Multiple sequence alignment - TraesCS6D01G247500

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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 TraesCS6D01G247500 chr6D 100.000 4845 0 0 1 4845 350936344 350931500 0.000000e+00 8948.0
1 TraesCS6D01G247500 chr6A 93.348 2766 111 33 565 3296 492792178 492794904 0.000000e+00 4021.0
2 TraesCS6D01G247500 chr6A 93.473 1241 43 20 3334 4547 492794908 492796137 0.000000e+00 1808.0
3 TraesCS6D01G247500 chr6A 93.052 403 23 5 1 402 492790302 492790700 6.990000e-163 584.0
4 TraesCS6D01G247500 chr6A 93.706 143 3 6 379 517 492791727 492791867 4.910000e-50 209.0
5 TraesCS6D01G247500 chr6B 92.096 2366 134 32 1 2346 528905888 528908220 0.000000e+00 3284.0
6 TraesCS6D01G247500 chr6B 96.356 1811 45 12 2395 4193 528908708 528910509 0.000000e+00 2959.0
7 TraesCS6D01G247500 chr6B 84.263 699 44 24 4188 4839 528911576 528912255 5.330000e-174 621.0
8 TraesCS6D01G247500 chr5B 84.314 153 22 2 4 155 211581722 211581571 1.090000e-31 148.0
9 TraesCS6D01G247500 chr5D 83.226 155 26 0 4 158 200638118 200637964 5.050000e-30 143.0
10 TraesCS6D01G247500 chrUn 79.310 145 20 4 8 152 178686063 178685929 5.160000e-15 93.5
11 TraesCS6D01G247500 chrUn 79.310 145 20 4 8 152 386568273 386568139 5.160000e-15 93.5


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 TraesCS6D01G247500 chr6D 350931500 350936344 4844 True 8948.0 8948 100.00000 1 4845 1 chr6D.!!$R1 4844
1 TraesCS6D01G247500 chr6A 492790302 492796137 5835 False 1655.5 4021 93.39475 1 4547 4 chr6A.!!$F1 4546
2 TraesCS6D01G247500 chr6B 528905888 528912255 6367 False 2288.0 3284 90.90500 1 4839 3 chr6B.!!$F1 4838

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
135 136 0.447801 CGAGCCAACATGGTAAGCAC 59.552 55.0 7.61 0.62 40.46 4.40 F
519 1572 0.471617 CTATGAGGGGCCTGAACCTG 59.528 60.0 0.84 0.00 37.18 4.00 F
1416 2747 0.040067 GTTGCTTTGCAGGGTTCGAG 60.040 55.0 0.00 0.00 40.61 4.04 F
1429 2760 0.238553 GTTCGAGTGGCAAGGAAAGC 59.761 55.0 0.00 0.00 0.00 3.51 F
2351 3703 0.399833 TGCACCAGTTCATGCCACTA 59.600 50.0 0.00 0.00 41.33 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 2423 0.609406 TCCCGCCCGAGATCTATCTG 60.609 60.000 0.0 0.0 37.25 2.90 R
2490 4282 0.937304 GCGCTGTCAGTTCTGTTCAA 59.063 50.000 0.0 0.0 0.00 2.69 R
2960 4754 0.605319 TGTCCGGCTGTTCATTCCAC 60.605 55.000 0.0 0.0 0.00 4.02 R
3209 5003 2.295885 CCAAAGATGAGTGAGGGATGC 58.704 52.381 0.0 0.0 0.00 3.91 R
4166 5969 0.107312 CCATGGCCCTCACAGAAGAG 60.107 60.000 0.0 0.0 35.39 2.85 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
28 29 4.216042 TGAAGTGTACGTTATGTCTTCGGA 59.784 41.667 0.00 0.00 35.51 4.55
89 90 5.097742 TGGTCCATTCATCAGTTATCGTT 57.902 39.130 0.00 0.00 0.00 3.85
100 101 1.982958 AGTTATCGTTGGGTCCTTGGT 59.017 47.619 0.00 0.00 0.00 3.67
103 104 1.131303 ATCGTTGGGTCCTTGGTCCA 61.131 55.000 5.40 0.00 0.00 4.02
105 106 1.764571 CGTTGGGTCCTTGGTCCAGA 61.765 60.000 5.40 0.00 31.59 3.86
135 136 0.447801 CGAGCCAACATGGTAAGCAC 59.552 55.000 7.61 0.62 40.46 4.40
177 178 2.095847 GCGGTCCGAACGTATGCAA 61.096 57.895 17.49 0.00 0.00 4.08
191 192 1.039856 ATGCAAGCGTTTTGAGGGTT 58.960 45.000 0.00 0.00 0.00 4.11
243 244 2.348998 CTCGGGCAGAAGCAACCT 59.651 61.111 0.00 0.00 44.61 3.50
295 296 1.926511 GCAACCATGAAGACCTGGCG 61.927 60.000 0.00 0.00 35.66 5.69
319 320 6.634436 CGTTATATCAAGACACCCGTTACTAC 59.366 42.308 0.00 0.00 0.00 2.73
467 1518 6.566197 AATCTCAACACAAGAACATTCTCC 57.434 37.500 0.00 0.00 36.28 3.71
468 1519 5.296151 TCTCAACACAAGAACATTCTCCT 57.704 39.130 0.00 0.00 36.28 3.69
519 1572 0.471617 CTATGAGGGGCCTGAACCTG 59.528 60.000 0.84 0.00 37.18 4.00
528 1581 2.483188 GGGCCTGAACCTGTATACTTCG 60.483 54.545 0.84 0.00 0.00 3.79
532 1585 3.617263 CCTGAACCTGTATACTTCGTTGC 59.383 47.826 4.17 0.59 0.00 4.17
533 1586 3.247442 TGAACCTGTATACTTCGTTGCG 58.753 45.455 4.17 0.00 0.00 4.85
534 1587 2.288961 ACCTGTATACTTCGTTGCGG 57.711 50.000 4.17 0.00 0.00 5.69
559 1612 0.725686 CCTGCGTCTTGCTTGATCAG 59.274 55.000 0.00 0.00 46.63 2.90
572 1889 2.859165 TGATCAGGCCTCGTTTCTTT 57.141 45.000 0.00 0.00 0.00 2.52
582 1899 3.591023 CCTCGTTTCTTTCCCTCTCTTC 58.409 50.000 0.00 0.00 0.00 2.87
586 1903 3.078097 GTTTCTTTCCCTCTCTTCCTGC 58.922 50.000 0.00 0.00 0.00 4.85
680 1997 1.249407 GTGGACGAGAGGAGACAACT 58.751 55.000 0.00 0.00 0.00 3.16
689 2006 1.615883 GAGGAGACAACTGAGTCAGCA 59.384 52.381 20.31 0.00 40.98 4.41
834 2152 3.466712 TTGAGTTAGTAGTCAGTCGCG 57.533 47.619 0.00 0.00 35.24 5.87
899 2217 1.557832 CACCCACCGATTCCCTTCTAA 59.442 52.381 0.00 0.00 0.00 2.10
949 2268 2.819608 CAAACCACCGATCATTTCCACT 59.180 45.455 0.00 0.00 0.00 4.00
982 2305 4.161295 CCGAATCCAGCCAGGCGA 62.161 66.667 5.55 0.00 37.29 5.54
983 2306 2.125147 CGAATCCAGCCAGGCGAA 60.125 61.111 5.55 0.00 37.29 4.70
984 2307 2.176273 CGAATCCAGCCAGGCGAAG 61.176 63.158 5.55 0.00 37.29 3.79
1089 2417 1.220493 TCCCCCTCTAGCTTAGCATGA 59.780 52.381 7.07 2.97 0.00 3.07
1092 2420 1.346068 CCCTCTAGCTTAGCATGACCC 59.654 57.143 7.07 0.00 0.00 4.46
1094 2422 1.000283 CTCTAGCTTAGCATGACCCGG 60.000 57.143 7.07 0.00 0.00 5.73
1095 2423 0.601311 CTAGCTTAGCATGACCCGGC 60.601 60.000 7.07 0.00 0.00 6.13
1351 2682 0.250513 GAGGATCTCCCGTTTGCTGT 59.749 55.000 0.00 0.00 40.87 4.40
1369 2700 1.026718 GTTGCCGAGGGAGTGATTGG 61.027 60.000 0.00 0.00 0.00 3.16
1370 2701 2.514824 GCCGAGGGAGTGATTGGC 60.515 66.667 0.00 0.00 38.78 4.52
1416 2747 0.040067 GTTGCTTTGCAGGGTTCGAG 60.040 55.000 0.00 0.00 40.61 4.04
1429 2760 0.238553 GTTCGAGTGGCAAGGAAAGC 59.761 55.000 0.00 0.00 0.00 3.51
1492 2823 3.274288 GGTAAGCTTCTTATGCTGCTGT 58.726 45.455 0.00 0.00 41.03 4.40
1776 3111 3.635591 GTTCTTCCCAATCATCCACCAT 58.364 45.455 0.00 0.00 0.00 3.55
2011 3346 1.121378 GGGAGGTGAGCTAAGTACCC 58.879 60.000 0.00 0.00 35.03 3.69
2013 3348 2.468915 GGAGGTGAGCTAAGTACCCTT 58.531 52.381 0.00 0.00 35.03 3.95
2032 3367 7.215719 ACCCTTTTCTAGTTAGTTTTCATGC 57.784 36.000 0.00 0.00 0.00 4.06
2038 3387 7.658179 TTCTAGTTAGTTTTCATGCTCTGTG 57.342 36.000 0.00 0.00 0.00 3.66
2060 3409 5.947228 GCACCTGCACATATGTATTGTAT 57.053 39.130 8.32 0.00 41.59 2.29
2062 3411 7.615582 GCACCTGCACATATGTATTGTATAT 57.384 36.000 8.32 0.00 41.59 0.86
2063 3412 8.716646 GCACCTGCACATATGTATTGTATATA 57.283 34.615 8.32 0.00 41.59 0.86
2064 3413 9.161629 GCACCTGCACATATGTATTGTATATAA 57.838 33.333 8.32 0.00 41.59 0.98
2066 3415 9.366216 ACCTGCACATATGTATTGTATATAACG 57.634 33.333 8.32 0.00 0.00 3.18
2067 3416 8.817100 CCTGCACATATGTATTGTATATAACGG 58.183 37.037 8.32 0.00 0.00 4.44
2068 3417 8.710835 TGCACATATGTATTGTATATAACGGG 57.289 34.615 8.32 0.00 0.00 5.28
2069 3418 7.279090 TGCACATATGTATTGTATATAACGGGC 59.721 37.037 8.32 2.55 0.00 6.13
2070 3419 7.279090 GCACATATGTATTGTATATAACGGGCA 59.721 37.037 8.32 0.00 0.00 5.36
2071 3420 9.157104 CACATATGTATTGTATATAACGGGCAA 57.843 33.333 8.32 0.00 0.00 4.52
2072 3421 9.727859 ACATATGTATTGTATATAACGGGCAAA 57.272 29.630 6.56 0.00 0.00 3.68
2075 3424 8.856153 ATGTATTGTATATAACGGGCAAATGA 57.144 30.769 0.00 0.00 0.00 2.57
2076 3425 8.317891 TGTATTGTATATAACGGGCAAATGAG 57.682 34.615 0.00 0.00 0.00 2.90
2077 3426 8.151596 TGTATTGTATATAACGGGCAAATGAGA 58.848 33.333 0.00 0.00 0.00 3.27
2078 3427 9.162764 GTATTGTATATAACGGGCAAATGAGAT 57.837 33.333 0.00 0.00 0.00 2.75
2079 3428 7.433708 TTGTATATAACGGGCAAATGAGATG 57.566 36.000 0.00 0.00 0.00 2.90
2080 3429 6.530120 TGTATATAACGGGCAAATGAGATGT 58.470 36.000 0.00 0.00 0.00 3.06
2081 3430 7.672240 TGTATATAACGGGCAAATGAGATGTA 58.328 34.615 0.00 0.00 0.00 2.29
2082 3431 7.601130 TGTATATAACGGGCAAATGAGATGTAC 59.399 37.037 0.00 0.00 0.00 2.90
2083 3432 3.350219 AACGGGCAAATGAGATGTACT 57.650 42.857 0.00 0.00 0.00 2.73
2084 3433 3.350219 ACGGGCAAATGAGATGTACTT 57.650 42.857 0.00 0.00 0.00 2.24
2085 3434 3.009723 ACGGGCAAATGAGATGTACTTG 58.990 45.455 0.00 0.00 0.00 3.16
2086 3435 3.270027 CGGGCAAATGAGATGTACTTGA 58.730 45.455 0.00 0.00 0.00 3.02
2087 3436 3.689161 CGGGCAAATGAGATGTACTTGAA 59.311 43.478 0.00 0.00 0.00 2.69
2088 3437 4.336433 CGGGCAAATGAGATGTACTTGAAT 59.664 41.667 0.00 0.00 0.00 2.57
2089 3438 5.163622 CGGGCAAATGAGATGTACTTGAATT 60.164 40.000 0.00 0.00 0.00 2.17
2090 3439 6.038356 GGGCAAATGAGATGTACTTGAATTG 58.962 40.000 0.00 0.00 0.00 2.32
2118 3467 2.696506 GGTACCAACAAGTGCTAGTCC 58.303 52.381 7.15 0.00 0.00 3.85
2123 3472 4.833390 ACCAACAAGTGCTAGTCCTATTC 58.167 43.478 0.00 0.00 0.00 1.75
2170 3522 6.151817 AGCAGACCACTAAATCTTTGGATTTC 59.848 38.462 7.17 0.00 45.73 2.17
2239 3591 2.163818 TGCTTGGAGTACCTTTGTCG 57.836 50.000 0.00 0.00 37.04 4.35
2293 3645 5.645067 TGCAATGAGGTATGCATCTAATAGC 59.355 40.000 0.19 0.00 46.87 2.97
2297 3649 5.551233 TGAGGTATGCATCTAATAGCCAAC 58.449 41.667 0.19 0.00 0.00 3.77
2298 3650 5.071653 TGAGGTATGCATCTAATAGCCAACA 59.928 40.000 0.19 0.00 0.00 3.33
2322 3674 2.466846 TCTGGCTTCCTGCTATGTGTA 58.533 47.619 0.00 0.00 42.39 2.90
2323 3675 2.168521 TCTGGCTTCCTGCTATGTGTAC 59.831 50.000 0.00 0.00 42.39 2.90
2324 3676 1.905894 TGGCTTCCTGCTATGTGTACA 59.094 47.619 0.00 0.00 42.39 2.90
2325 3677 2.093500 TGGCTTCCTGCTATGTGTACAG 60.093 50.000 0.00 0.00 42.39 2.74
2326 3678 2.168521 GGCTTCCTGCTATGTGTACAGA 59.831 50.000 0.00 0.00 42.39 3.41
2327 3679 3.369471 GGCTTCCTGCTATGTGTACAGAA 60.369 47.826 0.00 0.00 42.39 3.02
2328 3680 4.446371 GCTTCCTGCTATGTGTACAGAAT 58.554 43.478 0.00 0.00 38.95 2.40
2349 3701 0.890542 TCTGCACCAGTTCATGCCAC 60.891 55.000 0.00 0.00 41.33 5.01
2351 3703 0.399833 TGCACCAGTTCATGCCACTA 59.600 50.000 0.00 0.00 41.33 2.74
2352 3704 1.202867 TGCACCAGTTCATGCCACTAA 60.203 47.619 0.00 0.00 41.33 2.24
2363 4133 4.464008 TCATGCCACTAATTCTGGATTCC 58.536 43.478 6.31 0.00 0.00 3.01
2377 4147 4.225942 TCTGGATTCCACTTTGTATCAGCT 59.774 41.667 0.00 0.00 0.00 4.24
2391 4161 5.614308 TGTATCAGCTTAACATGCATAGCT 58.386 37.500 14.62 14.62 44.34 3.32
2445 4236 9.890629 TGAATTCTAATATCTGCACTGTACTTT 57.109 29.630 7.05 0.00 0.00 2.66
2470 4261 5.897824 TCCTAGCACTAGTAGTGGCTTTATT 59.102 40.000 27.48 9.49 46.01 1.40
2473 4264 8.202137 CCTAGCACTAGTAGTGGCTTTATTTTA 58.798 37.037 27.48 10.23 46.01 1.52
2639 4431 8.324567 TGAATTATGTTTTCTTTGTTTCGTTGC 58.675 29.630 0.00 0.00 0.00 4.17
2689 4481 1.063006 CATTGCTCCGCCAATCGTG 59.937 57.895 0.00 0.00 33.35 4.35
2705 4497 0.580104 CGTGTTTCGTGGGAAGTCAC 59.420 55.000 0.00 0.00 36.45 3.67
2960 4754 7.601886 CCTTCTGCAGTTCATATACTTCCTATG 59.398 40.741 14.67 0.00 0.00 2.23
3178 4972 0.548031 CCCTTGCCTCCTATTCTGCA 59.452 55.000 0.00 0.00 0.00 4.41
3184 4978 5.182760 CCTTGCCTCCTATTCTGCATTTATC 59.817 44.000 0.00 0.00 33.08 1.75
3209 5003 1.804151 TCCTCATTCTTTGGTTTCGCG 59.196 47.619 0.00 0.00 0.00 5.87
3422 5216 7.129660 TCCTGCCCTCTAGCTATCTATAAGTAT 59.870 40.741 0.00 0.00 0.00 2.12
3687 5481 2.095617 TGAGCGAGCATGTCACATTTTG 60.096 45.455 0.00 0.00 0.00 2.44
3754 5551 1.480137 TGGTGTTTGCCAAGTTCCTTG 59.520 47.619 0.00 0.00 40.75 3.61
3887 5689 1.183030 AAGTCCACCGGTGTCATCGA 61.183 55.000 31.80 19.03 0.00 3.59
3972 5774 7.286316 AGTTATGGGAATAATTTGCCTCAGAAG 59.714 37.037 0.00 0.00 43.41 2.85
4019 5821 6.550108 TGGAAGAGAGTAGAAGTGTAACAACT 59.450 38.462 0.00 0.00 41.43 3.16
4076 5878 5.944007 TGTTTAAAGCCTTGGATCTTACCTC 59.056 40.000 0.00 0.00 0.00 3.85
4160 5963 2.032223 CTGCTGGTGAGCTGCTGT 59.968 61.111 7.01 0.00 46.39 4.40
4161 5964 2.031616 TGCTGGTGAGCTGCTGTC 59.968 61.111 7.01 0.00 46.39 3.51
4162 5965 2.346739 GCTGGTGAGCTGCTGTCT 59.653 61.111 7.01 0.00 42.52 3.41
4163 5966 1.302351 GCTGGTGAGCTGCTGTCTT 60.302 57.895 7.01 0.00 42.52 3.01
4164 5967 1.297456 GCTGGTGAGCTGCTGTCTTC 61.297 60.000 7.01 0.00 42.52 2.87
4165 5968 0.321021 CTGGTGAGCTGCTGTCTTCT 59.679 55.000 7.01 0.00 0.00 2.85
4166 5969 0.319728 TGGTGAGCTGCTGTCTTCTC 59.680 55.000 7.01 0.00 0.00 2.87
4174 5978 2.029110 GCTGCTGTCTTCTCTCTTCTGT 60.029 50.000 0.00 0.00 0.00 3.41
4219 7095 6.891908 ACCTAAAGACAGCAAAACCATATGAT 59.108 34.615 3.65 0.00 0.00 2.45
4220 7096 7.067494 ACCTAAAGACAGCAAAACCATATGATC 59.933 37.037 3.65 0.00 0.00 2.92
4248 7124 2.104622 TCTGTGCCTTGTGAAGTGATGA 59.895 45.455 0.00 0.00 0.00 2.92
4283 7159 3.028094 AGCCTTCATTGCAGATTCCAT 57.972 42.857 0.00 0.00 0.00 3.41
4299 7194 8.632679 GCAGATTCCATTTCTTATAAACATCCA 58.367 33.333 0.00 0.00 0.00 3.41
4305 7200 9.585369 TCCATTTCTTATAAACATCCATGCATA 57.415 29.630 0.00 0.00 0.00 3.14
4417 7316 2.418628 GCTTGCGCCATAACAAGAAGTA 59.581 45.455 4.18 0.00 44.89 2.24
4418 7317 3.119990 GCTTGCGCCATAACAAGAAGTAA 60.120 43.478 4.18 0.00 44.89 2.24
4460 7359 6.100404 ACAGAAAATATTGCATGTGGTTGT 57.900 33.333 0.00 0.00 0.00 3.32
4465 7364 8.367156 AGAAAATATTGCATGTGGTTGTACTTT 58.633 29.630 0.00 0.00 0.00 2.66
4474 7374 9.019656 TGCATGTGGTTGTACTTTATAGATTTT 57.980 29.630 0.00 0.00 0.00 1.82
4543 7443 4.082733 GCATGACAAAAGGTCCTAAGGAAC 60.083 45.833 0.00 0.00 46.38 3.62
4547 7447 3.136992 ACAAAAGGTCCTAAGGAACGGAA 59.863 43.478 0.00 0.00 45.53 4.30
4568 7468 6.093082 CGGAATCCTCCAAAGTTTAACGTAAT 59.907 38.462 0.00 0.00 42.58 1.89
4569 7469 7.361457 CGGAATCCTCCAAAGTTTAACGTAATT 60.361 37.037 0.00 0.00 42.58 1.40
4570 7470 7.966753 GGAATCCTCCAAAGTTTAACGTAATTC 59.033 37.037 0.00 0.00 41.96 2.17
4571 7471 6.806388 TCCTCCAAAGTTTAACGTAATTCC 57.194 37.500 0.00 0.00 0.00 3.01
4572 7472 6.536447 TCCTCCAAAGTTTAACGTAATTCCT 58.464 36.000 0.00 0.00 0.00 3.36
4573 7473 6.999871 TCCTCCAAAGTTTAACGTAATTCCTT 59.000 34.615 0.00 0.00 0.00 3.36
4574 7474 7.173735 TCCTCCAAAGTTTAACGTAATTCCTTC 59.826 37.037 0.00 0.00 0.00 3.46
4590 7490 7.459795 AATTCCTTCAATCAAAGAAGAGGTC 57.540 36.000 4.61 0.00 44.00 3.85
4600 7500 5.799213 TCAAAGAAGAGGTCCTTGATCTTC 58.201 41.667 12.54 11.13 46.02 2.87
4628 7528 5.142061 TCCAGAGATTTACGCTTGTTACA 57.858 39.130 0.00 0.00 0.00 2.41
4636 7536 5.425577 TTTACGCTTGTTACATTGCTTGA 57.574 34.783 8.63 0.00 0.00 3.02
4637 7537 5.621197 TTACGCTTGTTACATTGCTTGAT 57.379 34.783 8.63 0.00 0.00 2.57
4639 7539 5.621197 ACGCTTGTTACATTGCTTGATTA 57.379 34.783 8.63 0.00 0.00 1.75
4640 7540 6.194796 ACGCTTGTTACATTGCTTGATTAT 57.805 33.333 8.63 0.00 0.00 1.28
4641 7541 6.258160 ACGCTTGTTACATTGCTTGATTATC 58.742 36.000 8.63 0.00 0.00 1.75
4683 7584 9.667107 GAAAATGATATAGATTCCGGTAATCCA 57.333 33.333 17.64 9.13 44.44 3.41
4696 7597 0.322098 TAATCCACAACGGTGCCCAG 60.322 55.000 0.00 0.00 43.88 4.45
4724 7625 7.362662 TCAGATGCTTTGAATGAACAGTAAAC 58.637 34.615 0.00 0.00 0.00 2.01
4725 7626 7.013178 TCAGATGCTTTGAATGAACAGTAAACA 59.987 33.333 0.00 0.00 0.00 2.83
4726 7627 7.648908 CAGATGCTTTGAATGAACAGTAAACAA 59.351 33.333 0.00 0.00 0.00 2.83
4727 7628 8.362639 AGATGCTTTGAATGAACAGTAAACAAT 58.637 29.630 0.00 0.00 0.00 2.71
4728 7629 8.891671 ATGCTTTGAATGAACAGTAAACAATT 57.108 26.923 0.00 0.00 0.00 2.32
4729 7630 9.979578 ATGCTTTGAATGAACAGTAAACAATTA 57.020 25.926 0.00 0.00 0.00 1.40
4730 7631 9.979578 TGCTTTGAATGAACAGTAAACAATTAT 57.020 25.926 0.00 0.00 0.00 1.28
4772 7697 8.893563 TGTCATCCATTCTTTTTAGGGTATTT 57.106 30.769 0.00 0.00 0.00 1.40
4789 7714 6.621514 AGGGTATTTTCATCCATTCTAGGAGT 59.378 38.462 0.00 0.00 41.90 3.85
4791 7716 7.283329 GGTATTTTCATCCATTCTAGGAGTGT 58.717 38.462 0.00 0.00 41.90 3.55
4797 7722 4.574674 TCCATTCTAGGAGTGTGCAAAT 57.425 40.909 0.00 0.00 32.77 2.32
4798 7723 4.922206 TCCATTCTAGGAGTGTGCAAATT 58.078 39.130 0.00 0.00 32.77 1.82
4812 7737 8.430801 AGTGTGCAAATTTTTGTGCTAAAATA 57.569 26.923 5.05 0.00 41.48 1.40
4813 7738 8.887717 AGTGTGCAAATTTTTGTGCTAAAATAA 58.112 25.926 5.05 0.00 41.48 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.706962 TCAAGATGAAGATCTCCGAAGACA 59.293 41.667 0.00 0.00 38.03 3.41
28 29 6.378710 TCGACGTAATCAAGATGAAGATCT 57.621 37.500 0.00 0.00 41.00 2.75
89 90 3.900888 GTCTGGACCAAGGACCCA 58.099 61.111 5.18 5.22 0.00 4.51
177 178 0.463116 ACGTCAACCCTCAAAACGCT 60.463 50.000 0.00 0.00 36.85 5.07
191 192 5.970317 TCTTTAGTACATCTCCAACGTCA 57.030 39.130 0.00 0.00 0.00 4.35
243 244 7.013274 GCCTTTAACTAATGCATCTGGTCATTA 59.987 37.037 0.00 0.00 34.95 1.90
295 296 6.634436 CGTAGTAACGGGTGTCTTGATATAAC 59.366 42.308 0.00 0.00 45.50 1.89
319 320 2.665649 TAATGCACACCCACTACTCG 57.334 50.000 0.00 0.00 0.00 4.18
496 1549 1.559682 GTTCAGGCCCCTCATAGTGAA 59.440 52.381 0.00 0.00 0.00 3.18
500 1553 0.471617 CAGGTTCAGGCCCCTCATAG 59.528 60.000 0.00 0.00 0.00 2.23
501 1554 0.253160 ACAGGTTCAGGCCCCTCATA 60.253 55.000 0.00 0.00 0.00 2.15
519 1572 0.648958 GGTGCCGCAACGAAGTATAC 59.351 55.000 0.00 0.00 45.00 1.47
559 1612 0.325272 AGAGGGAAAGAAACGAGGCC 59.675 55.000 0.00 0.00 0.00 5.19
572 1889 3.697190 ATTCTAGCAGGAAGAGAGGGA 57.303 47.619 0.00 0.00 0.00 4.20
582 1899 2.002586 CGTGGTGTGAATTCTAGCAGG 58.997 52.381 7.05 12.39 0.00 4.85
586 1903 3.121279 CGTTGTCGTGGTGTGAATTCTAG 59.879 47.826 7.05 0.00 0.00 2.43
680 1997 4.248859 GTTGAGATTAGCTTGCTGACTCA 58.751 43.478 16.99 16.99 0.00 3.41
689 2006 4.030134 CGTCTACGGTTGAGATTAGCTT 57.970 45.455 0.00 0.00 35.37 3.74
715 2032 3.181475 GGTCTTCCGCACTATCAGATCAA 60.181 47.826 0.00 0.00 0.00 2.57
787 2104 2.702592 TCAGGTTCAAGTTGTTCGGT 57.297 45.000 2.11 0.00 0.00 4.69
834 2152 1.080434 GCGGTGGACTGACTCACTC 60.080 63.158 0.00 0.00 34.57 3.51
899 2217 3.612681 CGGTGTGACACGGGAGGT 61.613 66.667 14.60 0.00 34.83 3.85
923 2241 2.113860 ATGATCGGTGGTTTGGTCTG 57.886 50.000 0.00 0.00 0.00 3.51
984 2307 4.887987 ATCCTCGCAGCTCGCAGC 62.888 66.667 8.52 0.00 42.60 5.25
985 2308 2.341807 TACATCCTCGCAGCTCGCAG 62.342 60.000 8.52 5.31 42.60 5.18
986 2309 2.414785 TACATCCTCGCAGCTCGCA 61.415 57.895 8.52 0.00 42.60 5.10
987 2310 1.946650 GTACATCCTCGCAGCTCGC 60.947 63.158 0.00 0.00 38.27 5.03
989 2312 1.299468 CGGTACATCCTCGCAGCTC 60.299 63.158 0.00 0.00 0.00 4.09
1089 2417 0.896019 CCGAGATCTATCTGCCGGGT 60.896 60.000 2.18 0.00 39.35 5.28
1092 2420 1.214062 GCCCGAGATCTATCTGCCG 59.786 63.158 0.00 0.00 37.25 5.69
1094 2422 1.214062 CCGCCCGAGATCTATCTGC 59.786 63.158 0.00 0.00 37.25 4.26
1095 2423 0.609406 TCCCGCCCGAGATCTATCTG 60.609 60.000 0.00 0.00 37.25 2.90
1229 2560 2.400399 CGAAACTGGAACTGCGACTTA 58.600 47.619 0.00 0.00 0.00 2.24
1351 2682 1.299648 CCAATCACTCCCTCGGCAA 59.700 57.895 0.00 0.00 0.00 4.52
1416 2747 1.916697 GAGCTCGCTTTCCTTGCCAC 61.917 60.000 0.00 0.00 0.00 5.01
1492 2823 8.352201 CAAATCAACTGTAAGAATCCAAGACAA 58.648 33.333 0.00 0.00 37.43 3.18
1647 2982 3.346315 CACTGATGTAGACCCAATGCAA 58.654 45.455 0.00 0.00 0.00 4.08
1776 3111 4.381825 GCTGGTATTTCATTGGCAATGTCA 60.382 41.667 32.66 22.89 39.87 3.58
2011 3346 8.778358 ACAGAGCATGAAAACTAACTAGAAAAG 58.222 33.333 0.00 0.00 0.00 2.27
2013 3348 7.307989 GCACAGAGCATGAAAACTAACTAGAAA 60.308 37.037 0.00 0.00 44.79 2.52
2038 3387 5.947228 ATACAATACATATGTGCAGGTGC 57.053 39.130 18.81 0.00 42.50 5.01
2058 3407 7.903145 AGTACATCTCATTTGCCCGTTATATA 58.097 34.615 0.00 0.00 0.00 0.86
2059 3408 6.769512 AGTACATCTCATTTGCCCGTTATAT 58.230 36.000 0.00 0.00 0.00 0.86
2060 3409 6.169557 AGTACATCTCATTTGCCCGTTATA 57.830 37.500 0.00 0.00 0.00 0.98
2061 3410 5.036117 AGTACATCTCATTTGCCCGTTAT 57.964 39.130 0.00 0.00 0.00 1.89
2062 3411 4.481368 AGTACATCTCATTTGCCCGTTA 57.519 40.909 0.00 0.00 0.00 3.18
2063 3412 3.350219 AGTACATCTCATTTGCCCGTT 57.650 42.857 0.00 0.00 0.00 4.44
2064 3413 3.009723 CAAGTACATCTCATTTGCCCGT 58.990 45.455 0.00 0.00 0.00 5.28
2065 3414 3.270027 TCAAGTACATCTCATTTGCCCG 58.730 45.455 0.00 0.00 0.00 6.13
2066 3415 5.841957 ATTCAAGTACATCTCATTTGCCC 57.158 39.130 0.00 0.00 0.00 5.36
2067 3416 5.517770 GCAATTCAAGTACATCTCATTTGCC 59.482 40.000 0.00 0.00 0.00 4.52
2068 3417 6.094719 TGCAATTCAAGTACATCTCATTTGC 58.905 36.000 0.00 2.69 0.00 3.68
2069 3418 7.310664 ACTGCAATTCAAGTACATCTCATTTG 58.689 34.615 0.00 0.00 0.00 2.32
2070 3419 7.458409 ACTGCAATTCAAGTACATCTCATTT 57.542 32.000 0.00 0.00 0.00 2.32
2071 3420 7.458409 AACTGCAATTCAAGTACATCTCATT 57.542 32.000 0.00 0.00 0.00 2.57
2072 3421 7.310664 CAAACTGCAATTCAAGTACATCTCAT 58.689 34.615 0.00 0.00 0.00 2.90
2073 3422 6.294120 CCAAACTGCAATTCAAGTACATCTCA 60.294 38.462 0.00 0.00 0.00 3.27
2074 3423 6.088824 CCAAACTGCAATTCAAGTACATCTC 58.911 40.000 0.00 0.00 0.00 2.75
2075 3424 5.047802 CCCAAACTGCAATTCAAGTACATCT 60.048 40.000 0.00 0.00 0.00 2.90
2076 3425 5.163513 CCCAAACTGCAATTCAAGTACATC 58.836 41.667 0.00 0.00 0.00 3.06
2077 3426 4.588528 ACCCAAACTGCAATTCAAGTACAT 59.411 37.500 0.00 0.00 0.00 2.29
2078 3427 3.957497 ACCCAAACTGCAATTCAAGTACA 59.043 39.130 0.00 0.00 0.00 2.90
2079 3428 4.584327 ACCCAAACTGCAATTCAAGTAC 57.416 40.909 0.00 0.00 0.00 2.73
2080 3429 4.521256 GGTACCCAAACTGCAATTCAAGTA 59.479 41.667 0.00 0.00 0.00 2.24
2081 3430 3.320826 GGTACCCAAACTGCAATTCAAGT 59.679 43.478 0.00 0.00 0.00 3.16
2082 3431 3.320541 TGGTACCCAAACTGCAATTCAAG 59.679 43.478 10.07 0.00 0.00 3.02
2083 3432 3.300388 TGGTACCCAAACTGCAATTCAA 58.700 40.909 10.07 0.00 0.00 2.69
2084 3433 2.950781 TGGTACCCAAACTGCAATTCA 58.049 42.857 10.07 0.00 0.00 2.57
2085 3434 3.068873 TGTTGGTACCCAAACTGCAATTC 59.931 43.478 10.07 0.00 45.73 2.17
2086 3435 3.034635 TGTTGGTACCCAAACTGCAATT 58.965 40.909 10.07 0.00 45.73 2.32
2087 3436 2.672098 TGTTGGTACCCAAACTGCAAT 58.328 42.857 10.07 0.00 45.73 3.56
2088 3437 2.145397 TGTTGGTACCCAAACTGCAA 57.855 45.000 10.07 0.00 45.73 4.08
2089 3438 2.028130 CTTGTTGGTACCCAAACTGCA 58.972 47.619 10.07 0.00 45.73 4.41
2090 3439 2.028876 ACTTGTTGGTACCCAAACTGC 58.971 47.619 10.07 0.00 45.73 4.40
2107 3456 6.739331 AATAGCAGAATAGGACTAGCACTT 57.261 37.500 0.00 0.00 0.00 3.16
2123 3472 6.707608 TGCTCCATTACAAGACATAATAGCAG 59.292 38.462 0.00 0.00 32.49 4.24
2144 3496 4.579869 TCCAAAGATTTAGTGGTCTGCTC 58.420 43.478 0.00 0.00 33.88 4.26
2170 3522 5.064452 CAGTTTAGAGTCTGCAAGCATAAGG 59.936 44.000 1.86 0.00 0.00 2.69
2239 3591 4.589374 AGAGGCCTATACCACATCAAGTAC 59.411 45.833 4.42 0.00 0.00 2.73
2293 3645 1.610522 CAGGAAGCCAGAAAGTGTTGG 59.389 52.381 0.00 0.00 37.53 3.77
2322 3674 4.558226 TGAACTGGTGCAGATATTCTGT 57.442 40.909 6.40 0.00 45.94 3.41
2323 3675 4.261072 GCATGAACTGGTGCAGATATTCTG 60.261 45.833 0.00 0.08 46.90 3.02
2324 3676 3.881688 GCATGAACTGGTGCAGATATTCT 59.118 43.478 0.00 0.00 40.94 2.40
2325 3677 3.004106 GGCATGAACTGGTGCAGATATTC 59.996 47.826 0.00 0.00 43.00 1.75
2326 3678 2.954318 GGCATGAACTGGTGCAGATATT 59.046 45.455 0.00 0.00 43.00 1.28
2327 3679 2.092267 TGGCATGAACTGGTGCAGATAT 60.092 45.455 0.00 0.00 43.00 1.63
2328 3680 1.281577 TGGCATGAACTGGTGCAGATA 59.718 47.619 0.00 0.00 43.00 1.98
2349 3701 8.737168 TGATACAAAGTGGAATCCAGAATTAG 57.263 34.615 0.27 0.00 32.34 1.73
2351 3703 6.096001 GCTGATACAAAGTGGAATCCAGAATT 59.904 38.462 0.27 0.00 32.34 2.17
2352 3704 5.591877 GCTGATACAAAGTGGAATCCAGAAT 59.408 40.000 0.27 0.00 32.34 2.40
2363 4133 5.941733 TGCATGTTAAGCTGATACAAAGTG 58.058 37.500 0.00 0.00 0.00 3.16
2426 4217 7.926555 GCTAGGAAAAGTACAGTGCAGATATTA 59.073 37.037 0.00 0.00 0.00 0.98
2445 4236 3.383698 AGCCACTACTAGTGCTAGGAA 57.616 47.619 5.39 0.00 44.63 3.36
2490 4282 0.937304 GCGCTGTCAGTTCTGTTCAA 59.063 50.000 0.00 0.00 0.00 2.69
2602 4394 7.099120 AGAAAACATAATTCAATCAGGTTGCC 58.901 34.615 0.00 0.00 37.74 4.52
2639 4431 1.342174 ACAAAAGCCAATGTGGAGCTG 59.658 47.619 0.00 0.00 40.96 4.24
2689 4481 2.473984 CGTTAGTGACTTCCCACGAAAC 59.526 50.000 0.00 0.00 41.67 2.78
2960 4754 0.605319 TGTCCGGCTGTTCATTCCAC 60.605 55.000 0.00 0.00 0.00 4.02
3178 4972 6.659242 ACCAAAGAATGAGGAACGTGATAAAT 59.341 34.615 0.00 0.00 0.00 1.40
3184 4978 4.537015 GAAACCAAAGAATGAGGAACGTG 58.463 43.478 0.00 0.00 0.00 4.49
3209 5003 2.295885 CCAAAGATGAGTGAGGGATGC 58.704 52.381 0.00 0.00 0.00 3.91
3498 5292 4.576463 ACTTTCTTCCAGCAGTAAACACTG 59.424 41.667 0.36 0.36 40.51 3.66
3539 5333 6.759497 AAGTTTACTGAAAAACTGTGCTCT 57.241 33.333 11.59 0.00 46.40 4.09
3754 5551 0.799534 CTGCTGGTATTTTGCGCTGC 60.800 55.000 9.73 0.00 0.00 5.25
3861 5663 1.549170 ACACCGGTGGACTTCTGTATC 59.451 52.381 36.47 0.00 34.19 2.24
3887 5689 3.349006 CAGAACCGCAGCACGCTT 61.349 61.111 0.00 0.00 41.76 4.68
3972 5774 8.696410 TCCAACAAATAAACAAACTTCTGAAC 57.304 30.769 0.00 0.00 0.00 3.18
4019 5821 8.812972 AGTTCCAGAGATAACACTAATACAACA 58.187 33.333 0.00 0.00 0.00 3.33
4076 5878 6.308766 GGCTTCAAACAACATGCAGTTTATAG 59.691 38.462 13.70 13.75 38.74 1.31
4160 5963 2.175202 GCCCTCACAGAAGAGAGAAGA 58.825 52.381 0.00 0.00 37.87 2.87
4161 5964 1.206849 GGCCCTCACAGAAGAGAGAAG 59.793 57.143 0.00 0.00 37.87 2.85
4162 5965 1.270907 GGCCCTCACAGAAGAGAGAA 58.729 55.000 0.00 0.00 37.87 2.87
4163 5966 0.115152 TGGCCCTCACAGAAGAGAGA 59.885 55.000 0.00 0.00 37.87 3.10
4164 5967 1.134461 CATGGCCCTCACAGAAGAGAG 60.134 57.143 0.00 0.00 37.87 3.20
4165 5968 0.907486 CATGGCCCTCACAGAAGAGA 59.093 55.000 0.00 0.00 37.87 3.10
4166 5969 0.107312 CCATGGCCCTCACAGAAGAG 60.107 60.000 0.00 0.00 35.39 2.85
4174 5978 0.548926 TCCAACTACCATGGCCCTCA 60.549 55.000 13.04 0.00 37.88 3.86
4219 7095 2.634453 TCACAAGGCACAGATGAGAAGA 59.366 45.455 0.00 0.00 0.00 2.87
4220 7096 3.049708 TCACAAGGCACAGATGAGAAG 57.950 47.619 0.00 0.00 0.00 2.85
4248 7124 3.846588 TGAAGGCTAGAAGATTCCTTGGT 59.153 43.478 2.21 0.00 38.90 3.67
4320 7218 1.819288 TCAGTGAAGGCTAGAAGGACG 59.181 52.381 0.00 0.00 0.00 4.79
4547 7447 7.173032 AGGAATTACGTTAAACTTTGGAGGAT 58.827 34.615 0.00 0.00 0.00 3.24
4568 7468 5.073691 AGGACCTCTTCTTTGATTGAAGGAA 59.926 40.000 0.00 0.00 40.73 3.36
4569 7469 4.599241 AGGACCTCTTCTTTGATTGAAGGA 59.401 41.667 0.00 0.00 40.73 3.36
4570 7470 4.916183 AGGACCTCTTCTTTGATTGAAGG 58.084 43.478 0.00 0.00 40.73 3.46
4571 7471 6.000219 TCAAGGACCTCTTCTTTGATTGAAG 59.000 40.000 0.00 0.00 43.49 3.02
4572 7472 5.940617 TCAAGGACCTCTTCTTTGATTGAA 58.059 37.500 0.00 0.00 43.49 2.69
4573 7473 5.567037 TCAAGGACCTCTTCTTTGATTGA 57.433 39.130 0.00 0.00 43.49 2.57
4590 7490 4.081972 TCTCTGGAAACGAGAAGATCAAGG 60.082 45.833 0.00 0.00 37.17 3.61
4600 7500 3.512680 AGCGTAAATCTCTGGAAACGAG 58.487 45.455 0.00 0.00 32.05 4.18
4663 7564 6.530534 CGTTGTGGATTACCGGAATCTATATC 59.469 42.308 9.46 7.83 43.20 1.63
4668 7569 2.419574 CCGTTGTGGATTACCGGAATCT 60.420 50.000 9.46 0.00 43.20 2.40
4674 7575 1.641123 GGCACCGTTGTGGATTACCG 61.641 60.000 0.00 0.00 42.99 4.02
4696 7597 3.192001 TGTTCATTCAAAGCATCTGAGCC 59.808 43.478 0.00 0.00 34.23 4.70
4748 7671 9.803315 GAAAATACCCTAAAAAGAATGGATGAC 57.197 33.333 0.00 0.00 0.00 3.06
4764 7687 6.621514 ACTCCTAGAATGGATGAAAATACCCT 59.378 38.462 0.00 0.00 35.30 4.34
4765 7688 6.712547 CACTCCTAGAATGGATGAAAATACCC 59.287 42.308 0.00 0.00 35.30 3.69
4772 7697 3.519107 TGCACACTCCTAGAATGGATGAA 59.481 43.478 0.00 0.00 35.30 2.57
4781 7706 5.735922 GCACAAAAATTTGCACACTCCTAGA 60.736 40.000 5.82 0.00 41.79 2.43
4789 7714 8.668353 TGTTATTTTAGCACAAAAATTTGCACA 58.332 25.926 5.82 0.00 41.79 4.57
4797 7722 9.823647 TCCTCAAATGTTATTTTAGCACAAAAA 57.176 25.926 1.01 0.00 33.15 1.94
4798 7723 9.474920 CTCCTCAAATGTTATTTTAGCACAAAA 57.525 29.630 0.00 0.00 0.00 2.44
4812 7737 2.799017 TGCATGAGCTCCTCAAATGTT 58.201 42.857 12.15 0.00 44.04 2.71
4813 7738 2.502142 TGCATGAGCTCCTCAAATGT 57.498 45.000 12.15 0.00 44.04 2.71


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

AutoCloner maintained by Alex Coulton.