Multiple sequence alignment - TraesCS1D01G421700

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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 TraesCS1D01G421700 chr1D 100.000 3363 0 0 1 3363 477433858 477437220 0.000000e+00 6211.0
1 TraesCS1D01G421700 chr1D 84.615 1170 116 32 1739 2871 477480184 477481326 0.000000e+00 1105.0
2 TraesCS1D01G421700 chr1D 82.105 475 49 18 1320 1775 477479670 477480127 1.140000e-99 374.0
3 TraesCS1D01G421700 chr1D 79.401 267 43 10 1143 1403 477434961 477435221 9.590000e-41 178.0
4 TraesCS1D01G421700 chr1D 79.401 267 43 10 1104 1364 477435000 477435260 9.590000e-41 178.0
5 TraesCS1D01G421700 chr1A 92.252 2349 136 30 779 3116 573817117 573819430 0.000000e+00 3288.0
6 TraesCS1D01G421700 chr1A 92.231 2317 131 19 1069 3363 573817360 573819649 0.000000e+00 3236.0
7 TraesCS1D01G421700 chr1A 83.531 1178 119 42 1735 2871 573921447 573922590 0.000000e+00 1031.0
8 TraesCS1D01G421700 chr1A 82.500 480 46 19 1318 1775 573920931 573921394 1.460000e-103 387.0
9 TraesCS1D01G421700 chr1A 89.623 212 19 2 1104 1315 573817473 573817681 1.990000e-67 267.0
10 TraesCS1D01G421700 chr1A 85.965 171 18 4 127 294 573816460 573816627 9.590000e-41 178.0
11 TraesCS1D01G421700 chr1A 82.927 205 26 8 1104 1305 573817512 573817710 3.450000e-40 176.0
12 TraesCS1D01G421700 chr1A 76.846 298 35 19 869 1143 573920683 573920969 1.630000e-28 137.0
13 TraesCS1D01G421700 chr1A 78.231 147 27 5 1101 1246 573817548 573817690 4.620000e-14 89.8
14 TraesCS1D01G421700 chr1B 90.495 1799 88 25 819 2587 665048567 665050312 0.000000e+00 2298.0
15 TraesCS1D01G421700 chr1B 83.316 977 84 31 1739 2689 665061335 665062258 0.000000e+00 828.0
16 TraesCS1D01G421700 chr1B 86.872 358 39 7 1 354 665044156 665044509 8.750000e-106 394.0
17 TraesCS1D01G421700 chr1B 83.376 391 42 10 1320 1691 665060835 665061221 1.160000e-89 340.0
18 TraesCS1D01G421700 chr1B 85.294 170 14 6 193 353 665047833 665048000 7.460000e-37 165.0
19 TraesCS1D01G421700 chr1B 82.081 173 31 0 1143 1315 665048841 665049013 7.520000e-32 148.0
20 TraesCS1D01G421700 chr7A 87.774 319 25 3 1417 1735 705667554 705667250 8.870000e-96 361.0
21 TraesCS1D01G421700 chr5A 90.517 232 16 1 1510 1735 41973612 41973843 5.450000e-78 302.0
22 TraesCS1D01G421700 chr5A 87.907 215 22 4 1510 1721 76127540 76127753 2.000000e-62 250.0
23 TraesCS1D01G421700 chr3A 89.252 214 23 0 2117 2330 434069272 434069059 5.530000e-68 268.0
24 TraesCS1D01G421700 chr5D 90.710 183 17 0 1518 1700 80205191 80205009 9.320000e-61 244.0
25 TraesCS1D01G421700 chr4A 80.631 222 36 6 2104 2323 143252301 143252517 7.460000e-37 165.0
26 TraesCS1D01G421700 chr4B 80.645 217 29 7 2112 2323 407056966 407056758 4.490000e-34 156.0
27 TraesCS1D01G421700 chr3B 81.022 137 16 9 1944 2077 13365300 13365429 2.140000e-17 100.0
28 TraesCS1D01G421700 chr2B 82.828 99 14 2 2112 2210 188855826 188855731 5.980000e-13 86.1
29 TraesCS1D01G421700 chr3D 100.000 31 0 0 1775 1805 5493897 5493867 1.300000e-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 TraesCS1D01G421700 chr1D 477433858 477437220 3362 False 2189.000000 6211 86.267333 1 3363 3 chr1D.!!$F1 3362
1 TraesCS1D01G421700 chr1D 477479670 477481326 1656 False 739.500000 1105 83.360000 1320 2871 2 chr1D.!!$F2 1551
2 TraesCS1D01G421700 chr1A 573816460 573819649 3189 False 1205.800000 3288 86.871500 127 3363 6 chr1A.!!$F1 3236
3 TraesCS1D01G421700 chr1A 573920683 573922590 1907 False 518.333333 1031 80.959000 869 2871 3 chr1A.!!$F2 2002
4 TraesCS1D01G421700 chr1B 665044156 665050312 6156 False 751.250000 2298 86.185500 1 2587 4 chr1B.!!$F1 2586
5 TraesCS1D01G421700 chr1B 665060835 665062258 1423 False 584.000000 828 83.346000 1320 2689 2 chr1B.!!$F2 1369

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
211 3701 0.036388 GCATCCCAGAAAGGTGTCGA 60.036 55.0 0.0 0.0 34.66 4.20 F
490 4036 0.105224 CATCTCTCCTCCAGCAGCAG 59.895 60.0 0.0 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 5836 0.179215 CTTCGTGACGCCATGCTTTC 60.179 55.0 0.0 0.0 0.00 2.62 R
2432 6431 1.631405 TACGAAAGGGAGGAACCGAA 58.369 50.0 0.0 0.0 40.11 4.30 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
22 23 3.141409 TTTGAACCAAAGAGGCCCC 57.859 52.632 0.00 0.00 43.14 5.80
33 34 1.415200 AGAGGCCCCTAGAAATCGAC 58.585 55.000 0.00 0.00 0.00 4.20
34 35 1.120530 GAGGCCCCTAGAAATCGACA 58.879 55.000 0.00 0.00 0.00 4.35
76 77 0.933796 AAACCAAACGCGGCATTTTG 59.066 45.000 12.47 11.98 33.30 2.44
87 88 3.199764 GCATTTTGAGCCAAAGCGT 57.800 47.368 1.52 0.00 46.67 5.07
99 100 1.066257 AAAGCGTGGCAGTTTGCTG 59.934 52.632 4.51 0.00 44.28 4.41
100 101 2.354074 AAAGCGTGGCAGTTTGCTGG 62.354 55.000 4.51 0.00 44.28 4.85
108 109 2.170187 TGGCAGTTTGCTGGAATTTTGT 59.830 40.909 0.67 0.00 44.28 2.83
111 112 2.219216 CAGTTTGCTGGAATTTTGTGCG 59.781 45.455 0.00 0.00 39.01 5.34
141 142 3.088532 TGTTCGAATTTAGCCAGGCATT 58.911 40.909 15.80 4.47 0.00 3.56
151 152 3.531934 AGCCAGGCATTTGCTATTTTC 57.468 42.857 15.80 0.00 41.70 2.29
154 155 2.195922 CAGGCATTTGCTATTTTCCGC 58.804 47.619 2.12 0.00 41.70 5.54
157 158 2.860136 GGCATTTGCTATTTTCCGCTTC 59.140 45.455 2.12 0.00 41.70 3.86
159 160 3.549070 GCATTTGCTATTTTCCGCTTCTG 59.451 43.478 0.00 0.00 38.21 3.02
169 173 2.420628 TCCGCTTCTGCAAAAACATG 57.579 45.000 0.00 0.00 39.64 3.21
200 3690 2.586079 CGCCGTAGTGCATCCCAG 60.586 66.667 0.00 0.00 0.00 4.45
206 3696 1.066143 CGTAGTGCATCCCAGAAAGGT 60.066 52.381 0.00 0.00 34.66 3.50
211 3701 0.036388 GCATCCCAGAAAGGTGTCGA 60.036 55.000 0.00 0.00 34.66 4.20
262 3756 2.574955 GGGTCACGGACAGCTGTCT 61.575 63.158 38.17 22.46 44.20 3.41
263 3757 1.080434 GGTCACGGACAGCTGTCTC 60.080 63.158 38.17 28.31 44.20 3.36
266 3760 0.900182 TCACGGACAGCTGTCTCCAT 60.900 55.000 38.17 22.16 44.20 3.41
281 3775 1.607178 CCATGGCAGGGCAGAAACA 60.607 57.895 4.75 0.00 0.00 2.83
290 3784 3.947841 GCAGAAACACACCGCGCA 61.948 61.111 8.75 0.00 0.00 6.09
294 3788 3.102107 GAAACACACCGCGCACACA 62.102 57.895 8.75 0.00 0.00 3.72
307 3801 1.714899 GCACACACACTGGACACACC 61.715 60.000 0.00 0.00 39.54 4.16
308 3802 0.107703 CACACACACTGGACACACCT 60.108 55.000 0.00 0.00 39.86 4.00
309 3803 0.107703 ACACACACTGGACACACCTG 60.108 55.000 0.00 0.00 42.26 4.00
312 3806 2.281761 CACTGGACACACCTGCCC 60.282 66.667 0.00 0.00 40.59 5.36
313 3807 2.772191 ACTGGACACACCTGCCCA 60.772 61.111 0.00 0.00 40.59 5.36
333 3832 2.286523 CCTGGTTCCGGAGACTGCT 61.287 63.158 3.34 0.00 0.00 4.24
334 3833 1.674057 CTGGTTCCGGAGACTGCTT 59.326 57.895 3.34 0.00 0.00 3.91
366 3889 1.271656 CCGGATCTCCACGGTTATACC 59.728 57.143 0.00 0.00 44.85 2.73
371 3894 2.823959 TCTCCACGGTTATACCCAGTT 58.176 47.619 0.00 0.00 33.75 3.16
372 3895 3.979911 TCTCCACGGTTATACCCAGTTA 58.020 45.455 0.00 0.00 33.75 2.24
429 3972 1.006519 CTCTCTCTCTCCACCCTCCAA 59.993 57.143 0.00 0.00 0.00 3.53
483 4029 3.531207 CGCCGCATCTCTCCTCCA 61.531 66.667 0.00 0.00 0.00 3.86
486 4032 2.429767 CCGCATCTCTCCTCCAGCA 61.430 63.158 0.00 0.00 0.00 4.41
490 4036 0.105224 CATCTCTCCTCCAGCAGCAG 59.895 60.000 0.00 0.00 0.00 4.24
545 4095 2.482333 CGGTTCGCTCGATCCTCCT 61.482 63.158 14.95 0.00 33.14 3.69
547 4097 1.384989 GGTTCGCTCGATCCTCCTGA 61.385 60.000 11.05 0.00 32.70 3.86
549 4099 1.135083 GTTCGCTCGATCCTCCTGAAA 60.135 52.381 0.00 0.00 0.00 2.69
550 4100 1.403814 TCGCTCGATCCTCCTGAAAT 58.596 50.000 0.00 0.00 0.00 2.17
551 4101 2.583143 TCGCTCGATCCTCCTGAAATA 58.417 47.619 0.00 0.00 0.00 1.40
561 4111 3.782523 TCCTCCTGAAATACTGCTTGGAT 59.217 43.478 0.00 0.00 0.00 3.41
565 4115 5.569355 TCCTGAAATACTGCTTGGATCAAA 58.431 37.500 0.00 0.00 0.00 2.69
567 4117 7.345691 TCCTGAAATACTGCTTGGATCAAATA 58.654 34.615 0.00 0.00 0.00 1.40
569 4119 7.333528 TGAAATACTGCTTGGATCAAATACC 57.666 36.000 0.00 0.00 0.00 2.73
605 4155 2.799502 TTTCAGTCGCGTCGCTCG 60.800 61.111 16.36 0.08 43.12 5.03
643 4197 0.740149 GGTTTCCACCCGTCGTTTTT 59.260 50.000 0.00 0.00 37.03 1.94
649 4203 4.144418 CCCGTCGTTTTTGGGTGA 57.856 55.556 0.00 0.00 38.18 4.02
652 4261 0.816421 CCGTCGTTTTTGGGTGAGGT 60.816 55.000 0.00 0.00 0.00 3.85
681 4290 5.672653 TTTGTTTGTTTGTTCGATCGTTG 57.327 34.783 15.94 0.00 0.00 4.10
683 4292 2.392933 TTGTTTGTTCGATCGTTGGC 57.607 45.000 15.94 4.68 0.00 4.52
692 4301 4.108299 ATCGTTGGCCGCCATGGA 62.108 61.111 18.40 13.84 42.00 3.41
716 4325 2.098870 GACGTTTCGCTGTGTTTGTTC 58.901 47.619 0.00 0.00 0.00 3.18
717 4326 1.735571 ACGTTTCGCTGTGTTTGTTCT 59.264 42.857 0.00 0.00 0.00 3.01
718 4327 2.222953 ACGTTTCGCTGTGTTTGTTCTC 60.223 45.455 0.00 0.00 0.00 2.87
720 4329 0.303493 TTCGCTGTGTTTGTTCTCGC 59.697 50.000 0.00 0.00 0.00 5.03
745 4413 1.010125 GTGCGTGCGTGTGTGATTT 60.010 52.632 0.00 0.00 0.00 2.17
759 4427 0.109781 TGATTTCGAGCCGCTTTTGC 60.110 50.000 0.00 0.00 43.23 3.68
760 4428 0.169009 GATTTCGAGCCGCTTTTGCT 59.831 50.000 0.00 0.00 44.80 3.91
761 4429 0.109597 ATTTCGAGCCGCTTTTGCTG 60.110 50.000 0.00 0.00 44.80 4.41
767 4435 2.564975 CCGCTTTTGCTGCTCTGG 59.435 61.111 0.00 0.00 44.80 3.86
768 4436 2.564975 CGCTTTTGCTGCTCTGGG 59.435 61.111 0.00 0.00 44.80 4.45
769 4437 1.968017 CGCTTTTGCTGCTCTGGGA 60.968 57.895 0.00 0.00 44.80 4.37
770 4438 1.881602 GCTTTTGCTGCTCTGGGAG 59.118 57.895 0.00 0.00 43.35 4.30
771 4439 1.593296 GCTTTTGCTGCTCTGGGAGG 61.593 60.000 0.00 0.00 43.35 4.30
772 4440 0.251077 CTTTTGCTGCTCTGGGAGGT 60.251 55.000 0.00 0.00 0.00 3.85
773 4441 0.538057 TTTTGCTGCTCTGGGAGGTG 60.538 55.000 0.00 0.00 0.00 4.00
774 4442 3.557903 TTGCTGCTCTGGGAGGTGC 62.558 63.158 0.00 0.00 0.00 5.01
776 4444 4.463879 CTGCTCTGGGAGGTGCGG 62.464 72.222 0.00 0.00 0.00 5.69
795 4463 0.647925 GCTTGCGATCGAGTTCCTTC 59.352 55.000 21.57 0.00 0.00 3.46
796 4464 1.281899 CTTGCGATCGAGTTCCTTCC 58.718 55.000 21.57 0.00 0.00 3.46
819 4487 1.165907 TTCTGAAACAGCCGGTGCAG 61.166 55.000 1.90 0.00 41.13 4.41
823 4491 4.873810 AACAGCCGGTGCAGTGCA 62.874 61.111 15.37 15.37 37.29 4.57
824 4492 4.873810 ACAGCCGGTGCAGTGCAA 62.874 61.111 21.67 0.56 41.47 4.08
825 4493 3.367743 CAGCCGGTGCAGTGCAAT 61.368 61.111 21.67 0.50 41.47 3.56
826 4494 3.367743 AGCCGGTGCAGTGCAATG 61.368 61.111 21.67 14.95 41.47 2.82
828 4496 3.367743 CCGGTGCAGTGCAATGCT 61.368 61.111 35.48 4.94 46.63 3.79
859 4527 2.579787 GTCCCGTGCTCGATCGTG 60.580 66.667 15.94 14.19 39.71 4.35
860 4528 2.748647 TCCCGTGCTCGATCGTGA 60.749 61.111 20.54 0.00 39.71 4.35
861 4529 2.278206 CCCGTGCTCGATCGTGAG 60.278 66.667 20.54 10.26 39.71 3.51
911 4592 3.969287 TCTGCTGCAGAGATTTACTGT 57.031 42.857 27.35 0.00 35.39 3.55
914 4595 5.354767 TCTGCTGCAGAGATTTACTGTATG 58.645 41.667 27.35 0.00 35.39 2.39
947 4629 7.915923 GGGATTTTTCTTCGAATATTTCTGACC 59.084 37.037 0.00 0.00 0.00 4.02
960 4642 0.815734 TCTGACCTTCCGATCCGTTC 59.184 55.000 0.00 0.00 0.00 3.95
1018 4701 1.617536 ATGCAGGAAGCTCCCCTCA 60.618 57.895 4.75 7.04 45.94 3.86
1072 4809 3.948719 GACCGGTGTGCTTCCCCA 61.949 66.667 14.63 0.00 0.00 4.96
1118 4855 4.410400 CTGCACCCCCTTCGTCCC 62.410 72.222 0.00 0.00 0.00 4.46
1121 4858 4.388499 CACCCCCTTCGTCCCGTG 62.388 72.222 0.00 0.00 0.00 4.94
1152 4889 2.107141 CCGATCGGCACCTCCTTC 59.893 66.667 23.37 0.00 0.00 3.46
1153 4890 2.278857 CGATCGGCACCTCCTTCG 60.279 66.667 7.38 0.00 33.76 3.79
1154 4891 2.893398 GATCGGCACCTCCTTCGT 59.107 61.111 0.00 0.00 0.00 3.85
1155 4892 1.227002 GATCGGCACCTCCTTCGTC 60.227 63.158 0.00 0.00 0.00 4.20
1156 4893 2.630592 GATCGGCACCTCCTTCGTCC 62.631 65.000 0.00 0.00 0.00 4.79
1157 4894 4.452733 CGGCACCTCCTTCGTCCC 62.453 72.222 0.00 0.00 0.00 4.46
1158 4895 4.452733 GGCACCTCCTTCGTCCCG 62.453 72.222 0.00 0.00 0.00 5.14
1159 4896 3.692406 GCACCTCCTTCGTCCCGT 61.692 66.667 0.00 0.00 0.00 5.28
1160 4897 2.261671 CACCTCCTTCGTCCCGTG 59.738 66.667 0.00 0.00 0.00 4.94
1161 4898 3.692406 ACCTCCTTCGTCCCGTGC 61.692 66.667 0.00 0.00 0.00 5.34
1162 4899 4.796231 CCTCCTTCGTCCCGTGCG 62.796 72.222 0.00 0.00 0.00 5.34
1277 5014 3.646715 CGCCCCCTTCACCCAGAA 61.647 66.667 0.00 0.00 34.41 3.02
1284 5021 1.380302 CTTCACCCAGAACCCCAGG 59.620 63.158 0.00 0.00 31.61 4.45
1316 5053 4.259131 CACCCCGTTCACCCCGTT 62.259 66.667 0.00 0.00 0.00 4.44
1318 5055 3.943691 CCCCGTTCACCCCGTTCA 61.944 66.667 0.00 0.00 0.00 3.18
1321 5058 2.667199 CGTTCACCCCGTTCACCC 60.667 66.667 0.00 0.00 0.00 4.61
1322 5059 2.281970 GTTCACCCCGTTCACCCC 60.282 66.667 0.00 0.00 0.00 4.95
1323 5060 3.943691 TTCACCCCGTTCACCCCG 61.944 66.667 0.00 0.00 0.00 5.73
1602 5486 0.865769 GCGTCATCAACAACGACCTT 59.134 50.000 0.00 0.00 41.29 3.50
1855 5844 2.182537 GCGGCAAGGGAAAGCATG 59.817 61.111 0.00 0.00 0.00 4.06
1929 5918 2.160205 TCCACTCGTTCGACTGAATCT 58.840 47.619 0.00 0.00 36.29 2.40
1971 5970 0.165944 CACCTGTTCGACGATTTGCC 59.834 55.000 0.00 0.00 0.00 4.52
2020 6019 4.651008 TTCGTGGGCGTGGACGTC 62.651 66.667 7.13 7.13 44.28 4.34
2331 6330 4.838152 CCGCCACTCCATCACCCG 62.838 72.222 0.00 0.00 0.00 5.28
2375 6374 0.882042 CCCCTGATCGCTACACATGC 60.882 60.000 0.00 0.00 0.00 4.06
2432 6431 2.534990 CTTCACTCCCTCACTCCTTCT 58.465 52.381 0.00 0.00 0.00 2.85
2481 6485 3.902881 TGCCACATTGGAAAACAAACT 57.097 38.095 0.00 0.00 43.46 2.66
2625 6644 6.438741 TGCTTTATTGTTACATGGGGATTGAA 59.561 34.615 0.00 0.00 0.00 2.69
2643 6662 4.868172 TGAACTGGGATTCTGGATCATT 57.132 40.909 0.00 0.00 36.43 2.57
2658 6677 7.504403 TCTGGATCATTAGAGAGGTGAATTTC 58.496 38.462 0.00 0.00 0.00 2.17
2671 6690 6.160459 AGAGGTGAATTTCTATATGTTGGGGT 59.840 38.462 0.00 0.00 0.00 4.95
2709 6731 9.734620 CATGGTTTGTTATATAGTCATTGGTTG 57.265 33.333 0.00 0.00 0.00 3.77
2710 6732 9.693739 ATGGTTTGTTATATAGTCATTGGTTGA 57.306 29.630 0.00 0.00 0.00 3.18
2738 6760 4.631813 ACATGATCTTTGTTCCTTAGTCGC 59.368 41.667 0.00 0.00 0.00 5.19
2742 6764 3.054878 TCTTTGTTCCTTAGTCGCGTTC 58.945 45.455 5.77 0.31 0.00 3.95
2792 6831 9.478019 GATGTAACTAAATCTCAATTCGTGTTG 57.522 33.333 0.00 0.00 0.00 3.33
2833 6872 3.369892 GCAGGAAGATCAGGCTACTTCAA 60.370 47.826 21.05 0.00 40.89 2.69
3009 7049 2.710096 TAGGACTGCATTAGTTGGGC 57.290 50.000 0.00 0.00 40.53 5.36
3024 7064 5.053978 AGTTGGGCTTATAAGGAAGATGG 57.946 43.478 14.28 0.00 0.00 3.51
3086 7126 2.575279 AGCAAGATCATCTTCCACACCT 59.425 45.455 0.00 0.00 33.78 4.00
3097 7137 4.648651 TCTTCCACACCTAGCCTAAAAAC 58.351 43.478 0.00 0.00 0.00 2.43
3098 7138 4.103469 TCTTCCACACCTAGCCTAAAAACA 59.897 41.667 0.00 0.00 0.00 2.83
3099 7139 3.746940 TCCACACCTAGCCTAAAAACAC 58.253 45.455 0.00 0.00 0.00 3.32
3100 7140 3.136809 TCCACACCTAGCCTAAAAACACA 59.863 43.478 0.00 0.00 0.00 3.72
3101 7141 3.502211 CCACACCTAGCCTAAAAACACAG 59.498 47.826 0.00 0.00 0.00 3.66
3102 7142 3.058224 CACACCTAGCCTAAAAACACAGC 60.058 47.826 0.00 0.00 0.00 4.40
3103 7143 3.181443 ACACCTAGCCTAAAAACACAGCT 60.181 43.478 0.00 0.00 37.58 4.24
3104 7144 3.189287 CACCTAGCCTAAAAACACAGCTG 59.811 47.826 13.48 13.48 35.03 4.24
3105 7145 3.181443 ACCTAGCCTAAAAACACAGCTGT 60.181 43.478 15.25 15.25 35.03 4.40
3106 7146 3.821033 CCTAGCCTAAAAACACAGCTGTT 59.179 43.478 18.94 4.70 42.81 3.16
3129 7169 9.825109 TGTTTGCTAAAAACTAAATTTTAGGCT 57.175 25.926 18.05 0.00 46.08 4.58
3185 7225 7.037873 ACCCGAACCTATATGGATGCTATTTTA 60.038 37.037 0.00 0.00 39.71 1.52
3247 7287 4.006780 ACCAATCCAAATGAACAAAGCC 57.993 40.909 0.00 0.00 0.00 4.35
3260 7300 5.656480 TGAACAAAGCCTAAAACCAAAGTC 58.344 37.500 0.00 0.00 0.00 3.01
3279 7319 2.668280 GCGGTCGTGAGAAGCCAAC 61.668 63.158 0.00 0.00 45.01 3.77
3304 7345 1.854280 ACCCCTAAACTTTCACCACCA 59.146 47.619 0.00 0.00 0.00 4.17
3337 7378 4.113815 CCGCCTCCATCCCAGCAA 62.114 66.667 0.00 0.00 0.00 3.91
3347 7388 2.449464 CATCCCAGCAAATTCAGGTCA 58.551 47.619 0.00 0.00 0.00 4.02
3350 7391 1.402968 CCCAGCAAATTCAGGTCATCG 59.597 52.381 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.991920 CTAGGGGCCTCTTTGGTTCA 59.008 55.000 12.52 0.00 38.35 3.18
10 11 2.746472 CGATTTCTAGGGGCCTCTTTGG 60.746 54.545 12.52 1.29 39.35 3.28
87 88 2.170187 ACAAAATTCCAGCAAACTGCCA 59.830 40.909 0.00 0.00 46.52 4.92
99 100 1.713932 GACGCTTTCGCACAAAATTCC 59.286 47.619 0.00 0.00 39.84 3.01
100 101 2.401720 CAGACGCTTTCGCACAAAATTC 59.598 45.455 0.00 0.00 39.84 2.17
108 109 0.872451 TTCGAACAGACGCTTTCGCA 60.872 50.000 0.00 6.18 43.44 5.10
111 112 4.082447 GCTAAATTCGAACAGACGCTTTC 58.918 43.478 0.00 0.00 0.00 2.62
116 117 2.348666 CCTGGCTAAATTCGAACAGACG 59.651 50.000 11.55 4.26 0.00 4.18
118 119 2.290008 TGCCTGGCTAAATTCGAACAGA 60.290 45.455 21.03 0.00 0.00 3.41
120 121 2.192664 TGCCTGGCTAAATTCGAACA 57.807 45.000 21.03 0.00 0.00 3.18
141 142 2.158559 TGCAGAAGCGGAAAATAGCAA 58.841 42.857 0.00 0.00 46.23 3.91
151 152 0.785979 GCATGTTTTTGCAGAAGCGG 59.214 50.000 0.00 0.00 46.23 5.52
159 160 1.888512 TCCTCCTCTGCATGTTTTTGC 59.111 47.619 0.00 0.00 43.07 3.68
169 173 4.828925 GGCGTGCTCCTCCTCTGC 62.829 72.222 0.00 0.00 0.00 4.26
171 175 3.640257 TACGGCGTGCTCCTCCTCT 62.640 63.158 24.86 0.00 0.00 3.69
188 192 1.985159 ACACCTTTCTGGGATGCACTA 59.015 47.619 0.00 0.00 41.11 2.74
200 3690 0.036388 TGCCCTCATCGACACCTTTC 60.036 55.000 0.00 0.00 0.00 2.62
206 3696 3.381983 ACGCTGCCCTCATCGACA 61.382 61.111 0.00 0.00 35.59 4.35
211 3701 4.827087 CGAGCACGCTGCCCTCAT 62.827 66.667 0.00 0.00 46.52 2.90
262 3756 1.304381 GTTTCTGCCCTGCCATGGA 60.304 57.895 18.40 0.00 0.00 3.41
263 3757 1.607178 TGTTTCTGCCCTGCCATGG 60.607 57.895 7.63 7.63 0.00 3.66
266 3760 1.827789 GTGTGTTTCTGCCCTGCCA 60.828 57.895 0.00 0.00 0.00 4.92
281 3775 4.830765 AGTGTGTGTGCGCGGTGT 62.831 61.111 8.83 0.00 0.00 4.16
290 3784 0.107703 CAGGTGTGTCCAGTGTGTGT 60.108 55.000 0.00 0.00 39.02 3.72
294 3788 2.510906 GGCAGGTGTGTCCAGTGT 59.489 61.111 0.00 0.00 39.02 3.55
307 3801 4.722700 CGGAACCAGGGTGGGCAG 62.723 72.222 0.00 0.00 43.37 4.85
312 3806 1.913762 AGTCTCCGGAACCAGGGTG 60.914 63.158 5.23 0.00 0.00 4.61
313 3807 1.913762 CAGTCTCCGGAACCAGGGT 60.914 63.158 5.23 0.00 0.00 4.34
366 3889 1.850755 ACTGGGGGTGGGTAACTGG 60.851 63.158 0.00 0.00 0.00 4.00
371 3894 2.605295 CGTCACTGGGGGTGGGTA 60.605 66.667 0.00 0.00 45.38 3.69
389 3928 2.042435 AGAGGAGGCGGAGGAAGG 60.042 66.667 0.00 0.00 0.00 3.46
391 3930 1.076632 GAGAGAGGAGGCGGAGGAA 60.077 63.158 0.00 0.00 0.00 3.36
506 4052 4.093952 CTGCCGGCTTGCTGTTCG 62.094 66.667 29.70 0.57 0.00 3.95
508 4054 4.586235 ACCTGCCGGCTTGCTGTT 62.586 61.111 29.70 1.40 0.00 3.16
534 4084 3.320541 AGCAGTATTTCAGGAGGATCGAG 59.679 47.826 0.00 0.00 34.37 4.04
545 4095 6.321181 GGGTATTTGATCCAAGCAGTATTTCA 59.679 38.462 0.00 0.00 0.00 2.69
547 4097 6.435164 AGGGTATTTGATCCAAGCAGTATTT 58.565 36.000 0.00 0.00 0.00 1.40
549 4099 5.370880 AGAGGGTATTTGATCCAAGCAGTAT 59.629 40.000 0.00 0.00 0.00 2.12
550 4100 4.721776 AGAGGGTATTTGATCCAAGCAGTA 59.278 41.667 0.00 0.00 0.00 2.74
551 4101 3.525199 AGAGGGTATTTGATCCAAGCAGT 59.475 43.478 0.00 0.00 0.00 4.40
561 4111 2.832129 ACTCAAGCGAGAGGGTATTTGA 59.168 45.455 12.15 0.00 42.34 2.69
565 4115 4.406003 ACAATTACTCAAGCGAGAGGGTAT 59.594 41.667 12.15 1.50 42.34 2.73
567 4117 2.567615 ACAATTACTCAAGCGAGAGGGT 59.432 45.455 12.15 0.00 42.34 4.34
569 4119 4.690748 TGAAACAATTACTCAAGCGAGAGG 59.309 41.667 12.15 0.00 42.34 3.69
605 4155 1.750572 CTCTGACTGATCAAGCGCGC 61.751 60.000 26.66 26.66 33.30 6.86
662 4271 2.466205 GCCAACGATCGAACAAACAAAC 59.534 45.455 24.34 0.00 0.00 2.93
692 4301 0.599204 AACACAGCGAAACGTCCGAT 60.599 50.000 13.43 4.98 0.00 4.18
697 4306 1.735571 AGAACAAACACAGCGAAACGT 59.264 42.857 0.00 0.00 0.00 3.99
727 4395 0.991770 GAAATCACACACGCACGCAC 60.992 55.000 0.00 0.00 0.00 5.34
731 4399 0.451135 GCTCGAAATCACACACGCAC 60.451 55.000 0.00 0.00 0.00 5.34
736 4404 0.602638 AAGCGGCTCGAAATCACACA 60.603 50.000 1.45 0.00 0.00 3.72
745 4413 3.726517 GCAGCAAAAGCGGCTCGA 61.727 61.111 1.45 0.00 40.23 4.04
759 4427 4.463879 CCGCACCTCCCAGAGCAG 62.464 72.222 0.00 0.00 0.00 4.24
762 4430 3.710722 AAGCCGCACCTCCCAGAG 61.711 66.667 0.00 0.00 0.00 3.35
763 4431 4.020617 CAAGCCGCACCTCCCAGA 62.021 66.667 0.00 0.00 0.00 3.86
768 4436 3.567797 GATCGCAAGCCGCACCTC 61.568 66.667 0.00 0.00 42.60 3.85
771 4439 3.918220 CTCGATCGCAAGCCGCAC 61.918 66.667 11.09 0.00 42.60 5.34
772 4440 3.932580 AACTCGATCGCAAGCCGCA 62.933 57.895 11.09 0.00 42.60 5.69
773 4441 3.144120 GAACTCGATCGCAAGCCGC 62.144 63.158 11.09 0.00 36.73 6.53
774 4442 2.517450 GGAACTCGATCGCAAGCCG 61.517 63.158 11.09 0.00 38.61 5.52
775 4443 0.741221 AAGGAACTCGATCGCAAGCC 60.741 55.000 11.09 9.36 38.49 4.35
776 4444 0.647925 GAAGGAACTCGATCGCAAGC 59.352 55.000 11.09 0.00 38.49 4.01
777 4445 1.281899 GGAAGGAACTCGATCGCAAG 58.718 55.000 11.09 6.23 38.49 4.01
795 4463 0.447801 CCGGCTGTTTCAGAAATCGG 59.552 55.000 0.00 7.11 32.44 4.18
796 4464 1.135972 CACCGGCTGTTTCAGAAATCG 60.136 52.381 0.00 2.10 32.44 3.34
819 4487 2.810439 TTAAACCACCAGCATTGCAC 57.190 45.000 11.91 0.00 0.00 4.57
823 4491 3.192633 GGACGAATTAAACCACCAGCATT 59.807 43.478 0.00 0.00 0.00 3.56
824 4492 2.752903 GGACGAATTAAACCACCAGCAT 59.247 45.455 0.00 0.00 0.00 3.79
825 4493 2.156098 GGACGAATTAAACCACCAGCA 58.844 47.619 0.00 0.00 0.00 4.41
826 4494 1.471287 GGGACGAATTAAACCACCAGC 59.529 52.381 0.00 0.00 0.00 4.85
859 4527 4.617645 CGCTAGCATCCGTAATAACTTCTC 59.382 45.833 16.45 0.00 0.00 2.87
860 4528 4.547532 CGCTAGCATCCGTAATAACTTCT 58.452 43.478 16.45 0.00 0.00 2.85
861 4529 3.673809 CCGCTAGCATCCGTAATAACTTC 59.326 47.826 16.45 0.00 0.00 3.01
862 4530 3.650139 CCGCTAGCATCCGTAATAACTT 58.350 45.455 16.45 0.00 0.00 2.66
863 4531 2.609737 GCCGCTAGCATCCGTAATAACT 60.610 50.000 16.45 0.00 42.97 2.24
864 4532 1.725164 GCCGCTAGCATCCGTAATAAC 59.275 52.381 16.45 0.00 42.97 1.89
865 4533 2.074547 GCCGCTAGCATCCGTAATAA 57.925 50.000 16.45 0.00 42.97 1.40
866 4534 3.806591 GCCGCTAGCATCCGTAATA 57.193 52.632 16.45 0.00 42.97 0.98
867 4535 4.675404 GCCGCTAGCATCCGTAAT 57.325 55.556 16.45 0.00 42.97 1.89
908 4589 7.480542 CGAAGAAAAATCCCGTAAAACATACAG 59.519 37.037 0.00 0.00 0.00 2.74
910 4591 7.520686 TCGAAGAAAAATCCCGTAAAACATAC 58.479 34.615 0.00 0.00 0.00 2.39
911 4592 7.670009 TCGAAGAAAAATCCCGTAAAACATA 57.330 32.000 0.00 0.00 0.00 2.29
914 4595 9.563898 AATATTCGAAGAAAAATCCCGTAAAAC 57.436 29.630 3.35 0.00 45.90 2.43
1135 4872 2.107141 GAAGGAGGTGCCGATCGG 59.893 66.667 30.03 30.03 43.43 4.18
1136 4873 2.278857 CGAAGGAGGTGCCGATCG 60.279 66.667 8.51 8.51 43.43 3.69
1137 4874 1.227002 GACGAAGGAGGTGCCGATC 60.227 63.158 0.00 0.00 43.43 3.69
1138 4875 2.722201 GGACGAAGGAGGTGCCGAT 61.722 63.158 0.00 0.00 43.43 4.18
1139 4876 3.379445 GGACGAAGGAGGTGCCGA 61.379 66.667 0.00 0.00 43.43 5.54
1140 4877 4.452733 GGGACGAAGGAGGTGCCG 62.453 72.222 0.00 0.00 43.43 5.69
1177 4914 4.452733 GACGAAGGGGGTGCCGAG 62.453 72.222 0.00 0.00 0.00 4.63
1261 4998 2.035783 GTTCTGGGTGAAGGGGGC 59.964 66.667 0.00 0.00 35.01 5.80
1305 5042 2.281970 GGGGTGAACGGGGTGAAC 60.282 66.667 0.00 0.00 0.00 3.18
1309 5046 3.944945 GAACGGGGTGAACGGGGT 61.945 66.667 0.00 0.00 35.23 4.95
1310 5047 3.943691 TGAACGGGGTGAACGGGG 61.944 66.667 0.00 0.00 35.23 5.73
1316 5053 4.938074 TCGGGGTGAACGGGGTGA 62.938 66.667 0.00 0.00 0.00 4.02
1323 5060 4.410400 CTGGGGCTCGGGGTGAAC 62.410 72.222 0.00 0.00 0.00 3.18
1840 5829 2.580815 GCCATGCTTTCCCTTGCC 59.419 61.111 0.00 0.00 0.00 4.52
1841 5830 2.182537 CGCCATGCTTTCCCTTGC 59.817 61.111 0.00 0.00 0.00 4.01
1842 5831 1.243342 TGACGCCATGCTTTCCCTTG 61.243 55.000 0.00 0.00 0.00 3.61
1843 5832 1.074775 TGACGCCATGCTTTCCCTT 59.925 52.632 0.00 0.00 0.00 3.95
1844 5833 1.675641 GTGACGCCATGCTTTCCCT 60.676 57.895 0.00 0.00 0.00 4.20
1845 5834 2.877691 GTGACGCCATGCTTTCCC 59.122 61.111 0.00 0.00 0.00 3.97
1846 5835 1.573829 TTCGTGACGCCATGCTTTCC 61.574 55.000 0.00 0.00 0.00 3.13
1847 5836 0.179215 CTTCGTGACGCCATGCTTTC 60.179 55.000 0.00 0.00 0.00 2.62
1848 5837 1.868997 CTTCGTGACGCCATGCTTT 59.131 52.632 0.00 0.00 0.00 3.51
1971 5970 2.174107 CGCATTGCACAGACACCG 59.826 61.111 9.69 0.00 0.00 4.94
2331 6330 2.029307 GAGGGGGATGTAGTCGGCAC 62.029 65.000 0.00 0.00 0.00 5.01
2375 6374 4.147449 TCGGCGATGGAGCACTGG 62.147 66.667 4.99 0.00 39.27 4.00
2432 6431 1.631405 TACGAAAGGGAGGAACCGAA 58.369 50.000 0.00 0.00 40.11 4.30
2606 6616 4.711355 CCAGTTCAATCCCCATGTAACAAT 59.289 41.667 0.00 0.00 0.00 2.71
2625 6644 5.471424 TCTCTAATGATCCAGAATCCCAGT 58.529 41.667 0.00 0.00 33.01 4.00
2643 6662 8.651389 CCCAACATATAGAAATTCACCTCTCTA 58.349 37.037 0.00 0.00 0.00 2.43
2658 6677 7.827236 TGTAAGAAAGAACACCCCAACATATAG 59.173 37.037 0.00 0.00 0.00 1.31
2700 6721 8.298854 CAAAGATCATGTAACTTCAACCAATGA 58.701 33.333 0.00 0.00 35.85 2.57
2709 6731 9.220767 ACTAAGGAACAAAGATCATGTAACTTC 57.779 33.333 16.70 7.69 32.58 3.01
2710 6732 9.220767 GACTAAGGAACAAAGATCATGTAACTT 57.779 33.333 17.07 17.07 33.89 2.66
2742 6764 2.638480 TGCCCATAATTTCCTCTCGG 57.362 50.000 0.00 0.00 0.00 4.63
2761 6783 8.916654 CGAATTGAGATTTAGTTACATCGCTAT 58.083 33.333 0.00 0.00 0.00 2.97
2792 6831 3.843999 TGCCACAAGACAGAACAAAAAC 58.156 40.909 0.00 0.00 0.00 2.43
2874 6914 7.603180 ACATCTATACTTGACATGCTCCTAA 57.397 36.000 0.00 0.00 0.00 2.69
2940 6980 7.565323 AGAACATCAATCTTAAAGATCAGGC 57.435 36.000 0.00 0.00 32.89 4.85
3000 7040 6.601332 CCATCTTCCTTATAAGCCCAACTAA 58.399 40.000 6.99 0.00 0.00 2.24
3002 7042 4.689983 GCCATCTTCCTTATAAGCCCAACT 60.690 45.833 6.99 0.00 0.00 3.16
3009 7049 4.336889 TGTCCGCCATCTTCCTTATAAG 57.663 45.455 5.43 5.43 0.00 1.73
3024 7064 2.939103 ACTCTCAAGCATAATTGTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
3098 7138 9.161629 AAAATTTAGTTTTTAGCAAACAGCTGT 57.838 25.926 15.25 15.25 44.16 4.40
3103 7143 9.825109 AGCCTAAAATTTAGTTTTTAGCAAACA 57.175 25.926 11.34 0.00 43.27 2.83
3145 7185 0.539986 TCGGGTTAGTTGATGGAGCC 59.460 55.000 0.00 0.00 0.00 4.70
3155 7195 4.020485 GCATCCATATAGGTTCGGGTTAGT 60.020 45.833 0.00 0.00 39.02 2.24
3160 7200 5.359194 AATAGCATCCATATAGGTTCGGG 57.641 43.478 0.00 0.00 39.02 5.14
3247 7287 1.136446 CGACCGCGACTTTGGTTTTAG 60.136 52.381 8.23 0.00 38.99 1.85
3260 7300 4.717629 TGGCTTCTCACGACCGCG 62.718 66.667 0.00 0.00 44.79 6.46
3279 7319 3.244770 TGGTGAAAGTTTAGGGGTAGCAG 60.245 47.826 0.00 0.00 0.00 4.24
3290 7331 2.014128 CGACTGTGGTGGTGAAAGTTT 58.986 47.619 0.00 0.00 0.00 2.66
3304 7345 4.078516 GGGTTAGGCGGCGACTGT 62.079 66.667 28.54 1.42 0.00 3.55
3323 7364 2.029623 CTGAATTTGCTGGGATGGAGG 58.970 52.381 0.00 0.00 0.00 4.30
3328 7369 2.905415 TGACCTGAATTTGCTGGGAT 57.095 45.000 0.00 0.00 0.00 3.85
3336 7377 1.338674 TGGCGACGATGACCTGAATTT 60.339 47.619 0.00 0.00 0.00 1.82
3337 7378 0.249120 TGGCGACGATGACCTGAATT 59.751 50.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.