Multiple sequence alignment - TraesCS4B01G087200

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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 TraesCS4B01G087200 chr4B 100.000 6125 0 0 1 6125 87414580 87420704 0.000000e+00 11311
1 TraesCS4B01G087200 chr4A 91.780 5426 241 91 831 6125 537596685 537591334 0.000000e+00 7360
2 TraesCS4B01G087200 chr4A 90.780 282 7 3 96 374 537597467 537597202 5.840000e-95 359
3 TraesCS4B01G087200 chr4A 95.000 180 5 3 1 180 537597688 537597513 4.680000e-71 279
4 TraesCS4B01G087200 chr4A 94.048 84 2 2 760 840 537596797 537596714 2.320000e-24 124
5 TraesCS4B01G087200 chr4A 91.011 89 3 4 96 183 537597530 537597446 1.400000e-21 115
6 TraesCS4B01G087200 chr4D 92.286 2774 121 50 358 3066 58147250 58149995 0.000000e+00 3851
7 TraesCS4B01G087200 chr4D 92.899 2239 70 38 3062 5224 58152940 58155165 0.000000e+00 3171
8 TraesCS4B01G087200 chr4D 94.326 282 7 3 96 374 58146959 58147234 2.040000e-114 424
9 TraesCS4B01G087200 chr4D 82.890 526 22 16 5621 6122 58155407 58155888 1.590000e-110 411
10 TraesCS4B01G087200 chr4D 93.478 184 7 4 1 183 58146801 58146980 1.010000e-67 268
11 TraesCS4B01G087200 chr1A 78.835 704 116 23 1608 2304 320615576 320614899 1.570000e-120 444
12 TraesCS4B01G087200 chr1A 87.324 355 35 6 3114 3460 320614139 320613787 1.240000e-106 398
13 TraesCS4B01G087200 chr1B 85.955 356 39 3 3111 3457 572807539 572807892 2.700000e-98 370
14 TraesCS4B01G087200 chr3B 85.674 356 40 7 3114 3460 206053544 206053191 1.250000e-96 364
15 TraesCS4B01G087200 chr3B 85.169 236 29 5 2880 3112 205379137 205378905 2.850000e-58 237


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 TraesCS4B01G087200 chr4B 87414580 87420704 6124 False 11311.0 11311 100.0000 1 6125 1 chr4B.!!$F1 6124
1 TraesCS4B01G087200 chr4A 537591334 537597688 6354 True 1647.4 7360 92.5238 1 6125 5 chr4A.!!$R1 6124
2 TraesCS4B01G087200 chr4D 58146801 58155888 9087 False 1625.0 3851 91.1758 1 6122 5 chr4D.!!$F1 6121
3 TraesCS4B01G087200 chr1A 320613787 320615576 1789 True 421.0 444 83.0795 1608 3460 2 chr1A.!!$R1 1852

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
229 430 0.179009 AGACATGCATTGGGATCCGG 60.179 55.000 5.45 0.0 0.00 5.14 F
611 869 0.305922 GCGTCAATGCTATCTGGCAC 59.694 55.000 0.00 0.0 45.36 5.01 F
975 1300 1.613925 CCGCAGAATCCGAGATTAGGA 59.386 52.381 0.00 0.0 42.69 2.94 F
1447 1809 0.944311 CGTGCTACGGAACAACTGCT 60.944 55.000 1.40 0.0 38.08 4.24 F
2353 2744 0.591170 CGTGTTGGTTCAAGCCGAAT 59.409 50.000 0.00 0.0 35.63 3.34 F
4012 7435 0.694771 AGAGGACCAGCTTGATTGCA 59.305 50.000 0.00 0.0 34.99 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1463 0.252375 ATGTGGGGAAGGCAGCAAAT 60.252 50.000 0.00 0.0 0.00 2.32 R
1435 1797 0.320771 AGGCACTAGCAGTTGTTCCG 60.321 55.000 0.00 0.0 44.61 4.30 R
2245 2634 1.067516 GCACCAGTGATGTTGCAACTT 59.932 47.619 28.61 23.0 0.00 2.66 R
2725 3118 1.208165 AAGGTGTCCTTAGCCTGGGG 61.208 60.000 0.00 0.0 42.74 4.96 R
4110 7542 0.104487 TTTACCACAGAACCGCGTCA 59.896 50.000 4.92 0.0 0.00 4.35 R
5436 9011 0.320697 AGCGGAACTGTGTTCTACCC 59.679 55.000 9.81 0.0 0.00 3.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 4.992381 ATTCTTCTGAACAAGTACGCAC 57.008 40.909 0.00 0.00 34.71 5.34
54 55 2.390938 TCTTCTGAACAAGTACGCACG 58.609 47.619 0.00 0.00 0.00 5.34
224 425 2.040145 TCTTGACAGACATGCATTGGGA 59.960 45.455 0.00 0.00 0.00 4.37
225 426 2.812836 TGACAGACATGCATTGGGAT 57.187 45.000 0.00 0.00 0.00 3.85
226 427 2.646930 TGACAGACATGCATTGGGATC 58.353 47.619 0.00 0.00 0.00 3.36
227 428 1.952296 GACAGACATGCATTGGGATCC 59.048 52.381 1.92 1.92 0.00 3.36
228 429 0.949397 CAGACATGCATTGGGATCCG 59.051 55.000 5.45 0.00 0.00 4.18
229 430 0.179009 AGACATGCATTGGGATCCGG 60.179 55.000 5.45 0.00 0.00 5.14
230 431 1.152694 ACATGCATTGGGATCCGGG 60.153 57.895 5.45 0.00 0.00 5.73
231 432 1.151221 CATGCATTGGGATCCGGGA 59.849 57.895 5.45 0.00 0.00 5.14
232 433 0.892358 CATGCATTGGGATCCGGGAG 60.892 60.000 5.45 0.00 0.00 4.30
233 434 2.595754 GCATTGGGATCCGGGAGC 60.596 66.667 3.04 3.04 0.00 4.70
234 435 2.281070 CATTGGGATCCGGGAGCG 60.281 66.667 5.45 0.00 0.00 5.03
235 436 3.560251 ATTGGGATCCGGGAGCGG 61.560 66.667 5.45 0.00 0.00 5.52
263 464 1.003233 AGGCGCCTTGAGGTTTCTC 60.003 57.895 27.08 0.00 40.36 2.87
398 640 4.094739 TGATGATGTGCAGAAATTGTACGG 59.905 41.667 0.00 0.00 44.39 4.02
401 643 1.876799 TGTGCAGAAATTGTACGGTGG 59.123 47.619 0.00 0.00 44.39 4.61
497 740 5.844301 AATCAAATCCGCACAAAATTCAC 57.156 34.783 0.00 0.00 0.00 3.18
514 757 9.108284 CAAAATTCACAAAATGACCCTTTTACT 57.892 29.630 0.00 0.00 36.92 2.24
554 811 2.285969 ATGCTCCTGGCCTGAGGT 60.286 61.111 20.12 0.00 40.92 3.85
556 813 3.325753 GCTCCTGGCCTGAGGTGT 61.326 66.667 20.12 0.00 34.36 4.16
607 865 1.959042 AAGGGCGTCAATGCTATCTG 58.041 50.000 0.00 0.00 34.52 2.90
611 869 0.305922 GCGTCAATGCTATCTGGCAC 59.694 55.000 0.00 0.00 45.36 5.01
721 979 5.551233 AGATCAAATCTGTCCGTTTTCTCA 58.449 37.500 0.00 0.00 38.44 3.27
727 985 3.601435 TCTGTCCGTTTTCTCACACAAA 58.399 40.909 0.00 0.00 0.00 2.83
894 1207 3.074538 GCCAGTATCAAACCCTATCCCAT 59.925 47.826 0.00 0.00 0.00 4.00
895 1208 4.807643 GCCAGTATCAAACCCTATCCCATC 60.808 50.000 0.00 0.00 0.00 3.51
896 1209 4.599241 CCAGTATCAAACCCTATCCCATCT 59.401 45.833 0.00 0.00 0.00 2.90
915 1237 2.335712 CCTTTGGTCTTGGCGGCTC 61.336 63.158 11.43 0.00 0.00 4.70
975 1300 1.613925 CCGCAGAATCCGAGATTAGGA 59.386 52.381 0.00 0.00 42.69 2.94
978 1303 3.192422 CGCAGAATCCGAGATTAGGATCT 59.808 47.826 0.00 0.00 46.99 2.75
1035 1363 4.364817 CGGTTCCACCAGCGTAAA 57.635 55.556 0.00 0.00 38.47 2.01
1080 1428 7.576236 TCTTCTTCTTCTTTCGTTTTGCATAG 58.424 34.615 0.00 0.00 0.00 2.23
1111 1461 4.114997 CGCCGCCGCCAATCTTTT 62.115 61.111 0.00 0.00 0.00 2.27
1112 1462 2.506881 GCCGCCGCCAATCTTTTG 60.507 61.111 0.00 0.00 0.00 2.44
1113 1463 2.988688 GCCGCCGCCAATCTTTTGA 61.989 57.895 0.00 0.00 34.60 2.69
1154 1515 3.009473 TCCCCTTTCTCCATTCTTCAGTG 59.991 47.826 0.00 0.00 0.00 3.66
1159 1520 4.543590 TTCTCCATTCTTCAGTGTCTCC 57.456 45.455 0.00 0.00 0.00 3.71
1174 1535 5.586243 CAGTGTCTCCGTATCCATGAAATTT 59.414 40.000 0.00 0.00 0.00 1.82
1208 1570 7.252612 TCCCTGAAATATCACTGAGTTGTTA 57.747 36.000 0.00 0.00 0.00 2.41
1266 1628 3.128589 CCATCGTTTAATCAACCAGGTGG 59.871 47.826 0.00 0.00 42.17 4.61
1334 1696 1.950973 GCTCTCCGTCCAGGGACTTC 61.951 65.000 15.95 0.00 42.54 3.01
1404 1766 5.251700 TCCAGCTTTTCTATCCTTTTCCTCT 59.748 40.000 0.00 0.00 0.00 3.69
1407 1769 7.039434 CCAGCTTTTCTATCCTTTTCCTCTTTT 60.039 37.037 0.00 0.00 0.00 2.27
1408 1770 8.026026 CAGCTTTTCTATCCTTTTCCTCTTTTC 58.974 37.037 0.00 0.00 0.00 2.29
1435 1797 4.870426 TCAGATTTCTCATTTCCGTGCTAC 59.130 41.667 0.00 0.00 0.00 3.58
1447 1809 0.944311 CGTGCTACGGAACAACTGCT 60.944 55.000 1.40 0.00 38.08 4.24
1463 1825 5.046591 ACAACTGCTAGTGCCTTGTAGATTA 60.047 40.000 8.15 0.00 37.33 1.75
1469 1839 3.206150 AGTGCCTTGTAGATTAATGGCG 58.794 45.455 7.50 0.00 42.87 5.69
1473 1843 4.065088 GCCTTGTAGATTAATGGCGATGA 58.935 43.478 0.00 0.00 0.00 2.92
1477 1847 7.466455 GCCTTGTAGATTAATGGCGATGATATG 60.466 40.741 0.00 0.00 0.00 1.78
1478 1848 7.011763 CCTTGTAGATTAATGGCGATGATATGG 59.988 40.741 0.00 0.00 0.00 2.74
1484 1854 4.350368 AATGGCGATGATATGGTGTGTA 57.650 40.909 0.00 0.00 0.00 2.90
1485 1855 3.106242 TGGCGATGATATGGTGTGTAC 57.894 47.619 0.00 0.00 0.00 2.90
1528 1904 5.828859 TCCTTATCTCTGTACTTGTCTAGGC 59.171 44.000 0.00 0.00 0.00 3.93
1594 1971 1.874231 TGCCATTGCAGCAACATTTTG 59.126 42.857 10.85 4.21 44.23 2.44
1630 2010 6.199719 GCAAGGTGGTTATGTAGTAATACGAC 59.800 42.308 0.00 0.00 0.00 4.34
1695 2075 9.271828 CTTTTATTACCTGGCAACTTCATTTTT 57.728 29.630 0.00 0.00 37.61 1.94
1764 2144 7.924541 AGAGGGATACAGTTATGGTACAAAAA 58.075 34.615 0.00 0.00 40.76 1.94
1792 2172 3.066342 TCGGTAGGATGACGATCTTCAAC 59.934 47.826 5.94 3.45 0.00 3.18
1794 2174 3.132289 GGTAGGATGACGATCTTCAACCA 59.868 47.826 24.47 11.85 40.18 3.67
1811 2191 8.956426 TCTTCAACCACTTTGGAATATATTGTC 58.044 33.333 1.78 0.00 40.96 3.18
1933 2313 5.586643 GTCATGGATTCTTCAGGGTTAGTTC 59.413 44.000 0.00 0.00 0.00 3.01
2062 2443 5.301835 ACTCAGAGCATGCCATATAAACT 57.698 39.130 15.66 0.00 0.00 2.66
2245 2634 1.624312 TGTGCACCGGTCTAAATGGTA 59.376 47.619 15.69 0.00 33.82 3.25
2279 2668 2.595463 GTGCACAGGAGGCTTGCA 60.595 61.111 13.17 7.47 43.89 4.08
2297 2686 2.036992 TGCATTTTGGTTCAAGCCGAAT 59.963 40.909 0.00 0.00 35.63 3.34
2353 2744 0.591170 CGTGTTGGTTCAAGCCGAAT 59.409 50.000 0.00 0.00 35.63 3.34
2420 2813 2.628178 ACACTGTCTTCTTGATGTCCGA 59.372 45.455 0.00 0.00 0.00 4.55
2630 3023 2.557490 TGCTTTGCATAGCATGTTGTCA 59.443 40.909 25.36 2.80 45.72 3.58
2755 3149 6.776603 GGCTAAGGACACCTTATCTCTAACTA 59.223 42.308 10.14 0.00 44.01 2.24
2805 3199 5.693769 TCCTAACTTTAAGATGACAGGGG 57.306 43.478 0.00 0.00 0.00 4.79
2808 3202 5.648092 CCTAACTTTAAGATGACAGGGGTTG 59.352 44.000 0.00 0.00 0.00 3.77
2875 3269 9.090692 CTGCTAGTAAAAACTACGCCTTATTAA 57.909 33.333 0.00 0.00 0.00 1.40
3320 6741 5.061435 CAGCATCAGGTTCATAATCGTATCG 59.939 44.000 0.00 0.00 0.00 2.92
3337 6758 5.574055 TCGTATCGTTTGTTGTGACCTAATC 59.426 40.000 0.00 0.00 0.00 1.75
3378 6799 6.183360 GCTTGAGGCAGCTATCAAAGAATTTA 60.183 38.462 12.71 0.00 37.21 1.40
3521 6942 7.984050 CAGGTTACATTACTCATTGAGATGTCT 59.016 37.037 20.33 10.35 34.77 3.41
3553 6974 3.950395 CCAGCTCCTCTCCTTTATTTTGG 59.050 47.826 0.00 0.00 0.00 3.28
3557 6978 3.356290 TCCTCTCCTTTATTTTGGCAGC 58.644 45.455 0.00 0.00 0.00 5.25
3563 6984 3.507233 TCCTTTATTTTGGCAGCTGAGTG 59.493 43.478 20.43 0.00 0.00 3.51
3692 7113 6.537301 TGAACGTACAAACTTGAGACATCTTT 59.463 34.615 0.00 0.00 0.00 2.52
3725 7146 1.961277 CTGGTTGACCTGGTGACGC 60.961 63.158 2.82 0.00 36.82 5.19
3745 7166 3.257873 CGCTGGACCTATCATTCATCTCT 59.742 47.826 0.00 0.00 0.00 3.10
3773 7194 2.489329 GTGGTATGATTTGCTGTGCACT 59.511 45.455 19.41 0.00 38.71 4.40
3774 7195 3.689161 GTGGTATGATTTGCTGTGCACTA 59.311 43.478 19.41 3.54 38.71 2.74
3775 7196 4.336433 GTGGTATGATTTGCTGTGCACTAT 59.664 41.667 19.41 3.70 38.71 2.12
3776 7197 5.527214 GTGGTATGATTTGCTGTGCACTATA 59.473 40.000 19.41 0.59 38.71 1.31
3777 7198 5.759763 TGGTATGATTTGCTGTGCACTATAG 59.240 40.000 19.41 8.41 38.71 1.31
3796 7217 9.764363 CACTATAGTGTGGTGTGATACATTTAT 57.236 33.333 22.48 0.00 40.96 1.40
3808 7229 9.284968 GTGTGATACATTTATAGTGGCCTTATT 57.715 33.333 3.32 0.00 0.00 1.40
4006 7429 1.345741 TCAACTGAGAGGACCAGCTTG 59.654 52.381 0.00 0.00 35.14 4.01
4011 7434 1.339438 TGAGAGGACCAGCTTGATTGC 60.339 52.381 0.00 0.00 0.00 3.56
4012 7435 0.694771 AGAGGACCAGCTTGATTGCA 59.305 50.000 0.00 0.00 34.99 4.08
4018 7441 1.972795 ACCAGCTTGATTGCATTGGTT 59.027 42.857 0.00 0.00 32.83 3.67
4113 7545 9.807649 AAATGCATACATTAGGAAGAAAATGAC 57.192 29.630 0.00 0.00 45.90 3.06
4236 7668 3.047796 CTCTCCAATATTTTGCATGCGC 58.952 45.455 14.09 0.00 39.24 6.09
4251 7683 3.741476 CGCAAGGGCCTTCACTGC 61.741 66.667 17.86 16.96 36.38 4.40
4270 7702 7.165485 TCACTGCCAGCTTAAAGAAATTACTA 58.835 34.615 0.00 0.00 0.00 1.82
4352 7784 5.008613 GCAGTGGTCAAAGTAATGAAGACAA 59.991 40.000 0.00 0.00 0.00 3.18
4361 7793 8.181573 TCAAAGTAATGAAGACAAACTCAACAC 58.818 33.333 0.00 0.00 0.00 3.32
4429 7861 9.503399 CAGGTATAAAACAAGTTTCCTCTTAGT 57.497 33.333 0.00 0.00 31.45 2.24
4472 7905 9.685276 AGTTGATCATCATATGGAAAAGTACAA 57.315 29.630 2.13 0.00 0.00 2.41
4494 7927 2.795231 ATACTGATGCACAAGCCACT 57.205 45.000 0.00 0.00 41.13 4.00
4515 7948 7.335924 GCCACTGTATCTGTTTTTATCCTGTTA 59.664 37.037 0.00 0.00 0.00 2.41
4536 7969 3.739401 AGGTAGGAAAAGGTGGGATTG 57.261 47.619 0.00 0.00 0.00 2.67
4615 8048 7.766219 TTACTTCTGTTGCGTATCCTATTTC 57.234 36.000 0.00 0.00 0.00 2.17
4706 8165 6.801539 TCTTCTGCTTGATTACGATGTTTT 57.198 33.333 0.00 0.00 0.00 2.43
4707 8166 6.831769 TCTTCTGCTTGATTACGATGTTTTC 58.168 36.000 0.00 0.00 0.00 2.29
4716 8175 5.949354 TGATTACGATGTTTTCCCCTTGAAT 59.051 36.000 0.00 0.00 31.67 2.57
4717 8176 5.890424 TTACGATGTTTTCCCCTTGAATC 57.110 39.130 0.00 0.00 31.67 2.52
4722 8181 2.178984 TGTTTTCCCCTTGAATCCCACT 59.821 45.455 0.00 0.00 31.67 4.00
4742 8207 6.761714 CCCACTAGCAAATAGTACACTTAAGG 59.238 42.308 7.53 0.00 43.13 2.69
4845 8310 7.112779 CCTGAAGTAGACCAACCTATTCAATT 58.887 38.462 0.00 0.00 0.00 2.32
4847 8312 6.374333 TGAAGTAGACCAACCTATTCAATTGC 59.626 38.462 0.00 0.00 0.00 3.56
5031 8496 2.433838 CCACACGCAGAGGCAGAG 60.434 66.667 0.00 0.00 41.24 3.35
5035 8500 4.079850 ACGCAGAGGCAGAGGCAG 62.080 66.667 0.00 0.00 43.71 4.85
5047 8512 3.388703 GAGGCAGAGGCAGAGGCAG 62.389 68.421 0.00 0.00 43.71 4.85
5377 8947 7.094377 GGAATGAAACAATTAGCTCCAGTGTTA 60.094 37.037 10.96 0.00 32.32 2.41
5381 8951 8.081633 TGAAACAATTAGCTCCAGTGTTATTTG 58.918 33.333 10.96 0.00 32.32 2.32
5385 8960 8.421002 ACAATTAGCTCCAGTGTTATTTGTTTT 58.579 29.630 0.00 0.00 29.56 2.43
5418 8993 1.800586 GCATAGCATACGGGATGTGTG 59.199 52.381 1.50 0.30 42.16 3.82
5436 9011 2.575993 CTCCCTGTGCACCGAGAG 59.424 66.667 15.69 10.07 0.00 3.20
5459 9034 1.779569 AGAACACAGTTCCGCTTACG 58.220 50.000 6.29 0.00 39.67 3.18
5460 9035 1.338973 AGAACACAGTTCCGCTTACGA 59.661 47.619 6.29 0.00 43.93 3.43
5462 9037 2.450609 ACACAGTTCCGCTTACGATT 57.549 45.000 0.00 0.00 43.93 3.34
5481 9056 7.692908 ACGATTTTGTACCTTTTGTGATTTG 57.307 32.000 0.00 0.00 0.00 2.32
5489 9064 4.079253 ACCTTTTGTGATTTGGCTACGAT 58.921 39.130 0.00 0.00 0.00 3.73
5492 9067 2.779755 TGTGATTTGGCTACGATGGT 57.220 45.000 0.00 0.00 0.00 3.55
5530 9105 0.526211 TCGTTCCACTGATCTGACGG 59.474 55.000 6.60 6.55 0.00 4.79
5538 9113 1.066303 ACTGATCTGACGGAGCGATTC 59.934 52.381 6.60 0.00 32.20 2.52
5577 9152 2.170187 AGATGATGTGCAACCTCTCTCC 59.830 50.000 0.00 0.00 34.36 3.71
5583 9158 2.125350 CAACCTCTCTCCGCTGCC 60.125 66.667 0.00 0.00 0.00 4.85
5602 9177 6.237915 CGCTGCCATTTCCTTTTATTTTCATC 60.238 38.462 0.00 0.00 0.00 2.92
5646 9224 2.431419 TCTGTCGTGTCCAACCTACAAA 59.569 45.455 0.00 0.00 0.00 2.83
5671 9249 9.790389 AAGTTCATCGAGTAGTTAAGAGTATTG 57.210 33.333 0.00 0.00 0.00 1.90
5709 9287 3.244181 TGTTACCGACCCTTGTTTCTACC 60.244 47.826 0.00 0.00 0.00 3.18
5781 9361 2.251893 CGTTGAACTCTTAGCGGAGTC 58.748 52.381 9.68 5.70 44.67 3.36
5803 9404 6.070881 AGTCTGATCTCCTCATGTATATTGCC 60.071 42.308 0.00 0.00 32.10 4.52
5811 9412 0.034756 ATGTATATTGCCGCGCCTGA 59.965 50.000 0.00 0.00 0.00 3.86
5852 9453 1.549203 TGGATTTCCTTTCCAGCAGC 58.451 50.000 0.00 0.00 38.35 5.25
5865 9466 0.314578 CAGCAGCGCGTCTAAATTCG 60.315 55.000 8.43 0.00 0.00 3.34
5928 9529 4.714802 TCCTAGTCTAAGTGCAGGCAATAA 59.285 41.667 0.00 0.00 0.00 1.40
5929 9530 5.366768 TCCTAGTCTAAGTGCAGGCAATAAT 59.633 40.000 0.00 0.00 0.00 1.28
5930 9531 6.553476 TCCTAGTCTAAGTGCAGGCAATAATA 59.447 38.462 0.00 0.00 0.00 0.98
5985 9586 2.783135 TGGAGAACAAGAACCAGATGC 58.217 47.619 0.00 0.00 0.00 3.91
5986 9587 2.106338 TGGAGAACAAGAACCAGATGCA 59.894 45.455 0.00 0.00 0.00 3.96
5987 9588 2.485814 GGAGAACAAGAACCAGATGCAC 59.514 50.000 0.00 0.00 0.00 4.57
5988 9589 2.485814 GAGAACAAGAACCAGATGCACC 59.514 50.000 0.00 0.00 0.00 5.01
5989 9590 2.158623 AGAACAAGAACCAGATGCACCA 60.159 45.455 0.00 0.00 0.00 4.17
5990 9591 1.609208 ACAAGAACCAGATGCACCAC 58.391 50.000 0.00 0.00 0.00 4.16
5991 9592 1.133823 ACAAGAACCAGATGCACCACA 60.134 47.619 0.00 0.00 0.00 4.17
5992 9593 1.955778 CAAGAACCAGATGCACCACAA 59.044 47.619 0.00 0.00 0.00 3.33
5993 9594 2.559668 CAAGAACCAGATGCACCACAAT 59.440 45.455 0.00 0.00 0.00 2.71
5994 9595 2.165167 AGAACCAGATGCACCACAATG 58.835 47.619 0.00 0.00 0.00 2.82
5995 9596 1.203052 GAACCAGATGCACCACAATGG 59.797 52.381 0.00 0.00 45.02 3.16
6005 9606 3.537455 CCACAATGGTATGGGGCAT 57.463 52.632 0.00 0.00 36.99 4.40
6006 9607 2.673775 CCACAATGGTATGGGGCATA 57.326 50.000 0.00 0.00 36.99 3.14
6007 9608 3.173953 CCACAATGGTATGGGGCATAT 57.826 47.619 0.00 0.00 36.99 1.78
6008 9609 2.827322 CCACAATGGTATGGGGCATATG 59.173 50.000 0.00 0.00 36.99 1.78
6058 9659 3.519579 CAGACAGACAGATCCACATGAC 58.480 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 4.116747 ACTCCAGATTACTGCTTTCTCG 57.883 45.455 0.00 0.00 42.25 4.04
54 55 6.035112 CGTAAACTCCAGATTACTGCTTTCTC 59.965 42.308 5.51 0.00 42.25 2.87
228 429 4.779733 TCAGGACCTCCCGCTCCC 62.780 72.222 0.00 0.00 40.87 4.30
229 430 3.151022 CTCAGGACCTCCCGCTCC 61.151 72.222 0.00 0.00 40.87 4.70
230 431 3.151022 CCTCAGGACCTCCCGCTC 61.151 72.222 0.00 0.00 40.87 5.03
236 437 3.394836 AAGGCGCCTCAGGACCTC 61.395 66.667 32.93 0.00 31.00 3.85
237 438 3.710722 CAAGGCGCCTCAGGACCT 61.711 66.667 32.93 9.57 33.14 3.85
238 439 3.672295 CTCAAGGCGCCTCAGGACC 62.672 68.421 32.93 0.00 0.00 4.46
239 440 2.125350 CTCAAGGCGCCTCAGGAC 60.125 66.667 32.93 0.00 0.00 3.85
263 464 4.584325 TCTTTCAGAAATGAAACCAGTGGG 59.416 41.667 15.21 0.00 41.29 4.61
434 676 4.584327 AGAAAAGGGTCAAATTTGTCCG 57.416 40.909 22.67 0.00 37.27 4.79
484 727 4.318689 GGGTCATTTTGTGAATTTTGTGCG 60.319 41.667 0.00 0.00 38.90 5.34
497 740 4.708601 CGTCGAGTAAAAGGGTCATTTTG 58.291 43.478 3.95 0.00 34.35 2.44
527 770 3.267233 AGGAGCATGGCACCCCAA 61.267 61.111 0.95 0.00 46.14 4.12
554 811 2.752939 CGCGCCATCAAGCATGACA 61.753 57.895 0.00 0.00 38.69 3.58
556 813 3.204119 CCGCGCCATCAAGCATGA 61.204 61.111 0.00 0.00 40.57 3.07
575 833 1.449778 GCCCTTTGTCGAGGTAGCC 60.450 63.158 0.00 0.00 34.88 3.93
607 865 1.197721 CTGAACCTGAAATGTCGTGCC 59.802 52.381 0.00 0.00 0.00 5.01
611 869 0.443869 CGCCTGAACCTGAAATGTCG 59.556 55.000 0.00 0.00 0.00 4.35
656 914 9.586435 GAATGAACCGGATCTGAAAATATTTTT 57.414 29.630 9.46 0.00 0.00 1.94
727 985 2.948315 ACCCGCAAAATTTTGTGCAAAT 59.052 36.364 30.35 16.50 44.89 2.32
894 1207 1.374947 CCGCCAAGACCAAAGGAGA 59.625 57.895 0.00 0.00 0.00 3.71
895 1208 2.335712 GCCGCCAAGACCAAAGGAG 61.336 63.158 0.00 0.00 0.00 3.69
896 1209 2.282180 GCCGCCAAGACCAAAGGA 60.282 61.111 0.00 0.00 0.00 3.36
915 1237 1.760268 GAGAGAGATGCAAAGCGCCG 61.760 60.000 2.29 0.00 41.33 6.46
975 1300 1.388065 CCTCCTTCTCGACGGCAGAT 61.388 60.000 0.00 0.00 0.00 2.90
978 1303 2.282958 ACCTCCTTCTCGACGGCA 60.283 61.111 0.00 0.00 0.00 5.69
1021 1349 1.519408 GAGCTTTTACGCTGGTGGAA 58.481 50.000 0.00 0.00 41.08 3.53
1035 1363 2.596411 AGATTTAGGAGGGGGAGCTT 57.404 50.000 0.00 0.00 0.00 3.74
1103 1453 4.390909 GGAAGGCAGCAAATCAAAAGATTG 59.609 41.667 0.00 0.00 37.92 2.67
1105 1455 3.055602 GGGAAGGCAGCAAATCAAAAGAT 60.056 43.478 0.00 0.00 0.00 2.40
1106 1456 2.299867 GGGAAGGCAGCAAATCAAAAGA 59.700 45.455 0.00 0.00 0.00 2.52
1107 1457 2.613725 GGGGAAGGCAGCAAATCAAAAG 60.614 50.000 0.00 0.00 0.00 2.27
1111 1461 0.899717 GTGGGGAAGGCAGCAAATCA 60.900 55.000 0.00 0.00 0.00 2.57
1112 1462 0.899717 TGTGGGGAAGGCAGCAAATC 60.900 55.000 0.00 0.00 0.00 2.17
1113 1463 0.252375 ATGTGGGGAAGGCAGCAAAT 60.252 50.000 0.00 0.00 0.00 2.32
1154 1515 5.277538 GCTCAAATTTCATGGATACGGAGAC 60.278 44.000 0.00 0.00 42.51 3.36
1159 1520 4.498009 GGGTGCTCAAATTTCATGGATACG 60.498 45.833 0.00 0.00 42.51 3.06
1174 1535 1.002069 ATTTCAGGGATGGGTGCTCA 58.998 50.000 0.00 0.00 0.00 4.26
1208 1570 4.099419 GGTTCCACCAGAAGAAACATTTGT 59.901 41.667 0.00 0.00 38.42 2.83
1266 1628 5.408909 GCCTAACTGTGGAAGAAAAGAGTAC 59.591 44.000 0.00 0.00 0.00 2.73
1267 1629 5.307196 AGCCTAACTGTGGAAGAAAAGAGTA 59.693 40.000 0.00 0.00 0.00 2.59
1268 1630 4.103311 AGCCTAACTGTGGAAGAAAAGAGT 59.897 41.667 0.00 0.00 0.00 3.24
1334 1696 2.745884 TGGGATTTGACAGCCGCG 60.746 61.111 0.00 0.00 0.00 6.46
1404 1766 8.413229 ACGGAAATGAGAAATCTGAAAAGAAAA 58.587 29.630 0.00 0.00 0.00 2.29
1407 1769 6.568462 GCACGGAAATGAGAAATCTGAAAAGA 60.568 38.462 0.00 0.00 0.00 2.52
1408 1770 5.570589 GCACGGAAATGAGAAATCTGAAAAG 59.429 40.000 0.00 0.00 0.00 2.27
1411 1773 4.326826 AGCACGGAAATGAGAAATCTGAA 58.673 39.130 0.00 0.00 0.00 3.02
1412 1774 3.942829 AGCACGGAAATGAGAAATCTGA 58.057 40.909 0.00 0.00 0.00 3.27
1413 1775 4.259970 CGTAGCACGGAAATGAGAAATCTG 60.260 45.833 1.40 0.00 38.08 2.90
1435 1797 0.320771 AGGCACTAGCAGTTGTTCCG 60.321 55.000 0.00 0.00 44.61 4.30
1447 1809 4.100344 TCGCCATTAATCTACAAGGCACTA 59.900 41.667 11.51 0.00 42.10 2.74
1463 1825 3.213206 ACACACCATATCATCGCCATT 57.787 42.857 0.00 0.00 0.00 3.16
1469 1839 5.639506 GGCATACAGTACACACCATATCATC 59.360 44.000 0.00 0.00 0.00 2.92
1473 1843 4.653801 TGAGGCATACAGTACACACCATAT 59.346 41.667 0.00 0.00 0.00 1.78
1477 1847 3.543680 ATGAGGCATACAGTACACACC 57.456 47.619 0.00 0.00 0.00 4.16
1478 1848 4.503910 TGAATGAGGCATACAGTACACAC 58.496 43.478 0.00 0.00 0.00 3.82
1484 1854 4.080129 AGGAACATGAATGAGGCATACAGT 60.080 41.667 0.00 0.00 0.00 3.55
1485 1855 4.458397 AGGAACATGAATGAGGCATACAG 58.542 43.478 0.00 0.00 0.00 2.74
1594 1971 6.992715 ACATAACCACCTTGCAATCTAGTATC 59.007 38.462 0.00 0.00 0.00 2.24
1630 2010 4.081198 AGAGGCTGAAACTGTCCTATCTTG 60.081 45.833 0.00 0.00 0.00 3.02
1695 2075 4.508551 ACCATCACATCAATAAGAGGCA 57.491 40.909 0.00 0.00 0.00 4.75
1747 2127 5.451354 ACACCCTTTTTGTACCATAACTGT 58.549 37.500 0.00 0.00 0.00 3.55
1764 2144 1.035932 CGTCATCCTACCGACACCCT 61.036 60.000 0.00 0.00 32.24 4.34
2062 2443 6.005823 AGCTAATAGCATGCCATATGTTTCA 58.994 36.000 15.66 0.00 45.56 2.69
2096 2477 5.335976 GGCTCATTCTTTCCAGATTTCGTTT 60.336 40.000 0.00 0.00 0.00 3.60
2245 2634 1.067516 GCACCAGTGATGTTGCAACTT 59.932 47.619 28.61 23.00 0.00 2.66
2279 2668 3.317603 CCATTCGGCTTGAACCAAAAT 57.682 42.857 0.00 0.00 40.00 1.82
2420 2813 1.344065 TCCCGTTCATACACACCTGT 58.656 50.000 0.00 0.00 0.00 4.00
2589 2982 3.428045 GCATCAAACACCATAGCAACTCC 60.428 47.826 0.00 0.00 0.00 3.85
2630 3023 5.495926 AGGATGAGATTCAAAGTCAGTGT 57.504 39.130 0.00 0.00 0.00 3.55
2725 3118 1.208165 AAGGTGTCCTTAGCCTGGGG 61.208 60.000 0.00 0.00 42.74 4.96
2739 3133 8.532819 AGGAAGTTGTTAGTTAGAGATAAGGTG 58.467 37.037 0.00 0.00 0.00 4.00
2755 3149 8.706322 AGTACCATTCAAATTAGGAAGTTGTT 57.294 30.769 0.03 0.00 37.68 2.83
2805 3199 3.181458 TGGCTCCGATTAAGGGATACAAC 60.181 47.826 0.00 0.00 39.74 3.32
2808 3202 3.071167 AGTTGGCTCCGATTAAGGGATAC 59.929 47.826 0.00 0.00 31.99 2.24
2875 3269 3.766591 CAGGAGACAGACAACTAGATGGT 59.233 47.826 4.89 0.00 0.00 3.55
3320 6741 3.506067 CCCTGGATTAGGTCACAACAAAC 59.494 47.826 0.00 0.00 45.80 2.93
3378 6799 4.963318 TCTTTCCATCACAGTCAACTCT 57.037 40.909 0.00 0.00 0.00 3.24
3553 6974 0.603707 TAGCAACCACACTCAGCTGC 60.604 55.000 9.47 0.00 36.80 5.25
3692 7113 3.631453 CCAGTTGTGGCAGCTTAGA 57.369 52.632 0.00 0.00 36.89 2.10
3725 7146 8.365060 AGAATAGAGATGAATGATAGGTCCAG 57.635 38.462 0.00 0.00 0.00 3.86
3745 7166 6.404623 GCACAGCAAATCATACCACAAGAATA 60.405 38.462 0.00 0.00 0.00 1.75
3774 7195 9.764363 CACTATAAATGTATCACACCACACTAT 57.236 33.333 0.00 0.00 0.00 2.12
3775 7196 8.201464 CCACTATAAATGTATCACACCACACTA 58.799 37.037 0.00 0.00 0.00 2.74
3776 7197 7.047891 CCACTATAAATGTATCACACCACACT 58.952 38.462 0.00 0.00 0.00 3.55
3777 7198 6.238374 GCCACTATAAATGTATCACACCACAC 60.238 42.308 0.00 0.00 0.00 3.82
3779 7200 5.238650 GGCCACTATAAATGTATCACACCAC 59.761 44.000 0.00 0.00 0.00 4.16
3780 7201 5.131977 AGGCCACTATAAATGTATCACACCA 59.868 40.000 5.01 0.00 0.00 4.17
3781 7202 5.621193 AGGCCACTATAAATGTATCACACC 58.379 41.667 5.01 0.00 0.00 4.16
3782 7203 8.848474 ATAAGGCCACTATAAATGTATCACAC 57.152 34.615 5.01 0.00 0.00 3.82
3796 7217 5.995565 ACGAGCATATAATAAGGCCACTA 57.004 39.130 5.01 0.00 0.00 2.74
4011 7434 9.616634 CTTATAGCTACAATGCATAAACCAATG 57.383 33.333 0.00 0.00 34.99 2.82
4012 7435 8.796475 CCTTATAGCTACAATGCATAAACCAAT 58.204 33.333 0.00 0.00 34.99 3.16
4033 7456 8.528643 GTCCCTAAATGCAAACTAAAACCTTAT 58.471 33.333 0.00 0.00 0.00 1.73
4095 7527 3.374058 CCGCGTCATTTTCTTCCTAATGT 59.626 43.478 4.92 0.00 34.25 2.71
4108 7540 0.319083 TACCACAGAACCGCGTCATT 59.681 50.000 4.92 0.00 0.00 2.57
4109 7541 0.319083 TTACCACAGAACCGCGTCAT 59.681 50.000 4.92 0.00 0.00 3.06
4110 7542 0.104487 TTTACCACAGAACCGCGTCA 59.896 50.000 4.92 0.00 0.00 4.35
4111 7543 0.509929 GTTTACCACAGAACCGCGTC 59.490 55.000 4.92 0.00 0.00 5.19
4112 7544 0.105408 AGTTTACCACAGAACCGCGT 59.895 50.000 4.92 0.00 0.00 6.01
4113 7545 0.511221 CAGTTTACCACAGAACCGCG 59.489 55.000 0.00 0.00 0.00 6.46
4189 7621 3.915437 AAAACAGAAGCACAATACCGG 57.085 42.857 0.00 0.00 0.00 5.28
4472 7905 4.577693 CAGTGGCTTGTGCATCAGTATTAT 59.422 41.667 0.00 0.00 41.91 1.28
4515 7948 3.401342 ACAATCCCACCTTTTCCTACCTT 59.599 43.478 0.00 0.00 0.00 3.50
4588 8021 8.556213 AATAGGATACGCAACAGAAGTAAAAA 57.444 30.769 0.00 0.00 46.39 1.94
4589 8022 8.556213 AAATAGGATACGCAACAGAAGTAAAA 57.444 30.769 0.00 0.00 46.39 1.52
4611 8044 3.084039 TCCATGAAAAGCTCTGCGAAAT 58.916 40.909 0.00 0.00 0.00 2.17
4615 8048 4.825546 ATAATCCATGAAAAGCTCTGCG 57.174 40.909 0.00 0.00 0.00 5.18
4617 8050 7.541162 TGACAAATAATCCATGAAAAGCTCTG 58.459 34.615 0.00 0.00 0.00 3.35
4618 8051 7.707624 TGACAAATAATCCATGAAAAGCTCT 57.292 32.000 0.00 0.00 0.00 4.09
4706 8165 1.213296 GCTAGTGGGATTCAAGGGGA 58.787 55.000 0.00 0.00 0.00 4.81
4707 8166 0.918983 TGCTAGTGGGATTCAAGGGG 59.081 55.000 0.00 0.00 0.00 4.79
4716 8175 7.364408 CCTTAAGTGTACTATTTGCTAGTGGGA 60.364 40.741 0.97 0.00 40.94 4.37
4717 8176 6.761714 CCTTAAGTGTACTATTTGCTAGTGGG 59.238 42.308 0.97 0.00 40.94 4.61
4742 8207 8.360390 AGTCCAATATTCCAAGTTGAAGTTTTC 58.640 33.333 3.87 0.00 0.00 2.29
4751 8216 7.348274 TCTCAGGATAGTCCAATATTCCAAGTT 59.652 37.037 0.00 0.00 39.61 2.66
4752 8217 6.846505 TCTCAGGATAGTCCAATATTCCAAGT 59.153 38.462 0.00 0.00 39.61 3.16
4845 8310 3.694043 TCTAACACCTGTAATGCAGCA 57.306 42.857 0.00 0.00 43.71 4.41
4847 8312 6.161855 TCCTATCTAACACCTGTAATGCAG 57.838 41.667 0.00 0.00 44.63 4.41
5017 8482 4.383861 TGCCTCTGCCTCTGCGTG 62.384 66.667 0.00 0.00 41.78 5.34
5019 8484 3.719883 CTCTGCCTCTGCCTCTGCG 62.720 68.421 0.00 0.00 41.78 5.18
5024 8489 3.400928 CTGCCTCTGCCTCTGCCT 61.401 66.667 0.00 0.00 36.33 4.75
5027 8492 2.901813 CCTCTGCCTCTGCCTCTG 59.098 66.667 0.00 0.00 36.33 3.35
5031 8496 4.486503 CCTGCCTCTGCCTCTGCC 62.487 72.222 0.00 0.00 36.33 4.85
5098 8599 2.733669 CCTCTGGCTCTGGCTCTGG 61.734 68.421 0.00 0.00 38.73 3.86
5418 8993 3.655810 CTCTCGGTGCACAGGGAGC 62.656 68.421 29.82 6.21 32.25 4.70
5436 9011 0.320697 AGCGGAACTGTGTTCTACCC 59.679 55.000 9.81 0.00 0.00 3.69
5459 9034 6.705825 AGCCAAATCACAAAAGGTACAAAATC 59.294 34.615 0.00 0.00 0.00 2.17
5460 9035 6.591001 AGCCAAATCACAAAAGGTACAAAAT 58.409 32.000 0.00 0.00 0.00 1.82
5462 9037 5.606348 AGCCAAATCACAAAAGGTACAAA 57.394 34.783 0.00 0.00 0.00 2.83
5481 9056 4.377021 TGAATGTATTCACCATCGTAGCC 58.623 43.478 3.28 0.00 41.51 3.93
5492 9067 2.670905 CGAACTGCGGTGAATGTATTCA 59.329 45.455 0.00 3.28 39.26 2.57
5530 9105 3.125316 ACATTTTCCAGTTCGAATCGCTC 59.875 43.478 0.00 0.00 0.00 5.03
5538 9113 6.000891 TCATCTTGAACATTTTCCAGTTCG 57.999 37.500 0.00 0.00 45.34 3.95
5577 9152 4.928615 TGAAAATAAAAGGAAATGGCAGCG 59.071 37.500 0.00 0.00 0.00 5.18
5602 9177 1.556911 ACCCACCTGCACAGATAGAAG 59.443 52.381 0.00 0.00 0.00 2.85
5646 9224 8.958506 ACAATACTCTTAACTACTCGATGAACT 58.041 33.333 0.00 0.00 0.00 3.01
5671 9249 7.486870 GGTCGGTAACAAATTTCCAATGATAAC 59.513 37.037 0.00 0.00 0.00 1.89
5781 9361 5.107824 CGGCAATATACATGAGGAGATCAG 58.892 45.833 0.00 0.00 42.53 2.90
5803 9404 1.961277 AGGTCAGTTTTCAGGCGCG 60.961 57.895 0.00 0.00 0.00 6.86
5852 9453 1.201877 CCAACACCGAATTTAGACGCG 60.202 52.381 3.53 3.53 0.00 6.01
5928 9529 6.476378 ACTTTGGTGCTTAATCACACTCTAT 58.524 36.000 11.30 0.00 38.66 1.98
5929 9530 5.865085 ACTTTGGTGCTTAATCACACTCTA 58.135 37.500 11.30 0.00 38.66 2.43
5930 9531 4.718961 ACTTTGGTGCTTAATCACACTCT 58.281 39.130 11.30 0.00 38.66 3.24
5987 9588 2.673775 TATGCCCCATACCATTGTGG 57.326 50.000 0.00 0.00 45.02 4.17
5988 9589 3.256383 CACATATGCCCCATACCATTGTG 59.744 47.826 1.58 3.65 31.26 3.33
5989 9590 3.499338 CACATATGCCCCATACCATTGT 58.501 45.455 1.58 0.00 0.00 2.71
5990 9591 2.231964 GCACATATGCCCCATACCATTG 59.768 50.000 1.58 0.00 46.97 2.82
5991 9592 2.528564 GCACATATGCCCCATACCATT 58.471 47.619 1.58 0.00 46.97 3.16
5992 9593 2.220653 GCACATATGCCCCATACCAT 57.779 50.000 1.58 0.00 46.97 3.55
5993 9594 3.743714 GCACATATGCCCCATACCA 57.256 52.632 1.58 0.00 46.97 3.25


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

AutoCloner maintained by Alex Coulton.