Multiple sequence alignment - TraesCS2A01G384000

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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 TraesCS2A01G384000 chr2A 100.000 8301 0 0 1 8301 628729512 628737812 0.000000e+00 15330
1 TraesCS2A01G384000 chr2A 93.694 333 6 5 4592 4910 628732063 628732394 1.250000e-132 484
2 TraesCS2A01G384000 chr2D 96.933 3424 65 14 4907 8299 484854388 484857802 0.000000e+00 5705
3 TraesCS2A01G384000 chr2D 92.646 2230 138 22 2552 4763 349731795 349729574 0.000000e+00 3186
4 TraesCS2A01G384000 chr2D 97.482 1549 34 4 1002 2548 484852804 484854349 0.000000e+00 2639
5 TraesCS2A01G384000 chr2D 92.539 898 41 11 121 1008 484851436 484852317 0.000000e+00 1264
6 TraesCS2A01G384000 chr2D 92.566 417 30 1 2552 2967 392697392 392697808 1.540000e-166 597
7 TraesCS2A01G384000 chr2D 95.789 95 4 0 1 95 484851344 484851438 4.010000e-33 154
8 TraesCS2A01G384000 chr7A 93.459 2339 100 12 2622 4910 269963521 269961186 0.000000e+00 3422
9 TraesCS2A01G384000 chr7A 91.322 1256 89 8 3671 4908 245980852 245982105 0.000000e+00 1698
10 TraesCS2A01G384000 chr5D 93.438 2301 113 11 2619 4907 371789232 371791506 0.000000e+00 3378
11 TraesCS2A01G384000 chr5D 92.820 2298 146 11 2622 4906 387112332 387110041 0.000000e+00 3312
12 TraesCS2A01G384000 chr5D 91.645 1927 129 17 2994 4909 323024330 323022425 0.000000e+00 2638
13 TraesCS2A01G384000 chr4D 92.295 2401 134 15 2552 4906 455184069 455186464 0.000000e+00 3362
14 TraesCS2A01G384000 chr7D 93.599 2234 118 7 2551 4763 90628419 90626190 0.000000e+00 3310
15 TraesCS2A01G384000 chrUn 91.587 2306 166 19 2622 4906 26911199 26908901 0.000000e+00 3158
16 TraesCS2A01G384000 chr6D 90.729 2319 173 16 2622 4906 322585318 322583008 0.000000e+00 3053
17 TraesCS2A01G384000 chr2B 92.195 1973 101 31 6350 8300 569498184 569500125 0.000000e+00 2741
18 TraesCS2A01G384000 chr2B 99.115 226 2 0 6134 6359 569497443 569497668 2.790000e-109 407
19 TraesCS2A01G384000 chr3B 88.834 1424 143 3 3346 4753 741305447 741306870 0.000000e+00 1735
20 TraesCS2A01G384000 chr6A 90.450 1267 89 14 3653 4907 100317086 100318332 0.000000e+00 1640
21 TraesCS2A01G384000 chr6A 94.964 417 20 1 2552 2967 520839080 520839496 0.000000e+00 652
22 TraesCS2A01G384000 chr6A 94.245 417 20 2 2552 2967 100315948 100316361 1.180000e-177 634
23 TraesCS2A01G384000 chr6A 96.960 329 6 2 2552 2879 100318006 100318331 4.380000e-152 549
24 TraesCS2A01G384000 chr6A 93.958 331 9 3 4591 4910 100315947 100316277 2.690000e-134 490
25 TraesCS2A01G384000 chr6A 97.143 140 4 0 4767 4906 309874847 309874986 3.870000e-58 237
26 TraesCS2A01G384000 chr5A 84.829 1081 134 10 3716 4787 397152255 397153314 0.000000e+00 1061
27 TraesCS2A01G384000 chr3D 92.899 338 11 5 4584 4910 146058656 146058321 5.830000e-131 479
28 TraesCS2A01G384000 chr3D 92.803 264 8 3 4662 4914 146047928 146047665 1.020000e-98 372
29 TraesCS2A01G384000 chr4A 79.481 385 32 17 2552 2917 86290057 86289701 6.480000e-56 230
30 TraesCS2A01G384000 chr4A 78.415 366 44 22 2552 2889 117689250 117689608 1.090000e-48 206
31 TraesCS2A01G384000 chr4A 80.195 308 15 14 2552 2839 86286933 86286652 1.100000e-43 189
32 TraesCS2A01G384000 chr4A 83.568 213 19 11 2552 2760 117691470 117691670 1.420000e-42 185


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 TraesCS2A01G384000 chr2A 628729512 628737812 8300 False 15330.00 15330 100.00000 1 8301 1 chr2A.!!$F1 8300
1 TraesCS2A01G384000 chr2D 349729574 349731795 2221 True 3186.00 3186 92.64600 2552 4763 1 chr2D.!!$R1 2211
2 TraesCS2A01G384000 chr2D 484851344 484857802 6458 False 2440.50 5705 95.68575 1 8299 4 chr2D.!!$F2 8298
3 TraesCS2A01G384000 chr7A 269961186 269963521 2335 True 3422.00 3422 93.45900 2622 4910 1 chr7A.!!$R1 2288
4 TraesCS2A01G384000 chr7A 245980852 245982105 1253 False 1698.00 1698 91.32200 3671 4908 1 chr7A.!!$F1 1237
5 TraesCS2A01G384000 chr5D 371789232 371791506 2274 False 3378.00 3378 93.43800 2619 4907 1 chr5D.!!$F1 2288
6 TraesCS2A01G384000 chr5D 387110041 387112332 2291 True 3312.00 3312 92.82000 2622 4906 1 chr5D.!!$R2 2284
7 TraesCS2A01G384000 chr5D 323022425 323024330 1905 True 2638.00 2638 91.64500 2994 4909 1 chr5D.!!$R1 1915
8 TraesCS2A01G384000 chr4D 455184069 455186464 2395 False 3362.00 3362 92.29500 2552 4906 1 chr4D.!!$F1 2354
9 TraesCS2A01G384000 chr7D 90626190 90628419 2229 True 3310.00 3310 93.59900 2551 4763 1 chr7D.!!$R1 2212
10 TraesCS2A01G384000 chrUn 26908901 26911199 2298 True 3158.00 3158 91.58700 2622 4906 1 chrUn.!!$R1 2284
11 TraesCS2A01G384000 chr6D 322583008 322585318 2310 True 3053.00 3053 90.72900 2622 4906 1 chr6D.!!$R1 2284
12 TraesCS2A01G384000 chr2B 569497443 569500125 2682 False 1574.00 2741 95.65500 6134 8300 2 chr2B.!!$F1 2166
13 TraesCS2A01G384000 chr3B 741305447 741306870 1423 False 1735.00 1735 88.83400 3346 4753 1 chr3B.!!$F1 1407
14 TraesCS2A01G384000 chr6A 100315947 100318332 2385 False 828.25 1640 93.90325 2552 4910 4 chr6A.!!$F3 2358
15 TraesCS2A01G384000 chr5A 397152255 397153314 1059 False 1061.00 1061 84.82900 3716 4787 1 chr5A.!!$F1 1071
16 TraesCS2A01G384000 chr4A 86286652 86290057 3405 True 209.50 230 79.83800 2552 2917 2 chr4A.!!$R1 365

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
117 118 0.108329 CTGGAGTTGTAACGGGCGAT 60.108 55.000 0.00 0.00 0.00 4.58 F
337 338 0.246635 ATTGTCGGCGTGTCTTAGCT 59.753 50.000 6.85 0.00 0.00 3.32 F
338 339 0.666274 TTGTCGGCGTGTCTTAGCTG 60.666 55.000 6.85 0.00 40.87 4.24 F
1266 1769 1.726533 GGGTCGATGGAGTCCTCGTC 61.727 65.000 22.25 18.50 36.33 4.20 F
1855 2358 1.871039 GCTTTTGTCCAGAAGTGCGTA 59.129 47.619 0.33 0.00 0.00 4.42 F
3704 5595 0.673956 TCTGAGCTAGCTCGACACGT 60.674 55.000 33.55 4.31 45.48 4.49 F
4172 6066 0.531532 GATCTCCAGTCGGCCATGTG 60.532 60.000 2.24 0.00 0.00 3.21 F
5817 7844 0.039618 GACCCCAAGAAAGGCCATCA 59.960 55.000 5.01 0.00 0.00 3.07 F
5983 8010 0.105555 AGAGGGCTCCATCAGAGAGG 60.106 60.000 3.28 0.00 46.50 3.69 F
6794 9346 0.689623 CTGGGTTCTGAAGCTGGAGT 59.310 55.000 17.95 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1863 0.792640 ATCTCAAGAACACGCTTGCG 59.207 50.000 13.70 13.7 43.78 4.85 R
2309 2813 1.960763 TGCACGCGAGAAATGCAGT 60.961 52.632 15.93 0.0 44.17 4.40 R
2362 2867 3.009473 TGAGCAAGGGAAGCAGTTCTATT 59.991 43.478 0.00 0.0 32.72 1.73 R
2403 2908 1.471684 GCAAGGGAGATGTTCTGCTTG 59.528 52.381 0.00 0.0 35.01 4.01 R
3734 5625 0.108804 GGTGGCGAAGTCGATCTTGA 60.109 55.000 4.59 0.0 43.02 3.02 R
4580 6491 0.252197 GCCATAACACTTCTCCCCGT 59.748 55.000 0.00 0.0 0.00 5.28 R
5983 8010 1.174712 TTCTTGCTGCTTGCCACTCC 61.175 55.000 0.00 0.0 42.00 3.85 R
7005 9557 1.526917 CCATTGATCCGCCCACTCC 60.527 63.158 0.00 0.0 0.00 3.85 R
7036 9588 2.172505 TCTCAGTTTTGGGAAGTCTGCA 59.827 45.455 0.00 0.0 28.50 4.41 R
8117 10702 2.073252 ACTGATCTCCGCCATGTCTA 57.927 50.000 0.00 0.0 0.00 2.59 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
91 92 1.448013 GCTCACGAAGTACCAGCCC 60.448 63.158 0.00 0.00 41.61 5.19
92 93 1.153823 CTCACGAAGTACCAGCCCG 60.154 63.158 0.00 0.00 41.61 6.13
93 94 2.813908 CACGAAGTACCAGCCCGC 60.814 66.667 0.00 0.00 41.61 6.13
94 95 4.078516 ACGAAGTACCAGCCCGCC 62.079 66.667 0.00 0.00 41.94 6.13
95 96 3.771160 CGAAGTACCAGCCCGCCT 61.771 66.667 0.00 0.00 0.00 5.52
96 97 2.420568 CGAAGTACCAGCCCGCCTA 61.421 63.158 0.00 0.00 0.00 3.93
97 98 1.442148 GAAGTACCAGCCCGCCTAG 59.558 63.158 0.00 0.00 0.00 3.02
98 99 2.646117 GAAGTACCAGCCCGCCTAGC 62.646 65.000 0.00 0.00 0.00 3.42
99 100 3.155167 GTACCAGCCCGCCTAGCT 61.155 66.667 0.00 0.00 42.70 3.32
104 105 4.787280 AGCCCGCCTAGCTGGAGT 62.787 66.667 0.00 0.00 39.69 3.85
105 106 3.787001 GCCCGCCTAGCTGGAGTT 61.787 66.667 0.00 0.00 34.85 3.01
106 107 2.187946 CCCGCCTAGCTGGAGTTG 59.812 66.667 0.00 0.00 34.85 3.16
107 108 2.660064 CCCGCCTAGCTGGAGTTGT 61.660 63.158 0.00 0.00 34.85 3.32
108 109 1.327690 CCCGCCTAGCTGGAGTTGTA 61.328 60.000 0.00 0.00 34.85 2.41
109 110 0.535335 CCGCCTAGCTGGAGTTGTAA 59.465 55.000 0.00 0.00 38.35 2.41
110 111 1.641577 CGCCTAGCTGGAGTTGTAAC 58.358 55.000 0.00 0.00 38.35 2.50
111 112 1.641577 GCCTAGCTGGAGTTGTAACG 58.358 55.000 0.00 0.00 38.35 3.18
112 113 1.739371 GCCTAGCTGGAGTTGTAACGG 60.739 57.143 0.00 0.00 38.35 4.44
113 114 1.134788 CCTAGCTGGAGTTGTAACGGG 60.135 57.143 0.00 0.00 38.35 5.28
114 115 0.248289 TAGCTGGAGTTGTAACGGGC 59.752 55.000 0.00 0.00 0.00 6.13
115 116 2.388232 GCTGGAGTTGTAACGGGCG 61.388 63.158 0.00 0.00 0.00 6.13
116 117 1.290955 CTGGAGTTGTAACGGGCGA 59.709 57.895 0.00 0.00 0.00 5.54
117 118 0.108329 CTGGAGTTGTAACGGGCGAT 60.108 55.000 0.00 0.00 0.00 4.58
118 119 1.135527 CTGGAGTTGTAACGGGCGATA 59.864 52.381 0.00 0.00 0.00 2.92
119 120 1.758280 TGGAGTTGTAACGGGCGATAT 59.242 47.619 0.00 0.00 0.00 1.63
152 153 4.402056 TGTCGGCTAGGATTAGGAAAAG 57.598 45.455 0.00 0.00 0.00 2.27
155 156 5.046159 TGTCGGCTAGGATTAGGAAAAGAAA 60.046 40.000 0.00 0.00 0.00 2.52
157 158 6.373495 GTCGGCTAGGATTAGGAAAAGAAAAA 59.627 38.462 0.00 0.00 0.00 1.94
207 208 6.972901 CACGAAGTAAATACATCTACTCAGCA 59.027 38.462 0.00 0.00 41.61 4.41
327 328 1.067060 TGACTGATCCTATTGTCGGCG 59.933 52.381 0.00 0.00 32.64 6.46
337 338 0.246635 ATTGTCGGCGTGTCTTAGCT 59.753 50.000 6.85 0.00 0.00 3.32
338 339 0.666274 TTGTCGGCGTGTCTTAGCTG 60.666 55.000 6.85 0.00 40.87 4.24
343 344 2.391389 GCGTGTCTTAGCTGTGGCC 61.391 63.158 0.00 0.00 39.73 5.36
358 359 4.214971 GCTGTGGCCAAGATACATGATAAG 59.785 45.833 7.24 0.00 0.00 1.73
362 363 3.503748 GGCCAAGATACATGATAAGCCAC 59.496 47.826 0.00 0.00 37.80 5.01
387 395 6.537453 AGCAAGTACATGACTAGATTCACT 57.463 37.500 0.00 0.00 37.44 3.41
430 439 7.548427 CACATGAGCATATACCCTCTGATAAAG 59.452 40.741 0.00 0.00 0.00 1.85
588 597 5.971763 AGTAGCATCTTCTGTTGACCTAAG 58.028 41.667 0.00 0.00 0.00 2.18
604 613 9.352191 GTTGACCTAAGGTATTGATACTCTAGA 57.648 37.037 0.00 0.00 35.25 2.43
626 635 9.445786 CTAGAAACGTTTTAAAGCATTTCTTCA 57.554 29.630 24.36 11.66 40.09 3.02
632 641 8.192110 ACGTTTTAAAGCATTTCTTCAAAGGTA 58.808 29.630 2.86 0.00 40.09 3.08
703 712 2.206322 AGGGGCCATCATGTACCTTA 57.794 50.000 4.39 0.00 0.00 2.69
704 713 2.498441 AGGGGCCATCATGTACCTTAA 58.502 47.619 4.39 0.00 0.00 1.85
705 714 3.063650 AGGGGCCATCATGTACCTTAAT 58.936 45.455 4.39 0.00 0.00 1.40
706 715 3.467103 AGGGGCCATCATGTACCTTAATT 59.533 43.478 4.39 0.00 0.00 1.40
707 716 4.667858 AGGGGCCATCATGTACCTTAATTA 59.332 41.667 4.39 0.00 0.00 1.40
747 757 2.280628 CTCCGTTCTAATCCAAGCCAC 58.719 52.381 0.00 0.00 0.00 5.01
808 818 2.903784 ACATTATGCCCCGTCATAGCTA 59.096 45.455 0.00 0.00 31.33 3.32
809 819 3.326588 ACATTATGCCCCGTCATAGCTAA 59.673 43.478 0.00 0.00 31.33 3.09
810 820 4.019321 ACATTATGCCCCGTCATAGCTAAT 60.019 41.667 0.00 0.00 31.33 1.73
811 821 5.188948 ACATTATGCCCCGTCATAGCTAATA 59.811 40.000 0.00 0.00 31.33 0.98
812 822 3.895232 ATGCCCCGTCATAGCTAATAG 57.105 47.619 0.00 0.00 0.00 1.73
813 823 2.884320 TGCCCCGTCATAGCTAATAGA 58.116 47.619 0.00 0.00 0.00 1.98
814 824 3.441101 TGCCCCGTCATAGCTAATAGAT 58.559 45.455 0.00 0.00 0.00 1.98
900 910 6.307776 TGGAAGTACAAGAGAGAGAAAGAGA 58.692 40.000 0.00 0.00 0.00 3.10
925 935 9.542462 GAGTTTTGTACTATATGTTCCATAGCA 57.458 33.333 0.00 0.00 37.17 3.49
962 972 5.899547 TCTTGAACTATTGAGCTGGATCCTA 59.100 40.000 14.23 0.00 0.00 2.94
984 994 8.597167 TCCTAATATCCATACAATTCCTCACAG 58.403 37.037 0.00 0.00 0.00 3.66
1019 1522 2.643304 ACATGGCTGATCCTAGCATGAT 59.357 45.455 16.85 0.00 45.46 2.45
1071 1574 3.355378 CTTCATCAATAACACAGGGGCA 58.645 45.455 0.00 0.00 0.00 5.36
1103 1606 3.743396 ACTGCAAGACGTTTCTCATCTTC 59.257 43.478 0.00 0.00 37.43 2.87
1248 1751 1.869767 GTCGAATTATGGCTGAGCAGG 59.130 52.381 6.82 0.00 0.00 4.85
1251 1754 2.225467 GAATTATGGCTGAGCAGGGTC 58.775 52.381 6.82 0.00 0.00 4.46
1266 1769 1.726533 GGGTCGATGGAGTCCTCGTC 61.727 65.000 22.25 18.50 36.33 4.20
1531 2034 4.214310 TCTCTGGGAATTTTTCAACAGCA 58.786 39.130 0.00 0.00 36.64 4.41
1699 2202 7.792374 TGAGATTTGTTATATGCTTCCAGAC 57.208 36.000 0.00 0.00 0.00 3.51
1718 2221 7.479980 TCCAGACAAACTTAAAATGAACACAG 58.520 34.615 0.00 0.00 0.00 3.66
1722 2225 9.783256 AGACAAACTTAAAATGAACACAGTAAC 57.217 29.630 0.00 0.00 0.00 2.50
1740 2243 6.484308 ACAGTAACAAAAGTTAATGTACGCCT 59.516 34.615 16.68 0.00 43.38 5.52
1803 2306 8.549338 AAAACCTTCCATTTAAAACGTTTTCA 57.451 26.923 28.31 16.24 28.81 2.69
1819 2322 9.896263 AAACGTTTTCAACTAAACTTCAAGTAA 57.104 25.926 7.96 0.00 36.18 2.24
1855 2358 1.871039 GCTTTTGTCCAGAAGTGCGTA 59.129 47.619 0.33 0.00 0.00 4.42
2082 2585 8.713737 AAAGGTAGTATCGATCCTTTGTTTAC 57.286 34.615 21.72 4.88 45.01 2.01
2309 2813 4.211125 TCACAATGTTTTACCTTGCCTGA 58.789 39.130 0.00 0.00 28.56 3.86
2403 2908 5.819379 TGCTCAGATAGATTGGAATCAACAC 59.181 40.000 2.32 0.00 37.89 3.32
2521 3026 4.453478 TGAGTGAACATTCTCTCACAATGC 59.547 41.667 18.00 0.00 46.68 3.56
2530 3035 1.998315 CTCTCACAATGCGAACAGGAG 59.002 52.381 0.00 0.00 0.00 3.69
2548 3053 2.611518 GAGTGAGAGCATAAGCACGTT 58.388 47.619 0.00 0.00 45.49 3.99
2549 3054 2.996621 GAGTGAGAGCATAAGCACGTTT 59.003 45.455 0.00 0.00 45.49 3.60
2581 3086 1.306312 TTTAGCTAGGCCCACCGGA 60.306 57.895 9.46 0.00 42.76 5.14
2615 3121 8.554011 AGCCCACAAGTTATCTTAGGTTAATTA 58.446 33.333 4.43 0.00 32.07 1.40
2969 3707 4.735132 CGTGCCGATGACCACCGT 62.735 66.667 0.00 0.00 0.00 4.83
2988 4589 3.387091 CCGATGACGTCCACCCCA 61.387 66.667 14.12 0.00 37.88 4.96
3383 5049 4.340246 CCTCTGGCACCTGCAGCA 62.340 66.667 8.66 0.00 44.36 4.41
3507 5392 1.832608 CCCGATCCATCAGGTCCGA 60.833 63.158 0.00 0.00 34.47 4.55
3510 5395 1.893137 CCGATCCATCAGGTCCGATTA 59.107 52.381 0.00 0.00 34.47 1.75
3704 5595 0.673956 TCTGAGCTAGCTCGACACGT 60.674 55.000 33.55 4.31 45.48 4.49
4140 6034 4.838486 CGCGTGGACGAGGAGCTC 62.838 72.222 4.71 4.71 43.02 4.09
4172 6066 0.531532 GATCTCCAGTCGGCCATGTG 60.532 60.000 2.24 0.00 0.00 3.21
4212 6107 2.755064 CGCATGGTGGCCATCCAA 60.755 61.111 24.81 4.84 43.15 3.53
4510 6420 1.610038 TCGAGAAGGTGTTTGACGCTA 59.390 47.619 0.00 0.00 0.00 4.26
4534 6444 2.888464 ATCGCCTCGAGGAGTTCCGA 62.888 60.000 35.69 30.17 39.91 4.55
4580 6491 0.880278 GGACGAGCTGTTTGTGCAGA 60.880 55.000 0.00 0.00 38.70 4.26
4949 6976 8.063153 TGATTAACTTACCTATACTCCCACTGA 58.937 37.037 0.00 0.00 0.00 3.41
4955 6982 7.182206 ACTTACCTATACTCCCACTGAAACAAT 59.818 37.037 0.00 0.00 0.00 2.71
5012 7039 1.063616 CAGAAGATTGACTGCATGCGG 59.936 52.381 25.08 25.08 0.00 5.69
5184 7211 0.244721 GGCTTGCCTTGGAATGACAC 59.755 55.000 4.11 0.00 0.00 3.67
5300 7327 1.418334 AGAAGATGTCGGGATCCCAG 58.582 55.000 30.42 21.71 35.37 4.45
5817 7844 0.039618 GACCCCAAGAAAGGCCATCA 59.960 55.000 5.01 0.00 0.00 3.07
5876 7903 3.990469 GAGTTGCAAATCTGACTCTTCGA 59.010 43.478 19.13 0.00 36.47 3.71
5983 8010 0.105555 AGAGGGCTCCATCAGAGAGG 60.106 60.000 3.28 0.00 46.50 3.69
6418 8970 8.827832 ATGATCTGAACATTGATTCCCTAAAA 57.172 30.769 0.00 0.00 0.00 1.52
6494 9046 1.028330 CAAGACACATCCGCTGGCAT 61.028 55.000 0.00 0.00 0.00 4.40
6794 9346 0.689623 CTGGGTTCTGAAGCTGGAGT 59.310 55.000 17.95 0.00 0.00 3.85
7005 9557 7.448161 TGCCAAATATTACCAGAATATGACCAG 59.552 37.037 0.00 0.00 0.00 4.00
7038 9590 4.402851 TGGAACAGAGCACCATGC 57.597 55.556 0.00 0.00 45.46 4.06
7069 9621 6.214615 TCCCAAAACTGAGATCATTGGTACTA 59.785 38.462 11.04 0.00 39.07 1.82
7117 9669 1.704628 TGCATCCCAAGAGACTTTCCA 59.295 47.619 0.00 0.00 0.00 3.53
7142 9694 5.783360 TGTCTTGAAAGTATTAGGGTGGAGA 59.217 40.000 0.00 0.00 0.00 3.71
7247 9799 2.381961 TGGGAAAAGCTAGAATGGGGTT 59.618 45.455 0.00 0.00 0.00 4.11
7328 9880 5.456548 TCACTGCAACATGATGAAACAAT 57.543 34.783 7.22 0.00 0.00 2.71
7383 9935 8.496751 CAGAGTATGATGAATGTTCTGCATTAG 58.503 37.037 0.00 0.00 46.90 1.73
7426 9978 7.219535 CACACTCAAGCATAAGCAACAATATTC 59.780 37.037 0.00 0.00 45.49 1.75
7484 10036 0.761802 CCTAGGCCTGTGAAGATCCC 59.238 60.000 17.99 0.00 0.00 3.85
7742 10317 9.979578 TTGTGCATAGATTGTATTTTCAGTTTT 57.020 25.926 0.00 0.00 0.00 2.43
7811 10386 6.820656 CAGTTAGCTCATACCTGATTGACTTT 59.179 38.462 0.00 0.00 0.00 2.66
7817 10392 5.745227 TCATACCTGATTGACTTTCCTTCC 58.255 41.667 0.00 0.00 0.00 3.46
7825 10400 4.387026 TTGACTTTCCTTCCATGGTCAT 57.613 40.909 12.58 0.00 34.42 3.06
7847 10422 4.195225 GCTTATAGCATACCAGAGGGAC 57.805 50.000 0.00 0.00 41.89 4.46
7896 10472 1.826054 CCACGCAACACCTCCCAAA 60.826 57.895 0.00 0.00 0.00 3.28
7940 10517 9.566432 GTCTCCAGATTCACCATATATTCTTTT 57.434 33.333 0.00 0.00 0.00 2.27
8117 10702 2.391724 ATCGAACACCTTGCACCCGT 62.392 55.000 0.00 0.00 0.00 5.28
8145 10730 2.189342 GCGGAGATCAGTTCTTTCTCG 58.811 52.381 0.00 0.00 37.38 4.04
8222 10807 0.108567 GACCAAAGGTCGCTCTCTCC 60.109 60.000 0.00 0.00 43.14 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.120649 CGCTTAGTTGACTTGCCTACAAC 60.121 47.826 0.00 0.00 42.51 3.32
16 17 3.064207 CGCTTAGTTGACTTGCCTACAA 58.936 45.455 0.00 0.00 0.00 2.41
78 79 2.351336 CTAGGCGGGCTGGTACTTCG 62.351 65.000 15.11 0.00 0.00 3.79
91 92 1.641577 GTTACAACTCCAGCTAGGCG 58.358 55.000 0.00 0.00 37.29 5.52
92 93 1.641577 CGTTACAACTCCAGCTAGGC 58.358 55.000 0.00 0.00 37.29 3.93
93 94 1.134788 CCCGTTACAACTCCAGCTAGG 60.135 57.143 0.00 0.00 39.47 3.02
94 95 1.739371 GCCCGTTACAACTCCAGCTAG 60.739 57.143 0.00 0.00 0.00 3.42
95 96 0.248289 GCCCGTTACAACTCCAGCTA 59.752 55.000 0.00 0.00 0.00 3.32
96 97 1.003718 GCCCGTTACAACTCCAGCT 60.004 57.895 0.00 0.00 0.00 4.24
97 98 2.388232 CGCCCGTTACAACTCCAGC 61.388 63.158 0.00 0.00 0.00 4.85
98 99 0.108329 ATCGCCCGTTACAACTCCAG 60.108 55.000 0.00 0.00 0.00 3.86
99 100 1.184431 TATCGCCCGTTACAACTCCA 58.816 50.000 0.00 0.00 0.00 3.86
100 101 2.132762 CATATCGCCCGTTACAACTCC 58.867 52.381 0.00 0.00 0.00 3.85
101 102 1.525619 GCATATCGCCCGTTACAACTC 59.474 52.381 0.00 0.00 32.94 3.01
102 103 1.578583 GCATATCGCCCGTTACAACT 58.421 50.000 0.00 0.00 32.94 3.16
113 114 3.363970 CGACATAAGGTTTGGCATATCGC 60.364 47.826 0.00 0.00 41.28 4.58
114 115 3.186409 CCGACATAAGGTTTGGCATATCG 59.814 47.826 0.00 0.00 0.00 2.92
115 116 3.058224 GCCGACATAAGGTTTGGCATATC 60.058 47.826 6.43 0.00 45.55 1.63
116 117 2.884639 GCCGACATAAGGTTTGGCATAT 59.115 45.455 6.43 0.00 45.55 1.78
117 118 2.294074 GCCGACATAAGGTTTGGCATA 58.706 47.619 6.43 0.00 45.55 3.14
118 119 1.102978 GCCGACATAAGGTTTGGCAT 58.897 50.000 6.43 0.00 45.55 4.40
119 120 2.562125 GCCGACATAAGGTTTGGCA 58.438 52.632 6.43 0.00 45.55 4.92
168 169 1.937223 CTTCGTGTGCAAGTTACACCA 59.063 47.619 3.76 0.00 44.18 4.17
169 170 1.937899 ACTTCGTGTGCAAGTTACACC 59.062 47.619 3.76 0.00 44.18 4.16
172 173 6.879962 TGTATTTACTTCGTGTGCAAGTTAC 58.120 36.000 0.00 0.00 35.63 2.50
173 174 7.601130 AGATGTATTTACTTCGTGTGCAAGTTA 59.399 33.333 0.00 0.00 35.63 2.24
174 175 5.994887 TGTATTTACTTCGTGTGCAAGTT 57.005 34.783 0.00 0.00 35.63 2.66
175 176 5.932303 AGATGTATTTACTTCGTGTGCAAGT 59.068 36.000 0.00 0.00 37.80 3.16
179 180 6.750501 TGAGTAGATGTATTTACTTCGTGTGC 59.249 38.462 0.00 0.00 36.02 4.57
184 185 7.168302 CCTTGCTGAGTAGATGTATTTACTTCG 59.832 40.741 0.00 0.00 36.02 3.79
327 328 3.322514 TTGGCCACAGCTAAGACAC 57.677 52.632 3.88 0.00 34.09 3.67
337 338 4.136796 GCTTATCATGTATCTTGGCCACA 58.863 43.478 3.88 0.00 0.00 4.17
338 339 3.503748 GGCTTATCATGTATCTTGGCCAC 59.496 47.826 3.88 0.00 37.30 5.01
343 344 5.297527 TGCTTGTGGCTTATCATGTATCTTG 59.702 40.000 0.00 0.00 42.39 3.02
358 359 2.154462 AGTCATGTACTTGCTTGTGGC 58.846 47.619 3.90 0.00 33.35 5.01
362 363 6.815641 AGTGAATCTAGTCATGTACTTGCTTG 59.184 38.462 3.90 6.22 39.80 4.01
387 395 6.701841 GCTCATGTGATTCGACTATTCCTTTA 59.298 38.462 0.00 0.00 0.00 1.85
455 464 6.255453 ACAACGATTTGACTTTTCCAACAATG 59.745 34.615 0.00 0.00 36.48 2.82
529 538 1.134431 AGATGGCATGTACACGCATCA 60.134 47.619 16.66 5.78 0.00 3.07
604 613 8.387354 CCTTTGAAGAAATGCTTTAAAACGTTT 58.613 29.630 7.96 7.96 40.29 3.60
642 651 6.515832 CCTGTAAGCTTCCAATTTTCTGTTT 58.484 36.000 0.00 0.00 0.00 2.83
644 653 4.021981 GCCTGTAAGCTTCCAATTTTCTGT 60.022 41.667 0.00 0.00 0.00 3.41
651 660 1.005215 AGCAGCCTGTAAGCTTCCAAT 59.995 47.619 0.00 0.00 42.61 3.16
703 712 5.047306 GCACAGGGGCTAGTTTCTTTTAATT 60.047 40.000 0.00 0.00 0.00 1.40
704 713 4.462834 GCACAGGGGCTAGTTTCTTTTAAT 59.537 41.667 0.00 0.00 0.00 1.40
705 714 3.824443 GCACAGGGGCTAGTTTCTTTTAA 59.176 43.478 0.00 0.00 0.00 1.52
706 715 3.073946 AGCACAGGGGCTAGTTTCTTTTA 59.926 43.478 0.00 0.00 43.70 1.52
707 716 2.158460 AGCACAGGGGCTAGTTTCTTTT 60.158 45.455 0.00 0.00 43.70 2.27
714 723 3.077556 CGGAGCACAGGGGCTAGT 61.078 66.667 0.00 0.00 45.99 2.57
747 757 4.202295 TGCAGCTTCCTGGAATCTACATAG 60.202 45.833 12.13 2.01 36.41 2.23
775 785 3.003378 GGGCATAATGTAGAAAAGACCGC 59.997 47.826 0.00 0.00 0.00 5.68
778 788 4.196971 ACGGGGCATAATGTAGAAAAGAC 58.803 43.478 0.00 0.00 0.00 3.01
809 819 9.622637 ACTTCCTATTTAAGAGGGCTAATCTAT 57.377 33.333 5.75 0.00 34.56 1.98
810 820 8.871125 CACTTCCTATTTAAGAGGGCTAATCTA 58.129 37.037 5.75 0.00 34.56 1.98
811 821 7.348537 ACACTTCCTATTTAAGAGGGCTAATCT 59.651 37.037 5.75 0.00 34.56 2.40
812 822 7.510407 ACACTTCCTATTTAAGAGGGCTAATC 58.490 38.462 5.75 0.00 34.56 1.75
813 823 7.420330 GGACACTTCCTATTTAAGAGGGCTAAT 60.420 40.741 5.75 0.00 39.13 1.73
814 824 6.126854 GGACACTTCCTATTTAAGAGGGCTAA 60.127 42.308 5.75 0.00 39.13 3.09
822 832 6.940298 TCCAGTTTGGACACTTCCTATTTAAG 59.060 38.462 0.00 0.00 42.67 1.85
875 885 6.951198 TCTCTTTCTCTCTCTTGTACTTCCAT 59.049 38.462 0.00 0.00 0.00 3.41
929 939 8.137437 CAGCTCAATAGTTCAAGAAAGGAAAAA 58.863 33.333 0.00 0.00 0.00 1.94
938 948 4.718774 AGGATCCAGCTCAATAGTTCAAGA 59.281 41.667 15.82 0.00 0.00 3.02
962 972 8.274322 TGTTCTGTGAGGAATTGTATGGATATT 58.726 33.333 0.00 0.00 0.00 1.28
972 982 2.162681 GGGGTGTTCTGTGAGGAATTG 58.837 52.381 0.00 0.00 0.00 2.32
984 994 1.480545 GCCATGTAAATGGGGGTGTTC 59.519 52.381 14.08 0.00 41.94 3.18
1008 1018 3.881089 CTGCACAAATCATCATGCTAGGA 59.119 43.478 0.00 0.00 38.90 2.94
1103 1606 2.254951 TGCGCTTGATGCAAACGG 59.745 55.556 9.73 0.00 43.06 4.44
1248 1751 1.726533 GGACGAGGACTCCATCGACC 61.727 65.000 18.27 17.25 44.05 4.79
1251 1754 1.320344 TTGGGACGAGGACTCCATCG 61.320 60.000 12.65 12.65 44.36 3.84
1266 1769 1.750206 TGTTCGATGGCATCAATTGGG 59.250 47.619 25.88 9.58 0.00 4.12
1360 1863 0.792640 ATCTCAAGAACACGCTTGCG 59.207 50.000 13.70 13.70 43.78 4.85
1653 2156 8.435187 TCTCATCTAAATGTTCATCTAGGCAAT 58.565 33.333 0.00 0.00 34.32 3.56
1718 2221 7.856894 TCAAAGGCGTACATTAACTTTTGTTAC 59.143 33.333 0.00 0.00 43.76 2.50
1722 2225 6.435428 ACTCAAAGGCGTACATTAACTTTTG 58.565 36.000 0.00 0.00 29.64 2.44
1734 2237 7.380536 TGTAAAGAAATAGACTCAAAGGCGTA 58.619 34.615 0.00 0.00 0.00 4.42
1819 2322 6.131544 ACAAAAGCTCGATTTGTACACTTT 57.868 33.333 12.26 0.00 46.21 2.66
1855 2358 8.694540 TGTTGTAGGATTTTATAGCAAATGCAT 58.305 29.630 8.28 0.00 45.16 3.96
1872 2375 7.719193 TGAACTGAGAAATTTGATGTTGTAGGA 59.281 33.333 0.00 0.00 0.00 2.94
1873 2376 7.805071 GTGAACTGAGAAATTTGATGTTGTAGG 59.195 37.037 0.00 0.00 0.00 3.18
2081 2584 9.474313 TTCCTTTTATCTAATTAATGCCACTGT 57.526 29.630 0.00 0.00 0.00 3.55
2082 2585 9.956720 CTTCCTTTTATCTAATTAATGCCACTG 57.043 33.333 0.00 0.00 0.00 3.66
2309 2813 1.960763 TGCACGCGAGAAATGCAGT 60.961 52.632 15.93 0.00 44.17 4.40
2362 2867 3.009473 TGAGCAAGGGAAGCAGTTCTATT 59.991 43.478 0.00 0.00 32.72 1.73
2403 2908 1.471684 GCAAGGGAGATGTTCTGCTTG 59.528 52.381 0.00 0.00 35.01 4.01
2462 2967 3.569250 TTGCCGGACTGATTTAAAAGC 57.431 42.857 5.05 0.00 0.00 3.51
2469 2974 2.198827 TGTTCATTGCCGGACTGATT 57.801 45.000 5.05 0.00 0.00 2.57
2521 3026 3.443037 CTTATGCTCTCACTCCTGTTCG 58.557 50.000 0.00 0.00 0.00 3.95
2530 3035 4.330074 ACATAAACGTGCTTATGCTCTCAC 59.670 41.667 16.38 0.00 41.19 3.51
2548 3053 4.159244 AGCTAAACCGGCCATAACATAA 57.841 40.909 0.00 0.00 0.00 1.90
2549 3054 3.849563 AGCTAAACCGGCCATAACATA 57.150 42.857 0.00 0.00 0.00 2.29
2581 3086 6.067217 AGATAACTTGTGGGCTAAGATTGT 57.933 37.500 0.00 0.00 0.00 2.71
3507 5392 3.159347 GACGGGGAGGGCGGTAAT 61.159 66.667 0.00 0.00 0.00 1.89
3545 5430 1.224592 GGCGATGGTGAAGACCCAT 59.775 57.895 0.00 0.00 45.37 4.00
3682 5573 0.253327 TGTCGAGCTAGCTCAGAGGA 59.747 55.000 36.92 25.50 42.86 3.71
3704 5595 2.333417 GGTGTCTGAGTCGGAGCGA 61.333 63.158 0.58 0.00 0.00 4.93
3734 5625 0.108804 GGTGGCGAAGTCGATCTTGA 60.109 55.000 4.59 0.00 43.02 3.02
3876 5767 0.249322 CGAGGGCGTAATACCAGGTG 60.249 60.000 0.76 0.00 0.00 4.00
3995 5889 2.203938 AGGTGAAGGGAAGGCGGA 60.204 61.111 0.00 0.00 0.00 5.54
4084 5978 2.747686 GACAAAGAGGTCGGCCCA 59.252 61.111 0.08 0.00 34.66 5.36
4212 6107 0.620410 TCCGGGATGGTGATTCCTGT 60.620 55.000 0.00 0.00 37.86 4.00
4510 6420 0.681564 ACTCCTCGAGGCGATCAACT 60.682 55.000 27.68 0.97 34.61 3.16
4534 6444 0.608308 GTAAGGTGGGGAAGCGCTTT 60.608 55.000 25.84 8.10 0.00 3.51
4573 6484 1.837051 ACTTCTCCCCGTCTGCACA 60.837 57.895 0.00 0.00 0.00 4.57
4580 6491 0.252197 GCCATAACACTTCTCCCCGT 59.748 55.000 0.00 0.00 0.00 5.28
4763 6715 2.365105 TAGGGTTCCGGCTCCCAG 60.365 66.667 27.39 0.00 45.64 4.45
4764 6716 2.365105 CTAGGGTTCCGGCTCCCA 60.365 66.667 27.39 16.25 45.64 4.37
4765 6717 3.862991 GCTAGGGTTCCGGCTCCC 61.863 72.222 21.26 21.26 43.71 4.30
4855 6882 1.221021 CGGAGGTTGTAGGGGAAGC 59.779 63.158 0.00 0.00 0.00 3.86
5184 7211 1.524355 CACGAGTTTGCACTGTCTCTG 59.476 52.381 0.00 0.00 31.22 3.35
5300 7327 4.752146 CTTTTGATTTCAGAATCTGGGGC 58.248 43.478 10.71 0.00 41.80 5.80
5817 7844 5.784177 CTGACAACAGGCTACGGATTATAT 58.216 41.667 0.00 0.00 40.14 0.86
5876 7903 5.743636 ATAATGTGGTGCATTTTGACCTT 57.256 34.783 0.00 0.00 44.82 3.50
5983 8010 1.174712 TTCTTGCTGCTTGCCACTCC 61.175 55.000 0.00 0.00 42.00 3.85
6794 9346 8.194104 GTGATAGATAGAAAGCTTCTCAAGTGA 58.806 37.037 0.00 0.00 41.14 3.41
7005 9557 1.526917 CCATTGATCCGCCCACTCC 60.527 63.158 0.00 0.00 0.00 3.85
7036 9588 2.172505 TCTCAGTTTTGGGAAGTCTGCA 59.827 45.455 0.00 0.00 28.50 4.41
7038 9590 4.645535 TGATCTCAGTTTTGGGAAGTCTG 58.354 43.478 0.00 0.00 37.36 3.51
7069 9621 2.972713 TCTCAGCTTTGGTAGGTCAGTT 59.027 45.455 0.00 0.00 30.51 3.16
7117 9669 6.443849 TCTCCACCCTAATACTTTCAAGACAT 59.556 38.462 0.00 0.00 0.00 3.06
7142 9694 2.582052 TGTTTTCAGATTCGGGCAGTT 58.418 42.857 0.00 0.00 0.00 3.16
7247 9799 2.239402 TGCTCTCCATTATGTCCTTGCA 59.761 45.455 0.00 0.00 0.00 4.08
7383 9935 3.057033 AGTGTGGCAGATGAAATTGAAGC 60.057 43.478 0.00 0.00 0.00 3.86
7426 9978 2.393271 AGAGGTTGATTGAGGAAGCG 57.607 50.000 0.00 0.00 0.00 4.68
7632 10206 6.974622 GTCACTTGTTTGTGAATCTGAACATT 59.025 34.615 0.00 0.00 46.77 2.71
7735 10310 5.809001 AGGATATGCTCTGTGAAAAACTGA 58.191 37.500 0.00 0.00 35.63 3.41
7736 10311 6.506500 AAGGATATGCTCTGTGAAAAACTG 57.493 37.500 0.00 0.00 0.00 3.16
7737 10312 8.635765 TTAAAGGATATGCTCTGTGAAAAACT 57.364 30.769 0.00 0.00 0.00 2.66
7738 10313 9.860898 ATTTAAAGGATATGCTCTGTGAAAAAC 57.139 29.630 0.00 0.00 0.00 2.43
7739 10314 9.859427 CATTTAAAGGATATGCTCTGTGAAAAA 57.141 29.630 0.00 0.00 0.00 1.94
7740 10315 7.975616 GCATTTAAAGGATATGCTCTGTGAAAA 59.024 33.333 3.61 0.00 41.04 2.29
7741 10316 7.416664 GGCATTTAAAGGATATGCTCTGTGAAA 60.417 37.037 3.61 0.00 43.17 2.69
7742 10317 6.039717 GGCATTTAAAGGATATGCTCTGTGAA 59.960 38.462 3.61 0.00 43.17 3.18
7811 10386 4.505566 GCTATAAGCATGACCATGGAAGGA 60.506 45.833 21.47 0.00 41.89 3.36
7896 10472 5.112686 GGAGACTGATATTTCGTTGCTTCT 58.887 41.667 0.00 0.00 0.00 2.85
7940 10517 3.761218 TGAGCCTTGTGACTTTTTGTTCA 59.239 39.130 0.00 0.00 0.00 3.18
8117 10702 2.073252 ACTGATCTCCGCCATGTCTA 57.927 50.000 0.00 0.00 0.00 2.59
8222 10807 3.688159 GCCCAGTGCAAGCCCAAG 61.688 66.667 0.00 0.00 40.77 3.61


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

AutoCloner maintained by Alex Coulton.