Multiple sequence alignment - TraesCS6D01G071200

Loading Multiple Alignment...

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 TraesCS6D01G071200 chr6D 100.000 8642 0 0 1 8642 36091220 36082579 0.000000e+00 15959.0
1 TraesCS6D01G071200 chr6D 85.010 1034 123 22 6647 7670 35717632 35716621 0.000000e+00 1022.0
2 TraesCS6D01G071200 chr6D 85.961 869 90 22 7783 8641 35715966 35715120 0.000000e+00 900.0
3 TraesCS6D01G071200 chr6D 79.453 1134 171 33 6643 7754 35641695 35640602 0.000000e+00 747.0
4 TraesCS6D01G071200 chr6D 80.000 1030 157 27 6642 7635 35667142 35666126 0.000000e+00 715.0
5 TraesCS6D01G071200 chr6D 87.954 606 65 6 8041 8642 35639843 35639242 0.000000e+00 708.0
6 TraesCS6D01G071200 chr6D 99.417 343 1 1 1143 1485 36084922 36084581 9.530000e-174 621.0
7 TraesCS6D01G071200 chr6D 99.417 343 1 1 6299 6640 36090078 36089736 9.530000e-174 621.0
8 TraesCS6D01G071200 chr6D 87.887 355 41 2 792 1145 35717988 35717635 4.830000e-112 416.0
9 TraesCS6D01G071200 chr6D 83.376 391 51 12 766 1146 36106098 36105712 4.960000e-92 350.0
10 TraesCS6D01G071200 chr6D 86.636 217 25 3 7783 7995 35640055 35639839 4.030000e-58 237.0
11 TraesCS6D01G071200 chr6D 92.157 51 3 1 7830 7880 27537715 27537666 4.330000e-08 71.3
12 TraesCS6D01G071200 chr1D 98.764 5500 64 3 1143 6642 6392673 6398168 0.000000e+00 9777.0
13 TraesCS6D01G071200 chr1D 98.708 5494 68 2 1147 6640 6387524 6393014 0.000000e+00 9749.0
14 TraesCS6D01G071200 chr1D 98.399 5495 82 4 1147 6640 464017955 464012466 0.000000e+00 9655.0
15 TraesCS6D01G071200 chr1D 75.109 5034 1155 80 1470 6451 418666918 418661931 0.000000e+00 2265.0
16 TraesCS6D01G071200 chr1D 97.935 339 7 0 6302 6640 6387524 6387862 9.660000e-164 588.0
17 TraesCS6D01G071200 chr1D 97.093 344 9 1 1143 1486 464012807 464012465 5.820000e-161 579.0
18 TraesCS6D01G071200 chr1D 96.793 343 10 1 1143 1485 6397825 6398166 9.730000e-159 571.0
19 TraesCS6D01G071200 chr1D 82.906 585 82 12 6641 7223 37880387 37880955 2.150000e-140 510.0
20 TraesCS6D01G071200 chr3D 98.341 4821 76 3 1822 6641 560156882 560152065 0.000000e+00 8456.0
21 TraesCS6D01G071200 chr3D 74.986 5469 1247 97 1144 6545 588367365 588361951 0.000000e+00 2409.0
22 TraesCS6D01G071200 chr3D 77.021 1101 236 17 5456 6545 475657431 475658525 4.430000e-172 616.0
23 TraesCS6D01G071200 chr3D 96.610 354 11 1 1147 1500 560157230 560156878 3.480000e-163 586.0
24 TraesCS6D01G071200 chr3D 97.345 339 9 0 6302 6640 560157230 560156892 2.090000e-160 577.0
25 TraesCS6D01G071200 chr3D 96.793 343 10 1 1143 1485 560152407 560152066 9.730000e-159 571.0
26 TraesCS6D01G071200 chr5B 94.320 2729 99 20 3825 6546 690368417 690365738 0.000000e+00 4130.0
27 TraesCS6D01G071200 chr5B 95.694 720 31 0 2174 2893 690369145 690368426 0.000000e+00 1158.0
28 TraesCS6D01G071200 chr5B 92.901 493 29 2 1556 2042 690389977 690389485 0.000000e+00 712.0
29 TraesCS6D01G071200 chr5B 96.503 143 4 1 2037 2178 690375064 690374922 1.450000e-57 235.0
30 TraesCS6D01G071200 chr7D 98.220 2360 40 1 1136 3495 24111386 24113743 0.000000e+00 4124.0
31 TraesCS6D01G071200 chr7D 97.368 342 9 0 6299 6640 24111394 24111735 4.500000e-162 582.0
32 TraesCS6D01G071200 chr6A 94.630 2011 69 9 6641 8642 39670385 39668405 0.000000e+00 3079.0
33 TraesCS6D01G071200 chr6A 94.080 2010 81 8 6641 8642 39628593 39626614 0.000000e+00 3018.0
34 TraesCS6D01G071200 chr6A 93.936 2012 82 10 6641 8642 39580805 39578824 0.000000e+00 3003.0
35 TraesCS6D01G071200 chr6A 93.927 494 29 1 654 1147 39670872 39670380 0.000000e+00 745.0
36 TraesCS6D01G071200 chr6A 82.401 858 107 24 6914 7754 39548260 39547430 0.000000e+00 708.0
37 TraesCS6D01G071200 chr6A 81.921 885 116 24 6914 7781 39590373 39589516 0.000000e+00 708.0
38 TraesCS6D01G071200 chr6A 87.954 606 64 7 8041 8642 39588760 39588160 0.000000e+00 706.0
39 TraesCS6D01G071200 chr6A 87.624 606 67 6 8041 8642 39546643 39546042 0.000000e+00 697.0
40 TraesCS6D01G071200 chr6A 82.630 829 103 22 6975 7786 39638109 39637305 0.000000e+00 695.0
41 TraesCS6D01G071200 chr6A 87.129 606 69 6 8041 8642 39636552 39635952 0.000000e+00 678.0
42 TraesCS6D01G071200 chr6A 92.701 411 28 1 739 1147 39628998 39628588 7.470000e-165 592.0
43 TraesCS6D01G071200 chr6A 91.241 411 34 2 739 1147 39581210 39580800 7.580000e-155 558.0
44 TraesCS6D01G071200 chr6A 84.979 466 25 14 209 644 39671304 39670854 1.720000e-116 431.0
45 TraesCS6D01G071200 chr6A 88.235 119 11 3 31 148 39862375 39862259 1.170000e-28 139.0
46 TraesCS6D01G071200 chr6A 92.105 76 5 1 127 202 39857908 39857834 1.190000e-18 106.0
47 TraesCS6D01G071200 chr6B 76.741 5370 1133 85 1319 6645 659193419 659198715 0.000000e+00 2891.0
48 TraesCS6D01G071200 chr6B 95.347 1139 43 3 6641 7776 75525931 75524800 0.000000e+00 1801.0
49 TraesCS6D01G071200 chr6B 94.251 835 19 6 7812 8642 75524587 75523778 0.000000e+00 1249.0
50 TraesCS6D01G071200 chr6B 84.948 1156 142 20 6643 7786 75423105 75421970 0.000000e+00 1142.0
51 TraesCS6D01G071200 chr6B 80.118 1524 250 34 1321 2818 76327941 76326445 0.000000e+00 1086.0
52 TraesCS6D01G071200 chr6B 87.429 875 78 24 7783 8642 75044721 75043864 0.000000e+00 977.0
53 TraesCS6D01G071200 chr6B 87.765 850 45 21 318 1147 75526736 75525926 0.000000e+00 939.0
54 TraesCS6D01G071200 chr6B 84.083 867 98 21 7783 8642 75421423 75420590 0.000000e+00 800.0
55 TraesCS6D01G071200 chr6B 87.467 383 43 4 768 1146 75423484 75423103 3.700000e-118 436.0
56 TraesCS6D01G071200 chr6B 86.807 379 47 2 771 1146 75510362 75509984 3.730000e-113 420.0
57 TraesCS6D01G071200 chr6B 92.014 288 22 1 30 316 75527286 75526999 3.760000e-108 403.0
58 TraesCS6D01G071200 chr6B 84.328 402 53 7 719 1117 75514630 75514236 1.360000e-102 385.0
59 TraesCS6D01G071200 chr6B 85.993 307 34 6 737 1042 76153380 76153082 3.890000e-83 320.0
60 TraesCS6D01G071200 chr3A 75.142 5467 1230 102 1147 6542 95120262 95125670 0.000000e+00 2447.0
61 TraesCS6D01G071200 chr5D 75.059 5477 1230 110 1147 6545 533420549 533425967 0.000000e+00 2422.0
62 TraesCS6D01G071200 chr7A 74.977 4340 1008 65 2256 6545 580687637 580683326 0.000000e+00 1927.0
63 TraesCS6D01G071200 chr7A 75.827 1088 214 34 1147 2204 580689113 580688045 2.780000e-139 507.0
64 TraesCS6D01G071200 chr1B 74.642 4263 1011 60 2323 6546 497344584 497348815 0.000000e+00 1820.0
65 TraesCS6D01G071200 chr1B 75.730 1199 229 44 1147 2308 497332447 497333620 5.900000e-151 545.0
66 TraesCS6D01G071200 chr1B 83.333 564 86 5 6641 7203 57615554 57616110 1.660000e-141 514.0
67 TraesCS6D01G071200 chr1B 80.142 564 77 19 7242 7786 57616188 57616735 1.050000e-103 388.0
68 TraesCS6D01G071200 chr5A 75.849 1089 212 36 1147 2204 115669905 115670973 2.780000e-139 507.0


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 TraesCS6D01G071200 chr6D 36082579 36091220 8641 True 15959.000000 15959 100.000000 1 8642 1 chr6D.!!$R3 8641
1 TraesCS6D01G071200 chr6D 35715120 35717988 2868 True 779.333333 1022 86.286000 792 8641 3 chr6D.!!$R8 7849
2 TraesCS6D01G071200 chr6D 35666126 35667142 1016 True 715.000000 715 80.000000 6642 7635 1 chr6D.!!$R2 993
3 TraesCS6D01G071200 chr6D 35639242 35641695 2453 True 564.000000 747 84.681000 6643 8642 3 chr6D.!!$R7 1999
4 TraesCS6D01G071200 chr1D 6387524 6393014 5490 False 9749.000000 9749 98.708000 1147 6640 1 chr1D.!!$F1 5493
5 TraesCS6D01G071200 chr1D 6392673 6398168 5495 False 5174.000000 9777 97.778500 1143 6642 2 chr1D.!!$F4 5499
6 TraesCS6D01G071200 chr1D 464012465 464017955 5490 True 5117.000000 9655 97.746000 1143 6640 2 chr1D.!!$R2 5497
7 TraesCS6D01G071200 chr1D 418661931 418666918 4987 True 2265.000000 2265 75.109000 1470 6451 1 chr1D.!!$R1 4981
8 TraesCS6D01G071200 chr1D 37880387 37880955 568 False 510.000000 510 82.906000 6641 7223 1 chr1D.!!$F3 582
9 TraesCS6D01G071200 chr3D 560152065 560156882 4817 True 8456.000000 8456 98.341000 1822 6641 1 chr3D.!!$R1 4819
10 TraesCS6D01G071200 chr3D 588361951 588367365 5414 True 2409.000000 2409 74.986000 1144 6545 1 chr3D.!!$R3 5401
11 TraesCS6D01G071200 chr3D 475657431 475658525 1094 False 616.000000 616 77.021000 5456 6545 1 chr3D.!!$F1 1089
12 TraesCS6D01G071200 chr5B 690365738 690369145 3407 True 2644.000000 4130 95.007000 2174 6546 2 chr5B.!!$R3 4372
13 TraesCS6D01G071200 chr7D 24111386 24113743 2357 False 2353.000000 4124 97.794000 1136 6640 2 chr7D.!!$F1 5504
14 TraesCS6D01G071200 chr6A 39626614 39628998 2384 True 1805.000000 3018 93.390500 739 8642 2 chr6A.!!$R6 7903
15 TraesCS6D01G071200 chr6A 39578824 39581210 2386 True 1780.500000 3003 92.588500 739 8642 2 chr6A.!!$R4 7903
16 TraesCS6D01G071200 chr6A 39668405 39671304 2899 True 1418.333333 3079 91.178667 209 8642 3 chr6A.!!$R8 8433
17 TraesCS6D01G071200 chr6A 39588160 39590373 2213 True 707.000000 708 84.937500 6914 8642 2 chr6A.!!$R5 1728
18 TraesCS6D01G071200 chr6A 39546042 39548260 2218 True 702.500000 708 85.012500 6914 8642 2 chr6A.!!$R3 1728
19 TraesCS6D01G071200 chr6A 39635952 39638109 2157 True 686.500000 695 84.879500 6975 8642 2 chr6A.!!$R7 1667
20 TraesCS6D01G071200 chr6B 659193419 659198715 5296 False 2891.000000 2891 76.741000 1319 6645 1 chr6B.!!$F1 5326
21 TraesCS6D01G071200 chr6B 75523778 75527286 3508 True 1098.000000 1801 92.344250 30 8642 4 chr6B.!!$R6 8612
22 TraesCS6D01G071200 chr6B 76326445 76327941 1496 True 1086.000000 1086 80.118000 1321 2818 1 chr6B.!!$R3 1497
23 TraesCS6D01G071200 chr6B 75043864 75044721 857 True 977.000000 977 87.429000 7783 8642 1 chr6B.!!$R1 859
24 TraesCS6D01G071200 chr6B 75420590 75423484 2894 True 792.666667 1142 85.499333 768 8642 3 chr6B.!!$R4 7874
25 TraesCS6D01G071200 chr6B 75509984 75514630 4646 True 402.500000 420 85.567500 719 1146 2 chr6B.!!$R5 427
26 TraesCS6D01G071200 chr3A 95120262 95125670 5408 False 2447.000000 2447 75.142000 1147 6542 1 chr3A.!!$F1 5395
27 TraesCS6D01G071200 chr5D 533420549 533425967 5418 False 2422.000000 2422 75.059000 1147 6545 1 chr5D.!!$F1 5398
28 TraesCS6D01G071200 chr7A 580683326 580689113 5787 True 1217.000000 1927 75.402000 1147 6545 2 chr7A.!!$R1 5398
29 TraesCS6D01G071200 chr1B 497344584 497348815 4231 False 1820.000000 1820 74.642000 2323 6546 1 chr1B.!!$F2 4223
30 TraesCS6D01G071200 chr1B 497332447 497333620 1173 False 545.000000 545 75.730000 1147 2308 1 chr1B.!!$F1 1161
31 TraesCS6D01G071200 chr1B 57615554 57616735 1181 False 451.000000 514 81.737500 6641 7786 2 chr1B.!!$F3 1145
32 TraesCS6D01G071200 chr5A 115669905 115670973 1068 False 507.000000 507 75.849000 1147 2204 1 chr5A.!!$F1 1057

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
980 1282 0.889306 CTCCTCGGTTTCTTCGACCT 59.111 55.000 0.00 0.00 34.95 3.85 F
1841 2180 0.039437 GAGCACTTCGTCTTCGGACA 60.039 55.000 0.00 0.00 44.65 4.02 F
3048 3755 0.893727 AATTCTCGTTGTGTGGGGGC 60.894 55.000 0.00 0.00 0.00 5.80 F
3823 4552 0.617935 TGGATGAATTGTCCGGAGCA 59.382 50.000 3.06 3.03 38.64 4.26 F
4900 5637 0.944311 GGTATGCACAGGATACGGCG 60.944 60.000 4.80 4.80 46.39 6.46 F
6765 7512 1.071071 CAACACTTCCGGGTGGTCTTA 59.929 52.381 14.34 0.00 41.09 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3048 3755 1.673665 GGCTGCAGTCCTTGGAGTG 60.674 63.158 16.64 17.66 46.12 3.51 R
3488 4217 1.875514 GTGCTGCAAACACATCTGAGA 59.124 47.619 2.77 0.00 37.96 3.27 R
4619 5356 1.129326 GATTGAAGGTACGATCGCCG 58.871 55.000 16.60 0.00 45.44 6.46 R
5273 6011 2.083774 GCAATTGAATCGTCCTGACCA 58.916 47.619 10.34 0.00 0.00 4.02 R
6902 7670 0.038166 CCCAACTAGCACACCCATGT 59.962 55.000 0.00 0.00 40.80 3.21 R
8485 11390 2.787680 GCAACCGAGCACTAGTATTACG 59.212 50.000 0.00 0.00 0.00 3.18 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
59 60 8.237267 GTCAAAACTGATCTTACATTTTCGGAT 58.763 33.333 0.00 0.00 0.00 4.18
69 70 3.347216 ACATTTTCGGATGGAGGAAGTG 58.653 45.455 0.00 0.00 0.00 3.16
85 86 4.757149 AGGAAGTGTCTCTTTGTGCATTAC 59.243 41.667 0.00 0.00 36.40 1.89
88 89 4.718961 AGTGTCTCTTTGTGCATTACCTT 58.281 39.130 0.00 0.00 0.00 3.50
93 94 3.826157 CTCTTTGTGCATTACCTTTGGGA 59.174 43.478 0.00 0.00 36.25 4.37
105 106 3.697166 ACCTTTGGGAATGGATGTACAC 58.303 45.455 0.00 0.00 36.25 2.90
141 143 2.091055 AGGAGGCTAGTAGGAGATGCAA 60.091 50.000 0.00 0.00 0.00 4.08
151 153 0.961019 GGAGATGCAAGTTGTTGGCA 59.039 50.000 4.48 0.00 33.87 4.92
276 289 3.758300 CTCTGGTTTTGTTGTGTCACAC 58.242 45.455 4.80 0.00 34.56 3.82
279 292 3.149981 TGGTTTTGTTGTGTCACACTGA 58.850 40.909 9.90 0.00 35.11 3.41
303 316 1.202734 CGGAGATGTCATGGCATCCTT 60.203 52.381 31.58 17.86 44.58 3.36
316 329 8.295288 GTCATGGCATCCTTTAGAAATTGATAG 58.705 37.037 0.00 0.00 0.00 2.08
317 330 7.449395 TCATGGCATCCTTTAGAAATTGATAGG 59.551 37.037 0.00 0.00 0.00 2.57
318 331 6.672593 TGGCATCCTTTAGAAATTGATAGGT 58.327 36.000 0.00 0.00 0.00 3.08
319 332 7.125391 TGGCATCCTTTAGAAATTGATAGGTT 58.875 34.615 0.00 0.00 0.00 3.50
320 333 8.278639 TGGCATCCTTTAGAAATTGATAGGTTA 58.721 33.333 0.00 0.00 0.00 2.85
321 334 8.568794 GGCATCCTTTAGAAATTGATAGGTTAC 58.431 37.037 0.00 0.00 0.00 2.50
322 335 9.120538 GCATCCTTTAGAAATTGATAGGTTACA 57.879 33.333 0.00 0.00 0.00 2.41
465 757 9.521841 TGTTGATTATGTGTACATTTTTAGGGA 57.478 29.630 0.00 0.00 37.76 4.20
495 787 9.217278 TGTAACTTTGTACAACTTTCAAGTGTA 57.783 29.630 8.07 1.84 39.66 2.90
563 855 2.368439 AGGCAAGAAATCTGCGCATTA 58.632 42.857 12.24 1.91 0.00 1.90
630 924 6.354130 GCTCTCTCTCTCTCTACCTAAAAGA 58.646 44.000 0.00 0.00 0.00 2.52
631 925 6.826741 GCTCTCTCTCTCTCTACCTAAAAGAA 59.173 42.308 0.00 0.00 0.00 2.52
632 926 7.338449 GCTCTCTCTCTCTCTACCTAAAAGAAA 59.662 40.741 0.00 0.00 0.00 2.52
633 927 9.408648 CTCTCTCTCTCTCTACCTAAAAGAAAT 57.591 37.037 0.00 0.00 0.00 2.17
634 928 9.184523 TCTCTCTCTCTCTACCTAAAAGAAATG 57.815 37.037 0.00 0.00 0.00 2.32
635 929 9.184523 CTCTCTCTCTCTACCTAAAAGAAATGA 57.815 37.037 0.00 0.00 0.00 2.57
636 930 9.184523 TCTCTCTCTCTACCTAAAAGAAATGAG 57.815 37.037 0.00 0.00 0.00 2.90
637 931 8.887264 TCTCTCTCTACCTAAAAGAAATGAGT 57.113 34.615 0.00 0.00 0.00 3.41
638 932 9.315363 TCTCTCTCTACCTAAAAGAAATGAGTT 57.685 33.333 0.00 0.00 0.00 3.01
639 933 9.936759 CTCTCTCTACCTAAAAGAAATGAGTTT 57.063 33.333 0.00 0.00 0.00 2.66
642 936 9.284968 TCTCTACCTAAAAGAAATGAGTTTTGG 57.715 33.333 0.00 0.00 0.00 3.28
643 937 8.404107 TCTACCTAAAAGAAATGAGTTTTGGG 57.596 34.615 8.03 8.03 45.22 4.12
646 940 7.713764 CCTAAAAGAAATGAGTTTTGGGTTG 57.286 36.000 2.68 0.00 38.70 3.77
647 941 7.272244 CCTAAAAGAAATGAGTTTTGGGTTGT 58.728 34.615 2.68 0.00 38.70 3.32
648 942 7.438160 CCTAAAAGAAATGAGTTTTGGGTTGTC 59.562 37.037 2.68 0.00 38.70 3.18
649 943 6.544928 AAAGAAATGAGTTTTGGGTTGTCT 57.455 33.333 0.00 0.00 0.00 3.41
650 944 5.774498 AGAAATGAGTTTTGGGTTGTCTC 57.226 39.130 0.00 0.00 0.00 3.36
651 945 5.200483 AGAAATGAGTTTTGGGTTGTCTCA 58.800 37.500 0.00 0.00 39.05 3.27
652 946 5.656416 AGAAATGAGTTTTGGGTTGTCTCAA 59.344 36.000 0.00 0.00 38.38 3.02
653 947 5.930837 AATGAGTTTTGGGTTGTCTCAAA 57.069 34.783 0.00 0.00 38.38 2.69
654 948 5.930837 ATGAGTTTTGGGTTGTCTCAAAA 57.069 34.783 2.45 2.45 39.58 2.44
655 949 5.730296 TGAGTTTTGGGTTGTCTCAAAAA 57.270 34.783 7.43 0.00 42.23 1.94
688 982 1.751351 TGGGCTTCTATCTCACTGACG 59.249 52.381 0.00 0.00 0.00 4.35
856 1158 4.554036 GCCTCCCACCAGATCCGC 62.554 72.222 0.00 0.00 0.00 5.54
980 1282 0.889306 CTCCTCGGTTTCTTCGACCT 59.111 55.000 0.00 0.00 34.95 3.85
1046 1348 0.741221 GGCTACTTCTCCTTGTGCCG 60.741 60.000 0.00 0.00 0.00 5.69
1277 1588 1.296715 GCGAGGAGTGGGTGAACAT 59.703 57.895 0.00 0.00 0.00 2.71
1375 1692 1.268948 GGCGGCTACCTACTTAGAACG 60.269 57.143 0.00 0.00 0.00 3.95
1841 2180 0.039437 GAGCACTTCGTCTTCGGACA 60.039 55.000 0.00 0.00 44.65 4.02
2466 3173 1.153369 CGATCATGGTCCAACGCCT 60.153 57.895 0.00 0.00 0.00 5.52
3048 3755 0.893727 AATTCTCGTTGTGTGGGGGC 60.894 55.000 0.00 0.00 0.00 5.80
3487 4216 3.138283 TCCAACACCTCTTGGATGAGTTT 59.862 43.478 0.00 0.00 44.05 2.66
3488 4217 3.891366 CCAACACCTCTTGGATGAGTTTT 59.109 43.478 0.00 0.00 43.19 2.43
3529 4258 1.460255 CAAGGCCTTCCTCCCAACA 59.540 57.895 17.29 0.00 43.40 3.33
3823 4552 0.617935 TGGATGAATTGTCCGGAGCA 59.382 50.000 3.06 3.03 38.64 4.26
4348 5082 4.700213 GCTAAACCCTTGACTCATTTGCTA 59.300 41.667 0.00 0.00 0.00 3.49
4764 5501 4.083855 GCTGCGCTACAAAATATGCTATCA 60.084 41.667 9.73 0.00 0.00 2.15
4900 5637 0.944311 GGTATGCACAGGATACGGCG 60.944 60.000 4.80 4.80 46.39 6.46
4904 5641 1.227263 GCACAGGATACGGCGACAT 60.227 57.895 16.62 6.12 46.39 3.06
5273 6011 3.571401 GGATTTCATCGAAGGATTGCCAT 59.429 43.478 0.00 0.00 36.29 4.40
5415 6153 4.528596 AGTTTACAGACTGCATGGACTACT 59.471 41.667 1.25 0.00 0.00 2.57
5477 6215 3.757493 CAGATTCTGGCAAGAGCTCTTTT 59.243 43.478 26.44 3.81 41.70 2.27
5883 6622 5.717119 CTTTGAAATTGGGGATTCTGTCTG 58.283 41.667 0.00 0.00 0.00 3.51
6211 6952 1.611977 CGTTGGTCTGGTGACACTCTA 59.388 52.381 5.39 0.00 44.61 2.43
6432 7173 1.296715 GCGAGGAGTGGGTGAACAT 59.703 57.895 0.00 0.00 0.00 2.71
6591 7338 6.466812 TGATGTGCTTGTAAGAAGAGAATCA 58.533 36.000 0.00 0.00 37.82 2.57
6593 7340 8.260114 TGATGTGCTTGTAAGAAGAGAATCATA 58.740 33.333 0.00 0.00 37.82 2.15
6616 7363 4.755266 ACTCTGAACCACATACATACCC 57.245 45.455 0.00 0.00 0.00 3.69
6765 7512 1.071071 CAACACTTCCGGGTGGTCTTA 59.929 52.381 14.34 0.00 41.09 2.10
6799 7546 2.813754 ACAAACGAGCAGCAACATACAT 59.186 40.909 0.00 0.00 0.00 2.29
6821 7568 2.104253 CCATCGCCCGCGTTTACTT 61.104 57.895 4.92 0.00 40.74 2.24
6881 7628 3.434309 CACTTCCATCCAAACTTCCCAT 58.566 45.455 0.00 0.00 0.00 4.00
6902 7670 8.988060 TCCCATCAAGAGTCATATGTACTTTAA 58.012 33.333 1.90 0.00 0.00 1.52
7160 7928 0.036732 ACCGATTGTGATGGTGCTGT 59.963 50.000 0.00 0.00 33.91 4.40
7554 8379 4.936411 GCTGGATGATCTCCTCAACATATG 59.064 45.833 0.00 0.00 45.21 1.78
7802 9423 2.541762 GTGGAGCGAGCTTAAGCATAAG 59.458 50.000 28.39 16.55 45.16 1.73
8013 9683 4.313020 AATATCTCATCAATGCCCCCTC 57.687 45.455 0.00 0.00 0.00 4.30
8016 9686 0.816825 CTCATCAATGCCCCCTCGTG 60.817 60.000 0.00 0.00 0.00 4.35
8017 9687 1.224315 CATCAATGCCCCCTCGTGA 59.776 57.895 0.00 0.00 0.00 4.35
8018 9688 0.394216 CATCAATGCCCCCTCGTGAA 60.394 55.000 0.00 0.00 0.00 3.18
8019 9689 0.552848 ATCAATGCCCCCTCGTGAAT 59.447 50.000 0.00 0.00 0.00 2.57
8020 9690 0.331278 TCAATGCCCCCTCGTGAATT 59.669 50.000 0.00 0.00 0.00 2.17
8021 9691 1.185315 CAATGCCCCCTCGTGAATTT 58.815 50.000 0.00 0.00 0.00 1.82
8022 9692 2.025793 TCAATGCCCCCTCGTGAATTTA 60.026 45.455 0.00 0.00 0.00 1.40
8023 9693 2.348411 ATGCCCCCTCGTGAATTTAG 57.652 50.000 0.00 0.00 0.00 1.85
8024 9694 1.281419 TGCCCCCTCGTGAATTTAGA 58.719 50.000 0.00 0.00 0.00 2.10
8025 9695 1.843851 TGCCCCCTCGTGAATTTAGAT 59.156 47.619 0.00 0.00 0.00 1.98
8026 9696 2.241176 TGCCCCCTCGTGAATTTAGATT 59.759 45.455 0.00 0.00 0.00 2.40
8027 9697 3.288092 GCCCCCTCGTGAATTTAGATTT 58.712 45.455 0.00 0.00 0.00 2.17
8378 11069 6.049790 GTGATTCTTATGTTGTCCCCTCTAC 58.950 44.000 0.00 0.00 0.00 2.59
8379 11070 5.964477 TGATTCTTATGTTGTCCCCTCTACT 59.036 40.000 0.00 0.00 0.00 2.57
8406 11099 8.966868 CAAGTAATTGATACCCAACAATACCTT 58.033 33.333 0.00 0.00 37.63 3.50
8485 11390 3.940209 TGCTGTTCATTTGGGATTGTC 57.060 42.857 0.00 0.00 0.00 3.18
8606 11689 7.891561 ACTCACATATGTAATCTCCTTCTAGC 58.108 38.462 8.32 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.630415 TCCTCCATCCGAAAATGTAAGAT 57.370 39.130 0.00 0.00 0.00 2.40
55 56 1.479709 AGAGACACTTCCTCCATCCG 58.520 55.000 0.00 0.00 0.00 4.18
59 60 2.485479 GCACAAAGAGACACTTCCTCCA 60.485 50.000 0.00 0.00 37.93 3.86
69 70 4.321230 CCCAAAGGTAATGCACAAAGAGAC 60.321 45.833 0.00 0.00 0.00 3.36
85 86 2.682856 CGTGTACATCCATTCCCAAAGG 59.317 50.000 0.00 0.00 0.00 3.11
88 89 2.303311 TGTCGTGTACATCCATTCCCAA 59.697 45.455 0.00 0.00 31.43 4.12
105 106 1.469251 CCTCCTACAACCGTGATGTCG 60.469 57.143 0.00 0.00 32.27 4.35
113 114 1.955080 CCTACTAGCCTCCTACAACCG 59.045 57.143 0.00 0.00 0.00 4.44
141 143 1.274167 CAAGCCATCATGCCAACAACT 59.726 47.619 0.00 0.00 0.00 3.16
151 153 2.029649 GCTGTTTCACACAAGCCATCAT 60.030 45.455 0.00 0.00 33.87 2.45
171 173 9.651913 TTTCCTCAATAATGAACTTTTTATGGC 57.348 29.630 0.00 0.00 34.49 4.40
203 205 0.251341 ACTACAAAAGCCCTGCCAGG 60.251 55.000 2.91 2.91 34.30 4.45
276 289 2.819115 CCATGACATCTCCGACTTCAG 58.181 52.381 0.00 0.00 0.00 3.02
279 292 0.904649 TGCCATGACATCTCCGACTT 59.095 50.000 0.00 0.00 0.00 3.01
303 316 9.675464 AATCCGTTGTAACCTATCAATTTCTAA 57.325 29.630 0.00 0.00 0.00 2.10
316 329 4.119442 TCTGCTCTAATCCGTTGTAACC 57.881 45.455 0.00 0.00 0.00 2.85
317 330 6.074249 GCTTATCTGCTCTAATCCGTTGTAAC 60.074 42.308 0.00 0.00 0.00 2.50
318 331 5.983720 GCTTATCTGCTCTAATCCGTTGTAA 59.016 40.000 0.00 0.00 0.00 2.41
319 332 5.302059 AGCTTATCTGCTCTAATCCGTTGTA 59.698 40.000 0.00 0.00 39.34 2.41
320 333 4.100189 AGCTTATCTGCTCTAATCCGTTGT 59.900 41.667 0.00 0.00 39.34 3.32
321 334 4.626042 AGCTTATCTGCTCTAATCCGTTG 58.374 43.478 0.00 0.00 39.34 4.10
322 335 4.946478 AGCTTATCTGCTCTAATCCGTT 57.054 40.909 0.00 0.00 39.34 4.44
323 336 5.623368 GCATAGCTTATCTGCTCTAATCCGT 60.623 44.000 0.00 0.00 42.97 4.69
343 617 3.623060 GCTTCGAAGGAAAGATGTGCATA 59.377 43.478 25.77 0.00 0.00 3.14
630 924 5.930837 TTGAGACAACCCAAAACTCATTT 57.069 34.783 0.00 0.00 37.43 2.32
631 925 5.930837 TTTGAGACAACCCAAAACTCATT 57.069 34.783 0.00 0.00 37.43 2.57
632 926 5.930837 TTTTGAGACAACCCAAAACTCAT 57.069 34.783 0.00 0.00 37.35 2.90
633 927 5.730296 TTTTTGAGACAACCCAAAACTCA 57.270 34.783 0.00 0.00 40.60 3.41
657 951 6.777580 TGAGATAGAAGCCCAAAACTCTTTTT 59.222 34.615 0.00 0.00 35.15 1.94
661 955 4.534103 AGTGAGATAGAAGCCCAAAACTCT 59.466 41.667 0.00 0.00 0.00 3.24
688 982 1.984321 GAGACGAGAGGAGTCACGCC 61.984 65.000 0.00 0.00 40.09 5.68
870 1172 1.984570 CTTGGAGACGAGGGAGGCA 60.985 63.158 0.00 0.00 38.28 4.75
980 1282 4.820716 CCATTGCAGGTTTGAAATTGGAAA 59.179 37.500 4.17 0.00 29.61 3.13
1046 1348 1.063412 GTCGCCATTTTCGCCGTTTC 61.063 55.000 0.00 0.00 0.00 2.78
1277 1588 1.354031 TGCTTTATGCTTCCTGGGTCA 59.646 47.619 0.00 0.00 43.37 4.02
1375 1692 4.035612 AGGAAAAGGGAAAGGAACTAGC 57.964 45.455 0.00 0.00 38.49 3.42
3048 3755 1.673665 GGCTGCAGTCCTTGGAGTG 60.674 63.158 16.64 17.66 46.12 3.51
3487 4216 2.291465 GTGCTGCAAACACATCTGAGAA 59.709 45.455 2.77 0.00 37.96 2.87
3488 4217 1.875514 GTGCTGCAAACACATCTGAGA 59.124 47.619 2.77 0.00 37.96 3.27
3529 4258 4.993584 GGAATACGATGATCACATGCTCTT 59.006 41.667 0.00 0.00 36.82 2.85
4619 5356 1.129326 GATTGAAGGTACGATCGCCG 58.871 55.000 16.60 0.00 45.44 6.46
4764 5501 2.427095 GCTCCATTATCCGCACCTTTTT 59.573 45.455 0.00 0.00 0.00 1.94
4900 5637 6.969993 AAGTCCTCCACTATCTTCTATGTC 57.030 41.667 0.00 0.00 32.30 3.06
4904 5641 6.366340 CCTGTAAGTCCTCCACTATCTTCTA 58.634 44.000 0.00 0.00 32.30 2.10
5273 6011 2.083774 GCAATTGAATCGTCCTGACCA 58.916 47.619 10.34 0.00 0.00 4.02
5415 6153 6.944096 TCTCGGTCGGATAGAATAGAATCTA 58.056 40.000 0.00 0.00 36.41 1.98
5477 6215 2.239681 AGGGTTGTTTGGGTTTGTCA 57.760 45.000 0.00 0.00 0.00 3.58
5883 6622 6.919721 TGAACATAAGGTTGGAGTTTAATGC 58.080 36.000 0.00 0.00 40.63 3.56
6016 6755 2.621998 GACGGGATGGATCTTCGAAGTA 59.378 50.000 23.85 11.78 0.00 2.24
6211 6952 3.663815 ATCCTCCCACGTCGGCTCT 62.664 63.158 0.00 0.00 0.00 4.09
6432 7173 1.354031 TGCTTTATGCTTCCTGGGTCA 59.646 47.619 0.00 0.00 43.37 4.02
6591 7338 7.093902 CGGGTATGTATGTGGTTCAGAGTATAT 60.094 40.741 0.00 0.00 0.00 0.86
6593 7340 5.010719 CGGGTATGTATGTGGTTCAGAGTAT 59.989 44.000 0.00 0.00 0.00 2.12
6616 7363 1.169577 AGGACTGCACTACTGTCTCG 58.830 55.000 3.40 0.00 44.37 4.04
6765 7512 3.643763 CTCGTTTGTCTCTGTGCTTACT 58.356 45.455 0.00 0.00 0.00 2.24
6821 7568 0.752658 CCATATGGCAGTCTCCGACA 59.247 55.000 9.29 0.00 34.60 4.35
6881 7628 9.599866 CCATGTTAAAGTACATATGACTCTTGA 57.400 33.333 10.38 1.54 36.64 3.02
6902 7670 0.038166 CCCAACTAGCACACCCATGT 59.962 55.000 0.00 0.00 40.80 3.21
7160 7928 3.330701 AGTTCTTCCTAGCACCCATGAAA 59.669 43.478 0.00 0.00 0.00 2.69
7554 8379 2.162408 CCAAAAAGAAGACTCCATCGCC 59.838 50.000 0.00 0.00 0.00 5.54
7628 8462 4.865365 GCAGAACTGGTTAGCTACAGTAAG 59.135 45.833 15.26 10.27 46.49 2.34
7802 9423 5.012871 ACCTGAAGGGAGAAGTTACCTAAAC 59.987 44.000 0.56 0.00 40.27 2.01
7912 9535 7.008021 ACGAGTAGATAAACAAAACCCCTAA 57.992 36.000 0.00 0.00 0.00 2.69
8378 11069 8.621286 GGTATTGTTGGGTATCAATTACTTGAG 58.379 37.037 1.80 0.00 44.32 3.02
8379 11070 8.333235 AGGTATTGTTGGGTATCAATTACTTGA 58.667 33.333 0.00 0.00 45.15 3.02
8485 11390 2.787680 GCAACCGAGCACTAGTATTACG 59.212 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.