Multiple sequence alignment - TraesCS7A01G313800

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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 TraesCS7A01G313800 chr7A 100.000 7147 0 0 1 7147 447494132 447501278 0.000000e+00 13199.0
1 TraesCS7A01G313800 chr7A 87.671 146 15 3 3125 3270 706907582 706907440 4.430000e-37 167.0
2 TraesCS7A01G313800 chr7A 94.521 73 4 0 1848 1920 447495914 447495986 5.860000e-21 113.0
3 TraesCS7A01G313800 chr7A 94.521 73 4 0 1783 1855 447495979 447496051 5.860000e-21 113.0
4 TraesCS7A01G313800 chr7D 97.462 3467 65 13 3127 6577 394066597 394070056 0.000000e+00 5893.0
5 TraesCS7A01G313800 chr7D 95.944 2663 92 7 1 2657 394063733 394066385 0.000000e+00 4305.0
6 TraesCS7A01G313800 chr7D 88.652 141 13 3 3126 3266 1972169 1972306 1.230000e-37 169.0
7 TraesCS7A01G313800 chr7D 93.671 79 4 1 1842 1920 394065505 394065582 4.530000e-22 117.0
8 TraesCS7A01G313800 chr7D 94.521 73 4 0 1783 1855 394065575 394065647 5.860000e-21 113.0
9 TraesCS7A01G313800 chr7D 96.364 55 1 1 2648 2701 394066542 394066596 9.880000e-14 89.8
10 TraesCS7A01G313800 chr7B 95.869 3486 103 20 3140 6597 393858727 393862199 0.000000e+00 5602.0
11 TraesCS7A01G313800 chr7B 94.969 1769 63 11 1 1764 393855728 393857475 0.000000e+00 2750.0
12 TraesCS7A01G313800 chr7B 92.726 1251 59 8 1474 2697 393857468 393858713 0.000000e+00 1777.0
13 TraesCS7A01G313800 chr7B 91.389 511 21 8 1267 1777 734671853 734672340 0.000000e+00 678.0
14 TraesCS7A01G313800 chr7B 83.721 645 73 17 3265 3881 20344924 20344284 1.340000e-161 580.0
15 TraesCS7A01G313800 chr7B 91.831 355 22 6 6600 6948 187597151 187597504 8.330000e-134 488.0
16 TraesCS7A01G313800 chr7B 87.843 255 24 5 6894 7147 187597483 187597731 7.010000e-75 292.0
17 TraesCS7A01G313800 chr7B 86.957 161 16 4 4056 4216 191210392 191210237 7.370000e-40 176.0
18 TraesCS7A01G313800 chr7B 88.793 116 10 3 2463 2575 20345055 20344940 9.670000e-29 139.0
19 TraesCS7A01G313800 chr7B 93.151 73 5 0 1783 1855 393857842 393857914 2.730000e-19 108.0
20 TraesCS7A01G313800 chr7B 86.000 100 12 2 1211 1308 652703614 652703515 9.810000e-19 106.0
21 TraesCS7A01G313800 chr2A 97.091 550 13 2 6601 7147 420406741 420407290 0.000000e+00 924.0
22 TraesCS7A01G313800 chr2A 95.446 549 23 2 6601 7147 320838243 320837695 0.000000e+00 874.0
23 TraesCS7A01G313800 chr2A 84.902 457 60 8 1987 2441 315762308 315762757 3.040000e-123 453.0
24 TraesCS7A01G313800 chr2A 92.593 54 3 1 2590 2642 527781773 527781826 7.690000e-10 76.8
25 TraesCS7A01G313800 chr3A 96.721 549 16 2 6601 7147 13398207 13398755 0.000000e+00 913.0
26 TraesCS7A01G313800 chr3A 88.276 145 14 3 3127 3270 36337479 36337337 3.430000e-38 171.0
27 TraesCS7A01G313800 chr3A 80.952 105 19 1 2588 2691 453671038 453670934 1.650000e-11 82.4
28 TraesCS7A01G313800 chr3B 90.339 590 31 11 1267 1855 601207873 601208437 0.000000e+00 750.0
29 TraesCS7A01G313800 chr3B 95.302 149 5 2 1845 1992 601208362 601208509 1.200000e-57 235.0
30 TraesCS7A01G313800 chr3B 88.542 96 9 2 1211 1304 743753621 743753716 1.630000e-21 115.0
31 TraesCS7A01G313800 chr3B 88.542 96 9 2 1211 1304 743765916 743766011 1.630000e-21 115.0
32 TraesCS7A01G313800 chr3B 86.869 99 11 2 1211 1307 451159402 451159304 7.580000e-20 110.0
33 TraesCS7A01G313800 chr3B 78.231 147 22 7 2590 2734 765011401 765011539 1.280000e-12 86.1
34 TraesCS7A01G313800 chr1D 87.654 567 47 15 6601 7147 3980135 3979572 7.820000e-179 638.0
35 TraesCS7A01G313800 chr1D 85.057 87 12 1 2583 2668 256285345 256285259 3.550000e-13 87.9
36 TraesCS7A01G313800 chr4B 83.841 656 72 13 3256 3881 240108632 240109283 1.720000e-165 593.0
37 TraesCS7A01G313800 chr4B 90.000 130 11 2 2463 2591 240108514 240108642 4.430000e-37 167.0
38 TraesCS7A01G313800 chr4B 84.066 182 16 7 3523 3692 429219980 429220160 5.740000e-36 163.0
39 TraesCS7A01G313800 chr4B 84.722 144 19 3 6988 7128 128528550 128528407 2.690000e-29 141.0
40 TraesCS7A01G313800 chr4B 81.935 155 14 6 2466 2616 314654941 314654797 1.260000e-22 119.0
41 TraesCS7A01G313800 chr1B 91.981 424 24 6 2723 3142 668079213 668079630 2.870000e-163 586.0
42 TraesCS7A01G313800 chr1B 83.667 649 73 21 3261 3881 569854832 569854189 1.340000e-161 580.0
43 TraesCS7A01G313800 chr1B 88.506 435 22 5 1422 1855 484304111 484303704 1.070000e-137 501.0
44 TraesCS7A01G313800 chr1B 91.716 169 8 2 2723 2890 888819 888656 5.580000e-56 230.0
45 TraesCS7A01G313800 chr1B 93.617 141 8 1 1853 1992 484303772 484303632 7.270000e-50 209.0
46 TraesCS7A01G313800 chr1B 96.639 119 4 0 1267 1385 484304224 484304106 1.570000e-46 198.0
47 TraesCS7A01G313800 chr1B 92.523 107 8 0 2591 2697 357240997 357240891 3.450000e-33 154.0
48 TraesCS7A01G313800 chr5B 83.511 655 76 16 3256 3881 117961036 117961687 3.720000e-162 582.0
49 TraesCS7A01G313800 chr5B 87.309 457 49 8 1987 2441 634121778 634121329 1.370000e-141 514.0
50 TraesCS7A01G313800 chr5B 88.550 131 13 2 2463 2591 117960916 117961046 2.670000e-34 158.0
51 TraesCS7A01G313800 chr5B 81.868 182 20 6 3523 3692 205573492 205573312 2.690000e-29 141.0
52 TraesCS7A01G313800 chr5B 77.064 109 18 6 2585 2691 83874640 83874743 1.000000e-03 56.5
53 TraesCS7A01G313800 chr6A 91.335 427 24 8 2723 3142 161415272 161415692 8.040000e-159 571.0
54 TraesCS7A01G313800 chr6A 90.376 426 29 7 2723 3141 161175381 161175801 3.770000e-152 549.0
55 TraesCS7A01G313800 chr1A 91.315 426 24 9 2723 3141 106504555 106504136 2.890000e-158 569.0
56 TraesCS7A01G313800 chr1A 87.079 178 21 2 2264 2441 558001241 558001416 4.370000e-47 200.0
57 TraesCS7A01G313800 chr1A 91.034 145 10 3 3127 3270 53033477 53033335 7.320000e-45 193.0
58 TraesCS7A01G313800 chr2D 86.871 457 52 7 1987 2441 52284086 52284536 8.270000e-139 505.0
59 TraesCS7A01G313800 chr2D 90.683 161 14 1 1462 1622 390316168 390316327 5.620000e-51 213.0
60 TraesCS7A01G313800 chr3D 86.681 458 52 8 1987 2441 412102902 412103353 3.850000e-137 499.0
61 TraesCS7A01G313800 chr3D 86.433 457 54 6 1987 2441 30970176 30970626 1.790000e-135 494.0
62 TraesCS7A01G313800 chr3D 87.692 325 37 3 2117 2441 477613644 477613323 6.770000e-100 375.0
63 TraesCS7A01G313800 chr6B 88.095 420 38 6 2727 3141 718332664 718332252 8.330000e-134 488.0
64 TraesCS7A01G313800 chr6B 86.957 161 15 4 4056 4216 480265741 480265895 7.370000e-40 176.0
65 TraesCS7A01G313800 chr4A 87.681 414 42 5 2723 3132 729919792 729919384 2.330000e-129 473.0
66 TraesCS7A01G313800 chr2B 87.059 425 41 9 2722 3137 762236307 762236726 1.090000e-127 468.0
67 TraesCS7A01G313800 chr2B 90.402 323 23 4 2826 3140 762236731 762237053 1.110000e-112 418.0
68 TraesCS7A01G313800 chr2B 81.319 182 21 6 3523 3692 685737934 685738114 1.250000e-27 135.0
69 TraesCS7A01G313800 chr5A 89.490 314 30 2 2830 3140 129676581 129676894 1.870000e-105 394.0
70 TraesCS7A01G313800 chr5A 89.362 141 13 2 3130 3270 397510256 397510394 7.370000e-40 176.0
71 TraesCS7A01G313800 chr5A 88.652 141 13 3 3127 3266 160017713 160017851 1.230000e-37 169.0
72 TraesCS7A01G313800 chr4D 80.000 555 68 27 6599 7128 92179416 92178880 3.150000e-98 370.0
73 TraesCS7A01G313800 chrUn 89.205 176 12 5 2719 2892 141693660 141693830 5.620000e-51 213.0
74 TraesCS7A01G313800 chrUn 97.059 34 1 0 1 34 26924302 26924269 2.780000e-04 58.4
75 TraesCS7A01G313800 chr6D 89.437 142 12 3 3127 3267 460588148 460588009 7.370000e-40 176.0
76 TraesCS7A01G313800 chr6D 85.263 95 10 4 1211 1302 173970444 173970351 2.120000e-15 95.3
77 TraesCS7A01G313800 chr6D 81.250 80 14 1 2590 2668 284396879 284396800 5.990000e-06 63.9
78 TraesCS7A01G313800 chr5D 88.276 145 14 3 3127 3270 36205505 36205363 3.430000e-38 171.0
79 TraesCS7A01G313800 chr5D 85.806 155 18 4 3124 3276 305191696 305191848 2.060000e-35 161.0


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 TraesCS7A01G313800 chr7A 447494132 447501278 7146 False 13199.000000 13199 100.000000 1 7147 1 chr7A.!!$F1 7146
1 TraesCS7A01G313800 chr7D 394063733 394070056 6323 False 2103.560000 5893 95.592400 1 6577 5 chr7D.!!$F2 6576
2 TraesCS7A01G313800 chr7B 393855728 393862199 6471 False 2559.250000 5602 94.178750 1 6597 4 chr7B.!!$F3 6596
3 TraesCS7A01G313800 chr7B 187597151 187597731 580 False 390.000000 488 89.837000 6600 7147 2 chr7B.!!$F2 547
4 TraesCS7A01G313800 chr7B 20344284 20345055 771 True 359.500000 580 86.257000 2463 3881 2 chr7B.!!$R3 1418
5 TraesCS7A01G313800 chr2A 420406741 420407290 549 False 924.000000 924 97.091000 6601 7147 1 chr2A.!!$F2 546
6 TraesCS7A01G313800 chr2A 320837695 320838243 548 True 874.000000 874 95.446000 6601 7147 1 chr2A.!!$R1 546
7 TraesCS7A01G313800 chr3A 13398207 13398755 548 False 913.000000 913 96.721000 6601 7147 1 chr3A.!!$F1 546
8 TraesCS7A01G313800 chr3B 601207873 601208509 636 False 492.500000 750 92.820500 1267 1992 2 chr3B.!!$F4 725
9 TraesCS7A01G313800 chr1D 3979572 3980135 563 True 638.000000 638 87.654000 6601 7147 1 chr1D.!!$R1 546
10 TraesCS7A01G313800 chr4B 240108514 240109283 769 False 380.000000 593 86.920500 2463 3881 2 chr4B.!!$F2 1418
11 TraesCS7A01G313800 chr1B 569854189 569854832 643 True 580.000000 580 83.667000 3261 3881 1 chr1B.!!$R3 620
12 TraesCS7A01G313800 chr1B 484303632 484304224 592 True 302.666667 501 92.920667 1267 1992 3 chr1B.!!$R4 725
13 TraesCS7A01G313800 chr5B 117960916 117961687 771 False 370.000000 582 86.030500 2463 3881 2 chr5B.!!$F2 1418
14 TraesCS7A01G313800 chr2B 762236307 762237053 746 False 443.000000 468 88.730500 2722 3140 2 chr2B.!!$F2 418
15 TraesCS7A01G313800 chr4D 92178880 92179416 536 True 370.000000 370 80.000000 6599 7128 1 chr4D.!!$R1 529

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
143 144 0.659427 CCTTAGTCCGACGCGTCATA 59.341 55.000 35.71 21.68 0.00 2.15 F
252 253 1.279271 AGAAGATCCCAAACCACCTCG 59.721 52.381 0.00 0.00 0.00 4.63 F
744 748 1.433471 CATACCACTCGCTCGCTCA 59.567 57.895 0.00 0.00 0.00 4.26 F
925 931 1.459450 ATTCGTTCCCCATTTCGGTG 58.541 50.000 0.00 0.00 0.00 4.94 F
2781 3313 0.249868 TCGGCTTGAAGACACACCTG 60.250 55.000 0.00 0.00 0.00 4.00 F
2952 3490 0.031994 GCGGTTCATTGTGGCAGTTT 59.968 50.000 0.00 0.00 0.00 2.66 F
3048 3589 0.584876 AACGCGTTTAGTTGCTCACC 59.415 50.000 20.79 0.00 0.00 4.02 F
3543 4295 1.272872 TGTACTACCTGGACTCACCCC 60.273 57.143 0.00 0.00 38.00 4.95 F
4784 5570 1.899142 GGAAGCCTGACAGAGTCTTCT 59.101 52.381 20.84 3.34 34.98 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1363 0.037697 ACGTCCTAATCAAGCACGCA 60.038 50.000 0.00 0.00 33.73 5.24 R
2157 2497 0.323816 TGGTTGTCTTGCCCACACAA 60.324 50.000 0.00 0.00 0.00 3.33 R
2242 2582 1.589716 GGCAACCATCACAGTCAGCC 61.590 60.000 0.00 0.00 33.13 4.85 R
2824 3356 0.168128 GCCGCTGATGGTGTTTACAC 59.832 55.000 4.43 4.43 45.72 2.90 R
4084 4870 1.068741 GCGTCGATAAGTCTTCCCCAT 59.931 52.381 0.00 0.00 0.00 4.00 R
4487 5273 2.201732 CGGTGGAAGTCATCATAACCG 58.798 52.381 0.00 0.00 41.52 4.44 R
5009 5795 1.528586 CCAAGAGTGACAGCTCGTTTG 59.471 52.381 0.00 0.00 40.26 2.93 R
5438 6224 1.160137 CTTTCTCCCTGTTCTTGCGG 58.840 55.000 0.00 0.00 0.00 5.69 R
6466 7266 0.904865 AGTCGTCAATGCAGGGGAGA 60.905 55.000 0.00 0.00 0.00 3.71 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
27 28 9.881649 TTTCTTATGGCATGCATTAACATTTTA 57.118 25.926 21.36 0.00 0.00 1.52
143 144 0.659427 CCTTAGTCCGACGCGTCATA 59.341 55.000 35.71 21.68 0.00 2.15
175 176 1.641577 GTCACTCGCCTTATCCACAC 58.358 55.000 0.00 0.00 0.00 3.82
178 179 1.883084 CTCGCCTTATCCACACCGC 60.883 63.158 0.00 0.00 0.00 5.68
252 253 1.279271 AGAAGATCCCAAACCACCTCG 59.721 52.381 0.00 0.00 0.00 4.63
334 335 7.504924 TCTATTGCCCCTAAAATATTCAACG 57.495 36.000 0.00 0.00 0.00 4.10
651 654 1.434773 CCCTATCCATCCCTCTCTCCA 59.565 57.143 0.00 0.00 0.00 3.86
744 748 1.433471 CATACCACTCGCTCGCTCA 59.567 57.895 0.00 0.00 0.00 4.26
748 752 2.695759 CCACTCGCTCGCTCACTCT 61.696 63.158 0.00 0.00 0.00 3.24
830 836 3.359950 AGGAAACCCTAGGTACGTACTG 58.640 50.000 24.07 14.39 33.12 2.74
906 912 2.441532 CCGTCTCCCCCGCTCTAA 60.442 66.667 0.00 0.00 0.00 2.10
921 927 3.002348 CGCTCTAATTCGTTCCCCATTTC 59.998 47.826 0.00 0.00 0.00 2.17
922 928 3.002348 GCTCTAATTCGTTCCCCATTTCG 59.998 47.826 0.00 0.00 0.00 3.46
923 929 3.537580 TCTAATTCGTTCCCCATTTCGG 58.462 45.455 0.00 0.00 0.00 4.30
924 930 2.209690 AATTCGTTCCCCATTTCGGT 57.790 45.000 0.00 0.00 0.00 4.69
925 931 1.459450 ATTCGTTCCCCATTTCGGTG 58.541 50.000 0.00 0.00 0.00 4.94
977 986 3.724508 TTGGTTGGTGCTGTAATTGTG 57.275 42.857 0.00 0.00 0.00 3.33
1334 1343 9.169592 TGTAATTAATAGCTTCCCTGTTGTTAC 57.830 33.333 0.00 0.00 33.22 2.50
1354 1363 1.886655 CGGGGCTGGTTTTAGAGCTTT 60.887 52.381 0.00 0.00 35.42 3.51
1381 1390 5.350365 GTGCTTGATTAGGACGTAATGTTGA 59.650 40.000 5.16 0.00 35.39 3.18
1394 1403 4.965762 CGTAATGTTGATGTGCTGCTATTG 59.034 41.667 0.00 0.00 0.00 1.90
1399 1408 5.003160 TGTTGATGTGCTGCTATTGTTACT 58.997 37.500 0.00 0.00 0.00 2.24
1411 1420 4.878397 GCTATTGTTACTGCTTCAGTGGAT 59.122 41.667 9.52 1.99 45.01 3.41
1574 1625 5.192927 AGTTTTTGTGTCTCATTGAGGTGA 58.807 37.500 13.59 0.00 0.00 4.02
1676 2011 8.050778 TGATTGTTTGACTGTTCACTAGTTTT 57.949 30.769 0.00 0.00 0.00 2.43
1792 2128 4.875544 GCATGAAGCAGTTTATCGGTTA 57.124 40.909 0.00 0.00 44.79 2.85
1799 2135 2.733026 GCAGTTTATCGGTTACGTGTGT 59.267 45.455 0.00 0.00 41.85 3.72
1940 2277 4.338118 CGGGTAATGGCAATTACAATCTGT 59.662 41.667 22.60 0.00 46.80 3.41
2045 2385 4.697514 CTCTGCTTTTTCGATCCATAGGA 58.302 43.478 0.00 0.00 35.55 2.94
2094 2434 3.182182 GGTACTGTAAATTCGTCCGTCC 58.818 50.000 0.00 0.00 0.00 4.79
2112 2452 6.257630 GTCCGTCCGAGTATATTATCTACCTC 59.742 46.154 0.00 0.00 0.00 3.85
2157 2497 7.657761 CAGTTAGTTGATACCACTGACTTTTCT 59.342 37.037 0.00 0.00 37.90 2.52
2221 2561 4.041444 AGACAGAGCACTTCAGATTCCTTT 59.959 41.667 0.00 0.00 0.00 3.11
2242 2582 5.384063 TTTACTTGTAACATGTGCCATGG 57.616 39.130 7.63 7.63 0.00 3.66
2342 2682 4.072131 GTTGGCCATCTCTTGTTCTGTTA 58.928 43.478 6.09 0.00 0.00 2.41
2383 2723 8.049117 TGTATTCCTCTAATTGTTTCAGCTCAT 58.951 33.333 0.00 0.00 0.00 2.90
2394 2734 5.744171 TGTTTCAGCTCATAATTCTAGCCA 58.256 37.500 3.67 0.00 36.92 4.75
2697 3229 7.459795 TGCCAATTATGTGATTAGTGTTGAA 57.540 32.000 0.00 0.00 0.00 2.69
2698 3230 7.312154 TGCCAATTATGTGATTAGTGTTGAAC 58.688 34.615 0.00 0.00 0.00 3.18
2700 3232 7.485913 GCCAATTATGTGATTAGTGTTGAACTG 59.514 37.037 0.00 0.00 40.26 3.16
2701 3233 8.514594 CCAATTATGTGATTAGTGTTGAACTGT 58.485 33.333 0.00 0.00 40.26 3.55
2702 3234 9.897744 CAATTATGTGATTAGTGTTGAACTGTT 57.102 29.630 0.00 0.00 40.26 3.16
2703 3235 9.897744 AATTATGTGATTAGTGTTGAACTGTTG 57.102 29.630 0.00 0.00 40.26 3.33
2737 3269 4.116961 TGGTATGACTAGTAAATGCGCAC 58.883 43.478 14.90 0.00 0.00 5.34
2774 3306 7.180748 GTGTAATCTTAATTCGGCTTGAAGAC 58.819 38.462 0.00 0.00 40.65 3.01
2776 3308 5.803020 ATCTTAATTCGGCTTGAAGACAC 57.197 39.130 0.00 0.00 40.65 3.67
2781 3313 0.249868 TCGGCTTGAAGACACACCTG 60.250 55.000 0.00 0.00 0.00 4.00
2784 3316 2.508526 GGCTTGAAGACACACCTGAAT 58.491 47.619 0.00 0.00 0.00 2.57
2785 3317 2.887152 GGCTTGAAGACACACCTGAATT 59.113 45.455 0.00 0.00 0.00 2.17
2786 3318 3.319122 GGCTTGAAGACACACCTGAATTT 59.681 43.478 0.00 0.00 0.00 1.82
2787 3319 4.202151 GGCTTGAAGACACACCTGAATTTT 60.202 41.667 0.00 0.00 0.00 1.82
2788 3320 4.978580 GCTTGAAGACACACCTGAATTTTC 59.021 41.667 0.00 0.00 0.00 2.29
2800 3332 9.023967 CACACCTGAATTTTCTTTTCTTTACAG 57.976 33.333 0.00 0.00 0.00 2.74
2865 3398 4.384647 GCAGGTCCATCTCTTCCTACAAAT 60.385 45.833 0.00 0.00 0.00 2.32
2871 3404 4.641989 CCATCTCTTCCTACAAATGGGTTG 59.358 45.833 0.00 0.00 43.43 3.77
2878 3411 8.713708 TCTTCCTACAAATGGGTTGAAAATTA 57.286 30.769 0.00 0.00 39.87 1.40
2904 3441 0.326927 TTCAACGGAGAATCACCCCC 59.673 55.000 0.00 0.00 36.25 5.40
2915 3453 1.698874 ATCACCCCCTGATTCCCTTT 58.301 50.000 0.00 0.00 35.99 3.11
2924 3462 4.102681 CCCCTGATTCCCTTTCTTACGTAT 59.897 45.833 0.00 0.00 0.00 3.06
2925 3463 5.057149 CCCTGATTCCCTTTCTTACGTATG 58.943 45.833 0.00 0.00 0.00 2.39
2928 3466 5.345702 TGATTCCCTTTCTTACGTATGTCG 58.654 41.667 8.18 0.00 46.00 4.35
2940 3478 2.284276 TATGTCGTGGGGCGGTTCA 61.284 57.895 0.00 0.00 41.72 3.18
2952 3490 0.031994 GCGGTTCATTGTGGCAGTTT 59.968 50.000 0.00 0.00 0.00 2.66
2953 3491 1.930371 GCGGTTCATTGTGGCAGTTTC 60.930 52.381 0.00 0.00 0.00 2.78
2955 3493 1.963515 GGTTCATTGTGGCAGTTTCCT 59.036 47.619 0.00 0.00 0.00 3.36
2963 3501 3.892284 TGTGGCAGTTTCCTTTCTTGTA 58.108 40.909 0.00 0.00 0.00 2.41
2997 3536 2.046292 GGAAGGGAATCAGGGAGAGAG 58.954 57.143 0.00 0.00 0.00 3.20
2998 3537 2.046292 GAAGGGAATCAGGGAGAGAGG 58.954 57.143 0.00 0.00 0.00 3.69
3001 3542 2.252408 AGGGAATCAGGGAGAGAGGATT 59.748 50.000 0.00 0.00 32.97 3.01
3008 3549 3.900601 TCAGGGAGAGAGGATTGATTAGC 59.099 47.826 0.00 0.00 0.00 3.09
3016 3557 6.276847 AGAGAGGATTGATTAGCAGTAAACG 58.723 40.000 0.00 0.00 0.00 3.60
3048 3589 0.584876 AACGCGTTTAGTTGCTCACC 59.415 50.000 20.79 0.00 0.00 4.02
3063 3604 4.780815 TGCTCACCATTAGGACAATAAGG 58.219 43.478 0.00 0.00 38.69 2.69
3065 3606 4.816925 GCTCACCATTAGGACAATAAGGAC 59.183 45.833 0.00 0.00 38.69 3.85
3066 3607 5.396884 GCTCACCATTAGGACAATAAGGACT 60.397 44.000 0.00 0.00 38.69 3.85
3099 3640 2.934364 GCTAATGGATGGCCGAGATCTG 60.934 54.545 0.00 0.00 36.79 2.90
3352 4093 2.736721 TGTTAAGAAGCTGTGCATCGTC 59.263 45.455 0.00 0.00 31.18 4.20
3353 4094 2.736721 GTTAAGAAGCTGTGCATCGTCA 59.263 45.455 0.00 0.00 31.18 4.35
3368 4109 4.321230 GCATCGTCATTTGTTTCCCTTTCT 60.321 41.667 0.00 0.00 0.00 2.52
3498 4247 1.299541 CACATTGGGCGTGGAGTATC 58.700 55.000 0.00 0.00 0.00 2.24
3543 4295 1.272872 TGTACTACCTGGACTCACCCC 60.273 57.143 0.00 0.00 38.00 4.95
3603 4355 3.944015 AGGCATTGACTTCAGTTGCTATC 59.056 43.478 13.02 1.80 37.15 2.08
3751 4526 9.985318 CAAATGTGCAATTTCTTGAGTTTAAAA 57.015 25.926 0.00 0.00 34.04 1.52
3895 4678 4.080015 TCCAAGTCTAATACATTGTGGGGG 60.080 45.833 0.00 0.00 0.00 5.40
4487 5273 5.729510 ACAGGTTCTGATCTTAAAGAGCTC 58.270 41.667 5.27 5.27 35.18 4.09
4784 5570 1.899142 GGAAGCCTGACAGAGTCTTCT 59.101 52.381 20.84 3.34 34.98 2.85
5174 5960 6.809428 TGATCTCTCCCTTGATATACCATCT 58.191 40.000 0.00 0.00 0.00 2.90
5305 6091 3.511477 AGAAGCTGAGGAGGTACAAGAA 58.489 45.455 0.00 0.00 0.00 2.52
5438 6224 4.989279 ACTGATAACAATTGCCATGGAC 57.011 40.909 18.40 7.64 0.00 4.02
5465 6251 0.539051 ACAGGGAGAAAGAGATGGCG 59.461 55.000 0.00 0.00 0.00 5.69
5527 6313 4.023980 AGTGAAGACATCGTCAAGGGATA 58.976 43.478 0.00 0.00 36.21 2.59
5633 6419 1.667212 GTGATCGATGATGTGCTTGCA 59.333 47.619 0.54 0.00 0.00 4.08
5720 6506 2.358003 GCACGCTCACTTGCCTCT 60.358 61.111 0.00 0.00 35.11 3.69
5762 6548 3.790437 CTGAGATGCTGGGGCGGT 61.790 66.667 0.00 0.00 42.25 5.68
5819 6605 3.846588 AGATAACAAAGCTCCTGGAGGAA 59.153 43.478 24.43 3.50 44.91 3.36
5831 6617 1.107538 TGGAGGAATACGAGAGCGGG 61.108 60.000 0.00 0.00 43.17 6.13
6157 6943 0.245539 TCGACTTGAACCGATGACCC 59.754 55.000 0.00 0.00 0.00 4.46
6314 7108 2.270986 CCCTCTTGCTTGTGGTGGC 61.271 63.158 0.00 0.00 0.00 5.01
6345 7139 5.423290 TGTCTAGATCTTTGCATCTCTGGAA 59.577 40.000 0.00 0.00 34.75 3.53
6495 7295 2.658325 GCATTGACGACTTGTGATTTGC 59.342 45.455 0.00 0.00 0.00 3.68
6580 7380 2.230025 CTGTGGCTATCACCCTATCTCG 59.770 54.545 0.00 0.00 45.48 4.04
6584 7384 3.321111 TGGCTATCACCCTATCTCGAAAC 59.679 47.826 0.00 0.00 0.00 2.78
6597 7397 7.040340 CCCTATCTCGAAACGCTATGGATATAT 60.040 40.741 0.00 0.00 0.00 0.86
6648 7448 0.460311 CTTCCGATTACACCGGCTCT 59.540 55.000 0.00 0.00 46.10 4.09
6660 7460 3.118884 ACACCGGCTCTTGATTACGTTAT 60.119 43.478 0.00 0.00 0.00 1.89
6745 7546 3.283751 CCAAAAACGGCCATATGGACTA 58.716 45.455 26.47 0.00 42.58 2.59
6774 7576 1.276622 AACACCGCTCCTCTGGTAAT 58.723 50.000 0.00 0.00 36.50 1.89
6900 7724 4.385405 GAGCCCGTGAGCAGCAGT 62.385 66.667 0.00 0.00 34.23 4.40
6912 7736 1.084370 GCAGCAGTACCGCGATCTTT 61.084 55.000 8.23 0.00 36.85 2.52
7065 7984 1.650314 CGCCATCATCAGCAACAGCA 61.650 55.000 0.00 0.00 0.00 4.41
7071 7990 1.065272 TCATCAGCAACAGCATGGCTA 60.065 47.619 0.00 0.00 43.62 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 8.610896 TCTTTTTGTATTTTGAGCCAACATTTG 58.389 29.630 0.00 0.00 0.00 2.32
52 53 7.945033 TGATCTTTTTGTATTTTGAGCCAAC 57.055 32.000 0.00 0.00 0.00 3.77
143 144 3.771160 GTGACGGGCCGGATGAGT 61.771 66.667 31.78 7.70 0.00 3.41
252 253 1.664649 GGGTTTTGCTTTGCTCGGC 60.665 57.895 0.00 0.00 0.00 5.54
294 295 0.040646 TAGATGAGTGGTCGGTGGGT 59.959 55.000 0.00 0.00 0.00 4.51
353 354 1.122632 TGGGGCGTGGAGTACTTTGA 61.123 55.000 0.00 0.00 0.00 2.69
439 440 4.802051 CCATCCCCACGTGGCAGG 62.802 72.222 29.75 24.64 0.00 4.85
651 654 1.098712 GGAGACGAGACTGAGCCGAT 61.099 60.000 0.00 0.00 0.00 4.18
830 836 0.969894 ACGCCCTATCCAGACATAGC 59.030 55.000 0.00 0.00 0.00 2.97
904 910 3.353370 ACCGAAATGGGGAACGAATTA 57.647 42.857 0.00 0.00 44.64 1.40
906 912 3.970205 ACCGAAATGGGGAACGAAT 57.030 47.368 0.00 0.00 44.64 3.34
1334 1343 0.322546 AAGCTCTAAAACCAGCCCCG 60.323 55.000 0.00 0.00 36.17 5.73
1354 1363 0.037697 ACGTCCTAATCAAGCACGCA 60.038 50.000 0.00 0.00 33.73 5.24
1381 1390 3.614092 AGCAGTAACAATAGCAGCACAT 58.386 40.909 0.00 0.00 0.00 3.21
1394 1403 2.159653 CGCAATCCACTGAAGCAGTAAC 60.160 50.000 0.00 0.00 43.43 2.50
1399 1408 1.725641 CTACGCAATCCACTGAAGCA 58.274 50.000 0.00 0.00 0.00 3.91
1411 1420 1.535028 CATGAACAACAGGCTACGCAA 59.465 47.619 0.00 0.00 0.00 4.85
1574 1625 3.246416 ACCTCCATATAACGAGAGCCT 57.754 47.619 0.00 0.00 0.00 4.58
1651 1986 7.624360 AAACTAGTGAACAGTCAAACAATCA 57.376 32.000 0.00 0.00 34.87 2.57
1676 2011 2.811431 ACTGCAACAAATCGAAATCGGA 59.189 40.909 2.63 0.00 40.29 4.55
1786 2122 2.859526 TAACACACACACGTAACCGA 57.140 45.000 0.00 0.00 37.88 4.69
1792 2128 3.127895 AGCACAAATTAACACACACACGT 59.872 39.130 0.00 0.00 0.00 4.49
1799 2135 2.550606 GTCGGGAGCACAAATTAACACA 59.449 45.455 0.00 0.00 0.00 3.72
1940 2277 5.109210 CAACATAGAAGAATGCTACACGGA 58.891 41.667 0.00 0.00 0.00 4.69
2019 2356 1.061276 GGATCGAAAAAGCAGAGCGAC 59.939 52.381 0.00 0.00 33.52 5.19
2020 2357 1.337728 TGGATCGAAAAAGCAGAGCGA 60.338 47.619 0.00 0.00 35.32 4.93
2021 2358 1.078709 TGGATCGAAAAAGCAGAGCG 58.921 50.000 0.00 0.00 0.00 5.03
2022 2359 3.249559 CCTATGGATCGAAAAAGCAGAGC 59.750 47.826 0.00 0.00 0.00 4.09
2034 2374 4.638421 GGATCTGAGTACTCCTATGGATCG 59.362 50.000 20.11 0.00 31.96 3.69
2084 2424 5.240891 AGATAATATACTCGGACGGACGAA 58.759 41.667 0.00 0.00 42.98 3.85
2094 2434 9.621629 ATCAGGAAGAGGTAGATAATATACTCG 57.378 37.037 0.00 0.00 0.00 4.18
2112 2452 7.821846 ACTAACTGAAAGCTTCTTATCAGGAAG 59.178 37.037 23.29 20.72 42.76 3.46
2157 2497 0.323816 TGGTTGTCTTGCCCACACAA 60.324 50.000 0.00 0.00 0.00 3.33
2242 2582 1.589716 GGCAACCATCACAGTCAGCC 61.590 60.000 0.00 0.00 33.13 4.85
2342 2682 6.617371 AGAGGAATACAAACAGACCATATCCT 59.383 38.462 0.00 0.00 0.00 3.24
2394 2734 8.055181 ACACATAGATATTGACCAACTTCCATT 58.945 33.333 0.00 0.00 0.00 3.16
2410 2750 8.366359 AGGACATGCATACATACACATAGATA 57.634 34.615 0.00 0.00 33.67 1.98
2668 3200 5.918576 CACTAATCACATAATTGGCATGCAG 59.081 40.000 21.36 5.18 0.00 4.41
2697 3229 9.547753 GTCATACCAAATATCAGTATCAACAGT 57.452 33.333 0.00 0.00 0.00 3.55
2698 3230 9.770097 AGTCATACCAAATATCAGTATCAACAG 57.230 33.333 0.00 0.00 0.00 3.16
2728 3260 2.725450 CGTTGCACGTGCGCATTT 60.725 55.556 33.22 0.00 45.83 2.32
2750 3282 6.876789 TGTCTTCAAGCCGAATTAAGATTACA 59.123 34.615 0.00 0.00 31.69 2.41
2774 3306 8.925161 TGTAAAGAAAAGAAAATTCAGGTGTG 57.075 30.769 0.00 0.00 0.00 3.82
2776 3308 9.801873 TTCTGTAAAGAAAAGAAAATTCAGGTG 57.198 29.630 0.00 0.00 0.00 4.00
2824 3356 0.168128 GCCGCTGATGGTGTTTACAC 59.832 55.000 4.43 4.43 45.72 2.90
2826 3358 0.447801 CTGCCGCTGATGGTGTTTAC 59.552 55.000 0.00 0.00 0.00 2.01
2878 3411 6.289064 GGGTGATTCTCCGTTGAATTAGTAT 58.711 40.000 0.00 0.00 36.86 2.12
2886 3423 0.546747 AGGGGGTGATTCTCCGTTGA 60.547 55.000 0.00 0.00 37.63 3.18
2904 3441 5.459107 CGACATACGTAAGAAAGGGAATCAG 59.541 44.000 4.57 0.00 43.62 2.90
2928 3466 2.635443 CCACAATGAACCGCCCCAC 61.635 63.158 0.00 0.00 0.00 4.61
2934 3472 1.335872 GGAAACTGCCACAATGAACCG 60.336 52.381 0.00 0.00 0.00 4.44
2940 3478 3.706086 ACAAGAAAGGAAACTGCCACAAT 59.294 39.130 0.00 0.00 42.68 2.71
2955 3493 9.333724 CTTCCTTAGTACACCTTTTACAAGAAA 57.666 33.333 0.00 0.00 30.57 2.52
2963 3501 5.917545 TTCCCTTCCTTAGTACACCTTTT 57.082 39.130 0.00 0.00 0.00 2.27
2973 3511 3.645687 CTCTCCCTGATTCCCTTCCTTAG 59.354 52.174 0.00 0.00 0.00 2.18
2997 3536 3.308866 ACGCGTTTACTGCTAATCAATCC 59.691 43.478 5.58 0.00 0.00 3.01
2998 3537 4.516092 ACGCGTTTACTGCTAATCAATC 57.484 40.909 5.58 0.00 0.00 2.67
3001 3542 4.201647 GCTAAACGCGTTTACTGCTAATCA 60.202 41.667 34.03 16.42 34.23 2.57
3008 3549 4.634349 TTAGTGCTAAACGCGTTTACTG 57.366 40.909 33.09 27.17 43.27 2.74
3033 3574 4.092968 GTCCTAATGGTGAGCAACTAAACG 59.907 45.833 0.00 0.00 34.23 3.60
3048 3589 5.050490 CCGACAGTCCTTATTGTCCTAATG 58.950 45.833 0.00 0.00 38.72 1.90
3063 3604 5.297547 TCCATTAGCATTAATCCGACAGTC 58.702 41.667 0.00 0.00 0.00 3.51
3065 3606 5.122869 CCATCCATTAGCATTAATCCGACAG 59.877 44.000 0.00 0.00 0.00 3.51
3066 3607 5.003160 CCATCCATTAGCATTAATCCGACA 58.997 41.667 0.00 0.00 0.00 4.35
3099 3640 0.393537 CCCAGTGAGGCAGATCCAAC 60.394 60.000 0.00 0.00 37.29 3.77
3498 4247 3.692257 ACACTTCACTGAAGATCCCAG 57.308 47.619 23.08 10.24 41.71 4.45
3543 4295 6.939627 TGTAAAATCTAACCATATGCGTTCG 58.060 36.000 11.39 7.29 0.00 3.95
3895 4678 2.529632 AGAATTCCCCAAACTCAAGGC 58.470 47.619 0.65 0.00 0.00 4.35
4084 4870 1.068741 GCGTCGATAAGTCTTCCCCAT 59.931 52.381 0.00 0.00 0.00 4.00
4272 5058 9.456147 AACCACATAACAAGTTAACAGCATATA 57.544 29.630 8.61 0.00 0.00 0.86
4487 5273 2.201732 CGGTGGAAGTCATCATAACCG 58.798 52.381 0.00 0.00 41.52 4.44
4784 5570 5.599999 TTTGTAAAACTTGCAAGCCCTTA 57.400 34.783 26.27 16.82 36.63 2.69
5009 5795 1.528586 CCAAGAGTGACAGCTCGTTTG 59.471 52.381 0.00 0.00 40.26 2.93
5174 5960 5.988310 ATGTCTGGAATTGAGATTTTGCA 57.012 34.783 0.00 0.00 0.00 4.08
5305 6091 3.916035 TGTATCATAGACACAGCCTCCT 58.084 45.455 0.00 0.00 0.00 3.69
5438 6224 1.160137 CTTTCTCCCTGTTCTTGCGG 58.840 55.000 0.00 0.00 0.00 5.69
5465 6251 6.183360 TGCTTAATGAGGATAGGAGAACTGAC 60.183 42.308 0.00 0.00 0.00 3.51
5527 6313 5.884232 TCTGCAGATTCAAGAAGCATTATGT 59.116 36.000 13.74 0.00 34.35 2.29
5633 6419 5.396213 GCCAATCTCATCTAAGTTCAGAGGT 60.396 44.000 0.00 0.00 0.00 3.85
5735 6521 1.001487 CAGCATCTCAGTAGCCTCTCG 60.001 57.143 0.00 0.00 0.00 4.04
5819 6605 4.889112 TCGCCCCCGCTCTCGTAT 62.889 66.667 0.00 0.00 0.00 3.06
5831 6617 2.056906 ATGCTTCCCCTACATCGCCC 62.057 60.000 0.00 0.00 0.00 6.13
6157 6943 1.022982 TTGATGCTTCCTGCTCGCTG 61.023 55.000 0.00 0.00 43.37 5.18
6314 7108 2.799412 GCAAAGATCTAGACATGAGCCG 59.201 50.000 0.00 0.00 0.00 5.52
6345 7139 3.256631 CAGCAAGAACAGCAAAGGGTATT 59.743 43.478 0.00 0.00 0.00 1.89
6403 7197 7.962995 TCTCCTCTGTTCTACTTGATGTAAT 57.037 36.000 0.00 0.00 0.00 1.89
6466 7266 0.904865 AGTCGTCAATGCAGGGGAGA 60.905 55.000 0.00 0.00 0.00 3.71
6495 7295 2.642139 AGTTTCGGCATGATGCTTTG 57.358 45.000 17.84 7.85 44.28 2.77
6561 7361 2.515854 TCGAGATAGGGTGATAGCCAC 58.484 52.381 0.00 0.00 44.95 5.01
6571 7371 2.557056 TCCATAGCGTTTCGAGATAGGG 59.443 50.000 0.00 0.00 0.00 3.53
6580 7380 4.204573 GCGTCGATATATCCATAGCGTTTC 59.795 45.833 7.15 0.00 44.75 2.78
6584 7384 2.286242 ACGCGTCGATATATCCATAGCG 60.286 50.000 24.71 24.71 45.59 4.26
6597 7397 3.641986 GCCAACCAAACGCGTCGA 61.642 61.111 14.44 0.00 0.00 4.20
6648 7448 6.542574 AACAAACACCGATAACGTAATCAA 57.457 33.333 0.00 0.00 37.88 2.57
6660 7460 2.690786 CCCGATCTAAACAAACACCGA 58.309 47.619 0.00 0.00 0.00 4.69
6745 7546 1.271217 GGAGCGGTGTTTTCCCTTACT 60.271 52.381 0.00 0.00 0.00 2.24
6774 7576 2.054140 GAAAACCAGAACGTGCGGCA 62.054 55.000 0.00 0.00 0.00 5.69
7065 7984 0.178990 GGCGGAGGGAAATTAGCCAT 60.179 55.000 0.00 0.00 43.65 4.40
7071 7990 1.078426 CAGACGGCGGAGGGAAATT 60.078 57.895 13.24 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.