Multiple sequence alignment - TraesCS7D01G355800

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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 TraesCS7D01G355800 chr7D 100.000 4401 0 0 1 4401 459474496 459470096 0.000000e+00 8128.0
1 TraesCS7D01G355800 chr7D 81.358 1502 252 16 1971 3455 459464437 459462947 0.000000e+00 1197.0
2 TraesCS7D01G355800 chr7D 81.158 1502 249 23 1973 3454 459605859 459604372 0.000000e+00 1175.0
3 TraesCS7D01G355800 chr7D 80.502 1513 263 22 1971 3464 459431609 459430110 0.000000e+00 1131.0
4 TraesCS7D01G355800 chr7D 81.739 115 8 8 3832 3939 69414612 69414720 2.820000e-12 84.2
5 TraesCS7D01G355800 chr7B 96.068 2518 81 9 631 3133 481624785 481622271 0.000000e+00 4085.0
6 TraesCS7D01G355800 chr7B 81.516 1504 244 20 1971 3454 481616062 481614573 0.000000e+00 1206.0
7 TraesCS7D01G355800 chr7B 84.896 576 73 14 3828 4394 17654719 17654149 1.780000e-158 569.0
8 TraesCS7D01G355800 chr7B 79.796 589 95 8 3828 4399 634577145 634577726 1.470000e-109 407.0
9 TraesCS7D01G355800 chr7B 90.196 204 12 4 3630 3825 481621254 481621051 4.370000e-65 259.0
10 TraesCS7D01G355800 chr7A 95.273 1925 84 5 1163 3086 540749417 540751335 0.000000e+00 3044.0
11 TraesCS7D01G355800 chr7A 79.741 3480 655 37 5 3464 540202925 540206374 0.000000e+00 2475.0
12 TraesCS7D01G355800 chr7A 80.515 1591 277 19 1973 3543 540757522 540759099 0.000000e+00 1190.0
13 TraesCS7D01G355800 chr7A 92.282 609 28 9 3150 3758 540751336 540751925 0.000000e+00 846.0
14 TraesCS7D01G355800 chr4D 79.743 3505 630 56 8 3464 500301060 500304532 0.000000e+00 2466.0
15 TraesCS7D01G355800 chr4D 78.447 1545 316 16 9 1545 500152049 500153584 0.000000e+00 992.0
16 TraesCS7D01G355800 chr4D 88.356 584 48 10 3835 4401 315085142 315084562 0.000000e+00 684.0
17 TraesCS7D01G355800 chr4B 79.628 3495 640 50 13 3464 643629227 643632692 0.000000e+00 2444.0
18 TraesCS7D01G355800 chr4B 79.098 3502 660 55 13 3464 643528291 643531770 0.000000e+00 2346.0
19 TraesCS7D01G355800 chr4B 78.823 3518 668 61 1 3464 643481952 643485446 0.000000e+00 2298.0
20 TraesCS7D01G355800 chr4B 79.111 1733 339 22 13 1734 643535607 643537327 0.000000e+00 1173.0
21 TraesCS7D01G355800 chr4B 79.330 1553 302 17 8 1551 643557988 643559530 0.000000e+00 1072.0
22 TraesCS7D01G355800 chr4B 83.211 816 122 13 2666 3471 643537753 643538563 0.000000e+00 734.0
23 TraesCS7D01G355800 chr4B 82.487 571 72 13 3832 4399 451459776 451460321 3.980000e-130 475.0
24 TraesCS7D01G355800 chr5A 79.611 3497 638 56 13 3464 680981299 680984765 0.000000e+00 2438.0
25 TraesCS7D01G355800 chr5A 79.641 3453 622 60 13 3411 680921390 680924815 0.000000e+00 2407.0
26 TraesCS7D01G355800 chr5A 79.148 3496 661 52 13 3464 680865608 680869079 0.000000e+00 2355.0
27 TraesCS7D01G355800 chrUn 79.377 3501 652 54 16 3467 60417101 60413622 0.000000e+00 2401.0
28 TraesCS7D01G355800 chrUn 79.177 3501 667 40 16 3471 16761073 16757590 0.000000e+00 2370.0
29 TraesCS7D01G355800 chrUn 79.323 2631 476 49 885 3467 60473869 60471259 0.000000e+00 1783.0
30 TraesCS7D01G355800 chrUn 79.324 769 152 7 12 777 389276474 389275710 2.330000e-147 532.0
31 TraesCS7D01G355800 chrUn 81.404 570 88 15 3833 4394 277592880 277592321 2.410000e-122 449.0
32 TraesCS7D01G355800 chr2D 87.136 583 59 6 3835 4401 27583462 27582880 0.000000e+00 647.0
33 TraesCS7D01G355800 chr1D 92.088 455 36 0 3947 4401 342845854 342846308 3.710000e-180 641.0
34 TraesCS7D01G355800 chr1D 86.757 589 56 8 3832 4399 326290541 326291128 1.730000e-178 636.0
35 TraesCS7D01G355800 chr1D 86.919 581 53 9 3835 4399 156123803 156124376 8.030000e-177 630.0
36 TraesCS7D01G355800 chr1D 82.837 571 67 15 3830 4399 377802727 377802187 2.380000e-132 483.0
37 TraesCS7D01G355800 chr1D 80.874 549 59 19 3832 4364 480552572 480553090 1.480000e-104 390.0
38 TraesCS7D01G355800 chr4A 86.815 584 55 11 3835 4401 160250014 160250592 2.230000e-177 632.0
39 TraesCS7D01G355800 chr1A 86.348 586 60 8 3832 4399 203811320 203810737 4.830000e-174 621.0
40 TraesCS7D01G355800 chr5B 85.069 576 63 10 3847 4401 323871505 323872078 2.300000e-157 566.0
41 TraesCS7D01G355800 chr5B 81.695 590 80 15 3830 4399 683988646 683989227 2.400000e-127 466.0
42 TraesCS7D01G355800 chr3B 81.404 570 88 15 3833 4394 765725415 765724856 2.410000e-122 449.0


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 TraesCS7D01G355800 chr7D 459470096 459474496 4400 True 8128.000000 8128 100.000000 1 4401 1 chr7D.!!$R3 4400
1 TraesCS7D01G355800 chr7D 459462947 459464437 1490 True 1197.000000 1197 81.358000 1971 3455 1 chr7D.!!$R2 1484
2 TraesCS7D01G355800 chr7D 459604372 459605859 1487 True 1175.000000 1175 81.158000 1973 3454 1 chr7D.!!$R4 1481
3 TraesCS7D01G355800 chr7D 459430110 459431609 1499 True 1131.000000 1131 80.502000 1971 3464 1 chr7D.!!$R1 1493
4 TraesCS7D01G355800 chr7B 481621051 481624785 3734 True 2172.000000 4085 93.132000 631 3825 2 chr7B.!!$R3 3194
5 TraesCS7D01G355800 chr7B 481614573 481616062 1489 True 1206.000000 1206 81.516000 1971 3454 1 chr7B.!!$R2 1483
6 TraesCS7D01G355800 chr7B 17654149 17654719 570 True 569.000000 569 84.896000 3828 4394 1 chr7B.!!$R1 566
7 TraesCS7D01G355800 chr7B 634577145 634577726 581 False 407.000000 407 79.796000 3828 4399 1 chr7B.!!$F1 571
8 TraesCS7D01G355800 chr7A 540202925 540206374 3449 False 2475.000000 2475 79.741000 5 3464 1 chr7A.!!$F1 3459
9 TraesCS7D01G355800 chr7A 540749417 540751925 2508 False 1945.000000 3044 93.777500 1163 3758 2 chr7A.!!$F3 2595
10 TraesCS7D01G355800 chr7A 540757522 540759099 1577 False 1190.000000 1190 80.515000 1973 3543 1 chr7A.!!$F2 1570
11 TraesCS7D01G355800 chr4D 500301060 500304532 3472 False 2466.000000 2466 79.743000 8 3464 1 chr4D.!!$F2 3456
12 TraesCS7D01G355800 chr4D 500152049 500153584 1535 False 992.000000 992 78.447000 9 1545 1 chr4D.!!$F1 1536
13 TraesCS7D01G355800 chr4D 315084562 315085142 580 True 684.000000 684 88.356000 3835 4401 1 chr4D.!!$R1 566
14 TraesCS7D01G355800 chr4B 643629227 643632692 3465 False 2444.000000 2444 79.628000 13 3464 1 chr4B.!!$F4 3451
15 TraesCS7D01G355800 chr4B 643481952 643485446 3494 False 2298.000000 2298 78.823000 1 3464 1 chr4B.!!$F2 3463
16 TraesCS7D01G355800 chr4B 643528291 643538563 10272 False 1417.666667 2346 80.473333 13 3471 3 chr4B.!!$F5 3458
17 TraesCS7D01G355800 chr4B 643557988 643559530 1542 False 1072.000000 1072 79.330000 8 1551 1 chr4B.!!$F3 1543
18 TraesCS7D01G355800 chr4B 451459776 451460321 545 False 475.000000 475 82.487000 3832 4399 1 chr4B.!!$F1 567
19 TraesCS7D01G355800 chr5A 680981299 680984765 3466 False 2438.000000 2438 79.611000 13 3464 1 chr5A.!!$F3 3451
20 TraesCS7D01G355800 chr5A 680921390 680924815 3425 False 2407.000000 2407 79.641000 13 3411 1 chr5A.!!$F2 3398
21 TraesCS7D01G355800 chr5A 680865608 680869079 3471 False 2355.000000 2355 79.148000 13 3464 1 chr5A.!!$F1 3451
22 TraesCS7D01G355800 chrUn 60413622 60417101 3479 True 2401.000000 2401 79.377000 16 3467 1 chrUn.!!$R2 3451
23 TraesCS7D01G355800 chrUn 16757590 16761073 3483 True 2370.000000 2370 79.177000 16 3471 1 chrUn.!!$R1 3455
24 TraesCS7D01G355800 chrUn 60471259 60473869 2610 True 1783.000000 1783 79.323000 885 3467 1 chrUn.!!$R3 2582
25 TraesCS7D01G355800 chrUn 389275710 389276474 764 True 532.000000 532 79.324000 12 777 1 chrUn.!!$R5 765
26 TraesCS7D01G355800 chrUn 277592321 277592880 559 True 449.000000 449 81.404000 3833 4394 1 chrUn.!!$R4 561
27 TraesCS7D01G355800 chr2D 27582880 27583462 582 True 647.000000 647 87.136000 3835 4401 1 chr2D.!!$R1 566
28 TraesCS7D01G355800 chr1D 326290541 326291128 587 False 636.000000 636 86.757000 3832 4399 1 chr1D.!!$F2 567
29 TraesCS7D01G355800 chr1D 156123803 156124376 573 False 630.000000 630 86.919000 3835 4399 1 chr1D.!!$F1 564
30 TraesCS7D01G355800 chr1D 377802187 377802727 540 True 483.000000 483 82.837000 3830 4399 1 chr1D.!!$R1 569
31 TraesCS7D01G355800 chr1D 480552572 480553090 518 False 390.000000 390 80.874000 3832 4364 1 chr1D.!!$F4 532
32 TraesCS7D01G355800 chr4A 160250014 160250592 578 False 632.000000 632 86.815000 3835 4401 1 chr4A.!!$F1 566
33 TraesCS7D01G355800 chr1A 203810737 203811320 583 True 621.000000 621 86.348000 3832 4399 1 chr1A.!!$R1 567
34 TraesCS7D01G355800 chr5B 323871505 323872078 573 False 566.000000 566 85.069000 3847 4401 1 chr5B.!!$F1 554
35 TraesCS7D01G355800 chr5B 683988646 683989227 581 False 466.000000 466 81.695000 3830 4399 1 chr5B.!!$F2 569
36 TraesCS7D01G355800 chr3B 765724856 765725415 559 True 449.000000 449 81.404000 3833 4394 1 chr3B.!!$R1 561

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
60 61 0.035881 CAAGCTCTCAGGTCCAAGCA 59.964 55.000 7.91 0.0 37.22 3.91 F
197 198 0.107456 CTGGCTCCATATCCGCTTGT 59.893 55.000 0.00 0.0 0.00 3.16 F
198 199 0.179048 TGGCTCCATATCCGCTTGTG 60.179 55.000 0.00 0.0 0.00 3.33 F
780 8097 0.249322 CCATACCTCCTGTAACGGCG 60.249 60.000 4.80 4.8 31.94 6.46 F
1884 9224 1.202842 TCCACTCTCGGACAGTGTGTA 60.203 52.381 11.64 0.0 42.73 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 8584 3.565516 GCCTGCTTTTAGCTTGTTGTAC 58.434 45.455 0.00 0.0 42.97 2.90 R
1758 9098 5.116180 CCAGAGAAGTAGTTGTGTGACAAA 58.884 41.667 6.19 0.0 40.15 2.83 R
2105 9445 6.131264 TCATTTCCTTGGATTGATACTGCAT 58.869 36.000 0.00 0.0 0.00 3.96 R
2668 10041 1.780309 TCTTTCACCATGTCCAAGGGT 59.220 47.619 0.00 0.0 34.59 4.34 R
3651 11625 0.039618 TCCCCAATCTGGTTCCAAGC 59.960 55.000 0.00 0.0 35.17 4.01 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
23 24 3.498774 ACCAAGAATGACAGACAAGCT 57.501 42.857 0.00 0.00 0.00 3.74
42 43 2.811873 GCTCTCCTTTGCTTCAAGTCCA 60.812 50.000 0.00 0.00 0.00 4.02
57 58 0.687354 GTCCAAGCTCTCAGGTCCAA 59.313 55.000 0.00 0.00 0.00 3.53
58 59 0.979665 TCCAAGCTCTCAGGTCCAAG 59.020 55.000 0.00 0.00 0.00 3.61
60 61 0.035881 CAAGCTCTCAGGTCCAAGCA 59.964 55.000 7.91 0.00 37.22 3.91
64 65 0.108233 CTCTCAGGTCCAAGCAGAGC 60.108 60.000 0.00 0.00 34.42 4.09
71 72 2.219164 TCCAAGCAGAGCTCTGGCA 61.219 57.895 37.86 11.62 43.94 4.92
90 91 2.244117 ATCATGGAGCAACGCGTCCT 62.244 55.000 14.44 12.70 33.57 3.85
95 96 4.719369 AGCAACGCGTCCTCGGAC 62.719 66.667 14.44 6.01 41.40 4.79
97 98 4.351938 CAACGCGTCCTCGGACCA 62.352 66.667 14.44 0.00 41.76 4.02
103 104 2.262915 GTCCTCGGACCACTGCAG 59.737 66.667 13.48 13.48 39.08 4.41
129 130 3.503363 GGATCACCTGCAGTGCGC 61.503 66.667 13.81 0.00 46.81 6.09
161 162 1.071605 GTGTCATTGCACTCGACCTC 58.928 55.000 6.83 0.00 36.51 3.85
191 192 1.023513 GCATCGCTGGCTCCATATCC 61.024 60.000 0.00 0.00 0.00 2.59
192 193 0.738762 CATCGCTGGCTCCATATCCG 60.739 60.000 0.00 0.00 0.00 4.18
197 198 0.107456 CTGGCTCCATATCCGCTTGT 59.893 55.000 0.00 0.00 0.00 3.16
198 199 0.179048 TGGCTCCATATCCGCTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
199 200 1.510480 GGCTCCATATCCGCTTGTGC 61.510 60.000 0.00 0.00 0.00 4.57
212 213 4.947147 TGTGCCGCCAACCTCACC 62.947 66.667 0.00 0.00 0.00 4.02
218 219 2.032681 GCCAACCTCACCGCTCTT 59.967 61.111 0.00 0.00 0.00 2.85
220 221 0.741221 GCCAACCTCACCGCTCTTAG 60.741 60.000 0.00 0.00 0.00 2.18
230 231 0.537188 CCGCTCTTAGAAGGCTCCAA 59.463 55.000 0.00 0.00 0.00 3.53
358 359 1.338105 TGAACTCTCTGCATGTTCCCG 60.338 52.381 14.81 0.00 39.24 5.14
364 365 1.811266 CTGCATGTTCCCGACTCCG 60.811 63.158 0.00 0.00 0.00 4.63
371 372 0.535797 GTTCCCGACTCCGAATCCTT 59.464 55.000 0.00 0.00 38.22 3.36
437 438 0.455633 GCCAATGCAAGCGTCTTCAG 60.456 55.000 0.00 0.00 37.47 3.02
525 526 0.926846 GTGCATGCTAGTTCTCGCTC 59.073 55.000 20.33 0.00 0.00 5.03
591 592 4.261072 GCCTTTCTCTCACATACGTCGATA 60.261 45.833 0.00 0.00 0.00 2.92
608 609 3.059884 CGATATTGGGACGAATGGTCTG 58.940 50.000 0.00 0.00 45.35 3.51
667 7984 4.017808 TCTCTCCAAGTACTTAGGCTCAC 58.982 47.826 8.04 0.00 0.00 3.51
717 8034 3.056304 GAGACTCTCTTCAACACTGCAC 58.944 50.000 0.00 0.00 0.00 4.57
739 8056 0.609957 CTTGTTGCCATCTGCCTCCA 60.610 55.000 0.00 0.00 40.16 3.86
756 8073 0.868406 CCAAACAGAACAGCCTCGTC 59.132 55.000 0.00 0.00 0.00 4.20
777 8094 2.480759 CGGTTCCATACCTCCTGTAACG 60.481 54.545 0.00 0.00 45.40 3.18
780 8097 0.249322 CCATACCTCCTGTAACGGCG 60.249 60.000 4.80 4.80 31.94 6.46
782 8099 1.340248 CATACCTCCTGTAACGGCGAT 59.660 52.381 16.62 3.59 31.94 4.58
784 8101 1.477553 ACCTCCTGTAACGGCGATAA 58.522 50.000 16.62 0.00 0.00 1.75
785 8102 1.826720 ACCTCCTGTAACGGCGATAAA 59.173 47.619 16.62 0.00 0.00 1.40
792 8124 2.028294 TGTAACGGCGATAAACTCCCAA 60.028 45.455 16.62 0.00 0.00 4.12
892 8224 7.063426 TGCTTGAACTTCGTCTTACAGATAATG 59.937 37.037 0.00 0.00 0.00 1.90
893 8225 6.887376 TGAACTTCGTCTTACAGATAATGC 57.113 37.500 0.00 0.00 0.00 3.56
911 8243 3.712016 TGCTTTAGTTGGGAGCATACA 57.288 42.857 0.00 0.00 41.15 2.29
1048 8380 2.685100 CAAACAACTCCCTCGTAGGAC 58.315 52.381 2.84 0.00 37.67 3.85
1049 8381 2.005370 AACAACTCCCTCGTAGGACA 57.995 50.000 2.84 0.00 37.67 4.02
1210 8549 6.823286 TTACTGGATTCATACCATCCTTCA 57.177 37.500 0.82 0.00 40.99 3.02
1245 8584 9.341899 CCAAATTTAAAGGAACTAGATTTGTCG 57.658 33.333 0.00 0.00 38.49 4.35
1623 8963 7.461749 TGAGTTCTCTAAAACTGGATTGGAAT 58.538 34.615 1.53 0.00 39.55 3.01
1758 9098 2.894731 TCACTCACTGGAGAGTTGGAT 58.105 47.619 0.00 0.00 46.26 3.41
1776 9116 6.038271 AGTTGGATTTGTCACACAACTACTTC 59.962 38.462 9.24 0.00 46.88 3.01
1884 9224 1.202842 TCCACTCTCGGACAGTGTGTA 60.203 52.381 11.64 0.00 42.73 2.90
2105 9445 2.931325 GTGGTATATTTGACAACGCGGA 59.069 45.455 12.47 0.00 0.00 5.54
2775 10148 2.111043 AACCACTGTGCACCTCCG 59.889 61.111 15.69 1.79 0.00 4.63
2850 10223 4.284829 TGCATATGTCACTGACTTTGGA 57.715 40.909 10.54 4.22 33.15 3.53
2882 10255 8.853077 AGATTTCTGTTCACTACATCAAATGA 57.147 30.769 0.00 0.00 35.85 2.57
3134 10521 6.567687 TGTTACAAATGATAACAGGGTGTG 57.432 37.500 0.00 0.00 37.56 3.82
3141 10528 2.647299 TGATAACAGGGTGTGGTCCAAT 59.353 45.455 0.00 0.00 0.00 3.16
3198 11128 7.864882 TCACGAATTTGTTGATGAAGCATTTAA 59.135 29.630 0.00 0.00 0.00 1.52
3384 11314 5.075493 CCTTAGAATCAAGCATATGGCCTT 58.925 41.667 3.32 0.00 46.50 4.35
3519 11463 6.706270 CAGTTGGTGACACTTGTAGAAAGTAT 59.294 38.462 5.39 0.00 42.67 2.12
3619 11563 1.634757 TATTTGTGCGAGCAGTGCCG 61.635 55.000 12.58 15.96 0.00 5.69
3639 11583 5.006649 TGCCGAATCAAATCAAGTTAGATCG 59.993 40.000 0.00 0.00 0.00 3.69
3651 11625 5.066634 TCAAGTTAGATCGTCTAGAAGCTGG 59.933 44.000 0.15 0.00 29.56 4.85
3667 11641 3.362040 TGGCTTGGAACCAGATTGG 57.638 52.632 0.00 0.00 45.02 3.16
3677 11651 3.704566 GGAACCAGATTGGGGATTAAACC 59.295 47.826 0.00 0.00 43.37 3.27
3767 11747 1.416243 CAAGCCCATGCCCAATATGT 58.584 50.000 0.00 0.00 38.69 2.29
3825 11807 2.686106 GGCCGTCCCAGAACCCTA 60.686 66.667 0.00 0.00 0.00 3.53
3826 11808 2.295602 GGCCGTCCCAGAACCCTAA 61.296 63.158 0.00 0.00 0.00 2.69
3859 11845 1.534163 GGATTTCGCCCCGCTTTATAC 59.466 52.381 0.00 0.00 0.00 1.47
3882 11868 0.235665 AAGCAACGATCAACAGCACG 59.764 50.000 0.00 0.00 0.00 5.34
3940 11936 2.042979 ACACCCAAGGCAGGATACAAAT 59.957 45.455 0.00 0.00 41.41 2.32
3967 11980 2.752030 TCCCTAGCACTACAAGAGCAT 58.248 47.619 0.00 0.00 34.13 3.79
3981 11995 2.265467 GAGCATCCGGGGGCTACAAA 62.265 60.000 18.73 0.00 41.22 2.83
3982 11996 1.823899 GCATCCGGGGGCTACAAAG 60.824 63.158 0.00 0.00 0.00 2.77
4025 12040 1.663643 GTGAAGCCGCATATGACGAAA 59.336 47.619 17.40 0.70 0.00 3.46
4065 12080 2.770164 CTTCAAGAAGGGGACGACAT 57.230 50.000 1.86 0.00 34.87 3.06
4155 12170 2.738147 CGACGACGCCTTCAAGAAT 58.262 52.632 0.00 0.00 0.00 2.40
4168 12183 4.515191 CCTTCAAGAATGGAACGAGTTTCA 59.485 41.667 0.00 0.00 35.70 2.69
4232 12248 2.815211 CCACACACCGCCATCGAG 60.815 66.667 0.00 0.00 38.10 4.04
4377 12394 1.908793 CACCACCTCACCCGAGACT 60.909 63.158 0.00 0.00 42.34 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.683822 GGAGAGCTTGTCTGTCATTCTTG 59.316 47.826 0.00 0.00 36.86 3.02
6 7 3.582208 AGGAGAGCTTGTCTGTCATTCTT 59.418 43.478 0.00 0.00 36.86 2.52
23 24 3.480470 CTTGGACTTGAAGCAAAGGAGA 58.520 45.455 0.00 0.00 0.00 3.71
42 43 0.324285 CTGCTTGGACCTGAGAGCTT 59.676 55.000 0.00 0.00 36.16 3.74
57 58 0.179043 CATGATGCCAGAGCTCTGCT 60.179 55.000 34.09 21.70 43.88 4.24
58 59 1.167155 CCATGATGCCAGAGCTCTGC 61.167 60.000 34.09 27.97 42.47 4.26
60 61 0.759959 CTCCATGATGCCAGAGCTCT 59.240 55.000 11.45 11.45 40.80 4.09
64 65 1.022735 GTTGCTCCATGATGCCAGAG 58.977 55.000 0.00 0.00 0.00 3.35
71 72 1.815421 GGACGCGTTGCTCCATGAT 60.815 57.895 15.53 0.00 0.00 2.45
90 91 4.007644 CCAGCTGCAGTGGTCCGA 62.008 66.667 16.64 0.00 0.00 4.55
103 104 4.101448 AGGTGATCCCGTGCCAGC 62.101 66.667 0.00 0.00 38.74 4.85
134 135 2.434185 GCAATGACACGGCGAGGA 60.434 61.111 16.62 0.00 0.00 3.71
140 141 1.626654 GGTCGAGTGCAATGACACGG 61.627 60.000 15.17 0.95 45.45 4.94
170 171 2.475371 ATATGGAGCCAGCGATGCCC 62.475 60.000 0.00 0.00 0.00 5.36
177 178 1.072159 AAGCGGATATGGAGCCAGC 59.928 57.895 0.00 0.00 32.90 4.85
192 193 4.043200 GAGGTTGGCGGCACAAGC 62.043 66.667 12.92 19.04 46.26 4.01
212 213 1.205893 AGTTGGAGCCTTCTAAGAGCG 59.794 52.381 0.00 0.00 0.00 5.03
213 214 4.100189 TGATAGTTGGAGCCTTCTAAGAGC 59.900 45.833 0.00 0.00 0.00 4.09
215 216 6.013725 TGTTTGATAGTTGGAGCCTTCTAAGA 60.014 38.462 0.00 0.00 0.00 2.10
218 219 5.755409 TGTTTGATAGTTGGAGCCTTCTA 57.245 39.130 0.00 0.00 0.00 2.10
220 221 4.518970 TGTTGTTTGATAGTTGGAGCCTTC 59.481 41.667 0.00 0.00 0.00 3.46
230 231 3.498397 CGTGGAAGCTGTTGTTTGATAGT 59.502 43.478 0.00 0.00 0.00 2.12
358 359 2.484264 CACAAACCAAGGATTCGGAGTC 59.516 50.000 0.00 0.00 0.00 3.36
364 365 4.099419 AGTTGTTCCACAAACCAAGGATTC 59.901 41.667 0.00 0.00 40.15 2.52
400 401 1.773856 GCCAAGGCTAGGAGGGATCC 61.774 65.000 1.92 1.92 38.26 3.36
407 408 1.076777 GCATTGGCCAAGGCTAGGA 60.077 57.895 40.05 10.10 43.87 2.94
437 438 4.864704 TTTGTTGCCAAGGTTAATCTCC 57.135 40.909 0.00 0.00 0.00 3.71
458 459 1.000866 GATGCCCCCTTGGAGCTTT 59.999 57.895 0.00 0.00 35.39 3.51
491 492 2.105006 TGCACAGCTCAGGAAGATTC 57.895 50.000 0.00 0.00 0.00 2.52
571 572 6.206498 CCAATATCGACGTATGTGAGAGAAA 58.794 40.000 0.00 0.00 0.00 2.52
573 574 4.215613 CCCAATATCGACGTATGTGAGAGA 59.784 45.833 0.00 0.00 0.00 3.10
574 575 4.215613 TCCCAATATCGACGTATGTGAGAG 59.784 45.833 0.00 0.00 0.00 3.20
591 592 2.169352 CTCTCAGACCATTCGTCCCAAT 59.831 50.000 0.00 0.00 43.08 3.16
667 7984 6.583562 AGTTCCCCAGTAAGATTATTTCTCG 58.416 40.000 0.00 0.00 31.78 4.04
696 8013 3.056304 GTGCAGTGTTGAAGAGAGTCTC 58.944 50.000 12.54 12.54 0.00 3.36
739 8056 0.600255 CCGACGAGGCTGTTCTGTTT 60.600 55.000 0.00 0.00 0.00 2.83
777 8094 8.793592 AGATATTTAATTTGGGAGTTTATCGCC 58.206 33.333 0.00 0.00 40.09 5.54
892 8224 4.261801 TCTTGTATGCTCCCAACTAAAGC 58.738 43.478 0.00 0.00 36.56 3.51
893 8225 5.734720 TCTCTTGTATGCTCCCAACTAAAG 58.265 41.667 0.00 0.00 0.00 1.85
911 8243 5.221621 GGCTGAATATGACCTAAGCTCTCTT 60.222 44.000 0.00 0.00 36.35 2.85
1048 8380 6.038271 GTGTAGCCAATATTGAAGGGTAGTTG 59.962 42.308 17.23 0.00 36.20 3.16
1049 8381 6.120220 GTGTAGCCAATATTGAAGGGTAGTT 58.880 40.000 17.23 0.00 36.20 2.24
1210 8549 7.508687 AGTTCCTTTAAATTTGGCAATGAACT 58.491 30.769 16.14 16.14 0.00 3.01
1245 8584 3.565516 GCCTGCTTTTAGCTTGTTGTAC 58.434 45.455 0.00 0.00 42.97 2.90
1623 8963 7.801893 TCCAGGTATCTTTCCAGTAAAGTTA 57.198 36.000 0.00 0.00 44.27 2.24
1758 9098 5.116180 CCAGAGAAGTAGTTGTGTGACAAA 58.884 41.667 6.19 0.00 40.15 2.83
1884 9224 6.409524 TGCATTTCAAGATTCTCCAAAACT 57.590 33.333 0.00 0.00 0.00 2.66
2105 9445 6.131264 TCATTTCCTTGGATTGATACTGCAT 58.869 36.000 0.00 0.00 0.00 3.96
2279 9627 6.248433 TGCACTCTCTTCCTCCAATAAATTT 58.752 36.000 0.00 0.00 0.00 1.82
2668 10041 1.780309 TCTTTCACCATGTCCAAGGGT 59.220 47.619 0.00 0.00 34.59 4.34
2675 10048 8.273780 AGTCAGAATATTTCTTTCACCATGTC 57.726 34.615 0.00 0.00 38.11 3.06
2775 10148 4.437930 GGCTTCAAGTCACAATGTATCAGC 60.438 45.833 0.00 0.00 0.00 4.26
2850 10223 6.759272 TGTAGTGAACAGAAATCTTGCTAGT 58.241 36.000 0.00 0.00 33.01 2.57
2882 10255 8.680903 CCAAACTTGCTGAACTATCTTGATATT 58.319 33.333 0.00 0.00 0.00 1.28
3134 10521 7.153985 TCATTGAGTTTTTCATCAATTGGACC 58.846 34.615 5.42 0.00 42.11 4.46
3198 11128 5.647658 TCGACAACCTCATGCATATTCTTTT 59.352 36.000 0.00 0.00 0.00 2.27
3208 11138 0.107703 TGGGATCGACAACCTCATGC 60.108 55.000 0.00 0.00 0.00 4.06
3384 11314 2.523245 TGCTTCATACACCCATTTGCA 58.477 42.857 0.00 0.00 0.00 4.08
3464 11399 7.428826 ACTGAATTTCAAAATGGAGAAGTCAC 58.571 34.615 0.01 0.00 0.00 3.67
3519 11463 9.305555 AGAAAATGAGATGGAAAAAGAGAATGA 57.694 29.630 0.00 0.00 0.00 2.57
3531 11475 9.130661 TCACTTGTAAAAAGAAAATGAGATGGA 57.869 29.630 0.00 0.00 0.00 3.41
3619 11563 9.737427 TCTAGACGATCTAACTTGATTTGATTC 57.263 33.333 0.00 0.00 33.55 2.52
3639 11583 2.351455 GTTCCAAGCCAGCTTCTAGAC 58.649 52.381 0.90 0.00 33.42 2.59
3651 11625 0.039618 TCCCCAATCTGGTTCCAAGC 59.960 55.000 0.00 0.00 35.17 4.01
3667 11641 5.429130 ACTTCAGATTCGAGGTTTAATCCC 58.571 41.667 0.00 0.00 33.44 3.85
3677 11651 5.288232 GTCATGTTCAGACTTCAGATTCGAG 59.712 44.000 0.00 0.00 33.29 4.04
3767 11747 2.885135 ATGTTCTTGATCTGGGCACA 57.115 45.000 0.00 0.00 0.00 4.57
3796 11778 1.448013 GACGGCCAGGTACAAGCTC 60.448 63.158 2.24 0.00 0.00 4.09
3859 11845 3.848019 GTGCTGTTGATCGTTGCTTTATG 59.152 43.478 0.00 0.00 0.00 1.90
3882 11868 1.133869 GGTCGTGCATTTGTACCGC 59.866 57.895 0.00 0.00 0.00 5.68
3967 11980 2.204029 ACCTTTGTAGCCCCCGGA 60.204 61.111 0.73 0.00 0.00 5.14
3997 12011 1.021390 ATGCGGCTTCACTTCTTCGG 61.021 55.000 0.00 0.00 0.00 4.30
4089 12104 2.959421 AGGGGAAACTCTGATCCTCT 57.041 50.000 0.00 0.00 42.28 3.69
4155 12170 1.595929 GGCGGTGAAACTCGTTCCA 60.596 57.895 0.00 0.00 36.74 3.53
4186 12202 4.336280 GGGTGAAAACCTGCTCTATCTTT 58.664 43.478 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.