Multiple sequence alignment - TraesCS3A01G061900

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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 TraesCS3A01G061900 chr3A 100.000 2561 0 0 1 2561 37188181 37190741 0.000000e+00 4730
1 TraesCS3A01G061900 chr3A 96.463 1442 45 5 932 2371 37296924 37298361 0.000000e+00 2375
2 TraesCS3A01G061900 chr3A 88.333 1440 141 13 934 2359 36921648 36923074 0.000000e+00 1703
3 TraesCS3A01G061900 chrUn 89.463 1452 116 20 934 2359 267178805 267177365 0.000000e+00 1801
4 TraesCS3A01G061900 chrUn 91.333 1200 73 10 934 2118 38679549 38678366 0.000000e+00 1611
5 TraesCS3A01G061900 chrUn 84.005 769 102 14 935 1689 38670044 38669283 0.000000e+00 719
6 TraesCS3A01G061900 chr3B 89.463 1452 116 20 934 2359 45282317 45283757 0.000000e+00 1801
7 TraesCS3A01G061900 chr3B 89.873 1412 115 19 965 2359 45285558 45286958 0.000000e+00 1790
8 TraesCS3A01G061900 chr3D 89.437 1439 128 11 934 2359 27059783 27058356 0.000000e+00 1794
9 TraesCS3A01G061900 chr3D 94.093 1185 50 12 934 2106 26678111 26679287 0.000000e+00 1783
10 TraesCS3A01G061900 chr3D 94.979 936 42 3 1 936 442387863 442388793 0.000000e+00 1463
11 TraesCS3A01G061900 chr3D 94.338 936 48 3 1 936 573882207 573881277 0.000000e+00 1430
12 TraesCS3A01G061900 chr1A 94.444 936 48 2 1 936 582290901 582291832 0.000000e+00 1437
13 TraesCS3A01G061900 chr1A 94.231 936 50 2 1 936 45286514 45287445 0.000000e+00 1426
14 TraesCS3A01G061900 chr7D 94.036 939 46 7 1 936 2476526 2477457 0.000000e+00 1415
15 TraesCS3A01G061900 chr4D 93.823 939 48 7 1 936 490393103 490394034 0.000000e+00 1404
16 TraesCS3A01G061900 chr6D 93.717 939 49 7 1 936 61466492 61467423 0.000000e+00 1399
17 TraesCS3A01G061900 chr6D 93.717 939 47 8 1 936 54918741 54917812 0.000000e+00 1397
18 TraesCS3A01G061900 chr6D 97.479 119 2 1 2443 2561 291678171 291678288 4.320000e-48 202
19 TraesCS3A01G061900 chr6D 96.629 89 3 0 2367 2455 291678059 291678147 5.710000e-32 148
20 TraesCS3A01G061900 chr1D 93.291 939 53 7 1 936 484576350 484577281 0.000000e+00 1376
21 TraesCS3A01G061900 chr1D 96.410 195 6 1 2367 2561 391070304 391070497 1.140000e-83 320
22 TraesCS3A01G061900 chr4B 90.506 158 8 1 2367 2524 667395228 667395378 4.320000e-48 202


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 TraesCS3A01G061900 chr3A 37188181 37190741 2560 False 4730.0 4730 100.000 1 2561 1 chr3A.!!$F2 2560
1 TraesCS3A01G061900 chr3A 37296924 37298361 1437 False 2375.0 2375 96.463 932 2371 1 chr3A.!!$F3 1439
2 TraesCS3A01G061900 chr3A 36921648 36923074 1426 False 1703.0 1703 88.333 934 2359 1 chr3A.!!$F1 1425
3 TraesCS3A01G061900 chrUn 267177365 267178805 1440 True 1801.0 1801 89.463 934 2359 1 chrUn.!!$R3 1425
4 TraesCS3A01G061900 chrUn 38678366 38679549 1183 True 1611.0 1611 91.333 934 2118 1 chrUn.!!$R2 1184
5 TraesCS3A01G061900 chrUn 38669283 38670044 761 True 719.0 719 84.005 935 1689 1 chrUn.!!$R1 754
6 TraesCS3A01G061900 chr3B 45282317 45286958 4641 False 1795.5 1801 89.668 934 2359 2 chr3B.!!$F1 1425
7 TraesCS3A01G061900 chr3D 27058356 27059783 1427 True 1794.0 1794 89.437 934 2359 1 chr3D.!!$R1 1425
8 TraesCS3A01G061900 chr3D 26678111 26679287 1176 False 1783.0 1783 94.093 934 2106 1 chr3D.!!$F1 1172
9 TraesCS3A01G061900 chr3D 442387863 442388793 930 False 1463.0 1463 94.979 1 936 1 chr3D.!!$F2 935
10 TraesCS3A01G061900 chr3D 573881277 573882207 930 True 1430.0 1430 94.338 1 936 1 chr3D.!!$R2 935
11 TraesCS3A01G061900 chr1A 582290901 582291832 931 False 1437.0 1437 94.444 1 936 1 chr1A.!!$F2 935
12 TraesCS3A01G061900 chr1A 45286514 45287445 931 False 1426.0 1426 94.231 1 936 1 chr1A.!!$F1 935
13 TraesCS3A01G061900 chr7D 2476526 2477457 931 False 1415.0 1415 94.036 1 936 1 chr7D.!!$F1 935
14 TraesCS3A01G061900 chr4D 490393103 490394034 931 False 1404.0 1404 93.823 1 936 1 chr4D.!!$F1 935
15 TraesCS3A01G061900 chr6D 61466492 61467423 931 False 1399.0 1399 93.717 1 936 1 chr6D.!!$F1 935
16 TraesCS3A01G061900 chr6D 54917812 54918741 929 True 1397.0 1397 93.717 1 936 1 chr6D.!!$R1 935
17 TraesCS3A01G061900 chr1D 484576350 484577281 931 False 1376.0 1376 93.291 1 936 1 chr1D.!!$F2 935

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
79 80 0.17668 ATGTCTGCCACTGATCGGTC 59.823 55.0 3.54 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 5245 1.311859 TCCAGAGCTGTTTGCAAGTG 58.688 50.0 0.0 0.0 45.94 3.16 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
47 48 2.034939 TGGAATGCTTCAGTGCAAACAG 59.965 45.455 0.00 0.00 46.61 3.16
48 49 2.035066 GGAATGCTTCAGTGCAAACAGT 59.965 45.455 0.00 0.00 46.61 3.55
79 80 0.176680 ATGTCTGCCACTGATCGGTC 59.823 55.000 3.54 0.00 0.00 4.79
95 96 0.460987 GGTCGTCTGCTCTTGATGGG 60.461 60.000 0.00 0.00 0.00 4.00
103 104 1.198713 GCTCTTGATGGGGACTCTCA 58.801 55.000 0.00 0.00 0.00 3.27
104 105 1.556911 GCTCTTGATGGGGACTCTCAA 59.443 52.381 0.00 0.00 33.60 3.02
121 122 3.058450 CTCAATCTCGTCTGATGATGCC 58.942 50.000 0.00 0.00 0.00 4.40
146 147 3.508402 TGAGTATCGCAGTCTTGTTGGTA 59.492 43.478 0.00 0.00 38.61 3.25
225 226 2.429610 GTCAATTTCTGCATGCTCCCAT 59.570 45.455 20.33 3.23 0.00 4.00
259 260 3.058224 GGTCAGCTGTGAAGCGTATTTTT 60.058 43.478 14.67 0.00 40.27 1.94
312 313 2.338785 GCTTCTTCAGCCTGCACCC 61.339 63.158 0.00 0.00 43.65 4.61
402 403 2.084546 GGATATGCGGTATTCCTTGGC 58.915 52.381 0.00 0.00 0.00 4.52
420 421 1.134670 GGCTCTAACTTGATCGCCTGT 60.135 52.381 0.00 0.00 34.80 4.00
480 481 8.030106 AGTACTGAAGCTGAGTATAAAGTTGTC 58.970 37.037 8.68 0.00 0.00 3.18
486 487 4.031878 GCTGAGTATAAAGTTGTCGCTGAC 59.968 45.833 2.32 2.32 0.00 3.51
726 727 3.807553 TCAACTTGCTGACATCTTCACA 58.192 40.909 0.00 0.00 0.00 3.58
797 798 1.953686 GCTTTGTACTTCAGGCCACAA 59.046 47.619 5.01 2.10 0.00 3.33
800 801 4.798574 CTTTGTACTTCAGGCCACAATTC 58.201 43.478 5.01 0.00 31.45 2.17
837 838 6.205464 GGGTGTTAGACTGTATATACGTAGCA 59.795 42.308 8.33 3.44 0.00 3.49
1011 1024 2.366480 CTGAGCTCATGAGGAGGCCG 62.366 65.000 23.89 0.00 44.22 6.13
1079 1094 1.401539 GGGACAAGAAATTGTGAGCGC 60.402 52.381 0.00 0.00 34.90 5.92
1088 1103 2.907910 ATTGTGAGCGCAACTGAATC 57.092 45.000 11.47 0.00 0.00 2.52
1162 1177 2.356535 CCTATTGCACCTCTCCTTGCTT 60.357 50.000 0.00 0.00 39.62 3.91
1196 1212 0.450583 GCTGACTGTACCATCGACGA 59.549 55.000 0.00 0.00 0.00 4.20
1311 1327 7.020827 ACCTGAAAGATTTACAGATGAAGGA 57.979 36.000 0.00 0.00 34.07 3.36
1330 1346 4.922206 AGGAAATGCTAGGAATGTCAACA 58.078 39.130 0.00 0.00 0.00 3.33
1589 1612 7.386848 TCGAGCTAAGCTAAATACTTTGTGTTT 59.613 33.333 0.00 0.00 39.88 2.83
1932 5165 6.833342 ACAAAATGAAAACTCACATGCTTC 57.167 33.333 0.00 0.00 0.00 3.86
2002 5245 7.655328 CAGATACCAAGGACAATGAATCTCTAC 59.345 40.741 0.00 0.00 0.00 2.59
2065 5311 2.554142 ACACGCATCTACCATGACATG 58.446 47.619 8.56 8.56 0.00 3.21
2250 5500 5.633830 TTATCCTCAACTTCGAGTACGTT 57.366 39.130 0.00 0.00 40.69 3.99
2302 5552 4.664392 AGACTCCGAAACCTAGAAGAAGA 58.336 43.478 0.00 0.00 0.00 2.87
2364 5614 1.555992 CCAACTGGTGGGTATTACGGA 59.444 52.381 3.05 0.00 44.64 4.69
2365 5615 2.624636 CAACTGGTGGGTATTACGGAC 58.375 52.381 0.00 0.00 0.00 4.79
2366 5616 2.235402 CAACTGGTGGGTATTACGGACT 59.765 50.000 0.00 0.00 0.00 3.85
2367 5617 2.543635 ACTGGTGGGTATTACGGACTT 58.456 47.619 0.00 0.00 0.00 3.01
2368 5618 3.711863 ACTGGTGGGTATTACGGACTTA 58.288 45.455 0.00 0.00 0.00 2.24
2369 5619 4.292643 ACTGGTGGGTATTACGGACTTAT 58.707 43.478 0.00 0.00 0.00 1.73
2370 5620 4.100498 ACTGGTGGGTATTACGGACTTATG 59.900 45.833 0.00 0.00 0.00 1.90
2372 5622 3.389002 GGTGGGTATTACGGACTTATGGT 59.611 47.826 0.00 0.00 0.00 3.55
2373 5623 4.141642 GGTGGGTATTACGGACTTATGGTT 60.142 45.833 0.00 0.00 0.00 3.67
2374 5624 5.052481 GTGGGTATTACGGACTTATGGTTC 58.948 45.833 0.00 0.00 0.00 3.62
2379 5629 2.677971 CGGACTTATGGTTCGCCTG 58.322 57.895 0.00 0.00 40.27 4.85
2380 5630 1.429148 CGGACTTATGGTTCGCCTGC 61.429 60.000 0.00 0.00 40.27 4.85
2381 5631 1.429148 GGACTTATGGTTCGCCTGCG 61.429 60.000 4.92 4.92 38.36 5.18
2382 5632 2.036764 GACTTATGGTTCGCCTGCGC 62.037 60.000 6.67 0.00 39.59 6.09
2383 5633 2.822255 TTATGGTTCGCCTGCGCC 60.822 61.111 4.18 3.92 39.59 6.53
2384 5634 3.323758 TTATGGTTCGCCTGCGCCT 62.324 57.895 4.18 0.00 39.59 5.52
2387 5637 4.752879 GGTTCGCCTGCGCCTGTA 62.753 66.667 4.18 0.00 39.59 2.74
2388 5638 3.488090 GTTCGCCTGCGCCTGTAC 61.488 66.667 4.18 0.00 39.59 2.90
2389 5639 3.691342 TTCGCCTGCGCCTGTACT 61.691 61.111 4.18 0.00 39.59 2.73
2390 5640 3.932580 TTCGCCTGCGCCTGTACTG 62.933 63.158 4.18 0.00 39.59 2.74
2394 5644 4.087892 CTGCGCCTGTACTGGGCT 62.088 66.667 23.06 0.00 46.73 5.19
2395 5645 4.393155 TGCGCCTGTACTGGGCTG 62.393 66.667 23.06 18.03 46.73 4.85
2398 5648 3.721706 GCCTGTACTGGGCTGCCT 61.722 66.667 19.68 0.70 45.57 4.75
2399 5649 2.270205 CCTGTACTGGGCTGCCTG 59.730 66.667 19.68 14.03 0.00 4.85
2400 5650 2.596851 CCTGTACTGGGCTGCCTGT 61.597 63.158 19.68 18.85 0.00 4.00
2401 5651 1.376466 CTGTACTGGGCTGCCTGTT 59.624 57.895 19.68 5.19 0.00 3.16
2402 5652 0.613260 CTGTACTGGGCTGCCTGTTA 59.387 55.000 19.68 4.17 0.00 2.41
2403 5653 0.613260 TGTACTGGGCTGCCTGTTAG 59.387 55.000 19.68 13.74 0.00 2.34
2404 5654 0.613777 GTACTGGGCTGCCTGTTAGT 59.386 55.000 19.68 18.25 0.00 2.24
2405 5655 1.003233 GTACTGGGCTGCCTGTTAGTT 59.997 52.381 19.68 6.05 0.00 2.24
2406 5656 0.250901 ACTGGGCTGCCTGTTAGTTG 60.251 55.000 19.68 2.91 0.00 3.16
2407 5657 0.962356 CTGGGCTGCCTGTTAGTTGG 60.962 60.000 19.68 0.00 0.00 3.77
2408 5658 1.678970 GGGCTGCCTGTTAGTTGGG 60.679 63.158 19.68 0.00 0.00 4.12
2409 5659 2.343426 GGCTGCCTGTTAGTTGGGC 61.343 63.158 12.43 0.00 45.45 5.36
2410 5660 2.343426 GCTGCCTGTTAGTTGGGCC 61.343 63.158 0.00 0.00 44.71 5.80
2411 5661 1.380302 CTGCCTGTTAGTTGGGCCT 59.620 57.895 4.53 0.00 44.71 5.19
2412 5662 0.678048 CTGCCTGTTAGTTGGGCCTC 60.678 60.000 4.53 0.00 44.71 4.70
2413 5663 1.133809 TGCCTGTTAGTTGGGCCTCT 61.134 55.000 4.53 6.05 44.71 3.69
2414 5664 0.678048 GCCTGTTAGTTGGGCCTCTG 60.678 60.000 4.53 0.00 39.96 3.35
2415 5665 0.693049 CCTGTTAGTTGGGCCTCTGT 59.307 55.000 4.53 0.00 0.00 3.41
2416 5666 1.339151 CCTGTTAGTTGGGCCTCTGTC 60.339 57.143 4.53 2.50 0.00 3.51
2417 5667 1.347707 CTGTTAGTTGGGCCTCTGTCA 59.652 52.381 4.53 6.59 0.00 3.58
2418 5668 1.071699 TGTTAGTTGGGCCTCTGTCAC 59.928 52.381 4.53 3.66 0.00 3.67
2419 5669 0.690762 TTAGTTGGGCCTCTGTCACC 59.309 55.000 4.53 0.00 0.00 4.02
2420 5670 1.541310 TAGTTGGGCCTCTGTCACCG 61.541 60.000 4.53 0.00 0.00 4.94
2421 5671 2.525629 TTGGGCCTCTGTCACCGA 60.526 61.111 4.53 0.00 0.00 4.69
2422 5672 2.144078 TTGGGCCTCTGTCACCGAA 61.144 57.895 4.53 0.00 0.00 4.30
2423 5673 2.111999 TTGGGCCTCTGTCACCGAAG 62.112 60.000 4.53 0.00 0.00 3.79
2424 5674 2.283529 GGGCCTCTGTCACCGAAGA 61.284 63.158 0.84 0.00 0.00 2.87
2425 5675 1.216710 GGCCTCTGTCACCGAAGAG 59.783 63.158 0.00 0.00 39.76 2.85
2436 5686 3.853104 CCGAAGAGGTATGTTGCCA 57.147 52.632 0.00 0.00 34.51 4.92
2437 5687 1.656652 CCGAAGAGGTATGTTGCCAG 58.343 55.000 0.00 0.00 34.51 4.85
2438 5688 1.656652 CGAAGAGGTATGTTGCCAGG 58.343 55.000 0.00 0.00 0.00 4.45
2439 5689 1.066143 CGAAGAGGTATGTTGCCAGGT 60.066 52.381 0.00 0.00 0.00 4.00
2440 5690 2.633488 GAAGAGGTATGTTGCCAGGTC 58.367 52.381 0.00 0.00 0.00 3.85
2441 5691 0.912486 AGAGGTATGTTGCCAGGTCC 59.088 55.000 0.00 0.00 0.00 4.46
2442 5692 0.462047 GAGGTATGTTGCCAGGTCCG 60.462 60.000 0.00 0.00 0.00 4.79
2443 5693 0.907704 AGGTATGTTGCCAGGTCCGA 60.908 55.000 0.00 0.00 0.00 4.55
2444 5694 0.743345 GGTATGTTGCCAGGTCCGAC 60.743 60.000 0.00 0.00 0.00 4.79
2445 5695 0.249398 GTATGTTGCCAGGTCCGACT 59.751 55.000 0.00 0.00 0.00 4.18
2446 5696 0.535335 TATGTTGCCAGGTCCGACTC 59.465 55.000 0.00 0.00 0.00 3.36
2447 5697 2.047179 GTTGCCAGGTCCGACTCC 60.047 66.667 0.00 0.00 0.00 3.85
2448 5698 2.525629 TTGCCAGGTCCGACTCCA 60.526 61.111 0.00 0.00 0.00 3.86
2449 5699 1.918293 TTGCCAGGTCCGACTCCAT 60.918 57.895 0.00 0.00 0.00 3.41
2450 5700 1.899437 TTGCCAGGTCCGACTCCATC 61.899 60.000 0.00 0.00 0.00 3.51
2451 5701 2.060980 GCCAGGTCCGACTCCATCT 61.061 63.158 0.00 0.00 0.00 2.90
2452 5702 2.022240 GCCAGGTCCGACTCCATCTC 62.022 65.000 0.00 0.00 0.00 2.75
2453 5703 1.395826 CCAGGTCCGACTCCATCTCC 61.396 65.000 0.00 0.00 0.00 3.71
2454 5704 0.684479 CAGGTCCGACTCCATCTCCA 60.684 60.000 0.00 0.00 0.00 3.86
2455 5705 0.041238 AGGTCCGACTCCATCTCCAA 59.959 55.000 0.00 0.00 0.00 3.53
2456 5706 1.123928 GGTCCGACTCCATCTCCAAT 58.876 55.000 0.00 0.00 0.00 3.16
2457 5707 2.091278 AGGTCCGACTCCATCTCCAATA 60.091 50.000 0.00 0.00 0.00 1.90
2458 5708 2.036089 GGTCCGACTCCATCTCCAATAC 59.964 54.545 0.00 0.00 0.00 1.89
2459 5709 2.959707 GTCCGACTCCATCTCCAATACT 59.040 50.000 0.00 0.00 0.00 2.12
2460 5710 3.004944 GTCCGACTCCATCTCCAATACTC 59.995 52.174 0.00 0.00 0.00 2.59
2461 5711 2.297597 CCGACTCCATCTCCAATACTCC 59.702 54.545 0.00 0.00 0.00 3.85
2462 5712 2.959030 CGACTCCATCTCCAATACTCCA 59.041 50.000 0.00 0.00 0.00 3.86
2463 5713 3.576118 CGACTCCATCTCCAATACTCCAT 59.424 47.826 0.00 0.00 0.00 3.41
2464 5714 4.321601 CGACTCCATCTCCAATACTCCATC 60.322 50.000 0.00 0.00 0.00 3.51
2465 5715 3.576118 ACTCCATCTCCAATACTCCATCG 59.424 47.826 0.00 0.00 0.00 3.84
2466 5716 2.300152 TCCATCTCCAATACTCCATCGC 59.700 50.000 0.00 0.00 0.00 4.58
2467 5717 2.301296 CCATCTCCAATACTCCATCGCT 59.699 50.000 0.00 0.00 0.00 4.93
2468 5718 3.511540 CCATCTCCAATACTCCATCGCTA 59.488 47.826 0.00 0.00 0.00 4.26
2469 5719 4.161189 CCATCTCCAATACTCCATCGCTAT 59.839 45.833 0.00 0.00 0.00 2.97
2470 5720 5.337894 CCATCTCCAATACTCCATCGCTATT 60.338 44.000 0.00 0.00 0.00 1.73
2471 5721 6.127338 CCATCTCCAATACTCCATCGCTATTA 60.127 42.308 0.00 0.00 0.00 0.98
2472 5722 7.418368 CCATCTCCAATACTCCATCGCTATTAT 60.418 40.741 0.00 0.00 0.00 1.28
2473 5723 7.482169 TCTCCAATACTCCATCGCTATTATT 57.518 36.000 0.00 0.00 0.00 1.40
2474 5724 7.548097 TCTCCAATACTCCATCGCTATTATTC 58.452 38.462 0.00 0.00 0.00 1.75
2475 5725 6.640518 TCCAATACTCCATCGCTATTATTCC 58.359 40.000 0.00 0.00 0.00 3.01
2476 5726 6.440647 TCCAATACTCCATCGCTATTATTCCT 59.559 38.462 0.00 0.00 0.00 3.36
2477 5727 7.618117 TCCAATACTCCATCGCTATTATTCCTA 59.382 37.037 0.00 0.00 0.00 2.94
2478 5728 8.424918 CCAATACTCCATCGCTATTATTCCTAT 58.575 37.037 0.00 0.00 0.00 2.57
2479 5729 9.823647 CAATACTCCATCGCTATTATTCCTATT 57.176 33.333 0.00 0.00 0.00 1.73
2481 5731 6.879400 ACTCCATCGCTATTATTCCTATTCC 58.121 40.000 0.00 0.00 0.00 3.01
2482 5732 6.670027 ACTCCATCGCTATTATTCCTATTCCT 59.330 38.462 0.00 0.00 0.00 3.36
2483 5733 7.839705 ACTCCATCGCTATTATTCCTATTCCTA 59.160 37.037 0.00 0.00 0.00 2.94
2484 5734 8.783660 TCCATCGCTATTATTCCTATTCCTAT 57.216 34.615 0.00 0.00 0.00 2.57
2485 5735 9.877222 TCCATCGCTATTATTCCTATTCCTATA 57.123 33.333 0.00 0.00 0.00 1.31
2512 5762 8.579682 AAAAATAAATCTCCATCGCTATTTGC 57.420 30.769 0.00 0.00 38.57 3.68
2513 5763 7.516198 AAATAAATCTCCATCGCTATTTGCT 57.484 32.000 0.00 0.00 40.11 3.91
2514 5764 4.825546 AAATCTCCATCGCTATTTGCTG 57.174 40.909 0.00 0.00 40.11 4.41
2515 5765 3.758755 ATCTCCATCGCTATTTGCTGA 57.241 42.857 0.00 0.00 40.11 4.26
2516 5766 3.758755 TCTCCATCGCTATTTGCTGAT 57.241 42.857 0.00 0.00 40.11 2.90
2517 5767 3.657634 TCTCCATCGCTATTTGCTGATC 58.342 45.455 0.00 0.00 40.11 2.92
2518 5768 3.323115 TCTCCATCGCTATTTGCTGATCT 59.677 43.478 0.00 0.00 40.11 2.75
2519 5769 3.657634 TCCATCGCTATTTGCTGATCTC 58.342 45.455 0.00 0.00 40.11 2.75
2520 5770 2.740981 CCATCGCTATTTGCTGATCTCC 59.259 50.000 0.00 0.00 40.11 3.71
2521 5771 3.556633 CCATCGCTATTTGCTGATCTCCT 60.557 47.826 0.00 0.00 40.11 3.69
2522 5772 3.827008 TCGCTATTTGCTGATCTCCTT 57.173 42.857 0.00 0.00 40.11 3.36
2523 5773 3.722147 TCGCTATTTGCTGATCTCCTTC 58.278 45.455 0.00 0.00 40.11 3.46
2524 5774 2.805099 CGCTATTTGCTGATCTCCTTCC 59.195 50.000 0.00 0.00 40.11 3.46
2525 5775 3.494048 CGCTATTTGCTGATCTCCTTCCT 60.494 47.826 0.00 0.00 40.11 3.36
2526 5776 4.459330 GCTATTTGCTGATCTCCTTCCTT 58.541 43.478 0.00 0.00 38.95 3.36
2527 5777 4.886489 GCTATTTGCTGATCTCCTTCCTTT 59.114 41.667 0.00 0.00 38.95 3.11
2528 5778 5.008514 GCTATTTGCTGATCTCCTTCCTTTC 59.991 44.000 0.00 0.00 38.95 2.62
2529 5779 4.647564 TTTGCTGATCTCCTTCCTTTCT 57.352 40.909 0.00 0.00 0.00 2.52
2530 5780 5.762179 TTTGCTGATCTCCTTCCTTTCTA 57.238 39.130 0.00 0.00 0.00 2.10
2531 5781 4.744795 TGCTGATCTCCTTCCTTTCTAC 57.255 45.455 0.00 0.00 0.00 2.59
2532 5782 4.357325 TGCTGATCTCCTTCCTTTCTACT 58.643 43.478 0.00 0.00 0.00 2.57
2533 5783 4.404073 TGCTGATCTCCTTCCTTTCTACTC 59.596 45.833 0.00 0.00 0.00 2.59
2534 5784 4.202212 GCTGATCTCCTTCCTTTCTACTCC 60.202 50.000 0.00 0.00 0.00 3.85
2535 5785 4.947883 TGATCTCCTTCCTTTCTACTCCA 58.052 43.478 0.00 0.00 0.00 3.86
2536 5786 5.533112 TGATCTCCTTCCTTTCTACTCCAT 58.467 41.667 0.00 0.00 0.00 3.41
2537 5787 6.683537 TGATCTCCTTCCTTTCTACTCCATA 58.316 40.000 0.00 0.00 0.00 2.74
2538 5788 7.309091 TGATCTCCTTCCTTTCTACTCCATAT 58.691 38.462 0.00 0.00 0.00 1.78
2539 5789 7.453126 TGATCTCCTTCCTTTCTACTCCATATC 59.547 40.741 0.00 0.00 0.00 1.63
2540 5790 6.683537 TCTCCTTCCTTTCTACTCCATATCA 58.316 40.000 0.00 0.00 0.00 2.15
2541 5791 6.551601 TCTCCTTCCTTTCTACTCCATATCAC 59.448 42.308 0.00 0.00 0.00 3.06
2542 5792 5.302059 TCCTTCCTTTCTACTCCATATCACG 59.698 44.000 0.00 0.00 0.00 4.35
2543 5793 5.302059 CCTTCCTTTCTACTCCATATCACGA 59.698 44.000 0.00 0.00 0.00 4.35
2544 5794 6.015010 CCTTCCTTTCTACTCCATATCACGAT 60.015 42.308 0.00 0.00 0.00 3.73
2545 5795 6.576662 TCCTTTCTACTCCATATCACGATC 57.423 41.667 0.00 0.00 0.00 3.69
2546 5796 6.068670 TCCTTTCTACTCCATATCACGATCA 58.931 40.000 0.00 0.00 0.00 2.92
2547 5797 6.016192 TCCTTTCTACTCCATATCACGATCAC 60.016 42.308 0.00 0.00 0.00 3.06
2548 5798 5.358298 TTCTACTCCATATCACGATCACG 57.642 43.478 0.00 0.00 45.75 4.35
2549 5799 2.423926 ACTCCATATCACGATCACGC 57.576 50.000 0.00 0.00 43.96 5.34
2550 5800 1.957177 ACTCCATATCACGATCACGCT 59.043 47.619 0.00 0.00 43.96 5.07
2551 5801 2.287849 ACTCCATATCACGATCACGCTG 60.288 50.000 0.00 0.00 43.96 5.18
2552 5802 0.786581 CCATATCACGATCACGCTGC 59.213 55.000 0.00 0.00 43.96 5.25
2553 5803 0.432361 CATATCACGATCACGCTGCG 59.568 55.000 21.91 21.91 43.96 5.18
2554 5804 1.278172 ATATCACGATCACGCTGCGC 61.278 55.000 23.51 0.00 43.96 6.09
2555 5805 2.336400 TATCACGATCACGCTGCGCT 62.336 55.000 23.51 7.04 43.96 5.92
2556 5806 4.200851 CACGATCACGCTGCGCTG 62.201 66.667 23.51 18.54 43.96 5.18
2557 5807 4.724602 ACGATCACGCTGCGCTGT 62.725 61.111 23.51 10.49 43.96 4.40
2558 5808 3.906649 CGATCACGCTGCGCTGTC 61.907 66.667 23.51 15.49 0.00 3.51
2559 5809 3.906649 GATCACGCTGCGCTGTCG 61.907 66.667 23.51 22.08 39.07 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.461127 GCAGACATCGGAGTGACAAAC 59.539 52.381 0.00 0.00 0.00 2.93
48 49 1.608025 GGCAGACATCGGAGTGACAAA 60.608 52.381 0.00 0.00 0.00 2.83
79 80 0.460987 GTCCCCATCAAGAGCAGACG 60.461 60.000 0.00 0.00 0.00 4.18
95 96 3.629855 TCATCAGACGAGATTGAGAGTCC 59.370 47.826 0.00 0.00 34.41 3.85
103 104 2.433604 AGTGGCATCATCAGACGAGATT 59.566 45.455 0.00 0.00 0.00 2.40
104 105 2.037901 AGTGGCATCATCAGACGAGAT 58.962 47.619 0.00 0.00 0.00 2.75
121 122 3.223423 ACAAGACTGCGATACTCAGTG 57.777 47.619 0.00 0.00 44.09 3.66
146 147 7.202011 CCTGGTAATAGTAAGGTATTGCAGACT 60.202 40.741 0.00 0.00 29.27 3.24
225 226 2.303890 ACAGCTGACCAATGAGATGTCA 59.696 45.455 23.35 0.00 33.63 3.58
259 260 3.521560 CAGTAAGGCAGACATAGCGAAA 58.478 45.455 0.00 0.00 0.00 3.46
260 261 2.738643 GCAGTAAGGCAGACATAGCGAA 60.739 50.000 0.00 0.00 0.00 4.70
261 262 1.202417 GCAGTAAGGCAGACATAGCGA 60.202 52.381 0.00 0.00 0.00 4.93
402 403 4.210120 GCATTACAGGCGATCAAGTTAGAG 59.790 45.833 0.00 0.00 0.00 2.43
692 693 2.686915 GCAAGTTGATCCTTGGATGAGG 59.313 50.000 7.16 0.00 41.70 3.86
726 727 1.064017 TGTGGTTGTGGAAGAGGCTTT 60.064 47.619 0.00 0.00 0.00 3.51
797 798 2.566746 ACACCCTCCCTCAATCTGAAT 58.433 47.619 0.00 0.00 0.00 2.57
800 801 3.107601 TCTAACACCCTCCCTCAATCTG 58.892 50.000 0.00 0.00 0.00 2.90
874 875 7.473511 GCTCTTTCATTGTATAGAGGTACCCAT 60.474 40.741 8.74 2.25 35.72 4.00
889 892 0.890683 GGGGTGTGGCTCTTTCATTG 59.109 55.000 0.00 0.00 0.00 2.82
1011 1024 2.436417 TGTAGCTTTCCCATGAAGTGC 58.564 47.619 0.00 0.00 34.25 4.40
1079 1094 4.221342 CACCATGTTGTTCGATTCAGTTG 58.779 43.478 0.00 0.00 0.00 3.16
1088 1103 2.736721 CTCAGGTACACCATGTTGTTCG 59.263 50.000 0.00 0.00 38.89 3.95
1162 1177 4.349503 AGCCATGGCAAGGTGCGA 62.350 61.111 37.18 0.00 46.21 5.10
1311 1327 7.147846 CCCTTAATGTTGACATTCCTAGCATTT 60.148 37.037 12.28 0.00 44.67 2.32
1330 1346 9.895138 CAAGAAATGAAAATCATTCCCCTTAAT 57.105 29.630 6.09 0.00 45.57 1.40
1601 1626 3.976015 ACACCTTCTTCCCAAGAAAACA 58.024 40.909 0.61 0.00 46.13 2.83
2002 5245 1.311859 TCCAGAGCTGTTTGCAAGTG 58.688 50.000 0.00 0.00 45.94 3.16
2143 5389 2.401583 TTTGTGCCATCGTAGATGCT 57.598 45.000 4.60 0.00 45.12 3.79
2163 5409 7.173907 CCTGCGGATCAAATTTAGATCTGTAAT 59.826 37.037 24.59 2.30 46.06 1.89
2250 5500 7.212976 GCATTGTGATATTGAGGAAGTAGAGA 58.787 38.462 0.00 0.00 0.00 3.10
2302 5552 1.668419 GTAACTGCATCCTCGGCAAT 58.332 50.000 0.00 0.00 41.39 3.56
2359 5609 1.135527 CAGGCGAACCATAAGTCCGTA 59.864 52.381 0.00 0.00 39.06 4.02
2361 5611 1.429148 GCAGGCGAACCATAAGTCCG 61.429 60.000 0.00 0.00 39.06 4.79
2362 5612 1.429148 CGCAGGCGAACCATAAGTCC 61.429 60.000 8.15 0.00 42.83 3.85
2364 5614 2.106683 GCGCAGGCGAACCATAAGT 61.107 57.895 18.96 0.00 42.83 2.24
2365 5615 2.709475 GCGCAGGCGAACCATAAG 59.291 61.111 18.96 0.00 42.83 1.73
2382 5632 2.129555 AACAGGCAGCCCAGTACAGG 62.130 60.000 8.22 0.00 29.65 4.00
2383 5633 0.613260 TAACAGGCAGCCCAGTACAG 59.387 55.000 8.22 0.00 29.65 2.74
2384 5634 0.613260 CTAACAGGCAGCCCAGTACA 59.387 55.000 8.22 0.00 29.65 2.90
2385 5635 0.613777 ACTAACAGGCAGCCCAGTAC 59.386 55.000 8.22 0.00 29.65 2.73
2386 5636 1.003118 CAACTAACAGGCAGCCCAGTA 59.997 52.381 8.22 0.00 29.65 2.74
2387 5637 0.250901 CAACTAACAGGCAGCCCAGT 60.251 55.000 8.22 4.25 31.28 4.00
2388 5638 0.962356 CCAACTAACAGGCAGCCCAG 60.962 60.000 8.22 3.47 0.00 4.45
2389 5639 1.074775 CCAACTAACAGGCAGCCCA 59.925 57.895 8.22 0.00 0.00 5.36
2390 5640 1.678970 CCCAACTAACAGGCAGCCC 60.679 63.158 8.22 0.00 0.00 5.19
2391 5641 2.343426 GCCCAACTAACAGGCAGCC 61.343 63.158 1.84 1.84 46.34 4.85
2392 5642 3.278157 GCCCAACTAACAGGCAGC 58.722 61.111 0.00 0.00 46.34 5.25
2395 5645 0.678048 CAGAGGCCCAACTAACAGGC 60.678 60.000 0.00 0.00 46.37 4.85
2396 5646 0.693049 ACAGAGGCCCAACTAACAGG 59.307 55.000 0.00 0.00 0.00 4.00
2397 5647 1.347707 TGACAGAGGCCCAACTAACAG 59.652 52.381 0.00 0.00 0.00 3.16
2398 5648 1.071699 GTGACAGAGGCCCAACTAACA 59.928 52.381 0.00 0.00 0.00 2.41
2399 5649 1.610886 GGTGACAGAGGCCCAACTAAC 60.611 57.143 0.00 0.00 0.00 2.34
2400 5650 0.690762 GGTGACAGAGGCCCAACTAA 59.309 55.000 0.00 0.00 0.00 2.24
2401 5651 1.541310 CGGTGACAGAGGCCCAACTA 61.541 60.000 0.00 0.00 0.00 2.24
2402 5652 2.883828 CGGTGACAGAGGCCCAACT 61.884 63.158 0.00 0.00 0.00 3.16
2403 5653 2.358737 CGGTGACAGAGGCCCAAC 60.359 66.667 0.00 0.00 0.00 3.77
2404 5654 2.111999 CTTCGGTGACAGAGGCCCAA 62.112 60.000 0.00 0.00 0.00 4.12
2405 5655 2.525629 TTCGGTGACAGAGGCCCA 60.526 61.111 0.00 0.00 0.00 5.36
2406 5656 2.232298 CTCTTCGGTGACAGAGGCCC 62.232 65.000 0.00 0.00 0.00 5.80
2407 5657 1.216710 CTCTTCGGTGACAGAGGCC 59.783 63.158 0.00 0.00 0.00 5.19
2408 5658 1.216710 CCTCTTCGGTGACAGAGGC 59.783 63.158 4.74 0.00 41.02 4.70
2409 5659 2.659800 ACCTCTTCGGTGACAGAGG 58.340 57.895 14.01 14.01 46.80 3.69
2414 5664 5.731694 TGGCAACATACCTCTTCGGTGAC 62.732 52.174 0.00 0.00 45.46 3.67
2415 5665 3.674084 TGGCAACATACCTCTTCGGTGA 61.674 50.000 0.00 0.00 45.46 4.02
2416 5666 1.338674 TGGCAACATACCTCTTCGGTG 60.339 52.381 0.00 0.00 45.46 4.94
2418 5668 3.853104 TGGCAACATACCTCTTCGG 57.147 52.632 0.00 0.00 46.17 4.30
2430 5680 2.047179 GGAGTCGGACCTGGCAAC 60.047 66.667 4.14 0.00 0.00 4.17
2431 5681 1.899437 GATGGAGTCGGACCTGGCAA 61.899 60.000 4.14 0.00 0.00 4.52
2432 5682 2.284625 ATGGAGTCGGACCTGGCA 60.285 61.111 4.14 0.00 0.00 4.92
2433 5683 2.022240 GAGATGGAGTCGGACCTGGC 62.022 65.000 4.14 0.00 0.00 4.85
2434 5684 1.395826 GGAGATGGAGTCGGACCTGG 61.396 65.000 4.14 0.00 0.00 4.45
2435 5685 0.684479 TGGAGATGGAGTCGGACCTG 60.684 60.000 4.14 0.00 0.00 4.00
2436 5686 0.041238 TTGGAGATGGAGTCGGACCT 59.959 55.000 4.14 0.00 0.00 3.85
2437 5687 1.123928 ATTGGAGATGGAGTCGGACC 58.876 55.000 4.14 0.00 0.00 4.46
2438 5688 2.959707 AGTATTGGAGATGGAGTCGGAC 59.040 50.000 0.00 0.00 0.00 4.79
2439 5689 3.223435 GAGTATTGGAGATGGAGTCGGA 58.777 50.000 0.00 0.00 0.00 4.55
2440 5690 2.297597 GGAGTATTGGAGATGGAGTCGG 59.702 54.545 0.00 0.00 0.00 4.79
2441 5691 2.959030 TGGAGTATTGGAGATGGAGTCG 59.041 50.000 0.00 0.00 0.00 4.18
2442 5692 4.321601 CGATGGAGTATTGGAGATGGAGTC 60.322 50.000 0.00 0.00 0.00 3.36
2443 5693 3.576118 CGATGGAGTATTGGAGATGGAGT 59.424 47.826 0.00 0.00 0.00 3.85
2444 5694 3.616076 GCGATGGAGTATTGGAGATGGAG 60.616 52.174 0.00 0.00 0.00 3.86
2445 5695 2.300152 GCGATGGAGTATTGGAGATGGA 59.700 50.000 0.00 0.00 0.00 3.41
2446 5696 2.301296 AGCGATGGAGTATTGGAGATGG 59.699 50.000 0.00 0.00 0.00 3.51
2447 5697 3.674528 AGCGATGGAGTATTGGAGATG 57.325 47.619 0.00 0.00 0.00 2.90
2448 5698 7.667575 ATAATAGCGATGGAGTATTGGAGAT 57.332 36.000 0.00 0.00 0.00 2.75
2449 5699 7.363880 GGAATAATAGCGATGGAGTATTGGAGA 60.364 40.741 0.00 0.00 0.00 3.71
2450 5700 6.758886 GGAATAATAGCGATGGAGTATTGGAG 59.241 42.308 0.00 0.00 0.00 3.86
2451 5701 6.440647 AGGAATAATAGCGATGGAGTATTGGA 59.559 38.462 0.00 0.00 0.00 3.53
2452 5702 6.644347 AGGAATAATAGCGATGGAGTATTGG 58.356 40.000 0.00 0.00 0.00 3.16
2453 5703 9.823647 AATAGGAATAATAGCGATGGAGTATTG 57.176 33.333 0.00 0.00 0.00 1.90
2455 5705 8.643324 GGAATAGGAATAATAGCGATGGAGTAT 58.357 37.037 0.00 0.00 0.00 2.12
2456 5706 7.839705 AGGAATAGGAATAATAGCGATGGAGTA 59.160 37.037 0.00 0.00 0.00 2.59
2457 5707 6.670027 AGGAATAGGAATAATAGCGATGGAGT 59.330 38.462 0.00 0.00 0.00 3.85
2458 5708 7.118496 AGGAATAGGAATAATAGCGATGGAG 57.882 40.000 0.00 0.00 0.00 3.86
2459 5709 8.783660 ATAGGAATAGGAATAATAGCGATGGA 57.216 34.615 0.00 0.00 0.00 3.41
2487 5737 8.579682 GCAAATAGCGATGGAGATTTATTTTT 57.420 30.769 0.00 0.00 0.00 1.94
2504 5754 4.084011 AGGAAGGAGATCAGCAAATAGC 57.916 45.455 0.00 0.00 46.19 2.97
2505 5755 6.355747 AGAAAGGAAGGAGATCAGCAAATAG 58.644 40.000 0.00 0.00 0.00 1.73
2506 5756 6.319048 AGAAAGGAAGGAGATCAGCAAATA 57.681 37.500 0.00 0.00 0.00 1.40
2507 5757 5.190357 AGAAAGGAAGGAGATCAGCAAAT 57.810 39.130 0.00 0.00 0.00 2.32
2508 5758 4.647564 AGAAAGGAAGGAGATCAGCAAA 57.352 40.909 0.00 0.00 0.00 3.68
2509 5759 4.780021 AGTAGAAAGGAAGGAGATCAGCAA 59.220 41.667 0.00 0.00 0.00 3.91
2510 5760 4.357325 AGTAGAAAGGAAGGAGATCAGCA 58.643 43.478 0.00 0.00 0.00 4.41
2511 5761 4.202212 GGAGTAGAAAGGAAGGAGATCAGC 60.202 50.000 0.00 0.00 0.00 4.26
2512 5762 4.959210 TGGAGTAGAAAGGAAGGAGATCAG 59.041 45.833 0.00 0.00 0.00 2.90
2513 5763 4.947883 TGGAGTAGAAAGGAAGGAGATCA 58.052 43.478 0.00 0.00 0.00 2.92
2514 5764 7.453126 TGATATGGAGTAGAAAGGAAGGAGATC 59.547 40.741 0.00 0.00 0.00 2.75
2515 5765 7.234577 GTGATATGGAGTAGAAAGGAAGGAGAT 59.765 40.741 0.00 0.00 0.00 2.75
2516 5766 6.551601 GTGATATGGAGTAGAAAGGAAGGAGA 59.448 42.308 0.00 0.00 0.00 3.71
2517 5767 6.515862 CGTGATATGGAGTAGAAAGGAAGGAG 60.516 46.154 0.00 0.00 0.00 3.69
2518 5768 5.302059 CGTGATATGGAGTAGAAAGGAAGGA 59.698 44.000 0.00 0.00 0.00 3.36
2519 5769 5.302059 TCGTGATATGGAGTAGAAAGGAAGG 59.698 44.000 0.00 0.00 0.00 3.46
2520 5770 6.392625 TCGTGATATGGAGTAGAAAGGAAG 57.607 41.667 0.00 0.00 0.00 3.46
2521 5771 6.549736 TGATCGTGATATGGAGTAGAAAGGAA 59.450 38.462 0.00 0.00 0.00 3.36
2522 5772 6.016192 GTGATCGTGATATGGAGTAGAAAGGA 60.016 42.308 0.00 0.00 0.00 3.36
2523 5773 6.153067 GTGATCGTGATATGGAGTAGAAAGG 58.847 44.000 0.00 0.00 0.00 3.11
2524 5774 5.853810 CGTGATCGTGATATGGAGTAGAAAG 59.146 44.000 0.00 0.00 0.00 2.62
2525 5775 5.758924 CGTGATCGTGATATGGAGTAGAAA 58.241 41.667 0.00 0.00 0.00 2.52
2526 5776 4.320275 GCGTGATCGTGATATGGAGTAGAA 60.320 45.833 0.00 0.00 39.49 2.10
2527 5777 3.188667 GCGTGATCGTGATATGGAGTAGA 59.811 47.826 0.00 0.00 39.49 2.59
2528 5778 3.189495 AGCGTGATCGTGATATGGAGTAG 59.811 47.826 0.00 0.00 39.49 2.57
2529 5779 3.058224 CAGCGTGATCGTGATATGGAGTA 60.058 47.826 0.00 0.00 39.49 2.59
2530 5780 1.957177 AGCGTGATCGTGATATGGAGT 59.043 47.619 0.00 0.00 39.49 3.85
2531 5781 2.323059 CAGCGTGATCGTGATATGGAG 58.677 52.381 0.00 0.00 39.49 3.86
2532 5782 1.602920 GCAGCGTGATCGTGATATGGA 60.603 52.381 0.00 0.00 39.49 3.41
2533 5783 0.786581 GCAGCGTGATCGTGATATGG 59.213 55.000 0.00 0.00 39.49 2.74
2534 5784 0.432361 CGCAGCGTGATCGTGATATG 59.568 55.000 6.65 0.00 39.49 1.78
2535 5785 2.801388 CGCAGCGTGATCGTGATAT 58.199 52.632 6.65 0.00 39.49 1.63
2536 5786 4.302154 CGCAGCGTGATCGTGATA 57.698 55.556 6.65 0.00 39.49 2.15


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

AutoCloner maintained by Alex Coulton.