Multiple sequence alignment - TraesCS2D01G561400

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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 TraesCS2D01G561400 chr2D 100.000 3117 0 0 1 3117 633712074 633708958 0.000000e+00 5757
1 TraesCS2D01G561400 chr2D 90.458 524 24 6 2494 3006 48168524 48169032 0.000000e+00 667
2 TraesCS2D01G561400 chr2D 85.150 532 40 13 2494 3003 67551677 67552191 2.770000e-140 508
3 TraesCS2D01G561400 chr2D 83.275 568 38 15 2494 3006 470437671 470438236 1.310000e-128 470
4 TraesCS2D01G561400 chr2B 91.297 2275 118 29 1 2221 776709842 776707594 0.000000e+00 3031
5 TraesCS2D01G561400 chr2B 97.468 79 2 0 2396 2474 677961568 677961646 5.420000e-28 135
6 TraesCS2D01G561400 chr2B 97.403 77 2 0 2396 2472 773010703 773010779 7.010000e-27 132
7 TraesCS2D01G561400 chr2A 90.375 1600 71 24 676 2235 779889731 779891287 0.000000e+00 2025
8 TraesCS2D01G561400 chr2A 91.323 461 18 8 167 611 779888962 779889416 7.390000e-171 610
9 TraesCS2D01G561400 chr2A 81.995 411 34 17 2494 2870 3830843 3830439 2.330000e-81 313
10 TraesCS2D01G561400 chr2A 87.288 118 5 4 3010 3117 779891627 779891744 3.260000e-25 126
11 TraesCS2D01G561400 chr7D 89.454 531 26 5 2494 3006 607113801 607114319 0.000000e+00 643
12 TraesCS2D01G561400 chr7D 87.203 547 35 9 2494 3006 266322675 266323220 9.630000e-165 590
13 TraesCS2D01G561400 chr7D 91.447 152 12 1 2241 2392 607112319 607112469 1.130000e-49 207
14 TraesCS2D01G561400 chr1D 89.293 523 27 5 2494 3003 453551560 453552066 2.040000e-176 628
15 TraesCS2D01G561400 chr1D 84.768 302 22 11 2727 3006 9007319 9007618 6.580000e-72 281
16 TraesCS2D01G561400 chr1D 90.000 150 12 2 2246 2395 478251443 478251297 1.140000e-44 191
17 TraesCS2D01G561400 chr1D 88.125 160 15 4 2239 2397 423279041 423279197 1.480000e-43 187
18 TraesCS2D01G561400 chr1D 96.203 79 3 0 2396 2474 7062224 7062302 2.520000e-26 130
19 TraesCS2D01G561400 chr1D 96.203 79 3 0 2396 2474 453551538 453551460 2.520000e-26 130
20 TraesCS2D01G561400 chr6D 88.000 550 31 13 2494 3011 58897779 58898325 4.420000e-173 617
21 TraesCS2D01G561400 chr6D 85.231 562 35 18 2494 3009 10675046 10674487 4.580000e-148 534
22 TraesCS2D01G561400 chr6D 83.186 565 38 16 2494 3003 300325429 300325991 6.090000e-127 464
23 TraesCS2D01G561400 chr6D 80.627 542 43 13 2494 3003 292724677 292724166 2.280000e-96 363
24 TraesCS2D01G561400 chr6D 90.385 156 14 1 2242 2397 456367253 456367099 1.470000e-48 204
25 TraesCS2D01G561400 chr6D 90.000 150 14 1 2246 2395 58896244 58896392 3.170000e-45 193
26 TraesCS2D01G561400 chr4D 86.727 550 34 17 2494 3007 32247770 32248316 2.700000e-160 575
27 TraesCS2D01G561400 chr4D 86.069 524 50 9 2494 3003 486790572 486791086 2.730000e-150 542
28 TraesCS2D01G561400 chr4D 84.683 568 28 20 2494 3006 81327530 81326967 2.140000e-141 512
29 TraesCS2D01G561400 chr4D 86.111 432 23 6 2494 2890 3506504 3506933 6.180000e-117 431
30 TraesCS2D01G561400 chr4D 85.203 419 35 14 2494 2890 28418702 28418289 3.740000e-109 405
31 TraesCS2D01G561400 chr3D 86.679 548 36 14 2494 3006 40756747 40756202 9.700000e-160 573
32 TraesCS2D01G561400 chr3D 84.561 570 31 18 2494 3008 81741908 81741341 2.140000e-141 512
33 TraesCS2D01G561400 chr3D 96.203 79 3 0 2396 2474 394933387 394933465 2.520000e-26 130
34 TraesCS2D01G561400 chr3D 96.203 79 3 0 2396 2474 556036663 556036741 2.520000e-26 130
35 TraesCS2D01G561400 chr3D 96.203 79 3 0 2396 2474 597309509 597309587 2.520000e-26 130
36 TraesCS2D01G561400 chr6A 84.803 533 56 9 2494 3005 495146439 495146967 2.140000e-141 512
37 TraesCS2D01G561400 chr7A 84.230 539 64 9 2494 3015 251248831 251249365 3.590000e-139 505
38 TraesCS2D01G561400 chr5D 84.854 548 27 21 2494 3006 57214391 57213865 4.640000e-138 501
39 TraesCS2D01G561400 chr5D 90.000 150 14 1 2246 2395 543593411 543593559 3.170000e-45 193
40 TraesCS2D01G561400 chr5A 80.708 565 41 24 2494 3003 411880241 411880792 8.160000e-101 377
41 TraesCS2D01G561400 chr1A 84.936 312 22 12 2716 3005 79171617 79171925 3.040000e-75 292
42 TraesCS2D01G561400 chr4B 90.667 150 14 0 2246 2395 391160796 391160647 1.900000e-47 200
43 TraesCS2D01G561400 chr4B 89.744 156 15 1 2240 2395 52650367 52650521 6.820000e-47 198
44 TraesCS2D01G561400 chr4A 91.216 148 12 1 2246 2393 638282127 638282273 1.900000e-47 200
45 TraesCS2D01G561400 chr5B 97.468 79 2 0 2396 2474 425360622 425360544 5.420000e-28 135
46 TraesCS2D01G561400 chr3B 97.468 79 2 0 2396 2474 132078775 132078697 5.420000e-28 135


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 TraesCS2D01G561400 chr2D 633708958 633712074 3116 True 5757.000000 5757 100.0000 1 3117 1 chr2D.!!$R1 3116
1 TraesCS2D01G561400 chr2D 48168524 48169032 508 False 667.000000 667 90.4580 2494 3006 1 chr2D.!!$F1 512
2 TraesCS2D01G561400 chr2D 67551677 67552191 514 False 508.000000 508 85.1500 2494 3003 1 chr2D.!!$F2 509
3 TraesCS2D01G561400 chr2D 470437671 470438236 565 False 470.000000 470 83.2750 2494 3006 1 chr2D.!!$F3 512
4 TraesCS2D01G561400 chr2B 776707594 776709842 2248 True 3031.000000 3031 91.2970 1 2221 1 chr2B.!!$R1 2220
5 TraesCS2D01G561400 chr2A 779888962 779891744 2782 False 920.333333 2025 89.6620 167 3117 3 chr2A.!!$F1 2950
6 TraesCS2D01G561400 chr7D 266322675 266323220 545 False 590.000000 590 87.2030 2494 3006 1 chr7D.!!$F1 512
7 TraesCS2D01G561400 chr7D 607112319 607114319 2000 False 425.000000 643 90.4505 2241 3006 2 chr7D.!!$F2 765
8 TraesCS2D01G561400 chr1D 453551560 453552066 506 False 628.000000 628 89.2930 2494 3003 1 chr1D.!!$F4 509
9 TraesCS2D01G561400 chr6D 10674487 10675046 559 True 534.000000 534 85.2310 2494 3009 1 chr6D.!!$R1 515
10 TraesCS2D01G561400 chr6D 300325429 300325991 562 False 464.000000 464 83.1860 2494 3003 1 chr6D.!!$F1 509
11 TraesCS2D01G561400 chr6D 58896244 58898325 2081 False 405.000000 617 89.0000 2246 3011 2 chr6D.!!$F2 765
12 TraesCS2D01G561400 chr6D 292724166 292724677 511 True 363.000000 363 80.6270 2494 3003 1 chr6D.!!$R2 509
13 TraesCS2D01G561400 chr4D 32247770 32248316 546 False 575.000000 575 86.7270 2494 3007 1 chr4D.!!$F2 513
14 TraesCS2D01G561400 chr4D 486790572 486791086 514 False 542.000000 542 86.0690 2494 3003 1 chr4D.!!$F3 509
15 TraesCS2D01G561400 chr4D 81326967 81327530 563 True 512.000000 512 84.6830 2494 3006 1 chr4D.!!$R2 512
16 TraesCS2D01G561400 chr3D 40756202 40756747 545 True 573.000000 573 86.6790 2494 3006 1 chr3D.!!$R1 512
17 TraesCS2D01G561400 chr3D 81741341 81741908 567 True 512.000000 512 84.5610 2494 3008 1 chr3D.!!$R2 514
18 TraesCS2D01G561400 chr6A 495146439 495146967 528 False 512.000000 512 84.8030 2494 3005 1 chr6A.!!$F1 511
19 TraesCS2D01G561400 chr7A 251248831 251249365 534 False 505.000000 505 84.2300 2494 3015 1 chr7A.!!$F1 521
20 TraesCS2D01G561400 chr5D 57213865 57214391 526 True 501.000000 501 84.8540 2494 3006 1 chr5D.!!$R1 512
21 TraesCS2D01G561400 chr5A 411880241 411880792 551 False 377.000000 377 80.7080 2494 3003 1 chr5A.!!$F1 509

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
994 1327 0.466189 ACCAACTTGACACCAGCCAG 60.466 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 2768 0.03918 TTGTGAGAGGACCGGCTAGA 59.961 55.0 0.0 0.0 0.0 2.43 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
79 83 3.085443 AGCAAGACCTTCATCGTATCG 57.915 47.619 0.00 0.00 0.00 2.92
112 116 6.147985 AGCTAAAAAGTACTACTTGCAAGAGC 59.852 38.462 32.50 23.17 38.66 4.09
228 233 1.706287 GCCGCCGTTGAGAATCTTCC 61.706 60.000 0.00 0.00 34.92 3.46
269 291 3.098958 CACACGCGTTGCCAATGC 61.099 61.111 10.22 11.64 40.02 3.56
409 437 0.582960 CAACCACCGGTCAACGTAAC 59.417 55.000 2.59 0.00 42.24 2.50
423 451 2.063266 ACGTAACCACACACGCTTATG 58.937 47.619 0.00 0.00 41.80 1.90
424 452 1.201877 CGTAACCACACACGCTTATGC 60.202 52.381 0.00 0.00 0.00 3.14
553 595 1.195115 GACAGTGCTGAGGTATCCCA 58.805 55.000 6.17 0.00 0.00 4.37
559 601 2.105477 GTGCTGAGGTATCCCATGACAT 59.895 50.000 0.00 0.00 0.00 3.06
642 828 2.384382 GTTGCAACCATTCAACACGAG 58.616 47.619 19.15 0.00 41.46 4.18
646 832 2.436417 CAACCATTCAACACGAGGGAT 58.564 47.619 0.00 0.00 0.00 3.85
710 1001 1.195115 TGCCTAGCTCGATGGAAACT 58.805 50.000 0.00 0.00 0.00 2.66
777 1076 2.608752 GCACATGGAGCCAGAAAAGTTG 60.609 50.000 0.00 0.00 0.00 3.16
799 1116 6.147864 TGACACAAAATTTCTGGAAAGAGG 57.852 37.500 0.00 0.00 33.32 3.69
833 1150 3.982475 TGAGAACAGAGACACATGTGAC 58.018 45.455 31.94 25.13 0.00 3.67
836 1153 2.140065 ACAGAGACACATGTGACACG 57.860 50.000 31.94 19.92 0.00 4.49
895 1212 3.015293 AAGTCAATCACGCGCGCAG 62.015 57.895 32.58 24.87 0.00 5.18
954 1286 6.120507 AGCTCCAACATCTAGAAAGAAACT 57.879 37.500 0.00 0.00 34.73 2.66
994 1327 0.466189 ACCAACTTGACACCAGCCAG 60.466 55.000 0.00 0.00 0.00 4.85
995 1328 1.656441 CAACTTGACACCAGCCAGC 59.344 57.895 0.00 0.00 0.00 4.85
996 1329 1.529244 AACTTGACACCAGCCAGCC 60.529 57.895 0.00 0.00 0.00 4.85
997 1330 2.113774 CTTGACACCAGCCAGCCA 59.886 61.111 0.00 0.00 0.00 4.75
1053 1386 1.369625 CCACTACATCGGTGGCTTTC 58.630 55.000 0.00 0.00 45.97 2.62
1072 1405 6.416514 GCTTTCAACATTTTCTTTCTGCAAG 58.583 36.000 0.00 0.00 0.00 4.01
1124 1457 1.267806 GCTGTAAGAAGCAAGCAAGCA 59.732 47.619 3.19 0.00 43.01 3.91
1125 1458 2.287788 GCTGTAAGAAGCAAGCAAGCAA 60.288 45.455 3.19 0.00 43.01 3.91
1126 1459 3.562505 CTGTAAGAAGCAAGCAAGCAAG 58.437 45.455 3.19 0.00 34.07 4.01
1127 1460 2.287788 TGTAAGAAGCAAGCAAGCAAGC 60.288 45.455 3.19 0.00 36.85 4.01
1128 1461 0.748450 AAGAAGCAAGCAAGCAAGCA 59.252 45.000 10.52 0.00 36.85 3.91
1129 1462 0.748450 AGAAGCAAGCAAGCAAGCAA 59.252 45.000 10.52 0.00 36.85 3.91
1130 1463 0.857287 GAAGCAAGCAAGCAAGCAAC 59.143 50.000 10.52 2.01 36.85 4.17
1131 1464 0.462789 AAGCAAGCAAGCAAGCAACT 59.537 45.000 10.52 0.00 36.85 3.16
1142 1475 2.010497 GCAAGCAACTAGGAGCTAACC 58.990 52.381 11.02 0.00 40.90 2.85
1157 1490 0.976641 TAACCAGCCAGTCAGGTGAG 59.023 55.000 0.00 0.00 40.61 3.51
1249 1582 1.453155 AACAAGGATAAGCTGCCACG 58.547 50.000 0.00 0.00 0.00 4.94
1395 1728 1.079612 CTGGTGCTGATCGTGCTCA 60.080 57.895 11.02 8.64 0.00 4.26
1542 1875 2.738521 CGTTCGAGGTGCAGGTGG 60.739 66.667 0.00 0.00 0.00 4.61
1544 1877 1.668151 GTTCGAGGTGCAGGTGGTC 60.668 63.158 0.00 0.00 0.00 4.02
1545 1878 3.220999 TTCGAGGTGCAGGTGGTCG 62.221 63.158 0.00 0.00 0.00 4.79
1819 2152 2.032528 CGCCCTCAAGCTGTGGAA 59.967 61.111 0.00 0.00 33.04 3.53
1835 2168 1.153147 GAAGATGACGGGGAAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
1836 2169 1.910580 GAAGATGACGGGGAAGGCCA 61.911 60.000 5.01 0.00 35.15 5.36
1837 2170 2.124695 GATGACGGGGAAGGCCAC 60.125 66.667 5.01 0.00 35.15 5.01
2032 2371 6.030849 CCGTTCCTGTCGATCTATATTGATC 58.969 44.000 14.87 14.87 39.40 2.92
2165 2510 6.992063 TTTGCTATGAATTTCTCTGGAGAC 57.008 37.500 0.00 0.00 37.14 3.36
2194 2539 7.684937 ATAAAGAGAAGATATTGGCTCATGC 57.315 36.000 0.00 0.00 38.76 4.06
2203 2548 0.109153 TTGGCTCATGCACACAGTCT 59.891 50.000 0.00 0.00 41.91 3.24
2204 2549 0.109153 TGGCTCATGCACACAGTCTT 59.891 50.000 0.00 0.00 41.91 3.01
2205 2550 0.520404 GGCTCATGCACACAGTCTTG 59.480 55.000 0.00 0.00 41.91 3.02
2235 2580 3.699038 GGTTTTCAGGCTTATGCACCATA 59.301 43.478 2.72 0.00 41.91 2.74
2236 2581 4.202050 GGTTTTCAGGCTTATGCACCATAG 60.202 45.833 2.72 0.00 41.91 2.23
2237 2582 3.931907 TTCAGGCTTATGCACCATAGT 57.068 42.857 2.72 0.00 41.91 2.12
2238 2583 3.931907 TCAGGCTTATGCACCATAGTT 57.068 42.857 2.72 0.00 41.91 2.24
2239 2584 3.544684 TCAGGCTTATGCACCATAGTTG 58.455 45.455 2.72 0.00 41.91 3.16
2244 2589 4.520492 GGCTTATGCACCATAGTTGCTTAT 59.480 41.667 2.72 0.00 41.91 1.73
2262 2607 0.833287 ATAGCATCTCCAACAGCCGT 59.167 50.000 0.00 0.00 0.00 5.68
2291 2636 3.887777 CGTCGCGCCATAAAATTGA 57.112 47.368 0.00 0.00 0.00 2.57
2292 2637 2.383298 CGTCGCGCCATAAAATTGAT 57.617 45.000 0.00 0.00 0.00 2.57
2303 2648 6.417635 CGCCATAAAATTGATCATTTTAGCGT 59.582 34.615 24.98 13.75 46.12 5.07
2395 2740 2.813908 GCCGAAACTCCATCGCGT 60.814 61.111 5.77 0.00 38.93 6.01
2397 2742 1.736645 CCGAAACTCCATCGCGTGT 60.737 57.895 5.77 0.00 38.93 4.49
2398 2743 0.457166 CCGAAACTCCATCGCGTGTA 60.457 55.000 5.77 0.00 38.93 2.90
2399 2744 0.638746 CGAAACTCCATCGCGTGTAC 59.361 55.000 5.77 0.00 33.07 2.90
2401 2746 0.319083 AAACTCCATCGCGTGTACCA 59.681 50.000 5.77 0.00 0.00 3.25
2402 2747 0.319083 AACTCCATCGCGTGTACCAA 59.681 50.000 5.77 0.00 0.00 3.67
2404 2749 0.999406 CTCCATCGCGTGTACCAAAG 59.001 55.000 5.77 0.00 0.00 2.77
2405 2750 1.017177 TCCATCGCGTGTACCAAAGC 61.017 55.000 5.77 0.00 0.00 3.51
2406 2751 1.295357 CCATCGCGTGTACCAAAGCA 61.295 55.000 5.77 0.00 0.00 3.91
2407 2752 0.726827 CATCGCGTGTACCAAAGCAT 59.273 50.000 5.77 0.00 0.00 3.79
2410 2755 0.796312 CGCGTGTACCAAAGCATCTT 59.204 50.000 0.00 0.00 0.00 2.40
2412 2757 2.350388 CGCGTGTACCAAAGCATCTTTT 60.350 45.455 0.00 0.00 0.00 2.27
2413 2758 2.979813 GCGTGTACCAAAGCATCTTTTG 59.020 45.455 0.00 0.00 37.70 2.44
2414 2759 3.304391 GCGTGTACCAAAGCATCTTTTGA 60.304 43.478 0.37 0.00 39.79 2.69
2415 2760 4.615912 GCGTGTACCAAAGCATCTTTTGAT 60.616 41.667 0.37 0.00 39.79 2.57
2416 2761 5.088739 CGTGTACCAAAGCATCTTTTGATC 58.911 41.667 0.37 0.00 39.79 2.92
2419 2764 6.374333 GTGTACCAAAGCATCTTTTGATCCTA 59.626 38.462 0.37 0.00 39.79 2.94
2420 2765 6.945435 TGTACCAAAGCATCTTTTGATCCTAA 59.055 34.615 0.37 0.00 39.79 2.69
2421 2766 6.916360 ACCAAAGCATCTTTTGATCCTAAA 57.084 33.333 0.37 0.00 39.79 1.85
2422 2767 7.301868 ACCAAAGCATCTTTTGATCCTAAAA 57.698 32.000 0.37 0.00 39.79 1.52
2423 2768 7.910584 ACCAAAGCATCTTTTGATCCTAAAAT 58.089 30.769 0.37 0.00 39.79 1.82
2424 2769 8.037166 ACCAAAGCATCTTTTGATCCTAAAATC 58.963 33.333 0.37 0.00 39.79 2.17
2425 2770 8.255905 CCAAAGCATCTTTTGATCCTAAAATCT 58.744 33.333 0.37 0.00 39.79 2.40
2428 2773 8.164058 AGCATCTTTTGATCCTAAAATCTAGC 57.836 34.615 0.00 0.00 36.97 3.42
2429 2774 7.230309 AGCATCTTTTGATCCTAAAATCTAGCC 59.770 37.037 0.00 0.00 36.97 3.93
2431 2776 6.055588 TCTTTTGATCCTAAAATCTAGCCGG 58.944 40.000 0.00 0.00 0.00 6.13
2432 2777 5.367945 TTTGATCCTAAAATCTAGCCGGT 57.632 39.130 1.90 0.00 0.00 5.28
2433 2778 4.602340 TGATCCTAAAATCTAGCCGGTC 57.398 45.455 1.90 0.00 0.00 4.79
2437 2782 2.966516 CCTAAAATCTAGCCGGTCCTCT 59.033 50.000 1.90 0.00 0.00 3.69
2439 2784 2.160721 AAATCTAGCCGGTCCTCTCA 57.839 50.000 1.90 0.00 0.00 3.27
2441 2786 0.259065 ATCTAGCCGGTCCTCTCACA 59.741 55.000 1.90 0.00 0.00 3.58
2442 2787 0.039180 TCTAGCCGGTCCTCTCACAA 59.961 55.000 1.90 0.00 0.00 3.33
2444 2789 2.092049 TCTAGCCGGTCCTCTCACAATA 60.092 50.000 1.90 0.00 0.00 1.90
2445 2790 1.115467 AGCCGGTCCTCTCACAATAG 58.885 55.000 1.90 0.00 0.00 1.73
2450 4101 3.535561 CGGTCCTCTCACAATAGCAAAT 58.464 45.455 0.00 0.00 0.00 2.32
2451 4102 3.941483 CGGTCCTCTCACAATAGCAAATT 59.059 43.478 0.00 0.00 0.00 1.82
2452 4103 4.201851 CGGTCCTCTCACAATAGCAAATTG 60.202 45.833 9.54 9.54 35.29 2.32
2454 4105 4.096984 GTCCTCTCACAATAGCAAATTGGG 59.903 45.833 14.18 11.06 33.91 4.12
2455 4106 3.181483 CCTCTCACAATAGCAAATTGGGC 60.181 47.826 14.18 0.00 32.72 5.36
2467 4118 3.609879 GCAAATTGGGCTTGCAAAATCAC 60.610 43.478 0.00 0.00 46.78 3.06
2468 4119 3.488778 AATTGGGCTTGCAAAATCACA 57.511 38.095 0.00 0.00 0.00 3.58
2471 4122 1.483827 TGGGCTTGCAAAATCACACAA 59.516 42.857 0.00 0.00 0.00 3.33
2485 4136 3.301352 CACAAGCGTGCATGATCAC 57.699 52.632 10.93 0.00 36.06 3.06
2486 4137 0.518195 CACAAGCGTGCATGATCACA 59.482 50.000 10.93 0.00 36.06 3.58
2487 4138 0.518636 ACAAGCGTGCATGATCACAC 59.481 50.000 10.93 1.49 36.80 3.82
2488 4139 0.518195 CAAGCGTGCATGATCACACA 59.482 50.000 10.93 6.37 36.57 3.72
2489 4140 1.069091 CAAGCGTGCATGATCACACAA 60.069 47.619 10.93 0.00 36.57 3.33
2490 4141 0.800631 AGCGTGCATGATCACACAAG 59.199 50.000 10.93 11.33 36.57 3.16
2491 4142 0.795735 GCGTGCATGATCACACAAGC 60.796 55.000 17.56 17.56 36.57 4.01
2492 4143 0.519792 CGTGCATGATCACACAAGCG 60.520 55.000 14.69 6.41 36.57 4.68
2621 4285 1.544246 CCTATCATGCCATCCGACGTA 59.456 52.381 0.00 0.00 0.00 3.57
2622 4286 2.029380 CCTATCATGCCATCCGACGTAA 60.029 50.000 0.00 0.00 0.00 3.18
2723 4452 7.789341 TTTGTGCGTTTGATGTTGTATTATC 57.211 32.000 0.00 0.00 0.00 1.75
2835 4609 7.600375 TGTGTTTGATCTTTTTGCTTGTGTTTA 59.400 29.630 0.00 0.00 0.00 2.01
2915 4815 2.579201 GCGGCTGCTGGAGTTAGA 59.421 61.111 11.21 0.00 38.39 2.10
3037 4994 4.899239 GGCGGGGCGTCATGAGAG 62.899 72.222 0.00 0.00 0.00 3.20
3039 4996 3.461773 CGGGGCGTCATGAGAGGT 61.462 66.667 0.00 0.00 32.37 3.85
3067 5028 4.821805 GTCCAGAATCAGTTCCAAAGTTCA 59.178 41.667 0.00 0.00 34.81 3.18
3098 5065 3.442273 CGCACCTAGCCAAATTCCTTTAA 59.558 43.478 0.00 0.00 41.38 1.52
3101 5068 5.650703 GCACCTAGCCAAATTCCTTTAACTA 59.349 40.000 0.00 0.00 37.23 2.24
3109 5076 7.122799 AGCCAAATTCCTTTAACTACTCCAATC 59.877 37.037 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 21 1.069513 TCAGTTTGTACCGGTGGAGTG 59.930 52.381 19.93 12.83 0.00 3.51
79 83 0.167251 TACTTTTTAGCTTGCGCCGC 59.833 50.000 4.18 0.00 36.60 6.53
228 233 8.173130 GTGTTTCAAGTAATAATCCCGTGTTAG 58.827 37.037 0.00 0.00 0.00 2.34
269 291 2.480419 ACCTTTCTCTTTCACATTCGCG 59.520 45.455 0.00 0.00 0.00 5.87
424 452 4.383861 TCTCAGCCGTGCAGCCAG 62.384 66.667 0.00 0.00 0.00 4.85
529 571 0.538746 TACCTCAGCACTGTCGTGGA 60.539 55.000 0.00 0.00 41.51 4.02
553 595 4.124970 CACAACGATCTCCATCATGTCAT 58.875 43.478 0.00 0.00 30.10 3.06
642 828 1.327764 GTTGCACTTCGATCGAATCCC 59.672 52.381 29.22 19.40 33.28 3.85
646 832 0.781787 CACGTTGCACTTCGATCGAA 59.218 50.000 27.54 27.54 0.00 3.71
777 1076 4.984785 GCCTCTTTCCAGAAATTTTGTGTC 59.015 41.667 5.66 0.00 0.00 3.67
833 1150 0.591236 CGTTTGAAACAGTGGCCGTG 60.591 55.000 8.93 0.00 0.00 4.94
836 1153 1.673920 TCTTCGTTTGAAACAGTGGCC 59.326 47.619 8.93 0.00 32.66 5.36
954 1286 1.723608 CGTTGGTTGGTGCTGCTTGA 61.724 55.000 0.00 0.00 0.00 3.02
994 1327 4.278419 GGGTCCAAGTTTATATGTGATGGC 59.722 45.833 0.00 0.00 0.00 4.40
995 1328 4.515191 CGGGTCCAAGTTTATATGTGATGG 59.485 45.833 0.00 0.00 0.00 3.51
996 1329 5.364778 TCGGGTCCAAGTTTATATGTGATG 58.635 41.667 0.00 0.00 0.00 3.07
997 1330 5.623956 TCGGGTCCAAGTTTATATGTGAT 57.376 39.130 0.00 0.00 0.00 3.06
1053 1386 4.121317 TGGCTTGCAGAAAGAAAATGTTG 58.879 39.130 0.00 0.00 38.24 3.33
1072 1405 2.467826 GCTCGCAGGATGAACTGGC 61.468 63.158 0.00 0.00 39.69 4.85
1124 1457 2.355209 GCTGGTTAGCTCCTAGTTGCTT 60.355 50.000 11.18 0.00 46.57 3.91
1125 1458 1.208293 GCTGGTTAGCTCCTAGTTGCT 59.792 52.381 10.80 10.80 46.57 3.91
1126 1459 1.657822 GCTGGTTAGCTCCTAGTTGC 58.342 55.000 0.00 0.00 46.57 4.17
1142 1475 0.902048 TCTCCTCACCTGACTGGCTG 60.902 60.000 0.00 0.00 40.22 4.85
1157 1490 0.817229 GGTAGCTTGCCATGCTCTCC 60.817 60.000 8.52 9.21 41.46 3.71
1223 1556 3.192212 GCAGCTTATCCTTGTTTTGCTCT 59.808 43.478 0.00 0.00 0.00 4.09
1261 1594 4.944372 GCCGGTCGCCATAGTCGG 62.944 72.222 1.90 0.00 43.13 4.79
1264 1597 4.530857 GCAGCCGGTCGCCATAGT 62.531 66.667 1.90 0.00 38.78 2.12
1442 1775 1.749258 GAACGTGGGGATCTTGGGC 60.749 63.158 0.00 0.00 0.00 5.36
1542 1875 2.808321 GTTCGGGTTCTCGGCGAC 60.808 66.667 4.99 0.00 0.00 5.19
1604 1937 2.665185 AGCTCCGTGCCGTTGAAC 60.665 61.111 0.00 0.00 44.23 3.18
1679 2012 2.764128 TCCCCCTGGAGCGTGATC 60.764 66.667 0.00 0.00 35.03 2.92
1784 2117 0.657840 CGCCAAACTTGATCCGGATC 59.342 55.000 33.41 33.41 38.29 3.36
1790 2123 0.960364 TGAGGGCGCCAAACTTGATC 60.960 55.000 30.85 12.31 0.00 2.92
1819 2152 2.285368 TGGCCTTCCCCGTCATCT 60.285 61.111 3.32 0.00 0.00 2.90
1835 2168 1.667830 CACCACCAGGCTACACGTG 60.668 63.158 15.48 15.48 39.06 4.49
1836 2169 2.741092 CACCACCAGGCTACACGT 59.259 61.111 0.00 0.00 39.06 4.49
1837 2170 2.047274 CCACCACCAGGCTACACG 60.047 66.667 0.00 0.00 39.06 4.49
2032 2371 0.455802 CCATCTGCCGATCGATCTCG 60.456 60.000 22.43 12.40 41.45 4.04
2141 2485 6.259608 CGTCTCCAGAGAAATTCATAGCAAAT 59.740 38.462 0.00 0.00 39.48 2.32
2165 2510 9.645059 TGAGCCAATATCTTCTCTTTATTATCG 57.355 33.333 0.00 0.00 0.00 2.92
2203 2548 1.203523 GCCTGAAAACCACACACACAA 59.796 47.619 0.00 0.00 0.00 3.33
2204 2549 0.814457 GCCTGAAAACCACACACACA 59.186 50.000 0.00 0.00 0.00 3.72
2205 2550 1.102978 AGCCTGAAAACCACACACAC 58.897 50.000 0.00 0.00 0.00 3.82
2239 2584 2.810852 GGCTGTTGGAGATGCTATAAGC 59.189 50.000 0.00 0.00 42.82 3.09
2244 2589 0.108186 CACGGCTGTTGGAGATGCTA 60.108 55.000 0.00 0.00 0.00 3.49
2275 2620 4.566545 AATGATCAATTTTATGGCGCGA 57.433 36.364 12.10 0.00 0.00 5.87
2282 2627 6.074888 GCGCACGCTAAAATGATCAATTTTAT 60.075 34.615 13.74 2.87 45.36 1.40
2283 2628 5.229052 GCGCACGCTAAAATGATCAATTTTA 59.771 36.000 13.74 15.06 45.63 1.52
2291 2636 4.974468 CGCGCACGCTAAAATGAT 57.026 50.000 13.70 0.00 39.32 2.45
2303 2648 2.582226 CTCTACCGATTGCGCGCA 60.582 61.111 33.09 33.09 35.83 6.09
2344 2689 4.830765 ATATGCCACGTGCGCGGT 62.831 61.111 25.20 6.78 45.60 5.68
2346 2691 1.608966 CTAGATATGCCACGTGCGCG 61.609 60.000 19.78 19.78 45.60 6.86
2347 2692 0.597637 ACTAGATATGCCACGTGCGC 60.598 55.000 18.49 18.49 45.60 6.09
2348 2693 1.787155 GAACTAGATATGCCACGTGCG 59.213 52.381 10.91 4.74 45.60 5.34
2349 2694 2.797156 CTGAACTAGATATGCCACGTGC 59.203 50.000 10.91 6.53 41.77 5.34
2350 2695 2.797156 GCTGAACTAGATATGCCACGTG 59.203 50.000 9.08 9.08 0.00 4.49
2351 2696 2.543861 CGCTGAACTAGATATGCCACGT 60.544 50.000 0.00 0.00 0.00 4.49
2352 2697 2.054363 CGCTGAACTAGATATGCCACG 58.946 52.381 0.00 0.00 0.00 4.94
2353 2698 1.795286 GCGCTGAACTAGATATGCCAC 59.205 52.381 0.00 0.00 0.00 5.01
2354 2699 1.602920 CGCGCTGAACTAGATATGCCA 60.603 52.381 5.56 0.00 0.00 4.92
2395 2740 5.324409 AGGATCAAAAGATGCTTTGGTACA 58.676 37.500 0.00 0.00 33.31 2.90
2397 2742 8.415950 TTTTAGGATCAAAAGATGCTTTGGTA 57.584 30.769 4.85 0.00 37.00 3.25
2398 2743 6.916360 TTTAGGATCAAAAGATGCTTTGGT 57.084 33.333 4.85 0.00 37.00 3.67
2399 2744 8.255905 AGATTTTAGGATCAAAAGATGCTTTGG 58.744 33.333 4.85 0.00 37.00 3.28
2402 2747 8.628280 GCTAGATTTTAGGATCAAAAGATGCTT 58.372 33.333 4.85 0.00 34.98 3.91
2404 2749 7.366513 GGCTAGATTTTAGGATCAAAAGATGC 58.633 38.462 0.00 0.00 31.29 3.91
2405 2750 7.308229 CCGGCTAGATTTTAGGATCAAAAGATG 60.308 40.741 0.00 0.00 31.29 2.90
2406 2751 6.712547 CCGGCTAGATTTTAGGATCAAAAGAT 59.287 38.462 0.00 0.00 31.29 2.40
2407 2752 6.055588 CCGGCTAGATTTTAGGATCAAAAGA 58.944 40.000 0.00 0.00 31.29 2.52
2410 2755 5.365619 GACCGGCTAGATTTTAGGATCAAA 58.634 41.667 0.00 0.00 0.00 2.69
2412 2757 3.323979 GGACCGGCTAGATTTTAGGATCA 59.676 47.826 0.00 0.00 0.00 2.92
2413 2758 3.579151 AGGACCGGCTAGATTTTAGGATC 59.421 47.826 0.00 0.00 0.00 3.36
2414 2759 3.579151 GAGGACCGGCTAGATTTTAGGAT 59.421 47.826 0.00 0.00 0.00 3.24
2415 2760 2.963782 GAGGACCGGCTAGATTTTAGGA 59.036 50.000 0.00 0.00 0.00 2.94
2416 2761 2.966516 AGAGGACCGGCTAGATTTTAGG 59.033 50.000 0.00 0.00 0.00 2.69
2419 2764 2.168728 GTGAGAGGACCGGCTAGATTTT 59.831 50.000 0.00 0.00 0.00 1.82
2420 2765 1.757699 GTGAGAGGACCGGCTAGATTT 59.242 52.381 0.00 0.00 0.00 2.17
2421 2766 1.342076 TGTGAGAGGACCGGCTAGATT 60.342 52.381 0.00 0.00 0.00 2.40
2422 2767 0.259065 TGTGAGAGGACCGGCTAGAT 59.741 55.000 0.00 0.00 0.00 1.98
2423 2768 0.039180 TTGTGAGAGGACCGGCTAGA 59.961 55.000 0.00 0.00 0.00 2.43
2424 2769 1.115467 ATTGTGAGAGGACCGGCTAG 58.885 55.000 0.00 0.00 0.00 3.42
2425 2770 2.307768 CTATTGTGAGAGGACCGGCTA 58.692 52.381 0.00 0.00 0.00 3.93
2426 2771 1.115467 CTATTGTGAGAGGACCGGCT 58.885 55.000 0.00 0.00 0.00 5.52
2427 2772 0.530870 GCTATTGTGAGAGGACCGGC 60.531 60.000 0.00 0.00 0.00 6.13
2428 2773 0.824109 TGCTATTGTGAGAGGACCGG 59.176 55.000 0.00 0.00 0.00 5.28
2429 2774 2.672961 TTGCTATTGTGAGAGGACCG 57.327 50.000 0.00 0.00 0.00 4.79
2431 2776 4.096984 CCCAATTTGCTATTGTGAGAGGAC 59.903 45.833 10.03 0.00 0.00 3.85
2432 2777 4.272489 CCCAATTTGCTATTGTGAGAGGA 58.728 43.478 10.03 0.00 0.00 3.71
2433 2778 3.181483 GCCCAATTTGCTATTGTGAGAGG 60.181 47.826 10.03 5.98 0.00 3.69
2437 2782 3.617045 GCAAGCCCAATTTGCTATTGTGA 60.617 43.478 10.03 0.00 45.64 3.58
2439 2784 2.976589 GCAAGCCCAATTTGCTATTGT 58.023 42.857 10.03 0.00 45.64 2.71
2450 4101 1.483827 TGTGTGATTTTGCAAGCCCAA 59.516 42.857 0.00 0.00 0.00 4.12
2451 4102 1.117994 TGTGTGATTTTGCAAGCCCA 58.882 45.000 0.00 0.00 0.00 5.36
2452 4103 2.137523 CTTGTGTGATTTTGCAAGCCC 58.862 47.619 0.00 0.00 33.14 5.19
2455 4106 2.216940 CACGCTTGTGTGATTTTGCAAG 59.783 45.455 8.46 0.00 42.55 4.01
2459 4110 1.837648 TGCACGCTTGTGTGATTTTG 58.162 45.000 17.16 0.00 45.65 2.44
2460 4111 2.034432 TCATGCACGCTTGTGTGATTTT 59.966 40.909 17.16 0.00 45.65 1.82
2462 4113 1.237533 TCATGCACGCTTGTGTGATT 58.762 45.000 17.16 1.77 45.65 2.57
2467 4118 0.518195 TGTGATCATGCACGCTTGTG 59.482 50.000 0.00 0.00 46.67 3.33
2468 4119 0.518636 GTGTGATCATGCACGCTTGT 59.481 50.000 0.00 0.00 43.87 3.16
2471 4122 0.800631 CTTGTGTGATCATGCACGCT 59.199 50.000 15.18 0.00 46.53 5.07
2474 4125 0.518636 ACGCTTGTGTGATCATGCAC 59.481 50.000 9.04 9.04 38.03 4.57
2477 4128 0.518195 TGCACGCTTGTGTGATCATG 59.482 50.000 17.16 0.00 45.65 3.07
2478 4129 0.518636 GTGCACGCTTGTGTGATCAT 59.481 50.000 17.16 0.00 45.65 2.45
2485 4136 2.898181 TCATATTGTGCACGCTTGTG 57.102 45.000 13.13 7.99 46.67 3.33
2486 4137 3.009026 TGATCATATTGTGCACGCTTGT 58.991 40.909 13.13 0.00 0.00 3.16
2487 4138 3.678915 TGATCATATTGTGCACGCTTG 57.321 42.857 13.13 7.40 0.00 4.01
2488 4139 3.059393 CGATGATCATATTGTGCACGCTT 60.059 43.478 13.13 1.60 0.00 4.68
2489 4140 2.477754 CGATGATCATATTGTGCACGCT 59.522 45.455 13.13 4.16 0.00 5.07
2490 4141 2.476241 TCGATGATCATATTGTGCACGC 59.524 45.455 13.13 0.00 0.00 5.34
2491 4142 3.983344 TCTCGATGATCATATTGTGCACG 59.017 43.478 13.13 5.53 0.00 5.34
2492 4143 5.912360 TTCTCGATGATCATATTGTGCAC 57.088 39.130 10.75 10.75 0.00 4.57
2621 4285 2.885676 GATCATCATGCGCCGCGTT 61.886 57.895 15.34 0.00 0.00 4.84
2622 4286 3.341043 GATCATCATGCGCCGCGT 61.341 61.111 15.34 0.00 0.00 6.01
2723 4452 9.961266 TTATCGTTCAATACAACAAATAGTTCG 57.039 29.630 0.00 0.00 38.74 3.95
2835 4609 4.082841 TCGCACAAACAACATATGCATTCT 60.083 37.500 3.54 0.00 36.02 2.40
3036 4993 0.916358 CTGATTCTGGACCCCCACCT 60.916 60.000 0.00 0.00 37.58 4.00
3037 4994 1.208165 ACTGATTCTGGACCCCCACC 61.208 60.000 0.00 0.00 37.58 4.61
3039 4996 0.991920 GAACTGATTCTGGACCCCCA 59.008 55.000 0.00 0.00 40.95 4.96
3067 5028 0.392595 GGCTAGGTGCGGCTTAACTT 60.393 55.000 0.00 0.00 44.05 2.66


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

AutoCloner maintained by Alex Coulton.