Multiple sequence alignment - TraesCS7D01G489900

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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 TraesCS7D01G489900 chr7D 100.000 3427 0 0 1 3427 599400008 599396582 0.000000e+00 6329.0
1 TraesCS7D01G489900 chr7D 79.660 1765 271 57 686 2397 599193806 599192077 0.000000e+00 1190.0
2 TraesCS7D01G489900 chr7D 80.510 549 91 13 1056 1596 599269169 599268629 1.140000e-109 407.0
3 TraesCS7D01G489900 chr7D 83.904 292 16 7 100 374 240638441 240638164 2.040000e-62 250.0
4 TraesCS7D01G489900 chr7D 99.029 103 1 0 3325 3427 390861369 390861471 5.840000e-43 185.0
5 TraesCS7D01G489900 chr7D 94.340 106 6 0 3322 3427 579340672 579340777 2.740000e-36 163.0
6 TraesCS7D01G489900 chr7D 78.327 263 35 14 464 708 599193806 599193548 2.130000e-32 150.0
7 TraesCS7D01G489900 chr7D 91.262 103 9 0 3325 3427 78629392 78629494 1.280000e-29 141.0
8 TraesCS7D01G489900 chr7A 94.255 2646 115 20 1 2614 691523678 691521038 0.000000e+00 4010.0
9 TraesCS7D01G489900 chr7A 90.629 1526 112 9 967 2463 691675678 691677201 0.000000e+00 1997.0
10 TraesCS7D01G489900 chr7A 92.291 467 31 3 2612 3075 691516097 691515633 0.000000e+00 658.0
11 TraesCS7D01G489900 chr7A 90.816 392 22 4 382 770 691674630 691675010 2.360000e-141 512.0
12 TraesCS7D01G489900 chr7A 95.652 253 10 1 3074 3325 691515579 691515327 4.120000e-109 405.0
13 TraesCS7D01G489900 chr7A 81.150 313 30 18 512 812 691523085 691522790 1.240000e-54 224.0
14 TraesCS7D01G489900 chr7A 82.353 238 27 9 161 388 691674110 691674342 3.490000e-45 193.0
15 TraesCS7D01G489900 chr7A 81.739 230 39 2 1056 1282 691474063 691473834 4.510000e-44 189.0
16 TraesCS7D01G489900 chr7A 77.947 263 36 14 464 708 691448630 691448372 9.910000e-31 145.0
17 TraesCS7D01G489900 chr7B 95.996 1948 74 2 530 2474 678737123 678735177 0.000000e+00 3162.0
18 TraesCS7D01G489900 chr7B 92.353 1713 122 6 765 2472 678850657 678852365 0.000000e+00 2429.0
19 TraesCS7D01G489900 chr7B 80.411 1460 223 38 1056 2469 678664033 678662591 0.000000e+00 1053.0
20 TraesCS7D01G489900 chr7B 89.591 538 40 9 185 716 678849529 678850056 0.000000e+00 669.0
21 TraesCS7D01G489900 chr7B 89.069 494 29 7 1 494 678738004 678737536 1.060000e-164 590.0
22 TraesCS7D01G489900 chr7B 77.539 837 137 38 686 1498 678648391 678647582 1.120000e-124 457.0
23 TraesCS7D01G489900 chr7B 83.924 367 44 11 512 866 678737073 678736710 1.520000e-88 337.0
24 TraesCS7D01G489900 chr7B 87.845 181 18 2 613 789 678850657 678850837 3.470000e-50 209.0
25 TraesCS7D01G489900 chr7B 86.188 181 22 2 689 866 678850657 678850837 3.490000e-45 193.0
26 TraesCS7D01G489900 chr7B 94.175 103 6 0 3325 3427 614613927 614613825 1.270000e-34 158.0
27 TraesCS7D01G489900 chr7B 77.186 263 39 13 464 708 678648391 678648132 2.150000e-27 134.0
28 TraesCS7D01G489900 chr7B 100.000 42 0 0 492 533 678737375 678737334 1.020000e-10 78.7
29 TraesCS7D01G489900 chr6A 94.020 602 36 0 2474 3075 447799833 447799232 0.000000e+00 913.0
30 TraesCS7D01G489900 chr6A 93.586 608 38 1 2469 3075 572774825 572775432 0.000000e+00 905.0
31 TraesCS7D01G489900 chr6A 93.522 602 39 0 2474 3075 447804741 447804140 0.000000e+00 896.0
32 TraesCS7D01G489900 chr6A 93.092 608 40 2 2469 3075 572760853 572761459 0.000000e+00 889.0
33 TraesCS7D01G489900 chr6A 92.447 609 44 2 2469 3075 572768094 572768702 0.000000e+00 869.0
34 TraesCS7D01G489900 chr6A 91.694 602 42 2 2474 3075 447802273 447801680 0.000000e+00 828.0
35 TraesCS7D01G489900 chr6A 91.820 599 41 2 2477 3075 447807196 447806606 0.000000e+00 828.0
36 TraesCS7D01G489900 chr6A 96.047 253 9 1 3074 3325 447799178 447798926 8.850000e-111 411.0
37 TraesCS7D01G489900 chr6A 96.032 252 10 0 3074 3325 447804086 447803835 8.850000e-111 411.0
38 TraesCS7D01G489900 chr6A 96.032 252 9 1 3074 3325 447806552 447806302 3.180000e-110 409.0
39 TraesCS7D01G489900 chr6A 95.238 252 12 0 3074 3325 447801626 447801375 1.920000e-107 399.0
40 TraesCS7D01G489900 chr6A 95.238 252 12 0 3074 3325 572761513 572761764 1.920000e-107 399.0
41 TraesCS7D01G489900 chr6A 95.238 252 12 0 3074 3325 572768756 572769007 1.920000e-107 399.0
42 TraesCS7D01G489900 chr6A 95.238 252 12 0 3074 3325 572775486 572775737 1.920000e-107 399.0
43 TraesCS7D01G489900 chr1A 93.226 561 38 0 2515 3075 50521545 50522105 0.000000e+00 826.0
44 TraesCS7D01G489900 chr1A 96.047 253 9 1 3074 3325 50522159 50522411 8.850000e-111 411.0
45 TraesCS7D01G489900 chr1A 91.346 104 7 2 3325 3427 561391258 561391156 1.280000e-29 141.0
46 TraesCS7D01G489900 chr4B 77.834 591 113 9 1134 1709 12840339 12840926 1.960000e-92 350.0
47 TraesCS7D01G489900 chr4B 86.920 237 14 8 154 373 648554448 648554684 2.040000e-62 250.0
48 TraesCS7D01G489900 chr4B 83.333 294 18 16 97 373 220075758 220075479 3.420000e-60 243.0
49 TraesCS7D01G489900 chr4B 83.276 293 18 10 98 373 70104681 70104403 1.230000e-59 241.0
50 TraesCS7D01G489900 chr4B 82.095 296 21 13 100 377 284629954 284629673 1.240000e-54 224.0
51 TraesCS7D01G489900 chr4B 76.208 269 45 13 461 713 12828180 12828445 1.290000e-24 124.0
52 TraesCS7D01G489900 chr1B 85.526 304 18 15 94 373 353557963 353557662 9.300000e-76 294.0
53 TraesCS7D01G489900 chr1B 83.333 294 18 9 98 374 677921205 677920926 3.420000e-60 243.0
54 TraesCS7D01G489900 chr1B 83.276 293 18 10 98 373 612400215 612400493 1.230000e-59 241.0
55 TraesCS7D01G489900 chr2B 83.276 293 18 10 98 373 737765028 737765306 1.230000e-59 241.0
56 TraesCS7D01G489900 chr5B 82.993 294 19 10 98 374 276945299 276945020 1.590000e-58 237.0
57 TraesCS7D01G489900 chr5B 77.027 222 32 8 95 313 383025327 383025532 3.620000e-20 110.0
58 TraesCS7D01G489900 chr2A 82.253 293 20 15 100 374 395632520 395632242 1.240000e-54 224.0
59 TraesCS7D01G489900 chr4D 84.388 237 19 11 154 373 494256314 494256549 2.070000e-52 217.0
60 TraesCS7D01G489900 chr4D 82.418 182 17 5 98 278 446993946 446993779 9.910000e-31 145.0
61 TraesCS7D01G489900 chr1D 86.047 215 15 3 100 313 212862519 212862719 2.070000e-52 217.0
62 TraesCS7D01G489900 chr1D 92.727 110 7 1 3318 3427 413810924 413810816 1.270000e-34 158.0
63 TraesCS7D01G489900 chr1D 93.243 74 2 3 92 165 432326381 432326451 4.680000e-19 106.0
64 TraesCS7D01G489900 chr2D 98.058 103 2 0 3325 3427 6435785 6435887 2.720000e-41 180.0
65 TraesCS7D01G489900 chr2D 95.146 103 5 0 3325 3427 481671821 481671923 2.740000e-36 163.0
66 TraesCS7D01G489900 chr3D 85.405 185 10 7 94 275 246977083 246976913 3.510000e-40 176.0
67 TraesCS7D01G489900 chr3D 93.519 108 6 1 3321 3427 45625114 45625221 3.540000e-35 159.0
68 TraesCS7D01G489900 chr3A 78.626 262 32 11 154 397 312677180 312677435 5.920000e-33 152.0
69 TraesCS7D01G489900 chr6D 79.638 221 18 9 96 313 88785345 88785149 2.150000e-27 134.0


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 TraesCS7D01G489900 chr7D 599396582 599400008 3426 True 6329.000000 6329 100.000000 1 3427 1 chr7D.!!$R3 3426
1 TraesCS7D01G489900 chr7D 599192077 599193806 1729 True 670.000000 1190 78.993500 464 2397 2 chr7D.!!$R4 1933
2 TraesCS7D01G489900 chr7D 599268629 599269169 540 True 407.000000 407 80.510000 1056 1596 1 chr7D.!!$R2 540
3 TraesCS7D01G489900 chr7A 691521038 691523678 2640 True 2117.000000 4010 87.702500 1 2614 2 chr7A.!!$R4 2613
4 TraesCS7D01G489900 chr7A 691674110 691677201 3091 False 900.666667 1997 87.932667 161 2463 3 chr7A.!!$F1 2302
5 TraesCS7D01G489900 chr7A 691515327 691516097 770 True 531.500000 658 93.971500 2612 3325 2 chr7A.!!$R3 713
6 TraesCS7D01G489900 chr7B 678662591 678664033 1442 True 1053.000000 1053 80.411000 1056 2469 1 chr7B.!!$R2 1413
7 TraesCS7D01G489900 chr7B 678735177 678738004 2827 True 1041.925000 3162 92.247250 1 2474 4 chr7B.!!$R4 2473
8 TraesCS7D01G489900 chr7B 678849529 678852365 2836 False 875.000000 2429 88.994250 185 2472 4 chr7B.!!$F1 2287
9 TraesCS7D01G489900 chr7B 678647582 678648391 809 True 295.500000 457 77.362500 464 1498 2 chr7B.!!$R3 1034
10 TraesCS7D01G489900 chr6A 572774825 572775737 912 False 652.000000 905 94.412000 2469 3325 2 chr6A.!!$F3 856
11 TraesCS7D01G489900 chr6A 572760853 572761764 911 False 644.000000 889 94.165000 2469 3325 2 chr6A.!!$F1 856
12 TraesCS7D01G489900 chr6A 447798926 447807196 8270 True 636.875000 913 94.300625 2474 3325 8 chr6A.!!$R1 851
13 TraesCS7D01G489900 chr6A 572768094 572769007 913 False 634.000000 869 93.842500 2469 3325 2 chr6A.!!$F2 856
14 TraesCS7D01G489900 chr1A 50521545 50522411 866 False 618.500000 826 94.636500 2515 3325 2 chr1A.!!$F1 810
15 TraesCS7D01G489900 chr4B 12840339 12840926 587 False 350.000000 350 77.834000 1134 1709 1 chr4B.!!$F2 575

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
872 2200 2.912956 AGCCAAAACCTCCTCTACATGA 59.087 45.455 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 4224 0.98423 ATCGGGAGGCTGAGAAACAA 59.016 50.0 0.0 0.0 0.0 2.83 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
64 65 9.920946 AAATTTATAACACCACTCACCATCTAT 57.079 29.630 0.00 0.00 0.00 1.98
71 72 4.405680 CACCACTCACCATCTATCTTGGTA 59.594 45.833 0.00 0.00 45.71 3.25
327 344 8.504811 TCCTCATTAACATATATGTCTTGGGA 57.495 34.615 18.52 17.77 40.80 4.37
424 734 5.411361 TCATAGTACATGGAAGTGTGCAAAC 59.589 40.000 0.00 0.00 37.20 2.93
629 1320 7.609960 TCAATTCATAGTAAATGCAGCCAAAA 58.390 30.769 0.00 0.00 0.00 2.44
800 2127 4.287552 GAACCCTCCTCTACATGGAAGTA 58.712 47.826 0.00 0.00 32.61 2.24
872 2200 2.912956 AGCCAAAACCTCCTCTACATGA 59.087 45.455 0.00 0.00 0.00 3.07
1016 2644 1.092921 TGCACGGACCAACACAAGTC 61.093 55.000 0.00 0.00 0.00 3.01
1149 2786 1.221466 ACTGTTGACGATGCCACACG 61.221 55.000 0.00 0.00 0.00 4.49
1453 3090 3.309436 CTTCCACCCGCGGACATCA 62.309 63.158 30.73 6.41 33.75 3.07
1541 3178 2.528127 ACGTCACCCCCATCCACA 60.528 61.111 0.00 0.00 0.00 4.17
1667 3316 2.280524 CGGGTTTCGACAGCCACA 60.281 61.111 19.09 0.00 42.43 4.17
1747 3396 2.052237 CAACGTCACGGCTTGCAC 60.052 61.111 0.35 0.00 0.00 4.57
2572 4273 1.300931 GTCTCACGTGCAGCCAAGA 60.301 57.895 11.67 4.31 0.00 3.02
2675 6835 2.425592 GCAAACCCAAGCCCCAAC 59.574 61.111 0.00 0.00 0.00 3.77
2743 6903 1.032114 CGGCTCCCAAATCAAGTCCC 61.032 60.000 0.00 0.00 0.00 4.46
2771 6931 1.899814 AGGCCTCGTATGAAGACAACA 59.100 47.619 0.00 0.00 0.00 3.33
2900 9522 2.095314 TGATAACTAACGACGTTCCGCA 60.095 45.455 17.94 5.62 0.00 5.69
2901 9523 2.414058 TAACTAACGACGTTCCGCAA 57.586 45.000 17.94 0.00 0.00 4.85
2928 11998 2.271607 GACGAGTCTGATGAGGCGCA 62.272 60.000 10.83 0.00 0.00 6.09
2955 12025 2.693864 CTGGATGGCCTCCCCTGT 60.694 66.667 15.98 0.00 44.23 4.00
3000 12070 1.587613 GCAGTCTCTCGTGATCCGC 60.588 63.158 0.00 0.00 36.19 5.54
3056 12127 4.072839 GCAGAGTAATAGTATTTGCCCCC 58.927 47.826 0.00 0.00 0.00 5.40
3063 12134 5.869649 AATAGTATTTGCCCCCAATGAAC 57.130 39.130 0.00 0.00 0.00 3.18
3069 12140 1.454847 GCCCCCAATGAACGGCATA 60.455 57.895 0.00 0.00 41.25 3.14
3090 12216 2.105477 AGTGTGCCTTGTTCAGATCAGT 59.895 45.455 0.00 0.00 0.00 3.41
3268 12396 2.352805 CAGAAGTGGGCTGGGGTC 59.647 66.667 0.00 0.00 0.00 4.46
3287 12415 3.365364 GGTCGCTTTCTCCACTTTTGATG 60.365 47.826 0.00 0.00 0.00 3.07
3325 12453 5.796935 CAGCAAGTCACTATCCAAAATTTCG 59.203 40.000 0.00 0.00 0.00 3.46
3326 12454 5.705441 AGCAAGTCACTATCCAAAATTTCGA 59.295 36.000 0.00 0.00 0.00 3.71
3327 12455 6.206634 AGCAAGTCACTATCCAAAATTTCGAA 59.793 34.615 0.00 0.00 0.00 3.71
3328 12456 6.861055 GCAAGTCACTATCCAAAATTTCGAAA 59.139 34.615 13.91 13.91 0.00 3.46
3329 12457 7.061094 GCAAGTCACTATCCAAAATTTCGAAAG 59.939 37.037 16.80 2.24 0.00 2.62
3330 12458 7.745620 AGTCACTATCCAAAATTTCGAAAGT 57.254 32.000 16.80 11.21 0.00 2.66
3331 12459 7.584987 AGTCACTATCCAAAATTTCGAAAGTG 58.415 34.615 16.80 14.29 34.54 3.16
3332 12460 6.305638 GTCACTATCCAAAATTTCGAAAGTGC 59.694 38.462 16.80 7.79 33.54 4.40
3333 12461 6.206634 TCACTATCCAAAATTTCGAAAGTGCT 59.793 34.615 16.80 2.15 33.54 4.40
3334 12462 7.389330 TCACTATCCAAAATTTCGAAAGTGCTA 59.611 33.333 16.80 5.92 33.54 3.49
3335 12463 8.184192 CACTATCCAAAATTTCGAAAGTGCTAT 58.816 33.333 16.80 11.53 0.00 2.97
3336 12464 8.739972 ACTATCCAAAATTTCGAAAGTGCTATT 58.260 29.630 16.80 2.02 0.00 1.73
3337 12465 9.226345 CTATCCAAAATTTCGAAAGTGCTATTC 57.774 33.333 16.80 0.00 0.00 1.75
3338 12466 7.214467 TCCAAAATTTCGAAAGTGCTATTCT 57.786 32.000 16.80 0.00 0.00 2.40
3339 12467 7.083858 TCCAAAATTTCGAAAGTGCTATTCTG 58.916 34.615 16.80 1.73 0.00 3.02
3340 12468 7.040755 TCCAAAATTTCGAAAGTGCTATTCTGA 60.041 33.333 16.80 1.88 0.00 3.27
3341 12469 7.272084 CCAAAATTTCGAAAGTGCTATTCTGAG 59.728 37.037 16.80 0.00 0.00 3.35
3342 12470 4.928661 TTTCGAAAGTGCTATTCTGAGC 57.071 40.909 6.47 0.00 43.16 4.26
3343 12471 2.893637 TCGAAAGTGCTATTCTGAGCC 58.106 47.619 0.00 0.00 42.11 4.70
3344 12472 1.936547 CGAAAGTGCTATTCTGAGCCC 59.063 52.381 0.00 0.00 42.11 5.19
3345 12473 1.936547 GAAAGTGCTATTCTGAGCCCG 59.063 52.381 0.00 0.00 42.11 6.13
3346 12474 1.195115 AAGTGCTATTCTGAGCCCGA 58.805 50.000 0.00 0.00 42.11 5.14
3347 12475 0.749649 AGTGCTATTCTGAGCCCGAG 59.250 55.000 0.00 0.00 42.11 4.63
3348 12476 0.878086 GTGCTATTCTGAGCCCGAGC 60.878 60.000 0.00 0.00 42.11 5.03
3358 12486 2.894387 GCCCGAGCTCAGATGCAC 60.894 66.667 15.40 0.00 35.50 4.57
3359 12487 2.202987 CCCGAGCTCAGATGCACC 60.203 66.667 15.40 0.00 34.99 5.01
3360 12488 2.729479 CCCGAGCTCAGATGCACCT 61.729 63.158 15.40 0.00 34.99 4.00
3361 12489 1.521010 CCGAGCTCAGATGCACCTG 60.521 63.158 15.40 0.00 34.99 4.00
3362 12490 1.217511 CGAGCTCAGATGCACCTGT 59.782 57.895 15.40 0.00 35.71 4.00
3363 12491 0.390866 CGAGCTCAGATGCACCTGTT 60.391 55.000 15.40 0.00 35.71 3.16
3364 12492 1.134995 CGAGCTCAGATGCACCTGTTA 60.135 52.381 15.40 0.00 35.71 2.41
3365 12493 2.482664 CGAGCTCAGATGCACCTGTTAT 60.483 50.000 15.40 0.00 35.71 1.89
3366 12494 3.129871 GAGCTCAGATGCACCTGTTATC 58.870 50.000 8.25 0.70 35.71 1.75
3367 12495 2.158842 AGCTCAGATGCACCTGTTATCC 60.159 50.000 8.25 0.00 35.71 2.59
3368 12496 2.158842 GCTCAGATGCACCTGTTATCCT 60.159 50.000 8.25 0.00 35.71 3.24
3369 12497 3.070159 GCTCAGATGCACCTGTTATCCTA 59.930 47.826 8.25 0.00 35.71 2.94
3370 12498 4.443457 GCTCAGATGCACCTGTTATCCTAA 60.443 45.833 8.25 0.00 35.71 2.69
3371 12499 5.023533 TCAGATGCACCTGTTATCCTAAC 57.976 43.478 8.25 0.00 35.71 2.34
3372 12500 4.130118 CAGATGCACCTGTTATCCTAACC 58.870 47.826 0.00 0.00 0.00 2.85
3373 12501 2.684001 TGCACCTGTTATCCTAACCG 57.316 50.000 0.00 0.00 0.00 4.44
3374 12502 1.903860 TGCACCTGTTATCCTAACCGT 59.096 47.619 0.00 0.00 0.00 4.83
3375 12503 2.303600 TGCACCTGTTATCCTAACCGTT 59.696 45.455 0.00 0.00 0.00 4.44
3376 12504 2.934553 GCACCTGTTATCCTAACCGTTC 59.065 50.000 0.00 0.00 0.00 3.95
3377 12505 3.369157 GCACCTGTTATCCTAACCGTTCT 60.369 47.826 0.00 0.00 0.00 3.01
3378 12506 4.828829 CACCTGTTATCCTAACCGTTCTT 58.171 43.478 0.00 0.00 0.00 2.52
3379 12507 4.868734 CACCTGTTATCCTAACCGTTCTTC 59.131 45.833 0.00 0.00 0.00 2.87
3380 12508 4.529377 ACCTGTTATCCTAACCGTTCTTCA 59.471 41.667 0.00 0.00 0.00 3.02
3381 12509 5.109903 CCTGTTATCCTAACCGTTCTTCAG 58.890 45.833 0.00 0.00 0.00 3.02
3382 12510 4.501071 TGTTATCCTAACCGTTCTTCAGC 58.499 43.478 0.00 0.00 0.00 4.26
3383 12511 2.295253 ATCCTAACCGTTCTTCAGCG 57.705 50.000 0.00 0.00 0.00 5.18
3384 12512 0.389426 TCCTAACCGTTCTTCAGCGC 60.389 55.000 0.00 0.00 0.00 5.92
3385 12513 1.359459 CCTAACCGTTCTTCAGCGCC 61.359 60.000 2.29 0.00 0.00 6.53
3386 12514 0.669318 CTAACCGTTCTTCAGCGCCA 60.669 55.000 2.29 0.00 0.00 5.69
3387 12515 0.249953 TAACCGTTCTTCAGCGCCAA 60.250 50.000 2.29 0.00 0.00 4.52
3388 12516 1.507141 AACCGTTCTTCAGCGCCAAG 61.507 55.000 2.29 7.13 0.00 3.61
3410 12538 3.884900 GCTCCCGCGTGTGTATTT 58.115 55.556 4.92 0.00 0.00 1.40
3411 12539 1.713830 GCTCCCGCGTGTGTATTTC 59.286 57.895 4.92 0.00 0.00 2.17
3412 12540 1.017177 GCTCCCGCGTGTGTATTTCA 61.017 55.000 4.92 0.00 0.00 2.69
3413 12541 0.719465 CTCCCGCGTGTGTATTTCAC 59.281 55.000 4.92 0.00 46.31 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.323792 CCAAGATAGATGGTGAGTGGTGTT 60.324 45.833 0.00 0.00 33.08 3.32
47 48 3.198635 CCAAGATAGATGGTGAGTGGTGT 59.801 47.826 0.00 0.00 33.08 4.16
71 72 7.399674 AGGGCTCAATTTATAAATCTCTCCT 57.600 36.000 11.08 11.16 0.00 3.69
189 190 7.974501 GCATGACACTACACTTATGTTACTACT 59.025 37.037 0.00 0.00 40.48 2.57
629 1320 2.159043 CGCACTTCCATGTAGATGAGGT 60.159 50.000 0.46 0.00 0.00 3.85
738 1708 7.657336 TGAACCAAAAATCCTCTGTTGTTATC 58.343 34.615 0.00 0.00 0.00 1.75
872 2200 3.275617 TGCGTATCCCTTGCATACTTT 57.724 42.857 0.00 0.00 32.86 2.66
1016 2644 4.406069 CAAACACATCGACTGGCTAATTG 58.594 43.478 0.00 0.00 0.00 2.32
1453 3090 3.310860 GAGGTGGCGGAATGACGGT 62.311 63.158 0.00 0.00 0.00 4.83
1667 3316 4.057428 GACACCGGCGAGCACTCT 62.057 66.667 9.30 0.00 0.00 3.24
1747 3396 1.040339 AGAGGCAGTAGGAGAAGCGG 61.040 60.000 0.00 0.00 0.00 5.52
2381 4078 4.145807 ACCACATCAAATCGGGTTGTTTA 58.854 39.130 0.00 0.00 0.00 2.01
2523 4224 0.984230 ATCGGGAGGCTGAGAAACAA 59.016 50.000 0.00 0.00 0.00 2.83
2764 6924 2.025887 GGGAATCATCTGGGTGTTGTCT 60.026 50.000 0.00 0.00 0.00 3.41
2771 6931 1.486726 GTTCGAGGGAATCATCTGGGT 59.513 52.381 0.00 0.00 34.05 4.51
2900 9522 3.570125 TCATCAGACTCGTCTTCACAGTT 59.430 43.478 0.00 0.00 37.98 3.16
2901 9523 3.149981 TCATCAGACTCGTCTTCACAGT 58.850 45.455 0.00 0.00 37.98 3.55
2928 11998 2.046314 CCATCCAGGGCGTCGTTT 60.046 61.111 0.00 0.00 0.00 3.60
3000 12070 4.582656 AGACTACAGCACTATAGCTTCCTG 59.417 45.833 0.00 4.12 43.70 3.86
3009 12079 3.634448 CAGGCTACAGACTACAGCACTAT 59.366 47.826 9.11 0.00 37.02 2.12
3069 12140 2.105477 ACTGATCTGAACAAGGCACACT 59.895 45.455 6.60 0.00 0.00 3.55
3075 12146 2.486472 AGCCACTGATCTGAACAAGG 57.514 50.000 6.60 2.83 0.00 3.61
3076 12147 3.057736 CCAAAGCCACTGATCTGAACAAG 60.058 47.826 6.60 0.00 0.00 3.16
3077 12148 2.886523 CCAAAGCCACTGATCTGAACAA 59.113 45.455 6.60 0.00 0.00 2.83
3090 12216 0.675633 GAAAAGCTGAGCCAAAGCCA 59.324 50.000 0.00 0.00 41.82 4.75
3268 12396 3.003689 ACACATCAAAAGTGGAGAAAGCG 59.996 43.478 0.00 0.00 41.21 4.68
3325 12453 1.936547 CGGGCTCAGAATAGCACTTTC 59.063 52.381 0.00 0.00 44.07 2.62
3326 12454 1.555075 TCGGGCTCAGAATAGCACTTT 59.445 47.619 0.00 0.00 44.07 2.66
3327 12455 1.137872 CTCGGGCTCAGAATAGCACTT 59.862 52.381 0.00 0.00 44.07 3.16
3328 12456 0.749649 CTCGGGCTCAGAATAGCACT 59.250 55.000 0.00 0.00 44.07 4.40
3329 12457 0.878086 GCTCGGGCTCAGAATAGCAC 60.878 60.000 0.00 0.00 44.64 4.40
3330 12458 1.443407 GCTCGGGCTCAGAATAGCA 59.557 57.895 0.00 0.00 44.64 3.49
3331 12459 4.352386 GCTCGGGCTCAGAATAGC 57.648 61.111 0.00 0.00 41.99 2.97
3341 12469 2.894387 GTGCATCTGAGCTCGGGC 60.894 66.667 22.38 18.22 39.06 6.13
3342 12470 2.202987 GGTGCATCTGAGCTCGGG 60.203 66.667 22.38 11.19 34.99 5.14
3343 12471 1.521010 CAGGTGCATCTGAGCTCGG 60.521 63.158 23.04 16.98 36.93 4.63
3344 12472 0.390866 AACAGGTGCATCTGAGCTCG 60.391 55.000 33.21 6.05 38.11 5.03
3345 12473 2.680312 TAACAGGTGCATCTGAGCTC 57.320 50.000 33.21 6.82 38.11 4.09
3346 12474 2.158842 GGATAACAGGTGCATCTGAGCT 60.159 50.000 33.21 18.16 38.11 4.09
3347 12475 2.158842 AGGATAACAGGTGCATCTGAGC 60.159 50.000 33.21 14.55 38.11 4.26
3348 12476 3.834489 AGGATAACAGGTGCATCTGAG 57.166 47.619 33.21 8.51 38.11 3.35
3349 12477 4.141711 GGTTAGGATAACAGGTGCATCTGA 60.142 45.833 33.21 12.67 38.11 3.27
3350 12478 4.130118 GGTTAGGATAACAGGTGCATCTG 58.870 47.826 25.51 25.51 40.40 2.90
3351 12479 3.181465 CGGTTAGGATAACAGGTGCATCT 60.181 47.826 0.00 0.00 0.00 2.90
3352 12480 3.131396 CGGTTAGGATAACAGGTGCATC 58.869 50.000 0.00 0.00 0.00 3.91
3353 12481 2.504175 ACGGTTAGGATAACAGGTGCAT 59.496 45.455 0.00 0.00 0.00 3.96
3354 12482 1.903860 ACGGTTAGGATAACAGGTGCA 59.096 47.619 5.13 0.00 0.00 4.57
3355 12483 2.685850 ACGGTTAGGATAACAGGTGC 57.314 50.000 5.13 0.00 0.00 5.01
3356 12484 4.467198 AGAACGGTTAGGATAACAGGTG 57.533 45.455 0.00 0.00 0.00 4.00
3357 12485 4.529377 TGAAGAACGGTTAGGATAACAGGT 59.471 41.667 0.00 0.00 0.00 4.00
3358 12486 5.080969 TGAAGAACGGTTAGGATAACAGG 57.919 43.478 0.00 0.00 0.00 4.00
3359 12487 4.567159 GCTGAAGAACGGTTAGGATAACAG 59.433 45.833 0.00 0.00 0.00 3.16
3360 12488 4.501071 GCTGAAGAACGGTTAGGATAACA 58.499 43.478 0.00 0.00 0.00 2.41
3361 12489 3.550678 CGCTGAAGAACGGTTAGGATAAC 59.449 47.826 0.00 0.00 0.00 1.89
3362 12490 3.777478 CGCTGAAGAACGGTTAGGATAA 58.223 45.455 0.00 0.00 0.00 1.75
3363 12491 2.480759 GCGCTGAAGAACGGTTAGGATA 60.481 50.000 0.00 0.00 0.00 2.59
3364 12492 1.739371 GCGCTGAAGAACGGTTAGGAT 60.739 52.381 0.00 0.00 0.00 3.24
3365 12493 0.389426 GCGCTGAAGAACGGTTAGGA 60.389 55.000 0.00 0.00 0.00 2.94
3366 12494 1.359459 GGCGCTGAAGAACGGTTAGG 61.359 60.000 7.64 0.00 0.00 2.69
3367 12495 0.669318 TGGCGCTGAAGAACGGTTAG 60.669 55.000 7.64 0.00 0.00 2.34
3368 12496 0.249953 TTGGCGCTGAAGAACGGTTA 60.250 50.000 7.64 0.00 0.00 2.85
3369 12497 1.507141 CTTGGCGCTGAAGAACGGTT 61.507 55.000 7.64 0.00 0.00 4.44
3370 12498 1.961277 CTTGGCGCTGAAGAACGGT 60.961 57.895 7.64 0.00 0.00 4.83
3371 12499 2.863153 CTTGGCGCTGAAGAACGG 59.137 61.111 7.64 0.00 0.00 4.44
3372 12500 2.174349 GCTTGGCGCTGAAGAACG 59.826 61.111 19.71 0.00 35.14 3.95
3394 12522 3.131326 TGAAATACACACGCGGGAG 57.869 52.632 19.19 10.92 0.00 4.30


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

AutoCloner maintained by Alex Coulton.