Multiple sequence alignment - TraesCS7A01G187200

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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 TraesCS7A01G187200 chr7A 100.000 4706 0 0 1 4706 142987110 142982405 0.000000e+00 8691.0
1 TraesCS7A01G187200 chr7D 94.891 4463 151 28 30 4447 140806850 140802420 0.000000e+00 6907.0
2 TraesCS7A01G187200 chr7D 95.676 185 6 2 4520 4704 140801922 140801740 3.560000e-76 296.0
3 TraesCS7A01G187200 chr7D 92.188 64 5 0 3600 3663 511117079 511117016 1.800000e-14 91.6
4 TraesCS7A01G187200 chr7D 100.000 30 0 0 1 30 148261252 148261223 6.580000e-04 56.5
5 TraesCS7A01G187200 chr7D 100.000 30 0 0 1 30 154326477 154326448 6.580000e-04 56.5
6 TraesCS7A01G187200 chr7D 100.000 30 0 0 1 30 265940078 265940049 6.580000e-04 56.5
7 TraesCS7A01G187200 chr7B 95.094 3975 127 22 504 4447 105884858 105880921 0.000000e+00 6198.0
8 TraesCS7A01G187200 chr7B 91.371 197 7 1 4520 4706 105880423 105880227 1.300000e-65 261.0
9 TraesCS7A01G187200 chr7B 95.455 66 2 1 4467 4532 15305713 15305649 2.320000e-18 104.0
10 TraesCS7A01G187200 chr7B 98.305 59 1 0 4466 4524 457401465 457401407 2.320000e-18 104.0
11 TraesCS7A01G187200 chr7B 98.077 52 1 0 247 298 718533188 718533239 1.800000e-14 91.6
12 TraesCS7A01G187200 chr7B 98.077 52 1 0 247 298 718565982 718566033 1.800000e-14 91.6
13 TraesCS7A01G187200 chr7B 98.077 52 1 0 247 298 718590270 718590321 1.800000e-14 91.6
14 TraesCS7A01G187200 chr6A 77.769 1228 220 34 1030 2239 541229219 541228027 0.000000e+00 706.0
15 TraesCS7A01G187200 chr6D 77.824 1195 213 32 1030 2207 394724180 394725339 0.000000e+00 691.0
16 TraesCS7A01G187200 chr6D 88.487 304 34 1 3405 3708 73792611 73792913 2.680000e-97 366.0
17 TraesCS7A01G187200 chr6D 96.226 53 2 0 246 298 172136341 172136393 2.330000e-13 87.9
18 TraesCS7A01G187200 chr6D 100.000 30 0 0 1 30 304042297 304042268 6.580000e-04 56.5
19 TraesCS7A01G187200 chr6B 78.717 1076 193 20 1157 2217 590913506 590912452 0.000000e+00 686.0
20 TraesCS7A01G187200 chr6B 78.956 613 69 37 3402 3994 564364819 564364247 3.460000e-96 363.0
21 TraesCS7A01G187200 chr6B 93.939 66 4 0 4464 4529 684445305 684445370 3.000000e-17 100.0
22 TraesCS7A01G187200 chr5B 80.504 595 70 29 3414 3994 2053846 2053284 9.420000e-112 414.0
23 TraesCS7A01G187200 chr2D 79.732 597 74 31 3411 3994 81653498 81654060 5.710000e-104 388.0
24 TraesCS7A01G187200 chr2D 86.905 84 10 1 4464 4546 544576195 544576278 5.010000e-15 93.5
25 TraesCS7A01G187200 chr1B 85.377 212 21 5 3405 3616 577972142 577972343 1.330000e-50 211.0
26 TraesCS7A01G187200 chr1B 94.643 56 2 1 246 300 366490337 366490282 8.390000e-13 86.1
27 TraesCS7A01G187200 chr3A 86.842 190 17 5 3100 3284 169101449 169101635 6.170000e-49 206.0
28 TraesCS7A01G187200 chr3A 87.692 65 6 2 231 295 632729706 632729644 1.820000e-09 75.0
29 TraesCS7A01G187200 chr5D 84.186 215 24 4 3405 3619 277314234 277314030 2.870000e-47 200.0
30 TraesCS7A01G187200 chr3B 91.579 95 4 3 3100 3192 235921550 235921458 1.370000e-25 128.0
31 TraesCS7A01G187200 chr4A 92.958 71 4 1 4467 4537 448094405 448094336 8.330000e-18 102.0
32 TraesCS7A01G187200 chr4A 86.905 84 10 1 4464 4546 28558176 28558259 5.010000e-15 93.5
33 TraesCS7A01G187200 chr3D 98.276 58 1 0 4464 4521 74370078 74370135 8.330000e-18 102.0
34 TraesCS7A01G187200 chr3D 98.246 57 1 0 4467 4523 94848773 94848717 3.000000e-17 100.0
35 TraesCS7A01G187200 chr3D 98.246 57 1 0 4467 4523 529146046 529145990 3.000000e-17 100.0
36 TraesCS7A01G187200 chr3D 95.745 47 2 0 246 292 8779717 8779671 5.050000e-10 76.8
37 TraesCS7A01G187200 chr3D 100.000 30 0 0 1 30 132213273 132213244 6.580000e-04 56.5
38 TraesCS7A01G187200 chr3D 100.000 30 0 0 1 30 199968349 199968320 6.580000e-04 56.5
39 TraesCS7A01G187200 chr3D 100.000 30 0 0 1 30 200006037 200006008 6.580000e-04 56.5
40 TraesCS7A01G187200 chr3D 100.000 30 0 0 1 30 467366655 467366684 6.580000e-04 56.5
41 TraesCS7A01G187200 chr3D 100.000 30 0 0 1 30 611486140 611486169 6.580000e-04 56.5
42 TraesCS7A01G187200 chrUn 98.077 52 1 0 247 298 313633701 313633752 1.800000e-14 91.6


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 TraesCS7A01G187200 chr7A 142982405 142987110 4705 True 8691.0 8691 100.0000 1 4706 1 chr7A.!!$R1 4705
1 TraesCS7A01G187200 chr7D 140801740 140806850 5110 True 3601.5 6907 95.2835 30 4704 2 chr7D.!!$R5 4674
2 TraesCS7A01G187200 chr7B 105880227 105884858 4631 True 3229.5 6198 93.2325 504 4706 2 chr7B.!!$R3 4202
3 TraesCS7A01G187200 chr6A 541228027 541229219 1192 True 706.0 706 77.7690 1030 2239 1 chr6A.!!$R1 1209
4 TraesCS7A01G187200 chr6D 394724180 394725339 1159 False 691.0 691 77.8240 1030 2207 1 chr6D.!!$F3 1177
5 TraesCS7A01G187200 chr6B 590912452 590913506 1054 True 686.0 686 78.7170 1157 2217 1 chr6B.!!$R2 1060
6 TraesCS7A01G187200 chr6B 564364247 564364819 572 True 363.0 363 78.9560 3402 3994 1 chr6B.!!$R1 592
7 TraesCS7A01G187200 chr5B 2053284 2053846 562 True 414.0 414 80.5040 3414 3994 1 chr5B.!!$R1 580
8 TraesCS7A01G187200 chr2D 81653498 81654060 562 False 388.0 388 79.7320 3411 3994 1 chr2D.!!$F1 583

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
666 674 0.165944 CGAAACATCGCACCCTCAAC 59.834 55.0 0.00 0.0 0.00 3.18 F
2007 2032 0.112995 TGGTGCAGAAGGATTTGGCT 59.887 50.0 0.00 0.0 0.00 4.75 F
2250 2275 0.662619 TGAGTTGCGGCACTCTTTTG 59.337 50.0 23.33 0.0 43.32 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 2558 1.487142 TGTTTCCCAAGAGTTCCGTCA 59.513 47.619 0.00 0.0 0.0 4.35 R
3640 3683 1.059098 ACATGCTTGGTCCACAGAGA 58.941 50.000 4.44 0.0 0.0 3.10 R
4089 4155 1.661480 GCTCACAACATGGCAGCAA 59.339 52.632 0.00 0.0 0.0 3.91 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
70 71 3.410631 TGTCAGAATTTCCCGTGCTTA 57.589 42.857 0.00 0.00 0.00 3.09
84 85 4.083696 CCCGTGCTTACTAAACGAAATTGT 60.084 41.667 0.00 0.00 39.64 2.71
93 94 3.556625 CGAAATTGTCGTCGCCCA 58.443 55.556 0.00 0.00 45.09 5.36
101 102 0.172578 TGTCGTCGCCCAGATAACAG 59.827 55.000 0.00 0.00 0.00 3.16
110 111 2.369394 CCCAGATAACAGAACTTGCCC 58.631 52.381 0.00 0.00 0.00 5.36
141 142 6.866248 AGGTTTGATTTGTTATGCTTTAACCG 59.134 34.615 0.00 0.00 37.10 4.44
160 161 8.749841 TTAACCGGTGATGAATTTTTAACATG 57.250 30.769 8.52 0.00 0.00 3.21
161 162 6.582677 ACCGGTGATGAATTTTTAACATGA 57.417 33.333 6.12 0.00 0.00 3.07
162 163 6.386654 ACCGGTGATGAATTTTTAACATGAC 58.613 36.000 6.12 0.00 0.00 3.06
167 168 9.520204 GGTGATGAATTTTTAACATGACCATAG 57.480 33.333 0.00 0.00 43.82 2.23
197 198 7.744678 TTAGATACTTGGTTTTAGCTACCCT 57.255 36.000 1.64 0.00 34.66 4.34
198 199 5.990668 AGATACTTGGTTTTAGCTACCCTG 58.009 41.667 1.64 0.00 34.66 4.45
202 203 0.251073 GGTTTTAGCTACCCTGCCGA 59.749 55.000 0.00 0.00 0.00 5.54
223 224 8.349983 TGCCGATTCTAAATATAAGCCTTTTTC 58.650 33.333 0.00 0.00 0.00 2.29
362 367 3.294038 AGATCATCAGGAGGGCAAAAG 57.706 47.619 0.00 0.00 0.00 2.27
363 368 1.680207 GATCATCAGGAGGGCAAAAGC 59.320 52.381 0.00 0.00 0.00 3.51
413 419 5.649395 ACCAGATAACAGAACCAACATCATG 59.351 40.000 0.00 0.00 0.00 3.07
451 457 5.310451 AGACCAAACTGTTAAGCCGATAAA 58.690 37.500 0.00 0.00 0.00 1.40
474 480 2.543848 CGACTGCAACTAAAGCACAGAA 59.456 45.455 0.00 0.00 37.02 3.02
656 664 3.175152 CTCTTCTCACTCCGAAACATCG 58.825 50.000 0.00 0.00 0.00 3.84
663 671 1.079405 TCCGAAACATCGCACCCTC 60.079 57.895 0.00 0.00 0.00 4.30
666 674 0.165944 CGAAACATCGCACCCTCAAC 59.834 55.000 0.00 0.00 0.00 3.18
694 702 1.227674 GGGCTCACCGCTAATGAGG 60.228 63.158 9.84 0.00 43.26 3.86
698 706 2.588877 CACCGCTAATGAGGCCCG 60.589 66.667 0.00 0.00 36.56 6.13
710 718 1.718757 GAGGCCCGCATGTCATTGAC 61.719 60.000 9.93 9.93 0.00 3.18
746 754 1.605453 GGTTTATCCGGTGGCCAGA 59.395 57.895 5.11 0.00 0.00 3.86
975 985 4.177673 CCCCCTACTCGGCTACTC 57.822 66.667 0.00 0.00 0.00 2.59
976 986 1.531128 CCCCCTACTCGGCTACTCC 60.531 68.421 0.00 0.00 0.00 3.85
1368 1381 4.516195 GAGAAGGAGGCCCGCGAC 62.516 72.222 8.23 0.00 37.58 5.19
2007 2032 0.112995 TGGTGCAGAAGGATTTGGCT 59.887 50.000 0.00 0.00 0.00 4.75
2243 2268 4.030452 GCTGGTGAGTTGCGGCAC 62.030 66.667 0.05 0.00 0.00 5.01
2250 2275 0.662619 TGAGTTGCGGCACTCTTTTG 59.337 50.000 23.33 0.00 43.32 2.44
2251 2276 0.663153 GAGTTGCGGCACTCTTTTGT 59.337 50.000 18.85 0.00 40.23 2.83
2252 2277 1.065551 GAGTTGCGGCACTCTTTTGTT 59.934 47.619 18.85 0.00 40.23 2.83
2253 2278 2.289547 GAGTTGCGGCACTCTTTTGTTA 59.710 45.455 18.85 0.00 40.23 2.41
2254 2279 2.032924 AGTTGCGGCACTCTTTTGTTAC 59.967 45.455 0.05 0.00 0.00 2.50
2255 2280 1.669604 TGCGGCACTCTTTTGTTACA 58.330 45.000 0.00 0.00 0.00 2.41
2256 2281 2.017782 TGCGGCACTCTTTTGTTACAA 58.982 42.857 0.00 0.00 0.00 2.41
2257 2282 2.223386 TGCGGCACTCTTTTGTTACAAC 60.223 45.455 0.00 0.00 0.00 3.32
2258 2283 2.857104 GCGGCACTCTTTTGTTACAACC 60.857 50.000 0.00 0.00 0.00 3.77
2259 2284 2.356382 CGGCACTCTTTTGTTACAACCA 59.644 45.455 0.00 0.00 0.00 3.67
2260 2285 3.004315 CGGCACTCTTTTGTTACAACCAT 59.996 43.478 0.00 0.00 0.00 3.55
2261 2286 4.214545 CGGCACTCTTTTGTTACAACCATA 59.785 41.667 0.00 0.00 0.00 2.74
2262 2287 5.106317 CGGCACTCTTTTGTTACAACCATAT 60.106 40.000 0.00 0.00 0.00 1.78
2263 2288 6.092748 GGCACTCTTTTGTTACAACCATATG 58.907 40.000 0.00 0.00 0.00 1.78
2340 2365 8.147058 TGCATCAGTTATTTGTTATGTTTGGTT 58.853 29.630 0.00 0.00 0.00 3.67
2353 2378 8.478877 TGTTATGTTTGGTTTTTGATAGGTGTT 58.521 29.630 0.00 0.00 0.00 3.32
2395 2420 6.313744 ACAATTTCACTAACTTAGGTGCAC 57.686 37.500 8.80 8.80 33.91 4.57
2398 2423 3.738830 TCACTAACTTAGGTGCACGTT 57.261 42.857 18.35 14.49 33.91 3.99
2415 2440 7.042523 GGTGCACGTTCTACTTAAGTTTCTTTA 60.043 37.037 14.49 0.00 0.00 1.85
2436 2461 3.851458 TCACTGCCATTATGCTCATCT 57.149 42.857 0.00 0.00 0.00 2.90
2453 2478 2.397044 TCTTGGGATTTGGCACCTTT 57.603 45.000 0.00 0.00 0.00 3.11
2454 2479 3.534357 TCTTGGGATTTGGCACCTTTA 57.466 42.857 0.00 0.00 0.00 1.85
2471 2496 6.591448 GCACCTTTATTTCCCTTGAATTTCTG 59.409 38.462 0.00 0.00 0.00 3.02
2497 2522 9.819267 GGAGTGAGCATTAAGTATAGTAGTTTT 57.181 33.333 0.00 0.00 0.00 2.43
2516 2541 8.974408 GTAGTTTTGTTCCCAAACATCATTTAC 58.026 33.333 0.00 0.00 44.59 2.01
2535 2561 9.535878 TCATTTACCTGGTAAAATGTTTTTGAC 57.464 29.630 29.80 0.00 40.62 3.18
2586 2612 4.084171 GCTCGACATTGACCACATATGATG 60.084 45.833 10.38 4.04 0.00 3.07
2603 2629 8.644216 ACATATGATGCATAAATGTTCCACAAT 58.356 29.630 10.38 0.00 29.74 2.71
2616 2642 4.288366 TGTTCCACAATTAGATGGACTGGA 59.712 41.667 5.05 0.00 44.80 3.86
2655 2681 7.989741 ACAATGTGATCTTATATAGCATAGGCC 59.010 37.037 0.00 0.00 42.56 5.19
2657 2683 5.656859 TGTGATCTTATATAGCATAGGCCGT 59.343 40.000 0.00 0.00 42.56 5.68
2663 2689 7.061054 TCTTATATAGCATAGGCCGTCTGTAT 58.939 38.462 0.00 4.35 42.56 2.29
2685 2711 8.802856 TGTATTGTTTCACAACTCAAAATTTCG 58.197 29.630 0.00 0.00 41.40 3.46
2831 2857 6.210784 GGTTAGGGATGCCTTCTTTTTAGTTT 59.789 38.462 12.53 0.00 0.00 2.66
2967 2998 8.863872 ATACCTAAATATGTGCCATTACCTTC 57.136 34.615 0.00 0.00 0.00 3.46
2976 3007 4.898861 TGTGCCATTACCTTCTTTTCCTTT 59.101 37.500 0.00 0.00 0.00 3.11
3082 3124 4.207165 GTTGTATGTGGTATGGCCTTGAT 58.793 43.478 3.32 0.00 38.35 2.57
3640 3683 4.632538 GTTGCTTTCAACCAGTACAAGT 57.367 40.909 0.00 0.00 45.15 3.16
4116 4182 2.228582 CCATGTTGTGAGCGAAATTCCA 59.771 45.455 0.00 0.00 0.00 3.53
4291 4370 0.030638 TGCTTGCTTTTCTTCCACGC 59.969 50.000 0.00 0.00 0.00 5.34
4296 4375 4.545610 CTTGCTTTTCTTCCACGCATTTA 58.454 39.130 0.00 0.00 0.00 1.40
4310 4389 5.301805 CCACGCATTTAATTATCTTCCCCTT 59.698 40.000 0.00 0.00 0.00 3.95
4316 4396 7.452813 GCATTTAATTATCTTCCCCTTGAGGAT 59.547 37.037 0.00 0.00 42.08 3.24
4413 4501 4.766373 TCCATTGCTTGCTGACTTTTCATA 59.234 37.500 0.00 0.00 0.00 2.15
4438 4526 4.589908 ACTTGCACCGATTCCTTAGAAAT 58.410 39.130 0.00 0.00 35.09 2.17
4439 4527 4.396166 ACTTGCACCGATTCCTTAGAAATG 59.604 41.667 0.00 0.00 35.09 2.32
4443 4531 3.118038 CACCGATTCCTTAGAAATGGGGA 60.118 47.826 0.00 0.00 36.37 4.81
4445 4533 3.883489 CCGATTCCTTAGAAATGGGGAAC 59.117 47.826 0.00 0.00 40.10 3.62
4446 4534 4.385310 CCGATTCCTTAGAAATGGGGAACT 60.385 45.833 0.00 0.00 40.10 3.01
4448 4536 5.066505 CGATTCCTTAGAAATGGGGAACTTG 59.933 44.000 0.00 0.00 40.10 3.16
4449 4537 3.697166 TCCTTAGAAATGGGGAACTTGC 58.303 45.455 0.00 0.00 0.00 4.01
4451 4539 3.193479 CCTTAGAAATGGGGAACTTGCAC 59.807 47.826 0.00 0.00 0.00 4.57
4452 4540 1.632589 AGAAATGGGGAACTTGCACC 58.367 50.000 0.00 0.00 0.00 5.01
4454 4542 0.178975 AAATGGGGAACTTGCACCGA 60.179 50.000 0.00 0.00 0.00 4.69
4455 4543 0.039618 AATGGGGAACTTGCACCGAT 59.960 50.000 0.00 0.00 0.00 4.18
4457 4545 0.608035 TGGGGAACTTGCACCGATTC 60.608 55.000 0.00 0.00 0.00 2.52
4458 4546 1.313091 GGGGAACTTGCACCGATTCC 61.313 60.000 8.35 8.35 40.00 3.01
4459 4547 0.322546 GGGAACTTGCACCGATTCCT 60.323 55.000 14.05 0.00 40.47 3.36
4460 4548 1.534729 GGAACTTGCACCGATTCCTT 58.465 50.000 9.26 0.00 38.08 3.36
4461 4549 2.617021 GGGAACTTGCACCGATTCCTTA 60.617 50.000 14.05 0.00 40.47 2.69
4462 4550 2.678336 GGAACTTGCACCGATTCCTTAG 59.322 50.000 9.26 0.00 38.08 2.18
4463 4551 3.596214 GAACTTGCACCGATTCCTTAGA 58.404 45.455 0.00 0.00 0.00 2.10
4464 4552 3.695830 ACTTGCACCGATTCCTTAGAA 57.304 42.857 0.00 0.00 36.15 2.10
4469 4583 3.694072 TGCACCGATTCCTTAGAAATTGG 59.306 43.478 0.00 0.00 35.09 3.16
4471 4585 4.438744 GCACCGATTCCTTAGAAATTGGTG 60.439 45.833 21.72 21.72 41.78 4.17
4472 4586 3.694566 ACCGATTCCTTAGAAATTGGTGC 59.305 43.478 2.10 0.00 35.09 5.01
4477 4591 6.708054 CGATTCCTTAGAAATTGGTGCTAGAT 59.292 38.462 0.00 0.00 35.09 1.98
4478 4592 7.872993 CGATTCCTTAGAAATTGGTGCTAGATA 59.127 37.037 0.00 0.00 35.09 1.98
4479 4593 8.910351 ATTCCTTAGAAATTGGTGCTAGATAC 57.090 34.615 0.00 0.00 35.09 2.24
4488 4602 6.889301 ATTGGTGCTAGATACATCCATTTG 57.111 37.500 0.00 0.00 0.00 2.32
4489 4603 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
4490 4604 5.614308 TGGTGCTAGATACATCCATTTGAG 58.386 41.667 0.00 0.00 0.00 3.02
4491 4605 4.999950 GGTGCTAGATACATCCATTTGAGG 59.000 45.833 0.00 0.00 0.00 3.86
4492 4606 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
4493 4607 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
4494 4608 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
4495 4609 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
4497 4611 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
4498 4612 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
4499 4613 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
4500 4614 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
4501 4615 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
4502 4616 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
4504 4618 4.039124 TCCATTTGAGGGACAAGCTTTTTC 59.961 41.667 0.00 0.00 39.77 2.29
4505 4619 3.708563 TTTGAGGGACAAGCTTTTTCG 57.291 42.857 0.00 0.00 39.77 3.46
4506 4620 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
4507 4621 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
4508 4622 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
4509 4623 1.133915 AGGGACAAGCTTTTTCGGACA 60.134 47.619 0.00 0.00 0.00 4.02
4510 4624 1.266989 GGGACAAGCTTTTTCGGACAG 59.733 52.381 0.00 0.00 0.00 3.51
4511 4625 2.218603 GGACAAGCTTTTTCGGACAGA 58.781 47.619 0.00 0.00 0.00 3.41
4512 4626 2.224314 GGACAAGCTTTTTCGGACAGAG 59.776 50.000 0.00 0.00 0.00 3.35
4513 4627 2.222027 ACAAGCTTTTTCGGACAGAGG 58.778 47.619 0.00 0.00 0.00 3.69
4514 4628 1.537202 CAAGCTTTTTCGGACAGAGGG 59.463 52.381 0.00 0.00 0.00 4.30
4515 4629 1.056660 AGCTTTTTCGGACAGAGGGA 58.943 50.000 0.00 0.00 0.00 4.20
4516 4630 1.002544 AGCTTTTTCGGACAGAGGGAG 59.997 52.381 0.00 0.00 0.00 4.30
4517 4631 1.270893 GCTTTTTCGGACAGAGGGAGT 60.271 52.381 0.00 0.00 0.00 3.85
4518 4632 2.028385 GCTTTTTCGGACAGAGGGAGTA 60.028 50.000 0.00 0.00 0.00 2.59
4535 5053 9.780186 AGAGGGAGTATATGCAAAAACTAATAC 57.220 33.333 0.00 0.00 0.00 1.89
4683 5211 9.543018 CTCTTACGACAATTGGAATTTACTTTC 57.457 33.333 10.83 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.695830 AGTAAGCACGGGAAATTCTGA 57.304 42.857 0.00 0.00 0.00 3.27
55 56 4.389687 TCGTTTAGTAAGCACGGGAAATTC 59.610 41.667 7.16 0.00 34.61 2.17
84 85 1.135199 GTTCTGTTATCTGGGCGACGA 60.135 52.381 0.00 0.00 0.00 4.20
86 87 2.673368 CAAGTTCTGTTATCTGGGCGAC 59.327 50.000 0.00 0.00 0.00 5.19
91 92 3.071874 TGGGCAAGTTCTGTTATCTGG 57.928 47.619 0.00 0.00 0.00 3.86
92 93 5.452078 TTTTGGGCAAGTTCTGTTATCTG 57.548 39.130 0.00 0.00 0.00 2.90
118 119 6.643360 ACCGGTTAAAGCATAACAAATCAAAC 59.357 34.615 0.00 0.00 0.00 2.93
129 130 6.767524 AAATTCATCACCGGTTAAAGCATA 57.232 33.333 2.97 0.00 0.00 3.14
141 142 9.520204 CTATGGTCATGTTAAAAATTCATCACC 57.480 33.333 0.00 0.00 34.21 4.02
195 196 5.491982 AGGCTTATATTTAGAATCGGCAGG 58.508 41.667 0.00 0.00 0.00 4.85
197 198 7.817418 AAAAGGCTTATATTTAGAATCGGCA 57.183 32.000 0.00 0.00 0.00 5.69
198 199 8.349983 TGAAAAAGGCTTATATTTAGAATCGGC 58.650 33.333 0.00 0.00 0.00 5.54
265 267 6.043358 ACTCCCTCTGTTCCTAAATATAAGCC 59.957 42.308 0.00 0.00 0.00 4.35
266 268 7.068686 ACTCCCTCTGTTCCTAAATATAAGC 57.931 40.000 0.00 0.00 0.00 3.09
282 284 8.528543 ACTACTCTATTCCTAATACTCCCTCT 57.471 38.462 0.00 0.00 0.00 3.69
362 367 4.347876 ATTTTATAAAATGGAGCCTGGGGC 59.652 41.667 20.14 0.00 41.95 5.80
395 401 3.760738 TGGCATGATGTTGGTTCTGTTA 58.239 40.909 0.00 0.00 0.00 2.41
400 406 1.273048 TGCTTGGCATGATGTTGGTTC 59.727 47.619 4.32 0.00 31.71 3.62
413 419 1.340889 TGGTCTTTGAACATGCTTGGC 59.659 47.619 4.44 0.00 0.00 4.52
451 457 2.738846 CTGTGCTTTAGTTGCAGTCGAT 59.261 45.455 0.00 0.00 41.41 3.59
454 460 3.608008 GCTTCTGTGCTTTAGTTGCAGTC 60.608 47.826 0.00 0.00 41.41 3.51
467 473 4.568152 TGTTTTCTTTAGGCTTCTGTGC 57.432 40.909 0.00 0.00 0.00 4.57
474 480 8.007405 ACATGTAGTTTTGTTTTCTTTAGGCT 57.993 30.769 0.00 0.00 0.00 4.58
501 508 4.059511 TCGACAGACTCGGCAAAATTTTA 58.940 39.130 2.44 0.00 43.16 1.52
582 590 5.048224 GCCTGGCTAGATTTACGACATACTA 60.048 44.000 12.43 0.00 0.00 1.82
583 591 4.262079 GCCTGGCTAGATTTACGACATACT 60.262 45.833 12.43 0.00 0.00 2.12
584 592 3.988517 GCCTGGCTAGATTTACGACATAC 59.011 47.826 12.43 0.00 0.00 2.39
585 593 3.895656 AGCCTGGCTAGATTTACGACATA 59.104 43.478 21.98 0.00 36.99 2.29
656 664 1.200716 CACATGACATGTTGAGGGTGC 59.799 52.381 18.52 0.00 42.70 5.01
663 671 1.200716 GTGAGCCCACATGACATGTTG 59.799 52.381 18.52 14.84 42.70 3.33
666 674 1.371337 CGGTGAGCCCACATGACATG 61.371 60.000 14.02 14.02 44.93 3.21
694 702 1.430632 CTGTCAATGACATGCGGGC 59.569 57.895 17.10 0.00 41.94 6.13
698 706 0.795735 GCGTGCTGTCAATGACATGC 60.796 55.000 17.10 20.18 41.94 4.06
728 736 0.746923 GTCTGGCCACCGGATAAACC 60.747 60.000 9.46 2.22 41.38 3.27
743 751 4.747810 ACTCTTTGCTTTTGGTTTGTCTG 58.252 39.130 0.00 0.00 0.00 3.51
746 754 3.513515 TGGACTCTTTGCTTTTGGTTTGT 59.486 39.130 0.00 0.00 0.00 2.83
902 911 1.445582 GCGAAATGGAGACGGACGT 60.446 57.895 0.00 0.00 0.00 4.34
973 983 4.024984 TGGGGACTGGGGAGGGAG 62.025 72.222 0.00 0.00 0.00 4.30
974 984 4.348495 GTGGGGACTGGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
975 985 4.354943 AGTGGGGACTGGGGAGGG 62.355 72.222 0.00 0.00 0.00 4.30
976 986 2.689034 GAGTGGGGACTGGGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
1404 1417 1.370064 CGTGTCGAACCCCTCCTTT 59.630 57.895 0.00 0.00 0.00 3.11
2257 2282 5.384063 TGTTGCAAGTTGTAACCATATGG 57.616 39.130 27.24 20.68 41.35 2.74
2258 2283 7.062138 GTGAATGTTGCAAGTTGTAACCATATG 59.938 37.037 27.24 0.00 41.35 1.78
2259 2284 7.039784 AGTGAATGTTGCAAGTTGTAACCATAT 60.040 33.333 27.24 15.42 41.35 1.78
2260 2285 6.264292 AGTGAATGTTGCAAGTTGTAACCATA 59.736 34.615 27.24 14.05 41.35 2.74
2261 2286 5.068987 AGTGAATGTTGCAAGTTGTAACCAT 59.931 36.000 27.24 18.56 41.35 3.55
2262 2287 4.400884 AGTGAATGTTGCAAGTTGTAACCA 59.599 37.500 27.24 18.03 41.35 3.67
2263 2288 4.932146 AGTGAATGTTGCAAGTTGTAACC 58.068 39.130 27.24 16.09 41.35 2.85
2340 2365 8.871629 ACCACAATACATAACACCTATCAAAA 57.128 30.769 0.00 0.00 0.00 2.44
2382 2407 5.458041 AAGTAGAACGTGCACCTAAGTTA 57.542 39.130 12.15 0.00 0.00 2.24
2398 2423 8.372459 TGGCAGTGATAAAGAAACTTAAGTAGA 58.628 33.333 8.92 0.00 0.00 2.59
2415 2440 4.368565 AGATGAGCATAATGGCAGTGAT 57.631 40.909 0.00 0.00 35.83 3.06
2422 2447 5.279306 CCAAATCCCAAGATGAGCATAATGG 60.279 44.000 6.91 6.91 31.29 3.16
2436 2461 4.019771 GGAAATAAAGGTGCCAAATCCCAA 60.020 41.667 0.00 0.00 0.00 4.12
2453 2478 6.789268 TCACTCCAGAAATTCAAGGGAAATA 58.211 36.000 0.00 0.00 36.43 1.40
2454 2479 5.644188 TCACTCCAGAAATTCAAGGGAAAT 58.356 37.500 0.00 0.00 36.43 2.17
2471 2496 9.819267 AAAACTACTATACTTAATGCTCACTCC 57.181 33.333 0.00 0.00 0.00 3.85
2516 2541 5.189659 TCCGTCAAAAACATTTTACCAGG 57.810 39.130 0.00 0.00 0.00 4.45
2532 2558 1.487142 TGTTTCCCAAGAGTTCCGTCA 59.513 47.619 0.00 0.00 0.00 4.35
2535 2561 2.548480 GAGTTGTTTCCCAAGAGTTCCG 59.452 50.000 0.00 0.00 32.51 4.30
2603 2629 4.574674 ATGCAAAGTCCAGTCCATCTAA 57.425 40.909 0.00 0.00 0.00 2.10
2685 2711 6.653740 ACAAGATGGTAAAGTACTAACTTGCC 59.346 38.462 16.39 8.59 46.49 4.52
3057 3099 4.249638 AGGCCATACCACATACAACATT 57.750 40.909 5.01 0.00 43.14 2.71
3170 3212 7.092038 TGGCCATCATATATAAATGCTTAGGGA 60.092 37.037 0.00 0.00 0.00 4.20
3276 3318 7.015487 ACAGGCATTACATATGTGGCATATTTT 59.985 33.333 18.81 0.97 40.49 1.82
3640 3683 1.059098 ACATGCTTGGTCCACAGAGA 58.941 50.000 4.44 0.00 0.00 3.10
4029 4092 6.146898 CCGTTAGTGAAACAAAATAAGGTGG 58.853 40.000 0.00 0.00 41.43 4.61
4076 4142 3.221771 TGGCAGCAACATACTCAAAACT 58.778 40.909 0.00 0.00 0.00 2.66
4089 4155 1.661480 GCTCACAACATGGCAGCAA 59.339 52.632 0.00 0.00 0.00 3.91
4116 4182 4.160642 TGCTGATGAAGTGCCAATCTAT 57.839 40.909 0.00 0.00 0.00 1.98
4252 4318 8.397906 GCAAGCATTTACAGTCACATAAAGATA 58.602 33.333 0.00 0.00 0.00 1.98
4291 4370 8.946797 ATCCTCAAGGGGAAGATAATTAAATG 57.053 34.615 0.00 0.00 39.02 2.32
4316 4396 9.369904 GTCCGTGATAAGTACCAAAGTATTTAA 57.630 33.333 0.00 0.00 35.03 1.52
4381 4469 6.485984 AGTCAGCAAGCAATGGAGATAATAAG 59.514 38.462 0.00 0.00 0.00 1.73
4413 4501 4.394729 TCTAAGGAATCGGTGCAAGTTTT 58.605 39.130 0.00 0.00 0.00 2.43
4438 4526 0.608035 GAATCGGTGCAAGTTCCCCA 60.608 55.000 0.00 0.00 0.00 4.96
4439 4527 1.313091 GGAATCGGTGCAAGTTCCCC 61.313 60.000 8.65 0.00 35.24 4.81
4443 4531 3.695830 TCTAAGGAATCGGTGCAAGTT 57.304 42.857 0.00 0.00 0.00 2.66
4445 4533 5.335127 CAATTTCTAAGGAATCGGTGCAAG 58.665 41.667 0.00 0.00 0.00 4.01
4446 4534 4.157656 CCAATTTCTAAGGAATCGGTGCAA 59.842 41.667 0.00 0.00 0.00 4.08
4448 4536 3.694566 ACCAATTTCTAAGGAATCGGTGC 59.305 43.478 0.00 0.00 31.12 5.01
4449 4537 4.438744 GCACCAATTTCTAAGGAATCGGTG 60.439 45.833 13.32 13.32 42.21 4.94
4451 4539 3.947834 AGCACCAATTTCTAAGGAATCGG 59.052 43.478 0.00 0.00 0.00 4.18
4452 4540 6.049149 TCTAGCACCAATTTCTAAGGAATCG 58.951 40.000 0.00 0.00 0.00 3.34
4454 4542 8.494433 TGTATCTAGCACCAATTTCTAAGGAAT 58.506 33.333 0.00 0.00 0.00 3.01
4455 4543 7.857456 TGTATCTAGCACCAATTTCTAAGGAA 58.143 34.615 0.00 0.00 0.00 3.36
4457 4545 7.389053 GGATGTATCTAGCACCAATTTCTAAGG 59.611 40.741 0.00 0.00 0.00 2.69
4458 4546 7.933577 TGGATGTATCTAGCACCAATTTCTAAG 59.066 37.037 0.00 0.00 0.00 2.18
4459 4547 7.801104 TGGATGTATCTAGCACCAATTTCTAA 58.199 34.615 0.00 0.00 0.00 2.10
4460 4548 7.373617 TGGATGTATCTAGCACCAATTTCTA 57.626 36.000 0.00 0.00 0.00 2.10
4461 4549 6.252599 TGGATGTATCTAGCACCAATTTCT 57.747 37.500 0.00 0.00 0.00 2.52
4462 4550 7.516198 AATGGATGTATCTAGCACCAATTTC 57.484 36.000 0.00 0.00 0.00 2.17
4463 4551 7.560991 TCAAATGGATGTATCTAGCACCAATTT 59.439 33.333 0.00 0.00 0.00 1.82
4464 4552 7.062322 TCAAATGGATGTATCTAGCACCAATT 58.938 34.615 0.00 0.00 0.00 2.32
4469 4583 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
4471 4585 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
4472 4586 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
4477 4591 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
4478 4592 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
4479 4593 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
4488 4602 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
4489 4603 1.133915 TGTCCGAAAAAGCTTGTCCCT 60.134 47.619 0.00 0.00 0.00 4.20
4490 4604 1.266989 CTGTCCGAAAAAGCTTGTCCC 59.733 52.381 0.00 0.00 0.00 4.46
4491 4605 2.218603 TCTGTCCGAAAAAGCTTGTCC 58.781 47.619 0.00 0.00 0.00 4.02
4492 4606 2.224314 CCTCTGTCCGAAAAAGCTTGTC 59.776 50.000 0.00 0.00 0.00 3.18
4493 4607 2.222027 CCTCTGTCCGAAAAAGCTTGT 58.778 47.619 0.00 0.00 0.00 3.16
4494 4608 1.537202 CCCTCTGTCCGAAAAAGCTTG 59.463 52.381 0.00 0.00 0.00 4.01
4495 4609 1.420138 TCCCTCTGTCCGAAAAAGCTT 59.580 47.619 0.00 0.00 0.00 3.74
4497 4611 1.270893 ACTCCCTCTGTCCGAAAAAGC 60.271 52.381 0.00 0.00 0.00 3.51
4498 4612 2.841442 ACTCCCTCTGTCCGAAAAAG 57.159 50.000 0.00 0.00 0.00 2.27
4499 4613 5.684030 GCATATACTCCCTCTGTCCGAAAAA 60.684 44.000 0.00 0.00 0.00 1.94
4500 4614 4.202223 GCATATACTCCCTCTGTCCGAAAA 60.202 45.833 0.00 0.00 0.00 2.29
4501 4615 3.321111 GCATATACTCCCTCTGTCCGAAA 59.679 47.826 0.00 0.00 0.00 3.46
4502 4616 2.891580 GCATATACTCCCTCTGTCCGAA 59.108 50.000 0.00 0.00 0.00 4.30
4504 4618 2.239400 TGCATATACTCCCTCTGTCCG 58.761 52.381 0.00 0.00 0.00 4.79
4505 4619 4.689612 TTTGCATATACTCCCTCTGTCC 57.310 45.455 0.00 0.00 0.00 4.02
4506 4620 6.116126 AGTTTTTGCATATACTCCCTCTGTC 58.884 40.000 0.00 0.00 0.00 3.51
4507 4621 6.067217 AGTTTTTGCATATACTCCCTCTGT 57.933 37.500 0.00 0.00 0.00 3.41
4508 4622 8.682936 ATTAGTTTTTGCATATACTCCCTCTG 57.317 34.615 3.72 0.00 0.00 3.35
4509 4623 9.780186 GTATTAGTTTTTGCATATACTCCCTCT 57.220 33.333 3.72 0.00 0.00 3.69
4510 4624 9.780186 AGTATTAGTTTTTGCATATACTCCCTC 57.220 33.333 3.72 0.00 0.00 4.30
4535 5053 3.265791 GCATACAGAGGACAGGAACAAG 58.734 50.000 0.00 0.00 0.00 3.16
4663 5191 9.061610 GTACATGAAAGTAAATTCCAATTGTCG 57.938 33.333 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.