Multiple sequence alignment - TraesCS3B01G183600

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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 TraesCS3B01G183600 chr3B 100.000 3280 0 0 1 3280 194765814 194762535 0.000000e+00 6058.0
1 TraesCS3B01G183600 chr3B 100.000 2875 0 0 3597 6471 194762218 194759344 0.000000e+00 5310.0
2 TraesCS3B01G183600 chr3B 81.416 791 108 24 3875 4652 195100059 195099295 1.540000e-170 610.0
3 TraesCS3B01G183600 chr3B 83.268 508 70 10 2453 2954 195101264 195100766 2.750000e-123 453.0
4 TraesCS3B01G183600 chr3A 94.300 2035 84 18 1163 3179 154037595 154035575 0.000000e+00 3086.0
5 TraesCS3B01G183600 chr3A 95.080 1504 70 4 3597 5099 154035249 154033749 0.000000e+00 2364.0
6 TraesCS3B01G183600 chr3A 93.175 1392 68 14 5097 6470 154033590 154032208 0.000000e+00 2019.0
7 TraesCS3B01G183600 chr3A 88.953 1041 62 26 167 1174 154038637 154037617 0.000000e+00 1236.0
8 TraesCS3B01G183600 chr3A 81.830 798 98 30 3875 4652 154073977 154073207 1.530000e-175 627.0
9 TraesCS3B01G183600 chr3A 84.430 456 64 3 2453 2907 154075163 154074714 5.950000e-120 442.0
10 TraesCS3B01G183600 chr3A 93.878 147 7 2 1 145 154038881 154038735 3.040000e-53 220.0
11 TraesCS3B01G183600 chr3A 86.364 66 9 0 4903 4968 154072999 154072934 9.000000e-09 73.1
12 TraesCS3B01G183600 chr3D 95.188 1808 78 6 3945 5745 136405503 136403698 0.000000e+00 2848.0
13 TraesCS3B01G183600 chr3D 94.674 1258 52 9 1929 3179 136407230 136405981 0.000000e+00 1938.0
14 TraesCS3B01G183600 chr3D 89.083 1200 56 36 1 1174 136409293 136408143 0.000000e+00 1421.0
15 TraesCS3B01G183600 chr3D 95.396 782 20 7 1163 1931 136408121 136407343 0.000000e+00 1230.0
16 TraesCS3B01G183600 chr3D 89.356 761 30 12 5750 6471 136403650 136402902 0.000000e+00 909.0
17 TraesCS3B01G183600 chr3D 81.234 794 104 29 3875 4652 136416453 136415689 3.340000e-167 599.0
18 TraesCS3B01G183600 chr3D 92.128 343 25 1 3597 3937 136405885 136405543 3.510000e-132 483.0
19 TraesCS3B01G183600 chr3D 85.922 412 53 4 2514 2922 136417603 136417194 9.960000e-118 435.0
20 TraesCS3B01G183600 chr3D 87.097 62 7 1 4903 4964 136415483 136415423 1.160000e-07 69.4
21 TraesCS3B01G183600 chr3D 91.489 47 3 1 3704 3750 136405550 136405505 5.420000e-06 63.9
22 TraesCS3B01G183600 chr1A 81.553 309 42 5 6177 6470 186213496 186213188 2.330000e-59 241.0
23 TraesCS3B01G183600 chr1D 80.906 309 44 5 6177 6470 127505029 127504721 5.050000e-56 230.0
24 TraesCS3B01G183600 chr1D 98.630 73 1 0 3207 3279 276823056 276822984 5.270000e-26 130.0
25 TraesCS3B01G183600 chr1B 80.583 309 45 5 6177 6470 246455156 246454848 2.350000e-54 224.0
26 TraesCS3B01G183600 chr2D 78.169 284 56 6 6190 6470 498228526 498228246 6.670000e-40 176.0
27 TraesCS3B01G183600 chr2D 93.902 82 4 1 3198 3279 589522245 589522325 8.810000e-24 122.0
28 TraesCS3B01G183600 chr2D 90.909 88 6 2 3192 3279 32020707 32020792 4.100000e-22 117.0
29 TraesCS3B01G183600 chr6B 95.455 110 2 1 641 750 662096792 662096898 8.630000e-39 172.0
30 TraesCS3B01G183600 chr6B 95.062 81 4 0 3199 3279 472612053 472612133 1.890000e-25 128.0
31 TraesCS3B01G183600 chr6B 89.247 93 8 2 3188 3279 458503587 458503496 1.470000e-21 115.0
32 TraesCS3B01G183600 chr6A 98.630 73 1 0 3207 3279 93285788 93285716 5.270000e-26 130.0
33 TraesCS3B01G183600 chr2A 96.104 77 3 0 3203 3279 161948678 161948602 6.810000e-25 126.0
34 TraesCS3B01G183600 chr2A 95.000 80 4 0 3200 3279 350738126 350738205 6.810000e-25 126.0
35 TraesCS3B01G183600 chr2A 92.135 89 5 2 3192 3279 51498540 51498627 2.450000e-24 124.0


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 TraesCS3B01G183600 chr3B 194759344 194765814 6470 True 5684.000000 6058 100.000000 1 6471 2 chr3B.!!$R1 6470
1 TraesCS3B01G183600 chr3B 195099295 195101264 1969 True 531.500000 610 82.342000 2453 4652 2 chr3B.!!$R2 2199
2 TraesCS3B01G183600 chr3A 154032208 154038881 6673 True 1785.000000 3086 93.077200 1 6470 5 chr3A.!!$R1 6469
3 TraesCS3B01G183600 chr3A 154072934 154075163 2229 True 380.700000 627 84.208000 2453 4968 3 chr3A.!!$R2 2515
4 TraesCS3B01G183600 chr3D 136402902 136409293 6391 True 1270.414286 2848 92.473429 1 6471 7 chr3D.!!$R1 6470
5 TraesCS3B01G183600 chr3D 136415423 136417603 2180 True 367.800000 599 84.751000 2514 4964 3 chr3D.!!$R2 2450

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
446 540 0.739561 ACCTCGCGATGGTTCTCTAC 59.260 55.000 20.13 0.00 33.34 2.59 F
586 692 0.758734 GCCCCCATAATGCTTTTCCC 59.241 55.000 0.00 0.00 0.00 3.97 F
1954 2251 0.606401 ATGGTGTTCGTGCTTGAGGG 60.606 55.000 0.00 0.00 0.00 4.30 F
2318 2619 0.685785 TGTTGCTTTGCTCCCCAACA 60.686 50.000 8.68 8.68 43.51 3.33 F
3632 4302 1.808945 CGTTCTCTGCATTTCTTGGCT 59.191 47.619 0.00 0.00 0.00 4.75 F
3873 4546 1.081892 AATGTGTCAGCGACTCATGC 58.918 50.000 19.39 0.00 43.11 4.06 F
5143 6056 1.225637 GATTTGTACCACGCGTGCG 60.226 57.895 33.17 26.37 46.03 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2234 0.534203 TTCCCTCAAGCACGAACACC 60.534 55.000 0.00 0.00 0.00 4.16 R
2306 2607 1.425066 ACTCATCTTGTTGGGGAGCAA 59.575 47.619 0.00 0.00 0.00 3.91 R
2975 3281 1.826385 AGGACCTTTGGATGCTTTCG 58.174 50.000 0.00 0.00 0.00 3.46 R
3846 4519 2.603560 GTCGCTGACACATTAGGTTAGC 59.396 50.000 0.00 0.00 42.49 3.09 R
5138 6051 0.725784 GGCATGAAGAACAACGCACG 60.726 55.000 0.00 0.00 34.18 5.34 R
5439 6355 0.872021 CAAGCTGGTAGACGCGATCC 60.872 60.000 15.93 9.86 0.00 3.36 R
5994 7014 0.608640 CAGATACAGATACCCCGGGC 59.391 60.000 17.73 0.00 0.00 6.13 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
63 65 2.347490 GGGTCGAGCTTTGCCTCA 59.653 61.111 15.18 0.00 0.00 3.86
188 267 3.933048 GACCGACCGTCTCCTCCCA 62.933 68.421 0.00 0.00 38.57 4.37
209 295 3.699894 CTGCACCTCACCTCGCCT 61.700 66.667 0.00 0.00 0.00 5.52
210 296 3.655810 CTGCACCTCACCTCGCCTC 62.656 68.421 0.00 0.00 0.00 4.70
211 297 4.459089 GCACCTCACCTCGCCTCC 62.459 72.222 0.00 0.00 0.00 4.30
212 298 2.681778 CACCTCACCTCGCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
213 299 2.363147 ACCTCACCTCGCCTCCTC 60.363 66.667 0.00 0.00 0.00 3.71
214 300 3.522731 CCTCACCTCGCCTCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
215 301 4.200283 CTCACCTCGCCTCCTCGC 62.200 72.222 0.00 0.00 0.00 5.03
237 323 2.930682 CCTTTTTCTCGCCTACTACTGC 59.069 50.000 0.00 0.00 0.00 4.40
241 327 0.814410 TCTCGCCTACTACTGCCGAG 60.814 60.000 0.00 0.00 32.93 4.63
262 348 1.076513 TGCACCCCTACTACTGACTGA 59.923 52.381 0.00 0.00 0.00 3.41
263 349 2.176889 GCACCCCTACTACTGACTGAA 58.823 52.381 0.00 0.00 0.00 3.02
264 350 2.094130 GCACCCCTACTACTGACTGAAC 60.094 54.545 0.00 0.00 0.00 3.18
351 445 2.043450 CCGGTCTGCTCCTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
353 447 2.899505 GGTCTGCTCCTCCTCTGC 59.100 66.667 0.00 0.00 0.00 4.26
354 448 1.685421 GGTCTGCTCCTCCTCTGCT 60.685 63.158 0.00 0.00 0.00 4.24
355 449 1.516892 GTCTGCTCCTCCTCTGCTG 59.483 63.158 0.00 0.00 0.00 4.41
359 453 3.478274 CTCCTCCTCTGCTGCCCC 61.478 72.222 0.00 0.00 0.00 5.80
363 457 4.804420 TCCTCTGCTGCCCCCGAT 62.804 66.667 0.00 0.00 0.00 4.18
364 458 3.801997 CCTCTGCTGCCCCCGATT 61.802 66.667 0.00 0.00 0.00 3.34
365 459 2.203126 CTCTGCTGCCCCCGATTC 60.203 66.667 0.00 0.00 0.00 2.52
366 460 3.764160 CTCTGCTGCCCCCGATTCC 62.764 68.421 0.00 0.00 0.00 3.01
382 476 1.599606 TTCCGTCCTGCTCTGCTCTC 61.600 60.000 0.00 0.00 0.00 3.20
392 486 1.686115 GCTCTGCTCTCTTCTCCTCCT 60.686 57.143 0.00 0.00 0.00 3.69
397 491 3.448934 TGCTCTCTTCTCCTCCTTGATT 58.551 45.455 0.00 0.00 0.00 2.57
446 540 0.739561 ACCTCGCGATGGTTCTCTAC 59.260 55.000 20.13 0.00 33.34 2.59
447 541 1.025812 CCTCGCGATGGTTCTCTACT 58.974 55.000 10.36 0.00 0.00 2.57
448 542 1.002251 CCTCGCGATGGTTCTCTACTC 60.002 57.143 10.36 0.00 0.00 2.59
449 543 1.944024 CTCGCGATGGTTCTCTACTCT 59.056 52.381 10.36 0.00 0.00 3.24
450 544 2.356382 CTCGCGATGGTTCTCTACTCTT 59.644 50.000 10.36 0.00 0.00 2.85
575 681 3.007940 CGATGATACTCTTTGCCCCCATA 59.992 47.826 0.00 0.00 0.00 2.74
579 685 1.780503 ACTCTTTGCCCCCATAATGC 58.219 50.000 0.00 0.00 0.00 3.56
583 689 3.180507 TCTTTGCCCCCATAATGCTTTT 58.819 40.909 0.00 0.00 0.00 2.27
584 690 3.197549 TCTTTGCCCCCATAATGCTTTTC 59.802 43.478 0.00 0.00 0.00 2.29
585 691 1.494960 TGCCCCCATAATGCTTTTCC 58.505 50.000 0.00 0.00 0.00 3.13
586 692 0.758734 GCCCCCATAATGCTTTTCCC 59.241 55.000 0.00 0.00 0.00 3.97
587 693 1.423584 CCCCCATAATGCTTTTCCCC 58.576 55.000 0.00 0.00 0.00 4.81
625 734 2.286950 TGATGTTCTTGCGTGCTTTGTC 60.287 45.455 0.00 0.00 0.00 3.18
812 932 2.965147 ACAAGAAATCAACCAAGTGGGG 59.035 45.455 1.69 0.00 42.91 4.96
972 1096 2.407090 GTTTCATGCTTTTCAGGTGCC 58.593 47.619 0.00 0.00 0.00 5.01
973 1097 1.702182 TTCATGCTTTTCAGGTGCCA 58.298 45.000 0.00 0.00 0.00 4.92
990 1115 0.758734 CCATCTCTGTGGGCGGATTA 59.241 55.000 0.00 0.00 35.55 1.75
998 1123 3.964688 TCTGTGGGCGGATTAGATTAGAA 59.035 43.478 0.00 0.00 0.00 2.10
1024 1149 3.304324 GGTTCTCAAGAAGCTGCTTCAAC 60.304 47.826 35.77 29.05 45.93 3.18
1102 1227 8.385898 TGTACCTTCAATAGTTAACTTGGTTG 57.614 34.615 14.49 15.50 0.00 3.77
1103 1228 7.994334 TGTACCTTCAATAGTTAACTTGGTTGT 59.006 33.333 14.49 7.39 0.00 3.32
1112 1237 6.584185 AGTTAACTTGGTTGTTTTGTCAGT 57.416 33.333 1.12 0.00 0.00 3.41
1168 1301 6.239458 CCTTGCCCTCTTTAAAACAATAACCA 60.239 38.462 0.00 0.00 0.00 3.67
1212 1380 3.212685 TGATGCATGTGTGTGTTCTTGA 58.787 40.909 2.46 0.00 0.00 3.02
1233 1401 3.448093 TGAAACTGCATACCAATGGGA 57.552 42.857 3.55 0.00 38.05 4.37
1277 1445 9.905713 AATAACAGAATAATTAGAGGCTGTTGA 57.094 29.630 22.16 13.42 43.81 3.18
1426 1601 3.710326 ATGAATGCATGTCTGTGATGC 57.290 42.857 0.00 0.00 45.45 3.91
1429 1604 2.413310 ATGCATGTCTGTGATGCTCA 57.587 45.000 0.00 0.00 45.45 4.26
1546 1721 6.186420 TCTATTTATGCAGGCAAGTCCATA 57.814 37.500 0.00 0.00 37.29 2.74
1587 1762 4.526970 AGCTTCGGATGACCAATGTTAAT 58.473 39.130 0.00 0.00 35.59 1.40
1787 1968 1.270274 ACATGCAAAAGAAGATGCGCA 59.730 42.857 14.96 14.96 45.47 6.09
1937 2234 8.417106 GGATGTCAGGGATATACTACATGTATG 58.583 40.741 5.91 3.59 41.55 2.39
1940 2237 7.178451 TGTCAGGGATATACTACATGTATGGTG 59.822 40.741 5.91 0.00 41.55 4.17
1944 2241 7.033791 GGGATATACTACATGTATGGTGTTCG 58.966 42.308 5.91 0.00 41.55 3.95
1954 2251 0.606401 ATGGTGTTCGTGCTTGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
2030 2327 1.471119 ATGGCATCCTGCTTTCACTG 58.529 50.000 0.00 0.00 44.28 3.66
2069 2366 3.294214 AGCTGGCTTTCATTAGGAATGG 58.706 45.455 0.00 0.00 39.38 3.16
2111 2408 2.475487 GCAGTAACCTGTCGTTGAACTC 59.525 50.000 0.00 0.00 41.02 3.01
2112 2409 3.713288 CAGTAACCTGTCGTTGAACTCA 58.287 45.455 0.00 0.00 35.79 3.41
2114 2411 4.150627 CAGTAACCTGTCGTTGAACTCATG 59.849 45.833 0.00 0.00 35.79 3.07
2115 2412 3.469008 AACCTGTCGTTGAACTCATGA 57.531 42.857 0.00 0.00 31.79 3.07
2174 2471 3.092301 GGCTCCCAGCAAAGAAATACTT 58.908 45.455 0.00 0.00 44.75 2.24
2240 2541 4.110036 CCAGCTACTGGTAATTTTTGGC 57.890 45.455 5.43 0.00 45.82 4.52
2241 2542 3.427503 CCAGCTACTGGTAATTTTTGGCG 60.428 47.826 5.43 0.00 45.82 5.69
2318 2619 0.685785 TGTTGCTTTGCTCCCCAACA 60.686 50.000 8.68 8.68 43.51 3.33
2379 2680 3.740115 TGTACAGGCTTGTTCTTCTTCC 58.260 45.455 6.84 0.00 38.76 3.46
2654 2958 3.657634 TCTCATCGATGATAAAGGCAGC 58.342 45.455 27.43 0.00 36.02 5.25
2827 3131 2.715749 TCCTGCCACCAATATGTGAG 57.284 50.000 0.00 0.00 38.55 3.51
2832 3136 2.092267 TGCCACCAATATGTGAGCAGAT 60.092 45.455 0.00 0.00 37.44 2.90
2975 3281 4.188462 TCATGACATTGACGGTGAATACC 58.812 43.478 0.00 0.00 43.89 2.73
3036 3342 8.340618 ACTGTTGTTTGTGCTGATTATATCTT 57.659 30.769 0.00 0.00 0.00 2.40
3210 3880 5.637006 TGGTGCCATTTTTGTATGTACTC 57.363 39.130 0.00 0.00 0.00 2.59
3211 3881 4.461081 TGGTGCCATTTTTGTATGTACTCC 59.539 41.667 0.00 0.00 0.00 3.85
3213 3883 4.705023 GTGCCATTTTTGTATGTACTCCCT 59.295 41.667 0.00 0.00 0.00 4.20
3214 3884 4.947388 TGCCATTTTTGTATGTACTCCCTC 59.053 41.667 0.00 0.00 0.00 4.30
3215 3885 5.193679 GCCATTTTTGTATGTACTCCCTCT 58.806 41.667 0.00 0.00 0.00 3.69
3216 3886 5.066505 GCCATTTTTGTATGTACTCCCTCTG 59.933 44.000 0.00 0.00 0.00 3.35
3219 3889 7.827236 CCATTTTTGTATGTACTCCCTCTGTAA 59.173 37.037 0.00 0.00 0.00 2.41
3220 3890 9.226606 CATTTTTGTATGTACTCCCTCTGTAAA 57.773 33.333 0.00 0.00 0.00 2.01
3221 3891 8.842358 TTTTTGTATGTACTCCCTCTGTAAAG 57.158 34.615 0.00 0.00 0.00 1.85
3222 3892 7.786046 TTTGTATGTACTCCCTCTGTAAAGA 57.214 36.000 0.00 0.00 0.00 2.52
3223 3893 7.786046 TTGTATGTACTCCCTCTGTAAAGAA 57.214 36.000 0.00 0.00 0.00 2.52
3224 3894 7.786046 TGTATGTACTCCCTCTGTAAAGAAA 57.214 36.000 0.00 0.00 0.00 2.52
3225 3895 8.375493 TGTATGTACTCCCTCTGTAAAGAAAT 57.625 34.615 0.00 0.00 0.00 2.17
3226 3896 9.483489 TGTATGTACTCCCTCTGTAAAGAAATA 57.517 33.333 0.00 0.00 0.00 1.40
3233 3903 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
3234 3904 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
3235 3905 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
3236 3906 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
3266 3936 6.663944 ACTAAAATAGTGATCCAAACGCTC 57.336 37.500 0.00 0.00 37.69 5.03
3267 3937 6.407202 ACTAAAATAGTGATCCAAACGCTCT 58.593 36.000 0.00 0.00 37.69 4.09
3268 3938 6.879458 ACTAAAATAGTGATCCAAACGCTCTT 59.121 34.615 0.00 0.00 37.69 2.85
3269 3939 8.038944 ACTAAAATAGTGATCCAAACGCTCTTA 58.961 33.333 0.00 0.00 37.69 2.10
3270 3940 7.865706 AAAATAGTGATCCAAACGCTCTTAT 57.134 32.000 0.00 0.00 0.00 1.73
3271 3941 8.958119 AAAATAGTGATCCAAACGCTCTTATA 57.042 30.769 0.00 0.00 0.00 0.98
3272 3942 9.561069 AAAATAGTGATCCAAACGCTCTTATAT 57.439 29.630 0.00 0.00 0.00 0.86
3273 3943 9.561069 AAATAGTGATCCAAACGCTCTTATATT 57.439 29.630 0.00 0.00 0.00 1.28
3274 3944 9.561069 AATAGTGATCCAAACGCTCTTATATTT 57.439 29.630 0.00 0.00 0.00 1.40
3275 3945 7.484035 AGTGATCCAAACGCTCTTATATTTC 57.516 36.000 0.00 0.00 0.00 2.17
3276 3946 7.275920 AGTGATCCAAACGCTCTTATATTTCT 58.724 34.615 0.00 0.00 0.00 2.52
3277 3947 7.770897 AGTGATCCAAACGCTCTTATATTTCTT 59.229 33.333 0.00 0.00 0.00 2.52
3278 3948 8.398665 GTGATCCAAACGCTCTTATATTTCTTT 58.601 33.333 0.00 0.00 0.00 2.52
3279 3949 8.397906 TGATCCAAACGCTCTTATATTTCTTTG 58.602 33.333 0.00 0.00 0.00 2.77
3632 4302 1.808945 CGTTCTCTGCATTTCTTGGCT 59.191 47.619 0.00 0.00 0.00 4.75
3695 4365 3.245052 GCACTCCTGCAATAATCCCCTAT 60.245 47.826 0.00 0.00 43.62 2.57
3793 4465 6.280855 TCATTCGATACTTGGAGAAGAACA 57.719 37.500 0.00 0.00 32.98 3.18
3804 4476 6.607198 ACTTGGAGAAGAACAGGAAAAATGAA 59.393 34.615 0.00 0.00 32.98 2.57
3846 4519 7.502226 TCAAATTAGGTTGGCATATCACTAAGG 59.498 37.037 0.00 0.00 0.00 2.69
3873 4546 1.081892 AATGTGTCAGCGACTCATGC 58.918 50.000 19.39 0.00 43.11 4.06
3899 4573 3.698029 TTGCACTGCAGTCTTTCTTTC 57.302 42.857 18.64 0.00 40.61 2.62
3928 4609 9.362151 AGGATTTACACCTGAAATCAGTTTTTA 57.638 29.630 9.43 0.00 42.59 1.52
4162 4886 6.016610 TCCCCTTCTTTTTCAACTTTATCACG 60.017 38.462 0.00 0.00 0.00 4.35
4179 4903 5.633830 ATCACGACAAATGCAATCTCTTT 57.366 34.783 0.00 0.00 0.00 2.52
4339 5063 2.489329 CAAGTCGAATTCCACCATGCTT 59.511 45.455 0.00 0.00 0.00 3.91
4570 5295 6.713450 TGGTAAAAAGATGTCTTGGTTACTCC 59.287 38.462 18.93 10.88 37.39 3.85
4578 5303 1.559682 TCTTGGTTACTCCTCATGGCC 59.440 52.381 0.00 0.00 37.07 5.36
4809 5561 7.962441 ACACCCTAATAGCTGAATTTTGTTTT 58.038 30.769 0.00 0.00 0.00 2.43
4840 5592 2.787473 TTGTACCTGCCATCTCCTTG 57.213 50.000 0.00 0.00 0.00 3.61
5138 6051 2.695359 TCCTTCAGATTTGTACCACGC 58.305 47.619 0.00 0.00 0.00 5.34
5143 6056 1.225637 GATTTGTACCACGCGTGCG 60.226 57.895 33.17 26.37 46.03 5.34
5179 6092 5.327091 CCACTGAATTCATTCTTACAAGCG 58.673 41.667 8.96 0.00 37.67 4.68
5189 6102 1.871039 TCTTACAAGCGTTTCACCTGC 59.129 47.619 0.00 0.00 0.00 4.85
5212 6125 2.608752 GCAGCATTTTGAGACCCTTGTG 60.609 50.000 0.00 0.00 0.00 3.33
5478 6400 2.048603 GCCAGACCTGACCATTGCC 61.049 63.158 0.00 0.00 0.00 4.52
5507 6429 3.895998 CCTACTTAGGGAGTAACTCGGT 58.104 50.000 0.00 0.00 40.25 4.69
5509 6431 4.819088 CCTACTTAGGGAGTAACTCGGTAC 59.181 50.000 0.00 0.00 40.25 3.34
5545 6467 1.234821 TCACAATCCACACGAAAGGC 58.765 50.000 0.00 0.00 0.00 4.35
5599 6521 8.099364 ACTGTAGATGAATTGGTTGTAGTTTG 57.901 34.615 0.00 0.00 0.00 2.93
5601 6523 7.001674 TGTAGATGAATTGGTTGTAGTTTGGT 58.998 34.615 0.00 0.00 0.00 3.67
5603 6525 9.005777 GTAGATGAATTGGTTGTAGTTTGGTAA 57.994 33.333 0.00 0.00 0.00 2.85
5702 6624 3.005367 TGACGTGTTGATAGCTTCAGTGA 59.995 43.478 0.00 0.00 35.27 3.41
5724 6646 5.540337 TGACTCTGGAAGTGTGAATAGAACT 59.460 40.000 0.00 0.00 41.37 3.01
5766 6748 7.787028 ACCACTAGCAAAATAAAAACAAGGAA 58.213 30.769 0.00 0.00 0.00 3.36
5775 6757 9.276397 CAAAATAAAAACAAGGAAGCAAAACAG 57.724 29.630 0.00 0.00 0.00 3.16
5785 6767 6.521151 AGGAAGCAAAACAGAAGGATATTG 57.479 37.500 0.00 0.00 0.00 1.90
5797 6779 6.071728 ACAGAAGGATATTGCAAAACTTCAGG 60.072 38.462 24.60 20.30 37.41 3.86
5826 6808 4.543692 CACAATCTTCAGCTTTCAGGTTG 58.456 43.478 7.67 7.67 35.18 3.77
5865 6856 8.824781 CAGACATGTTTCCATCTAATCTAACTG 58.175 37.037 0.00 0.00 0.00 3.16
5889 6880 5.624344 AAAAGAATGTCTGCATCTCACAG 57.376 39.130 0.00 0.00 33.50 3.66
5898 6912 4.093115 GTCTGCATCTCACAGAACTTGATG 59.907 45.833 0.00 0.00 45.32 3.07
5994 7014 5.535406 AGGAGGGTTTACAGTGATATACGAG 59.465 44.000 0.00 0.00 0.00 4.18
5996 7016 4.038883 AGGGTTTACAGTGATATACGAGCC 59.961 45.833 0.00 0.00 0.00 4.70
6048 7068 3.119316 CCAGTAGTCCTACAAGCACTCAG 60.119 52.174 7.19 0.00 38.48 3.35
6063 7083 1.072331 ACTCAGAAAACCCGATGCAGT 59.928 47.619 0.00 0.00 0.00 4.40
6326 7349 2.360475 GGGTCCTTGGTGAGCAGC 60.360 66.667 0.00 0.00 34.46 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 51 2.048222 CGGTGAGGCAAAGCTCGA 60.048 61.111 0.00 0.00 0.00 4.04
77 79 2.687200 CCACACGGATGGGAGGGA 60.687 66.667 0.00 0.00 35.95 4.20
105 108 1.971695 GTTTGCAGGGAGGGGAACG 60.972 63.158 0.00 0.00 0.00 3.95
188 267 1.599047 CGAGGTGAGGTGCAGGAAT 59.401 57.895 0.00 0.00 0.00 3.01
209 295 1.375523 GCGAGAAAAAGGGCGAGGA 60.376 57.895 0.00 0.00 0.00 3.71
210 296 2.399356 GGCGAGAAAAAGGGCGAGG 61.399 63.158 0.00 0.00 0.00 4.63
211 297 0.108329 TAGGCGAGAAAAAGGGCGAG 60.108 55.000 0.00 0.00 0.00 5.03
212 298 0.390735 GTAGGCGAGAAAAAGGGCGA 60.391 55.000 0.00 0.00 0.00 5.54
213 299 0.391263 AGTAGGCGAGAAAAAGGGCG 60.391 55.000 0.00 0.00 0.00 6.13
214 300 2.093606 AGTAGTAGGCGAGAAAAAGGGC 60.094 50.000 0.00 0.00 0.00 5.19
215 301 3.522553 CAGTAGTAGGCGAGAAAAAGGG 58.477 50.000 0.00 0.00 0.00 3.95
216 302 2.930682 GCAGTAGTAGGCGAGAAAAAGG 59.069 50.000 0.00 0.00 0.00 3.11
237 323 0.683504 AGTAGTAGGGGTGCACTCGG 60.684 60.000 17.98 0.00 0.00 4.63
241 327 1.204941 CAGTCAGTAGTAGGGGTGCAC 59.795 57.143 8.80 8.80 0.00 4.57
248 334 2.108970 GGGGGTTCAGTCAGTAGTAGG 58.891 57.143 0.00 0.00 0.00 3.18
353 447 4.547367 GGACGGAATCGGGGGCAG 62.547 72.222 0.00 0.00 41.39 4.85
355 449 4.547367 CAGGACGGAATCGGGGGC 62.547 72.222 0.00 0.00 41.39 5.80
359 453 1.227089 CAGAGCAGGACGGAATCGG 60.227 63.158 0.00 0.00 41.39 4.18
361 455 0.529555 GAGCAGAGCAGGACGGAATC 60.530 60.000 0.00 0.00 0.00 2.52
362 456 0.975040 AGAGCAGAGCAGGACGGAAT 60.975 55.000 0.00 0.00 0.00 3.01
363 457 1.599606 GAGAGCAGAGCAGGACGGAA 61.600 60.000 0.00 0.00 0.00 4.30
364 458 2.036414 AGAGCAGAGCAGGACGGA 59.964 61.111 0.00 0.00 0.00 4.69
365 459 1.603236 AAGAGAGCAGAGCAGGACGG 61.603 60.000 0.00 0.00 0.00 4.79
366 460 0.179140 GAAGAGAGCAGAGCAGGACG 60.179 60.000 0.00 0.00 0.00 4.79
367 461 1.134946 GAGAAGAGAGCAGAGCAGGAC 59.865 57.143 0.00 0.00 0.00 3.85
368 462 1.473258 GAGAAGAGAGCAGAGCAGGA 58.527 55.000 0.00 0.00 0.00 3.86
369 463 0.461135 GGAGAAGAGAGCAGAGCAGG 59.539 60.000 0.00 0.00 0.00 4.85
382 476 3.008330 CAGCACAATCAAGGAGGAGAAG 58.992 50.000 0.00 0.00 0.00 2.85
392 486 1.001487 CGAGCAAACCAGCACAATCAA 60.001 47.619 0.00 0.00 36.85 2.57
397 491 1.785041 GAAGCGAGCAAACCAGCACA 61.785 55.000 0.00 0.00 36.85 4.57
446 540 5.793952 CGCACAATCAATCAAAAGAGAAGAG 59.206 40.000 0.00 0.00 0.00 2.85
447 541 5.469760 TCGCACAATCAATCAAAAGAGAAGA 59.530 36.000 0.00 0.00 0.00 2.87
448 542 5.692814 TCGCACAATCAATCAAAAGAGAAG 58.307 37.500 0.00 0.00 0.00 2.85
449 543 5.687770 TCGCACAATCAATCAAAAGAGAA 57.312 34.783 0.00 0.00 0.00 2.87
450 544 5.645067 AGATCGCACAATCAATCAAAAGAGA 59.355 36.000 0.00 0.00 0.00 3.10
503 606 5.400485 CAGAAAGAAAACGAAAGATTGCAGG 59.600 40.000 0.00 0.00 0.00 4.85
625 734 1.002468 CCCAGCAACAGACAAAACGAG 60.002 52.381 0.00 0.00 0.00 4.18
972 1096 1.688735 TCTAATCCGCCCACAGAGATG 59.311 52.381 0.00 0.00 0.00 2.90
973 1097 2.088104 TCTAATCCGCCCACAGAGAT 57.912 50.000 0.00 0.00 0.00 2.75
990 1115 7.047271 GCTTCTTGAGAACCATCTTCTAATCT 58.953 38.462 0.00 0.00 35.54 2.40
998 1123 2.305343 AGCAGCTTCTTGAGAACCATCT 59.695 45.455 0.00 0.00 39.10 2.90
1024 1149 4.654091 TTTTCTTGCCAACTCCAAAGAG 57.346 40.909 0.00 0.00 46.36 2.85
1086 1211 8.745590 ACTGACAAAACAACCAAGTTAACTATT 58.254 29.630 8.92 1.27 0.00 1.73
1087 1212 8.288689 ACTGACAAAACAACCAAGTTAACTAT 57.711 30.769 8.92 0.00 0.00 2.12
1089 1214 6.584185 ACTGACAAAACAACCAAGTTAACT 57.416 33.333 1.12 1.12 0.00 2.24
1102 1227 1.792118 GCACCCCCGACTGACAAAAC 61.792 60.000 0.00 0.00 0.00 2.43
1103 1228 1.527380 GCACCCCCGACTGACAAAA 60.527 57.895 0.00 0.00 0.00 2.44
1112 1237 1.634865 ATCATGTGATGCACCCCCGA 61.635 55.000 0.00 0.00 32.73 5.14
1212 1380 3.701040 GTCCCATTGGTATGCAGTTTCAT 59.299 43.478 1.20 0.00 0.00 2.57
1233 1401 7.442969 TCTGTTATTCCAACAAATTACGACTGT 59.557 33.333 0.00 0.00 0.00 3.55
1277 1445 5.905331 TCCTGACATAACTATCTGGACCATT 59.095 40.000 0.00 0.00 37.86 3.16
1426 1601 4.920376 ACAAACTCCAAAACATCGTTGAG 58.080 39.130 0.00 0.00 0.00 3.02
1429 1604 8.788806 TGATATAACAAACTCCAAAACATCGTT 58.211 29.630 0.00 0.00 0.00 3.85
1546 1721 1.630878 CTACCTTGCCAAAGAGGGTCT 59.369 52.381 0.00 0.00 37.36 3.85
1587 1762 7.333174 GGAGGAACAAACAGAACATTTCAAAAA 59.667 33.333 0.00 0.00 0.00 1.94
1756 1937 8.044060 TCTTCTTTTGCATGTAGTAAGAATGG 57.956 34.615 17.26 10.77 35.14 3.16
1787 1968 2.816087 CAACCACTGAAGTAGCTGCATT 59.184 45.455 4.12 0.00 0.00 3.56
1866 2047 7.813645 ACTAAACTAATTGCTTCCTTAAACCG 58.186 34.615 0.00 0.00 0.00 4.44
1937 2234 0.534203 TTCCCTCAAGCACGAACACC 60.534 55.000 0.00 0.00 0.00 4.16
1940 2237 3.071479 TGTAATTCCCTCAAGCACGAAC 58.929 45.455 0.00 0.00 0.00 3.95
1944 2241 6.759497 AATAGTTGTAATTCCCTCAAGCAC 57.241 37.500 0.00 0.00 0.00 4.40
2016 2313 6.899393 TGTTAAATTCAGTGAAAGCAGGAT 57.101 33.333 10.14 0.00 0.00 3.24
2019 2316 7.140705 TGTCATGTTAAATTCAGTGAAAGCAG 58.859 34.615 10.14 0.00 0.00 4.24
2030 2327 7.260603 AGCCAGCTAATTGTCATGTTAAATTC 58.739 34.615 0.00 0.00 0.00 2.17
2069 2366 3.801293 GCCATTTCATTAATGCCTGCTCC 60.801 47.826 10.76 0.00 41.93 4.70
2153 2450 2.728007 AGTATTTCTTTGCTGGGAGCC 58.272 47.619 0.00 0.00 41.51 4.70
2228 2528 3.636282 AGACACACGCCAAAAATTACC 57.364 42.857 0.00 0.00 0.00 2.85
2240 2541 6.457392 CCATCATCAAGGATAAAAGACACACG 60.457 42.308 0.00 0.00 0.00 4.49
2241 2542 6.183360 CCCATCATCAAGGATAAAAGACACAC 60.183 42.308 0.00 0.00 0.00 3.82
2306 2607 1.425066 ACTCATCTTGTTGGGGAGCAA 59.575 47.619 0.00 0.00 0.00 3.91
2310 2611 3.184628 AGATCACTCATCTTGTTGGGGA 58.815 45.455 0.00 0.00 38.95 4.81
2379 2680 7.008266 CACTAGCAACTACGGCATTTTAATTTG 59.992 37.037 0.00 0.00 0.00 2.32
2792 3096 6.071616 GGTGGCAGGAAATTAATTCACAGTTA 60.072 38.462 14.03 0.00 39.98 2.24
2827 3131 2.223203 CGTCCAATCTTTGCTCATCTGC 60.223 50.000 0.00 0.00 0.00 4.26
2832 3136 3.629855 TGTTTTCGTCCAATCTTTGCTCA 59.370 39.130 0.00 0.00 0.00 4.26
2947 3253 5.109210 TCACCGTCAATGTCATGATAGTTC 58.891 41.667 0.00 0.00 0.00 3.01
2975 3281 1.826385 AGGACCTTTGGATGCTTTCG 58.174 50.000 0.00 0.00 0.00 3.46
3096 3402 6.032956 AGTTCAGATACGGTGTTGTGAATA 57.967 37.500 8.13 0.00 0.00 1.75
3190 3860 4.705023 AGGGAGTACATACAAAAATGGCAC 59.295 41.667 0.00 0.00 0.00 5.01
3210 3880 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
3243 3913 6.407202 AGAGCGTTTGGATCACTATTTTAGT 58.593 36.000 0.00 0.00 40.28 2.24
3244 3914 6.910536 AGAGCGTTTGGATCACTATTTTAG 57.089 37.500 0.00 0.00 32.03 1.85
3245 3915 8.958119 ATAAGAGCGTTTGGATCACTATTTTA 57.042 30.769 0.00 0.00 32.03 1.52
3246 3916 7.865706 ATAAGAGCGTTTGGATCACTATTTT 57.134 32.000 0.00 0.00 32.03 1.82
3247 3917 9.561069 AATATAAGAGCGTTTGGATCACTATTT 57.439 29.630 0.00 0.00 32.03 1.40
3248 3918 9.561069 AAATATAAGAGCGTTTGGATCACTATT 57.439 29.630 0.00 0.00 32.03 1.73
3249 3919 9.209175 GAAATATAAGAGCGTTTGGATCACTAT 57.791 33.333 0.00 0.00 32.03 2.12
3250 3920 8.421784 AGAAATATAAGAGCGTTTGGATCACTA 58.578 33.333 0.00 0.00 32.03 2.74
3251 3921 7.275920 AGAAATATAAGAGCGTTTGGATCACT 58.724 34.615 0.00 0.00 32.03 3.41
3252 3922 7.484035 AGAAATATAAGAGCGTTTGGATCAC 57.516 36.000 0.00 0.00 32.03 3.06
3253 3923 8.397906 CAAAGAAATATAAGAGCGTTTGGATCA 58.602 33.333 0.00 0.00 32.03 2.92
3254 3924 8.773762 CAAAGAAATATAAGAGCGTTTGGATC 57.226 34.615 0.00 0.00 0.00 3.36
3632 4302 5.769662 ACATACAAGATGTTGCCAGAAAAGA 59.230 36.000 1.83 0.00 37.14 2.52
3688 4358 6.723977 AGTCTTTTAATTGTTGCAATAGGGGA 59.276 34.615 0.59 0.00 0.00 4.81
3811 4484 4.501400 GCCAACCTAATTTGACAGTTGCTT 60.501 41.667 0.00 0.00 37.17 3.91
3828 4501 3.214696 AGCCTTAGTGATATGCCAACC 57.785 47.619 0.00 0.00 0.00 3.77
3846 4519 2.603560 GTCGCTGACACATTAGGTTAGC 59.396 50.000 0.00 0.00 42.49 3.09
3873 4546 4.157289 AGAAAGACTGCAGTGCAAATATGG 59.843 41.667 27.27 8.77 38.41 2.74
3899 4573 6.674694 CTGATTTCAGGTGTAAATCCTCTG 57.325 41.667 0.00 0.00 40.89 3.35
3928 4609 9.990360 AAATTGAGACCCACGTTTTTATTAATT 57.010 25.926 0.00 0.00 0.00 1.40
4162 4886 9.076596 GGTAATTGTAAAGAGATTGCATTTGTC 57.923 33.333 0.00 0.00 33.42 3.18
4200 4924 6.931838 CCTGAATGGTAGTACACTTTCTGTA 58.068 40.000 2.06 0.00 33.91 2.74
4339 5063 2.502947 CTGGATGGAGATCAACACCTGA 59.497 50.000 0.00 0.00 38.81 3.86
4570 5295 6.118170 TGAGAATCTTCTTTTAGGCCATGAG 58.882 40.000 5.01 0.00 37.73 2.90
4578 5303 6.808008 TGGCAACTGAGAATCTTCTTTTAG 57.192 37.500 0.00 0.00 35.70 1.85
4770 5522 2.693267 GGGTGTCCCAGTAATCTGTC 57.307 55.000 0.00 0.00 44.65 3.51
4815 5567 3.763897 GGAGATGGCAGGTACAATTGTTT 59.236 43.478 17.78 0.07 0.00 2.83
4840 5592 8.268850 TGACTTATCACAGCTAAAAAGGAATC 57.731 34.615 0.00 0.00 0.00 2.52
5138 6051 0.725784 GGCATGAAGAACAACGCACG 60.726 55.000 0.00 0.00 34.18 5.34
5143 6056 3.988379 TTCAGTGGCATGAAGAACAAC 57.012 42.857 0.00 0.00 34.31 3.32
5189 6102 1.542492 AGGGTCTCAAAATGCTGCAG 58.458 50.000 10.11 10.11 0.00 4.41
5212 6125 1.875963 CTCGTGGAAATGGTGCACC 59.124 57.895 29.67 29.67 45.34 5.01
5439 6355 0.872021 CAAGCTGGTAGACGCGATCC 60.872 60.000 15.93 9.86 0.00 3.36
5478 6400 7.621796 AGTTACTCCCTAAGTAGGTGAATTTG 58.378 38.462 3.71 0.00 41.47 2.32
5545 6467 3.107601 TCACCCCTAGACTTCTTCCATG 58.892 50.000 0.00 0.00 0.00 3.66
5599 6521 3.078837 TCTTCCAGAAACGGCAATTACC 58.921 45.455 0.00 0.00 0.00 2.85
5601 6523 4.584874 TCATCTTCCAGAAACGGCAATTA 58.415 39.130 0.00 0.00 0.00 1.40
5603 6525 3.071874 TCATCTTCCAGAAACGGCAAT 57.928 42.857 0.00 0.00 0.00 3.56
5683 6605 3.579709 AGTCACTGAAGCTATCAACACG 58.420 45.455 0.00 0.00 37.67 4.49
5702 6624 7.179338 ACATAGTTCTATTCACACTTCCAGAGT 59.821 37.037 0.00 0.00 39.89 3.24
5724 6646 3.081061 GTGGTCATCAAAGTGGCACATA 58.919 45.455 21.41 1.89 44.52 2.29
5766 6748 5.726980 TTGCAATATCCTTCTGTTTTGCT 57.273 34.783 0.00 0.00 39.98 3.91
5775 6757 5.105063 GCCTGAAGTTTTGCAATATCCTTC 58.895 41.667 0.00 9.97 0.00 3.46
5785 6767 1.142474 GCACATGCCTGAAGTTTTGC 58.858 50.000 0.00 0.00 34.31 3.68
5797 6779 1.201647 AGCTGAAGATTGTGCACATGC 59.798 47.619 22.39 15.48 42.50 4.06
5826 6808 8.522830 TGGAAACATGTCTGATTAAATCTTTCC 58.477 33.333 0.00 4.50 35.71 3.13
5865 6856 6.369890 TCTGTGAGATGCAGACATTCTTTTAC 59.630 38.462 0.00 0.00 37.98 2.01
5898 6912 2.223272 GCTAACGGCTGCTAATTGAACC 60.223 50.000 0.00 0.00 38.06 3.62
5935 6949 4.387862 CGGTGATTTCCGTTATATACCTGC 59.612 45.833 0.00 0.00 44.77 4.85
5958 6972 1.558233 ACCCTCCTGTACTGTACTGC 58.442 55.000 17.98 0.00 0.00 4.40
5994 7014 0.608640 CAGATACAGATACCCCGGGC 59.391 60.000 17.73 0.00 0.00 6.13
5996 7016 4.601084 AGATACAGATACAGATACCCCGG 58.399 47.826 0.00 0.00 0.00 5.73
6048 7068 3.596214 TCTAGAACTGCATCGGGTTTTC 58.404 45.455 0.00 0.00 0.00 2.29
6063 7083 4.439700 CGGCCAGTTCGAGTATTTCTAGAA 60.440 45.833 2.24 0.00 35.90 2.10
6107 7127 2.202878 TTATCGGCTGGCGCTGTC 60.203 61.111 19.55 0.71 43.19 3.51
6226 7249 2.281484 TGAACTGGGCGCTTGTCC 60.281 61.111 7.64 0.00 38.10 4.02


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

AutoCloner maintained by Alex Coulton.