Multiple sequence alignment - TraesCS4A01G493500

Loading Multiple Alignment...

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 TraesCS4A01G493500 chr4A 100.000 5418 0 0 1 5418 742018937 742024354 0.000000e+00 10006
1 TraesCS4A01G493500 chr4A 89.340 3424 297 37 824 4216 740124073 740120687 0.000000e+00 4239
2 TraesCS4A01G493500 chr4A 85.644 2034 260 28 2193 4213 742159752 742157738 0.000000e+00 2109
3 TraesCS4A01G493500 chr4A 86.573 1914 230 15 2324 4216 739886463 739888370 0.000000e+00 2085
4 TraesCS4A01G493500 chr4A 88.578 1252 137 5 2966 4216 741805168 741806414 0.000000e+00 1515
5 TraesCS4A01G493500 chr4A 82.203 1843 228 62 386 2192 739605120 739606898 0.000000e+00 1495
6 TraesCS4A01G493500 chr4A 87.116 1203 146 8 3017 4216 741505834 741504638 0.000000e+00 1354
7 TraesCS4A01G493500 chr4A 86.121 1124 95 41 4323 5418 740497446 740498536 0.000000e+00 1155
8 TraesCS4A01G493500 chr4A 91.821 758 51 10 4325 5075 739609267 739610020 0.000000e+00 1046
9 TraesCS4A01G493500 chr4A 87.636 922 66 23 4448 5355 740134415 740133528 0.000000e+00 1027
10 TraesCS4A01G493500 chr4A 85.790 943 112 15 810 1748 742161150 742160226 0.000000e+00 979
11 TraesCS4A01G493500 chr4A 86.475 902 82 23 4239 5126 733984338 733983463 0.000000e+00 953
12 TraesCS4A01G493500 chr4A 87.402 762 63 21 4320 5062 733822145 733822892 0.000000e+00 845
13 TraesCS4A01G493500 chr4A 83.144 967 102 38 4231 5155 739888912 739889859 0.000000e+00 826
14 TraesCS4A01G493500 chr4A 89.456 588 53 8 4835 5416 740119728 740119144 0.000000e+00 734
15 TraesCS4A01G493500 chr4A 80.786 916 157 11 845 1758 741420759 741421657 0.000000e+00 699
16 TraesCS4A01G493500 chr4A 83.231 811 87 30 4372 5155 741504315 741503527 0.000000e+00 699
17 TraesCS4A01G493500 chr4A 87.002 577 59 15 4846 5418 733808767 733809331 2.130000e-178 636
18 TraesCS4A01G493500 chr4A 89.720 321 21 4 6 315 739983433 739983114 3.040000e-107 399
19 TraesCS4A01G493500 chr4A 90.096 313 16 5 6 309 739604506 739604812 5.090000e-105 392
20 TraesCS4A01G493500 chr4A 89.904 208 16 3 109 312 740152002 740151796 4.160000e-66 263
21 TraesCS4A01G493500 chr4A 90.270 185 15 2 3 186 740489158 740489340 7.010000e-59 239
22 TraesCS4A01G493500 chr4A 90.000 150 9 2 7 150 741362354 741362205 7.160000e-44 189
23 TraesCS4A01G493500 chr4A 88.462 156 14 2 157 309 740493829 740493983 9.270000e-43 185
24 TraesCS4A01G493500 chr4A 89.552 134 8 2 7 134 741406821 741406688 1.210000e-36 165
25 TraesCS4A01G493500 chr4A 90.909 99 8 1 217 315 741362190 741362093 1.220000e-26 132
26 TraesCS4A01G493500 chr4A 91.954 87 7 0 4238 4324 741504409 741504323 7.370000e-24 122
27 TraesCS4A01G493500 chr4A 95.833 72 3 0 309 380 742018546 742018475 3.430000e-22 117
28 TraesCS4A01G493500 chr7A 81.666 3398 494 82 856 4210 3156012 3152701 0.000000e+00 2704
29 TraesCS4A01G493500 chr7A 87.653 2041 227 20 2194 4216 3842815 3840782 0.000000e+00 2350
30 TraesCS4A01G493500 chr7A 85.263 2056 253 26 2193 4213 3804732 3802692 0.000000e+00 2073
31 TraesCS4A01G493500 chr7A 83.317 2038 296 29 2211 4216 2800573 2798548 0.000000e+00 1840
32 TraesCS4A01G493500 chr7A 86.170 1222 163 5 2256 3476 2685992 2684776 0.000000e+00 1315
33 TraesCS4A01G493500 chr7A 87.892 1115 91 26 4320 5416 3840328 3839240 0.000000e+00 1271
34 TraesCS4A01G493500 chr7A 88.828 913 87 9 832 1744 3844195 3843298 0.000000e+00 1107
35 TraesCS4A01G493500 chr7A 92.738 661 48 0 812 1472 3807733 3807073 0.000000e+00 955
36 TraesCS4A01G493500 chr7A 88.265 784 80 9 4637 5414 2126310 2125533 0.000000e+00 928
37 TraesCS4A01G493500 chr7A 81.606 984 157 17 853 1829 2805906 2804940 0.000000e+00 793
38 TraesCS4A01G493500 chr7A 83.802 747 85 24 4325 5055 3802026 3801300 0.000000e+00 676
39 TraesCS4A01G493500 chr7A 89.487 390 30 7 391 777 3808397 3808016 2.930000e-132 483
40 TraesCS4A01G493500 chr7D 88.004 2034 215 20 2194 4216 4009339 4007324 0.000000e+00 2377
41 TraesCS4A01G493500 chr7D 85.012 2035 273 27 2193 4210 3551291 3549272 0.000000e+00 2039
42 TraesCS4A01G493500 chr7D 84.907 1981 277 19 2238 4210 2903508 2901542 0.000000e+00 1982
43 TraesCS4A01G493500 chr7D 88.940 1085 93 19 4320 5391 4006766 4005696 0.000000e+00 1314
44 TraesCS4A01G493500 chr7D 88.251 1098 83 21 4330 5416 3421374 3420312 0.000000e+00 1271
45 TraesCS4A01G493500 chr7D 88.692 902 87 9 850 1751 4010596 4009710 0.000000e+00 1086
46 TraesCS4A01G493500 chr7D 87.470 830 70 18 4593 5414 2508419 2507616 0.000000e+00 926
47 TraesCS4A01G493500 chr7D 78.029 1370 216 53 853 2193 2904911 2903598 0.000000e+00 784
48 TraesCS4A01G493500 chr7D 90.112 536 43 8 4884 5414 2665117 2664587 0.000000e+00 688
49 TraesCS4A01G493500 chr7D 87.214 524 37 13 4268 4773 2678687 2678176 2.190000e-158 569
50 TraesCS4A01G493500 chr7D 94.848 330 13 2 5091 5418 2676437 2676110 3.740000e-141 512
51 TraesCS4A01G493500 chr7D 90.260 154 15 0 4325 4478 2509967 2509814 9.200000e-48 202
52 TraesCS4A01G493500 chr1D 83.448 2042 297 36 2193 4216 464795433 464797451 0.000000e+00 1860
53 TraesCS4A01G493500 chr1D 95.455 66 3 0 309 374 406720 406785 7.420000e-19 106
54 TraesCS4A01G493500 chr1D 93.056 72 5 0 309 380 42271030 42270959 7.420000e-19 106
55 TraesCS4A01G493500 chr1D 95.455 66 3 0 309 374 417369732 417369797 7.420000e-19 106
56 TraesCS4A01G493500 chr1D 93.056 72 5 0 309 380 427593882 427593811 7.420000e-19 106
57 TraesCS4A01G493500 chr4B 98.485 66 1 0 309 374 586860040 586860105 3.430000e-22 117
58 TraesCS4A01G493500 chr7B 96.970 66 2 0 309 374 616840697 616840762 1.600000e-20 111
59 TraesCS4A01G493500 chr5D 96.970 66 2 0 309 374 407376705 407376770 1.600000e-20 111
60 TraesCS4A01G493500 chr2A 92.105 76 4 2 311 385 3971038 3971112 7.420000e-19 106


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 TraesCS4A01G493500 chr4A 742018937 742024354 5417 False 10006.000000 10006 100.000000 1 5418 1 chr4A.!!$F6 5417
1 TraesCS4A01G493500 chr4A 740119144 740124073 4929 True 2486.500000 4239 89.398000 824 5416 2 chr4A.!!$R7 4592
2 TraesCS4A01G493500 chr4A 742157738 742161150 3412 True 1544.000000 2109 85.717000 810 4213 2 chr4A.!!$R10 3403
3 TraesCS4A01G493500 chr4A 741805168 741806414 1246 False 1515.000000 1515 88.578000 2966 4216 1 chr4A.!!$F5 1250
4 TraesCS4A01G493500 chr4A 739886463 739889859 3396 False 1455.500000 2085 84.858500 2324 5155 2 chr4A.!!$F8 2831
5 TraesCS4A01G493500 chr4A 740133528 740134415 887 True 1027.000000 1027 87.636000 4448 5355 1 chr4A.!!$R3 907
6 TraesCS4A01G493500 chr4A 739604506 739610020 5514 False 977.666667 1495 88.040000 6 5075 3 chr4A.!!$F7 5069
7 TraesCS4A01G493500 chr4A 733983463 733984338 875 True 953.000000 953 86.475000 4239 5126 1 chr4A.!!$R1 887
8 TraesCS4A01G493500 chr4A 733822145 733822892 747 False 845.000000 845 87.402000 4320 5062 1 chr4A.!!$F2 742
9 TraesCS4A01G493500 chr4A 741503527 741505834 2307 True 725.000000 1354 87.433667 3017 5155 3 chr4A.!!$R9 2138
10 TraesCS4A01G493500 chr4A 741420759 741421657 898 False 699.000000 699 80.786000 845 1758 1 chr4A.!!$F4 913
11 TraesCS4A01G493500 chr4A 740493829 740498536 4707 False 670.000000 1155 87.291500 157 5418 2 chr4A.!!$F9 5261
12 TraesCS4A01G493500 chr4A 733808767 733809331 564 False 636.000000 636 87.002000 4846 5418 1 chr4A.!!$F1 572
13 TraesCS4A01G493500 chr7A 3152701 3156012 3311 True 2704.000000 2704 81.666000 856 4210 1 chr7A.!!$R5 3354
14 TraesCS4A01G493500 chr7A 2798548 2800573 2025 True 1840.000000 1840 83.317000 2211 4216 1 chr7A.!!$R3 2005
15 TraesCS4A01G493500 chr7A 3839240 3844195 4955 True 1576.000000 2350 88.124333 832 5416 3 chr7A.!!$R7 4584
16 TraesCS4A01G493500 chr7A 2684776 2685992 1216 True 1315.000000 1315 86.170000 2256 3476 1 chr7A.!!$R2 1220
17 TraesCS4A01G493500 chr7A 3801300 3808397 7097 True 1046.750000 2073 87.822500 391 5055 4 chr7A.!!$R6 4664
18 TraesCS4A01G493500 chr7A 2125533 2126310 777 True 928.000000 928 88.265000 4637 5414 1 chr7A.!!$R1 777
19 TraesCS4A01G493500 chr7A 2804940 2805906 966 True 793.000000 793 81.606000 853 1829 1 chr7A.!!$R4 976
20 TraesCS4A01G493500 chr7D 3549272 3551291 2019 True 2039.000000 2039 85.012000 2193 4210 1 chr7D.!!$R3 2017
21 TraesCS4A01G493500 chr7D 4005696 4010596 4900 True 1592.333333 2377 88.545333 850 5391 3 chr7D.!!$R7 4541
22 TraesCS4A01G493500 chr7D 2901542 2904911 3369 True 1383.000000 1982 81.468000 853 4210 2 chr7D.!!$R6 3357
23 TraesCS4A01G493500 chr7D 3420312 3421374 1062 True 1271.000000 1271 88.251000 4330 5416 1 chr7D.!!$R2 1086
24 TraesCS4A01G493500 chr7D 2664587 2665117 530 True 688.000000 688 90.112000 4884 5414 1 chr7D.!!$R1 530
25 TraesCS4A01G493500 chr7D 2507616 2509967 2351 True 564.000000 926 88.865000 4325 5414 2 chr7D.!!$R4 1089
26 TraesCS4A01G493500 chr7D 2676110 2678687 2577 True 540.500000 569 91.031000 4268 5418 2 chr7D.!!$R5 1150
27 TraesCS4A01G493500 chr1D 464795433 464797451 2018 False 1860.000000 1860 83.448000 2193 4216 1 chr1D.!!$F3 2023

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
248 255 0.606401 CTGATTGCCAGGTTGACCGT 60.606 55.0 0.00 0.0 42.08 4.83 F
351 364 0.612744 TCACATGACGGGCAATGAGA 59.387 50.0 0.00 0.0 0.00 3.27 F
353 366 0.745845 ACATGACGGGCAATGAGAGC 60.746 55.0 0.00 0.0 0.00 4.09 F
1782 4050 0.178068 TTAGATGAAGGGCAGCCGAC 59.822 55.0 5.00 0.0 31.91 4.79 F
2245 4703 0.333993 AAGGAGGCTGGCATTCATGT 59.666 50.0 3.38 0.0 0.00 3.21 F
3759 6277 0.319555 CGCTTTCTCCACAACTCCGA 60.320 55.0 0.00 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 3560 1.000396 AGATGTCTTGCCAAGGCCC 60.000 57.895 6.59 0.0 41.09 5.80 R
1782 4050 2.546795 CCTCTTTCTCGGGATTCATCGG 60.547 54.545 0.00 0.0 0.00 4.18 R
1921 4204 2.811431 CGCAAACCCTCAATGTAAGACA 59.189 45.455 0.00 0.0 0.00 3.41 R
3162 5661 0.526096 CACCGCACATGGCAATAAGC 60.526 55.000 0.00 0.0 45.17 3.09 R
4004 6528 0.892063 GACCGGCATATCTCCCTCTC 59.108 60.000 0.00 0.0 0.00 3.20 R
4791 9978 1.610886 CGAAACCCCAAGACCCTCTTC 60.611 57.143 0.00 0.0 33.78 2.87 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
40 41 7.042051 TGTGCAAGTAGATTTTGAGTTAGTCAC 60.042 37.037 0.00 0.00 33.71 3.67
62 63 5.516696 CACAGTACTATTTCATCACCACTCG 59.483 44.000 0.00 0.00 0.00 4.18
90 91 4.513318 TCTGTTTCACGACACATGCATTAA 59.487 37.500 0.00 0.00 0.00 1.40
101 102 6.183360 CGACACATGCATTAATTGAAAGTTGG 60.183 38.462 0.00 0.00 0.00 3.77
150 151 4.174411 TGATAGACGAACCTTGTGTCAG 57.826 45.455 0.00 0.00 35.09 3.51
154 155 1.151777 ACGAACCTTGTGTCAGTGCG 61.152 55.000 0.00 0.00 0.00 5.34
173 174 1.956477 CGGCTAAAAGGGCATGCTTAT 59.044 47.619 18.92 0.35 0.00 1.73
184 185 3.244840 GGGCATGCTTATCTCTCCAGATT 60.245 47.826 18.92 0.00 40.18 2.40
210 211 9.743581 TGCATGAATTACATATATGGAACAGAT 57.256 29.630 12.71 2.47 44.98 2.90
222 229 2.978978 TGGAACAGATTGAACAGGAGGA 59.021 45.455 0.00 0.00 0.00 3.71
247 254 2.174334 CTGATTGCCAGGTTGACCG 58.826 57.895 0.00 0.00 42.08 4.79
248 255 0.606401 CTGATTGCCAGGTTGACCGT 60.606 55.000 0.00 0.00 42.08 4.83
291 304 3.353836 GTGGTGCCGTGAACGCAT 61.354 61.111 0.00 0.00 38.18 4.73
309 322 4.216042 ACGCATTTGATGATGAAGTTGACA 59.784 37.500 0.00 0.00 0.00 3.58
312 325 5.575606 GCATTTGATGATGAAGTTGACAAGG 59.424 40.000 0.00 0.00 0.00 3.61
315 328 6.748333 TTGATGATGAAGTTGACAAGGATC 57.252 37.500 0.00 0.00 0.00 3.36
316 329 5.807909 TGATGATGAAGTTGACAAGGATCA 58.192 37.500 0.00 0.00 0.00 2.92
317 330 5.878669 TGATGATGAAGTTGACAAGGATCAG 59.121 40.000 0.00 0.00 0.00 2.90
318 331 5.488262 TGATGAAGTTGACAAGGATCAGA 57.512 39.130 0.00 0.00 0.00 3.27
319 332 5.485620 TGATGAAGTTGACAAGGATCAGAG 58.514 41.667 0.00 0.00 0.00 3.35
321 334 5.296151 TGAAGTTGACAAGGATCAGAGTT 57.704 39.130 0.00 0.00 0.00 3.01
322 335 5.684704 TGAAGTTGACAAGGATCAGAGTTT 58.315 37.500 0.00 0.00 0.00 2.66
323 336 5.760253 TGAAGTTGACAAGGATCAGAGTTTC 59.240 40.000 0.00 0.00 0.00 2.78
324 337 4.646572 AGTTGACAAGGATCAGAGTTTCC 58.353 43.478 0.00 0.00 0.00 3.13
325 338 3.703001 TGACAAGGATCAGAGTTTCCC 57.297 47.619 0.00 0.00 32.05 3.97
326 339 2.305927 TGACAAGGATCAGAGTTTCCCC 59.694 50.000 0.00 0.00 32.05 4.81
327 340 2.573915 GACAAGGATCAGAGTTTCCCCT 59.426 50.000 0.00 0.00 32.05 4.79
329 342 3.777522 ACAAGGATCAGAGTTTCCCCTAG 59.222 47.826 0.00 0.00 32.05 3.02
330 343 4.033709 CAAGGATCAGAGTTTCCCCTAGA 58.966 47.826 0.00 0.00 32.05 2.43
331 344 3.922375 AGGATCAGAGTTTCCCCTAGAG 58.078 50.000 0.00 0.00 32.05 2.43
332 345 3.273618 AGGATCAGAGTTTCCCCTAGAGT 59.726 47.826 0.00 0.00 32.05 3.24
333 346 3.639561 GGATCAGAGTTTCCCCTAGAGTC 59.360 52.174 0.00 0.00 0.00 3.36
335 348 3.432378 TCAGAGTTTCCCCTAGAGTCAC 58.568 50.000 0.00 0.00 0.00 3.67
338 351 3.772025 AGAGTTTCCCCTAGAGTCACATG 59.228 47.826 0.00 0.00 0.00 3.21
339 352 3.769844 GAGTTTCCCCTAGAGTCACATGA 59.230 47.826 0.00 0.00 0.00 3.07
340 353 3.515901 AGTTTCCCCTAGAGTCACATGAC 59.484 47.826 0.00 3.72 45.08 3.06
350 363 0.729116 GTCACATGACGGGCAATGAG 59.271 55.000 0.00 0.00 35.12 2.90
351 364 0.612744 TCACATGACGGGCAATGAGA 59.387 50.000 0.00 0.00 0.00 3.27
352 365 1.012086 CACATGACGGGCAATGAGAG 58.988 55.000 0.00 0.00 0.00 3.20
353 366 0.745845 ACATGACGGGCAATGAGAGC 60.746 55.000 0.00 0.00 0.00 4.09
360 373 3.918220 GCAATGAGAGCCGCGACG 61.918 66.667 8.23 0.00 0.00 5.12
361 374 2.202610 CAATGAGAGCCGCGACGA 60.203 61.111 8.23 0.00 0.00 4.20
362 375 2.202623 AATGAGAGCCGCGACGAC 60.203 61.111 8.23 0.00 0.00 4.34
363 376 4.538283 ATGAGAGCCGCGACGACG 62.538 66.667 8.23 2.12 42.93 5.12
373 433 4.238385 CGACGACGCCTTCAAGAA 57.762 55.556 0.00 0.00 0.00 2.52
374 434 2.513159 CGACGACGCCTTCAAGAAA 58.487 52.632 0.00 0.00 0.00 2.52
422 667 7.504926 AACATAATGGGGTACTAGTTCTCAA 57.495 36.000 0.00 0.00 0.00 3.02
423 668 7.691993 ACATAATGGGGTACTAGTTCTCAAT 57.308 36.000 0.00 0.00 0.00 2.57
516 762 3.123790 TCGTACCATGTGCATTTAACACG 59.876 43.478 0.00 0.00 41.03 4.49
522 768 1.876799 TGTGCATTTAACACGGTCAGG 59.123 47.619 0.00 0.00 41.03 3.86
530 776 1.204146 AACACGGTCAGGGCATAGAT 58.796 50.000 0.00 0.00 0.00 1.98
531 777 2.082140 ACACGGTCAGGGCATAGATA 57.918 50.000 0.00 0.00 0.00 1.98
534 780 2.300152 CACGGTCAGGGCATAGATACAT 59.700 50.000 0.00 0.00 0.00 2.29
558 804 3.126171 TGATTAGTTGTACCAATGCACGC 59.874 43.478 0.00 0.00 0.00 5.34
559 805 1.444836 TAGTTGTACCAATGCACGCC 58.555 50.000 0.00 0.00 0.00 5.68
596 842 1.560923 CACGGTCAAAGCCTAGATCG 58.439 55.000 0.00 1.57 43.60 3.69
664 910 1.139654 CATGCTTAGCTGTAGGGCTCA 59.860 52.381 5.60 0.00 42.97 4.26
714 960 7.645058 TGAGAATGGAAGACAAGTTTCTTTT 57.355 32.000 3.02 0.00 35.90 2.27
796 1050 4.596585 CCCACCCCACCCACACAC 62.597 72.222 0.00 0.00 0.00 3.82
802 1056 2.518349 CCACCCACACACCACACC 60.518 66.667 0.00 0.00 0.00 4.16
965 1477 2.743928 GCAGACAGGCGTCAAGGG 60.744 66.667 11.04 1.21 45.23 3.95
1174 1686 2.023673 TCAAGCCACACAAACTCAAGG 58.976 47.619 0.00 0.00 0.00 3.61
1308 1820 1.108727 TGTACAGGGTCCACGACGTT 61.109 55.000 0.00 0.00 32.65 3.99
1372 1884 2.035442 GCTCTGTTCAAGGACCGGC 61.035 63.158 0.00 0.00 0.00 6.13
1404 1916 7.696755 TCGTTGGTATTGATGATTCATTGAAG 58.303 34.615 5.21 0.00 0.00 3.02
1405 1917 7.552330 TCGTTGGTATTGATGATTCATTGAAGA 59.448 33.333 5.21 0.00 0.00 2.87
1482 3560 7.445945 AGATACTCTCTATTTTTGGATTCGGG 58.554 38.462 0.00 0.00 30.26 5.14
1526 3604 3.242739 GCCAAAGCACTGTATGATAACCG 60.243 47.826 0.00 0.00 39.53 4.44
1640 3718 4.689612 AGCTAAAGCATCGGGATTCTAA 57.310 40.909 4.54 0.00 45.16 2.10
1661 3739 7.735917 TCTAACTTATCGTCATGGGATGAAAT 58.264 34.615 9.57 0.00 42.13 2.17
1674 3752 3.378112 GGGATGAAATGCAGTTGATCGAA 59.622 43.478 17.82 0.00 35.75 3.71
1765 4031 6.189133 AGTAAATGGGAAAATTAGCGGGTTA 58.811 36.000 0.00 0.00 0.00 2.85
1772 4040 5.008712 GGGAAAATTAGCGGGTTAGATGAAG 59.991 44.000 0.00 0.00 0.00 3.02
1782 4050 0.178068 TTAGATGAAGGGCAGCCGAC 59.822 55.000 5.00 0.00 31.91 4.79
1810 4082 2.600790 TCCCGAGAAAGAGGTACACAA 58.399 47.619 0.00 0.00 0.00 3.33
1856 4136 8.671384 TTCATACATGTAAGTAGTAAATGGGC 57.329 34.615 10.14 0.00 32.27 5.36
1868 4150 7.221450 AGTAGTAAATGGGCGAAAATAGCATA 58.779 34.615 0.00 0.00 36.08 3.14
1942 4227 2.811431 TGTCTTACATTGAGGGTTTGCG 59.189 45.455 0.00 0.00 0.00 4.85
1964 4249 3.877508 GTGGCCTATGGTCATTCTTGTAC 59.122 47.826 3.32 0.00 40.40 2.90
1981 4268 5.748152 TCTTGTACATTTTGCAAAAGACTGC 59.252 36.000 27.08 15.98 42.95 4.40
2072 4387 5.687770 TGTTCGCCCACATTCATATATTG 57.312 39.130 0.00 0.00 0.00 1.90
2236 4694 0.622665 AGATTCCACAAGGAGGCTGG 59.377 55.000 0.00 0.00 46.74 4.85
2245 4703 0.333993 AAGGAGGCTGGCATTCATGT 59.666 50.000 3.38 0.00 0.00 3.21
2339 4810 2.098934 GCGTTATGGATGCCAATGACAA 59.901 45.455 0.00 0.00 36.95 3.18
2404 4877 3.391049 GAACTAGTCAAGACCGCTTTGT 58.609 45.455 0.00 0.00 30.14 2.83
2566 5039 5.649395 GCTGCAATAGAATGGCCTAATCATA 59.351 40.000 3.32 0.00 0.00 2.15
2575 5048 7.068702 AGAATGGCCTAATCATATTCCAACAA 58.931 34.615 3.32 0.00 0.00 2.83
2656 5129 3.826466 GCTAGTTTGCTTGCTGGTAAAG 58.174 45.455 0.00 0.00 39.71 1.85
2922 5395 5.560722 TTGGTGAGAGGTACTTCAATGAA 57.439 39.130 7.82 0.00 41.55 2.57
2997 5494 0.390124 TAACTGGGTGTCGTGTCCAC 59.610 55.000 0.00 0.00 0.00 4.02
3015 5512 6.645003 GTGTCCACGACATAATGCTTGATATA 59.355 38.462 0.00 0.00 44.63 0.86
3162 5661 3.664276 CGTCAACATTACAAGCAAGGTCG 60.664 47.826 0.00 0.00 0.00 4.79
3258 5757 1.819632 CCCCTGGTATTCGCACAGC 60.820 63.158 0.00 0.00 0.00 4.40
3318 5820 0.984995 GGCACCTCAAACTAGGGAGT 59.015 55.000 0.00 0.00 41.32 3.85
3366 5868 8.380742 AGGAAATAGGACATCTGAAGTTCTTA 57.619 34.615 4.17 0.00 0.00 2.10
3424 5929 3.772025 ACTTCCAGAGAGTATTGGTGGAG 59.228 47.826 0.00 0.00 38.53 3.86
3461 5966 9.248417 CAAGTGCTTGAACATTTGTGAAACAGG 62.248 40.741 6.08 0.00 45.69 4.00
3658 6169 2.028567 GCTGAGTCTGTAGCCAAACTCT 60.029 50.000 0.00 0.00 39.09 3.24
3730 6248 0.944238 TCATGAGGAGATCCCCTGGA 59.056 55.000 0.00 0.00 36.49 3.86
3759 6277 0.319555 CGCTTTCTCCACAACTCCGA 60.320 55.000 0.00 0.00 0.00 4.55
3807 6325 1.210155 GCTGGTGGCAACGATCAAC 59.790 57.895 0.00 0.00 41.35 3.18
4004 6528 1.083015 CAACGGTTGGCTCGTTTCG 60.083 57.895 13.03 0.00 46.85 3.46
4036 6560 0.250513 GCCGGTCCTTGAATCACTCT 59.749 55.000 1.90 0.00 0.00 3.24
4045 6569 2.479566 TGAATCACTCTGGTTCAGGC 57.520 50.000 0.00 0.00 42.07 4.85
4056 6580 1.339055 TGGTTCAGGCTCATAGCACAC 60.339 52.381 0.78 0.00 44.75 3.82
4137 6661 2.920490 GCTTAAGAGAGTCAGCGTCTTG 59.080 50.000 6.67 0.00 32.73 3.02
4154 6678 2.711009 TCTTGTTATATGCCCCTCCTGG 59.289 50.000 0.00 0.00 0.00 4.45
4183 6707 0.803117 GAAGGCTAAGGAAACGGTGC 59.197 55.000 0.00 0.00 0.00 5.01
4216 6742 1.836999 TATGCTGCCCAACCGTGTCT 61.837 55.000 0.00 0.00 0.00 3.41
4220 7465 1.202651 GCTGCCCAACCGTGTCTATAT 60.203 52.381 0.00 0.00 0.00 0.86
4293 7886 5.376854 AAATAACAGCAGTTGCCAGTAAG 57.623 39.130 4.52 0.00 43.38 2.34
4297 7890 1.211190 GCAGTTGCCAGTAAGCTGC 59.789 57.895 0.00 0.00 44.24 5.25
4451 8209 6.258899 GCGGAAAAAGAAAAGATATCAGGAC 58.741 40.000 5.32 0.00 0.00 3.85
4776 9962 2.609459 CTGTTGCTTCGTTGTTCACTCT 59.391 45.455 0.00 0.00 0.00 3.24
4791 9978 9.657121 GTTGTTCACTCTGAAAAAGAATTCTAG 57.343 33.333 8.75 1.95 38.22 2.43
4903 10142 2.159572 GCGTGTGTGTCTTGTTCTTTGT 60.160 45.455 0.00 0.00 0.00 2.83
5284 12183 2.754946 ACGGGCGAAAGAAGTATCAA 57.245 45.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.787085 ATCTACTTGCACAACTACTTTGAC 57.213 37.500 0.00 0.00 38.73 3.18
40 41 5.651530 ACGAGTGGTGATGAAATAGTACTG 58.348 41.667 5.39 0.00 0.00 2.74
126 127 6.096987 ACTGACACAAGGTTCGTCTATCATAT 59.903 38.462 0.00 0.00 0.00 1.78
127 128 5.417894 ACTGACACAAGGTTCGTCTATCATA 59.582 40.000 0.00 0.00 0.00 2.15
128 129 4.220821 ACTGACACAAGGTTCGTCTATCAT 59.779 41.667 0.00 0.00 0.00 2.45
129 130 3.572682 ACTGACACAAGGTTCGTCTATCA 59.427 43.478 0.00 0.00 0.00 2.15
130 131 3.921021 CACTGACACAAGGTTCGTCTATC 59.079 47.826 0.00 0.00 0.00 2.08
136 137 1.564622 CGCACTGACACAAGGTTCG 59.435 57.895 0.00 0.00 0.00 3.95
150 151 1.139520 CATGCCCTTTTAGCCGCAC 59.860 57.895 0.00 0.00 33.31 5.34
154 155 3.225940 AGATAAGCATGCCCTTTTAGCC 58.774 45.455 15.66 3.24 0.00 3.93
173 174 5.993055 TGTAATTCATGCAATCTGGAGAGA 58.007 37.500 0.00 0.00 0.00 3.10
184 185 9.743581 ATCTGTTCCATATATGTAATTCATGCA 57.256 29.630 11.73 0.00 37.91 3.96
210 211 0.108585 GGCACTGTCCTCCTGTTCAA 59.891 55.000 0.00 0.00 0.00 2.69
291 304 6.716173 TGATCCTTGTCAACTTCATCATCAAA 59.284 34.615 0.00 0.00 0.00 2.69
309 322 4.265078 ACTCTAGGGGAAACTCTGATCCTT 60.265 45.833 0.00 0.00 44.95 3.36
312 325 4.098807 GTGACTCTAGGGGAAACTCTGATC 59.901 50.000 0.00 0.00 44.95 2.92
315 328 3.165875 TGTGACTCTAGGGGAAACTCTG 58.834 50.000 0.00 0.00 44.95 3.35
316 329 6.565976 GTCATGTGACTCTAGGGGAAACTCT 61.566 48.000 5.91 0.00 42.77 3.24
317 330 3.769844 TCATGTGACTCTAGGGGAAACTC 59.230 47.826 0.00 0.00 0.00 3.01
318 331 3.515901 GTCATGTGACTCTAGGGGAAACT 59.484 47.826 5.91 0.00 41.65 2.66
319 332 3.676324 CGTCATGTGACTCTAGGGGAAAC 60.676 52.174 11.03 0.00 42.66 2.78
321 334 2.100197 CGTCATGTGACTCTAGGGGAA 58.900 52.381 11.03 0.00 42.66 3.97
322 335 1.685180 CCGTCATGTGACTCTAGGGGA 60.685 57.143 11.03 0.00 42.66 4.81
323 336 0.747255 CCGTCATGTGACTCTAGGGG 59.253 60.000 11.03 0.72 42.66 4.79
324 337 0.747255 CCCGTCATGTGACTCTAGGG 59.253 60.000 11.03 9.78 42.66 3.53
325 338 0.103208 GCCCGTCATGTGACTCTAGG 59.897 60.000 11.03 7.53 42.66 3.02
326 339 0.817654 TGCCCGTCATGTGACTCTAG 59.182 55.000 11.03 0.00 42.66 2.43
327 340 1.262417 TTGCCCGTCATGTGACTCTA 58.738 50.000 11.03 0.00 42.66 2.43
329 342 0.729116 CATTGCCCGTCATGTGACTC 59.271 55.000 11.03 1.87 42.66 3.36
330 343 0.324614 TCATTGCCCGTCATGTGACT 59.675 50.000 11.03 0.00 42.66 3.41
331 344 0.729116 CTCATTGCCCGTCATGTGAC 59.271 55.000 3.07 3.07 41.47 3.67
332 345 0.612744 TCTCATTGCCCGTCATGTGA 59.387 50.000 0.00 0.00 0.00 3.58
333 346 1.012086 CTCTCATTGCCCGTCATGTG 58.988 55.000 0.00 0.00 0.00 3.21
335 348 1.442526 GGCTCTCATTGCCCGTCATG 61.443 60.000 0.00 0.00 44.32 3.07
342 355 3.567797 GTCGCGGCTCTCATTGCC 61.568 66.667 1.90 0.00 46.42 4.52
344 357 2.202610 TCGTCGCGGCTCTCATTG 60.203 61.111 9.90 0.00 0.00 2.82
345 358 2.202623 GTCGTCGCGGCTCTCATT 60.203 61.111 9.90 0.00 0.00 2.57
346 359 4.538283 CGTCGTCGCGGCTCTCAT 62.538 66.667 9.90 0.00 0.00 2.90
495 741 3.412654 CGTGTTAAATGCACATGGTACG 58.587 45.455 0.00 0.00 36.71 3.67
508 754 2.568062 TCTATGCCCTGACCGTGTTAAA 59.432 45.455 0.00 0.00 0.00 1.52
516 762 3.324846 TCACATGTATCTATGCCCTGACC 59.675 47.826 0.00 0.00 0.00 4.02
522 768 7.969536 ACAACTAATCACATGTATCTATGCC 57.030 36.000 0.00 0.00 0.00 4.40
558 804 2.755836 GCTAAATGCACATGGTACGG 57.244 50.000 0.00 0.00 42.31 4.02
596 842 3.062774 GCTTTGGTTCAGCTAATCTCGTC 59.937 47.826 0.00 0.00 34.15 4.20
676 922 8.428852 TCTTCCATTCTCATATATTTTGTCCGA 58.571 33.333 0.00 0.00 0.00 4.55
731 977 7.594015 TCACACACTCGTCTTTATAGTTCTTTC 59.406 37.037 0.00 0.00 0.00 2.62
735 981 5.800941 CCTCACACACTCGTCTTTATAGTTC 59.199 44.000 0.00 0.00 0.00 3.01
779 1033 4.596585 GTGTGTGGGTGGGGTGGG 62.597 72.222 0.00 0.00 0.00 4.61
780 1034 4.596585 GGTGTGTGGGTGGGGTGG 62.597 72.222 0.00 0.00 0.00 4.61
781 1035 3.814906 TGGTGTGTGGGTGGGGTG 61.815 66.667 0.00 0.00 0.00 4.61
782 1036 3.816090 GTGGTGTGTGGGTGGGGT 61.816 66.667 0.00 0.00 0.00 4.95
787 1041 3.018193 TGGGTGTGGTGTGTGGGT 61.018 61.111 0.00 0.00 0.00 4.51
788 1042 2.518349 GTGGGTGTGGTGTGTGGG 60.518 66.667 0.00 0.00 0.00 4.61
791 1045 1.377987 GTGTGTGGGTGTGGTGTGT 60.378 57.895 0.00 0.00 0.00 3.72
792 1046 2.118404 GGTGTGTGGGTGTGGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
793 1047 2.274104 GGTGTGTGGGTGTGGTGT 59.726 61.111 0.00 0.00 0.00 4.16
796 1050 2.113139 GAGGGTGTGTGGGTGTGG 59.887 66.667 0.00 0.00 0.00 4.17
802 1056 2.116983 CTGAGGGTGAGGGTGTGTGG 62.117 65.000 0.00 0.00 0.00 4.17
906 1418 0.250901 GTTGGCCAAGCTTGAGGAGA 60.251 55.000 28.05 6.71 0.00 3.71
941 1453 4.099170 CGCCTGTCTGCAGCTTGC 62.099 66.667 9.47 8.00 45.29 4.01
965 1477 7.566760 TCTCTCTTGAGATACTCAACATCTC 57.433 40.000 9.67 5.57 44.27 2.75
1015 1527 2.203280 CACGTCCCCAACCTTGCA 60.203 61.111 0.00 0.00 0.00 4.08
1144 1656 1.980772 GTGGCTTGATGGCTGGCTT 60.981 57.895 2.00 0.00 42.34 4.35
1174 1686 2.437281 TCCCCATCTTCTTCATGAGCTC 59.563 50.000 6.82 6.82 0.00 4.09
1289 1801 1.108727 AACGTCGTGGACCCTGTACA 61.109 55.000 0.00 0.00 0.00 2.90
1372 1884 4.183865 TCATCAATACCAACGAGCTCTTG 58.816 43.478 12.85 14.24 0.00 3.02
1404 1916 7.041508 CCATCACTCATTATCTTGGTTAGCTTC 60.042 40.741 0.00 0.00 0.00 3.86
1405 1917 6.769822 CCATCACTCATTATCTTGGTTAGCTT 59.230 38.462 0.00 0.00 0.00 3.74
1482 3560 1.000396 AGATGTCTTGCCAAGGCCC 60.000 57.895 6.59 0.00 41.09 5.80
1526 3604 4.913924 CACTACAATCAAACTCTGCTTTGC 59.086 41.667 0.00 0.00 32.10 3.68
1640 3718 4.516698 GCATTTCATCCCATGACGATAAGT 59.483 41.667 0.00 0.00 39.39 2.24
1661 3739 2.731451 CGAAGTTCTTCGATCAACTGCA 59.269 45.455 24.63 0.00 46.52 4.41
1674 3752 5.769484 TCTCAAGTAACAGTCGAAGTTCT 57.231 39.130 7.68 3.83 0.00 3.01
1765 4031 2.586792 GTCGGCTGCCCTTCATCT 59.413 61.111 14.12 0.00 0.00 2.90
1772 4040 3.757248 ATTCATCGGTCGGCTGCCC 62.757 63.158 14.12 0.00 0.00 5.36
1782 4050 2.546795 CCTCTTTCTCGGGATTCATCGG 60.547 54.545 0.00 0.00 0.00 4.18
1856 4136 6.265577 CCTTCTGGGTTTTATGCTATTTTCG 58.734 40.000 0.00 0.00 0.00 3.46
1906 4189 8.944029 CAATGTAAGACAATGTCTCAGAAAGAT 58.056 33.333 17.02 0.72 42.59 2.40
1912 4195 5.583854 CCCTCAATGTAAGACAATGTCTCAG 59.416 44.000 17.02 1.26 42.59 3.35
1921 4204 2.811431 CGCAAACCCTCAATGTAAGACA 59.189 45.455 0.00 0.00 0.00 3.41
1922 4205 2.812011 ACGCAAACCCTCAATGTAAGAC 59.188 45.455 0.00 0.00 0.00 3.01
1923 4206 2.811431 CACGCAAACCCTCAATGTAAGA 59.189 45.455 0.00 0.00 0.00 2.10
1942 4227 3.004752 ACAAGAATGACCATAGGCCAC 57.995 47.619 5.01 0.00 0.00 5.01
2005 4309 5.582689 AATTATGGCAAAGAAGGTAGTGC 57.417 39.130 0.00 0.00 36.24 4.40
2159 4475 3.868077 CCATTTCATCGTCCAGAACTCTC 59.132 47.826 0.00 0.00 0.00 3.20
2375 4847 4.003648 GGTCTTGACTAGTTCCCATGTTG 58.996 47.826 0.00 0.00 0.00 3.33
2404 4877 2.359214 TGCTTCCGCAATTGTTACACAA 59.641 40.909 7.40 0.00 44.62 3.33
2656 5129 2.814336 CCTTAGACCAAAACTCCACAGC 59.186 50.000 0.00 0.00 0.00 4.40
2922 5395 6.392354 CATTATCATGCTTTTGTTCACCAGT 58.608 36.000 0.00 0.00 0.00 4.00
2948 5421 7.455953 TGCCATTATACTCATCTTCCTCTACAT 59.544 37.037 0.00 0.00 0.00 2.29
3162 5661 0.526096 CACCGCACATGGCAATAAGC 60.526 55.000 0.00 0.00 45.17 3.09
3258 5757 4.277672 CCAACATGCTCAAGATGATTAGGG 59.722 45.833 0.00 0.00 0.00 3.53
3318 5820 3.653164 TGGGAGCTCACTGATACCAATA 58.347 45.455 18.70 0.00 0.00 1.90
3366 5868 2.344592 TCACCCAAGTCCAATACCAGT 58.655 47.619 0.00 0.00 0.00 4.00
3461 5966 3.635433 CAGCATGGCACTACAATGC 57.365 52.632 0.34 0.34 45.34 3.56
3658 6169 4.824479 TGTCTATGACTTGGATCTTGCA 57.176 40.909 0.00 0.00 33.15 4.08
3730 6248 2.484264 GTGGAGAAAGCGCATACTGTTT 59.516 45.455 11.47 0.00 0.00 2.83
3741 6259 1.270358 ACTCGGAGTTGTGGAGAAAGC 60.270 52.381 4.45 0.00 0.00 3.51
3807 6325 1.377333 GTTGGGAAGAAGCGAGGGG 60.377 63.158 0.00 0.00 0.00 4.79
4004 6528 0.892063 GACCGGCATATCTCCCTCTC 59.108 60.000 0.00 0.00 0.00 3.20
4036 6560 0.983467 TGTGCTATGAGCCTGAACCA 59.017 50.000 0.00 0.00 41.51 3.67
4045 6569 3.131755 TCATCACTGGAGTGTGCTATGAG 59.868 47.826 6.68 0.00 45.76 2.90
4056 6580 2.812591 GCTAATGCCATCATCACTGGAG 59.187 50.000 0.00 0.00 35.70 3.86
4154 6678 1.680249 CCTTAGCCTTCTTGTGCTCCC 60.680 57.143 0.00 0.00 39.00 4.30
4183 6707 2.381589 CAGCATATCAATTGCACGCTG 58.618 47.619 18.16 18.16 42.62 5.18
4307 7905 5.991328 AAGATACACGCAGATTGGTAATG 57.009 39.130 0.00 0.00 0.00 1.90
4451 8209 0.946221 AGAGCAAACAGACGGAAGCG 60.946 55.000 0.00 0.00 0.00 4.68
4686 9864 5.464030 TTACTACGAAAGGCAGAGAAACT 57.536 39.130 0.00 0.00 0.00 2.66
4776 9962 7.978925 AGACCCTCTTCTAGAATTCTTTTTCA 58.021 34.615 14.36 0.00 0.00 2.69
4791 9978 1.610886 CGAAACCCCAAGACCCTCTTC 60.611 57.143 0.00 0.00 33.78 2.87
4903 10142 4.324331 CCCCCTAAACCAAAAACCAAAACA 60.324 41.667 0.00 0.00 0.00 2.83
5284 12183 7.768807 TTTTGGTACATAAACAAGCCATACT 57.231 32.000 0.00 0.00 39.30 2.12
5303 12202 6.209391 ACTCCTCACCTTTACATCAATTTTGG 59.791 38.462 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.