Multiple sequence alignment - TraesCS2A01G097200

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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 TraesCS2A01G097200 chr2A 100.000 2981 0 0 1 2981 51009654 51006674 0.000000e+00 5505.0
1 TraesCS2A01G097200 chr2D 91.313 1911 63 30 459 2320 48132554 48134410 0.000000e+00 2514.0
2 TraesCS2A01G097200 chr2D 87.558 643 52 11 2360 2981 48134413 48135048 0.000000e+00 719.0
3 TraesCS2A01G097200 chr2D 85.082 429 46 11 1 411 48131532 48131960 3.550000e-114 422.0
4 TraesCS2A01G097200 chr2D 76.203 395 73 14 1 377 624237534 624237925 3.920000e-44 189.0
5 TraesCS2A01G097200 chr2B 91.933 1847 53 23 523 2323 75846928 75848724 0.000000e+00 2497.0
6 TraesCS2A01G097200 chr2B 83.249 591 47 20 2411 2981 75848763 75849321 2.060000e-136 496.0
7 TraesCS2A01G097200 chr2B 75.567 397 78 14 1 379 653616633 653617028 8.490000e-41 178.0
8 TraesCS2A01G097200 chr2B 82.895 76 12 1 247 321 88972630 88972705 1.920000e-07 67.6
9 TraesCS2A01G097200 chr4D 88.997 309 34 0 1160 1468 315597323 315597631 1.680000e-102 383.0
10 TraesCS2A01G097200 chr4D 76.774 155 26 10 242 391 38596258 38596109 8.860000e-11 78.7
11 TraesCS2A01G097200 chr4B 88.599 307 35 0 1160 1466 393406270 393406576 1.010000e-99 374.0
12 TraesCS2A01G097200 chr4B 86.408 103 12 2 247 347 539501294 539501396 8.730000e-21 111.0
13 TraesCS2A01G097200 chr4A 88.562 306 35 0 1163 1468 159294850 159294545 3.630000e-99 372.0
14 TraesCS2A01G097200 chr3D 81.463 410 72 4 1061 1468 525917784 525917377 1.710000e-87 333.0
15 TraesCS2A01G097200 chr1A 81.875 320 51 5 1160 1477 58946920 58947234 2.280000e-66 263.0
16 TraesCS2A01G097200 chr1A 87.879 198 22 2 1160 1356 569139382 569139186 6.430000e-57 231.0
17 TraesCS2A01G097200 chr7D 77.916 403 67 16 1 383 474355005 474355405 6.430000e-57 231.0
18 TraesCS2A01G097200 chr1D 77.273 418 78 12 1 402 220416777 220417193 2.310000e-56 230.0
19 TraesCS2A01G097200 chr1D 75.758 396 70 17 1 371 7376907 7376513 3.050000e-40 176.0
20 TraesCS2A01G097200 chr1D 75.495 404 71 16 1 377 425563685 425564087 3.950000e-39 172.0
21 TraesCS2A01G097200 chr1D 76.803 319 56 11 1 302 359695044 359694727 2.380000e-36 163.0
22 TraesCS2A01G097200 chr1B 86.634 202 25 2 1156 1356 659780379 659780179 3.870000e-54 222.0
23 TraesCS2A01G097200 chr5A 74.866 374 68 13 1 358 367778514 367778877 2.390000e-31 147.0
24 TraesCS2A01G097200 chr5A 93.023 43 3 0 435 477 106810857 106810815 2.480000e-06 63.9
25 TraesCS2A01G097200 chr6B 79.670 182 36 1 1 182 615588342 615588162 2.410000e-26 130.0
26 TraesCS2A01G097200 chr3A 79.006 181 36 2 2 181 501010152 501010331 4.040000e-24 122.0
27 TraesCS2A01G097200 chr7A 83.193 119 18 2 247 364 13175087 13175204 1.130000e-19 108.0
28 TraesCS2A01G097200 chr7A 73.514 185 45 4 299 480 94393942 94393759 1.920000e-07 67.6
29 TraesCS2A01G097200 chr3B 72.868 387 78 19 2 370 347997122 347996745 1.130000e-19 108.0
30 TraesCS2A01G097200 chr3B 75.124 201 41 9 282 477 160618766 160618962 5.290000e-13 86.1
31 TraesCS2A01G097200 chr7B 83.673 98 12 3 263 358 65592131 65592226 4.090000e-14 89.8


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 TraesCS2A01G097200 chr2A 51006674 51009654 2980 True 5505.000000 5505 100.000000 1 2981 1 chr2A.!!$R1 2980
1 TraesCS2A01G097200 chr2D 48131532 48135048 3516 False 1218.333333 2514 87.984333 1 2981 3 chr2D.!!$F2 2980
2 TraesCS2A01G097200 chr2B 75846928 75849321 2393 False 1496.500000 2497 87.591000 523 2981 2 chr2B.!!$F3 2458

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
454 473 0.037046 GCATTTGAGGTGGCTTTGGG 60.037 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2961 0.394938 TAAGAGCGTTCTTGGCACCA 59.605 50.0 22.97 0.31 43.41 4.17 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
48 50 4.301505 GCATCTTCTGGGCGACAA 57.698 55.556 0.00 0.00 0.00 3.18
54 56 0.807667 CTTCTGGGCGACAATCTCCG 60.808 60.000 0.00 0.00 0.00 4.63
67 69 1.399714 ATCTCCGCCTTACATGACGA 58.600 50.000 0.00 0.00 0.00 4.20
69 71 1.134367 TCTCCGCCTTACATGACGAAG 59.866 52.381 0.00 0.00 0.00 3.79
72 74 1.752501 CGCCTTACATGACGAAGCCG 61.753 60.000 0.00 0.00 42.50 5.52
146 148 1.065928 CGGGCCAGACGACATCTAC 59.934 63.158 4.39 0.00 35.15 2.59
151 153 1.004595 CCAGACGACATCTACGACGA 58.995 55.000 0.00 0.00 35.15 4.20
153 155 1.392510 CAGACGACATCTACGACGACA 59.607 52.381 0.00 0.00 35.15 4.35
184 186 1.692042 AGGTGAGGATGGGGAGCAG 60.692 63.158 0.00 0.00 0.00 4.24
185 187 1.997874 GGTGAGGATGGGGAGCAGT 60.998 63.158 0.00 0.00 0.00 4.40
195 197 1.341156 GGGGAGCAGTAGTGGCAGAT 61.341 60.000 0.00 0.00 0.00 2.90
197 199 0.539051 GGAGCAGTAGTGGCAGATGT 59.461 55.000 0.00 0.00 0.00 3.06
198 200 1.065854 GGAGCAGTAGTGGCAGATGTT 60.066 52.381 0.00 0.00 0.00 2.71
199 201 2.005451 GAGCAGTAGTGGCAGATGTTG 58.995 52.381 0.00 0.00 0.00 3.33
200 202 1.089920 GCAGTAGTGGCAGATGTTGG 58.910 55.000 0.00 0.00 0.00 3.77
201 203 1.611673 GCAGTAGTGGCAGATGTTGGT 60.612 52.381 0.00 0.00 0.00 3.67
203 205 0.804989 GTAGTGGCAGATGTTGGTGC 59.195 55.000 0.00 0.00 39.08 5.01
207 222 1.001181 GTGGCAGATGTTGGTGCAATT 59.999 47.619 0.00 0.00 41.75 2.32
218 233 0.321346 GGTGCAATTTTGGAGGGTGG 59.679 55.000 0.00 0.00 0.00 4.61
240 258 2.270858 GGGAGGAGGAGGAAGAGTTTT 58.729 52.381 0.00 0.00 0.00 2.43
248 266 5.536538 GGAGGAGGAAGAGTTTTGTGATTTT 59.463 40.000 0.00 0.00 0.00 1.82
267 285 0.758310 TGGTGCAATTTGCTGTGGGA 60.758 50.000 21.19 0.00 45.31 4.37
314 332 3.941188 CGCCCAGACGCCCCATAT 61.941 66.667 0.00 0.00 0.00 1.78
315 333 2.032681 GCCCAGACGCCCCATATC 59.967 66.667 0.00 0.00 0.00 1.63
316 334 2.520536 GCCCAGACGCCCCATATCT 61.521 63.158 0.00 0.00 0.00 1.98
317 335 1.372683 CCCAGACGCCCCATATCTG 59.627 63.158 0.00 0.00 39.70 2.90
318 336 1.302033 CCAGACGCCCCATATCTGC 60.302 63.158 0.00 0.00 38.84 4.26
325 344 1.837439 CGCCCCATATCTGCCCTATAA 59.163 52.381 0.00 0.00 0.00 0.98
339 358 7.196187 TCTGCCCTATAATTGGACTGGATATA 58.804 38.462 0.00 0.00 0.00 0.86
347 366 3.360740 TGGACTGGATATATGGGGTGT 57.639 47.619 0.00 0.00 0.00 4.16
351 370 0.981183 TGGATATATGGGGTGTCGGC 59.019 55.000 0.00 0.00 0.00 5.54
370 389 0.889186 CCAGTCCCAACGTTTGAGGG 60.889 60.000 14.59 14.59 44.22 4.30
402 421 6.544928 AGAGTTTGTCTGGGTTGAAATTTT 57.455 33.333 0.00 0.00 32.57 1.82
403 422 7.654022 AGAGTTTGTCTGGGTTGAAATTTTA 57.346 32.000 0.00 0.00 32.57 1.52
411 430 4.153411 TGGGTTGAAATTTTATGACCGGT 58.847 39.130 6.92 6.92 0.00 5.28
413 432 4.218852 GGGTTGAAATTTTATGACCGGTCA 59.781 41.667 37.79 37.79 44.59 4.02
414 433 5.279056 GGGTTGAAATTTTATGACCGGTCAA 60.279 40.000 39.04 24.29 43.58 3.18
415 434 6.394809 GGTTGAAATTTTATGACCGGTCAAT 58.605 36.000 39.04 27.55 43.58 2.57
416 435 7.363094 GGGTTGAAATTTTATGACCGGTCAATA 60.363 37.037 39.04 26.50 43.58 1.90
417 436 8.030106 GGTTGAAATTTTATGACCGGTCAATAA 58.970 33.333 39.04 30.04 43.58 1.40
418 437 8.856247 GTTGAAATTTTATGACCGGTCAATAAC 58.144 33.333 39.04 23.06 43.58 1.89
429 448 0.451783 GTCAATAACCAAGCAGCCCG 59.548 55.000 0.00 0.00 0.00 6.13
430 449 0.326595 TCAATAACCAAGCAGCCCGA 59.673 50.000 0.00 0.00 0.00 5.14
431 450 1.064758 TCAATAACCAAGCAGCCCGAT 60.065 47.619 0.00 0.00 0.00 4.18
433 452 0.546122 ATAACCAAGCAGCCCGATGA 59.454 50.000 0.00 0.00 0.00 2.92
434 453 0.107703 TAACCAAGCAGCCCGATGAG 60.108 55.000 0.00 0.00 0.00 2.90
445 464 0.107017 CCCGATGAGGCATTTGAGGT 60.107 55.000 0.00 0.00 39.21 3.85
446 465 1.019673 CCGATGAGGCATTTGAGGTG 58.980 55.000 0.00 0.00 0.00 4.00
447 466 1.019673 CGATGAGGCATTTGAGGTGG 58.980 55.000 0.00 0.00 0.00 4.61
448 467 0.743097 GATGAGGCATTTGAGGTGGC 59.257 55.000 0.00 0.00 41.96 5.01
454 473 0.037046 GCATTTGAGGTGGCTTTGGG 60.037 55.000 0.00 0.00 0.00 4.12
455 474 0.037046 CATTTGAGGTGGCTTTGGGC 60.037 55.000 0.00 0.00 40.90 5.36
456 475 1.535204 ATTTGAGGTGGCTTTGGGCG 61.535 55.000 0.00 0.00 42.94 6.13
457 476 2.920076 TTTGAGGTGGCTTTGGGCGT 62.920 55.000 0.00 0.00 42.94 5.68
458 477 3.056328 GAGGTGGCTTTGGGCGTC 61.056 66.667 0.00 0.00 42.94 5.19
459 478 4.660938 AGGTGGCTTTGGGCGTCC 62.661 66.667 0.00 0.00 42.94 4.79
481 1045 5.069914 TCCGGCTGTAGATGCTCTTATTTTA 59.930 40.000 0.00 0.00 0.00 1.52
484 1048 7.041098 CCGGCTGTAGATGCTCTTATTTTATTT 60.041 37.037 0.00 0.00 0.00 1.40
505 1075 4.325028 TTTAAAGAGGCAGTACGACACA 57.675 40.909 0.00 0.00 0.00 3.72
533 1104 2.231478 CAGTGAAGTCTACACCGGACAT 59.769 50.000 9.46 0.00 38.82 3.06
564 1135 0.308684 CAAAGCAAAGCAGCACGAGA 59.691 50.000 0.00 0.00 36.85 4.04
691 1262 5.343325 GCTTTTTCGAGTTTGGTTCATCATC 59.657 40.000 0.00 0.00 0.00 2.92
692 1263 6.384258 TTTTTCGAGTTTGGTTCATCATCA 57.616 33.333 0.00 0.00 0.00 3.07
693 1264 5.611796 TTTCGAGTTTGGTTCATCATCAG 57.388 39.130 0.00 0.00 0.00 2.90
694 1265 4.535526 TCGAGTTTGGTTCATCATCAGA 57.464 40.909 0.00 0.00 0.00 3.27
695 1266 5.089970 TCGAGTTTGGTTCATCATCAGAT 57.910 39.130 0.00 0.00 33.87 2.90
708 1279 5.827666 CATCATCAGATGCATGCTTAAACA 58.172 37.500 20.33 0.00 44.61 2.83
755 1326 1.610102 CCGATCTGCCTTCCATCATCC 60.610 57.143 0.00 0.00 0.00 3.51
771 1342 4.838904 TCATCCATCCTCATCATCATCC 57.161 45.455 0.00 0.00 0.00 3.51
772 1343 3.197116 TCATCCATCCTCATCATCATCCG 59.803 47.826 0.00 0.00 0.00 4.18
782 1353 0.738975 TCATCATCCGTCGTCCAGTC 59.261 55.000 0.00 0.00 0.00 3.51
783 1354 0.741326 CATCATCCGTCGTCCAGTCT 59.259 55.000 0.00 0.00 0.00 3.24
784 1355 1.947456 CATCATCCGTCGTCCAGTCTA 59.053 52.381 0.00 0.00 0.00 2.59
814 1385 0.106268 TCAAGTCCAAGCCAAGCCAA 60.106 50.000 0.00 0.00 0.00 4.52
815 1386 0.316204 CAAGTCCAAGCCAAGCCAAG 59.684 55.000 0.00 0.00 0.00 3.61
816 1387 1.466851 AAGTCCAAGCCAAGCCAAGC 61.467 55.000 0.00 0.00 0.00 4.01
817 1388 2.601367 TCCAAGCCAAGCCAAGCC 60.601 61.111 0.00 0.00 0.00 4.35
818 1389 2.918802 CCAAGCCAAGCCAAGCCA 60.919 61.111 0.00 0.00 0.00 4.75
933 1539 2.112815 CCCGCCCTTTTCATCGTCC 61.113 63.158 0.00 0.00 0.00 4.79
965 1571 4.609866 TCACCCATATAGAGATCCGGAT 57.390 45.455 19.21 19.21 0.00 4.18
966 1572 5.727243 TCACCCATATAGAGATCCGGATA 57.273 43.478 19.15 1.03 0.00 2.59
967 1573 5.696030 TCACCCATATAGAGATCCGGATAG 58.304 45.833 19.15 0.11 0.00 2.08
968 1574 4.279671 CACCCATATAGAGATCCGGATAGC 59.720 50.000 19.15 12.46 0.00 2.97
990 1596 1.016130 GCTGCTAGCTTCGCTTGTCA 61.016 55.000 17.23 0.00 40.44 3.58
1034 1649 2.123251 GGGGATGAGAGGCGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
1036 1651 1.152652 GGGATGAGAGGCGAGGAGA 60.153 63.158 0.00 0.00 0.00 3.71
1472 2090 3.803082 CATCCACGCCGCCAACAG 61.803 66.667 0.00 0.00 0.00 3.16
1485 2103 4.394712 AACAGCTCCGGCGAAGGG 62.395 66.667 9.30 0.00 44.37 3.95
1605 2223 3.119096 GCCGACGTGGAGCTTTCC 61.119 66.667 0.00 0.00 42.00 3.13
1635 2253 2.202146 CTGTCGTCGTCGTCGTCC 60.202 66.667 11.41 4.92 38.33 4.79
1814 2435 0.248458 GAACAACAGCACCACCAACG 60.248 55.000 0.00 0.00 0.00 4.10
1836 2463 2.047844 GAGTCGCAGCTGCTTGGA 60.048 61.111 34.22 22.27 39.32 3.53
2076 2711 2.736670 AGCGCTCCAATAATCCCTTT 57.263 45.000 2.64 0.00 0.00 3.11
2213 2853 7.940850 TCCTTTTGGACTTTACTCATTCTTTG 58.059 34.615 0.00 0.00 45.19 2.77
2311 2951 1.391577 TGAATCAACCATGCATCCCG 58.608 50.000 0.00 0.00 0.00 5.14
2313 2953 2.233271 GAATCAACCATGCATCCCGAT 58.767 47.619 0.00 0.00 0.00 4.18
2315 2955 0.545646 TCAACCATGCATCCCGATCA 59.454 50.000 0.00 0.00 0.00 2.92
2316 2956 0.949397 CAACCATGCATCCCGATCAG 59.051 55.000 0.00 0.00 0.00 2.90
2318 2958 1.970114 CCATGCATCCCGATCAGGC 60.970 63.158 0.00 0.00 39.21 4.85
2319 2959 1.072678 CATGCATCCCGATCAGGCT 59.927 57.895 0.00 0.00 39.21 4.58
2320 2960 1.072678 ATGCATCCCGATCAGGCTG 59.927 57.895 8.58 8.58 39.21 4.85
2321 2961 1.703014 ATGCATCCCGATCAGGCTGT 61.703 55.000 15.27 1.47 39.21 4.40
2322 2962 1.890979 GCATCCCGATCAGGCTGTG 60.891 63.158 15.27 4.48 39.21 3.66
2323 2963 1.227764 CATCCCGATCAGGCTGTGG 60.228 63.158 15.27 14.33 39.21 4.17
2324 2964 1.690633 ATCCCGATCAGGCTGTGGT 60.691 57.895 15.27 1.78 39.21 4.16
2325 2965 1.976132 ATCCCGATCAGGCTGTGGTG 61.976 60.000 15.27 9.19 39.21 4.17
2326 2966 2.821366 CCGATCAGGCTGTGGTGC 60.821 66.667 15.27 0.00 0.00 5.01
2334 2974 2.639286 GCTGTGGTGCCAAGAACG 59.361 61.111 0.00 0.00 0.00 3.95
2335 2975 2.639286 CTGTGGTGCCAAGAACGC 59.361 61.111 0.00 0.00 0.00 4.84
2336 2976 1.893808 CTGTGGTGCCAAGAACGCT 60.894 57.895 0.00 0.00 0.00 5.07
2337 2977 1.845809 CTGTGGTGCCAAGAACGCTC 61.846 60.000 0.00 0.00 0.00 5.03
2338 2978 1.598130 GTGGTGCCAAGAACGCTCT 60.598 57.895 0.00 0.00 0.00 4.09
2339 2979 1.148273 TGGTGCCAAGAACGCTCTT 59.852 52.632 0.00 0.00 42.96 2.85
2340 2980 0.394938 TGGTGCCAAGAACGCTCTTA 59.605 50.000 0.00 0.00 40.05 2.10
2341 2981 1.003118 TGGTGCCAAGAACGCTCTTAT 59.997 47.619 0.00 0.00 40.05 1.73
2342 2982 2.235155 TGGTGCCAAGAACGCTCTTATA 59.765 45.455 0.00 0.00 40.05 0.98
2343 2983 3.118408 TGGTGCCAAGAACGCTCTTATAT 60.118 43.478 0.00 0.00 40.05 0.86
2344 2984 3.877508 GGTGCCAAGAACGCTCTTATATT 59.122 43.478 0.00 0.00 40.05 1.28
2345 2985 5.054477 GGTGCCAAGAACGCTCTTATATTA 58.946 41.667 0.00 0.00 40.05 0.98
2346 2986 5.701290 GGTGCCAAGAACGCTCTTATATTAT 59.299 40.000 0.00 0.00 40.05 1.28
2347 2987 6.347725 GGTGCCAAGAACGCTCTTATATTATG 60.348 42.308 0.00 0.00 40.05 1.90
2348 2988 6.423905 GTGCCAAGAACGCTCTTATATTATGA 59.576 38.462 0.00 0.00 40.05 2.15
2349 2989 6.989759 TGCCAAGAACGCTCTTATATTATGAA 59.010 34.615 0.00 0.00 40.05 2.57
2350 2990 7.497579 TGCCAAGAACGCTCTTATATTATGAAA 59.502 33.333 0.00 0.00 40.05 2.69
2351 2991 7.798982 GCCAAGAACGCTCTTATATTATGAAAC 59.201 37.037 0.00 0.00 40.05 2.78
2352 2992 9.046296 CCAAGAACGCTCTTATATTATGAAACT 57.954 33.333 0.00 0.00 40.05 2.66
2358 2998 8.867097 ACGCTCTTATATTATGAAACTAAGGGA 58.133 33.333 0.00 0.00 0.00 4.20
2378 3018 8.996651 AAGGGAGTAATTAATTAATCTGTGGG 57.003 34.615 26.21 0.00 37.47 4.61
2385 3025 9.274206 GTAATTAATTAATCTGTGGGGAGAGAC 57.726 37.037 11.08 0.00 0.00 3.36
2403 3043 6.210385 GGAGAGACCTCTAATCTTCATGCATA 59.790 42.308 0.00 0.00 40.61 3.14
2462 3102 8.226819 TCGTCAAGTAGATCAAGATTATGAGT 57.773 34.615 0.00 0.00 31.76 3.41
2477 3117 7.978982 AGATTATGAGTATGTGACAAAGCAAC 58.021 34.615 0.00 0.00 0.00 4.17
2487 3127 3.122780 GTGACAAAGCAACCACAACAAAC 59.877 43.478 0.00 0.00 0.00 2.93
2488 3128 3.006323 TGACAAAGCAACCACAACAAACT 59.994 39.130 0.00 0.00 0.00 2.66
2491 3131 3.436700 AAGCAACCACAACAAACTAGC 57.563 42.857 0.00 0.00 0.00 3.42
2496 3145 4.455877 GCAACCACAACAAACTAGCTAGAT 59.544 41.667 27.45 13.16 0.00 1.98
2538 3187 2.409975 ACCGACCACAGTTTTGTATCG 58.590 47.619 6.56 6.56 41.34 2.92
2565 3218 3.678951 TTGCTCGATCGCATGCCCA 62.679 57.895 13.15 0.00 40.04 5.36
2660 3322 8.845413 AAAGATAAGCAGATATTTCAGCTAGG 57.155 34.615 3.60 0.00 43.21 3.02
2663 3325 1.462670 GCAGATATTTCAGCTAGGCGC 59.537 52.381 0.00 0.00 39.57 6.53
2749 3419 1.485838 GATGATGGCGAGCGTCACTG 61.486 60.000 0.00 0.00 30.16 3.66
2759 3429 0.250513 AGCGTCACTGAGAATTCCCC 59.749 55.000 0.65 0.00 0.00 4.81
2760 3430 0.250513 GCGTCACTGAGAATTCCCCT 59.749 55.000 0.65 0.00 0.00 4.79
2775 3445 3.955650 TCCCCTAGAAAAAGAGACACG 57.044 47.619 0.00 0.00 0.00 4.49
2779 3449 1.057636 TAGAAAAAGAGACACGCGCG 58.942 50.000 30.96 30.96 0.00 6.86
2785 3455 0.949105 AAGAGACACGCGCGGAATTT 60.949 50.000 35.22 16.77 0.00 1.82
2787 3457 0.717224 GAGACACGCGCGGAATTTAA 59.283 50.000 35.22 0.00 0.00 1.52
2789 3459 0.519792 GACACGCGCGGAATTTAACC 60.520 55.000 35.22 8.24 0.00 2.85
2791 3461 0.110147 CACGCGCGGAATTTAACCAA 60.110 50.000 35.22 0.00 0.00 3.67
2792 3462 0.167251 ACGCGCGGAATTTAACCAAG 59.833 50.000 35.22 0.47 0.00 3.61
2793 3463 1.131618 CGCGCGGAATTTAACCAAGC 61.132 55.000 24.84 0.00 0.00 4.01
2794 3464 0.109504 GCGCGGAATTTAACCAAGCA 60.110 50.000 8.83 0.00 32.53 3.91
2795 3465 1.613270 CGCGGAATTTAACCAAGCAC 58.387 50.000 0.00 0.00 0.00 4.40
2796 3466 1.068885 CGCGGAATTTAACCAAGCACA 60.069 47.619 0.00 0.00 0.00 4.57
2797 3467 2.605823 CGCGGAATTTAACCAAGCACAA 60.606 45.455 0.00 0.00 0.00 3.33
2851 3523 2.476051 CGACCGCAATCAGCACAC 59.524 61.111 0.00 0.00 46.13 3.82
2856 3528 0.098200 CCGCAATCAGCACACAGATG 59.902 55.000 0.00 0.00 46.13 2.90
2933 3605 1.732259 CTGTGTGCGGAAAGGATGTAC 59.268 52.381 0.00 0.00 0.00 2.90
2934 3606 1.346395 TGTGTGCGGAAAGGATGTACT 59.654 47.619 0.00 0.00 0.00 2.73
2969 3645 3.740832 GCTTTAGTTTTTGGCATGTCCAC 59.259 43.478 8.18 0.00 46.55 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.659957 GATTGTCGCCCAGAAGATGC 59.340 55.000 0.00 0.00 0.00 3.91
48 50 1.399714 TCGTCATGTAAGGCGGAGAT 58.600 50.000 0.00 0.00 0.00 2.75
54 56 0.459585 TCGGCTTCGTCATGTAAGGC 60.460 55.000 16.23 16.23 42.96 4.35
55 57 1.927174 CTTCGGCTTCGTCATGTAAGG 59.073 52.381 0.00 0.00 35.06 2.69
67 69 2.047179 GCGTCCCTTCTTCGGCTT 60.047 61.111 0.00 0.00 0.00 4.35
72 74 2.506438 CGTCGGCGTCCCTTCTTC 60.506 66.667 6.85 0.00 0.00 2.87
131 133 0.589229 CGTCGTAGATGTCGTCTGGC 60.589 60.000 4.73 0.00 40.67 4.85
133 135 1.392510 TGTCGTCGTAGATGTCGTCTG 59.607 52.381 4.73 0.00 45.22 3.51
134 136 1.659601 CTGTCGTCGTAGATGTCGTCT 59.340 52.381 0.00 0.00 45.22 4.18
138 140 2.348685 CCGATCTGTCGTCGTAGATGTC 60.349 54.545 15.82 6.29 46.25 3.06
146 148 2.408022 GGTCCCGATCTGTCGTCG 59.592 66.667 0.00 0.00 46.25 5.12
151 153 2.442272 CCTCCGGTCCCGATCTGT 60.442 66.667 7.42 0.00 42.83 3.41
153 155 2.442272 CACCTCCGGTCCCGATCT 60.442 66.667 7.42 0.00 42.83 2.75
159 161 2.435693 CCATCCTCACCTCCGGTCC 61.436 68.421 0.00 0.00 31.02 4.46
163 165 2.041922 TCCCCATCCTCACCTCCG 60.042 66.667 0.00 0.00 0.00 4.63
184 186 0.804989 GCACCAACATCTGCCACTAC 59.195 55.000 0.00 0.00 0.00 2.73
185 187 0.399833 TGCACCAACATCTGCCACTA 59.600 50.000 0.00 0.00 31.97 2.74
195 197 1.415659 CCCTCCAAAATTGCACCAACA 59.584 47.619 0.00 0.00 0.00 3.33
197 199 1.415659 CACCCTCCAAAATTGCACCAA 59.584 47.619 0.00 0.00 0.00 3.67
198 200 1.047002 CACCCTCCAAAATTGCACCA 58.953 50.000 0.00 0.00 0.00 4.17
199 201 0.321346 CCACCCTCCAAAATTGCACC 59.679 55.000 0.00 0.00 0.00 5.01
200 202 0.320683 GCCACCCTCCAAAATTGCAC 60.321 55.000 0.00 0.00 0.00 4.57
201 203 1.814772 CGCCACCCTCCAAAATTGCA 61.815 55.000 0.00 0.00 0.00 4.08
203 205 1.591183 CCGCCACCCTCCAAAATTG 59.409 57.895 0.00 0.00 0.00 2.32
207 222 3.646715 CTCCCGCCACCCTCCAAA 61.647 66.667 0.00 0.00 0.00 3.28
218 233 2.042843 TCTTCCTCCTCCTCCCGC 60.043 66.667 0.00 0.00 0.00 6.13
302 320 2.520536 GGGCAGATATGGGGCGTCT 61.521 63.158 0.00 0.00 0.00 4.18
310 328 6.070021 TCCAGTCCAATTATAGGGCAGATATG 60.070 42.308 0.00 0.00 31.65 1.78
311 329 6.032039 TCCAGTCCAATTATAGGGCAGATAT 58.968 40.000 0.00 0.00 31.65 1.63
312 330 5.411493 TCCAGTCCAATTATAGGGCAGATA 58.589 41.667 0.00 0.00 31.65 1.98
313 331 4.242811 TCCAGTCCAATTATAGGGCAGAT 58.757 43.478 0.00 0.00 31.65 2.90
314 332 3.664320 TCCAGTCCAATTATAGGGCAGA 58.336 45.455 0.00 0.00 31.65 4.26
315 333 4.647564 ATCCAGTCCAATTATAGGGCAG 57.352 45.455 0.00 0.00 31.65 4.85
316 334 7.147320 CCATATATCCAGTCCAATTATAGGGCA 60.147 40.741 0.00 0.00 31.65 5.36
317 335 7.227156 CCATATATCCAGTCCAATTATAGGGC 58.773 42.308 0.00 0.00 0.00 5.19
318 336 7.202223 CCCCATATATCCAGTCCAATTATAGGG 60.202 44.444 0.00 0.00 0.00 3.53
325 344 4.251169 ACACCCCATATATCCAGTCCAAT 58.749 43.478 0.00 0.00 0.00 3.16
339 358 3.717294 GACTGGCCGACACCCCAT 61.717 66.667 0.00 0.00 0.00 4.00
347 366 3.109592 AAACGTTGGGACTGGCCGA 62.110 57.895 0.00 0.00 37.63 5.54
351 370 0.889186 CCCTCAAACGTTGGGACTGG 60.889 60.000 15.47 8.46 43.47 4.00
370 389 3.304458 CCCAGACAAACTCTTTAAACGGC 60.304 47.826 0.00 0.00 0.00 5.68
411 430 0.326595 TCGGGCTGCTTGGTTATTGA 59.673 50.000 0.00 0.00 0.00 2.57
413 432 1.064758 TCATCGGGCTGCTTGGTTATT 60.065 47.619 0.00 0.00 0.00 1.40
414 433 0.546122 TCATCGGGCTGCTTGGTTAT 59.454 50.000 0.00 0.00 0.00 1.89
415 434 0.107703 CTCATCGGGCTGCTTGGTTA 60.108 55.000 0.00 0.00 0.00 2.85
416 435 1.377725 CTCATCGGGCTGCTTGGTT 60.378 57.895 0.00 0.00 0.00 3.67
417 436 2.270205 CTCATCGGGCTGCTTGGT 59.730 61.111 0.00 0.00 0.00 3.67
418 437 2.515523 CCTCATCGGGCTGCTTGG 60.516 66.667 0.00 0.00 0.00 3.61
426 445 0.107017 ACCTCAAATGCCTCATCGGG 60.107 55.000 0.00 0.00 0.00 5.14
427 446 1.019673 CACCTCAAATGCCTCATCGG 58.980 55.000 0.00 0.00 0.00 4.18
429 448 0.743097 GCCACCTCAAATGCCTCATC 59.257 55.000 0.00 0.00 0.00 2.92
430 449 0.333993 AGCCACCTCAAATGCCTCAT 59.666 50.000 0.00 0.00 0.00 2.90
431 450 0.112995 AAGCCACCTCAAATGCCTCA 59.887 50.000 0.00 0.00 0.00 3.86
433 452 0.971386 CAAAGCCACCTCAAATGCCT 59.029 50.000 0.00 0.00 0.00 4.75
434 453 0.037046 CCAAAGCCACCTCAAATGCC 60.037 55.000 0.00 0.00 0.00 4.40
436 455 0.037046 GCCCAAAGCCACCTCAAATG 60.037 55.000 0.00 0.00 34.35 2.32
437 456 1.535204 CGCCCAAAGCCACCTCAAAT 61.535 55.000 0.00 0.00 38.78 2.32
438 457 2.199652 CGCCCAAAGCCACCTCAAA 61.200 57.895 0.00 0.00 38.78 2.69
439 458 2.597217 CGCCCAAAGCCACCTCAA 60.597 61.111 0.00 0.00 38.78 3.02
441 460 3.056328 GACGCCCAAAGCCACCTC 61.056 66.667 0.00 0.00 38.78 3.85
442 461 4.660938 GGACGCCCAAAGCCACCT 62.661 66.667 0.00 0.00 38.78 4.00
448 467 3.599285 TACAGCCGGACGCCCAAAG 62.599 63.158 5.05 0.00 38.78 2.77
449 468 3.599285 CTACAGCCGGACGCCCAAA 62.599 63.158 5.05 0.00 38.78 3.28
450 469 4.077184 CTACAGCCGGACGCCCAA 62.077 66.667 5.05 0.00 38.78 4.12
454 473 2.962253 GCATCTACAGCCGGACGC 60.962 66.667 5.05 0.00 37.98 5.19
455 474 1.299468 GAGCATCTACAGCCGGACG 60.299 63.158 5.05 0.00 0.00 4.79
456 475 4.740235 GAGCATCTACAGCCGGAC 57.260 61.111 5.05 0.00 0.00 4.79
481 1045 5.761234 TGTGTCGTACTGCCTCTTTAAAAAT 59.239 36.000 0.00 0.00 0.00 1.82
484 1048 4.325028 TGTGTCGTACTGCCTCTTTAAA 57.675 40.909 0.00 0.00 0.00 1.52
486 1050 3.319972 AGTTGTGTCGTACTGCCTCTTTA 59.680 43.478 0.00 0.00 0.00 1.85
487 1051 2.102588 AGTTGTGTCGTACTGCCTCTTT 59.897 45.455 0.00 0.00 0.00 2.52
488 1052 1.687123 AGTTGTGTCGTACTGCCTCTT 59.313 47.619 0.00 0.00 0.00 2.85
489 1053 1.000163 CAGTTGTGTCGTACTGCCTCT 60.000 52.381 0.00 0.00 35.79 3.69
490 1054 1.000607 TCAGTTGTGTCGTACTGCCTC 60.001 52.381 0.00 0.00 41.16 4.70
491 1055 1.000163 CTCAGTTGTGTCGTACTGCCT 60.000 52.381 0.00 0.00 41.16 4.75
494 1058 2.054363 CTGCTCAGTTGTGTCGTACTG 58.946 52.381 0.00 0.00 42.41 2.74
495 1059 1.681793 ACTGCTCAGTTGTGTCGTACT 59.318 47.619 0.00 0.00 38.83 2.73
505 1075 3.243907 GGTGTAGACTTCACTGCTCAGTT 60.244 47.826 11.46 0.00 40.20 3.16
533 1104 3.743899 GCTTTGCTTTGATTTTGACCCCA 60.744 43.478 0.00 0.00 0.00 4.96
691 1262 5.657474 AGGATTTGTTTAAGCATGCATCTG 58.343 37.500 21.98 0.00 0.00 2.90
692 1263 5.163478 GGAGGATTTGTTTAAGCATGCATCT 60.163 40.000 21.98 6.32 0.00 2.90
693 1264 5.045872 GGAGGATTTGTTTAAGCATGCATC 58.954 41.667 21.98 10.94 0.00 3.91
694 1265 4.467082 TGGAGGATTTGTTTAAGCATGCAT 59.533 37.500 21.98 11.22 29.44 3.96
695 1266 3.831333 TGGAGGATTTGTTTAAGCATGCA 59.169 39.130 21.98 0.00 31.95 3.96
696 1267 4.176271 GTGGAGGATTTGTTTAAGCATGC 58.824 43.478 10.51 10.51 0.00 4.06
708 1279 1.674322 CCGCAACCGTGGAGGATTT 60.674 57.895 0.00 0.00 46.55 2.17
737 1308 2.945080 TGGATGATGGAAGGCAGATC 57.055 50.000 0.00 0.00 0.00 2.75
738 1309 2.041350 GGATGGATGATGGAAGGCAGAT 59.959 50.000 0.00 0.00 0.00 2.90
739 1310 1.422781 GGATGGATGATGGAAGGCAGA 59.577 52.381 0.00 0.00 0.00 4.26
740 1311 1.424302 AGGATGGATGATGGAAGGCAG 59.576 52.381 0.00 0.00 0.00 4.85
755 1326 2.029560 ACGACGGATGATGATGAGGATG 60.030 50.000 0.00 0.00 0.00 3.51
771 1342 3.260740 AGAGTTAGTAGACTGGACGACG 58.739 50.000 0.00 0.00 0.00 5.12
772 1343 5.625921 AAAGAGTTAGTAGACTGGACGAC 57.374 43.478 0.00 0.00 0.00 4.34
814 1385 1.302511 CGTGGTAGCTTGGTTGGCT 60.303 57.895 0.00 0.00 43.02 4.75
815 1386 2.332654 CCGTGGTAGCTTGGTTGGC 61.333 63.158 0.00 0.00 0.00 4.52
816 1387 0.250553 TTCCGTGGTAGCTTGGTTGG 60.251 55.000 0.00 0.00 0.00 3.77
817 1388 1.821216 ATTCCGTGGTAGCTTGGTTG 58.179 50.000 0.00 0.00 0.00 3.77
818 1389 2.355412 GGTATTCCGTGGTAGCTTGGTT 60.355 50.000 0.00 0.00 0.00 3.67
933 1539 7.627311 TCTCTATATGGGTGATCAAATGATGG 58.373 38.462 0.00 0.00 34.37 3.51
984 1590 0.518636 CCATCGCCACAACTGACAAG 59.481 55.000 0.00 0.00 0.00 3.16
990 1596 3.049674 CACGCCATCGCCACAACT 61.050 61.111 0.00 0.00 39.84 3.16
1482 2100 2.758327 TGCGCTATCACGTCCCCT 60.758 61.111 9.73 0.00 34.88 4.79
1485 2103 2.962253 GCCTGCGCTATCACGTCC 60.962 66.667 9.73 0.00 34.88 4.79
1833 2460 3.680786 CACCACGTCTCGGCTCCA 61.681 66.667 0.00 0.00 0.00 3.86
1836 2463 3.681835 GACCACCACGTCTCGGCT 61.682 66.667 0.00 0.00 0.00 5.52
2213 2853 2.973694 TCACTCCGTATTTACCCAGC 57.026 50.000 0.00 0.00 0.00 4.85
2318 2958 1.845809 GAGCGTTCTTGGCACCACAG 61.846 60.000 0.00 0.00 0.00 3.66
2319 2959 1.891919 GAGCGTTCTTGGCACCACA 60.892 57.895 0.00 0.00 0.00 4.17
2320 2960 1.166531 AAGAGCGTTCTTGGCACCAC 61.167 55.000 14.17 0.00 42.04 4.16
2321 2961 0.394938 TAAGAGCGTTCTTGGCACCA 59.605 50.000 22.97 0.31 43.41 4.17
2322 2962 1.739067 ATAAGAGCGTTCTTGGCACC 58.261 50.000 22.97 0.00 43.41 5.01
2323 2963 6.423905 TCATAATATAAGAGCGTTCTTGGCAC 59.576 38.462 22.97 0.00 43.41 5.01
2324 2964 6.521162 TCATAATATAAGAGCGTTCTTGGCA 58.479 36.000 22.97 9.18 43.41 4.92
2325 2965 7.421530 TTCATAATATAAGAGCGTTCTTGGC 57.578 36.000 22.97 0.00 43.41 4.52
2326 2966 9.046296 AGTTTCATAATATAAGAGCGTTCTTGG 57.954 33.333 22.97 5.44 43.41 3.61
2331 2971 9.490379 CCCTTAGTTTCATAATATAAGAGCGTT 57.510 33.333 0.00 0.00 0.00 4.84
2332 2972 8.867097 TCCCTTAGTTTCATAATATAAGAGCGT 58.133 33.333 0.00 0.00 0.00 5.07
2333 2973 9.360093 CTCCCTTAGTTTCATAATATAAGAGCG 57.640 37.037 0.00 0.00 0.00 5.03
2353 2993 8.004801 CCCCACAGATTAATTAATTACTCCCTT 58.995 37.037 17.41 4.51 0.00 3.95
2354 2994 7.352522 TCCCCACAGATTAATTAATTACTCCCT 59.647 37.037 17.41 1.20 0.00 4.20
2355 2995 7.523415 TCCCCACAGATTAATTAATTACTCCC 58.477 38.462 17.41 0.00 0.00 4.30
2356 2996 8.437575 TCTCCCCACAGATTAATTAATTACTCC 58.562 37.037 17.41 7.08 0.00 3.85
2358 2998 9.225682 TCTCTCCCCACAGATTAATTAATTACT 57.774 33.333 11.92 2.62 0.00 2.24
2365 3005 4.375313 AGGTCTCTCCCCACAGATTAATT 58.625 43.478 0.00 0.00 36.75 1.40
2378 3018 4.343526 TGCATGAAGATTAGAGGTCTCTCC 59.656 45.833 3.49 0.00 40.83 3.71
2385 3025 9.064706 AGAATGTTTATGCATGAAGATTAGAGG 57.935 33.333 21.64 0.00 0.00 3.69
2457 3097 4.216257 GTGGTTGCTTTGTCACATACTCAT 59.784 41.667 0.00 0.00 0.00 2.90
2462 3102 3.696548 TGTTGTGGTTGCTTTGTCACATA 59.303 39.130 0.00 0.00 39.45 2.29
2464 3104 1.889170 TGTTGTGGTTGCTTTGTCACA 59.111 42.857 0.00 0.00 38.21 3.58
2470 3110 3.447229 AGCTAGTTTGTTGTGGTTGCTTT 59.553 39.130 0.00 0.00 0.00 3.51
2477 3117 6.801539 TTCAATCTAGCTAGTTTGTTGTGG 57.198 37.500 30.25 14.18 35.53 4.17
2487 3127 6.699204 ACACGTGATCAATTCAATCTAGCTAG 59.301 38.462 25.01 15.01 35.70 3.42
2488 3128 6.476706 CACACGTGATCAATTCAATCTAGCTA 59.523 38.462 25.01 0.00 35.70 3.32
2491 3131 5.496387 GCACACGTGATCAATTCAATCTAG 58.504 41.667 25.01 0.00 35.70 2.43
2496 3145 2.592796 CGCACACGTGATCAATTCAA 57.407 45.000 25.01 0.00 35.70 2.69
2538 3187 1.531883 GCGATCGAGCAAATGGTTTCC 60.532 52.381 21.57 0.00 37.05 3.13
2565 3218 9.901172 ACCGAATACTTTTTATAGTTTGGAGAT 57.099 29.630 0.00 0.00 0.00 2.75
2749 3419 6.596106 GTGTCTCTTTTTCTAGGGGAATTCTC 59.404 42.308 5.23 0.00 33.53 2.87
2759 3429 1.057847 CGCGCGTGTCTCTTTTTCTAG 59.942 52.381 24.19 0.00 0.00 2.43
2760 3430 1.057636 CGCGCGTGTCTCTTTTTCTA 58.942 50.000 24.19 0.00 0.00 2.10
2775 3445 0.109504 TGCTTGGTTAAATTCCGCGC 60.110 50.000 0.00 0.00 0.00 6.86
2779 3449 3.988819 TGCTTGTGCTTGGTTAAATTCC 58.011 40.909 0.00 0.00 40.48 3.01
2785 3455 3.781079 GCATATGCTTGTGCTTGGTTA 57.219 42.857 20.64 0.00 37.05 2.85
2838 3508 0.522705 GCATCTGTGTGCTGATTGCG 60.523 55.000 0.00 0.00 46.63 4.85
2872 3544 4.208460 GTGCGTTGCTAATCATATGTACGT 59.792 41.667 1.90 0.00 0.00 3.57
2875 3547 5.276631 CGTTGTGCGTTGCTAATCATATGTA 60.277 40.000 1.90 0.00 35.54 2.29
2876 3548 4.494035 CGTTGTGCGTTGCTAATCATATGT 60.494 41.667 1.90 0.00 35.54 2.29
2877 3549 3.961860 CGTTGTGCGTTGCTAATCATATG 59.038 43.478 0.00 0.00 35.54 1.78
2878 3550 3.002246 CCGTTGTGCGTTGCTAATCATAT 59.998 43.478 0.00 0.00 39.32 1.78
2902 3574 3.128375 CACACAGTTTGCCCCACC 58.872 61.111 0.00 0.00 0.00 4.61
2933 3605 4.250116 ACTAAAGCGATGGATGCTAGAG 57.750 45.455 0.00 0.00 43.14 2.43
2934 3606 4.672587 AACTAAAGCGATGGATGCTAGA 57.327 40.909 0.00 0.00 43.14 2.43


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

AutoCloner maintained by Alex Coulton.