Multiple sequence alignment - TraesCS1D01G300500

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 TraesCS1D01G300500 chr1D 100.000 3018 0 0 1 3018 398552284 398549267 0.000000e+00 5574.0
1 TraesCS1D01G300500 chr1D 89.696 1349 89 25 764 2096 398468096 398466782 0.000000e+00 1676.0
2 TraesCS1D01G300500 chr1D 78.049 1025 149 46 999 1974 398853107 398852110 7.260000e-161 577.0
3 TraesCS1D01G300500 chr1D 82.712 295 43 6 2726 3018 398465004 398464716 3.860000e-64 255.0
4 TraesCS1D01G300500 chr1D 79.403 335 32 30 7 334 398475653 398475349 5.100000e-48 202.0
5 TraesCS1D01G300500 chr1D 100.000 28 0 0 793 820 398551465 398551492 5.000000e-03 52.8
6 TraesCS1D01G300500 chr1A 89.872 2192 124 53 1 2154 495457464 495455333 0.000000e+00 2728.0
7 TraesCS1D01G300500 chr1A 89.671 881 75 12 2150 3018 495455219 495454343 0.000000e+00 1109.0
8 TraesCS1D01G300500 chr1A 77.507 1027 148 54 1001 1974 495579952 495578956 9.520000e-150 540.0
9 TraesCS1D01G300500 chr1B 78.439 1025 146 47 999 1974 534151674 534150676 1.550000e-167 599.0


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 TraesCS1D01G300500 chr1D 398549267 398552284 3017 True 5574.0 5574 100.0000 1 3018 1 chr1D.!!$R2 3017
1 TraesCS1D01G300500 chr1D 398464716 398468096 3380 True 965.5 1676 86.2040 764 3018 2 chr1D.!!$R4 2254
2 TraesCS1D01G300500 chr1D 398852110 398853107 997 True 577.0 577 78.0490 999 1974 1 chr1D.!!$R3 975
3 TraesCS1D01G300500 chr1A 495454343 495457464 3121 True 1918.5 2728 89.7715 1 3018 2 chr1A.!!$R2 3017
4 TraesCS1D01G300500 chr1A 495578956 495579952 996 True 540.0 540 77.5070 1001 1974 1 chr1A.!!$R1 973
5 TraesCS1D01G300500 chr1B 534150676 534151674 998 True 599.0 599 78.4390 999 1974 1 chr1B.!!$R1 975

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
932 965 0.102120 GCAGATCCAGAGTCACGGAG 59.898 60.0 7.33 0.0 33.97 4.63 F
979 1012 0.320374 CTGCAAACGGGGAGTAGTGA 59.680 55.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 1902 0.108756 GGTCACCTTCAGTCGTAGGC 60.109 60.0 0.00 0.0 33.04 3.93 R
2573 2846 0.396278 CCAATGGGCCTCTTCTTCCC 60.396 60.0 4.53 0.0 40.47 3.97 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
33 35 4.810191 GATACTCCTTGAGGTGTGTCTT 57.190 45.455 16.78 1.99 42.62 3.01
34 36 2.918712 ACTCCTTGAGGTGTGTCTTG 57.081 50.000 4.07 0.00 40.10 3.02
35 37 2.398588 ACTCCTTGAGGTGTGTCTTGA 58.601 47.619 4.07 0.00 40.10 3.02
36 38 2.366916 ACTCCTTGAGGTGTGTCTTGAG 59.633 50.000 4.07 0.00 40.10 3.02
37 39 2.366916 CTCCTTGAGGTGTGTCTTGAGT 59.633 50.000 0.00 0.00 36.34 3.41
38 40 2.365617 TCCTTGAGGTGTGTCTTGAGTC 59.634 50.000 0.00 0.00 36.34 3.36
57 59 0.457851 CTTGACGTGCTAGCTAGGCT 59.542 55.000 22.10 0.00 43.41 4.58
71 73 3.077359 GCTAGGCTGTCAAGTTGTCATT 58.923 45.455 2.11 0.00 0.00 2.57
79 81 5.506151 GCTGTCAAGTTGTCATTGTTCATCA 60.506 40.000 2.11 0.00 0.00 3.07
127 129 2.741145 GATACAGAGGGAGGTCAGTGT 58.259 52.381 0.00 0.00 0.00 3.55
128 130 1.924731 TACAGAGGGAGGTCAGTGTG 58.075 55.000 0.00 0.00 0.00 3.82
130 132 0.542938 CAGAGGGAGGTCAGTGTGGA 60.543 60.000 0.00 0.00 0.00 4.02
131 133 0.252012 AGAGGGAGGTCAGTGTGGAG 60.252 60.000 0.00 0.00 0.00 3.86
134 136 2.262915 GAGGTCAGTGTGGAGCCG 59.737 66.667 0.00 0.00 35.95 5.52
135 137 3.941657 GAGGTCAGTGTGGAGCCGC 62.942 68.421 0.00 0.00 35.95 6.53
136 138 4.008933 GGTCAGTGTGGAGCCGCT 62.009 66.667 0.00 0.00 0.00 5.52
137 139 2.433318 GTCAGTGTGGAGCCGCTC 60.433 66.667 12.27 12.27 0.00 5.03
209 212 6.456795 AGAGCTAGATTTTGCCCATAAAAC 57.543 37.500 0.00 0.00 32.86 2.43
213 216 7.449247 AGCTAGATTTTGCCCATAAAACAAAA 58.551 30.769 0.00 2.97 44.64 2.44
214 217 7.387673 AGCTAGATTTTGCCCATAAAACAAAAC 59.612 33.333 0.00 0.00 43.70 2.43
221 224 6.222038 TGCCCATAAAACAAAACTGTTACA 57.778 33.333 0.00 0.00 0.00 2.41
226 229 7.114247 CCCATAAAACAAAACTGTTACATCACG 59.886 37.037 0.00 0.00 0.00 4.35
235 238 6.509418 AACTGTTACATCACGCCAAAATAT 57.491 33.333 0.00 0.00 0.00 1.28
308 316 6.187727 TGGACTGAGTAAAGGAGAATTTGT 57.812 37.500 0.00 0.00 0.00 2.83
310 318 7.918076 TGGACTGAGTAAAGGAGAATTTGTAT 58.082 34.615 0.00 0.00 0.00 2.29
316 324 8.103305 TGAGTAAAGGAGAATTTGTATCAGCTT 58.897 33.333 0.00 0.00 0.00 3.74
317 325 9.601217 GAGTAAAGGAGAATTTGTATCAGCTTA 57.399 33.333 0.00 0.00 0.00 3.09
318 326 9.959721 AGTAAAGGAGAATTTGTATCAGCTTAA 57.040 29.630 0.00 0.00 0.00 1.85
321 329 8.814038 AAGGAGAATTTGTATCAGCTTAATGT 57.186 30.769 0.00 0.00 0.00 2.71
322 330 8.814038 AGGAGAATTTGTATCAGCTTAATGTT 57.186 30.769 0.00 0.00 0.00 2.71
323 331 8.680903 AGGAGAATTTGTATCAGCTTAATGTTG 58.319 33.333 0.00 0.00 0.00 3.33
324 332 7.433425 GGAGAATTTGTATCAGCTTAATGTTGC 59.567 37.037 0.00 0.00 0.00 4.17
325 333 8.059798 AGAATTTGTATCAGCTTAATGTTGCT 57.940 30.769 0.00 0.00 40.54 3.91
326 334 9.177608 AGAATTTGTATCAGCTTAATGTTGCTA 57.822 29.630 0.00 0.00 37.81 3.49
327 335 9.787532 GAATTTGTATCAGCTTAATGTTGCTAA 57.212 29.630 0.00 0.00 37.81 3.09
329 337 9.740239 ATTTGTATCAGCTTAATGTTGCTAATG 57.260 29.630 0.00 0.00 37.81 1.90
330 338 6.728200 TGTATCAGCTTAATGTTGCTAATGC 58.272 36.000 0.00 0.00 37.81 3.56
331 339 4.637483 TCAGCTTAATGTTGCTAATGCC 57.363 40.909 0.00 0.00 37.81 4.40
332 340 4.015764 TCAGCTTAATGTTGCTAATGCCA 58.984 39.130 0.00 0.00 37.81 4.92
333 341 4.462132 TCAGCTTAATGTTGCTAATGCCAA 59.538 37.500 0.00 0.00 37.81 4.52
334 342 4.563976 CAGCTTAATGTTGCTAATGCCAAC 59.436 41.667 0.00 0.00 37.81 3.77
335 343 4.220382 AGCTTAATGTTGCTAATGCCAACA 59.780 37.500 9.08 9.08 41.02 3.33
338 346 4.605640 AATGTTGCTAATGCCAACAAGT 57.394 36.364 10.49 0.75 40.57 3.16
351 359 2.353605 CCAACAAGTTGCCAACTGTGTT 60.354 45.455 21.67 21.67 41.91 3.32
366 374 0.811281 GTGTTACAGCTGAATGGGGC 59.189 55.000 23.35 3.66 0.00 5.80
367 375 0.403655 TGTTACAGCTGAATGGGGCA 59.596 50.000 23.35 6.27 0.00 5.36
368 376 1.202989 TGTTACAGCTGAATGGGGCAA 60.203 47.619 23.35 0.00 0.00 4.52
369 377 1.892474 GTTACAGCTGAATGGGGCAAA 59.108 47.619 23.35 0.00 0.00 3.68
382 392 2.173782 TGGGGCAAAGTCAACTTCTGTA 59.826 45.455 0.00 0.00 34.61 2.74
384 394 3.211045 GGGCAAAGTCAACTTCTGTACA 58.789 45.455 0.00 0.00 34.61 2.90
400 410 0.981183 TACAGGACGATGGTTGGCTT 59.019 50.000 0.00 0.00 0.00 4.35
402 412 1.349688 ACAGGACGATGGTTGGCTTAA 59.650 47.619 0.00 0.00 0.00 1.85
403 413 2.224670 ACAGGACGATGGTTGGCTTAAA 60.225 45.455 0.00 0.00 0.00 1.52
404 414 3.016736 CAGGACGATGGTTGGCTTAAAT 58.983 45.455 0.00 0.00 0.00 1.40
467 477 0.248289 AGTTGCATGAAATGGCCAGC 59.752 50.000 13.05 8.73 46.86 4.85
475 485 0.458669 GAAATGGCCAGCATGAGGTG 59.541 55.000 13.05 0.00 39.69 4.00
490 500 2.218603 GAGGTGCTTCCGAAAGAAACA 58.781 47.619 0.00 0.00 41.99 2.83
492 502 2.554032 AGGTGCTTCCGAAAGAAACATG 59.446 45.455 0.00 0.00 41.99 3.21
513 523 0.750546 CACCTGATGCTGATGGGTGG 60.751 60.000 0.00 0.00 42.39 4.61
517 527 2.043652 ATGCTGATGGGTGGGTGC 60.044 61.111 0.00 0.00 0.00 5.01
518 528 3.667217 ATGCTGATGGGTGGGTGCC 62.667 63.158 0.00 0.00 0.00 5.01
519 529 4.365111 GCTGATGGGTGGGTGCCA 62.365 66.667 0.00 0.00 0.00 4.92
520 530 2.685366 CTGATGGGTGGGTGCCAT 59.315 61.111 0.00 0.00 35.28 4.40
521 531 1.922057 CTGATGGGTGGGTGCCATA 59.078 57.895 0.00 0.00 35.28 2.74
522 532 0.179009 CTGATGGGTGGGTGCCATAG 60.179 60.000 0.00 0.00 35.28 2.23
523 533 0.623031 TGATGGGTGGGTGCCATAGA 60.623 55.000 0.00 0.00 35.28 1.98
524 534 0.550914 GATGGGTGGGTGCCATAGAA 59.449 55.000 0.00 0.00 35.28 2.10
559 569 4.331717 TCGTCTTGTCTTTTGTGAAGTTCC 59.668 41.667 0.00 0.00 0.00 3.62
586 596 0.523072 CCAGTCAAGATTTGCACCCG 59.477 55.000 0.00 0.00 0.00 5.28
587 597 1.238439 CAGTCAAGATTTGCACCCGT 58.762 50.000 0.00 0.00 0.00 5.28
588 598 1.069022 CAGTCAAGATTTGCACCCGTG 60.069 52.381 0.00 0.00 0.00 4.94
606 616 5.883673 ACCCGTGCTTTCTTATAATTTGCTA 59.116 36.000 0.00 0.00 0.00 3.49
682 704 1.603172 GGGTGAGTGTGAACTCTCGTG 60.603 57.143 7.35 0.00 38.83 4.35
696 718 2.034066 CGTGTTGGTCCCCTGCAT 59.966 61.111 0.00 0.00 0.00 3.96
705 727 0.671251 GTCCCCTGCATAGACTCTCG 59.329 60.000 0.00 0.00 0.00 4.04
714 736 6.405508 CCCTGCATAGACTCTCGTTAGTTTAA 60.406 42.308 0.00 0.00 0.00 1.52
791 815 1.363744 CGGTCATTGCTCTCACTTCC 58.636 55.000 0.00 0.00 0.00 3.46
911 944 0.392998 GCTTCCTTCCATCGAGGCAA 60.393 55.000 0.00 0.00 37.29 4.52
912 945 1.661341 CTTCCTTCCATCGAGGCAAG 58.339 55.000 0.00 0.00 37.29 4.01
916 949 1.078214 TTCCATCGAGGCAAGGCAG 60.078 57.895 0.00 0.00 37.29 4.85
925 958 0.913451 AGGCAAGGCAGATCCAGAGT 60.913 55.000 0.00 0.00 37.29 3.24
927 960 0.251354 GCAAGGCAGATCCAGAGTCA 59.749 55.000 0.00 0.00 37.29 3.41
930 963 1.142748 GGCAGATCCAGAGTCACGG 59.857 63.158 0.00 0.00 34.01 4.94
931 964 1.323271 GGCAGATCCAGAGTCACGGA 61.323 60.000 3.96 3.96 35.27 4.69
932 965 0.102120 GCAGATCCAGAGTCACGGAG 59.898 60.000 7.33 0.00 33.97 4.63
936 969 2.174639 AGATCCAGAGTCACGGAGAGAT 59.825 50.000 7.33 0.00 33.97 2.75
938 971 3.866703 TCCAGAGTCACGGAGAGATAT 57.133 47.619 0.00 0.00 0.00 1.63
940 973 5.506730 TCCAGAGTCACGGAGAGATATAT 57.493 43.478 0.00 0.00 0.00 0.86
942 975 6.645306 TCCAGAGTCACGGAGAGATATATAG 58.355 44.000 0.00 0.00 0.00 1.31
943 976 6.440965 TCCAGAGTCACGGAGAGATATATAGA 59.559 42.308 0.00 0.00 0.00 1.98
944 977 7.038231 TCCAGAGTCACGGAGAGATATATAGAA 60.038 40.741 0.00 0.00 0.00 2.10
945 978 7.279981 CCAGAGTCACGGAGAGATATATAGAAG 59.720 44.444 0.00 0.00 0.00 2.85
946 979 7.822334 CAGAGTCACGGAGAGATATATAGAAGT 59.178 40.741 0.00 0.00 0.00 3.01
947 980 9.038072 AGAGTCACGGAGAGATATATAGAAGTA 57.962 37.037 0.00 0.00 0.00 2.24
968 1001 2.740981 AGAAAGATCTCAGCTGCAAACG 59.259 45.455 9.47 0.00 0.00 3.60
979 1012 0.320374 CTGCAAACGGGGAGTAGTGA 59.680 55.000 0.00 0.00 0.00 3.41
1040 1076 1.669115 CTGCTTCAGTGGTGTCCGG 60.669 63.158 0.00 0.00 0.00 5.14
1288 1327 4.092091 CGAAAAGAAGGTAAGCTAGCTGTG 59.908 45.833 20.16 0.00 36.50 3.66
1355 1425 3.650139 AGCAACGACTTAACAAGATCGT 58.350 40.909 0.00 9.28 42.58 3.73
1380 1455 4.751093 TTCCAGGATGCGCGCGAA 62.751 61.111 37.18 27.72 31.97 4.70
1444 1519 1.964223 GAGGACGGCTTCATATGGAGA 59.036 52.381 15.70 0.00 0.00 3.71
1657 1738 2.612972 GGAAGAGGACGTCAAGATGCAA 60.613 50.000 18.91 0.00 0.00 4.08
1798 1900 1.671901 CGGAGGGAGGAGAAGCAGAC 61.672 65.000 0.00 0.00 0.00 3.51
1800 1902 1.671901 GAGGGAGGAGAAGCAGACGG 61.672 65.000 0.00 0.00 0.00 4.79
1801 1903 2.185608 GGAGGAGAAGCAGACGGC 59.814 66.667 0.00 0.00 45.30 5.68
1829 1931 2.880890 CTGAAGGTGACCAAAGTTGAGG 59.119 50.000 3.63 0.00 0.00 3.86
2043 2146 3.334691 GTGAATTTCCTCGTGTGATGGA 58.665 45.455 0.00 0.00 0.00 3.41
2103 2206 5.741011 TGGATTTCTTCTACTATGGCGTTT 58.259 37.500 0.00 0.00 0.00 3.60
2145 2253 3.088194 AGCATGAAAGCAAGTGTGTTG 57.912 42.857 0.00 0.00 36.85 3.33
2184 2415 7.067008 TGGTTAATGTATTGCCTTTAGAGCTTC 59.933 37.037 0.00 0.00 0.00 3.86
2192 2442 5.886960 TGCCTTTAGAGCTTCAGAAATTC 57.113 39.130 0.00 0.00 0.00 2.17
2195 2445 5.675827 GCCTTTAGAGCTTCAGAAATTCTGC 60.676 44.000 17.58 6.89 43.95 4.26
2201 2451 4.333690 AGCTTCAGAAATTCTGCTGTCAT 58.666 39.130 17.58 0.00 43.95 3.06
2205 2455 5.072040 TCAGAAATTCTGCTGTCATCGTA 57.928 39.130 17.58 0.00 43.95 3.43
2206 2456 5.478407 TCAGAAATTCTGCTGTCATCGTAA 58.522 37.500 17.58 0.00 43.95 3.18
2211 2461 3.443099 TCTGCTGTCATCGTAATCCTG 57.557 47.619 0.00 0.00 0.00 3.86
2213 2463 3.119291 CTGCTGTCATCGTAATCCTGTC 58.881 50.000 0.00 0.00 0.00 3.51
2215 2465 2.159099 GCTGTCATCGTAATCCTGTCCA 60.159 50.000 0.00 0.00 0.00 4.02
2222 2472 5.363868 TCATCGTAATCCTGTCCATCTCTTT 59.636 40.000 0.00 0.00 0.00 2.52
2252 2502 2.158561 AATGGCGGCAAAGTCAAGGC 62.159 55.000 18.31 0.00 0.00 4.35
2253 2503 3.294493 GGCGGCAAAGTCAAGGCA 61.294 61.111 3.07 0.00 0.00 4.75
2255 2505 2.956987 CGGCAAAGTCAAGGCAGG 59.043 61.111 0.00 0.00 0.00 4.85
2299 2549 2.032071 GTGGTGACGAAGGTGGGG 59.968 66.667 0.00 0.00 0.00 4.96
2401 2652 3.967326 AGATGATTGGTGGGAAGACGATA 59.033 43.478 0.00 0.00 0.00 2.92
2443 2694 1.367659 ACGAGAGTACGACTAGTGGC 58.632 55.000 0.00 0.00 46.88 5.01
2458 2709 0.179020 GTGGCCATTCATCGATGGGA 60.179 55.000 24.61 14.28 45.47 4.37
2492 2763 3.280295 GGGAGAGAGTAGACGATGACAA 58.720 50.000 0.00 0.00 0.00 3.18
2494 2765 4.193090 GGAGAGAGTAGACGATGACAAGA 58.807 47.826 0.00 0.00 0.00 3.02
2503 2774 8.101654 AGTAGACGATGACAAGATCCTATAAC 57.898 38.462 0.00 0.00 0.00 1.89
2535 2806 0.036022 TGGTGGATCAACATGCGACA 59.964 50.000 1.86 0.00 0.00 4.35
2562 2835 0.389948 CCGGAGACAAAAGGAGGACG 60.390 60.000 0.00 0.00 0.00 4.79
2565 2838 2.805657 CGGAGACAAAAGGAGGACGTTT 60.806 50.000 0.00 0.00 35.96 3.60
2573 2846 0.035458 AGGAGGACGTTTGAGGCAAG 59.965 55.000 0.00 0.00 0.00 4.01
2574 2847 0.955919 GGAGGACGTTTGAGGCAAGG 60.956 60.000 0.00 0.00 0.00 3.61
2586 2859 1.379176 GGCAAGGGAAGAAGAGGCC 60.379 63.158 0.00 0.00 0.00 5.19
2590 2863 1.006400 CAAGGGAAGAAGAGGCCCATT 59.994 52.381 0.00 0.00 44.55 3.16
2633 2906 1.548719 GGCGGCCAAAAGATAAAAGGT 59.451 47.619 15.62 0.00 0.00 3.50
2637 2910 3.181490 CGGCCAAAAGATAAAAGGTAGGC 60.181 47.826 2.24 0.00 38.84 3.93
2638 2911 4.386867 GCCAAAAGATAAAAGGTAGGCC 57.613 45.455 0.00 0.00 33.68 5.19
2644 2917 3.865571 AGATAAAAGGTAGGCCGGGATA 58.134 45.455 2.18 0.00 40.50 2.59
2645 2918 4.237018 AGATAAAAGGTAGGCCGGGATAA 58.763 43.478 2.18 0.00 40.50 1.75
2648 2921 0.030399 AAGGTAGGCCGGGATAAGGT 60.030 55.000 2.18 0.00 40.50 3.50
2651 2924 1.553704 GGTAGGCCGGGATAAGGTATG 59.446 57.143 2.18 0.00 0.00 2.39
2666 2947 7.713073 GGATAAGGTATGTTTGAGAGAAAGAGG 59.287 40.741 0.00 0.00 0.00 3.69
2667 2948 6.688073 AAGGTATGTTTGAGAGAAAGAGGA 57.312 37.500 0.00 0.00 0.00 3.71
2705 2986 4.520874 TGGATGCAACGGATCTAACAAAAA 59.479 37.500 0.00 0.00 0.00 1.94
2707 2988 6.375736 TGGATGCAACGGATCTAACAAAAATA 59.624 34.615 0.00 0.00 0.00 1.40
2751 4165 1.885887 TCCGATTTGAGGCAACCAAAG 59.114 47.619 0.00 0.00 39.17 2.77
2771 4185 3.883669 AGAGGTCAATCTGATCTTTGGC 58.116 45.455 0.00 0.00 38.10 4.52
2772 4186 2.611292 GAGGTCAATCTGATCTTTGGCG 59.389 50.000 0.00 0.00 38.10 5.69
2776 4191 3.003068 GTCAATCTGATCTTTGGCGATGG 59.997 47.826 0.00 0.00 0.00 3.51
2782 4197 1.943340 GATCTTTGGCGATGGAACTCC 59.057 52.381 0.00 0.00 0.00 3.85
2833 4249 0.758734 TCCGATGGGATCAAGCGATT 59.241 50.000 6.84 0.00 37.43 3.34
2834 4250 1.140852 TCCGATGGGATCAAGCGATTT 59.859 47.619 6.84 0.00 37.43 2.17
2870 4286 1.882623 CAGCTTTGGTCAAACCCTCTC 59.117 52.381 0.00 0.00 37.50 3.20
2872 4288 2.155279 GCTTTGGTCAAACCCTCTCTC 58.845 52.381 0.00 0.00 37.50 3.20
2969 4386 2.362717 GTCCCTGGAGATTAGGAACGAG 59.637 54.545 0.00 0.00 37.52 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 1.613925 AGCTAGCACGTCAAGACTCAA 59.386 47.619 18.83 0.00 0.00 3.02
33 35 1.248486 AGCTAGCACGTCAAGACTCA 58.752 50.000 18.83 0.00 0.00 3.41
34 36 2.223386 CCTAGCTAGCACGTCAAGACTC 60.223 54.545 18.83 0.00 0.00 3.36
35 37 1.746220 CCTAGCTAGCACGTCAAGACT 59.254 52.381 18.83 0.00 0.00 3.24
36 38 1.799548 GCCTAGCTAGCACGTCAAGAC 60.800 57.143 18.83 0.00 0.00 3.01
37 39 0.456221 GCCTAGCTAGCACGTCAAGA 59.544 55.000 18.83 0.00 0.00 3.02
38 40 0.457851 AGCCTAGCTAGCACGTCAAG 59.542 55.000 18.83 4.08 36.99 3.02
57 59 6.262720 TGATGATGAACAATGACAACTTGACA 59.737 34.615 0.00 0.00 0.00 3.58
71 73 6.957920 TTGAGTTTTTCCTGATGATGAACA 57.042 33.333 0.00 0.00 0.00 3.18
79 81 6.779539 AGGATCAACTTTGAGTTTTTCCTGAT 59.220 34.615 15.36 5.79 41.67 2.90
199 201 6.926272 TGATGTAACAGTTTTGTTTTATGGGC 59.074 34.615 0.00 0.00 45.01 5.36
200 202 7.114247 CGTGATGTAACAGTTTTGTTTTATGGG 59.886 37.037 0.00 0.00 45.01 4.00
209 212 3.617540 TGGCGTGATGTAACAGTTTTG 57.382 42.857 0.00 0.00 0.00 2.44
213 216 7.618502 TTATATTTTGGCGTGATGTAACAGT 57.381 32.000 0.00 0.00 0.00 3.55
214 217 7.431084 GGTTTATATTTTGGCGTGATGTAACAG 59.569 37.037 0.00 0.00 0.00 3.16
221 224 5.906113 TGTGGTTTATATTTTGGCGTGAT 57.094 34.783 0.00 0.00 0.00 3.06
226 229 8.819643 TTAACACTTGTGGTTTATATTTTGGC 57.180 30.769 5.72 0.00 0.00 4.52
264 267 7.502561 AGTCCAAAGTAAACTTGAGTGCTATTT 59.497 33.333 0.00 0.00 36.12 1.40
267 270 5.758296 CAGTCCAAAGTAAACTTGAGTGCTA 59.242 40.000 0.00 0.00 36.12 3.49
269 272 4.574828 TCAGTCCAAAGTAAACTTGAGTGC 59.425 41.667 10.81 0.00 36.12 4.40
270 273 5.817816 ACTCAGTCCAAAGTAAACTTGAGTG 59.182 40.000 10.55 10.22 36.12 3.51
308 316 5.827267 TGGCATTAGCAACATTAAGCTGATA 59.173 36.000 0.00 0.00 44.61 2.15
310 318 4.015764 TGGCATTAGCAACATTAAGCTGA 58.984 39.130 0.00 0.00 44.61 4.26
316 324 5.720371 ACTTGTTGGCATTAGCAACATTA 57.280 34.783 6.35 0.00 44.61 1.90
317 325 4.605640 ACTTGTTGGCATTAGCAACATT 57.394 36.364 6.35 0.00 44.61 2.71
318 326 4.309099 CAACTTGTTGGCATTAGCAACAT 58.691 39.130 6.35 0.00 44.61 2.71
319 327 3.715495 CAACTTGTTGGCATTAGCAACA 58.285 40.909 5.65 0.00 44.61 3.33
320 328 2.476241 GCAACTTGTTGGCATTAGCAAC 59.524 45.455 14.30 0.00 44.61 4.17
321 329 2.547642 GGCAACTTGTTGGCATTAGCAA 60.548 45.455 27.42 0.00 45.56 3.91
322 330 1.000731 GGCAACTTGTTGGCATTAGCA 59.999 47.619 27.42 0.00 45.56 3.49
323 331 1.713597 GGCAACTTGTTGGCATTAGC 58.286 50.000 27.42 7.87 45.56 3.09
329 337 0.175531 ACAGTTGGCAACTTGTTGGC 59.824 50.000 29.32 26.24 46.33 4.52
330 338 1.204467 ACACAGTTGGCAACTTGTTGG 59.796 47.619 29.32 19.65 40.46 3.77
331 339 2.652941 ACACAGTTGGCAACTTGTTG 57.347 45.000 29.32 25.31 40.46 3.33
332 340 3.508012 TGTAACACAGTTGGCAACTTGTT 59.492 39.130 35.16 35.16 40.46 2.83
333 341 3.085533 TGTAACACAGTTGGCAACTTGT 58.914 40.909 29.32 28.10 40.46 3.16
334 342 3.694734 CTGTAACACAGTTGGCAACTTG 58.305 45.455 29.32 27.55 41.19 3.16
351 359 1.075374 ACTTTGCCCCATTCAGCTGTA 59.925 47.619 14.67 4.08 0.00 2.74
358 366 2.893489 AGAAGTTGACTTTGCCCCATTC 59.107 45.455 0.00 0.00 36.11 2.67
366 374 4.209288 CGTCCTGTACAGAAGTTGACTTTG 59.791 45.833 24.68 6.37 36.11 2.77
367 375 4.098960 TCGTCCTGTACAGAAGTTGACTTT 59.901 41.667 24.68 0.00 36.11 2.66
368 376 3.635373 TCGTCCTGTACAGAAGTTGACTT 59.365 43.478 24.68 0.00 39.23 3.01
369 377 3.220110 TCGTCCTGTACAGAAGTTGACT 58.780 45.455 24.68 0.00 0.00 3.41
382 392 0.981183 TAAGCCAACCATCGTCCTGT 59.019 50.000 0.00 0.00 0.00 4.00
384 394 2.871096 TTTAAGCCAACCATCGTCCT 57.129 45.000 0.00 0.00 0.00 3.85
435 445 2.877097 TGCAACTGAAGGAGGCATAA 57.123 45.000 0.00 0.00 0.00 1.90
440 450 3.119245 CCATTTCATGCAACTGAAGGAGG 60.119 47.826 3.16 3.80 36.55 4.30
467 477 2.099141 TCTTTCGGAAGCACCTCATG 57.901 50.000 0.00 0.00 36.31 3.07
475 485 1.269448 TGGCATGTTTCTTTCGGAAGC 59.731 47.619 0.00 0.00 35.16 3.86
476 486 2.351738 GGTGGCATGTTTCTTTCGGAAG 60.352 50.000 0.00 0.00 35.16 3.46
490 500 0.467474 CCATCAGCATCAGGTGGCAT 60.467 55.000 0.00 0.00 43.32 4.40
492 502 1.826921 CCCATCAGCATCAGGTGGC 60.827 63.158 0.00 0.00 43.32 5.01
513 523 1.094785 ACGTGCATTTCTATGGCACC 58.905 50.000 10.03 0.00 36.39 5.01
517 527 2.472861 CGAGCTACGTGCATTTCTATGG 59.527 50.000 0.00 0.00 45.94 2.74
518 528 3.760264 CGAGCTACGTGCATTTCTATG 57.240 47.619 0.00 0.00 45.94 2.23
606 616 6.374333 ACCGTGATTTGATTACATGCTTTACT 59.626 34.615 0.00 0.00 0.00 2.24
612 622 4.970003 GCTTACCGTGATTTGATTACATGC 59.030 41.667 0.00 0.00 0.00 4.06
619 629 3.350219 AGGTGCTTACCGTGATTTGAT 57.650 42.857 0.00 0.00 34.28 2.57
621 631 5.560966 ATTTAGGTGCTTACCGTGATTTG 57.439 39.130 0.00 0.00 34.28 2.32
624 634 4.196971 GGAATTTAGGTGCTTACCGTGAT 58.803 43.478 0.00 0.00 34.28 3.06
705 727 2.222223 CGCGTCGCTGAGTTAAACTAAC 60.222 50.000 16.36 0.00 38.94 2.34
911 944 1.326213 CCGTGACTCTGGATCTGCCT 61.326 60.000 0.00 0.00 37.63 4.75
912 945 1.142748 CCGTGACTCTGGATCTGCC 59.857 63.158 0.00 0.00 37.10 4.85
916 949 2.045561 TCTCTCCGTGACTCTGGATC 57.954 55.000 0.00 0.00 32.83 3.36
938 971 7.503902 TGCAGCTGAGATCTTTCTACTTCTATA 59.496 37.037 20.43 0.00 30.30 1.31
940 973 5.654209 TGCAGCTGAGATCTTTCTACTTCTA 59.346 40.000 20.43 0.00 30.30 2.10
942 975 4.753233 TGCAGCTGAGATCTTTCTACTTC 58.247 43.478 20.43 0.00 30.30 3.01
943 976 4.815533 TGCAGCTGAGATCTTTCTACTT 57.184 40.909 20.43 0.00 30.30 2.24
944 977 4.815533 TTGCAGCTGAGATCTTTCTACT 57.184 40.909 20.43 0.00 30.30 2.57
945 978 4.201666 CGTTTGCAGCTGAGATCTTTCTAC 60.202 45.833 20.43 0.00 30.30 2.59
946 979 3.928992 CGTTTGCAGCTGAGATCTTTCTA 59.071 43.478 20.43 0.00 30.30 2.10
947 980 2.740981 CGTTTGCAGCTGAGATCTTTCT 59.259 45.455 20.43 0.00 33.88 2.52
960 993 0.320374 TCACTACTCCCCGTTTGCAG 59.680 55.000 0.00 0.00 0.00 4.41
968 1001 6.786122 AGAATCTAGACTATCACTACTCCCC 58.214 44.000 0.00 0.00 0.00 4.81
979 1012 6.889722 GCCATGTCCTCTAGAATCTAGACTAT 59.110 42.308 15.47 5.69 0.00 2.12
1288 1327 3.861569 GCGCAAGACTACATCATTACC 57.138 47.619 0.30 0.00 43.02 2.85
1322 1391 2.671177 CGTTGCTCGCCTGAACTGG 61.671 63.158 0.00 0.00 0.00 4.00
1355 1425 1.812571 GCGCATCCTGGAAAAAGAGAA 59.187 47.619 0.30 0.00 0.00 2.87
1444 1519 1.640917 TCTCCTTCTGCCCGTACTTT 58.359 50.000 0.00 0.00 0.00 2.66
1632 1707 2.877866 TCTTGACGTCCTCTTCCTCTT 58.122 47.619 14.12 0.00 0.00 2.85
1657 1738 1.415374 CGAAGTTGATGACGAACGGT 58.585 50.000 0.00 0.00 0.00 4.83
1769 1871 1.526887 CTCCCTCCGGCAAGCATAA 59.473 57.895 0.00 0.00 0.00 1.90
1798 1900 1.153823 CACCTTCAGTCGTAGGCCG 60.154 63.158 0.00 0.00 33.04 6.13
1800 1902 0.108756 GGTCACCTTCAGTCGTAGGC 60.109 60.000 0.00 0.00 33.04 3.93
1801 1903 1.254026 TGGTCACCTTCAGTCGTAGG 58.746 55.000 0.00 0.00 35.84 3.18
2043 2146 9.813826 AAAATTAAGTTGGCCATCTAGCTATAT 57.186 29.630 16.73 2.20 0.00 0.86
2103 2206 1.868997 GCTCAGCGCTAGTGCAAAA 59.131 52.632 28.83 13.10 39.64 2.44
2116 2224 0.797249 GCTTTCATGCTTGCGCTCAG 60.797 55.000 9.73 5.81 36.97 3.35
2184 2415 5.784750 TTACGATGACAGCAGAATTTCTG 57.215 39.130 19.92 19.92 46.90 3.02
2192 2442 3.119291 GACAGGATTACGATGACAGCAG 58.881 50.000 0.00 0.00 0.00 4.24
2195 2445 3.801114 TGGACAGGATTACGATGACAG 57.199 47.619 0.00 0.00 0.00 3.51
2201 2451 4.956700 AGAAAGAGATGGACAGGATTACGA 59.043 41.667 0.00 0.00 0.00 3.43
2205 2455 4.537688 TGGAAGAAAGAGATGGACAGGATT 59.462 41.667 0.00 0.00 0.00 3.01
2206 2456 4.107072 TGGAAGAAAGAGATGGACAGGAT 58.893 43.478 0.00 0.00 0.00 3.24
2211 2461 6.824305 TTGAAATGGAAGAAAGAGATGGAC 57.176 37.500 0.00 0.00 0.00 4.02
2252 2502 4.704833 CCAGTGACGGTGCCCCTG 62.705 72.222 0.00 0.00 0.00 4.45
2255 2505 4.643387 AAGCCAGTGACGGTGCCC 62.643 66.667 0.00 0.00 0.00 5.36
2266 2516 1.556911 ACCACCTCTATGACAAGCCAG 59.443 52.381 0.00 0.00 0.00 4.85
2299 2549 2.288886 CCTTAACCACTATAGAGCGGGC 60.289 54.545 6.78 0.00 0.00 6.13
2318 2568 3.580319 GCACCCACCCCTGAACCT 61.580 66.667 0.00 0.00 0.00 3.50
2341 2592 1.078637 GGGTTCTTCTACGGTGGCC 60.079 63.158 0.00 0.00 0.00 5.36
2349 2600 2.263540 GTGGCGCGGGTTCTTCTA 59.736 61.111 8.83 0.00 0.00 2.10
2401 2652 0.889186 GTGGTCCTTGGCATTCACGT 60.889 55.000 0.00 0.00 0.00 4.49
2434 2685 2.890808 TCGATGAATGGCCACTAGTC 57.109 50.000 8.16 3.83 0.00 2.59
2443 2694 2.983229 GATCCTCCCATCGATGAATGG 58.017 52.381 26.86 21.65 44.96 3.16
2458 2709 2.902846 CTCCCGCTCGTCGATCCT 60.903 66.667 0.00 0.00 41.67 3.24
2466 2717 1.492319 CGTCTACTCTCTCCCGCTCG 61.492 65.000 0.00 0.00 0.00 5.03
2492 2763 5.713861 ACCGCGGTAAATAGTTATAGGATCT 59.286 40.000 33.34 0.00 0.00 2.75
2494 2765 5.337009 CCACCGCGGTAAATAGTTATAGGAT 60.337 44.000 33.70 0.00 0.00 3.24
2526 2797 2.397751 GGCAGCTATTGTCGCATGT 58.602 52.632 0.00 0.00 0.00 3.21
2535 2806 2.359900 CTTTTGTCTCCGGCAGCTATT 58.640 47.619 0.00 0.00 0.00 1.73
2562 2835 2.816672 CTCTTCTTCCCTTGCCTCAAAC 59.183 50.000 0.00 0.00 0.00 2.93
2565 2838 0.987294 CCTCTTCTTCCCTTGCCTCA 59.013 55.000 0.00 0.00 0.00 3.86
2573 2846 0.396278 CCAATGGGCCTCTTCTTCCC 60.396 60.000 4.53 0.00 40.47 3.97
2574 2847 0.625849 TCCAATGGGCCTCTTCTTCC 59.374 55.000 4.53 0.00 0.00 3.46
2586 2859 2.028420 TCATTGTCGAGCTCCAATGG 57.972 50.000 29.68 18.74 45.05 3.16
2590 2863 0.904649 ACCATCATTGTCGAGCTCCA 59.095 50.000 8.47 0.00 0.00 3.86
2633 2906 2.708037 ACATACCTTATCCCGGCCTA 57.292 50.000 0.00 0.00 0.00 3.93
2637 2910 4.344102 TCTCTCAAACATACCTTATCCCGG 59.656 45.833 0.00 0.00 0.00 5.73
2638 2911 5.531122 TCTCTCAAACATACCTTATCCCG 57.469 43.478 0.00 0.00 0.00 5.14
2644 2917 6.688073 TCCTCTTTCTCTCAAACATACCTT 57.312 37.500 0.00 0.00 0.00 3.50
2645 2918 6.688073 TTCCTCTTTCTCTCAAACATACCT 57.312 37.500 0.00 0.00 0.00 3.08
2648 2921 6.272324 TCCCTTTCCTCTTTCTCTCAAACATA 59.728 38.462 0.00 0.00 0.00 2.29
2651 2924 4.974399 TCCCTTTCCTCTTTCTCTCAAAC 58.026 43.478 0.00 0.00 0.00 2.93
2666 2947 3.611766 GCATCCAACGAGTTTTCCCTTTC 60.612 47.826 0.00 0.00 0.00 2.62
2667 2948 2.296190 GCATCCAACGAGTTTTCCCTTT 59.704 45.455 0.00 0.00 0.00 3.11
2751 4165 2.611292 CGCCAAAGATCAGATTGACCTC 59.389 50.000 0.00 0.00 0.00 3.85
2771 4185 4.409342 CTCTGCGGAGTTCCATCG 57.591 61.111 14.84 0.00 35.03 3.84
2782 4197 1.667724 GGATGTTCAATGGACTCTGCG 59.332 52.381 0.00 0.00 0.00 5.18
2794 4209 6.176896 TCGGAGTTGAATTATTGGATGTTCA 58.823 36.000 0.00 0.00 0.00 3.18
2833 4249 2.092968 AGCTGATATGAACGGCCTTCAA 60.093 45.455 17.79 10.20 42.37 2.69
2834 4250 1.486310 AGCTGATATGAACGGCCTTCA 59.514 47.619 16.66 16.66 43.28 3.02


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

AutoCloner maintained by Alex Coulton.