Multiple sequence alignment - TraesCS1D01G067200

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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 TraesCS1D01G067200 chr1D 100.000 3348 0 0 876 4223 48884296 48887643 0.000000e+00 6183.0
1 TraesCS1D01G067200 chr1D 100.000 543 0 0 1 543 48883421 48883963 0.000000e+00 1003.0
2 TraesCS1D01G067200 chr1D 93.030 330 6 7 3681 3993 48900521 48900850 2.300000e-127 466.0
3 TraesCS1D01G067200 chr1D 83.430 519 34 25 3417 3902 48914103 48914602 6.480000e-118 435.0
4 TraesCS1D01G067200 chr1D 84.681 235 18 10 3182 3405 48913895 48914122 7.110000e-53 219.0
5 TraesCS1D01G067200 chr1D 86.224 196 14 3 4008 4191 49220632 49220826 2.580000e-47 200.0
6 TraesCS1D01G067200 chr1D 85.864 191 16 5 4010 4191 48916510 48916698 4.310000e-45 193.0
7 TraesCS1D01G067200 chr1D 83.085 201 17 9 4008 4191 48900910 48901110 2.610000e-37 167.0
8 TraesCS1D01G067200 chr1D 100.000 29 0 0 4191 4219 48901146 48901174 2.000000e-03 54.7
9 TraesCS1D01G067200 chr1B 91.314 3166 168 52 890 3999 68944206 68947320 0.000000e+00 4224.0
10 TraesCS1D01G067200 chr1B 82.387 511 25 29 55 543 68943671 68944138 6.620000e-103 385.0
11 TraesCS1D01G067200 chr1B 88.770 187 17 3 4008 4191 68947418 68947603 4.250000e-55 226.0
12 TraesCS1D01G067200 chr1B 88.571 175 14 5 3764 3933 69236386 69236559 1.540000e-49 207.0
13 TraesCS1D01G067200 chr1A 93.676 2530 116 17 890 3398 48783993 48786499 0.000000e+00 3746.0
14 TraesCS1D01G067200 chr1A 81.421 366 29 24 3590 3933 48789689 48790037 3.240000e-66 263.0
15 TraesCS1D01G067200 chr1A 91.573 178 13 2 3417 3593 48789411 48789587 1.170000e-60 244.0
16 TraesCS1D01G067200 chr1A 80.756 291 20 11 87 362 48783598 48783867 1.200000e-45 195.0
17 TraesCS1D01G067200 chr7A 88.462 468 38 8 1565 2023 620859636 620859176 6.170000e-153 551.0
18 TraesCS1D01G067200 chr7D 77.096 489 101 9 2299 2783 176160304 176160785 5.380000e-69 272.0
19 TraesCS1D01G067200 chr6A 83.740 246 18 8 1796 2031 220743160 220742927 3.310000e-51 213.0
20 TraesCS1D01G067200 chr2B 92.174 115 9 0 1962 2076 281873307 281873421 3.380000e-36 163.0
21 TraesCS1D01G067200 chr2B 97.727 44 1 0 2432 2475 281873463 281873506 4.530000e-10 76.8
22 TraesCS1D01G067200 chr2B 97.368 38 1 0 2490 2527 281873504 281873541 9.800000e-07 65.8
23 TraesCS1D01G067200 chr4B 85.542 83 12 0 2502 2584 124917638 124917556 2.090000e-13 87.9
24 TraesCS1D01G067200 chr4B 80.000 90 14 4 2530 2617 377938866 377938779 3.520000e-06 63.9
25 TraesCS1D01G067200 chr4D 80.000 90 14 4 2530 2617 303519072 303518985 3.520000e-06 63.9
26 TraesCS1D01G067200 chr4A 80.000 90 14 4 2530 2617 175856484 175856571 3.520000e-06 63.9


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 TraesCS1D01G067200 chr1D 48883421 48887643 4222 False 3593.000000 6183 100.000000 1 4223 2 chr1D.!!$F2 4222
1 TraesCS1D01G067200 chr1D 48913895 48916698 2803 False 282.333333 435 84.658333 3182 4191 3 chr1D.!!$F4 1009
2 TraesCS1D01G067200 chr1D 48900521 48901174 653 False 229.233333 466 92.038333 3681 4219 3 chr1D.!!$F3 538
3 TraesCS1D01G067200 chr1B 68943671 68947603 3932 False 1611.666667 4224 87.490333 55 4191 3 chr1B.!!$F2 4136
4 TraesCS1D01G067200 chr1A 48783598 48790037 6439 False 1112.000000 3746 86.856500 87 3933 4 chr1A.!!$F1 3846

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
29 30 0.034756 TGGGTGACACGAACCATCTG 59.965 55.0 0.00 0.0 39.65 2.90 F
154 159 0.104120 TCGCGTCCCATACTTCCATG 59.896 55.0 5.77 0.0 0.00 3.66 F
1056 1105 0.178935 CTCCCCTCCTCCTCCTCATC 60.179 65.0 0.00 0.0 0.00 2.92 F
1594 1655 0.795085 CGTCTTCGTGTCCTACTCGT 59.205 55.0 2.04 0.0 36.59 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1876 1.079127 CGGAGTGGATGGAAGCGTT 60.079 57.895 0.00 0.0 0.00 4.84 R
1824 1885 3.474570 GGGAGCTGCGGAGTGGAT 61.475 66.667 5.62 0.0 0.00 3.41 R
2796 2872 1.136252 CATTCGACGAGGTTGTTGCAG 60.136 52.381 0.00 0.0 0.00 4.41 R
3232 3308 0.391130 TCCGCATTTCAAGAGGACCG 60.391 55.000 0.00 0.0 29.61 4.79 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
18 19 3.474083 TCTGAGACCATGGGTGACA 57.526 52.632 18.09 9.56 35.25 3.58
19 20 0.976641 TCTGAGACCATGGGTGACAC 59.023 55.000 18.09 0.00 35.25 3.67
20 21 0.390340 CTGAGACCATGGGTGACACG 60.390 60.000 18.09 2.10 35.25 4.49
21 22 0.830023 TGAGACCATGGGTGACACGA 60.830 55.000 18.09 0.00 35.25 4.35
22 23 0.320374 GAGACCATGGGTGACACGAA 59.680 55.000 18.09 0.00 35.25 3.85
23 24 0.034896 AGACCATGGGTGACACGAAC 59.965 55.000 18.09 0.00 35.25 3.95
24 25 0.953960 GACCATGGGTGACACGAACC 60.954 60.000 18.09 0.00 35.25 3.62
25 26 1.072332 CCATGGGTGACACGAACCA 59.928 57.895 2.85 4.75 39.65 3.67
26 27 0.322456 CCATGGGTGACACGAACCAT 60.322 55.000 2.85 8.56 44.17 3.55
27 28 1.086696 CATGGGTGACACGAACCATC 58.913 55.000 10.83 0.00 41.56 3.51
28 29 0.984230 ATGGGTGACACGAACCATCT 59.016 50.000 8.56 0.00 39.41 2.90
29 30 0.034756 TGGGTGACACGAACCATCTG 59.965 55.000 0.00 0.00 39.65 2.90
30 31 1.298859 GGGTGACACGAACCATCTGC 61.299 60.000 0.00 0.00 39.65 4.26
31 32 0.320771 GGTGACACGAACCATCTGCT 60.321 55.000 0.00 0.00 37.65 4.24
32 33 1.512926 GTGACACGAACCATCTGCTT 58.487 50.000 0.00 0.00 0.00 3.91
33 34 2.611971 GGTGACACGAACCATCTGCTTA 60.612 50.000 0.00 0.00 37.65 3.09
34 35 2.412089 GTGACACGAACCATCTGCTTAC 59.588 50.000 0.00 0.00 0.00 2.34
35 36 1.654105 GACACGAACCATCTGCTTACG 59.346 52.381 0.00 0.00 0.00 3.18
36 37 1.000506 ACACGAACCATCTGCTTACGT 59.999 47.619 0.00 0.00 0.00 3.57
37 38 1.654105 CACGAACCATCTGCTTACGTC 59.346 52.381 0.00 0.00 0.00 4.34
38 39 1.271379 ACGAACCATCTGCTTACGTCA 59.729 47.619 0.00 0.00 0.00 4.35
39 40 1.654105 CGAACCATCTGCTTACGTCAC 59.346 52.381 0.00 0.00 0.00 3.67
40 41 2.000447 GAACCATCTGCTTACGTCACC 59.000 52.381 0.00 0.00 0.00 4.02
41 42 0.249398 ACCATCTGCTTACGTCACCC 59.751 55.000 0.00 0.00 0.00 4.61
42 43 0.806102 CCATCTGCTTACGTCACCCG 60.806 60.000 0.00 0.00 44.03 5.28
43 44 1.153628 ATCTGCTTACGTCACCCGC 60.154 57.895 0.00 0.00 41.42 6.13
44 45 1.884075 ATCTGCTTACGTCACCCGCA 61.884 55.000 0.00 0.00 41.42 5.69
45 46 1.666553 CTGCTTACGTCACCCGCAA 60.667 57.895 0.00 0.00 41.42 4.85
46 47 1.225376 CTGCTTACGTCACCCGCAAA 61.225 55.000 0.00 0.00 41.42 3.68
47 48 0.814410 TGCTTACGTCACCCGCAAAA 60.814 50.000 0.00 0.00 41.42 2.44
48 49 0.308376 GCTTACGTCACCCGCAAAAA 59.692 50.000 0.00 0.00 41.42 1.94
110 111 1.300971 CCATCCAGCTGTTCACGTGG 61.301 60.000 17.00 7.34 0.00 4.94
146 151 3.896133 GCCGAGTCGCGTCCCATA 61.896 66.667 7.12 0.00 38.67 2.74
148 153 2.478890 CCGAGTCGCGTCCCATACT 61.479 63.158 7.12 0.00 38.67 2.12
149 154 1.432251 CGAGTCGCGTCCCATACTT 59.568 57.895 5.77 0.00 34.64 2.24
150 155 0.591741 CGAGTCGCGTCCCATACTTC 60.592 60.000 5.77 0.00 34.64 3.01
151 156 0.248949 GAGTCGCGTCCCATACTTCC 60.249 60.000 5.77 0.00 0.00 3.46
152 157 0.968901 AGTCGCGTCCCATACTTCCA 60.969 55.000 5.77 0.00 0.00 3.53
153 158 0.104304 GTCGCGTCCCATACTTCCAT 59.896 55.000 5.77 0.00 0.00 3.41
154 159 0.104120 TCGCGTCCCATACTTCCATG 59.896 55.000 5.77 0.00 0.00 3.66
155 160 1.498865 CGCGTCCCATACTTCCATGC 61.499 60.000 0.00 0.00 0.00 4.06
156 161 1.166531 GCGTCCCATACTTCCATGCC 61.167 60.000 0.00 0.00 0.00 4.40
157 162 0.535102 CGTCCCATACTTCCATGCCC 60.535 60.000 0.00 0.00 0.00 5.36
158 163 0.550914 GTCCCATACTTCCATGCCCA 59.449 55.000 0.00 0.00 0.00 5.36
159 164 1.145738 GTCCCATACTTCCATGCCCAT 59.854 52.381 0.00 0.00 0.00 4.00
166 171 0.892358 CTTCCATGCCCATCCATCCG 60.892 60.000 0.00 0.00 0.00 4.18
168 173 2.203379 CATGCCCATCCATCCGCA 60.203 61.111 0.00 0.00 35.35 5.69
172 177 2.271821 CCCATCCATCCGCACACA 59.728 61.111 0.00 0.00 0.00 3.72
173 178 1.378382 CCCATCCATCCGCACACAA 60.378 57.895 0.00 0.00 0.00 3.33
182 187 1.141645 TCCGCACACAAACATACGTC 58.858 50.000 0.00 0.00 0.00 4.34
324 343 3.716006 CGCCGTGACAGCAACAGG 61.716 66.667 0.00 0.00 0.00 4.00
392 424 2.556287 CAGCGCACGAGGGAAAAC 59.444 61.111 11.47 0.00 0.00 2.43
393 425 3.041940 AGCGCACGAGGGAAAACG 61.042 61.111 11.47 0.00 0.00 3.60
394 426 4.736631 GCGCACGAGGGAAAACGC 62.737 66.667 0.30 0.00 39.49 4.84
395 427 4.084888 CGCACGAGGGAAAACGCC 62.085 66.667 0.00 0.00 0.00 5.68
396 428 2.975799 GCACGAGGGAAAACGCCA 60.976 61.111 0.00 0.00 0.00 5.69
416 448 4.038080 CCACGGCCGCAAAAGGTC 62.038 66.667 28.58 0.00 0.00 3.85
420 452 4.404654 GGCCGCAAAAGGTCGCAG 62.405 66.667 0.00 0.00 0.00 5.18
421 453 3.353836 GCCGCAAAAGGTCGCAGA 61.354 61.111 0.00 0.00 0.00 4.26
422 454 2.863153 CCGCAAAAGGTCGCAGAG 59.137 61.111 0.00 0.00 36.95 3.35
431 463 2.570706 GTCGCAGAGCAGAGCAGA 59.429 61.111 0.00 0.00 36.95 4.26
432 464 1.141449 GTCGCAGAGCAGAGCAGAT 59.859 57.895 0.00 0.00 36.95 2.90
433 465 0.871163 GTCGCAGAGCAGAGCAGATC 60.871 60.000 0.00 0.00 36.95 2.75
434 466 1.592131 CGCAGAGCAGAGCAGATCC 60.592 63.158 0.00 0.00 0.00 3.36
435 467 1.227615 GCAGAGCAGAGCAGATCCC 60.228 63.158 0.00 0.00 0.00 3.85
436 468 1.688269 GCAGAGCAGAGCAGATCCCT 61.688 60.000 0.00 0.00 0.00 4.20
437 469 0.390124 CAGAGCAGAGCAGATCCCTC 59.610 60.000 3.41 3.41 0.00 4.30
438 470 0.760189 AGAGCAGAGCAGATCCCTCC 60.760 60.000 7.23 0.00 30.70 4.30
439 471 0.760189 GAGCAGAGCAGATCCCTCCT 60.760 60.000 7.23 0.14 0.00 3.69
440 472 0.760189 AGCAGAGCAGATCCCTCCTC 60.760 60.000 7.23 0.67 0.00 3.71
441 473 2.040330 CAGAGCAGATCCCTCCTCG 58.960 63.158 7.23 0.00 0.00 4.63
442 474 0.754957 CAGAGCAGATCCCTCCTCGT 60.755 60.000 7.23 0.00 0.00 4.18
443 475 0.467290 AGAGCAGATCCCTCCTCGTC 60.467 60.000 7.23 0.00 0.00 4.20
444 476 1.791103 GAGCAGATCCCTCCTCGTCG 61.791 65.000 0.00 0.00 0.00 5.12
445 477 2.122167 GCAGATCCCTCCTCGTCGT 61.122 63.158 0.00 0.00 0.00 4.34
446 478 2.026522 CAGATCCCTCCTCGTCGTC 58.973 63.158 0.00 0.00 0.00 4.20
447 479 0.748367 CAGATCCCTCCTCGTCGTCA 60.748 60.000 0.00 0.00 0.00 4.35
448 480 0.748729 AGATCCCTCCTCGTCGTCAC 60.749 60.000 0.00 0.00 0.00 3.67
449 481 1.726533 GATCCCTCCTCGTCGTCACC 61.727 65.000 0.00 0.00 0.00 4.02
450 482 3.450115 CCCTCCTCGTCGTCACCC 61.450 72.222 0.00 0.00 0.00 4.61
451 483 3.812019 CCTCCTCGTCGTCACCCG 61.812 72.222 0.00 0.00 38.13 5.28
452 484 3.054503 CTCCTCGTCGTCACCCGT 61.055 66.667 0.00 0.00 37.94 5.28
453 485 3.036783 CTCCTCGTCGTCACCCGTC 62.037 68.421 0.00 0.00 37.94 4.79
454 486 4.456253 CCTCGTCGTCACCCGTCG 62.456 72.222 0.00 0.00 46.86 5.12
468 500 2.383527 CGTCGCTCACTGCCTTTCC 61.384 63.158 0.00 0.00 38.78 3.13
512 554 1.229336 CCCCCACCACTCTGACTCT 60.229 63.158 0.00 0.00 0.00 3.24
892 934 3.161557 GCCCCGCTAATCCCATCT 58.838 61.111 0.00 0.00 0.00 2.90
893 935 1.003233 GCCCCGCTAATCCCATCTC 60.003 63.158 0.00 0.00 0.00 2.75
894 936 1.768684 GCCCCGCTAATCCCATCTCA 61.769 60.000 0.00 0.00 0.00 3.27
895 937 0.987294 CCCCGCTAATCCCATCTCAT 59.013 55.000 0.00 0.00 0.00 2.90
1028 1077 2.360350 AATGGCCACGCTCACCAG 60.360 61.111 8.16 0.00 36.78 4.00
1055 1104 1.673928 CCTCCCCTCCTCCTCCTCAT 61.674 65.000 0.00 0.00 0.00 2.90
1056 1105 0.178935 CTCCCCTCCTCCTCCTCATC 60.179 65.000 0.00 0.00 0.00 2.92
1057 1106 0.931250 TCCCCTCCTCCTCCTCATCA 60.931 60.000 0.00 0.00 0.00 3.07
1066 1115 2.633481 CTCCTCCTCATCAGCATCATCA 59.367 50.000 0.00 0.00 0.00 3.07
1069 1118 3.601435 CTCCTCATCAGCATCATCATCC 58.399 50.000 0.00 0.00 0.00 3.51
1143 1204 3.946201 ACGCTCAAGCTGCTGGGT 61.946 61.111 1.35 2.31 39.32 4.51
1594 1655 0.795085 CGTCTTCGTGTCCTACTCGT 59.205 55.000 2.04 0.00 36.59 4.18
1740 1801 2.282958 AGCTTCTCGACCCCGTCA 60.283 61.111 0.00 0.00 37.05 4.35
1743 1804 2.993264 TTCTCGACCCCGTCACCC 60.993 66.667 0.00 0.00 37.05 4.61
1824 1885 2.342279 CTCGACCCAACGCTTCCA 59.658 61.111 0.00 0.00 0.00 3.53
1895 1971 1.571460 CGACCAGCTCAGTTGCAAC 59.429 57.895 22.17 22.17 34.99 4.17
2703 2779 1.878522 GCCGGAGTACATGCTGACG 60.879 63.158 5.05 0.00 0.00 4.35
2988 3064 2.913054 TAGTGCAGATGCTGAGCGGC 62.913 60.000 6.35 1.40 42.66 6.53
3099 3175 3.488090 GACTACAACGCGCTGGGC 61.488 66.667 14.82 6.64 38.69 5.36
3114 3190 2.047179 GGCCTGAACCTGTCGGAC 60.047 66.667 0.00 0.00 34.07 4.79
3138 3214 2.815298 CTCCTCGTCCGACTCGCTC 61.815 68.421 0.00 0.00 0.00 5.03
3195 3271 1.292223 CCACGACATCGGGTTCAGT 59.708 57.895 6.21 0.00 42.08 3.41
3338 3426 7.118496 AGAGTCCTAACATATCTCTTTGTGG 57.882 40.000 0.00 0.00 32.52 4.17
3374 6396 6.519679 TTTCAGATGGTTCATTGGATCAAG 57.480 37.500 0.00 0.00 0.00 3.02
3379 6401 6.152323 CAGATGGTTCATTGGATCAAGTTTCT 59.848 38.462 0.00 0.00 0.00 2.52
3383 6405 7.209475 TGGTTCATTGGATCAAGTTTCTTTTC 58.791 34.615 0.00 0.00 0.00 2.29
3385 6407 7.436933 GTTCATTGGATCAAGTTTCTTTTCCT 58.563 34.615 0.00 0.00 0.00 3.36
3387 6409 8.021898 TCATTGGATCAAGTTTCTTTTCCTTT 57.978 30.769 0.00 0.00 0.00 3.11
3388 6410 8.485392 TCATTGGATCAAGTTTCTTTTCCTTTT 58.515 29.630 0.00 0.00 0.00 2.27
3389 6411 8.768019 CATTGGATCAAGTTTCTTTTCCTTTTC 58.232 33.333 0.00 0.00 0.00 2.29
3390 6412 7.660030 TGGATCAAGTTTCTTTTCCTTTTCT 57.340 32.000 0.00 0.00 0.00 2.52
3391 6413 8.078060 TGGATCAAGTTTCTTTTCCTTTTCTT 57.922 30.769 0.00 0.00 0.00 2.52
3392 6414 8.197439 TGGATCAAGTTTCTTTTCCTTTTCTTC 58.803 33.333 0.00 0.00 0.00 2.87
3393 6415 8.417106 GGATCAAGTTTCTTTTCCTTTTCTTCT 58.583 33.333 0.00 0.00 0.00 2.85
3394 6416 9.457110 GATCAAGTTTCTTTTCCTTTTCTTCTC 57.543 33.333 0.00 0.00 0.00 2.87
3395 6417 8.581253 TCAAGTTTCTTTTCCTTTTCTTCTCT 57.419 30.769 0.00 0.00 0.00 3.10
3396 6418 9.025041 TCAAGTTTCTTTTCCTTTTCTTCTCTT 57.975 29.630 0.00 0.00 0.00 2.85
3397 6419 9.295214 CAAGTTTCTTTTCCTTTTCTTCTCTTC 57.705 33.333 0.00 0.00 0.00 2.87
3398 6420 8.815565 AGTTTCTTTTCCTTTTCTTCTCTTCT 57.184 30.769 0.00 0.00 0.00 2.85
3399 6421 8.681806 AGTTTCTTTTCCTTTTCTTCTCTTCTG 58.318 33.333 0.00 0.00 0.00 3.02
3400 6422 8.462811 GTTTCTTTTCCTTTTCTTCTCTTCTGT 58.537 33.333 0.00 0.00 0.00 3.41
3401 6423 8.581253 TTCTTTTCCTTTTCTTCTCTTCTGTT 57.419 30.769 0.00 0.00 0.00 3.16
3402 6424 8.214721 TCTTTTCCTTTTCTTCTCTTCTGTTC 57.785 34.615 0.00 0.00 0.00 3.18
3403 6425 6.944234 TTTCCTTTTCTTCTCTTCTGTTCC 57.056 37.500 0.00 0.00 0.00 3.62
3404 6426 5.896073 TCCTTTTCTTCTCTTCTGTTCCT 57.104 39.130 0.00 0.00 0.00 3.36
3405 6427 5.859495 TCCTTTTCTTCTCTTCTGTTCCTC 58.141 41.667 0.00 0.00 0.00 3.71
3406 6428 5.604650 TCCTTTTCTTCTCTTCTGTTCCTCT 59.395 40.000 0.00 0.00 0.00 3.69
3407 6429 5.700373 CCTTTTCTTCTCTTCTGTTCCTCTG 59.300 44.000 0.00 0.00 0.00 3.35
3408 6430 6.463614 CCTTTTCTTCTCTTCTGTTCCTCTGA 60.464 42.308 0.00 0.00 0.00 3.27
3409 6431 6.485830 TTTCTTCTCTTCTGTTCCTCTGAA 57.514 37.500 0.00 0.00 33.95 3.02
3410 6432 6.485830 TTCTTCTCTTCTGTTCCTCTGAAA 57.514 37.500 0.00 0.00 34.51 2.69
3411 6433 6.485830 TCTTCTCTTCTGTTCCTCTGAAAA 57.514 37.500 0.00 0.00 34.51 2.29
3412 6434 6.889198 TCTTCTCTTCTGTTCCTCTGAAAAA 58.111 36.000 0.00 0.00 34.51 1.94
3413 6435 6.763610 TCTTCTCTTCTGTTCCTCTGAAAAAC 59.236 38.462 0.00 0.00 34.51 2.43
3414 6436 6.240549 TCTCTTCTGTTCCTCTGAAAAACT 57.759 37.500 4.19 0.00 34.51 2.66
3415 6437 7.361457 TCTCTTCTGTTCCTCTGAAAAACTA 57.639 36.000 4.19 0.00 34.51 2.24
3416 6438 7.967908 TCTCTTCTGTTCCTCTGAAAAACTAT 58.032 34.615 4.19 0.00 34.51 2.12
3417 6439 8.432805 TCTCTTCTGTTCCTCTGAAAAACTATT 58.567 33.333 4.19 0.00 34.51 1.73
3418 6440 8.980481 TCTTCTGTTCCTCTGAAAAACTATTT 57.020 30.769 4.19 0.00 34.51 1.40
3419 6441 9.408648 TCTTCTGTTCCTCTGAAAAACTATTTT 57.591 29.630 4.19 0.00 41.37 1.82
3546 6585 3.648067 TGAGATCTTGGTGGTGGATATCC 59.352 47.826 15.39 15.39 29.76 2.59
3547 6586 3.648067 GAGATCTTGGTGGTGGATATCCA 59.352 47.826 20.98 20.98 45.30 3.41
3562 6601 2.781403 ATCCATCCATCCCCTTTTGG 57.219 50.000 0.00 0.00 39.97 3.28
3608 6752 7.960195 CAGATGCTACTATACTAGAATCACACG 59.040 40.741 0.00 0.00 0.00 4.49
3633 6777 1.203287 GAAGAGGGATGGCTTGTTTGC 59.797 52.381 0.00 0.00 0.00 3.68
3958 8919 5.230182 TGATGCTGTTGTCTAACACTACTG 58.770 41.667 0.00 0.00 41.66 2.74
3999 8963 6.308015 AGTGGTGGTAATCATAGCAAAGTA 57.692 37.500 0.00 0.00 40.93 2.24
4000 8964 6.349300 AGTGGTGGTAATCATAGCAAAGTAG 58.651 40.000 0.00 0.00 40.93 2.57
4219 9325 8.755696 TTTCAATCGTATCCAAAAATTTCTGG 57.244 30.769 3.98 3.98 0.00 3.86
4220 9326 6.329496 TCAATCGTATCCAAAAATTTCTGGC 58.671 36.000 5.60 0.00 32.33 4.85
4221 9327 5.913137 ATCGTATCCAAAAATTTCTGGCA 57.087 34.783 5.60 0.00 32.33 4.92
4222 9328 5.309323 TCGTATCCAAAAATTTCTGGCAG 57.691 39.130 8.58 8.58 32.33 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.976641 GTGTCACCCATGGTCTCAGA 59.023 55.000 11.73 0.00 31.02 3.27
1 2 0.390340 CGTGTCACCCATGGTCTCAG 60.390 60.000 11.73 0.00 31.02 3.35
2 3 0.830023 TCGTGTCACCCATGGTCTCA 60.830 55.000 11.73 1.58 31.02 3.27
3 4 0.320374 TTCGTGTCACCCATGGTCTC 59.680 55.000 11.73 0.00 31.02 3.36
4 5 0.034896 GTTCGTGTCACCCATGGTCT 59.965 55.000 11.73 0.00 31.02 3.85
5 6 0.953960 GGTTCGTGTCACCCATGGTC 60.954 60.000 11.73 0.00 31.02 4.02
6 7 1.072505 GGTTCGTGTCACCCATGGT 59.927 57.895 11.73 0.00 35.62 3.55
7 8 0.322456 ATGGTTCGTGTCACCCATGG 60.322 55.000 4.14 4.14 36.36 3.66
8 9 1.086696 GATGGTTCGTGTCACCCATG 58.913 55.000 14.76 0.00 37.81 3.66
9 10 0.984230 AGATGGTTCGTGTCACCCAT 59.016 50.000 10.91 10.91 40.34 4.00
10 11 0.034756 CAGATGGTTCGTGTCACCCA 59.965 55.000 2.38 2.38 32.71 4.51
11 12 1.298859 GCAGATGGTTCGTGTCACCC 61.299 60.000 0.00 0.00 32.71 4.61
12 13 0.320771 AGCAGATGGTTCGTGTCACC 60.321 55.000 0.00 0.00 34.52 4.02
13 14 1.512926 AAGCAGATGGTTCGTGTCAC 58.487 50.000 0.00 0.00 0.00 3.67
14 15 2.683968 GTAAGCAGATGGTTCGTGTCA 58.316 47.619 0.00 0.00 37.00 3.58
15 16 1.654105 CGTAAGCAGATGGTTCGTGTC 59.346 52.381 0.00 0.00 37.00 3.67
16 17 1.000506 ACGTAAGCAGATGGTTCGTGT 59.999 47.619 15.90 6.22 45.62 4.49
17 18 1.654105 GACGTAAGCAGATGGTTCGTG 59.346 52.381 19.25 7.65 45.62 4.35
18 19 1.271379 TGACGTAAGCAGATGGTTCGT 59.729 47.619 16.32 16.32 45.62 3.85
19 20 1.654105 GTGACGTAAGCAGATGGTTCG 59.346 52.381 0.00 7.58 45.62 3.95
20 21 2.000447 GGTGACGTAAGCAGATGGTTC 59.000 52.381 0.00 0.00 45.62 3.62
21 22 1.338769 GGGTGACGTAAGCAGATGGTT 60.339 52.381 4.14 2.51 45.62 3.67
22 23 0.249398 GGGTGACGTAAGCAGATGGT 59.751 55.000 4.14 0.00 45.62 3.55
23 24 0.806102 CGGGTGACGTAAGCAGATGG 60.806 60.000 4.14 0.00 45.62 3.51
24 25 1.421410 GCGGGTGACGTAAGCAGATG 61.421 60.000 6.42 0.00 46.52 2.90
25 26 1.153628 GCGGGTGACGTAAGCAGAT 60.154 57.895 6.42 0.00 46.52 2.90
26 27 2.089887 TTGCGGGTGACGTAAGCAGA 62.090 55.000 6.42 0.00 42.23 4.26
27 28 1.666553 TTGCGGGTGACGTAAGCAG 60.667 57.895 4.14 0.50 42.23 4.24
28 29 2.422165 TTGCGGGTGACGTAAGCA 59.578 55.556 4.14 1.74 42.23 3.91
46 47 5.977129 CACGTAAGCAGATGGTTTTCTTTTT 59.023 36.000 2.20 0.00 45.62 1.94
47 48 5.507315 CCACGTAAGCAGATGGTTTTCTTTT 60.507 40.000 2.20 0.00 45.62 2.27
48 49 4.023193 CCACGTAAGCAGATGGTTTTCTTT 60.023 41.667 2.20 0.00 45.62 2.52
49 50 3.502211 CCACGTAAGCAGATGGTTTTCTT 59.498 43.478 2.20 0.00 45.62 2.52
50 51 3.074412 CCACGTAAGCAGATGGTTTTCT 58.926 45.455 2.20 0.00 45.62 2.52
51 52 2.414161 GCCACGTAAGCAGATGGTTTTC 60.414 50.000 2.20 0.00 45.62 2.29
52 53 1.539827 GCCACGTAAGCAGATGGTTTT 59.460 47.619 2.20 0.00 45.62 2.43
53 54 1.165270 GCCACGTAAGCAGATGGTTT 58.835 50.000 2.20 0.00 45.62 3.27
84 85 1.667724 GAACAGCTGGATGGAACGATG 59.332 52.381 19.93 0.00 0.00 3.84
94 95 2.280797 GCCACGTGAACAGCTGGA 60.281 61.111 19.30 0.00 0.00 3.86
110 111 3.148279 AGGTCGACCTGGATCGGC 61.148 66.667 35.89 14.02 46.55 5.54
119 120 4.176851 GACTCGGCGAGGTCGACC 62.177 72.222 36.81 27.67 46.52 4.79
146 151 0.186873 GGATGGATGGGCATGGAAGT 59.813 55.000 0.00 0.00 0.00 3.01
148 153 1.151221 CGGATGGATGGGCATGGAA 59.849 57.895 0.00 0.00 0.00 3.53
149 154 2.838360 CGGATGGATGGGCATGGA 59.162 61.111 0.00 0.00 0.00 3.41
150 155 2.987547 GCGGATGGATGGGCATGG 60.988 66.667 0.00 0.00 0.00 3.66
151 156 2.203379 TGCGGATGGATGGGCATG 60.203 61.111 0.00 0.00 0.00 4.06
152 157 2.203394 GTGCGGATGGATGGGCAT 60.203 61.111 0.00 0.00 37.77 4.40
153 158 3.726144 TGTGCGGATGGATGGGCA 61.726 61.111 0.00 0.00 0.00 5.36
154 159 3.211963 GTGTGCGGATGGATGGGC 61.212 66.667 0.00 0.00 0.00 5.36
155 160 0.964860 TTTGTGTGCGGATGGATGGG 60.965 55.000 0.00 0.00 0.00 4.00
156 161 0.171007 GTTTGTGTGCGGATGGATGG 59.829 55.000 0.00 0.00 0.00 3.51
157 162 0.880441 TGTTTGTGTGCGGATGGATG 59.120 50.000 0.00 0.00 0.00 3.51
158 163 1.838112 ATGTTTGTGTGCGGATGGAT 58.162 45.000 0.00 0.00 0.00 3.41
159 164 2.080693 GTATGTTTGTGTGCGGATGGA 58.919 47.619 0.00 0.00 0.00 3.41
166 171 2.139917 TGGAGACGTATGTTTGTGTGC 58.860 47.619 0.00 0.00 0.00 4.57
168 173 2.413837 GCTGGAGACGTATGTTTGTGT 58.586 47.619 0.00 0.00 0.00 3.72
172 177 1.076533 CGCGCTGGAGACGTATGTTT 61.077 55.000 5.56 0.00 0.00 2.83
173 178 1.516386 CGCGCTGGAGACGTATGTT 60.516 57.895 5.56 0.00 0.00 2.71
414 446 0.871163 GATCTGCTCTGCTCTGCGAC 60.871 60.000 0.00 0.00 0.00 5.19
415 447 1.436748 GATCTGCTCTGCTCTGCGA 59.563 57.895 0.00 0.00 0.00 5.10
416 448 1.592131 GGATCTGCTCTGCTCTGCG 60.592 63.158 0.00 0.00 0.00 5.18
420 452 0.760189 AGGAGGGATCTGCTCTGCTC 60.760 60.000 0.00 0.00 43.01 4.26
421 453 1.314170 AGGAGGGATCTGCTCTGCT 59.686 57.895 0.00 0.00 41.55 4.24
422 454 3.968773 AGGAGGGATCTGCTCTGC 58.031 61.111 0.00 0.00 37.03 4.26
426 458 1.826054 CGACGAGGAGGGATCTGCT 60.826 63.158 0.00 0.00 44.63 4.24
427 459 2.065906 GACGACGAGGAGGGATCTGC 62.066 65.000 0.00 0.00 0.00 4.26
428 460 0.748367 TGACGACGAGGAGGGATCTG 60.748 60.000 0.00 0.00 0.00 2.90
429 461 0.748729 GTGACGACGAGGAGGGATCT 60.749 60.000 0.00 0.00 0.00 2.75
430 462 1.726533 GGTGACGACGAGGAGGGATC 61.727 65.000 0.00 0.00 0.00 3.36
431 463 1.753463 GGTGACGACGAGGAGGGAT 60.753 63.158 0.00 0.00 0.00 3.85
432 464 2.360852 GGTGACGACGAGGAGGGA 60.361 66.667 0.00 0.00 0.00 4.20
433 465 3.450115 GGGTGACGACGAGGAGGG 61.450 72.222 0.00 0.00 0.00 4.30
444 476 2.430921 CAGTGAGCGACGGGTGAC 60.431 66.667 0.00 0.00 0.00 3.67
445 477 4.357947 GCAGTGAGCGACGGGTGA 62.358 66.667 0.00 0.00 0.00 4.02
454 486 2.359230 AGCGGAAAGGCAGTGAGC 60.359 61.111 0.00 0.00 44.65 4.26
455 487 1.018226 CAGAGCGGAAAGGCAGTGAG 61.018 60.000 0.00 0.00 34.64 3.51
490 532 4.087892 CAGAGTGGTGGGGGAGCG 62.088 72.222 0.00 0.00 0.00 5.03
891 933 2.364970 GTGAGGTGGGAGATGAGATGAG 59.635 54.545 0.00 0.00 0.00 2.90
892 934 2.392662 GTGAGGTGGGAGATGAGATGA 58.607 52.381 0.00 0.00 0.00 2.92
893 935 1.415659 GGTGAGGTGGGAGATGAGATG 59.584 57.143 0.00 0.00 0.00 2.90
894 936 1.293458 AGGTGAGGTGGGAGATGAGAT 59.707 52.381 0.00 0.00 0.00 2.75
895 937 0.712979 AGGTGAGGTGGGAGATGAGA 59.287 55.000 0.00 0.00 0.00 3.27
937 981 3.465403 CGGGGGAGTGAGCTGAGG 61.465 72.222 0.00 0.00 0.00 3.86
1055 1104 1.976404 GGAGGAGGATGATGATGCTGA 59.024 52.381 0.00 0.00 28.67 4.26
1056 1105 1.979308 AGGAGGAGGATGATGATGCTG 59.021 52.381 0.00 0.00 28.67 4.41
1057 1106 2.259012 GAGGAGGAGGATGATGATGCT 58.741 52.381 0.00 0.00 31.83 3.79
1066 1115 1.826054 CGTCAGCGAGGAGGAGGAT 60.826 63.158 0.00 0.00 41.33 3.24
1069 1118 4.200283 GGCGTCAGCGAGGAGGAG 62.200 72.222 0.00 0.00 46.35 3.69
1143 1204 2.202946 TTGTTGAGGTGCGCGTCA 60.203 55.556 18.08 18.08 37.68 4.35
1242 1303 3.760035 GTGGAGAAGCCCGCGAGA 61.760 66.667 8.23 0.00 34.97 4.04
1815 1876 1.079127 CGGAGTGGATGGAAGCGTT 60.079 57.895 0.00 0.00 0.00 4.84
1824 1885 3.474570 GGGAGCTGCGGAGTGGAT 61.475 66.667 5.62 0.00 0.00 3.41
2796 2872 1.136252 CATTCGACGAGGTTGTTGCAG 60.136 52.381 0.00 0.00 0.00 4.41
2880 2956 1.797211 GCATCTCCCCCTCGTCGTAG 61.797 65.000 0.00 0.00 0.00 3.51
2970 3046 2.125229 CCGCTCAGCATCTGCACT 60.125 61.111 4.79 0.00 45.16 4.40
3018 3094 1.817099 GAAGCTCATGGACGGCCTG 60.817 63.158 9.82 4.34 34.31 4.85
3060 3136 3.699894 ACGCTGTCCTGGAGGCTG 61.700 66.667 16.19 12.71 34.44 4.85
3099 3175 1.213013 CTCGTCCGACAGGTTCAGG 59.787 63.158 0.00 0.00 39.05 3.86
3138 3214 2.872001 GTGAGCGACGACGAGCTG 60.872 66.667 22.49 2.37 44.69 4.24
3232 3308 0.391130 TCCGCATTTCAAGAGGACCG 60.391 55.000 0.00 0.00 29.61 4.79
3367 6388 8.417106 AGAAGAAAAGGAAAAGAAACTTGATCC 58.583 33.333 0.00 0.00 0.00 3.36
3374 6396 8.462811 ACAGAAGAGAAGAAAAGGAAAAGAAAC 58.537 33.333 0.00 0.00 0.00 2.78
3379 6401 7.119387 AGGAACAGAAGAGAAGAAAAGGAAAA 58.881 34.615 0.00 0.00 0.00 2.29
3383 6405 5.700373 CAGAGGAACAGAAGAGAAGAAAAGG 59.300 44.000 0.00 0.00 0.00 3.11
3385 6407 6.485830 TCAGAGGAACAGAAGAGAAGAAAA 57.514 37.500 0.00 0.00 0.00 2.29
3387 6409 6.485830 TTTCAGAGGAACAGAAGAGAAGAA 57.514 37.500 0.00 0.00 31.35 2.52
3388 6410 6.485830 TTTTCAGAGGAACAGAAGAGAAGA 57.514 37.500 0.00 0.00 31.35 2.87
3389 6411 6.765512 AGTTTTTCAGAGGAACAGAAGAGAAG 59.234 38.462 2.05 0.00 31.35 2.85
3390 6412 6.653989 AGTTTTTCAGAGGAACAGAAGAGAA 58.346 36.000 2.05 0.00 31.35 2.87
3391 6413 6.240549 AGTTTTTCAGAGGAACAGAAGAGA 57.759 37.500 2.05 0.00 31.35 3.10
3392 6414 8.614469 AATAGTTTTTCAGAGGAACAGAAGAG 57.386 34.615 2.05 0.00 31.35 2.85
3393 6415 8.980481 AAATAGTTTTTCAGAGGAACAGAAGA 57.020 30.769 2.05 0.00 31.35 2.87
3394 6416 9.670719 GAAAATAGTTTTTCAGAGGAACAGAAG 57.329 33.333 6.37 0.00 46.55 2.85
3409 6431 9.599866 CAGGAACAAAAGAAGGAAAATAGTTTT 57.400 29.630 0.00 0.00 35.12 2.43
3410 6432 7.710907 GCAGGAACAAAAGAAGGAAAATAGTTT 59.289 33.333 0.00 0.00 0.00 2.66
3411 6433 7.147742 TGCAGGAACAAAAGAAGGAAAATAGTT 60.148 33.333 0.00 0.00 0.00 2.24
3412 6434 6.323739 TGCAGGAACAAAAGAAGGAAAATAGT 59.676 34.615 0.00 0.00 0.00 2.12
3413 6435 6.748132 TGCAGGAACAAAAGAAGGAAAATAG 58.252 36.000 0.00 0.00 0.00 1.73
3414 6436 6.723298 TGCAGGAACAAAAGAAGGAAAATA 57.277 33.333 0.00 0.00 0.00 1.40
3415 6437 5.612725 TGCAGGAACAAAAGAAGGAAAAT 57.387 34.783 0.00 0.00 0.00 1.82
3416 6438 5.413309 TTGCAGGAACAAAAGAAGGAAAA 57.587 34.783 0.00 0.00 0.00 2.29
3417 6439 5.413309 TTTGCAGGAACAAAAGAAGGAAA 57.587 34.783 0.00 0.00 36.62 3.13
3418 6440 5.413309 TTTTGCAGGAACAAAAGAAGGAA 57.587 34.783 0.00 0.00 42.88 3.36
3419 6441 5.413309 TTTTTGCAGGAACAAAAGAAGGA 57.587 34.783 3.06 0.00 46.84 3.36
3456 6485 4.082125 AGATCCGAACAAAAGGAGCAAAT 58.918 39.130 2.57 0.00 44.72 2.32
3458 6487 3.140325 AGATCCGAACAAAAGGAGCAA 57.860 42.857 2.57 0.00 44.72 3.91
3464 6493 1.804151 TCGCCAAGATCCGAACAAAAG 59.196 47.619 0.00 0.00 0.00 2.27
3546 6585 0.826062 GTGCCAAAAGGGGATGGATG 59.174 55.000 0.00 0.00 40.18 3.51
3547 6586 0.413037 TGTGCCAAAAGGGGATGGAT 59.587 50.000 0.00 0.00 40.18 3.41
3548 6587 0.541764 GTGTGCCAAAAGGGGATGGA 60.542 55.000 0.00 0.00 40.18 3.41
3549 6588 0.831288 TGTGTGCCAAAAGGGGATGG 60.831 55.000 0.00 0.00 40.18 3.51
3562 6601 1.191096 CTTTTGCTTGTCGTGTGTGC 58.809 50.000 0.00 0.00 0.00 4.57
3608 6752 2.238395 ACAAGCCATCCCTCTTCTTCTC 59.762 50.000 0.00 0.00 0.00 2.87
3633 6777 0.669318 CCAAGCTTGGCATTGCACAG 60.669 55.000 31.70 5.10 42.21 3.66
3958 8919 4.322101 CACTTTGTGTGGTACGATTAGC 57.678 45.455 0.00 0.00 42.68 3.09
3999 8963 0.464036 TGACTGACGTTGGCACTTCT 59.536 50.000 0.00 0.00 0.00 2.85
4000 8964 0.861837 CTGACTGACGTTGGCACTTC 59.138 55.000 0.00 0.00 0.00 3.01
4054 9107 2.125178 GTGGGACCCACGAGATAGG 58.875 63.158 27.79 0.00 44.95 2.57


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

AutoCloner maintained by Alex Coulton.