Multiple sequence alignment - TraesCS5D01G055400

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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 TraesCS5D01G055400 chr5D 100.000 6376 0 0 1 6376 52053582 52059957 0.000000e+00 11775.0
1 TraesCS5D01G055400 chr5D 92.941 170 11 1 4541 4710 6162092 6162260 4.940000e-61 246.0
2 TraesCS5D01G055400 chr5D 92.262 168 12 1 4541 4708 6260085 6260251 2.970000e-58 237.0
3 TraesCS5D01G055400 chr5D 91.765 170 13 1 4541 4710 503306690 503306522 1.070000e-57 235.0
4 TraesCS5D01G055400 chr5D 91.765 170 13 1 4541 4710 512405731 512405563 1.070000e-57 235.0
5 TraesCS5D01G055400 chr5A 94.567 4804 146 42 57 4793 41301858 41306613 0.000000e+00 7319.0
6 TraesCS5D01G055400 chr5A 93.485 1581 56 19 4824 6376 41306614 41308175 0.000000e+00 2305.0
7 TraesCS5D01G055400 chr5B 93.931 2768 109 22 525 3255 55179032 55181777 0.000000e+00 4126.0
8 TraesCS5D01G055400 chr5B 94.415 2650 99 22 3745 6373 55182994 55185615 0.000000e+00 4028.0
9 TraesCS5D01G055400 chr5B 96.620 503 17 0 3241 3743 55182330 55182832 0.000000e+00 835.0
10 TraesCS5D01G055400 chr5B 91.133 406 11 9 114 508 55178242 55178633 1.570000e-145 527.0
11 TraesCS5D01G055400 chr7D 92.353 170 12 1 4541 4710 231596079 231596247 2.300000e-59 241.0
12 TraesCS5D01G055400 chr1D 92.727 165 11 1 4546 4710 254449830 254449667 2.970000e-58 237.0
13 TraesCS5D01G055400 chr7B 91.176 170 14 1 4541 4710 137679680 137679512 4.970000e-56 230.0
14 TraesCS5D01G055400 chr7B 89.130 46 4 1 18 63 272121575 272121619 8.930000e-04 56.5
15 TraesCS5D01G055400 chr6B 92.308 65 5 0 963 1027 145900601 145900665 6.810000e-15 93.5
16 TraesCS5D01G055400 chr4B 91.111 45 4 0 18 62 128034497 128034541 1.920000e-05 62.1
17 TraesCS5D01G055400 chr6D 96.774 31 1 0 20 50 471908909 471908939 1.200000e-02 52.8


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 TraesCS5D01G055400 chr5D 52053582 52059957 6375 False 11775 11775 100.00000 1 6376 1 chr5D.!!$F3 6375
1 TraesCS5D01G055400 chr5A 41301858 41308175 6317 False 4812 7319 94.02600 57 6376 2 chr5A.!!$F1 6319
2 TraesCS5D01G055400 chr5B 55178242 55185615 7373 False 2379 4126 94.02475 114 6373 4 chr5B.!!$F1 6259

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
526 559 0.033208 AGTGGAGCCAGAGAGAGAGG 60.033 60.0 0.00 0.0 0.00 3.69 F
532 941 0.550914 GCCAGAGAGAGAGGGAGAGA 59.449 60.0 0.00 0.0 0.00 3.10 F
1900 2385 0.037326 CGCACTGTTTCAGGGAGCTA 60.037 55.0 3.02 0.0 36.97 3.32 F
2032 2517 0.307760 CGTTGCTGGAGGTTGTTCAC 59.692 55.0 0.00 0.0 0.00 3.18 F
3553 4605 1.133809 TGGTGCCAGGTTAGAAGCCT 61.134 55.0 0.00 0.0 36.66 4.58 F
4397 5609 0.178950 TGCCAGGTGAGTCTGTCTCT 60.179 55.0 3.71 0.0 43.13 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 2080 0.267960 AAGGTCAGATATCCCCCGGT 59.732 55.000 0.00 0.00 0.00 5.28 R
2013 2498 0.307760 GTGAACAACCTCCAGCAACG 59.692 55.000 0.00 0.00 0.00 4.10 R
3423 4475 1.270907 AACTCTACCCCACTCTGCAG 58.729 55.000 7.63 7.63 0.00 4.41 R
3579 4631 1.676529 GCTGGAGCGATACACTCACTA 59.323 52.381 0.00 0.00 35.79 2.74 R
4806 6018 1.649664 CCATGAGCAAAGGAGTCGAG 58.350 55.000 0.00 0.00 0.00 4.04 R
6327 7579 0.036732 TGACACATCCTTCCACTGGC 59.963 55.000 0.00 0.00 0.00 4.85 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
21 22 3.958704 CATGCTCTCTCACCGTACTAAG 58.041 50.000 0.00 0.00 0.00 2.18
22 23 1.743958 TGCTCTCTCACCGTACTAAGC 59.256 52.381 0.00 0.00 0.00 3.09
23 24 2.018515 GCTCTCTCACCGTACTAAGCT 58.981 52.381 0.00 0.00 0.00 3.74
24 25 2.424246 GCTCTCTCACCGTACTAAGCTT 59.576 50.000 3.48 3.48 0.00 3.74
25 26 3.732471 GCTCTCTCACCGTACTAAGCTTG 60.732 52.174 9.86 1.57 0.00 4.01
26 27 3.418995 TCTCTCACCGTACTAAGCTTGT 58.581 45.455 9.86 7.95 0.00 3.16
27 28 4.582869 TCTCTCACCGTACTAAGCTTGTA 58.417 43.478 9.86 6.92 0.00 2.41
28 29 4.394300 TCTCTCACCGTACTAAGCTTGTAC 59.606 45.833 20.29 20.29 37.50 2.90
29 30 4.330250 TCTCACCGTACTAAGCTTGTACT 58.670 43.478 24.11 12.56 38.39 2.73
30 31 4.394300 TCTCACCGTACTAAGCTTGTACTC 59.606 45.833 24.11 10.00 38.39 2.59
31 32 3.441572 TCACCGTACTAAGCTTGTACTCC 59.558 47.826 24.11 9.53 38.39 3.85
32 33 2.757314 ACCGTACTAAGCTTGTACTCCC 59.243 50.000 24.11 9.29 38.39 4.30
33 34 3.022406 CCGTACTAAGCTTGTACTCCCT 58.978 50.000 24.11 0.00 38.39 4.20
34 35 3.066481 CCGTACTAAGCTTGTACTCCCTC 59.934 52.174 24.11 8.58 38.39 4.30
35 36 3.946558 CGTACTAAGCTTGTACTCCCTCT 59.053 47.826 24.11 0.00 38.39 3.69
36 37 5.121811 CGTACTAAGCTTGTACTCCCTCTA 58.878 45.833 24.11 0.00 38.39 2.43
37 38 5.764192 CGTACTAAGCTTGTACTCCCTCTAT 59.236 44.000 24.11 0.00 38.39 1.98
38 39 6.933521 CGTACTAAGCTTGTACTCCCTCTATA 59.066 42.308 24.11 0.00 38.39 1.31
39 40 7.443575 CGTACTAAGCTTGTACTCCCTCTATAA 59.556 40.741 24.11 0.00 38.39 0.98
40 41 9.129532 GTACTAAGCTTGTACTCCCTCTATAAA 57.870 37.037 21.76 0.00 37.76 1.40
41 42 8.009622 ACTAAGCTTGTACTCCCTCTATAAAC 57.990 38.462 9.86 0.00 0.00 2.01
42 43 7.840210 ACTAAGCTTGTACTCCCTCTATAAACT 59.160 37.037 9.86 0.00 0.00 2.66
43 44 9.352191 CTAAGCTTGTACTCCCTCTATAAACTA 57.648 37.037 9.86 0.00 0.00 2.24
44 45 8.605325 AAGCTTGTACTCCCTCTATAAACTAA 57.395 34.615 0.00 0.00 0.00 2.24
45 46 8.785184 AGCTTGTACTCCCTCTATAAACTAAT 57.215 34.615 0.00 0.00 0.00 1.73
46 47 9.878737 AGCTTGTACTCCCTCTATAAACTAATA 57.121 33.333 0.00 0.00 0.00 0.98
265 285 3.020984 CTCTCTCTAACCACCCACTCTC 58.979 54.545 0.00 0.00 0.00 3.20
332 359 3.060736 TCGACAGTTACTGCTCTCTCT 57.939 47.619 12.80 0.00 34.37 3.10
333 360 3.004171 TCGACAGTTACTGCTCTCTCTC 58.996 50.000 12.80 0.00 34.37 3.20
334 361 3.006940 CGACAGTTACTGCTCTCTCTCT 58.993 50.000 12.80 0.00 34.37 3.10
335 362 3.063452 CGACAGTTACTGCTCTCTCTCTC 59.937 52.174 12.80 0.00 34.37 3.20
336 363 4.261801 GACAGTTACTGCTCTCTCTCTCT 58.738 47.826 12.80 0.00 34.37 3.10
337 364 4.662278 ACAGTTACTGCTCTCTCTCTCTT 58.338 43.478 12.80 0.00 34.37 2.85
338 365 4.700213 ACAGTTACTGCTCTCTCTCTCTTC 59.300 45.833 12.80 0.00 34.37 2.87
339 366 4.096382 CAGTTACTGCTCTCTCTCTCTTCC 59.904 50.000 0.00 0.00 0.00 3.46
340 367 4.018415 AGTTACTGCTCTCTCTCTCTTCCT 60.018 45.833 0.00 0.00 0.00 3.36
341 368 3.004752 ACTGCTCTCTCTCTCTTCCTC 57.995 52.381 0.00 0.00 0.00 3.71
342 369 2.578021 ACTGCTCTCTCTCTCTTCCTCT 59.422 50.000 0.00 0.00 0.00 3.69
343 370 3.209410 CTGCTCTCTCTCTCTTCCTCTC 58.791 54.545 0.00 0.00 0.00 3.20
344 371 2.846206 TGCTCTCTCTCTCTTCCTCTCT 59.154 50.000 0.00 0.00 0.00 3.10
345 372 3.118261 TGCTCTCTCTCTCTTCCTCTCTC 60.118 52.174 0.00 0.00 0.00 3.20
467 494 3.067106 TCCTTCTTTTGTCACGAGATGC 58.933 45.455 0.00 0.00 0.00 3.91
508 535 2.203337 CACCACCACCACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
526 559 0.033208 AGTGGAGCCAGAGAGAGAGG 60.033 60.000 0.00 0.00 0.00 3.69
532 941 0.550914 GCCAGAGAGAGAGGGAGAGA 59.449 60.000 0.00 0.00 0.00 3.10
774 1198 0.977395 GTCATATAGCTCCGGGGCTT 59.023 55.000 38.12 23.99 42.97 4.35
857 1281 2.125512 CGTCCGCCCCTCTTCTTG 60.126 66.667 0.00 0.00 0.00 3.02
863 1287 1.223211 GCCCCTCTTCTTGGAGCTC 59.777 63.158 4.71 4.71 32.43 4.09
868 1292 1.273606 CCTCTTCTTGGAGCTCGTTCA 59.726 52.381 7.83 0.00 32.43 3.18
882 1306 1.133450 TCGTTCAATTGGTTTGGGGGA 60.133 47.619 5.42 0.00 35.92 4.81
1041 1472 4.329545 CAGGGGTGGACGTGGGTG 62.330 72.222 0.00 0.00 0.00 4.61
1370 1805 3.946907 CTTTGGCAAAGCAGCAGC 58.053 55.556 25.46 0.00 42.56 5.25
1431 1867 4.406648 TCGCTATCTGATTGTGGATTGT 57.593 40.909 11.63 0.00 0.00 2.71
1602 2058 7.540474 TTCTATCTGTCCACTGTTAAAGACT 57.460 36.000 0.00 0.00 0.00 3.24
1646 2103 2.174854 CCGGGGGATATCTGACCTTTTT 59.825 50.000 2.05 0.00 0.00 1.94
1647 2104 3.477530 CGGGGGATATCTGACCTTTTTC 58.522 50.000 2.05 0.00 0.00 2.29
1648 2105 3.118038 CGGGGGATATCTGACCTTTTTCA 60.118 47.826 2.05 0.00 0.00 2.69
1649 2106 4.464947 GGGGGATATCTGACCTTTTTCAG 58.535 47.826 2.05 0.00 43.93 3.02
1650 2107 3.885901 GGGGATATCTGACCTTTTTCAGC 59.114 47.826 2.05 0.00 42.52 4.26
1651 2108 4.385754 GGGGATATCTGACCTTTTTCAGCT 60.386 45.833 2.05 0.00 42.52 4.24
1652 2109 5.163195 GGGGATATCTGACCTTTTTCAGCTA 60.163 44.000 2.05 0.00 42.52 3.32
1653 2110 5.994668 GGGATATCTGACCTTTTTCAGCTAG 59.005 44.000 2.05 0.00 42.52 3.42
1655 2112 6.928492 GGATATCTGACCTTTTTCAGCTAGAG 59.072 42.308 2.05 0.00 42.52 2.43
1656 2113 5.753721 ATCTGACCTTTTTCAGCTAGAGT 57.246 39.130 0.00 0.00 42.52 3.24
1657 2114 6.859112 ATCTGACCTTTTTCAGCTAGAGTA 57.141 37.500 0.00 0.00 42.52 2.59
1729 2186 4.347876 TCATCTCTCCTGTTGTTTTCTCCA 59.652 41.667 0.00 0.00 0.00 3.86
1758 2215 6.089016 CACTTTTCTTATTGCAATGCAGACAG 59.911 38.462 22.27 19.20 40.61 3.51
1760 2217 6.816134 TTTCTTATTGCAATGCAGACAGTA 57.184 33.333 22.27 5.52 40.61 2.74
1778 2235 6.610830 AGACAGTATCTCTTGTTCCATCATCT 59.389 38.462 0.00 0.00 28.16 2.90
1779 2236 7.782168 AGACAGTATCTCTTGTTCCATCATCTA 59.218 37.037 0.00 0.00 28.16 1.98
1780 2237 8.311395 ACAGTATCTCTTGTTCCATCATCTAA 57.689 34.615 0.00 0.00 0.00 2.10
1782 2239 9.205719 CAGTATCTCTTGTTCCATCATCTAATG 57.794 37.037 0.00 0.00 0.00 1.90
1784 2241 9.770097 GTATCTCTTGTTCCATCATCTAATGAA 57.230 33.333 0.00 0.00 43.50 2.57
1787 2244 8.324306 TCTCTTGTTCCATCATCTAATGAACTT 58.676 33.333 0.00 0.00 43.50 2.66
1788 2245 8.272545 TCTTGTTCCATCATCTAATGAACTTG 57.727 34.615 0.00 0.00 43.50 3.16
1822 2305 7.819900 AGTAACTTCTGCTTACAAGTAAGGATG 59.180 37.037 18.60 13.04 41.52 3.51
1900 2385 0.037326 CGCACTGTTTCAGGGAGCTA 60.037 55.000 3.02 0.00 36.97 3.32
1913 2398 1.432270 GGAGCTATTGCGGCAGTCAC 61.432 60.000 0.00 0.00 45.42 3.67
2013 2498 1.230324 GGATTACCGGCATGCTTCTC 58.770 55.000 18.92 6.21 0.00 2.87
2032 2517 0.307760 CGTTGCTGGAGGTTGTTCAC 59.692 55.000 0.00 0.00 0.00 3.18
2048 2533 4.206375 TGTTCACCTGAATTGCTTCTGAA 58.794 39.130 0.00 0.00 36.33 3.02
2049 2534 4.644234 TGTTCACCTGAATTGCTTCTGAAA 59.356 37.500 0.00 0.00 36.33 2.69
2054 2539 6.716628 TCACCTGAATTGCTTCTGAAATTACT 59.283 34.615 0.00 0.00 31.82 2.24
2061 2546 9.630098 GAATTGCTTCTGAAATTACTTCATTCA 57.370 29.630 0.00 0.00 43.20 2.57
2254 2739 8.545229 TCTCTTTTCTGACAAATGATCTTCTC 57.455 34.615 0.00 0.00 0.00 2.87
2389 2874 3.309296 TCCTGAAAGTGAACCAGAGACT 58.691 45.455 0.00 0.00 0.00 3.24
2571 3056 2.421073 CTCGGAGCAAAAGCATCAATCA 59.579 45.455 0.00 0.00 0.00 2.57
2642 3127 6.479990 CACTTTAAGCTGAACGATCATCCATA 59.520 38.462 0.00 0.00 34.37 2.74
2651 3136 7.482654 TGAACGATCATCCATATTTCTGTTC 57.517 36.000 0.00 0.00 34.23 3.18
2786 3271 3.741344 GCAAGTACTTGGGAGTATATGCG 59.259 47.826 31.42 7.00 40.12 4.73
2835 3320 6.951256 TTTCTCAAATCTGACAGTGTATCG 57.049 37.500 1.59 0.00 0.00 2.92
2850 3335 6.481976 ACAGTGTATCGTTTCTTGATCACAAA 59.518 34.615 0.00 0.00 35.49 2.83
2868 3353 9.334693 GATCACAAATGTGTTATTTGACTCTTC 57.665 33.333 16.60 5.25 45.76 2.87
2963 3448 3.594134 ACAGCTGAGGAAAGAAGAATCG 58.406 45.455 23.35 0.00 0.00 3.34
3085 3570 6.317789 TGATCTTGTTAAGTTTTGGAGCAG 57.682 37.500 0.00 0.00 0.00 4.24
3092 3577 5.359576 TGTTAAGTTTTGGAGCAGACAATGT 59.640 36.000 0.00 0.00 0.00 2.71
3127 3612 4.415596 TCTGCACATTCCCCTTTGTAATT 58.584 39.130 0.00 0.00 0.00 1.40
3131 3616 5.777732 TGCACATTCCCCTTTGTAATTTACT 59.222 36.000 7.99 0.00 0.00 2.24
3134 3619 8.308207 GCACATTCCCCTTTGTAATTTACTTTA 58.692 33.333 7.99 0.00 0.00 1.85
3161 3646 9.896645 TGATATTATTATCCTTTGGAGCTCATC 57.103 33.333 17.19 4.45 34.05 2.92
3548 4600 1.340017 GCAAGATGGTGCCAGGTTAGA 60.340 52.381 0.00 0.00 38.66 2.10
3553 4605 1.133809 TGGTGCCAGGTTAGAAGCCT 61.134 55.000 0.00 0.00 36.66 4.58
3579 4631 5.931724 GCATGTACTTTTAGGGCATTTGTTT 59.068 36.000 0.00 0.00 0.00 2.83
3581 4633 7.275560 GCATGTACTTTTAGGGCATTTGTTTAG 59.724 37.037 0.00 0.00 0.00 1.85
3586 4638 6.549736 ACTTTTAGGGCATTTGTTTAGTGAGT 59.450 34.615 0.00 0.00 0.00 3.41
3692 4744 6.128172 GGGTGGAAAATAGATATTCTGCATCG 60.128 42.308 0.00 0.00 0.00 3.84
4206 5418 5.737860 TGCTGAATACAAGACATCACTGAT 58.262 37.500 0.00 0.00 0.00 2.90
4214 5426 5.802465 ACAAGACATCACTGATGAATCACT 58.198 37.500 23.30 11.74 42.09 3.41
4299 5511 8.862550 AATTCTGTTCTTTCTTGATTGTTCAC 57.137 30.769 0.00 0.00 0.00 3.18
4300 5512 7.630242 TTCTGTTCTTTCTTGATTGTTCACT 57.370 32.000 0.00 0.00 0.00 3.41
4301 5513 7.251704 TCTGTTCTTTCTTGATTGTTCACTC 57.748 36.000 0.00 0.00 0.00 3.51
4397 5609 0.178950 TGCCAGGTGAGTCTGTCTCT 60.179 55.000 3.71 0.00 43.13 3.10
4544 5756 5.885230 TGATCCATGTTTGATTCACTGAC 57.115 39.130 0.00 0.00 0.00 3.51
4551 5763 6.238842 CCATGTTTGATTCACTGACAAAGACT 60.239 38.462 0.00 0.00 34.86 3.24
4580 5792 8.674173 AGATAGACTGGATTAGAAGGATCTGTA 58.326 37.037 0.00 0.00 37.10 2.74
4693 5905 6.426937 GTGTACAGCCCCATAATAATAGTGTG 59.573 42.308 0.00 0.00 0.00 3.82
4849 6069 9.344772 TGGCTGAATTTAGTCTTTGTAGTTTAA 57.655 29.630 3.31 0.00 0.00 1.52
4896 6116 7.648039 TGTAAATAGGTTCAGTTGGTTGTTT 57.352 32.000 0.00 0.00 0.00 2.83
4908 6128 6.601613 TCAGTTGGTTGTTTGATCTTGTAAGT 59.398 34.615 0.00 0.00 0.00 2.24
4970 6190 8.637986 CATGTTAAGCTCTCTAGAAAGTAGGAT 58.362 37.037 0.00 0.00 0.00 3.24
5053 6277 6.353323 TGATAATAAGGAAAGGATGTTGCGA 58.647 36.000 0.00 0.00 0.00 5.10
5058 6283 2.489329 AGGAAAGGATGTTGCGATGTTG 59.511 45.455 0.00 0.00 0.00 3.33
5091 6316 1.268625 GGGCAACACTTCTTTAACCCG 59.731 52.381 0.00 0.00 39.74 5.28
5096 6321 4.201980 GCAACACTTCTTTAACCCGTTCTT 60.202 41.667 0.00 0.00 0.00 2.52
5195 6420 0.901124 ATAGGATGCCGCAGAGATCC 59.099 55.000 0.00 0.46 35.96 3.36
5198 6423 1.146930 GATGCCGCAGAGATCCCAA 59.853 57.895 0.00 0.00 0.00 4.12
5523 6750 7.562454 ACTAATTTTGTCCGAAAGAGAAACA 57.438 32.000 0.00 0.00 37.46 2.83
5654 6889 3.088194 TCGAAACACGAGTAGCTGTTT 57.912 42.857 0.00 0.00 46.45 2.83
5687 6922 0.176449 CATCAGTGCAGGGATCGACA 59.824 55.000 0.00 0.00 0.00 4.35
5709 6944 1.812571 CGAAAAGAATGGTGACCTGGG 59.187 52.381 2.11 0.00 0.00 4.45
5749 6984 1.081840 GTGTTGCGCTGCTCTTTCC 60.082 57.895 9.73 0.00 0.00 3.13
5839 7076 6.857848 AGAAGAGAAGGGAAAAGGAAGAAAT 58.142 36.000 0.00 0.00 0.00 2.17
5861 7098 7.929941 AATCTGAAAAGAGATGGTAGAAACC 57.070 36.000 0.00 0.00 46.98 3.27
5930 7168 6.042777 GCTCACTGCTCTGTAACATTATACA 58.957 40.000 0.00 0.00 38.95 2.29
5994 7232 1.003223 GTTTGTCCTGTAACACGCCAC 60.003 52.381 0.00 0.00 0.00 5.01
6069 7310 9.396022 GATTGTCTCCTATTTACCATTTCTTGA 57.604 33.333 0.00 0.00 0.00 3.02
6081 7322 6.610075 ACCATTTCTTGATGCTGGTTAATT 57.390 33.333 0.00 0.00 36.86 1.40
6097 7338 5.189934 TGGTTAATTTGTTTTCCTGGGTGTT 59.810 36.000 0.00 0.00 0.00 3.32
6120 7361 1.610522 GATTTGCTGCAAGTGAGTGGT 59.389 47.619 15.36 0.00 35.30 4.16
6195 7436 1.248486 TGTCTGTCTGAGAGGAACCG 58.752 55.000 1.65 0.00 0.00 4.44
6296 7546 1.219213 GGATCCTCCCTCCTCTTCTGA 59.781 57.143 3.84 0.00 0.00 3.27
6327 7579 0.824109 TACCATCTTGAGCCCAGACG 59.176 55.000 0.00 0.00 0.00 4.18
6331 7583 2.249413 ATCTTGAGCCCAGACGCCAG 62.249 60.000 0.00 0.00 0.00 4.85
6338 7590 2.046892 CCAGACGCCAGTGGAAGG 60.047 66.667 15.20 3.32 35.67 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.793801 GCTTAGTACGGTGAGAGAGCATG 60.794 52.174 0.00 0.00 0.00 4.06
1 2 2.359531 GCTTAGTACGGTGAGAGAGCAT 59.640 50.000 0.00 0.00 0.00 3.79
2 3 1.743958 GCTTAGTACGGTGAGAGAGCA 59.256 52.381 0.00 0.00 0.00 4.26
4 5 3.440872 ACAAGCTTAGTACGGTGAGAGAG 59.559 47.826 0.00 0.00 0.00 3.20
8 9 4.438472 GGAGTACAAGCTTAGTACGGTGAG 60.438 50.000 22.29 3.47 44.92 3.51
9 10 3.441572 GGAGTACAAGCTTAGTACGGTGA 59.558 47.826 22.29 0.61 44.92 4.02
10 11 3.428589 GGGAGTACAAGCTTAGTACGGTG 60.429 52.174 22.29 5.24 44.92 4.94
12 13 3.022406 AGGGAGTACAAGCTTAGTACGG 58.978 50.000 22.29 5.83 44.92 4.02
13 14 3.946558 AGAGGGAGTACAAGCTTAGTACG 59.053 47.826 22.29 6.42 44.92 3.67
14 15 8.688747 TTATAGAGGGAGTACAAGCTTAGTAC 57.311 38.462 21.63 21.63 41.59 2.73
15 16 9.129532 GTTTATAGAGGGAGTACAAGCTTAGTA 57.870 37.037 0.00 1.51 0.00 1.82
16 17 7.840210 AGTTTATAGAGGGAGTACAAGCTTAGT 59.160 37.037 0.00 2.56 0.00 2.24
17 18 8.240267 AGTTTATAGAGGGAGTACAAGCTTAG 57.760 38.462 0.00 0.00 0.00 2.18
18 19 9.705103 TTAGTTTATAGAGGGAGTACAAGCTTA 57.295 33.333 0.00 0.00 0.00 3.09
19 20 8.605325 TTAGTTTATAGAGGGAGTACAAGCTT 57.395 34.615 0.00 0.00 0.00 3.74
20 21 8.785184 ATTAGTTTATAGAGGGAGTACAAGCT 57.215 34.615 0.00 0.00 0.00 3.74
142 144 9.498176 GTGGGTGTAGTACTAATTATTAATGGG 57.502 37.037 3.61 0.00 0.00 4.00
164 169 3.450096 TCTGAGAAGATGATGACTGTGGG 59.550 47.826 0.00 0.00 0.00 4.61
239 253 2.024846 TGGGTGGTTAGAGAGAGAGAGG 60.025 54.545 0.00 0.00 0.00 3.69
248 268 1.546961 ACGAGAGTGGGTGGTTAGAG 58.453 55.000 0.00 0.00 46.97 2.43
249 269 3.759865 ACGAGAGTGGGTGGTTAGA 57.240 52.632 0.00 0.00 46.97 2.10
265 285 1.079127 GTGGGGGTGATGACTGACG 60.079 63.158 0.00 0.00 0.00 4.35
332 359 1.850345 GGGAGGAGAGAGAGGAAGAGA 59.150 57.143 0.00 0.00 0.00 3.10
333 360 1.568597 TGGGAGGAGAGAGAGGAAGAG 59.431 57.143 0.00 0.00 0.00 2.85
334 361 1.687492 TGGGAGGAGAGAGAGGAAGA 58.313 55.000 0.00 0.00 0.00 2.87
335 362 2.107366 GTTGGGAGGAGAGAGAGGAAG 58.893 57.143 0.00 0.00 0.00 3.46
336 363 1.273324 GGTTGGGAGGAGAGAGAGGAA 60.273 57.143 0.00 0.00 0.00 3.36
337 364 0.336737 GGTTGGGAGGAGAGAGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
338 365 0.689412 GGGTTGGGAGGAGAGAGAGG 60.689 65.000 0.00 0.00 0.00 3.69
339 366 0.338120 AGGGTTGGGAGGAGAGAGAG 59.662 60.000 0.00 0.00 0.00 3.20
340 367 1.695065 TAGGGTTGGGAGGAGAGAGA 58.305 55.000 0.00 0.00 0.00 3.10
341 368 2.552093 TTAGGGTTGGGAGGAGAGAG 57.448 55.000 0.00 0.00 0.00 3.20
342 369 2.592512 AGATTAGGGTTGGGAGGAGAGA 59.407 50.000 0.00 0.00 0.00 3.10
343 370 2.969262 GAGATTAGGGTTGGGAGGAGAG 59.031 54.545 0.00 0.00 0.00 3.20
344 371 2.592512 AGAGATTAGGGTTGGGAGGAGA 59.407 50.000 0.00 0.00 0.00 3.71
345 372 2.969262 GAGAGATTAGGGTTGGGAGGAG 59.031 54.545 0.00 0.00 0.00 3.69
467 494 2.511600 CTAGTTTGGGGCGAGCCG 60.512 66.667 8.14 0.00 36.85 5.52
508 535 1.042559 CCCTCTCTCTCTGGCTCCAC 61.043 65.000 0.00 0.00 0.00 4.02
511 544 0.550914 TCTCCCTCTCTCTCTGGCTC 59.449 60.000 0.00 0.00 0.00 4.70
515 548 1.811558 CGCTCTCTCCCTCTCTCTCTG 60.812 61.905 0.00 0.00 0.00 3.35
526 559 2.888051 GCTTTCGCCGCTCTCTCC 60.888 66.667 0.00 0.00 0.00 3.71
582 1000 0.941542 TGGTAAAATAGCGGCGATGC 59.058 50.000 12.98 0.00 0.00 3.91
583 1001 1.263217 GGTGGTAAAATAGCGGCGATG 59.737 52.381 12.98 0.00 0.00 3.84
584 1002 1.589803 GGTGGTAAAATAGCGGCGAT 58.410 50.000 12.98 7.15 0.00 4.58
774 1198 2.038269 GCGGAAAACCAGCGGATCA 61.038 57.895 0.00 0.00 0.00 2.92
855 1279 2.270352 ACCAATTGAACGAGCTCCAA 57.730 45.000 8.47 7.26 0.00 3.53
857 1281 2.351738 CCAAACCAATTGAACGAGCTCC 60.352 50.000 8.47 0.00 41.85 4.70
863 1287 1.333177 TCCCCCAAACCAATTGAACG 58.667 50.000 7.12 0.00 41.85 3.95
868 1292 3.117701 CCAACTTTTCCCCCAAACCAATT 60.118 43.478 0.00 0.00 0.00 2.32
882 1306 1.470805 GCACCGCAAGAACCAACTTTT 60.471 47.619 0.00 0.00 43.02 2.27
1041 1472 1.446966 GACGTGCTTCTGGGAGAGC 60.447 63.158 0.00 0.00 0.00 4.09
1372 1807 8.511604 ACAAATCCTTATCCAGTAAACATCTG 57.488 34.615 0.00 0.00 0.00 2.90
1373 1808 8.328758 TGACAAATCCTTATCCAGTAAACATCT 58.671 33.333 0.00 0.00 0.00 2.90
1431 1867 9.953565 ACTTTAGTAAAGATGCAACCTAACATA 57.046 29.630 25.87 0.00 41.02 2.29
1525 1981 7.656412 AGCATGACATCAGATTACACTAGTAG 58.344 38.462 0.00 0.00 0.00 2.57
1526 1982 7.588497 AGCATGACATCAGATTACACTAGTA 57.412 36.000 0.00 0.00 0.00 1.82
1527 1983 6.477053 AGCATGACATCAGATTACACTAGT 57.523 37.500 0.00 0.00 0.00 2.57
1624 2080 0.267960 AAGGTCAGATATCCCCCGGT 59.732 55.000 0.00 0.00 0.00 5.28
1646 2103 3.434940 TCAGTGGTGTACTCTAGCTGA 57.565 47.619 0.00 3.91 37.60 4.26
1647 2104 4.158579 TGATTCAGTGGTGTACTCTAGCTG 59.841 45.833 0.00 1.69 37.60 4.24
1648 2105 4.344978 TGATTCAGTGGTGTACTCTAGCT 58.655 43.478 0.00 0.00 37.60 3.32
1649 2106 4.158764 ACTGATTCAGTGGTGTACTCTAGC 59.841 45.833 18.35 0.00 43.63 3.42
1650 2107 5.906113 ACTGATTCAGTGGTGTACTCTAG 57.094 43.478 18.35 0.00 43.63 2.43
1651 2108 7.614192 TGATTACTGATTCAGTGGTGTACTCTA 59.386 37.037 26.01 2.40 45.01 2.43
1652 2109 6.437477 TGATTACTGATTCAGTGGTGTACTCT 59.563 38.462 26.01 1.03 45.01 3.24
1653 2110 6.631016 TGATTACTGATTCAGTGGTGTACTC 58.369 40.000 26.01 11.77 45.01 2.59
1655 2112 5.292101 GCTGATTACTGATTCAGTGGTGTAC 59.708 44.000 26.01 12.95 45.01 2.90
1656 2113 5.046663 TGCTGATTACTGATTCAGTGGTGTA 60.047 40.000 26.01 5.90 45.01 2.90
1657 2114 4.256920 GCTGATTACTGATTCAGTGGTGT 58.743 43.478 26.01 11.07 45.01 4.16
1729 2186 4.632688 GCATTGCAATAAGAAAAGTGGCAT 59.367 37.500 12.53 0.00 0.00 4.40
1822 2305 4.079253 TCCTTCTTACATGGGAAACTTGC 58.921 43.478 0.00 0.00 0.00 4.01
1900 2385 0.608130 TAGTGAGTGACTGCCGCAAT 59.392 50.000 0.00 0.00 35.96 3.56
1913 2398 2.947852 GCGTATAGCCCATGTAGTGAG 58.052 52.381 0.00 0.00 40.81 3.51
1941 2426 4.331968 TGCCAAACAGTCCTACAATAAGG 58.668 43.478 0.00 0.00 38.06 2.69
2013 2498 0.307760 GTGAACAACCTCCAGCAACG 59.692 55.000 0.00 0.00 0.00 4.10
2032 2517 7.596494 TGAAGTAATTTCAGAAGCAATTCAGG 58.404 34.615 0.00 0.00 40.82 3.86
2061 2546 8.613034 AGATGAGGATGATCAAATAAATAGGCT 58.387 33.333 0.00 0.00 27.93 4.58
2254 2739 2.806608 ATCCTTGCAGCAACTTGTTG 57.193 45.000 2.83 8.95 0.00 3.33
2317 2802 0.531532 CATCCGTGGCTGGATCAGAC 60.532 60.000 8.61 0.00 45.80 3.51
2389 2874 1.891919 GGGCTTTGCAGACGACACA 60.892 57.895 0.00 0.00 0.00 3.72
2571 3056 8.792830 TCTGTATTCCTTTTTCAATTCGATCT 57.207 30.769 0.00 0.00 0.00 2.75
2642 3127 5.711976 CACCAGGACAATAAGGAACAGAAAT 59.288 40.000 0.00 0.00 0.00 2.17
2651 3136 4.021192 ACAAAATGCACCAGGACAATAAGG 60.021 41.667 0.00 0.00 0.00 2.69
2850 3335 9.520515 ACCTTTATGAAGAGTCAAATAACACAT 57.479 29.630 0.00 0.00 37.30 3.21
2868 3353 4.096984 ACGACTAGACCGGTTACCTTTATG 59.903 45.833 9.42 0.00 0.00 1.90
2963 3448 1.596727 GATCTCTGAGTCATTTGCCGC 59.403 52.381 4.32 0.00 0.00 6.53
3034 3519 5.967674 GCAAATCAAAGACATCTACATTCCG 59.032 40.000 0.00 0.00 0.00 4.30
3085 3570 6.369890 TGCAGAAAACTAGAGATCACATTGTC 59.630 38.462 0.00 0.00 0.00 3.18
3092 3577 5.877012 GGAATGTGCAGAAAACTAGAGATCA 59.123 40.000 0.00 0.00 0.00 2.92
3161 3646 9.135189 TGGTATCTGAGGAATTTTTCAATATGG 57.865 33.333 0.00 0.00 0.00 2.74
3163 3648 8.840321 CGTGGTATCTGAGGAATTTTTCAATAT 58.160 33.333 0.00 0.00 0.00 1.28
3175 3660 2.022195 GTAGCACGTGGTATCTGAGGA 58.978 52.381 28.23 4.58 0.00 3.71
3419 4471 1.902508 TCTACCCCACTCTGCAGAAAG 59.097 52.381 18.85 12.64 0.00 2.62
3423 4475 1.270907 AACTCTACCCCACTCTGCAG 58.729 55.000 7.63 7.63 0.00 4.41
3548 4600 4.781934 CCCTAAAAGTACATGCTAGGCTT 58.218 43.478 0.00 0.00 0.00 4.35
3553 4605 5.949354 ACAAATGCCCTAAAAGTACATGCTA 59.051 36.000 0.00 0.00 0.00 3.49
3579 4631 1.676529 GCTGGAGCGATACACTCACTA 59.323 52.381 0.00 0.00 35.79 2.74
3581 4633 2.964911 GCTGGAGCGATACACTCAC 58.035 57.895 0.00 0.00 35.79 3.51
3692 4744 4.694339 AGACACAGAACTGTACCTTCAAC 58.306 43.478 7.15 0.00 42.83 3.18
4206 5418 7.213216 TGCATGCTTTAAGTTAAGTGATTCA 57.787 32.000 20.33 0.00 0.00 2.57
4214 5426 9.703892 AAAATACACATGCATGCTTTAAGTTAA 57.296 25.926 26.53 2.91 0.00 2.01
4295 5507 6.918067 TTTCTATCTGGAGTGAAGAGTGAA 57.082 37.500 0.00 0.00 0.00 3.18
4296 5508 7.068839 GGTATTTCTATCTGGAGTGAAGAGTGA 59.931 40.741 0.00 0.00 0.00 3.41
4297 5509 7.147828 TGGTATTTCTATCTGGAGTGAAGAGTG 60.148 40.741 0.00 0.00 0.00 3.51
4298 5510 6.897966 TGGTATTTCTATCTGGAGTGAAGAGT 59.102 38.462 0.00 0.00 0.00 3.24
4299 5511 7.353414 TGGTATTTCTATCTGGAGTGAAGAG 57.647 40.000 0.00 0.00 0.00 2.85
4300 5512 7.619698 TCTTGGTATTTCTATCTGGAGTGAAGA 59.380 37.037 0.00 0.00 0.00 2.87
4301 5513 7.786030 TCTTGGTATTTCTATCTGGAGTGAAG 58.214 38.462 0.00 0.00 0.00 3.02
4544 5756 8.690884 TCTAATCCAGTCTATCTGAAGTCTTTG 58.309 37.037 0.00 0.00 46.27 2.77
4551 5763 8.231007 AGATCCTTCTAATCCAGTCTATCTGAA 58.769 37.037 0.00 0.00 46.27 3.02
4604 5816 6.099341 GCGACAAGGGAATATTTGAAACAAT 58.901 36.000 0.00 0.00 0.00 2.71
4626 5838 5.121298 CCAATCTGTTGAGATATGGTATGCG 59.879 44.000 0.00 0.00 38.03 4.73
4693 5905 6.923508 CCTCCAATAAGTTTTCTTTTGGACAC 59.076 38.462 14.31 0.00 43.43 3.67
4806 6018 1.649664 CCATGAGCAAAGGAGTCGAG 58.350 55.000 0.00 0.00 0.00 4.04
4849 6069 6.070538 ACAAAGTAGAGCAATCTGGACTATGT 60.071 38.462 0.00 0.00 0.00 2.29
4896 6116 8.988060 TGGTATTCTATCCAACTTACAAGATCA 58.012 33.333 0.00 0.00 0.00 2.92
4908 6128 9.681062 CTAAAAGGAAGTTGGTATTCTATCCAA 57.319 33.333 0.00 0.00 40.77 3.53
4970 6190 3.719268 ACCTGCAATACATGTTCTGGA 57.281 42.857 2.30 2.09 0.00 3.86
5053 6277 5.999205 TGCCCATTTTTCAGATACAACAT 57.001 34.783 0.00 0.00 0.00 2.71
5058 6283 5.391312 AGTGTTGCCCATTTTTCAGATAC 57.609 39.130 0.00 0.00 0.00 2.24
5186 6411 2.275318 CGAGAACTTTGGGATCTCTGC 58.725 52.381 0.00 0.00 37.93 4.26
5493 6719 5.529430 TCTTTCGGACAAAATTAGTTGCTCA 59.471 36.000 0.00 0.00 31.29 4.26
5687 6922 2.884639 CCAGGTCACCATTCTTTTCGTT 59.115 45.455 0.00 0.00 0.00 3.85
5749 6984 3.664107 TCTTCCCTTCAGTGATGTTTCG 58.336 45.455 0.00 0.00 0.00 3.46
5839 7076 5.479306 CGGTTTCTACCATCTCTTTTCAGA 58.521 41.667 0.00 0.00 45.31 3.27
5861 7098 1.647545 CCATGGTTACACAGCAGCCG 61.648 60.000 2.57 0.00 35.97 5.52
5930 7168 7.956328 TCCACAAGATGTTAGTAGTATCAGT 57.044 36.000 0.00 0.00 0.00 3.41
6069 7310 5.512921 CCCAGGAAAACAAATTAACCAGCAT 60.513 40.000 0.00 0.00 0.00 3.79
6081 7322 3.374042 TCAGAACACCCAGGAAAACAA 57.626 42.857 0.00 0.00 0.00 2.83
6097 7338 2.551032 CACTCACTTGCAGCAAATCAGA 59.449 45.455 9.65 4.07 0.00 3.27
6120 7361 4.457257 CGTGAGATCTGTCTATATCAGCCA 59.543 45.833 0.00 0.00 33.97 4.75
6139 7380 3.682858 GCCTAAAAATAGAGTGCACGTGA 59.317 43.478 22.23 1.04 0.00 4.35
6195 7436 3.217626 CTGAAAACCATAGCCTGATCCC 58.782 50.000 0.00 0.00 0.00 3.85
6327 7579 0.036732 TGACACATCCTTCCACTGGC 59.963 55.000 0.00 0.00 0.00 4.85
6331 7583 5.282055 TCATAGATGACACATCCTTCCAC 57.718 43.478 7.93 0.00 0.00 4.02
6338 7590 7.658982 ACCACATACATTCATAGATGACACATC 59.341 37.037 3.87 3.87 36.36 3.06


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

AutoCloner maintained by Alex Coulton.