Multiple sequence alignment - TraesCS5D01G221700

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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 TraesCS5D01G221700 chr5D 100.000 3517 0 0 1 3517 329256798 329260314 0.000000e+00 6495.0
1 TraesCS5D01G221700 chr5D 92.920 113 5 2 661 773 329257342 329257451 1.010000e-35 161.0
2 TraesCS5D01G221700 chr5D 92.920 113 5 2 545 654 329257458 329257570 1.010000e-35 161.0
3 TraesCS5D01G221700 chr5D 95.699 93 4 0 2518 2610 388098089 388097997 2.190000e-32 150.0
4 TraesCS5D01G221700 chr5A 93.317 1990 93 24 548 2519 427372327 427370360 0.000000e+00 2902.0
5 TraesCS5D01G221700 chr5A 90.467 514 42 4 1 508 427373375 427372863 0.000000e+00 671.0
6 TraesCS5D01G221700 chr5A 95.057 263 13 0 3027 3289 541939993 541940255 7.020000e-112 414.0
7 TraesCS5D01G221700 chr5A 100.000 97 0 0 2599 2695 427370363 427370267 2.790000e-41 180.0
8 TraesCS5D01G221700 chr5A 94.231 104 5 1 545 648 427372211 427372109 1.310000e-34 158.0
9 TraesCS5D01G221700 chr5A 88.710 124 9 4 651 772 427372342 427372222 2.830000e-31 147.0
10 TraesCS5D01G221700 chr5A 92.233 103 6 2 2518 2618 580286932 580286830 1.020000e-30 145.0
11 TraesCS5D01G221700 chr5A 80.405 148 25 3 1671 1816 430244677 430244532 3.710000e-20 110.0
12 TraesCS5D01G221700 chr5A 100.000 44 0 0 508 551 427372623 427372580 8.090000e-12 82.4
13 TraesCS5D01G221700 chr5B 91.991 1748 90 25 807 2517 382359303 382361037 0.000000e+00 2407.0
14 TraesCS5D01G221700 chr5B 75.197 1649 302 67 923 2501 378848886 378850497 0.000000e+00 680.0
15 TraesCS5D01G221700 chr5B 93.561 264 17 0 3027 3290 517196942 517197205 9.150000e-106 394.0
16 TraesCS5D01G221700 chr5B 87.611 339 13 5 346 683 382358809 382359119 1.990000e-97 366.0
17 TraesCS5D01G221700 chr5B 91.241 137 6 5 672 806 382359138 382359270 7.760000e-42 182.0
18 TraesCS5D01G221700 chr5B 91.892 111 6 2 663 773 382358984 382359091 6.080000e-33 152.0
19 TraesCS5D01G221700 chr5B 94.048 84 5 0 2816 2899 382362812 382362895 1.020000e-25 128.0
20 TraesCS5D01G221700 chr3D 98.544 618 9 0 2900 3517 571996043 571996660 0.000000e+00 1092.0
21 TraesCS5D01G221700 chr6A 92.462 199 15 0 3319 3517 548398150 548397952 5.750000e-73 285.0
22 TraesCS5D01G221700 chr3A 95.570 158 7 0 3319 3476 571406248 571406091 1.620000e-63 254.0
23 TraesCS5D01G221700 chr2A 94.340 159 8 1 3316 3473 614566946 614567104 3.510000e-60 243.0
24 TraesCS5D01G221700 chr2A 93.506 154 10 0 3320 3473 718483979 718484132 2.730000e-56 230.0
25 TraesCS5D01G221700 chr2A 82.645 121 18 3 409 529 734155999 734156116 1.730000e-18 104.0
26 TraesCS5D01G221700 chr2A 93.878 49 3 0 3469 3517 614567122 614567170 1.350000e-09 75.0
27 TraesCS5D01G221700 chr2A 95.122 41 2 0 3477 3517 718484158 718484198 8.150000e-07 65.8
28 TraesCS5D01G221700 chr6D 97.638 127 3 0 2900 3026 60392672 60392546 5.910000e-53 219.0
29 TraesCS5D01G221700 chr6D 90.566 106 10 0 2510 2615 448291715 448291820 1.320000e-29 141.0
30 TraesCS5D01G221700 chr6D 79.630 162 22 8 3363 3517 153304875 153305032 4.800000e-19 106.0
31 TraesCS5D01G221700 chr6D 79.012 162 22 9 3363 3517 894721 894565 2.230000e-17 100.0
32 TraesCS5D01G221700 chr6D 94.737 38 2 0 47 84 465139569 465139532 3.790000e-05 60.2
33 TraesCS5D01G221700 chr7D 95.238 126 6 0 2901 3026 620312004 620312129 2.140000e-47 200.0
34 TraesCS5D01G221700 chr7D 96.552 87 3 0 2900 2986 488127693 488127607 1.020000e-30 145.0
35 TraesCS5D01G221700 chr7D 91.228 57 3 2 31 86 103208574 103208629 3.760000e-10 76.8
36 TraesCS5D01G221700 chrUn 90.566 106 10 0 2510 2615 110731959 110732064 1.320000e-29 141.0
37 TraesCS5D01G221700 chrUn 100.000 32 0 0 56 87 115097547 115097578 3.790000e-05 60.2
38 TraesCS5D01G221700 chr4D 90.566 106 10 0 2510 2615 68726336 68726231 1.320000e-29 141.0
39 TraesCS5D01G221700 chr4B 90.566 106 10 0 2510 2615 668162928 668163033 1.320000e-29 141.0
40 TraesCS5D01G221700 chr4B 90.566 106 10 0 2510 2615 668489821 668489926 1.320000e-29 141.0
41 TraesCS5D01G221700 chr4B 90.566 106 10 0 2510 2615 669101780 669101675 1.320000e-29 141.0
42 TraesCS5D01G221700 chr1D 90.566 106 10 0 2510 2615 489134101 489133996 1.320000e-29 141.0
43 TraesCS5D01G221700 chr1A 93.333 90 6 0 2937 3026 164463217 164463128 2.200000e-27 134.0
44 TraesCS5D01G221700 chr7A 84.127 63 9 1 672 733 25921970 25921908 3.790000e-05 60.2


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 TraesCS5D01G221700 chr5D 329256798 329260314 3516 False 2272.333333 6495 95.280000 1 3517 3 chr5D.!!$F1 3516
1 TraesCS5D01G221700 chr5A 427370267 427373375 3108 True 690.066667 2902 94.454167 1 2695 6 chr5A.!!$R3 2694
2 TraesCS5D01G221700 chr5B 378848886 378850497 1611 False 680.000000 680 75.197000 923 2501 1 chr5B.!!$F1 1578
3 TraesCS5D01G221700 chr5B 382358809 382362895 4086 False 647.000000 2407 91.356600 346 2899 5 chr5B.!!$F3 2553
4 TraesCS5D01G221700 chr3D 571996043 571996660 617 False 1092.000000 1092 98.544000 2900 3517 1 chr3D.!!$F1 617

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
24 25 0.179145 CGTGGACTGATACGGGACAC 60.179 60.0 0.00 0.0 36.71 3.67 F
30 31 0.462047 CTGATACGGGACACCCTTGC 60.462 60.0 5.27 0.0 42.67 4.01 F
1048 1629 0.321671 CGCCCTCTTCTGTCTCCAAA 59.678 55.0 0.00 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1013 1594 0.745468 GGCGAGAAGGGAGAATACGT 59.255 55.000 0.00 0.00 0.00 3.57 R
1600 2215 1.473257 GCCGAGGATCATGCACTGTAA 60.473 52.381 0.00 0.00 33.23 2.41 R
2823 3596 0.179059 TCACTTTGTTGCTCGAGCCA 60.179 50.000 33.23 21.55 41.18 4.75 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
23 24 2.186155 CGTGGACTGATACGGGACA 58.814 57.895 0.00 0.00 36.71 4.02
24 25 0.179145 CGTGGACTGATACGGGACAC 60.179 60.000 0.00 0.00 36.71 3.67
26 27 0.974010 TGGACTGATACGGGACACCC 60.974 60.000 0.00 0.00 41.09 4.61
30 31 0.462047 CTGATACGGGACACCCTTGC 60.462 60.000 5.27 0.00 42.67 4.01
35 36 3.070576 GGGACACCCTTGCATGGC 61.071 66.667 13.15 0.00 41.34 4.40
41 42 3.136123 CCCTTGCATGGCTGTCCG 61.136 66.667 13.15 0.00 34.14 4.79
52 53 2.338620 CTGTCCGGACACTTGCGA 59.661 61.111 33.23 10.87 39.29 5.10
53 54 1.734477 CTGTCCGGACACTTGCGAG 60.734 63.158 33.23 17.70 39.29 5.03
74 75 0.875059 GGTTTGAGAGTCCGCTTTGG 59.125 55.000 0.00 0.00 40.09 3.28
98 99 4.706962 AGATGCCCTAAAACAACATTCCTC 59.293 41.667 0.00 0.00 0.00 3.71
127 128 4.389772 GCAATCGTGCCATGAAGC 57.610 55.556 0.00 0.00 45.68 3.86
128 129 1.507630 GCAATCGTGCCATGAAGCA 59.492 52.632 9.13 0.00 45.68 3.91
148 149 3.205338 CAGGGTTTTCTTTGGCCAAAAG 58.795 45.455 29.93 22.59 45.76 2.27
161 162 6.827586 TTGGCCAAAAGATACTACGAAATT 57.172 33.333 17.98 0.00 0.00 1.82
165 166 6.458342 GGCCAAAAGATACTACGAAATTGGAG 60.458 42.308 0.00 0.00 38.64 3.86
181 182 3.758755 TGGAGCGAGCATGAAGATATT 57.241 42.857 0.00 0.00 0.00 1.28
234 235 4.020573 TCTGGCGAAAGATCTTTGGTCTTA 60.021 41.667 27.83 16.86 34.97 2.10
242 243 7.389607 CGAAAGATCTTTGGTCTTACCCTAAAA 59.610 37.037 25.12 0.00 37.50 1.52
249 250 5.245584 TGGTCTTACCCTAAAACCGATTT 57.754 39.130 0.00 0.00 37.50 2.17
276 277 3.097614 AGTGGACCGCTCTTATGTACTT 58.902 45.455 0.29 0.00 0.00 2.24
339 343 4.718961 AGAAGTAAAATGTGCTCTGGTGT 58.281 39.130 0.00 0.00 0.00 4.16
344 348 8.630054 AAGTAAAATGTGCTCTGGTGTAATAA 57.370 30.769 0.00 0.00 0.00 1.40
425 432 9.307121 CTATGTATGTCCTCTCTGTTTTAACTG 57.693 37.037 0.00 0.00 0.00 3.16
464 471 4.739195 TGGTTTTCTTTCACTGGTTTTCG 58.261 39.130 0.00 0.00 0.00 3.46
780 1319 3.942130 AGTAAGTGCAAAATCCTTGCC 57.058 42.857 6.98 0.00 44.32 4.52
908 1479 9.362151 ACTCCATTGACTGTTTCCTAAAATAAA 57.638 29.630 0.00 0.00 0.00 1.40
955 1536 3.852536 GCAGCGTCTACTATAATTAGCCG 59.147 47.826 0.00 0.00 0.00 5.52
1013 1594 1.609239 CAGCCATGGAGCTTACCCA 59.391 57.895 18.40 0.00 42.61 4.51
1048 1629 0.321671 CGCCCTCTTCTGTCTCCAAA 59.678 55.000 0.00 0.00 0.00 3.28
1104 1685 4.821589 GCCCTCGGCGACTCCAAG 62.822 72.222 4.99 0.00 39.62 3.61
1302 1886 9.545105 ACACTTTGCTCAAAATTTGATTTGATA 57.455 25.926 9.02 0.00 45.45 2.15
1334 1943 9.399797 TGAATATTTGAGCATTGAGTCTATGTT 57.600 29.630 14.71 9.64 0.00 2.71
1339 1948 5.414360 TGAGCATTGAGTCTATGTTCTGTC 58.586 41.667 23.92 11.66 35.18 3.51
1342 1951 6.105333 AGCATTGAGTCTATGTTCTGTCTTC 58.895 40.000 14.71 0.00 0.00 2.87
1346 1955 5.700846 TGAGTCTATGTTCTGTCTTCGTTC 58.299 41.667 0.00 0.00 0.00 3.95
1347 1956 5.061920 AGTCTATGTTCTGTCTTCGTTCC 57.938 43.478 0.00 0.00 0.00 3.62
1351 1960 3.928727 TGTTCTGTCTTCGTTCCGTAT 57.071 42.857 0.00 0.00 0.00 3.06
1437 2049 2.377310 CGTCAATTTCGCCGTCGGT 61.377 57.895 13.94 0.00 36.13 4.69
1440 2052 2.031465 AATTTCGCCGTCGGTGGT 59.969 55.556 23.98 8.53 33.43 4.16
1597 2212 1.142097 GCTCCCTTGTCTAGCCGTC 59.858 63.158 0.00 0.00 0.00 4.79
1598 2213 1.817209 CTCCCTTGTCTAGCCGTCC 59.183 63.158 0.00 0.00 0.00 4.79
1599 2214 2.005960 CTCCCTTGTCTAGCCGTCCG 62.006 65.000 0.00 0.00 0.00 4.79
1600 2215 2.348888 CCCTTGTCTAGCCGTCCGT 61.349 63.158 0.00 0.00 0.00 4.69
1609 2224 1.525718 TAGCCGTCCGTTACAGTGCA 61.526 55.000 0.00 0.00 0.00 4.57
1611 2226 1.966493 GCCGTCCGTTACAGTGCATG 61.966 60.000 0.00 0.00 0.00 4.06
1614 2229 1.588404 CGTCCGTTACAGTGCATGATC 59.412 52.381 0.00 0.00 0.00 2.92
1617 2232 2.159099 TCCGTTACAGTGCATGATCCTC 60.159 50.000 0.00 0.00 0.00 3.71
1653 2268 6.109359 ACATACTGAGAAACTGCTTGATACC 58.891 40.000 0.00 0.00 0.00 2.73
1663 2278 1.754803 TGCTTGATACCTACAGGACCG 59.245 52.381 1.29 0.00 38.94 4.79
1825 2441 5.053091 CGCTGATGTATGTTTACATTTTGCG 60.053 40.000 17.56 17.56 46.64 4.85
1881 2497 2.891112 ACACACCATTTTTGCACTGTG 58.109 42.857 2.76 2.76 36.03 3.66
1884 2500 3.491639 CACACCATTTTTGCACTGTGATG 59.508 43.478 12.86 5.75 32.44 3.07
1886 2502 4.141981 ACACCATTTTTGCACTGTGATGAA 60.142 37.500 12.86 0.00 0.00 2.57
1889 2505 5.467399 ACCATTTTTGCACTGTGATGAAATG 59.533 36.000 22.34 22.34 34.49 2.32
1890 2506 5.106869 CCATTTTTGCACTGTGATGAAATGG 60.107 40.000 27.76 27.76 42.92 3.16
1892 2508 3.646611 TTGCACTGTGATGAAATGGTG 57.353 42.857 12.86 0.00 0.00 4.17
1893 2509 1.270274 TGCACTGTGATGAAATGGTGC 59.730 47.619 12.86 8.63 46.65 5.01
1894 2510 1.270274 GCACTGTGATGAAATGGTGCA 59.730 47.619 12.86 0.00 46.02 4.57
1895 2511 2.670229 GCACTGTGATGAAATGGTGCAG 60.670 50.000 12.86 0.00 46.02 4.41
1901 2540 4.022935 TGTGATGAAATGGTGCAGAACTTC 60.023 41.667 0.00 0.00 0.00 3.01
2090 2729 1.967319 AGTACCACAACACCAAGCTG 58.033 50.000 0.00 0.00 0.00 4.24
2162 2801 2.031495 AGGCTGACTTCTACAACCCT 57.969 50.000 0.00 0.00 0.00 4.34
2189 2828 0.549169 AGATCCTCCAAAACCCCGGA 60.549 55.000 0.73 0.00 0.00 5.14
2217 2856 4.675190 GGTACGTAAGGAAAAGAAAGCC 57.325 45.455 0.00 0.00 46.39 4.35
2218 2857 3.438087 GGTACGTAAGGAAAAGAAAGCCC 59.562 47.826 0.00 0.00 46.39 5.19
2219 2858 3.217681 ACGTAAGGAAAAGAAAGCCCA 57.782 42.857 0.00 0.00 46.39 5.36
2220 2859 3.146847 ACGTAAGGAAAAGAAAGCCCAG 58.853 45.455 0.00 0.00 46.39 4.45
2221 2860 3.181448 ACGTAAGGAAAAGAAAGCCCAGA 60.181 43.478 0.00 0.00 46.39 3.86
2222 2861 3.818773 CGTAAGGAAAAGAAAGCCCAGAA 59.181 43.478 0.00 0.00 0.00 3.02
2223 2862 4.083271 CGTAAGGAAAAGAAAGCCCAGAAG 60.083 45.833 0.00 0.00 0.00 2.85
2224 2863 3.602205 AGGAAAAGAAAGCCCAGAAGT 57.398 42.857 0.00 0.00 0.00 3.01
2225 2864 3.916035 AGGAAAAGAAAGCCCAGAAGTT 58.084 40.909 0.00 0.00 0.00 2.66
2226 2865 3.891977 AGGAAAAGAAAGCCCAGAAGTTC 59.108 43.478 0.00 0.00 0.00 3.01
2227 2866 3.891977 GGAAAAGAAAGCCCAGAAGTTCT 59.108 43.478 0.00 0.00 31.69 3.01
2228 2867 5.070685 GGAAAAGAAAGCCCAGAAGTTCTA 58.929 41.667 4.74 0.00 30.24 2.10
2229 2868 5.048643 GGAAAAGAAAGCCCAGAAGTTCTAC 60.049 44.000 4.74 0.00 30.24 2.59
2239 2878 1.070134 AGAAGTTCTACCTGCGTGCAA 59.930 47.619 2.75 0.00 0.00 4.08
2517 3182 7.162082 GCCCATACTGAATGCTAATAACTAGT 58.838 38.462 0.00 0.00 33.92 2.57
2518 3183 8.311836 GCCCATACTGAATGCTAATAACTAGTA 58.688 37.037 0.00 0.00 33.92 1.82
2519 3184 9.640963 CCCATACTGAATGCTAATAACTAGTAC 57.359 37.037 0.00 0.00 33.92 2.73
2523 3188 7.953752 ACTGAATGCTAATAACTAGTACTCCC 58.046 38.462 0.00 0.00 0.00 4.30
2524 3189 7.785506 ACTGAATGCTAATAACTAGTACTCCCT 59.214 37.037 0.00 0.00 0.00 4.20
2525 3190 8.179509 TGAATGCTAATAACTAGTACTCCCTC 57.820 38.462 0.00 0.00 0.00 4.30
2526 3191 8.005388 TGAATGCTAATAACTAGTACTCCCTCT 58.995 37.037 0.00 0.00 0.00 3.69
2527 3192 7.768807 ATGCTAATAACTAGTACTCCCTCTG 57.231 40.000 0.00 0.00 0.00 3.35
2528 3193 6.670617 TGCTAATAACTAGTACTCCCTCTGT 58.329 40.000 0.00 0.00 0.00 3.41
2529 3194 7.809238 TGCTAATAACTAGTACTCCCTCTGTA 58.191 38.462 0.00 0.00 0.00 2.74
2530 3195 8.277197 TGCTAATAACTAGTACTCCCTCTGTAA 58.723 37.037 0.00 0.00 0.00 2.41
2531 3196 9.129532 GCTAATAACTAGTACTCCCTCTGTAAA 57.870 37.037 0.00 0.00 0.00 2.01
2544 3209 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2545 3210 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2546 3211 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2547 3212 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2548 3213 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2721 3471 4.752101 AGTTAGCATAGACAATTGATCCGC 59.248 41.667 13.59 7.87 0.00 5.54
2722 3472 2.498167 AGCATAGACAATTGATCCGCC 58.502 47.619 13.59 0.00 0.00 6.13
2723 3473 1.537202 GCATAGACAATTGATCCGCCC 59.463 52.381 13.59 0.00 0.00 6.13
2724 3474 2.849942 CATAGACAATTGATCCGCCCA 58.150 47.619 13.59 0.00 0.00 5.36
2725 3475 3.415212 CATAGACAATTGATCCGCCCAT 58.585 45.455 13.59 0.00 0.00 4.00
2726 3476 4.578871 CATAGACAATTGATCCGCCCATA 58.421 43.478 13.59 0.00 0.00 2.74
2727 3477 2.851195 AGACAATTGATCCGCCCATAC 58.149 47.619 13.59 0.00 0.00 2.39
2729 3479 2.549754 GACAATTGATCCGCCCATACTG 59.450 50.000 13.59 0.00 0.00 2.74
2730 3480 2.172505 ACAATTGATCCGCCCATACTGA 59.827 45.455 13.59 0.00 0.00 3.41
2731 3481 3.213506 CAATTGATCCGCCCATACTGAA 58.786 45.455 0.00 0.00 0.00 3.02
2733 3483 2.549064 TGATCCGCCCATACTGAATG 57.451 50.000 0.00 0.00 35.15 2.67
2734 3484 1.160137 GATCCGCCCATACTGAATGC 58.840 55.000 0.00 0.00 33.92 3.56
2737 3487 1.070134 TCCGCCCATACTGAATGCTAC 59.930 52.381 0.00 0.00 33.92 3.58
2738 3488 1.070758 CCGCCCATACTGAATGCTACT 59.929 52.381 0.00 0.00 33.92 2.57
2739 3489 2.299013 CCGCCCATACTGAATGCTACTA 59.701 50.000 0.00 0.00 33.92 1.82
2741 3491 3.330267 GCCCATACTGAATGCTACTAGC 58.670 50.000 0.61 0.61 42.82 3.42
2742 3492 3.007398 GCCCATACTGAATGCTACTAGCT 59.993 47.826 9.49 0.00 42.97 3.32
2743 3493 4.503991 GCCCATACTGAATGCTACTAGCTT 60.504 45.833 9.49 0.17 42.97 3.74
2744 3494 5.615289 CCCATACTGAATGCTACTAGCTTT 58.385 41.667 9.49 8.99 42.97 3.51
2745 3495 6.058183 CCCATACTGAATGCTACTAGCTTTT 58.942 40.000 9.49 3.52 42.97 2.27
2746 3496 6.543831 CCCATACTGAATGCTACTAGCTTTTT 59.456 38.462 9.49 1.23 42.97 1.94
2782 3555 5.427378 TGAATGCTACTAGCTATTGTTGCA 58.573 37.500 19.15 19.15 45.33 4.08
2807 3580 4.237724 TGCTGTACTTCTGATCTGAAACG 58.762 43.478 14.97 7.95 0.00 3.60
2823 3596 3.249799 TGAAACGCATCGTGAAACTCAAT 59.750 39.130 0.00 0.00 39.99 2.57
2824 3597 2.880822 ACGCATCGTGAAACTCAATG 57.119 45.000 0.00 0.00 39.18 2.82
2825 3598 1.464608 ACGCATCGTGAAACTCAATGG 59.535 47.619 0.00 0.00 39.18 3.16
2826 3599 1.791555 CGCATCGTGAAACTCAATGGC 60.792 52.381 0.00 0.00 31.75 4.40
2845 5075 2.404215 GCTCGAGCAACAAAGTGAGTA 58.596 47.619 31.91 0.00 41.59 2.59
2862 5092 9.583765 AAAGTGAGTAGAACGGAAATTATACTC 57.416 33.333 11.53 11.53 46.53 2.59
2867 5097 5.490139 AGAACGGAAATTATACTCGACGA 57.510 39.130 0.00 0.00 0.00 4.20
2868 5098 5.508872 AGAACGGAAATTATACTCGACGAG 58.491 41.667 22.97 22.97 35.52 4.18
3017 5247 1.710816 CTCCCTTATCTCTTCCGCCT 58.289 55.000 0.00 0.00 0.00 5.52
3120 5350 2.978010 CAAGAACAAGGGCGCCGT 60.978 61.111 22.54 20.09 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.974010 GGGTGTCCCGTATCAGTCCA 60.974 60.000 0.00 0.00 32.13 4.02
23 24 2.036256 GGACAGCCATGCAAGGGT 59.964 61.111 6.90 6.90 42.11 4.34
24 25 3.136123 CGGACAGCCATGCAAGGG 61.136 66.667 10.51 6.76 43.76 3.95
26 27 2.046023 TCCGGACAGCCATGCAAG 60.046 61.111 0.00 0.00 0.00 4.01
30 31 1.003355 AAGTGTCCGGACAGCCATG 60.003 57.895 37.04 0.00 42.74 3.66
35 36 1.734477 CTCGCAAGTGTCCGGACAG 60.734 63.158 37.04 25.62 42.74 3.51
41 42 0.868406 CAAACCTCTCGCAAGTGTCC 59.132 55.000 0.00 0.00 39.48 4.02
52 53 1.343069 AAGCGGACTCTCAAACCTCT 58.657 50.000 0.00 0.00 0.00 3.69
53 54 1.801178 CAAAGCGGACTCTCAAACCTC 59.199 52.381 0.00 0.00 0.00 3.85
74 75 4.706962 AGGAATGTTGTTTTAGGGCATCTC 59.293 41.667 0.00 0.00 0.00 2.75
98 99 2.919229 GCACGATTGCCAGAATCTTTTG 59.081 45.455 0.00 0.00 43.66 2.44
127 128 2.998316 TTTGGCCAAAGAAAACCCTG 57.002 45.000 27.13 0.00 0.00 4.45
128 129 3.111484 TCTTTTGGCCAAAGAAAACCCT 58.889 40.909 28.79 0.00 46.68 4.34
148 149 3.425858 GCTCGCTCCAATTTCGTAGTATC 59.574 47.826 0.00 0.00 0.00 2.24
156 157 2.679837 TCTTCATGCTCGCTCCAATTTC 59.320 45.455 0.00 0.00 0.00 2.17
161 162 3.758755 AATATCTTCATGCTCGCTCCA 57.241 42.857 0.00 0.00 0.00 3.86
165 166 6.589523 ACTCTCATTAATATCTTCATGCTCGC 59.410 38.462 0.00 0.00 0.00 5.03
181 182 7.228314 TCCGAAAGAGAAAGAACTCTCATTA 57.772 36.000 0.00 0.00 45.08 1.90
262 263 4.033990 TCTGAGCAAGTACATAAGAGCG 57.966 45.455 0.00 0.00 0.00 5.03
263 264 6.045318 TCATTCTGAGCAAGTACATAAGAGC 58.955 40.000 0.00 0.00 0.00 4.09
266 267 8.659925 AGATTCATTCTGAGCAAGTACATAAG 57.340 34.615 0.00 0.00 31.79 1.73
312 313 8.946085 CACCAGAGCACATTTTACTTCTAATAA 58.054 33.333 0.00 0.00 0.00 1.40
359 363 8.857098 TCGATTACTATCAACCTAATAGCAACT 58.143 33.333 0.00 0.00 31.17 3.16
464 471 0.375803 AGACGTGTGCGGTTTTCAAC 59.624 50.000 0.00 0.00 43.45 3.18
474 481 2.853281 GCTAAACCAACAAGACGTGTGC 60.853 50.000 0.00 0.00 40.60 4.57
657 1163 5.105997 GCCAAATGAATCAGCACTTACTCTT 60.106 40.000 0.00 0.00 0.00 2.85
780 1319 9.277783 CAGGAGGTACTAATTGAATAAGATTGG 57.722 37.037 0.00 0.00 41.55 3.16
860 1431 7.373617 AGTTACCATGTTTTTCTTTTGGGAT 57.626 32.000 0.00 0.00 0.00 3.85
955 1536 1.706287 GAAAATCAGAGGCGCCCGAC 61.706 60.000 26.15 15.48 0.00 4.79
1013 1594 0.745468 GGCGAGAAGGGAGAATACGT 59.255 55.000 0.00 0.00 0.00 3.57
1104 1685 2.100631 CAGGTTGCCGGTGTCGATC 61.101 63.158 1.90 0.00 39.00 3.69
1315 1899 5.798132 ACAGAACATAGACTCAATGCTCAA 58.202 37.500 0.00 0.00 0.00 3.02
1319 1903 5.005203 CGAAGACAGAACATAGACTCAATGC 59.995 44.000 0.00 0.00 0.00 3.56
1346 1955 2.470821 CAAACTCCTCGGCTAATACGG 58.529 52.381 0.00 0.00 0.00 4.02
1347 1956 2.159142 ACCAAACTCCTCGGCTAATACG 60.159 50.000 0.00 0.00 0.00 3.06
1351 1960 1.549170 GAGACCAAACTCCTCGGCTAA 59.451 52.381 0.00 0.00 0.00 3.09
1597 2212 2.205074 GAGGATCATGCACTGTAACGG 58.795 52.381 0.00 0.00 33.17 4.44
1598 2213 1.854743 CGAGGATCATGCACTGTAACG 59.145 52.381 0.00 0.00 33.17 3.18
1599 2214 2.205074 CCGAGGATCATGCACTGTAAC 58.795 52.381 0.00 0.00 33.17 2.50
1600 2215 1.473257 GCCGAGGATCATGCACTGTAA 60.473 52.381 0.00 0.00 33.23 2.41
1609 2224 3.641436 TGTATGTAACAGCCGAGGATCAT 59.359 43.478 0.00 0.00 33.01 2.45
1611 2226 3.728076 TGTATGTAACAGCCGAGGATC 57.272 47.619 0.00 0.00 33.01 3.36
1614 2229 4.037565 TCAGTATGTATGTAACAGCCGAGG 59.962 45.833 0.00 0.00 42.70 4.63
1617 2232 5.183014 TCTCAGTATGTATGTAACAGCCG 57.817 43.478 0.00 0.00 42.70 5.52
1653 2268 1.478510 AGCATTCACTCGGTCCTGTAG 59.521 52.381 0.00 0.00 0.00 2.74
1825 2441 7.936950 AAGCTGAAGCAAAACTAAAGAAATC 57.063 32.000 4.90 0.00 45.16 2.17
1881 2497 4.771590 TGAAGTTCTGCACCATTTCATC 57.228 40.909 4.17 0.00 0.00 2.92
1884 2500 5.183904 AGGTAATGAAGTTCTGCACCATTTC 59.816 40.000 17.18 3.30 0.00 2.17
1886 2502 4.666512 AGGTAATGAAGTTCTGCACCATT 58.333 39.130 17.18 6.74 0.00 3.16
1889 2505 3.191371 CCAAGGTAATGAAGTTCTGCACC 59.809 47.826 4.17 8.10 0.00 5.01
1890 2506 3.821033 ACCAAGGTAATGAAGTTCTGCAC 59.179 43.478 4.17 0.00 0.00 4.57
1892 2508 5.001232 TGTACCAAGGTAATGAAGTTCTGC 58.999 41.667 4.17 0.00 31.86 4.26
1893 2509 6.485313 TGTTGTACCAAGGTAATGAAGTTCTG 59.515 38.462 4.17 0.00 31.86 3.02
1894 2510 6.597562 TGTTGTACCAAGGTAATGAAGTTCT 58.402 36.000 4.17 0.00 31.86 3.01
1895 2511 6.072673 CCTGTTGTACCAAGGTAATGAAGTTC 60.073 42.308 0.00 0.00 31.86 3.01
1901 2540 3.190535 GCACCTGTTGTACCAAGGTAATG 59.809 47.826 10.05 2.10 31.86 1.90
1925 2564 4.250464 CGTAAGTTGCACCTCCTTTGATA 58.750 43.478 0.00 0.00 0.00 2.15
2090 2729 3.682315 CCGTCGATCGCATCACGC 61.682 66.667 18.37 0.25 43.23 5.34
2162 2801 4.040461 GGGTTTTGGAGGATCTCGATGATA 59.960 45.833 0.00 0.00 35.14 2.15
2189 2828 1.243902 TTCCTTACGTACCGAACCGT 58.756 50.000 0.00 0.00 40.87 4.83
2206 2845 5.048643 GGTAGAACTTCTGGGCTTTCTTTTC 60.049 44.000 1.17 0.00 30.89 2.29
2214 2853 0.615850 GCAGGTAGAACTTCTGGGCT 59.384 55.000 1.17 0.00 0.00 5.19
2215 2854 0.741221 CGCAGGTAGAACTTCTGGGC 60.741 60.000 1.17 0.00 35.34 5.36
2216 2855 0.608640 ACGCAGGTAGAACTTCTGGG 59.391 55.000 1.17 14.66 43.92 4.45
2217 2856 1.714794 CACGCAGGTAGAACTTCTGG 58.285 55.000 1.17 0.00 0.00 3.86
2218 2857 1.071605 GCACGCAGGTAGAACTTCTG 58.928 55.000 1.17 0.00 0.00 3.02
2219 2858 0.679505 TGCACGCAGGTAGAACTTCT 59.320 50.000 0.00 0.00 0.00 2.85
2220 2859 1.461127 CTTGCACGCAGGTAGAACTTC 59.539 52.381 0.00 0.00 0.00 3.01
2221 2860 1.512926 CTTGCACGCAGGTAGAACTT 58.487 50.000 0.00 0.00 0.00 2.66
2222 2861 0.320771 CCTTGCACGCAGGTAGAACT 60.321 55.000 0.22 0.00 0.00 3.01
2223 2862 1.298859 CCCTTGCACGCAGGTAGAAC 61.299 60.000 2.31 0.00 0.00 3.01
2224 2863 1.003839 CCCTTGCACGCAGGTAGAA 60.004 57.895 2.31 0.00 0.00 2.10
2225 2864 1.764571 AACCCTTGCACGCAGGTAGA 61.765 55.000 3.62 0.00 30.63 2.59
2226 2865 0.889186 AAACCCTTGCACGCAGGTAG 60.889 55.000 3.62 0.00 30.63 3.18
2227 2866 1.149627 AAACCCTTGCACGCAGGTA 59.850 52.632 3.62 0.00 30.63 3.08
2228 2867 2.123897 AAACCCTTGCACGCAGGT 60.124 55.556 2.31 0.00 0.00 4.00
2229 2868 2.336088 CAAACCCTTGCACGCAGG 59.664 61.111 0.00 0.00 0.00 4.85
2239 2878 3.565307 TCAGAAAACTCATGCAAACCCT 58.435 40.909 0.00 0.00 0.00 4.34
2426 3091 3.050275 GTGGCCTCCGTGAAGTGC 61.050 66.667 3.32 0.00 0.00 4.40
2518 3183 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2519 3184 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2520 3185 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2521 3186 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2522 3187 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2582 3247 9.597681 TCTCTAATACTCCCTCCGTAAATTAAT 57.402 33.333 0.00 0.00 0.00 1.40
2583 3248 9.075678 CTCTCTAATACTCCCTCCGTAAATTAA 57.924 37.037 0.00 0.00 0.00 1.40
2584 3249 7.668886 CCTCTCTAATACTCCCTCCGTAAATTA 59.331 40.741 0.00 0.00 0.00 1.40
2585 3250 6.494146 CCTCTCTAATACTCCCTCCGTAAATT 59.506 42.308 0.00 0.00 0.00 1.82
2586 3251 6.011481 CCTCTCTAATACTCCCTCCGTAAAT 58.989 44.000 0.00 0.00 0.00 1.40
2587 3252 5.133322 TCCTCTCTAATACTCCCTCCGTAAA 59.867 44.000 0.00 0.00 0.00 2.01
2588 3253 4.662179 TCCTCTCTAATACTCCCTCCGTAA 59.338 45.833 0.00 0.00 0.00 3.18
2589 3254 4.237843 TCCTCTCTAATACTCCCTCCGTA 58.762 47.826 0.00 0.00 0.00 4.02
2590 3255 3.054576 TCCTCTCTAATACTCCCTCCGT 58.945 50.000 0.00 0.00 0.00 4.69
2591 3256 3.681593 CTCCTCTCTAATACTCCCTCCG 58.318 54.545 0.00 0.00 0.00 4.63
2592 3257 3.427573 GCTCCTCTCTAATACTCCCTCC 58.572 54.545 0.00 0.00 0.00 4.30
2593 3258 3.427573 GGCTCCTCTCTAATACTCCCTC 58.572 54.545 0.00 0.00 0.00 4.30
2594 3259 2.111077 GGGCTCCTCTCTAATACTCCCT 59.889 54.545 0.00 0.00 0.00 4.20
2595 3260 2.531771 GGGCTCCTCTCTAATACTCCC 58.468 57.143 0.00 0.00 0.00 4.30
2596 3261 2.164338 CGGGCTCCTCTCTAATACTCC 58.836 57.143 0.00 0.00 0.00 3.85
2700 3365 4.065088 GGCGGATCAATTGTCTATGCTAA 58.935 43.478 5.13 0.00 0.00 3.09
2702 3367 2.498167 GGCGGATCAATTGTCTATGCT 58.502 47.619 5.13 0.00 0.00 3.79
2703 3368 1.537202 GGGCGGATCAATTGTCTATGC 59.463 52.381 5.13 4.82 0.00 3.14
2704 3369 2.849942 TGGGCGGATCAATTGTCTATG 58.150 47.619 5.13 0.00 0.00 2.23
2705 3370 3.795688 ATGGGCGGATCAATTGTCTAT 57.204 42.857 5.13 0.00 0.00 1.98
2716 3466 0.767375 AGCATTCAGTATGGGCGGAT 59.233 50.000 0.00 0.00 36.16 4.18
2718 3468 1.070758 AGTAGCATTCAGTATGGGCGG 59.929 52.381 0.00 0.00 36.16 6.13
2719 3469 2.533266 AGTAGCATTCAGTATGGGCG 57.467 50.000 0.00 0.00 36.16 6.13
2721 3471 4.881019 AGCTAGTAGCATTCAGTATGGG 57.119 45.455 23.77 0.00 45.56 4.00
2722 3472 7.559590 AAAAAGCTAGTAGCATTCAGTATGG 57.440 36.000 23.77 0.00 45.56 2.74
2746 3496 8.883731 GCTAGTAGCATTCAGATTGTCTAAAAA 58.116 33.333 17.47 0.00 41.89 1.94
2747 3497 8.260818 AGCTAGTAGCATTCAGATTGTCTAAAA 58.739 33.333 23.77 0.00 45.56 1.52
2748 3498 7.786030 AGCTAGTAGCATTCAGATTGTCTAAA 58.214 34.615 23.77 0.00 45.56 1.85
2750 3500 6.968263 AGCTAGTAGCATTCAGATTGTCTA 57.032 37.500 23.77 0.00 45.56 2.59
2752 3502 7.655328 ACAATAGCTAGTAGCATTCAGATTGTC 59.345 37.037 23.77 0.00 45.56 3.18
2755 3505 7.041508 GCAACAATAGCTAGTAGCATTCAGATT 60.042 37.037 23.77 9.90 45.56 2.40
2757 3507 5.755375 GCAACAATAGCTAGTAGCATTCAGA 59.245 40.000 23.77 2.58 45.56 3.27
2759 3509 5.427378 TGCAACAATAGCTAGTAGCATTCA 58.573 37.500 23.77 11.69 45.56 2.57
2762 3512 6.093219 GCATATGCAACAATAGCTAGTAGCAT 59.907 38.462 23.77 22.62 41.86 3.79
2763 3513 5.409520 GCATATGCAACAATAGCTAGTAGCA 59.590 40.000 23.77 14.60 41.86 3.49
2766 3539 6.524734 ACAGCATATGCAACAATAGCTAGTA 58.475 36.000 28.62 0.00 45.16 1.82
2782 3555 6.699204 CGTTTCAGATCAGAAGTACAGCATAT 59.301 38.462 0.54 0.00 0.00 1.78
2783 3556 6.036470 CGTTTCAGATCAGAAGTACAGCATA 58.964 40.000 0.54 0.00 0.00 3.14
2807 3580 1.470098 AGCCATTGAGTTTCACGATGC 59.530 47.619 0.00 0.00 0.00 3.91
2823 3596 0.179059 TCACTTTGTTGCTCGAGCCA 60.179 50.000 33.23 21.55 41.18 4.75
2824 3597 0.514691 CTCACTTTGTTGCTCGAGCC 59.485 55.000 33.23 19.84 41.18 4.70
2825 3598 1.221414 ACTCACTTTGTTGCTCGAGC 58.779 50.000 30.42 30.42 42.50 5.03
2826 3599 3.902150 TCTACTCACTTTGTTGCTCGAG 58.098 45.455 8.45 8.45 0.00 4.04
2845 5075 5.490139 TCGTCGAGTATAATTTCCGTTCT 57.510 39.130 0.00 0.00 0.00 3.01
2867 5097 4.730949 TGTTTATAACTGGACGCTAGCT 57.269 40.909 13.93 0.00 0.00 3.32
2868 5098 5.789710 TTTGTTTATAACTGGACGCTAGC 57.210 39.130 4.06 4.06 0.00 3.42
2981 5211 1.471851 GGAGGAAGAGAGTTAAGCGGC 60.472 57.143 0.00 0.00 0.00 6.53
3017 5247 4.100084 CAGGGTGGGAGCGCATCA 62.100 66.667 11.47 0.94 0.00 3.07
3336 5566 3.322466 CCCCTCTGCTTCACCGGT 61.322 66.667 0.00 0.00 0.00 5.28
3361 5591 1.717937 GATGCTTCATCGCAACGCT 59.282 52.632 0.00 0.00 44.06 5.07


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

AutoCloner maintained by Alex Coulton.