Multiple sequence alignment - TraesCS5A01G210300

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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 TraesCS5A01G210300 chr5A 100.000 4560 0 0 1 4560 423743857 423748416 0.000000e+00 8421.0
1 TraesCS5A01G210300 chr5A 84.653 1629 181 37 1959 3557 423681179 423682768 0.000000e+00 1559.0
2 TraesCS5A01G210300 chr5A 89.781 685 47 18 1122 1799 423680408 423681076 0.000000e+00 856.0
3 TraesCS5A01G210300 chr5A 79.466 599 97 19 3804 4385 121257074 121256485 7.110000e-108 401.0
4 TraesCS5A01G210300 chr5A 92.527 281 20 1 1236 1515 430508317 430508037 7.110000e-108 401.0
5 TraesCS5A01G210300 chr5A 88.710 62 5 2 1799 1859 423681092 423681152 1.760000e-09 75.0
6 TraesCS5A01G210300 chr5B 90.323 2883 177 38 955 3797 377843478 377846298 0.000000e+00 3685.0
7 TraesCS5A01G210300 chr5B 84.031 2605 265 77 1122 3645 377698587 377701121 0.000000e+00 2366.0
8 TraesCS5A01G210300 chr5B 80.857 700 130 3 2641 3338 378069970 378070667 8.630000e-152 547.0
9 TraesCS5A01G210300 chr5B 81.599 663 72 31 1119 1754 378510562 378511201 1.890000e-138 503.0
10 TraesCS5A01G210300 chr5B 84.512 523 60 13 1236 1754 377978340 377978845 8.810000e-137 497.0
11 TraesCS5A01G210300 chr5B 84.030 526 70 13 1236 1754 378068455 378068973 1.140000e-135 494.0
12 TraesCS5A01G210300 chr5B 90.877 285 20 3 1 279 680235127 680234843 1.200000e-100 377.0
13 TraesCS5A01G210300 chr5B 87.273 220 24 3 1959 2178 378511551 378511766 9.800000e-62 248.0
14 TraesCS5A01G210300 chr5B 84.729 203 25 5 1959 2159 378069298 378069496 1.000000e-46 198.0
15 TraesCS5A01G210300 chr5D 85.448 2467 248 59 1122 3542 325422710 325425111 0.000000e+00 2464.0
16 TraesCS5A01G210300 chr5D 85.444 529 57 15 1236 1754 326118243 326118761 2.420000e-147 532.0
17 TraesCS5A01G210300 chr5D 91.815 281 22 1 1236 1515 325663796 325664076 1.540000e-104 390.0
18 TraesCS5A01G210300 chr5D 86.818 220 25 3 1959 2178 326119111 326119326 4.560000e-60 243.0
19 TraesCS5A01G210300 chr5D 93.750 144 7 2 955 1098 325462442 325462583 9.940000e-52 215.0
20 TraesCS5A01G210300 chr5D 83.333 222 30 6 1959 2178 325664562 325664778 1.000000e-46 198.0
21 TraesCS5A01G210300 chr5D 91.034 145 13 0 1610 1754 325664136 325664280 3.600000e-46 196.0
22 TraesCS5A01G210300 chr5D 88.961 154 17 0 1601 1754 325647300 325647453 1.670000e-44 191.0
23 TraesCS5A01G210300 chr5D 85.976 164 22 1 2015 2178 325647681 325647843 1.690000e-39 174.0
24 TraesCS5A01G210300 chr6A 100.000 968 0 0 1 968 440257193 440256226 0.000000e+00 1788.0
25 TraesCS5A01G210300 chr6A 81.210 628 113 5 3804 4427 135265708 135265082 6.810000e-138 501.0
26 TraesCS5A01G210300 chr2D 100.000 968 0 0 1 968 2354266 2355233 0.000000e+00 1788.0
27 TraesCS5A01G210300 chr2D 100.000 968 0 0 1 968 608746969 608747936 0.000000e+00 1788.0
28 TraesCS5A01G210300 chr2D 93.693 761 44 3 3804 4560 554560677 554561437 0.000000e+00 1136.0
29 TraesCS5A01G210300 chr6D 99.897 970 1 0 1 970 334239783 334240752 0.000000e+00 1786.0
30 TraesCS5A01G210300 chr6B 99.897 969 1 0 1 969 696415735 696414767 0.000000e+00 1784.0
31 TraesCS5A01G210300 chr4A 99.693 976 2 1 1 976 351577999 351577025 0.000000e+00 1784.0
32 TraesCS5A01G210300 chr4A 94.294 333 17 2 1 331 630042926 630043258 4.070000e-140 508.0
33 TraesCS5A01G210300 chr3D 86.911 764 93 4 3804 4560 43772838 43772075 0.000000e+00 850.0
34 TraesCS5A01G210300 chr2A 80.311 579 98 13 3803 4374 208114698 208115267 1.520000e-114 424.0
35 TraesCS5A01G210300 chr7A 89.076 238 25 1 732 968 537496625 537496388 1.240000e-75 294.0
36 TraesCS5A01G210300 chr7A 77.368 190 39 4 4036 4222 274504223 274504411 4.820000e-20 110.0
37 TraesCS5A01G210300 chr1A 86.275 51 5 1 4450 4500 558077735 558077783 2.000000e-03 54.7


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 TraesCS5A01G210300 chr5A 423743857 423748416 4559 False 8421.000000 8421 100.000000 1 4560 1 chr5A.!!$F1 4559
1 TraesCS5A01G210300 chr5A 423680408 423682768 2360 False 830.000000 1559 87.714667 1122 3557 3 chr5A.!!$F2 2435
2 TraesCS5A01G210300 chr5A 121256485 121257074 589 True 401.000000 401 79.466000 3804 4385 1 chr5A.!!$R1 581
3 TraesCS5A01G210300 chr5B 377843478 377846298 2820 False 3685.000000 3685 90.323000 955 3797 1 chr5B.!!$F2 2842
4 TraesCS5A01G210300 chr5B 377698587 377701121 2534 False 2366.000000 2366 84.031000 1122 3645 1 chr5B.!!$F1 2523
5 TraesCS5A01G210300 chr5B 377978340 377978845 505 False 497.000000 497 84.512000 1236 1754 1 chr5B.!!$F3 518
6 TraesCS5A01G210300 chr5B 378068455 378070667 2212 False 413.000000 547 83.205333 1236 3338 3 chr5B.!!$F4 2102
7 TraesCS5A01G210300 chr5B 378510562 378511766 1204 False 375.500000 503 84.436000 1119 2178 2 chr5B.!!$F5 1059
8 TraesCS5A01G210300 chr5D 325422710 325425111 2401 False 2464.000000 2464 85.448000 1122 3542 1 chr5D.!!$F1 2420
9 TraesCS5A01G210300 chr5D 326118243 326119326 1083 False 387.500000 532 86.131000 1236 2178 2 chr5D.!!$F5 942
10 TraesCS5A01G210300 chr5D 325663796 325664778 982 False 261.333333 390 88.727333 1236 2178 3 chr5D.!!$F4 942
11 TraesCS5A01G210300 chr6A 440256226 440257193 967 True 1788.000000 1788 100.000000 1 968 1 chr6A.!!$R2 967
12 TraesCS5A01G210300 chr6A 135265082 135265708 626 True 501.000000 501 81.210000 3804 4427 1 chr6A.!!$R1 623
13 TraesCS5A01G210300 chr2D 2354266 2355233 967 False 1788.000000 1788 100.000000 1 968 1 chr2D.!!$F1 967
14 TraesCS5A01G210300 chr2D 608746969 608747936 967 False 1788.000000 1788 100.000000 1 968 1 chr2D.!!$F3 967
15 TraesCS5A01G210300 chr2D 554560677 554561437 760 False 1136.000000 1136 93.693000 3804 4560 1 chr2D.!!$F2 756
16 TraesCS5A01G210300 chr6D 334239783 334240752 969 False 1786.000000 1786 99.897000 1 970 1 chr6D.!!$F1 969
17 TraesCS5A01G210300 chr6B 696414767 696415735 968 True 1784.000000 1784 99.897000 1 969 1 chr6B.!!$R1 968
18 TraesCS5A01G210300 chr4A 351577025 351577999 974 True 1784.000000 1784 99.693000 1 976 1 chr4A.!!$R1 975
19 TraesCS5A01G210300 chr3D 43772075 43772838 763 True 850.000000 850 86.911000 3804 4560 1 chr3D.!!$R1 756
20 TraesCS5A01G210300 chr2A 208114698 208115267 569 False 424.000000 424 80.311000 3803 4374 1 chr2A.!!$F1 571

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
998 999 0.248843 CCAGCCTCTCAGGTCTCAAC 59.751 60.0 0.00 0.00 37.8 3.18 F
1078 1079 1.026718 CACAGCTCCCGGGAACATTC 61.027 60.0 26.68 11.16 0.0 2.67 F
2311 2535 0.108585 TCCAAGTTCCAGGCTGACAC 59.891 55.0 17.94 11.89 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2281 2505 0.038310 GAACTTGGAAGGGACCCAGG 59.962 60.0 14.60 0.00 36.89 4.45 R
2601 2849 0.320374 TAGGTGAAACGTCTGGCCAG 59.680 55.0 27.87 27.87 38.12 4.85 R
4105 4396 0.458543 CCGTCGTCTTCATCAGTGGG 60.459 60.0 0.00 0.00 0.00 4.61 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
998 999 0.248843 CCAGCCTCTCAGGTCTCAAC 59.751 60.000 0.00 0.00 37.80 3.18
1007 1008 2.491693 CTCAGGTCTCAACTGTCTCCTC 59.508 54.545 0.00 0.00 37.25 3.71
1008 1009 2.158460 TCAGGTCTCAACTGTCTCCTCA 60.158 50.000 0.00 0.00 37.25 3.86
1009 1010 2.230992 CAGGTCTCAACTGTCTCCTCAG 59.769 54.545 0.00 0.00 40.80 3.35
1010 1011 1.548269 GGTCTCAACTGTCTCCTCAGG 59.452 57.143 0.00 0.00 39.48 3.86
1036 1037 4.755629 GGTCTCACCTTTCTCCTTAAACAC 59.244 45.833 0.00 0.00 34.73 3.32
1041 1042 4.642885 CACCTTTCTCCTTAAACACCACAA 59.357 41.667 0.00 0.00 0.00 3.33
1042 1043 4.643334 ACCTTTCTCCTTAAACACCACAAC 59.357 41.667 0.00 0.00 0.00 3.32
1043 1044 4.261031 CCTTTCTCCTTAAACACCACAACG 60.261 45.833 0.00 0.00 0.00 4.10
1044 1045 2.215196 TCTCCTTAAACACCACAACGC 58.785 47.619 0.00 0.00 0.00 4.84
1045 1046 1.944024 CTCCTTAAACACCACAACGCA 59.056 47.619 0.00 0.00 0.00 5.24
1074 1075 2.670148 ATCCACAGCTCCCGGGAAC 61.670 63.158 26.68 21.56 32.25 3.62
1078 1079 1.026718 CACAGCTCCCGGGAACATTC 61.027 60.000 26.68 11.16 0.00 2.67
1079 1080 1.452108 CAGCTCCCGGGAACATTCC 60.452 63.158 26.68 8.61 46.82 3.01
1315 1337 2.954753 GAACCTGCACGCCTTCACG 61.955 63.158 0.00 0.00 39.50 4.35
1515 1537 1.227943 TGGTGAGTGCCAACAGAGC 60.228 57.895 0.00 0.00 37.61 4.09
1564 1589 4.335315 GGTCGATCAAATGCTTGGTGATTA 59.665 41.667 0.00 0.00 32.18 1.75
1607 1645 5.003402 CGACGGAATATTTTGCATGTTGTTC 59.997 40.000 0.00 0.00 0.00 3.18
1661 1699 2.033424 GCACAAGAACCTGGTGAAACTC 59.967 50.000 0.00 0.00 37.60 3.01
1760 1861 2.260844 TCAAAGGTGAGTTGCTGAGG 57.739 50.000 0.00 0.00 0.00 3.86
1816 1948 3.023946 AGTACATGAGCGATGATCTGC 57.976 47.619 0.00 1.93 35.80 4.26
1818 1950 2.616634 ACATGAGCGATGATCTGCTT 57.383 45.000 11.75 0.00 42.60 3.91
1854 1996 7.382488 GCCTTTATTCTCTGTTTCCTTTTTGTC 59.618 37.037 0.00 0.00 0.00 3.18
1956 2172 3.320541 TGGTGCAAACTTATTGGTCTTGG 59.679 43.478 0.00 0.00 0.00 3.61
1964 2180 5.304686 ACTTATTGGTCTTGGTCTGTTGA 57.695 39.130 0.00 0.00 0.00 3.18
1973 2189 1.225855 TGGTCTGTTGATCAACGTGC 58.774 50.000 28.55 20.68 43.94 5.34
2012 2229 7.118496 CTGAAATATCCTACTGTCTTCAGGT 57.882 40.000 0.00 0.00 45.14 4.00
2013 2230 8.239038 CTGAAATATCCTACTGTCTTCAGGTA 57.761 38.462 0.00 0.00 45.14 3.08
2030 2247 3.323115 CAGGTAGCATCAATGGCTCTCTA 59.677 47.826 0.00 0.00 42.62 2.43
2167 2384 1.153329 CGGTAAGCCACCCGCAATA 60.153 57.895 0.00 0.00 45.52 1.90
2251 2475 5.126061 GTCACCTGCCATGACTGAATAATTT 59.874 40.000 0.00 0.00 42.68 1.82
2254 2478 5.359009 ACCTGCCATGACTGAATAATTTCTG 59.641 40.000 0.00 0.00 36.98 3.02
2255 2479 5.359009 CCTGCCATGACTGAATAATTTCTGT 59.641 40.000 0.00 0.00 44.01 3.41
2257 2481 7.067372 CCTGCCATGACTGAATAATTTCTGTAA 59.933 37.037 0.00 0.00 42.15 2.41
2307 2531 0.610232 CCCTTCCAAGTTCCAGGCTG 60.610 60.000 7.75 7.75 0.00 4.85
2308 2532 0.401738 CCTTCCAAGTTCCAGGCTGA 59.598 55.000 17.94 0.00 0.00 4.26
2309 2533 1.528129 CTTCCAAGTTCCAGGCTGAC 58.472 55.000 17.94 7.20 0.00 3.51
2310 2534 0.843309 TTCCAAGTTCCAGGCTGACA 59.157 50.000 17.94 0.00 0.00 3.58
2311 2535 0.108585 TCCAAGTTCCAGGCTGACAC 59.891 55.000 17.94 11.89 0.00 3.67
2312 2536 0.179020 CCAAGTTCCAGGCTGACACA 60.179 55.000 17.94 0.00 0.00 3.72
2313 2537 1.679139 CAAGTTCCAGGCTGACACAA 58.321 50.000 17.94 0.00 0.00 3.33
2314 2538 2.023673 CAAGTTCCAGGCTGACACAAA 58.976 47.619 17.94 0.00 0.00 2.83
2315 2539 2.624838 CAAGTTCCAGGCTGACACAAAT 59.375 45.455 17.94 0.00 0.00 2.32
2316 2540 2.949447 AGTTCCAGGCTGACACAAATT 58.051 42.857 17.94 0.00 0.00 1.82
2317 2541 4.098914 AGTTCCAGGCTGACACAAATTA 57.901 40.909 17.94 0.00 0.00 1.40
2318 2542 4.666512 AGTTCCAGGCTGACACAAATTAT 58.333 39.130 17.94 0.00 0.00 1.28
2319 2543 5.079643 AGTTCCAGGCTGACACAAATTATT 58.920 37.500 17.94 0.00 0.00 1.40
2320 2544 5.539955 AGTTCCAGGCTGACACAAATTATTT 59.460 36.000 17.94 0.00 0.00 1.40
2321 2545 6.041979 AGTTCCAGGCTGACACAAATTATTTT 59.958 34.615 17.94 0.00 0.00 1.82
2425 2651 1.067416 GACAGCACTGACGTGACCA 59.933 57.895 4.31 0.00 43.97 4.02
2431 2674 1.000607 GCACTGACGTGACCAGAACTA 60.001 52.381 9.51 0.00 43.97 2.24
2451 2694 4.721776 ACTAGGAAGGTTCTTGGATGCATA 59.278 41.667 0.00 0.00 0.00 3.14
2452 2695 4.803329 AGGAAGGTTCTTGGATGCATAT 57.197 40.909 0.00 0.00 0.00 1.78
2456 2699 4.096190 AGGTTCTTGGATGCATATCAGG 57.904 45.455 0.00 2.09 34.90 3.86
2477 2720 3.307339 GGCTTGAGAAATCCAGTCTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2492 2735 0.766288 TGTCTGACCCCCACATCACA 60.766 55.000 5.17 0.00 0.00 3.58
2545 2791 8.511321 CACTGTCCAGCTTACACAAATAAATAA 58.489 33.333 0.00 0.00 0.00 1.40
2603 2851 8.455903 TCTTATTTCATCTTATCTTTGGGCTG 57.544 34.615 0.00 0.00 0.00 4.85
2638 2898 8.754991 TTCACCTAACCAAATTTGAACTTCTA 57.245 30.769 19.86 1.28 0.00 2.10
2761 3021 2.488355 TACGCAGCGCCTGAGTAC 59.512 61.111 16.61 0.00 42.25 2.73
2950 3210 1.030488 TGATGGACTCGACCCTCGAC 61.030 60.000 1.34 0.00 44.82 4.20
3025 3285 0.260230 TGAGCCAAAACCCCAAGTCA 59.740 50.000 0.00 0.00 0.00 3.41
3124 3384 3.010420 TGTGTTCACCATTGTCGTTGAA 58.990 40.909 0.37 0.00 0.00 2.69
3163 3423 1.814429 TGAAGGTGGAGGTTGAGGAA 58.186 50.000 0.00 0.00 0.00 3.36
3253 3513 1.077086 TGGCATTGTGCTCCATGGT 59.923 52.632 12.58 0.00 44.28 3.55
3257 3517 0.813184 CATTGTGCTCCATGGTGACC 59.187 55.000 17.98 7.05 0.00 4.02
3353 3617 5.104652 GGGGCTTAGTGGTTCAAGAGTATAA 60.105 44.000 0.00 0.00 0.00 0.98
3361 3625 6.555360 AGTGGTTCAAGAGTATAATAGGGGAG 59.445 42.308 0.00 0.00 0.00 4.30
3444 3708 5.202640 GGTGTCACATCGTTTGTTTAGAAC 58.797 41.667 5.12 0.00 36.00 3.01
3451 3715 5.007332 ACATCGTTTGTTTAGAACTGTGGAC 59.993 40.000 0.00 0.00 33.74 4.02
3456 3722 3.191669 TGTTTAGAACTGTGGACGTGTG 58.808 45.455 0.00 0.00 0.00 3.82
3486 3752 5.643379 TTTCTTCATGATAGTGGCAAACC 57.357 39.130 0.00 0.00 0.00 3.27
3514 3780 2.495669 AGTTTGGTTTGGATTATGGCCG 59.504 45.455 0.00 0.00 0.00 6.13
3600 3879 8.356657 CACTTTCAAATAGTTGGTCCAACATTA 58.643 33.333 31.59 18.95 45.66 1.90
3621 3900 8.017373 ACATTATGAATCGTTGACAAGTGAAAG 58.983 33.333 0.00 0.00 0.00 2.62
3622 3901 7.490962 TTATGAATCGTTGACAAGTGAAAGT 57.509 32.000 0.00 0.00 0.00 2.66
3623 3902 5.155509 TGAATCGTTGACAAGTGAAAGTG 57.844 39.130 0.00 0.00 0.00 3.16
3624 3903 4.873259 TGAATCGTTGACAAGTGAAAGTGA 59.127 37.500 0.00 0.00 0.00 3.41
3627 3906 5.216566 TCGTTGACAAGTGAAAGTGAAAG 57.783 39.130 0.00 0.00 0.00 2.62
3628 3907 4.693566 TCGTTGACAAGTGAAAGTGAAAGT 59.306 37.500 0.00 0.00 0.00 2.66
3629 3908 4.788100 CGTTGACAAGTGAAAGTGAAAGTG 59.212 41.667 0.00 0.00 0.00 3.16
3630 3909 5.390461 CGTTGACAAGTGAAAGTGAAAGTGA 60.390 40.000 0.00 0.00 0.00 3.41
3633 3912 6.611381 TGACAAGTGAAAGTGAAAGTGAAAG 58.389 36.000 0.00 0.00 0.00 2.62
3645 3924 6.375455 AGTGAAAGTGAAAGTGAAAGTGACAT 59.625 34.615 0.00 0.00 0.00 3.06
3646 3925 6.688813 GTGAAAGTGAAAGTGAAAGTGACATC 59.311 38.462 0.00 0.00 0.00 3.06
3647 3926 5.757850 AAGTGAAAGTGAAAGTGACATCC 57.242 39.130 0.00 0.00 0.00 3.51
3649 3928 5.059833 AGTGAAAGTGAAAGTGACATCCTC 58.940 41.667 0.00 0.00 0.00 3.71
3650 3929 4.816385 GTGAAAGTGAAAGTGACATCCTCA 59.184 41.667 0.00 0.00 0.00 3.86
3651 3930 5.049818 GTGAAAGTGAAAGTGACATCCTCAG 60.050 44.000 0.00 0.00 0.00 3.35
3652 3931 4.696479 AAGTGAAAGTGACATCCTCAGT 57.304 40.909 0.00 0.00 33.53 3.41
3653 3932 4.696479 AGTGAAAGTGACATCCTCAGTT 57.304 40.909 0.00 0.00 43.39 3.16
3654 3933 5.808366 AGTGAAAGTGACATCCTCAGTTA 57.192 39.130 0.00 0.00 41.06 2.24
3655 3934 6.174720 AGTGAAAGTGACATCCTCAGTTAA 57.825 37.500 0.00 0.00 41.06 2.01
3656 3935 6.773638 AGTGAAAGTGACATCCTCAGTTAAT 58.226 36.000 0.00 0.00 41.06 1.40
3657 3936 7.227156 AGTGAAAGTGACATCCTCAGTTAATT 58.773 34.615 0.00 0.00 41.06 1.40
3658 3937 7.389053 AGTGAAAGTGACATCCTCAGTTAATTC 59.611 37.037 0.00 0.00 41.06 2.17
3659 3938 6.655003 TGAAAGTGACATCCTCAGTTAATTCC 59.345 38.462 0.00 0.00 41.06 3.01
3660 3939 4.759782 AGTGACATCCTCAGTTAATTCCG 58.240 43.478 0.00 0.00 0.00 4.30
3661 3940 3.871594 GTGACATCCTCAGTTAATTCCGG 59.128 47.826 0.00 0.00 0.00 5.14
3662 3941 2.872858 GACATCCTCAGTTAATTCCGGC 59.127 50.000 0.00 0.00 0.00 6.13
3663 3942 2.222027 CATCCTCAGTTAATTCCGGCC 58.778 52.381 0.00 0.00 0.00 6.13
3664 3943 1.281419 TCCTCAGTTAATTCCGGCCA 58.719 50.000 2.24 0.00 0.00 5.36
3665 3944 1.631388 TCCTCAGTTAATTCCGGCCAA 59.369 47.619 2.24 0.00 0.00 4.52
3666 3945 2.040545 TCCTCAGTTAATTCCGGCCAAA 59.959 45.455 2.24 0.00 0.00 3.28
3667 3946 2.823154 CCTCAGTTAATTCCGGCCAAAA 59.177 45.455 2.24 0.00 0.00 2.44
3668 3947 3.447229 CCTCAGTTAATTCCGGCCAAAAT 59.553 43.478 2.24 0.00 0.00 1.82
3669 3948 4.642885 CCTCAGTTAATTCCGGCCAAAATA 59.357 41.667 2.24 0.00 0.00 1.40
3670 3949 5.126384 CCTCAGTTAATTCCGGCCAAAATAA 59.874 40.000 2.24 0.00 0.00 1.40
3671 3950 6.350612 CCTCAGTTAATTCCGGCCAAAATAAA 60.351 38.462 2.24 0.00 0.00 1.40
3672 3951 7.176589 TCAGTTAATTCCGGCCAAAATAAAT 57.823 32.000 2.24 0.00 0.00 1.40
3673 3952 8.294954 TCAGTTAATTCCGGCCAAAATAAATA 57.705 30.769 2.24 0.00 0.00 1.40
3674 3953 8.750298 TCAGTTAATTCCGGCCAAAATAAATAA 58.250 29.630 2.24 0.00 0.00 1.40
3681 3960 7.419711 TCCGGCCAAAATAAATAAATAACCA 57.580 32.000 2.24 0.00 0.00 3.67
3701 3980 3.567164 CCAGGAGCATATACAAAAGCCTG 59.433 47.826 0.00 0.00 40.92 4.85
3711 3990 7.878127 GCATATACAAAAGCCTGTCTTATCCTA 59.122 37.037 0.00 0.00 33.88 2.94
3712 3991 9.778741 CATATACAAAAGCCTGTCTTATCCTAA 57.221 33.333 0.00 0.00 33.88 2.69
3714 3993 6.374417 ACAAAAGCCTGTCTTATCCTAAGA 57.626 37.500 0.00 0.00 33.88 2.10
3749 4031 6.602179 GCAAAATAATGCAAGAAGAAAACCC 58.398 36.000 0.00 0.00 45.70 4.11
3775 4057 2.559668 ACAAGTTGATGTTGATGGCCTG 59.440 45.455 10.54 0.00 0.00 4.85
3776 4058 2.821378 CAAGTTGATGTTGATGGCCTGA 59.179 45.455 3.32 0.00 0.00 3.86
3777 4059 2.719739 AGTTGATGTTGATGGCCTGAG 58.280 47.619 3.32 0.00 0.00 3.35
3797 4079 7.253422 CCTGAGTTAATGATGTCAATTTGGAC 58.747 38.462 0.00 0.00 38.29 4.02
3798 4080 7.156876 TGAGTTAATGATGTCAATTTGGACC 57.843 36.000 0.00 0.00 36.97 4.46
3799 4081 6.947733 TGAGTTAATGATGTCAATTTGGACCT 59.052 34.615 0.00 0.00 36.97 3.85
3800 4082 7.121168 TGAGTTAATGATGTCAATTTGGACCTC 59.879 37.037 0.00 0.00 36.97 3.85
3801 4083 6.947733 AGTTAATGATGTCAATTTGGACCTCA 59.052 34.615 6.43 6.43 43.38 3.86
3909 4192 3.443099 GTTCTTTTGAGCCAGCTTTGT 57.557 42.857 0.00 0.00 0.00 2.83
3929 4212 0.116342 TCCTCCTAGGTTGTGGAGCA 59.884 55.000 9.08 0.00 46.23 4.26
3938 4221 1.301322 TTGTGGAGCAATCGCGTGA 60.301 52.632 5.77 0.00 45.49 4.35
4105 4396 5.805728 TCTCCTACTCCTTTTGATGTTTCC 58.194 41.667 0.00 0.00 0.00 3.13
4116 4407 3.805066 TGATGTTTCCCCACTGATGAA 57.195 42.857 0.00 0.00 0.00 2.57
4159 4462 2.126071 CCGACTGGCGACGTGATT 60.126 61.111 3.46 0.00 44.57 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
990 991 1.548269 CCTGAGGAGACAGTTGAGACC 59.452 57.143 0.00 0.00 36.30 3.85
998 999 0.614415 AGACCTGCCTGAGGAGACAG 60.614 60.000 0.65 0.00 46.33 3.51
1022 1023 3.065648 GCGTTGTGGTGTTTAAGGAGAAA 59.934 43.478 0.00 0.00 0.00 2.52
1036 1037 4.335647 AGGGGAGCTGCGTTGTGG 62.336 66.667 0.00 0.00 0.00 4.17
1044 1045 2.124403 GTGGATGCAGGGGAGCTG 60.124 66.667 0.00 0.00 34.99 4.24
1045 1046 2.611800 TGTGGATGCAGGGGAGCT 60.612 61.111 0.00 0.00 34.99 4.09
1074 1075 2.353889 CCGAGCAACAGATCAAGGAATG 59.646 50.000 0.00 0.00 0.00 2.67
1078 1079 1.466167 CAACCGAGCAACAGATCAAGG 59.534 52.381 0.00 0.00 0.00 3.61
1079 1080 1.135859 GCAACCGAGCAACAGATCAAG 60.136 52.381 0.00 0.00 0.00 3.02
1207 1211 0.109342 ATCTCGGGCTGCCCTTATTG 59.891 55.000 33.39 18.68 42.67 1.90
1225 1235 1.448540 CAGGTTCTTCAGCGGCGAT 60.449 57.895 12.98 0.00 0.00 4.58
1515 1537 1.660607 CATTCGTGGTCGACAATGAGG 59.339 52.381 18.91 9.43 46.03 3.86
1564 1589 2.360350 CAGTTGGCATCGTGGGCT 60.360 61.111 0.00 0.00 0.00 5.19
1607 1645 3.058639 CGAGAAAGAAAACTTCAGCCTGG 60.059 47.826 0.00 0.00 0.00 4.45
1661 1699 0.945099 TCTCGTAGCAGTAGCCGATG 59.055 55.000 0.00 0.00 43.56 3.84
1746 1784 1.228245 TTGGCCTCAGCAACTCACC 60.228 57.895 3.32 0.00 42.56 4.02
1754 1792 1.032014 TTGAACTTGTTGGCCTCAGC 58.968 50.000 3.32 0.00 38.76 4.26
1760 1861 5.544136 ACAAATTTGTTGAACTTGTTGGC 57.456 34.783 18.13 0.00 38.47 4.52
1812 1944 1.130054 AGGCAGGGAACAGAAGCAGA 61.130 55.000 0.00 0.00 0.00 4.26
1816 1948 4.593956 AGAATAAAGGCAGGGAACAGAAG 58.406 43.478 0.00 0.00 0.00 2.85
1818 1950 3.846588 AGAGAATAAAGGCAGGGAACAGA 59.153 43.478 0.00 0.00 0.00 3.41
1854 1996 3.198635 TGCTCTCTTATCCCCTTGACTTG 59.801 47.826 0.00 0.00 0.00 3.16
1883 2028 2.095853 AGATATGTTCGTTTGCAAGGCG 59.904 45.455 16.15 16.15 0.00 5.52
1922 2076 3.317993 AGTTTGCACCAACAATCCAGTAC 59.682 43.478 4.19 0.00 0.00 2.73
1932 2136 4.584327 AGACCAATAAGTTTGCACCAAC 57.416 40.909 0.00 0.00 0.00 3.77
1956 2172 1.398960 GCTGCACGTTGATCAACAGAC 60.399 52.381 32.06 21.84 41.20 3.51
1964 2180 0.729116 GCTACATGCTGCACGTTGAT 59.271 50.000 13.93 0.00 38.95 2.57
1994 2210 5.125367 TGCTACCTGAAGACAGTAGGATA 57.875 43.478 0.00 0.00 42.05 2.59
2011 2228 3.070159 TGGTAGAGAGCCATTGATGCTAC 59.930 47.826 0.00 0.00 39.69 3.58
2012 2229 3.308401 TGGTAGAGAGCCATTGATGCTA 58.692 45.455 0.00 0.00 39.69 3.49
2013 2230 2.121948 TGGTAGAGAGCCATTGATGCT 58.878 47.619 0.00 0.00 43.03 3.79
2030 2247 1.371467 TCATCCTTGTCACCCATGGT 58.629 50.000 11.73 0.00 39.02 3.55
2037 2254 1.936547 GGCGATCTTCATCCTTGTCAC 59.063 52.381 0.00 0.00 0.00 3.67
2120 2337 3.243839 GCAAGATGTTGGAGGCTTTGAAA 60.244 43.478 4.57 0.00 33.87 2.69
2167 2384 4.405358 TGTTGGAACTGAAAAAGCCTGAAT 59.595 37.500 0.00 0.00 0.00 2.57
2281 2505 0.038310 GAACTTGGAAGGGACCCAGG 59.962 60.000 14.60 0.00 36.89 4.45
2369 2593 9.835389 AGACCAGAAATTTTCAAAATGAAATGA 57.165 25.926 11.53 0.00 44.75 2.57
2431 2674 4.166725 TGATATGCATCCAAGAACCTTCCT 59.833 41.667 0.19 0.00 0.00 3.36
2451 2694 3.522750 AGACTGGATTTCTCAAGCCTGAT 59.477 43.478 3.48 0.00 39.21 2.90
2452 2695 2.909006 AGACTGGATTTCTCAAGCCTGA 59.091 45.455 3.48 0.00 39.21 3.86
2456 2699 3.683822 CAGACAGACTGGATTTCTCAAGC 59.316 47.826 7.51 0.00 42.39 4.01
2477 2720 1.454104 GTGTGTGATGTGGGGGTCA 59.546 57.895 0.00 0.00 0.00 4.02
2511 2757 3.788227 AAGCTGGACAGTGATGGTTAA 57.212 42.857 0.00 0.00 0.00 2.01
2545 2791 6.833416 TGTTTATATGCCTCTAATTTGCAGGT 59.167 34.615 0.00 0.00 38.58 4.00
2598 2846 3.056328 GAAACGTCTGGCCAGCCC 61.056 66.667 28.91 18.95 34.56 5.19
2599 2847 2.281484 TGAAACGTCTGGCCAGCC 60.281 61.111 28.91 17.17 0.00 4.85
2601 2849 0.320374 TAGGTGAAACGTCTGGCCAG 59.680 55.000 27.87 27.87 38.12 4.85
2603 2851 1.154197 GTTAGGTGAAACGTCTGGCC 58.846 55.000 0.00 0.00 38.12 5.36
2692 2952 2.665185 GTTGCGTCGCCTTGAGGT 60.665 61.111 15.88 0.00 37.57 3.85
2746 3006 2.202797 ATGTACTCAGGCGCTGCG 60.203 61.111 19.17 19.17 0.00 5.18
2755 3015 0.464036 GGCCCGTCATGATGTACTCA 59.536 55.000 13.81 0.00 38.53 3.41
2761 3021 1.670811 GTTAAGTGGCCCGTCATGATG 59.329 52.381 8.03 8.03 0.00 3.07
2833 3093 1.447314 GTCCACGGATTGTCGTCCC 60.447 63.158 0.00 0.00 41.86 4.46
2950 3210 0.729116 CCTTGCACGAGTATTGGCAG 59.271 55.000 0.00 0.00 37.59 4.85
3025 3285 1.274650 ACCTCCCTCATGGATGGTCTT 60.275 52.381 0.00 0.00 44.07 3.01
3068 3328 3.942115 GGAAAGAAGTCTTCCATGCCTAC 59.058 47.826 9.04 0.00 34.61 3.18
3124 3384 2.030027 TGTCCATCACCTTGTCCTCT 57.970 50.000 0.00 0.00 0.00 3.69
3163 3423 1.039856 GGTGATGGTGTTGGTGCTTT 58.960 50.000 0.00 0.00 0.00 3.51
3253 3513 2.983030 GCAACATGCCCGTGGTCA 60.983 61.111 0.00 0.00 37.42 4.02
3353 3617 2.982488 CAATCCTAACTGCCTCCCCTAT 59.018 50.000 0.00 0.00 0.00 2.57
3361 3625 6.902771 TCTATCTCTACAATCCTAACTGCC 57.097 41.667 0.00 0.00 0.00 4.85
3444 3708 2.225068 AGAAAGACACACGTCCACAG 57.775 50.000 0.00 0.00 43.73 3.66
3451 3715 6.048073 TCATGAAGAAAAGAAAGACACACG 57.952 37.500 0.00 0.00 0.00 4.49
3456 3722 7.094634 TGCCACTATCATGAAGAAAAGAAAGAC 60.095 37.037 0.00 0.00 0.00 3.01
3486 3752 6.073112 CCATAATCCAAACCAAACTTTTGCAG 60.073 38.462 0.00 0.00 36.86 4.41
3514 3780 5.043248 CACACATCTTTGAACAAGAAACCC 58.957 41.667 0.00 0.00 0.00 4.11
3566 3845 5.691754 CCAACTATTTGAAAGTGAAAGTGGC 59.308 40.000 0.00 0.00 34.24 5.01
3567 3846 6.805713 ACCAACTATTTGAAAGTGAAAGTGG 58.194 36.000 0.00 0.00 34.24 4.00
3600 3879 5.527214 TCACTTTCACTTGTCAACGATTCAT 59.473 36.000 0.00 0.00 0.00 2.57
3621 3900 5.938322 TGTCACTTTCACTTTCACTTTCAC 58.062 37.500 0.00 0.00 0.00 3.18
3622 3901 6.183360 GGATGTCACTTTCACTTTCACTTTCA 60.183 38.462 0.00 0.00 0.00 2.69
3623 3902 6.038714 AGGATGTCACTTTCACTTTCACTTTC 59.961 38.462 0.00 0.00 0.00 2.62
3624 3903 5.888161 AGGATGTCACTTTCACTTTCACTTT 59.112 36.000 0.00 0.00 0.00 2.66
3627 3906 4.816385 TGAGGATGTCACTTTCACTTTCAC 59.184 41.667 0.00 0.00 0.00 3.18
3628 3907 5.034852 TGAGGATGTCACTTTCACTTTCA 57.965 39.130 0.00 0.00 0.00 2.69
3629 3908 5.059833 ACTGAGGATGTCACTTTCACTTTC 58.940 41.667 0.00 0.00 0.00 2.62
3630 3909 5.041191 ACTGAGGATGTCACTTTCACTTT 57.959 39.130 0.00 0.00 0.00 2.66
3633 3912 7.361286 GGAATTAACTGAGGATGTCACTTTCAC 60.361 40.741 0.00 0.00 0.00 3.18
3645 3924 1.281419 TGGCCGGAATTAACTGAGGA 58.719 50.000 5.05 0.00 0.00 3.71
3646 3925 2.122783 TTGGCCGGAATTAACTGAGG 57.877 50.000 5.05 0.00 0.00 3.86
3647 3926 4.718940 ATTTTGGCCGGAATTAACTGAG 57.281 40.909 5.05 0.00 0.00 3.35
3649 3928 8.934507 TTATTTATTTTGGCCGGAATTAACTG 57.065 30.769 5.05 0.00 0.00 3.16
3654 3933 9.332502 GGTTATTTATTTATTTTGGCCGGAATT 57.667 29.630 5.05 0.94 0.00 2.17
3655 3934 8.487028 TGGTTATTTATTTATTTTGGCCGGAAT 58.513 29.630 5.05 3.22 0.00 3.01
3656 3935 7.848128 TGGTTATTTATTTATTTTGGCCGGAA 58.152 30.769 5.05 0.00 0.00 4.30
3657 3936 7.418025 CCTGGTTATTTATTTATTTTGGCCGGA 60.418 37.037 5.05 0.00 0.00 5.14
3658 3937 6.704050 CCTGGTTATTTATTTATTTTGGCCGG 59.296 38.462 0.00 0.00 0.00 6.13
3659 3938 7.493367 TCCTGGTTATTTATTTATTTTGGCCG 58.507 34.615 0.00 0.00 0.00 6.13
3660 3939 7.441157 GCTCCTGGTTATTTATTTATTTTGGCC 59.559 37.037 0.00 0.00 0.00 5.36
3661 3940 7.984617 TGCTCCTGGTTATTTATTTATTTTGGC 59.015 33.333 0.00 0.00 0.00 4.52
3672 3951 8.846211 GCTTTTGTATATGCTCCTGGTTATTTA 58.154 33.333 0.00 0.00 0.00 1.40
3673 3952 7.201911 GGCTTTTGTATATGCTCCTGGTTATTT 60.202 37.037 0.00 0.00 0.00 1.40
3674 3953 6.265422 GGCTTTTGTATATGCTCCTGGTTATT 59.735 38.462 0.00 0.00 0.00 1.40
3679 3958 3.567164 CAGGCTTTTGTATATGCTCCTGG 59.433 47.826 0.00 0.00 36.96 4.45
3681 3960 4.164988 AGACAGGCTTTTGTATATGCTCCT 59.835 41.667 0.00 0.00 0.00 3.69
3689 3968 8.090788 TCTTAGGATAAGACAGGCTTTTGTAT 57.909 34.615 0.00 0.00 38.05 2.29
3727 4006 8.094548 GGTAGGGTTTTCTTCTTGCATTATTTT 58.905 33.333 0.00 0.00 0.00 1.82
3728 4007 7.234577 TGGTAGGGTTTTCTTCTTGCATTATTT 59.765 33.333 0.00 0.00 0.00 1.40
3749 4031 4.379813 GCCATCAACATCAACTTGTGGTAG 60.380 45.833 0.00 0.00 0.00 3.18
3775 4057 7.396540 AGGTCCAAATTGACATCATTAACTC 57.603 36.000 0.00 0.00 36.97 3.01
3776 4058 7.396540 GAGGTCCAAATTGACATCATTAACT 57.603 36.000 5.89 0.00 43.58 2.24
3797 4079 2.048503 GGACCGTTGGACGTGAGG 60.049 66.667 0.00 0.00 40.58 3.86
3798 4080 2.430244 CGGACCGTTGGACGTGAG 60.430 66.667 5.48 0.00 40.58 3.51
3799 4081 3.980989 CCGGACCGTTGGACGTGA 61.981 66.667 13.94 0.00 40.58 4.35
3929 4212 0.888619 TCCTCAGACTTCACGCGATT 59.111 50.000 15.93 0.00 0.00 3.34
3938 4221 4.079970 TGTTCTATCACGTCCTCAGACTT 58.920 43.478 0.00 0.00 41.16 3.01
4105 4396 0.458543 CCGTCGTCTTCATCAGTGGG 60.459 60.000 0.00 0.00 0.00 4.61
4158 4461 2.475172 GGGTCCCCTCCCAAACCAA 61.475 63.158 0.00 0.00 46.30 3.67
4159 4462 2.861974 GGGTCCCCTCCCAAACCA 60.862 66.667 0.00 0.00 46.30 3.67
4192 4496 3.141272 ACCAGTATAGGAGAAGAGGGAGG 59.859 52.174 0.00 0.00 0.00 4.30
4414 4718 0.970937 CTAGAAGGAGACACGGCCCA 60.971 60.000 0.00 0.00 0.00 5.36
4478 4782 3.310860 GAGCGCGGGGGAAGAGAAA 62.311 63.158 8.83 0.00 0.00 2.52
4500 4804 3.766096 GGGGTCCCCAATGCCCAT 61.766 66.667 23.53 0.00 44.65 4.00
4538 4842 2.358737 CACCCGAAGAGGCACCAC 60.359 66.667 0.00 0.00 39.21 4.16


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

AutoCloner maintained by Alex Coulton.