Multiple sequence alignment - TraesCS7B01G330100

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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 TraesCS7B01G330100 chr7B 100.000 6165 0 0 1 6165 585516153 585509989 0.000000e+00 11385.0
1 TraesCS7B01G330100 chr7B 95.423 1748 66 10 2611 4347 204089119 204087375 0.000000e+00 2772.0
2 TraesCS7B01G330100 chr7B 95.358 1745 68 8 2612 4347 577132847 577131107 0.000000e+00 2761.0
3 TraesCS7B01G330100 chr7B 95.066 1743 71 9 2613 4347 329690327 329688592 0.000000e+00 2728.0
4 TraesCS7B01G330100 chr7B 93.633 1822 98 5 504 2325 585627270 585625467 0.000000e+00 2706.0
5 TraesCS7B01G330100 chr7B 85.392 1992 245 21 661 2613 604101177 604099193 0.000000e+00 2025.0
6 TraesCS7B01G330100 chr7B 92.227 1338 87 11 50 1387 585573484 585572164 0.000000e+00 1879.0
7 TraesCS7B01G330100 chr7B 91.006 1034 82 7 465 1494 585761229 585760203 0.000000e+00 1384.0
8 TraesCS7B01G330100 chr7B 93.103 812 56 0 4347 5158 585579310 585578499 0.000000e+00 1190.0
9 TraesCS7B01G330100 chr7B 87.348 988 98 16 5186 6165 47502504 47501536 0.000000e+00 1107.0
10 TraesCS7B01G330100 chr7B 90.764 812 75 0 4347 5158 604099198 604098387 0.000000e+00 1085.0
11 TraesCS7B01G330100 chr7B 85.986 421 47 5 1 419 585627675 585627265 2.040000e-119 440.0
12 TraesCS7B01G330100 chr7B 84.767 407 45 10 24 425 585629924 585629530 5.790000e-105 392.0
13 TraesCS7B01G330100 chr7B 83.133 415 49 14 24 431 586045260 586044860 5.880000e-95 359.0
14 TraesCS7B01G330100 chr7D 94.956 2617 118 7 1 2613 541967877 541965271 0.000000e+00 4089.0
15 TraesCS7B01G330100 chr7D 90.870 1621 138 8 991 2607 541502442 541500828 0.000000e+00 2165.0
16 TraesCS7B01G330100 chr7D 84.678 1958 256 30 689 2613 556719926 556717980 0.000000e+00 1914.0
17 TraesCS7B01G330100 chr7D 89.814 1453 133 8 1174 2613 542099621 542098171 0.000000e+00 1849.0
18 TraesCS7B01G330100 chr7D 94.581 812 44 0 4347 5158 541965276 541964465 0.000000e+00 1256.0
19 TraesCS7B01G330100 chr7D 92.488 812 57 4 4347 5157 542098176 542097368 0.000000e+00 1158.0
20 TraesCS7B01G330100 chr7D 91.626 812 68 0 4347 5158 556717985 556717174 0.000000e+00 1123.0
21 TraesCS7B01G330100 chr7D 90.390 385 34 3 478 861 542100006 542099624 2.570000e-138 503.0
22 TraesCS7B01G330100 chr7D 84.076 471 60 10 464 932 542008384 542007927 2.040000e-119 440.0
23 TraesCS7B01G330100 chr7D 87.200 375 39 4 1 372 542123463 542123095 9.560000e-113 418.0
24 TraesCS7B01G330100 chr7D 84.438 347 40 7 464 797 541503035 541502690 4.610000e-86 329.0
25 TraesCS7B01G330100 chr1B 95.655 1749 58 10 2612 4347 426517999 426516256 0.000000e+00 2793.0
26 TraesCS7B01G330100 chr1B 95.186 1745 67 11 2612 4347 426537399 426535663 0.000000e+00 2741.0
27 TraesCS7B01G330100 chr1B 91.360 1007 78 5 5159 6165 321879999 321880996 0.000000e+00 1369.0
28 TraesCS7B01G330100 chr1B 90.999 1011 78 8 5162 6165 249514775 249515779 0.000000e+00 1351.0
29 TraesCS7B01G330100 chr6B 95.348 1741 69 6 2614 4347 701958187 701959922 0.000000e+00 2756.0
30 TraesCS7B01G330100 chr6B 95.148 1752 71 10 2606 4347 211776102 211774355 0.000000e+00 2752.0
31 TraesCS7B01G330100 chr6B 90.837 1004 71 8 5162 6165 221406334 221405352 0.000000e+00 1325.0
32 TraesCS7B01G330100 chr6B 90.538 1004 74 6 5162 6165 502314515 502313533 0.000000e+00 1308.0
33 TraesCS7B01G330100 chr6B 89.757 986 90 7 5187 6165 19039565 19038584 0.000000e+00 1251.0
34 TraesCS7B01G330100 chr4B 95.183 1744 71 7 2612 4347 423153352 423155090 0.000000e+00 2743.0
35 TraesCS7B01G330100 chr4B 90.990 1010 68 12 5162 6165 182238962 182237970 0.000000e+00 1339.0
36 TraesCS7B01G330100 chr5B 95.083 1749 67 10 2613 4347 267978756 267980499 0.000000e+00 2736.0
37 TraesCS7B01G330100 chr5B 89.143 1004 96 7 5162 6165 108182721 108181731 0.000000e+00 1238.0
38 TraesCS7B01G330100 chr5B 89.542 1004 65 19 5162 6165 225099884 225098921 0.000000e+00 1236.0
39 TraesCS7B01G330100 chr5B 89.535 946 86 10 5228 6165 461826824 461825884 0.000000e+00 1186.0
40 TraesCS7B01G330100 chr7A 84.813 1982 260 30 663 2611 642327793 642325820 0.000000e+00 1954.0
41 TraesCS7B01G330100 chr7A 91.133 812 72 0 4347 5158 642325823 642325012 0.000000e+00 1101.0
42 TraesCS7B01G330100 chr7A 87.422 803 96 4 4347 5145 735763275 735762474 0.000000e+00 918.0
43 TraesCS7B01G330100 chr7A 90.547 603 52 3 1 603 624851692 624851095 0.000000e+00 793.0
44 TraesCS7B01G330100 chr7A 94.074 405 18 3 50 454 624822163 624821765 1.470000e-170 610.0
45 TraesCS7B01G330100 chr7A 83.777 413 51 9 24 431 624853846 624853445 1.620000e-100 377.0
46 TraesCS7B01G330100 chrUn 84.648 1648 238 9 971 2613 88843052 88844689 0.000000e+00 1628.0
47 TraesCS7B01G330100 chrUn 84.569 1646 242 6 971 2613 88864123 88865759 0.000000e+00 1622.0
48 TraesCS7B01G330100 chrUn 87.920 803 92 4 4347 5145 88865754 88866555 0.000000e+00 941.0
49 TraesCS7B01G330100 chrUn 87.547 803 95 4 4347 5145 365695854 365695053 0.000000e+00 924.0
50 TraesCS7B01G330100 chrUn 85.915 852 117 2 1764 2613 365696699 365695849 0.000000e+00 905.0
51 TraesCS7B01G330100 chr2B 89.683 504 43 5 5668 6165 575140075 575140575 8.720000e-178 634.0
52 TraesCS7B01G330100 chr4A 92.308 39 0 1 435 470 709902979 709902941 1.100000e-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 TraesCS7B01G330100 chr7B 585509989 585516153 6164 True 11385.000000 11385 100.000000 1 6165 1 chr7B.!!$R5 6164
1 TraesCS7B01G330100 chr7B 204087375 204089119 1744 True 2772.000000 2772 95.423000 2611 4347 1 chr7B.!!$R2 1736
2 TraesCS7B01G330100 chr7B 577131107 577132847 1740 True 2761.000000 2761 95.358000 2612 4347 1 chr7B.!!$R4 1735
3 TraesCS7B01G330100 chr7B 329688592 329690327 1735 True 2728.000000 2728 95.066000 2613 4347 1 chr7B.!!$R3 1734
4 TraesCS7B01G330100 chr7B 585572164 585573484 1320 True 1879.000000 1879 92.227000 50 1387 1 chr7B.!!$R6 1337
5 TraesCS7B01G330100 chr7B 604098387 604101177 2790 True 1555.000000 2025 88.078000 661 5158 2 chr7B.!!$R11 4497
6 TraesCS7B01G330100 chr7B 585760203 585761229 1026 True 1384.000000 1384 91.006000 465 1494 1 chr7B.!!$R8 1029
7 TraesCS7B01G330100 chr7B 585578499 585579310 811 True 1190.000000 1190 93.103000 4347 5158 1 chr7B.!!$R7 811
8 TraesCS7B01G330100 chr7B 585625467 585629924 4457 True 1179.333333 2706 88.128667 1 2325 3 chr7B.!!$R10 2324
9 TraesCS7B01G330100 chr7B 47501536 47502504 968 True 1107.000000 1107 87.348000 5186 6165 1 chr7B.!!$R1 979
10 TraesCS7B01G330100 chr7D 541964465 541967877 3412 True 2672.500000 4089 94.768500 1 5158 2 chr7D.!!$R4 5157
11 TraesCS7B01G330100 chr7D 556717174 556719926 2752 True 1518.500000 1914 88.152000 689 5158 2 chr7D.!!$R6 4469
12 TraesCS7B01G330100 chr7D 541500828 541503035 2207 True 1247.000000 2165 87.654000 464 2607 2 chr7D.!!$R3 2143
13 TraesCS7B01G330100 chr7D 542097368 542100006 2638 True 1170.000000 1849 90.897333 478 5157 3 chr7D.!!$R5 4679
14 TraesCS7B01G330100 chr1B 426516256 426517999 1743 True 2793.000000 2793 95.655000 2612 4347 1 chr1B.!!$R1 1735
15 TraesCS7B01G330100 chr1B 426535663 426537399 1736 True 2741.000000 2741 95.186000 2612 4347 1 chr1B.!!$R2 1735
16 TraesCS7B01G330100 chr1B 321879999 321880996 997 False 1369.000000 1369 91.360000 5159 6165 1 chr1B.!!$F2 1006
17 TraesCS7B01G330100 chr1B 249514775 249515779 1004 False 1351.000000 1351 90.999000 5162 6165 1 chr1B.!!$F1 1003
18 TraesCS7B01G330100 chr6B 701958187 701959922 1735 False 2756.000000 2756 95.348000 2614 4347 1 chr6B.!!$F1 1733
19 TraesCS7B01G330100 chr6B 211774355 211776102 1747 True 2752.000000 2752 95.148000 2606 4347 1 chr6B.!!$R2 1741
20 TraesCS7B01G330100 chr6B 221405352 221406334 982 True 1325.000000 1325 90.837000 5162 6165 1 chr6B.!!$R3 1003
21 TraesCS7B01G330100 chr6B 502313533 502314515 982 True 1308.000000 1308 90.538000 5162 6165 1 chr6B.!!$R4 1003
22 TraesCS7B01G330100 chr6B 19038584 19039565 981 True 1251.000000 1251 89.757000 5187 6165 1 chr6B.!!$R1 978
23 TraesCS7B01G330100 chr4B 423153352 423155090 1738 False 2743.000000 2743 95.183000 2612 4347 1 chr4B.!!$F1 1735
24 TraesCS7B01G330100 chr4B 182237970 182238962 992 True 1339.000000 1339 90.990000 5162 6165 1 chr4B.!!$R1 1003
25 TraesCS7B01G330100 chr5B 267978756 267980499 1743 False 2736.000000 2736 95.083000 2613 4347 1 chr5B.!!$F1 1734
26 TraesCS7B01G330100 chr5B 108181731 108182721 990 True 1238.000000 1238 89.143000 5162 6165 1 chr5B.!!$R1 1003
27 TraesCS7B01G330100 chr5B 225098921 225099884 963 True 1236.000000 1236 89.542000 5162 6165 1 chr5B.!!$R2 1003
28 TraesCS7B01G330100 chr5B 461825884 461826824 940 True 1186.000000 1186 89.535000 5228 6165 1 chr5B.!!$R3 937
29 TraesCS7B01G330100 chr7A 642325012 642327793 2781 True 1527.500000 1954 87.973000 663 5158 2 chr7A.!!$R4 4495
30 TraesCS7B01G330100 chr7A 735762474 735763275 801 True 918.000000 918 87.422000 4347 5145 1 chr7A.!!$R2 798
31 TraesCS7B01G330100 chr7A 624851095 624853846 2751 True 585.000000 793 87.162000 1 603 2 chr7A.!!$R3 602
32 TraesCS7B01G330100 chrUn 88843052 88844689 1637 False 1628.000000 1628 84.648000 971 2613 1 chrUn.!!$F1 1642
33 TraesCS7B01G330100 chrUn 88864123 88866555 2432 False 1281.500000 1622 86.244500 971 5145 2 chrUn.!!$F2 4174
34 TraesCS7B01G330100 chrUn 365695053 365696699 1646 True 914.500000 924 86.731000 1764 5145 2 chrUn.!!$R1 3381
35 TraesCS7B01G330100 chr2B 575140075 575140575 500 False 634.000000 634 89.683000 5668 6165 1 chr2B.!!$F1 497

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
707 2989 1.795286 GTGCAAAGACCTCTTCTGACG 59.205 52.381 0.0 0.0 34.61 4.35 F
1454 3914 0.038744 CAGAGCTTTGACCACCCCAT 59.961 55.000 0.0 0.0 0.00 4.00 F
3304 5802 0.254747 CAAGGCCCATTAGTTCCCGA 59.745 55.000 0.0 0.0 0.00 5.14 F
4917 7430 0.524180 GCCGCACATAAGCTTCTTGC 60.524 55.000 0.0 9.5 43.29 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 5090 0.250166 ACTACGTTCCCCAACAGCAC 60.250 55.000 0.00 0.0 32.14 4.40 R
3324 5825 1.072505 GGAGAAAACCGGAGTGCCA 59.927 57.895 9.46 0.0 0.00 4.92 R
5004 7517 0.247460 CTCATCGTCTTGGAGGCACA 59.753 55.000 0.00 0.0 0.00 4.57 R
6014 8564 0.530744 AGCGATCCAAGACGTAAGCA 59.469 50.000 0.00 0.0 45.62 3.91 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
54 2313 5.246307 ACTAGCAACATAGACCACTTTTCC 58.754 41.667 0.00 0.00 0.00 3.13
88 2347 6.884836 TGAACTATGTAGCAGTAGAAGTGAGA 59.115 38.462 0.00 0.00 0.00 3.27
105 2364 8.153550 AGAAGTGAGAGCCGATTATTTATGAAT 58.846 33.333 0.00 0.00 0.00 2.57
177 2438 7.756722 CCAACTGAATATTGGTGAAAATCAGTC 59.243 37.037 6.04 0.00 43.64 3.51
196 2457 6.662755 TCAGTCCTAGTTAACTATCCGGTAA 58.337 40.000 15.57 0.00 0.00 2.85
233 2494 3.510719 TGAATTTAAAGCAGCGCAATCC 58.489 40.909 11.47 0.00 0.00 3.01
261 2522 6.374333 TCTTTTATTTACGGATGAAAGCAGCT 59.626 34.615 0.00 0.00 34.44 4.24
397 2658 6.488769 TGTTAGGTTTCAGTCACTTTCCTA 57.511 37.500 0.00 0.00 0.00 2.94
476 2738 7.065683 GGTACAGAGGTAGTACTTCACTAGTTC 59.934 44.444 14.23 5.64 40.48 3.01
613 2889 3.450457 TCAGTTGGGTGCAAAAAGAACAT 59.550 39.130 0.00 0.00 0.00 2.71
707 2989 1.795286 GTGCAAAGACCTCTTCTGACG 59.205 52.381 0.00 0.00 34.61 4.35
945 3266 5.717178 ACAGTCTCTACATTTCAAGCCTCTA 59.283 40.000 0.00 0.00 0.00 2.43
1128 3580 1.219124 GCTCGTCTCCAGCAATGGA 59.781 57.895 0.00 0.00 36.82 3.41
1340 3800 2.231478 CCGTGATCTGGTCTACACAAGT 59.769 50.000 0.00 0.00 33.56 3.16
1373 3833 4.446371 AGAAATATCACCACTGCTGCTAC 58.554 43.478 0.00 0.00 0.00 3.58
1454 3914 0.038744 CAGAGCTTTGACCACCCCAT 59.961 55.000 0.00 0.00 0.00 4.00
1510 3971 1.462238 AAGGTCACAGGCCTGGAGT 60.462 57.895 35.42 13.49 36.30 3.85
1530 3991 2.857748 GTGCCGTTTTGTTTCTTGGAAG 59.142 45.455 0.00 0.00 0.00 3.46
1673 4138 2.095768 GCAAATACTTCGCTGCACTTCA 60.096 45.455 0.00 0.00 34.87 3.02
1675 4140 4.726416 CAAATACTTCGCTGCACTTCAAT 58.274 39.130 0.00 0.00 0.00 2.57
1797 4262 3.206150 GGTTACTCGCCATGTCATTGAT 58.794 45.455 0.00 0.00 0.00 2.57
1863 4328 5.070823 AGGATTGGGTAATGATCAATGCT 57.929 39.130 0.00 0.00 42.10 3.79
1871 4336 5.105392 GGGTAATGATCAATGCTCAACCAAA 60.105 40.000 0.00 0.00 28.97 3.28
1940 4405 7.390823 TGCACTGATAATAAAGTTCCACACTA 58.609 34.615 0.00 0.00 32.94 2.74
2078 4543 5.296780 CACACACCACAGACAAGTTCTATTT 59.703 40.000 0.00 0.00 31.12 1.40
2276 4752 5.009631 TGACACTACCAATTCAAATGGAGG 58.990 41.667 0.00 0.00 40.56 4.30
2302 4778 7.846644 ACTCTTTATCTTCATCTTTCTGCTG 57.153 36.000 0.00 0.00 0.00 4.41
2409 4889 5.957771 TTGCACTCATCCTCCTACTAATT 57.042 39.130 0.00 0.00 0.00 1.40
2452 4932 8.762645 ACAAGAGATCTGGTCAAATACAGAATA 58.237 33.333 0.00 0.00 45.81 1.75
2512 4992 4.153986 CAATGATCTTCAACGAGCAACAC 58.846 43.478 0.00 0.00 32.53 3.32
2607 5089 2.110901 AGCAGTGAAGAGGCTTGATG 57.889 50.000 0.00 0.00 33.21 3.07
2608 5090 1.093159 GCAGTGAAGAGGCTTGATGG 58.907 55.000 0.00 0.00 0.00 3.51
2609 5091 1.612726 GCAGTGAAGAGGCTTGATGGT 60.613 52.381 0.00 0.00 0.00 3.55
2675 5158 4.070009 GCAAGATCATGGTGATGCATAGA 58.930 43.478 0.00 0.00 37.20 1.98
2753 5236 2.030096 TGACAACGCGGTTGATGTAGTA 60.030 45.455 22.26 4.28 45.28 1.82
2787 5270 0.323633 TCCGACCGATCCAAGTACCA 60.324 55.000 0.00 0.00 0.00 3.25
2915 5401 3.243401 TGACGATGATGATGTTCTACCGG 60.243 47.826 0.00 0.00 0.00 5.28
3176 5665 1.690985 GAAGGAGTGGGAGAGGGGG 60.691 68.421 0.00 0.00 0.00 5.40
3304 5802 0.254747 CAAGGCCCATTAGTTCCCGA 59.745 55.000 0.00 0.00 0.00 5.14
3570 6075 7.618117 TGTAGACATGACCTAGAACTATTTCCA 59.382 37.037 0.00 0.00 31.28 3.53
3757 6262 1.968493 ACCGGCAAGTCTCTTTACTCA 59.032 47.619 0.00 0.00 0.00 3.41
3762 6267 5.168569 CGGCAAGTCTCTTTACTCATTACA 58.831 41.667 0.00 0.00 0.00 2.41
3851 6361 1.182385 GCCCAGAGATACCTCTCCGG 61.182 65.000 0.00 0.00 46.38 5.14
3873 6383 3.557595 GCAATCGGAGTGACAAATCCTAG 59.442 47.826 9.97 0.00 33.12 3.02
3944 6454 7.293535 AGAGCTCCTTTATAATCACCCAGTTAT 59.706 37.037 10.93 0.00 0.00 1.89
4017 6527 8.768955 GTTGCATAATCTCATAGTTGTAGGAAG 58.231 37.037 0.00 0.00 0.00 3.46
4077 6587 4.408182 AACGATCAAGTGCTAGGCTAAT 57.592 40.909 0.00 0.00 0.00 1.73
4116 6626 9.716531 GTCAATCACATCATTCTCCTAATGATA 57.283 33.333 11.71 0.02 43.38 2.15
4195 6705 9.587772 TCTTTGATTAATGAGCTAGTCAAGTAC 57.412 33.333 0.00 0.00 39.19 2.73
4259 6769 7.390440 CACATGTATCATGTTTCCGGGTAATAT 59.610 37.037 11.89 0.00 0.00 1.28
4334 6844 9.965902 AATATCTTTATTATTGCCTCTAGGGTG 57.034 33.333 0.00 0.00 37.43 4.61
4359 6869 4.640771 TTCCTTCAGGTGCTTATCAAGT 57.359 40.909 0.00 0.00 36.34 3.16
4398 6908 3.672808 CTGAAGTGAGCTCAATTGGAGT 58.327 45.455 32.03 9.70 45.88 3.85
4486 6996 9.225201 CTTGTTTATGAATACATGTCAAATCGG 57.775 33.333 0.00 0.00 37.87 4.18
4525 7038 9.421806 CATTTATTTGGAAGCAACTCAATGTTA 57.578 29.630 0.00 0.00 37.07 2.41
4535 7048 7.759489 AGCAACTCAATGTTAAATTGGACTA 57.241 32.000 0.00 0.00 37.07 2.59
4553 7066 5.552371 TGGACTACTAGGTATCAGATAGGCT 59.448 44.000 0.00 0.00 0.00 4.58
4561 7074 5.081032 AGGTATCAGATAGGCTTAGGTGTC 58.919 45.833 0.00 0.00 0.00 3.67
4593 7106 1.134401 GGCCTACTTGCATGACAGCTA 60.134 52.381 6.60 0.00 34.99 3.32
4653 7166 5.536554 AACATACTTCTTGATGCTTCACG 57.463 39.130 1.02 0.52 0.00 4.35
4668 7181 3.716601 CTTCACGCCTTCCAAAAATTGT 58.283 40.909 0.00 0.00 0.00 2.71
4676 7189 5.983118 CGCCTTCCAAAAATTGTAGACTTTT 59.017 36.000 0.00 0.00 0.00 2.27
4731 7244 5.871524 GCAGAGTATTGACAACAATGAGAGA 59.128 40.000 0.00 0.00 44.97 3.10
4750 7263 4.777896 AGAGAAACTACAGGATACCTTGCA 59.222 41.667 0.00 0.00 37.17 4.08
4803 7316 5.625311 CACCAAAAGTCGATGTTTTTAGCTC 59.375 40.000 0.00 0.00 0.00 4.09
4819 7332 1.904771 CTCCGGGATGGTGTTGCTA 59.095 57.895 0.00 0.00 39.52 3.49
4839 7352 9.561069 GTTGCTAGAAATAATATCTGGAAGGAA 57.439 33.333 0.00 0.00 0.00 3.36
4856 7369 2.028930 AGGAAGAACTCATGTCCGTCAC 60.029 50.000 0.00 0.00 35.19 3.67
4861 7374 1.153823 CTCATGTCCGTCACGTCCC 60.154 63.158 0.00 0.00 0.00 4.46
4917 7430 0.524180 GCCGCACATAAGCTTCTTGC 60.524 55.000 0.00 9.50 43.29 4.01
4932 7445 2.820767 CTTGCAGGAGACGTCGGGAC 62.821 65.000 10.46 1.81 0.00 4.46
5000 7513 2.243602 AATTGCTTGCAAGGTTGTGG 57.756 45.000 27.10 1.70 0.00 4.17
5004 7517 0.177836 GCTTGCAAGGTTGTGGGTTT 59.822 50.000 27.10 0.00 0.00 3.27
5062 7575 3.074390 TGGGACATGTGGTTCAGATTCTT 59.926 43.478 1.15 0.00 0.00 2.52
5248 7761 3.561528 GCTTAGGGGTCAAGTAAGCCTTT 60.562 47.826 2.53 0.00 41.83 3.11
5312 7825 9.270640 AGATGTATCAATCTAATCAAGCAAGAC 57.729 33.333 0.00 0.00 35.09 3.01
5396 7909 2.370445 TGCCCTCCTTCTAGCAGCC 61.370 63.158 0.00 0.00 0.00 4.85
5397 7910 2.370445 GCCCTCCTTCTAGCAGCCA 61.370 63.158 0.00 0.00 0.00 4.75
5472 7985 4.069232 CCGTCTCTTCCGCTGCCA 62.069 66.667 0.00 0.00 0.00 4.92
5490 8003 1.837051 AGTCACCTTGTCGCCTCCA 60.837 57.895 0.00 0.00 0.00 3.86
5567 8080 2.442643 CCCCGCCGTCCTTACCTA 60.443 66.667 0.00 0.00 0.00 3.08
5580 8096 3.002038 CTTACCTAGGAGGACGTGTCT 57.998 52.381 17.98 0.00 37.67 3.41
5623 8139 2.722201 GCGGTCCAGGAGATCCGTT 61.722 63.158 16.36 0.00 39.72 4.44
5654 8170 2.666207 GTCATACGGGCCACACCA 59.334 61.111 4.39 0.00 42.05 4.17
5701 8217 2.587753 CGTTGTGGCTGTCGTGGT 60.588 61.111 0.00 0.00 0.00 4.16
5725 8241 2.425592 CACACCAGACGGCCTTCA 59.574 61.111 12.41 0.00 34.57 3.02
5910 8459 3.217743 AGCTCGGCCGCCTAGTAC 61.218 66.667 23.51 3.92 0.00 2.73
5922 8472 1.895866 GCCTAGTACGGGATGCCCTAT 60.896 57.143 11.26 0.00 42.67 2.57
5956 8506 1.945354 GACCTCGTTCCCATCAGCGA 61.945 60.000 0.00 0.00 0.00 4.93
6019 8569 2.126618 CGTCGCCGTCAGTGCTTA 60.127 61.111 0.00 0.00 0.00 3.09
6043 8593 3.845259 GGATCGCTACCCGCCACA 61.845 66.667 0.00 0.00 36.73 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 2313 9.891828 CTACTGCTACATAGTTCATAAGAAGAG 57.108 37.037 0.00 0.00 33.63 2.85
88 2347 5.222130 ACCCCTCATTCATAAATAATCGGCT 60.222 40.000 0.00 0.00 0.00 5.52
105 2364 2.780693 CCTCTCCCTCACCCCTCA 59.219 66.667 0.00 0.00 0.00 3.86
177 2438 7.817962 CCATCATTTACCGGATAGTTAACTAGG 59.182 40.741 19.58 16.95 0.00 3.02
196 2457 5.920193 AAATTCATCCGTCAACCATCATT 57.080 34.783 0.00 0.00 0.00 2.57
233 2494 7.535139 TGCTTTCATCCGTAAATAAAAGAAGG 58.465 34.615 0.00 0.00 0.00 3.46
364 2625 9.101655 GTGACTGAAACCTAACAAAAGTAACTA 57.898 33.333 0.00 0.00 0.00 2.24
379 2640 6.694877 AAGTTTAGGAAAGTGACTGAAACC 57.305 37.500 0.00 0.00 0.00 3.27
613 2889 4.391830 GTGGTTTAATGATGAGAGCGACAA 59.608 41.667 0.00 0.00 0.00 3.18
707 2989 4.765449 GGTTACCCGGCGGACCAC 62.765 72.222 30.79 19.33 34.57 4.16
787 3078 3.010696 GGAAAGGGTGGAGGAAGAAGAAT 59.989 47.826 0.00 0.00 0.00 2.40
945 3266 3.836949 CTTCTTGTTGTTGTTGCTGTGT 58.163 40.909 0.00 0.00 0.00 3.72
1128 3580 3.984200 GAAGCCGAGCGCGTACCTT 62.984 63.158 8.43 8.14 44.76 3.50
1373 3833 3.589988 AGATTTCCACTACTCAACAGCG 58.410 45.455 0.00 0.00 0.00 5.18
1510 3971 2.755655 TCTTCCAAGAAACAAAACGGCA 59.244 40.909 0.00 0.00 30.73 5.69
1530 3991 1.880819 TAGCCGGGTCGACCAAGTTC 61.881 60.000 34.40 19.69 40.22 3.01
1673 4138 1.102978 GTGGCGGGCTGACATTTATT 58.897 50.000 4.49 0.00 38.42 1.40
1675 4140 0.392461 GAGTGGCGGGCTGACATTTA 60.392 55.000 4.49 0.00 38.42 1.40
1797 4262 1.176619 TCTTCGCTTGACCCGAGACA 61.177 55.000 0.00 0.00 35.96 3.41
1863 4328 2.997980 TCACACTGAGCTTTTGGTTGA 58.002 42.857 0.00 0.00 0.00 3.18
1871 4336 2.708051 CATGGACATCACACTGAGCTT 58.292 47.619 0.00 0.00 0.00 3.74
1940 4405 1.985159 TGAAGCCCTCCATACAGTTGT 59.015 47.619 0.00 0.00 0.00 3.32
2045 4510 3.127895 GTCTGTGGTGTGTGTTTTGCTTA 59.872 43.478 0.00 0.00 0.00 3.09
2097 4562 0.545071 CTTTTGGGGCATTCTGGGGT 60.545 55.000 0.00 0.00 0.00 4.95
2276 4752 8.389603 CAGCAGAAAGATGAAGATAAAGAGTTC 58.610 37.037 0.00 0.00 35.00 3.01
2291 4767 6.939163 ACTTTGTACATCTTCAGCAGAAAGAT 59.061 34.615 0.00 0.00 34.16 2.40
2302 4778 9.952341 GTTGTTTTTCAAACTTTGTACATCTTC 57.048 29.630 0.00 0.00 37.81 2.87
2452 4932 7.528996 TGATTCCATCACAAACTTCAGATTT 57.471 32.000 0.00 0.00 33.59 2.17
2534 5015 1.064017 ACAGAACCAAAACTGCCTCCA 60.064 47.619 0.00 0.00 37.61 3.86
2607 5089 0.953960 CTACGTTCCCCAACAGCACC 60.954 60.000 0.00 0.00 32.14 5.01
2608 5090 0.250166 ACTACGTTCCCCAACAGCAC 60.250 55.000 0.00 0.00 32.14 4.40
2609 5091 1.340088 TACTACGTTCCCCAACAGCA 58.660 50.000 0.00 0.00 32.14 4.41
2675 5158 1.344763 CAACACTCTCCCCTCTCGTTT 59.655 52.381 0.00 0.00 0.00 3.60
2753 5236 1.396301 GTCGGATCGTGAAGACGTACT 59.604 52.381 0.00 0.00 46.20 2.73
2979 5465 1.666553 CGTTCCTTAGCCGTGTGCA 60.667 57.895 0.00 0.00 44.83 4.57
3259 5754 2.487265 GCCCTAGTGGAGAGAGAGAGAG 60.487 59.091 1.75 0.00 35.39 3.20
3260 5755 1.493022 GCCCTAGTGGAGAGAGAGAGA 59.507 57.143 1.75 0.00 35.39 3.10
3324 5825 1.072505 GGAGAAAACCGGAGTGCCA 59.927 57.895 9.46 0.00 0.00 4.92
3433 5935 1.115467 GAGTCCCGGATGTGATCACT 58.885 55.000 25.55 11.93 0.00 3.41
3497 6000 4.434989 GCATGCTTAACGTTACGATGACAA 60.435 41.667 13.03 0.00 0.00 3.18
3570 6075 4.080526 AGGTTCCGCTATTGGTTATTGACT 60.081 41.667 0.00 0.00 0.00 3.41
3757 6262 7.877612 TGAGTACGGAATGATGCATTATGTAAT 59.122 33.333 4.51 2.81 33.90 1.89
3762 6267 7.065085 GCTAATGAGTACGGAATGATGCATTAT 59.935 37.037 0.00 0.00 33.90 1.28
3851 6361 2.359900 AGGATTTGTCACTCCGATTGC 58.640 47.619 0.00 0.00 36.62 3.56
3873 6383 2.602878 TGAGTTGGCGTATTTCGAGAC 58.397 47.619 0.00 0.00 42.86 3.36
3944 6454 1.666700 GTGCTACCAAACGTCACAACA 59.333 47.619 0.00 0.00 0.00 3.33
4017 6527 9.846248 ATTGCTTTCTTCATGACTTATACAAAC 57.154 29.630 0.00 0.00 0.00 2.93
4077 6587 3.181435 TGTGATTGACTTGACCCATTCCA 60.181 43.478 0.00 0.00 0.00 3.53
4116 6626 6.376864 TGTTGTCATTTGATTAACGGGATCAT 59.623 34.615 0.00 0.00 33.82 2.45
4195 6705 4.507710 ACATAATGTCACTAGTGTGCCTG 58.492 43.478 21.99 14.56 43.49 4.85
4312 6822 6.824958 ACACCCTAGAGGCAATAATAAAGA 57.175 37.500 0.00 0.00 40.58 2.52
4333 6843 6.061022 TGATAAGCACCTGAAGGAAATACA 57.939 37.500 2.62 0.00 38.94 2.29
4334 6844 6.599638 ACTTGATAAGCACCTGAAGGAAATAC 59.400 38.462 2.62 0.00 38.94 1.89
4359 6869 5.411831 TTCAGCTCTGAATTGCTTCTCTA 57.588 39.130 8.14 0.00 43.90 2.43
4398 6908 7.517614 TTAACTAAATTGATGTGCTGGACAA 57.482 32.000 5.98 0.00 38.36 3.18
4486 6996 7.630242 TCCAAATAAATGGACATCAAGAGAC 57.370 36.000 0.00 0.00 44.52 3.36
4525 7038 9.315363 CCTATCTGATACCTAGTAGTCCAATTT 57.685 37.037 0.00 0.00 0.00 1.82
4535 7048 6.183361 ACACCTAAGCCTATCTGATACCTAGT 60.183 42.308 0.00 0.00 0.00 2.57
4553 7066 1.053424 AACCCTCTTGCGACACCTAA 58.947 50.000 0.00 0.00 0.00 2.69
4561 7074 1.745489 GTAGGCCAACCCTCTTGCG 60.745 63.158 5.01 0.00 44.96 4.85
4593 7106 1.957177 AGTGTATGATGCGGTCTCGAT 59.043 47.619 0.00 0.00 39.00 3.59
4653 7166 7.177498 CAAAAGTCTACAATTTTTGGAAGGC 57.823 36.000 1.98 0.00 39.57 4.35
4668 7181 3.766545 AGCTTTGCCATCCAAAAGTCTA 58.233 40.909 0.00 0.00 42.51 2.59
4676 7189 3.168035 TCCTAAAAGCTTTGCCATCCA 57.832 42.857 13.54 0.00 0.00 3.41
4731 7244 3.587506 AGGTGCAAGGTATCCTGTAGTTT 59.412 43.478 0.00 0.00 32.13 2.66
4750 7263 1.073284 ACACCGGTAAGCAATTCAGGT 59.927 47.619 6.87 0.00 0.00 4.00
4758 7271 3.514706 TGTAATAGGAACACCGGTAAGCA 59.485 43.478 6.87 0.00 0.00 3.91
4803 7316 0.251916 TTCTAGCAACACCATCCCGG 59.748 55.000 0.00 0.00 42.50 5.73
4839 7352 0.959553 ACGTGACGGACATGAGTTCT 59.040 50.000 10.66 0.00 38.72 3.01
4861 7374 1.968017 ATCAGTGTTGCCACCGCTG 60.968 57.895 0.00 0.00 42.88 5.18
4917 7430 0.388649 CAAAGTCCCGACGTCTCCTG 60.389 60.000 14.70 0.00 36.20 3.86
4932 7445 5.295292 CCATGTAGCTTGTGATCTACCAAAG 59.705 44.000 0.00 0.00 35.50 2.77
4969 7482 2.919229 GCAAGCAATTTCAACCTCATCG 59.081 45.455 0.00 0.00 0.00 3.84
5000 7513 0.534203 TCGTCTTGGAGGCACAAACC 60.534 55.000 0.00 0.00 0.00 3.27
5004 7517 0.247460 CTCATCGTCTTGGAGGCACA 59.753 55.000 0.00 0.00 0.00 4.57
5047 7560 3.754965 CCCTTCAAGAATCTGAACCACA 58.245 45.455 0.00 0.00 32.00 4.17
5062 7575 3.173151 TGTGATCTCAACTAGCCCTTCA 58.827 45.455 0.00 0.00 0.00 3.02
5160 7673 6.324512 TCATTAGGCCCATTACGTACTCTAAA 59.675 38.462 0.00 0.00 0.00 1.85
5378 7891 2.370445 GGCTGCTAGAAGGAGGGCA 61.370 63.158 0.00 0.00 33.92 5.36
5396 7909 7.012704 AGCTAGCTGATACCAAATTGTTATGTG 59.987 37.037 18.57 0.00 0.00 3.21
5397 7910 7.056635 AGCTAGCTGATACCAAATTGTTATGT 58.943 34.615 18.57 0.00 0.00 2.29
5562 8075 1.064906 CCAGACACGTCCTCCTAGGTA 60.065 57.143 9.08 0.00 36.53 3.08
5567 8080 2.283966 CCCCAGACACGTCCTCCT 60.284 66.667 0.00 0.00 0.00 3.69
5623 8139 0.693622 TATGACCCGGCCAAGAACAA 59.306 50.000 2.24 0.00 0.00 2.83
5701 8217 4.063967 CGTCTGGTGTGGCGGCTA 62.064 66.667 11.43 0.00 0.00 3.93
5746 8262 2.543802 CGATGGATGGCAGCTGCTG 61.544 63.158 35.82 24.80 41.70 4.41
5747 8263 2.203167 CGATGGATGGCAGCTGCT 60.203 61.111 35.82 19.70 41.70 4.24
5748 8264 3.962421 GCGATGGATGGCAGCTGC 61.962 66.667 30.88 30.88 41.14 5.25
5778 8294 2.203669 TGCCATTGCAGCCAAGGT 60.204 55.556 0.00 0.00 44.23 3.50
5922 8472 4.034258 GTCGTCGCACTCCCGTCA 62.034 66.667 0.00 0.00 0.00 4.35
6013 8563 0.645868 GCGATCCAAGACGTAAGCAC 59.354 55.000 0.00 0.00 45.62 4.40
6014 8564 0.530744 AGCGATCCAAGACGTAAGCA 59.469 50.000 0.00 0.00 45.62 3.91
6019 8569 1.814527 GGGTAGCGATCCAAGACGT 59.185 57.895 0.00 0.00 0.00 4.34
6109 8659 2.353839 CAGCTGCAAACCACGCAC 60.354 61.111 0.00 0.00 35.08 5.34


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

AutoCloner maintained by Alex Coulton.