Multiple sequence alignment - TraesCS7B01G312100

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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 TraesCS7B01G312100 chr7B 100.000 3489 0 0 1 3489 557461670 557458182 0.000000e+00 6444
1 TraesCS7B01G312100 chr7B 88.094 1411 144 16 980 2372 557491664 557490260 0.000000e+00 1653
2 TraesCS7B01G312100 chr7B 85.485 1433 190 15 947 2369 528871558 528872982 0.000000e+00 1478
3 TraesCS7B01G312100 chr7B 85.541 1404 178 18 983 2369 557257487 557256092 0.000000e+00 1445
4 TraesCS7B01G312100 chr7B 84.407 1443 183 25 947 2369 73174094 73175514 0.000000e+00 1380
5 TraesCS7B01G312100 chr7D 95.016 1565 64 4 982 2532 523128204 523126640 0.000000e+00 2446
6 TraesCS7B01G312100 chr7D 87.181 1412 155 17 980 2372 523133871 523132467 0.000000e+00 1581
7 TraesCS7B01G312100 chr7D 85.425 1434 190 16 947 2369 500773662 500775087 0.000000e+00 1472
8 TraesCS7B01G312100 chr7D 86.652 1341 162 11 1046 2369 523057020 523055680 0.000000e+00 1469
9 TraesCS7B01G312100 chr7D 85.487 1385 175 20 947 2316 113581454 113582827 0.000000e+00 1421
10 TraesCS7B01G312100 chr7A 85.834 1433 186 14 947 2369 566788158 566789583 0.000000e+00 1506
11 TraesCS7B01G312100 chr7A 86.422 1392 165 17 999 2372 603553298 603551913 0.000000e+00 1502
12 TraesCS7B01G312100 chr7A 86.172 1374 170 8 1012 2369 603331690 603330321 0.000000e+00 1467
13 TraesCS7B01G312100 chr7A 84.699 915 108 16 2587 3489 733620812 733619918 0.000000e+00 885
14 TraesCS7B01G312100 chr6D 95.815 908 28 5 2587 3489 393611741 393610839 0.000000e+00 1458
15 TraesCS7B01G312100 chr1B 90.422 877 49 21 99 952 111966965 111966101 0.000000e+00 1122
16 TraesCS7B01G312100 chr4A 86.902 962 95 21 1 949 625787624 625788567 0.000000e+00 1050
17 TraesCS7B01G312100 chrUn 86.770 907 95 17 18 909 364831339 364832235 0.000000e+00 987
18 TraesCS7B01G312100 chr3A 85.361 970 111 22 6 951 43734782 43733820 0.000000e+00 976
19 TraesCS7B01G312100 chr3A 85.155 970 112 22 6 951 43144772 43143811 0.000000e+00 965
20 TraesCS7B01G312100 chr3A 78.507 777 96 32 2589 3339 723578522 723579253 8.890000e-121 444
21 TraesCS7B01G312100 chr2A 85.667 914 100 17 2587 3488 569013968 569013074 0.000000e+00 933
22 TraesCS7B01G312100 chr2A 83.429 694 89 18 2566 3243 307702558 307703241 3.820000e-174 621
23 TraesCS7B01G312100 chr2A 79.800 599 75 23 2587 3169 706523682 706524250 9.080000e-106 394
24 TraesCS7B01G312100 chr6A 84.401 968 114 25 1 952 18875350 18876296 0.000000e+00 917
25 TraesCS7B01G312100 chr6A 84.167 960 110 30 6 949 144531808 144530875 0.000000e+00 893
26 TraesCS7B01G312100 chr6A 83.817 964 116 33 1 945 587703628 587702686 0.000000e+00 880
27 TraesCS7B01G312100 chr6A 82.886 783 102 18 2587 3351 385811125 385811893 0.000000e+00 675
28 TraesCS7B01G312100 chr6A 82.886 783 100 19 2587 3351 385730584 385731350 0.000000e+00 673
29 TraesCS7B01G312100 chr1A 83.454 967 117 29 1 949 572567008 572566067 0.000000e+00 859
30 TraesCS7B01G312100 chr6B 82.631 783 104 18 2587 3351 426451469 426450701 0.000000e+00 664
31 TraesCS7B01G312100 chr6B 82.565 499 57 18 2868 3351 426769978 426769495 2.510000e-111 412
32 TraesCS7B01G312100 chr3B 82.857 770 85 22 2589 3339 794534119 794534860 0.000000e+00 647
33 TraesCS7B01G312100 chr2B 83.333 630 62 18 2888 3489 364955702 364956316 3.060000e-150 542
34 TraesCS7B01G312100 chr3D 87.140 451 51 5 2587 3032 426839931 426840379 4.020000e-139 505
35 TraesCS7B01G312100 chr1D 83.117 385 42 14 2981 3351 348726967 348727342 2.600000e-86 329


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 TraesCS7B01G312100 chr7B 557458182 557461670 3488 True 6444 6444 100.000 1 3489 1 chr7B.!!$R2 3488
1 TraesCS7B01G312100 chr7B 557490260 557491664 1404 True 1653 1653 88.094 980 2372 1 chr7B.!!$R3 1392
2 TraesCS7B01G312100 chr7B 528871558 528872982 1424 False 1478 1478 85.485 947 2369 1 chr7B.!!$F2 1422
3 TraesCS7B01G312100 chr7B 557256092 557257487 1395 True 1445 1445 85.541 983 2369 1 chr7B.!!$R1 1386
4 TraesCS7B01G312100 chr7B 73174094 73175514 1420 False 1380 1380 84.407 947 2369 1 chr7B.!!$F1 1422
5 TraesCS7B01G312100 chr7D 523126640 523128204 1564 True 2446 2446 95.016 982 2532 1 chr7D.!!$R2 1550
6 TraesCS7B01G312100 chr7D 523132467 523133871 1404 True 1581 1581 87.181 980 2372 1 chr7D.!!$R3 1392
7 TraesCS7B01G312100 chr7D 500773662 500775087 1425 False 1472 1472 85.425 947 2369 1 chr7D.!!$F2 1422
8 TraesCS7B01G312100 chr7D 523055680 523057020 1340 True 1469 1469 86.652 1046 2369 1 chr7D.!!$R1 1323
9 TraesCS7B01G312100 chr7D 113581454 113582827 1373 False 1421 1421 85.487 947 2316 1 chr7D.!!$F1 1369
10 TraesCS7B01G312100 chr7A 566788158 566789583 1425 False 1506 1506 85.834 947 2369 1 chr7A.!!$F1 1422
11 TraesCS7B01G312100 chr7A 603551913 603553298 1385 True 1502 1502 86.422 999 2372 1 chr7A.!!$R2 1373
12 TraesCS7B01G312100 chr7A 603330321 603331690 1369 True 1467 1467 86.172 1012 2369 1 chr7A.!!$R1 1357
13 TraesCS7B01G312100 chr7A 733619918 733620812 894 True 885 885 84.699 2587 3489 1 chr7A.!!$R3 902
14 TraesCS7B01G312100 chr6D 393610839 393611741 902 True 1458 1458 95.815 2587 3489 1 chr6D.!!$R1 902
15 TraesCS7B01G312100 chr1B 111966101 111966965 864 True 1122 1122 90.422 99 952 1 chr1B.!!$R1 853
16 TraesCS7B01G312100 chr4A 625787624 625788567 943 False 1050 1050 86.902 1 949 1 chr4A.!!$F1 948
17 TraesCS7B01G312100 chrUn 364831339 364832235 896 False 987 987 86.770 18 909 1 chrUn.!!$F1 891
18 TraesCS7B01G312100 chr3A 43733820 43734782 962 True 976 976 85.361 6 951 1 chr3A.!!$R2 945
19 TraesCS7B01G312100 chr3A 43143811 43144772 961 True 965 965 85.155 6 951 1 chr3A.!!$R1 945
20 TraesCS7B01G312100 chr3A 723578522 723579253 731 False 444 444 78.507 2589 3339 1 chr3A.!!$F1 750
21 TraesCS7B01G312100 chr2A 569013074 569013968 894 True 933 933 85.667 2587 3488 1 chr2A.!!$R1 901
22 TraesCS7B01G312100 chr2A 307702558 307703241 683 False 621 621 83.429 2566 3243 1 chr2A.!!$F1 677
23 TraesCS7B01G312100 chr2A 706523682 706524250 568 False 394 394 79.800 2587 3169 1 chr2A.!!$F2 582
24 TraesCS7B01G312100 chr6A 18875350 18876296 946 False 917 917 84.401 1 952 1 chr6A.!!$F1 951
25 TraesCS7B01G312100 chr6A 144530875 144531808 933 True 893 893 84.167 6 949 1 chr6A.!!$R1 943
26 TraesCS7B01G312100 chr6A 587702686 587703628 942 True 880 880 83.817 1 945 1 chr6A.!!$R2 944
27 TraesCS7B01G312100 chr6A 385811125 385811893 768 False 675 675 82.886 2587 3351 1 chr6A.!!$F3 764
28 TraesCS7B01G312100 chr6A 385730584 385731350 766 False 673 673 82.886 2587 3351 1 chr6A.!!$F2 764
29 TraesCS7B01G312100 chr1A 572566067 572567008 941 True 859 859 83.454 1 949 1 chr1A.!!$R1 948
30 TraesCS7B01G312100 chr6B 426450701 426451469 768 True 664 664 82.631 2587 3351 1 chr6B.!!$R1 764
31 TraesCS7B01G312100 chr3B 794534119 794534860 741 False 647 647 82.857 2589 3339 1 chr3B.!!$F1 750
32 TraesCS7B01G312100 chr2B 364955702 364956316 614 False 542 542 83.333 2888 3489 1 chr2B.!!$F1 601

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
924 957 0.028110 GCGATTTTTAGCGCCTCCTG 59.972 55.0 2.29 0.0 46.93 3.86 F
974 1007 0.107643 TTCATCACGCTTGTGGGACA 59.892 50.0 0.00 0.0 44.00 4.02 F
1471 1531 0.530870 GTCTATGCCCAAGCTCGTCC 60.531 60.0 0.00 0.0 40.80 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2397 0.323542 AATCAGAGGACGACGACCCT 60.324 55.0 12.78 12.38 35.02 4.34 R
2462 2554 0.402504 AAACTCACGGGCCCATTACA 59.597 50.0 24.92 0.00 0.00 2.41 R
2547 2639 0.459934 CAGCTACTGCACTCTCCAGC 60.460 60.0 0.00 0.00 42.74 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
22 23 1.229209 AAGGCTCAACTCCGAGGGA 60.229 57.895 0.00 0.00 33.36 4.20
129 134 2.400158 CGCTCCGTCCTTCTCTCGT 61.400 63.158 0.00 0.00 0.00 4.18
148 153 4.436998 GACGTGGGAGCTCGTGGG 62.437 72.222 7.83 0.00 40.39 4.61
189 194 2.040464 GGGGCATCCTCCTCCTCA 60.040 66.667 0.00 0.00 0.00 3.86
203 208 4.514577 CTCATCCGGCCGCTCGTT 62.515 66.667 22.85 0.00 0.00 3.85
301 308 2.202756 GCATCGACGACTCCACCC 60.203 66.667 0.00 0.00 0.00 4.61
302 309 2.494918 CATCGACGACTCCACCCC 59.505 66.667 0.00 0.00 0.00 4.95
303 310 2.052690 CATCGACGACTCCACCCCT 61.053 63.158 0.00 0.00 0.00 4.79
483 491 1.080230 CCTGGATGAGATAGCCGCG 60.080 63.158 0.00 0.00 37.80 6.46
543 557 2.571096 GACAGCGACGACGACGAG 60.571 66.667 22.94 15.68 42.66 4.18
664 691 1.400113 CGACTACACGCGGTTCTACAA 60.400 52.381 12.47 0.00 0.00 2.41
728 760 2.766400 GGGAGACGACGAGGAGCAG 61.766 68.421 0.00 0.00 0.00 4.24
788 820 1.904144 TATGAACGAACTCGCCGAAG 58.096 50.000 0.00 0.00 44.43 3.79
796 828 0.942252 AACTCGCCGAAGTTTGGTTC 59.058 50.000 10.98 0.00 36.02 3.62
802 834 2.470999 CGCCGAAGTTTGGTTCAATTTG 59.529 45.455 10.98 0.00 0.00 2.32
816 848 1.486644 AATTTGCGCCGTGTTTGTGC 61.487 50.000 4.18 0.00 39.63 4.57
817 849 4.560856 TTGCGCCGTGTTTGTGCC 62.561 61.111 4.18 0.00 38.44 5.01
826 858 3.852572 GCCGTGTTTGTGCCGTAATTTAA 60.853 43.478 0.00 0.00 0.00 1.52
840 872 9.798885 TGCCGTAATTTAAATTTTCAAAAATCG 57.201 25.926 18.14 9.28 37.62 3.34
850 883 4.413800 AAAAATCGTGGGCGCCGC 62.414 61.111 22.54 15.11 38.14 6.53
914 947 4.968370 CCCGAGGGGCGATTTTTA 57.032 55.556 0.00 0.00 44.57 1.52
915 948 2.702847 CCCGAGGGGCGATTTTTAG 58.297 57.895 0.00 0.00 44.57 1.85
916 949 1.444917 CCCGAGGGGCGATTTTTAGC 61.445 60.000 0.00 0.00 44.57 3.09
917 950 1.641677 CGAGGGGCGATTTTTAGCG 59.358 57.895 0.00 0.00 44.57 4.26
922 955 4.998294 GCGATTTTTAGCGCCTCC 57.002 55.556 2.29 0.00 46.93 4.30
923 956 2.394604 GCGATTTTTAGCGCCTCCT 58.605 52.632 2.29 0.00 46.93 3.69
924 957 0.028110 GCGATTTTTAGCGCCTCCTG 59.972 55.000 2.29 0.00 46.93 3.86
925 958 1.651987 CGATTTTTAGCGCCTCCTGA 58.348 50.000 2.29 0.00 0.00 3.86
926 959 2.006888 CGATTTTTAGCGCCTCCTGAA 58.993 47.619 2.29 0.00 0.00 3.02
927 960 2.030946 CGATTTTTAGCGCCTCCTGAAG 59.969 50.000 2.29 0.00 0.00 3.02
935 968 2.045926 CCTCCTGAAGGCCAACGG 60.046 66.667 5.01 2.92 38.67 4.44
947 980 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
948 981 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
949 982 0.392193 CAACGGCTGGAGATGCTCTT 60.392 55.000 0.00 0.00 0.00 2.85
950 983 1.134699 CAACGGCTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
951 984 1.418334 ACGGCTGGAGATGCTCTTAT 58.582 50.000 0.00 0.00 0.00 1.73
962 995 5.700373 GGAGATGCTCTTATTCCTTCATCAC 59.300 44.000 0.00 0.00 34.42 3.06
965 998 3.118629 TGCTCTTATTCCTTCATCACGCT 60.119 43.478 0.00 0.00 0.00 5.07
967 1000 4.260538 GCTCTTATTCCTTCATCACGCTTG 60.261 45.833 0.00 0.00 0.00 4.01
971 1004 0.321564 TCCTTCATCACGCTTGTGGG 60.322 55.000 0.00 0.00 44.00 4.61
974 1007 0.107643 TTCATCACGCTTGTGGGACA 59.892 50.000 0.00 0.00 44.00 4.02
1010 1043 2.093447 CCCGAGCTTCCACTAAATCTGT 60.093 50.000 0.00 0.00 0.00 3.41
1020 1053 4.346709 TCCACTAAATCTGTGAGTTGGACA 59.653 41.667 0.00 0.00 37.60 4.02
1086 1119 2.112297 GTGTTCCCTTGGCCACGA 59.888 61.111 11.54 1.03 0.00 4.35
1095 1128 3.177194 TTGGCCACGACAGGGACAG 62.177 63.158 3.88 0.00 46.14 3.51
1105 1138 1.221840 CAGGGACAGATCAACCCCG 59.778 63.158 15.17 4.95 44.21 5.73
1121 1154 2.753966 CCGTGCTCCATTTCGCCAG 61.754 63.158 0.00 0.00 0.00 4.85
1146 1179 4.477975 GTCGACGCCGGAGTCCAG 62.478 72.222 29.37 18.05 37.85 3.86
1170 1203 3.649277 CTTCCTCCACACCGAGCGG 62.649 68.421 7.48 7.48 42.03 5.52
1276 1312 0.540923 CTTCTTGGAGCTCCTGGAGG 59.459 60.000 32.28 23.81 36.82 4.30
1362 1422 1.516386 CGTTGTCGCCGATAGCACT 60.516 57.895 0.00 0.00 44.04 4.40
1389 1449 3.255379 GCCTTCGACATCGCCGAC 61.255 66.667 0.00 0.00 39.60 4.79
1429 1489 2.661537 CCTTCGTCACGCACAGCA 60.662 61.111 0.00 0.00 0.00 4.41
1471 1531 0.530870 GTCTATGCCCAAGCTCGTCC 60.531 60.000 0.00 0.00 40.80 4.79
1511 1571 3.519973 CTGCAGACGACCTGGTGCA 62.520 63.158 8.42 6.39 43.50 4.57
1665 1725 1.939381 GCACTCATAGTCAACACCGCA 60.939 52.381 0.00 0.00 0.00 5.69
1710 1770 4.134187 CACATCGCGTCGTGCACC 62.134 66.667 12.15 0.00 46.97 5.01
1788 1850 4.135153 CTGTGGCGGGAGGACGAG 62.135 72.222 0.00 0.00 35.47 4.18
2143 2211 1.973812 GTGTGCTGGCCCTTCTTCC 60.974 63.158 0.00 0.00 0.00 3.46
2159 2230 1.070134 CTTCCTCGACCAGACCAACAA 59.930 52.381 0.00 0.00 0.00 2.83
2340 2422 1.201647 GGTCGTCGTCCTCTGATTTCA 59.798 52.381 0.91 0.00 0.00 2.69
2389 2471 2.158827 TGAAGCACTGTGTGAAGCCTAA 60.159 45.455 9.86 0.00 35.23 2.69
2457 2539 6.675565 GGGGGTGGAAAGTATTATAGGAAAA 58.324 40.000 0.00 0.00 0.00 2.29
2462 2554 7.061054 GTGGAAAGTATTATAGGAAAAGGCCT 58.939 38.462 0.00 0.00 42.15 5.19
2490 2582 2.595386 GCCCGTGAGTTTAGCATTTTG 58.405 47.619 0.00 0.00 0.00 2.44
2496 2588 2.562298 TGAGTTTAGCATTTTGGGGCTG 59.438 45.455 0.00 0.00 41.25 4.85
2505 2597 1.126488 TTTTGGGGCTGAACAATGCA 58.874 45.000 0.00 0.00 0.00 3.96
2506 2598 0.680618 TTTGGGGCTGAACAATGCAG 59.319 50.000 0.00 0.00 36.47 4.41
2511 2603 0.610232 GGCTGAACAATGCAGTCCCT 60.610 55.000 0.00 0.00 35.81 4.20
2532 2624 1.038130 ACGGCTGCCTCTAGGTGTAG 61.038 60.000 17.92 0.00 37.57 2.74
2533 2625 1.739338 CGGCTGCCTCTAGGTGTAGG 61.739 65.000 17.92 0.00 37.57 3.18
2538 2630 3.926729 CCTCTAGGTGTAGGCCTCA 57.073 57.895 9.68 4.34 39.94 3.86
2539 2631 2.390225 CCTCTAGGTGTAGGCCTCAT 57.610 55.000 9.68 0.00 39.94 2.90
2540 2632 1.967066 CCTCTAGGTGTAGGCCTCATG 59.033 57.143 9.68 0.51 39.94 3.07
2541 2633 2.424957 CCTCTAGGTGTAGGCCTCATGA 60.425 54.545 9.68 0.00 39.94 3.07
2542 2634 2.625790 CTCTAGGTGTAGGCCTCATGAC 59.374 54.545 9.68 1.31 39.94 3.06
2543 2635 1.338337 CTAGGTGTAGGCCTCATGACG 59.662 57.143 9.68 0.00 39.94 4.35
2544 2636 0.324368 AGGTGTAGGCCTCATGACGA 60.324 55.000 9.68 0.00 32.39 4.20
2545 2637 0.103208 GGTGTAGGCCTCATGACGAG 59.897 60.000 9.68 0.00 41.89 4.18
2552 2644 3.621225 CTCATGACGAGGGCTGGA 58.379 61.111 0.00 0.00 38.18 3.86
2553 2645 1.440893 CTCATGACGAGGGCTGGAG 59.559 63.158 0.00 0.00 38.18 3.86
2554 2646 1.000359 TCATGACGAGGGCTGGAGA 60.000 57.895 0.00 0.00 0.00 3.71
2555 2647 1.039785 TCATGACGAGGGCTGGAGAG 61.040 60.000 0.00 0.00 0.00 3.20
2556 2648 1.000993 ATGACGAGGGCTGGAGAGT 59.999 57.895 0.00 0.00 0.00 3.24
2557 2649 1.326213 ATGACGAGGGCTGGAGAGTG 61.326 60.000 0.00 0.00 0.00 3.51
2558 2650 3.363844 GACGAGGGCTGGAGAGTGC 62.364 68.421 0.00 0.00 0.00 4.40
2559 2651 3.385384 CGAGGGCTGGAGAGTGCA 61.385 66.667 0.00 0.00 0.00 4.57
2560 2652 2.583520 GAGGGCTGGAGAGTGCAG 59.416 66.667 0.00 0.00 38.97 4.41
2561 2653 2.203907 AGGGCTGGAGAGTGCAGT 60.204 61.111 0.00 0.00 38.17 4.40
2562 2654 0.972983 GAGGGCTGGAGAGTGCAGTA 60.973 60.000 0.00 0.00 38.17 2.74
2563 2655 0.975040 AGGGCTGGAGAGTGCAGTAG 60.975 60.000 0.00 0.00 38.17 2.57
2564 2656 1.153469 GGCTGGAGAGTGCAGTAGC 60.153 63.158 5.60 5.60 38.17 3.58
2565 2657 1.612395 GGCTGGAGAGTGCAGTAGCT 61.612 60.000 12.56 0.00 38.17 3.32
2566 2658 0.459934 GCTGGAGAGTGCAGTAGCTG 60.460 60.000 6.76 0.00 38.17 4.24
2576 2668 3.766644 CAGTAGCTGCACTATGCCA 57.233 52.632 4.12 0.00 44.23 4.92
2577 2669 2.028420 CAGTAGCTGCACTATGCCAA 57.972 50.000 4.12 0.00 44.23 4.52
2578 2670 1.938577 CAGTAGCTGCACTATGCCAAG 59.061 52.381 4.12 0.00 44.23 3.61
2579 2671 1.833630 AGTAGCTGCACTATGCCAAGA 59.166 47.619 4.12 0.00 44.23 3.02
2580 2672 2.158986 AGTAGCTGCACTATGCCAAGAG 60.159 50.000 4.12 0.00 44.23 2.85
2581 2673 0.747283 AGCTGCACTATGCCAAGAGC 60.747 55.000 1.02 0.72 44.23 4.09
2628 2720 1.956170 CATCCGGCCTGCATCGTAC 60.956 63.158 0.00 0.00 0.00 3.67
2714 2813 3.753272 GGTGTACTTGCATGACATGAGTT 59.247 43.478 19.76 2.45 0.00 3.01
2742 2842 6.294176 GCTCATCAAGATGTTGTTTGGTAAGT 60.294 38.462 9.66 0.00 39.72 2.24
2773 2873 6.554784 AGGCCAAATAATATGATGGATGTGA 58.445 36.000 5.01 0.00 34.82 3.58
2870 2979 9.932699 CAGATATCTTTGCTGATTGAAGTAAAG 57.067 33.333 1.33 8.05 45.73 1.85
3018 3132 9.797642 TCTATGTGTATTCCATTATCAGCATTT 57.202 29.630 0.00 0.00 0.00 2.32
3159 3293 6.599638 ACAAAACTAGCTTGTCTCTCTTGTTT 59.400 34.615 0.07 0.00 37.37 2.83
3245 3384 7.367285 TGCACAAATTACTCATGAAGTTAACC 58.633 34.615 0.88 0.00 39.55 2.85
3246 3385 7.013750 TGCACAAATTACTCATGAAGTTAACCA 59.986 33.333 0.88 0.00 39.55 3.67
3247 3386 7.865385 GCACAAATTACTCATGAAGTTAACCAA 59.135 33.333 0.88 0.00 39.55 3.67
3248 3387 9.743057 CACAAATTACTCATGAAGTTAACCAAA 57.257 29.630 0.88 0.00 39.55 3.28
3474 3678 1.401800 CGTGTGCATACGTGGTCTACA 60.402 52.381 25.65 0.00 39.13 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.229209 TCCCTCGGAGTTGAGCCTT 60.229 57.895 4.02 0.00 34.56 4.35
98 99 3.902086 GAGCGGGGTACTCGAGCC 61.902 72.222 13.61 6.43 45.83 4.70
101 102 4.415150 ACGGAGCGGGGTACTCGA 62.415 66.667 12.01 0.00 34.87 4.04
102 103 3.885521 GACGGAGCGGGGTACTCG 61.886 72.222 0.00 0.00 34.87 4.18
129 134 3.733960 CACGAGCTCCCACGTCGA 61.734 66.667 8.47 0.00 40.76 4.20
471 479 3.998911 TTTGCGCGCGGCTATCTCA 62.999 57.895 33.06 16.18 44.05 3.27
525 533 3.978867 CTCGTCGTCGTCGCTGTCC 62.979 68.421 7.01 0.00 38.33 4.02
579 594 3.655211 CCTGCTGCAACCCTCCCT 61.655 66.667 3.02 0.00 0.00 4.20
664 691 0.824759 GTTCTACATGCCGAGGAGGT 59.175 55.000 0.00 0.00 43.70 3.85
718 750 0.256464 ACTACTAGGCTGCTCCTCGT 59.744 55.000 0.00 4.96 43.20 4.18
764 796 4.422840 TCGGCGAGTTCGTTCATATTTAA 58.577 39.130 4.99 0.00 42.22 1.52
765 797 4.031418 TCGGCGAGTTCGTTCATATTTA 57.969 40.909 4.99 0.00 42.22 1.40
788 820 0.506506 CGGCGCAAATTGAACCAAAC 59.493 50.000 10.83 0.00 0.00 2.93
796 828 0.229247 CACAAACACGGCGCAAATTG 59.771 50.000 10.83 10.20 0.00 2.32
826 858 2.478514 GCGCCCACGATTTTTGAAAATT 59.521 40.909 0.00 0.00 43.93 1.82
850 883 2.184322 CGTGATGTCCCCCAGTCG 59.816 66.667 0.00 0.00 0.00 4.18
900 933 1.355563 GCGCTAAAAATCGCCCCTC 59.644 57.895 0.00 0.00 45.01 4.30
901 934 3.509659 GCGCTAAAAATCGCCCCT 58.490 55.556 0.00 0.00 45.01 4.79
906 939 1.651987 TCAGGAGGCGCTAAAAATCG 58.348 50.000 7.64 0.00 0.00 3.34
907 940 2.356069 CCTTCAGGAGGCGCTAAAAATC 59.644 50.000 7.64 0.00 39.09 2.17
908 941 2.369394 CCTTCAGGAGGCGCTAAAAAT 58.631 47.619 7.64 0.00 39.09 1.82
909 942 1.821216 CCTTCAGGAGGCGCTAAAAA 58.179 50.000 7.64 0.00 39.09 1.94
910 943 3.551259 CCTTCAGGAGGCGCTAAAA 57.449 52.632 7.64 0.00 39.09 1.52
919 952 2.747855 GCCGTTGGCCTTCAGGAG 60.748 66.667 3.32 0.00 44.06 3.69
930 963 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
941 974 4.084118 GCGTGATGAAGGAATAAGAGCATC 60.084 45.833 0.00 0.00 34.32 3.91
942 975 3.812053 GCGTGATGAAGGAATAAGAGCAT 59.188 43.478 0.00 0.00 0.00 3.79
943 976 3.118629 AGCGTGATGAAGGAATAAGAGCA 60.119 43.478 0.00 0.00 0.00 4.26
944 977 3.462021 AGCGTGATGAAGGAATAAGAGC 58.538 45.455 0.00 0.00 0.00 4.09
945 978 4.872691 ACAAGCGTGATGAAGGAATAAGAG 59.127 41.667 6.65 0.00 0.00 2.85
946 979 4.631377 CACAAGCGTGATGAAGGAATAAGA 59.369 41.667 6.65 0.00 46.80 2.10
947 980 4.201851 CCACAAGCGTGATGAAGGAATAAG 60.202 45.833 6.65 0.00 46.80 1.73
948 981 3.689161 CCACAAGCGTGATGAAGGAATAA 59.311 43.478 6.65 0.00 46.80 1.40
949 982 3.270027 CCACAAGCGTGATGAAGGAATA 58.730 45.455 6.65 0.00 46.80 1.75
950 983 2.086869 CCACAAGCGTGATGAAGGAAT 58.913 47.619 6.65 0.00 46.80 3.01
951 984 1.522668 CCACAAGCGTGATGAAGGAA 58.477 50.000 6.65 0.00 46.80 3.36
962 995 2.896801 GCACAGTGTCCCACAAGCG 61.897 63.158 1.61 0.00 36.74 4.68
965 998 1.372838 CGTTGCACAGTGTCCCACAA 61.373 55.000 1.61 0.00 36.74 3.33
967 1000 3.022287 CGTTGCACAGTGTCCCAC 58.978 61.111 1.61 0.00 34.10 4.61
971 1004 4.012895 CCGGCGTTGCACAGTGTC 62.013 66.667 6.01 0.00 0.00 3.67
1010 1043 1.227823 CGGCAGGTTGTCCAACTCA 60.228 57.895 9.79 0.00 40.94 3.41
1020 1053 3.747976 GCGGCAAATCGGCAGGTT 61.748 61.111 0.00 0.00 41.26 3.50
1086 1119 1.553690 CGGGGTTGATCTGTCCCTGT 61.554 60.000 16.03 0.00 41.46 4.00
1095 1128 0.394352 AATGGAGCACGGGGTTGATC 60.394 55.000 0.00 0.00 0.00 2.92
1105 1138 2.334946 TGCTGGCGAAATGGAGCAC 61.335 57.895 0.00 0.00 36.54 4.40
1140 1173 0.907230 GGAGGAAGCTGACCTGGACT 60.907 60.000 16.03 0.00 37.93 3.85
1146 1179 1.003233 GGTGTGGAGGAAGCTGACC 60.003 63.158 2.38 2.38 0.00 4.02
1170 1203 0.733223 GAGCAAGACGACGGAGGTTC 60.733 60.000 0.00 0.00 0.00 3.62
1389 1449 2.356793 GATGGGATGCCGAGCTCG 60.357 66.667 29.06 29.06 39.44 5.03
1429 1489 4.742201 CGCCAGGTAGCTGCACGT 62.742 66.667 16.62 0.00 0.00 4.49
1665 1725 4.148825 GACCGCTCCATGGACGCT 62.149 66.667 24.50 15.57 0.00 5.07
1873 1935 3.056107 CCGGTGAGGAATTCAGTGAACTA 60.056 47.826 7.96 0.00 45.00 2.24
2000 2065 4.547905 CGACGACGCGCCCTATGT 62.548 66.667 5.73 0.00 0.00 2.29
2071 2139 1.639298 GAGTTCCATCCTGCGTGTGC 61.639 60.000 0.00 0.00 43.20 4.57
2143 2211 0.944311 CGGTTGTTGGTCTGGTCGAG 60.944 60.000 0.00 0.00 0.00 4.04
2189 2260 2.093075 CAGATGTCCTTCATGTCCAGCT 60.093 50.000 0.00 0.00 36.83 4.24
2318 2397 0.323542 AATCAGAGGACGACGACCCT 60.324 55.000 12.78 12.38 35.02 4.34
2437 2519 7.013369 CAGGCCTTTTCCTATAATACTTTCCAC 59.987 40.741 0.00 0.00 33.95 4.02
2440 2522 9.623000 TTACAGGCCTTTTCCTATAATACTTTC 57.377 33.333 0.00 0.00 33.95 2.62
2462 2554 0.402504 AAACTCACGGGCCCATTACA 59.597 50.000 24.92 0.00 0.00 2.41
2490 2582 1.598701 GGACTGCATTGTTCAGCCCC 61.599 60.000 0.00 0.00 35.04 5.80
2496 2588 0.798776 CGTGAGGGACTGCATTGTTC 59.201 55.000 0.00 0.00 41.55 3.18
2511 2603 2.037367 ACCTAGAGGCAGCCGTGA 59.963 61.111 5.55 0.00 39.32 4.35
2535 2627 1.039785 TCTCCAGCCCTCGTCATGAG 61.040 60.000 0.00 0.00 44.83 2.90
2536 2628 1.000359 TCTCCAGCCCTCGTCATGA 60.000 57.895 0.00 0.00 0.00 3.07
2537 2629 1.326213 ACTCTCCAGCCCTCGTCATG 61.326 60.000 0.00 0.00 0.00 3.07
2538 2630 1.000993 ACTCTCCAGCCCTCGTCAT 59.999 57.895 0.00 0.00 0.00 3.06
2539 2631 1.979155 CACTCTCCAGCCCTCGTCA 60.979 63.158 0.00 0.00 0.00 4.35
2540 2632 2.888863 CACTCTCCAGCCCTCGTC 59.111 66.667 0.00 0.00 0.00 4.20
2541 2633 3.386237 GCACTCTCCAGCCCTCGT 61.386 66.667 0.00 0.00 0.00 4.18
2542 2634 3.368190 CTGCACTCTCCAGCCCTCG 62.368 68.421 0.00 0.00 0.00 4.63
2543 2635 0.972983 TACTGCACTCTCCAGCCCTC 60.973 60.000 0.00 0.00 33.65 4.30
2544 2636 0.975040 CTACTGCACTCTCCAGCCCT 60.975 60.000 0.00 0.00 33.65 5.19
2545 2637 1.519719 CTACTGCACTCTCCAGCCC 59.480 63.158 0.00 0.00 33.65 5.19
2546 2638 1.153469 GCTACTGCACTCTCCAGCC 60.153 63.158 0.00 0.00 39.41 4.85
2547 2639 0.459934 CAGCTACTGCACTCTCCAGC 60.460 60.000 0.00 0.00 42.74 4.85
2548 2640 3.737127 CAGCTACTGCACTCTCCAG 57.263 57.895 0.00 0.00 42.74 3.86
2573 2665 2.899339 GCCCTCGATGCTCTTGGC 60.899 66.667 0.15 0.00 42.22 4.52
2574 2666 2.587194 CGCCCTCGATGCTCTTGG 60.587 66.667 5.65 0.00 38.10 3.61
2575 2667 2.169789 CACGCCCTCGATGCTCTTG 61.170 63.158 5.65 0.00 39.41 3.02
2576 2668 2.172483 AACACGCCCTCGATGCTCTT 62.172 55.000 5.65 0.00 39.41 2.85
2577 2669 2.172483 AAACACGCCCTCGATGCTCT 62.172 55.000 5.65 0.00 39.41 4.09
2578 2670 1.741770 AAACACGCCCTCGATGCTC 60.742 57.895 5.65 0.00 39.41 4.26
2579 2671 2.034879 CAAACACGCCCTCGATGCT 61.035 57.895 5.65 0.00 39.41 3.79
2580 2672 2.480555 CAAACACGCCCTCGATGC 59.519 61.111 0.00 0.00 39.41 3.91
2581 2673 1.234615 AACCAAACACGCCCTCGATG 61.235 55.000 0.00 0.00 39.41 3.84
2582 2674 0.536460 AAACCAAACACGCCCTCGAT 60.536 50.000 0.00 0.00 39.41 3.59
2583 2675 1.153127 AAACCAAACACGCCCTCGA 60.153 52.632 0.00 0.00 39.41 4.04
2584 2676 1.281656 GAAACCAAACACGCCCTCG 59.718 57.895 0.00 0.00 42.43 4.63
2585 2677 0.822121 AGGAAACCAAACACGCCCTC 60.822 55.000 0.00 0.00 0.00 4.30
2628 2720 4.479993 CCCAGCCAAGCTCCCTCG 62.480 72.222 0.00 0.00 36.40 4.63
2714 2813 4.701651 CCAAACAACATCTTGATGAGCCTA 59.298 41.667 16.43 0.00 0.00 3.93
2742 2842 6.295405 CCATCATATTATTTGGCCTCATGCAA 60.295 38.462 3.32 0.00 43.89 4.08
3159 3293 3.027412 AGATCAGCTAGCGAGGAAGAAA 58.973 45.455 9.55 0.00 0.00 2.52
3272 3432 8.891985 TCTAGCTGTGAGATCCTATTGATTAT 57.108 34.615 0.00 0.00 32.41 1.28


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

AutoCloner maintained by Alex Coulton.