Multiple sequence alignment - TraesCS4A01G168300

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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 TraesCS4A01G168300 chr4A 100.000 3827 0 0 1 3827 420021345 420017519 0.000000e+00 7068.0
1 TraesCS4A01G168300 chr4A 92.857 126 9 0 1 126 226037389 226037514 2.350000e-42 183.0
2 TraesCS4A01G168300 chr4A 96.491 57 0 2 525 581 420020773 420020719 4.070000e-15 93.5
3 TraesCS4A01G168300 chr4A 96.491 57 0 2 573 627 420020821 420020765 4.070000e-15 93.5
4 TraesCS4A01G168300 chr2D 96.134 2121 73 7 1710 3827 52284362 52286476 0.000000e+00 3454.0
5 TraesCS4A01G168300 chr5B 95.710 2121 59 10 1710 3827 634121503 634119412 0.000000e+00 3384.0
6 TraesCS4A01G168300 chr5B 98.462 195 1 2 784 977 654755925 654755732 3.660000e-90 342.0
7 TraesCS4A01G168300 chr2A 95.059 2024 94 6 1710 3731 315762583 315764602 0.000000e+00 3179.0
8 TraesCS4A01G168300 chr2A 93.333 690 32 5 1010 1697 6476236 6476913 0.000000e+00 1007.0
9 TraesCS4A01G168300 chr2A 94.064 438 16 2 1010 1447 6474013 6474440 0.000000e+00 656.0
10 TraesCS4A01G168300 chr2A 83.893 298 24 8 1830 2127 755370074 755370347 2.930000e-66 263.0
11 TraesCS4A01G168300 chr3D 96.049 1949 71 5 1710 3657 477613497 477611554 0.000000e+00 3168.0
12 TraesCS4A01G168300 chr3D 96.907 1584 46 3 1710 3291 30970452 30972034 0.000000e+00 2651.0
13 TraesCS4A01G168300 chr3D 91.310 1634 120 12 1710 3340 412103178 412104792 0.000000e+00 2211.0
14 TraesCS4A01G168300 chr3D 95.221 544 23 1 3287 3827 30972850 30973393 0.000000e+00 857.0
15 TraesCS4A01G168300 chr3D 95.455 176 8 0 3652 3827 477571265 477571090 8.090000e-72 281.0
16 TraesCS4A01G168300 chr1A 98.278 1684 28 1 2145 3827 558014399 558016082 0.000000e+00 2948.0
17 TraesCS4A01G168300 chr1A 98.893 1174 12 1 974 2147 558000507 558001679 0.000000e+00 2095.0
18 TraesCS4A01G168300 chr1A 98.104 791 11 4 1 789 557999738 558000526 0.000000e+00 1375.0
19 TraesCS4A01G168300 chr1A 100.000 57 0 0 525 581 558000308 558000364 5.230000e-19 106.0
20 TraesCS4A01G168300 chr1A 96.364 55 0 2 575 627 558000262 558000316 5.270000e-14 89.8
21 TraesCS4A01G168300 chr7A 97.398 1499 38 1 1758 3256 299430986 299429489 0.000000e+00 2551.0
22 TraesCS4A01G168300 chr7A 95.161 682 17 5 1047 1723 299431654 299430984 0.000000e+00 1062.0
23 TraesCS4A01G168300 chr7A 95.034 584 26 3 3246 3827 299415275 299414693 0.000000e+00 915.0
24 TraesCS4A01G168300 chr7A 97.191 534 14 1 1 534 299433020 299432488 0.000000e+00 902.0
25 TraesCS4A01G168300 chr7A 95.000 260 10 3 530 786 299431909 299431650 4.600000e-109 405.0
26 TraesCS4A01G168300 chr7A 100.000 186 0 0 788 973 323738820 323738635 1.020000e-90 344.0
27 TraesCS4A01G168300 chr7A 100.000 54 0 0 528 581 299431862 299431809 2.430000e-17 100.0
28 TraesCS4A01G168300 chr6D 91.912 952 64 8 2803 3744 169715444 169716392 0.000000e+00 1319.0
29 TraesCS4A01G168300 chr6D 91.440 257 22 0 2382 2638 169714691 169714947 1.690000e-93 353.0
30 TraesCS4A01G168300 chr6D 92.857 126 9 0 1 126 158118691 158118816 2.350000e-42 183.0
31 TraesCS4A01G168300 chr7B 95.627 686 21 1 1012 1697 125885180 125885856 0.000000e+00 1092.0
32 TraesCS4A01G168300 chr7B 90.679 633 39 9 1070 1694 83991738 83991118 0.000000e+00 824.0
33 TraesCS4A01G168300 chr7B 96.089 358 14 0 1 358 84107320 84106963 5.510000e-163 584.0
34 TraesCS4A01G168300 chr7B 91.274 424 30 5 360 783 83992151 83991735 4.290000e-159 571.0
35 TraesCS4A01G168300 chr7B 100.000 187 0 0 787 973 690699406 690699592 2.830000e-91 346.0
36 TraesCS4A01G168300 chr7B 97.487 199 4 1 787 985 252794268 252794465 4.740000e-89 339.0
37 TraesCS4A01G168300 chr7B 93.607 219 8 5 757 973 344312630 344312416 4.770000e-84 322.0
38 TraesCS4A01G168300 chr7B 89.671 213 17 5 1710 1919 393858258 393858468 2.270000e-67 267.0
39 TraesCS4A01G168300 chr7B 92.727 55 2 1 573 627 83991988 83991936 1.140000e-10 78.7
40 TraesCS4A01G168300 chr3B 88.305 838 60 12 2956 3789 726179274 726178471 0.000000e+00 970.0
41 TraesCS4A01G168300 chr3B 90.515 738 49 8 967 1695 99766003 99766728 0.000000e+00 955.0
42 TraesCS4A01G168300 chr3B 87.817 394 40 4 188 581 99765485 99765870 4.510000e-124 455.0
43 TraesCS4A01G168300 chr3B 94.764 191 9 1 1 191 99756457 99756646 2.890000e-76 296.0
44 TraesCS4A01G168300 chr3B 86.735 98 11 2 3701 3797 242876272 242876368 1.450000e-19 108.0
45 TraesCS4A01G168300 chr7D 81.240 629 78 17 966 1583 33058529 33057930 4.480000e-129 472.0
46 TraesCS4A01G168300 chrUn 79.930 573 75 13 1020 1583 193297082 193296541 6.000000e-103 385.0
47 TraesCS4A01G168300 chrUn 92.638 163 12 0 2640 2802 394864046 394864208 6.390000e-58 235.0
48 TraesCS4A01G168300 chr5A 99.474 190 1 0 785 974 664552840 664553029 2.830000e-91 346.0
49 TraesCS4A01G168300 chr5A 89.011 91 7 2 2248 2338 600890327 600890414 4.040000e-20 110.0
50 TraesCS4A01G168300 chr4B 100.000 187 0 0 787 973 588430817 588431003 2.830000e-91 346.0
51 TraesCS4A01G168300 chr3A 98.969 194 1 1 784 977 724318924 724319116 2.830000e-91 346.0
52 TraesCS4A01G168300 chr2B 98.462 195 3 0 779 973 331010407 331010213 1.020000e-90 344.0
53 TraesCS4A01G168300 chr6B 92.857 126 9 0 1 126 288649901 288649776 2.350000e-42 183.0
54 TraesCS4A01G168300 chr6A 92.913 127 8 1 1 126 210798704 210798830 2.350000e-42 183.0
55 TraesCS4A01G168300 chr1B 92.063 126 10 0 1 126 677611372 677611497 1.090000e-40 178.0


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 TraesCS4A01G168300 chr4A 420017519 420021345 3826 True 2418.333333 7068 97.660667 1 3827 3 chr4A.!!$R1 3826
1 TraesCS4A01G168300 chr2D 52284362 52286476 2114 False 3454.000000 3454 96.134000 1710 3827 1 chr2D.!!$F1 2117
2 TraesCS4A01G168300 chr5B 634119412 634121503 2091 True 3384.000000 3384 95.710000 1710 3827 1 chr5B.!!$R1 2117
3 TraesCS4A01G168300 chr2A 315762583 315764602 2019 False 3179.000000 3179 95.059000 1710 3731 1 chr2A.!!$F1 2021
4 TraesCS4A01G168300 chr2A 6474013 6476913 2900 False 831.500000 1007 93.698500 1010 1697 2 chr2A.!!$F3 687
5 TraesCS4A01G168300 chr3D 477611554 477613497 1943 True 3168.000000 3168 96.049000 1710 3657 1 chr3D.!!$R2 1947
6 TraesCS4A01G168300 chr3D 412103178 412104792 1614 False 2211.000000 2211 91.310000 1710 3340 1 chr3D.!!$F1 1630
7 TraesCS4A01G168300 chr3D 30970452 30973393 2941 False 1754.000000 2651 96.064000 1710 3827 2 chr3D.!!$F2 2117
8 TraesCS4A01G168300 chr1A 558014399 558016082 1683 False 2948.000000 2948 98.278000 2145 3827 1 chr1A.!!$F1 1682
9 TraesCS4A01G168300 chr1A 557999738 558001679 1941 False 916.450000 2095 98.340250 1 2147 4 chr1A.!!$F2 2146
10 TraesCS4A01G168300 chr7A 299429489 299433020 3531 True 1004.000000 2551 96.950000 1 3256 5 chr7A.!!$R3 3255
11 TraesCS4A01G168300 chr7A 299414693 299415275 582 True 915.000000 915 95.034000 3246 3827 1 chr7A.!!$R1 581
12 TraesCS4A01G168300 chr6D 169714691 169716392 1701 False 836.000000 1319 91.676000 2382 3744 2 chr6D.!!$F2 1362
13 TraesCS4A01G168300 chr7B 125885180 125885856 676 False 1092.000000 1092 95.627000 1012 1697 1 chr7B.!!$F1 685
14 TraesCS4A01G168300 chr7B 83991118 83992151 1033 True 491.233333 824 91.560000 360 1694 3 chr7B.!!$R3 1334
15 TraesCS4A01G168300 chr3B 726178471 726179274 803 True 970.000000 970 88.305000 2956 3789 1 chr3B.!!$R1 833
16 TraesCS4A01G168300 chr3B 99765485 99766728 1243 False 705.000000 955 89.166000 188 1695 2 chr3B.!!$F3 1507
17 TraesCS4A01G168300 chr7D 33057930 33058529 599 True 472.000000 472 81.240000 966 1583 1 chr7D.!!$R1 617
18 TraesCS4A01G168300 chrUn 193296541 193297082 541 True 385.000000 385 79.930000 1020 1583 1 chrUn.!!$R1 563

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
797 1389 0.106967 GTTGGAGATGAAGGGGAGCC 60.107 60.0 0.0 0.0 0.00 4.70 F
848 1440 0.107831 CCAAGAGGTCACGGGTTCAA 59.892 55.0 0.0 0.0 0.00 2.69 F
894 1486 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.0 0.0 0.0 37.28 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 5169 1.391485 CTCCAATCTATATGCGCGTGC 59.609 52.381 15.48 15.48 43.20 5.34 R
2825 6002 1.604278 GGTGGTGCAAACTCAAGTCTC 59.396 52.381 0.00 0.00 0.00 3.36 R
3017 6199 6.369065 GGAGTAACACTCAAGGTTATGTCAAG 59.631 42.308 8.47 0.00 46.79 3.02 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
130 131 7.553044 GTGTAGTGGAAGGATAGTTTATTTGCT 59.447 37.037 0.00 0.00 0.00 3.91
331 333 6.403878 GCCTATGGCCGATTAAATAGAACTA 58.596 40.000 0.00 0.00 44.06 2.24
524 526 1.602771 GTAGGCCTGGGTGAAGTCC 59.397 63.158 17.99 0.00 0.00 3.85
525 527 1.987855 TAGGCCTGGGTGAAGTCCG 60.988 63.158 17.99 0.00 0.00 4.79
662 1254 0.532862 CGAGAGCAGGTTGTGGTTGT 60.533 55.000 0.00 0.00 36.87 3.32
777 1369 8.970020 TGGCATATTTGTTTTCAGAGTATTGAT 58.030 29.630 0.00 0.00 0.00 2.57
778 1370 9.241317 GGCATATTTGTTTTCAGAGTATTGATG 57.759 33.333 0.00 0.00 0.00 3.07
779 1371 9.793252 GCATATTTGTTTTCAGAGTATTGATGT 57.207 29.630 0.00 0.00 0.00 3.06
783 1375 7.815840 TTGTTTTCAGAGTATTGATGTTGGA 57.184 32.000 0.00 0.00 0.00 3.53
784 1376 7.439157 TGTTTTCAGAGTATTGATGTTGGAG 57.561 36.000 0.00 0.00 0.00 3.86
785 1377 7.223584 TGTTTTCAGAGTATTGATGTTGGAGA 58.776 34.615 0.00 0.00 0.00 3.71
786 1378 7.884877 TGTTTTCAGAGTATTGATGTTGGAGAT 59.115 33.333 0.00 0.00 0.00 2.75
787 1379 7.854557 TTTCAGAGTATTGATGTTGGAGATG 57.145 36.000 0.00 0.00 0.00 2.90
788 1380 6.796785 TCAGAGTATTGATGTTGGAGATGA 57.203 37.500 0.00 0.00 0.00 2.92
789 1381 7.186570 TCAGAGTATTGATGTTGGAGATGAA 57.813 36.000 0.00 0.00 0.00 2.57
790 1382 7.270779 TCAGAGTATTGATGTTGGAGATGAAG 58.729 38.462 0.00 0.00 0.00 3.02
791 1383 6.482641 CAGAGTATTGATGTTGGAGATGAAGG 59.517 42.308 0.00 0.00 0.00 3.46
792 1384 5.688807 AGTATTGATGTTGGAGATGAAGGG 58.311 41.667 0.00 0.00 0.00 3.95
793 1385 3.370840 TTGATGTTGGAGATGAAGGGG 57.629 47.619 0.00 0.00 0.00 4.79
794 1386 2.561187 TGATGTTGGAGATGAAGGGGA 58.439 47.619 0.00 0.00 0.00 4.81
795 1387 2.507058 TGATGTTGGAGATGAAGGGGAG 59.493 50.000 0.00 0.00 0.00 4.30
796 1388 0.620556 TGTTGGAGATGAAGGGGAGC 59.379 55.000 0.00 0.00 0.00 4.70
797 1389 0.106967 GTTGGAGATGAAGGGGAGCC 60.107 60.000 0.00 0.00 0.00 4.70
798 1390 0.253347 TTGGAGATGAAGGGGAGCCT 60.253 55.000 0.00 0.00 0.00 4.58
799 1391 0.253347 TGGAGATGAAGGGGAGCCTT 60.253 55.000 0.00 0.00 0.00 4.35
800 1392 0.182299 GGAGATGAAGGGGAGCCTTG 59.818 60.000 0.00 0.00 0.00 3.61
801 1393 0.182299 GAGATGAAGGGGAGCCTTGG 59.818 60.000 0.00 0.00 0.00 3.61
802 1394 1.454663 GATGAAGGGGAGCCTTGGC 60.455 63.158 2.97 2.97 0.00 4.52
803 1395 3.350031 ATGAAGGGGAGCCTTGGCG 62.350 63.158 5.95 0.00 0.00 5.69
811 1403 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
812 1404 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
813 1405 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
814 1406 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
815 1407 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
816 1408 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
817 1409 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
822 1414 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
823 1415 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
824 1416 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
825 1417 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
826 1418 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
827 1419 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
828 1420 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
829 1421 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
830 1422 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
831 1423 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
832 1424 2.195567 GCTGCTGCCTTGTGACCAA 61.196 57.895 3.85 0.00 0.00 3.67
833 1425 1.954528 CTGCTGCCTTGTGACCAAG 59.045 57.895 0.00 0.00 46.33 3.61
846 1438 4.695560 CCAAGAGGTCACGGGTTC 57.304 61.111 0.00 0.00 0.00 3.62
847 1439 1.752198 CCAAGAGGTCACGGGTTCA 59.248 57.895 0.00 0.00 0.00 3.18
848 1440 0.107831 CCAAGAGGTCACGGGTTCAA 59.892 55.000 0.00 0.00 0.00 2.69
849 1441 1.512926 CAAGAGGTCACGGGTTCAAG 58.487 55.000 0.00 0.00 0.00 3.02
850 1442 1.129058 AAGAGGTCACGGGTTCAAGT 58.871 50.000 0.00 0.00 0.00 3.16
851 1443 0.680061 AGAGGTCACGGGTTCAAGTC 59.320 55.000 0.00 0.00 0.00 3.01
852 1444 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
853 1445 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
854 1446 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
855 1447 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
856 1448 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
857 1449 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
858 1450 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
859 1451 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
860 1452 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
874 1466 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
875 1467 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
876 1468 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
877 1469 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
878 1470 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
879 1471 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
880 1472 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
881 1473 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
882 1474 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
883 1475 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
884 1476 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
885 1477 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
886 1478 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
887 1479 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
888 1480 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
889 1481 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
890 1482 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
891 1483 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
892 1484 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
893 1485 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
894 1486 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
895 1487 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
896 1488 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
897 1489 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
898 1490 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
899 1491 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
900 1492 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
901 1493 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
902 1494 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
903 1495 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
904 1496 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
905 1497 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
906 1498 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
907 1499 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
908 1500 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
909 1501 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
910 1502 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
911 1503 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
916 1508 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
917 1509 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
918 1510 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
919 1511 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
920 1512 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
921 1513 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
922 1514 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
923 1515 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
924 1516 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
931 1523 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
958 1550 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
959 1551 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
960 1552 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
961 1553 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
962 1554 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
963 1555 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
1490 4321 7.492669 CCATGACTATATGCGGTTCCTATAAAG 59.507 40.741 0.00 0.00 0.00 1.85
1708 4547 3.507622 GGAGGCTGCTGAACAAGTTTATT 59.492 43.478 0.00 0.00 0.00 1.40
1902 4742 2.133742 CTGGAACTTGTGCTTGCCCG 62.134 60.000 0.00 0.00 0.00 6.13
2060 4902 1.683385 GAGGTGGTGCTCTTGCTTTTT 59.317 47.619 0.00 0.00 40.48 1.94
2196 5040 3.137533 AGAAGAGTTTTCTGCACTGAGC 58.862 45.455 0.00 0.00 45.96 4.26
2289 5133 6.980397 GGAACAATTGTGTGTCTTGATCTTTT 59.020 34.615 12.82 0.00 38.27 2.27
2325 5169 5.869344 GGTTTTGCAGCCTAGAATTTTTAGG 59.131 40.000 8.34 8.34 40.57 2.69
2365 5210 8.948631 TTGGAGCATCTAATAGTAGTTGAAAG 57.051 34.615 11.47 0.00 31.24 2.62
2434 5279 2.440409 ACATCATGGTCTTCTTGTGCC 58.560 47.619 0.00 0.00 0.00 5.01
2726 5756 2.180276 GGAGAAGGAGAGGTACAGCAA 58.820 52.381 0.00 0.00 0.00 3.91
2825 6002 8.432359 CGATTCAATTGCCATTGATAATGATTG 58.568 33.333 13.48 4.91 46.68 2.67
3017 6199 9.635520 TCAGACTTTAGTTTGCTAATACTGTAC 57.364 33.333 0.00 0.00 37.09 2.90
3075 6257 7.530426 AAGTGGATTGAGCTTTTTGTTATCT 57.470 32.000 0.00 0.00 0.00 1.98
3321 7325 4.563580 GGACACTCTTGCTTGATACAAGGA 60.564 45.833 12.36 7.49 43.79 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 5.542779 AGTTGAGAAACTGTGTCATAGGAC 58.457 41.667 0.00 0.00 44.57 3.85
349 351 2.873094 TTCCTCGAGGTGTCTCACTA 57.127 50.000 30.17 5.42 39.95 2.74
524 526 1.653094 AACACACACACACCTTGCCG 61.653 55.000 0.00 0.00 0.00 5.69
525 527 0.179140 CAACACACACACACCTTGCC 60.179 55.000 0.00 0.00 0.00 4.52
585 1177 2.239402 TGCCTCCATCTATCTGCAACAA 59.761 45.455 0.00 0.00 0.00 2.83
642 1234 0.532862 CAACCACAACCTGCTCTCGT 60.533 55.000 0.00 0.00 0.00 4.18
662 1254 6.267699 CGGAGGGGAATACATATATATGCAGA 59.732 42.308 20.46 8.47 37.19 4.26
777 1369 0.620556 GCTCCCCTTCATCTCCAACA 59.379 55.000 0.00 0.00 0.00 3.33
778 1370 0.106967 GGCTCCCCTTCATCTCCAAC 60.107 60.000 0.00 0.00 0.00 3.77
779 1371 0.253347 AGGCTCCCCTTCATCTCCAA 60.253 55.000 0.00 0.00 38.74 3.53
780 1372 1.397823 AGGCTCCCCTTCATCTCCA 59.602 57.895 0.00 0.00 38.74 3.86
781 1373 4.409257 AGGCTCCCCTTCATCTCC 57.591 61.111 0.00 0.00 38.74 3.71
793 1385 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
794 1386 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
795 1387 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
796 1388 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
797 1389 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
798 1390 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
799 1391 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
800 1392 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
804 1396 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
805 1397 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
806 1398 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
807 1399 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
808 1400 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
809 1401 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
810 1402 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
811 1403 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
812 1404 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
813 1405 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
814 1406 2.195567 TTGGTCACAAGGCAGCAGC 61.196 57.895 0.00 0.00 41.10 5.25
815 1407 4.162592 TTGGTCACAAGGCAGCAG 57.837 55.556 0.00 0.00 31.73 4.24
829 1421 0.107831 TTGAACCCGTGACCTCTTGG 59.892 55.000 0.00 0.00 39.83 3.61
830 1422 1.202651 ACTTGAACCCGTGACCTCTTG 60.203 52.381 0.00 0.00 0.00 3.02
831 1423 1.070289 GACTTGAACCCGTGACCTCTT 59.930 52.381 0.00 0.00 0.00 2.85
832 1424 0.680061 GACTTGAACCCGTGACCTCT 59.320 55.000 0.00 0.00 0.00 3.69
833 1425 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
834 1426 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
835 1427 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
836 1428 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
837 1429 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
838 1430 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
839 1431 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
840 1432 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
841 1433 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
842 1434 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
843 1435 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
844 1436 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
845 1437 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
846 1438 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
847 1439 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
848 1440 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
849 1441 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
850 1442 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
851 1443 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
852 1444 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
864 1456 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
865 1457 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
866 1458 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
867 1459 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
868 1460 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
869 1461 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
870 1462 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
871 1463 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
872 1464 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
873 1465 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
874 1466 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
875 1467 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
876 1468 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
877 1469 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
878 1470 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
879 1471 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
880 1472 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
881 1473 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
882 1474 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
883 1475 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
884 1476 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
885 1477 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
886 1478 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
887 1479 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
888 1480 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
889 1481 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
890 1482 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
900 1492 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
901 1493 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
902 1494 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
903 1495 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
904 1496 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
905 1497 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
906 1498 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
907 1499 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
914 1506 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
930 1522 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
933 1525 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
934 1526 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
935 1527 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
936 1528 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
942 1534 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
943 1535 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
944 1536 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
945 1537 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
946 1538 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
979 1574 6.586344 TCATCTTAAGGTCATCTCCAACATC 58.414 40.000 1.85 0.00 0.00 3.06
1490 4321 5.062558 GCAATCATTAAACATGCAACAGGAC 59.937 40.000 0.00 0.00 37.00 3.85
1579 4410 7.452880 TCTTGATCTGGAAAAATAACAGTGG 57.547 36.000 0.00 0.00 34.02 4.00
1708 4547 6.202937 GTGGAACAATTCACACGACAAATAA 58.797 36.000 0.00 0.00 44.16 1.40
1875 4715 5.817816 GCAAGCACAAGTTCCAGTATATAGT 59.182 40.000 0.00 0.00 0.00 2.12
2289 5133 3.516615 CTGCAAAACCAAAGAAAACGGA 58.483 40.909 0.00 0.00 0.00 4.69
2325 5169 1.391485 CTCCAATCTATATGCGCGTGC 59.609 52.381 15.48 15.48 43.20 5.34
2434 5279 4.974368 TCTACACCAACCAAACAACAAG 57.026 40.909 0.00 0.00 0.00 3.16
2825 6002 1.604278 GGTGGTGCAAACTCAAGTCTC 59.396 52.381 0.00 0.00 0.00 3.36
3017 6199 6.369065 GGAGTAACACTCAAGGTTATGTCAAG 59.631 42.308 8.47 0.00 46.79 3.02
3075 6257 2.612212 GAGTTTGCTTTCAAGACACCGA 59.388 45.455 0.00 0.00 33.12 4.69
3321 7325 5.348986 GGTCAGTGTACGACATGTTCATAT 58.651 41.667 0.00 0.00 34.97 1.78
3615 7625 3.008049 ACCAAACAGCCCTGACTACTAAG 59.992 47.826 1.69 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.