Multiple sequence alignment - TraesCS3D01G512300

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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 TraesCS3D01G512300 chr3D 100.000 3647 0 0 1 3647 596892598 596888952 0.000000e+00 6735.0
1 TraesCS3D01G512300 chr3D 78.215 661 115 23 1966 2613 578243306 578242662 2.640000e-106 396.0
2 TraesCS3D01G512300 chr3D 74.362 901 204 20 1711 2602 579429348 579430230 3.460000e-95 359.0
3 TraesCS3D01G512300 chr3D 84.058 138 19 3 2963 3099 290858257 290858122 2.960000e-26 130.0
4 TraesCS3D01G512300 chr3D 81.884 138 25 0 2976 3113 251316011 251316148 2.300000e-22 117.0
5 TraesCS3D01G512300 chr3D 82.482 137 16 6 2968 3103 127342848 127342719 2.980000e-21 113.0
6 TraesCS3D01G512300 chr3B 90.181 2322 156 34 1352 3647 802998404 803000679 0.000000e+00 2959.0
7 TraesCS3D01G512300 chr3B 90.881 1272 97 13 1465 2725 802929956 802928693 0.000000e+00 1688.0
8 TraesCS3D01G512300 chr3B 81.541 1116 117 50 363 1428 802932150 802931074 0.000000e+00 837.0
9 TraesCS3D01G512300 chr3B 86.422 626 40 22 640 1233 802997722 802998334 0.000000e+00 643.0
10 TraesCS3D01G512300 chr3B 88.100 521 47 8 2 510 802997081 802997598 4.030000e-169 604.0
11 TraesCS3D01G512300 chr3B 78.215 661 115 22 1966 2613 771533209 771532565 2.640000e-106 396.0
12 TraesCS3D01G512300 chr3B 73.579 897 218 15 1711 2602 773843724 773844606 3.510000e-85 326.0
13 TraesCS3D01G512300 chr3B 92.500 160 5 2 460 619 802997598 802997750 4.740000e-54 222.0
14 TraesCS3D01G512300 chr3B 83.333 138 20 3 2963 3099 383706443 383706308 1.380000e-24 124.0
15 TraesCS3D01G512300 chr3B 88.889 72 5 3 157 226 74334413 74334343 6.490000e-13 86.1
16 TraesCS3D01G512300 chr3B 90.476 63 6 0 169 231 31540131 31540193 2.330000e-12 84.2
17 TraesCS3D01G512300 chr3B 90.476 63 6 0 169 231 31557806 31557868 2.330000e-12 84.2
18 TraesCS3D01G512300 chr3B 85.897 78 10 1 157 233 475463198 475463121 8.390000e-12 82.4
19 TraesCS3D01G512300 chr3A 76.335 693 139 20 1893 2574 712553167 712553845 7.500000e-92 348.0
20 TraesCS3D01G512300 chr3A 74.571 700 151 22 1924 2614 713623124 713622443 7.710000e-72 281.0
21 TraesCS3D01G512300 chr3A 85.484 124 18 0 2977 3100 8867714 8867837 2.960000e-26 130.0
22 TraesCS3D01G512300 chr3A 82.609 138 24 0 2976 3113 332556293 332556156 4.950000e-24 122.0
23 TraesCS3D01G512300 chr3A 86.047 86 12 0 145 230 53225272 53225187 3.880000e-15 93.5
24 TraesCS3D01G512300 chrUn 73.567 855 207 15 1711 2560 41302672 41303512 3.540000e-80 309.0
25 TraesCS3D01G512300 chrUn 82.000 100 16 2 3334 3432 182868731 182868633 2.330000e-12 84.2
26 TraesCS3D01G512300 chr6B 86.131 137 13 4 2969 3103 46424663 46424795 3.800000e-30 143.0
27 TraesCS3D01G512300 chr1B 83.607 122 19 1 2977 3098 316256121 316256241 2.980000e-21 113.0
28 TraesCS3D01G512300 chr6A 85.714 84 12 0 147 230 109489593 109489510 5.020000e-14 89.8
29 TraesCS3D01G512300 chr2A 88.158 76 8 1 157 232 21463642 21463716 5.020000e-14 89.8
30 TraesCS3D01G512300 chr5B 81.818 99 17 1 3334 3432 676056917 676056820 8.390000e-12 82.4
31 TraesCS3D01G512300 chr4A 83.750 80 12 1 3334 3413 542992175 542992253 1.400000e-09 75.0
32 TraesCS3D01G512300 chr7D 85.135 74 8 3 157 230 106576213 106576143 5.050000e-09 73.1
33 TraesCS3D01G512300 chr4D 83.333 78 13 0 3334 3411 82443717 82443794 5.050000e-09 73.1
34 TraesCS3D01G512300 chr2D 90.741 54 5 0 3343 3396 170605695 170605642 5.050000e-09 73.1
35 TraesCS3D01G512300 chr2B 90.196 51 5 0 3334 3384 63058071 63058021 2.350000e-07 67.6


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 TraesCS3D01G512300 chr3D 596888952 596892598 3646 True 6735.0 6735 100.00000 1 3647 1 chr3D.!!$R4 3646
1 TraesCS3D01G512300 chr3D 578242662 578243306 644 True 396.0 396 78.21500 1966 2613 1 chr3D.!!$R3 647
2 TraesCS3D01G512300 chr3D 579429348 579430230 882 False 359.0 359 74.36200 1711 2602 1 chr3D.!!$F2 891
3 TraesCS3D01G512300 chr3B 802928693 802932150 3457 True 1262.5 1688 86.21100 363 2725 2 chr3B.!!$R5 2362
4 TraesCS3D01G512300 chr3B 802997081 803000679 3598 False 1107.0 2959 89.30075 2 3647 4 chr3B.!!$F4 3645
5 TraesCS3D01G512300 chr3B 771532565 771533209 644 True 396.0 396 78.21500 1966 2613 1 chr3B.!!$R4 647
6 TraesCS3D01G512300 chr3B 773843724 773844606 882 False 326.0 326 73.57900 1711 2602 1 chr3B.!!$F3 891
7 TraesCS3D01G512300 chr3A 712553167 712553845 678 False 348.0 348 76.33500 1893 2574 1 chr3A.!!$F2 681
8 TraesCS3D01G512300 chr3A 713622443 713623124 681 True 281.0 281 74.57100 1924 2614 1 chr3A.!!$R3 690
9 TraesCS3D01G512300 chrUn 41302672 41303512 840 False 309.0 309 73.56700 1711 2560 1 chrUn.!!$F1 849

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
66 72 0.036732 AAGCAAGATGGACGGAAGCA 59.963 50.0 0.00 0.0 0.00 3.91 F
333 344 0.108804 GCACGCAGCACCTAGTCTAA 60.109 55.0 0.00 0.0 44.79 2.10 F
1195 1338 1.306148 TCGGTCGATCTCGCAGTAAT 58.694 50.0 0.00 0.0 39.60 1.89 F
1261 1411 0.178891 TTCCTTCTCCAGCCAGACCT 60.179 55.0 0.00 0.0 0.00 3.85 F
1920 3190 0.179073 GTGACCCGTCATATGCAGCT 60.179 55.0 0.03 0.0 42.18 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1316 0.029567 ACTGCGAGATCGACCGATTC 59.970 55.0 6.39 5.68 43.02 2.52 R
1250 1400 0.032615 AGAGGAGTAGGTCTGGCTGG 60.033 60.0 0.00 0.00 0.00 4.85 R
2465 3744 0.034089 AATGAGGCCCTGGTTGTAGC 60.034 55.0 0.00 0.00 0.00 3.58 R
2515 3794 0.681887 TACGTCTCGATTGCCCCTGA 60.682 55.0 0.00 0.00 0.00 3.86 R
3620 4916 0.784778 CGTCTCTCGTGAAGCAAACC 59.215 55.0 0.00 0.00 34.52 3.27 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
26 27 0.040781 CCGCGGTTACACAAAGGTTG 60.041 55.000 19.50 0.00 0.00 3.77
35 36 0.310854 CACAAAGGTTGGCCTCGTTC 59.689 55.000 3.32 0.00 46.33 3.95
36 37 0.822121 ACAAAGGTTGGCCTCGTTCC 60.822 55.000 3.32 0.00 46.33 3.62
37 38 0.821711 CAAAGGTTGGCCTCGTTCCA 60.822 55.000 3.32 0.00 46.33 3.53
44 45 1.698506 TGGCCTCGTTCCAAATGTTT 58.301 45.000 3.32 0.00 0.00 2.83
45 46 1.339610 TGGCCTCGTTCCAAATGTTTG 59.660 47.619 3.32 0.00 37.90 2.93
53 59 4.803088 TCGTTCCAAATGTTTGAAAGCAAG 59.197 37.500 7.04 0.00 40.55 4.01
59 65 5.178067 CCAAATGTTTGAAAGCAAGATGGAC 59.822 40.000 7.04 0.00 40.55 4.02
66 72 0.036732 AAGCAAGATGGACGGAAGCA 59.963 50.000 0.00 0.00 0.00 3.91
68 74 1.098050 GCAAGATGGACGGAAGCATT 58.902 50.000 0.00 0.00 0.00 3.56
82 88 1.139989 AGCATTGACTTGTGACGTCG 58.860 50.000 11.62 0.00 34.17 5.12
86 92 2.115348 TTGACTTGTGACGTCGACTC 57.885 50.000 14.70 10.63 34.17 3.36
89 95 2.050714 TTGTGACGTCGACTCGGC 60.051 61.111 14.70 3.84 39.54 5.54
116 122 2.804931 CGCGATGACGTGCACTCA 60.805 61.111 16.19 16.96 42.78 3.41
125 131 1.661509 CGTGCACTCAGAAGCGTCA 60.662 57.895 16.19 0.00 0.00 4.35
188 194 9.419297 GGTGAAAGTTTCTAAAGTTTGACTTTT 57.581 29.630 18.41 4.59 45.38 2.27
225 231 9.797642 ATATGCACTACATTATGAAATGAAGGA 57.202 29.630 0.00 0.00 44.50 3.36
226 232 7.936496 TGCACTACATTATGAAATGAAGGAA 57.064 32.000 0.00 0.00 44.50 3.36
258 269 9.045223 ACTATAATATGTCGACACGTAGTAACA 57.955 33.333 22.71 5.91 41.61 2.41
264 275 5.443261 TGTCGACACGTAGTAACAAGTAAG 58.557 41.667 15.76 0.00 41.61 2.34
333 344 0.108804 GCACGCAGCACCTAGTCTAA 60.109 55.000 0.00 0.00 44.79 2.10
435 448 2.164422 GGAAACTAAACCTGAGCATGCC 59.836 50.000 15.66 6.65 0.00 4.40
501 564 3.507786 CGTTGATATCACCGAACAGACA 58.492 45.455 16.82 0.00 33.43 3.41
583 687 4.885413 GGCATGATTGCTTATTAATGCCA 58.115 39.130 17.29 0.00 46.23 4.92
584 688 5.484715 GGCATGATTGCTTATTAATGCCAT 58.515 37.500 17.29 0.00 46.23 4.40
585 689 5.579511 GGCATGATTGCTTATTAATGCCATC 59.420 40.000 17.29 2.00 46.23 3.51
586 690 6.395629 GCATGATTGCTTATTAATGCCATCT 58.604 36.000 0.00 0.00 45.77 2.90
587 691 6.530534 GCATGATTGCTTATTAATGCCATCTC 59.469 38.462 0.00 0.00 45.77 2.75
588 692 7.599171 CATGATTGCTTATTAATGCCATCTCA 58.401 34.615 11.03 3.88 33.98 3.27
589 693 7.585579 TGATTGCTTATTAATGCCATCTCAA 57.414 32.000 11.03 2.45 33.98 3.02
654 758 9.773328 AAACAAGTGTATGTATGATTGATTTCG 57.227 29.630 0.00 0.00 32.02 3.46
655 759 8.492673 ACAAGTGTATGTATGATTGATTTCGT 57.507 30.769 0.00 0.00 0.00 3.85
656 760 8.946085 ACAAGTGTATGTATGATTGATTTCGTT 58.054 29.630 0.00 0.00 0.00 3.85
705 812 7.412346 GCATGTATGATCGATTCAACATCTACC 60.412 40.741 14.08 4.40 38.03 3.18
706 813 7.049799 TGTATGATCGATTCAACATCTACCA 57.950 36.000 0.00 0.00 38.03 3.25
709 816 4.803613 TGATCGATTCAACATCTACCAACG 59.196 41.667 0.00 0.00 0.00 4.10
839 960 2.510664 TGGAAAACCCAAGTGGCAC 58.489 52.632 10.29 10.29 43.29 5.01
865 987 7.334421 CCTTGCTGTTACATTAGCTAGAGAAAA 59.666 37.037 8.78 0.00 42.67 2.29
866 988 7.596749 TGCTGTTACATTAGCTAGAGAAAAC 57.403 36.000 0.00 2.93 40.52 2.43
868 990 6.037281 GCTGTTACATTAGCTAGAGAAAACCC 59.963 42.308 0.00 0.00 36.99 4.11
869 991 7.011499 TGTTACATTAGCTAGAGAAAACCCA 57.989 36.000 0.00 0.00 0.00 4.51
870 992 7.103641 TGTTACATTAGCTAGAGAAAACCCAG 58.896 38.462 0.00 0.00 0.00 4.45
926 1059 6.954102 TCTCACTATATAAGGCTGGCTAATGA 59.046 38.462 3.41 0.00 0.00 2.57
999 1141 2.324860 GGTTGACGCCATTAAGCAAAC 58.675 47.619 0.00 0.00 0.00 2.93
1058 1201 6.478344 GCCTCTCTAGTGTACTGATTCATTTG 59.522 42.308 0.00 0.00 0.00 2.32
1062 1205 9.778741 TCTCTAGTGTACTGATTCATTTGTTTT 57.221 29.630 0.00 0.00 0.00 2.43
1105 1248 7.061210 CACATATGTAGTTATGAGCGCTCTTAC 59.939 40.741 35.27 27.39 34.37 2.34
1122 1265 6.367969 CGCTCTTACTCCTACAAAAGCTTTTA 59.632 38.462 23.44 9.04 0.00 1.52
1165 1308 8.918202 TGACTATTTGTAAGTGGACTGAAAAT 57.082 30.769 0.00 0.00 0.00 1.82
1195 1338 1.306148 TCGGTCGATCTCGCAGTAAT 58.694 50.000 0.00 0.00 39.60 1.89
1197 1340 2.222678 TCGGTCGATCTCGCAGTAATAC 59.777 50.000 0.00 0.00 39.60 1.89
1204 1347 6.418226 GTCGATCTCGCAGTAATACTTGAATT 59.582 38.462 0.00 0.00 39.60 2.17
1244 1394 1.981256 TTTTCCTCCACCAGCTGTTC 58.019 50.000 13.81 0.00 0.00 3.18
1250 1400 0.687354 TCCACCAGCTGTTCCTTCTC 59.313 55.000 13.81 0.00 0.00 2.87
1258 1408 0.979665 CTGTTCCTTCTCCAGCCAGA 59.020 55.000 0.00 0.00 0.00 3.86
1261 1411 0.178891 TTCCTTCTCCAGCCAGACCT 60.179 55.000 0.00 0.00 0.00 3.85
1317 1468 1.601419 CCTTCTTCGGTGCGGTCCTA 61.601 60.000 0.00 0.00 0.00 2.94
1326 1477 2.288025 TGCGGTCCTAACCAGTCCC 61.288 63.158 0.00 0.00 46.86 4.46
1338 1489 1.038280 CCAGTCCCTACCGGTGATAC 58.962 60.000 19.93 10.16 0.00 2.24
1339 1490 1.411216 CCAGTCCCTACCGGTGATACT 60.411 57.143 19.93 12.41 0.00 2.12
1346 1497 2.304092 CTACCGGTGATACTGCTACCA 58.696 52.381 19.93 0.00 34.10 3.25
1374 1526 2.126307 CCCTGTCTCGAGCACACG 60.126 66.667 7.81 7.19 0.00 4.49
1403 1556 1.937191 ATCCAAGGGGCGTCAAAAAT 58.063 45.000 0.00 0.00 0.00 1.82
1409 1562 4.064388 CAAGGGGCGTCAAAAATGAAAAT 58.936 39.130 0.00 0.00 0.00 1.82
1410 1563 4.350368 AGGGGCGTCAAAAATGAAAATT 57.650 36.364 0.00 0.00 0.00 1.82
1423 1576 9.632807 CAAAAATGAAAATTATGACCCGAACTA 57.367 29.630 0.00 0.00 0.00 2.24
1431 1584 0.251653 TGACCCGAACTAGTGAGCCT 60.252 55.000 0.00 0.00 0.00 4.58
1433 1586 0.251653 ACCCGAACTAGTGAGCCTCA 60.252 55.000 0.00 0.00 0.00 3.86
1434 1587 0.457851 CCCGAACTAGTGAGCCTCAG 59.542 60.000 0.00 0.00 0.00 3.35
1496 2756 2.902846 CGGCGAGATCCGGAGTCT 60.903 66.667 11.34 13.00 45.38 3.24
1518 2785 3.316573 CTCACAAGGTCTCCGCCCC 62.317 68.421 0.00 0.00 0.00 5.80
1519 2786 4.410400 CACAAGGTCTCCGCCCCC 62.410 72.222 0.00 0.00 0.00 5.40
1520 2787 4.658786 ACAAGGTCTCCGCCCCCT 62.659 66.667 0.00 0.00 0.00 4.79
1521 2788 3.787001 CAAGGTCTCCGCCCCCTC 61.787 72.222 0.00 0.00 0.00 4.30
1570 2838 6.037726 CCTACACAAATTTTAATTACGGGCC 58.962 40.000 0.00 0.00 0.00 5.80
1583 2851 5.562298 ATTACGGGCCACTTGTAGATAAT 57.438 39.130 4.39 0.00 0.00 1.28
1597 2866 7.541091 ACTTGTAGATAATCCACGCGTATTATG 59.459 37.037 24.67 14.82 30.32 1.90
1602 2871 8.630278 AGATAATCCACGCGTATTATGATTAC 57.370 34.615 24.67 13.75 30.32 1.89
1603 2872 7.705325 AGATAATCCACGCGTATTATGATTACC 59.295 37.037 24.67 16.52 30.32 2.85
1604 2873 4.587584 TCCACGCGTATTATGATTACCA 57.412 40.909 13.44 0.00 0.00 3.25
1684 2954 2.139917 TGATCCAAACAAGTTCCGACG 58.860 47.619 0.00 0.00 0.00 5.12
1687 2957 1.666700 TCCAAACAAGTTCCGACGTTG 59.333 47.619 0.00 0.00 0.00 4.10
1863 3133 1.489649 AGTGGCATCTTCCTCATCCTG 59.510 52.381 0.00 0.00 0.00 3.86
1917 3187 1.142965 CCGTGACCCGTCATATGCA 59.857 57.895 0.03 0.00 42.18 3.96
1920 3190 0.179073 GTGACCCGTCATATGCAGCT 60.179 55.000 0.03 0.00 42.18 4.24
2037 3310 2.194056 CTCCCGGCCATGCAGAAT 59.806 61.111 2.24 0.00 0.00 2.40
2163 3439 1.201429 TCAGGGACCCTTCTGGCTTC 61.201 60.000 11.56 0.00 37.83 3.86
2280 3556 0.370273 GGCTCAACTATGCGACGTTG 59.630 55.000 0.00 0.00 41.30 4.10
2682 3970 1.334779 CGTCTATGTACGTAGCTGGCC 60.335 57.143 16.06 0.00 38.07 5.36
2690 3978 2.176273 CGTAGCTGGCCTGTCATGC 61.176 63.158 11.69 2.74 0.00 4.06
2693 3981 0.179037 TAGCTGGCCTGTCATGCATC 60.179 55.000 11.69 0.00 0.00 3.91
2708 3996 1.885157 CATCCATGCGTTGCCACTT 59.115 52.632 0.00 0.00 0.00 3.16
2727 4015 7.545265 TGCCACTTGTTGAATAAAAATAGATGC 59.455 33.333 0.00 0.00 0.00 3.91
2765 4053 4.762289 AGCCTATGAACGAATCTTCCTT 57.238 40.909 0.00 0.00 0.00 3.36
2998 4287 3.359950 ACTACCTTCGTCCCGAATTAGT 58.640 45.455 11.82 11.82 44.85 2.24
3118 4407 8.723311 CGGAGGTAATATGTTTTAAACTTGTCA 58.277 33.333 9.33 0.00 0.00 3.58
3128 4417 8.527567 TGTTTTAAACTTGTCAGAAAAACCAG 57.472 30.769 9.33 0.00 36.48 4.00
3129 4418 7.600752 TGTTTTAAACTTGTCAGAAAAACCAGG 59.399 33.333 9.33 0.00 36.48 4.45
3130 4419 6.844097 TTAAACTTGTCAGAAAAACCAGGT 57.156 33.333 0.00 0.00 0.00 4.00
3131 4420 5.738619 AAACTTGTCAGAAAAACCAGGTT 57.261 34.783 0.00 0.00 0.00 3.50
3132 4421 4.718940 ACTTGTCAGAAAAACCAGGTTG 57.281 40.909 5.30 0.00 0.00 3.77
3133 4422 3.119137 ACTTGTCAGAAAAACCAGGTTGC 60.119 43.478 5.30 0.00 0.00 4.17
3134 4423 2.733956 TGTCAGAAAAACCAGGTTGCT 58.266 42.857 5.30 1.02 0.00 3.91
3135 4424 2.426738 TGTCAGAAAAACCAGGTTGCTG 59.573 45.455 17.92 17.92 0.00 4.41
3144 4433 2.800881 CCAGGTTGCTGGTTTTCTTC 57.199 50.000 0.00 0.00 39.56 2.87
3149 4438 4.453819 CAGGTTGCTGGTTTTCTTCTAGAG 59.546 45.833 0.00 0.00 0.00 2.43
3165 4454 5.808366 TCTAGAGCCAGAAGTTTCTTTCA 57.192 39.130 0.00 0.00 34.74 2.69
3229 4518 2.266372 CCCGTGGCGTATGTTGGA 59.734 61.111 0.00 0.00 0.00 3.53
3269 4558 2.330231 AACAACAATTCATCCACGCG 57.670 45.000 3.53 3.53 0.00 6.01
3279 4568 2.578786 TCATCCACGCGTAGAATAGGA 58.421 47.619 13.44 14.45 0.00 2.94
3280 4569 2.552743 TCATCCACGCGTAGAATAGGAG 59.447 50.000 13.44 7.68 32.46 3.69
3329 4618 1.671379 GAACCTGTCACGGAAGCCC 60.671 63.158 0.00 0.00 0.00 5.19
3355 4644 1.618343 GGGTCAGTTTTGATGGGTTGG 59.382 52.381 0.00 0.00 35.39 3.77
3359 4648 1.273327 CAGTTTTGATGGGTTGGGAGC 59.727 52.381 0.00 0.00 0.00 4.70
3402 4691 2.690778 GGCGCCAGGTGTCATGTTC 61.691 63.158 24.80 0.00 0.00 3.18
3458 4754 6.772716 TGCACTTTTGGACTCTAGAGAATTTT 59.227 34.615 26.57 2.82 0.00 1.82
3470 4766 8.138074 ACTCTAGAGAATTTTGTTTGGCTTTTC 58.862 33.333 26.57 0.00 0.00 2.29
3472 4768 8.695456 TCTAGAGAATTTTGTTTGGCTTTTCTT 58.305 29.630 0.00 0.00 0.00 2.52
3512 4808 6.153851 CCCCTAGGTTTCGGAAAATAAATTGT 59.846 38.462 8.29 0.00 0.00 2.71
3515 4811 7.968405 CCTAGGTTTCGGAAAATAAATTGTCTG 59.032 37.037 4.46 0.00 32.71 3.51
3516 4812 7.284919 AGGTTTCGGAAAATAAATTGTCTGT 57.715 32.000 4.46 0.00 33.14 3.41
3517 4813 8.398878 AGGTTTCGGAAAATAAATTGTCTGTA 57.601 30.769 4.46 0.00 33.14 2.74
3518 4814 9.020731 AGGTTTCGGAAAATAAATTGTCTGTAT 57.979 29.630 4.46 0.00 33.14 2.29
3631 4927 0.312102 GAGGCACAGGTTTGCTTCAC 59.688 55.000 2.64 0.00 45.50 3.18
3642 4938 0.664466 TTGCTTCACGAGAGACGCAG 60.664 55.000 0.00 0.00 42.58 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.167781 AACCTTTGTGTAACCGCGGG 61.168 55.000 31.76 11.88 34.36 6.13
9 10 0.318360 GCCAACCTTTGTGTAACCGC 60.318 55.000 0.00 0.00 34.36 5.68
26 27 1.611491 TCAAACATTTGGAACGAGGCC 59.389 47.619 0.00 0.00 38.66 5.19
35 36 5.178067 GTCCATCTTGCTTTCAAACATTTGG 59.822 40.000 4.58 0.00 38.66 3.28
36 37 5.107760 CGTCCATCTTGCTTTCAAACATTTG 60.108 40.000 0.00 0.00 39.48 2.32
37 38 4.984161 CGTCCATCTTGCTTTCAAACATTT 59.016 37.500 0.00 0.00 0.00 2.32
44 45 2.426522 CTTCCGTCCATCTTGCTTTCA 58.573 47.619 0.00 0.00 0.00 2.69
45 46 1.131315 GCTTCCGTCCATCTTGCTTTC 59.869 52.381 0.00 0.00 0.00 2.62
53 59 2.029838 AGTCAATGCTTCCGTCCATC 57.970 50.000 0.00 0.00 0.00 3.51
59 65 1.136252 CGTCACAAGTCAATGCTTCCG 60.136 52.381 0.00 0.00 0.00 4.30
66 72 2.662700 GAGTCGACGTCACAAGTCAAT 58.337 47.619 17.16 0.00 38.46 2.57
68 74 0.041576 CGAGTCGACGTCACAAGTCA 60.042 55.000 17.16 0.00 38.46 3.41
101 107 0.987715 CTTCTGAGTGCACGTCATCG 59.012 55.000 12.01 5.40 43.34 3.84
110 116 1.070309 CAAGTTGACGCTTCTGAGTGC 60.070 52.381 0.00 0.00 36.87 4.40
160 166 8.117813 AGTCAAACTTTAGAAACTTTCACCAA 57.882 30.769 4.34 0.00 0.00 3.67
199 205 9.797642 TCCTTCATTTCATAATGTAGTGCATAT 57.202 29.630 0.00 0.00 41.54 1.78
200 206 9.625747 TTCCTTCATTTCATAATGTAGTGCATA 57.374 29.630 0.00 0.00 41.54 3.14
201 207 8.523915 TTCCTTCATTTCATAATGTAGTGCAT 57.476 30.769 0.00 0.00 41.54 3.96
202 208 7.611467 ACTTCCTTCATTTCATAATGTAGTGCA 59.389 33.333 0.00 0.00 41.54 4.57
203 209 7.989826 ACTTCCTTCATTTCATAATGTAGTGC 58.010 34.615 0.00 0.00 41.54 4.40
237 243 6.615088 ACTTGTTACTACGTGTCGACATATT 58.385 36.000 23.12 11.37 0.00 1.28
240 246 4.494350 ACTTGTTACTACGTGTCGACAT 57.506 40.909 23.12 9.40 0.00 3.06
241 247 3.969117 ACTTGTTACTACGTGTCGACA 57.031 42.857 15.76 15.76 0.00 4.35
242 248 4.319377 GCTTACTTGTTACTACGTGTCGAC 59.681 45.833 9.11 9.11 0.00 4.20
243 249 4.466828 GCTTACTTGTTACTACGTGTCGA 58.533 43.478 0.00 0.00 0.00 4.20
244 250 3.605486 GGCTTACTTGTTACTACGTGTCG 59.395 47.826 0.00 0.00 0.00 4.35
245 251 4.549458 TGGCTTACTTGTTACTACGTGTC 58.451 43.478 0.00 0.00 0.00 3.67
258 269 6.916360 TTGAAGGAAAATGATGGCTTACTT 57.084 33.333 0.00 0.00 0.00 2.24
264 275 4.354587 GTCGATTGAAGGAAAATGATGGC 58.645 43.478 0.00 0.00 0.00 4.40
299 310 2.074942 GTGCACGCACGTATTAGCA 58.925 52.632 6.38 0.00 37.19 3.49
333 344 4.633126 CGAGAATGGTTGTTCACATCTCAT 59.367 41.667 7.81 0.00 34.91 2.90
392 403 4.502016 CTGTACCTAGTCACTAGTCGACA 58.498 47.826 19.50 10.01 35.77 4.35
435 448 3.448686 ACGAGCTCGACCTTAAATGATG 58.551 45.455 40.58 8.52 43.02 3.07
487 550 3.067106 GTTGTCATGTCTGTTCGGTGAT 58.933 45.455 0.00 0.00 0.00 3.06
501 564 1.070821 CGCACGATGTCAGTTGTCAT 58.929 50.000 0.00 0.00 0.00 3.06
581 685 6.367149 ACGAAATCGATCATACATTGAGATGG 59.633 38.462 10.16 0.00 43.02 3.51
582 686 7.343614 ACGAAATCGATCATACATTGAGATG 57.656 36.000 10.16 0.00 43.02 2.90
583 687 7.953158 AACGAAATCGATCATACATTGAGAT 57.047 32.000 10.16 0.00 43.02 2.75
584 688 9.129209 GATAACGAAATCGATCATACATTGAGA 57.871 33.333 10.16 0.00 43.02 3.27
585 689 8.915654 TGATAACGAAATCGATCATACATTGAG 58.084 33.333 10.16 0.00 43.02 3.02
586 690 8.810652 TGATAACGAAATCGATCATACATTGA 57.189 30.769 10.16 0.00 43.02 2.57
587 691 8.703336 ACTGATAACGAAATCGATCATACATTG 58.297 33.333 10.16 0.07 43.02 2.82
588 692 8.818141 ACTGATAACGAAATCGATCATACATT 57.182 30.769 10.16 0.00 43.02 2.71
589 693 8.818141 AACTGATAACGAAATCGATCATACAT 57.182 30.769 10.16 0.00 43.02 2.29
628 732 9.773328 CGAAATCAATCATACATACACTTGTTT 57.227 29.630 0.00 0.00 0.00 2.83
629 733 8.946085 ACGAAATCAATCATACATACACTTGTT 58.054 29.630 0.00 0.00 0.00 2.83
630 734 8.492673 ACGAAATCAATCATACATACACTTGT 57.507 30.769 0.00 0.00 0.00 3.16
657 761 9.252962 CATGCACTTCTTTTTCTAAAAACTGAT 57.747 29.630 0.00 0.00 34.46 2.90
658 762 8.250332 ACATGCACTTCTTTTTCTAAAAACTGA 58.750 29.630 0.00 0.00 34.46 3.41
659 763 8.411318 ACATGCACTTCTTTTTCTAAAAACTG 57.589 30.769 0.00 0.00 34.46 3.16
665 769 8.390354 CGATCATACATGCACTTCTTTTTCTAA 58.610 33.333 0.00 0.00 0.00 2.10
666 770 7.763985 TCGATCATACATGCACTTCTTTTTCTA 59.236 33.333 0.00 0.00 0.00 2.10
667 771 6.595326 TCGATCATACATGCACTTCTTTTTCT 59.405 34.615 0.00 0.00 0.00 2.52
668 772 6.775088 TCGATCATACATGCACTTCTTTTTC 58.225 36.000 0.00 0.00 0.00 2.29
669 773 6.741992 TCGATCATACATGCACTTCTTTTT 57.258 33.333 0.00 0.00 0.00 1.94
670 774 6.932356 ATCGATCATACATGCACTTCTTTT 57.068 33.333 0.00 0.00 0.00 2.27
705 812 2.559998 AACTTGTTGGACTTGCGTTG 57.440 45.000 0.00 0.00 0.00 4.10
706 813 2.159296 GGAAACTTGTTGGACTTGCGTT 60.159 45.455 0.00 0.00 0.00 4.84
709 816 3.518634 TTGGAAACTTGTTGGACTTGC 57.481 42.857 0.00 0.00 0.00 4.01
747 859 5.189928 ACGTGCCATTTGACCATTTCTATA 58.810 37.500 0.00 0.00 0.00 1.31
752 864 2.606795 CGAACGTGCCATTTGACCATTT 60.607 45.455 0.00 0.00 0.00 2.32
753 865 1.068610 CGAACGTGCCATTTGACCATT 60.069 47.619 0.00 0.00 0.00 3.16
754 866 0.521291 CGAACGTGCCATTTGACCAT 59.479 50.000 0.00 0.00 0.00 3.55
755 867 1.945522 CGAACGTGCCATTTGACCA 59.054 52.632 0.00 0.00 0.00 4.02
756 868 1.442017 GCGAACGTGCCATTTGACC 60.442 57.895 0.00 0.00 0.00 4.02
757 869 0.725784 CTGCGAACGTGCCATTTGAC 60.726 55.000 0.00 0.00 0.00 3.18
758 870 1.573932 CTGCGAACGTGCCATTTGA 59.426 52.632 0.00 0.00 0.00 2.69
759 871 1.442520 CCTGCGAACGTGCCATTTG 60.443 57.895 0.00 0.00 0.00 2.32
839 960 5.907207 TCTCTAGCTAATGTAACAGCAAGG 58.093 41.667 0.00 0.00 40.36 3.61
926 1059 1.427368 TGGCTTGTTCCCATAAGTGGT 59.573 47.619 0.00 0.00 44.48 4.16
945 1080 4.439700 CCTCAAATATGTGCTTTGCTCCTG 60.440 45.833 0.00 0.00 34.36 3.86
999 1141 0.882042 GCAGATGCGTACCTCCCATG 60.882 60.000 0.00 0.00 0.00 3.66
1076 1219 5.241728 AGCGCTCATAACTACATATGTGAGA 59.758 40.000 18.81 6.17 36.15 3.27
1140 1283 8.918202 ATTTTCAGTCCACTTACAAATAGTCA 57.082 30.769 0.00 0.00 0.00 3.41
1173 1316 0.029567 ACTGCGAGATCGACCGATTC 59.970 55.000 6.39 5.68 43.02 2.52
1185 1328 7.481798 GGTTTTCAATTCAAGTATTACTGCGAG 59.518 37.037 0.00 0.00 0.00 5.03
1188 1331 7.375053 TGGGTTTTCAATTCAAGTATTACTGC 58.625 34.615 0.00 0.00 0.00 4.40
1195 1338 5.189659 CCGTTGGGTTTTCAATTCAAGTA 57.810 39.130 0.00 0.00 0.00 2.24
1218 1362 2.698274 GCTGGTGGAGGAAAAAGGAAAA 59.302 45.455 0.00 0.00 0.00 2.29
1244 1394 0.827368 GTAGGTCTGGCTGGAGAAGG 59.173 60.000 0.00 0.00 0.00 3.46
1250 1400 0.032615 AGAGGAGTAGGTCTGGCTGG 60.033 60.000 0.00 0.00 0.00 4.85
1258 1408 1.094269 AAGGGTGGAGAGGAGTAGGT 58.906 55.000 0.00 0.00 0.00 3.08
1261 1411 1.276622 GCAAAGGGTGGAGAGGAGTA 58.723 55.000 0.00 0.00 0.00 2.59
1300 1451 0.037975 GTTAGGACCGCACCGAAGAA 60.038 55.000 0.00 0.00 34.73 2.52
1326 1477 2.293677 CTGGTAGCAGTATCACCGGTAG 59.706 54.545 6.87 1.53 34.55 3.18
1338 1489 0.528684 GACGCCTTAGCTGGTAGCAG 60.529 60.000 17.67 17.67 45.56 4.24
1339 1490 1.515954 GACGCCTTAGCTGGTAGCA 59.484 57.895 0.00 0.00 45.56 3.49
1346 1497 1.305381 AGACAGGGACGCCTTAGCT 60.305 57.895 0.00 0.00 36.60 3.32
1374 1526 1.403647 GCCCCTTGGATTAAACAACGC 60.404 52.381 0.00 0.00 0.00 4.84
1403 1556 6.703319 TCACTAGTTCGGGTCATAATTTTCA 58.297 36.000 0.00 0.00 0.00 2.69
1409 1562 2.429610 GGCTCACTAGTTCGGGTCATAA 59.570 50.000 0.00 0.00 0.00 1.90
1410 1563 2.029623 GGCTCACTAGTTCGGGTCATA 58.970 52.381 0.00 0.00 0.00 2.15
1431 1584 1.378119 TCGCCGGTAGAGAAGCTGA 60.378 57.895 1.90 0.00 0.00 4.26
1433 1586 1.677966 TGTCGCCGGTAGAGAAGCT 60.678 57.895 1.90 0.00 0.00 3.74
1434 1587 1.516603 GTGTCGCCGGTAGAGAAGC 60.517 63.158 1.90 0.00 0.00 3.86
1436 1589 2.693762 CCGTGTCGCCGGTAGAGAA 61.694 63.158 1.90 0.00 43.07 2.87
1437 1590 3.129502 CCGTGTCGCCGGTAGAGA 61.130 66.667 1.90 0.00 43.07 3.10
1518 2785 9.709495 CAATTATCATAGAGAAGAAGAAGGAGG 57.291 37.037 0.00 0.00 0.00 4.30
1521 2788 9.487790 GGTCAATTATCATAGAGAAGAAGAAGG 57.512 37.037 0.00 0.00 0.00 3.46
1558 2826 4.822685 TCTACAAGTGGCCCGTAATTAA 57.177 40.909 0.00 0.00 0.00 1.40
1570 2838 3.444916 ACGCGTGGATTATCTACAAGTG 58.555 45.455 12.93 3.21 0.00 3.16
1583 2851 4.587584 TGGTAATCATAATACGCGTGGA 57.412 40.909 24.59 11.68 0.00 4.02
1620 2889 8.902806 TCAGCAATTAAGGACCATGTATAAAAG 58.097 33.333 0.00 0.00 0.00 2.27
1628 2897 6.400568 ACAAAATCAGCAATTAAGGACCATG 58.599 36.000 0.00 0.00 0.00 3.66
1632 2901 6.922957 TGACAACAAAATCAGCAATTAAGGAC 59.077 34.615 0.00 0.00 0.00 3.85
1643 2912 6.505044 TCAGATCCATGACAACAAAATCAG 57.495 37.500 0.00 0.00 0.00 2.90
1684 2954 2.916716 CGGCTGCACAAACATAATCAAC 59.083 45.455 0.50 0.00 0.00 3.18
1687 2957 2.518949 CACGGCTGCACAAACATAATC 58.481 47.619 0.50 0.00 0.00 1.75
1863 3133 3.458163 TCGAGCCCACCGACATCC 61.458 66.667 0.00 0.00 0.00 3.51
2465 3744 0.034089 AATGAGGCCCTGGTTGTAGC 60.034 55.000 0.00 0.00 0.00 3.58
2515 3794 0.681887 TACGTCTCGATTGCCCCTGA 60.682 55.000 0.00 0.00 0.00 3.86
2699 3987 8.810652 TCTATTTTTATTCAACAAGTGGCAAC 57.189 30.769 0.00 0.00 0.00 4.17
2708 3996 6.851609 AGCACGCATCTATTTTTATTCAACA 58.148 32.000 0.00 0.00 0.00 3.33
2727 4015 1.135972 GGCTACATTGTCACAAGCACG 60.136 52.381 10.56 0.00 34.85 5.34
2832 4121 8.983307 AAATGTTCATTTGTTTGTTTTGCAAT 57.017 23.077 0.00 0.00 36.89 3.56
2998 4287 8.984891 TTCGTAGTTAGATAAATTTCCGACAA 57.015 30.769 0.00 0.00 0.00 3.18
3042 4331 9.955102 TGTCTATATACGGATGTATCTAACACT 57.045 33.333 0.00 0.00 42.09 3.55
3126 4415 4.389374 TCTAGAAGAAAACCAGCAACCTG 58.611 43.478 0.00 0.00 38.85 4.00
3127 4416 4.646572 CTCTAGAAGAAAACCAGCAACCT 58.353 43.478 0.00 0.00 0.00 3.50
3128 4417 3.189495 GCTCTAGAAGAAAACCAGCAACC 59.811 47.826 0.00 0.00 0.00 3.77
3129 4418 3.189495 GGCTCTAGAAGAAAACCAGCAAC 59.811 47.826 0.00 0.00 0.00 4.17
3130 4419 3.181445 TGGCTCTAGAAGAAAACCAGCAA 60.181 43.478 0.00 0.00 0.00 3.91
3131 4420 2.371841 TGGCTCTAGAAGAAAACCAGCA 59.628 45.455 0.00 0.00 0.00 4.41
3132 4421 3.006247 CTGGCTCTAGAAGAAAACCAGC 58.994 50.000 0.00 0.00 34.91 4.85
3133 4422 4.543590 TCTGGCTCTAGAAGAAAACCAG 57.456 45.455 12.14 12.14 39.43 4.00
3134 4423 4.974645 TTCTGGCTCTAGAAGAAAACCA 57.025 40.909 3.36 0.07 33.08 3.67
3142 4431 6.174720 TGAAAGAAACTTCTGGCTCTAGAA 57.825 37.500 0.00 0.00 37.65 2.10
3143 4432 5.808366 TGAAAGAAACTTCTGGCTCTAGA 57.192 39.130 0.00 0.00 37.65 2.43
3144 4433 5.180304 GGTTGAAAGAAACTTCTGGCTCTAG 59.820 44.000 0.00 0.00 37.65 2.43
3149 4438 4.590850 ATGGTTGAAAGAAACTTCTGGC 57.409 40.909 0.00 0.00 37.65 4.85
3250 4539 1.606668 ACGCGTGGATGAATTGTTGTT 59.393 42.857 12.93 0.00 0.00 2.83
3264 4553 1.001597 GGTCCTCCTATTCTACGCGTG 60.002 57.143 24.59 12.26 0.00 5.34
3267 4556 1.700955 TGGGTCCTCCTATTCTACGC 58.299 55.000 0.00 0.00 36.20 4.42
3269 4558 4.217983 CGTACATGGGTCCTCCTATTCTAC 59.782 50.000 0.00 0.00 32.46 2.59
3279 4568 3.377253 TTACTCTCGTACATGGGTCCT 57.623 47.619 0.00 0.00 0.00 3.85
3280 4569 4.098960 TCAATTACTCTCGTACATGGGTCC 59.901 45.833 0.00 0.00 0.00 4.46
3329 4618 3.763897 CCCATCAAAACTGACCCTTAAGG 59.236 47.826 15.14 15.14 43.78 2.69
3340 4629 1.632589 GCTCCCAACCCATCAAAACT 58.367 50.000 0.00 0.00 0.00 2.66
3386 4675 1.300971 CCAGAACATGACACCTGGCG 61.301 60.000 0.00 0.00 39.59 5.69
3389 4678 1.432514 CGTCCAGAACATGACACCTG 58.567 55.000 0.00 0.70 0.00 4.00
3436 4732 8.753497 AACAAAATTCTCTAGAGTCCAAAAGT 57.247 30.769 19.21 8.66 0.00 2.66
3437 4733 9.455847 CAAACAAAATTCTCTAGAGTCCAAAAG 57.544 33.333 19.21 8.10 0.00 2.27
3446 4742 8.237811 AGAAAAGCCAAACAAAATTCTCTAGA 57.762 30.769 0.00 0.00 0.00 2.43
3482 4778 2.629017 TCCGAAACCTAGGGGTAACT 57.371 50.000 14.81 0.00 46.67 2.24
3544 4840 6.772233 TGTCTCCATGAGAAGAAAATTTGTGA 59.228 34.615 0.00 0.00 40.59 3.58
3620 4916 0.784778 CGTCTCTCGTGAAGCAAACC 59.215 55.000 0.00 0.00 34.52 3.27


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

AutoCloner maintained by Alex Coulton.