Multiple sequence alignment - TraesCS3B01G565100

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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 TraesCS3B01G565100 chr3B 100.000 3455 0 0 1 3455 798156102 798159556 0.000000e+00 6381.0
1 TraesCS3B01G565100 chr3B 87.447 1649 191 11 944 2589 798199850 798201485 0.000000e+00 1884.0
2 TraesCS3B01G565100 chr3B 89.293 495 48 4 1 492 798176264 798176756 1.760000e-172 616.0
3 TraesCS3B01G565100 chr3B 96.188 341 12 1 1 340 798148294 798148634 1.080000e-154 556.0
4 TraesCS3B01G565100 chr3A 92.764 1769 119 8 824 2589 725233295 725235057 0.000000e+00 2549.0
5 TraesCS3B01G565100 chr3A 85.078 1595 198 21 881 2460 745207444 745209013 0.000000e+00 1591.0
6 TraesCS3B01G565100 chr3A 90.255 1057 89 10 1476 2530 725362698 725363742 0.000000e+00 1369.0
7 TraesCS3B01G565100 chr3A 94.363 479 25 2 1 478 725147847 725148324 0.000000e+00 734.0
8 TraesCS3B01G565100 chr3A 91.767 498 31 7 49 541 725230531 725231023 0.000000e+00 684.0
9 TraesCS3B01G565100 chr3A 80.638 439 68 12 7 432 724795183 724794749 1.200000e-84 324.0
10 TraesCS3B01G565100 chr3A 84.135 208 27 5 576 778 725232920 725233126 2.720000e-46 196.0
11 TraesCS3B01G565100 chr3D 85.151 1724 213 20 889 2597 593911506 593909811 0.000000e+00 1725.0
12 TraesCS3B01G565100 chr3D 86.088 1567 199 9 981 2533 594510001 594511562 0.000000e+00 1668.0
13 TraesCS3B01G565100 chr3D 85.400 1589 204 15 1012 2588 593770551 593768979 0.000000e+00 1624.0
14 TraesCS3B01G565100 chr3D 92.089 493 33 3 1 492 594501565 594502052 0.000000e+00 689.0
15 TraesCS3B01G565100 chr3D 93.023 43 3 0 539 581 598422864 598422822 2.880000e-06 63.9
16 TraesCS3B01G565100 chrUn 84.561 1684 226 18 928 2597 288267008 288265345 0.000000e+00 1639.0
17 TraesCS3B01G565100 chrUn 84.145 1684 235 15 928 2598 41880841 41882505 0.000000e+00 1602.0
18 TraesCS3B01G565100 chr7B 92.325 873 64 2 2586 3455 581310688 581309816 0.000000e+00 1238.0
19 TraesCS3B01G565100 chr7B 91.982 873 67 3 2586 3455 494592995 494593867 0.000000e+00 1221.0
20 TraesCS3B01G565100 chr7B 86.567 67 6 3 2878 2944 239753962 239754025 1.720000e-08 71.3
21 TraesCS3B01G565100 chr5B 80.203 394 55 18 5 379 539615916 539615527 1.220000e-69 274.0
22 TraesCS3B01G565100 chr5B 82.639 288 47 2 3168 3452 654361755 654362042 5.720000e-63 252.0
23 TraesCS3B01G565100 chr5A 82.792 308 42 10 79 379 559618112 559617809 7.350000e-67 265.0
24 TraesCS3B01G565100 chr6B 72.961 233 49 11 1017 1244 706898408 706898631 6.190000e-08 69.4
25 TraesCS3B01G565100 chr6B 95.238 42 1 1 540 580 143631478 143631437 8.000000e-07 65.8
26 TraesCS3B01G565100 chr4A 100.000 36 0 0 543 578 612687676 612687641 2.230000e-07 67.6
27 TraesCS3B01G565100 chr2D 97.500 40 0 1 540 578 537414405 537414444 2.230000e-07 67.6
28 TraesCS3B01G565100 chr4B 93.182 44 1 2 540 581 614295322 614295365 2.880000e-06 63.9
29 TraesCS3B01G565100 chr1D 95.122 41 1 1 540 579 472010124 472010164 2.880000e-06 63.9
30 TraesCS3B01G565100 chr1B 95.122 41 1 1 540 579 19358372 19358332 2.880000e-06 63.9
31 TraesCS3B01G565100 chr1B 95.122 41 1 1 540 579 19394937 19394897 2.880000e-06 63.9
32 TraesCS3B01G565100 chr1B 94.595 37 2 0 495 531 262529199 262529163 1.340000e-04 58.4
33 TraesCS3B01G565100 chr4D 95.000 40 1 1 540 578 495347322 495347361 1.040000e-05 62.1


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 TraesCS3B01G565100 chr3B 798156102 798159556 3454 False 6381 6381 100.000000 1 3455 1 chr3B.!!$F2 3454
1 TraesCS3B01G565100 chr3B 798199850 798201485 1635 False 1884 1884 87.447000 944 2589 1 chr3B.!!$F4 1645
2 TraesCS3B01G565100 chr3A 745207444 745209013 1569 False 1591 1591 85.078000 881 2460 1 chr3A.!!$F3 1579
3 TraesCS3B01G565100 chr3A 725362698 725363742 1044 False 1369 1369 90.255000 1476 2530 1 chr3A.!!$F2 1054
4 TraesCS3B01G565100 chr3A 725230531 725235057 4526 False 1143 2549 89.555333 49 2589 3 chr3A.!!$F4 2540
5 TraesCS3B01G565100 chr3D 593909811 593911506 1695 True 1725 1725 85.151000 889 2597 1 chr3D.!!$R2 1708
6 TraesCS3B01G565100 chr3D 594510001 594511562 1561 False 1668 1668 86.088000 981 2533 1 chr3D.!!$F2 1552
7 TraesCS3B01G565100 chr3D 593768979 593770551 1572 True 1624 1624 85.400000 1012 2588 1 chr3D.!!$R1 1576
8 TraesCS3B01G565100 chrUn 288265345 288267008 1663 True 1639 1639 84.561000 928 2597 1 chrUn.!!$R1 1669
9 TraesCS3B01G565100 chrUn 41880841 41882505 1664 False 1602 1602 84.145000 928 2598 1 chrUn.!!$F1 1670
10 TraesCS3B01G565100 chr7B 581309816 581310688 872 True 1238 1238 92.325000 2586 3455 1 chr7B.!!$R1 869
11 TraesCS3B01G565100 chr7B 494592995 494593867 872 False 1221 1221 91.982000 2586 3455 1 chr7B.!!$F2 869

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
36 37 0.030908 CGAGTCGGATGGGAAGCTAC 59.969 60.0 4.10 0.0 0.00 3.58 F
515 519 0.099791 ACAAAAAGGTCCGTGCGTTG 59.900 50.0 0.00 0.0 0.00 4.10 F
554 558 0.105607 ATCTCCCCTAGAACCGGGAC 60.106 60.0 6.32 0.0 43.72 4.46 F
993 3000 0.394216 CCAATCTGCCACCGATCCAA 60.394 55.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 3983 0.960861 GCCAGTGCCCAACCTAGTTC 60.961 60.0 0.00 0.0 0.00 3.01 R
2171 4209 0.535335 TTCTACCGACTCATGGTGGC 59.465 55.0 0.00 0.0 40.73 5.01 R
2285 4323 3.149981 CCTAGATACTGCATCCTCGACA 58.850 50.0 0.00 0.0 33.75 4.35 R
2744 4785 0.456995 GAGGCCAGAAGAAGTCGTCG 60.457 60.0 5.01 0.0 0.00 5.12 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
17 18 3.924507 ATTTGCCGGCACCTCATC 58.075 55.556 32.95 0.00 0.00 2.92
18 19 2.114670 ATTTGCCGGCACCTCATCG 61.115 57.895 32.95 0.00 0.00 3.84
19 20 2.535485 ATTTGCCGGCACCTCATCGA 62.535 55.000 32.95 9.33 0.00 3.59
20 21 3.664025 TTGCCGGCACCTCATCGAG 62.664 63.158 32.95 0.00 0.00 4.04
21 22 4.148825 GCCGGCACCTCATCGAGT 62.149 66.667 24.80 0.00 0.00 4.18
22 23 2.105128 CCGGCACCTCATCGAGTC 59.895 66.667 0.00 0.00 0.00 3.36
23 24 2.278206 CGGCACCTCATCGAGTCG 60.278 66.667 6.09 6.09 0.00 4.18
24 25 2.105128 GGCACCTCATCGAGTCGG 59.895 66.667 13.54 0.00 0.00 4.79
25 26 2.415608 GGCACCTCATCGAGTCGGA 61.416 63.158 13.54 1.76 0.00 4.55
26 27 1.736586 GCACCTCATCGAGTCGGAT 59.263 57.895 13.54 2.16 0.00 4.18
27 28 0.596083 GCACCTCATCGAGTCGGATG 60.596 60.000 13.54 14.35 44.10 3.51
28 29 0.031314 CACCTCATCGAGTCGGATGG 59.969 60.000 13.54 12.12 43.18 3.51
29 30 1.109920 ACCTCATCGAGTCGGATGGG 61.110 60.000 13.54 14.02 43.21 4.00
30 31 0.823769 CCTCATCGAGTCGGATGGGA 60.824 60.000 19.85 8.59 45.84 4.37
31 32 1.032794 CTCATCGAGTCGGATGGGAA 58.967 55.000 13.54 0.00 45.84 3.97
32 33 1.000827 CTCATCGAGTCGGATGGGAAG 60.001 57.143 13.54 5.49 45.84 3.46
33 34 0.598680 CATCGAGTCGGATGGGAAGC 60.599 60.000 13.54 0.00 40.07 3.86
34 35 0.757188 ATCGAGTCGGATGGGAAGCT 60.757 55.000 13.54 0.00 0.00 3.74
35 36 0.106868 TCGAGTCGGATGGGAAGCTA 60.107 55.000 13.54 0.00 0.00 3.32
36 37 0.030908 CGAGTCGGATGGGAAGCTAC 59.969 60.000 4.10 0.00 0.00 3.58
37 38 1.404843 GAGTCGGATGGGAAGCTACT 58.595 55.000 0.00 0.00 0.00 2.57
38 39 1.338655 GAGTCGGATGGGAAGCTACTC 59.661 57.143 0.00 0.00 0.00 2.59
39 40 1.112113 GTCGGATGGGAAGCTACTCA 58.888 55.000 0.00 0.00 0.00 3.41
40 41 1.689273 GTCGGATGGGAAGCTACTCAT 59.311 52.381 0.00 0.00 33.28 2.90
41 42 1.688735 TCGGATGGGAAGCTACTCATG 59.311 52.381 0.00 0.00 30.48 3.07
42 43 1.270518 CGGATGGGAAGCTACTCATGG 60.271 57.143 0.00 0.00 30.48 3.66
43 44 1.771255 GGATGGGAAGCTACTCATGGT 59.229 52.381 0.00 0.00 30.48 3.55
44 45 2.972713 GGATGGGAAGCTACTCATGGTA 59.027 50.000 0.00 0.00 30.48 3.25
45 46 3.391296 GGATGGGAAGCTACTCATGGTAA 59.609 47.826 0.00 0.00 30.48 2.85
46 47 4.141482 GGATGGGAAGCTACTCATGGTAAA 60.141 45.833 0.00 0.00 30.48 2.01
47 48 4.487714 TGGGAAGCTACTCATGGTAAAG 57.512 45.455 0.00 0.00 0.00 1.85
57 58 3.195610 ACTCATGGTAAAGCATCGTCAGA 59.804 43.478 0.00 0.00 0.00 3.27
65 66 0.976641 AGCATCGTCAGAACCTCCAA 59.023 50.000 0.00 0.00 0.00 3.53
107 108 6.382869 ACTCTCAAAGTGGATGTTTTGAAG 57.617 37.500 1.91 5.06 41.30 3.02
108 109 5.186996 TCTCAAAGTGGATGTTTTGAAGC 57.813 39.130 1.91 0.00 41.30 3.86
109 110 4.644234 TCTCAAAGTGGATGTTTTGAAGCA 59.356 37.500 1.91 0.00 41.30 3.91
110 111 4.935702 TCAAAGTGGATGTTTTGAAGCAG 58.064 39.130 0.00 0.00 39.57 4.24
111 112 4.644234 TCAAAGTGGATGTTTTGAAGCAGA 59.356 37.500 0.00 0.00 39.57 4.26
112 113 4.843220 AAGTGGATGTTTTGAAGCAGAG 57.157 40.909 0.00 0.00 0.00 3.35
113 114 4.090761 AGTGGATGTTTTGAAGCAGAGA 57.909 40.909 0.00 0.00 0.00 3.10
142 144 2.282391 GCATGGGTGCCACTGACA 60.282 61.111 0.00 0.00 45.76 3.58
158 160 4.899239 CAGAAGGGCTAGGCGGCG 62.899 72.222 10.58 0.51 39.52 6.46
189 191 6.473521 CACTCTTCGTTAGCATGAATTTCTC 58.526 40.000 0.00 0.00 0.00 2.87
203 205 2.543777 TTTCTCCAAGTCTGTTCCGG 57.456 50.000 0.00 0.00 0.00 5.14
211 213 0.320697 AGTCTGTTCCGGCACCTTAC 59.679 55.000 0.56 0.00 0.00 2.34
212 214 1.012486 GTCTGTTCCGGCACCTTACG 61.012 60.000 0.56 0.00 0.00 3.18
309 311 5.335127 CCCGTCAAAGATTTGTGATGATTC 58.665 41.667 5.29 0.00 39.18 2.52
334 336 0.918983 CAACATGGCTCTTCCCCCTA 59.081 55.000 0.00 0.00 0.00 3.53
348 350 2.022428 TCCCCCTAGAGATGGTGCTTTA 60.022 50.000 0.00 0.00 0.00 1.85
398 400 6.253727 ACGTTGCAGTCTAAGATTAGATTTCG 59.746 38.462 5.64 7.78 41.43 3.46
440 442 6.931838 TGTATTTCCTCTCATAGTGTTTCGT 58.068 36.000 0.00 0.00 0.00 3.85
447 449 5.048153 TCTCATAGTGTTTCGTGACAGAG 57.952 43.478 0.00 0.00 0.00 3.35
457 459 1.686587 TCGTGACAGAGAAAGGCTTGA 59.313 47.619 0.00 0.00 0.00 3.02
505 509 9.636789 ACTCTTTACCATTACTAACAAAAAGGT 57.363 29.630 0.00 0.00 0.00 3.50
507 511 9.070179 TCTTTACCATTACTAACAAAAAGGTCC 57.930 33.333 0.00 0.00 0.00 4.46
511 515 4.816786 TTACTAACAAAAAGGTCCGTGC 57.183 40.909 0.00 0.00 0.00 5.34
513 517 1.600485 CTAACAAAAAGGTCCGTGCGT 59.400 47.619 0.00 0.00 0.00 5.24
514 518 0.812549 AACAAAAAGGTCCGTGCGTT 59.187 45.000 0.00 0.00 0.00 4.84
515 519 0.099791 ACAAAAAGGTCCGTGCGTTG 59.900 50.000 0.00 0.00 0.00 4.10
516 520 1.065109 AAAAAGGTCCGTGCGTTGC 59.935 52.632 0.00 0.00 0.00 4.17
517 521 1.658686 AAAAAGGTCCGTGCGTTGCA 61.659 50.000 0.00 0.00 35.60 4.08
519 523 2.331019 AAAGGTCCGTGCGTTGCAAC 62.331 55.000 19.89 19.89 41.47 4.17
551 555 3.240302 ACATAATCTCCCCTAGAACCGG 58.760 50.000 0.00 0.00 37.89 5.28
552 556 2.393630 TAATCTCCCCTAGAACCGGG 57.606 55.000 6.32 0.00 37.89 5.73
553 557 0.640495 AATCTCCCCTAGAACCGGGA 59.360 55.000 6.32 4.60 46.52 5.14
554 558 0.105607 ATCTCCCCTAGAACCGGGAC 60.106 60.000 6.32 0.00 43.72 4.46
555 559 1.219824 TCTCCCCTAGAACCGGGACT 61.220 60.000 6.32 7.19 43.72 3.85
557 561 0.554792 TCCCCTAGAACCGGGACTAG 59.445 60.000 22.13 22.13 43.72 2.57
559 563 1.496429 CCCCTAGAACCGGGACTAGTA 59.504 57.143 24.89 4.45 44.90 1.82
560 564 2.580962 CCCTAGAACCGGGACTAGTAC 58.419 57.143 24.89 0.00 44.90 2.73
561 565 2.580962 CCTAGAACCGGGACTAGTACC 58.419 57.143 24.89 14.92 35.65 3.34
562 566 2.580962 CTAGAACCGGGACTAGTACCC 58.419 57.143 19.06 17.48 43.57 3.69
564 568 1.109609 GAACCGGGACTAGTACCCTG 58.890 60.000 19.06 16.85 44.72 4.45
565 569 0.411058 AACCGGGACTAGTACCCTGT 59.589 55.000 19.06 17.43 44.65 4.00
566 570 0.411058 ACCGGGACTAGTACCCTGTT 59.589 55.000 19.06 0.00 41.07 3.16
567 571 1.203225 ACCGGGACTAGTACCCTGTTT 60.203 52.381 19.06 0.00 41.07 2.83
571 575 4.019174 CGGGACTAGTACCCTGTTTTCTA 58.981 47.826 19.06 0.00 44.72 2.10
572 576 4.142293 CGGGACTAGTACCCTGTTTTCTAC 60.142 50.000 19.06 0.00 44.72 2.59
573 577 5.022122 GGGACTAGTACCCTGTTTTCTACT 58.978 45.833 13.90 0.00 43.65 2.57
577 2443 7.148103 GGACTAGTACCCTGTTTTCTACTAGTG 60.148 44.444 17.09 0.00 46.18 2.74
590 2456 5.584551 TCTACTAGTGAGGCCATCTGATA 57.415 43.478 5.01 0.00 0.00 2.15
591 2457 5.317808 TCTACTAGTGAGGCCATCTGATAC 58.682 45.833 5.01 0.00 0.00 2.24
592 2458 3.916035 ACTAGTGAGGCCATCTGATACA 58.084 45.455 5.01 0.00 0.00 2.29
604 2470 4.868734 CCATCTGATACATGGATGATGTCG 59.131 45.833 14.22 0.88 41.91 4.35
629 2495 4.785301 TGACATCATCCAATTCCTTCTCC 58.215 43.478 0.00 0.00 0.00 3.71
644 2510 2.755952 TCTCCTGCAGCCTATGACTA 57.244 50.000 8.66 0.00 0.00 2.59
649 2515 5.420421 TCTCCTGCAGCCTATGACTATATTC 59.580 44.000 8.66 0.00 0.00 1.75
692 2558 0.618680 AGCTCCTGGGTGACTATGCA 60.619 55.000 0.00 0.00 0.00 3.96
706 2572 4.063689 GACTATGCATCTGGGATGAACAG 58.936 47.826 0.19 2.37 37.30 3.16
708 2574 2.885135 TGCATCTGGGATGAACAGTT 57.115 45.000 11.16 0.00 37.25 3.16
712 2578 5.076182 TGCATCTGGGATGAACAGTTTTTA 58.924 37.500 11.16 0.00 37.25 1.52
713 2579 5.538053 TGCATCTGGGATGAACAGTTTTTAA 59.462 36.000 11.16 0.00 37.25 1.52
714 2580 6.041409 TGCATCTGGGATGAACAGTTTTTAAA 59.959 34.615 11.16 0.00 37.25 1.52
716 2582 7.440856 GCATCTGGGATGAACAGTTTTTAAAAA 59.559 33.333 9.31 9.31 37.25 1.94
765 2646 3.409570 GGTTCTGGGTCAGTTAAGGTTC 58.590 50.000 0.00 0.00 32.61 3.62
813 2757 4.819761 TCTCATGCGGCCGACAGC 62.820 66.667 33.48 12.12 42.60 4.40
909 2913 1.783071 GTAGAGGCTAAGCTGACCCT 58.217 55.000 0.00 0.00 0.00 4.34
993 3000 0.394216 CCAATCTGCCACCGATCCAA 60.394 55.000 0.00 0.00 0.00 3.53
1065 3078 2.663188 GACATCCTCCGCCGCATC 60.663 66.667 0.00 0.00 0.00 3.91
1284 3304 3.702048 GTCTACCCGCACCAGGCA 61.702 66.667 0.00 0.00 45.17 4.75
1291 3311 1.741770 CCGCACCAGGCAAGAGTAC 60.742 63.158 0.00 0.00 45.17 2.73
1301 3321 2.312140 AGGCAAGAGTACTCCAGTCCTA 59.688 50.000 19.38 0.00 0.00 2.94
1400 3435 1.429825 CGTTGAAACCGTGGTGCAA 59.570 52.632 0.00 0.00 0.00 4.08
1467 3502 4.211920 ACCATGTTTTCCTCTTTCCGAAA 58.788 39.130 0.00 0.00 0.00 3.46
1594 3629 7.635423 TGTGTTGTCAATGTTAATGTACTCAC 58.365 34.615 0.00 0.00 0.00 3.51
1833 3871 1.372128 CTGCGGTCCAAAAAGCTGC 60.372 57.895 0.00 0.00 0.00 5.25
1844 3882 1.071605 AAAAGCTGCTACTCGCTTCG 58.928 50.000 0.90 0.00 45.03 3.79
1942 3980 4.097892 GGATGCTAACCGAATTGACCAATT 59.902 41.667 7.62 7.62 43.14 2.32
1945 3983 4.155826 TGCTAACCGAATTGACCAATTGAG 59.844 41.667 12.17 6.32 40.77 3.02
1973 4011 2.669569 GGCACTGGCACATGACGT 60.670 61.111 0.00 0.00 43.71 4.34
1996 4034 1.672854 CCTCAACCTGCATGGCCATG 61.673 60.000 36.80 36.80 41.60 3.66
2025 4063 8.674263 TTCGTACTCTTAAAATACAACCCAAA 57.326 30.769 0.00 0.00 0.00 3.28
2134 4172 7.069344 TGACTCTGAATATTCATGGGACTCTA 58.931 38.462 18.26 0.00 36.46 2.43
2428 4466 5.192327 GAAATTATCCATGCCACCTGAAG 57.808 43.478 0.00 0.00 0.00 3.02
2461 4499 5.739630 CGATCTAGTTATACATAGCGCTTGG 59.260 44.000 18.68 11.29 0.00 3.61
2466 4504 4.040461 AGTTATACATAGCGCTTGGGATGT 59.960 41.667 23.02 23.02 36.52 3.06
2478 4516 1.923356 TGGGATGTTCCTTGCCTTTC 58.077 50.000 0.00 0.00 36.57 2.62
2611 4652 0.387202 TTTTGGAATGTGTGTGGCCG 59.613 50.000 0.00 0.00 0.00 6.13
2612 4653 0.466372 TTTGGAATGTGTGTGGCCGA 60.466 50.000 0.00 0.00 0.00 5.54
2657 4698 0.901827 TCCGCTCTGTAATTGCCTCA 59.098 50.000 0.00 0.00 0.00 3.86
2663 4704 4.006319 GCTCTGTAATTGCCTCAGTTTCT 58.994 43.478 0.00 0.00 0.00 2.52
2666 4707 3.686016 TGTAATTGCCTCAGTTTCTCCC 58.314 45.455 0.00 0.00 0.00 4.30
2696 4737 6.826668 TGTCTGTCTTCAAGAATCCAAACTA 58.173 36.000 0.00 0.00 0.00 2.24
2727 4768 1.717194 GCCGTTCCTTGTTCGTGATA 58.283 50.000 0.00 0.00 0.00 2.15
2761 4802 0.038526 TTCGACGACTTCTTCTGGCC 60.039 55.000 0.00 0.00 0.00 5.36
2762 4803 0.894184 TCGACGACTTCTTCTGGCCT 60.894 55.000 3.32 0.00 0.00 5.19
2822 4863 0.458716 GTAGCAGCCGTGTCTTCCTC 60.459 60.000 0.00 0.00 0.00 3.71
2832 4873 1.143073 GTGTCTTCCTCACCAACCCTT 59.857 52.381 0.00 0.00 0.00 3.95
2862 4903 3.440415 ATCACGTCTCCGCAGCGA 61.440 61.111 18.75 1.08 37.70 4.93
2906 4947 0.773644 ATTGGTGGCTCACTGGAGTT 59.226 50.000 5.48 0.00 43.37 3.01
2942 4983 1.921230 GACGACGCCAAGATCTCTTTC 59.079 52.381 0.00 0.00 33.11 2.62
2990 5031 0.179073 CTATCTCTGGCCCGTGGTTG 60.179 60.000 0.00 0.00 0.00 3.77
2996 5037 4.029809 GGCCCGTGGTTGCTAGGT 62.030 66.667 0.00 0.00 0.00 3.08
3038 5079 4.100963 TCCTCTGCTAGTGACAAGAACAAA 59.899 41.667 0.00 0.00 0.00 2.83
3096 5137 2.152830 GCTTCATCTCTGATCATGGCC 58.847 52.381 0.00 0.00 0.00 5.36
3098 5139 3.007723 GCTTCATCTCTGATCATGGCCTA 59.992 47.826 3.32 0.00 0.00 3.93
3116 5157 3.580458 GCCTACATGACATCTACCTCCAT 59.420 47.826 0.00 0.00 0.00 3.41
3149 5190 2.649034 TGGTCGAACGAGCAGGAC 59.351 61.111 21.82 0.00 46.01 3.85
3274 5315 1.076923 GTCCCCTGCTCCTCGACTA 60.077 63.158 0.00 0.00 0.00 2.59
3279 5320 1.408405 CCCTGCTCCTCGACTACACTA 60.408 57.143 0.00 0.00 0.00 2.74
3292 5333 3.231818 ACTACACTACTTGCTCTGGTGT 58.768 45.455 0.00 0.00 42.58 4.16
3308 5349 2.124860 GTAGGCCGGCGTTTCCAT 60.125 61.111 28.71 5.65 34.01 3.41
3333 5374 4.764771 GCCATTGGCCTGCCCTCA 62.765 66.667 17.28 0.00 44.06 3.86
3446 5490 2.266055 AGCCTACAACGCTGGAGC 59.734 61.111 0.00 0.00 34.56 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.114670 CGATGAGGTGCCGGCAAAT 61.115 57.895 34.66 23.50 0.00 2.32
1 2 2.745884 CGATGAGGTGCCGGCAAA 60.746 61.111 34.66 17.93 0.00 3.68
2 3 3.664025 CTCGATGAGGTGCCGGCAA 62.664 63.158 34.66 17.35 0.00 4.52
3 4 4.147449 CTCGATGAGGTGCCGGCA 62.147 66.667 29.03 29.03 0.00 5.69
4 5 4.148825 ACTCGATGAGGTGCCGGC 62.149 66.667 22.73 22.73 33.35 6.13
5 6 2.105128 GACTCGATGAGGTGCCGG 59.895 66.667 0.00 0.00 33.35 6.13
6 7 2.278206 CGACTCGATGAGGTGCCG 60.278 66.667 0.00 0.00 33.35 5.69
7 8 1.739338 ATCCGACTCGATGAGGTGCC 61.739 60.000 0.00 0.00 33.35 5.01
8 9 0.596083 CATCCGACTCGATGAGGTGC 60.596 60.000 0.00 0.00 41.92 5.01
9 10 0.031314 CCATCCGACTCGATGAGGTG 59.969 60.000 0.00 0.00 41.92 4.00
10 11 1.109920 CCCATCCGACTCGATGAGGT 61.110 60.000 0.00 0.00 41.92 3.85
11 12 0.823769 TCCCATCCGACTCGATGAGG 60.824 60.000 0.00 6.18 41.92 3.86
12 13 1.000827 CTTCCCATCCGACTCGATGAG 60.001 57.143 0.00 0.00 41.92 2.90
13 14 1.032794 CTTCCCATCCGACTCGATGA 58.967 55.000 0.00 0.00 41.92 2.92
14 15 0.598680 GCTTCCCATCCGACTCGATG 60.599 60.000 0.00 2.42 39.54 3.84
15 16 0.757188 AGCTTCCCATCCGACTCGAT 60.757 55.000 0.00 0.00 0.00 3.59
16 17 0.106868 TAGCTTCCCATCCGACTCGA 60.107 55.000 0.00 0.00 0.00 4.04
17 18 0.030908 GTAGCTTCCCATCCGACTCG 59.969 60.000 0.00 0.00 0.00 4.18
18 19 1.338655 GAGTAGCTTCCCATCCGACTC 59.661 57.143 0.00 0.00 0.00 3.36
19 20 1.342076 TGAGTAGCTTCCCATCCGACT 60.342 52.381 0.00 0.00 0.00 4.18
20 21 1.112113 TGAGTAGCTTCCCATCCGAC 58.888 55.000 0.00 0.00 0.00 4.79
21 22 1.688735 CATGAGTAGCTTCCCATCCGA 59.311 52.381 0.00 0.00 0.00 4.55
22 23 1.270518 CCATGAGTAGCTTCCCATCCG 60.271 57.143 0.00 0.00 0.00 4.18
23 24 1.771255 ACCATGAGTAGCTTCCCATCC 59.229 52.381 0.00 0.00 0.00 3.51
24 25 4.689612 TTACCATGAGTAGCTTCCCATC 57.310 45.455 0.00 0.00 30.92 3.51
25 26 4.687219 GCTTTACCATGAGTAGCTTCCCAT 60.687 45.833 0.00 0.00 30.92 4.00
26 27 3.370527 GCTTTACCATGAGTAGCTTCCCA 60.371 47.826 0.00 0.00 30.92 4.37
27 28 3.206964 GCTTTACCATGAGTAGCTTCCC 58.793 50.000 0.00 0.00 30.92 3.97
28 29 3.873910 TGCTTTACCATGAGTAGCTTCC 58.126 45.455 0.00 0.00 30.92 3.46
29 30 4.210120 CGATGCTTTACCATGAGTAGCTTC 59.790 45.833 0.00 4.96 30.92 3.86
30 31 4.122776 CGATGCTTTACCATGAGTAGCTT 58.877 43.478 0.00 0.00 30.92 3.74
31 32 3.133003 ACGATGCTTTACCATGAGTAGCT 59.867 43.478 0.00 0.00 30.92 3.32
32 33 3.458189 ACGATGCTTTACCATGAGTAGC 58.542 45.455 0.00 0.00 30.92 3.58
33 34 4.682787 TGACGATGCTTTACCATGAGTAG 58.317 43.478 0.00 0.00 30.92 2.57
34 35 4.401202 TCTGACGATGCTTTACCATGAGTA 59.599 41.667 0.00 0.00 0.00 2.59
35 36 3.195610 TCTGACGATGCTTTACCATGAGT 59.804 43.478 0.00 0.00 0.00 3.41
36 37 3.785486 TCTGACGATGCTTTACCATGAG 58.215 45.455 0.00 0.00 0.00 2.90
37 38 3.885724 TCTGACGATGCTTTACCATGA 57.114 42.857 0.00 0.00 0.00 3.07
38 39 3.063997 GGTTCTGACGATGCTTTACCATG 59.936 47.826 0.00 0.00 0.00 3.66
39 40 3.055094 AGGTTCTGACGATGCTTTACCAT 60.055 43.478 0.00 0.00 0.00 3.55
40 41 2.301870 AGGTTCTGACGATGCTTTACCA 59.698 45.455 0.00 0.00 0.00 3.25
41 42 2.930682 GAGGTTCTGACGATGCTTTACC 59.069 50.000 0.00 0.00 0.00 2.85
42 43 2.930682 GGAGGTTCTGACGATGCTTTAC 59.069 50.000 0.00 0.00 0.00 2.01
43 44 2.565391 TGGAGGTTCTGACGATGCTTTA 59.435 45.455 0.00 0.00 0.00 1.85
44 45 1.347707 TGGAGGTTCTGACGATGCTTT 59.652 47.619 0.00 0.00 0.00 3.51
45 46 0.976641 TGGAGGTTCTGACGATGCTT 59.023 50.000 0.00 0.00 0.00 3.91
46 47 0.976641 TTGGAGGTTCTGACGATGCT 59.023 50.000 0.00 0.00 0.00 3.79
47 48 1.079503 GTTGGAGGTTCTGACGATGC 58.920 55.000 0.00 0.00 0.00 3.91
104 105 2.346847 CGTGTGTGCTAATCTCTGCTTC 59.653 50.000 0.00 0.00 0.00 3.86
105 106 2.341257 CGTGTGTGCTAATCTCTGCTT 58.659 47.619 0.00 0.00 0.00 3.91
107 108 0.371645 GCGTGTGTGCTAATCTCTGC 59.628 55.000 0.00 0.00 0.00 4.26
108 109 1.713597 TGCGTGTGTGCTAATCTCTG 58.286 50.000 0.00 0.00 35.36 3.35
109 110 2.274437 CATGCGTGTGTGCTAATCTCT 58.726 47.619 0.00 0.00 35.36 3.10
110 111 1.328680 CCATGCGTGTGTGCTAATCTC 59.671 52.381 4.96 0.00 35.36 2.75
111 112 1.372582 CCATGCGTGTGTGCTAATCT 58.627 50.000 4.96 0.00 35.36 2.40
112 113 0.378257 CCCATGCGTGTGTGCTAATC 59.622 55.000 4.96 0.00 35.36 1.75
113 114 0.322456 ACCCATGCGTGTGTGCTAAT 60.322 50.000 4.96 0.00 35.36 1.73
134 136 0.539051 CCTAGCCCTTCTGTCAGTGG 59.461 60.000 0.00 3.94 0.00 4.00
158 160 1.897641 CTAACGAAGAGTGCTCGACC 58.102 55.000 0.00 0.00 34.09 4.79
189 191 1.966451 GGTGCCGGAACAGACTTGG 60.966 63.158 16.38 0.00 0.00 3.61
211 213 0.749649 CATCTTCCTCCACCTCTCCG 59.250 60.000 0.00 0.00 0.00 4.63
212 214 1.872773 ACATCTTCCTCCACCTCTCC 58.127 55.000 0.00 0.00 0.00 3.71
309 311 1.815003 GGAAGAGCCATGTTGTTCCAG 59.185 52.381 14.74 0.00 36.50 3.86
334 336 5.726980 TTGCATTTTAAAGCACCATCTCT 57.273 34.783 1.87 0.00 41.05 3.10
422 424 3.824443 TGTCACGAAACACTATGAGAGGA 59.176 43.478 0.00 0.00 0.00 3.71
436 438 2.102420 TCAAGCCTTTCTCTGTCACGAA 59.898 45.455 0.00 0.00 0.00 3.85
440 442 6.293407 CGTAAAAATCAAGCCTTTCTCTGTCA 60.293 38.462 0.00 0.00 0.00 3.58
447 449 8.515473 ACATAAACGTAAAAATCAAGCCTTTC 57.485 30.769 0.00 0.00 0.00 2.62
502 506 3.276846 GTTGCAACGCACGGACCT 61.277 61.111 14.90 0.00 38.71 3.85
529 533 3.646637 CCGGTTCTAGGGGAGATTATGTT 59.353 47.826 0.00 0.00 32.88 2.71
530 534 3.240302 CCGGTTCTAGGGGAGATTATGT 58.760 50.000 0.00 0.00 32.88 2.29
541 545 2.580962 GGTACTAGTCCCGGTTCTAGG 58.419 57.143 24.29 12.77 38.24 3.02
542 546 2.580962 GGGTACTAGTCCCGGTTCTAG 58.419 57.143 21.11 21.11 39.37 2.43
544 548 3.604024 GGGTACTAGTCCCGGTTCT 57.396 57.895 12.78 0.15 35.27 3.01
551 555 7.332213 CTAGTAGAAAACAGGGTACTAGTCC 57.668 44.000 0.00 0.27 39.62 3.85
554 558 7.067251 CCTCACTAGTAGAAAACAGGGTACTAG 59.933 44.444 3.59 11.94 45.59 2.57
555 559 6.888632 CCTCACTAGTAGAAAACAGGGTACTA 59.111 42.308 3.59 0.00 0.00 1.82
557 561 5.624052 GCCTCACTAGTAGAAAACAGGGTAC 60.624 48.000 3.59 0.00 0.00 3.34
559 563 3.261137 GCCTCACTAGTAGAAAACAGGGT 59.739 47.826 3.59 0.00 0.00 4.34
560 564 3.369576 GGCCTCACTAGTAGAAAACAGGG 60.370 52.174 3.59 0.00 0.00 4.45
561 565 3.260884 TGGCCTCACTAGTAGAAAACAGG 59.739 47.826 3.32 2.74 0.00 4.00
562 566 4.537135 TGGCCTCACTAGTAGAAAACAG 57.463 45.455 3.32 0.00 0.00 3.16
564 568 5.105310 TCAGATGGCCTCACTAGTAGAAAAC 60.105 44.000 3.32 0.00 0.00 2.43
565 569 5.023452 TCAGATGGCCTCACTAGTAGAAAA 58.977 41.667 3.32 0.00 0.00 2.29
566 570 4.610333 TCAGATGGCCTCACTAGTAGAAA 58.390 43.478 3.32 0.00 0.00 2.52
567 571 4.251103 TCAGATGGCCTCACTAGTAGAA 57.749 45.455 3.32 0.00 0.00 2.10
571 575 3.916035 TGTATCAGATGGCCTCACTAGT 58.084 45.455 3.32 0.00 0.00 2.57
572 576 4.322574 CCATGTATCAGATGGCCTCACTAG 60.323 50.000 3.32 0.00 34.21 2.57
573 577 3.580022 CCATGTATCAGATGGCCTCACTA 59.420 47.826 3.32 0.00 34.21 2.74
577 2443 3.262660 TCATCCATGTATCAGATGGCCTC 59.737 47.826 3.32 0.00 40.35 4.70
604 2470 4.952335 AGAAGGAATTGGATGATGTCAACC 59.048 41.667 2.63 2.63 39.04 3.77
629 2495 5.065704 ACGAATATAGTCATAGGCTGCAG 57.934 43.478 10.11 10.11 0.00 4.41
686 2552 4.082665 ACTGTTCATCCCAGATGCATAG 57.917 45.455 0.00 0.00 34.04 2.23
735 2601 2.325393 GACCCAGAACCCATAGCCGG 62.325 65.000 0.00 0.00 0.00 6.13
742 2608 1.702957 CCTTAACTGACCCAGAACCCA 59.297 52.381 0.45 0.00 35.18 4.51
743 2609 1.703513 ACCTTAACTGACCCAGAACCC 59.296 52.381 0.45 0.00 35.18 4.11
765 2646 5.351465 ACACGTGTTCCATCAGCTAAAATAG 59.649 40.000 17.22 0.00 0.00 1.73
892 2896 0.980231 CCAGGGTCAGCTTAGCCTCT 60.980 60.000 15.76 0.00 45.56 3.69
909 2913 3.831911 TCGTATATGAGATGTGATGGCCA 59.168 43.478 8.56 8.56 0.00 5.36
993 3000 2.670148 GGCTGGGTCCATCCTCGTT 61.670 63.158 2.82 0.00 36.25 3.85
1014 3027 2.970324 GGAAAGCACGTGCCGTCA 60.970 61.111 35.51 0.00 43.38 4.35
1022 3035 0.999406 CACATCGTAGGGAAAGCACG 59.001 55.000 0.00 0.00 37.03 5.34
1029 3042 1.101635 CGAGGAGCACATCGTAGGGA 61.102 60.000 10.06 0.00 43.73 4.20
1078 3091 2.964978 GCACTGGGAAGCGCAAAT 59.035 55.556 11.47 0.00 0.00 2.32
1106 3119 3.850095 TTGACGATGTCGCGCCACA 62.850 57.895 11.04 11.04 44.43 4.17
1266 3286 3.391382 GCCTGGTGCGGGTAGACT 61.391 66.667 0.00 0.00 31.34 3.24
1284 3304 4.712337 CCATTGTAGGACTGGAGTACTCTT 59.288 45.833 21.88 7.31 38.81 2.85
1291 3311 3.788672 GGCCATTGTAGGACTGGAG 57.211 57.895 0.00 0.00 32.29 3.86
1301 3321 0.985490 GAGGAGGAGGAGGCCATTGT 60.985 60.000 5.01 0.00 0.00 2.71
1385 3417 1.876799 CATAGTTGCACCACGGTTTCA 59.123 47.619 0.00 0.00 0.00 2.69
1389 3421 1.674322 GCCATAGTTGCACCACGGT 60.674 57.895 0.00 0.00 0.00 4.83
1400 3435 1.424638 AGCCAAGGATACGCCATAGT 58.575 50.000 0.00 0.00 46.39 2.12
1467 3502 2.370718 CTCCTTGAGCAGACCACCT 58.629 57.895 0.00 0.00 0.00 4.00
1844 3882 3.729163 GCTTGCTAAGACTGATTTTCCGC 60.729 47.826 0.00 0.00 0.00 5.54
1854 3892 4.584325 CCTCTCTCATAGCTTGCTAAGACT 59.416 45.833 6.42 0.00 0.00 3.24
1942 3980 1.347707 CAGTGCCCAACCTAGTTCTCA 59.652 52.381 0.00 0.00 0.00 3.27
1945 3983 0.960861 GCCAGTGCCCAACCTAGTTC 60.961 60.000 0.00 0.00 0.00 3.01
1973 4011 1.296392 CCATGCAGGTTGAGGTCGA 59.704 57.895 0.00 0.00 0.00 4.20
1996 4034 8.385858 GGGTTGTATTTTAAGAGTACGAATCAC 58.614 37.037 0.00 0.00 0.00 3.06
2025 4063 6.608405 TGCTTCCAACAATCTTCCATATCATT 59.392 34.615 0.00 0.00 0.00 2.57
2036 4074 2.564062 CCACCATTGCTTCCAACAATCT 59.436 45.455 0.00 0.00 35.58 2.40
2134 4172 4.271696 TGTCGATGAAGTTGTCCTCATT 57.728 40.909 0.00 0.00 0.00 2.57
2171 4209 0.535335 TTCTACCGACTCATGGTGGC 59.465 55.000 0.00 0.00 40.73 5.01
2285 4323 3.149981 CCTAGATACTGCATCCTCGACA 58.850 50.000 0.00 0.00 33.75 4.35
2461 4499 3.282885 CCTAGAAAGGCAAGGAACATCC 58.717 50.000 0.00 0.00 35.64 3.51
2478 4516 6.336566 CACATAGCCATGTAGATAAGCCTAG 58.663 44.000 0.00 0.00 43.73 3.02
2555 4596 5.501897 CGACTAACTGAAAGCAACGAAACTT 60.502 40.000 0.00 0.00 37.60 2.66
2556 4597 4.025979 CGACTAACTGAAAGCAACGAAACT 60.026 41.667 0.00 0.00 37.60 2.66
2561 4602 4.647291 ATTCGACTAACTGAAAGCAACG 57.353 40.909 0.00 0.00 37.60 4.10
2570 4611 4.227538 ACACGACTCAATTCGACTAACTG 58.772 43.478 0.00 0.00 41.78 3.16
2611 4652 4.056125 GCTTGGCCCCGCAGTTTC 62.056 66.667 0.00 0.00 0.00 2.78
2651 4692 2.024176 TACAGGGAGAAACTGAGGCA 57.976 50.000 0.00 0.00 39.24 4.75
2657 4698 4.841246 AGACAGACAATACAGGGAGAAACT 59.159 41.667 0.00 0.00 0.00 2.66
2663 4704 4.838423 TCTTGAAGACAGACAATACAGGGA 59.162 41.667 0.00 0.00 0.00 4.20
2666 4707 6.875726 TGGATTCTTGAAGACAGACAATACAG 59.124 38.462 0.00 0.00 0.00 2.74
2713 4754 2.027561 CCAAGGGTATCACGAACAAGGA 60.028 50.000 0.00 0.00 0.00 3.36
2727 4768 3.647771 GAACTCGGCCCCAAGGGT 61.648 66.667 4.11 0.00 46.51 4.34
2744 4785 0.456995 GAGGCCAGAAGAAGTCGTCG 60.457 60.000 5.01 0.00 0.00 5.12
2809 4850 1.070786 TTGGTGAGGAAGACACGGC 59.929 57.895 0.00 0.00 38.90 5.68
2818 4859 1.410932 CCACAAAAGGGTTGGTGAGGA 60.411 52.381 0.00 0.00 40.67 3.71
2832 4873 2.038426 AGACGTGATGATCACCCACAAA 59.962 45.455 19.01 0.00 44.20 2.83
2862 4903 2.581354 GCCAGAGACAGCGGTCAT 59.419 61.111 19.33 4.37 46.80 3.06
2942 4983 4.069232 TCGTGGAGCTCGGCAAGG 62.069 66.667 7.83 0.00 0.00 3.61
2990 5031 3.055819 TCATGTTGAAGTCTCCACCTAGC 60.056 47.826 0.00 0.00 0.00 3.42
2996 5037 4.478206 GGAGATCATGTTGAAGTCTCCA 57.522 45.455 16.79 0.00 45.44 3.86
3038 5079 2.586079 CGGCGGTTGATGCGATCT 60.586 61.111 0.00 0.00 0.00 2.75
3075 5116 1.799403 GCCATGATCAGAGATGAAGCG 59.201 52.381 0.09 0.00 0.00 4.68
3096 5137 4.020751 CCCATGGAGGTAGATGTCATGTAG 60.021 50.000 15.22 0.00 34.94 2.74
3098 5139 2.707791 CCCATGGAGGTAGATGTCATGT 59.292 50.000 15.22 0.00 34.94 3.21
3274 5315 2.563179 CCTACACCAGAGCAAGTAGTGT 59.437 50.000 0.00 0.00 43.65 3.55
3279 5320 1.679898 GGCCTACACCAGAGCAAGT 59.320 57.895 0.00 0.00 0.00 3.16
3292 5333 0.609681 AAAATGGAAACGCCGGCCTA 60.610 50.000 23.46 4.61 40.66 3.93
3333 5374 1.477685 ATGGTCTGGTCGAACCCGTT 61.478 55.000 0.00 0.00 37.50 4.44
3342 5383 2.000429 GCATTTTGCATGGTCTGGTC 58.000 50.000 0.00 0.00 44.26 4.02


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

AutoCloner maintained by Alex Coulton.