Multiple sequence alignment - TraesCS4B01G065700

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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 TraesCS4B01G065700 chr4B 100.000 3596 0 0 1 3596 58600546 58596951 0.000000e+00 6641.0
1 TraesCS4B01G065700 chr4B 97.430 817 19 2 2780 3596 58569408 58568594 0.000000e+00 1391.0
2 TraesCS4B01G065700 chr4B 92.571 175 10 2 1780 1954 58598677 58598506 7.710000e-62 248.0
3 TraesCS4B01G065700 chr4B 92.571 175 10 2 1870 2041 58598767 58598593 7.710000e-62 248.0
4 TraesCS4B01G065700 chr4D 92.935 1288 48 22 1592 2875 40124609 40123361 0.000000e+00 1834.0
5 TraesCS4B01G065700 chr4D 92.523 963 35 12 645 1593 40125580 40124641 0.000000e+00 1345.0
6 TraesCS4B01G065700 chr4D 82.485 491 37 22 2883 3335 40123387 40122908 5.630000e-103 385.0
7 TraesCS4B01G065700 chr4D 96.825 126 4 0 1829 1954 40124321 40124196 1.010000e-50 211.0
8 TraesCS4B01G065700 chr4D 96.522 115 4 0 1867 1981 40124435 40124321 1.320000e-44 191.0
9 TraesCS4B01G065700 chr4A 92.195 1294 47 21 1592 2875 559945938 559947187 0.000000e+00 1781.0
10 TraesCS4B01G065700 chr4A 89.730 779 32 16 847 1593 559945144 559945906 0.000000e+00 952.0
11 TraesCS4B01G065700 chr4A 97.610 251 6 0 3346 3596 743718817 743719067 7.130000e-117 431.0
12 TraesCS4B01G065700 chr4A 80.967 331 33 19 2883 3206 559947162 559947469 6.000000e-58 235.0
13 TraesCS4B01G065700 chr4A 93.651 126 7 1 1829 1954 559946238 559946362 1.700000e-43 187.0
14 TraesCS4B01G065700 chr4A 95.536 112 5 0 1870 1981 559946127 559946238 2.850000e-41 180.0
15 TraesCS4B01G065700 chr4A 76.703 279 47 17 122 396 500852660 500852396 4.840000e-29 139.0
16 TraesCS4B01G065700 chr4A 74.286 315 56 22 79 388 14158441 14158147 3.800000e-20 110.0
17 TraesCS4B01G065700 chr3B 87.818 550 51 11 1 546 571943857 571943320 6.550000e-177 630.0
18 TraesCS4B01G065700 chr3B 98.008 251 5 0 3346 3596 769212697 769212447 1.530000e-118 436.0
19 TraesCS4B01G065700 chr3B 78.448 116 14 11 143 254 22591618 22591510 8.330000e-07 65.8
20 TraesCS4B01G065700 chr3B 88.462 52 5 1 143 194 738321467 738321517 1.080000e-05 62.1
21 TraesCS4B01G065700 chr6D 85.464 571 45 18 2 546 363818695 363819253 8.720000e-156 560.0
22 TraesCS4B01G065700 chr6D 83.333 582 83 10 2032 2600 434019750 434020330 3.180000e-145 525.0
23 TraesCS4B01G065700 chr6D 91.843 331 24 2 1003 1333 434017603 434017930 3.270000e-125 459.0
24 TraesCS4B01G065700 chr7B 85.231 562 46 16 1 542 485524937 485525481 8.780000e-151 544.0
25 TraesCS4B01G065700 chr7B 100.000 30 0 0 225 254 677415159 677415130 5.020000e-04 56.5
26 TraesCS4B01G065700 chr6B 83.477 581 80 11 2037 2605 656511369 656511945 8.840000e-146 527.0
27 TraesCS4B01G065700 chr6B 90.909 341 25 3 996 1333 656509565 656509902 1.520000e-123 453.0
28 TraesCS4B01G065700 chr6B 77.632 228 28 19 207 424 32742181 32742395 2.270000e-22 117.0
29 TraesCS4B01G065700 chr6A 83.741 572 78 9 2046 2605 580279610 580280178 8.840000e-146 527.0
30 TraesCS4B01G065700 chr6A 91.765 340 22 3 997 1333 580278069 580278405 5.440000e-128 468.0
31 TraesCS4B01G065700 chrUn 90.380 395 20 7 1201 1593 362176467 362176845 1.490000e-138 503.0
32 TraesCS4B01G065700 chrUn 88.811 143 6 5 1690 1832 362177004 362177136 2.220000e-37 167.0
33 TraesCS4B01G065700 chrUn 97.849 93 2 0 2883 2975 477459885 477459977 1.030000e-35 161.0
34 TraesCS4B01G065700 chr5D 90.380 395 20 7 1201 1593 254898197 254898575 1.490000e-138 503.0
35 TraesCS4B01G065700 chr5D 90.380 395 20 7 1201 1593 254901418 254901796 1.490000e-138 503.0
36 TraesCS4B01G065700 chr5D 88.384 396 22 11 1201 1593 220891171 220891545 4.230000e-124 455.0
37 TraesCS4B01G065700 chr5D 82.066 513 22 20 2883 3334 154529182 154528679 1.220000e-99 374.0
38 TraesCS4B01G065700 chr5D 85.000 240 33 3 2357 2595 478965933 478965696 1.290000e-59 241.0
39 TraesCS4B01G065700 chr5D 88.811 143 6 5 1690 1832 220891704 220891836 2.220000e-37 167.0
40 TraesCS4B01G065700 chr5D 88.811 143 6 5 1690 1832 254898734 254898866 2.220000e-37 167.0
41 TraesCS4B01G065700 chr5D 88.811 143 6 5 1690 1832 254901955 254902087 2.220000e-37 167.0
42 TraesCS4B01G065700 chr5D 92.857 98 7 0 1592 1689 220891577 220891674 3.740000e-30 143.0
43 TraesCS4B01G065700 chr2B 98.008 251 5 0 3346 3596 147501563 147501813 1.530000e-118 436.0
44 TraesCS4B01G065700 chr2B 97.610 251 6 0 3346 3596 47687952 47687702 7.130000e-117 431.0
45 TraesCS4B01G065700 chr2B 97.610 251 6 0 3346 3596 47714483 47714233 7.130000e-117 431.0
46 TraesCS4B01G065700 chr2B 76.074 163 25 13 25 180 584470801 584470956 4.980000e-09 73.1
47 TraesCS4B01G065700 chr1B 98.008 251 5 0 3346 3596 662564782 662565032 1.530000e-118 436.0
48 TraesCS4B01G065700 chr1B 97.610 251 6 0 3346 3596 651297756 651297506 7.130000e-117 431.0
49 TraesCS4B01G065700 chr5B 97.610 251 6 0 3346 3596 640139344 640139094 7.130000e-117 431.0
50 TraesCS4B01G065700 chr5B 82.066 513 22 16 2883 3334 177194411 177194914 1.220000e-99 374.0
51 TraesCS4B01G065700 chr5B 83.333 114 14 4 1081 1193 586847516 586847407 2.280000e-17 100.0
52 TraesCS4B01G065700 chr5A 82.066 513 22 19 2883 3334 263508692 263509195 1.220000e-99 374.0
53 TraesCS4B01G065700 chr2A 81.532 509 28 18 2883 3334 406455101 406454602 3.410000e-95 359.0
54 TraesCS4B01G065700 chr2A 81.139 509 30 18 2883 3334 394755072 394755571 7.390000e-92 348.0
55 TraesCS4B01G065700 chr1A 83.333 318 32 8 183 479 131275342 131275659 1.270000e-69 274.0
56 TraesCS4B01G065700 chr1A 77.311 357 55 23 1 339 131275066 131275414 1.700000e-43 187.0


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 TraesCS4B01G065700 chr4B 58596951 58600546 3595 True 2379.0 6641 95.047333 1 3596 3 chr4B.!!$R2 3595
1 TraesCS4B01G065700 chr4B 58568594 58569408 814 True 1391.0 1391 97.430000 2780 3596 1 chr4B.!!$R1 816
2 TraesCS4B01G065700 chr4D 40122908 40125580 2672 True 793.2 1834 92.258000 645 3335 5 chr4D.!!$R1 2690
3 TraesCS4B01G065700 chr4A 559945144 559947469 2325 False 667.0 1781 90.415800 847 3206 5 chr4A.!!$F2 2359
4 TraesCS4B01G065700 chr3B 571943320 571943857 537 True 630.0 630 87.818000 1 546 1 chr3B.!!$R2 545
5 TraesCS4B01G065700 chr6D 363818695 363819253 558 False 560.0 560 85.464000 2 546 1 chr6D.!!$F1 544
6 TraesCS4B01G065700 chr6D 434017603 434020330 2727 False 492.0 525 87.588000 1003 2600 2 chr6D.!!$F2 1597
7 TraesCS4B01G065700 chr7B 485524937 485525481 544 False 544.0 544 85.231000 1 542 1 chr7B.!!$F1 541
8 TraesCS4B01G065700 chr6B 656509565 656511945 2380 False 490.0 527 87.193000 996 2605 2 chr6B.!!$F2 1609
9 TraesCS4B01G065700 chr6A 580278069 580280178 2109 False 497.5 527 87.753000 997 2605 2 chr6A.!!$F1 1608
10 TraesCS4B01G065700 chrUn 362176467 362177136 669 False 335.0 503 89.595500 1201 1832 2 chrUn.!!$F2 631
11 TraesCS4B01G065700 chr5D 154528679 154529182 503 True 374.0 374 82.066000 2883 3334 1 chr5D.!!$R1 451
12 TraesCS4B01G065700 chr5D 254898197 254902087 3890 False 335.0 503 89.595500 1201 1832 4 chr5D.!!$F2 631
13 TraesCS4B01G065700 chr5D 220891171 220891836 665 False 255.0 455 90.017333 1201 1832 3 chr5D.!!$F1 631
14 TraesCS4B01G065700 chr5B 177194411 177194914 503 False 374.0 374 82.066000 2883 3334 1 chr5B.!!$F1 451
15 TraesCS4B01G065700 chr5A 263508692 263509195 503 False 374.0 374 82.066000 2883 3334 1 chr5A.!!$F1 451
16 TraesCS4B01G065700 chr1A 131275066 131275659 593 False 230.5 274 80.322000 1 479 2 chr1A.!!$F1 478

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
841 1009 0.031585 GGAAACGCAACCAAAGGTCC 59.968 55.0 0.0 0.0 33.12 4.46 F
925 1093 0.174845 TAGCCGTCAACCAATCCGAG 59.825 55.0 0.0 0.0 0.00 4.63 F
1912 6952 0.250901 ACACTGCTGTTGGTCCATCC 60.251 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 6934 0.037303 AGGATGGACCAACAGCAGTG 59.963 55.0 0.0 0.0 42.04 3.66 R
2199 7698 1.103803 GCCTGTCCAGAGTATCGACA 58.896 55.0 0.0 0.0 42.67 4.35 R
3531 9130 1.217057 ATGGCACCCTTCCTGTCCAT 61.217 55.0 0.0 0.0 0.00 3.41 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
94 97 8.606040 AATCATTGGTTTGGAAAAAGTACATG 57.394 30.769 0.00 0.00 0.00 3.21
131 251 8.211116 AGAAATGTTCATGCATTTGAAAACAA 57.789 26.923 13.85 0.00 45.68 2.83
132 252 8.675504 AGAAATGTTCATGCATTTGAAAACAAA 58.324 25.926 13.85 0.00 45.68 2.83
221 342 4.986659 GCATGCAATTGAAAGAAGTTCACT 59.013 37.500 14.21 0.00 46.09 3.41
244 365 9.352784 CACTAGATTTTGAAAACAAGTTCACAA 57.647 29.630 0.00 0.00 37.24 3.33
275 419 8.716646 AAAAAGGTTCATCAGTTTTGGTTAAG 57.283 30.769 0.00 0.00 0.00 1.85
465 633 9.292195 AGAAAAGAAAGGGATCACGTATTTTTA 57.708 29.630 8.00 0.00 0.00 1.52
469 637 9.687210 AAGAAAGGGATCACGTATTTTTAAAAC 57.313 29.630 0.00 0.00 0.00 2.43
472 640 9.819267 AAAGGGATCACGTATTTTTAAAACAAA 57.181 25.926 0.00 0.00 0.00 2.83
522 690 6.584184 GCTGAAAAGGAGAAAAAGAATGTAGC 59.416 38.462 0.00 0.00 0.00 3.58
525 693 7.920682 TGAAAAGGAGAAAAAGAATGTAGCAAC 59.079 33.333 0.00 0.00 0.00 4.17
546 714 2.669569 CGTCAGGTGGGTTGGCTG 60.670 66.667 0.00 0.00 0.00 4.85
547 715 2.282462 GTCAGGTGGGTTGGCTGG 60.282 66.667 0.00 0.00 0.00 4.85
548 716 3.579302 TCAGGTGGGTTGGCTGGG 61.579 66.667 0.00 0.00 0.00 4.45
561 729 3.546543 CTGGGCCGCGGGATAGAA 61.547 66.667 29.38 0.00 0.00 2.10
562 730 2.847234 TGGGCCGCGGGATAGAAT 60.847 61.111 29.38 0.00 0.00 2.40
563 731 2.047179 GGGCCGCGGGATAGAATC 60.047 66.667 29.38 6.97 0.00 2.52
564 732 2.741092 GGCCGCGGGATAGAATCA 59.259 61.111 29.38 0.00 0.00 2.57
565 733 1.668151 GGCCGCGGGATAGAATCAC 60.668 63.158 29.38 5.28 0.00 3.06
602 770 6.809297 TTTTAGCGTTTTAAAAACCGAAGG 57.191 33.333 13.34 0.00 39.43 3.46
603 771 6.558909 TTTTAGCGTTTTAAAAACCGAAGGA 58.441 32.000 13.34 0.00 38.55 3.36
604 772 7.031975 TTTTAGCGTTTTAAAAACCGAAGGAA 58.968 30.769 13.34 2.39 38.55 3.36
605 773 7.543520 TTTTAGCGTTTTAAAAACCGAAGGAAA 59.456 29.630 13.34 6.62 38.55 3.13
627 795 4.397832 GTAACTGGGCCGGCCGAA 62.398 66.667 38.22 27.51 36.85 4.30
628 796 3.638316 TAACTGGGCCGGCCGAAA 61.638 61.111 38.22 24.89 36.85 3.46
629 797 3.615509 TAACTGGGCCGGCCGAAAG 62.616 63.158 38.22 33.34 36.85 2.62
642 810 3.460648 CGAAAGCGGAGGAGGATTT 57.539 52.632 0.00 0.00 0.00 2.17
643 811 2.596904 CGAAAGCGGAGGAGGATTTA 57.403 50.000 0.00 0.00 0.00 1.40
644 812 2.474816 CGAAAGCGGAGGAGGATTTAG 58.525 52.381 0.00 0.00 0.00 1.85
645 813 2.214347 GAAAGCGGAGGAGGATTTAGC 58.786 52.381 0.00 0.00 0.00 3.09
646 814 0.470341 AAGCGGAGGAGGATTTAGCC 59.530 55.000 0.00 0.00 0.00 3.93
647 815 1.071642 GCGGAGGAGGATTTAGCCC 59.928 63.158 0.00 0.00 0.00 5.19
648 816 1.411651 GCGGAGGAGGATTTAGCCCT 61.412 60.000 0.00 0.00 36.57 5.19
668 836 2.215942 TAAAAGGGCCCAGCTTCTTC 57.784 50.000 27.56 0.00 0.00 2.87
669 837 0.484655 AAAAGGGCCCAGCTTCTTCT 59.515 50.000 27.56 0.00 0.00 2.85
743 911 4.522114 AGCTTGCCCTTTGCTTTTAAAAA 58.478 34.783 1.66 0.00 42.00 1.94
807 975 4.370917 GGTGTGTCTACAAACCGACTTAA 58.629 43.478 6.70 0.00 43.72 1.85
840 1008 3.562639 GGAAACGCAACCAAAGGTC 57.437 52.632 0.00 0.00 33.12 3.85
841 1009 0.031585 GGAAACGCAACCAAAGGTCC 59.968 55.000 0.00 0.00 33.12 4.46
842 1010 0.031585 GAAACGCAACCAAAGGTCCC 59.968 55.000 0.00 0.00 33.12 4.46
843 1011 0.684805 AAACGCAACCAAAGGTCCCA 60.685 50.000 0.00 0.00 33.12 4.37
844 1012 0.684805 AACGCAACCAAAGGTCCCAA 60.685 50.000 0.00 0.00 33.12 4.12
845 1013 1.362355 CGCAACCAAAGGTCCCAAC 59.638 57.895 0.00 0.00 33.12 3.77
881 1049 0.320771 CCAGCCCGCAGTCCATATAC 60.321 60.000 0.00 0.00 0.00 1.47
925 1093 0.174845 TAGCCGTCAACCAATCCGAG 59.825 55.000 0.00 0.00 0.00 4.63
1194 1390 4.719369 GTCGTCAAGCTCGCCCGT 62.719 66.667 0.00 0.00 0.00 5.28
1336 1532 4.690719 CACGCGCCCCAGGTTGTA 62.691 66.667 5.73 0.00 0.00 2.41
1352 1548 1.950828 TGTACGTCGATCCTCTCTCC 58.049 55.000 0.00 0.00 0.00 3.71
1381 1580 5.010112 CCACCTAGATCATCGTTACATCTGT 59.990 44.000 0.00 0.00 0.00 3.41
1382 1581 5.917447 CACCTAGATCATCGTTACATCTGTG 59.083 44.000 0.00 0.00 0.00 3.66
1383 1582 5.594725 ACCTAGATCATCGTTACATCTGTGT 59.405 40.000 0.00 0.00 42.39 3.72
1384 1583 6.096987 ACCTAGATCATCGTTACATCTGTGTT 59.903 38.462 0.00 0.00 39.77 3.32
1385 1584 6.980978 CCTAGATCATCGTTACATCTGTGTTT 59.019 38.462 0.00 0.00 39.77 2.83
1419 1890 4.608948 TGTTGTTTGTCACCAAAGGTTT 57.391 36.364 0.00 0.00 41.09 3.27
1466 1938 1.881973 CTGCTGTGCTGGTTGTGTAAT 59.118 47.619 0.00 0.00 0.00 1.89
1467 1939 3.073678 CTGCTGTGCTGGTTGTGTAATA 58.926 45.455 0.00 0.00 0.00 0.98
1468 1940 2.811431 TGCTGTGCTGGTTGTGTAATAC 59.189 45.455 0.00 0.00 0.00 1.89
1469 1941 3.074412 GCTGTGCTGGTTGTGTAATACT 58.926 45.455 0.00 0.00 0.00 2.12
1470 1942 3.125316 GCTGTGCTGGTTGTGTAATACTC 59.875 47.826 0.00 0.00 0.00 2.59
1481 1958 7.287005 TGGTTGTGTAATACTCCTAGGACATAG 59.713 40.741 7.62 0.02 0.00 2.23
1513 2502 2.848302 GCACATCTGCTACGAAAATTGC 59.152 45.455 0.00 0.00 40.63 3.56
1514 2503 3.670359 GCACATCTGCTACGAAAATTGCA 60.670 43.478 0.00 0.00 40.63 4.08
1516 2505 2.873170 TCTGCTACGAAAATTGCACG 57.127 45.000 0.00 0.00 0.00 5.34
1535 2531 7.751047 TGCACGAGTTATACATTAAGAGAAC 57.249 36.000 0.00 0.00 0.00 3.01
1623 5875 1.140852 TGCAGGCCATGTATAGTGTCC 59.859 52.381 5.01 0.00 0.00 4.02
1667 6074 3.067180 AGTTGTGAACTTGTGATGCCTTG 59.933 43.478 0.00 0.00 39.04 3.61
1697 6188 2.101750 GGAGTAGCTTAGAGGTTCCTGC 59.898 54.545 0.00 0.00 0.00 4.85
1750 6245 3.756082 AATTTCCTTCCATAGGCCACA 57.244 42.857 5.01 0.00 44.37 4.17
1754 6249 1.707989 TCCTTCCATAGGCCACACAAA 59.292 47.619 5.01 0.00 44.37 2.83
1755 6250 2.311542 TCCTTCCATAGGCCACACAAAT 59.688 45.455 5.01 0.00 44.37 2.32
1816 6818 1.004044 AGCCTGAACACTGCTATTGCT 59.996 47.619 0.00 0.00 40.48 3.91
1817 6819 1.131883 GCCTGAACACTGCTATTGCTG 59.868 52.381 4.58 4.58 42.70 4.41
1832 6872 3.650281 TTGCTGCTCCATCCTTATTGA 57.350 42.857 0.00 0.00 0.00 2.57
1855 6895 3.440522 GGTTCTGAAGTCCCTAAACATGC 59.559 47.826 0.00 0.00 0.00 4.06
1887 6927 0.744414 GGCCATTGCTCACGCTCTAA 60.744 55.000 0.00 0.00 37.74 2.10
1889 6929 1.009829 CCATTGCTCACGCTCTAACC 58.990 55.000 0.00 0.00 36.97 2.85
1893 6933 0.966179 TGCTCACGCTCTAACCTGAA 59.034 50.000 0.00 0.00 36.97 3.02
1894 6934 1.336887 TGCTCACGCTCTAACCTGAAC 60.337 52.381 0.00 0.00 36.97 3.18
1896 6936 2.329379 CTCACGCTCTAACCTGAACAC 58.671 52.381 0.00 0.00 0.00 3.32
1897 6937 1.961394 TCACGCTCTAACCTGAACACT 59.039 47.619 0.00 0.00 0.00 3.55
1899 6939 1.071605 CGCTCTAACCTGAACACTGC 58.928 55.000 0.00 0.00 0.00 4.40
1900 6940 1.337260 CGCTCTAACCTGAACACTGCT 60.337 52.381 0.00 0.00 0.00 4.24
1901 6941 2.072298 GCTCTAACCTGAACACTGCTG 58.928 52.381 0.00 0.00 0.00 4.41
1902 6942 2.548920 GCTCTAACCTGAACACTGCTGT 60.549 50.000 0.00 0.00 0.00 4.40
1903 6943 3.733337 CTCTAACCTGAACACTGCTGTT 58.267 45.455 0.00 0.00 43.71 3.16
1904 6944 3.466836 TCTAACCTGAACACTGCTGTTG 58.533 45.455 0.00 0.00 40.93 3.33
1905 6945 1.392589 AACCTGAACACTGCTGTTGG 58.607 50.000 0.00 0.00 40.93 3.77
1907 6947 0.947244 CCTGAACACTGCTGTTGGTC 59.053 55.000 0.00 0.89 40.93 4.02
1908 6948 0.947244 CTGAACACTGCTGTTGGTCC 59.053 55.000 0.00 0.00 40.93 4.46
1911 6951 1.537202 GAACACTGCTGTTGGTCCATC 59.463 52.381 0.00 0.00 40.93 3.51
1912 6952 0.250901 ACACTGCTGTTGGTCCATCC 60.251 55.000 0.00 0.00 0.00 3.51
1914 6954 0.773644 ACTGCTGTTGGTCCATCCTT 59.226 50.000 0.00 0.00 37.07 3.36
2013 7493 4.044065 TGGTCCATCCTTATTGTGGTTCTT 59.956 41.667 0.00 0.00 37.07 2.52
2014 7494 5.016831 GGTCCATCCTTATTGTGGTTCTTT 58.983 41.667 0.00 0.00 34.61 2.52
2199 7698 1.972588 AGTGCCCCTACAAGGATCTT 58.027 50.000 0.00 0.00 37.67 2.40
2316 7824 4.299586 TGCTGTTTATCAAGATGGTGGA 57.700 40.909 0.00 0.00 0.00 4.02
2412 7920 2.049156 CTCGAGCTGTTCCGTGCA 60.049 61.111 0.00 0.00 0.00 4.57
2617 8125 1.333619 TGCTGCCTTCGTTTCTCAAAC 59.666 47.619 0.00 0.00 38.02 2.93
2621 8129 2.755655 TGCCTTCGTTTCTCAAACCAAA 59.244 40.909 0.00 0.00 38.14 3.28
2766 8274 5.752955 ACACATGTGGATTTTGTTTGTAAGC 59.247 36.000 28.64 0.00 34.19 3.09
2768 8276 5.752955 ACATGTGGATTTTGTTTGTAAGCAC 59.247 36.000 0.00 0.00 0.00 4.40
2776 8284 2.147958 TGTTTGTAAGCACGGGATGAC 58.852 47.619 0.00 0.00 0.00 3.06
2803 8311 9.269453 AGTTTCGTACTTAAATTTTGTAGAGCT 57.731 29.630 0.00 0.00 31.29 4.09
2870 8381 6.550938 TCAGGCTCTATTTTCTTCTCATCA 57.449 37.500 0.00 0.00 0.00 3.07
3003 8514 3.879998 TCTGAGAGTAGAGCGTTCATCT 58.120 45.455 1.01 1.71 0.00 2.90
3392 8991 2.032634 TAGCTGAAAGGCGCAACCG 61.033 57.895 10.83 0.00 46.52 4.44
3439 9038 5.039333 GCATGATGAGTTATTCCAACTTGC 58.961 41.667 0.00 0.00 0.00 4.01
3445 9044 4.176271 GAGTTATTCCAACTTGCCATTGC 58.824 43.478 0.00 0.00 38.26 3.56
3497 9096 6.989169 GCCATTCACATTCTCAATAGAGTACT 59.011 38.462 0.00 0.00 42.66 2.73
3531 9130 2.937873 GCCCAAAACACCGTATGAGCTA 60.938 50.000 0.00 0.00 0.00 3.32
3536 9135 3.454371 AACACCGTATGAGCTATGGAC 57.546 47.619 0.02 0.00 38.62 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.918630 CTGGTGAACATTTTTCAAATTAGAGAT 57.081 29.630 0.00 0.00 0.00 2.75
77 80 6.819146 TCAAAACCCATGTACTTTTTCCAAAC 59.181 34.615 0.00 0.00 0.00 2.93
94 97 7.387397 TGCATGAACATTTCTTTATCAAAACCC 59.613 33.333 0.00 0.00 0.00 4.11
131 251 8.364142 TGAACTTTATTTCAAAATCCGGTGATT 58.636 29.630 0.00 0.00 35.32 2.57
132 252 7.891561 TGAACTTTATTTCAAAATCCGGTGAT 58.108 30.769 0.00 0.00 32.42 3.06
212 333 9.788960 ACTTGTTTTCAAAATCTAGTGAACTTC 57.211 29.630 0.00 0.00 39.47 3.01
249 371 9.810545 CTTAACCAAAACTGATGAACCTTTTTA 57.189 29.630 0.00 0.00 0.00 1.52
449 617 9.465985 TTCTTTGTTTTAAAAATACGTGATCCC 57.534 29.630 1.31 0.00 0.00 3.85
498 666 7.651808 TGCTACATTCTTTTTCTCCTTTTCAG 58.348 34.615 0.00 0.00 0.00 3.02
522 690 0.746563 AACCCACCTGACGTGTGTTG 60.747 55.000 0.00 0.00 40.94 3.33
525 693 1.891919 CCAACCCACCTGACGTGTG 60.892 63.158 0.00 0.00 41.26 3.82
546 714 2.047179 GATTCTATCCCGCGGCCC 60.047 66.667 22.85 0.00 0.00 5.80
547 715 1.668151 GTGATTCTATCCCGCGGCC 60.668 63.158 22.85 0.00 0.00 6.13
548 716 2.022129 CGTGATTCTATCCCGCGGC 61.022 63.158 22.85 3.47 0.00 6.53
549 717 0.594602 TACGTGATTCTATCCCGCGG 59.405 55.000 21.04 21.04 33.34 6.46
550 718 1.266175 ACTACGTGATTCTATCCCGCG 59.734 52.381 0.00 0.00 33.34 6.46
551 719 3.666374 CGTACTACGTGATTCTATCCCGC 60.666 52.174 0.00 0.00 36.74 6.13
552 720 3.666374 GCGTACTACGTGATTCTATCCCG 60.666 52.174 10.23 0.00 44.73 5.14
553 721 3.251729 TGCGTACTACGTGATTCTATCCC 59.748 47.826 10.23 0.00 44.73 3.85
554 722 4.478843 TGCGTACTACGTGATTCTATCC 57.521 45.455 10.23 0.00 44.73 2.59
555 723 5.450171 ACATGCGTACTACGTGATTCTATC 58.550 41.667 10.23 0.00 44.73 2.08
556 724 5.434352 ACATGCGTACTACGTGATTCTAT 57.566 39.130 10.23 0.00 44.73 1.98
557 725 4.888038 ACATGCGTACTACGTGATTCTA 57.112 40.909 10.23 0.00 44.73 2.10
558 726 3.777465 ACATGCGTACTACGTGATTCT 57.223 42.857 10.23 0.00 44.73 2.40
559 727 4.835199 AAACATGCGTACTACGTGATTC 57.165 40.909 10.23 0.00 44.73 2.52
560 728 5.600908 AAAAACATGCGTACTACGTGATT 57.399 34.783 10.23 4.04 44.73 2.57
561 729 5.220340 GCTAAAAACATGCGTACTACGTGAT 60.220 40.000 10.23 0.77 44.73 3.06
562 730 4.090354 GCTAAAAACATGCGTACTACGTGA 59.910 41.667 10.23 0.00 44.73 4.35
563 731 4.320491 GCTAAAAACATGCGTACTACGTG 58.680 43.478 10.23 4.37 44.73 4.49
564 732 3.059834 CGCTAAAAACATGCGTACTACGT 59.940 43.478 10.23 0.00 44.73 3.57
565 733 3.580389 CGCTAAAAACATGCGTACTACG 58.420 45.455 4.12 4.12 45.88 3.51
604 772 1.183030 GCCGGCCCAGTTACCTTTTT 61.183 55.000 18.11 0.00 0.00 1.94
605 773 1.605451 GCCGGCCCAGTTACCTTTT 60.605 57.895 18.11 0.00 0.00 2.27
606 774 2.035155 GCCGGCCCAGTTACCTTT 59.965 61.111 18.11 0.00 0.00 3.11
607 775 4.043100 GGCCGGCCCAGTTACCTT 62.043 66.667 36.64 0.00 0.00 3.50
610 778 3.905437 TTTCGGCCGGCCCAGTTAC 62.905 63.158 39.24 13.53 0.00 2.50
611 779 3.615509 CTTTCGGCCGGCCCAGTTA 62.616 63.158 39.24 18.85 0.00 2.24
624 792 2.474816 CTAAATCCTCCTCCGCTTTCG 58.525 52.381 0.00 0.00 0.00 3.46
625 793 2.214347 GCTAAATCCTCCTCCGCTTTC 58.786 52.381 0.00 0.00 0.00 2.62
626 794 1.134068 GGCTAAATCCTCCTCCGCTTT 60.134 52.381 0.00 0.00 0.00 3.51
627 795 0.470341 GGCTAAATCCTCCTCCGCTT 59.530 55.000 0.00 0.00 0.00 4.68
628 796 1.411651 GGGCTAAATCCTCCTCCGCT 61.412 60.000 0.00 0.00 0.00 5.52
629 797 1.071642 GGGCTAAATCCTCCTCCGC 59.928 63.158 0.00 0.00 0.00 5.54
630 798 1.132500 AAGGGCTAAATCCTCCTCCG 58.868 55.000 0.00 0.00 32.59 4.63
631 799 4.790718 TTTAAGGGCTAAATCCTCCTCC 57.209 45.455 0.00 0.00 32.59 4.30
632 800 5.133941 CCTTTTAAGGGCTAAATCCTCCTC 58.866 45.833 0.32 0.00 42.66 3.71
633 801 5.130705 CCTTTTAAGGGCTAAATCCTCCT 57.869 43.478 0.32 0.00 42.66 3.69
646 814 1.186200 GAAGCTGGGCCCTTTTAAGG 58.814 55.000 25.70 5.37 46.06 2.69
647 815 2.222227 AGAAGCTGGGCCCTTTTAAG 57.778 50.000 25.70 13.01 0.00 1.85
648 816 2.110011 AGAAGAAGCTGGGCCCTTTTAA 59.890 45.455 25.70 0.00 0.00 1.52
691 859 1.381872 ATAGGTGAGCCCAGCGAGT 60.382 57.895 0.00 0.00 44.94 4.18
743 911 3.947834 CGATAAGCCAGAAAATTCCACCT 59.052 43.478 0.00 0.00 0.00 4.00
750 918 5.343249 GCAATGTTCGATAAGCCAGAAAAT 58.657 37.500 0.00 0.00 0.00 1.82
790 958 7.149063 CGTTTCTACTTAAGTCGGTTTGTAGAC 60.149 40.741 12.39 0.00 35.01 2.59
807 975 2.796593 CGTTTCCGTTTCCGTTTCTACT 59.203 45.455 0.00 0.00 0.00 2.57
831 999 0.996762 TGGGAGTTGGGACCTTTGGT 60.997 55.000 0.00 0.00 39.44 3.67
836 1004 1.464198 AGCTTGGGAGTTGGGACCT 60.464 57.895 0.00 0.00 0.00 3.85
838 1006 0.690762 TACAGCTTGGGAGTTGGGAC 59.309 55.000 0.00 0.00 38.31 4.46
839 1007 0.984230 CTACAGCTTGGGAGTTGGGA 59.016 55.000 0.00 0.00 38.31 4.37
840 1008 0.984230 TCTACAGCTTGGGAGTTGGG 59.016 55.000 0.00 0.00 38.31 4.12
841 1009 1.625818 ACTCTACAGCTTGGGAGTTGG 59.374 52.381 6.45 0.00 38.31 3.77
842 1010 2.354203 GGACTCTACAGCTTGGGAGTTG 60.354 54.545 11.81 0.00 39.71 3.16
843 1011 1.903183 GGACTCTACAGCTTGGGAGTT 59.097 52.381 11.81 0.02 35.74 3.01
844 1012 1.203187 TGGACTCTACAGCTTGGGAGT 60.203 52.381 10.74 10.74 37.31 3.85
845 1013 1.480137 CTGGACTCTACAGCTTGGGAG 59.520 57.143 5.39 5.39 0.00 4.30
908 1076 2.750888 GCTCGGATTGGTTGACGGC 61.751 63.158 0.00 0.00 0.00 5.68
910 1078 1.375396 TGGCTCGGATTGGTTGACG 60.375 57.895 0.00 0.00 0.00 4.35
925 1093 4.626081 AGCTGTGGGACGTGTGGC 62.626 66.667 0.00 0.00 0.00 5.01
1336 1532 1.600023 GATGGAGAGAGGATCGACGT 58.400 55.000 0.00 0.00 42.67 4.34
1352 1548 2.251818 ACGATGATCTAGGTGGGGATG 58.748 52.381 0.00 0.00 0.00 3.51
1381 1580 8.353684 ACAAACAACATATTATCCGACAAAACA 58.646 29.630 0.00 0.00 0.00 2.83
1382 1581 8.736751 ACAAACAACATATTATCCGACAAAAC 57.263 30.769 0.00 0.00 0.00 2.43
1383 1582 8.568794 TGACAAACAACATATTATCCGACAAAA 58.431 29.630 0.00 0.00 0.00 2.44
1384 1583 8.018520 GTGACAAACAACATATTATCCGACAAA 58.981 33.333 0.00 0.00 0.00 2.83
1385 1584 7.361371 GGTGACAAACAACATATTATCCGACAA 60.361 37.037 0.00 0.00 36.04 3.18
1419 1890 3.848191 GCTTCAAAACACGCGAATCAAGA 60.848 43.478 15.93 0.33 0.00 3.02
1466 1938 5.908562 ACTAGCACTATGTCCTAGGAGTA 57.091 43.478 13.15 7.66 34.32 2.59
1467 1939 4.799715 ACTAGCACTATGTCCTAGGAGT 57.200 45.455 13.15 6.79 34.32 3.85
1468 1940 6.276847 CAAAACTAGCACTATGTCCTAGGAG 58.723 44.000 13.15 2.52 34.32 3.69
1469 1941 5.395324 GCAAAACTAGCACTATGTCCTAGGA 60.395 44.000 7.62 7.62 34.32 2.94
1470 1942 4.811557 GCAAAACTAGCACTATGTCCTAGG 59.188 45.833 0.82 0.82 34.32 3.02
1513 2502 7.043325 GCAGGTTCTCTTAATGTATAACTCGTG 60.043 40.741 0.00 0.00 0.00 4.35
1514 2503 6.979238 GCAGGTTCTCTTAATGTATAACTCGT 59.021 38.462 0.00 0.00 0.00 4.18
1516 2505 7.201145 TCGCAGGTTCTCTTAATGTATAACTC 58.799 38.462 0.00 0.00 0.00 3.01
1535 2531 7.028962 TGAAATTGATTAAACTCAATCGCAGG 58.971 34.615 5.06 0.00 43.37 4.85
1667 6074 4.023021 CCTCTAAGCTACTCCATAACCGAC 60.023 50.000 0.00 0.00 0.00 4.79
1697 6188 2.352421 CCATCAGCCAAGAAACAGCTTG 60.352 50.000 0.00 0.00 43.74 4.01
1755 6250 8.726988 GGCTAAATAGACAAGTTACATTTGTGA 58.273 33.333 0.00 0.00 38.78 3.58
1832 6872 4.807643 GCATGTTTAGGGACTTCAGAACCT 60.808 45.833 0.00 0.00 41.75 3.50
1855 6895 2.885554 GCAATGGCCTATAAGATGGGGG 60.886 54.545 3.32 0.00 0.00 5.40
1887 6927 0.255890 ACCAACAGCAGTGTTCAGGT 59.744 50.000 0.00 0.00 43.88 4.00
1889 6929 0.947244 GGACCAACAGCAGTGTTCAG 59.053 55.000 0.00 0.00 43.88 3.02
1893 6933 0.250901 GGATGGACCAACAGCAGTGT 60.251 55.000 0.00 0.00 39.19 3.55
1894 6934 0.037303 AGGATGGACCAACAGCAGTG 59.963 55.000 0.00 0.00 42.04 3.66
1896 6936 2.787473 TAAGGATGGACCAACAGCAG 57.213 50.000 0.00 0.00 42.04 4.24
1897 6937 3.245229 ACAATAAGGATGGACCAACAGCA 60.245 43.478 0.00 0.00 42.04 4.41
1899 6939 3.696051 CCACAATAAGGATGGACCAACAG 59.304 47.826 0.00 0.00 42.04 3.16
1900 6940 3.075283 ACCACAATAAGGATGGACCAACA 59.925 43.478 0.00 0.00 42.04 3.33
1901 6941 3.697166 ACCACAATAAGGATGGACCAAC 58.303 45.455 0.00 0.00 42.04 3.77
1902 6942 4.044065 AGAACCACAATAAGGATGGACCAA 59.956 41.667 0.00 0.00 42.04 3.67
1903 6943 3.591527 AGAACCACAATAAGGATGGACCA 59.408 43.478 0.00 0.00 42.04 4.02
1904 6944 3.947834 CAGAACCACAATAAGGATGGACC 59.052 47.826 0.00 0.00 36.94 4.46
1905 6945 4.843728 TCAGAACCACAATAAGGATGGAC 58.156 43.478 0.00 0.00 36.94 4.02
1907 6947 5.256474 ACTTCAGAACCACAATAAGGATGG 58.744 41.667 0.00 0.00 39.57 3.51
1908 6948 5.355350 GGACTTCAGAACCACAATAAGGATG 59.645 44.000 0.00 0.00 0.00 3.51
1911 6951 4.010349 GGGACTTCAGAACCACAATAAGG 58.990 47.826 0.00 0.00 0.00 2.69
1912 6952 4.911390 AGGGACTTCAGAACCACAATAAG 58.089 43.478 0.00 0.00 27.25 1.73
1914 6954 6.183361 TGTTTAGGGACTTCAGAACCACAATA 60.183 38.462 0.00 0.00 41.75 1.90
2013 7493 2.583101 TGGGGGCATGTTTATGGACTAA 59.417 45.455 0.00 0.00 34.79 2.24
2014 7494 2.209758 TGGGGGCATGTTTATGGACTA 58.790 47.619 0.00 0.00 34.79 2.59
2199 7698 1.103803 GCCTGTCCAGAGTATCGACA 58.896 55.000 0.00 0.00 42.67 4.35
2246 7754 3.243670 TGAGCTCTTAGCAGGATCATTCG 60.244 47.826 16.19 0.00 45.56 3.34
2316 7824 2.433145 CTGCGCCTCATGTCGTGT 60.433 61.111 4.18 0.00 0.00 4.49
2617 8125 6.312672 CAGTAACAAACTTTTCCCTGTTTTGG 59.687 38.462 0.00 0.00 35.76 3.28
2621 8129 4.142026 GGCAGTAACAAACTTTTCCCTGTT 60.142 41.667 0.00 0.00 35.76 3.16
2672 8180 8.109634 ACTTCAAAGACCATACCAATAAGACAT 58.890 33.333 0.00 0.00 0.00 3.06
2766 8274 1.990563 GTACGAAACTGTCATCCCGTG 59.009 52.381 0.00 0.00 0.00 4.94
2768 8276 2.649331 AGTACGAAACTGTCATCCCG 57.351 50.000 0.00 0.00 36.93 5.14
2776 8284 9.314501 GCTCTACAAAATTTAAGTACGAAACTG 57.685 33.333 0.00 1.25 38.88 3.16
2803 8311 4.393371 GCTGGTAACCAAACAAAGCAAAAA 59.607 37.500 0.00 0.00 33.26 1.94
2831 8340 1.342174 CCTGAAGCTTGTGGCACAAAT 59.658 47.619 30.66 20.53 44.16 2.32
3003 8514 3.325870 CAGCATCGAAAGACAACCACTA 58.674 45.455 0.00 0.00 46.97 2.74
3177 8747 1.577328 CTTTGCACAGCACTACGGGG 61.577 60.000 0.00 0.00 38.71 5.73
3324 8923 7.387397 GGCATTTTGTGAATGGTTTTTCTCATA 59.613 33.333 1.47 0.00 31.40 2.15
3392 8991 4.509970 TGCGCACCATATCAATAAGTGTAC 59.490 41.667 5.66 0.00 0.00 2.90
3439 9038 2.751259 CCTCCATCCATAATCGCAATGG 59.249 50.000 4.62 4.62 44.51 3.16
3445 9044 2.847327 AGCACCTCCATCCATAATCG 57.153 50.000 0.00 0.00 0.00 3.34
3531 9130 1.217057 ATGGCACCCTTCCTGTCCAT 61.217 55.000 0.00 0.00 0.00 3.41
3536 9135 2.276740 GGGATGGCACCCTTCCTG 59.723 66.667 15.34 0.00 44.40 3.86


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

AutoCloner maintained by Alex Coulton.