Multiple sequence alignment - TraesCS2A01G100400

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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 TraesCS2A01G100400 chr2A 100.000 4158 0 0 1 4158 53440199 53444356 0.000000e+00 7679.0
1 TraesCS2A01G100400 chr2A 96.438 758 23 1 3401 4158 753015621 753014868 0.000000e+00 1247.0
2 TraesCS2A01G100400 chr2A 95.544 763 31 3 3396 4158 80985574 80986333 0.000000e+00 1218.0
3 TraesCS2A01G100400 chr2B 91.856 1584 96 15 1 1563 80554546 80556117 0.000000e+00 2180.0
4 TraesCS2A01G100400 chr2B 89.470 1396 60 40 1984 3320 80556536 80557903 0.000000e+00 1683.0
5 TraesCS2A01G100400 chr2B 83.995 881 91 30 709 1563 77496286 77495430 0.000000e+00 800.0
6 TraesCS2A01G100400 chr2B 90.296 371 22 7 1561 1924 80556154 80556517 1.350000e-129 473.0
7 TraesCS2A01G100400 chr2B 88.496 339 36 3 20 355 243559675 243559337 1.390000e-109 407.0
8 TraesCS2A01G100400 chr2B 91.154 260 21 2 1580 1837 77495369 77495110 6.610000e-93 351.0
9 TraesCS2A01G100400 chr2D 88.874 1474 74 42 1984 3396 52042341 52043785 0.000000e+00 1731.0
10 TraesCS2A01G100400 chr2D 88.346 1270 82 40 1984 3215 42717009 42715768 0.000000e+00 1465.0
11 TraesCS2A01G100400 chr2D 87.991 916 52 20 681 1563 52041033 52041923 0.000000e+00 1029.0
12 TraesCS2A01G100400 chr2D 91.680 637 28 13 943 1561 42718057 42717428 0.000000e+00 859.0
13 TraesCS2A01G100400 chr2D 92.529 348 18 4 1580 1923 52041979 52042322 3.730000e-135 492.0
14 TraesCS2A01G100400 chr2D 91.081 370 20 6 1561 1924 42717389 42717027 4.830000e-134 488.0
15 TraesCS2A01G100400 chr2D 90.909 319 17 4 476 787 42721024 42720711 6.430000e-113 418.0
16 TraesCS2A01G100400 chr2D 88.000 75 9 0 1 75 474180226 474180300 5.730000e-14 89.8
17 TraesCS2A01G100400 chr2D 87.097 62 8 0 808 869 42720708 42720647 2.070000e-08 71.3
18 TraesCS2A01G100400 chr5A 97.500 760 18 1 3399 4158 704842064 704841306 0.000000e+00 1297.0
19 TraesCS2A01G100400 chr5A 96.199 763 27 2 3396 4158 5693673 5694433 0.000000e+00 1247.0
20 TraesCS2A01G100400 chr5A 87.165 709 78 9 3395 4098 2419256 2419956 0.000000e+00 793.0
21 TraesCS2A01G100400 chr5A 97.351 453 11 1 3706 4158 493818809 493819260 0.000000e+00 769.0
22 TraesCS2A01G100400 chr5A 94.062 320 19 0 3396 3715 493818086 493818405 1.740000e-133 486.0
23 TraesCS2A01G100400 chr5A 87.535 361 41 4 1 358 456445182 456445541 8.320000e-112 414.0
24 TraesCS2A01G100400 chr5A 89.328 253 25 2 1 252 118249734 118249483 2.410000e-82 316.0
25 TraesCS2A01G100400 chr5A 87.069 232 28 2 1 231 693131919 693131689 1.150000e-65 261.0
26 TraesCS2A01G100400 chr1A 96.296 756 27 1 3399 4154 478364666 478363912 0.000000e+00 1240.0
27 TraesCS2A01G100400 chr1A 94.444 486 27 0 3399 3884 146189417 146188932 0.000000e+00 749.0
28 TraesCS2A01G100400 chr1A 82.626 495 63 19 2661 3152 531241324 531241798 2.310000e-112 416.0
29 TraesCS2A01G100400 chr1A 89.091 220 22 2 1992 2210 531240062 531240280 5.300000e-69 272.0
30 TraesCS2A01G100400 chr6A 95.078 772 34 2 3387 4158 551838685 551839452 0.000000e+00 1212.0
31 TraesCS2A01G100400 chr4A 96.882 449 12 2 3706 4154 558645042 558645488 0.000000e+00 750.0
32 TraesCS2A01G100400 chr4A 86.833 281 23 11 1953 2230 594126029 594126298 6.760000e-78 302.0
33 TraesCS2A01G100400 chr1D 82.318 509 67 21 2661 3150 432800692 432801196 1.790000e-113 420.0
34 TraesCS2A01G100400 chr1D 88.785 214 22 2 1992 2204 432798724 432798936 1.150000e-65 261.0
35 TraesCS2A01G100400 chr1D 84.127 252 26 6 1 252 431815583 431815346 8.990000e-57 231.0
36 TraesCS2A01G100400 chr6D 90.580 276 26 0 1072 1347 449117097 449116822 2.360000e-97 366.0
37 TraesCS2A01G100400 chr7A 88.489 278 31 1 1 277 174451307 174451584 6.660000e-88 335.0
38 TraesCS2A01G100400 chr7A 91.837 49 4 0 1167 1215 635649579 635649531 7.460000e-08 69.4
39 TraesCS2A01G100400 chr1B 90.361 249 23 1 2666 2913 584160193 584160441 4.010000e-85 326.0
40 TraesCS2A01G100400 chr1B 87.554 233 25 4 1992 2222 584158848 584159078 2.460000e-67 267.0
41 TraesCS2A01G100400 chr4B 88.538 253 23 3 1 252 75207535 75207782 6.760000e-78 302.0
42 TraesCS2A01G100400 chr4B 90.050 201 15 4 1953 2153 17389717 17389522 5.330000e-64 255.0
43 TraesCS2A01G100400 chr4B 89.062 128 14 0 1710 1837 17389929 17389802 4.300000e-35 159.0
44 TraesCS2A01G100400 chr4D 92.188 64 5 0 12 75 105900089 105900152 1.590000e-14 91.6


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 TraesCS2A01G100400 chr2A 53440199 53444356 4157 False 7679.000000 7679 100.000000 1 4158 1 chr2A.!!$F1 4157
1 TraesCS2A01G100400 chr2A 753014868 753015621 753 True 1247.000000 1247 96.438000 3401 4158 1 chr2A.!!$R1 757
2 TraesCS2A01G100400 chr2A 80985574 80986333 759 False 1218.000000 1218 95.544000 3396 4158 1 chr2A.!!$F2 762
3 TraesCS2A01G100400 chr2B 80554546 80557903 3357 False 1445.333333 2180 90.540667 1 3320 3 chr2B.!!$F1 3319
4 TraesCS2A01G100400 chr2B 77495110 77496286 1176 True 575.500000 800 87.574500 709 1837 2 chr2B.!!$R2 1128
5 TraesCS2A01G100400 chr2D 52041033 52043785 2752 False 1084.000000 1731 89.798000 681 3396 3 chr2D.!!$F2 2715
6 TraesCS2A01G100400 chr2D 42715768 42721024 5256 True 660.260000 1465 89.822600 476 3215 5 chr2D.!!$R1 2739
7 TraesCS2A01G100400 chr5A 704841306 704842064 758 True 1297.000000 1297 97.500000 3399 4158 1 chr5A.!!$R3 759
8 TraesCS2A01G100400 chr5A 5693673 5694433 760 False 1247.000000 1247 96.199000 3396 4158 1 chr5A.!!$F2 762
9 TraesCS2A01G100400 chr5A 2419256 2419956 700 False 793.000000 793 87.165000 3395 4098 1 chr5A.!!$F1 703
10 TraesCS2A01G100400 chr5A 493818086 493819260 1174 False 627.500000 769 95.706500 3396 4158 2 chr5A.!!$F4 762
11 TraesCS2A01G100400 chr1A 478363912 478364666 754 True 1240.000000 1240 96.296000 3399 4154 1 chr1A.!!$R2 755
12 TraesCS2A01G100400 chr1A 531240062 531241798 1736 False 344.000000 416 85.858500 1992 3152 2 chr1A.!!$F1 1160
13 TraesCS2A01G100400 chr6A 551838685 551839452 767 False 1212.000000 1212 95.078000 3387 4158 1 chr6A.!!$F1 771
14 TraesCS2A01G100400 chr1D 432798724 432801196 2472 False 340.500000 420 85.551500 1992 3150 2 chr1D.!!$F1 1158
15 TraesCS2A01G100400 chr1B 584158848 584160441 1593 False 296.500000 326 88.957500 1992 2913 2 chr1B.!!$F1 921

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
122 124 0.036022 GAGTGCCTCTGGTTTGCTCT 59.964 55.0 0.00 0.00 0.0 4.09 F
125 127 0.037326 TGCCTCTGGTTTGCTCTACG 60.037 55.0 0.00 0.00 0.0 3.51 F
1976 4615 0.111266 GTCCTAATTACATGCGCGCG 60.111 55.0 28.44 28.44 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 4596 0.111266 CGCGCGCATGTAATTAGGAC 60.111 55.0 32.61 0.00 0.00 3.85 R
1980 4619 0.865639 GTGTTCTGCCAACGCAACAC 60.866 55.0 4.77 4.77 46.66 3.32 R
3392 8002 0.035439 ACGGGCATTCCACTGGTTAG 60.035 55.0 0.00 0.00 34.36 2.34 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
32 33 9.277565 CGAAGATGTAAAATGGTGATGTAAAAG 57.722 33.333 0.00 0.00 0.00 2.27
35 36 8.028938 AGATGTAAAATGGTGATGTAAAAGTGC 58.971 33.333 0.00 0.00 0.00 4.40
38 39 8.147058 TGTAAAATGGTGATGTAAAAGTGCAAT 58.853 29.630 0.00 0.00 0.00 3.56
53 55 3.119245 AGTGCAATTCCAACAGATGATGC 60.119 43.478 0.00 0.00 0.00 3.91
80 82 7.715265 ATGAAGATGTAAACTAGTTATGCCG 57.285 36.000 8.92 0.00 0.00 5.69
83 85 2.542597 TGTAAACTAGTTATGCCGCCG 58.457 47.619 8.92 0.00 0.00 6.46
87 89 1.324740 ACTAGTTATGCCGCCGGTGA 61.325 55.000 18.79 0.00 0.00 4.02
91 93 3.961838 TTATGCCGCCGGTGACCAC 62.962 63.158 18.79 3.35 0.00 4.16
122 124 0.036022 GAGTGCCTCTGGTTTGCTCT 59.964 55.000 0.00 0.00 0.00 4.09
125 127 0.037326 TGCCTCTGGTTTGCTCTACG 60.037 55.000 0.00 0.00 0.00 3.51
209 211 1.481056 AACGAGAGGAGTTGGGGTGG 61.481 60.000 0.00 0.00 0.00 4.61
212 214 3.256960 GAGGAGTTGGGGTGGCCA 61.257 66.667 0.00 0.00 0.00 5.36
218 220 0.759060 AGTTGGGGTGGCCAAAACTC 60.759 55.000 7.24 0.57 28.82 3.01
267 269 2.113139 CACAACTTGCTCGGGGGT 59.887 61.111 0.00 0.00 0.00 4.95
279 281 4.106925 GGGGGTGAGGCTGCAGAG 62.107 72.222 20.43 0.00 0.00 3.35
301 303 2.830514 GGGGAGGCCGGATAAAGGG 61.831 68.421 5.05 0.00 0.00 3.95
339 341 2.457366 ACTCCAGGAGTTTAAGTGCG 57.543 50.000 17.31 0.00 40.28 5.34
362 364 2.642700 GGACGCGGCAAACATGTT 59.357 55.556 17.00 4.92 0.00 2.71
444 446 9.449719 AAATATGTTAACAAGAGTCCTTCGATT 57.550 29.630 13.23 0.00 0.00 3.34
458 460 3.555547 CCTTCGATTCATGCGTACATCAA 59.444 43.478 0.00 0.00 32.87 2.57
460 462 4.972286 TCGATTCATGCGTACATCAATC 57.028 40.909 0.00 0.00 39.61 2.67
486 488 2.099756 GAGCACCCATTCCTATTTGTGC 59.900 50.000 4.37 4.37 47.00 4.57
535 537 3.077359 GACATCTCTGGGAAGGTGTTTG 58.923 50.000 0.00 0.00 40.69 2.93
583 585 1.082756 CTGGTCGCGAACAAAGCAC 60.083 57.895 28.96 4.89 34.19 4.40
624 633 2.022129 GCTGTCACGTGGAAGTCCG 61.022 63.158 17.00 0.00 39.43 4.79
805 814 2.032071 CCGTCAGTTCACCCCACC 59.968 66.667 0.00 0.00 0.00 4.61
829 838 2.186076 CTCCACGTACAATCTTCTCGC 58.814 52.381 0.00 0.00 0.00 5.03
888 1848 4.760220 TCCCCCTCCCCTGCCTTC 62.760 72.222 0.00 0.00 0.00 3.46
1365 3940 1.375396 CATCAAGGTCAACGCCGGA 60.375 57.895 5.05 0.00 0.00 5.14
1425 4004 2.644992 CGTTGCCAAGCCCTGTTC 59.355 61.111 0.00 0.00 0.00 3.18
1490 4078 0.839277 ATCCAGCCGTCCATGATCAA 59.161 50.000 0.00 0.00 0.00 2.57
1502 4090 2.436417 CATGATCAAAGGTTCACGGGT 58.564 47.619 0.00 0.00 0.00 5.28
1503 4091 1.890876 TGATCAAAGGTTCACGGGTG 58.109 50.000 0.00 0.00 0.00 4.61
1521 4109 2.671682 GGAGGAAGGAGGCGCTTT 59.328 61.111 7.64 0.00 0.00 3.51
1542 4130 2.577059 GAATCGTGGGCGTCAGGA 59.423 61.111 0.00 0.00 43.32 3.86
1565 4192 1.745489 GGCCCCACGAAGATCACAC 60.745 63.158 0.00 0.00 0.00 3.82
1577 4204 7.277760 CCACGAAGATCACACTATCACATTTTA 59.722 37.037 0.00 0.00 0.00 1.52
1578 4205 8.323854 CACGAAGATCACACTATCACATTTTAG 58.676 37.037 0.00 0.00 0.00 1.85
1604 4239 9.423061 GTGCTTCAAACTAATTTACCATTGAAT 57.577 29.630 0.00 0.00 36.52 2.57
1682 4318 1.227823 CCCACAACTTGGTCGCAGA 60.228 57.895 0.00 0.00 45.25 4.26
1763 4399 4.082523 ACGATCGTGCAGTGGGGG 62.083 66.667 22.06 0.00 0.00 5.40
1889 4525 4.406943 CCTTCAAGGTACGTACGTAACTC 58.593 47.826 38.08 24.88 46.74 3.01
1890 4526 4.083324 CCTTCAAGGTACGTACGTAACTCA 60.083 45.833 38.08 27.11 46.74 3.41
1891 4527 4.404507 TCAAGGTACGTACGTAACTCAC 57.595 45.455 38.08 24.28 46.74 3.51
1892 4528 3.188460 TCAAGGTACGTACGTAACTCACC 59.812 47.826 38.08 30.65 46.74 4.02
1893 4529 2.778299 AGGTACGTACGTAACTCACCA 58.222 47.619 34.42 9.59 44.49 4.17
1894 4530 3.347216 AGGTACGTACGTAACTCACCAT 58.653 45.455 34.42 16.19 44.49 3.55
1922 4561 4.341783 GTCCCTGCTGCCAGTGCT 62.342 66.667 0.00 0.00 37.38 4.40
1923 4562 4.025858 TCCCTGCTGCCAGTGCTC 62.026 66.667 0.00 0.00 37.38 4.26
1924 4563 4.031129 CCCTGCTGCCAGTGCTCT 62.031 66.667 0.00 0.00 37.38 4.09
1925 4564 2.746671 CCTGCTGCCAGTGCTCTG 60.747 66.667 8.84 8.84 41.01 3.35
1932 4571 3.390521 CCAGTGCTCTGCCCGGTA 61.391 66.667 10.32 0.00 40.09 4.02
1933 4572 2.125512 CAGTGCTCTGCCCGGTAC 60.126 66.667 0.00 0.00 34.79 3.34
1934 4573 3.989698 CAGTGCTCTGCCCGGTACG 62.990 68.421 0.00 0.00 43.03 3.67
1951 4590 2.659897 GCCATACAGAGCGCGAGG 60.660 66.667 12.10 0.00 0.00 4.63
1953 4592 1.589993 CCATACAGAGCGCGAGGTG 60.590 63.158 12.10 5.23 45.11 4.00
1954 4593 1.589993 CATACAGAGCGCGAGGTGG 60.590 63.158 12.10 0.00 45.11 4.61
1955 4594 2.786495 ATACAGAGCGCGAGGTGGG 61.786 63.158 12.10 0.00 45.11 4.61
1962 4601 3.066190 CGCGAGGTGGGTGTCCTA 61.066 66.667 0.00 0.00 35.20 2.94
1963 4602 2.642254 CGCGAGGTGGGTGTCCTAA 61.642 63.158 0.00 0.00 35.20 2.69
1964 4603 1.905512 GCGAGGTGGGTGTCCTAAT 59.094 57.895 0.00 0.00 35.20 1.73
1965 4604 0.252197 GCGAGGTGGGTGTCCTAATT 59.748 55.000 0.00 0.00 35.20 1.40
1966 4605 1.483415 GCGAGGTGGGTGTCCTAATTA 59.517 52.381 0.00 0.00 35.20 1.40
1967 4606 2.740904 GCGAGGTGGGTGTCCTAATTAC 60.741 54.545 0.00 0.00 35.20 1.89
1968 4607 2.498481 CGAGGTGGGTGTCCTAATTACA 59.502 50.000 0.00 0.00 35.20 2.41
1969 4608 3.134081 CGAGGTGGGTGTCCTAATTACAT 59.866 47.826 0.00 0.00 35.20 2.29
1970 4609 4.451900 GAGGTGGGTGTCCTAATTACATG 58.548 47.826 0.00 0.00 35.20 3.21
1971 4610 2.949644 GGTGGGTGTCCTAATTACATGC 59.050 50.000 0.00 0.00 0.00 4.06
1972 4611 2.612212 GTGGGTGTCCTAATTACATGCG 59.388 50.000 0.00 0.00 0.00 4.73
1973 4612 1.602377 GGGTGTCCTAATTACATGCGC 59.398 52.381 0.00 0.00 0.00 6.09
1974 4613 1.260561 GGTGTCCTAATTACATGCGCG 59.739 52.381 0.00 0.00 0.00 6.86
1975 4614 0.934496 TGTCCTAATTACATGCGCGC 59.066 50.000 27.26 27.26 0.00 6.86
1976 4615 0.111266 GTCCTAATTACATGCGCGCG 60.111 55.000 28.44 28.44 0.00 6.86
1977 4616 1.438710 CCTAATTACATGCGCGCGC 60.439 57.895 45.02 45.02 42.35 6.86
1978 4617 1.784396 CTAATTACATGCGCGCGCG 60.784 57.895 45.73 45.73 45.51 6.86
2224 5366 2.038007 TGCTCGCCCTCCTCTTCT 59.962 61.111 0.00 0.00 0.00 2.85
2227 5369 1.819905 CTCGCCCTCCTCTTCTTCC 59.180 63.158 0.00 0.00 0.00 3.46
2228 5370 0.686112 CTCGCCCTCCTCTTCTTCCT 60.686 60.000 0.00 0.00 0.00 3.36
2229 5371 0.684805 TCGCCCTCCTCTTCTTCCTC 60.685 60.000 0.00 0.00 0.00 3.71
2231 5373 0.684805 GCCCTCCTCTTCTTCCTCGA 60.685 60.000 0.00 0.00 0.00 4.04
2232 5374 2.032151 GCCCTCCTCTTCTTCCTCGAT 61.032 57.143 0.00 0.00 0.00 3.59
2233 5375 1.686052 CCCTCCTCTTCTTCCTCGATG 59.314 57.143 0.00 0.00 0.00 3.84
2235 5377 1.068434 CTCCTCTTCTTCCTCGATGCC 59.932 57.143 0.00 0.00 0.00 4.40
2236 5378 1.118838 CCTCTTCTTCCTCGATGCCT 58.881 55.000 0.00 0.00 0.00 4.75
2237 5379 2.091830 TCCTCTTCTTCCTCGATGCCTA 60.092 50.000 0.00 0.00 0.00 3.93
2251 5393 0.033306 TGCCTAATGCTCCATTGCCA 60.033 50.000 0.94 0.00 42.00 4.92
2253 5395 1.751733 GCCTAATGCTCCATTGCCAGA 60.752 52.381 0.94 0.00 35.54 3.86
2270 5425 2.947652 CCAGACCTTCCATGCAATACTG 59.052 50.000 0.00 0.00 0.00 2.74
2307 5495 4.211374 AGAAAAACAGAGCATGTACGACAC 59.789 41.667 0.00 0.00 43.00 3.67
2460 6269 3.783362 CTGTCCGTTTGTGCCCCCA 62.783 63.158 0.00 0.00 0.00 4.96
2512 6617 0.923403 CCACATGCTCGATACACGTG 59.077 55.000 15.48 15.48 43.13 4.49
2527 6632 4.921470 ACACGTGAAATATTTCGGTCTG 57.079 40.909 25.01 15.06 40.01 3.51
2579 6794 9.956797 CATGTTTTCTGTTTTGTTTTTCTACAG 57.043 29.630 0.00 0.00 38.00 2.74
2610 6856 2.810650 CACGGTGGCACTAGAATCTAC 58.189 52.381 18.45 0.00 0.00 2.59
2658 6921 3.678072 GTGTATATGACTGTGTGCGTGTT 59.322 43.478 0.00 0.00 0.00 3.32
2659 6922 3.677596 TGTATATGACTGTGTGCGTGTTG 59.322 43.478 0.00 0.00 0.00 3.33
2660 6923 2.232756 TATGACTGTGTGCGTGTTGT 57.767 45.000 0.00 0.00 0.00 3.32
2663 6926 1.705337 GACTGTGTGCGTGTTGTGCT 61.705 55.000 0.00 0.00 0.00 4.40
2664 6927 0.461163 ACTGTGTGCGTGTTGTGCTA 60.461 50.000 0.00 0.00 0.00 3.49
2671 7209 2.680913 CGTGTTGTGCTAGCAGGGC 61.681 63.158 20.03 11.32 0.00 5.19
2920 7462 3.590127 GCTGTACGCTCCTATTCCC 57.410 57.895 2.99 0.00 35.14 3.97
2921 7463 0.033642 GCTGTACGCTCCTATTCCCC 59.966 60.000 2.99 0.00 35.14 4.81
2922 7464 1.705873 CTGTACGCTCCTATTCCCCT 58.294 55.000 0.00 0.00 0.00 4.79
2928 7470 0.104934 GCTCCTATTCCCCTCCTCCA 60.105 60.000 0.00 0.00 0.00 3.86
2938 7528 2.046292 CCCCTCCTCCATTCTCTCTTC 58.954 57.143 0.00 0.00 0.00 2.87
2968 7558 2.123640 CTCCGTCCTCTCCCCTCC 60.124 72.222 0.00 0.00 0.00 4.30
2969 7559 3.742248 CTCCGTCCTCTCCCCTCCC 62.742 73.684 0.00 0.00 0.00 4.30
2990 7581 1.019278 CGGTTTCTGACGGTGGATGG 61.019 60.000 0.00 0.00 0.00 3.51
2992 7583 1.439679 GTTTCTGACGGTGGATGGTC 58.560 55.000 0.00 0.00 0.00 4.02
3166 7760 2.041819 AGGATCTGACCGGGGTCC 60.042 66.667 14.95 2.85 43.97 4.46
3184 7778 2.462503 CCGTTCCATGTAACACGGG 58.537 57.895 12.20 0.00 46.92 5.28
3186 7780 1.791662 GTTCCATGTAACACGGGCG 59.208 57.895 0.00 0.00 0.00 6.13
3225 7835 2.903135 AGAAGAGGGAGTGGAAAGACAG 59.097 50.000 0.00 0.00 0.00 3.51
3230 7840 1.971357 GGGAGTGGAAAGACAGAGTGA 59.029 52.381 0.00 0.00 0.00 3.41
3231 7841 2.368875 GGGAGTGGAAAGACAGAGTGAA 59.631 50.000 0.00 0.00 0.00 3.18
3255 7865 9.173939 GAATGAATTTATACAGATTCTTTGGCG 57.826 33.333 0.00 0.00 32.86 5.69
3261 7871 2.863809 ACAGATTCTTTGGCGGTCTTT 58.136 42.857 0.00 0.00 0.00 2.52
3294 7904 2.333581 GCGTGTTTTCAACCCGGG 59.666 61.111 22.25 22.25 0.00 5.73
3343 7953 2.436646 CCCTCGCTGGAAACGCAT 60.437 61.111 0.00 0.00 38.35 4.73
3349 7959 1.298157 CGCTGGAAACGCATGGAAGA 61.298 55.000 0.00 0.00 0.00 2.87
3392 8002 3.528009 GCAAGTGCTCGAATATTAGGC 57.472 47.619 0.00 0.00 38.21 3.93
3397 8007 4.884247 AGTGCTCGAATATTAGGCTAACC 58.116 43.478 9.55 0.00 0.00 2.85
3536 8147 1.551883 GCAAGGTGGGCATCTGATTTT 59.448 47.619 0.00 0.00 0.00 1.82
3607 8218 5.336531 CGGTAGTCATTGTGTCTCCTTAACT 60.337 44.000 0.00 0.00 0.00 2.24
3618 8229 4.933400 TGTCTCCTTAACTAACCAAATCGC 59.067 41.667 0.00 0.00 0.00 4.58
3639 8250 4.379499 CGCTCGCTAACTGGATATATGTCA 60.379 45.833 1.63 0.00 0.00 3.58
3742 8766 2.656002 TCCTCAGACTTATAGTGCGCT 58.344 47.619 9.73 4.58 0.00 5.92
3863 8887 2.859806 GCCTGACAATGACACTGCAAAC 60.860 50.000 0.00 0.00 0.00 2.93
3889 8913 7.571613 CGGTTCAAGTCCGTGTCAAATATTAAA 60.572 37.037 0.00 0.00 42.62 1.52
3941 8968 2.692557 CCAACAAACACATCACCCTTGA 59.307 45.455 0.00 0.00 35.73 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.277565 CTTTTACATCACCATTTTACATCTTCG 57.722 33.333 0.00 0.00 0.00 3.79
10 11 7.812191 TGCACTTTTACATCACCATTTTACATC 59.188 33.333 0.00 0.00 0.00 3.06
18 19 5.245751 TGGAATTGCACTTTTACATCACCAT 59.754 36.000 0.00 0.00 0.00 3.55
21 22 5.982516 TGTTGGAATTGCACTTTTACATCAC 59.017 36.000 0.00 0.00 0.00 3.06
32 33 3.184541 GCATCATCTGTTGGAATTGCAC 58.815 45.455 0.00 0.00 31.73 4.57
35 36 6.103330 TCATTTGCATCATCTGTTGGAATTG 58.897 36.000 0.00 9.33 32.63 2.32
38 39 5.477637 TCTTCATTTGCATCATCTGTTGGAA 59.522 36.000 0.00 0.00 0.00 3.53
53 55 9.722056 GGCATAACTAGTTTACATCTTCATTTG 57.278 33.333 14.49 0.00 0.00 2.32
87 89 3.515316 CTCCGACGTGCTTGGTGGT 62.515 63.158 0.00 0.00 0.00 4.16
112 114 0.034337 GTCACCCGTAGAGCAAACCA 59.966 55.000 0.00 0.00 0.00 3.67
122 124 1.301087 CTGCAAACCGTCACCCGTA 60.301 57.895 0.00 0.00 33.66 4.02
125 127 4.025401 CGCTGCAAACCGTCACCC 62.025 66.667 0.00 0.00 0.00 4.61
140 142 2.442188 CCGTAGAGCCAAACGTCGC 61.442 63.158 0.00 0.00 37.40 5.19
186 188 1.608283 CCCCAACTCCTCTCGTTTGTC 60.608 57.143 0.00 0.00 0.00 3.18
187 189 0.396811 CCCCAACTCCTCTCGTTTGT 59.603 55.000 0.00 0.00 0.00 2.83
209 211 1.869690 GCTCCTGTCGAGTTTTGGC 59.130 57.895 0.00 0.00 41.10 4.52
212 214 3.498676 CTCGCTCCTGTCGAGTTTT 57.501 52.632 4.44 0.00 45.86 2.43
218 220 3.500642 TCGAGCTCGCTCCTGTCG 61.501 66.667 30.97 5.49 39.77 4.35
254 256 3.322466 CCTCACCCCCGAGCAAGT 61.322 66.667 0.00 0.00 0.00 3.16
265 267 2.745492 GTGCTCTGCAGCCTCACC 60.745 66.667 9.47 0.00 46.26 4.02
267 269 4.383861 CCGTGCTCTGCAGCCTCA 62.384 66.667 9.47 3.46 46.26 3.86
320 322 1.692519 ACGCACTTAAACTCCTGGAGT 59.307 47.619 23.49 23.49 45.64 3.85
332 334 2.126618 CGTCCGAGCACGCACTTA 60.127 61.111 0.00 0.00 38.29 2.24
377 379 6.844696 ATGGTATGTCATTGACGTATTCAC 57.155 37.500 19.02 10.50 36.59 3.18
378 380 8.585018 AGATATGGTATGTCATTGACGTATTCA 58.415 33.333 19.02 18.78 36.59 2.57
418 420 9.449719 AATCGAAGGACTCTTGTTAACATATTT 57.550 29.630 9.56 0.00 32.52 1.40
444 446 2.607180 CCAACGATTGATGTACGCATGA 59.393 45.455 0.00 0.00 35.07 3.07
486 488 2.993899 ACCGAGTTTAACAATCTGCTCG 59.006 45.455 0.00 0.00 43.45 5.03
535 537 0.743097 GACATGATTGCCCAAGCTCC 59.257 55.000 0.00 0.00 40.80 4.70
624 633 1.136110 CCTCGCTCTTCTCTTCCTTCC 59.864 57.143 0.00 0.00 0.00 3.46
631 640 3.144193 CCGCCCTCGCTCTTCTCT 61.144 66.667 0.00 0.00 0.00 3.10
632 641 4.214327 CCCGCCCTCGCTCTTCTC 62.214 72.222 0.00 0.00 0.00 2.87
634 643 4.516195 GACCCGCCCTCGCTCTTC 62.516 72.222 0.00 0.00 0.00 2.87
805 814 3.914312 AGAAGATTGTACGTGGAGTGTG 58.086 45.455 0.00 0.00 0.00 3.82
938 1900 4.736896 GGTGACTGGACGGACGGC 62.737 72.222 0.00 0.00 0.00 5.68
939 1901 3.299977 TGGTGACTGGACGGACGG 61.300 66.667 0.00 0.00 0.00 4.79
1365 3940 2.063266 CAATGCACGTACGTGTAGGTT 58.937 47.619 39.56 27.97 46.90 3.50
1425 4004 0.612732 TCCAATGGAGGCAGCAAAGG 60.613 55.000 0.00 0.00 0.00 3.11
1490 4078 2.526046 CCTCCCACCCGTGAACCTT 61.526 63.158 0.00 0.00 0.00 3.50
1502 4090 4.722535 AGCGCCTCCTTCCTCCCA 62.723 66.667 2.29 0.00 0.00 4.37
1503 4091 2.878089 GAAAGCGCCTCCTTCCTCCC 62.878 65.000 2.29 0.00 0.00 4.30
1521 4109 2.225791 CTGACGCCCACGATTCCAGA 62.226 60.000 0.00 0.00 43.93 3.86
1542 4130 1.203001 TGATCTTCGTGGGGCCTTTTT 60.203 47.619 0.84 0.00 0.00 1.94
1577 4204 8.177119 TCAATGGTAAATTAGTTTGAAGCACT 57.823 30.769 0.00 0.00 0.00 4.40
1578 4205 8.810652 TTCAATGGTAAATTAGTTTGAAGCAC 57.189 30.769 0.00 0.00 31.53 4.40
1604 4239 4.530710 AATGCCACAGTAGTTCGAAGTA 57.469 40.909 8.66 8.66 0.00 2.24
1882 4518 1.082117 GGCGGTGATGGTGAGTTACG 61.082 60.000 0.00 0.00 0.00 3.18
1883 4519 1.082117 CGGCGGTGATGGTGAGTTAC 61.082 60.000 0.00 0.00 0.00 2.50
1885 4521 2.047274 CGGCGGTGATGGTGAGTT 60.047 61.111 0.00 0.00 0.00 3.01
1886 4522 4.760047 GCGGCGGTGATGGTGAGT 62.760 66.667 9.78 0.00 0.00 3.41
1916 4555 2.125512 GTACCGGGCAGAGCACTG 60.126 66.667 6.32 6.80 45.91 3.66
1917 4556 3.760035 CGTACCGGGCAGAGCACT 61.760 66.667 6.32 0.00 0.00 4.40
1921 4560 2.495409 TATGGCGTACCGGGCAGAG 61.495 63.158 6.32 0.00 46.24 3.35
1922 4561 2.442458 TATGGCGTACCGGGCAGA 60.442 61.111 6.32 0.00 46.24 4.26
1923 4562 2.279918 GTATGGCGTACCGGGCAG 60.280 66.667 6.32 0.00 46.24 4.85
1925 4564 2.279918 CTGTATGGCGTACCGGGC 60.280 66.667 14.04 0.00 39.70 6.13
1927 4566 1.299926 GCTCTGTATGGCGTACCGG 60.300 63.158 14.04 0.00 39.70 5.28
1928 4567 1.657487 CGCTCTGTATGGCGTACCG 60.657 63.158 14.04 8.10 45.34 4.02
1934 4573 2.659897 CCTCGCGCTCTGTATGGC 60.660 66.667 5.56 0.00 0.00 4.40
1935 4574 1.589993 CACCTCGCGCTCTGTATGG 60.590 63.158 5.56 0.00 0.00 2.74
1938 4577 3.449227 CCCACCTCGCGCTCTGTA 61.449 66.667 5.56 0.00 0.00 2.74
1945 4584 1.956629 ATTAGGACACCCACCTCGCG 61.957 60.000 0.00 0.00 38.76 5.87
1946 4585 0.252197 AATTAGGACACCCACCTCGC 59.748 55.000 0.00 0.00 38.76 5.03
1947 4586 2.498481 TGTAATTAGGACACCCACCTCG 59.502 50.000 0.00 0.00 38.76 4.63
1948 4587 4.451900 CATGTAATTAGGACACCCACCTC 58.548 47.826 0.00 0.00 38.76 3.85
1949 4588 3.371595 GCATGTAATTAGGACACCCACCT 60.372 47.826 0.00 0.00 41.05 4.00
1950 4589 2.949644 GCATGTAATTAGGACACCCACC 59.050 50.000 0.00 0.00 33.88 4.61
1951 4590 2.612212 CGCATGTAATTAGGACACCCAC 59.388 50.000 0.00 0.00 33.88 4.61
1952 4591 2.912771 CGCATGTAATTAGGACACCCA 58.087 47.619 0.00 0.00 33.88 4.51
1953 4592 1.602377 GCGCATGTAATTAGGACACCC 59.398 52.381 0.30 0.00 0.00 4.61
1954 4593 1.260561 CGCGCATGTAATTAGGACACC 59.739 52.381 8.75 0.00 0.00 4.16
1955 4594 1.332904 GCGCGCATGTAATTAGGACAC 60.333 52.381 29.10 0.00 0.00 3.67
1956 4595 0.934496 GCGCGCATGTAATTAGGACA 59.066 50.000 29.10 0.00 0.00 4.02
1957 4596 0.111266 CGCGCGCATGTAATTAGGAC 60.111 55.000 32.61 0.00 0.00 3.85
1958 4597 1.827315 GCGCGCGCATGTAATTAGGA 61.827 55.000 46.11 0.00 41.49 2.94
1959 4598 1.438710 GCGCGCGCATGTAATTAGG 60.439 57.895 46.11 11.55 41.49 2.69
1960 4599 4.099924 GCGCGCGCATGTAATTAG 57.900 55.556 46.11 12.36 41.49 1.73
1978 4617 3.462333 TTCTGCCAACGCAACACGC 62.462 57.895 0.00 0.00 46.66 5.34
1979 4618 1.654137 GTTCTGCCAACGCAACACG 60.654 57.895 0.00 0.00 46.66 4.49
1980 4619 0.865639 GTGTTCTGCCAACGCAACAC 60.866 55.000 4.77 4.77 46.66 3.32
1981 4620 1.431440 GTGTTCTGCCAACGCAACA 59.569 52.632 4.70 0.00 46.66 3.33
1982 4621 1.654137 CGTGTTCTGCCAACGCAAC 60.654 57.895 9.21 0.00 46.66 4.17
2210 5352 0.684805 GAGGAAGAAGAGGAGGGCGA 60.685 60.000 0.00 0.00 0.00 5.54
2211 5353 1.819905 GAGGAAGAAGAGGAGGGCG 59.180 63.158 0.00 0.00 0.00 6.13
2214 5356 1.068434 GCATCGAGGAAGAAGAGGAGG 59.932 57.143 0.00 0.00 0.00 4.30
2233 5375 0.672342 CTGGCAATGGAGCATTAGGC 59.328 55.000 0.00 0.00 45.30 3.93
2235 5377 1.952296 GGTCTGGCAATGGAGCATTAG 59.048 52.381 0.17 0.00 32.35 1.73
2236 5378 1.565759 AGGTCTGGCAATGGAGCATTA 59.434 47.619 7.10 0.00 32.35 1.90
2237 5379 0.333993 AGGTCTGGCAATGGAGCATT 59.666 50.000 7.10 0.00 34.04 3.56
2270 5425 1.284982 TTTTCTCTCTCTGCGTGCGC 61.285 55.000 9.85 9.85 42.35 6.09
2275 5430 2.411409 GCTCTGTTTTTCTCTCTCTGCG 59.589 50.000 0.00 0.00 0.00 5.18
2307 5495 1.066908 TGTTTGCCGGCTCTCTTTTTG 59.933 47.619 29.70 0.00 0.00 2.44
2512 6617 4.267928 CACGAGACCAGACCGAAATATTTC 59.732 45.833 16.79 16.79 0.00 2.17
2579 6794 2.594962 CCACCGTGCTCGTGAACAC 61.595 63.158 7.47 0.00 35.01 3.32
2610 6856 0.784178 CGTCACACGTCCATTCTGTG 59.216 55.000 0.00 0.00 36.74 3.66
2915 7457 2.252408 AGAGAGAATGGAGGAGGGGAAT 59.748 50.000 0.00 0.00 0.00 3.01
2916 7458 1.653918 AGAGAGAATGGAGGAGGGGAA 59.346 52.381 0.00 0.00 0.00 3.97
2917 7459 1.324014 AGAGAGAATGGAGGAGGGGA 58.676 55.000 0.00 0.00 0.00 4.81
2918 7460 2.046292 GAAGAGAGAATGGAGGAGGGG 58.954 57.143 0.00 0.00 0.00 4.79
2919 7461 2.046292 GGAAGAGAGAATGGAGGAGGG 58.954 57.143 0.00 0.00 0.00 4.30
2920 7462 3.044873 AGGAAGAGAGAATGGAGGAGG 57.955 52.381 0.00 0.00 0.00 4.30
2921 7463 5.427378 GAAAAGGAAGAGAGAATGGAGGAG 58.573 45.833 0.00 0.00 0.00 3.69
2922 7464 4.226168 GGAAAAGGAAGAGAGAATGGAGGA 59.774 45.833 0.00 0.00 0.00 3.71
2928 7470 3.328050 ACGGTGGAAAAGGAAGAGAGAAT 59.672 43.478 0.00 0.00 0.00 2.40
2990 7581 3.186001 GTCCTGCATCATCATTCATCGAC 59.814 47.826 0.00 0.00 0.00 4.20
2992 7583 2.157085 CGTCCTGCATCATCATTCATCG 59.843 50.000 0.00 0.00 0.00 3.84
3082 7676 3.102107 CTCCTCGTCGGTGAGCTCG 62.102 68.421 9.64 0.00 34.56 5.03
3183 7777 4.088762 CATGACGTGTGTGCCGCC 62.089 66.667 0.00 0.00 0.00 6.13
3184 7778 1.561717 TTACATGACGTGTGTGCCGC 61.562 55.000 10.67 0.00 42.24 6.53
3186 7780 2.139917 TCTTTACATGACGTGTGTGCC 58.860 47.619 10.67 0.00 42.24 5.01
3196 7790 4.425772 TCCACTCCCTCTTCTTTACATGA 58.574 43.478 0.00 0.00 0.00 3.07
3230 7840 8.137437 CCGCCAAAGAATCTGTATAAATTCATT 58.863 33.333 0.00 0.00 34.91 2.57
3231 7841 7.285401 ACCGCCAAAGAATCTGTATAAATTCAT 59.715 33.333 0.00 0.00 34.91 2.57
3261 7871 3.972276 GCACTCGCCGCCCAAAAA 61.972 61.111 0.00 0.00 0.00 1.94
3307 7917 2.025727 CCGATCGAGTACCGTGCC 59.974 66.667 18.66 0.00 39.75 5.01
3343 7953 6.479972 AAATACGGACTATCATGTCTTCCA 57.520 37.500 0.00 0.00 37.16 3.53
3378 7988 4.686554 CACTGGTTAGCCTAATATTCGAGC 59.313 45.833 0.00 0.00 35.27 5.03
3380 7990 4.897076 TCCACTGGTTAGCCTAATATTCGA 59.103 41.667 0.00 0.00 35.27 3.71
3391 8001 1.376609 CGGGCATTCCACTGGTTAGC 61.377 60.000 0.00 0.00 34.36 3.09
3392 8002 0.035439 ACGGGCATTCCACTGGTTAG 60.035 55.000 0.00 0.00 34.36 2.34
3397 8007 3.803082 CGCACGGGCATTCCACTG 61.803 66.667 11.77 0.00 41.24 3.66
3425 8035 3.417101 ACACATGGACATTCGGCTTTTA 58.583 40.909 0.00 0.00 0.00 1.52
3536 8147 9.249457 GAGTCTTTATTTGTCGATGTATGATGA 57.751 33.333 0.00 0.00 0.00 2.92
3607 8218 2.927477 CAGTTAGCGAGCGATTTGGTTA 59.073 45.455 0.00 0.00 0.00 2.85
3618 8229 6.856895 TGATGACATATATCCAGTTAGCGAG 58.143 40.000 0.00 0.00 0.00 5.03
3672 8283 2.475466 GCACCCATGGATGCGTGAG 61.475 63.158 17.36 0.00 38.51 3.51
3889 8913 1.935933 CCGCAGTTAATAGCTTCGGT 58.064 50.000 7.00 0.00 37.83 4.69
3941 8968 6.627087 AGCCATGGTGCACTATATACTTAT 57.373 37.500 15.99 0.00 0.00 1.73
4107 9135 6.000219 ACTTAGTGCACATCTGTTGAGATTT 59.000 36.000 21.04 0.00 36.75 2.17


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

AutoCloner maintained by Alex Coulton.