Multiple sequence alignment - TraesCS7D01G305100

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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 TraesCS7D01G305100 chr7D 100.000 6804 0 0 1 6804 386665411 386658608 0.000000e+00 12565.0
1 TraesCS7D01G305100 chr7D 93.186 2084 99 16 4229 6277 51685914 51683839 0.000000e+00 3022.0
2 TraesCS7D01G305100 chr7D 93.603 1485 67 7 2774 4230 51687480 51685996 0.000000e+00 2191.0
3 TraesCS7D01G305100 chr7D 88.169 1065 82 25 338 1391 51689345 51688314 0.000000e+00 1229.0
4 TraesCS7D01G305100 chr7D 86.994 692 41 21 1662 2346 51688135 51687486 0.000000e+00 734.0
5 TraesCS7D01G305100 chr7D 86.723 354 25 3 6 337 51691976 51691623 2.320000e-99 374.0
6 TraesCS7D01G305100 chr7D 92.188 128 10 0 6275 6402 51683637 51683510 1.510000e-41 182.0
7 TraesCS7D01G305100 chr7D 91.803 122 9 1 6683 6804 452442584 452442464 1.170000e-37 169.0
8 TraesCS7D01G305100 chr7A 94.242 4741 165 40 1535 6242 436075031 436070366 0.000000e+00 7143.0
9 TraesCS7D01G305100 chr7A 92.891 3123 159 20 3332 6402 54191229 54188118 0.000000e+00 4479.0
10 TraesCS7D01G305100 chr7A 94.750 1657 66 8 3332 4970 54150285 54148632 0.000000e+00 2558.0
11 TraesCS7D01G305100 chr7A 89.596 1461 90 21 4966 6400 54147588 54146164 0.000000e+00 1799.0
12 TraesCS7D01G305100 chr7A 88.703 1434 89 32 2 1391 54194096 54192692 0.000000e+00 1683.0
13 TraesCS7D01G305100 chr7A 90.616 1087 61 13 441 1514 436076208 436075150 0.000000e+00 1404.0
14 TraesCS7D01G305100 chr7A 95.187 561 26 1 2774 3334 54191855 54191296 0.000000e+00 885.0
15 TraesCS7D01G305100 chr7A 85.106 658 50 16 1696 2346 54151720 54151104 4.480000e-176 628.0
16 TraesCS7D01G305100 chr7A 84.127 693 60 21 1662 2346 54192511 54191861 5.790000e-175 625.0
17 TraesCS7D01G305100 chr7A 96.100 359 14 0 2774 3132 54151098 54150740 2.730000e-163 586.0
18 TraesCS7D01G305100 chr7A 94.712 208 11 0 3127 3334 54150584 54150377 2.370000e-84 324.0
19 TraesCS7D01G305100 chr7A 84.877 324 16 4 1 299 436095238 436094923 5.160000e-76 296.0
20 TraesCS7D01G305100 chr7A 87.709 179 8 7 6430 6608 436070315 436070151 5.380000e-46 196.0
21 TraesCS7D01G305100 chr7A 88.525 122 9 5 6685 6804 55359268 55359386 7.110000e-30 143.0
22 TraesCS7D01G305100 chr7B 95.547 2740 86 11 3335 6070 381511310 381508603 0.000000e+00 4351.0
23 TraesCS7D01G305100 chr7B 93.266 1975 77 26 1362 3327 381513325 381511398 0.000000e+00 2859.0
24 TraesCS7D01G305100 chr7B 90.654 1391 73 16 26 1379 381514706 381513336 0.000000e+00 1796.0
25 TraesCS7D01G305100 chr7B 86.878 221 21 6 6430 6647 381508573 381508358 2.450000e-59 241.0
26 TraesCS7D01G305100 chr7B 95.082 122 6 0 6683 6804 713242595 713242474 6.960000e-45 193.0
27 TraesCS7D01G305100 chr7B 94.167 120 7 0 6683 6802 661432426 661432545 4.190000e-42 183.0
28 TraesCS7D01G305100 chr4A 93.769 1926 85 15 2718 4611 666061250 666059328 0.000000e+00 2859.0
29 TraesCS7D01G305100 chr4A 89.186 1498 98 20 1 1453 666063581 666062103 0.000000e+00 1810.0
30 TraesCS7D01G305100 chr4A 93.696 1047 55 6 4873 5913 666058517 666057476 0.000000e+00 1557.0
31 TraesCS7D01G305100 chr4A 85.616 730 48 19 1662 2376 666061934 666061247 0.000000e+00 713.0
32 TraesCS7D01G305100 chr4A 86.549 565 44 14 5902 6437 666057453 666056892 1.630000e-165 593.0
33 TraesCS7D01G305100 chr4A 94.872 234 12 0 4648 4881 666059328 666059095 3.880000e-97 366.0
34 TraesCS7D01G305100 chr5B 89.355 310 30 1 5186 5495 100048073 100048379 2.980000e-103 387.0
35 TraesCS7D01G305100 chr5B 87.121 264 30 3 4885 5147 100047813 100048073 5.160000e-76 296.0
36 TraesCS7D01G305100 chrUn 89.137 313 28 4 5186 5495 26776026 26776335 1.070000e-102 385.0
37 TraesCS7D01G305100 chrUn 88.417 259 26 3 4885 5142 26775766 26776021 6.630000e-80 309.0
38 TraesCS7D01G305100 chr5A 87.419 310 36 3 5186 5495 493022222 493022528 3.020000e-93 353.0
39 TraesCS7D01G305100 chr5A 87.879 264 28 3 4885 5147 493021962 493022222 2.380000e-79 307.0
40 TraesCS7D01G305100 chr3D 99.200 125 1 0 6680 6804 591372313 591372437 6.870000e-55 226.0
41 TraesCS7D01G305100 chr3D 91.228 57 5 0 6275 6331 285121515 285121459 2.030000e-10 78.7
42 TraesCS7D01G305100 chr3D 96.970 33 1 0 6299 6331 81716515 81716547 1.000000e-03 56.5
43 TraesCS7D01G305100 chr5D 95.082 122 6 0 6683 6804 40984954 40984833 6.960000e-45 193.0
44 TraesCS7D01G305100 chr1D 94.309 123 6 1 6683 6804 40500072 40499950 3.240000e-43 187.0
45 TraesCS7D01G305100 chr3B 88.618 123 7 7 6685 6804 4304700 4304818 7.110000e-30 143.0
46 TraesCS7D01G305100 chr3B 88.525 122 9 5 6685 6804 447018231 447018349 7.110000e-30 143.0
47 TraesCS7D01G305100 chr3B 96.970 33 1 0 6299 6331 127931610 127931642 1.000000e-03 56.5
48 TraesCS7D01G305100 chr3A 91.228 57 5 0 6275 6331 373346337 373346281 2.030000e-10 78.7
49 TraesCS7D01G305100 chr2D 80.460 87 17 0 3775 3861 580257064 580257150 4.400000e-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 TraesCS7D01G305100 chr7D 386658608 386665411 6803 True 12565.000000 12565 100.000000 1 6804 1 chr7D.!!$R1 6803
1 TraesCS7D01G305100 chr7D 51683510 51691976 8466 True 1288.666667 3022 90.143833 6 6402 6 chr7D.!!$R3 6396
2 TraesCS7D01G305100 chr7A 436070151 436076208 6057 True 2914.333333 7143 90.855667 441 6608 3 chr7A.!!$R4 6167
3 TraesCS7D01G305100 chr7A 54188118 54194096 5978 True 1918.000000 4479 90.227000 2 6402 4 chr7A.!!$R3 6400
4 TraesCS7D01G305100 chr7A 54146164 54151720 5556 True 1179.000000 2558 92.052800 1696 6400 5 chr7A.!!$R2 4704
5 TraesCS7D01G305100 chr7B 381508358 381514706 6348 True 2311.750000 4351 91.586250 26 6647 4 chr7B.!!$R2 6621
6 TraesCS7D01G305100 chr4A 666056892 666063581 6689 True 1316.333333 2859 90.614667 1 6437 6 chr4A.!!$R1 6436
7 TraesCS7D01G305100 chr5B 100047813 100048379 566 False 341.500000 387 88.238000 4885 5495 2 chr5B.!!$F1 610
8 TraesCS7D01G305100 chrUn 26775766 26776335 569 False 347.000000 385 88.777000 4885 5495 2 chrUn.!!$F1 610
9 TraesCS7D01G305100 chr5A 493021962 493022528 566 False 330.000000 353 87.649000 4885 5495 2 chr5A.!!$F1 610

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
711 3020 0.036732 GTCAACATCCTGCACTCCCA 59.963 55.000 0.00 0.0 0.00 4.37 F
1749 4268 0.676782 GCAGGTGCCCGAGTAATTGT 60.677 55.000 0.00 0.0 34.31 2.71 F
2548 5092 1.939934 GCAAGTTTGGCTTTTGGTTCC 59.060 47.619 0.00 0.0 34.69 3.62 F
3329 6059 2.806244 ACGTCTAGCATGGTGAAAACAC 59.194 45.455 7.89 0.0 0.00 3.32 F
4267 7235 2.415090 GCTGATCACTGACATGGTTTGC 60.415 50.000 0.00 0.0 0.00 3.68 F
5433 10062 0.108138 GGTGGTGGTGCTAGCTACTG 60.108 60.000 17.23 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 4396 0.582005 GTTGTCGCGCTTCAGAGTTT 59.418 50.000 5.56 0.0 0.00 2.66 R
3438 6262 3.935203 ACTCTGCATGATTTGTAAGACGG 59.065 43.478 0.00 0.0 0.00 4.79 R
3780 6611 1.135402 GTAGCTTTTGGCCACAATCCG 60.135 52.381 3.88 0.0 43.05 4.18 R
4667 7645 2.285827 TTGAAAAACAGGTGGCAACG 57.714 45.000 0.00 0.0 42.51 4.10 R
5550 10182 0.467384 CTGGATCAGAGGTGGCGAAT 59.533 55.000 0.00 0.0 32.44 3.34 R
6505 11413 1.181786 CTCCTCCTCTTGTCTTCGCT 58.818 55.000 0.00 0.0 0.00 4.93 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
57 58 1.003580 GAGAAGAGCCATGGGTCACAA 59.996 52.381 38.01 0.00 44.24 3.33
86 87 1.059835 GACGTGCTCGATGCTCTTTTC 59.940 52.381 16.04 0.00 43.37 2.29
247 269 6.682861 GCTTGGAAGTTTATCAACAGTTTGGT 60.683 38.462 0.00 0.00 35.05 3.67
404 2704 4.387862 CACGCCAGAGTTTAACGAGTATTT 59.612 41.667 0.00 0.00 0.00 1.40
461 2761 6.889177 TGAAATTAGGGTAGTGCAATCAATGA 59.111 34.615 0.00 0.00 0.00 2.57
462 2762 6.699575 AATTAGGGTAGTGCAATCAATGAC 57.300 37.500 0.00 0.00 0.00 3.06
532 2832 6.723515 TGAAAAATCTATGGGTTCATTCCACA 59.276 34.615 0.00 0.00 37.08 4.17
703 3012 3.499737 GCCGCCGTCAACATCCTG 61.500 66.667 0.00 0.00 0.00 3.86
710 3019 1.021390 CGTCAACATCCTGCACTCCC 61.021 60.000 0.00 0.00 0.00 4.30
711 3020 0.036732 GTCAACATCCTGCACTCCCA 59.963 55.000 0.00 0.00 0.00 4.37
948 3259 7.254227 ACAATACATGTTTAGTGTCGTTGTT 57.746 32.000 2.30 0.00 40.06 2.83
1001 3313 4.862641 ACACCTTAGGCATCTTACCAAT 57.137 40.909 0.00 0.00 0.00 3.16
1027 3339 4.222145 CCCTTACTCCAACTACTTGCTACA 59.778 45.833 0.00 0.00 0.00 2.74
1082 3421 1.434696 GGTCCAATGGCAAGATGCG 59.565 57.895 0.00 0.00 46.21 4.73
1090 3429 4.022068 CCAATGGCAAGATGCGGTATAAAT 60.022 41.667 0.00 0.00 46.21 1.40
1103 3442 3.672310 GGTATAAATCGCGTCGCAAAAA 58.328 40.909 18.75 0.00 0.00 1.94
1135 3474 6.257193 GGTACATGGAAAATACTGTTACTCCG 59.743 42.308 0.00 0.00 0.00 4.63
1316 3667 8.311395 AGTATGAGTGATTTTCCTCATAGTGA 57.689 34.615 13.46 0.00 46.13 3.41
1366 3717 2.242043 AGTTGAGGCAAAATCCAGGTG 58.758 47.619 0.00 0.00 0.00 4.00
1367 3718 0.968405 TTGAGGCAAAATCCAGGTGC 59.032 50.000 0.00 0.00 37.55 5.01
1386 3767 4.681025 GGTGCATCAACTTGTTGTACAATG 59.319 41.667 12.26 5.69 37.48 2.82
1533 3920 5.560722 AAAAAGGGGATTTGGTTGTAAGG 57.439 39.130 0.00 0.00 0.00 2.69
1617 4130 4.214437 GTTTGCTATTGATATGCTCGTGC 58.786 43.478 1.71 1.71 40.20 5.34
1619 4132 2.037641 TGCTATTGATATGCTCGTGCCT 59.962 45.455 7.05 0.00 38.71 4.75
1683 4196 9.221933 CAACAACCCAATTACTGTACTACATTA 57.778 33.333 0.00 0.00 0.00 1.90
1688 4201 9.969001 ACCCAATTACTGTACTACATTAAATGT 57.031 29.630 10.92 0.00 46.92 2.71
1694 4207 7.753309 ACTGTACTACATTAAATGTTTGCCA 57.247 32.000 0.00 0.00 41.63 4.92
1742 4261 1.003839 TAAACTGCAGGTGCCCGAG 60.004 57.895 19.93 0.00 41.18 4.63
1749 4268 0.676782 GCAGGTGCCCGAGTAATTGT 60.677 55.000 0.00 0.00 34.31 2.71
1787 4313 9.132521 CATCAAAGTTTTGTATCACTTGATTCC 57.867 33.333 0.00 0.00 39.18 3.01
1836 4371 8.335532 AGAAAATGTAAATCTGATTTCCACGA 57.664 30.769 18.22 0.00 33.82 4.35
1860 4395 4.079253 GTGCTTAAACCCCAAATCTCTCA 58.921 43.478 0.00 0.00 0.00 3.27
1861 4396 4.522789 GTGCTTAAACCCCAAATCTCTCAA 59.477 41.667 0.00 0.00 0.00 3.02
2029 4570 2.684104 GGAAGGGGAAGGGGAAGC 59.316 66.667 0.00 0.00 0.00 3.86
2030 4571 2.272471 GAAGGGGAAGGGGAAGCG 59.728 66.667 0.00 0.00 0.00 4.68
2031 4572 3.339093 AAGGGGAAGGGGAAGCGG 61.339 66.667 0.00 0.00 0.00 5.52
2032 4573 3.883822 AAGGGGAAGGGGAAGCGGA 62.884 63.158 0.00 0.00 0.00 5.54
2033 4574 3.335729 GGGGAAGGGGAAGCGGAA 61.336 66.667 0.00 0.00 0.00 4.30
2034 4575 2.272471 GGGAAGGGGAAGCGGAAG 59.728 66.667 0.00 0.00 0.00 3.46
2035 4576 2.272471 GGAAGGGGAAGCGGAAGG 59.728 66.667 0.00 0.00 0.00 3.46
2036 4577 2.438614 GAAGGGGAAGCGGAAGGC 60.439 66.667 0.00 0.00 44.05 4.35
2348 4892 9.651913 TTTAGATTTGGGAATGTTCTTAATTGC 57.348 29.630 0.00 0.00 0.00 3.56
2548 5092 1.939934 GCAAGTTTGGCTTTTGGTTCC 59.060 47.619 0.00 0.00 34.69 3.62
2680 5225 3.696548 GTGGAGGGAATTGTTGAGAATCC 59.303 47.826 0.00 0.00 0.00 3.01
3167 5885 7.950512 TGCTTATTTGATGTCCTTTCTGAAAA 58.049 30.769 4.18 0.00 0.00 2.29
3235 5954 8.737168 TTCGAGATGATGATTTGGACTTTTAT 57.263 30.769 0.00 0.00 0.00 1.40
3329 6059 2.806244 ACGTCTAGCATGGTGAAAACAC 59.194 45.455 7.89 0.00 0.00 3.32
3422 6246 6.254157 TCCTAAACTAATGATTACGAACGTGC 59.746 38.462 10.14 0.00 0.00 5.34
3438 6262 6.007677 CGAACGTGCAGTAAGTTTCTTATTC 58.992 40.000 0.00 0.00 30.94 1.75
3683 6511 2.978156 TGATTTTTGCTGGAGGAGGT 57.022 45.000 0.00 0.00 0.00 3.85
3780 6611 4.702131 ACTTCACTGCCCAAAGATATGTTC 59.298 41.667 0.00 0.00 0.00 3.18
3864 6704 3.716431 AGGATCATGGCCAATTTTCTGT 58.284 40.909 10.96 0.00 0.00 3.41
3865 6705 4.098894 AGGATCATGGCCAATTTTCTGTT 58.901 39.130 10.96 0.00 0.00 3.16
3866 6706 4.081309 AGGATCATGGCCAATTTTCTGTTG 60.081 41.667 10.96 0.00 0.00 3.33
3911 6756 7.881232 CACCCTAGTTCAGTTTTCTTACCAATA 59.119 37.037 0.00 0.00 0.00 1.90
4110 6995 8.598041 ACTAACTGTCCTTTCATTCATACTTCT 58.402 33.333 0.00 0.00 0.00 2.85
4267 7235 2.415090 GCTGATCACTGACATGGTTTGC 60.415 50.000 0.00 0.00 0.00 3.68
4271 7239 4.455533 TGATCACTGACATGGTTTGCTAAC 59.544 41.667 2.11 2.11 0.00 2.34
5263 9885 9.626045 CAGGGTTAGATGAAATTCAAAAAGTAC 57.374 33.333 0.00 0.00 0.00 2.73
5393 10019 2.348666 CGAACAAGTTCAGCTATTCCCG 59.651 50.000 12.86 0.00 39.46 5.14
5433 10062 0.108138 GGTGGTGGTGCTAGCTACTG 60.108 60.000 17.23 0.00 0.00 2.74
5666 10310 9.617975 CATCATAGTTTTTCTTCTTTCAAGTCC 57.382 33.333 0.00 0.00 0.00 3.85
5707 10357 6.148480 GCATAAGAATTGTGTGTCACTCTTCT 59.852 38.462 4.27 4.43 39.60 2.85
5708 10358 7.308229 GCATAAGAATTGTGTGTCACTCTTCTT 60.308 37.037 18.50 18.50 42.36 2.52
5709 10359 6.610741 AAGAATTGTGTGTCACTCTTCTTC 57.389 37.500 12.81 9.68 39.27 2.87
5818 10468 2.812358 ATTGAAGCAACCGAAAACCC 57.188 45.000 0.00 0.00 0.00 4.11
5872 10522 0.555769 TTTGAGCTTGACTTGGGGGT 59.444 50.000 0.00 0.00 0.00 4.95
5916 10603 1.211949 TGGTACCCATCAGCCTTTAGC 59.788 52.381 10.07 0.00 44.25 3.09
5941 10629 0.548510 AGCTGGGGGAATGAGCTTAC 59.451 55.000 0.00 0.00 40.19 2.34
5948 10636 3.769300 GGGGGAATGAGCTTACAATGTTT 59.231 43.478 0.00 0.00 0.00 2.83
5968 10656 9.744468 AATGTTTTAAGTTAGGATGTTGTTGAC 57.256 29.630 0.00 0.00 0.00 3.18
5983 10671 1.732259 GTTGACTCGATGATTTGCCGT 59.268 47.619 0.00 0.00 0.00 5.68
5988 10676 3.123804 ACTCGATGATTTGCCGTATGTC 58.876 45.455 0.00 0.00 0.00 3.06
6016 10704 9.390795 CAGTTTATTATGTTTGCTCTATCATGC 57.609 33.333 0.00 0.00 0.00 4.06
6094 10784 0.823356 TTGAGTTGCCTGAACCTGCC 60.823 55.000 0.00 0.00 34.80 4.85
6144 10834 3.733684 CGAAACACTTTGTTGGGTGAAGG 60.734 47.826 0.00 0.00 40.14 3.46
6203 10904 1.082756 CTTGTTGTGCCGTCTTCGC 60.083 57.895 0.00 0.00 35.54 4.70
6266 10967 0.865639 GATGTAAATGGCGCCGCAAC 60.866 55.000 23.90 17.21 0.00 4.17
6348 11253 3.612479 GCTTATAAATGGCGCATTCCCTG 60.612 47.826 10.83 0.00 32.43 4.45
6415 11323 1.214853 GGAGACCGGTTCCTCGTTC 59.785 63.158 21.61 3.47 0.00 3.95
6428 11336 1.270305 CCTCGTTCTGTTCCTCAAGCA 60.270 52.381 0.00 0.00 0.00 3.91
6444 11352 6.702723 TCCTCAAGCATTTCTTTTCAAATGTG 59.297 34.615 7.54 0.74 43.16 3.21
6446 11354 7.011669 CCTCAAGCATTTCTTTTCAAATGTGTT 59.988 33.333 7.54 0.77 43.16 3.32
6447 11355 7.686519 TCAAGCATTTCTTTTCAAATGTGTTG 58.313 30.769 7.54 10.37 43.16 3.33
6448 11356 6.051646 AGCATTTCTTTTCAAATGTGTTGC 57.948 33.333 7.54 0.00 43.16 4.17
6449 11357 5.818857 AGCATTTCTTTTCAAATGTGTTGCT 59.181 32.000 7.54 0.00 43.16 3.91
6450 11358 5.905181 GCATTTCTTTTCAAATGTGTTGCTG 59.095 36.000 7.54 0.00 43.16 4.41
6503 11411 0.324943 TTGGTCTGAAGCTAGTGGCC 59.675 55.000 0.00 0.00 43.05 5.36
6504 11412 0.545309 TGGTCTGAAGCTAGTGGCCT 60.545 55.000 3.32 0.00 43.05 5.19
6505 11413 1.273041 TGGTCTGAAGCTAGTGGCCTA 60.273 52.381 3.32 0.00 43.05 3.93
6516 11424 0.247736 AGTGGCCTAGCGAAGACAAG 59.752 55.000 3.32 0.00 0.00 3.16
6517 11425 0.246635 GTGGCCTAGCGAAGACAAGA 59.753 55.000 3.32 0.00 0.00 3.02
6518 11426 0.532573 TGGCCTAGCGAAGACAAGAG 59.467 55.000 3.32 0.00 0.00 2.85
6534 11442 6.252995 AGACAAGAGGAGGAGGATATGATAC 58.747 44.000 0.00 0.00 0.00 2.24
6608 11519 0.392595 GGCCGGGAAAGAAATCGTCT 60.393 55.000 2.18 0.00 38.69 4.18
6610 11521 1.130561 GCCGGGAAAGAAATCGTCTTG 59.869 52.381 2.18 0.00 46.36 3.02
6637 11548 3.190878 GCCATTGGCGACCTCAAG 58.809 61.111 12.82 0.00 39.62 3.02
6638 11549 1.675641 GCCATTGGCGACCTCAAGT 60.676 57.895 12.82 0.00 39.62 3.16
6641 11552 0.798776 CATTGGCGACCTCAAGTCAC 59.201 55.000 0.00 0.00 46.69 3.67
6642 11553 0.396435 ATTGGCGACCTCAAGTCACA 59.604 50.000 0.00 0.00 46.69 3.58
6643 11554 0.531974 TTGGCGACCTCAAGTCACAC 60.532 55.000 0.00 0.00 46.69 3.82
6644 11555 2.022129 GGCGACCTCAAGTCACACG 61.022 63.158 0.00 0.00 46.69 4.49
6645 11556 1.007734 GCGACCTCAAGTCACACGA 60.008 57.895 0.00 0.00 46.69 4.35
6646 11557 0.388649 GCGACCTCAAGTCACACGAT 60.389 55.000 0.00 0.00 46.69 3.73
6647 11558 1.340658 CGACCTCAAGTCACACGATG 58.659 55.000 0.00 0.00 46.69 3.84
6648 11559 1.335964 CGACCTCAAGTCACACGATGT 60.336 52.381 0.00 0.00 46.69 3.06
6649 11560 2.755650 GACCTCAAGTCACACGATGTT 58.244 47.619 0.00 0.00 45.55 2.71
6650 11561 3.131396 GACCTCAAGTCACACGATGTTT 58.869 45.455 0.00 0.00 45.55 2.83
6651 11562 3.541632 ACCTCAAGTCACACGATGTTTT 58.458 40.909 0.00 0.00 0.00 2.43
6652 11563 3.945285 ACCTCAAGTCACACGATGTTTTT 59.055 39.130 0.00 0.00 0.00 1.94
6688 11599 3.271250 CAACAGTGCAATAGGCCCT 57.729 52.632 0.00 0.00 43.89 5.19
6689 11600 1.098050 CAACAGTGCAATAGGCCCTC 58.902 55.000 0.00 0.00 43.89 4.30
6690 11601 0.392998 AACAGTGCAATAGGCCCTCG 60.393 55.000 0.00 0.00 43.89 4.63
6691 11602 2.182842 CAGTGCAATAGGCCCTCGC 61.183 63.158 0.00 0.00 43.89 5.03
6692 11603 3.272334 GTGCAATAGGCCCTCGCG 61.272 66.667 0.00 0.00 43.89 5.87
6693 11604 3.781307 TGCAATAGGCCCTCGCGT 61.781 61.111 5.77 0.00 43.89 6.01
6694 11605 2.967615 GCAATAGGCCCTCGCGTC 60.968 66.667 5.77 0.00 36.11 5.19
6695 11606 2.280186 CAATAGGCCCTCGCGTCC 60.280 66.667 5.77 3.58 34.31 4.79
6696 11607 3.547513 AATAGGCCCTCGCGTCCC 61.548 66.667 5.77 2.31 34.31 4.46
6697 11608 4.541648 ATAGGCCCTCGCGTCCCT 62.542 66.667 5.77 10.20 34.31 4.20
6751 11662 4.499116 CCCTCCACCGGATCCCCT 62.499 72.222 9.46 0.00 0.00 4.79
6752 11663 2.844839 CCTCCACCGGATCCCCTC 60.845 72.222 9.46 0.00 0.00 4.30
6753 11664 2.844839 CTCCACCGGATCCCCTCC 60.845 72.222 9.46 0.00 41.07 4.30
6754 11665 3.364964 TCCACCGGATCCCCTCCT 61.365 66.667 9.46 0.00 42.47 3.69
6755 11666 2.844839 CCACCGGATCCCCTCCTC 60.845 72.222 9.46 0.00 42.47 3.71
6756 11667 2.041922 CACCGGATCCCCTCCTCA 60.042 66.667 9.46 0.00 42.47 3.86
6757 11668 2.041819 ACCGGATCCCCTCCTCAC 60.042 66.667 9.46 0.00 42.47 3.51
6758 11669 2.283809 CCGGATCCCCTCCTCACT 59.716 66.667 6.06 0.00 42.47 3.41
6759 11670 1.834822 CCGGATCCCCTCCTCACTC 60.835 68.421 6.06 0.00 42.47 3.51
6760 11671 1.834822 CGGATCCCCTCCTCACTCC 60.835 68.421 6.06 0.00 42.47 3.85
6761 11672 1.460497 GGATCCCCTCCTCACTCCC 60.460 68.421 0.00 0.00 41.29 4.30
6762 11673 1.460497 GATCCCCTCCTCACTCCCC 60.460 68.421 0.00 0.00 0.00 4.81
6763 11674 1.949449 ATCCCCTCCTCACTCCCCT 60.949 63.158 0.00 0.00 0.00 4.79
6764 11675 1.967343 ATCCCCTCCTCACTCCCCTC 61.967 65.000 0.00 0.00 0.00 4.30
6765 11676 2.041405 CCCTCCTCACTCCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
6766 11677 2.041405 CCTCCTCACTCCCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
6767 11678 2.041405 CTCCTCACTCCCCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
6768 11679 2.540910 TCCTCACTCCCCTCCCCT 60.541 66.667 0.00 0.00 0.00 4.79
6769 11680 2.041405 CCTCACTCCCCTCCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
6770 11681 2.443016 CTCACTCCCCTCCCCTCG 60.443 72.222 0.00 0.00 0.00 4.63
6771 11682 4.779733 TCACTCCCCTCCCCTCGC 62.780 72.222 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.597404 TGCAATGTGCCATTGTTCTTAA 57.403 36.364 21.41 5.98 44.23 1.85
57 58 1.956170 CGAGCACGTCTTTGCCTGT 60.956 57.895 0.00 0.00 44.14 4.00
86 87 2.154462 AGTCTGGATTTCTGCCAAACG 58.846 47.619 0.00 0.00 31.66 3.60
247 269 3.798515 TCCTGCTTTAGACCTCCCTTTA 58.201 45.455 0.00 0.00 0.00 1.85
363 2663 3.741388 GCGTGCATCTAGTCCCTACATTT 60.741 47.826 0.00 0.00 0.00 2.32
408 2708 7.398829 AGGATTATTCGAGTAGCTAGATCTCA 58.601 38.462 0.00 0.00 0.00 3.27
532 2832 3.069729 GCCCGACACCTTATAGAATGTCT 59.930 47.826 3.18 0.00 39.45 3.41
703 3012 4.899352 AGATAATGGATACTGGGAGTGC 57.101 45.455 0.00 0.00 37.61 4.40
710 3019 6.090483 ACACGAGGAAGATAATGGATACTG 57.910 41.667 0.00 0.00 37.61 2.74
711 3020 6.551601 AGAACACGAGGAAGATAATGGATACT 59.448 38.462 0.00 0.00 37.61 2.12
948 3259 7.236019 TGTGGGGTTTTCTAGATAGTTGTCTAA 59.764 37.037 0.00 0.00 30.74 2.10
1001 3313 3.007614 GCAAGTAGTTGGAGTAAGGGTCA 59.992 47.826 12.19 0.00 33.87 4.02
1027 3339 2.045926 GTTCGGGGTGCTCATGCT 60.046 61.111 0.00 0.00 40.48 3.79
1082 3421 3.307339 TTTTGCGACGCGATTTATACC 57.693 42.857 15.93 0.00 0.00 2.73
1090 3429 1.071107 CACTTACTTTTTGCGACGCGA 60.071 47.619 15.93 11.15 0.00 5.87
1097 3436 5.699097 TCCATGTACCACTTACTTTTTGC 57.301 39.130 0.00 0.00 0.00 3.68
1103 3442 7.686434 ACAGTATTTTCCATGTACCACTTACT 58.314 34.615 0.00 0.00 0.00 2.24
1352 3703 0.896923 TGATGCACCTGGATTTTGCC 59.103 50.000 0.00 0.00 35.26 4.52
1366 3717 4.870363 ACCATTGTACAACAAGTTGATGC 58.130 39.130 18.90 8.93 41.94 3.91
1367 3718 6.738114 AGAACCATTGTACAACAAGTTGATG 58.262 36.000 18.90 10.94 41.94 3.07
1386 3767 2.162408 GAGCTACCACAATGCAAGAACC 59.838 50.000 0.00 0.00 0.00 3.62
1526 3913 2.224523 CCTCTGCAACTGGACCTTACAA 60.225 50.000 0.00 0.00 0.00 2.41
1532 3919 2.360475 GCCCTCTGCAACTGGACC 60.360 66.667 0.00 0.00 40.77 4.46
1553 4040 2.633488 GACTGTAACTGAGATTGGGCC 58.367 52.381 0.00 0.00 0.00 5.80
1558 4045 6.126863 TGGATTTGGACTGTAACTGAGATT 57.873 37.500 0.00 0.00 0.00 2.40
1610 4123 1.086696 TTGCAAATAGAGGCACGAGC 58.913 50.000 0.00 0.00 40.23 5.03
1617 4130 6.229733 TGGGTTTTCAAATTGCAAATAGAGG 58.770 36.000 1.71 0.00 0.00 3.69
1619 4132 9.213799 GTTATGGGTTTTCAAATTGCAAATAGA 57.786 29.630 1.71 0.00 0.00 1.98
1709 4224 6.653320 CCTGCAGTTTACACTTGGATTTAGTA 59.347 38.462 13.81 0.00 0.00 1.82
1710 4225 5.473504 CCTGCAGTTTACACTTGGATTTAGT 59.526 40.000 13.81 0.00 0.00 2.24
1711 4226 5.473504 ACCTGCAGTTTACACTTGGATTTAG 59.526 40.000 13.81 0.00 0.00 1.85
1763 4282 8.463930 AGGAATCAAGTGATACAAAACTTTGA 57.536 30.769 9.12 0.00 36.35 2.69
1836 4371 3.076032 AGAGATTTGGGGTTTAAGCACCT 59.924 43.478 12.25 0.00 36.97 4.00
1860 4395 1.003866 GTTGTCGCGCTTCAGAGTTTT 60.004 47.619 5.56 0.00 0.00 2.43
1861 4396 0.582005 GTTGTCGCGCTTCAGAGTTT 59.418 50.000 5.56 0.00 0.00 2.66
1957 4498 3.353836 GGCGGCGTCTGCAAAGAA 61.354 61.111 9.37 0.00 45.35 2.52
2007 4548 3.023735 CCCTTCCCCTTCCCCCTG 61.024 72.222 0.00 0.00 0.00 4.45
2271 4815 2.673368 CCACAGAAGGCTTACACGATTC 59.327 50.000 0.00 0.00 0.00 2.52
2348 4892 2.125912 CTCCCGCTCAACCACTCG 60.126 66.667 0.00 0.00 0.00 4.18
2548 5092 4.165779 CCAATCGAAGGTCCAAATTTTCG 58.834 43.478 4.28 4.28 42.61 3.46
2680 5225 6.403309 GCCTATGGAAAAGAAAACTAAGACCG 60.403 42.308 0.00 0.00 0.00 4.79
3235 5954 7.561021 TGTATAGCAGAAACACAACTTTTCA 57.439 32.000 0.00 0.00 35.72 2.69
3329 6059 6.320494 AGAATAGATCTGCTAGGTTGTACG 57.680 41.667 5.18 0.00 36.88 3.67
3422 6246 8.752766 TGTAAGACGGAATAAGAAACTTACTG 57.247 34.615 0.54 0.00 38.96 2.74
3438 6262 3.935203 ACTCTGCATGATTTGTAAGACGG 59.065 43.478 0.00 0.00 0.00 4.79
3683 6511 5.046878 ACTCAATACTTCATTACGGTGACCA 60.047 40.000 1.11 0.00 0.00 4.02
3780 6611 1.135402 GTAGCTTTTGGCCACAATCCG 60.135 52.381 3.88 0.00 43.05 4.18
3834 6666 3.889815 TGGCCATGATCCTAACAAAGAG 58.110 45.455 0.00 0.00 0.00 2.85
3865 6705 1.659233 CCAAACGAGCATTGGCACA 59.341 52.632 0.00 0.00 44.61 4.57
3866 6706 4.557942 CCAAACGAGCATTGGCAC 57.442 55.556 0.00 0.00 44.61 5.01
3991 6867 6.549736 TGGCAGACAGCTATATTTAGAGTGTA 59.450 38.462 0.00 0.00 44.79 2.90
4110 6995 4.631234 AGGGTGGAAGTCCTGATATAACA 58.369 43.478 0.00 0.00 36.82 2.41
4267 7235 6.027749 GGCCAAAATTCTATGACAACGTTAG 58.972 40.000 0.00 0.00 0.00 2.34
4271 7239 4.433186 TGGCCAAAATTCTATGACAACG 57.567 40.909 0.61 0.00 0.00 4.10
4654 7632 3.429085 GTGGCAACGCTAATCTTTGATG 58.571 45.455 0.00 0.00 46.04 3.07
4667 7645 2.285827 TTGAAAAACAGGTGGCAACG 57.714 45.000 0.00 0.00 42.51 4.10
4711 7689 4.809958 CGAAGCAGATCAGATGTTCTCATT 59.190 41.667 0.00 0.00 34.06 2.57
4856 7834 9.003658 CAGAACTAGTTTGGATCAGTACAAAAT 57.996 33.333 10.02 0.00 39.79 1.82
5263 9885 4.675114 GCAAACGATTAACCACAAGAGTTG 59.325 41.667 0.00 0.00 0.00 3.16
5375 10001 3.914426 ATCGGGAATAGCTGAACTTGT 57.086 42.857 0.00 0.00 0.00 3.16
5393 10019 3.204526 CACATGCAGAGGAGGAGAAATC 58.795 50.000 0.00 0.00 0.00 2.17
5433 10062 4.935205 TGTACATGCAGGAACATACAAGTC 59.065 41.667 4.84 0.00 0.00 3.01
5550 10182 0.467384 CTGGATCAGAGGTGGCGAAT 59.533 55.000 0.00 0.00 32.44 3.34
5606 10250 5.757320 AGCACACATGAGAAGCTATATCAAC 59.243 40.000 0.00 0.00 33.06 3.18
5608 10252 5.541953 AGCACACATGAGAAGCTATATCA 57.458 39.130 0.00 0.00 33.06 2.15
5666 10310 2.656973 GCGCCAACACCAAAACCG 60.657 61.111 0.00 0.00 0.00 4.44
5707 10357 5.277974 CGTGCTGAAGAATGGAAGAAAAGAA 60.278 40.000 0.00 0.00 0.00 2.52
5708 10358 4.214119 CGTGCTGAAGAATGGAAGAAAAGA 59.786 41.667 0.00 0.00 0.00 2.52
5709 10359 4.214119 TCGTGCTGAAGAATGGAAGAAAAG 59.786 41.667 0.00 0.00 0.00 2.27
5872 10522 4.271533 CCGACTAAGTAAGCACACAACAAA 59.728 41.667 0.00 0.00 0.00 2.83
5941 10629 9.743057 TCAACAACATCCTAACTTAAAACATTG 57.257 29.630 0.00 0.00 0.00 2.82
5948 10636 6.751157 TCGAGTCAACAACATCCTAACTTAA 58.249 36.000 0.00 0.00 0.00 1.85
5968 10656 3.384668 AGACATACGGCAAATCATCGAG 58.615 45.455 0.00 0.00 0.00 4.04
5983 10671 9.890629 AGAGCAAACATAATAAACTGAGACATA 57.109 29.630 0.00 0.00 0.00 2.29
6094 10784 2.483583 TGTGTTAAAAGCCAGCAACG 57.516 45.000 0.00 0.00 0.00 4.10
6104 10794 6.750963 GTGTTTCGTTTGGGTATGTGTTAAAA 59.249 34.615 0.00 0.00 0.00 1.52
6105 10795 6.095160 AGTGTTTCGTTTGGGTATGTGTTAAA 59.905 34.615 0.00 0.00 0.00 1.52
6106 10796 5.589452 AGTGTTTCGTTTGGGTATGTGTTAA 59.411 36.000 0.00 0.00 0.00 2.01
6166 10859 4.399303 ACAAGAGAAATTTAGGCCATTCCG 59.601 41.667 5.01 0.00 40.77 4.30
6203 10904 2.241880 ACGCGTTCCAAACAGACCG 61.242 57.895 5.58 0.00 0.00 4.79
6244 10945 2.551912 CGGCGCCATTTACATCCCC 61.552 63.158 28.98 0.00 0.00 4.81
6266 10967 2.414957 GGGAAAATGAACTAAACGGGCG 60.415 50.000 0.00 0.00 0.00 6.13
6348 11253 4.274950 TCTTGACAAATTTCCGTGGAGTTC 59.725 41.667 0.00 0.00 0.00 3.01
6376 11281 1.442526 GCGACTGATGCAGGAATGGG 61.443 60.000 0.00 0.00 35.51 4.00
6382 11287 4.147449 TCCCGCGACTGATGCAGG 62.147 66.667 8.23 0.00 35.51 4.85
6415 11323 5.835257 TGAAAAGAAATGCTTGAGGAACAG 58.165 37.500 0.00 0.00 36.80 3.16
6428 11336 7.201635 GGTTCAGCAACACATTTGAAAAGAAAT 60.202 33.333 0.00 0.00 33.70 2.17
6444 11352 3.063485 GAGAGACTTCAGGTTCAGCAAC 58.937 50.000 0.00 0.00 0.00 4.17
6446 11354 2.603021 AGAGAGACTTCAGGTTCAGCA 58.397 47.619 0.00 0.00 0.00 4.41
6447 11355 3.130340 CCTAGAGAGACTTCAGGTTCAGC 59.870 52.174 0.00 0.00 0.00 4.26
6448 11356 3.130340 GCCTAGAGAGACTTCAGGTTCAG 59.870 52.174 0.00 0.00 0.00 3.02
6449 11357 3.093057 GCCTAGAGAGACTTCAGGTTCA 58.907 50.000 0.00 0.00 0.00 3.18
6450 11358 3.361786 AGCCTAGAGAGACTTCAGGTTC 58.638 50.000 0.00 0.00 0.00 3.62
6486 11394 1.410882 CTAGGCCACTAGCTTCAGACC 59.589 57.143 5.01 0.00 40.21 3.85
6503 11411 2.357637 CTCCTCCTCTTGTCTTCGCTAG 59.642 54.545 0.00 0.00 0.00 3.42
6504 11412 2.370349 CTCCTCCTCTTGTCTTCGCTA 58.630 52.381 0.00 0.00 0.00 4.26
6505 11413 1.181786 CTCCTCCTCTTGTCTTCGCT 58.818 55.000 0.00 0.00 0.00 4.93
6516 11424 5.126384 CCTTTCGTATCATATCCTCCTCCTC 59.874 48.000 0.00 0.00 0.00 3.71
6517 11425 5.020132 CCTTTCGTATCATATCCTCCTCCT 58.980 45.833 0.00 0.00 0.00 3.69
6518 11426 4.773149 ACCTTTCGTATCATATCCTCCTCC 59.227 45.833 0.00 0.00 0.00 4.30
6534 11442 2.642700 CCAAACGGCCACCTTTCG 59.357 61.111 2.24 0.00 0.00 3.46
6567 11478 2.602267 ATCACGACCACCCGACCA 60.602 61.111 0.00 0.00 0.00 4.02
6608 11519 1.243342 CCAATGGCTGCGAGGAACAA 61.243 55.000 0.00 0.00 0.00 2.83
6610 11521 3.056313 GCCAATGGCTGCGAGGAAC 62.056 63.158 18.47 0.00 46.69 3.62
6675 11586 3.272334 CGCGAGGGCCTATTGCAC 61.272 66.667 20.64 2.05 46.89 4.57
6676 11587 3.733344 GACGCGAGGGCCTATTGCA 62.733 63.158 15.93 0.00 43.89 4.08
6677 11588 2.967615 GACGCGAGGGCCTATTGC 60.968 66.667 15.93 10.68 40.16 3.56
6678 11589 2.280186 GGACGCGAGGGCCTATTG 60.280 66.667 15.93 0.56 35.02 1.90
6679 11590 3.547513 GGGACGCGAGGGCCTATT 61.548 66.667 15.93 0.00 35.02 1.73
6680 11591 4.541648 AGGGACGCGAGGGCCTAT 62.542 66.667 15.93 0.00 35.02 2.57
6734 11645 4.499116 AGGGGATCCGGTGGAGGG 62.499 72.222 5.45 0.00 34.05 4.30
6735 11646 2.844839 GAGGGGATCCGGTGGAGG 60.845 72.222 5.45 0.00 34.05 4.30
6736 11647 2.844839 GGAGGGGATCCGGTGGAG 60.845 72.222 5.45 0.00 38.67 3.86
6744 11655 1.460497 GGGGAGTGAGGAGGGGATC 60.460 68.421 0.00 0.00 0.00 3.36
6745 11656 1.949449 AGGGGAGTGAGGAGGGGAT 60.949 63.158 0.00 0.00 0.00 3.85
6746 11657 2.540910 AGGGGAGTGAGGAGGGGA 60.541 66.667 0.00 0.00 0.00 4.81
6747 11658 2.041405 GAGGGGAGTGAGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
6748 11659 2.041405 GGAGGGGAGTGAGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
6749 11660 2.041405 GGGAGGGGAGTGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
6750 11661 2.041405 GGGGAGGGGAGTGAGGAG 60.041 72.222 0.00 0.00 0.00 3.69
6751 11662 2.540910 AGGGGAGGGGAGTGAGGA 60.541 66.667 0.00 0.00 0.00 3.71
6752 11663 2.041405 GAGGGGAGGGGAGTGAGG 60.041 72.222 0.00 0.00 0.00 3.86
6753 11664 2.443016 CGAGGGGAGGGGAGTGAG 60.443 72.222 0.00 0.00 0.00 3.51
6754 11665 4.779733 GCGAGGGGAGGGGAGTGA 62.780 72.222 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.