Multiple sequence alignment - TraesCS6A01G314500

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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 TraesCS6A01G314500 chr6A 100.000 2751 0 0 1 2751 551086172 551088922 0.000000e+00 5081.0
1 TraesCS6A01G314500 chr6A 100.000 1099 0 0 3109 4207 551089280 551090378 0.000000e+00 2030.0
2 TraesCS6A01G314500 chr6A 78.987 395 68 7 97 479 183225775 183225384 5.400000e-64 255.0
3 TraesCS6A01G314500 chr6A 88.506 87 7 3 3610 3695 88767583 88767667 7.440000e-18 102.0
4 TraesCS6A01G314500 chr6D 86.205 2124 180 57 1 2062 404591334 404593406 0.000000e+00 2194.0
5 TraesCS6A01G314500 chr6D 92.424 924 50 11 3110 4019 404593910 404594827 0.000000e+00 1301.0
6 TraesCS6A01G314500 chr6D 94.094 508 17 6 2252 2751 404593406 404593908 0.000000e+00 760.0
7 TraesCS6A01G314500 chr6D 78.320 512 91 10 102 598 262746740 262746234 3.160000e-81 313.0
8 TraesCS6A01G314500 chr6D 95.181 166 7 1 3783 3948 289352865 289352701 1.160000e-65 261.0
9 TraesCS6A01G314500 chr6D 95.395 152 7 0 4038 4189 404594812 404594963 4.200000e-60 243.0
10 TraesCS6A01G314500 chr6D 91.250 80 6 1 3617 3695 72021808 72021729 1.600000e-19 108.0
11 TraesCS6A01G314500 chr6D 91.250 80 6 1 3617 3695 72021729 72021808 1.600000e-19 108.0
12 TraesCS6A01G314500 chr6B 92.326 1251 54 17 1506 2751 606962867 606964080 0.000000e+00 1740.0
13 TraesCS6A01G314500 chr6B 89.588 874 37 23 678 1510 606961879 606962739 0.000000e+00 1061.0
14 TraesCS6A01G314500 chr6B 91.189 681 31 8 3109 3772 606964083 606964751 0.000000e+00 898.0
15 TraesCS6A01G314500 chr6B 97.403 154 4 0 4036 4189 606965205 606965358 3.230000e-66 263.0
16 TraesCS6A01G314500 chr6B 98.701 77 0 1 3944 4019 606965146 606965222 7.340000e-28 135.0
17 TraesCS6A01G314500 chr6B 84.127 63 10 0 588 650 42615788 42615850 1.260000e-05 62.1
18 TraesCS6A01G314500 chr5B 81.996 511 77 7 102 600 589664873 589664366 1.810000e-113 420.0
19 TraesCS6A01G314500 chr4D 78.370 638 97 17 1 601 19338384 19339017 3.970000e-100 375.0
20 TraesCS6A01G314500 chr2A 78.974 585 91 17 22 580 617430034 617429456 1.850000e-98 370.0
21 TraesCS6A01G314500 chr3B 80.077 517 86 11 97 600 564761926 564762438 6.650000e-98 368.0
22 TraesCS6A01G314500 chr3B 87.059 85 6 2 3617 3696 637059392 637059476 1.610000e-14 91.6
23 TraesCS6A01G314500 chr5A 79.513 493 82 13 97 580 475780174 475780656 2.420000e-87 333.0
24 TraesCS6A01G314500 chr5A 92.571 175 13 0 3782 3956 526657957 526657783 6.980000e-63 252.0
25 TraesCS6A01G314500 chr5A 77.604 192 36 5 97 284 45251548 45251736 4.450000e-20 110.0
26 TraesCS6A01G314500 chr4A 77.208 566 98 17 62 600 17404535 17403974 6.840000e-78 302.0
27 TraesCS6A01G314500 chr3A 78.175 504 83 20 97 580 78184259 78183763 3.180000e-76 296.0
28 TraesCS6A01G314500 chr3D 77.668 506 94 12 97 590 498428067 498428565 1.480000e-74 291.0
29 TraesCS6A01G314500 chr3D 95.152 165 8 0 3784 3948 433161449 433161285 1.160000e-65 261.0
30 TraesCS6A01G314500 chr3D 73.492 547 111 17 47 578 444933543 444934070 4.320000e-40 176.0
31 TraesCS6A01G314500 chr7D 94.118 170 10 0 3783 3952 23497593 23497762 4.170000e-65 259.0
32 TraesCS6A01G314500 chr7D 88.636 88 7 2 3617 3703 351567800 351567885 2.070000e-18 104.0
33 TraesCS6A01G314500 chr7A 94.578 166 9 0 3784 3949 443397796 443397631 1.500000e-64 257.0
34 TraesCS6A01G314500 chr7A 77.511 458 82 14 160 600 152336925 152336472 5.400000e-64 255.0
35 TraesCS6A01G314500 chr7A 89.773 88 6 2 3617 3703 398912531 398912616 4.450000e-20 110.0
36 TraesCS6A01G314500 chr5D 94.578 166 9 0 3783 3948 48669131 48668966 1.500000e-64 257.0
37 TraesCS6A01G314500 chr1D 94.048 168 10 0 3783 3950 220154299 220154132 5.400000e-64 255.0
38 TraesCS6A01G314500 chr1D 92.614 176 13 0 3777 3952 140136974 140137149 1.940000e-63 254.0
39 TraesCS6A01G314500 chr1D 80.757 317 46 12 292 600 431763889 431764198 2.530000e-57 233.0
40 TraesCS6A01G314500 chr1A 87.209 86 5 2 3617 3696 568396161 568396076 4.480000e-15 93.5
41 TraesCS6A01G314500 chr7B 97.059 34 1 0 617 650 681685778 681685745 1.630000e-04 58.4


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 TraesCS6A01G314500 chr6A 551086172 551090378 4206 False 3555.5 5081 100.0000 1 4207 2 chr6A.!!$F2 4206
1 TraesCS6A01G314500 chr6D 404591334 404594963 3629 False 1124.5 2194 92.0295 1 4189 4 chr6D.!!$F2 4188
2 TraesCS6A01G314500 chr6D 262746234 262746740 506 True 313.0 313 78.3200 102 598 1 chr6D.!!$R2 496
3 TraesCS6A01G314500 chr6B 606961879 606965358 3479 False 819.4 1740 93.8414 678 4189 5 chr6B.!!$F2 3511
4 TraesCS6A01G314500 chr5B 589664366 589664873 507 True 420.0 420 81.9960 102 600 1 chr5B.!!$R1 498
5 TraesCS6A01G314500 chr4D 19338384 19339017 633 False 375.0 375 78.3700 1 601 1 chr4D.!!$F1 600
6 TraesCS6A01G314500 chr2A 617429456 617430034 578 True 370.0 370 78.9740 22 580 1 chr2A.!!$R1 558
7 TraesCS6A01G314500 chr3B 564761926 564762438 512 False 368.0 368 80.0770 97 600 1 chr3B.!!$F1 503
8 TraesCS6A01G314500 chr4A 17403974 17404535 561 True 302.0 302 77.2080 62 600 1 chr4A.!!$R1 538

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
234 257 0.039035 GGAGGGCATGTGGTGGTTTA 59.961 55.0 0.00 0.0 0.00 2.01 F
1256 1362 0.178068 GCTGCCAATCGAGTCCCTAA 59.822 55.0 0.00 0.0 0.00 2.69 F
2039 2295 1.136828 TTGCAGTACCTGGTGGAGTT 58.863 50.0 10.23 0.0 37.04 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2416 0.249573 CCCCAAGCAAGTGCAAACTG 60.250 55.0 6.00 0.00 45.16 3.16 R
2278 2534 0.314935 AGTTTGATGGCCTGTTTGCG 59.685 50.0 3.32 0.00 0.00 4.85 R
4027 4690 0.820871 ACCACTTCTTTGCCGCAAAA 59.179 45.0 18.78 5.14 32.75 2.44 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
73 81 1.153168 ATCTGCGGTGGATTTCGGG 60.153 57.895 0.00 0.00 0.00 5.14
108 129 3.364889 AGGCTCCGTTTTTAGTTTTGC 57.635 42.857 0.00 0.00 0.00 3.68
112 133 4.214758 GGCTCCGTTTTTAGTTTTGCTAGA 59.785 41.667 0.00 0.00 0.00 2.43
129 150 1.531423 AGAGTTTGTGCCATGCTCAG 58.469 50.000 0.00 0.00 33.64 3.35
143 166 1.536943 GCTCAGGAAGACGAGGTGGT 61.537 60.000 0.00 0.00 0.00 4.16
146 169 1.913762 AGGAAGACGAGGTGGTGGG 60.914 63.158 0.00 0.00 0.00 4.61
158 181 0.469144 GTGGTGGGGGCTTCTTGAAA 60.469 55.000 0.00 0.00 0.00 2.69
228 251 1.852157 ATCGTTGGAGGGCATGTGGT 61.852 55.000 0.00 0.00 0.00 4.16
234 257 0.039035 GGAGGGCATGTGGTGGTTTA 59.961 55.000 0.00 0.00 0.00 2.01
265 289 4.090588 TCGTGGGATCGGTTGGCC 62.091 66.667 0.00 0.00 0.00 5.36
268 292 1.749258 GTGGGATCGGTTGGCCTTC 60.749 63.158 3.32 0.00 0.00 3.46
284 308 2.633488 CCTTCTTCTTCGGTGGATTCC 58.367 52.381 0.00 0.00 0.00 3.01
311 345 6.916387 CCTTCGTTCATCTACGTATATGTGTT 59.084 38.462 17.48 0.00 42.01 3.32
325 359 0.323816 TGTGTTTGCAGGTTGGACCA 60.324 50.000 0.00 0.00 41.95 4.02
371 405 1.962306 GGCGGCGGTTGTTGTTCTA 60.962 57.895 9.78 0.00 0.00 2.10
372 406 1.495951 GCGGCGGTTGTTGTTCTAG 59.504 57.895 9.78 0.00 0.00 2.43
373 407 1.226030 GCGGCGGTTGTTGTTCTAGT 61.226 55.000 9.78 0.00 0.00 2.57
380 414 2.353579 GGTTGTTGTTCTAGTGCGTTGT 59.646 45.455 0.00 0.00 0.00 3.32
382 416 4.408694 GTTGTTGTTCTAGTGCGTTGTTT 58.591 39.130 0.00 0.00 0.00 2.83
391 426 1.073284 AGTGCGTTGTTTCTATGGGGT 59.927 47.619 0.00 0.00 0.00 4.95
394 429 2.007608 GCGTTGTTTCTATGGGGTCTC 58.992 52.381 0.00 0.00 0.00 3.36
403 438 1.278985 CTATGGGGTCTCAGCACAACA 59.721 52.381 0.00 0.00 30.29 3.33
429 464 7.037438 ACTTTTCGACTGTCTACTACAACAAA 58.963 34.615 6.21 0.00 37.74 2.83
438 473 5.830991 TGTCTACTACAACAAAATTTGCCCT 59.169 36.000 5.52 0.00 34.29 5.19
580 615 8.723942 ACTACCTTGACAATTGATGAATAGAC 57.276 34.615 13.59 0.00 0.00 2.59
590 625 8.190784 ACAATTGATGAATAGACCGGAAATTTC 58.809 33.333 13.59 9.83 0.00 2.17
620 658 2.815478 TCACATTTTGCCGGTGAAAAC 58.185 42.857 13.66 0.00 38.50 2.43
628 666 0.671251 GCCGGTGAAAACAATGGTCA 59.329 50.000 1.90 0.00 0.00 4.02
659 697 5.636837 ACATAAAAATATGACACACCGTGC 58.363 37.500 0.00 0.00 36.98 5.34
664 702 4.419522 AATATGACACACCGTGCTTTTC 57.580 40.909 0.00 0.00 36.98 2.29
667 705 2.088423 TGACACACCGTGCTTTTCTTT 58.912 42.857 0.00 0.00 36.98 2.52
668 706 2.490115 TGACACACCGTGCTTTTCTTTT 59.510 40.909 0.00 0.00 36.98 2.27
669 707 2.851824 GACACACCGTGCTTTTCTTTTG 59.148 45.455 0.00 0.00 36.98 2.44
735 774 3.270877 GGGTGATGACTTGTATCCACAC 58.729 50.000 0.00 0.00 33.30 3.82
814 853 1.963985 ATTCTGCTCCAGTCTTCCCT 58.036 50.000 0.00 0.00 32.61 4.20
828 898 4.097589 AGTCTTCCCTACGAAAATAGACGG 59.902 45.833 0.00 0.00 30.84 4.79
837 907 3.742369 ACGAAAATAGACGGCGAAAAGAA 59.258 39.130 16.62 0.00 0.00 2.52
838 908 4.211794 ACGAAAATAGACGGCGAAAAGAAA 59.788 37.500 16.62 0.00 0.00 2.52
839 909 5.141568 CGAAAATAGACGGCGAAAAGAAAA 58.858 37.500 16.62 0.00 0.00 2.29
840 910 5.280678 CGAAAATAGACGGCGAAAAGAAAAG 59.719 40.000 16.62 0.00 0.00 2.27
1137 1243 2.885676 CGATTCATCGCCGGCTTGG 61.886 63.158 26.68 13.38 43.84 3.61
1177 1283 3.744719 GAACCCCCGCCGCTTTTC 61.745 66.667 0.00 0.00 0.00 2.29
1200 1306 4.311606 GGGTTGTTGGATTATGCGTTTTT 58.688 39.130 0.00 0.00 0.00 1.94
1201 1307 5.471257 GGGTTGTTGGATTATGCGTTTTTA 58.529 37.500 0.00 0.00 0.00 1.52
1203 1309 6.592220 GGGTTGTTGGATTATGCGTTTTTATT 59.408 34.615 0.00 0.00 0.00 1.40
1204 1310 7.118535 GGGTTGTTGGATTATGCGTTTTTATTT 59.881 33.333 0.00 0.00 0.00 1.40
1205 1311 9.141400 GGTTGTTGGATTATGCGTTTTTATTTA 57.859 29.630 0.00 0.00 0.00 1.40
1241 1347 0.528924 TCATGGAATGCTGTTGCTGC 59.471 50.000 0.00 0.00 46.21 5.25
1256 1362 0.178068 GCTGCCAATCGAGTCCCTAA 59.822 55.000 0.00 0.00 0.00 2.69
1355 1461 1.337071 GATGCGTCGGAGGAGACAATA 59.663 52.381 1.18 0.00 40.98 1.90
1399 1505 1.152777 TGGTCAGTGTTTGCCCCAG 60.153 57.895 0.00 0.00 0.00 4.45
1427 1540 4.096382 CCATTCTACATGTTTTCCCCTTCG 59.904 45.833 2.30 0.00 0.00 3.79
1489 1602 7.094805 GCTTACCTGAAACTGTATTGATGTCAA 60.095 37.037 0.00 0.00 40.51 3.18
1618 1864 2.480555 GCATTGACGCCTTCACCG 59.519 61.111 0.00 0.00 32.26 4.94
1717 1963 5.591472 CAGATTTCAGGACATTAATGAGGCA 59.409 40.000 22.16 0.00 0.00 4.75
1773 2019 4.998788 TCAGTATCCTCATGTTCAACTCG 58.001 43.478 0.00 0.00 0.00 4.18
1961 2216 8.993121 CGAGTAATCCTAAACATTGCATTAGAT 58.007 33.333 6.41 0.00 32.10 1.98
1970 2225 7.658525 AAACATTGCATTAGATTACATGGGA 57.341 32.000 0.00 0.00 0.00 4.37
1987 2242 2.178984 TGGGAAGTTCATTTGGTCCCTT 59.821 45.455 5.01 0.00 46.97 3.95
2009 2264 7.041098 CCCTTTATAATTTAGACGCTGCTGAAT 60.041 37.037 0.00 0.00 0.00 2.57
2024 2280 3.831333 TGCTGAATTACCTGGATTTTGCA 59.169 39.130 0.00 3.19 0.00 4.08
2039 2295 1.136828 TTGCAGTACCTGGTGGAGTT 58.863 50.000 10.23 0.00 37.04 3.01
2044 2300 3.323243 CAGTACCTGGTGGAGTTTTACG 58.677 50.000 10.23 0.00 37.04 3.18
2074 2330 9.905713 TGACTGCCATAAGACTAAGAATAATTT 57.094 29.630 0.00 0.00 0.00 1.82
2110 2366 3.589988 AGTTAGAAGATGTCAAGCGTGG 58.410 45.455 0.00 0.00 0.00 4.94
2113 2369 2.851195 AGAAGATGTCAAGCGTGGTTT 58.149 42.857 0.00 0.00 0.00 3.27
2158 2414 6.435292 AGGGACTAAATAGTTCTGTGTTGT 57.565 37.500 0.00 0.00 36.02 3.32
2159 2415 7.549147 AGGGACTAAATAGTTCTGTGTTGTA 57.451 36.000 0.00 0.00 36.02 2.41
2160 2416 7.384477 AGGGACTAAATAGTTCTGTGTTGTAC 58.616 38.462 0.00 0.00 36.02 2.90
2278 2534 1.198637 GCAAGTCAGTCATTGCCTCAC 59.801 52.381 0.00 0.00 44.76 3.51
2303 2559 3.022557 ACAGGCCATCAAACTATGCAT 57.977 42.857 5.01 3.79 0.00 3.96
2383 2644 0.754957 TTGTTGCACACCTTGGAGGG 60.755 55.000 0.00 0.00 40.58 4.30
2403 2664 2.550978 GTGGTCGCATGCATTAGTAGT 58.449 47.619 19.57 0.00 0.00 2.73
2433 2694 3.184541 GCCATCATTTGTTGATCACTGC 58.815 45.455 0.00 0.00 43.40 4.40
2435 2696 2.617250 TCATTTGTTGATCACTGCGC 57.383 45.000 0.00 0.00 0.00 6.09
2473 2734 5.329035 AGTTTTGCACTGACTGTCAAAAT 57.671 34.783 12.16 0.00 37.65 1.82
2649 2912 2.094762 AACGGCAGGAGTATGACAAC 57.905 50.000 0.00 0.00 0.00 3.32
3212 3475 0.180406 ACTCGGTGTGGTGAGCTTTT 59.820 50.000 0.00 0.00 35.61 2.27
3226 3489 2.820197 GAGCTTTTTCAGGGGTACAAGG 59.180 50.000 0.00 0.00 0.00 3.61
3243 3506 0.972983 AGGGTCTGCGTCTATGTGCT 60.973 55.000 0.00 0.00 0.00 4.40
3244 3507 0.108138 GGGTCTGCGTCTATGTGCTT 60.108 55.000 0.00 0.00 0.00 3.91
3281 3544 6.148315 GTGTGTAGTTGTAAAATCCCACCTAC 59.852 42.308 0.00 0.00 28.66 3.18
3338 3608 1.859080 GGCTTAGCGTTTCATCCTACG 59.141 52.381 0.00 0.00 40.55 3.51
3547 3817 1.439679 CGCTGTGTTCTTTACTCCCC 58.560 55.000 0.00 0.00 0.00 4.81
3548 3818 1.270625 CGCTGTGTTCTTTACTCCCCA 60.271 52.381 0.00 0.00 0.00 4.96
3551 3821 3.826729 GCTGTGTTCTTTACTCCCCAAAT 59.173 43.478 0.00 0.00 0.00 2.32
3661 3933 5.779529 AGACGTTTTAGGTCACTAGTGAA 57.220 39.130 26.74 9.43 41.85 3.18
3709 3984 7.760607 TGGAGTGAGTATCTTATAGGAGTGAT 58.239 38.462 0.00 0.00 34.92 3.06
3789 4452 8.075761 TCAGTTTTCTCTTACCTTATACTCCC 57.924 38.462 0.00 0.00 0.00 4.30
3798 4461 1.969208 CCTTATACTCCCTCCGTTCCC 59.031 57.143 0.00 0.00 0.00 3.97
3803 4466 0.328258 ACTCCCTCCGTTCCCAAATG 59.672 55.000 0.00 0.00 0.00 2.32
3813 4476 5.134661 TCCGTTCCCAAATGTAAGTCTTTT 58.865 37.500 0.00 0.00 0.00 2.27
3814 4477 5.595133 TCCGTTCCCAAATGTAAGTCTTTTT 59.405 36.000 0.00 0.00 0.00 1.94
3853 4516 9.461312 AAGTGACTACATATGGAGCAAAATAAA 57.539 29.630 15.30 0.00 0.00 1.40
3866 4529 8.677300 TGGAGCAAAATAAATGAATCTACACTC 58.323 33.333 0.00 0.00 0.00 3.51
3904 4567 7.946655 CATACATTCGTATGTTGTAGTCCAT 57.053 36.000 13.12 0.00 46.70 3.41
3905 4568 8.365399 CATACATTCGTATGTTGTAGTCCATT 57.635 34.615 13.12 0.00 46.70 3.16
3912 4575 7.747888 TCGTATGTTGTAGTCCATTTGAAATG 58.252 34.615 10.84 10.84 0.00 2.32
3917 4580 8.684386 TGTTGTAGTCCATTTGAAATGTCTAA 57.316 30.769 15.93 4.89 0.00 2.10
4012 4675 2.233271 CACCAATGCTCAAGAAGTGGT 58.767 47.619 4.25 4.25 39.96 4.16
4013 4676 2.624838 CACCAATGCTCAAGAAGTGGTT 59.375 45.455 7.40 0.00 37.26 3.67
4014 4677 3.820467 CACCAATGCTCAAGAAGTGGTTA 59.180 43.478 7.40 0.00 37.26 2.85
4015 4678 4.460382 CACCAATGCTCAAGAAGTGGTTAT 59.540 41.667 7.40 0.00 37.26 1.89
4016 4679 5.647658 CACCAATGCTCAAGAAGTGGTTATA 59.352 40.000 7.40 0.00 37.26 0.98
4017 4680 6.319658 CACCAATGCTCAAGAAGTGGTTATAT 59.680 38.462 7.40 0.00 37.26 0.86
4018 4681 6.891908 ACCAATGCTCAAGAAGTGGTTATATT 59.108 34.615 4.25 0.00 35.89 1.28
4019 4682 8.052748 ACCAATGCTCAAGAAGTGGTTATATTA 58.947 33.333 4.25 0.00 35.89 0.98
4020 4683 9.071276 CCAATGCTCAAGAAGTGGTTATATTAT 57.929 33.333 0.00 0.00 0.00 1.28
4172 4836 9.573133 CAGATAAAATTTACAAGGTGGTTGATC 57.427 33.333 0.00 0.00 38.60 2.92
4189 4853 5.349817 GGTTGATCATGTGGCTATATTCTCG 59.650 44.000 0.00 0.00 0.00 4.04
4190 4854 4.498241 TGATCATGTGGCTATATTCTCGC 58.502 43.478 0.00 0.00 0.00 5.03
4191 4855 4.021192 TGATCATGTGGCTATATTCTCGCA 60.021 41.667 0.00 0.00 0.00 5.10
4192 4856 3.653344 TCATGTGGCTATATTCTCGCAC 58.347 45.455 0.00 0.00 0.00 5.34
4193 4857 3.069443 TCATGTGGCTATATTCTCGCACA 59.931 43.478 0.00 0.00 0.00 4.57
4194 4858 2.821546 TGTGGCTATATTCTCGCACAC 58.178 47.619 0.00 0.00 0.00 3.82
4195 4859 2.167487 TGTGGCTATATTCTCGCACACA 59.833 45.455 0.00 0.00 34.69 3.72
4196 4860 3.181466 TGTGGCTATATTCTCGCACACAT 60.181 43.478 0.00 0.00 33.30 3.21
4197 4861 3.430218 GTGGCTATATTCTCGCACACATC 59.570 47.826 0.00 0.00 0.00 3.06
4198 4862 3.321968 TGGCTATATTCTCGCACACATCT 59.678 43.478 0.00 0.00 0.00 2.90
4199 4863 4.522789 TGGCTATATTCTCGCACACATCTA 59.477 41.667 0.00 0.00 0.00 1.98
4200 4864 5.098893 GGCTATATTCTCGCACACATCTAG 58.901 45.833 0.00 0.00 0.00 2.43
4201 4865 5.106118 GGCTATATTCTCGCACACATCTAGA 60.106 44.000 0.00 0.00 0.00 2.43
4202 4866 5.797934 GCTATATTCTCGCACACATCTAGAC 59.202 44.000 0.00 0.00 0.00 2.59
4203 4867 5.774498 ATATTCTCGCACACATCTAGACA 57.226 39.130 0.00 0.00 0.00 3.41
4204 4868 2.921634 TCTCGCACACATCTAGACAC 57.078 50.000 0.00 0.00 0.00 3.67
4205 4869 1.130561 TCTCGCACACATCTAGACACG 59.869 52.381 0.00 0.00 0.00 4.49
4206 4870 0.879090 TCGCACACATCTAGACACGT 59.121 50.000 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.647158 GGAGAAGAAGCGGACCGGT 61.647 63.158 13.98 13.98 40.00 5.28
88 96 2.956333 AGCAAAACTAAAAACGGAGCCT 59.044 40.909 0.00 0.00 0.00 4.58
129 150 2.663196 CCCACCACCTCGTCTTCC 59.337 66.667 0.00 0.00 0.00 3.46
143 166 2.692709 TCATTTTCAAGAAGCCCCCA 57.307 45.000 0.00 0.00 0.00 4.96
146 169 6.701340 ACCTTATTTCATTTTCAAGAAGCCC 58.299 36.000 0.00 0.00 0.00 5.19
158 181 2.850568 ACGGGGAGGACCTTATTTCATT 59.149 45.455 0.00 0.00 40.03 2.57
228 251 3.181479 CGAGATCCGTTGGAGATAAACCA 60.181 47.826 0.00 0.00 34.05 3.67
258 281 0.250770 ACCGAAGAAGAAGGCCAACC 60.251 55.000 5.01 0.00 0.00 3.77
284 308 2.463553 TACGTAGATGAACGAAGGCG 57.536 50.000 3.10 0.00 45.68 5.52
285 309 5.342525 CACATATACGTAGATGAACGAAGGC 59.657 44.000 31.07 0.00 45.68 4.35
286 320 6.436261 ACACATATACGTAGATGAACGAAGG 58.564 40.000 31.07 15.28 45.68 3.46
311 345 0.958091 CGAAATGGTCCAACCTGCAA 59.042 50.000 0.00 0.00 39.58 4.08
325 359 5.860941 TGAAGAGAAGCCTAGATCGAAAT 57.139 39.130 0.00 0.00 0.00 2.17
358 392 1.214367 ACGCACTAGAACAACAACCG 58.786 50.000 0.00 0.00 0.00 4.44
359 393 2.353579 ACAACGCACTAGAACAACAACC 59.646 45.455 0.00 0.00 0.00 3.77
366 400 4.092968 CCCATAGAAACAACGCACTAGAAC 59.907 45.833 0.00 0.00 0.00 3.01
368 402 3.369052 CCCCATAGAAACAACGCACTAGA 60.369 47.826 0.00 0.00 0.00 2.43
371 405 1.073284 ACCCCATAGAAACAACGCACT 59.927 47.619 0.00 0.00 0.00 4.40
372 406 1.467342 GACCCCATAGAAACAACGCAC 59.533 52.381 0.00 0.00 0.00 5.34
373 407 1.349688 AGACCCCATAGAAACAACGCA 59.650 47.619 0.00 0.00 0.00 5.24
380 414 2.265367 TGTGCTGAGACCCCATAGAAA 58.735 47.619 0.00 0.00 0.00 2.52
382 416 1.555075 GTTGTGCTGAGACCCCATAGA 59.445 52.381 0.00 0.00 0.00 1.98
391 426 3.063452 GTCGAAAAGTTGTTGTGCTGAGA 59.937 43.478 0.00 0.00 0.00 3.27
394 429 3.100817 CAGTCGAAAAGTTGTTGTGCTG 58.899 45.455 0.00 0.00 0.00 4.41
403 438 6.567050 TGTTGTAGTAGACAGTCGAAAAGTT 58.433 36.000 0.00 0.00 39.88 2.66
429 464 1.829222 CTCATTGGAGCAGGGCAAATT 59.171 47.619 0.00 0.00 33.67 1.82
473 508 0.445436 GTACTCGAACGAGCCGAAGA 59.555 55.000 21.47 0.99 45.54 2.87
484 519 3.251729 AGCAACGACTACAAGTACTCGAA 59.748 43.478 13.57 0.00 0.00 3.71
610 648 3.444703 TTTGACCATTGTTTTCACCGG 57.555 42.857 0.00 0.00 0.00 5.28
611 649 5.982465 AATTTTGACCATTGTTTTCACCG 57.018 34.783 0.00 0.00 0.00 4.94
612 650 7.708752 TGTCTAATTTTGACCATTGTTTTCACC 59.291 33.333 8.23 0.00 33.83 4.02
647 685 1.745232 AAGAAAAGCACGGTGTGTCA 58.255 45.000 10.24 0.00 35.75 3.58
656 694 3.819564 AACCCCTCAAAAGAAAAGCAC 57.180 42.857 0.00 0.00 0.00 4.40
659 697 5.451381 GGTGTGTAACCCCTCAAAAGAAAAG 60.451 44.000 0.00 0.00 44.02 2.27
814 853 4.484236 TCTTTTCGCCGTCTATTTTCGTA 58.516 39.130 0.00 0.00 0.00 3.43
912 992 1.627297 CCTTCCTTCCTTCCGGGGAG 61.627 65.000 0.00 0.00 40.49 4.30
958 1042 2.965462 CGCGGGGATTACCTTCGC 60.965 66.667 0.00 0.00 46.14 4.70
959 1043 1.299926 CTCGCGGGGATTACCTTCG 60.300 63.158 6.13 0.00 40.03 3.79
960 1044 1.069258 CCTCGCGGGGATTACCTTC 59.931 63.158 24.25 0.00 40.03 3.46
1173 1279 3.366476 CGCATAATCCAACAACCCGAAAA 60.366 43.478 0.00 0.00 0.00 2.29
1177 1283 1.091537 ACGCATAATCCAACAACCCG 58.908 50.000 0.00 0.00 0.00 5.28
1241 1347 6.037610 CAGAAAAAGATTAGGGACTCGATTGG 59.962 42.308 0.00 0.00 41.75 3.16
1256 1362 5.279156 GCAACCTCATCCAACAGAAAAAGAT 60.279 40.000 0.00 0.00 0.00 2.40
1328 1434 1.960689 TCCTCCGACGCATCATAATCA 59.039 47.619 0.00 0.00 0.00 2.57
1355 1461 0.739561 GACGGATGTAGCTCGACCTT 59.260 55.000 0.00 0.00 0.00 3.50
1399 1505 2.919666 AAACATGTAGAATGGCGTGC 57.080 45.000 0.00 0.00 0.00 5.34
1403 1509 3.365472 AGGGGAAAACATGTAGAATGGC 58.635 45.455 0.00 0.00 0.00 4.40
1427 1540 0.863144 TTTCAGACCGCACGCTTTAC 59.137 50.000 0.00 0.00 0.00 2.01
1603 1848 0.606604 ACTACGGTGAAGGCGTCAAT 59.393 50.000 4.28 0.00 38.23 2.57
1618 1864 8.697292 AGGAGAAAATAGTAGATTGGTCACTAC 58.303 37.037 0.00 0.00 39.15 2.73
1717 1963 0.251165 ACCAAAGCGCACCTTGGTAT 60.251 50.000 29.30 13.81 34.96 2.73
1798 2045 4.266976 GCTGCTTGCACATCATGATAAAAC 59.733 41.667 8.15 0.00 42.31 2.43
1961 2216 4.770010 GGACCAAATGAACTTCCCATGTAA 59.230 41.667 0.00 0.00 0.00 2.41
1987 2242 8.770828 GGTAATTCAGCAGCGTCTAAATTATAA 58.229 33.333 0.00 0.00 0.00 0.98
2009 2264 4.650972 AGGTACTGCAAAATCCAGGTAA 57.349 40.909 0.00 0.00 37.18 2.85
2024 2280 3.233507 TCGTAAAACTCCACCAGGTACT 58.766 45.455 0.00 0.00 43.88 2.73
2039 2295 7.050970 AGTCTTATGGCAGTCATATCGTAAA 57.949 36.000 0.00 0.00 38.08 2.01
2074 2330 5.244402 TCTTCTAACTCACGAATGGTACCAA 59.756 40.000 20.76 2.16 0.00 3.67
2079 2335 5.047306 TGACATCTTCTAACTCACGAATGGT 60.047 40.000 0.00 0.00 0.00 3.55
2082 2338 5.578727 GCTTGACATCTTCTAACTCACGAAT 59.421 40.000 0.00 0.00 0.00 3.34
2135 2391 6.435292 ACAACACAGAACTATTTAGTCCCT 57.565 37.500 0.00 0.00 34.99 4.20
2156 2412 2.098934 CCAAGCAAGTGCAAACTGTACA 59.901 45.455 6.00 0.00 45.16 2.90
2157 2413 2.543653 CCCAAGCAAGTGCAAACTGTAC 60.544 50.000 6.00 0.00 45.16 2.90
2158 2414 1.680735 CCCAAGCAAGTGCAAACTGTA 59.319 47.619 6.00 0.00 45.16 2.74
2159 2415 0.461135 CCCAAGCAAGTGCAAACTGT 59.539 50.000 6.00 0.00 45.16 3.55
2160 2416 0.249573 CCCCAAGCAAGTGCAAACTG 60.250 55.000 6.00 0.00 45.16 3.16
2245 2501 1.349688 TGACTTGCCCTAAATGGACGT 59.650 47.619 0.00 0.00 38.35 4.34
2246 2502 2.009774 CTGACTTGCCCTAAATGGACG 58.990 52.381 0.00 0.00 38.35 4.79
2278 2534 0.314935 AGTTTGATGGCCTGTTTGCG 59.685 50.000 3.32 0.00 0.00 4.85
2303 2559 9.128404 TCCGCTAGTTTCTTAGTATGATCTAAA 57.872 33.333 0.00 0.00 30.88 1.85
2333 2593 7.223387 GGCTCAAATGTCATGACCAAATAAATC 59.777 37.037 22.85 4.98 0.00 2.17
2334 2594 7.043565 GGCTCAAATGTCATGACCAAATAAAT 58.956 34.615 22.85 5.12 0.00 1.40
2335 2595 6.014755 TGGCTCAAATGTCATGACCAAATAAA 60.015 34.615 22.85 2.70 30.40 1.40
2336 2596 5.479724 TGGCTCAAATGTCATGACCAAATAA 59.520 36.000 22.85 3.48 30.40 1.40
2338 2598 3.833650 TGGCTCAAATGTCATGACCAAAT 59.166 39.130 22.85 7.35 30.40 2.32
2383 2644 2.550978 ACTACTAATGCATGCGACCAC 58.449 47.619 14.09 0.00 0.00 4.16
2403 2664 4.282957 TCAACAAATGATGGCCAGCTTTTA 59.717 37.500 28.11 14.44 31.50 1.52
2516 2778 1.003116 GCTAAAGCAGATGCATCGTGG 60.003 52.381 20.67 14.98 45.16 4.94
2649 2912 6.548441 TCCTGAACGTATAAAACACCTTTG 57.452 37.500 0.00 0.00 0.00 2.77
2724 2987 2.325082 GCGTGTGGTGGTGATGGTC 61.325 63.158 0.00 0.00 0.00 4.02
3212 3475 1.358152 CAGACCCTTGTACCCCTGAA 58.642 55.000 0.00 0.00 0.00 3.02
3226 3489 1.661112 GAAAGCACATAGACGCAGACC 59.339 52.381 0.00 0.00 0.00 3.85
3243 3506 2.224185 ACTACACACATCAGCCACGAAA 60.224 45.455 0.00 0.00 0.00 3.46
3244 3507 1.343142 ACTACACACATCAGCCACGAA 59.657 47.619 0.00 0.00 0.00 3.85
3281 3544 6.604735 AGTACTGTGCTAAACTTTGTGAAG 57.395 37.500 0.00 0.00 38.87 3.02
3709 3984 9.802039 AAAGATAAGTTACTTGGTGACCAATTA 57.198 29.630 18.64 13.91 43.07 1.40
3737 4019 3.777106 TCACTGAGCATTTCTCCAAGT 57.223 42.857 0.00 0.00 41.18 3.16
3789 4452 3.939066 AGACTTACATTTGGGAACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
3827 4490 9.461312 TTTATTTTGCTCCATATGTAGTCACTT 57.539 29.630 1.24 0.00 0.00 3.16
3828 4491 9.632638 ATTTATTTTGCTCCATATGTAGTCACT 57.367 29.630 1.24 0.00 0.00 3.41
3830 4493 9.625747 TCATTTATTTTGCTCCATATGTAGTCA 57.374 29.630 1.24 0.00 0.00 3.41
3840 4503 8.579850 AGTGTAGATTCATTTATTTTGCTCCA 57.420 30.769 0.00 0.00 0.00 3.86
3887 4550 7.389330 ACATTTCAAATGGACTACAACATACGA 59.611 33.333 14.70 0.00 0.00 3.43
3898 4561 9.136323 AGACTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 0.00 3.85
3899 4562 9.750125 AAGACTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.04 0.00 4.02
3917 4580 7.991460 CCCTCCGTTCCTAAATATAAGACTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3922 4585 6.379579 ACTCCCTCCGTTCCTAAATATAAGA 58.620 40.000 0.00 0.00 0.00 2.10
3926 4589 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
4017 4680 9.646427 ACTTCTTTGCCGCAAAAATAATAATAA 57.354 25.926 18.78 3.19 32.75 1.40
4018 4681 9.081997 CACTTCTTTGCCGCAAAAATAATAATA 57.918 29.630 18.78 0.00 32.75 0.98
4019 4682 7.064490 CCACTTCTTTGCCGCAAAAATAATAAT 59.936 33.333 18.78 0.00 32.75 1.28
4020 4683 6.367422 CCACTTCTTTGCCGCAAAAATAATAA 59.633 34.615 18.78 6.61 32.75 1.40
4021 4684 5.866633 CCACTTCTTTGCCGCAAAAATAATA 59.133 36.000 18.78 0.00 32.75 0.98
4022 4685 4.690280 CCACTTCTTTGCCGCAAAAATAAT 59.310 37.500 18.78 2.35 32.75 1.28
4023 4686 4.054671 CCACTTCTTTGCCGCAAAAATAA 58.945 39.130 18.78 12.22 32.75 1.40
4024 4687 3.068873 ACCACTTCTTTGCCGCAAAAATA 59.931 39.130 18.78 5.68 32.75 1.40
4025 4688 2.158971 ACCACTTCTTTGCCGCAAAAAT 60.159 40.909 18.78 3.01 32.75 1.82
4026 4689 1.205893 ACCACTTCTTTGCCGCAAAAA 59.794 42.857 18.78 14.07 32.75 1.94
4027 4690 0.820871 ACCACTTCTTTGCCGCAAAA 59.179 45.000 18.78 5.14 32.75 2.44
4028 4691 0.820871 AACCACTTCTTTGCCGCAAA 59.179 45.000 17.39 17.39 0.00 3.68
4029 4692 1.681538 TAACCACTTCTTTGCCGCAA 58.318 45.000 0.38 0.38 0.00 4.85
4030 4693 1.904287 ATAACCACTTCTTTGCCGCA 58.096 45.000 0.00 0.00 0.00 5.69
4031 4694 4.632538 AATATAACCACTTCTTTGCCGC 57.367 40.909 0.00 0.00 0.00 6.53
4032 4695 7.964545 GTTAAATATAACCACTTCTTTGCCG 57.035 36.000 0.00 0.00 36.25 5.69
4112 4776 2.354704 CCCTCTCATCGTTGGTGCTTAA 60.355 50.000 0.00 0.00 0.00 1.85
4137 4801 8.253113 CCTTGTAAATTTTATCTGCTCCAATGT 58.747 33.333 0.00 0.00 0.00 2.71
4172 4836 3.185188 GTGTGCGAGAATATAGCCACATG 59.815 47.826 0.00 0.00 33.81 3.21


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

AutoCloner maintained by Alex Coulton.