Multiple sequence alignment - TraesCS4D01G314500

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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 TraesCS4D01G314500 chr4D 100.000 6115 0 0 1 6115 480823573 480829687 0.000000e+00 11293
1 TraesCS4D01G314500 chr4D 89.571 163 17 0 3830 3992 85011281 85011119 2.230000e-49 207
2 TraesCS4D01G314500 chr4D 79.252 294 33 17 5664 5932 501319690 501319400 4.870000e-41 180
3 TraesCS4D01G314500 chr4D 90.909 110 6 3 616 721 337260385 337260494 1.780000e-30 145
4 TraesCS4D01G314500 chr4D 92.941 85 5 1 5317 5401 480828806 480828889 8.320000e-24 122
5 TraesCS4D01G314500 chr4D 92.941 85 5 1 5234 5317 480828889 480828973 8.320000e-24 122
6 TraesCS4D01G314500 chr4B 94.140 4795 178 35 1362 6115 608669810 608674542 0.000000e+00 7203
7 TraesCS4D01G314500 chr4B 87.159 880 55 36 518 1368 608668827 608669677 0.000000e+00 946
8 TraesCS4D01G314500 chr4B 88.423 501 24 14 1 489 608668121 608668599 1.910000e-159 573
9 TraesCS4D01G314500 chr4B 89.262 149 9 6 507 652 608668583 608668727 4.870000e-41 180
10 TraesCS4D01G314500 chr4B 95.294 85 4 0 5317 5401 608673678 608673762 1.070000e-27 135
11 TraesCS4D01G314500 chr4B 90.476 84 7 1 5234 5317 608673762 608673844 6.480000e-20 110
12 TraesCS4D01G314500 chr5A 94.214 3249 119 19 2775 5981 662729548 662726327 0.000000e+00 4894
13 TraesCS4D01G314500 chr5A 96.031 1159 40 4 1583 2739 662730699 662729545 0.000000e+00 1881
14 TraesCS4D01G314500 chr5A 86.131 1096 88 39 507 1554 662731771 662730692 0.000000e+00 1123
15 TraesCS4D01G314500 chr5A 81.729 509 39 21 14 489 662732242 662731755 5.790000e-100 375
16 TraesCS4D01G314500 chr5A 81.090 312 43 10 5636 5933 3346694 3347003 1.020000e-57 235
17 TraesCS4D01G314500 chr5A 92.941 85 5 1 5317 5401 662727066 662726983 8.320000e-24 122
18 TraesCS4D01G314500 chr5A 89.412 85 8 1 5234 5317 662726983 662726899 8.380000e-19 106
19 TraesCS4D01G314500 chr6D 83.062 307 39 9 5639 5933 388957279 388956974 3.630000e-67 267
20 TraesCS4D01G314500 chr6D 89.634 164 17 0 3831 3994 472535989 472535826 6.210000e-50 209
21 TraesCS4D01G314500 chr6D 92.593 108 4 3 613 719 63710484 63710380 1.060000e-32 152
22 TraesCS4D01G314500 chr3D 82.026 306 41 8 5638 5931 401175453 401175756 1.320000e-61 248
23 TraesCS4D01G314500 chr3A 81.759 307 40 10 5638 5931 521633071 521633374 6.120000e-60 243
24 TraesCS4D01G314500 chr3A 79.545 308 49 9 5639 5933 599416253 599415947 2.230000e-49 207
25 TraesCS4D01G314500 chr3B 81.699 306 41 9 5638 5931 526964451 526964753 2.200000e-59 241
26 TraesCS4D01G314500 chr3B 77.778 306 52 11 5639 5932 687620846 687621147 2.270000e-39 174
27 TraesCS4D01G314500 chr3B 77.451 306 53 11 5639 5932 687650694 687650995 1.050000e-37 169
28 TraesCS4D01G314500 chr5B 80.323 310 46 8 5636 5932 582402238 582401931 2.870000e-53 220
29 TraesCS4D01G314500 chr1A 82.490 257 33 7 5637 5881 532736809 532737065 1.330000e-51 215
30 TraesCS4D01G314500 chr1A 87.179 156 19 1 3831 3986 262830285 262830439 6.300000e-40 176
31 TraesCS4D01G314500 chr2D 79.421 311 48 7 5638 5934 107932483 107932791 8.030000e-49 206
32 TraesCS4D01G314500 chr2D 87.654 162 18 2 3831 3991 35507242 35507082 2.910000e-43 187
33 TraesCS4D01G314500 chr2B 79.385 325 42 9 5622 5932 377087544 377087231 8.030000e-49 206
34 TraesCS4D01G314500 chr2B 93.137 102 2 4 619 720 258656074 258656170 1.780000e-30 145
35 TraesCS4D01G314500 chr7A 87.730 163 18 1 3831 3991 701493630 701493468 8.090000e-44 189
36 TraesCS4D01G314500 chr7A 78.755 273 41 9 5672 5931 538155609 538155341 3.790000e-37 167
37 TraesCS4D01G314500 chr7A 84.524 168 22 3 3833 3998 86235170 86235005 4.900000e-36 163
38 TraesCS4D01G314500 chr6B 78.502 307 48 12 5637 5930 204445865 204445564 1.050000e-42 185
39 TraesCS4D01G314500 chr2A 86.164 159 20 2 3834 3991 601705998 601705841 2.930000e-38 171
40 TraesCS4D01G314500 chr1D 96.939 98 1 2 624 721 267593125 267593030 4.900000e-36 163
41 TraesCS4D01G314500 chr6A 93.396 106 6 1 617 722 80820458 80820354 8.210000e-34 156
42 TraesCS4D01G314500 chr4A 94.949 99 4 1 624 721 135355029 135354931 2.950000e-33 154
43 TraesCS4D01G314500 chr5D 90.909 110 6 3 610 719 302378491 302378386 1.780000e-30 145


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 TraesCS4D01G314500 chr4D 480823573 480829687 6114 False 3845.666667 11293 95.294000 1 6115 3 chr4D.!!$F2 6114
1 TraesCS4D01G314500 chr4B 608668121 608674542 6421 False 1524.500000 7203 90.792333 1 6115 6 chr4B.!!$F1 6114
2 TraesCS4D01G314500 chr5A 662726327 662732242 5915 True 1416.833333 4894 90.076333 14 5981 6 chr5A.!!$R1 5967

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
821 1084 0.038744 CCAAGCCCAAGACAGTCCAT 59.961 55.0 0.00 0.00 0.00 3.41 F
1160 1449 0.037590 TCACCTCCACGGGGAAATTG 59.962 55.0 8.34 5.07 44.06 2.32 F
1331 1625 0.601558 GGTCAGCCTGTTCGTGTAGA 59.398 55.0 0.00 0.00 0.00 2.59 F
1616 2054 0.792640 CTGATGGTGACTGTGCGTTC 59.207 55.0 0.00 0.00 0.00 3.95 F
2076 2514 1.656587 TGGTAATGGCCACTCTCTGT 58.343 50.0 8.16 0.00 32.81 3.41 F
3587 4053 1.707632 TGCATGGTTACGCAATTTGC 58.292 45.0 11.42 11.42 40.69 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2746 3184 1.067635 CCAATTTTCAAGCACCTCCGG 60.068 52.381 0.00 0.0 0.00 5.14 R
2748 3186 3.321968 ACTTCCAATTTTCAAGCACCTCC 59.678 43.478 0.00 0.0 0.00 4.30 R
2875 3314 3.846360 CAGTAGAAACCTAACGACCAGG 58.154 50.000 0.00 0.0 39.25 4.45 R
3438 3878 4.297768 ACCTATAAGGGGCGGTACTTAAA 58.702 43.478 0.00 0.0 40.58 1.52 R
3626 4092 1.227556 GTATAGCACACCAGGGGCG 60.228 63.158 0.00 0.0 0.00 6.13 R
5381 5857 0.965363 GATGCCGAGCTGGGGAAAAA 60.965 55.000 14.02 0.0 38.63 1.94 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
36 37 2.679059 GCACCTAATCTTCTGCTGCTGA 60.679 50.000 5.03 5.03 0.00 4.26
59 61 1.380246 TGTGAGCCCGGGTACGTAT 60.380 57.895 24.63 0.77 38.78 3.06
81 83 1.343069 GGAGGTCACTGTTGGAGAGT 58.657 55.000 0.00 0.00 0.00 3.24
82 84 1.694696 GGAGGTCACTGTTGGAGAGTT 59.305 52.381 0.00 0.00 0.00 3.01
218 254 3.452474 GATGGATCAGAGTCGTGAAAGG 58.548 50.000 0.00 0.00 0.00 3.11
222 258 0.596577 TCAGAGTCGTGAAAGGGACG 59.403 55.000 0.00 0.00 38.20 4.79
252 291 5.840940 AAAAGAATGTACGTAGCACAGTC 57.159 39.130 8.88 8.88 40.39 3.51
277 316 0.810648 GCGATTTTGGGCACTGATGA 59.189 50.000 0.00 0.00 0.00 2.92
406 446 6.207810 TGGAGTAGTCTGACTTCTTCTTCTTC 59.792 42.308 19.55 6.65 0.00 2.87
407 447 6.433093 GGAGTAGTCTGACTTCTTCTTCTTCT 59.567 42.308 16.53 0.33 0.00 2.85
408 448 7.039993 GGAGTAGTCTGACTTCTTCTTCTTCTT 60.040 40.741 16.53 0.00 0.00 2.52
409 449 7.882179 AGTAGTCTGACTTCTTCTTCTTCTTC 58.118 38.462 16.53 0.00 0.00 2.87
410 450 6.976934 AGTCTGACTTCTTCTTCTTCTTCT 57.023 37.500 4.06 0.00 0.00 2.85
411 451 7.360113 AGTCTGACTTCTTCTTCTTCTTCTT 57.640 36.000 4.06 0.00 0.00 2.52
412 452 7.433680 AGTCTGACTTCTTCTTCTTCTTCTTC 58.566 38.462 4.06 0.00 0.00 2.87
413 453 6.645003 GTCTGACTTCTTCTTCTTCTTCTTCC 59.355 42.308 0.00 0.00 0.00 3.46
467 511 1.474879 TGACCGAGAATGTGCGTGATA 59.525 47.619 0.00 0.00 0.00 2.15
482 526 3.119316 GCGTGATAGTCCCATCTGATAGG 60.119 52.174 0.00 0.00 0.00 2.57
485 529 4.469227 GTGATAGTCCCATCTGATAGGCAT 59.531 45.833 0.00 0.00 0.00 4.40
486 530 4.468868 TGATAGTCCCATCTGATAGGCATG 59.531 45.833 0.00 0.00 0.00 4.06
487 531 2.699160 AGTCCCATCTGATAGGCATGT 58.301 47.619 0.00 0.00 0.00 3.21
488 532 3.051581 AGTCCCATCTGATAGGCATGTT 58.948 45.455 0.00 0.00 0.00 2.71
489 533 3.461085 AGTCCCATCTGATAGGCATGTTT 59.539 43.478 0.00 0.00 0.00 2.83
490 534 4.079558 AGTCCCATCTGATAGGCATGTTTT 60.080 41.667 0.00 0.00 0.00 2.43
491 535 4.646492 GTCCCATCTGATAGGCATGTTTTT 59.354 41.667 0.00 0.00 0.00 1.94
512 556 3.735704 TTTTTGCGGGGACATCTGA 57.264 47.368 0.00 0.00 0.00 3.27
513 557 2.214376 TTTTTGCGGGGACATCTGAT 57.786 45.000 0.00 0.00 0.00 2.90
514 558 3.358111 TTTTTGCGGGGACATCTGATA 57.642 42.857 0.00 0.00 0.00 2.15
515 559 2.620251 TTTGCGGGGACATCTGATAG 57.380 50.000 0.00 0.00 0.00 2.08
516 560 0.758734 TTGCGGGGACATCTGATAGG 59.241 55.000 0.00 0.00 0.00 2.57
517 561 1.004440 GCGGGGACATCTGATAGGC 60.004 63.158 0.00 0.00 0.00 3.93
518 562 1.758440 GCGGGGACATCTGATAGGCA 61.758 60.000 0.00 0.00 0.00 4.75
519 563 0.979665 CGGGGACATCTGATAGGCAT 59.020 55.000 0.00 0.00 0.00 4.40
568 614 4.199432 ACACTGCTGTTATCTGAAGAGG 57.801 45.455 0.00 0.00 0.00 3.69
593 640 2.096496 GCAGATGAATCACCCTTGAACG 59.904 50.000 0.00 0.00 34.61 3.95
613 663 3.870419 ACGTGCACAAATTTCAGCAAAAT 59.130 34.783 18.64 2.79 39.30 1.82
720 979 6.017109 CACTAAACTACAGCCACTTTGATGTT 60.017 38.462 0.00 0.00 0.00 2.71
722 981 4.836125 ACTACAGCCACTTTGATGTTTG 57.164 40.909 0.00 0.00 0.00 2.93
748 1007 8.897752 GCAAAGAGGAATCATCTTATTTGTAGT 58.102 33.333 10.71 0.00 42.51 2.73
759 1018 8.421784 TCATCTTATTTGTAGTGTATGACCTCC 58.578 37.037 0.00 0.00 0.00 4.30
760 1019 7.727578 TCTTATTTGTAGTGTATGACCTCCA 57.272 36.000 0.00 0.00 0.00 3.86
761 1020 7.782049 TCTTATTTGTAGTGTATGACCTCCAG 58.218 38.462 0.00 0.00 0.00 3.86
762 1021 7.618117 TCTTATTTGTAGTGTATGACCTCCAGA 59.382 37.037 0.00 0.00 0.00 3.86
763 1022 6.814954 ATTTGTAGTGTATGACCTCCAGAT 57.185 37.500 0.00 0.00 0.00 2.90
819 1082 0.329596 ATCCAAGCCCAAGACAGTCC 59.670 55.000 0.00 0.00 0.00 3.85
820 1083 1.059584 TCCAAGCCCAAGACAGTCCA 61.060 55.000 0.00 0.00 0.00 4.02
821 1084 0.038744 CCAAGCCCAAGACAGTCCAT 59.961 55.000 0.00 0.00 0.00 3.41
822 1085 1.457346 CAAGCCCAAGACAGTCCATC 58.543 55.000 0.00 0.00 0.00 3.51
836 1099 0.920763 TCCATCTGGGCTGGATTGGT 60.921 55.000 0.00 0.00 37.87 3.67
837 1100 0.466922 CCATCTGGGCTGGATTGGTC 60.467 60.000 0.00 0.00 35.70 4.02
838 1101 0.256752 CATCTGGGCTGGATTGGTCA 59.743 55.000 0.00 0.00 0.00 4.02
839 1102 1.133575 CATCTGGGCTGGATTGGTCAT 60.134 52.381 0.00 0.00 0.00 3.06
840 1103 1.002069 TCTGGGCTGGATTGGTCATT 58.998 50.000 0.00 0.00 0.00 2.57
841 1104 2.204463 TCTGGGCTGGATTGGTCATTA 58.796 47.619 0.00 0.00 0.00 1.90
843 1106 1.064017 TGGGCTGGATTGGTCATTACC 60.064 52.381 0.00 0.00 46.98 2.85
853 1116 0.623723 GGTCATTACCAAGCCCAGGA 59.376 55.000 0.00 0.00 45.98 3.86
855 1118 0.251916 TCATTACCAAGCCCAGGACG 59.748 55.000 0.00 0.00 0.00 4.79
859 1122 4.410400 CCAAGCCCAGGACGGACC 62.410 72.222 0.00 0.00 36.56 4.46
860 1123 4.760047 CAAGCCCAGGACGGACCG 62.760 72.222 13.61 13.61 44.74 4.79
884 1151 2.983592 GTCAAGCCCCACCAACCG 60.984 66.667 0.00 0.00 0.00 4.44
934 1202 1.606601 GCTCAAAACCCCTCCACCC 60.607 63.158 0.00 0.00 0.00 4.61
956 1224 3.134081 CCGCATTCTTAGGGTTTCCTCTA 59.866 47.826 0.00 0.00 43.66 2.43
988 1260 4.717313 GGCAACTCCACCCCCGAC 62.717 72.222 0.00 0.00 34.01 4.79
1149 1437 1.685765 CCTGACCCGATCACCTCCA 60.686 63.158 0.00 0.00 32.37 3.86
1160 1449 0.037590 TCACCTCCACGGGGAAATTG 59.962 55.000 8.34 5.07 44.06 2.32
1166 1455 1.014352 CCACGGGGAAATTGACGATC 58.986 55.000 0.00 0.00 35.59 3.69
1211 1505 1.139095 GTTACGCCTGGACTCGAGG 59.861 63.158 18.41 2.71 0.00 4.63
1331 1625 0.601558 GGTCAGCCTGTTCGTGTAGA 59.398 55.000 0.00 0.00 0.00 2.59
1422 1857 6.094048 AGTTGCAAATATAGCGAATGTGTCTT 59.906 34.615 0.00 0.00 33.85 3.01
1520 1957 5.048991 TCGTGAGATTTTTCTTAGCAAACCC 60.049 40.000 0.00 0.00 33.31 4.11
1521 1958 5.470368 GTGAGATTTTTCTTAGCAAACCCC 58.530 41.667 0.00 0.00 0.00 4.95
1546 1983 3.465210 TGAGGGGTATGGATAAATTGGCA 59.535 43.478 0.00 0.00 0.00 4.92
1610 2047 4.100963 TCAAGTTGTACTGATGGTGACTGT 59.899 41.667 2.11 0.00 0.00 3.55
1616 2054 0.792640 CTGATGGTGACTGTGCGTTC 59.207 55.000 0.00 0.00 0.00 3.95
1802 2240 9.690434 CTTTGTAGAAATACTGCTCGATTTAAC 57.310 33.333 0.00 0.00 32.51 2.01
1825 2263 6.449698 ACCATTTGTTGAGTAAAGAAGCATG 58.550 36.000 0.00 0.00 0.00 4.06
1908 2346 2.644299 TGGTGTGGACAATCCTCAGAAT 59.356 45.455 0.00 0.00 40.30 2.40
1997 2435 4.763793 AGCAATTCTTTTCTCTGCTGCTTA 59.236 37.500 0.00 0.00 41.65 3.09
2009 2447 7.668525 TCTCTGCTGCTTATATGAATGAATG 57.331 36.000 0.00 0.00 0.00 2.67
2068 2506 4.155709 TCTTTGTCATTTGGTAATGGCCA 58.844 39.130 8.56 8.56 44.06 5.36
2076 2514 1.656587 TGGTAATGGCCACTCTCTGT 58.343 50.000 8.16 0.00 32.81 3.41
2136 2574 7.043590 GCATGAAAAATCTGCATGTATGTTCTC 60.044 37.037 0.00 0.00 41.01 2.87
2440 2878 8.777413 CATACTTGTGAGTGATTCTTTTCTTGA 58.223 33.333 0.00 0.00 36.60 3.02
2480 2918 5.986135 GGCAATCTACTTAGTGTCGATGAAT 59.014 40.000 0.00 0.00 32.37 2.57
2679 3117 5.505324 GCAACTCATCTGCATATGTCCTTTC 60.505 44.000 11.42 0.00 39.69 2.62
2684 3122 7.071069 TCATCTGCATATGTCCTTTCACTAT 57.929 36.000 11.42 0.00 0.00 2.12
2685 3123 7.512130 TCATCTGCATATGTCCTTTCACTATT 58.488 34.615 11.42 0.00 0.00 1.73
2686 3124 7.994911 TCATCTGCATATGTCCTTTCACTATTT 59.005 33.333 11.42 0.00 0.00 1.40
2717 3155 4.024670 TGGACATGATTGGAATGCATTGA 58.975 39.130 18.59 2.79 0.00 2.57
2746 3184 8.950208 AGCTATCGCCCTATAATTTATTCTTC 57.050 34.615 0.00 0.00 36.60 2.87
2748 3186 7.042658 GCTATCGCCCTATAATTTATTCTTCCG 60.043 40.741 0.00 0.00 0.00 4.30
2786 3224 6.584185 TTGGAAGTTAGAATTAAAGGGTGC 57.416 37.500 0.00 0.00 0.00 5.01
2972 3411 9.559732 TGCACTGCATATAAGTTAATTATCTGT 57.440 29.630 0.00 0.00 32.86 3.41
3045 3484 1.763968 AGTCTATGTGCCAGCGACTA 58.236 50.000 0.00 0.00 33.53 2.59
3057 3496 3.615351 GCCAGCGACTATCCTTCTATTCC 60.615 52.174 0.00 0.00 0.00 3.01
3072 3511 4.328536 TCTATTCCGCTGCTTAACCAAAA 58.671 39.130 0.00 0.00 0.00 2.44
3073 3512 4.762765 TCTATTCCGCTGCTTAACCAAAAA 59.237 37.500 0.00 0.00 0.00 1.94
3376 3816 2.967362 TGTTCAGGTTAGTATGCACGG 58.033 47.619 0.00 0.00 0.00 4.94
3426 3866 6.959361 TGTCAGCTCTGTTGTTTCTAAAATC 58.041 36.000 0.00 0.00 0.00 2.17
3438 3878 7.562454 TGTTTCTAAAATCGACCTTGAAAGT 57.438 32.000 0.00 0.00 0.00 2.66
3455 3895 4.041444 TGAAAGTTTAAGTACCGCCCCTTA 59.959 41.667 0.00 0.00 0.00 2.69
3457 3897 5.955961 AAGTTTAAGTACCGCCCCTTATA 57.044 39.130 0.00 0.00 0.00 0.98
3523 3989 7.624360 AATTTCATTTGGCTGAGATTACGTA 57.376 32.000 0.00 0.00 30.58 3.57
3587 4053 1.707632 TGCATGGTTACGCAATTTGC 58.292 45.000 11.42 11.42 40.69 3.68
3598 4064 4.989279 ACGCAATTTGCCTGATCTAATT 57.011 36.364 15.45 0.00 41.12 1.40
3626 4092 5.140454 ACAAACTGATATAATTCCCTGGCC 58.860 41.667 0.00 0.00 0.00 5.36
3674 4140 2.147958 TGTAACGGTGGTTCATGCTTC 58.852 47.619 0.00 0.00 37.58 3.86
3743 4209 4.689345 CACCTTAAGAAAGTCAACCCTACG 59.311 45.833 3.36 0.00 0.00 3.51
3799 4265 4.326826 CCTAGATTCAACTGCCACTCAAA 58.673 43.478 0.00 0.00 0.00 2.69
3829 4295 7.581011 AATTTCATTTTCAACGCCTAACATC 57.419 32.000 0.00 0.00 0.00 3.06
3955 4421 7.060421 TCATTTTGTTGAACTAAAGAGGGTCT 58.940 34.615 10.35 0.00 0.00 3.85
4009 4475 7.426606 TGCCTACCTAACATACAGTGAAATA 57.573 36.000 0.00 0.00 0.00 1.40
4010 4476 7.270047 TGCCTACCTAACATACAGTGAAATAC 58.730 38.462 0.00 0.00 0.00 1.89
4011 4477 7.125204 TGCCTACCTAACATACAGTGAAATACT 59.875 37.037 0.00 0.00 41.36 2.12
4079 4545 6.856135 AATGATGCATAGTACAGACACATG 57.144 37.500 0.00 0.00 0.00 3.21
4510 4976 8.378565 AGGTAGAATCTCATTTCTTCTTTGTGA 58.621 33.333 0.00 0.00 37.20 3.58
4511 4977 9.003658 GGTAGAATCTCATTTCTTCTTTGTGAA 57.996 33.333 0.00 0.00 37.20 3.18
4599 5072 4.461781 CAGTCCATGAAATTGAAGGAGCTT 59.538 41.667 0.00 0.00 0.00 3.74
5292 5767 6.719829 AGTTTCCACATGCATATGATCATCAT 59.280 34.615 12.53 5.24 40.72 2.45
5322 5798 0.612229 CCCAGCTCGGCATCTCATAT 59.388 55.000 0.00 0.00 0.00 1.78
5368 5844 6.363882 TCCATAAGTTTCCACATGCATATGA 58.636 36.000 6.52 0.00 37.73 2.15
5381 5857 8.520351 CCACATGCATATGATCATCAACTATTT 58.480 33.333 12.53 0.00 37.73 1.40
5382 5858 9.908152 CACATGCATATGATCATCAACTATTTT 57.092 29.630 12.53 0.00 37.73 1.82
5421 5899 3.003897 TCGGTGTTCATTTAGCCAACAAC 59.996 43.478 0.00 0.00 34.87 3.32
5436 5914 4.839121 CCAACAACCTGTAGGCAGTTATA 58.161 43.478 7.87 0.00 41.02 0.98
5525 6005 6.888632 ACCTCATCTTTCTGCAAATAGTTGAT 59.111 34.615 7.18 0.00 36.83 2.57
5536 6016 4.263911 GCAAATAGTTGATTCTTCTTGCGC 59.736 41.667 7.18 0.00 36.83 6.09
5584 6064 4.701651 TCAGGATTGAGTGAATCGCATTTT 59.298 37.500 0.00 0.00 41.45 1.82
5632 6112 7.496920 TGTGAAATCATTGATCTCCACATCTAC 59.503 37.037 17.36 2.70 0.00 2.59
5773 6253 9.717942 TTTTTCCATAGTATTCATTTTGTTGGG 57.282 29.630 0.00 0.00 0.00 4.12
5831 6311 5.596361 TCCTTTGTTTTTCCTGTGCTATCAA 59.404 36.000 0.00 0.00 0.00 2.57
5864 6344 9.869757 CCAAAATTTTATAGGGTACAAAAGGAG 57.130 33.333 2.44 0.00 0.00 3.69
5904 6384 8.490355 CCTGTGTTTTTCTTATTCTTGCATTTC 58.510 33.333 0.00 0.00 0.00 2.17
5915 6395 5.824904 TTCTTGCATTTCTAGAATCCTGC 57.175 39.130 20.15 20.15 32.89 4.85
5932 6412 0.908910 TGCGAATCAAAGAGGCCCTA 59.091 50.000 0.00 0.00 0.00 3.53
5968 6453 1.213182 TGGTGTACAAAGTGCAAGGGA 59.787 47.619 0.00 0.00 28.81 4.20
5972 6457 2.890311 TGTACAAAGTGCAAGGGAATGG 59.110 45.455 0.00 0.00 0.00 3.16
6057 6542 2.557924 GTCATTCATGGTTGGACTGCAA 59.442 45.455 0.00 0.00 0.00 4.08
6070 6555 0.254178 ACTGCAATGGAGCGATCCTT 59.746 50.000 22.18 12.31 37.31 3.36
6071 6556 0.661552 CTGCAATGGAGCGATCCTTG 59.338 55.000 22.18 21.18 37.31 3.61
6082 6567 2.770048 ATCCTTGGCGCCCTAGCT 60.770 61.111 26.77 8.42 36.60 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.133668 GCAGAAGATTAGGTGCCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
11 12 0.255890 GCAGAAGATTAGGTGCCCCA 59.744 55.000 0.00 0.00 0.00 4.96
12 13 0.548510 AGCAGAAGATTAGGTGCCCC 59.451 55.000 0.00 0.00 36.54 5.80
26 27 1.079612 CACACGGATCAGCAGCAGA 60.080 57.895 0.00 0.00 0.00 4.26
81 83 2.167693 AGAAACGTGGTGACTCACTCAA 59.832 45.455 9.08 0.00 35.63 3.02
82 84 1.754803 AGAAACGTGGTGACTCACTCA 59.245 47.619 9.08 3.13 35.63 3.41
234 270 3.226346 TGGACTGTGCTACGTACATTC 57.774 47.619 0.00 0.00 30.04 2.67
237 273 2.353307 CCATTGGACTGTGCTACGTACA 60.353 50.000 0.00 0.00 0.00 2.90
238 274 2.268298 CCATTGGACTGTGCTACGTAC 58.732 52.381 0.00 0.00 0.00 3.67
239 275 1.404986 GCCATTGGACTGTGCTACGTA 60.405 52.381 6.95 0.00 0.00 3.57
240 276 0.673644 GCCATTGGACTGTGCTACGT 60.674 55.000 6.95 0.00 0.00 3.57
241 277 1.695893 CGCCATTGGACTGTGCTACG 61.696 60.000 6.95 0.00 0.00 3.51
244 280 0.322816 AATCGCCATTGGACTGTGCT 60.323 50.000 6.95 0.00 0.00 4.40
245 281 0.527565 AAATCGCCATTGGACTGTGC 59.472 50.000 6.95 0.00 0.00 4.57
246 282 2.598589 CAAAATCGCCATTGGACTGTG 58.401 47.619 6.95 0.00 0.00 3.66
252 291 0.740516 GTGCCCAAAATCGCCATTGG 60.741 55.000 0.00 0.00 44.61 3.16
283 322 3.177600 CCGTCGGCAAATGGACTG 58.822 61.111 0.00 0.00 0.00 3.51
336 375 2.358898 ACACATTCTTTGACCTGTGCAC 59.641 45.455 10.75 10.75 42.07 4.57
370 409 4.336713 TCAGACTACTCCAGTGATCATTCG 59.663 45.833 0.00 0.00 37.72 3.34
467 511 2.699160 ACATGCCTATCAGATGGGACT 58.301 47.619 16.97 0.00 31.57 3.85
494 538 2.214376 ATCAGATGTCCCCGCAAAAA 57.786 45.000 0.00 0.00 0.00 1.94
495 539 2.421388 CCTATCAGATGTCCCCGCAAAA 60.421 50.000 0.00 0.00 0.00 2.44
496 540 1.140852 CCTATCAGATGTCCCCGCAAA 59.859 52.381 0.00 0.00 0.00 3.68
497 541 0.758734 CCTATCAGATGTCCCCGCAA 59.241 55.000 0.00 0.00 0.00 4.85
498 542 1.758440 GCCTATCAGATGTCCCCGCA 61.758 60.000 0.00 0.00 0.00 5.69
499 543 1.004440 GCCTATCAGATGTCCCCGC 60.004 63.158 0.00 0.00 0.00 6.13
500 544 0.979665 ATGCCTATCAGATGTCCCCG 59.020 55.000 0.00 0.00 0.00 5.73
501 545 1.701847 ACATGCCTATCAGATGTCCCC 59.298 52.381 0.00 0.00 0.00 4.81
502 546 3.144506 CAACATGCCTATCAGATGTCCC 58.855 50.000 0.00 0.00 29.93 4.46
503 547 3.812053 GTCAACATGCCTATCAGATGTCC 59.188 47.826 0.00 0.00 29.93 4.02
504 548 3.492383 CGTCAACATGCCTATCAGATGTC 59.508 47.826 0.00 0.00 29.93 3.06
505 549 3.118629 ACGTCAACATGCCTATCAGATGT 60.119 43.478 0.00 0.00 31.54 3.06
506 550 3.246936 CACGTCAACATGCCTATCAGATG 59.753 47.826 0.00 0.00 0.00 2.90
507 551 3.461061 CACGTCAACATGCCTATCAGAT 58.539 45.455 0.00 0.00 0.00 2.90
508 552 2.892374 CACGTCAACATGCCTATCAGA 58.108 47.619 0.00 0.00 0.00 3.27
509 553 1.328680 GCACGTCAACATGCCTATCAG 59.671 52.381 0.00 0.00 35.73 2.90
510 554 1.338579 TGCACGTCAACATGCCTATCA 60.339 47.619 0.00 0.00 41.33 2.15
511 555 1.368641 TGCACGTCAACATGCCTATC 58.631 50.000 0.00 0.00 41.33 2.08
512 556 1.739466 CTTGCACGTCAACATGCCTAT 59.261 47.619 0.00 0.00 41.33 2.57
513 557 1.155889 CTTGCACGTCAACATGCCTA 58.844 50.000 0.00 0.00 41.33 3.93
514 558 0.534877 TCTTGCACGTCAACATGCCT 60.535 50.000 0.00 0.00 41.33 4.75
515 559 0.310543 TTCTTGCACGTCAACATGCC 59.689 50.000 0.00 0.00 41.33 4.40
516 560 1.780860 GTTTCTTGCACGTCAACATGC 59.219 47.619 0.00 0.00 42.40 4.06
517 561 2.384382 GGTTTCTTGCACGTCAACATG 58.616 47.619 9.19 0.00 0.00 3.21
518 562 1.336755 GGGTTTCTTGCACGTCAACAT 59.663 47.619 9.19 0.00 0.00 2.71
519 563 0.736053 GGGTTTCTTGCACGTCAACA 59.264 50.000 9.19 0.00 0.00 3.33
568 614 3.118261 TCAAGGGTGATTCATCTGCCTAC 60.118 47.826 0.00 0.00 0.00 3.18
593 640 5.406767 TGATTTTGCTGAAATTTGTGCAC 57.593 34.783 10.75 10.75 38.06 4.57
622 672 4.331443 GCCACACTTACCCTTTTTGTTTTG 59.669 41.667 0.00 0.00 0.00 2.44
623 673 4.224147 AGCCACACTTACCCTTTTTGTTTT 59.776 37.500 0.00 0.00 0.00 2.43
633 892 1.675641 CCAGCAGCCACACTTACCC 60.676 63.158 0.00 0.00 0.00 3.69
636 895 0.698238 AATCCCAGCAGCCACACTTA 59.302 50.000 0.00 0.00 0.00 2.24
720 979 8.125978 ACAAATAAGATGATTCCTCTTTGCAA 57.874 30.769 9.12 0.00 34.81 4.08
722 981 8.897752 ACTACAAATAAGATGATTCCTCTTTGC 58.102 33.333 9.12 0.00 34.81 3.68
748 1007 5.186215 TGAAACGTTATCTGGAGGTCATACA 59.814 40.000 0.00 0.00 0.00 2.29
749 1008 5.657474 TGAAACGTTATCTGGAGGTCATAC 58.343 41.667 0.00 0.00 0.00 2.39
754 1013 7.881232 TCTTATTTTGAAACGTTATCTGGAGGT 59.119 33.333 0.00 0.00 0.00 3.85
755 1014 8.263940 TCTTATTTTGAAACGTTATCTGGAGG 57.736 34.615 0.00 0.00 0.00 4.30
757 1016 9.887406 GTTTCTTATTTTGAAACGTTATCTGGA 57.113 29.630 0.00 0.00 42.16 3.86
791 1054 1.523938 GGGCTTGGATCCGTACAGC 60.524 63.158 7.39 11.43 0.00 4.40
819 1082 0.256752 TGACCAATCCAGCCCAGATG 59.743 55.000 0.00 0.00 0.00 2.90
820 1083 1.229131 ATGACCAATCCAGCCCAGAT 58.771 50.000 0.00 0.00 0.00 2.90
821 1084 1.002069 AATGACCAATCCAGCCCAGA 58.998 50.000 0.00 0.00 0.00 3.86
822 1085 2.301346 GTAATGACCAATCCAGCCCAG 58.699 52.381 0.00 0.00 0.00 4.45
836 1099 0.251916 CGTCCTGGGCTTGGTAATGA 59.748 55.000 0.00 0.00 0.00 2.57
837 1100 0.748005 CCGTCCTGGGCTTGGTAATG 60.748 60.000 0.00 0.00 0.00 1.90
838 1101 0.912487 TCCGTCCTGGGCTTGGTAAT 60.912 55.000 0.00 0.00 38.76 1.89
839 1102 1.536907 TCCGTCCTGGGCTTGGTAA 60.537 57.895 0.00 0.00 38.76 2.85
840 1103 2.120940 TCCGTCCTGGGCTTGGTA 59.879 61.111 0.00 0.00 38.76 3.25
841 1104 3.637273 GTCCGTCCTGGGCTTGGT 61.637 66.667 0.00 0.00 40.15 3.67
843 1106 4.760047 CGGTCCGTCCTGGGCTTG 62.760 72.222 2.08 0.00 44.07 4.01
848 1111 4.112341 GTCGTCGGTCCGTCCTGG 62.112 72.222 11.88 0.00 40.09 4.45
860 1123 3.998672 TGGGGCTTGACCGTCGTC 61.999 66.667 0.00 0.00 40.62 4.20
861 1124 4.309950 GTGGGGCTTGACCGTCGT 62.310 66.667 0.00 0.00 40.62 4.34
934 1202 2.092914 AGAGGAAACCCTAAGAATGCGG 60.093 50.000 0.00 0.00 33.25 5.69
1128 1416 0.976073 GAGGTGATCGGGTCAGGGAA 60.976 60.000 0.00 0.00 37.56 3.97
1149 1437 1.553248 TCTGATCGTCAATTTCCCCGT 59.447 47.619 0.00 0.00 0.00 5.28
1160 1449 7.697710 TCATAATTTGCACATTTTCTGATCGTC 59.302 33.333 2.94 0.00 0.00 4.20
1211 1505 5.826737 TGCTCTATGTAGTCTACCTTACCAC 59.173 44.000 7.56 0.00 0.00 4.16
1378 1813 7.259882 TGCAACTTTGAATATAGCAATCCAAG 58.740 34.615 0.00 0.00 0.00 3.61
1380 1815 6.772360 TGCAACTTTGAATATAGCAATCCA 57.228 33.333 0.00 0.00 0.00 3.41
1497 1932 5.154222 GGGTTTGCTAAGAAAAATCTCACG 58.846 41.667 0.00 0.00 0.00 4.35
1520 1957 6.426587 CCAATTTATCCATACCCCTCATAGG 58.573 44.000 0.00 0.00 34.30 2.57
1521 1958 5.888161 GCCAATTTATCCATACCCCTCATAG 59.112 44.000 0.00 0.00 0.00 2.23
1560 1997 6.582677 ACGTATCTGATTAGGGAGAGATTG 57.417 41.667 0.00 0.00 0.00 2.67
1564 2001 6.150396 ACAAACGTATCTGATTAGGGAGAG 57.850 41.667 0.00 0.00 0.00 3.20
1802 2240 6.449698 ACATGCTTCTTTACTCAACAAATGG 58.550 36.000 0.00 0.00 0.00 3.16
1825 2263 1.205417 CCCATGGCCAATCAGACAAAC 59.795 52.381 10.96 0.00 0.00 2.93
1908 2346 3.244630 GGGTGGTATCATACGCCCATTTA 60.245 47.826 16.98 0.00 41.36 1.40
2009 2447 6.036953 GGACATGATCAGACACTTGAATCTTC 59.963 42.308 0.00 0.00 0.00 2.87
2440 2878 5.014858 AGATTGCCTGACAGAATCAACATT 58.985 37.500 15.53 0.42 36.69 2.71
2480 2918 7.918076 ACACACTCTGAAGGAGGAAATAAATA 58.082 34.615 0.00 0.00 45.83 1.40
2485 2923 4.020128 GGTACACACTCTGAAGGAGGAAAT 60.020 45.833 0.00 0.00 45.83 2.17
2743 3181 1.604604 TTTTCAAGCACCTCCGGAAG 58.395 50.000 5.23 0.57 0.00 3.46
2746 3184 1.067635 CCAATTTTCAAGCACCTCCGG 60.068 52.381 0.00 0.00 0.00 5.14
2748 3186 3.321968 ACTTCCAATTTTCAAGCACCTCC 59.678 43.478 0.00 0.00 0.00 4.30
2875 3314 3.846360 CAGTAGAAACCTAACGACCAGG 58.154 50.000 0.00 0.00 39.25 4.45
2972 3411 6.882610 ATCAGCAAATCTCACAACAGTAAA 57.117 33.333 0.00 0.00 0.00 2.01
3045 3484 4.381411 GTTAAGCAGCGGAATAGAAGGAT 58.619 43.478 0.00 0.00 0.00 3.24
3106 3545 9.846248 GTTCAGCAATAAGAAATGAACAATAGT 57.154 29.630 10.57 0.00 45.67 2.12
3426 3866 4.376717 GCGGTACTTAAACTTTCAAGGTCG 60.377 45.833 0.00 0.00 0.00 4.79
3438 3878 4.297768 ACCTATAAGGGGCGGTACTTAAA 58.702 43.478 0.00 0.00 40.58 1.52
3455 3895 6.491714 AGATGCAGTTGACAAGATACCTAT 57.508 37.500 0.00 0.00 0.00 2.57
3457 3897 4.833478 AGATGCAGTTGACAAGATACCT 57.167 40.909 0.00 0.00 0.00 3.08
3523 3989 6.656270 TCAATGCTTCAAGTGAGAATGTATGT 59.344 34.615 0.00 0.00 0.00 2.29
3598 4064 9.573166 CCAGGGAATTATATCAGTTTGTATGAA 57.427 33.333 0.00 0.00 0.00 2.57
3626 4092 1.227556 GTATAGCACACCAGGGGCG 60.228 63.158 0.00 0.00 0.00 6.13
3743 4209 7.039270 ACCTTTGTTTTGGACATTTAGACAAC 58.961 34.615 0.00 0.00 38.26 3.32
3799 4265 9.868277 TTAGGCGTTGAAAATGAAATTAATGAT 57.132 25.926 0.00 0.00 33.67 2.45
3829 4295 2.568509 AGGTTCCAAATTTGCATCCCTG 59.431 45.455 12.92 0.00 0.00 4.45
3870 4336 5.852282 AGTTCATTTGGTTGCAGTAAGTT 57.148 34.783 0.00 0.00 0.00 2.66
3928 4394 7.060421 ACCCTCTTTAGTTCAACAAAATGAGA 58.940 34.615 14.96 0.98 0.00 3.27
3965 4431 3.814283 GCATGCAAATTTGGAACCTTGAA 59.186 39.130 16.71 0.00 30.51 2.69
4079 4545 2.219674 CGTGCTTTGAGAATCGGCTATC 59.780 50.000 0.00 0.00 38.61 2.08
4189 4655 4.564782 TGTCCTGCAGAGAGATCATTTT 57.435 40.909 17.39 0.00 0.00 1.82
4413 4879 4.791411 GCATCCACGCAAACTTCTTTTACA 60.791 41.667 0.00 0.00 0.00 2.41
4511 4977 2.029838 CTTCCATAAGCTTCGGTGCT 57.970 50.000 0.00 0.00 46.40 4.40
4557 5030 2.238144 CTGAGATGGAGCCTGGAAAGAA 59.762 50.000 0.00 0.00 0.00 2.52
4563 5036 0.979709 TGGACTGAGATGGAGCCTGG 60.980 60.000 0.00 0.00 0.00 4.45
4616 5089 6.727824 AGTCGGAGAAAATAGTTGATTGTG 57.272 37.500 0.00 0.00 39.69 3.33
4632 5105 1.666700 CGTCTACAGGAGAAGTCGGAG 59.333 57.143 0.00 0.00 35.37 4.63
4689 5162 1.268999 GCCAAACGACAATGTGAAGCA 60.269 47.619 0.00 0.00 0.00 3.91
5322 5798 5.067283 GGAGCAAAGTTTGTTTGGAGACTTA 59.933 40.000 16.70 0.00 32.44 2.24
5381 5857 0.965363 GATGCCGAGCTGGGGAAAAA 60.965 55.000 14.02 0.00 38.63 1.94
5382 5858 1.378514 GATGCCGAGCTGGGGAAAA 60.379 57.895 14.02 0.00 38.63 2.29
5436 5914 7.872138 TCAGGATTAACTGAACAAATATCCCT 58.128 34.615 0.00 0.00 44.03 4.20
5525 6005 1.668751 AGTGAAAACGCGCAAGAAGAA 59.331 42.857 5.73 0.00 43.02 2.52
5536 6016 1.933181 TCAGACAGCACAGTGAAAACG 59.067 47.619 4.15 0.00 0.00 3.60
5584 6064 6.146347 CACAATGCACAAACATGATTGATTCA 59.854 34.615 21.13 14.57 39.12 2.57
5773 6253 5.532779 AGAGGTTTGAGTGGATGAAAAGTTC 59.467 40.000 0.00 0.00 0.00 3.01
5780 6260 4.437682 ACAAAGAGGTTTGAGTGGATGA 57.562 40.909 4.91 0.00 45.22 2.92
5831 6311 9.369672 TGTACCCTATAAAATTTTGGAAGTGTT 57.630 29.630 13.76 0.00 0.00 3.32
5864 6344 1.139058 ACACAGGAACAGAGTGTCACC 59.861 52.381 0.00 0.00 42.36 4.02
5904 6384 4.749099 CCTCTTTGATTCGCAGGATTCTAG 59.251 45.833 0.00 0.00 0.00 2.43
5915 6395 1.134401 TGCTAGGGCCTCTTTGATTCG 60.134 52.381 10.74 0.00 37.74 3.34
5932 6412 7.124573 TGTACACCAAAGTCATATCTATGCT 57.875 36.000 0.00 0.00 33.76 3.79
5968 6453 1.811860 GCATCGCTTTGCCTCCATT 59.188 52.632 0.00 0.00 36.60 3.16
6048 6533 0.462581 GATCGCTCCATTGCAGTCCA 60.463 55.000 0.00 0.00 0.00 4.02
6057 6542 2.109799 CGCCAAGGATCGCTCCAT 59.890 61.111 8.23 0.00 44.79 3.41
6070 6555 2.359850 CACAAAGCTAGGGCGCCA 60.360 61.111 30.85 7.71 44.37 5.69
6071 6556 3.815396 GCACAAAGCTAGGGCGCC 61.815 66.667 21.18 21.18 44.37 6.53


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

AutoCloner maintained by Alex Coulton.