Multiple sequence alignment - TraesCS4B01G187900

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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 TraesCS4B01G187900 chr4B 100.000 7394 0 0 1 7394 408960142 408952749 0.000000e+00 13655.0
1 TraesCS4B01G187900 chr4D 95.904 4980 131 23 156 5110 329011075 329006144 0.000000e+00 7998.0
2 TraesCS4B01G187900 chr4D 96.390 1219 33 3 5275 6489 329005969 329004758 0.000000e+00 1997.0
3 TraesCS4B01G187900 chr4D 88.837 860 43 26 6477 7333 329001243 329000434 0.000000e+00 1007.0
4 TraesCS4B01G187900 chr4D 97.902 143 3 0 21 163 329013774 329013632 1.590000e-61 248.0
5 TraesCS4B01G187900 chr4D 97.333 75 2 0 7320 7394 329000224 329000150 2.170000e-25 128.0
6 TraesCS4B01G187900 chr4A 95.287 4286 129 31 874 5126 141118162 141122407 0.000000e+00 6728.0
7 TraesCS4B01G187900 chr4A 93.967 779 40 5 6618 7394 141124170 141124943 0.000000e+00 1171.0
8 TraesCS4B01G187900 chr4A 91.652 587 30 8 5299 5882 141122829 141123399 0.000000e+00 795.0
9 TraesCS4B01G187900 chr4A 89.828 580 43 6 5911 6484 141123505 141124074 0.000000e+00 730.0
10 TraesCS4B01G187900 chr4A 94.536 183 6 4 5125 5304 141122489 141122670 5.650000e-71 279.0
11 TraesCS4B01G187900 chr4A 91.216 148 12 1 9 156 671960158 671960012 4.520000e-47 200.0
12 TraesCS4B01G187900 chr2D 97.579 2396 48 5 2440 4826 407216995 407219389 0.000000e+00 4095.0
13 TraesCS4B01G187900 chr2D 96.473 1219 35 2 5275 6489 407220115 407221329 0.000000e+00 2006.0
14 TraesCS4B01G187900 chr2D 95.582 1245 40 6 1028 2259 407215758 407217000 0.000000e+00 1980.0
15 TraesCS4B01G187900 chr2D 87.791 860 52 27 6478 7333 407223661 407224471 0.000000e+00 957.0
16 TraesCS4B01G187900 chr2D 97.270 403 11 0 21 423 407208970 407208568 0.000000e+00 684.0
17 TraesCS4B01G187900 chr2D 93.275 342 12 4 566 899 407208109 407208447 1.850000e-135 494.0
18 TraesCS4B01G187900 chr2D 95.987 299 7 3 4817 5110 407219414 407219712 1.440000e-131 481.0
19 TraesCS4B01G187900 chr2D 93.443 122 4 2 887 1008 407208566 407208449 2.120000e-40 178.0
20 TraesCS4B01G187900 chr2D 89.394 132 10 2 329 460 278396630 278396757 5.940000e-36 163.0
21 TraesCS4B01G187900 chr2D 97.333 75 2 0 7320 7394 407224489 407224563 2.170000e-25 128.0
22 TraesCS4B01G187900 chr2D 95.745 47 2 0 21 67 407208059 407208105 7.960000e-10 76.8
23 TraesCS4B01G187900 chr1B 97.374 1942 43 6 2866 4801 135942030 135943969 0.000000e+00 3297.0
24 TraesCS4B01G187900 chr1B 95.615 2007 64 10 1080 3069 135940035 135942034 0.000000e+00 3197.0
25 TraesCS4B01G187900 chr1B 96.654 1315 32 5 5275 6582 135957940 135959249 0.000000e+00 2174.0
26 TraesCS4B01G187900 chr1B 90.870 701 44 12 6694 7394 135960178 135960858 0.000000e+00 922.0
27 TraesCS4B01G187900 chr1B 88.928 569 23 11 403 964 135938165 135938700 0.000000e+00 665.0
28 TraesCS4B01G187900 chr1B 95.278 360 7 3 4795 5144 135957561 135957920 5.010000e-156 562.0
29 TraesCS4B01G187900 chr1B 97.872 188 4 0 182 369 135937978 135938165 7.150000e-85 326.0
30 TraesCS4B01G187900 chr1B 84.615 286 23 9 154 430 29581496 29581223 1.580000e-66 265.0
31 TraesCS4B01G187900 chr1B 96.748 123 4 0 21 143 135937857 135937979 9.720000e-49 206.0
32 TraesCS4B01G187900 chr1B 95.918 49 2 0 970 1018 135938754 135938706 6.150000e-11 80.5
33 TraesCS4B01G187900 chr1B 97.619 42 1 0 6634 6675 135960137 135960178 1.030000e-08 73.1
34 TraesCS4B01G187900 chr1B 94.444 36 2 0 6580 6615 135960111 135960146 1.000000e-03 56.5
35 TraesCS4B01G187900 chrUn 96.654 1315 32 5 5275 6582 326354676 326355985 0.000000e+00 2174.0
36 TraesCS4B01G187900 chrUn 95.556 360 6 3 4795 5144 326354297 326354656 1.080000e-157 568.0
37 TraesCS4B01G187900 chr7D 81.013 632 80 28 6775 7394 113714445 113715048 4.040000e-127 466.0
38 TraesCS4B01G187900 chr7B 80.757 634 84 24 6775 7394 73328932 73329541 1.880000e-125 460.0
39 TraesCS4B01G187900 chr7B 82.261 513 54 20 6894 7394 73233455 73233942 6.910000e-110 409.0
40 TraesCS4B01G187900 chr7B 82.227 512 52 22 6894 7392 73311190 73311675 8.930000e-109 405.0
41 TraesCS4B01G187900 chr7B 81.029 311 42 14 154 460 595525488 595525785 1.600000e-56 231.0
42 TraesCS4B01G187900 chr7A 80.854 632 79 29 6775 7394 118573634 118574235 6.760000e-125 459.0
43 TraesCS4B01G187900 chr5B 82.699 289 33 10 154 430 595292003 595291720 2.670000e-59 241.0
44 TraesCS4B01G187900 chr3B 87.678 211 20 4 256 466 130254645 130254441 2.670000e-59 241.0
45 TraesCS4B01G187900 chr3B 91.216 148 12 1 9 156 730552935 730552789 4.520000e-47 200.0
46 TraesCS4B01G187900 chr3D 85.153 229 26 6 237 464 83699013 83698792 2.080000e-55 228.0
47 TraesCS4B01G187900 chr3D 88.406 138 12 2 329 466 575392447 575392314 5.940000e-36 163.0
48 TraesCS4B01G187900 chr1A 81.139 281 34 15 154 430 518050765 518050500 2.700000e-49 207.0
49 TraesCS4B01G187900 chr1A 80.071 281 37 15 154 430 586704516 586704781 2.720000e-44 191.0
50 TraesCS4B01G187900 chr2A 91.892 148 11 1 9 156 591660647 591660501 9.720000e-49 206.0
51 TraesCS4B01G187900 chr5A 90.541 148 13 1 9 156 549015493 549015639 2.100000e-45 195.0
52 TraesCS4B01G187900 chr3A 87.879 165 18 2 296 460 746445346 746445184 7.570000e-45 193.0
53 TraesCS4B01G187900 chr3A 79.359 281 39 15 154 430 54339294 54339559 5.890000e-41 180.0
54 TraesCS4B01G187900 chr2B 87.500 160 12 2 313 466 436539386 436539543 2.120000e-40 178.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G187900 chr4B 408952749 408960142 7393 True 13655.000000 13655 100.000000 1 7394 1 chr4B.!!$R1 7393
1 TraesCS4B01G187900 chr4D 329000150 329013774 13624 True 2275.600000 7998 95.273200 21 7394 5 chr4D.!!$R1 7373
2 TraesCS4B01G187900 chr4A 141118162 141124943 6781 False 1940.600000 6728 93.054000 874 7394 5 chr4A.!!$F1 6520
3 TraesCS4B01G187900 chr2D 407215758 407224563 8805 False 1607.833333 4095 95.124167 1028 7394 6 chr2D.!!$F3 6366
4 TraesCS4B01G187900 chr2D 407208449 407208970 521 True 431.000000 684 95.356500 21 1008 2 chr2D.!!$R1 987
5 TraesCS4B01G187900 chr1B 135937857 135943969 6112 False 1538.200000 3297 95.307400 21 4801 5 chr1B.!!$F1 4780
6 TraesCS4B01G187900 chr1B 135957561 135960858 3297 False 757.520000 2174 94.973000 4795 7394 5 chr1B.!!$F2 2599
7 TraesCS4B01G187900 chrUn 326354297 326355985 1688 False 1371.000000 2174 96.105000 4795 6582 2 chrUn.!!$F1 1787
8 TraesCS4B01G187900 chr7D 113714445 113715048 603 False 466.000000 466 81.013000 6775 7394 1 chr7D.!!$F1 619
9 TraesCS4B01G187900 chr7B 73328932 73329541 609 False 460.000000 460 80.757000 6775 7394 1 chr7B.!!$F3 619
10 TraesCS4B01G187900 chr7A 118573634 118574235 601 False 459.000000 459 80.854000 6775 7394 1 chr7A.!!$F1 619

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
904 3480 0.179084 CGGGGCAAGAAATAGCGAGA 60.179 55.0 0.00 0.0 0.00 4.04 F
1613 5428 0.321919 GCAGTGGAGATGTCCTTGCA 60.322 55.0 24.24 0.0 45.77 4.08 F
3063 7089 0.817013 ACGCTATGTTGCCATTTGGG 59.183 50.0 0.00 0.0 40.85 4.12 F
3975 8008 0.817654 GCAGGGGCATAACCTTGTTC 59.182 55.0 0.00 0.0 39.60 3.18 F
3997 8030 0.036388 TTCTCCACTTGGGACGATGC 60.036 55.0 0.00 0.0 42.15 3.91 F
5525 9988 0.183492 TGCTGATGATAGTTGCCCCC 59.817 55.0 0.00 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 5738 2.060567 ATGCCACTGCTGTCACACCT 62.061 55.0 0.00 0.0 38.71 4.00 R
3259 7285 0.744771 GGACTCGGACAAGGCAATCC 60.745 60.0 0.00 0.0 0.00 3.01 R
3986 8019 0.323302 TAGTTGCTGCATCGTCCCAA 59.677 50.0 1.84 0.0 0.00 4.12 R
5638 10101 0.740868 TCTGCTCAATGTGTAGCCGC 60.741 55.0 0.00 0.0 37.97 6.53 R
5912 10457 4.142204 TGCACACATCTGCAAAAGAAAGAA 60.142 37.5 0.00 0.0 44.28 2.52 R
6939 15896 0.770557 TAGTGGGGGCTGGTGAAAGT 60.771 55.0 0.00 0.0 0.00 2.66 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
226 2791 8.883731 AGGATTACTGAATGTTGATTTTACTCG 58.116 33.333 0.00 0.00 0.00 4.18
270 2835 3.845860 AGAGGGTTCTCTCACTGTACAA 58.154 45.455 0.00 0.00 46.79 2.41
373 2938 8.131731 AGTTTACTGAATCTTGTTTCTTTCTGC 58.868 33.333 0.00 0.00 0.00 4.26
397 2962 1.109920 TGGCTAGTGATCCTCGGCTC 61.110 60.000 9.44 0.00 33.13 4.70
400 2965 2.442413 GCTAGTGATCCTCGGCTCTAT 58.558 52.381 0.00 0.00 0.00 1.98
458 3023 1.759445 AGTAGACAAGCATCATCGGCT 59.241 47.619 0.00 0.00 45.15 5.52
501 3066 5.978919 TCGTACGTACATATTGATGTTTCCC 59.021 40.000 24.50 0.00 44.18 3.97
522 3087 1.476085 TGTCAAATTGGCTTATGCGGG 59.524 47.619 0.00 0.00 40.82 6.13
523 3088 1.476488 GTCAAATTGGCTTATGCGGGT 59.524 47.619 0.00 0.00 40.82 5.28
524 3089 1.476085 TCAAATTGGCTTATGCGGGTG 59.524 47.619 0.00 0.00 40.82 4.61
525 3090 1.204467 CAAATTGGCTTATGCGGGTGT 59.796 47.619 0.00 0.00 40.82 4.16
526 3091 2.425312 CAAATTGGCTTATGCGGGTGTA 59.575 45.455 0.00 0.00 40.82 2.90
527 3092 2.656947 ATTGGCTTATGCGGGTGTAT 57.343 45.000 0.00 0.00 40.82 2.29
528 3093 1.674359 TTGGCTTATGCGGGTGTATG 58.326 50.000 0.00 0.00 40.82 2.39
529 3094 0.817634 TGGCTTATGCGGGTGTATGC 60.818 55.000 0.00 0.00 40.82 3.14
530 3095 1.569493 GCTTATGCGGGTGTATGCG 59.431 57.895 0.00 0.00 0.00 4.73
605 3171 1.971695 CCCCGCCTTCAACCTGAAC 60.972 63.158 0.00 0.00 32.21 3.18
606 3172 2.325082 CCCGCCTTCAACCTGAACG 61.325 63.158 0.00 0.00 32.21 3.95
607 3173 1.597027 CCGCCTTCAACCTGAACGT 60.597 57.895 0.00 0.00 32.21 3.99
726 3292 4.840005 GTAGCAGGCAGGGGCGTC 62.840 72.222 0.00 0.00 42.47 5.19
820 3386 4.316823 AGCCGTCCTCCTGGTCCA 62.317 66.667 0.00 0.00 34.23 4.02
847 3413 4.309950 GTCAAGGTCGGCGTGGGT 62.310 66.667 6.85 0.00 0.00 4.51
870 3436 2.683933 GGGAACTCGAGCCAGGGA 60.684 66.667 13.61 0.00 0.00 4.20
903 3479 1.776034 GCGGGGCAAGAAATAGCGAG 61.776 60.000 0.00 0.00 0.00 5.03
904 3480 0.179084 CGGGGCAAGAAATAGCGAGA 60.179 55.000 0.00 0.00 0.00 4.04
908 3484 2.747446 GGGCAAGAAATAGCGAGAAACA 59.253 45.455 0.00 0.00 0.00 2.83
932 3512 1.771854 TGCTGTTTCTGTTAGGGTGGA 59.228 47.619 0.00 0.00 0.00 4.02
933 3513 2.173782 TGCTGTTTCTGTTAGGGTGGAA 59.826 45.455 0.00 0.00 0.00 3.53
1187 4992 0.906756 CTCCTCACCTCCTTCAGCCA 60.907 60.000 0.00 0.00 0.00 4.75
1191 4996 1.079543 CACCTCCTTCAGCCACTCG 60.080 63.158 0.00 0.00 0.00 4.18
1215 5020 3.114647 CTTCCTCGCCCTCTCGTCG 62.115 68.421 0.00 0.00 0.00 5.12
1244 5049 1.353103 GCATCAAGGTGCGGAATCG 59.647 57.895 0.00 0.00 35.10 3.34
1371 5176 2.683933 AGTTCGCCGACATCCCCT 60.684 61.111 0.00 0.00 0.00 4.79
1503 5308 4.521075 GCTGTTGCTATCTGGCGA 57.479 55.556 0.00 0.00 36.03 5.54
1504 5309 2.009888 GCTGTTGCTATCTGGCGAC 58.990 57.895 0.00 0.00 44.44 5.19
1509 5314 2.105128 GCTATCTGGCGACGTGCT 59.895 61.111 0.00 0.00 45.43 4.40
1510 5315 2.233654 GCTATCTGGCGACGTGCTG 61.234 63.158 0.00 0.00 45.43 4.41
1511 5316 1.139734 CTATCTGGCGACGTGCTGT 59.860 57.895 0.00 0.00 45.43 4.40
1512 5317 1.142185 CTATCTGGCGACGTGCTGTG 61.142 60.000 0.00 0.00 45.43 3.66
1513 5318 1.873270 TATCTGGCGACGTGCTGTGT 61.873 55.000 0.00 0.00 45.43 3.72
1514 5319 3.705638 CTGGCGACGTGCTGTGTG 61.706 66.667 0.00 0.00 45.43 3.82
1515 5320 4.522689 TGGCGACGTGCTGTGTGT 62.523 61.111 0.00 0.00 45.43 3.72
1516 5321 4.000557 GGCGACGTGCTGTGTGTG 62.001 66.667 0.00 0.00 45.43 3.82
1517 5322 4.649954 GCGACGTGCTGTGTGTGC 62.650 66.667 0.00 0.00 41.73 4.57
1518 5323 4.339809 CGACGTGCTGTGTGTGCG 62.340 66.667 0.00 0.00 0.00 5.34
1557 5372 4.275936 GTGTTTTTGCCTAGCAGAAGAAGA 59.724 41.667 0.00 0.00 40.61 2.87
1571 5386 1.223211 GAAGAGGAAGGCTGGGAGC 59.777 63.158 0.00 0.00 41.46 4.70
1601 5416 3.636231 CTTGGGACGGGCAGTGGA 61.636 66.667 0.00 0.00 0.00 4.02
1613 5428 0.321919 GCAGTGGAGATGTCCTTGCA 60.322 55.000 24.24 0.00 45.77 4.08
1818 5633 1.807742 TGTTTAAGCACATACCCGCAC 59.192 47.619 0.00 0.00 0.00 5.34
1923 5738 6.326375 GGTGTGTGTTTTGTATTTGTTCAGA 58.674 36.000 0.00 0.00 0.00 3.27
2188 6013 6.392354 CACTATGGATGTTTTTGCATCTGTT 58.608 36.000 6.11 0.00 43.41 3.16
2280 6105 8.974408 TGATCGTAATGACCTTTATATTCAACG 58.026 33.333 0.00 0.00 0.00 4.10
2371 6198 7.015680 TGGCCTAGAATCTCTAAATGATCTCT 58.984 38.462 3.32 0.00 0.00 3.10
2627 6457 9.315525 CTTTGAGCTAAGGGTCTTTTAGTATAC 57.684 37.037 0.00 0.00 40.29 1.47
2895 6921 1.831736 GTATGCCCTCCTGTACTGTGT 59.168 52.381 0.00 0.00 0.00 3.72
3063 7089 0.817013 ACGCTATGTTGCCATTTGGG 59.183 50.000 0.00 0.00 40.85 4.12
3112 7138 6.836527 AGTTCAAGCTGTATACTCTCTATGGT 59.163 38.462 4.17 0.00 0.00 3.55
3188 7214 7.618019 AGGAGAAATAGATGTGTTGGCTATA 57.382 36.000 0.00 0.00 0.00 1.31
3259 7285 3.717707 TGCGCAATAAGAAGCCTACTAG 58.282 45.455 8.16 0.00 0.00 2.57
3541 7567 5.066375 TGCTAATGTTCATCAGTTATGGTGC 59.934 40.000 0.00 0.00 37.47 5.01
3615 7643 4.290942 TCAAACCCTGTTTACAAATGGGT 58.709 39.130 12.67 12.67 44.21 4.51
3726 7759 1.950909 ACTATCACTGCTCTAGACCGC 59.049 52.381 0.00 0.00 0.00 5.68
3780 7813 5.529430 TCCGAAGCTTCATACACAAGAAAAA 59.471 36.000 25.47 0.00 0.00 1.94
3975 8008 0.817654 GCAGGGGCATAACCTTGTTC 59.182 55.000 0.00 0.00 39.60 3.18
3986 8019 3.933861 AACCTTGTTCTGTTCTCCACT 57.066 42.857 0.00 0.00 0.00 4.00
3997 8030 0.036388 TTCTCCACTTGGGACGATGC 60.036 55.000 0.00 0.00 42.15 3.91
4198 8234 6.827586 ATTTAGTTCCGGTGCAAAGAATTA 57.172 33.333 0.00 0.00 0.00 1.40
4254 8290 5.132502 AGGAAATATGGCGTCATTGATCAA 58.867 37.500 8.30 11.26 34.96 2.57
4411 8447 7.875554 TCACTGTTTGCATCTTTACTATGTACA 59.124 33.333 0.00 0.00 0.00 2.90
4770 8806 7.044798 CCTGGAGAAGGTACTATTTCTTCTTG 58.955 42.308 11.21 6.61 44.82 3.02
4812 8848 3.367703 GGAGCTTGTTGCATTGCATAACT 60.368 43.478 12.95 10.36 45.94 2.24
4813 8849 4.240096 GAGCTTGTTGCATTGCATAACTT 58.760 39.130 12.95 0.00 45.94 2.66
4814 8850 3.991773 AGCTTGTTGCATTGCATAACTTG 59.008 39.130 12.95 6.96 45.94 3.16
4815 8851 3.423907 GCTTGTTGCATTGCATAACTTGC 60.424 43.478 12.95 12.34 46.09 4.01
5069 9151 8.455903 TGTGTACTGTATTATGGAGTACTACC 57.544 38.462 1.66 3.60 41.71 3.18
5110 9198 1.571919 GGTTGTGCTATAGCGACTGG 58.428 55.000 19.55 0.00 45.83 4.00
5148 9361 1.867233 AGATAATGCACAACGCGGATC 59.133 47.619 12.47 0.00 46.97 3.36
5198 9411 4.489306 ACAATCAGGGTAGTTTAGCTCC 57.511 45.455 0.00 0.00 0.00 4.70
5300 9759 4.990543 TGTTCAGAATGTTCGTGATGTC 57.009 40.909 0.00 0.00 37.40 3.06
5310 9769 7.817478 AGAATGTTCGTGATGTCACTGTTATTA 59.183 33.333 11.03 0.00 44.34 0.98
5489 9952 2.139118 GTGTGAAGAGCAGTCTGGAAC 58.861 52.381 1.14 0.00 31.37 3.62
5525 9988 0.183492 TGCTGATGATAGTTGCCCCC 59.817 55.000 0.00 0.00 0.00 5.40
5638 10101 2.967362 TGGCAGTGACAAGTTATACGG 58.033 47.619 0.00 0.00 0.00 4.02
5644 10107 1.750206 TGACAAGTTATACGGCGGCTA 59.250 47.619 13.24 0.00 0.00 3.93
5765 10229 2.098770 GGGAGAGAAATGCAACATCAGC 59.901 50.000 0.00 0.00 0.00 4.26
5909 10454 5.945784 TGCCACTAATCTAAGCAAAACTGAT 59.054 36.000 0.00 0.00 0.00 2.90
5910 10455 6.434028 TGCCACTAATCTAAGCAAAACTGATT 59.566 34.615 0.00 0.00 0.00 2.57
5911 10456 6.749118 GCCACTAATCTAAGCAAAACTGATTG 59.251 38.462 0.00 0.00 0.00 2.67
5912 10457 7.575720 GCCACTAATCTAAGCAAAACTGATTGT 60.576 37.037 0.00 0.00 32.80 2.71
6121 10666 5.455392 GTTGACAAGGATGTGAAAGATGTG 58.545 41.667 0.00 0.00 40.74 3.21
6226 10771 4.811024 TCTGAAAATAGTGACGATGATGCC 59.189 41.667 0.00 0.00 0.00 4.40
6265 10810 1.137872 GTTGGCATGTCTCCGAGAGAT 59.862 52.381 2.17 2.17 40.98 2.75
6267 10812 1.137675 TGGCATGTCTCCGAGAGATTG 59.862 52.381 5.31 3.66 40.98 2.67
6283 10828 5.844004 AGAGATTGTTCGACTTTGTGTACT 58.156 37.500 0.00 0.00 0.00 2.73
6307 10852 8.416329 ACTGTCAAGATGTATTTTTCAAGCTTT 58.584 29.630 0.00 0.00 0.00 3.51
6315 10864 9.860898 GATGTATTTTTCAAGCTTTCCATAGTT 57.139 29.630 0.00 0.00 0.00 2.24
6363 10914 5.222631 GGAAGGTTGCACTAATTTTGACAG 58.777 41.667 0.00 0.00 0.00 3.51
6516 14597 1.490910 CCCCTGGAATCCTAAGTCACC 59.509 57.143 0.00 0.00 0.00 4.02
6532 14613 2.160417 GTCACCGCGTACTAGTACAAGT 59.840 50.000 28.03 19.53 35.87 3.16
6710 15659 0.041982 AACCACACCAACCCCAAGTT 59.958 50.000 0.00 0.00 40.16 2.66
6820 15773 0.318120 GGTGCCAATTGGACAACAGG 59.682 55.000 29.02 0.00 37.39 4.00
6825 15778 2.288395 GCCAATTGGACAACAGGTTCTG 60.288 50.000 29.02 0.00 37.39 3.02
6836 15789 3.188159 ACAGGTTCTGCTTCGTTAACA 57.812 42.857 6.39 0.00 34.37 2.41
6939 15896 0.834687 ACTCGACCCTGGCTTTGGTA 60.835 55.000 0.00 0.00 34.20 3.25
6967 15927 1.918800 GCCCCCACTACTCACCAGT 60.919 63.158 0.00 0.00 36.55 4.00
6969 15929 0.544357 CCCCCACTACTCACCAGTCA 60.544 60.000 0.00 0.00 33.62 3.41
6971 15931 0.608640 CCCACTACTCACCAGTCACC 59.391 60.000 0.00 0.00 33.62 4.02
6972 15932 1.338107 CCACTACTCACCAGTCACCA 58.662 55.000 0.00 0.00 33.62 4.17
6973 15933 1.000955 CCACTACTCACCAGTCACCAC 59.999 57.143 0.00 0.00 33.62 4.16
6974 15934 1.686587 CACTACTCACCAGTCACCACA 59.313 52.381 0.00 0.00 33.62 4.17
6975 15935 1.687123 ACTACTCACCAGTCACCACAC 59.313 52.381 0.00 0.00 33.62 3.82
6976 15936 1.000955 CTACTCACCAGTCACCACACC 59.999 57.143 0.00 0.00 33.62 4.16
7101 16064 2.957680 ACTCAACACATCATTTGCACCA 59.042 40.909 0.00 0.00 0.00 4.17
7308 16275 2.092429 TCAGGCAGTTCAACTTCACCTT 60.092 45.455 1.39 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.357034 TTCAACGCGTGAGGAGGC 60.357 61.111 14.98 0.00 37.61 4.70
5 6 1.289066 TCTTCAACGCGTGAGGAGG 59.711 57.895 14.98 12.00 37.43 4.30
6 7 4.966005 TCTTCAACGCGTGAGGAG 57.034 55.556 14.98 13.56 37.43 3.69
7 8 1.289066 CCTCTTCAACGCGTGAGGA 59.711 57.895 29.77 23.25 46.53 3.71
8 9 0.108615 ATCCTCTTCAACGCGTGAGG 60.109 55.000 28.43 28.43 45.36 3.86
9 10 0.994995 CATCCTCTTCAACGCGTGAG 59.005 55.000 14.98 15.19 37.61 3.51
10 11 0.317160 ACATCCTCTTCAACGCGTGA 59.683 50.000 14.98 10.15 0.00 4.35
11 12 1.126846 GAACATCCTCTTCAACGCGTG 59.873 52.381 14.98 7.52 0.00 5.34
12 13 1.429463 GAACATCCTCTTCAACGCGT 58.571 50.000 5.58 5.58 0.00 6.01
13 14 0.721718 GGAACATCCTCTTCAACGCG 59.278 55.000 3.53 3.53 32.53 6.01
14 15 2.100605 AGGAACATCCTCTTCAACGC 57.899 50.000 0.00 0.00 45.66 4.84
50 51 2.199236 ACGAAACGACAACTCTGGTTC 58.801 47.619 0.00 0.00 32.73 3.62
55 56 0.938168 GGCGACGAAACGACAACTCT 60.938 55.000 0.00 0.00 41.34 3.24
226 2791 7.565680 TCTAAATCTGAAACATAACTCCCCTC 58.434 38.462 0.00 0.00 0.00 4.30
270 2835 7.624549 AGTGTACATAAAGACACAGGATTCAT 58.375 34.615 0.00 0.00 46.83 2.57
397 2962 8.191446 AGACACAAACTACTGCAGTGTATATAG 58.809 37.037 29.57 18.98 42.86 1.31
400 2965 6.340962 AGACACAAACTACTGCAGTGTATA 57.659 37.500 29.57 8.34 42.86 1.47
479 3044 6.759827 ACAGGGAAACATCAATATGTACGTAC 59.240 38.462 18.90 18.90 45.79 3.67
501 3066 2.480073 CCCGCATAAGCCAATTTGACAG 60.480 50.000 0.00 0.00 37.52 3.51
605 3171 1.757574 TTGTTCGTTCCACGTAGACG 58.242 50.000 10.21 10.21 43.14 4.18
606 3172 3.306703 TGTTTTGTTCGTTCCACGTAGAC 59.693 43.478 0.00 0.00 43.14 2.59
607 3173 3.519579 TGTTTTGTTCGTTCCACGTAGA 58.480 40.909 0.00 0.00 43.14 2.59
613 3179 3.269538 TCTCCTGTTTTGTTCGTTCCA 57.730 42.857 0.00 0.00 0.00 3.53
726 3292 1.831389 CTGTGAACTGAACCACGCCG 61.831 60.000 0.00 0.00 36.15 6.46
730 3296 0.531974 TCGGCTGTGAACTGAACCAC 60.532 55.000 0.00 0.00 0.00 4.16
820 3386 0.905357 CGACCTTGACTCCCATTCCT 59.095 55.000 0.00 0.00 0.00 3.36
829 3395 4.003788 CCCACGCCGACCTTGACT 62.004 66.667 0.00 0.00 0.00 3.41
847 3413 2.649034 GCTCGAGTTCCCACGACA 59.351 61.111 15.13 0.00 34.82 4.35
908 3484 3.632145 CACCCTAACAGAAACAGCAAACT 59.368 43.478 0.00 0.00 0.00 2.66
932 3512 1.146359 ACGGGCTAGGGTTTTCCTTTT 59.854 47.619 0.00 0.00 45.47 2.27
933 3513 0.775542 ACGGGCTAGGGTTTTCCTTT 59.224 50.000 0.00 0.00 45.47 3.11
1155 4960 4.208686 AGGAGGTCGCGAATCGGC 62.209 66.667 12.06 0.00 43.18 5.54
1187 4992 3.576004 CGAGGAAGTCGGACGAGT 58.424 61.111 1.89 0.00 45.58 4.18
1244 5049 3.585990 CATGGATGGGCGGCGTTC 61.586 66.667 9.37 1.68 0.00 3.95
1281 5086 0.611714 TCGGGTTAACAGAGGAAGCC 59.388 55.000 8.10 0.00 39.38 4.35
1340 5145 1.862806 GAACTCCGTCTGCAAGTGC 59.137 57.895 0.00 0.00 42.50 4.40
1495 5300 2.433145 CACAGCACGTCGCCAGAT 60.433 61.111 6.39 0.00 44.04 2.90
1503 5308 3.563088 CACGCACACACAGCACGT 61.563 61.111 0.00 0.00 37.47 4.49
1504 5309 3.563088 ACACGCACACACAGCACG 61.563 61.111 0.00 0.00 0.00 5.34
1509 5314 3.559344 GACGCACACGCACACACA 61.559 61.111 0.00 0.00 45.53 3.72
1510 5315 2.373524 AATGACGCACACGCACACAC 62.374 55.000 0.00 0.00 45.53 3.82
1511 5316 2.176926 AATGACGCACACGCACACA 61.177 52.632 0.00 0.00 45.53 3.72
1512 5317 1.722163 CAATGACGCACACGCACAC 60.722 57.895 0.00 0.00 45.53 3.82
1513 5318 2.630872 CAATGACGCACACGCACA 59.369 55.556 0.00 0.00 45.53 4.57
1514 5319 2.796617 GCAATGACGCACACGCAC 60.797 61.111 0.00 0.00 45.53 5.34
1515 5320 2.953605 GAGCAATGACGCACACGCA 61.954 57.895 8.38 0.00 45.53 5.24
1516 5321 2.202222 GAGCAATGACGCACACGC 60.202 61.111 0.00 0.00 45.53 5.34
1518 5323 1.154599 CACGAGCAATGACGCACAC 60.155 57.895 0.00 0.00 0.00 3.82
1557 5372 3.080121 CGAGCTCCCAGCCTTCCT 61.080 66.667 8.47 0.00 43.77 3.36
1571 5386 3.485431 CCAAGCACGAGCAGCGAG 61.485 66.667 7.77 0.00 45.49 5.03
1601 5416 0.109086 CGTCGAGTGCAAGGACATCT 60.109 55.000 11.97 0.00 0.00 2.90
1818 5633 3.989817 GCAAACAAAGCCAAGATTACAGG 59.010 43.478 0.00 0.00 0.00 4.00
1923 5738 2.060567 ATGCCACTGCTGTCACACCT 62.061 55.000 0.00 0.00 38.71 4.00
2099 5922 9.646427 GAGAGTAGTGAAACACTGAAAATAGAT 57.354 33.333 13.62 0.00 45.01 1.98
2524 6354 9.098355 CAGATAGATAAAGTTCGGATTTCACAA 57.902 33.333 0.00 0.00 0.00 3.33
2525 6355 8.258007 ACAGATAGATAAAGTTCGGATTTCACA 58.742 33.333 0.00 0.00 0.00 3.58
3063 7089 2.552743 GACTTTTACCACTGCCCAACTC 59.447 50.000 0.00 0.00 0.00 3.01
3112 7138 2.107378 TCCACAAAGATTGCTGGGTGTA 59.893 45.455 9.97 0.00 34.61 2.90
3188 7214 6.328672 AGAAATAGCAGATACCAACCTCAGAT 59.671 38.462 0.00 0.00 0.00 2.90
3259 7285 0.744771 GGACTCGGACAAGGCAATCC 60.745 60.000 0.00 0.00 0.00 3.01
3661 7690 1.605710 CAGCCCAAGATTCGCCATTAG 59.394 52.381 0.00 0.00 0.00 1.73
3780 7813 7.119992 GGTTTTGTTACACCATGTTTCCTTTTT 59.880 33.333 0.00 0.00 32.74 1.94
3943 7976 1.386533 CCCCTGCAGTTGATAGCTTG 58.613 55.000 13.81 0.00 0.00 4.01
3975 8008 0.679505 TCGTCCCAAGTGGAGAACAG 59.320 55.000 0.00 0.00 46.38 3.16
3986 8019 0.323302 TAGTTGCTGCATCGTCCCAA 59.677 50.000 1.84 0.00 0.00 4.12
3997 8030 5.679734 AGTTGTCACAGAATTAGTTGCTG 57.320 39.130 0.00 0.00 35.81 4.41
4198 8234 5.058149 TCAATGCATATGCTGTCGTTTTT 57.942 34.783 27.13 6.58 42.66 1.94
4254 8290 1.682684 AGGATGGCCGACGAGACTT 60.683 57.895 0.00 0.00 39.96 3.01
4443 8479 4.039852 ACACAACATCAAAATTGTACCCCC 59.960 41.667 0.00 0.00 36.92 5.40
4770 8806 3.194968 TCCAACTAGTACTGCTAAGTGGC 59.805 47.826 5.39 0.00 37.19 5.01
4813 8849 9.836864 AGAAACAAACAGACATATAGATATGCA 57.163 29.630 9.05 0.00 42.98 3.96
4817 8853 8.988060 TGGGAGAAACAAACAGACATATAGATA 58.012 33.333 0.00 0.00 0.00 1.98
4818 8854 7.861629 TGGGAGAAACAAACAGACATATAGAT 58.138 34.615 0.00 0.00 0.00 1.98
4887 8965 6.100004 ACTACAAATCTAGACAATGTCACCG 58.900 40.000 16.38 3.40 34.60 4.94
5069 9151 4.697352 CCCTTCTCCATAACAAGAACACTG 59.303 45.833 0.00 0.00 0.00 3.66
5198 9411 7.383029 TGACAAAGCAAAATTCTTATTGAGCTG 59.617 33.333 0.00 0.00 35.86 4.24
5264 9477 5.227569 TCTGAACATGGTGATGTAACTGT 57.772 39.130 0.00 0.00 42.30 3.55
5267 9480 6.500684 ACATTCTGAACATGGTGATGTAAC 57.499 37.500 0.00 0.00 42.30 2.50
5269 9482 5.351189 CGAACATTCTGAACATGGTGATGTA 59.649 40.000 0.00 0.00 42.30 2.29
5272 9485 4.154737 CACGAACATTCTGAACATGGTGAT 59.845 41.667 0.00 0.00 0.00 3.06
5273 9486 3.498018 CACGAACATTCTGAACATGGTGA 59.502 43.478 0.00 0.00 0.00 4.02
5300 9759 7.415206 GGTTGCCAGGAAACTATAATAACAGTG 60.415 40.741 10.46 0.00 40.21 3.66
5310 9769 4.082125 CAAAGAGGTTGCCAGGAAACTAT 58.918 43.478 10.46 0.00 40.21 2.12
5517 9980 2.365582 CTATACAAGTGTGGGGGCAAC 58.634 52.381 0.00 0.00 0.00 4.17
5525 9988 8.932945 TTCAAGATCTAAGCTATACAAGTGTG 57.067 34.615 0.00 0.00 0.00 3.82
5638 10101 0.740868 TCTGCTCAATGTGTAGCCGC 60.741 55.000 0.00 0.00 37.97 6.53
5644 10107 6.170846 TCTATGATCATCTGCTCAATGTGT 57.829 37.500 12.53 0.00 0.00 3.72
5765 10229 4.196193 TGTGATCCAAATAAGGTAAGGCG 58.804 43.478 0.00 0.00 0.00 5.52
5909 10454 5.806502 CACACATCTGCAAAAGAAAGAACAA 59.193 36.000 0.00 0.00 38.79 2.83
5910 10455 5.342433 CACACATCTGCAAAAGAAAGAACA 58.658 37.500 0.00 0.00 38.79 3.18
5911 10456 4.207841 GCACACATCTGCAAAAGAAAGAAC 59.792 41.667 0.00 0.00 38.79 3.01
5912 10457 4.142204 TGCACACATCTGCAAAAGAAAGAA 60.142 37.500 0.00 0.00 44.28 2.52
6076 10621 8.846211 TCAACCTAAGGAAAGTGAAAAACATAG 58.154 33.333 0.00 0.00 0.00 2.23
6082 10627 6.096282 CCTTGTCAACCTAAGGAAAGTGAAAA 59.904 38.462 0.00 0.00 44.98 2.29
6226 10771 2.196749 ACAATGCTGCGATTCTACTCG 58.803 47.619 0.00 0.00 41.54 4.18
6265 10810 4.496360 TGACAGTACACAAAGTCGAACAA 58.504 39.130 0.00 0.00 33.83 2.83
6267 10812 4.802039 TCTTGACAGTACACAAAGTCGAAC 59.198 41.667 0.00 0.00 33.83 3.95
6283 10828 7.867403 GGAAAGCTTGAAAAATACATCTTGACA 59.133 33.333 0.00 0.00 0.00 3.58
6307 10852 5.049267 GCGGTTTTACAAACTCAACTATGGA 60.049 40.000 0.00 0.00 0.00 3.41
6315 10864 1.015109 TGCGCGGTTTTACAAACTCA 58.985 45.000 8.83 0.00 0.00 3.41
6363 10914 4.068599 GCCTTTCAGATATTACCTCCTGC 58.931 47.826 0.00 0.00 0.00 4.85
6516 14597 5.290643 ACTCTCTTACTTGTACTAGTACGCG 59.709 44.000 24.36 19.72 38.85 6.01
6853 15808 2.032681 GGGTCTGAAAGCACGCCT 59.967 61.111 0.00 0.00 0.00 5.52
6907 15864 4.037446 CAGGGTCGAGTTTTTCCAAATTGA 59.963 41.667 0.00 0.00 0.00 2.57
6939 15896 0.770557 TAGTGGGGGCTGGTGAAAGT 60.771 55.000 0.00 0.00 0.00 2.66
6967 15927 1.147376 CTTGAACGGGGTGTGGTGA 59.853 57.895 0.00 0.00 0.00 4.02
6969 15929 2.203294 GCTTGAACGGGGTGTGGT 60.203 61.111 0.00 0.00 0.00 4.16
6971 15931 0.817634 TGAAGCTTGAACGGGGTGTG 60.818 55.000 2.10 0.00 0.00 3.82
6972 15932 0.818040 GTGAAGCTTGAACGGGGTGT 60.818 55.000 2.10 0.00 0.00 4.16
6973 15933 1.515521 GGTGAAGCTTGAACGGGGTG 61.516 60.000 2.10 0.00 0.00 4.61
6974 15934 1.228154 GGTGAAGCTTGAACGGGGT 60.228 57.895 2.10 0.00 0.00 4.95
6975 15935 0.821711 TTGGTGAAGCTTGAACGGGG 60.822 55.000 2.10 0.00 0.00 5.73
6976 15936 1.028905 TTTGGTGAAGCTTGAACGGG 58.971 50.000 2.10 0.00 0.00 5.28
7068 16031 1.742831 GTGTTGAGTTGTGGCTGTTGA 59.257 47.619 0.00 0.00 0.00 3.18
7101 16064 2.417924 GCTGTGATGATCAAGGACGACT 60.418 50.000 0.00 0.00 0.00 4.18
7308 16275 2.869646 CGTGACGCGTGGTACCTA 59.130 61.111 20.70 0.00 35.54 3.08


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

AutoCloner maintained by Alex Coulton.