Multiple sequence alignment - TraesCS1D01G145000

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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 TraesCS1D01G145000 chr1D 100.000 7262 0 0 1 7262 200223038 200215777 0.000000e+00 13411.0
1 TraesCS1D01G145000 chr1D 93.333 105 6 1 4593 4696 275529302 275529198 3.510000e-33 154.0
2 TraesCS1D01G145000 chr1D 88.525 61 6 1 3998 4058 399943458 399943399 1.010000e-08 73.1
3 TraesCS1D01G145000 chr1A 97.188 2489 62 5 202 2688 253384910 253382428 0.000000e+00 4202.0
4 TraesCS1D01G145000 chr1A 96.507 1918 47 10 2687 4599 253382304 253380402 0.000000e+00 3153.0
5 TraesCS1D01G145000 chr1A 97.970 1724 32 3 4692 6414 253380404 253378683 0.000000e+00 2987.0
6 TraesCS1D01G145000 chr1A 89.236 864 75 12 6408 7262 35108791 35109645 0.000000e+00 1064.0
7 TraesCS1D01G145000 chr1A 91.707 205 12 4 1 203 253385587 253385386 5.550000e-71 279.0
8 TraesCS1D01G145000 chr1A 86.441 59 7 1 3998 4056 496307755 496307698 6.080000e-06 63.9
9 TraesCS1D01G145000 chr1B 93.153 2629 138 17 423 3034 287704462 287707065 0.000000e+00 3819.0
10 TraesCS1D01G145000 chr1B 96.560 814 28 0 4692 5505 287708572 287709385 0.000000e+00 1349.0
11 TraesCS1D01G145000 chr1B 92.803 931 43 16 3188 4109 287707092 287708007 0.000000e+00 1327.0
12 TraesCS1D01G145000 chr1B 85.681 859 106 13 6413 7262 178884349 178885199 0.000000e+00 889.0
13 TraesCS1D01G145000 chr1B 94.485 544 25 2 5873 6414 287709906 287710446 0.000000e+00 833.0
14 TraesCS1D01G145000 chr1B 90.177 509 32 8 4106 4599 287708069 287708574 0.000000e+00 647.0
15 TraesCS1D01G145000 chr1B 93.252 326 21 1 28 352 287700994 287701319 5.100000e-131 479.0
16 TraesCS1D01G145000 chr1B 88.435 294 25 5 5550 5835 287709381 287709673 5.390000e-91 346.0
17 TraesCS1D01G145000 chr1B 94.898 98 5 0 4597 4694 677585804 677585901 3.510000e-33 154.0
18 TraesCS1D01G145000 chr1B 97.101 69 2 0 5766 5834 287709832 287709900 4.600000e-22 117.0
19 TraesCS1D01G145000 chr1B 88.525 61 6 1 3998 4058 536660462 536660403 1.010000e-08 73.1
20 TraesCS1D01G145000 chr1B 100.000 30 0 0 4004 4033 330198456 330198485 1.000000e-03 56.5
21 TraesCS1D01G145000 chr6A 92.890 858 48 7 6411 7262 188416550 188415700 0.000000e+00 1234.0
22 TraesCS1D01G145000 chr6A 82.750 829 122 15 6410 7231 228530741 228529927 0.000000e+00 719.0
23 TraesCS1D01G145000 chr4A 90.326 858 69 9 6412 7262 712476568 712477418 0.000000e+00 1112.0
24 TraesCS1D01G145000 chr7A 87.967 856 80 9 6412 7262 493633146 493633983 0.000000e+00 989.0
25 TraesCS1D01G145000 chr7A 93.827 162 6 2 3033 3194 451519972 451519815 2.620000e-59 241.0
26 TraesCS1D01G145000 chr7A 100.000 32 0 0 4004 4035 148481516 148481485 7.870000e-05 60.2
27 TraesCS1D01G145000 chr5B 86.496 859 103 10 6412 7262 416553658 416554511 0.000000e+00 931.0
28 TraesCS1D01G145000 chr5B 95.918 98 4 0 4596 4693 638485377 638485474 7.540000e-35 159.0
29 TraesCS1D01G145000 chr6D 83.160 867 123 16 6409 7262 55109087 55108231 0.000000e+00 771.0
30 TraesCS1D01G145000 chr7D 82.381 840 130 13 6409 7238 51698222 51699053 0.000000e+00 715.0
31 TraesCS1D01G145000 chr7D 93.413 167 8 1 3028 3194 83345017 83344854 2.020000e-60 244.0
32 TraesCS1D01G145000 chr5D 96.154 156 6 0 3032 3187 242367932 242368087 9.350000e-64 255.0
33 TraesCS1D01G145000 chr5D 94.268 157 6 1 3032 3188 101809757 101809910 3.390000e-58 237.0
34 TraesCS1D01G145000 chr5D 100.000 30 0 0 1266 1295 484247621 484247592 1.000000e-03 56.5
35 TraesCS1D01G145000 chr4D 93.333 165 6 2 3032 3194 291203379 291203218 9.420000e-59 239.0
36 TraesCS1D01G145000 chr2A 93.293 164 8 1 3032 3195 239584475 239584315 9.420000e-59 239.0
37 TraesCS1D01G145000 chr2A 95.098 102 5 0 4592 4693 27741253 27741354 2.100000e-35 161.0
38 TraesCS1D01G145000 chr5A 93.252 163 8 2 3032 3194 181621360 181621201 3.390000e-58 237.0
39 TraesCS1D01G145000 chr5A 94.268 157 6 1 3032 3188 422444302 422444455 3.390000e-58 237.0
40 TraesCS1D01G145000 chr6B 94.118 102 6 0 4595 4696 475446851 475446750 9.750000e-34 156.0
41 TraesCS1D01G145000 chr6B 87.692 130 15 1 4564 4693 43237090 43237218 4.540000e-32 150.0
42 TraesCS1D01G145000 chr6B 79.412 102 9 9 4002 4094 506725754 506725852 2.190000e-05 62.1
43 TraesCS1D01G145000 chr3A 94.175 103 5 1 4593 4694 614663638 614663536 9.750000e-34 156.0
44 TraesCS1D01G145000 chrUn 87.692 130 15 1 4564 4693 94040227 94040355 4.540000e-32 150.0
45 TraesCS1D01G145000 chr3B 90.991 111 9 1 4590 4700 12406666 12406775 1.630000e-31 148.0
46 TraesCS1D01G145000 chr7B 77.885 104 17 5 4004 4107 109926823 109926726 7.870000e-05 60.2


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 TraesCS1D01G145000 chr1D 200215777 200223038 7261 True 13411.000 13411 100.00000 1 7262 1 chr1D.!!$R1 7261
1 TraesCS1D01G145000 chr1A 253378683 253385587 6904 True 2655.250 4202 95.84300 1 6414 4 chr1A.!!$R2 6413
2 TraesCS1D01G145000 chr1A 35108791 35109645 854 False 1064.000 1064 89.23600 6408 7262 1 chr1A.!!$F1 854
3 TraesCS1D01G145000 chr1B 287700994 287710446 9452 False 1114.625 3819 93.24575 28 6414 8 chr1B.!!$F4 6386
4 TraesCS1D01G145000 chr1B 178884349 178885199 850 False 889.000 889 85.68100 6413 7262 1 chr1B.!!$F1 849
5 TraesCS1D01G145000 chr6A 188415700 188416550 850 True 1234.000 1234 92.89000 6411 7262 1 chr6A.!!$R1 851
6 TraesCS1D01G145000 chr6A 228529927 228530741 814 True 719.000 719 82.75000 6410 7231 1 chr6A.!!$R2 821
7 TraesCS1D01G145000 chr4A 712476568 712477418 850 False 1112.000 1112 90.32600 6412 7262 1 chr4A.!!$F1 850
8 TraesCS1D01G145000 chr7A 493633146 493633983 837 False 989.000 989 87.96700 6412 7262 1 chr7A.!!$F1 850
9 TraesCS1D01G145000 chr5B 416553658 416554511 853 False 931.000 931 86.49600 6412 7262 1 chr5B.!!$F1 850
10 TraesCS1D01G145000 chr6D 55108231 55109087 856 True 771.000 771 83.16000 6409 7262 1 chr6D.!!$R1 853
11 TraesCS1D01G145000 chr7D 51698222 51699053 831 False 715.000 715 82.38100 6409 7238 1 chr7D.!!$F1 829

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
541 4094 0.314302 CCGCCGATCTTATCCTCGTT 59.686 55.000 0.00 0.0 33.11 3.85 F
1340 4895 1.026718 GCTGGTCTACGCCTTGCAAT 61.027 55.000 0.00 0.0 0.00 3.56 F
1341 4896 1.453155 CTGGTCTACGCCTTGCAATT 58.547 50.000 0.00 0.0 0.00 2.32 F
1449 5004 1.529244 GGTTGCACCAGAGGCTGTT 60.529 57.895 0.00 0.0 38.42 3.16 F
3099 6799 1.186200 AGAGACTGCATACGGAGCAA 58.814 50.000 0.00 0.0 42.17 3.91 F
3221 6921 1.750399 CCTCACCCTTGATTGGCCG 60.750 63.158 0.00 0.0 0.00 6.13 F
4614 8404 1.961133 ATACTCCCTCCGACCCAAAA 58.039 50.000 0.00 0.0 0.00 2.44 F
5550 9340 0.971447 AACCTCTCGTACCTGAGCCC 60.971 60.000 4.71 0.0 35.90 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 5100 0.096976 CAACCTGCTGAATAACCGCG 59.903 55.000 0.00 0.00 0.00 6.46 R
2709 6403 1.689813 TCTACAACTCTGGCGGTTTGA 59.310 47.619 14.62 1.30 0.00 2.69 R
3087 6787 2.677836 TCACTCATTTTGCTCCGTATGC 59.322 45.455 0.00 0.00 0.00 3.14 R
3244 6944 4.052518 ACCCCAGAGCCATGGCAC 62.053 66.667 37.18 31.11 44.88 5.01 R
4677 8467 0.042131 ATTGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37 R
4678 8468 1.201424 AATTGTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46 R
6225 10253 0.110509 CTTTGCGCGCTAGCCATATG 60.111 55.000 33.29 7.96 41.18 1.78 R
6716 10754 0.675633 GCTTGGTGACATTTGGCAGT 59.324 50.000 0.00 0.00 42.32 4.40 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
115 119 6.183360 CGCTATAAGTTGCCCAATGTCTTTTA 60.183 38.462 0.00 0.00 0.00 1.52
200 681 0.458025 CTGTCGACCCGGAACTAAGC 60.458 60.000 14.12 0.00 0.00 3.09
274 755 2.682352 GTCCTCCTCGTACTTAGTGTCC 59.318 54.545 0.00 0.00 0.00 4.02
284 765 5.803461 TCGTACTTAGTGTCCAATTTGATCG 59.197 40.000 0.00 0.00 0.00 3.69
286 767 5.862924 ACTTAGTGTCCAATTTGATCGTG 57.137 39.130 0.00 0.00 0.00 4.35
472 4025 2.280552 CCGGACGTGGGGAAGAAGA 61.281 63.158 0.00 0.00 0.00 2.87
489 4042 4.706035 AGAAGAGGTCTGCATCATCAATC 58.294 43.478 6.50 4.75 34.29 2.67
493 4046 2.697229 AGGTCTGCATCATCAATCGAGA 59.303 45.455 0.00 0.00 0.00 4.04
541 4094 0.314302 CCGCCGATCTTATCCTCGTT 59.686 55.000 0.00 0.00 33.11 3.85
572 4125 1.153549 GCGGCTCGGATTCAACTCT 60.154 57.895 0.00 0.00 0.00 3.24
643 4196 1.212616 GTCCGAGCTGTGTATGCATC 58.787 55.000 0.19 0.00 0.00 3.91
782 4337 3.810310 AGAAGCTCTCGGAATTTCGAT 57.190 42.857 9.77 0.00 38.55 3.59
783 4338 3.712187 AGAAGCTCTCGGAATTTCGATC 58.288 45.455 9.77 3.88 38.55 3.69
881 4436 4.270808 AGCGCAGAATTTTGTTCCTTTTTG 59.729 37.500 11.47 0.00 0.00 2.44
898 4453 1.861542 TTGCGGCTGTTTTGATCCGG 61.862 55.000 0.00 0.00 41.96 5.14
907 4462 2.293122 TGTTTTGATCCGGCAGTTCTTG 59.707 45.455 0.00 0.00 0.00 3.02
925 4480 1.941734 GCGAATCACTCTCTCCGCG 60.942 63.158 0.00 0.00 33.42 6.46
1340 4895 1.026718 GCTGGTCTACGCCTTGCAAT 61.027 55.000 0.00 0.00 0.00 3.56
1341 4896 1.453155 CTGGTCTACGCCTTGCAATT 58.547 50.000 0.00 0.00 0.00 2.32
1449 5004 1.529244 GGTTGCACCAGAGGCTGTT 60.529 57.895 0.00 0.00 38.42 3.16
1545 5100 1.815003 CTTGAGCATTTGGTGGAGACC 59.185 52.381 0.00 0.00 43.48 3.85
1818 5380 2.557056 AGTAGTTCGCTGAGCACACTTA 59.443 45.455 10.40 0.00 0.00 2.24
2282 5845 2.753849 GCTGGGGCCGTATTGCAA 60.754 61.111 0.00 0.00 0.00 4.08
2323 5886 6.381481 TTCTATGCCTGTTTGCAGATATTG 57.619 37.500 0.00 0.00 45.93 1.90
2483 6046 7.967178 ACGTGCCTTGTTACTTGTATAAATAC 58.033 34.615 0.00 0.00 0.00 1.89
2600 6169 7.017551 TCCCAGCTATACCTGACATCATTAAAT 59.982 37.037 0.00 0.00 34.77 1.40
2601 6170 8.321353 CCCAGCTATACCTGACATCATTAAATA 58.679 37.037 0.00 0.00 34.77 1.40
2602 6171 9.725019 CCAGCTATACCTGACATCATTAAATAA 57.275 33.333 0.00 0.00 34.77 1.40
2643 6212 4.560128 TGTTTCACTCTGACAGCACTATC 58.440 43.478 0.00 0.00 0.00 2.08
2682 6251 3.550639 GCTCAAACAAGCAGTGCAATACA 60.551 43.478 19.20 0.00 42.05 2.29
2715 6409 3.058639 CAGTACAGAGCTTGCTTCAAACC 60.059 47.826 0.00 0.00 0.00 3.27
2826 6524 5.806502 CCGTGACACGTTTATATTAAGGACA 59.193 40.000 25.18 0.00 40.58 4.02
3052 6752 5.897824 CACCTACTCCCTCTGTTCCTAAATA 59.102 44.000 0.00 0.00 0.00 1.40
3053 6753 6.041069 CACCTACTCCCTCTGTTCCTAAATAG 59.959 46.154 0.00 0.00 0.00 1.73
3092 6792 7.441017 AGAGATTCCAATAAGAGACTGCATAC 58.559 38.462 0.00 0.00 0.00 2.39
3099 6799 1.186200 AGAGACTGCATACGGAGCAA 58.814 50.000 0.00 0.00 42.17 3.91
3110 6810 4.201950 GCATACGGAGCAAAATGAGTGAAT 60.202 41.667 0.00 0.00 0.00 2.57
3221 6921 1.750399 CCTCACCCTTGATTGGCCG 60.750 63.158 0.00 0.00 0.00 6.13
3511 7217 8.685427 CCCATGAACAAGTCAAAATACATGATA 58.315 33.333 0.00 0.00 40.50 2.15
3711 7418 3.162666 ACTGATTTCCACCTACGACTGA 58.837 45.455 0.00 0.00 0.00 3.41
3730 7437 4.809426 ACTGACAGTAGTTTTTCCTGTTCG 59.191 41.667 6.24 0.00 39.43 3.95
4059 7768 7.154656 TGCGATGTGCTTATTCTATAATCTGT 58.845 34.615 0.00 0.00 46.63 3.41
4138 7912 4.382457 CGTGCATTTGTGTTGTTATGAAGG 59.618 41.667 0.00 0.00 0.00 3.46
4371 8146 5.273208 TCCTATTTGAAGCTAGTGGAGAGT 58.727 41.667 0.00 0.00 0.00 3.24
4599 8389 7.101054 TGGCATTCACGTTTAGTCTTTATACT 58.899 34.615 0.00 0.00 0.00 2.12
4600 8390 7.277098 TGGCATTCACGTTTAGTCTTTATACTC 59.723 37.037 0.00 0.00 0.00 2.59
4601 8391 7.254353 GGCATTCACGTTTAGTCTTTATACTCC 60.254 40.741 0.00 0.00 0.00 3.85
4602 8392 7.254353 GCATTCACGTTTAGTCTTTATACTCCC 60.254 40.741 0.00 0.00 0.00 4.30
4603 8393 7.472334 TTCACGTTTAGTCTTTATACTCCCT 57.528 36.000 0.00 0.00 0.00 4.20
4604 8394 7.093322 TCACGTTTAGTCTTTATACTCCCTC 57.907 40.000 0.00 0.00 0.00 4.30
4605 8395 6.096001 TCACGTTTAGTCTTTATACTCCCTCC 59.904 42.308 0.00 0.00 0.00 4.30
4606 8396 5.067023 ACGTTTAGTCTTTATACTCCCTCCG 59.933 44.000 0.00 0.00 0.00 4.63
4607 8397 5.297776 CGTTTAGTCTTTATACTCCCTCCGA 59.702 44.000 0.00 0.00 0.00 4.55
4608 8398 6.502652 GTTTAGTCTTTATACTCCCTCCGAC 58.497 44.000 0.00 0.00 0.00 4.79
4609 8399 3.564264 AGTCTTTATACTCCCTCCGACC 58.436 50.000 0.00 0.00 0.00 4.79
4610 8400 2.627221 GTCTTTATACTCCCTCCGACCC 59.373 54.545 0.00 0.00 0.00 4.46
4611 8401 2.245546 TCTTTATACTCCCTCCGACCCA 59.754 50.000 0.00 0.00 0.00 4.51
4612 8402 2.852714 TTATACTCCCTCCGACCCAA 57.147 50.000 0.00 0.00 0.00 4.12
4613 8403 2.852714 TATACTCCCTCCGACCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
4614 8404 1.961133 ATACTCCCTCCGACCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4615 8405 1.961133 TACTCCCTCCGACCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4616 8406 1.961133 ACTCCCTCCGACCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4617 8407 2.271777 ACTCCCTCCGACCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4618 8408 2.238898 ACTCCCTCCGACCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4619 8409 2.238898 CTCCCTCCGACCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4620 8410 2.026636 TCCCTCCGACCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4621 8411 2.026636 CCCTCCGACCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
4622 8412 3.007635 CCTCCGACCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
4623 8413 3.307480 CCTCCGACCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
4624 8414 3.933332 CTCCGACCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
4625 8415 3.325425 TCCGACCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
4626 8416 4.069304 CCGACCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4627 8417 4.083484 CCGACCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4628 8418 4.755123 CGACCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
4629 8419 5.238650 CGACCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
4630 8420 6.238648 CGACCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
4631 8421 6.805713 ACCCAAAATAAGTGACTCAACTTTG 58.194 36.000 0.00 0.00 40.77 2.77
4632 8422 6.379988 ACCCAAAATAAGTGACTCAACTTTGT 59.620 34.615 0.00 0.00 40.77 2.83
4633 8423 7.558444 ACCCAAAATAAGTGACTCAACTTTGTA 59.442 33.333 0.00 0.00 40.77 2.41
4634 8424 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
4635 8425 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
4641 8431 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
4642 8432 9.880157 AAGTGACTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
4643 8433 9.880157 AGTGACTCAACTTTGTACTAACTTTAA 57.120 29.630 0.00 0.00 0.00 1.52
4669 8459 9.701098 ATACAAAATTAGTACAAACTCGAGTCA 57.299 29.630 20.33 1.60 37.15 3.41
4670 8460 7.848491 ACAAAATTAGTACAAACTCGAGTCAC 58.152 34.615 20.33 14.01 37.15 3.67
4671 8461 7.709613 ACAAAATTAGTACAAACTCGAGTCACT 59.290 33.333 20.33 19.79 37.15 3.41
4672 8462 8.548721 CAAAATTAGTACAAACTCGAGTCACTT 58.451 33.333 20.33 6.87 37.15 3.16
4673 8463 9.754382 AAAATTAGTACAAACTCGAGTCACTTA 57.246 29.630 20.33 13.29 37.15 2.24
4674 8464 9.924650 AAATTAGTACAAACTCGAGTCACTTAT 57.075 29.630 20.33 14.79 37.15 1.73
4675 8465 9.924650 AATTAGTACAAACTCGAGTCACTTATT 57.075 29.630 20.33 18.90 37.15 1.40
4676 8466 9.924650 ATTAGTACAAACTCGAGTCACTTATTT 57.075 29.630 20.33 4.41 37.15 1.40
4677 8467 9.754382 TTAGTACAAACTCGAGTCACTTATTTT 57.246 29.630 20.33 3.59 37.15 1.82
4678 8468 8.073355 AGTACAAACTCGAGTCACTTATTTTG 57.927 34.615 20.33 18.12 0.00 2.44
4679 8469 6.300354 ACAAACTCGAGTCACTTATTTTGG 57.700 37.500 20.33 0.00 0.00 3.28
4680 8470 5.238650 ACAAACTCGAGTCACTTATTTTGGG 59.761 40.000 20.33 0.00 0.00 4.12
4681 8471 4.884668 ACTCGAGTCACTTATTTTGGGA 57.115 40.909 13.58 0.00 0.00 4.37
4682 8472 4.566987 ACTCGAGTCACTTATTTTGGGAC 58.433 43.478 13.58 0.00 0.00 4.46
4683 8473 3.581755 TCGAGTCACTTATTTTGGGACG 58.418 45.455 0.00 0.00 33.84 4.79
4684 8474 2.671396 CGAGTCACTTATTTTGGGACGG 59.329 50.000 0.00 0.00 33.84 4.79
4685 8475 3.615592 CGAGTCACTTATTTTGGGACGGA 60.616 47.826 0.00 0.00 33.84 4.69
4686 8476 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
4687 8477 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4688 8478 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4689 8479 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4690 8480 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4740 8530 7.820386 TCATTTCCTCGCTTGTATTACAACTTA 59.180 33.333 5.14 0.00 33.96 2.24
5508 9298 5.814705 ACTTCTTGCTTAGATTCCATTCTCG 59.185 40.000 0.00 0.00 31.54 4.04
5510 9300 3.475566 TGCTTAGATTCCATTCTCGGG 57.524 47.619 0.00 0.00 0.00 5.14
5511 9301 2.771943 TGCTTAGATTCCATTCTCGGGT 59.228 45.455 0.00 0.00 0.00 5.28
5550 9340 0.971447 AACCTCTCGTACCTGAGCCC 60.971 60.000 4.71 0.00 35.90 5.19
5551 9341 1.379977 CCTCTCGTACCTGAGCCCA 60.380 63.158 4.71 0.00 35.90 5.36
5608 9398 8.630054 TTGTTTAGAATAAAGCAGTACCATGT 57.370 30.769 0.00 0.00 0.00 3.21
5674 9465 2.415090 GCGATGCTGAATTTGCAGACTT 60.415 45.455 11.64 0.00 44.04 3.01
5865 9891 5.175491 CACATGCAAACAAACTTGGTGATAC 59.825 40.000 0.00 0.00 0.00 2.24
5866 9892 5.068987 ACATGCAAACAAACTTGGTGATACT 59.931 36.000 0.00 0.00 0.00 2.12
5867 9893 6.264292 ACATGCAAACAAACTTGGTGATACTA 59.736 34.615 0.00 0.00 0.00 1.82
5868 9894 6.312399 TGCAAACAAACTTGGTGATACTAG 57.688 37.500 0.00 0.00 0.00 2.57
5869 9895 5.825679 TGCAAACAAACTTGGTGATACTAGT 59.174 36.000 0.00 0.00 0.00 2.57
5870 9896 6.993308 TGCAAACAAACTTGGTGATACTAGTA 59.007 34.615 4.77 4.77 0.00 1.82
5871 9897 7.172532 TGCAAACAAACTTGGTGATACTAGTAG 59.827 37.037 8.85 0.00 0.00 2.57
5873 9899 9.268268 CAAACAAACTTGGTGATACTAGTAGAA 57.732 33.333 8.85 0.00 0.00 2.10
5874 9900 9.841295 AAACAAACTTGGTGATACTAGTAGAAA 57.159 29.630 8.85 0.00 0.00 2.52
6177 10205 3.525800 AATTGTGTAAGCTGGAACCCT 57.474 42.857 0.00 0.00 0.00 4.34
6225 10253 1.740043 GCGATGACCGTACAGTTCGC 61.740 60.000 11.36 11.36 39.68 4.70
6244 10272 0.110509 CATATGGCTAGCGCGCAAAG 60.111 55.000 35.10 28.86 36.88 2.77
6285 10313 8.750298 TGAAAAGTTTTGTATGTTTTCCCTGTA 58.250 29.630 5.36 0.00 37.87 2.74
6519 10549 4.253685 TCTGGCGATCAAGGAGTAAAAAG 58.746 43.478 0.00 0.00 0.00 2.27
6577 10615 2.029918 GGCTAGAAAAACAGCAGGTTGG 60.030 50.000 0.00 0.00 40.35 3.77
6715 10753 2.412847 CGGAAAGTGCATTCGTTTCTCC 60.413 50.000 11.31 0.00 31.96 3.71
6716 10754 2.552315 GGAAAGTGCATTCGTTTCTCCA 59.448 45.455 11.31 0.00 31.96 3.86
6982 11025 3.071206 GGCCAGCCTCGTCTCTGA 61.071 66.667 0.00 0.00 32.26 3.27
7096 11139 3.840666 TGAAGTTAGTCTTGAGCATCCCT 59.159 43.478 0.00 0.00 36.40 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.757237 TGACACAAATGACCTGCAAAATATT 58.243 32.000 0.00 0.00 0.00 1.28
89 93 3.118408 AGACATTGGGCAACTTATAGCGA 60.118 43.478 0.00 0.00 0.00 4.93
92 96 8.902806 TCATAAAAGACATTGGGCAACTTATAG 58.097 33.333 0.00 0.00 0.00 1.31
93 97 8.815565 TCATAAAAGACATTGGGCAACTTATA 57.184 30.769 0.00 0.00 0.00 0.98
136 140 6.549736 AGCCTAGAAATACACCACTTTTGTTT 59.450 34.615 0.00 0.00 0.00 2.83
148 152 5.646360 GCCTTGTACAAAGCCTAGAAATACA 59.354 40.000 16.86 0.00 0.00 2.29
200 681 0.747283 GCTCATGAAGACCAGCCCTG 60.747 60.000 0.00 0.00 0.00 4.45
274 755 6.317088 AGTAGTCAAATGCACGATCAAATTG 58.683 36.000 0.00 0.00 0.00 2.32
428 3981 8.319146 GGTTCATAATCTCCCTCGGATTTTATA 58.681 37.037 0.00 0.00 35.40 0.98
472 4025 2.697229 TCTCGATTGATGATGCAGACCT 59.303 45.455 0.00 0.00 0.00 3.85
489 4042 4.372656 AGTTGGTTTTGTTCTCTCTCTCG 58.627 43.478 0.00 0.00 0.00 4.04
493 4046 3.467803 CCGAGTTGGTTTTGTTCTCTCT 58.532 45.455 0.00 0.00 0.00 3.10
541 4094 4.143333 GCCGCCCGAGCTCACTAA 62.143 66.667 15.40 0.00 36.60 2.24
572 4125 1.479323 GTGGCCGTCCATTCTACACTA 59.521 52.381 0.00 0.00 45.62 2.74
643 4196 6.072119 GGCCGATAAAAGTAGATATTTTGGGG 60.072 42.308 0.00 0.00 32.38 4.96
782 4337 3.260205 ACAGGAAAAATGGGAGGAGAGA 58.740 45.455 0.00 0.00 0.00 3.10
783 4338 3.009473 TGACAGGAAAAATGGGAGGAGAG 59.991 47.826 0.00 0.00 0.00 3.20
881 4436 2.485122 CCGGATCAAAACAGCCGC 59.515 61.111 0.00 0.00 42.29 6.53
907 4462 1.941734 CGCGGAGAGAGTGATTCGC 60.942 63.158 0.00 0.00 39.79 4.70
936 4491 3.070302 AGCAATAGCAAAACCCGGAAAAA 59.930 39.130 0.73 0.00 45.49 1.94
1089 4644 0.106619 AACCGAGGGAGTAGAGCGAT 60.107 55.000 0.00 0.00 0.00 4.58
1224 4779 2.672961 TGCCGGTAAGAGAGTCAATG 57.327 50.000 1.90 0.00 0.00 2.82
1545 5100 0.096976 CAACCTGCTGAATAACCGCG 59.903 55.000 0.00 0.00 0.00 6.46
1818 5380 9.686683 AAAGACCTTATGTAAATAGACATGCTT 57.313 29.630 0.00 0.00 40.31 3.91
2199 5762 4.765856 AGTGTACGTAAACAGTCATCTCCT 59.234 41.667 17.99 0.00 0.00 3.69
2202 5765 8.086522 ACAAATAGTGTACGTAAACAGTCATCT 58.913 33.333 17.99 1.80 39.29 2.90
2203 5766 8.160342 CACAAATAGTGTACGTAAACAGTCATC 58.840 37.037 17.99 0.00 43.40 2.92
2204 5767 8.014322 CACAAATAGTGTACGTAAACAGTCAT 57.986 34.615 17.99 3.09 43.40 3.06
2205 5768 7.397512 CACAAATAGTGTACGTAAACAGTCA 57.602 36.000 17.99 0.00 43.40 3.41
2282 5845 8.854117 GGCATAGAAATTTCAAGTATCCATCTT 58.146 33.333 19.99 0.00 0.00 2.40
2323 5886 5.173131 CCAAACTTCGTTTTTATGAGCACAC 59.827 40.000 0.00 0.00 33.10 3.82
2643 6212 5.947228 TTGAGCAATGTTCCAAGAGTTAG 57.053 39.130 0.00 0.00 0.00 2.34
2709 6403 1.689813 TCTACAACTCTGGCGGTTTGA 59.310 47.619 14.62 1.30 0.00 2.69
2715 6409 3.119291 CAGCTTATCTACAACTCTGGCG 58.881 50.000 0.00 0.00 0.00 5.69
2826 6524 4.774726 TCAGATTCAGCAGAGGTAAAGAGT 59.225 41.667 0.00 0.00 0.00 3.24
3087 6787 2.677836 TCACTCATTTTGCTCCGTATGC 59.322 45.455 0.00 0.00 0.00 3.14
3092 6792 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3244 6944 4.052518 ACCCCAGAGCCATGGCAC 62.053 66.667 37.18 31.11 44.88 5.01
3438 7143 7.530426 AATGGCAAAACTCTTCTTATTCAGT 57.470 32.000 0.00 0.00 0.00 3.41
3450 7155 5.988561 TGGTAACATCAAAATGGCAAAACTC 59.011 36.000 0.00 0.00 46.17 3.01
3511 7217 5.334879 GGTTTGACTGCATGTACTCGAAAAT 60.335 40.000 0.00 0.00 0.00 1.82
3711 7418 5.910614 AGTACGAACAGGAAAAACTACTGT 58.089 37.500 0.00 0.00 46.59 3.55
3730 7437 5.116528 GCCGTAACAAAAGCAATGAAAGTAC 59.883 40.000 0.00 0.00 0.00 2.73
4059 7768 8.178313 TGTCTCTAGTTCTGTGACTATTTTCA 57.822 34.615 0.00 0.00 32.07 2.69
4138 7912 4.324267 ACCCAGTTAACTTATGCAGTGAC 58.676 43.478 5.07 0.00 35.12 3.67
4355 8130 2.828520 CCTCAACTCTCCACTAGCTTCA 59.171 50.000 0.00 0.00 0.00 3.02
4464 8252 8.843262 ACTACCTTTAAACGAGCTGTAAAAATT 58.157 29.630 0.00 0.00 0.00 1.82
4599 8389 2.026636 CACTTATTTTGGGTCGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4600 8390 2.026636 TCACTTATTTTGGGTCGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4601 8391 3.007635 GTCACTTATTTTGGGTCGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4602 8392 3.933332 GAGTCACTTATTTTGGGTCGGAG 59.067 47.826 0.00 0.00 0.00 4.63
4603 8393 3.325425 TGAGTCACTTATTTTGGGTCGGA 59.675 43.478 0.00 0.00 0.00 4.55
4604 8394 3.670625 TGAGTCACTTATTTTGGGTCGG 58.329 45.455 0.00 0.00 0.00 4.79
4605 8395 4.755123 AGTTGAGTCACTTATTTTGGGTCG 59.245 41.667 0.00 0.00 0.00 4.79
4606 8396 6.635030 AAGTTGAGTCACTTATTTTGGGTC 57.365 37.500 0.00 0.00 35.10 4.46
4607 8397 6.379988 ACAAAGTTGAGTCACTTATTTTGGGT 59.620 34.615 12.94 0.00 35.87 4.51
4608 8398 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
4609 8399 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
4615 8405 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
4616 8406 8.788325 AAAGTTAGTACAAAGTTGAGTCACTT 57.212 30.769 0.00 0.00 38.74 3.16
4617 8407 9.880157 TTAAAGTTAGTACAAAGTTGAGTCACT 57.120 29.630 0.00 0.00 0.00 3.41
4643 8433 9.701098 TGACTCGAGTTTGTACTAATTTTGTAT 57.299 29.630 21.08 0.00 33.84 2.29
4644 8434 8.971321 GTGACTCGAGTTTGTACTAATTTTGTA 58.029 33.333 21.08 0.00 33.84 2.41
4645 8435 7.709613 AGTGACTCGAGTTTGTACTAATTTTGT 59.290 33.333 21.08 0.00 33.84 2.83
4646 8436 8.073355 AGTGACTCGAGTTTGTACTAATTTTG 57.927 34.615 21.08 0.00 33.84 2.44
4647 8437 8.658499 AAGTGACTCGAGTTTGTACTAATTTT 57.342 30.769 21.08 4.43 33.84 1.82
4648 8438 9.924650 ATAAGTGACTCGAGTTTGTACTAATTT 57.075 29.630 21.08 9.24 33.84 1.82
4649 8439 9.924650 AATAAGTGACTCGAGTTTGTACTAATT 57.075 29.630 21.08 9.45 33.84 1.40
4650 8440 9.924650 AAATAAGTGACTCGAGTTTGTACTAAT 57.075 29.630 21.08 10.15 33.84 1.73
4651 8441 9.754382 AAAATAAGTGACTCGAGTTTGTACTAA 57.246 29.630 21.08 1.57 33.84 2.24
4652 8442 9.188588 CAAAATAAGTGACTCGAGTTTGTACTA 57.811 33.333 21.08 7.42 33.84 1.82
4653 8443 7.170998 CCAAAATAAGTGACTCGAGTTTGTACT 59.829 37.037 21.08 17.56 37.31 2.73
4654 8444 7.288672 CCAAAATAAGTGACTCGAGTTTGTAC 58.711 38.462 21.08 15.71 0.00 2.90
4655 8445 6.425721 CCCAAAATAAGTGACTCGAGTTTGTA 59.574 38.462 21.08 10.21 0.00 2.41
4656 8446 5.238650 CCCAAAATAAGTGACTCGAGTTTGT 59.761 40.000 21.08 5.70 0.00 2.83
4657 8447 5.468746 TCCCAAAATAAGTGACTCGAGTTTG 59.531 40.000 21.08 16.23 0.00 2.93
4658 8448 5.469084 GTCCCAAAATAAGTGACTCGAGTTT 59.531 40.000 21.08 12.75 0.00 2.66
4659 8449 4.995487 GTCCCAAAATAAGTGACTCGAGTT 59.005 41.667 21.08 6.08 0.00 3.01
4660 8450 4.566987 GTCCCAAAATAAGTGACTCGAGT 58.433 43.478 20.18 20.18 0.00 4.18
4661 8451 3.612860 CGTCCCAAAATAAGTGACTCGAG 59.387 47.826 11.84 11.84 0.00 4.04
4662 8452 3.581755 CGTCCCAAAATAAGTGACTCGA 58.418 45.455 0.00 0.00 0.00 4.04
4663 8453 2.671396 CCGTCCCAAAATAAGTGACTCG 59.329 50.000 0.00 0.00 0.00 4.18
4664 8454 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
4665 8455 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
4666 8456 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
4667 8457 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
4668 8458 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4669 8459 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4670 8460 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4671 8461 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4672 8462 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4673 8463 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4674 8464 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
4675 8465 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
4676 8466 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
4677 8467 0.042131 ATTGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
4678 8468 1.201424 AATTGTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
4679 8469 4.141779 ACATAAATTGTACTCCCTCCGTCC 60.142 45.833 0.00 0.00 36.57 4.79
4680 8470 4.809426 CACATAAATTGTACTCCCTCCGTC 59.191 45.833 0.00 0.00 36.57 4.79
4681 8471 4.224370 ACACATAAATTGTACTCCCTCCGT 59.776 41.667 0.00 0.00 36.57 4.69
4682 8472 4.766375 ACACATAAATTGTACTCCCTCCG 58.234 43.478 0.00 0.00 36.57 4.63
4683 8473 7.773690 ACATAACACATAAATTGTACTCCCTCC 59.226 37.037 0.00 0.00 36.57 4.30
4684 8474 8.732746 ACATAACACATAAATTGTACTCCCTC 57.267 34.615 0.00 0.00 36.57 4.30
4740 8530 5.838521 AGGGGTTAGACATGACAACAATTTT 59.161 36.000 0.00 0.00 0.00 1.82
5550 9340 7.891561 TCCTTGTTTCAAAATACCACCTAATG 58.108 34.615 0.00 0.00 0.00 1.90
5551 9341 8.485578 TTCCTTGTTTCAAAATACCACCTAAT 57.514 30.769 0.00 0.00 0.00 1.73
5608 9398 4.261994 GCAAGAGCATAAAACCTCCAAACA 60.262 41.667 0.00 0.00 41.58 2.83
5674 9465 6.485830 AAGAATACTACTTCTGGCTATGCA 57.514 37.500 0.00 0.00 35.67 3.96
5710 9501 5.163581 GCAATGATCAGCAAGAATACTGGTT 60.164 40.000 0.09 0.00 34.57 3.67
5805 9831 3.769739 ACTAATGTGTCTGCTTCCACA 57.230 42.857 5.58 5.58 44.91 4.17
5841 9867 3.519579 TCACCAAGTTTGTTTGCATGTG 58.480 40.909 0.00 0.00 0.00 3.21
5865 9891 9.186837 TGTAGTGGTCCTCTAAATTTCTACTAG 57.813 37.037 2.17 0.00 0.00 2.57
5866 9892 9.186837 CTGTAGTGGTCCTCTAAATTTCTACTA 57.813 37.037 2.17 0.00 0.00 1.82
5867 9893 7.894364 TCTGTAGTGGTCCTCTAAATTTCTACT 59.106 37.037 2.17 0.00 0.00 2.57
5868 9894 7.975058 GTCTGTAGTGGTCCTCTAAATTTCTAC 59.025 40.741 2.17 0.00 0.00 2.59
5869 9895 7.672660 TGTCTGTAGTGGTCCTCTAAATTTCTA 59.327 37.037 2.17 0.00 0.00 2.10
5870 9896 6.497259 TGTCTGTAGTGGTCCTCTAAATTTCT 59.503 38.462 2.17 0.00 0.00 2.52
5871 9897 6.698380 TGTCTGTAGTGGTCCTCTAAATTTC 58.302 40.000 2.17 0.00 0.00 2.17
5873 9899 6.681729 TTGTCTGTAGTGGTCCTCTAAATT 57.318 37.500 2.17 0.00 0.00 1.82
5874 9900 6.465084 GTTTGTCTGTAGTGGTCCTCTAAAT 58.535 40.000 2.17 0.00 0.00 1.40
5925 9951 6.389906 ACAGCAGGTTGATTTAAACATTAGC 58.610 36.000 0.00 0.00 0.00 3.09
6177 10205 3.329889 AACATCTGGGGCCTCGCA 61.330 61.111 0.84 0.00 0.00 5.10
6207 10235 0.455464 TGCGAACTGTACGGTCATCG 60.455 55.000 19.90 19.90 45.88 3.84
6225 10253 0.110509 CTTTGCGCGCTAGCCATATG 60.111 55.000 33.29 7.96 41.18 1.78
6244 10272 4.986622 ACTTTTCAAGTCAAACTGTGAGC 58.013 39.130 0.00 0.00 37.02 4.26
6246 10274 7.206687 ACAAAACTTTTCAAGTCAAACTGTGA 58.793 30.769 0.00 0.00 41.91 3.58
6285 10313 9.840427 GCATACAGTCAAAATGTACAACTATTT 57.160 29.630 0.00 0.00 36.04 1.40
6564 10602 1.490490 TGAGAGACCAACCTGCTGTTT 59.510 47.619 0.00 0.00 34.00 2.83
6577 10615 1.969923 CTGGGATCCTCCATGAGAGAC 59.030 57.143 12.58 0.00 46.50 3.36
6715 10753 1.603678 GCTTGGTGACATTTGGCAGTG 60.604 52.381 0.00 1.03 42.32 3.66
6716 10754 0.675633 GCTTGGTGACATTTGGCAGT 59.324 50.000 0.00 0.00 42.32 4.40
6982 11025 2.779755 TATGGTGCAATGACCGTCTT 57.220 45.000 0.00 0.00 39.07 3.01
7060 11103 4.934602 ACTAACTTCAGAAATCTGCTCTGC 59.065 41.667 5.53 0.00 43.46 4.26
7096 11139 3.924144 GCATACAACTGCCAATTCCAAA 58.076 40.909 0.00 0.00 36.10 3.28


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

AutoCloner maintained by Alex Coulton.