Multiple sequence alignment - TraesCS1D01G302000

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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 TraesCS1D01G302000 chr1D 100.000 8842 0 0 1 8842 399939304 399948145 0.000000e+00 16329.0
1 TraesCS1D01G302000 chr1D 87.156 109 14 0 1659 1767 433198518 433198410 3.350000e-24 124.0
2 TraesCS1D01G302000 chr1D 88.525 61 6 1 4096 4155 200218981 200219041 1.230000e-08 73.1
3 TraesCS1D01G302000 chr1A 96.543 5728 170 15 1699 7405 496305300 496311020 0.000000e+00 9455.0
4 TraesCS1D01G302000 chr1A 93.756 1121 56 8 7394 8510 496311110 496312220 0.000000e+00 1670.0
5 TraesCS1D01G302000 chr1A 93.252 978 56 5 1 975 352313957 352312987 0.000000e+00 1432.0
6 TraesCS1D01G302000 chr1A 95.556 720 26 3 994 1713 496304573 496305286 0.000000e+00 1147.0
7 TraesCS1D01G302000 chr1A 97.196 321 8 1 8464 8783 496312219 496312539 7.810000e-150 542.0
8 TraesCS1D01G302000 chr1A 88.525 61 6 1 4096 4155 253380943 253381003 1.230000e-08 73.1
9 TraesCS1D01G302000 chr1B 93.552 3350 138 33 1248 4564 536657590 536660894 0.000000e+00 4918.0
10 TraesCS1D01G302000 chr1B 93.993 1798 92 8 5609 7405 536662186 536663968 0.000000e+00 2708.0
11 TraesCS1D01G302000 chr1B 90.261 1458 115 18 7401 8842 536664061 536665507 0.000000e+00 1881.0
12 TraesCS1D01G302000 chr1B 95.330 878 39 2 4726 5602 536661205 536662081 0.000000e+00 1393.0
13 TraesCS1D01G302000 chr1B 85.130 269 22 13 994 1253 536654711 536654970 8.810000e-65 259.0
14 TraesCS1D01G302000 chr1B 92.899 169 12 0 4556 4724 536660926 536661094 6.860000e-61 246.0
15 TraesCS1D01G302000 chr1B 83.333 66 8 3 4084 4148 330198521 330198458 3.450000e-04 58.4
16 TraesCS1D01G302000 chr4D 96.509 974 32 1 1 972 46051391 46052364 0.000000e+00 1609.0
17 TraesCS1D01G302000 chr4D 87.156 109 14 0 1659 1767 365085382 365085274 3.350000e-24 124.0
18 TraesCS1D01G302000 chr6A 93.648 976 50 7 1 973 613601704 613602670 0.000000e+00 1448.0
19 TraesCS1D01G302000 chr3D 93.545 976 49 8 1 972 573449910 573450875 0.000000e+00 1441.0
20 TraesCS1D01G302000 chr3D 85.841 226 32 0 6930 7155 447579726 447579501 3.190000e-59 241.0
21 TraesCS1D01G302000 chr3D 85.965 171 20 2 1901 2068 87395882 87395713 7.050000e-41 180.0
22 TraesCS1D01G302000 chr3D 85.890 163 21 2 2265 2426 87395354 87395193 1.180000e-38 172.0
23 TraesCS1D01G302000 chr2D 93.354 978 51 9 1 973 556343594 556342626 0.000000e+00 1434.0
24 TraesCS1D01G302000 chr2D 88.991 109 12 0 1659 1767 42028462 42028354 1.550000e-27 135.0
25 TraesCS1D01G302000 chrUn 93.033 976 56 7 1 972 47641674 47640707 0.000000e+00 1415.0
26 TraesCS1D01G302000 chr5B 93.040 977 54 8 1 973 408963944 408964910 0.000000e+00 1415.0
27 TraesCS1D01G302000 chr5A 92.952 979 58 7 1 975 560727495 560726524 0.000000e+00 1415.0
28 TraesCS1D01G302000 chr5A 78.659 328 42 21 2026 2336 54730386 54730702 9.060000e-45 193.0
29 TraesCS1D01G302000 chr5A 88.073 109 13 0 1659 1767 696917115 696917007 7.200000e-26 130.0
30 TraesCS1D01G302000 chr5A 87.500 88 10 1 1659 1746 303720064 303719978 5.650000e-17 100.0
31 TraesCS1D01G302000 chr3B 93.018 974 59 4 1 972 8615966 8616932 0.000000e+00 1413.0
32 TraesCS1D01G302000 chr3B 88.073 109 13 0 1659 1767 793155278 793155170 7.200000e-26 130.0
33 TraesCS1D01G302000 chr2A 77.657 461 60 24 1350 1793 34166647 34166213 3.190000e-59 241.0
34 TraesCS1D01G302000 chr6B 87.719 57 5 2 4098 4152 506725810 506725754 2.060000e-06 65.8
35 TraesCS1D01G302000 chr7B 96.774 31 1 0 4118 4148 109926791 109926821 1.600000e-02 52.8
36 TraesCS1D01G302000 chr7A 73.913 161 29 4 3991 4148 148481364 148481514 1.600000e-02 52.8


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 TraesCS1D01G302000 chr1D 399939304 399948145 8841 False 16329.000000 16329 100.000000 1 8842 1 chr1D.!!$F2 8841
1 TraesCS1D01G302000 chr1A 496304573 496312539 7966 False 3203.500000 9455 95.762750 994 8783 4 chr1A.!!$F2 7789
2 TraesCS1D01G302000 chr1A 352312987 352313957 970 True 1432.000000 1432 93.252000 1 975 1 chr1A.!!$R1 974
3 TraesCS1D01G302000 chr1B 536654711 536665507 10796 False 1900.833333 4918 91.860833 994 8842 6 chr1B.!!$F1 7848
4 TraesCS1D01G302000 chr4D 46051391 46052364 973 False 1609.000000 1609 96.509000 1 972 1 chr4D.!!$F1 971
5 TraesCS1D01G302000 chr6A 613601704 613602670 966 False 1448.000000 1448 93.648000 1 973 1 chr6A.!!$F1 972
6 TraesCS1D01G302000 chr3D 573449910 573450875 965 False 1441.000000 1441 93.545000 1 972 1 chr3D.!!$F1 971
7 TraesCS1D01G302000 chr2D 556342626 556343594 968 True 1434.000000 1434 93.354000 1 973 1 chr2D.!!$R2 972
8 TraesCS1D01G302000 chrUn 47640707 47641674 967 True 1415.000000 1415 93.033000 1 972 1 chrUn.!!$R1 971
9 TraesCS1D01G302000 chr5B 408963944 408964910 966 False 1415.000000 1415 93.040000 1 973 1 chr5B.!!$F1 972
10 TraesCS1D01G302000 chr5A 560726524 560727495 971 True 1415.000000 1415 92.952000 1 975 1 chr5A.!!$R2 974
11 TraesCS1D01G302000 chr3B 8615966 8616932 966 False 1413.000000 1413 93.018000 1 972 1 chr3B.!!$F1 971

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
507 509 0.685097 TTGGAGTAGCAGCGGTTCTT 59.315 50.000 0.00 0.00 0.00 2.52 F
1018 1028 1.017387 GATGGCTACTTTTGGAGGCG 58.983 55.000 0.00 0.00 40.99 5.52 F
1410 4059 1.202806 TGGACAGGAGTTTTCTGCCAG 60.203 52.381 0.00 0.00 39.13 4.85 F
2730 5414 2.233271 GGGACCGATACCGAAGTCATA 58.767 52.381 0.00 0.00 38.22 2.15 F
3567 6251 0.735471 GCACTAGCCCTGCTAAAAGC 59.265 55.000 0.00 0.00 40.82 3.51 F
3762 6447 0.810648 TCGCATGCATTTTCAGGGAC 59.189 50.000 19.57 0.00 0.00 4.46 F
4180 6866 1.552337 TCCTGCTTCAGACATCTGTCC 59.448 52.381 8.70 0.24 45.85 4.02 F
5773 8733 1.550976 CCTCTGACCAGTTACTCCCAC 59.449 57.143 0.00 0.00 0.00 4.61 F
6337 9297 2.357009 GCATCATCGCAATCTGGTTTCT 59.643 45.455 0.00 0.00 0.00 2.52 F
7088 10049 1.079819 TCTTTCGAGGCTTGCTCCG 60.080 57.895 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 4859 4.699735 ACAAGCAATCAACATCGGAATACA 59.300 37.500 0.00 0.0 0.00 2.29 R
2924 5608 4.575885 TGGGAAAGAAATAGACTTCCACG 58.424 43.478 2.40 0.0 0.00 4.94 R
3066 5750 2.821969 AGGTGCCTTTGCTAATTCTGTG 59.178 45.455 0.00 0.0 38.71 3.66 R
3613 6297 0.311790 ATGCCACGTTCAAAGTGCAG 59.688 50.000 0.00 0.0 38.22 4.41 R
4604 7356 0.831307 GCCGGAATAGTCTTGAGGGT 59.169 55.000 5.05 0.0 0.00 4.34 R
4992 7854 1.422024 AGAGGCTGTCTATCGGAGCTA 59.578 52.381 0.00 0.0 31.71 3.32 R
6024 8984 2.759191 TGAATAAGATGCCTGCTAGCG 58.241 47.619 10.77 4.9 34.65 4.26 R
7088 10049 0.472471 TCCCTTCAATATCCGGCACC 59.528 55.000 0.00 0.0 0.00 5.01 R
7695 10766 0.601558 GTGTCCGTAGTCTCCAGCAA 59.398 55.000 0.00 0.0 0.00 3.91 R
8038 11110 1.413812 TCACTGCTCATGTCACTGTGT 59.586 47.619 7.79 0.0 35.50 3.72 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
42 43 1.536072 CGGTGATGATCGGTGGTACTG 60.536 57.143 0.00 0.00 0.00 2.74
186 188 3.118408 GGCTCTGGTGGTCATACATGTTA 60.118 47.826 2.30 0.00 0.00 2.41
507 509 0.685097 TTGGAGTAGCAGCGGTTCTT 59.315 50.000 0.00 0.00 0.00 2.52
857 862 3.168528 GGGGAGGAGCGCCCATAA 61.169 66.667 15.92 0.00 45.54 1.90
884 889 1.275666 CCGGGGATGTAGCCATATCA 58.724 55.000 0.00 0.00 0.00 2.15
975 985 6.093633 GTGCCTCGGATTTATTCTAACAGTTT 59.906 38.462 0.00 0.00 0.00 2.66
976 986 6.315393 TGCCTCGGATTTATTCTAACAGTTTC 59.685 38.462 0.00 0.00 0.00 2.78
977 987 6.539103 GCCTCGGATTTATTCTAACAGTTTCT 59.461 38.462 0.00 0.00 0.00 2.52
978 988 7.466050 GCCTCGGATTTATTCTAACAGTTTCTG 60.466 40.741 0.00 0.00 37.52 3.02
979 989 7.303634 TCGGATTTATTCTAACAGTTTCTGC 57.696 36.000 0.00 0.00 34.37 4.26
980 990 7.103641 TCGGATTTATTCTAACAGTTTCTGCT 58.896 34.615 0.00 0.00 34.37 4.24
981 991 7.606456 TCGGATTTATTCTAACAGTTTCTGCTT 59.394 33.333 0.00 0.00 34.37 3.91
982 992 8.879759 CGGATTTATTCTAACAGTTTCTGCTTA 58.120 33.333 0.00 0.00 34.37 3.09
992 1002 9.922305 CTAACAGTTTCTGCTTAATTATACAGC 57.078 33.333 9.38 5.75 34.37 4.40
1004 1014 3.924918 TTATACAGCGAGAGAGATGGC 57.075 47.619 0.00 0.00 0.00 4.40
1018 1028 1.017387 GATGGCTACTTTTGGAGGCG 58.983 55.000 0.00 0.00 40.99 5.52
1024 1034 2.347731 CTACTTTTGGAGGCGTCTTCC 58.652 52.381 6.34 0.00 0.00 3.46
1035 1045 2.654912 CGTCTTCCGCGTGGTTGTC 61.655 63.158 16.01 6.10 36.30 3.18
1183 1209 5.629079 ACAAGGAAAACCGATTGATCTTC 57.371 39.130 0.00 0.00 0.00 2.87
1410 4059 1.202806 TGGACAGGAGTTTTCTGCCAG 60.203 52.381 0.00 0.00 39.13 4.85
1434 4083 6.652062 AGATAATCAATGATGCGCTTCATGTA 59.348 34.615 31.95 24.19 36.48 2.29
1523 4172 8.693625 CATTCTATATGAGCTCTGGTCATCATA 58.306 37.037 16.19 2.89 45.91 2.15
1579 4228 7.282224 ACAGACAAGATTGTTTACAAGCAGTAA 59.718 33.333 12.72 0.00 44.03 2.24
1884 4561 4.556501 CGTAATGTGCAACCTGTCATGTTT 60.557 41.667 0.00 0.00 34.36 2.83
1978 4655 5.105392 AGGTCAGTCTTTTATCTCAGCTGAG 60.105 44.000 33.73 33.73 43.36 3.35
2073 4750 8.534333 TTAAGACTTGCTACACTTCAGTATTG 57.466 34.615 0.00 0.00 0.00 1.90
2079 4756 5.606505 TGCTACACTTCAGTATTGTCAACA 58.393 37.500 0.00 0.00 0.00 3.33
2182 4859 9.227777 GAGTAACCAGTCAGTAAAACCATAATT 57.772 33.333 0.00 0.00 0.00 1.40
2183 4860 9.010029 AGTAACCAGTCAGTAAAACCATAATTG 57.990 33.333 0.00 0.00 0.00 2.32
2405 5087 7.420002 CCTTCGATATGCAAAGAAATCAATGA 58.580 34.615 0.00 0.00 0.00 2.57
2730 5414 2.233271 GGGACCGATACCGAAGTCATA 58.767 52.381 0.00 0.00 38.22 2.15
2810 5494 7.766219 ATGCTTTGCTAATTGATGTTCAATC 57.234 32.000 3.39 0.00 45.57 2.67
2924 5608 5.416271 TCCCATTACTTCTTCACCTGTAC 57.584 43.478 0.00 0.00 0.00 2.90
2950 5634 7.469456 CGTGGAAGTCTATTTCTTTCCCAAAAA 60.469 37.037 0.14 0.00 0.00 1.94
3066 5750 3.084786 CAATTTGTCTGGACCTCTTCCC 58.915 50.000 0.00 0.00 45.17 3.97
3394 6078 8.299570 CCAGTTTTATTAAGCAACATCTCAACT 58.700 33.333 0.00 0.00 0.00 3.16
3413 6097 6.422333 TCAACTTGCCAATGTCTAATATCCA 58.578 36.000 0.00 0.00 0.00 3.41
3440 6124 4.543692 TCTTACACTTACACTGAGTTCGC 58.456 43.478 0.00 0.00 0.00 4.70
3530 6214 4.322123 CCTGATCTGAGTGCCATATCTGAG 60.322 50.000 0.38 0.00 32.66 3.35
3567 6251 0.735471 GCACTAGCCCTGCTAAAAGC 59.265 55.000 0.00 0.00 40.82 3.51
3691 6375 6.317140 TGAGATAGCAGTTTGACAATCCATTC 59.683 38.462 0.00 0.00 0.00 2.67
3721 6406 6.436847 TCATGCATTTCAGGAAATAACTCCAA 59.563 34.615 6.92 0.00 38.84 3.53
3762 6447 0.810648 TCGCATGCATTTTCAGGGAC 59.189 50.000 19.57 0.00 0.00 4.46
3807 6492 6.260936 CAGGACCAATACCAACTAATAAGCTG 59.739 42.308 0.00 0.00 0.00 4.24
3945 6630 2.967201 TGTCCCGTTAAACTTCTCAGGA 59.033 45.455 0.00 0.00 0.00 3.86
4065 6750 5.815740 TGTAGTCTTTGTTTGAACCACTCTC 59.184 40.000 0.00 0.00 0.00 3.20
4070 6756 2.143122 TGTTTGAACCACTCTCGCATC 58.857 47.619 0.00 0.00 0.00 3.91
4177 6863 4.815308 CCTAAATCCTGCTTCAGACATCTG 59.185 45.833 2.24 2.24 45.08 2.90
4180 6866 1.552337 TCCTGCTTCAGACATCTGTCC 59.448 52.381 8.70 0.24 45.85 4.02
4322 7033 7.001674 ACAAAATCACCCTGTATGAGTTGTTA 58.998 34.615 0.00 0.00 35.97 2.41
4362 7074 9.845305 GCAAATACAGTCATACGTAAATAGTTC 57.155 33.333 0.00 0.00 0.00 3.01
4423 7135 6.518493 AGATGTGCATGACAAGTTCATTTTT 58.482 32.000 0.00 0.00 42.87 1.94
4589 7341 2.754002 TGCATTTTTCGATCATGCAGGA 59.246 40.909 17.96 2.36 46.53 3.86
4597 7349 1.938577 CGATCATGCAGGAACTTCCAG 59.061 52.381 4.62 3.18 39.61 3.86
4604 7356 6.899089 TCATGCAGGAACTTCCAGAATAATA 58.101 36.000 10.57 0.00 39.61 0.98
4992 7854 3.261897 CCTGTCTGTGGGAATTCTAGTGT 59.738 47.826 5.23 0.00 0.00 3.55
5080 7942 4.844884 ACTCTAGCCTAATTTGTTCACCC 58.155 43.478 0.00 0.00 0.00 4.61
5420 8282 6.789457 TCCAGATATCTTTGGTCCATATGAGT 59.211 38.462 1.33 0.00 35.89 3.41
5467 8329 5.876651 ATGCAGATGGTATGTACTCTTCA 57.123 39.130 0.00 0.00 0.00 3.02
5554 8416 9.989869 GAGTACTAAATAGTGGCAATTTTCTTC 57.010 33.333 0.00 0.00 37.10 2.87
5555 8417 9.515226 AGTACTAAATAGTGGCAATTTTCTTCA 57.485 29.630 0.00 0.00 37.10 3.02
5773 8733 1.550976 CCTCTGACCAGTTACTCCCAC 59.449 57.143 0.00 0.00 0.00 4.61
6033 8993 2.536928 GCAAATAAACGTCGCTAGCAGG 60.537 50.000 16.45 10.01 0.00 4.85
6208 9168 6.594547 GTCAAGGAGGTTATGGAAAAGTCTAC 59.405 42.308 0.00 0.00 0.00 2.59
6211 9171 5.189934 AGGAGGTTATGGAAAAGTCTACAGG 59.810 44.000 0.00 0.00 0.00 4.00
6229 9189 3.051803 ACAGGGGAACTCTAGATGATGGA 60.052 47.826 0.00 0.00 0.00 3.41
6244 9204 7.893124 AGATGATGGAGAAATTGTAGCAATT 57.107 32.000 1.68 1.68 0.00 2.32
6302 9262 3.368531 GGAGTTCTGCACGGAAATAGAGT 60.369 47.826 0.00 0.00 0.00 3.24
6337 9297 2.357009 GCATCATCGCAATCTGGTTTCT 59.643 45.455 0.00 0.00 0.00 2.52
6555 9515 4.076394 ACATGCCAAATGGTACTTTACGT 58.924 39.130 0.71 0.00 37.57 3.57
6729 9690 6.537355 CCAGGGCTCTTAATTCAAGATCATA 58.463 40.000 0.00 0.00 42.44 2.15
6843 9804 2.882137 GGACCATTCGACCTGTTCAAAA 59.118 45.455 0.00 0.00 0.00 2.44
7088 10049 1.079819 TCTTTCGAGGCTTGCTCCG 60.080 57.895 0.00 0.00 0.00 4.63
7238 10200 3.753294 TCTTTTCGGCAGGGATATCTC 57.247 47.619 2.05 0.00 0.00 2.75
7405 10475 9.636965 CTTTAAACTGTAATTTTTGCTTGCTTC 57.363 29.630 0.00 0.00 0.00 3.86
7457 10527 6.454795 ACATGAATTTAAGTGGAACGCAAAT 58.545 32.000 0.00 0.00 45.86 2.32
7526 10597 4.556699 GCGTACCAATCAGGCAATATTTCC 60.557 45.833 0.00 0.00 43.14 3.13
7621 10692 2.415608 GCCAGGATGAGACCGACGA 61.416 63.158 0.00 0.00 39.69 4.20
7721 10792 1.018226 AGACTACGGACACGGACTCG 61.018 60.000 0.00 0.00 46.48 4.18
7737 10808 4.556898 CGGACTCGGGTGATATGAGTAAAG 60.557 50.000 0.00 0.00 42.71 1.85
7739 10810 3.961408 ACTCGGGTGATATGAGTAAAGCT 59.039 43.478 0.00 0.00 40.98 3.74
7784 10855 6.730344 GGGACTTCCTTTGTCACACAGACA 62.730 50.000 0.00 0.00 44.98 3.41
7880 10952 9.301153 CATAGGATTTTAACTTGTAAATGTGGC 57.699 33.333 0.00 0.00 0.00 5.01
7893 10965 3.569250 AATGTGGCGATGTTTTGTACC 57.431 42.857 0.00 0.00 0.00 3.34
7898 10970 2.230025 TGGCGATGTTTTGTACCATTGG 59.770 45.455 0.00 0.00 0.00 3.16
7902 10974 4.380023 GCGATGTTTTGTACCATTGGCTTA 60.380 41.667 1.54 0.00 0.00 3.09
7903 10975 5.331902 CGATGTTTTGTACCATTGGCTTAG 58.668 41.667 1.54 0.00 0.00 2.18
7904 10976 4.513198 TGTTTTGTACCATTGGCTTAGC 57.487 40.909 1.54 0.00 0.00 3.09
7906 10978 4.526262 TGTTTTGTACCATTGGCTTAGCAT 59.474 37.500 6.53 0.00 0.00 3.79
7907 10979 5.712446 TGTTTTGTACCATTGGCTTAGCATA 59.288 36.000 6.53 0.00 0.00 3.14
7916 10988 2.316108 TGGCTTAGCATACTCGGATCA 58.684 47.619 6.53 0.00 0.00 2.92
7922 10994 5.107298 GCTTAGCATACTCGGATCATTTGTC 60.107 44.000 0.00 0.00 0.00 3.18
7981 11053 9.424319 TGTAAACTAGAGAATGTGAATGAGAAC 57.576 33.333 0.00 0.00 0.00 3.01
7996 11068 7.712639 GTGAATGAGAACAGCTGAGGAATATTA 59.287 37.037 23.35 0.00 0.00 0.98
8007 11079 7.443575 CAGCTGAGGAATATTAACATAGCTTGT 59.556 37.037 8.42 0.00 41.53 3.16
8010 11082 6.202762 TGAGGAATATTAACATAGCTTGTGCG 59.797 38.462 0.00 0.00 45.42 5.34
8016 11088 2.113860 ACATAGCTTGTGCGTTCCAT 57.886 45.000 0.00 0.00 45.42 3.41
8019 11091 4.199310 ACATAGCTTGTGCGTTCCATAAT 58.801 39.130 0.00 0.00 45.42 1.28
8038 11110 9.679661 TCCATAATTTTAGAAGCTTCATGTACA 57.320 29.630 27.57 0.00 0.00 2.90
8054 11126 2.102252 TGTACACACAGTGACATGAGCA 59.898 45.455 7.81 0.00 36.96 4.26
8058 11130 1.413812 ACACAGTGACATGAGCAGTGA 59.586 47.619 24.56 0.00 38.64 3.41
8064 11136 3.514706 AGTGACATGAGCAGTGATTCTCT 59.485 43.478 0.00 0.00 0.00 3.10
8083 11155 4.125703 CTCTCTTATGCTGGACATTCCAC 58.874 47.826 0.00 0.00 42.67 4.02
8109 11181 2.148768 CAGAAGCTTCATGTGCACAGA 58.851 47.619 27.57 18.53 0.00 3.41
8110 11182 2.551032 CAGAAGCTTCATGTGCACAGAA 59.449 45.455 27.57 23.55 0.00 3.02
8111 11183 3.190744 CAGAAGCTTCATGTGCACAGAAT 59.809 43.478 27.57 12.99 0.00 2.40
8159 11234 4.826733 ACACATAAGCATGGTGAGAAACAA 59.173 37.500 0.00 0.00 36.39 2.83
8235 11310 5.105473 TGCTAGATTACTGGTACCAGAACAC 60.105 44.000 41.87 28.39 46.30 3.32
8286 11361 9.188588 CAATATGCTGATAATTGGCTAAAAGTG 57.811 33.333 0.00 0.00 0.00 3.16
8578 11702 3.979101 TCACTGTCCACATCAGCATTA 57.021 42.857 0.00 0.00 36.50 1.90
8679 11804 4.838986 TGAAGGGCTATAGATGTAGAACCC 59.161 45.833 3.21 1.74 36.29 4.11
8687 11812 7.502561 GGCTATAGATGTAGAACCCAAAAATGT 59.497 37.037 3.21 0.00 0.00 2.71
8724 11849 5.948992 AAGAACAAATTGCTAGACCTGAC 57.051 39.130 0.00 0.00 0.00 3.51
8759 11884 2.352342 TGAGTATGCATGCAACACGATG 59.648 45.455 26.68 0.00 0.00 3.84
8793 11926 7.175119 TCGATGATAGTCATACTTTGGGTCTAG 59.825 40.741 0.00 0.00 37.20 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.898574 CACTCAACCCCCACTGCAC 60.899 63.158 0.00 0.00 0.00 4.57
107 109 0.526954 CTCGCCGCTATTACCACGTT 60.527 55.000 0.00 0.00 0.00 3.99
186 188 4.569943 AGTCAAATACGCAGTTGTCTCAT 58.430 39.130 0.00 0.00 37.78 2.90
303 305 3.334691 ACAACTCACATATTGGGTGTCG 58.665 45.455 0.00 0.00 38.32 4.35
507 509 5.132648 ACATTGGACTTGAGCTTATCCCATA 59.867 40.000 0.00 0.00 0.00 2.74
857 862 3.420197 TACATCCCCGGGGCCTGAT 62.420 63.158 35.53 23.57 34.68 2.90
884 889 5.238650 CCAAGATTTGTTAACGAGGTTCACT 59.761 40.000 0.26 0.00 0.00 3.41
975 985 6.486993 TCTCTCTCGCTGTATAATTAAGCAGA 59.513 38.462 18.20 12.85 36.73 4.26
976 986 6.673106 TCTCTCTCGCTGTATAATTAAGCAG 58.327 40.000 12.58 12.58 36.73 4.24
977 987 6.635030 TCTCTCTCGCTGTATAATTAAGCA 57.365 37.500 8.07 1.48 36.73 3.91
978 988 6.529829 CCATCTCTCTCGCTGTATAATTAAGC 59.470 42.308 0.00 0.00 0.00 3.09
979 989 6.529829 GCCATCTCTCTCGCTGTATAATTAAG 59.470 42.308 0.00 0.00 0.00 1.85
980 990 6.209589 AGCCATCTCTCTCGCTGTATAATTAA 59.790 38.462 0.00 0.00 0.00 1.40
981 991 5.712446 AGCCATCTCTCTCGCTGTATAATTA 59.288 40.000 0.00 0.00 0.00 1.40
982 992 4.526262 AGCCATCTCTCTCGCTGTATAATT 59.474 41.667 0.00 0.00 0.00 1.40
983 993 4.085733 AGCCATCTCTCTCGCTGTATAAT 58.914 43.478 0.00 0.00 0.00 1.28
984 994 3.491342 AGCCATCTCTCTCGCTGTATAA 58.509 45.455 0.00 0.00 0.00 0.98
985 995 3.147553 AGCCATCTCTCTCGCTGTATA 57.852 47.619 0.00 0.00 0.00 1.47
986 996 1.993956 AGCCATCTCTCTCGCTGTAT 58.006 50.000 0.00 0.00 0.00 2.29
987 997 2.158740 AGTAGCCATCTCTCTCGCTGTA 60.159 50.000 0.00 0.00 32.76 2.74
988 998 1.028905 GTAGCCATCTCTCTCGCTGT 58.971 55.000 0.00 0.00 32.76 4.40
989 999 1.317613 AGTAGCCATCTCTCTCGCTG 58.682 55.000 0.00 0.00 32.76 5.18
990 1000 2.065899 AAGTAGCCATCTCTCTCGCT 57.934 50.000 0.00 0.00 35.34 4.93
991 1001 2.863137 CAAAAGTAGCCATCTCTCTCGC 59.137 50.000 0.00 0.00 0.00 5.03
992 1002 3.131223 TCCAAAAGTAGCCATCTCTCTCG 59.869 47.826 0.00 0.00 0.00 4.04
1004 1014 2.347731 GGAAGACGCCTCCAAAAGTAG 58.652 52.381 0.00 0.00 0.00 2.57
1018 1028 2.315386 GGACAACCACGCGGAAGAC 61.315 63.158 12.47 0.00 35.59 3.01
1024 1034 4.988598 AGCCAGGACAACCACGCG 62.989 66.667 3.53 3.53 37.48 6.01
1033 1043 1.451028 GGAGCATCACAGCCAGGAC 60.451 63.158 0.00 0.00 36.25 3.85
1035 1045 2.124403 GGGAGCATCACAGCCAGG 60.124 66.667 0.00 0.00 39.41 4.45
1239 1265 9.967245 GTGAAAGGTTGAAAAATAAAAGAACAC 57.033 29.630 0.00 0.00 0.00 3.32
1244 1270 7.227992 TGCGTGAAAGGTTGAAAAATAAAAG 57.772 32.000 0.00 0.00 0.00 2.27
1245 1271 7.596749 TTGCGTGAAAGGTTGAAAAATAAAA 57.403 28.000 0.00 0.00 0.00 1.52
1249 1275 5.063312 CAGTTTGCGTGAAAGGTTGAAAAAT 59.937 36.000 0.00 0.00 0.00 1.82
1410 4059 5.696822 ACATGAAGCGCATCATTGATTATC 58.303 37.500 24.38 0.00 37.96 1.75
1505 4154 5.627182 AAACTATGATGACCAGAGCTCAT 57.373 39.130 17.77 0.00 37.62 2.90
1506 4155 5.426689 AAAACTATGATGACCAGAGCTCA 57.573 39.130 17.77 0.00 37.62 4.26
1552 4201 6.060028 TGCTTGTAAACAATCTTGTCTGTC 57.940 37.500 0.00 0.00 41.31 3.51
1579 4228 8.366359 AGACATTAGCATTTAATTGGAAAGGT 57.634 30.769 0.00 0.00 0.00 3.50
1903 4580 8.049117 TCCTCTTAAATAACTGTCTGCATTGAT 58.951 33.333 0.00 0.00 0.00 2.57
1978 4655 9.077674 CACATCAGAGTAATACTTACAGTGTTC 57.922 37.037 0.00 0.00 38.60 3.18
2073 4750 7.639850 CGACACCATGAATTTGTATATGTTGAC 59.360 37.037 0.00 0.00 0.00 3.18
2079 4756 9.692749 CTACTACGACACCATGAATTTGTATAT 57.307 33.333 0.00 0.00 0.00 0.86
2182 4859 4.699735 ACAAGCAATCAACATCGGAATACA 59.300 37.500 0.00 0.00 0.00 2.29
2183 4860 5.065218 AGACAAGCAATCAACATCGGAATAC 59.935 40.000 0.00 0.00 0.00 1.89
2730 5414 6.815089 TGTTTCACATTTCTTAAGTTGGCAT 58.185 32.000 1.63 0.00 0.00 4.40
2810 5494 5.652994 ACAGAGGTTAGAGCTAAGTTCAG 57.347 43.478 0.00 0.00 0.00 3.02
2891 5575 5.501156 AGAAGTAATGGGATTCTCCACAAC 58.499 41.667 0.00 0.00 39.97 3.32
2924 5608 4.575885 TGGGAAAGAAATAGACTTCCACG 58.424 43.478 2.40 0.00 0.00 4.94
2950 5634 8.437575 TCCTACTAAACTTTCACAAGGAGAATT 58.562 33.333 0.00 0.00 33.82 2.17
2951 5635 7.974504 TCCTACTAAACTTTCACAAGGAGAAT 58.025 34.615 0.00 0.00 33.82 2.40
3066 5750 2.821969 AGGTGCCTTTGCTAATTCTGTG 59.178 45.455 0.00 0.00 38.71 3.66
3394 6078 9.812347 AGAATTATGGATATTAGACATTGGCAA 57.188 29.630 0.68 0.68 0.00 4.52
3413 6097 9.355215 CGAACTCAGTGTAAGTGTAAGAATTAT 57.645 33.333 0.00 0.00 38.75 1.28
3440 6124 3.996480 AGAAAAGTTCTCCTCAGTTCCG 58.004 45.455 0.00 0.00 34.07 4.30
3530 6214 1.541147 TGCACTCACAAATAGCCAAGC 59.459 47.619 0.00 0.00 0.00 4.01
3605 6289 2.030363 CGTTCAAAGTGCAGGCCATAAA 60.030 45.455 5.01 0.00 0.00 1.40
3613 6297 0.311790 ATGCCACGTTCAAAGTGCAG 59.688 50.000 0.00 0.00 38.22 4.41
3691 6375 8.680903 AGTTATTTCCTGAAATGCATGAACTAG 58.319 33.333 13.92 0.00 40.83 2.57
3721 6406 7.121759 TGCGAGTAATAGTAGTTTAGACACCTT 59.878 37.037 0.00 0.00 0.00 3.50
3762 6447 3.476552 TGTCAGTTTGTTCCAGCTAAGG 58.523 45.455 0.00 0.00 0.00 2.69
3807 6492 2.802816 CAGAGTAGTGATATTTGGCGCC 59.197 50.000 22.73 22.73 0.00 6.53
3865 6550 6.347725 CCAGAAAACAGAAATTAGTCGAGTGG 60.348 42.308 2.10 0.00 0.00 4.00
3945 6630 7.939588 ACTTACAAAAGCTGAAGATTAGGAAGT 59.060 33.333 5.81 5.81 36.05 3.01
4065 6750 9.173939 GTGAAAAATTATCCAATAGAAGATGCG 57.826 33.333 0.00 0.00 0.00 4.73
4177 6863 1.494824 ACGTTTGCAGTAAGACGGAC 58.505 50.000 11.37 0.00 39.63 4.79
4180 6866 7.213706 CACATTATTTACGTTTGCAGTAAGACG 59.786 37.037 0.00 6.97 41.00 4.18
4225 6911 5.023533 TCAATATACACCTGCAGAACCTC 57.976 43.478 17.39 0.00 0.00 3.85
4226 6912 5.130975 TGATCAATATACACCTGCAGAACCT 59.869 40.000 17.39 0.00 0.00 3.50
4227 6913 5.368145 TGATCAATATACACCTGCAGAACC 58.632 41.667 17.39 0.00 0.00 3.62
4228 6914 6.540189 AGTTGATCAATATACACCTGCAGAAC 59.460 38.462 17.39 6.17 0.00 3.01
4289 7000 3.763897 ACAGGGTGATTTTGTAGCAATCC 59.236 43.478 0.00 0.00 30.64 3.01
4295 7006 6.655003 ACAACTCATACAGGGTGATTTTGTAG 59.345 38.462 0.00 0.00 33.46 2.74
4589 7341 7.182930 AGTCTTGAGGGTATTATTCTGGAAGTT 59.817 37.037 0.00 0.00 33.76 2.66
4597 7349 7.097834 CCGGAATAGTCTTGAGGGTATTATTC 58.902 42.308 0.00 0.00 0.00 1.75
4604 7356 0.831307 GCCGGAATAGTCTTGAGGGT 59.169 55.000 5.05 0.00 0.00 4.34
4803 7664 7.228314 TGTAGCAACTCTAACTAGACAACAT 57.772 36.000 0.00 0.00 0.00 2.71
4928 7790 8.023128 GCACAAAATGACAACAGTAGTGATTAT 58.977 33.333 4.09 0.00 34.57 1.28
4992 7854 1.422024 AGAGGCTGTCTATCGGAGCTA 59.578 52.381 0.00 0.00 31.71 3.32
5080 7942 4.513692 TCGTAATTTTTATCCGATGGGCAG 59.486 41.667 0.00 0.00 0.00 4.85
5420 8282 6.773976 AGAACCAAGTGTGAAATTGAGAAA 57.226 33.333 0.00 0.00 0.00 2.52
5506 8368 5.776358 TCCCACATGGCCTAAAATTAGAAT 58.224 37.500 3.32 0.00 32.47 2.40
5554 8416 5.705441 TGACCAAACTAACAGAAAGGCTATG 59.295 40.000 0.00 0.00 0.00 2.23
5555 8417 5.876357 TGACCAAACTAACAGAAAGGCTAT 58.124 37.500 0.00 0.00 0.00 2.97
5718 8678 8.623903 GCCATAGAAACAAATGAATCATGAGTA 58.376 33.333 0.09 0.00 0.00 2.59
5794 8754 9.730420 GGATATTCTGTAAAAATTACGCACAAT 57.270 29.630 0.00 0.00 0.00 2.71
6024 8984 2.759191 TGAATAAGATGCCTGCTAGCG 58.241 47.619 10.77 4.90 34.65 4.26
6033 8993 4.513318 GGTGCTACCTCTTGAATAAGATGC 59.487 45.833 0.00 0.00 41.83 3.91
6208 9168 3.577848 CTCCATCATCTAGAGTTCCCCTG 59.422 52.174 0.00 0.00 0.00 4.45
6211 9171 5.878406 TTTCTCCATCATCTAGAGTTCCC 57.122 43.478 0.00 0.00 0.00 3.97
6229 9189 5.047660 TGCCCGTTTAATTGCTACAATTTCT 60.048 36.000 10.52 0.00 0.00 2.52
6244 9204 2.238646 AGAATCCTCATGTGCCCGTTTA 59.761 45.455 0.00 0.00 0.00 2.01
6302 9262 4.023792 GCGATGATGCAATCTGGATAACAA 60.024 41.667 0.00 0.00 45.81 2.83
6337 9297 5.709631 TGCTTCATCACAATAGCCAACTAAA 59.290 36.000 0.00 0.00 32.73 1.85
6478 9438 5.469373 TCGAATGACAGCATGAATAACAC 57.531 39.130 0.00 0.00 39.69 3.32
6555 9515 7.331934 GCTGTGTACTTACAAGAAAGATGATCA 59.668 37.037 0.00 0.00 38.04 2.92
6680 9641 1.210538 TTGGATGAGCAGGATCAGCT 58.789 50.000 11.22 11.22 46.82 4.24
6843 9804 7.775053 TGAGGTGCTTAATTTAGGAAAACAT 57.225 32.000 0.00 0.00 0.00 2.71
6953 9914 6.214615 TGTGTAGATACAGAATTCCCTTGGAA 59.785 38.462 0.65 0.00 40.49 3.53
7088 10049 0.472471 TCCCTTCAATATCCGGCACC 59.528 55.000 0.00 0.00 0.00 5.01
7215 10177 5.053978 AGATATCCCTGCCGAAAAGAAAT 57.946 39.130 0.00 0.00 0.00 2.17
7238 10200 4.339530 TGAGTCAGGAAGTATTCTGGATCG 59.660 45.833 0.00 0.00 46.56 3.69
7396 10358 3.380954 TGTCATTTTCTGTGAAGCAAGCA 59.619 39.130 0.00 0.00 0.00 3.91
7551 10622 2.034687 GCAGTCTGGTGGGCACAT 59.965 61.111 0.00 0.00 0.00 3.21
7556 10627 2.569059 CTATTGATGCAGTCTGGTGGG 58.431 52.381 1.14 0.00 0.00 4.61
7559 10630 3.370953 GGAACCTATTGATGCAGTCTGGT 60.371 47.826 1.14 0.00 0.00 4.00
7621 10692 1.988107 TCTCTGACATGGAAGGCCTTT 59.012 47.619 21.54 2.04 34.31 3.11
7684 10755 5.441718 AGTCTCCAGCAAATTAAGATCCA 57.558 39.130 0.00 0.00 0.00 3.41
7692 10763 2.301870 TGTCCGTAGTCTCCAGCAAATT 59.698 45.455 0.00 0.00 0.00 1.82
7693 10764 1.899814 TGTCCGTAGTCTCCAGCAAAT 59.100 47.619 0.00 0.00 0.00 2.32
7695 10766 0.601558 GTGTCCGTAGTCTCCAGCAA 59.398 55.000 0.00 0.00 0.00 3.91
7715 10786 4.796618 GCTTTACTCATATCACCCGAGTCC 60.797 50.000 0.00 0.00 40.41 3.85
7721 10792 5.880332 TGACAAAGCTTTACTCATATCACCC 59.120 40.000 12.25 0.00 0.00 4.61
7737 10808 3.698029 TGCTGAAGAAGTTGACAAAGC 57.302 42.857 0.00 0.00 0.00 3.51
7739 10810 3.181501 CGGTTGCTGAAGAAGTTGACAAA 60.182 43.478 0.00 0.00 0.00 2.83
7784 10855 2.165030 GCTTGCATTAACACTGCCAGAT 59.835 45.455 0.00 0.00 38.89 2.90
7893 10965 3.111853 TCCGAGTATGCTAAGCCAATG 57.888 47.619 0.00 0.00 0.00 2.82
7898 10970 4.752101 ACAAATGATCCGAGTATGCTAAGC 59.248 41.667 0.00 0.00 0.00 3.09
7902 10974 4.679373 AGACAAATGATCCGAGTATGCT 57.321 40.909 0.00 0.00 0.00 3.79
7903 10975 4.572389 ACAAGACAAATGATCCGAGTATGC 59.428 41.667 0.00 0.00 0.00 3.14
7904 10976 6.756542 TGTACAAGACAAATGATCCGAGTATG 59.243 38.462 0.00 0.00 34.15 2.39
7906 10978 6.275494 TGTACAAGACAAATGATCCGAGTA 57.725 37.500 0.00 0.00 34.15 2.59
7907 10979 5.147330 TGTACAAGACAAATGATCCGAGT 57.853 39.130 0.00 0.00 34.15 4.18
7940 11012 9.593134 CTCTAGTTTACATCAAAGCTGACTAAT 57.407 33.333 0.00 0.00 33.30 1.73
7981 11053 7.443575 ACAAGCTATGTTAATATTCCTCAGCTG 59.556 37.037 7.63 7.63 40.06 4.24
7996 11068 1.890876 TGGAACGCACAAGCTATGTT 58.109 45.000 0.00 0.00 41.46 2.71
8007 11079 6.150307 TGAAGCTTCTAAAATTATGGAACGCA 59.850 34.615 26.09 0.00 0.00 5.24
8016 11088 9.278978 TGTGTGTACATGAAGCTTCTAAAATTA 57.721 29.630 26.09 5.44 0.00 1.40
8019 11091 6.765989 ACTGTGTGTACATGAAGCTTCTAAAA 59.234 34.615 26.09 7.35 35.97 1.52
8038 11110 1.413812 TCACTGCTCATGTCACTGTGT 59.586 47.619 7.79 0.00 35.50 3.72
8041 11113 3.597255 AGAATCACTGCTCATGTCACTG 58.403 45.455 0.00 0.00 0.00 3.66
8054 11126 4.713814 TGTCCAGCATAAGAGAGAATCACT 59.286 41.667 0.00 0.00 37.77 3.41
8058 11130 5.131642 TGGAATGTCCAGCATAAGAGAGAAT 59.868 40.000 0.00 0.00 42.67 2.40
8083 11155 4.384846 GTGCACATGAAGCTTCTGAAATTG 59.615 41.667 26.09 15.44 0.00 2.32
8159 11234 2.033801 GTGTGTCTCAAGCACTGCAATT 59.966 45.455 3.30 0.00 37.70 2.32
8235 11310 6.421202 GTCGGCCTAGATTACATGTAAAGAAG 59.579 42.308 21.57 16.74 0.00 2.85
8408 11486 8.091449 CCATCAGTCCTGAAATATAGGTACTTC 58.909 40.741 0.37 0.00 43.58 3.01
8646 11770 6.439636 TCTATAGCCCTTCACATGCTATTT 57.560 37.500 8.36 0.00 43.82 1.40
8724 11849 6.164408 TGCATACTCAAACAGTGATAAACG 57.836 37.500 0.00 0.00 36.43 3.60
8759 11884 1.611006 TGACTATCATCGAGCTGAGGC 59.389 52.381 0.00 0.00 39.06 4.70
8793 11926 4.695217 TGGTTAAATCGATGGTCAAAGC 57.305 40.909 0.00 0.07 0.00 3.51
8810 11943 9.840427 GCGCATATAACTCATATTTTATTGGTT 57.160 29.630 0.30 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.