Multiple sequence alignment - TraesCS6D01G267500

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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 TraesCS6D01G267500 chr6D 100.000 5684 0 0 1 5684 377542280 377547963 0.000000e+00 10497
1 TraesCS6D01G267500 chr6D 100.000 214 0 0 6053 6266 377548332 377548545 4.550000e-106 396
2 TraesCS6D01G267500 chr6B 95.191 3660 133 25 2046 5684 563996929 564000566 0.000000e+00 5744
3 TraesCS6D01G267500 chr6B 89.723 1479 94 29 602 2045 563995356 563996811 0.000000e+00 1836
4 TraesCS6D01G267500 chr6B 88.079 604 46 13 1 579 227837834 227837232 0.000000e+00 693
5 TraesCS6D01G267500 chr6B 92.453 371 26 2 1 369 578657103 578656733 4.300000e-146 529
6 TraesCS6D01G267500 chr6B 97.183 213 5 1 6054 6266 564000598 564000809 5.970000e-95 359
7 TraesCS6D01G267500 chr6A 94.674 3624 131 26 2046 5648 519206502 519210084 0.000000e+00 5566
8 TraesCS6D01G267500 chr6A 93.833 1200 45 8 853 2045 519205255 519206432 0.000000e+00 1779
9 TraesCS6D01G267500 chr6A 90.278 576 36 5 3 576 601670008 601670565 0.000000e+00 736
10 TraesCS6D01G267500 chr6A 93.333 360 23 1 1 359 24835792 24836151 1.200000e-146 531
11 TraesCS6D01G267500 chr6A 90.746 389 29 7 191 575 24836124 24836509 4.330000e-141 512
12 TraesCS6D01G267500 chr6A 96.209 211 8 0 577 787 519205048 519205258 4.650000e-91 346
13 TraesCS6D01G267500 chr4D 96.213 581 20 2 1 580 345432718 345433297 0.000000e+00 950
14 TraesCS6D01G267500 chr4D 93.318 449 25 5 121 567 223879210 223878765 0.000000e+00 658
15 TraesCS6D01G267500 chr4D 88.889 198 17 4 1832 2027 399723057 399723251 8.120000e-59 239
16 TraesCS6D01G267500 chr4D 92.771 83 6 0 1 83 223879291 223879209 3.070000e-23 121
17 TraesCS6D01G267500 chr3D 94.310 580 30 2 1 577 71973841 71973262 0.000000e+00 885
18 TraesCS6D01G267500 chr5D 92.466 584 38 6 1 581 95957482 95956902 0.000000e+00 830
19 TraesCS6D01G267500 chr5D 95.331 257 12 0 324 580 396948983 396948727 5.850000e-110 409
20 TraesCS6D01G267500 chr7D 92.411 448 28 6 138 581 563341939 563342384 8.860000e-178 634
21 TraesCS6D01G267500 chr7A 90.439 387 35 2 191 576 200063281 200062896 5.600000e-140 508
22 TraesCS6D01G267500 chr4B 86.869 198 18 5 1832 2027 493764672 493764863 1.370000e-51 215
23 TraesCS6D01G267500 chr5B 89.726 146 13 2 1 144 272677454 272677599 1.070000e-42 185


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 TraesCS6D01G267500 chr6D 377542280 377548545 6265 False 5446.500000 10497 100.000000 1 6266 2 chr6D.!!$F1 6265
1 TraesCS6D01G267500 chr6B 563995356 564000809 5453 False 2646.333333 5744 94.032333 602 6266 3 chr6B.!!$F1 5664
2 TraesCS6D01G267500 chr6B 227837232 227837834 602 True 693.000000 693 88.079000 1 579 1 chr6B.!!$R1 578
3 TraesCS6D01G267500 chr6A 519205048 519210084 5036 False 2563.666667 5566 94.905333 577 5648 3 chr6A.!!$F3 5071
4 TraesCS6D01G267500 chr6A 601670008 601670565 557 False 736.000000 736 90.278000 3 576 1 chr6A.!!$F1 573
5 TraesCS6D01G267500 chr6A 24835792 24836509 717 False 521.500000 531 92.039500 1 575 2 chr6A.!!$F2 574
6 TraesCS6D01G267500 chr4D 345432718 345433297 579 False 950.000000 950 96.213000 1 580 1 chr4D.!!$F1 579
7 TraesCS6D01G267500 chr4D 223878765 223879291 526 True 389.500000 658 93.044500 1 567 2 chr4D.!!$R1 566
8 TraesCS6D01G267500 chr3D 71973262 71973841 579 True 885.000000 885 94.310000 1 577 1 chr3D.!!$R1 576
9 TraesCS6D01G267500 chr5D 95956902 95957482 580 True 830.000000 830 92.466000 1 581 1 chr5D.!!$R1 580

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
811 975 0.035820 TGTTAACTGGGCCGGACATC 60.036 55.000 21.81 7.35 0.00 3.06 F
827 991 0.318784 CATCCTTACCGCTCGCCTAC 60.319 60.000 0.00 0.00 0.00 3.18 F
1119 1317 0.631753 CCTCCTCCTCCTCCAGTGTA 59.368 60.000 0.00 0.00 0.00 2.90 F
1925 2130 0.684535 TGCCTTCACTGGAATGACGA 59.315 50.000 0.00 0.00 31.34 4.20 F
2869 3194 1.881973 TCTTCCTGAAGTGCACAATGC 59.118 47.619 21.04 5.48 39.39 3.56 F
3290 3619 0.036577 AGGCTGTGTCTCTGCATGAC 60.037 55.000 11.62 11.62 41.72 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 2004 1.824852 GAAATTGCCCGTTCCCTGATT 59.175 47.619 0.00 0.00 0.00 2.57 R
2033 2238 2.435422 CAAACCCCCATTTTGGAATGC 58.565 47.619 0.00 0.00 40.96 3.56 R
2740 3064 2.711009 ACAGGAGAAATGTGGGACTTGA 59.289 45.455 0.00 0.00 0.00 3.02 R
3199 3525 5.415701 ACAGAAAAGGGTGCACAATATACTG 59.584 40.000 20.43 20.31 0.00 2.74 R
3955 4293 0.442699 GAACATCGAACCAACGAGGC 59.557 55.000 0.00 0.00 45.67 4.70 R
5282 5627 0.322906 GAAACCTTCAGGGGGCAGAG 60.323 60.000 0.00 0.00 40.27 3.35 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
22 23 1.733041 GTGACGCAGCTGCTCGTTA 60.733 57.895 34.22 20.28 39.22 3.18
175 176 3.769739 AGCTTCTACCACAACATCACA 57.230 42.857 0.00 0.00 0.00 3.58
231 238 1.065564 GCAGGAATGCAGAGAAGAGGT 60.066 52.381 0.00 0.00 34.41 3.85
232 239 2.617532 GCAGGAATGCAGAGAAGAGGTT 60.618 50.000 0.00 0.00 34.41 3.50
519 671 3.797353 AGCGCGGGGATCCAACAT 61.797 61.111 15.23 0.00 0.00 2.71
762 915 8.194104 TGAAATCTTTTCAAAACCGATGAAAGA 58.806 29.630 0.37 0.00 44.83 2.52
791 955 2.074376 TGCAAAAACGTTCGTGTACG 57.926 45.000 0.00 0.00 46.52 3.67
809 973 1.071814 GTGTTAACTGGGCCGGACA 59.928 57.895 21.81 10.58 0.00 4.02
810 974 0.322187 GTGTTAACTGGGCCGGACAT 60.322 55.000 21.81 7.34 0.00 3.06
811 975 0.035820 TGTTAACTGGGCCGGACATC 60.036 55.000 21.81 7.35 0.00 3.06
812 976 0.746923 GTTAACTGGGCCGGACATCC 60.747 60.000 21.81 2.78 0.00 3.51
813 977 0.912487 TTAACTGGGCCGGACATCCT 60.912 55.000 21.81 0.00 0.00 3.24
814 978 0.912487 TAACTGGGCCGGACATCCTT 60.912 55.000 21.81 3.91 0.00 3.36
815 979 0.912487 AACTGGGCCGGACATCCTTA 60.912 55.000 21.81 0.00 0.00 2.69
816 980 1.146263 CTGGGCCGGACATCCTTAC 59.854 63.158 11.00 0.00 0.00 2.34
817 981 2.325393 CTGGGCCGGACATCCTTACC 62.325 65.000 11.00 0.00 0.00 2.85
818 982 2.108362 GGCCGGACATCCTTACCG 59.892 66.667 5.05 0.00 45.24 4.02
819 983 2.588034 GCCGGACATCCTTACCGC 60.588 66.667 5.05 0.00 44.45 5.68
820 984 3.090219 GCCGGACATCCTTACCGCT 62.090 63.158 5.05 0.00 44.45 5.52
821 985 1.067582 CCGGACATCCTTACCGCTC 59.932 63.158 0.00 0.00 44.45 5.03
822 986 1.299165 CGGACATCCTTACCGCTCG 60.299 63.158 0.00 0.00 40.19 5.03
823 987 1.591863 GGACATCCTTACCGCTCGC 60.592 63.158 0.00 0.00 0.00 5.03
824 988 1.591863 GACATCCTTACCGCTCGCC 60.592 63.158 0.00 0.00 0.00 5.54
825 989 2.017559 GACATCCTTACCGCTCGCCT 62.018 60.000 0.00 0.00 0.00 5.52
826 990 0.754217 ACATCCTTACCGCTCGCCTA 60.754 55.000 0.00 0.00 0.00 3.93
827 991 0.318784 CATCCTTACCGCTCGCCTAC 60.319 60.000 0.00 0.00 0.00 3.18
828 992 1.461911 ATCCTTACCGCTCGCCTACC 61.462 60.000 0.00 0.00 0.00 3.18
829 993 2.025727 CTTACCGCTCGCCTACCG 59.974 66.667 0.00 0.00 38.61 4.02
830 994 3.480225 CTTACCGCTCGCCTACCGG 62.480 68.421 0.00 0.00 46.97 5.28
1091 1286 4.722535 TCAGCTCCGCCCCTTCCT 62.723 66.667 0.00 0.00 0.00 3.36
1092 1287 4.168291 CAGCTCCGCCCCTTCCTC 62.168 72.222 0.00 0.00 0.00 3.71
1093 1288 4.406763 AGCTCCGCCCCTTCCTCT 62.407 66.667 0.00 0.00 0.00 3.69
1094 1289 3.855853 GCTCCGCCCCTTCCTCTC 61.856 72.222 0.00 0.00 0.00 3.20
1095 1290 3.157949 CTCCGCCCCTTCCTCTCC 61.158 72.222 0.00 0.00 0.00 3.71
1096 1291 3.684628 TCCGCCCCTTCCTCTCCT 61.685 66.667 0.00 0.00 0.00 3.69
1097 1292 3.157949 CCGCCCCTTCCTCTCCTC 61.158 72.222 0.00 0.00 0.00 3.71
1098 1293 3.157949 CGCCCCTTCCTCTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
1099 1294 2.370633 GCCCCTTCCTCTCCTCCT 59.629 66.667 0.00 0.00 0.00 3.69
1100 1295 1.764454 GCCCCTTCCTCTCCTCCTC 60.764 68.421 0.00 0.00 0.00 3.71
1101 1296 1.074850 CCCCTTCCTCTCCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
1102 1297 1.598856 CCCCTTCCTCTCCTCCTCCT 61.599 65.000 0.00 0.00 0.00 3.69
1116 1314 1.589399 CCTCCTCCTCCTCCTCCAGT 61.589 65.000 0.00 0.00 0.00 4.00
1119 1317 0.631753 CCTCCTCCTCCTCCAGTGTA 59.368 60.000 0.00 0.00 0.00 2.90
1420 1624 8.659925 AGAAATGATCATACAATCTGTCTCAC 57.340 34.615 9.04 0.00 0.00 3.51
1439 1643 3.075283 TCACCAGTCACAACCCCATTAAT 59.925 43.478 0.00 0.00 0.00 1.40
1442 1646 3.430453 CAGTCACAACCCCATTAATGGT 58.570 45.455 28.62 12.16 46.65 3.55
1479 1683 2.890808 ACTGTCTTTCTTGTGCTCGA 57.109 45.000 0.00 0.00 0.00 4.04
1480 1684 3.393089 ACTGTCTTTCTTGTGCTCGAT 57.607 42.857 0.00 0.00 0.00 3.59
1481 1685 3.321497 ACTGTCTTTCTTGTGCTCGATC 58.679 45.455 0.00 0.00 0.00 3.69
1482 1686 2.328473 TGTCTTTCTTGTGCTCGATCG 58.672 47.619 9.36 9.36 0.00 3.69
1715 1919 6.127897 CCCAAGTGATAAGATGAGTGGTTTTC 60.128 42.308 0.00 0.00 0.00 2.29
1717 1921 5.178797 AGTGATAAGATGAGTGGTTTTCGG 58.821 41.667 0.00 0.00 0.00 4.30
1722 1926 5.373812 AAGATGAGTGGTTTTCGGGATAT 57.626 39.130 0.00 0.00 0.00 1.63
1747 1951 5.947228 TTCTCAATCTTGTACAGCCTTTG 57.053 39.130 0.00 0.06 0.00 2.77
1770 1974 1.067142 TGTCATTGTAGGACTCGCACC 60.067 52.381 0.00 0.00 36.26 5.01
1790 1994 3.257393 CCGAGATAGATGCATACTTGGC 58.743 50.000 0.00 0.00 0.00 4.52
1797 2001 1.103398 ATGCATACTTGGCGGCTTCC 61.103 55.000 11.43 0.00 0.00 3.46
1800 2004 2.305607 ATACTTGGCGGCTTCCCCA 61.306 57.895 11.43 0.00 0.00 4.96
1910 2115 1.140312 TTCTCCTCTGTTTGGTGCCT 58.860 50.000 0.00 0.00 0.00 4.75
1925 2130 0.684535 TGCCTTCACTGGAATGACGA 59.315 50.000 0.00 0.00 31.34 4.20
1948 2153 6.267496 ACTTATGGTTTTGGCAGATACAAC 57.733 37.500 0.00 0.00 0.00 3.32
2033 2238 2.563179 ACCGCTGCTATATTACTCCCTG 59.437 50.000 0.00 0.00 0.00 4.45
2035 2240 2.029020 CGCTGCTATATTACTCCCTGCA 60.029 50.000 0.00 0.00 0.00 4.41
2078 2400 4.289672 AGAACTATTCTTGTGACATGGGGT 59.710 41.667 0.00 0.00 36.36 4.95
2145 2467 6.291377 ACACTGCCATTAATCGATTATGTCT 58.709 36.000 18.18 2.10 0.00 3.41
2571 2893 9.155975 CTGTACTTTTCTGCTATAAGAACATGT 57.844 33.333 0.00 0.00 35.92 3.21
2583 2905 3.592898 AGAACATGTACACTGCATCGA 57.407 42.857 0.00 0.00 0.00 3.59
2658 2980 2.930950 TGGGCAGATATGCTTAACCAC 58.069 47.619 12.80 0.00 34.73 4.16
2740 3064 6.128486 TGTTGTATGGGATTATGAAGCACAT 58.872 36.000 0.00 0.00 44.30 3.21
2869 3194 1.881973 TCTTCCTGAAGTGCACAATGC 59.118 47.619 21.04 5.48 39.39 3.56
3176 3502 6.399639 TTTGGTTTTACAGAACTGGGAATC 57.600 37.500 6.76 0.04 34.19 2.52
3225 3554 7.120579 CAGTATATTGTGCACCCTTTTCTGTAA 59.879 37.037 15.69 0.00 0.00 2.41
3288 3617 2.467962 CAGGCTGTGTCTCTGCATG 58.532 57.895 6.28 4.45 43.57 4.06
3289 3618 2.369654 AGGCTGTGTCTCTGCATGA 58.630 52.632 0.00 0.00 41.72 3.07
3290 3619 0.036577 AGGCTGTGTCTCTGCATGAC 60.037 55.000 11.62 11.62 41.72 3.06
3291 3620 0.036577 GGCTGTGTCTCTGCATGACT 60.037 55.000 17.19 0.00 41.72 3.41
3292 3621 1.077123 GCTGTGTCTCTGCATGACTG 58.923 55.000 17.19 10.53 40.09 3.51
3687 4021 4.400884 TCAGAGTAAGTGCTCTCATCCTTC 59.599 45.833 0.00 0.00 43.37 3.46
3762 4096 6.381498 TCATTAGACTGGGGTATTTGTTGA 57.619 37.500 0.00 0.00 0.00 3.18
3926 4260 4.681942 GCTATATCTTGTGTCGATGGTGTC 59.318 45.833 0.00 0.00 0.00 3.67
3955 4293 3.111853 TGAGTGTCTTGGTGCTTACAG 57.888 47.619 0.00 0.00 0.00 2.74
4021 4360 3.115554 CCTGCTCACGTTTTGGAAAAAG 58.884 45.455 0.00 0.00 34.28 2.27
4036 4375 4.874966 TGGAAAAAGTGAATTTGCAGTTGG 59.125 37.500 0.00 0.00 33.90 3.77
4176 4516 2.711542 AGGGCAACGAAAATGACTAGG 58.288 47.619 0.00 0.00 37.60 3.02
4243 4584 3.340814 AAGATCGTGGCAATCAACTCT 57.659 42.857 2.27 0.00 0.00 3.24
4244 4585 3.340814 AGATCGTGGCAATCAACTCTT 57.659 42.857 2.27 0.00 0.00 2.85
4455 4796 0.898320 AAGAGTGGATCTGGTCACCG 59.102 55.000 0.00 0.00 38.67 4.94
4554 4895 4.967442 TCAGTCCTCCTGAGATGATTCAAT 59.033 41.667 0.00 0.00 45.34 2.57
4580 4921 4.737855 TGAGGAGGTTAGTGCTGTTATC 57.262 45.455 0.00 0.00 0.00 1.75
4732 5073 1.107538 TTATCCCGAGCTGGACGAGG 61.108 60.000 0.00 0.00 42.00 4.63
4916 5257 8.592105 AATCATTTGGCACCAATATTATTTCG 57.408 30.769 2.31 0.00 35.70 3.46
4924 5265 7.704472 TGGCACCAATATTATTTCGTTGAAATC 59.296 33.333 7.96 0.00 40.77 2.17
4925 5266 7.704472 GGCACCAATATTATTTCGTTGAAATCA 59.296 33.333 7.96 0.00 40.77 2.57
4926 5267 8.745837 GCACCAATATTATTTCGTTGAAATCAG 58.254 33.333 7.96 0.00 40.77 2.90
4940 5285 7.012894 TCGTTGAAATCAGTTTAAGTCAACCAT 59.987 33.333 8.34 0.00 34.51 3.55
5053 5398 1.446099 GTGCATCAGCGAACGGAGA 60.446 57.895 0.00 0.00 46.23 3.71
5083 5428 3.852286 TCGTTCACAATACGTAAGCCAT 58.148 40.909 0.00 0.00 45.62 4.40
5240 5585 6.100792 GCTTAAAGCTCTGTCACTATTCAC 57.899 41.667 0.00 0.00 38.45 3.18
5267 5612 9.745018 TGGTCTCAGAAATCTCTTCAAATAAAT 57.255 29.630 0.00 0.00 0.00 1.40
5275 5620 7.607615 AATCTCTTCAAATAAATGGATGGGG 57.392 36.000 0.00 0.00 0.00 4.96
5282 5627 7.716799 TCAAATAAATGGATGGGGTATATGC 57.283 36.000 0.00 0.00 0.00 3.14
5297 5642 1.348008 TATGCTCTGCCCCCTGAAGG 61.348 60.000 0.00 0.00 0.00 3.46
5304 5649 2.361230 CCCCCTGAAGGTTTCGGC 60.361 66.667 0.00 0.00 34.66 5.54
5315 5660 1.210155 GTTTCGGCGAGCAATGCTT 59.790 52.632 9.91 0.00 39.88 3.91
5321 5666 2.084681 GCGAGCAATGCTTGTGTGC 61.085 57.895 22.18 11.85 41.74 4.57
5328 5673 0.823356 AATGCTTGTGTGCCTCCGTT 60.823 50.000 0.00 0.00 0.00 4.44
5360 5705 9.396022 GGTAAATTCTCAATCTGTCCTCATTTA 57.604 33.333 0.00 0.00 0.00 1.40
5363 5708 8.729805 AATTCTCAATCTGTCCTCATTTAGTC 57.270 34.615 0.00 0.00 0.00 2.59
5364 5709 6.857437 TCTCAATCTGTCCTCATTTAGTCA 57.143 37.500 0.00 0.00 0.00 3.41
5365 5710 7.429374 TCTCAATCTGTCCTCATTTAGTCAT 57.571 36.000 0.00 0.00 0.00 3.06
5366 5711 7.855375 TCTCAATCTGTCCTCATTTAGTCATT 58.145 34.615 0.00 0.00 0.00 2.57
5367 5712 8.324306 TCTCAATCTGTCCTCATTTAGTCATTT 58.676 33.333 0.00 0.00 0.00 2.32
5368 5713 8.868522 TCAATCTGTCCTCATTTAGTCATTTT 57.131 30.769 0.00 0.00 0.00 1.82
5369 5714 8.950210 TCAATCTGTCCTCATTTAGTCATTTTC 58.050 33.333 0.00 0.00 0.00 2.29
5379 5724 8.934023 TCATTTAGTCATTTTCTACCACCTTT 57.066 30.769 0.00 0.00 0.00 3.11
5381 5726 6.569179 TTAGTCATTTTCTACCACCTTTGC 57.431 37.500 0.00 0.00 0.00 3.68
5390 5735 0.536460 ACCACCTTTGCCGTCGAAAT 60.536 50.000 0.00 0.00 0.00 2.17
5393 5738 0.889186 ACCTTTGCCGTCGAAATGCT 60.889 50.000 0.00 0.00 0.00 3.79
5406 5751 5.088739 GTCGAAATGCTGTATTTTCACTGG 58.911 41.667 5.21 0.00 39.06 4.00
5409 5754 5.391312 AAATGCTGTATTTTCACTGGACC 57.609 39.130 0.00 0.00 35.47 4.46
5422 5767 0.323633 CTGGACCCCACATGATGCAA 60.324 55.000 0.00 0.00 0.00 4.08
5654 6005 7.083858 CGCATCTGTTTATCTTTTCTTTTGGA 58.916 34.615 0.00 0.00 0.00 3.53
6083 6434 0.320073 TTTTCGGGTCGCCTGTACTG 60.320 55.000 0.00 0.00 0.00 2.74
6109 6460 0.106708 TCTATCATGCCCAAGACGCC 59.893 55.000 0.00 0.00 0.00 5.68
6132 6483 1.741401 CATTCGCGCTTCCTGTCCA 60.741 57.895 5.56 0.00 0.00 4.02
6148 6499 0.901580 TCCAGTTCTACCGGTGGACC 60.902 60.000 21.61 14.46 34.03 4.46
6212 6563 2.536365 GGACACGCTATCGAAACATGA 58.464 47.619 0.00 0.00 39.41 3.07
6247 6598 7.087639 ACGCCATTGAAAAATCGAGAAAATTA 58.912 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.227674 GGATCGCCGGAAGCAAGAT 60.228 57.895 5.05 0.00 44.04 2.40
62 63 0.526211 CATCTTGGTGACGACCTCGA 59.474 55.000 0.78 0.00 43.58 4.04
231 238 6.111382 TGCAAAAATTTCACAACATCTCCAA 58.889 32.000 0.00 0.00 0.00 3.53
232 239 5.668471 TGCAAAAATTTCACAACATCTCCA 58.332 33.333 0.00 0.00 0.00 3.86
478 630 1.807226 CCGTCCGATGTAGTGCTCA 59.193 57.895 0.00 0.00 0.00 4.26
519 671 1.604147 ATATCCGCCGCATCGATGGA 61.604 55.000 26.00 15.04 35.32 3.41
616 768 5.925397 ACACGTTGTACATTTTCCGTATACA 59.075 36.000 3.32 0.00 0.00 2.29
762 915 5.518487 ACGAACGTTTTTGCAAAGATGAAAT 59.482 32.000 24.25 12.22 0.00 2.17
791 955 0.322187 ATGTCCGGCCCAGTTAACAC 60.322 55.000 8.61 0.00 0.00 3.32
797 961 1.306654 TAAGGATGTCCGGCCCAGT 60.307 57.895 0.00 0.00 42.08 4.00
809 973 1.461911 GGTAGGCGAGCGGTAAGGAT 61.462 60.000 0.00 0.00 0.00 3.24
810 974 2.123428 GGTAGGCGAGCGGTAAGGA 61.123 63.158 0.00 0.00 0.00 3.36
811 975 2.416260 GGTAGGCGAGCGGTAAGG 59.584 66.667 0.00 0.00 0.00 2.69
812 976 2.025727 CGGTAGGCGAGCGGTAAG 59.974 66.667 11.42 0.00 45.37 2.34
818 982 4.344474 CGATCCCGGTAGGCGAGC 62.344 72.222 0.00 0.00 35.76 5.03
819 983 2.593725 TCGATCCCGGTAGGCGAG 60.594 66.667 0.00 0.00 35.76 5.03
820 984 2.593725 CTCGATCCCGGTAGGCGA 60.594 66.667 0.00 3.13 35.76 5.54
821 985 2.593725 TCTCGATCCCGGTAGGCG 60.594 66.667 0.00 0.00 35.76 5.52
822 986 1.228184 TCTCTCGATCCCGGTAGGC 60.228 63.158 0.00 0.00 35.76 3.93
823 987 0.108963 ACTCTCTCGATCCCGGTAGG 59.891 60.000 0.00 0.00 36.24 3.18
824 988 1.071071 AGACTCTCTCGATCCCGGTAG 59.929 57.143 0.00 0.00 36.24 3.18
825 989 1.070445 GAGACTCTCTCGATCCCGGTA 59.930 57.143 0.00 0.00 33.35 4.02
826 990 0.179040 GAGACTCTCTCGATCCCGGT 60.179 60.000 0.00 0.00 33.35 5.28
827 991 2.624169 GAGACTCTCTCGATCCCGG 58.376 63.158 0.00 0.00 33.35 5.73
844 1008 2.047655 GTTGTGACGATGGGGCGA 60.048 61.111 0.00 0.00 34.83 5.54
939 1134 1.744014 GGGGCTTATCCGCTCGTTA 59.256 57.895 0.00 0.00 43.89 3.18
1088 1283 0.996762 GGAGGAGGAGGAGGAGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1091 1286 0.996762 GGAGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
1092 1287 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1093 1288 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1094 1289 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1095 1290 1.292941 TGGAGGAGGAGGAGGAGGAG 61.293 65.000 0.00 0.00 0.00 3.69
1096 1291 1.230650 TGGAGGAGGAGGAGGAGGA 60.231 63.158 0.00 0.00 0.00 3.71
1097 1292 1.232792 CTGGAGGAGGAGGAGGAGG 59.767 68.421 0.00 0.00 0.00 4.30
1098 1293 0.396974 CACTGGAGGAGGAGGAGGAG 60.397 65.000 0.00 0.00 0.00 3.69
1099 1294 1.149782 ACACTGGAGGAGGAGGAGGA 61.150 60.000 0.00 0.00 0.00 3.71
1100 1295 0.631753 TACACTGGAGGAGGAGGAGG 59.368 60.000 0.00 0.00 0.00 4.30
1101 1296 1.770294 GTACACTGGAGGAGGAGGAG 58.230 60.000 0.00 0.00 0.00 3.69
1102 1297 0.034380 CGTACACTGGAGGAGGAGGA 60.034 60.000 0.00 0.00 0.00 3.71
1116 1314 3.766691 GAGAAGCGGGGGCGTACA 61.767 66.667 0.00 0.00 0.00 2.90
1420 1624 2.760092 CCATTAATGGGGTTGTGACTGG 59.240 50.000 24.61 0.00 44.31 4.00
1439 1643 8.458573 ACAGTAATTGTGAAAACTGAATACCA 57.541 30.769 10.10 0.00 41.47 3.25
1479 1683 2.416836 CCATTCCTACACACGACACGAT 60.417 50.000 0.00 0.00 0.00 3.73
1480 1684 1.068125 CCATTCCTACACACGACACGA 60.068 52.381 0.00 0.00 0.00 4.35
1481 1685 1.068125 TCCATTCCTACACACGACACG 60.068 52.381 0.00 0.00 0.00 4.49
1482 1686 2.607187 CTCCATTCCTACACACGACAC 58.393 52.381 0.00 0.00 0.00 3.67
1704 1908 4.771114 ATGATATCCCGAAAACCACTCA 57.229 40.909 0.00 0.00 0.00 3.41
1715 1919 7.154656 TGTACAAGATTGAGAATGATATCCCG 58.845 38.462 0.00 0.00 0.00 5.14
1717 1921 7.118971 GGCTGTACAAGATTGAGAATGATATCC 59.881 40.741 0.00 0.00 0.00 2.59
1722 1926 5.426689 AGGCTGTACAAGATTGAGAATGA 57.573 39.130 0.00 0.00 0.00 2.57
1747 1951 3.064207 TGCGAGTCCTACAATGACAAAC 58.936 45.455 0.00 0.00 35.15 2.93
1770 1974 2.919859 CGCCAAGTATGCATCTATCTCG 59.080 50.000 0.19 0.00 0.00 4.04
1800 2004 1.824852 GAAATTGCCCGTTCCCTGATT 59.175 47.619 0.00 0.00 0.00 2.57
1910 2115 4.020573 ACCATAAGTCGTCATTCCAGTGAA 60.021 41.667 0.00 0.00 34.33 3.18
1925 2130 5.106317 CGTTGTATCTGCCAAAACCATAAGT 60.106 40.000 0.00 0.00 0.00 2.24
2033 2238 2.435422 CAAACCCCCATTTTGGAATGC 58.565 47.619 0.00 0.00 40.96 3.56
2078 2400 7.561722 TGAAATAAAATGGAATCCCCGTGAATA 59.438 33.333 0.00 0.00 37.93 1.75
2119 2441 7.283127 AGACATAATCGATTAATGGCAGTGTTT 59.717 33.333 21.05 11.36 0.00 2.83
2131 2453 6.581166 CGACGAATTCCAGACATAATCGATTA 59.419 38.462 19.63 19.63 0.00 1.75
2145 2467 2.813474 CGGCTGCGACGAATTCCA 60.813 61.111 0.00 0.00 35.20 3.53
2198 2520 9.944663 GCTGTATTCGGAACATTTAATTAATCA 57.055 29.630 0.00 0.00 0.00 2.57
2348 2670 5.226396 CGGCACCAAACTCAAAAATCAATA 58.774 37.500 0.00 0.00 0.00 1.90
2396 2718 4.164988 AGGACCATCTAAAGTTCTCCATGG 59.835 45.833 4.97 4.97 37.42 3.66
2549 2871 8.936864 GTGTACATGTTCTTATAGCAGAAAAGT 58.063 33.333 2.30 0.00 34.50 2.66
2571 2893 4.693095 TGCAAAATAGTTCGATGCAGTGTA 59.307 37.500 3.59 0.00 41.67 2.90
2583 2905 6.870971 TCTAAACGAACCTGCAAAATAGTT 57.129 33.333 0.00 0.00 0.00 2.24
2658 2980 5.440610 AGAAAATGTAATACCTCAGGGCTG 58.559 41.667 0.00 0.00 35.63 4.85
2714 3038 6.606796 TGTGCTTCATAATCCCATACAACATT 59.393 34.615 0.00 0.00 0.00 2.71
2715 3039 6.128486 TGTGCTTCATAATCCCATACAACAT 58.872 36.000 0.00 0.00 0.00 2.71
2726 3050 4.883585 TGGGACTTGATGTGCTTCATAATC 59.116 41.667 0.00 0.00 36.83 1.75
2740 3064 2.711009 ACAGGAGAAATGTGGGACTTGA 59.289 45.455 0.00 0.00 0.00 3.02
3196 3522 6.319658 AGAAAAGGGTGCACAATATACTGATG 59.680 38.462 20.43 0.00 0.00 3.07
3197 3523 6.319658 CAGAAAAGGGTGCACAATATACTGAT 59.680 38.462 20.43 0.00 0.00 2.90
3198 3524 5.647658 CAGAAAAGGGTGCACAATATACTGA 59.352 40.000 20.43 0.00 0.00 3.41
3199 3525 5.415701 ACAGAAAAGGGTGCACAATATACTG 59.584 40.000 20.43 20.31 0.00 2.74
3225 3554 9.461312 TTCATACTTTAAATGCCAGTCTATTGT 57.539 29.630 0.00 0.00 0.00 2.71
3248 3577 6.875726 CCTGTACAAGACTCAAGATGATTTCA 59.124 38.462 0.00 0.00 0.00 2.69
3926 4260 3.125829 CACCAAGACACTCAAATGGATCG 59.874 47.826 0.00 0.00 35.16 3.69
3955 4293 0.442699 GAACATCGAACCAACGAGGC 59.557 55.000 0.00 0.00 45.67 4.70
4021 4360 2.028748 AGATGCCCAACTGCAAATTCAC 60.029 45.455 0.00 0.00 45.84 3.18
4176 4516 5.064441 AGCATTTCTCCAGTTTTATGTGC 57.936 39.130 0.00 0.00 0.00 4.57
4243 4584 3.153919 GTGGATGGTGCCAAGAAGTTAA 58.846 45.455 0.00 0.00 40.20 2.01
4244 4585 2.554344 GGTGGATGGTGCCAAGAAGTTA 60.554 50.000 0.00 0.00 40.20 2.24
4455 4796 4.700692 GGGGAAACTTTCAGACCTGATAAC 59.299 45.833 0.01 0.00 39.64 1.89
4554 4895 1.699634 AGCACTAACCTCCTCAAAGCA 59.300 47.619 0.00 0.00 0.00 3.91
4580 4921 5.865552 CAGTTCTGAAAATAATTGGTGCCAG 59.134 40.000 0.00 0.00 0.00 4.85
4732 5073 4.873259 GTCCAAGATAAACTGAAGAGCCTC 59.127 45.833 0.00 0.00 0.00 4.70
4898 5239 6.516739 TTCAACGAAATAATATTGGTGCCA 57.483 33.333 0.00 0.00 0.00 4.92
4916 5257 8.871686 AATGGTTGACTTAAACTGATTTCAAC 57.128 30.769 4.10 4.10 36.47 3.18
4940 5285 2.955660 CCTTGGCGCCCTGAAATATTAA 59.044 45.455 26.77 6.12 0.00 1.40
5053 5398 5.657474 ACGTATTGTGAACGATACAGGATT 58.343 37.500 17.17 0.00 42.90 3.01
5059 5404 4.799949 TGGCTTACGTATTGTGAACGATAC 59.200 41.667 9.85 9.85 42.90 2.24
5083 5428 3.237746 AGCTAGGCTGCAAGATCTATGA 58.762 45.455 0.50 0.00 37.57 2.15
5134 5479 1.813513 AATGTGAGACGCCAAGGAAG 58.186 50.000 0.00 0.00 0.00 3.46
5240 5585 8.783833 TTATTTGAAGAGATTTCTGAGACCAG 57.216 34.615 0.00 0.00 41.74 4.00
5267 5612 1.630369 GCAGAGCATATACCCCATCCA 59.370 52.381 0.00 0.00 0.00 3.41
5268 5613 1.065126 GGCAGAGCATATACCCCATCC 60.065 57.143 0.00 0.00 0.00 3.51
5275 5620 1.352083 TCAGGGGGCAGAGCATATAC 58.648 55.000 0.00 0.00 0.00 1.47
5282 5627 0.322906 GAAACCTTCAGGGGGCAGAG 60.323 60.000 0.00 0.00 40.27 3.35
5297 5642 1.067199 CAAGCATTGCTCGCCGAAAC 61.067 55.000 12.39 0.00 40.39 2.78
5315 5660 0.813610 CAAGTCAACGGAGGCACACA 60.814 55.000 0.00 0.00 0.00 3.72
5321 5666 4.324267 AGAATTTACCAAGTCAACGGAGG 58.676 43.478 0.00 0.00 28.83 4.30
5328 5673 6.655003 GGACAGATTGAGAATTTACCAAGTCA 59.345 38.462 0.00 0.00 28.83 3.41
5360 5705 3.826729 GGCAAAGGTGGTAGAAAATGACT 59.173 43.478 0.00 0.00 0.00 3.41
5361 5706 3.365969 CGGCAAAGGTGGTAGAAAATGAC 60.366 47.826 0.00 0.00 0.00 3.06
5362 5707 2.817258 CGGCAAAGGTGGTAGAAAATGA 59.183 45.455 0.00 0.00 0.00 2.57
5363 5708 2.556622 ACGGCAAAGGTGGTAGAAAATG 59.443 45.455 0.00 0.00 0.00 2.32
5364 5709 2.817844 GACGGCAAAGGTGGTAGAAAAT 59.182 45.455 0.00 0.00 0.00 1.82
5365 5710 2.223745 GACGGCAAAGGTGGTAGAAAA 58.776 47.619 0.00 0.00 0.00 2.29
5366 5711 1.874739 CGACGGCAAAGGTGGTAGAAA 60.875 52.381 0.00 0.00 0.00 2.52
5367 5712 0.320073 CGACGGCAAAGGTGGTAGAA 60.320 55.000 0.00 0.00 0.00 2.10
5368 5713 1.180456 TCGACGGCAAAGGTGGTAGA 61.180 55.000 0.00 0.00 0.00 2.59
5369 5714 0.320073 TTCGACGGCAAAGGTGGTAG 60.320 55.000 0.00 0.00 0.00 3.18
5379 5724 1.732941 AATACAGCATTTCGACGGCA 58.267 45.000 0.00 0.00 0.00 5.69
5381 5726 4.088648 GTGAAAATACAGCATTTCGACGG 58.911 43.478 0.00 0.00 38.16 4.79
5390 5735 2.554344 GGGGTCCAGTGAAAATACAGCA 60.554 50.000 0.00 0.00 0.00 4.41
5393 5738 2.443632 TGTGGGGTCCAGTGAAAATACA 59.556 45.455 0.00 0.00 32.34 2.29
5406 5751 1.410153 GGAATTGCATCATGTGGGGTC 59.590 52.381 0.00 0.00 0.00 4.46
5409 5754 2.104967 ACTGGAATTGCATCATGTGGG 58.895 47.619 0.00 0.00 0.00 4.61
5422 5767 1.747444 ACAGGAGGTGGAACTGGAAT 58.253 50.000 0.00 0.00 36.57 3.01
6083 6434 2.988010 TGGGCATGATAGACAGACAC 57.012 50.000 0.00 0.00 0.00 3.67
6109 6460 1.812922 AGGAAGCGCGAATGCTCTG 60.813 57.895 12.10 0.00 46.60 3.35
6132 6483 0.964358 CGAGGTCCACCGGTAGAACT 60.964 60.000 21.19 21.19 42.08 3.01
6148 6499 1.079405 ACACAATACCGCCACCGAG 60.079 57.895 0.00 0.00 36.29 4.63
6212 6563 4.582701 TTTCAATGGCGTTGAGTGATTT 57.417 36.364 20.42 0.00 46.85 2.17


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

AutoCloner maintained by Alex Coulton.