Multiple sequence alignment - TraesCS1B01G137000

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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 TraesCS1B01G137000 chr1B 100.000 2335 0 0 1 2335 174782916 174785250 0.000000e+00 4313.0
1 TraesCS1B01G137000 chr1B 80.930 645 120 3 1651 2294 445662065 445661423 7.450000e-140 507.0
2 TraesCS1B01G137000 chr1B 81.340 418 34 21 972 1383 174763145 174763524 1.360000e-77 300.0
3 TraesCS1B01G137000 chr1B 85.714 287 20 7 972 1258 175275521 175275786 1.370000e-72 283.0
4 TraesCS1B01G137000 chr1A 83.051 1652 165 62 7 1598 124188815 124190411 0.000000e+00 1393.0
5 TraesCS1B01G137000 chr1A 82.821 390 30 14 962 1350 124786908 124787261 4.840000e-82 315.0
6 TraesCS1B01G137000 chr1A 78.555 429 47 23 962 1383 124181233 124181623 8.340000e-60 241.0
7 TraesCS1B01G137000 chr1D 84.652 1251 84 41 407 1598 114082690 114083891 0.000000e+00 1147.0
8 TraesCS1B01G137000 chr1D 86.957 414 33 8 7 408 114081946 114082350 1.650000e-121 446.0
9 TraesCS1B01G137000 chr1D 82.297 418 33 21 972 1383 114064797 114065179 8.050000e-85 324.0
10 TraesCS1B01G137000 chr1D 82.741 394 34 19 972 1361 114313342 114313705 1.040000e-83 320.0
11 TraesCS1B01G137000 chr2D 93.913 690 42 0 1604 2293 25074255 25073566 0.000000e+00 1042.0
12 TraesCS1B01G137000 chr2D 90.883 691 62 1 1604 2293 19388852 19388162 0.000000e+00 926.0
13 TraesCS1B01G137000 chr2D 86.036 666 91 2 1609 2273 625461633 625460969 0.000000e+00 713.0
14 TraesCS1B01G137000 chr7B 93.245 681 46 0 1606 2286 417555616 417554936 0.000000e+00 1003.0
15 TraesCS1B01G137000 chr7D 91.172 691 60 1 1604 2293 61143633 61142943 0.000000e+00 937.0
16 TraesCS1B01G137000 chr2B 90.630 683 41 9 1604 2286 718635914 718635255 0.000000e+00 885.0
17 TraesCS1B01G137000 chr2A 85.277 686 100 1 1609 2294 369204845 369205529 0.000000e+00 706.0
18 TraesCS1B01G137000 chrUn 91.142 508 45 0 1780 2287 64824331 64824838 0.000000e+00 689.0
19 TraesCS1B01G137000 chrUn 91.713 181 15 0 1604 1784 64822430 64822610 3.850000e-63 252.0
20 TraesCS1B01G137000 chr3D 82.278 237 30 11 985 1212 86237277 86237044 6.580000e-46 195.0
21 TraesCS1B01G137000 chr6A 100.000 29 0 0 2303 2331 502918514 502918542 1.000000e-03 54.7


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 TraesCS1B01G137000 chr1B 174782916 174785250 2334 False 4313.0 4313 100.0000 1 2335 1 chr1B.!!$F2 2334
1 TraesCS1B01G137000 chr1B 445661423 445662065 642 True 507.0 507 80.9300 1651 2294 1 chr1B.!!$R1 643
2 TraesCS1B01G137000 chr1A 124188815 124190411 1596 False 1393.0 1393 83.0510 7 1598 1 chr1A.!!$F2 1591
3 TraesCS1B01G137000 chr1D 114081946 114083891 1945 False 796.5 1147 85.8045 7 1598 2 chr1D.!!$F3 1591
4 TraesCS1B01G137000 chr2D 25073566 25074255 689 True 1042.0 1042 93.9130 1604 2293 1 chr2D.!!$R2 689
5 TraesCS1B01G137000 chr2D 19388162 19388852 690 True 926.0 926 90.8830 1604 2293 1 chr2D.!!$R1 689
6 TraesCS1B01G137000 chr2D 625460969 625461633 664 True 713.0 713 86.0360 1609 2273 1 chr2D.!!$R3 664
7 TraesCS1B01G137000 chr7B 417554936 417555616 680 True 1003.0 1003 93.2450 1606 2286 1 chr7B.!!$R1 680
8 TraesCS1B01G137000 chr7D 61142943 61143633 690 True 937.0 937 91.1720 1604 2293 1 chr7D.!!$R1 689
9 TraesCS1B01G137000 chr2B 718635255 718635914 659 True 885.0 885 90.6300 1604 2286 1 chr2B.!!$R1 682
10 TraesCS1B01G137000 chr2A 369204845 369205529 684 False 706.0 706 85.2770 1609 2294 1 chr2A.!!$F1 685
11 TraesCS1B01G137000 chrUn 64822430 64824838 2408 False 470.5 689 91.4275 1604 2287 2 chrUn.!!$F1 683

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
397 415 0.037017 TGGTGGGTGGTAATGGTTCG 59.963 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 4493 0.042188 CCAAAGCGTTCGACACAGTG 60.042 55.0 0.0 0.0 0.0 3.66 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
26 27 2.556622 ACCAAAACTGTAGCCATTTCCG 59.443 45.455 0.00 0.00 0.00 4.30
39 40 3.077359 CCATTTCCGAAGTTCTTCAGCT 58.923 45.455 12.15 0.00 0.00 4.24
45 46 1.447945 GAAGTTCTTCAGCTGAGCCC 58.552 55.000 17.43 6.58 0.00 5.19
47 48 1.063183 AGTTCTTCAGCTGAGCCCTT 58.937 50.000 17.43 1.41 0.00 3.95
76 77 1.269569 TGCTTCGCGAGACAGAAGAAA 60.270 47.619 9.59 0.00 44.76 2.52
77 78 1.792949 GCTTCGCGAGACAGAAGAAAA 59.207 47.619 9.59 0.00 44.76 2.29
95 96 0.669077 AATAAAACACCGGCGCACAA 59.331 45.000 10.83 0.00 0.00 3.33
105 106 1.369568 GGCGCACAACGGTTAACAC 60.370 57.895 10.83 0.00 43.93 3.32
124 125 0.040425 CCACACGGTTTAGCAAGTGC 60.040 55.000 0.00 0.00 38.08 4.40
129 130 0.096976 CGGTTTAGCAAGTGCCATCG 59.903 55.000 0.00 0.00 43.38 3.84
135 136 2.945984 CAAGTGCCATCGTGCGTT 59.054 55.556 0.00 0.00 0.00 4.84
183 184 2.985847 GCCCACAGGTTCAGCCAC 60.986 66.667 0.00 0.00 40.61 5.01
186 187 1.601759 CCACAGGTTCAGCCACTGG 60.602 63.158 0.00 0.00 40.61 4.00
188 189 0.037303 CACAGGTTCAGCCACTGGAT 59.963 55.000 0.00 0.00 40.61 3.41
190 191 0.742281 CAGGTTCAGCCACTGGATCG 60.742 60.000 0.00 0.00 40.61 3.69
216 217 8.525290 GCTAATGCCATTTGGGAATAGTATAT 57.475 34.615 12.91 0.00 40.07 0.86
300 313 4.162698 TGATACTACTACCGGGCAAACAAT 59.837 41.667 6.32 0.00 0.00 2.71
301 314 3.428413 ACTACTACCGGGCAAACAATT 57.572 42.857 6.32 0.00 0.00 2.32
302 315 3.078837 ACTACTACCGGGCAAACAATTG 58.921 45.455 6.32 3.24 39.65 2.32
320 333 0.885879 TGCGTAACTGGTCGACTGAT 59.114 50.000 16.46 6.34 0.00 2.90
322 335 1.654105 GCGTAACTGGTCGACTGATTG 59.346 52.381 16.46 4.13 0.00 2.67
341 354 3.838244 TGAAGGCAGAGTACTTTGTGT 57.162 42.857 14.34 0.22 0.00 3.72
348 361 8.685838 AAGGCAGAGTACTTTGTGTAATTAAA 57.314 30.769 14.34 0.00 32.25 1.52
351 364 9.983804 GGCAGAGTACTTTGTGTAATTAAATAC 57.016 33.333 14.34 0.00 32.25 1.89
397 415 0.037017 TGGTGGGTGGTAATGGTTCG 59.963 55.000 0.00 0.00 0.00 3.95
425 790 9.172820 CAGTTCGTAGTATATAATGTAACGCAA 57.827 33.333 0.00 0.00 0.00 4.85
427 792 7.786305 TCGTAGTATATAATGTAACGCAAGC 57.214 36.000 0.00 0.00 45.62 4.01
428 793 6.520790 TCGTAGTATATAATGTAACGCAAGCG 59.479 38.462 13.50 13.50 46.03 4.68
429 794 6.520790 CGTAGTATATAATGTAACGCAAGCGA 59.479 38.462 22.30 0.00 42.83 4.93
430 795 6.686130 AGTATATAATGTAACGCAAGCGAC 57.314 37.500 22.30 10.30 42.83 5.19
431 796 6.210796 AGTATATAATGTAACGCAAGCGACA 58.789 36.000 22.30 15.80 42.83 4.35
463 828 6.879400 AGTTCCTTTCACATAGACATAGTCC 58.121 40.000 0.00 0.00 32.18 3.85
510 879 5.067283 ACAATCAACTTGTGAAGGTTGGTAC 59.933 40.000 0.00 0.00 46.37 3.34
544 917 8.481132 CGTAGCAGCTATAATGTTTTTGATTC 57.519 34.615 5.14 0.00 0.00 2.52
549 927 9.403110 GCAGCTATAATGTTTTTGATTCATAGG 57.597 33.333 0.00 0.00 0.00 2.57
559 937 8.190122 TGTTTTTGATTCATAGGTGCATCATAC 58.810 33.333 0.00 0.00 37.73 2.39
568 946 3.115390 AGGTGCATCATACTGTTAGGGT 58.885 45.455 0.00 0.00 0.00 4.34
614 992 7.607250 AGTATAGTTTGTTGAGGAGAAGACAG 58.393 38.462 0.00 0.00 0.00 3.51
644 1027 4.321718 CGCCATAATGTTCAGATCCAGAT 58.678 43.478 0.00 0.00 0.00 2.90
654 1037 6.414732 TGTTCAGATCCAGATTTAATCGGTT 58.585 36.000 12.76 7.17 0.00 4.44
662 1045 9.273016 GATCCAGATTTAATCGGTTTTCAGATA 57.727 33.333 12.76 0.00 33.89 1.98
665 1048 8.338259 CCAGATTTAATCGGTTTTCAGATACAG 58.662 37.037 4.57 0.00 33.89 2.74
667 1050 9.838339 AGATTTAATCGGTTTTCAGATACAGAT 57.162 29.630 0.00 0.00 33.89 2.90
674 1057 9.613428 ATCGGTTTTCAGATACAGATTTAATCA 57.387 29.630 7.74 0.00 33.29 2.57
675 1058 9.098355 TCGGTTTTCAGATACAGATTTAATCAG 57.902 33.333 7.74 1.67 0.00 2.90
676 1059 8.883731 CGGTTTTCAGATACAGATTTAATCAGT 58.116 33.333 7.74 7.89 33.38 3.41
677 1060 9.994432 GGTTTTCAGATACAGATTTAATCAGTG 57.006 33.333 12.27 3.43 31.17 3.66
681 1064 9.942850 TTCAGATACAGATTTAATCAGTGTTCA 57.057 29.630 12.27 0.00 31.17 3.18
682 1065 9.591792 TCAGATACAGATTTAATCAGTGTTCAG 57.408 33.333 12.27 7.09 31.17 3.02
683 1066 9.591792 CAGATACAGATTTAATCAGTGTTCAGA 57.408 33.333 12.27 0.00 31.17 3.27
686 1069 7.856145 ACAGATTTAATCAGTGTTCAGATCC 57.144 36.000 7.74 0.00 0.00 3.36
687 1070 7.397221 ACAGATTTAATCAGTGTTCAGATCCA 58.603 34.615 7.74 0.00 0.00 3.41
688 1071 7.551974 ACAGATTTAATCAGTGTTCAGATCCAG 59.448 37.037 7.74 0.00 0.00 3.86
689 1072 7.767659 CAGATTTAATCAGTGTTCAGATCCAGA 59.232 37.037 7.74 0.00 0.00 3.86
690 1073 8.492782 AGATTTAATCAGTGTTCAGATCCAGAT 58.507 33.333 7.74 0.00 0.00 2.90
691 1074 9.118300 GATTTAATCAGTGTTCAGATCCAGATT 57.882 33.333 0.00 0.00 0.00 2.40
692 1075 8.868522 TTTAATCAGTGTTCAGATCCAGATTT 57.131 30.769 0.00 0.00 0.00 2.17
693 1076 9.958180 TTTAATCAGTGTTCAGATCCAGATTTA 57.042 29.630 0.00 0.00 0.00 1.40
694 1077 9.958180 TTAATCAGTGTTCAGATCCAGATTTAA 57.042 29.630 0.00 0.00 0.00 1.52
695 1078 7.856145 ATCAGTGTTCAGATCCAGATTTAAC 57.144 36.000 0.00 0.00 0.00 2.01
696 1079 6.768483 TCAGTGTTCAGATCCAGATTTAACA 58.232 36.000 0.00 0.00 0.00 2.41
697 1080 6.650807 TCAGTGTTCAGATCCAGATTTAACAC 59.349 38.462 17.35 17.35 43.32 3.32
698 1081 6.427853 CAGTGTTCAGATCCAGATTTAACACA 59.572 38.462 22.24 6.58 44.66 3.72
699 1082 6.652481 AGTGTTCAGATCCAGATTTAACACAG 59.348 38.462 22.24 0.00 44.66 3.66
700 1083 6.650807 GTGTTCAGATCCAGATTTAACACAGA 59.349 38.462 18.79 0.00 42.81 3.41
701 1084 7.173218 GTGTTCAGATCCAGATTTAACACAGAA 59.827 37.037 18.79 0.00 42.81 3.02
702 1085 7.719193 TGTTCAGATCCAGATTTAACACAGAAA 59.281 33.333 0.00 0.00 0.00 2.52
703 1086 7.672983 TCAGATCCAGATTTAACACAGAAAC 57.327 36.000 0.00 0.00 0.00 2.78
704 1087 7.223584 TCAGATCCAGATTTAACACAGAAACA 58.776 34.615 0.00 0.00 0.00 2.83
705 1088 7.719193 TCAGATCCAGATTTAACACAGAAACAA 59.281 33.333 0.00 0.00 0.00 2.83
706 1089 8.517878 CAGATCCAGATTTAACACAGAAACAAT 58.482 33.333 0.00 0.00 0.00 2.71
707 1090 8.517878 AGATCCAGATTTAACACAGAAACAATG 58.482 33.333 0.00 0.00 0.00 2.82
708 1091 6.446318 TCCAGATTTAACACAGAAACAATGC 58.554 36.000 0.00 0.00 0.00 3.56
709 1092 6.265196 TCCAGATTTAACACAGAAACAATGCT 59.735 34.615 0.00 0.00 0.00 3.79
712 1095 8.292448 CAGATTTAACACAGAAACAATGCTAGT 58.708 33.333 0.00 0.00 0.00 2.57
720 1103 7.170998 ACACAGAAACAATGCTAGTACAAGTAC 59.829 37.037 2.18 2.18 36.35 2.73
748 1166 1.151450 GGGACATGCGGGGAATCAT 59.849 57.895 0.00 0.00 0.00 2.45
784 1202 2.870435 GCCTCTAAAACAAGCAGACCGA 60.870 50.000 0.00 0.00 0.00 4.69
833 1251 4.349365 GGGAATGGATCAACCCTAAAACA 58.651 43.478 0.00 0.00 39.28 2.83
850 1268 6.595716 CCTAAAACAAGATCTCATTTCCGACT 59.404 38.462 0.00 0.00 0.00 4.18
857 1275 4.952957 AGATCTCATTTCCGACTTCTCTCA 59.047 41.667 0.00 0.00 0.00 3.27
878 1312 7.542890 TCTCATCTAAGCTCTAACACAGAAAG 58.457 38.462 0.00 0.00 31.12 2.62
885 1319 3.866449 GCTCTAACACAGAAAGGACTGGG 60.866 52.174 0.00 0.00 45.62 4.45
890 1324 2.430465 CACAGAAAGGACTGGGTGATG 58.570 52.381 0.00 0.00 41.59 3.07
934 1368 3.411351 GTACACGCACGGGCACAG 61.411 66.667 11.77 0.00 41.24 3.66
1123 1573 1.313129 GCCTTCTCCTCCTCCTCCT 59.687 63.158 0.00 0.00 0.00 3.69
1299 1755 1.586028 CCCGAAAGTCGTTCCCGTA 59.414 57.895 0.00 0.00 38.40 4.02
1332 1788 3.077556 AAGGAGACGGCGGATGCT 61.078 61.111 13.24 6.85 42.25 3.79
1368 1824 1.014044 TTAGCTCGGTCGCTTGCTTG 61.014 55.000 0.00 0.00 41.30 4.01
1421 1878 2.472695 TTCGGTTTGGTGAGAGATGG 57.527 50.000 0.00 0.00 0.00 3.51
1424 1881 1.001974 CGGTTTGGTGAGAGATGGTGA 59.998 52.381 0.00 0.00 0.00 4.02
1428 1885 1.561643 TGGTGAGAGATGGTGAGGAC 58.438 55.000 0.00 0.00 0.00 3.85
1451 1908 4.568152 GTTGTAAACTGTGAATGCTGGT 57.432 40.909 0.00 0.00 45.32 4.00
1482 1939 1.062275 AGATGGAGAGCTGGAGATGGT 60.062 52.381 0.00 0.00 0.00 3.55
1485 1942 1.694133 GGAGAGCTGGAGATGGTGGG 61.694 65.000 0.00 0.00 0.00 4.61
1501 1972 2.963101 GGTGGGAATTTATAACCAGGGC 59.037 50.000 0.00 0.00 32.84 5.19
1536 2007 4.524318 ATAGGAACGGCGCGTGGG 62.524 66.667 6.90 0.00 39.99 4.61
1587 2058 2.863853 CGTGACGCATGATCGCCTG 61.864 63.158 0.00 0.00 0.00 4.85
1598 2069 0.250209 GATCGCCTGGACTCATGCAT 60.250 55.000 0.00 0.00 34.78 3.96
1599 2070 0.182061 ATCGCCTGGACTCATGCATT 59.818 50.000 0.00 0.00 34.78 3.56
1600 2071 0.035152 TCGCCTGGACTCATGCATTT 60.035 50.000 0.00 0.00 34.78 2.32
1601 2072 0.813184 CGCCTGGACTCATGCATTTT 59.187 50.000 0.00 0.00 34.78 1.82
1602 2073 1.202222 CGCCTGGACTCATGCATTTTC 60.202 52.381 0.00 0.00 34.78 2.29
1640 2112 2.388232 CGCTCCACCTACAAACGCC 61.388 63.158 0.00 0.00 0.00 5.68
1661 2133 1.951424 GCAGTCGGGACTACTCACTCT 60.951 57.143 0.21 0.00 40.20 3.24
1669 2141 3.117436 GGGACTACTCACTCTCTACCCAT 60.117 52.174 0.00 0.00 35.41 4.00
1709 2181 0.876342 GCTATCCACTTCGCCCTTCG 60.876 60.000 0.00 0.00 40.15 3.79
1746 2218 0.962356 CAAGCCTTGCCTTCCGTGAT 60.962 55.000 0.00 0.00 0.00 3.06
1784 3981 0.457443 CTGTAGTGATGGAGCAGCGA 59.543 55.000 0.00 0.00 0.00 4.93
2006 4203 1.629861 TCAGCAGGATGTGGTCAATGA 59.370 47.619 0.00 0.00 39.31 2.57
2041 4238 2.042831 GCAGAACGGGCAAGCATCT 61.043 57.895 0.00 0.00 0.00 2.90
2287 4484 0.034059 GCTGGATCCCATGTAGTCGG 59.966 60.000 9.90 0.00 30.82 4.79
2288 4485 0.681733 CTGGATCCCATGTAGTCGGG 59.318 60.000 9.90 0.00 44.60 5.14
2294 4491 1.531748 CCATGTAGTCGGGGCCATT 59.468 57.895 4.39 0.00 0.00 3.16
2295 4492 0.106719 CCATGTAGTCGGGGCCATTT 60.107 55.000 4.39 0.00 0.00 2.32
2296 4493 1.308998 CATGTAGTCGGGGCCATTTC 58.691 55.000 4.39 0.00 0.00 2.17
2297 4494 0.916086 ATGTAGTCGGGGCCATTTCA 59.084 50.000 4.39 0.00 0.00 2.69
2298 4495 0.035820 TGTAGTCGGGGCCATTTCAC 60.036 55.000 4.39 0.00 0.00 3.18
2299 4496 0.252197 GTAGTCGGGGCCATTTCACT 59.748 55.000 4.39 0.85 0.00 3.41
2300 4497 0.251916 TAGTCGGGGCCATTTCACTG 59.748 55.000 4.39 0.00 0.00 3.66
2301 4498 1.303317 GTCGGGGCCATTTCACTGT 60.303 57.895 4.39 0.00 0.00 3.55
2302 4499 1.303236 TCGGGGCCATTTCACTGTG 60.303 57.895 4.39 0.17 0.00 3.66
2303 4500 1.603455 CGGGGCCATTTCACTGTGT 60.603 57.895 4.39 0.00 0.00 3.72
2304 4501 1.586154 CGGGGCCATTTCACTGTGTC 61.586 60.000 4.39 0.00 0.00 3.67
2305 4502 1.586154 GGGGCCATTTCACTGTGTCG 61.586 60.000 4.39 0.00 0.00 4.35
2306 4503 0.605319 GGGCCATTTCACTGTGTCGA 60.605 55.000 4.39 0.00 0.00 4.20
2307 4504 1.234821 GGCCATTTCACTGTGTCGAA 58.765 50.000 7.79 2.49 0.00 3.71
2308 4505 1.069227 GGCCATTTCACTGTGTCGAAC 60.069 52.381 7.79 0.00 0.00 3.95
2309 4506 1.398451 GCCATTTCACTGTGTCGAACG 60.398 52.381 7.79 0.00 0.00 3.95
2310 4507 1.398451 CCATTTCACTGTGTCGAACGC 60.398 52.381 7.79 0.00 0.00 4.84
2311 4508 1.526887 CATTTCACTGTGTCGAACGCT 59.473 47.619 7.79 0.00 0.00 5.07
2312 4509 1.647346 TTTCACTGTGTCGAACGCTT 58.353 45.000 7.79 0.00 0.00 4.68
2313 4510 1.647346 TTCACTGTGTCGAACGCTTT 58.353 45.000 7.79 0.00 0.00 3.51
2314 4511 0.927537 TCACTGTGTCGAACGCTTTG 59.072 50.000 7.79 0.00 0.00 2.77
2315 4512 0.042188 CACTGTGTCGAACGCTTTGG 60.042 55.000 0.00 0.00 0.00 3.28
2316 4513 0.179094 ACTGTGTCGAACGCTTTGGA 60.179 50.000 0.00 0.00 0.00 3.53
2317 4514 1.148310 CTGTGTCGAACGCTTTGGAT 58.852 50.000 0.00 0.00 0.00 3.41
2318 4515 2.288579 ACTGTGTCGAACGCTTTGGATA 60.289 45.455 0.00 0.00 0.00 2.59
2319 4516 2.930040 CTGTGTCGAACGCTTTGGATAT 59.070 45.455 0.00 0.00 0.00 1.63
2320 4517 2.670905 TGTGTCGAACGCTTTGGATATG 59.329 45.455 0.00 0.00 0.00 1.78
2321 4518 2.671396 GTGTCGAACGCTTTGGATATGT 59.329 45.455 0.00 0.00 0.00 2.29
2322 4519 2.927477 TGTCGAACGCTTTGGATATGTC 59.073 45.455 0.00 0.00 0.00 3.06
2323 4520 2.284417 GTCGAACGCTTTGGATATGTCC 59.716 50.000 0.60 0.60 45.31 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.335661 GGAAATGGCTACAGTTTTGGTGTAG 60.336 44.000 5.99 5.99 46.92 2.74
2 3 4.521256 GGAAATGGCTACAGTTTTGGTGTA 59.479 41.667 0.00 0.00 34.65 2.90
3 4 3.320826 GGAAATGGCTACAGTTTTGGTGT 59.679 43.478 0.00 0.00 34.65 4.16
4 5 3.611530 CGGAAATGGCTACAGTTTTGGTG 60.612 47.826 0.00 0.00 34.65 4.17
5 6 2.556622 CGGAAATGGCTACAGTTTTGGT 59.443 45.455 0.00 0.00 34.65 3.67
18 19 3.077359 AGCTGAAGAACTTCGGAAATGG 58.923 45.455 22.55 4.37 46.23 3.16
26 27 1.003003 AGGGCTCAGCTGAAGAACTTC 59.997 52.381 18.85 7.51 39.91 3.01
39 40 2.764269 AGCATCCTAGTAAAGGGCTCA 58.236 47.619 0.00 0.00 46.55 4.26
76 77 0.669077 TTGTGCGCCGGTGTTTTATT 59.331 45.000 17.91 0.00 0.00 1.40
77 78 0.039888 GTTGTGCGCCGGTGTTTTAT 60.040 50.000 17.91 0.00 0.00 1.40
105 106 0.040425 GCACTTGCTAAACCGTGTGG 60.040 55.000 0.00 0.00 38.67 4.17
147 148 0.110509 CTGCGCCATATCATTCGTGC 60.111 55.000 4.18 0.00 0.00 5.34
172 173 1.599047 CGATCCAGTGGCTGAACCT 59.401 57.895 3.51 0.00 40.22 3.50
193 194 9.461312 GTGATATACTATTCCCAAATGGCATTA 57.539 33.333 14.05 0.00 0.00 1.90
205 206 6.565999 GCTTTGTTGCCGTGATATACTATTCC 60.566 42.308 0.00 0.00 0.00 3.01
216 217 1.029408 AGTGTGCTTTGTTGCCGTGA 61.029 50.000 0.00 0.00 0.00 4.35
243 244 2.165641 GCCGGCAGCTTTACCTTAAATT 59.834 45.455 24.80 0.00 38.99 1.82
300 313 0.669619 TCAGTCGACCAGTTACGCAA 59.330 50.000 13.01 0.00 0.00 4.85
301 314 0.885879 ATCAGTCGACCAGTTACGCA 59.114 50.000 13.01 0.00 0.00 5.24
302 315 1.654105 CAATCAGTCGACCAGTTACGC 59.346 52.381 13.01 0.00 0.00 4.42
303 316 3.211803 TCAATCAGTCGACCAGTTACG 57.788 47.619 13.01 0.00 0.00 3.18
304 317 3.927142 CCTTCAATCAGTCGACCAGTTAC 59.073 47.826 13.01 0.00 0.00 2.50
305 318 3.616560 GCCTTCAATCAGTCGACCAGTTA 60.617 47.826 13.01 0.00 0.00 2.24
306 319 2.872038 GCCTTCAATCAGTCGACCAGTT 60.872 50.000 13.01 1.27 0.00 3.16
307 320 1.338200 GCCTTCAATCAGTCGACCAGT 60.338 52.381 13.01 0.00 0.00 4.00
320 333 4.150897 ACACAAAGTACTCTGCCTTCAA 57.849 40.909 0.00 0.00 0.00 2.69
322 335 6.803154 AATTACACAAAGTACTCTGCCTTC 57.197 37.500 0.00 0.00 30.91 3.46
341 354 9.841880 CGATCTCCAGATCTTCGTATTTAATTA 57.158 33.333 13.51 0.00 46.58 1.40
348 361 4.557695 GCAACGATCTCCAGATCTTCGTAT 60.558 45.833 17.24 7.47 46.58 3.06
351 364 2.123342 GCAACGATCTCCAGATCTTCG 58.877 52.381 13.51 11.29 46.58 3.79
366 379 0.742990 ACCCACCATGATACGCAACG 60.743 55.000 0.00 0.00 0.00 4.10
397 415 8.835160 GCGTTACATTATATACTACGAACTGAC 58.165 37.037 0.00 0.00 0.00 3.51
425 790 1.080434 GAACTCCTCGCTTGTCGCT 60.080 57.895 0.00 0.00 38.27 4.93
426 791 2.095252 GGAACTCCTCGCTTGTCGC 61.095 63.158 0.00 0.00 38.27 5.19
427 792 1.587054 AGGAACTCCTCGCTTGTCG 59.413 57.895 0.00 0.00 44.77 4.35
463 828 2.523168 GTTGGGTTGGGGTGGGTG 60.523 66.667 0.00 0.00 0.00 4.61
530 903 8.747471 TGATGCACCTATGAATCAAAAACATTA 58.253 29.630 0.00 0.00 46.35 1.90
544 917 5.221722 ACCCTAACAGTATGATGCACCTATG 60.222 44.000 0.00 0.00 39.69 2.23
549 927 8.557029 GTTATTTACCCTAACAGTATGATGCAC 58.443 37.037 0.00 0.00 39.69 4.57
559 937 6.653320 TGCTTCTGTGTTATTTACCCTAACAG 59.347 38.462 0.00 0.00 39.17 3.16
626 1004 9.224267 CCGATTAAATCTGGATCTGAACATTAT 57.776 33.333 0.00 0.00 0.00 1.28
627 1005 8.210946 ACCGATTAAATCTGGATCTGAACATTA 58.789 33.333 0.00 0.00 0.00 1.90
629 1007 6.595682 ACCGATTAAATCTGGATCTGAACAT 58.404 36.000 0.00 0.00 0.00 2.71
630 1008 5.989477 ACCGATTAAATCTGGATCTGAACA 58.011 37.500 0.00 0.00 0.00 3.18
662 1045 7.397221 TGGATCTGAACACTGATTAAATCTGT 58.603 34.615 0.00 0.00 41.36 3.41
665 1048 8.674263 ATCTGGATCTGAACACTGATTAAATC 57.326 34.615 0.00 0.00 0.00 2.17
667 1050 8.868522 AAATCTGGATCTGAACACTGATTAAA 57.131 30.769 0.00 0.00 33.20 1.52
668 1051 9.958180 TTAAATCTGGATCTGAACACTGATTAA 57.042 29.630 0.00 0.00 33.20 1.40
669 1052 9.383519 GTTAAATCTGGATCTGAACACTGATTA 57.616 33.333 0.00 0.00 33.20 1.75
670 1053 7.884877 TGTTAAATCTGGATCTGAACACTGATT 59.115 33.333 0.00 0.00 34.40 2.57
671 1054 7.335422 GTGTTAAATCTGGATCTGAACACTGAT 59.665 37.037 17.96 0.00 41.09 2.90
673 1056 6.427853 TGTGTTAAATCTGGATCTGAACACTG 59.572 38.462 21.69 0.00 43.42 3.66
674 1057 6.533730 TGTGTTAAATCTGGATCTGAACACT 58.466 36.000 21.69 0.00 43.42 3.55
675 1058 6.650807 TCTGTGTTAAATCTGGATCTGAACAC 59.349 38.462 18.19 18.19 43.35 3.32
676 1059 6.768483 TCTGTGTTAAATCTGGATCTGAACA 58.232 36.000 0.00 0.00 0.00 3.18
677 1060 7.672983 TTCTGTGTTAAATCTGGATCTGAAC 57.327 36.000 0.00 0.00 0.00 3.18
678 1061 7.719193 TGTTTCTGTGTTAAATCTGGATCTGAA 59.281 33.333 0.00 0.00 0.00 3.02
679 1062 7.223584 TGTTTCTGTGTTAAATCTGGATCTGA 58.776 34.615 0.00 0.00 0.00 3.27
680 1063 7.439157 TGTTTCTGTGTTAAATCTGGATCTG 57.561 36.000 0.00 0.00 0.00 2.90
681 1064 8.517878 CATTGTTTCTGTGTTAAATCTGGATCT 58.482 33.333 0.00 0.00 0.00 2.75
682 1065 7.274250 GCATTGTTTCTGTGTTAAATCTGGATC 59.726 37.037 0.00 0.00 0.00 3.36
683 1066 7.039504 AGCATTGTTTCTGTGTTAAATCTGGAT 60.040 33.333 0.00 0.00 0.00 3.41
684 1067 6.265196 AGCATTGTTTCTGTGTTAAATCTGGA 59.735 34.615 0.00 0.00 0.00 3.86
685 1068 6.449698 AGCATTGTTTCTGTGTTAAATCTGG 58.550 36.000 0.00 0.00 0.00 3.86
686 1069 8.292448 ACTAGCATTGTTTCTGTGTTAAATCTG 58.708 33.333 0.00 0.00 0.00 2.90
687 1070 8.396272 ACTAGCATTGTTTCTGTGTTAAATCT 57.604 30.769 0.00 0.00 0.00 2.40
688 1071 9.543018 GTACTAGCATTGTTTCTGTGTTAAATC 57.457 33.333 0.00 0.00 0.00 2.17
689 1072 9.062524 TGTACTAGCATTGTTTCTGTGTTAAAT 57.937 29.630 0.00 0.00 0.00 1.40
690 1073 8.439993 TGTACTAGCATTGTTTCTGTGTTAAA 57.560 30.769 0.00 0.00 0.00 1.52
691 1074 8.439993 TTGTACTAGCATTGTTTCTGTGTTAA 57.560 30.769 0.00 0.00 0.00 2.01
692 1075 7.713507 ACTTGTACTAGCATTGTTTCTGTGTTA 59.286 33.333 4.10 0.00 0.00 2.41
693 1076 6.542370 ACTTGTACTAGCATTGTTTCTGTGTT 59.458 34.615 4.10 0.00 0.00 3.32
694 1077 6.055588 ACTTGTACTAGCATTGTTTCTGTGT 58.944 36.000 4.10 0.00 0.00 3.72
695 1078 6.545504 ACTTGTACTAGCATTGTTTCTGTG 57.454 37.500 4.10 0.00 0.00 3.66
696 1079 6.649557 GGTACTTGTACTAGCATTGTTTCTGT 59.350 38.462 4.10 0.00 0.00 3.41
697 1080 6.649141 TGGTACTTGTACTAGCATTGTTTCTG 59.351 38.462 4.10 0.00 0.00 3.02
698 1081 6.649557 GTGGTACTTGTACTAGCATTGTTTCT 59.350 38.462 4.10 0.00 0.00 2.52
699 1082 6.425721 TGTGGTACTTGTACTAGCATTGTTTC 59.574 38.462 4.10 0.00 0.00 2.78
700 1083 6.292923 TGTGGTACTTGTACTAGCATTGTTT 58.707 36.000 4.10 0.00 0.00 2.83
701 1084 5.860611 TGTGGTACTTGTACTAGCATTGTT 58.139 37.500 4.10 0.00 0.00 2.83
702 1085 5.245301 TCTGTGGTACTTGTACTAGCATTGT 59.755 40.000 4.10 0.00 0.00 2.71
703 1086 5.720202 TCTGTGGTACTTGTACTAGCATTG 58.280 41.667 4.10 0.00 0.00 2.82
704 1087 5.995565 TCTGTGGTACTTGTACTAGCATT 57.004 39.130 4.10 0.00 0.00 3.56
705 1088 5.894393 AGATCTGTGGTACTTGTACTAGCAT 59.106 40.000 4.10 0.00 0.00 3.79
706 1089 5.125578 CAGATCTGTGGTACTTGTACTAGCA 59.874 44.000 14.95 0.00 0.00 3.49
707 1090 5.450688 CCAGATCTGTGGTACTTGTACTAGC 60.451 48.000 21.11 0.00 32.32 3.42
708 1091 5.067936 CCCAGATCTGTGGTACTTGTACTAG 59.932 48.000 21.11 2.56 35.60 2.57
709 1092 4.954202 CCCAGATCTGTGGTACTTGTACTA 59.046 45.833 21.11 2.21 35.60 1.82
712 1095 3.767673 GTCCCAGATCTGTGGTACTTGTA 59.232 47.826 21.11 2.43 35.60 2.41
720 1103 0.812811 CGCATGTCCCAGATCTGTGG 60.813 60.000 21.11 19.93 37.34 4.17
748 1166 3.266510 AGAGGCGCAGATGTTTCAATA 57.733 42.857 10.83 0.00 0.00 1.90
807 1225 2.577970 AGGGTTGATCCATTCCCTTCT 58.422 47.619 7.89 0.00 46.99 2.85
833 1251 5.420421 TGAGAGAAGTCGGAAATGAGATCTT 59.580 40.000 0.00 0.00 0.00 2.40
850 1268 6.887002 TCTGTGTTAGAGCTTAGATGAGAGAA 59.113 38.462 0.00 0.00 0.00 2.87
857 1275 6.439058 AGTCCTTTCTGTGTTAGAGCTTAGAT 59.561 38.462 0.00 0.00 36.61 1.98
885 1319 2.208431 CTCTTTCGATCTGGGCATCAC 58.792 52.381 0.00 0.00 0.00 3.06
887 1321 1.542108 CCCTCTTTCGATCTGGGCATC 60.542 57.143 0.00 0.00 0.00 3.91
890 1324 0.541863 TTCCCTCTTTCGATCTGGGC 59.458 55.000 8.01 0.00 37.83 5.36
900 1334 4.262335 CGTGTACCTAGTTGTTCCCTCTTT 60.262 45.833 0.00 0.00 0.00 2.52
907 1341 1.717645 CGTGCGTGTACCTAGTTGTTC 59.282 52.381 0.00 0.00 0.00 3.18
934 1368 0.239347 GACACAACCAGACATGCTGC 59.761 55.000 10.54 0.00 43.50 5.25
939 1373 1.667830 CGCCGACACAACCAGACAT 60.668 57.895 0.00 0.00 0.00 3.06
948 1382 3.923864 AGCCAACTCGCCGACACA 61.924 61.111 0.00 0.00 0.00 3.72
1332 1788 2.203549 TAATGGCCATGGCACCGTCA 62.204 55.000 36.56 24.92 41.84 4.35
1334 1790 1.453745 CTAATGGCCATGGCACCGT 60.454 57.895 36.56 19.59 41.84 4.83
1368 1824 3.058363 CCCGTAGTAGAATCTTACGAGCC 60.058 52.174 14.08 0.00 36.38 4.70
1421 1878 4.439057 TCACAGTTTACAACAGTCCTCAC 58.561 43.478 0.00 0.00 0.00 3.51
1424 1881 4.275936 GCATTCACAGTTTACAACAGTCCT 59.724 41.667 0.00 0.00 0.00 3.85
1428 1885 4.036734 ACCAGCATTCACAGTTTACAACAG 59.963 41.667 0.00 0.00 0.00 3.16
1449 1906 0.391661 TCCATCTCGCAAGCTCAACC 60.392 55.000 0.00 0.00 37.18 3.77
1450 1907 1.005340 CTCCATCTCGCAAGCTCAAC 58.995 55.000 0.00 0.00 37.18 3.18
1451 1908 0.897621 TCTCCATCTCGCAAGCTCAA 59.102 50.000 0.00 0.00 37.18 3.02
1482 1939 4.017037 TCTTGCCCTGGTTATAAATTCCCA 60.017 41.667 0.00 0.00 0.00 4.37
1485 1942 5.445964 TCCTCTTGCCCTGGTTATAAATTC 58.554 41.667 0.00 0.00 0.00 2.17
1501 1972 4.898265 TCCTATCCACTCTTCATCCTCTTG 59.102 45.833 0.00 0.00 0.00 3.02
1544 2015 2.909965 GAAAAGCGCACCCCCACA 60.910 61.111 11.47 0.00 0.00 4.17
1576 2047 1.509703 CATGAGTCCAGGCGATCATG 58.490 55.000 11.70 11.70 42.04 3.07
1577 2048 0.250209 GCATGAGTCCAGGCGATCAT 60.250 55.000 0.00 0.00 40.39 2.45
1584 2055 2.165030 GTGGAAAATGCATGAGTCCAGG 59.835 50.000 20.87 0.00 39.02 4.45
1585 2056 2.821378 TGTGGAAAATGCATGAGTCCAG 59.179 45.455 20.87 0.00 39.02 3.86
1587 2058 5.581126 TTATGTGGAAAATGCATGAGTCC 57.419 39.130 14.00 14.00 0.00 3.85
1598 2069 6.127869 CGGTGGATTGTACATTATGTGGAAAA 60.128 38.462 8.26 0.00 0.00 2.29
1599 2070 5.355630 CGGTGGATTGTACATTATGTGGAAA 59.644 40.000 8.26 0.29 0.00 3.13
1600 2071 4.878971 CGGTGGATTGTACATTATGTGGAA 59.121 41.667 8.26 0.96 0.00 3.53
1601 2072 4.447290 CGGTGGATTGTACATTATGTGGA 58.553 43.478 8.26 0.00 0.00 4.02
1602 2073 3.003275 GCGGTGGATTGTACATTATGTGG 59.997 47.826 8.26 0.00 0.00 4.17
1640 2112 1.136984 GTGAGTAGTCCCGACTGCG 59.863 63.158 7.63 0.00 46.57 5.18
1661 2133 4.742012 GATCTTCTGGTAGGATGGGTAGA 58.258 47.826 0.00 0.00 0.00 2.59
1669 2141 2.437085 TGCTCGATCTTCTGGTAGGA 57.563 50.000 0.00 0.00 0.00 2.94
1709 2181 2.250237 GGCAGCAGGCGAGCTTATC 61.250 63.158 4.73 0.00 43.70 1.75
1746 2218 0.322456 GCAGGTAGTTGGGCACATCA 60.322 55.000 0.00 0.00 0.00 3.07
1784 3981 2.350388 GGAATGCAATTGTGTTCGACGT 60.350 45.455 7.40 0.00 36.07 4.34
1944 4141 1.328279 TTGGAGAACTCTGTGCTCGA 58.672 50.000 1.86 0.00 39.04 4.04
2264 4461 0.319728 CTACATGGGATCCAGCTCCG 59.680 60.000 15.23 0.00 36.75 4.63
2287 4484 0.605319 TCGACACAGTGAAATGGCCC 60.605 55.000 7.81 0.00 0.00 5.80
2288 4485 1.069227 GTTCGACACAGTGAAATGGCC 60.069 52.381 7.81 0.00 0.00 5.36
2294 4491 1.326245 CAAAGCGTTCGACACAGTGAA 59.674 47.619 7.81 0.00 0.00 3.18
2295 4492 0.927537 CAAAGCGTTCGACACAGTGA 59.072 50.000 7.81 0.00 0.00 3.41
2296 4493 0.042188 CCAAAGCGTTCGACACAGTG 60.042 55.000 0.00 0.00 0.00 3.66
2297 4494 0.179094 TCCAAAGCGTTCGACACAGT 60.179 50.000 0.00 0.00 0.00 3.55
2298 4495 1.148310 ATCCAAAGCGTTCGACACAG 58.852 50.000 0.00 0.00 0.00 3.66
2299 4496 2.442212 TATCCAAAGCGTTCGACACA 57.558 45.000 0.00 0.00 0.00 3.72
2300 4497 2.671396 ACATATCCAAAGCGTTCGACAC 59.329 45.455 0.00 0.00 0.00 3.67
2301 4498 2.927477 GACATATCCAAAGCGTTCGACA 59.073 45.455 0.00 0.00 0.00 4.35
2302 4499 2.284417 GGACATATCCAAAGCGTTCGAC 59.716 50.000 0.00 0.00 45.47 4.20
2303 4500 2.546778 GGACATATCCAAAGCGTTCGA 58.453 47.619 0.00 0.00 45.47 3.71


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

AutoCloner maintained by Alex Coulton.