Multiple sequence alignment - TraesCS4D01G259900

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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 TraesCS4D01G259900 chr4D 100.000 3841 0 0 1 3841 428973438 428969598 0.000000e+00 7094.0
1 TraesCS4D01G259900 chr4D 82.238 563 80 12 1 545 49087403 49086843 5.810000e-128 468.0
2 TraesCS4D01G259900 chr4A 92.175 3246 171 37 657 3841 37299658 37302881 0.000000e+00 4510.0
3 TraesCS4D01G259900 chr4B 91.759 3240 171 47 658 3841 527011435 527008236 0.000000e+00 4416.0
4 TraesCS4D01G259900 chr1B 84.574 551 71 10 1 545 270383923 270384465 5.650000e-148 534.0
5 TraesCS4D01G259900 chr1A 84.817 382 53 2 1 378 243603491 243603111 2.800000e-101 379.0
6 TraesCS4D01G259900 chr1A 85.143 175 19 5 370 544 243602685 243602518 5.100000e-39 172.0
7 TraesCS4D01G259900 chr5B 87.415 294 30 4 1 289 678906868 678907159 7.950000e-87 331.0
8 TraesCS4D01G259900 chr5D 83.523 176 25 3 2075 2246 372296812 372296987 1.100000e-35 161.0
9 TraesCS4D01G259900 chr3D 83.523 176 25 3 2075 2246 275629926 275630101 1.100000e-35 161.0
10 TraesCS4D01G259900 chr3D 96.875 32 1 0 546 577 378781742 378781711 2.000000e-03 54.7
11 TraesCS4D01G259900 chr5A 82.955 176 26 3 2075 2246 523751175 523751350 5.140000e-34 156.0
12 TraesCS4D01G259900 chr5A 87.387 111 14 0 546 656 535653088 535653198 1.120000e-25 128.0
13 TraesCS4D01G259900 chr2D 82.778 180 24 5 1 175 428702814 428702991 1.850000e-33 154.0
14 TraesCS4D01G259900 chr7D 85.217 115 13 4 544 656 351351825 351351937 8.720000e-22 115.0
15 TraesCS4D01G259900 chr3B 87.342 79 9 1 582 659 708502757 708502835 5.290000e-14 89.8
16 TraesCS4D01G259900 chr6B 84.211 76 10 2 582 656 25922635 25922709 5.320000e-09 73.1


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 TraesCS4D01G259900 chr4D 428969598 428973438 3840 True 7094.0 7094 100.000 1 3841 1 chr4D.!!$R2 3840
1 TraesCS4D01G259900 chr4D 49086843 49087403 560 True 468.0 468 82.238 1 545 1 chr4D.!!$R1 544
2 TraesCS4D01G259900 chr4A 37299658 37302881 3223 False 4510.0 4510 92.175 657 3841 1 chr4A.!!$F1 3184
3 TraesCS4D01G259900 chr4B 527008236 527011435 3199 True 4416.0 4416 91.759 658 3841 1 chr4B.!!$R1 3183
4 TraesCS4D01G259900 chr1B 270383923 270384465 542 False 534.0 534 84.574 1 545 1 chr1B.!!$F1 544
5 TraesCS4D01G259900 chr1A 243602518 243603491 973 True 275.5 379 84.980 1 544 2 chr1A.!!$R1 543

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
559 1004 0.246910 TAGGCACCGTATTTGCACGA 59.753 50.0 0.00 0.0 44.69 4.35 F
2070 2517 0.467804 GTTGCCTCTGGATCCTCCTC 59.532 60.0 14.23 0.0 37.46 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 2792 0.896940 ACAACATCCTGCAGCCCAAG 60.897 55.0 8.66 0.0 0.00 3.61 R
3624 4146 0.803768 CTGTCCAGAATGCGGTCTCG 60.804 60.0 0.00 0.0 39.81 4.04 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 7.600065 TCTCTTTATATGCACTAACGGATACC 58.400 38.462 0.00 0.00 0.00 2.73
38 39 0.458669 CGGATACCTTGGCGTAGTGT 59.541 55.000 0.00 0.00 0.00 3.55
80 81 5.869888 ACGTTCAAGGTCTACAGATTGATTC 59.130 40.000 0.00 0.00 32.13 2.52
116 119 7.418840 TTTTTCTGCAAAATTATTCATGCGT 57.581 28.000 9.86 0.00 41.61 5.24
120 123 3.119673 TGCAAAATTATTCATGCGTCCGT 60.120 39.130 9.86 0.00 41.61 4.69
135 138 2.735823 GTCCGTGTTACGAACTTCTGT 58.264 47.619 2.52 0.00 46.05 3.41
171 178 3.589288 AGATGGGCCCTAAATTAGCCTAG 59.411 47.826 25.70 0.00 46.31 3.02
177 184 4.103627 GGCCCTAAATTAGCCTAGTTACCA 59.896 45.833 0.00 0.00 43.62 3.25
223 230 1.115467 CTACTGACTAGTGGCCCCAG 58.885 60.000 0.00 3.29 37.78 4.45
279 286 6.878923 TCTTTATCTGATTGACGGACACAAAT 59.121 34.615 0.00 0.00 36.66 2.32
285 292 4.578516 TGATTGACGGACACAAATTTGACT 59.421 37.500 24.64 8.50 0.00 3.41
294 301 4.183101 ACACAAATTTGACTGGCTGTTTG 58.817 39.130 24.64 10.33 33.92 2.93
334 341 3.988976 AGTTGTGCATATCCACTGTCT 57.011 42.857 0.00 0.00 36.68 3.41
335 342 4.292186 AGTTGTGCATATCCACTGTCTT 57.708 40.909 0.00 0.00 36.68 3.01
338 345 2.571202 TGTGCATATCCACTGTCTTCCA 59.429 45.455 0.00 0.00 36.68 3.53
339 346 3.008923 TGTGCATATCCACTGTCTTCCAA 59.991 43.478 0.00 0.00 36.68 3.53
343 350 0.321653 ATCCACTGTCTTCCAACGCC 60.322 55.000 0.00 0.00 0.00 5.68
344 351 1.227823 CCACTGTCTTCCAACGCCA 60.228 57.895 0.00 0.00 0.00 5.69
364 371 1.345741 AGTGGGATGGATATGCGTCTG 59.654 52.381 15.15 0.00 0.00 3.51
380 821 4.453136 TGCGTCTGAGTGTTTTATTAACCC 59.547 41.667 0.00 0.00 0.00 4.11
407 848 1.200020 GGTTCGAACCTCATTTGCCTG 59.800 52.381 34.98 0.00 45.75 4.85
410 851 3.904800 TCGAACCTCATTTGCCTGATA 57.095 42.857 0.00 0.00 0.00 2.15
452 896 7.621683 TGAGGCCTTTTGTGGGTAATTAAATAT 59.378 33.333 6.77 0.00 0.00 1.28
522 967 0.602638 TTTGTGCACTCCTAGCCACG 60.603 55.000 19.41 0.00 0.00 4.94
556 1001 3.162448 GGTAGGCACCGTATTTGCA 57.838 52.632 0.00 0.00 42.12 4.08
557 1002 0.730840 GGTAGGCACCGTATTTGCAC 59.269 55.000 0.00 0.00 42.12 4.57
558 1003 0.372334 GTAGGCACCGTATTTGCACG 59.628 55.000 0.00 0.00 42.12 5.34
559 1004 0.246910 TAGGCACCGTATTTGCACGA 59.753 50.000 0.00 0.00 44.69 4.35
560 1005 1.019278 AGGCACCGTATTTGCACGAG 61.019 55.000 0.00 0.00 44.69 4.18
561 1006 1.017177 GGCACCGTATTTGCACGAGA 61.017 55.000 0.00 0.00 44.69 4.04
562 1007 0.793861 GCACCGTATTTGCACGAGAA 59.206 50.000 0.00 0.00 44.69 2.87
563 1008 1.463528 GCACCGTATTTGCACGAGAAC 60.464 52.381 0.00 0.00 44.69 3.01
564 1009 1.795872 CACCGTATTTGCACGAGAACA 59.204 47.619 0.00 0.00 44.69 3.18
565 1010 1.796459 ACCGTATTTGCACGAGAACAC 59.204 47.619 0.00 0.00 44.69 3.32
566 1011 1.795872 CCGTATTTGCACGAGAACACA 59.204 47.619 0.00 0.00 44.69 3.72
567 1012 2.222213 CCGTATTTGCACGAGAACACAA 59.778 45.455 0.00 0.00 44.69 3.33
568 1013 3.469629 CGTATTTGCACGAGAACACAAG 58.530 45.455 0.00 0.00 44.69 3.16
569 1014 3.059868 CGTATTTGCACGAGAACACAAGT 60.060 43.478 0.00 0.00 44.69 3.16
570 1015 4.551990 CGTATTTGCACGAGAACACAAGTT 60.552 41.667 0.00 0.00 44.69 2.66
571 1016 2.823196 TTGCACGAGAACACAAGTTG 57.177 45.000 0.00 0.00 38.30 3.16
572 1017 2.017138 TGCACGAGAACACAAGTTGA 57.983 45.000 10.54 0.00 38.30 3.18
573 1018 2.351455 TGCACGAGAACACAAGTTGAA 58.649 42.857 10.54 0.00 38.30 2.69
574 1019 2.942376 TGCACGAGAACACAAGTTGAAT 59.058 40.909 10.54 0.00 38.30 2.57
575 1020 3.376859 TGCACGAGAACACAAGTTGAATT 59.623 39.130 10.54 2.89 38.30 2.17
576 1021 4.572795 TGCACGAGAACACAAGTTGAATTA 59.427 37.500 10.54 0.00 38.30 1.40
577 1022 5.238432 TGCACGAGAACACAAGTTGAATTAT 59.762 36.000 10.54 0.22 38.30 1.28
578 1023 5.790495 GCACGAGAACACAAGTTGAATTATC 59.210 40.000 10.54 8.80 38.30 1.75
579 1024 6.565811 GCACGAGAACACAAGTTGAATTATCA 60.566 38.462 10.54 0.00 38.30 2.15
580 1025 7.521529 CACGAGAACACAAGTTGAATTATCAT 58.478 34.615 10.54 0.00 38.30 2.45
581 1026 8.655970 CACGAGAACACAAGTTGAATTATCATA 58.344 33.333 10.54 0.00 38.30 2.15
582 1027 9.214957 ACGAGAACACAAGTTGAATTATCATAA 57.785 29.630 10.54 0.00 38.30 1.90
618 1063 9.924650 TTTTAAGTTTTAGCACCAAACTAAACA 57.075 25.926 7.99 0.00 42.47 2.83
620 1065 9.738832 TTAAGTTTTAGCACCAAACTAAACATC 57.261 29.630 7.99 0.00 42.47 3.06
621 1066 6.435428 AGTTTTAGCACCAAACTAAACATCG 58.565 36.000 6.23 0.00 41.68 3.84
622 1067 6.261381 AGTTTTAGCACCAAACTAAACATCGA 59.739 34.615 6.23 0.00 41.68 3.59
623 1068 6.621316 TTTAGCACCAAACTAAACATCGAA 57.379 33.333 0.00 0.00 35.28 3.71
624 1069 6.811253 TTAGCACCAAACTAAACATCGAAT 57.189 33.333 0.00 0.00 0.00 3.34
625 1070 5.046910 AGCACCAAACTAAACATCGAATG 57.953 39.130 0.00 0.00 0.00 2.67
626 1071 3.608073 GCACCAAACTAAACATCGAATGC 59.392 43.478 0.00 0.00 0.00 3.56
627 1072 4.793071 CACCAAACTAAACATCGAATGCA 58.207 39.130 0.00 0.00 0.00 3.96
628 1073 5.218885 CACCAAACTAAACATCGAATGCAA 58.781 37.500 0.00 0.00 0.00 4.08
629 1074 5.343058 CACCAAACTAAACATCGAATGCAAG 59.657 40.000 0.00 0.00 0.00 4.01
630 1075 5.009610 ACCAAACTAAACATCGAATGCAAGT 59.990 36.000 0.00 0.00 0.00 3.16
631 1076 5.920273 CCAAACTAAACATCGAATGCAAGTT 59.080 36.000 0.00 0.00 33.77 2.66
632 1077 7.081349 CCAAACTAAACATCGAATGCAAGTTA 58.919 34.615 0.00 0.00 32.76 2.24
633 1078 7.754924 CCAAACTAAACATCGAATGCAAGTTAT 59.245 33.333 0.00 0.00 32.76 1.89
634 1079 8.577939 CAAACTAAACATCGAATGCAAGTTATG 58.422 33.333 0.00 0.00 32.76 1.90
635 1080 7.377766 ACTAAACATCGAATGCAAGTTATGT 57.622 32.000 0.00 0.00 0.00 2.29
636 1081 7.243487 ACTAAACATCGAATGCAAGTTATGTG 58.757 34.615 8.35 1.42 0.00 3.21
637 1082 5.878332 AACATCGAATGCAAGTTATGTGA 57.122 34.783 8.35 0.00 0.00 3.58
638 1083 5.221891 ACATCGAATGCAAGTTATGTGAC 57.778 39.130 0.00 0.00 0.00 3.67
639 1084 4.937620 ACATCGAATGCAAGTTATGTGACT 59.062 37.500 0.00 0.00 0.00 3.41
640 1085 5.063944 ACATCGAATGCAAGTTATGTGACTC 59.936 40.000 0.00 0.00 0.00 3.36
641 1086 3.932710 TCGAATGCAAGTTATGTGACTCC 59.067 43.478 0.00 0.00 0.00 3.85
642 1087 3.935203 CGAATGCAAGTTATGTGACTCCT 59.065 43.478 0.00 0.00 0.00 3.69
643 1088 5.105513 TCGAATGCAAGTTATGTGACTCCTA 60.106 40.000 0.00 0.00 0.00 2.94
644 1089 5.233050 CGAATGCAAGTTATGTGACTCCTAG 59.767 44.000 0.00 0.00 0.00 3.02
645 1090 5.683876 ATGCAAGTTATGTGACTCCTAGT 57.316 39.130 0.00 0.00 0.00 2.57
646 1091 4.820897 TGCAAGTTATGTGACTCCTAGTG 58.179 43.478 0.00 0.00 0.00 2.74
647 1092 4.526650 TGCAAGTTATGTGACTCCTAGTGA 59.473 41.667 0.00 0.00 0.00 3.41
648 1093 5.187772 TGCAAGTTATGTGACTCCTAGTGAT 59.812 40.000 0.00 0.00 0.00 3.06
649 1094 6.379988 TGCAAGTTATGTGACTCCTAGTGATA 59.620 38.462 0.00 0.00 0.00 2.15
650 1095 7.069950 TGCAAGTTATGTGACTCCTAGTGATAT 59.930 37.037 0.00 0.00 0.00 1.63
651 1096 7.928706 GCAAGTTATGTGACTCCTAGTGATATT 59.071 37.037 0.00 0.00 0.00 1.28
654 1099 9.080097 AGTTATGTGACTCCTAGTGATATTACC 57.920 37.037 0.00 0.00 0.00 2.85
655 1100 9.080097 GTTATGTGACTCCTAGTGATATTACCT 57.920 37.037 0.00 0.00 0.00 3.08
656 1101 9.656323 TTATGTGACTCCTAGTGATATTACCTT 57.344 33.333 0.00 0.00 0.00 3.50
707 1152 4.082245 CGGTGATTTTGGCCTGTTTAATCT 60.082 41.667 3.32 0.00 0.00 2.40
709 1154 5.410924 GTGATTTTGGCCTGTTTAATCTCC 58.589 41.667 3.32 0.00 0.00 3.71
772 1218 3.601586 CGCGTATCAGCAAAAGGATTACG 60.602 47.826 0.00 0.00 36.85 3.18
793 1239 2.551270 GTGTTGCGCAAGGACTCG 59.449 61.111 25.78 0.00 37.48 4.18
900 1346 1.201429 ATCACCAAGCGACCTTCCCT 61.201 55.000 0.00 0.00 0.00 4.20
901 1347 1.672356 CACCAAGCGACCTTCCCTG 60.672 63.158 0.00 0.00 0.00 4.45
941 1387 4.215742 CCGGTCGCCGCCATTCTA 62.216 66.667 12.03 0.00 46.86 2.10
1051 1497 4.113815 CCAGGGCCGCCTTCATCA 62.114 66.667 9.86 0.00 0.00 3.07
1158 1604 2.264794 GCCACCACCTTCGACGAT 59.735 61.111 0.00 0.00 0.00 3.73
1283 1729 7.174426 AGCGCTAAACTTTCCTAATTACTTGTT 59.826 33.333 8.99 0.00 0.00 2.83
1295 1741 8.537858 TCCTAATTACTTGTTACTTCTCCTTCC 58.462 37.037 0.00 0.00 0.00 3.46
1296 1742 7.491696 CCTAATTACTTGTTACTTCTCCTTCCG 59.508 40.741 0.00 0.00 0.00 4.30
1298 1744 2.970640 ACTTGTTACTTCTCCTTCCGGT 59.029 45.455 0.00 0.00 0.00 5.28
1299 1745 3.006644 ACTTGTTACTTCTCCTTCCGGTC 59.993 47.826 0.00 0.00 0.00 4.79
1313 1759 4.386711 CTTCCGGTCTCCTTTGTTTTACT 58.613 43.478 0.00 0.00 0.00 2.24
1506 1952 1.342174 TCTGTTGTCCGGTGTAAGACC 59.658 52.381 0.00 0.00 42.07 3.85
1586 2033 3.891049 AGGCACCCTTCATGTTTATCTC 58.109 45.455 0.00 0.00 0.00 2.75
1590 2037 4.333926 GCACCCTTCATGTTTATCTCTGAC 59.666 45.833 0.00 0.00 0.00 3.51
1598 2045 3.585862 TGTTTATCTCTGACGTTCCTGC 58.414 45.455 0.00 0.00 0.00 4.85
1697 2144 3.581024 TCCATTGCATGTTCTGAAAGC 57.419 42.857 0.00 0.00 0.00 3.51
1702 2149 4.325028 TTGCATGTTCTGAAAGCATTGT 57.675 36.364 12.25 0.00 34.87 2.71
1718 2165 3.629398 GCATTGTCTGATCCAAACCCTAG 59.371 47.826 0.00 0.00 0.00 3.02
1728 2175 7.016661 TCTGATCCAAACCCTAGAAATATCTCC 59.983 40.741 0.00 0.00 37.10 3.71
1737 2184 5.163447 CCCTAGAAATATCTCCACGTGTCAA 60.163 44.000 15.65 0.00 37.10 3.18
1894 2341 1.067516 ACTTGTGTTCATGCAACCAGC 59.932 47.619 0.00 0.00 45.96 4.85
2033 2480 4.024725 CAGAAGCATCTAAGCATGAAGAGC 60.025 45.833 0.00 2.36 36.85 4.09
2068 2515 1.144936 CGTTGCCTCTGGATCCTCC 59.855 63.158 14.23 0.00 36.96 4.30
2069 2516 1.333636 CGTTGCCTCTGGATCCTCCT 61.334 60.000 14.23 0.00 37.46 3.69
2070 2517 0.467804 GTTGCCTCTGGATCCTCCTC 59.532 60.000 14.23 0.00 37.46 3.71
2193 2640 2.153645 TGATGTGTTGTGGAGTCATGC 58.846 47.619 0.00 0.00 0.00 4.06
2232 2679 6.054295 CCTGCTAGCATCAGAAGATAAGTTT 58.946 40.000 19.72 0.00 33.54 2.66
2334 2792 8.019094 AGCATTGTTGTTTATTTACGGTTCTAC 58.981 33.333 0.00 0.00 0.00 2.59
2540 2998 0.813821 CAGACCTCAGCGAGTCATCA 59.186 55.000 0.00 0.00 0.00 3.07
2563 3021 0.038709 GTCACTGACGAAGCTGAGCT 60.039 55.000 0.00 0.00 42.56 4.09
2731 3189 3.424105 GGGCCAGAGCAAGGGGAT 61.424 66.667 4.39 0.00 42.56 3.85
2843 3301 0.878523 TGCTCAAGCGTGCGTAGTTT 60.879 50.000 0.00 0.00 45.83 2.66
2845 3303 1.721804 GCTCAAGCGTGCGTAGTTTTC 60.722 52.381 0.00 0.00 0.00 2.29
2853 3311 5.144359 AGCGTGCGTAGTTTTCAATAAAAG 58.856 37.500 0.00 0.00 35.29 2.27
2921 3379 4.802999 CTTTTTGAGCCAGACAGGATTTC 58.197 43.478 0.00 0.00 41.22 2.17
2968 3426 2.190161 TCAAATGGTCGATTCTACGCG 58.810 47.619 3.53 3.53 0.00 6.01
3027 3485 0.751643 GGTGGCTGTGTGTTCACCTT 60.752 55.000 0.00 0.00 44.43 3.50
3028 3486 1.102978 GTGGCTGTGTGTTCACCTTT 58.897 50.000 0.37 0.00 43.26 3.11
3051 3510 3.366679 GGTGAACATGTTCTGCAAGATGG 60.367 47.826 32.57 0.00 46.36 3.51
3093 3569 7.562454 AGTTTTCTTTTGGACTCGTGATAAA 57.438 32.000 0.00 0.00 0.00 1.40
3189 3666 3.785486 TGTACATATCTGTGCAGTGCTC 58.215 45.455 17.60 13.76 42.17 4.26
3190 3667 3.448660 TGTACATATCTGTGCAGTGCTCT 59.551 43.478 17.60 0.00 42.17 4.09
3198 3675 2.169352 CTGTGCAGTGCTCTAGGGTTAT 59.831 50.000 17.60 0.00 0.00 1.89
3221 3698 4.101585 TCCCAACATGCCTGAGTATCTAAG 59.898 45.833 0.00 0.00 34.92 2.18
3246 3723 7.455638 AGTTACTCTATGTGGTAAGGTTGGTAA 59.544 37.037 0.00 0.00 0.00 2.85
3373 3871 0.741221 GTCCCGTGCCTCACTCATTC 60.741 60.000 0.00 0.00 31.34 2.67
3392 3890 7.716998 ACTCATTCGCCTTTCTATTAACATCAT 59.283 33.333 0.00 0.00 0.00 2.45
3430 3928 9.751542 TGACTTTCTACTAGCATAATTCTTAGC 57.248 33.333 0.00 0.00 0.00 3.09
3522 4020 2.092968 TCTTGCTCCAGACAGTTGTGTT 60.093 45.455 0.00 0.00 36.88 3.32
3531 4029 6.119536 TCCAGACAGTTGTGTTTCACTTAAT 58.880 36.000 1.72 0.00 36.88 1.40
3533 4031 6.183360 CCAGACAGTTGTGTTTCACTTAATGT 60.183 38.462 1.72 5.29 36.88 2.71
3535 4033 8.394877 CAGACAGTTGTGTTTCACTTAATGTTA 58.605 33.333 1.72 0.00 36.88 2.41
3537 4035 9.730420 GACAGTTGTGTTTCACTTAATGTTAAT 57.270 29.630 1.72 0.00 36.88 1.40
3565 4086 8.877864 AATAGACCATTGGAAACATTTACTCA 57.122 30.769 10.37 0.00 42.32 3.41
3588 4109 0.588252 ACTGAGCATGCGTGTTTGAC 59.412 50.000 13.01 0.00 0.00 3.18
3614 4136 6.205101 AGATGTGGATTCTGAAAAATCTGC 57.795 37.500 0.00 0.00 36.19 4.26
3624 4146 2.030540 TGAAAAATCTGCTGTGAGCTGC 60.031 45.455 0.00 0.00 42.97 5.25
3655 4177 6.701841 CGCATTCTGGACAGTTAATACACTAT 59.298 38.462 0.00 0.00 0.00 2.12
3671 4193 3.076621 CACTATCATAACATGGGCGCAT 58.923 45.455 11.00 11.00 0.00 4.73
3699 4221 6.756542 GCTCAAATGTTACAAAGTTTCAACCT 59.243 34.615 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.197116 AGCTAAACACTACGCCAAGGTAT 59.803 43.478 0.00 0.00 0.00 2.73
26 27 2.000447 GGAGCTAAACACTACGCCAAG 59.000 52.381 0.00 0.00 0.00 3.61
38 39 2.500098 ACGTGGAAGCATAGGAGCTAAA 59.500 45.455 0.00 0.00 45.89 1.85
109 112 0.039346 TTCGTAACACGGACGCATGA 60.039 50.000 0.00 0.00 42.81 3.07
116 119 3.441496 AACAGAAGTTCGTAACACGGA 57.559 42.857 0.00 0.00 42.81 4.69
120 123 3.872771 GGGTCAAACAGAAGTTCGTAACA 59.127 43.478 0.00 0.00 36.84 2.41
135 138 2.566833 CCATCTGTCAGTGGGTCAAA 57.433 50.000 11.56 0.00 0.00 2.69
223 230 9.209175 CATACTGTCTAATGGGTAATTTAGAGC 57.791 37.037 0.00 0.00 0.00 4.09
279 286 2.435372 AGACCAAACAGCCAGTCAAA 57.565 45.000 0.00 0.00 0.00 2.69
310 317 6.237901 AGACAGTGGATATGCACAACTAAAA 58.762 36.000 26.61 0.00 0.00 1.52
324 331 0.321653 GGCGTTGGAAGACAGTGGAT 60.322 55.000 0.00 0.00 0.00 3.41
326 333 1.227823 TGGCGTTGGAAGACAGTGG 60.228 57.895 0.00 0.00 0.00 4.00
327 334 2.238353 CTGGCGTTGGAAGACAGTG 58.762 57.895 0.00 0.00 39.80 3.66
334 341 1.303236 CATCCCACTGGCGTTGGAA 60.303 57.895 5.78 0.00 38.34 3.53
335 342 2.350895 CATCCCACTGGCGTTGGA 59.649 61.111 5.78 5.43 39.09 3.53
338 345 1.140312 ATATCCATCCCACTGGCGTT 58.860 50.000 0.00 0.00 36.16 4.84
339 346 0.397941 CATATCCATCCCACTGGCGT 59.602 55.000 0.00 0.00 36.16 5.68
343 350 1.345741 AGACGCATATCCATCCCACTG 59.654 52.381 0.00 0.00 0.00 3.66
344 351 1.345741 CAGACGCATATCCATCCCACT 59.654 52.381 0.00 0.00 0.00 4.00
478 923 1.669440 GTGACCCTAACACGCCAGA 59.331 57.895 0.00 0.00 0.00 3.86
479 924 1.375523 GGTGACCCTAACACGCCAG 60.376 63.158 0.00 0.00 38.90 4.85
501 946 0.472044 TGGCTAGGAGTGCACAAACA 59.528 50.000 21.04 5.01 0.00 2.83
503 948 0.602638 CGTGGCTAGGAGTGCACAAA 60.603 55.000 21.04 0.00 0.00 2.83
540 985 0.246910 TCGTGCAAATACGGTGCCTA 59.753 50.000 0.00 0.00 43.85 3.93
545 990 1.796459 GTGTTCTCGTGCAAATACGGT 59.204 47.619 0.00 0.00 43.85 4.83
546 991 1.795872 TGTGTTCTCGTGCAAATACGG 59.204 47.619 0.00 0.00 43.85 4.02
547 992 3.059868 ACTTGTGTTCTCGTGCAAATACG 60.060 43.478 0.00 0.00 44.98 3.06
548 993 4.468095 ACTTGTGTTCTCGTGCAAATAC 57.532 40.909 0.00 0.00 0.00 1.89
549 994 4.572795 TCAACTTGTGTTCTCGTGCAAATA 59.427 37.500 0.00 0.00 33.52 1.40
550 995 3.376859 TCAACTTGTGTTCTCGTGCAAAT 59.623 39.130 0.00 0.00 33.52 2.32
551 996 2.744741 TCAACTTGTGTTCTCGTGCAAA 59.255 40.909 0.00 0.00 33.52 3.68
552 997 2.351455 TCAACTTGTGTTCTCGTGCAA 58.649 42.857 0.00 0.00 33.52 4.08
553 998 2.017138 TCAACTTGTGTTCTCGTGCA 57.983 45.000 0.00 0.00 33.52 4.57
554 999 3.609103 ATTCAACTTGTGTTCTCGTGC 57.391 42.857 0.00 0.00 33.52 5.34
555 1000 6.887368 TGATAATTCAACTTGTGTTCTCGTG 58.113 36.000 0.00 0.00 33.52 4.35
556 1001 7.672983 ATGATAATTCAACTTGTGTTCTCGT 57.327 32.000 0.00 0.00 34.96 4.18
592 1037 9.924650 TGTTTAGTTTGGTGCTAAAACTTAAAA 57.075 25.926 14.31 9.04 43.60 1.52
594 1039 9.738832 GATGTTTAGTTTGGTGCTAAAACTTAA 57.261 29.630 14.31 10.34 43.60 1.85
595 1040 8.071368 CGATGTTTAGTTTGGTGCTAAAACTTA 58.929 33.333 14.31 5.94 43.60 2.24
596 1041 6.915843 CGATGTTTAGTTTGGTGCTAAAACTT 59.084 34.615 14.31 0.81 43.60 2.66
597 1042 6.261381 TCGATGTTTAGTTTGGTGCTAAAACT 59.739 34.615 13.79 13.79 46.72 2.66
598 1043 6.432107 TCGATGTTTAGTTTGGTGCTAAAAC 58.568 36.000 0.00 2.47 39.29 2.43
599 1044 6.621316 TCGATGTTTAGTTTGGTGCTAAAA 57.379 33.333 0.00 0.00 39.29 1.52
600 1045 6.621316 TTCGATGTTTAGTTTGGTGCTAAA 57.379 33.333 0.00 0.00 36.44 1.85
601 1046 6.607689 CATTCGATGTTTAGTTTGGTGCTAA 58.392 36.000 0.00 0.00 0.00 3.09
602 1047 5.391523 GCATTCGATGTTTAGTTTGGTGCTA 60.392 40.000 0.00 0.00 0.00 3.49
603 1048 4.615912 GCATTCGATGTTTAGTTTGGTGCT 60.616 41.667 0.00 0.00 0.00 4.40
604 1049 3.608073 GCATTCGATGTTTAGTTTGGTGC 59.392 43.478 0.00 0.00 0.00 5.01
605 1050 4.793071 TGCATTCGATGTTTAGTTTGGTG 58.207 39.130 0.00 0.00 0.00 4.17
606 1051 5.009610 ACTTGCATTCGATGTTTAGTTTGGT 59.990 36.000 0.00 0.00 0.00 3.67
607 1052 5.460646 ACTTGCATTCGATGTTTAGTTTGG 58.539 37.500 0.00 0.00 0.00 3.28
608 1053 6.991485 AACTTGCATTCGATGTTTAGTTTG 57.009 33.333 0.00 0.00 29.56 2.93
609 1054 8.296713 ACATAACTTGCATTCGATGTTTAGTTT 58.703 29.630 7.68 0.00 33.12 2.66
610 1055 7.750458 CACATAACTTGCATTCGATGTTTAGTT 59.250 33.333 0.00 0.00 34.34 2.24
611 1056 7.119116 TCACATAACTTGCATTCGATGTTTAGT 59.881 33.333 0.00 0.00 0.00 2.24
612 1057 7.426456 GTCACATAACTTGCATTCGATGTTTAG 59.574 37.037 0.00 0.00 0.00 1.85
613 1058 7.119116 AGTCACATAACTTGCATTCGATGTTTA 59.881 33.333 0.00 0.00 0.00 2.01
614 1059 6.072508 AGTCACATAACTTGCATTCGATGTTT 60.073 34.615 0.00 0.00 0.00 2.83
615 1060 5.412594 AGTCACATAACTTGCATTCGATGTT 59.587 36.000 0.00 0.00 0.00 2.71
616 1061 4.937620 AGTCACATAACTTGCATTCGATGT 59.062 37.500 0.00 0.00 0.00 3.06
617 1062 5.475273 AGTCACATAACTTGCATTCGATG 57.525 39.130 0.00 0.00 0.00 3.84
618 1063 4.572389 GGAGTCACATAACTTGCATTCGAT 59.428 41.667 0.00 0.00 0.00 3.59
619 1064 3.932710 GGAGTCACATAACTTGCATTCGA 59.067 43.478 0.00 0.00 0.00 3.71
620 1065 3.935203 AGGAGTCACATAACTTGCATTCG 59.065 43.478 0.00 0.00 0.00 3.34
621 1066 6.036517 CACTAGGAGTCACATAACTTGCATTC 59.963 42.308 0.00 0.00 0.00 2.67
622 1067 5.877012 CACTAGGAGTCACATAACTTGCATT 59.123 40.000 0.00 0.00 0.00 3.56
623 1068 5.187772 TCACTAGGAGTCACATAACTTGCAT 59.812 40.000 0.00 0.00 0.00 3.96
624 1069 4.526650 TCACTAGGAGTCACATAACTTGCA 59.473 41.667 0.00 0.00 0.00 4.08
625 1070 5.073311 TCACTAGGAGTCACATAACTTGC 57.927 43.478 0.00 0.00 0.00 4.01
628 1073 9.080097 GGTAATATCACTAGGAGTCACATAACT 57.920 37.037 0.00 0.00 0.00 2.24
629 1074 9.080097 AGGTAATATCACTAGGAGTCACATAAC 57.920 37.037 0.00 0.00 0.00 1.89
630 1075 9.656323 AAGGTAATATCACTAGGAGTCACATAA 57.344 33.333 0.00 0.00 0.00 1.90
632 1077 9.656323 TTAAGGTAATATCACTAGGAGTCACAT 57.344 33.333 0.00 0.00 0.00 3.21
633 1078 9.483489 TTTAAGGTAATATCACTAGGAGTCACA 57.517 33.333 0.00 0.00 0.00 3.58
664 1109 2.639286 CCAAACTGGAGCACGCAC 59.361 61.111 0.00 0.00 40.96 5.34
709 1154 0.778815 GAATCACGCCGCTTATCTCG 59.221 55.000 0.00 0.00 0.00 4.04
823 1269 2.203209 GGACGGATGATGGGGTGC 60.203 66.667 0.00 0.00 0.00 5.01
884 1330 1.841556 TCAGGGAAGGTCGCTTGGT 60.842 57.895 0.00 0.00 37.59 3.67
885 1331 1.376037 GTCAGGGAAGGTCGCTTGG 60.376 63.158 0.00 0.00 37.59 3.61
941 1387 1.146263 GATCGATCAAAGCCCGGGT 59.854 57.895 24.63 5.98 0.00 5.28
1134 1580 4.265056 AAGGTGGTGGCCGTGGAC 62.265 66.667 0.00 0.00 0.00 4.02
1158 1604 3.021473 GCGGTCGGGGATGTACCAA 62.021 63.158 0.00 0.00 41.20 3.67
1268 1714 9.939802 GAAGGAGAAGTAACAAGTAATTAGGAA 57.060 33.333 0.00 0.00 0.00 3.36
1270 1716 7.491696 CGGAAGGAGAAGTAACAAGTAATTAGG 59.508 40.741 0.00 0.00 0.00 2.69
1295 1741 6.872020 TCAATCTAGTAAAACAAAGGAGACCG 59.128 38.462 0.00 0.00 0.00 4.79
1296 1742 8.794335 ATCAATCTAGTAAAACAAAGGAGACC 57.206 34.615 0.00 0.00 0.00 3.85
1313 1759 4.455533 GGCCGCATGACATTAATCAATCTA 59.544 41.667 0.00 0.00 30.82 1.98
1328 1774 1.597797 ATCACCAGTTTGGCCGCATG 61.598 55.000 0.00 0.00 42.67 4.06
1332 1778 1.821216 AACTATCACCAGTTTGGCCG 58.179 50.000 0.00 0.00 42.67 6.13
1506 1952 3.689161 TGAACGCTCCTGATACCAATTTG 59.311 43.478 0.00 0.00 0.00 2.32
1586 2033 3.190738 TTGGGGGCAGGAACGTCAG 62.191 63.158 0.00 0.00 0.00 3.51
1590 2037 2.672996 CACTTGGGGGCAGGAACG 60.673 66.667 0.00 0.00 0.00 3.95
1598 2045 2.919494 GCAAACGAGCACTTGGGGG 61.919 63.158 0.00 0.00 0.00 5.40
1697 2144 5.102953 TCTAGGGTTTGGATCAGACAATG 57.897 43.478 0.00 0.00 0.00 2.82
1702 2149 7.016661 GGAGATATTTCTAGGGTTTGGATCAGA 59.983 40.741 0.00 0.00 30.30 3.27
1718 2165 6.258727 ACATGATTGACACGTGGAGATATTTC 59.741 38.462 21.57 6.04 0.00 2.17
1728 2175 4.686091 ACAACTCTACATGATTGACACGTG 59.314 41.667 15.48 15.48 0.00 4.49
1797 2244 5.334105 GCGGCATACATATGAAAAGGTACAG 60.334 44.000 10.38 0.00 35.75 2.74
1894 2341 1.338973 CCATGGGAATCAATCTTGGCG 59.661 52.381 2.85 0.00 0.00 5.69
2033 2480 3.728864 GCAACGGATAAACTGTCATGCTG 60.729 47.826 0.00 0.00 38.12 4.41
2068 2515 2.159653 GGCTTCAATAACACGTGCAGAG 60.160 50.000 17.22 5.46 0.00 3.35
2069 2516 1.804151 GGCTTCAATAACACGTGCAGA 59.196 47.619 17.22 3.63 0.00 4.26
2070 2517 1.806542 AGGCTTCAATAACACGTGCAG 59.193 47.619 17.22 0.99 0.00 4.41
2334 2792 0.896940 ACAACATCCTGCAGCCCAAG 60.897 55.000 8.66 0.00 0.00 3.61
2490 2948 7.713507 CGGGAAGATACATGAACCAAGTTATTA 59.286 37.037 0.00 0.00 0.00 0.98
2506 2964 3.025262 AGGTCTGAGAACGGGAAGATAC 58.975 50.000 0.00 0.00 0.00 2.24
2540 2998 1.409064 TCAGCTTCGTCAGTGACACTT 59.591 47.619 22.66 0.94 32.09 3.16
2744 3202 6.494491 TGAAATCCTTCTTGGTGTTGATGATT 59.506 34.615 0.00 0.00 37.07 2.57
2843 3301 5.321102 TGCCAGCTCCTTACTTTTATTGAA 58.679 37.500 0.00 0.00 0.00 2.69
2845 3303 4.943705 TCTGCCAGCTCCTTACTTTTATTG 59.056 41.667 0.00 0.00 0.00 1.90
2853 3311 0.107945 CCACTCTGCCAGCTCCTTAC 60.108 60.000 0.00 0.00 0.00 2.34
2939 3397 7.921786 AGAATCGACCATTTGATGAACTAAA 57.078 32.000 0.00 0.00 0.00 1.85
2968 3426 2.248487 CTTAACGTCGACCTGTACAGC 58.752 52.381 17.86 3.87 0.00 4.40
3027 3485 3.286353 TCTTGCAGAACATGTTCACCAA 58.714 40.909 33.92 30.20 41.84 3.67
3028 3486 2.929641 TCTTGCAGAACATGTTCACCA 58.070 42.857 33.92 26.74 41.84 4.17
3085 3561 8.837059 GTTGCAGTAACAACTAAATTTATCACG 58.163 33.333 0.00 0.00 45.20 4.35
3115 3592 4.985409 GGCTAAACCAGAACGAGATCATAG 59.015 45.833 0.00 0.00 38.86 2.23
3198 3675 2.481441 AGATACTCAGGCATGTTGGGA 58.519 47.619 0.00 0.00 0.00 4.37
3202 3679 7.425224 AGTAACTTAGATACTCAGGCATGTT 57.575 36.000 0.00 0.00 0.00 2.71
3203 3680 7.045126 GAGTAACTTAGATACTCAGGCATGT 57.955 40.000 20.09 0.00 45.52 3.21
3221 3698 6.046290 ACCAACCTTACCACATAGAGTAAC 57.954 41.667 0.00 0.00 0.00 2.50
3246 3723 9.290988 TGTCAATATTGTTGTGTAGGTGTTATT 57.709 29.630 14.97 0.00 0.00 1.40
3302 3782 7.752695 AGCAGCTGTTGTTATATCTGTAAAAC 58.247 34.615 16.64 0.00 0.00 2.43
3303 3783 7.921786 AGCAGCTGTTGTTATATCTGTAAAA 57.078 32.000 16.64 0.00 0.00 1.52
3358 3851 2.456119 GGCGAATGAGTGAGGCACG 61.456 63.158 0.00 0.00 39.64 5.34
3373 3871 7.482654 TCAGAATGATGTTAATAGAAAGGCG 57.517 36.000 0.00 0.00 42.56 5.52
3406 3904 7.868415 CCGCTAAGAATTATGCTAGTAGAAAGT 59.132 37.037 0.00 0.00 0.00 2.66
3414 3912 5.753438 TGTGTTCCGCTAAGAATTATGCTAG 59.247 40.000 0.00 0.00 0.00 3.42
3430 3928 2.282555 CGCATACAGATCTTGTGTTCCG 59.717 50.000 0.00 0.00 41.10 4.30
3531 4029 9.967451 TGTTTCCAATGGTCTATTCTATTAACA 57.033 29.630 0.00 0.00 0.00 2.41
3539 4037 8.956426 TGAGTAAATGTTTCCAATGGTCTATTC 58.044 33.333 0.00 0.00 0.00 1.75
3549 4070 8.378172 CTCAGTACTTGAGTAAATGTTTCCAA 57.622 34.615 11.84 0.00 46.77 3.53
3565 4086 2.169832 AACACGCATGCTCAGTACTT 57.830 45.000 17.13 0.00 0.00 2.24
3588 4109 7.914346 GCAGATTTTTCAGAATCCACATCTTAG 59.086 37.037 0.00 0.00 36.84 2.18
3614 4136 2.505777 CGGTCTCGCAGCTCACAG 60.506 66.667 0.00 0.00 0.00 3.66
3624 4146 0.803768 CTGTCCAGAATGCGGTCTCG 60.804 60.000 0.00 0.00 39.81 4.04
3655 4177 1.811965 GCATATGCGCCCATGTTATGA 59.188 47.619 12.82 0.00 32.85 2.15
3671 4193 9.243637 GTTGAAACTTTGTAACATTTGAGCATA 57.756 29.630 0.00 0.00 0.00 3.14
3699 4221 3.469008 TTCTTCTCGGAAGAAACAGCA 57.531 42.857 20.05 3.98 40.95 4.41


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

AutoCloner maintained by Alex Coulton.