Multiple sequence alignment - TraesCS1D01G378400

Loading Multiple Alignment...

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 TraesCS1D01G378400 chr1D 100.000 3239 0 0 1 3239 454459421 454456183 0.000000e+00 5982.0
1 TraesCS1D01G378400 chr1D 90.023 1724 116 27 711 2403 454768808 454770506 0.000000e+00 2180.0
2 TraesCS1D01G378400 chr1D 86.667 1785 151 35 837 2579 454493966 454492227 0.000000e+00 1897.0
3 TraesCS1D01G378400 chr1D 87.127 1507 97 39 722 2154 454812461 454813944 0.000000e+00 1618.0
4 TraesCS1D01G378400 chr1D 90.123 486 40 5 2733 3215 454648520 454649000 2.740000e-175 625.0
5 TraesCS1D01G378400 chr1D 83.828 303 32 10 125 427 454494866 454494581 4.120000e-69 272.0
6 TraesCS1D01G378400 chr1D 96.124 129 5 0 1 129 462466088 462465960 9.100000e-51 211.0
7 TraesCS1D01G378400 chr1D 95.726 117 5 0 1 117 204026637 204026753 4.270000e-44 189.0
8 TraesCS1D01G378400 chr1D 81.377 247 24 12 122 362 454811520 454811750 7.140000e-42 182.0
9 TraesCS1D01G378400 chr1D 80.147 272 26 10 194 453 454768308 454768563 9.230000e-41 178.0
10 TraesCS1D01G378400 chr1D 86.207 145 7 1 1 132 216318511 216318367 9.370000e-31 145.0
11 TraesCS1D01G378400 chr1D 87.023 131 3 7 1 117 371744869 371744999 5.640000e-28 135.0
12 TraesCS1D01G378400 chr1D 100.000 31 0 0 678 708 454494550 454494520 1.260000e-04 58.4
13 TraesCS1D01G378400 chr1B 88.161 1985 172 31 711 2654 625082305 625084267 0.000000e+00 2305.0
14 TraesCS1D01G378400 chr1B 88.715 1533 111 36 825 2332 624970668 624972163 0.000000e+00 1816.0
15 TraesCS1D01G378400 chr1B 87.542 1485 110 43 723 2154 625144942 625146404 0.000000e+00 1648.0
16 TraesCS1D01G378400 chr1B 93.944 677 37 3 2567 3239 624977796 624978472 0.000000e+00 1020.0
17 TraesCS1D01G378400 chr1B 80.724 773 104 26 1958 2716 625052002 625052743 7.850000e-156 560.0
18 TraesCS1D01G378400 chr1B 92.958 213 9 3 2326 2536 624977590 624977798 4.060000e-79 305.0
19 TraesCS1D01G378400 chr1B 82.848 309 32 13 139 445 624969866 624970155 1.150000e-64 257.0
20 TraesCS1D01G378400 chr1B 80.997 321 31 12 122 422 625081736 625082046 9.040000e-56 228.0
21 TraesCS1D01G378400 chr1B 82.927 246 25 8 122 362 625143354 625143587 4.240000e-49 206.0
22 TraesCS1D01G378400 chr1B 90.164 61 5 1 122 182 625046028 625046087 9.630000e-11 78.7
23 TraesCS1D01G378400 chr1A 91.785 1473 59 28 963 2410 548772380 548773815 0.000000e+00 1993.0
24 TraesCS1D01G378400 chr1A 89.557 1398 106 14 962 2330 548733331 548734717 0.000000e+00 1736.0
25 TraesCS1D01G378400 chr1A 87.659 1491 102 48 722 2154 548789046 548790512 0.000000e+00 1659.0
26 TraesCS1D01G378400 chr1A 89.286 336 30 2 122 451 548771551 548771886 1.800000e-112 416.0
27 TraesCS1D01G378400 chr1A 86.380 279 16 8 674 952 548772039 548772295 5.290000e-73 285.0
28 TraesCS1D01G378400 chr1A 82.583 333 37 14 122 453 548732584 548732896 1.140000e-69 274.0
29 TraesCS1D01G378400 chr1A 80.894 246 26 9 122 362 548787992 548788221 1.190000e-39 174.0
30 TraesCS1D01G378400 chr3A 84.119 806 89 21 1096 1883 482184545 482183761 0.000000e+00 743.0
31 TraesCS1D01G378400 chr3A 88.172 186 21 1 507 691 648037450 648037265 1.510000e-53 220.0
32 TraesCS1D01G378400 chr3D 82.609 874 107 35 1183 2046 362070340 362069502 0.000000e+00 730.0
33 TraesCS1D01G378400 chr3D 93.252 163 11 0 509 671 87925999 87926161 1.160000e-59 241.0
34 TraesCS1D01G378400 chr3D 88.889 117 10 2 4 117 462840301 462840417 1.210000e-29 141.0
35 TraesCS1D01G378400 chr5A 93.252 163 11 0 509 671 320214243 320214405 1.160000e-59 241.0
36 TraesCS1D01G378400 chr5A 91.279 172 15 0 508 679 558675660 558675489 5.400000e-58 235.0
37 TraesCS1D01G378400 chr5A 87.705 122 8 4 1 117 51668208 51668327 5.640000e-28 135.0
38 TraesCS1D01G378400 chr4D 92.683 164 12 0 509 672 386984667 386984830 1.500000e-58 237.0
39 TraesCS1D01G378400 chr4D 91.617 167 14 0 506 672 334164387 334164553 6.990000e-57 231.0
40 TraesCS1D01G378400 chr4D 79.928 279 38 11 1201 1478 484620960 484621221 4.270000e-44 189.0
41 TraesCS1D01G378400 chr4B 92.121 165 13 0 508 672 406389459 406389295 1.940000e-57 233.0
42 TraesCS1D01G378400 chr4B 81.132 212 36 4 2413 2621 647764804 647764594 2.000000e-37 167.0
43 TraesCS1D01G378400 chr2D 91.176 170 14 1 502 671 296364217 296364049 2.510000e-56 230.0
44 TraesCS1D01G378400 chr2D 89.256 121 8 2 1 116 12526996 12526876 2.600000e-31 147.0
45 TraesCS1D01G378400 chr2B 91.176 170 14 1 502 671 366017511 366017679 2.510000e-56 230.0
46 TraesCS1D01G378400 chr2B 92.373 118 8 1 1 117 731032349 731032466 2.000000e-37 167.0
47 TraesCS1D01G378400 chr7D 88.806 134 2 1 1 121 66103001 66103134 5.600000e-33 152.0
48 TraesCS1D01G378400 chr7D 86.029 136 6 2 1 123 162015849 162015714 2.030000e-27 134.0
49 TraesCS1D01G378400 chr6A 79.717 212 39 4 2413 2621 590370941 590371151 2.010000e-32 150.0
50 TraesCS1D01G378400 chr6A 79.245 212 40 4 2413 2621 457075037 457075247 9.370000e-31 145.0
51 TraesCS1D01G378400 chr5B 79.717 212 39 4 2413 2621 638783251 638783461 2.010000e-32 150.0
52 TraesCS1D01G378400 chr2A 79.717 212 39 4 2413 2621 138922431 138922641 2.010000e-32 150.0
53 TraesCS1D01G378400 chr3B 79.717 212 38 5 2413 2621 12765120 12765329 7.240000e-32 148.0
54 TraesCS1D01G378400 chr4A 79.245 212 40 4 2413 2621 69306058 69305848 9.370000e-31 145.0


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 TraesCS1D01G378400 chr1D 454456183 454459421 3238 True 5982.000000 5982 100.000000 1 3239 1 chr1D.!!$R2 3238
1 TraesCS1D01G378400 chr1D 454768308 454770506 2198 False 1179.000000 2180 85.085000 194 2403 2 chr1D.!!$F4 2209
2 TraesCS1D01G378400 chr1D 454811520 454813944 2424 False 900.000000 1618 84.252000 122 2154 2 chr1D.!!$F5 2032
3 TraesCS1D01G378400 chr1D 454492227 454494866 2639 True 742.466667 1897 90.165000 125 2579 3 chr1D.!!$R4 2454
4 TraesCS1D01G378400 chr1B 625081736 625084267 2531 False 1266.500000 2305 84.579000 122 2654 2 chr1B.!!$F5 2532
5 TraesCS1D01G378400 chr1B 624969866 624972163 2297 False 1036.500000 1816 85.781500 139 2332 2 chr1B.!!$F3 2193
6 TraesCS1D01G378400 chr1B 625143354 625146404 3050 False 927.000000 1648 85.234500 122 2154 2 chr1B.!!$F6 2032
7 TraesCS1D01G378400 chr1B 624977590 624978472 882 False 662.500000 1020 93.451000 2326 3239 2 chr1B.!!$F4 913
8 TraesCS1D01G378400 chr1B 625052002 625052743 741 False 560.000000 560 80.724000 1958 2716 1 chr1B.!!$F2 758
9 TraesCS1D01G378400 chr1A 548732584 548734717 2133 False 1005.000000 1736 86.070000 122 2330 2 chr1A.!!$F1 2208
10 TraesCS1D01G378400 chr1A 548787992 548790512 2520 False 916.500000 1659 84.276500 122 2154 2 chr1A.!!$F3 2032
11 TraesCS1D01G378400 chr1A 548771551 548773815 2264 False 898.000000 1993 89.150333 122 2410 3 chr1A.!!$F2 2288
12 TraesCS1D01G378400 chr3A 482183761 482184545 784 True 743.000000 743 84.119000 1096 1883 1 chr3A.!!$R1 787
13 TraesCS1D01G378400 chr3D 362069502 362070340 838 True 730.000000 730 82.609000 1183 2046 1 chr3D.!!$R1 863

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
523 1980 0.098200 GCAAATACTCCCGCCGTTTC 59.902 55.0 0.0 0.0 0.00 2.78 F
898 3231 0.533755 ACACACACTTGCCTCTGCTC 60.534 55.0 0.0 0.0 38.71 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 4278 0.673644 CCCCTTTGTGAGCACGTAGG 60.674 60.0 11.65 11.65 35.51 3.18 R
2596 5149 0.456628 TCGTCAGTGACCGTTGTTGA 59.543 50.0 17.57 4.30 0.00 3.18 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
65 66 3.741476 CGGCAAGAAGGTGCTGGC 61.741 66.667 0.00 0.00 45.49 4.85
66 67 3.741476 GGCAAGAAGGTGCTGGCG 61.741 66.667 0.00 0.00 44.31 5.69
67 68 3.741476 GCAAGAAGGTGCTGGCGG 61.741 66.667 0.00 0.00 41.51 6.13
68 69 3.741476 CAAGAAGGTGCTGGCGGC 61.741 66.667 12.43 12.43 42.22 6.53
143 144 0.613260 AGGAGATGCGTTACTTGGCA 59.387 50.000 0.00 0.00 44.29 4.92
144 145 1.009829 GGAGATGCGTTACTTGGCAG 58.990 55.000 0.00 0.00 43.27 4.85
283 302 1.317613 GCCAACCAGTGTGTTCATCA 58.682 50.000 0.00 0.00 0.00 3.07
289 308 4.290711 ACCAGTGTGTTCATCATCATCA 57.709 40.909 0.00 0.00 0.00 3.07
298 317 7.010460 GTGTGTTCATCATCATCATCGTCTTTA 59.990 37.037 0.00 0.00 0.00 1.85
467 1868 9.884814 AATACTAATATCAAGTACTCCCTCTGT 57.115 33.333 0.00 0.00 32.47 3.41
468 1869 7.589958 ACTAATATCAAGTACTCCCTCTGTG 57.410 40.000 0.00 0.00 0.00 3.66
469 1870 7.355101 ACTAATATCAAGTACTCCCTCTGTGA 58.645 38.462 0.00 0.00 0.00 3.58
470 1871 6.723298 AATATCAAGTACTCCCTCTGTGAG 57.277 41.667 0.00 0.00 35.92 3.51
482 1883 7.437748 ACTCCCTCTGTGAGAATATAAAATCG 58.562 38.462 0.00 0.00 33.95 3.34
515 1972 8.959705 AACTAAAGTACTATGCAAATACTCCC 57.040 34.615 0.00 0.00 0.00 4.30
516 1973 7.208080 ACTAAAGTACTATGCAAATACTCCCG 58.792 38.462 0.00 3.68 0.00 5.14
517 1974 3.991367 AGTACTATGCAAATACTCCCGC 58.009 45.455 0.00 0.00 0.00 6.13
518 1975 2.256117 ACTATGCAAATACTCCCGCC 57.744 50.000 0.00 0.00 0.00 6.13
519 1976 1.148310 CTATGCAAATACTCCCGCCG 58.852 55.000 0.00 0.00 0.00 6.46
520 1977 0.466543 TATGCAAATACTCCCGCCGT 59.533 50.000 0.00 0.00 0.00 5.68
521 1978 0.393808 ATGCAAATACTCCCGCCGTT 60.394 50.000 0.00 0.00 0.00 4.44
522 1979 0.606944 TGCAAATACTCCCGCCGTTT 60.607 50.000 0.00 0.00 0.00 3.60
523 1980 0.098200 GCAAATACTCCCGCCGTTTC 59.902 55.000 0.00 0.00 0.00 2.78
524 1981 1.734163 CAAATACTCCCGCCGTTTCT 58.266 50.000 0.00 0.00 0.00 2.52
525 1982 2.896168 CAAATACTCCCGCCGTTTCTA 58.104 47.619 0.00 0.00 0.00 2.10
526 1983 3.264104 CAAATACTCCCGCCGTTTCTAA 58.736 45.455 0.00 0.00 0.00 2.10
527 1984 3.615224 AATACTCCCGCCGTTTCTAAA 57.385 42.857 0.00 0.00 0.00 1.85
528 1985 3.832615 ATACTCCCGCCGTTTCTAAAT 57.167 42.857 0.00 0.00 0.00 1.40
529 1986 4.942761 ATACTCCCGCCGTTTCTAAATA 57.057 40.909 0.00 0.00 0.00 1.40
530 1987 3.832615 ACTCCCGCCGTTTCTAAATAT 57.167 42.857 0.00 0.00 0.00 1.28
531 1988 4.942761 ACTCCCGCCGTTTCTAAATATA 57.057 40.909 0.00 0.00 0.00 0.86
532 1989 5.280654 ACTCCCGCCGTTTCTAAATATAA 57.719 39.130 0.00 0.00 0.00 0.98
533 1990 5.295152 ACTCCCGCCGTTTCTAAATATAAG 58.705 41.667 0.00 0.00 0.00 1.73
534 1991 5.163374 ACTCCCGCCGTTTCTAAATATAAGT 60.163 40.000 0.00 0.00 0.00 2.24
535 1992 5.291971 TCCCGCCGTTTCTAAATATAAGTC 58.708 41.667 0.00 0.00 0.00 3.01
536 1993 5.069516 TCCCGCCGTTTCTAAATATAAGTCT 59.930 40.000 0.00 0.00 0.00 3.24
537 1994 5.756833 CCCGCCGTTTCTAAATATAAGTCTT 59.243 40.000 0.00 0.00 0.00 3.01
538 1995 6.259387 CCCGCCGTTTCTAAATATAAGTCTTT 59.741 38.462 0.00 0.00 0.00 2.52
539 1996 7.201670 CCCGCCGTTTCTAAATATAAGTCTTTT 60.202 37.037 0.00 0.00 0.00 2.27
540 1997 8.179615 CCGCCGTTTCTAAATATAAGTCTTTTT 58.820 33.333 0.00 0.00 0.00 1.94
567 2024 9.658799 AGAGATTTCAATATGGATTACATACGG 57.341 33.333 0.00 0.00 44.41 4.02
568 2025 9.653287 GAGATTTCAATATGGATTACATACGGA 57.347 33.333 0.00 0.00 44.41 4.69
569 2026 9.658799 AGATTTCAATATGGATTACATACGGAG 57.341 33.333 0.00 0.00 44.41 4.63
570 2027 7.667043 TTTCAATATGGATTACATACGGAGC 57.333 36.000 0.00 0.00 44.41 4.70
571 2028 6.353404 TCAATATGGATTACATACGGAGCA 57.647 37.500 0.00 0.00 44.41 4.26
572 2029 6.764379 TCAATATGGATTACATACGGAGCAA 58.236 36.000 0.00 0.00 44.41 3.91
573 2030 7.220740 TCAATATGGATTACATACGGAGCAAA 58.779 34.615 0.00 0.00 44.41 3.68
574 2031 7.717436 TCAATATGGATTACATACGGAGCAAAA 59.283 33.333 0.00 0.00 44.41 2.44
575 2032 8.514594 CAATATGGATTACATACGGAGCAAAAT 58.485 33.333 0.00 0.00 44.41 1.82
576 2033 5.749596 TGGATTACATACGGAGCAAAATG 57.250 39.130 0.00 0.00 0.00 2.32
577 2034 5.432645 TGGATTACATACGGAGCAAAATGA 58.567 37.500 0.00 0.00 0.00 2.57
578 2035 5.527214 TGGATTACATACGGAGCAAAATGAG 59.473 40.000 0.00 0.00 0.00 2.90
579 2036 5.527582 GGATTACATACGGAGCAAAATGAGT 59.472 40.000 0.00 0.00 0.00 3.41
580 2037 5.794687 TTACATACGGAGCAAAATGAGTG 57.205 39.130 0.00 0.00 0.00 3.51
581 2038 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
582 2039 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
583 2040 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
584 2041 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
585 2042 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
586 2043 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
587 2044 5.431765 ACGGAGCAAAATGAGTGAATCTAT 58.568 37.500 0.00 0.00 0.00 1.98
588 2045 6.582636 ACGGAGCAAAATGAGTGAATCTATA 58.417 36.000 0.00 0.00 0.00 1.31
589 2046 6.480320 ACGGAGCAAAATGAGTGAATCTATAC 59.520 38.462 0.00 0.00 0.00 1.47
590 2047 6.703607 CGGAGCAAAATGAGTGAATCTATACT 59.296 38.462 0.00 0.00 0.00 2.12
591 2048 7.095857 CGGAGCAAAATGAGTGAATCTATACTC 60.096 40.741 0.00 0.00 42.77 2.59
592 2049 7.930865 GGAGCAAAATGAGTGAATCTATACTCT 59.069 37.037 0.00 0.00 42.86 3.24
593 2050 9.973450 GAGCAAAATGAGTGAATCTATACTCTA 57.027 33.333 0.00 0.00 42.86 2.43
614 2071 9.228949 ACTCTAAAGTATGTCTATATACACCCG 57.771 37.037 0.00 0.00 36.27 5.28
615 2072 9.228949 CTCTAAAGTATGTCTATATACACCCGT 57.771 37.037 0.00 0.00 36.27 5.28
672 2129 9.557061 CTTATATTTAGGAACAAAGGGAGTACC 57.443 37.037 0.00 0.00 40.67 3.34
757 2603 9.097257 CACATATGAAAGACAAAAACAAAACCT 57.903 29.630 10.38 0.00 0.00 3.50
770 2616 2.037121 ACAAAACCTTAAGCCCATGTGC 59.963 45.455 0.00 0.00 0.00 4.57
852 3171 0.753262 ACACTCACACTCACCTCCAC 59.247 55.000 0.00 0.00 0.00 4.02
873 3206 6.509280 TCCACCTCCTCTCATCCTCTATATAA 59.491 42.308 0.00 0.00 0.00 0.98
874 3207 6.605594 CCACCTCCTCTCATCCTCTATATAAC 59.394 46.154 0.00 0.00 0.00 1.89
875 3208 7.178573 CACCTCCTCTCATCCTCTATATAACA 58.821 42.308 0.00 0.00 0.00 2.41
876 3209 7.122055 CACCTCCTCTCATCCTCTATATAACAC 59.878 44.444 0.00 0.00 0.00 3.32
883 3216 7.559897 TCTCATCCTCTATATAACACACACACA 59.440 37.037 0.00 0.00 0.00 3.72
898 3231 0.533755 ACACACACTTGCCTCTGCTC 60.534 55.000 0.00 0.00 38.71 4.26
980 3404 4.835615 CCCTCCTAGCTAAGCATCTTCTTA 59.164 45.833 0.00 0.00 0.00 2.10
983 3407 7.096551 CCTCCTAGCTAAGCATCTTCTTAATC 58.903 42.308 0.00 0.00 0.00 1.75
1197 3655 3.249189 AGGCTGCCGTCCTCCAAA 61.249 61.111 13.96 0.00 0.00 3.28
1466 3924 2.472909 GCAAGCACATCTACCCCGC 61.473 63.158 0.00 0.00 0.00 6.13
1902 4396 1.261480 ACCAGCTCTTCATCGACTGT 58.739 50.000 0.00 0.00 0.00 3.55
1946 4443 2.095469 GACGACGACGACGACCTC 59.905 66.667 25.15 9.57 42.66 3.85
2154 4687 0.731417 TAGACTTCGCGCTGACCTAC 59.269 55.000 5.56 0.00 0.00 3.18
2200 4733 2.168521 CCGAGGCCAAGAGATCAACTAA 59.831 50.000 5.01 0.00 0.00 2.24
2221 4754 0.838122 AGGAGTACAAGCAGCAGGGT 60.838 55.000 0.00 0.00 0.00 4.34
2224 4757 0.250467 AGTACAAGCAGCAGGGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
2321 4857 5.171476 CAAATACTCTTGACCGACTCACAT 58.829 41.667 0.00 0.00 0.00 3.21
2322 4858 6.330278 CAAATACTCTTGACCGACTCACATA 58.670 40.000 0.00 0.00 0.00 2.29
2323 4859 5.759506 ATACTCTTGACCGACTCACATAG 57.240 43.478 0.00 0.00 0.00 2.23
2324 4860 3.422796 ACTCTTGACCGACTCACATAGT 58.577 45.455 0.00 0.00 42.80 2.12
2441 4991 9.624373 ACATCAGAAGTAATAGAAATTGCATCT 57.376 29.630 0.00 0.00 36.56 2.90
2479 5029 5.696724 ACCTAGCGATGAGTACAAATATTGC 59.303 40.000 0.00 0.00 0.00 3.56
2537 5090 2.335712 CGGAGCTGGGCAAACCTTC 61.336 63.158 0.00 0.00 41.11 3.46
2554 5107 2.438411 CTTCTGGTAGGAGACAGTCGT 58.562 52.381 0.00 0.00 36.17 4.34
2561 5114 0.110678 AGGAGACAGTCGTGAGGTCA 59.889 55.000 0.00 0.00 34.04 4.02
2596 5149 0.033894 AAAGGACCAACACACCGGTT 60.034 50.000 2.97 0.00 34.99 4.44
2644 5197 5.138800 ACGTAAATCGAAATGATCCAACG 57.861 39.130 0.00 0.00 42.86 4.10
2695 5248 3.261897 AGTCGAATCCAAGTTGATCCACT 59.738 43.478 3.87 0.00 0.00 4.00
2734 5287 2.076622 ATCCAACGAGATCCGCCGAG 62.077 60.000 6.74 0.37 43.32 4.63
2788 5341 0.801067 CGTCGCTACTGTTAGGCCAC 60.801 60.000 5.01 0.00 0.00 5.01
2806 5359 1.382146 CCCAAGTAGTAGCCCCGGA 60.382 63.158 0.73 0.00 0.00 5.14
2811 5364 0.040794 AGTAGTAGCCCCGGAAGTGT 59.959 55.000 0.73 0.00 0.00 3.55
2841 5394 7.707893 TCCATTTCTTTCTTCTTTGCTTCTTTG 59.292 33.333 0.00 0.00 0.00 2.77
2948 5501 6.751514 ATCGCCACACATTAGAAAAACATA 57.248 33.333 0.00 0.00 0.00 2.29
2982 5535 7.101652 TGGAAACAGTGTGCAAGTAATTTTA 57.898 32.000 0.00 0.00 35.01 1.52
3017 5570 8.922676 TCTTACTCTTCAAAACAATATCGTGAC 58.077 33.333 0.00 0.00 0.00 3.67
3039 5592 9.677567 GTGACATTTTATAAGTGTTCATGTGTT 57.322 29.630 6.93 0.00 0.00 3.32
3169 5724 9.202273 ACAAAATGTTCATGCGTTACAAAATAT 57.798 25.926 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.741476 CAGCACCTTCTTGCCGCC 61.741 66.667 0.00 0.00 44.14 6.13
47 48 3.741476 CCAGCACCTTCTTGCCGC 61.741 66.667 0.00 0.00 44.14 6.53
48 49 3.741476 GCCAGCACCTTCTTGCCG 61.741 66.667 0.00 0.00 44.14 5.69
49 50 3.741476 CGCCAGCACCTTCTTGCC 61.741 66.667 0.00 0.00 44.14 4.52
50 51 3.741476 CCGCCAGCACCTTCTTGC 61.741 66.667 0.00 0.00 43.34 4.01
51 52 3.741476 GCCGCCAGCACCTTCTTG 61.741 66.667 0.00 0.00 42.97 3.02
104 105 4.415332 TTCCACTCGCGTCGCCTC 62.415 66.667 12.44 0.00 0.00 4.70
105 106 4.421479 CTTCCACTCGCGTCGCCT 62.421 66.667 12.44 0.00 0.00 5.52
108 109 3.175240 CTGCTTCCACTCGCGTCG 61.175 66.667 5.77 0.58 0.00 5.12
109 110 2.811317 CCTGCTTCCACTCGCGTC 60.811 66.667 5.77 0.00 0.00 5.19
110 111 3.288308 CTCCTGCTTCCACTCGCGT 62.288 63.158 5.77 0.00 0.00 6.01
111 112 2.290122 ATCTCCTGCTTCCACTCGCG 62.290 60.000 0.00 0.00 0.00 5.87
112 113 0.809241 CATCTCCTGCTTCCACTCGC 60.809 60.000 0.00 0.00 0.00 5.03
113 114 3.359194 CATCTCCTGCTTCCACTCG 57.641 57.895 0.00 0.00 0.00 4.18
123 124 1.009829 GCCAAGTAACGCATCTCCTG 58.990 55.000 0.00 0.00 0.00 3.86
143 144 2.306219 GGAGGAAGAAAAGTAGTGGCCT 59.694 50.000 3.32 0.00 0.00 5.19
144 145 2.618302 GGGAGGAAGAAAAGTAGTGGCC 60.618 54.545 0.00 0.00 0.00 5.36
216 217 2.685388 TGTGGTTGCGTGAGAAATTCAA 59.315 40.909 0.00 0.00 37.61 2.69
261 262 0.323816 TGAACACACTGGTTGGCCAA 60.324 50.000 16.05 16.05 45.51 4.52
270 271 4.569564 ACGATGATGATGATGAACACACTG 59.430 41.667 0.00 0.00 0.00 3.66
313 332 3.799281 ATGGCGGTGTTAATGGAAATG 57.201 42.857 0.00 0.00 0.00 2.32
314 337 5.923733 TTTATGGCGGTGTTAATGGAAAT 57.076 34.783 0.00 0.00 0.00 2.17
317 340 7.001674 AGATATTTTATGGCGGTGTTAATGGA 58.998 34.615 0.00 0.00 0.00 3.41
319 342 8.999431 AGTAGATATTTTATGGCGGTGTTAATG 58.001 33.333 0.00 0.00 0.00 1.90
325 348 7.870954 TCAACTAGTAGATATTTTATGGCGGTG 59.129 37.037 3.59 0.00 0.00 4.94
326 349 7.871463 GTCAACTAGTAGATATTTTATGGCGGT 59.129 37.037 3.59 0.00 0.00 5.68
442 1755 9.303116 CACAGAGGGAGTACTTGATATTAGTAT 57.697 37.037 0.00 0.00 31.31 2.12
460 1861 8.438676 AAACGATTTTATATTCTCACAGAGGG 57.561 34.615 0.00 0.00 0.00 4.30
507 1964 3.615224 TTTAGAAACGGCGGGAGTATT 57.385 42.857 13.24 0.00 0.00 1.89
508 1965 3.832615 ATTTAGAAACGGCGGGAGTAT 57.167 42.857 13.24 0.00 0.00 2.12
509 1966 4.942761 ATATTTAGAAACGGCGGGAGTA 57.057 40.909 13.24 0.00 0.00 2.59
510 1967 3.832615 ATATTTAGAAACGGCGGGAGT 57.167 42.857 13.24 0.00 0.00 3.85
511 1968 5.295152 ACTTATATTTAGAAACGGCGGGAG 58.705 41.667 13.24 0.00 0.00 4.30
512 1969 5.069516 AGACTTATATTTAGAAACGGCGGGA 59.930 40.000 13.24 0.00 0.00 5.14
513 1970 5.295152 AGACTTATATTTAGAAACGGCGGG 58.705 41.667 13.24 0.00 0.00 6.13
514 1971 6.839820 AAGACTTATATTTAGAAACGGCGG 57.160 37.500 13.24 0.00 0.00 6.13
541 1998 9.658799 CCGTATGTAATCCATATTGAAATCTCT 57.341 33.333 0.00 0.00 38.29 3.10
542 1999 9.653287 TCCGTATGTAATCCATATTGAAATCTC 57.347 33.333 0.00 0.00 38.29 2.75
543 2000 9.658799 CTCCGTATGTAATCCATATTGAAATCT 57.341 33.333 0.00 0.00 38.29 2.40
544 2001 8.391106 GCTCCGTATGTAATCCATATTGAAATC 58.609 37.037 0.00 0.00 38.29 2.17
545 2002 7.882791 TGCTCCGTATGTAATCCATATTGAAAT 59.117 33.333 0.00 0.00 38.29 2.17
546 2003 7.220740 TGCTCCGTATGTAATCCATATTGAAA 58.779 34.615 0.00 0.00 38.29 2.69
547 2004 6.764379 TGCTCCGTATGTAATCCATATTGAA 58.236 36.000 0.00 0.00 38.29 2.69
548 2005 6.353404 TGCTCCGTATGTAATCCATATTGA 57.647 37.500 0.00 0.00 38.29 2.57
549 2006 7.433708 TTTGCTCCGTATGTAATCCATATTG 57.566 36.000 0.00 0.00 38.29 1.90
550 2007 8.514594 CATTTTGCTCCGTATGTAATCCATATT 58.485 33.333 0.00 0.00 38.29 1.28
551 2008 7.882791 TCATTTTGCTCCGTATGTAATCCATAT 59.117 33.333 0.00 0.00 38.29 1.78
552 2009 7.220740 TCATTTTGCTCCGTATGTAATCCATA 58.779 34.615 0.00 0.00 34.86 2.74
553 2010 6.061441 TCATTTTGCTCCGTATGTAATCCAT 58.939 36.000 0.00 0.00 37.58 3.41
554 2011 5.432645 TCATTTTGCTCCGTATGTAATCCA 58.567 37.500 0.00 0.00 0.00 3.41
555 2012 5.527582 ACTCATTTTGCTCCGTATGTAATCC 59.472 40.000 0.00 0.00 0.00 3.01
556 2013 6.257849 TCACTCATTTTGCTCCGTATGTAATC 59.742 38.462 0.00 0.00 0.00 1.75
557 2014 6.112734 TCACTCATTTTGCTCCGTATGTAAT 58.887 36.000 0.00 0.00 0.00 1.89
558 2015 5.483811 TCACTCATTTTGCTCCGTATGTAA 58.516 37.500 0.00 0.00 0.00 2.41
559 2016 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
560 2017 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
561 2018 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
562 2019 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
563 2020 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
564 2021 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
565 2022 5.998454 ATAGATTCACTCATTTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
566 2023 7.930865 AGAGTATAGATTCACTCATTTTGCTCC 59.069 37.037 4.70 0.00 42.99 4.70
567 2024 8.885494 AGAGTATAGATTCACTCATTTTGCTC 57.115 34.615 4.70 0.00 42.99 4.26
588 2045 9.228949 CGGGTGTATATAGACATACTTTAGAGT 57.771 37.037 11.75 0.00 39.97 3.24
589 2046 9.228949 ACGGGTGTATATAGACATACTTTAGAG 57.771 37.037 11.75 0.00 33.37 2.43
642 2099 9.853177 CTCCCTTTGTTCCTAAATATAAGTCAT 57.147 33.333 0.00 0.00 0.00 3.06
643 2100 8.832735 ACTCCCTTTGTTCCTAAATATAAGTCA 58.167 33.333 0.00 0.00 0.00 3.41
646 2103 9.557061 GGTACTCCCTTTGTTCCTAAATATAAG 57.443 37.037 0.00 0.00 0.00 1.73
647 2104 9.060137 TGGTACTCCCTTTGTTCCTAAATATAA 57.940 33.333 0.00 0.00 0.00 0.98
648 2105 8.626917 TGGTACTCCCTTTGTTCCTAAATATA 57.373 34.615 0.00 0.00 0.00 0.86
649 2106 7.519347 TGGTACTCCCTTTGTTCCTAAATAT 57.481 36.000 0.00 0.00 0.00 1.28
650 2107 6.956102 TGGTACTCCCTTTGTTCCTAAATA 57.044 37.500 0.00 0.00 0.00 1.40
651 2108 5.853572 TGGTACTCCCTTTGTTCCTAAAT 57.146 39.130 0.00 0.00 0.00 1.40
652 2109 5.649970 TTGGTACTCCCTTTGTTCCTAAA 57.350 39.130 0.00 0.00 0.00 1.85
653 2110 5.104024 TGTTTGGTACTCCCTTTGTTCCTAA 60.104 40.000 0.00 0.00 0.00 2.69
654 2111 4.412858 TGTTTGGTACTCCCTTTGTTCCTA 59.587 41.667 0.00 0.00 0.00 2.94
655 2112 3.203487 TGTTTGGTACTCCCTTTGTTCCT 59.797 43.478 0.00 0.00 0.00 3.36
656 2113 3.558033 TGTTTGGTACTCCCTTTGTTCC 58.442 45.455 0.00 0.00 0.00 3.62
657 2114 4.399934 TGTTGTTTGGTACTCCCTTTGTTC 59.600 41.667 0.00 0.00 0.00 3.18
658 2115 4.158949 GTGTTGTTTGGTACTCCCTTTGTT 59.841 41.667 0.00 0.00 0.00 2.83
659 2116 3.697542 GTGTTGTTTGGTACTCCCTTTGT 59.302 43.478 0.00 0.00 0.00 2.83
660 2117 3.951680 AGTGTTGTTTGGTACTCCCTTTG 59.048 43.478 0.00 0.00 0.00 2.77
661 2118 4.245251 AGTGTTGTTTGGTACTCCCTTT 57.755 40.909 0.00 0.00 0.00 3.11
662 2119 3.945640 AGTGTTGTTTGGTACTCCCTT 57.054 42.857 0.00 0.00 0.00 3.95
663 2120 3.244457 GCTAGTGTTGTTTGGTACTCCCT 60.244 47.826 0.00 0.00 0.00 4.20
664 2121 3.072211 GCTAGTGTTGTTTGGTACTCCC 58.928 50.000 0.00 0.00 0.00 4.30
665 2122 3.735591 TGCTAGTGTTGTTTGGTACTCC 58.264 45.455 0.00 0.00 0.00 3.85
666 2123 4.755123 ACATGCTAGTGTTGTTTGGTACTC 59.245 41.667 0.00 0.00 0.00 2.59
720 2564 9.586435 TTGTCTTTCATATGTGTGTAGTAGATG 57.414 33.333 1.90 0.00 0.00 2.90
757 2603 1.846007 ATTTCCGCACATGGGCTTAA 58.154 45.000 19.64 9.10 0.00 1.85
823 2693 1.417890 AGTGTGAGTGTGGCTAAGCTT 59.582 47.619 3.48 3.48 0.00 3.74
852 3171 7.122055 GTGTGTTATATAGAGGATGAGAGGAGG 59.878 44.444 0.00 0.00 0.00 4.30
873 3206 0.322456 AGGCAAGTGTGTGTGTGTGT 60.322 50.000 0.00 0.00 0.00 3.72
874 3207 0.378257 GAGGCAAGTGTGTGTGTGTG 59.622 55.000 0.00 0.00 0.00 3.82
875 3208 0.253044 AGAGGCAAGTGTGTGTGTGT 59.747 50.000 0.00 0.00 0.00 3.72
876 3209 0.659427 CAGAGGCAAGTGTGTGTGTG 59.341 55.000 0.00 0.00 0.00 3.82
883 3216 1.676384 GAGGAGCAGAGGCAAGTGT 59.324 57.895 0.00 0.00 44.61 3.55
898 3231 0.827368 GAGGCAGTTGGTAGAGGAGG 59.173 60.000 0.00 0.00 0.00 4.30
955 3305 2.604139 AGATGCTTAGCTAGGAGGGAC 58.396 52.381 7.11 0.00 0.00 4.46
958 3308 4.953940 AAGAAGATGCTTAGCTAGGAGG 57.046 45.455 7.11 0.00 0.00 4.30
980 3404 0.747255 CCGATCACCACCGAGAGATT 59.253 55.000 0.00 0.00 0.00 2.40
983 3407 0.031314 CATCCGATCACCACCGAGAG 59.969 60.000 0.00 0.00 0.00 3.20
1350 3808 3.305177 GAGCGGGCGGAAGTTGGTA 62.305 63.158 0.00 0.00 0.00 3.25
1569 4060 3.666253 TCGAACAGGTGCTCGCGA 61.666 61.111 9.26 9.26 34.03 5.87
1787 4278 0.673644 CCCCTTTGTGAGCACGTAGG 60.674 60.000 11.65 11.65 35.51 3.18
1845 4336 1.526575 GGTAGAACCCGACCACGTCA 61.527 60.000 0.00 0.00 37.90 4.35
1902 4396 2.283824 GGTCTTGGACCGGAGCTTA 58.716 57.895 9.46 0.00 43.14 3.09
1938 4432 1.515736 CGCGTTAAGGGAGGTCGTC 60.516 63.158 0.00 0.00 34.27 4.20
1939 4433 2.570181 CGCGTTAAGGGAGGTCGT 59.430 61.111 0.00 0.00 34.27 4.34
1940 4434 2.202703 CCGCGTTAAGGGAGGTCG 60.203 66.667 4.92 0.00 34.27 4.79
2007 4507 2.197605 TGCCGTGAGAAGGTCGACA 61.198 57.895 18.91 0.00 0.00 4.35
2040 4564 2.109181 GCCATGCCGTACTCCTCC 59.891 66.667 0.00 0.00 0.00 4.30
2154 4687 0.957395 GTGAGGTGGTGGCATGTCTG 60.957 60.000 0.00 0.00 0.00 3.51
2185 4718 7.386851 TGTACTCCTTTTAGTTGATCTCTTGG 58.613 38.462 0.00 0.00 0.00 3.61
2200 4733 1.271597 CCCTGCTGCTTGTACTCCTTT 60.272 52.381 0.00 0.00 0.00 3.11
2221 4754 5.491070 ACAAGTCTATAGAGCAAATGCACA 58.509 37.500 1.64 0.00 45.16 4.57
2224 4757 5.007136 GGTGACAAGTCTATAGAGCAAATGC 59.993 44.000 1.64 0.00 42.49 3.56
2441 4991 5.485209 TCGCTAGGTGATCTATGAGACTA 57.515 43.478 0.00 0.00 0.00 2.59
2479 5029 1.160137 GGTGCACCTTAGACTTGCTG 58.840 55.000 29.12 0.00 37.16 4.41
2537 5090 1.740585 CTCACGACTGTCTCCTACCAG 59.259 57.143 6.21 0.00 34.82 4.00
2544 5097 1.202087 CGATGACCTCACGACTGTCTC 60.202 57.143 6.21 0.00 0.00 3.36
2554 5107 1.112113 GCCTTAGGACGATGACCTCA 58.888 55.000 0.69 0.00 38.76 3.86
2561 5114 0.546598 CTTTGGGGCCTTAGGACGAT 59.453 55.000 0.69 0.00 0.00 3.73
2596 5149 0.456628 TCGTCAGTGACCGTTGTTGA 59.543 50.000 17.57 4.30 0.00 3.18
2644 5197 5.158494 TCATATGTGTTCACGTGTCTACAC 58.842 41.667 27.96 27.96 43.15 2.90
2695 5248 6.990798 TGGATTTTATCATTGTTTGTCTGCA 58.009 32.000 0.00 0.00 0.00 4.41
2755 5308 2.624811 GACGCATGATGCTCGCTG 59.375 61.111 16.17 1.64 42.25 5.18
2777 5330 1.628846 ACTACTTGGGTGGCCTAACAG 59.371 52.381 3.32 0.00 0.00 3.16
2788 5341 0.979187 TTCCGGGGCTACTACTTGGG 60.979 60.000 0.00 0.00 0.00 4.12
2806 5359 5.537674 AGAAGAAAGAAATGGATGCACACTT 59.462 36.000 0.00 0.00 0.00 3.16
2811 5364 5.011329 AGCAAAGAAGAAAGAAATGGATGCA 59.989 36.000 0.00 0.00 0.00 3.96
2906 5459 9.988350 GTGGCGATATTTCATACTATATTTTGG 57.012 33.333 0.00 0.00 0.00 3.28
2924 5477 6.751514 ATGTTTTTCTAATGTGTGGCGATA 57.248 33.333 0.00 0.00 0.00 2.92
2948 5501 5.301551 TGCACACTGTTTCCAATGAGTTAAT 59.698 36.000 0.00 0.00 0.00 1.40
2957 5510 5.590530 AATTACTTGCACACTGTTTCCAA 57.409 34.783 0.00 0.00 0.00 3.53
2990 5543 9.140286 TCACGATATTGTTTTGAAGAGTAAGAG 57.860 33.333 0.00 0.00 0.00 2.85
2993 5546 8.596271 TGTCACGATATTGTTTTGAAGAGTAA 57.404 30.769 0.00 0.00 0.00 2.24
3010 5563 8.946085 ACATGAACACTTATAAAATGTCACGAT 58.054 29.630 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.