Multiple sequence alignment - TraesCS6B01G219300

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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 TraesCS6B01G219300 chr6B 100.000 3171 0 0 1 3171 308472416 308475586 0.000000e+00 5856.0
1 TraesCS6B01G219300 chr6B 100.000 1450 0 0 3352 4801 308475767 308477216 0.000000e+00 2678.0
2 TraesCS6B01G219300 chr6B 97.898 904 19 0 1 904 633350480 633351383 0.000000e+00 1565.0
3 TraesCS6B01G219300 chr6B 86.944 360 45 2 3480 3839 320983891 320983534 2.080000e-108 403.0
4 TraesCS6B01G219300 chr6B 84.573 363 45 8 4322 4674 48121796 48121435 2.750000e-92 350.0
5 TraesCS6B01G219300 chr6B 100.000 122 0 0 2950 3071 308475304 308475425 4.830000e-55 226.0
6 TraesCS6B01G219300 chr6B 100.000 122 0 0 2889 3010 308475365 308475486 4.830000e-55 226.0
7 TraesCS6B01G219300 chr6B 100.000 61 0 0 3011 3071 308475304 308475364 3.930000e-21 113.0
8 TraesCS6B01G219300 chr6B 100.000 61 0 0 2889 2949 308475426 308475486 3.930000e-21 113.0
9 TraesCS6B01G219300 chr6D 97.630 2110 43 5 904 3010 260020496 260022601 0.000000e+00 3613.0
10 TraesCS6B01G219300 chr6D 95.448 1340 57 3 3465 4801 260023016 260024354 0.000000e+00 2134.0
11 TraesCS6B01G219300 chr6D 97.297 222 6 0 2950 3171 260022480 260022701 1.260000e-100 377.0
12 TraesCS6B01G219300 chr6D 85.612 139 17 3 3839 3975 177411115 177410978 5.010000e-30 143.0
13 TraesCS6B01G219300 chr6D 100.000 62 0 0 3406 3467 260022932 260022993 1.090000e-21 115.0
14 TraesCS6B01G219300 chr6D 98.361 61 1 0 2889 2949 260022541 260022601 1.830000e-19 108.0
15 TraesCS6B01G219300 chr6A 97.608 2090 43 5 923 3010 370679554 370677470 0.000000e+00 3576.0
16 TraesCS6B01G219300 chr6A 93.878 1421 47 12 3401 4801 370677160 370675760 0.000000e+00 2106.0
17 TraesCS6B01G219300 chr6A 98.119 904 17 0 1 904 538053412 538054315 0.000000e+00 1576.0
18 TraesCS6B01G219300 chr6A 97.685 216 5 0 2952 3167 370677589 370677374 5.870000e-99 372.0
19 TraesCS6B01G219300 chr6A 84.211 361 41 6 3494 3839 254439149 254439508 2.140000e-88 337.0
20 TraesCS6B01G219300 chr6A 98.361 61 1 0 2889 2949 370677530 370677470 1.830000e-19 108.0
21 TraesCS6B01G219300 chr2B 98.234 906 14 2 1 904 742107685 742108590 0.000000e+00 1583.0
22 TraesCS6B01G219300 chr2B 98.119 904 14 2 1 904 340547793 340548693 0.000000e+00 1572.0
23 TraesCS6B01G219300 chr7B 98.119 904 17 0 1 904 23391466 23392369 0.000000e+00 1576.0
24 TraesCS6B01G219300 chr7B 89.881 336 28 5 3970 4300 946642 946308 1.230000e-115 427.0
25 TraesCS6B01G219300 chr7B 86.029 136 16 3 3839 3972 285351502 285351636 5.010000e-30 143.0
26 TraesCS6B01G219300 chr3A 98.119 904 16 1 1 904 521604635 521605537 0.000000e+00 1574.0
27 TraesCS6B01G219300 chr3A 87.719 57 7 0 3467 3523 661984899 661984955 3.100000e-07 67.6
28 TraesCS6B01G219300 chr5B 98.011 905 18 0 1 905 700993600 700994504 0.000000e+00 1572.0
29 TraesCS6B01G219300 chr5B 89.911 337 28 4 3970 4301 101020638 101020303 3.430000e-116 429.0
30 TraesCS6B01G219300 chr5B 86.047 129 16 2 3854 3981 157031264 157031137 2.330000e-28 137.0
31 TraesCS6B01G219300 chr1B 97.903 906 17 2 1 904 57742896 57741991 0.000000e+00 1567.0
32 TraesCS6B01G219300 chr1B 97.380 916 20 4 1 915 472397366 472396454 0.000000e+00 1555.0
33 TraesCS6B01G219300 chr1B 86.943 314 39 2 4303 4614 340345700 340346013 7.640000e-93 351.0
34 TraesCS6B01G219300 chr1B 85.714 133 14 4 3029 3157 222306745 222306876 8.380000e-28 135.0
35 TraesCS6B01G219300 chr1B 87.288 118 13 2 3027 3144 222306957 222307072 3.010000e-27 134.0
36 TraesCS6B01G219300 chr1D 91.014 345 24 6 3967 4304 174199271 174199615 4.380000e-125 459.0
37 TraesCS6B01G219300 chr1D 83.862 378 48 11 4303 4670 138267570 138267196 9.890000e-92 348.0
38 TraesCS6B01G219300 chr1D 89.333 150 12 3 3022 3170 211688639 211688785 8.210000e-43 185.0
39 TraesCS6B01G219300 chr1D 83.766 154 17 7 3825 3975 148520748 148520600 6.480000e-29 139.0
40 TraesCS6B01G219300 chr1D 85.075 134 17 3 3839 3972 68657146 68657276 3.010000e-27 134.0
41 TraesCS6B01G219300 chrUn 90.588 340 27 3 3967 4301 24296412 24296073 3.410000e-121 446.0
42 TraesCS6B01G219300 chrUn 88.889 252 28 0 3582 3833 76188748 76188497 1.300000e-80 311.0
43 TraesCS6B01G219300 chrUn 87.983 233 28 0 3601 3833 76137975 76137743 4.730000e-70 276.0
44 TraesCS6B01G219300 chrUn 90.123 81 8 0 3752 3832 465284770 465284850 6.570000e-19 106.0
45 TraesCS6B01G219300 chr4D 89.706 340 30 3 3967 4301 286963489 286963828 3.430000e-116 429.0
46 TraesCS6B01G219300 chr4D 89.412 340 31 3 3967 4301 212073222 212072883 1.600000e-114 424.0
47 TraesCS6B01G219300 chr4D 90.551 127 10 2 4675 4800 286963470 286963595 2.970000e-37 167.0
48 TraesCS6B01G219300 chr4D 90.551 127 10 2 4675 4800 441294134 441294259 2.970000e-37 167.0
49 TraesCS6B01G219300 chr3D 89.412 340 31 3 3967 4301 545201905 545201566 1.600000e-114 424.0
50 TraesCS6B01G219300 chr3D 83.684 380 50 7 4303 4672 400455144 400455521 9.890000e-92 348.0
51 TraesCS6B01G219300 chr3D 88.889 144 16 0 3027 3170 126947274 126947131 1.370000e-40 178.0
52 TraesCS6B01G219300 chr3D 89.764 127 11 2 4675 4800 126965319 126965194 1.380000e-35 161.0
53 TraesCS6B01G219300 chr3D 87.705 122 14 1 3854 3975 585427902 585427782 1.800000e-29 141.0
54 TraesCS6B01G219300 chr4A 83.990 381 51 8 4303 4674 704001062 704000683 1.640000e-94 357.0
55 TraesCS6B01G219300 chr4A 90.551 127 10 2 4675 4800 551222252 551222377 2.970000e-37 167.0
56 TraesCS6B01G219300 chr4A 88.333 120 12 2 3869 3988 741534335 741534218 5.010000e-30 143.0
57 TraesCS6B01G219300 chr4A 87.719 57 7 0 3467 3523 29793405 29793349 3.100000e-07 67.6
58 TraesCS6B01G219300 chr7A 86.943 314 39 2 4303 4614 719608951 719609264 7.640000e-93 351.0
59 TraesCS6B01G219300 chr7A 91.946 149 11 1 3022 3170 126583604 126583751 1.750000e-49 207.0
60 TraesCS6B01G219300 chr2A 86.943 314 39 2 4303 4614 48457683 48457996 7.640000e-93 351.0
61 TraesCS6B01G219300 chr2A 89.474 57 6 0 3467 3523 113384863 113384919 6.670000e-09 73.1
62 TraesCS6B01G219300 chr4B 82.902 386 50 12 4303 4674 68126456 68126839 2.770000e-87 333.0
63 TraesCS6B01G219300 chr7D 78.990 495 86 14 2407 2898 511124223 511124702 5.990000e-84 322.0
64 TraesCS6B01G219300 chr1A 88.841 233 26 0 3497 3729 589551672 589551904 2.190000e-73 287.0
65 TraesCS6B01G219300 chr1A 89.764 127 11 2 4675 4800 291683267 291683142 1.380000e-35 161.0
66 TraesCS6B01G219300 chr1A 89.286 56 6 0 3467 3522 292897768 292897713 2.400000e-08 71.3
67 TraesCS6B01G219300 chr2D 90.551 127 10 2 4675 4800 643163792 643163917 2.970000e-37 167.0
68 TraesCS6B01G219300 chr5D 88.636 132 15 0 3562 3693 5821783 5821652 1.380000e-35 161.0
69 TraesCS6B01G219300 chr5D 89.764 127 10 2 4675 4800 69890617 69890741 4.970000e-35 159.0
70 TraesCS6B01G219300 chr5D 88.496 113 11 2 3060 3171 4304146 4304035 8.380000e-28 135.0
71 TraesCS6B01G219300 chr5D 89.706 68 6 1 3467 3534 5821855 5821789 8.560000e-13 86.1
72 TraesCS6B01G219300 chr5A 89.189 111 7 4 3061 3170 109953339 109953233 3.010000e-27 134.0
73 TraesCS6B01G219300 chr5A 89.091 55 6 0 3469 3523 564774687 564774633 8.620000e-08 69.4


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 TraesCS6B01G219300 chr6B 308472416 308477216 4800 False 1535.333333 5856 100.0000 1 4801 6 chr6B.!!$F2 4800
1 TraesCS6B01G219300 chr6B 633350480 633351383 903 False 1565.000000 1565 97.8980 1 904 1 chr6B.!!$F1 903
2 TraesCS6B01G219300 chr6D 260020496 260024354 3858 False 1269.400000 3613 97.7472 904 4801 5 chr6D.!!$F1 3897
3 TraesCS6B01G219300 chr6A 538053412 538054315 903 False 1576.000000 1576 98.1190 1 904 1 chr6A.!!$F2 903
4 TraesCS6B01G219300 chr6A 370675760 370679554 3794 True 1540.500000 3576 96.8830 923 4801 4 chr6A.!!$R1 3878
5 TraesCS6B01G219300 chr2B 742107685 742108590 905 False 1583.000000 1583 98.2340 1 904 1 chr2B.!!$F2 903
6 TraesCS6B01G219300 chr2B 340547793 340548693 900 False 1572.000000 1572 98.1190 1 904 1 chr2B.!!$F1 903
7 TraesCS6B01G219300 chr7B 23391466 23392369 903 False 1576.000000 1576 98.1190 1 904 1 chr7B.!!$F1 903
8 TraesCS6B01G219300 chr3A 521604635 521605537 902 False 1574.000000 1574 98.1190 1 904 1 chr3A.!!$F1 903
9 TraesCS6B01G219300 chr5B 700993600 700994504 904 False 1572.000000 1572 98.0110 1 905 1 chr5B.!!$F1 904
10 TraesCS6B01G219300 chr1B 57741991 57742896 905 True 1567.000000 1567 97.9030 1 904 1 chr1B.!!$R1 903
11 TraesCS6B01G219300 chr1B 472396454 472397366 912 True 1555.000000 1555 97.3800 1 915 1 chr1B.!!$R2 914

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
503 504 2.785679 GTCGTGCATTTATCTTGCCAC 58.214 47.619 0.00 0.00 39.39 5.01 F
1074 1080 0.912006 GCTCACCCCTCTCCTTCCTT 60.912 60.000 0.00 0.00 0.00 3.36 F
1831 1838 1.473258 TGGTTCTGCACTTTGCTTGT 58.527 45.000 0.00 0.00 45.31 3.16 F
3020 3028 0.179054 GGGATAGTTCGAACAGGGCC 60.179 60.000 28.78 21.69 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2106 0.178967 TCTGCACCCATGGAAAAGCA 60.179 50.0 15.22 15.71 0.00 3.91 R
2756 2764 0.396435 TTCACGTGCAGATTCCCACT 59.604 50.0 11.67 0.00 0.00 4.00 R
3367 3375 0.178068 CCCCTTCACATCCTACGTGG 59.822 60.0 0.00 0.00 35.03 4.94 R
4719 4763 1.900237 ACGCGTACATACTTTCCGAC 58.100 50.0 11.67 0.00 0.00 4.79 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
274 275 5.449297 TTATCAGTTGGTGATGGGAATGA 57.551 39.130 0.00 0.00 46.09 2.57
304 305 5.815233 TTTCTCTCTCTGACTGTGGATTT 57.185 39.130 0.00 0.00 0.00 2.17
503 504 2.785679 GTCGTGCATTTATCTTGCCAC 58.214 47.619 0.00 0.00 39.39 5.01
523 524 5.664457 CCACTAATGTTCTGTGATGCTCTA 58.336 41.667 0.00 0.00 33.95 2.43
626 627 7.462571 ACCTTGAACCTGTTTTATAATCCAC 57.537 36.000 0.00 0.00 0.00 4.02
713 716 6.353404 TGGATATGTGTGTGTGTTAGAGAA 57.647 37.500 0.00 0.00 0.00 2.87
893 898 3.339464 CGTTGCAACGCACGGGTA 61.339 61.111 35.89 0.00 46.06 3.69
907 912 4.670735 CGCACGGGTATTTTTCTAGTTTGG 60.671 45.833 0.00 0.00 0.00 3.28
908 913 4.456566 GCACGGGTATTTTTCTAGTTTGGA 59.543 41.667 0.00 0.00 0.00 3.53
909 914 5.124936 GCACGGGTATTTTTCTAGTTTGGAT 59.875 40.000 0.00 0.00 0.00 3.41
910 915 6.316890 GCACGGGTATTTTTCTAGTTTGGATA 59.683 38.462 0.00 0.00 0.00 2.59
1001 1007 2.838225 CCCCGACTACCTCGCCAT 60.838 66.667 0.00 0.00 41.46 4.40
1026 1032 2.720561 TTCGCTTTCTCGTCGTCGCA 62.721 55.000 0.00 0.00 36.96 5.10
1074 1080 0.912006 GCTCACCCCTCTCCTTCCTT 60.912 60.000 0.00 0.00 0.00 3.36
1106 1112 1.599797 CCCGCCCTTTTGTCGTCTT 60.600 57.895 0.00 0.00 0.00 3.01
1121 1127 2.510238 CTTCCCTCTTCGCCGCTG 60.510 66.667 0.00 0.00 0.00 5.18
1409 1415 4.373116 GTTCGAGGTGAGCGGGCA 62.373 66.667 0.00 0.00 0.00 5.36
1478 1484 5.932303 TGTAGTGTTCTTGGAATTCACTAGC 59.068 40.000 7.93 2.12 40.60 3.42
1831 1838 1.473258 TGGTTCTGCACTTTGCTTGT 58.527 45.000 0.00 0.00 45.31 3.16
1888 1895 6.499699 TGATATGATATCAAGGTGCCTCTCTT 59.500 38.462 12.47 0.00 0.00 2.85
2108 2115 7.179269 AGGTAATAATAACCTGTGCTTTTCCA 58.821 34.615 0.00 0.00 45.78 3.53
2133 2140 6.252995 TGGGTGCAGAATTCTTATTACCTTT 58.747 36.000 18.92 0.00 0.00 3.11
2159 2166 7.769970 TGTGTGAGATATGCATTTCATGTAGAA 59.230 33.333 17.81 0.00 36.63 2.10
2450 2457 7.178451 GGGAAATGAAAACAAGGGAAGATAGAA 59.822 37.037 0.00 0.00 0.00 2.10
2575 2583 3.423539 AGCACAGGAAAGCATCTTACA 57.576 42.857 0.00 0.00 0.00 2.41
2774 2782 0.320683 CAGTGGGAATCTGCACGTGA 60.321 55.000 22.23 3.45 0.00 4.35
2808 2816 6.072112 TCCTGCAAAATACTGTTCAACTTC 57.928 37.500 0.00 0.00 0.00 3.01
3007 3015 7.561356 ACCTATCAAATTGGTCTTTTGGGATAG 59.439 37.037 0.00 0.00 32.92 2.08
3008 3016 7.561356 CCTATCAAATTGGTCTTTTGGGATAGT 59.439 37.037 0.00 0.00 35.31 2.12
3009 3017 7.797121 ATCAAATTGGTCTTTTGGGATAGTT 57.203 32.000 0.00 0.00 35.31 2.24
3010 3018 7.227049 TCAAATTGGTCTTTTGGGATAGTTC 57.773 36.000 0.00 0.00 35.31 3.01
3011 3019 5.897377 AATTGGTCTTTTGGGATAGTTCG 57.103 39.130 0.00 0.00 0.00 3.95
3012 3020 4.627284 TTGGTCTTTTGGGATAGTTCGA 57.373 40.909 0.00 0.00 0.00 3.71
3013 3021 4.627284 TGGTCTTTTGGGATAGTTCGAA 57.373 40.909 0.00 0.00 0.00 3.71
3014 3022 4.320870 TGGTCTTTTGGGATAGTTCGAAC 58.679 43.478 20.71 20.71 0.00 3.95
3015 3023 4.202377 TGGTCTTTTGGGATAGTTCGAACA 60.202 41.667 28.78 15.65 0.00 3.18
3016 3024 4.392138 GGTCTTTTGGGATAGTTCGAACAG 59.608 45.833 28.78 14.38 0.00 3.16
3017 3025 4.392138 GTCTTTTGGGATAGTTCGAACAGG 59.608 45.833 28.78 7.35 0.00 4.00
3018 3026 3.343941 TTTGGGATAGTTCGAACAGGG 57.656 47.619 28.78 0.00 0.00 4.45
3019 3027 0.539986 TGGGATAGTTCGAACAGGGC 59.460 55.000 28.78 14.85 0.00 5.19
3020 3028 0.179054 GGGATAGTTCGAACAGGGCC 60.179 60.000 28.78 21.69 0.00 5.80
3021 3029 0.831307 GGATAGTTCGAACAGGGCCT 59.169 55.000 28.78 0.00 0.00 5.19
3022 3030 2.037144 GGATAGTTCGAACAGGGCCTA 58.963 52.381 28.78 12.47 0.00 3.93
3023 3031 2.433239 GGATAGTTCGAACAGGGCCTAA 59.567 50.000 28.78 0.00 0.00 2.69
3024 3032 3.492829 GGATAGTTCGAACAGGGCCTAAG 60.493 52.174 28.78 0.00 0.00 2.18
3025 3033 1.349067 AGTTCGAACAGGGCCTAAGT 58.651 50.000 28.78 0.00 0.00 2.24
3026 3034 2.532843 AGTTCGAACAGGGCCTAAGTA 58.467 47.619 28.78 0.00 0.00 2.24
3027 3035 3.105283 AGTTCGAACAGGGCCTAAGTAT 58.895 45.455 28.78 1.52 0.00 2.12
3028 3036 4.284178 AGTTCGAACAGGGCCTAAGTATA 58.716 43.478 28.78 0.00 0.00 1.47
3029 3037 4.900054 AGTTCGAACAGGGCCTAAGTATAT 59.100 41.667 28.78 0.40 0.00 0.86
3030 3038 5.365895 AGTTCGAACAGGGCCTAAGTATATT 59.634 40.000 28.78 0.00 0.00 1.28
3031 3039 6.552350 AGTTCGAACAGGGCCTAAGTATATTA 59.448 38.462 28.78 0.00 0.00 0.98
3032 3040 7.234988 AGTTCGAACAGGGCCTAAGTATATTAT 59.765 37.037 28.78 0.00 0.00 1.28
3033 3041 8.526147 GTTCGAACAGGGCCTAAGTATATTATA 58.474 37.037 23.12 0.00 0.00 0.98
3034 3042 8.834004 TCGAACAGGGCCTAAGTATATTATAT 57.166 34.615 5.28 0.00 0.00 0.86
3035 3043 8.910944 TCGAACAGGGCCTAAGTATATTATATC 58.089 37.037 5.28 0.00 0.00 1.63
3036 3044 8.915036 CGAACAGGGCCTAAGTATATTATATCT 58.085 37.037 5.28 0.00 0.00 1.98
3038 3046 8.785184 ACAGGGCCTAAGTATATTATATCTCC 57.215 38.462 5.28 0.00 0.00 3.71
3039 3047 8.579259 ACAGGGCCTAAGTATATTATATCTCCT 58.421 37.037 5.28 0.00 0.00 3.69
3040 3048 9.084533 CAGGGCCTAAGTATATTATATCTCCTC 57.915 40.741 5.28 0.00 0.00 3.71
3041 3049 9.031724 AGGGCCTAAGTATATTATATCTCCTCT 57.968 37.037 2.82 0.00 0.00 3.69
3056 3064 8.980832 ATATCTCCTCTACCTATCAAATTGGT 57.019 34.615 0.00 0.00 41.29 3.67
3057 3065 6.732896 TCTCCTCTACCTATCAAATTGGTC 57.267 41.667 0.00 0.00 39.17 4.02
3058 3066 6.444704 TCTCCTCTACCTATCAAATTGGTCT 58.555 40.000 0.00 0.00 39.17 3.85
3059 3067 6.903534 TCTCCTCTACCTATCAAATTGGTCTT 59.096 38.462 0.00 0.00 39.17 3.01
3060 3068 7.403231 TCTCCTCTACCTATCAAATTGGTCTTT 59.597 37.037 0.00 0.00 39.17 2.52
3061 3069 7.928873 TCCTCTACCTATCAAATTGGTCTTTT 58.071 34.615 0.00 0.00 39.17 2.27
3062 3070 7.829211 TCCTCTACCTATCAAATTGGTCTTTTG 59.171 37.037 0.00 0.00 39.17 2.44
3063 3071 7.067494 CCTCTACCTATCAAATTGGTCTTTTGG 59.933 40.741 0.00 0.00 39.17 3.28
3064 3072 6.889722 TCTACCTATCAAATTGGTCTTTTGGG 59.110 38.462 0.00 0.00 39.17 4.12
3065 3073 5.650283 ACCTATCAAATTGGTCTTTTGGGA 58.350 37.500 0.00 0.00 32.92 4.37
3066 3074 6.263754 ACCTATCAAATTGGTCTTTTGGGAT 58.736 36.000 0.00 0.00 32.92 3.85
3067 3075 7.418378 ACCTATCAAATTGGTCTTTTGGGATA 58.582 34.615 0.00 0.00 32.92 2.59
3075 3083 4.403734 TGGTCTTTTGGGATAGTTGGTTC 58.596 43.478 0.00 0.00 0.00 3.62
3148 3156 1.078490 TCCCTGCATTTTCCCCAATCA 59.922 47.619 0.00 0.00 0.00 2.57
3163 3171 5.088730 CCCCAATCATTTATCCACATCCAT 58.911 41.667 0.00 0.00 0.00 3.41
3374 3382 6.287107 GTTGACAATTCCATATCCACGTAG 57.713 41.667 0.00 0.00 0.00 3.51
3375 3383 4.956085 TGACAATTCCATATCCACGTAGG 58.044 43.478 0.00 0.00 39.47 3.18
3385 3393 1.191535 TCCACGTAGGATGTGAAGGG 58.808 55.000 3.02 0.00 43.07 3.95
3386 3394 0.178068 CCACGTAGGATGTGAAGGGG 59.822 60.000 0.32 0.00 41.22 4.79
3387 3395 0.178068 CACGTAGGATGTGAAGGGGG 59.822 60.000 0.00 0.00 37.29 5.40
3534 3567 2.632996 TCACCCTGGTGTAAACTCTCTG 59.367 50.000 15.60 0.00 45.55 3.35
3680 3713 2.635714 TCTCAAGCATGCATGTGGTAG 58.364 47.619 26.79 18.48 0.00 3.18
3696 3729 1.817447 GGTAGTCTTACCTCACACGCT 59.183 52.381 0.00 0.00 45.01 5.07
3733 3766 4.466370 TCTCACGGTGGATGTTAAGAAGAT 59.534 41.667 8.50 0.00 0.00 2.40
3780 3813 5.481473 ACCTCACATGCATTTTGGTTCTTAT 59.519 36.000 0.00 0.00 0.00 1.73
3857 3890 9.599866 CCAAGGGTATGTATGTATGTATGTATG 57.400 37.037 0.00 0.00 0.00 2.39
3887 3921 7.833285 ACAATACAAATGTTTCCTACAACCT 57.167 32.000 0.00 0.00 40.89 3.50
3926 3960 7.119116 CACCACTTGAGTTTTGTATGCTGTATA 59.881 37.037 0.00 0.00 0.00 1.47
3928 3962 9.325198 CCACTTGAGTTTTGTATGCTGTATATA 57.675 33.333 0.00 0.00 0.00 0.86
3966 4000 6.935208 TCAGAGAGTATGTATGCGTAGTATGT 59.065 38.462 0.00 0.00 32.95 2.29
3977 4011 7.858879 TGTATGCGTAGTATGTTGTATGTAGTG 59.141 37.037 0.00 0.00 32.95 2.74
4458 4494 5.159273 TGCATGTGAGTCCATAGTGTTTA 57.841 39.130 0.00 0.00 0.00 2.01
4620 4656 9.990360 TTGACAGATACTACATACAAAACTCAA 57.010 29.630 0.00 0.00 0.00 3.02
4708 4752 9.585099 CCACTTGCATTTTGTATGTTGTATATT 57.415 29.630 0.00 0.00 0.00 1.28
4740 4784 2.778386 GTCGGAAAGTATGTACGCGTAC 59.222 50.000 36.15 36.15 37.36 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 275 5.306678 ACAGTCAGAGAGAGAAATTGGAACT 59.693 40.000 0.00 0.00 0.00 3.01
304 305 2.595463 AAGCGCTTCTTGCCTGCA 60.595 55.556 18.98 0.00 38.78 4.41
503 504 6.259387 TGCATTAGAGCATCACAGAACATTAG 59.741 38.462 0.00 0.00 40.11 1.73
523 524 5.484998 AGATAACCAATTCCCAAAGTGCATT 59.515 36.000 0.00 0.00 0.00 3.56
626 627 1.327460 ACGCGCTAGTGCATAACAATG 59.673 47.619 26.75 11.00 39.64 2.82
713 716 0.933700 CCCCTCTCCCTCTCTCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
855 860 3.759618 CGGGGCCACATTAACTTTAAGAA 59.240 43.478 5.46 0.00 0.00 2.52
1001 1007 1.003839 ACGAGAAAGCGAATGGCCA 60.004 52.632 8.56 8.56 45.17 5.36
1026 1032 0.173708 GGGAGACGACGAGCATTTCT 59.826 55.000 0.00 0.00 0.00 2.52
1121 1127 1.827789 TGGTGTTTGTGGAGGCAGC 60.828 57.895 0.00 0.00 0.00 5.25
1200 1206 1.152881 GATGCCCATTCGCCTCCTT 60.153 57.895 0.00 0.00 0.00 3.36
1409 1415 3.011119 TGCTTCGGTTACACAAACTTGT 58.989 40.909 0.00 0.00 43.36 3.16
1428 1434 3.044305 CCGCGCCTAAGCCTATGC 61.044 66.667 0.00 0.00 34.57 3.14
1478 1484 1.005340 GCTGCTCTTGACCGAATCAG 58.995 55.000 0.00 0.00 38.99 2.90
1525 1531 7.272244 TCAACCTCACATACATCGTCATATTT 58.728 34.615 0.00 0.00 0.00 1.40
1539 1545 6.119536 TGTTTGTAGTCTTTCAACCTCACAT 58.880 36.000 0.00 0.00 0.00 3.21
1831 1838 8.202461 TCTTTTACTTGAGAAGAGGAACCATA 57.798 34.615 0.00 0.00 0.00 2.74
2027 2034 8.553085 TCTCCTCTATTGACAATAATTCCTCA 57.447 34.615 9.14 0.00 0.00 3.86
2092 2099 2.158385 ACCCATGGAAAAGCACAGGTTA 60.158 45.455 15.22 0.00 0.00 2.85
2093 2100 1.341080 CCCATGGAAAAGCACAGGTT 58.659 50.000 15.22 0.00 0.00 3.50
2094 2101 0.188342 ACCCATGGAAAAGCACAGGT 59.812 50.000 15.22 0.00 0.00 4.00
2099 2106 0.178967 TCTGCACCCATGGAAAAGCA 60.179 50.000 15.22 15.71 0.00 3.91
2108 2115 6.018433 AGGTAATAAGAATTCTGCACCCAT 57.982 37.500 9.17 0.00 0.00 4.00
2159 2166 8.897872 ATTTTTCTGCTGAATTTCAAATGACT 57.102 26.923 6.88 0.00 31.56 3.41
2450 2457 6.542735 GCGTTCCTTTCCTATTCCTCTATTTT 59.457 38.462 0.00 0.00 0.00 1.82
2507 2514 1.002134 ATGGTTCCCTCTGCCGTTG 60.002 57.895 0.00 0.00 0.00 4.10
2575 2583 5.106157 GCAATGTCCTTTTAGCTGTACACAT 60.106 40.000 0.00 0.00 0.00 3.21
2748 2756 2.779430 TGCAGATTCCCACTGATACCAT 59.221 45.455 0.00 0.00 37.54 3.55
2756 2764 0.396435 TTCACGTGCAGATTCCCACT 59.604 50.000 11.67 0.00 0.00 4.00
3007 3015 3.538634 ATACTTAGGCCCTGTTCGAAC 57.461 47.619 21.42 21.42 0.00 3.95
3008 3016 5.881923 AATATACTTAGGCCCTGTTCGAA 57.118 39.130 0.00 0.00 0.00 3.71
3009 3017 8.834004 ATATAATATACTTAGGCCCTGTTCGA 57.166 34.615 0.00 0.00 0.00 3.71
3010 3018 8.915036 AGATATAATATACTTAGGCCCTGTTCG 58.085 37.037 0.00 0.00 0.00 3.95
3012 3020 9.214962 GGAGATATAATATACTTAGGCCCTGTT 57.785 37.037 0.00 0.00 0.00 3.16
3013 3021 8.579259 AGGAGATATAATATACTTAGGCCCTGT 58.421 37.037 0.00 0.00 0.00 4.00
3014 3022 9.084533 GAGGAGATATAATATACTTAGGCCCTG 57.915 40.741 0.00 0.00 0.00 4.45
3015 3023 9.031724 AGAGGAGATATAATATACTTAGGCCCT 57.968 37.037 0.00 0.00 0.00 5.19
3031 3039 8.980832 ACCAATTTGATAGGTAGAGGAGATAT 57.019 34.615 0.00 0.00 32.92 1.63
3032 3040 8.235230 AGACCAATTTGATAGGTAGAGGAGATA 58.765 37.037 0.00 0.00 35.36 1.98
3033 3041 7.079048 AGACCAATTTGATAGGTAGAGGAGAT 58.921 38.462 0.00 0.00 35.36 2.75
3034 3042 6.444704 AGACCAATTTGATAGGTAGAGGAGA 58.555 40.000 0.00 0.00 35.36 3.71
3035 3043 6.739331 AGACCAATTTGATAGGTAGAGGAG 57.261 41.667 0.00 0.00 35.36 3.69
3036 3044 7.510675 AAAGACCAATTTGATAGGTAGAGGA 57.489 36.000 0.00 0.00 35.36 3.71
3037 3045 7.067494 CCAAAAGACCAATTTGATAGGTAGAGG 59.933 40.741 0.00 0.00 39.56 3.69
3038 3046 7.067494 CCCAAAAGACCAATTTGATAGGTAGAG 59.933 40.741 0.00 0.00 39.56 2.43
3039 3047 6.889722 CCCAAAAGACCAATTTGATAGGTAGA 59.110 38.462 0.00 0.00 39.56 2.59
3040 3048 6.889722 TCCCAAAAGACCAATTTGATAGGTAG 59.110 38.462 0.00 0.00 39.56 3.18
3041 3049 6.795590 TCCCAAAAGACCAATTTGATAGGTA 58.204 36.000 0.00 0.00 39.56 3.08
3042 3050 5.650283 TCCCAAAAGACCAATTTGATAGGT 58.350 37.500 0.00 0.00 39.56 3.08
3043 3051 6.796785 ATCCCAAAAGACCAATTTGATAGG 57.203 37.500 0.00 0.00 39.56 2.57
3044 3052 8.525290 ACTATCCCAAAAGACCAATTTGATAG 57.475 34.615 0.00 0.00 39.56 2.08
3045 3053 8.748412 CAACTATCCCAAAAGACCAATTTGATA 58.252 33.333 0.00 0.00 39.56 2.15
3046 3054 7.310609 CCAACTATCCCAAAAGACCAATTTGAT 60.311 37.037 0.00 0.00 39.56 2.57
3047 3055 6.014669 CCAACTATCCCAAAAGACCAATTTGA 60.015 38.462 0.00 0.00 39.56 2.69
3048 3056 6.165577 CCAACTATCCCAAAAGACCAATTTG 58.834 40.000 0.00 0.00 37.48 2.32
3049 3057 5.843969 ACCAACTATCCCAAAAGACCAATTT 59.156 36.000 0.00 0.00 0.00 1.82
3050 3058 5.402630 ACCAACTATCCCAAAAGACCAATT 58.597 37.500 0.00 0.00 0.00 2.32
3051 3059 5.010708 ACCAACTATCCCAAAAGACCAAT 57.989 39.130 0.00 0.00 0.00 3.16
3052 3060 4.463050 ACCAACTATCCCAAAAGACCAA 57.537 40.909 0.00 0.00 0.00 3.67
3053 3061 4.141135 TGAACCAACTATCCCAAAAGACCA 60.141 41.667 0.00 0.00 0.00 4.02
3054 3062 4.403734 TGAACCAACTATCCCAAAAGACC 58.596 43.478 0.00 0.00 0.00 3.85
3055 3063 6.318900 CCTATGAACCAACTATCCCAAAAGAC 59.681 42.308 0.00 0.00 0.00 3.01
3056 3064 6.216662 TCCTATGAACCAACTATCCCAAAAGA 59.783 38.462 0.00 0.00 0.00 2.52
3057 3065 6.423182 TCCTATGAACCAACTATCCCAAAAG 58.577 40.000 0.00 0.00 0.00 2.27
3058 3066 6.395780 TCCTATGAACCAACTATCCCAAAA 57.604 37.500 0.00 0.00 0.00 2.44
3059 3067 6.395780 TTCCTATGAACCAACTATCCCAAA 57.604 37.500 0.00 0.00 0.00 3.28
3060 3068 6.590656 ATTCCTATGAACCAACTATCCCAA 57.409 37.500 0.00 0.00 32.13 4.12
3061 3069 7.739444 AGATATTCCTATGAACCAACTATCCCA 59.261 37.037 0.00 0.00 32.13 4.37
3062 3070 8.152023 AGATATTCCTATGAACCAACTATCCC 57.848 38.462 0.00 0.00 32.13 3.85
3067 3075 9.784531 CATGTTAGATATTCCTATGAACCAACT 57.215 33.333 0.00 0.00 32.13 3.16
3148 3156 3.394274 TCCCGACATGGATGTGGATAAAT 59.606 43.478 0.00 0.00 41.95 1.40
3351 3359 5.236478 CCTACGTGGATATGGAATTGTCAAC 59.764 44.000 0.00 0.00 38.35 3.18
3352 3360 5.129650 TCCTACGTGGATATGGAATTGTCAA 59.870 40.000 0.00 0.00 40.56 3.18
3353 3361 4.651962 TCCTACGTGGATATGGAATTGTCA 59.348 41.667 0.00 0.00 40.56 3.58
3354 3362 5.209818 TCCTACGTGGATATGGAATTGTC 57.790 43.478 0.00 0.00 40.56 3.18
3367 3375 0.178068 CCCCTTCACATCCTACGTGG 59.822 60.000 0.00 0.00 35.03 4.94
3368 3376 0.178068 CCCCCTTCACATCCTACGTG 59.822 60.000 0.00 0.00 35.63 4.49
3369 3377 2.604118 CCCCCTTCACATCCTACGT 58.396 57.895 0.00 0.00 0.00 3.57
3389 3397 7.624077 AGGAGATATGATATACTTAACACCCCC 59.376 40.741 0.00 0.00 0.00 5.40
3390 3398 8.611051 AGGAGATATGATATACTTAACACCCC 57.389 38.462 0.00 0.00 0.00 4.95
3391 3399 9.482175 AGAGGAGATATGATATACTTAACACCC 57.518 37.037 0.00 0.00 0.00 4.61
3472 3480 6.538742 TCACCCGAAATGATGAATAGACTTTC 59.461 38.462 0.00 0.00 0.00 2.62
3534 3567 7.867403 ACAACATTCAAAAGGAATCATGTGTAC 59.133 33.333 0.00 0.00 44.41 2.90
3599 3632 7.334858 TGCATGTGAGGTAAGATTACAACATA 58.665 34.615 13.21 8.08 34.67 2.29
3680 3713 2.059541 GTCAAGCGTGTGAGGTAAGAC 58.940 52.381 0.00 0.00 0.00 3.01
3696 3729 4.035091 CACCGTGAGAAAGAAATGTGTCAA 59.965 41.667 0.00 0.00 0.00 3.18
3780 3813 2.700371 CTCATGCACCCTATAGTCACCA 59.300 50.000 0.00 0.00 0.00 4.17
3943 3977 7.228906 ACAACATACTACGCATACATACTCTCT 59.771 37.037 0.00 0.00 0.00 3.10
3955 3989 6.031471 CACACTACATACAACATACTACGCA 58.969 40.000 0.00 0.00 0.00 5.24
3988 4022 5.112220 ACGCGTACATATTCTCCGATTTA 57.888 39.130 11.67 0.00 0.00 1.40
4620 4656 2.158204 ACCAGTGGTAGTTACCCTCACT 60.158 50.000 14.87 0.66 45.87 3.41
4719 4763 1.900237 ACGCGTACATACTTTCCGAC 58.100 50.000 11.67 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.