Multiple sequence alignment - TraesCS1D01G001100

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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 TraesCS1D01G001100 chr1D 100.000 3042 0 0 1 3042 261615 258574 0.000000e+00 5618.0
1 TraesCS1D01G001100 chr1D 90.072 1934 155 12 299 2216 252116 250204 0.000000e+00 2473.0
2 TraesCS1D01G001100 chr1D 89.830 1701 143 17 1207 2883 322683 320989 0.000000e+00 2156.0
3 TraesCS1D01G001100 chr1D 87.839 1217 121 13 1343 2558 381528 380338 0.000000e+00 1402.0
4 TraesCS1D01G001100 chr1D 87.906 1108 80 15 393 1487 323541 322475 0.000000e+00 1254.0
5 TraesCS1D01G001100 chr1D 84.026 1083 101 40 299 1370 382901 381880 0.000000e+00 976.0
6 TraesCS1D01G001100 chr1D 89.728 662 65 1 2250 2911 236679 236021 0.000000e+00 843.0
7 TraesCS1D01G001100 chr1A 85.096 2610 252 48 299 2884 4032611 4035107 0.000000e+00 2538.0
8 TraesCS1D01G001100 chr1A 85.063 2611 249 49 299 2883 4040596 4043091 0.000000e+00 2531.0
9 TraesCS1D01G001100 chr1A 84.038 2437 266 42 299 2710 3909669 3912007 0.000000e+00 2231.0
10 TraesCS1D01G001100 chr1A 85.190 1580 191 21 1324 2888 3846409 3844858 0.000000e+00 1581.0
11 TraesCS1D01G001100 chr1A 86.969 1082 89 21 323 1387 3847878 3846832 0.000000e+00 1170.0
12 TraesCS1D01G001100 chr1A 91.753 97 6 2 85 181 3942557 3942651 1.900000e-27 134.0
13 TraesCS1D01G001100 chr1B 88.296 1931 166 23 301 2216 5141294 5143179 0.000000e+00 2259.0
14 TraesCS1D01G001100 chr1B 84.933 2104 203 31 299 2367 4993367 4991343 0.000000e+00 2025.0
15 TraesCS1D01G001100 chr1B 93.282 1176 71 7 319 1488 5136323 5137496 0.000000e+00 1727.0
16 TraesCS1D01G001100 chr1B 92.738 1198 79 5 1717 2914 5137869 5139058 0.000000e+00 1724.0
17 TraesCS1D01G001100 chr1B 84.825 1397 153 15 1164 2558 4965801 4967140 0.000000e+00 1351.0
18 TraesCS1D01G001100 chr1B 86.620 1151 105 28 373 1503 5056252 5057373 0.000000e+00 1227.0
19 TraesCS1D01G001100 chr1B 86.644 1153 95 27 370 1487 5098629 5099757 0.000000e+00 1221.0
20 TraesCS1D01G001100 chr1B 88.627 976 103 5 1908 2883 5100315 5101282 0.000000e+00 1181.0
21 TraesCS1D01G001100 chr1B 89.044 931 100 2 1717 2647 5057758 5058686 0.000000e+00 1153.0
22 TraesCS1D01G001100 chr1B 87.000 800 50 16 1177 1932 5099518 5100307 0.000000e+00 852.0
23 TraesCS1D01G001100 chr1B 90.169 651 59 3 2262 2911 5143197 5143843 0.000000e+00 843.0
24 TraesCS1D01G001100 chr1B 86.689 586 60 10 1164 1731 5057148 5057733 4.280000e-178 634.0
25 TraesCS1D01G001100 chr1B 93.269 416 23 1 1 411 5135916 5136331 2.590000e-170 608.0
26 TraesCS1D01G001100 chr1B 86.406 537 43 7 1207 1734 5137287 5137802 7.370000e-156 560.0
27 TraesCS1D01G001100 chr1B 91.480 223 18 1 82 304 5141036 5141257 3.810000e-79 305.0
28 TraesCS1D01G001100 chr1B 91.346 208 17 1 97 304 5055879 5056085 1.790000e-72 283.0
29 TraesCS1D01G001100 chr1B 90.385 208 19 1 97 304 5098259 5098465 3.860000e-69 272.0
30 TraesCS1D01G001100 chr1B 86.385 213 24 5 299 508 5056118 5056328 8.480000e-56 228.0
31 TraesCS1D01G001100 chr1B 87.597 129 16 0 176 304 4993528 4993400 1.890000e-32 150.0
32 TraesCS1D01G001100 chr1B 84.848 132 18 2 2913 3042 288806372 288806503 6.840000e-27 132.0
33 TraesCS1D01G001100 chr4B 95.690 116 5 0 2927 3042 626003008 626002893 1.440000e-43 187.0
34 TraesCS1D01G001100 chr4B 91.358 81 7 0 1 81 68958055 68958135 8.920000e-21 111.0
35 TraesCS1D01G001100 chr4A 95.690 116 5 0 2927 3042 476148733 476148848 1.440000e-43 187.0
36 TraesCS1D01G001100 chr4A 100.000 29 0 0 2911 2939 476148701 476148729 2.000000e-03 54.7
37 TraesCS1D01G001100 chr7A 93.103 116 8 0 2927 3042 597641646 597641531 1.450000e-38 171.0
38 TraesCS1D01G001100 chr7A 86.822 129 16 1 2915 3042 626327959 626328087 3.160000e-30 143.0
39 TraesCS1D01G001100 chr2A 92.241 116 8 1 2928 3042 755780218 755780103 2.430000e-36 163.0
40 TraesCS1D01G001100 chr2A 91.358 81 7 0 1 81 176566555 176566635 8.920000e-21 111.0
41 TraesCS1D01G001100 chr5A 87.597 129 15 1 2915 3042 10042803 10042675 6.800000e-32 148.0
42 TraesCS1D01G001100 chr5A 90.588 85 7 1 2915 2998 570527264 570527348 8.920000e-21 111.0
43 TraesCS1D01G001100 chr5D 92.771 83 6 0 1 83 185207559 185207477 1.480000e-23 121.0
44 TraesCS1D01G001100 chr5D 91.358 81 7 0 1 81 259534469 259534549 8.920000e-21 111.0
45 TraesCS1D01G001100 chr5B 91.667 84 7 0 1 84 294566453 294566370 1.920000e-22 117.0
46 TraesCS1D01G001100 chr7D 83.465 127 17 4 2914 3038 98998504 98998628 6.890000e-22 115.0
47 TraesCS1D01G001100 chr2D 92.500 80 5 1 3 82 563960743 563960665 2.480000e-21 113.0
48 TraesCS1D01G001100 chr2D 90.123 81 8 0 1 81 34585621 34585701 4.150000e-19 106.0
49 TraesCS1D01G001100 chr2B 91.250 80 7 0 2 81 662345873 662345952 3.210000e-20 110.0


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 TraesCS1D01G001100 chr1D 258574 261615 3041 True 5618.000000 5618 100.000000 1 3042 1 chr1D.!!$R3 3041
1 TraesCS1D01G001100 chr1D 250204 252116 1912 True 2473.000000 2473 90.072000 299 2216 1 chr1D.!!$R2 1917
2 TraesCS1D01G001100 chr1D 320989 323541 2552 True 1705.000000 2156 88.868000 393 2883 2 chr1D.!!$R4 2490
3 TraesCS1D01G001100 chr1D 380338 382901 2563 True 1189.000000 1402 85.932500 299 2558 2 chr1D.!!$R5 2259
4 TraesCS1D01G001100 chr1D 236021 236679 658 True 843.000000 843 89.728000 2250 2911 1 chr1D.!!$R1 661
5 TraesCS1D01G001100 chr1A 4032611 4035107 2496 False 2538.000000 2538 85.096000 299 2884 1 chr1A.!!$F3 2585
6 TraesCS1D01G001100 chr1A 4040596 4043091 2495 False 2531.000000 2531 85.063000 299 2883 1 chr1A.!!$F4 2584
7 TraesCS1D01G001100 chr1A 3909669 3912007 2338 False 2231.000000 2231 84.038000 299 2710 1 chr1A.!!$F1 2411
8 TraesCS1D01G001100 chr1A 3844858 3847878 3020 True 1375.500000 1581 86.079500 323 2888 2 chr1A.!!$R1 2565
9 TraesCS1D01G001100 chr1B 4965801 4967140 1339 False 1351.000000 1351 84.825000 1164 2558 1 chr1B.!!$F1 1394
10 TraesCS1D01G001100 chr1B 5135916 5143843 7927 False 1146.571429 2259 90.805714 1 2914 7 chr1B.!!$F5 2913
11 TraesCS1D01G001100 chr1B 4991343 4993528 2185 True 1087.500000 2025 86.265000 176 2367 2 chr1B.!!$R1 2191
12 TraesCS1D01G001100 chr1B 5098259 5101282 3023 False 881.500000 1221 88.164000 97 2883 4 chr1B.!!$F4 2786
13 TraesCS1D01G001100 chr1B 5055879 5058686 2807 False 705.000000 1227 88.016800 97 2647 5 chr1B.!!$F3 2550

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
995 1262 2.037772 AGGCCTGCAATATTAGACTCCG 59.962 50.0 3.11 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2957 8940 0.035458 GGCTGGTCCTAATCGGGATG 59.965 60.0 0.0 0.0 37.73 3.51 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
32 33 5.651576 TGCAGCTCATATTATGTTGGTCAAA 59.348 36.000 3.67 0.00 0.00 2.69
51 52 9.837681 TGGTCAAATTATAGATCTAGGGATACA 57.162 33.333 8.70 0.00 39.74 2.29
81 82 5.363101 CCTTATAAACCGGAAAGGAGGTAC 58.637 45.833 9.46 0.00 45.00 3.34
92 98 6.271566 CGGAAAGGAGGTACTAGATAAACAC 58.728 44.000 0.00 0.00 41.55 3.32
101 107 7.732996 AGGTACTAGATAAACACGCCAATAAT 58.267 34.615 0.00 0.00 36.02 1.28
260 266 6.363577 AGTAACAACAGTTGTCATGAACAG 57.636 37.500 19.41 0.00 44.59 3.16
276 282 3.888323 TGAACAGCTTGGACTAAATGCAA 59.112 39.130 0.00 0.00 36.08 4.08
277 283 4.340666 TGAACAGCTTGGACTAAATGCAAA 59.659 37.500 0.00 0.00 38.30 3.68
355 401 9.780413 ATTAAGACGTGTAAAGCTAGTACTAAC 57.220 33.333 3.76 0.00 0.00 2.34
356 402 7.446001 AAGACGTGTAAAGCTAGTACTAACT 57.554 36.000 3.76 1.67 39.91 2.24
498 750 9.411801 GATGAGTCATGTATTGATAACGTGTAT 57.588 33.333 11.20 0.00 36.54 2.29
530 783 4.183865 TCAGCTTGTTCATCTTACCATCG 58.816 43.478 0.00 0.00 0.00 3.84
600 854 7.380065 CAGAACGAACATTAGAATACTAGCCTC 59.620 40.741 0.00 0.00 0.00 4.70
640 895 6.701145 TGCACAAGGACACAAATTTAGTTA 57.299 33.333 0.00 0.00 0.00 2.24
688 947 9.429600 GTTTATGTCTAACAACTTGTACAACAC 57.570 33.333 3.59 0.00 0.00 3.32
799 1058 9.220767 GAGTCACTACCAATTATCAAGTTTTCT 57.779 33.333 0.00 0.00 0.00 2.52
881 1142 2.418692 TGTATGTAGTGCCACCAAACG 58.581 47.619 0.00 0.00 0.00 3.60
995 1262 2.037772 AGGCCTGCAATATTAGACTCCG 59.962 50.000 3.11 0.00 0.00 4.63
1070 1338 4.860907 CGTAGTAGTTAACGCAAATCCACT 59.139 41.667 0.00 0.00 31.66 4.00
1184 1455 1.468985 CACAACAACAACCAGTCCCA 58.531 50.000 0.00 0.00 0.00 4.37
1426 2352 0.323816 TCCCAGCAACCACAACAACA 60.324 50.000 0.00 0.00 0.00 3.33
1431 2357 3.688673 CCAGCAACCACAACAACAATTTT 59.311 39.130 0.00 0.00 0.00 1.82
1433 2359 4.630940 CAGCAACCACAACAACAATTTTCT 59.369 37.500 0.00 0.00 0.00 2.52
1527 2516 3.005554 CAGCCATCTCTACAACAACAGG 58.994 50.000 0.00 0.00 0.00 4.00
1575 2564 1.067516 AGCAATGCAAACCTGTGTCAC 59.932 47.619 8.35 0.00 0.00 3.67
1693 2682 1.019673 CAGTGTGCAGCCATCCATAC 58.980 55.000 0.00 0.00 0.00 2.39
1698 2687 1.146041 GCAGCCATCCATACCGTCA 59.854 57.895 0.00 0.00 0.00 4.35
1700 2689 1.001974 GCAGCCATCCATACCGTCATA 59.998 52.381 0.00 0.00 0.00 2.15
1926 3110 3.443052 TCCATCATCAAGGCACCATTTT 58.557 40.909 0.00 0.00 0.00 1.82
1932 3116 0.388907 CAAGGCACCATTTTCCAGCG 60.389 55.000 0.00 0.00 0.00 5.18
2016 3203 5.353123 TCATCGTTGCTTAGTTGATTTACCC 59.647 40.000 0.00 0.00 0.00 3.69
2078 3266 3.936203 GTGACCCCGACCAGTGCA 61.936 66.667 0.00 0.00 0.00 4.57
2080 3268 2.351276 GACCCCGACCAGTGCAAT 59.649 61.111 0.00 0.00 0.00 3.56
2122 3310 5.095490 AGACAAAGAAAGTTCAAGTTTGCG 58.905 37.500 0.00 0.00 32.45 4.85
2258 3450 5.132502 TCTACCGATTAATGGTCGACCTAA 58.867 41.667 33.39 24.17 41.40 2.69
2328 3520 2.359531 GACCGAGCAGCTATCAGTTAGT 59.640 50.000 0.00 0.00 0.00 2.24
2350 3542 2.772568 TTTCCTGAACATTGCACACG 57.227 45.000 0.00 0.00 0.00 4.49
2412 3604 5.056480 GGCCATTTTAGCAGAAAAACAAGT 58.944 37.500 0.00 0.00 31.50 3.16
2495 8474 1.234821 TTGAGTTTGATGGCACCGAC 58.765 50.000 0.00 0.00 0.00 4.79
2517 8497 6.521133 CGACACATTCTTCAAAGCAATTCTAC 59.479 38.462 0.00 0.00 0.00 2.59
2522 8502 5.241403 TCTTCAAAGCAATTCTACAGGGA 57.759 39.130 0.00 0.00 0.00 4.20
2641 8622 5.567423 GCCAAACATGCCATTAAACTCTTCT 60.567 40.000 0.00 0.00 0.00 2.85
2647 8628 7.118723 ACATGCCATTAAACTCTTCTTATGGA 58.881 34.615 0.00 0.00 0.00 3.41
2650 8631 9.866655 ATGCCATTAAACTCTTCTTATGGATTA 57.133 29.630 0.00 0.00 0.00 1.75
2668 8649 5.104360 TGGATTATTGGAGAGAGGGAAACAG 60.104 44.000 0.00 0.00 0.00 3.16
2679 8660 4.911390 AGAGGGAAACAGTTTACAGATGG 58.089 43.478 10.57 0.00 0.00 3.51
2698 8679 6.863126 CAGATGGCAAACAAAACTTAAGTAGG 59.137 38.462 8.92 4.15 0.00 3.18
2814 8795 8.402798 TCAATCTAGGAACACAAAGCAAATAA 57.597 30.769 0.00 0.00 0.00 1.40
2917 8900 8.876275 AGTAACAAACTTAACATTGTACGAGA 57.124 30.769 0.00 0.00 38.75 4.04
2918 8901 9.316730 AGTAACAAACTTAACATTGTACGAGAA 57.683 29.630 0.00 0.00 38.75 2.87
2919 8902 9.577003 GTAACAAACTTAACATTGTACGAGAAG 57.423 33.333 0.00 0.00 38.75 2.85
2920 8903 7.781548 ACAAACTTAACATTGTACGAGAAGT 57.218 32.000 0.00 0.00 37.96 3.01
2921 8904 7.848491 ACAAACTTAACATTGTACGAGAAGTC 58.152 34.615 0.00 0.00 37.96 3.01
2922 8905 7.042254 ACAAACTTAACATTGTACGAGAAGTCC 60.042 37.037 0.00 0.00 37.96 3.85
2923 8906 6.092955 ACTTAACATTGTACGAGAAGTCCA 57.907 37.500 0.00 0.00 0.00 4.02
2924 8907 6.698380 ACTTAACATTGTACGAGAAGTCCAT 58.302 36.000 0.00 0.00 0.00 3.41
2925 8908 6.812160 ACTTAACATTGTACGAGAAGTCCATC 59.188 38.462 0.00 0.00 0.00 3.51
2926 8909 3.770666 ACATTGTACGAGAAGTCCATCG 58.229 45.455 0.00 0.00 44.36 3.84
2927 8910 2.273370 TTGTACGAGAAGTCCATCGC 57.727 50.000 0.00 0.00 42.61 4.58
2928 8911 1.460504 TGTACGAGAAGTCCATCGCT 58.539 50.000 0.00 0.00 42.61 4.93
2929 8912 1.132453 TGTACGAGAAGTCCATCGCTG 59.868 52.381 0.00 0.00 42.61 5.18
2930 8913 0.100682 TACGAGAAGTCCATCGCTGC 59.899 55.000 0.00 0.00 42.61 5.25
2931 8914 1.153765 CGAGAAGTCCATCGCTGCA 60.154 57.895 0.00 0.00 31.42 4.41
2932 8915 1.416813 CGAGAAGTCCATCGCTGCAC 61.417 60.000 0.00 0.00 31.42 4.57
2933 8916 1.416813 GAGAAGTCCATCGCTGCACG 61.417 60.000 0.00 2.79 45.62 5.34
2934 8917 3.088500 GAAGTCCATCGCTGCACGC 62.089 63.158 0.00 1.51 43.23 5.34
2935 8918 3.881952 AAGTCCATCGCTGCACGCA 62.882 57.895 0.00 0.00 43.23 5.24
2936 8919 3.857854 GTCCATCGCTGCACGCAG 61.858 66.667 14.73 14.73 46.15 5.18
2966 8949 2.676608 TGGCACAGCATCCCGATT 59.323 55.556 0.00 0.00 0.00 3.34
2967 8950 1.911471 TGGCACAGCATCCCGATTA 59.089 52.632 0.00 0.00 0.00 1.75
2968 8951 0.179048 TGGCACAGCATCCCGATTAG 60.179 55.000 0.00 0.00 0.00 1.73
2969 8952 0.886490 GGCACAGCATCCCGATTAGG 60.886 60.000 0.00 0.00 40.63 2.69
2970 8953 0.106708 GCACAGCATCCCGATTAGGA 59.893 55.000 0.00 0.00 45.00 2.94
2971 8954 1.871080 CACAGCATCCCGATTAGGAC 58.129 55.000 0.00 0.00 45.00 3.85
2972 8955 0.759346 ACAGCATCCCGATTAGGACC 59.241 55.000 0.00 0.00 45.00 4.46
2973 8956 0.758734 CAGCATCCCGATTAGGACCA 59.241 55.000 0.00 0.00 45.00 4.02
2974 8957 1.051812 AGCATCCCGATTAGGACCAG 58.948 55.000 0.00 0.00 45.00 4.00
2975 8958 0.603975 GCATCCCGATTAGGACCAGC 60.604 60.000 0.00 0.00 45.00 4.85
2976 8959 0.035458 CATCCCGATTAGGACCAGCC 59.965 60.000 0.00 0.00 45.00 4.85
2977 8960 0.399949 ATCCCGATTAGGACCAGCCA 60.400 55.000 0.00 0.00 45.00 4.75
2978 8961 0.619255 TCCCGATTAGGACCAGCCAA 60.619 55.000 0.00 0.00 45.00 4.52
2979 8962 0.254747 CCCGATTAGGACCAGCCAAA 59.745 55.000 0.00 0.00 45.00 3.28
2980 8963 1.668419 CCGATTAGGACCAGCCAAAG 58.332 55.000 0.00 0.00 45.00 2.77
2981 8964 1.065418 CCGATTAGGACCAGCCAAAGT 60.065 52.381 0.00 0.00 45.00 2.66
2982 8965 2.009774 CGATTAGGACCAGCCAAAGTG 58.990 52.381 0.00 0.00 40.02 3.16
2983 8966 1.745653 GATTAGGACCAGCCAAAGTGC 59.254 52.381 0.00 0.00 40.02 4.40
2984 8967 0.771127 TTAGGACCAGCCAAAGTGCT 59.229 50.000 0.00 0.00 44.00 4.40
2985 8968 1.651737 TAGGACCAGCCAAAGTGCTA 58.348 50.000 0.00 0.00 40.32 3.49
2986 8969 0.036875 AGGACCAGCCAAAGTGCTAC 59.963 55.000 0.00 0.00 40.32 3.58
2987 8970 0.036875 GGACCAGCCAAAGTGCTACT 59.963 55.000 0.00 0.00 40.32 2.57
2988 8971 1.545651 GGACCAGCCAAAGTGCTACTT 60.546 52.381 0.00 0.00 40.32 2.24
2989 8972 1.537202 GACCAGCCAAAGTGCTACTTG 59.463 52.381 2.88 0.00 40.32 3.16
2990 8973 0.883833 CCAGCCAAAGTGCTACTTGG 59.116 55.000 6.84 6.84 40.32 3.61
2991 8974 1.545428 CCAGCCAAAGTGCTACTTGGA 60.545 52.381 13.39 0.00 40.32 3.53
2992 8975 1.808945 CAGCCAAAGTGCTACTTGGAG 59.191 52.381 13.39 3.69 40.32 3.86
2993 8976 1.421646 AGCCAAAGTGCTACTTGGAGT 59.578 47.619 13.39 0.00 38.66 3.85
2994 8977 2.637872 AGCCAAAGTGCTACTTGGAGTA 59.362 45.455 13.39 0.00 38.66 2.59
2995 8978 3.264450 AGCCAAAGTGCTACTTGGAGTAT 59.736 43.478 13.39 0.00 38.66 2.12
2996 8979 4.469945 AGCCAAAGTGCTACTTGGAGTATA 59.530 41.667 13.39 0.00 38.66 1.47
2997 8980 4.811557 GCCAAAGTGCTACTTGGAGTATAG 59.188 45.833 13.39 0.00 38.66 1.31
2998 8981 5.627040 GCCAAAGTGCTACTTGGAGTATAGT 60.627 44.000 13.39 0.00 38.66 2.12
2999 8982 5.812642 CCAAAGTGCTACTTGGAGTATAGTG 59.187 44.000 5.61 0.00 38.66 2.74
3000 8983 4.657436 AGTGCTACTTGGAGTATAGTGC 57.343 45.455 0.00 0.00 29.08 4.40
3001 8984 4.023980 AGTGCTACTTGGAGTATAGTGCA 58.976 43.478 0.00 0.00 29.08 4.57
3002 8985 4.113354 GTGCTACTTGGAGTATAGTGCAC 58.887 47.826 9.40 9.40 39.60 4.57
3003 8986 3.132289 TGCTACTTGGAGTATAGTGCACC 59.868 47.826 14.63 0.00 29.08 5.01
3004 8987 2.961526 ACTTGGAGTATAGTGCACCG 57.038 50.000 14.63 0.00 0.00 4.94
3005 8988 1.134788 ACTTGGAGTATAGTGCACCGC 60.135 52.381 14.63 0.00 0.00 5.68
3006 8989 0.177141 TTGGAGTATAGTGCACCGCC 59.823 55.000 14.63 9.92 0.00 6.13
3007 8990 1.299926 GGAGTATAGTGCACCGCCG 60.300 63.158 14.63 0.00 0.00 6.46
3008 8991 1.731433 GGAGTATAGTGCACCGCCGA 61.731 60.000 14.63 0.00 0.00 5.54
3009 8992 0.594284 GAGTATAGTGCACCGCCGAC 60.594 60.000 14.63 5.06 0.00 4.79
3010 8993 1.942712 GTATAGTGCACCGCCGACG 60.943 63.158 14.63 0.00 39.67 5.12
3011 8994 2.114051 TATAGTGCACCGCCGACGA 61.114 57.895 14.63 0.00 43.93 4.20
3012 8995 2.055310 TATAGTGCACCGCCGACGAG 62.055 60.000 14.63 0.00 43.93 4.18
3021 9004 3.776656 GCCGACGAGCGTTATGTT 58.223 55.556 0.00 0.00 38.67 2.71
3022 9005 2.075761 GCCGACGAGCGTTATGTTT 58.924 52.632 0.00 0.00 38.67 2.83
3023 9006 0.024619 GCCGACGAGCGTTATGTTTC 59.975 55.000 0.00 0.00 38.67 2.78
3024 9007 0.293723 CCGACGAGCGTTATGTTTCG 59.706 55.000 0.00 0.00 38.67 3.46
3026 9009 2.168384 CGACGAGCGTTATGTTTCGTA 58.832 47.619 0.00 0.00 45.23 3.43
3027 9010 2.780014 CGACGAGCGTTATGTTTCGTAT 59.220 45.455 0.00 0.00 45.23 3.06
3028 9011 3.961860 CGACGAGCGTTATGTTTCGTATA 59.038 43.478 0.00 0.00 45.23 1.47
3029 9012 4.610122 CGACGAGCGTTATGTTTCGTATAT 59.390 41.667 0.00 0.00 45.23 0.86
3030 9013 5.439821 CGACGAGCGTTATGTTTCGTATATG 60.440 44.000 0.00 0.00 45.23 1.78
3031 9014 5.276270 ACGAGCGTTATGTTTCGTATATGT 58.724 37.500 0.00 0.00 43.64 2.29
3032 9015 5.745294 ACGAGCGTTATGTTTCGTATATGTT 59.255 36.000 0.00 0.00 43.64 2.71
3033 9016 6.056424 CGAGCGTTATGTTTCGTATATGTTG 58.944 40.000 0.00 0.00 0.00 3.33
3034 9017 6.291427 CGAGCGTTATGTTTCGTATATGTTGT 60.291 38.462 0.00 0.00 0.00 3.32
3035 9018 7.096925 CGAGCGTTATGTTTCGTATATGTTGTA 60.097 37.037 0.00 0.00 0.00 2.41
3036 9019 8.583810 AGCGTTATGTTTCGTATATGTTGTAT 57.416 30.769 0.00 0.00 0.00 2.29
3037 9020 9.037737 AGCGTTATGTTTCGTATATGTTGTATT 57.962 29.630 0.00 0.00 0.00 1.89
3038 9021 9.298113 GCGTTATGTTTCGTATATGTTGTATTC 57.702 33.333 0.00 0.00 0.00 1.75
3039 9022 9.494679 CGTTATGTTTCGTATATGTTGTATTCG 57.505 33.333 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.756195 TTGACCAACATAATATGAGCTGC 57.244 39.130 7.33 0.00 0.00 5.25
42 43 8.599792 GGTTTATAAGGCTTGTATGTATCCCTA 58.400 37.037 10.69 0.00 0.00 3.53
50 51 6.238648 CCTTTCCGGTTTATAAGGCTTGTATG 60.239 42.308 10.69 0.00 31.59 2.39
51 52 5.826208 CCTTTCCGGTTTATAAGGCTTGTAT 59.174 40.000 10.69 0.00 31.59 2.29
81 82 6.706270 AGTCCATTATTGGCGTGTTTATCTAG 59.294 38.462 0.00 0.00 43.29 2.43
92 98 3.689161 TGTCAAGAAGTCCATTATTGGCG 59.311 43.478 0.00 0.00 45.54 5.69
192 198 8.542497 TCGAGCATTTACAAAGTAAATAGTGT 57.458 30.769 13.07 1.64 0.00 3.55
403 534 8.316946 TCAATACATGACTCATCATATTCCCTC 58.683 37.037 0.00 0.00 44.13 4.30
498 750 8.621532 AAGATGAACAAGCTGAAGTAATGTTA 57.378 30.769 0.00 0.00 34.59 2.41
600 854 7.066163 TCCTTGTGCATGTTGTTAAGATAGATG 59.934 37.037 0.00 0.00 0.00 2.90
640 895 2.684881 CAAATCTTCATAGCTTGCGGGT 59.315 45.455 0.00 0.00 0.00 5.28
809 1068 8.199449 AGTTGCCTTTTTATGGTTCATATCATG 58.801 33.333 0.00 0.00 0.00 3.07
881 1142 6.375377 TCGAACTAATTATTTGGTGTGTTGC 58.625 36.000 0.00 0.00 0.00 4.17
926 1189 9.868389 GTTTCTTTTCATTATTGCTTTCCTTTG 57.132 29.630 0.00 0.00 0.00 2.77
995 1262 4.130118 GTGTGAAGGATGGATGATGGTAC 58.870 47.826 0.00 0.00 0.00 3.34
1070 1338 8.603898 TTGTTAGGATGAGTAAGGTCTTCATA 57.396 34.615 0.00 0.00 0.00 2.15
1184 1455 0.773644 AGAATGGTTGGTGAGGCTGT 59.226 50.000 0.00 0.00 0.00 4.40
1426 2352 3.037549 TGTTGTTGGGGCTGAGAAAATT 58.962 40.909 0.00 0.00 0.00 1.82
1431 2357 2.238521 GAATTGTTGTTGGGGCTGAGA 58.761 47.619 0.00 0.00 0.00 3.27
1433 2359 1.337118 GGAATTGTTGTTGGGGCTGA 58.663 50.000 0.00 0.00 0.00 4.26
1527 2516 3.259123 AGGAAATTCTTGCATGGGTTCAC 59.741 43.478 0.00 0.00 0.00 3.18
1575 2564 0.539051 GACCAGAGGGATGACACCAG 59.461 60.000 0.00 0.00 38.05 4.00
1693 2682 4.142752 GCATGATGATGGAATGTATGACGG 60.143 45.833 0.00 0.00 0.00 4.79
1698 2687 4.403734 TGCTGCATGATGATGGAATGTAT 58.596 39.130 0.00 0.00 28.12 2.29
1700 2689 2.661718 TGCTGCATGATGATGGAATGT 58.338 42.857 0.00 0.00 28.12 2.71
1932 3116 2.125269 ACCAATGCCGGCGACTAC 60.125 61.111 23.90 0.00 0.00 2.73
2033 3220 2.289756 TGGTGCACGCCAGTTTATTCTA 60.290 45.455 11.45 0.00 33.97 2.10
2034 3221 1.165270 GGTGCACGCCAGTTTATTCT 58.835 50.000 11.45 0.00 0.00 2.40
2078 3266 7.734942 TGTCTTTTATTCCCAAGCTTGAAATT 58.265 30.769 28.05 12.96 0.00 1.82
2080 3268 6.723298 TGTCTTTTATTCCCAAGCTTGAAA 57.277 33.333 28.05 20.10 0.00 2.69
2122 3310 3.058293 TGGAACAATGACAAGCGATGTTC 60.058 43.478 8.10 8.10 45.61 3.18
2258 3450 5.013079 TCAATCGGCCTATAAACTGGATCAT 59.987 40.000 0.00 0.00 0.00 2.45
2328 3520 3.304592 CGTGTGCAATGTTCAGGAAATCA 60.305 43.478 0.00 0.00 0.00 2.57
2412 3604 4.079844 TGATGGATGGTTTCTAATCAGGCA 60.080 41.667 0.00 0.00 0.00 4.75
2495 8474 6.805271 CCTGTAGAATTGCTTTGAAGAATGTG 59.195 38.462 0.00 0.00 0.00 3.21
2517 8497 1.699634 TCACCTCTTTGGAGTTCCCTG 59.300 52.381 0.00 0.00 37.86 4.45
2522 8502 6.381133 AGTTTGATTTTCACCTCTTTGGAGTT 59.619 34.615 0.00 0.00 37.86 3.01
2554 8535 6.405731 GCATGCTTTATCTTTTACCATGTGGA 60.406 38.462 11.37 0.00 38.94 4.02
2641 8622 7.128728 TGTTTCCCTCTCTCCAATAATCCATAA 59.871 37.037 0.00 0.00 0.00 1.90
2647 8628 6.394345 AACTGTTTCCCTCTCTCCAATAAT 57.606 37.500 0.00 0.00 0.00 1.28
2650 8631 4.731313 AAACTGTTTCCCTCTCTCCAAT 57.269 40.909 0.00 0.00 0.00 3.16
2654 8635 5.470047 TCTGTAAACTGTTTCCCTCTCTC 57.530 43.478 9.38 0.00 0.00 3.20
2668 8649 6.902224 AAGTTTTGTTTGCCATCTGTAAAC 57.098 33.333 0.00 0.00 46.19 2.01
2679 8660 7.649057 ACTGATCCTACTTAAGTTTTGTTTGC 58.351 34.615 14.49 0.00 0.00 3.68
2765 8746 8.641541 TGAGATAAGTCAATATCACAGTGCATA 58.358 33.333 0.00 0.00 35.22 3.14
2814 8795 4.141413 TGGAGTCCATAGCAGCAAATGTAT 60.141 41.667 8.12 0.00 0.00 2.29
2893 8876 9.577003 CTTCTCGTACAATGTTAAGTTTGTTAC 57.423 33.333 7.93 4.99 37.29 2.50
2894 8877 9.316730 ACTTCTCGTACAATGTTAAGTTTGTTA 57.683 29.630 7.93 0.00 37.29 2.41
2895 8878 8.205131 ACTTCTCGTACAATGTTAAGTTTGTT 57.795 30.769 7.93 0.00 37.29 2.83
2901 8884 6.020599 CGATGGACTTCTCGTACAATGTTAAG 60.021 42.308 0.00 0.00 40.61 1.85
2911 8894 0.100682 GCAGCGATGGACTTCTCGTA 59.899 55.000 1.46 0.00 37.23 3.43
2912 8895 1.153745 GCAGCGATGGACTTCTCGT 60.154 57.895 1.46 0.00 37.23 4.18
2913 8896 1.153765 TGCAGCGATGGACTTCTCG 60.154 57.895 1.46 0.00 37.92 4.04
2914 8897 1.416813 CGTGCAGCGATGGACTTCTC 61.417 60.000 22.79 0.00 44.77 2.87
2915 8898 1.446792 CGTGCAGCGATGGACTTCT 60.447 57.895 22.79 0.00 44.77 2.85
2916 8899 3.084579 CGTGCAGCGATGGACTTC 58.915 61.111 22.79 0.00 44.77 3.01
2917 8900 3.121030 GCGTGCAGCGATGGACTT 61.121 61.111 22.79 0.00 44.77 3.01
2948 8931 0.179048 TAATCGGGATGCTGTGCCAG 60.179 55.000 0.00 0.00 38.45 4.85
2949 8932 0.179048 CTAATCGGGATGCTGTGCCA 60.179 55.000 0.00 0.00 38.45 4.92
2950 8933 0.886490 CCTAATCGGGATGCTGTGCC 60.886 60.000 0.00 0.00 34.40 5.01
2951 8934 0.106708 TCCTAATCGGGATGCTGTGC 59.893 55.000 0.00 0.00 0.00 4.57
2952 8935 1.541233 GGTCCTAATCGGGATGCTGTG 60.541 57.143 0.00 0.00 37.73 3.66
2953 8936 0.759346 GGTCCTAATCGGGATGCTGT 59.241 55.000 0.00 0.00 37.73 4.40
2954 8937 0.758734 TGGTCCTAATCGGGATGCTG 59.241 55.000 0.00 0.00 37.73 4.41
2955 8938 1.051812 CTGGTCCTAATCGGGATGCT 58.948 55.000 0.00 0.00 37.73 3.79
2956 8939 0.603975 GCTGGTCCTAATCGGGATGC 60.604 60.000 0.00 0.00 37.73 3.91
2957 8940 0.035458 GGCTGGTCCTAATCGGGATG 59.965 60.000 0.00 0.00 37.73 3.51
2958 8941 0.399949 TGGCTGGTCCTAATCGGGAT 60.400 55.000 0.00 0.00 37.73 3.85
2959 8942 0.619255 TTGGCTGGTCCTAATCGGGA 60.619 55.000 0.00 0.00 35.26 5.14
2960 8943 0.254747 TTTGGCTGGTCCTAATCGGG 59.745 55.000 0.00 0.00 35.26 5.14
2961 8944 1.065418 ACTTTGGCTGGTCCTAATCGG 60.065 52.381 0.00 0.00 35.26 4.18
2962 8945 2.009774 CACTTTGGCTGGTCCTAATCG 58.990 52.381 0.00 0.00 35.26 3.34
2963 8946 1.745653 GCACTTTGGCTGGTCCTAATC 59.254 52.381 0.00 0.00 35.26 1.75
2964 8947 1.355720 AGCACTTTGGCTGGTCCTAAT 59.644 47.619 0.00 0.00 43.89 1.73
2965 8948 0.771127 AGCACTTTGGCTGGTCCTAA 59.229 50.000 0.00 0.00 43.89 2.69
2966 8949 1.278127 GTAGCACTTTGGCTGGTCCTA 59.722 52.381 0.00 0.00 45.44 2.94
2967 8950 0.036875 GTAGCACTTTGGCTGGTCCT 59.963 55.000 0.00 0.00 45.44 3.85
2968 8951 0.036875 AGTAGCACTTTGGCTGGTCC 59.963 55.000 0.00 0.00 45.44 4.46
2969 8952 1.537202 CAAGTAGCACTTTGGCTGGTC 59.463 52.381 0.00 0.00 45.44 4.02
2970 8953 1.609208 CAAGTAGCACTTTGGCTGGT 58.391 50.000 0.00 0.00 45.44 4.00
2971 8954 0.883833 CCAAGTAGCACTTTGGCTGG 59.116 55.000 0.00 0.00 45.44 4.85
2972 8955 1.808945 CTCCAAGTAGCACTTTGGCTG 59.191 52.381 7.92 1.74 45.44 4.85
2974 8957 1.897560 ACTCCAAGTAGCACTTTGGC 58.102 50.000 7.92 0.00 36.03 4.52
2975 8958 5.812642 CACTATACTCCAAGTAGCACTTTGG 59.187 44.000 6.75 6.75 36.03 3.28
2976 8959 5.292101 GCACTATACTCCAAGTAGCACTTTG 59.708 44.000 0.00 0.00 36.03 2.77
2977 8960 5.046591 TGCACTATACTCCAAGTAGCACTTT 60.047 40.000 0.00 0.00 36.03 2.66
2978 8961 4.466370 TGCACTATACTCCAAGTAGCACTT 59.534 41.667 0.00 0.00 39.39 3.16
2979 8962 4.023980 TGCACTATACTCCAAGTAGCACT 58.976 43.478 0.00 0.00 33.66 4.40
2980 8963 4.113354 GTGCACTATACTCCAAGTAGCAC 58.887 47.826 10.32 11.16 40.26 4.40
2981 8964 3.132289 GGTGCACTATACTCCAAGTAGCA 59.868 47.826 17.98 0.00 33.66 3.49
2982 8965 3.718815 GGTGCACTATACTCCAAGTAGC 58.281 50.000 17.98 0.00 33.66 3.58
2983 8966 3.795826 GCGGTGCACTATACTCCAAGTAG 60.796 52.174 17.98 0.00 33.66 2.57
2984 8967 2.100252 GCGGTGCACTATACTCCAAGTA 59.900 50.000 17.98 0.00 34.82 2.24
2985 8968 1.134788 GCGGTGCACTATACTCCAAGT 60.135 52.381 17.98 0.00 0.00 3.16
2986 8969 1.571919 GCGGTGCACTATACTCCAAG 58.428 55.000 17.98 0.00 0.00 3.61
2987 8970 0.177141 GGCGGTGCACTATACTCCAA 59.823 55.000 17.98 0.00 0.00 3.53
2988 8971 1.820581 GGCGGTGCACTATACTCCA 59.179 57.895 17.98 0.00 0.00 3.86
2989 8972 1.299926 CGGCGGTGCACTATACTCC 60.300 63.158 17.98 3.21 0.00 3.85
2990 8973 0.594284 GTCGGCGGTGCACTATACTC 60.594 60.000 17.98 0.00 0.00 2.59
2991 8974 1.436336 GTCGGCGGTGCACTATACT 59.564 57.895 17.98 0.00 0.00 2.12
2992 8975 1.942712 CGTCGGCGGTGCACTATAC 60.943 63.158 17.98 7.44 0.00 1.47
2993 8976 2.055310 CTCGTCGGCGGTGCACTATA 62.055 60.000 17.98 0.00 38.89 1.31
2994 8977 3.411418 CTCGTCGGCGGTGCACTAT 62.411 63.158 17.98 0.00 38.89 2.12
2995 8978 4.111016 CTCGTCGGCGGTGCACTA 62.111 66.667 17.98 0.00 38.89 2.74
3004 8987 0.024619 GAAACATAACGCTCGTCGGC 59.975 55.000 0.00 0.00 43.86 5.54
3005 8988 0.293723 CGAAACATAACGCTCGTCGG 59.706 55.000 0.00 0.00 43.86 4.79
3006 8989 0.979811 ACGAAACATAACGCTCGTCG 59.020 50.000 0.00 0.00 40.29 5.12
3007 8990 5.397534 ACATATACGAAACATAACGCTCGTC 59.602 40.000 0.00 0.00 43.06 4.20
3008 8991 5.276270 ACATATACGAAACATAACGCTCGT 58.724 37.500 1.36 1.36 45.71 4.18
3009 8992 5.801176 ACATATACGAAACATAACGCTCG 57.199 39.130 0.00 0.00 37.33 5.03
3010 8993 6.929896 ACAACATATACGAAACATAACGCTC 58.070 36.000 0.00 0.00 0.00 5.03
3011 8994 6.897259 ACAACATATACGAAACATAACGCT 57.103 33.333 0.00 0.00 0.00 5.07
3012 8995 9.298113 GAATACAACATATACGAAACATAACGC 57.702 33.333 0.00 0.00 0.00 4.84
3013 8996 9.494679 CGAATACAACATATACGAAACATAACG 57.505 33.333 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.