Multiple sequence alignment - TraesCS1B01G407500

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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 TraesCS1B01G407500 chr1B 100.000 3086 0 0 1 3086 634599743 634602828 0.000000e+00 5699.0
1 TraesCS1B01G407500 chr1B 95.086 1567 36 16 1503 3037 634413638 634412081 0.000000e+00 2429.0
2 TraesCS1B01G407500 chr1B 95.607 1070 27 8 443 1510 634419414 634418363 0.000000e+00 1698.0
3 TraesCS1B01G407500 chr1B 100.000 527 0 0 3321 3847 634603063 634603589 0.000000e+00 974.0
4 TraesCS1B01G407500 chr1B 91.429 105 9 0 3 107 627920691 627920587 1.110000e-30 145.0
5 TraesCS1B01G407500 chr1D 90.028 1755 89 49 1313 3036 461487017 461485318 0.000000e+00 2193.0
6 TraesCS1B01G407500 chr1D 90.020 992 47 16 327 1288 461488051 461487082 0.000000e+00 1236.0
7 TraesCS1B01G407500 chr1D 86.182 977 60 47 2151 3085 461506875 461505932 0.000000e+00 987.0
8 TraesCS1B01G407500 chr1D 86.468 739 26 19 111 789 461537048 461536324 0.000000e+00 743.0
9 TraesCS1B01G407500 chr1D 89.522 544 39 13 1142 1668 461533956 461533414 0.000000e+00 673.0
10 TraesCS1B01G407500 chr1D 91.385 325 18 3 834 1152 461536328 461536008 1.640000e-118 436.0
11 TraesCS1B01G407500 chr1D 92.517 294 20 2 3554 3847 461505636 461505345 1.650000e-113 420.0
12 TraesCS1B01G407500 chr1D 95.628 183 8 0 1809 1991 461533419 461533237 1.050000e-75 294.0
13 TraesCS1B01G407500 chr1D 96.319 163 4 2 1984 2145 461507081 461506920 2.280000e-67 267.0
14 TraesCS1B01G407500 chr1D 76.087 276 51 13 1357 1626 414775960 414776226 3.120000e-26 130.0
15 TraesCS1B01G407500 chr1D 100.000 38 0 0 3321 3358 461505839 461505802 1.920000e-08 71.3
16 TraesCS1B01G407500 chr1A 88.751 1849 106 45 327 2139 552952852 552951070 0.000000e+00 2169.0
17 TraesCS1B01G407500 chr1A 85.435 920 63 30 2149 3037 552951017 552950138 0.000000e+00 891.0
18 TraesCS1B01G407500 chr1A 92.381 105 8 0 4 108 16097738 16097634 2.390000e-32 150.0
19 TraesCS1B01G407500 chrUn 89.095 917 57 32 775 1668 218154320 218155216 0.000000e+00 1099.0
20 TraesCS1B01G407500 chrUn 89.095 917 57 32 775 1668 246424049 246423153 0.000000e+00 1099.0
21 TraesCS1B01G407500 chrUn 100.000 404 0 0 1107 1510 478319186 478319589 0.000000e+00 747.0
22 TraesCS1B01G407500 chrUn 88.259 494 37 11 2595 3085 218156090 218156565 4.310000e-159 571.0
23 TraesCS1B01G407500 chrUn 88.259 494 37 11 2595 3085 246422279 246421804 4.310000e-159 571.0
24 TraesCS1B01G407500 chrUn 97.264 329 7 2 1809 2136 218155211 218155538 1.210000e-154 556.0
25 TraesCS1B01G407500 chrUn 96.988 332 8 2 1809 2139 246423158 246422828 1.210000e-154 556.0
26 TraesCS1B01G407500 chrUn 90.431 418 32 6 3433 3845 218156780 218157194 9.400000e-151 544.0
27 TraesCS1B01G407500 chrUn 90.431 418 32 6 3433 3845 246421589 246421175 9.400000e-151 544.0
28 TraesCS1B01G407500 chrUn 90.850 306 12 5 477 778 218148911 218149204 2.790000e-106 396.0
29 TraesCS1B01G407500 chrUn 90.850 306 12 5 477 778 246429458 246429165 2.790000e-106 396.0
30 TraesCS1B01G407500 chrUn 82.005 389 25 21 2149 2521 218155592 218155951 4.860000e-74 289.0
31 TraesCS1B01G407500 chrUn 81.888 392 26 21 2149 2524 246422777 246422415 4.860000e-74 289.0
32 TraesCS1B01G407500 chr7A 84.783 322 46 2 1822 2143 71145257 71144939 1.720000e-83 320.0
33 TraesCS1B01G407500 chr7A 86.404 228 24 7 2618 2842 71144021 71143798 3.840000e-60 243.0
34 TraesCS1B01G407500 chr7A 88.701 177 20 0 1096 1272 71146016 71145840 2.330000e-52 217.0
35 TraesCS1B01G407500 chr7A 92.000 75 6 0 1594 1668 71145339 71145265 5.260000e-19 106.0
36 TraesCS1B01G407500 chr7D 85.079 315 42 4 1822 2135 68791019 68791329 2.230000e-82 316.0
37 TraesCS1B01G407500 chr7D 87.440 207 23 3 2618 2823 68792220 68792424 6.430000e-58 235.0
38 TraesCS1B01G407500 chr7D 89.266 177 19 0 1096 1272 68790279 68790455 5.000000e-54 222.0
39 TraesCS1B01G407500 chr7D 82.927 205 35 0 1349 1553 68790455 68790659 6.560000e-43 185.0
40 TraesCS1B01G407500 chr7D 92.308 104 7 1 4 107 45195449 45195347 3.100000e-31 147.0
41 TraesCS1B01G407500 chr7D 85.859 99 14 0 1570 1668 68790913 68791011 5.260000e-19 106.0
42 TraesCS1B01G407500 chr7B 84.211 323 46 4 1822 2143 9751234 9751552 3.730000e-80 309.0
43 TraesCS1B01G407500 chr7B 86.996 223 20 9 2607 2823 9752810 9753029 3.840000e-60 243.0
44 TraesCS1B01G407500 chr7B 83.902 205 33 0 1349 1553 9750657 9750861 3.030000e-46 196.0
45 TraesCS1B01G407500 chr7B 92.000 75 6 0 1594 1668 9751152 9751226 5.260000e-19 106.0
46 TraesCS1B01G407500 chr4A 95.327 107 5 0 1 107 14722866 14722972 1.840000e-38 171.0
47 TraesCS1B01G407500 chr4A 93.458 107 7 0 1 107 14756503 14756609 3.980000e-35 159.0
48 TraesCS1B01G407500 chr4A 91.667 108 5 1 4 107 658187602 658187709 3.100000e-31 147.0
49 TraesCS1B01G407500 chr6A 93.458 107 7 0 1 107 601270924 601271030 3.980000e-35 159.0
50 TraesCS1B01G407500 chr3D 92.453 106 8 0 3 108 85412276 85412171 6.660000e-33 152.0
51 TraesCS1B01G407500 chr2B 90.385 104 10 0 4 107 787349838 787349735 1.860000e-28 137.0


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 TraesCS1B01G407500 chr1B 634599743 634603589 3846 False 3336.500 5699 100.00000 1 3847 2 chr1B.!!$F1 3846
1 TraesCS1B01G407500 chr1B 634412081 634413638 1557 True 2429.000 2429 95.08600 1503 3037 1 chr1B.!!$R2 1534
2 TraesCS1B01G407500 chr1B 634418363 634419414 1051 True 1698.000 1698 95.60700 443 1510 1 chr1B.!!$R3 1067
3 TraesCS1B01G407500 chr1D 461485318 461488051 2733 True 1714.500 2193 90.02400 327 3036 2 chr1D.!!$R1 2709
4 TraesCS1B01G407500 chr1D 461533237 461537048 3811 True 536.500 743 90.75075 111 1991 4 chr1D.!!$R3 1880
5 TraesCS1B01G407500 chr1D 461505345 461507081 1736 True 436.325 987 93.75450 1984 3847 4 chr1D.!!$R2 1863
6 TraesCS1B01G407500 chr1A 552950138 552952852 2714 True 1530.000 2169 87.09300 327 3037 2 chr1A.!!$R2 2710
7 TraesCS1B01G407500 chrUn 218154320 218157194 2874 False 611.800 1099 89.41080 775 3845 5 chrUn.!!$F3 3070
8 TraesCS1B01G407500 chrUn 246421175 246424049 2874 True 611.800 1099 89.33220 775 3845 5 chrUn.!!$R2 3070
9 TraesCS1B01G407500 chr7A 71143798 71146016 2218 True 221.500 320 87.97200 1096 2842 4 chr7A.!!$R1 1746
10 TraesCS1B01G407500 chr7D 68790279 68792424 2145 False 212.800 316 86.11420 1096 2823 5 chr7D.!!$F1 1727
11 TraesCS1B01G407500 chr7B 9750657 9753029 2372 False 213.500 309 86.77725 1349 2823 4 chr7B.!!$F1 1474

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
55 56 0.028902 GCTTTGCCGGCGGTTATAAG 59.971 55.0 28.82 23.09 0.00 1.73 F
56 57 0.028902 CTTTGCCGGCGGTTATAAGC 59.971 55.0 28.82 11.60 0.00 3.09 F
92 93 0.179119 GTGGCACTCGGCGTATAACT 60.179 55.0 11.13 0.00 46.16 2.24 F
733 793 0.250295 TTTTCTCCCTGGCAGACACG 60.250 55.0 17.94 0.00 0.00 4.49 F
2491 5658 0.180406 AGTAATGGTGGATCGGCACC 59.820 55.0 12.78 12.78 41.64 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 1207 0.098025 AAGTTGAACACCGCGTTGTG 59.902 50.000 10.96 12.19 38.19 3.33 R
2386 5529 8.640091 TGAATGATTTGAAGATCTTCTACTCG 57.360 34.615 30.45 0.00 40.14 4.18 R
2437 5581 5.181748 TGCCAGCTCTAGATCTTCTTTTTC 58.818 41.667 0.00 0.00 0.00 2.29 R
2540 5723 1.220529 ACGTGCATCAACAGTGTCAG 58.779 50.000 0.00 0.00 0.00 3.51 R
3470 7177 0.235665 ACGCGCACTTTCATTGTCTG 59.764 50.000 5.73 0.00 0.00 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
25 26 2.244000 GCTTTTGCCGAGTGTAGCA 58.756 52.632 0.00 0.00 40.15 3.49
26 27 0.110192 GCTTTTGCCGAGTGTAGCAC 60.110 55.000 0.00 0.00 39.10 4.40
27 28 2.474387 GCTTTTGCCGAGTGTAGCACT 61.474 52.381 0.97 0.97 43.06 4.40
28 29 4.307696 GCTTTTGCCGAGTGTAGCACTC 62.308 54.545 16.70 16.70 45.47 3.51
35 36 3.217242 AGTGTAGCACTCGGCAAAG 57.783 52.632 0.00 0.00 41.21 2.77
36 37 0.320771 AGTGTAGCACTCGGCAAAGG 60.321 55.000 0.00 0.00 41.21 3.11
40 41 3.042560 GCACTCGGCAAAGGCTTT 58.957 55.556 6.68 6.68 43.97 3.51
41 42 1.372128 GCACTCGGCAAAGGCTTTG 60.372 57.895 30.74 30.74 43.97 2.77
52 53 3.138128 GGCTTTGCCGGCGGTTAT 61.138 61.111 28.82 0.00 39.62 1.89
53 54 1.820481 GGCTTTGCCGGCGGTTATA 60.820 57.895 28.82 11.17 39.62 0.98
54 55 1.378124 GGCTTTGCCGGCGGTTATAA 61.378 55.000 28.82 14.66 39.62 0.98
55 56 0.028902 GCTTTGCCGGCGGTTATAAG 59.971 55.000 28.82 23.09 0.00 1.73
56 57 0.028902 CTTTGCCGGCGGTTATAAGC 59.971 55.000 28.82 11.60 0.00 3.09
63 64 3.938653 GCGGTTATAAGCCCTTTGC 57.061 52.632 9.01 2.80 41.71 3.68
64 65 0.384309 GCGGTTATAAGCCCTTTGCC 59.616 55.000 9.01 0.00 42.71 4.52
65 66 0.661020 CGGTTATAAGCCCTTTGCCG 59.339 55.000 9.01 1.17 42.71 5.69
66 67 1.744456 CGGTTATAAGCCCTTTGCCGA 60.744 52.381 9.01 0.00 42.71 5.54
67 68 1.674441 GGTTATAAGCCCTTTGCCGAC 59.326 52.381 3.16 0.00 42.71 4.79
68 69 2.640184 GTTATAAGCCCTTTGCCGACT 58.360 47.619 0.00 0.00 42.71 4.18
69 70 2.325583 TATAAGCCCTTTGCCGACTG 57.674 50.000 0.00 0.00 42.71 3.51
70 71 0.328258 ATAAGCCCTTTGCCGACTGT 59.672 50.000 0.00 0.00 42.71 3.55
71 72 0.321298 TAAGCCCTTTGCCGACTGTC 60.321 55.000 0.00 0.00 42.71 3.51
72 73 2.032681 GCCCTTTGCCGACTGTCT 59.967 61.111 6.21 0.00 0.00 3.41
73 74 2.328099 GCCCTTTGCCGACTGTCTG 61.328 63.158 6.21 0.05 0.00 3.51
74 75 1.071471 CCCTTTGCCGACTGTCTGT 59.929 57.895 6.21 0.00 0.00 3.41
75 76 1.230635 CCCTTTGCCGACTGTCTGTG 61.231 60.000 6.21 0.00 0.00 3.66
76 77 1.230635 CCTTTGCCGACTGTCTGTGG 61.231 60.000 6.21 1.09 0.00 4.17
77 78 1.845809 CTTTGCCGACTGTCTGTGGC 61.846 60.000 15.58 15.58 40.67 5.01
78 79 2.601194 TTTGCCGACTGTCTGTGGCA 62.601 55.000 19.63 19.63 44.74 4.92
79 80 3.044305 GCCGACTGTCTGTGGCAC 61.044 66.667 11.55 11.55 40.29 5.01
80 81 2.737180 CCGACTGTCTGTGGCACT 59.263 61.111 19.83 0.00 0.00 4.40
81 82 1.373497 CCGACTGTCTGTGGCACTC 60.373 63.158 19.83 9.79 0.00 3.51
82 83 1.730902 CGACTGTCTGTGGCACTCG 60.731 63.158 19.83 14.25 0.00 4.18
83 84 1.373497 GACTGTCTGTGGCACTCGG 60.373 63.158 19.83 15.41 0.00 4.63
84 85 2.740055 CTGTCTGTGGCACTCGGC 60.740 66.667 19.83 11.83 43.74 5.54
85 86 4.662961 TGTCTGTGGCACTCGGCG 62.663 66.667 19.83 0.00 46.16 6.46
86 87 4.664677 GTCTGTGGCACTCGGCGT 62.665 66.667 19.83 0.00 46.16 5.68
87 88 2.986979 TCTGTGGCACTCGGCGTA 60.987 61.111 19.83 0.00 46.16 4.42
88 89 2.184322 CTGTGGCACTCGGCGTAT 59.816 61.111 19.83 0.00 46.16 3.06
89 90 1.033202 TCTGTGGCACTCGGCGTATA 61.033 55.000 19.83 0.00 46.16 1.47
90 91 0.179121 CTGTGGCACTCGGCGTATAA 60.179 55.000 19.83 0.00 46.16 0.98
91 92 0.458889 TGTGGCACTCGGCGTATAAC 60.459 55.000 19.83 0.02 46.16 1.89
92 93 0.179119 GTGGCACTCGGCGTATAACT 60.179 55.000 11.13 0.00 46.16 2.24
93 94 1.066002 GTGGCACTCGGCGTATAACTA 59.934 52.381 11.13 0.00 46.16 2.24
94 95 1.335810 TGGCACTCGGCGTATAACTAG 59.664 52.381 6.85 0.00 46.16 2.57
95 96 1.605710 GGCACTCGGCGTATAACTAGA 59.394 52.381 6.85 0.00 46.16 2.43
96 97 2.228343 GGCACTCGGCGTATAACTAGAT 59.772 50.000 6.85 0.00 46.16 1.98
97 98 3.305199 GGCACTCGGCGTATAACTAGATT 60.305 47.826 6.85 0.00 46.16 2.40
98 99 3.913163 GCACTCGGCGTATAACTAGATTC 59.087 47.826 6.85 0.00 0.00 2.52
99 100 4.474113 CACTCGGCGTATAACTAGATTCC 58.526 47.826 6.85 0.00 0.00 3.01
100 101 4.023450 CACTCGGCGTATAACTAGATTCCA 60.023 45.833 6.85 0.00 0.00 3.53
101 102 4.215827 ACTCGGCGTATAACTAGATTCCAG 59.784 45.833 6.85 0.00 0.00 3.86
102 103 4.139786 TCGGCGTATAACTAGATTCCAGT 58.860 43.478 6.85 0.00 0.00 4.00
103 104 5.308014 TCGGCGTATAACTAGATTCCAGTA 58.692 41.667 6.85 0.00 0.00 2.74
104 105 5.410746 TCGGCGTATAACTAGATTCCAGTAG 59.589 44.000 6.85 0.00 0.00 2.57
105 106 5.180868 CGGCGTATAACTAGATTCCAGTAGT 59.819 44.000 0.00 0.00 0.00 2.73
106 107 6.380190 GGCGTATAACTAGATTCCAGTAGTG 58.620 44.000 0.00 0.00 29.71 2.74
107 108 6.380190 GCGTATAACTAGATTCCAGTAGTGG 58.620 44.000 10.66 10.66 46.63 4.00
108 109 6.380190 CGTATAACTAGATTCCAGTAGTGGC 58.620 44.000 12.14 0.00 44.60 5.01
109 110 5.810080 ATAACTAGATTCCAGTAGTGGCC 57.190 43.478 12.14 0.00 44.60 5.36
188 189 2.203280 CCACTGAACACCGGCCAA 60.203 61.111 0.00 0.00 0.00 4.52
242 247 1.526887 GTATGTTCCACATCATCGCGG 59.473 52.381 6.13 0.00 39.88 6.46
248 253 0.798009 CCACATCATCGCGGCAAAAC 60.798 55.000 6.13 0.00 0.00 2.43
262 267 3.250762 CGGCAAAACTCAAGATGACTGAA 59.749 43.478 0.00 0.00 0.00 3.02
324 329 3.515901 TCTCTTTCTTTCTCCCTAGGTGC 59.484 47.826 8.29 0.00 0.00 5.01
387 392 5.705905 GGTTGCATAGAGAAAGTTGTTACCT 59.294 40.000 0.00 0.00 0.00 3.08
411 416 0.750850 TCCGATCGATTGGGGTCTTC 59.249 55.000 28.01 0.00 31.87 2.87
435 440 7.523415 TCCTTCCCAACTATCTTTTGTACTTT 58.477 34.615 0.00 0.00 0.00 2.66
436 441 8.002459 TCCTTCCCAACTATCTTTTGTACTTTT 58.998 33.333 0.00 0.00 0.00 2.27
437 442 9.292195 CCTTCCCAACTATCTTTTGTACTTTTA 57.708 33.333 0.00 0.00 0.00 1.52
475 480 8.260270 TGAATCTTAACATTCAGATCACACAG 57.740 34.615 2.37 0.00 37.77 3.66
570 621 2.027653 TGTGCGTCCTTTGGTATCATGA 60.028 45.455 0.00 0.00 0.00 3.07
599 655 3.001634 CGTAGCATGCTGACCTTTACATG 59.998 47.826 30.42 8.27 42.20 3.21
623 683 3.380479 TCGGAGAATAATAAGGCGGTG 57.620 47.619 0.00 0.00 0.00 4.94
624 684 2.036733 TCGGAGAATAATAAGGCGGTGG 59.963 50.000 0.00 0.00 0.00 4.61
625 685 2.224209 CGGAGAATAATAAGGCGGTGGT 60.224 50.000 0.00 0.00 0.00 4.16
626 686 3.139077 GGAGAATAATAAGGCGGTGGTG 58.861 50.000 0.00 0.00 0.00 4.17
627 687 3.139077 GAGAATAATAAGGCGGTGGTGG 58.861 50.000 0.00 0.00 0.00 4.61
628 688 2.775384 AGAATAATAAGGCGGTGGTGGA 59.225 45.455 0.00 0.00 0.00 4.02
629 689 2.632987 ATAATAAGGCGGTGGTGGAC 57.367 50.000 0.00 0.00 0.00 4.02
630 690 1.575419 TAATAAGGCGGTGGTGGACT 58.425 50.000 0.00 0.00 0.00 3.85
714 774 4.401925 CAAAGGTCAAAGGGAGAGACAAT 58.598 43.478 0.00 0.00 34.04 2.71
729 789 2.376518 AGACAATTTTCTCCCTGGCAGA 59.623 45.455 17.94 0.00 0.00 4.26
733 793 0.250295 TTTTCTCCCTGGCAGACACG 60.250 55.000 17.94 0.00 0.00 4.49
1016 1103 0.537188 ACGATGGGAACGATGAGCTT 59.463 50.000 0.00 0.00 34.70 3.74
2491 5658 0.180406 AGTAATGGTGGATCGGCACC 59.820 55.000 12.78 12.78 41.64 5.01
2935 6603 5.622770 TTTATTCGAGCTTGAGTTTTCCC 57.377 39.130 4.04 0.00 0.00 3.97
3037 6718 6.663944 ACTCTCGAATAAATTGTTAGTGCC 57.336 37.500 0.00 0.00 0.00 5.01
3076 6757 3.428999 CGTCGGCGAATTCCCTATATGAT 60.429 47.826 12.92 0.00 41.33 2.45
3085 6766 7.467811 GCGAATTCCCTATATGATGCTTATTGG 60.468 40.741 0.00 0.00 0.00 3.16
3409 7116 2.813474 CCCATTCGCGTTCGAGCA 60.813 61.111 5.77 0.00 46.34 4.26
3410 7117 2.173669 CCCATTCGCGTTCGAGCAT 61.174 57.895 5.77 0.00 46.34 3.79
3411 7118 1.705337 CCCATTCGCGTTCGAGCATT 61.705 55.000 5.77 0.00 46.34 3.56
3412 7119 0.587242 CCATTCGCGTTCGAGCATTG 60.587 55.000 5.77 0.00 46.34 2.82
3413 7120 0.587242 CATTCGCGTTCGAGCATTGG 60.587 55.000 5.77 0.00 46.34 3.16
3414 7121 1.019278 ATTCGCGTTCGAGCATTGGT 61.019 50.000 5.77 0.00 46.34 3.67
3415 7122 1.225376 TTCGCGTTCGAGCATTGGTT 61.225 50.000 5.77 0.00 46.34 3.67
3416 7123 1.509787 CGCGTTCGAGCATTGGTTG 60.510 57.895 0.00 0.00 38.10 3.77
3424 7131 2.887360 GCATTGGTTGCCGAGCAT 59.113 55.556 0.00 0.00 46.15 3.79
3428 7135 0.899717 ATTGGTTGCCGAGCATTGGT 60.900 50.000 0.00 0.00 43.65 3.67
3445 7152 2.357760 TTGCCGCGTGGTCCTTAC 60.358 61.111 17.91 0.00 37.67 2.34
3447 7154 2.125269 GCCGCGTGGTCCTTACAT 60.125 61.111 17.91 0.00 37.67 2.29
3452 7159 2.940410 CCGCGTGGTCCTTACATATTTT 59.060 45.455 6.91 0.00 0.00 1.82
3492 7199 0.380378 ACAATGAAAGTGCGCGTTGT 59.620 45.000 8.43 4.66 38.89 3.32
3510 7220 1.092921 GTCGCGCCCATACATTCCAA 61.093 55.000 0.00 0.00 0.00 3.53
3512 7222 0.029300 CGCGCCCATACATTCCAAAG 59.971 55.000 0.00 0.00 0.00 2.77
3521 7231 8.356657 CGCCCATACATTCCAAAGAAATAATAA 58.643 33.333 0.00 0.00 35.09 1.40
3576 7288 7.881142 TCAAATAATGGTTCAAGTTACAGTGG 58.119 34.615 0.00 0.00 0.00 4.00
3657 7369 2.836636 TGAGAGGCCACATCTCTACT 57.163 50.000 18.44 0.00 43.03 2.57
3671 7383 3.849911 TCTCTACTTTGGATGCTCAACG 58.150 45.455 0.00 0.00 0.00 4.10
3748 7460 6.072175 CCCGAAGAAGAAAAACACCAATGATA 60.072 38.462 0.00 0.00 0.00 2.15
3767 7479 6.161855 TGATATTGTCTGTGATGGTACCTC 57.838 41.667 14.36 8.80 0.00 3.85
3778 7490 5.425217 TGTGATGGTACCTCATAGTTGACAT 59.575 40.000 14.36 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.597217 TCGGCAAAAGCCACCTGG 60.597 61.111 7.34 0.00 38.53 4.45
1 2 1.898574 ACTCGGCAAAAGCCACCTG 60.899 57.895 7.34 0.00 0.00 4.00
2 3 1.898574 CACTCGGCAAAAGCCACCT 60.899 57.895 7.34 0.00 0.00 4.00
4 5 0.517316 CTACACTCGGCAAAAGCCAC 59.483 55.000 7.34 0.00 0.00 5.01
5 6 1.234615 GCTACACTCGGCAAAAGCCA 61.235 55.000 7.34 0.00 0.00 4.75
6 7 1.234615 TGCTACACTCGGCAAAAGCC 61.235 55.000 0.00 0.00 35.40 4.35
7 8 0.110192 GTGCTACACTCGGCAAAAGC 60.110 55.000 0.00 0.00 40.26 3.51
8 9 1.512926 AGTGCTACACTCGGCAAAAG 58.487 50.000 0.00 0.00 41.21 2.27
9 10 3.698250 AGTGCTACACTCGGCAAAA 57.302 47.368 0.00 0.00 41.21 2.44
18 19 1.912371 GCCTTTGCCGAGTGCTACAC 61.912 60.000 0.00 0.00 42.00 2.90
19 20 1.671054 GCCTTTGCCGAGTGCTACA 60.671 57.895 0.00 0.00 42.00 2.74
20 21 0.955919 AAGCCTTTGCCGAGTGCTAC 60.956 55.000 0.00 0.00 42.00 3.58
21 22 0.250727 AAAGCCTTTGCCGAGTGCTA 60.251 50.000 0.00 0.00 42.00 3.49
22 23 1.529244 AAAGCCTTTGCCGAGTGCT 60.529 52.632 0.00 0.00 42.00 4.40
23 24 1.372128 CAAAGCCTTTGCCGAGTGC 60.372 57.895 3.91 0.00 38.69 4.40
24 25 4.950744 CAAAGCCTTTGCCGAGTG 57.049 55.556 3.91 0.00 38.69 3.51
35 36 1.378124 TTATAACCGCCGGCAAAGCC 61.378 55.000 28.98 0.00 46.75 4.35
36 37 0.028902 CTTATAACCGCCGGCAAAGC 59.971 55.000 28.98 0.00 0.00 3.51
37 38 0.028902 GCTTATAACCGCCGGCAAAG 59.971 55.000 28.98 17.06 0.00 2.77
38 39 1.378124 GGCTTATAACCGCCGGCAAA 61.378 55.000 28.98 8.49 36.45 3.68
39 40 1.820481 GGCTTATAACCGCCGGCAA 60.820 57.895 28.98 11.09 36.45 4.52
40 41 2.203098 GGCTTATAACCGCCGGCA 60.203 61.111 28.98 7.02 36.45 5.69
44 45 0.384309 GCAAAGGGCTTATAACCGCC 59.616 55.000 7.12 7.12 45.55 6.13
45 46 0.384309 GGCAAAGGGCTTATAACCGC 59.616 55.000 0.00 0.00 44.01 5.68
46 47 0.661020 CGGCAAAGGGCTTATAACCG 59.339 55.000 0.00 0.00 44.01 4.44
47 48 1.674441 GTCGGCAAAGGGCTTATAACC 59.326 52.381 0.00 0.00 44.01 2.85
48 49 2.354821 CAGTCGGCAAAGGGCTTATAAC 59.645 50.000 0.00 0.00 44.01 1.89
49 50 2.026636 ACAGTCGGCAAAGGGCTTATAA 60.027 45.455 0.00 0.00 44.01 0.98
50 51 1.557832 ACAGTCGGCAAAGGGCTTATA 59.442 47.619 0.00 0.00 44.01 0.98
51 52 0.328258 ACAGTCGGCAAAGGGCTTAT 59.672 50.000 0.00 0.00 44.01 1.73
52 53 0.321298 GACAGTCGGCAAAGGGCTTA 60.321 55.000 0.00 0.00 44.01 3.09
53 54 1.600916 GACAGTCGGCAAAGGGCTT 60.601 57.895 0.00 0.00 44.01 4.35
54 55 2.032681 GACAGTCGGCAAAGGGCT 59.967 61.111 0.00 0.00 44.01 5.19
55 56 2.032681 AGACAGTCGGCAAAGGGC 59.967 61.111 0.00 0.00 43.74 5.19
56 57 1.071471 ACAGACAGTCGGCAAAGGG 59.929 57.895 0.00 0.00 0.00 3.95
57 58 1.230635 CCACAGACAGTCGGCAAAGG 61.231 60.000 0.00 0.00 0.00 3.11
58 59 1.845809 GCCACAGACAGTCGGCAAAG 61.846 60.000 11.91 0.00 41.29 2.77
59 60 1.891919 GCCACAGACAGTCGGCAAA 60.892 57.895 11.91 0.00 41.29 3.68
60 61 2.280797 GCCACAGACAGTCGGCAA 60.281 61.111 11.91 0.00 41.29 4.52
61 62 3.545574 TGCCACAGACAGTCGGCA 61.546 61.111 14.75 14.75 45.66 5.69
62 63 3.044305 GTGCCACAGACAGTCGGC 61.044 66.667 10.28 10.28 41.71 5.54
63 64 1.373497 GAGTGCCACAGACAGTCGG 60.373 63.158 0.00 0.00 0.00 4.79
64 65 4.251760 GAGTGCCACAGACAGTCG 57.748 61.111 0.00 0.00 0.00 4.18
65 66 1.373497 CCGAGTGCCACAGACAGTC 60.373 63.158 0.00 0.00 34.71 3.51
66 67 2.737180 CCGAGTGCCACAGACAGT 59.263 61.111 0.00 0.00 0.00 3.55
67 68 2.740055 GCCGAGTGCCACAGACAG 60.740 66.667 0.00 0.00 0.00 3.51
68 69 4.662961 CGCCGAGTGCCACAGACA 62.663 66.667 0.00 0.00 36.24 3.41
69 70 2.558554 ATACGCCGAGTGCCACAGAC 62.559 60.000 0.00 0.00 36.24 3.51
70 71 1.033202 TATACGCCGAGTGCCACAGA 61.033 55.000 0.00 0.00 36.24 3.41
71 72 0.179121 TTATACGCCGAGTGCCACAG 60.179 55.000 0.00 0.00 36.24 3.66
72 73 0.458889 GTTATACGCCGAGTGCCACA 60.459 55.000 0.00 0.00 36.24 4.17
73 74 0.179119 AGTTATACGCCGAGTGCCAC 60.179 55.000 0.00 0.00 36.24 5.01
74 75 1.335810 CTAGTTATACGCCGAGTGCCA 59.664 52.381 0.00 0.00 36.24 4.92
75 76 1.605710 TCTAGTTATACGCCGAGTGCC 59.394 52.381 0.00 0.00 36.24 5.01
76 77 3.555917 ATCTAGTTATACGCCGAGTGC 57.444 47.619 0.00 0.00 0.00 4.40
77 78 4.023450 TGGAATCTAGTTATACGCCGAGTG 60.023 45.833 0.00 0.00 0.00 3.51
78 79 4.139786 TGGAATCTAGTTATACGCCGAGT 58.860 43.478 0.00 0.00 0.00 4.18
79 80 4.215827 ACTGGAATCTAGTTATACGCCGAG 59.784 45.833 0.00 0.00 0.00 4.63
80 81 4.139786 ACTGGAATCTAGTTATACGCCGA 58.860 43.478 0.00 0.00 0.00 5.54
81 82 4.500603 ACTGGAATCTAGTTATACGCCG 57.499 45.455 0.00 0.00 0.00 6.46
82 83 6.380190 CACTACTGGAATCTAGTTATACGCC 58.620 44.000 4.22 0.00 0.00 5.68
83 84 6.380190 CCACTACTGGAATCTAGTTATACGC 58.620 44.000 4.22 0.00 40.55 4.42
84 85 6.380190 GCCACTACTGGAATCTAGTTATACG 58.620 44.000 4.22 0.00 40.55 3.06
85 86 6.569994 CGGCCACTACTGGAATCTAGTTATAC 60.570 46.154 4.22 0.00 40.55 1.47
86 87 5.475909 CGGCCACTACTGGAATCTAGTTATA 59.524 44.000 4.22 0.00 40.55 0.98
87 88 4.281182 CGGCCACTACTGGAATCTAGTTAT 59.719 45.833 4.22 0.00 40.55 1.89
88 89 3.635373 CGGCCACTACTGGAATCTAGTTA 59.365 47.826 4.22 0.00 40.55 2.24
89 90 2.431057 CGGCCACTACTGGAATCTAGTT 59.569 50.000 4.22 0.00 40.55 2.24
90 91 2.032620 CGGCCACTACTGGAATCTAGT 58.967 52.381 2.24 4.36 40.55 2.57
91 92 1.341531 CCGGCCACTACTGGAATCTAG 59.658 57.143 2.24 0.00 40.55 2.43
92 93 1.063492 TCCGGCCACTACTGGAATCTA 60.063 52.381 2.24 0.00 42.29 1.98
93 94 0.325296 TCCGGCCACTACTGGAATCT 60.325 55.000 2.24 0.00 42.29 2.40
94 95 0.105039 CTCCGGCCACTACTGGAATC 59.895 60.000 2.24 0.00 44.58 2.52
95 96 1.338136 CCTCCGGCCACTACTGGAAT 61.338 60.000 2.24 0.00 44.58 3.01
96 97 1.987855 CCTCCGGCCACTACTGGAA 60.988 63.158 2.24 0.00 44.58 3.53
97 98 2.363795 CCTCCGGCCACTACTGGA 60.364 66.667 2.24 0.00 43.03 3.86
98 99 1.550130 TTTCCTCCGGCCACTACTGG 61.550 60.000 2.24 0.00 41.13 4.00
99 100 0.323629 TTTTCCTCCGGCCACTACTG 59.676 55.000 2.24 0.00 0.00 2.74
100 101 1.286248 ATTTTCCTCCGGCCACTACT 58.714 50.000 2.24 0.00 0.00 2.57
101 102 2.994186 TATTTTCCTCCGGCCACTAC 57.006 50.000 2.24 0.00 0.00 2.73
102 103 5.091552 AGATATATTTTCCTCCGGCCACTA 58.908 41.667 2.24 0.00 0.00 2.74
103 104 3.910627 AGATATATTTTCCTCCGGCCACT 59.089 43.478 2.24 0.00 0.00 4.00
104 105 4.287766 AGATATATTTTCCTCCGGCCAC 57.712 45.455 2.24 0.00 0.00 5.01
105 106 4.993705 AAGATATATTTTCCTCCGGCCA 57.006 40.909 2.24 0.00 0.00 5.36
106 107 6.051179 AGTAAGATATATTTTCCTCCGGCC 57.949 41.667 0.00 0.00 0.00 6.13
107 108 7.040494 GGTAGTAAGATATATTTTCCTCCGGC 58.960 42.308 0.00 0.00 0.00 6.13
108 109 8.130671 TGGTAGTAAGATATATTTTCCTCCGG 57.869 38.462 0.00 0.00 0.00 5.14
188 189 5.714806 ACGTGGAATTCCTATGGACATTTTT 59.285 36.000 24.73 0.00 36.82 1.94
204 205 4.079446 CACCAGCCAACGTGGAAT 57.921 55.556 8.04 0.00 40.96 3.01
242 247 6.072838 TCAGATTCAGTCATCTTGAGTTTTGC 60.073 38.462 0.00 0.00 30.50 3.68
248 253 7.333672 TGAATGTTCAGATTCAGTCATCTTGAG 59.666 37.037 0.00 0.00 37.41 3.02
324 329 4.142600 GGAACTCACGAAAAGATTGGATGG 60.143 45.833 0.00 0.00 0.00 3.51
387 392 0.386476 CCCCAATCGATCGGACGTAA 59.614 55.000 16.41 0.00 34.70 3.18
411 416 7.761038 AAAGTACAAAAGATAGTTGGGAAGG 57.239 36.000 0.00 0.00 0.00 3.46
475 480 0.468029 CACCTGCCCATATGGAACCC 60.468 60.000 24.00 8.76 37.39 4.11
570 621 1.114627 TCAGCATGCTACGATCCTGT 58.885 50.000 22.19 0.00 34.76 4.00
599 655 3.933332 CCGCCTTATTATTCTCCGATTCC 59.067 47.826 0.00 0.00 0.00 3.01
623 683 0.250513 GAGATCACCACCAGTCCACC 59.749 60.000 0.00 0.00 0.00 4.61
624 684 1.205893 GAGAGATCACCACCAGTCCAC 59.794 57.143 0.00 0.00 0.00 4.02
625 685 1.203174 TGAGAGATCACCACCAGTCCA 60.203 52.381 0.00 0.00 0.00 4.02
626 686 1.205893 GTGAGAGATCACCACCAGTCC 59.794 57.143 0.00 0.00 34.74 3.85
627 687 1.135257 CGTGAGAGATCACCACCAGTC 60.135 57.143 0.00 0.00 37.33 3.51
628 688 0.891373 CGTGAGAGATCACCACCAGT 59.109 55.000 0.00 0.00 37.33 4.00
629 689 0.891373 ACGTGAGAGATCACCACCAG 59.109 55.000 0.00 0.00 37.33 4.00
630 690 0.603065 CACGTGAGAGATCACCACCA 59.397 55.000 10.90 0.00 37.33 4.17
714 774 0.250295 CGTGTCTGCCAGGGAGAAAA 60.250 55.000 13.20 0.99 0.00 2.29
729 789 7.345392 TCCTACCCTTTAGTATTTTATCCGTGT 59.655 37.037 0.00 0.00 0.00 4.49
1105 1207 0.098025 AAGTTGAACACCGCGTTGTG 59.902 50.000 10.96 12.19 38.19 3.33
2386 5529 8.640091 TGAATGATTTGAAGATCTTCTACTCG 57.360 34.615 30.45 0.00 40.14 4.18
2437 5581 5.181748 TGCCAGCTCTAGATCTTCTTTTTC 58.818 41.667 0.00 0.00 0.00 2.29
2491 5658 1.433053 TTTGTTGGGCGTGTCAGTCG 61.433 55.000 0.00 0.00 0.00 4.18
2540 5723 1.220529 ACGTGCATCAACAGTGTCAG 58.779 50.000 0.00 0.00 0.00 3.51
2541 5724 1.597195 GAACGTGCATCAACAGTGTCA 59.403 47.619 0.00 0.00 0.00 3.58
2908 6571 9.620660 GGAAAACTCAAGCTCGAATAAAATAAA 57.379 29.630 0.00 0.00 0.00 1.40
2915 6583 4.280436 TGGGAAAACTCAAGCTCGAATA 57.720 40.909 0.00 0.00 0.00 1.75
3008 6689 6.575162 AACAATTTATTCGAGAGTTGCCTT 57.425 33.333 0.00 0.00 0.00 4.35
3037 6718 2.202756 GTAAGTCGCTCCGGGCAG 60.203 66.667 14.17 0.77 41.91 4.85
3383 7089 2.514592 GCGAATGGGCTAGCTGCA 60.515 61.111 15.72 0.00 45.15 4.41
3409 7116 0.899717 ACCAATGCTCGGCAACCAAT 60.900 50.000 2.68 0.00 43.62 3.16
3410 7117 1.112315 AACCAATGCTCGGCAACCAA 61.112 50.000 2.68 0.00 43.62 3.67
3411 7118 1.530419 AACCAATGCTCGGCAACCA 60.530 52.632 2.68 0.00 43.62 3.67
3412 7119 1.080569 CAACCAATGCTCGGCAACC 60.081 57.895 2.68 0.00 43.62 3.77
3413 7120 4.557942 CAACCAATGCTCGGCAAC 57.442 55.556 2.68 0.00 43.62 4.17
3422 7129 3.609214 GACCACGCGGCAACCAATG 62.609 63.158 12.47 0.00 34.57 2.82
3423 7130 3.361977 GACCACGCGGCAACCAAT 61.362 61.111 12.47 0.00 34.57 3.16
3428 7135 2.357760 GTAAGGACCACGCGGCAA 60.358 61.111 12.47 0.00 34.57 4.52
3462 7169 5.569059 CGCACTTTCATTGTCTGGTATTTTC 59.431 40.000 0.00 0.00 0.00 2.29
3463 7170 5.460646 CGCACTTTCATTGTCTGGTATTTT 58.539 37.500 0.00 0.00 0.00 1.82
3470 7177 0.235665 ACGCGCACTTTCATTGTCTG 59.764 50.000 5.73 0.00 0.00 3.51
3492 7199 0.393132 TTTGGAATGTATGGGCGCGA 60.393 50.000 12.10 0.00 0.00 5.87
3576 7288 2.095919 GTCAATGGTTGCGGACTGTTAC 60.096 50.000 0.00 0.00 0.00 2.50
3657 7369 2.254546 ACTGACGTTGAGCATCCAAA 57.745 45.000 0.00 0.00 0.00 3.28
3671 7383 5.751243 TTTGTGCTAGGAAAGAAACTGAC 57.249 39.130 0.00 0.00 0.00 3.51
3717 7429 4.037565 GTGTTTTTCTTCTTCGGGATTGGT 59.962 41.667 0.00 0.00 0.00 3.67
3748 7460 5.663106 ACTATGAGGTACCATCACAGACAAT 59.337 40.000 19.97 6.62 0.00 2.71
3767 7479 3.455910 TCCTCCCTTGGATGTCAACTATG 59.544 47.826 0.00 0.00 0.00 2.23
3778 7490 4.329638 TTTTGCATATTCCTCCCTTGGA 57.670 40.909 0.00 0.00 0.00 3.53
3806 7518 7.147846 TGCATCTATATCATATCGCAAGGAAGA 60.148 37.037 0.00 0.00 38.47 2.87
3811 7523 8.194433 AGTTTGCATCTATATCATATCGCAAG 57.806 34.615 0.00 0.00 39.10 4.01


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

AutoCloner maintained by Alex Coulton.