Multiple sequence alignment - TraesCS7A01G265700

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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 TraesCS7A01G265700 chr7A 100.000 6033 0 0 1 6033 266982214 266976182 0.000000e+00 11141
1 TraesCS7A01G265700 chr7A 89.860 286 27 2 3371 3655 697199464 697199180 3.440000e-97 366
2 TraesCS7A01G265700 chr7A 89.510 286 28 2 3371 3655 697176854 697176570 1.600000e-95 361
3 TraesCS7A01G265700 chr7A 91.228 114 6 2 5065 5177 27488178 27488288 1.050000e-32 152
4 TraesCS7A01G265700 chr7D 95.146 2122 68 17 1773 3864 253151098 253153214 0.000000e+00 3315
5 TraesCS7A01G265700 chr7D 93.797 2144 99 17 3897 6024 253153211 253155336 0.000000e+00 3192
6 TraesCS7A01G265700 chr7D 92.849 1762 90 16 1 1746 253149360 253151101 0.000000e+00 2523
7 TraesCS7A01G265700 chr7B 94.358 2127 86 13 3896 6015 230211522 230213621 0.000000e+00 3232
8 TraesCS7A01G265700 chr7B 94.010 1419 69 5 1404 2808 230209132 230210548 0.000000e+00 2135
9 TraesCS7A01G265700 chr7B 95.344 988 28 9 2886 3862 230210544 230211524 0.000000e+00 1554
10 TraesCS7A01G265700 chr7B 94.505 819 24 7 696 1502 230208313 230209122 0.000000e+00 1243
11 TraesCS7A01G265700 chr7B 88.707 549 55 5 148 693 230206434 230206978 0.000000e+00 664
12 TraesCS7A01G265700 chr7B 89.879 247 18 6 4453 4699 77187227 77187466 1.630000e-80 311
13 TraesCS7A01G265700 chr7B 86.920 237 31 0 4746 4982 77187465 77187701 3.580000e-67 267
14 TraesCS7A01G265700 chr7B 92.000 75 4 2 5083 5156 77187713 77187786 2.970000e-18 104
15 TraesCS7A01G265700 chr4A 93.293 328 16 4 12 337 121510314 121510637 4.230000e-131 479
16 TraesCS7A01G265700 chr4A 93.069 101 5 2 5082 5181 703413136 703413235 4.870000e-31 147
17 TraesCS7A01G265700 chr6D 91.445 339 23 4 1 337 337237573 337237907 1.530000e-125 460
18 TraesCS7A01G265700 chr2B 91.202 341 22 6 1 338 478200527 478200862 1.980000e-124 457
19 TraesCS7A01G265700 chr4B 91.793 329 20 5 13 338 426089304 426088980 9.220000e-123 451
20 TraesCS7A01G265700 chr4B 88.192 271 29 1 4716 4983 322656637 322656367 2.710000e-83 320
21 TraesCS7A01G265700 chr4B 90.678 118 6 2 5065 5181 322656372 322656259 1.050000e-32 152
22 TraesCS7A01G265700 chr4B 88.136 118 10 2 5065 5181 621863678 621863564 2.930000e-28 137
23 TraesCS7A01G265700 chr5A 90.855 339 26 3 1 337 536338402 536338737 3.320000e-122 449
24 TraesCS7A01G265700 chr5A 90.517 232 16 5 4468 4699 37615290 37615515 9.830000e-78 302
25 TraesCS7A01G265700 chr5A 88.584 219 21 2 4746 4960 37615514 37615732 4.640000e-66 263
26 TraesCS7A01G265700 chr4D 91.265 332 21 6 11 339 126901020 126901346 4.290000e-121 446
27 TraesCS7A01G265700 chr4D 90.058 342 27 5 1 339 359207589 359207252 2.580000e-118 436
28 TraesCS7A01G265700 chr1D 91.034 290 24 2 3367 3655 437805196 437805484 2.040000e-104 390
29 TraesCS7A01G265700 chrUn 90.345 290 26 2 3367 3655 256116838 256116550 4.410000e-101 379
30 TraesCS7A01G265700 chrUn 90.345 290 26 2 3367 3655 356149657 356149945 4.410000e-101 379
31 TraesCS7A01G265700 chrUn 87.562 201 20 4 2448 2646 94388228 94388031 1.690000e-55 228
32 TraesCS7A01G265700 chrUn 87.500 200 20 4 2448 2645 94444908 94444712 6.080000e-55 226
33 TraesCS7A01G265700 chrUn 87.000 200 21 4 2448 2645 94309456 94309260 2.830000e-53 220
34 TraesCS7A01G265700 chrUn 87.000 200 21 4 2448 2645 94363579 94363383 2.830000e-53 220
35 TraesCS7A01G265700 chrUn 87.000 200 21 5 2448 2645 94412990 94412794 2.830000e-53 220
36 TraesCS7A01G265700 chrUn 86.452 155 17 3 2448 2601 470498393 470498242 3.740000e-37 167
37 TraesCS7A01G265700 chr5B 90.345 290 26 2 3367 3655 660878168 660878456 4.410000e-101 379
38 TraesCS7A01G265700 chr5B 90.345 290 26 2 3367 3655 660924117 660924405 4.410000e-101 379
39 TraesCS7A01G265700 chr3B 93.617 94 6 0 5597 5690 380513194 380513287 2.270000e-29 141
40 TraesCS7A01G265700 chr3B 90.099 101 8 2 5082 5181 573600358 573600457 4.910000e-26 130
41 TraesCS7A01G265700 chr6B 88.136 118 10 2 5065 5181 712640033 712640147 2.930000e-28 137


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 TraesCS7A01G265700 chr7A 266976182 266982214 6032 True 11141.000000 11141 100.000000 1 6033 1 chr7A.!!$R1 6032
1 TraesCS7A01G265700 chr7D 253149360 253155336 5976 False 3010.000000 3315 93.930667 1 6024 3 chr7D.!!$F1 6023
2 TraesCS7A01G265700 chr7B 230206434 230213621 7187 False 1765.600000 3232 93.384800 148 6015 5 chr7B.!!$F2 5867
3 TraesCS7A01G265700 chr7B 77187227 77187786 559 False 227.333333 311 89.599667 4453 5156 3 chr7B.!!$F1 703

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
43 44 0.111253 AGTGGCTGAGGGTTTTGGAG 59.889 55.0 0.00 0.00 0.0 3.86 F
370 373 0.680280 TCTTCTCGCCGCCTAGTTCT 60.680 55.0 0.00 0.00 0.0 3.01 F
442 445 0.833287 CTCCCGATTCACCACCATCT 59.167 55.0 0.00 0.00 0.0 2.90 F
2106 3567 0.392863 TTGCATGCGTCATAGGCAGT 60.393 50.0 14.09 0.00 42.6 4.40 F
2920 4396 1.419381 TCATTACGGGGAGCTGCATA 58.581 50.0 7.79 0.00 0.0 3.14 F
3880 5377 0.174389 ATGTGTCAGCGCTGTCTAGG 59.826 55.0 34.70 10.73 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 3002 2.591753 CATGCCCTGACGTCCCAT 59.408 61.111 14.12 7.61 0.0 4.00 R
2082 3543 2.096069 GCCTATGACGCATGCAATACAG 60.096 50.000 19.57 8.45 0.0 2.74 R
2437 3912 2.478879 CCACCTGTCACGTTTCCAAAAC 60.479 50.000 0.00 0.00 0.0 2.43 R
3865 5362 0.458716 GAACCCTAGACAGCGCTGAC 60.459 60.000 42.03 35.06 0.0 3.51 R
4108 5605 0.534203 GACAAGTGCCAAAGGACGGA 60.534 55.000 0.00 0.00 0.0 4.69 R
5356 6865 0.391597 AAGAACGAGCGGAGACCAAA 59.608 50.000 0.00 0.00 0.0 3.28 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
29 30 1.560505 ATGGAATGTGGGAAAGTGGC 58.439 50.000 0.00 0.00 0.00 5.01
43 44 0.111253 AGTGGCTGAGGGTTTTGGAG 59.889 55.000 0.00 0.00 0.00 3.86
61 62 4.592942 TGGAGCAATATCTTCAAGCACTT 58.407 39.130 0.00 0.00 0.00 3.16
78 79 3.748048 GCACTTGAGCAACTAAGTCATGA 59.252 43.478 0.00 0.00 35.08 3.07
80 81 5.447010 GCACTTGAGCAACTAAGTCATGATC 60.447 44.000 0.00 0.00 35.08 2.92
91 92 9.903682 CAACTAAGTCATGATCAAAAACTCATT 57.096 29.630 0.00 0.00 29.74 2.57
148 149 6.599244 TCAATGTGATCTTGGATCACTTAACC 59.401 38.462 28.84 11.95 46.25 2.85
153 154 7.286546 TGTGATCTTGGATCACTTAACCAAAAA 59.713 33.333 28.84 11.63 46.25 1.94
154 155 8.306761 GTGATCTTGGATCACTTAACCAAAAAT 58.693 33.333 24.66 0.00 43.62 1.82
155 156 9.527157 TGATCTTGGATCACTTAACCAAAAATA 57.473 29.630 6.17 0.00 42.02 1.40
200 201 7.658575 GCCAATATGTTTCCATAGCATTTTGAT 59.341 33.333 0.00 0.00 36.99 2.57
354 357 5.480422 ACTTTCAAAAGTCAACACCCTTCTT 59.520 36.000 2.30 0.00 45.65 2.52
365 368 2.423898 CCCTTCTTCTCGCCGCCTA 61.424 63.158 0.00 0.00 0.00 3.93
370 373 0.680280 TCTTCTCGCCGCCTAGTTCT 60.680 55.000 0.00 0.00 0.00 3.01
382 385 1.202463 CCTAGTTCTGCTCACCATCGG 60.202 57.143 0.00 0.00 0.00 4.18
405 408 1.395954 CTATGGTTCTCGTCGTCGTCA 59.604 52.381 1.33 0.00 38.33 4.35
442 445 0.833287 CTCCCGATTCACCACCATCT 59.167 55.000 0.00 0.00 0.00 2.90
446 449 1.012086 CGATTCACCACCATCTGCTG 58.988 55.000 0.00 0.00 0.00 4.41
475 478 4.740822 GGCGCCCACAACCCTCAT 62.741 66.667 18.11 0.00 0.00 2.90
490 493 0.882042 CTCATCGGCCAATCCTTCGG 60.882 60.000 2.24 0.00 0.00 4.30
523 526 3.430862 GAGCACCGCATTGCCGAA 61.431 61.111 2.41 0.00 44.14 4.30
555 558 7.973388 CGTCATTCTCTCTTCATCTCTTTTAGT 59.027 37.037 0.00 0.00 0.00 2.24
585 588 6.872920 ACGTGTTGGCATGGATATTTATTTT 58.127 32.000 0.00 0.00 35.99 1.82
626 629 5.417580 AGTGCTAGGTTTTCTGTCAAAAACA 59.582 36.000 17.45 0.00 46.28 2.83
659 662 6.053113 GAGAATCAGTGCGATCTGTTACGC 62.053 50.000 0.00 0.00 44.89 4.42
664 668 2.202690 CGATCTGTTACGCCCGCA 60.203 61.111 0.00 0.00 0.00 5.69
703 2039 3.128068 CCGGCACCAATTCTTTAACCTAC 59.872 47.826 0.00 0.00 0.00 3.18
715 2051 6.661740 TCTTTAACCTACCCCCAAATGTAT 57.338 37.500 0.00 0.00 0.00 2.29
747 2087 6.846283 GCAATTAACTGCATCGTAACTACATC 59.154 38.462 3.59 0.00 42.17 3.06
769 2110 3.414269 TCAGCATCATTTGTGAAGAGCA 58.586 40.909 0.00 0.00 0.00 4.26
919 2262 4.814041 GGCCTCCTCCTCCCTGCT 62.814 72.222 0.00 0.00 0.00 4.24
956 2301 1.271325 TGAAGCGGAGGCAAATTGAGA 60.271 47.619 0.00 0.00 43.41 3.27
977 2322 1.612739 AGACGAAACCCTCCTCCCC 60.613 63.158 0.00 0.00 0.00 4.81
978 2323 1.612739 GACGAAACCCTCCTCCCCT 60.613 63.158 0.00 0.00 0.00 4.79
979 2324 1.151877 ACGAAACCCTCCTCCCCTT 60.152 57.895 0.00 0.00 0.00 3.95
1306 2651 3.675698 CGTCAAGCAGGTAGACTCTTTTC 59.324 47.826 0.00 0.00 0.00 2.29
1439 2900 4.413189 TGGAGATGGCCTCTGATTTGATTA 59.587 41.667 3.32 0.00 41.66 1.75
1475 2936 5.109210 TCCATAACTTCATCACACATCGAC 58.891 41.667 0.00 0.00 0.00 4.20
1541 3002 3.998913 TGTTGGCAATAGAGATGACCA 57.001 42.857 1.92 0.00 0.00 4.02
1570 3031 1.619827 CAGGGCATGGCTTTCTTGAAA 59.380 47.619 19.78 0.00 0.00 2.69
1589 3050 7.958567 TCTTGAAAATTTGTATACGGTTAAGCG 59.041 33.333 24.36 24.36 0.00 4.68
1769 3230 8.135586 TGGGTGGGGTTAGATATAAGATGATAT 58.864 37.037 0.00 0.00 0.00 1.63
1770 3231 8.652290 GGGTGGGGTTAGATATAAGATGATATC 58.348 40.741 0.00 0.00 38.56 1.63
1805 3266 4.320641 GGTATTTTTGTAAGCGGCAACTCA 60.321 41.667 1.45 0.00 0.00 3.41
1866 3327 5.913137 TTCTGGATAAAAATGGCACGAAT 57.087 34.783 0.00 0.00 0.00 3.34
1956 3417 9.988815 AGAGAGATAAATAAGATTTGCGTGTAT 57.011 29.630 0.00 0.00 0.00 2.29
1970 3431 4.252878 TGCGTGTATGTCAAGTCATCAAT 58.747 39.130 0.00 0.00 0.00 2.57
2082 3543 3.682858 TCTTTCTGTAGTATTGCAACCGC 59.317 43.478 0.00 0.00 39.24 5.68
2106 3567 0.392863 TTGCATGCGTCATAGGCAGT 60.393 50.000 14.09 0.00 42.60 4.40
2287 3762 4.865776 TGCACCCTTTCTGTTTTTATTCG 58.134 39.130 0.00 0.00 0.00 3.34
2345 3820 9.696917 TGTGTACTAGCTTTACCTTTTTACTAC 57.303 33.333 0.00 0.00 0.00 2.73
2660 4135 7.938140 AATTTAGCAATAGAAGTAGGCACAA 57.062 32.000 0.00 0.00 0.00 3.33
2715 4190 9.300681 TGATATAGCCATAATTTTCTTCTTGGG 57.699 33.333 0.00 0.00 0.00 4.12
2804 4279 9.575783 GCAGGTAATCTTCTACTATATGTAAGC 57.424 37.037 0.00 0.00 0.00 3.09
2859 4335 7.432350 AAAATGTTGCTTTGACACTTTGAAA 57.568 28.000 0.00 0.00 26.84 2.69
2879 4355 8.999220 TTGAAATATGAAATGTGCTTGCATTA 57.001 26.923 0.00 0.00 38.03 1.90
2920 4396 1.419381 TCATTACGGGGAGCTGCATA 58.581 50.000 7.79 0.00 0.00 3.14
2936 4412 3.156293 TGCATACCATTCTTTGTGTGCT 58.844 40.909 11.60 0.00 46.06 4.40
2997 4473 3.104843 ACTTCTCCAATATCAGCGAGC 57.895 47.619 0.00 0.00 0.00 5.03
3141 4618 4.330074 GCATTACGTACATCAACAGAGCTT 59.670 41.667 0.00 0.00 0.00 3.74
3181 4658 8.670135 CCAAATCGTCATATTTACCTGTTTACA 58.330 33.333 0.00 0.00 0.00 2.41
3183 4660 9.444600 AAATCGTCATATTTACCTGTTTACACT 57.555 29.630 0.00 0.00 0.00 3.55
3212 4689 5.627499 TTGGATATGCATATTCTTTCCGC 57.373 39.130 22.81 7.67 0.00 5.54
3233 4712 4.662145 GCTATTGACAGCGCAAGTAATTT 58.338 39.130 11.47 0.00 41.68 1.82
3601 5098 5.886960 ATGTCATGCTTCTGAAACTTACC 57.113 39.130 0.00 0.00 0.00 2.85
3746 5243 3.500448 TGGGTGCAATGTTGAAGACTA 57.500 42.857 0.00 0.00 0.00 2.59
3862 5359 9.627123 TGCTTTTTGCTAATAAGGTCTGTATAT 57.373 29.630 0.00 0.00 43.37 0.86
3863 5360 9.884465 GCTTTTTGCTAATAAGGTCTGTATATG 57.116 33.333 0.00 0.00 38.95 1.78
3866 5363 9.899661 TTTTGCTAATAAGGTCTGTATATGTGT 57.100 29.630 0.00 0.00 0.00 3.72
3867 5364 9.542462 TTTGCTAATAAGGTCTGTATATGTGTC 57.458 33.333 0.00 0.00 0.00 3.67
3868 5365 8.245195 TGCTAATAAGGTCTGTATATGTGTCA 57.755 34.615 0.00 0.00 0.00 3.58
3869 5366 8.360390 TGCTAATAAGGTCTGTATATGTGTCAG 58.640 37.037 0.00 0.00 0.00 3.51
3870 5367 7.329717 GCTAATAAGGTCTGTATATGTGTCAGC 59.670 40.741 0.00 0.00 0.00 4.26
3871 5368 3.717400 AGGTCTGTATATGTGTCAGCG 57.283 47.619 0.00 0.00 0.00 5.18
3872 5369 2.128035 GGTCTGTATATGTGTCAGCGC 58.872 52.381 0.00 0.00 0.00 5.92
3873 5370 2.223829 GGTCTGTATATGTGTCAGCGCT 60.224 50.000 2.64 2.64 0.00 5.92
3874 5371 2.791560 GTCTGTATATGTGTCAGCGCTG 59.208 50.000 31.53 31.53 0.00 5.18
3875 5372 2.427095 TCTGTATATGTGTCAGCGCTGT 59.573 45.455 34.70 19.18 0.00 4.40
3876 5373 2.791560 CTGTATATGTGTCAGCGCTGTC 59.208 50.000 34.70 29.65 0.00 3.51
3877 5374 2.427095 TGTATATGTGTCAGCGCTGTCT 59.573 45.455 34.70 17.26 0.00 3.41
3878 5375 3.630312 TGTATATGTGTCAGCGCTGTCTA 59.370 43.478 34.70 22.29 0.00 2.59
3879 5376 2.851805 TATGTGTCAGCGCTGTCTAG 57.148 50.000 34.70 11.54 0.00 2.43
3880 5377 0.174389 ATGTGTCAGCGCTGTCTAGG 59.826 55.000 34.70 10.73 0.00 3.02
3881 5378 1.153745 GTGTCAGCGCTGTCTAGGG 60.154 63.158 34.70 9.93 39.68 3.53
3882 5379 1.606601 TGTCAGCGCTGTCTAGGGT 60.607 57.895 34.70 0.00 38.97 4.34
3883 5380 1.185618 TGTCAGCGCTGTCTAGGGTT 61.186 55.000 34.70 0.00 38.97 4.11
3884 5381 0.458716 GTCAGCGCTGTCTAGGGTTC 60.459 60.000 34.70 12.36 38.97 3.62
3885 5382 1.517257 CAGCGCTGTCTAGGGTTCG 60.517 63.158 29.24 0.00 38.97 3.95
3886 5383 2.202756 GCGCTGTCTAGGGTTCGG 60.203 66.667 0.00 0.00 38.97 4.30
3887 5384 2.494918 CGCTGTCTAGGGTTCGGG 59.505 66.667 0.00 0.00 32.59 5.14
3888 5385 2.348888 CGCTGTCTAGGGTTCGGGT 61.349 63.158 0.00 0.00 32.59 5.28
3889 5386 1.033746 CGCTGTCTAGGGTTCGGGTA 61.034 60.000 0.00 0.00 32.59 3.69
3890 5387 1.411041 GCTGTCTAGGGTTCGGGTAT 58.589 55.000 0.00 0.00 0.00 2.73
3891 5388 1.761198 GCTGTCTAGGGTTCGGGTATT 59.239 52.381 0.00 0.00 0.00 1.89
3892 5389 2.961062 GCTGTCTAGGGTTCGGGTATTA 59.039 50.000 0.00 0.00 0.00 0.98
3893 5390 3.243670 GCTGTCTAGGGTTCGGGTATTAC 60.244 52.174 0.00 0.00 0.00 1.89
3894 5391 3.956199 CTGTCTAGGGTTCGGGTATTACA 59.044 47.826 0.00 0.00 0.00 2.41
3895 5392 4.352009 TGTCTAGGGTTCGGGTATTACAA 58.648 43.478 0.00 0.00 0.00 2.41
3896 5393 4.964262 TGTCTAGGGTTCGGGTATTACAAT 59.036 41.667 0.00 0.00 0.00 2.71
3897 5394 6.135454 TGTCTAGGGTTCGGGTATTACAATA 58.865 40.000 0.00 0.00 0.00 1.90
3957 5454 6.983906 TGAGTCATATCATAGCTTCTTCCA 57.016 37.500 0.00 0.00 0.00 3.53
4003 5500 7.533900 CGTAAGATATTTTCACACCTGTTTGTG 59.466 37.037 0.00 0.00 44.39 3.33
4108 5605 3.444703 GTCATCTTGACTGCTATCCGT 57.555 47.619 0.45 0.00 43.73 4.69
4109 5606 3.376540 GTCATCTTGACTGCTATCCGTC 58.623 50.000 0.45 0.00 43.73 4.79
4294 5794 7.837202 ATTGGTCATTTCATGTTTTATGCAG 57.163 32.000 0.00 0.00 0.00 4.41
4299 5799 8.385111 GGTCATTTCATGTTTTATGCAGAATTG 58.615 33.333 0.00 0.00 0.00 2.32
4311 5811 9.806203 TTTTATGCAGAATTGGAAGTAATCATG 57.194 29.630 0.00 0.00 0.00 3.07
4355 5858 5.049405 CACAAAACTGTCCTATGTGTTCCTC 60.049 44.000 0.00 0.00 37.27 3.71
4366 5869 3.917329 TGTGTTCCTCGTCTGTCTTAG 57.083 47.619 0.00 0.00 0.00 2.18
4427 5930 3.205338 TCGGTTATCCACTTGCATCATG 58.795 45.455 0.00 0.00 0.00 3.07
4713 6216 9.178758 CAGGTATCTATCATGTACTACAGCATA 57.821 37.037 0.00 0.00 0.00 3.14
4813 6319 0.106819 CTGGAATGAGGCAAGGGAGG 60.107 60.000 0.00 0.00 0.00 4.30
5053 6559 0.893727 GGTACCCTGTTGCCCTGTTG 60.894 60.000 0.00 0.00 0.00 3.33
5160 6666 3.557185 ACATGCGTCAGTATACTGCATTG 59.443 43.478 25.31 19.52 43.24 2.82
5335 6844 8.948631 ATACTACATGTCAACTGATAGGTTTG 57.051 34.615 0.00 0.00 32.69 2.93
5356 6865 2.945668 GTTCTTCACTGGTCTGCAAACT 59.054 45.455 0.00 0.00 0.00 2.66
5358 6867 3.620488 TCTTCACTGGTCTGCAAACTTT 58.380 40.909 0.00 0.00 0.00 2.66
5406 6915 0.539438 TTCGCATTCCCTTTGCTGGT 60.539 50.000 0.00 0.00 37.96 4.00
5423 6932 4.254709 TGCGGTCTTGCTGGTGCT 62.255 61.111 0.00 0.00 40.48 4.40
5427 6936 2.595463 GTCTTGCTGGTGCTGGCA 60.595 61.111 0.00 0.00 40.48 4.92
5543 7052 2.046892 GGAAGCTCTTGCCGCAGA 60.047 61.111 0.00 0.00 40.80 4.26
5559 7068 0.179936 CAGAAGATGGTGGCCTCCTC 59.820 60.000 23.90 17.56 0.00 3.71
5582 7091 2.416244 TTCGCGCTCTCGACTTTGGT 62.416 55.000 5.56 0.00 38.30 3.67
5776 7288 1.661178 CGTAGTACGTGTGCGAGTGTT 60.661 52.381 14.62 0.00 42.00 3.32
5788 7300 0.034059 CGAGTGTTCCTTGCCTGAGT 59.966 55.000 0.00 0.00 0.00 3.41
5823 7335 2.102578 GTATTGGCTTTGGCATCTGGT 58.897 47.619 0.00 0.00 38.08 4.00
5927 7439 2.156051 GACGAAGAACCTGCCGGAGT 62.156 60.000 5.05 0.00 0.00 3.85
5952 7464 1.522668 CTGATGTTTTGGTCGCCTCA 58.477 50.000 0.00 0.00 0.00 3.86
6024 7536 4.114058 CAAACCCAGTTTGCATAGGATG 57.886 45.455 7.22 0.00 44.59 3.51
6025 7537 3.737559 AACCCAGTTTGCATAGGATGA 57.262 42.857 0.00 0.00 0.00 2.92
6026 7538 3.959495 ACCCAGTTTGCATAGGATGAT 57.041 42.857 0.00 0.00 0.00 2.45
6027 7539 3.559069 ACCCAGTTTGCATAGGATGATG 58.441 45.455 0.00 0.00 0.00 3.07
6028 7540 3.202818 ACCCAGTTTGCATAGGATGATGA 59.797 43.478 0.00 0.00 0.00 2.92
6029 7541 4.209538 CCCAGTTTGCATAGGATGATGAA 58.790 43.478 0.00 0.00 0.00 2.57
6030 7542 4.831155 CCCAGTTTGCATAGGATGATGAAT 59.169 41.667 0.00 0.00 0.00 2.57
6031 7543 6.005823 CCCAGTTTGCATAGGATGATGAATA 58.994 40.000 0.00 0.00 0.00 1.75
6032 7544 6.491062 CCCAGTTTGCATAGGATGATGAATAA 59.509 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.094026 GCCACTTTCCCACATTCCATTC 60.094 50.000 0.00 0.00 0.00 2.67
29 30 4.530875 AGATATTGCTCCAAAACCCTCAG 58.469 43.478 0.00 0.00 0.00 3.35
61 62 7.229306 AGTTTTTGATCATGACTTAGTTGCTCA 59.771 33.333 0.00 0.00 0.00 4.26
91 92 7.648770 AGGAAAGCCAATACTATTAAAAGGGA 58.351 34.615 0.00 0.00 36.29 4.20
148 149 8.758715 CAAAAGCTCCAAGACTCTTTATTTTTG 58.241 33.333 0.00 0.59 0.00 2.44
153 154 4.460731 GGCAAAAGCTCCAAGACTCTTTAT 59.539 41.667 0.00 0.00 0.00 1.40
154 155 3.821033 GGCAAAAGCTCCAAGACTCTTTA 59.179 43.478 0.00 0.00 0.00 1.85
155 156 2.625314 GGCAAAAGCTCCAAGACTCTTT 59.375 45.455 0.00 0.00 0.00 2.52
200 201 0.327924 GACATGTGGATGTGGACCCA 59.672 55.000 1.15 0.00 43.22 4.51
297 299 6.428295 TCTCCGGATGGTTTTGGTAATTAAT 58.572 36.000 3.57 0.00 36.30 1.40
298 300 5.817784 TCTCCGGATGGTTTTGGTAATTAA 58.182 37.500 3.57 0.00 36.30 1.40
299 301 5.438698 TCTCCGGATGGTTTTGGTAATTA 57.561 39.130 3.57 0.00 36.30 1.40
354 357 3.064987 GCAGAACTAGGCGGCGAGA 62.065 63.158 25.32 3.53 0.00 4.04
365 368 2.366469 ACCGATGGTGAGCAGAACT 58.634 52.632 0.00 0.00 32.98 3.01
382 385 1.546834 GACGACGAGAACCATAGCAC 58.453 55.000 0.00 0.00 0.00 4.40
385 388 1.395954 TGACGACGACGAGAACCATAG 59.604 52.381 15.32 0.00 42.66 2.23
387 390 0.168348 CTGACGACGACGAGAACCAT 59.832 55.000 15.32 0.00 42.66 3.55
405 408 3.022406 GGAGGTGGTCTATACGTTCACT 58.978 50.000 0.00 0.00 0.00 3.41
459 462 3.134127 GATGAGGGTTGTGGGCGC 61.134 66.667 0.00 0.00 0.00 6.53
490 493 1.583967 CTCACCGACGTCGATCTGC 60.584 63.158 37.65 0.00 43.02 4.26
523 526 4.808414 TGAAGAGAGAATGACGAATGGT 57.192 40.909 0.00 0.00 0.00 3.55
533 536 8.811017 TCACACTAAAAGAGATGAAGAGAGAAT 58.189 33.333 0.00 0.00 0.00 2.40
555 558 0.884259 CCATGCCAACACGTCTCACA 60.884 55.000 0.00 0.00 0.00 3.58
585 588 0.550914 ACTTGCAGGGTTGACTTGGA 59.449 50.000 0.00 0.00 0.00 3.53
626 629 3.335579 GCACTGATTCTCGTTTAACCCT 58.664 45.455 0.00 0.00 0.00 4.34
631 634 4.105486 CAGATCGCACTGATTCTCGTTTA 58.895 43.478 3.24 0.00 39.94 2.01
685 689 4.021229 GGGGGTAGGTTAAAGAATTGGTG 58.979 47.826 0.00 0.00 0.00 4.17
693 697 9.074576 GATAATACATTTGGGGGTAGGTTAAAG 57.925 37.037 0.00 0.00 0.00 1.85
694 2030 8.793720 AGATAATACATTTGGGGGTAGGTTAAA 58.206 33.333 0.00 0.00 0.00 1.52
703 2039 5.867903 TTGCAAGATAATACATTTGGGGG 57.132 39.130 0.00 0.00 0.00 5.40
732 2068 3.706698 TGCTGAGATGTAGTTACGATGC 58.293 45.455 0.00 0.00 0.00 3.91
747 2087 3.439129 TGCTCTTCACAAATGATGCTGAG 59.561 43.478 0.00 0.00 33.85 3.35
769 2110 9.618890 TCTCAAAATATCTCGGATTTTCTTCAT 57.381 29.630 0.00 0.00 34.93 2.57
857 2200 3.835395 ACACCACCAAAACAAAGGAGAAA 59.165 39.130 0.00 0.00 0.00 2.52
858 2201 3.194542 CACACCACCAAAACAAAGGAGAA 59.805 43.478 0.00 0.00 0.00 2.87
859 2202 2.757868 CACACCACCAAAACAAAGGAGA 59.242 45.455 0.00 0.00 0.00 3.71
860 2203 2.159114 CCACACCACCAAAACAAAGGAG 60.159 50.000 0.00 0.00 0.00 3.69
861 2204 1.827969 CCACACCACCAAAACAAAGGA 59.172 47.619 0.00 0.00 0.00 3.36
874 2217 2.626255 TACAAAAGGCGGCCACACCA 62.626 55.000 23.09 0.00 39.03 4.17
918 2261 4.381505 GCTTCAGGTACAAGGAAGAGAGAG 60.382 50.000 18.80 0.00 40.28 3.20
919 2262 3.511934 GCTTCAGGTACAAGGAAGAGAGA 59.488 47.826 18.80 0.00 40.28 3.10
956 2301 1.249469 GGAGGAGGGTTTCGTCTCGT 61.249 60.000 0.00 0.00 39.93 4.18
977 2322 0.548510 GATTGGAGTGGGGAGGGAAG 59.451 60.000 0.00 0.00 0.00 3.46
978 2323 0.121197 AGATTGGAGTGGGGAGGGAA 59.879 55.000 0.00 0.00 0.00 3.97
979 2324 0.326618 GAGATTGGAGTGGGGAGGGA 60.327 60.000 0.00 0.00 0.00 4.20
1541 3002 2.591753 CATGCCCTGACGTCCCAT 59.408 61.111 14.12 7.61 0.00 4.00
1570 3031 5.277634 GGATGCGCTTAACCGTATACAAATT 60.278 40.000 9.73 0.00 34.76 1.82
1614 3075 3.327757 AGAAGCATAACACTGGGAGAACA 59.672 43.478 0.00 0.00 0.00 3.18
1674 3135 5.047306 CCAGAGTACAATCTCACTACCACAA 60.047 44.000 0.00 0.00 36.97 3.33
1676 3137 4.463186 ACCAGAGTACAATCTCACTACCAC 59.537 45.833 0.00 0.00 36.97 4.16
1769 3230 6.403866 ACAAAAATACCATTGCTCAACAGA 57.596 33.333 0.00 0.00 0.00 3.41
1770 3231 7.148755 GCTTACAAAAATACCATTGCTCAACAG 60.149 37.037 0.00 0.00 0.00 3.16
1866 3327 5.279708 CCCAAAATACCACATAACAAGGCAA 60.280 40.000 0.00 0.00 0.00 4.52
1956 3417 5.945191 TCTGCCAAATATTGATGACTTGACA 59.055 36.000 0.00 0.00 0.00 3.58
1970 3431 5.310331 TGGAGGATCACATATCTGCCAAATA 59.690 40.000 0.00 0.00 36.25 1.40
2082 3543 2.096069 GCCTATGACGCATGCAATACAG 60.096 50.000 19.57 8.45 0.00 2.74
2106 3567 9.184523 CATATTACCCTCAAAAGGTGAAACATA 57.815 33.333 0.00 0.00 41.59 2.29
2296 3771 7.816513 CACAGAGTCAATTTCAACTATCTGAGA 59.183 37.037 5.92 0.00 0.00 3.27
2437 3912 2.478879 CCACCTGTCACGTTTCCAAAAC 60.479 50.000 0.00 0.00 0.00 2.43
2568 4043 8.316946 ACATGAGAGTAAACAGAATGATCAAGA 58.683 33.333 0.00 0.00 39.69 3.02
2571 4046 9.538508 CATACATGAGAGTAAACAGAATGATCA 57.461 33.333 0.00 0.00 39.69 2.92
2578 4053 9.778741 AAAGAAACATACATGAGAGTAAACAGA 57.221 29.630 0.00 0.00 0.00 3.41
2805 4280 9.986833 CATTTTCGAATGTGTCAATAATCTGTA 57.013 29.630 0.00 0.00 0.00 2.74
2806 4281 7.970061 CCATTTTCGAATGTGTCAATAATCTGT 59.030 33.333 0.00 0.00 0.00 3.41
2807 4282 8.183536 TCCATTTTCGAATGTGTCAATAATCTG 58.816 33.333 0.00 0.00 0.00 2.90
2808 4283 8.279970 TCCATTTTCGAATGTGTCAATAATCT 57.720 30.769 0.00 0.00 0.00 2.40
2809 4284 8.909708 TTCCATTTTCGAATGTGTCAATAATC 57.090 30.769 0.00 0.00 0.00 1.75
2810 4285 9.703892 TTTTCCATTTTCGAATGTGTCAATAAT 57.296 25.926 0.00 0.00 0.00 1.28
2811 4286 9.534565 TTTTTCCATTTTCGAATGTGTCAATAA 57.465 25.926 0.00 0.00 0.00 1.40
2850 4326 7.095565 TGCAAGCACATTTCATATTTCAAAGTG 60.096 33.333 0.00 0.00 0.00 3.16
2859 4335 9.203421 CATCAATAATGCAAGCACATTTCATAT 57.797 29.630 0.00 0.00 40.64 1.78
3046 4523 1.004560 CCACTGTCATCGGCACTGT 60.005 57.895 0.00 0.00 0.00 3.55
3090 4567 7.420800 CAGGCAACAAGGATCTATCAATTAAC 58.579 38.462 0.00 0.00 41.41 2.01
3141 4618 6.693466 TGACGATTTGGTTGAGATACTTACA 58.307 36.000 0.00 0.00 0.00 2.41
3233 4712 7.175467 AGCAGCAATATAAAGTATATGCAAGCA 59.825 33.333 12.89 0.00 35.01 3.91
3306 4785 3.888583 TGCTTTATCACTGCATGGATGA 58.111 40.909 9.77 0.00 0.00 2.92
3553 5046 7.227156 AGCAAATAGAAGATTCCACGGATTAT 58.773 34.615 0.00 0.00 0.00 1.28
3862 5359 1.586541 CCTAGACAGCGCTGACACA 59.413 57.895 42.03 25.28 0.00 3.72
3863 5360 1.153745 CCCTAGACAGCGCTGACAC 60.154 63.158 42.03 29.06 0.00 3.67
3864 5361 1.185618 AACCCTAGACAGCGCTGACA 61.186 55.000 42.03 24.05 0.00 3.58
3865 5362 0.458716 GAACCCTAGACAGCGCTGAC 60.459 60.000 42.03 35.06 0.00 3.51
3866 5363 1.890894 GAACCCTAGACAGCGCTGA 59.109 57.895 42.03 20.48 0.00 4.26
3867 5364 1.517257 CGAACCCTAGACAGCGCTG 60.517 63.158 34.89 34.89 0.00 5.18
3868 5365 2.711922 CCGAACCCTAGACAGCGCT 61.712 63.158 2.64 2.64 0.00 5.92
3869 5366 2.202756 CCGAACCCTAGACAGCGC 60.203 66.667 0.00 0.00 0.00 5.92
3870 5367 1.033746 TACCCGAACCCTAGACAGCG 61.034 60.000 0.00 0.00 0.00 5.18
3871 5368 1.411041 ATACCCGAACCCTAGACAGC 58.589 55.000 0.00 0.00 0.00 4.40
3872 5369 3.956199 TGTAATACCCGAACCCTAGACAG 59.044 47.826 0.00 0.00 0.00 3.51
3873 5370 3.979911 TGTAATACCCGAACCCTAGACA 58.020 45.455 0.00 0.00 0.00 3.41
3874 5371 5.541953 ATTGTAATACCCGAACCCTAGAC 57.458 43.478 0.00 0.00 0.00 2.59
3875 5372 7.011994 TCATATTGTAATACCCGAACCCTAGA 58.988 38.462 0.00 0.00 0.00 2.43
3876 5373 7.235935 TCATATTGTAATACCCGAACCCTAG 57.764 40.000 0.00 0.00 0.00 3.02
3877 5374 7.676893 AGATCATATTGTAATACCCGAACCCTA 59.323 37.037 0.00 0.00 0.00 3.53
3878 5375 6.500751 AGATCATATTGTAATACCCGAACCCT 59.499 38.462 0.00 0.00 0.00 4.34
3879 5376 6.708285 AGATCATATTGTAATACCCGAACCC 58.292 40.000 0.00 0.00 0.00 4.11
3880 5377 9.530633 GATAGATCATATTGTAATACCCGAACC 57.469 37.037 0.00 0.00 0.00 3.62
3928 5425 7.960262 AGAAGCTATGATATGACTCATCAACA 58.040 34.615 0.00 0.00 38.69 3.33
3957 5454 5.689383 ACGAACAACAGATACATTGCTTT 57.311 34.783 0.00 0.00 0.00 3.51
4003 5500 5.466393 ACAGCAAAATAGAAACAACATTGGC 59.534 36.000 0.00 0.00 0.00 4.52
4107 5604 0.818040 ACAAGTGCCAAAGGACGGAC 60.818 55.000 0.00 0.00 0.00 4.79
4108 5605 0.534203 GACAAGTGCCAAAGGACGGA 60.534 55.000 0.00 0.00 0.00 4.69
4109 5606 0.535102 AGACAAGTGCCAAAGGACGG 60.535 55.000 0.00 0.00 0.00 4.79
4280 5780 7.230849 ACTTCCAATTCTGCATAAAACATGA 57.769 32.000 0.00 0.00 0.00 3.07
4311 5811 2.164827 TGTGCATGCTCACAATCAATCC 59.835 45.455 20.33 0.00 43.27 3.01
4355 5858 4.640789 AGCCAGAATACTAAGACAGACG 57.359 45.455 0.00 0.00 0.00 4.18
4366 5869 9.717942 AATGACAAATAGATCTAGCCAGAATAC 57.282 33.333 8.70 0.00 33.50 1.89
4427 5930 8.499162 CAGTCAAATATAATAGCTACACCAAGC 58.501 37.037 0.00 0.00 43.11 4.01
4455 5958 2.897326 TCACTAAGCAGGCTTACACTCA 59.103 45.455 9.56 0.00 37.47 3.41
4537 6040 6.770746 AAGCATCTTCTACAATGAAGCATT 57.229 33.333 0.00 0.00 42.15 3.56
4686 6189 7.231467 TGCTGTAGTACATGATAGATACCTGA 58.769 38.462 2.82 0.00 0.00 3.86
4721 6224 9.525826 AGACAATCCATTCTTAAAGTTTCTGAT 57.474 29.630 0.00 0.00 0.00 2.90
5053 6559 4.410400 CTGCCAACCCCTCCCGAC 62.410 72.222 0.00 0.00 0.00 4.79
5311 6817 7.903145 ACAAACCTATCAGTTGACATGTAGTA 58.097 34.615 0.00 0.00 0.00 1.82
5312 6818 6.769512 ACAAACCTATCAGTTGACATGTAGT 58.230 36.000 0.00 0.00 0.00 2.73
5332 6838 2.997980 TGCAGACCAGTGAAGAACAAA 58.002 42.857 0.00 0.00 0.00 2.83
5335 6844 2.945668 AGTTTGCAGACCAGTGAAGAAC 59.054 45.455 3.32 0.00 0.00 3.01
5356 6865 0.391597 AAGAACGAGCGGAGACCAAA 59.608 50.000 0.00 0.00 0.00 3.28
5358 6867 1.289066 CAAGAACGAGCGGAGACCA 59.711 57.895 0.00 0.00 0.00 4.02
5406 6915 4.254709 AGCACCAGCAAGACCGCA 62.255 61.111 0.00 0.00 45.49 5.69
5427 6936 4.873810 TGCAACAGCAGTGGCCGT 62.874 61.111 6.11 0.00 44.45 5.68
5487 6996 2.224992 TGCCAGGAAGAATGCTTTACCA 60.225 45.455 0.00 0.00 33.61 3.25
5543 7052 3.036429 GCGAGGAGGCCACCATCTT 62.036 63.158 22.29 0.00 0.00 2.40
5582 7091 2.282110 CACCATTGGGCGTGGACA 60.282 61.111 7.78 0.00 39.12 4.02
5776 7288 1.601759 GCAGCAACTCAGGCAAGGA 60.602 57.895 0.00 0.00 0.00 3.36
5788 7300 1.270274 CAATACTGGCACAAGCAGCAA 59.730 47.619 0.00 0.00 44.61 3.91
5823 7335 4.179361 CCCAACAGGCAGCAGAAA 57.821 55.556 0.00 0.00 0.00 2.52
5899 7411 2.221981 CAGGTTCTTCGTCAAGCAACTC 59.778 50.000 0.00 0.00 0.00 3.01
5927 7439 1.879380 CGACCAAAACATCAGCCAAGA 59.121 47.619 0.00 0.00 0.00 3.02
5952 7464 1.251251 GGCAGTTCATTGGCAAGACT 58.749 50.000 5.96 6.95 42.68 3.24


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

AutoCloner maintained by Alex Coulton.