Multiple sequence alignment - TraesCS1B01G109400

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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 TraesCS1B01G109400 chr1B 100.000 4129 0 0 1 4129 121403118 121407246 0.000000e+00 7625.0
1 TraesCS1B01G109400 chr1B 95.385 65 3 0 659 723 121350456 121350520 2.030000e-18 104.0
2 TraesCS1B01G109400 chr1B 92.537 67 5 0 659 725 121279730 121279796 3.400000e-16 97.1
3 TraesCS1B01G109400 chr1B 100.000 34 0 0 3373 3406 121406357 121406390 3.450000e-06 63.9
4 TraesCS1B01G109400 chr1B 100.000 34 0 0 3240 3273 121406490 121406523 3.450000e-06 63.9
5 TraesCS1B01G109400 chr1A 90.699 2817 144 56 477 3242 108921616 108924365 0.000000e+00 3642.0
6 TraesCS1B01G109400 chr1A 92.308 832 44 11 3314 4129 108924381 108925208 0.000000e+00 1164.0
7 TraesCS1B01G109400 chr1A 86.262 313 26 11 128 438 108918610 108918907 1.430000e-84 324.0
8 TraesCS1B01G109400 chr1A 93.846 65 4 0 659 723 108909483 108909547 9.450000e-17 99.0
9 TraesCS1B01G109400 chr1A 90.164 61 4 1 659 719 108817522 108817580 1.230000e-10 78.7
10 TraesCS1B01G109400 chr1D 91.151 2181 113 34 1 2138 77837422 77839565 0.000000e+00 2885.0
11 TraesCS1B01G109400 chr1D 93.711 1113 43 12 2145 3242 77839658 77840758 0.000000e+00 1642.0
12 TraesCS1B01G109400 chr1D 96.983 663 18 1 3314 3974 77840774 77841436 0.000000e+00 1112.0
13 TraesCS1B01G109400 chr1D 91.573 178 5 2 3962 4129 77848293 77848470 1.920000e-58 237.0
14 TraesCS1B01G109400 chr1D 81.600 125 15 6 600 718 77759160 77759282 3.400000e-16 97.1
15 TraesCS1B01G109400 chr5D 77.863 524 89 21 1376 1886 326118246 326118755 2.410000e-77 300.0
16 TraesCS1B01G109400 chr5D 81.111 270 48 3 1378 1645 325422829 325423097 3.230000e-51 213.0
17 TraesCS1B01G109400 chr5D 88.028 142 17 0 1745 1886 325423176 325423317 7.100000e-38 169.0
18 TraesCS1B01G109400 chr5D 87.075 147 15 4 1738 1882 325647299 325647443 3.300000e-36 163.0
19 TraesCS1B01G109400 chr5D 86.806 144 16 3 1741 1882 325664128 325664270 1.540000e-34 158.0
20 TraesCS1B01G109400 chr5B 77.132 516 99 17 1376 1882 378068458 378068963 8.740000e-72 281.0
21 TraesCS1B01G109400 chr5B 81.550 271 49 1 1376 1645 378510703 378510973 5.370000e-54 222.0
22 TraesCS1B01G109400 chr5B 80.970 268 49 2 1376 1642 377978343 377978609 1.160000e-50 211.0
23 TraesCS1B01G109400 chr5B 87.050 139 16 2 1745 1882 378511054 378511191 5.530000e-34 156.0
24 TraesCS1B01G109400 chr5A 81.853 259 45 2 1385 1642 430508305 430508048 2.500000e-52 217.0
25 TraesCS1B01G109400 chr4D 79.787 282 53 4 1745 2024 283882645 283882366 7.000000e-48 202.0


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 TraesCS1B01G109400 chr1B 121403118 121407246 4128 False 2584.266667 7625 100.000000 1 4129 3 chr1B.!!$F3 4128
1 TraesCS1B01G109400 chr1A 108918610 108925208 6598 False 1710.000000 3642 89.756333 128 4129 3 chr1A.!!$F3 4001
2 TraesCS1B01G109400 chr1D 77837422 77841436 4014 False 1879.666667 2885 93.948333 1 3974 3 chr1D.!!$F3 3973
3 TraesCS1B01G109400 chr5D 326118246 326118755 509 False 300.000000 300 77.863000 1376 1886 1 chr5D.!!$F3 510
4 TraesCS1B01G109400 chr5B 378068458 378068963 505 False 281.000000 281 77.132000 1376 1882 1 chr5B.!!$F2 506

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
842 3545 0.539986 GTGAATAGTCAAGCCCGGGA 59.460 55.0 29.31 0.0 34.87 5.14 F
1022 3746 0.040692 CTTCGTCGTCAACCAGTCGA 60.041 55.0 0.00 0.0 35.49 4.20 F
2534 5372 0.178068 AGTACATCATGACGGGGCAC 59.822 55.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2750 5588 0.179163 GGCTCAAGCATTTGTACGCC 60.179 55.000 4.13 0.0 44.36 5.68 R
2923 5761 0.667792 GTCAGCCTTCCACTCGTCAC 60.668 60.000 0.00 0.0 0.00 3.67 R
4020 6862 1.003545 CGCAAGCGATACATTTGGGAG 60.004 52.381 9.11 0.0 42.83 4.30 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
26 27 7.278424 GCAAAACTGCAATGTTATGATAACCAT 59.722 33.333 12.39 4.17 35.65 3.55
27 28 8.597227 CAAAACTGCAATGTTATGATAACCATG 58.403 33.333 12.39 11.63 36.71 3.66
28 29 7.408756 AACTGCAATGTTATGATAACCATGT 57.591 32.000 12.39 1.54 36.71 3.21
42 43 7.592938 TGATAACCATGTTGCTAAGTTTCTTG 58.407 34.615 0.00 0.00 0.00 3.02
51 52 1.468914 CTAAGTTTCTTGGAAGGCGCC 59.531 52.381 21.89 21.89 0.00 6.53
53 54 1.901464 GTTTCTTGGAAGGCGCCCA 60.901 57.895 26.15 11.99 0.00 5.36
84 85 4.455533 GGCTGTCACAGACAAACATCATAA 59.544 41.667 9.70 0.00 42.26 1.90
116 117 4.704833 TGCCTCCGAAGCACAGGC 62.705 66.667 2.04 2.04 45.19 4.85
117 118 4.704833 GCCTCCGAAGCACAGGCA 62.705 66.667 4.27 0.00 44.42 4.75
118 119 2.032528 CCTCCGAAGCACAGGCAA 59.967 61.111 0.00 0.00 44.61 4.52
119 120 2.328099 CCTCCGAAGCACAGGCAAC 61.328 63.158 0.00 0.00 44.61 4.17
157 158 6.128634 CGACTCCTTGACCTGTAAAATTGTAC 60.129 42.308 0.00 0.00 0.00 2.90
195 196 2.954868 CACGTACGGCCGATCAGC 60.955 66.667 35.90 15.00 0.00 4.26
242 243 1.208052 CCAACCTGTCGATCATCTGGT 59.792 52.381 8.98 8.98 37.46 4.00
244 245 1.852633 ACCTGTCGATCATCTGGTCA 58.147 50.000 8.98 0.00 31.93 4.02
250 251 3.448660 TGTCGATCATCTGGTCACTCAAT 59.551 43.478 0.00 0.00 0.00 2.57
264 265 5.465935 GTCACTCAATATTCTCCGATCTCC 58.534 45.833 0.00 0.00 0.00 3.71
265 266 5.242838 GTCACTCAATATTCTCCGATCTCCT 59.757 44.000 0.00 0.00 0.00 3.69
266 267 5.475220 TCACTCAATATTCTCCGATCTCCTC 59.525 44.000 0.00 0.00 0.00 3.71
268 269 4.740902 TCAATATTCTCCGATCTCCTCCA 58.259 43.478 0.00 0.00 0.00 3.86
287 288 3.373748 TCCACACGTGTCATTATTCATGC 59.626 43.478 20.49 0.00 32.13 4.06
294 295 5.008019 ACGTGTCATTATTCATGCAAGGATC 59.992 40.000 0.00 0.00 32.13 3.36
302 316 5.988310 ATTCATGCAAGGATCAACAGAAA 57.012 34.783 0.00 0.00 0.00 2.52
303 317 5.787953 TTCATGCAAGGATCAACAGAAAA 57.212 34.783 0.00 0.00 0.00 2.29
306 320 3.963665 TGCAAGGATCAACAGAAAAACG 58.036 40.909 0.00 0.00 0.00 3.60
307 321 3.629855 TGCAAGGATCAACAGAAAAACGA 59.370 39.130 0.00 0.00 0.00 3.85
308 322 3.975035 GCAAGGATCAACAGAAAAACGAC 59.025 43.478 0.00 0.00 0.00 4.34
309 323 4.211389 CAAGGATCAACAGAAAAACGACG 58.789 43.478 0.00 0.00 0.00 5.12
350 364 3.423154 CGGAAGTTGCACCCGCTC 61.423 66.667 3.58 0.00 39.64 5.03
355 369 3.730761 GTTGCACCCGCTCTGCTG 61.731 66.667 0.00 0.00 39.64 4.41
356 370 4.254709 TTGCACCCGCTCTGCTGT 62.255 61.111 0.00 0.00 39.64 4.40
357 371 4.994471 TGCACCCGCTCTGCTGTG 62.994 66.667 0.00 0.00 39.64 3.66
382 396 0.729690 GAGGCGAGATTTGCTGGAAC 59.270 55.000 0.00 0.00 0.00 3.62
388 402 3.012518 CGAGATTTGCTGGAACCAGATT 58.987 45.455 22.96 5.25 46.30 2.40
389 403 3.064545 CGAGATTTGCTGGAACCAGATTC 59.935 47.826 22.96 12.77 46.30 2.52
390 404 4.268359 GAGATTTGCTGGAACCAGATTCT 58.732 43.478 22.96 16.44 46.30 2.40
392 406 1.538047 TTGCTGGAACCAGATTCTGC 58.462 50.000 22.96 8.95 46.30 4.26
512 3196 2.093235 GCAGAAGAACATGGACCTAGCT 60.093 50.000 0.00 0.00 0.00 3.32
529 3213 4.219725 CCTAGCTAGAAGAGGCAAGTATCC 59.780 50.000 22.70 0.00 0.00 2.59
551 3238 6.853720 TCCTCTCTCGTACTAAAACATTCAG 58.146 40.000 0.00 0.00 0.00 3.02
555 3242 5.779922 TCTCGTACTAAAACATTCAGCTGT 58.220 37.500 14.67 0.00 0.00 4.40
601 3292 1.004560 CACGTGGCCTGACATCTGT 60.005 57.895 7.95 0.00 0.00 3.41
623 3314 3.308595 TCACTAGTTAATTTGCATCGCCG 59.691 43.478 0.00 0.00 0.00 6.46
692 3393 0.816421 CCTCACGTTTTCCACCCGTT 60.816 55.000 0.00 0.00 31.46 4.44
736 3437 1.203313 GCACGTAAAGCGGTGTGAC 59.797 57.895 6.96 0.00 46.52 3.67
787 3488 3.866582 CCCGTGGCATCTCCCTCC 61.867 72.222 0.00 0.00 0.00 4.30
842 3545 0.539986 GTGAATAGTCAAGCCCGGGA 59.460 55.000 29.31 0.00 34.87 5.14
882 3596 1.946768 TGCTTTTTGTTCGCTACTGCT 59.053 42.857 0.00 0.00 36.97 4.24
944 3658 2.192861 TCAAGGCAAGCCAACACCG 61.193 57.895 14.40 0.00 38.92 4.94
1021 3745 1.606350 GCTTCGTCGTCAACCAGTCG 61.606 60.000 0.00 0.00 0.00 4.18
1022 3746 0.040692 CTTCGTCGTCAACCAGTCGA 60.041 55.000 0.00 0.00 35.49 4.20
1023 3747 0.040692 TTCGTCGTCAACCAGTCGAG 60.041 55.000 0.00 0.00 38.40 4.04
1024 3748 1.162181 TCGTCGTCAACCAGTCGAGT 61.162 55.000 0.00 0.00 38.40 4.18
1025 3749 0.725118 CGTCGTCAACCAGTCGAGTC 60.725 60.000 0.00 0.00 38.40 3.36
1031 3755 1.202891 TCAACCAGTCGAGTCTCTCCA 60.203 52.381 0.00 0.00 0.00 3.86
1032 3756 1.613925 CAACCAGTCGAGTCTCTCCAA 59.386 52.381 0.00 0.00 0.00 3.53
1054 3778 2.476199 CCCATCTCCTCTTCAACTCCT 58.524 52.381 0.00 0.00 0.00 3.69
1057 3781 3.517100 CCATCTCCTCTTCAACTCCTCAA 59.483 47.826 0.00 0.00 0.00 3.02
1073 3797 1.098712 TCAAACCCTCACACCGCAAC 61.099 55.000 0.00 0.00 0.00 4.17
1101 3825 2.481276 GCTCAACCAAGAAACCAACCAC 60.481 50.000 0.00 0.00 0.00 4.16
1103 3827 3.436243 TCAACCAAGAAACCAACCACTT 58.564 40.909 0.00 0.00 0.00 3.16
1136 3860 0.599204 TCGTTGCCAGTTCTTCCGTC 60.599 55.000 0.00 0.00 0.00 4.79
1170 3894 0.824109 TGAGCGGTCCATCTTCGATT 59.176 50.000 12.85 0.00 0.00 3.34
1171 3895 2.028876 TGAGCGGTCCATCTTCGATTA 58.971 47.619 12.85 0.00 0.00 1.75
1201 3930 1.626654 CGTGTCACCGATGGCTTCAC 61.627 60.000 0.00 0.00 0.00 3.18
1239 3968 2.989253 TTCTGCTGCGTCGGAGGA 60.989 61.111 15.95 12.02 0.00 3.71
1303 4032 3.744719 CGTCTTCCACGCCGAGGA 61.745 66.667 0.00 0.00 42.87 3.71
1308 4037 3.578968 TTCCACGCCGAGGAGGAGA 62.579 63.158 2.97 0.00 43.02 3.71
1317 4046 0.753848 CGAGGAGGAGAAGAGGGGAC 60.754 65.000 0.00 0.00 0.00 4.46
1318 4047 0.336737 GAGGAGGAGAAGAGGGGACA 59.663 60.000 0.00 0.00 0.00 4.02
1320 4049 0.336737 GGAGGAGAAGAGGGGACAGA 59.663 60.000 0.00 0.00 0.00 3.41
1324 4053 1.199615 GAGAAGAGGGGACAGAAGGG 58.800 60.000 0.00 0.00 0.00 3.95
1428 4157 2.575525 CTCTCGCTGACGCTGTCG 60.576 66.667 4.65 0.00 39.84 4.35
1596 4325 1.291272 GGTCGCCGTCAAGTACCTT 59.709 57.895 0.00 0.00 0.00 3.50
1702 4431 4.604976 GGATGCATGAGCTGTCAAATAAC 58.395 43.478 2.46 0.00 42.74 1.89
1829 4566 3.127352 CTACGAGGAGGAGCACCGC 62.127 68.421 0.00 0.00 41.83 5.68
1853 4590 1.520787 GGCGTACGAGTTCATGGGG 60.521 63.158 21.65 0.00 0.00 4.96
1877 4614 1.376942 CAGCCTGGAGAAGCACCTG 60.377 63.158 0.00 0.00 0.00 4.00
2128 4865 4.245660 GACGGATGAATGTCAAAGTCTGA 58.754 43.478 0.00 0.00 35.20 3.27
2144 4881 2.031683 GTCTGACACCCGTTTCAAACAG 59.968 50.000 2.24 0.00 0.00 3.16
2145 4882 0.736053 TGACACCCGTTTCAAACAGC 59.264 50.000 0.22 0.00 0.00 4.40
2146 4883 1.021968 GACACCCGTTTCAAACAGCT 58.978 50.000 0.22 0.00 0.00 4.24
2147 4884 0.738389 ACACCCGTTTCAAACAGCTG 59.262 50.000 13.48 13.48 0.00 4.24
2149 4886 1.007387 CCCGTTTCAAACAGCTGGC 60.007 57.895 19.93 0.00 0.00 4.85
2150 4887 1.007387 CCGTTTCAAACAGCTGGCC 60.007 57.895 19.93 0.00 0.00 5.36
2232 5055 5.241728 GCCCATTTCTCACATAAATCCTACC 59.758 44.000 0.00 0.00 0.00 3.18
2257 5083 6.376864 CCACAATCAATAAATCTGTACCCACA 59.623 38.462 0.00 0.00 0.00 4.17
2258 5084 7.093988 CCACAATCAATAAATCTGTACCCACAA 60.094 37.037 0.00 0.00 33.22 3.33
2259 5085 8.469200 CACAATCAATAAATCTGTACCCACAAT 58.531 33.333 0.00 0.00 33.22 2.71
2260 5086 8.686334 ACAATCAATAAATCTGTACCCACAATC 58.314 33.333 0.00 0.00 33.22 2.67
2261 5087 8.685427 CAATCAATAAATCTGTACCCACAATCA 58.315 33.333 0.00 0.00 33.22 2.57
2313 5151 4.022762 ACAGATACAGCTTAGCACGATAGG 60.023 45.833 7.07 0.00 43.77 2.57
2329 5167 5.346551 CACGATAGGAACGTTGTCATGTTAA 59.653 40.000 5.00 0.00 42.07 2.01
2330 5168 5.575606 ACGATAGGAACGTTGTCATGTTAAG 59.424 40.000 5.00 0.00 41.18 1.85
2331 5169 5.575606 CGATAGGAACGTTGTCATGTTAAGT 59.424 40.000 5.00 0.00 31.82 2.24
2332 5170 6.748658 CGATAGGAACGTTGTCATGTTAAGTA 59.251 38.462 5.00 0.00 31.82 2.24
2349 5187 9.658799 ATGTTAAGTACATGCATATATCACTCC 57.341 33.333 0.00 0.00 45.71 3.85
2350 5188 8.646900 TGTTAAGTACATGCATATATCACTCCA 58.353 33.333 0.00 0.00 0.00 3.86
2351 5189 9.144747 GTTAAGTACATGCATATATCACTCCAG 57.855 37.037 0.00 0.00 0.00 3.86
2352 5190 6.924913 AGTACATGCATATATCACTCCAGT 57.075 37.500 0.00 0.00 0.00 4.00
2388 5226 8.398665 CACAAGTTATCTTTGCCTAACCTAATC 58.601 37.037 0.00 0.00 0.00 1.75
2426 5264 1.136305 GACTATACCGCCAAGCTGTCA 59.864 52.381 0.00 0.00 0.00 3.58
2534 5372 0.178068 AGTACATCATGACGGGGCAC 59.822 55.000 0.00 0.00 0.00 5.01
2654 5492 0.811616 GCTTGGTCGACTATGCCAGG 60.812 60.000 23.75 11.72 33.41 4.45
2723 5561 0.391130 TGGAATGCCAGTACTCGTGC 60.391 55.000 0.00 0.00 39.92 5.34
2750 5588 3.414700 GAACTGGCCGCACGAGTG 61.415 66.667 0.00 0.00 37.41 3.51
2891 5729 4.103357 CAGTCGTAGTGGAAAATACCGAG 58.897 47.826 0.00 0.00 0.00 4.63
2902 5740 4.913345 GGAAAATACCGAGAAAAACGTTGG 59.087 41.667 0.00 0.00 0.00 3.77
2905 5743 1.589803 ACCGAGAAAAACGTTGGGAG 58.410 50.000 0.00 0.00 0.00 4.30
2923 5761 3.118992 GGGAGCAAAGGAAAGCTTATTGG 60.119 47.826 0.00 0.00 42.04 3.16
2993 5831 1.817099 GCAGAGCCACCAAGATCGG 60.817 63.158 0.00 0.00 0.00 4.18
3074 5912 0.036306 CCATCGGGCCTTATACCACC 59.964 60.000 0.84 0.00 0.00 4.61
3160 5998 1.477295 ACAGAGCTTAGTTAGGACCGC 59.523 52.381 0.00 0.00 0.00 5.68
3242 6080 3.306225 GGGTGTAACACAAGTCACGGATA 60.306 47.826 0.00 0.00 42.56 2.59
3243 6081 3.924686 GGTGTAACACAAGTCACGGATAG 59.075 47.826 0.00 0.00 39.98 2.08
3244 6082 4.553323 GTGTAACACAAGTCACGGATAGT 58.447 43.478 0.00 0.00 36.32 2.12
3245 6083 4.384846 GTGTAACACAAGTCACGGATAGTG 59.615 45.833 0.00 0.00 44.70 2.74
3255 6093 0.537188 ACGGATAGTGAAGCTGGGTG 59.463 55.000 0.00 0.00 0.00 4.61
3256 6094 0.537188 CGGATAGTGAAGCTGGGTGT 59.463 55.000 0.00 0.00 0.00 4.16
3257 6095 1.754803 CGGATAGTGAAGCTGGGTGTA 59.245 52.381 0.00 0.00 0.00 2.90
3258 6096 2.167693 CGGATAGTGAAGCTGGGTGTAA 59.832 50.000 0.00 0.00 0.00 2.41
3259 6097 3.369052 CGGATAGTGAAGCTGGGTGTAAA 60.369 47.826 0.00 0.00 0.00 2.01
3260 6098 4.683400 CGGATAGTGAAGCTGGGTGTAAAT 60.683 45.833 0.00 0.00 0.00 1.40
3261 6099 4.576463 GGATAGTGAAGCTGGGTGTAAATG 59.424 45.833 0.00 0.00 0.00 2.32
3262 6100 2.162681 AGTGAAGCTGGGTGTAAATGC 58.837 47.619 0.00 0.00 0.00 3.56
3263 6101 1.202348 GTGAAGCTGGGTGTAAATGCC 59.798 52.381 0.00 0.00 0.00 4.40
3264 6102 1.202989 TGAAGCTGGGTGTAAATGCCA 60.203 47.619 0.00 0.00 0.00 4.92
3265 6103 1.892474 GAAGCTGGGTGTAAATGCCAA 59.108 47.619 0.00 0.00 0.00 4.52
3266 6104 2.008242 AGCTGGGTGTAAATGCCAAA 57.992 45.000 0.00 0.00 0.00 3.28
3267 6105 2.324541 AGCTGGGTGTAAATGCCAAAA 58.675 42.857 0.00 0.00 0.00 2.44
3268 6106 2.299867 AGCTGGGTGTAAATGCCAAAAG 59.700 45.455 0.00 0.00 0.00 2.27
3269 6107 2.037121 GCTGGGTGTAAATGCCAAAAGT 59.963 45.455 0.00 0.00 0.00 2.66
3270 6108 3.494223 GCTGGGTGTAAATGCCAAAAGTT 60.494 43.478 0.00 0.00 0.00 2.66
3271 6109 4.702831 CTGGGTGTAAATGCCAAAAGTTT 58.297 39.130 0.00 0.00 0.00 2.66
3272 6110 5.104259 TGGGTGTAAATGCCAAAAGTTTT 57.896 34.783 0.00 0.00 0.00 2.43
3273 6111 6.235231 TGGGTGTAAATGCCAAAAGTTTTA 57.765 33.333 0.00 0.00 0.00 1.52
3274 6112 6.831976 TGGGTGTAAATGCCAAAAGTTTTAT 58.168 32.000 0.00 0.00 0.00 1.40
3275 6113 7.283329 TGGGTGTAAATGCCAAAAGTTTTATT 58.717 30.769 0.00 0.00 0.00 1.40
3276 6114 7.442666 TGGGTGTAAATGCCAAAAGTTTTATTC 59.557 33.333 0.00 0.00 0.00 1.75
3277 6115 7.659799 GGGTGTAAATGCCAAAAGTTTTATTCT 59.340 33.333 0.00 0.00 0.00 2.40
3278 6116 9.051679 GGTGTAAATGCCAAAAGTTTTATTCTT 57.948 29.630 0.00 0.00 0.00 2.52
3471 6312 9.411801 TCAAAGTATATAAATAGCAAGCGAGAG 57.588 33.333 0.00 0.00 0.00 3.20
3536 6377 8.189119 TGTTAGAAAAAGTTGCTCCCATAATT 57.811 30.769 0.00 0.00 0.00 1.40
3551 6392 3.354397 CATAATTCGGTTTCTGCGCTTC 58.646 45.455 9.73 0.00 0.00 3.86
3552 6393 1.234821 AATTCGGTTTCTGCGCTTCA 58.765 45.000 9.73 0.00 0.00 3.02
3632 6473 8.594550 GCCTCTAGTATACCATCCTTTTCATTA 58.405 37.037 0.00 0.00 0.00 1.90
3705 6546 6.930731 TGGAAAGCCTTTATGGTATGAAAAC 58.069 36.000 0.00 0.00 38.35 2.43
3808 6649 9.323985 CTGTAAAATGGTTCATTTCCTTTCAAA 57.676 29.630 6.37 0.00 42.32 2.69
4034 6876 9.489084 TCAATTCTATTACTCCCAAATGTATCG 57.511 33.333 0.00 0.00 0.00 2.92
4035 6877 7.907214 ATTCTATTACTCCCAAATGTATCGC 57.093 36.000 0.00 0.00 0.00 4.58
4039 6886 2.017049 ACTCCCAAATGTATCGCTTGC 58.983 47.619 0.00 0.00 0.00 4.01
4053 6900 2.624364 TCGCTTGCGGTAATATAGGTGA 59.376 45.455 15.10 0.00 0.00 4.02
4124 6976 5.425196 TTGGTAGCTTACGGTTTCCTAAT 57.575 39.130 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.313292 ACATGGTTATCATAACATTGCAGTTTT 58.687 29.630 9.79 0.00 34.12 2.43
26 27 3.317993 GCCTTCCAAGAAACTTAGCAACA 59.682 43.478 0.00 0.00 0.00 3.33
27 28 3.609409 CGCCTTCCAAGAAACTTAGCAAC 60.609 47.826 0.00 0.00 0.00 4.17
28 29 2.552315 CGCCTTCCAAGAAACTTAGCAA 59.448 45.455 0.00 0.00 0.00 3.91
53 54 4.918360 TGTGACAGCCCCACCCCT 62.918 66.667 0.00 0.00 33.80 4.79
57 58 0.465460 TTTGTCTGTGACAGCCCCAC 60.465 55.000 7.93 1.23 43.69 4.61
105 106 0.317269 CTTGTGTTGCCTGTGCTTCG 60.317 55.000 0.00 0.00 38.71 3.79
117 118 0.810031 AGTCGCGAGCAACTTGTGTT 60.810 50.000 10.24 0.00 36.75 3.32
118 119 1.215655 GAGTCGCGAGCAACTTGTGT 61.216 55.000 10.24 0.00 0.00 3.72
119 120 1.488957 GAGTCGCGAGCAACTTGTG 59.511 57.895 10.24 0.00 0.00 3.33
133 134 6.935208 AGTACAATTTTACAGGTCAAGGAGTC 59.065 38.462 4.66 0.00 0.00 3.36
157 158 5.220043 CGTGCACAATACTCTTTTCTACGAG 60.220 44.000 18.64 0.00 0.00 4.18
217 218 0.904649 TGATCGACAGGTTGGATGCT 59.095 50.000 0.00 0.00 0.00 3.79
242 243 5.389520 AGGAGATCGGAGAATATTGAGTGA 58.610 41.667 0.00 0.00 43.58 3.41
244 245 4.770010 GGAGGAGATCGGAGAATATTGAGT 59.230 45.833 0.00 0.00 43.58 3.41
250 251 3.223435 GTGTGGAGGAGATCGGAGAATA 58.777 50.000 0.00 0.00 43.58 1.75
264 265 4.494690 GCATGAATAATGACACGTGTGGAG 60.495 45.833 28.82 0.00 38.72 3.86
265 266 3.373748 GCATGAATAATGACACGTGTGGA 59.626 43.478 28.82 12.99 38.72 4.02
266 267 3.126686 TGCATGAATAATGACACGTGTGG 59.873 43.478 28.82 0.00 38.72 4.17
268 269 4.142622 CCTTGCATGAATAATGACACGTGT 60.143 41.667 23.64 23.64 38.72 4.49
287 288 4.025229 TCGTCGTTTTTCTGTTGATCCTTG 60.025 41.667 0.00 0.00 0.00 3.61
294 295 1.647748 CGCTCGTCGTTTTTCTGTTG 58.352 50.000 0.00 0.00 0.00 3.33
302 316 1.136446 GTGTTTATGCGCTCGTCGTTT 60.136 47.619 9.73 0.00 41.07 3.60
303 317 0.437295 GTGTTTATGCGCTCGTCGTT 59.563 50.000 9.73 0.00 41.07 3.85
306 320 0.294887 CTCGTGTTTATGCGCTCGTC 59.705 55.000 9.73 0.00 0.00 4.20
307 321 0.109458 TCTCGTGTTTATGCGCTCGT 60.109 50.000 9.73 0.00 0.00 4.18
308 322 0.989164 TTCTCGTGTTTATGCGCTCG 59.011 50.000 9.73 2.45 0.00 5.03
309 323 1.060698 GGTTCTCGTGTTTATGCGCTC 59.939 52.381 9.73 0.00 0.00 5.03
350 364 4.729918 GCCTCCCACCCACAGCAG 62.730 72.222 0.00 0.00 0.00 4.24
355 369 2.198304 AAATCTCGCCTCCCACCCAC 62.198 60.000 0.00 0.00 0.00 4.61
356 370 1.923395 AAATCTCGCCTCCCACCCA 60.923 57.895 0.00 0.00 0.00 4.51
357 371 1.452108 CAAATCTCGCCTCCCACCC 60.452 63.158 0.00 0.00 0.00 4.61
358 372 2.115291 GCAAATCTCGCCTCCCACC 61.115 63.158 0.00 0.00 0.00 4.61
529 3213 6.252441 CAGCTGAATGTTTTAGTACGAGAGAG 59.748 42.308 8.42 0.00 0.00 3.20
577 3268 0.107410 TGTCAGGCCACGTGAAAACT 60.107 50.000 19.30 6.28 30.04 2.66
601 3292 3.308595 CGGCGATGCAAATTAACTAGTGA 59.691 43.478 0.00 0.00 0.00 3.41
623 3314 1.153449 TGGCCGTGATTGACCGATC 60.153 57.895 0.00 0.00 0.00 3.69
661 3362 1.205064 CGTGAGGTTGCTTGAAGCG 59.795 57.895 13.05 0.00 46.26 4.68
743 3444 2.420129 GGTAATCTGGAATCTGGTGCGT 60.420 50.000 0.00 0.00 0.00 5.24
842 3545 0.664767 GCAGACGAGTCGTTGAGCTT 60.665 55.000 20.91 0.00 41.37 3.74
1021 3745 1.760029 GAGATGGGGTTGGAGAGACTC 59.240 57.143 0.00 0.00 0.00 3.36
1022 3746 1.623834 GGAGATGGGGTTGGAGAGACT 60.624 57.143 0.00 0.00 0.00 3.24
1023 3747 0.833949 GGAGATGGGGTTGGAGAGAC 59.166 60.000 0.00 0.00 0.00 3.36
1024 3748 0.719015 AGGAGATGGGGTTGGAGAGA 59.281 55.000 0.00 0.00 0.00 3.10
1025 3749 1.127343 GAGGAGATGGGGTTGGAGAG 58.873 60.000 0.00 0.00 0.00 3.20
1031 3755 2.573915 GAGTTGAAGAGGAGATGGGGTT 59.426 50.000 0.00 0.00 0.00 4.11
1032 3756 2.192263 GAGTTGAAGAGGAGATGGGGT 58.808 52.381 0.00 0.00 0.00 4.95
1054 3778 1.098712 GTTGCGGTGTGAGGGTTTGA 61.099 55.000 0.00 0.00 0.00 2.69
1057 3781 1.227853 GAGTTGCGGTGTGAGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
1073 3797 2.260844 TTCTTGGTTGAGCCTGTGAG 57.739 50.000 0.00 0.00 38.35 3.51
1153 3877 1.068741 GGTAATCGAAGATGGACCGCT 59.931 52.381 0.00 0.00 45.12 5.52
1180 3904 1.352156 GAAGCCATCGGTGACACGAC 61.352 60.000 0.00 0.00 46.64 4.34
1201 3930 2.233922 ACATAGACCTCCACGTCTTTGG 59.766 50.000 11.93 0.00 42.64 3.28
1204 3933 3.193691 CAGAACATAGACCTCCACGTCTT 59.806 47.826 0.00 0.00 40.23 3.01
1207 3936 1.204941 GCAGAACATAGACCTCCACGT 59.795 52.381 0.00 0.00 0.00 4.49
1259 3988 2.949678 CTTCGTCGTCGGCATCGG 60.950 66.667 1.55 0.00 37.69 4.18
1260 3989 2.949678 CCTTCGTCGTCGGCATCG 60.950 66.667 1.55 0.00 37.69 3.84
1261 3990 2.582498 CCCTTCGTCGTCGGCATC 60.582 66.667 1.55 0.00 37.69 3.91
1262 3991 4.814294 GCCCTTCGTCGTCGGCAT 62.814 66.667 12.86 0.00 37.69 4.40
1303 4032 1.273552 CCTTCTGTCCCCTCTTCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
1308 4037 2.294078 CGCCCTTCTGTCCCCTCTT 61.294 63.158 0.00 0.00 0.00 2.85
1431 4160 1.896660 GAAGGCGTGCAGGTTGGAA 60.897 57.895 8.40 0.00 0.00 3.53
1596 4325 2.041115 CGAGCTGGAGTCGAGGTCA 61.041 63.158 27.05 1.06 39.92 4.02
1702 4431 1.334869 GTTGGCGCAATAATGGAGGAG 59.665 52.381 10.83 0.00 0.00 3.69
1829 4566 0.735978 TGAACTCGTACGCCAGCATG 60.736 55.000 11.24 0.00 0.00 4.06
1853 4590 3.672295 CTTCTCCAGGCTGCCGGTC 62.672 68.421 22.65 0.00 0.00 4.79
1877 4614 1.696832 GGCCGTCGATGCTTCTGAAC 61.697 60.000 9.38 0.00 0.00 3.18
2090 4827 2.301870 TCCGTCCACAAGTTGCTCTATT 59.698 45.455 1.81 0.00 0.00 1.73
2128 4865 3.184736 AGCTGTTTGAAACGGGTGT 57.815 47.368 19.53 0.00 46.01 4.16
2144 4881 2.672996 TTTTCCAGCGAGGCCAGC 60.673 61.111 14.50 14.50 37.29 4.85
2145 4882 2.694760 GCTTTTCCAGCGAGGCCAG 61.695 63.158 5.01 0.00 39.29 4.85
2146 4883 2.672996 GCTTTTCCAGCGAGGCCA 60.673 61.111 5.01 0.00 39.29 5.36
2232 5055 6.376864 TGTGGGTACAGATTTATTGATTGTGG 59.623 38.462 0.00 0.00 31.91 4.17
2257 5083 9.793252 GTTGCTTTGATACTGACATAATTGATT 57.207 29.630 0.00 0.00 0.00 2.57
2258 5084 8.959548 TGTTGCTTTGATACTGACATAATTGAT 58.040 29.630 0.00 0.00 0.00 2.57
2259 5085 8.334263 TGTTGCTTTGATACTGACATAATTGA 57.666 30.769 0.00 0.00 0.00 2.57
2260 5086 7.219535 GCTGTTGCTTTGATACTGACATAATTG 59.780 37.037 0.00 0.00 36.03 2.32
2261 5087 7.253422 GCTGTTGCTTTGATACTGACATAATT 58.747 34.615 0.00 0.00 36.03 1.40
2329 5167 6.924913 ACTGGAGTGATATATGCATGTACT 57.075 37.500 10.16 3.00 0.00 2.73
2330 5168 6.931281 ACAACTGGAGTGATATATGCATGTAC 59.069 38.462 10.16 0.00 0.00 2.90
2331 5169 6.930722 CACAACTGGAGTGATATATGCATGTA 59.069 38.462 10.16 7.68 39.30 2.29
2332 5170 5.761726 CACAACTGGAGTGATATATGCATGT 59.238 40.000 10.16 5.06 39.30 3.21
2337 5175 7.334171 TGACAAACACAACTGGAGTGATATATG 59.666 37.037 8.43 3.53 40.16 1.78
2366 5204 6.768381 GCAGATTAGGTTAGGCAAAGATAACT 59.232 38.462 0.00 0.00 33.36 2.24
2543 5381 3.293262 GAAGCTATAGACGTCGCTCTTG 58.707 50.000 14.72 4.48 31.30 3.02
2555 5393 1.215655 GCACCACGCCGAAGCTATAG 61.216 60.000 0.00 0.00 36.60 1.31
2623 5461 0.250901 GACCAAGCTTTGCTCCCTGA 60.251 55.000 0.00 0.00 38.25 3.86
2642 5480 0.320771 GGTATGGCCTGGCATAGTCG 60.321 60.000 22.05 0.00 0.00 4.18
2654 5492 1.210478 TCCTGCTTCTTGAGGTATGGC 59.790 52.381 0.00 0.00 0.00 4.40
2750 5588 0.179163 GGCTCAAGCATTTGTACGCC 60.179 55.000 4.13 0.00 44.36 5.68
2891 5729 2.100087 TCCTTTGCTCCCAACGTTTTTC 59.900 45.455 0.00 0.00 0.00 2.29
2902 5740 3.511540 ACCAATAAGCTTTCCTTTGCTCC 59.488 43.478 3.20 0.00 38.75 4.70
2905 5743 4.237724 GTCACCAATAAGCTTTCCTTTGC 58.762 43.478 3.20 0.00 34.95 3.68
2923 5761 0.667792 GTCAGCCTTCCACTCGTCAC 60.668 60.000 0.00 0.00 0.00 3.67
2975 5813 1.817099 CCGATCTTGGTGGCTCTGC 60.817 63.158 0.00 0.00 0.00 4.26
2993 5831 2.022240 TTGGGAACTTTTGCCGGTGC 62.022 55.000 1.90 0.00 45.31 5.01
3065 5903 1.798446 CGTTGTAGCGCGGTGGTATAA 60.798 52.381 23.02 2.48 32.25 0.98
3160 5998 8.660373 CATTTTGCTACTCTTACTCCTTTACAG 58.340 37.037 0.00 0.00 0.00 2.74
3242 6080 2.162681 GCATTTACACCCAGCTTCACT 58.837 47.619 0.00 0.00 0.00 3.41
3243 6081 1.202348 GGCATTTACACCCAGCTTCAC 59.798 52.381 0.00 0.00 0.00 3.18
3244 6082 1.202989 TGGCATTTACACCCAGCTTCA 60.203 47.619 0.00 0.00 0.00 3.02
3245 6083 1.544724 TGGCATTTACACCCAGCTTC 58.455 50.000 0.00 0.00 0.00 3.86
3248 6086 2.037121 ACTTTTGGCATTTACACCCAGC 59.963 45.455 0.00 0.00 0.00 4.85
3249 6087 4.335400 AACTTTTGGCATTTACACCCAG 57.665 40.909 0.00 0.00 0.00 4.45
3480 6321 9.719355 GGTAACAAAATTACCATTTCAGGAAAT 57.281 29.630 10.34 1.50 42.97 2.17
3484 6325 8.364142 TGAAGGTAACAAAATTACCATTTCAGG 58.636 33.333 16.19 0.00 45.23 3.86
3536 6377 1.019278 GGATGAAGCGCAGAAACCGA 61.019 55.000 11.47 0.00 0.00 4.69
3632 6473 6.814954 TCTGGCTTTATCCATAGACTTCTT 57.185 37.500 0.00 0.00 35.22 2.52
3705 6546 6.949352 ATATGTCACTTTTATGGAAGCTGG 57.051 37.500 0.00 0.00 0.00 4.85
3941 6783 6.010850 AGGTATACTGGTGATACATGATCGT 58.989 40.000 0.00 0.00 37.38 3.73
4015 6857 5.468746 GCAAGCGATACATTTGGGAGTAATA 59.531 40.000 0.00 0.00 0.00 0.98
4020 6862 1.003545 CGCAAGCGATACATTTGGGAG 60.004 52.381 9.11 0.00 42.83 4.30
4034 6876 3.988517 GAGTCACCTATATTACCGCAAGC 59.011 47.826 0.00 0.00 0.00 4.01
4035 6877 4.557205 GGAGTCACCTATATTACCGCAAG 58.443 47.826 0.00 0.00 35.41 4.01
4039 6886 3.152341 ACGGGAGTCACCTATATTACCG 58.848 50.000 0.00 0.00 40.62 4.02


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

AutoCloner maintained by Alex Coulton.