Multiple sequence alignment - TraesCS2B01G000900

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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 TraesCS2B01G000900 chr2B 100.000 2561 0 0 1 2561 452112 449552 0.000000e+00 4730.0
1 TraesCS2B01G000900 chr2B 94.875 2595 82 15 5 2561 18881 21462 0.000000e+00 4008.0
2 TraesCS2B01G000900 chr2B 100.000 1927 0 0 2964 4890 449149 447223 0.000000e+00 3559.0
3 TraesCS2B01G000900 chr2B 92.216 1683 71 25 4 1663 122185 120540 0.000000e+00 2327.0
4 TraesCS2B01G000900 chr2B 95.134 1233 44 7 3187 4415 21463 22683 0.000000e+00 1930.0
5 TraesCS2B01G000900 chr2B 95.364 906 42 0 1655 2560 119882 118977 0.000000e+00 1441.0
6 TraesCS2B01G000900 chr2B 88.144 641 69 5 3187 3823 118977 118340 0.000000e+00 756.0
7 TraesCS2B01G000900 chr2B 94.737 304 13 1 4590 4890 40286 40589 2.060000e-128 470.0
8 TraesCS2B01G000900 chr2B 87.931 348 28 7 4338 4684 112656 112322 9.860000e-107 398.0
9 TraesCS2B01G000900 chr2B 96.444 225 8 0 2969 3193 710836118 710836342 5.980000e-99 372.0
10 TraesCS2B01G000900 chr2B 95.694 209 9 0 4476 4684 22703 22911 2.180000e-88 337.0
11 TraesCS2B01G000900 chr2B 95.283 212 9 1 4121 4331 113754 113543 7.840000e-88 335.0
12 TraesCS2B01G000900 chr2B 77.541 423 86 9 3231 3648 121167 120749 3.780000e-61 246.0
13 TraesCS2B01G000900 chr2B 77.143 420 92 4 1036 1453 448882 448465 1.760000e-59 241.0
14 TraesCS2B01G000900 chr2B 77.251 422 88 8 3231 3648 451077 450660 1.760000e-59 241.0
15 TraesCS2B01G000900 chr2B 73.534 665 158 16 3222 3879 19933 20586 2.280000e-58 237.0
16 TraesCS2B01G000900 chr2B 94.309 123 5 1 3973 4095 113864 113744 2.320000e-43 187.0
17 TraesCS2B01G000900 chr2B 94.737 38 2 0 4441 4478 447620 447583 5.290000e-05 60.2
18 TraesCS2B01G000900 chr2B 94.737 38 2 0 4493 4530 447672 447635 5.290000e-05 60.2
19 TraesCS2B01G000900 chr2B 96.970 33 1 0 4446 4478 112508 112476 6.840000e-04 56.5
20 TraesCS2B01G000900 chr2D 93.350 1970 113 10 593 2560 1961708 1959755 0.000000e+00 2896.0
21 TraesCS2B01G000900 chr2D 88.985 1498 94 34 3187 4655 1959755 1958300 0.000000e+00 1786.0
22 TraesCS2B01G000900 chr2D 85.263 285 33 6 263 544 27620386 27620664 8.010000e-73 285.0
23 TraesCS2B01G000900 chr2D 77.518 427 85 9 3231 3653 1961275 1960856 3.780000e-61 246.0
24 TraesCS2B01G000900 chr2D 93.220 59 4 0 165 223 1961764 1961706 2.420000e-13 87.9
25 TraesCS2B01G000900 chr2D 94.737 38 2 0 4686 4723 1958299 1958262 5.290000e-05 60.2
26 TraesCS2B01G000900 chr2D 100.000 29 0 0 4637 4665 1958963 1958935 2.000000e-03 54.7
27 TraesCS2B01G000900 chr2A 93.091 1708 80 16 3187 4890 1858926 1857253 0.000000e+00 2466.0
28 TraesCS2B01G000900 chr2A 92.259 1731 112 14 835 2560 1860639 1858926 0.000000e+00 2435.0
29 TraesCS2B01G000900 chr2A 96.889 225 7 0 2969 3193 83951016 83950792 1.280000e-100 377.0
30 TraesCS2B01G000900 chr2A 88.934 244 24 3 1 243 1862574 1862333 1.030000e-76 298.0
31 TraesCS2B01G000900 chr2A 89.316 234 14 6 566 794 1862348 1862121 2.880000e-72 283.0
32 TraesCS2B01G000900 chr2A 76.376 436 92 9 3222 3653 1860454 1860026 1.770000e-54 224.0
33 TraesCS2B01G000900 chr2A 94.595 37 2 0 4442 4478 1857633 1857597 1.900000e-04 58.4
34 TraesCS2B01G000900 chr1A 97.778 225 5 0 2969 3193 19500493 19500269 5.940000e-104 388.0
35 TraesCS2B01G000900 chr7B 96.889 225 7 0 2969 3193 742400267 742400043 1.280000e-100 377.0
36 TraesCS2B01G000900 chr7B 74.444 450 107 8 1033 1477 693923459 693923905 2.320000e-43 187.0
37 TraesCS2B01G000900 chr4D 90.813 283 24 2 262 544 311188005 311188285 1.280000e-100 377.0
38 TraesCS2B01G000900 chr4D 87.676 284 30 4 262 544 4070740 4071019 4.720000e-85 326.0
39 TraesCS2B01G000900 chr1B 96.889 225 7 0 2969 3193 19417391 19417615 1.280000e-100 377.0
40 TraesCS2B01G000900 chr1B 96.000 225 9 0 2969 3193 687569367 687569143 2.780000e-97 366.0
41 TraesCS2B01G000900 chr3B 96.889 225 6 1 2969 3193 812818730 812818507 4.620000e-100 375.0
42 TraesCS2B01G000900 chr3B 89.399 283 27 2 262 543 820946056 820946336 2.170000e-93 353.0
43 TraesCS2B01G000900 chr6B 96.000 225 9 0 2969 3193 713875578 713875802 2.780000e-97 366.0
44 TraesCS2B01G000900 chr6B 88.112 286 31 3 262 544 61169 60884 2.180000e-88 337.0
45 TraesCS2B01G000900 chr4A 96.000 225 9 0 2969 3193 78259670 78259894 2.780000e-97 366.0
46 TraesCS2B01G000900 chr7D 91.860 258 17 3 287 544 79120722 79120975 1.670000e-94 357.0
47 TraesCS2B01G000900 chr7D 72.200 1277 296 43 1030 2285 983049 981811 2.180000e-88 337.0
48 TraesCS2B01G000900 chr7D 72.757 613 127 32 1026 1621 982261 981672 2.340000e-38 171.0
49 TraesCS2B01G000900 chr7D 73.444 482 106 19 1026 1496 608809875 608809405 1.410000e-35 161.0
50 TraesCS2B01G000900 chr7D 72.340 611 127 30 1026 1618 480857 480271 2.360000e-33 154.0
51 TraesCS2B01G000900 chr7D 72.363 474 91 28 1026 1489 915746 915303 4.000000e-21 113.0
52 TraesCS2B01G000900 chr4B 88.028 284 30 3 262 544 116138786 116139066 2.820000e-87 333.0


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 TraesCS2B01G000900 chr2B 447223 452112 4889 True 1481.900000 4730 90.644667 1 4890 6 chr2B.!!$R3 4889
1 TraesCS2B01G000900 chr2B 18881 22911 4030 False 1628.000000 4008 89.809250 5 4684 4 chr2B.!!$F3 4679
2 TraesCS2B01G000900 chr2B 118340 122185 3845 True 1192.500000 2327 88.316250 4 3823 4 chr2B.!!$R2 3819
3 TraesCS2B01G000900 chr2B 112322 113864 1542 True 244.125000 398 93.623250 3973 4684 4 chr2B.!!$R1 711
4 TraesCS2B01G000900 chr2D 1958262 1961764 3502 True 855.133333 2896 91.301667 165 4723 6 chr2D.!!$R1 4558
5 TraesCS2B01G000900 chr2A 1857253 1862574 5321 True 960.733333 2466 89.095167 1 4890 6 chr2A.!!$R2 4889
6 TraesCS2B01G000900 chr7D 981672 983049 1377 True 254.000000 337 72.478500 1026 2285 2 chr7D.!!$R4 1259

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
493 515 0.823460 TGTGTGCATCCGAGCTATGA 59.177 50.0 0.00 0.0 34.99 2.15 F
1078 2563 0.385029 TGCATTTGACTGCACCACAC 59.615 50.0 0.00 0.0 46.76 3.82 F
1889 4052 0.948623 TTGATTGCACCACCTCGACG 60.949 55.0 0.00 0.0 0.00 5.12 F
3102 5265 1.340088 TTGCATGTGAGCCCATGTTT 58.660 45.0 9.53 0.0 43.33 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 4052 0.823356 TCACCTTGTTCCAAGCTGGC 60.823 55.000 0.00 0.0 37.47 4.85 R
2963 5126 2.027837 GGAATGGGTGTAACTACCGTGT 60.028 50.000 0.00 0.0 41.79 4.49 R
3650 5820 2.056577 GTACTTACGTGCTTGTTCGCT 58.943 47.619 0.00 0.0 0.00 4.93 R
4451 7597 0.798776 CAAGGCGCTGACTTCGAAAT 59.201 50.000 7.64 0.0 0.00 2.17 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
175 176 2.076100 CTACGAGCCATTGAACTGCAA 58.924 47.619 0.00 0.00 41.53 4.08
265 266 1.755179 AGCCTTTGATGGTTGGATCG 58.245 50.000 0.00 0.00 0.00 3.69
289 311 0.951558 TTCCTTCTTGAAGGCGTTGC 59.048 50.000 21.16 0.00 39.80 4.17
307 329 2.997980 TGCTGTTGAAGAACCTTGTCA 58.002 42.857 0.00 0.00 0.00 3.58
330 352 2.227388 CCTTGTGGTGTCATGAGAAAGC 59.773 50.000 0.00 0.00 0.00 3.51
386 408 2.101783 TGCGGATTTGATGCTTTGGAT 58.898 42.857 0.00 0.00 0.00 3.41
447 469 1.003545 CTTTGCTATTCGCCGATGTGG 60.004 52.381 0.00 0.00 42.50 4.17
485 507 1.588824 ATGTTGGCTGTGTGCATCCG 61.589 55.000 0.00 0.00 45.15 4.18
493 515 0.823460 TGTGTGCATCCGAGCTATGA 59.177 50.000 0.00 0.00 34.99 2.15
523 545 1.854126 GTGTGTGCTCATTGTGTTTGC 59.146 47.619 0.00 0.00 0.00 3.68
535 557 6.932947 TCATTGTGTTTGCATCCATTTGATA 58.067 32.000 0.00 0.00 30.56 2.15
545 567 7.692460 TGCATCCATTTGATACTTCATATCC 57.308 36.000 0.00 0.00 39.29 2.59
547 569 7.175467 TGCATCCATTTGATACTTCATATCCAC 59.825 37.037 0.00 0.00 39.29 4.02
550 572 8.267620 TCCATTTGATACTTCATATCCACTCT 57.732 34.615 0.00 0.00 39.29 3.24
551 573 8.717717 TCCATTTGATACTTCATATCCACTCTT 58.282 33.333 0.00 0.00 39.29 2.85
556 578 9.914131 TTGATACTTCATATCCACTCTTTATCG 57.086 33.333 0.00 0.00 39.29 2.92
670 709 2.492088 GACCACCATAAACCTTTCTGGC 59.508 50.000 2.83 0.00 37.79 4.85
671 710 2.158385 ACCACCATAAACCTTTCTGGCA 60.158 45.455 2.83 0.00 37.79 4.92
672 711 3.099141 CCACCATAAACCTTTCTGGCAT 58.901 45.455 2.83 0.00 37.79 4.40
673 712 4.264172 ACCACCATAAACCTTTCTGGCATA 60.264 41.667 2.83 0.00 37.79 3.14
674 713 4.895297 CCACCATAAACCTTTCTGGCATAT 59.105 41.667 2.83 0.00 37.79 1.78
675 714 6.068010 CCACCATAAACCTTTCTGGCATATA 58.932 40.000 2.83 0.00 37.79 0.86
676 715 6.016276 CCACCATAAACCTTTCTGGCATATAC 60.016 42.308 2.83 0.00 37.79 1.47
689 728 8.800370 TTCTGGCATATACATTTCTTGTGTTA 57.200 30.769 0.00 0.00 39.48 2.41
759 802 1.103398 AGAGCGCAACTGCCAAGTTT 61.103 50.000 11.47 0.00 44.47 2.66
832 1143 5.183331 TGCTTTACTAAGAGAAAGAGAGCGA 59.817 40.000 0.00 0.00 35.12 4.93
839 2323 7.832769 ACTAAGAGAAAGAGAGCGAAACTTAT 58.167 34.615 0.00 0.00 0.00 1.73
877 2361 9.577110 CAGCTACATACACAAATTGATGAAAAT 57.423 29.630 0.00 0.00 0.00 1.82
942 2426 9.802039 ATTTTCCTTACACATGAGTTAGGTAAA 57.198 29.630 24.11 24.11 39.85 2.01
1078 2563 0.385029 TGCATTTGACTGCACCACAC 59.615 50.000 0.00 0.00 46.76 3.82
1098 2583 1.610554 CGACCCCGGACTGGTACAAT 61.611 60.000 0.73 0.00 38.70 2.71
1212 2700 6.583912 ACTTACACGTCGGATATGAAATTG 57.416 37.500 0.00 0.00 0.00 2.32
1829 3992 4.024670 TGATGAATGGCCAATGTTGATGA 58.975 39.130 10.96 0.00 0.00 2.92
1889 4052 0.948623 TTGATTGCACCACCTCGACG 60.949 55.000 0.00 0.00 0.00 5.12
2261 4424 3.750371 TCACACATTTACTCTTGGTGGG 58.250 45.455 0.00 0.00 34.27 4.61
2560 4723 6.875726 TCATGATATATGCTTGCTAGGAACAC 59.124 38.462 0.00 0.00 0.00 3.32
2983 5146 3.323751 ACACGGTAGTTACACCCATTC 57.676 47.619 0.00 0.00 34.90 2.67
2984 5147 2.027837 ACACGGTAGTTACACCCATTCC 60.028 50.000 0.00 0.00 34.90 3.01
2985 5148 2.235402 CACGGTAGTTACACCCATTCCT 59.765 50.000 0.00 0.00 34.90 3.36
2986 5149 2.498885 ACGGTAGTTACACCCATTCCTC 59.501 50.000 0.00 0.00 34.90 3.71
2987 5150 2.498481 CGGTAGTTACACCCATTCCTCA 59.502 50.000 0.00 0.00 34.90 3.86
2988 5151 3.134081 CGGTAGTTACACCCATTCCTCAT 59.866 47.826 0.00 0.00 34.90 2.90
2989 5152 4.342951 CGGTAGTTACACCCATTCCTCATA 59.657 45.833 0.00 0.00 34.90 2.15
2990 5153 5.011738 CGGTAGTTACACCCATTCCTCATAT 59.988 44.000 0.00 0.00 34.90 1.78
2991 5154 6.231211 GGTAGTTACACCCATTCCTCATATG 58.769 44.000 0.00 0.00 31.91 1.78
2992 5155 4.718961 AGTTACACCCATTCCTCATATGC 58.281 43.478 0.00 0.00 0.00 3.14
2993 5156 4.413520 AGTTACACCCATTCCTCATATGCT 59.586 41.667 0.00 0.00 0.00 3.79
2994 5157 5.606749 AGTTACACCCATTCCTCATATGCTA 59.393 40.000 0.00 0.00 0.00 3.49
2995 5158 4.357918 ACACCCATTCCTCATATGCTAC 57.642 45.455 0.00 0.00 0.00 3.58
2996 5159 3.073062 ACACCCATTCCTCATATGCTACC 59.927 47.826 0.00 0.00 0.00 3.18
2997 5160 3.072915 CACCCATTCCTCATATGCTACCA 59.927 47.826 0.00 0.00 0.00 3.25
2998 5161 3.918912 ACCCATTCCTCATATGCTACCAT 59.081 43.478 0.00 0.00 35.44 3.55
2999 5162 4.263639 ACCCATTCCTCATATGCTACCATG 60.264 45.833 0.00 0.00 32.85 3.66
3000 5163 4.263639 CCCATTCCTCATATGCTACCATGT 60.264 45.833 0.00 0.00 32.85 3.21
3001 5164 4.698780 CCATTCCTCATATGCTACCATGTG 59.301 45.833 0.00 0.00 40.66 3.21
3002 5165 5.513614 CCATTCCTCATATGCTACCATGTGA 60.514 44.000 0.00 3.67 44.21 3.58
3003 5166 5.830799 TTCCTCATATGCTACCATGTGAT 57.169 39.130 0.00 0.00 44.94 3.06
3004 5167 6.933514 TTCCTCATATGCTACCATGTGATA 57.066 37.500 0.00 0.00 44.94 2.15
3005 5168 6.535963 TCCTCATATGCTACCATGTGATAG 57.464 41.667 0.00 0.00 44.94 2.08
3006 5169 6.019108 TCCTCATATGCTACCATGTGATAGT 58.981 40.000 0.00 0.00 44.94 2.12
3007 5170 7.182060 TCCTCATATGCTACCATGTGATAGTA 58.818 38.462 0.00 0.00 44.94 1.82
3008 5171 7.841222 TCCTCATATGCTACCATGTGATAGTAT 59.159 37.037 0.00 0.00 44.94 2.12
3009 5172 9.136323 CCTCATATGCTACCATGTGATAGTATA 57.864 37.037 0.00 8.25 44.94 1.47
3015 5178 9.928618 ATGCTACCATGTGATAGTATATACTCT 57.071 33.333 18.68 9.55 37.73 3.24
3075 5238 9.422681 TCTAAGATACTCCAAAGCTAACTATGT 57.577 33.333 0.00 0.00 0.00 2.29
3076 5239 9.469807 CTAAGATACTCCAAAGCTAACTATGTG 57.530 37.037 0.00 0.00 0.00 3.21
3077 5240 7.661536 AGATACTCCAAAGCTAACTATGTGA 57.338 36.000 0.00 0.00 0.00 3.58
3078 5241 8.079211 AGATACTCCAAAGCTAACTATGTGAA 57.921 34.615 0.00 0.00 0.00 3.18
3079 5242 8.540388 AGATACTCCAAAGCTAACTATGTGAAA 58.460 33.333 0.00 0.00 0.00 2.69
3080 5243 9.162764 GATACTCCAAAGCTAACTATGTGAAAA 57.837 33.333 0.00 0.00 0.00 2.29
3081 5244 7.817418 ACTCCAAAGCTAACTATGTGAAAAA 57.183 32.000 0.00 0.00 0.00 1.94
3098 5261 3.706600 AAAAATTGCATGTGAGCCCAT 57.293 38.095 0.00 0.00 0.00 4.00
3099 5262 2.684001 AAATTGCATGTGAGCCCATG 57.316 45.000 0.00 4.66 44.07 3.66
3100 5263 1.563924 AATTGCATGTGAGCCCATGT 58.436 45.000 9.53 0.00 43.33 3.21
3101 5264 1.563924 ATTGCATGTGAGCCCATGTT 58.436 45.000 9.53 0.00 43.33 2.71
3102 5265 1.340088 TTGCATGTGAGCCCATGTTT 58.660 45.000 9.53 0.00 43.33 2.83
3103 5266 1.340088 TGCATGTGAGCCCATGTTTT 58.660 45.000 9.53 0.00 43.33 2.43
3104 5267 1.693062 TGCATGTGAGCCCATGTTTTT 59.307 42.857 9.53 0.00 43.33 1.94
3105 5268 2.896044 TGCATGTGAGCCCATGTTTTTA 59.104 40.909 9.53 0.00 43.33 1.52
3106 5269 3.514706 TGCATGTGAGCCCATGTTTTTAT 59.485 39.130 9.53 0.00 43.33 1.40
3107 5270 4.708909 TGCATGTGAGCCCATGTTTTTATA 59.291 37.500 9.53 0.00 43.33 0.98
3108 5271 5.186603 TGCATGTGAGCCCATGTTTTTATAA 59.813 36.000 9.53 0.00 43.33 0.98
3109 5272 6.127111 TGCATGTGAGCCCATGTTTTTATAAT 60.127 34.615 9.53 0.00 43.33 1.28
3110 5273 7.069208 TGCATGTGAGCCCATGTTTTTATAATA 59.931 33.333 9.53 0.00 43.33 0.98
3111 5274 8.090214 GCATGTGAGCCCATGTTTTTATAATAT 58.910 33.333 9.53 0.00 43.33 1.28
3112 5275 9.985730 CATGTGAGCCCATGTTTTTATAATATT 57.014 29.630 0.00 0.00 37.91 1.28
3152 5315 9.646336 CATATTTGTACGTAAAAAGGAGTATGC 57.354 33.333 15.76 0.00 0.00 3.14
3153 5316 7.916914 ATTTGTACGTAAAAAGGAGTATGCT 57.083 32.000 15.76 0.00 40.15 3.79
3154 5317 6.956299 TTGTACGTAAAAAGGAGTATGCTC 57.044 37.500 1.56 1.56 33.13 4.26
3155 5318 6.028146 TGTACGTAAAAAGGAGTATGCTCA 57.972 37.500 13.14 0.00 43.37 4.26
3156 5319 6.457355 TGTACGTAAAAAGGAGTATGCTCAA 58.543 36.000 13.14 0.00 43.37 3.02
3157 5320 6.930164 TGTACGTAAAAAGGAGTATGCTCAAA 59.070 34.615 13.14 0.00 43.37 2.69
3158 5321 6.870971 ACGTAAAAAGGAGTATGCTCAAAA 57.129 33.333 13.14 0.00 43.37 2.44
3159 5322 7.448748 ACGTAAAAAGGAGTATGCTCAAAAT 57.551 32.000 13.14 0.00 43.37 1.82
3160 5323 8.556213 ACGTAAAAAGGAGTATGCTCAAAATA 57.444 30.769 13.14 0.00 43.37 1.40
3161 5324 9.174166 ACGTAAAAAGGAGTATGCTCAAAATAT 57.826 29.630 13.14 0.00 43.37 1.28
3277 5444 3.189287 GCATTTGACAGTACCACCTCAAG 59.811 47.826 0.00 0.00 0.00 3.02
3425 5595 6.197655 TGAAAATAGTTGATTCGACCGATACG 59.802 38.462 0.15 0.00 0.00 3.06
3623 5793 2.353505 GGACTTCGTCTCCAAAGTACCC 60.354 54.545 0.00 0.00 35.90 3.69
3659 5829 2.730672 CGGCGGAGAAGCGAACAAG 61.731 63.158 0.00 0.00 38.18 3.16
3704 5874 9.383519 GAGATACACTAATCCAAGTTTCATGAA 57.616 33.333 3.38 3.38 0.00 2.57
4058 6269 1.072505 GAAACAAGGAGGGGCACGA 59.927 57.895 0.00 0.00 0.00 4.35
4066 6277 1.402896 GGAGGGGCACGAGATGATGA 61.403 60.000 0.00 0.00 0.00 2.92
4067 6278 0.465705 GAGGGGCACGAGATGATGAA 59.534 55.000 0.00 0.00 0.00 2.57
4120 6335 2.573083 CGCCACCTTTGCCACCAAT 61.573 57.895 0.00 0.00 0.00 3.16
4122 6337 1.187567 GCCACCTTTGCCACCAATCT 61.188 55.000 0.00 0.00 0.00 2.40
4238 6469 4.341806 TCGAATACGGCCAGTCCTTATTTA 59.658 41.667 2.24 0.00 38.82 1.40
4245 6476 4.382685 CGGCCAGTCCTTATTTACTTCTGA 60.383 45.833 2.24 0.00 0.00 3.27
4333 6567 5.586643 GCTTTACTCTATCAAGTTTCCCCTG 59.413 44.000 0.00 0.00 0.00 4.45
4336 7450 5.428184 ACTCTATCAAGTTTCCCCTGAAG 57.572 43.478 0.00 0.00 0.00 3.02
4421 7567 8.262601 AGAATGATGGTCCATACATACAGTTA 57.737 34.615 3.72 0.00 0.00 2.24
4422 7568 8.370940 AGAATGATGGTCCATACATACAGTTAG 58.629 37.037 3.72 0.00 0.00 2.34
4423 7569 6.419484 TGATGGTCCATACATACAGTTAGG 57.581 41.667 3.72 0.00 0.00 2.69
4424 7570 5.903010 TGATGGTCCATACATACAGTTAGGT 59.097 40.000 3.72 0.00 0.00 3.08
4425 7571 6.385759 TGATGGTCCATACATACAGTTAGGTT 59.614 38.462 3.72 0.00 0.00 3.50
4426 7572 7.565768 TGATGGTCCATACATACAGTTAGGTTA 59.434 37.037 3.72 0.00 0.00 2.85
4428 7574 6.183360 TGGTCCATACATACAGTTAGGTTAGC 60.183 42.308 0.00 0.00 0.00 3.09
4429 7575 6.041751 GGTCCATACATACAGTTAGGTTAGCT 59.958 42.308 0.00 0.00 0.00 3.32
4430 7576 7.232127 GGTCCATACATACAGTTAGGTTAGCTA 59.768 40.741 0.00 0.00 0.00 3.32
4431 7577 8.298140 GTCCATACATACAGTTAGGTTAGCTAG 58.702 40.741 0.00 0.00 0.00 3.42
4432 7578 7.039923 TCCATACATACAGTTAGGTTAGCTAGC 60.040 40.741 6.62 6.62 0.00 3.42
4435 7581 3.528597 ACAGTTAGGTTAGCTAGCTGC 57.471 47.619 26.87 18.49 38.59 5.25
4451 7597 7.772332 GCTAGCTGCTGTTAATTTCTACTAA 57.228 36.000 13.43 0.00 38.95 2.24
4452 7598 8.371770 GCTAGCTGCTGTTAATTTCTACTAAT 57.628 34.615 13.43 0.00 38.95 1.73
4453 7599 8.831550 GCTAGCTGCTGTTAATTTCTACTAATT 58.168 33.333 13.43 0.00 38.95 1.40
4456 7602 8.391106 AGCTGCTGTTAATTTCTACTAATTTCG 58.609 33.333 0.00 0.00 0.00 3.46
4465 7611 6.627690 TTTCTACTAATTTCGAAGTCAGCG 57.372 37.500 0.00 0.00 0.00 5.18
4466 7612 4.103357 TCTACTAATTTCGAAGTCAGCGC 58.897 43.478 0.00 0.00 0.00 5.92
4467 7613 2.000447 ACTAATTTCGAAGTCAGCGCC 59.000 47.619 2.29 0.00 0.00 6.53
4468 7614 2.271800 CTAATTTCGAAGTCAGCGCCT 58.728 47.619 2.29 0.00 0.00 5.52
4469 7615 1.523758 AATTTCGAAGTCAGCGCCTT 58.476 45.000 2.29 0.00 0.00 4.35
4470 7616 0.798776 ATTTCGAAGTCAGCGCCTTG 59.201 50.000 2.29 0.00 0.00 3.61
4471 7617 1.227999 TTTCGAAGTCAGCGCCTTGG 61.228 55.000 2.29 1.75 0.00 3.61
4472 7618 3.793144 CGAAGTCAGCGCCTTGGC 61.793 66.667 2.29 0.00 0.00 4.52
4473 7619 3.793144 GAAGTCAGCGCCTTGGCG 61.793 66.667 27.32 27.32 38.18 5.69
4474 7620 4.626081 AAGTCAGCGCCTTGGCGT 62.626 61.111 30.53 17.15 38.18 5.68
4485 7631 2.415357 CGCCTTGGCGTACAATTTTGAT 60.415 45.455 24.03 0.00 38.65 2.57
4624 7795 2.981302 CTCAGCGGGTGGTCATGA 59.019 61.111 7.42 0.00 0.00 3.07
4676 7847 1.258982 GCGGAGTGATTAACGATGCAG 59.741 52.381 0.00 0.00 0.00 4.41
4728 7899 3.151958 GAGATCTTAGCGGCCGCCA 62.152 63.158 44.47 32.33 43.17 5.69
4818 7989 6.329460 AGTCCCTTAAGTTTACAAGAAGTCCT 59.671 38.462 0.97 0.00 0.00 3.85
4868 8039 6.039829 GGTGAATTTCAGTCCCTCATATTTCC 59.960 42.308 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 3.751698 GCGGGTCAATGTAGACTTTTCTT 59.248 43.478 0.00 0.00 38.57 2.52
175 176 9.981114 CCTAGTAAATGTGAACCTTTCATTTTT 57.019 29.630 7.48 4.26 42.47 1.94
232 233 6.071728 CCATCAAAGGCTAGATCAAGTTGTTT 60.072 38.462 2.11 0.00 0.00 2.83
289 311 4.392940 AGGATGACAAGGTTCTTCAACAG 58.607 43.478 0.00 0.00 33.70 3.16
307 329 4.330250 CTTTCTCATGACACCACAAGGAT 58.670 43.478 0.00 0.00 38.69 3.24
330 352 1.942657 CAATGACCTTATCCGCACCAG 59.057 52.381 0.00 0.00 0.00 4.00
447 469 6.400940 CCAACATCAACACACACAAGAAAAAC 60.401 38.462 0.00 0.00 0.00 2.43
485 507 1.369321 CCCGGCCTCTTCATAGCTC 59.631 63.158 0.00 0.00 0.00 4.09
493 515 4.643387 GCACACACCCGGCCTCTT 62.643 66.667 0.00 0.00 0.00 2.85
523 545 8.859236 AGTGGATATGAAGTATCAAATGGATG 57.141 34.615 0.00 0.00 40.86 3.51
535 557 6.978674 TCCGATAAAGAGTGGATATGAAGT 57.021 37.500 0.00 0.00 0.00 3.01
564 602 2.198406 TCTGTCAAGTTGTTCGGTTCG 58.802 47.619 2.11 0.00 0.00 3.95
839 2323 8.499403 TGTGTATGTAGCTGCACATAAAAATA 57.501 30.769 19.27 9.39 41.74 1.40
877 2361 9.489084 GAGCCATAGACACACATAATATGTAAA 57.511 33.333 5.49 0.00 42.70 2.01
1098 2583 4.707448 ACCAACCAAAACACATTGTCTACA 59.293 37.500 0.00 0.00 0.00 2.74
1212 2700 3.614616 CGTTTATCTCAGCAGAGTCAACC 59.385 47.826 5.98 0.00 42.66 3.77
1546 3041 3.255888 TGCGAAGACCCTGTAGCATATAG 59.744 47.826 0.00 0.00 0.00 1.31
1889 4052 0.823356 TCACCTTGTTCCAAGCTGGC 60.823 55.000 0.00 0.00 37.47 4.85
2261 4424 7.900782 AATACGTACTTGGTTATATGCATCC 57.099 36.000 0.19 0.00 0.00 3.51
2963 5126 2.027837 GGAATGGGTGTAACTACCGTGT 60.028 50.000 0.00 0.00 41.79 4.49
2964 5127 2.235402 AGGAATGGGTGTAACTACCGTG 59.765 50.000 0.00 0.00 41.79 4.94
2965 5128 2.498885 GAGGAATGGGTGTAACTACCGT 59.501 50.000 0.00 0.00 41.79 4.83
2966 5129 2.498481 TGAGGAATGGGTGTAACTACCG 59.502 50.000 0.00 0.00 41.79 4.02
2967 5130 4.772886 ATGAGGAATGGGTGTAACTACC 57.227 45.455 0.00 0.00 40.10 3.18
2968 5131 5.701290 GCATATGAGGAATGGGTGTAACTAC 59.299 44.000 6.97 0.00 36.74 2.73
2969 5132 5.606749 AGCATATGAGGAATGGGTGTAACTA 59.393 40.000 6.97 0.00 36.74 2.24
2970 5133 4.413520 AGCATATGAGGAATGGGTGTAACT 59.586 41.667 6.97 0.00 36.74 2.24
2971 5134 4.718961 AGCATATGAGGAATGGGTGTAAC 58.281 43.478 6.97 0.00 0.00 2.50
2972 5135 5.221843 GGTAGCATATGAGGAATGGGTGTAA 60.222 44.000 6.97 0.00 0.00 2.41
2973 5136 4.286032 GGTAGCATATGAGGAATGGGTGTA 59.714 45.833 6.97 0.00 0.00 2.90
2974 5137 3.073062 GGTAGCATATGAGGAATGGGTGT 59.927 47.826 6.97 0.00 0.00 4.16
2975 5138 3.072915 TGGTAGCATATGAGGAATGGGTG 59.927 47.826 6.97 0.00 0.00 4.61
2976 5139 3.326521 TGGTAGCATATGAGGAATGGGT 58.673 45.455 6.97 0.00 0.00 4.51
2977 5140 4.263639 ACATGGTAGCATATGAGGAATGGG 60.264 45.833 7.18 0.00 0.00 4.00
2978 5141 4.698780 CACATGGTAGCATATGAGGAATGG 59.301 45.833 7.41 0.00 0.00 3.16
2979 5142 5.554070 TCACATGGTAGCATATGAGGAATG 58.446 41.667 11.71 5.71 0.00 2.67
2980 5143 5.830799 TCACATGGTAGCATATGAGGAAT 57.169 39.130 11.71 0.00 0.00 3.01
2981 5144 5.830799 ATCACATGGTAGCATATGAGGAA 57.169 39.130 19.57 0.00 0.00 3.36
2982 5145 6.019108 ACTATCACATGGTAGCATATGAGGA 58.981 40.000 19.57 10.28 0.00 3.71
2983 5146 6.291648 ACTATCACATGGTAGCATATGAGG 57.708 41.667 19.57 16.25 0.00 3.86
2989 5152 9.928618 AGAGTATATACTATCACATGGTAGCAT 57.071 33.333 15.42 0.40 36.50 3.79
3049 5212 9.422681 ACATAGTTAGCTTTGGAGTATCTTAGA 57.577 33.333 0.00 0.00 33.73 2.10
3050 5213 9.469807 CACATAGTTAGCTTTGGAGTATCTTAG 57.530 37.037 0.00 0.00 33.73 2.18
3051 5214 9.197306 TCACATAGTTAGCTTTGGAGTATCTTA 57.803 33.333 0.00 0.00 33.73 2.10
3052 5215 8.079211 TCACATAGTTAGCTTTGGAGTATCTT 57.921 34.615 0.00 0.00 33.73 2.40
3053 5216 7.661536 TCACATAGTTAGCTTTGGAGTATCT 57.338 36.000 0.00 0.00 33.73 1.98
3054 5217 8.718102 TTTCACATAGTTAGCTTTGGAGTATC 57.282 34.615 0.00 0.00 0.00 2.24
3055 5218 9.515226 TTTTTCACATAGTTAGCTTTGGAGTAT 57.485 29.630 0.00 0.00 0.00 2.12
3056 5219 8.911918 TTTTTCACATAGTTAGCTTTGGAGTA 57.088 30.769 0.00 0.00 0.00 2.59
3057 5220 7.817418 TTTTTCACATAGTTAGCTTTGGAGT 57.183 32.000 0.00 0.00 0.00 3.85
3078 5241 3.340034 CATGGGCTCACATGCAATTTTT 58.660 40.909 0.00 0.00 41.43 1.94
3079 5242 2.980568 CATGGGCTCACATGCAATTTT 58.019 42.857 0.00 0.00 41.43 1.82
3080 5243 2.684001 CATGGGCTCACATGCAATTT 57.316 45.000 0.00 0.00 41.43 1.82
3126 5289 9.646336 GCATACTCCTTTTTACGTACAAATATG 57.354 33.333 15.08 15.08 0.00 1.78
3127 5290 9.609346 AGCATACTCCTTTTTACGTACAAATAT 57.391 29.630 7.32 0.93 0.00 1.28
3128 5291 9.090692 GAGCATACTCCTTTTTACGTACAAATA 57.909 33.333 7.32 0.00 36.90 1.40
3129 5292 7.604927 TGAGCATACTCCTTTTTACGTACAAAT 59.395 33.333 7.32 0.00 42.74 2.32
3130 5293 6.930164 TGAGCATACTCCTTTTTACGTACAAA 59.070 34.615 6.71 6.71 42.74 2.83
3131 5294 6.457355 TGAGCATACTCCTTTTTACGTACAA 58.543 36.000 0.00 0.00 42.74 2.41
3132 5295 6.028146 TGAGCATACTCCTTTTTACGTACA 57.972 37.500 0.00 0.00 42.74 2.90
3133 5296 6.956299 TTGAGCATACTCCTTTTTACGTAC 57.044 37.500 0.00 0.00 42.74 3.67
3134 5297 7.966246 TTTTGAGCATACTCCTTTTTACGTA 57.034 32.000 0.00 0.00 42.74 3.57
3135 5298 6.870971 TTTTGAGCATACTCCTTTTTACGT 57.129 33.333 0.00 0.00 42.74 3.57
3249 5416 4.457603 GGTGGTACTGTCAAATGCATACAA 59.542 41.667 0.00 0.00 0.00 2.41
3277 5444 4.947388 TGTCCACAGTTTTATAATCTGGGC 59.053 41.667 16.91 7.27 32.02 5.36
3425 5595 6.150318 GCTTCTTTTGTAGCCTTTTAACTCC 58.850 40.000 0.00 0.00 36.94 3.85
3650 5820 2.056577 GTACTTACGTGCTTGTTCGCT 58.943 47.619 0.00 0.00 0.00 4.93
3659 5829 4.491676 TCTCCAATCTTGTACTTACGTGC 58.508 43.478 0.00 0.00 0.00 5.34
3720 5890 2.604914 GCGTCATACATGAGTGAGTTGG 59.395 50.000 0.00 0.00 37.51 3.77
4058 6269 2.094675 CTGGGCGGTTTTTCATCATCT 58.905 47.619 0.00 0.00 0.00 2.90
4093 6308 2.853290 AAAGGTGGCGACGACTCGT 61.853 57.895 3.08 3.08 45.10 4.18
4333 6567 0.935196 AGCGAACACGGTTCAACTTC 59.065 50.000 14.43 0.00 34.06 3.01
4336 7450 1.774639 TCTAGCGAACACGGTTCAAC 58.225 50.000 14.43 7.68 38.63 3.18
4430 7576 8.391106 CGAAATTAGTAGAAATTAACAGCAGCT 58.609 33.333 0.00 0.00 0.00 4.24
4431 7577 8.388103 TCGAAATTAGTAGAAATTAACAGCAGC 58.612 33.333 0.00 0.00 0.00 5.25
4440 7586 7.674240 GCGCTGACTTCGAAATTAGTAGAAATT 60.674 37.037 0.00 0.00 0.00 1.82
4441 7587 6.237861 GCGCTGACTTCGAAATTAGTAGAAAT 60.238 38.462 0.00 0.00 0.00 2.17
4444 7590 4.103357 GCGCTGACTTCGAAATTAGTAGA 58.897 43.478 0.00 0.00 0.00 2.59
4447 7593 2.000447 GGCGCTGACTTCGAAATTAGT 59.000 47.619 7.64 0.00 0.00 2.24
4451 7597 0.798776 CAAGGCGCTGACTTCGAAAT 59.201 50.000 7.64 0.00 0.00 2.17
4452 7598 1.227999 CCAAGGCGCTGACTTCGAAA 61.228 55.000 7.64 0.00 0.00 3.46
4453 7599 1.667830 CCAAGGCGCTGACTTCGAA 60.668 57.895 7.64 0.00 0.00 3.71
4454 7600 2.048222 CCAAGGCGCTGACTTCGA 60.048 61.111 7.64 0.00 0.00 3.71
4465 7611 2.715737 TCAAAATTGTACGCCAAGGC 57.284 45.000 0.00 0.00 36.25 4.35
4466 7612 5.469479 AGAAATCAAAATTGTACGCCAAGG 58.531 37.500 0.00 0.00 36.25 3.61
4467 7613 6.148948 TGAGAAATCAAAATTGTACGCCAAG 58.851 36.000 0.00 0.00 36.25 3.61
4468 7614 6.078202 TGAGAAATCAAAATTGTACGCCAA 57.922 33.333 0.00 0.00 37.49 4.52
4469 7615 5.697473 TGAGAAATCAAAATTGTACGCCA 57.303 34.783 0.00 0.00 0.00 5.69
4470 7616 7.581011 ATTTGAGAAATCAAAATTGTACGCC 57.419 32.000 7.43 0.00 42.04 5.68
4471 7617 7.475256 GCAATTTGAGAAATCAAAATTGTACGC 59.525 33.333 22.03 12.51 42.04 4.42
4472 7618 8.702438 AGCAATTTGAGAAATCAAAATTGTACG 58.298 29.630 22.03 8.85 42.04 3.67
4609 7780 1.300971 CTTGTCATGACCACCCGCTG 61.301 60.000 22.85 0.00 0.00 5.18
4624 7795 5.247110 TCTCCTCTGCTAGTCAATTTCTTGT 59.753 40.000 0.00 0.00 33.87 3.16
4676 7847 4.089923 GTGATTTGTGCGGAAATTTGTAGC 59.910 41.667 0.00 0.00 0.00 3.58
4728 7899 8.955794 AGGTAGAATTCTCTCTTCTAGTATCCT 58.044 37.037 12.24 0.00 36.23 3.24
4789 7960 9.910267 ACTTCTTGTAAACTTAAGGGACTAAAA 57.090 29.630 7.53 0.00 38.49 1.52
4796 7967 6.531021 TGAGGACTTCTTGTAAACTTAAGGG 58.469 40.000 7.53 0.00 0.00 3.95
4818 7989 4.657814 AAAAAGTTGAGGGGCTAGATGA 57.342 40.909 0.00 0.00 0.00 2.92
4844 8015 6.603201 TGGAAATATGAGGGACTGAAATTCAC 59.397 38.462 0.00 0.00 41.55 3.18
4852 8023 6.588719 TTTGTTTGGAAATATGAGGGACTG 57.411 37.500 0.00 0.00 41.55 3.51


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

AutoCloner maintained by Alex Coulton.