Multiple sequence alignment - TraesCS1D01G249900

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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 TraesCS1D01G249900 chr1D 100.000 2683 0 0 975 3657 342232003 342229321 0.000000e+00 4955.0
1 TraesCS1D01G249900 chr1D 100.000 592 0 0 1 592 342232977 342232386 0.000000e+00 1094.0
2 TraesCS1D01G249900 chr1D 77.907 430 77 14 9 428 366208493 366208072 6.060000e-63 252.0
3 TraesCS1D01G249900 chr1B 90.151 1127 73 19 975 2079 458387532 458386422 0.000000e+00 1432.0
4 TraesCS1D01G249900 chr1B 90.292 958 57 10 2017 2965 458386416 458385486 0.000000e+00 1221.0
5 TraesCS1D01G249900 chr1B 84.812 586 59 16 7 569 212426504 212425926 2.470000e-156 562.0
6 TraesCS1D01G249900 chr1B 87.759 482 52 3 1 475 458388308 458387827 1.150000e-154 556.0
7 TraesCS1D01G249900 chr1B 93.333 180 10 1 3079 3256 458385487 458385308 7.790000e-67 265.0
8 TraesCS1D01G249900 chr1B 93.103 116 6 2 455 569 458387805 458387691 6.280000e-38 169.0
9 TraesCS1D01G249900 chr1B 89.076 119 13 0 2962 3080 555753213 555753095 8.180000e-32 148.0
10 TraesCS1D01G249900 chr1A 94.356 939 37 3 975 1911 441956985 441956061 0.000000e+00 1426.0
11 TraesCS1D01G249900 chr1A 93.719 605 31 4 1910 2507 441955803 441955199 0.000000e+00 900.0
12 TraesCS1D01G249900 chr1A 96.112 463 16 1 2503 2965 441955146 441954686 0.000000e+00 754.0
13 TraesCS1D01G249900 chr1A 94.925 335 17 0 3082 3416 441954684 441954350 3.240000e-145 525.0
14 TraesCS1D01G249900 chr1A 93.133 233 14 2 3426 3657 441954271 441954040 1.260000e-89 340.0
15 TraesCS1D01G249900 chr6D 85.448 591 52 18 4 569 162265177 162264596 5.260000e-163 584.0
16 TraesCS1D01G249900 chr6D 77.640 161 22 11 328 481 162273839 162273686 6.510000e-13 86.1
17 TraesCS1D01G249900 chr4D 79.212 457 83 5 4 448 220017128 220016672 1.280000e-79 307.0
18 TraesCS1D01G249900 chr4D 91.925 161 12 1 3257 3416 220367606 220367446 1.320000e-54 224.0
19 TraesCS1D01G249900 chr4A 92.169 166 12 1 3254 3418 115567074 115567239 2.200000e-57 233.0
20 TraesCS1D01G249900 chr2A 76.765 439 85 15 8 439 148872304 148871876 2.840000e-56 230.0
21 TraesCS1D01G249900 chr2A 87.970 133 15 1 2949 3080 611025259 611025391 4.890000e-34 156.0
22 TraesCS1D01G249900 chr3D 91.463 164 13 1 3254 3416 324319111 324319274 1.320000e-54 224.0
23 TraesCS1D01G249900 chr3D 91.304 161 13 1 3257 3416 313292528 313292368 6.150000e-53 219.0
24 TraesCS1D01G249900 chr5D 90.854 164 14 1 3254 3416 67584593 67584756 6.150000e-53 219.0
25 TraesCS1D01G249900 chr5D 91.304 161 13 1 3257 3416 277243271 277243111 6.150000e-53 219.0
26 TraesCS1D01G249900 chr3B 91.304 161 13 1 3257 3416 415934408 415934248 6.150000e-53 219.0
27 TraesCS1D01G249900 chr3B 77.966 295 58 7 50 340 82405550 82405841 1.040000e-40 178.0
28 TraesCS1D01G249900 chr3B 90.598 117 11 0 2964 3080 54809407 54809291 4.890000e-34 156.0
29 TraesCS1D01G249900 chr2B 91.304 161 13 1 3257 3416 227853466 227853306 6.150000e-53 219.0
30 TraesCS1D01G249900 chr2B 91.597 119 10 0 2962 3080 624544491 624544373 8.120000e-37 165.0
31 TraesCS1D01G249900 chr5B 92.623 122 9 0 2959 3080 485568828 485568949 3.750000e-40 176.0
32 TraesCS1D01G249900 chr6A 79.859 283 22 21 312 569 503530865 503530593 1.350000e-39 174.0
33 TraesCS1D01G249900 chr6A 92.437 119 9 0 2964 3082 537483619 537483501 1.750000e-38 171.0
34 TraesCS1D01G249900 chr6A 76.667 300 57 10 51 342 486832117 486832411 1.760000e-33 154.0
35 TraesCS1D01G249900 chr6A 89.831 118 12 0 2963 3080 595781867 595781984 6.320000e-33 152.0
36 TraesCS1D01G249900 chr6B 90.323 124 9 3 2959 3081 257495841 257495962 3.780000e-35 159.0
37 TraesCS1D01G249900 chr7B 89.344 122 12 1 2960 3081 188605904 188605784 6.320000e-33 152.0
38 TraesCS1D01G249900 chr4B 84.043 94 14 1 352 444 247640726 247640633 5.030000e-14 89.8


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 TraesCS1D01G249900 chr1D 342229321 342232977 3656 True 3024.5 4955 100.0000 1 3657 2 chr1D.!!$R2 3656
1 TraesCS1D01G249900 chr1B 458385308 458388308 3000 True 728.6 1432 90.9276 1 3256 5 chr1B.!!$R3 3255
2 TraesCS1D01G249900 chr1B 212425926 212426504 578 True 562.0 562 84.8120 7 569 1 chr1B.!!$R1 562
3 TraesCS1D01G249900 chr1A 441954040 441956985 2945 True 789.0 1426 94.4490 975 3657 5 chr1A.!!$R1 2682
4 TraesCS1D01G249900 chr6D 162264596 162265177 581 True 584.0 584 85.4480 4 569 1 chr6D.!!$R1 565

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
565 634 0.113190 TCAGAGTCCACTGCTCAGGA 59.887 55.000 1.66 0.0 37.75 3.86 F
566 635 1.193323 CAGAGTCCACTGCTCAGGAT 58.807 55.000 1.66 0.0 36.11 3.24 F
1340 1446 1.336125 GATTCGGGTAGTACGGGACAG 59.664 57.143 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2845 0.753867 TGTGTAGGCACTCGTTTCCA 59.246 50.000 0.00 0.00 45.44 3.53 R
2389 2846 2.094762 ATGTGTAGGCACTCGTTTCC 57.905 50.000 0.00 0.00 45.44 3.13 R
3306 3828 1.600957 CATGGATAGCAAGCTTCCACG 59.399 52.381 20.41 13.24 42.09 4.94 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 2.925170 AAGGCCGTCTGCACCTCT 60.925 61.111 0.00 0.00 43.89 3.69
40 41 2.941333 CACCTCTGCGCACTTGTG 59.059 61.111 5.66 10.11 0.00 3.33
83 84 4.544689 CGGGAGAGCAGCGTCTCG 62.545 72.222 5.77 5.77 43.54 4.04
104 105 4.087892 AGCGCGGTGAGATTGGCT 62.088 61.111 11.39 0.00 0.00 4.75
121 128 2.204136 TGTCTGCTCCCCCATGGT 60.204 61.111 11.73 0.00 34.77 3.55
195 202 0.685131 TCTAAGCGGATCGAACCCCA 60.685 55.000 6.09 0.00 0.00 4.96
196 203 0.393077 CTAAGCGGATCGAACCCCAT 59.607 55.000 6.09 0.00 0.00 4.00
207 214 2.841266 TCGAACCCCATGTAGGATTTCA 59.159 45.455 6.04 0.00 41.22 2.69
222 229 0.886938 TTTCATGCGCTTCACCGGAA 60.887 50.000 9.46 0.00 30.90 4.30
235 242 0.744414 ACCGGAATGAATCGCACCTG 60.744 55.000 9.46 0.00 0.00 4.00
238 245 1.027357 GGAATGAATCGCACCTGCAT 58.973 50.000 0.00 0.00 42.21 3.96
240 247 1.672363 GAATGAATCGCACCTGCATCA 59.328 47.619 0.00 0.00 42.21 3.07
360 368 1.198867 CGGTTGGATTTGATCGCACAA 59.801 47.619 0.00 0.00 0.00 3.33
389 397 1.758906 GGGGACGAGGAGAGGAAGG 60.759 68.421 0.00 0.00 0.00 3.46
391 399 2.776913 GGACGAGGAGAGGAAGGCG 61.777 68.421 0.00 0.00 0.00 5.52
430 438 5.692928 AGAAAGGGGATGAGATTCAGATTG 58.307 41.667 0.00 0.00 0.00 2.67
440 449 5.478407 TGAGATTCAGATTGTGAGCGTTTA 58.522 37.500 0.00 0.00 36.21 2.01
461 512 2.162681 TCTTGCTGATCTGTCTCACGA 58.837 47.619 1.27 0.00 0.00 4.35
462 513 2.163211 TCTTGCTGATCTGTCTCACGAG 59.837 50.000 1.27 0.00 0.00 4.18
481 532 6.049149 CACGAGATCCAGGTGTTTAATACAT 58.951 40.000 0.00 0.00 39.39 2.29
492 560 3.940221 TGTTTAATACATACACGCACCCC 59.060 43.478 0.00 0.00 0.00 4.95
528 597 4.751431 GGCTCAGCCCAAACTCAT 57.249 55.556 3.37 0.00 44.06 2.90
565 634 0.113190 TCAGAGTCCACTGCTCAGGA 59.887 55.000 1.66 0.00 37.75 3.86
566 635 1.193323 CAGAGTCCACTGCTCAGGAT 58.807 55.000 1.66 0.00 36.11 3.24
575 680 1.695239 TGCTCAGGATGGCCCATCT 60.695 57.895 22.58 6.76 40.39 2.90
1254 1360 4.150359 GTCGGGGTAATATTCTCTCTCCA 58.850 47.826 0.00 0.00 0.00 3.86
1319 1425 4.774726 TGGGATACTAGATCTTGCATCTCC 59.225 45.833 12.89 13.08 0.00 3.71
1323 1429 6.127479 GGATACTAGATCTTGCATCTCCGATT 60.127 42.308 14.51 0.00 0.00 3.34
1340 1446 1.336125 GATTCGGGTAGTACGGGACAG 59.664 57.143 0.00 0.00 0.00 3.51
1387 1493 7.138736 AGACATGTTTCTCGTAATTTTGTTGG 58.861 34.615 0.00 0.00 0.00 3.77
1596 1721 5.241506 TCTTCTGAAAATCGCATTGAAGGTT 59.758 36.000 0.00 0.00 32.77 3.50
1613 1738 3.019564 AGGTTGTATGCTCTGCCAATTC 58.980 45.455 0.00 0.00 0.00 2.17
1622 1747 2.223433 GCTCTGCCAATTCTTCATTCCG 60.223 50.000 0.00 0.00 0.00 4.30
1624 1749 3.273434 TCTGCCAATTCTTCATTCCGAG 58.727 45.455 0.00 0.00 0.00 4.63
1806 1933 2.722094 TGTGGAATGCCTTGGTGATAC 58.278 47.619 0.00 0.00 34.31 2.24
1843 1970 6.851222 AAATTCAGCTGACTATGTAATCGG 57.149 37.500 18.03 0.00 0.00 4.18
1868 1995 9.897744 GGGTATTGTGTGTAATGATCATATTTG 57.102 33.333 9.04 0.00 0.00 2.32
1902 2029 5.772393 TTTAATAGTGTCCTGGACCACAT 57.228 39.130 23.42 10.74 0.00 3.21
1940 2326 8.233868 TCTTGTCACGTATGATTAACAATTTGG 58.766 33.333 0.78 0.00 37.14 3.28
1979 2365 9.702494 CATATTCCATGCAGATATACATATCGT 57.298 33.333 0.00 0.00 43.01 3.73
2109 2559 1.603678 GGCACAACATCCTTTGCACAG 60.604 52.381 0.00 0.00 36.66 3.66
2285 2739 4.561105 CTTCCGCAGTTCTCTCTTAAACT 58.439 43.478 0.00 0.00 36.16 2.66
2305 2760 6.496144 AACTCCCGTTAGCCTATATTTCTT 57.504 37.500 0.00 0.00 0.00 2.52
2387 2844 8.297426 TCTCTTGTATATACTTCTACAATGCCG 58.703 37.037 13.89 0.00 37.26 5.69
2388 2845 7.948357 TCTTGTATATACTTCTACAATGCCGT 58.052 34.615 13.89 0.00 37.26 5.68
2389 2846 7.865889 TCTTGTATATACTTCTACAATGCCGTG 59.134 37.037 13.89 0.00 37.26 4.94
2428 2891 5.355071 CACATTTTAGCTTAGCACAGGATGA 59.645 40.000 7.07 0.00 39.69 2.92
2514 3034 6.128200 TGTTCACTCATTGAGTATGATTGTGC 60.128 38.462 18.59 4.77 41.37 4.57
2525 3045 6.484977 TGAGTATGATTGTGCACAACTTTGTA 59.515 34.615 33.29 18.23 39.91 2.41
2533 3053 4.142293 TGTGCACAACTTTGTATTGCTCAA 60.142 37.500 19.28 0.00 39.91 3.02
2777 3297 2.841442 ACTCTCTTGCTGGGTGTTAC 57.159 50.000 0.00 0.00 0.00 2.50
2800 3320 2.026822 CACTCCCTTTGAGCACTATGGT 60.027 50.000 0.00 0.00 45.61 3.55
2818 3338 2.708861 TGGTACCAATCTGTTCCACAGT 59.291 45.455 13.60 0.00 46.03 3.55
2819 3339 3.074412 GGTACCAATCTGTTCCACAGTG 58.926 50.000 7.15 0.00 46.03 3.66
2920 3440 6.321945 TCTCATATGTAATTGGCATGCTGTTT 59.678 34.615 18.92 10.76 0.00 2.83
2973 3493 5.995565 TTGGTTGATATATACTCCCTCCG 57.004 43.478 0.00 0.00 0.00 4.63
2974 3494 5.006896 TGGTTGATATATACTCCCTCCGT 57.993 43.478 0.00 0.00 0.00 4.69
2975 3495 5.014858 TGGTTGATATATACTCCCTCCGTC 58.985 45.833 0.00 0.00 0.00 4.79
2976 3496 4.401837 GGTTGATATATACTCCCTCCGTCC 59.598 50.000 0.00 0.00 0.00 4.79
2977 3497 5.262804 GTTGATATATACTCCCTCCGTCCT 58.737 45.833 0.00 0.00 0.00 3.85
2978 3498 4.856509 TGATATATACTCCCTCCGTCCTG 58.143 47.826 0.00 0.00 0.00 3.86
2979 3499 4.538891 TGATATATACTCCCTCCGTCCTGA 59.461 45.833 0.00 0.00 0.00 3.86
2980 3500 3.897657 ATATACTCCCTCCGTCCTGAA 57.102 47.619 0.00 0.00 0.00 3.02
2981 3501 2.544844 ATACTCCCTCCGTCCTGAAA 57.455 50.000 0.00 0.00 0.00 2.69
2982 3502 2.544844 TACTCCCTCCGTCCTGAAAT 57.455 50.000 0.00 0.00 0.00 2.17
2983 3503 2.544844 ACTCCCTCCGTCCTGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
2984 3504 2.108970 ACTCCCTCCGTCCTGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
2985 3505 2.292323 ACTCCCTCCGTCCTGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
2986 3506 2.766828 CTCCCTCCGTCCTGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
2987 3507 2.500098 TCCCTCCGTCCTGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
2988 3508 2.236395 CCCTCCGTCCTGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
2989 3509 3.522553 CCTCCGTCCTGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
2990 3510 3.179830 CTCCGTCCTGAAATACTTGTCG 58.820 50.000 0.00 0.00 0.00 4.35
2991 3511 2.821378 TCCGTCCTGAAATACTTGTCGA 59.179 45.455 0.00 0.00 0.00 4.20
2992 3512 3.256383 TCCGTCCTGAAATACTTGTCGAA 59.744 43.478 0.00 0.00 0.00 3.71
2993 3513 3.612860 CCGTCCTGAAATACTTGTCGAAG 59.387 47.826 0.00 0.00 35.07 3.79
2994 3514 4.482386 CGTCCTGAAATACTTGTCGAAGA 58.518 43.478 0.00 0.00 32.98 2.87
2995 3515 4.921515 CGTCCTGAAATACTTGTCGAAGAA 59.078 41.667 0.00 0.00 39.69 2.52
2996 3516 5.404366 CGTCCTGAAATACTTGTCGAAGAAA 59.596 40.000 0.00 0.00 39.69 2.52
2997 3517 6.090898 CGTCCTGAAATACTTGTCGAAGAAAT 59.909 38.462 0.00 0.00 39.69 2.17
2998 3518 7.237173 GTCCTGAAATACTTGTCGAAGAAATG 58.763 38.462 0.00 0.00 39.69 2.32
2999 3519 6.371548 TCCTGAAATACTTGTCGAAGAAATGG 59.628 38.462 0.00 0.00 39.69 3.16
3000 3520 6.149474 CCTGAAATACTTGTCGAAGAAATGGT 59.851 38.462 0.00 0.00 39.69 3.55
3001 3521 7.308589 CCTGAAATACTTGTCGAAGAAATGGTT 60.309 37.037 0.00 0.00 39.69 3.67
3002 3522 8.610248 TGAAATACTTGTCGAAGAAATGGTTA 57.390 30.769 0.00 0.00 39.69 2.85
3003 3523 9.058174 TGAAATACTTGTCGAAGAAATGGTTAA 57.942 29.630 0.00 0.00 39.69 2.01
3004 3524 9.887406 GAAATACTTGTCGAAGAAATGGTTAAA 57.113 29.630 0.00 0.00 39.69 1.52
3008 3528 8.574196 ACTTGTCGAAGAAATGGTTAAAATTG 57.426 30.769 0.00 0.00 39.69 2.32
3009 3529 7.651704 ACTTGTCGAAGAAATGGTTAAAATTGG 59.348 33.333 0.00 0.00 39.69 3.16
3010 3530 7.278461 TGTCGAAGAAATGGTTAAAATTGGA 57.722 32.000 0.00 0.00 39.69 3.53
3011 3531 7.891561 TGTCGAAGAAATGGTTAAAATTGGAT 58.108 30.769 0.00 0.00 39.69 3.41
3012 3532 7.812191 TGTCGAAGAAATGGTTAAAATTGGATG 59.188 33.333 0.00 0.00 39.69 3.51
3013 3533 7.812669 GTCGAAGAAATGGTTAAAATTGGATGT 59.187 33.333 0.00 0.00 39.69 3.06
3014 3534 9.015367 TCGAAGAAATGGTTAAAATTGGATGTA 57.985 29.630 0.00 0.00 0.00 2.29
3015 3535 9.801873 CGAAGAAATGGTTAAAATTGGATGTAT 57.198 29.630 0.00 0.00 0.00 2.29
3053 3573 7.005062 ACGTCTAAATTCATTCATTTCTCCG 57.995 36.000 0.00 0.00 0.00 4.63
3054 3574 6.816640 ACGTCTAAATTCATTCATTTCTCCGA 59.183 34.615 0.00 0.00 0.00 4.55
3055 3575 7.119997 CGTCTAAATTCATTCATTTCTCCGAC 58.880 38.462 0.00 0.00 0.00 4.79
3056 3576 7.201522 CGTCTAAATTCATTCATTTCTCCGACA 60.202 37.037 0.00 0.00 0.00 4.35
3057 3577 8.450964 GTCTAAATTCATTCATTTCTCCGACAA 58.549 33.333 0.00 0.00 0.00 3.18
3058 3578 8.668353 TCTAAATTCATTCATTTCTCCGACAAG 58.332 33.333 0.00 0.00 0.00 3.16
3059 3579 6.824305 AATTCATTCATTTCTCCGACAAGT 57.176 33.333 0.00 0.00 0.00 3.16
3060 3580 7.921786 AATTCATTCATTTCTCCGACAAGTA 57.078 32.000 0.00 0.00 0.00 2.24
3061 3581 8.511604 AATTCATTCATTTCTCCGACAAGTAT 57.488 30.769 0.00 0.00 0.00 2.12
3062 3582 7.921786 TTCATTCATTTCTCCGACAAGTATT 57.078 32.000 0.00 0.00 0.00 1.89
3063 3583 7.921786 TCATTCATTTCTCCGACAAGTATTT 57.078 32.000 0.00 0.00 0.00 1.40
3064 3584 7.974675 TCATTCATTTCTCCGACAAGTATTTC 58.025 34.615 0.00 0.00 0.00 2.17
3065 3585 6.403333 TTCATTTCTCCGACAAGTATTTCG 57.597 37.500 0.00 0.00 34.93 3.46
3072 3592 3.173668 CGACAAGTATTTCGGGATGGA 57.826 47.619 0.00 0.00 0.00 3.41
3073 3593 3.123804 CGACAAGTATTTCGGGATGGAG 58.876 50.000 0.00 0.00 0.00 3.86
3074 3594 3.467803 GACAAGTATTTCGGGATGGAGG 58.532 50.000 0.00 0.00 0.00 4.30
3075 3595 2.172717 ACAAGTATTTCGGGATGGAGGG 59.827 50.000 0.00 0.00 0.00 4.30
3076 3596 2.438021 CAAGTATTTCGGGATGGAGGGA 59.562 50.000 0.00 0.00 0.00 4.20
3077 3597 2.330216 AGTATTTCGGGATGGAGGGAG 58.670 52.381 0.00 0.00 0.00 4.30
3116 3636 1.342496 TCTGAAGGAGAGTGTGCTGTG 59.658 52.381 0.00 0.00 0.00 3.66
3180 3700 7.068962 TCCATTGTTGCAACTTGATATGATCAT 59.931 33.333 28.61 13.81 39.39 2.45
3188 3708 4.466827 ACTTGATATGATCATGCCTTGCA 58.533 39.130 18.72 4.49 44.86 4.08
3256 3778 7.377398 CACATGAATTCCTTATTTGTTGGACA 58.623 34.615 0.00 0.00 0.00 4.02
3270 3792 4.582869 TGTTGGACAGATCTGAAGGATTG 58.417 43.478 29.27 0.90 34.33 2.67
3299 3821 2.375174 ACCAAAGAACTAGCCATGGACA 59.625 45.455 18.40 0.00 0.00 4.02
3300 3822 3.181434 ACCAAAGAACTAGCCATGGACAA 60.181 43.478 18.40 0.00 0.00 3.18
3349 3871 1.734465 CCAGAACCTTGAGTTGATCGC 59.266 52.381 0.00 0.00 39.40 4.58
3392 3914 6.001460 CCTCTAGTGTACCCAAATTGTTTGA 58.999 40.000 4.11 0.00 43.26 2.69
3401 3923 7.827236 TGTACCCAAATTGTTTGAGACTATAGG 59.173 37.037 4.43 0.00 43.26 2.57
3427 3964 9.255304 GCTTTGTTGTTGTTGAATTCCTTATTA 57.745 29.630 2.27 0.00 0.00 0.98
3454 4044 5.398711 CGCACGTCTATTATTTAGTCACTCC 59.601 44.000 0.00 0.00 0.00 3.85
3459 4049 6.224584 GTCTATTATTTAGTCACTCCTGGGC 58.775 44.000 0.00 0.00 0.00 5.36
3496 4086 5.472148 CAGTTTTGCTGGCAAATAGATTCA 58.528 37.500 19.27 2.52 44.14 2.57
3497 4087 5.575606 CAGTTTTGCTGGCAAATAGATTCAG 59.424 40.000 19.27 0.00 44.14 3.02
3538 4129 2.477825 CTTGGTATCATCTGTGGCGAG 58.522 52.381 0.00 0.00 0.00 5.03
3539 4130 1.485124 TGGTATCATCTGTGGCGAGT 58.515 50.000 0.00 0.00 0.00 4.18
3557 4148 1.134521 AGTTGCGTGTCCTTTGTCTCA 60.135 47.619 0.00 0.00 0.00 3.27
3581 4172 8.358895 TCAACTCTTTGACATGCATTTTCAATA 58.641 29.630 17.37 10.38 36.79 1.90
3595 4186 7.922278 TGCATTTTCAATAACTTGATATGCTCC 59.078 33.333 22.46 7.81 46.68 4.70
3635 4226 7.250445 TGATGAACCATCATATTTCAGTTCG 57.750 36.000 5.61 0.00 46.30 3.95
3636 4227 5.484173 TGAACCATCATATTTCAGTTCGC 57.516 39.130 0.00 0.00 37.11 4.70
3648 4239 2.703416 TCAGTTCGCATTTCTGCTCAT 58.297 42.857 0.00 0.00 46.65 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.594775 CTTGCCCACAAGTGCGCA 61.595 61.111 5.66 5.66 46.84 6.09
40 41 1.301677 CGAAGAGAAGGTGCTTGCCC 61.302 60.000 0.00 0.00 0.00 5.36
83 84 1.493950 CCAATCTCACCGCGCTCATC 61.494 60.000 5.56 0.00 0.00 2.92
104 105 2.204136 ACCATGGGGGAGCAGACA 60.204 61.111 18.09 0.00 41.15 3.41
176 183 0.685131 TGGGGTTCGATCCGCTTAGA 60.685 55.000 24.85 7.09 40.43 2.10
195 202 3.313526 GTGAAGCGCATGAAATCCTACAT 59.686 43.478 11.47 0.00 0.00 2.29
196 203 2.677836 GTGAAGCGCATGAAATCCTACA 59.322 45.455 11.47 0.00 0.00 2.74
207 214 0.676466 TTCATTCCGGTGAAGCGCAT 60.676 50.000 11.47 0.00 33.41 4.73
222 229 1.753930 TTGATGCAGGTGCGATTCAT 58.246 45.000 0.00 0.00 45.83 2.57
238 245 3.744214 GCCAGATCGGTAACATCCATTGA 60.744 47.826 5.66 0.00 36.97 2.57
240 247 2.487265 GGCCAGATCGGTAACATCCATT 60.487 50.000 0.00 0.00 36.97 3.16
257 264 3.399181 CCGCTACTCCCTTGGCCA 61.399 66.667 0.00 0.00 0.00 5.36
350 358 3.191162 CCAAATTCCTCTTTGTGCGATCA 59.809 43.478 0.00 0.00 34.90 2.92
354 362 1.067635 CCCCAAATTCCTCTTTGTGCG 60.068 52.381 0.00 0.00 34.90 5.34
360 368 1.282157 CCTCGTCCCCAAATTCCTCTT 59.718 52.381 0.00 0.00 0.00 2.85
389 397 4.253257 CCTACCTCCGCTCGTCGC 62.253 72.222 0.00 0.00 36.73 5.19
391 399 0.747283 TTCTCCTACCTCCGCTCGTC 60.747 60.000 0.00 0.00 0.00 4.20
397 405 0.032416 TCCCCTTTCTCCTACCTCCG 60.032 60.000 0.00 0.00 0.00 4.63
430 438 3.868077 AGATCAGCAAGATAAACGCTCAC 59.132 43.478 0.00 0.00 37.00 3.51
440 449 2.757314 TCGTGAGACAGATCAGCAAGAT 59.243 45.455 0.00 0.00 35.47 2.40
461 512 6.984474 CGTGTATGTATTAAACACCTGGATCT 59.016 38.462 0.00 0.00 42.09 2.75
462 513 6.292703 GCGTGTATGTATTAAACACCTGGATC 60.293 42.308 0.00 0.00 42.09 3.36
528 597 3.173965 CTGAGGGAGAAAGGGTCAAGTA 58.826 50.000 0.00 0.00 0.00 2.24
565 634 4.042187 GGTGTTATCTCTTAGATGGGCCAT 59.958 45.833 21.39 21.39 35.37 4.40
566 635 3.391296 GGTGTTATCTCTTAGATGGGCCA 59.609 47.826 9.61 9.61 35.37 5.36
1319 1425 0.308993 GTCCCGTACTACCCGAATCG 59.691 60.000 0.00 0.00 0.00 3.34
1323 1429 0.107508 CTCTGTCCCGTACTACCCGA 60.108 60.000 0.00 0.00 0.00 5.14
1340 1446 6.922957 GTCTCTGATCATAAGAATGTGGACTC 59.077 42.308 8.98 0.00 34.50 3.36
1387 1493 9.189723 GCATTATTCCTATTTGATCTTGAAAGC 57.810 33.333 0.00 0.00 0.00 3.51
1596 1721 3.954200 TGAAGAATTGGCAGAGCATACA 58.046 40.909 0.00 0.00 0.00 2.29
1613 1738 0.905357 ACCCTGACCTCGGAATGAAG 59.095 55.000 0.00 0.00 0.00 3.02
1622 1747 5.561679 AGAACATAAGAAAACCCTGACCTC 58.438 41.667 0.00 0.00 0.00 3.85
1624 1749 6.040504 ACAAAGAACATAAGAAAACCCTGACC 59.959 38.462 0.00 0.00 0.00 4.02
1764 1891 7.972277 CCACATTGTCAAGAAATTATTGGAGAG 59.028 37.037 0.24 0.00 0.00 3.20
1829 1956 6.127281 ACACACAATACCCGATTACATAGTCA 60.127 38.462 0.00 0.00 0.00 3.41
1830 1957 6.278363 ACACACAATACCCGATTACATAGTC 58.722 40.000 0.00 0.00 0.00 2.59
1868 1995 7.012421 CAGGACACTATTAAAAGCCCTACAATC 59.988 40.741 0.00 0.00 0.00 2.67
2267 2721 3.254892 GGGAGTTTAAGAGAGAACTGCG 58.745 50.000 0.00 0.00 42.81 5.18
2285 2739 6.552350 ACAGTAAGAAATATAGGCTAACGGGA 59.448 38.462 0.00 0.00 0.00 5.14
2305 2760 4.871933 TCAGAAGATGCAGTTCACAGTA 57.128 40.909 12.75 0.00 0.00 2.74
2387 2844 1.145803 GTGTAGGCACTCGTTTCCAC 58.854 55.000 0.00 0.00 42.13 4.02
2388 2845 0.753867 TGTGTAGGCACTCGTTTCCA 59.246 50.000 0.00 0.00 45.44 3.53
2389 2846 2.094762 ATGTGTAGGCACTCGTTTCC 57.905 50.000 0.00 0.00 45.44 3.13
2456 2919 6.644592 TGCTTAACCAAAATACAGCAACAATC 59.355 34.615 0.00 0.00 34.38 2.67
2514 3034 8.164153 GCATTAATTGAGCAATACAAAGTTGTG 58.836 33.333 6.94 0.00 42.31 3.33
2525 3045 9.938280 ATTTAGCATATGCATTAATTGAGCAAT 57.062 25.926 28.62 6.05 45.16 3.56
2777 3297 3.529533 CATAGTGCTCAAAGGGAGTGAG 58.470 50.000 0.00 0.00 45.88 3.51
2818 3338 4.507710 GACCAGACATAGCAATCACTTCA 58.492 43.478 0.00 0.00 0.00 3.02
2819 3339 3.553511 CGACCAGACATAGCAATCACTTC 59.446 47.826 0.00 0.00 0.00 3.01
2920 3440 2.365617 AGCTTGTCCAAAAGAGACGAGA 59.634 45.455 11.47 0.00 45.15 4.04
2963 3483 2.544844 ATTTCAGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
2964 3484 2.108970 GTATTTCAGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
2965 3485 2.389715 AGTATTTCAGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
2966 3486 2.500098 CAAGTATTTCAGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
2967 3487 2.236395 ACAAGTATTTCAGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
2968 3488 3.522553 GACAAGTATTTCAGGACGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
2969 3489 3.119602 TCGACAAGTATTTCAGGACGGAG 60.120 47.826 0.00 0.00 0.00 4.63
2970 3490 2.821378 TCGACAAGTATTTCAGGACGGA 59.179 45.455 0.00 0.00 0.00 4.69
2971 3491 3.226346 TCGACAAGTATTTCAGGACGG 57.774 47.619 0.00 0.00 0.00 4.79
2972 3492 4.482386 TCTTCGACAAGTATTTCAGGACG 58.518 43.478 0.00 0.00 0.00 4.79
2973 3493 6.780706 TTTCTTCGACAAGTATTTCAGGAC 57.219 37.500 0.00 0.00 0.00 3.85
2974 3494 6.371548 CCATTTCTTCGACAAGTATTTCAGGA 59.628 38.462 0.00 0.00 0.00 3.86
2975 3495 6.149474 ACCATTTCTTCGACAAGTATTTCAGG 59.851 38.462 0.00 0.00 0.00 3.86
2976 3496 7.133891 ACCATTTCTTCGACAAGTATTTCAG 57.866 36.000 0.00 0.00 0.00 3.02
2977 3497 7.504924 AACCATTTCTTCGACAAGTATTTCA 57.495 32.000 0.00 0.00 0.00 2.69
2978 3498 9.887406 TTTAACCATTTCTTCGACAAGTATTTC 57.113 29.630 0.00 0.00 0.00 2.17
2982 3502 9.672086 CAATTTTAACCATTTCTTCGACAAGTA 57.328 29.630 0.00 0.00 0.00 2.24
2983 3503 7.651704 CCAATTTTAACCATTTCTTCGACAAGT 59.348 33.333 0.00 0.00 0.00 3.16
2984 3504 7.865385 TCCAATTTTAACCATTTCTTCGACAAG 59.135 33.333 0.00 0.00 0.00 3.16
2985 3505 7.717568 TCCAATTTTAACCATTTCTTCGACAA 58.282 30.769 0.00 0.00 0.00 3.18
2986 3506 7.278461 TCCAATTTTAACCATTTCTTCGACA 57.722 32.000 0.00 0.00 0.00 4.35
2987 3507 7.812669 ACATCCAATTTTAACCATTTCTTCGAC 59.187 33.333 0.00 0.00 0.00 4.20
2988 3508 7.891561 ACATCCAATTTTAACCATTTCTTCGA 58.108 30.769 0.00 0.00 0.00 3.71
2989 3509 9.801873 ATACATCCAATTTTAACCATTTCTTCG 57.198 29.630 0.00 0.00 0.00 3.79
3027 3547 8.765219 CGGAGAAATGAATGAATTTAGACGTAT 58.235 33.333 0.00 0.00 29.89 3.06
3028 3548 7.977293 TCGGAGAAATGAATGAATTTAGACGTA 59.023 33.333 0.00 0.00 29.89 3.57
3029 3549 6.816640 TCGGAGAAATGAATGAATTTAGACGT 59.183 34.615 0.00 0.00 29.89 4.34
3030 3550 7.119997 GTCGGAGAAATGAATGAATTTAGACG 58.880 38.462 0.00 0.00 39.69 4.18
3031 3551 7.974675 TGTCGGAGAAATGAATGAATTTAGAC 58.025 34.615 0.00 0.00 39.69 2.59
3032 3552 8.560355 TTGTCGGAGAAATGAATGAATTTAGA 57.440 30.769 0.00 0.00 39.69 2.10
3033 3553 8.454106 ACTTGTCGGAGAAATGAATGAATTTAG 58.546 33.333 0.00 0.00 39.69 1.85
3034 3554 8.335532 ACTTGTCGGAGAAATGAATGAATTTA 57.664 30.769 0.00 0.00 39.69 1.40
3035 3555 7.219484 ACTTGTCGGAGAAATGAATGAATTT 57.781 32.000 0.00 0.00 39.69 1.82
3036 3556 6.824305 ACTTGTCGGAGAAATGAATGAATT 57.176 33.333 0.00 0.00 39.69 2.17
3037 3557 8.511604 AATACTTGTCGGAGAAATGAATGAAT 57.488 30.769 0.00 0.00 39.69 2.57
3038 3558 7.921786 AATACTTGTCGGAGAAATGAATGAA 57.078 32.000 0.00 0.00 39.69 2.57
3039 3559 7.201522 CGAAATACTTGTCGGAGAAATGAATGA 60.202 37.037 0.00 0.00 39.69 2.57
3040 3560 6.901887 CGAAATACTTGTCGGAGAAATGAATG 59.098 38.462 0.00 0.00 39.69 2.67
3041 3561 7.005062 CGAAATACTTGTCGGAGAAATGAAT 57.995 36.000 0.00 0.00 39.69 2.57
3042 3562 6.403333 CGAAATACTTGTCGGAGAAATGAA 57.597 37.500 0.00 0.00 39.69 2.57
3052 3572 3.123804 CTCCATCCCGAAATACTTGTCG 58.876 50.000 0.00 0.00 37.01 4.35
3053 3573 3.467803 CCTCCATCCCGAAATACTTGTC 58.532 50.000 0.00 0.00 0.00 3.18
3054 3574 2.172717 CCCTCCATCCCGAAATACTTGT 59.827 50.000 0.00 0.00 0.00 3.16
3055 3575 2.438021 TCCCTCCATCCCGAAATACTTG 59.562 50.000 0.00 0.00 0.00 3.16
3056 3576 2.706190 CTCCCTCCATCCCGAAATACTT 59.294 50.000 0.00 0.00 0.00 2.24
3057 3577 2.330216 CTCCCTCCATCCCGAAATACT 58.670 52.381 0.00 0.00 0.00 2.12
3058 3578 2.047830 ACTCCCTCCATCCCGAAATAC 58.952 52.381 0.00 0.00 0.00 1.89
3059 3579 2.489528 ACTCCCTCCATCCCGAAATA 57.510 50.000 0.00 0.00 0.00 1.40
3060 3580 2.489528 TACTCCCTCCATCCCGAAAT 57.510 50.000 0.00 0.00 0.00 2.17
3061 3581 2.489528 ATACTCCCTCCATCCCGAAA 57.510 50.000 0.00 0.00 0.00 3.46
3062 3582 2.489528 AATACTCCCTCCATCCCGAA 57.510 50.000 0.00 0.00 0.00 4.30
3063 3583 2.489528 AAATACTCCCTCCATCCCGA 57.510 50.000 0.00 0.00 0.00 5.14
3064 3584 3.477530 GAAAAATACTCCCTCCATCCCG 58.522 50.000 0.00 0.00 0.00 5.14
3065 3585 3.463704 AGGAAAAATACTCCCTCCATCCC 59.536 47.826 0.00 0.00 32.95 3.85
3066 3586 4.797912 AGGAAAAATACTCCCTCCATCC 57.202 45.455 0.00 0.00 32.95 3.51
3067 3587 4.339530 GCAAGGAAAAATACTCCCTCCATC 59.660 45.833 0.00 0.00 32.95 3.51
3068 3588 4.264352 TGCAAGGAAAAATACTCCCTCCAT 60.264 41.667 0.00 0.00 32.95 3.41
3069 3589 3.075283 TGCAAGGAAAAATACTCCCTCCA 59.925 43.478 0.00 0.00 32.95 3.86
3070 3590 3.697166 TGCAAGGAAAAATACTCCCTCC 58.303 45.455 0.00 0.00 32.95 4.30
3071 3591 5.418840 TGAATGCAAGGAAAAATACTCCCTC 59.581 40.000 0.00 0.00 32.95 4.30
3072 3592 5.332743 TGAATGCAAGGAAAAATACTCCCT 58.667 37.500 0.00 0.00 32.95 4.20
3073 3593 5.659440 TGAATGCAAGGAAAAATACTCCC 57.341 39.130 0.00 0.00 32.95 4.30
3074 3594 6.976925 CAGATGAATGCAAGGAAAAATACTCC 59.023 38.462 0.00 0.00 0.00 3.85
3075 3595 7.765307 TCAGATGAATGCAAGGAAAAATACTC 58.235 34.615 0.00 0.00 0.00 2.59
3076 3596 7.707624 TCAGATGAATGCAAGGAAAAATACT 57.292 32.000 0.00 0.00 0.00 2.12
3077 3597 7.490402 CCTTCAGATGAATGCAAGGAAAAATAC 59.510 37.037 0.00 0.00 36.48 1.89
3180 3700 5.409520 GTCGATAAGATTATCATGCAAGGCA 59.590 40.000 11.94 0.00 39.55 4.75
3256 3778 5.306678 GGTGATACTCCAATCCTTCAGATCT 59.693 44.000 0.00 0.00 32.47 2.75
3270 3792 4.081087 TGGCTAGTTCTTTGGTGATACTCC 60.081 45.833 0.00 0.00 0.00 3.85
3299 3821 4.643387 AAGCTTCCACGCGCCCTT 62.643 61.111 5.73 0.00 34.40 3.95
3306 3828 1.600957 CATGGATAGCAAGCTTCCACG 59.399 52.381 20.41 13.24 42.09 4.94
3318 3840 2.947652 CAAGGTTCTGGCACATGGATAG 59.052 50.000 0.00 0.00 38.20 2.08
3384 3906 7.448469 ACAACAAAGCCTATAGTCTCAAACAAT 59.552 33.333 0.00 0.00 0.00 2.71
3392 3914 6.296026 TCAACAACAACAAAGCCTATAGTCT 58.704 36.000 0.00 0.00 0.00 3.24
3401 3923 7.713764 ATAAGGAATTCAACAACAACAAAGC 57.286 32.000 7.93 0.00 0.00 3.51
3427 3964 5.175126 GTGACTAAATAATAGACGTGCGCAT 59.825 40.000 15.91 0.00 0.00 4.73
3428 3965 4.501559 GTGACTAAATAATAGACGTGCGCA 59.498 41.667 5.66 5.66 0.00 6.09
3454 4044 1.146263 GAGTACATTCGGGGCCCAG 59.854 63.158 26.86 21.96 0.00 4.45
3459 4049 2.747446 CAAAACTGGAGTACATTCGGGG 59.253 50.000 0.00 0.00 0.00 5.73
3489 4079 6.094603 GCAAGGAAAAAGAGATGCTGAATCTA 59.905 38.462 0.00 0.00 46.12 1.98
3491 4081 5.100943 GCAAGGAAAAAGAGATGCTGAATC 58.899 41.667 0.00 0.00 35.29 2.52
3492 4082 4.525487 TGCAAGGAAAAAGAGATGCTGAAT 59.475 37.500 0.00 0.00 34.97 2.57
3493 4083 3.890756 TGCAAGGAAAAAGAGATGCTGAA 59.109 39.130 0.00 0.00 34.97 3.02
3495 4085 3.928727 TGCAAGGAAAAAGAGATGCTG 57.071 42.857 0.00 0.00 34.97 4.41
3496 4086 3.368116 GCATGCAAGGAAAAAGAGATGCT 60.368 43.478 14.21 0.00 33.69 3.79
3497 4087 2.928116 GCATGCAAGGAAAAAGAGATGC 59.072 45.455 14.21 0.00 0.00 3.91
3498 4088 4.451629 AGCATGCAAGGAAAAAGAGATG 57.548 40.909 21.98 0.00 0.00 2.90
3538 4129 1.295792 TGAGACAAAGGACACGCAAC 58.704 50.000 0.00 0.00 0.00 4.17
3539 4130 1.668751 GTTGAGACAAAGGACACGCAA 59.331 47.619 0.00 0.00 0.00 4.85
3547 4138 5.755813 CATGTCAAAGAGTTGAGACAAAGG 58.244 41.667 0.00 0.00 44.44 3.11
3557 4148 8.981647 GTTATTGAAAATGCATGTCAAAGAGTT 58.018 29.630 22.87 12.87 35.07 3.01
3581 4172 4.225942 TCAGGTTCAGGAGCATATCAAGTT 59.774 41.667 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.