Multiple sequence alignment - TraesCS5B01G378800

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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 TraesCS5B01G378800 chr5B 100.000 3054 0 0 1 3054 556971509 556974562 0.000000e+00 5640
1 TraesCS5B01G378800 chr5B 93.297 2029 105 16 323 2341 684764529 684762522 0.000000e+00 2964
2 TraesCS5B01G378800 chr5B 91.894 1505 80 17 361 1857 684749985 684751455 0.000000e+00 2065
3 TraesCS5B01G378800 chr5B 79.131 1519 266 37 531 2016 557070167 557071667 0.000000e+00 1002
4 TraesCS5B01G378800 chr5B 77.719 947 162 33 531 1462 684776429 684775517 4.480000e-148 534
5 TraesCS5B01G378800 chr5B 89.426 331 13 2 4 312 684749274 684749604 6.140000e-107 398
6 TraesCS5B01G378800 chr5B 89.426 331 13 2 4 312 684764925 684764595 6.140000e-107 398
7 TraesCS5B01G378800 chr5B 77.479 484 102 6 664 1143 557350336 557350816 1.790000e-72 283
8 TraesCS5B01G378800 chr5D 94.134 2523 95 18 323 2840 543298196 543300670 0.000000e+00 3790
9 TraesCS5B01G378800 chr5D 79.513 1518 255 41 531 2010 543306034 543307533 0.000000e+00 1029
10 TraesCS5B01G378800 chr5D 89.759 332 14 2 1 312 543297803 543298134 1.020000e-109 407
11 TraesCS5B01G378800 chr4A 92.289 2516 140 29 341 2840 625921952 625919475 0.000000e+00 3522
12 TraesCS5B01G378800 chr4A 79.315 1518 264 36 531 2016 625901731 625900232 0.000000e+00 1018
13 TraesCS5B01G378800 chr4A 73.840 1315 302 31 677 1969 695981507 695980213 4.580000e-133 484
14 TraesCS5B01G378800 chr1B 97.209 215 5 1 2841 3054 677620894 677621108 2.240000e-96 363
15 TraesCS5B01G378800 chr3D 95.794 214 9 0 2841 3054 251295672 251295459 2.250000e-91 346
16 TraesCS5B01G378800 chr3B 93.488 215 14 0 2840 3054 688104035 688104249 1.370000e-83 320
17 TraesCS5B01G378800 chr3B 87.615 218 20 4 2840 3054 67274742 67274955 2.350000e-61 246
18 TraesCS5B01G378800 chr4B 92.056 214 17 0 2841 3054 630091976 630091763 4.950000e-78 302
19 TraesCS5B01G378800 chr4B 92.019 213 14 3 2841 3051 491470204 491470415 2.300000e-76 296
20 TraesCS5B01G378800 chr7D 91.943 211 17 0 2844 3054 589088507 589088717 2.300000e-76 296
21 TraesCS5B01G378800 chr6D 87.615 218 25 2 2838 3054 61568393 61568609 5.050000e-63 252
22 TraesCS5B01G378800 chr1D 88.208 212 23 2 2844 3054 42051852 42051642 5.050000e-63 252


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 TraesCS5B01G378800 chr5B 556971509 556974562 3053 False 5640.0 5640 100.0000 1 3054 1 chr5B.!!$F1 3053
1 TraesCS5B01G378800 chr5B 684762522 684764925 2403 True 1681.0 2964 91.3615 4 2341 2 chr5B.!!$R2 2337
2 TraesCS5B01G378800 chr5B 684749274 684751455 2181 False 1231.5 2065 90.6600 4 1857 2 chr5B.!!$F4 1853
3 TraesCS5B01G378800 chr5B 557070167 557071667 1500 False 1002.0 1002 79.1310 531 2016 1 chr5B.!!$F2 1485
4 TraesCS5B01G378800 chr5B 684775517 684776429 912 True 534.0 534 77.7190 531 1462 1 chr5B.!!$R1 931
5 TraesCS5B01G378800 chr5D 543297803 543300670 2867 False 2098.5 3790 91.9465 1 2840 2 chr5D.!!$F2 2839
6 TraesCS5B01G378800 chr5D 543306034 543307533 1499 False 1029.0 1029 79.5130 531 2010 1 chr5D.!!$F1 1479
7 TraesCS5B01G378800 chr4A 625919475 625921952 2477 True 3522.0 3522 92.2890 341 2840 1 chr4A.!!$R2 2499
8 TraesCS5B01G378800 chr4A 625900232 625901731 1499 True 1018.0 1018 79.3150 531 2016 1 chr4A.!!$R1 1485
9 TraesCS5B01G378800 chr4A 695980213 695981507 1294 True 484.0 484 73.8400 677 1969 1 chr4A.!!$R3 1292

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
312 338 0.106967 TGCAACCACTACAGGTGCAA 60.107 50.0 0.12 0.0 42.25 4.08 F
313 339 0.310854 GCAACCACTACAGGTGCAAC 59.689 55.0 0.00 0.0 42.25 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1678 1.134965 GGTCAGAAGATCCACGTCCTG 60.135 57.143 0.00 0.0 0.0 3.86 R
2201 2665 2.555664 AGGCCAGAGAAATCCAGAGAA 58.444 47.619 5.01 0.0 0.0 2.87 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
114 137 1.271926 ACTAGCGTTTTGGATTGGGCT 60.272 47.619 0.00 0.00 34.69 5.19
218 241 1.360192 GTTTGTGTCACAGGCTGCC 59.640 57.895 15.89 11.65 0.00 4.85
312 338 0.106967 TGCAACCACTACAGGTGCAA 60.107 50.000 0.12 0.00 42.25 4.08
313 339 0.310854 GCAACCACTACAGGTGCAAC 59.689 55.000 0.00 0.00 42.25 4.17
395 772 4.546570 CCGGACTTGATTTCCTGTTTTTC 58.453 43.478 0.00 0.00 0.00 2.29
402 779 9.196552 GACTTGATTTCCTGTTTTTCAATTAGG 57.803 33.333 0.00 0.00 0.00 2.69
451 835 7.048512 AGTTTCTTTCTGTATACATAGGTGGC 58.951 38.462 5.91 0.00 0.00 5.01
495 879 1.947597 TTGCGCCCATCAGGATTTGC 61.948 55.000 4.18 0.00 38.24 3.68
942 1337 2.415090 GCTCACAAGATTCAAAGCGCAT 60.415 45.455 11.47 0.00 0.00 4.73
1014 1410 1.153369 CGGGATGATTGTGGTCGCT 60.153 57.895 0.00 0.00 0.00 4.93
1032 1431 1.238439 CTGCAACCAACAACCTCGAT 58.762 50.000 0.00 0.00 0.00 3.59
1038 1437 4.062293 CAACCAACAACCTCGATTCACTA 58.938 43.478 0.00 0.00 0.00 2.74
1160 1563 1.270550 GGTTTGCACTCCACATCCTTG 59.729 52.381 0.00 0.00 0.00 3.61
1171 1574 7.864379 GCACTCCACATCCTTGAAAATATTATG 59.136 37.037 0.00 0.00 0.00 1.90
1200 1634 0.540454 CTTGGCAGCCTCTGATGAGA 59.460 55.000 14.15 0.00 42.73 3.27
1206 1640 2.903798 CAGCCTCTGATGAGAAACCTC 58.096 52.381 0.00 0.00 42.73 3.85
1244 1678 0.244721 GATGCAGGTGTTGAAAGCCC 59.755 55.000 0.00 0.00 0.00 5.19
1687 2134 2.284258 AGCGAGGTGAGCTCCCTT 60.284 61.111 20.63 2.75 41.83 3.95
1700 2147 1.461268 TCCCTTGCCCTGACTGACA 60.461 57.895 0.00 0.00 0.00 3.58
2114 2577 6.295575 CCTTCTTCATCCTAACAGTTGAGACT 60.296 42.308 0.00 0.00 36.25 3.24
2243 2707 6.352308 GCCTTTTCTCCTTTCCTACTACAGAT 60.352 42.308 0.00 0.00 0.00 2.90
2245 2709 8.103935 CCTTTTCTCCTTTCCTACTACAGATTT 58.896 37.037 0.00 0.00 0.00 2.17
2246 2710 9.157104 CTTTTCTCCTTTCCTACTACAGATTTC 57.843 37.037 0.00 0.00 0.00 2.17
2498 2962 6.994421 AATTCCATAAGGTTTGACCAACTT 57.006 33.333 0.00 0.00 41.95 2.66
2499 2963 6.994421 ATTCCATAAGGTTTGACCAACTTT 57.006 33.333 0.00 0.00 41.95 2.66
2500 2964 8.485578 AATTCCATAAGGTTTGACCAACTTTA 57.514 30.769 0.00 0.00 41.95 1.85
2501 2965 8.664669 ATTCCATAAGGTTTGACCAACTTTAT 57.335 30.769 0.00 2.11 44.51 1.40
2506 2970 6.800072 AAGGTTTGACCAACTTTATGGAAA 57.200 33.333 0.00 0.00 43.54 3.13
2507 2971 6.800072 AGGTTTGACCAACTTTATGGAAAA 57.200 33.333 0.00 0.00 43.54 2.29
2508 2972 7.373617 AGGTTTGACCAACTTTATGGAAAAT 57.626 32.000 0.00 0.00 43.54 1.82
2509 2973 7.216494 AGGTTTGACCAACTTTATGGAAAATG 58.784 34.615 0.00 0.00 43.54 2.32
2510 2974 7.070571 AGGTTTGACCAACTTTATGGAAAATGA 59.929 33.333 0.00 0.00 43.54 2.57
2511 2975 7.877612 GGTTTGACCAACTTTATGGAAAATGAT 59.122 33.333 0.00 0.00 43.54 2.45
2512 2976 9.271828 GTTTGACCAACTTTATGGAAAATGATT 57.728 29.630 0.00 0.00 43.54 2.57
2513 2977 9.487790 TTTGACCAACTTTATGGAAAATGATTC 57.512 29.630 0.00 0.00 43.54 2.52
2514 2978 8.421249 TGACCAACTTTATGGAAAATGATTCT 57.579 30.769 0.00 0.00 43.54 2.40
2515 2979 9.527157 TGACCAACTTTATGGAAAATGATTCTA 57.473 29.630 0.00 0.00 43.54 2.10
2579 3043 3.081804 GGATTTCAATTGTCCCACGTCT 58.918 45.455 5.13 0.00 0.00 4.18
2607 3072 5.060940 GCAAAATCGGCTTACACTCAATTTC 59.939 40.000 0.00 0.00 0.00 2.17
2840 3306 5.121298 CACACACAATGTTCAGAGGTGATAG 59.879 44.000 6.33 0.00 40.64 2.08
2841 3307 5.012046 ACACACAATGTTCAGAGGTGATAGA 59.988 40.000 6.33 0.00 38.98 1.98
2842 3308 5.579904 CACACAATGTTCAGAGGTGATAGAG 59.420 44.000 0.00 0.00 33.82 2.43
2843 3309 5.247110 ACACAATGTTCAGAGGTGATAGAGT 59.753 40.000 0.00 0.00 33.82 3.24
2844 3310 5.579904 CACAATGTTCAGAGGTGATAGAGTG 59.420 44.000 0.00 0.00 30.85 3.51
2845 3311 5.481824 ACAATGTTCAGAGGTGATAGAGTGA 59.518 40.000 0.00 0.00 30.85 3.41
2846 3312 6.014242 ACAATGTTCAGAGGTGATAGAGTGAA 60.014 38.462 0.00 0.00 30.85 3.18
2847 3313 6.805016 ATGTTCAGAGGTGATAGAGTGAAT 57.195 37.500 0.00 0.00 30.85 2.57
2848 3314 6.611613 TGTTCAGAGGTGATAGAGTGAATT 57.388 37.500 0.00 0.00 30.85 2.17
2849 3315 6.401394 TGTTCAGAGGTGATAGAGTGAATTG 58.599 40.000 0.00 0.00 30.85 2.32
2850 3316 5.016051 TCAGAGGTGATAGAGTGAATTGC 57.984 43.478 0.00 0.00 0.00 3.56
2851 3317 4.467438 TCAGAGGTGATAGAGTGAATTGCA 59.533 41.667 0.00 0.00 0.00 4.08
2852 3318 5.046376 TCAGAGGTGATAGAGTGAATTGCAA 60.046 40.000 0.00 0.00 0.00 4.08
2853 3319 5.645067 CAGAGGTGATAGAGTGAATTGCAAA 59.355 40.000 1.71 0.00 0.00 3.68
2854 3320 6.149973 CAGAGGTGATAGAGTGAATTGCAAAA 59.850 38.462 1.71 0.00 0.00 2.44
2855 3321 6.716628 AGAGGTGATAGAGTGAATTGCAAAAA 59.283 34.615 1.71 0.00 0.00 1.94
2872 3338 3.626028 AAAAACATCGACACTTCAGGC 57.374 42.857 0.00 0.00 0.00 4.85
2873 3339 2.254546 AAACATCGACACTTCAGGCA 57.745 45.000 0.00 0.00 0.00 4.75
2874 3340 2.254546 AACATCGACACTTCAGGCAA 57.745 45.000 0.00 0.00 0.00 4.52
2875 3341 1.800805 ACATCGACACTTCAGGCAAG 58.199 50.000 0.00 0.00 38.21 4.01
2876 3342 1.081892 CATCGACACTTCAGGCAAGG 58.918 55.000 0.00 0.00 36.26 3.61
2877 3343 0.687354 ATCGACACTTCAGGCAAGGT 59.313 50.000 0.00 0.00 36.26 3.50
2878 3344 0.468226 TCGACACTTCAGGCAAGGTT 59.532 50.000 0.00 0.00 36.26 3.50
2879 3345 1.134220 TCGACACTTCAGGCAAGGTTT 60.134 47.619 0.00 0.00 36.26 3.27
2880 3346 1.002468 CGACACTTCAGGCAAGGTTTG 60.002 52.381 0.00 0.00 36.26 2.93
2881 3347 2.024414 GACACTTCAGGCAAGGTTTGT 58.976 47.619 0.00 0.00 36.26 2.83
2882 3348 3.211045 GACACTTCAGGCAAGGTTTGTA 58.789 45.455 0.00 0.00 36.26 2.41
2883 3349 3.214328 ACACTTCAGGCAAGGTTTGTAG 58.786 45.455 0.00 0.00 36.26 2.74
2884 3350 2.554032 CACTTCAGGCAAGGTTTGTAGG 59.446 50.000 0.00 0.00 36.26 3.18
2885 3351 2.441750 ACTTCAGGCAAGGTTTGTAGGA 59.558 45.455 0.00 0.00 36.26 2.94
2886 3352 3.117663 ACTTCAGGCAAGGTTTGTAGGAA 60.118 43.478 0.00 0.00 36.26 3.36
2887 3353 2.858745 TCAGGCAAGGTTTGTAGGAAC 58.141 47.619 0.00 0.00 0.00 3.62
2896 3362 4.929819 GGTTTGTAGGAACCACACATTT 57.070 40.909 2.08 0.00 46.66 2.32
2898 3364 5.765176 GGTTTGTAGGAACCACACATTTAC 58.235 41.667 2.08 0.00 46.66 2.01
2899 3365 5.445845 GTTTGTAGGAACCACACATTTACG 58.554 41.667 0.00 0.00 0.00 3.18
2900 3366 3.666274 TGTAGGAACCACACATTTACGG 58.334 45.455 0.00 0.00 0.00 4.02
2901 3367 3.324268 TGTAGGAACCACACATTTACGGA 59.676 43.478 0.00 0.00 0.00 4.69
2902 3368 3.495434 AGGAACCACACATTTACGGAA 57.505 42.857 0.00 0.00 0.00 4.30
2903 3369 4.028993 AGGAACCACACATTTACGGAAT 57.971 40.909 0.00 0.00 0.00 3.01
2904 3370 4.403734 AGGAACCACACATTTACGGAATT 58.596 39.130 0.00 0.00 0.00 2.17
2905 3371 4.217550 AGGAACCACACATTTACGGAATTG 59.782 41.667 0.68 0.68 0.00 2.32
2906 3372 4.022676 GGAACCACACATTTACGGAATTGT 60.023 41.667 2.02 2.02 30.96 2.71
2907 3373 4.497473 ACCACACATTTACGGAATTGTG 57.503 40.909 26.26 26.26 45.83 3.33
2908 3374 3.241701 CCACACATTTACGGAATTGTGC 58.758 45.455 27.29 0.00 44.95 4.57
2909 3375 3.241701 CACACATTTACGGAATTGTGCC 58.758 45.455 27.29 0.00 44.95 5.01
2910 3376 2.230266 ACACATTTACGGAATTGTGCCC 59.770 45.455 27.29 0.00 44.95 5.36
2911 3377 2.230025 CACATTTACGGAATTGTGCCCA 59.770 45.455 19.37 0.00 39.04 5.36
2912 3378 2.894126 ACATTTACGGAATTGTGCCCAA 59.106 40.909 7.10 0.00 29.99 4.12
2913 3379 3.322254 ACATTTACGGAATTGTGCCCAAA 59.678 39.130 7.10 0.00 33.44 3.28
2914 3380 4.202264 ACATTTACGGAATTGTGCCCAAAA 60.202 37.500 7.10 0.00 33.44 2.44
2915 3381 3.372660 TTACGGAATTGTGCCCAAAAC 57.627 42.857 0.00 0.00 33.44 2.43
2916 3382 0.391228 ACGGAATTGTGCCCAAAACC 59.609 50.000 0.00 0.00 33.44 3.27
2917 3383 0.390860 CGGAATTGTGCCCAAAACCA 59.609 50.000 8.02 0.00 33.44 3.67
2918 3384 1.871822 CGGAATTGTGCCCAAAACCAC 60.872 52.381 8.02 0.00 33.44 4.16
2919 3385 1.416030 GGAATTGTGCCCAAAACCACT 59.584 47.619 3.69 0.00 33.44 4.00
2920 3386 2.630580 GGAATTGTGCCCAAAACCACTA 59.369 45.455 3.69 0.00 33.44 2.74
2921 3387 3.070302 GGAATTGTGCCCAAAACCACTAA 59.930 43.478 3.69 0.00 33.44 2.24
2922 3388 4.262851 GGAATTGTGCCCAAAACCACTAAT 60.263 41.667 3.69 0.00 33.44 1.73
2923 3389 4.972751 ATTGTGCCCAAAACCACTAATT 57.027 36.364 0.00 0.00 33.44 1.40
2924 3390 4.762289 TTGTGCCCAAAACCACTAATTT 57.238 36.364 0.00 0.00 33.26 1.82
2925 3391 4.762289 TGTGCCCAAAACCACTAATTTT 57.238 36.364 0.00 0.00 33.26 1.82
2926 3392 5.104259 TGTGCCCAAAACCACTAATTTTT 57.896 34.783 0.00 0.00 33.26 1.94
2962 3428 1.687563 AAAAACACTAGTTGGCGGCT 58.312 45.000 11.43 0.00 38.17 5.52
2963 3429 1.687563 AAAACACTAGTTGGCGGCTT 58.312 45.000 11.43 0.00 38.17 4.35
2964 3430 1.687563 AAACACTAGTTGGCGGCTTT 58.312 45.000 11.43 0.00 38.17 3.51
2965 3431 0.951558 AACACTAGTTGGCGGCTTTG 59.048 50.000 11.43 0.67 36.39 2.77
2966 3432 0.889186 ACACTAGTTGGCGGCTTTGG 60.889 55.000 11.43 0.00 0.00 3.28
2967 3433 0.889186 CACTAGTTGGCGGCTTTGGT 60.889 55.000 11.43 0.67 0.00 3.67
2968 3434 0.605589 ACTAGTTGGCGGCTTTGGTC 60.606 55.000 11.43 0.00 0.00 4.02
2969 3435 1.635663 CTAGTTGGCGGCTTTGGTCG 61.636 60.000 11.43 0.00 44.16 4.79
2970 3436 2.102109 TAGTTGGCGGCTTTGGTCGA 62.102 55.000 11.43 0.00 44.06 4.20
2971 3437 2.033448 TTGGCGGCTTTGGTCGAT 59.967 55.556 11.43 0.00 44.06 3.59
2972 3438 1.602323 TTGGCGGCTTTGGTCGATT 60.602 52.632 11.43 0.00 44.06 3.34
2973 3439 1.175983 TTGGCGGCTTTGGTCGATTT 61.176 50.000 11.43 0.00 44.06 2.17
2974 3440 1.154035 GGCGGCTTTGGTCGATTTG 60.154 57.895 0.00 0.00 44.06 2.32
2975 3441 1.582610 GGCGGCTTTGGTCGATTTGA 61.583 55.000 0.00 0.00 44.06 2.69
2976 3442 0.451783 GCGGCTTTGGTCGATTTGAT 59.548 50.000 0.00 0.00 44.06 2.57
2977 3443 1.795162 GCGGCTTTGGTCGATTTGATG 60.795 52.381 0.00 0.00 44.06 3.07
2978 3444 1.737236 CGGCTTTGGTCGATTTGATGA 59.263 47.619 0.00 0.00 44.06 2.92
2979 3445 2.476185 CGGCTTTGGTCGATTTGATGAC 60.476 50.000 0.00 0.00 44.06 3.06
2980 3446 2.476185 GGCTTTGGTCGATTTGATGACG 60.476 50.000 0.00 0.00 35.95 4.35
2981 3447 2.415168 GCTTTGGTCGATTTGATGACGA 59.585 45.455 0.00 0.00 35.95 4.20
2982 3448 3.063997 GCTTTGGTCGATTTGATGACGAT 59.936 43.478 0.00 0.00 38.27 3.73
2983 3449 4.437390 GCTTTGGTCGATTTGATGACGATT 60.437 41.667 0.00 0.00 38.27 3.34
2984 3450 5.220586 GCTTTGGTCGATTTGATGACGATTA 60.221 40.000 0.00 0.00 38.27 1.75
2985 3451 6.511767 GCTTTGGTCGATTTGATGACGATTAT 60.512 38.462 0.00 0.00 38.27 1.28
2986 3452 5.905480 TGGTCGATTTGATGACGATTATG 57.095 39.130 0.00 0.00 38.27 1.90
2987 3453 5.596845 TGGTCGATTTGATGACGATTATGA 58.403 37.500 0.00 0.00 38.27 2.15
2988 3454 5.462068 TGGTCGATTTGATGACGATTATGAC 59.538 40.000 0.00 0.00 38.27 3.06
2989 3455 5.462068 GGTCGATTTGATGACGATTATGACA 59.538 40.000 0.00 0.00 38.27 3.58
2990 3456 6.346120 GGTCGATTTGATGACGATTATGACAG 60.346 42.308 0.00 0.00 38.27 3.51
2991 3457 6.417930 GTCGATTTGATGACGATTATGACAGA 59.582 38.462 0.00 0.00 38.27 3.41
2992 3458 7.115520 GTCGATTTGATGACGATTATGACAGAT 59.884 37.037 0.00 0.00 38.27 2.90
2993 3459 7.115378 TCGATTTGATGACGATTATGACAGATG 59.885 37.037 0.00 0.00 0.00 2.90
2994 3460 6.849588 TTTGATGACGATTATGACAGATGG 57.150 37.500 0.00 0.00 0.00 3.51
2995 3461 4.886579 TGATGACGATTATGACAGATGGG 58.113 43.478 0.00 0.00 0.00 4.00
2996 3462 3.111853 TGACGATTATGACAGATGGGC 57.888 47.619 0.00 0.00 0.00 5.36
2997 3463 2.224281 TGACGATTATGACAGATGGGCC 60.224 50.000 0.00 0.00 0.00 5.80
2998 3464 1.072331 ACGATTATGACAGATGGGCCC 59.928 52.381 17.59 17.59 0.00 5.80
2999 3465 1.611673 CGATTATGACAGATGGGCCCC 60.612 57.143 22.27 4.15 0.00 5.80
3000 3466 0.401738 ATTATGACAGATGGGCCCCG 59.598 55.000 22.27 7.78 0.00 5.73
3001 3467 0.986019 TTATGACAGATGGGCCCCGT 60.986 55.000 22.27 11.50 0.00 5.28
3002 3468 0.986019 TATGACAGATGGGCCCCGTT 60.986 55.000 22.27 3.44 0.00 4.44
3003 3469 1.863155 ATGACAGATGGGCCCCGTTT 61.863 55.000 22.27 0.25 0.00 3.60
3004 3470 1.202099 TGACAGATGGGCCCCGTTTA 61.202 55.000 22.27 0.00 0.00 2.01
3005 3471 0.182775 GACAGATGGGCCCCGTTTAT 59.817 55.000 22.27 4.98 0.00 1.40
3006 3472 0.106719 ACAGATGGGCCCCGTTTATG 60.107 55.000 22.27 11.59 0.00 1.90
3007 3473 1.152756 AGATGGGCCCCGTTTATGC 60.153 57.895 22.27 0.00 0.00 3.14
3008 3474 2.123468 ATGGGCCCCGTTTATGCC 60.123 61.111 22.27 0.00 44.59 4.40
3009 3475 4.805768 TGGGCCCCGTTTATGCCG 62.806 66.667 22.27 0.00 46.31 5.69
3010 3476 4.493049 GGGCCCCGTTTATGCCGA 62.493 66.667 12.23 0.00 46.31 5.54
3011 3477 3.206957 GGCCCCGTTTATGCCGAC 61.207 66.667 0.00 0.00 35.08 4.79
3012 3478 3.569690 GCCCCGTTTATGCCGACG 61.570 66.667 0.00 0.00 38.90 5.12
3013 3479 2.125431 CCCCGTTTATGCCGACGT 60.125 61.111 0.00 0.00 37.56 4.34
3014 3480 2.457778 CCCCGTTTATGCCGACGTG 61.458 63.158 0.00 0.00 37.56 4.49
3015 3481 2.457778 CCCGTTTATGCCGACGTGG 61.458 63.158 0.00 0.00 37.56 4.94
3028 3494 3.484547 CGTGGCCTAACGGTTCGC 61.485 66.667 3.32 0.11 39.89 4.70
3029 3495 2.357760 GTGGCCTAACGGTTCGCA 60.358 61.111 3.32 0.27 0.00 5.10
3030 3496 2.047655 TGGCCTAACGGTTCGCAG 60.048 61.111 3.32 0.00 0.00 5.18
3031 3497 2.818274 GGCCTAACGGTTCGCAGG 60.818 66.667 13.01 8.93 36.07 4.85
3032 3498 3.497031 GCCTAACGGTTCGCAGGC 61.497 66.667 15.30 15.30 45.85 4.85
3033 3499 2.047655 CCTAACGGTTCGCAGGCA 60.048 61.111 0.00 0.00 0.00 4.75
3034 3500 1.669760 CCTAACGGTTCGCAGGCAA 60.670 57.895 0.00 0.00 0.00 4.52
3035 3501 1.495951 CTAACGGTTCGCAGGCAAC 59.504 57.895 0.00 0.00 0.00 4.17
3049 3515 1.997669 GGCAACTCCGTTAGACAGAG 58.002 55.000 0.00 0.00 0.00 3.35
3050 3516 1.404315 GGCAACTCCGTTAGACAGAGG 60.404 57.143 0.00 0.00 31.70 3.69
3051 3517 1.544691 GCAACTCCGTTAGACAGAGGA 59.455 52.381 0.00 0.00 31.70 3.71
3052 3518 2.166664 GCAACTCCGTTAGACAGAGGAT 59.833 50.000 0.00 0.00 31.66 3.24
3053 3519 3.368531 GCAACTCCGTTAGACAGAGGATT 60.369 47.826 0.00 0.00 31.66 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 137 1.135141 GTAAAGCGGCATGGCATTGAA 60.135 47.619 20.37 3.19 34.64 2.69
138 161 0.458669 CAGGGCTAGCAATTTGGCAG 59.541 55.000 18.24 0.00 35.83 4.85
375 751 9.196552 CTAATTGAAAAACAGGAAATCAAGTCC 57.803 33.333 0.00 0.00 33.91 3.85
395 772 4.067896 AGTGAGTGACAACTGCCTAATTG 58.932 43.478 0.00 0.00 36.52 2.32
402 779 3.198068 TGAAAGAGTGAGTGACAACTGC 58.802 45.455 0.00 0.00 36.52 4.40
443 827 2.043992 TGTAAGCATACCGCCACCTAT 58.956 47.619 0.00 0.00 44.04 2.57
451 835 3.245284 CCTGTCGATTTGTAAGCATACCG 59.755 47.826 0.00 0.00 0.00 4.02
495 879 1.200948 GCTGCTTCCTAAGTTTGGCAG 59.799 52.381 8.17 8.17 46.51 4.85
797 1185 4.202441 CCCACATGATTCTCCTCGAATTT 58.798 43.478 0.00 0.00 42.31 1.82
942 1337 3.845178 CAGCTGATTAACGGTGTGTCTA 58.155 45.455 8.42 0.00 0.00 2.59
1014 1410 1.606668 GAATCGAGGTTGTTGGTTGCA 59.393 47.619 0.00 0.00 0.00 4.08
1032 1431 4.640771 AACAAGGGCTTGATCTAGTGAA 57.359 40.909 6.05 0.00 42.93 3.18
1038 1437 3.636153 GACCTAACAAGGGCTTGATCT 57.364 47.619 0.00 0.00 42.93 2.75
1160 1563 6.355638 CAAGACGACGCCTCATAATATTTTC 58.644 40.000 0.00 0.00 0.00 2.29
1171 1574 2.811317 CTGCCAAGACGACGCCTC 60.811 66.667 0.00 0.00 0.00 4.70
1244 1678 1.134965 GGTCAGAAGATCCACGTCCTG 60.135 57.143 0.00 0.00 0.00 3.86
1687 2134 3.080641 CCCATGTCAGTCAGGGCA 58.919 61.111 0.00 0.00 45.50 5.36
2040 2499 7.602517 AGACCATTCATTTACTTCTTCTTCG 57.397 36.000 0.00 0.00 0.00 3.79
2201 2665 2.555664 AGGCCAGAGAAATCCAGAGAA 58.444 47.619 5.01 0.00 0.00 2.87
2243 2707 3.724508 ATGCCAAAACACATCACGAAA 57.275 38.095 0.00 0.00 0.00 3.46
2245 2709 6.691754 ATAATATGCCAAAACACATCACGA 57.308 33.333 0.00 0.00 0.00 4.35
2246 2710 6.751425 ACAATAATATGCCAAAACACATCACG 59.249 34.615 0.00 0.00 0.00 4.35
2463 2927 9.588096 AAACCTTATGGAATTTGACTTAGAACT 57.412 29.630 0.81 0.00 37.04 3.01
2520 2984 7.836685 ACCCACCAATTTTTCCATAAAGTTTTT 59.163 29.630 0.00 0.00 0.00 1.94
2521 2985 7.284261 CACCCACCAATTTTTCCATAAAGTTTT 59.716 33.333 0.00 0.00 0.00 2.43
2522 2986 6.770303 CACCCACCAATTTTTCCATAAAGTTT 59.230 34.615 0.00 0.00 0.00 2.66
2523 2987 6.295249 CACCCACCAATTTTTCCATAAAGTT 58.705 36.000 0.00 0.00 0.00 2.66
2524 2988 5.744594 GCACCCACCAATTTTTCCATAAAGT 60.745 40.000 0.00 0.00 0.00 2.66
2525 2989 4.694982 GCACCCACCAATTTTTCCATAAAG 59.305 41.667 0.00 0.00 0.00 1.85
2526 2990 4.505742 GGCACCCACCAATTTTTCCATAAA 60.506 41.667 0.00 0.00 0.00 1.40
2579 3043 1.810151 GTGTAAGCCGATTTTGCTCCA 59.190 47.619 0.00 0.00 38.34 3.86
2736 3201 2.505405 CATGGATGGAGAATCTGCCTG 58.495 52.381 0.00 0.00 35.43 4.85
2852 3318 2.948979 TGCCTGAAGTGTCGATGTTTTT 59.051 40.909 0.00 0.00 0.00 1.94
2853 3319 2.571212 TGCCTGAAGTGTCGATGTTTT 58.429 42.857 0.00 0.00 0.00 2.43
2854 3320 2.254546 TGCCTGAAGTGTCGATGTTT 57.745 45.000 0.00 0.00 0.00 2.83
2855 3321 2.146342 CTTGCCTGAAGTGTCGATGTT 58.854 47.619 0.00 0.00 0.00 2.71
2856 3322 1.609061 CCTTGCCTGAAGTGTCGATGT 60.609 52.381 0.00 0.00 0.00 3.06
2857 3323 1.081892 CCTTGCCTGAAGTGTCGATG 58.918 55.000 0.00 0.00 0.00 3.84
2858 3324 0.687354 ACCTTGCCTGAAGTGTCGAT 59.313 50.000 0.00 0.00 0.00 3.59
2859 3325 0.468226 AACCTTGCCTGAAGTGTCGA 59.532 50.000 0.00 0.00 0.00 4.20
2860 3326 1.002468 CAAACCTTGCCTGAAGTGTCG 60.002 52.381 0.00 0.00 0.00 4.35
2861 3327 2.024414 ACAAACCTTGCCTGAAGTGTC 58.976 47.619 0.00 0.00 0.00 3.67
2862 3328 2.143876 ACAAACCTTGCCTGAAGTGT 57.856 45.000 0.00 0.00 0.00 3.55
2863 3329 2.554032 CCTACAAACCTTGCCTGAAGTG 59.446 50.000 0.00 0.00 0.00 3.16
2864 3330 2.441750 TCCTACAAACCTTGCCTGAAGT 59.558 45.455 0.00 0.00 0.00 3.01
2865 3331 3.140325 TCCTACAAACCTTGCCTGAAG 57.860 47.619 0.00 0.00 0.00 3.02
2866 3332 3.219281 GTTCCTACAAACCTTGCCTGAA 58.781 45.455 0.00 0.00 0.00 3.02
2867 3333 2.488347 GGTTCCTACAAACCTTGCCTGA 60.488 50.000 0.00 0.00 44.45 3.86
2868 3334 1.886542 GGTTCCTACAAACCTTGCCTG 59.113 52.381 0.00 0.00 44.45 4.85
2869 3335 2.287977 GGTTCCTACAAACCTTGCCT 57.712 50.000 0.00 0.00 44.45 4.75
2876 3342 5.445845 CGTAAATGTGTGGTTCCTACAAAC 58.554 41.667 4.34 0.00 0.00 2.93
2877 3343 4.515944 CCGTAAATGTGTGGTTCCTACAAA 59.484 41.667 4.34 0.00 0.00 2.83
2878 3344 4.066490 CCGTAAATGTGTGGTTCCTACAA 58.934 43.478 4.34 0.00 0.00 2.41
2879 3345 3.324268 TCCGTAAATGTGTGGTTCCTACA 59.676 43.478 0.00 0.00 0.00 2.74
2880 3346 3.929094 TCCGTAAATGTGTGGTTCCTAC 58.071 45.455 0.00 0.00 0.00 3.18
2881 3347 4.620589 TTCCGTAAATGTGTGGTTCCTA 57.379 40.909 0.00 0.00 0.00 2.94
2882 3348 3.495434 TTCCGTAAATGTGTGGTTCCT 57.505 42.857 0.00 0.00 0.00 3.36
2883 3349 4.022676 ACAATTCCGTAAATGTGTGGTTCC 60.023 41.667 0.00 0.00 0.00 3.62
2884 3350 4.915085 CACAATTCCGTAAATGTGTGGTTC 59.085 41.667 1.06 0.00 35.28 3.62
2885 3351 4.794655 GCACAATTCCGTAAATGTGTGGTT 60.795 41.667 10.17 0.00 37.13 3.67
2886 3352 3.305064 GCACAATTCCGTAAATGTGTGGT 60.305 43.478 10.17 0.00 37.13 4.16
2887 3353 3.241701 GCACAATTCCGTAAATGTGTGG 58.758 45.455 10.17 0.00 37.13 4.17
2888 3354 3.241701 GGCACAATTCCGTAAATGTGTG 58.758 45.455 10.17 11.90 38.28 3.82
2889 3355 2.230266 GGGCACAATTCCGTAAATGTGT 59.770 45.455 10.17 1.93 33.04 3.72
2890 3356 2.230025 TGGGCACAATTCCGTAAATGTG 59.770 45.455 4.68 4.68 33.34 3.21
2891 3357 2.520069 TGGGCACAATTCCGTAAATGT 58.480 42.857 0.00 0.00 0.00 2.71
2892 3358 3.584406 TTGGGCACAATTCCGTAAATG 57.416 42.857 0.00 0.00 0.00 2.32
2893 3359 4.311606 GTTTTGGGCACAATTCCGTAAAT 58.688 39.130 0.06 0.00 36.29 1.40
2894 3360 3.492829 GGTTTTGGGCACAATTCCGTAAA 60.493 43.478 0.06 0.00 36.29 2.01
2895 3361 2.036089 GGTTTTGGGCACAATTCCGTAA 59.964 45.455 0.06 0.00 36.29 3.18
2896 3362 1.614413 GGTTTTGGGCACAATTCCGTA 59.386 47.619 0.06 0.00 36.29 4.02
2897 3363 0.391228 GGTTTTGGGCACAATTCCGT 59.609 50.000 0.06 0.00 36.29 4.69
2898 3364 0.390860 TGGTTTTGGGCACAATTCCG 59.609 50.000 0.06 0.00 36.29 4.30
2899 3365 1.416030 AGTGGTTTTGGGCACAATTCC 59.584 47.619 0.06 9.00 36.29 3.01
2900 3366 2.908688 AGTGGTTTTGGGCACAATTC 57.091 45.000 0.06 0.00 36.29 2.17
2901 3367 4.972751 ATTAGTGGTTTTGGGCACAATT 57.027 36.364 0.06 0.00 36.29 2.32
2902 3368 4.972751 AATTAGTGGTTTTGGGCACAAT 57.027 36.364 0.06 0.00 36.29 2.71
2903 3369 4.762289 AAATTAGTGGTTTTGGGCACAA 57.238 36.364 0.00 0.00 34.07 3.33
2904 3370 4.762289 AAAATTAGTGGTTTTGGGCACA 57.238 36.364 0.00 0.00 0.00 4.57
2943 3409 1.687563 AGCCGCCAACTAGTGTTTTT 58.312 45.000 0.00 0.00 33.52 1.94
2944 3410 1.687563 AAGCCGCCAACTAGTGTTTT 58.312 45.000 0.00 0.00 33.52 2.43
2945 3411 1.336755 CAAAGCCGCCAACTAGTGTTT 59.663 47.619 0.00 0.00 33.52 2.83
2946 3412 0.951558 CAAAGCCGCCAACTAGTGTT 59.048 50.000 0.00 0.00 36.75 3.32
2947 3413 0.889186 CCAAAGCCGCCAACTAGTGT 60.889 55.000 0.00 0.00 0.00 3.55
2948 3414 0.889186 ACCAAAGCCGCCAACTAGTG 60.889 55.000 0.00 0.00 0.00 2.74
2949 3415 0.605589 GACCAAAGCCGCCAACTAGT 60.606 55.000 0.00 0.00 0.00 2.57
2950 3416 1.635663 CGACCAAAGCCGCCAACTAG 61.636 60.000 0.00 0.00 0.00 2.57
2951 3417 1.669760 CGACCAAAGCCGCCAACTA 60.670 57.895 0.00 0.00 0.00 2.24
2952 3418 2.748058 ATCGACCAAAGCCGCCAACT 62.748 55.000 0.00 0.00 0.00 3.16
2953 3419 1.862602 AATCGACCAAAGCCGCCAAC 61.863 55.000 0.00 0.00 0.00 3.77
2954 3420 1.175983 AAATCGACCAAAGCCGCCAA 61.176 50.000 0.00 0.00 0.00 4.52
2955 3421 1.602323 AAATCGACCAAAGCCGCCA 60.602 52.632 0.00 0.00 0.00 5.69
2956 3422 1.154035 CAAATCGACCAAAGCCGCC 60.154 57.895 0.00 0.00 0.00 6.13
2957 3423 0.451783 ATCAAATCGACCAAAGCCGC 59.548 50.000 0.00 0.00 0.00 6.53
2958 3424 1.737236 TCATCAAATCGACCAAAGCCG 59.263 47.619 0.00 0.00 0.00 5.52
2959 3425 2.476185 CGTCATCAAATCGACCAAAGCC 60.476 50.000 0.00 0.00 0.00 4.35
2960 3426 2.415168 TCGTCATCAAATCGACCAAAGC 59.585 45.455 0.00 0.00 0.00 3.51
2961 3427 4.864916 ATCGTCATCAAATCGACCAAAG 57.135 40.909 0.00 0.00 36.46 2.77
2962 3428 6.536941 TCATAATCGTCATCAAATCGACCAAA 59.463 34.615 0.00 0.00 36.46 3.28
2963 3429 6.019075 GTCATAATCGTCATCAAATCGACCAA 60.019 38.462 0.00 0.00 36.46 3.67
2964 3430 5.462068 GTCATAATCGTCATCAAATCGACCA 59.538 40.000 0.00 0.00 36.46 4.02
2965 3431 5.462068 TGTCATAATCGTCATCAAATCGACC 59.538 40.000 0.00 0.00 36.46 4.79
2966 3432 6.417930 TCTGTCATAATCGTCATCAAATCGAC 59.582 38.462 0.00 0.00 36.46 4.20
2967 3433 6.503524 TCTGTCATAATCGTCATCAAATCGA 58.496 36.000 0.00 0.00 37.96 3.59
2968 3434 6.753897 TCTGTCATAATCGTCATCAAATCG 57.246 37.500 0.00 0.00 0.00 3.34
2969 3435 7.360691 CCCATCTGTCATAATCGTCATCAAATC 60.361 40.741 0.00 0.00 0.00 2.17
2970 3436 6.429078 CCCATCTGTCATAATCGTCATCAAAT 59.571 38.462 0.00 0.00 0.00 2.32
2971 3437 5.759763 CCCATCTGTCATAATCGTCATCAAA 59.240 40.000 0.00 0.00 0.00 2.69
2972 3438 5.299949 CCCATCTGTCATAATCGTCATCAA 58.700 41.667 0.00 0.00 0.00 2.57
2973 3439 4.800582 GCCCATCTGTCATAATCGTCATCA 60.801 45.833 0.00 0.00 0.00 3.07
2974 3440 3.681897 GCCCATCTGTCATAATCGTCATC 59.318 47.826 0.00 0.00 0.00 2.92
2975 3441 3.557898 GGCCCATCTGTCATAATCGTCAT 60.558 47.826 0.00 0.00 0.00 3.06
2976 3442 2.224281 GGCCCATCTGTCATAATCGTCA 60.224 50.000 0.00 0.00 0.00 4.35
2977 3443 2.417719 GGCCCATCTGTCATAATCGTC 58.582 52.381 0.00 0.00 0.00 4.20
2978 3444 1.072331 GGGCCCATCTGTCATAATCGT 59.928 52.381 19.95 0.00 0.00 3.73
2979 3445 1.611673 GGGGCCCATCTGTCATAATCG 60.612 57.143 26.86 0.00 0.00 3.34
2980 3446 1.611673 CGGGGCCCATCTGTCATAATC 60.612 57.143 26.86 0.00 0.00 1.75
2981 3447 0.401738 CGGGGCCCATCTGTCATAAT 59.598 55.000 26.86 0.00 0.00 1.28
2982 3448 0.986019 ACGGGGCCCATCTGTCATAA 60.986 55.000 26.86 0.00 0.00 1.90
2983 3449 0.986019 AACGGGGCCCATCTGTCATA 60.986 55.000 26.86 0.00 0.00 2.15
2984 3450 1.863155 AAACGGGGCCCATCTGTCAT 61.863 55.000 26.86 6.16 0.00 3.06
2985 3451 1.202099 TAAACGGGGCCCATCTGTCA 61.202 55.000 26.86 5.09 0.00 3.58
2986 3452 0.182775 ATAAACGGGGCCCATCTGTC 59.817 55.000 26.86 3.25 0.00 3.51
2987 3453 0.106719 CATAAACGGGGCCCATCTGT 60.107 55.000 26.86 13.49 0.00 3.41
2988 3454 1.455383 GCATAAACGGGGCCCATCTG 61.455 60.000 26.86 12.75 0.00 2.90
2989 3455 1.152756 GCATAAACGGGGCCCATCT 60.153 57.895 26.86 8.03 0.00 2.90
2990 3456 2.200337 GGCATAAACGGGGCCCATC 61.200 63.158 26.86 5.93 41.90 3.51
2991 3457 2.123468 GGCATAAACGGGGCCCAT 60.123 61.111 26.86 3.28 41.90 4.00
2992 3458 4.805768 CGGCATAAACGGGGCCCA 62.806 66.667 26.86 1.48 44.90 5.36
2993 3459 4.493049 TCGGCATAAACGGGGCCC 62.493 66.667 15.76 15.76 44.90 5.80
2994 3460 3.206957 GTCGGCATAAACGGGGCC 61.207 66.667 0.00 0.00 44.27 5.80
2995 3461 3.569690 CGTCGGCATAAACGGGGC 61.570 66.667 0.00 0.00 35.32 5.80
2996 3462 2.125431 ACGTCGGCATAAACGGGG 60.125 61.111 0.00 0.00 42.99 5.73
2997 3463 2.457778 CCACGTCGGCATAAACGGG 61.458 63.158 0.00 0.00 42.99 5.28
2998 3464 3.086309 CCACGTCGGCATAAACGG 58.914 61.111 0.00 0.00 42.99 4.44
3007 3473 3.578515 AACCGTTAGGCCACGTCGG 62.579 63.158 21.03 21.03 45.53 4.79
3008 3474 2.048877 AACCGTTAGGCCACGTCG 60.049 61.111 13.90 8.45 42.76 5.12
3009 3475 2.090524 CGAACCGTTAGGCCACGTC 61.091 63.158 13.90 5.69 42.76 4.34
3010 3476 2.048877 CGAACCGTTAGGCCACGT 60.049 61.111 13.90 0.00 42.76 4.49
3011 3477 3.484547 GCGAACCGTTAGGCCACG 61.485 66.667 5.01 7.16 42.76 4.94
3012 3478 2.357760 TGCGAACCGTTAGGCCAC 60.358 61.111 5.01 0.00 42.76 5.01
3013 3479 2.047655 CTGCGAACCGTTAGGCCA 60.048 61.111 5.01 0.00 42.76 5.36
3014 3480 2.818274 CCTGCGAACCGTTAGGCC 60.818 66.667 0.00 0.00 42.76 5.19
3015 3481 3.497031 GCCTGCGAACCGTTAGGC 61.497 66.667 16.29 16.29 45.59 3.93
3016 3482 1.669760 TTGCCTGCGAACCGTTAGG 60.670 57.895 0.00 0.00 45.13 2.69
3017 3483 0.949105 AGTTGCCTGCGAACCGTTAG 60.949 55.000 0.00 0.00 0.00 2.34
3018 3484 0.947180 GAGTTGCCTGCGAACCGTTA 60.947 55.000 0.00 0.00 0.00 3.18
3019 3485 2.203153 AGTTGCCTGCGAACCGTT 60.203 55.556 0.00 0.00 0.00 4.44
3020 3486 2.665185 GAGTTGCCTGCGAACCGT 60.665 61.111 0.00 0.00 0.00 4.83
3021 3487 3.423154 GGAGTTGCCTGCGAACCG 61.423 66.667 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.