Multiple sequence alignment - TraesCS2A01G473600

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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 TraesCS2A01G473600 chr2A 100.000 3848 0 0 1 3848 715252053 715248206 0.000000e+00 7107.0
1 TraesCS2A01G473600 chr2A 89.739 536 37 6 3327 3848 41626836 41627367 0.000000e+00 669.0
2 TraesCS2A01G473600 chr2A 84.516 310 40 6 3000 3303 715210306 715209999 2.250000e-77 300.0
3 TraesCS2A01G473600 chr2A 82.721 272 40 4 3000 3270 715216481 715216216 6.430000e-58 235.0
4 TraesCS2A01G473600 chr2B 89.685 2288 129 44 711 2943 693316384 693314149 0.000000e+00 2819.0
5 TraesCS2A01G473600 chr2B 84.194 310 41 6 3000 3303 693154911 693154604 1.050000e-75 294.0
6 TraesCS2A01G473600 chr2B 87.783 221 24 2 3003 3220 693180787 693180567 4.930000e-64 255.0
7 TraesCS2A01G473600 chr2B 82.042 284 42 7 3000 3281 693305710 693305434 2.310000e-57 233.0
8 TraesCS2A01G473600 chr2D 89.189 2331 145 52 702 2971 577078665 577076381 0.000000e+00 2809.0
9 TraesCS2A01G473600 chr2D 88.172 279 33 0 3326 3604 93262716 93262994 2.220000e-87 333.0
10 TraesCS2A01G473600 chr2D 92.929 198 12 2 3133 3328 577059688 577059491 1.750000e-73 287.0
11 TraesCS2A01G473600 chr2D 90.385 208 18 2 2711 2917 577024061 577023855 4.900000e-69 272.0
12 TraesCS2A01G473600 chr2D 98.551 138 2 0 3000 3137 577076041 577075904 1.070000e-60 244.0
13 TraesCS2A01G473600 chr2D 81.625 283 45 5 3000 3281 577023594 577023318 1.080000e-55 228.0
14 TraesCS2A01G473600 chr2D 82.203 236 37 4 3351 3585 6459073 6458842 8.430000e-47 198.0
15 TraesCS2A01G473600 chr1B 96.000 700 27 1 1 700 633308527 633309225 0.000000e+00 1136.0
16 TraesCS2A01G473600 chr1B 84.121 529 76 3 3327 3848 153129660 153129133 4.440000e-139 505.0
17 TraesCS2A01G473600 chr7D 95.714 700 29 1 2 700 77497000 77497699 0.000000e+00 1125.0
18 TraesCS2A01G473600 chr7D 95.150 701 33 1 1 700 147588097 147587397 0.000000e+00 1105.0
19 TraesCS2A01G473600 chr7D 94.437 701 37 2 1 701 66593061 66592363 0.000000e+00 1077.0
20 TraesCS2A01G473600 chr7D 79.508 366 66 8 3327 3689 5475791 5476150 6.380000e-63 252.0
21 TraesCS2A01G473600 chr5D 95.546 696 31 0 1 696 539447818 539448513 0.000000e+00 1114.0
22 TraesCS2A01G473600 chr1D 94.595 703 37 1 3 704 365897694 365898396 0.000000e+00 1086.0
23 TraesCS2A01G473600 chr6D 94.548 697 36 2 1 696 427315914 427316609 0.000000e+00 1075.0
24 TraesCS2A01G473600 chr6D 82.353 238 32 8 3351 3585 55678005 55678235 8.430000e-47 198.0
25 TraesCS2A01G473600 chr6D 80.303 264 49 3 3351 3613 31261345 31261084 3.030000e-46 196.0
26 TraesCS2A01G473600 chr3D 93.822 696 42 1 1 696 417079755 417080449 0.000000e+00 1046.0
27 TraesCS2A01G473600 chr7A 93.324 704 45 2 1 702 507405185 507405888 0.000000e+00 1038.0
28 TraesCS2A01G473600 chr7A 94.906 530 20 2 3326 3848 608533309 608533838 0.000000e+00 822.0
29 TraesCS2A01G473600 chr7A 90.875 526 32 6 3326 3837 25704752 25704229 0.000000e+00 691.0
30 TraesCS2A01G473600 chr7A 89.299 542 37 4 3327 3848 545710282 545710822 0.000000e+00 660.0
31 TraesCS2A01G473600 chr4B 85.547 512 50 11 3352 3848 537153527 537153025 7.370000e-142 514.0
32 TraesCS2A01G473600 chr5B 86.017 472 54 5 3326 3792 589341061 589340597 2.670000e-136 496.0
33 TraesCS2A01G473600 chr5B 82.472 542 70 14 3328 3848 703943634 703943097 5.860000e-123 451.0
34 TraesCS2A01G473600 chr5B 97.297 37 1 0 3812 3848 640538997 640538961 3.210000e-06 63.9
35 TraesCS2A01G473600 chr6B 85.239 481 53 8 3327 3792 716999354 716998877 2.690000e-131 479.0
36 TraesCS2A01G473600 chr3A 85.252 278 38 2 3327 3604 739534288 739534562 2.260000e-72 283.0


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 TraesCS2A01G473600 chr2A 715248206 715252053 3847 True 7107.0 7107 100.000 1 3848 1 chr2A.!!$R3 3847
1 TraesCS2A01G473600 chr2A 41626836 41627367 531 False 669.0 669 89.739 3327 3848 1 chr2A.!!$F1 521
2 TraesCS2A01G473600 chr2B 693314149 693316384 2235 True 2819.0 2819 89.685 711 2943 1 chr2B.!!$R4 2232
3 TraesCS2A01G473600 chr2D 577075904 577078665 2761 True 1526.5 2809 93.870 702 3137 2 chr2D.!!$R4 2435
4 TraesCS2A01G473600 chr2D 577023318 577024061 743 True 250.0 272 86.005 2711 3281 2 chr2D.!!$R3 570
5 TraesCS2A01G473600 chr1B 633308527 633309225 698 False 1136.0 1136 96.000 1 700 1 chr1B.!!$F1 699
6 TraesCS2A01G473600 chr1B 153129133 153129660 527 True 505.0 505 84.121 3327 3848 1 chr1B.!!$R1 521
7 TraesCS2A01G473600 chr7D 77497000 77497699 699 False 1125.0 1125 95.714 2 700 1 chr7D.!!$F2 698
8 TraesCS2A01G473600 chr7D 147587397 147588097 700 True 1105.0 1105 95.150 1 700 1 chr7D.!!$R2 699
9 TraesCS2A01G473600 chr7D 66592363 66593061 698 True 1077.0 1077 94.437 1 701 1 chr7D.!!$R1 700
10 TraesCS2A01G473600 chr5D 539447818 539448513 695 False 1114.0 1114 95.546 1 696 1 chr5D.!!$F1 695
11 TraesCS2A01G473600 chr1D 365897694 365898396 702 False 1086.0 1086 94.595 3 704 1 chr1D.!!$F1 701
12 TraesCS2A01G473600 chr6D 427315914 427316609 695 False 1075.0 1075 94.548 1 696 1 chr6D.!!$F2 695
13 TraesCS2A01G473600 chr3D 417079755 417080449 694 False 1046.0 1046 93.822 1 696 1 chr3D.!!$F1 695
14 TraesCS2A01G473600 chr7A 507405185 507405888 703 False 1038.0 1038 93.324 1 702 1 chr7A.!!$F1 701
15 TraesCS2A01G473600 chr7A 608533309 608533838 529 False 822.0 822 94.906 3326 3848 1 chr7A.!!$F3 522
16 TraesCS2A01G473600 chr7A 25704229 25704752 523 True 691.0 691 90.875 3326 3837 1 chr7A.!!$R1 511
17 TraesCS2A01G473600 chr7A 545710282 545710822 540 False 660.0 660 89.299 3327 3848 1 chr7A.!!$F2 521
18 TraesCS2A01G473600 chr4B 537153025 537153527 502 True 514.0 514 85.547 3352 3848 1 chr4B.!!$R1 496
19 TraesCS2A01G473600 chr5B 703943097 703943634 537 True 451.0 451 82.472 3328 3848 1 chr5B.!!$R3 520

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
821 835 0.248825 ATGACGACGCTCTGATCTGC 60.249 55.0 0.00 0.0 0.00 4.26 F
1520 1564 0.322975 CAGGTAGCTGTGGTGCTCTT 59.677 55.0 13.89 0.0 42.97 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 1923 0.034670 ACCTACCGGAGTAGCGAACT 60.035 55.0 9.46 0.0 44.05 3.01 R
3278 3700 0.033894 GAAAAGGTGGCCCCCGATAA 60.034 55.0 0.00 0.0 0.00 1.75 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
121 122 2.027745 ACATGACCATTGAGAACGAGCT 60.028 45.455 0.00 0.00 0.00 4.09
179 180 2.031870 GGCATTCCTGTTAACCCCATC 58.968 52.381 2.48 0.00 0.00 3.51
219 220 4.038763 TCAGACGTTTCATGAAGGTGTACT 59.961 41.667 16.19 7.09 36.54 2.73
654 658 7.747155 TTACGGTCCAAATTTTACATCTTCA 57.253 32.000 0.00 0.00 0.00 3.02
655 659 6.642707 ACGGTCCAAATTTTACATCTTCAA 57.357 33.333 0.00 0.00 0.00 2.69
661 665 9.597999 GTCCAAATTTTACATCTTCAATTTTGC 57.402 29.630 0.00 0.00 28.44 3.68
682 686 6.085555 TGCACCGTCAAAATTTAAACCATA 57.914 33.333 0.00 0.00 0.00 2.74
706 710 3.510388 TGAAGATGCTGTAAGGAGTCG 57.490 47.619 0.00 0.00 38.10 4.18
713 717 3.024547 TGCTGTAAGGAGTCGAGCTAAT 58.975 45.455 0.00 0.00 0.00 1.73
747 751 1.995484 CACTTGGCTCGATACACACTG 59.005 52.381 0.00 0.00 0.00 3.66
818 832 3.171705 GGATGACGACGCTCTGATC 57.828 57.895 0.00 0.00 0.00 2.92
819 833 0.665835 GGATGACGACGCTCTGATCT 59.334 55.000 0.00 0.00 0.00 2.75
820 834 1.599171 GGATGACGACGCTCTGATCTG 60.599 57.143 0.00 0.00 0.00 2.90
821 835 0.248825 ATGACGACGCTCTGATCTGC 60.249 55.000 0.00 0.00 0.00 4.26
822 836 1.308783 TGACGACGCTCTGATCTGCT 61.309 55.000 0.00 0.00 0.00 4.24
826 840 2.027314 CGCTCTGATCTGCTCCCG 59.973 66.667 0.00 0.00 0.00 5.14
858 876 2.126580 GTCCACCGACCGTCTTCG 60.127 66.667 0.00 0.00 38.80 3.79
922 945 1.611519 AAAGGAAATCCACCGCGAAA 58.388 45.000 8.23 0.00 38.89 3.46
965 991 4.394078 CGTCGACAACGCGGAGGA 62.394 66.667 17.16 0.00 45.76 3.71
966 992 2.804090 GTCGACAACGCGGAGGAC 60.804 66.667 12.47 6.68 39.58 3.85
967 993 4.047059 TCGACAACGCGGAGGACC 62.047 66.667 12.47 0.00 39.58 4.46
1083 1109 4.682334 TCCAGGTACCACCGCCGA 62.682 66.667 15.94 0.00 44.90 5.54
1100 1126 1.674057 GACCACCAGTAGCAGCAGT 59.326 57.895 0.00 0.00 0.00 4.40
1111 1137 2.033757 CAGCAGTGCCAGCTCCTT 59.966 61.111 12.58 0.00 41.14 3.36
1113 1139 2.749441 GCAGTGCCAGCTCCTTCC 60.749 66.667 2.85 0.00 0.00 3.46
1245 1273 1.755959 TGGTGTTGCTGCATTCTGTTT 59.244 42.857 1.84 0.00 0.00 2.83
1392 1427 2.179018 CGAAAATGTGGCCCTGCG 59.821 61.111 0.00 0.00 0.00 5.18
1410 1445 1.587088 GGCGCGCATGAATTTCAGG 60.587 57.895 34.42 6.69 0.00 3.86
1416 1451 1.741706 CGCATGAATTTCAGGTGCTCT 59.258 47.619 18.09 0.00 31.90 4.09
1421 1456 0.962356 AATTTCAGGTGCTCTGCGGG 60.962 55.000 0.00 0.00 43.06 6.13
1436 1480 2.671682 GGGAGAGAGGGCCAACAC 59.328 66.667 6.18 0.00 0.00 3.32
1453 1497 3.498774 ACACTGGGATATCCAAGCATC 57.501 47.619 24.15 6.30 46.51 3.91
1455 1499 3.181447 ACACTGGGATATCCAAGCATCTG 60.181 47.826 24.15 17.14 46.51 2.90
1473 1517 2.047465 CTCTCGTGCCTTGCTGCT 60.047 61.111 0.00 0.00 0.00 4.24
1476 1520 2.669569 TCGTGCCTTGCTGCTTCC 60.670 61.111 0.00 0.00 0.00 3.46
1480 1524 3.130160 GCCTTGCTGCTTCCCTCG 61.130 66.667 0.00 0.00 0.00 4.63
1491 1535 1.202475 GCTTCCCTCGTCTTCATCTCC 60.202 57.143 0.00 0.00 0.00 3.71
1514 1558 1.853963 CCTAGTCAGGTAGCTGTGGT 58.146 55.000 20.76 9.67 37.15 4.16
1516 1560 0.895530 TAGTCAGGTAGCTGTGGTGC 59.104 55.000 20.76 8.09 0.00 5.01
1518 1562 0.390472 GTCAGGTAGCTGTGGTGCTC 60.390 60.000 20.76 2.21 42.97 4.26
1520 1564 0.322975 CAGGTAGCTGTGGTGCTCTT 59.677 55.000 13.89 0.00 42.97 2.85
1526 1570 1.002544 AGCTGTGGTGCTCTTCTAACC 59.997 52.381 0.00 0.00 39.34 2.85
1538 1582 6.867816 GTGCTCTTCTAACCTATCATCAGATG 59.132 42.308 3.71 3.71 35.67 2.90
1541 1585 6.753180 TCTTCTAACCTATCATCAGATGCAC 58.247 40.000 5.41 0.00 35.67 4.57
1542 1586 5.126396 TCTAACCTATCATCAGATGCACG 57.874 43.478 5.41 0.00 35.67 5.34
1545 1589 2.961741 ACCTATCATCAGATGCACGTCT 59.038 45.455 5.41 0.00 35.67 4.18
1546 1590 3.386078 ACCTATCATCAGATGCACGTCTT 59.614 43.478 5.41 0.00 35.67 3.01
1548 1592 5.069119 ACCTATCATCAGATGCACGTCTTAA 59.931 40.000 5.41 0.00 35.67 1.85
1550 1594 5.725110 ATCATCAGATGCACGTCTTAAAC 57.275 39.130 5.41 0.00 31.91 2.01
1551 1595 3.932710 TCATCAGATGCACGTCTTAAACC 59.067 43.478 5.41 0.00 0.00 3.27
1552 1596 2.333926 TCAGATGCACGTCTTAAACCG 58.666 47.619 0.00 0.00 0.00 4.44
1553 1597 1.393539 CAGATGCACGTCTTAAACCGG 59.606 52.381 0.00 0.00 0.00 5.28
1659 1716 9.708092 AAAAACAGAGATAGTCAGTAAGGTTAC 57.292 33.333 0.00 0.00 0.00 2.50
1660 1717 7.407393 AACAGAGATAGTCAGTAAGGTTACC 57.593 40.000 0.00 0.00 34.19 2.85
1866 1923 0.391130 CCGCCAAGAACTTCGATCCA 60.391 55.000 0.00 0.00 0.00 3.41
1881 1938 0.683504 ATCCAGTTCGCTACTCCGGT 60.684 55.000 0.00 0.00 33.85 5.28
1935 1992 1.118965 TCGCTGGTCAGGGACAAGAA 61.119 55.000 12.72 0.00 44.07 2.52
1984 2041 4.760530 TTACAGCAGCCTCATACTGAAT 57.239 40.909 0.00 0.00 37.32 2.57
2022 2083 6.989659 TCTGGTTTACGAAGACAGAATAGTT 58.010 36.000 0.00 0.00 35.45 2.24
2027 2088 9.148104 GGTTTACGAAGACAGAATAGTTGTATT 57.852 33.333 0.00 0.00 33.10 1.89
2232 2306 1.467734 GTGCAATGCCTGTCTCAAGAG 59.532 52.381 1.53 0.00 0.00 2.85
2247 2321 2.809861 AAGAGGACATGGCTGGTGCG 62.810 60.000 0.00 0.00 40.82 5.34
2343 2417 4.160329 CCAAGCTACCCTATGATGTCCTA 58.840 47.826 0.00 0.00 0.00 2.94
2349 2423 1.546476 CCCTATGATGTCCTAGCGACC 59.454 57.143 8.36 0.00 41.18 4.79
2490 2564 8.133024 AGCCATCTTAATGTAGATTCTAGAGG 57.867 38.462 0.00 0.00 32.60 3.69
2508 2582 5.211174 AGAGGGTAGTACTTTGTGTTGTC 57.789 43.478 0.00 0.00 0.00 3.18
2547 2621 3.865446 TGATGCACTCGTGATCTGAAAT 58.135 40.909 0.39 0.00 0.00 2.17
2548 2622 5.009854 TGATGCACTCGTGATCTGAAATA 57.990 39.130 0.39 0.00 0.00 1.40
2550 2624 6.051074 TGATGCACTCGTGATCTGAAATAAT 58.949 36.000 0.39 0.00 0.00 1.28
2552 2626 6.741992 TGCACTCGTGATCTGAAATAATTT 57.258 33.333 0.39 0.00 0.00 1.82
2553 2627 6.545508 TGCACTCGTGATCTGAAATAATTTG 58.454 36.000 0.39 0.00 0.00 2.32
2583 2657 6.127338 TGACACTGAACCAGATATACTCAAGG 60.127 42.308 0.45 0.00 35.18 3.61
2586 2660 5.067936 ACTGAACCAGATATACTCAAGGACG 59.932 44.000 0.45 0.00 35.18 4.79
2663 2737 2.544685 CTACGACCCAAGCAAGATCAG 58.455 52.381 0.00 0.00 0.00 2.90
2850 2924 5.077424 GCCGAAGTGTATTTCAAGTAAACG 58.923 41.667 0.00 0.00 0.00 3.60
2874 2948 1.746615 CCATCCGCTGTTCCACTGG 60.747 63.158 0.00 0.00 0.00 4.00
2894 2968 0.179234 TCGGTGTTTGCTTCTCCACA 59.821 50.000 0.00 0.00 0.00 4.17
2925 3003 9.277783 AGCTGCACTTTGATAAATATAAGTAGG 57.722 33.333 1.02 0.00 30.19 3.18
2926 3004 8.017946 GCTGCACTTTGATAAATATAAGTAGGC 58.982 37.037 0.00 0.00 30.19 3.93
2966 3044 3.249080 TCCGTCGAGAAACCATGAAAAAC 59.751 43.478 0.00 0.00 0.00 2.43
2971 3064 4.824537 TCGAGAAACCATGAAAAACCATGA 59.175 37.500 5.54 0.00 44.98 3.07
2974 3067 6.478344 CGAGAAACCATGAAAAACCATGAAAA 59.522 34.615 5.54 0.00 44.98 2.29
2978 3084 9.271828 GAAACCATGAAAAACCATGAAAACTAT 57.728 29.630 5.54 0.00 44.98 2.12
2989 3095 6.750148 ACCATGAAAACTATATCTCGGAGAC 58.250 40.000 10.41 0.00 0.00 3.36
3151 3572 1.379044 GGTTCTACCCGGACGGAGA 60.379 63.158 13.13 5.16 37.50 3.71
3152 3573 1.661498 GGTTCTACCCGGACGGAGAC 61.661 65.000 13.13 3.28 37.50 3.36
3153 3574 0.962356 GTTCTACCCGGACGGAGACA 60.962 60.000 13.13 0.00 37.50 3.41
3154 3575 0.679002 TTCTACCCGGACGGAGACAG 60.679 60.000 13.13 3.71 37.50 3.51
3155 3576 2.044650 TACCCGGACGGAGACAGG 60.045 66.667 13.13 0.00 37.28 4.00
3161 3582 2.053277 GGACGGAGACAGGGAGGAC 61.053 68.421 0.00 0.00 0.00 3.85
3163 3584 3.827898 CGGAGACAGGGAGGACGC 61.828 72.222 0.00 0.00 0.00 5.19
3164 3585 2.363147 GGAGACAGGGAGGACGCT 60.363 66.667 0.00 0.00 39.90 5.07
3189 3610 1.956170 CACGCGTCAGCCTTCTTGT 60.956 57.895 9.86 0.00 41.18 3.16
3194 3615 1.194772 GCGTCAGCCTTCTTGTGTTAC 59.805 52.381 0.00 0.00 37.42 2.50
3202 3623 2.427506 CTTCTTGTGTTACCTCAGCCC 58.572 52.381 0.00 0.00 0.00 5.19
3220 3641 2.351276 GGCCAAGGACGTGGTGAT 59.649 61.111 0.00 0.00 41.12 3.06
3226 3647 2.217750 CAAGGACGTGGTGATGACAAA 58.782 47.619 0.00 0.00 0.00 2.83
3229 3650 2.631062 AGGACGTGGTGATGACAAACTA 59.369 45.455 0.00 0.00 0.00 2.24
3230 3651 3.070446 AGGACGTGGTGATGACAAACTAA 59.930 43.478 0.00 0.00 0.00 2.24
3231 3652 4.000988 GGACGTGGTGATGACAAACTAAT 58.999 43.478 0.00 0.00 0.00 1.73
3272 3694 3.604400 GCAACGTGCAAGCAACTG 58.396 55.556 0.00 0.00 44.26 3.16
3278 3700 2.123769 TGCAAGCAACTGGGCAGT 60.124 55.556 0.00 0.00 44.94 4.40
3286 3708 3.320359 ACTGGGCAGTTATCGGGG 58.680 61.111 0.00 0.00 38.83 5.73
3287 3709 2.375345 ACTGGGCAGTTATCGGGGG 61.375 63.158 0.00 0.00 38.83 5.40
3288 3710 3.774599 CTGGGCAGTTATCGGGGGC 62.775 68.421 0.00 0.00 0.00 5.80
3289 3711 4.581093 GGGCAGTTATCGGGGGCC 62.581 72.222 0.00 0.00 43.86 5.80
3290 3712 3.804329 GGCAGTTATCGGGGGCCA 61.804 66.667 4.39 0.00 44.01 5.36
3291 3713 2.516225 GCAGTTATCGGGGGCCAC 60.516 66.667 4.39 0.00 0.00 5.01
3292 3714 2.192175 CAGTTATCGGGGGCCACC 59.808 66.667 16.67 16.67 39.11 4.61
3293 3715 2.042261 AGTTATCGGGGGCCACCT 59.958 61.111 25.09 6.77 40.03 4.00
3294 3716 1.618447 AGTTATCGGGGGCCACCTT 60.618 57.895 25.09 12.48 40.03 3.50
3295 3717 1.212250 AGTTATCGGGGGCCACCTTT 61.212 55.000 25.09 12.06 40.03 3.11
3296 3718 0.323999 GTTATCGGGGGCCACCTTTT 60.324 55.000 25.09 9.14 40.03 2.27
3297 3719 0.033894 TTATCGGGGGCCACCTTTTC 60.034 55.000 25.09 0.00 40.03 2.29
3298 3720 0.917333 TATCGGGGGCCACCTTTTCT 60.917 55.000 25.09 4.06 40.03 2.52
3299 3721 2.211468 ATCGGGGGCCACCTTTTCTC 62.211 60.000 25.09 0.00 40.03 2.87
3300 3722 2.037367 GGGGGCCACCTTTTCTCC 59.963 66.667 20.04 0.00 40.03 3.71
3301 3723 2.851045 GGGGCCACCTTTTCTCCA 59.149 61.111 4.39 0.00 36.80 3.86
3302 3724 1.304464 GGGGCCACCTTTTCTCCAG 60.304 63.158 4.39 0.00 36.80 3.86
3303 3725 1.304464 GGGCCACCTTTTCTCCAGG 60.304 63.158 4.39 0.00 37.45 4.45
3304 3726 1.304464 GGCCACCTTTTCTCCAGGG 60.304 63.158 0.00 0.00 35.46 4.45
3305 3727 1.304464 GCCACCTTTTCTCCAGGGG 60.304 63.158 0.00 0.00 35.46 4.79
3306 3728 1.789576 GCCACCTTTTCTCCAGGGGA 61.790 60.000 0.00 0.00 36.89 4.81
3307 3729 0.777446 CCACCTTTTCTCCAGGGGAA 59.223 55.000 0.00 0.00 36.89 3.97
3308 3730 1.272147 CCACCTTTTCTCCAGGGGAAG 60.272 57.143 0.82 0.00 36.89 3.46
3309 3731 1.705186 CACCTTTTCTCCAGGGGAAGA 59.295 52.381 0.82 0.00 36.89 2.87
3310 3732 2.108250 CACCTTTTCTCCAGGGGAAGAA 59.892 50.000 0.82 0.00 36.89 2.52
3311 3733 2.789399 ACCTTTTCTCCAGGGGAAGAAA 59.211 45.455 0.82 0.00 35.46 2.52
3312 3734 3.206639 ACCTTTTCTCCAGGGGAAGAAAA 59.793 43.478 0.82 7.95 36.96 2.29
3313 3735 4.140686 ACCTTTTCTCCAGGGGAAGAAAAT 60.141 41.667 12.72 0.58 37.74 1.82
3314 3736 4.221482 CCTTTTCTCCAGGGGAAGAAAATG 59.779 45.833 12.72 8.20 37.74 2.32
3315 3737 4.740154 TTTCTCCAGGGGAAGAAAATGA 57.260 40.909 0.82 0.00 31.33 2.57
3316 3738 4.953781 TTCTCCAGGGGAAGAAAATGAT 57.046 40.909 0.00 0.00 0.00 2.45
3317 3739 6.401537 TTTCTCCAGGGGAAGAAAATGATA 57.598 37.500 0.82 0.00 31.33 2.15
3318 3740 5.373812 TCTCCAGGGGAAGAAAATGATAC 57.626 43.478 0.00 0.00 0.00 2.24
3319 3741 4.166144 TCTCCAGGGGAAGAAAATGATACC 59.834 45.833 0.00 0.00 0.00 2.73
3320 3742 4.119155 TCCAGGGGAAGAAAATGATACCT 58.881 43.478 0.00 0.00 0.00 3.08
3321 3743 4.079787 TCCAGGGGAAGAAAATGATACCTG 60.080 45.833 0.00 0.00 42.88 4.00
3322 3744 4.210331 CAGGGGAAGAAAATGATACCTGG 58.790 47.826 0.00 0.00 40.31 4.45
3323 3745 3.205282 AGGGGAAGAAAATGATACCTGGG 59.795 47.826 0.00 0.00 0.00 4.45
3324 3746 3.566351 GGGAAGAAAATGATACCTGGGG 58.434 50.000 0.00 0.00 0.00 4.96
3444 3866 2.722201 GCCTTCGGATGACCTCGGT 61.722 63.158 0.00 0.00 0.00 4.69
3610 4051 1.290324 CTGCGAGTGTGGCTAGTGT 59.710 57.895 0.00 0.00 0.00 3.55
3641 4082 3.842923 CCTCCAGATCGCGCCACT 61.843 66.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 2.099141 TCCAAGCTCGTTCTCAATGG 57.901 50.000 0.00 0.00 0.00 3.16
146 147 4.141088 ACAGGAATGCCCATCAAGTGATAT 60.141 41.667 0.00 0.00 37.41 1.63
179 180 0.516877 TGATGCGCTGTTCTTTTCGG 59.483 50.000 9.73 0.00 0.00 4.30
219 220 1.379527 TCGCTGTCTCTAATCTCGCA 58.620 50.000 0.00 0.00 0.00 5.10
631 635 7.747155 TTGAAGATGTAAAATTTGGACCGTA 57.253 32.000 0.00 0.00 0.00 4.02
632 636 6.642707 TTGAAGATGTAAAATTTGGACCGT 57.357 33.333 0.00 0.00 0.00 4.83
682 686 6.040955 TCGACTCCTTACAGCATCTTCAATAT 59.959 38.462 0.00 0.00 0.00 1.28
696 700 4.548991 TCGAATTAGCTCGACTCCTTAC 57.451 45.455 0.00 0.00 42.69 2.34
706 710 1.143183 TGGCCCGTCGAATTAGCTC 59.857 57.895 0.00 0.00 0.00 4.09
713 717 2.504274 AAGTGAGTGGCCCGTCGAA 61.504 57.895 0.00 0.00 0.00 3.71
922 945 0.818938 GACGTTTTGTTGGGGTTGGT 59.181 50.000 0.00 0.00 0.00 3.67
960 986 3.756727 GTCGGTGTCGGGTCCTCC 61.757 72.222 0.00 0.00 36.95 4.30
961 987 4.112341 CGTCGGTGTCGGGTCCTC 62.112 72.222 0.00 0.00 36.95 3.71
1075 1101 3.642778 CTACTGGTGGTCGGCGGTG 62.643 68.421 7.21 0.00 0.00 4.94
1083 1109 1.372683 CACTGCTGCTACTGGTGGT 59.627 57.895 0.00 0.00 0.00 4.16
1100 1126 2.665000 CGAAGGAAGGAGCTGGCA 59.335 61.111 0.00 0.00 0.00 4.92
1113 1139 4.727235 AAAGCGAAGAAACTAACCGAAG 57.273 40.909 0.00 0.00 0.00 3.79
1245 1273 8.940952 TGAATGTGAAATTCGTATCATGTACAA 58.059 29.630 0.00 0.00 0.00 2.41
1286 1317 0.737715 CACGCCTGCCTGTAACTCTC 60.738 60.000 0.00 0.00 0.00 3.20
1392 1427 1.587088 CCTGAAATTCATGCGCGCC 60.587 57.895 30.77 10.98 0.00 6.53
1421 1456 1.298014 CCAGTGTTGGCCCTCTCTC 59.702 63.158 0.00 0.00 37.73 3.20
1428 1463 0.550914 TGGATATCCCAGTGTTGGCC 59.449 55.000 19.34 0.00 43.58 5.36
1453 1497 2.047465 AGCAAGGCACGAGAGCAG 60.047 61.111 0.00 0.00 35.83 4.24
1455 1499 3.797546 GCAGCAAGGCACGAGAGC 61.798 66.667 0.00 0.00 0.00 4.09
1473 1517 1.486211 GGGAGATGAAGACGAGGGAA 58.514 55.000 0.00 0.00 0.00 3.97
1476 1520 0.461961 GTGGGGAGATGAAGACGAGG 59.538 60.000 0.00 0.00 0.00 4.63
1480 1524 2.696187 GACTAGGTGGGGAGATGAAGAC 59.304 54.545 0.00 0.00 0.00 3.01
1507 1551 1.002544 AGGTTAGAAGAGCACCACAGC 59.997 52.381 0.00 0.00 32.43 4.40
1508 1552 4.160439 TGATAGGTTAGAAGAGCACCACAG 59.840 45.833 0.00 0.00 32.43 3.66
1509 1553 4.093743 TGATAGGTTAGAAGAGCACCACA 58.906 43.478 0.00 0.00 32.43 4.17
1510 1554 4.737855 TGATAGGTTAGAAGAGCACCAC 57.262 45.455 0.00 0.00 32.43 4.16
1511 1555 4.962362 TGATGATAGGTTAGAAGAGCACCA 59.038 41.667 0.00 0.00 32.43 4.17
1512 1556 5.303078 TCTGATGATAGGTTAGAAGAGCACC 59.697 44.000 0.00 0.00 0.00 5.01
1514 1558 6.518032 GCATCTGATGATAGGTTAGAAGAGCA 60.518 42.308 21.30 0.00 0.00 4.26
1516 1560 6.867816 GTGCATCTGATGATAGGTTAGAAGAG 59.132 42.308 21.30 0.00 0.00 2.85
1518 1562 5.632764 CGTGCATCTGATGATAGGTTAGAAG 59.367 44.000 21.30 0.00 0.00 2.85
1520 1564 4.584743 ACGTGCATCTGATGATAGGTTAGA 59.415 41.667 21.30 0.00 0.00 2.10
1526 1570 6.074088 GGTTTAAGACGTGCATCTGATGATAG 60.074 42.308 21.30 12.30 0.00 2.08
1538 1582 1.193874 CTGAACCGGTTTAAGACGTGC 59.806 52.381 23.22 5.56 0.00 5.34
1541 1585 3.243336 CTCTCTGAACCGGTTTAAGACG 58.757 50.000 23.22 18.35 0.00 4.18
1542 1586 2.994578 GCTCTCTGAACCGGTTTAAGAC 59.005 50.000 23.22 8.76 0.00 3.01
1545 1589 3.478857 TTGCTCTCTGAACCGGTTTAA 57.521 42.857 23.22 12.31 0.00 1.52
1546 1590 3.478857 TTTGCTCTCTGAACCGGTTTA 57.521 42.857 23.22 17.20 0.00 2.01
1548 1592 2.039084 AGATTTGCTCTCTGAACCGGTT 59.961 45.455 22.50 22.50 0.00 4.44
1550 1594 2.005451 CAGATTTGCTCTCTGAACCGG 58.995 52.381 0.00 0.00 42.22 5.28
1551 1595 1.396301 GCAGATTTGCTCTCTGAACCG 59.604 52.381 12.87 0.00 46.95 4.44
1576 1630 5.124645 TGAAATGGATAATTTGGCAATGGC 58.875 37.500 0.00 0.00 38.64 4.40
1658 1715 3.148084 CGGGTCTCAACTGGTGGT 58.852 61.111 0.00 0.00 0.00 4.16
1659 1716 2.358737 GCGGGTCTCAACTGGTGG 60.359 66.667 0.00 0.00 0.00 4.61
1660 1717 2.738521 CGCGGGTCTCAACTGGTG 60.739 66.667 0.00 0.00 0.00 4.17
1866 1923 0.034670 ACCTACCGGAGTAGCGAACT 60.035 55.000 9.46 0.00 44.05 3.01
1881 1938 0.907704 ATGCCACCTCGAACCACCTA 60.908 55.000 0.00 0.00 0.00 3.08
1935 1992 2.260822 ACCTGAGTACAATGGCAGTCT 58.739 47.619 0.00 0.00 0.00 3.24
1999 2056 6.645415 ACAACTATTCTGTCTTCGTAAACCAG 59.355 38.462 0.00 0.00 0.00 4.00
2000 2057 6.518493 ACAACTATTCTGTCTTCGTAAACCA 58.482 36.000 0.00 0.00 0.00 3.67
2001 2058 8.699283 ATACAACTATTCTGTCTTCGTAAACC 57.301 34.615 0.00 0.00 0.00 3.27
2048 2111 6.036083 GCTTGCTTACGATAATTCAGTTGAGA 59.964 38.462 0.00 0.00 0.00 3.27
2049 2112 6.036517 AGCTTGCTTACGATAATTCAGTTGAG 59.963 38.462 0.00 0.00 0.00 3.02
2050 2113 5.874810 AGCTTGCTTACGATAATTCAGTTGA 59.125 36.000 0.00 0.00 0.00 3.18
2051 2114 6.111768 AGCTTGCTTACGATAATTCAGTTG 57.888 37.500 0.00 0.00 0.00 3.16
2083 2157 3.632145 ACCAGCAATTTTCCGATCATACC 59.368 43.478 0.00 0.00 0.00 2.73
2232 2306 4.408821 TCCGCACCAGCCATGTCC 62.409 66.667 0.00 0.00 37.52 4.02
2247 2321 1.142060 TCCCTCTCGAGATCAGTCTCC 59.858 57.143 17.03 0.00 46.67 3.71
2298 2372 1.373873 GAACGGGAGTGTCGGGAAC 60.374 63.158 0.00 0.00 46.69 3.62
2313 2387 4.347000 TCATAGGGTAGCTTGGGTATGAAC 59.653 45.833 0.00 0.00 0.00 3.18
2343 2417 0.524862 AATTGTCGTAGTCGGTCGCT 59.475 50.000 0.00 0.00 37.69 4.93
2349 2423 0.835740 CGGCGTAATTGTCGTAGTCG 59.164 55.000 0.00 0.00 38.55 4.18
2373 2447 0.397941 TGGTGTCCTTTGCTCCAGAG 59.602 55.000 0.00 0.00 0.00 3.35
2490 2564 5.045872 ACTTCGACAACACAAAGTACTACC 58.954 41.667 0.00 0.00 30.47 3.18
2508 2582 4.979197 GCATCAGATAGTTAGGTGACTTCG 59.021 45.833 0.00 0.00 43.67 3.79
2652 2726 0.674895 GCGTGTCCCTGATCTTGCTT 60.675 55.000 0.00 0.00 0.00 3.91
2850 2924 1.212751 GAACAGCGGATGGGTTTGC 59.787 57.895 0.00 0.00 0.00 3.68
2874 2948 0.586802 GTGGAGAAGCAAACACCGAC 59.413 55.000 0.00 0.00 0.00 4.79
2894 2968 2.472695 TATCAAAGTGCAGCTTCCGT 57.527 45.000 0.00 0.00 36.17 4.69
2926 3004 0.322008 GACTGAAGCCACTGAAGGGG 60.322 60.000 0.00 0.00 0.00 4.79
2966 3044 5.859114 CGTCTCCGAGATATAGTTTTCATGG 59.141 44.000 0.33 0.00 35.63 3.66
2971 3064 4.499357 GCACCGTCTCCGAGATATAGTTTT 60.499 45.833 0.33 0.00 35.63 2.43
2974 3067 2.152830 GCACCGTCTCCGAGATATAGT 58.847 52.381 0.33 0.00 35.63 2.12
2978 3084 1.826921 GGGCACCGTCTCCGAGATA 60.827 63.158 0.33 0.00 40.86 1.98
3029 3450 0.669318 TGGTCACCTCGAAATCGTGC 60.669 55.000 0.00 0.00 40.80 5.34
3171 3592 1.956170 ACAAGAAGGCTGACGCGTG 60.956 57.895 20.70 3.71 36.88 5.34
3181 3602 2.427506 GGCTGAGGTAACACAAGAAGG 58.572 52.381 0.00 0.00 36.48 3.46
3184 3605 0.320374 CGGGCTGAGGTAACACAAGA 59.680 55.000 0.00 0.00 36.48 3.02
3189 3610 3.712907 GGCCGGGCTGAGGTAACA 61.713 66.667 22.87 0.00 41.41 2.41
3202 3623 3.605749 ATCACCACGTCCTTGGCCG 62.606 63.158 0.00 0.00 40.77 6.13
3211 3632 4.894784 AGATTAGTTTGTCATCACCACGT 58.105 39.130 0.00 0.00 0.00 4.49
3214 3635 7.227873 TGGTTAAGATTAGTTTGTCATCACCA 58.772 34.615 0.00 0.00 0.00 4.17
3220 3641 7.144722 CAGCATGGTTAAGATTAGTTTGTCA 57.855 36.000 0.00 0.00 0.00 3.58
3271 3693 3.804329 GCCCCCGATAACTGCCCA 61.804 66.667 0.00 0.00 0.00 5.36
3272 3694 4.581093 GGCCCCCGATAACTGCCC 62.581 72.222 0.00 0.00 36.07 5.36
3278 3700 0.033894 GAAAAGGTGGCCCCCGATAA 60.034 55.000 0.00 0.00 0.00 1.75
3281 3703 2.856988 AGAAAAGGTGGCCCCCGA 60.857 61.111 0.00 0.00 0.00 5.14
3282 3704 2.361230 GAGAAAAGGTGGCCCCCG 60.361 66.667 0.00 0.00 0.00 5.73
3283 3705 2.037367 GGAGAAAAGGTGGCCCCC 59.963 66.667 0.00 0.00 0.00 5.40
3284 3706 1.304464 CTGGAGAAAAGGTGGCCCC 60.304 63.158 0.00 0.03 0.00 5.80
3285 3707 1.304464 CCTGGAGAAAAGGTGGCCC 60.304 63.158 0.00 0.00 0.00 5.80
3286 3708 1.304464 CCCTGGAGAAAAGGTGGCC 60.304 63.158 0.00 0.00 32.45 5.36
3287 3709 1.304464 CCCCTGGAGAAAAGGTGGC 60.304 63.158 0.00 0.00 32.45 5.01
3288 3710 0.777446 TTCCCCTGGAGAAAAGGTGG 59.223 55.000 0.00 0.00 31.21 4.61
3289 3711 1.705186 TCTTCCCCTGGAGAAAAGGTG 59.295 52.381 0.00 0.00 31.21 4.00
3290 3712 2.133858 TCTTCCCCTGGAGAAAAGGT 57.866 50.000 0.00 0.00 31.21 3.50
3291 3713 3.525800 TTTCTTCCCCTGGAGAAAAGG 57.474 47.619 6.59 0.00 31.33 3.11
3292 3714 5.079643 TCATTTTCTTCCCCTGGAGAAAAG 58.920 41.667 19.98 14.40 39.54 2.27
3293 3715 5.073437 TCATTTTCTTCCCCTGGAGAAAA 57.927 39.130 18.49 18.49 39.97 2.29
3294 3716 4.740154 TCATTTTCTTCCCCTGGAGAAA 57.260 40.909 5.27 5.27 31.89 2.52
3295 3717 4.953781 ATCATTTTCTTCCCCTGGAGAA 57.046 40.909 0.00 0.00 31.21 2.87
3296 3718 4.166144 GGTATCATTTTCTTCCCCTGGAGA 59.834 45.833 0.00 0.00 31.21 3.71
3297 3719 4.166919 AGGTATCATTTTCTTCCCCTGGAG 59.833 45.833 0.00 0.00 31.21 3.86
3298 3720 4.079787 CAGGTATCATTTTCTTCCCCTGGA 60.080 45.833 0.00 0.00 35.65 3.86
3299 3721 4.210331 CAGGTATCATTTTCTTCCCCTGG 58.790 47.826 0.00 0.00 35.65 4.45
3300 3722 4.210331 CCAGGTATCATTTTCTTCCCCTG 58.790 47.826 0.00 0.00 38.33 4.45
3301 3723 3.205282 CCCAGGTATCATTTTCTTCCCCT 59.795 47.826 0.00 0.00 0.00 4.79
3302 3724 3.566351 CCCAGGTATCATTTTCTTCCCC 58.434 50.000 0.00 0.00 0.00 4.81
3303 3725 3.566351 CCCCAGGTATCATTTTCTTCCC 58.434 50.000 0.00 0.00 0.00 3.97
3304 3726 2.959030 GCCCCAGGTATCATTTTCTTCC 59.041 50.000 0.00 0.00 0.00 3.46
3305 3727 3.631250 TGCCCCAGGTATCATTTTCTTC 58.369 45.455 0.00 0.00 0.00 2.87
3306 3728 3.756082 TGCCCCAGGTATCATTTTCTT 57.244 42.857 0.00 0.00 0.00 2.52
3307 3729 3.437052 GGATGCCCCAGGTATCATTTTCT 60.437 47.826 12.83 0.00 44.71 2.52
3308 3730 2.893489 GGATGCCCCAGGTATCATTTTC 59.107 50.000 12.83 0.00 44.71 2.29
3309 3731 2.247111 TGGATGCCCCAGGTATCATTTT 59.753 45.455 12.83 0.00 44.71 1.82
3310 3732 1.858910 TGGATGCCCCAGGTATCATTT 59.141 47.619 12.83 0.00 44.71 2.32
3311 3733 1.533187 TGGATGCCCCAGGTATCATT 58.467 50.000 12.83 0.00 44.71 2.57
3312 3734 3.280030 TGGATGCCCCAGGTATCAT 57.720 52.632 12.83 0.00 44.71 2.45
3313 3735 4.849529 TGGATGCCCCAGGTATCA 57.150 55.556 12.83 0.00 44.71 2.15
3320 3742 0.899717 GCTTGTTTCTGGATGCCCCA 60.900 55.000 0.00 0.00 44.25 4.96
3321 3743 0.899717 TGCTTGTTTCTGGATGCCCC 60.900 55.000 0.00 0.00 0.00 5.80
3322 3744 1.134907 CATGCTTGTTTCTGGATGCCC 60.135 52.381 0.00 0.00 0.00 5.36
3323 3745 1.820519 TCATGCTTGTTTCTGGATGCC 59.179 47.619 0.00 0.00 33.08 4.40
3324 3746 2.229543 TGTCATGCTTGTTTCTGGATGC 59.770 45.455 0.00 0.00 33.08 3.91
3380 3802 0.036306 AAAAACTGATCCGACGGCCT 59.964 50.000 9.66 0.00 0.00 5.19
3641 4082 0.972883 GCCACCCAATTTTACAGGCA 59.027 50.000 0.00 0.00 40.29 4.75
3797 4244 3.792736 GCGGTATGGCAGGGACCA 61.793 66.667 14.27 0.00 45.82 4.02


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

AutoCloner maintained by Alex Coulton.