Multiple sequence alignment - TraesCS5A01G030900

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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 TraesCS5A01G030900 chr5A 100.000 3112 0 0 1 3112 28227138 28230249 0.000000e+00 5747.0
1 TraesCS5A01G030900 chr5A 81.818 297 19 14 2829 3112 28237275 28237549 1.880000e-52 217.0
2 TraesCS5A01G030900 chr5B 86.164 2067 123 72 546 2510 33557880 33555875 0.000000e+00 2082.0
3 TraesCS5A01G030900 chr5B 90.226 532 43 6 1 527 33558506 33557979 0.000000e+00 686.0
4 TraesCS5A01G030900 chr5B 80.353 397 30 10 2717 3112 33555601 33555252 1.110000e-64 257.0
5 TraesCS5A01G030900 chr5B 91.667 96 8 0 2582 2677 33555878 33555783 1.950000e-27 134.0
6 TraesCS5A01G030900 chr5D 89.070 1473 71 32 1002 2423 40183040 40184473 0.000000e+00 1746.0
7 TraesCS5A01G030900 chr5D 91.470 551 42 4 1 547 40181738 40182287 0.000000e+00 752.0
8 TraesCS5A01G030900 chr5D 88.641 449 24 9 2675 3112 40184812 40185244 3.560000e-144 521.0
9 TraesCS5A01G030900 chr5D 90.741 270 12 4 725 986 40182644 40182908 6.390000e-92 348.0
10 TraesCS5A01G030900 chr5D 85.882 170 14 7 546 710 40182365 40182529 4.130000e-39 172.0
11 TraesCS5A01G030900 chr4D 89.377 546 52 3 7 547 291532273 291532817 0.000000e+00 682.0
12 TraesCS5A01G030900 chr4D 80.299 1005 85 46 1423 2402 291586925 291587841 0.000000e+00 654.0
13 TraesCS5A01G030900 chr4D 84.688 320 31 14 1033 1340 291586578 291586891 1.400000e-78 303.0
14 TraesCS5A01G030900 chr4D 81.100 291 26 13 725 1004 291578273 291578545 4.070000e-49 206.0
15 TraesCS5A01G030900 chr7B 80.088 904 96 42 1003 1853 719146548 719147420 2.070000e-166 595.0
16 TraesCS5A01G030900 chr7B 90.871 241 16 3 1879 2113 719147410 719147650 5.010000e-83 318.0
17 TraesCS5A01G030900 chr7B 85.542 83 4 4 2505 2583 700274419 700274497 2.570000e-11 80.5
18 TraesCS5A01G030900 chr2D 93.421 76 5 0 1742 1817 64158324 64158399 2.540000e-21 113.0
19 TraesCS5A01G030900 chr2A 93.333 75 5 0 1743 1817 65653835 65653909 9.120000e-21 111.0
20 TraesCS5A01G030900 chr2B 92.000 75 6 0 1743 1817 100326793 100326867 4.240000e-19 106.0
21 TraesCS5A01G030900 chr3D 90.909 55 5 0 2523 2577 29699436 29699490 1.200000e-09 75.0
22 TraesCS5A01G030900 chr1B 90.000 60 2 2 2524 2583 629488780 629488835 1.200000e-09 75.0
23 TraesCS5A01G030900 chr1B 88.525 61 3 2 2505 2561 121930090 121930150 1.550000e-08 71.3
24 TraesCS5A01G030900 chr3A 88.525 61 3 2 2505 2561 37802092 37802152 1.550000e-08 71.3
25 TraesCS5A01G030900 chr1D 88.525 61 3 2 2523 2583 81473 81529 1.550000e-08 71.3
26 TraesCS5A01G030900 chr6D 83.133 83 5 5 2505 2583 187277441 187277364 2.000000e-07 67.6
27 TraesCS5A01G030900 chr4B 88.889 54 6 0 2523 2576 89379062 89379009 2.000000e-07 67.6
28 TraesCS5A01G030900 chr3B 88.235 51 2 2 2534 2584 671671115 671671069 1.210000e-04 58.4


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 TraesCS5A01G030900 chr5A 28227138 28230249 3111 False 5747.00 5747 100.0000 1 3112 1 chr5A.!!$F1 3111
1 TraesCS5A01G030900 chr5B 33555252 33558506 3254 True 789.75 2082 87.1025 1 3112 4 chr5B.!!$R1 3111
2 TraesCS5A01G030900 chr5D 40181738 40185244 3506 False 707.80 1746 89.1608 1 3112 5 chr5D.!!$F1 3111
3 TraesCS5A01G030900 chr4D 291532273 291532817 544 False 682.00 682 89.3770 7 547 1 chr4D.!!$F1 540
4 TraesCS5A01G030900 chr4D 291586578 291587841 1263 False 478.50 654 82.4935 1033 2402 2 chr4D.!!$F3 1369
5 TraesCS5A01G030900 chr7B 719146548 719147650 1102 False 456.50 595 85.4795 1003 2113 2 chr7B.!!$F2 1110

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
711 816 0.381801 CATGCTCCCAACAATACGGC 59.618 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2680 3291 0.107017 AAGGTGATTGGGCCTCATCG 60.107 55.0 4.53 0.0 33.24 3.84 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
90 91 6.127619 GGGATGGAAGAGTTTAGAACAAATGG 60.128 42.308 0.00 0.00 0.00 3.16
254 257 7.671827 CATGCATTTTGATGTTTCTGTGTATG 58.328 34.615 0.00 0.00 0.00 2.39
353 359 7.751793 TGAAAGGTTTTAGAACAAACGAGAAAC 59.248 33.333 0.00 0.00 37.50 2.78
354 360 6.127810 AGGTTTTAGAACAAACGAGAAACC 57.872 37.500 6.93 6.93 42.86 3.27
375 381 3.560239 CCCTTGTGTTTTGGGGTTTGTTT 60.560 43.478 0.00 0.00 37.37 2.83
467 473 2.754946 TCCAACGGTCAATAGTGTCC 57.245 50.000 0.00 0.00 0.00 4.02
487 494 4.976116 GTCCGAATTTGCTATATTTGCACC 59.024 41.667 3.06 0.00 40.40 5.01
560 650 6.782298 ACAGAGCGATCATAATCATTGAAG 57.218 37.500 2.38 0.00 31.76 3.02
597 687 4.119442 ACTTTAGTTATCGCGTGGATGT 57.881 40.909 5.77 0.00 36.55 3.06
649 742 2.031163 AGTGGAGTTGCCGTGCTC 59.969 61.111 0.00 0.00 40.66 4.26
651 744 3.611674 TGGAGTTGCCGTGCTCGA 61.612 61.111 10.21 0.00 40.66 4.04
652 745 3.112709 GGAGTTGCCGTGCTCGAC 61.113 66.667 10.21 0.00 39.71 4.20
702 807 5.104402 TCACTCTCAAATATCATGCTCCCAA 60.104 40.000 0.00 0.00 0.00 4.12
706 811 6.131264 TCTCAAATATCATGCTCCCAACAAT 58.869 36.000 0.00 0.00 0.00 2.71
707 812 7.289310 TCTCAAATATCATGCTCCCAACAATA 58.711 34.615 0.00 0.00 0.00 1.90
708 813 7.229306 TCTCAAATATCATGCTCCCAACAATAC 59.771 37.037 0.00 0.00 0.00 1.89
709 814 5.947228 AATATCATGCTCCCAACAATACG 57.053 39.130 0.00 0.00 0.00 3.06
710 815 2.036958 TCATGCTCCCAACAATACGG 57.963 50.000 0.00 0.00 0.00 4.02
711 816 0.381801 CATGCTCCCAACAATACGGC 59.618 55.000 0.00 0.00 0.00 5.68
712 817 0.751643 ATGCTCCCAACAATACGGCC 60.752 55.000 0.00 0.00 0.00 6.13
713 818 2.469516 GCTCCCAACAATACGGCCG 61.470 63.158 26.86 26.86 0.00 6.13
714 819 2.437002 TCCCAACAATACGGCCGC 60.437 61.111 28.58 0.00 0.00 6.53
715 820 3.514362 CCCAACAATACGGCCGCC 61.514 66.667 28.58 0.00 0.00 6.13
902 1123 3.071206 GCTCCCAGCGTCCTGAGA 61.071 66.667 0.00 0.00 41.77 3.27
903 1124 3.074999 GCTCCCAGCGTCCTGAGAG 62.075 68.421 0.00 0.00 44.26 3.20
948 1169 0.767446 CCATCCTCATCCTGCTCCCT 60.767 60.000 0.00 0.00 0.00 4.20
996 1229 4.767255 CCCAGAGCGCACTCCCAC 62.767 72.222 11.47 0.00 44.65 4.61
997 1230 4.007644 CCAGAGCGCACTCCCACA 62.008 66.667 11.47 0.00 44.65 4.17
1092 1429 0.524862 TCAAGAGCGTCGAAGGTACC 59.475 55.000 2.73 2.73 0.00 3.34
1099 1436 1.513586 GTCGAAGGTACCAGCGTCG 60.514 63.158 15.94 16.38 45.99 5.12
1108 1445 2.842188 TACCAGCGTCGCCCTCCTTA 62.842 60.000 14.86 0.00 0.00 2.69
1109 1446 2.577059 CAGCGTCGCCCTCCTTAA 59.423 61.111 14.86 0.00 0.00 1.85
1144 1496 3.725740 CGCTGCATTTTCGGCTTAATTAG 59.274 43.478 0.00 0.00 36.24 1.73
1178 1530 4.992294 CGCGCGTTTTGGTTGGGG 62.992 66.667 24.19 0.00 0.00 4.96
1181 1539 2.279851 GCGTTTTGGTTGGGGTGC 60.280 61.111 0.00 0.00 0.00 5.01
1491 1906 1.519719 CCCGAGAAGAAGCCTGAGG 59.480 63.158 0.00 0.00 0.00 3.86
1541 1959 0.979665 CTGACAAAGAGGAGGAGGCA 59.020 55.000 0.00 0.00 0.00 4.75
1563 1987 2.174349 CAAGCGACGAGGCAAAGC 59.826 61.111 0.00 0.00 34.64 3.51
1720 2192 4.552365 CCTGTCCCATGCGCCGAT 62.552 66.667 4.18 0.00 0.00 4.18
1745 2229 1.209127 GCACCACGAATTCAACCCG 59.791 57.895 6.22 0.00 0.00 5.28
1746 2230 1.512156 GCACCACGAATTCAACCCGT 61.512 55.000 6.22 0.00 36.95 5.28
1747 2231 1.798283 CACCACGAATTCAACCCGTA 58.202 50.000 6.22 0.00 34.91 4.02
1748 2232 1.461897 CACCACGAATTCAACCCGTAC 59.538 52.381 6.22 0.00 34.91 3.67
1749 2233 0.717224 CCACGAATTCAACCCGTACG 59.283 55.000 8.69 8.69 34.91 3.67
1750 2234 0.717224 CACGAATTCAACCCGTACGG 59.283 55.000 27.68 27.68 34.91 4.02
1751 2235 1.015607 ACGAATTCAACCCGTACGGC 61.016 55.000 29.15 11.33 34.52 5.68
1838 2322 3.905678 CCGGAGCAGGGCTACTCG 61.906 72.222 0.00 0.80 39.88 4.18
1839 2323 4.577246 CGGAGCAGGGCTACTCGC 62.577 72.222 0.00 0.00 39.88 5.03
1840 2324 3.151022 GGAGCAGGGCTACTCGCT 61.151 66.667 0.00 0.00 39.88 4.93
2148 2648 2.046700 CCGCCGGAAAAGTAGCCA 60.047 61.111 5.05 0.00 0.00 4.75
2202 2709 4.237976 CCTCTCTGGTTGTAGGTAGAGA 57.762 50.000 0.00 0.00 42.31 3.10
2203 2710 3.949113 CCTCTCTGGTTGTAGGTAGAGAC 59.051 52.174 0.00 0.00 40.36 3.36
2204 2711 4.567958 CCTCTCTGGTTGTAGGTAGAGACA 60.568 50.000 0.00 0.00 40.36 3.41
2205 2712 4.590918 TCTCTGGTTGTAGGTAGAGACAG 58.409 47.826 0.00 0.00 40.36 3.51
2265 2780 6.136155 TCTCCTTGACCAATCCTTTTTCTTT 58.864 36.000 0.00 0.00 0.00 2.52
2398 2925 5.064314 AGATCTTCCACCCTACTAGTACC 57.936 47.826 0.00 0.00 0.00 3.34
2450 2978 9.598517 GACATGAGAGAGAGAAACATAAAAGAT 57.401 33.333 0.00 0.00 0.00 2.40
2456 2984 9.360093 AGAGAGAGAAACATAAAAGATAACACG 57.640 33.333 0.00 0.00 0.00 4.49
2457 2985 8.480643 AGAGAGAAACATAAAAGATAACACGG 57.519 34.615 0.00 0.00 0.00 4.94
2458 2986 8.311836 AGAGAGAAACATAAAAGATAACACGGA 58.688 33.333 0.00 0.00 0.00 4.69
2459 2987 9.099454 GAGAGAAACATAAAAGATAACACGGAT 57.901 33.333 0.00 0.00 0.00 4.18
2460 2988 9.449719 AGAGAAACATAAAAGATAACACGGATT 57.550 29.630 0.00 0.00 0.00 3.01
2514 3042 5.915175 GAGGAATTAATTACTCAGTCCCGT 58.085 41.667 28.43 4.51 45.20 5.28
2515 3043 7.047460 GAGGAATTAATTACTCAGTCCCGTA 57.953 40.000 28.43 0.00 45.20 4.02
2516 3044 7.427989 AGGAATTAATTACTCAGTCCCGTAA 57.572 36.000 7.14 0.00 0.00 3.18
2517 3045 8.030913 AGGAATTAATTACTCAGTCCCGTAAT 57.969 34.615 7.14 0.00 37.79 1.89
2518 3046 9.151177 AGGAATTAATTACTCAGTCCCGTAATA 57.849 33.333 7.14 0.00 35.80 0.98
2519 3047 9.939802 GGAATTAATTACTCAGTCCCGTAATAT 57.060 33.333 2.93 0.00 35.80 1.28
2521 3049 8.773404 ATTAATTACTCAGTCCCGTAATATGC 57.227 34.615 0.00 0.00 35.80 3.14
2522 3050 2.795175 ACTCAGTCCCGTAATATGCG 57.205 50.000 0.00 0.00 0.00 4.73
2523 3051 2.029623 ACTCAGTCCCGTAATATGCGT 58.970 47.619 0.00 0.00 0.00 5.24
2524 3052 2.429610 ACTCAGTCCCGTAATATGCGTT 59.570 45.455 0.00 0.00 0.00 4.84
2525 3053 3.118884 ACTCAGTCCCGTAATATGCGTTT 60.119 43.478 0.00 0.00 0.00 3.60
2526 3054 3.864243 TCAGTCCCGTAATATGCGTTTT 58.136 40.909 0.00 0.00 0.00 2.43
2527 3055 4.255301 TCAGTCCCGTAATATGCGTTTTT 58.745 39.130 0.00 0.00 0.00 1.94
2528 3056 4.093703 TCAGTCCCGTAATATGCGTTTTTG 59.906 41.667 0.00 0.00 0.00 2.44
2529 3057 4.093703 CAGTCCCGTAATATGCGTTTTTGA 59.906 41.667 0.00 0.00 0.00 2.69
2530 3058 4.093850 AGTCCCGTAATATGCGTTTTTGAC 59.906 41.667 0.00 0.00 0.00 3.18
2531 3059 4.001652 TCCCGTAATATGCGTTTTTGACA 58.998 39.130 0.00 0.00 0.00 3.58
2532 3060 4.092816 CCCGTAATATGCGTTTTTGACAC 58.907 43.478 0.00 0.00 0.00 3.67
2533 3061 4.142773 CCCGTAATATGCGTTTTTGACACT 60.143 41.667 0.00 0.00 0.00 3.55
2534 3062 5.063691 CCCGTAATATGCGTTTTTGACACTA 59.936 40.000 0.00 0.00 0.00 2.74
2535 3063 6.238266 CCCGTAATATGCGTTTTTGACACTAT 60.238 38.462 0.00 0.00 0.00 2.12
2536 3064 7.184106 CCGTAATATGCGTTTTTGACACTATT 58.816 34.615 0.00 0.00 0.00 1.73
2537 3065 7.163520 CCGTAATATGCGTTTTTGACACTATTG 59.836 37.037 0.00 0.00 0.00 1.90
2538 3066 7.690637 CGTAATATGCGTTTTTGACACTATTGT 59.309 33.333 0.00 0.00 39.32 2.71
2539 3067 9.976255 GTAATATGCGTTTTTGACACTATTGTA 57.024 29.630 0.00 0.00 35.47 2.41
2541 3069 5.994887 TGCGTTTTTGACACTATTGTAGT 57.005 34.783 0.00 0.00 40.28 2.73
2554 3082 6.071463 CACTATTGTAGTGTCAAAAACGCTC 58.929 40.000 8.58 0.00 45.69 5.03
2555 3083 5.989777 ACTATTGTAGTGTCAAAAACGCTCT 59.010 36.000 0.00 0.00 45.69 4.09
2556 3084 5.751243 ATTGTAGTGTCAAAAACGCTCTT 57.249 34.783 0.00 0.00 45.69 2.85
2557 3085 6.854496 ATTGTAGTGTCAAAAACGCTCTTA 57.146 33.333 0.00 0.00 45.69 2.10
2558 3086 6.854496 TTGTAGTGTCAAAAACGCTCTTAT 57.146 33.333 0.00 0.00 45.69 1.73
2559 3087 7.949903 TTGTAGTGTCAAAAACGCTCTTATA 57.050 32.000 0.00 0.00 45.69 0.98
2560 3088 8.542497 TTGTAGTGTCAAAAACGCTCTTATAT 57.458 30.769 0.00 0.00 45.69 0.86
2561 3089 8.181487 TGTAGTGTCAAAAACGCTCTTATATC 57.819 34.615 0.00 0.00 45.69 1.63
2562 3090 7.815549 TGTAGTGTCAAAAACGCTCTTATATCA 59.184 33.333 0.00 0.00 45.69 2.15
2563 3091 7.061752 AGTGTCAAAAACGCTCTTATATCAC 57.938 36.000 0.00 0.00 45.69 3.06
2564 3092 6.874134 AGTGTCAAAAACGCTCTTATATCACT 59.126 34.615 0.00 0.00 45.69 3.41
2565 3093 6.955963 GTGTCAAAAACGCTCTTATATCACTG 59.044 38.462 0.00 0.00 35.42 3.66
2566 3094 6.092122 TGTCAAAAACGCTCTTATATCACTGG 59.908 38.462 0.00 0.00 0.00 4.00
2567 3095 6.312918 GTCAAAAACGCTCTTATATCACTGGA 59.687 38.462 0.00 0.00 0.00 3.86
2568 3096 6.312918 TCAAAAACGCTCTTATATCACTGGAC 59.687 38.462 0.00 0.00 0.00 4.02
2569 3097 3.627732 ACGCTCTTATATCACTGGACG 57.372 47.619 0.00 0.00 0.00 4.79
2570 3098 2.293677 ACGCTCTTATATCACTGGACGG 59.706 50.000 0.00 0.00 0.00 4.79
2571 3099 2.552743 CGCTCTTATATCACTGGACGGA 59.447 50.000 0.00 0.00 0.00 4.69
2572 3100 3.609644 CGCTCTTATATCACTGGACGGAC 60.610 52.174 0.00 0.00 0.00 4.79
2573 3101 3.609644 GCTCTTATATCACTGGACGGACG 60.610 52.174 0.00 0.00 0.00 4.79
2574 3102 2.882761 TCTTATATCACTGGACGGACGG 59.117 50.000 0.00 0.00 0.00 4.79
2575 3103 2.643995 TATATCACTGGACGGACGGA 57.356 50.000 0.00 0.00 0.00 4.69
2576 3104 1.319541 ATATCACTGGACGGACGGAG 58.680 55.000 0.00 0.00 0.00 4.63
2577 3105 0.750546 TATCACTGGACGGACGGAGG 60.751 60.000 0.00 0.00 0.00 4.30
2578 3106 3.760035 CACTGGACGGACGGAGGG 61.760 72.222 0.00 0.00 0.00 4.30
2579 3107 3.975591 ACTGGACGGACGGAGGGA 61.976 66.667 0.00 0.00 0.00 4.20
2580 3108 3.141488 CTGGACGGACGGAGGGAG 61.141 72.222 0.00 0.00 0.00 4.30
2596 3124 3.354467 AGGGAGTAGTAGAAAGGTCGTG 58.646 50.000 0.00 0.00 0.00 4.35
2597 3125 2.426381 GGGAGTAGTAGAAAGGTCGTGG 59.574 54.545 0.00 0.00 0.00 4.94
2599 3127 3.128415 GGAGTAGTAGAAAGGTCGTGGTC 59.872 52.174 0.00 0.00 0.00 4.02
2661 3193 1.372087 CGATTCTTGTGGCCAGCTCC 61.372 60.000 5.11 0.00 0.00 4.70
2662 3194 1.000396 ATTCTTGTGGCCAGCTCCC 60.000 57.895 5.11 0.00 0.00 4.30
2680 3291 1.299014 CGAGCAGCCTCTGACGATC 60.299 63.158 0.00 0.00 35.94 3.69
2684 3409 0.938637 GCAGCCTCTGACGATCGATG 60.939 60.000 24.34 11.01 32.44 3.84
2702 3429 1.076705 GAGGCCCAATCACCTTCCC 60.077 63.158 0.00 0.00 36.05 3.97
2789 3577 3.964909 CAACTTGTTTAGGTTGGTGCTC 58.035 45.455 0.00 0.00 39.08 4.26
2843 3631 4.573900 AGCCTTTTCATATAGCTCATCGG 58.426 43.478 0.00 0.00 0.00 4.18
2846 3634 4.623167 CCTTTTCATATAGCTCATCGGTCG 59.377 45.833 0.00 0.00 0.00 4.79
2861 3649 1.815421 GTCGCTCATGCCGAATGGT 60.815 57.895 9.37 0.00 36.86 3.55
2862 3650 1.815003 TCGCTCATGCCGAATGGTG 60.815 57.895 5.93 0.00 36.86 4.17
2863 3651 2.108514 CGCTCATGCCGAATGGTGT 61.109 57.895 0.01 0.00 36.86 4.16
2864 3652 1.430632 GCTCATGCCGAATGGTGTG 59.569 57.895 0.00 0.00 36.86 3.82
2865 3653 1.996786 GCTCATGCCGAATGGTGTGG 61.997 60.000 0.00 0.00 36.86 4.17
2890 3678 0.318699 GCCGGTTTGTTTGAAGGCTC 60.319 55.000 1.90 0.00 41.21 4.70
2906 3694 6.653020 TGAAGGCTCTTGAATATAAGCAAGA 58.347 36.000 15.62 15.62 45.83 3.02
2938 3742 5.722263 CTTGCCCACATGTTAATGATTTGA 58.278 37.500 0.00 0.00 37.24 2.69
2939 3743 5.936187 TGCCCACATGTTAATGATTTGAT 57.064 34.783 0.00 0.00 37.24 2.57
2940 3744 6.297080 TGCCCACATGTTAATGATTTGATT 57.703 33.333 0.00 0.00 37.24 2.57
2941 3745 6.709281 TGCCCACATGTTAATGATTTGATTT 58.291 32.000 0.00 0.00 37.24 2.17
2942 3746 7.845037 TGCCCACATGTTAATGATTTGATTTA 58.155 30.769 0.00 0.00 37.24 1.40
2943 3747 7.763528 TGCCCACATGTTAATGATTTGATTTAC 59.236 33.333 0.00 0.00 37.24 2.01
2944 3748 7.224557 GCCCACATGTTAATGATTTGATTTACC 59.775 37.037 0.00 0.00 37.24 2.85
2973 3777 0.818445 CTCAGCCTGGGTGATCATGC 60.818 60.000 27.10 0.00 39.36 4.06
2982 3786 4.770531 CCTGGGTGATCATGCATGATTTAT 59.229 41.667 36.12 20.31 46.84 1.40
3067 3878 2.774687 ATTGTGGGTTGCGGGGGTAC 62.775 60.000 0.00 0.00 0.00 3.34
3107 3918 1.579429 GTGGTGGACAAATCGTGCC 59.421 57.895 0.00 0.00 34.43 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 2.859165 TCTCACATCACAAACCTCCC 57.141 50.000 0.00 0.00 0.00 4.30
254 257 8.667987 TTTTACTTCACGATTTACAATGCATC 57.332 30.769 0.00 0.00 0.00 3.91
333 339 6.127810 AGGGTTTCTCGTTTGTTCTAAAAC 57.872 37.500 0.00 0.00 36.81 2.43
353 359 1.557371 ACAAACCCCAAAACACAAGGG 59.443 47.619 0.00 0.00 45.75 3.95
354 360 3.342377 AACAAACCCCAAAACACAAGG 57.658 42.857 0.00 0.00 0.00 3.61
375 381 7.936496 TTCATGGTTGAGCTTAATCACAATA 57.064 32.000 6.30 0.00 32.27 1.90
407 413 6.855836 ACAAATTCTGCCACATGTACTATTG 58.144 36.000 0.00 0.00 0.00 1.90
467 473 3.974401 CCGGTGCAAATATAGCAAATTCG 59.026 43.478 4.51 6.79 44.64 3.34
468 474 3.735746 GCCGGTGCAAATATAGCAAATTC 59.264 43.478 1.90 0.00 44.64 2.17
487 494 0.749091 TGGATGAAGCCAATCTGCCG 60.749 55.000 0.00 0.00 34.31 5.69
543 554 5.835911 ACGCTCTTCAATGATTATGATCG 57.164 39.130 0.00 0.00 34.91 3.69
555 645 1.952990 TGCCATCAAAACGCTCTTCAA 59.047 42.857 0.00 0.00 0.00 2.69
560 650 2.422276 AAGTTGCCATCAAAACGCTC 57.578 45.000 0.00 0.00 33.37 5.03
627 720 2.281070 CGGCAACTCCACTGCACT 60.281 61.111 0.00 0.00 41.78 4.40
628 721 2.591715 ACGGCAACTCCACTGCAC 60.592 61.111 0.00 0.00 41.78 4.57
649 742 3.433957 TGACAATTTATGTTGGTCGGTCG 59.566 43.478 0.00 0.00 44.12 4.79
651 744 5.007034 TGATGACAATTTATGTTGGTCGGT 58.993 37.500 0.00 0.00 44.12 4.69
652 745 5.559427 TGATGACAATTTATGTTGGTCGG 57.441 39.130 0.00 0.00 44.12 4.79
695 800 2.469516 CGGCCGTATTGTTGGGAGC 61.470 63.158 19.50 0.00 0.00 4.70
702 807 4.085204 TTCCGGCGGCCGTATTGT 62.085 61.111 36.22 0.00 46.80 2.71
715 820 1.002033 CGTTCCTAGGTATCCGTTCCG 60.002 57.143 9.08 0.00 0.00 4.30
718 823 2.428530 GTTCCGTTCCTAGGTATCCGTT 59.571 50.000 9.08 0.00 0.00 4.44
719 824 2.027385 GTTCCGTTCCTAGGTATCCGT 58.973 52.381 9.08 0.00 0.00 4.69
720 825 1.002033 CGTTCCGTTCCTAGGTATCCG 60.002 57.143 9.08 6.89 0.00 4.18
721 826 1.339291 CCGTTCCGTTCCTAGGTATCC 59.661 57.143 9.08 0.00 0.00 2.59
723 828 2.442236 TCCGTTCCGTTCCTAGGTAT 57.558 50.000 9.08 0.00 0.00 2.73
760 975 1.211743 GCGGCCGTATTGTTAGTACC 58.788 55.000 28.70 0.08 0.00 3.34
813 1032 1.518572 GAGTACGACCACATGGCCG 60.519 63.158 4.96 4.96 46.81 6.13
899 1120 1.102978 GAGTCTGTGGCTCTCCTCTC 58.897 60.000 0.00 0.00 0.00 3.20
900 1121 0.679640 CGAGTCTGTGGCTCTCCTCT 60.680 60.000 0.00 0.00 0.00 3.69
901 1122 0.678366 TCGAGTCTGTGGCTCTCCTC 60.678 60.000 0.00 0.00 0.00 3.71
902 1123 0.679640 CTCGAGTCTGTGGCTCTCCT 60.680 60.000 3.62 0.00 0.00 3.69
903 1124 1.806568 CTCGAGTCTGTGGCTCTCC 59.193 63.158 3.62 0.00 0.00 3.71
948 1169 1.400629 CGTCGTCTCGCTTCTTGGTTA 60.401 52.381 0.00 0.00 0.00 2.85
996 1229 1.504912 AGGTCTGGAGATCCATGGTG 58.495 55.000 12.58 0.00 46.46 4.17
997 1230 2.122768 GAAGGTCTGGAGATCCATGGT 58.877 52.381 12.58 0.00 46.46 3.55
1008 1345 1.079543 CCTCAGCACGAAGGTCTGG 60.080 63.158 0.00 0.00 0.00 3.86
1092 1429 0.462047 AATTAAGGAGGGCGACGCTG 60.462 55.000 20.77 0.00 0.00 5.18
1099 1436 1.422024 GGGAGGAGAATTAAGGAGGGC 59.578 57.143 0.00 0.00 0.00 5.19
1107 1444 1.760875 AGCGGCGGGAGGAGAATTA 60.761 57.895 9.78 0.00 0.00 1.40
1108 1445 3.083997 AGCGGCGGGAGGAGAATT 61.084 61.111 9.78 0.00 0.00 2.17
1109 1446 3.854669 CAGCGGCGGGAGGAGAAT 61.855 66.667 9.78 0.00 0.00 2.40
1144 1496 1.266466 GCGACGACCACTTAGTAAGC 58.734 55.000 9.92 0.00 0.00 3.09
1147 1499 1.135315 GCGCGACGACCACTTAGTA 59.865 57.895 12.10 0.00 0.00 1.82
1178 1530 4.687215 TCCTGCACGCCTGAGCAC 62.687 66.667 0.00 0.00 36.75 4.40
1369 1745 2.825836 CATCCTTGCTGCCGTCCC 60.826 66.667 0.00 0.00 0.00 4.46
1416 1801 2.435586 CTGCGGCTCCTTCACAGG 60.436 66.667 0.00 0.00 42.50 4.00
1417 1802 2.435586 CCTGCGGCTCCTTCACAG 60.436 66.667 0.00 0.00 0.00 3.66
1418 1803 4.704833 GCCTGCGGCTCCTTCACA 62.705 66.667 11.61 0.00 46.69 3.58
1475 1860 4.511636 GCCTCAGGCTTCTTCTCG 57.488 61.111 9.09 0.00 46.69 4.04
1491 1906 1.134551 AGATTCTGCTTCCTTCTCCGC 60.135 52.381 0.00 0.00 0.00 5.54
1541 1959 1.098712 TTGCCTCGTCGCTTGGTTTT 61.099 50.000 0.00 0.00 0.00 2.43
1645 2084 2.892425 CCTCGGCCTCGTCATTGC 60.892 66.667 0.00 0.00 37.69 3.56
1646 2085 2.892425 GCCTCGGCCTCGTCATTG 60.892 66.667 0.00 0.00 37.69 2.82
1647 2086 4.514577 CGCCTCGGCCTCGTCATT 62.515 66.667 0.00 0.00 37.98 2.57
1722 2206 2.202171 GAATTCGTGGTGCGCGTG 60.202 61.111 8.43 0.00 41.07 5.34
1733 2217 1.711500 GCCGTACGGGTTGAATTCG 59.289 57.895 33.98 6.45 38.44 3.34
2202 2709 4.760715 TCGAAGAGAGTAACAAGCTACTGT 59.239 41.667 0.00 0.00 32.14 3.55
2203 2710 5.298197 TCGAAGAGAGTAACAAGCTACTG 57.702 43.478 0.00 0.00 32.14 2.74
2204 2711 6.326375 CAATCGAAGAGAGTAACAAGCTACT 58.674 40.000 0.00 0.00 43.63 2.57
2205 2712 5.517054 CCAATCGAAGAGAGTAACAAGCTAC 59.483 44.000 0.00 0.00 43.63 3.58
2346 2864 8.195436 TGATGCTACTACTACATGTAAAGGTTC 58.805 37.037 7.06 1.92 0.00 3.62
2348 2866 7.655521 TGATGCTACTACTACATGTAAAGGT 57.344 36.000 7.06 4.35 0.00 3.50
2416 2944 8.642432 TGTTTCTCTCTCTCATGTCTTTTTAGA 58.358 33.333 0.00 0.00 0.00 2.10
2424 2952 8.994429 TCTTTTATGTTTCTCTCTCTCATGTC 57.006 34.615 0.00 0.00 0.00 3.06
2504 3032 2.795175 ACGCATATTACGGGACTGAG 57.205 50.000 0.45 0.00 34.00 3.35
2506 3034 4.093703 TCAAAAACGCATATTACGGGACTG 59.906 41.667 0.45 0.00 34.00 3.51
2507 3035 4.093850 GTCAAAAACGCATATTACGGGACT 59.906 41.667 0.45 0.00 34.00 3.85
2508 3036 4.142859 TGTCAAAAACGCATATTACGGGAC 60.143 41.667 0.45 0.00 34.00 4.46
2509 3037 4.001652 TGTCAAAAACGCATATTACGGGA 58.998 39.130 0.45 0.00 34.00 5.14
2510 3038 4.092816 GTGTCAAAAACGCATATTACGGG 58.907 43.478 0.45 0.00 38.31 5.28
2511 3039 4.965062 AGTGTCAAAAACGCATATTACGG 58.035 39.130 0.45 0.00 41.03 4.02
2512 3040 7.690637 ACAATAGTGTCAAAAACGCATATTACG 59.309 33.333 0.00 0.00 41.03 3.18
2513 3041 8.889849 ACAATAGTGTCAAAAACGCATATTAC 57.110 30.769 0.00 0.00 41.03 1.89
2515 3043 8.726988 ACTACAATAGTGTCAAAAACGCATATT 58.273 29.630 0.00 0.00 41.03 1.28
2516 3044 8.263940 ACTACAATAGTGTCAAAAACGCATAT 57.736 30.769 0.00 0.00 41.03 1.78
2517 3045 7.661127 ACTACAATAGTGTCAAAAACGCATA 57.339 32.000 0.00 0.00 41.03 3.14
2518 3046 6.554334 ACTACAATAGTGTCAAAAACGCAT 57.446 33.333 0.00 0.00 41.03 4.73
2519 3047 5.994887 ACTACAATAGTGTCAAAAACGCA 57.005 34.783 0.00 0.00 41.03 5.24
2531 3059 5.989777 AGAGCGTTTTTGACACTACAATAGT 59.010 36.000 0.00 0.00 40.28 2.12
2532 3060 6.467723 AGAGCGTTTTTGACACTACAATAG 57.532 37.500 0.00 0.00 0.00 1.73
2533 3061 6.854496 AAGAGCGTTTTTGACACTACAATA 57.146 33.333 0.00 0.00 0.00 1.90
2534 3062 5.751243 AAGAGCGTTTTTGACACTACAAT 57.249 34.783 0.00 0.00 0.00 2.71
2535 3063 6.854496 ATAAGAGCGTTTTTGACACTACAA 57.146 33.333 0.00 0.00 0.00 2.41
2536 3064 7.815549 TGATATAAGAGCGTTTTTGACACTACA 59.184 33.333 0.00 0.00 0.00 2.74
2537 3065 8.108782 GTGATATAAGAGCGTTTTTGACACTAC 58.891 37.037 0.00 0.00 0.00 2.73
2538 3066 8.033038 AGTGATATAAGAGCGTTTTTGACACTA 58.967 33.333 0.00 0.00 32.05 2.74
2539 3067 6.874134 AGTGATATAAGAGCGTTTTTGACACT 59.126 34.615 0.00 0.00 0.00 3.55
2540 3068 6.955963 CAGTGATATAAGAGCGTTTTTGACAC 59.044 38.462 0.00 0.00 0.00 3.67
2541 3069 6.092122 CCAGTGATATAAGAGCGTTTTTGACA 59.908 38.462 0.00 0.00 0.00 3.58
2542 3070 6.312918 TCCAGTGATATAAGAGCGTTTTTGAC 59.687 38.462 0.00 0.00 0.00 3.18
2543 3071 6.312918 GTCCAGTGATATAAGAGCGTTTTTGA 59.687 38.462 0.00 0.00 0.00 2.69
2544 3072 6.478588 GTCCAGTGATATAAGAGCGTTTTTG 58.521 40.000 0.00 0.00 0.00 2.44
2545 3073 5.291128 CGTCCAGTGATATAAGAGCGTTTTT 59.709 40.000 0.00 0.00 0.00 1.94
2546 3074 4.804139 CGTCCAGTGATATAAGAGCGTTTT 59.196 41.667 0.00 0.00 0.00 2.43
2547 3075 4.360563 CGTCCAGTGATATAAGAGCGTTT 58.639 43.478 0.00 0.00 0.00 3.60
2548 3076 3.243434 CCGTCCAGTGATATAAGAGCGTT 60.243 47.826 0.00 0.00 0.00 4.84
2549 3077 2.293677 CCGTCCAGTGATATAAGAGCGT 59.706 50.000 0.00 0.00 0.00 5.07
2550 3078 2.552743 TCCGTCCAGTGATATAAGAGCG 59.447 50.000 0.00 0.00 0.00 5.03
2551 3079 3.609644 CGTCCGTCCAGTGATATAAGAGC 60.610 52.174 0.00 0.00 0.00 4.09
2552 3080 3.058155 CCGTCCGTCCAGTGATATAAGAG 60.058 52.174 0.00 0.00 0.00 2.85
2553 3081 2.882761 CCGTCCGTCCAGTGATATAAGA 59.117 50.000 0.00 0.00 0.00 2.10
2554 3082 2.882761 TCCGTCCGTCCAGTGATATAAG 59.117 50.000 0.00 0.00 0.00 1.73
2555 3083 2.882761 CTCCGTCCGTCCAGTGATATAA 59.117 50.000 0.00 0.00 0.00 0.98
2556 3084 2.501261 CTCCGTCCGTCCAGTGATATA 58.499 52.381 0.00 0.00 0.00 0.86
2557 3085 1.319541 CTCCGTCCGTCCAGTGATAT 58.680 55.000 0.00 0.00 0.00 1.63
2558 3086 0.750546 CCTCCGTCCGTCCAGTGATA 60.751 60.000 0.00 0.00 0.00 2.15
2559 3087 2.052690 CCTCCGTCCGTCCAGTGAT 61.053 63.158 0.00 0.00 0.00 3.06
2560 3088 2.675423 CCTCCGTCCGTCCAGTGA 60.675 66.667 0.00 0.00 0.00 3.41
2561 3089 3.760035 CCCTCCGTCCGTCCAGTG 61.760 72.222 0.00 0.00 0.00 3.66
2562 3090 3.940506 CTCCCTCCGTCCGTCCAGT 62.941 68.421 0.00 0.00 0.00 4.00
2563 3091 2.547640 TACTCCCTCCGTCCGTCCAG 62.548 65.000 0.00 0.00 0.00 3.86
2564 3092 2.547640 CTACTCCCTCCGTCCGTCCA 62.548 65.000 0.00 0.00 0.00 4.02
2565 3093 1.823041 CTACTCCCTCCGTCCGTCC 60.823 68.421 0.00 0.00 0.00 4.79
2566 3094 0.179000 TACTACTCCCTCCGTCCGTC 59.821 60.000 0.00 0.00 0.00 4.79
2567 3095 0.179936 CTACTACTCCCTCCGTCCGT 59.820 60.000 0.00 0.00 0.00 4.69
2568 3096 0.467384 TCTACTACTCCCTCCGTCCG 59.533 60.000 0.00 0.00 0.00 4.79
2569 3097 2.725221 TTCTACTACTCCCTCCGTCC 57.275 55.000 0.00 0.00 0.00 4.79
2570 3098 2.950975 CCTTTCTACTACTCCCTCCGTC 59.049 54.545 0.00 0.00 0.00 4.79
2571 3099 2.311243 ACCTTTCTACTACTCCCTCCGT 59.689 50.000 0.00 0.00 0.00 4.69
2572 3100 2.950975 GACCTTTCTACTACTCCCTCCG 59.049 54.545 0.00 0.00 0.00 4.63
2573 3101 2.950975 CGACCTTTCTACTACTCCCTCC 59.049 54.545 0.00 0.00 0.00 4.30
2574 3102 3.377798 CACGACCTTTCTACTACTCCCTC 59.622 52.174 0.00 0.00 0.00 4.30
2575 3103 3.354467 CACGACCTTTCTACTACTCCCT 58.646 50.000 0.00 0.00 0.00 4.20
2576 3104 2.426381 CCACGACCTTTCTACTACTCCC 59.574 54.545 0.00 0.00 0.00 4.30
2577 3105 3.087781 ACCACGACCTTTCTACTACTCC 58.912 50.000 0.00 0.00 0.00 3.85
2578 3106 4.009002 AGACCACGACCTTTCTACTACTC 58.991 47.826 0.00 0.00 0.00 2.59
2579 3107 3.757493 CAGACCACGACCTTTCTACTACT 59.243 47.826 0.00 0.00 0.00 2.57
2580 3108 3.505293 ACAGACCACGACCTTTCTACTAC 59.495 47.826 0.00 0.00 0.00 2.73
2596 3124 2.019984 GATTGGATTGGAGCACAGACC 58.980 52.381 0.00 0.00 0.00 3.85
2597 3125 2.715046 TGATTGGATTGGAGCACAGAC 58.285 47.619 0.00 0.00 0.00 3.51
2599 3127 2.223735 GCATGATTGGATTGGAGCACAG 60.224 50.000 0.00 0.00 0.00 3.66
2641 3173 1.372087 GAGCTGGCCACAAGAATCGG 61.372 60.000 0.00 0.00 0.00 4.18
2642 3174 1.372087 GGAGCTGGCCACAAGAATCG 61.372 60.000 0.00 0.00 0.00 3.34
2661 3193 2.676016 GATCGTCAGAGGCTGCTCGG 62.676 65.000 0.00 0.00 32.88 4.63
2662 3194 1.299014 GATCGTCAGAGGCTGCTCG 60.299 63.158 0.00 0.00 33.12 5.03
2680 3291 0.107017 AAGGTGATTGGGCCTCATCG 60.107 55.000 4.53 0.00 33.24 3.84
2684 3409 1.076705 GGGAAGGTGATTGGGCCTC 60.077 63.158 4.53 0.00 33.24 4.70
2702 3429 3.670627 GCTAAACTTGATCGGTGGCAAAG 60.671 47.826 0.00 0.00 0.00 2.77
2743 3531 4.445453 CTGCTGAGCCATCACACTAATTA 58.555 43.478 0.23 0.00 0.00 1.40
2744 3532 3.276857 CTGCTGAGCCATCACACTAATT 58.723 45.455 0.23 0.00 0.00 1.40
2745 3533 2.915349 CTGCTGAGCCATCACACTAAT 58.085 47.619 0.23 0.00 0.00 1.73
2746 3534 1.676916 GCTGCTGAGCCATCACACTAA 60.677 52.381 0.23 0.00 39.57 2.24
2747 3535 0.107993 GCTGCTGAGCCATCACACTA 60.108 55.000 0.23 0.00 39.57 2.74
2843 3631 1.815421 ACCATTCGGCATGAGCGAC 60.815 57.895 0.00 0.00 43.41 5.19
2846 3634 1.430632 CACACCATTCGGCATGAGC 59.569 57.895 0.00 0.00 34.31 4.26
2861 3649 4.514585 AAACCGGCCAGCACCACA 62.515 61.111 0.00 0.00 0.00 4.17
2862 3650 3.977244 CAAACCGGCCAGCACCAC 61.977 66.667 0.00 0.00 0.00 4.16
2863 3651 4.514585 ACAAACCGGCCAGCACCA 62.515 61.111 0.00 0.00 0.00 4.17
2864 3652 2.791868 AAACAAACCGGCCAGCACC 61.792 57.895 0.00 0.00 0.00 5.01
2865 3653 1.591327 CAAACAAACCGGCCAGCAC 60.591 57.895 0.00 0.00 0.00 4.40
2890 3678 5.008415 CACAGCCCTCTTGCTTATATTCAAG 59.992 44.000 7.71 7.71 40.32 3.02
2910 3698 1.246649 TAACATGTGGGCAAGCACAG 58.753 50.000 0.00 0.00 34.58 3.66
2960 3764 5.977489 ATAAATCATGCATGATCACCCAG 57.023 39.130 35.88 5.62 46.22 4.45
3010 3815 5.599732 AGCTGACTCTAATGAGCATAACAG 58.400 41.667 0.00 0.00 43.85 3.16
3011 3816 5.604758 AGCTGACTCTAATGAGCATAACA 57.395 39.130 0.00 0.00 43.85 2.41
3012 3817 8.087750 AGATTAGCTGACTCTAATGAGCATAAC 58.912 37.037 0.00 0.00 43.85 1.89
3029 3834 7.198390 CCACAATAATGAAACCAGATTAGCTG 58.802 38.462 0.00 0.00 44.49 4.24
3071 3882 9.975218 GTCCACCACCTTTCCATTATTATATAT 57.025 33.333 0.00 0.00 0.00 0.86
3072 3883 8.950480 TGTCCACCACCTTTCCATTATTATATA 58.050 33.333 0.00 0.00 0.00 0.86
3073 3884 7.821566 TGTCCACCACCTTTCCATTATTATAT 58.178 34.615 0.00 0.00 0.00 0.86
3074 3885 7.214460 TGTCCACCACCTTTCCATTATTATA 57.786 36.000 0.00 0.00 0.00 0.98
3075 3886 6.086011 TGTCCACCACCTTTCCATTATTAT 57.914 37.500 0.00 0.00 0.00 1.28
3088 3899 1.579429 GCACGATTTGTCCACCACC 59.421 57.895 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.