Multiple sequence alignment - TraesCS1D01G283900

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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 TraesCS1D01G283900 chr1D 100.000 3067 0 0 1 3067 382217953 382221019 0.000000e+00 5664
1 TraesCS1D01G283900 chr1D 86.316 380 49 3 2421 2800 144771933 144771557 7.910000e-111 411
2 TraesCS1D01G283900 chr1D 86.026 229 28 3 71 296 487695024 487694797 3.060000e-60 243
3 TraesCS1D01G283900 chr1A 89.413 2078 126 34 288 2306 482327874 482329916 0.000000e+00 2532
4 TraesCS1D01G283900 chr1A 89.420 293 29 2 5 296 482327513 482327804 4.830000e-98 368
5 TraesCS1D01G283900 chr1A 95.714 70 3 0 2311 2380 482330564 482330633 2.500000e-21 113
6 TraesCS1D01G283900 chr7D 95.903 659 15 3 2421 3067 510790890 510790232 0.000000e+00 1057
7 TraesCS1D01G283900 chr7D 95.296 659 19 6 2421 3067 510798196 510797538 0.000000e+00 1035
8 TraesCS1D01G283900 chr7D 81.612 881 132 17 1038 1906 452140897 452140035 0.000000e+00 702
9 TraesCS1D01G283900 chr7D 88.286 350 34 5 2421 2768 470542706 470543050 2.200000e-111 412
10 TraesCS1D01G283900 chr7D 84.234 222 31 3 70 289 227572416 227572635 2.400000e-51 213
11 TraesCS1D01G283900 chr2D 95.525 514 11 3 2566 3067 537583653 537583140 0.000000e+00 811
12 TraesCS1D01G283900 chr2D 89.143 350 32 6 2421 2768 327896830 327896485 6.080000e-117 431
13 TraesCS1D01G283900 chr2D 86.649 382 47 4 2421 2800 20341335 20340956 1.320000e-113 420
14 TraesCS1D01G283900 chr6D 95.499 511 11 3 2566 3064 41043726 41044236 0.000000e+00 806
15 TraesCS1D01G283900 chr6D 95.499 511 11 3 2566 3064 41047996 41048506 0.000000e+00 806
16 TraesCS1D01G283900 chr6D 95.108 511 13 3 2566 3064 41055792 41056302 0.000000e+00 795
17 TraesCS1D01G283900 chr6D 85.678 391 50 6 2421 2809 119602986 119602600 1.020000e-109 407
18 TraesCS1D01G283900 chr7A 81.158 881 136 15 1038 1906 545519793 545520655 0.000000e+00 680
19 TraesCS1D01G283900 chr7A 84.440 482 55 7 73 536 725210151 725210630 1.000000e-124 457
20 TraesCS1D01G283900 chr7A 83.784 259 35 3 290 547 239771054 239771306 3.950000e-59 239
21 TraesCS1D01G283900 chr7A 85.778 225 29 2 70 292 239770755 239770978 5.110000e-58 235
22 TraesCS1D01G283900 chr7B 81.105 778 119 14 1038 1804 468058475 468059235 5.660000e-167 597
23 TraesCS1D01G283900 chr7B 82.249 676 100 11 1038 1706 474435280 474434618 1.600000e-157 566
24 TraesCS1D01G283900 chr7B 84.581 227 28 6 72 296 584258975 584259196 5.150000e-53 219
25 TraesCS1D01G283900 chr4D 86.842 380 42 7 2421 2798 248694446 248694073 4.730000e-113 418
26 TraesCS1D01G283900 chr5D 86.792 371 49 0 2421 2791 178082487 178082857 6.120000e-112 414
27 TraesCS1D01G283900 chr6B 85.222 406 53 7 2663 3064 447375360 447375762 7.910000e-111 411
28 TraesCS1D01G283900 chr6B 85.185 405 52 8 2663 3063 309467896 309467496 2.850000e-110 409
29 TraesCS1D01G283900 chr6B 85.714 392 50 6 2676 3064 447367748 447368136 2.850000e-110 409
30 TraesCS1D01G283900 chr6A 89.224 232 25 0 288 519 416647778 416647547 1.080000e-74 291
31 TraesCS1D01G283900 chr6A 86.161 224 29 2 74 296 416648070 416647848 1.100000e-59 241
32 TraesCS1D01G283900 chr4B 88.938 226 23 2 288 512 629941852 629942076 8.380000e-71 278
33 TraesCS1D01G283900 chr4B 83.262 233 31 7 71 296 629941551 629941782 1.110000e-49 207
34 TraesCS1D01G283900 chr3D 87.556 225 25 2 74 296 549971 549748 1.090000e-64 257
35 TraesCS1D01G283900 chr5B 85.398 226 30 2 73 296 505713985 505713761 6.610000e-57 231
36 TraesCS1D01G283900 chr5B 85.185 189 28 0 294 482 74373331 74373143 8.680000e-46 195
37 TraesCS1D01G283900 chr3B 85.027 187 24 3 113 296 421232042 421231857 1.450000e-43 187


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 TraesCS1D01G283900 chr1D 382217953 382221019 3066 False 5664.000000 5664 100.000000 1 3067 1 chr1D.!!$F1 3066
1 TraesCS1D01G283900 chr1A 482327513 482330633 3120 False 1004.333333 2532 91.515667 5 2380 3 chr1A.!!$F1 2375
2 TraesCS1D01G283900 chr7D 510790232 510790890 658 True 1057.000000 1057 95.903000 2421 3067 1 chr7D.!!$R2 646
3 TraesCS1D01G283900 chr7D 510797538 510798196 658 True 1035.000000 1035 95.296000 2421 3067 1 chr7D.!!$R3 646
4 TraesCS1D01G283900 chr7D 452140035 452140897 862 True 702.000000 702 81.612000 1038 1906 1 chr7D.!!$R1 868
5 TraesCS1D01G283900 chr2D 537583140 537583653 513 True 811.000000 811 95.525000 2566 3067 1 chr2D.!!$R3 501
6 TraesCS1D01G283900 chr6D 41043726 41048506 4780 False 806.000000 806 95.499000 2566 3064 2 chr6D.!!$F2 498
7 TraesCS1D01G283900 chr6D 41055792 41056302 510 False 795.000000 795 95.108000 2566 3064 1 chr6D.!!$F1 498
8 TraesCS1D01G283900 chr7A 545519793 545520655 862 False 680.000000 680 81.158000 1038 1906 1 chr7A.!!$F1 868
9 TraesCS1D01G283900 chr7A 239770755 239771306 551 False 237.000000 239 84.781000 70 547 2 chr7A.!!$F3 477
10 TraesCS1D01G283900 chr7B 468058475 468059235 760 False 597.000000 597 81.105000 1038 1804 1 chr7B.!!$F1 766
11 TraesCS1D01G283900 chr7B 474434618 474435280 662 True 566.000000 566 82.249000 1038 1706 1 chr7B.!!$R1 668
12 TraesCS1D01G283900 chr6A 416647547 416648070 523 True 266.000000 291 87.692500 74 519 2 chr6A.!!$R1 445
13 TraesCS1D01G283900 chr4B 629941551 629942076 525 False 242.500000 278 86.100000 71 512 2 chr4B.!!$F1 441

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
982 1083 0.179 ATTTAGGGTGAGCAGAGCGG 59.821 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2917 3740 0.03101 GGAGGTAGGTGGGTGGATCT 60.031 60.0 0.0 0.0 0.0 2.75 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
24 26 1.512926 AATGGAACGTCACTGAGTGC 58.487 50.000 7.93 2.31 32.98 4.40
37 39 1.823610 CTGAGTGCATGGTCTGAGAGA 59.176 52.381 0.00 0.00 0.00 3.10
144 149 6.270231 AGAAGTTAGACATAGTTCCACCAAGT 59.730 38.462 0.00 0.00 0.00 3.16
192 197 6.563422 GGCATTGCATTACTCAAATACTTCA 58.437 36.000 11.39 0.00 0.00 3.02
239 245 8.045720 AGGCTTCATCCTTAATCTTGGTAATA 57.954 34.615 0.00 0.00 30.82 0.98
273 279 2.106683 GCGGCTATGTTGCGGAAGT 61.107 57.895 0.00 0.00 35.67 3.01
355 439 3.039588 GACGTCGCGAAGGCCAAA 61.040 61.111 25.31 0.00 35.02 3.28
401 485 3.996363 CTCTCATTGTGAACCGACATTGA 59.004 43.478 0.00 0.00 35.78 2.57
410 494 3.323691 TGAACCGACATTGAAAGAGGAGA 59.676 43.478 0.00 0.00 0.00 3.71
415 499 4.118410 CGACATTGAAAGAGGAGATGAGG 58.882 47.826 0.00 0.00 0.00 3.86
417 501 3.265221 ACATTGAAAGAGGAGATGAGGCA 59.735 43.478 0.00 0.00 0.00 4.75
577 668 1.136828 ACTACAAGGGTGCTCCACAA 58.863 50.000 7.20 0.00 35.86 3.33
607 698 1.302832 GCAGTGGACTGTTCCCTGG 60.303 63.158 8.54 0.00 45.45 4.45
613 704 1.208165 GGACTGTTCCCTGGGTGGAT 61.208 60.000 13.56 0.00 38.35 3.41
616 707 1.203050 ACTGTTCCCTGGGTGGATTTG 60.203 52.381 13.56 0.91 38.35 2.32
640 731 0.751277 CACCAACAGTGTCTGCCCAA 60.751 55.000 0.00 0.00 41.93 4.12
661 762 5.887598 CCAAGTGGAGATGGACAATTCAATA 59.112 40.000 0.00 0.00 39.12 1.90
663 764 7.069085 CCAAGTGGAGATGGACAATTCAATATT 59.931 37.037 0.00 0.00 39.12 1.28
666 767 8.057623 AGTGGAGATGGACAATTCAATATTTCT 58.942 33.333 0.00 0.00 0.00 2.52
668 769 7.503566 TGGAGATGGACAATTCAATATTTCTCC 59.496 37.037 14.51 14.51 43.67 3.71
669 770 7.040132 GGAGATGGACAATTCAATATTTCTCCC 60.040 40.741 11.84 0.00 39.61 4.30
670 771 6.488006 AGATGGACAATTCAATATTTCTCCCG 59.512 38.462 0.00 0.00 0.00 5.14
671 772 4.338118 TGGACAATTCAATATTTCTCCCGC 59.662 41.667 0.00 0.00 0.00 6.13
673 774 5.763204 GGACAATTCAATATTTCTCCCGCTA 59.237 40.000 0.00 0.00 0.00 4.26
674 775 6.431234 GGACAATTCAATATTTCTCCCGCTAT 59.569 38.462 0.00 0.00 0.00 2.97
675 776 7.206981 ACAATTCAATATTTCTCCCGCTATG 57.793 36.000 0.00 0.00 0.00 2.23
676 777 6.998074 ACAATTCAATATTTCTCCCGCTATGA 59.002 34.615 0.00 0.00 0.00 2.15
718 819 4.103311 TGACTAGTCATGGAGAGCTAGCTA 59.897 45.833 21.74 1.43 34.27 3.32
774 875 0.679321 GAGCCTTCTTCCTTGCCCAG 60.679 60.000 0.00 0.00 0.00 4.45
789 890 1.730902 CCAGATCGCTCATACGCCG 60.731 63.158 0.00 0.00 0.00 6.46
801 902 0.673644 ATACGCCGTTGAAAGCTGCT 60.674 50.000 0.00 0.00 0.00 4.24
821 922 4.102996 TGCTGCTATCCACCATATCTTGAA 59.897 41.667 0.00 0.00 0.00 2.69
826 927 9.458727 CTGCTATCCACCATATCTTGAAATTAT 57.541 33.333 0.00 0.00 0.00 1.28
835 936 7.946219 ACCATATCTTGAAATTATGCTCATCCA 59.054 33.333 0.00 0.00 0.00 3.41
836 937 8.967918 CCATATCTTGAAATTATGCTCATCCAT 58.032 33.333 0.00 0.00 0.00 3.41
848 949 0.673985 TCATCCATGTCGACCCGATC 59.326 55.000 14.12 0.00 38.42 3.69
866 967 1.081906 CAGCTGCAACGTCGCATTT 60.082 52.632 0.00 0.00 42.06 2.32
868 969 1.207593 GCTGCAACGTCGCATTTCT 59.792 52.632 0.00 0.00 42.06 2.52
887 988 1.992667 CTAGCTGCGAATTCGTCAACA 59.007 47.619 27.24 16.05 42.22 3.33
893 994 4.209288 GCTGCGAATTCGTCAACATATAGT 59.791 41.667 27.24 0.00 42.22 2.12
961 1062 1.002746 TAATCAAGCCGCCAGTGCA 60.003 52.632 0.00 0.00 37.32 4.57
971 1072 1.476833 CCGCCAGTGCATATTTAGGGT 60.477 52.381 0.00 0.00 37.32 4.34
972 1073 1.603802 CGCCAGTGCATATTTAGGGTG 59.396 52.381 0.00 0.00 37.32 4.61
973 1074 2.744823 CGCCAGTGCATATTTAGGGTGA 60.745 50.000 0.00 0.00 37.32 4.02
974 1075 2.880890 GCCAGTGCATATTTAGGGTGAG 59.119 50.000 0.00 0.00 37.47 3.51
975 1076 2.880890 CCAGTGCATATTTAGGGTGAGC 59.119 50.000 0.00 0.00 0.00 4.26
976 1077 3.544684 CAGTGCATATTTAGGGTGAGCA 58.455 45.455 0.00 0.00 0.00 4.26
977 1078 3.562973 CAGTGCATATTTAGGGTGAGCAG 59.437 47.826 0.00 0.00 0.00 4.24
978 1079 3.455910 AGTGCATATTTAGGGTGAGCAGA 59.544 43.478 0.00 0.00 0.00 4.26
979 1080 3.812053 GTGCATATTTAGGGTGAGCAGAG 59.188 47.826 0.00 0.00 0.00 3.35
980 1081 2.810852 GCATATTTAGGGTGAGCAGAGC 59.189 50.000 0.00 0.00 0.00 4.09
981 1082 2.890808 TATTTAGGGTGAGCAGAGCG 57.109 50.000 0.00 0.00 0.00 5.03
982 1083 0.179000 ATTTAGGGTGAGCAGAGCGG 59.821 55.000 0.00 0.00 0.00 5.52
983 1084 2.521958 TTTAGGGTGAGCAGAGCGGC 62.522 60.000 0.00 0.00 0.00 6.53
988 1089 4.724602 TGAGCAGAGCGGCGTGTC 62.725 66.667 9.37 5.98 39.27 3.67
989 1090 4.427661 GAGCAGAGCGGCGTGTCT 62.428 66.667 9.37 8.52 39.27 3.41
990 1091 3.923563 GAGCAGAGCGGCGTGTCTT 62.924 63.158 9.37 0.00 39.27 3.01
991 1092 3.782244 GCAGAGCGGCGTGTCTTG 61.782 66.667 9.37 7.46 0.00 3.02
992 1093 2.356313 CAGAGCGGCGTGTCTTGT 60.356 61.111 9.37 0.00 0.00 3.16
999 1100 1.078759 CGGCGTGTCTTGTGATCCTC 61.079 60.000 0.00 0.00 0.00 3.71
1025 1126 4.486503 GCCAGCTCCAGCCTCCAG 62.487 72.222 0.00 0.00 43.38 3.86
1035 1136 2.026879 GCCTCCAGCTCGATCGAC 59.973 66.667 15.15 11.39 38.99 4.20
1036 1137 2.725008 CCTCCAGCTCGATCGACC 59.275 66.667 15.15 8.19 0.00 4.79
1345 1455 4.083862 AAGGTCTCCTTCGCGCCC 62.084 66.667 0.00 0.00 40.17 6.13
1741 1860 2.358737 CAGACCGGCAAGACCACC 60.359 66.667 0.00 0.00 39.03 4.61
1834 1953 0.462759 CGGGCTTCTTCATCTGGTCC 60.463 60.000 0.00 0.00 0.00 4.46
1910 2029 1.134401 AGATCGTCGCCAACCATTGAT 60.134 47.619 0.00 0.00 0.00 2.57
1911 2030 1.261619 GATCGTCGCCAACCATTGATC 59.738 52.381 0.00 0.00 0.00 2.92
1913 2032 0.652592 CGTCGCCAACCATTGATCTC 59.347 55.000 0.00 0.00 0.00 2.75
1916 2044 0.461870 CGCCAACCATTGATCTCCGA 60.462 55.000 0.00 0.00 0.00 4.55
1920 2048 1.665679 CAACCATTGATCTCCGAACGG 59.334 52.381 6.94 6.94 0.00 4.44
1921 2049 1.191535 ACCATTGATCTCCGAACGGA 58.808 50.000 15.13 15.13 42.90 4.69
1932 2060 0.248621 CCGAACGGACGGTATACACC 60.249 60.000 7.53 4.29 46.70 4.16
1954 2082 9.270640 ACACCGTACTACTACTATCAATAAGAG 57.729 37.037 0.00 0.00 0.00 2.85
1955 2083 9.270640 CACCGTACTACTACTATCAATAAGAGT 57.729 37.037 0.00 0.00 0.00 3.24
1979 2113 0.179000 AGGATTGCCAAGAGCCGTAG 59.821 55.000 0.00 0.00 42.71 3.51
1980 2114 0.178068 GGATTGCCAAGAGCCGTAGA 59.822 55.000 0.00 0.00 42.71 2.59
1982 2116 2.565841 GATTGCCAAGAGCCGTAGAAT 58.434 47.619 0.00 0.00 42.71 2.40
2003 2152 4.024143 TGCGCGCGTGCAATCTTT 62.024 55.556 41.72 0.00 43.02 2.52
2004 2153 2.097538 GCGCGCGTGCAATCTTTA 59.902 55.556 37.29 0.00 42.97 1.85
2005 2154 1.511043 GCGCGCGTGCAATCTTTAA 60.511 52.632 37.29 0.00 42.97 1.52
2006 2155 1.062873 GCGCGCGTGCAATCTTTAAA 61.063 50.000 37.29 0.00 42.97 1.52
2007 2156 1.534028 CGCGCGTGCAATCTTTAAAT 58.466 45.000 24.19 0.00 42.97 1.40
2008 2157 1.508725 CGCGCGTGCAATCTTTAAATC 59.491 47.619 24.19 0.00 42.97 2.17
2009 2158 2.514902 GCGCGTGCAATCTTTAAATCA 58.485 42.857 17.66 0.00 42.15 2.57
2010 2159 3.108144 GCGCGTGCAATCTTTAAATCAT 58.892 40.909 17.66 0.00 42.15 2.45
2051 2211 3.944055 ACTGTATGAGAGTGGTGTGAC 57.056 47.619 0.00 0.00 0.00 3.67
2066 2226 4.236935 GGTGTGACGACCGTAAGAATAAA 58.763 43.478 0.00 0.00 43.02 1.40
2068 2228 4.919754 GTGTGACGACCGTAAGAATAAAGT 59.080 41.667 0.00 0.00 43.02 2.66
2078 2238 6.113411 CCGTAAGAATAAAGTGGATGGTTCT 58.887 40.000 0.00 0.00 43.02 3.01
2081 2241 5.779241 AGAATAAAGTGGATGGTTCTGGA 57.221 39.130 0.00 0.00 0.00 3.86
2084 2244 6.604795 AGAATAAAGTGGATGGTTCTGGAATG 59.395 38.462 0.00 0.00 0.00 2.67
2095 2255 3.057946 GGTTCTGGAATGAAGTGAAGCAC 60.058 47.826 0.00 0.00 35.85 4.40
2100 2260 2.095718 GGAATGAAGTGAAGCACCGTTC 60.096 50.000 0.00 0.00 34.49 3.95
2101 2261 1.148310 ATGAAGTGAAGCACCGTTCG 58.852 50.000 0.00 0.00 34.49 3.95
2108 2268 0.669318 GAAGCACCGTTCGTCCATCA 60.669 55.000 0.00 0.00 0.00 3.07
2111 2271 1.292223 CACCGTTCGTCCATCACCT 59.708 57.895 0.00 0.00 0.00 4.00
2117 2277 1.550976 GTTCGTCCATCACCTTCCTCT 59.449 52.381 0.00 0.00 0.00 3.69
2140 2300 2.186903 CGTCCCCTCCATGTTCGG 59.813 66.667 0.00 0.00 0.00 4.30
2141 2301 2.124695 GTCCCCTCCATGTTCGGC 60.125 66.667 0.00 0.00 0.00 5.54
2144 2304 2.671070 CCCTCCATGTTCGGCTGT 59.329 61.111 0.00 0.00 0.00 4.40
2158 2318 2.981302 CTGTCGACCATCCTGCCA 59.019 61.111 14.12 0.00 0.00 4.92
2194 2362 5.390567 CCTCTTCGGATGGTTTTAACTTTCG 60.391 44.000 0.00 0.00 33.16 3.46
2195 2363 4.453136 TCTTCGGATGGTTTTAACTTTCGG 59.547 41.667 0.00 0.00 0.00 4.30
2199 2367 4.155280 CGGATGGTTTTAACTTTCGGTGAT 59.845 41.667 0.00 0.00 0.00 3.06
2202 2370 7.225145 CGGATGGTTTTAACTTTCGGTGATATA 59.775 37.037 0.00 0.00 0.00 0.86
2203 2371 8.895737 GGATGGTTTTAACTTTCGGTGATATAA 58.104 33.333 0.00 0.00 0.00 0.98
2204 2372 9.712359 GATGGTTTTAACTTTCGGTGATATAAC 57.288 33.333 0.00 0.00 0.00 1.89
2216 2384 7.402811 TCGGTGATATAACGATGAAATTCAC 57.597 36.000 0.00 0.00 33.28 3.18
2217 2385 7.207383 TCGGTGATATAACGATGAAATTCACT 58.793 34.615 0.00 0.00 34.23 3.41
2218 2386 7.169140 TCGGTGATATAACGATGAAATTCACTG 59.831 37.037 0.00 0.00 39.46 3.66
2219 2387 7.169140 CGGTGATATAACGATGAAATTCACTGA 59.831 37.037 0.00 0.00 40.15 3.41
2220 2388 8.826710 GGTGATATAACGATGAAATTCACTGAA 58.173 33.333 0.00 0.00 34.23 3.02
2248 2416 9.558396 TTCACCAAAAATATTTCAGCAATTTCT 57.442 25.926 0.10 0.00 0.00 2.52
2347 3158 0.178947 TTTTGGTCCTGGGCCGAAAT 60.179 50.000 25.56 0.00 35.18 2.17
2380 3191 8.550376 CAAAATCACCGAAATTCAATCAACTTT 58.450 29.630 0.00 0.00 0.00 2.66
2381 3192 7.873739 AATCACCGAAATTCAATCAACTTTC 57.126 32.000 0.00 0.00 0.00 2.62
2382 3193 6.633500 TCACCGAAATTCAATCAACTTTCT 57.367 33.333 0.00 0.00 0.00 2.52
2383 3194 6.437928 TCACCGAAATTCAATCAACTTTCTG 58.562 36.000 0.00 0.00 0.00 3.02
2384 3195 6.039270 TCACCGAAATTCAATCAACTTTCTGT 59.961 34.615 0.00 0.00 0.00 3.41
2385 3196 6.697019 CACCGAAATTCAATCAACTTTCTGTT 59.303 34.615 0.00 0.00 39.92 3.16
2411 3222 9.904198 TGTTGATGAAATATATCTGAAACTGGA 57.096 29.630 0.00 0.00 0.00 3.86
2583 3394 1.504359 CTTGCCTTCGTTGACCGTTA 58.496 50.000 0.00 0.00 37.94 3.18
2585 3396 0.104487 TGCCTTCGTTGACCGTTACA 59.896 50.000 0.00 0.00 37.94 2.41
2594 3405 1.416243 TGACCGTTACAGGACCAACT 58.584 50.000 0.00 0.00 34.73 3.16
2768 3579 3.253220 TCTCTTTTGGCCTACCTAACCA 58.747 45.455 3.32 0.00 36.63 3.67
2769 3580 3.263425 TCTCTTTTGGCCTACCTAACCAG 59.737 47.826 3.32 0.00 34.28 4.00
2819 3630 3.559069 GATGATCCAAAATGCTCCCTCA 58.441 45.455 0.00 0.00 0.00 3.86
2917 3740 0.994050 TCCTCCTCGGGATCTCTCCA 60.994 60.000 0.00 0.00 44.08 3.86
3064 3887 3.003173 CCGCAACCCTCCTCCTCA 61.003 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.480419 CTCAGTGACGTTCCATTTCCAC 59.520 50.000 0.00 0.00 0.00 4.02
2 3 2.480419 CACTCAGTGACGTTCCATTTCC 59.520 50.000 0.00 0.00 35.23 3.13
3 4 2.096218 GCACTCAGTGACGTTCCATTTC 60.096 50.000 9.70 0.00 35.23 2.17
11 12 0.319900 GACCATGCACTCAGTGACGT 60.320 55.000 9.70 0.00 35.23 4.34
24 26 2.167281 ACCGTTGATCTCTCAGACCATG 59.833 50.000 0.00 0.00 31.68 3.66
93 95 8.464770 TCTTAATTGATGAAAAAGGCAAATCG 57.535 30.769 0.00 0.00 0.00 3.34
166 171 2.937469 TTTGAGTAATGCAATGCCGG 57.063 45.000 1.53 0.00 0.00 6.13
239 245 0.458669 CCGCCACTACTACCGTCATT 59.541 55.000 0.00 0.00 0.00 2.57
340 424 4.084888 GGTTTGGCCTTCGCGACG 62.085 66.667 9.15 7.07 35.02 5.12
345 429 4.513198 TTAAGAATTGGTTTGGCCTTCG 57.487 40.909 3.32 0.00 38.35 3.79
355 439 4.019681 TGTGGACGGAGATTAAGAATTGGT 60.020 41.667 0.00 0.00 0.00 3.67
401 485 0.539051 CGGTGCCTCATCTCCTCTTT 59.461 55.000 0.00 0.00 0.00 2.52
410 494 0.976641 TTCAAGAGACGGTGCCTCAT 59.023 50.000 0.00 0.00 33.25 2.90
415 499 0.249911 ACAGGTTCAAGAGACGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
417 501 2.561569 CAAACAGGTTCAAGAGACGGT 58.438 47.619 0.00 0.00 0.00 4.83
461 545 4.096003 CAACGTCGGGGATGGCCT 62.096 66.667 3.32 0.00 0.00 5.19
607 698 1.602323 TGGTGACGCCAAATCCACC 60.602 57.895 4.92 0.00 45.94 4.61
640 731 8.057623 AGAAATATTGAATTGTCCATCTCCACT 58.942 33.333 0.00 0.00 0.00 4.00
661 762 3.393800 CGTCAATCATAGCGGGAGAAAT 58.606 45.455 0.00 0.00 0.00 2.17
663 764 1.538204 GCGTCAATCATAGCGGGAGAA 60.538 52.381 0.00 0.00 0.00 2.87
666 767 0.464036 AAGCGTCAATCATAGCGGGA 59.536 50.000 0.00 0.00 34.34 5.14
668 769 2.096713 GCTTAAGCGTCAATCATAGCGG 60.097 50.000 12.53 0.00 34.34 5.52
669 770 2.096713 GGCTTAAGCGTCAATCATAGCG 60.097 50.000 20.80 0.00 43.26 4.26
670 771 2.872245 TGGCTTAAGCGTCAATCATAGC 59.128 45.455 20.80 3.41 43.26 2.97
671 772 5.088141 CTTGGCTTAAGCGTCAATCATAG 57.912 43.478 20.80 4.95 43.26 2.23
718 819 1.893808 CAAGTCCTGGCGTGCAAGT 60.894 57.895 0.59 0.00 0.00 3.16
774 875 0.594028 TCAACGGCGTATGAGCGATC 60.594 55.000 15.20 0.00 38.18 3.69
801 902 9.234827 CATAATTTCAAGATATGGTGGATAGCA 57.765 33.333 0.00 0.00 38.89 3.49
821 922 4.067896 GGTCGACATGGATGAGCATAATT 58.932 43.478 18.91 0.00 0.00 1.40
826 927 1.522092 GGGTCGACATGGATGAGCA 59.478 57.895 18.91 0.00 31.98 4.26
835 936 1.439228 CAGCTGATCGGGTCGACAT 59.561 57.895 18.91 1.65 39.18 3.06
836 937 2.885113 CAGCTGATCGGGTCGACA 59.115 61.111 18.91 0.00 39.18 4.35
866 967 2.259618 GTTGACGAATTCGCAGCTAGA 58.740 47.619 27.03 8.32 44.43 2.43
868 969 2.073117 TGTTGACGAATTCGCAGCTA 57.927 45.000 27.03 11.21 44.43 3.32
887 988 3.087031 CGATGGGGTACGTGGACTATAT 58.913 50.000 0.00 0.00 0.00 0.86
893 994 0.688418 AATCCGATGGGGTACGTGGA 60.688 55.000 0.00 0.00 37.00 4.02
957 1058 3.808728 TCTGCTCACCCTAAATATGCAC 58.191 45.455 0.00 0.00 0.00 4.57
961 1062 2.037772 CCGCTCTGCTCACCCTAAATAT 59.962 50.000 0.00 0.00 0.00 1.28
971 1072 4.724602 GACACGCCGCTCTGCTCA 62.725 66.667 0.00 0.00 0.00 4.26
972 1073 3.923563 AAGACACGCCGCTCTGCTC 62.924 63.158 0.00 0.00 0.00 4.26
973 1074 3.996124 AAGACACGCCGCTCTGCT 61.996 61.111 0.00 0.00 0.00 4.24
974 1075 3.782244 CAAGACACGCCGCTCTGC 61.782 66.667 0.00 0.00 0.00 4.26
975 1076 2.356313 ACAAGACACGCCGCTCTG 60.356 61.111 0.00 0.00 0.00 3.35
976 1077 2.159819 ATCACAAGACACGCCGCTCT 62.160 55.000 0.00 0.00 0.00 4.09
977 1078 1.687494 GATCACAAGACACGCCGCTC 61.687 60.000 0.00 0.00 0.00 5.03
978 1079 1.738099 GATCACAAGACACGCCGCT 60.738 57.895 0.00 0.00 0.00 5.52
979 1080 2.740714 GGATCACAAGACACGCCGC 61.741 63.158 0.00 0.00 0.00 6.53
980 1081 1.078759 GAGGATCACAAGACACGCCG 61.079 60.000 0.00 0.00 33.17 6.46
981 1082 0.037326 TGAGGATCACAAGACACGCC 60.037 55.000 0.00 0.00 42.56 5.68
982 1083 3.514777 TGAGGATCACAAGACACGC 57.485 52.632 0.00 0.00 42.56 5.34
999 1100 2.046507 GGAGCTGGCCTCTGTGTG 60.047 66.667 3.32 0.00 40.57 3.82
1024 1125 3.219928 ATGGCGGTCGATCGAGCT 61.220 61.111 35.85 20.42 40.14 4.09
1025 1126 3.032609 CATGGCGGTCGATCGAGC 61.033 66.667 31.90 31.90 39.05 5.03
1027 1128 2.411701 GTCATGGCGGTCGATCGA 59.588 61.111 24.71 15.15 0.00 3.59
1028 1129 2.930012 TTCGTCATGGCGGTCGATCG 62.930 60.000 21.18 15.15 32.54 3.69
1029 1130 1.226859 TTCGTCATGGCGGTCGATC 60.227 57.895 21.18 0.00 32.54 3.69
1030 1131 1.518572 GTTCGTCATGGCGGTCGAT 60.519 57.895 21.18 0.00 32.54 3.59
1031 1132 2.126228 GTTCGTCATGGCGGTCGA 60.126 61.111 21.18 6.80 0.00 4.20
1032 1133 3.541831 CGTTCGTCATGGCGGTCG 61.542 66.667 21.18 19.60 0.00 4.79
1033 1134 3.186047 CCGTTCGTCATGGCGGTC 61.186 66.667 21.18 12.02 39.41 4.79
1034 1135 4.752879 CCCGTTCGTCATGGCGGT 62.753 66.667 21.18 0.00 42.36 5.68
1035 1136 3.359515 TACCCGTTCGTCATGGCGG 62.360 63.158 21.18 12.32 43.40 6.13
1036 1137 2.162754 GTACCCGTTCGTCATGGCG 61.163 63.158 14.91 14.91 0.00 5.69
1345 1455 2.258591 CACGAGTCCACGGAGGTG 59.741 66.667 0.00 0.00 43.99 4.00
1354 1464 3.948719 TTGGCCACCCACGAGTCC 61.949 66.667 3.88 0.00 41.97 3.85
1951 2079 5.372373 GCTCTTGGCAATCCTAATAACTCT 58.628 41.667 0.00 0.00 41.35 3.24
1952 2080 4.517075 GGCTCTTGGCAATCCTAATAACTC 59.483 45.833 0.00 0.00 44.01 3.01
1954 2082 3.251004 CGGCTCTTGGCAATCCTAATAAC 59.749 47.826 0.00 0.00 44.01 1.89
1955 2083 3.118038 ACGGCTCTTGGCAATCCTAATAA 60.118 43.478 0.00 0.00 44.01 1.40
1963 2097 2.717639 ATTCTACGGCTCTTGGCAAT 57.282 45.000 0.00 0.00 44.01 3.56
1979 2113 2.644707 GCACGCGCGCACTTATTC 60.645 61.111 32.58 8.28 0.00 1.75
1980 2114 2.252127 ATTGCACGCGCGCACTTATT 62.252 50.000 32.58 5.07 42.87 1.40
1982 2116 3.361455 GATTGCACGCGCGCACTTA 62.361 57.895 32.58 8.00 42.87 2.24
2004 2153 9.328845 AGTTTTGCAAACAAGTATGAATGATTT 57.671 25.926 12.39 0.00 37.04 2.17
2005 2154 8.891671 AGTTTTGCAAACAAGTATGAATGATT 57.108 26.923 12.39 0.00 37.04 2.57
2006 2155 9.410556 GTAGTTTTGCAAACAAGTATGAATGAT 57.589 29.630 12.39 0.00 37.04 2.45
2007 2156 8.629158 AGTAGTTTTGCAAACAAGTATGAATGA 58.371 29.630 12.39 0.00 37.04 2.57
2008 2157 8.693504 CAGTAGTTTTGCAAACAAGTATGAATG 58.306 33.333 12.39 0.00 37.04 2.67
2009 2158 8.413229 ACAGTAGTTTTGCAAACAAGTATGAAT 58.587 29.630 12.39 0.00 37.04 2.57
2010 2159 7.767261 ACAGTAGTTTTGCAAACAAGTATGAA 58.233 30.769 12.39 0.00 37.04 2.57
2051 2211 4.506654 CCATCCACTTTATTCTTACGGTCG 59.493 45.833 0.00 0.00 0.00 4.79
2066 2226 3.331889 ACTTCATTCCAGAACCATCCACT 59.668 43.478 0.00 0.00 0.00 4.00
2068 2228 3.330405 TCACTTCATTCCAGAACCATCCA 59.670 43.478 0.00 0.00 0.00 3.41
2078 2238 1.202758 ACGGTGCTTCACTTCATTCCA 60.203 47.619 0.00 0.00 34.40 3.53
2081 2241 1.531149 CGAACGGTGCTTCACTTCATT 59.469 47.619 0.00 0.00 34.40 2.57
2084 2244 0.507358 GACGAACGGTGCTTCACTTC 59.493 55.000 0.00 0.00 34.40 3.01
2095 2255 0.739813 GGAAGGTGATGGACGAACGG 60.740 60.000 0.00 0.00 0.00 4.44
2100 2260 1.827969 AGAAGAGGAAGGTGATGGACG 59.172 52.381 0.00 0.00 0.00 4.79
2101 2261 2.169561 GGAGAAGAGGAAGGTGATGGAC 59.830 54.545 0.00 0.00 0.00 4.02
2108 2268 0.615261 GGACGGGAGAAGAGGAAGGT 60.615 60.000 0.00 0.00 0.00 3.50
2111 2271 1.305887 GGGGACGGGAGAAGAGGAA 60.306 63.158 0.00 0.00 0.00 3.36
2117 2277 1.689233 CATGGAGGGGACGGGAGAA 60.689 63.158 0.00 0.00 0.00 2.87
2140 2300 2.512515 GGCAGGATGGTCGACAGC 60.513 66.667 18.91 10.37 35.86 4.40
2141 2301 1.448540 GTGGCAGGATGGTCGACAG 60.449 63.158 18.91 0.63 35.86 3.51
2144 2304 4.451150 GCGTGGCAGGATGGTCGA 62.451 66.667 12.03 0.00 35.86 4.20
2158 2318 1.299976 GAAGAGGTGATTGGGGCGT 59.700 57.895 0.00 0.00 0.00 5.68
2194 2362 8.365399 TCAGTGAATTTCATCGTTATATCACC 57.635 34.615 1.78 0.00 37.29 4.02
2216 2384 8.991026 TGCTGAAATATTTTTGGTGAAATTCAG 58.009 29.630 1.43 0.00 40.39 3.02
2217 2385 8.899427 TGCTGAAATATTTTTGGTGAAATTCA 57.101 26.923 1.43 0.00 31.96 2.57
2222 2390 9.558396 AGAAATTGCTGAAATATTTTTGGTGAA 57.442 25.926 1.43 0.00 0.00 3.18
2223 2391 8.991026 CAGAAATTGCTGAAATATTTTTGGTGA 58.009 29.630 7.80 0.00 38.14 4.02
2224 2392 8.776470 ACAGAAATTGCTGAAATATTTTTGGTG 58.224 29.630 20.85 0.00 39.20 4.17
2225 2393 8.907222 ACAGAAATTGCTGAAATATTTTTGGT 57.093 26.923 20.85 0.00 39.20 3.67
2335 3146 1.079888 GTTTGCATTTCGGCCCAGG 60.080 57.895 0.00 0.00 0.00 4.45
2338 3149 0.250081 TTTGGTTTGCATTTCGGCCC 60.250 50.000 0.00 0.00 0.00 5.80
2347 3158 3.526931 TTTCGGTGATTTTGGTTTGCA 57.473 38.095 0.00 0.00 0.00 4.08
2385 3196 9.904198 TCCAGTTTCAGATATATTTCATCAACA 57.096 29.630 0.00 0.00 0.00 3.33
2391 3202 9.958180 TTCACTTCCAGTTTCAGATATATTTCA 57.042 29.630 0.00 0.00 0.00 2.69
2396 3207 9.739276 ACATTTTCACTTCCAGTTTCAGATATA 57.261 29.630 0.00 0.00 0.00 0.86
2397 3208 8.517878 CACATTTTCACTTCCAGTTTCAGATAT 58.482 33.333 0.00 0.00 0.00 1.63
2398 3209 7.719193 TCACATTTTCACTTCCAGTTTCAGATA 59.281 33.333 0.00 0.00 0.00 1.98
2399 3210 6.547141 TCACATTTTCACTTCCAGTTTCAGAT 59.453 34.615 0.00 0.00 0.00 2.90
2400 3211 5.885352 TCACATTTTCACTTCCAGTTTCAGA 59.115 36.000 0.00 0.00 0.00 3.27
2401 3212 5.973565 GTCACATTTTCACTTCCAGTTTCAG 59.026 40.000 0.00 0.00 0.00 3.02
2402 3213 5.448496 CGTCACATTTTCACTTCCAGTTTCA 60.448 40.000 0.00 0.00 0.00 2.69
2403 3214 4.970003 CGTCACATTTTCACTTCCAGTTTC 59.030 41.667 0.00 0.00 0.00 2.78
2404 3215 4.733523 GCGTCACATTTTCACTTCCAGTTT 60.734 41.667 0.00 0.00 0.00 2.66
2405 3216 3.243068 GCGTCACATTTTCACTTCCAGTT 60.243 43.478 0.00 0.00 0.00 3.16
2406 3217 2.290641 GCGTCACATTTTCACTTCCAGT 59.709 45.455 0.00 0.00 0.00 4.00
2407 3218 2.350772 GGCGTCACATTTTCACTTCCAG 60.351 50.000 0.00 0.00 0.00 3.86
2408 3219 1.606668 GGCGTCACATTTTCACTTCCA 59.393 47.619 0.00 0.00 0.00 3.53
2409 3220 1.068541 GGGCGTCACATTTTCACTTCC 60.069 52.381 0.00 0.00 0.00 3.46
2410 3221 1.068541 GGGGCGTCACATTTTCACTTC 60.069 52.381 0.00 0.00 0.00 3.01
2411 3222 0.958822 GGGGCGTCACATTTTCACTT 59.041 50.000 0.00 0.00 0.00 3.16
2412 3223 1.234615 CGGGGCGTCACATTTTCACT 61.235 55.000 0.00 0.00 0.00 3.41
2413 3224 1.209127 CGGGGCGTCACATTTTCAC 59.791 57.895 0.00 0.00 0.00 3.18
2414 3225 0.953471 CTCGGGGCGTCACATTTTCA 60.953 55.000 0.00 0.00 0.00 2.69
2415 3226 0.672401 TCTCGGGGCGTCACATTTTC 60.672 55.000 0.00 0.00 0.00 2.29
2416 3227 0.953960 GTCTCGGGGCGTCACATTTT 60.954 55.000 0.00 0.00 0.00 1.82
2417 3228 1.375523 GTCTCGGGGCGTCACATTT 60.376 57.895 0.00 0.00 0.00 2.32
2418 3229 2.264794 GTCTCGGGGCGTCACATT 59.735 61.111 0.00 0.00 0.00 2.71
2419 3230 3.771160 GGTCTCGGGGCGTCACAT 61.771 66.667 0.00 0.00 0.00 3.21
2583 3394 5.535030 GGAAACAAAATCTAGTTGGTCCTGT 59.465 40.000 8.29 0.00 34.14 4.00
2585 3396 5.077564 GGGAAACAAAATCTAGTTGGTCCT 58.922 41.667 12.44 0.00 35.85 3.85
2594 3405 4.766891 CAGGCAAGAGGGAAACAAAATCTA 59.233 41.667 0.00 0.00 0.00 1.98
2768 3579 0.170561 CGGACGGTCGAAGATGAACT 59.829 55.000 1.43 0.00 40.67 3.01
2769 3580 0.169672 TCGGACGGTCGAAGATGAAC 59.830 55.000 1.43 0.00 40.67 3.18
2819 3630 8.971894 ACTAGGGGTGGACTGCTATATATATAT 58.028 37.037 10.10 10.10 0.00 0.86
2917 3740 0.031010 GGAGGTAGGTGGGTGGATCT 60.031 60.000 0.00 0.00 0.00 2.75
2971 3794 1.103803 CTCTCCTCCGGATCGAACAA 58.896 55.000 3.57 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.