Multiple sequence alignment - TraesCS1D01G241000

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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 TraesCS1D01G241000 chr1D 100.000 5395 0 0 1 5395 331300016 331305410 0.000000e+00 9963.0
1 TraesCS1D01G241000 chr1A 93.622 3810 146 34 863 4595 428546347 428550136 0.000000e+00 5600.0
2 TraesCS1D01G241000 chr1A 92.734 867 40 14 4 868 428544871 428545716 0.000000e+00 1230.0
3 TraesCS1D01G241000 chr1A 89.406 387 21 7 4994 5372 428577198 428577572 2.270000e-128 470.0
4 TraesCS1D01G241000 chr1A 83.333 174 23 5 4461 4629 428191183 428191355 7.240000e-34 156.0
5 TraesCS1D01G241000 chr1A 83.077 195 10 11 4771 4962 428577022 428577196 7.240000e-34 156.0
6 TraesCS1D01G241000 chr1B 92.518 3876 186 51 831 4632 445742345 445746190 0.000000e+00 5456.0
7 TraesCS1D01G241000 chr1B 84.019 826 85 19 50 849 445741068 445741872 0.000000e+00 750.0
8 TraesCS1D01G241000 chr1B 84.636 371 26 13 5018 5372 445749646 445750001 1.860000e-89 340.0
9 TraesCS1D01G241000 chr1B 91.603 131 7 2 4771 4898 445746182 445746311 1.540000e-40 178.0
10 TraesCS1D01G241000 chr1B 75.000 236 52 6 173 404 486824482 486824714 9.560000e-18 102.0
11 TraesCS1D01G241000 chr3B 78.877 374 61 13 247 607 470492469 470492101 2.510000e-58 237.0
12 TraesCS1D01G241000 chr3A 72.385 478 102 19 112 572 638491399 638491863 2.040000e-24 124.0
13 TraesCS1D01G241000 chrUn 79.856 139 24 4 106 242 328115673 328115809 1.240000e-16 99.0
14 TraesCS1D01G241000 chr2B 93.023 43 2 1 531 572 467860204 467860246 1.620000e-05 62.1
15 TraesCS1D01G241000 chr2A 78.095 105 13 7 505 607 532858051 532858147 2.100000e-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 TraesCS1D01G241000 chr1D 331300016 331305410 5394 False 9963 9963 100.0000 1 5395 1 chr1D.!!$F1 5394
1 TraesCS1D01G241000 chr1A 428544871 428550136 5265 False 3415 5600 93.1780 4 4595 2 chr1A.!!$F2 4591
2 TraesCS1D01G241000 chr1A 428577022 428577572 550 False 313 470 86.2415 4771 5372 2 chr1A.!!$F3 601
3 TraesCS1D01G241000 chr1B 445741068 445750001 8933 False 1681 5456 88.1940 50 5372 4 chr1B.!!$F2 5322

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
659 671 0.250901 AAGATGCCCAGACGTTGCTT 60.251 50.000 0.00 0.00 0.00 3.91 F
777 800 1.382522 TCCTTGCTCAATCCATTCGC 58.617 50.000 0.00 0.00 0.00 4.70 F
1365 2522 1.671979 CGTGTCGAGGTACCTCCATA 58.328 55.000 31.78 18.19 39.77 2.74 F
1525 2682 2.782341 AGCTCCTCTATGCCAGGAAAAT 59.218 45.455 0.00 0.00 39.69 1.82 F
3108 4302 1.557099 ATACAGAACTGAGTCCGCCA 58.443 50.000 8.87 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 3555 1.271379 ACAGGGTGTATGAGGCAACAC 60.271 52.381 0.00 0.0 44.19 3.32 R
2613 3804 1.305201 ACTTACCACAGTTTGTGCCG 58.695 50.000 3.72 0.0 46.51 5.69 R
2831 4022 1.276622 GGGGGAAAGAGTGCAGACTA 58.723 55.000 0.00 0.0 30.16 2.59 R
3421 4624 0.748005 CCCACCACTAAATCCTGCGG 60.748 60.000 0.00 0.0 0.00 5.69 R
4686 5930 0.035317 ATTTCAGTCGCTGCCACTCA 59.965 50.000 0.00 0.0 0.00 3.41 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
427 428 3.446507 GCAATGAATGTGCTTGGGG 57.553 52.632 0.00 0.00 39.00 4.96
471 482 9.022915 GTTGTACCACAAAAACTTAACCATAAC 57.977 33.333 0.00 0.00 40.15 1.89
573 585 2.315925 AATCGGATGTGCGAGACATT 57.684 45.000 2.63 0.00 45.90 2.71
659 671 0.250901 AAGATGCCCAGACGTTGCTT 60.251 50.000 0.00 0.00 0.00 3.91
668 680 4.312443 CCCAGACGTTGCTTAAAACTCTA 58.688 43.478 0.00 0.00 0.00 2.43
676 688 8.652810 ACGTTGCTTAAAACTCTAAAACTCTA 57.347 30.769 0.00 0.00 0.00 2.43
777 800 1.382522 TCCTTGCTCAATCCATTCGC 58.617 50.000 0.00 0.00 0.00 4.70
846 1360 4.654262 AGCTACTGTAATGGGCTAAAGCTA 59.346 41.667 1.39 0.00 41.70 3.32
849 1363 6.317893 GCTACTGTAATGGGCTAAAGCTAAAA 59.682 38.462 1.39 0.00 41.70 1.52
869 2020 7.975616 GCTAAAATTTCTTCCACATCTGCATTA 59.024 33.333 0.00 0.00 0.00 1.90
1122 2279 2.304761 GTCACCCACCTAAATCCAGTCA 59.695 50.000 0.00 0.00 0.00 3.41
1365 2522 1.671979 CGTGTCGAGGTACCTCCATA 58.328 55.000 31.78 18.19 39.77 2.74
1379 2536 8.170730 AGGTACCTCCATATTTTTCTTCTTTGT 58.829 33.333 9.21 0.00 39.02 2.83
1525 2682 2.782341 AGCTCCTCTATGCCAGGAAAAT 59.218 45.455 0.00 0.00 39.69 1.82
1562 2719 4.142966 GGTTTCATTTACCGAACTTCTCCG 60.143 45.833 0.00 0.00 0.00 4.63
1576 2738 4.911390 ACTTCTCCGTTTCATTTCATCCT 58.089 39.130 0.00 0.00 0.00 3.24
1754 2918 5.684704 ACAAGAATCGGATACCACATCATT 58.315 37.500 0.00 0.00 0.00 2.57
1755 2919 5.528690 ACAAGAATCGGATACCACATCATTG 59.471 40.000 0.00 0.00 0.00 2.82
1776 2940 5.947228 TGTCTTTCCTTGCAATAACTCAG 57.053 39.130 0.00 0.00 0.00 3.35
1905 3069 9.414295 GAATTGATCAATTGTCAGTTTCATCAA 57.586 29.630 32.89 13.88 40.77 2.57
2067 3256 7.823310 CCTAATCTCGATACACTAGCCTTAGTA 59.177 40.741 0.00 0.00 38.05 1.82
2091 3280 7.790782 AGAGGTAAATCTGTCTTCTTCTTCT 57.209 36.000 0.00 0.00 0.00 2.85
2092 3281 8.201242 AGAGGTAAATCTGTCTTCTTCTTCTT 57.799 34.615 0.00 0.00 0.00 2.52
2093 3282 8.311109 AGAGGTAAATCTGTCTTCTTCTTCTTC 58.689 37.037 0.00 0.00 0.00 2.87
2094 3283 8.201242 AGGTAAATCTGTCTTCTTCTTCTTCT 57.799 34.615 0.00 0.00 0.00 2.85
2095 3284 8.655901 AGGTAAATCTGTCTTCTTCTTCTTCTT 58.344 33.333 0.00 0.00 0.00 2.52
2096 3285 8.931775 GGTAAATCTGTCTTCTTCTTCTTCTTC 58.068 37.037 0.00 0.00 0.00 2.87
2122 3311 8.916628 TTCATGCTATATACTTTGCCATTGTA 57.083 30.769 0.00 0.00 0.00 2.41
2176 3365 6.490040 TCCCTTCTCAACCTATGAAAACAAAG 59.510 38.462 0.00 0.00 37.67 2.77
2252 3441 4.878397 ACTTGGACTTGTTTGTTCAGAGAG 59.122 41.667 0.00 0.00 0.00 3.20
2395 3586 6.065976 TCATACACCCTGTTTCTGATCAAT 57.934 37.500 0.00 0.00 0.00 2.57
2613 3804 3.922850 GCTTGGAAAAGCTTTATGTGCTC 59.077 43.478 13.10 4.92 42.32 4.26
2831 4022 9.131791 ACTACAAGGTGACACTTAATTTGAAAT 57.868 29.630 5.39 0.00 0.00 2.17
2847 4038 6.560253 TTTGAAATAGTCTGCACTCTTTCC 57.440 37.500 10.68 0.00 41.68 3.13
2878 4069 8.815141 TTTGGAACAGTTTCATTCATGTAATG 57.185 30.769 0.00 10.06 44.04 1.90
2984 4177 5.303078 TGATTGTTTTCCTTTCCCGATTTCA 59.697 36.000 0.00 0.00 0.00 2.69
2985 4178 5.799827 TTGTTTTCCTTTCCCGATTTCAT 57.200 34.783 0.00 0.00 0.00 2.57
2986 4179 6.902771 TTGTTTTCCTTTCCCGATTTCATA 57.097 33.333 0.00 0.00 0.00 2.15
2987 4180 7.475137 TTGTTTTCCTTTCCCGATTTCATAT 57.525 32.000 0.00 0.00 0.00 1.78
2988 4181 6.862209 TGTTTTCCTTTCCCGATTTCATATG 58.138 36.000 0.00 0.00 0.00 1.78
2989 4182 6.435904 TGTTTTCCTTTCCCGATTTCATATGT 59.564 34.615 1.90 0.00 0.00 2.29
2990 4183 6.449635 TTTCCTTTCCCGATTTCATATGTG 57.550 37.500 1.90 0.00 0.00 3.21
2992 4185 3.004734 CCTTTCCCGATTTCATATGTGGC 59.995 47.826 1.90 0.00 0.00 5.01
2993 4186 3.289407 TTCCCGATTTCATATGTGGCA 57.711 42.857 1.90 0.00 0.00 4.92
2994 4187 2.849942 TCCCGATTTCATATGTGGCAG 58.150 47.619 1.90 0.00 0.00 4.85
2995 4188 2.172505 TCCCGATTTCATATGTGGCAGT 59.827 45.455 1.90 0.00 0.00 4.40
2998 4191 3.378112 CCGATTTCATATGTGGCAGTGTT 59.622 43.478 1.90 0.00 0.00 3.32
3001 4194 5.064579 CGATTTCATATGTGGCAGTGTTGTA 59.935 40.000 1.90 0.00 0.00 2.41
3108 4302 1.557099 ATACAGAACTGAGTCCGCCA 58.443 50.000 8.87 0.00 0.00 5.69
3191 4385 1.802636 GGTGGATGTCATTGCACCG 59.197 57.895 9.14 0.00 46.24 4.94
3210 4404 2.398498 CGTCATGCTACAGGTATGCTC 58.602 52.381 0.00 0.00 37.83 4.26
3211 4405 2.223805 CGTCATGCTACAGGTATGCTCA 60.224 50.000 0.00 0.00 37.83 4.26
3212 4406 3.126831 GTCATGCTACAGGTATGCTCAC 58.873 50.000 0.00 0.00 37.83 3.51
3233 4432 6.179756 TCACCGCATATATCCATTGCTTTAT 58.820 36.000 0.00 0.00 34.23 1.40
3269 4469 5.021033 AGTCAGGCATCACTCTCAAATAG 57.979 43.478 0.00 0.00 0.00 1.73
3360 4562 6.076981 TCCCGTCGTATATAGTTCTTTTCC 57.923 41.667 0.00 0.00 0.00 3.13
3417 4620 2.774439 AACTAAAAGTGCCTGTTGCG 57.226 45.000 0.00 0.00 45.60 4.85
3421 4624 1.921243 AAAAGTGCCTGTTGCGAAAC 58.079 45.000 0.00 0.00 45.60 2.78
3468 4671 4.035112 TGGGAGTACCGAAATATTCTGGT 58.965 43.478 14.09 14.09 44.64 4.00
3713 4916 1.066257 CACTTGTGTGCTGTTGGGC 59.934 57.895 0.00 0.00 37.38 5.36
3983 5188 3.144506 CATCATCGCCTTCCTGCTAAAT 58.855 45.455 0.00 0.00 0.00 1.40
3996 5201 5.488341 TCCTGCTAAATCTGGTTAGTGAAC 58.512 41.667 0.00 0.00 34.20 3.18
4174 5381 0.106669 GGGGAAGGGCAAGGTACATC 60.107 60.000 0.00 0.00 0.00 3.06
4368 5578 3.678717 AAGGACGGACGCATCGACG 62.679 63.158 0.00 0.00 37.01 5.12
4401 5611 4.689345 AGCAGAATAAACCGTGAAGTGTAC 59.311 41.667 0.00 0.00 0.00 2.90
4411 5621 6.132791 ACCGTGAAGTGTACTGTATCATAG 57.867 41.667 0.00 0.00 0.00 2.23
4419 5650 5.878669 AGTGTACTGTATCATAGACACACGA 59.121 40.000 9.59 0.00 39.67 4.35
4423 5654 4.645136 ACTGTATCATAGACACACGACCAT 59.355 41.667 0.00 0.00 0.00 3.55
4431 5662 2.202743 ACACGACCATGCGATCCG 60.203 61.111 0.00 0.00 34.83 4.18
4481 5717 3.570926 AATGAGTGCACAGCAGAAATG 57.429 42.857 21.04 0.00 40.08 2.32
4551 5795 3.465403 CTCCCCCGACAGGCTCAG 61.465 72.222 0.00 0.00 35.76 3.35
4563 5807 1.558756 CAGGCTCAGGGATCAACTCTT 59.441 52.381 0.00 0.00 0.00 2.85
4570 5814 4.836825 TCAGGGATCAACTCTTCAATGAC 58.163 43.478 0.00 0.00 0.00 3.06
4573 5817 2.029728 GGATCAACTCTTCAATGACGCG 59.970 50.000 3.53 3.53 0.00 6.01
4580 5824 4.355437 ACTCTTCAATGACGCGATAGAAG 58.645 43.478 15.93 17.45 39.76 2.85
4582 5826 4.105486 TCTTCAATGACGCGATAGAAGTG 58.895 43.478 15.93 2.64 35.30 3.16
4589 5833 1.202110 ACGCGATAGAAGTGTGTACCG 60.202 52.381 15.93 0.00 39.76 4.02
4595 5839 5.634896 CGATAGAAGTGTGTACCGTTAGTT 58.365 41.667 0.00 0.00 39.76 2.24
4599 5843 5.527033 AGAAGTGTGTACCGTTAGTTTCTC 58.473 41.667 0.00 0.00 0.00 2.87
4607 5851 2.436911 ACCGTTAGTTTCTCCACTTGGT 59.563 45.455 0.00 0.00 36.34 3.67
4609 5853 3.250040 CCGTTAGTTTCTCCACTTGGTTG 59.750 47.826 0.00 0.00 36.34 3.77
4610 5854 3.875134 CGTTAGTTTCTCCACTTGGTTGT 59.125 43.478 0.00 0.00 36.34 3.32
4612 5856 5.163693 CGTTAGTTTCTCCACTTGGTTGTTT 60.164 40.000 0.00 0.00 36.34 2.83
4613 5857 4.718940 AGTTTCTCCACTTGGTTGTTTG 57.281 40.909 0.00 0.00 36.34 2.93
4614 5858 3.119137 AGTTTCTCCACTTGGTTGTTTGC 60.119 43.478 0.00 0.00 36.34 3.68
4617 5861 1.067250 CCACTTGGTTGTTTGCCCG 59.933 57.895 0.00 0.00 0.00 6.13
4618 5862 1.388065 CCACTTGGTTGTTTGCCCGA 61.388 55.000 0.00 0.00 0.00 5.14
4619 5863 0.673437 CACTTGGTTGTTTGCCCGAT 59.327 50.000 0.00 0.00 0.00 4.18
4620 5864 1.883275 CACTTGGTTGTTTGCCCGATA 59.117 47.619 0.00 0.00 0.00 2.92
4621 5865 2.095263 CACTTGGTTGTTTGCCCGATAG 60.095 50.000 0.00 0.00 0.00 2.08
4622 5866 2.159382 CTTGGTTGTTTGCCCGATAGT 58.841 47.619 0.00 0.00 0.00 2.12
4624 5868 2.588620 TGGTTGTTTGCCCGATAGTTT 58.411 42.857 0.00 0.00 0.00 2.66
4625 5869 2.294791 TGGTTGTTTGCCCGATAGTTTG 59.705 45.455 0.00 0.00 0.00 2.93
4626 5870 2.554893 GGTTGTTTGCCCGATAGTTTGA 59.445 45.455 0.00 0.00 0.00 2.69
4627 5871 3.004944 GGTTGTTTGCCCGATAGTTTGAA 59.995 43.478 0.00 0.00 0.00 2.69
4628 5872 4.226761 GTTGTTTGCCCGATAGTTTGAAG 58.773 43.478 0.00 0.00 0.00 3.02
4629 5873 2.817258 TGTTTGCCCGATAGTTTGAAGG 59.183 45.455 0.00 0.00 0.00 3.46
4630 5874 3.078837 GTTTGCCCGATAGTTTGAAGGA 58.921 45.455 0.00 0.00 0.00 3.36
4631 5875 3.426787 TTGCCCGATAGTTTGAAGGAA 57.573 42.857 0.00 0.00 0.00 3.36
4632 5876 2.706890 TGCCCGATAGTTTGAAGGAAC 58.293 47.619 0.00 0.00 0.00 3.62
4633 5877 1.664151 GCCCGATAGTTTGAAGGAACG 59.336 52.381 0.00 0.00 34.74 3.95
4634 5878 2.277084 CCCGATAGTTTGAAGGAACGG 58.723 52.381 0.00 0.00 39.02 4.44
4635 5879 2.093869 CCCGATAGTTTGAAGGAACGGA 60.094 50.000 0.00 0.00 41.30 4.69
4636 5880 3.592059 CCGATAGTTTGAAGGAACGGAA 58.408 45.455 0.00 0.00 41.30 4.30
4637 5881 3.617263 CCGATAGTTTGAAGGAACGGAAG 59.383 47.826 0.00 0.00 41.30 3.46
4650 5894 2.846039 ACGGAAGTACTCTGCATACG 57.154 50.000 0.00 0.00 46.88 3.06
4651 5895 1.404391 ACGGAAGTACTCTGCATACGG 59.596 52.381 0.00 0.00 46.88 4.02
4652 5896 1.404391 CGGAAGTACTCTGCATACGGT 59.596 52.381 0.00 0.00 0.00 4.83
4653 5897 2.615447 CGGAAGTACTCTGCATACGGTA 59.385 50.000 0.00 0.00 0.00 4.02
4654 5898 3.303857 CGGAAGTACTCTGCATACGGTAG 60.304 52.174 0.00 0.00 0.00 3.18
4655 5899 3.881688 GGAAGTACTCTGCATACGGTAGA 59.118 47.826 0.00 0.00 36.73 2.59
4656 5900 4.519730 GGAAGTACTCTGCATACGGTAGAT 59.480 45.833 0.00 0.00 37.62 1.98
4657 5901 5.440234 AAGTACTCTGCATACGGTAGATG 57.560 43.478 0.00 0.00 37.62 2.90
4658 5902 4.715713 AGTACTCTGCATACGGTAGATGA 58.284 43.478 0.00 0.00 37.62 2.92
4659 5903 5.317808 AGTACTCTGCATACGGTAGATGAT 58.682 41.667 0.00 0.00 37.62 2.45
4660 5904 6.473758 AGTACTCTGCATACGGTAGATGATA 58.526 40.000 0.00 0.00 37.62 2.15
4661 5905 7.113437 AGTACTCTGCATACGGTAGATGATAT 58.887 38.462 0.00 0.00 37.62 1.63
4662 5906 6.443934 ACTCTGCATACGGTAGATGATATC 57.556 41.667 0.00 0.00 37.62 1.63
4663 5907 6.184068 ACTCTGCATACGGTAGATGATATCT 58.816 40.000 3.98 0.00 43.33 1.98
4664 5908 6.094742 ACTCTGCATACGGTAGATGATATCTG 59.905 42.308 3.98 0.00 40.51 2.90
4665 5909 6.180472 TCTGCATACGGTAGATGATATCTGA 58.820 40.000 3.98 0.00 40.51 3.27
4666 5910 6.830838 TCTGCATACGGTAGATGATATCTGAT 59.169 38.462 3.98 0.00 40.51 2.90
4667 5911 7.340487 TCTGCATACGGTAGATGATATCTGATT 59.660 37.037 3.98 0.00 40.51 2.57
4668 5912 7.840931 TGCATACGGTAGATGATATCTGATTT 58.159 34.615 3.98 0.00 40.51 2.17
4669 5913 8.966868 TGCATACGGTAGATGATATCTGATTTA 58.033 33.333 3.98 0.00 40.51 1.40
4670 5914 9.973450 GCATACGGTAGATGATATCTGATTTAT 57.027 33.333 3.98 0.00 40.51 1.40
4687 5931 9.952188 TCTGATTTATATACGACAGAGACTTTG 57.048 33.333 0.00 0.00 32.04 2.77
4688 5932 9.952188 CTGATTTATATACGACAGAGACTTTGA 57.048 33.333 0.00 0.00 0.00 2.69
4689 5933 9.952188 TGATTTATATACGACAGAGACTTTGAG 57.048 33.333 0.00 0.00 0.00 3.02
4690 5934 9.953697 GATTTATATACGACAGAGACTTTGAGT 57.046 33.333 0.00 2.62 0.00 3.41
4691 5935 9.737427 ATTTATATACGACAGAGACTTTGAGTG 57.263 33.333 0.00 0.00 0.00 3.51
4692 5936 2.802787 ACGACAGAGACTTTGAGTGG 57.197 50.000 0.00 0.00 0.00 4.00
4693 5937 1.269831 ACGACAGAGACTTTGAGTGGC 60.270 52.381 0.00 0.00 0.00 5.01
4694 5938 1.269778 CGACAGAGACTTTGAGTGGCA 60.270 52.381 0.00 0.00 0.00 4.92
4695 5939 2.411904 GACAGAGACTTTGAGTGGCAG 58.588 52.381 0.00 0.00 0.00 4.85
4696 5940 1.155042 CAGAGACTTTGAGTGGCAGC 58.845 55.000 0.00 0.00 0.00 5.25
4697 5941 0.320247 AGAGACTTTGAGTGGCAGCG 60.320 55.000 0.00 0.00 0.00 5.18
4698 5942 0.319900 GAGACTTTGAGTGGCAGCGA 60.320 55.000 0.00 0.00 0.00 4.93
4699 5943 0.601311 AGACTTTGAGTGGCAGCGAC 60.601 55.000 0.00 0.00 0.00 5.19
4700 5944 0.601311 GACTTTGAGTGGCAGCGACT 60.601 55.000 10.26 10.26 0.00 4.18
4701 5945 0.882042 ACTTTGAGTGGCAGCGACTG 60.882 55.000 15.73 2.91 34.12 3.51
4702 5946 0.601046 CTTTGAGTGGCAGCGACTGA 60.601 55.000 15.73 3.19 32.44 3.41
4703 5947 0.179059 TTTGAGTGGCAGCGACTGAA 60.179 50.000 15.73 10.28 32.44 3.02
4704 5948 0.179059 TTGAGTGGCAGCGACTGAAA 60.179 50.000 15.73 6.49 32.44 2.69
4705 5949 0.035317 TGAGTGGCAGCGACTGAAAT 59.965 50.000 15.73 0.00 32.44 2.17
4706 5950 1.275010 TGAGTGGCAGCGACTGAAATA 59.725 47.619 15.73 0.00 32.44 1.40
4707 5951 2.093500 TGAGTGGCAGCGACTGAAATAT 60.093 45.455 15.73 0.00 32.44 1.28
4708 5952 2.283298 AGTGGCAGCGACTGAAATATG 58.717 47.619 9.62 0.00 32.44 1.78
4709 5953 2.093500 AGTGGCAGCGACTGAAATATGA 60.093 45.455 9.62 0.00 32.44 2.15
4710 5954 2.030946 GTGGCAGCGACTGAAATATGAC 59.969 50.000 10.46 0.00 32.44 3.06
4711 5955 2.279741 GGCAGCGACTGAAATATGACA 58.720 47.619 10.46 0.00 32.44 3.58
4712 5956 2.286294 GGCAGCGACTGAAATATGACAG 59.714 50.000 10.46 7.56 39.65 3.51
4713 5957 3.190079 GCAGCGACTGAAATATGACAGA 58.810 45.455 13.86 0.00 37.54 3.41
4714 5958 3.618594 GCAGCGACTGAAATATGACAGAA 59.381 43.478 13.86 0.00 37.54 3.02
4715 5959 4.093408 GCAGCGACTGAAATATGACAGAAA 59.907 41.667 13.86 0.00 37.54 2.52
4716 5960 5.220739 GCAGCGACTGAAATATGACAGAAAT 60.221 40.000 13.86 0.00 37.54 2.17
4717 5961 6.417327 CAGCGACTGAAATATGACAGAAATC 58.583 40.000 13.86 3.68 37.54 2.17
4718 5962 6.257411 CAGCGACTGAAATATGACAGAAATCT 59.743 38.462 13.86 5.19 37.54 2.40
4719 5963 7.436376 CAGCGACTGAAATATGACAGAAATCTA 59.564 37.037 13.86 0.00 37.54 1.98
4720 5964 7.981789 AGCGACTGAAATATGACAGAAATCTAA 59.018 33.333 13.86 0.00 37.54 2.10
4721 5965 8.768955 GCGACTGAAATATGACAGAAATCTAAT 58.231 33.333 13.86 0.00 37.54 1.73
4724 5968 9.911788 ACTGAAATATGACAGAAATCTAATGGT 57.088 29.630 13.86 0.00 37.54 3.55
4755 5999 2.932855 TGGTACACAAATCGGTTGGA 57.067 45.000 0.00 0.00 41.97 3.53
4756 6000 3.210232 TGGTACACAAATCGGTTGGAA 57.790 42.857 0.00 0.00 41.97 3.53
4757 6001 3.552875 TGGTACACAAATCGGTTGGAAA 58.447 40.909 0.00 0.00 41.97 3.13
4758 6002 3.952323 TGGTACACAAATCGGTTGGAAAA 59.048 39.130 0.00 0.00 41.97 2.29
4759 6003 4.036971 TGGTACACAAATCGGTTGGAAAAG 59.963 41.667 0.00 0.00 41.97 2.27
4760 6004 4.276431 GGTACACAAATCGGTTGGAAAAGA 59.724 41.667 0.00 0.00 41.97 2.52
4761 6005 4.568152 ACACAAATCGGTTGGAAAAGAG 57.432 40.909 0.00 0.00 41.97 2.85
4762 6006 3.243401 ACACAAATCGGTTGGAAAAGAGC 60.243 43.478 0.00 0.00 41.97 4.09
4763 6007 2.955660 ACAAATCGGTTGGAAAAGAGCA 59.044 40.909 0.00 0.00 41.97 4.26
4764 6008 3.004734 ACAAATCGGTTGGAAAAGAGCAG 59.995 43.478 0.00 0.00 41.97 4.24
4765 6009 2.568623 ATCGGTTGGAAAAGAGCAGT 57.431 45.000 0.00 0.00 0.00 4.40
4766 6010 1.593196 TCGGTTGGAAAAGAGCAGTG 58.407 50.000 0.00 0.00 0.00 3.66
4767 6011 0.040067 CGGTTGGAAAAGAGCAGTGC 60.040 55.000 7.13 7.13 0.00 4.40
4768 6012 1.322442 GGTTGGAAAAGAGCAGTGCT 58.678 50.000 19.86 19.86 43.88 4.40
4784 6028 3.985925 CAGTGCTCTTCAAGAAAAATGGC 59.014 43.478 0.00 0.00 0.00 4.40
4789 6033 4.802999 CTCTTCAAGAAAAATGGCTCCAC 58.197 43.478 0.00 0.00 0.00 4.02
4808 6052 4.646945 TCCACTGAAGAGCCTTGTCTATAG 59.353 45.833 0.00 0.00 0.00 1.31
4809 6053 4.404073 CCACTGAAGAGCCTTGTCTATAGT 59.596 45.833 0.00 0.00 0.00 2.12
4814 6058 5.592282 TGAAGAGCCTTGTCTATAGTCAGAG 59.408 44.000 0.00 1.90 0.00 3.35
4885 6132 4.511527 CAAATGAGGCATGTCTACAGACT 58.488 43.478 0.00 0.00 44.99 3.24
4898 6145 5.778241 TGTCTACAGACTGGTTATTGGAAGA 59.222 40.000 7.51 0.00 44.99 2.87
4899 6146 6.440647 TGTCTACAGACTGGTTATTGGAAGAT 59.559 38.462 7.51 0.00 44.99 2.40
4902 6149 6.319048 ACAGACTGGTTATTGGAAGATCAT 57.681 37.500 7.51 0.00 0.00 2.45
4903 6150 6.352516 ACAGACTGGTTATTGGAAGATCATC 58.647 40.000 7.51 0.00 0.00 2.92
4904 6151 6.070021 ACAGACTGGTTATTGGAAGATCATCA 60.070 38.462 7.51 0.00 0.00 3.07
4905 6152 6.259608 CAGACTGGTTATTGGAAGATCATCAC 59.740 42.308 0.00 0.00 0.00 3.06
4906 6153 6.157645 AGACTGGTTATTGGAAGATCATCACT 59.842 38.462 0.00 0.00 0.00 3.41
4908 6155 6.825721 ACTGGTTATTGGAAGATCATCACTTC 59.174 38.462 0.00 0.00 41.79 3.01
4913 6226 9.565213 GTTATTGGAAGATCATCACTTCTTTTG 57.435 33.333 0.00 0.00 42.07 2.44
4981 9471 3.195661 GTTAATACCACGAGAGGCCAAG 58.804 50.000 5.01 0.00 0.00 3.61
4982 9472 1.568504 AATACCACGAGAGGCCAAGA 58.431 50.000 5.01 0.00 0.00 3.02
4983 9473 1.115467 ATACCACGAGAGGCCAAGAG 58.885 55.000 5.01 0.00 0.00 2.85
4984 9474 0.970937 TACCACGAGAGGCCAAGAGG 60.971 60.000 5.01 3.53 38.23 3.69
4985 9475 1.984570 CCACGAGAGGCCAAGAGGA 60.985 63.158 5.01 0.00 36.89 3.71
4986 9476 1.216710 CACGAGAGGCCAAGAGGAC 59.783 63.158 5.01 0.00 46.64 3.85
5057 9547 2.431057 ACTCCTATGGGACGAATGACAC 59.569 50.000 0.00 0.00 36.57 3.67
5070 9560 6.128007 GGACGAATGACACACATAGGAAAATT 60.128 38.462 0.00 0.00 38.38 1.82
5107 9597 4.815308 TCCGAAAATCCTACAAAACGAACA 59.185 37.500 0.00 0.00 0.00 3.18
5136 9637 3.365265 GTTGCCCTCCAAGCACGG 61.365 66.667 0.00 0.00 40.69 4.94
5142 9643 0.179073 CCCTCCAAGCACGGATGTAG 60.179 60.000 0.00 0.00 33.56 2.74
5143 9644 0.537188 CCTCCAAGCACGGATGTAGT 59.463 55.000 0.00 0.00 33.56 2.73
5144 9645 1.754803 CCTCCAAGCACGGATGTAGTA 59.245 52.381 0.00 0.00 33.56 1.82
5159 9660 0.249120 TAGTACATGCGTGCTGCCTT 59.751 50.000 5.64 0.00 45.60 4.35
5168 9669 1.571460 GTGCTGCCTTCTGAACACG 59.429 57.895 0.00 0.00 0.00 4.49
5241 9749 0.532862 AGAAACGGTGTGCTGAGTGG 60.533 55.000 0.00 0.00 0.00 4.00
5243 9751 1.095228 AAACGGTGTGCTGAGTGGTG 61.095 55.000 0.00 0.00 0.00 4.17
5299 9809 0.244721 GCTGGTTTGCAAAGGGCTAG 59.755 55.000 13.26 9.53 45.15 3.42
5300 9810 1.620822 CTGGTTTGCAAAGGGCTAGT 58.379 50.000 13.26 0.00 45.15 2.57
5301 9811 2.790433 CTGGTTTGCAAAGGGCTAGTA 58.210 47.619 13.26 0.00 45.15 1.82
5302 9812 2.488153 CTGGTTTGCAAAGGGCTAGTAC 59.512 50.000 13.26 0.00 45.15 2.73
5303 9813 2.107552 TGGTTTGCAAAGGGCTAGTACT 59.892 45.455 13.26 0.00 45.15 2.73
5304 9814 3.328343 TGGTTTGCAAAGGGCTAGTACTA 59.672 43.478 13.26 1.89 45.15 1.82
5329 9839 4.894784 ACTGAAGAAAAATAGGACTCGCA 58.105 39.130 0.00 0.00 0.00 5.10
5330 9840 4.932200 ACTGAAGAAAAATAGGACTCGCAG 59.068 41.667 0.00 0.00 0.00 5.18
5331 9841 3.684788 TGAAGAAAAATAGGACTCGCAGC 59.315 43.478 0.00 0.00 0.00 5.25
5372 9882 1.457346 CTGCAAAGGGACTGTCCATC 58.543 55.000 26.94 11.68 40.86 3.51
5373 9883 0.770499 TGCAAAGGGACTGTCCATCA 59.230 50.000 26.94 12.61 40.86 3.07
5374 9884 1.144708 TGCAAAGGGACTGTCCATCAA 59.855 47.619 26.94 5.36 40.86 2.57
5375 9885 1.815003 GCAAAGGGACTGTCCATCAAG 59.185 52.381 26.94 14.60 40.86 3.02
5376 9886 2.815589 GCAAAGGGACTGTCCATCAAGT 60.816 50.000 26.94 3.30 40.86 3.16
5377 9887 3.490348 CAAAGGGACTGTCCATCAAGTT 58.510 45.455 26.94 9.54 40.86 2.66
5378 9888 2.867109 AGGGACTGTCCATCAAGTTG 57.133 50.000 26.94 0.00 38.64 3.16
5379 9889 1.168714 GGGACTGTCCATCAAGTTGC 58.831 55.000 26.94 3.83 38.64 4.17
5380 9890 1.271597 GGGACTGTCCATCAAGTTGCT 60.272 52.381 26.94 0.00 38.64 3.91
5381 9891 2.508526 GGACTGTCCATCAAGTTGCTT 58.491 47.619 21.70 0.00 36.28 3.91
5382 9892 2.887152 GGACTGTCCATCAAGTTGCTTT 59.113 45.455 21.70 0.00 36.28 3.51
5383 9893 3.304928 GGACTGTCCATCAAGTTGCTTTG 60.305 47.826 21.70 0.00 36.28 2.77
5384 9894 2.624838 ACTGTCCATCAAGTTGCTTTGG 59.375 45.455 11.14 11.14 0.00 3.28
5385 9895 1.340889 TGTCCATCAAGTTGCTTTGGC 59.659 47.619 12.10 9.13 39.26 4.52
5386 9896 1.615392 GTCCATCAAGTTGCTTTGGCT 59.385 47.619 12.10 0.00 39.59 4.75
5387 9897 2.036346 GTCCATCAAGTTGCTTTGGCTT 59.964 45.455 12.10 0.00 39.59 4.35
5388 9898 2.297033 TCCATCAAGTTGCTTTGGCTTC 59.703 45.455 12.10 0.00 39.59 3.86
5389 9899 2.611224 CCATCAAGTTGCTTTGGCTTCC 60.611 50.000 0.00 0.00 39.59 3.46
5390 9900 0.667993 TCAAGTTGCTTTGGCTTCCG 59.332 50.000 0.00 0.00 39.59 4.30
5391 9901 0.385390 CAAGTTGCTTTGGCTTCCGT 59.615 50.000 0.00 0.00 39.59 4.69
5392 9902 0.668535 AAGTTGCTTTGGCTTCCGTC 59.331 50.000 0.00 0.00 39.59 4.79
5393 9903 1.082104 GTTGCTTTGGCTTCCGTCG 60.082 57.895 0.00 0.00 39.59 5.12
5394 9904 1.227704 TTGCTTTGGCTTCCGTCGA 60.228 52.632 0.00 0.00 39.59 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.695526 TTGTTATCGTTTTAGAGCACTAAACTA 57.304 29.630 14.85 5.34 44.80 2.24
2 3 9.654417 TTTTGTTATCGTTTTAGAGCACTAAAC 57.346 29.630 14.85 9.87 44.80 2.01
21 22 6.783708 ACATCAAACTCCCTTGTTTTGTTA 57.216 33.333 0.00 0.00 37.98 2.41
427 428 3.130340 ACAACAACATTGATAATCCCCGC 59.870 43.478 0.00 0.00 0.00 6.13
463 474 5.106436 GGAATTTTTCCTCGACGTTATGGTT 60.106 40.000 0.00 0.00 46.57 3.67
638 650 0.955428 GCAACGTCTGGGCATCTTCA 60.955 55.000 0.00 0.00 0.00 3.02
646 658 3.139077 AGAGTTTTAAGCAACGTCTGGG 58.861 45.455 0.00 0.00 0.00 4.45
652 664 8.975439 TCTAGAGTTTTAGAGTTTTAAGCAACG 58.025 33.333 0.00 0.00 0.00 4.10
668 680 5.105269 GGAACCTCGGATCTTCTAGAGTTTT 60.105 44.000 0.00 0.00 0.00 2.43
763 786 2.028130 CCTGGCGAATGGATTGAGC 58.972 57.895 0.00 0.00 0.00 4.26
777 800 2.168728 GACCACTTCTACTAAGGCCTGG 59.831 54.545 5.69 5.02 0.00 4.45
846 1360 8.316214 ACATAATGCAGATGTGGAAGAAATTTT 58.684 29.630 14.52 0.00 36.18 1.82
849 1363 7.414222 AACATAATGCAGATGTGGAAGAAAT 57.586 32.000 15.66 0.00 37.59 2.17
869 2020 1.332375 CGTTTCCGTCCACACAAACAT 59.668 47.619 0.00 0.00 0.00 2.71
1103 2260 3.433306 TTGACTGGATTTAGGTGGGTG 57.567 47.619 0.00 0.00 0.00 4.61
1122 2279 6.156256 TCAGGTTGTATGTACTGCTAGGAATT 59.844 38.462 0.00 0.00 0.00 2.17
1365 2522 9.768662 AGCAATGTCAATACAAAGAAGAAAAAT 57.231 25.926 0.00 0.00 39.58 1.82
1424 2581 2.171237 CACTGGTTCCAGATCCTATGCA 59.829 50.000 23.45 0.00 37.49 3.96
1511 2668 3.382546 CAGGTTCCATTTTCCTGGCATAG 59.617 47.826 0.00 0.00 43.30 2.23
1562 2719 7.275888 TGCATATGGTAGGATGAAATGAAAC 57.724 36.000 4.56 0.00 0.00 2.78
1593 2755 1.355720 ACCAAGCTGGCAAGAGGTAAT 59.644 47.619 0.00 0.00 42.67 1.89
1754 2918 4.761739 CCTGAGTTATTGCAAGGAAAGACA 59.238 41.667 4.94 2.85 0.00 3.41
1755 2919 5.003804 TCCTGAGTTATTGCAAGGAAAGAC 58.996 41.667 4.94 0.00 0.00 3.01
1776 2940 3.744660 AGTCAAGTCCATGAGTTGTTCC 58.255 45.455 10.52 2.63 41.92 3.62
1932 3100 6.914665 TCCATAACATCAAGAATGGGAATCT 58.085 36.000 0.00 0.00 39.51 2.40
1933 3101 7.286316 ACTTCCATAACATCAAGAATGGGAATC 59.714 37.037 0.00 0.00 39.51 2.52
2067 3256 7.790782 AGAAGAAGAAGACAGATTTACCTCT 57.209 36.000 0.00 0.00 0.00 3.69
2091 3280 7.992608 TGGCAAAGTATATAGCATGAAGAAGAA 59.007 33.333 0.00 0.00 0.00 2.52
2092 3281 7.508687 TGGCAAAGTATATAGCATGAAGAAGA 58.491 34.615 0.00 0.00 0.00 2.87
2093 3282 7.734924 TGGCAAAGTATATAGCATGAAGAAG 57.265 36.000 0.00 0.00 0.00 2.85
2094 3283 8.570488 CAATGGCAAAGTATATAGCATGAAGAA 58.430 33.333 0.00 0.00 0.00 2.52
2095 3284 7.720957 ACAATGGCAAAGTATATAGCATGAAGA 59.279 33.333 0.00 0.00 0.00 2.87
2096 3285 7.879070 ACAATGGCAAAGTATATAGCATGAAG 58.121 34.615 0.00 0.00 0.00 3.02
2122 3311 3.387374 ATCACAAGATACAGCAGCTAGCT 59.613 43.478 12.68 12.68 43.80 3.32
2176 3365 3.613299 CAGATATCTGTCATCATGAGCGC 59.387 47.826 22.42 0.00 39.09 5.92
2199 3388 9.436957 TGTTCAAAGATCCTATGTTCTTTACTC 57.563 33.333 4.39 0.94 38.07 2.59
2252 3441 6.996879 GTCCCTAGAATTGGGGTATAGAAAAC 59.003 42.308 0.00 0.00 44.67 2.43
2335 3526 4.232221 CGTCATAGTGTAACGTCTTTGGT 58.768 43.478 0.00 0.00 45.86 3.67
2364 3555 1.271379 ACAGGGTGTATGAGGCAACAC 60.271 52.381 0.00 0.00 44.19 3.32
2558 3749 2.755103 TCTACAGATCTCAAAGCTGCGA 59.245 45.455 0.00 0.00 33.03 5.10
2613 3804 1.305201 ACTTACCACAGTTTGTGCCG 58.695 50.000 3.72 0.00 46.51 5.69
2831 4022 1.276622 GGGGGAAAGAGTGCAGACTA 58.723 55.000 0.00 0.00 30.16 2.59
2847 4038 4.622260 ATGAAACTGTTCCAAAATGGGG 57.378 40.909 0.00 0.00 38.32 4.96
2878 4069 7.145932 ACTGTTGATTGTAGAAGTAAATGGC 57.854 36.000 0.00 0.00 0.00 4.40
2984 4177 8.836413 GTTATACAATACAACACTGCCACATAT 58.164 33.333 0.00 0.00 0.00 1.78
2985 4178 8.044309 AGTTATACAATACAACACTGCCACATA 58.956 33.333 0.00 0.00 0.00 2.29
2986 4179 6.884295 AGTTATACAATACAACACTGCCACAT 59.116 34.615 0.00 0.00 0.00 3.21
2987 4180 6.148645 CAGTTATACAATACAACACTGCCACA 59.851 38.462 0.00 0.00 0.00 4.17
2988 4181 6.148811 ACAGTTATACAATACAACACTGCCAC 59.851 38.462 0.00 0.00 34.72 5.01
2989 4182 6.148645 CACAGTTATACAATACAACACTGCCA 59.851 38.462 0.00 0.00 34.72 4.92
2990 4183 6.370442 TCACAGTTATACAATACAACACTGCC 59.630 38.462 0.00 0.00 34.72 4.85
2992 4185 7.117667 TGCTCACAGTTATACAATACAACACTG 59.882 37.037 0.00 0.00 36.93 3.66
2993 4186 7.158697 TGCTCACAGTTATACAATACAACACT 58.841 34.615 0.00 0.00 0.00 3.55
2994 4187 7.359262 TGCTCACAGTTATACAATACAACAC 57.641 36.000 0.00 0.00 0.00 3.32
2995 4188 9.830975 ATATGCTCACAGTTATACAATACAACA 57.169 29.630 0.00 0.00 0.00 3.33
2998 4191 8.773645 GCAATATGCTCACAGTTATACAATACA 58.226 33.333 0.00 0.00 40.96 2.29
3001 4194 7.040892 CCTGCAATATGCTCACAGTTATACAAT 60.041 37.037 3.78 0.00 45.31 2.71
3104 4298 3.558505 CAATGAAGAGACAGTTTTGGCG 58.441 45.455 0.00 0.00 37.43 5.69
3108 4302 5.625150 AGTAGGCAATGAAGAGACAGTTTT 58.375 37.500 0.00 0.00 0.00 2.43
3191 4385 3.126831 GTGAGCATACCTGTAGCATGAC 58.873 50.000 0.00 0.00 0.00 3.06
3210 4404 4.771590 AAAGCAATGGATATATGCGGTG 57.228 40.909 0.00 1.71 44.60 4.94
3211 4405 7.466746 AAATAAAGCAATGGATATATGCGGT 57.533 32.000 0.00 0.00 44.60 5.68
3233 4432 8.250332 GTGATGCCTGACTTTTTATGGATAAAA 58.750 33.333 1.22 1.22 39.65 1.52
3269 4469 6.019762 GGTGCAAGTAAAACTATTAGTTCGC 58.980 40.000 9.45 6.77 37.47 4.70
3360 4562 6.371389 GGAAGAAACTGTTGGAATAGAAACG 58.629 40.000 0.00 0.00 0.00 3.60
3417 4620 2.161609 CACCACTAAATCCTGCGGTTTC 59.838 50.000 0.00 0.00 0.00 2.78
3421 4624 0.748005 CCCACCACTAAATCCTGCGG 60.748 60.000 0.00 0.00 0.00 5.69
3468 4671 2.906389 AGGGTGCTGAGTCATAGAAACA 59.094 45.455 0.00 0.00 0.00 2.83
3843 5048 3.058293 TGACTGCTGCAAAATAAGGAACG 60.058 43.478 3.02 0.00 0.00 3.95
3983 5188 3.325870 CAGCATTCGTTCACTAACCAGA 58.674 45.455 0.00 0.00 31.46 3.86
3996 5201 2.159212 TCCATCCAAAATGCAGCATTCG 60.159 45.455 21.10 14.56 32.43 3.34
4174 5381 8.376889 TGAGAGCATATAATATAGAGAGCGAG 57.623 38.462 0.00 0.00 0.00 5.03
4266 5476 5.941733 TGAAATCCATTCATGAACACTTCG 58.058 37.500 11.07 0.00 43.08 3.79
4390 5600 6.687531 GTGTCTATGATACAGTACACTTCACG 59.312 42.308 0.00 0.00 35.50 4.35
4401 5611 4.632538 TGGTCGTGTGTCTATGATACAG 57.367 45.455 0.00 0.00 34.57 2.74
4411 5621 1.421410 GGATCGCATGGTCGTGTGTC 61.421 60.000 0.00 2.21 0.00 3.67
4419 5650 1.040646 ATCTACACGGATCGCATGGT 58.959 50.000 0.00 0.00 0.00 3.55
4423 5654 5.163784 GCTAATACTATCTACACGGATCGCA 60.164 44.000 0.00 0.00 0.00 5.10
4431 5662 8.879759 TGTTTTGCTTGCTAATACTATCTACAC 58.120 33.333 0.00 0.00 0.00 2.90
4462 5698 2.511659 ACATTTCTGCTGTGCACTCAT 58.488 42.857 19.41 0.00 33.79 2.90
4481 5717 2.731976 CCACTCGCTGTCTGAACTAAAC 59.268 50.000 0.00 0.00 0.00 2.01
4551 5795 2.352960 GCGTCATTGAAGAGTTGATCCC 59.647 50.000 3.64 0.00 0.00 3.85
4563 5807 3.179048 CACACTTCTATCGCGTCATTGA 58.821 45.455 5.77 0.00 0.00 2.57
4570 5814 1.202110 ACGGTACACACTTCTATCGCG 60.202 52.381 0.00 0.00 0.00 5.87
4573 5817 7.311408 AGAAACTAACGGTACACACTTCTATC 58.689 38.462 0.00 0.00 0.00 2.08
4580 5824 3.737774 GTGGAGAAACTAACGGTACACAC 59.262 47.826 0.00 0.00 0.00 3.82
4582 5826 4.248691 AGTGGAGAAACTAACGGTACAC 57.751 45.455 0.00 0.00 0.00 2.90
4589 5833 5.830000 AACAACCAAGTGGAGAAACTAAC 57.170 39.130 3.83 0.00 38.94 2.34
4595 5839 1.754226 GGCAAACAACCAAGTGGAGAA 59.246 47.619 3.83 0.00 38.94 2.87
4599 5843 1.067250 CGGGCAAACAACCAAGTGG 59.933 57.895 0.00 0.00 42.17 4.00
4607 5851 3.254657 CCTTCAAACTATCGGGCAAACAA 59.745 43.478 0.00 0.00 0.00 2.83
4609 5853 3.078837 TCCTTCAAACTATCGGGCAAAC 58.921 45.455 0.00 0.00 0.00 2.93
4610 5854 3.426787 TCCTTCAAACTATCGGGCAAA 57.573 42.857 0.00 0.00 0.00 3.68
4612 5856 2.706890 GTTCCTTCAAACTATCGGGCA 58.293 47.619 0.00 0.00 0.00 5.36
4613 5857 1.664151 CGTTCCTTCAAACTATCGGGC 59.336 52.381 0.00 0.00 0.00 6.13
4614 5858 2.093869 TCCGTTCCTTCAAACTATCGGG 60.094 50.000 0.00 0.00 37.72 5.14
4617 5861 6.396450 AGTACTTCCGTTCCTTCAAACTATC 58.604 40.000 0.00 0.00 0.00 2.08
4618 5862 6.210984 AGAGTACTTCCGTTCCTTCAAACTAT 59.789 38.462 0.00 0.00 0.00 2.12
4619 5863 5.537674 AGAGTACTTCCGTTCCTTCAAACTA 59.462 40.000 0.00 0.00 0.00 2.24
4620 5864 4.344390 AGAGTACTTCCGTTCCTTCAAACT 59.656 41.667 0.00 0.00 0.00 2.66
4621 5865 4.448060 CAGAGTACTTCCGTTCCTTCAAAC 59.552 45.833 0.00 0.00 0.00 2.93
4622 5866 4.628074 CAGAGTACTTCCGTTCCTTCAAA 58.372 43.478 0.00 0.00 0.00 2.69
4624 5868 2.029290 GCAGAGTACTTCCGTTCCTTCA 60.029 50.000 0.00 0.00 0.00 3.02
4625 5869 2.029290 TGCAGAGTACTTCCGTTCCTTC 60.029 50.000 0.00 0.00 0.00 3.46
4626 5870 1.968493 TGCAGAGTACTTCCGTTCCTT 59.032 47.619 0.00 0.00 0.00 3.36
4627 5871 1.629043 TGCAGAGTACTTCCGTTCCT 58.371 50.000 0.00 0.00 0.00 3.36
4628 5872 2.674796 ATGCAGAGTACTTCCGTTCC 57.325 50.000 0.00 0.00 0.00 3.62
4629 5873 3.106672 CGTATGCAGAGTACTTCCGTTC 58.893 50.000 0.00 0.00 0.00 3.95
4630 5874 2.159282 CCGTATGCAGAGTACTTCCGTT 60.159 50.000 0.00 0.00 0.00 4.44
4631 5875 1.404391 CCGTATGCAGAGTACTTCCGT 59.596 52.381 0.00 0.00 0.00 4.69
4632 5876 1.404391 ACCGTATGCAGAGTACTTCCG 59.596 52.381 0.00 0.00 0.00 4.30
4633 5877 3.881688 TCTACCGTATGCAGAGTACTTCC 59.118 47.826 0.00 0.00 0.00 3.46
4634 5878 5.238868 TCATCTACCGTATGCAGAGTACTTC 59.761 44.000 0.00 0.00 0.00 3.01
4635 5879 5.131067 TCATCTACCGTATGCAGAGTACTT 58.869 41.667 0.00 0.00 0.00 2.24
4636 5880 4.715713 TCATCTACCGTATGCAGAGTACT 58.284 43.478 0.00 0.00 0.00 2.73
4637 5881 5.630661 ATCATCTACCGTATGCAGAGTAC 57.369 43.478 0.00 0.00 0.00 2.73
4638 5882 7.281100 CAGATATCATCTACCGTATGCAGAGTA 59.719 40.741 5.32 0.00 37.58 2.59
4639 5883 6.094742 CAGATATCATCTACCGTATGCAGAGT 59.905 42.308 5.32 0.00 37.58 3.24
4640 5884 6.317391 TCAGATATCATCTACCGTATGCAGAG 59.683 42.308 5.32 0.00 37.58 3.35
4641 5885 6.180472 TCAGATATCATCTACCGTATGCAGA 58.820 40.000 5.32 0.00 37.58 4.26
4642 5886 6.442513 TCAGATATCATCTACCGTATGCAG 57.557 41.667 5.32 0.00 37.58 4.41
4643 5887 7.410120 AATCAGATATCATCTACCGTATGCA 57.590 36.000 5.32 0.00 37.58 3.96
4644 5888 9.973450 ATAAATCAGATATCATCTACCGTATGC 57.027 33.333 5.32 0.00 37.58 3.14
4661 5905 9.952188 CAAAGTCTCTGTCGTATATAAATCAGA 57.048 33.333 9.87 9.87 0.00 3.27
4662 5906 9.952188 TCAAAGTCTCTGTCGTATATAAATCAG 57.048 33.333 0.00 0.00 0.00 2.90
4663 5907 9.952188 CTCAAAGTCTCTGTCGTATATAAATCA 57.048 33.333 0.00 0.00 0.00 2.57
4664 5908 9.953697 ACTCAAAGTCTCTGTCGTATATAAATC 57.046 33.333 0.00 0.00 0.00 2.17
4665 5909 9.737427 CACTCAAAGTCTCTGTCGTATATAAAT 57.263 33.333 0.00 0.00 0.00 1.40
4666 5910 8.188799 CCACTCAAAGTCTCTGTCGTATATAAA 58.811 37.037 0.00 0.00 0.00 1.40
4667 5911 7.681304 GCCACTCAAAGTCTCTGTCGTATATAA 60.681 40.741 0.00 0.00 0.00 0.98
4668 5912 6.238676 GCCACTCAAAGTCTCTGTCGTATATA 60.239 42.308 0.00 0.00 0.00 0.86
4669 5913 5.450688 GCCACTCAAAGTCTCTGTCGTATAT 60.451 44.000 0.00 0.00 0.00 0.86
4670 5914 4.142447 GCCACTCAAAGTCTCTGTCGTATA 60.142 45.833 0.00 0.00 0.00 1.47
4671 5915 3.367498 GCCACTCAAAGTCTCTGTCGTAT 60.367 47.826 0.00 0.00 0.00 3.06
4672 5916 2.030185 GCCACTCAAAGTCTCTGTCGTA 60.030 50.000 0.00 0.00 0.00 3.43
4673 5917 1.269831 GCCACTCAAAGTCTCTGTCGT 60.270 52.381 0.00 0.00 0.00 4.34
4674 5918 1.269778 TGCCACTCAAAGTCTCTGTCG 60.270 52.381 0.00 0.00 0.00 4.35
4675 5919 2.411904 CTGCCACTCAAAGTCTCTGTC 58.588 52.381 0.00 0.00 0.00 3.51
4676 5920 1.542108 GCTGCCACTCAAAGTCTCTGT 60.542 52.381 0.00 0.00 0.00 3.41
4677 5921 1.155042 GCTGCCACTCAAAGTCTCTG 58.845 55.000 0.00 0.00 0.00 3.35
4678 5922 0.320247 CGCTGCCACTCAAAGTCTCT 60.320 55.000 0.00 0.00 0.00 3.10
4679 5923 0.319900 TCGCTGCCACTCAAAGTCTC 60.320 55.000 0.00 0.00 0.00 3.36
4680 5924 0.601311 GTCGCTGCCACTCAAAGTCT 60.601 55.000 0.00 0.00 0.00 3.24
4681 5925 0.601311 AGTCGCTGCCACTCAAAGTC 60.601 55.000 0.00 0.00 0.00 3.01
4682 5926 0.882042 CAGTCGCTGCCACTCAAAGT 60.882 55.000 0.00 0.00 0.00 2.66
4683 5927 0.601046 TCAGTCGCTGCCACTCAAAG 60.601 55.000 0.00 0.00 0.00 2.77
4684 5928 0.179059 TTCAGTCGCTGCCACTCAAA 60.179 50.000 0.00 0.00 0.00 2.69
4685 5929 0.179059 TTTCAGTCGCTGCCACTCAA 60.179 50.000 0.00 0.00 0.00 3.02
4686 5930 0.035317 ATTTCAGTCGCTGCCACTCA 59.965 50.000 0.00 0.00 0.00 3.41
4687 5931 2.010145 TATTTCAGTCGCTGCCACTC 57.990 50.000 0.00 0.00 0.00 3.51
4688 5932 2.093500 TCATATTTCAGTCGCTGCCACT 60.093 45.455 0.00 0.00 0.00 4.00
4689 5933 2.030946 GTCATATTTCAGTCGCTGCCAC 59.969 50.000 0.00 0.00 0.00 5.01
4690 5934 2.279741 GTCATATTTCAGTCGCTGCCA 58.720 47.619 0.00 0.00 0.00 4.92
4691 5935 2.279741 TGTCATATTTCAGTCGCTGCC 58.720 47.619 0.00 0.00 0.00 4.85
4692 5936 3.190079 TCTGTCATATTTCAGTCGCTGC 58.810 45.455 2.45 0.00 33.89 5.25
4693 5937 5.784750 TTTCTGTCATATTTCAGTCGCTG 57.215 39.130 1.02 1.02 33.89 5.18
4694 5938 6.344500 AGATTTCTGTCATATTTCAGTCGCT 58.656 36.000 4.49 0.00 33.89 4.93
4695 5939 6.595772 AGATTTCTGTCATATTTCAGTCGC 57.404 37.500 4.49 0.00 33.89 5.19
4698 5942 9.911788 ACCATTAGATTTCTGTCATATTTCAGT 57.088 29.630 4.49 0.00 33.89 3.41
4724 5968 9.537192 CCGATTTGTGTACCATAGTTAGAATTA 57.463 33.333 0.00 0.00 0.00 1.40
4725 5969 8.044908 ACCGATTTGTGTACCATAGTTAGAATT 58.955 33.333 0.00 0.00 0.00 2.17
4726 5970 7.562135 ACCGATTTGTGTACCATAGTTAGAAT 58.438 34.615 0.00 0.00 0.00 2.40
4727 5971 6.938507 ACCGATTTGTGTACCATAGTTAGAA 58.061 36.000 0.00 0.00 0.00 2.10
4728 5972 6.534475 ACCGATTTGTGTACCATAGTTAGA 57.466 37.500 0.00 0.00 0.00 2.10
4729 5973 6.036735 CCAACCGATTTGTGTACCATAGTTAG 59.963 42.308 0.00 0.00 32.71 2.34
4730 5974 5.875910 CCAACCGATTTGTGTACCATAGTTA 59.124 40.000 0.00 0.00 32.71 2.24
4731 5975 4.698304 CCAACCGATTTGTGTACCATAGTT 59.302 41.667 0.00 0.00 32.71 2.24
4732 5976 4.020039 TCCAACCGATTTGTGTACCATAGT 60.020 41.667 0.00 0.00 32.71 2.12
4733 5977 4.509616 TCCAACCGATTTGTGTACCATAG 58.490 43.478 0.00 0.00 32.71 2.23
4734 5978 4.554960 TCCAACCGATTTGTGTACCATA 57.445 40.909 0.00 0.00 32.71 2.74
4735 5979 3.426787 TCCAACCGATTTGTGTACCAT 57.573 42.857 0.00 0.00 32.71 3.55
4736 5980 2.932855 TCCAACCGATTTGTGTACCA 57.067 45.000 0.00 0.00 32.71 3.25
4737 5981 4.276431 TCTTTTCCAACCGATTTGTGTACC 59.724 41.667 0.00 0.00 32.71 3.34
4738 5982 5.427036 TCTTTTCCAACCGATTTGTGTAC 57.573 39.130 0.00 0.00 32.71 2.90
4739 5983 4.023536 GCTCTTTTCCAACCGATTTGTGTA 60.024 41.667 0.00 0.00 32.71 2.90
4740 5984 3.243401 GCTCTTTTCCAACCGATTTGTGT 60.243 43.478 0.00 0.00 32.71 3.72
4741 5985 3.243367 TGCTCTTTTCCAACCGATTTGTG 60.243 43.478 0.00 0.00 32.71 3.33
4742 5986 2.955660 TGCTCTTTTCCAACCGATTTGT 59.044 40.909 0.00 0.00 32.71 2.83
4743 5987 3.004734 ACTGCTCTTTTCCAACCGATTTG 59.995 43.478 0.00 0.00 34.63 2.32
4744 5988 3.004734 CACTGCTCTTTTCCAACCGATTT 59.995 43.478 0.00 0.00 0.00 2.17
4745 5989 2.554032 CACTGCTCTTTTCCAACCGATT 59.446 45.455 0.00 0.00 0.00 3.34
4746 5990 2.154462 CACTGCTCTTTTCCAACCGAT 58.846 47.619 0.00 0.00 0.00 4.18
4747 5991 1.593196 CACTGCTCTTTTCCAACCGA 58.407 50.000 0.00 0.00 0.00 4.69
4748 5992 0.040067 GCACTGCTCTTTTCCAACCG 60.040 55.000 0.00 0.00 0.00 4.44
4749 5993 1.322442 AGCACTGCTCTTTTCCAACC 58.678 50.000 0.00 0.00 30.62 3.77
4760 6004 4.261909 CCATTTTTCTTGAAGAGCACTGCT 60.262 41.667 2.22 2.22 43.88 4.24
4761 6005 3.985925 CCATTTTTCTTGAAGAGCACTGC 59.014 43.478 0.00 0.00 0.00 4.40
4762 6006 3.985925 GCCATTTTTCTTGAAGAGCACTG 59.014 43.478 0.00 0.00 0.00 3.66
4763 6007 3.893813 AGCCATTTTTCTTGAAGAGCACT 59.106 39.130 4.96 0.00 0.00 4.40
4764 6008 4.233005 GAGCCATTTTTCTTGAAGAGCAC 58.767 43.478 4.96 0.00 0.00 4.40
4765 6009 3.256631 GGAGCCATTTTTCTTGAAGAGCA 59.743 43.478 4.96 0.00 0.00 4.26
4766 6010 3.256631 TGGAGCCATTTTTCTTGAAGAGC 59.743 43.478 0.00 0.00 0.00 4.09
4767 6011 4.522022 AGTGGAGCCATTTTTCTTGAAGAG 59.478 41.667 0.00 0.00 0.00 2.85
4768 6012 4.279169 CAGTGGAGCCATTTTTCTTGAAGA 59.721 41.667 0.00 0.00 0.00 2.87
4769 6013 4.279169 TCAGTGGAGCCATTTTTCTTGAAG 59.721 41.667 0.00 0.00 0.00 3.02
4784 6028 1.622811 AGACAAGGCTCTTCAGTGGAG 59.377 52.381 0.00 0.00 0.00 3.86
4789 6033 5.592282 TCTGACTATAGACAAGGCTCTTCAG 59.408 44.000 6.78 5.17 0.00 3.02
4808 6052 4.738124 TGATCTTCGTTCACATCTCTGAC 58.262 43.478 0.00 0.00 0.00 3.51
4809 6053 4.460731 ACTGATCTTCGTTCACATCTCTGA 59.539 41.667 0.00 0.00 0.00 3.27
4814 6058 3.190874 GGGACTGATCTTCGTTCACATC 58.809 50.000 0.00 0.00 0.00 3.06
4885 6132 6.962182 AGAAGTGATGATCTTCCAATAACCA 58.038 36.000 6.17 0.00 41.27 3.67
4902 6149 6.294675 CCAATATTCAGCACCAAAAGAAGTGA 60.295 38.462 0.00 0.00 36.01 3.41
4903 6150 5.865552 CCAATATTCAGCACCAAAAGAAGTG 59.134 40.000 0.00 0.00 37.05 3.16
4904 6151 5.047092 CCCAATATTCAGCACCAAAAGAAGT 60.047 40.000 0.00 0.00 0.00 3.01
4905 6152 5.413499 CCCAATATTCAGCACCAAAAGAAG 58.587 41.667 0.00 0.00 0.00 2.85
4906 6153 4.322650 GCCCAATATTCAGCACCAAAAGAA 60.323 41.667 2.08 0.00 0.00 2.52
4908 6155 3.196254 AGCCCAATATTCAGCACCAAAAG 59.804 43.478 8.53 0.00 0.00 2.27
4913 6226 0.947244 CGAGCCCAATATTCAGCACC 59.053 55.000 8.53 0.76 0.00 5.01
4966 9456 2.286523 CCTCTTGGCCTCTCGTGGT 61.287 63.158 3.32 0.00 0.00 4.16
4989 9479 9.661563 TCGTGTTCATATTGGTCTAATTTAAGT 57.338 29.630 0.00 0.00 0.00 2.24
4992 9482 9.825109 TGATCGTGTTCATATTGGTCTAATTTA 57.175 29.630 0.00 0.00 0.00 1.40
5045 9535 3.520290 TCCTATGTGTGTCATTCGTCC 57.480 47.619 0.00 0.00 37.91 4.79
5107 9597 1.003718 GGGCAACGAGTACAGGCTT 60.004 57.895 0.00 0.00 37.60 4.35
5136 9637 1.258982 GCAGCACGCATGTACTACATC 59.741 52.381 0.00 0.00 36.53 3.06
5142 9643 1.021390 AGAAGGCAGCACGCATGTAC 61.021 55.000 0.00 0.00 45.17 2.90
5143 9644 1.020861 CAGAAGGCAGCACGCATGTA 61.021 55.000 0.00 0.00 45.17 2.29
5144 9645 2.033141 AGAAGGCAGCACGCATGT 59.967 55.556 0.00 0.00 45.17 3.21
5152 9653 2.558313 GCGTGTTCAGAAGGCAGC 59.442 61.111 0.00 0.00 0.00 5.25
5159 9660 0.741574 ACGTGTTTGGCGTGTTCAGA 60.742 50.000 0.00 0.00 41.33 3.27
5168 9669 1.408422 GATTTGCTCACGTGTTTGGC 58.592 50.000 16.51 15.34 0.00 4.52
5259 9767 3.307199 GCTGGTAGCCCTTAACTACACAA 60.307 47.826 3.60 0.00 41.49 3.33
5301 9811 8.460428 CGAGTCCTATTTTTCTTCAGTAGTAGT 58.540 37.037 0.00 0.00 0.00 2.73
5302 9812 7.432838 GCGAGTCCTATTTTTCTTCAGTAGTAG 59.567 40.741 0.00 0.00 0.00 2.57
5303 9813 7.094075 TGCGAGTCCTATTTTTCTTCAGTAGTA 60.094 37.037 0.00 0.00 0.00 1.82
5304 9814 6.100668 GCGAGTCCTATTTTTCTTCAGTAGT 58.899 40.000 0.00 0.00 0.00 2.73
5324 9834 1.450134 TTGGTAGGCATGCTGCGAG 60.450 57.895 18.92 0.00 46.21 5.03
5372 9882 0.385390 ACGGAAGCCAAAGCAACTTG 59.615 50.000 0.00 0.00 43.56 3.16
5373 9883 0.668535 GACGGAAGCCAAAGCAACTT 59.331 50.000 0.00 0.00 43.56 2.66
5374 9884 1.507141 CGACGGAAGCCAAAGCAACT 61.507 55.000 0.00 0.00 43.56 3.16
5375 9885 1.082104 CGACGGAAGCCAAAGCAAC 60.082 57.895 0.00 0.00 43.56 4.17
5376 9886 1.227704 TCGACGGAAGCCAAAGCAA 60.228 52.632 0.00 0.00 43.56 3.91
5377 9887 2.423874 TCGACGGAAGCCAAAGCA 59.576 55.556 0.00 0.00 43.56 3.91


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

AutoCloner maintained by Alex Coulton.