Multiple sequence alignment - TraesCS1B01G313300

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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 TraesCS1B01G313300 chr1B 100.000 4191 0 0 1 4191 536777052 536772862 0.000000e+00 7740.0
1 TraesCS1B01G313300 chr1B 93.372 347 20 1 379 722 647910408 647910062 1.040000e-140 510.0
2 TraesCS1B01G313300 chr1B 88.889 63 7 0 3803 3865 68073372 68073310 1.250000e-10 78.7
3 TraesCS1B01G313300 chr1D 92.372 2635 105 35 772 3373 400066935 400064364 0.000000e+00 3664.0
4 TraesCS1B01G313300 chr1D 93.590 390 23 1 3804 4191 400063574 400063185 7.810000e-162 580.0
5 TraesCS1B01G313300 chr1D 84.211 247 31 3 3521 3759 400064024 400063778 2.520000e-57 233.0
6 TraesCS1B01G313300 chr1D 96.721 61 2 0 774 834 400070207 400070147 7.410000e-18 102.0
7 TraesCS1B01G313300 chr1D 88.889 63 7 0 3803 3865 48391358 48391296 1.250000e-10 78.7
8 TraesCS1B01G313300 chr1A 92.888 2278 107 21 774 3000 496482564 496480291 0.000000e+00 3258.0
9 TraesCS1B01G313300 chr1A 86.631 561 45 9 2828 3373 496480507 496479962 1.000000e-165 593.0
10 TraesCS1B01G313300 chr1A 93.077 390 25 1 3804 4191 496479202 496478813 1.690000e-158 569.0
11 TraesCS1B01G313300 chr1A 84.746 177 21 5 3516 3687 496479563 496479388 5.570000e-39 172.0
12 TraesCS1B01G313300 chr3A 91.678 733 35 2 1 707 514261839 514262571 0.000000e+00 992.0
13 TraesCS1B01G313300 chr3B 94.621 409 18 2 307 711 82309234 82308826 7.650000e-177 630.0
14 TraesCS1B01G313300 chr3B 94.294 333 18 1 379 711 181333915 181334246 3.740000e-140 508.0
15 TraesCS1B01G313300 chr3B 90.390 333 9 2 1 311 82338664 82338333 2.330000e-112 416.0
16 TraesCS1B01G313300 chr7D 96.697 333 11 0 379 711 428708631 428708963 4.730000e-154 555.0
17 TraesCS1B01G313300 chr7D 90.164 61 6 0 3803 3863 494749890 494749950 3.470000e-11 80.5
18 TraesCS1B01G313300 chr3D 94.294 333 19 0 379 711 424472246 424471914 1.040000e-140 510.0
19 TraesCS1B01G313300 chr3D 89.231 65 6 1 3799 3863 71517781 71517844 3.470000e-11 80.5
20 TraesCS1B01G313300 chrUn 95.848 289 9 1 422 707 439380380 439380668 8.210000e-127 464.0
21 TraesCS1B01G313300 chr5D 96.113 283 10 1 429 711 526270064 526269783 1.060000e-125 460.0
22 TraesCS1B01G313300 chr7A 91.592 333 20 2 379 711 364464013 364463689 1.780000e-123 453.0
23 TraesCS1B01G313300 chr7A 90.476 63 5 1 3794 3856 187460737 187460676 9.660000e-12 82.4
24 TraesCS1B01G313300 chr6B 93.103 58 4 0 3802 3859 470793477 470793420 7.470000e-13 86.1
25 TraesCS1B01G313300 chr7B 90.164 61 6 0 3803 3863 522721419 522721479 3.470000e-11 80.5
26 TraesCS1B01G313300 chr2B 89.796 49 4 1 664 711 424379676 424379628 1.260000e-05 62.1


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 TraesCS1B01G313300 chr1B 536772862 536777052 4190 True 7740.00 7740 100.0000 1 4191 1 chr1B.!!$R2 4190
1 TraesCS1B01G313300 chr1D 400063185 400070207 7022 True 1144.75 3664 91.7235 772 4191 4 chr1D.!!$R2 3419
2 TraesCS1B01G313300 chr1A 496478813 496482564 3751 True 1148.00 3258 89.3355 774 4191 4 chr1A.!!$R1 3417
3 TraesCS1B01G313300 chr3A 514261839 514262571 732 False 992.00 992 91.6780 1 707 1 chr3A.!!$F1 706


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
566 593 0.040336 ACTATATGTGAGCCGCGACG 60.040 55.0 8.23 0.0 0.00 5.12 F
1947 5281 0.482446 TGGAGGCAAGTCCATTTGGT 59.518 50.0 0.00 0.0 41.99 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 5497 0.032540 TCATCATCGGCGACATGAGG 59.967 55.0 22.79 19.81 33.48 3.86 R
3226 6606 0.038983 TGCGTGCGTGTACATACAGT 60.039 50.0 0.00 0.00 36.78 3.55 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
23 24 4.070716 GCGAATCCATTCCATGAATCTCT 58.929 43.478 0.00 0.00 33.28 3.10
44 45 4.698304 TCTCCTCTCTCTTTTCTTCTCGTC 59.302 45.833 0.00 0.00 0.00 4.20
99 104 3.118482 TGCAAGTCAATCCTGATCTCTCC 60.118 47.826 0.00 0.00 33.05 3.71
241 268 2.409651 GTGAGCTCGCCTCTACCG 59.590 66.667 16.69 0.00 41.35 4.02
249 276 3.445888 GCCTCTACCGGCCTCTAC 58.554 66.667 0.00 0.00 44.41 2.59
320 347 0.472161 GGAGTACCCCATCCTCCTCC 60.472 65.000 0.00 0.00 41.31 4.30
408 435 2.586079 CACATAGGCGAGCACCGG 60.586 66.667 0.00 0.00 39.04 5.28
566 593 0.040336 ACTATATGTGAGCCGCGACG 60.040 55.000 8.23 0.00 0.00 5.12
617 644 0.974383 GGAAGGAGTGGAAGAACCGA 59.026 55.000 0.00 0.00 42.61 4.69
677 704 1.102978 GAGTGGTGTGGCAGTTTTGT 58.897 50.000 0.00 0.00 0.00 2.83
682 709 2.292016 TGGTGTGGCAGTTTTGTAATCG 59.708 45.455 0.00 0.00 0.00 3.34
689 716 2.668279 GCAGTTTTGTAATCGGGCACAG 60.668 50.000 0.00 0.00 0.00 3.66
707 734 4.582656 GCACAGGGTTGCCAAATACATATA 59.417 41.667 0.00 0.00 36.42 0.86
708 735 5.243730 GCACAGGGTTGCCAAATACATATAT 59.756 40.000 0.00 0.00 36.42 0.86
709 736 6.570378 GCACAGGGTTGCCAAATACATATATC 60.570 42.308 0.00 0.00 36.42 1.63
710 737 5.705441 ACAGGGTTGCCAAATACATATATCG 59.295 40.000 0.00 0.00 0.00 2.92
711 738 5.937540 CAGGGTTGCCAAATACATATATCGA 59.062 40.000 0.00 0.00 0.00 3.59
712 739 6.429692 CAGGGTTGCCAAATACATATATCGAA 59.570 38.462 0.00 0.00 0.00 3.71
713 740 7.121168 CAGGGTTGCCAAATACATATATCGAAT 59.879 37.037 0.00 0.00 0.00 3.34
714 741 7.121168 AGGGTTGCCAAATACATATATCGAATG 59.879 37.037 0.00 0.00 0.00 2.67
715 742 7.094377 GGGTTGCCAAATACATATATCGAATGT 60.094 37.037 6.47 6.47 40.57 2.71
716 743 8.296713 GGTTGCCAAATACATATATCGAATGTT 58.703 33.333 6.54 0.00 38.49 2.71
717 744 9.329913 GTTGCCAAATACATATATCGAATGTTC 57.670 33.333 6.54 0.00 38.49 3.18
718 745 8.614469 TGCCAAATACATATATCGAATGTTCA 57.386 30.769 6.54 0.00 38.49 3.18
719 746 9.061435 TGCCAAATACATATATCGAATGTTCAA 57.939 29.630 6.54 0.00 38.49 2.69
720 747 9.891828 GCCAAATACATATATCGAATGTTCAAA 57.108 29.630 6.54 0.00 38.49 2.69
758 785 9.228949 AGTACAATGTATCCTACTCTATTACGG 57.771 37.037 0.00 0.00 0.00 4.02
759 786 9.224267 GTACAATGTATCCTACTCTATTACGGA 57.776 37.037 0.00 0.00 0.00 4.69
760 787 8.338072 ACAATGTATCCTACTCTATTACGGAG 57.662 38.462 0.00 0.00 36.92 4.63
762 789 9.445878 CAATGTATCCTACTCTATTACGGAGTA 57.554 37.037 0.00 0.00 45.11 2.59
789 816 7.123160 TGATTACGAATGAAAATTCACGTCA 57.877 32.000 13.01 5.67 39.53 4.35
848 4149 1.070038 CTAAAAACGCGGGCGAGTTA 58.930 50.000 20.98 12.47 42.83 2.24
1460 4769 1.410882 CTTTCTCCCATCTCCTCCGTC 59.589 57.143 0.00 0.00 0.00 4.79
1475 4784 3.115892 GTCGCCGTTGCCGAATCA 61.116 61.111 0.00 0.00 36.36 2.57
1604 4913 0.959553 AAGACGAGACGAAGCAAGGA 59.040 50.000 0.00 0.00 0.00 3.36
1667 4976 1.783250 AAAGTGCCCCCACAGAGGAG 61.783 60.000 0.00 0.00 44.53 3.69
1743 5056 4.776837 ACCTGTTCCATGGAAATATGCAAA 59.223 37.500 28.64 0.10 35.75 3.68
1744 5057 5.426185 ACCTGTTCCATGGAAATATGCAAAT 59.574 36.000 28.64 9.72 35.75 2.32
1745 5058 5.756347 CCTGTTCCATGGAAATATGCAAATG 59.244 40.000 28.64 10.07 35.75 2.32
1747 5060 5.104859 TGTTCCATGGAAATATGCAAATGCT 60.105 36.000 28.64 0.00 37.65 3.79
1748 5061 4.951254 TCCATGGAAATATGCAAATGCTG 58.049 39.130 13.46 0.00 42.66 4.41
1808 5137 2.040278 CCTCCCAACATTTCTCACCTCA 59.960 50.000 0.00 0.00 0.00 3.86
1876 5210 1.142097 GAGAGCCCTACGTTCCAGC 59.858 63.158 0.00 0.00 0.00 4.85
1940 5274 3.984193 ATGCGCTGGAGGCAAGTCC 62.984 63.158 9.73 0.00 44.66 3.85
1941 5275 4.704833 GCGCTGGAGGCAAGTCCA 62.705 66.667 0.00 2.06 44.82 4.02
1947 5281 0.482446 TGGAGGCAAGTCCATTTGGT 59.518 50.000 0.00 0.00 41.99 3.67
1955 5290 4.020662 GGCAAGTCCATTTGGTTAATTCCA 60.021 41.667 0.00 0.00 36.34 3.53
1960 5295 3.192422 TCCATTTGGTTAATTCCAGCGTG 59.808 43.478 0.00 0.00 38.80 5.34
1961 5296 3.510719 CATTTGGTTAATTCCAGCGTGG 58.489 45.455 0.00 0.00 38.80 4.94
1965 5311 1.448985 GTTAATTCCAGCGTGGCAGA 58.551 50.000 0.00 0.00 37.47 4.26
2253 5604 2.093921 CGTTGGTGTTGGGGTTTCTTTT 60.094 45.455 0.00 0.00 0.00 2.27
2264 5616 7.290248 TGTTGGGGTTTCTTTTGTTATGGAATA 59.710 33.333 0.00 0.00 0.00 1.75
2274 5626 6.683974 TTTGTTATGGAATAAGAGCAGCTC 57.316 37.500 15.25 15.25 39.94 4.09
2525 5877 4.560716 CGTACTCCTGAAAGACATGGTTGA 60.561 45.833 0.00 0.00 34.07 3.18
2689 6045 2.091610 AGAGGACATCATCGAGGAGGAA 60.092 50.000 19.38 0.00 0.00 3.36
2740 6099 4.252570 AGAAGAATACGAGGAGGAGGAA 57.747 45.455 0.00 0.00 0.00 3.36
2807 6169 2.268920 CCCCCTCACATCACACCG 59.731 66.667 0.00 0.00 0.00 4.94
2887 6249 2.610859 GCCCCCAAGTCTCCCTCA 60.611 66.667 0.00 0.00 0.00 3.86
2889 6251 1.538876 CCCCCAAGTCTCCCTCACA 60.539 63.158 0.00 0.00 0.00 3.58
2899 6261 2.509336 CCCTCACATCGCACCGAC 60.509 66.667 0.00 0.00 39.18 4.79
2905 6267 1.670730 ACATCGCACCGACAATGCA 60.671 52.632 0.00 0.00 43.57 3.96
2946 6308 4.717629 CTCTCGCCGCACCGACAA 62.718 66.667 0.00 0.00 33.12 3.18
2947 6309 3.989698 CTCTCGCCGCACCGACAAT 62.990 63.158 0.00 0.00 33.12 2.71
2948 6310 3.853330 CTCGCCGCACCGACAATG 61.853 66.667 0.00 0.00 33.12 2.82
2949 6311 4.673298 TCGCCGCACCGACAATGT 62.673 61.111 0.00 0.00 31.36 2.71
2950 6312 4.444024 CGCCGCACCGACAATGTG 62.444 66.667 0.00 0.00 36.79 3.21
2955 6317 4.063529 CACCGACAATGTGCCAGT 57.936 55.556 0.00 0.00 0.00 4.00
2956 6318 2.330254 CACCGACAATGTGCCAGTT 58.670 52.632 0.00 0.00 0.00 3.16
2957 6319 1.518325 CACCGACAATGTGCCAGTTA 58.482 50.000 0.00 0.00 0.00 2.24
2958 6320 1.196808 CACCGACAATGTGCCAGTTAC 59.803 52.381 0.00 0.00 0.00 2.50
2959 6321 1.071699 ACCGACAATGTGCCAGTTACT 59.928 47.619 0.00 0.00 0.00 2.24
2960 6322 1.464608 CCGACAATGTGCCAGTTACTG 59.535 52.381 5.22 5.22 0.00 2.74
2961 6323 2.143122 CGACAATGTGCCAGTTACTGT 58.857 47.619 11.68 0.00 0.00 3.55
2962 6324 2.157668 CGACAATGTGCCAGTTACTGTC 59.842 50.000 11.68 0.00 0.00 3.51
3057 6434 0.749091 AGCACAGACAACAGCAGCAA 60.749 50.000 0.00 0.00 0.00 3.91
3213 6593 1.801309 GCGGCCTTTGGTGTTTGCTA 61.801 55.000 0.00 0.00 0.00 3.49
3367 6747 5.982356 TGGATCTGTGATTCTTAGTTCCTG 58.018 41.667 13.86 0.00 33.48 3.86
3370 6750 6.705381 GGATCTGTGATTCTTAGTTCCTGATG 59.295 42.308 0.00 0.00 30.94 3.07
3371 6751 6.611613 TCTGTGATTCTTAGTTCCTGATGT 57.388 37.500 0.00 0.00 0.00 3.06
3372 6752 7.718334 TCTGTGATTCTTAGTTCCTGATGTA 57.282 36.000 0.00 0.00 0.00 2.29
3373 6753 7.776107 TCTGTGATTCTTAGTTCCTGATGTAG 58.224 38.462 0.00 0.00 0.00 2.74
3375 6755 5.755861 GTGATTCTTAGTTCCTGATGTAGGC 59.244 44.000 0.00 0.00 46.87 3.93
3376 6756 4.755266 TTCTTAGTTCCTGATGTAGGCC 57.245 45.455 0.00 0.00 46.87 5.19
3377 6757 3.039011 TCTTAGTTCCTGATGTAGGCCC 58.961 50.000 0.00 0.00 46.87 5.80
3378 6758 2.868964 TAGTTCCTGATGTAGGCCCT 57.131 50.000 0.00 0.00 46.87 5.19
3379 6759 1.207791 AGTTCCTGATGTAGGCCCTG 58.792 55.000 0.00 0.00 46.87 4.45
3380 6760 0.912486 GTTCCTGATGTAGGCCCTGT 59.088 55.000 0.00 0.00 46.87 4.00
3381 6761 1.282157 GTTCCTGATGTAGGCCCTGTT 59.718 52.381 0.00 0.00 46.87 3.16
3382 6762 1.204146 TCCTGATGTAGGCCCTGTTC 58.796 55.000 0.00 0.00 46.87 3.18
3383 6763 0.179073 CCTGATGTAGGCCCTGTTCG 60.179 60.000 0.00 0.00 40.38 3.95
3384 6764 0.179073 CTGATGTAGGCCCTGTTCGG 60.179 60.000 0.00 0.00 0.00 4.30
3385 6765 0.907704 TGATGTAGGCCCTGTTCGGT 60.908 55.000 0.00 0.00 0.00 4.69
3386 6766 1.117150 GATGTAGGCCCTGTTCGGTA 58.883 55.000 0.00 0.00 0.00 4.02
3387 6767 1.483415 GATGTAGGCCCTGTTCGGTAA 59.517 52.381 0.00 0.00 0.00 2.85
3388 6768 1.575419 TGTAGGCCCTGTTCGGTAAT 58.425 50.000 0.00 0.00 0.00 1.89
3389 6769 1.483415 TGTAGGCCCTGTTCGGTAATC 59.517 52.381 0.00 0.00 0.00 1.75
3390 6770 1.483415 GTAGGCCCTGTTCGGTAATCA 59.517 52.381 0.00 0.00 0.00 2.57
3391 6771 1.213296 AGGCCCTGTTCGGTAATCAT 58.787 50.000 0.00 0.00 0.00 2.45
3392 6772 1.141053 AGGCCCTGTTCGGTAATCATC 59.859 52.381 0.00 0.00 0.00 2.92
3393 6773 1.594331 GCCCTGTTCGGTAATCATCC 58.406 55.000 0.00 0.00 0.00 3.51
3395 6775 1.217882 CCTGTTCGGTAATCATCCGC 58.782 55.000 0.00 0.00 46.49 5.54
3396 6776 1.202533 CCTGTTCGGTAATCATCCGCT 60.203 52.381 0.00 0.00 46.49 5.52
3397 6777 2.128035 CTGTTCGGTAATCATCCGCTC 58.872 52.381 0.00 0.00 46.49 5.03
3398 6778 1.202486 TGTTCGGTAATCATCCGCTCC 60.202 52.381 0.00 0.00 46.49 4.70
3399 6779 1.068741 GTTCGGTAATCATCCGCTCCT 59.931 52.381 0.00 0.00 46.49 3.69
3400 6780 0.673985 TCGGTAATCATCCGCTCCTG 59.326 55.000 0.00 0.00 46.49 3.86
3401 6781 0.319900 CGGTAATCATCCGCTCCTGG 60.320 60.000 0.00 0.00 41.48 4.45
3402 6782 1.048601 GGTAATCATCCGCTCCTGGA 58.951 55.000 0.00 0.00 43.58 3.86
3403 6783 1.416401 GGTAATCATCCGCTCCTGGAA 59.584 52.381 0.00 0.00 42.46 3.53
3404 6784 2.039084 GGTAATCATCCGCTCCTGGAAT 59.961 50.000 0.00 0.00 42.46 3.01
3405 6785 2.557920 AATCATCCGCTCCTGGAATC 57.442 50.000 0.00 0.00 42.46 2.52
3406 6786 1.727062 ATCATCCGCTCCTGGAATCT 58.273 50.000 0.00 0.00 42.46 2.40
3407 6787 0.755079 TCATCCGCTCCTGGAATCTG 59.245 55.000 0.00 0.00 42.46 2.90
3408 6788 0.883814 CATCCGCTCCTGGAATCTGC 60.884 60.000 0.00 0.00 42.46 4.26
3409 6789 1.340399 ATCCGCTCCTGGAATCTGCA 61.340 55.000 0.00 0.00 42.46 4.41
3410 6790 1.523258 CCGCTCCTGGAATCTGCAG 60.523 63.158 7.63 7.63 35.43 4.41
3411 6791 1.519246 CGCTCCTGGAATCTGCAGA 59.481 57.895 20.79 20.79 38.14 4.26
3412 6792 0.530211 CGCTCCTGGAATCTGCAGAG 60.530 60.000 22.96 7.76 38.14 3.35
3413 6793 0.814812 GCTCCTGGAATCTGCAGAGC 60.815 60.000 22.96 15.89 38.14 4.09
3414 6794 0.540454 CTCCTGGAATCTGCAGAGCA 59.460 55.000 22.96 0.00 38.14 4.26
3431 6811 3.461843 CAGAAAACTGCAACTCCGC 57.538 52.632 0.00 0.00 0.00 5.54
3432 6812 0.040067 CAGAAAACTGCAACTCCGCC 60.040 55.000 0.00 0.00 0.00 6.13
3433 6813 0.465460 AGAAAACTGCAACTCCGCCA 60.465 50.000 0.00 0.00 0.00 5.69
3434 6814 0.598065 GAAAACTGCAACTCCGCCAT 59.402 50.000 0.00 0.00 0.00 4.40
3435 6815 1.000274 GAAAACTGCAACTCCGCCATT 60.000 47.619 0.00 0.00 0.00 3.16
3436 6816 0.598065 AAACTGCAACTCCGCCATTC 59.402 50.000 0.00 0.00 0.00 2.67
3437 6817 0.250901 AACTGCAACTCCGCCATTCT 60.251 50.000 0.00 0.00 0.00 2.40
3438 6818 0.957395 ACTGCAACTCCGCCATTCTG 60.957 55.000 0.00 0.00 0.00 3.02
3439 6819 0.674581 CTGCAACTCCGCCATTCTGA 60.675 55.000 0.00 0.00 0.00 3.27
3440 6820 0.250684 TGCAACTCCGCCATTCTGAA 60.251 50.000 0.00 0.00 0.00 3.02
3441 6821 0.169009 GCAACTCCGCCATTCTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
3442 6822 1.813513 CAACTCCGCCATTCTGAACT 58.186 50.000 0.00 0.00 0.00 3.01
3443 6823 1.466167 CAACTCCGCCATTCTGAACTG 59.534 52.381 0.00 0.00 0.00 3.16
3444 6824 0.687354 ACTCCGCCATTCTGAACTGT 59.313 50.000 0.00 0.00 0.00 3.55
3445 6825 1.899814 ACTCCGCCATTCTGAACTGTA 59.100 47.619 0.00 0.00 0.00 2.74
3446 6826 2.093973 ACTCCGCCATTCTGAACTGTAG 60.094 50.000 0.00 0.00 0.00 2.74
3447 6827 1.009829 CCGCCATTCTGAACTGTAGC 58.990 55.000 0.00 0.00 0.00 3.58
3448 6828 1.406069 CCGCCATTCTGAACTGTAGCT 60.406 52.381 0.00 0.00 0.00 3.32
3449 6829 1.929836 CGCCATTCTGAACTGTAGCTC 59.070 52.381 0.00 0.00 0.00 4.09
3450 6830 2.284190 GCCATTCTGAACTGTAGCTCC 58.716 52.381 0.00 0.00 0.00 4.70
3451 6831 2.911484 CCATTCTGAACTGTAGCTCCC 58.089 52.381 0.00 0.00 0.00 4.30
3452 6832 2.420687 CCATTCTGAACTGTAGCTCCCC 60.421 54.545 0.00 0.00 0.00 4.81
3453 6833 1.276622 TTCTGAACTGTAGCTCCCCC 58.723 55.000 0.00 0.00 0.00 5.40
3454 6834 0.116342 TCTGAACTGTAGCTCCCCCA 59.884 55.000 0.00 0.00 0.00 4.96
3455 6835 0.984230 CTGAACTGTAGCTCCCCCAA 59.016 55.000 0.00 0.00 0.00 4.12
3456 6836 0.690762 TGAACTGTAGCTCCCCCAAC 59.309 55.000 0.00 0.00 0.00 3.77
3457 6837 0.984995 GAACTGTAGCTCCCCCAACT 59.015 55.000 0.00 0.00 0.00 3.16
3458 6838 0.984995 AACTGTAGCTCCCCCAACTC 59.015 55.000 0.00 0.00 0.00 3.01
3459 6839 0.910088 ACTGTAGCTCCCCCAACTCC 60.910 60.000 0.00 0.00 0.00 3.85
3460 6840 1.961180 CTGTAGCTCCCCCAACTCCG 61.961 65.000 0.00 0.00 0.00 4.63
3461 6841 3.081409 TAGCTCCCCCAACTCCGC 61.081 66.667 0.00 0.00 0.00 5.54
3462 6842 3.618855 TAGCTCCCCCAACTCCGCT 62.619 63.158 0.00 0.00 0.00 5.52
3463 6843 4.785453 GCTCCCCCAACTCCGCTG 62.785 72.222 0.00 0.00 0.00 5.18
3464 6844 4.785453 CTCCCCCAACTCCGCTGC 62.785 72.222 0.00 0.00 0.00 5.25
3477 6857 4.344865 GCTGCCGGAGTTGGGGAA 62.345 66.667 5.05 0.00 0.00 3.97
3478 6858 2.359975 CTGCCGGAGTTGGGGAAC 60.360 66.667 5.05 0.00 0.00 3.62
3479 6859 4.323477 TGCCGGAGTTGGGGAACG 62.323 66.667 5.05 0.00 0.00 3.95
3482 6862 2.264794 CGGAGTTGGGGAACGGAG 59.735 66.667 0.00 0.00 0.00 4.63
3483 6863 2.046217 GGAGTTGGGGAACGGAGC 60.046 66.667 0.00 0.00 0.00 4.70
3484 6864 2.434359 GAGTTGGGGAACGGAGCG 60.434 66.667 0.00 0.00 0.00 5.03
3485 6865 2.920912 AGTTGGGGAACGGAGCGA 60.921 61.111 0.00 0.00 0.00 4.93
3486 6866 2.240162 GAGTTGGGGAACGGAGCGAT 62.240 60.000 0.00 0.00 0.00 4.58
3487 6867 0.974010 AGTTGGGGAACGGAGCGATA 60.974 55.000 0.00 0.00 0.00 2.92
3488 6868 0.808847 GTTGGGGAACGGAGCGATAC 60.809 60.000 0.00 0.00 0.00 2.24
3489 6869 1.963464 TTGGGGAACGGAGCGATACC 61.963 60.000 0.00 0.00 0.00 2.73
3496 6876 4.014065 GGAGCGATACCGAACAGC 57.986 61.111 0.00 0.00 38.22 4.40
3497 6877 1.141019 GGAGCGATACCGAACAGCA 59.859 57.895 0.00 0.00 38.22 4.41
3498 6878 1.146358 GGAGCGATACCGAACAGCAC 61.146 60.000 0.00 0.00 38.22 4.40
3499 6879 0.457853 GAGCGATACCGAACAGCACA 60.458 55.000 0.00 0.00 38.22 4.57
3514 6894 6.972901 CGAACAGCACAGTAATATCAACTCTA 59.027 38.462 0.00 0.00 0.00 2.43
3515 6895 7.166638 CGAACAGCACAGTAATATCAACTCTAG 59.833 40.741 0.00 0.00 0.00 2.43
3516 6896 6.276847 ACAGCACAGTAATATCAACTCTAGC 58.723 40.000 0.00 0.00 0.00 3.42
3517 6897 6.127338 ACAGCACAGTAATATCAACTCTAGCA 60.127 38.462 0.00 0.00 0.00 3.49
3518 6898 6.420306 CAGCACAGTAATATCAACTCTAGCAG 59.580 42.308 0.00 0.00 0.00 4.24
3536 7310 8.621532 TCTAGCAGAAACACATAAAACTTCAT 57.378 30.769 0.00 0.00 0.00 2.57
3553 7327 6.259550 ACTTCATCTACAGATTTTGGTTGC 57.740 37.500 0.00 0.00 31.21 4.17
3565 7339 4.320608 TTTTGGTTGCTCCATTCAGAAC 57.679 40.909 2.36 0.00 46.60 3.01
3566 7340 1.909700 TGGTTGCTCCATTCAGAACC 58.090 50.000 0.00 0.00 41.93 3.62
3568 7342 1.541588 GGTTGCTCCATTCAGAACCAC 59.458 52.381 0.00 0.00 36.79 4.16
3622 7397 1.896220 CCAGTTTAAGGCAGCTGTGA 58.104 50.000 16.64 0.00 0.00 3.58
3623 7398 2.440409 CCAGTTTAAGGCAGCTGTGAT 58.560 47.619 16.64 4.04 0.00 3.06
3626 7401 4.458989 CCAGTTTAAGGCAGCTGTGATAAA 59.541 41.667 16.64 14.19 0.00 1.40
3634 7409 2.159393 GCAGCTGTGATAAATGCGGAAA 60.159 45.455 16.64 0.00 0.00 3.13
3637 7412 3.316308 AGCTGTGATAAATGCGGAAATCC 59.684 43.478 0.00 0.00 0.00 3.01
3663 7440 3.706600 AACGTTGCCCCTACAATTAGA 57.293 42.857 0.00 0.00 0.00 2.10
3666 7443 3.754850 ACGTTGCCCCTACAATTAGAAAC 59.245 43.478 0.00 0.00 0.00 2.78
3667 7444 3.181514 CGTTGCCCCTACAATTAGAAACG 60.182 47.826 0.00 0.00 0.00 3.60
3668 7445 2.993937 TGCCCCTACAATTAGAAACGG 58.006 47.619 0.00 0.00 0.00 4.44
3669 7446 2.572556 TGCCCCTACAATTAGAAACGGA 59.427 45.455 0.00 0.00 0.00 4.69
3670 7447 3.201266 TGCCCCTACAATTAGAAACGGAT 59.799 43.478 0.00 0.00 0.00 4.18
3671 7448 3.564225 GCCCCTACAATTAGAAACGGATG 59.436 47.826 0.00 0.00 0.00 3.51
3672 7449 3.564225 CCCCTACAATTAGAAACGGATGC 59.436 47.826 0.00 0.00 0.00 3.91
3673 7450 4.451900 CCCTACAATTAGAAACGGATGCT 58.548 43.478 0.00 0.00 0.00 3.79
3676 7453 6.540914 CCCTACAATTAGAAACGGATGCTTTA 59.459 38.462 0.00 0.00 0.00 1.85
3677 7454 7.254795 CCCTACAATTAGAAACGGATGCTTTAG 60.255 40.741 0.00 0.00 0.00 1.85
3679 7456 7.865706 ACAATTAGAAACGGATGCTTTAGAT 57.134 32.000 0.00 0.00 0.00 1.98
3695 7633 9.844257 ATGCTTTAGATTAATGTTAGAAGCTCT 57.156 29.630 19.31 10.55 39.08 4.09
3700 7638 9.587772 TTAGATTAATGTTAGAAGCTCTCACAC 57.412 33.333 0.00 0.00 33.93 3.82
3715 7653 2.990479 CACCAGGTGGGGTCTAGC 59.010 66.667 12.40 0.00 39.79 3.42
3719 7657 1.550130 CCAGGTGGGGTCTAGCGAAA 61.550 60.000 0.00 0.00 0.00 3.46
3723 7661 1.202545 GGTGGGGTCTAGCGAAAGATC 60.203 57.143 0.00 0.00 0.00 2.75
3749 7687 3.433306 AGGCAAGCCTTACACAATGTA 57.567 42.857 8.02 0.00 45.70 2.29
3760 7698 2.699954 ACACAATGTAAGAAGCTCCGG 58.300 47.619 0.00 0.00 0.00 5.14
3761 7699 2.009774 CACAATGTAAGAAGCTCCGGG 58.990 52.381 0.00 0.00 0.00 5.73
3763 7701 2.304761 ACAATGTAAGAAGCTCCGGGAA 59.695 45.455 0.00 0.00 0.00 3.97
3764 7702 3.244770 ACAATGTAAGAAGCTCCGGGAAA 60.245 43.478 0.00 0.00 0.00 3.13
3765 7703 2.762535 TGTAAGAAGCTCCGGGAAAG 57.237 50.000 0.00 0.00 0.00 2.62
3767 7705 1.553704 GTAAGAAGCTCCGGGAAAGGA 59.446 52.381 0.00 0.00 38.80 3.36
3769 7707 1.290134 AGAAGCTCCGGGAAAGGATT 58.710 50.000 0.00 0.00 39.96 3.01
3770 7708 2.478292 AGAAGCTCCGGGAAAGGATTA 58.522 47.619 0.00 0.00 39.96 1.75
3774 7733 2.299297 AGCTCCGGGAAAGGATTATACG 59.701 50.000 0.00 0.00 39.96 3.06
3798 7757 0.323725 AGCCTTACCCCAGTGCAATG 60.324 55.000 7.29 7.29 0.00 2.82
3799 7758 0.611896 GCCTTACCCCAGTGCAATGT 60.612 55.000 13.82 0.00 0.00 2.71
3800 7759 1.923356 CCTTACCCCAGTGCAATGTT 58.077 50.000 13.82 0.00 0.00 2.71
3801 7760 2.882229 GCCTTACCCCAGTGCAATGTTA 60.882 50.000 13.82 0.00 0.00 2.41
3802 7761 3.016736 CCTTACCCCAGTGCAATGTTAG 58.983 50.000 13.82 3.66 0.00 2.34
3839 7810 1.939838 GCACAAGTGGGGAGTACTTCG 60.940 57.143 0.00 0.00 36.29 3.79
3840 7811 1.343465 CACAAGTGGGGAGTACTTCGT 59.657 52.381 0.00 0.00 36.29 3.85
3842 7813 0.886563 AAGTGGGGAGTACTTCGTCG 59.113 55.000 0.00 0.00 33.28 5.12
3859 7830 4.552365 GCTGCGCCAGGCCTATCA 62.552 66.667 3.98 0.00 42.61 2.15
3882 7853 3.000041 TCAAACGCTCACATCCATACAC 59.000 45.455 0.00 0.00 0.00 2.90
3889 7860 3.553511 GCTCACATCCATACACGAGAAAG 59.446 47.826 0.00 0.00 0.00 2.62
3931 7904 3.668447 TCAGCTCTGGTCAGAACAATTC 58.332 45.455 2.13 0.00 36.94 2.17
4025 7998 2.571212 ACACCACACATTGTTCACGAT 58.429 42.857 0.00 0.00 0.00 3.73
4035 8008 4.761739 ACATTGTTCACGATCAATCAAGGT 59.238 37.500 0.00 0.00 32.85 3.50
4106 8079 8.433421 AACTTTAGGTACACATTATTCATCCG 57.567 34.615 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.399219 TGACGAGAAGAAAAGAGAGAGGA 58.601 43.478 0.00 0.00 0.00 3.71
44 45 1.851021 TTGATTCGCCGGTGCAGTTG 61.851 55.000 11.05 0.00 37.32 3.16
99 104 4.158579 GCTTGGTAAGAAAAGGAAGGATGG 59.841 45.833 0.00 0.00 0.00 3.51
224 251 2.409651 CGGTAGAGGCGAGCTCAC 59.590 66.667 15.40 3.30 0.00 3.51
536 563 1.113517 ACATATAGTGGTCGCCGCCT 61.114 55.000 5.92 0.84 33.99 5.52
636 663 1.191489 TGTCCCTTCGGTCAGCATCA 61.191 55.000 0.00 0.00 0.00 3.07
642 669 2.203523 TCGGTGTCCCTTCGGTCA 60.204 61.111 0.00 0.00 0.00 4.02
645 672 2.261671 CACTCGGTGTCCCTTCGG 59.738 66.667 0.00 0.00 0.00 4.30
677 704 1.377987 GCAACCCTGTGCCCGATTA 60.378 57.895 0.00 0.00 38.66 1.75
689 716 6.811253 TTCGATATATGTATTTGGCAACCC 57.189 37.500 0.00 0.00 0.00 4.11
732 759 9.228949 CCGTAATAGAGTAGGATACATTGTACT 57.771 37.037 0.00 0.00 46.26 2.73
733 760 9.224267 TCCGTAATAGAGTAGGATACATTGTAC 57.776 37.037 0.00 0.00 46.26 2.90
734 761 9.445878 CTCCGTAATAGAGTAGGATACATTGTA 57.554 37.037 0.00 0.00 46.26 2.41
735 762 7.943447 ACTCCGTAATAGAGTAGGATACATTGT 59.057 37.037 0.00 0.00 46.26 2.71
736 763 8.338072 ACTCCGTAATAGAGTAGGATACATTG 57.662 38.462 0.00 0.00 46.26 2.82
747 774 9.881649 TCGTAATCATATACTCCGTAATAGAGT 57.118 33.333 0.00 0.00 46.22 3.24
755 782 9.706691 ATTTTCATTCGTAATCATATACTCCGT 57.293 29.630 0.00 0.00 0.00 4.69
762 789 9.864034 GACGTGAATTTTCATTCGTAATCATAT 57.136 29.630 0.00 0.00 41.77 1.78
763 790 8.874816 TGACGTGAATTTTCATTCGTAATCATA 58.125 29.630 0.00 0.00 41.77 2.15
764 791 7.747888 TGACGTGAATTTTCATTCGTAATCAT 58.252 30.769 0.00 0.00 41.77 2.45
765 792 7.123160 TGACGTGAATTTTCATTCGTAATCA 57.877 32.000 0.00 2.32 41.77 2.57
766 793 8.429739 TTTGACGTGAATTTTCATTCGTAATC 57.570 30.769 0.00 0.29 41.77 1.75
767 794 8.789881 TTTTGACGTGAATTTTCATTCGTAAT 57.210 26.923 0.00 0.00 41.77 1.89
768 795 8.525071 GTTTTTGACGTGAATTTTCATTCGTAA 58.475 29.630 0.00 0.70 41.77 3.18
769 796 7.097369 CGTTTTTGACGTGAATTTTCATTCGTA 60.097 33.333 0.00 0.00 46.49 3.43
770 797 6.290851 CGTTTTTGACGTGAATTTTCATTCGT 60.291 34.615 8.21 8.21 46.49 3.85
771 798 6.049651 CGTTTTTGACGTGAATTTTCATTCG 58.950 36.000 0.00 0.00 46.49 3.34
789 816 1.782028 GCACCCGTCTGCTCGTTTTT 61.782 55.000 0.00 0.00 34.06 1.94
848 4149 0.321298 ATGGCCGTTGCTTCGTAACT 60.321 50.000 0.00 0.00 37.74 2.24
1218 4522 2.764128 GGGGACGAGGAGGATGCA 60.764 66.667 0.00 0.00 0.00 3.96
1360 4667 0.108329 GTCGACGTGATGGGGTCATT 60.108 55.000 0.00 0.00 39.48 2.57
1361 4668 1.515954 GTCGACGTGATGGGGTCAT 59.484 57.895 0.00 0.00 39.48 3.06
1604 4913 3.971702 GCCAGAAGCCCCCACAGT 61.972 66.667 0.00 0.00 34.35 3.55
1631 4940 0.248012 TTTCGTCGAGCATGGCCTTA 59.752 50.000 3.32 0.00 0.00 2.69
1687 4996 2.821366 GACTGCCGGCTGATGTGG 60.821 66.667 36.36 15.54 0.00 4.17
1745 5058 0.737219 GATGACATGGTGAAGGCAGC 59.263 55.000 0.00 0.00 42.72 5.25
1747 5060 0.697658 TGGATGACATGGTGAAGGCA 59.302 50.000 0.00 0.00 0.00 4.75
1748 5061 1.098050 GTGGATGACATGGTGAAGGC 58.902 55.000 0.00 0.00 0.00 4.35
1750 5063 2.026915 TGGAGTGGATGACATGGTGAAG 60.027 50.000 0.00 0.00 0.00 3.02
1808 5137 2.612672 CGTGATTGAGCTTGCTGATGAT 59.387 45.455 0.00 0.00 0.00 2.45
1893 5227 0.744771 GCCCTCCCATGTCGAACTTC 60.745 60.000 0.00 0.00 0.00 3.01
1940 5274 3.510719 CCACGCTGGAATTAACCAAATG 58.489 45.455 0.00 0.00 40.96 2.32
1941 5275 2.094234 GCCACGCTGGAATTAACCAAAT 60.094 45.455 8.04 0.00 40.96 2.32
1947 5281 1.277842 TCTCTGCCACGCTGGAATTAA 59.722 47.619 8.04 0.00 40.96 1.40
1955 5290 2.492090 GACGATCTCTGCCACGCT 59.508 61.111 0.00 0.00 0.00 5.07
1960 5295 0.171455 ACAAGTCGACGATCTCTGCC 59.829 55.000 10.46 0.00 0.00 4.85
1961 5296 1.135660 TGACAAGTCGACGATCTCTGC 60.136 52.381 10.46 0.00 0.00 4.26
1965 5311 0.811915 CCCTGACAAGTCGACGATCT 59.188 55.000 10.46 0.00 0.00 2.75
2146 5497 0.032540 TCATCATCGGCGACATGAGG 59.967 55.000 22.79 19.81 33.48 3.86
2253 5604 4.444876 GGGAGCTGCTCTTATTCCATAACA 60.445 45.833 27.09 0.00 0.00 2.41
2274 5626 4.838152 CACCTGATCCACGGCGGG 62.838 72.222 13.24 7.16 36.60 6.13
2689 6045 6.096282 CCTCCTCGTATTCTTCTTCTTCTTCT 59.904 42.308 0.00 0.00 0.00 2.85
2740 6099 4.057428 GTGTCGTGCTCGGCCTCT 62.057 66.667 10.59 0.00 41.33 3.69
2876 6238 0.247736 GTGCGATGTGAGGGAGACTT 59.752 55.000 0.00 0.00 0.00 3.01
2887 6249 1.670730 TGCATTGTCGGTGCGATGT 60.671 52.632 0.00 0.00 45.37 3.06
2889 6251 2.398554 GGTGCATTGTCGGTGCGAT 61.399 57.895 0.00 0.00 45.37 4.58
2929 6291 3.989698 ATTGTCGGTGCGGCGAGAG 62.990 63.158 12.98 0.00 32.50 3.20
2930 6292 4.063967 ATTGTCGGTGCGGCGAGA 62.064 61.111 12.98 0.08 32.50 4.04
2931 6293 3.853330 CATTGTCGGTGCGGCGAG 61.853 66.667 12.98 0.00 32.50 5.03
2932 6294 4.673298 ACATTGTCGGTGCGGCGA 62.673 61.111 12.98 0.00 32.50 5.54
2933 6295 4.444024 CACATTGTCGGTGCGGCG 62.444 66.667 0.51 0.51 32.50 6.46
2938 6300 1.196808 GTAACTGGCACATTGTCGGTG 59.803 52.381 0.00 0.00 41.37 4.94
2939 6301 1.071699 AGTAACTGGCACATTGTCGGT 59.928 47.619 0.00 0.00 44.65 4.69
2940 6302 1.464608 CAGTAACTGGCACATTGTCGG 59.535 52.381 0.00 0.00 38.20 4.79
2941 6303 2.143122 ACAGTAACTGGCACATTGTCG 58.857 47.619 0.00 0.00 38.20 4.35
2942 6304 2.484264 GGACAGTAACTGGCACATTGTC 59.516 50.000 0.00 6.25 42.18 3.18
2943 6305 2.504367 GGACAGTAACTGGCACATTGT 58.496 47.619 0.00 0.00 42.18 2.71
2944 6306 1.812571 GGGACAGTAACTGGCACATTG 59.187 52.381 0.00 0.00 43.56 2.82
2945 6307 2.200373 GGGACAGTAACTGGCACATT 57.800 50.000 0.00 0.00 43.56 2.71
2946 6308 3.957288 GGGACAGTAACTGGCACAT 57.043 52.632 0.00 0.00 43.56 3.21
2948 6310 0.107831 TGTGGGACAGTAACTGGCAC 59.892 55.000 0.00 0.00 44.54 5.01
2949 6311 0.396435 CTGTGGGACAGTAACTGGCA 59.604 55.000 0.00 0.00 42.18 4.92
2950 6312 3.233355 CTGTGGGACAGTAACTGGC 57.767 57.895 0.00 0.00 41.80 4.85
2959 6321 3.311110 GAGGGCGACTGTGGGACA 61.311 66.667 0.00 0.00 0.00 4.02
2960 6322 2.997897 AGAGGGCGACTGTGGGAC 60.998 66.667 0.00 0.00 0.00 4.46
2961 6323 2.680352 GAGAGGGCGACTGTGGGA 60.680 66.667 0.00 0.00 0.00 4.37
2962 6324 4.135153 CGAGAGGGCGACTGTGGG 62.135 72.222 0.00 0.00 0.00 4.61
2984 6346 1.795170 GCAACCGGCACATTGTCAGT 61.795 55.000 0.00 0.00 43.97 3.41
2986 6348 3.038280 GCAACCGGCACATTGTCA 58.962 55.556 0.00 0.00 43.97 3.58
3057 6434 2.434884 CAACTCCGATGGCAGCGT 60.435 61.111 24.41 2.11 0.00 5.07
3226 6606 0.038983 TGCGTGCGTGTACATACAGT 60.039 50.000 0.00 0.00 36.78 3.55
3227 6607 1.006079 CATGCGTGCGTGTACATACAG 60.006 52.381 0.00 0.00 36.78 2.74
3228 6608 0.995728 CATGCGTGCGTGTACATACA 59.004 50.000 0.00 0.00 0.00 2.29
3229 6609 0.996462 ACATGCGTGCGTGTACATAC 59.004 50.000 17.53 0.00 43.52 2.39
3230 6610 2.097791 TCTACATGCGTGCGTGTACATA 59.902 45.455 19.96 8.40 43.52 2.29
3322 6702 9.740710 ATCCATGGATATGATGCTCATATTATG 57.259 33.333 26.25 20.17 46.75 1.90
3323 6703 9.961264 GATCCATGGATATGATGCTCATATTAT 57.039 33.333 27.38 0.00 46.75 1.28
3343 6723 6.385176 TCAGGAACTAAGAATCACAGATCCAT 59.615 38.462 11.14 0.00 36.02 3.41
3347 6727 7.192852 ACATCAGGAACTAAGAATCACAGAT 57.807 36.000 0.00 0.00 36.02 2.90
3367 6747 1.117150 TACCGAACAGGGCCTACATC 58.883 55.000 5.28 3.85 46.96 3.06
3370 6750 1.483415 TGATTACCGAACAGGGCCTAC 59.517 52.381 5.28 0.00 46.96 3.18
3371 6751 1.868713 TGATTACCGAACAGGGCCTA 58.131 50.000 5.28 0.00 46.96 3.93
3372 6752 1.141053 GATGATTACCGAACAGGGCCT 59.859 52.381 0.00 0.00 46.96 5.19
3373 6753 1.594331 GATGATTACCGAACAGGGCC 58.406 55.000 0.00 0.00 46.96 5.80
3374 6754 1.594331 GGATGATTACCGAACAGGGC 58.406 55.000 0.00 0.00 46.96 5.19
3383 6763 1.048601 TCCAGGAGCGGATGATTACC 58.951 55.000 0.00 0.00 0.00 2.85
3384 6764 2.910688 TTCCAGGAGCGGATGATTAC 57.089 50.000 0.00 0.00 34.19 1.89
3385 6765 3.007290 CAGATTCCAGGAGCGGATGATTA 59.993 47.826 0.00 0.00 34.19 1.75
3386 6766 2.053244 AGATTCCAGGAGCGGATGATT 58.947 47.619 0.00 0.00 34.19 2.57
3387 6767 1.347050 CAGATTCCAGGAGCGGATGAT 59.653 52.381 0.00 0.00 34.19 2.45
3388 6768 0.755079 CAGATTCCAGGAGCGGATGA 59.245 55.000 0.00 0.00 34.19 2.92
3389 6769 0.883814 GCAGATTCCAGGAGCGGATG 60.884 60.000 0.00 0.00 34.19 3.51
3390 6770 1.340399 TGCAGATTCCAGGAGCGGAT 61.340 55.000 0.00 0.00 34.19 4.18
3391 6771 1.964608 CTGCAGATTCCAGGAGCGGA 61.965 60.000 8.42 0.00 33.54 5.54
3392 6772 1.523258 CTGCAGATTCCAGGAGCGG 60.523 63.158 8.42 0.00 0.00 5.52
3393 6773 0.530211 CTCTGCAGATTCCAGGAGCG 60.530 60.000 18.63 0.00 0.00 5.03
3394 6774 0.814812 GCTCTGCAGATTCCAGGAGC 60.815 60.000 18.63 10.76 0.00 4.70
3395 6775 0.540454 TGCTCTGCAGATTCCAGGAG 59.460 55.000 18.63 3.76 33.32 3.69
3396 6776 2.687781 TGCTCTGCAGATTCCAGGA 58.312 52.632 18.63 3.09 33.32 3.86
3414 6794 0.465460 TGGCGGAGTTGCAGTTTTCT 60.465 50.000 0.00 0.00 36.28 2.52
3415 6795 0.598065 ATGGCGGAGTTGCAGTTTTC 59.402 50.000 0.00 0.00 36.28 2.29
3416 6796 1.000274 GAATGGCGGAGTTGCAGTTTT 60.000 47.619 0.00 0.00 36.28 2.43
3417 6797 0.598065 GAATGGCGGAGTTGCAGTTT 59.402 50.000 0.00 0.00 36.28 2.66
3418 6798 0.250901 AGAATGGCGGAGTTGCAGTT 60.251 50.000 0.00 0.00 36.28 3.16
3419 6799 0.957395 CAGAATGGCGGAGTTGCAGT 60.957 55.000 0.00 0.00 36.28 4.40
3420 6800 0.674581 TCAGAATGGCGGAGTTGCAG 60.675 55.000 0.00 0.00 36.16 4.41
3421 6801 0.250684 TTCAGAATGGCGGAGTTGCA 60.251 50.000 0.00 0.00 36.16 4.08
3422 6802 0.169009 GTTCAGAATGGCGGAGTTGC 59.831 55.000 0.00 0.00 36.16 4.17
3423 6803 1.466167 CAGTTCAGAATGGCGGAGTTG 59.534 52.381 0.00 0.00 36.16 3.16
3424 6804 1.072331 ACAGTTCAGAATGGCGGAGTT 59.928 47.619 0.00 0.00 36.16 3.01
3425 6805 0.687354 ACAGTTCAGAATGGCGGAGT 59.313 50.000 0.00 0.00 36.16 3.85
3426 6806 2.544685 CTACAGTTCAGAATGGCGGAG 58.455 52.381 0.00 0.00 36.16 4.63
3427 6807 1.405526 GCTACAGTTCAGAATGGCGGA 60.406 52.381 0.00 0.00 36.16 5.54
3428 6808 1.009829 GCTACAGTTCAGAATGGCGG 58.990 55.000 0.00 0.00 36.16 6.13
3429 6809 1.929836 GAGCTACAGTTCAGAATGGCG 59.070 52.381 0.00 0.00 36.16 5.69
3430 6810 2.284190 GGAGCTACAGTTCAGAATGGC 58.716 52.381 0.00 0.00 36.16 4.40
3431 6811 2.420687 GGGGAGCTACAGTTCAGAATGG 60.421 54.545 0.00 0.00 36.16 3.16
3432 6812 2.420687 GGGGGAGCTACAGTTCAGAATG 60.421 54.545 0.00 0.00 37.54 2.67
3433 6813 1.840635 GGGGGAGCTACAGTTCAGAAT 59.159 52.381 0.00 0.00 0.00 2.40
3434 6814 1.276622 GGGGGAGCTACAGTTCAGAA 58.723 55.000 0.00 0.00 0.00 3.02
3435 6815 0.116342 TGGGGGAGCTACAGTTCAGA 59.884 55.000 0.00 0.00 0.00 3.27
3436 6816 0.984230 TTGGGGGAGCTACAGTTCAG 59.016 55.000 0.00 0.00 0.00 3.02
3437 6817 0.690762 GTTGGGGGAGCTACAGTTCA 59.309 55.000 0.00 0.00 0.00 3.18
3438 6818 0.984995 AGTTGGGGGAGCTACAGTTC 59.015 55.000 0.00 0.00 0.00 3.01
3439 6819 0.984995 GAGTTGGGGGAGCTACAGTT 59.015 55.000 0.00 0.00 0.00 3.16
3440 6820 0.910088 GGAGTTGGGGGAGCTACAGT 60.910 60.000 0.00 0.00 0.00 3.55
3441 6821 1.908483 GGAGTTGGGGGAGCTACAG 59.092 63.158 0.00 0.00 0.00 2.74
3442 6822 1.987855 CGGAGTTGGGGGAGCTACA 60.988 63.158 0.00 0.00 0.00 2.74
3443 6823 2.901042 CGGAGTTGGGGGAGCTAC 59.099 66.667 0.00 0.00 0.00 3.58
3444 6824 3.081409 GCGGAGTTGGGGGAGCTA 61.081 66.667 0.00 0.00 0.00 3.32
3446 6826 4.785453 CAGCGGAGTTGGGGGAGC 62.785 72.222 0.00 0.00 34.22 4.70
3447 6827 4.785453 GCAGCGGAGTTGGGGGAG 62.785 72.222 0.00 0.00 39.81 4.30
3460 6840 4.344865 TTCCCCAACTCCGGCAGC 62.345 66.667 0.00 0.00 0.00 5.25
3461 6841 2.359975 GTTCCCCAACTCCGGCAG 60.360 66.667 0.00 0.00 0.00 4.85
3462 6842 4.323477 CGTTCCCCAACTCCGGCA 62.323 66.667 0.00 0.00 0.00 5.69
3464 6844 3.310860 CTCCGTTCCCCAACTCCGG 62.311 68.421 0.00 0.00 39.98 5.14
3465 6845 2.264794 CTCCGTTCCCCAACTCCG 59.735 66.667 0.00 0.00 0.00 4.63
3466 6846 2.046217 GCTCCGTTCCCCAACTCC 60.046 66.667 0.00 0.00 0.00 3.85
3467 6847 2.240162 ATCGCTCCGTTCCCCAACTC 62.240 60.000 0.00 0.00 0.00 3.01
3468 6848 0.974010 TATCGCTCCGTTCCCCAACT 60.974 55.000 0.00 0.00 0.00 3.16
3469 6849 0.808847 GTATCGCTCCGTTCCCCAAC 60.809 60.000 0.00 0.00 0.00 3.77
3470 6850 1.518774 GTATCGCTCCGTTCCCCAA 59.481 57.895 0.00 0.00 0.00 4.12
3471 6851 2.428925 GGTATCGCTCCGTTCCCCA 61.429 63.158 0.00 0.00 0.00 4.96
3472 6852 2.420466 GGTATCGCTCCGTTCCCC 59.580 66.667 0.00 0.00 0.00 4.81
3473 6853 2.008268 TTCGGTATCGCTCCGTTCCC 62.008 60.000 11.16 0.00 46.86 3.97
3474 6854 0.869028 GTTCGGTATCGCTCCGTTCC 60.869 60.000 11.16 0.00 46.86 3.62
3475 6855 0.179156 TGTTCGGTATCGCTCCGTTC 60.179 55.000 11.16 7.41 46.86 3.95
3476 6856 0.179145 CTGTTCGGTATCGCTCCGTT 60.179 55.000 11.16 0.00 46.86 4.44
3477 6857 1.432251 CTGTTCGGTATCGCTCCGT 59.568 57.895 11.16 0.00 46.86 4.69
3479 6859 1.141019 TGCTGTTCGGTATCGCTCC 59.859 57.895 0.00 0.00 36.13 4.70
3480 6860 0.457853 TGTGCTGTTCGGTATCGCTC 60.458 55.000 0.00 0.00 36.13 5.03
3481 6861 0.458543 CTGTGCTGTTCGGTATCGCT 60.459 55.000 0.00 0.00 36.13 4.93
3482 6862 0.736325 ACTGTGCTGTTCGGTATCGC 60.736 55.000 0.00 0.00 36.13 4.58
3483 6863 2.554806 TACTGTGCTGTTCGGTATCG 57.445 50.000 0.00 0.00 37.82 2.92
3484 6864 6.213677 TGATATTACTGTGCTGTTCGGTATC 58.786 40.000 0.00 0.00 0.00 2.24
3485 6865 6.156748 TGATATTACTGTGCTGTTCGGTAT 57.843 37.500 0.00 0.00 0.00 2.73
3486 6866 5.585820 TGATATTACTGTGCTGTTCGGTA 57.414 39.130 0.00 0.00 0.00 4.02
3487 6867 4.465632 TGATATTACTGTGCTGTTCGGT 57.534 40.909 0.00 0.00 0.00 4.69
3488 6868 4.870426 AGTTGATATTACTGTGCTGTTCGG 59.130 41.667 0.00 0.00 0.00 4.30
3489 6869 5.807520 AGAGTTGATATTACTGTGCTGTTCG 59.192 40.000 0.00 0.00 0.00 3.95
3490 6870 7.043059 GCTAGAGTTGATATTACTGTGCTGTTC 60.043 40.741 0.00 0.00 0.00 3.18
3491 6871 6.758886 GCTAGAGTTGATATTACTGTGCTGTT 59.241 38.462 0.00 0.00 0.00 3.16
3492 6872 6.127338 TGCTAGAGTTGATATTACTGTGCTGT 60.127 38.462 0.00 0.00 0.00 4.40
3493 6873 6.276091 TGCTAGAGTTGATATTACTGTGCTG 58.724 40.000 0.00 0.00 0.00 4.41
3494 6874 6.322456 TCTGCTAGAGTTGATATTACTGTGCT 59.678 38.462 0.00 0.00 0.00 4.40
3495 6875 6.507900 TCTGCTAGAGTTGATATTACTGTGC 58.492 40.000 0.00 0.00 0.00 4.57
3496 6876 8.812329 GTTTCTGCTAGAGTTGATATTACTGTG 58.188 37.037 0.00 0.00 0.00 3.66
3497 6877 8.531982 TGTTTCTGCTAGAGTTGATATTACTGT 58.468 33.333 0.00 0.00 0.00 3.55
3498 6878 8.812329 GTGTTTCTGCTAGAGTTGATATTACTG 58.188 37.037 0.00 0.00 0.00 2.74
3499 6879 8.531982 TGTGTTTCTGCTAGAGTTGATATTACT 58.468 33.333 0.00 0.00 0.00 2.24
3514 6894 7.516198 AGATGAAGTTTTATGTGTTTCTGCT 57.484 32.000 0.00 0.00 0.00 4.24
3515 6895 8.289618 TGTAGATGAAGTTTTATGTGTTTCTGC 58.710 33.333 0.00 0.00 0.00 4.26
3516 6896 9.817365 CTGTAGATGAAGTTTTATGTGTTTCTG 57.183 33.333 0.00 0.00 0.00 3.02
3517 6897 9.778741 TCTGTAGATGAAGTTTTATGTGTTTCT 57.221 29.630 0.00 0.00 0.00 2.52
3536 7310 4.365514 TGGAGCAACCAAAATCTGTAGA 57.634 40.909 0.11 0.00 46.75 2.59
3553 7327 4.763793 AGAATGTTGTGGTTCTGAATGGAG 59.236 41.667 0.00 0.00 33.64 3.86
3565 7339 2.129607 GCTTGTGCAAGAATGTTGTGG 58.870 47.619 15.31 0.00 40.79 4.17
3566 7340 3.088194 AGCTTGTGCAAGAATGTTGTG 57.912 42.857 15.31 0.00 40.79 3.33
3568 7342 4.224433 CAGTAGCTTGTGCAAGAATGTTG 58.776 43.478 15.31 3.62 40.79 3.33
3604 7379 5.627499 TTTATCACAGCTGCCTTAAACTG 57.373 39.130 15.27 1.53 36.22 3.16
3622 7397 6.127842 ACGTTTTACTGGATTTCCGCATTTAT 60.128 34.615 0.00 0.00 39.43 1.40
3623 7398 5.181622 ACGTTTTACTGGATTTCCGCATTTA 59.818 36.000 0.00 0.00 39.43 1.40
3626 7401 3.078837 ACGTTTTACTGGATTTCCGCAT 58.921 40.909 0.00 0.00 39.43 4.73
3634 7409 1.074889 AGGGGCAACGTTTTACTGGAT 59.925 47.619 0.00 0.00 37.60 3.41
3637 7412 2.496111 TGTAGGGGCAACGTTTTACTG 58.504 47.619 0.00 0.00 37.60 2.74
3663 7440 9.391006 TCTAACATTAATCTAAAGCATCCGTTT 57.609 29.630 0.00 0.00 0.00 3.60
3666 7443 8.012241 GCTTCTAACATTAATCTAAAGCATCCG 58.988 37.037 10.42 0.00 38.16 4.18
3667 7444 9.061435 AGCTTCTAACATTAATCTAAAGCATCC 57.939 33.333 14.78 0.00 40.14 3.51
3669 7446 9.844257 AGAGCTTCTAACATTAATCTAAAGCAT 57.156 29.630 14.78 5.59 40.14 3.79
3670 7447 9.319143 GAGAGCTTCTAACATTAATCTAAAGCA 57.681 33.333 14.78 0.00 40.14 3.91
3671 7448 9.319143 TGAGAGCTTCTAACATTAATCTAAAGC 57.681 33.333 0.00 0.00 38.46 3.51
3676 7453 7.044798 GGTGTGAGAGCTTCTAACATTAATCT 58.955 38.462 6.63 0.00 39.87 2.40
3677 7454 6.818644 TGGTGTGAGAGCTTCTAACATTAATC 59.181 38.462 6.63 0.00 39.87 1.75
3679 7456 6.109156 TGGTGTGAGAGCTTCTAACATTAA 57.891 37.500 6.63 0.00 39.87 1.40
3700 7638 1.550130 TTTCGCTAGACCCCACCTGG 61.550 60.000 0.00 0.00 0.00 4.45
3715 7653 3.242870 GGCTTGCCTTGTATGATCTTTCG 60.243 47.826 4.11 0.00 0.00 3.46
3719 7657 3.659183 AAGGCTTGCCTTGTATGATCT 57.341 42.857 24.19 0.00 0.00 2.75
3723 7661 3.081061 TGTGTAAGGCTTGCCTTGTATG 58.919 45.455 30.51 0.00 0.00 2.39
3740 7678 2.615493 CCCGGAGCTTCTTACATTGTGT 60.615 50.000 0.73 0.00 0.00 3.72
3742 7680 1.906574 TCCCGGAGCTTCTTACATTGT 59.093 47.619 0.73 0.00 0.00 2.71
3749 7687 1.290134 ATCCTTTCCCGGAGCTTCTT 58.710 50.000 0.73 0.00 36.31 2.52
3751 7689 3.493767 ATAATCCTTTCCCGGAGCTTC 57.506 47.619 0.73 0.00 36.31 3.86
3759 7697 3.665190 CTGCCTCGTATAATCCTTTCCC 58.335 50.000 0.00 0.00 0.00 3.97
3760 7698 3.067833 GCTGCCTCGTATAATCCTTTCC 58.932 50.000 0.00 0.00 0.00 3.13
3761 7699 3.067833 GGCTGCCTCGTATAATCCTTTC 58.932 50.000 12.43 0.00 0.00 2.62
3763 7701 2.330216 AGGCTGCCTCGTATAATCCTT 58.670 47.619 17.22 0.00 0.00 3.36
3764 7702 2.016905 AGGCTGCCTCGTATAATCCT 57.983 50.000 17.22 0.00 0.00 3.24
3765 7703 2.841442 AAGGCTGCCTCGTATAATCC 57.159 50.000 23.61 0.00 30.89 3.01
3767 7705 2.302157 GGGTAAGGCTGCCTCGTATAAT 59.698 50.000 23.61 6.86 30.89 1.28
3769 7707 1.335145 GGGTAAGGCTGCCTCGTATA 58.665 55.000 23.61 7.77 30.89 1.47
3770 7708 1.408453 GGGGTAAGGCTGCCTCGTAT 61.408 60.000 23.61 8.92 30.89 3.06
3774 7733 2.301738 ACTGGGGTAAGGCTGCCTC 61.302 63.158 23.61 10.46 30.89 4.70
3856 7827 3.346315 TGGATGTGAGCGTTTGAATGAT 58.654 40.909 0.00 0.00 0.00 2.45
3859 7830 4.094887 GTGTATGGATGTGAGCGTTTGAAT 59.905 41.667 0.00 0.00 0.00 2.57
3882 7853 4.201910 TGGCTCTTCAAAAACACTTTCTCG 60.202 41.667 0.00 0.00 0.00 4.04
3889 7860 4.105486 GAGTTGTGGCTCTTCAAAAACAC 58.895 43.478 0.00 0.00 32.99 3.32
3931 7904 3.889815 TGAGATCCAAATTGGCTGGTAG 58.110 45.455 7.24 0.00 37.47 3.18
4001 7974 2.602660 GTGAACAATGTGTGGTGTTTGC 59.397 45.455 0.00 0.00 38.07 3.68
4008 7981 3.894782 TTGATCGTGAACAATGTGTGG 57.105 42.857 0.00 0.00 0.00 4.17
4025 7998 1.786441 ACCCTTTCCCACCTTGATTGA 59.214 47.619 0.00 0.00 0.00 2.57
4035 8008 6.296145 CCTTGCAAATTATTTACCCTTTCCCA 60.296 38.462 0.00 0.00 0.00 4.37



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

AutoCloner maintained by Alex Coulton.