Multiple sequence alignment - TraesCS1D01G338300

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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 TraesCS1D01G338300 chr1D 100.000 5626 0 0 1 5626 427613905 427619530 0.000000e+00 10390.0
1 TraesCS1D01G338300 chr1A 91.831 4321 223 61 237 4501 522949211 522953457 0.000000e+00 5904.0
2 TraesCS1D01G338300 chr1A 88.615 1054 90 19 4582 5626 522954250 522955282 0.000000e+00 1254.0
3 TraesCS1D01G338300 chr1A 85.673 349 46 3 5150 5494 572015136 572014788 1.150000e-96 364.0
4 TraesCS1D01G338300 chr1A 95.833 48 1 1 4497 4543 522953469 522953516 6.040000e-10 76.8
5 TraesCS1D01G338300 chr1B 93.084 2328 105 18 1989 4295 579783372 579785664 0.000000e+00 3356.0
6 TraesCS1D01G338300 chr1B 89.304 1393 68 17 4281 5626 579787971 579789329 0.000000e+00 1672.0
7 TraesCS1D01G338300 chr1B 92.335 1122 49 10 903 1992 579782187 579783303 0.000000e+00 1561.0
8 TraesCS1D01G338300 chr1B 87.751 498 50 5 43 536 579781607 579782097 6.320000e-159 571.0
9 TraesCS1D01G338300 chr1B 75.480 469 91 19 3202 3654 181099590 181099130 2.050000e-49 207.0
10 TraesCS1D01G338300 chr1B 81.690 213 30 6 662 870 350800280 350800487 9.690000e-38 169.0
11 TraesCS1D01G338300 chr5B 88.342 772 74 10 4868 5626 92233091 92233859 0.000000e+00 913.0
12 TraesCS1D01G338300 chr5D 87.150 786 69 16 4857 5626 84900046 84900815 0.000000e+00 863.0
13 TraesCS1D01G338300 chr5D 94.915 59 0 2 1 56 257029136 257029078 7.760000e-14 89.8
14 TraesCS1D01G338300 chr5A 86.624 785 75 14 4857 5626 79284225 79284994 0.000000e+00 841.0
15 TraesCS1D01G338300 chr5A 88.571 70 4 3 1 67 445647153 445647221 1.300000e-11 82.4
16 TraesCS1D01G338300 chr2B 84.848 165 19 5 743 903 592765175 592765337 1.620000e-35 161.0
17 TraesCS1D01G338300 chr2B 96.364 55 0 2 1 53 619373842 619373896 7.760000e-14 89.8
18 TraesCS1D01G338300 chr2B 74.603 252 36 15 677 904 186381999 186381752 1.000000e-12 86.1
19 TraesCS1D01G338300 chr4D 81.675 191 26 5 688 870 47502576 47502765 3.510000e-32 150.0
20 TraesCS1D01G338300 chr2A 77.647 255 47 6 658 904 644249128 644249380 4.540000e-31 147.0
21 TraesCS1D01G338300 chr7D 78.059 237 37 11 664 889 45001744 45001512 9.830000e-28 135.0
22 TraesCS1D01G338300 chr7D 77.169 219 32 11 664 872 29756912 29756702 1.660000e-20 111.0
23 TraesCS1D01G338300 chr7D 94.643 56 1 1 1 56 144163971 144163918 1.000000e-12 86.1
24 TraesCS1D01G338300 chr3A 77.434 226 40 9 673 889 745458877 745458654 2.130000e-24 124.0
25 TraesCS1D01G338300 chr3A 76.623 231 41 11 676 901 726719936 726720158 1.280000e-21 115.0
26 TraesCS1D01G338300 chr3B 76.667 240 40 10 677 906 73784311 73784078 9.900000e-23 119.0
27 TraesCS1D01G338300 chr7B 74.638 276 43 18 658 911 531683786 531684056 4.640000e-16 97.1
28 TraesCS1D01G338300 chr7A 98.077 52 0 1 1 51 549603516 549603567 7.760000e-14 89.8
29 TraesCS1D01G338300 chr2D 96.364 55 0 2 1 54 68834892 68834945 7.760000e-14 89.8
30 TraesCS1D01G338300 chr2D 96.364 55 0 2 1 54 68892783 68892730 7.760000e-14 89.8
31 TraesCS1D01G338300 chr2D 90.769 65 4 2 1 64 176543081 176543018 1.000000e-12 86.1
32 TraesCS1D01G338300 chr3D 96.226 53 2 0 1 53 604990447 604990395 2.790000e-13 87.9


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 TraesCS1D01G338300 chr1D 427613905 427619530 5625 False 10390.0 10390 100.0000 1 5626 1 chr1D.!!$F1 5625
1 TraesCS1D01G338300 chr1A 522949211 522955282 6071 False 2411.6 5904 92.0930 237 5626 3 chr1A.!!$F1 5389
2 TraesCS1D01G338300 chr1B 579781607 579789329 7722 False 1790.0 3356 90.6185 43 5626 4 chr1B.!!$F2 5583
3 TraesCS1D01G338300 chr5B 92233091 92233859 768 False 913.0 913 88.3420 4868 5626 1 chr5B.!!$F1 758
4 TraesCS1D01G338300 chr5D 84900046 84900815 769 False 863.0 863 87.1500 4857 5626 1 chr5D.!!$F1 769
5 TraesCS1D01G338300 chr5A 79284225 79284994 769 False 841.0 841 86.6240 4857 5626 1 chr5A.!!$F1 769

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
733 742 0.027194 CAGGCTTGCGATGATGTTCG 59.973 55.000 0.00 0.00 41.99 3.95 F
854 867 0.035534 TAGGGTGTGCATGCGTTCAT 60.036 50.000 14.09 2.99 0.00 2.57 F
855 868 0.035534 AGGGTGTGCATGCGTTCATA 60.036 50.000 14.09 0.00 0.00 2.15 F
2277 2434 0.396556 AACGGCAAAAAGACTGGGGT 60.397 50.000 0.00 0.00 0.00 4.95 F
2545 2704 1.286553 TGGTCCAAACTGGTCCTGTTT 59.713 47.619 18.42 18.42 44.55 2.83 F
4261 4442 1.455383 CGTGGCCCTGCAGTTTTTCT 61.455 55.000 13.81 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2434 0.107752 TGCGATGGCATACAGAAGCA 60.108 50.000 0.00 3.15 46.21 3.91 R
2444 2602 1.211457 AGCAAGGCCTCACCATCTAAG 59.789 52.381 5.23 0.00 43.14 2.18 R
2668 2830 2.037901 TCCAACAATTTTGCAGGCAGA 58.962 42.857 0.00 0.00 0.00 4.26 R
3804 3982 2.280524 TCCACCGGACTGTTTGCG 60.281 61.111 9.46 0.00 39.13 4.85 R
4407 6909 3.071874 ACTGAATTTGCGAATCCTCCA 57.928 42.857 0.00 0.00 0.00 3.86 R
5388 8653 0.251077 CAAAGGGCACAGAGAAGGCT 60.251 55.000 0.00 0.00 0.00 4.58 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
22 23 5.938438 CAATTACCAAAACCAAACATGGG 57.062 39.130 0.00 0.00 37.26 4.00
23 24 4.632327 ATTACCAAAACCAAACATGGGG 57.368 40.909 0.00 0.00 37.26 4.96
24 25 1.135960 ACCAAAACCAAACATGGGGG 58.864 50.000 0.00 0.00 37.26 5.40
25 26 0.250684 CCAAAACCAAACATGGGGGC 60.251 55.000 0.00 0.00 0.00 5.80
26 27 0.471617 CAAAACCAAACATGGGGGCA 59.528 50.000 0.00 0.00 0.00 5.36
27 28 0.472044 AAAACCAAACATGGGGGCAC 59.528 50.000 0.00 0.00 0.00 5.01
39 40 3.365535 GGGCACCGCATGTTCTTT 58.634 55.556 0.00 0.00 40.86 2.52
40 41 1.212751 GGGCACCGCATGTTCTTTC 59.787 57.895 0.00 0.00 40.86 2.62
41 42 1.523154 GGGCACCGCATGTTCTTTCA 61.523 55.000 0.00 0.00 40.86 2.69
80 81 1.538047 TGCAAGATTCAGGCCTTGTC 58.462 50.000 0.00 0.81 41.21 3.18
81 82 1.202915 TGCAAGATTCAGGCCTTGTCA 60.203 47.619 0.00 0.00 41.21 3.58
89 90 3.657398 TCAGGCCTTGTCATCATCATT 57.343 42.857 0.00 0.00 0.00 2.57
95 96 7.124599 TCAGGCCTTGTCATCATCATTTTTATT 59.875 33.333 0.00 0.00 0.00 1.40
98 99 7.011669 GGCCTTGTCATCATCATTTTTATTTGG 59.988 37.037 0.00 0.00 0.00 3.28
123 124 8.984764 GGCACATACATAAAAGACGTATAATCA 58.015 33.333 0.00 0.00 0.00 2.57
171 172 7.121382 ACCCTATTGTCATGTGATCAAAAGAT 58.879 34.615 0.00 0.00 0.00 2.40
176 177 6.245115 TGTCATGTGATCAAAAGATGTGTC 57.755 37.500 0.00 0.00 0.00 3.67
199 200 3.190118 GGTGAGCTCTTCATTTGGTTGAG 59.810 47.826 16.19 0.00 38.29 3.02
210 211 1.956043 TGGTTGAGCCATTTCACGC 59.044 52.632 0.00 0.00 43.61 5.34
211 212 0.821301 TGGTTGAGCCATTTCACGCA 60.821 50.000 0.00 0.00 43.61 5.24
213 214 1.408422 GTTGAGCCATTTCACGCAAC 58.592 50.000 0.00 0.00 38.94 4.17
221 222 4.082300 AGCCATTTCACGCAACAAATATGA 60.082 37.500 0.00 0.00 0.00 2.15
235 236 8.830580 GCAACAAATATGAGCTTCTATGACTAA 58.169 33.333 0.00 0.00 0.00 2.24
325 327 5.921962 ATTCATAAAAAGGGTCCAAGCTC 57.078 39.130 0.00 0.00 0.00 4.09
332 334 0.618458 AGGGTCCAAGCTCGCATTTA 59.382 50.000 0.00 0.00 0.00 1.40
339 341 1.421410 AAGCTCGCATTTAGCCGACG 61.421 55.000 0.00 0.00 41.02 5.12
462 468 2.690778 GCGGAACTCATGGTGTGGC 61.691 63.158 0.00 0.00 0.00 5.01
470 476 1.475280 CTCATGGTGTGGCATTCCTTG 59.525 52.381 15.43 15.43 0.00 3.61
491 497 4.973396 TGATCGTCAAATCAAGTTGATGC 58.027 39.130 18.94 8.97 42.07 3.91
497 503 1.825090 AATCAAGTTGATGCGCTCCA 58.175 45.000 18.94 3.17 37.15 3.86
510 516 2.183409 GCTCCAATGCGAATGGTGT 58.817 52.632 2.62 0.00 39.09 4.16
525 531 1.437573 GTGTCGGATGGATCGAGCA 59.562 57.895 1.84 0.00 37.31 4.26
531 537 1.000274 CGGATGGATCGAGCACATGTA 60.000 52.381 1.84 0.00 0.00 2.29
537 543 2.604855 GGATCGAGCACATGTACTACCG 60.605 54.545 1.84 0.00 0.00 4.02
554 560 0.448990 CCGCACACTCATTCATGTGG 59.551 55.000 6.51 0.00 45.21 4.17
567 573 1.065199 TCATGTGGGAGTGCCATTCTC 60.065 52.381 6.66 0.00 35.15 2.87
568 574 0.994247 ATGTGGGAGTGCCATTCTCA 59.006 50.000 6.66 0.00 35.15 3.27
573 579 2.827322 TGGGAGTGCCATTCTCATTTTG 59.173 45.455 0.00 0.00 35.15 2.44
574 580 3.091545 GGGAGTGCCATTCTCATTTTGA 58.908 45.455 0.00 0.00 35.15 2.69
575 581 3.703052 GGGAGTGCCATTCTCATTTTGAT 59.297 43.478 0.00 0.00 35.15 2.57
659 668 2.034558 AGTTGTGCACATGCTTTGTACC 59.965 45.455 22.39 0.00 42.66 3.34
660 669 0.958091 TGTGCACATGCTTTGTACCC 59.042 50.000 17.42 0.00 42.66 3.69
668 677 0.402504 TGCTTTGTACCCGGGTTCAT 59.597 50.000 35.42 9.51 0.00 2.57
671 680 2.510613 CTTTGTACCCGGGTTCATGTT 58.489 47.619 35.42 7.20 0.00 2.71
674 683 1.276989 TGTACCCGGGTTCATGTTCTC 59.723 52.381 35.42 11.33 0.00 2.87
675 684 0.533491 TACCCGGGTTCATGTTCTCG 59.467 55.000 35.42 0.00 0.00 4.04
678 687 0.246635 CCGGGTTCATGTTCTCGACT 59.753 55.000 12.14 0.00 0.00 4.18
679 688 1.337823 CCGGGTTCATGTTCTCGACTT 60.338 52.381 12.14 0.00 0.00 3.01
680 689 1.726791 CGGGTTCATGTTCTCGACTTG 59.273 52.381 6.37 0.00 35.36 3.16
686 695 5.637810 GGTTCATGTTCTCGACTTGACATTA 59.362 40.000 0.00 0.00 40.80 1.90
687 696 6.147164 GGTTCATGTTCTCGACTTGACATTAA 59.853 38.462 0.00 0.00 40.80 1.40
690 699 5.530519 TGTTCTCGACTTGACATTAATGC 57.469 39.130 15.48 8.85 0.00 3.56
696 705 4.395854 TCGACTTGACATTAATGCTTGCAT 59.604 37.500 15.48 1.81 0.00 3.96
701 710 8.638685 ACTTGACATTAATGCTTGCATTATTC 57.361 30.769 23.25 19.45 0.00 1.75
711 720 8.652810 AATGCTTGCATTATTCTTGGATTTAC 57.347 30.769 17.88 0.00 0.00 2.01
713 722 7.483307 TGCTTGCATTATTCTTGGATTTACTC 58.517 34.615 0.00 0.00 0.00 2.59
714 723 6.920210 GCTTGCATTATTCTTGGATTTACTCC 59.080 38.462 0.00 0.00 45.19 3.85
724 733 1.406887 GGATTTACTCCAGGCTTGCGA 60.407 52.381 0.00 0.00 44.26 5.10
733 742 0.027194 CAGGCTTGCGATGATGTTCG 59.973 55.000 0.00 0.00 41.99 3.95
736 745 1.135689 GGCTTGCGATGATGTTCGTTT 60.136 47.619 0.00 0.00 41.16 3.60
739 748 3.062099 GCTTGCGATGATGTTCGTTTAGA 59.938 43.478 0.00 0.00 41.16 2.10
740 749 4.780324 GCTTGCGATGATGTTCGTTTAGAG 60.780 45.833 0.00 0.00 41.16 2.43
742 751 3.119280 TGCGATGATGTTCGTTTAGAGGA 60.119 43.478 0.00 0.00 41.16 3.71
743 752 3.487574 GCGATGATGTTCGTTTAGAGGAG 59.512 47.826 0.00 0.00 41.16 3.69
744 753 4.733815 GCGATGATGTTCGTTTAGAGGAGA 60.734 45.833 0.00 0.00 41.16 3.71
745 754 4.735822 CGATGATGTTCGTTTAGAGGAGAC 59.264 45.833 0.00 0.00 34.46 3.36
764 777 1.012086 CGTTCCCGTCGACTATGAGA 58.988 55.000 14.70 0.00 0.00 3.27
766 779 1.741706 GTTCCCGTCGACTATGAGACA 59.258 52.381 14.70 0.00 37.23 3.41
767 780 1.376543 TCCCGTCGACTATGAGACAC 58.623 55.000 14.70 0.00 37.23 3.67
770 783 1.064208 CCGTCGACTATGAGACACCTG 59.936 57.143 14.70 0.00 37.23 4.00
771 784 1.532090 CGTCGACTATGAGACACCTGC 60.532 57.143 14.70 0.00 37.23 4.85
795 808 6.817396 CGATGACTTCGTAAAATCTCAACAA 58.183 36.000 2.72 0.00 43.01 2.83
796 809 7.456253 CGATGACTTCGTAAAATCTCAACAAT 58.544 34.615 2.72 0.00 43.01 2.71
797 810 7.423598 CGATGACTTCGTAAAATCTCAACAATG 59.576 37.037 2.72 0.00 43.01 2.82
799 812 6.204688 TGACTTCGTAAAATCTCAACAATGCT 59.795 34.615 0.00 0.00 0.00 3.79
800 813 7.386573 TGACTTCGTAAAATCTCAACAATGCTA 59.613 33.333 0.00 0.00 0.00 3.49
801 814 8.268850 ACTTCGTAAAATCTCAACAATGCTAT 57.731 30.769 0.00 0.00 0.00 2.97
802 815 8.177663 ACTTCGTAAAATCTCAACAATGCTATG 58.822 33.333 0.00 0.00 0.00 2.23
804 817 5.682862 CGTAAAATCTCAACAATGCTATGCC 59.317 40.000 0.00 0.00 0.00 4.40
805 818 3.976793 AATCTCAACAATGCTATGCCG 57.023 42.857 0.00 0.00 0.00 5.69
811 824 0.816825 ACAATGCTATGCCGGCTCAG 60.817 55.000 29.70 23.95 0.00 3.35
812 825 1.895707 AATGCTATGCCGGCTCAGC 60.896 57.895 32.94 32.94 34.56 4.26
822 835 3.609703 GGCTCAGCCTCTCGAAGA 58.390 61.111 9.09 0.00 46.69 2.87
832 845 2.556189 GCCTCTCGAAGATGCTCATAGA 59.444 50.000 0.00 0.00 33.80 1.98
834 847 3.191162 CCTCTCGAAGATGCTCATAGAGG 59.809 52.174 9.84 9.84 38.19 3.69
844 857 1.069358 GCTCATAGAGGTAGGGTGTGC 59.931 57.143 0.00 0.00 0.00 4.57
845 858 2.388735 CTCATAGAGGTAGGGTGTGCA 58.611 52.381 0.00 0.00 0.00 4.57
846 859 2.968574 CTCATAGAGGTAGGGTGTGCAT 59.031 50.000 0.00 0.00 0.00 3.96
847 860 2.700371 TCATAGAGGTAGGGTGTGCATG 59.300 50.000 0.00 0.00 0.00 4.06
850 863 2.046314 GGTAGGGTGTGCATGCGT 60.046 61.111 14.09 0.00 0.00 5.24
851 864 1.674322 GGTAGGGTGTGCATGCGTT 60.674 57.895 14.09 0.00 0.00 4.84
852 865 1.644786 GGTAGGGTGTGCATGCGTTC 61.645 60.000 14.09 6.79 0.00 3.95
853 866 0.953471 GTAGGGTGTGCATGCGTTCA 60.953 55.000 14.09 9.46 0.00 3.18
854 867 0.035534 TAGGGTGTGCATGCGTTCAT 60.036 50.000 14.09 2.99 0.00 2.57
855 868 0.035534 AGGGTGTGCATGCGTTCATA 60.036 50.000 14.09 0.00 0.00 2.15
856 869 0.808125 GGGTGTGCATGCGTTCATAA 59.192 50.000 14.09 0.00 0.00 1.90
857 870 1.202177 GGGTGTGCATGCGTTCATAAG 60.202 52.381 14.09 0.00 0.00 1.73
859 872 1.093972 TGTGCATGCGTTCATAAGGG 58.906 50.000 14.09 0.00 0.00 3.95
860 873 1.094785 GTGCATGCGTTCATAAGGGT 58.905 50.000 14.09 0.00 0.00 4.34
861 874 1.093972 TGCATGCGTTCATAAGGGTG 58.906 50.000 14.09 0.00 0.00 4.61
862 875 1.339535 TGCATGCGTTCATAAGGGTGA 60.340 47.619 14.09 0.00 0.00 4.02
873 906 5.598416 TCATAAGGGTGAGTGTATGTGAG 57.402 43.478 0.00 0.00 0.00 3.51
874 907 2.770164 AAGGGTGAGTGTATGTGAGC 57.230 50.000 0.00 0.00 0.00 4.26
880 913 2.917971 GTGAGTGTATGTGAGCGACTTC 59.082 50.000 0.00 0.00 0.00 3.01
889 922 1.918609 GTGAGCGACTTCGATTGTACC 59.081 52.381 2.02 0.00 43.02 3.34
890 923 1.189403 GAGCGACTTCGATTGTACCG 58.811 55.000 2.02 0.00 43.02 4.02
892 925 0.638746 GCGACTTCGATTGTACCGTG 59.361 55.000 2.02 0.00 43.02 4.94
895 928 2.727798 CGACTTCGATTGTACCGTGTTT 59.272 45.455 0.00 0.00 43.02 2.83
1299 1334 2.660064 GGTCCACCAGATGCTCCGT 61.660 63.158 0.00 0.00 35.64 4.69
1353 1388 1.075151 CTCCTCCCTCCAGGTACCC 60.075 68.421 8.74 0.00 36.75 3.69
1410 1452 1.876156 GGGTTTGCTGTCTCTGACTTG 59.124 52.381 0.00 0.00 33.15 3.16
1411 1453 1.876156 GGTTTGCTGTCTCTGACTTGG 59.124 52.381 0.00 0.00 33.15 3.61
1710 1764 2.492088 TGTTCAGTGATCAGGTACCTCG 59.508 50.000 12.84 8.23 0.00 4.63
1714 1768 2.027751 GATCAGGTACCTCGCCGC 59.972 66.667 12.84 0.00 0.00 6.53
1748 1802 4.591072 TCCCTTTTTGAATGGTTTAGTGGG 59.409 41.667 0.00 0.00 0.00 4.61
1802 1856 5.301298 TCATGTGGATGAAATTGTGTGTTCA 59.699 36.000 0.00 0.00 35.55 3.18
1819 1873 6.929606 GTGTGTTCAACTAGTATGACCTTCTT 59.070 38.462 0.00 0.00 0.00 2.52
1820 1874 8.086522 GTGTGTTCAACTAGTATGACCTTCTTA 58.913 37.037 0.00 0.00 0.00 2.10
1886 1950 1.480789 TGCCAGTTAGCTCCGTCATA 58.519 50.000 0.00 0.00 0.00 2.15
1926 1990 1.404181 GCTGTGTGATCCTTCGTAGCA 60.404 52.381 0.00 0.00 0.00 3.49
2060 2215 7.148000 TGGAGTACATGTGACAAAATTGTTCAA 60.148 33.333 9.11 0.00 42.43 2.69
2097 2252 2.279582 ATGTTTCGGTAGCAGTCTCG 57.720 50.000 0.00 0.00 0.00 4.04
2158 2315 1.028905 TTGTCGGCCACTTCTTTTGG 58.971 50.000 2.24 0.00 37.17 3.28
2262 2419 4.991056 CCACACCTTCATATGAGATAACGG 59.009 45.833 5.39 1.19 0.00 4.44
2277 2434 0.396556 AACGGCAAAAAGACTGGGGT 60.397 50.000 0.00 0.00 0.00 4.95
2283 2440 2.310538 CAAAAAGACTGGGGTGCTTCT 58.689 47.619 0.00 0.00 0.00 2.85
2356 2514 9.073475 TGTGTTACAGCATTATTTTTCTAACCT 57.927 29.630 0.00 0.00 0.00 3.50
2434 2592 5.408079 AATGGGTCCCAACTAATGATGAT 57.592 39.130 16.55 0.00 36.95 2.45
2444 2602 6.429385 CCCAACTAATGATGATCTTCCTAAGC 59.571 42.308 6.17 0.00 0.00 3.09
2513 2671 4.002906 AGATTCGGTAGTTGTGCAAAGA 57.997 40.909 0.00 0.00 0.00 2.52
2519 2677 4.576873 TCGGTAGTTGTGCAAAGATTTTGA 59.423 37.500 5.77 0.00 0.00 2.69
2545 2704 1.286553 TGGTCCAAACTGGTCCTGTTT 59.713 47.619 18.42 18.42 44.55 2.83
2559 2718 9.856162 ACTGGTCCTGTTTAATTTTAGTTTCTA 57.144 29.630 0.00 0.00 0.00 2.10
2619 2781 8.725405 TTTGATATGGTAATGAACACGTGTAT 57.275 30.769 23.69 10.14 0.00 2.29
2627 2789 7.041030 TGGTAATGAACACGTGTATGTTTGATT 60.041 33.333 23.69 13.82 42.89 2.57
2665 2827 8.021396 GTCCTGCTTTTCGTTATTCTTTACAAT 58.979 33.333 0.00 0.00 0.00 2.71
2666 2828 9.221933 TCCTGCTTTTCGTTATTCTTTACAATA 57.778 29.630 0.00 0.00 0.00 1.90
2687 2849 2.137523 GTCTGCCTGCAAAATTGTTGG 58.862 47.619 0.00 0.00 0.00 3.77
2723 2885 3.120041 TCGTCAATATGTGCACGTATGG 58.880 45.455 27.92 25.26 34.45 2.74
2737 2899 4.768145 CACGTATGGTGTTGTTACTTGTG 58.232 43.478 0.00 0.00 41.89 3.33
2744 2906 5.676552 TGGTGTTGTTACTTGTGAGTACAT 58.323 37.500 0.00 0.00 38.07 2.29
2785 2953 7.881142 TGGTGATTGTAACTTACCTTTTCATG 58.119 34.615 0.00 0.00 32.68 3.07
2786 2954 7.504238 TGGTGATTGTAACTTACCTTTTCATGT 59.496 33.333 0.00 0.00 32.68 3.21
2787 2955 9.005777 GGTGATTGTAACTTACCTTTTCATGTA 57.994 33.333 0.00 0.00 0.00 2.29
3263 3440 1.705186 GGGCCCCTATTTGATGCTCTA 59.295 52.381 12.23 0.00 0.00 2.43
3633 3811 5.228945 AGAAATCCTATTACATGGACCCG 57.771 43.478 0.00 0.00 34.90 5.28
3804 3982 2.872370 CAGCAAATGGTCAAGCTTAGC 58.128 47.619 0.00 0.00 34.61 3.09
4261 4442 1.455383 CGTGGCCCTGCAGTTTTTCT 61.455 55.000 13.81 0.00 0.00 2.52
4407 6909 1.077716 GCGGTTGGACCCTAGCATT 60.078 57.895 0.00 0.00 33.75 3.56
4650 7880 4.136796 TGTTCTGGTCACTGGAATTTCTG 58.863 43.478 0.00 0.00 0.00 3.02
4668 7898 3.222603 TCTGTTCTTTTTCCCTTCTGGC 58.777 45.455 0.00 0.00 0.00 4.85
4702 7933 7.387673 CACACTGGAAGAATACAGTATTGTTCA 59.612 37.037 30.27 20.50 45.21 3.18
4939 8193 0.892755 CTCGCCTACTAACCACCACA 59.107 55.000 0.00 0.00 0.00 4.17
4967 8221 4.395959 TGGCGAGTATAACAAACCCTAG 57.604 45.455 0.00 0.00 0.00 3.02
4980 8234 3.345508 AACCCTAGATTCCGACAAACC 57.654 47.619 0.00 0.00 0.00 3.27
5199 8464 2.440980 GCTTGGATCTGGCCCCAC 60.441 66.667 0.00 0.00 31.11 4.61
5208 8473 4.731853 TGGCCCCACCCGATGAGA 62.732 66.667 0.00 0.00 37.83 3.27
5229 8494 1.291877 GCCAATGCTTCTCGACACGT 61.292 55.000 0.00 0.00 33.53 4.49
5259 8524 0.519077 CCACTTTCTCGCCTTTGCTC 59.481 55.000 0.00 0.00 34.43 4.26
5316 8581 1.278637 GTTCTTCACGGCAACCACG 59.721 57.895 0.00 0.00 37.36 4.94
5388 8653 0.473694 TGAGCTTGGAGACCTTCCCA 60.474 55.000 0.00 0.00 46.19 4.37
5462 8731 5.474532 AGAAGTTGATCTGCAAAGCAATGTA 59.525 36.000 0.00 0.00 38.41 2.29
5501 8771 5.551760 CAGCTATCACTGTTTGGGTTAAG 57.448 43.478 0.00 0.00 32.78 1.85
5511 8781 3.181434 TGTTTGGGTTAAGTCATGAGGCT 60.181 43.478 0.00 0.00 0.00 4.58
5520 8790 6.258947 GGTTAAGTCATGAGGCTACAAAGATC 59.741 42.308 0.00 0.00 0.00 2.75
5521 8799 5.690464 AAGTCATGAGGCTACAAAGATCT 57.310 39.130 0.00 0.00 0.00 2.75
5573 8851 1.407979 GAGCGACCCGATTTCTCCTAA 59.592 52.381 0.00 0.00 0.00 2.69
5574 8852 1.409427 AGCGACCCGATTTCTCCTAAG 59.591 52.381 0.00 0.00 0.00 2.18
5583 8861 0.902531 TTTCTCCTAAGACCTGGCCG 59.097 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.759183 CCCCATGTTTGGTTTTGGTAATTG 59.241 41.667 0.00 0.00 41.91 2.32
2 3 3.329225 CCCCCATGTTTGGTTTTGGTAAT 59.671 43.478 0.00 0.00 41.91 1.89
3 4 2.706190 CCCCCATGTTTGGTTTTGGTAA 59.294 45.455 0.00 0.00 41.91 2.85
4 5 2.330216 CCCCCATGTTTGGTTTTGGTA 58.670 47.619 0.00 0.00 41.91 3.25
5 6 1.135960 CCCCCATGTTTGGTTTTGGT 58.864 50.000 0.00 0.00 41.91 3.67
6 7 0.250684 GCCCCCATGTTTGGTTTTGG 60.251 55.000 0.00 0.00 41.91 3.28
7 8 0.471617 TGCCCCCATGTTTGGTTTTG 59.528 50.000 0.00 0.00 41.91 2.44
8 9 0.472044 GTGCCCCCATGTTTGGTTTT 59.528 50.000 0.00 0.00 41.91 2.43
9 10 1.414866 GGTGCCCCCATGTTTGGTTT 61.415 55.000 0.00 0.00 41.91 3.27
10 11 1.841103 GGTGCCCCCATGTTTGGTT 60.841 57.895 0.00 0.00 41.91 3.67
11 12 2.203773 GGTGCCCCCATGTTTGGT 60.204 61.111 0.00 0.00 41.91 3.67
12 13 3.381136 CGGTGCCCCCATGTTTGG 61.381 66.667 0.00 0.00 43.23 3.28
13 14 4.067913 GCGGTGCCCCCATGTTTG 62.068 66.667 0.00 0.00 0.00 2.93
14 15 3.903281 ATGCGGTGCCCCCATGTTT 62.903 57.895 0.00 0.00 0.00 2.83
15 16 4.380945 ATGCGGTGCCCCCATGTT 62.381 61.111 0.00 0.00 0.00 2.71
18 19 4.380945 AACATGCGGTGCCCCCAT 62.381 61.111 0.00 0.00 0.00 4.00
20 21 4.740822 AGAACATGCGGTGCCCCC 62.741 66.667 0.00 0.00 0.00 5.40
21 22 2.212900 GAAAGAACATGCGGTGCCCC 62.213 60.000 0.00 0.00 0.00 5.80
22 23 1.212751 GAAAGAACATGCGGTGCCC 59.787 57.895 0.00 0.00 0.00 5.36
23 24 0.313672 TTGAAAGAACATGCGGTGCC 59.686 50.000 0.00 0.00 0.00 5.01
24 25 1.987770 CATTGAAAGAACATGCGGTGC 59.012 47.619 0.00 0.00 0.00 5.01
25 26 2.598589 CCATTGAAAGAACATGCGGTG 58.401 47.619 0.00 0.00 0.00 4.94
26 27 1.067635 GCCATTGAAAGAACATGCGGT 60.068 47.619 0.00 0.00 0.00 5.68
27 28 1.067706 TGCCATTGAAAGAACATGCGG 60.068 47.619 0.00 0.00 0.00 5.69
28 29 2.350899 TGCCATTGAAAGAACATGCG 57.649 45.000 0.00 0.00 0.00 4.73
29 30 4.247258 TGATTGCCATTGAAAGAACATGC 58.753 39.130 0.00 0.00 0.00 4.06
30 31 6.674519 GCATTGATTGCCATTGAAAGAACATG 60.675 38.462 0.00 0.00 46.15 3.21
31 32 5.353123 GCATTGATTGCCATTGAAAGAACAT 59.647 36.000 0.00 0.00 46.15 2.71
32 33 4.691685 GCATTGATTGCCATTGAAAGAACA 59.308 37.500 0.00 0.00 46.15 3.18
33 34 5.212589 GCATTGATTGCCATTGAAAGAAC 57.787 39.130 0.00 0.00 46.15 3.01
58 59 2.901839 ACAAGGCCTGAATCTTGCAATT 59.098 40.909 5.69 0.00 42.82 2.32
59 60 2.494870 GACAAGGCCTGAATCTTGCAAT 59.505 45.455 5.69 0.00 42.82 3.56
63 64 3.349927 TGATGACAAGGCCTGAATCTTG 58.650 45.455 5.69 1.07 44.14 3.02
73 74 7.466320 GCCAAATAAAAATGATGATGACAAGGC 60.466 37.037 0.00 0.00 0.00 4.35
80 81 9.315525 TGTATGTGCCAAATAAAAATGATGATG 57.684 29.630 0.00 0.00 0.00 3.07
89 90 9.347934 CGTCTTTTATGTATGTGCCAAATAAAA 57.652 29.630 0.00 0.00 33.76 1.52
95 96 8.719560 TTATACGTCTTTTATGTATGTGCCAA 57.280 30.769 0.00 0.00 39.98 4.52
111 112 8.786826 TCAAGAAAACCATTGATTATACGTCT 57.213 30.769 0.00 0.00 30.67 4.18
123 124 7.381323 GGTTCATCTTCATCAAGAAAACCATT 58.619 34.615 16.99 0.00 46.27 3.16
171 172 0.969149 ATGAAGAGCTCACCGACACA 59.031 50.000 17.77 5.34 36.69 3.72
176 177 1.813513 ACCAAATGAAGAGCTCACCG 58.186 50.000 17.77 0.00 36.69 4.94
199 200 4.172505 TCATATTTGTTGCGTGAAATGGC 58.827 39.130 0.00 0.00 0.00 4.40
206 207 4.346734 AGAAGCTCATATTTGTTGCGTG 57.653 40.909 0.00 0.00 0.00 5.34
208 209 6.018425 AGTCATAGAAGCTCATATTTGTTGCG 60.018 38.462 0.00 0.00 0.00 4.85
241 242 9.561069 AAGTTGTAGATTAAGTTGTGAGAACAT 57.439 29.630 0.00 0.00 0.00 2.71
300 301 5.543790 AGCTTGGACCCTTTTTATGAATTGT 59.456 36.000 0.00 0.00 0.00 2.71
303 304 4.399303 CGAGCTTGGACCCTTTTTATGAAT 59.601 41.667 0.00 0.00 0.00 2.57
311 313 0.251341 AATGCGAGCTTGGACCCTTT 60.251 50.000 2.37 0.00 0.00 3.11
312 314 0.251341 AAATGCGAGCTTGGACCCTT 60.251 50.000 2.37 0.00 0.00 3.95
313 315 0.618458 TAAATGCGAGCTTGGACCCT 59.382 50.000 2.37 0.00 0.00 4.34
325 327 1.136197 TGTTTTCGTCGGCTAAATGCG 60.136 47.619 0.00 0.00 44.05 4.73
332 334 2.172851 TTATGGTGTTTTCGTCGGCT 57.827 45.000 0.00 0.00 0.00 5.52
432 438 2.301870 TGAGTTCCGCTCTACCATTTGT 59.698 45.455 0.00 0.00 44.41 2.83
470 476 4.024438 CGCATCAACTTGATTTGACGATC 58.976 43.478 1.17 0.00 38.31 3.69
497 503 1.016627 CATCCGACACCATTCGCATT 58.983 50.000 0.00 0.00 37.70 3.56
510 516 0.032540 CATGTGCTCGATCCATCCGA 59.967 55.000 0.00 0.00 34.61 4.55
525 531 1.890489 TGAGTGTGCGGTAGTACATGT 59.110 47.619 2.69 2.69 44.41 3.21
531 537 2.028112 ACATGAATGAGTGTGCGGTAGT 60.028 45.455 0.00 0.00 0.00 2.73
537 543 1.741706 CTCCCACATGAATGAGTGTGC 59.258 52.381 0.00 0.00 43.28 4.57
554 560 4.996788 ATCAAAATGAGAATGGCACTCC 57.003 40.909 0.00 0.00 33.95 3.85
659 668 0.246635 AGTCGAGAACATGAACCCGG 59.753 55.000 0.00 0.00 0.00 5.73
660 669 1.726791 CAAGTCGAGAACATGAACCCG 59.273 52.381 0.00 0.00 0.00 5.28
668 677 5.237815 AGCATTAATGTCAAGTCGAGAACA 58.762 37.500 16.61 0.00 0.00 3.18
671 680 4.093408 GCAAGCATTAATGTCAAGTCGAGA 59.907 41.667 16.61 0.00 0.00 4.04
674 683 4.082274 TGCAAGCATTAATGTCAAGTCG 57.918 40.909 16.61 1.11 0.00 4.18
686 695 8.480501 AGTAAATCCAAGAATAATGCAAGCATT 58.519 29.630 22.19 22.19 46.85 3.56
687 696 8.015185 AGTAAATCCAAGAATAATGCAAGCAT 57.985 30.769 0.86 0.86 38.46 3.79
711 720 0.463295 ACATCATCGCAAGCCTGGAG 60.463 55.000 0.00 0.00 37.18 3.86
713 722 0.379669 GAACATCATCGCAAGCCTGG 59.620 55.000 0.00 0.00 37.18 4.45
714 723 0.027194 CGAACATCATCGCAAGCCTG 59.973 55.000 0.00 0.00 35.85 4.85
716 725 0.447801 AACGAACATCATCGCAAGCC 59.552 50.000 0.00 0.00 46.51 4.35
724 733 4.158025 ACGTCTCCTCTAAACGAACATCAT 59.842 41.667 0.71 0.00 39.59 2.45
759 772 1.189752 AGTCATCGCAGGTGTCTCAT 58.810 50.000 0.00 0.00 0.00 2.90
760 773 0.969149 AAGTCATCGCAGGTGTCTCA 59.031 50.000 0.00 0.00 0.00 3.27
764 777 4.578913 CGAAGTCATCGCAGGTGT 57.421 55.556 0.00 0.00 45.89 4.16
781 794 5.682862 CGGCATAGCATTGTTGAGATTTTAC 59.317 40.000 0.00 0.00 0.00 2.01
783 796 4.440525 CCGGCATAGCATTGTTGAGATTTT 60.441 41.667 0.00 0.00 0.00 1.82
793 806 1.947013 CTGAGCCGGCATAGCATTG 59.053 57.895 31.54 6.36 0.00 2.82
795 808 2.281345 GCTGAGCCGGCATAGCAT 60.281 61.111 35.55 15.86 35.55 3.79
796 809 4.552365 GGCTGAGCCGGCATAGCA 62.552 66.667 38.40 25.98 39.62 3.49
812 825 3.191162 CCTCTATGAGCATCTTCGAGAGG 59.809 52.174 10.32 10.32 40.56 3.69
820 833 3.116939 ACACCCTACCTCTATGAGCATCT 60.117 47.826 0.00 0.00 34.92 2.90
822 835 2.968574 CACACCCTACCTCTATGAGCAT 59.031 50.000 0.00 0.00 0.00 3.79
832 845 2.124507 AACGCATGCACACCCTACCT 62.125 55.000 19.57 0.00 0.00 3.08
834 847 0.953471 TGAACGCATGCACACCCTAC 60.953 55.000 19.57 0.49 0.00 3.18
844 857 2.352651 CACTCACCCTTATGAACGCATG 59.647 50.000 0.00 0.00 35.94 4.06
845 858 2.027192 ACACTCACCCTTATGAACGCAT 60.027 45.455 0.00 0.00 38.54 4.73
846 859 1.346395 ACACTCACCCTTATGAACGCA 59.654 47.619 0.00 0.00 0.00 5.24
847 860 2.094762 ACACTCACCCTTATGAACGC 57.905 50.000 0.00 0.00 0.00 4.84
850 863 5.626809 GCTCACATACACTCACCCTTATGAA 60.627 44.000 0.00 0.00 0.00 2.57
851 864 4.141937 GCTCACATACACTCACCCTTATGA 60.142 45.833 0.00 0.00 0.00 2.15
852 865 4.122776 GCTCACATACACTCACCCTTATG 58.877 47.826 0.00 0.00 0.00 1.90
853 866 3.181475 CGCTCACATACACTCACCCTTAT 60.181 47.826 0.00 0.00 0.00 1.73
854 867 2.165641 CGCTCACATACACTCACCCTTA 59.834 50.000 0.00 0.00 0.00 2.69
855 868 1.066858 CGCTCACATACACTCACCCTT 60.067 52.381 0.00 0.00 0.00 3.95
856 869 0.532573 CGCTCACATACACTCACCCT 59.467 55.000 0.00 0.00 0.00 4.34
857 870 0.530744 TCGCTCACATACACTCACCC 59.469 55.000 0.00 0.00 0.00 4.61
859 872 2.638556 AGTCGCTCACATACACTCAC 57.361 50.000 0.00 0.00 0.00 3.51
860 873 2.414161 CGAAGTCGCTCACATACACTCA 60.414 50.000 0.00 0.00 0.00 3.41
861 874 2.159558 TCGAAGTCGCTCACATACACTC 60.160 50.000 0.00 0.00 39.60 3.51
862 875 1.810755 TCGAAGTCGCTCACATACACT 59.189 47.619 0.00 0.00 39.60 3.55
873 906 0.638746 CACGGTACAATCGAAGTCGC 59.361 55.000 0.00 0.00 39.60 5.19
874 907 1.973138 ACACGGTACAATCGAAGTCG 58.027 50.000 0.00 0.00 41.45 4.18
917 952 1.152271 TCCCTCCCTCTCTTTCCTTGT 59.848 52.381 0.00 0.00 0.00 3.16
918 953 1.836802 CTCCCTCCCTCTCTTTCCTTG 59.163 57.143 0.00 0.00 0.00 3.61
1353 1388 1.341089 GGAAAGGCTAGGGTTTGGAGG 60.341 57.143 0.00 0.00 0.00 4.30
1507 1549 3.371063 GTGGCGTCGTCCTCCTCA 61.371 66.667 0.00 0.00 0.00 3.86
1710 1764 2.247437 GGGAGACATCAATCGCGGC 61.247 63.158 6.13 0.00 0.00 6.53
1714 1768 5.627499 TTCAAAAAGGGAGACATCAATCG 57.373 39.130 0.00 0.00 0.00 3.34
1762 1816 3.191791 CACATGACTGATGATGGCACAAA 59.808 43.478 0.00 0.00 37.43 2.83
1763 1817 2.750712 CACATGACTGATGATGGCACAA 59.249 45.455 0.00 0.00 37.43 3.33
1802 1856 9.924010 AGTCAGTATAAGAAGGTCATACTAGTT 57.076 33.333 0.00 0.00 34.50 2.24
1820 1874 9.856488 CACTAACAGTACACATTTAGTCAGTAT 57.144 33.333 0.00 0.00 33.44 2.12
1886 1950 3.008330 GCACATCAGAATGCTTCAGTCT 58.992 45.455 3.26 0.00 39.45 3.24
2060 2215 8.079809 CCGAAACATACTGGTTCAGTTAAAAAT 58.920 33.333 5.86 0.00 44.00 1.82
2076 2231 3.106672 CGAGACTGCTACCGAAACATAC 58.893 50.000 0.00 0.00 0.00 2.39
2097 2252 1.680338 AGTCCACACCAACAAAGAGC 58.320 50.000 0.00 0.00 0.00 4.09
2222 2379 4.267536 GTGTGGGACTAAGGGGTTATTTC 58.732 47.826 0.00 0.00 0.00 2.17
2233 2390 5.277250 TCTCATATGAAGGTGTGGGACTAA 58.723 41.667 6.90 0.00 0.00 2.24
2262 2419 0.752658 AAGCACCCCAGTCTTTTTGC 59.247 50.000 0.00 0.00 0.00 3.68
2277 2434 0.107752 TGCGATGGCATACAGAAGCA 60.108 50.000 0.00 3.15 46.21 3.91
2356 2514 1.762370 TGTGACCTGTGCTTCTCAGAA 59.238 47.619 0.00 0.00 35.20 3.02
2415 2573 4.713792 AGATCATCATTAGTTGGGACCC 57.286 45.455 2.45 2.45 0.00 4.46
2418 2576 7.690301 GCTTAGGAAGATCATCATTAGTTGGGA 60.690 40.741 0.00 0.00 0.00 4.37
2419 2577 6.429385 GCTTAGGAAGATCATCATTAGTTGGG 59.571 42.308 0.00 0.00 0.00 4.12
2420 2578 7.222872 AGCTTAGGAAGATCATCATTAGTTGG 58.777 38.462 0.00 0.00 0.00 3.77
2421 2579 8.674263 AAGCTTAGGAAGATCATCATTAGTTG 57.326 34.615 0.00 0.00 0.00 3.16
2434 2592 4.651503 CCTCACCATCTAAGCTTAGGAAGA 59.348 45.833 28.81 15.35 0.00 2.87
2444 2602 1.211457 AGCAAGGCCTCACCATCTAAG 59.789 52.381 5.23 0.00 43.14 2.18
2513 2671 6.126796 ACCAGTTTGGACCAGAAATTCAAAAT 60.127 34.615 1.40 0.00 40.96 1.82
2596 2758 7.269316 ACATACACGTGTTCATTACCATATCA 58.731 34.615 28.55 3.18 0.00 2.15
2619 2781 5.304101 AGGACCACAAAAGCATAATCAAACA 59.696 36.000 0.00 0.00 0.00 2.83
2627 2789 2.584835 AGCAGGACCACAAAAGCATA 57.415 45.000 0.00 0.00 0.00 3.14
2665 2827 3.005684 CCAACAATTTTGCAGGCAGACTA 59.994 43.478 0.00 0.00 0.00 2.59
2666 2828 2.224113 CCAACAATTTTGCAGGCAGACT 60.224 45.455 0.00 0.00 0.00 3.24
2668 2830 2.037901 TCCAACAATTTTGCAGGCAGA 58.962 42.857 0.00 0.00 0.00 4.26
2669 2831 2.529780 TCCAACAATTTTGCAGGCAG 57.470 45.000 0.00 0.00 0.00 4.85
2687 2849 4.668576 TTGACGAGCACTTTGATTGATC 57.331 40.909 0.00 0.00 0.00 2.92
2717 2879 4.748102 ACTCACAAGTAACAACACCATACG 59.252 41.667 0.00 0.00 32.59 3.06
2723 2885 8.361592 AGTTATGTACTCACAAGTAACAACAC 57.638 34.615 0.00 0.00 39.66 3.32
2744 2906 3.572642 TCACCAGACAGACCAAGAGTTA 58.427 45.455 0.00 0.00 0.00 2.24
2755 2918 5.794894 AGGTAAGTTACAATCACCAGACAG 58.205 41.667 14.81 0.00 0.00 3.51
2816 2984 6.428465 TCTGCAATCAAAGGTACGACAAAATA 59.572 34.615 0.00 0.00 0.00 1.40
2897 3065 0.947244 GCAGGTTATTGAGGCCATCG 59.053 55.000 5.01 0.00 0.00 3.84
3044 3212 1.444119 GGCCGACTGTTGTGAGCAAA 61.444 55.000 0.00 0.00 36.22 3.68
3263 3440 4.751767 TTTTCCTTGGACTTTTGCACAT 57.248 36.364 0.00 0.00 0.00 3.21
3633 3811 2.357009 CTCATAGTTGCTGGATGGTTGC 59.643 50.000 0.00 0.00 0.00 4.17
3804 3982 2.280524 TCCACCGGACTGTTTGCG 60.281 61.111 9.46 0.00 39.13 4.85
4407 6909 3.071874 ACTGAATTTGCGAATCCTCCA 57.928 42.857 0.00 0.00 0.00 3.86
4474 6984 5.989477 TCATACGAATCCTCAACCATTCTT 58.011 37.500 0.00 0.00 0.00 2.52
4600 7823 9.988350 GCTAACATTTATTTCTTTCGATCAGAA 57.012 29.630 3.92 3.92 37.01 3.02
4620 7843 3.402110 CAGTGACCAGAACATGCTAACA 58.598 45.455 0.00 0.00 0.00 2.41
4650 7880 2.227194 TCGCCAGAAGGGAAAAAGAAC 58.773 47.619 0.00 0.00 40.01 3.01
4668 7898 3.303881 TTCTTCCAGTGTGAGACATCG 57.696 47.619 0.00 0.00 0.00 3.84
4846 8090 4.517285 ACTCCATTATGTCTTGCGTTGAT 58.483 39.130 0.00 0.00 0.00 2.57
4939 8193 6.038936 GGGTTTGTTATACTCGCCATGTTATT 59.961 38.462 0.00 0.00 0.00 1.40
4967 8221 2.415512 CTCCTTTCGGTTTGTCGGAATC 59.584 50.000 0.00 0.00 35.79 2.52
4980 8234 2.599082 CGCTACTAGTTTGCTCCTTTCG 59.401 50.000 0.00 0.00 0.00 3.46
4986 8240 7.326547 GGATTTATCTACGCTACTAGTTTGCTC 59.673 40.741 0.00 0.00 0.00 4.26
5127 8390 0.257039 GAAGCACACCCCCATCTGAT 59.743 55.000 0.00 0.00 0.00 2.90
5199 8464 2.537560 GCATTGGCGTCTCATCGGG 61.538 63.158 0.00 0.00 0.00 5.14
5235 8500 2.436824 GGCGAGAAAGTGGCCCTC 60.437 66.667 0.00 0.00 44.24 4.30
5388 8653 0.251077 CAAAGGGCACAGAGAAGGCT 60.251 55.000 0.00 0.00 0.00 4.58
5496 8766 7.010923 CAGATCTTTGTAGCCTCATGACTTAAC 59.989 40.741 0.00 0.00 0.00 2.01
5498 8768 6.381133 TCAGATCTTTGTAGCCTCATGACTTA 59.619 38.462 0.00 0.00 0.00 2.24
5501 8771 4.808364 GTCAGATCTTTGTAGCCTCATGAC 59.192 45.833 0.00 0.00 0.00 3.06
5511 8781 5.470098 GCTTGAGGTTTGTCAGATCTTTGTA 59.530 40.000 0.00 0.00 0.00 2.41
5520 8790 1.876156 GTGGAGCTTGAGGTTTGTCAG 59.124 52.381 0.00 0.00 0.00 3.51
5521 8799 1.810031 CGTGGAGCTTGAGGTTTGTCA 60.810 52.381 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.