Multiple sequence alignment - TraesCS6A01G118000

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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 TraesCS6A01G118000 chr6A 100.000 4918 0 0 1 4918 88846939 88851856 0.000000e+00 9082
1 TraesCS6A01G118000 chr6B 92.146 4316 185 58 2 4227 146695910 146700161 0.000000e+00 5951
2 TraesCS6A01G118000 chr6B 94.783 115 6 0 4793 4907 146708122 146708236 3.910000e-41 180
3 TraesCS6A01G118000 chr6B 89.516 124 6 2 4363 4480 671146810 671146688 3.070000e-32 150
4 TraesCS6A01G118000 chr6D 92.845 3438 145 54 1 3362 72139866 72143278 0.000000e+00 4892
5 TraesCS6A01G118000 chr6D 95.770 922 25 8 3364 4278 72143439 72144353 0.000000e+00 1474
6 TraesCS6A01G118000 chr6D 93.593 437 21 4 4481 4917 72170751 72171180 0.000000e+00 645
7 TraesCS6A01G118000 chr6D 94.624 93 5 0 4269 4361 72170673 72170765 1.430000e-30 145
8 TraesCS6A01G118000 chr2B 83.861 632 69 19 3695 4326 68602015 68602613 5.520000e-159 571
9 TraesCS6A01G118000 chr2B 81.201 633 81 20 3695 4325 39734914 39735510 4.450000e-130 475
10 TraesCS6A01G118000 chr2B 84.074 270 24 9 2717 2981 68601680 68601935 4.920000e-60 243
11 TraesCS6A01G118000 chr3A 82.704 636 69 21 3695 4325 688425574 688424975 1.210000e-145 527
12 TraesCS6A01G118000 chr3A 92.254 142 5 3 2718 2857 688436502 688436639 3.880000e-46 196
13 TraesCS6A01G118000 chr1D 84.340 530 53 17 3695 4224 486701536 486701037 4.420000e-135 492
14 TraesCS6A01G118000 chr1D 81.849 584 67 21 3695 4274 308188483 308189031 5.800000e-124 455
15 TraesCS6A01G118000 chr1D 86.555 119 12 4 4363 4480 452579799 452579914 1.440000e-25 128
16 TraesCS6A01G118000 chr4B 82.504 583 64 21 3695 4274 527326927 527326380 1.240000e-130 477
17 TraesCS6A01G118000 chr4B 83.585 530 57 17 3695 4224 566610707 566610208 2.070000e-128 470
18 TraesCS6A01G118000 chr7D 81.102 635 81 23 3695 4325 298811879 298812478 5.760000e-129 472
19 TraesCS6A01G118000 chr7D 83.208 530 58 16 3695 4224 162186122 162185624 1.610000e-124 457
20 TraesCS6A01G118000 chr7D 86.885 122 14 2 4361 4480 295294141 295294262 8.590000e-28 135
21 TraesCS6A01G118000 chr2D 83.019 530 59 16 3695 4224 408489820 408489322 7.510000e-123 451
22 TraesCS6A01G118000 chr2D 89.516 124 6 6 4361 4480 10069664 10069544 3.070000e-32 150
23 TraesCS6A01G118000 chr2D 86.777 121 9 6 4362 4479 642785969 642786085 1.440000e-25 128
24 TraesCS6A01G118000 chr1A 83.019 530 59 16 3695 4224 45647766 45647268 7.510000e-123 451
25 TraesCS6A01G118000 chr1A 87.500 120 8 7 4363 4480 544570543 544570429 1.110000e-26 132
26 TraesCS6A01G118000 chr3D 80.220 637 85 23 3695 4328 173629205 173628607 1.620000e-119 440
27 TraesCS6A01G118000 chr5D 94.915 118 3 2 4363 4478 271849075 271849191 1.090000e-41 182
28 TraesCS6A01G118000 chr5B 91.270 126 8 3 4357 4480 658446344 658446220 8.470000e-38 169
29 TraesCS6A01G118000 chr5B 95.506 89 4 0 3668 3756 296940137 296940049 5.130000e-30 143
30 TraesCS6A01G118000 chr7B 88.333 120 8 6 4363 4480 287161115 287161000 6.640000e-29 139


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 TraesCS6A01G118000 chr6A 88846939 88851856 4917 False 9082 9082 100.0000 1 4918 1 chr6A.!!$F1 4917
1 TraesCS6A01G118000 chr6B 146695910 146700161 4251 False 5951 5951 92.1460 2 4227 1 chr6B.!!$F1 4225
2 TraesCS6A01G118000 chr6D 72139866 72144353 4487 False 3183 4892 94.3075 1 4278 2 chr6D.!!$F1 4277
3 TraesCS6A01G118000 chr6D 72170673 72171180 507 False 395 645 94.1085 4269 4917 2 chr6D.!!$F2 648
4 TraesCS6A01G118000 chr2B 39734914 39735510 596 False 475 475 81.2010 3695 4325 1 chr2B.!!$F1 630
5 TraesCS6A01G118000 chr2B 68601680 68602613 933 False 407 571 83.9675 2717 4326 2 chr2B.!!$F2 1609
6 TraesCS6A01G118000 chr3A 688424975 688425574 599 True 527 527 82.7040 3695 4325 1 chr3A.!!$R1 630
7 TraesCS6A01G118000 chr1D 308188483 308189031 548 False 455 455 81.8490 3695 4274 1 chr1D.!!$F1 579
8 TraesCS6A01G118000 chr4B 527326380 527326927 547 True 477 477 82.5040 3695 4274 1 chr4B.!!$R1 579
9 TraesCS6A01G118000 chr7D 298811879 298812478 599 False 472 472 81.1020 3695 4325 1 chr7D.!!$F2 630
10 TraesCS6A01G118000 chr3D 173628607 173629205 598 True 440 440 80.2200 3695 4328 1 chr3D.!!$R1 633

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
537 581 0.110486 GACTTCTTCCCCTTGCCACA 59.890 55.0 0.00 0.0 0.00 4.17 F
1989 2062 0.603707 CGGCAGCACCAGAGAAGAAA 60.604 55.0 0.00 0.0 39.03 2.52 F
2055 2128 0.178891 AGGAGGAGGAGCTGTCCAAA 60.179 55.0 13.16 0.0 46.80 3.28 F
2214 2287 0.373716 GCAAAGGGTCTATGTTCGCG 59.626 55.0 0.00 0.0 0.00 5.87 F
3238 3398 0.543277 TTGGGCCAGTGATAGAGCAG 59.457 55.0 6.23 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2123 0.321210 TCCTCGCATTTCGCTTTGGA 60.321 50.000 0.00 0.00 39.08 3.53 R
3126 3286 0.895100 GCTCAATTGCCTGTGGTCCA 60.895 55.000 0.00 0.00 0.00 4.02 R
3238 3398 1.602920 GGGCTAACAGTTTGTTGCAGC 60.603 52.381 4.78 6.46 41.30 5.25 R
3815 4138 1.897802 TCAGTAAACCCCGAAGACTCC 59.102 52.381 0.00 0.00 0.00 3.85 R
4720 5067 0.178992 CCTCCTGAGATCGAGGCTCT 60.179 60.000 13.50 3.42 39.36 4.09 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
36 37 1.210478 TGTGAGCCCAGGAATTCTAGC 59.790 52.381 5.23 3.68 0.00 3.42
38 39 2.092699 GTGAGCCCAGGAATTCTAGCTT 60.093 50.000 5.23 0.00 35.27 3.74
41 42 2.092158 AGCCCAGGAATTCTAGCTTTCC 60.092 50.000 6.78 6.78 41.46 3.13
51 52 1.272490 TCTAGCTTTCCTGTGACCGTG 59.728 52.381 0.00 0.00 0.00 4.94
87 88 0.523072 CAGGGCAAATTGGTCTCACG 59.477 55.000 0.00 0.00 0.00 4.35
124 125 2.161855 TGCAAATCCCAGATGACACAC 58.838 47.619 0.00 0.00 0.00 3.82
145 146 2.418628 CCACGATTCCAACACATGTACC 59.581 50.000 0.00 0.00 0.00 3.34
146 147 3.070748 CACGATTCCAACACATGTACCA 58.929 45.455 0.00 0.00 0.00 3.25
173 191 2.853430 ACCACCTAGAGAGAGGAGAGA 58.147 52.381 0.00 0.00 39.15 3.10
174 192 2.777692 ACCACCTAGAGAGAGGAGAGAG 59.222 54.545 0.00 0.00 39.15 3.20
175 193 3.045634 CCACCTAGAGAGAGGAGAGAGA 58.954 54.545 0.00 0.00 39.15 3.10
176 194 3.071602 CCACCTAGAGAGAGGAGAGAGAG 59.928 56.522 0.00 0.00 39.15 3.20
177 195 3.967326 CACCTAGAGAGAGGAGAGAGAGA 59.033 52.174 0.00 0.00 39.15 3.10
304 325 1.858301 TAAAACCCCACCCCCTCCC 60.858 63.158 0.00 0.00 0.00 4.30
337 359 1.282653 CCCTTTCTTCCTCCTCCCCC 61.283 65.000 0.00 0.00 0.00 5.40
370 392 2.193248 CCGCAATTCCCTCCCTCC 59.807 66.667 0.00 0.00 0.00 4.30
371 393 2.378634 CCGCAATTCCCTCCCTCCT 61.379 63.158 0.00 0.00 0.00 3.69
426 458 4.896482 TCCCTAGTTAGCATTCCTCTTCTC 59.104 45.833 0.00 0.00 0.00 2.87
457 489 2.292267 CCATCTCCAATCCCAAAGACG 58.708 52.381 0.00 0.00 0.00 4.18
521 565 1.981636 CTCTGCTCCTGGCTTGACT 59.018 57.895 0.00 0.00 42.39 3.41
527 571 1.948144 GCTCCTGGCTTGACTTCTTCC 60.948 57.143 0.00 0.00 38.06 3.46
537 581 0.110486 GACTTCTTCCCCTTGCCACA 59.890 55.000 0.00 0.00 0.00 4.17
556 600 1.139947 GACAGAGGAGTACGGCAGC 59.860 63.158 0.00 0.00 0.00 5.25
557 601 2.286127 GACAGAGGAGTACGGCAGCC 62.286 65.000 0.00 0.00 0.00 4.85
570 614 1.144936 GCAGCCGCTGTAGAATCCT 59.855 57.895 21.29 0.00 33.43 3.24
827 879 1.669604 GCCGAGAAGGAAGGGAATTC 58.330 55.000 0.00 0.00 45.00 2.17
838 890 0.618981 AGGGAATTCCTCGGTTGACC 59.381 55.000 23.63 4.06 44.06 4.02
847 899 1.611673 CCTCGGTTGACCAGCAATCTT 60.612 52.381 0.51 0.00 39.03 2.40
848 900 1.734465 CTCGGTTGACCAGCAATCTTC 59.266 52.381 0.51 0.00 39.03 2.87
849 901 0.804989 CGGTTGACCAGCAATCTTCC 59.195 55.000 0.51 0.00 39.03 3.46
926 984 1.463674 GGCGGTGGAGTTCATTGATT 58.536 50.000 0.00 0.00 0.00 2.57
928 986 2.083774 GCGGTGGAGTTCATTGATTGA 58.916 47.619 0.00 0.00 0.00 2.57
929 987 2.684881 GCGGTGGAGTTCATTGATTGAT 59.315 45.455 0.00 0.00 33.34 2.57
936 994 3.812053 GAGTTCATTGATTGATCGGAGGG 59.188 47.826 0.00 0.00 33.34 4.30
940 998 3.144506 CATTGATTGATCGGAGGGGAAG 58.855 50.000 0.00 0.00 0.00 3.46
941 999 2.174685 TGATTGATCGGAGGGGAAGA 57.825 50.000 0.00 0.00 0.00 2.87
942 1000 2.042464 TGATTGATCGGAGGGGAAGAG 58.958 52.381 0.00 0.00 0.00 2.85
943 1001 2.320781 GATTGATCGGAGGGGAAGAGA 58.679 52.381 0.00 0.00 0.00 3.10
944 1002 1.781786 TTGATCGGAGGGGAAGAGAG 58.218 55.000 0.00 0.00 0.00 3.20
1662 1735 1.962822 CATCGACGGCATCATGGGG 60.963 63.158 0.00 0.00 0.00 4.96
1687 1760 3.443045 CCATGGAGGCCAACACGC 61.443 66.667 5.56 0.00 36.95 5.34
1758 1831 0.980231 ACCTCAGGAGCCTCATGGTC 60.980 60.000 6.52 0.00 40.86 4.02
1929 2002 3.148084 CCACCACCGACAGAACCT 58.852 61.111 0.00 0.00 0.00 3.50
1989 2062 0.603707 CGGCAGCACCAGAGAAGAAA 60.604 55.000 0.00 0.00 39.03 2.52
2026 2099 4.224818 AGAAGAAGGTGAAGATGGAGAAGG 59.775 45.833 0.00 0.00 0.00 3.46
2050 2123 2.297129 GCCAAGGAGGAGGAGCTGT 61.297 63.158 0.00 0.00 41.22 4.40
2055 2128 0.178891 AGGAGGAGGAGCTGTCCAAA 60.179 55.000 13.16 0.00 46.80 3.28
2057 2130 0.392327 GAGGAGGAGCTGTCCAAAGC 60.392 60.000 13.16 0.00 46.80 3.51
2073 2146 2.897350 GCGAAATGCGAGGAGGGG 60.897 66.667 0.00 0.00 44.57 4.79
2145 2218 1.668151 GACAAAGGCGCCGAAGACT 60.668 57.895 23.20 0.00 0.00 3.24
2214 2287 0.373716 GCAAAGGGTCTATGTTCGCG 59.626 55.000 0.00 0.00 0.00 5.87
2354 2428 8.445275 TGAGCTAACAGTAACTCAAATTTTCA 57.555 30.769 0.00 0.00 36.27 2.69
2440 2526 7.721402 AGATGATGTTACCTCTTCTATGACAC 58.279 38.462 4.71 0.00 0.00 3.67
2449 2535 7.868906 ACCTCTTCTATGACACTCTTACTAC 57.131 40.000 0.00 0.00 0.00 2.73
2450 2536 7.403671 ACCTCTTCTATGACACTCTTACTACA 58.596 38.462 0.00 0.00 0.00 2.74
2455 2541 7.265647 TCTATGACACTCTTACTACATCAGC 57.734 40.000 0.00 0.00 0.00 4.26
2472 2560 7.928307 ACATCAGCTAAATTACAGACATGTT 57.072 32.000 0.00 0.00 41.01 2.71
2549 2649 8.429237 TTCAGTTCCACCACCATAATTAAATT 57.571 30.769 0.00 0.00 0.00 1.82
2550 2650 8.429237 TCAGTTCCACCACCATAATTAAATTT 57.571 30.769 0.00 0.00 0.00 1.82
2551 2651 8.527810 TCAGTTCCACCACCATAATTAAATTTC 58.472 33.333 0.00 0.00 0.00 2.17
2552 2652 7.487829 CAGTTCCACCACCATAATTAAATTTCG 59.512 37.037 0.00 0.00 0.00 3.46
2553 2653 6.458232 TCCACCACCATAATTAAATTTCGG 57.542 37.500 0.00 0.00 0.00 4.30
2554 2654 5.361285 TCCACCACCATAATTAAATTTCGGG 59.639 40.000 0.00 0.00 0.00 5.14
2556 2656 6.039616 CACCACCATAATTAAATTTCGGGTG 58.960 40.000 0.00 0.00 43.13 4.61
2557 2657 5.047188 CCACCATAATTAAATTTCGGGTGC 58.953 41.667 0.00 0.00 42.37 5.01
2558 2658 5.047188 CACCATAATTAAATTTCGGGTGCC 58.953 41.667 0.00 0.00 38.22 5.01
2560 2660 5.068591 ACCATAATTAAATTTCGGGTGCCTC 59.931 40.000 0.00 0.00 0.00 4.70
2562 2662 2.188062 TTAAATTTCGGGTGCCTCGT 57.812 45.000 0.00 0.00 0.00 4.18
2563 2663 1.444836 TAAATTTCGGGTGCCTCGTG 58.555 50.000 0.00 0.00 0.00 4.35
2698 2812 6.683974 ACCACATGCTTGATAAGTTGATAC 57.316 37.500 6.60 0.00 0.00 2.24
2739 2853 5.763698 GGAACTGGTATCAACTATTAAGCCC 59.236 44.000 0.00 0.00 0.00 5.19
2740 2854 5.968676 ACTGGTATCAACTATTAAGCCCA 57.031 39.130 0.00 0.00 0.00 5.36
2741 2855 6.515512 ACTGGTATCAACTATTAAGCCCAT 57.484 37.500 0.00 0.00 0.00 4.00
2856 2973 9.189723 CTGTAAGTACACACCTTTTAAGAGTAC 57.810 37.037 0.00 0.00 31.93 2.73
2865 2984 7.876068 CACACCTTTTAAGAGTACCACTGATAA 59.124 37.037 0.00 0.00 0.00 1.75
2883 3002 9.354673 CACTGATAATCCAGTAACCCATAAAAT 57.645 33.333 0.00 0.00 44.87 1.82
2884 3003 9.574516 ACTGATAATCCAGTAACCCATAAAATC 57.425 33.333 0.00 0.00 44.82 2.17
2889 3008 6.057321 TCCAGTAACCCATAAAATCGAAGT 57.943 37.500 0.00 0.00 0.00 3.01
2947 3068 1.132453 GCGAATCCTGGCAAACCTAAC 59.868 52.381 0.00 0.00 36.63 2.34
3002 3123 5.680619 AGTCCAGTGAACACATGAGTTTTA 58.319 37.500 9.96 0.49 0.00 1.52
3103 3225 8.519799 TTGGATAAACTAGATTCAACCATTCC 57.480 34.615 0.00 0.00 0.00 3.01
3126 3286 8.523915 TCCATTATGCTCAATTATTCAACAGT 57.476 30.769 0.00 0.00 0.00 3.55
3238 3398 0.543277 TTGGGCCAGTGATAGAGCAG 59.457 55.000 6.23 0.00 0.00 4.24
3247 3407 2.079158 GTGATAGAGCAGCTGCAACAA 58.921 47.619 38.24 21.49 45.16 2.83
3362 3522 3.402628 TCTGTCCAGCTTCTTTGTACC 57.597 47.619 0.00 0.00 0.00 3.34
3395 3714 3.198068 ACACACGATGGCATCATTACTC 58.802 45.455 25.88 0.00 32.98 2.59
3409 3728 7.387948 GGCATCATTACTCACCTTACGATTTAT 59.612 37.037 0.00 0.00 0.00 1.40
3728 4047 9.252962 ACTGATGCTTGAAAGAATAAAAAGTTG 57.747 29.630 0.00 0.00 0.00 3.16
3815 4138 2.785477 ACGTGTCTACTTTGTCGAAACG 59.215 45.455 11.59 11.59 42.20 3.60
3990 4325 4.330347 CCTTTTTAGCTTCTCTCGTTAGCC 59.670 45.833 0.00 0.00 35.53 3.93
4239 4582 7.763985 TCCGGATATATGTTATGTTATGCACAG 59.236 37.037 0.00 0.00 39.40 3.66
4265 4611 4.929211 GGTGCTGTTTCATCCATTTTTACC 59.071 41.667 0.00 0.00 0.00 2.85
4289 4635 2.762887 TCTGAAATCACTCGCTCCATCT 59.237 45.455 0.00 0.00 0.00 2.90
4327 4674 1.934525 CATGCACAGCAAAGCAAAACA 59.065 42.857 0.00 0.00 43.62 2.83
4330 4677 1.190763 GCACAGCAAAGCAAAACATCG 59.809 47.619 0.00 0.00 0.00 3.84
4347 4694 3.598019 ATCGCACAGATGGCAAATTTT 57.402 38.095 0.00 0.00 38.36 1.82
4348 4695 2.674954 TCGCACAGATGGCAAATTTTG 58.325 42.857 4.72 4.72 0.00 2.44
4349 4696 2.035704 TCGCACAGATGGCAAATTTTGT 59.964 40.909 10.65 0.00 0.00 2.83
4350 4697 3.254411 TCGCACAGATGGCAAATTTTGTA 59.746 39.130 10.65 1.54 0.00 2.41
4351 4698 3.609373 CGCACAGATGGCAAATTTTGTAG 59.391 43.478 10.65 0.00 0.00 2.74
4352 4699 4.559153 GCACAGATGGCAAATTTTGTAGT 58.441 39.130 10.65 0.00 0.00 2.73
4353 4700 4.622740 GCACAGATGGCAAATTTTGTAGTC 59.377 41.667 10.65 6.40 0.00 2.59
4354 4701 5.163513 CACAGATGGCAAATTTTGTAGTCC 58.836 41.667 10.65 4.18 0.00 3.85
4355 4702 4.832266 ACAGATGGCAAATTTTGTAGTCCA 59.168 37.500 10.65 9.28 0.00 4.02
4356 4703 5.304101 ACAGATGGCAAATTTTGTAGTCCAA 59.696 36.000 10.65 0.00 0.00 3.53
4357 4704 6.183360 ACAGATGGCAAATTTTGTAGTCCAAA 60.183 34.615 10.65 0.00 41.25 3.28
4383 4730 2.406205 TTTTTGAACGGTCACGGGG 58.594 52.632 0.44 0.00 46.48 5.73
4384 4731 1.102222 TTTTTGAACGGTCACGGGGG 61.102 55.000 0.44 0.00 46.48 5.40
4401 4748 2.993853 GGAGAGCTTCCCCACCTG 59.006 66.667 0.00 0.00 40.37 4.00
4402 4749 1.613630 GGAGAGCTTCCCCACCTGA 60.614 63.158 0.00 0.00 40.37 3.86
4403 4750 1.201429 GGAGAGCTTCCCCACCTGAA 61.201 60.000 0.00 0.00 40.37 3.02
4404 4751 0.915364 GAGAGCTTCCCCACCTGAAT 59.085 55.000 0.00 0.00 0.00 2.57
4405 4752 2.119495 GAGAGCTTCCCCACCTGAATA 58.881 52.381 0.00 0.00 0.00 1.75
4406 4753 2.708325 GAGAGCTTCCCCACCTGAATAT 59.292 50.000 0.00 0.00 0.00 1.28
4407 4754 3.904339 GAGAGCTTCCCCACCTGAATATA 59.096 47.826 0.00 0.00 0.00 0.86
4408 4755 4.507342 AGAGCTTCCCCACCTGAATATAT 58.493 43.478 0.00 0.00 0.00 0.86
4409 4756 4.916424 AGAGCTTCCCCACCTGAATATATT 59.084 41.667 0.00 0.00 0.00 1.28
4410 4757 6.091555 AGAGCTTCCCCACCTGAATATATTA 58.908 40.000 0.00 0.00 0.00 0.98
4411 4758 6.013293 AGAGCTTCCCCACCTGAATATATTAC 60.013 42.308 0.00 0.00 0.00 1.89
4412 4759 5.014228 AGCTTCCCCACCTGAATATATTACC 59.986 44.000 0.00 0.00 0.00 2.85
4413 4760 5.222048 GCTTCCCCACCTGAATATATTACCA 60.222 44.000 0.00 0.00 0.00 3.25
4414 4761 5.836024 TCCCCACCTGAATATATTACCAC 57.164 43.478 0.00 0.00 0.00 4.16
4415 4762 5.482580 TCCCCACCTGAATATATTACCACT 58.517 41.667 0.00 0.00 0.00 4.00
4416 4763 5.546499 TCCCCACCTGAATATATTACCACTC 59.454 44.000 0.00 0.00 0.00 3.51
4417 4764 5.309543 CCCCACCTGAATATATTACCACTCA 59.690 44.000 0.00 0.00 0.00 3.41
4418 4765 6.183361 CCCCACCTGAATATATTACCACTCAA 60.183 42.308 0.00 0.00 0.00 3.02
4419 4766 7.287061 CCCACCTGAATATATTACCACTCAAA 58.713 38.462 0.00 0.00 0.00 2.69
4420 4767 7.944554 CCCACCTGAATATATTACCACTCAAAT 59.055 37.037 0.00 0.00 0.00 2.32
4421 4768 8.786898 CCACCTGAATATATTACCACTCAAATG 58.213 37.037 0.00 0.00 0.00 2.32
4422 4769 9.559732 CACCTGAATATATTACCACTCAAATGA 57.440 33.333 0.00 0.00 0.00 2.57
4429 4776 9.965902 ATATATTACCACTCAAATGAAGGATCC 57.034 33.333 2.48 2.48 0.00 3.36
4430 4777 2.991250 ACCACTCAAATGAAGGATCCG 58.009 47.619 5.98 0.00 0.00 4.18
4431 4778 2.571653 ACCACTCAAATGAAGGATCCGA 59.428 45.455 5.98 0.00 0.00 4.55
4432 4779 3.201290 CCACTCAAATGAAGGATCCGAG 58.799 50.000 5.98 7.53 0.00 4.63
4433 4780 3.118629 CCACTCAAATGAAGGATCCGAGA 60.119 47.826 15.06 0.49 0.00 4.04
4434 4781 4.507710 CACTCAAATGAAGGATCCGAGAA 58.492 43.478 15.06 0.53 0.00 2.87
4435 4782 5.121811 CACTCAAATGAAGGATCCGAGAAT 58.878 41.667 15.06 2.73 0.00 2.40
4436 4783 5.587844 CACTCAAATGAAGGATCCGAGAATT 59.412 40.000 15.06 7.98 0.00 2.17
4437 4784 6.763135 CACTCAAATGAAGGATCCGAGAATTA 59.237 38.462 15.06 0.00 0.00 1.40
4438 4785 6.763610 ACTCAAATGAAGGATCCGAGAATTAC 59.236 38.462 15.06 0.72 0.00 1.89
4439 4786 6.649155 TCAAATGAAGGATCCGAGAATTACA 58.351 36.000 5.98 0.00 0.00 2.41
4440 4787 6.763135 TCAAATGAAGGATCCGAGAATTACAG 59.237 38.462 5.98 1.01 0.00 2.74
4441 4788 4.060038 TGAAGGATCCGAGAATTACAGC 57.940 45.455 5.98 0.00 0.00 4.40
4442 4789 3.450817 TGAAGGATCCGAGAATTACAGCA 59.549 43.478 5.98 0.00 0.00 4.41
4443 4790 3.742433 AGGATCCGAGAATTACAGCAG 57.258 47.619 5.98 0.00 0.00 4.24
4444 4791 3.300388 AGGATCCGAGAATTACAGCAGA 58.700 45.455 5.98 0.00 0.00 4.26
4445 4792 3.706594 AGGATCCGAGAATTACAGCAGAA 59.293 43.478 5.98 0.00 0.00 3.02
4446 4793 4.162320 AGGATCCGAGAATTACAGCAGAAA 59.838 41.667 5.98 0.00 0.00 2.52
4447 4794 5.059833 GGATCCGAGAATTACAGCAGAAAT 58.940 41.667 0.00 0.00 0.00 2.17
4448 4795 6.042093 AGGATCCGAGAATTACAGCAGAAATA 59.958 38.462 5.98 0.00 0.00 1.40
4449 4796 6.876257 GGATCCGAGAATTACAGCAGAAATAT 59.124 38.462 0.00 0.00 0.00 1.28
4450 4797 7.148507 GGATCCGAGAATTACAGCAGAAATATG 60.149 40.741 0.00 0.00 0.00 1.78
4451 4798 5.991606 TCCGAGAATTACAGCAGAAATATGG 59.008 40.000 0.00 0.00 0.00 2.74
4452 4799 5.180117 CCGAGAATTACAGCAGAAATATGGG 59.820 44.000 0.00 0.00 0.00 4.00
4453 4800 5.760253 CGAGAATTACAGCAGAAATATGGGT 59.240 40.000 0.00 0.00 0.00 4.51
4454 4801 6.929049 CGAGAATTACAGCAGAAATATGGGTA 59.071 38.462 0.00 0.00 0.00 3.69
4455 4802 7.095607 CGAGAATTACAGCAGAAATATGGGTAC 60.096 40.741 0.00 0.00 0.00 3.34
4456 4803 7.573710 AGAATTACAGCAGAAATATGGGTACA 58.426 34.615 0.00 0.00 0.00 2.90
4457 4804 8.052748 AGAATTACAGCAGAAATATGGGTACAA 58.947 33.333 0.00 0.00 0.00 2.41
4458 4805 8.766994 AATTACAGCAGAAATATGGGTACAAT 57.233 30.769 0.00 0.00 0.00 2.71
4459 4806 8.766994 ATTACAGCAGAAATATGGGTACAATT 57.233 30.769 0.00 0.00 0.00 2.32
4460 4807 8.588290 TTACAGCAGAAATATGGGTACAATTT 57.412 30.769 0.00 0.00 0.00 1.82
4461 4808 7.480760 ACAGCAGAAATATGGGTACAATTTT 57.519 32.000 0.00 0.00 0.00 1.82
4462 4809 7.547227 ACAGCAGAAATATGGGTACAATTTTC 58.453 34.615 0.00 2.41 34.40 2.29
4463 4810 7.178274 ACAGCAGAAATATGGGTACAATTTTCA 59.822 33.333 0.00 0.00 35.59 2.69
4464 4811 7.489113 CAGCAGAAATATGGGTACAATTTTCAC 59.511 37.037 0.00 0.30 35.59 3.18
4465 4812 7.397192 AGCAGAAATATGGGTACAATTTTCACT 59.603 33.333 0.00 2.08 35.59 3.41
4466 4813 7.702348 GCAGAAATATGGGTACAATTTTCACTC 59.298 37.037 0.00 0.00 35.59 3.51
4467 4814 8.739039 CAGAAATATGGGTACAATTTTCACTCA 58.261 33.333 0.00 0.00 35.59 3.41
4468 4815 8.960591 AGAAATATGGGTACAATTTTCACTCAG 58.039 33.333 0.00 0.00 35.59 3.35
4469 4816 8.877864 AAATATGGGTACAATTTTCACTCAGA 57.122 30.769 0.00 0.00 0.00 3.27
4470 4817 8.877864 AATATGGGTACAATTTTCACTCAGAA 57.122 30.769 0.00 0.00 0.00 3.02
4471 4818 6.824305 ATGGGTACAATTTTCACTCAGAAG 57.176 37.500 0.00 0.00 37.57 2.85
4472 4819 5.070001 TGGGTACAATTTTCACTCAGAAGG 58.930 41.667 0.00 0.00 37.57 3.46
4473 4820 4.459337 GGGTACAATTTTCACTCAGAAGGG 59.541 45.833 0.00 0.00 37.57 3.95
4474 4821 5.313712 GGTACAATTTTCACTCAGAAGGGA 58.686 41.667 0.00 0.00 37.57 4.20
4475 4822 5.946377 GGTACAATTTTCACTCAGAAGGGAT 59.054 40.000 0.00 0.00 34.04 3.85
4476 4823 6.434340 GGTACAATTTTCACTCAGAAGGGATT 59.566 38.462 0.00 0.00 34.04 3.01
4477 4824 6.336842 ACAATTTTCACTCAGAAGGGATTG 57.663 37.500 0.00 0.00 34.04 2.67
4478 4825 5.166398 CAATTTTCACTCAGAAGGGATTGC 58.834 41.667 0.00 0.00 34.04 3.56
4479 4826 3.507162 TTTCACTCAGAAGGGATTGCA 57.493 42.857 0.00 0.00 34.04 4.08
4480 4827 3.726557 TTCACTCAGAAGGGATTGCAT 57.273 42.857 0.00 0.00 34.04 3.96
4562 4909 3.057315 ACATCACCTGAAAATTCAAGCGG 60.057 43.478 0.00 0.00 36.64 5.52
4587 4934 2.052157 GACTAGAATCGCATGCGTACC 58.948 52.381 36.50 25.15 40.74 3.34
4588 4935 1.681793 ACTAGAATCGCATGCGTACCT 59.318 47.619 36.50 29.50 40.74 3.08
4598 4945 2.398498 CATGCGTACCTGTCATAGCTC 58.602 52.381 0.00 0.00 0.00 4.09
4601 4948 1.860399 GCGTACCTGTCATAGCTCACG 60.860 57.143 0.00 0.00 0.00 4.35
4604 4951 1.330655 ACCTGTCATAGCTCACGGGG 61.331 60.000 18.18 10.23 42.67 5.73
4608 4955 0.039074 GTCATAGCTCACGGGGATCG 60.039 60.000 0.00 0.00 45.88 3.69
4720 5067 2.645802 ACTGCAAAGTGGGTTCGTTAA 58.354 42.857 0.00 0.00 0.00 2.01
4721 5068 2.616842 ACTGCAAAGTGGGTTCGTTAAG 59.383 45.455 0.00 0.00 0.00 1.85
4733 5080 3.364946 GTTCGTTAAGAGCCTCGATCTC 58.635 50.000 6.70 6.70 32.54 2.75
4812 5159 3.613030 ACCCGTGTGTTTTGTTAAGTCT 58.387 40.909 0.00 0.00 0.00 3.24
4813 5160 4.768583 ACCCGTGTGTTTTGTTAAGTCTA 58.231 39.130 0.00 0.00 0.00 2.59
4824 5171 5.599999 TTGTTAAGTCTAGATCTGAGGCC 57.400 43.478 5.18 0.00 0.00 5.19
4839 5186 1.596477 GGCCGTGCAGATCTGATCC 60.596 63.158 27.04 13.80 0.00 3.36
4856 5203 0.690192 TCCGATGGCCTGAGAAAACA 59.310 50.000 3.32 0.00 0.00 2.83
4917 5264 2.280389 CCCCTCACATCATCGCCG 60.280 66.667 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.210478 GCTAGAATTCCTGGGCTCACA 59.790 52.381 0.65 0.00 0.00 3.58
36 37 1.302511 CCCCACGGTCACAGGAAAG 60.303 63.158 0.00 0.00 0.00 2.62
38 39 2.122769 TCCCCACGGTCACAGGAA 60.123 61.111 0.00 0.00 0.00 3.36
41 42 4.394712 GGCTCCCCACGGTCACAG 62.395 72.222 0.00 0.00 0.00 3.66
51 52 2.440980 GTGCTTCCATGGCTCCCC 60.441 66.667 6.96 0.00 0.00 4.81
87 88 2.923121 TGCAATGGATAAGTGGAGAGC 58.077 47.619 0.00 0.00 0.00 4.09
124 125 2.418628 GGTACATGTGTTGGAATCGTGG 59.581 50.000 9.11 0.00 0.00 4.94
145 146 4.121317 CTCTCTCTAGGTGGTACGTACTG 58.879 52.174 24.07 8.78 0.00 2.74
146 147 3.134442 CCTCTCTCTAGGTGGTACGTACT 59.866 52.174 24.07 7.98 31.46 2.73
173 191 3.773154 GCCCCCTCCCTCCTCTCT 61.773 72.222 0.00 0.00 0.00 3.10
174 192 4.890306 GGCCCCCTCCCTCCTCTC 62.890 77.778 0.00 0.00 0.00 3.20
225 246 2.124693 GTCGCTCTCCTCCCTCTGG 61.125 68.421 0.00 0.00 0.00 3.86
304 325 1.004862 GAAAGGGTTCAAGAGGAGGGG 59.995 57.143 0.00 0.00 33.61 4.79
337 359 4.506255 GGGGGATTGGAGGCGGTG 62.506 72.222 0.00 0.00 0.00 4.94
370 392 4.978099 AGGCTAGAGAGAGAGATGAGAAG 58.022 47.826 0.00 0.00 0.00 2.85
371 393 5.376625 GAAGGCTAGAGAGAGAGATGAGAA 58.623 45.833 0.00 0.00 0.00 2.87
426 458 1.147153 GGAGATGGGCGAAGGGAAG 59.853 63.158 0.00 0.00 0.00 3.46
521 565 0.110486 GTCTGTGGCAAGGGGAAGAA 59.890 55.000 0.00 0.00 0.00 2.52
527 571 1.002868 CCTCTGTCTGTGGCAAGGG 60.003 63.158 0.00 0.00 0.00 3.95
537 581 1.316706 GCTGCCGTACTCCTCTGTCT 61.317 60.000 0.00 0.00 0.00 3.41
556 600 0.460311 ACGGAAGGATTCTACAGCGG 59.540 55.000 0.00 0.00 46.56 5.52
557 601 1.536284 GGACGGAAGGATTCTACAGCG 60.536 57.143 0.00 0.00 46.56 5.18
558 602 1.202545 GGGACGGAAGGATTCTACAGC 60.203 57.143 0.00 0.00 46.56 4.40
560 604 1.007963 AGGGGACGGAAGGATTCTACA 59.992 52.381 0.00 0.00 46.56 2.74
561 605 1.790818 AGGGGACGGAAGGATTCTAC 58.209 55.000 0.00 0.00 46.56 2.59
562 606 3.917324 ATAGGGGACGGAAGGATTCTA 57.083 47.619 0.00 0.00 46.56 2.10
563 607 2.797285 ATAGGGGACGGAAGGATTCT 57.203 50.000 0.00 0.00 46.56 2.40
564 608 3.859061 AAATAGGGGACGGAAGGATTC 57.141 47.619 0.00 0.00 46.67 2.52
565 609 3.268595 ACAAAATAGGGGACGGAAGGATT 59.731 43.478 0.00 0.00 0.00 3.01
566 610 2.850568 ACAAAATAGGGGACGGAAGGAT 59.149 45.455 0.00 0.00 0.00 3.24
570 614 4.076394 CAAGAACAAAATAGGGGACGGAA 58.924 43.478 0.00 0.00 0.00 4.30
616 660 0.972983 ACCTGGGATGGACTCGACTG 60.973 60.000 0.00 0.00 0.00 3.51
722 770 1.579429 CTTTTCCGAGGGGCAAACG 59.421 57.895 0.00 0.00 0.00 3.60
827 879 0.036010 AGATTGCTGGTCAACCGAGG 60.036 55.000 0.00 0.00 37.53 4.63
838 890 2.017049 CTAAACCCCGGAAGATTGCTG 58.983 52.381 0.73 0.00 0.00 4.41
847 899 1.288188 CTAAACCCCTAAACCCCGGA 58.712 55.000 0.73 0.00 0.00 5.14
848 900 0.256752 CCTAAACCCCTAAACCCCGG 59.743 60.000 0.00 0.00 0.00 5.73
849 901 1.288188 TCCTAAACCCCTAAACCCCG 58.712 55.000 0.00 0.00 0.00 5.73
916 974 2.880890 CCCCTCCGATCAATCAATGAAC 59.119 50.000 0.00 0.00 42.54 3.18
919 977 2.936919 TCCCCTCCGATCAATCAATG 57.063 50.000 0.00 0.00 0.00 2.82
926 984 0.105964 CCTCTCTTCCCCTCCGATCA 60.106 60.000 0.00 0.00 0.00 2.92
928 986 0.187361 CTCCTCTCTTCCCCTCCGAT 59.813 60.000 0.00 0.00 0.00 4.18
929 987 1.615814 CTCCTCTCTTCCCCTCCGA 59.384 63.158 0.00 0.00 0.00 4.55
936 994 2.445682 TACTCCAGCTCCTCTCTTCC 57.554 55.000 0.00 0.00 0.00 3.46
940 998 4.499019 CGAGAATTTACTCCAGCTCCTCTC 60.499 50.000 0.00 0.00 33.83 3.20
941 999 3.383185 CGAGAATTTACTCCAGCTCCTCT 59.617 47.826 0.00 0.00 33.83 3.69
942 1000 3.491792 CCGAGAATTTACTCCAGCTCCTC 60.492 52.174 0.00 0.00 33.83 3.71
943 1001 2.432510 CCGAGAATTTACTCCAGCTCCT 59.567 50.000 0.00 0.00 33.83 3.69
944 1002 2.827652 CCGAGAATTTACTCCAGCTCC 58.172 52.381 0.00 0.00 33.83 4.70
1008 1075 2.189521 CCCGTGGGTATGCAGGAC 59.810 66.667 0.00 0.00 0.00 3.85
1447 1520 4.090057 GTTCTTGCAGGCGTCGGC 62.090 66.667 11.43 11.43 38.90 5.54
1909 1982 3.228017 TTCTGTCGGTGGTGGCGA 61.228 61.111 0.00 0.00 0.00 5.54
1917 1990 2.031163 GCTGCAGGTTCTGTCGGT 59.969 61.111 17.12 0.00 33.43 4.69
1989 2062 5.530543 CACCTTCTTCTTCTTCTTGCTCTTT 59.469 40.000 0.00 0.00 0.00 2.52
2026 2099 1.225704 CCTCCTCCTTGGCCATCAC 59.774 63.158 6.09 0.00 35.26 3.06
2050 2123 0.321210 TCCTCGCATTTCGCTTTGGA 60.321 50.000 0.00 0.00 39.08 3.53
2055 2128 2.187946 CCCTCCTCGCATTTCGCT 59.812 61.111 0.00 0.00 39.08 4.93
2057 2130 2.203070 CCCCCTCCTCGCATTTCG 60.203 66.667 0.00 0.00 40.15 3.46
2073 2146 1.745489 GTCCAGTGTTCCATCGGCC 60.745 63.158 0.00 0.00 0.00 6.13
2305 2379 6.258230 TCAAAATTATGTTGCAGTCTCCTG 57.742 37.500 0.00 0.00 41.91 3.86
2312 2386 7.756272 TGTTAGCTCATCAAAATTATGTTGCAG 59.244 33.333 0.00 0.00 32.02 4.41
2408 2493 5.144159 AGAGGTAACATCATCTACAGGGA 57.856 43.478 0.00 0.00 41.41 4.20
2449 2535 9.282247 GAAAACATGTCTGTAATTTAGCTGATG 57.718 33.333 0.00 0.00 33.36 3.07
2450 2536 9.013229 TGAAAACATGTCTGTAATTTAGCTGAT 57.987 29.630 0.00 0.00 33.36 2.90
2472 2560 9.996554 TTCAGAGTAACTCATATCAGTTTGAAA 57.003 29.630 0.00 0.00 37.75 2.69
2556 2656 1.728490 GAAATGGGGATGCACGAGGC 61.728 60.000 0.00 0.00 45.13 4.70
2557 2657 0.107017 AGAAATGGGGATGCACGAGG 60.107 55.000 0.00 0.00 0.00 4.63
2558 2658 1.672881 GAAGAAATGGGGATGCACGAG 59.327 52.381 0.00 0.00 0.00 4.18
2560 2660 0.740737 GGAAGAAATGGGGATGCACG 59.259 55.000 0.00 0.00 0.00 5.34
2562 2662 0.623194 TCGGAAGAAATGGGGATGCA 59.377 50.000 0.00 0.00 37.03 3.96
2563 2663 1.025041 GTCGGAAGAAATGGGGATGC 58.975 55.000 0.00 0.00 45.01 3.91
2671 2785 5.048083 TCAACTTATCAAGCATGTGGTTTCC 60.048 40.000 0.00 0.00 32.86 3.13
2698 2812 3.628005 CCACAATATGGCAGTTGCG 57.372 52.632 13.41 6.03 43.24 4.85
2856 2973 4.771114 TGGGTTACTGGATTATCAGTGG 57.229 45.455 7.65 0.00 46.29 4.00
2865 2984 6.659824 ACTTCGATTTTATGGGTTACTGGAT 58.340 36.000 0.00 0.00 0.00 3.41
2928 3049 1.743394 GGTTAGGTTTGCCAGGATTCG 59.257 52.381 0.00 0.00 37.19 3.34
2935 3056 4.668138 AATCTAAGGGTTAGGTTTGCCA 57.332 40.909 0.00 0.00 32.82 4.92
2936 3057 5.014202 TGAAATCTAAGGGTTAGGTTTGCC 58.986 41.667 9.19 0.00 44.36 4.52
3094 3216 9.199982 GAATAATTGAGCATAATGGAATGGTTG 57.800 33.333 0.00 0.00 37.69 3.77
3103 3225 8.407832 TCCACTGTTGAATAATTGAGCATAATG 58.592 33.333 0.00 0.00 0.00 1.90
3126 3286 0.895100 GCTCAATTGCCTGTGGTCCA 60.895 55.000 0.00 0.00 0.00 4.02
3238 3398 1.602920 GGGCTAACAGTTTGTTGCAGC 60.603 52.381 4.78 6.46 41.30 5.25
3247 3407 3.525800 ACTGAATTGGGGCTAACAGTT 57.474 42.857 0.00 0.00 35.52 3.16
3362 3522 3.186409 CCATCGTGTGTCCAAACTACAAG 59.814 47.826 0.00 0.00 0.00 3.16
3395 3714 4.178540 ACCGTGTCATAAATCGTAAGGTG 58.821 43.478 0.00 0.00 38.47 4.00
3409 3728 9.448294 GTTTTACATTGTTATTAAACCGTGTCA 57.552 29.630 0.00 0.00 35.28 3.58
3490 3809 5.814705 GGTTCATCCTTGATTAGTGAGACTG 59.185 44.000 0.00 0.00 0.00 3.51
3728 4047 7.591426 GTGCTTGGCTTACAAATATTATACTGC 59.409 37.037 0.00 0.00 38.91 4.40
3764 4087 2.300152 GTGATCTGGTGTGAGGAGTGAA 59.700 50.000 0.00 0.00 0.00 3.18
3815 4138 1.897802 TCAGTAAACCCCGAAGACTCC 59.102 52.381 0.00 0.00 0.00 3.85
3963 4294 2.615493 CGAGAGAAGCTAAAAAGGGCCA 60.615 50.000 6.18 0.00 0.00 5.36
3965 4296 2.701107 ACGAGAGAAGCTAAAAAGGGC 58.299 47.619 0.00 0.00 0.00 5.19
3968 4299 4.929808 TGGCTAACGAGAGAAGCTAAAAAG 59.070 41.667 0.00 0.00 41.24 2.27
3990 4325 3.574284 CTCACTCACTGAGGTCTCTTG 57.426 52.381 10.86 0.00 42.69 3.02
4048 4389 4.031314 GCAAAACTCCGAAACACAAAGAAC 59.969 41.667 0.00 0.00 0.00 3.01
4239 4582 4.460948 AAATGGATGAAACAGCACCATC 57.539 40.909 0.00 0.00 39.93 3.51
4265 4611 2.165234 TGGAGCGAGTGATTTCAGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
4304 4650 2.312722 TTGCTTTGCTGTGCATGTTT 57.687 40.000 0.00 0.00 38.76 2.83
4327 4674 3.255725 CAAAATTTGCCATCTGTGCGAT 58.744 40.909 0.00 0.00 0.00 4.58
4330 4677 4.559153 ACTACAAAATTTGCCATCTGTGC 58.441 39.130 5.52 0.00 0.00 4.57
4365 4712 1.102222 CCCCCGTGACCGTTCAAAAA 61.102 55.000 0.00 0.00 31.90 1.94
4366 4713 1.526455 CCCCCGTGACCGTTCAAAA 60.526 57.895 0.00 0.00 31.90 2.44
4367 4714 2.111460 CCCCCGTGACCGTTCAAA 59.889 61.111 0.00 0.00 31.90 2.69
4384 4731 1.201429 TTCAGGTGGGGAAGCTCTCC 61.201 60.000 6.43 6.43 44.54 3.71
4385 4732 0.915364 ATTCAGGTGGGGAAGCTCTC 59.085 55.000 0.00 0.00 33.14 3.20
4386 4733 2.270434 TATTCAGGTGGGGAAGCTCT 57.730 50.000 0.00 0.00 33.14 4.09
4387 4734 4.917906 ATATATTCAGGTGGGGAAGCTC 57.082 45.455 0.00 0.00 33.14 4.09
4388 4735 5.014228 GGTAATATATTCAGGTGGGGAAGCT 59.986 44.000 0.00 0.00 36.97 3.74
4389 4736 5.222048 TGGTAATATATTCAGGTGGGGAAGC 60.222 44.000 0.00 0.00 0.00 3.86
4390 4737 6.044404 AGTGGTAATATATTCAGGTGGGGAAG 59.956 42.308 0.00 0.00 0.00 3.46
4391 4738 5.914716 AGTGGTAATATATTCAGGTGGGGAA 59.085 40.000 0.00 0.00 0.00 3.97
4392 4739 5.482580 AGTGGTAATATATTCAGGTGGGGA 58.517 41.667 0.00 0.00 0.00 4.81
4393 4740 5.309543 TGAGTGGTAATATATTCAGGTGGGG 59.690 44.000 0.00 0.00 0.00 4.96
4394 4741 6.433847 TGAGTGGTAATATATTCAGGTGGG 57.566 41.667 0.00 0.00 0.00 4.61
4395 4742 8.786898 CATTTGAGTGGTAATATATTCAGGTGG 58.213 37.037 0.00 0.00 0.00 4.61
4396 4743 9.559732 TCATTTGAGTGGTAATATATTCAGGTG 57.440 33.333 0.00 0.00 0.00 4.00
4403 4750 9.965902 GGATCCTTCATTTGAGTGGTAATATAT 57.034 33.333 3.84 0.00 0.00 0.86
4404 4751 8.094548 CGGATCCTTCATTTGAGTGGTAATATA 58.905 37.037 10.75 0.00 0.00 0.86
4405 4752 6.936900 CGGATCCTTCATTTGAGTGGTAATAT 59.063 38.462 10.75 0.00 0.00 1.28
4406 4753 6.099125 TCGGATCCTTCATTTGAGTGGTAATA 59.901 38.462 10.75 0.00 0.00 0.98
4407 4754 5.104527 TCGGATCCTTCATTTGAGTGGTAAT 60.105 40.000 10.75 0.00 0.00 1.89
4408 4755 4.224147 TCGGATCCTTCATTTGAGTGGTAA 59.776 41.667 10.75 0.00 0.00 2.85
4409 4756 3.772572 TCGGATCCTTCATTTGAGTGGTA 59.227 43.478 10.75 0.00 0.00 3.25
4410 4757 2.571653 TCGGATCCTTCATTTGAGTGGT 59.428 45.455 10.75 0.00 0.00 4.16
4411 4758 3.118629 TCTCGGATCCTTCATTTGAGTGG 60.119 47.826 10.75 0.00 0.00 4.00
4412 4759 4.128925 TCTCGGATCCTTCATTTGAGTG 57.871 45.455 10.75 0.00 0.00 3.51
4413 4760 4.826274 TTCTCGGATCCTTCATTTGAGT 57.174 40.909 10.75 0.00 0.00 3.41
4414 4761 6.763135 TGTAATTCTCGGATCCTTCATTTGAG 59.237 38.462 10.75 7.18 0.00 3.02
4415 4762 6.649155 TGTAATTCTCGGATCCTTCATTTGA 58.351 36.000 10.75 0.00 0.00 2.69
4416 4763 6.512415 GCTGTAATTCTCGGATCCTTCATTTG 60.512 42.308 10.75 0.00 0.00 2.32
4417 4764 5.529060 GCTGTAATTCTCGGATCCTTCATTT 59.471 40.000 10.75 1.00 0.00 2.32
4418 4765 5.059833 GCTGTAATTCTCGGATCCTTCATT 58.940 41.667 10.75 5.49 0.00 2.57
4419 4766 4.101585 TGCTGTAATTCTCGGATCCTTCAT 59.898 41.667 10.75 0.00 0.00 2.57
4420 4767 3.450817 TGCTGTAATTCTCGGATCCTTCA 59.549 43.478 10.75 0.00 0.00 3.02
4421 4768 4.054671 CTGCTGTAATTCTCGGATCCTTC 58.945 47.826 10.75 0.00 0.00 3.46
4422 4769 3.706594 TCTGCTGTAATTCTCGGATCCTT 59.293 43.478 10.75 0.00 0.00 3.36
4423 4770 3.300388 TCTGCTGTAATTCTCGGATCCT 58.700 45.455 10.75 0.00 0.00 3.24
4424 4771 3.735237 TCTGCTGTAATTCTCGGATCC 57.265 47.619 0.00 0.00 0.00 3.36
4425 4772 7.148507 CCATATTTCTGCTGTAATTCTCGGATC 60.149 40.741 1.00 0.00 0.00 3.36
4426 4773 6.652481 CCATATTTCTGCTGTAATTCTCGGAT 59.348 38.462 1.00 0.00 0.00 4.18
4427 4774 5.991606 CCATATTTCTGCTGTAATTCTCGGA 59.008 40.000 1.00 0.00 0.00 4.55
4428 4775 5.180117 CCCATATTTCTGCTGTAATTCTCGG 59.820 44.000 1.00 0.00 0.00 4.63
4429 4776 5.760253 ACCCATATTTCTGCTGTAATTCTCG 59.240 40.000 1.00 0.00 0.00 4.04
4430 4777 7.715249 TGTACCCATATTTCTGCTGTAATTCTC 59.285 37.037 1.00 0.00 0.00 2.87
4431 4778 7.573710 TGTACCCATATTTCTGCTGTAATTCT 58.426 34.615 1.00 0.00 0.00 2.40
4432 4779 7.801716 TGTACCCATATTTCTGCTGTAATTC 57.198 36.000 1.00 0.00 0.00 2.17
4433 4780 8.766994 ATTGTACCCATATTTCTGCTGTAATT 57.233 30.769 1.00 0.00 0.00 1.40
4434 4781 8.766994 AATTGTACCCATATTTCTGCTGTAAT 57.233 30.769 1.36 1.36 0.00 1.89
4435 4782 8.588290 AAATTGTACCCATATTTCTGCTGTAA 57.412 30.769 0.00 0.00 0.00 2.41
4436 4783 8.588290 AAAATTGTACCCATATTTCTGCTGTA 57.412 30.769 0.00 0.00 0.00 2.74
4437 4784 7.178274 TGAAAATTGTACCCATATTTCTGCTGT 59.822 33.333 0.00 0.00 31.69 4.40
4438 4785 7.489113 GTGAAAATTGTACCCATATTTCTGCTG 59.511 37.037 0.00 0.00 31.69 4.41
4439 4786 7.397192 AGTGAAAATTGTACCCATATTTCTGCT 59.603 33.333 0.00 0.00 31.69 4.24
4440 4787 7.547227 AGTGAAAATTGTACCCATATTTCTGC 58.453 34.615 0.00 0.00 31.69 4.26
4441 4788 8.739039 TGAGTGAAAATTGTACCCATATTTCTG 58.261 33.333 0.00 0.00 31.69 3.02
4442 4789 8.877864 TGAGTGAAAATTGTACCCATATTTCT 57.122 30.769 0.00 0.00 31.69 2.52
4443 4790 8.956426 TCTGAGTGAAAATTGTACCCATATTTC 58.044 33.333 0.00 0.00 0.00 2.17
4444 4791 8.877864 TCTGAGTGAAAATTGTACCCATATTT 57.122 30.769 0.00 0.00 0.00 1.40
4445 4792 8.877864 TTCTGAGTGAAAATTGTACCCATATT 57.122 30.769 0.00 0.00 0.00 1.28
4446 4793 7.557719 CCTTCTGAGTGAAAATTGTACCCATAT 59.442 37.037 0.00 0.00 33.79 1.78
4447 4794 6.884295 CCTTCTGAGTGAAAATTGTACCCATA 59.116 38.462 0.00 0.00 33.79 2.74
4448 4795 5.711976 CCTTCTGAGTGAAAATTGTACCCAT 59.288 40.000 0.00 0.00 33.79 4.00
4449 4796 5.070001 CCTTCTGAGTGAAAATTGTACCCA 58.930 41.667 0.00 0.00 33.79 4.51
4450 4797 4.459337 CCCTTCTGAGTGAAAATTGTACCC 59.541 45.833 0.00 0.00 33.79 3.69
4451 4798 5.313712 TCCCTTCTGAGTGAAAATTGTACC 58.686 41.667 0.00 0.00 33.79 3.34
4452 4799 7.308435 CAATCCCTTCTGAGTGAAAATTGTAC 58.692 38.462 0.00 0.00 32.28 2.90
4453 4800 6.071952 GCAATCCCTTCTGAGTGAAAATTGTA 60.072 38.462 0.00 0.00 34.76 2.41
4454 4801 5.279156 GCAATCCCTTCTGAGTGAAAATTGT 60.279 40.000 0.00 0.00 34.76 2.71
4455 4802 5.166398 GCAATCCCTTCTGAGTGAAAATTG 58.834 41.667 0.00 0.00 35.05 2.32
4456 4803 4.834496 TGCAATCCCTTCTGAGTGAAAATT 59.166 37.500 0.00 0.00 32.28 1.82
4457 4804 4.410099 TGCAATCCCTTCTGAGTGAAAAT 58.590 39.130 0.00 0.00 32.28 1.82
4458 4805 3.831323 TGCAATCCCTTCTGAGTGAAAA 58.169 40.909 0.00 0.00 32.28 2.29
4459 4806 3.507162 TGCAATCCCTTCTGAGTGAAA 57.493 42.857 0.00 0.00 32.28 2.69
4460 4807 3.726557 ATGCAATCCCTTCTGAGTGAA 57.273 42.857 0.00 0.00 32.28 3.18
4461 4808 3.245016 ACAATGCAATCCCTTCTGAGTGA 60.245 43.478 0.00 0.00 32.28 3.41
4462 4809 3.087031 ACAATGCAATCCCTTCTGAGTG 58.913 45.455 0.00 0.00 33.66 3.51
4463 4810 3.446442 ACAATGCAATCCCTTCTGAGT 57.554 42.857 0.00 0.00 0.00 3.41
4464 4811 4.521146 ACTACAATGCAATCCCTTCTGAG 58.479 43.478 0.00 0.00 0.00 3.35
4465 4812 4.517285 GACTACAATGCAATCCCTTCTGA 58.483 43.478 0.00 0.00 0.00 3.27
4466 4813 3.629398 GGACTACAATGCAATCCCTTCTG 59.371 47.826 0.00 0.00 0.00 3.02
4467 4814 3.266772 TGGACTACAATGCAATCCCTTCT 59.733 43.478 0.00 0.00 0.00 2.85
4468 4815 3.620488 TGGACTACAATGCAATCCCTTC 58.380 45.455 0.00 0.00 0.00 3.46
4469 4816 3.737559 TGGACTACAATGCAATCCCTT 57.262 42.857 0.00 0.00 0.00 3.95
4470 4817 3.737559 TTGGACTACAATGCAATCCCT 57.262 42.857 0.00 0.00 33.18 4.20
4471 4818 4.220602 ACTTTTGGACTACAATGCAATCCC 59.779 41.667 0.00 0.00 39.21 3.85
4472 4819 5.391312 ACTTTTGGACTACAATGCAATCC 57.609 39.130 0.00 0.00 39.21 3.01
4473 4820 8.863049 CAATTACTTTTGGACTACAATGCAATC 58.137 33.333 0.00 0.00 39.21 2.67
4474 4821 8.584157 TCAATTACTTTTGGACTACAATGCAAT 58.416 29.630 0.00 0.00 39.21 3.56
4475 4822 7.946207 TCAATTACTTTTGGACTACAATGCAA 58.054 30.769 0.00 0.00 39.21 4.08
4476 4823 7.446931 TCTCAATTACTTTTGGACTACAATGCA 59.553 33.333 0.00 0.00 39.21 3.96
4477 4824 7.816640 TCTCAATTACTTTTGGACTACAATGC 58.183 34.615 0.00 0.00 39.21 3.56
4527 4874 5.573219 TCAGGTGATGTTTCAGATTTCCAT 58.427 37.500 0.00 0.00 30.85 3.41
4562 4909 1.506493 CATGCGATTCTAGTCCCAGC 58.494 55.000 0.00 0.00 0.00 4.85
4587 4934 1.000283 GATCCCCGTGAGCTATGACAG 60.000 57.143 0.00 0.00 0.00 3.51
4588 4935 1.040646 GATCCCCGTGAGCTATGACA 58.959 55.000 0.00 0.00 0.00 3.58
4604 4951 4.570663 CCCTCACCGTCGGCGATC 62.571 72.222 12.93 6.12 41.33 3.69
4608 4955 1.366854 GAAATTCCCTCACCGTCGGC 61.367 60.000 12.28 0.00 0.00 5.54
4706 5053 1.697982 AGGCTCTTAACGAACCCACTT 59.302 47.619 0.00 0.00 0.00 3.16
4720 5067 0.178992 CCTCCTGAGATCGAGGCTCT 60.179 60.000 13.50 3.42 39.36 4.09
4721 5068 0.179004 TCCTCCTGAGATCGAGGCTC 60.179 60.000 3.87 3.87 44.61 4.70
4733 5080 2.521547 AAAAAGAGCCCATCCTCCTG 57.478 50.000 0.00 0.00 32.17 3.86
4812 5159 0.395724 TCTGCACGGCCTCAGATCTA 60.396 55.000 13.17 0.00 34.69 1.98
4813 5160 1.047596 ATCTGCACGGCCTCAGATCT 61.048 55.000 19.87 6.54 44.23 2.75
4824 5171 1.416373 CATCGGATCAGATCTGCACG 58.584 55.000 18.36 19.54 35.60 5.34
4839 5186 1.402968 CCATGTTTTCTCAGGCCATCG 59.597 52.381 5.01 0.00 0.00 3.84
4856 5203 2.680370 GGAAGAACCCGCCTCCCAT 61.680 63.158 0.00 0.00 0.00 4.00
4895 5242 4.552365 ATGATGTGAGGGGCGGCG 62.552 66.667 0.51 0.51 0.00 6.46


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

AutoCloner maintained by Alex Coulton.