Multiple sequence alignment - TraesCS4A01G312400

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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 TraesCS4A01G312400 chr4A 100.000 2858 0 0 1 2858 603541551 603538694 0.000000e+00 5278
1 TraesCS4A01G312400 chr4D 91.919 1819 96 30 848 2648 1230605 1232390 0.000000e+00 2497
2 TraesCS4A01G312400 chr4D 92.791 541 26 5 1 539 1229738 1230267 0.000000e+00 771
3 TraesCS4A01G312400 chr4D 81.184 473 83 5 1204 1670 362131913 362131441 2.690000e-100 375
4 TraesCS4A01G312400 chr4D 79.894 189 10 11 619 782 1230303 1230488 2.330000e-21 113
5 TraesCS4A01G312400 chr4B 88.067 1433 70 49 780 2141 654039 652637 0.000000e+00 1605
6 TraesCS4A01G312400 chr4B 88.567 726 47 17 1 714 654855 654154 0.000000e+00 848
7 TraesCS4A01G312400 chr4B 87.013 385 38 9 2232 2608 652405 652025 9.470000e-115 424
8 TraesCS4A01G312400 chr6D 86.842 1216 91 37 935 2116 26350856 26352036 0.000000e+00 1295
9 TraesCS4A01G312400 chr6D 85.595 479 63 3 1189 1661 462422969 462423447 5.500000e-137 497
10 TraesCS4A01G312400 chr6D 77.536 414 38 31 120 523 26350075 26350443 6.250000e-47 198
11 TraesCS4A01G312400 chr6D 84.146 82 7 4 639 715 26350490 26350570 1.100000e-09 75
12 TraesCS4A01G312400 chr6B 86.672 1223 87 46 935 2135 48551766 48552934 0.000000e+00 1286
13 TraesCS4A01G312400 chr6B 85.626 487 63 4 1180 1661 704890658 704891142 3.290000e-139 505
14 TraesCS4A01G312400 chr6A 87.132 1189 84 40 961 2124 27772625 27773769 0.000000e+00 1284
15 TraesCS4A01G312400 chr6A 85.832 487 62 4 1180 1661 609176277 609176761 7.060000e-141 510


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 TraesCS4A01G312400 chr4A 603538694 603541551 2857 True 5278.000000 5278 100.000000 1 2858 1 chr4A.!!$R1 2857
1 TraesCS4A01G312400 chr4D 1229738 1232390 2652 False 1127.000000 2497 88.201333 1 2648 3 chr4D.!!$F1 2647
2 TraesCS4A01G312400 chr4B 652025 654855 2830 True 959.000000 1605 87.882333 1 2608 3 chr4B.!!$R1 2607
3 TraesCS4A01G312400 chr6D 26350075 26352036 1961 False 522.666667 1295 82.841333 120 2116 3 chr6D.!!$F2 1996
4 TraesCS4A01G312400 chr6B 48551766 48552934 1168 False 1286.000000 1286 86.672000 935 2135 1 chr6B.!!$F1 1200
5 TraesCS4A01G312400 chr6A 27772625 27773769 1144 False 1284.000000 1284 87.132000 961 2124 1 chr6A.!!$F1 1163

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
567 592 0.035317 CCTCAGCTAGTGCACACCAA 59.965 55.0 21.04 0.04 42.74 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 2115 0.036732 TCTTGATGCTTGGAGGCGTT 59.963 50.0 0.0 0.0 34.52 4.84 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
34 35 0.970427 GGTTGGTGGGGCTGGTAATG 60.970 60.000 0.00 0.00 0.00 1.90
60 61 3.953612 GCCAATCCACATTTGATGGTAGA 59.046 43.478 0.00 0.00 38.47 2.59
86 88 8.788325 AGGGTGACTCATTTTTAAGTATACAC 57.212 34.615 5.50 0.00 0.00 2.90
89 91 8.995220 GGTGACTCATTTTTAAGTATACACACA 58.005 33.333 5.50 0.00 0.00 3.72
104 106 3.074412 ACACACATGTAGGCAGCTAAAC 58.926 45.455 0.00 0.00 37.26 2.01
145 147 6.606796 TGGTCCATGCAATCATACAAAGTATT 59.393 34.615 0.00 0.00 0.00 1.89
146 148 7.123997 TGGTCCATGCAATCATACAAAGTATTT 59.876 33.333 0.00 0.00 40.26 1.40
147 149 7.981225 GGTCCATGCAATCATACAAAGTATTTT 59.019 33.333 0.00 0.00 35.03 1.82
148 150 9.369904 GTCCATGCAATCATACAAAGTATTTTT 57.630 29.630 0.00 0.00 35.03 1.94
213 222 9.598517 CACCGTAAAATATAGGTAAACCAAGTA 57.401 33.333 1.26 0.00 38.89 2.24
232 243 1.295020 AATAGGGGTGCACTTAGCCA 58.705 50.000 17.98 0.00 44.83 4.75
242 253 5.450550 GGGTGCACTTAGCCATAATTTTCTC 60.451 44.000 17.98 0.00 44.83 2.87
406 431 3.438183 ACTAGAAGGTACCCATCAACGT 58.562 45.455 8.74 3.71 0.00 3.99
487 512 1.439143 AGTCTTCCTCCCCCTCTTCTT 59.561 52.381 0.00 0.00 0.00 2.52
488 513 1.834896 GTCTTCCTCCCCCTCTTCTTC 59.165 57.143 0.00 0.00 0.00 2.87
489 514 1.725182 TCTTCCTCCCCCTCTTCTTCT 59.275 52.381 0.00 0.00 0.00 2.85
535 560 5.660533 TGGATCCTCCATATATACACCACA 58.339 41.667 14.23 0.00 42.67 4.17
536 561 5.483937 TGGATCCTCCATATATACACCACAC 59.516 44.000 14.23 0.00 42.67 3.82
537 562 5.483937 GGATCCTCCATATATACACCACACA 59.516 44.000 3.84 0.00 36.28 3.72
538 563 5.801531 TCCTCCATATATACACCACACAC 57.198 43.478 0.00 0.00 0.00 3.82
539 564 5.464069 TCCTCCATATATACACCACACACT 58.536 41.667 0.00 0.00 0.00 3.55
540 565 5.538813 TCCTCCATATATACACCACACACTC 59.461 44.000 0.00 0.00 0.00 3.51
541 566 5.447624 TCCATATATACACCACACACTCG 57.552 43.478 0.00 0.00 0.00 4.18
542 567 3.987868 CCATATATACACCACACACTCGC 59.012 47.826 0.00 0.00 0.00 5.03
543 568 4.262036 CCATATATACACCACACACTCGCT 60.262 45.833 0.00 0.00 0.00 4.93
544 569 2.647529 TATACACCACACACTCGCTG 57.352 50.000 0.00 0.00 0.00 5.18
545 570 0.966179 ATACACCACACACTCGCTGA 59.034 50.000 0.00 0.00 0.00 4.26
546 571 0.313987 TACACCACACACTCGCTGAG 59.686 55.000 4.36 4.36 35.52 3.35
547 572 1.665916 CACCACACACTCGCTGAGG 60.666 63.158 9.75 0.00 33.35 3.86
548 573 2.740055 CCACACACTCGCTGAGGC 60.740 66.667 9.75 0.00 33.35 4.70
549 574 2.740055 CACACACTCGCTGAGGCC 60.740 66.667 0.00 0.00 33.35 5.19
550 575 2.919856 ACACACTCGCTGAGGCCT 60.920 61.111 3.86 3.86 33.35 5.19
551 576 2.125753 CACACTCGCTGAGGCCTC 60.126 66.667 26.78 26.78 33.35 4.70
552 577 2.601666 ACACTCGCTGAGGCCTCA 60.602 61.111 33.04 33.04 38.06 3.86
567 592 0.035317 CCTCAGCTAGTGCACACCAA 59.965 55.000 21.04 0.04 42.74 3.67
582 624 2.099098 ACACCAACAAAAAGAAGGAGCG 59.901 45.455 0.00 0.00 0.00 5.03
608 650 6.533367 GCCAAAATCTCATACTAGATCGATCC 59.467 42.308 21.66 4.34 35.10 3.36
628 671 3.099905 CCATCGATGGGGATCTAGCTAA 58.900 50.000 32.99 0.00 44.31 3.09
629 672 3.708631 CCATCGATGGGGATCTAGCTAAT 59.291 47.826 32.99 0.00 44.31 1.73
631 674 5.355596 CATCGATGGGGATCTAGCTAATTC 58.644 45.833 17.96 0.00 0.00 2.17
632 675 4.678256 TCGATGGGGATCTAGCTAATTCT 58.322 43.478 0.00 0.00 0.00 2.40
633 676 4.707448 TCGATGGGGATCTAGCTAATTCTC 59.293 45.833 0.00 0.00 0.00 2.87
634 677 4.142049 CGATGGGGATCTAGCTAATTCTCC 60.142 50.000 12.64 12.64 0.00 3.71
635 678 4.213531 TGGGGATCTAGCTAATTCTCCA 57.786 45.455 16.68 16.68 36.39 3.86
636 679 3.904339 TGGGGATCTAGCTAATTCTCCAC 59.096 47.826 16.68 11.31 33.80 4.02
637 680 3.262151 GGGGATCTAGCTAATTCTCCACC 59.738 52.174 14.09 8.48 0.00 4.61
641 684 5.961421 GGATCTAGCTAATTCTCCACCCTAT 59.039 44.000 0.00 0.00 0.00 2.57
768 856 7.543172 TGCTCATGAAATCAAAAGATAACAAGC 59.457 33.333 0.00 0.00 0.00 4.01
769 857 7.758528 GCTCATGAAATCAAAAGATAACAAGCT 59.241 33.333 0.00 0.00 0.00 3.74
773 861 8.862325 TGAAATCAAAAGATAACAAGCTAGGA 57.138 30.769 0.00 0.00 0.00 2.94
774 862 8.950210 TGAAATCAAAAGATAACAAGCTAGGAG 58.050 33.333 0.00 0.00 0.00 3.69
775 863 6.934048 ATCAAAAGATAACAAGCTAGGAGC 57.066 37.500 0.00 0.00 42.84 4.70
799 909 6.582672 GCTGGTTCTTAATTCTGTAAACAAGC 59.417 38.462 0.00 0.00 36.75 4.01
829 943 5.411361 TCACATGTATGGTTGTTGCTAGTTC 59.589 40.000 0.00 0.00 0.00 3.01
830 944 4.700213 ACATGTATGGTTGTTGCTAGTTCC 59.300 41.667 0.00 0.00 0.00 3.62
842 957 4.386867 TGCTAGTTCCTTCGATTCGATT 57.613 40.909 9.96 0.00 35.23 3.34
845 960 4.085517 GCTAGTTCCTTCGATTCGATTTCG 60.086 45.833 9.96 10.97 35.23 3.46
892 1035 0.894184 CAGATCCAGGGCATCATGGC 60.894 60.000 1.56 1.56 43.95 4.40
904 1047 2.223203 GCATCATGGCGAAGAAGACAAG 60.223 50.000 0.00 0.00 30.05 3.16
937 1086 4.722193 GCTTGCTAGCCACCAAGA 57.278 55.556 13.29 0.00 41.74 3.02
948 1113 2.165998 GCCACCAAGAAAGAAGAGCAT 58.834 47.619 0.00 0.00 0.00 3.79
970 1135 6.513066 GCATATCAAGAAAGGAAGCAAGCTAG 60.513 42.308 0.00 0.00 0.00 3.42
971 1136 3.679389 TCAAGAAAGGAAGCAAGCTAGG 58.321 45.455 0.00 0.00 0.00 3.02
1545 1739 4.874977 GTCTACCTCGCAGGCGGC 62.875 72.222 14.24 0.00 39.63 6.53
1734 1928 0.617249 CAGGTGCTCCTCTTCCTCCT 60.617 60.000 3.81 0.00 43.07 3.69
1872 2066 4.782156 CCCTACTAGCTACCTACCTAGCTA 59.218 50.000 7.52 7.52 46.35 3.32
1906 2100 0.390998 GTCAGGACTTCAGGAGCAGC 60.391 60.000 0.00 0.00 0.00 5.25
1920 2115 1.374631 GCAGCTCGTCCATGTGTCA 60.375 57.895 0.00 0.00 0.00 3.58
1924 2119 1.781555 CTCGTCCATGTGTCAACGC 59.218 57.895 0.00 0.00 35.22 4.84
1993 2213 6.377996 ACCAATAACTAGAGAATTGCATTGCA 59.622 34.615 7.38 7.38 36.47 4.08
1994 2214 7.069085 ACCAATAACTAGAGAATTGCATTGCAT 59.931 33.333 12.95 0.00 38.76 3.96
1995 2215 8.570488 CCAATAACTAGAGAATTGCATTGCATA 58.430 33.333 12.95 4.15 38.76 3.14
2127 2373 3.004106 CCTTTTACTGCCTGCAGATATGC 59.996 47.826 24.88 10.73 46.30 3.14
2234 2628 8.711170 TCAACTTAACTAGATATTTAGGTGGGG 58.289 37.037 1.10 0.00 0.00 4.96
2245 2639 2.961536 TAGGTGGGGAGAAGGAATGA 57.038 50.000 0.00 0.00 0.00 2.57
2253 2647 5.709164 GTGGGGAGAAGGAATGATGAATATG 59.291 44.000 0.00 0.00 0.00 1.78
2275 2669 4.988540 TGTATACATAGCTCGTTTCATGCC 59.011 41.667 0.08 0.00 0.00 4.40
2324 2721 6.493116 CCTGACATTGCTGAGAAATATTGAC 58.507 40.000 0.00 0.00 0.00 3.18
2366 2764 6.331845 TCGCAATGATGTTGCAAGATTAATT 58.668 32.000 10.81 10.76 45.14 1.40
2379 2777 7.441017 TGCAAGATTAATTAGTTTTGCTTGGT 58.559 30.769 26.02 0.00 40.96 3.67
2382 2780 7.775053 AGATTAATTAGTTTTGCTTGGTCCA 57.225 32.000 0.00 0.00 0.00 4.02
2398 2799 6.040166 GCTTGGTCCAATAGATCAATGTCAAT 59.960 38.462 4.34 0.00 44.64 2.57
2453 2854 9.978044 ACTAAACTAAACTTTACTCGAGTCATT 57.022 29.630 23.89 12.95 0.00 2.57
2483 2884 5.296813 AGCAAATTTTACTCGATGGACAC 57.703 39.130 0.00 0.00 0.00 3.67
2495 2897 2.679059 CGATGGACACTGCTCATCCTTT 60.679 50.000 0.00 0.00 35.22 3.11
2516 2918 6.818142 CCTTTGGTTACATGAATTTCATTCCC 59.182 38.462 9.19 7.55 34.28 3.97
2521 2923 6.762661 GGTTACATGAATTTCATTCCCCATTG 59.237 38.462 9.19 0.54 34.28 2.82
2529 2931 1.565759 TCATTCCCCATTGCTAGCACT 59.434 47.619 19.17 9.85 0.00 4.40
2597 2999 6.009589 TGTGTGGTCATTTCATCAGGTTTAT 58.990 36.000 0.00 0.00 0.00 1.40
2598 3000 7.171653 TGTGTGGTCATTTCATCAGGTTTATA 58.828 34.615 0.00 0.00 0.00 0.98
2599 3001 7.833682 TGTGTGGTCATTTCATCAGGTTTATAT 59.166 33.333 0.00 0.00 0.00 0.86
2610 3012 7.999679 TCATCAGGTTTATATGCCTTTTTGAG 58.000 34.615 0.00 0.00 31.73 3.02
2624 3026 0.911769 TTTGAGTCGCATGATCCCCT 59.088 50.000 0.00 0.00 0.00 4.79
2628 3030 2.503765 TGAGTCGCATGATCCCCTAAAA 59.496 45.455 0.00 0.00 0.00 1.52
2629 3031 2.872858 GAGTCGCATGATCCCCTAAAAC 59.127 50.000 0.00 0.00 0.00 2.43
2630 3032 2.238646 AGTCGCATGATCCCCTAAAACA 59.761 45.455 0.00 0.00 0.00 2.83
2631 3033 3.117888 AGTCGCATGATCCCCTAAAACAT 60.118 43.478 0.00 0.00 0.00 2.71
2632 3034 4.102524 AGTCGCATGATCCCCTAAAACATA 59.897 41.667 0.00 0.00 0.00 2.29
2633 3035 5.003804 GTCGCATGATCCCCTAAAACATAT 58.996 41.667 0.00 0.00 0.00 1.78
2634 3036 5.003160 TCGCATGATCCCCTAAAACATATG 58.997 41.667 0.00 0.00 0.00 1.78
2636 3038 5.473162 CGCATGATCCCCTAAAACATATGAA 59.527 40.000 10.38 0.00 0.00 2.57
2637 3039 6.151648 CGCATGATCCCCTAAAACATATGAAT 59.848 38.462 10.38 0.00 0.00 2.57
2638 3040 7.336679 CGCATGATCCCCTAAAACATATGAATA 59.663 37.037 10.38 0.00 0.00 1.75
2639 3041 9.193806 GCATGATCCCCTAAAACATATGAATAT 57.806 33.333 10.38 0.00 0.00 1.28
2642 3044 9.905713 TGATCCCCTAAAACATATGAATATAGC 57.094 33.333 10.38 0.00 0.00 2.97
2643 3045 9.905713 GATCCCCTAAAACATATGAATATAGCA 57.094 33.333 10.38 0.00 0.00 3.49
2659 3061 9.743581 TGAATATAGCATAATTCCATCACATGT 57.256 29.630 0.00 0.00 32.25 3.21
2661 3063 9.743581 AATATAGCATAATTCCATCACATGTCA 57.256 29.630 0.00 0.00 0.00 3.58
2662 3064 9.916360 ATATAGCATAATTCCATCACATGTCAT 57.084 29.630 0.00 0.00 0.00 3.06
2663 3065 6.327279 AGCATAATTCCATCACATGTCATG 57.673 37.500 11.41 11.41 0.00 3.07
2664 3066 6.066032 AGCATAATTCCATCACATGTCATGA 58.934 36.000 19.77 0.00 0.00 3.07
2665 3067 6.206829 AGCATAATTCCATCACATGTCATGAG 59.793 38.462 19.77 11.75 0.00 2.90
2666 3068 6.569801 GCATAATTCCATCACATGTCATGAGG 60.570 42.308 19.77 14.01 0.00 3.86
2667 3069 4.515028 ATTCCATCACATGTCATGAGGT 57.485 40.909 19.77 4.91 0.00 3.85
2668 3070 4.305539 TTCCATCACATGTCATGAGGTT 57.694 40.909 19.77 3.84 0.00 3.50
2669 3071 4.305539 TCCATCACATGTCATGAGGTTT 57.694 40.909 19.77 0.00 0.00 3.27
2670 3072 4.011698 TCCATCACATGTCATGAGGTTTG 58.988 43.478 19.77 6.90 0.00 2.93
2671 3073 3.760151 CCATCACATGTCATGAGGTTTGT 59.240 43.478 19.77 0.00 0.00 2.83
2672 3074 4.380128 CCATCACATGTCATGAGGTTTGTG 60.380 45.833 19.77 15.79 36.64 3.33
2673 3075 3.148412 TCACATGTCATGAGGTTTGTGG 58.852 45.455 19.77 7.98 36.13 4.17
2674 3076 2.886523 CACATGTCATGAGGTTTGTGGT 59.113 45.455 19.77 0.00 32.78 4.16
2675 3077 2.886523 ACATGTCATGAGGTTTGTGGTG 59.113 45.455 19.77 0.00 0.00 4.17
2676 3078 1.979855 TGTCATGAGGTTTGTGGTGG 58.020 50.000 0.00 0.00 0.00 4.61
2677 3079 1.247567 GTCATGAGGTTTGTGGTGGG 58.752 55.000 0.00 0.00 0.00 4.61
2678 3080 1.144691 TCATGAGGTTTGTGGTGGGA 58.855 50.000 0.00 0.00 0.00 4.37
2679 3081 1.710244 TCATGAGGTTTGTGGTGGGAT 59.290 47.619 0.00 0.00 0.00 3.85
2680 3082 2.109834 TCATGAGGTTTGTGGTGGGATT 59.890 45.455 0.00 0.00 0.00 3.01
2681 3083 1.993956 TGAGGTTTGTGGTGGGATTG 58.006 50.000 0.00 0.00 0.00 2.67
2682 3084 1.216678 TGAGGTTTGTGGTGGGATTGT 59.783 47.619 0.00 0.00 0.00 2.71
2683 3085 1.613437 GAGGTTTGTGGTGGGATTGTG 59.387 52.381 0.00 0.00 0.00 3.33
2684 3086 0.678950 GGTTTGTGGTGGGATTGTGG 59.321 55.000 0.00 0.00 0.00 4.17
2685 3087 1.698506 GTTTGTGGTGGGATTGTGGA 58.301 50.000 0.00 0.00 0.00 4.02
2686 3088 2.247358 GTTTGTGGTGGGATTGTGGAT 58.753 47.619 0.00 0.00 0.00 3.41
2687 3089 3.426615 GTTTGTGGTGGGATTGTGGATA 58.573 45.455 0.00 0.00 0.00 2.59
2688 3090 4.023291 GTTTGTGGTGGGATTGTGGATAT 58.977 43.478 0.00 0.00 0.00 1.63
2689 3091 3.576078 TGTGGTGGGATTGTGGATATC 57.424 47.619 0.00 0.00 0.00 1.63
2690 3092 3.122480 TGTGGTGGGATTGTGGATATCT 58.878 45.455 2.05 0.00 0.00 1.98
2691 3093 3.527253 TGTGGTGGGATTGTGGATATCTT 59.473 43.478 2.05 0.00 0.00 2.40
2692 3094 3.885297 GTGGTGGGATTGTGGATATCTTG 59.115 47.826 2.05 0.00 0.00 3.02
2693 3095 3.527253 TGGTGGGATTGTGGATATCTTGT 59.473 43.478 2.05 0.00 0.00 3.16
2694 3096 4.017591 TGGTGGGATTGTGGATATCTTGTT 60.018 41.667 2.05 0.00 0.00 2.83
2695 3097 4.339247 GGTGGGATTGTGGATATCTTGTTG 59.661 45.833 2.05 0.00 0.00 3.33
2696 3098 3.953612 TGGGATTGTGGATATCTTGTTGC 59.046 43.478 2.05 0.00 0.00 4.17
2697 3099 3.003689 GGGATTGTGGATATCTTGTTGCG 59.996 47.826 2.05 0.00 0.00 4.85
2698 3100 3.876914 GGATTGTGGATATCTTGTTGCGA 59.123 43.478 2.05 0.00 0.00 5.10
2699 3101 4.024556 GGATTGTGGATATCTTGTTGCGAG 60.025 45.833 2.05 0.00 0.00 5.03
2700 3102 2.905075 TGTGGATATCTTGTTGCGAGG 58.095 47.619 2.05 0.00 0.00 4.63
2701 3103 2.499693 TGTGGATATCTTGTTGCGAGGA 59.500 45.455 2.05 0.00 0.00 3.71
2702 3104 3.055458 TGTGGATATCTTGTTGCGAGGAA 60.055 43.478 2.05 0.00 0.00 3.36
2703 3105 3.557595 GTGGATATCTTGTTGCGAGGAAG 59.442 47.826 2.05 0.00 0.00 3.46
2704 3106 3.450817 TGGATATCTTGTTGCGAGGAAGA 59.549 43.478 2.05 0.00 0.00 2.87
2705 3107 4.101585 TGGATATCTTGTTGCGAGGAAGAT 59.898 41.667 11.32 11.32 39.31 2.40
2706 3108 4.688413 GGATATCTTGTTGCGAGGAAGATC 59.312 45.833 10.28 0.00 37.55 2.75
2707 3109 2.386661 TCTTGTTGCGAGGAAGATCC 57.613 50.000 0.00 0.00 36.58 3.36
2708 3110 1.623311 TCTTGTTGCGAGGAAGATCCA 59.377 47.619 0.00 0.00 39.61 3.41
2709 3111 2.237143 TCTTGTTGCGAGGAAGATCCAT 59.763 45.455 0.00 0.00 39.61 3.41
2710 3112 3.450817 TCTTGTTGCGAGGAAGATCCATA 59.549 43.478 0.00 0.00 39.61 2.74
2711 3113 4.101585 TCTTGTTGCGAGGAAGATCCATAT 59.898 41.667 0.00 0.00 39.61 1.78
2712 3114 4.422073 TGTTGCGAGGAAGATCCATATT 57.578 40.909 0.00 0.00 39.61 1.28
2713 3115 4.129380 TGTTGCGAGGAAGATCCATATTG 58.871 43.478 0.00 0.00 39.61 1.90
2714 3116 3.407424 TGCGAGGAAGATCCATATTGG 57.593 47.619 0.00 0.00 39.61 3.16
2728 3130 6.078456 TCCATATTGGATTGTCTTGGTTCT 57.922 37.500 0.00 0.00 42.67 3.01
2729 3131 6.493166 TCCATATTGGATTGTCTTGGTTCTT 58.507 36.000 0.00 0.00 42.67 2.52
2730 3132 6.953520 TCCATATTGGATTGTCTTGGTTCTTT 59.046 34.615 0.00 0.00 42.67 2.52
2731 3133 7.454380 TCCATATTGGATTGTCTTGGTTCTTTT 59.546 33.333 0.00 0.00 42.67 2.27
2732 3134 8.096414 CCATATTGGATTGTCTTGGTTCTTTTT 58.904 33.333 0.00 0.00 40.96 1.94
2757 3159 9.588774 TTTCTTTATGTTTTGTAAGACGATTCG 57.411 29.630 4.14 4.14 0.00 3.34
2758 3160 7.231607 TCTTTATGTTTTGTAAGACGATTCGC 58.768 34.615 5.86 0.00 0.00 4.70
2759 3161 6.715344 TTATGTTTTGTAAGACGATTCGCT 57.285 33.333 5.86 1.57 0.00 4.93
2760 3162 4.640805 TGTTTTGTAAGACGATTCGCTC 57.359 40.909 5.86 3.47 0.00 5.03
2768 3170 3.704843 CGATTCGCTCGGCATCAA 58.295 55.556 0.00 0.00 43.82 2.57
2769 3171 1.273887 CGATTCGCTCGGCATCAAC 59.726 57.895 0.00 0.00 43.82 3.18
2770 3172 1.148157 CGATTCGCTCGGCATCAACT 61.148 55.000 0.00 0.00 43.82 3.16
2771 3173 1.852942 GATTCGCTCGGCATCAACTA 58.147 50.000 0.00 0.00 0.00 2.24
2772 3174 2.201732 GATTCGCTCGGCATCAACTAA 58.798 47.619 0.00 0.00 0.00 2.24
2773 3175 2.309528 TTCGCTCGGCATCAACTAAT 57.690 45.000 0.00 0.00 0.00 1.73
2774 3176 3.446310 TTCGCTCGGCATCAACTAATA 57.554 42.857 0.00 0.00 0.00 0.98
2775 3177 3.660501 TCGCTCGGCATCAACTAATAT 57.339 42.857 0.00 0.00 0.00 1.28
2776 3178 4.776795 TCGCTCGGCATCAACTAATATA 57.223 40.909 0.00 0.00 0.00 0.86
2777 3179 4.733850 TCGCTCGGCATCAACTAATATAG 58.266 43.478 0.00 0.00 0.00 1.31
2778 3180 4.457949 TCGCTCGGCATCAACTAATATAGA 59.542 41.667 0.00 0.00 0.00 1.98
2779 3181 4.795795 CGCTCGGCATCAACTAATATAGAG 59.204 45.833 0.00 0.00 0.00 2.43
2780 3182 5.105752 GCTCGGCATCAACTAATATAGAGG 58.894 45.833 0.00 0.00 0.00 3.69
2781 3183 5.073311 TCGGCATCAACTAATATAGAGGC 57.927 43.478 0.00 0.00 37.10 4.70
2785 3187 5.181748 GCATCAACTAATATAGAGGCCAGG 58.818 45.833 5.01 0.00 32.21 4.45
2786 3188 5.280215 GCATCAACTAATATAGAGGCCAGGT 60.280 44.000 5.01 0.00 32.21 4.00
2787 3189 5.808366 TCAACTAATATAGAGGCCAGGTG 57.192 43.478 5.01 0.00 0.00 4.00
2788 3190 4.040461 TCAACTAATATAGAGGCCAGGTGC 59.960 45.833 5.01 0.00 40.16 5.01
2789 3191 2.563179 ACTAATATAGAGGCCAGGTGCG 59.437 50.000 5.01 0.00 42.61 5.34
2790 3192 0.035458 AATATAGAGGCCAGGTGCGC 59.965 55.000 5.01 0.00 42.61 6.09
2791 3193 0.833834 ATATAGAGGCCAGGTGCGCT 60.834 55.000 9.73 0.00 42.61 5.92
2792 3194 0.178973 TATAGAGGCCAGGTGCGCTA 60.179 55.000 9.73 0.00 42.61 4.26
2793 3195 0.833834 ATAGAGGCCAGGTGCGCTAT 60.834 55.000 9.73 0.00 42.61 2.97
2794 3196 1.464376 TAGAGGCCAGGTGCGCTATC 61.464 60.000 9.73 0.00 42.61 2.08
2795 3197 3.083349 AGGCCAGGTGCGCTATCA 61.083 61.111 9.73 0.00 42.61 2.15
2796 3198 2.124736 GGCCAGGTGCGCTATCAA 60.125 61.111 9.73 0.00 42.61 2.57
2797 3199 2.472909 GGCCAGGTGCGCTATCAAC 61.473 63.158 9.73 0.00 42.61 3.18
2798 3200 2.472909 GCCAGGTGCGCTATCAACC 61.473 63.158 9.73 7.46 0.00 3.77
2799 3201 1.221840 CCAGGTGCGCTATCAACCT 59.778 57.895 9.73 10.12 0.00 3.50
2800 3202 0.392998 CCAGGTGCGCTATCAACCTT 60.393 55.000 13.30 0.00 0.00 3.50
2801 3203 1.453155 CAGGTGCGCTATCAACCTTT 58.547 50.000 13.30 0.00 0.00 3.11
2802 3204 1.398390 CAGGTGCGCTATCAACCTTTC 59.602 52.381 13.30 0.00 0.00 2.62
2803 3205 1.279271 AGGTGCGCTATCAACCTTTCT 59.721 47.619 9.73 0.00 0.00 2.52
2804 3206 1.398390 GGTGCGCTATCAACCTTTCTG 59.602 52.381 9.73 0.00 0.00 3.02
2805 3207 2.346803 GTGCGCTATCAACCTTTCTGA 58.653 47.619 9.73 0.00 0.00 3.27
2806 3208 2.742053 GTGCGCTATCAACCTTTCTGAA 59.258 45.455 9.73 0.00 0.00 3.02
2807 3209 3.188460 GTGCGCTATCAACCTTTCTGAAA 59.812 43.478 9.73 2.44 0.00 2.69
2808 3210 3.818210 TGCGCTATCAACCTTTCTGAAAA 59.182 39.130 9.73 0.00 0.00 2.29
2809 3211 4.277174 TGCGCTATCAACCTTTCTGAAAAA 59.723 37.500 9.73 0.00 0.00 1.94
2838 3240 7.754851 TTAGTTATCTATGGTCGTAGCATCA 57.245 36.000 3.40 0.00 37.51 3.07
2839 3241 6.650427 AGTTATCTATGGTCGTAGCATCAA 57.350 37.500 3.40 0.00 37.51 2.57
2840 3242 7.050970 AGTTATCTATGGTCGTAGCATCAAA 57.949 36.000 3.40 0.00 37.51 2.69
2841 3243 7.497595 AGTTATCTATGGTCGTAGCATCAAAA 58.502 34.615 3.40 0.00 37.51 2.44
2842 3244 7.653713 AGTTATCTATGGTCGTAGCATCAAAAG 59.346 37.037 3.40 0.00 37.51 2.27
2843 3245 5.592104 TCTATGGTCGTAGCATCAAAAGA 57.408 39.130 3.40 0.15 37.51 2.52
2844 3246 5.972935 TCTATGGTCGTAGCATCAAAAGAA 58.027 37.500 3.40 0.00 37.51 2.52
2845 3247 6.582636 TCTATGGTCGTAGCATCAAAAGAAT 58.417 36.000 3.40 0.00 37.51 2.40
2846 3248 4.944962 TGGTCGTAGCATCAAAAGAATG 57.055 40.909 0.00 0.00 0.00 2.67
2847 3249 4.323417 TGGTCGTAGCATCAAAAGAATGT 58.677 39.130 0.00 0.00 0.00 2.71
2848 3250 4.391830 TGGTCGTAGCATCAAAAGAATGTC 59.608 41.667 0.00 0.00 0.00 3.06
2849 3251 4.631813 GGTCGTAGCATCAAAAGAATGTCT 59.368 41.667 0.00 0.00 0.00 3.41
2850 3252 5.122396 GGTCGTAGCATCAAAAGAATGTCTT 59.878 40.000 0.00 0.00 38.59 3.01
2852 3254 7.078228 GTCGTAGCATCAAAAGAATGTCTTTT 58.922 34.615 9.62 9.62 46.87 2.27
2853 3255 7.591426 GTCGTAGCATCAAAAGAATGTCTTTTT 59.409 33.333 12.19 2.58 46.87 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.099881 ACCATCAAATGTGGATTGGCATAC 59.900 41.667 0.00 0.00 39.12 2.39
60 61 9.227777 GTGTATACTTAAAAATGAGTCACCCTT 57.772 33.333 4.17 0.00 0.00 3.95
86 88 4.764679 TTTGTTTAGCTGCCTACATGTG 57.235 40.909 9.11 0.00 0.00 3.21
89 91 4.344104 ACCATTTGTTTAGCTGCCTACAT 58.656 39.130 0.00 0.00 0.00 2.29
213 222 1.295020 TGGCTAAGTGCACCCCTATT 58.705 50.000 14.63 3.09 45.15 1.73
215 224 2.184088 TATGGCTAAGTGCACCCCTA 57.816 50.000 14.63 1.98 45.15 3.53
242 253 7.765307 ACATGGCATTTGTTCTTCTTACATAG 58.235 34.615 0.00 0.00 0.00 2.23
344 369 3.950395 GCCTCCAAGCTAATTCACTTCAT 59.050 43.478 0.00 0.00 0.00 2.57
406 431 2.308570 AGGGATGCATGAGGTGTGTTAA 59.691 45.455 2.46 0.00 0.00 2.01
487 512 3.706600 GCTAGCTAGCTAGAGGGTAGA 57.293 52.381 42.59 15.67 46.56 2.59
531 556 2.740055 GCCTCAGCGAGTGTGTGG 60.740 66.667 0.00 0.00 0.00 4.17
534 559 2.125753 GAGGCCTCAGCGAGTGTG 60.126 66.667 28.43 0.00 41.24 3.82
535 560 2.601666 TGAGGCCTCAGCGAGTGT 60.602 61.111 32.00 0.00 41.24 3.55
543 568 1.610379 TGCACTAGCTGAGGCCTCA 60.610 57.895 33.04 33.04 42.74 3.86
544 569 1.153469 GTGCACTAGCTGAGGCCTC 60.153 63.158 26.78 26.78 42.74 4.70
545 570 1.915266 TGTGCACTAGCTGAGGCCT 60.915 57.895 19.41 3.86 42.74 5.19
546 571 1.743252 GTGTGCACTAGCTGAGGCC 60.743 63.158 19.41 0.00 42.74 5.19
547 572 1.743252 GGTGTGCACTAGCTGAGGC 60.743 63.158 19.41 0.00 42.74 4.70
548 573 0.035317 TTGGTGTGCACTAGCTGAGG 59.965 55.000 19.41 0.00 42.74 3.86
549 574 1.151668 GTTGGTGTGCACTAGCTGAG 58.848 55.000 19.41 0.00 42.74 3.35
550 575 0.467804 TGTTGGTGTGCACTAGCTGA 59.532 50.000 19.41 5.03 42.74 4.26
551 576 1.308047 TTGTTGGTGTGCACTAGCTG 58.692 50.000 19.41 0.00 42.74 4.24
552 577 2.051334 TTTGTTGGTGTGCACTAGCT 57.949 45.000 19.41 0.00 42.74 3.32
553 578 2.861462 TTTTGTTGGTGTGCACTAGC 57.139 45.000 19.41 14.06 42.57 3.42
554 579 4.630894 TCTTTTTGTTGGTGTGCACTAG 57.369 40.909 19.41 0.00 0.00 2.57
555 580 4.142271 CCTTCTTTTTGTTGGTGTGCACTA 60.142 41.667 19.41 1.23 0.00 2.74
556 581 3.368323 CCTTCTTTTTGTTGGTGTGCACT 60.368 43.478 19.41 0.00 0.00 4.40
557 582 2.929398 CCTTCTTTTTGTTGGTGTGCAC 59.071 45.455 10.75 10.75 0.00 4.57
558 583 2.828520 TCCTTCTTTTTGTTGGTGTGCA 59.171 40.909 0.00 0.00 0.00 4.57
559 584 3.447742 CTCCTTCTTTTTGTTGGTGTGC 58.552 45.455 0.00 0.00 0.00 4.57
567 592 0.467290 TGGCCGCTCCTTCTTTTTGT 60.467 50.000 0.00 0.00 35.26 2.83
582 624 5.784177 TCGATCTAGTATGAGATTTTGGCC 58.216 41.667 0.00 0.00 36.27 5.36
608 650 5.128499 AGAATTAGCTAGATCCCCATCGATG 59.872 44.000 18.76 18.76 33.75 3.84
625 668 5.896073 AACCAGATAGGGTGGAGAATTAG 57.104 43.478 0.00 0.00 41.32 1.73
628 671 4.111577 TCAAACCAGATAGGGTGGAGAAT 58.888 43.478 0.00 0.00 41.32 2.40
629 672 3.526899 TCAAACCAGATAGGGTGGAGAA 58.473 45.455 0.00 0.00 41.32 2.87
631 674 4.510167 AATCAAACCAGATAGGGTGGAG 57.490 45.455 0.00 0.00 41.32 3.86
632 675 4.141482 GCTAATCAAACCAGATAGGGTGGA 60.141 45.833 0.00 0.00 41.32 4.02
633 676 4.137543 GCTAATCAAACCAGATAGGGTGG 58.862 47.826 0.00 0.00 41.32 4.61
634 677 4.818546 CAGCTAATCAAACCAGATAGGGTG 59.181 45.833 0.00 0.00 41.32 4.61
635 678 4.687219 GCAGCTAATCAAACCAGATAGGGT 60.687 45.833 0.00 0.00 45.04 4.34
636 679 3.817647 GCAGCTAATCAAACCAGATAGGG 59.182 47.826 0.00 0.00 43.89 3.53
637 680 4.454678 TGCAGCTAATCAAACCAGATAGG 58.545 43.478 0.00 0.00 45.67 2.57
641 684 5.243507 TGAAATTGCAGCTAATCAAACCAGA 59.756 36.000 0.00 0.00 0.00 3.86
768 856 5.983540 ACAGAATTAAGAACCAGCTCCTAG 58.016 41.667 0.00 0.00 0.00 3.02
769 857 7.490657 TTACAGAATTAAGAACCAGCTCCTA 57.509 36.000 0.00 0.00 0.00 2.94
770 858 4.917906 ACAGAATTAAGAACCAGCTCCT 57.082 40.909 0.00 0.00 0.00 3.69
771 859 6.430000 TGTTTACAGAATTAAGAACCAGCTCC 59.570 38.462 0.00 0.00 0.00 4.70
773 861 7.522236 GCTTGTTTACAGAATTAAGAACCAGCT 60.522 37.037 0.00 0.00 34.71 4.24
774 862 6.582672 GCTTGTTTACAGAATTAAGAACCAGC 59.417 38.462 0.00 0.00 31.63 4.85
775 863 7.648142 TGCTTGTTTACAGAATTAAGAACCAG 58.352 34.615 0.00 0.00 0.00 4.00
777 865 8.515414 AGATGCTTGTTTACAGAATTAAGAACC 58.485 33.333 0.00 0.00 0.00 3.62
799 909 6.261603 AGCAACAACCATACATGTGATAGATG 59.738 38.462 9.11 3.47 0.00 2.90
842 957 8.610035 CAAATGAAATGAAGATGAGAGATCGAA 58.390 33.333 0.00 0.00 0.00 3.71
852 990 9.181805 GATCTGCATACAAATGAAATGAAGATG 57.818 33.333 19.56 0.00 43.23 2.90
904 1047 7.645735 GGCTAGCAAGCTTTCTTGATTAATTAC 59.354 37.037 18.24 0.00 45.72 1.89
931 1080 6.715280 TCTTGATATGCTCTTCTTTCTTGGT 58.285 36.000 0.00 0.00 0.00 3.67
934 1083 8.105829 TCCTTTCTTGATATGCTCTTCTTTCTT 58.894 33.333 0.00 0.00 0.00 2.52
935 1084 7.628234 TCCTTTCTTGATATGCTCTTCTTTCT 58.372 34.615 0.00 0.00 0.00 2.52
936 1085 7.856145 TCCTTTCTTGATATGCTCTTCTTTC 57.144 36.000 0.00 0.00 0.00 2.62
937 1086 7.148103 GCTTCCTTTCTTGATATGCTCTTCTTT 60.148 37.037 0.00 0.00 0.00 2.52
948 1113 5.045578 ACCTAGCTTGCTTCCTTTCTTGATA 60.046 40.000 0.00 0.00 0.00 2.15
970 1135 4.473477 AACCTAACTGATCTGTGCTACC 57.527 45.455 5.96 0.00 0.00 3.18
971 1136 5.127356 ACCTAACCTAACTGATCTGTGCTAC 59.873 44.000 5.96 0.00 0.00 3.58
1446 1640 0.746923 TCTCGAATCTTCCGCGGAGA 60.747 55.000 29.20 25.75 0.00 3.71
1593 1787 3.014538 ATCACCATGACGGGCCCA 61.015 61.111 24.92 1.51 40.22 5.36
1734 1928 3.936203 GGGTCGCCGGCCATCATA 61.936 66.667 23.46 0.00 0.00 2.15
1871 2065 4.038522 GTCCTGACTGCTTGATGCTATCTA 59.961 45.833 0.00 0.00 43.37 1.98
1872 2066 3.036819 TCCTGACTGCTTGATGCTATCT 58.963 45.455 0.00 0.00 43.37 1.98
1873 2067 3.129871 GTCCTGACTGCTTGATGCTATC 58.870 50.000 0.00 0.00 43.37 2.08
1874 2068 2.770802 AGTCCTGACTGCTTGATGCTAT 59.229 45.455 0.00 0.00 40.75 2.97
1884 2078 0.390998 GCTCCTGAAGTCCTGACTGC 60.391 60.000 0.00 0.00 41.58 4.40
1906 2100 1.626654 GGCGTTGACACATGGACGAG 61.627 60.000 0.00 0.00 37.69 4.18
1920 2115 0.036732 TCTTGATGCTTGGAGGCGTT 59.963 50.000 0.00 0.00 34.52 4.84
1924 2119 3.555527 TCTGATCTTGATGCTTGGAGG 57.444 47.619 0.00 0.00 0.00 4.30
2226 2505 2.961536 TCATTCCTTCTCCCCACCTA 57.038 50.000 0.00 0.00 0.00 3.08
2230 2624 5.373555 ACATATTCATCATTCCTTCTCCCCA 59.626 40.000 0.00 0.00 0.00 4.96
2231 2625 5.885465 ACATATTCATCATTCCTTCTCCCC 58.115 41.667 0.00 0.00 0.00 4.81
2253 2647 4.988540 TGGCATGAAACGAGCTATGTATAC 59.011 41.667 0.00 0.00 0.00 1.47
2275 2669 5.886992 TCTTGTGCTCATAGAATTGCAATG 58.113 37.500 13.82 1.09 37.17 2.82
2287 2681 0.689055 TGTCAGGCTCTTGTGCTCAT 59.311 50.000 0.00 0.00 0.00 2.90
2324 2721 4.735985 TGCGAGAAATGTGGAATTCATTG 58.264 39.130 7.93 0.00 35.95 2.82
2366 2764 6.480763 TGATCTATTGGACCAAGCAAAACTA 58.519 36.000 13.43 0.00 0.00 2.24
2421 2822 8.306761 TCGAGTAAAGTTTAGTTTAGTTAGGGG 58.693 37.037 4.48 0.00 0.00 4.79
2422 2823 9.351570 CTCGAGTAAAGTTTAGTTTAGTTAGGG 57.648 37.037 3.62 0.00 0.00 3.53
2423 2824 9.905171 ACTCGAGTAAAGTTTAGTTTAGTTAGG 57.095 33.333 18.46 0.00 0.00 2.69
2478 2879 1.271597 ACCAAAGGATGAGCAGTGTCC 60.272 52.381 0.00 0.00 0.00 4.02
2483 2884 4.264253 TCATGTAACCAAAGGATGAGCAG 58.736 43.478 0.00 0.00 0.00 4.24
2516 2918 3.004629 TGTCAAAACAGTGCTAGCAATGG 59.995 43.478 38.91 25.44 45.01 3.16
2521 2923 3.971032 ACTTGTCAAAACAGTGCTAGC 57.029 42.857 8.10 8.10 36.57 3.42
2529 2931 4.180057 GGCAACATCAACTTGTCAAAACA 58.820 39.130 0.00 0.00 0.00 2.83
2597 2999 3.342719 TCATGCGACTCAAAAAGGCATA 58.657 40.909 0.00 0.00 42.00 3.14
2598 3000 2.161855 TCATGCGACTCAAAAAGGCAT 58.838 42.857 0.00 0.00 44.51 4.40
2599 3001 1.603456 TCATGCGACTCAAAAAGGCA 58.397 45.000 0.00 0.00 38.09 4.75
2610 3012 2.639065 TGTTTTAGGGGATCATGCGAC 58.361 47.619 0.00 0.00 0.00 5.19
2633 3035 9.743581 ACATGTGATGGAATTATGCTATATTCA 57.256 29.630 0.00 0.00 33.43 2.57
2636 3038 9.916360 ATGACATGTGATGGAATTATGCTATAT 57.084 29.630 1.15 0.00 33.60 0.86
2637 3039 9.169592 CATGACATGTGATGGAATTATGCTATA 57.830 33.333 16.63 0.00 33.60 1.31
2638 3040 7.886446 TCATGACATGTGATGGAATTATGCTAT 59.114 33.333 22.73 0.00 33.60 2.97
2639 3041 7.225725 TCATGACATGTGATGGAATTATGCTA 58.774 34.615 22.73 0.00 33.60 3.49
2640 3042 6.066032 TCATGACATGTGATGGAATTATGCT 58.934 36.000 22.73 0.00 33.60 3.79
2641 3043 6.321848 TCATGACATGTGATGGAATTATGC 57.678 37.500 22.73 0.00 33.60 3.14
2642 3044 6.489022 ACCTCATGACATGTGATGGAATTATG 59.511 38.462 22.73 5.33 33.60 1.90
2643 3045 6.607970 ACCTCATGACATGTGATGGAATTAT 58.392 36.000 22.73 3.23 33.60 1.28
2648 3050 4.011698 CAAACCTCATGACATGTGATGGA 58.988 43.478 22.73 10.40 33.60 3.41
2649 3051 3.760151 ACAAACCTCATGACATGTGATGG 59.240 43.478 22.73 11.98 33.60 3.51
2650 3052 4.380128 CCACAAACCTCATGACATGTGATG 60.380 45.833 18.11 18.11 40.32 3.07
2651 3053 3.760151 CCACAAACCTCATGACATGTGAT 59.240 43.478 17.09 0.00 40.32 3.06
2652 3054 3.148412 CCACAAACCTCATGACATGTGA 58.852 45.455 17.09 0.00 40.32 3.58
2653 3055 2.886523 ACCACAAACCTCATGACATGTG 59.113 45.455 14.98 12.36 38.25 3.21
2654 3056 2.886523 CACCACAAACCTCATGACATGT 59.113 45.455 14.98 0.00 0.00 3.21
2655 3057 2.229543 CCACCACAAACCTCATGACATG 59.770 50.000 9.28 9.28 0.00 3.21
2656 3058 2.517959 CCACCACAAACCTCATGACAT 58.482 47.619 0.00 0.00 0.00 3.06
2657 3059 1.478471 CCCACCACAAACCTCATGACA 60.478 52.381 0.00 0.00 0.00 3.58
2658 3060 1.202879 TCCCACCACAAACCTCATGAC 60.203 52.381 0.00 0.00 0.00 3.06
2659 3061 1.144691 TCCCACCACAAACCTCATGA 58.855 50.000 0.00 0.00 0.00 3.07
2660 3062 2.220653 ATCCCACCACAAACCTCATG 57.779 50.000 0.00 0.00 0.00 3.07
2661 3063 2.158325 ACAATCCCACCACAAACCTCAT 60.158 45.455 0.00 0.00 0.00 2.90
2662 3064 1.216678 ACAATCCCACCACAAACCTCA 59.783 47.619 0.00 0.00 0.00 3.86
2663 3065 1.613437 CACAATCCCACCACAAACCTC 59.387 52.381 0.00 0.00 0.00 3.85
2664 3066 1.703411 CACAATCCCACCACAAACCT 58.297 50.000 0.00 0.00 0.00 3.50
2665 3067 0.678950 CCACAATCCCACCACAAACC 59.321 55.000 0.00 0.00 0.00 3.27
2666 3068 1.698506 TCCACAATCCCACCACAAAC 58.301 50.000 0.00 0.00 0.00 2.93
2667 3069 2.692709 ATCCACAATCCCACCACAAA 57.307 45.000 0.00 0.00 0.00 2.83
2668 3070 3.527253 AGATATCCACAATCCCACCACAA 59.473 43.478 0.00 0.00 0.00 3.33
2669 3071 3.122480 AGATATCCACAATCCCACCACA 58.878 45.455 0.00 0.00 0.00 4.17
2670 3072 3.864789 AGATATCCACAATCCCACCAC 57.135 47.619 0.00 0.00 0.00 4.16
2671 3073 3.527253 ACAAGATATCCACAATCCCACCA 59.473 43.478 0.00 0.00 0.00 4.17
2672 3074 4.170468 ACAAGATATCCACAATCCCACC 57.830 45.455 0.00 0.00 0.00 4.61
2673 3075 4.202050 GCAACAAGATATCCACAATCCCAC 60.202 45.833 0.00 0.00 0.00 4.61
2674 3076 3.953612 GCAACAAGATATCCACAATCCCA 59.046 43.478 0.00 0.00 0.00 4.37
2675 3077 3.003689 CGCAACAAGATATCCACAATCCC 59.996 47.826 0.00 0.00 0.00 3.85
2676 3078 3.876914 TCGCAACAAGATATCCACAATCC 59.123 43.478 0.00 0.00 0.00 3.01
2677 3079 4.024556 CCTCGCAACAAGATATCCACAATC 60.025 45.833 0.00 0.00 0.00 2.67
2678 3080 3.879295 CCTCGCAACAAGATATCCACAAT 59.121 43.478 0.00 0.00 0.00 2.71
2679 3081 3.055458 TCCTCGCAACAAGATATCCACAA 60.055 43.478 0.00 0.00 0.00 3.33
2680 3082 2.499693 TCCTCGCAACAAGATATCCACA 59.500 45.455 0.00 0.00 0.00 4.17
2681 3083 3.179443 TCCTCGCAACAAGATATCCAC 57.821 47.619 0.00 0.00 0.00 4.02
2682 3084 3.450817 TCTTCCTCGCAACAAGATATCCA 59.549 43.478 0.00 0.00 0.00 3.41
2683 3085 4.060038 TCTTCCTCGCAACAAGATATCC 57.940 45.455 0.00 0.00 0.00 2.59
2684 3086 4.688413 GGATCTTCCTCGCAACAAGATATC 59.312 45.833 0.00 0.00 37.07 1.63
2685 3087 4.101585 TGGATCTTCCTCGCAACAAGATAT 59.898 41.667 0.00 0.00 37.07 1.63
2686 3088 3.450817 TGGATCTTCCTCGCAACAAGATA 59.549 43.478 0.00 0.00 37.07 1.98
2687 3089 2.237143 TGGATCTTCCTCGCAACAAGAT 59.763 45.455 0.00 0.00 39.17 2.40
2688 3090 1.623311 TGGATCTTCCTCGCAACAAGA 59.377 47.619 0.00 0.00 37.46 3.02
2689 3091 2.099141 TGGATCTTCCTCGCAACAAG 57.901 50.000 0.00 0.00 37.46 3.16
2690 3092 2.787473 ATGGATCTTCCTCGCAACAA 57.213 45.000 0.00 0.00 37.46 2.83
2691 3093 4.129380 CAATATGGATCTTCCTCGCAACA 58.871 43.478 0.00 0.00 37.46 3.33
2692 3094 3.499918 CCAATATGGATCTTCCTCGCAAC 59.500 47.826 0.00 0.00 40.96 4.17
2693 3095 3.390967 TCCAATATGGATCTTCCTCGCAA 59.609 43.478 0.00 0.00 42.67 4.85
2694 3096 2.972021 TCCAATATGGATCTTCCTCGCA 59.028 45.455 0.00 0.00 42.67 5.10
2695 3097 3.685139 TCCAATATGGATCTTCCTCGC 57.315 47.619 0.00 0.00 42.67 5.03
2706 3108 6.780457 AAGAACCAAGACAATCCAATATGG 57.220 37.500 0.00 0.00 39.43 2.74
2731 3133 9.588774 CGAATCGTCTTACAAAACATAAAGAAA 57.411 29.630 0.00 0.00 30.24 2.52
2732 3134 7.742963 GCGAATCGTCTTACAAAACATAAAGAA 59.257 33.333 4.07 0.00 30.24 2.52
2733 3135 7.117236 AGCGAATCGTCTTACAAAACATAAAGA 59.883 33.333 4.07 0.00 0.00 2.52
2734 3136 7.234384 AGCGAATCGTCTTACAAAACATAAAG 58.766 34.615 4.07 0.00 0.00 1.85
2735 3137 7.124347 AGCGAATCGTCTTACAAAACATAAA 57.876 32.000 4.07 0.00 0.00 1.40
2736 3138 6.453265 CGAGCGAATCGTCTTACAAAACATAA 60.453 38.462 4.07 0.00 46.62 1.90
2737 3139 5.004061 CGAGCGAATCGTCTTACAAAACATA 59.996 40.000 4.07 0.00 46.62 2.29
2738 3140 4.201589 CGAGCGAATCGTCTTACAAAACAT 60.202 41.667 4.07 0.00 46.62 2.71
2739 3141 3.120616 CGAGCGAATCGTCTTACAAAACA 59.879 43.478 4.07 0.00 46.62 2.83
2740 3142 3.646303 CGAGCGAATCGTCTTACAAAAC 58.354 45.455 4.07 0.00 46.62 2.43
2741 3143 3.965209 CGAGCGAATCGTCTTACAAAA 57.035 42.857 4.07 0.00 46.62 2.44
2752 3154 1.852942 TAGTTGATGCCGAGCGAATC 58.147 50.000 0.00 0.00 0.00 2.52
2753 3155 2.309528 TTAGTTGATGCCGAGCGAAT 57.690 45.000 0.00 0.00 0.00 3.34
2754 3156 2.309528 ATTAGTTGATGCCGAGCGAA 57.690 45.000 0.00 0.00 0.00 4.70
2755 3157 3.660501 ATATTAGTTGATGCCGAGCGA 57.339 42.857 0.00 0.00 0.00 4.93
2756 3158 4.733850 TCTATATTAGTTGATGCCGAGCG 58.266 43.478 0.00 0.00 0.00 5.03
2757 3159 5.105752 CCTCTATATTAGTTGATGCCGAGC 58.894 45.833 0.00 0.00 0.00 5.03
2758 3160 5.105752 GCCTCTATATTAGTTGATGCCGAG 58.894 45.833 0.00 0.00 0.00 4.63
2759 3161 4.081642 GGCCTCTATATTAGTTGATGCCGA 60.082 45.833 0.00 0.00 0.00 5.54
2760 3162 4.184629 GGCCTCTATATTAGTTGATGCCG 58.815 47.826 0.00 0.00 0.00 5.69
2761 3163 5.165961 TGGCCTCTATATTAGTTGATGCC 57.834 43.478 3.32 0.00 35.75 4.40
2762 3164 5.181748 CCTGGCCTCTATATTAGTTGATGC 58.818 45.833 3.32 0.00 0.00 3.91
2763 3165 6.169094 CACCTGGCCTCTATATTAGTTGATG 58.831 44.000 3.32 0.00 0.00 3.07
2764 3166 5.280215 GCACCTGGCCTCTATATTAGTTGAT 60.280 44.000 3.32 0.00 36.11 2.57
2765 3167 4.040461 GCACCTGGCCTCTATATTAGTTGA 59.960 45.833 3.32 0.00 36.11 3.18
2766 3168 4.319177 GCACCTGGCCTCTATATTAGTTG 58.681 47.826 3.32 0.00 36.11 3.16
2767 3169 3.006967 CGCACCTGGCCTCTATATTAGTT 59.993 47.826 3.32 0.00 40.31 2.24
2768 3170 2.563179 CGCACCTGGCCTCTATATTAGT 59.437 50.000 3.32 0.00 40.31 2.24
2769 3171 2.675317 GCGCACCTGGCCTCTATATTAG 60.675 54.545 3.32 0.00 40.31 1.73
2770 3172 1.275291 GCGCACCTGGCCTCTATATTA 59.725 52.381 3.32 0.00 40.31 0.98
2771 3173 0.035458 GCGCACCTGGCCTCTATATT 59.965 55.000 3.32 0.00 40.31 1.28
2772 3174 0.833834 AGCGCACCTGGCCTCTATAT 60.834 55.000 11.47 0.00 40.31 0.86
2773 3175 0.178973 TAGCGCACCTGGCCTCTATA 60.179 55.000 11.47 0.00 40.31 1.31
2774 3176 0.833834 ATAGCGCACCTGGCCTCTAT 60.834 55.000 11.47 0.00 40.31 1.98
2775 3177 1.457643 ATAGCGCACCTGGCCTCTA 60.458 57.895 11.47 0.00 40.31 2.43
2776 3178 2.765807 ATAGCGCACCTGGCCTCT 60.766 61.111 11.47 0.00 40.31 3.69
2777 3179 2.280457 GATAGCGCACCTGGCCTC 60.280 66.667 11.47 0.00 40.31 4.70
2778 3180 2.669133 TTGATAGCGCACCTGGCCT 61.669 57.895 11.47 0.00 40.31 5.19
2779 3181 2.124736 TTGATAGCGCACCTGGCC 60.125 61.111 11.47 0.00 40.31 5.36
2780 3182 2.472909 GGTTGATAGCGCACCTGGC 61.473 63.158 11.47 0.00 39.90 4.85
2781 3183 0.392998 AAGGTTGATAGCGCACCTGG 60.393 55.000 16.27 0.00 0.00 4.45
2782 3184 1.398390 GAAAGGTTGATAGCGCACCTG 59.602 52.381 16.27 0.00 0.00 4.00
2783 3185 1.279271 AGAAAGGTTGATAGCGCACCT 59.721 47.619 11.47 10.84 0.00 4.00
2784 3186 1.398390 CAGAAAGGTTGATAGCGCACC 59.602 52.381 11.47 8.17 0.00 5.01
2785 3187 2.346803 TCAGAAAGGTTGATAGCGCAC 58.653 47.619 11.47 0.00 0.00 5.34
2786 3188 2.760634 TCAGAAAGGTTGATAGCGCA 57.239 45.000 11.47 0.00 0.00 6.09
2787 3189 4.419522 TTTTCAGAAAGGTTGATAGCGC 57.580 40.909 0.00 0.00 0.00 5.92
2812 3214 9.457436 TGATGCTACGACCATAGATAACTAATA 57.543 33.333 0.00 0.00 32.04 0.98
2813 3215 8.349568 TGATGCTACGACCATAGATAACTAAT 57.650 34.615 0.00 0.00 32.04 1.73
2814 3216 7.754851 TGATGCTACGACCATAGATAACTAA 57.245 36.000 0.00 0.00 32.04 2.24
2815 3217 7.754851 TTGATGCTACGACCATAGATAACTA 57.245 36.000 0.00 0.00 0.00 2.24
2816 3218 6.650427 TTGATGCTACGACCATAGATAACT 57.350 37.500 0.00 0.00 0.00 2.24
2817 3219 7.652105 TCTTTTGATGCTACGACCATAGATAAC 59.348 37.037 0.00 0.00 0.00 1.89
2818 3220 7.722363 TCTTTTGATGCTACGACCATAGATAA 58.278 34.615 0.00 0.00 0.00 1.75
2819 3221 7.284919 TCTTTTGATGCTACGACCATAGATA 57.715 36.000 0.00 0.00 0.00 1.98
2820 3222 6.161855 TCTTTTGATGCTACGACCATAGAT 57.838 37.500 0.00 0.00 0.00 1.98
2821 3223 5.592104 TCTTTTGATGCTACGACCATAGA 57.408 39.130 0.00 0.00 0.00 1.98
2822 3224 6.258727 ACATTCTTTTGATGCTACGACCATAG 59.741 38.462 0.00 0.00 0.00 2.23
2823 3225 6.112734 ACATTCTTTTGATGCTACGACCATA 58.887 36.000 0.00 0.00 0.00 2.74
2824 3226 4.943705 ACATTCTTTTGATGCTACGACCAT 59.056 37.500 0.00 0.00 0.00 3.55
2825 3227 4.323417 ACATTCTTTTGATGCTACGACCA 58.677 39.130 0.00 0.00 0.00 4.02
2826 3228 4.631813 AGACATTCTTTTGATGCTACGACC 59.368 41.667 0.00 0.00 0.00 4.79
2827 3229 5.786401 AGACATTCTTTTGATGCTACGAC 57.214 39.130 0.00 0.00 0.00 4.34
2828 3230 6.801539 AAAGACATTCTTTTGATGCTACGA 57.198 33.333 0.00 0.00 43.62 3.43


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

AutoCloner maintained by Alex Coulton.