Multiple sequence alignment - TraesCS4D01G345600

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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 TraesCS4D01G345600 chr4D 100.000 3263 0 0 1 3263 500150951 500154213 0.000000e+00 6026.0
1 TraesCS4D01G345600 chr4D 99.326 3263 22 0 1 3263 500192536 500195798 0.000000e+00 5904.0
2 TraesCS4D01G345600 chr4D 99.282 2648 17 2 1 2647 500196203 500198849 0.000000e+00 4783.0
3 TraesCS4D01G345600 chr4D 98.789 578 7 0 1 578 500163169 500163746 0.000000e+00 1029.0
4 TraesCS4D01G345600 chr4D 98.270 578 10 0 1 578 500167094 500167671 0.000000e+00 1013.0
5 TraesCS4D01G345600 chr4D 98.270 578 10 0 1 578 500179764 500180341 0.000000e+00 1013.0
6 TraesCS4D01G345600 chr4D 90.609 394 37 0 2638 3031 500198470 500198863 1.280000e-144 523.0
7 TraesCS4D01G345600 chr4D 92.437 238 15 2 3028 3262 500200238 500200475 1.800000e-88 337.0
8 TraesCS4D01G345600 chr4D 100.000 112 0 0 3923 4034 500154873 500154984 1.470000e-49 207.0
9 TraesCS4D01G345600 chr4D 97.297 111 3 0 3924 4034 500200479 500200589 5.320000e-44 189.0
10 TraesCS4D01G345600 chr4B 96.442 2052 46 13 597 2647 643481484 643483509 0.000000e+00 3360.0
11 TraesCS4D01G345600 chr4B 87.254 1781 203 12 885 2647 643528062 643529836 0.000000e+00 2010.0
12 TraesCS4D01G345600 chr4B 88.235 629 65 6 2638 3263 643559159 643559781 0.000000e+00 743.0
13 TraesCS4D01G345600 chr4B 90.355 394 38 0 2638 3031 643483130 643483523 5.980000e-143 518.0
14 TraesCS4D01G345600 chr4B 89.899 396 38 2 2637 3031 643536772 643537166 3.600000e-140 508.0
15 TraesCS4D01G345600 chr4B 92.050 239 16 2 3028 3263 643531225 643531463 2.320000e-87 333.0
16 TraesCS4D01G345600 chr4B 92.593 108 8 0 3923 4030 643559818 643559925 5.400000e-34 156.0
17 TraesCS4D01G345600 chr4B 88.462 78 7 2 760 837 643557706 643557781 4.290000e-15 93.5
18 TraesCS4D01G345600 chrUn 100.000 1559 0 0 360 1918 389277216 389275658 0.000000e+00 2880.0
19 TraesCS4D01G345600 chrUn 92.125 1562 117 6 947 2505 60475434 60473876 0.000000e+00 2198.0
20 TraesCS4D01G345600 chrUn 89.671 1704 171 5 947 2647 60491694 60489993 0.000000e+00 2167.0
21 TraesCS4D01G345600 chrUn 87.592 1773 197 13 893 2647 16761298 16759531 0.000000e+00 2034.0
22 TraesCS4D01G345600 chrUn 87.592 1773 197 13 893 2647 60417326 60415559 0.000000e+00 2034.0
23 TraesCS4D01G345600 chrUn 98.443 578 9 0 1 578 280132084 280131507 0.000000e+00 1018.0
24 TraesCS4D01G345600 chrUn 98.443 578 9 0 1 578 321598961 321598384 0.000000e+00 1018.0
25 TraesCS4D01G345600 chrUn 98.270 578 10 0 1 578 265235410 265234833 0.000000e+00 1013.0
26 TraesCS4D01G345600 chrUn 98.270 578 10 0 1 578 321598087 321597510 0.000000e+00 1013.0
27 TraesCS4D01G345600 chrUn 88.806 402 44 1 2631 3031 60473582 60473181 3.620000e-135 492.0
28 TraesCS4D01G345600 chrUn 88.557 402 45 1 2631 3031 60490380 60489979 1.690000e-133 486.0
29 TraesCS4D01G345600 chrUn 92.469 239 14 3 3028 3263 60471806 60471569 4.990000e-89 339.0
30 TraesCS4D01G345600 chrUn 92.050 239 16 2 3028 3263 16758142 16757904 2.320000e-87 333.0
31 TraesCS4D01G345600 chrUn 91.632 239 17 2 3028 3263 60414170 60413932 1.080000e-85 327.0
32 TraesCS4D01G345600 chrUn 99.099 111 1 0 3923 4033 60413930 60413820 2.460000e-47 200.0
33 TraesCS4D01G345600 chrUn 97.321 112 3 0 3923 4034 16757902 16757791 1.480000e-44 191.0
34 TraesCS4D01G345600 chrUn 91.071 112 10 0 3923 4034 60485704 60485593 6.980000e-33 152.0
35 TraesCS4D01G345600 chrUn 89.157 83 7 2 760 842 60475604 60475524 7.130000e-18 102.0
36 TraesCS4D01G345600 chrUn 92.157 51 4 0 787 837 60491804 60491754 5.590000e-09 73.1
37 TraesCS4D01G345600 chrUn 92.157 51 4 0 787 837 318521347 318521397 5.590000e-09 73.1
38 TraesCS4D01G345600 chr5A 87.373 1774 199 14 893 2647 680921168 680922935 0.000000e+00 2012.0
39 TraesCS4D01G345600 chr5A 89.801 402 40 1 2631 3031 680866773 680867174 7.730000e-142 514.0
40 TraesCS4D01G345600 chr5A 89.367 395 40 2 2638 3031 680982465 680982858 2.800000e-136 496.0
41 TraesCS4D01G345600 chr5A 92.469 239 15 2 3028 3263 680924323 680924561 4.990000e-89 339.0
42 TraesCS4D01G345600 chr5A 92.017 238 16 2 3029 3263 680868535 680868772 8.360000e-87 331.0
43 TraesCS4D01G345600 chr5A 98.214 112 2 0 3923 4034 680924563 680924674 3.180000e-46 196.0
44 TraesCS4D01G345600 chr5A 87.500 88 9 2 755 842 680865277 680865362 2.570000e-17 100.0
45 TraesCS4D01G345600 chr7B 93.694 111 7 0 3923 4033 481665617 481665507 2.490000e-37 167.0
46 TraesCS4D01G345600 chr7A 92.793 111 8 0 3923 4033 540206072 540206182 1.160000e-35 161.0
47 TraesCS4D01G345600 chr7D 90.991 111 10 0 3923 4033 459743436 459743326 2.510000e-32 150.0


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 TraesCS4D01G345600 chr4D 500150951 500154984 4033 False 3116.500000 6026 100.000000 1 4034 2 chr4D.!!$F2 4033
1 TraesCS4D01G345600 chr4D 500192536 500200589 8053 False 2347.200000 5904 95.790200 1 4034 5 chr4D.!!$F4 4033
2 TraesCS4D01G345600 chr4D 500163169 500167671 4502 False 1021.000000 1029 98.529500 1 578 2 chr4D.!!$F3 577
3 TraesCS4D01G345600 chr4D 500179764 500180341 577 False 1013.000000 1013 98.270000 1 578 1 chr4D.!!$F1 577
4 TraesCS4D01G345600 chr4B 643481484 643483523 2039 False 1939.000000 3360 93.398500 597 3031 2 chr4B.!!$F2 2434
5 TraesCS4D01G345600 chr4B 643528062 643531463 3401 False 1171.500000 2010 89.652000 885 3263 2 chr4B.!!$F3 2378
6 TraesCS4D01G345600 chr4B 643557706 643559925 2219 False 330.833333 743 89.763333 760 4030 3 chr4B.!!$F4 3270
7 TraesCS4D01G345600 chrUn 389275658 389277216 1558 True 2880.000000 2880 100.000000 360 1918 1 chrUn.!!$R4 1558
8 TraesCS4D01G345600 chrUn 280131507 280132084 577 True 1018.000000 1018 98.443000 1 578 1 chrUn.!!$R3 577
9 TraesCS4D01G345600 chrUn 321597510 321598961 1451 True 1015.500000 1018 98.356500 1 578 2 chrUn.!!$R9 577
10 TraesCS4D01G345600 chrUn 265234833 265235410 577 True 1013.000000 1013 98.270000 1 578 1 chrUn.!!$R2 577
11 TraesCS4D01G345600 chrUn 60489979 60491804 1825 True 908.700000 2167 90.128333 787 3031 3 chrUn.!!$R8 2244
12 TraesCS4D01G345600 chrUn 60413820 60417326 3506 True 853.666667 2034 92.774333 893 4033 3 chrUn.!!$R6 3140
13 TraesCS4D01G345600 chrUn 16757791 16761298 3507 True 852.666667 2034 92.321000 893 4034 3 chrUn.!!$R5 3141
14 TraesCS4D01G345600 chrUn 60471569 60475604 4035 True 782.750000 2198 90.639250 760 3263 4 chrUn.!!$R7 2503
15 TraesCS4D01G345600 chr5A 680921168 680924674 3506 False 849.000000 2012 92.685333 893 4034 3 chr5A.!!$F3 3141
16 TraesCS4D01G345600 chr5A 680865277 680868772 3495 False 315.000000 514 89.772667 755 3263 3 chr5A.!!$F2 2508

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
75 950 2.124901 CCGCGATTGGGCTTGGTA 60.125 61.111 8.23 0.0 0.0 3.25 F
232 1544 3.008594 ACAATCCGTATGAACCCTGTTGA 59.991 43.478 0.00 0.0 0.0 3.18 F
2644 11310 2.113860 ATCCGTTGCACATAACAGCT 57.886 45.000 0.00 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 10917 4.819630 GGCAATGAACCGAAGAATGGTATA 59.180 41.667 0.00 0.00 39.29 1.47 R
2649 11315 3.587061 AGCCGAAATATGGTATGGATCCA 59.413 43.478 18.88 18.88 39.41 3.41 R
3948 13777 9.459640 CCTCATGAATATTCTTTGTAAATGCTG 57.540 33.333 16.24 6.37 0.00 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 950 2.124901 CCGCGATTGGGCTTGGTA 60.125 61.111 8.23 0.00 0.00 3.25
232 1544 3.008594 ACAATCCGTATGAACCCTGTTGA 59.991 43.478 0.00 0.00 0.00 3.18
2643 11309 2.286418 GCTATCCGTTGCACATAACAGC 60.286 50.000 0.00 0.00 0.00 4.40
2644 11310 2.113860 ATCCGTTGCACATAACAGCT 57.886 45.000 0.00 0.00 0.00 4.24
2647 11313 3.403968 TCCGTTGCACATAACAGCTTTA 58.596 40.909 0.00 0.00 0.00 1.85
2649 11315 3.188460 CCGTTGCACATAACAGCTTTACT 59.812 43.478 0.00 0.00 0.00 2.24
2662 11328 4.978099 CAGCTTTACTGGATCCATACCAT 58.022 43.478 16.63 1.41 43.19 3.55
2665 11331 7.170965 CAGCTTTACTGGATCCATACCATATT 58.829 38.462 16.63 0.00 43.19 1.28
2669 11335 5.165961 ACTGGATCCATACCATATTTCGG 57.834 43.478 16.63 0.70 36.79 4.30
2670 11336 3.941483 CTGGATCCATACCATATTTCGGC 59.059 47.826 16.63 0.00 36.79 5.54
2671 11337 3.587061 TGGATCCATACCATATTTCGGCT 59.413 43.478 11.44 0.00 32.03 5.52
2673 11339 4.323485 GGATCCATACCATATTTCGGCTCA 60.323 45.833 6.95 0.00 0.00 4.26
2674 11340 4.908601 TCCATACCATATTTCGGCTCAT 57.091 40.909 0.00 0.00 0.00 2.90
2675 11341 5.241403 TCCATACCATATTTCGGCTCATT 57.759 39.130 0.00 0.00 0.00 2.57
2676 11342 5.003160 TCCATACCATATTTCGGCTCATTG 58.997 41.667 0.00 0.00 0.00 2.82
2706 11372 1.523758 AGGAACTCGATTTGGCACAC 58.476 50.000 0.00 0.00 39.29 3.82
2707 11373 1.202758 AGGAACTCGATTTGGCACACA 60.203 47.619 0.00 0.00 39.29 3.72
2708 11374 1.606668 GGAACTCGATTTGGCACACAA 59.393 47.619 0.00 0.00 39.29 3.33
2709 11375 2.604614 GGAACTCGATTTGGCACACAAC 60.605 50.000 0.00 0.00 39.29 3.32
2710 11376 1.674359 ACTCGATTTGGCACACAACA 58.326 45.000 0.00 0.00 39.29 3.33
2711 11377 2.020720 ACTCGATTTGGCACACAACAA 58.979 42.857 0.00 0.00 39.29 2.83
2712 11378 2.033299 ACTCGATTTGGCACACAACAAG 59.967 45.455 0.00 0.00 39.29 3.16
2713 11379 1.130955 CGATTTGGCACACAACAAGC 58.869 50.000 0.00 0.00 39.29 4.01
2714 11380 1.269206 CGATTTGGCACACAACAAGCT 60.269 47.619 0.00 0.00 39.29 3.74
2715 11381 2.031245 CGATTTGGCACACAACAAGCTA 60.031 45.455 0.00 0.00 39.29 3.32
2716 11382 3.568538 GATTTGGCACACAACAAGCTAG 58.431 45.455 0.00 0.00 39.29 3.42
2717 11383 2.340210 TTGGCACACAACAAGCTAGA 57.660 45.000 0.00 0.00 39.29 2.43
2718 11384 2.340210 TGGCACACAACAAGCTAGAA 57.660 45.000 0.00 0.00 0.00 2.10
2719 11385 2.221169 TGGCACACAACAAGCTAGAAG 58.779 47.619 0.00 0.00 0.00 2.85
2720 11386 1.068954 GGCACACAACAAGCTAGAAGC 60.069 52.381 0.00 0.00 42.84 3.86
2721 11387 1.603802 GCACACAACAAGCTAGAAGCA 59.396 47.619 1.22 0.00 45.56 3.91
2722 11388 2.350197 GCACACAACAAGCTAGAAGCAG 60.350 50.000 1.22 0.00 45.56 4.24
2723 11389 3.133691 CACACAACAAGCTAGAAGCAGA 58.866 45.455 1.22 0.00 45.56 4.26
2724 11390 3.750130 CACACAACAAGCTAGAAGCAGAT 59.250 43.478 1.22 0.00 45.56 2.90
2725 11391 3.750130 ACACAACAAGCTAGAAGCAGATG 59.250 43.478 1.22 1.64 45.56 2.90
2726 11392 3.999001 CACAACAAGCTAGAAGCAGATGA 59.001 43.478 1.22 0.00 45.56 2.92
2727 11393 4.634883 CACAACAAGCTAGAAGCAGATGAT 59.365 41.667 1.22 0.00 45.56 2.45
2728 11394 5.123502 CACAACAAGCTAGAAGCAGATGATT 59.876 40.000 1.22 0.00 45.56 2.57
2729 11395 5.123502 ACAACAAGCTAGAAGCAGATGATTG 59.876 40.000 1.22 0.00 45.56 2.67
2730 11396 4.197750 ACAAGCTAGAAGCAGATGATTGG 58.802 43.478 1.22 0.00 45.56 3.16
2731 11397 3.488778 AGCTAGAAGCAGATGATTGGG 57.511 47.619 1.22 0.00 45.56 4.12
2732 11398 2.106166 AGCTAGAAGCAGATGATTGGGG 59.894 50.000 1.22 0.00 45.56 4.96
2733 11399 2.105477 GCTAGAAGCAGATGATTGGGGA 59.895 50.000 0.00 0.00 41.89 4.81
2734 11400 3.244840 GCTAGAAGCAGATGATTGGGGAT 60.245 47.826 0.00 0.00 41.89 3.85
2735 11401 3.967467 AGAAGCAGATGATTGGGGATT 57.033 42.857 0.00 0.00 0.00 3.01
2736 11402 4.261411 AGAAGCAGATGATTGGGGATTT 57.739 40.909 0.00 0.00 0.00 2.17
2737 11403 3.958798 AGAAGCAGATGATTGGGGATTTG 59.041 43.478 0.00 0.00 0.00 2.32
2738 11404 3.393426 AGCAGATGATTGGGGATTTGT 57.607 42.857 0.00 0.00 0.00 2.83
2739 11405 3.294214 AGCAGATGATTGGGGATTTGTC 58.706 45.455 0.00 0.00 0.00 3.18
2740 11406 3.053095 AGCAGATGATTGGGGATTTGTCT 60.053 43.478 0.00 0.00 0.00 3.41
2741 11407 3.317430 GCAGATGATTGGGGATTTGTCTC 59.683 47.826 0.00 0.00 0.00 3.36
2742 11408 4.789807 CAGATGATTGGGGATTTGTCTCT 58.210 43.478 0.00 0.00 0.00 3.10
2743 11409 5.198965 CAGATGATTGGGGATTTGTCTCTT 58.801 41.667 0.00 0.00 0.00 2.85
2744 11410 5.298777 CAGATGATTGGGGATTTGTCTCTTC 59.701 44.000 0.00 0.00 0.00 2.87
2745 11411 4.656100 TGATTGGGGATTTGTCTCTTCA 57.344 40.909 0.00 0.00 0.00 3.02
2746 11412 4.335416 TGATTGGGGATTTGTCTCTTCAC 58.665 43.478 0.00 0.00 0.00 3.18
2747 11413 4.043310 TGATTGGGGATTTGTCTCTTCACT 59.957 41.667 0.00 0.00 0.00 3.41
2748 11414 5.250543 TGATTGGGGATTTGTCTCTTCACTA 59.749 40.000 0.00 0.00 0.00 2.74
2749 11415 5.779241 TTGGGGATTTGTCTCTTCACTAT 57.221 39.130 0.00 0.00 0.00 2.12
2750 11416 5.359194 TGGGGATTTGTCTCTTCACTATC 57.641 43.478 0.00 0.00 0.00 2.08
2751 11417 5.032846 TGGGGATTTGTCTCTTCACTATCT 58.967 41.667 0.00 0.00 0.00 1.98
2752 11418 6.202331 TGGGGATTTGTCTCTTCACTATCTA 58.798 40.000 0.00 0.00 0.00 1.98
2753 11419 6.672218 TGGGGATTTGTCTCTTCACTATCTAA 59.328 38.462 0.00 0.00 0.00 2.10
2754 11420 7.348274 TGGGGATTTGTCTCTTCACTATCTAAT 59.652 37.037 0.00 0.00 0.00 1.73
2755 11421 8.214364 GGGGATTTGTCTCTTCACTATCTAATT 58.786 37.037 0.00 0.00 0.00 1.40
2756 11422 9.050601 GGGATTTGTCTCTTCACTATCTAATTG 57.949 37.037 0.00 0.00 0.00 2.32
2757 11423 8.555361 GGATTTGTCTCTTCACTATCTAATTGC 58.445 37.037 0.00 0.00 0.00 3.56
2758 11424 9.323985 GATTTGTCTCTTCACTATCTAATTGCT 57.676 33.333 0.00 0.00 0.00 3.91
2759 11425 8.709386 TTTGTCTCTTCACTATCTAATTGCTC 57.291 34.615 0.00 0.00 0.00 4.26
2760 11426 6.810911 TGTCTCTTCACTATCTAATTGCTCC 58.189 40.000 0.00 0.00 0.00 4.70
2761 11427 6.381133 TGTCTCTTCACTATCTAATTGCTCCA 59.619 38.462 0.00 0.00 0.00 3.86
2762 11428 6.922957 GTCTCTTCACTATCTAATTGCTCCAG 59.077 42.308 0.00 0.00 0.00 3.86
2764 11430 5.663106 TCTTCACTATCTAATTGCTCCAGGT 59.337 40.000 0.00 0.00 0.00 4.00
2768 11434 5.525378 CACTATCTAATTGCTCCAGGTTGAC 59.475 44.000 0.00 0.00 0.00 3.18
2777 11443 2.345760 CCAGGTTGACCATGCTGGC 61.346 63.158 2.56 0.00 42.67 4.85
2778 11444 2.036256 AGGTTGACCATGCTGGCC 59.964 61.111 0.00 0.00 42.67 5.36
2785 11451 1.380785 ACCATGCTGGCCTTGGATG 60.381 57.895 18.59 18.59 42.67 3.51
2786 11452 2.131709 CCATGCTGGCCTTGGATGG 61.132 63.158 25.78 25.78 44.58 3.51
2787 11453 1.076559 CATGCTGGCCTTGGATGGA 60.077 57.895 18.05 0.00 31.08 3.41
2808 11474 6.523840 TGGAAACAATCTCAAAGGGAAATTG 58.476 36.000 0.00 0.00 37.44 2.32
2811 11477 3.903090 ACAATCTCAAAGGGAAATTGCCA 59.097 39.130 6.25 0.00 0.00 4.92
2812 11478 4.347583 ACAATCTCAAAGGGAAATTGCCAA 59.652 37.500 6.25 0.00 0.00 4.52
2813 11479 4.813750 ATCTCAAAGGGAAATTGCCAAG 57.186 40.909 6.25 0.00 0.00 3.61
2814 11480 3.575805 TCTCAAAGGGAAATTGCCAAGT 58.424 40.909 6.25 0.00 0.00 3.16
2815 11481 3.966665 TCTCAAAGGGAAATTGCCAAGTT 59.033 39.130 6.25 0.00 0.00 2.66
2816 11482 4.039124 TCTCAAAGGGAAATTGCCAAGTTC 59.961 41.667 9.03 9.03 34.92 3.01
2820 11486 6.269769 TCAAAGGGAAATTGCCAAGTTCTATT 59.730 34.615 16.17 9.14 35.90 1.73
2832 11498 4.635765 CCAAGTTCTATTGGCGATCTTTCA 59.364 41.667 0.00 0.00 43.12 2.69
2833 11499 5.123820 CCAAGTTCTATTGGCGATCTTTCAA 59.876 40.000 0.00 0.00 43.12 2.69
2835 11501 6.183309 AGTTCTATTGGCGATCTTTCAAAC 57.817 37.500 0.00 0.00 0.00 2.93
2836 11502 5.705441 AGTTCTATTGGCGATCTTTCAAACA 59.295 36.000 0.00 0.00 0.00 2.83
2837 11503 5.801350 TCTATTGGCGATCTTTCAAACAG 57.199 39.130 0.00 0.00 0.00 3.16
2839 11505 0.881118 TGGCGATCTTTCAAACAGCC 59.119 50.000 0.00 0.00 43.05 4.85
2840 11506 1.168714 GGCGATCTTTCAAACAGCCT 58.831 50.000 0.00 0.00 39.92 4.58
2841 11507 1.541588 GGCGATCTTTCAAACAGCCTT 59.458 47.619 0.00 0.00 39.92 4.35
2842 11508 2.589014 GCGATCTTTCAAACAGCCTTG 58.411 47.619 0.00 0.00 0.00 3.61
2843 11509 2.226437 GCGATCTTTCAAACAGCCTTGA 59.774 45.455 0.00 0.00 33.48 3.02
2844 11510 3.814945 CGATCTTTCAAACAGCCTTGAC 58.185 45.455 0.00 0.00 35.07 3.18
2845 11511 3.499918 CGATCTTTCAAACAGCCTTGACT 59.500 43.478 0.00 0.00 35.07 3.41
2846 11512 4.377841 CGATCTTTCAAACAGCCTTGACTC 60.378 45.833 0.00 0.00 35.07 3.36
2847 11513 2.872245 TCTTTCAAACAGCCTTGACTCG 59.128 45.455 0.00 0.00 35.07 4.18
2848 11514 2.325583 TTCAAACAGCCTTGACTCGT 57.674 45.000 0.00 0.00 35.07 4.18
2849 11515 2.325583 TCAAACAGCCTTGACTCGTT 57.674 45.000 0.00 0.00 30.31 3.85
2850 11516 1.939934 TCAAACAGCCTTGACTCGTTG 59.060 47.619 0.00 0.00 30.31 4.10
2851 11517 1.670811 CAAACAGCCTTGACTCGTTGT 59.329 47.619 0.00 0.00 0.00 3.32
2852 11518 1.299541 AACAGCCTTGACTCGTTGTG 58.700 50.000 0.00 0.00 0.00 3.33
2853 11519 0.532862 ACAGCCTTGACTCGTTGTGG 60.533 55.000 0.00 0.00 0.00 4.17
2854 11520 1.598130 AGCCTTGACTCGTTGTGGC 60.598 57.895 0.00 0.00 40.54 5.01
2855 11521 1.598130 GCCTTGACTCGTTGTGGCT 60.598 57.895 0.00 0.00 37.58 4.75
2856 11522 1.845809 GCCTTGACTCGTTGTGGCTG 61.846 60.000 0.00 0.00 37.58 4.85
2857 11523 0.249868 CCTTGACTCGTTGTGGCTGA 60.250 55.000 0.00 0.00 0.00 4.26
2858 11524 1.143305 CTTGACTCGTTGTGGCTGAG 58.857 55.000 0.00 0.00 35.85 3.35
2859 11525 0.464036 TTGACTCGTTGTGGCTGAGT 59.536 50.000 0.00 0.00 45.18 3.41
2866 11604 2.663279 GTTGTGGCTGAGTAACAACG 57.337 50.000 13.84 0.00 42.84 4.10
2868 11606 2.605837 TGTGGCTGAGTAACAACGAA 57.394 45.000 0.00 0.00 0.00 3.85
2869 11607 2.907634 TGTGGCTGAGTAACAACGAAA 58.092 42.857 0.00 0.00 0.00 3.46
2871 11609 3.880490 TGTGGCTGAGTAACAACGAAATT 59.120 39.130 0.00 0.00 0.00 1.82
2878 11616 6.295039 TGAGTAACAACGAAATTTCTGGAC 57.705 37.500 15.92 10.37 0.00 4.02
2879 11617 5.237779 TGAGTAACAACGAAATTTCTGGACC 59.762 40.000 15.92 6.50 0.00 4.46
2880 11618 5.374071 AGTAACAACGAAATTTCTGGACCT 58.626 37.500 15.92 3.71 0.00 3.85
2883 11621 8.316214 AGTAACAACGAAATTTCTGGACCTATA 58.684 33.333 15.92 0.00 0.00 1.31
2887 11625 5.425630 ACGAAATTTCTGGACCTATACCAC 58.574 41.667 15.92 0.00 33.57 4.16
2888 11626 4.814771 CGAAATTTCTGGACCTATACCACC 59.185 45.833 15.92 0.00 33.57 4.61
2889 11627 4.417426 AATTTCTGGACCTATACCACCG 57.583 45.455 0.00 0.00 33.57 4.94
2892 11630 1.133575 TCTGGACCTATACCACCGGAG 60.134 57.143 9.46 0.00 33.56 4.63
2893 11631 0.928505 TGGACCTATACCACCGGAGA 59.071 55.000 9.46 0.00 32.03 3.71
2898 11636 1.002087 CCTATACCACCGGAGATTGGC 59.998 57.143 9.46 0.00 34.36 4.52
2900 11638 0.916086 ATACCACCGGAGATTGGCAA 59.084 50.000 9.46 0.68 34.36 4.52
2901 11639 0.035820 TACCACCGGAGATTGGCAAC 60.036 55.000 9.46 0.00 34.36 4.17
2904 11642 0.609131 CACCGGAGATTGGCAACCTT 60.609 55.000 9.46 0.00 0.00 3.50
2905 11643 0.988832 ACCGGAGATTGGCAACCTTA 59.011 50.000 9.46 0.00 0.00 2.69
2906 11644 1.353022 ACCGGAGATTGGCAACCTTAA 59.647 47.619 9.46 0.00 0.00 1.85
2907 11645 2.017049 CCGGAGATTGGCAACCTTAAG 58.983 52.381 0.00 0.00 0.00 1.85
2908 11646 2.355716 CCGGAGATTGGCAACCTTAAGA 60.356 50.000 0.00 0.00 0.00 2.10
2909 11647 2.939103 CGGAGATTGGCAACCTTAAGAG 59.061 50.000 0.00 0.00 0.00 2.85
2910 11648 2.685388 GGAGATTGGCAACCTTAAGAGC 59.315 50.000 0.00 5.06 0.00 4.09
2915 11653 1.743996 GGCAACCTTAAGAGCCTCAG 58.256 55.000 19.84 0.00 43.70 3.35
2916 11654 1.003696 GGCAACCTTAAGAGCCTCAGT 59.996 52.381 19.84 0.54 43.70 3.41
2917 11655 2.236395 GGCAACCTTAAGAGCCTCAGTA 59.764 50.000 19.84 0.00 43.70 2.74
2918 11656 3.263261 GCAACCTTAAGAGCCTCAGTAC 58.737 50.000 3.36 0.00 0.00 2.73
2919 11657 3.306780 GCAACCTTAAGAGCCTCAGTACA 60.307 47.826 3.36 0.00 0.00 2.90
2920 11658 4.624125 GCAACCTTAAGAGCCTCAGTACAT 60.624 45.833 3.36 0.00 0.00 2.29
2921 11659 5.491982 CAACCTTAAGAGCCTCAGTACATT 58.508 41.667 3.36 0.00 0.00 2.71
2922 11660 5.091261 ACCTTAAGAGCCTCAGTACATTG 57.909 43.478 3.36 0.00 0.00 2.82
2923 11661 4.532521 ACCTTAAGAGCCTCAGTACATTGT 59.467 41.667 3.36 0.00 0.00 2.71
2924 11662 5.720041 ACCTTAAGAGCCTCAGTACATTGTA 59.280 40.000 3.36 0.00 0.00 2.41
2925 11663 6.043411 CCTTAAGAGCCTCAGTACATTGTAC 58.957 44.000 17.43 17.43 0.00 2.90
2926 11664 6.351033 CCTTAAGAGCCTCAGTACATTGTACA 60.351 42.308 24.80 8.00 0.00 2.90
2927 11665 5.683876 AAGAGCCTCAGTACATTGTACAT 57.316 39.130 24.80 10.37 0.00 2.29
2928 11666 5.016051 AGAGCCTCAGTACATTGTACATG 57.984 43.478 24.80 19.22 0.00 3.21
2929 11667 4.122776 GAGCCTCAGTACATTGTACATGG 58.877 47.826 24.80 21.79 0.00 3.66
2930 11668 3.774766 AGCCTCAGTACATTGTACATGGA 59.225 43.478 24.80 17.93 0.00 3.41
2931 11669 4.410228 AGCCTCAGTACATTGTACATGGAT 59.590 41.667 24.80 18.77 0.00 3.41
2932 11670 5.104360 AGCCTCAGTACATTGTACATGGATT 60.104 40.000 24.80 13.49 0.00 3.01
2933 11671 6.099701 AGCCTCAGTACATTGTACATGGATTA 59.900 38.462 24.80 7.25 0.00 1.75
2934 11672 6.202954 GCCTCAGTACATTGTACATGGATTAC 59.797 42.308 24.80 9.67 0.00 1.89
2935 11673 7.272244 CCTCAGTACATTGTACATGGATTACA 58.728 38.462 24.80 0.00 0.00 2.41
2936 11674 7.768582 CCTCAGTACATTGTACATGGATTACAA 59.231 37.037 24.80 9.15 42.23 2.41
2937 11675 9.330063 CTCAGTACATTGTACATGGATTACAAT 57.670 33.333 24.80 12.19 46.47 2.71
2938 11676 9.679661 TCAGTACATTGTACATGGATTACAATT 57.320 29.630 24.80 10.24 44.26 2.32
2970 11708 6.399639 GGTAATATACCACCAACAATTGGG 57.600 41.667 10.83 4.76 46.48 4.12
2971 11709 6.130569 GGTAATATACCACCAACAATTGGGA 58.869 40.000 10.83 0.00 46.48 4.37
2972 11710 6.608002 GGTAATATACCACCAACAATTGGGAA 59.392 38.462 10.83 0.00 46.48 3.97
2973 11711 7.124448 GGTAATATACCACCAACAATTGGGAAA 59.876 37.037 10.83 0.00 46.48 3.13
2982 11720 5.692613 CAACAATTGGGAAATTGCACAAT 57.307 34.783 8.21 8.21 42.37 2.71
2983 11721 6.074544 CAACAATTGGGAAATTGCACAATT 57.925 33.333 19.35 19.35 42.37 2.32
2984 11722 6.461231 CCAACAATTGGGAAATTGCACAATTT 60.461 34.615 21.98 18.62 45.51 1.82
2985 11723 8.418332 CCAACAATTGGGAAATTGCACAATTTG 61.418 37.037 21.98 18.09 45.42 2.32
2995 11733 6.843069 AATTGCACAATTTGGTCAAACTAC 57.157 33.333 2.77 0.00 37.74 2.73
2998 11736 4.400884 TGCACAATTTGGTCAAACTACACT 59.599 37.500 0.78 0.00 32.51 3.55
3001 11739 6.636850 GCACAATTTGGTCAAACTACACTTAG 59.363 38.462 0.78 0.00 32.51 2.18
3004 11742 5.744666 TTTGGTCAAACTACACTTAGCAC 57.255 39.130 0.00 0.00 0.00 4.40
3006 11744 4.771903 TGGTCAAACTACACTTAGCACAA 58.228 39.130 0.00 0.00 0.00 3.33
3011 11749 7.193595 GTCAAACTACACTTAGCACAAAACAT 58.806 34.615 0.00 0.00 0.00 2.71
3022 11760 2.137523 CACAAAACATGCTTTCAGGCC 58.862 47.619 0.00 0.00 0.00 5.19
3024 11762 2.224113 ACAAAACATGCTTTCAGGCCAG 60.224 45.455 5.01 0.00 0.00 4.85
3052 12877 0.179018 GGATACATCCCACCAGGTGC 60.179 60.000 14.98 0.00 41.20 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 950 1.616865 TCGACACGACCCAAGAGAAAT 59.383 47.619 0.00 0.00 0.00 2.17
232 1544 6.357367 ACAGAAACCAGATGACTACAAGTTT 58.643 36.000 0.00 0.00 0.00 2.66
2286 10917 4.819630 GGCAATGAACCGAAGAATGGTATA 59.180 41.667 0.00 0.00 39.29 1.47
2643 11309 7.334421 CCGAAATATGGTATGGATCCAGTAAAG 59.666 40.741 21.33 2.48 38.42 1.85
2644 11310 7.165485 CCGAAATATGGTATGGATCCAGTAAA 58.835 38.462 21.33 6.51 38.42 2.01
2647 11313 4.565652 GCCGAAATATGGTATGGATCCAGT 60.566 45.833 21.33 10.87 38.42 4.00
2649 11315 3.587061 AGCCGAAATATGGTATGGATCCA 59.413 43.478 18.88 18.88 39.41 3.41
2652 11318 4.908601 TGAGCCGAAATATGGTATGGAT 57.091 40.909 0.00 0.00 0.00 3.41
2653 11319 4.908601 ATGAGCCGAAATATGGTATGGA 57.091 40.909 0.00 0.00 0.00 3.41
2654 11320 4.379813 GCAATGAGCCGAAATATGGTATGG 60.380 45.833 0.00 0.00 37.23 2.74
2655 11321 4.726416 GCAATGAGCCGAAATATGGTATG 58.274 43.478 0.00 0.00 37.23 2.39
2678 11344 5.163513 CCAAATCGAGTTCCTCCAAATTTG 58.836 41.667 11.40 11.40 34.65 2.32
2679 11345 4.321974 GCCAAATCGAGTTCCTCCAAATTT 60.322 41.667 0.00 0.00 0.00 1.82
2680 11346 3.193479 GCCAAATCGAGTTCCTCCAAATT 59.807 43.478 0.00 0.00 0.00 1.82
2681 11347 2.755103 GCCAAATCGAGTTCCTCCAAAT 59.245 45.455 0.00 0.00 0.00 2.32
2683 11349 1.073125 TGCCAAATCGAGTTCCTCCAA 59.927 47.619 0.00 0.00 0.00 3.53
2684 11350 0.690192 TGCCAAATCGAGTTCCTCCA 59.310 50.000 0.00 0.00 0.00 3.86
2685 11351 1.087501 GTGCCAAATCGAGTTCCTCC 58.912 55.000 0.00 0.00 0.00 4.30
2686 11352 1.464997 GTGTGCCAAATCGAGTTCCTC 59.535 52.381 0.00 0.00 0.00 3.71
2687 11353 1.202758 TGTGTGCCAAATCGAGTTCCT 60.203 47.619 0.00 0.00 0.00 3.36
2688 11354 1.234821 TGTGTGCCAAATCGAGTTCC 58.765 50.000 0.00 0.00 0.00 3.62
2689 11355 2.032799 TGTTGTGTGCCAAATCGAGTTC 59.967 45.455 0.00 0.00 34.07 3.01
2690 11356 2.020720 TGTTGTGTGCCAAATCGAGTT 58.979 42.857 0.00 0.00 34.07 3.01
2691 11357 1.674359 TGTTGTGTGCCAAATCGAGT 58.326 45.000 0.00 0.00 34.07 4.18
2692 11358 2.653890 CTTGTTGTGTGCCAAATCGAG 58.346 47.619 0.00 0.00 34.07 4.04
2693 11359 1.268999 GCTTGTTGTGTGCCAAATCGA 60.269 47.619 0.00 0.00 34.07 3.59
2694 11360 1.130955 GCTTGTTGTGTGCCAAATCG 58.869 50.000 0.00 0.00 34.07 3.34
2695 11361 2.514205 AGCTTGTTGTGTGCCAAATC 57.486 45.000 0.00 0.00 34.07 2.17
2696 11362 3.221771 TCTAGCTTGTTGTGTGCCAAAT 58.778 40.909 0.00 0.00 34.07 2.32
2697 11363 2.649190 TCTAGCTTGTTGTGTGCCAAA 58.351 42.857 0.00 0.00 34.07 3.28
2698 11364 2.340210 TCTAGCTTGTTGTGTGCCAA 57.660 45.000 0.00 0.00 0.00 4.52
2699 11365 2.221169 CTTCTAGCTTGTTGTGTGCCA 58.779 47.619 0.00 0.00 0.00 4.92
2700 11366 1.068954 GCTTCTAGCTTGTTGTGTGCC 60.069 52.381 0.00 0.00 38.45 5.01
2701 11367 1.603802 TGCTTCTAGCTTGTTGTGTGC 59.396 47.619 0.00 0.00 42.97 4.57
2702 11368 3.133691 TCTGCTTCTAGCTTGTTGTGTG 58.866 45.455 0.00 0.00 42.97 3.82
2703 11369 3.475566 TCTGCTTCTAGCTTGTTGTGT 57.524 42.857 0.00 0.00 42.97 3.72
2704 11370 3.999001 TCATCTGCTTCTAGCTTGTTGTG 59.001 43.478 0.00 0.00 42.97 3.33
2705 11371 4.277515 TCATCTGCTTCTAGCTTGTTGT 57.722 40.909 0.00 0.00 42.97 3.32
2706 11372 5.448768 CCAATCATCTGCTTCTAGCTTGTTG 60.449 44.000 0.00 0.00 42.97 3.33
2707 11373 4.639310 CCAATCATCTGCTTCTAGCTTGTT 59.361 41.667 0.00 0.00 42.97 2.83
2708 11374 4.197750 CCAATCATCTGCTTCTAGCTTGT 58.802 43.478 0.00 0.00 42.97 3.16
2709 11375 3.564644 CCCAATCATCTGCTTCTAGCTTG 59.435 47.826 0.00 0.00 42.97 4.01
2710 11376 3.434739 CCCCAATCATCTGCTTCTAGCTT 60.435 47.826 0.00 0.00 42.97 3.74
2711 11377 2.106166 CCCCAATCATCTGCTTCTAGCT 59.894 50.000 0.00 0.00 42.97 3.32
2712 11378 2.105477 TCCCCAATCATCTGCTTCTAGC 59.895 50.000 0.00 0.00 42.82 3.42
2713 11379 4.637387 ATCCCCAATCATCTGCTTCTAG 57.363 45.455 0.00 0.00 0.00 2.43
2714 11380 5.135383 CAAATCCCCAATCATCTGCTTCTA 58.865 41.667 0.00 0.00 0.00 2.10
2715 11381 3.958798 CAAATCCCCAATCATCTGCTTCT 59.041 43.478 0.00 0.00 0.00 2.85
2716 11382 3.703052 ACAAATCCCCAATCATCTGCTTC 59.297 43.478 0.00 0.00 0.00 3.86
2717 11383 3.703052 GACAAATCCCCAATCATCTGCTT 59.297 43.478 0.00 0.00 0.00 3.91
2718 11384 3.053095 AGACAAATCCCCAATCATCTGCT 60.053 43.478 0.00 0.00 0.00 4.24
2719 11385 3.294214 AGACAAATCCCCAATCATCTGC 58.706 45.455 0.00 0.00 0.00 4.26
2720 11386 4.789807 AGAGACAAATCCCCAATCATCTG 58.210 43.478 0.00 0.00 0.00 2.90
2721 11387 5.044624 TGAAGAGACAAATCCCCAATCATCT 60.045 40.000 0.00 0.00 0.00 2.90
2722 11388 5.067023 GTGAAGAGACAAATCCCCAATCATC 59.933 44.000 0.00 0.00 0.00 2.92
2723 11389 4.952335 GTGAAGAGACAAATCCCCAATCAT 59.048 41.667 0.00 0.00 0.00 2.45
2724 11390 4.043310 AGTGAAGAGACAAATCCCCAATCA 59.957 41.667 0.00 0.00 0.00 2.57
2725 11391 4.593956 AGTGAAGAGACAAATCCCCAATC 58.406 43.478 0.00 0.00 0.00 2.67
2726 11392 4.664688 AGTGAAGAGACAAATCCCCAAT 57.335 40.909 0.00 0.00 0.00 3.16
2727 11393 5.488919 AGATAGTGAAGAGACAAATCCCCAA 59.511 40.000 0.00 0.00 0.00 4.12
2728 11394 5.032846 AGATAGTGAAGAGACAAATCCCCA 58.967 41.667 0.00 0.00 0.00 4.96
2729 11395 5.622346 AGATAGTGAAGAGACAAATCCCC 57.378 43.478 0.00 0.00 0.00 4.81
2730 11396 9.050601 CAATTAGATAGTGAAGAGACAAATCCC 57.949 37.037 0.00 0.00 0.00 3.85
2731 11397 8.555361 GCAATTAGATAGTGAAGAGACAAATCC 58.445 37.037 0.00 0.00 0.00 3.01
2732 11398 9.323985 AGCAATTAGATAGTGAAGAGACAAATC 57.676 33.333 0.00 0.00 0.00 2.17
2733 11399 9.323985 GAGCAATTAGATAGTGAAGAGACAAAT 57.676 33.333 0.00 0.00 0.00 2.32
2734 11400 7.766278 GGAGCAATTAGATAGTGAAGAGACAAA 59.234 37.037 0.00 0.00 0.00 2.83
2735 11401 7.093333 TGGAGCAATTAGATAGTGAAGAGACAA 60.093 37.037 0.00 0.00 0.00 3.18
2736 11402 6.381133 TGGAGCAATTAGATAGTGAAGAGACA 59.619 38.462 0.00 0.00 0.00 3.41
2737 11403 6.810911 TGGAGCAATTAGATAGTGAAGAGAC 58.189 40.000 0.00 0.00 0.00 3.36
2738 11404 6.041409 CCTGGAGCAATTAGATAGTGAAGAGA 59.959 42.308 0.00 0.00 0.00 3.10
2739 11405 6.183360 ACCTGGAGCAATTAGATAGTGAAGAG 60.183 42.308 0.00 0.00 0.00 2.85
2740 11406 5.663106 ACCTGGAGCAATTAGATAGTGAAGA 59.337 40.000 0.00 0.00 0.00 2.87
2741 11407 5.923204 ACCTGGAGCAATTAGATAGTGAAG 58.077 41.667 0.00 0.00 0.00 3.02
2742 11408 5.957771 ACCTGGAGCAATTAGATAGTGAA 57.042 39.130 0.00 0.00 0.00 3.18
2743 11409 5.425217 TCAACCTGGAGCAATTAGATAGTGA 59.575 40.000 0.00 0.00 0.00 3.41
2744 11410 5.525378 GTCAACCTGGAGCAATTAGATAGTG 59.475 44.000 0.00 0.00 0.00 2.74
2745 11411 5.396884 GGTCAACCTGGAGCAATTAGATAGT 60.397 44.000 0.00 0.00 35.43 2.12
2746 11412 5.059833 GGTCAACCTGGAGCAATTAGATAG 58.940 45.833 0.00 0.00 35.43 2.08
2747 11413 4.473196 TGGTCAACCTGGAGCAATTAGATA 59.527 41.667 0.00 0.00 41.86 1.98
2748 11414 3.266772 TGGTCAACCTGGAGCAATTAGAT 59.733 43.478 0.00 0.00 41.86 1.98
2749 11415 2.642311 TGGTCAACCTGGAGCAATTAGA 59.358 45.455 0.00 0.00 41.86 2.10
2750 11416 3.071874 TGGTCAACCTGGAGCAATTAG 57.928 47.619 0.00 0.00 41.86 1.73
2751 11417 3.355378 CATGGTCAACCTGGAGCAATTA 58.645 45.455 0.00 0.00 46.98 1.40
2752 11418 2.173519 CATGGTCAACCTGGAGCAATT 58.826 47.619 0.00 0.00 46.98 2.32
2753 11419 1.843368 CATGGTCAACCTGGAGCAAT 58.157 50.000 0.00 0.00 46.98 3.56
2754 11420 0.895100 GCATGGTCAACCTGGAGCAA 60.895 55.000 0.00 0.00 46.98 3.91
2756 11422 1.001641 AGCATGGTCAACCTGGAGC 60.002 57.895 0.00 0.00 36.82 4.70
2757 11423 2.864114 CAGCATGGTCAACCTGGAG 58.136 57.895 0.00 0.00 36.82 3.86
2777 11443 5.337009 CCTTTGAGATTGTTTCCATCCAAGG 60.337 44.000 0.00 0.00 0.00 3.61
2778 11444 5.337009 CCCTTTGAGATTGTTTCCATCCAAG 60.337 44.000 0.00 0.00 0.00 3.61
2785 11451 5.409520 GCAATTTCCCTTTGAGATTGTTTCC 59.590 40.000 7.12 0.00 43.85 3.13
2786 11452 5.409520 GGCAATTTCCCTTTGAGATTGTTTC 59.590 40.000 7.12 0.00 43.85 2.78
2787 11453 5.163216 TGGCAATTTCCCTTTGAGATTGTTT 60.163 36.000 7.12 0.00 43.85 2.83
2793 11459 3.575805 ACTTGGCAATTTCCCTTTGAGA 58.424 40.909 0.00 0.00 0.00 3.27
2794 11460 4.039609 AGAACTTGGCAATTTCCCTTTGAG 59.960 41.667 22.10 0.25 0.00 3.02
2798 11464 5.046376 CCAATAGAACTTGGCAATTTCCCTT 60.046 40.000 22.10 14.72 39.32 3.95
2799 11465 4.467438 CCAATAGAACTTGGCAATTTCCCT 59.533 41.667 22.10 10.78 39.32 4.20
2811 11477 6.206634 TGTTTGAAAGATCGCCAATAGAACTT 59.793 34.615 0.00 0.00 33.13 2.66
2812 11478 5.705441 TGTTTGAAAGATCGCCAATAGAACT 59.295 36.000 0.00 0.00 0.00 3.01
2813 11479 5.938322 TGTTTGAAAGATCGCCAATAGAAC 58.062 37.500 0.00 0.00 0.00 3.01
2814 11480 5.391950 GCTGTTTGAAAGATCGCCAATAGAA 60.392 40.000 0.00 0.00 0.00 2.10
2815 11481 4.094887 GCTGTTTGAAAGATCGCCAATAGA 59.905 41.667 0.00 0.00 0.00 1.98
2816 11482 4.346129 GCTGTTTGAAAGATCGCCAATAG 58.654 43.478 0.00 0.00 0.00 1.73
2820 11486 0.881118 GGCTGTTTGAAAGATCGCCA 59.119 50.000 1.24 0.00 36.16 5.69
2823 11489 3.499918 AGTCAAGGCTGTTTGAAAGATCG 59.500 43.478 0.00 0.00 38.69 3.69
2824 11490 4.377841 CGAGTCAAGGCTGTTTGAAAGATC 60.378 45.833 0.00 0.00 38.69 2.75
2826 11492 2.872245 CGAGTCAAGGCTGTTTGAAAGA 59.128 45.455 0.00 0.00 38.69 2.52
2827 11493 2.614057 ACGAGTCAAGGCTGTTTGAAAG 59.386 45.455 0.00 0.00 38.69 2.62
2828 11494 2.639065 ACGAGTCAAGGCTGTTTGAAA 58.361 42.857 0.00 0.00 38.69 2.69
2829 11495 2.325583 ACGAGTCAAGGCTGTTTGAA 57.674 45.000 0.00 0.00 38.69 2.69
2830 11496 1.939934 CAACGAGTCAAGGCTGTTTGA 59.060 47.619 0.00 0.00 34.83 2.69
2832 11498 1.670811 CACAACGAGTCAAGGCTGTTT 59.329 47.619 0.00 0.00 0.00 2.83
2833 11499 1.299541 CACAACGAGTCAAGGCTGTT 58.700 50.000 0.00 0.00 0.00 3.16
2835 11501 1.845809 GCCACAACGAGTCAAGGCTG 61.846 60.000 0.00 0.00 39.02 4.85
2836 11502 1.598130 GCCACAACGAGTCAAGGCT 60.598 57.895 0.00 0.00 39.02 4.58
2837 11503 1.598130 AGCCACAACGAGTCAAGGC 60.598 57.895 0.00 0.00 42.31 4.35
2839 11505 1.143305 CTCAGCCACAACGAGTCAAG 58.857 55.000 0.00 0.00 0.00 3.02
2840 11506 0.464036 ACTCAGCCACAACGAGTCAA 59.536 50.000 0.00 0.00 35.02 3.18
2841 11507 1.324383 TACTCAGCCACAACGAGTCA 58.676 50.000 0.00 0.00 40.41 3.41
2842 11508 2.059541 GTTACTCAGCCACAACGAGTC 58.940 52.381 0.00 0.00 40.41 3.36
2843 11509 1.411246 TGTTACTCAGCCACAACGAGT 59.589 47.619 0.00 0.00 42.49 4.18
2844 11510 2.148916 TGTTACTCAGCCACAACGAG 57.851 50.000 0.00 0.00 0.00 4.18
2845 11511 2.206750 GTTGTTACTCAGCCACAACGA 58.793 47.619 4.35 0.00 40.56 3.85
2846 11512 2.663279 GTTGTTACTCAGCCACAACG 57.337 50.000 4.35 0.00 40.56 4.10
2847 11513 2.206750 TCGTTGTTACTCAGCCACAAC 58.793 47.619 8.96 8.96 44.54 3.32
2848 11514 2.605837 TCGTTGTTACTCAGCCACAA 57.394 45.000 0.00 0.00 0.00 3.33
2849 11515 2.605837 TTCGTTGTTACTCAGCCACA 57.394 45.000 0.00 0.00 0.00 4.17
2850 11516 4.483476 AATTTCGTTGTTACTCAGCCAC 57.517 40.909 0.00 0.00 0.00 5.01
2851 11517 4.819630 AGAAATTTCGTTGTTACTCAGCCA 59.180 37.500 12.42 0.00 0.00 4.75
2852 11518 5.147162 CAGAAATTTCGTTGTTACTCAGCC 58.853 41.667 12.42 0.00 0.00 4.85
2853 11519 5.049680 TCCAGAAATTTCGTTGTTACTCAGC 60.050 40.000 12.42 0.00 0.00 4.26
2854 11520 6.363473 GTCCAGAAATTTCGTTGTTACTCAG 58.637 40.000 12.42 0.00 0.00 3.35
2855 11521 5.237779 GGTCCAGAAATTTCGTTGTTACTCA 59.762 40.000 12.42 0.00 0.00 3.41
2856 11522 5.469084 AGGTCCAGAAATTTCGTTGTTACTC 59.531 40.000 12.42 3.08 0.00 2.59
2857 11523 5.374071 AGGTCCAGAAATTTCGTTGTTACT 58.626 37.500 12.42 4.25 0.00 2.24
2858 11524 5.684550 AGGTCCAGAAATTTCGTTGTTAC 57.315 39.130 12.42 6.97 0.00 2.50
2859 11525 7.550196 GGTATAGGTCCAGAAATTTCGTTGTTA 59.450 37.037 12.42 3.77 0.00 2.41
2866 11604 4.814771 CGGTGGTATAGGTCCAGAAATTTC 59.185 45.833 10.33 10.33 35.49 2.17
2868 11606 3.135895 CCGGTGGTATAGGTCCAGAAATT 59.864 47.826 0.00 0.00 35.49 1.82
2869 11607 2.704065 CCGGTGGTATAGGTCCAGAAAT 59.296 50.000 0.00 0.00 35.49 2.17
2871 11609 1.288633 TCCGGTGGTATAGGTCCAGAA 59.711 52.381 0.00 0.00 35.49 3.02
2878 11616 1.002087 GCCAATCTCCGGTGGTATAGG 59.998 57.143 10.30 4.87 37.23 2.57
2879 11617 1.691976 TGCCAATCTCCGGTGGTATAG 59.308 52.381 10.30 0.00 37.23 1.31
2880 11618 1.796017 TGCCAATCTCCGGTGGTATA 58.204 50.000 10.30 0.00 37.23 1.47
2883 11621 1.303317 GTTGCCAATCTCCGGTGGT 60.303 57.895 10.30 0.00 37.23 4.16
2887 11625 2.017049 CTTAAGGTTGCCAATCTCCGG 58.983 52.381 0.00 0.00 0.00 5.14
2888 11626 2.939103 CTCTTAAGGTTGCCAATCTCCG 59.061 50.000 1.85 0.00 0.00 4.63
2889 11627 2.685388 GCTCTTAAGGTTGCCAATCTCC 59.315 50.000 1.85 0.00 0.00 3.71
2898 11636 4.537135 TGTACTGAGGCTCTTAAGGTTG 57.463 45.455 16.72 0.00 0.00 3.77
2900 11638 4.532521 ACAATGTACTGAGGCTCTTAAGGT 59.467 41.667 16.72 9.00 0.00 3.50
2901 11639 5.091261 ACAATGTACTGAGGCTCTTAAGG 57.909 43.478 16.72 3.61 0.00 2.69
2904 11642 6.406961 CCATGTACAATGTACTGAGGCTCTTA 60.407 42.308 22.22 4.21 0.00 2.10
2905 11643 5.423015 CATGTACAATGTACTGAGGCTCTT 58.577 41.667 22.22 5.25 0.00 2.85
2906 11644 4.141846 CCATGTACAATGTACTGAGGCTCT 60.142 45.833 22.22 0.00 0.00 4.09
2907 11645 4.122776 CCATGTACAATGTACTGAGGCTC 58.877 47.826 22.22 7.79 0.00 4.70
2908 11646 3.774766 TCCATGTACAATGTACTGAGGCT 59.225 43.478 22.22 0.00 0.00 4.58
2909 11647 4.137116 TCCATGTACAATGTACTGAGGC 57.863 45.455 22.22 0.00 0.00 4.70
2910 11648 7.272244 TGTAATCCATGTACAATGTACTGAGG 58.728 38.462 22.22 19.35 0.00 3.86
2963 11701 5.009811 ACCAAATTGTGCAATTTCCCAATTG 59.990 36.000 17.04 0.00 46.01 2.32
2964 11702 5.139001 ACCAAATTGTGCAATTTCCCAATT 58.861 33.333 17.04 5.21 46.01 2.32
2965 11703 4.727677 ACCAAATTGTGCAATTTCCCAAT 58.272 34.783 17.04 0.00 46.01 3.16
2966 11704 4.133078 GACCAAATTGTGCAATTTCCCAA 58.867 39.130 17.04 0.00 46.01 4.12
2967 11705 3.135348 TGACCAAATTGTGCAATTTCCCA 59.865 39.130 17.04 12.79 46.01 4.37
2968 11706 3.737850 TGACCAAATTGTGCAATTTCCC 58.262 40.909 17.04 10.97 46.01 3.97
2969 11707 5.296531 AGTTTGACCAAATTGTGCAATTTCC 59.703 36.000 17.04 11.23 46.01 3.13
2970 11708 6.362210 AGTTTGACCAAATTGTGCAATTTC 57.638 33.333 17.04 9.42 46.01 2.17
2972 11710 6.257630 GTGTAGTTTGACCAAATTGTGCAATT 59.742 34.615 4.48 4.48 42.35 2.32
2973 11711 5.752955 GTGTAGTTTGACCAAATTGTGCAAT 59.247 36.000 0.00 0.00 32.36 3.56
2974 11712 5.105554 AGTGTAGTTTGACCAAATTGTGCAA 60.106 36.000 0.00 0.00 32.36 4.08
2975 11713 4.400884 AGTGTAGTTTGACCAAATTGTGCA 59.599 37.500 0.00 0.00 32.36 4.57
2976 11714 4.932146 AGTGTAGTTTGACCAAATTGTGC 58.068 39.130 0.00 0.00 32.36 4.57
2977 11715 6.636850 GCTAAGTGTAGTTTGACCAAATTGTG 59.363 38.462 0.00 0.00 32.36 3.33
2978 11716 6.320164 TGCTAAGTGTAGTTTGACCAAATTGT 59.680 34.615 0.00 0.00 32.36 2.71
2979 11717 6.636850 GTGCTAAGTGTAGTTTGACCAAATTG 59.363 38.462 0.00 0.00 32.36 2.32
2980 11718 6.320164 TGTGCTAAGTGTAGTTTGACCAAATT 59.680 34.615 0.00 0.00 32.36 1.82
2981 11719 5.825679 TGTGCTAAGTGTAGTTTGACCAAAT 59.174 36.000 0.00 0.00 32.36 2.32
2982 11720 5.186942 TGTGCTAAGTGTAGTTTGACCAAA 58.813 37.500 0.00 0.00 0.00 3.28
2983 11721 4.771903 TGTGCTAAGTGTAGTTTGACCAA 58.228 39.130 0.00 0.00 0.00 3.67
2984 11722 4.409718 TGTGCTAAGTGTAGTTTGACCA 57.590 40.909 0.00 0.00 0.00 4.02
2985 11723 5.744666 TTTGTGCTAAGTGTAGTTTGACC 57.255 39.130 0.00 0.00 0.00 4.02
2986 11724 6.548171 TGTTTTGTGCTAAGTGTAGTTTGAC 58.452 36.000 0.00 0.00 0.00 3.18
2987 11725 6.745159 TGTTTTGTGCTAAGTGTAGTTTGA 57.255 33.333 0.00 0.00 0.00 2.69
2988 11726 6.074888 GCATGTTTTGTGCTAAGTGTAGTTTG 60.075 38.462 0.00 0.00 39.45 2.93
3001 11739 1.528161 GCCTGAAAGCATGTTTTGTGC 59.472 47.619 12.62 8.03 42.81 4.57
3004 11742 2.036217 TCTGGCCTGAAAGCATGTTTTG 59.964 45.455 12.62 0.00 0.00 2.44
3006 11744 1.999648 TCTGGCCTGAAAGCATGTTT 58.000 45.000 10.32 0.00 0.00 2.83
3011 11749 0.405198 TGGAATCTGGCCTGAAAGCA 59.595 50.000 17.04 0.00 0.00 3.91
3015 11753 2.775418 TCCTATGGAATCTGGCCTGAA 58.225 47.619 17.04 0.00 0.00 3.02
3016 11754 2.494888 TCCTATGGAATCTGGCCTGA 57.505 50.000 15.40 15.40 0.00 3.86
3018 11756 3.874316 TGTATCCTATGGAATCTGGCCT 58.126 45.455 3.32 0.00 34.34 5.19
3022 11760 5.338708 GGTGGGATGTATCCTATGGAATCTG 60.339 48.000 10.53 0.00 46.35 2.90
3024 11762 4.536090 TGGTGGGATGTATCCTATGGAATC 59.464 45.833 10.53 0.00 46.35 2.52
3076 12902 7.339466 ACAACTCTGTAAGGAACAAACTGAATT 59.661 33.333 0.00 0.00 37.74 2.17
3081 12907 6.646267 TGTACAACTCTGTAAGGAACAAACT 58.354 36.000 0.00 0.00 39.75 2.66
3153 12980 1.570813 TCGCTTCGCATTCCATACTG 58.429 50.000 0.00 0.00 0.00 2.74
3170 12999 3.808728 ACATCACCCTTGGTTGATATCG 58.191 45.455 0.00 0.00 31.02 2.92
3948 13777 9.459640 CCTCATGAATATTCTTTGTAAATGCTG 57.540 33.333 16.24 6.37 0.00 4.41


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

AutoCloner maintained by Alex Coulton.