Multiple sequence alignment - TraesCS4B01G175700

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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 TraesCS4B01G175700 chr4B 100.000 6478 0 0 1 6478 386028343 386021866 0.000000e+00 11963.0
1 TraesCS4B01G175700 chr4A 95.620 2329 49 25 663 2965 166297134 166299435 0.000000e+00 3687.0
2 TraesCS4B01G175700 chr4A 96.326 1252 22 10 4373 5621 166299427 166300657 0.000000e+00 2036.0
3 TraesCS4B01G175700 chr4A 94.560 625 30 3 5857 6478 166301367 166301990 0.000000e+00 963.0
4 TraesCS4B01G175700 chr4A 92.683 656 38 4 1 656 56289395 56290040 0.000000e+00 937.0
5 TraesCS4B01G175700 chr4A 90.107 657 57 6 1 657 74591372 74592020 0.000000e+00 846.0
6 TraesCS4B01G175700 chr4A 86.525 141 9 6 5904 6035 166301274 166301413 5.230000e-31 147.0
7 TraesCS4B01G175700 chr4A 79.817 109 18 4 5440 5546 502866478 502866584 6.960000e-10 76.8
8 TraesCS4B01G175700 chr4D 96.357 2196 47 17 777 2965 308952762 308950593 0.000000e+00 3581.0
9 TraesCS4B01G175700 chr4D 96.336 1474 40 6 4387 5858 308950581 308949120 0.000000e+00 2410.0
10 TraesCS4B01G175700 chr4D 96.629 623 20 1 5857 6478 308949082 308948460 0.000000e+00 1033.0
11 TraesCS4B01G175700 chr4D 85.227 528 34 17 3872 4372 7047367 7047877 2.700000e-138 503.0
12 TraesCS4B01G175700 chr4D 82.670 427 46 15 2966 3387 7046306 7046709 2.870000e-93 353.0
13 TraesCS4B01G175700 chr4D 85.816 141 10 6 5904 6035 308949175 308949036 2.440000e-29 141.0
14 TraesCS4B01G175700 chr4D 78.899 109 19 4 5440 5546 90842344 90842450 3.240000e-08 71.3
15 TraesCS4B01G175700 chr3A 93.465 658 37 3 1 658 731025045 731025696 0.000000e+00 972.0
16 TraesCS4B01G175700 chr3A 91.159 656 47 6 1 656 713566722 713566078 0.000000e+00 880.0
17 TraesCS4B01G175700 chr3A 82.830 530 36 26 3872 4374 730325746 730325245 2.160000e-114 424.0
18 TraesCS4B01G175700 chr3A 83.807 352 47 6 6055 6403 742622114 742621770 6.260000e-85 326.0
19 TraesCS4B01G175700 chr3A 79.091 330 40 13 3084 3412 39707696 39707395 3.960000e-47 200.0
20 TraesCS4B01G175700 chr3A 93.548 124 8 0 2966 3089 39708409 39708286 1.110000e-42 185.0
21 TraesCS4B01G175700 chr3D 92.988 656 38 5 1 656 591375331 591375978 0.000000e+00 950.0
22 TraesCS4B01G175700 chr3D 81.818 451 71 6 2966 3410 473820907 473820462 1.030000e-97 368.0
23 TraesCS4B01G175700 chr3D 87.732 269 16 3 4104 4372 91689576 91689325 1.370000e-76 298.0
24 TraesCS4B01G175700 chr3D 80.094 427 50 17 2966 3387 91690816 91690420 1.060000e-72 285.0
25 TraesCS4B01G175700 chr3D 92.222 180 14 0 3872 4051 91689762 91689583 8.340000e-64 255.0
26 TraesCS4B01G175700 chr3D 84.100 239 29 7 3877 4108 473819943 473819707 8.450000e-54 222.0
27 TraesCS4B01G175700 chr7B 94.608 612 27 3 1 610 337357744 337358351 0.000000e+00 942.0
28 TraesCS4B01G175700 chr7B 78.670 361 58 16 3472 3819 708570976 708570622 8.450000e-54 222.0
29 TraesCS4B01G175700 chr7B 79.805 307 50 7 3519 3817 686164133 686163831 5.090000e-51 213.0
30 TraesCS4B01G175700 chr7B 79.868 303 51 8 3523 3819 708569481 708569183 5.090000e-51 213.0
31 TraesCS4B01G175700 chr5A 89.939 656 53 6 1 655 461908810 461909453 0.000000e+00 833.0
32 TraesCS4B01G175700 chr5A 82.222 360 46 11 6056 6410 67331325 67331671 1.770000e-75 294.0
33 TraesCS4B01G175700 chr1A 85.178 533 53 19 5857 6373 521976610 521977132 2.070000e-144 523.0
34 TraesCS4B01G175700 chr1A 83.144 528 45 17 3872 4372 549506870 549506360 5.960000e-120 442.0
35 TraesCS4B01G175700 chr6A 93.396 318 17 1 1 318 84965206 84964893 9.830000e-128 468.0
36 TraesCS4B01G175700 chr6A 84.158 404 30 10 281 655 84929171 84928773 1.720000e-95 361.0
37 TraesCS4B01G175700 chr2A 82.420 529 49 22 3872 4373 84243730 84243219 7.770000e-114 422.0
38 TraesCS4B01G175700 chr2A 87.732 269 16 10 4104 4372 327181888 327182139 1.370000e-76 298.0
39 TraesCS4B01G175700 chr2A 88.312 231 27 0 3872 4102 327181626 327181856 1.780000e-70 278.0
40 TraesCS4B01G175700 chr5D 84.108 409 56 7 118 525 560525994 560525594 2.830000e-103 387.0
41 TraesCS4B01G175700 chr3B 82.812 448 45 16 2966 3412 27201444 27201028 7.930000e-99 372.0
42 TraesCS4B01G175700 chr3B 87.037 270 18 8 4104 4373 459089361 459089613 8.220000e-74 289.0
43 TraesCS4B01G175700 chr1B 82.472 445 49 13 2969 3412 264013768 264013352 4.770000e-96 363.0
44 TraesCS4B01G175700 chr1B 87.645 259 14 8 4114 4372 263982981 263982741 1.060000e-72 285.0
45 TraesCS4B01G175700 chr1B 94.667 75 4 0 3872 3946 264012732 264012658 4.100000e-22 117.0
46 TraesCS4B01G175700 chr2B 80.467 471 63 12 2962 3412 583387119 583386658 3.740000e-87 333.0
47 TraesCS4B01G175700 chr2B 83.240 358 39 13 6056 6406 694937811 694938154 6.310000e-80 309.0
48 TraesCS4B01G175700 chr2B 83.099 355 40 13 6056 6404 188082431 188082091 8.160000e-79 305.0
49 TraesCS4B01G175700 chr2B 78.970 466 51 17 2964 3412 671038721 671038286 2.300000e-69 274.0
50 TraesCS4B01G175700 chr2B 85.185 270 20 11 4104 4372 671037458 671037208 6.440000e-65 259.0
51 TraesCS4B01G175700 chr2B 83.465 254 20 7 4124 4373 583385780 583385545 3.930000e-52 217.0
52 TraesCS4B01G175700 chr2B 79.394 330 39 13 3084 3412 24204787 24205088 8.510000e-49 206.0
53 TraesCS4B01G175700 chr2B 93.548 124 8 0 2966 3089 24204077 24204200 1.110000e-42 185.0
54 TraesCS4B01G175700 chr2B 87.500 104 12 1 3872 3975 583386037 583385935 1.140000e-22 119.0
55 TraesCS4B01G175700 chr2B 83.146 89 15 0 4001 4089 671037585 671037497 1.500000e-11 82.4
56 TraesCS4B01G175700 chr5B 84.591 318 35 11 3511 3819 395708563 395708251 2.930000e-78 303.0
57 TraesCS4B01G175700 chr5B 82.353 374 42 16 6056 6423 550750803 550750448 2.930000e-78 303.0
58 TraesCS4B01G175700 chr6B 82.633 357 44 12 6056 6409 438944207 438944548 3.800000e-77 300.0
59 TraesCS4B01G175700 chr1D 84.385 301 39 4 2964 3257 328452969 328452670 8.220000e-74 289.0
60 TraesCS4B01G175700 chr1D 89.944 179 11 4 3235 3412 7700384 7700212 2.350000e-54 224.0
61 TraesCS4B01G175700 chr1D 83.682 239 30 6 3877 4108 328447042 328446806 3.930000e-52 217.0
62 TraesCS4B01G175700 chr7A 88.889 207 23 0 3872 4078 616228085 616228291 8.340000e-64 255.0
63 TraesCS4B01G175700 chr6D 89.583 96 10 0 4277 4372 1408789 1408694 8.820000e-24 122.0
64 TraesCS4B01G175700 chr7D 77.725 211 33 11 4550 4757 217874989 217875188 4.100000e-22 117.0


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 TraesCS4B01G175700 chr4B 386021866 386028343 6477 True 11963.000000 11963 100.000000 1 6478 1 chr4B.!!$R1 6477
1 TraesCS4B01G175700 chr4A 166297134 166301990 4856 False 1708.250000 3687 93.257750 663 6478 4 chr4A.!!$F4 5815
2 TraesCS4B01G175700 chr4A 56289395 56290040 645 False 937.000000 937 92.683000 1 656 1 chr4A.!!$F1 655
3 TraesCS4B01G175700 chr4A 74591372 74592020 648 False 846.000000 846 90.107000 1 657 1 chr4A.!!$F2 656
4 TraesCS4B01G175700 chr4D 308948460 308952762 4302 True 1791.250000 3581 93.784500 777 6478 4 chr4D.!!$R1 5701
5 TraesCS4B01G175700 chr4D 7046306 7047877 1571 False 428.000000 503 83.948500 2966 4372 2 chr4D.!!$F2 1406
6 TraesCS4B01G175700 chr3A 731025045 731025696 651 False 972.000000 972 93.465000 1 658 1 chr3A.!!$F1 657
7 TraesCS4B01G175700 chr3A 713566078 713566722 644 True 880.000000 880 91.159000 1 656 1 chr3A.!!$R1 655
8 TraesCS4B01G175700 chr3A 730325245 730325746 501 True 424.000000 424 82.830000 3872 4374 1 chr3A.!!$R2 502
9 TraesCS4B01G175700 chr3D 591375331 591375978 647 False 950.000000 950 92.988000 1 656 1 chr3D.!!$F1 655
10 TraesCS4B01G175700 chr3D 473819707 473820907 1200 True 295.000000 368 82.959000 2966 4108 2 chr3D.!!$R2 1142
11 TraesCS4B01G175700 chr3D 91689325 91690816 1491 True 279.333333 298 86.682667 2966 4372 3 chr3D.!!$R1 1406
12 TraesCS4B01G175700 chr7B 337357744 337358351 607 False 942.000000 942 94.608000 1 610 1 chr7B.!!$F1 609
13 TraesCS4B01G175700 chr7B 708569183 708570976 1793 True 217.500000 222 79.269000 3472 3819 2 chr7B.!!$R2 347
14 TraesCS4B01G175700 chr5A 461908810 461909453 643 False 833.000000 833 89.939000 1 655 1 chr5A.!!$F2 654
15 TraesCS4B01G175700 chr1A 521976610 521977132 522 False 523.000000 523 85.178000 5857 6373 1 chr1A.!!$F1 516
16 TraesCS4B01G175700 chr1A 549506360 549506870 510 True 442.000000 442 83.144000 3872 4372 1 chr1A.!!$R1 500
17 TraesCS4B01G175700 chr2A 84243219 84243730 511 True 422.000000 422 82.420000 3872 4373 1 chr2A.!!$R1 501
18 TraesCS4B01G175700 chr2A 327181626 327182139 513 False 288.000000 298 88.022000 3872 4372 2 chr2A.!!$F1 500
19 TraesCS4B01G175700 chr1B 264012658 264013768 1110 True 240.000000 363 88.569500 2969 3946 2 chr1B.!!$R2 977
20 TraesCS4B01G175700 chr2B 583385545 583387119 1574 True 223.000000 333 83.810667 2962 4373 3 chr2B.!!$R2 1411
21 TraesCS4B01G175700 chr2B 671037208 671038721 1513 True 205.133333 274 82.433667 2964 4372 3 chr2B.!!$R3 1408

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
257 263 0.610785 ACCACTTTTATGCCCCGGTG 60.611 55.0 0.00 0.00 0.00 4.94 F
1201 1243 0.394216 AAGGTATGCGCATGCTTCCA 60.394 50.0 32.52 11.22 43.34 3.53 F
2333 2375 0.389817 GCTCCGGGTCAATTTTTGGC 60.390 55.0 0.00 0.00 33.62 4.52 F
3632 5170 0.036671 GGGAGAGTGGGTACGTTTGG 60.037 60.0 0.00 0.00 0.00 3.28 F
4005 5766 0.041833 AGAGGAGCTCAAGTAGGGCA 59.958 55.0 17.19 0.00 32.06 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1291 0.541392 CGATCCCCACAGGTTCATCA 59.459 55.000 0.00 0.00 34.41 3.07 R
3067 3127 1.471684 GTACTGGTGACCGTAGAGTGG 59.528 57.143 2.87 0.00 0.00 4.00 R
3759 5495 0.101579 ACACAAAAGTTTTCCGGCCG 59.898 50.000 21.04 21.04 0.00 6.13 R
4891 6714 1.542915 CCGAGTAGTTCCAGGAAACGA 59.457 52.381 2.45 0.00 34.27 3.85 R
5669 7939 1.559682 AGAAAAATAGGCCGAGCTGGA 59.440 47.619 0.00 0.00 42.00 3.86 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
257 263 0.610785 ACCACTTTTATGCCCCGGTG 60.611 55.000 0.00 0.00 0.00 4.94
295 301 8.758633 ATAAGATGGTAACTTACGTATCATGC 57.241 34.615 0.00 0.00 33.58 4.06
296 302 6.156748 AGATGGTAACTTACGTATCATGCA 57.843 37.500 0.00 0.00 37.61 3.96
297 303 6.759272 AGATGGTAACTTACGTATCATGCAT 58.241 36.000 0.00 0.00 37.61 3.96
309 315 6.621613 ACGTATCATGCATAGACGTGATAAT 58.378 36.000 23.89 7.95 45.49 1.28
373 379 3.915536 TCGTCGAAACATACCAACATGA 58.084 40.909 0.00 0.00 0.00 3.07
422 428 7.796660 CGAGACGAATCTTTTATGTGAAAACAA 59.203 33.333 0.00 0.00 34.34 2.83
471 477 8.171840 TGTGCTACAAAATGTTTTAAAGTTTGC 58.828 29.630 0.00 0.00 33.46 3.68
657 668 1.671850 CGGTCGTTAGCACAGTCCATT 60.672 52.381 0.00 0.00 0.00 3.16
658 669 2.416296 CGGTCGTTAGCACAGTCCATTA 60.416 50.000 0.00 0.00 0.00 1.90
659 670 3.737047 CGGTCGTTAGCACAGTCCATTAT 60.737 47.826 0.00 0.00 0.00 1.28
660 671 4.498513 CGGTCGTTAGCACAGTCCATTATA 60.499 45.833 0.00 0.00 0.00 0.98
661 672 4.982916 GGTCGTTAGCACAGTCCATTATAG 59.017 45.833 0.00 0.00 0.00 1.31
671 682 6.992715 GCACAGTCCATTATAGATACCACTTT 59.007 38.462 0.00 0.00 0.00 2.66
682 693 9.802039 TTATAGATACCACTTTTTGAAACCACT 57.198 29.630 0.00 0.00 0.00 4.00
683 694 6.391227 AGATACCACTTTTTGAAACCACTG 57.609 37.500 0.00 0.00 0.00 3.66
708 719 9.624697 TGATTTTCTTGAAATTAGTGAAATCCG 57.375 29.630 0.00 0.00 38.06 4.18
726 737 8.792633 TGAAATCCGTTTTCTAAAATGAGTGAT 58.207 29.630 8.61 1.86 43.50 3.06
886 928 5.286082 GCACGGCAAGATTTACTATTTTGTG 59.714 40.000 0.00 0.00 0.00 3.33
892 934 7.121315 GGCAAGATTTACTATTTTGTGGAGTCT 59.879 37.037 0.00 0.00 0.00 3.24
893 935 8.515414 GCAAGATTTACTATTTTGTGGAGTCTT 58.485 33.333 0.00 0.00 0.00 3.01
896 938 9.014297 AGATTTACTATTTTGTGGAGTCTTTGG 57.986 33.333 0.00 0.00 0.00 3.28
897 939 8.934023 ATTTACTATTTTGTGGAGTCTTTGGA 57.066 30.769 0.00 0.00 0.00 3.53
928 970 2.949705 GAAGGATCCTTCCCGCAGCC 62.950 65.000 35.48 15.10 44.76 4.85
948 990 1.276622 GAGTTCCTTCCCCAGCTGTA 58.723 55.000 13.81 0.00 0.00 2.74
949 991 1.840635 GAGTTCCTTCCCCAGCTGTAT 59.159 52.381 13.81 0.00 0.00 2.29
950 992 2.239907 GAGTTCCTTCCCCAGCTGTATT 59.760 50.000 13.81 0.00 0.00 1.89
951 993 2.239907 AGTTCCTTCCCCAGCTGTATTC 59.760 50.000 13.81 0.00 0.00 1.75
952 994 0.830648 TCCTTCCCCAGCTGTATTCG 59.169 55.000 13.81 0.00 0.00 3.34
979 1021 0.930726 AAGTTCCAAGTCCAACCCCA 59.069 50.000 0.00 0.00 0.00 4.96
986 1028 0.771755 AAGTCCAACCCCACTTCTCC 59.228 55.000 0.00 0.00 0.00 3.71
987 1029 1.134438 AGTCCAACCCCACTTCTCCC 61.134 60.000 0.00 0.00 0.00 4.30
988 1030 1.850755 TCCAACCCCACTTCTCCCC 60.851 63.158 0.00 0.00 0.00 4.81
989 1031 1.852626 CCAACCCCACTTCTCCCCT 60.853 63.158 0.00 0.00 0.00 4.79
990 1032 1.685820 CAACCCCACTTCTCCCCTC 59.314 63.158 0.00 0.00 0.00 4.30
1095 1137 1.420430 GTCCTCCCAATCACCGGATA 58.580 55.000 9.46 0.00 32.09 2.59
1113 1155 0.533491 TACCGGAATCAACCAGGACG 59.467 55.000 9.46 0.00 0.00 4.79
1201 1243 0.394216 AAGGTATGCGCATGCTTCCA 60.394 50.000 32.52 11.22 43.34 3.53
1249 1291 3.501062 GCGTTAGGTTTTGAAGTTAGGCT 59.499 43.478 0.00 0.00 0.00 4.58
1270 1312 0.541863 ATGAACCTGTGGGGATCGAC 59.458 55.000 0.00 0.00 39.43 4.20
1555 1597 6.014584 TCTGACTCTTTTTCTGGCATAGTACA 60.015 38.462 0.00 0.00 0.00 2.90
1845 1887 9.525409 GATGATGATAGGAAAAAGGAACAATTG 57.475 33.333 3.24 3.24 0.00 2.32
2210 2252 8.725148 TGAGCTTTTGTTCTAGATGAATTTCTC 58.275 33.333 0.00 0.00 36.99 2.87
2229 2271 2.797156 CTCGTGGCTATTGATGTACTGC 59.203 50.000 0.00 0.00 0.00 4.40
2333 2375 0.389817 GCTCCGGGTCAATTTTTGGC 60.390 55.000 0.00 0.00 33.62 4.52
2382 2424 4.816385 ACGAAACCAGCAATCCAGTATATG 59.184 41.667 0.00 0.00 0.00 1.78
2572 2614 1.078143 GGAAAGCTCGGACATGCCT 60.078 57.895 0.00 0.00 0.00 4.75
2796 2838 9.261035 TCTCCTTTGAATAGTCTTGACTCTTAT 57.739 33.333 6.55 0.00 0.00 1.73
2990 3034 9.435570 AGAGTAAATTACATCTATGGTACCTGT 57.564 33.333 14.36 11.07 0.00 4.00
3013 3057 5.584551 ACTTGATCCTAGGGTTCACTTTT 57.415 39.130 9.46 0.00 32.00 2.27
3049 3109 4.070009 GGAAAGGTCAAAATACGGTCACT 58.930 43.478 0.00 0.00 0.00 3.41
3067 3127 3.050275 GAGGTTGCCAGGACGTGC 61.050 66.667 0.00 0.00 0.00 5.34
3096 3156 1.135721 GGTCACCAGTACCGTATCCAC 59.864 57.143 0.00 0.00 0.00 4.02
3102 3162 3.887716 ACCAGTACCGTATCCACTGTATC 59.112 47.826 0.00 0.00 38.39 2.24
3105 3165 4.820173 CAGTACCGTATCCACTGTATCTCA 59.180 45.833 0.00 0.00 35.91 3.27
3135 3210 5.594725 TGGCAAATACACCTCTCTCTACTAG 59.405 44.000 0.00 0.00 0.00 2.57
3154 3230 6.215495 ACTAGCACTCCTCTCTGAAATTAC 57.785 41.667 0.00 0.00 0.00 1.89
3177 3253 3.049912 TCGAACATCTTATCCGCATTCG 58.950 45.455 0.00 0.00 38.96 3.34
3179 3255 2.533266 ACATCTTATCCGCATTCGCT 57.467 45.000 0.00 0.00 35.30 4.93
3188 3264 2.956987 GCATTCGCTGTTGCACCT 59.043 55.556 0.00 0.00 38.72 4.00
3191 3267 0.592637 CATTCGCTGTTGCACCTCAA 59.407 50.000 0.00 0.00 39.64 3.02
3195 3271 2.924105 GCTGTTGCACCTCAAGCCC 61.924 63.158 0.00 0.00 39.41 5.19
3206 3282 4.748144 CAAGCCCAGCTCCCACCC 62.748 72.222 0.00 0.00 38.25 4.61
3219 3295 2.512896 CACCCCTGCCATAGCTCC 59.487 66.667 0.00 0.00 40.80 4.70
3276 3352 3.802685 GTGGTCCATGAACGATACTAAGC 59.197 47.826 0.00 0.00 0.00 3.09
3293 3369 4.536489 ACTAAGCTGGTTTCCTAGACCATT 59.464 41.667 2.45 0.00 45.56 3.16
3308 3384 1.631388 ACCATTACACACGGAATCCCA 59.369 47.619 0.00 0.00 0.00 4.37
3309 3385 2.014128 CCATTACACACGGAATCCCAC 58.986 52.381 0.00 0.00 0.00 4.61
3310 3386 2.014128 CATTACACACGGAATCCCACC 58.986 52.381 0.00 0.00 0.00 4.61
3315 3391 1.995626 CACGGAATCCCACCCTCCT 60.996 63.158 0.00 0.00 0.00 3.69
3345 3421 4.097741 CACCCAACTTGAAGTTCATCAACA 59.902 41.667 7.75 0.00 36.03 3.33
3408 3485 4.759096 GTGCGTGCGTGGCCAATC 62.759 66.667 7.24 2.00 0.00 2.67
3420 3497 3.813596 CCAATCGGCCGAAGAAGG 58.186 61.111 34.66 25.54 0.00 3.46
3450 3527 3.058160 CGAAGCAAGCCCTGGTGG 61.058 66.667 0.00 0.00 35.42 4.61
3468 3545 4.293648 CGGACGTGCCTGTGTGGA 62.294 66.667 0.00 0.00 38.35 4.02
3469 3546 2.665185 GGACGTGCCTGTGTGGAC 60.665 66.667 0.00 0.00 38.35 4.02
3470 3547 2.665185 GACGTGCCTGTGTGGACC 60.665 66.667 0.00 0.00 38.35 4.46
3484 3561 2.583868 GACCGTGTGTGTGCGTGA 60.584 61.111 0.00 0.00 0.00 4.35
3487 3564 2.585869 CCGTGTGTGTGCGTGAGTC 61.586 63.158 0.00 0.00 0.00 3.36
3491 3568 1.592669 GTGTGTGCGTGAGTCAGCT 60.593 57.895 13.40 0.00 0.00 4.24
3493 3570 1.592669 GTGTGCGTGAGTCAGCTGT 60.593 57.895 14.67 0.00 0.00 4.40
3494 3571 1.592400 TGTGCGTGAGTCAGCTGTG 60.592 57.895 14.67 0.00 0.00 3.66
3495 3572 1.592669 GTGCGTGAGTCAGCTGTGT 60.593 57.895 14.67 1.40 0.00 3.72
3496 3573 1.592400 TGCGTGAGTCAGCTGTGTG 60.592 57.895 14.67 0.42 0.00 3.82
3497 3574 1.592669 GCGTGAGTCAGCTGTGTGT 60.593 57.895 14.67 0.00 0.00 3.72
3498 3575 1.825285 GCGTGAGTCAGCTGTGTGTG 61.825 60.000 14.67 2.06 0.00 3.82
3499 3576 1.825285 CGTGAGTCAGCTGTGTGTGC 61.825 60.000 14.67 0.55 0.00 4.57
3500 3577 1.592400 TGAGTCAGCTGTGTGTGCG 60.592 57.895 14.67 0.00 35.28 5.34
3501 3578 2.947890 GAGTCAGCTGTGTGTGCGC 61.948 63.158 14.67 0.00 35.28 6.09
3521 3796 3.948719 GCGTGTGGGTTCAGGGGA 61.949 66.667 0.00 0.00 0.00 4.81
3526 3801 1.846124 GTGGGTTCAGGGGAGTGGA 60.846 63.158 0.00 0.00 0.00 4.02
3618 3893 3.371063 GACGTGGCGAGTGGGAGA 61.371 66.667 0.00 0.00 0.00 3.71
3619 3894 3.343788 GACGTGGCGAGTGGGAGAG 62.344 68.421 0.00 0.00 0.00 3.20
3625 5163 1.681327 GCGAGTGGGAGAGTGGGTA 60.681 63.158 0.00 0.00 0.00 3.69
3629 5167 0.178941 AGTGGGAGAGTGGGTACGTT 60.179 55.000 0.00 0.00 0.00 3.99
3632 5170 0.036671 GGGAGAGTGGGTACGTTTGG 60.037 60.000 0.00 0.00 0.00 3.28
3694 5430 1.819632 CCCCCTGTGTAATCGCTGC 60.820 63.158 0.00 0.00 0.00 5.25
3695 5431 1.819632 CCCCTGTGTAATCGCTGCC 60.820 63.158 0.00 0.00 0.00 4.85
3696 5432 1.819632 CCCTGTGTAATCGCTGCCC 60.820 63.158 0.00 0.00 0.00 5.36
3697 5433 1.078497 CCTGTGTAATCGCTGCCCA 60.078 57.895 0.00 0.00 0.00 5.36
3702 5438 0.249447 TGTAATCGCTGCCCAGATCG 60.249 55.000 0.00 0.00 0.00 3.69
3706 5442 2.081425 ATCGCTGCCCAGATCGAGTC 62.081 60.000 0.00 0.00 34.30 3.36
3709 5445 2.362503 TGCCCAGATCGAGTCCGT 60.363 61.111 0.00 0.00 37.05 4.69
3723 5459 1.144969 GTCCGTGCTCGATGTGAAAA 58.855 50.000 10.21 0.00 39.71 2.29
3725 5461 2.159627 GTCCGTGCTCGATGTGAAAAAT 59.840 45.455 10.21 0.00 39.71 1.82
3732 5468 6.247165 CGTGCTCGATGTGAAAAATAGAAAAG 59.753 38.462 1.00 0.00 39.71 2.27
3737 5473 5.856455 CGATGTGAAAAATAGAAAAGCCGTT 59.144 36.000 0.00 0.00 0.00 4.44
3767 5503 2.975799 GTGTTTGAGCGGCCGGAA 60.976 61.111 29.38 0.00 0.00 4.30
3768 5504 2.203224 TGTTTGAGCGGCCGGAAA 60.203 55.556 29.38 1.73 0.00 3.13
3769 5505 1.824329 TGTTTGAGCGGCCGGAAAA 60.824 52.632 29.38 6.82 0.00 2.29
3770 5506 1.371267 GTTTGAGCGGCCGGAAAAC 60.371 57.895 29.38 9.78 0.00 2.43
3771 5507 1.527380 TTTGAGCGGCCGGAAAACT 60.527 52.632 29.38 15.32 0.00 2.66
3772 5508 1.104577 TTTGAGCGGCCGGAAAACTT 61.105 50.000 29.38 0.00 0.00 2.66
3773 5509 1.104577 TTGAGCGGCCGGAAAACTTT 61.105 50.000 29.38 0.00 0.00 2.66
3774 5510 1.104577 TGAGCGGCCGGAAAACTTTT 61.105 50.000 29.38 0.00 0.00 2.27
3775 5511 0.663269 GAGCGGCCGGAAAACTTTTG 60.663 55.000 29.38 0.00 0.00 2.44
3776 5512 1.066752 GCGGCCGGAAAACTTTTGT 59.933 52.632 29.38 0.00 0.00 2.83
3779 5515 1.566404 GGCCGGAAAACTTTTGTGTG 58.434 50.000 5.05 0.00 0.00 3.82
3781 5517 1.470805 GCCGGAAAACTTTTGTGTGCT 60.471 47.619 5.05 0.00 0.00 4.40
3783 5519 2.857748 CCGGAAAACTTTTGTGTGCTTC 59.142 45.455 0.00 0.00 0.00 3.86
3784 5520 2.857748 CGGAAAACTTTTGTGTGCTTCC 59.142 45.455 0.00 0.00 33.17 3.46
3785 5521 3.428862 CGGAAAACTTTTGTGTGCTTCCT 60.429 43.478 0.00 0.00 33.79 3.36
3786 5522 4.112634 GGAAAACTTTTGTGTGCTTCCTC 58.887 43.478 0.00 0.00 33.47 3.71
3788 5524 2.736670 ACTTTTGTGTGCTTCCTCCT 57.263 45.000 0.00 0.00 0.00 3.69
3789 5525 2.576615 ACTTTTGTGTGCTTCCTCCTC 58.423 47.619 0.00 0.00 0.00 3.71
3790 5526 2.173569 ACTTTTGTGTGCTTCCTCCTCT 59.826 45.455 0.00 0.00 0.00 3.69
3791 5527 2.550830 TTTGTGTGCTTCCTCCTCTC 57.449 50.000 0.00 0.00 0.00 3.20
3792 5528 0.687354 TTGTGTGCTTCCTCCTCTCC 59.313 55.000 0.00 0.00 0.00 3.71
3793 5529 1.216710 GTGTGCTTCCTCCTCTCCG 59.783 63.158 0.00 0.00 0.00 4.63
3794 5530 1.984570 TGTGCTTCCTCCTCTCCGG 60.985 63.158 0.00 0.00 0.00 5.14
3795 5531 3.077556 TGCTTCCTCCTCTCCGGC 61.078 66.667 0.00 0.00 0.00 6.13
3796 5532 3.855853 GCTTCCTCCTCTCCGGCC 61.856 72.222 0.00 0.00 0.00 6.13
3797 5533 3.532155 CTTCCTCCTCTCCGGCCG 61.532 72.222 21.04 21.04 0.00 6.13
3798 5534 4.377760 TTCCTCCTCTCCGGCCGT 62.378 66.667 26.12 0.00 0.00 5.68
3801 5537 3.827898 CTCCTCTCCGGCCGTGTC 61.828 72.222 26.12 0.00 0.00 3.67
3802 5538 4.361971 TCCTCTCCGGCCGTGTCT 62.362 66.667 26.12 0.00 0.00 3.41
3803 5539 2.439701 CCTCTCCGGCCGTGTCTA 60.440 66.667 26.12 3.46 0.00 2.59
3804 5540 2.772691 CCTCTCCGGCCGTGTCTAC 61.773 68.421 26.12 0.00 0.00 2.59
3830 5569 3.760035 CCGTCGTGCACTAGGGCT 61.760 66.667 19.73 0.00 34.04 5.19
3831 5570 2.412323 CCGTCGTGCACTAGGGCTA 61.412 63.158 19.73 1.30 34.04 3.93
3832 5571 1.064296 CGTCGTGCACTAGGGCTAG 59.936 63.158 19.73 12.11 39.04 3.42
3833 5572 1.227002 GTCGTGCACTAGGGCTAGC 60.227 63.158 19.73 6.04 36.66 3.42
3834 5573 1.379977 TCGTGCACTAGGGCTAGCT 60.380 57.895 19.73 0.00 36.66 3.32
3835 5574 1.227089 CGTGCACTAGGGCTAGCTG 60.227 63.158 19.73 5.56 36.66 4.24
3836 5575 1.522580 GTGCACTAGGGCTAGCTGC 60.523 63.158 19.73 16.25 38.96 5.25
3924 5685 1.544246 TCTCGGAGCATGTCGAAGAAA 59.456 47.619 0.00 0.00 39.69 2.52
3960 5721 4.752879 AGCGCGCCACCGTATTGT 62.753 61.111 30.33 0.79 36.67 2.71
4005 5766 0.041833 AGAGGAGCTCAAGTAGGGCA 59.958 55.000 17.19 0.00 32.06 5.36
4051 5817 2.251642 GCACGAAGAAAGGCGGTGT 61.252 57.895 0.00 0.00 0.00 4.16
4052 5818 1.860078 CACGAAGAAAGGCGGTGTC 59.140 57.895 0.00 0.00 0.00 3.67
4082 5848 2.485479 GGTTGTTGACAGAAGAGAGCCA 60.485 50.000 0.00 0.00 0.00 4.75
4102 5868 0.914644 AGCAGCCATGTGGTACATCT 59.085 50.000 0.35 0.00 44.52 2.90
4142 5947 2.354510 GGTTCATTCATCGGATGCGAAA 59.645 45.455 14.89 4.60 0.00 3.46
4143 5948 3.181501 GGTTCATTCATCGGATGCGAAAA 60.182 43.478 14.89 11.70 0.00 2.29
4147 5952 0.732571 TCATCGGATGCGAAAAAGGC 59.267 50.000 14.89 0.00 0.00 4.35
4195 6002 2.805657 GCAAGTCAACCGTTAGGACAGT 60.806 50.000 4.96 0.00 41.02 3.55
4269 6080 4.569943 AGAGTGACACATTTACGCAATCT 58.430 39.130 8.59 0.00 0.00 2.40
4270 6081 4.627467 AGAGTGACACATTTACGCAATCTC 59.373 41.667 8.59 0.00 29.09 2.75
4271 6082 4.314961 AGTGACACATTTACGCAATCTCA 58.685 39.130 8.59 0.00 0.00 3.27
4272 6083 4.389992 AGTGACACATTTACGCAATCTCAG 59.610 41.667 8.59 0.00 0.00 3.35
4273 6084 4.152402 GTGACACATTTACGCAATCTCAGT 59.848 41.667 0.00 0.00 0.00 3.41
4274 6085 4.152223 TGACACATTTACGCAATCTCAGTG 59.848 41.667 0.00 0.00 0.00 3.66
4275 6086 4.314961 ACACATTTACGCAATCTCAGTGA 58.685 39.130 0.00 0.00 0.00 3.41
4276 6087 4.937620 ACACATTTACGCAATCTCAGTGAT 59.062 37.500 0.00 0.00 36.89 3.06
4277 6088 6.106003 ACACATTTACGCAATCTCAGTGATA 58.894 36.000 0.00 0.00 34.45 2.15
4278 6089 6.036083 ACACATTTACGCAATCTCAGTGATAC 59.964 38.462 0.00 0.00 34.45 2.24
4279 6090 5.232202 ACATTTACGCAATCTCAGTGATACG 59.768 40.000 0.00 6.37 39.36 3.06
4280 6091 1.560923 ACGCAATCTCAGTGATACGC 58.439 50.000 0.00 0.00 37.97 4.42
4281 6092 1.135112 ACGCAATCTCAGTGATACGCA 60.135 47.619 0.00 0.00 37.97 5.24
4282 6093 1.926510 CGCAATCTCAGTGATACGCAA 59.073 47.619 0.00 0.00 34.96 4.85
4283 6094 2.541346 CGCAATCTCAGTGATACGCAAT 59.459 45.455 0.00 0.00 34.96 3.56
4284 6095 3.362401 CGCAATCTCAGTGATACGCAATC 60.362 47.826 0.00 0.00 34.96 2.67
4302 6113 4.115516 CAATCTCAGTGACCGTATTCTGG 58.884 47.826 0.00 0.00 0.00 3.86
4599 6420 3.695830 AAATTGCTAGAACTCGGTCCA 57.304 42.857 0.00 0.00 0.00 4.02
4619 6440 8.135529 CGGTCCAAAGAAAACTAAAATTTCTCT 58.864 33.333 2.35 0.00 44.22 3.10
4862 6685 4.370364 TTTTGCGCTTCTCACTTTTTCT 57.630 36.364 9.73 0.00 0.00 2.52
4891 6714 6.070656 TGTTCCATCTTCAAAGTCAGGAATT 58.929 36.000 12.69 0.00 35.51 2.17
4922 6745 3.487209 GGAACTACTCGGACGAGATGAAC 60.487 52.174 26.41 14.08 44.53 3.18
5211 7034 7.123247 ACAATGCTGGACAAATAATAGAGCTTT 59.877 33.333 0.00 0.00 0.00 3.51
5278 7101 1.920835 GGGGCTCAGACTGAAGGGT 60.921 63.158 6.61 0.00 0.00 4.34
5279 7102 1.492993 GGGGCTCAGACTGAAGGGTT 61.493 60.000 6.61 0.00 0.00 4.11
5280 7103 1.276622 GGGCTCAGACTGAAGGGTTA 58.723 55.000 6.61 0.00 0.00 2.85
5281 7104 1.066071 GGGCTCAGACTGAAGGGTTAC 60.066 57.143 6.61 0.00 0.00 2.50
5306 7129 5.728637 ACTTATGATGTGTCAGTGTCTGA 57.271 39.130 0.00 0.00 37.87 3.27
5307 7130 6.291648 ACTTATGATGTGTCAGTGTCTGAT 57.708 37.500 2.80 0.00 42.73 2.90
5308 7131 6.104665 ACTTATGATGTGTCAGTGTCTGATG 58.895 40.000 2.80 0.00 42.73 3.07
5309 7132 4.813750 ATGATGTGTCAGTGTCTGATGA 57.186 40.909 2.80 0.00 42.73 2.92
5310 7133 4.813750 TGATGTGTCAGTGTCTGATGAT 57.186 40.909 2.80 0.00 42.73 2.45
5311 7134 5.920193 TGATGTGTCAGTGTCTGATGATA 57.080 39.130 2.80 0.00 42.73 2.15
5312 7135 5.899299 TGATGTGTCAGTGTCTGATGATAG 58.101 41.667 2.80 0.00 42.73 2.08
5313 7136 5.653769 TGATGTGTCAGTGTCTGATGATAGA 59.346 40.000 2.80 0.00 42.73 1.98
5428 7252 5.598005 ACACAGACATCCAAAAATTTGAGGA 59.402 36.000 12.67 12.67 40.55 3.71
5435 7259 8.017418 ACATCCAAAAATTTGAGGAGTTGTAA 57.983 30.769 14.85 0.00 40.55 2.41
5484 7308 0.878416 TGCTTTTGGCGGTACATCAC 59.122 50.000 0.00 0.00 45.43 3.06
5486 7310 1.434555 CTTTTGGCGGTACATCACGA 58.565 50.000 0.00 0.00 0.00 4.35
5517 7342 6.460781 CCTTTTAAAGGTCCACAAATTACCC 58.539 40.000 15.16 0.00 43.95 3.69
5563 7388 6.302313 GTGAAAAACGATTCGTAAGTTCATGG 59.698 38.462 23.38 0.00 39.99 3.66
5669 7939 5.251764 CACTTGAGAGATCCAGGTTTGATT 58.748 41.667 0.00 0.00 0.00 2.57
5837 8108 6.545508 TCAAATATGCTATTATCGTGCATGC 58.454 36.000 11.82 11.82 45.52 4.06
5842 8113 5.535043 TGCTATTATCGTGCATGCTAATG 57.465 39.130 20.33 13.11 36.82 1.90
6183 8504 7.466185 CGACAACAAAAGTGTAAACAGATACCA 60.466 37.037 0.00 0.00 36.80 3.25
6347 8672 2.093306 TTTGCTCATGTCGTCGGATT 57.907 45.000 0.00 0.00 0.00 3.01
6385 8710 1.753463 TTTTTCCCCGGTGCAACGT 60.753 52.632 24.60 0.00 38.12 3.99
6454 8779 1.072806 TGCAGCTTTCAGACTCACCAT 59.927 47.619 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.368248 TGGGCTAAGTAAGGTATCACGT 58.632 45.455 0.00 0.00 0.00 4.49
294 300 7.599245 AGGCTAAGTAAATTATCACGTCTATGC 59.401 37.037 0.00 0.00 0.00 3.14
295 301 8.916654 CAGGCTAAGTAAATTATCACGTCTATG 58.083 37.037 0.00 0.00 0.00 2.23
296 302 8.088981 CCAGGCTAAGTAAATTATCACGTCTAT 58.911 37.037 0.00 0.00 0.00 1.98
297 303 7.431249 CCAGGCTAAGTAAATTATCACGTCTA 58.569 38.462 0.00 0.00 0.00 2.59
309 315 1.663911 TCAGGCCCAGGCTAAGTAAA 58.336 50.000 8.89 0.00 41.60 2.01
351 357 4.500127 TCATGTTGGTATGTTTCGACGAT 58.500 39.130 0.00 0.00 0.00 3.73
398 404 9.965824 AATTGTTTTCACATAAAAGATTCGTCT 57.034 25.926 0.00 0.00 31.06 4.18
434 440 8.279970 ACATTTTGTAGCACAAATCATAGCTA 57.720 30.769 12.95 0.00 46.17 3.32
549 556 4.403137 GACTTTGCATGCGCGCCA 62.403 61.111 30.77 17.20 42.97 5.69
592 600 2.383298 CGAACAATCGCCGCAAATAT 57.617 45.000 0.00 0.00 42.96 1.28
606 617 2.823924 TTTAGCTACAGGCACGAACA 57.176 45.000 0.00 0.00 44.79 3.18
617 628 2.210961 GGACGGCAGGATTTTAGCTAC 58.789 52.381 0.00 0.00 0.00 3.58
657 668 9.226606 CAGTGGTTTCAAAAAGTGGTATCTATA 57.773 33.333 0.00 0.00 0.00 1.31
658 669 7.942341 TCAGTGGTTTCAAAAAGTGGTATCTAT 59.058 33.333 0.00 0.00 0.00 1.98
659 670 7.284074 TCAGTGGTTTCAAAAAGTGGTATCTA 58.716 34.615 0.00 0.00 0.00 1.98
660 671 6.126409 TCAGTGGTTTCAAAAAGTGGTATCT 58.874 36.000 0.00 0.00 0.00 1.98
661 672 6.385649 TCAGTGGTTTCAAAAAGTGGTATC 57.614 37.500 0.00 0.00 0.00 2.24
671 682 9.447157 AATTTCAAGAAAATCAGTGGTTTCAAA 57.553 25.926 17.26 11.62 36.54 2.69
682 693 9.624697 CGGATTTCACTAATTTCAAGAAAATCA 57.375 29.630 0.00 0.00 36.54 2.57
683 694 9.626045 ACGGATTTCACTAATTTCAAGAAAATC 57.374 29.630 0.00 0.00 36.54 2.17
886 928 2.795329 TCCAAAGCATCCAAAGACTCC 58.205 47.619 0.00 0.00 0.00 3.85
892 934 2.754552 CCTTCGATCCAAAGCATCCAAA 59.245 45.455 0.00 0.00 0.00 3.28
893 935 2.026356 TCCTTCGATCCAAAGCATCCAA 60.026 45.455 0.00 0.00 0.00 3.53
894 936 1.559219 TCCTTCGATCCAAAGCATCCA 59.441 47.619 0.00 0.00 0.00 3.41
895 937 2.332063 TCCTTCGATCCAAAGCATCC 57.668 50.000 0.00 0.00 0.00 3.51
928 970 1.078848 CAGCTGGGGAAGGAACTCG 60.079 63.158 5.57 0.00 38.49 4.18
948 990 2.859165 TGGAACTTGGAAGAGCGAAT 57.141 45.000 0.00 0.00 0.00 3.34
949 991 2.158813 ACTTGGAACTTGGAAGAGCGAA 60.159 45.455 0.00 0.00 0.00 4.70
950 992 1.416401 ACTTGGAACTTGGAAGAGCGA 59.584 47.619 0.00 0.00 0.00 4.93
951 993 1.801178 GACTTGGAACTTGGAAGAGCG 59.199 52.381 0.00 0.00 0.00 5.03
952 994 2.155279 GGACTTGGAACTTGGAAGAGC 58.845 52.381 0.00 0.00 0.00 4.09
979 1021 2.788589 GAGGGGGAGGGGAGAAGT 59.211 66.667 0.00 0.00 0.00 3.01
988 1030 4.806339 AGAAGCGGGGAGGGGGAG 62.806 72.222 0.00 0.00 0.00 4.30
989 1031 4.348495 AAGAAGCGGGGAGGGGGA 62.348 66.667 0.00 0.00 0.00 4.81
990 1032 3.798511 GAAGAAGCGGGGAGGGGG 61.799 72.222 0.00 0.00 0.00 5.40
1095 1137 1.189524 TCGTCCTGGTTGATTCCGGT 61.190 55.000 0.00 0.00 32.33 5.28
1113 1155 2.044551 ACGTACCGAGGGGTCCTC 60.045 66.667 3.96 3.96 46.01 3.71
1201 1243 5.744666 TTTCACGATTTCGAAAAACTCCT 57.255 34.783 15.66 0.00 43.02 3.69
1249 1291 0.541392 CGATCCCCACAGGTTCATCA 59.459 55.000 0.00 0.00 34.41 3.07
1270 1312 2.488347 CCCACCAAATTATACTCCCCCG 60.488 54.545 0.00 0.00 0.00 5.73
1555 1597 2.159000 TCAGATTGCTCGCTGACATGAT 60.159 45.455 0.00 0.00 36.31 2.45
1671 1713 1.340248 CCGCCACCGTCATAACTAGAT 59.660 52.381 0.00 0.00 0.00 1.98
1845 1887 4.836125 TGAGAAAAGAAATGACCAGTGC 57.164 40.909 0.00 0.00 0.00 4.40
2157 2199 6.185114 ACTTCCAAGATAGAGCATTGCTAT 57.815 37.500 11.96 11.46 39.88 2.97
2210 2252 1.867233 GGCAGTACATCAATAGCCACG 59.133 52.381 0.00 0.00 41.63 4.94
2229 2271 6.654161 CAGAATTAAGATCATGGCTAGGAAGG 59.346 42.308 0.00 0.00 0.00 3.46
2333 2375 3.243401 CCGAAGAAAAGGGAAACAACCTG 60.243 47.826 0.00 0.00 38.63 4.00
2382 2424 4.760204 ACATGTTACCTGCAAAGGACTAAC 59.240 41.667 0.00 0.00 0.00 2.34
2982 3026 3.896272 CCCTAGGATCAAGTACAGGTACC 59.104 52.174 11.48 2.73 36.75 3.34
2990 3034 6.043938 ACAAAAGTGAACCCTAGGATCAAGTA 59.956 38.462 11.48 0.00 36.30 2.24
3013 3057 4.346709 TGACCTTTCCTGAATACAGTGACA 59.653 41.667 0.00 0.00 42.05 3.58
3049 3109 2.425592 CACGTCCTGGCAACCTCA 59.574 61.111 0.00 0.00 0.00 3.86
3067 3127 1.471684 GTACTGGTGACCGTAGAGTGG 59.528 57.143 2.87 0.00 0.00 4.00
3096 3156 3.599730 TTGCCACTCAGTGAGATACAG 57.400 47.619 26.86 10.50 35.23 2.74
3102 3162 2.744202 GGTGTATTTGCCACTCAGTGAG 59.256 50.000 18.83 18.83 35.23 3.51
3105 3165 2.639839 AGAGGTGTATTTGCCACTCAGT 59.360 45.455 0.00 0.00 33.31 3.41
3135 3210 3.851098 ACGTAATTTCAGAGAGGAGTGC 58.149 45.455 0.00 0.00 0.00 4.40
3154 3230 1.835121 TGCGGATAAGATGTTCGACG 58.165 50.000 0.00 0.00 0.00 5.12
3177 3253 2.647297 GGCTTGAGGTGCAACAGC 59.353 61.111 3.64 3.86 39.98 4.40
3179 3255 1.529010 CTGGGCTTGAGGTGCAACA 60.529 57.895 3.64 0.00 39.98 3.33
3188 3264 3.650950 GGTGGGAGCTGGGCTTGA 61.651 66.667 0.00 0.00 39.88 3.02
3206 3282 2.834688 CTGGGGAGCTATGGCAGG 59.165 66.667 3.10 0.00 41.70 4.85
3252 3328 5.601662 CTTAGTATCGTTCATGGACCACAT 58.398 41.667 0.00 0.00 41.57 3.21
3270 3346 3.517612 TGGTCTAGGAAACCAGCTTAGT 58.482 45.455 0.00 0.00 41.84 2.24
3293 3369 0.545787 AGGGTGGGATTCCGTGTGTA 60.546 55.000 0.00 0.00 35.24 2.90
3308 3384 3.570212 GGTGTGGCACAGGAGGGT 61.570 66.667 22.75 0.00 41.80 4.34
3309 3385 4.351054 GGGTGTGGCACAGGAGGG 62.351 72.222 22.75 0.00 41.80 4.30
3310 3386 3.132029 TTGGGTGTGGCACAGGAGG 62.132 63.158 22.75 0.00 41.80 4.30
3315 3391 0.323816 TTCAAGTTGGGTGTGGCACA 60.324 50.000 17.96 17.96 35.86 4.57
3391 3468 4.759096 GATTGGCCACGCACGCAC 62.759 66.667 3.88 0.00 0.00 5.34
3403 3480 2.472909 GCCTTCTTCGGCCGATTGG 61.473 63.158 31.56 26.29 44.41 3.16
3404 3481 3.102097 GCCTTCTTCGGCCGATTG 58.898 61.111 31.56 24.07 44.41 2.67
3432 3509 3.741476 CACCAGGGCTTGCTTCGC 61.741 66.667 0.00 0.00 0.00 4.70
3433 3510 3.058160 CCACCAGGGCTTGCTTCG 61.058 66.667 0.00 0.00 0.00 3.79
3451 3528 4.293648 TCCACACAGGCACGTCCG 62.294 66.667 0.00 0.00 40.77 4.79
3452 3529 2.665185 GTCCACACAGGCACGTCC 60.665 66.667 0.00 0.00 37.29 4.79
3453 3530 2.665185 GGTCCACACAGGCACGTC 60.665 66.667 0.00 0.00 37.29 4.34
3454 3531 4.602259 CGGTCCACACAGGCACGT 62.602 66.667 0.00 0.00 37.29 4.49
3455 3532 4.602259 ACGGTCCACACAGGCACG 62.602 66.667 0.00 0.00 40.54 5.34
3456 3533 2.972505 CACGGTCCACACAGGCAC 60.973 66.667 0.00 0.00 37.29 5.01
3457 3534 3.475494 ACACGGTCCACACAGGCA 61.475 61.111 0.00 0.00 37.29 4.75
3458 3535 2.972505 CACACGGTCCACACAGGC 60.973 66.667 0.00 0.00 37.29 4.85
3459 3536 1.887242 CACACACGGTCCACACAGG 60.887 63.158 0.00 0.00 39.47 4.00
3460 3537 1.153449 ACACACACGGTCCACACAG 60.153 57.895 0.00 0.00 0.00 3.66
3461 3538 1.448717 CACACACACGGTCCACACA 60.449 57.895 0.00 0.00 0.00 3.72
3462 3539 2.819552 GCACACACACGGTCCACAC 61.820 63.158 0.00 0.00 0.00 3.82
3463 3540 2.512745 GCACACACACGGTCCACA 60.513 61.111 0.00 0.00 0.00 4.17
3464 3541 3.636043 CGCACACACACGGTCCAC 61.636 66.667 0.00 0.00 0.00 4.02
3465 3542 4.150203 ACGCACACACACGGTCCA 62.150 61.111 0.00 0.00 0.00 4.02
3466 3543 3.636043 CACGCACACACACGGTCC 61.636 66.667 0.00 0.00 0.00 4.46
3467 3544 2.583868 TCACGCACACACACGGTC 60.584 61.111 0.00 0.00 0.00 4.79
3468 3545 2.584970 CTCACGCACACACACGGT 60.585 61.111 0.00 0.00 0.00 4.83
3469 3546 2.584970 ACTCACGCACACACACGG 60.585 61.111 0.00 0.00 0.00 4.94
3470 3547 1.811217 CTGACTCACGCACACACACG 61.811 60.000 0.00 0.00 0.00 4.49
3484 3561 2.969238 GCGCACACACAGCTGACT 60.969 61.111 23.35 0.65 0.00 3.41
3506 3583 1.073199 CACTCCCCTGAACCCACAC 59.927 63.158 0.00 0.00 0.00 3.82
3508 3585 1.846124 TCCACTCCCCTGAACCCAC 60.846 63.158 0.00 0.00 0.00 4.61
3510 3587 2.603652 GGTCCACTCCCCTGAACCC 61.604 68.421 0.00 0.00 0.00 4.11
3513 3590 3.319198 GCGGTCCACTCCCCTGAA 61.319 66.667 0.00 0.00 0.00 3.02
3602 3877 3.374402 CTCTCCCACTCGCCACGT 61.374 66.667 0.00 0.00 0.00 4.49
3618 3893 2.031465 CGCCCAAACGTACCCACT 59.969 61.111 0.00 0.00 0.00 4.00
3619 3894 3.729698 GCGCCCAAACGTACCCAC 61.730 66.667 0.00 0.00 34.88 4.61
3647 5185 1.741327 TTATACCCGCGGGCTCTGAC 61.741 60.000 43.58 0.00 39.32 3.51
3648 5186 1.456145 TTATACCCGCGGGCTCTGA 60.456 57.895 43.58 23.69 39.32 3.27
3649 5187 1.006102 CTTATACCCGCGGGCTCTG 60.006 63.158 43.58 25.09 39.32 3.35
3650 5188 1.152610 TCTTATACCCGCGGGCTCT 60.153 57.895 43.58 28.97 39.32 4.09
3652 5190 2.505167 GGTCTTATACCCGCGGGCT 61.505 63.158 43.58 31.96 43.16 5.19
3694 5430 2.105128 GCACGGACTCGATCTGGG 59.895 66.667 8.07 5.47 40.54 4.45
3695 5431 1.064946 GAGCACGGACTCGATCTGG 59.935 63.158 8.07 0.00 38.12 3.86
3696 5432 4.700037 GAGCACGGACTCGATCTG 57.300 61.111 0.00 0.00 40.11 2.90
3702 5438 0.109272 TTCACATCGAGCACGGACTC 60.109 55.000 3.11 0.00 40.21 3.36
3706 5442 2.900122 ATTTTTCACATCGAGCACGG 57.100 45.000 3.11 0.00 40.21 4.94
3709 5445 6.086222 GCTTTTCTATTTTTCACATCGAGCA 58.914 36.000 0.00 0.00 0.00 4.26
3723 5459 1.127951 CGCACGAACGGCTTTTCTATT 59.872 47.619 0.00 0.00 0.00 1.73
3725 5461 2.146954 CGCACGAACGGCTTTTCTA 58.853 52.632 0.00 0.00 0.00 2.10
3751 5487 1.824329 TTTTCCGGCCGCTCAAACA 60.824 52.632 22.85 0.85 0.00 2.83
3752 5488 1.371267 GTTTTCCGGCCGCTCAAAC 60.371 57.895 22.85 22.13 0.00 2.93
3753 5489 1.104577 AAGTTTTCCGGCCGCTCAAA 61.105 50.000 22.85 15.14 0.00 2.69
3755 5491 1.104577 AAAAGTTTTCCGGCCGCTCA 61.105 50.000 22.85 1.77 0.00 4.26
3756 5492 0.663269 CAAAAGTTTTCCGGCCGCTC 60.663 55.000 22.85 7.39 0.00 5.03
3758 5494 1.066752 ACAAAAGTTTTCCGGCCGC 59.933 52.632 22.85 5.42 0.00 6.53
3759 5495 0.101579 ACACAAAAGTTTTCCGGCCG 59.898 50.000 21.04 21.04 0.00 6.13
3760 5496 1.566404 CACACAAAAGTTTTCCGGCC 58.434 50.000 0.00 0.00 0.00 6.13
3761 5497 0.927537 GCACACAAAAGTTTTCCGGC 59.072 50.000 0.00 0.00 0.00 6.13
3763 5499 2.857748 GGAAGCACACAAAAGTTTTCCG 59.142 45.455 0.00 0.00 0.00 4.30
3764 5500 4.112634 GAGGAAGCACACAAAAGTTTTCC 58.887 43.478 0.00 0.00 34.91 3.13
3765 5501 4.112634 GGAGGAAGCACACAAAAGTTTTC 58.887 43.478 0.00 0.00 0.00 2.29
3766 5502 3.769300 AGGAGGAAGCACACAAAAGTTTT 59.231 39.130 0.00 0.00 0.00 2.43
3767 5503 3.365472 AGGAGGAAGCACACAAAAGTTT 58.635 40.909 0.00 0.00 0.00 2.66
3768 5504 2.952310 GAGGAGGAAGCACACAAAAGTT 59.048 45.455 0.00 0.00 0.00 2.66
3769 5505 2.173569 AGAGGAGGAAGCACACAAAAGT 59.826 45.455 0.00 0.00 0.00 2.66
3770 5506 2.810852 GAGAGGAGGAAGCACACAAAAG 59.189 50.000 0.00 0.00 0.00 2.27
3771 5507 2.487265 GGAGAGGAGGAAGCACACAAAA 60.487 50.000 0.00 0.00 0.00 2.44
3772 5508 1.072331 GGAGAGGAGGAAGCACACAAA 59.928 52.381 0.00 0.00 0.00 2.83
3773 5509 0.687354 GGAGAGGAGGAAGCACACAA 59.313 55.000 0.00 0.00 0.00 3.33
3774 5510 1.536073 CGGAGAGGAGGAAGCACACA 61.536 60.000 0.00 0.00 0.00 3.72
3775 5511 1.216710 CGGAGAGGAGGAAGCACAC 59.783 63.158 0.00 0.00 0.00 3.82
3776 5512 1.984570 CCGGAGAGGAGGAAGCACA 60.985 63.158 0.00 0.00 45.00 4.57
3779 5515 3.855853 GGCCGGAGAGGAGGAAGC 61.856 72.222 5.05 0.00 45.00 3.86
3781 5517 4.377760 ACGGCCGGAGAGGAGGAA 62.378 66.667 31.76 0.00 45.00 3.36
3784 5520 2.888464 TAGACACGGCCGGAGAGGAG 62.888 65.000 31.76 11.97 45.00 3.69
3785 5521 2.975265 TAGACACGGCCGGAGAGGA 61.975 63.158 31.76 6.98 45.00 3.71
3786 5522 2.439701 TAGACACGGCCGGAGAGG 60.440 66.667 31.76 15.31 44.97 3.69
3788 5524 3.129502 CGTAGACACGGCCGGAGA 61.130 66.667 31.76 6.75 44.59 3.71
3797 5533 4.396854 GGCGATCACCGTAGACAC 57.603 61.111 0.00 0.00 41.15 3.67
3809 5545 2.102357 CTAGTGCACGACGGCGAT 59.898 61.111 22.49 0.00 41.64 4.58
3819 5555 2.903357 GCAGCTAGCCCTAGTGCA 59.097 61.111 18.10 0.00 38.66 4.57
3838 5577 3.818121 TTCCCCTCGCGTGTGTTGG 62.818 63.158 5.77 0.00 0.00 3.77
3839 5578 2.280524 TTCCCCTCGCGTGTGTTG 60.281 61.111 5.77 0.00 0.00 3.33
3840 5579 2.280592 GTTCCCCTCGCGTGTGTT 60.281 61.111 5.77 0.00 0.00 3.32
3841 5580 4.309950 GGTTCCCCTCGCGTGTGT 62.310 66.667 5.77 0.00 0.00 3.72
3888 5649 1.805495 CGAGATGACTACGAGGTCGGA 60.805 57.143 4.13 0.00 44.95 4.55
3957 5718 1.372499 CCCGCTCTTCGTCGAACAA 60.372 57.895 2.90 0.00 36.19 2.83
3960 5721 4.430765 GCCCCGCTCTTCGTCGAA 62.431 66.667 7.57 7.57 36.19 3.71
4035 5801 1.663702 CGACACCGCCTTTCTTCGT 60.664 57.895 0.00 0.00 0.00 3.85
4036 5802 0.942410 TTCGACACCGCCTTTCTTCG 60.942 55.000 0.00 0.00 35.37 3.79
4051 5817 3.887110 TCTGTCAACAACCTCTACTTCGA 59.113 43.478 0.00 0.00 0.00 3.71
4052 5818 4.238761 TCTGTCAACAACCTCTACTTCG 57.761 45.455 0.00 0.00 0.00 3.79
4082 5848 1.283029 AGATGTACCACATGGCTGCTT 59.717 47.619 0.00 0.00 39.27 3.91
4142 5947 2.241685 AGCTCATCCTTCTCATGCCTTT 59.758 45.455 0.00 0.00 0.00 3.11
4143 5948 1.845143 AGCTCATCCTTCTCATGCCTT 59.155 47.619 0.00 0.00 0.00 4.35
4147 5952 1.948145 GGCAAGCTCATCCTTCTCATG 59.052 52.381 0.00 0.00 0.00 3.07
4195 6002 8.806429 ATTTCACTGATGTGGTATATGTTGAA 57.194 30.769 0.00 0.00 43.94 2.69
4227 6035 4.724022 GGTCACCGCTACCGTATG 57.276 61.111 0.00 0.00 0.00 2.39
4269 6080 3.443681 TCACTGAGATTGCGTATCACTGA 59.556 43.478 8.86 2.58 35.59 3.41
4270 6081 3.549471 GTCACTGAGATTGCGTATCACTG 59.451 47.826 0.00 2.58 35.59 3.66
4271 6082 3.429547 GGTCACTGAGATTGCGTATCACT 60.430 47.826 0.00 0.00 35.59 3.41
4272 6083 2.860735 GGTCACTGAGATTGCGTATCAC 59.139 50.000 0.00 0.00 35.59 3.06
4273 6084 2.479560 CGGTCACTGAGATTGCGTATCA 60.480 50.000 0.00 0.00 35.59 2.15
4274 6085 2.120232 CGGTCACTGAGATTGCGTATC 58.880 52.381 0.00 0.00 0.00 2.24
4275 6086 1.476891 ACGGTCACTGAGATTGCGTAT 59.523 47.619 0.00 0.00 0.00 3.06
4276 6087 0.885879 ACGGTCACTGAGATTGCGTA 59.114 50.000 0.00 0.00 0.00 4.42
4277 6088 0.885879 TACGGTCACTGAGATTGCGT 59.114 50.000 0.00 0.00 0.00 5.24
4278 6089 2.209838 ATACGGTCACTGAGATTGCG 57.790 50.000 0.00 0.00 0.00 4.85
4279 6090 3.553511 CAGAATACGGTCACTGAGATTGC 59.446 47.826 0.00 0.00 32.90 3.56
4280 6091 4.115516 CCAGAATACGGTCACTGAGATTG 58.884 47.826 0.00 0.00 32.90 2.67
4281 6092 3.430929 GCCAGAATACGGTCACTGAGATT 60.431 47.826 0.00 0.00 32.90 2.40
4282 6093 2.101582 GCCAGAATACGGTCACTGAGAT 59.898 50.000 0.00 0.00 32.90 2.75
4283 6094 1.476891 GCCAGAATACGGTCACTGAGA 59.523 52.381 0.00 0.00 32.90 3.27
4284 6095 1.204704 TGCCAGAATACGGTCACTGAG 59.795 52.381 0.00 0.00 32.90 3.35
4378 6193 9.031537 TGATCAGACAAAACTAGGAGTATGTAA 57.968 33.333 0.00 0.00 31.27 2.41
4379 6194 8.589701 TGATCAGACAAAACTAGGAGTATGTA 57.410 34.615 0.00 0.00 31.27 2.29
4380 6195 7.482169 TGATCAGACAAAACTAGGAGTATGT 57.518 36.000 0.00 0.00 33.03 2.29
4619 6440 4.035441 GGTGCTACGAAAAAGTTAACACCA 59.965 41.667 8.61 0.00 43.52 4.17
4891 6714 1.542915 CCGAGTAGTTCCAGGAAACGA 59.457 52.381 2.45 0.00 34.27 3.85
4922 6745 4.333649 ACAATAGAGGTGATCAAACGCATG 59.666 41.667 0.00 0.00 0.00 4.06
5211 7034 2.295629 TCTCACGGCAAATCAAATGCAA 59.704 40.909 0.00 0.00 45.60 4.08
5278 7101 8.803235 AGACACTGACACATCATAAGTAAGTAA 58.197 33.333 0.00 0.00 33.22 2.24
5279 7102 8.244113 CAGACACTGACACATCATAAGTAAGTA 58.756 37.037 0.00 0.00 33.22 2.24
5280 7103 7.039714 TCAGACACTGACACATCATAAGTAAGT 60.040 37.037 0.00 0.00 35.39 2.24
5281 7104 7.315890 TCAGACACTGACACATCATAAGTAAG 58.684 38.462 0.00 0.00 35.39 2.34
5306 7129 9.182214 GGCCATACACAATTTATCATCTATCAT 57.818 33.333 0.00 0.00 0.00 2.45
5307 7130 7.611467 GGGCCATACACAATTTATCATCTATCA 59.389 37.037 4.39 0.00 0.00 2.15
5308 7131 7.067494 GGGGCCATACACAATTTATCATCTATC 59.933 40.741 4.39 0.00 0.00 2.08
5309 7132 6.891908 GGGGCCATACACAATTTATCATCTAT 59.108 38.462 4.39 0.00 0.00 1.98
5310 7133 6.045459 AGGGGCCATACACAATTTATCATCTA 59.955 38.462 4.39 0.00 0.00 1.98
5311 7134 5.079643 GGGGCCATACACAATTTATCATCT 58.920 41.667 4.39 0.00 0.00 2.90
5312 7135 5.079643 AGGGGCCATACACAATTTATCATC 58.920 41.667 4.39 0.00 0.00 2.92
5313 7136 5.078683 AGGGGCCATACACAATTTATCAT 57.921 39.130 4.39 0.00 0.00 2.45
5470 7294 1.880271 TTTTCGTGATGTACCGCCAA 58.120 45.000 0.00 0.00 0.00 4.52
5546 7371 4.174009 ACAGTCCATGAACTTACGAATCG 58.826 43.478 0.00 0.00 0.00 3.34
5563 7388 7.009907 CGCCTGGTAATAAACTAAAGTACAGTC 59.990 40.741 0.00 0.00 0.00 3.51
5669 7939 1.559682 AGAAAAATAGGCCGAGCTGGA 59.440 47.619 0.00 0.00 42.00 3.86
6018 8338 7.915293 ATGTACTCAATTTAAATGGTGTCGA 57.085 32.000 12.45 3.30 0.00 4.20


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

AutoCloner maintained by Alex Coulton.