Multiple sequence alignment - TraesCS6B01G168200

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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 TraesCS6B01G168200 chr6B 100.000 3031 0 0 1 3031 178020320 178017290 0.000000e+00 5598.0
1 TraesCS6B01G168200 chr6B 97.727 44 0 1 1693 1735 178018590 178018547 1.170000e-09 75.0
2 TraesCS6B01G168200 chr6B 97.727 44 0 1 1731 1774 178018628 178018586 1.170000e-09 75.0
3 TraesCS6B01G168200 chr6B 93.478 46 3 0 519 564 125631577 125631532 5.420000e-08 69.4
4 TraesCS6B01G168200 chr6B 100.000 32 0 0 148 179 178024051 178024020 3.260000e-05 60.2
5 TraesCS6B01G168200 chr6B 100.000 28 0 0 2768 2795 178017512 178017485 5.000000e-03 52.8
6 TraesCS6B01G168200 chr6B 100.000 28 0 0 2809 2836 178017553 178017526 5.000000e-03 52.8
7 TraesCS6B01G168200 chr6D 98.523 745 10 1 992 1735 94764926 94765670 0.000000e+00 1314.0
8 TraesCS6B01G168200 chr6D 95.736 469 6 4 1731 2197 94765627 94766083 0.000000e+00 743.0
9 TraesCS6B01G168200 chr6D 98.155 271 2 1 2531 2798 94766479 94766749 1.270000e-128 470.0
10 TraesCS6B01G168200 chr6D 97.683 259 6 0 2198 2456 94766221 94766479 2.140000e-121 446.0
11 TraesCS6B01G168200 chr6D 99.495 198 1 0 2834 3031 94768060 94768257 7.990000e-96 361.0
12 TraesCS6B01G168200 chr6D 100.000 28 0 0 2809 2836 94766719 94766746 5.000000e-03 52.8
13 TraesCS6B01G168200 chr3D 92.848 741 53 0 992 1732 333012317 333011577 0.000000e+00 1075.0
14 TraesCS6B01G168200 chr3D 87.352 506 21 11 1734 2197 333011613 333011109 9.560000e-150 540.0
15 TraesCS6B01G168200 chr3D 93.431 274 12 1 2531 2798 333010646 333010373 4.710000e-108 401.0
16 TraesCS6B01G168200 chr3D 86.880 343 25 10 552 888 567288511 567288839 1.720000e-97 366.0
17 TraesCS6B01G168200 chr3D 94.372 231 11 2 2231 2459 333010874 333010644 1.340000e-93 353.0
18 TraesCS6B01G168200 chr3D 91.489 141 4 1 2899 3031 333009282 333009142 1.430000e-43 187.0
19 TraesCS6B01G168200 chr3D 91.860 86 7 0 1798 1883 45765420 45765335 1.480000e-23 121.0
20 TraesCS6B01G168200 chr3D 100.000 28 0 0 2809 2836 333010403 333010376 5.000000e-03 52.8
21 TraesCS6B01G168200 chr3A 91.946 745 59 1 992 1735 450712595 450711851 0.000000e+00 1042.0
22 TraesCS6B01G168200 chr3A 92.276 479 34 2 44 521 531414915 531415391 0.000000e+00 676.0
23 TraesCS6B01G168200 chr3A 90.551 381 20 11 1734 2099 450711891 450711512 9.770000e-135 490.0
24 TraesCS6B01G168200 chr3A 93.208 265 17 1 2196 2459 450711437 450711173 3.660000e-104 388.0
25 TraesCS6B01G168200 chr3A 92.116 241 13 1 2564 2798 450702298 450702058 4.840000e-88 335.0
26 TraesCS6B01G168200 chr3A 96.241 133 5 0 2899 3031 450700962 450700830 5.090000e-53 219.0
27 TraesCS6B01G168200 chr3A 92.453 106 8 0 2 107 531414818 531414923 5.230000e-33 152.0
28 TraesCS6B01G168200 chr3A 93.421 76 3 2 2457 2532 342813376 342813303 8.880000e-21 111.0
29 TraesCS6B01G168200 chr3A 100.000 28 0 0 2809 2836 450702088 450702061 5.000000e-03 52.8
30 TraesCS6B01G168200 chr7D 92.798 486 30 4 39 521 154630865 154631348 0.000000e+00 699.0
31 TraesCS6B01G168200 chr7D 92.442 344 18 2 552 894 154631483 154631819 4.540000e-133 484.0
32 TraesCS6B01G168200 chr7D 79.842 506 63 20 2 469 42714825 42714321 1.740000e-87 333.0
33 TraesCS6B01G168200 chr7D 94.286 105 6 0 2 106 154630775 154630879 8.700000e-36 161.0
34 TraesCS6B01G168200 chr7D 89.041 73 7 1 2828 2900 195653922 195653851 4.160000e-14 89.8
35 TraesCS6B01G168200 chr5D 92.735 468 29 4 55 521 483989025 483989488 0.000000e+00 671.0
36 TraesCS6B01G168200 chr5D 92.068 353 14 4 552 890 483989622 483989974 4.540000e-133 484.0
37 TraesCS6B01G168200 chr5D 78.717 343 54 10 569 893 545266316 545265975 8.510000e-51 211.0
38 TraesCS6B01G168200 chr3B 92.747 455 30 3 1282 1735 432261900 432261448 0.000000e+00 654.0
39 TraesCS6B01G168200 chr3B 85.941 505 18 13 1734 2197 432261488 432260996 9.770000e-135 490.0
40 TraesCS6B01G168200 chr3B 78.628 758 115 27 1007 1722 71430138 71429386 2.750000e-125 459.0
41 TraesCS6B01G168200 chr3B 94.891 274 7 2 2531 2798 432260599 432260327 3.610000e-114 422.0
42 TraesCS6B01G168200 chr3B 93.609 266 15 2 2196 2459 432260862 432260597 2.190000e-106 396.0
43 TraesCS6B01G168200 chr3B 95.489 133 6 0 2899 3031 432259237 432259105 2.370000e-51 213.0
44 TraesCS6B01G168200 chr3B 100.000 28 0 0 2809 2836 432260357 432260330 5.000000e-03 52.8
45 TraesCS6B01G168200 chr6A 87.601 371 24 8 552 900 564152386 564152756 7.820000e-111 411.0
46 TraesCS6B01G168200 chr6A 89.831 295 22 6 552 838 564155003 564155297 3.690000e-99 372.0
47 TraesCS6B01G168200 chr6A 86.275 357 27 13 552 900 564202426 564202768 4.770000e-98 368.0
48 TraesCS6B01G168200 chr6A 87.500 56 7 0 516 571 461625257 461625312 7.010000e-07 65.8
49 TraesCS6B01G168200 chr4D 87.744 359 27 7 552 894 106676265 106676622 1.310000e-108 403.0
50 TraesCS6B01G168200 chr4D 86.957 92 3 2 2457 2539 303843553 303843462 8.950000e-16 95.3
51 TraesCS6B01G168200 chr4D 80.000 120 7 6 107 211 362521569 362521452 4.190000e-09 73.1
52 TraesCS6B01G168200 chr2D 86.807 379 26 10 539 895 179904207 179904583 4.710000e-108 401.0
53 TraesCS6B01G168200 chr2D 91.045 67 6 0 2834 2900 69220103 69220037 1.160000e-14 91.6
54 TraesCS6B01G168200 chr5A 87.288 354 29 6 552 890 365120546 365120898 1.020000e-104 390.0
55 TraesCS6B01G168200 chr1A 86.127 346 35 4 134 469 275144223 275143881 7.990000e-96 361.0
56 TraesCS6B01G168200 chr1A 79.109 359 56 7 552 894 572859455 572859810 2.350000e-56 230.0
57 TraesCS6B01G168200 chr1A 92.958 71 2 3 2462 2532 62578130 62578063 1.920000e-17 100.0
58 TraesCS6B01G168200 chr1A 97.500 40 1 0 519 558 364384905 364384944 5.420000e-08 69.4
59 TraesCS6B01G168200 chr1A 97.500 40 1 0 519 558 364438669 364438708 5.420000e-08 69.4
60 TraesCS6B01G168200 chr1A 100.000 29 0 0 107 135 275144265 275144237 2.000000e-03 54.7
61 TraesCS6B01G168200 chr1D 84.330 351 40 8 554 893 252549225 252548879 2.250000e-86 329.0
62 TraesCS6B01G168200 chr1D 93.506 77 2 2 2457 2533 169060335 169060262 8.880000e-21 111.0
63 TraesCS6B01G168200 chr4A 80.165 363 46 9 132 469 650072867 650072506 6.490000e-62 248.0
64 TraesCS6B01G168200 chr4A 92.647 68 5 0 2834 2901 636365160 636365227 6.920000e-17 99.0
65 TraesCS6B01G168200 chr1B 92.308 78 4 2 2456 2532 39849973 39849897 3.190000e-20 110.0
66 TraesCS6B01G168200 chr1B 94.444 54 3 0 2445 2498 40194693 40194746 1.940000e-12 84.2
67 TraesCS6B01G168200 chr1B 93.478 46 3 0 519 564 397140728 397140683 5.420000e-08 69.4
68 TraesCS6B01G168200 chr4B 93.151 73 4 1 2828 2900 453219903 453219974 4.130000e-19 106.0
69 TraesCS6B01G168200 chr4B 88.889 81 6 3 2457 2537 4715108 4715185 2.490000e-16 97.1
70 TraesCS6B01G168200 chr4B 91.176 68 6 0 2834 2901 576192155 576192222 3.220000e-15 93.5
71 TraesCS6B01G168200 chr4B 94.444 54 2 1 2445 2498 139757875 139757823 6.960000e-12 82.4
72 TraesCS6B01G168200 chr4B 94.000 50 2 1 2490 2539 379084931 379084883 1.170000e-09 75.0
73 TraesCS6B01G168200 chr4B 97.619 42 1 0 519 560 27650930 27650971 4.190000e-09 73.1
74 TraesCS6B01G168200 chr7A 95.385 65 3 0 831 895 367123170 367123106 1.490000e-18 104.0
75 TraesCS6B01G168200 chr7A 97.500 40 1 0 519 558 240361509 240361548 5.420000e-08 69.4
76 TraesCS6B01G168200 chr2A 90.411 73 6 1 2831 2903 740369694 740369765 8.950000e-16 95.3
77 TraesCS6B01G168200 chr2B 91.045 67 6 0 2834 2900 101412110 101412176 1.160000e-14 91.6
78 TraesCS6B01G168200 chr2B 93.478 46 3 0 519 564 494169726 494169681 5.420000e-08 69.4
79 TraesCS6B01G168200 chr5B 89.189 74 5 3 2457 2529 702514342 702514413 4.160000e-14 89.8
80 TraesCS6B01G168200 chr5B 85.057 87 8 5 2449 2532 696437611 696437527 1.940000e-12 84.2
81 TraesCS6B01G168200 chr7B 87.671 73 8 1 2828 2900 159549526 159549455 1.940000e-12 84.2


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 TraesCS6B01G168200 chr6B 178017290 178020320 3030 True 1170.720000 5598 99.090800 1 3031 5 chr6B.!!$R3 3030
1 TraesCS6B01G168200 chr6D 94764926 94768257 3331 False 564.466667 1314 98.265333 992 3031 6 chr6D.!!$F1 2039
2 TraesCS6B01G168200 chr3D 333009142 333012317 3175 True 434.800000 1075 93.248667 992 3031 6 chr3D.!!$R2 2039
3 TraesCS6B01G168200 chr3A 450711173 450712595 1422 True 640.000000 1042 91.901667 992 2459 3 chr3A.!!$R3 1467
4 TraesCS6B01G168200 chr3A 531414818 531415391 573 False 414.000000 676 92.364500 2 521 2 chr3A.!!$F1 519
5 TraesCS6B01G168200 chr3A 450700830 450702298 1468 True 202.266667 335 96.119000 2564 3031 3 chr3A.!!$R2 467
6 TraesCS6B01G168200 chr7D 154630775 154631819 1044 False 448.000000 699 93.175333 2 894 3 chr7D.!!$F1 892
7 TraesCS6B01G168200 chr7D 42714321 42714825 504 True 333.000000 333 79.842000 2 469 1 chr7D.!!$R1 467
8 TraesCS6B01G168200 chr5D 483989025 483989974 949 False 577.500000 671 92.401500 55 890 2 chr5D.!!$F1 835
9 TraesCS6B01G168200 chr3B 71429386 71430138 752 True 459.000000 459 78.628000 1007 1722 1 chr3B.!!$R1 715
10 TraesCS6B01G168200 chr3B 432259105 432261900 2795 True 371.300000 654 93.779500 1282 3031 6 chr3B.!!$R2 1749
11 TraesCS6B01G168200 chr6A 564152386 564155297 2911 False 391.500000 411 88.716000 552 900 2 chr6A.!!$F3 348

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
985 3810 0.035458 ATATAAGAGCCACAGCGCCC 59.965 55.0 2.29 0.0 46.67 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2515 5682 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.0 0.0 0.0 0.0 4.12 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
86 143 0.397816 CGACCTCCTTCCTCCTCCAT 60.398 60.000 0.00 0.00 0.00 3.41
190 247 4.033709 CTCCCTCCATTCTCCAAAGTAGA 58.966 47.826 0.00 0.00 0.00 2.59
212 269 1.612442 TCCCCTTTCCTCCCACTCG 60.612 63.158 0.00 0.00 0.00 4.18
253 310 6.017192 TCCTGTACAAGTAGAAAGAGGATGT 58.983 40.000 0.00 0.00 0.00 3.06
291 360 4.639755 TGTCATATTGTCGCCAATTGATGT 59.360 37.500 7.12 0.00 41.50 3.06
347 418 8.187354 TGCATATTGCTTGTCATATTTTTGTG 57.813 30.769 0.75 0.00 45.31 3.33
397 468 2.950433 AGTATTGCTGCACATTGTTGC 58.050 42.857 0.00 4.81 43.31 4.17
513 587 1.898154 CGGATCCCGTTGAAGAGGT 59.102 57.895 6.06 0.00 42.73 3.85
521 595 1.419374 CGTTGAAGAGGTGGAGAACG 58.581 55.000 0.00 0.00 0.00 3.95
523 597 2.352814 CGTTGAAGAGGTGGAGAACGAT 60.353 50.000 0.00 0.00 38.71 3.73
525 599 4.174762 GTTGAAGAGGTGGAGAACGATAC 58.825 47.826 0.00 0.00 0.00 2.24
526 600 3.427573 TGAAGAGGTGGAGAACGATACA 58.572 45.455 0.00 0.00 0.00 2.29
527 601 3.192844 TGAAGAGGTGGAGAACGATACAC 59.807 47.826 0.00 0.00 0.00 2.90
530 604 1.192428 GGTGGAGAACGATACACCCT 58.808 55.000 9.44 0.00 45.85 4.34
531 605 2.381911 GGTGGAGAACGATACACCCTA 58.618 52.381 9.44 0.00 45.85 3.53
532 606 2.963782 GGTGGAGAACGATACACCCTAT 59.036 50.000 9.44 0.00 45.85 2.57
533 607 4.147321 GGTGGAGAACGATACACCCTATA 58.853 47.826 9.44 0.00 45.85 1.31
534 608 4.771054 GGTGGAGAACGATACACCCTATAT 59.229 45.833 9.44 0.00 45.85 0.86
536 610 6.239515 GGTGGAGAACGATACACCCTATATTT 60.240 42.308 9.44 0.00 45.85 1.40
537 611 7.039504 GGTGGAGAACGATACACCCTATATTTA 60.040 40.741 9.44 0.00 45.85 1.40
538 612 8.027771 GTGGAGAACGATACACCCTATATTTAG 58.972 40.741 0.00 0.00 0.00 1.85
539 613 7.177921 TGGAGAACGATACACCCTATATTTAGG 59.822 40.741 2.37 2.37 44.17 2.69
682 3486 2.350007 GCAAAACGGTCGTTCTATTGCA 60.350 45.455 25.74 0.00 43.30 4.08
696 3500 7.334671 TCGTTCTATTGCAACCAATGTACATAA 59.665 33.333 9.21 0.00 41.58 1.90
784 3588 6.525121 TTCACAGTGAAATCTACAGTTTCG 57.475 37.500 13.90 0.00 38.18 3.46
844 3669 4.401525 CTGAAAGTTCACAGCTCACATC 57.598 45.455 0.00 0.00 32.90 3.06
845 3670 4.063689 CTGAAAGTTCACAGCTCACATCT 58.936 43.478 0.00 0.00 32.90 2.90
890 3715 0.312102 GCTCAACCAAACACAGCCTC 59.688 55.000 0.00 0.00 0.00 4.70
894 3719 1.066002 CAACCAAACACAGCCTCAGTG 59.934 52.381 0.00 0.00 42.56 3.66
899 3724 4.863707 CACAGCCTCAGTGTGTGT 57.136 55.556 3.95 0.00 40.44 3.72
900 3725 3.986970 CACAGCCTCAGTGTGTGTA 57.013 52.632 3.95 0.00 40.44 2.90
901 3726 1.788258 CACAGCCTCAGTGTGTGTAG 58.212 55.000 3.95 0.00 40.44 2.74
902 3727 1.341209 CACAGCCTCAGTGTGTGTAGA 59.659 52.381 3.95 0.00 40.44 2.59
903 3728 1.615883 ACAGCCTCAGTGTGTGTAGAG 59.384 52.381 0.00 0.00 0.00 2.43
904 3729 0.605589 AGCCTCAGTGTGTGTAGAGC 59.394 55.000 0.00 0.00 0.00 4.09
905 3730 0.605589 GCCTCAGTGTGTGTAGAGCT 59.394 55.000 0.00 0.00 0.00 4.09
906 3731 1.819288 GCCTCAGTGTGTGTAGAGCTA 59.181 52.381 0.00 0.00 0.00 3.32
907 3732 2.416162 GCCTCAGTGTGTGTAGAGCTAC 60.416 54.545 0.74 0.74 36.63 3.58
908 3733 3.085533 CCTCAGTGTGTGTAGAGCTACT 58.914 50.000 8.91 0.00 37.00 2.57
909 3734 4.262617 CCTCAGTGTGTGTAGAGCTACTA 58.737 47.826 8.91 0.00 37.00 1.82
910 3735 4.884744 CCTCAGTGTGTGTAGAGCTACTAT 59.115 45.833 8.91 0.00 37.00 2.12
911 3736 5.008217 CCTCAGTGTGTGTAGAGCTACTATC 59.992 48.000 8.91 1.62 37.00 2.08
912 3737 5.746284 TCAGTGTGTGTAGAGCTACTATCT 58.254 41.667 8.91 0.00 37.00 1.98
913 3738 6.885922 TCAGTGTGTGTAGAGCTACTATCTA 58.114 40.000 8.91 0.00 37.00 1.98
914 3739 6.762187 TCAGTGTGTGTAGAGCTACTATCTAC 59.238 42.308 8.91 6.24 46.16 2.59
939 3764 9.369904 ACAGTATAATTTGATTTGATTTGTGCC 57.630 29.630 0.00 0.00 0.00 5.01
940 3765 8.819974 CAGTATAATTTGATTTGATTTGTGCCC 58.180 33.333 0.00 0.00 0.00 5.36
941 3766 6.907206 ATAATTTGATTTGATTTGTGCCCG 57.093 33.333 0.00 0.00 0.00 6.13
942 3767 2.739885 TTGATTTGATTTGTGCCCGG 57.260 45.000 0.00 0.00 0.00 5.73
943 3768 0.246086 TGATTTGATTTGTGCCCGGC 59.754 50.000 1.04 1.04 0.00 6.13
944 3769 0.460109 GATTTGATTTGTGCCCGGCC 60.460 55.000 7.03 0.00 0.00 6.13
945 3770 1.898330 ATTTGATTTGTGCCCGGCCC 61.898 55.000 7.03 0.00 0.00 5.80
960 3785 3.537874 CCCGACCTCCCCACGATC 61.538 72.222 0.00 0.00 0.00 3.69
961 3786 3.900892 CCGACCTCCCCACGATCG 61.901 72.222 14.88 14.88 0.00 3.69
962 3787 4.570663 CGACCTCCCCACGATCGC 62.571 72.222 16.60 0.00 0.00 4.58
963 3788 3.148279 GACCTCCCCACGATCGCT 61.148 66.667 16.60 0.00 0.00 4.93
964 3789 1.826921 GACCTCCCCACGATCGCTA 60.827 63.158 16.60 0.00 0.00 4.26
965 3790 1.380785 ACCTCCCCACGATCGCTAA 60.381 57.895 16.60 0.00 0.00 3.09
966 3791 0.974010 ACCTCCCCACGATCGCTAAA 60.974 55.000 16.60 0.00 0.00 1.85
967 3792 0.393077 CCTCCCCACGATCGCTAAAT 59.607 55.000 16.60 0.00 0.00 1.40
968 3793 1.616865 CCTCCCCACGATCGCTAAATA 59.383 52.381 16.60 0.00 0.00 1.40
969 3794 2.233922 CCTCCCCACGATCGCTAAATAT 59.766 50.000 16.60 0.00 0.00 1.28
970 3795 3.446161 CCTCCCCACGATCGCTAAATATA 59.554 47.826 16.60 0.00 0.00 0.86
971 3796 4.081862 CCTCCCCACGATCGCTAAATATAA 60.082 45.833 16.60 0.00 0.00 0.98
972 3797 5.068234 TCCCCACGATCGCTAAATATAAG 57.932 43.478 16.60 0.00 0.00 1.73
973 3798 4.768448 TCCCCACGATCGCTAAATATAAGA 59.232 41.667 16.60 0.00 0.00 2.10
974 3799 5.103000 CCCCACGATCGCTAAATATAAGAG 58.897 45.833 16.60 0.00 0.00 2.85
975 3800 4.563184 CCCACGATCGCTAAATATAAGAGC 59.437 45.833 16.60 0.00 0.00 4.09
976 3801 4.563184 CCACGATCGCTAAATATAAGAGCC 59.437 45.833 16.60 0.00 32.35 4.70
977 3802 5.161358 CACGATCGCTAAATATAAGAGCCA 58.839 41.667 16.60 0.00 32.35 4.75
978 3803 5.061064 CACGATCGCTAAATATAAGAGCCAC 59.939 44.000 16.60 0.00 32.35 5.01
979 3804 5.161358 CGATCGCTAAATATAAGAGCCACA 58.839 41.667 0.26 0.00 32.35 4.17
980 3805 5.287274 CGATCGCTAAATATAAGAGCCACAG 59.713 44.000 0.26 0.00 32.35 3.66
981 3806 4.307432 TCGCTAAATATAAGAGCCACAGC 58.693 43.478 0.00 0.00 40.32 4.40
982 3807 3.121944 CGCTAAATATAAGAGCCACAGCG 59.878 47.826 0.00 0.00 46.67 5.18
983 3808 3.120511 GCTAAATATAAGAGCCACAGCGC 60.121 47.826 0.00 0.00 46.67 5.92
984 3809 1.884235 AATATAAGAGCCACAGCGCC 58.116 50.000 2.29 0.00 46.67 6.53
985 3810 0.035458 ATATAAGAGCCACAGCGCCC 59.965 55.000 2.29 0.00 46.67 6.13
986 3811 2.040009 TATAAGAGCCACAGCGCCCC 62.040 60.000 2.29 0.00 46.67 5.80
1597 4459 1.601903 GCTCAACATGACCACGTTTCA 59.398 47.619 0.00 0.00 0.00 2.69
1688 4550 0.251253 AACTCTCGACGTTCTCCCCT 60.251 55.000 0.00 0.00 0.00 4.79
1701 4563 3.636231 CCCCTGTGGCGTTCTGGA 61.636 66.667 0.00 0.00 0.00 3.86
1702 4564 2.671070 CCCTGTGGCGTTCTGGAT 59.329 61.111 0.00 0.00 0.00 3.41
1703 4565 1.746615 CCCTGTGGCGTTCTGGATG 60.747 63.158 0.00 0.00 0.00 3.51
1704 4566 1.003355 CCTGTGGCGTTCTGGATGT 60.003 57.895 0.00 0.00 0.00 3.06
1705 4567 0.249120 CCTGTGGCGTTCTGGATGTA 59.751 55.000 0.00 0.00 0.00 2.29
1706 4568 1.645034 CTGTGGCGTTCTGGATGTAG 58.355 55.000 0.00 0.00 0.00 2.74
1707 4569 0.391130 TGTGGCGTTCTGGATGTAGC 60.391 55.000 0.00 0.00 0.00 3.58
1708 4570 0.108138 GTGGCGTTCTGGATGTAGCT 60.108 55.000 0.00 0.00 0.00 3.32
1709 4571 1.136305 GTGGCGTTCTGGATGTAGCTA 59.864 52.381 0.00 0.00 0.00 3.32
1710 4572 1.136305 TGGCGTTCTGGATGTAGCTAC 59.864 52.381 17.30 17.30 0.00 3.58
1711 4573 1.136305 GGCGTTCTGGATGTAGCTACA 59.864 52.381 27.91 27.91 40.98 2.74
1712 4574 2.464865 GCGTTCTGGATGTAGCTACAG 58.535 52.381 29.05 16.89 39.92 2.74
1713 4575 2.464865 CGTTCTGGATGTAGCTACAGC 58.535 52.381 29.61 29.61 41.56 4.40
1714 4576 2.159240 CGTTCTGGATGTAGCTACAGCA 60.159 50.000 35.45 23.09 43.89 4.41
1715 4577 3.676049 CGTTCTGGATGTAGCTACAGCAA 60.676 47.826 35.45 27.50 43.89 3.91
1716 4578 4.253685 GTTCTGGATGTAGCTACAGCAAA 58.746 43.478 35.45 24.89 43.89 3.68
1717 4579 4.128925 TCTGGATGTAGCTACAGCAAAG 57.871 45.455 35.45 30.39 43.89 2.77
1718 4580 3.118629 TCTGGATGTAGCTACAGCAAAGG 60.119 47.826 35.45 23.28 43.89 3.11
1719 4581 2.837591 TGGATGTAGCTACAGCAAAGGA 59.162 45.455 35.45 15.92 43.89 3.36
1720 4582 3.263170 TGGATGTAGCTACAGCAAAGGAA 59.737 43.478 35.45 15.72 43.89 3.36
1721 4583 4.261801 GGATGTAGCTACAGCAAAGGAAA 58.738 43.478 35.45 9.71 43.89 3.13
1722 4584 4.095036 GGATGTAGCTACAGCAAAGGAAAC 59.905 45.833 35.45 17.09 43.89 2.78
1723 4585 4.351874 TGTAGCTACAGCAAAGGAAACT 57.648 40.909 22.67 0.00 44.27 2.66
1724 4586 4.065088 TGTAGCTACAGCAAAGGAAACTG 58.935 43.478 22.67 0.00 42.14 3.16
1725 4587 1.882623 AGCTACAGCAAAGGAAACTGC 59.117 47.619 3.70 0.00 42.14 4.40
1727 4589 2.095516 GCTACAGCAAAGGAAACTGCTC 60.096 50.000 0.00 0.00 45.79 4.26
1728 4590 2.057137 ACAGCAAAGGAAACTGCTCA 57.943 45.000 0.00 0.00 45.79 4.26
1729 4591 2.590821 ACAGCAAAGGAAACTGCTCAT 58.409 42.857 0.00 0.00 45.79 2.90
1730 4592 2.295349 ACAGCAAAGGAAACTGCTCATG 59.705 45.455 0.00 0.00 45.79 3.07
1731 4593 1.271656 AGCAAAGGAAACTGCTCATGC 59.728 47.619 0.00 0.00 45.79 4.06
1732 4594 1.973138 CAAAGGAAACTGCTCATGCG 58.027 50.000 0.00 0.00 42.68 4.73
1733 4595 1.267806 CAAAGGAAACTGCTCATGCGT 59.732 47.619 0.00 0.00 42.68 5.24
1734 4596 1.609208 AAGGAAACTGCTCATGCGTT 58.391 45.000 0.00 0.00 42.68 4.84
1735 4597 1.160137 AGGAAACTGCTCATGCGTTC 58.840 50.000 0.00 0.00 43.34 3.95
1736 4598 1.160137 GGAAACTGCTCATGCGTTCT 58.840 50.000 0.00 0.00 43.34 3.01
1737 4599 1.135859 GGAAACTGCTCATGCGTTCTG 60.136 52.381 0.00 0.00 43.34 3.02
1738 4600 0.877071 AAACTGCTCATGCGTTCTGG 59.123 50.000 0.00 0.00 43.34 3.86
1922 4795 9.594038 CAAAATATATGTATACTCCACGCAAAC 57.406 33.333 4.17 0.00 0.00 2.93
2084 4963 7.103641 TCGGAGCTCTTAATTGTTAATTCTGT 58.896 34.615 14.64 0.00 32.38 3.41
2372 5538 3.139077 AGAACACAATCAGGTTTCGGAC 58.861 45.455 0.00 0.00 0.00 4.79
2392 5558 5.394224 CGGACTCACTTTATGGAGAAGCTAA 60.394 44.000 0.00 0.00 35.17 3.09
2463 5630 9.802039 TGCCGATAAAATAATATTTTACTCCCT 57.198 29.630 17.40 4.76 0.00 4.20
2469 5636 8.687292 AAAATAATATTTTACTCCCTCCGTCC 57.313 34.615 9.04 0.00 0.00 4.79
2470 5637 4.701651 AATATTTTACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
2471 5638 1.961133 ATTTTACTCCCTCCGTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
2472 5639 1.732117 TTTTACTCCCTCCGTCCCAA 58.268 50.000 0.00 0.00 0.00 4.12
2473 5640 1.732117 TTTACTCCCTCCGTCCCAAA 58.268 50.000 0.00 0.00 0.00 3.28
2474 5641 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
2475 5642 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2476 5643 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2477 5644 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2478 5645 2.026542 ACTCCCTCCGTCCCAAAATAAC 60.027 50.000 0.00 0.00 0.00 1.89
2479 5646 2.238898 CTCCCTCCGTCCCAAAATAACT 59.761 50.000 0.00 0.00 0.00 2.24
2480 5647 2.026636 TCCCTCCGTCCCAAAATAACTG 60.027 50.000 0.00 0.00 0.00 3.16
2481 5648 2.290705 CCCTCCGTCCCAAAATAACTGT 60.291 50.000 0.00 0.00 0.00 3.55
2482 5649 3.007635 CCTCCGTCCCAAAATAACTGTC 58.992 50.000 0.00 0.00 0.00 3.51
2483 5650 3.307480 CCTCCGTCCCAAAATAACTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2484 5651 3.933332 CTCCGTCCCAAAATAACTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2485 5652 3.325425 TCCGTCCCAAAATAACTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2486 5653 4.069304 CCGTCCCAAAATAACTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2487 5654 4.083484 CCGTCCCAAAATAACTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2488 5655 4.755123 CGTCCCAAAATAACTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2489 5656 5.238650 CGTCCCAAAATAACTGTCTCAACTT 59.761 40.000 0.00 0.00 0.00 2.66
2490 5657 6.238648 CGTCCCAAAATAACTGTCTCAACTTT 60.239 38.462 0.00 0.00 0.00 2.66
2491 5658 6.918022 GTCCCAAAATAACTGTCTCAACTTTG 59.082 38.462 0.00 0.00 0.00 2.77
2492 5659 6.605594 TCCCAAAATAACTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 0.00 2.83
2493 5660 7.776030 TCCCAAAATAACTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 0.00 2.41
2494 5661 7.860872 CCCAAAATAACTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 0.00 2.90
2495 5662 8.621286 CCAAAATAACTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 0.00 2.73
2499 5666 9.915629 AATAACTGTCTCAACTTTGTACTAGAG 57.084 33.333 0.00 0.00 0.00 2.43
2500 5667 5.774630 ACTGTCTCAACTTTGTACTAGAGC 58.225 41.667 0.00 0.00 0.00 4.09
2501 5668 5.536916 ACTGTCTCAACTTTGTACTAGAGCT 59.463 40.000 0.00 0.00 0.00 4.09
2502 5669 6.041069 ACTGTCTCAACTTTGTACTAGAGCTT 59.959 38.462 0.00 0.00 0.00 3.74
2503 5670 6.216569 TGTCTCAACTTTGTACTAGAGCTTG 58.783 40.000 0.00 0.00 0.00 4.01
2504 5671 6.040504 TGTCTCAACTTTGTACTAGAGCTTGA 59.959 38.462 0.00 0.00 0.00 3.02
2505 5672 6.584563 GTCTCAACTTTGTACTAGAGCTTGAG 59.415 42.308 0.00 14.38 36.34 3.02
2506 5673 6.490381 TCTCAACTTTGTACTAGAGCTTGAGA 59.510 38.462 16.79 16.79 39.85 3.27
2507 5674 6.448006 TCAACTTTGTACTAGAGCTTGAGAC 58.552 40.000 0.00 0.00 0.00 3.36
2508 5675 5.049398 ACTTTGTACTAGAGCTTGAGACG 57.951 43.478 0.00 0.00 0.00 4.18
2509 5676 3.489180 TTGTACTAGAGCTTGAGACGC 57.511 47.619 0.00 0.00 0.00 5.19
2510 5677 2.712709 TGTACTAGAGCTTGAGACGCT 58.287 47.619 0.00 0.00 41.15 5.07
2511 5678 3.082548 TGTACTAGAGCTTGAGACGCTT 58.917 45.455 0.00 0.00 37.96 4.68
2512 5679 4.259356 TGTACTAGAGCTTGAGACGCTTA 58.741 43.478 0.00 0.00 37.96 3.09
2513 5680 4.882427 TGTACTAGAGCTTGAGACGCTTAT 59.118 41.667 0.00 0.00 37.96 1.73
2514 5681 4.993029 ACTAGAGCTTGAGACGCTTATT 57.007 40.909 0.00 0.00 37.96 1.40
2515 5682 5.331876 ACTAGAGCTTGAGACGCTTATTT 57.668 39.130 0.00 0.00 37.96 1.40
2516 5683 5.725362 ACTAGAGCTTGAGACGCTTATTTT 58.275 37.500 0.00 0.00 37.96 1.82
2517 5684 4.935885 AGAGCTTGAGACGCTTATTTTG 57.064 40.909 0.00 0.00 37.96 2.44
2518 5685 3.686726 AGAGCTTGAGACGCTTATTTTGG 59.313 43.478 0.00 0.00 37.96 3.28
2519 5686 2.749621 AGCTTGAGACGCTTATTTTGGG 59.250 45.455 0.00 0.00 32.98 4.12
2520 5687 2.747446 GCTTGAGACGCTTATTTTGGGA 59.253 45.455 0.00 0.00 0.00 4.37
2521 5688 3.426292 GCTTGAGACGCTTATTTTGGGAC 60.426 47.826 0.00 0.00 0.00 4.46
2522 5689 2.343101 TGAGACGCTTATTTTGGGACG 58.657 47.619 0.00 0.00 0.00 4.79
2523 5690 1.664151 GAGACGCTTATTTTGGGACGG 59.336 52.381 0.00 0.00 0.00 4.79
2524 5691 1.276989 AGACGCTTATTTTGGGACGGA 59.723 47.619 0.00 0.00 0.00 4.69
2525 5692 1.664151 GACGCTTATTTTGGGACGGAG 59.336 52.381 0.00 0.00 0.00 4.63
2526 5693 1.014352 CGCTTATTTTGGGACGGAGG 58.986 55.000 0.00 0.00 0.00 4.30
2527 5694 1.389555 GCTTATTTTGGGACGGAGGG 58.610 55.000 0.00 0.00 0.00 4.30
2528 5695 1.064979 GCTTATTTTGGGACGGAGGGA 60.065 52.381 0.00 0.00 0.00 4.20
2529 5696 2.919228 CTTATTTTGGGACGGAGGGAG 58.081 52.381 0.00 0.00 0.00 4.30
2530 5697 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2571 5738 6.094325 TGCCGGGTCTACTTATTTACAATTTG 59.906 38.462 2.18 0.00 0.00 2.32
2798 5972 4.587584 AATTGTGCATCACATGTTCACA 57.412 36.364 12.98 12.98 44.16 3.58
2799 5973 4.794278 ATTGTGCATCACATGTTCACAT 57.206 36.364 16.01 7.84 44.16 3.21
2822 6875 5.152804 TGTGCATCACATGTTCGTTAATTG 58.847 37.500 0.00 0.00 39.62 2.32
2823 6876 5.153513 GTGCATCACATGTTCGTTAATTGT 58.846 37.500 0.00 0.00 34.08 2.71
2825 6878 4.030529 GCATCACATGTTCGTTAATTGTGC 59.969 41.667 0.00 0.00 38.02 4.57
2827 6880 5.369685 TCACATGTTCGTTAATTGTGCAT 57.630 34.783 0.00 0.00 38.02 3.96
2830 6883 5.059587 CACATGTTCGTTAATTGTGCATCAC 59.940 40.000 0.00 0.00 32.24 3.06
2831 6884 4.820284 TGTTCGTTAATTGTGCATCACA 57.180 36.364 0.00 0.00 43.02 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.304282 GGCAAGCAATGGAGGAGGA 59.696 57.895 0.00 0.00 0.00 3.71
86 143 3.249189 AGGAGGTCCGGCAAGCAA 61.249 61.111 0.00 0.00 42.08 3.91
190 247 1.230281 TGGGAGGAAAGGGGAGCAT 60.230 57.895 0.00 0.00 0.00 3.79
262 328 3.802866 TGGCGACAATATGACATAGCAA 58.197 40.909 0.00 0.00 37.44 3.91
263 329 3.467374 TGGCGACAATATGACATAGCA 57.533 42.857 0.00 0.00 37.44 3.49
279 345 5.226396 TCCACTTTAAAACATCAATTGGCG 58.774 37.500 5.42 0.00 0.00 5.69
281 347 8.830201 TTCATCCACTTTAAAACATCAATTGG 57.170 30.769 5.42 0.00 0.00 3.16
291 360 7.117523 CGCATCCAAATTTCATCCACTTTAAAA 59.882 33.333 0.00 0.00 0.00 1.52
347 418 7.856145 AATCTCTTCCACTTCACATCAATAC 57.144 36.000 0.00 0.00 0.00 1.89
513 587 6.989155 AAATATAGGGTGTATCGTTCTCCA 57.011 37.500 0.00 0.00 0.00 3.86
536 610 7.627697 CCCATAATAATACTCCCTCCATTCCTA 59.372 40.741 0.00 0.00 0.00 2.94
537 611 6.448387 CCCATAATAATACTCCCTCCATTCCT 59.552 42.308 0.00 0.00 0.00 3.36
538 612 6.353951 CCCCATAATAATACTCCCTCCATTCC 60.354 46.154 0.00 0.00 0.00 3.01
539 613 6.217693 ACCCCATAATAATACTCCCTCCATTC 59.782 42.308 0.00 0.00 0.00 2.67
540 614 6.105411 ACCCCATAATAATACTCCCTCCATT 58.895 40.000 0.00 0.00 0.00 3.16
541 615 5.686667 ACCCCATAATAATACTCCCTCCAT 58.313 41.667 0.00 0.00 0.00 3.41
542 616 5.098663 GACCCCATAATAATACTCCCTCCA 58.901 45.833 0.00 0.00 0.00 3.86
544 618 6.697641 TTGACCCCATAATAATACTCCCTC 57.302 41.667 0.00 0.00 0.00 4.30
696 3500 5.636543 GTGCAAGTAGACCGTAAAATAGTGT 59.363 40.000 0.00 0.00 0.00 3.55
839 3664 3.499537 TGTAAAAGCTGCTGTGAGATGTG 59.500 43.478 1.35 0.00 0.00 3.21
840 3665 3.743521 TGTAAAAGCTGCTGTGAGATGT 58.256 40.909 1.35 0.00 0.00 3.06
841 3666 3.999001 TCTGTAAAAGCTGCTGTGAGATG 59.001 43.478 1.35 0.00 0.00 2.90
842 3667 4.277515 TCTGTAAAAGCTGCTGTGAGAT 57.722 40.909 1.35 0.00 0.00 2.75
843 3668 3.751479 TCTGTAAAAGCTGCTGTGAGA 57.249 42.857 1.35 0.00 0.00 3.27
844 3669 4.694509 AGATTCTGTAAAAGCTGCTGTGAG 59.305 41.667 1.35 0.00 0.00 3.51
845 3670 4.453478 CAGATTCTGTAAAAGCTGCTGTGA 59.547 41.667 1.35 0.00 36.04 3.58
890 3715 6.539103 TGTAGATAGTAGCTCTACACACACTG 59.461 42.308 8.30 0.00 46.23 3.66
894 3719 8.836268 ATACTGTAGATAGTAGCTCTACACAC 57.164 38.462 8.30 0.00 46.23 3.82
913 3738 9.369904 GGCACAAATCAAATCAAATTATACTGT 57.630 29.630 0.00 0.00 0.00 3.55
914 3739 8.819974 GGGCACAAATCAAATCAAATTATACTG 58.180 33.333 0.00 0.00 0.00 2.74
915 3740 7.706179 CGGGCACAAATCAAATCAAATTATACT 59.294 33.333 0.00 0.00 0.00 2.12
916 3741 7.042791 CCGGGCACAAATCAAATCAAATTATAC 60.043 37.037 0.00 0.00 0.00 1.47
917 3742 6.983307 CCGGGCACAAATCAAATCAAATTATA 59.017 34.615 0.00 0.00 0.00 0.98
918 3743 5.816777 CCGGGCACAAATCAAATCAAATTAT 59.183 36.000 0.00 0.00 0.00 1.28
919 3744 5.174395 CCGGGCACAAATCAAATCAAATTA 58.826 37.500 0.00 0.00 0.00 1.40
920 3745 4.002316 CCGGGCACAAATCAAATCAAATT 58.998 39.130 0.00 0.00 0.00 1.82
921 3746 3.598299 CCGGGCACAAATCAAATCAAAT 58.402 40.909 0.00 0.00 0.00 2.32
922 3747 2.869636 GCCGGGCACAAATCAAATCAAA 60.870 45.455 15.62 0.00 0.00 2.69
923 3748 1.337635 GCCGGGCACAAATCAAATCAA 60.338 47.619 15.62 0.00 0.00 2.57
924 3749 0.246086 GCCGGGCACAAATCAAATCA 59.754 50.000 15.62 0.00 0.00 2.57
925 3750 0.460109 GGCCGGGCACAAATCAAATC 60.460 55.000 25.33 0.00 0.00 2.17
926 3751 1.596408 GGCCGGGCACAAATCAAAT 59.404 52.632 25.33 0.00 0.00 2.32
927 3752 2.578714 GGGCCGGGCACAAATCAAA 61.579 57.895 30.95 0.00 0.00 2.69
928 3753 2.994417 GGGCCGGGCACAAATCAA 60.994 61.111 30.95 0.00 0.00 2.57
943 3768 3.537874 GATCGTGGGGAGGTCGGG 61.538 72.222 0.00 0.00 0.00 5.14
944 3769 3.900892 CGATCGTGGGGAGGTCGG 61.901 72.222 7.03 0.00 0.00 4.79
945 3770 4.570663 GCGATCGTGGGGAGGTCG 62.571 72.222 17.81 0.00 35.56 4.79
946 3771 1.389609 TTAGCGATCGTGGGGAGGTC 61.390 60.000 17.81 0.00 0.00 3.85
947 3772 0.974010 TTTAGCGATCGTGGGGAGGT 60.974 55.000 17.81 0.00 0.00 3.85
948 3773 0.393077 ATTTAGCGATCGTGGGGAGG 59.607 55.000 17.81 0.00 0.00 4.30
949 3774 3.594603 ATATTTAGCGATCGTGGGGAG 57.405 47.619 17.81 0.00 0.00 4.30
950 3775 4.768448 TCTTATATTTAGCGATCGTGGGGA 59.232 41.667 17.81 0.00 0.00 4.81
951 3776 5.068234 TCTTATATTTAGCGATCGTGGGG 57.932 43.478 17.81 0.00 0.00 4.96
952 3777 4.563184 GCTCTTATATTTAGCGATCGTGGG 59.437 45.833 17.81 0.00 0.00 4.61
953 3778 4.563184 GGCTCTTATATTTAGCGATCGTGG 59.437 45.833 17.81 0.00 37.11 4.94
954 3779 5.061064 GTGGCTCTTATATTTAGCGATCGTG 59.939 44.000 17.81 0.00 37.11 4.35
955 3780 5.162075 GTGGCTCTTATATTTAGCGATCGT 58.838 41.667 17.81 6.21 37.11 3.73
956 3781 5.161358 TGTGGCTCTTATATTTAGCGATCG 58.839 41.667 11.69 11.69 37.11 3.69
957 3782 5.062809 GCTGTGGCTCTTATATTTAGCGATC 59.937 44.000 0.00 0.00 37.11 3.69
958 3783 4.932200 GCTGTGGCTCTTATATTTAGCGAT 59.068 41.667 0.00 0.00 37.11 4.58
959 3784 4.307432 GCTGTGGCTCTTATATTTAGCGA 58.693 43.478 0.00 0.00 37.11 4.93
960 3785 3.121944 CGCTGTGGCTCTTATATTTAGCG 59.878 47.826 0.00 0.00 44.04 4.26
961 3786 3.120511 GCGCTGTGGCTCTTATATTTAGC 60.121 47.826 0.00 0.00 36.09 3.09
962 3787 3.433615 GGCGCTGTGGCTCTTATATTTAG 59.566 47.826 7.64 0.00 40.72 1.85
963 3788 3.399330 GGCGCTGTGGCTCTTATATTTA 58.601 45.455 7.64 0.00 40.72 1.40
964 3789 2.222027 GGCGCTGTGGCTCTTATATTT 58.778 47.619 7.64 0.00 40.72 1.40
965 3790 1.543429 GGGCGCTGTGGCTCTTATATT 60.543 52.381 14.60 0.00 44.11 1.28
966 3791 0.035458 GGGCGCTGTGGCTCTTATAT 59.965 55.000 14.60 0.00 44.11 0.86
967 3792 1.445942 GGGCGCTGTGGCTCTTATA 59.554 57.895 14.60 0.00 44.11 0.98
968 3793 2.190578 GGGCGCTGTGGCTCTTAT 59.809 61.111 14.60 0.00 44.11 1.73
969 3794 4.096003 GGGGCGCTGTGGCTCTTA 62.096 66.667 14.60 0.00 41.41 2.10
1211 4045 0.606401 AGAAGGTGCCACGGTTGATG 60.606 55.000 0.00 0.00 0.00 3.07
1597 4459 3.394940 TCCCTCACTATCGTACCTGAGAT 59.605 47.826 0.00 0.00 33.30 2.75
1688 4550 0.391130 GCTACATCCAGAACGCCACA 60.391 55.000 0.00 0.00 0.00 4.17
1701 4563 4.697352 CAGTTTCCTTTGCTGTAGCTACAT 59.303 41.667 26.22 4.74 42.66 2.29
1702 4564 4.065088 CAGTTTCCTTTGCTGTAGCTACA 58.935 43.478 24.63 24.63 42.66 2.74
1703 4565 3.120165 GCAGTTTCCTTTGCTGTAGCTAC 60.120 47.826 17.30 17.30 42.66 3.58
1704 4566 3.074412 GCAGTTTCCTTTGCTGTAGCTA 58.926 45.455 5.38 0.00 42.66 3.32
1705 4567 1.882623 GCAGTTTCCTTTGCTGTAGCT 59.117 47.619 5.38 0.00 42.66 3.32
1706 4568 2.338140 GCAGTTTCCTTTGCTGTAGC 57.662 50.000 0.00 0.00 42.50 3.58
1712 4574 1.706443 GCATGAGCAGTTTCCTTTGC 58.294 50.000 0.00 0.00 41.58 3.68
1713 4575 1.267806 ACGCATGAGCAGTTTCCTTTG 59.732 47.619 0.00 0.00 42.27 2.77
1714 4576 1.609208 ACGCATGAGCAGTTTCCTTT 58.391 45.000 0.00 0.00 42.27 3.11
1715 4577 1.537202 GAACGCATGAGCAGTTTCCTT 59.463 47.619 0.00 0.00 42.27 3.36
1716 4578 1.160137 GAACGCATGAGCAGTTTCCT 58.840 50.000 0.00 0.00 42.27 3.36
1717 4579 1.135859 CAGAACGCATGAGCAGTTTCC 60.136 52.381 0.00 0.00 42.27 3.13
1718 4580 1.135859 CCAGAACGCATGAGCAGTTTC 60.136 52.381 0.00 0.00 42.27 2.78
1719 4581 0.877071 CCAGAACGCATGAGCAGTTT 59.123 50.000 0.00 0.00 42.27 2.66
1720 4582 0.035317 TCCAGAACGCATGAGCAGTT 59.965 50.000 0.00 0.00 42.27 3.16
1721 4583 0.251354 ATCCAGAACGCATGAGCAGT 59.749 50.000 0.00 0.00 42.27 4.40
1722 4584 0.656259 CATCCAGAACGCATGAGCAG 59.344 55.000 0.00 0.00 42.27 4.24
1723 4585 0.036105 ACATCCAGAACGCATGAGCA 60.036 50.000 0.00 0.00 42.27 4.26
1724 4586 1.863454 CTACATCCAGAACGCATGAGC 59.137 52.381 0.00 0.00 37.42 4.26
1725 4587 1.863454 GCTACATCCAGAACGCATGAG 59.137 52.381 0.00 0.00 0.00 2.90
1726 4588 1.482182 AGCTACATCCAGAACGCATGA 59.518 47.619 0.00 0.00 0.00 3.07
1727 4589 1.945387 AGCTACATCCAGAACGCATG 58.055 50.000 0.00 0.00 0.00 4.06
1728 4590 2.430694 TGTAGCTACATCCAGAACGCAT 59.569 45.455 22.67 0.00 0.00 4.73
1729 4591 1.822371 TGTAGCTACATCCAGAACGCA 59.178 47.619 22.67 0.00 0.00 5.24
1730 4592 2.464865 CTGTAGCTACATCCAGAACGC 58.535 52.381 26.22 0.00 35.36 4.84
1731 4593 2.159240 TGCTGTAGCTACATCCAGAACG 60.159 50.000 26.22 13.22 42.66 3.95
1732 4594 3.526931 TGCTGTAGCTACATCCAGAAC 57.473 47.619 26.22 10.69 42.66 3.01
1733 4595 4.507710 CTTTGCTGTAGCTACATCCAGAA 58.492 43.478 26.22 18.28 42.66 3.02
1734 4596 3.118629 CCTTTGCTGTAGCTACATCCAGA 60.119 47.826 26.22 18.63 42.66 3.86
1735 4597 3.118629 TCCTTTGCTGTAGCTACATCCAG 60.119 47.826 26.22 18.61 42.66 3.86
1736 4598 2.837591 TCCTTTGCTGTAGCTACATCCA 59.162 45.455 26.22 21.61 42.66 3.41
1737 4599 3.543680 TCCTTTGCTGTAGCTACATCC 57.456 47.619 26.22 19.49 42.66 3.51
1738 4600 4.938226 AGTTTCCTTTGCTGTAGCTACATC 59.062 41.667 26.22 22.21 42.66 3.06
2084 4963 4.791411 GCTGAAACACGGTTTCTGCATTTA 60.791 41.667 31.79 14.34 46.08 1.40
2099 4978 9.462174 CAGAAATTAACATAAGTTGCTGAAACA 57.538 29.630 0.56 0.00 41.61 2.83
2372 5538 5.734720 TGGTTAGCTTCTCCATAAAGTGAG 58.265 41.667 0.00 0.00 0.00 3.51
2392 5558 8.908786 AATGAGTTTACATATCGATCAATGGT 57.091 30.769 0.00 0.00 0.00 3.55
2457 5624 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2458 5625 2.238898 AGTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2459 5626 2.026636 CAGTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2460 5627 2.290705 ACAGTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2461 5628 3.007635 GACAGTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2462 5629 3.933332 GAGACAGTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2463 5630 3.325425 TGAGACAGTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2464 5631 3.670625 TGAGACAGTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2465 5632 4.755123 AGTTGAGACAGTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
2466 5633 6.635030 AAGTTGAGACAGTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
2467 5634 6.605594 ACAAAGTTGAGACAGTTATTTTGGGA 59.394 34.615 0.00 0.00 0.00 4.37
2468 5635 6.805713 ACAAAGTTGAGACAGTTATTTTGGG 58.194 36.000 0.00 0.00 0.00 4.12
2469 5636 8.621286 AGTACAAAGTTGAGACAGTTATTTTGG 58.379 33.333 0.00 0.00 0.00 3.28
2473 5640 9.915629 CTCTAGTACAAAGTTGAGACAGTTATT 57.084 33.333 0.00 0.00 31.74 1.40
2474 5641 8.030106 GCTCTAGTACAAAGTTGAGACAGTTAT 58.970 37.037 0.00 0.00 31.74 1.89
2475 5642 7.230913 AGCTCTAGTACAAAGTTGAGACAGTTA 59.769 37.037 0.00 0.00 31.74 2.24
2476 5643 6.041069 AGCTCTAGTACAAAGTTGAGACAGTT 59.959 38.462 0.00 0.00 31.74 3.16
2477 5644 5.536916 AGCTCTAGTACAAAGTTGAGACAGT 59.463 40.000 0.00 0.00 31.74 3.55
2478 5645 6.019779 AGCTCTAGTACAAAGTTGAGACAG 57.980 41.667 0.00 0.00 31.74 3.51
2479 5646 6.040504 TCAAGCTCTAGTACAAAGTTGAGACA 59.959 38.462 0.00 0.00 31.74 3.41
2480 5647 6.448006 TCAAGCTCTAGTACAAAGTTGAGAC 58.552 40.000 0.00 0.00 31.74 3.36
2481 5648 6.490381 TCTCAAGCTCTAGTACAAAGTTGAGA 59.510 38.462 17.03 17.03 43.86 3.27
2482 5649 6.584563 GTCTCAAGCTCTAGTACAAAGTTGAG 59.415 42.308 14.52 14.52 40.56 3.02
2483 5650 6.448006 GTCTCAAGCTCTAGTACAAAGTTGA 58.552 40.000 0.00 0.00 0.00 3.18
2484 5651 5.343593 CGTCTCAAGCTCTAGTACAAAGTTG 59.656 44.000 0.00 0.00 0.00 3.16
2485 5652 5.462405 CGTCTCAAGCTCTAGTACAAAGTT 58.538 41.667 0.00 0.00 0.00 2.66
2486 5653 4.616373 GCGTCTCAAGCTCTAGTACAAAGT 60.616 45.833 0.00 0.00 0.00 2.66
2487 5654 3.854809 GCGTCTCAAGCTCTAGTACAAAG 59.145 47.826 0.00 0.00 0.00 2.77
2488 5655 3.506455 AGCGTCTCAAGCTCTAGTACAAA 59.494 43.478 0.00 0.00 41.83 2.83
2489 5656 3.082548 AGCGTCTCAAGCTCTAGTACAA 58.917 45.455 0.00 0.00 41.83 2.41
2490 5657 2.712709 AGCGTCTCAAGCTCTAGTACA 58.287 47.619 0.00 0.00 41.83 2.90
2491 5658 3.768468 AAGCGTCTCAAGCTCTAGTAC 57.232 47.619 0.00 0.00 45.31 2.73
2492 5659 6.452494 AAATAAGCGTCTCAAGCTCTAGTA 57.548 37.500 0.00 0.00 45.31 1.82
2493 5660 4.993029 AATAAGCGTCTCAAGCTCTAGT 57.007 40.909 0.00 0.00 45.31 2.57
2494 5661 5.006165 CCAAAATAAGCGTCTCAAGCTCTAG 59.994 44.000 0.00 0.00 45.31 2.43
2495 5662 4.870426 CCAAAATAAGCGTCTCAAGCTCTA 59.130 41.667 0.00 0.00 45.31 2.43
2496 5663 3.686726 CCAAAATAAGCGTCTCAAGCTCT 59.313 43.478 0.00 0.00 45.31 4.09
2497 5664 3.181506 CCCAAAATAAGCGTCTCAAGCTC 60.182 47.826 0.00 0.00 45.31 4.09
2499 5666 2.747446 TCCCAAAATAAGCGTCTCAAGC 59.253 45.455 0.00 0.00 0.00 4.01
2500 5667 3.181520 CGTCCCAAAATAAGCGTCTCAAG 60.182 47.826 0.00 0.00 0.00 3.02
2501 5668 2.739913 CGTCCCAAAATAAGCGTCTCAA 59.260 45.455 0.00 0.00 0.00 3.02
2502 5669 2.343101 CGTCCCAAAATAAGCGTCTCA 58.657 47.619 0.00 0.00 0.00 3.27
2503 5670 1.664151 CCGTCCCAAAATAAGCGTCTC 59.336 52.381 0.00 0.00 0.00 3.36
2504 5671 1.276989 TCCGTCCCAAAATAAGCGTCT 59.723 47.619 0.00 0.00 0.00 4.18
2505 5672 1.664151 CTCCGTCCCAAAATAAGCGTC 59.336 52.381 0.00 0.00 0.00 5.19
2506 5673 1.677820 CCTCCGTCCCAAAATAAGCGT 60.678 52.381 0.00 0.00 0.00 5.07
2507 5674 1.014352 CCTCCGTCCCAAAATAAGCG 58.986 55.000 0.00 0.00 0.00 4.68
2508 5675 1.064979 TCCCTCCGTCCCAAAATAAGC 60.065 52.381 0.00 0.00 0.00 3.09
2509 5676 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2510 5677 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2511 5678 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2512 5679 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2513 5680 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2514 5681 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2515 5682 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2516 5683 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
2517 5684 0.396695 TCATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
2518 5685 0.745468 GTCATGTACTCCCTCCGTCC 59.255 60.000 0.00 0.00 0.00 4.79
2519 5686 1.471119 TGTCATGTACTCCCTCCGTC 58.529 55.000 0.00 0.00 0.00 4.79
2520 5687 1.757118 CATGTCATGTACTCCCTCCGT 59.243 52.381 4.53 0.00 0.00 4.69
2521 5688 1.069204 CCATGTCATGTACTCCCTCCG 59.931 57.143 11.84 0.00 0.00 4.63
2522 5689 1.202698 GCCATGTCATGTACTCCCTCC 60.203 57.143 11.84 0.00 0.00 4.30
2523 5690 1.765314 AGCCATGTCATGTACTCCCTC 59.235 52.381 11.84 0.00 0.00 4.30
2524 5691 1.885049 AGCCATGTCATGTACTCCCT 58.115 50.000 11.84 0.00 0.00 4.20
2525 5692 3.838244 TTAGCCATGTCATGTACTCCC 57.162 47.619 11.84 0.00 0.00 4.30
2526 5693 3.499918 GCATTAGCCATGTCATGTACTCC 59.500 47.826 11.84 0.00 34.98 3.85
2527 5694 4.739046 GCATTAGCCATGTCATGTACTC 57.261 45.455 11.84 0.00 34.98 2.59
2800 5974 5.059587 CACAATTAACGAACATGTGATGCAC 59.940 40.000 0.00 0.00 43.01 4.57
2803 6849 5.152804 TGCACAATTAACGAACATGTGATG 58.847 37.500 0.00 0.00 43.01 3.07
2809 6855 5.369685 TGTGATGCACAATTAACGAACAT 57.630 34.783 0.00 0.00 41.69 2.71
2822 6875 6.437928 TCTTAGTTCAAAACATGTGATGCAC 58.562 36.000 0.00 2.38 34.56 4.57
2823 6876 6.631971 TCTTAGTTCAAAACATGTGATGCA 57.368 33.333 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.