Multiple sequence alignment - TraesCS7B01G012200

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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 TraesCS7B01G012200 chr7B 100.000 3968 0 0 1 3968 7733410 7729443 0.000000e+00 7328.0
1 TraesCS7B01G012200 chr7B 95.812 764 20 3 850 1613 10237419 10238170 0.000000e+00 1223.0
2 TraesCS7B01G012200 chr7B 81.596 614 88 17 1041 1634 34889077 34889685 5.960000e-133 484.0
3 TraesCS7B01G012200 chr7B 89.112 349 24 3 1740 2075 10238236 10238583 4.740000e-114 422.0
4 TraesCS7B01G012200 chr7B 81.096 529 76 11 1045 1560 7560706 7560189 6.180000e-108 401.0
5 TraesCS7B01G012200 chr7B 80.076 527 79 8 1045 1560 10582015 10582526 6.260000e-98 368.0
6 TraesCS7B01G012200 chr7B 88.618 246 15 1 2851 3096 7715956 7715724 1.800000e-73 287.0
7 TraesCS7B01G012200 chr7B 76.534 554 87 24 1181 1709 10061113 10061648 3.040000e-66 263.0
8 TraesCS7B01G012200 chr7B 93.976 166 9 1 2848 3012 10560662 10560827 2.370000e-62 250.0
9 TraesCS7B01G012200 chr7B 79.609 358 41 15 2725 3065 10239294 10239636 1.110000e-55 228.0
10 TraesCS7B01G012200 chr7B 79.420 345 44 14 1780 2101 7716861 7716521 6.680000e-53 219.0
11 TraesCS7B01G012200 chr7B 82.129 263 33 7 1838 2087 10559838 10560099 3.110000e-51 213.0
12 TraesCS7B01G012200 chr7B 92.982 57 4 0 3038 3094 10560827 10560883 2.540000e-12 84.2
13 TraesCS7B01G012200 chr7A 88.803 2992 162 63 1054 3968 71114685 71111790 0.000000e+00 3509.0
14 TraesCS7B01G012200 chr7A 92.552 1893 59 17 850 2718 70898731 70896897 0.000000e+00 2639.0
15 TraesCS7B01G012200 chr7A 79.583 671 91 24 1081 1717 85198906 85198248 4.710000e-119 438.0
16 TraesCS7B01G012200 chr7A 90.514 253 18 3 2848 3094 74644153 74644405 2.960000e-86 329.0
17 TraesCS7B01G012200 chr7A 81.174 409 68 8 1050 1452 70737083 70736678 1.780000e-83 320.0
18 TraesCS7B01G012200 chr7A 83.962 318 42 6 2725 3036 127762084 127761770 3.000000e-76 296.0
19 TraesCS7B01G012200 chr7A 79.822 337 42 16 1773 2087 74643284 74643616 5.160000e-54 222.0
20 TraesCS7B01G012200 chr7A 91.111 135 8 1 704 834 717046533 717046667 3.150000e-41 180.0
21 TraesCS7B01G012200 chr7A 87.898 157 12 5 703 852 717044271 717044427 1.130000e-40 178.0
22 TraesCS7B01G012200 chr7A 74.859 354 72 11 1773 2116 70267073 70266727 1.150000e-30 145.0
23 TraesCS7B01G012200 chr7A 75.214 351 52 21 2749 3071 70765477 70765134 2.490000e-27 134.0
24 TraesCS7B01G012200 chr7A 88.372 86 8 1 3093 3178 74604747 74604830 7.020000e-18 102.0
25 TraesCS7B01G012200 chr7A 96.429 56 1 1 965 1019 71114738 71114683 1.520000e-14 91.6
26 TraesCS7B01G012200 chr7A 97.297 37 1 0 1012 1048 47049277 47049313 3.310000e-06 63.9
27 TraesCS7B01G012200 chr7A 93.023 43 3 0 3093 3135 71112715 71112673 3.310000e-06 63.9
28 TraesCS7B01G012200 chr7A 100.000 34 0 0 1018 1051 634349398 634349365 3.310000e-06 63.9
29 TraesCS7B01G012200 chr7A 100.000 32 0 0 1017 1048 70233626 70233595 4.280000e-05 60.2
30 TraesCS7B01G012200 chr7A 100.000 31 0 0 1019 1049 86466476 86466506 1.540000e-04 58.4
31 TraesCS7B01G012200 chr7A 100.000 29 0 0 1019 1047 85199000 85198972 2.000000e-03 54.7
32 TraesCS7B01G012200 chr7A 92.105 38 2 1 3099 3135 70888163 70888126 7.000000e-03 52.8
33 TraesCS7B01G012200 chr7D 89.267 941 49 21 2207 3129 68929677 68930583 0.000000e+00 1131.0
34 TraesCS7B01G012200 chr7D 89.933 894 51 8 3077 3968 66505384 66504528 0.000000e+00 1116.0
35 TraesCS7B01G012200 chr7D 94.986 698 28 2 968 1665 66508555 66507865 0.000000e+00 1088.0
36 TraesCS7B01G012200 chr7D 92.756 704 33 9 962 1665 68928537 68929222 0.000000e+00 1002.0
37 TraesCS7B01G012200 chr7D 94.572 608 31 2 3363 3968 68931164 68931771 0.000000e+00 939.0
38 TraesCS7B01G012200 chr7D 84.367 774 58 27 1783 2525 66507796 66507055 0.000000e+00 701.0
39 TraesCS7B01G012200 chr7D 90.625 480 20 7 2658 3135 66507055 66506599 7.290000e-172 614.0
40 TraesCS7B01G012200 chr7D 82.211 579 75 15 997 1560 66376037 66375472 1.290000e-129 473.0
41 TraesCS7B01G012200 chr7D 93.291 313 21 0 1783 2095 68929291 68929603 2.790000e-126 462.0
42 TraesCS7B01G012200 chr7D 81.399 586 92 10 1050 1634 69019241 69019810 2.790000e-126 462.0
43 TraesCS7B01G012200 chr7D 81.206 564 95 6 1050 1609 66348256 66347700 1.010000e-120 444.0
44 TraesCS7B01G012200 chr7D 80.475 589 100 9 1050 1632 65940224 65939645 1.690000e-118 436.0
45 TraesCS7B01G012200 chr7D 81.295 556 79 11 1018 1560 69012881 69013424 1.020000e-115 427.0
46 TraesCS7B01G012200 chr7D 80.935 556 89 10 1080 1634 66367335 66366796 1.320000e-114 424.0
47 TraesCS7B01G012200 chr7D 89.706 340 12 2 3039 3377 68930556 68930873 2.850000e-111 412.0
48 TraesCS7B01G012200 chr7D 93.651 252 10 3 2851 3096 66413232 66412981 4.840000e-99 372.0
49 TraesCS7B01G012200 chr7D 87.550 249 16 2 2848 3096 68984979 68985212 1.400000e-69 274.0
50 TraesCS7B01G012200 chr7D 79.762 336 44 14 1773 2087 66415760 66415428 5.160000e-54 222.0
51 TraesCS7B01G012200 chr7D 95.536 112 5 0 2851 2962 69057140 69057251 3.150000e-41 180.0
52 TraesCS7B01G012200 chr7D 74.510 357 72 13 1773 2116 65902496 65902146 1.920000e-28 137.0
53 TraesCS7B01G012200 chr7D 74.644 351 49 24 2749 3071 66346086 66345748 6.970000e-23 119.0
54 TraesCS7B01G012200 chr7D 94.545 55 2 1 3039 3092 66506632 66506578 2.540000e-12 84.2
55 TraesCS7B01G012200 chr7D 95.349 43 2 0 3093 3135 66413048 66413006 7.120000e-08 69.4
56 TraesCS7B01G012200 chr6D 90.956 586 38 8 1 577 291623083 291622504 0.000000e+00 774.0
57 TraesCS7B01G012200 chr6D 94.667 75 2 1 599 673 291622515 291622443 9.010000e-22 115.0
58 TraesCS7B01G012200 chr6A 87.536 690 56 13 1 673 244163507 244164183 0.000000e+00 771.0
59 TraesCS7B01G012200 chr2A 87.101 690 58 13 1 673 178128372 178129047 0.000000e+00 752.0
60 TraesCS7B01G012200 chr3D 90.102 586 42 9 1 577 507634815 507634237 0.000000e+00 747.0
61 TraesCS7B01G012200 chr3D 97.917 48 1 0 626 673 507633182 507633135 2.540000e-12 84.2
62 TraesCS7B01G012200 chr5A 83.141 866 96 31 1 834 580293147 580292300 0.000000e+00 745.0
63 TraesCS7B01G012200 chr5A 88.567 586 52 8 1 577 566634091 566634670 0.000000e+00 697.0
64 TraesCS7B01G012200 chr5A 89.130 138 9 4 703 834 640073155 640073018 2.450000e-37 167.0
65 TraesCS7B01G012200 chr4D 89.761 586 45 8 1 577 318323079 318322500 0.000000e+00 736.0
66 TraesCS7B01G012200 chr4D 91.667 72 4 1 602 673 318322508 318322439 9.070000e-17 99.0
67 TraesCS7B01G012200 chr4A 92.289 415 23 3 49 454 716531225 716531639 7.390000e-162 580.0
68 TraesCS7B01G012200 chr4A 86.525 423 55 2 1 422 721807683 721808104 7.770000e-127 464.0
69 TraesCS7B01G012200 chr3A 79.724 868 99 39 1 834 297327619 297328443 1.250000e-154 556.0
70 TraesCS7B01G012200 chr3B 84.774 532 46 12 63 584 462058119 462057613 5.920000e-138 501.0
71 TraesCS7B01G012200 chr2B 81.803 610 71 20 1045 1615 135794904 135795512 3.590000e-130 475.0
72 TraesCS7B01G012200 chr2D 84.150 347 44 7 2725 3065 326453566 326453907 3.820000e-85 326.0
73 TraesCS7B01G012200 chrUn 88.199 161 11 6 703 855 410576496 410576336 6.770000e-43 185.0
74 TraesCS7B01G012200 chrUn 88.125 160 12 5 703 855 61934969 61935128 2.440000e-42 183.0
75 TraesCS7B01G012200 chrUn 88.125 160 12 5 703 855 379207092 379207251 2.440000e-42 183.0
76 TraesCS7B01G012200 chrUn 88.125 160 12 5 703 855 393316881 393317040 2.440000e-42 183.0
77 TraesCS7B01G012200 chr6B 96.429 112 3 1 724 834 687143357 687143468 2.440000e-42 183.0
78 TraesCS7B01G012200 chr1B 90.580 138 7 4 703 834 633696773 633696910 1.130000e-40 178.0
79 TraesCS7B01G012200 chr1A 82.051 156 19 9 2809 2958 589873184 589873336 1.500000e-24 124.0


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 TraesCS7B01G012200 chr7B 7729443 7733410 3967 True 7328.000000 7328 100.000000 1 3968 1 chr7B.!!$R2 3967
1 TraesCS7B01G012200 chr7B 10237419 10239636 2217 False 624.333333 1223 88.177667 850 3065 3 chr7B.!!$F4 2215
2 TraesCS7B01G012200 chr7B 34889077 34889685 608 False 484.000000 484 81.596000 1041 1634 1 chr7B.!!$F3 593
3 TraesCS7B01G012200 chr7B 7560189 7560706 517 True 401.000000 401 81.096000 1045 1560 1 chr7B.!!$R1 515
4 TraesCS7B01G012200 chr7B 10582015 10582526 511 False 368.000000 368 80.076000 1045 1560 1 chr7B.!!$F2 515
5 TraesCS7B01G012200 chr7B 10061113 10061648 535 False 263.000000 263 76.534000 1181 1709 1 chr7B.!!$F1 528
6 TraesCS7B01G012200 chr7B 7715724 7716861 1137 True 253.000000 287 84.019000 1780 3096 2 chr7B.!!$R3 1316
7 TraesCS7B01G012200 chr7A 70896897 70898731 1834 True 2639.000000 2639 92.552000 850 2718 1 chr7A.!!$R6 1868
8 TraesCS7B01G012200 chr7A 71111790 71114738 2948 True 1221.500000 3509 92.751667 965 3968 3 chr7A.!!$R9 3003
9 TraesCS7B01G012200 chr7A 74643284 74644405 1121 False 275.500000 329 85.168000 1773 3094 2 chr7A.!!$F4 1321
10 TraesCS7B01G012200 chr7A 85198248 85199000 752 True 246.350000 438 89.791500 1019 1717 2 chr7A.!!$R10 698
11 TraesCS7B01G012200 chr7D 68928537 68931771 3234 False 789.200000 1131 91.918400 962 3968 5 chr7D.!!$F5 3006
12 TraesCS7B01G012200 chr7D 66504528 66508555 4027 True 720.640000 1116 90.891200 968 3968 5 chr7D.!!$R7 3000
13 TraesCS7B01G012200 chr7D 66375472 66376037 565 True 473.000000 473 82.211000 997 1560 1 chr7D.!!$R4 563
14 TraesCS7B01G012200 chr7D 69019241 69019810 569 False 462.000000 462 81.399000 1050 1634 1 chr7D.!!$F3 584
15 TraesCS7B01G012200 chr7D 65939645 65940224 579 True 436.000000 436 80.475000 1050 1632 1 chr7D.!!$R2 582
16 TraesCS7B01G012200 chr7D 69012881 69013424 543 False 427.000000 427 81.295000 1018 1560 1 chr7D.!!$F2 542
17 TraesCS7B01G012200 chr7D 66366796 66367335 539 True 424.000000 424 80.935000 1080 1634 1 chr7D.!!$R3 554
18 TraesCS7B01G012200 chr7D 66345748 66348256 2508 True 281.500000 444 77.925000 1050 3071 2 chr7D.!!$R5 2021
19 TraesCS7B01G012200 chr7D 66412981 66415760 2779 True 221.133333 372 89.587333 1773 3135 3 chr7D.!!$R6 1362
20 TraesCS7B01G012200 chr6D 291622443 291623083 640 True 444.500000 774 92.811500 1 673 2 chr6D.!!$R1 672
21 TraesCS7B01G012200 chr6A 244163507 244164183 676 False 771.000000 771 87.536000 1 673 1 chr6A.!!$F1 672
22 TraesCS7B01G012200 chr2A 178128372 178129047 675 False 752.000000 752 87.101000 1 673 1 chr2A.!!$F1 672
23 TraesCS7B01G012200 chr3D 507633135 507634815 1680 True 415.600000 747 94.009500 1 673 2 chr3D.!!$R1 672
24 TraesCS7B01G012200 chr5A 580292300 580293147 847 True 745.000000 745 83.141000 1 834 1 chr5A.!!$R1 833
25 TraesCS7B01G012200 chr5A 566634091 566634670 579 False 697.000000 697 88.567000 1 577 1 chr5A.!!$F1 576
26 TraesCS7B01G012200 chr4D 318322439 318323079 640 True 417.500000 736 90.714000 1 673 2 chr4D.!!$R1 672
27 TraesCS7B01G012200 chr3A 297327619 297328443 824 False 556.000000 556 79.724000 1 834 1 chr3A.!!$F1 833
28 TraesCS7B01G012200 chr3B 462057613 462058119 506 True 501.000000 501 84.774000 63 584 1 chr3B.!!$R1 521
29 TraesCS7B01G012200 chr2B 135794904 135795512 608 False 475.000000 475 81.803000 1045 1615 1 chr2B.!!$F1 570

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
784 1880 0.032952 GCGTATTATGACTGGGCGGA 59.967 55.000 0.00 0.0 0.0 5.54 F
826 1922 0.322546 GGAGACCCAATCCGTGCTTT 60.323 55.000 0.00 0.0 0.0 3.51 F
827 1923 1.065709 GGAGACCCAATCCGTGCTTTA 60.066 52.381 0.00 0.0 0.0 1.85 F
1818 3055 1.360393 ACTGCAGTTTCCCTTCCCCA 61.360 55.000 15.25 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 3177 0.250467 GCACCAGCTTGTTCCTCAGA 60.250 55.000 0.00 0.0 37.91 3.27 R
2046 3310 2.049433 GACGACGGTGTGGAGGTG 60.049 66.667 0.00 0.0 0.00 4.00 R
2241 3945 2.614057 CAGACAGATTAATCCAACGGCC 59.386 50.000 11.92 0.0 0.00 6.13 R
3238 8330 0.316204 ACCGCGCAAGTACAACTAGT 59.684 50.000 8.75 0.0 41.68 2.57 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
54 56 7.013655 TCCTTTCCAGATTTCTTGAGAAAAGTG 59.986 37.037 9.96 9.80 45.81 3.16
284 287 3.681835 GACTGACCGACGCCACCT 61.682 66.667 0.00 0.00 0.00 4.00
285 288 3.222354 GACTGACCGACGCCACCTT 62.222 63.158 0.00 0.00 0.00 3.50
422 426 2.515901 GTGGAAGGTGTGGTGGCT 59.484 61.111 0.00 0.00 0.00 4.75
423 427 1.898574 GTGGAAGGTGTGGTGGCTG 60.899 63.158 0.00 0.00 0.00 4.85
424 428 2.075566 TGGAAGGTGTGGTGGCTGA 61.076 57.895 0.00 0.00 0.00 4.26
426 430 1.754745 GAAGGTGTGGTGGCTGAGA 59.245 57.895 0.00 0.00 0.00 3.27
427 431 0.321122 GAAGGTGTGGTGGCTGAGAG 60.321 60.000 0.00 0.00 0.00 3.20
429 433 1.056700 AGGTGTGGTGGCTGAGAGTT 61.057 55.000 0.00 0.00 0.00 3.01
472 485 4.029809 GGGCCGCCAGTAGGTTGT 62.030 66.667 12.58 0.00 37.19 3.32
555 569 4.312443 CTTTTACTTTGCTCCGAGGTGTA 58.688 43.478 0.00 0.00 0.00 2.90
576 590 6.642131 GTGTACCAGTTGTAGACGAATTGTAA 59.358 38.462 0.00 0.00 34.45 2.41
578 592 7.710044 TGTACCAGTTGTAGACGAATTGTAAAA 59.290 33.333 0.00 0.00 0.00 1.52
579 593 7.186021 ACCAGTTGTAGACGAATTGTAAAAG 57.814 36.000 0.00 0.00 0.00 2.27
580 594 6.987992 ACCAGTTGTAGACGAATTGTAAAAGA 59.012 34.615 0.00 0.00 0.00 2.52
581 595 7.042254 ACCAGTTGTAGACGAATTGTAAAAGAC 60.042 37.037 0.00 0.00 0.00 3.01
582 596 7.288672 CAGTTGTAGACGAATTGTAAAAGACC 58.711 38.462 0.00 0.00 0.00 3.85
585 599 7.647907 TGTAGACGAATTGTAAAAGACCTTC 57.352 36.000 0.00 0.00 0.00 3.46
601 615 7.659652 AAGACCTTCTTTTTAGAATCTGACG 57.340 36.000 0.00 0.00 31.57 4.35
602 616 6.994221 AGACCTTCTTTTTAGAATCTGACGA 58.006 36.000 0.00 0.00 0.00 4.20
603 617 7.442656 AGACCTTCTTTTTAGAATCTGACGAA 58.557 34.615 0.00 0.00 0.00 3.85
604 618 8.097662 AGACCTTCTTTTTAGAATCTGACGAAT 58.902 33.333 0.00 0.00 0.00 3.34
605 619 8.622948 ACCTTCTTTTTAGAATCTGACGAATT 57.377 30.769 0.00 0.00 0.00 2.17
606 620 8.507249 ACCTTCTTTTTAGAATCTGACGAATTG 58.493 33.333 0.00 0.00 0.00 2.32
607 621 8.507249 CCTTCTTTTTAGAATCTGACGAATTGT 58.493 33.333 0.00 0.00 0.00 2.71
624 679 1.975660 TGTAAAAGACCTGTGTGCCC 58.024 50.000 0.00 0.00 0.00 5.36
681 1777 3.479370 GCGATGTGCAGGACAGAC 58.521 61.111 0.00 0.00 45.45 3.51
683 1779 1.080501 CGATGTGCAGGACAGACGT 60.081 57.895 13.48 0.00 38.23 4.34
686 1782 2.683968 GATGTGCAGGACAGACGTAAA 58.316 47.619 0.00 0.00 38.23 2.01
687 1783 2.605837 TGTGCAGGACAGACGTAAAA 57.394 45.000 0.00 0.00 0.00 1.52
688 1784 2.907634 TGTGCAGGACAGACGTAAAAA 58.092 42.857 0.00 0.00 0.00 1.94
690 1786 3.880490 TGTGCAGGACAGACGTAAAAATT 59.120 39.130 0.00 0.00 0.00 1.82
693 1789 6.205853 TGTGCAGGACAGACGTAAAAATTATT 59.794 34.615 0.00 0.00 0.00 1.40
694 1790 7.081976 GTGCAGGACAGACGTAAAAATTATTT 58.918 34.615 0.00 0.00 0.00 1.40
695 1791 7.060633 GTGCAGGACAGACGTAAAAATTATTTG 59.939 37.037 0.00 0.00 0.00 2.32
696 1792 7.041030 TGCAGGACAGACGTAAAAATTATTTGA 60.041 33.333 0.00 0.00 0.00 2.69
697 1793 7.270579 GCAGGACAGACGTAAAAATTATTTGAC 59.729 37.037 0.00 0.00 0.00 3.18
699 1795 8.842280 AGGACAGACGTAAAAATTATTTGACAA 58.158 29.630 0.00 0.00 30.29 3.18
702 1798 9.240159 ACAGACGTAAAAATTATTTGACAAACC 57.760 29.630 1.94 0.00 30.29 3.27
703 1799 8.696175 CAGACGTAAAAATTATTTGACAAACCC 58.304 33.333 1.94 0.00 30.29 4.11
704 1800 8.414778 AGACGTAAAAATTATTTGACAAACCCA 58.585 29.630 1.94 0.00 30.29 4.51
705 1801 8.355272 ACGTAAAAATTATTTGACAAACCCAC 57.645 30.769 1.94 0.00 30.29 4.61
706 1802 7.167801 ACGTAAAAATTATTTGACAAACCCACG 59.832 33.333 1.94 7.25 30.29 4.94
707 1803 6.852858 AAAAATTATTTGACAAACCCACGG 57.147 33.333 1.94 0.00 0.00 4.94
709 1805 5.385509 AATTATTTGACAAACCCACGGAG 57.614 39.130 1.94 0.00 0.00 4.63
710 1806 1.616159 ATTTGACAAACCCACGGAGG 58.384 50.000 1.94 0.00 37.03 4.30
712 1808 2.112297 GACAAACCCACGGAGGCA 59.888 61.111 0.00 0.00 35.39 4.75
713 1809 1.527380 GACAAACCCACGGAGGCAA 60.527 57.895 0.00 0.00 35.39 4.52
714 1810 1.076632 ACAAACCCACGGAGGCAAA 60.077 52.632 0.00 0.00 35.39 3.68
715 1811 0.684805 ACAAACCCACGGAGGCAAAA 60.685 50.000 0.00 0.00 35.39 2.44
716 1812 0.461961 CAAACCCACGGAGGCAAAAA 59.538 50.000 0.00 0.00 35.39 1.94
717 1813 0.750249 AAACCCACGGAGGCAAAAAG 59.250 50.000 0.00 0.00 35.39 2.27
718 1814 1.112916 AACCCACGGAGGCAAAAAGG 61.113 55.000 0.00 0.00 35.39 3.11
719 1815 1.228429 CCCACGGAGGCAAAAAGGA 60.228 57.895 0.00 0.00 35.39 3.36
721 1817 0.313987 CCACGGAGGCAAAAAGGAAC 59.686 55.000 0.00 0.00 0.00 3.62
723 1819 1.266989 CACGGAGGCAAAAAGGAACTC 59.733 52.381 0.00 0.00 38.49 3.01
735 1831 6.016610 GCAAAAAGGAACTCATTAGTACCACA 60.017 38.462 0.00 0.00 38.49 4.17
739 1835 4.099573 AGGAACTCATTAGTACCACATCGG 59.900 45.833 0.00 0.00 36.21 4.18
753 1849 4.162812 CCACATCGGTTAATTCCAAAACG 58.837 43.478 0.00 0.00 38.38 3.60
754 1850 4.320641 CCACATCGGTTAATTCCAAAACGT 60.321 41.667 0.00 0.00 38.20 3.99
755 1851 5.106634 CCACATCGGTTAATTCCAAAACGTA 60.107 40.000 0.00 0.00 38.20 3.57
756 1852 6.372185 CACATCGGTTAATTCCAAAACGTAA 58.628 36.000 0.00 0.00 38.20 3.18
757 1853 7.024768 CACATCGGTTAATTCCAAAACGTAAT 58.975 34.615 0.00 0.00 38.20 1.89
758 1854 7.217447 CACATCGGTTAATTCCAAAACGTAATC 59.783 37.037 0.00 0.00 38.20 1.75
759 1855 5.856314 TCGGTTAATTCCAAAACGTAATCG 58.144 37.500 0.00 0.00 38.20 3.34
777 1873 7.989609 CGTAATCGTAAAAGCGTATTATGACT 58.010 34.615 4.08 0.00 32.66 3.41
778 1874 7.937817 CGTAATCGTAAAAGCGTATTATGACTG 59.062 37.037 4.08 0.00 32.66 3.51
779 1875 6.764877 ATCGTAAAAGCGTATTATGACTGG 57.235 37.500 4.08 0.00 32.66 4.00
780 1876 5.045215 TCGTAAAAGCGTATTATGACTGGG 58.955 41.667 0.00 0.00 0.00 4.45
781 1877 4.318546 CGTAAAAGCGTATTATGACTGGGC 60.319 45.833 0.00 0.00 0.00 5.36
782 1878 1.865865 AAGCGTATTATGACTGGGCG 58.134 50.000 0.00 0.00 0.00 6.13
783 1879 0.033504 AGCGTATTATGACTGGGCGG 59.966 55.000 0.00 0.00 0.00 6.13
784 1880 0.032952 GCGTATTATGACTGGGCGGA 59.967 55.000 0.00 0.00 0.00 5.54
785 1881 1.539496 GCGTATTATGACTGGGCGGAA 60.539 52.381 0.00 0.00 0.00 4.30
786 1882 2.828877 CGTATTATGACTGGGCGGAAA 58.171 47.619 0.00 0.00 0.00 3.13
787 1883 2.542595 CGTATTATGACTGGGCGGAAAC 59.457 50.000 0.00 0.00 0.00 2.78
801 1897 2.867456 GGAAACGTATTGTGACGGTG 57.133 50.000 0.00 0.00 43.33 4.94
802 1898 2.406130 GGAAACGTATTGTGACGGTGA 58.594 47.619 0.00 0.00 43.33 4.02
803 1899 2.801679 GGAAACGTATTGTGACGGTGAA 59.198 45.455 0.00 0.00 43.33 3.18
804 1900 3.363280 GGAAACGTATTGTGACGGTGAAC 60.363 47.826 0.00 0.00 43.33 3.18
805 1901 2.545106 AAACGTATTGTGACGGTGAACC 59.455 45.455 0.00 0.00 43.33 3.62
806 1902 1.073177 CGTATTGTGACGGTGAACCC 58.927 55.000 0.00 0.00 39.19 4.11
815 1911 2.926242 GGTGAACCCGGAGACCCA 60.926 66.667 0.73 0.00 0.00 4.51
816 1912 2.522367 GGTGAACCCGGAGACCCAA 61.522 63.158 0.73 0.00 0.00 4.12
817 1913 1.683441 GTGAACCCGGAGACCCAAT 59.317 57.895 0.73 0.00 0.00 3.16
818 1914 0.392595 GTGAACCCGGAGACCCAATC 60.393 60.000 0.73 0.00 0.00 2.67
819 1915 1.223763 GAACCCGGAGACCCAATCC 59.776 63.158 0.73 0.00 0.00 3.01
824 1920 2.990479 GGAGACCCAATCCGTGCT 59.010 61.111 0.00 0.00 0.00 4.40
825 1921 1.299976 GGAGACCCAATCCGTGCTT 59.700 57.895 0.00 0.00 0.00 3.91
826 1922 0.322546 GGAGACCCAATCCGTGCTTT 60.323 55.000 0.00 0.00 0.00 3.51
827 1923 1.065709 GGAGACCCAATCCGTGCTTTA 60.066 52.381 0.00 0.00 0.00 1.85
828 1924 2.421529 GGAGACCCAATCCGTGCTTTAT 60.422 50.000 0.00 0.00 0.00 1.40
829 1925 3.279434 GAGACCCAATCCGTGCTTTATT 58.721 45.455 0.00 0.00 0.00 1.40
830 1926 4.448210 GAGACCCAATCCGTGCTTTATTA 58.552 43.478 0.00 0.00 0.00 0.98
831 1927 5.048846 AGACCCAATCCGTGCTTTATTAT 57.951 39.130 0.00 0.00 0.00 1.28
832 1928 5.445964 AGACCCAATCCGTGCTTTATTATT 58.554 37.500 0.00 0.00 0.00 1.40
833 1929 6.597562 AGACCCAATCCGTGCTTTATTATTA 58.402 36.000 0.00 0.00 0.00 0.98
834 1930 7.057894 AGACCCAATCCGTGCTTTATTATTAA 58.942 34.615 0.00 0.00 0.00 1.40
835 1931 7.558444 AGACCCAATCCGTGCTTTATTATTAAA 59.442 33.333 0.00 0.00 0.00 1.52
836 1932 8.068892 ACCCAATCCGTGCTTTATTATTAAAA 57.931 30.769 0.00 0.00 0.00 1.52
837 1933 8.532819 ACCCAATCCGTGCTTTATTATTAAAAA 58.467 29.630 0.00 0.00 0.00 1.94
867 1963 7.619512 AGGGAGAGATAAAAGTGGGTTATAG 57.380 40.000 0.00 0.00 0.00 1.31
871 1967 9.682465 GGAGAGATAAAAGTGGGTTATAGTTTT 57.318 33.333 0.00 0.00 35.50 2.43
1147 2284 2.434185 CGGCATGTACCTGCACGT 60.434 61.111 22.26 0.00 44.12 4.49
1150 2287 2.452813 GCATGTACCTGCACGTCGG 61.453 63.158 17.08 0.00 41.87 4.79
1636 2862 2.224495 ATTTGCGCGAATTGGGTGGG 62.224 55.000 17.36 0.00 0.00 4.61
1818 3055 1.360393 ACTGCAGTTTCCCTTCCCCA 61.360 55.000 15.25 0.00 0.00 4.96
2056 3320 2.357517 CGTCTGGCACCTCCACAC 60.358 66.667 0.00 0.00 40.72 3.82
2174 3567 4.095782 GGAAAACAGTGTACTGAAACAGCA 59.904 41.667 18.18 0.00 46.59 4.41
2241 3945 2.223641 ACTGCTGTCTTTGCATTGTGTG 60.224 45.455 0.00 0.00 39.86 3.82
2242 3946 1.067364 TGCTGTCTTTGCATTGTGTGG 59.933 47.619 0.00 0.00 35.31 4.17
2270 3977 6.850752 TGGATTAATCTGTCTGTGTAGTCA 57.149 37.500 14.95 0.00 0.00 3.41
2286 3993 5.758784 GTGTAGTCAGAAGCTTAGTTGGTTT 59.241 40.000 0.00 0.00 0.00 3.27
2324 4228 6.609616 ACTCTTGGAACTTGAAAACCCAAATA 59.390 34.615 0.00 0.00 36.57 1.40
2347 4529 5.411831 AGTTCAGTCATATCAGTTCAGCA 57.588 39.130 0.00 0.00 0.00 4.41
2349 4531 5.816258 AGTTCAGTCATATCAGTTCAGCATG 59.184 40.000 0.00 0.00 37.54 4.06
2515 4755 3.964688 TGGGTGAAACTAGTCTGAACTGA 59.035 43.478 0.00 0.00 36.92 3.41
2614 4854 2.284190 GGACAGATGCTAGAAGGTTGC 58.716 52.381 0.00 0.00 0.00 4.17
2715 4998 2.979814 AGCAACCTGAAAACCCAAAC 57.020 45.000 0.00 0.00 0.00 2.93
2760 5160 5.923684 GGCATTCCATTGTTTCGAGTTTTTA 59.076 36.000 0.00 0.00 0.00 1.52
3044 6874 3.620226 GCTAAACTTGGTCCCTTCTCCTC 60.620 52.174 0.00 0.00 0.00 3.71
3075 6958 5.574188 AGGAAACCTATTTGCTGTTCTCAT 58.426 37.500 0.00 0.00 44.09 2.90
3100 8192 6.360370 TTCAGATATATACTGCTTGGTCCC 57.640 41.667 7.09 0.00 35.61 4.46
3245 8337 2.738147 CGAGGCGGAACACTAGTTG 58.262 57.895 0.00 0.00 38.30 3.16
3246 8338 0.038526 CGAGGCGGAACACTAGTTGT 60.039 55.000 0.00 0.00 41.74 3.32
3247 8339 1.200716 CGAGGCGGAACACTAGTTGTA 59.799 52.381 0.00 0.00 37.51 2.41
3248 8340 2.603953 GAGGCGGAACACTAGTTGTAC 58.396 52.381 0.00 0.00 37.51 2.90
3249 8341 2.230750 GAGGCGGAACACTAGTTGTACT 59.769 50.000 0.00 0.00 37.51 2.73
3250 8342 2.631545 AGGCGGAACACTAGTTGTACTT 59.368 45.455 0.00 0.00 37.51 2.24
3251 8343 2.735134 GGCGGAACACTAGTTGTACTTG 59.265 50.000 0.00 0.00 37.51 3.16
3252 8344 2.157085 GCGGAACACTAGTTGTACTTGC 59.843 50.000 0.00 0.00 37.51 4.01
3253 8345 2.407361 CGGAACACTAGTTGTACTTGCG 59.593 50.000 0.00 0.00 37.51 4.85
3254 8346 2.157085 GGAACACTAGTTGTACTTGCGC 59.843 50.000 0.00 0.00 37.51 6.09
3255 8347 1.415374 ACACTAGTTGTACTTGCGCG 58.585 50.000 0.00 0.00 36.32 6.86
3256 8348 0.713883 CACTAGTTGTACTTGCGCGG 59.286 55.000 8.83 0.00 0.00 6.46
3359 8451 5.059833 GTGTTTGGACAGAGAACTCTCAAT 58.940 41.667 9.34 0.00 45.21 2.57
3370 8462 2.169832 ACTCTCAATGGTGGTTGTCG 57.830 50.000 0.00 0.00 0.00 4.35
3760 9188 9.882996 GAATTTTTCATGAATTCAAAAAGGGTC 57.117 29.630 13.09 9.68 41.13 4.46
3945 9373 4.599036 GGGCTTCCCTTTGTGTGT 57.401 55.556 0.00 0.00 41.34 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.569404 AGAAATCTGGAAAGGAGCGAGT 59.431 45.455 0.00 0.00 0.00 4.18
29 30 7.013655 TCACTTTTCTCAAGAAATCTGGAAAGG 59.986 37.037 6.05 8.48 42.83 3.11
111 113 6.650807 TCAATAGAATCTGAACACGAGCTTTT 59.349 34.615 0.00 0.00 0.00 2.27
143 145 2.370189 ACCTCTTGTTCTTCCTCCACTG 59.630 50.000 0.00 0.00 0.00 3.66
284 287 0.038343 GACCGGTAGGCGTTGTGTAA 60.038 55.000 7.34 0.00 42.76 2.41
285 288 1.586028 GACCGGTAGGCGTTGTGTA 59.414 57.895 7.34 0.00 42.76 2.90
320 324 2.942796 CGGTGCTGTGGCTGGAGTA 61.943 63.158 0.00 0.00 39.59 2.59
422 426 0.252057 TCCCACGATCCCAACTCTCA 60.252 55.000 0.00 0.00 0.00 3.27
423 427 0.902531 TTCCCACGATCCCAACTCTC 59.097 55.000 0.00 0.00 0.00 3.20
424 428 0.613777 GTTCCCACGATCCCAACTCT 59.386 55.000 0.00 0.00 0.00 3.24
463 476 1.825474 CCACCGATCTCACAACCTACT 59.175 52.381 0.00 0.00 0.00 2.57
472 485 2.725312 GCTGCTCCCACCGATCTCA 61.725 63.158 0.00 0.00 0.00 3.27
503 516 1.135460 GGAGTTTAGGTCACGTCCTCG 60.135 57.143 0.00 0.00 38.86 4.63
555 569 6.987992 TCTTTTACAATTCGTCTACAACTGGT 59.012 34.615 0.00 0.00 0.00 4.00
578 592 6.994221 TCGTCAGATTCTAAAAAGAAGGTCT 58.006 36.000 0.00 0.00 0.00 3.85
579 593 7.653767 TTCGTCAGATTCTAAAAAGAAGGTC 57.346 36.000 0.00 0.00 0.00 3.85
580 594 8.507249 CAATTCGTCAGATTCTAAAAAGAAGGT 58.493 33.333 0.00 0.00 0.00 3.50
581 595 8.507249 ACAATTCGTCAGATTCTAAAAAGAAGG 58.493 33.333 0.00 0.00 0.00 3.46
593 607 6.710744 ACAGGTCTTTTACAATTCGTCAGATT 59.289 34.615 0.00 0.00 0.00 2.40
597 611 5.007234 CACACAGGTCTTTTACAATTCGTCA 59.993 40.000 0.00 0.00 0.00 4.35
598 612 5.440685 CACACAGGTCTTTTACAATTCGTC 58.559 41.667 0.00 0.00 0.00 4.20
599 613 4.261031 GCACACAGGTCTTTTACAATTCGT 60.261 41.667 0.00 0.00 0.00 3.85
600 614 4.219033 GCACACAGGTCTTTTACAATTCG 58.781 43.478 0.00 0.00 0.00 3.34
601 615 4.546570 GGCACACAGGTCTTTTACAATTC 58.453 43.478 0.00 0.00 0.00 2.17
602 616 3.320826 GGGCACACAGGTCTTTTACAATT 59.679 43.478 0.00 0.00 0.00 2.32
603 617 2.890945 GGGCACACAGGTCTTTTACAAT 59.109 45.455 0.00 0.00 0.00 2.71
604 618 2.092103 AGGGCACACAGGTCTTTTACAA 60.092 45.455 0.00 0.00 0.00 2.41
605 619 1.493022 AGGGCACACAGGTCTTTTACA 59.507 47.619 0.00 0.00 0.00 2.41
606 620 1.880027 CAGGGCACACAGGTCTTTTAC 59.120 52.381 0.00 0.00 0.00 2.01
607 621 1.493022 ACAGGGCACACAGGTCTTTTA 59.507 47.619 0.00 0.00 0.00 1.52
608 622 0.258774 ACAGGGCACACAGGTCTTTT 59.741 50.000 0.00 0.00 0.00 2.27
624 679 3.767230 CGTTCTCCGCACGCACAG 61.767 66.667 0.00 0.00 0.00 3.66
673 1769 8.385898 TGTCAAATAATTTTTACGTCTGTCCT 57.614 30.769 0.00 0.00 0.00 3.85
678 1774 8.414778 TGGGTTTGTCAAATAATTTTTACGTCT 58.585 29.630 0.40 0.00 0.00 4.18
679 1775 8.481641 GTGGGTTTGTCAAATAATTTTTACGTC 58.518 33.333 0.40 0.00 0.00 4.34
680 1776 7.167801 CGTGGGTTTGTCAAATAATTTTTACGT 59.832 33.333 0.40 0.00 0.00 3.57
681 1777 7.358517 CCGTGGGTTTGTCAAATAATTTTTACG 60.359 37.037 0.40 5.01 0.00 3.18
683 1779 7.723324 TCCGTGGGTTTGTCAAATAATTTTTA 58.277 30.769 0.40 0.00 0.00 1.52
686 1782 5.279256 CCTCCGTGGGTTTGTCAAATAATTT 60.279 40.000 0.40 0.00 0.00 1.82
687 1783 4.219725 CCTCCGTGGGTTTGTCAAATAATT 59.780 41.667 0.40 0.00 0.00 1.40
688 1784 3.761752 CCTCCGTGGGTTTGTCAAATAAT 59.238 43.478 0.40 0.00 0.00 1.28
690 1786 2.785562 CCTCCGTGGGTTTGTCAAATA 58.214 47.619 0.40 0.00 0.00 1.40
693 1789 1.527380 GCCTCCGTGGGTTTGTCAA 60.527 57.895 0.00 0.00 36.00 3.18
694 1790 2.112297 GCCTCCGTGGGTTTGTCA 59.888 61.111 0.00 0.00 36.00 3.58
695 1791 1.104577 TTTGCCTCCGTGGGTTTGTC 61.105 55.000 0.00 0.00 36.00 3.18
696 1792 0.684805 TTTTGCCTCCGTGGGTTTGT 60.685 50.000 0.00 0.00 36.00 2.83
697 1793 0.461961 TTTTTGCCTCCGTGGGTTTG 59.538 50.000 0.00 0.00 36.00 2.93
699 1795 1.112916 CCTTTTTGCCTCCGTGGGTT 61.113 55.000 0.00 0.00 36.00 4.11
701 1797 0.825840 TTCCTTTTTGCCTCCGTGGG 60.826 55.000 0.00 0.00 36.00 4.61
702 1798 0.313987 GTTCCTTTTTGCCTCCGTGG 59.686 55.000 0.00 0.00 39.35 4.94
703 1799 1.266989 GAGTTCCTTTTTGCCTCCGTG 59.733 52.381 0.00 0.00 0.00 4.94
704 1800 1.133915 TGAGTTCCTTTTTGCCTCCGT 60.134 47.619 0.00 0.00 0.00 4.69
705 1801 1.604604 TGAGTTCCTTTTTGCCTCCG 58.395 50.000 0.00 0.00 0.00 4.63
706 1802 4.767409 ACTAATGAGTTCCTTTTTGCCTCC 59.233 41.667 0.00 0.00 28.61 4.30
707 1803 5.966742 ACTAATGAGTTCCTTTTTGCCTC 57.033 39.130 0.00 0.00 28.61 4.70
709 1805 5.475564 TGGTACTAATGAGTTCCTTTTTGCC 59.524 40.000 7.36 0.00 42.27 4.52
710 1806 6.016610 TGTGGTACTAATGAGTTCCTTTTTGC 60.017 38.462 7.36 0.00 42.27 3.68
712 1808 7.119262 CGATGTGGTACTAATGAGTTCCTTTTT 59.881 37.037 7.36 0.00 42.27 1.94
713 1809 6.594159 CGATGTGGTACTAATGAGTTCCTTTT 59.406 38.462 7.36 0.00 42.27 2.27
714 1810 6.106673 CGATGTGGTACTAATGAGTTCCTTT 58.893 40.000 7.36 0.00 42.27 3.11
715 1811 5.395324 CCGATGTGGTACTAATGAGTTCCTT 60.395 44.000 7.36 0.00 42.27 3.36
716 1812 4.099573 CCGATGTGGTACTAATGAGTTCCT 59.900 45.833 7.36 0.00 42.27 3.36
717 1813 4.369182 CCGATGTGGTACTAATGAGTTCC 58.631 47.826 0.00 0.00 42.16 3.62
735 1831 6.480285 CGATTACGTTTTGGAATTAACCGAT 58.520 36.000 0.00 0.00 34.56 4.18
752 1848 7.937817 CAGTCATAATACGCTTTTACGATTACG 59.062 37.037 0.00 0.00 45.75 3.18
753 1849 8.212495 CCAGTCATAATACGCTTTTACGATTAC 58.788 37.037 0.00 0.00 36.70 1.89
754 1850 7.383029 CCCAGTCATAATACGCTTTTACGATTA 59.617 37.037 0.00 0.00 36.70 1.75
755 1851 6.202188 CCCAGTCATAATACGCTTTTACGATT 59.798 38.462 0.00 0.00 36.70 3.34
756 1852 5.694910 CCCAGTCATAATACGCTTTTACGAT 59.305 40.000 0.00 0.00 36.70 3.73
757 1853 5.045215 CCCAGTCATAATACGCTTTTACGA 58.955 41.667 0.00 0.00 36.70 3.43
758 1854 4.318546 GCCCAGTCATAATACGCTTTTACG 60.319 45.833 0.00 0.00 39.50 3.18
759 1855 4.318546 CGCCCAGTCATAATACGCTTTTAC 60.319 45.833 0.00 0.00 0.00 2.01
760 1856 3.805422 CGCCCAGTCATAATACGCTTTTA 59.195 43.478 0.00 0.00 0.00 1.52
761 1857 2.612212 CGCCCAGTCATAATACGCTTTT 59.388 45.455 0.00 0.00 0.00 2.27
762 1858 2.210116 CGCCCAGTCATAATACGCTTT 58.790 47.619 0.00 0.00 0.00 3.51
763 1859 1.540363 CCGCCCAGTCATAATACGCTT 60.540 52.381 0.00 0.00 0.00 4.68
764 1860 0.033504 CCGCCCAGTCATAATACGCT 59.966 55.000 0.00 0.00 0.00 5.07
765 1861 0.032952 TCCGCCCAGTCATAATACGC 59.967 55.000 0.00 0.00 0.00 4.42
766 1862 2.519377 TTCCGCCCAGTCATAATACG 57.481 50.000 0.00 0.00 0.00 3.06
767 1863 2.542595 CGTTTCCGCCCAGTCATAATAC 59.457 50.000 0.00 0.00 0.00 1.89
768 1864 2.168936 ACGTTTCCGCCCAGTCATAATA 59.831 45.455 0.00 0.00 37.70 0.98
769 1865 1.065709 ACGTTTCCGCCCAGTCATAAT 60.066 47.619 0.00 0.00 37.70 1.28
770 1866 0.322322 ACGTTTCCGCCCAGTCATAA 59.678 50.000 0.00 0.00 37.70 1.90
771 1867 1.184431 TACGTTTCCGCCCAGTCATA 58.816 50.000 0.00 0.00 37.70 2.15
772 1868 0.539986 ATACGTTTCCGCCCAGTCAT 59.460 50.000 0.00 0.00 37.70 3.06
773 1869 0.322322 AATACGTTTCCGCCCAGTCA 59.678 50.000 0.00 0.00 37.70 3.41
774 1870 0.725117 CAATACGTTTCCGCCCAGTC 59.275 55.000 0.00 0.00 37.70 3.51
775 1871 0.035739 ACAATACGTTTCCGCCCAGT 59.964 50.000 0.00 0.00 37.70 4.00
776 1872 0.446222 CACAATACGTTTCCGCCCAG 59.554 55.000 0.00 0.00 37.70 4.45
777 1873 0.035036 TCACAATACGTTTCCGCCCA 59.965 50.000 0.00 0.00 37.70 5.36
778 1874 0.445043 GTCACAATACGTTTCCGCCC 59.555 55.000 0.00 0.00 37.70 6.13
779 1875 0.094046 CGTCACAATACGTTTCCGCC 59.906 55.000 0.00 0.00 38.07 6.13
780 1876 0.094046 CCGTCACAATACGTTTCCGC 59.906 55.000 0.00 0.00 41.27 5.54
781 1877 1.125384 CACCGTCACAATACGTTTCCG 59.875 52.381 0.00 0.00 41.27 4.30
782 1878 2.406130 TCACCGTCACAATACGTTTCC 58.594 47.619 0.00 0.00 41.27 3.13
783 1879 3.363280 GGTTCACCGTCACAATACGTTTC 60.363 47.826 0.00 0.00 41.27 2.78
784 1880 2.545106 GGTTCACCGTCACAATACGTTT 59.455 45.455 0.00 0.00 41.27 3.60
785 1881 2.137523 GGTTCACCGTCACAATACGTT 58.862 47.619 0.00 0.00 41.27 3.99
786 1882 1.606224 GGGTTCACCGTCACAATACGT 60.606 52.381 0.00 0.00 41.27 3.57
787 1883 1.073177 GGGTTCACCGTCACAATACG 58.927 55.000 0.00 0.00 42.49 3.06
798 1894 1.848886 ATTGGGTCTCCGGGTTCACC 61.849 60.000 0.00 2.28 35.24 4.02
799 1895 0.392595 GATTGGGTCTCCGGGTTCAC 60.393 60.000 0.00 0.00 35.24 3.18
800 1896 1.559065 GGATTGGGTCTCCGGGTTCA 61.559 60.000 0.00 0.00 35.24 3.18
801 1897 1.223763 GGATTGGGTCTCCGGGTTC 59.776 63.158 0.00 0.00 35.24 3.62
802 1898 3.411700 GGATTGGGTCTCCGGGTT 58.588 61.111 0.00 0.00 35.24 4.11
807 1903 0.322546 AAAGCACGGATTGGGTCTCC 60.323 55.000 0.00 0.00 0.00 3.71
808 1904 2.396590 TAAAGCACGGATTGGGTCTC 57.603 50.000 0.00 0.00 0.00 3.36
809 1905 3.366052 AATAAAGCACGGATTGGGTCT 57.634 42.857 0.00 0.00 0.00 3.85
810 1906 5.767816 AATAATAAAGCACGGATTGGGTC 57.232 39.130 0.00 0.00 0.00 4.46
811 1907 7.648039 TTTAATAATAAAGCACGGATTGGGT 57.352 32.000 0.00 0.00 0.00 4.51
812 1908 8.934507 TTTTTAATAATAAAGCACGGATTGGG 57.065 30.769 0.00 0.00 32.80 4.12
836 1932 8.177456 ACCCACTTTTATCTCTCCCTAATTTTT 58.823 33.333 0.00 0.00 0.00 1.94
837 1933 7.709601 ACCCACTTTTATCTCTCCCTAATTTT 58.290 34.615 0.00 0.00 0.00 1.82
838 1934 7.285340 ACCCACTTTTATCTCTCCCTAATTT 57.715 36.000 0.00 0.00 0.00 1.82
839 1935 6.910259 ACCCACTTTTATCTCTCCCTAATT 57.090 37.500 0.00 0.00 0.00 1.40
840 1936 6.910259 AACCCACTTTTATCTCTCCCTAAT 57.090 37.500 0.00 0.00 0.00 1.73
841 1937 9.155785 CTATAACCCACTTTTATCTCTCCCTAA 57.844 37.037 0.00 0.00 0.00 2.69
842 1938 8.294690 ACTATAACCCACTTTTATCTCTCCCTA 58.705 37.037 0.00 0.00 0.00 3.53
843 1939 7.140304 ACTATAACCCACTTTTATCTCTCCCT 58.860 38.462 0.00 0.00 0.00 4.20
844 1940 7.376335 ACTATAACCCACTTTTATCTCTCCC 57.624 40.000 0.00 0.00 0.00 4.30
845 1941 9.682465 AAAACTATAACCCACTTTTATCTCTCC 57.318 33.333 0.00 0.00 0.00 3.71
1515 2706 2.425592 CTCCACGACCCAGTGCAA 59.574 61.111 0.00 0.00 40.59 4.08
1636 2862 0.523335 GGTCAAATTCCGACGCATGC 60.523 55.000 7.91 7.91 34.04 4.06
1686 2912 1.138247 CAAGAATTGCTCGCAGGCC 59.862 57.895 0.00 0.00 40.39 5.19
1818 3055 1.066143 CAACAGGGCGTCCAGTATTCT 60.066 52.381 9.71 0.00 32.11 2.40
1931 3177 0.250467 GCACCAGCTTGTTCCTCAGA 60.250 55.000 0.00 0.00 37.91 3.27
2043 3307 3.936203 GACGGTGTGGAGGTGCCA 61.936 66.667 0.00 0.00 46.96 4.92
2046 3310 2.049433 GACGACGGTGTGGAGGTG 60.049 66.667 0.00 0.00 0.00 4.00
2097 3361 6.101274 ACCCAAGGAGATTAGTAGGAAGTA 57.899 41.667 0.00 0.00 0.00 2.24
2241 3945 2.614057 CAGACAGATTAATCCAACGGCC 59.386 50.000 11.92 0.00 0.00 6.13
2242 3946 3.063997 CACAGACAGATTAATCCAACGGC 59.936 47.826 11.92 1.05 0.00 5.68
2286 3993 7.027874 AGTTCCAAGAGTGGGAATATGTAAA 57.972 36.000 0.00 0.00 45.55 2.01
2324 4228 5.798132 TGCTGAACTGATATGACTGAACTT 58.202 37.500 0.00 0.00 0.00 2.66
2614 4854 9.793252 CAAAACCAAACAATATCTATCTTCAGG 57.207 33.333 0.00 0.00 0.00 3.86
2663 4943 6.086222 CACTGGCGGCACATATTATTAAATC 58.914 40.000 7.97 0.00 0.00 2.17
2715 4998 6.103997 TGCCTAGAAAAATCTACGTAGTTGG 58.896 40.000 21.53 11.77 37.78 3.77
2760 5160 6.558488 AGATCAAGAAGAAAGCTGAGGTAT 57.442 37.500 0.00 0.00 0.00 2.73
3044 6874 6.071952 ACAGCAAATAGGTTTCCTACATTGTG 60.072 38.462 16.94 15.65 39.10 3.33
3075 6958 7.901322 AGGGACCAAGCAGTATATATCTGAATA 59.099 37.037 13.25 0.00 35.20 1.75
3100 8192 4.938226 GGTTTCCTACATTGTCAGGAGAAG 59.062 45.833 12.03 0.00 41.89 2.85
3235 8327 1.790623 CGCGCAAGTACAACTAGTGTT 59.209 47.619 8.75 0.00 38.87 3.32
3236 8328 1.415374 CGCGCAAGTACAACTAGTGT 58.585 50.000 8.75 0.00 40.67 3.55
3237 8329 0.713883 CCGCGCAAGTACAACTAGTG 59.286 55.000 8.75 0.00 41.68 2.74
3238 8330 0.316204 ACCGCGCAAGTACAACTAGT 59.684 50.000 8.75 0.00 41.68 2.57
3239 8331 2.267188 TACCGCGCAAGTACAACTAG 57.733 50.000 8.75 0.00 41.68 2.57
3240 8332 2.721274 TTACCGCGCAAGTACAACTA 57.279 45.000 8.75 0.00 41.68 2.24
3241 8333 2.088950 ATTACCGCGCAAGTACAACT 57.911 45.000 8.75 0.00 41.68 3.16
3242 8334 2.925563 ACTATTACCGCGCAAGTACAAC 59.074 45.455 8.75 0.00 41.68 3.32
3243 8335 3.235157 ACTATTACCGCGCAAGTACAA 57.765 42.857 8.75 0.00 41.68 2.41
3244 8336 2.945447 ACTATTACCGCGCAAGTACA 57.055 45.000 8.75 0.52 41.68 2.90
3245 8337 4.328667 CAAAACTATTACCGCGCAAGTAC 58.671 43.478 8.75 0.00 41.68 2.73
3246 8338 3.181518 GCAAAACTATTACCGCGCAAGTA 60.182 43.478 8.75 5.59 41.68 2.24
3247 8339 2.413634 GCAAAACTATTACCGCGCAAGT 60.414 45.455 8.75 6.78 41.68 3.16
3248 8340 2.173964 GCAAAACTATTACCGCGCAAG 58.826 47.619 8.75 0.00 43.44 4.01
3249 8341 1.535896 TGCAAAACTATTACCGCGCAA 59.464 42.857 8.75 0.00 0.00 4.85
3250 8342 1.129624 CTGCAAAACTATTACCGCGCA 59.870 47.619 8.75 0.00 0.00 6.09
3251 8343 1.129811 ACTGCAAAACTATTACCGCGC 59.870 47.619 0.00 0.00 0.00 6.86
3252 8344 2.413796 TCACTGCAAAACTATTACCGCG 59.586 45.455 0.00 0.00 0.00 6.46
3253 8345 4.413495 TTCACTGCAAAACTATTACCGC 57.587 40.909 0.00 0.00 0.00 5.68
3254 8346 5.123186 TCCATTCACTGCAAAACTATTACCG 59.877 40.000 0.00 0.00 0.00 4.02
3255 8347 6.404734 CCTCCATTCACTGCAAAACTATTACC 60.405 42.308 0.00 0.00 0.00 2.85
3256 8348 6.374333 TCCTCCATTCACTGCAAAACTATTAC 59.626 38.462 0.00 0.00 0.00 1.89
3359 8451 1.302431 CCATGAGCGACAACCACCA 60.302 57.895 0.00 0.00 0.00 4.17
3667 9093 7.543868 TGTGAACAATTTTCAAGTTCGTGAATT 59.456 29.630 2.53 0.00 43.36 2.17
3668 9094 7.032580 TGTGAACAATTTTCAAGTTCGTGAAT 58.967 30.769 2.53 0.00 43.36 2.57
3743 9170 9.506018 CTTTTTATGGACCCTTTTTGAATTCAT 57.494 29.630 9.40 0.00 0.00 2.57
3756 9183 6.773976 TCATGAACATCTTTTTATGGACCC 57.226 37.500 0.00 0.00 0.00 4.46
3790 9218 6.521151 TTTGCAAAACAAAATTGGGAACAT 57.479 29.167 10.02 0.00 45.22 2.71
3804 9232 5.931724 ACCCAACAATATAGCTTTGCAAAAC 59.068 36.000 13.84 9.04 0.00 2.43


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

AutoCloner maintained by Alex Coulton.