Multiple sequence alignment - TraesCS2B01G189500

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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 TraesCS2B01G189500 chr2B 100.000 4030 0 0 1 4030 165114123 165110094 0.000000e+00 7443.0
1 TraesCS2B01G189500 chr2B 87.569 724 79 10 1875 2594 43614780 43615496 0.000000e+00 828.0
2 TraesCS2B01G189500 chr2B 88.235 680 64 12 1924 2597 43630853 43630184 0.000000e+00 798.0
3 TraesCS2B01G189500 chr2B 86.874 419 41 10 2735 3141 43630062 43629646 1.320000e-124 457.0
4 TraesCS2B01G189500 chr2B 89.735 302 31 0 2734 3035 43615633 43615934 1.760000e-103 387.0
5 TraesCS2B01G189500 chr2B 83.125 320 30 14 11 314 793259816 793260127 1.850000e-68 270.0
6 TraesCS2B01G189500 chr2B 81.818 319 55 2 3715 4030 13061613 13061295 8.590000e-67 265.0
7 TraesCS2B01G189500 chr2B 78.626 393 61 19 799 1183 43613692 43614069 5.210000e-59 239.0
8 TraesCS2B01G189500 chr2B 82.000 200 32 4 1017 1213 43631804 43631606 2.490000e-37 167.0
9 TraesCS2B01G189500 chr2A 94.454 1713 83 5 1591 3293 116001477 115999767 0.000000e+00 2627.0
10 TraesCS2B01G189500 chr2A 91.103 798 61 10 781 1577 116002366 116001578 0.000000e+00 1072.0
11 TraesCS2B01G189500 chr2A 85.950 726 82 17 1880 2597 29878418 29877705 0.000000e+00 758.0
12 TraesCS2B01G189500 chr2A 86.957 690 64 17 1923 2592 29871287 29871970 0.000000e+00 752.0
13 TraesCS2B01G189500 chr2A 85.748 421 46 10 2734 3141 29877569 29877150 2.220000e-117 433.0
14 TraesCS2B01G189500 chr2A 90.728 302 28 0 2734 3035 29872083 29872384 1.740000e-108 403.0
15 TraesCS2B01G189500 chr2A 78.719 437 75 12 3610 4030 712966682 712967116 3.970000e-70 276.0
16 TraesCS2B01G189500 chr2A 78.523 447 74 13 3578 4008 412458917 412459357 1.430000e-69 274.0
17 TraesCS2B01G189500 chr2A 79.370 349 53 17 799 1138 29869855 29870193 1.130000e-55 228.0
18 TraesCS2B01G189500 chr2A 86.010 193 24 3 1017 1208 29879306 29879116 1.900000e-48 204.0
19 TraesCS2B01G189500 chr2A 81.148 122 21 2 3887 4007 192766304 192766424 3.320000e-16 97.1
20 TraesCS2B01G189500 chr2D 95.189 1455 50 6 1808 3254 114548616 114547174 0.000000e+00 2281.0
21 TraesCS2B01G189500 chr2D 92.406 935 58 11 670 1595 114549758 114548828 0.000000e+00 1321.0
22 TraesCS2B01G189500 chr2D 89.443 682 57 14 1923 2597 27763014 27762341 0.000000e+00 846.0
23 TraesCS2B01G189500 chr2D 86.401 728 82 16 1877 2594 27758418 27759138 0.000000e+00 780.0
24 TraesCS2B01G189500 chr2D 86.321 424 39 13 2735 3141 27762220 27761799 1.030000e-120 444.0
25 TraesCS2B01G189500 chr2D 91.391 302 26 0 2734 3035 27759251 27759552 8.060000e-112 414.0
26 TraesCS2B01G189500 chr2D 78.834 463 66 16 3506 3940 532196177 532196635 2.370000e-72 283.0
27 TraesCS2B01G189500 chr2D 94.400 125 5 2 1640 1763 114548733 114548610 1.480000e-44 191.0
28 TraesCS2B01G189500 chr2D 77.811 338 54 17 799 1130 27756950 27757272 5.320000e-44 189.0
29 TraesCS2B01G189500 chr2D 85.119 168 24 1 1041 1208 27764103 27763937 1.930000e-38 171.0
30 TraesCS2B01G189500 chr2D 94.444 36 2 0 3304 3339 388170263 388170298 5.630000e-04 56.5
31 TraesCS2B01G189500 chr2D 100.000 29 0 0 3416 3444 619141477 619141449 2.000000e-03 54.7
32 TraesCS2B01G189500 chr5D 85.185 513 60 11 95 598 381560453 381560958 2.780000e-141 512.0
33 TraesCS2B01G189500 chr5D 84.333 517 56 18 91 599 418944054 418944553 2.180000e-132 483.0
34 TraesCS2B01G189500 chr5D 79.359 562 70 18 3499 4030 393558140 393557595 1.780000e-93 353.0
35 TraesCS2B01G189500 chr7B 83.908 522 56 20 96 596 24003758 24004272 1.310000e-129 473.0
36 TraesCS2B01G189500 chr5B 83.626 513 65 14 96 596 429428182 429427677 7.890000e-127 464.0
37 TraesCS2B01G189500 chr5B 83.237 519 69 13 95 597 569216436 569215920 1.020000e-125 460.0
38 TraesCS2B01G189500 chr5B 83.044 519 60 19 96 596 696481466 696480958 2.860000e-121 446.0
39 TraesCS2B01G189500 chr5B 82.500 520 69 14 96 596 128344968 128344452 1.720000e-118 436.0
40 TraesCS2B01G189500 chr5B 80.519 231 18 13 11 231 611677093 611676880 6.980000e-33 152.0
41 TraesCS2B01G189500 chr1B 83.268 514 66 16 95 596 579006065 579006570 4.750000e-124 455.0
42 TraesCS2B01G189500 chr1B 81.712 514 74 16 96 596 568876286 568876792 1.040000e-110 411.0
43 TraesCS2B01G189500 chr1B 80.278 360 33 17 11 360 500704931 500704600 1.870000e-58 237.0
44 TraesCS2B01G189500 chr1B 75.200 250 57 4 3763 4010 4995290 4995044 3.290000e-21 113.0
45 TraesCS2B01G189500 chr6A 78.269 566 90 22 3495 4030 115337939 115337377 2.320000e-87 333.0
46 TraesCS2B01G189500 chr6A 80.420 143 24 4 3890 4030 48522575 48522715 5.510000e-19 106.0
47 TraesCS2B01G189500 chr3D 77.577 553 83 17 3495 4010 570144071 570143523 3.050000e-76 296.0
48 TraesCS2B01G189500 chr3D 78.295 129 16 6 3775 3892 34727767 34727894 5.590000e-09 73.1
49 TraesCS2B01G189500 chr3D 95.000 40 2 0 3888 3927 343492409 343492370 3.360000e-06 63.9
50 TraesCS2B01G189500 chr1D 83.916 286 43 3 3748 4030 362513781 362513496 1.850000e-68 270.0
51 TraesCS2B01G189500 chr6B 81.016 374 34 18 1 362 669505329 669504981 3.090000e-66 263.0
52 TraesCS2B01G189500 chr4A 80.697 373 39 18 1 362 669802380 669802730 4.000000e-65 259.0
53 TraesCS2B01G189500 chr4B 79.784 371 46 17 2 362 500505944 500506295 4.020000e-60 243.0
54 TraesCS2B01G189500 chr4B 81.818 275 22 13 1 265 21365193 21365449 5.280000e-49 206.0
55 TraesCS2B01G189500 chr3B 80.223 359 31 19 1 349 169184898 169185226 2.420000e-57 233.0
56 TraesCS2B01G189500 chr3B 81.369 263 19 15 1 252 171698956 171699199 1.910000e-43 187.0
57 TraesCS2B01G189500 chr3A 75.830 542 86 20 3504 4030 144326337 144326848 2.420000e-57 233.0
58 TraesCS2B01G189500 chr3A 100.000 30 0 0 3416 3445 698147018 698147047 5.630000e-04 56.5
59 TraesCS2B01G189500 chr4D 75.741 540 71 33 3506 4010 41075808 41076322 2.440000e-52 217.0
60 TraesCS2B01G189500 chr4D 80.368 163 30 2 3851 4012 273111299 273111460 5.470000e-24 122.0
61 TraesCS2B01G189500 chr7D 81.356 236 26 10 3729 3948 601690152 601689919 4.140000e-40 176.0
62 TraesCS2B01G189500 chr5A 84.932 73 11 0 3857 3929 119552946 119553018 1.550000e-09 75.0
63 TraesCS2B01G189500 chr5A 92.683 41 2 1 3405 3445 643571222 643571183 1.560000e-04 58.4
64 TraesCS2B01G189500 chr1A 100.000 29 0 0 3417 3445 343630848 343630820 2.000000e-03 54.7
65 TraesCS2B01G189500 chr1A 100.000 28 0 0 3418 3445 445550229 445550202 7.000000e-03 52.8
66 TraesCS2B01G189500 chr1A 100.000 28 0 0 3300 3327 500967351 500967378 7.000000e-03 52.8


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 TraesCS2B01G189500 chr2B 165110094 165114123 4029 True 7443.000000 7443 100.000000 1 4030 1 chr2B.!!$R2 4029
1 TraesCS2B01G189500 chr2B 43613692 43615934 2242 False 484.666667 828 85.310000 799 3035 3 chr2B.!!$F2 2236
2 TraesCS2B01G189500 chr2B 43629646 43631804 2158 True 474.000000 798 85.703000 1017 3141 3 chr2B.!!$R3 2124
3 TraesCS2B01G189500 chr2A 115999767 116002366 2599 True 1849.500000 2627 92.778500 781 3293 2 chr2A.!!$R2 2512
4 TraesCS2B01G189500 chr2A 29877150 29879306 2156 True 465.000000 758 85.902667 1017 3141 3 chr2A.!!$R1 2124
5 TraesCS2B01G189500 chr2A 29869855 29872384 2529 False 461.000000 752 85.685000 799 3035 3 chr2A.!!$F4 2236
6 TraesCS2B01G189500 chr2D 114547174 114549758 2584 True 1264.333333 2281 93.998333 670 3254 3 chr2D.!!$R3 2584
7 TraesCS2B01G189500 chr2D 27761799 27764103 2304 True 487.000000 846 86.961000 1041 3141 3 chr2D.!!$R2 2100
8 TraesCS2B01G189500 chr2D 27756950 27759552 2602 False 461.000000 780 85.201000 799 3035 3 chr2D.!!$F3 2236
9 TraesCS2B01G189500 chr5D 381560453 381560958 505 False 512.000000 512 85.185000 95 598 1 chr5D.!!$F1 503
10 TraesCS2B01G189500 chr5D 393557595 393558140 545 True 353.000000 353 79.359000 3499 4030 1 chr5D.!!$R1 531
11 TraesCS2B01G189500 chr7B 24003758 24004272 514 False 473.000000 473 83.908000 96 596 1 chr7B.!!$F1 500
12 TraesCS2B01G189500 chr5B 429427677 429428182 505 True 464.000000 464 83.626000 96 596 1 chr5B.!!$R2 500
13 TraesCS2B01G189500 chr5B 569215920 569216436 516 True 460.000000 460 83.237000 95 597 1 chr5B.!!$R3 502
14 TraesCS2B01G189500 chr5B 696480958 696481466 508 True 446.000000 446 83.044000 96 596 1 chr5B.!!$R5 500
15 TraesCS2B01G189500 chr5B 128344452 128344968 516 True 436.000000 436 82.500000 96 596 1 chr5B.!!$R1 500
16 TraesCS2B01G189500 chr1B 579006065 579006570 505 False 455.000000 455 83.268000 95 596 1 chr1B.!!$F2 501
17 TraesCS2B01G189500 chr1B 568876286 568876792 506 False 411.000000 411 81.712000 96 596 1 chr1B.!!$F1 500
18 TraesCS2B01G189500 chr6A 115337377 115337939 562 True 333.000000 333 78.269000 3495 4030 1 chr6A.!!$R1 535
19 TraesCS2B01G189500 chr3D 570143523 570144071 548 True 296.000000 296 77.577000 3495 4010 1 chr3D.!!$R2 515
20 TraesCS2B01G189500 chr3A 144326337 144326848 511 False 233.000000 233 75.830000 3504 4030 1 chr3A.!!$F1 526
21 TraesCS2B01G189500 chr4D 41075808 41076322 514 False 217.000000 217 75.741000 3506 4010 1 chr4D.!!$F1 504

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
651 737 0.035458 AGCGACAACAGCTAGCCTTT 59.965 50.0 12.13 1.28 44.05 3.11 F
1024 1129 0.824759 GGTACGCACCTTCTCCTCAT 59.175 55.0 0.00 0.00 42.11 2.90 F
1088 1194 0.865769 ATTCGTGTGGTTCTTGCGTC 59.134 50.0 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1971 0.597637 ACCTCAACGCTGACAGAACG 60.598 55.00 6.65 3.65 0.00 3.95 R
2798 3801 0.750911 GGATCTTGGGAGCCTTGCTG 60.751 60.00 0.00 0.00 44.03 4.41 R
3113 4126 5.099042 ACAAACTCCAGCCGATAAATACT 57.901 39.13 0.00 0.00 0.00 2.12 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
35 36 4.737353 AAACAGACGAAATAACCGAACC 57.263 40.909 0.00 0.00 0.00 3.62
36 37 2.331194 ACAGACGAAATAACCGAACCG 58.669 47.619 0.00 0.00 0.00 4.44
53 54 1.871077 CGGTAGCACGGGTTTTTCC 59.129 57.895 0.00 0.00 0.00 3.13
73 74 2.347490 TCTGAAAGAGGCACGCCC 59.653 61.111 3.95 0.00 38.67 6.13
74 75 3.121030 CTGAAAGAGGCACGCCCG 61.121 66.667 3.95 0.00 39.21 6.13
75 76 3.883744 CTGAAAGAGGCACGCCCGT 62.884 63.158 3.95 0.00 39.21 5.28
87 88 4.373116 GCCCGTGCCTCTGACGAA 62.373 66.667 0.00 0.00 39.21 3.85
88 89 2.342279 CCCGTGCCTCTGACGAAA 59.658 61.111 0.00 0.00 39.21 3.46
89 90 1.079127 CCCGTGCCTCTGACGAAAT 60.079 57.895 0.00 0.00 39.21 2.17
90 91 1.084370 CCCGTGCCTCTGACGAAATC 61.084 60.000 0.00 0.00 39.21 2.17
91 92 0.389817 CCGTGCCTCTGACGAAATCA 60.390 55.000 0.00 0.00 39.21 2.57
92 93 1.645034 CGTGCCTCTGACGAAATCAT 58.355 50.000 0.00 0.00 39.21 2.45
93 94 2.481276 CCGTGCCTCTGACGAAATCATA 60.481 50.000 0.00 0.00 39.21 2.15
147 148 1.372997 GCAAAGCCGTGACTCTCGA 60.373 57.895 2.07 0.00 0.00 4.04
315 333 4.008933 GGCACAGCCCTGACTCGT 62.009 66.667 1.69 0.00 44.06 4.18
328 371 4.124238 CCTGACTCGTGAAAGTAAAACCA 58.876 43.478 0.00 0.00 0.00 3.67
359 402 1.531578 GGAAGCAAAACCGTGACTCTC 59.468 52.381 0.00 0.00 0.00 3.20
364 407 1.531149 CAAAACCGTGACTCTCGCAAT 59.469 47.619 0.00 0.00 0.00 3.56
368 411 4.585955 AACCGTGACTCTCGCAATATAT 57.414 40.909 0.00 0.00 0.00 0.86
432 505 3.134021 TGGAAAACCAAAACGTCGAAC 57.866 42.857 0.00 0.00 0.00 3.95
433 506 2.159407 TGGAAAACCAAAACGTCGAACC 60.159 45.455 0.00 0.00 0.00 3.62
434 507 2.453080 GAAAACCAAAACGTCGAACCC 58.547 47.619 0.00 0.00 0.00 4.11
438 511 1.102222 CCAAAACGTCGAACCCCCAA 61.102 55.000 0.00 0.00 0.00 4.12
598 684 4.106197 CGCTCGTTAATTAGTTGCTCTCT 58.894 43.478 0.00 0.00 0.00 3.10
599 685 4.563184 CGCTCGTTAATTAGTTGCTCTCTT 59.437 41.667 0.00 0.00 0.00 2.85
600 686 5.062308 CGCTCGTTAATTAGTTGCTCTCTTT 59.938 40.000 0.00 0.00 0.00 2.52
601 687 6.401153 CGCTCGTTAATTAGTTGCTCTCTTTT 60.401 38.462 0.00 0.00 0.00 2.27
602 688 7.298854 GCTCGTTAATTAGTTGCTCTCTTTTT 58.701 34.615 0.00 0.00 0.00 1.94
646 732 3.878086 TTTTTGAGCGACAACAGCTAG 57.122 42.857 0.00 0.00 46.13 3.42
647 733 1.148310 TTTGAGCGACAACAGCTAGC 58.852 50.000 6.62 6.62 46.13 3.42
648 734 0.670546 TTGAGCGACAACAGCTAGCC 60.671 55.000 12.13 0.00 46.13 3.93
649 735 1.216710 GAGCGACAACAGCTAGCCT 59.783 57.895 12.13 0.00 46.13 4.58
650 736 0.390472 GAGCGACAACAGCTAGCCTT 60.390 55.000 12.13 0.00 46.13 4.35
651 737 0.035458 AGCGACAACAGCTAGCCTTT 59.965 50.000 12.13 1.28 44.05 3.11
652 738 0.875059 GCGACAACAGCTAGCCTTTT 59.125 50.000 12.13 0.00 0.00 2.27
653 739 1.266989 GCGACAACAGCTAGCCTTTTT 59.733 47.619 12.13 0.00 0.00 1.94
682 768 7.448748 ACAAACAGCTACTAGGTTTTATTGG 57.551 36.000 0.00 0.00 32.79 3.16
746 832 2.744823 CGACAACAGCATAGGCCCATTA 60.745 50.000 0.00 0.00 42.56 1.90
771 857 4.120589 CACTCTAGGCCGGTTTAATCTTC 58.879 47.826 1.90 0.00 0.00 2.87
781 867 5.413523 GCCGGTTTAATCTTCTCCAACTAAA 59.586 40.000 1.90 0.00 0.00 1.85
782 868 6.622245 GCCGGTTTAATCTTCTCCAACTAAAC 60.622 42.308 1.90 0.00 0.00 2.01
869 955 4.377760 TTCTCCCCGACGCCTCCT 62.378 66.667 0.00 0.00 0.00 3.69
1024 1129 0.824759 GGTACGCACCTTCTCCTCAT 59.175 55.000 0.00 0.00 42.11 2.90
1060 1166 1.466167 GATGTGATCTGCGTTTGTGCT 59.534 47.619 0.00 0.00 35.36 4.40
1088 1194 0.865769 ATTCGTGTGGTTCTTGCGTC 59.134 50.000 0.00 0.00 0.00 5.19
1228 1661 3.825014 TGTAGTCTAGTCACCACACTTCC 59.175 47.826 0.00 0.00 0.00 3.46
1230 1663 3.158676 AGTCTAGTCACCACACTTCCTC 58.841 50.000 0.00 0.00 0.00 3.71
1240 1673 3.181454 ACCACACTTCCTCTCGAAATTGT 60.181 43.478 0.00 0.00 30.30 2.71
1283 1716 2.737544 TGTGGTCGGCCTGTATTAGTA 58.262 47.619 7.97 0.00 35.27 1.82
1306 1740 5.471556 TGGTGGACTCGTTAAATCTGTTA 57.528 39.130 0.00 0.00 0.00 2.41
1309 1743 5.522824 GGTGGACTCGTTAAATCTGTTATCC 59.477 44.000 0.00 0.00 0.00 2.59
1314 1751 6.106673 ACTCGTTAAATCTGTTATCCTGTGG 58.893 40.000 0.00 0.00 0.00 4.17
1344 1781 1.961277 GGCGTGTTGACTGTGGAGG 60.961 63.158 0.00 0.00 0.00 4.30
1368 1807 7.819900 AGGATCTGTTCTGTTACATTGTTAGAC 59.180 37.037 0.00 0.00 0.00 2.59
1415 1876 7.019774 TGTGATTGCTGCTCTTATAAATGTC 57.980 36.000 0.00 0.00 0.00 3.06
1427 1888 6.958255 TCTTATAAATGTCATGGTGCGATTG 58.042 36.000 0.00 0.00 0.00 2.67
1454 1915 6.024552 TCTTGTTGAGAACTTTTGCTGTTT 57.975 33.333 0.00 0.00 0.00 2.83
1510 1971 5.808030 GCTGTTGTAGAGAACTAGAATGGAC 59.192 44.000 0.00 0.00 35.06 4.02
1559 2020 8.971321 TGTTCTTGTAACAGTTTCGATAACTAC 58.029 33.333 11.08 8.07 0.00 2.73
1571 2048 7.968956 AGTTTCGATAACTACACTATGTCACAG 59.031 37.037 10.11 0.00 0.00 3.66
1655 2276 3.747708 GCATAGAAACTACACCCATCCCC 60.748 52.174 0.00 0.00 0.00 4.81
1716 2337 8.763356 GCTAGTTATGTCTGATGATTTTCTCTG 58.237 37.037 0.00 0.00 0.00 3.35
1763 2445 7.226720 ACGAATAGTTTCAACTTCTTGTGATGT 59.773 33.333 0.00 0.00 40.37 3.06
1786 2470 7.881142 TGTTCAGTACTGATAATTTTTGGGTG 58.119 34.615 25.68 0.00 39.64 4.61
1792 2477 9.920946 AGTACTGATAATTTTTGGGTGACATAT 57.079 29.630 0.00 0.00 0.00 1.78
2264 3231 4.739046 ACTTCTTGCAGACATTTTCTCG 57.261 40.909 0.00 0.00 28.96 4.04
2265 3232 3.499918 ACTTCTTGCAGACATTTTCTCGG 59.500 43.478 0.00 0.00 28.96 4.63
2594 3561 2.033801 CACAAACAAGAAGGGTGAGCTG 59.966 50.000 0.00 0.00 0.00 4.24
2708 3706 1.466558 GCTTGTCTTGAGCCTGCTAAC 59.533 52.381 0.00 0.00 34.06 2.34
2718 3716 4.382291 TGAGCCTGCTAACGAAAAACTTA 58.618 39.130 0.00 0.00 0.00 2.24
2719 3717 4.817464 TGAGCCTGCTAACGAAAAACTTAA 59.183 37.500 0.00 0.00 0.00 1.85
2798 3801 2.396590 TATTTCCAGGCAAGACCGTC 57.603 50.000 0.00 0.00 46.52 4.79
2834 3837 2.310233 CCAGCGTCTTGTGACACCG 61.310 63.158 2.45 0.17 43.06 4.94
2987 3990 1.993653 CATGGCCAAGAGGAGGTCA 59.006 57.895 10.96 0.00 46.19 4.02
3113 4126 6.434018 TGATGATATTTTGCGTGAACATGA 57.566 33.333 0.00 0.00 0.00 3.07
3208 4223 9.199982 CCAAGTATTATCATCCATTTGAAATGC 57.800 33.333 12.26 0.00 0.00 3.56
3213 4228 8.674925 ATTATCATCCATTTGAAATGCCCTAT 57.325 30.769 12.26 5.99 0.00 2.57
3221 4236 9.432982 TCCATTTGAAATGCCCTATTACTTTAT 57.567 29.630 12.26 0.00 0.00 1.40
3284 4302 7.959658 ATATTCTGAATGAAATGTGTCCCAA 57.040 32.000 13.01 0.00 38.29 4.12
3285 4303 6.862469 ATTCTGAATGAAATGTGTCCCAAT 57.138 33.333 1.31 0.00 38.29 3.16
3287 4305 6.028146 TCTGAATGAAATGTGTCCCAATTG 57.972 37.500 0.00 0.00 0.00 2.32
3293 4311 9.434420 GAATGAAATGTGTCCCAATTGAAATTA 57.566 29.630 7.12 0.00 0.00 1.40
3294 4312 9.962809 AATGAAATGTGTCCCAATTGAAATTAT 57.037 25.926 7.12 0.00 0.00 1.28
3328 4346 7.747155 ATGAATCTCTATGCAAGATCAAAGG 57.253 36.000 0.00 0.00 32.29 3.11
3329 4347 6.892485 TGAATCTCTATGCAAGATCAAAGGA 58.108 36.000 0.00 0.00 32.29 3.36
3330 4348 7.341030 TGAATCTCTATGCAAGATCAAAGGAA 58.659 34.615 0.00 0.00 32.29 3.36
3331 4349 7.997223 TGAATCTCTATGCAAGATCAAAGGAAT 59.003 33.333 0.00 0.00 32.29 3.01
3332 4350 9.499479 GAATCTCTATGCAAGATCAAAGGAATA 57.501 33.333 0.00 0.00 32.29 1.75
3336 4354 9.381033 CTCTATGCAAGATCAAAGGAATATAGG 57.619 37.037 0.00 0.00 32.41 2.57
3337 4355 9.104713 TCTATGCAAGATCAAAGGAATATAGGA 57.895 33.333 0.00 0.00 0.00 2.94
3338 4356 9.902684 CTATGCAAGATCAAAGGAATATAGGAT 57.097 33.333 0.00 0.00 0.00 3.24
3341 4359 9.730705 TGCAAGATCAAAGGAATATAGGATTAG 57.269 33.333 0.00 0.00 0.00 1.73
3342 4360 9.171877 GCAAGATCAAAGGAATATAGGATTAGG 57.828 37.037 0.00 0.00 0.00 2.69
3345 4363 9.621239 AGATCAAAGGAATATAGGATTAGGACA 57.379 33.333 0.00 0.00 0.00 4.02
3351 4369 9.543231 AAGGAATATAGGATTAGGACATAACGA 57.457 33.333 0.00 0.00 0.00 3.85
3352 4370 9.191479 AGGAATATAGGATTAGGACATAACGAG 57.809 37.037 0.00 0.00 0.00 4.18
3353 4371 8.968969 GGAATATAGGATTAGGACATAACGAGT 58.031 37.037 0.00 0.00 0.00 4.18
3355 4373 9.756571 AATATAGGATTAGGACATAACGAGTCT 57.243 33.333 0.00 0.00 36.29 3.24
3356 4374 9.756571 ATATAGGATTAGGACATAACGAGTCTT 57.243 33.333 0.00 0.00 36.29 3.01
3357 4375 6.150396 AGGATTAGGACATAACGAGTCTTG 57.850 41.667 0.00 0.00 36.29 3.02
3358 4376 5.892119 AGGATTAGGACATAACGAGTCTTGA 59.108 40.000 0.00 0.00 36.29 3.02
3359 4377 5.978322 GGATTAGGACATAACGAGTCTTGAC 59.022 44.000 0.00 0.00 36.29 3.18
3360 4378 6.183360 GGATTAGGACATAACGAGTCTTGACT 60.183 42.308 2.59 2.59 36.29 3.41
3361 4379 4.442375 AGGACATAACGAGTCTTGACTG 57.558 45.455 8.11 3.80 36.29 3.51
3362 4380 4.079970 AGGACATAACGAGTCTTGACTGA 58.920 43.478 8.11 0.00 36.29 3.41
3363 4381 4.707448 AGGACATAACGAGTCTTGACTGAT 59.293 41.667 8.11 0.00 36.29 2.90
3364 4382 5.038033 GGACATAACGAGTCTTGACTGATC 58.962 45.833 8.11 0.00 36.29 2.92
3365 4383 5.000012 ACATAACGAGTCTTGACTGATCC 58.000 43.478 8.11 0.00 0.00 3.36
3366 4384 4.707448 ACATAACGAGTCTTGACTGATCCT 59.293 41.667 8.11 0.00 0.00 3.24
3367 4385 5.186021 ACATAACGAGTCTTGACTGATCCTT 59.814 40.000 8.11 0.00 0.00 3.36
3368 4386 3.584406 ACGAGTCTTGACTGATCCTTG 57.416 47.619 8.11 0.00 0.00 3.61
3369 4387 2.894126 ACGAGTCTTGACTGATCCTTGT 59.106 45.455 8.11 0.00 0.00 3.16
3370 4388 3.322254 ACGAGTCTTGACTGATCCTTGTT 59.678 43.478 8.11 0.00 0.00 2.83
3371 4389 4.202264 ACGAGTCTTGACTGATCCTTGTTT 60.202 41.667 8.11 0.00 0.00 2.83
3372 4390 5.010719 ACGAGTCTTGACTGATCCTTGTTTA 59.989 40.000 8.11 0.00 0.00 2.01
3373 4391 6.102663 CGAGTCTTGACTGATCCTTGTTTAT 58.897 40.000 8.11 0.00 0.00 1.40
3374 4392 7.093902 ACGAGTCTTGACTGATCCTTGTTTATA 60.094 37.037 8.11 0.00 0.00 0.98
3375 4393 7.759886 CGAGTCTTGACTGATCCTTGTTTATAA 59.240 37.037 8.11 0.00 0.00 0.98
3376 4394 9.606631 GAGTCTTGACTGATCCTTGTTTATAAT 57.393 33.333 8.11 0.00 0.00 1.28
3377 4395 9.388506 AGTCTTGACTGATCCTTGTTTATAATG 57.611 33.333 2.11 0.00 0.00 1.90
3378 4396 9.167311 GTCTTGACTGATCCTTGTTTATAATGT 57.833 33.333 0.00 0.00 0.00 2.71
3441 4459 8.621532 AACAGTTTTGCTAAATCACATCTAGA 57.378 30.769 0.00 0.00 0.00 2.43
3442 4460 8.798859 ACAGTTTTGCTAAATCACATCTAGAT 57.201 30.769 0.00 0.00 0.00 1.98
3443 4461 8.671921 ACAGTTTTGCTAAATCACATCTAGATG 58.328 33.333 27.63 27.63 44.15 2.90
3460 4478 9.689976 CATCTAGATGTCCTATGACTACTTTTG 57.310 37.037 22.42 0.00 42.28 2.44
3461 4479 8.824756 TCTAGATGTCCTATGACTACTTTTGT 57.175 34.615 0.00 0.00 42.28 2.83
3462 4480 8.904834 TCTAGATGTCCTATGACTACTTTTGTC 58.095 37.037 0.00 0.00 42.28 3.18
3463 4481 7.726033 AGATGTCCTATGACTACTTTTGTCT 57.274 36.000 0.00 0.00 42.28 3.41
3464 4482 8.140112 AGATGTCCTATGACTACTTTTGTCTT 57.860 34.615 0.00 0.00 42.28 3.01
3465 4483 8.598041 AGATGTCCTATGACTACTTTTGTCTTT 58.402 33.333 0.00 0.00 42.28 2.52
3466 4484 9.220767 GATGTCCTATGACTACTTTTGTCTTTT 57.779 33.333 0.00 0.00 42.28 2.27
3467 4485 8.603242 TGTCCTATGACTACTTTTGTCTTTTC 57.397 34.615 0.00 0.00 42.28 2.29
3468 4486 7.660208 TGTCCTATGACTACTTTTGTCTTTTCC 59.340 37.037 0.00 0.00 42.28 3.13
3469 4487 7.119407 GTCCTATGACTACTTTTGTCTTTTCCC 59.881 40.741 0.00 0.00 38.53 3.97
3470 4488 7.017254 TCCTATGACTACTTTTGTCTTTTCCCT 59.983 37.037 0.00 0.00 35.63 4.20
3471 4489 7.665974 CCTATGACTACTTTTGTCTTTTCCCTT 59.334 37.037 0.00 0.00 35.63 3.95
3472 4490 7.898014 ATGACTACTTTTGTCTTTTCCCTTT 57.102 32.000 0.00 0.00 35.63 3.11
3473 4491 7.712204 TGACTACTTTTGTCTTTTCCCTTTT 57.288 32.000 0.00 0.00 35.63 2.27
3474 4492 8.129496 TGACTACTTTTGTCTTTTCCCTTTTT 57.871 30.769 0.00 0.00 35.63 1.94
3475 4493 8.248253 TGACTACTTTTGTCTTTTCCCTTTTTC 58.752 33.333 0.00 0.00 35.63 2.29
3476 4494 8.362464 ACTACTTTTGTCTTTTCCCTTTTTCT 57.638 30.769 0.00 0.00 0.00 2.52
3477 4495 8.812972 ACTACTTTTGTCTTTTCCCTTTTTCTT 58.187 29.630 0.00 0.00 0.00 2.52
3478 4496 9.653287 CTACTTTTGTCTTTTCCCTTTTTCTTT 57.347 29.630 0.00 0.00 0.00 2.52
3479 4497 8.547967 ACTTTTGTCTTTTCCCTTTTTCTTTC 57.452 30.769 0.00 0.00 0.00 2.62
3480 4498 8.375506 ACTTTTGTCTTTTCCCTTTTTCTTTCT 58.624 29.630 0.00 0.00 0.00 2.52
3481 4499 9.869757 CTTTTGTCTTTTCCCTTTTTCTTTCTA 57.130 29.630 0.00 0.00 0.00 2.10
3531 4550 4.028131 ACCTAACCGATCCTCAATACACA 58.972 43.478 0.00 0.00 0.00 3.72
3537 4556 5.844004 ACCGATCCTCAATACACATTAGTC 58.156 41.667 0.00 0.00 0.00 2.59
3576 4596 0.035820 ACCGCCGCAAATCTTCCTAA 60.036 50.000 0.00 0.00 0.00 2.69
3581 4612 1.737793 CCGCAAATCTTCCTAACGCTT 59.262 47.619 0.00 0.00 0.00 4.68
3646 4682 0.686112 CTCCTCTTCTCCCCTTCGCT 60.686 60.000 0.00 0.00 0.00 4.93
3648 4684 0.972983 CCTCTTCTCCCCTTCGCTCA 60.973 60.000 0.00 0.00 0.00 4.26
3687 4749 0.921256 CCCCTTCTCCTCCCAATGGT 60.921 60.000 0.00 0.00 0.00 3.55
3700 4762 0.253044 CAATGGTCGGATGAGGTGGT 59.747 55.000 0.00 0.00 0.00 4.16
3703 4765 1.125093 TGGTCGGATGAGGTGGTTGT 61.125 55.000 0.00 0.00 0.00 3.32
3705 4767 1.485066 GGTCGGATGAGGTGGTTGTAT 59.515 52.381 0.00 0.00 0.00 2.29
3713 4775 0.838987 AGGTGGTTGTATGTCCCCGT 60.839 55.000 0.00 0.00 0.00 5.28
3722 4784 2.971095 TATGTCCCCGTCGCCGATCT 62.971 60.000 0.00 0.00 35.63 2.75
3737 4799 0.460284 GATCTGCAACGTGGATCCGT 60.460 55.000 7.39 0.00 44.23 4.69
3740 4802 2.742372 GCAACGTGGATCCGTGCT 60.742 61.111 17.60 0.00 41.65 4.40
3745 4807 2.124570 GTGGATCCGTGCTGCCAT 60.125 61.111 7.39 0.00 32.26 4.40
3867 4939 2.642254 CGCCAACGAGGACCTACCA 61.642 63.158 0.00 0.00 43.93 3.25
3936 5016 1.479709 CGAGAGACCCACAAGAGGAT 58.520 55.000 0.00 0.00 0.00 3.24
3948 5028 0.042131 AAGAGGATGTGGGTCGGGTA 59.958 55.000 0.00 0.00 0.00 3.69
3961 5041 2.046604 GGGTAGTTCCACACGGCC 60.047 66.667 0.00 0.00 38.11 6.13
3965 5045 1.904865 TAGTTCCACACGGCCGAGT 60.905 57.895 35.90 29.23 0.00 4.18
3969 5049 4.657824 CCACACGGCCGAGTTCGT 62.658 66.667 35.90 17.09 40.49 3.85
3990 5070 1.386525 GCCATGGAGTACGACCGGTA 61.387 60.000 18.40 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.513376 GGTTCGGTTATTTCGTCTGTTTTT 58.487 37.500 0.00 0.00 0.00 1.94
13 14 4.318974 CGGTTCGGTTATTTCGTCTGTTTT 60.319 41.667 0.00 0.00 0.00 2.43
14 15 3.184986 CGGTTCGGTTATTTCGTCTGTTT 59.815 43.478 0.00 0.00 0.00 2.83
15 16 2.733026 CGGTTCGGTTATTTCGTCTGTT 59.267 45.455 0.00 0.00 0.00 3.16
16 17 2.331194 CGGTTCGGTTATTTCGTCTGT 58.669 47.619 0.00 0.00 0.00 3.41
17 18 1.657094 CCGGTTCGGTTATTTCGTCTG 59.343 52.381 0.00 0.00 42.73 3.51
18 19 2.000429 CCGGTTCGGTTATTTCGTCT 58.000 50.000 0.00 0.00 42.73 4.18
30 31 3.578515 AACCCGTGCTACCGGTTCG 62.579 63.158 15.04 13.01 46.66 3.95
31 32 0.886043 AAAACCCGTGCTACCGGTTC 60.886 55.000 15.04 5.92 46.66 3.62
32 33 0.466007 AAAAACCCGTGCTACCGGTT 60.466 50.000 15.04 0.00 46.66 4.44
33 34 0.886043 GAAAAACCCGTGCTACCGGT 60.886 55.000 13.98 13.98 46.66 5.28
35 36 1.871077 GGAAAAACCCGTGCTACCG 59.129 57.895 0.00 0.00 0.00 4.02
45 46 3.005897 GCCTCTTTCAGAAGGGAAAAACC 59.994 47.826 0.00 0.00 35.21 3.27
46 47 3.636764 TGCCTCTTTCAGAAGGGAAAAAC 59.363 43.478 0.00 0.00 35.21 2.43
47 48 3.636764 GTGCCTCTTTCAGAAGGGAAAAA 59.363 43.478 0.00 0.00 35.21 1.94
48 49 3.222603 GTGCCTCTTTCAGAAGGGAAAA 58.777 45.455 0.00 0.00 35.21 2.29
49 50 2.810400 CGTGCCTCTTTCAGAAGGGAAA 60.810 50.000 0.00 0.00 35.21 3.13
50 51 1.270839 CGTGCCTCTTTCAGAAGGGAA 60.271 52.381 0.00 0.00 35.21 3.97
51 52 0.321671 CGTGCCTCTTTCAGAAGGGA 59.678 55.000 0.00 0.00 35.21 4.20
52 53 1.301677 GCGTGCCTCTTTCAGAAGGG 61.302 60.000 0.00 0.00 33.56 3.95
53 54 1.301677 GGCGTGCCTCTTTCAGAAGG 61.302 60.000 2.98 0.00 33.56 3.46
54 55 1.301677 GGGCGTGCCTCTTTCAGAAG 61.302 60.000 11.25 0.00 36.10 2.85
55 56 1.302511 GGGCGTGCCTCTTTCAGAA 60.303 57.895 11.25 0.00 36.10 3.02
56 57 2.347490 GGGCGTGCCTCTTTCAGA 59.653 61.111 11.25 0.00 36.10 3.27
57 58 3.121030 CGGGCGTGCCTCTTTCAG 61.121 66.667 11.25 0.00 36.10 3.02
58 59 3.936203 ACGGGCGTGCCTCTTTCA 61.936 61.111 11.25 0.00 36.10 2.69
59 60 3.423154 CACGGGCGTGCCTCTTTC 61.423 66.667 11.25 0.00 39.39 2.62
70 71 3.876589 TTTCGTCAGAGGCACGGGC 62.877 63.158 0.00 0.00 37.85 6.13
71 72 1.079127 ATTTCGTCAGAGGCACGGG 60.079 57.895 0.00 0.00 37.85 5.28
72 73 0.389817 TGATTTCGTCAGAGGCACGG 60.390 55.000 0.00 0.00 37.85 4.94
73 74 1.645034 ATGATTTCGTCAGAGGCACG 58.355 50.000 0.00 0.00 40.92 5.34
74 75 4.184629 AGTTATGATTTCGTCAGAGGCAC 58.815 43.478 0.00 0.00 40.92 5.01
75 76 4.160439 AGAGTTATGATTTCGTCAGAGGCA 59.840 41.667 0.00 0.00 40.92 4.75
76 77 4.688021 AGAGTTATGATTTCGTCAGAGGC 58.312 43.478 0.00 0.00 40.92 4.70
77 78 4.973051 CGAGAGTTATGATTTCGTCAGAGG 59.027 45.833 0.00 0.00 40.92 3.69
78 79 4.439449 GCGAGAGTTATGATTTCGTCAGAG 59.561 45.833 0.00 0.00 40.92 3.35
79 80 4.352039 GCGAGAGTTATGATTTCGTCAGA 58.648 43.478 0.00 0.00 40.92 3.27
80 81 3.178618 CGCGAGAGTTATGATTTCGTCAG 59.821 47.826 0.00 0.00 40.92 3.51
81 82 3.105937 CGCGAGAGTTATGATTTCGTCA 58.894 45.455 0.00 0.00 42.06 4.35
82 83 3.360533 TCGCGAGAGTTATGATTTCGTC 58.639 45.455 3.71 0.00 34.05 4.20
83 84 3.416119 TCGCGAGAGTTATGATTTCGT 57.584 42.857 3.71 0.00 34.05 3.85
84 85 4.741754 CTTTCGCGAGAGTTATGATTTCG 58.258 43.478 17.92 0.00 43.69 3.46
85 86 4.032900 TGCTTTCGCGAGAGTTATGATTTC 59.967 41.667 25.34 8.09 43.69 2.17
86 87 3.932710 TGCTTTCGCGAGAGTTATGATTT 59.067 39.130 25.34 0.00 43.69 2.17
87 88 3.307242 GTGCTTTCGCGAGAGTTATGATT 59.693 43.478 25.34 0.00 43.69 2.57
88 89 2.860735 GTGCTTTCGCGAGAGTTATGAT 59.139 45.455 25.34 0.00 43.69 2.45
89 90 2.259618 GTGCTTTCGCGAGAGTTATGA 58.740 47.619 25.34 0.00 43.69 2.15
90 91 1.992667 TGTGCTTTCGCGAGAGTTATG 59.007 47.619 25.34 7.32 43.69 1.90
91 92 1.993370 GTGTGCTTTCGCGAGAGTTAT 59.007 47.619 25.34 0.00 43.69 1.89
92 93 1.415374 GTGTGCTTTCGCGAGAGTTA 58.585 50.000 25.34 13.74 43.69 2.24
93 94 1.222115 GGTGTGCTTTCGCGAGAGTT 61.222 55.000 25.34 0.00 43.69 3.01
122 123 2.256461 CACGGCTTTGCTTCTGCC 59.744 61.111 0.00 0.00 42.94 4.85
125 126 0.394565 AGAGTCACGGCTTTGCTTCT 59.605 50.000 0.00 0.00 0.00 2.85
134 135 1.779569 TTTTTCTCGAGAGTCACGGC 58.220 50.000 15.94 0.00 0.00 5.68
303 321 1.629043 TACTTTCACGAGTCAGGGCT 58.371 50.000 0.00 0.00 0.00 5.19
307 325 5.679906 CATGGTTTTACTTTCACGAGTCAG 58.320 41.667 0.00 0.00 0.00 3.51
314 332 4.378459 CGAGAGGCATGGTTTTACTTTCAC 60.378 45.833 0.00 0.00 0.00 3.18
315 333 3.751175 CGAGAGGCATGGTTTTACTTTCA 59.249 43.478 0.00 0.00 0.00 2.69
397 468 4.081586 GGTTTTCCATCGGTCTTCTCTAGT 60.082 45.833 0.00 0.00 40.31 2.57
443 520 5.730802 GCGTTTTTGGCTTTTTAAACAGTTC 59.269 36.000 3.45 0.00 32.28 3.01
447 524 3.678548 ACGCGTTTTTGGCTTTTTAAACA 59.321 34.783 5.58 0.00 32.28 2.83
509 595 3.410516 CATTCGCCACGTGTCGCA 61.411 61.111 15.09 3.32 0.00 5.10
626 712 2.032030 GCTAGCTGTTGTCGCTCAAAAA 60.032 45.455 7.70 0.00 38.86 1.94
627 713 1.531149 GCTAGCTGTTGTCGCTCAAAA 59.469 47.619 7.70 0.00 38.86 2.44
628 714 1.148310 GCTAGCTGTTGTCGCTCAAA 58.852 50.000 7.70 0.00 38.86 2.69
629 715 0.670546 GGCTAGCTGTTGTCGCTCAA 60.671 55.000 15.72 0.00 38.86 3.02
630 716 1.079819 GGCTAGCTGTTGTCGCTCA 60.080 57.895 15.72 0.00 38.86 4.26
631 717 0.390472 AAGGCTAGCTGTTGTCGCTC 60.390 55.000 15.72 0.00 38.86 5.03
632 718 0.035458 AAAGGCTAGCTGTTGTCGCT 59.965 50.000 15.72 0.00 41.35 4.93
633 719 0.875059 AAAAGGCTAGCTGTTGTCGC 59.125 50.000 15.72 0.00 0.00 5.19
656 742 9.174166 CCAATAAAACCTAGTAGCTGTTTGTAT 57.826 33.333 0.00 0.00 32.85 2.29
657 743 8.158789 ACCAATAAAACCTAGTAGCTGTTTGTA 58.841 33.333 0.00 0.00 32.85 2.41
658 744 7.002276 ACCAATAAAACCTAGTAGCTGTTTGT 58.998 34.615 0.00 0.00 32.85 2.83
659 745 7.390718 AGACCAATAAAACCTAGTAGCTGTTTG 59.609 37.037 0.00 0.00 32.85 2.93
660 746 7.390718 CAGACCAATAAAACCTAGTAGCTGTTT 59.609 37.037 0.00 0.00 33.86 2.83
661 747 6.879458 CAGACCAATAAAACCTAGTAGCTGTT 59.121 38.462 0.00 0.00 0.00 3.16
662 748 6.013639 ACAGACCAATAAAACCTAGTAGCTGT 60.014 38.462 0.00 0.00 0.00 4.40
663 749 6.407202 ACAGACCAATAAAACCTAGTAGCTG 58.593 40.000 0.00 0.00 0.00 4.24
664 750 6.622427 ACAGACCAATAAAACCTAGTAGCT 57.378 37.500 0.00 0.00 0.00 3.32
665 751 8.959705 ATTACAGACCAATAAAACCTAGTAGC 57.040 34.615 0.00 0.00 0.00 3.58
674 760 9.461312 AGCTCACATTATTACAGACCAATAAAA 57.539 29.630 0.00 0.00 32.98 1.52
746 832 4.900054 AGATTAAACCGGCCTAGAGTGTAT 59.100 41.667 0.00 0.00 0.00 2.29
771 857 0.252197 CGGGAGGGGTTTAGTTGGAG 59.748 60.000 0.00 0.00 0.00 3.86
782 868 3.995506 ATTTTCAGCGCGGGAGGGG 62.996 63.158 8.83 0.00 43.89 4.79
869 955 8.150945 GGAAGATGTGATGAGCTTATAAAGGTA 58.849 37.037 0.00 0.00 39.77 3.08
1060 1166 2.741985 CACACGAATCAGGCGCCA 60.742 61.111 31.54 9.64 0.00 5.69
1088 1194 1.721489 CGCGATGTTCAACTGAAACCG 60.721 52.381 0.00 0.33 35.58 4.44
1228 1661 6.128445 ACTGAATAGCAACACAATTTCGAGAG 60.128 38.462 0.00 0.00 0.00 3.20
1230 1663 5.931532 ACTGAATAGCAACACAATTTCGAG 58.068 37.500 0.00 0.00 0.00 4.04
1240 1673 4.922206 AGGATCCAAACTGAATAGCAACA 58.078 39.130 15.82 0.00 0.00 3.33
1283 1716 4.553330 ACAGATTTAACGAGTCCACCAT 57.447 40.909 0.00 0.00 0.00 3.55
1306 1740 3.370953 GCCAAGTGTTAGATCCACAGGAT 60.371 47.826 12.84 0.00 46.28 3.24
1309 1743 2.002586 CGCCAAGTGTTAGATCCACAG 58.997 52.381 3.83 0.00 35.24 3.66
1344 1781 8.651588 CAGTCTAACAATGTAACAGAACAGATC 58.348 37.037 0.00 0.00 31.70 2.75
1368 1807 6.150474 ACAAATAATAGTTCCGACAAACCCAG 59.850 38.462 0.00 0.00 0.00 4.45
1415 1876 2.424601 ACAAGATTCCAATCGCACCATG 59.575 45.455 0.00 0.00 40.35 3.66
1427 1888 5.689068 CAGCAAAAGTTCTCAACAAGATTCC 59.311 40.000 0.00 0.00 32.82 3.01
1479 1940 3.565902 AGTTCTCTACAACAGCAAAAGCC 59.434 43.478 0.00 0.00 0.00 4.35
1510 1971 0.597637 ACCTCAACGCTGACAGAACG 60.598 55.000 6.65 3.65 0.00 3.95
1559 2020 6.915544 AATAGTGAATGCTGTGACATAGTG 57.084 37.500 0.87 0.00 0.00 2.74
1571 2048 8.519492 ACACATACAAACAAAATAGTGAATGC 57.481 30.769 0.00 0.00 0.00 3.56
1621 2218 2.875317 GTTTCTATGCTTAGCCCTCTGC 59.125 50.000 0.29 0.00 41.71 4.26
1655 2276 8.246180 AGACAAGTAGCAATTACATGAATTTGG 58.754 33.333 0.00 0.00 35.45 3.28
1716 2337 8.498192 TTCGTTGTTAATCGATACTATGCTAC 57.502 34.615 0.00 0.00 36.01 3.58
1763 2445 7.721842 TGTCACCCAAAAATTATCAGTACTGAA 59.278 33.333 28.43 14.41 43.58 3.02
1786 2470 9.998106 ATCACAGGGTACATAGTTAAATATGTC 57.002 33.333 26.77 18.82 43.61 3.06
1792 2477 5.045505 TGGCATCACAGGGTACATAGTTAAA 60.046 40.000 0.00 0.00 0.00 1.52
2594 3561 4.451096 TCAGTAAGCGAACAAATCAAGGAC 59.549 41.667 0.00 0.00 0.00 3.85
2798 3801 0.750911 GGATCTTGGGAGCCTTGCTG 60.751 60.000 0.00 0.00 44.03 4.41
3113 4126 5.099042 ACAAACTCCAGCCGATAAATACT 57.901 39.130 0.00 0.00 0.00 2.12
3302 4320 9.451002 CCTTTGATCTTGCATAGAGATTCATAT 57.549 33.333 1.03 0.00 36.02 1.78
3303 4321 8.654094 TCCTTTGATCTTGCATAGAGATTCATA 58.346 33.333 1.03 0.00 36.02 2.15
3304 4322 7.515586 TCCTTTGATCTTGCATAGAGATTCAT 58.484 34.615 1.03 0.00 36.02 2.57
3305 4323 6.892485 TCCTTTGATCTTGCATAGAGATTCA 58.108 36.000 1.03 0.30 36.02 2.57
3306 4324 7.798596 TTCCTTTGATCTTGCATAGAGATTC 57.201 36.000 1.03 0.00 36.02 2.52
3310 4328 9.381033 CCTATATTCCTTTGATCTTGCATAGAG 57.619 37.037 0.00 0.00 36.02 2.43
3311 4329 9.104713 TCCTATATTCCTTTGATCTTGCATAGA 57.895 33.333 0.00 0.00 37.28 1.98
3312 4330 9.902684 ATCCTATATTCCTTTGATCTTGCATAG 57.097 33.333 0.00 0.00 0.00 2.23
3315 4333 9.730705 CTAATCCTATATTCCTTTGATCTTGCA 57.269 33.333 0.00 0.00 0.00 4.08
3316 4334 9.171877 CCTAATCCTATATTCCTTTGATCTTGC 57.828 37.037 0.00 0.00 0.00 4.01
3319 4337 9.621239 TGTCCTAATCCTATATTCCTTTGATCT 57.379 33.333 0.00 0.00 0.00 2.75
3325 4343 9.543231 TCGTTATGTCCTAATCCTATATTCCTT 57.457 33.333 0.00 0.00 0.00 3.36
3326 4344 9.191479 CTCGTTATGTCCTAATCCTATATTCCT 57.809 37.037 0.00 0.00 0.00 3.36
3327 4345 8.968969 ACTCGTTATGTCCTAATCCTATATTCC 58.031 37.037 0.00 0.00 0.00 3.01
3329 4347 9.756571 AGACTCGTTATGTCCTAATCCTATATT 57.243 33.333 0.00 0.00 35.21 1.28
3330 4348 9.756571 AAGACTCGTTATGTCCTAATCCTATAT 57.243 33.333 0.00 0.00 35.21 0.86
3331 4349 9.011095 CAAGACTCGTTATGTCCTAATCCTATA 57.989 37.037 0.00 0.00 35.21 1.31
3332 4350 7.724506 TCAAGACTCGTTATGTCCTAATCCTAT 59.275 37.037 0.00 0.00 35.21 2.57
3333 4351 7.013083 GTCAAGACTCGTTATGTCCTAATCCTA 59.987 40.741 0.00 0.00 35.21 2.94
3334 4352 5.892119 TCAAGACTCGTTATGTCCTAATCCT 59.108 40.000 0.00 0.00 35.21 3.24
3335 4353 5.978322 GTCAAGACTCGTTATGTCCTAATCC 59.022 44.000 0.00 0.00 35.21 3.01
3336 4354 6.693545 CAGTCAAGACTCGTTATGTCCTAATC 59.306 42.308 0.00 0.00 40.20 1.75
3337 4355 6.377429 TCAGTCAAGACTCGTTATGTCCTAAT 59.623 38.462 0.00 0.00 40.20 1.73
3338 4356 5.708697 TCAGTCAAGACTCGTTATGTCCTAA 59.291 40.000 0.00 0.00 40.20 2.69
3339 4357 5.250982 TCAGTCAAGACTCGTTATGTCCTA 58.749 41.667 0.00 0.00 40.20 2.94
3340 4358 4.079970 TCAGTCAAGACTCGTTATGTCCT 58.920 43.478 0.00 0.00 40.20 3.85
3341 4359 4.436242 TCAGTCAAGACTCGTTATGTCC 57.564 45.455 0.00 0.00 40.20 4.02
3342 4360 5.038033 GGATCAGTCAAGACTCGTTATGTC 58.962 45.833 0.00 0.00 40.20 3.06
3343 4361 4.707448 AGGATCAGTCAAGACTCGTTATGT 59.293 41.667 0.00 0.00 40.20 2.29
3344 4362 5.255710 AGGATCAGTCAAGACTCGTTATG 57.744 43.478 0.00 0.00 40.20 1.90
3345 4363 5.186021 ACAAGGATCAGTCAAGACTCGTTAT 59.814 40.000 0.00 0.00 40.20 1.89
3346 4364 4.523173 ACAAGGATCAGTCAAGACTCGTTA 59.477 41.667 0.00 0.00 40.20 3.18
3347 4365 3.322254 ACAAGGATCAGTCAAGACTCGTT 59.678 43.478 0.00 0.00 40.20 3.85
3348 4366 2.894126 ACAAGGATCAGTCAAGACTCGT 59.106 45.455 0.00 0.00 40.20 4.18
3349 4367 3.584406 ACAAGGATCAGTCAAGACTCG 57.416 47.619 0.00 0.00 40.20 4.18
3350 4368 9.606631 ATTATAAACAAGGATCAGTCAAGACTC 57.393 33.333 0.00 0.00 40.20 3.36
3351 4369 9.388506 CATTATAAACAAGGATCAGTCAAGACT 57.611 33.333 0.00 0.00 43.61 3.24
3352 4370 9.167311 ACATTATAAACAAGGATCAGTCAAGAC 57.833 33.333 0.00 0.00 0.00 3.01
3415 4433 9.066892 TCTAGATGTGATTTAGCAAAACTGTTT 57.933 29.630 0.00 0.00 0.00 2.83
3416 4434 8.621532 TCTAGATGTGATTTAGCAAAACTGTT 57.378 30.769 0.00 0.00 0.00 3.16
3417 4435 8.671921 CATCTAGATGTGATTTAGCAAAACTGT 58.328 33.333 22.42 0.00 34.23 3.55
3434 4452 9.689976 CAAAAGTAGTCATAGGACATCTAGATG 57.310 37.037 27.63 27.63 46.80 2.90
3435 4453 9.427821 ACAAAAGTAGTCATAGGACATCTAGAT 57.572 33.333 10.58 0.00 46.80 1.98
3436 4454 8.824756 ACAAAAGTAGTCATAGGACATCTAGA 57.175 34.615 10.58 0.00 46.80 2.43
3437 4455 8.908903 AGACAAAAGTAGTCATAGGACATCTAG 58.091 37.037 10.58 4.51 46.80 2.43
3438 4456 8.824756 AGACAAAAGTAGTCATAGGACATCTA 57.175 34.615 10.58 0.00 46.80 1.98
3439 4457 7.726033 AGACAAAAGTAGTCATAGGACATCT 57.274 36.000 10.58 4.61 46.80 2.90
3440 4458 8.779354 AAAGACAAAAGTAGTCATAGGACATC 57.221 34.615 10.58 2.28 46.80 3.06
3441 4459 9.220767 GAAAAGACAAAAGTAGTCATAGGACAT 57.779 33.333 10.58 0.00 46.80 3.06
3442 4460 7.660208 GGAAAAGACAAAAGTAGTCATAGGACA 59.340 37.037 10.58 0.00 46.80 4.02
3443 4461 7.119407 GGGAAAAGACAAAAGTAGTCATAGGAC 59.881 40.741 0.00 0.00 44.66 3.85
3444 4462 7.017254 AGGGAAAAGACAAAAGTAGTCATAGGA 59.983 37.037 0.00 0.00 38.46 2.94
3445 4463 7.168905 AGGGAAAAGACAAAAGTAGTCATAGG 58.831 38.462 0.00 0.00 38.46 2.57
3446 4464 8.622948 AAGGGAAAAGACAAAAGTAGTCATAG 57.377 34.615 0.00 0.00 38.46 2.23
3447 4465 8.990163 AAAGGGAAAAGACAAAAGTAGTCATA 57.010 30.769 0.00 0.00 38.46 2.15
3448 4466 7.898014 AAAGGGAAAAGACAAAAGTAGTCAT 57.102 32.000 0.00 0.00 38.46 3.06
3449 4467 7.712204 AAAAGGGAAAAGACAAAAGTAGTCA 57.288 32.000 0.00 0.00 38.46 3.41
3450 4468 8.467598 AGAAAAAGGGAAAAGACAAAAGTAGTC 58.532 33.333 0.00 0.00 36.26 2.59
3451 4469 8.362464 AGAAAAAGGGAAAAGACAAAAGTAGT 57.638 30.769 0.00 0.00 0.00 2.73
3452 4470 9.653287 AAAGAAAAAGGGAAAAGACAAAAGTAG 57.347 29.630 0.00 0.00 0.00 2.57
3453 4471 9.647797 GAAAGAAAAAGGGAAAAGACAAAAGTA 57.352 29.630 0.00 0.00 0.00 2.24
3454 4472 8.375506 AGAAAGAAAAAGGGAAAAGACAAAAGT 58.624 29.630 0.00 0.00 0.00 2.66
3455 4473 8.777865 AGAAAGAAAAAGGGAAAAGACAAAAG 57.222 30.769 0.00 0.00 0.00 2.27
3481 4499 9.046296 CCGATAGAGAAGTACTGCATTTAAAAT 57.954 33.333 3.00 0.00 39.76 1.82
3482 4500 7.494625 CCCGATAGAGAAGTACTGCATTTAAAA 59.505 37.037 3.00 0.00 39.76 1.52
3483 4501 6.984474 CCCGATAGAGAAGTACTGCATTTAAA 59.016 38.462 3.00 0.00 39.76 1.52
3484 4502 6.322969 TCCCGATAGAGAAGTACTGCATTTAA 59.677 38.462 3.00 0.00 39.76 1.52
3485 4503 5.831525 TCCCGATAGAGAAGTACTGCATTTA 59.168 40.000 3.00 0.00 39.76 1.40
3486 4504 4.649674 TCCCGATAGAGAAGTACTGCATTT 59.350 41.667 3.00 0.00 39.76 2.32
3487 4505 4.038162 GTCCCGATAGAGAAGTACTGCATT 59.962 45.833 3.00 0.00 39.76 3.56
3488 4506 3.570550 GTCCCGATAGAGAAGTACTGCAT 59.429 47.826 3.00 0.00 39.76 3.96
3489 4507 2.950309 GTCCCGATAGAGAAGTACTGCA 59.050 50.000 3.00 0.00 39.76 4.41
3490 4508 2.293955 GGTCCCGATAGAGAAGTACTGC 59.706 54.545 0.00 0.00 39.76 4.40
3491 4509 3.822940 AGGTCCCGATAGAGAAGTACTG 58.177 50.000 0.00 0.00 39.76 2.74
3492 4510 5.375773 GTTAGGTCCCGATAGAGAAGTACT 58.624 45.833 0.00 0.00 39.76 2.73
3493 4511 4.518590 GGTTAGGTCCCGATAGAGAAGTAC 59.481 50.000 0.00 0.00 39.76 2.73
3557 4577 0.035820 TTAGGAAGATTTGCGGCGGT 60.036 50.000 9.78 0.00 0.00 5.68
3581 4612 0.952010 GAAGTTTTACTCGGCCGCCA 60.952 55.000 23.51 2.44 0.00 5.69
3687 4749 2.167693 GACATACAACCACCTCATCCGA 59.832 50.000 0.00 0.00 0.00 4.55
3700 4762 2.580276 GGCGACGGGGACATACAA 59.420 61.111 0.00 0.00 0.00 2.41
3713 4775 2.809174 CACGTTGCAGATCGGCGA 60.809 61.111 13.87 13.87 36.28 5.54
3722 4784 3.047280 GCACGGATCCACGTTGCA 61.047 61.111 13.41 0.00 46.25 4.08
3737 4799 3.479203 CCCTCGGGTATGGCAGCA 61.479 66.667 0.00 0.00 0.00 4.41
3847 4912 2.283388 TAGGTCCTCGTTGGCGGT 60.283 61.111 0.00 0.00 38.89 5.68
3936 5016 1.152290 TGGAACTACCCGACCCACA 60.152 57.895 0.00 0.00 38.00 4.17
3948 5028 2.710724 GAACTCGGCCGTGTGGAACT 62.711 60.000 31.37 16.77 38.04 3.01
3961 5041 1.811266 CTCCATGGCCACGAACTCG 60.811 63.158 8.16 0.00 46.33 4.18
3965 5045 1.216977 CGTACTCCATGGCCACGAA 59.783 57.895 21.09 0.00 34.66 3.85
3969 5049 2.717044 CGGTCGTACTCCATGGCCA 61.717 63.158 8.56 8.56 37.85 5.36
3990 5070 1.005394 CCGTGGTACCGAACTTGCT 60.005 57.895 7.57 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.