Multiple sequence alignment - TraesCS4B01G106500

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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 TraesCS4B01G106500 chr4B 100.000 4309 0 0 1 4309 115882669 115878361 0.000000e+00 7958.0
1 TraesCS4B01G106500 chr4B 80.152 1446 204 47 1903 3311 115846969 115845570 0.000000e+00 1003.0
2 TraesCS4B01G106500 chr4B 79.676 802 97 39 688 1465 115848301 115847542 6.390000e-143 518.0
3 TraesCS4B01G106500 chr4B 86.738 279 33 3 4031 4309 291896594 291896320 1.510000e-79 307.0
4 TraesCS4B01G106500 chr4B 93.204 103 5 2 1465 1566 115881104 115881205 2.680000e-32 150.0
5 TraesCS4B01G106500 chr4B 89.091 55 4 2 3851 3904 606081988 606081935 2.780000e-07 67.6
6 TraesCS4B01G106500 chr4A 93.524 1853 97 9 1562 3401 492031952 492030110 0.000000e+00 2736.0
7 TraesCS4B01G106500 chr4A 92.819 1490 84 14 23 1504 492033501 492032027 0.000000e+00 2137.0
8 TraesCS4B01G106500 chr4A 79.359 1061 149 47 1903 2948 491916538 491915533 0.000000e+00 682.0
9 TraesCS4B01G106500 chr4A 79.578 901 163 13 2350 3245 163280122 163281006 3.660000e-175 625.0
10 TraesCS4B01G106500 chr4A 91.429 315 23 3 3000 3311 491915424 491915111 3.080000e-116 429.0
11 TraesCS4B01G106500 chr4A 81.026 390 53 19 1124 1500 491917501 491917120 1.520000e-74 291.0
12 TraesCS4B01G106500 chr4A 81.250 368 45 17 688 1044 491917926 491917572 4.240000e-70 276.0
13 TraesCS4B01G106500 chr4A 95.294 85 4 0 3890 3974 492029995 492029911 7.520000e-28 135.0
14 TraesCS4B01G106500 chr4D 95.879 1650 63 3 1773 3422 81986519 81984875 0.000000e+00 2665.0
15 TraesCS4B01G106500 chr4D 89.826 1032 62 21 487 1496 81987965 81986955 0.000000e+00 1284.0
16 TraesCS4B01G106500 chr4D 81.013 869 113 38 2479 3321 81972568 81971726 1.010000e-180 643.0
17 TraesCS4B01G106500 chr4D 89.286 420 39 2 3890 4309 81984780 81984367 4.940000e-144 521.0
18 TraesCS4B01G106500 chr4D 83.074 514 76 9 1903 2415 81973252 81972749 1.410000e-124 457.0
19 TraesCS4B01G106500 chr4D 98.140 215 4 0 1562 1776 81986813 81986599 4.070000e-100 375.0
20 TraesCS4B01G106500 chr4D 88.015 267 23 8 3439 3700 386747367 386747629 1.510000e-79 307.0
21 TraesCS4B01G106500 chr4D 82.038 373 43 18 1134 1497 81974159 81973802 3.260000e-76 296.0
22 TraesCS4B01G106500 chr4D 82.535 355 37 18 708 1050 81974577 81974236 5.450000e-74 289.0
23 TraesCS4B01G106500 chr4D 84.746 295 28 13 3471 3760 481181048 481181330 3.280000e-71 279.0
24 TraesCS4B01G106500 chr4D 100.000 42 0 0 3399 3440 81984869 81984828 1.280000e-10 78.7
25 TraesCS4B01G106500 chr4D 95.000 40 2 0 1000 1039 81921721 81921682 3.600000e-06 63.9
26 TraesCS4B01G106500 chr4D 96.875 32 1 0 1535 1566 81986955 81986986 2.000000e-03 54.7
27 TraesCS4B01G106500 chr1D 79.506 1498 206 71 1875 3313 452626866 452625411 0.000000e+00 972.0
28 TraesCS4B01G106500 chr1D 84.672 274 40 2 4037 4309 357331768 357331496 5.490000e-69 272.0
29 TraesCS4B01G106500 chr1D 98.611 144 2 0 1134 1277 452627429 452627286 5.530000e-64 255.0
30 TraesCS4B01G106500 chr5B 78.292 1253 199 45 2095 3312 608202831 608204045 0.000000e+00 739.0
31 TraesCS4B01G106500 chr5B 80.737 706 108 14 1900 2597 608343387 608344072 3.820000e-145 525.0
32 TraesCS4B01G106500 chr5B 85.401 274 35 5 4037 4309 542689817 542690086 3.280000e-71 279.0
33 TraesCS4B01G106500 chr5B 79.240 342 46 18 1111 1444 608340786 608341110 9.380000e-52 215.0
34 TraesCS4B01G106500 chr5B 86.885 61 6 2 3845 3904 641736078 641736137 2.780000e-07 67.6
35 TraesCS4B01G106500 chr5B 88.889 54 3 3 3834 3884 631382552 631382605 3.600000e-06 63.9
36 TraesCS4B01G106500 chr1A 80.617 908 124 30 1875 2755 547393273 547392391 0.000000e+00 654.0
37 TraesCS4B01G106500 chr1A 81.608 734 104 22 1875 2591 547413983 547413264 2.890000e-161 579.0
38 TraesCS4B01G106500 chr1A 98.649 148 1 1 1134 1281 547417286 547417140 1.190000e-65 261.0
39 TraesCS4B01G106500 chr1A 98.611 144 2 0 1134 1277 547395709 547395566 5.530000e-64 255.0
40 TraesCS4B01G106500 chr1A 79.668 241 30 11 811 1049 547396008 547395785 5.770000e-34 156.0
41 TraesCS4B01G106500 chr7D 78.905 1005 179 23 2346 3341 188354568 188355548 0.000000e+00 651.0
42 TraesCS4B01G106500 chr7D 85.069 288 36 6 4024 4308 554245614 554245897 1.960000e-73 287.0
43 TraesCS4B01G106500 chr5A 77.922 1001 189 20 2346 3341 281327143 281326170 2.870000e-166 595.0
44 TraesCS4B01G106500 chr5A 77.545 1002 191 21 2346 3341 281328938 281327965 1.340000e-159 573.0
45 TraesCS4B01G106500 chr5A 79.138 719 106 29 1893 2590 397250321 397251016 1.410000e-124 457.0
46 TraesCS4B01G106500 chr5A 95.833 144 6 0 1134 1277 397249880 397250023 2.590000e-57 233.0
47 TraesCS4B01G106500 chr1B 82.016 734 90 25 1875 2591 622708112 622707404 1.730000e-163 586.0
48 TraesCS4B01G106500 chr1B 84.727 275 38 4 4033 4307 95300183 95299913 5.490000e-69 272.0
49 TraesCS4B01G106500 chr1B 98.611 144 2 0 1134 1277 622708751 622708608 5.530000e-64 255.0
50 TraesCS4B01G106500 chr1B 89.091 55 4 2 3851 3904 116219612 116219559 2.780000e-07 67.6
51 TraesCS4B01G106500 chr2A 77.778 1008 185 26 2350 3341 391958893 391957909 6.210000e-163 584.0
52 TraesCS4B01G106500 chr2A 86.364 264 35 1 4046 4309 764823848 764823586 1.960000e-73 287.0
53 TraesCS4B01G106500 chr5D 77.876 904 127 44 2447 3313 493121994 493122861 1.080000e-135 494.0
54 TraesCS4B01G106500 chr5D 82.477 331 43 12 3439 3760 422428234 422428558 4.240000e-70 276.0
55 TraesCS4B01G106500 chr5D 95.775 71 3 0 2680 2750 299834367 299834437 9.790000e-22 115.0
56 TraesCS4B01G106500 chr2B 85.276 326 38 10 3439 3760 749824756 749825075 1.160000e-85 327.0
57 TraesCS4B01G106500 chr2B 83.025 324 41 14 3444 3760 749820860 749821176 9.120000e-72 281.0
58 TraesCS4B01G106500 chr2B 90.164 61 3 1 1337 1394 351183325 351183385 4.620000e-10 76.8
59 TraesCS4B01G106500 chr2B 86.885 61 6 2 3845 3904 579631618 579631677 2.780000e-07 67.6
60 TraesCS4B01G106500 chr2B 86.885 61 6 2 3845 3904 587956112 587956171 2.780000e-07 67.6
61 TraesCS4B01G106500 chr2D 84.810 316 38 8 3439 3750 29015777 29015468 4.180000e-80 309.0
62 TraesCS4B01G106500 chr3A 87.452 263 29 4 4046 4307 181107966 181108225 2.520000e-77 300.0
63 TraesCS4B01G106500 chr3A 82.477 331 38 12 3439 3760 171346706 171346387 5.490000e-69 272.0
64 TraesCS4B01G106500 chr3D 86.081 273 34 4 4038 4309 458307331 458307600 1.520000e-74 291.0
65 TraesCS4B01G106500 chr6B 85.294 272 37 3 4039 4309 188870913 188870644 1.180000e-70 278.0
66 TraesCS4B01G106500 chr6B 89.091 55 4 2 3851 3904 188795233 188795180 2.780000e-07 67.6
67 TraesCS4B01G106500 chr3B 85.199 277 34 5 4032 4308 531405179 531405448 1.180000e-70 278.0
68 TraesCS4B01G106500 chr3B 82.623 305 42 11 3460 3760 642065494 642065791 4.270000e-65 259.0
69 TraesCS4B01G106500 chr3B 88.136 59 4 3 3847 3904 598645159 598645215 2.780000e-07 67.6
70 TraesCS4B01G106500 chr6D 82.566 304 41 9 3462 3760 13089201 13089497 1.540000e-64 257.0
71 TraesCS4B01G106500 chr6D 88.679 53 5 1 3851 3902 287017161 287017109 3.600000e-06 63.9


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 TraesCS4B01G106500 chr4B 115878361 115882669 4308 True 7958.000000 7958 100.000000 1 4309 1 chr4B.!!$R1 4308
1 TraesCS4B01G106500 chr4B 115845570 115848301 2731 True 760.500000 1003 79.914000 688 3311 2 chr4B.!!$R4 2623
2 TraesCS4B01G106500 chr4A 492029911 492033501 3590 True 1669.333333 2736 93.879000 23 3974 3 chr4A.!!$R2 3951
3 TraesCS4B01G106500 chr4A 163280122 163281006 884 False 625.000000 625 79.578000 2350 3245 1 chr4A.!!$F1 895
4 TraesCS4B01G106500 chr4A 491915111 491917926 2815 True 419.500000 682 83.266000 688 3311 4 chr4A.!!$R1 2623
5 TraesCS4B01G106500 chr4D 81984367 81987965 3598 True 984.740000 2665 94.626200 487 4309 5 chr4D.!!$R3 3822
6 TraesCS4B01G106500 chr4D 81971726 81974577 2851 True 421.250000 643 82.165000 708 3321 4 chr4D.!!$R2 2613
7 TraesCS4B01G106500 chr1D 452625411 452627429 2018 True 613.500000 972 89.058500 1134 3313 2 chr1D.!!$R2 2179
8 TraesCS4B01G106500 chr5B 608202831 608204045 1214 False 739.000000 739 78.292000 2095 3312 1 chr5B.!!$F2 1217
9 TraesCS4B01G106500 chr5B 608340786 608344072 3286 False 370.000000 525 79.988500 1111 2597 2 chr5B.!!$F5 1486
10 TraesCS4B01G106500 chr1A 547413264 547417286 4022 True 420.000000 579 90.128500 1134 2591 2 chr1A.!!$R2 1457
11 TraesCS4B01G106500 chr1A 547392391 547396008 3617 True 355.000000 654 86.298667 811 2755 3 chr1A.!!$R1 1944
12 TraesCS4B01G106500 chr7D 188354568 188355548 980 False 651.000000 651 78.905000 2346 3341 1 chr7D.!!$F1 995
13 TraesCS4B01G106500 chr5A 281326170 281328938 2768 True 584.000000 595 77.733500 2346 3341 2 chr5A.!!$R1 995
14 TraesCS4B01G106500 chr5A 397249880 397251016 1136 False 345.000000 457 87.485500 1134 2590 2 chr5A.!!$F1 1456
15 TraesCS4B01G106500 chr1B 622707404 622708751 1347 True 420.500000 586 90.313500 1134 2591 2 chr1B.!!$R3 1457
16 TraesCS4B01G106500 chr2A 391957909 391958893 984 True 584.000000 584 77.778000 2350 3341 1 chr2A.!!$R1 991
17 TraesCS4B01G106500 chr5D 493121994 493122861 867 False 494.000000 494 77.876000 2447 3313 1 chr5D.!!$F3 866
18 TraesCS4B01G106500 chr2B 749820860 749825075 4215 False 304.000000 327 84.150500 3439 3760 2 chr2B.!!$F4 321

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
794 803 0.245539 TGTTTCGGCTACCTTCTCCG 59.754 55.000 0.00 0.0 44.16 4.63 F
920 930 3.189287 CCTTCGTTCCTCACCAAAATCTG 59.811 47.826 0.00 0.0 0.00 2.90 F
2415 9524 2.028112 TGTAGGCCTTGCTGTAAGTGAG 60.028 50.000 12.58 0.0 35.30 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 9026 2.436646 GGACATGGTCACCTGGCG 60.437 66.667 0.00 0.0 33.68 5.69 R
2828 10115 1.613437 CACCTGGACCACAATTCAACC 59.387 52.381 0.00 0.0 0.00 3.77 R
3722 15036 0.034756 GTTGGCCCGGCAAGAAATTT 59.965 50.000 12.58 0.0 0.00 1.82 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
69 70 6.828785 ACAGGGGTGTTTAAATGCTAAGATAG 59.171 38.462 0.00 0.00 0.00 2.08
70 71 6.828785 CAGGGGTGTTTAAATGCTAAGATAGT 59.171 38.462 0.00 0.00 0.00 2.12
72 73 7.893833 AGGGGTGTTTAAATGCTAAGATAGTTT 59.106 33.333 0.00 0.00 0.00 2.66
129 130 6.106673 AGTATAGGAACATACAAGCACACAC 58.893 40.000 0.00 0.00 34.42 3.82
139 140 1.597195 CAAGCACACACACATACACGT 59.403 47.619 0.00 0.00 0.00 4.49
146 147 5.404096 CACACACACATACACGTCCTATAA 58.596 41.667 0.00 0.00 0.00 0.98
154 155 3.521947 ACACGTCCTATAAGCACCTTC 57.478 47.619 0.00 0.00 0.00 3.46
203 204 2.778299 TGATGAAGTTACCACAGGTGC 58.222 47.619 0.00 0.00 36.19 5.01
205 206 0.250124 TGAAGTTACCACAGGTGCCG 60.250 55.000 0.00 0.00 36.19 5.69
208 209 1.674322 GTTACCACAGGTGCCGCAT 60.674 57.895 0.00 0.00 36.19 4.73
226 227 2.679837 GCATTGTCGATGGGCATATAGG 59.320 50.000 2.16 0.00 36.21 2.57
233 234 4.081087 GTCGATGGGCATATAGGTTACCAT 60.081 45.833 3.51 9.19 41.11 3.55
285 286 1.074775 TCCACAAAAGGGCGAGCAT 59.925 52.632 0.00 0.00 0.00 3.79
287 288 0.451783 CCACAAAAGGGCGAGCATAC 59.548 55.000 0.00 0.00 0.00 2.39
307 308 6.072728 GCATACACACAACATTTAGGACTTCA 60.073 38.462 0.00 0.00 0.00 3.02
409 410 3.242091 CGAAGGAATGCACATAGTCAACG 60.242 47.826 0.00 0.00 0.00 4.10
412 413 5.276461 AGGAATGCACATAGTCAACGATA 57.724 39.130 0.00 0.00 0.00 2.92
437 438 2.097104 ACGTTTGTCAAGCGAATACACG 60.097 45.455 25.77 13.44 0.00 4.49
482 483 8.691194 AAAAAGAAGGTTACCTACTAGGGTAT 57.309 34.615 3.55 0.00 40.58 2.73
555 556 0.963962 CAAGGGCAAGCATCAACACT 59.036 50.000 0.00 0.00 0.00 3.55
590 591 6.127281 ACCATCAATCAATCAGCTTAATTGCA 60.127 34.615 11.98 0.00 34.73 4.08
591 592 6.759356 CCATCAATCAATCAGCTTAATTGCAA 59.241 34.615 0.00 0.00 34.73 4.08
593 594 7.821595 TCAATCAATCAGCTTAATTGCAAAG 57.178 32.000 1.71 0.00 34.73 2.77
594 595 7.604549 TCAATCAATCAGCTTAATTGCAAAGA 58.395 30.769 1.71 0.00 34.73 2.52
595 596 7.543172 TCAATCAATCAGCTTAATTGCAAAGAC 59.457 33.333 1.71 0.00 34.73 3.01
598 599 3.146066 TCAGCTTAATTGCAAAGACCGT 58.854 40.909 1.71 0.00 34.99 4.83
662 670 4.082523 CGTCCCGTGGTGCCATCT 62.083 66.667 0.00 0.00 0.00 2.90
670 678 2.369633 TGGTGCCATCTCATCCGCT 61.370 57.895 0.00 0.00 0.00 5.52
794 803 0.245539 TGTTTCGGCTACCTTCTCCG 59.754 55.000 0.00 0.00 44.16 4.63
920 930 3.189287 CCTTCGTTCCTCACCAAAATCTG 59.811 47.826 0.00 0.00 0.00 2.90
1081 1120 7.167968 CGAAAATTTGCTTGATCAGTGAAGAAA 59.832 33.333 0.00 0.00 0.00 2.52
1088 1127 4.277515 TGATCAGTGAAGAAACTCTGGG 57.722 45.455 0.00 0.00 33.81 4.45
1505 4558 9.927668 TTGGTGGAATCTTGAATCTTATTTTTC 57.072 29.630 0.00 0.00 0.00 2.29
1507 4560 8.458843 GGTGGAATCTTGAATCTTATTTTTCGA 58.541 33.333 0.00 0.00 0.00 3.71
1508 4561 9.840427 GTGGAATCTTGAATCTTATTTTTCGAA 57.160 29.630 0.00 0.00 0.00 3.71
1513 4566 9.860898 ATCTTGAATCTTATTTTTCGAAAAGGG 57.139 29.630 21.53 13.40 0.00 3.95
1514 4567 8.303876 TCTTGAATCTTATTTTTCGAAAAGGGG 58.696 33.333 21.53 13.69 0.00 4.79
1515 4568 6.394809 TGAATCTTATTTTTCGAAAAGGGGC 58.605 36.000 21.53 9.11 0.00 5.80
1516 4569 5.993748 ATCTTATTTTTCGAAAAGGGGCA 57.006 34.783 21.53 8.73 0.00 5.36
1517 4570 5.128992 TCTTATTTTTCGAAAAGGGGCAC 57.871 39.130 21.53 0.00 0.00 5.01
1518 4571 4.830600 TCTTATTTTTCGAAAAGGGGCACT 59.169 37.500 21.53 6.43 0.00 4.40
1561 4614 6.436847 TCAAGATTCCACCAAATTAATCAGCA 59.563 34.615 0.00 0.00 32.04 4.41
1562 4615 6.855763 AGATTCCACCAAATTAATCAGCAA 57.144 33.333 0.00 0.00 32.04 3.91
1563 4616 7.243604 AGATTCCACCAAATTAATCAGCAAA 57.756 32.000 0.00 0.00 32.04 3.68
2067 9150 2.431454 CCGGGGTGTGATGATCGGA 61.431 63.158 0.00 0.00 39.83 4.55
2226 9309 2.164422 TGTTCTCAGCTGTGGTATCTCG 59.836 50.000 14.67 0.00 0.00 4.04
2277 9374 5.828299 TTCCCAATGAAACATCGTATTCC 57.172 39.130 0.00 0.00 0.00 3.01
2290 9388 8.833231 AACATCGTATTCCTATTACCTTGATG 57.167 34.615 0.00 0.00 36.47 3.07
2291 9389 8.190326 ACATCGTATTCCTATTACCTTGATGA 57.810 34.615 0.00 0.00 34.94 2.92
2292 9390 8.816894 ACATCGTATTCCTATTACCTTGATGAT 58.183 33.333 0.00 0.00 34.94 2.45
2415 9524 2.028112 TGTAGGCCTTGCTGTAAGTGAG 60.028 50.000 12.58 0.00 35.30 3.51
2822 10109 5.928264 GGGATGCAAAATACTATGCCAAATC 59.072 40.000 0.00 0.00 41.87 2.17
2828 10115 6.201517 CAAAATACTATGCCAAATCCTCACG 58.798 40.000 0.00 0.00 0.00 4.35
2854 10143 0.840617 TTGTGGTCCAGGTGCTTGTA 59.159 50.000 0.00 0.00 0.00 2.41
2915 10205 2.173669 GGTCACGTCGATGCCATGG 61.174 63.158 7.63 7.63 0.00 3.66
2965 10255 6.887368 TGTATGTTCTCGACACAATTGAAAG 58.113 36.000 13.59 4.15 42.04 2.62
3074 10441 1.083895 TGTCCCCCATAAGGAGGCA 59.916 57.895 0.00 0.00 38.24 4.75
3188 10565 3.621558 AGTCGTGGAGATGTACATGAGA 58.378 45.455 14.43 0.63 33.64 3.27
3218 10601 2.288825 GGACGTGGAGAAGTTCATCACA 60.289 50.000 20.76 6.95 0.00 3.58
3346 10729 1.197721 CACCCTCGCTGCTTTAAACAG 59.802 52.381 11.27 11.27 38.22 3.16
3440 10851 1.021202 TGCTCACGGTTTGGTCTTTG 58.979 50.000 0.00 0.00 0.00 2.77
3441 10852 0.310854 GCTCACGGTTTGGTCTTTGG 59.689 55.000 0.00 0.00 0.00 3.28
3442 10853 0.951558 CTCACGGTTTGGTCTTTGGG 59.048 55.000 0.00 0.00 0.00 4.12
3443 10854 0.466555 TCACGGTTTGGTCTTTGGGG 60.467 55.000 0.00 0.00 0.00 4.96
3444 10855 1.830847 ACGGTTTGGTCTTTGGGGC 60.831 57.895 0.00 0.00 0.00 5.80
3445 10856 2.914908 CGGTTTGGTCTTTGGGGCG 61.915 63.158 0.00 0.00 0.00 6.13
3447 10858 2.915137 TTTGGTCTTTGGGGCGCC 60.915 61.111 21.18 21.18 0.00 6.53
3469 10880 3.551496 CTGTGGCCCCGCTTGAGAA 62.551 63.158 0.00 0.00 0.00 2.87
3470 10881 2.282180 GTGGCCCCGCTTGAGAAA 60.282 61.111 0.00 0.00 0.00 2.52
3476 10887 1.602920 GCCCCGCTTGAGAAAAAGTTG 60.603 52.381 0.00 0.00 0.00 3.16
3478 10889 2.543653 CCCCGCTTGAGAAAAAGTTGTG 60.544 50.000 0.00 0.00 0.00 3.33
3479 10890 2.099098 CCCGCTTGAGAAAAAGTTGTGT 59.901 45.455 0.00 0.00 0.00 3.72
3492 11118 6.740411 AAAAGTTGTGTGCATGTTTTCATT 57.260 29.167 0.00 0.00 38.64 2.57
3523 14836 1.674441 CATAGTGTTCTCGCCTCCGTA 59.326 52.381 0.00 0.00 35.54 4.02
3598 14912 8.687824 AAAGAAAAATAATTATCACCACAGCG 57.312 30.769 0.00 0.00 0.00 5.18
3599 14913 7.391148 AGAAAAATAATTATCACCACAGCGT 57.609 32.000 0.00 0.00 0.00 5.07
3601 14915 9.120538 AGAAAAATAATTATCACCACAGCGTAT 57.879 29.630 0.00 0.00 0.00 3.06
3603 14917 8.445275 AAAATAATTATCACCACAGCGTATCA 57.555 30.769 0.00 0.00 0.00 2.15
3604 14918 8.621532 AAATAATTATCACCACAGCGTATCAT 57.378 30.769 0.00 0.00 0.00 2.45
3605 14919 5.929697 AATTATCACCACAGCGTATCATG 57.070 39.130 0.00 0.00 0.00 3.07
3638 14952 8.711457 CACTTTGCATAACCCTTCATTTAAAAG 58.289 33.333 0.00 0.00 0.00 2.27
3767 15081 4.980805 GACACGTGGCGCCCTTCA 62.981 66.667 26.77 0.59 0.00 3.02
3772 15086 4.681978 GTGGCGCCCTTCACGAGT 62.682 66.667 26.77 0.00 0.00 4.18
3773 15087 2.992689 TGGCGCCCTTCACGAGTA 60.993 61.111 26.77 0.00 0.00 2.59
3774 15088 2.202756 GGCGCCCTTCACGAGTAG 60.203 66.667 18.11 0.00 0.00 2.57
3775 15089 2.886124 GCGCCCTTCACGAGTAGC 60.886 66.667 0.00 0.00 0.00 3.58
3776 15090 2.885861 CGCCCTTCACGAGTAGCT 59.114 61.111 0.00 0.00 0.00 3.32
3777 15091 1.215647 CGCCCTTCACGAGTAGCTT 59.784 57.895 0.00 0.00 0.00 3.74
3778 15092 0.454600 CGCCCTTCACGAGTAGCTTA 59.545 55.000 0.00 0.00 0.00 3.09
3779 15093 1.135199 CGCCCTTCACGAGTAGCTTAA 60.135 52.381 0.00 0.00 0.00 1.85
3780 15094 2.481449 CGCCCTTCACGAGTAGCTTAAT 60.481 50.000 0.00 0.00 0.00 1.40
3781 15095 2.866762 GCCCTTCACGAGTAGCTTAATG 59.133 50.000 0.00 0.00 0.00 1.90
3782 15096 3.458189 CCCTTCACGAGTAGCTTAATGG 58.542 50.000 0.00 0.00 0.00 3.16
3783 15097 3.458189 CCTTCACGAGTAGCTTAATGGG 58.542 50.000 0.00 0.00 0.00 4.00
3784 15098 3.118738 CCTTCACGAGTAGCTTAATGGGT 60.119 47.826 0.00 0.00 0.00 4.51
3785 15099 4.504858 CTTCACGAGTAGCTTAATGGGTT 58.495 43.478 0.00 0.00 0.00 4.11
3786 15100 4.546829 TCACGAGTAGCTTAATGGGTTT 57.453 40.909 0.00 0.00 0.00 3.27
3787 15101 5.664294 TCACGAGTAGCTTAATGGGTTTA 57.336 39.130 0.00 0.00 0.00 2.01
3788 15102 6.040209 TCACGAGTAGCTTAATGGGTTTAA 57.960 37.500 0.00 0.00 0.00 1.52
3789 15103 6.646267 TCACGAGTAGCTTAATGGGTTTAAT 58.354 36.000 0.00 0.00 0.00 1.40
3790 15104 7.784037 TCACGAGTAGCTTAATGGGTTTAATA 58.216 34.615 0.00 0.00 0.00 0.98
3791 15105 8.426489 TCACGAGTAGCTTAATGGGTTTAATAT 58.574 33.333 0.00 0.00 0.00 1.28
3792 15106 9.052759 CACGAGTAGCTTAATGGGTTTAATATT 57.947 33.333 0.00 0.00 0.00 1.28
3793 15107 9.623000 ACGAGTAGCTTAATGGGTTTAATATTT 57.377 29.630 0.00 0.00 0.00 1.40
3802 15116 9.646427 TTAATGGGTTTAATATTTCAAGTGTGC 57.354 29.630 0.00 0.00 0.00 4.57
3808 15122 1.832883 TATTTCAAGTGTGCCGCCAT 58.167 45.000 0.00 0.00 0.00 4.40
3814 15128 1.847798 AAGTGTGCCGCCATCCCTTA 61.848 55.000 0.00 0.00 0.00 2.69
3825 15139 3.431626 CGCCATCCCTTATGAGTGTACAA 60.432 47.826 0.00 0.00 37.86 2.41
3826 15140 4.523083 GCCATCCCTTATGAGTGTACAAA 58.477 43.478 0.00 0.00 37.86 2.83
3836 15150 8.901748 CCTTATGAGTGTACAAAAACATTTTCG 58.098 33.333 0.00 0.00 0.00 3.46
3837 15151 9.658475 CTTATGAGTGTACAAAAACATTTTCGA 57.342 29.630 0.00 0.00 0.00 3.71
3839 15153 8.918961 ATGAGTGTACAAAAACATTTTCGAAA 57.081 26.923 6.47 6.47 0.00 3.46
3840 15154 8.388319 TGAGTGTACAAAAACATTTTCGAAAG 57.612 30.769 10.98 3.11 0.00 2.62
3841 15155 8.024285 TGAGTGTACAAAAACATTTTCGAAAGT 58.976 29.630 10.98 5.26 0.00 2.66
3842 15156 9.493206 GAGTGTACAAAAACATTTTCGAAAGTA 57.507 29.630 10.98 4.66 0.00 2.24
3843 15157 9.843334 AGTGTACAAAAACATTTTCGAAAGTAA 57.157 25.926 10.98 0.00 0.00 2.24
3857 15171 7.982371 TTCGAAAGTAATATTCTCTTCGTCC 57.018 36.000 17.91 5.82 0.00 4.79
3858 15172 6.501781 TCGAAAGTAATATTCTCTTCGTCCC 58.498 40.000 17.91 4.29 0.00 4.46
3859 15173 6.095860 TCGAAAGTAATATTCTCTTCGTCCCA 59.904 38.462 17.91 4.42 0.00 4.37
3860 15174 6.924060 CGAAAGTAATATTCTCTTCGTCCCAT 59.076 38.462 13.50 0.00 0.00 4.00
3861 15175 8.080417 CGAAAGTAATATTCTCTTCGTCCCATA 58.920 37.037 13.50 0.00 0.00 2.74
3862 15176 9.760077 GAAAGTAATATTCTCTTCGTCCCATAA 57.240 33.333 0.00 0.00 0.00 1.90
3871 15185 9.930693 ATTCTCTTCGTCCCATAATATAAGAAC 57.069 33.333 0.00 0.00 0.00 3.01
3872 15186 7.591165 TCTCTTCGTCCCATAATATAAGAACG 58.409 38.462 0.00 0.00 0.00 3.95
3873 15187 7.230108 TCTCTTCGTCCCATAATATAAGAACGT 59.770 37.037 0.00 0.00 0.00 3.99
3874 15188 7.719483 TCTTCGTCCCATAATATAAGAACGTT 58.281 34.615 0.00 0.00 0.00 3.99
3875 15189 8.199449 TCTTCGTCCCATAATATAAGAACGTTT 58.801 33.333 0.46 0.00 0.00 3.60
3876 15190 8.721019 TTCGTCCCATAATATAAGAACGTTTT 57.279 30.769 0.46 0.00 0.00 2.43
3877 15191 8.721019 TCGTCCCATAATATAAGAACGTTTTT 57.279 30.769 9.22 9.22 0.00 1.94
3878 15192 8.605746 TCGTCCCATAATATAAGAACGTTTTTG 58.394 33.333 13.87 0.00 0.00 2.44
3879 15193 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3888 15202 7.989416 ATAAGAACGTTTTTGATACTTGGGA 57.011 32.000 13.87 0.00 0.00 4.37
3894 15208 4.154195 CGTTTTTGATACTTGGGACAGAGG 59.846 45.833 0.00 0.00 42.39 3.69
3896 15210 4.826274 TTTGATACTTGGGACAGAGGAG 57.174 45.455 0.00 0.00 42.39 3.69
3916 15230 5.717178 AGGAGTAATAGTCTGCAGTTTCTGA 59.283 40.000 14.67 0.00 32.44 3.27
4060 15374 5.437191 TTCTTAGAAAAGGAGGATGACCC 57.563 43.478 0.00 0.00 33.27 4.46
4071 15385 1.751563 GATGACCCTAGGCCTCTGC 59.248 63.158 9.68 0.00 0.00 4.26
4074 15388 1.050988 TGACCCTAGGCCTCTGCATC 61.051 60.000 9.68 2.37 40.13 3.91
4078 15392 1.071128 CTAGGCCTCTGCATCTGGC 59.929 63.158 9.68 14.11 45.42 4.85
4090 15404 0.591659 CATCTGGCCGATGCATTCAG 59.408 55.000 19.73 7.25 42.75 3.02
4136 15450 8.461222 CAAAGATCTTACAAAGTAATGCATCCA 58.539 33.333 8.75 0.00 0.00 3.41
4151 15465 4.476297 TGCATCCATAATTCTGAAGCCAT 58.524 39.130 0.00 0.00 0.00 4.40
4158 15472 5.121925 CCATAATTCTGAAGCCATCATCTCG 59.878 44.000 0.00 0.00 37.44 4.04
4188 15502 2.688446 TGTCGCTACTCCTATCCACTTG 59.312 50.000 0.00 0.00 0.00 3.16
4196 15510 3.713764 ACTCCTATCCACTTGATGAAGGG 59.286 47.826 0.00 0.00 34.76 3.95
4237 15551 2.605837 TACCAAACAGACTTCGCACA 57.394 45.000 0.00 0.00 0.00 4.57
4243 15557 2.475200 ACAGACTTCGCACAAAAAGC 57.525 45.000 0.00 0.00 0.00 3.51
4251 15565 3.552604 TCGCACAAAAAGCCTAACATC 57.447 42.857 0.00 0.00 0.00 3.06
4258 15572 6.681777 CACAAAAAGCCTAACATCTAAAGCT 58.318 36.000 0.00 0.00 0.00 3.74
4260 15574 6.490040 ACAAAAAGCCTAACATCTAAAGCTGA 59.510 34.615 0.00 0.00 0.00 4.26
4276 15590 0.469892 CTGAAGGCCCCAACCAAGTT 60.470 55.000 0.00 0.00 0.00 2.66
4278 15592 1.203001 TGAAGGCCCCAACCAAGTTAG 60.203 52.381 0.00 0.00 0.00 2.34
4280 15594 1.382914 AGGCCCCAACCAAGTTAGAT 58.617 50.000 0.00 0.00 0.00 1.98
4285 15599 1.472480 CCCAACCAAGTTAGATTGCCG 59.528 52.381 0.00 0.00 0.00 5.69
4286 15600 1.472480 CCAACCAAGTTAGATTGCCGG 59.528 52.381 0.00 0.00 0.00 6.13
4293 15607 0.252197 GTTAGATTGCCGGGTCTGGT 59.748 55.000 2.18 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.847224 AACAACCAGTTTTCTCTTCTAATAGAA 57.153 29.630 2.44 2.44 37.03 2.10
34 35 2.358322 ACACCCCTGTAAACAACCAG 57.642 50.000 0.00 0.00 0.00 4.00
112 113 3.961477 TGTGTGTGTGCTTGTATGTTC 57.039 42.857 0.00 0.00 0.00 3.18
117 118 2.797719 CGTGTATGTGTGTGTGCTTGTA 59.202 45.455 0.00 0.00 0.00 2.41
121 122 1.497991 GACGTGTATGTGTGTGTGCT 58.502 50.000 0.00 0.00 0.00 4.40
129 130 4.049186 GGTGCTTATAGGACGTGTATGTG 58.951 47.826 0.00 0.00 37.44 3.21
139 140 3.308035 TCCTCGAAGGTGCTTATAGGA 57.692 47.619 0.00 0.00 36.53 2.94
146 147 2.859165 TTCAATTCCTCGAAGGTGCT 57.141 45.000 0.00 0.00 36.53 4.40
154 155 1.498865 CCCGCCGATTCAATTCCTCG 61.499 60.000 0.00 0.00 0.00 4.63
203 204 0.884259 TATGCCCATCGACAATGCGG 60.884 55.000 0.00 0.00 33.71 5.69
205 206 2.679837 CCTATATGCCCATCGACAATGC 59.320 50.000 0.00 0.00 33.71 3.56
208 209 4.262721 GGTAACCTATATGCCCATCGACAA 60.263 45.833 0.00 0.00 0.00 3.18
266 267 1.244019 ATGCTCGCCCTTTTGTGGAC 61.244 55.000 0.00 0.00 0.00 4.02
285 286 6.261381 GGTTGAAGTCCTAAATGTTGTGTGTA 59.739 38.462 0.00 0.00 0.00 2.90
287 288 5.507315 GGGTTGAAGTCCTAAATGTTGTGTG 60.507 44.000 0.00 0.00 0.00 3.82
307 308 1.493022 TGCAACCTACTCAACTGGGTT 59.507 47.619 0.00 0.00 42.01 4.11
409 410 8.111836 TGTATTCGCTTGACAAACGTAAATATC 58.888 33.333 10.51 5.18 0.00 1.63
412 413 6.075280 GTGTATTCGCTTGACAAACGTAAAT 58.925 36.000 10.51 6.93 0.00 1.40
493 494 6.206600 TCGACGTCTTATCAAGTTTTTCAC 57.793 37.500 14.70 0.00 0.00 3.18
555 556 7.206789 TGATTGATTGATGGTTTAGGAGGTA 57.793 36.000 0.00 0.00 0.00 3.08
590 591 2.033299 TGTCGTTTCGTCTACGGTCTTT 59.967 45.455 2.24 0.00 39.38 2.52
591 592 1.603802 TGTCGTTTCGTCTACGGTCTT 59.396 47.619 2.24 0.00 39.38 3.01
593 594 1.974680 CTTGTCGTTTCGTCTACGGTC 59.025 52.381 2.24 0.00 39.38 4.79
594 595 1.335324 CCTTGTCGTTTCGTCTACGGT 60.335 52.381 2.24 0.00 39.38 4.83
595 596 1.069022 TCCTTGTCGTTTCGTCTACGG 60.069 52.381 2.24 0.00 39.38 4.02
598 599 4.572985 TTCTTCCTTGTCGTTTCGTCTA 57.427 40.909 0.00 0.00 0.00 2.59
662 670 0.035317 AGTTTGCTGTGAGCGGATGA 59.965 50.000 0.00 0.00 46.26 2.92
670 678 2.451490 TGGTTTTCCAGTTTGCTGTGA 58.549 42.857 0.00 0.00 46.22 3.58
837 846 4.942761 ATCGGCGAGTAATTAAGGGTAA 57.057 40.909 17.22 0.00 0.00 2.85
920 930 1.528161 GCTTTGCAGTTGGTTGATTGC 59.472 47.619 0.00 0.00 37.09 3.56
1081 1120 2.575279 AGCACTGATGAAATCCCAGAGT 59.425 45.455 0.00 0.00 44.73 3.24
1088 1127 6.532657 CCAAACCAATTAGCACTGATGAAATC 59.467 38.462 0.00 0.00 45.83 2.17
1287 1330 5.814705 CCTGAAACTATGGTCTGAATGTCTC 59.185 44.000 0.00 0.00 0.00 3.36
1349 1441 0.466555 AACCACGCCAAGTTAGCCAA 60.467 50.000 0.00 0.00 0.00 4.52
1501 4554 4.310357 GTAAAGTGCCCCTTTTCGAAAA 57.690 40.909 21.35 21.35 40.55 2.29
1507 4560 4.739587 TTTTTCGTAAAGTGCCCCTTTT 57.260 36.364 4.07 0.00 40.55 2.27
1534 4587 7.983484 GCTGATTAATTTGGTGGAATCTTGAAT 59.017 33.333 0.00 0.00 31.03 2.57
1539 4592 6.855763 TTGCTGATTAATTTGGTGGAATCT 57.144 33.333 0.00 0.00 31.03 2.40
1540 4593 7.387397 TGTTTTGCTGATTAATTTGGTGGAATC 59.613 33.333 0.00 0.00 0.00 2.52
1541 4594 7.222872 TGTTTTGCTGATTAATTTGGTGGAAT 58.777 30.769 0.00 0.00 0.00 3.01
1542 4595 6.586344 TGTTTTGCTGATTAATTTGGTGGAA 58.414 32.000 0.00 0.00 0.00 3.53
1544 4597 6.857777 TTGTTTTGCTGATTAATTTGGTGG 57.142 33.333 0.00 0.00 0.00 4.61
1546 4599 9.341078 AGATTTTGTTTTGCTGATTAATTTGGT 57.659 25.926 0.00 0.00 0.00 3.67
1555 4608 9.985730 TGATTCTTAAGATTTTGTTTTGCTGAT 57.014 25.926 5.89 0.00 0.00 2.90
1561 4614 9.710900 GTCCCATGATTCTTAAGATTTTGTTTT 57.289 29.630 5.89 0.00 0.00 2.43
1562 4615 8.869109 TGTCCCATGATTCTTAAGATTTTGTTT 58.131 29.630 5.89 0.00 0.00 2.83
1563 4616 8.421249 TGTCCCATGATTCTTAAGATTTTGTT 57.579 30.769 5.89 0.00 0.00 2.83
1943 9026 2.436646 GGACATGGTCACCTGGCG 60.437 66.667 0.00 0.00 33.68 5.69
2226 9309 6.876257 ACAATCAGAACAATCTCTTACCAGTC 59.124 38.462 0.00 0.00 32.03 3.51
2828 10115 1.613437 CACCTGGACCACAATTCAACC 59.387 52.381 0.00 0.00 0.00 3.77
2854 10143 1.971357 ACTCCACCGTTTGTCATCTCT 59.029 47.619 0.00 0.00 0.00 3.10
2965 10255 4.171005 CACCAATGCTCACAATGATCAAC 58.829 43.478 0.00 0.00 0.00 3.18
3074 10441 1.052124 TCGGGTGGGTCTTGAACACT 61.052 55.000 0.00 0.00 35.53 3.55
3188 10565 0.832135 TCTCCACGTCCAGCTCCTTT 60.832 55.000 0.00 0.00 0.00 3.11
3218 10601 1.956170 CGAGAAAGGCACGCTGTGT 60.956 57.895 9.76 0.00 35.75 3.72
3458 10869 2.099098 ACACAACTTTTTCTCAAGCGGG 59.901 45.455 0.00 0.00 0.00 6.13
3459 10870 3.108144 CACACAACTTTTTCTCAAGCGG 58.892 45.455 0.00 0.00 0.00 5.52
3469 10880 6.740411 AATGAAAACATGCACACAACTTTT 57.260 29.167 0.00 0.00 0.00 2.27
3470 10881 6.740411 AAATGAAAACATGCACACAACTTT 57.260 29.167 0.00 0.00 0.00 2.66
3502 11128 0.456221 CGGAGGCGAGAACACTATGT 59.544 55.000 0.00 0.00 0.00 2.29
3503 11129 0.456221 ACGGAGGCGAGAACACTATG 59.544 55.000 0.00 0.00 0.00 2.23
3505 11131 2.048444 ATACGGAGGCGAGAACACTA 57.952 50.000 0.00 0.00 0.00 2.74
3508 11134 3.872511 TTTTATACGGAGGCGAGAACA 57.127 42.857 0.00 0.00 0.00 3.18
3582 14896 5.931724 CCATGATACGCTGTGGTGATAATTA 59.068 40.000 0.00 0.00 0.00 1.40
3583 14897 4.756642 CCATGATACGCTGTGGTGATAATT 59.243 41.667 0.00 0.00 0.00 1.40
3586 14900 2.962421 TCCATGATACGCTGTGGTGATA 59.038 45.455 0.00 0.00 33.47 2.15
3591 14905 1.575244 CACTCCATGATACGCTGTGG 58.425 55.000 0.00 0.00 0.00 4.17
3592 14906 0.933097 GCACTCCATGATACGCTGTG 59.067 55.000 0.00 0.00 0.00 3.66
3593 14907 0.179073 GGCACTCCATGATACGCTGT 60.179 55.000 0.00 0.00 0.00 4.40
3595 14909 0.179073 GTGGCACTCCATGATACGCT 60.179 55.000 11.13 0.00 45.62 5.07
3596 14910 0.179073 AGTGGCACTCCATGATACGC 60.179 55.000 15.88 0.00 45.62 4.42
3597 14911 2.315925 AAGTGGCACTCCATGATACG 57.684 50.000 22.31 0.00 45.62 3.06
3598 14912 2.098117 GCAAAGTGGCACTCCATGATAC 59.902 50.000 22.31 4.79 45.62 2.24
3599 14913 2.290832 TGCAAAGTGGCACTCCATGATA 60.291 45.455 22.31 10.16 45.62 2.15
3601 14915 0.178995 TGCAAAGTGGCACTCCATGA 60.179 50.000 22.31 8.02 45.62 3.07
3603 14917 4.927557 TGCAAAGTGGCACTCCAT 57.072 50.000 22.31 7.68 45.62 3.41
3651 14965 7.524717 TTTTTCTTTTTAGATGGAGGTGAGG 57.475 36.000 0.00 0.00 0.00 3.86
3722 15036 0.034756 GTTGGCCCGGCAAGAAATTT 59.965 50.000 12.58 0.00 0.00 1.82
3724 15038 2.282783 GGTTGGCCCGGCAAGAAAT 61.283 57.895 12.58 0.00 0.00 2.17
3727 15041 4.659172 CTGGTTGGCCCGGCAAGA 62.659 66.667 12.58 0.00 35.15 3.02
3760 15074 2.667473 TTAAGCTACTCGTGAAGGGC 57.333 50.000 0.00 0.00 0.00 5.19
3761 15075 3.458189 CCATTAAGCTACTCGTGAAGGG 58.542 50.000 0.00 0.00 0.00 3.95
3762 15076 3.118738 ACCCATTAAGCTACTCGTGAAGG 60.119 47.826 0.00 0.00 0.00 3.46
3763 15077 4.124851 ACCCATTAAGCTACTCGTGAAG 57.875 45.455 0.00 0.00 0.00 3.02
3764 15078 4.546829 AACCCATTAAGCTACTCGTGAA 57.453 40.909 0.00 0.00 0.00 3.18
3765 15079 4.546829 AAACCCATTAAGCTACTCGTGA 57.453 40.909 0.00 0.00 0.00 4.35
3766 15080 6.920569 ATTAAACCCATTAAGCTACTCGTG 57.079 37.500 0.00 0.00 36.94 4.35
3767 15081 9.623000 AAATATTAAACCCATTAAGCTACTCGT 57.377 29.630 0.00 0.00 36.94 4.18
3774 15088 9.869757 ACACTTGAAATATTAAACCCATTAAGC 57.130 29.630 0.00 0.00 36.94 3.09
3776 15090 9.646427 GCACACTTGAAATATTAAACCCATTAA 57.354 29.630 0.00 0.00 37.86 1.40
3777 15091 8.254508 GGCACACTTGAAATATTAAACCCATTA 58.745 33.333 0.00 0.00 0.00 1.90
3778 15092 7.102993 GGCACACTTGAAATATTAAACCCATT 58.897 34.615 0.00 0.00 0.00 3.16
3779 15093 6.627065 CGGCACACTTGAAATATTAAACCCAT 60.627 38.462 0.00 0.00 0.00 4.00
3780 15094 5.336055 CGGCACACTTGAAATATTAAACCCA 60.336 40.000 0.00 0.00 0.00 4.51
3781 15095 5.099575 CGGCACACTTGAAATATTAAACCC 58.900 41.667 0.00 0.00 0.00 4.11
3782 15096 4.561213 GCGGCACACTTGAAATATTAAACC 59.439 41.667 0.00 0.00 0.00 3.27
3783 15097 4.561213 GGCGGCACACTTGAAATATTAAAC 59.439 41.667 3.07 0.00 0.00 2.01
3784 15098 4.218635 TGGCGGCACACTTGAAATATTAAA 59.781 37.500 7.97 0.00 0.00 1.52
3785 15099 3.759086 TGGCGGCACACTTGAAATATTAA 59.241 39.130 7.97 0.00 0.00 1.40
3786 15100 3.348119 TGGCGGCACACTTGAAATATTA 58.652 40.909 7.97 0.00 0.00 0.98
3787 15101 2.166829 TGGCGGCACACTTGAAATATT 58.833 42.857 7.97 0.00 0.00 1.28
3788 15102 1.832883 TGGCGGCACACTTGAAATAT 58.167 45.000 7.97 0.00 0.00 1.28
3789 15103 1.742831 GATGGCGGCACACTTGAAATA 59.257 47.619 16.34 0.00 0.00 1.40
3790 15104 0.527565 GATGGCGGCACACTTGAAAT 59.472 50.000 16.34 0.00 0.00 2.17
3791 15105 1.523154 GGATGGCGGCACACTTGAAA 61.523 55.000 16.34 0.00 0.00 2.69
3792 15106 1.971167 GGATGGCGGCACACTTGAA 60.971 57.895 16.34 0.00 0.00 2.69
3793 15107 2.359850 GGATGGCGGCACACTTGA 60.360 61.111 16.34 0.00 0.00 3.02
3794 15108 3.443045 GGGATGGCGGCACACTTG 61.443 66.667 16.34 0.00 0.00 3.16
3795 15109 1.847798 TAAGGGATGGCGGCACACTT 61.848 55.000 24.38 24.38 0.00 3.16
3802 15116 0.469917 ACACTCATAAGGGATGGCGG 59.530 55.000 0.00 0.00 36.08 6.13
3808 15122 8.472007 AAATGTTTTTGTACACTCATAAGGGA 57.528 30.769 0.00 0.00 0.00 4.20
3814 15128 8.918961 TTTCGAAAATGTTTTTGTACACTCAT 57.081 26.923 8.44 0.00 34.04 2.90
3836 15150 9.760077 TTATGGGACGAAGAGAATATTACTTTC 57.240 33.333 8.22 3.27 0.00 2.62
3845 15159 9.930693 GTTCTTATATTATGGGACGAAGAGAAT 57.069 33.333 0.00 0.00 0.00 2.40
3846 15160 8.080417 CGTTCTTATATTATGGGACGAAGAGAA 58.920 37.037 0.00 0.00 0.00 2.87
3847 15161 7.230108 ACGTTCTTATATTATGGGACGAAGAGA 59.770 37.037 14.76 0.00 0.00 3.10
3848 15162 7.368833 ACGTTCTTATATTATGGGACGAAGAG 58.631 38.462 14.76 0.00 0.00 2.85
3849 15163 7.281040 ACGTTCTTATATTATGGGACGAAGA 57.719 36.000 14.76 1.52 0.00 2.87
3850 15164 7.941795 AACGTTCTTATATTATGGGACGAAG 57.058 36.000 14.76 0.00 0.00 3.79
3851 15165 8.721019 AAAACGTTCTTATATTATGGGACGAA 57.279 30.769 0.00 0.00 0.00 3.85
3852 15166 8.605746 CAAAAACGTTCTTATATTATGGGACGA 58.394 33.333 0.00 0.00 0.00 4.20
3853 15167 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3862 15176 9.675464 TCCCAAGTATCAAAAACGTTCTTATAT 57.325 29.630 0.00 0.00 0.00 0.86
3863 15177 8.938906 GTCCCAAGTATCAAAAACGTTCTTATA 58.061 33.333 0.00 0.00 0.00 0.98
3864 15178 7.446013 TGTCCCAAGTATCAAAAACGTTCTTAT 59.554 33.333 0.00 0.00 0.00 1.73
3865 15179 6.766944 TGTCCCAAGTATCAAAAACGTTCTTA 59.233 34.615 0.00 0.00 0.00 2.10
3866 15180 5.591067 TGTCCCAAGTATCAAAAACGTTCTT 59.409 36.000 0.00 0.00 0.00 2.52
3867 15181 5.127491 TGTCCCAAGTATCAAAAACGTTCT 58.873 37.500 0.00 0.00 0.00 3.01
3868 15182 5.237779 TCTGTCCCAAGTATCAAAAACGTTC 59.762 40.000 0.00 0.00 0.00 3.95
3869 15183 5.127491 TCTGTCCCAAGTATCAAAAACGTT 58.873 37.500 0.00 0.00 0.00 3.99
3870 15184 4.710324 TCTGTCCCAAGTATCAAAAACGT 58.290 39.130 0.00 0.00 0.00 3.99
3871 15185 4.154195 CCTCTGTCCCAAGTATCAAAAACG 59.846 45.833 0.00 0.00 0.00 3.60
3872 15186 5.313712 TCCTCTGTCCCAAGTATCAAAAAC 58.686 41.667 0.00 0.00 0.00 2.43
3873 15187 5.073144 ACTCCTCTGTCCCAAGTATCAAAAA 59.927 40.000 0.00 0.00 0.00 1.94
3874 15188 4.597507 ACTCCTCTGTCCCAAGTATCAAAA 59.402 41.667 0.00 0.00 0.00 2.44
3875 15189 4.168101 ACTCCTCTGTCCCAAGTATCAAA 58.832 43.478 0.00 0.00 0.00 2.69
3876 15190 3.791320 ACTCCTCTGTCCCAAGTATCAA 58.209 45.455 0.00 0.00 0.00 2.57
3877 15191 3.474798 ACTCCTCTGTCCCAAGTATCA 57.525 47.619 0.00 0.00 0.00 2.15
3878 15192 6.778559 ACTATTACTCCTCTGTCCCAAGTATC 59.221 42.308 0.00 0.00 0.00 2.24
3879 15193 6.684538 ACTATTACTCCTCTGTCCCAAGTAT 58.315 40.000 0.00 0.00 0.00 2.12
3880 15194 6.068971 AGACTATTACTCCTCTGTCCCAAGTA 60.069 42.308 0.00 0.00 0.00 2.24
3881 15195 4.949121 ACTATTACTCCTCTGTCCCAAGT 58.051 43.478 0.00 0.00 0.00 3.16
3882 15196 5.068460 CAGACTATTACTCCTCTGTCCCAAG 59.932 48.000 0.00 0.00 0.00 3.61
3883 15197 4.956700 CAGACTATTACTCCTCTGTCCCAA 59.043 45.833 0.00 0.00 0.00 4.12
3884 15198 4.537751 CAGACTATTACTCCTCTGTCCCA 58.462 47.826 0.00 0.00 0.00 4.37
3885 15199 3.319689 GCAGACTATTACTCCTCTGTCCC 59.680 52.174 0.00 0.00 33.92 4.46
3886 15200 3.954904 TGCAGACTATTACTCCTCTGTCC 59.045 47.826 0.00 0.00 33.92 4.02
3887 15201 4.642885 ACTGCAGACTATTACTCCTCTGTC 59.357 45.833 23.35 0.00 33.92 3.51
3888 15202 4.605183 ACTGCAGACTATTACTCCTCTGT 58.395 43.478 23.35 0.00 33.92 3.41
3894 15208 6.626302 ACTCAGAAACTGCAGACTATTACTC 58.374 40.000 23.35 0.00 0.00 2.59
3896 15210 6.868864 TGAACTCAGAAACTGCAGACTATTAC 59.131 38.462 23.35 4.37 0.00 1.89
3916 15230 3.356529 AGGAAGATGCCGATTTGAACT 57.643 42.857 0.00 0.00 0.00 3.01
3977 15291 1.399727 CGCAAAACATCGGAAGTGGTC 60.400 52.381 0.00 0.00 0.00 4.02
3999 15313 5.971895 GCATTCTGCAAACAAAAAGAAGA 57.028 34.783 0.00 0.00 44.26 2.87
4038 15352 5.101529 AGGGTCATCCTCCTTTTCTAAGAA 58.898 41.667 0.00 0.00 44.06 2.52
4039 15353 4.699994 AGGGTCATCCTCCTTTTCTAAGA 58.300 43.478 0.00 0.00 44.06 2.10
4040 15354 5.071115 CCTAGGGTCATCCTCCTTTTCTAAG 59.929 48.000 0.00 0.00 44.06 2.18
4041 15355 4.969359 CCTAGGGTCATCCTCCTTTTCTAA 59.031 45.833 0.00 0.00 44.06 2.10
4042 15356 4.557705 CCTAGGGTCATCCTCCTTTTCTA 58.442 47.826 0.00 0.00 44.06 2.10
4060 15374 1.071128 GCCAGATGCAGAGGCCTAG 59.929 63.158 4.42 1.87 42.58 3.02
4061 15375 3.234349 GCCAGATGCAGAGGCCTA 58.766 61.111 4.42 0.00 42.58 3.93
4078 15392 2.589798 AAAATGGCTGAATGCATCGG 57.410 45.000 0.00 0.00 45.15 4.18
4125 15439 6.016024 TGGCTTCAGAATTATGGATGCATTAC 60.016 38.462 4.56 0.00 34.48 1.89
4130 15444 4.521639 TGATGGCTTCAGAATTATGGATGC 59.478 41.667 0.00 2.75 0.00 3.91
4136 15450 5.243981 CCGAGATGATGGCTTCAGAATTAT 58.756 41.667 9.09 0.00 37.89 1.28
4151 15465 1.731709 CGACAAATGTTGCCGAGATGA 59.268 47.619 0.00 0.00 38.91 2.92
4164 15478 3.961408 AGTGGATAGGAGTAGCGACAAAT 59.039 43.478 0.00 0.00 0.00 2.32
4176 15490 3.048600 CCCCTTCATCAAGTGGATAGGA 58.951 50.000 0.00 0.00 33.95 2.94
4188 15502 2.093500 GGATTTTTGGCACCCCTTCATC 60.093 50.000 0.00 0.00 0.00 2.92
4196 15510 1.069358 TCGGTTTGGATTTTTGGCACC 59.931 47.619 0.00 0.00 0.00 5.01
4237 15551 7.309438 CCTTCAGCTTTAGATGTTAGGCTTTTT 60.309 37.037 0.00 0.00 31.70 1.94
4243 15557 3.879892 GGCCTTCAGCTTTAGATGTTAGG 59.120 47.826 0.00 11.73 43.05 2.69
4251 15565 1.177401 GTTGGGGCCTTCAGCTTTAG 58.823 55.000 0.84 0.00 43.05 1.85
4258 15572 0.854218 TAACTTGGTTGGGGCCTTCA 59.146 50.000 0.84 0.00 0.00 3.02
4260 15574 1.154430 TCTAACTTGGTTGGGGCCTT 58.846 50.000 0.84 0.00 0.00 4.35
4276 15590 1.904771 CACCAGACCCGGCAATCTA 59.095 57.895 0.00 0.00 0.00 1.98
4278 15592 3.134127 GCACCAGACCCGGCAATC 61.134 66.667 0.00 0.00 0.00 2.67
4280 15594 4.947147 GTGCACCAGACCCGGCAA 62.947 66.667 5.22 0.00 38.10 4.52


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

AutoCloner maintained by Alex Coulton.