Multiple sequence alignment - TraesCS4B01G397500

Loading Multiple Alignment...

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 TraesCS4B01G397500 chr4B 100.000 3978 0 0 1 3978 671734852 671730875 0.000000e+00 7347.0
1 TraesCS4B01G397500 chr4B 84.108 409 37 16 2239 2631 671814265 671814661 1.750000e-98 370.0
2 TraesCS4B01G397500 chr4B 91.235 251 17 2 1376 1625 671814006 671814252 1.770000e-88 337.0
3 TraesCS4B01G397500 chr4B 80.836 287 49 6 230 511 193678182 193678467 1.860000e-53 220.0
4 TraesCS4B01G397500 chr4B 80.060 336 32 16 866 1180 671813451 671813772 2.410000e-52 217.0
5 TraesCS4B01G397500 chr4B 89.362 47 5 0 1671 1717 581520628 581520674 4.290000e-05 60.2
6 TraesCS4B01G397500 chr5A 95.310 2260 76 12 1733 3978 659201898 659204141 0.000000e+00 3559.0
7 TraesCS4B01G397500 chr5A 90.467 1091 76 17 550 1623 659184673 659185752 0.000000e+00 1413.0
8 TraesCS4B01G397500 chr5A 88.386 1016 81 15 1999 3000 709732358 709731366 0.000000e+00 1188.0
9 TraesCS4B01G397500 chr5A 92.761 373 24 3 1265 1635 659186186 659186557 1.630000e-148 536.0
10 TraesCS4B01G397500 chr5A 83.099 497 56 17 1993 2472 659185497 659185982 1.020000e-115 427.0
11 TraesCS4B01G397500 chr5A 79.921 508 71 15 1973 2457 709724476 709723977 1.060000e-90 344.0
12 TraesCS4B01G397500 chr5A 89.453 256 20 2 2254 2509 659186580 659186828 2.310000e-82 316.0
13 TraesCS4B01G397500 chr5A 83.526 346 33 16 727 1050 659197416 659197759 6.460000e-78 302.0
14 TraesCS4B01G397500 chr5A 83.268 257 34 4 1372 1623 709724451 709724199 1.110000e-55 228.0
15 TraesCS4B01G397500 chr5A 80.723 249 34 7 1999 2242 659186293 659186532 8.780000e-42 182.0
16 TraesCS4B01G397500 chr5A 82.787 122 15 5 1964 2080 709410520 709410640 1.960000e-18 104.0
17 TraesCS4B01G397500 chrUn 95.784 1257 48 5 1733 2986 30341380 30340126 0.000000e+00 2023.0
18 TraesCS4B01G397500 chrUn 91.478 1103 66 10 550 1635 30347661 30346570 0.000000e+00 1491.0
19 TraesCS4B01G397500 chrUn 81.565 575 61 25 727 1260 30342363 30341793 2.200000e-117 433.0
20 TraesCS4B01G397500 chrUn 91.892 259 19 1 2254 2512 30346547 30346291 1.050000e-95 361.0
21 TraesCS4B01G397500 chrUn 81.185 287 48 5 230 511 80031523 80031238 4.000000e-55 226.0
22 TraesCS4B01G397500 chrUn 84.211 152 24 0 2094 2245 30346743 30346592 8.910000e-32 148.0
23 TraesCS4B01G397500 chrUn 76.207 290 52 9 18 291 352658941 352659229 1.930000e-28 137.0
24 TraesCS4B01G397500 chrUn 76.207 290 52 9 18 291 468704360 468704648 1.930000e-28 137.0
25 TraesCS4B01G397500 chrUn 94.118 51 3 0 1672 1722 96733183 96733233 1.190000e-10 78.7
26 TraesCS4B01G397500 chr5D 90.814 479 30 5 3042 3519 495167705 495168170 2.610000e-176 628.0
27 TraesCS4B01G397500 chr5D 88.333 480 38 8 3042 3520 286181757 286181295 9.650000e-156 560.0
28 TraesCS4B01G397500 chr5D 94.643 224 11 1 3040 3262 510631342 510631119 2.940000e-91 346.0
29 TraesCS4B01G397500 chr5D 77.861 533 92 14 2 511 59013737 59013208 1.390000e-79 307.0
30 TraesCS4B01G397500 chr5D 76.525 541 94 17 2 509 218873890 218874430 8.480000e-67 265.0
31 TraesCS4B01G397500 chr5B 90.329 486 33 5 3029 3514 673286215 673286686 3.380000e-175 625.0
32 TraesCS4B01G397500 chr5B 78.713 202 41 2 22 221 293373907 293373706 2.490000e-27 134.0
33 TraesCS4B01G397500 chr5B 98.507 67 1 0 1733 1799 437184689 437184755 6.980000e-23 119.0
34 TraesCS4B01G397500 chr3D 90.188 479 33 4 3042 3519 62349522 62349987 2.630000e-171 612.0
35 TraesCS4B01G397500 chr3D 82.230 287 45 5 230 511 295535025 295535310 3.970000e-60 243.0
36 TraesCS4B01G397500 chr3D 94.521 73 4 0 1733 1805 10912426 10912498 3.250000e-21 113.0
37 TraesCS4B01G397500 chr3D 89.583 48 5 0 1671 1718 10912324 10912371 1.190000e-05 62.1
38 TraesCS4B01G397500 chr6B 90.208 480 28 7 3045 3519 17492012 17491547 3.400000e-170 608.0
39 TraesCS4B01G397500 chr6B 98.630 73 1 0 1733 1805 495761656 495761728 3.230000e-26 130.0
40 TraesCS4B01G397500 chr6B 97.260 73 2 0 1733 1805 550368790 550368862 1.500000e-24 124.0
41 TraesCS4B01G397500 chr6B 91.837 49 4 0 1671 1719 550368688 550368736 7.130000e-08 69.4
42 TraesCS4B01G397500 chr7D 89.813 481 34 5 3041 3520 543334317 543333851 1.580000e-168 603.0
43 TraesCS4B01G397500 chr7D 88.981 481 36 6 3041 3519 95279521 95279986 2.670000e-161 579.0
44 TraesCS4B01G397500 chr7D 80.247 810 125 22 2239 3040 408719253 408720035 9.590000e-161 577.0
45 TraesCS4B01G397500 chr7D 80.776 541 69 20 666 1180 408718016 408718547 1.340000e-104 390.0
46 TraesCS4B01G397500 chr7D 77.691 511 97 11 17 511 477982730 477983239 3.010000e-76 296.0
47 TraesCS4B01G397500 chr7D 97.260 73 2 0 1733 1805 140301955 140301883 1.500000e-24 124.0
48 TraesCS4B01G397500 chr7D 95.522 67 3 0 1297 1363 408718888 408718954 1.510000e-19 108.0
49 TraesCS4B01G397500 chr7D 90.385 52 5 0 1671 1722 140302057 140302006 7.130000e-08 69.4
50 TraesCS4B01G397500 chr1D 88.727 479 35 6 3042 3519 405171337 405171797 5.770000e-158 568.0
51 TraesCS4B01G397500 chr1D 86.765 476 45 6 3040 3513 208111918 208111459 7.620000e-142 514.0
52 TraesCS4B01G397500 chr1D 86.681 473 47 6 3042 3513 38553960 38553503 9.860000e-141 510.0
53 TraesCS4B01G397500 chr7A 81.919 542 61 17 666 1180 468831756 468832287 1.320000e-114 424.0
54 TraesCS4B01G397500 chr7A 89.427 227 22 1 2239 2465 468832992 468833216 6.510000e-73 285.0
55 TraesCS4B01G397500 chr7A 81.404 285 47 5 230 508 422487685 422487969 1.110000e-55 228.0
56 TraesCS4B01G397500 chr7A 81.481 270 45 4 247 511 592160120 592159851 2.410000e-52 217.0
57 TraesCS4B01G397500 chr7B 80.591 541 70 20 666 1180 423139006 423139537 6.240000e-103 385.0
58 TraesCS4B01G397500 chr7B 81.423 253 33 9 1372 1623 423139983 423140222 1.130000e-45 195.0
59 TraesCS4B01G397500 chr7B 95.522 67 3 0 1297 1363 423139873 423139939 1.510000e-19 108.0
60 TraesCS4B01G397500 chr6D 78.614 505 92 12 18 512 304619543 304619045 1.780000e-83 320.0
61 TraesCS4B01G397500 chr6D 77.713 516 90 17 13 510 458771313 458770805 3.890000e-75 292.0
62 TraesCS4B01G397500 chr2A 80.348 402 49 20 136 510 706680897 706680499 1.090000e-70 278.0
63 TraesCS4B01G397500 chr2A 95.714 70 3 0 1736 1805 624970217 624970148 3.250000e-21 113.0
64 TraesCS4B01G397500 chr3A 77.037 540 87 21 3 510 278639533 278640067 3.920000e-70 276.0
65 TraesCS4B01G397500 chr3B 78.973 409 60 21 120 508 657590963 657591365 5.100000e-64 255.0
66 TraesCS4B01G397500 chr2B 86.266 233 29 3 281 511 765328289 765328520 2.370000e-62 250.0
67 TraesCS4B01G397500 chr4D 75.601 541 101 13 1 511 133241202 133241741 5.140000e-59 239.0
68 TraesCS4B01G397500 chr2D 73.870 509 106 22 15 506 155725734 155725236 1.140000e-40 178.0
69 TraesCS4B01G397500 chr1A 97.260 73 2 0 1733 1805 365531479 365531407 1.500000e-24 124.0
70 TraesCS4B01G397500 chr1A 90.385 52 5 0 1671 1722 365531581 365531530 7.130000e-08 69.4


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 TraesCS4B01G397500 chr4B 671730875 671734852 3977 True 7347.000000 7347 100.000000 1 3978 1 chr4B.!!$R1 3977
1 TraesCS4B01G397500 chr4B 671813451 671814661 1210 False 308.000000 370 85.134333 866 2631 3 chr4B.!!$F3 1765
2 TraesCS4B01G397500 chr5A 659201898 659204141 2243 False 3559.000000 3559 95.310000 1733 3978 1 chr5A.!!$F2 2245
3 TraesCS4B01G397500 chr5A 709731366 709732358 992 True 1188.000000 1188 88.386000 1999 3000 1 chr5A.!!$R1 1001
4 TraesCS4B01G397500 chr5A 659184673 659186828 2155 False 574.800000 1413 87.300600 550 2509 5 chr5A.!!$F4 1959
5 TraesCS4B01G397500 chrUn 30340126 30347661 7535 True 891.200000 2023 88.986000 550 2986 5 chrUn.!!$R2 2436
6 TraesCS4B01G397500 chr5D 59013208 59013737 529 True 307.000000 307 77.861000 2 511 1 chr5D.!!$R1 509
7 TraesCS4B01G397500 chr5D 218873890 218874430 540 False 265.000000 265 76.525000 2 509 1 chr5D.!!$F1 507
8 TraesCS4B01G397500 chr7D 408718016 408720035 2019 False 358.333333 577 85.515000 666 3040 3 chr7D.!!$F3 2374
9 TraesCS4B01G397500 chr7D 477982730 477983239 509 False 296.000000 296 77.691000 17 511 1 chr7D.!!$F2 494
10 TraesCS4B01G397500 chr7A 468831756 468833216 1460 False 354.500000 424 85.673000 666 2465 2 chr7A.!!$F2 1799
11 TraesCS4B01G397500 chr7B 423139006 423140222 1216 False 229.333333 385 85.845333 666 1623 3 chr7B.!!$F1 957
12 TraesCS4B01G397500 chr6D 458770805 458771313 508 True 292.000000 292 77.713000 13 510 1 chr6D.!!$R2 497
13 TraesCS4B01G397500 chr3A 278639533 278640067 534 False 276.000000 276 77.037000 3 510 1 chr3A.!!$F1 507
14 TraesCS4B01G397500 chr4D 133241202 133241741 539 False 239.000000 239 75.601000 1 511 1 chr4D.!!$F1 510

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
55 56 0.033796 TCTCCACCCGAGGTCGTATT 60.034 55.0 0.00 0.0 39.30 1.89 F
1382 1719 0.169672 ATTGCGACTCTGCATTGCAC 59.830 50.0 7.38 0.0 45.78 4.57 F
1694 2032 0.168128 GCCGCACACCACTATTTGAC 59.832 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1995 0.030235 GCGGTGGGTTTGAGTGTTTC 59.970 55.000 0.00 0.00 0.00 2.78 R
2886 9263 3.064408 ACACATATCTTCAGTGCAATGCG 59.936 43.478 9.79 3.04 36.76 4.73 R
3435 9816 2.363788 TGAGATCCGTGCTACACAAC 57.636 50.000 0.00 0.00 33.40 3.32 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
34 35 2.029380 GGATAAAGTTGCTTTTGGGCGT 60.029 45.455 0.00 0.00 35.21 5.68
39 40 0.317854 GTTGCTTTTGGGCGTGTCTC 60.318 55.000 0.00 0.00 34.52 3.36
42 43 1.949257 CTTTTGGGCGTGTCTCCAC 59.051 57.895 0.00 0.00 38.27 4.02
53 54 1.377725 GTCTCCACCCGAGGTCGTA 60.378 63.158 0.00 0.00 39.30 3.43
55 56 0.033796 TCTCCACCCGAGGTCGTATT 60.034 55.000 0.00 0.00 39.30 1.89
66 67 2.429610 GAGGTCGTATTTAGCCTGTGGA 59.570 50.000 0.00 0.00 0.00 4.02
71 72 2.651455 GTATTTAGCCTGTGGAACCCC 58.349 52.381 0.00 0.00 34.36 4.95
78 79 0.397816 CCTGTGGAACCCCAAAACCA 60.398 55.000 0.00 0.00 45.59 3.67
81 82 1.834263 TGTGGAACCCCAAAACCAAAG 59.166 47.619 0.00 0.00 45.59 2.77
86 87 3.451540 GGAACCCCAAAACCAAAGTGTTA 59.548 43.478 0.00 0.00 0.00 2.41
95 96 7.013846 CCCAAAACCAAAGTGTTATCTTAGACA 59.986 37.037 0.00 0.00 0.00 3.41
100 101 7.039882 ACCAAAGTGTTATCTTAGACATACCG 58.960 38.462 0.00 0.00 0.00 4.02
207 222 5.104374 GTGATGGCCAATTGAACAACATAG 58.896 41.667 10.96 0.00 0.00 2.23
218 234 8.629986 CAATTGAACAACATAGAATCGACAAAC 58.370 33.333 0.00 0.00 0.00 2.93
219 235 6.852858 TGAACAACATAGAATCGACAAACA 57.147 33.333 0.00 0.00 0.00 2.83
255 292 5.675684 TTTCTTTTGCCCAGTTCTTCTTT 57.324 34.783 0.00 0.00 0.00 2.52
264 313 5.363580 TGCCCAGTTCTTCTTTTTCTCATTT 59.636 36.000 0.00 0.00 0.00 2.32
272 321 9.072294 GTTCTTCTTTTTCTCATTTTTCGTTCA 57.928 29.630 0.00 0.00 0.00 3.18
291 341 0.827507 ATTCTTTGTTGCAGGGCGGT 60.828 50.000 0.00 0.00 0.00 5.68
294 344 1.526575 CTTTGTTGCAGGGCGGTGAT 61.527 55.000 0.00 0.00 0.00 3.06
334 387 2.526873 AGGTCGACCTTGGGCAGT 60.527 61.111 31.69 7.13 46.09 4.40
364 417 3.991051 CACGCCACGACAGGGTCT 61.991 66.667 0.00 0.00 0.00 3.85
366 419 3.680786 CGCCACGACAGGGTCTCA 61.681 66.667 0.00 0.00 0.00 3.27
369 423 2.207229 CCACGACAGGGTCTCACCA 61.207 63.158 0.00 0.00 41.02 4.17
372 426 1.606601 CGACAGGGTCTCACCAGGA 60.607 63.158 0.00 0.00 41.02 3.86
376 430 1.152312 AGGGTCTCACCAGGACGTT 60.152 57.895 0.00 0.00 41.02 3.99
446 504 4.295119 CGGCCGGGTATCCTTCGG 62.295 72.222 20.10 0.00 45.84 4.30
449 507 2.108362 CCGGGTATCCTTCGGCAC 59.892 66.667 0.00 0.00 37.25 5.01
531 589 3.682372 TCGTGAGAGATGATTGACGAG 57.318 47.619 0.00 0.00 32.47 4.18
532 590 2.356069 TCGTGAGAGATGATTGACGAGG 59.644 50.000 0.00 0.00 32.47 4.63
533 591 2.356069 CGTGAGAGATGATTGACGAGGA 59.644 50.000 0.00 0.00 0.00 3.71
534 592 3.547813 CGTGAGAGATGATTGACGAGGAG 60.548 52.174 0.00 0.00 0.00 3.69
535 593 3.629855 GTGAGAGATGATTGACGAGGAGA 59.370 47.826 0.00 0.00 0.00 3.71
536 594 4.097135 GTGAGAGATGATTGACGAGGAGAA 59.903 45.833 0.00 0.00 0.00 2.87
537 595 4.706962 TGAGAGATGATTGACGAGGAGAAA 59.293 41.667 0.00 0.00 0.00 2.52
538 596 5.004922 AGAGATGATTGACGAGGAGAAAC 57.995 43.478 0.00 0.00 0.00 2.78
539 597 4.116238 GAGATGATTGACGAGGAGAAACC 58.884 47.826 0.00 0.00 39.35 3.27
540 598 3.515502 AGATGATTGACGAGGAGAAACCA 59.484 43.478 0.00 0.00 42.04 3.67
541 599 3.762407 TGATTGACGAGGAGAAACCAA 57.238 42.857 0.00 0.00 42.04 3.67
542 600 4.079980 TGATTGACGAGGAGAAACCAAA 57.920 40.909 0.00 0.00 42.04 3.28
543 601 4.065088 TGATTGACGAGGAGAAACCAAAG 58.935 43.478 0.00 0.00 42.04 2.77
544 602 2.543777 TGACGAGGAGAAACCAAAGG 57.456 50.000 0.00 0.00 42.04 3.11
545 603 1.766496 TGACGAGGAGAAACCAAAGGT 59.234 47.619 0.00 0.00 42.04 3.50
563 621 7.947890 ACCAAAGGTTTCCATCTCAAAGTAATA 59.052 33.333 0.00 0.00 27.29 0.98
571 629 9.567848 TTTCCATCTCAAAGTAATATTTTTCGC 57.432 29.630 0.00 0.00 0.00 4.70
577 635 7.484641 TCTCAAAGTAATATTTTTCGCACATGC 59.515 33.333 0.00 0.00 37.78 4.06
579 637 6.869421 AAGTAATATTTTTCGCACATGCAC 57.131 33.333 4.49 0.00 42.21 4.57
588 646 1.290009 GCACATGCACCTTTCACCC 59.710 57.895 0.00 0.00 41.59 4.61
589 647 1.966762 CACATGCACCTTTCACCCC 59.033 57.895 0.00 0.00 0.00 4.95
594 652 0.178975 TGCACCTTTCACCCCGAAAT 60.179 50.000 0.00 0.00 42.69 2.17
595 653 1.074084 TGCACCTTTCACCCCGAAATA 59.926 47.619 0.00 0.00 42.69 1.40
597 655 2.163613 GCACCTTTCACCCCGAAATAAG 59.836 50.000 0.00 0.00 42.69 1.73
610 668 3.013921 CGAAATAAGGCCAGCTGGTTAA 58.986 45.455 32.81 16.90 37.57 2.01
618 676 1.198408 GCCAGCTGGTTAACCGTTAAC 59.802 52.381 32.81 21.25 43.65 2.01
622 680 4.756135 CCAGCTGGTTAACCGTTAACTAAA 59.244 41.667 25.53 15.07 43.82 1.85
698 756 9.269415 GTTTAACAACACTACAACAAGTACAAG 57.731 33.333 0.00 0.00 32.54 3.16
733 794 5.678132 ACCGTTAAACAAGTACATCAACC 57.322 39.130 0.00 0.00 0.00 3.77
819 888 0.524862 CACCATTTGCTGCTCTGACC 59.475 55.000 0.00 0.00 0.00 4.02
842 921 3.142977 TCCCATAGAGGATAGCTCCAAGT 59.857 47.826 0.00 0.00 44.79 3.16
1205 1537 5.390613 ACGAAACTGAAACTGAAAACTGTG 58.609 37.500 0.00 0.00 0.00 3.66
1206 1538 5.180492 ACGAAACTGAAACTGAAAACTGTGA 59.820 36.000 0.00 0.00 0.00 3.58
1211 1543 5.529060 ACTGAAACTGAAAACTGTGAGGATC 59.471 40.000 0.00 0.00 0.00 3.36
1274 1607 6.710744 TGGTTTACCATCTCTTCTTCTTTCAC 59.289 38.462 0.00 0.00 42.01 3.18
1287 1624 6.942532 TCTTCTTTCACTGTATGCTTTGTT 57.057 33.333 0.00 0.00 0.00 2.83
1291 1628 7.985634 TCTTTCACTGTATGCTTTGTTTTTC 57.014 32.000 0.00 0.00 0.00 2.29
1294 1631 3.425193 CACTGTATGCTTTGTTTTTCGCC 59.575 43.478 0.00 0.00 0.00 5.54
1305 1642 1.713932 GTTTTTCGCCGTCAAAGATGC 59.286 47.619 0.00 0.00 0.00 3.91
1333 1670 1.134965 CCAACGCTTCTAGTCCTCAGG 60.135 57.143 0.00 0.00 0.00 3.86
1343 1680 2.777832 AGTCCTCAGGCAAGACATTC 57.222 50.000 0.00 0.00 32.82 2.67
1355 1692 4.151157 GGCAAGACATTCAGCAAAATGTTC 59.849 41.667 15.31 10.09 46.99 3.18
1370 1707 6.020678 GCAAAATGTTCAGGTAATATTGCGAC 60.021 38.462 0.00 0.00 30.16 5.19
1381 1718 1.736612 TATTGCGACTCTGCATTGCA 58.263 45.000 11.50 11.50 45.78 4.08
1382 1719 0.169672 ATTGCGACTCTGCATTGCAC 59.830 50.000 7.38 0.00 45.78 4.57
1407 1744 5.720202 TGTTCACATAACTAAGCGACTGAT 58.280 37.500 0.00 0.00 0.00 2.90
1408 1745 5.805486 TGTTCACATAACTAAGCGACTGATC 59.195 40.000 0.00 0.00 0.00 2.92
1427 1764 3.855630 GAGCATATCGACTCTGCGT 57.144 52.632 9.29 0.61 40.78 5.24
1428 1765 2.126914 GAGCATATCGACTCTGCGTT 57.873 50.000 9.29 0.00 40.78 4.84
1436 1773 6.509517 GCATATCGACTCTGCGTTTTAATTGA 60.510 38.462 0.00 0.00 0.00 2.57
1437 1774 4.903638 TCGACTCTGCGTTTTAATTGAG 57.096 40.909 0.00 0.00 0.00 3.02
1443 1781 4.783242 TCTGCGTTTTAATTGAGTGAAGC 58.217 39.130 0.00 0.00 0.00 3.86
1447 1785 4.492294 GCGTTTTAATTGAGTGAAGCGATC 59.508 41.667 0.00 0.00 0.00 3.69
1461 1799 6.641169 TGAAGCGATCACAGTTATCTATCT 57.359 37.500 0.00 0.00 31.50 1.98
1463 1801 7.142021 TGAAGCGATCACAGTTATCTATCTTC 58.858 38.462 0.00 10.91 31.50 2.87
1465 1803 5.772672 AGCGATCACAGTTATCTATCTTCCT 59.227 40.000 0.00 0.00 0.00 3.36
1467 1805 7.448777 AGCGATCACAGTTATCTATCTTCCTTA 59.551 37.037 0.00 0.00 0.00 2.69
1474 1812 8.584157 ACAGTTATCTATCTTCCTTATGCAGAG 58.416 37.037 0.00 0.00 0.00 3.35
1476 1814 9.545928 AGTTATCTATCTTCCTTATGCAGAGAT 57.454 33.333 0.00 0.00 0.00 2.75
1481 1819 8.801299 TCTATCTTCCTTATGCAGAGATTACAG 58.199 37.037 0.00 0.00 0.00 2.74
1482 1820 6.166984 TCTTCCTTATGCAGAGATTACAGG 57.833 41.667 0.00 0.00 0.00 4.00
1504 1842 3.883830 TCTCCATGCAAGAGACTCTTC 57.116 47.619 14.99 10.44 33.78 2.87
1505 1843 3.168292 TCTCCATGCAAGAGACTCTTCA 58.832 45.455 14.99 15.16 33.78 3.02
1506 1844 3.056250 TCTCCATGCAAGAGACTCTTCAC 60.056 47.826 14.99 10.71 33.78 3.18
1508 1846 3.071457 TCCATGCAAGAGACTCTTCACAA 59.929 43.478 14.99 1.89 33.78 3.33
1511 1849 5.064452 CCATGCAAGAGACTCTTCACAATAC 59.936 44.000 14.99 0.53 33.78 1.89
1513 1851 4.238514 GCAAGAGACTCTTCACAATACGT 58.761 43.478 14.99 0.00 33.78 3.57
1555 1893 1.985895 GGAAGAAGTGGAGGAAGGGAA 59.014 52.381 0.00 0.00 0.00 3.97
1559 1897 1.978580 GAAGTGGAGGAAGGGAACTCA 59.021 52.381 0.00 0.00 42.68 3.41
1566 1904 3.328050 GGAGGAAGGGAACTCAAAGAAGA 59.672 47.826 0.00 0.00 42.68 2.87
1569 1907 3.181443 GGAAGGGAACTCAAAGAAGACCA 60.181 47.826 0.00 0.00 42.68 4.02
1579 1917 5.817816 ACTCAAAGAAGACCAACAGTTGTAG 59.182 40.000 12.42 0.44 0.00 2.74
1627 1965 7.303634 GGTAACTTAACTGTACATGGACATG 57.696 40.000 12.19 8.51 44.15 3.21
1628 1966 6.315393 GGTAACTTAACTGTACATGGACATGG 59.685 42.308 12.19 3.20 42.91 3.66
1629 1967 4.261801 ACTTAACTGTACATGGACATGGC 58.738 43.478 12.19 9.10 42.91 4.40
1631 1969 2.408271 ACTGTACATGGACATGGCTG 57.592 50.000 12.19 1.56 42.91 4.85
1632 1970 1.908619 ACTGTACATGGACATGGCTGA 59.091 47.619 12.19 0.00 42.91 4.26
1633 1971 2.507058 ACTGTACATGGACATGGCTGAT 59.493 45.455 12.19 0.00 42.91 2.90
1634 1972 3.136763 CTGTACATGGACATGGCTGATC 58.863 50.000 12.19 0.00 42.91 2.92
1636 1974 3.966665 TGTACATGGACATGGCTGATCTA 59.033 43.478 6.68 0.00 42.91 1.98
1637 1975 4.594491 TGTACATGGACATGGCTGATCTAT 59.406 41.667 6.68 0.00 42.91 1.98
1638 1976 4.017177 ACATGGACATGGCTGATCTATG 57.983 45.455 15.94 1.73 42.91 2.23
1639 1977 2.556144 TGGACATGGCTGATCTATGC 57.444 50.000 0.00 0.00 37.18 3.14
1640 1978 1.770061 TGGACATGGCTGATCTATGCA 59.230 47.619 0.00 0.00 37.18 3.96
1641 1979 2.173143 TGGACATGGCTGATCTATGCAA 59.827 45.455 0.00 0.00 37.18 4.08
1642 1980 3.216800 GGACATGGCTGATCTATGCAAA 58.783 45.455 0.00 0.00 37.18 3.68
1643 1981 3.633525 GGACATGGCTGATCTATGCAAAA 59.366 43.478 0.00 0.00 37.18 2.44
1644 1982 4.261489 GGACATGGCTGATCTATGCAAAAG 60.261 45.833 0.00 0.00 37.18 2.27
1645 1983 4.529897 ACATGGCTGATCTATGCAAAAGA 58.470 39.130 4.75 4.75 37.18 2.52
1648 1986 6.774170 ACATGGCTGATCTATGCAAAAGAATA 59.226 34.615 6.25 0.00 37.18 1.75
1649 1987 7.286087 ACATGGCTGATCTATGCAAAAGAATAA 59.714 33.333 6.25 0.00 37.18 1.40
1650 1988 7.828508 TGGCTGATCTATGCAAAAGAATAAT 57.171 32.000 6.25 0.00 0.00 1.28
1651 1989 7.654568 TGGCTGATCTATGCAAAAGAATAATG 58.345 34.615 6.25 0.00 0.00 1.90
1652 1990 7.088905 GGCTGATCTATGCAAAAGAATAATGG 58.911 38.462 6.25 0.00 0.00 3.16
1654 1992 8.786898 GCTGATCTATGCAAAAGAATAATGGTA 58.213 33.333 6.25 0.00 0.00 3.25
1662 2000 9.995003 ATGCAAAAGAATAATGGTAAAGAAACA 57.005 25.926 0.00 0.00 0.00 2.83
1663 2001 9.255304 TGCAAAAGAATAATGGTAAAGAAACAC 57.745 29.630 0.00 0.00 0.00 3.32
1664 2002 9.476202 GCAAAAGAATAATGGTAAAGAAACACT 57.524 29.630 0.00 0.00 0.00 3.55
1670 2008 9.406828 GAATAATGGTAAAGAAACACTCAAACC 57.593 33.333 0.00 0.00 0.00 3.27
1671 2009 5.784578 ATGGTAAAGAAACACTCAAACCC 57.215 39.130 0.00 0.00 0.00 4.11
1672 2010 4.601084 TGGTAAAGAAACACTCAAACCCA 58.399 39.130 0.00 0.00 0.00 4.51
1673 2011 4.399934 TGGTAAAGAAACACTCAAACCCAC 59.600 41.667 0.00 0.00 0.00 4.61
1675 2013 1.675552 AGAAACACTCAAACCCACCG 58.324 50.000 0.00 0.00 0.00 4.94
1677 2015 1.388837 AAACACTCAAACCCACCGCC 61.389 55.000 0.00 0.00 0.00 6.13
1678 2016 3.353836 CACTCAAACCCACCGCCG 61.354 66.667 0.00 0.00 0.00 6.46
1689 2027 3.702048 ACCGCCGCACACCACTAT 61.702 61.111 0.00 0.00 0.00 2.12
1690 2028 2.435938 CCGCCGCACACCACTATT 60.436 61.111 0.00 0.00 0.00 1.73
1691 2029 2.038269 CCGCCGCACACCACTATTT 61.038 57.895 0.00 0.00 0.00 1.40
1692 2030 1.134487 CGCCGCACACCACTATTTG 59.866 57.895 0.00 0.00 0.00 2.32
1693 2031 1.295357 CGCCGCACACCACTATTTGA 61.295 55.000 0.00 0.00 0.00 2.69
1694 2032 0.168128 GCCGCACACCACTATTTGAC 59.832 55.000 0.00 0.00 0.00 3.18
1695 2033 0.802494 CCGCACACCACTATTTGACC 59.198 55.000 0.00 0.00 0.00 4.02
1696 2034 0.442310 CGCACACCACTATTTGACCG 59.558 55.000 0.00 0.00 0.00 4.79
1697 2035 1.519408 GCACACCACTATTTGACCGT 58.481 50.000 0.00 0.00 0.00 4.83
1701 2039 3.168773 CCACTATTTGACCGTGGGG 57.831 57.895 0.00 0.00 43.41 4.96
1703 2041 1.211949 CCACTATTTGACCGTGGGGAT 59.788 52.381 0.00 0.00 43.41 3.85
1704 2042 2.561569 CACTATTTGACCGTGGGGATC 58.438 52.381 0.00 0.00 36.97 3.36
1705 2043 1.489230 ACTATTTGACCGTGGGGATCC 59.511 52.381 1.92 1.92 36.97 3.36
1715 2053 4.191015 GGGGATCCCGTTCCAGGC 62.191 72.222 24.90 4.06 37.53 4.85
1717 2055 4.547367 GGATCCCGTTCCAGGCCG 62.547 72.222 0.00 0.00 35.72 6.13
1805 2347 3.189285 GCAAAGTTGACACAAGTTGCAT 58.811 40.909 18.99 0.00 37.38 3.96
1806 2348 3.243643 GCAAAGTTGACACAAGTTGCATC 59.756 43.478 18.99 1.28 37.38 3.91
1877 2490 3.821033 AGGTCGAGCTAACAAATGCTTTT 59.179 39.130 16.99 0.00 39.91 2.27
1924 2538 1.226435 CGACGCTGCTAGTCCTCAC 60.226 63.158 0.00 0.00 35.33 3.51
1997 2612 1.181098 ACTCCCATGTTGCCTTGCAC 61.181 55.000 0.00 0.00 38.71 4.57
2040 2659 1.486211 ACTAAGCGACTGGGCATACT 58.514 50.000 0.00 0.00 34.64 2.12
2165 2785 1.141019 GAGCTTGACGGCGATGGTA 59.859 57.895 16.62 0.00 37.29 3.25
2167 2787 0.739813 AGCTTGACGGCGATGGTAAC 60.740 55.000 16.62 0.00 37.29 2.50
2304 2961 6.394025 AACCTTAGTTTTTATGTTTCGCCA 57.606 33.333 0.00 0.00 29.61 5.69
2530 8896 5.128468 CGACTTTTAGTTTTACACGACTGC 58.872 41.667 0.00 0.00 0.00 4.40
2548 8917 3.318839 ACTGCACAAGCTAGCAATTTTCA 59.681 39.130 18.83 6.47 40.73 2.69
2701 9078 3.636300 TGCAAACTTTCAGGTAGCATTGT 59.364 39.130 0.00 0.00 0.00 2.71
2801 9178 1.747355 CATGGTCTTGGTCTCCATTGC 59.253 52.381 0.00 0.00 39.57 3.56
2886 9263 7.698130 GCACATATTCTTAATGAAACAGTCACC 59.302 37.037 0.00 0.00 39.72 4.02
3111 9492 5.353938 CCATTCATTTCCGCATCAAGATTT 58.646 37.500 0.00 0.00 0.00 2.17
3487 9868 3.261818 AGGGTATGGATAGGAGGTGTC 57.738 52.381 0.00 0.00 0.00 3.67
3488 9869 2.158143 AGGGTATGGATAGGAGGTGTCC 60.158 54.545 0.00 0.00 44.33 4.02
3557 9938 5.431765 TGCCTTGCCTTGTAAAAATGAAAA 58.568 33.333 0.00 0.00 0.00 2.29
3558 9939 5.882557 TGCCTTGCCTTGTAAAAATGAAAAA 59.117 32.000 0.00 0.00 0.00 1.94
3604 9985 3.893795 GCTTTTCTGCAGCGATCTC 57.106 52.632 9.47 0.00 0.00 2.75
3687 10068 8.227791 CCCCAGTTTGATTTATATAATCGTTCG 58.772 37.037 0.00 0.00 0.00 3.95
3719 10100 4.902443 TTTTGTTTTCCACGCATACTGA 57.098 36.364 0.00 0.00 0.00 3.41
3733 10123 7.224753 CCACGCATACTGAAAGAAATGTATACT 59.775 37.037 4.17 0.00 37.43 2.12
3793 10183 2.483876 TGAGAAGCGAAAAGGTGACAG 58.516 47.619 0.00 0.00 0.00 3.51
3794 10184 2.102420 TGAGAAGCGAAAAGGTGACAGA 59.898 45.455 0.00 0.00 0.00 3.41
3806 10198 1.461127 GGTGACAGACGTTCATGCTTC 59.539 52.381 0.00 0.00 0.00 3.86
3839 10231 4.737765 CGATCACCGAGAATCTTCTTCTTC 59.262 45.833 0.00 0.00 41.76 2.87
3894 10286 3.781079 TTGTTGTGTTCTTCTTGCTGG 57.219 42.857 0.00 0.00 0.00 4.85
3944 10336 8.961294 ATCTTGATTCTTCACCTAATCTCTTG 57.039 34.615 0.00 0.00 34.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.473162 GCCCAAAAGCAACTTTATCCATTTT 59.527 36.000 0.00 0.00 31.99 1.82
15 16 2.364002 ACACGCCCAAAAGCAACTTTAT 59.636 40.909 0.00 0.00 31.99 1.40
20 21 0.317854 GAGACACGCCCAAAAGCAAC 60.318 55.000 0.00 0.00 0.00 4.17
34 35 2.128290 TACGACCTCGGGTGGAGACA 62.128 60.000 11.06 0.00 46.23 3.41
39 40 1.537562 GCTAAATACGACCTCGGGTGG 60.538 57.143 0.00 2.21 44.95 4.61
42 43 1.038280 AGGCTAAATACGACCTCGGG 58.962 55.000 0.00 0.00 44.95 5.14
53 54 1.080638 TGGGGTTCCACAGGCTAAAT 58.919 50.000 0.00 0.00 38.32 1.40
55 56 0.854218 TTTGGGGTTCCACAGGCTAA 59.146 50.000 0.00 0.00 43.94 3.09
66 67 4.966168 AGATAACACTTTGGTTTTGGGGTT 59.034 37.500 0.00 0.00 32.29 4.11
78 79 9.886132 ATTTCGGTATGTCTAAGATAACACTTT 57.114 29.630 0.00 0.00 0.00 2.66
81 82 7.114529 CGGATTTCGGTATGTCTAAGATAACAC 59.885 40.741 0.00 0.00 34.75 3.32
86 87 5.535406 ACTCGGATTTCGGTATGTCTAAGAT 59.465 40.000 0.00 0.00 39.77 2.40
95 96 4.467198 AACTGAACTCGGATTTCGGTAT 57.533 40.909 19.11 9.64 40.92 2.73
100 101 7.590279 TCCAAAATTAACTGAACTCGGATTTC 58.410 34.615 1.47 1.47 0.00 2.17
175 187 1.288188 TTGGCCATCACCTCTCATCA 58.712 50.000 6.09 0.00 0.00 3.07
207 222 4.929808 AGTGGTAGATGTGTTTGTCGATTC 59.070 41.667 0.00 0.00 0.00 2.52
235 252 5.422012 AGAAAAAGAAGAACTGGGCAAAAGA 59.578 36.000 0.00 0.00 0.00 2.52
241 264 5.459536 AATGAGAAAAAGAAGAACTGGGC 57.540 39.130 0.00 0.00 0.00 5.36
255 292 8.925161 ACAAAGAATGAACGAAAAATGAGAAA 57.075 26.923 0.00 0.00 0.00 2.52
264 313 4.358851 CCTGCAACAAAGAATGAACGAAA 58.641 39.130 0.00 0.00 0.00 3.46
272 321 0.827507 ACCGCCCTGCAACAAAGAAT 60.828 50.000 0.00 0.00 0.00 2.40
291 341 1.132721 CCCCTAGGTCCTCATGGATCA 60.133 57.143 8.29 0.00 45.85 2.92
294 344 1.074471 GCCCCTAGGTCCTCATGGA 60.074 63.158 8.29 0.00 40.69 3.41
353 406 1.908793 CCTGGTGAGACCCTGTCGT 60.909 63.158 0.00 0.00 37.50 4.34
354 407 1.606601 TCCTGGTGAGACCCTGTCG 60.607 63.158 0.00 0.00 37.50 4.35
364 417 0.256464 AAACCCAAACGTCCTGGTGA 59.744 50.000 13.89 0.00 31.45 4.02
366 419 1.107945 CAAAACCCAAACGTCCTGGT 58.892 50.000 13.89 6.48 31.45 4.00
369 423 0.032912 ACCCAAAACCCAAACGTCCT 60.033 50.000 0.00 0.00 0.00 3.85
372 426 2.300433 GTAGACCCAAAACCCAAACGT 58.700 47.619 0.00 0.00 0.00 3.99
376 430 3.133183 GCTTTTGTAGACCCAAAACCCAA 59.867 43.478 0.00 0.00 38.90 4.12
449 507 3.857854 GTGATGCACCGCAGCTCG 61.858 66.667 5.76 0.00 45.80 5.03
469 527 1.299316 CGTGTACCGTTGACACCGT 60.299 57.895 6.24 0.00 43.53 4.83
488 546 2.096013 TGTTCGCACATGAAAACGTCAA 59.904 40.909 0.00 0.00 40.50 3.18
511 569 2.356069 CCTCGTCAATCATCTCTCACGA 59.644 50.000 0.00 0.00 35.17 4.35
512 570 2.356069 TCCTCGTCAATCATCTCTCACG 59.644 50.000 0.00 0.00 0.00 4.35
513 571 3.629855 TCTCCTCGTCAATCATCTCTCAC 59.370 47.826 0.00 0.00 0.00 3.51
514 572 3.891049 TCTCCTCGTCAATCATCTCTCA 58.109 45.455 0.00 0.00 0.00 3.27
515 573 4.909696 TTCTCCTCGTCAATCATCTCTC 57.090 45.455 0.00 0.00 0.00 3.20
516 574 4.142049 GGTTTCTCCTCGTCAATCATCTCT 60.142 45.833 0.00 0.00 0.00 3.10
517 575 4.116238 GGTTTCTCCTCGTCAATCATCTC 58.884 47.826 0.00 0.00 0.00 2.75
518 576 3.515502 TGGTTTCTCCTCGTCAATCATCT 59.484 43.478 0.00 0.00 37.07 2.90
519 577 3.861840 TGGTTTCTCCTCGTCAATCATC 58.138 45.455 0.00 0.00 37.07 2.92
520 578 3.981071 TGGTTTCTCCTCGTCAATCAT 57.019 42.857 0.00 0.00 37.07 2.45
521 579 3.762407 TTGGTTTCTCCTCGTCAATCA 57.238 42.857 0.00 0.00 37.07 2.57
522 580 3.437049 CCTTTGGTTTCTCCTCGTCAATC 59.563 47.826 0.00 0.00 37.07 2.67
523 581 3.181443 ACCTTTGGTTTCTCCTCGTCAAT 60.181 43.478 0.00 0.00 37.07 2.57
524 582 2.171870 ACCTTTGGTTTCTCCTCGTCAA 59.828 45.455 0.00 0.00 37.07 3.18
525 583 1.766496 ACCTTTGGTTTCTCCTCGTCA 59.234 47.619 0.00 0.00 37.07 4.35
526 584 2.545537 ACCTTTGGTTTCTCCTCGTC 57.454 50.000 0.00 0.00 37.07 4.20
537 595 4.546674 ACTTTGAGATGGAAACCTTTGGT 58.453 39.130 0.00 0.00 37.65 3.67
538 596 6.648879 TTACTTTGAGATGGAAACCTTTGG 57.351 37.500 0.00 0.00 0.00 3.28
545 603 9.567848 GCGAAAAATATTACTTTGAGATGGAAA 57.432 29.630 0.00 0.00 0.00 3.13
546 604 8.735315 TGCGAAAAATATTACTTTGAGATGGAA 58.265 29.630 0.00 0.00 0.00 3.53
547 605 8.181573 GTGCGAAAAATATTACTTTGAGATGGA 58.818 33.333 0.00 0.00 0.00 3.41
548 606 7.967854 TGTGCGAAAAATATTACTTTGAGATGG 59.032 33.333 0.00 0.00 0.00 3.51
563 621 2.818130 AAGGTGCATGTGCGAAAAAT 57.182 40.000 0.00 0.00 45.83 1.82
571 629 1.865788 CGGGGTGAAAGGTGCATGTG 61.866 60.000 0.00 0.00 0.00 3.21
588 646 0.394352 ACCAGCTGGCCTTATTTCGG 60.394 55.000 33.06 4.55 39.32 4.30
589 647 1.463674 AACCAGCTGGCCTTATTTCG 58.536 50.000 33.06 5.14 39.32 3.46
594 652 0.035820 CGGTTAACCAGCTGGCCTTA 60.036 55.000 33.06 20.96 39.32 2.69
595 653 1.303317 CGGTTAACCAGCTGGCCTT 60.303 57.895 33.06 22.05 39.32 4.35
597 655 0.321830 TAACGGTTAACCAGCTGGCC 60.322 55.000 33.06 23.26 39.32 5.36
622 680 9.284968 ACGTTGGCAATTAATTATAGCTCTATT 57.715 29.630 1.92 0.00 0.00 1.73
657 715 1.208844 TAAACCATTGGCTCCCCGGA 61.209 55.000 0.73 0.00 0.00 5.14
698 756 0.321830 TAACGGTTAACCAGCTGGCC 60.322 55.000 33.06 23.26 39.32 5.36
733 794 5.461078 GCTTGGAAATGGATGATTTGATTCG 59.539 40.000 0.00 0.00 34.18 3.34
819 888 3.464720 TGGAGCTATCCTCTATGGGAG 57.535 52.381 0.00 0.00 46.80 4.30
1137 1250 1.490490 AGAAGCTGGTTGGAGACACAA 59.510 47.619 0.00 0.00 42.67 3.33
1211 1543 4.416620 AGCTCTAAAGACATCGAAGTTCG 58.583 43.478 19.23 19.23 42.10 3.95
1222 1554 8.089597 AGGTTAAAACAGAGTAGCTCTAAAGAC 58.910 37.037 0.00 0.00 38.99 3.01
1227 1559 6.269307 ACCAAGGTTAAAACAGAGTAGCTCTA 59.731 38.462 0.00 0.00 38.99 2.43
1274 1607 2.656422 CGGCGAAAAACAAAGCATACAG 59.344 45.455 0.00 0.00 0.00 2.74
1287 1624 3.765349 GCATCTTTGACGGCGAAAA 57.235 47.368 16.62 12.94 0.00 2.29
1294 1631 0.248215 GCCCAATCGCATCTTTGACG 60.248 55.000 0.00 0.00 0.00 4.35
1305 1642 0.742990 TAGAAGCGTTGGCCCAATCG 60.743 55.000 0.00 6.77 41.24 3.34
1333 1670 4.746115 TGAACATTTTGCTGAATGTCTTGC 59.254 37.500 15.38 8.64 46.53 4.01
1343 1680 6.020440 CGCAATATTACCTGAACATTTTGCTG 60.020 38.462 0.00 0.00 35.88 4.41
1355 1692 3.457234 TGCAGAGTCGCAATATTACCTG 58.543 45.455 7.11 0.00 39.45 4.00
1370 1707 2.033675 TGTGAACAAGTGCAATGCAGAG 59.966 45.455 8.73 3.90 40.08 3.35
1381 1718 5.405571 CAGTCGCTTAGTTATGTGAACAAGT 59.594 40.000 0.00 0.00 0.00 3.16
1382 1719 5.633601 TCAGTCGCTTAGTTATGTGAACAAG 59.366 40.000 0.00 0.00 0.00 3.16
1408 1745 0.040870 ACGCAGAGTCGATATGCTCG 60.041 55.000 14.79 6.25 44.18 5.03
1409 1746 2.126914 AACGCAGAGTCGATATGCTC 57.873 50.000 14.79 5.48 44.18 4.26
1410 1747 2.586258 AAACGCAGAGTCGATATGCT 57.414 45.000 14.79 0.00 44.18 3.79
1416 1753 4.149922 CACTCAATTAAAACGCAGAGTCGA 59.850 41.667 0.00 0.00 34.39 4.20
1423 1760 3.248841 TCGCTTCACTCAATTAAAACGCA 59.751 39.130 0.00 0.00 0.00 5.24
1424 1761 3.805823 TCGCTTCACTCAATTAAAACGC 58.194 40.909 0.00 0.00 0.00 4.84
1425 1762 5.617609 TGATCGCTTCACTCAATTAAAACG 58.382 37.500 0.00 0.00 0.00 3.60
1443 1781 9.566530 CATAAGGAAGATAGATAACTGTGATCG 57.433 37.037 0.00 0.00 0.00 3.69
1447 1785 8.363390 TCTGCATAAGGAAGATAGATAACTGTG 58.637 37.037 0.00 0.00 0.00 3.66
1461 1799 6.556495 AGATCCTGTAATCTCTGCATAAGGAA 59.444 38.462 0.00 0.00 36.24 3.36
1463 1801 6.357579 AGATCCTGTAATCTCTGCATAAGG 57.642 41.667 0.00 0.00 29.89 2.69
1474 1812 4.965814 TCTTGCATGGAGATCCTGTAATC 58.034 43.478 0.00 0.00 36.82 1.75
1476 1814 4.033009 TCTCTTGCATGGAGATCCTGTAA 58.967 43.478 13.64 1.98 35.25 2.41
1481 1819 2.699846 AGAGTCTCTTGCATGGAGATCC 59.300 50.000 18.55 14.14 41.13 3.36
1482 1820 4.141981 TGAAGAGTCTCTTGCATGGAGATC 60.142 45.833 19.95 16.09 41.13 2.75
1505 1843 1.710013 CCGTCAAGCTCACGTATTGT 58.290 50.000 15.00 0.00 35.39 2.71
1506 1844 0.370273 GCCGTCAAGCTCACGTATTG 59.630 55.000 15.00 3.49 35.39 1.90
1508 1846 1.516386 CGCCGTCAAGCTCACGTAT 60.516 57.895 15.00 0.00 35.39 3.06
1511 1849 2.507102 ATCGCCGTCAAGCTCACG 60.507 61.111 10.50 10.50 36.99 4.35
1513 1851 2.202610 CGATCGCCGTCAAGCTCA 60.203 61.111 0.26 0.00 0.00 4.26
1535 1873 1.657804 TCCCTTCCTCCACTTCTTCC 58.342 55.000 0.00 0.00 0.00 3.46
1538 1876 2.261729 GAGTTCCCTTCCTCCACTTCT 58.738 52.381 0.00 0.00 0.00 2.85
1555 1893 4.589908 ACAACTGTTGGTCTTCTTTGAGT 58.410 39.130 23.15 0.00 34.12 3.41
1559 1897 4.523083 TGCTACAACTGTTGGTCTTCTTT 58.477 39.130 23.15 3.67 34.12 2.52
1566 1904 0.537371 GCCCTGCTACAACTGTTGGT 60.537 55.000 23.15 11.95 34.12 3.67
1569 1907 2.292828 ATTGCCCTGCTACAACTGTT 57.707 45.000 0.00 0.00 0.00 3.16
1579 1917 0.672342 CAGCCAGATAATTGCCCTGC 59.328 55.000 0.00 0.00 0.00 4.85
1612 1950 1.908619 TCAGCCATGTCCATGTACAGT 59.091 47.619 0.33 0.00 37.11 3.55
1613 1951 2.696989 TCAGCCATGTCCATGTACAG 57.303 50.000 0.33 0.00 37.11 2.74
1623 1961 4.529897 TCTTTTGCATAGATCAGCCATGT 58.470 39.130 0.00 0.00 0.00 3.21
1624 1962 5.509716 TTCTTTTGCATAGATCAGCCATG 57.490 39.130 0.00 0.00 0.00 3.66
1625 1963 7.828508 TTATTCTTTTGCATAGATCAGCCAT 57.171 32.000 0.00 0.00 0.00 4.40
1626 1964 7.255695 CCATTATTCTTTTGCATAGATCAGCCA 60.256 37.037 0.00 0.00 0.00 4.75
1627 1965 7.088905 CCATTATTCTTTTGCATAGATCAGCC 58.911 38.462 0.00 0.00 0.00 4.85
1628 1966 7.655490 ACCATTATTCTTTTGCATAGATCAGC 58.345 34.615 0.00 0.00 0.00 4.26
1636 1974 9.995003 TGTTTCTTTACCATTATTCTTTTGCAT 57.005 25.926 0.00 0.00 0.00 3.96
1637 1975 9.255304 GTGTTTCTTTACCATTATTCTTTTGCA 57.745 29.630 0.00 0.00 0.00 4.08
1638 1976 9.476202 AGTGTTTCTTTACCATTATTCTTTTGC 57.524 29.630 0.00 0.00 0.00 3.68
1644 1982 9.406828 GGTTTGAGTGTTTCTTTACCATTATTC 57.593 33.333 0.00 0.00 0.00 1.75
1645 1983 8.364894 GGGTTTGAGTGTTTCTTTACCATTATT 58.635 33.333 0.00 0.00 0.00 1.40
1648 1986 5.659079 TGGGTTTGAGTGTTTCTTTACCATT 59.341 36.000 0.00 0.00 0.00 3.16
1649 1987 5.068591 GTGGGTTTGAGTGTTTCTTTACCAT 59.931 40.000 0.00 0.00 0.00 3.55
1650 1988 4.399934 GTGGGTTTGAGTGTTTCTTTACCA 59.600 41.667 0.00 0.00 0.00 3.25
1651 1989 4.202080 GGTGGGTTTGAGTGTTTCTTTACC 60.202 45.833 0.00 0.00 0.00 2.85
1652 1990 4.496840 CGGTGGGTTTGAGTGTTTCTTTAC 60.497 45.833 0.00 0.00 0.00 2.01
1654 1992 2.425668 CGGTGGGTTTGAGTGTTTCTTT 59.574 45.455 0.00 0.00 0.00 2.52
1655 1993 2.021457 CGGTGGGTTTGAGTGTTTCTT 58.979 47.619 0.00 0.00 0.00 2.52
1656 1994 1.675552 CGGTGGGTTTGAGTGTTTCT 58.324 50.000 0.00 0.00 0.00 2.52
1657 1995 0.030235 GCGGTGGGTTTGAGTGTTTC 59.970 55.000 0.00 0.00 0.00 2.78
1658 1996 1.388837 GGCGGTGGGTTTGAGTGTTT 61.389 55.000 0.00 0.00 0.00 2.83
1659 1997 1.826487 GGCGGTGGGTTTGAGTGTT 60.826 57.895 0.00 0.00 0.00 3.32
1660 1998 2.203294 GGCGGTGGGTTTGAGTGT 60.203 61.111 0.00 0.00 0.00 3.55
1671 2009 3.950794 ATAGTGGTGTGCGGCGGTG 62.951 63.158 9.78 0.00 0.00 4.94
1672 2010 2.741486 AAATAGTGGTGTGCGGCGGT 62.741 55.000 9.78 0.00 0.00 5.68
1673 2011 2.038269 AAATAGTGGTGTGCGGCGG 61.038 57.895 9.78 0.00 0.00 6.13
1675 2013 0.168128 GTCAAATAGTGGTGTGCGGC 59.832 55.000 0.00 0.00 0.00 6.53
1677 2015 0.442310 CGGTCAAATAGTGGTGTGCG 59.558 55.000 0.00 0.00 0.00 5.34
1678 2016 1.196808 CACGGTCAAATAGTGGTGTGC 59.803 52.381 0.00 0.00 32.68 4.57
1684 2022 2.561569 GATCCCCACGGTCAAATAGTG 58.438 52.381 0.00 0.00 35.79 2.74
1685 2023 1.489230 GGATCCCCACGGTCAAATAGT 59.511 52.381 0.00 0.00 0.00 2.12
1686 2024 1.202770 GGGATCCCCACGGTCAAATAG 60.203 57.143 21.42 0.00 44.65 1.73
1687 2025 0.841289 GGGATCCCCACGGTCAAATA 59.159 55.000 21.42 0.00 44.65 1.40
1689 2027 2.961893 CGGGATCCCCACGGTCAAA 61.962 63.158 25.73 0.00 45.83 2.69
1690 2028 3.395702 CGGGATCCCCACGGTCAA 61.396 66.667 25.73 0.00 45.83 3.18
1691 2029 4.707768 ACGGGATCCCCACGGTCA 62.708 66.667 25.73 0.00 45.83 4.02
1692 2030 3.381333 GAACGGGATCCCCACGGTC 62.381 68.421 25.73 17.51 45.83 4.79
1693 2031 3.396570 GAACGGGATCCCCACGGT 61.397 66.667 25.73 14.17 45.83 4.83
1694 2032 4.171103 GGAACGGGATCCCCACGG 62.171 72.222 25.73 13.47 45.83 4.94
1695 2033 3.385749 CTGGAACGGGATCCCCACG 62.386 68.421 25.73 15.91 45.83 4.94
1696 2034 2.590092 CTGGAACGGGATCCCCAC 59.410 66.667 25.73 15.55 45.83 4.61
1717 2055 3.414700 CTGGACTGGACGCGTTGC 61.415 66.667 15.53 2.51 0.00 4.17
1719 2057 1.461091 TTCTCTGGACTGGACGCGTT 61.461 55.000 15.53 0.00 0.00 4.84
1721 2059 1.444553 GTTCTCTGGACTGGACGCG 60.445 63.158 3.53 3.53 0.00 6.01
1722 2060 1.079750 GGTTCTCTGGACTGGACGC 60.080 63.158 0.00 0.00 0.00 5.19
1723 2061 1.592223 GGGTTCTCTGGACTGGACG 59.408 63.158 0.00 0.00 0.00 4.79
1726 2064 1.903877 ATGCGGGTTCTCTGGACTGG 61.904 60.000 0.00 0.00 0.00 4.00
1729 2271 1.026718 CCAATGCGGGTTCTCTGGAC 61.027 60.000 0.00 0.00 0.00 4.02
1731 2273 0.322456 TTCCAATGCGGGTTCTCTGG 60.322 55.000 0.00 0.00 34.36 3.86
1805 2347 4.952460 AGAAGTGCAAACGGTAAACTAGA 58.048 39.130 0.00 0.00 0.00 2.43
1806 2348 5.668558 AAGAAGTGCAAACGGTAAACTAG 57.331 39.130 0.00 0.00 0.00 2.57
1844 2386 5.047590 TGTTAGCTCGACCTTGAATCTACAA 60.048 40.000 0.00 0.00 0.00 2.41
1924 2538 3.311106 ACATTTTGCTCAATGTCTTGCG 58.689 40.909 7.92 0.00 42.63 4.85
1997 2612 3.644823 TGTGAACAAATGCAATGCAGAG 58.355 40.909 14.98 8.37 43.65 3.35
2165 2785 2.666317 CCTTCCACCACTTCCTTTGTT 58.334 47.619 0.00 0.00 0.00 2.83
2167 2787 1.144913 TCCCTTCCACCACTTCCTTTG 59.855 52.381 0.00 0.00 0.00 2.77
2303 2960 3.723260 ACCTAAACCCAACGCATTTTTG 58.277 40.909 0.00 0.00 0.00 2.44
2304 2961 3.551250 CGACCTAAACCCAACGCATTTTT 60.551 43.478 0.00 0.00 0.00 1.94
2530 8896 4.456911 TCTCCTGAAAATTGCTAGCTTGTG 59.543 41.667 17.23 0.00 0.00 3.33
2687 9064 5.880332 GGAATAAGACACAATGCTACCTGAA 59.120 40.000 0.00 0.00 0.00 3.02
2701 9078 5.422331 AGATGTCTCTTTCCGGAATAAGACA 59.578 40.000 37.94 37.94 41.80 3.41
2886 9263 3.064408 ACACATATCTTCAGTGCAATGCG 59.936 43.478 9.79 3.04 36.76 4.73
3430 9811 3.510360 AGATCCGTGCTACACAACTAACT 59.490 43.478 0.00 0.00 33.40 2.24
3435 9816 2.363788 TGAGATCCGTGCTACACAAC 57.636 50.000 0.00 0.00 33.40 3.32
3557 9938 3.448660 GCCCTGCATTTCAAGTCCTTATT 59.551 43.478 0.00 0.00 0.00 1.40
3558 9939 3.026694 GCCCTGCATTTCAAGTCCTTAT 58.973 45.455 0.00 0.00 0.00 1.73
3604 9985 7.158021 AGATCTGTCAACTTCTCTAAAACAGG 58.842 38.462 0.00 0.00 34.77 4.00
3710 10091 9.464714 ACTAGTATACATTTCTTTCAGTATGCG 57.535 33.333 5.50 0.00 35.57 4.73
3746 10136 9.567776 TCCACACAAGTTCATAAATCTTAAGAA 57.432 29.630 9.71 0.00 0.00 2.52
3810 10202 3.600388 AGATTCTCGGTGATCGCTTTTT 58.400 40.909 6.18 0.00 39.05 1.94
3894 10286 3.916776 GCTTTGTTTCTGTATCTTGCAGC 59.083 43.478 0.00 0.00 34.21 5.25
3944 10336 2.037901 TGTCATCCTCAGCCTCATCTC 58.962 52.381 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.