Multiple sequence alignment - TraesCS2B01G598900

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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 TraesCS2B01G598900 chr2B 100.000 4999 0 0 1 4999 781798032 781793034 0.000000e+00 9232.0
1 TraesCS2B01G598900 chr2B 88.111 1085 109 12 1839 2921 781828620 781827554 0.000000e+00 1271.0
2 TraesCS2B01G598900 chr2B 85.946 1046 131 8 1839 2879 781807212 781806178 0.000000e+00 1103.0
3 TraesCS2B01G598900 chr2B 88.528 462 42 9 2916 3375 781805973 781805521 2.630000e-152 549.0
4 TraesCS2B01G598900 chr2B 85.371 458 57 3 2924 3379 781827506 781827057 2.730000e-127 466.0
5 TraesCS2B01G598900 chr2B 79.278 526 80 15 6 515 781830557 781830045 1.720000e-89 340.0
6 TraesCS2B01G598900 chr2B 87.762 286 15 11 4621 4905 781804187 781803921 2.900000e-82 316.0
7 TraesCS2B01G598900 chr2B 89.754 244 17 4 3379 3621 781827021 781826785 6.290000e-79 305.0
8 TraesCS2B01G598900 chr2B 84.354 147 18 3 4624 4769 784276558 784276416 6.750000e-29 139.0
9 TraesCS2B01G598900 chr2B 97.403 77 2 0 4869 4945 781793122 781793046 1.130000e-26 132.0
10 TraesCS2B01G598900 chr2B 97.403 77 2 0 4911 4987 781793164 781793088 1.130000e-26 132.0
11 TraesCS2B01G598900 chr2B 100.000 33 0 0 550 582 781830038 781830006 1.500000e-05 62.1
12 TraesCS2B01G598900 chr2D 89.356 2687 153 61 782 3379 648119634 648122276 0.000000e+00 3254.0
13 TraesCS2B01G598900 chr2D 86.686 1044 123 8 1839 2879 648102455 648103485 0.000000e+00 1144.0
14 TraesCS2B01G598900 chr2D 92.172 511 34 3 4438 4945 648123266 648123773 0.000000e+00 717.0
15 TraesCS2B01G598900 chr2D 89.333 525 25 11 1 501 648118922 648119439 9.130000e-177 630.0
16 TraesCS2B01G598900 chr2D 89.670 455 44 3 2925 3379 648103783 648104234 1.210000e-160 577.0
17 TraesCS2B01G598900 chr2D 85.496 524 33 10 3376 3897 648122304 648122786 1.610000e-139 507.0
18 TraesCS2B01G598900 chr2D 88.811 286 12 9 4621 4905 648112347 648112613 2.880000e-87 333.0
19 TraesCS2B01G598900 chr2D 81.073 317 56 4 6 320 647970287 647970601 2.990000e-62 250.0
20 TraesCS2B01G598900 chr2D 84.354 147 18 3 4624 4769 648355288 648355146 6.750000e-29 139.0
21 TraesCS2B01G598900 chr2D 93.478 92 6 0 4908 4999 648123694 648123785 2.430000e-28 137.0
22 TraesCS2B01G598900 chr2D 94.253 87 2 2 693 778 648119441 648119525 4.060000e-26 130.0
23 TraesCS2B01G598900 chrUn 91.537 2257 102 30 1176 3375 31313719 31311495 0.000000e+00 3027.0
24 TraesCS2B01G598900 chrUn 88.611 1001 102 8 1925 2918 31371327 31370332 0.000000e+00 1206.0
25 TraesCS2B01G598900 chrUn 87.536 1035 117 5 1848 2879 31327136 31326111 0.000000e+00 1186.0
26 TraesCS2B01G598900 chrUn 89.981 519 29 5 3378 3894 31311461 31310964 0.000000e+00 649.0
27 TraesCS2B01G598900 chrUn 89.871 464 43 4 2916 3379 31325877 31325418 1.200000e-165 593.0
28 TraesCS2B01G598900 chrUn 94.462 325 15 1 4621 4945 31309575 31309254 9.660000e-137 497.0
29 TraesCS2B01G598900 chrUn 86.623 456 51 2 2924 3379 31370281 31369836 3.480000e-136 496.0
30 TraesCS2B01G598900 chrUn 91.117 349 21 7 4087 4430 31310383 31310040 9.800000e-127 464.0
31 TraesCS2B01G598900 chrUn 87.762 286 15 9 4621 4905 31323767 31323501 2.900000e-82 316.0
32 TraesCS2B01G598900 chrUn 94.000 200 9 3 3890 4088 31310693 31310496 2.930000e-77 300.0
33 TraesCS2B01G598900 chrUn 87.766 188 17 3 4438 4622 31309815 31309631 1.090000e-51 215.0
34 TraesCS2B01G598900 chrUn 96.629 89 3 0 4911 4999 31309330 31309242 1.120000e-31 148.0
35 TraesCS2B01G598900 chrUn 82.667 150 21 3 4621 4769 31088705 31088850 1.460000e-25 128.0
36 TraesCS2B01G598900 chrUn 86.154 65 5 2 535 595 31372469 31372405 3.230000e-07 67.6
37 TraesCS2B01G598900 chrUn 94.737 38 2 0 4866 4903 31309291 31309254 5.400000e-05 60.2
38 TraesCS2B01G598900 chr5A 79.548 841 145 16 2046 2870 3313630 3314459 4.340000e-160 575.0
39 TraesCS2B01G598900 chr5D 92.256 297 6 7 1422 1705 8377105 8376813 6.030000e-109 405.0
40 TraesCS2B01G598900 chr5D 92.883 281 7 5 1422 1692 78436024 78435747 3.630000e-106 396.0
41 TraesCS2B01G598900 chr5D 93.694 111 2 3 1598 1705 403752962 403752854 1.440000e-35 161.0
42 TraesCS2B01G598900 chr5D 81.944 144 25 1 2977 3120 553625970 553625828 2.440000e-23 121.0
43 TraesCS2B01G598900 chr5D 80.272 147 27 2 3230 3375 6712219 6712074 5.290000e-20 110.0
44 TraesCS2B01G598900 chr7A 91.892 296 8 6 1422 1705 186108056 186107765 2.800000e-107 399.0
45 TraesCS2B01G598900 chr5B 78.035 692 110 25 2183 2848 6498022 6497347 1.010000e-106 398.0
46 TraesCS2B01G598900 chr7D 90.909 297 10 7 1422 1705 567809457 567809749 2.820000e-102 383.0
47 TraesCS2B01G598900 chr7D 86.000 350 48 1 1897 2245 489903661 489903312 1.700000e-99 374.0
48 TraesCS2B01G598900 chr7D 76.507 647 114 27 2249 2873 489903278 489902648 8.080000e-83 318.0
49 TraesCS2B01G598900 chr3A 89.899 297 13 7 1422 1705 731602437 731602729 2.840000e-97 366.0
50 TraesCS2B01G598900 chr4A 89.562 297 13 8 1422 1705 53815206 53815497 1.320000e-95 361.0
51 TraesCS2B01G598900 chr4A 83.333 144 23 1 2977 3120 614982831 614982973 1.130000e-26 132.0
52 TraesCS2B01G598900 chr4A 80.000 180 32 2 2977 3156 614908012 614908187 4.060000e-26 130.0
53 TraesCS2B01G598900 chr4A 81.944 144 25 1 2977 3120 615100687 615100829 2.440000e-23 121.0
54 TraesCS2B01G598900 chr7B 76.507 647 114 28 2249 2873 518395096 518394466 8.080000e-83 318.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G598900 chr2B 781793034 781798032 4998 True 9232.000000 9232 100.000000 1 4999 1 chr2B.!!$R1 4998
1 TraesCS2B01G598900 chr2B 781803921 781807212 3291 True 656.000000 1103 87.412000 1839 4905 3 chr2B.!!$R4 3066
2 TraesCS2B01G598900 chr2B 781826785 781830557 3772 True 488.820000 1271 88.502800 6 3621 5 chr2B.!!$R5 3615
3 TraesCS2B01G598900 chr2D 648118922 648123785 4863 False 895.833333 3254 90.681333 1 4999 6 chr2D.!!$F4 4998
4 TraesCS2B01G598900 chr2D 648102455 648104234 1779 False 860.500000 1144 88.178000 1839 3379 2 chr2D.!!$F3 1540
5 TraesCS2B01G598900 chrUn 31323501 31327136 3635 True 698.333333 1186 88.389667 1848 4905 3 chrUn.!!$R2 3057
6 TraesCS2B01G598900 chrUn 31309242 31313719 4477 True 670.025000 3027 92.528625 1176 4999 8 chrUn.!!$R1 3823
7 TraesCS2B01G598900 chrUn 31369836 31372469 2633 True 589.866667 1206 87.129333 535 3379 3 chrUn.!!$R3 2844
8 TraesCS2B01G598900 chr5A 3313630 3314459 829 False 575.000000 575 79.548000 2046 2870 1 chr5A.!!$F1 824
9 TraesCS2B01G598900 chr5B 6497347 6498022 675 True 398.000000 398 78.035000 2183 2848 1 chr5B.!!$R1 665
10 TraesCS2B01G598900 chr7D 489902648 489903661 1013 True 346.000000 374 81.253500 1897 2873 2 chr7D.!!$R1 976
11 TraesCS2B01G598900 chr7B 518394466 518395096 630 True 318.000000 318 76.507000 2249 2873 1 chr7B.!!$R1 624

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
527 553 0.035439 ACAGAGTTACATTGCCCCCG 60.035 55.000 0.00 0.00 0.0 5.73 F
528 554 1.077716 AGAGTTACATTGCCCCCGC 60.078 57.895 0.00 0.00 0.0 6.13 F
2013 2813 0.106708 GGATTCATGCAGCCGTCCTA 59.893 55.000 0.00 0.00 0.0 2.94 F
3460 4613 0.184692 TGTGCTGGTTGTTGGATCCA 59.815 50.000 11.44 11.44 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 2200 0.253327 AATGAAGAGAGTTCGGGCCC 59.747 55.0 13.57 13.57 0.00 5.80 R
2179 2979 0.523968 CACCAAAGATTGCGCCATCG 60.524 55.0 15.06 4.45 39.07 3.84 R
3516 4669 0.326927 CGGGAAAGCTGGGGAAACTA 59.673 55.0 0.00 0.00 0.00 2.24 R
4920 7374 0.108804 CCATGTCGCCGACACTAGTT 60.109 55.0 23.77 2.80 45.65 2.24 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
26 27 5.362263 ACTTGTTAGCGAGGTTAAAGTTGA 58.638 37.500 0.00 0.00 0.00 3.18
34 35 4.315803 CGAGGTTAAAGTTGATGTCTGGT 58.684 43.478 0.00 0.00 0.00 4.00
37 38 4.755123 AGGTTAAAGTTGATGTCTGGTTCG 59.245 41.667 0.00 0.00 0.00 3.95
133 134 2.282180 GCCCCAATGACACGGTGT 60.282 61.111 14.66 14.66 0.00 4.16
154 155 4.705991 TGTAGCAATGCAAATCCATCTTCA 59.294 37.500 8.35 0.00 0.00 3.02
254 255 7.883391 TCGGAATAACTTCTCAGTAGATCTT 57.117 36.000 0.00 0.00 30.68 2.40
316 318 5.128663 GGGAGTAATTTATGGCCATTGTTGT 59.871 40.000 26.37 8.64 0.00 3.32
317 319 6.351796 GGGAGTAATTTATGGCCATTGTTGTT 60.352 38.462 26.37 14.03 0.00 2.83
318 320 6.534793 GGAGTAATTTATGGCCATTGTTGTTG 59.465 38.462 26.37 0.00 0.00 3.33
359 362 4.114058 AGTGGCATGCATTCACAAATAC 57.886 40.909 21.36 0.00 34.17 1.89
377 403 2.729028 ACCGGATTTTGTATGAGGGG 57.271 50.000 9.46 0.00 0.00 4.79
388 414 5.640158 TTGTATGAGGGGGTATTTGGTAG 57.360 43.478 0.00 0.00 0.00 3.18
428 454 2.115427 TCCTGCTCGACCCATTATTCA 58.885 47.619 0.00 0.00 0.00 2.57
449 475 4.519350 TCATTGTTTGGTACGGTGCATAAA 59.481 37.500 0.00 0.00 0.00 1.40
459 485 8.332996 TGGTACGGTGCATAAAGTTTAATTAA 57.667 30.769 0.00 0.00 0.00 1.40
460 486 8.452534 TGGTACGGTGCATAAAGTTTAATTAAG 58.547 33.333 0.00 0.00 0.00 1.85
461 487 8.453320 GGTACGGTGCATAAAGTTTAATTAAGT 58.547 33.333 0.00 0.00 0.00 2.24
494 520 7.482169 TCAGGAAAAGTCTTCTAGCTCATTA 57.518 36.000 0.00 0.00 0.00 1.90
522 548 9.793252 ATTGATTATCAAACAGAGTTACATTGC 57.207 29.630 11.88 0.00 40.12 3.56
523 549 7.761409 TGATTATCAAACAGAGTTACATTGCC 58.239 34.615 0.00 0.00 0.00 4.52
524 550 6.509418 TTATCAAACAGAGTTACATTGCCC 57.491 37.500 0.00 0.00 0.00 5.36
525 551 3.153919 TCAAACAGAGTTACATTGCCCC 58.846 45.455 0.00 0.00 0.00 5.80
526 552 2.215942 AACAGAGTTACATTGCCCCC 57.784 50.000 0.00 0.00 0.00 5.40
527 553 0.035439 ACAGAGTTACATTGCCCCCG 60.035 55.000 0.00 0.00 0.00 5.73
528 554 1.077716 AGAGTTACATTGCCCCCGC 60.078 57.895 0.00 0.00 0.00 6.13
529 555 1.377987 GAGTTACATTGCCCCCGCA 60.378 57.895 0.00 0.00 45.49 5.69
605 635 5.461526 GTCATCTACCCAAAAACAAGCTTC 58.538 41.667 0.00 0.00 0.00 3.86
606 636 4.215399 TCATCTACCCAAAAACAAGCTTCG 59.785 41.667 0.00 0.00 0.00 3.79
607 637 3.547746 TCTACCCAAAAACAAGCTTCGT 58.452 40.909 0.00 0.00 0.00 3.85
608 638 3.949113 TCTACCCAAAAACAAGCTTCGTT 59.051 39.130 0.00 2.02 0.00 3.85
609 639 2.887337 ACCCAAAAACAAGCTTCGTTG 58.113 42.857 12.87 7.64 0.00 4.10
610 640 2.200899 CCCAAAAACAAGCTTCGTTGG 58.799 47.619 15.39 15.39 36.17 3.77
611 641 2.159170 CCCAAAAACAAGCTTCGTTGGA 60.159 45.455 20.69 0.00 38.20 3.53
612 642 3.516615 CCAAAAACAAGCTTCGTTGGAA 58.483 40.909 16.62 0.00 38.20 3.53
613 643 4.119136 CCAAAAACAAGCTTCGTTGGAAT 58.881 39.130 16.62 1.39 38.20 3.01
614 644 4.570369 CCAAAAACAAGCTTCGTTGGAATT 59.430 37.500 16.62 6.10 38.20 2.17
615 645 5.064579 CCAAAAACAAGCTTCGTTGGAATTT 59.935 36.000 16.62 10.22 38.20 1.82
616 646 5.966636 AAAACAAGCTTCGTTGGAATTTC 57.033 34.783 12.87 0.00 0.00 2.17
618 648 4.853924 ACAAGCTTCGTTGGAATTTCAT 57.146 36.364 0.00 0.00 0.00 2.57
619 649 4.798574 ACAAGCTTCGTTGGAATTTCATC 58.201 39.130 0.00 0.00 0.00 2.92
620 650 3.747099 AGCTTCGTTGGAATTTCATCG 57.253 42.857 10.41 10.41 0.00 3.84
621 651 3.334691 AGCTTCGTTGGAATTTCATCGA 58.665 40.909 14.53 14.53 37.17 3.59
622 652 3.751175 AGCTTCGTTGGAATTTCATCGAA 59.249 39.130 24.26 24.26 42.67 3.71
624 654 4.320953 GCTTCGTTGGAATTTCATCGAAAC 59.679 41.667 25.26 19.94 43.56 2.78
625 655 5.425577 TTCGTTGGAATTTCATCGAAACA 57.574 34.783 23.89 7.78 42.26 2.83
626 656 5.621197 TCGTTGGAATTTCATCGAAACAT 57.379 34.783 15.86 0.00 36.38 2.71
627 657 6.007936 TCGTTGGAATTTCATCGAAACATT 57.992 33.333 15.86 0.00 36.38 2.71
628 658 6.442952 TCGTTGGAATTTCATCGAAACATTT 58.557 32.000 15.86 0.00 36.38 2.32
629 659 6.580791 TCGTTGGAATTTCATCGAAACATTTC 59.419 34.615 15.86 0.00 36.38 2.17
660 690 9.794719 TCTAGCATAGTATGTGTAACTGTATCT 57.205 33.333 11.73 0.00 40.38 1.98
672 702 8.565416 TGTGTAACTGTATCTATAATCAGACCG 58.435 37.037 0.00 0.00 38.04 4.79
673 703 8.566260 GTGTAACTGTATCTATAATCAGACCGT 58.434 37.037 0.00 0.00 0.00 4.83
674 704 9.783081 TGTAACTGTATCTATAATCAGACCGTA 57.217 33.333 0.00 0.00 0.00 4.02
730 760 1.837439 ACCATAGAACATCCCTTGCGA 59.163 47.619 0.00 0.00 0.00 5.10
790 1085 9.573166 TTTTTCTTTTGAGATAGAAGACCATCA 57.427 29.630 0.00 0.00 32.43 3.07
851 1224 6.570692 CCCATCCAGAATTCTGAGAAATTTG 58.429 40.000 32.49 20.79 46.59 2.32
853 1226 7.256286 CCATCCAGAATTCTGAGAAATTTGTC 58.744 38.462 32.49 8.35 46.59 3.18
854 1227 6.824305 TCCAGAATTCTGAGAAATTTGTCC 57.176 37.500 32.49 0.00 46.59 4.02
856 1229 7.006509 TCCAGAATTCTGAGAAATTTGTCCTT 58.993 34.615 32.49 1.98 46.59 3.36
857 1230 7.506938 TCCAGAATTCTGAGAAATTTGTCCTTT 59.493 33.333 32.49 1.82 46.59 3.11
1041 1666 4.798682 TCCGGCCCTCTCCTTCCC 62.799 72.222 0.00 0.00 0.00 3.97
1058 1683 4.455137 CCCCTCCCCCACTCCCAT 62.455 72.222 0.00 0.00 0.00 4.00
1063 1712 3.797353 CCCCCACTCCCATCACGG 61.797 72.222 0.00 0.00 0.00 4.94
1088 1737 3.554342 AGCTAGCCCGCTCCCATG 61.554 66.667 12.13 0.00 34.57 3.66
1143 1793 4.699522 GTTCGCCTCCAACCCGCT 62.700 66.667 0.00 0.00 0.00 5.52
1169 1819 3.127533 GCACTCCACACCATCGCC 61.128 66.667 0.00 0.00 0.00 5.54
1219 1875 3.177228 AGGTACAACTGATCTTCCTGCT 58.823 45.455 0.00 0.00 0.00 4.24
1221 1877 4.160626 AGGTACAACTGATCTTCCTGCTAC 59.839 45.833 0.00 0.00 0.00 3.58
1285 1961 7.003482 TGCTCCTGTTTATATTGCCATTGATA 58.997 34.615 0.00 0.00 0.00 2.15
1296 1972 8.942338 ATATTGCCATTGATATCAATTCATGC 57.058 30.769 25.16 22.70 43.48 4.06
1306 1982 7.871853 TGATATCAATTCATGCTCATGTCAAG 58.128 34.615 1.98 0.83 39.72 3.02
1307 1983 7.501225 TGATATCAATTCATGCTCATGTCAAGT 59.499 33.333 1.98 0.00 39.72 3.16
1308 1984 5.970317 TCAATTCATGCTCATGTCAAGTT 57.030 34.783 9.41 0.00 39.72 2.66
1309 1985 5.705902 TCAATTCATGCTCATGTCAAGTTG 58.294 37.500 9.41 0.00 39.72 3.16
1310 1986 5.242171 TCAATTCATGCTCATGTCAAGTTGT 59.758 36.000 9.41 0.00 39.72 3.32
1311 1987 4.754372 TTCATGCTCATGTCAAGTTGTC 57.246 40.909 9.41 0.00 39.72 3.18
1312 1988 3.742385 TCATGCTCATGTCAAGTTGTCA 58.258 40.909 5.27 5.27 39.72 3.58
1313 1989 4.136051 TCATGCTCATGTCAAGTTGTCAA 58.864 39.130 6.89 0.00 39.72 3.18
1318 1994 4.790878 CTCATGTCAAGTTGTCAACCATG 58.209 43.478 18.95 18.95 32.25 3.66
1330 2006 4.370049 TGTCAACCATGCAATTGAACTTG 58.630 39.130 10.34 1.95 36.62 3.16
1350 2050 4.019792 TGCATACAGTTGGTGTCAATCT 57.980 40.909 0.00 0.00 40.94 2.40
1410 2131 5.237344 AGTGAGCACATGAACTGTTAACTTC 59.763 40.000 7.22 4.02 35.29 3.01
1417 2138 8.129211 GCACATGAACTGTTAACTTCTTTTACT 58.871 33.333 7.22 0.00 35.29 2.24
1431 2158 8.697507 ACTTCTTTTACTGATCACATTTCCTT 57.302 30.769 0.00 0.00 0.00 3.36
1494 2253 5.003804 AGAGTAGTTTTGTAATGGGCACAG 58.996 41.667 0.00 0.00 0.00 3.66
1557 2316 4.883026 GCACCATCTTTGCTGCTG 57.117 55.556 0.00 0.00 37.00 4.41
1565 2324 0.949397 TCTTTGCTGCTGCTGTTGAG 59.051 50.000 17.00 7.35 40.48 3.02
1572 2331 0.806868 TGCTGCTGTTGAGCTTATGC 59.193 50.000 0.00 0.00 46.39 3.14
1575 2334 1.400846 CTGCTGTTGAGCTTATGCCAG 59.599 52.381 0.00 0.00 46.39 4.85
1645 2404 9.638239 TTTTTGAAGCAGTGATTATTGGATTAC 57.362 29.630 0.00 0.00 0.00 1.89
1717 2476 1.737793 GTGCTACCCGGTTCAGATTTG 59.262 52.381 0.00 0.00 0.00 2.32
1719 2478 2.224670 TGCTACCCGGTTCAGATTTGTT 60.225 45.455 0.00 0.00 0.00 2.83
1720 2479 2.817844 GCTACCCGGTTCAGATTTGTTT 59.182 45.455 0.00 0.00 0.00 2.83
1721 2480 3.254903 GCTACCCGGTTCAGATTTGTTTT 59.745 43.478 0.00 0.00 0.00 2.43
1722 2481 4.261867 GCTACCCGGTTCAGATTTGTTTTT 60.262 41.667 0.00 0.00 0.00 1.94
1867 2658 9.665264 GAACTATATGCTTTTACATAAGGTTGC 57.335 33.333 0.00 0.00 36.17 4.17
1868 2659 8.746052 ACTATATGCTTTTACATAAGGTTGCA 57.254 30.769 0.00 0.00 36.17 4.08
1890 2681 0.960861 TTGTGTGACCGCCAACACAA 60.961 50.000 18.38 18.38 46.17 3.33
1942 2733 7.147828 TGTCTTCCTGTGTATCTAGGATTTCTG 60.148 40.741 0.00 0.00 42.38 3.02
1957 2756 6.186957 AGGATTTCTGCAATGTGTATACCAA 58.813 36.000 0.00 0.00 0.00 3.67
2013 2813 0.106708 GGATTCATGCAGCCGTCCTA 59.893 55.000 0.00 0.00 0.00 2.94
2063 2863 1.752198 CCCGTGGTTCCAAGAGTGA 59.248 57.895 6.36 0.00 0.00 3.41
2113 2913 0.463295 CAGCAGCCTGTCCGATGATT 60.463 55.000 0.00 0.00 34.31 2.57
2179 2979 2.139118 GCACAAGTCTTCTCTCACCAC 58.861 52.381 0.00 0.00 0.00 4.16
2444 3286 5.685520 AGGACAGTAATCTTTCCTTCTCC 57.314 43.478 0.00 0.00 45.41 3.71
2469 3311 3.094572 CCTCAAAACAATCAGGCTCCAT 58.905 45.455 0.00 0.00 0.00 3.41
2481 3323 2.681848 CAGGCTCCATTCTGTCATGTTC 59.318 50.000 0.00 0.00 0.00 3.18
2618 3460 1.590932 CATATCAGTGACTGCCAGCC 58.409 55.000 7.93 0.00 0.00 4.85
3030 4141 2.774799 GGGCGATTGGTGCATGACC 61.775 63.158 0.00 1.83 46.37 4.02
3168 4281 4.022242 TCTGCTACAACTCTTACTGACACC 60.022 45.833 0.00 0.00 0.00 4.16
3298 4411 4.384940 GAGAGGATCAAAATCTACTGCCC 58.615 47.826 0.00 0.00 37.82 5.36
3359 4472 3.766691 CCCACTGCCTGCAATGCC 61.767 66.667 1.53 0.00 0.00 4.40
3445 4598 3.434319 CCTGGTCCATGCGTGTGC 61.434 66.667 4.96 0.00 43.20 4.57
3459 4612 0.598065 GTGTGCTGGTTGTTGGATCC 59.402 55.000 4.20 4.20 0.00 3.36
3460 4613 0.184692 TGTGCTGGTTGTTGGATCCA 59.815 50.000 11.44 11.44 0.00 3.41
3514 4667 2.187958 TCTGGTGGGTATTCAGTCTGG 58.812 52.381 0.00 0.00 0.00 3.86
3515 4668 0.618458 TGGTGGGTATTCAGTCTGGC 59.382 55.000 0.00 0.00 0.00 4.85
3516 4669 0.912486 GGTGGGTATTCAGTCTGGCT 59.088 55.000 0.00 0.00 0.00 4.75
3560 4713 4.326826 CTTGAACAATTAGACCTGGAGCA 58.673 43.478 0.00 0.00 0.00 4.26
3569 4722 1.941999 GACCTGGAGCATTGCCTTGC 61.942 60.000 4.70 0.00 43.09 4.01
3571 4724 1.681327 CTGGAGCATTGCCTTGCCT 60.681 57.895 4.70 0.00 43.83 4.75
3642 4810 2.489938 TAGCAAATTCACGCTTCCCT 57.510 45.000 2.72 0.00 39.70 4.20
3653 4821 4.952460 TCACGCTTCCCTGGTTATATTAC 58.048 43.478 0.00 0.00 0.00 1.89
3654 4822 4.652421 TCACGCTTCCCTGGTTATATTACT 59.348 41.667 0.00 0.00 0.00 2.24
3660 4828 7.545965 CGCTTCCCTGGTTATATTACTTATCAG 59.454 40.741 0.00 0.00 0.00 2.90
3680 4849 3.066760 CAGGTTCCAGTCTTCCACAAAAC 59.933 47.826 0.00 0.00 0.00 2.43
3707 4876 4.510038 AGCCAGCTTTTGACTAACAATG 57.490 40.909 0.00 0.00 38.36 2.82
3708 4877 4.144297 AGCCAGCTTTTGACTAACAATGA 58.856 39.130 0.00 0.00 38.36 2.57
3729 4898 0.961019 TCAACTTTCATGTGCTGGGC 59.039 50.000 0.00 0.00 0.00 5.36
3764 4935 8.992835 ATGAGCAGTTGGATTCTTTAAAAATC 57.007 30.769 11.52 11.52 33.29 2.17
3785 5080 3.763360 TCAATATGGGCTTTCACCTTGTG 59.237 43.478 0.00 0.00 34.45 3.33
3811 5106 7.596248 GCAATAAAGAATTCTCTTGTGCTTTCA 59.404 33.333 19.22 0.00 41.23 2.69
3848 5323 6.986424 TTCGCTAGTACATTATTGATCACG 57.014 37.500 0.00 0.00 0.00 4.35
3881 5484 7.446013 TGGGTCAGTTTTATACCTTAACAGTTG 59.554 37.037 0.00 0.00 33.59 3.16
4024 5932 5.450137 CCAATGCATGCCAACTTTTTGAAAA 60.450 36.000 16.68 0.00 34.24 2.29
4029 5937 6.018098 TGCATGCCAACTTTTTGAAAATGTAG 60.018 34.615 16.68 6.10 34.24 2.74
4196 6221 3.187227 CGTTAGCTGCATGAAAACAGAGT 59.813 43.478 1.02 0.00 35.90 3.24
4218 6243 0.037326 TACTTCAACCAGCTCTGCCG 60.037 55.000 0.00 0.00 0.00 5.69
4221 6246 3.114616 CAACCAGCTCTGCCGTCG 61.115 66.667 0.00 0.00 0.00 5.12
4237 6262 1.659098 CGTCGAAATAAGACCACCTGC 59.341 52.381 0.00 0.00 35.33 4.85
4253 6278 3.316029 CACCTGCAGAACAATTCACAAGA 59.684 43.478 17.39 0.00 0.00 3.02
4254 6279 3.316308 ACCTGCAGAACAATTCACAAGAC 59.684 43.478 17.39 0.00 0.00 3.01
4376 6457 4.021280 TGCGGTACCAGACTGTAAAACATA 60.021 41.667 13.54 0.00 36.71 2.29
4380 6461 6.814644 CGGTACCAGACTGTAAAACATAATCA 59.185 38.462 13.54 0.00 0.00 2.57
4430 6511 9.676861 AGAAGACATGATTTCTGATCAAACATA 57.323 29.630 13.19 0.00 32.65 2.29
4472 6839 8.957028 CATGCAGGTTAATTAACAATACGATTG 58.043 33.333 25.59 12.81 37.92 2.67
4511 6883 0.394938 TCGTTTTACCAGCCAGCTCA 59.605 50.000 0.00 0.00 0.00 4.26
4589 6967 5.047660 TGTTAATTAGCACATGGGTGTTTCC 60.048 40.000 0.00 0.00 46.95 3.13
4644 7095 0.800683 TGCTAGACAATCGAACGCCG 60.801 55.000 0.00 0.00 40.25 6.46
4705 7156 1.762370 CAAGGCTGGGAAGGTTTTGTT 59.238 47.619 0.00 0.00 0.00 2.83
4723 7177 4.179579 GCGGTGGCGGCATCTTTC 62.180 66.667 20.91 4.17 0.00 2.62
4724 7178 2.436646 CGGTGGCGGCATCTTTCT 60.437 61.111 20.91 0.00 0.00 2.52
4725 7179 2.040544 CGGTGGCGGCATCTTTCTT 61.041 57.895 20.91 0.00 0.00 2.52
4906 7360 1.503542 GGCGACATGGCTTGACAAG 59.496 57.895 11.02 11.02 40.72 3.16
4917 7371 1.862815 GCTTGACAAGTGTTGCTGCTG 60.863 52.381 16.39 0.00 0.00 4.41
4918 7372 1.672363 CTTGACAAGTGTTGCTGCTGA 59.328 47.619 7.05 0.00 0.00 4.26
4919 7373 1.302366 TGACAAGTGTTGCTGCTGAG 58.698 50.000 0.00 0.00 0.00 3.35
4920 7374 1.134431 TGACAAGTGTTGCTGCTGAGA 60.134 47.619 0.00 0.00 0.00 3.27
4921 7375 1.942657 GACAAGTGTTGCTGCTGAGAA 59.057 47.619 0.00 0.00 0.00 2.87
4922 7376 1.672881 ACAAGTGTTGCTGCTGAGAAC 59.327 47.619 0.00 0.00 0.00 3.01
4923 7377 1.945394 CAAGTGTTGCTGCTGAGAACT 59.055 47.619 0.00 0.00 0.00 3.01
4924 7378 3.133691 CAAGTGTTGCTGCTGAGAACTA 58.866 45.455 0.00 0.00 0.00 2.24
4925 7379 3.037431 AGTGTTGCTGCTGAGAACTAG 57.963 47.619 0.00 0.00 0.00 2.57
4926 7380 2.366916 AGTGTTGCTGCTGAGAACTAGT 59.633 45.455 0.00 0.00 0.00 2.57
4927 7381 2.478134 GTGTTGCTGCTGAGAACTAGTG 59.522 50.000 0.00 0.00 0.00 2.74
4928 7382 2.103094 TGTTGCTGCTGAGAACTAGTGT 59.897 45.455 0.00 0.00 0.00 3.55
4929 7383 2.732412 TGCTGCTGAGAACTAGTGTC 57.268 50.000 0.00 0.00 0.00 3.67
4930 7384 1.068264 TGCTGCTGAGAACTAGTGTCG 60.068 52.381 0.00 0.00 0.00 4.35
4931 7385 1.734047 GCTGCTGAGAACTAGTGTCGG 60.734 57.143 0.00 2.95 0.00 4.79
4932 7386 0.243907 TGCTGAGAACTAGTGTCGGC 59.756 55.000 23.63 23.63 42.06 5.54
4933 7387 0.798771 GCTGAGAACTAGTGTCGGCG 60.799 60.000 18.75 0.00 33.10 6.46
4934 7388 0.803117 CTGAGAACTAGTGTCGGCGA 59.197 55.000 4.99 4.99 0.00 5.54
4935 7389 0.520404 TGAGAACTAGTGTCGGCGAC 59.480 55.000 31.68 31.68 0.00 5.19
4936 7390 0.520404 GAGAACTAGTGTCGGCGACA 59.480 55.000 36.29 36.29 40.50 4.35
4937 7391 1.132643 GAGAACTAGTGTCGGCGACAT 59.867 52.381 40.61 29.99 44.63 3.06
4938 7392 1.135373 AGAACTAGTGTCGGCGACATG 60.135 52.381 40.61 32.43 44.63 3.21
4939 7393 0.108804 AACTAGTGTCGGCGACATGG 60.109 55.000 40.61 31.98 44.63 3.66
4940 7394 1.878522 CTAGTGTCGGCGACATGGC 60.879 63.158 40.61 28.91 44.63 4.40
4941 7395 2.284798 CTAGTGTCGGCGACATGGCT 62.285 60.000 40.61 33.18 44.63 4.75
4942 7396 1.884075 TAGTGTCGGCGACATGGCTT 61.884 55.000 40.61 25.73 44.63 4.35
4943 7397 2.741985 TGTCGGCGACATGGCTTG 60.742 61.111 36.29 0.00 37.67 4.01
4944 7398 2.434185 GTCGGCGACATGGCTTGA 60.434 61.111 33.07 0.00 42.02 3.02
4945 7399 2.434185 TCGGCGACATGGCTTGAC 60.434 61.111 4.99 0.00 42.02 3.18
4946 7400 2.741985 CGGCGACATGGCTTGACA 60.742 61.111 0.00 0.00 42.02 3.58
4947 7401 2.324330 CGGCGACATGGCTTGACAA 61.324 57.895 0.00 0.00 42.02 3.18
4948 7402 1.503542 GGCGACATGGCTTGACAAG 59.496 57.895 11.02 11.02 40.72 3.16
4949 7403 1.237285 GGCGACATGGCTTGACAAGT 61.237 55.000 16.39 0.00 40.72 3.16
4950 7404 0.110056 GCGACATGGCTTGACAAGTG 60.110 55.000 16.39 9.49 0.00 3.16
4951 7405 1.229428 CGACATGGCTTGACAAGTGT 58.771 50.000 16.39 12.50 0.00 3.55
4952 7406 1.603802 CGACATGGCTTGACAAGTGTT 59.396 47.619 16.39 0.00 0.00 3.32
4953 7407 2.602933 CGACATGGCTTGACAAGTGTTG 60.603 50.000 16.39 12.30 0.00 3.33
4954 7408 1.067516 ACATGGCTTGACAAGTGTTGC 59.932 47.619 16.39 2.57 0.00 4.17
4955 7409 1.338973 CATGGCTTGACAAGTGTTGCT 59.661 47.619 16.39 0.00 0.00 3.91
4956 7410 0.740149 TGGCTTGACAAGTGTTGCTG 59.260 50.000 16.39 0.00 0.00 4.41
4957 7411 0.595825 GGCTTGACAAGTGTTGCTGC 60.596 55.000 16.39 0.00 0.00 5.25
4958 7412 0.383231 GCTTGACAAGTGTTGCTGCT 59.617 50.000 16.39 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.335579 GCTAAAAGACCGAACCAGACAT 58.664 45.455 0.00 0.00 0.00 3.06
37 38 2.483106 GGTTGAACTCGGCTAAAAGACC 59.517 50.000 0.00 0.00 0.00 3.85
133 134 5.361571 ACATGAAGATGGATTTGCATTGCTA 59.638 36.000 10.49 0.00 33.39 3.49
154 155 1.077501 CTGGCAATCACCCCGACAT 60.078 57.895 0.00 0.00 0.00 3.06
305 307 4.269844 CAGTTTACAACAACAACAATGGCC 59.730 41.667 0.00 0.00 0.00 5.36
359 362 1.214424 ACCCCCTCATACAAAATCCGG 59.786 52.381 0.00 0.00 0.00 5.14
377 403 7.715249 TCTTAGATCATGCAACTACCAAATACC 59.285 37.037 0.00 0.00 0.00 2.73
388 414 7.174599 AGCAGGAAATATCTTAGATCATGCAAC 59.825 37.037 18.14 2.15 46.73 4.17
428 454 4.521256 ACTTTATGCACCGTACCAAACAAT 59.479 37.500 0.00 0.00 0.00 2.71
470 496 6.365970 AATGAGCTAGAAGACTTTTCCTGA 57.634 37.500 0.00 0.00 0.00 3.86
510 536 1.077716 GCGGGGGCAATGTAACTCT 60.078 57.895 0.00 0.00 0.00 3.24
516 542 3.555967 TTTTTGCGGGGGCAATGT 58.444 50.000 2.00 0.00 0.00 2.71
532 558 7.010460 GCTTTTGAACAATGTAGCTCTGTTTTT 59.990 33.333 0.00 0.00 33.53 1.94
533 559 6.476706 GCTTTTGAACAATGTAGCTCTGTTTT 59.523 34.615 0.00 0.00 33.53 2.43
534 560 5.979517 GCTTTTGAACAATGTAGCTCTGTTT 59.020 36.000 0.00 0.00 33.53 2.83
535 561 5.067674 TGCTTTTGAACAATGTAGCTCTGTT 59.932 36.000 6.64 0.00 36.02 3.16
536 562 4.580167 TGCTTTTGAACAATGTAGCTCTGT 59.420 37.500 6.64 0.00 0.00 3.41
537 563 5.112220 TGCTTTTGAACAATGTAGCTCTG 57.888 39.130 6.64 0.00 0.00 3.35
538 564 5.772825 TTGCTTTTGAACAATGTAGCTCT 57.227 34.783 6.64 0.00 0.00 4.09
539 565 5.403466 CCTTTGCTTTTGAACAATGTAGCTC 59.597 40.000 6.64 0.00 0.00 4.09
540 566 5.291971 CCTTTGCTTTTGAACAATGTAGCT 58.708 37.500 6.64 0.00 0.00 3.32
541 567 4.084380 GCCTTTGCTTTTGAACAATGTAGC 60.084 41.667 0.00 0.00 33.53 3.58
542 568 5.049167 TGCCTTTGCTTTTGAACAATGTAG 58.951 37.500 0.00 0.00 38.71 2.74
543 569 5.016051 TGCCTTTGCTTTTGAACAATGTA 57.984 34.783 0.00 0.00 38.71 2.29
544 570 3.871485 TGCCTTTGCTTTTGAACAATGT 58.129 36.364 0.00 0.00 38.71 2.71
548 574 3.430651 CCTCTTGCCTTTGCTTTTGAACA 60.431 43.478 0.00 0.00 38.71 3.18
582 608 5.453567 AAGCTTGTTTTTGGGTAGATGAC 57.546 39.130 0.00 0.00 0.00 3.06
584 614 4.023193 ACGAAGCTTGTTTTTGGGTAGATG 60.023 41.667 2.10 0.00 0.00 2.90
595 625 5.004922 TGAAATTCCAACGAAGCTTGTTT 57.995 34.783 2.10 0.00 0.00 2.83
596 626 4.647424 TGAAATTCCAACGAAGCTTGTT 57.353 36.364 2.10 6.06 0.00 2.83
597 627 4.613622 CGATGAAATTCCAACGAAGCTTGT 60.614 41.667 2.10 0.00 34.84 3.16
601 631 3.740044 TCGATGAAATTCCAACGAAGC 57.260 42.857 0.00 0.00 38.17 3.86
605 635 6.689178 AAATGTTTCGATGAAATTCCAACG 57.311 33.333 0.00 0.00 33.97 4.10
631 661 8.160521 ACAGTTACACATACTATGCTAGAGAG 57.839 38.462 0.00 0.00 0.00 3.20
632 662 9.794719 ATACAGTTACACATACTATGCTAGAGA 57.205 33.333 0.00 0.00 0.00 3.10
634 664 9.794719 AGATACAGTTACACATACTATGCTAGA 57.205 33.333 0.00 0.00 0.00 2.43
647 677 8.566260 ACGGTCTGATTATAGATACAGTTACAC 58.434 37.037 0.00 0.00 0.00 2.90
648 678 8.687292 ACGGTCTGATTATAGATACAGTTACA 57.313 34.615 0.00 0.00 0.00 2.41
650 680 9.445878 CCTACGGTCTGATTATAGATACAGTTA 57.554 37.037 0.00 0.00 0.00 2.24
653 683 8.616942 CATCCTACGGTCTGATTATAGATACAG 58.383 40.741 0.00 0.00 0.00 2.74
654 684 8.326529 TCATCCTACGGTCTGATTATAGATACA 58.673 37.037 0.00 0.00 0.00 2.29
660 690 7.776618 ACAATCATCCTACGGTCTGATTATA 57.223 36.000 10.70 0.00 35.61 0.98
661 691 6.672266 ACAATCATCCTACGGTCTGATTAT 57.328 37.500 10.70 1.81 35.61 1.28
662 692 6.479972 AACAATCATCCTACGGTCTGATTA 57.520 37.500 10.70 0.00 35.61 1.75
663 693 5.359194 AACAATCATCCTACGGTCTGATT 57.641 39.130 7.27 7.27 36.97 2.57
664 694 5.359194 AAACAATCATCCTACGGTCTGAT 57.641 39.130 0.00 0.00 31.39 2.90
665 695 4.819105 AAACAATCATCCTACGGTCTGA 57.181 40.909 0.00 0.00 0.00 3.27
666 696 5.880054 AAAAACAATCATCCTACGGTCTG 57.120 39.130 0.00 0.00 0.00 3.51
685 715 3.305744 GCCGAGCAATTGGGAACTAAAAA 60.306 43.478 7.72 0.00 0.00 1.94
686 716 2.230266 GCCGAGCAATTGGGAACTAAAA 59.770 45.455 7.72 0.00 0.00 1.52
687 717 1.816224 GCCGAGCAATTGGGAACTAAA 59.184 47.619 7.72 0.00 0.00 1.85
688 718 1.271652 TGCCGAGCAATTGGGAACTAA 60.272 47.619 7.72 0.00 34.76 2.24
689 719 0.326595 TGCCGAGCAATTGGGAACTA 59.673 50.000 7.72 0.00 34.76 2.24
690 720 0.539438 TTGCCGAGCAATTGGGAACT 60.539 50.000 7.72 0.00 43.99 3.01
691 721 1.963679 TTGCCGAGCAATTGGGAAC 59.036 52.632 7.72 0.00 43.99 3.62
790 1085 5.413617 TGCTTCACACTAGCTACGCAAGT 62.414 47.826 0.00 0.00 44.84 3.16
851 1224 8.623903 TCTGCAAATATGACATCATAAAAGGAC 58.376 33.333 5.71 0.00 41.60 3.85
853 1226 9.976511 AATCTGCAAATATGACATCATAAAAGG 57.023 29.630 5.71 0.00 41.60 3.11
979 1523 4.548513 CGAGGGAGGGGAGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
1041 1666 4.455137 ATGGGAGTGGGGGAGGGG 62.455 72.222 0.00 0.00 0.00 4.79
1043 1668 2.042762 TGATGGGAGTGGGGGAGG 59.957 66.667 0.00 0.00 0.00 4.30
1045 1670 2.687200 CGTGATGGGAGTGGGGGA 60.687 66.667 0.00 0.00 0.00 4.81
1048 1673 4.838152 CGCCGTGATGGGAGTGGG 62.838 72.222 0.00 0.00 38.63 4.61
1049 1674 3.770040 TCGCCGTGATGGGAGTGG 61.770 66.667 0.00 0.00 38.63 4.00
1051 1676 4.129737 CGTCGCCGTGATGGGAGT 62.130 66.667 0.00 0.00 38.63 3.85
1127 1777 4.697756 CAGCGGGTTGGAGGCGAA 62.698 66.667 0.00 0.00 0.00 4.70
1149 1799 2.662596 GATGGTGTGGAGTGCGGA 59.337 61.111 0.00 0.00 0.00 5.54
1169 1819 4.451150 TAAGGCAGGTCGCAGGCG 62.451 66.667 7.46 7.46 45.17 5.52
1172 1822 2.265739 TGCTAAGGCAGGTCGCAG 59.734 61.111 0.00 0.00 44.28 5.18
1219 1875 4.101114 TCCCAGATTTGGTAAGCAGAGTA 58.899 43.478 0.96 0.00 43.40 2.59
1221 1877 3.634397 TCCCAGATTTGGTAAGCAGAG 57.366 47.619 0.96 0.00 43.40 3.35
1285 1961 6.071560 ACAACTTGACATGAGCATGAATTGAT 60.072 34.615 16.70 0.00 41.20 2.57
1296 1972 4.790878 CATGGTTGACAACTTGACATGAG 58.209 43.478 21.33 4.70 37.10 2.90
1306 1982 4.370917 AGTTCAATTGCATGGTTGACAAC 58.629 39.130 9.97 9.97 34.34 3.32
1307 1983 4.669206 AGTTCAATTGCATGGTTGACAA 57.331 36.364 0.00 0.00 34.34 3.18
1308 1984 4.370049 CAAGTTCAATTGCATGGTTGACA 58.630 39.130 0.00 0.90 34.34 3.58
1309 1985 4.977741 CAAGTTCAATTGCATGGTTGAC 57.022 40.909 0.00 5.75 34.34 3.18
1330 2006 4.726416 CAAGATTGACACCAACTGTATGC 58.274 43.478 0.00 0.00 34.72 3.14
1337 2037 4.241590 TCATTGCAAGATTGACACCAAC 57.758 40.909 4.94 0.00 34.72 3.77
1376 2076 9.750125 CAGTTCATGTGCTCACTTTAGTATATA 57.250 33.333 1.47 0.00 0.00 0.86
1392 2113 9.438291 CAGTAAAAGAAGTTAACAGTTCATGTG 57.562 33.333 8.61 0.00 43.00 3.21
1445 2195 1.807814 AGAGAGTTCGGGCCCATTAT 58.192 50.000 24.92 4.04 0.00 1.28
1450 2200 0.253327 AATGAAGAGAGTTCGGGCCC 59.747 55.000 13.57 13.57 0.00 5.80
1494 2253 6.166279 TGGTAATCAGTCACAGACAGAATTC 58.834 40.000 0.00 0.00 32.26 2.17
1565 2324 4.718940 AATTACAACACCTGGCATAAGC 57.281 40.909 0.00 0.00 41.10 3.09
1572 2331 6.642707 TCCAGTTTAAATTACAACACCTGG 57.357 37.500 8.63 8.63 38.60 4.45
1575 2334 7.151976 AGCATTCCAGTTTAAATTACAACACC 58.848 34.615 0.00 0.00 0.00 4.16
1623 2382 7.011389 CGAAGTAATCCAATAATCACTGCTTCA 59.989 37.037 0.00 0.00 0.00 3.02
1660 2419 8.677300 ACACACTAAATAGGAGCAATTATGTTG 58.323 33.333 0.00 0.00 0.00 3.33
1677 2436 9.211485 GTAGCACCTTTCTATTAACACACTAAA 57.789 33.333 0.00 0.00 0.00 1.85
1690 2449 1.551883 GAACCGGGTAGCACCTTTCTA 59.448 52.381 6.32 0.00 38.64 2.10
1868 2659 0.749818 TGTTGGCGGTCACACAATGT 60.750 50.000 0.00 0.00 0.00 2.71
1890 2681 5.633830 AACGATTTCAATCATGAAGCAGT 57.366 34.783 0.00 0.00 45.82 4.40
1923 2714 6.765036 ACATTGCAGAAATCCTAGATACACAG 59.235 38.462 0.00 0.00 0.00 3.66
1942 2733 8.876275 ATCAAAATCATTGGTATACACATTGC 57.124 30.769 5.01 0.00 0.00 3.56
1957 2756 8.434392 AGGGCAATGCTAAATAATCAAAATCAT 58.566 29.630 4.82 0.00 0.00 2.45
2013 2813 1.812571 GGTGCCGACATTTCATCAAGT 59.187 47.619 0.00 0.00 0.00 3.16
2063 2863 2.124819 CATTCCTGCTGCCTCGCT 60.125 61.111 0.00 0.00 0.00 4.93
2113 2913 1.545428 GGACATCACAAGGTGGAGCAA 60.545 52.381 0.00 0.00 33.87 3.91
2179 2979 0.523968 CACCAAAGATTGCGCCATCG 60.524 55.000 15.06 4.45 39.07 3.84
2444 3286 1.666888 GCCTGATTGTTTTGAGGTGCG 60.667 52.381 0.00 0.00 0.00 5.34
2481 3323 3.862845 GCGGCCTAAATAACCAATGTTTG 59.137 43.478 0.00 0.00 35.87 2.93
2764 3619 6.877855 AGATGTACATGATGATCCAATACTGC 59.122 38.462 14.43 0.00 0.00 4.40
3030 4141 1.291877 GCAGTGGGTACAAGTCAGCG 61.292 60.000 0.00 0.00 0.00 5.18
3168 4281 9.254133 CAGAATATCAACATCAAGGTAGTAGTG 57.746 37.037 0.00 0.00 0.00 2.74
3255 4368 2.439156 GCAAGGGTAGCTGCCTGG 60.439 66.667 21.02 11.16 32.18 4.45
3359 4472 0.935898 GCCACTCGATGCTGATCTTG 59.064 55.000 0.00 0.00 0.00 3.02
3393 4546 6.564125 CGTCTCCAAAACACTATTGTCTCAAC 60.564 42.308 0.00 0.00 33.55 3.18
3445 4598 2.288395 GCAGTTTGGATCCAACAACCAG 60.288 50.000 27.04 17.84 35.46 4.00
3459 4612 3.558505 CTTCCATTGACGAAGCAGTTTG 58.441 45.455 0.00 0.00 31.02 2.93
3460 4613 3.904136 CTTCCATTGACGAAGCAGTTT 57.096 42.857 0.00 0.00 31.02 2.66
3514 4667 1.464734 GGAAAGCTGGGGAAACTAGC 58.535 55.000 0.00 0.00 39.64 3.42
3515 4668 1.679032 CGGGAAAGCTGGGGAAACTAG 60.679 57.143 0.00 0.00 0.00 2.57
3516 4669 0.326927 CGGGAAAGCTGGGGAAACTA 59.673 55.000 0.00 0.00 0.00 2.24
3560 4713 1.368579 GTTGTGCAGGCAAGGCAAT 59.631 52.632 0.00 0.00 43.91 3.56
3569 4722 1.165907 TTTCTCAGCCGTTGTGCAGG 61.166 55.000 0.00 0.00 0.00 4.85
3571 4724 1.266718 GATTTTCTCAGCCGTTGTGCA 59.733 47.619 0.00 0.00 0.00 4.57
3642 4810 9.220906 ACTGGAACCTGATAAGTAATATAACCA 57.779 33.333 4.82 0.00 0.00 3.67
3653 4821 4.020218 TGTGGAAGACTGGAACCTGATAAG 60.020 45.833 4.82 0.00 0.00 1.73
3654 4822 3.907474 TGTGGAAGACTGGAACCTGATAA 59.093 43.478 4.82 0.00 0.00 1.75
3660 4828 3.020984 TGTTTTGTGGAAGACTGGAACC 58.979 45.455 0.00 0.00 0.00 3.62
3680 4849 5.008613 TGTTAGTCAAAAGCTGGCTAGTTTG 59.991 40.000 0.00 11.37 43.12 2.93
3707 4876 3.841643 CCCAGCACATGAAAGTTGAATC 58.158 45.455 0.00 0.00 0.00 2.52
3708 4877 2.028748 GCCCAGCACATGAAAGTTGAAT 60.029 45.455 0.00 0.00 0.00 2.57
3764 4935 3.676873 GCACAAGGTGAAAGCCCATATTG 60.677 47.826 0.00 0.00 35.23 1.90
3785 5080 7.596248 TGAAAGCACAAGAGAATTCTTTATTGC 59.404 33.333 20.31 18.99 41.71 3.56
3848 5323 6.838382 AGGTATAAAACTGACCCATACATCC 58.162 40.000 0.00 0.00 33.40 3.51
3912 5790 4.147133 GCAAATCTGTGAAGACGCTTTTTC 59.853 41.667 0.00 0.00 0.00 2.29
4024 5932 8.267620 TCATGGGTGATAGAATCTTTCTACAT 57.732 34.615 2.63 2.25 44.43 2.29
4029 5937 8.908786 TGTAATCATGGGTGATAGAATCTTTC 57.091 34.615 0.00 0.00 44.20 2.62
4160 6185 5.412594 TGCAGCTAACGATTCTCATTTTCTT 59.587 36.000 0.00 0.00 0.00 2.52
4167 6192 3.525268 TCATGCAGCTAACGATTCTCA 57.475 42.857 0.00 0.00 0.00 3.27
4176 6201 5.065914 AGAACTCTGTTTTCATGCAGCTAA 58.934 37.500 0.00 0.00 33.09 3.09
4196 6221 2.289694 GGCAGAGCTGGTTGAAGTAGAA 60.290 50.000 0.00 0.00 0.00 2.10
4218 6243 2.673368 CTGCAGGTGGTCTTATTTCGAC 59.327 50.000 5.57 0.00 0.00 4.20
4221 6246 4.072131 TGTTCTGCAGGTGGTCTTATTTC 58.928 43.478 15.13 0.00 0.00 2.17
4237 6262 6.267817 ACAATGTGTCTTGTGAATTGTTCTG 58.732 36.000 0.00 0.00 38.05 3.02
4347 6426 1.000955 CAGTCTGGTACCGCAACTCTT 59.999 52.381 7.57 0.00 0.00 2.85
4427 6508 8.077991 CCTGCATGGTTATTTGTAGTGATTATG 58.922 37.037 0.00 0.00 0.00 1.90
4430 6511 6.455360 CCTGCATGGTTATTTGTAGTGATT 57.545 37.500 0.00 0.00 0.00 2.57
4491 6858 1.079503 GAGCTGGCTGGTAAAACGAG 58.920 55.000 0.00 0.00 0.00 4.18
4494 6861 0.881796 GGTGAGCTGGCTGGTAAAAC 59.118 55.000 0.00 0.00 0.00 2.43
4511 6883 8.610369 AGTAGTAGTAGACTTTGGTAGTTAGGT 58.390 37.037 0.00 0.00 39.81 3.08
4560 6938 6.039717 ACACCCATGTGCTAATTAACATCATC 59.960 38.462 0.64 0.00 46.86 2.92
4644 7095 0.957888 GTCAGGAGGCAGCCAGAAAC 60.958 60.000 15.80 1.00 0.00 2.78
4723 7177 1.412074 CCCCATTCCATCCCCAAGAAG 60.412 57.143 0.00 0.00 0.00 2.85
4724 7178 0.636101 CCCCATTCCATCCCCAAGAA 59.364 55.000 0.00 0.00 0.00 2.52
4725 7179 1.948403 GCCCCATTCCATCCCCAAGA 61.948 60.000 0.00 0.00 0.00 3.02
4906 7360 2.478134 CACTAGTTCTCAGCAGCAACAC 59.522 50.000 0.00 0.00 0.00 3.32
4917 7371 0.520404 TGTCGCCGACACTAGTTCTC 59.480 55.000 17.22 0.00 37.67 2.87
4918 7372 1.135373 CATGTCGCCGACACTAGTTCT 60.135 52.381 23.77 1.10 45.65 3.01
4919 7373 1.269166 CATGTCGCCGACACTAGTTC 58.731 55.000 23.77 0.00 45.65 3.01
4920 7374 0.108804 CCATGTCGCCGACACTAGTT 60.109 55.000 23.77 2.80 45.65 2.24
4921 7375 1.511305 CCATGTCGCCGACACTAGT 59.489 57.895 23.77 3.24 45.65 2.57
4922 7376 1.878522 GCCATGTCGCCGACACTAG 60.879 63.158 23.77 14.73 45.65 2.57
4923 7377 1.884075 AAGCCATGTCGCCGACACTA 61.884 55.000 23.77 0.00 45.65 2.74
4924 7378 3.240134 AAGCCATGTCGCCGACACT 62.240 57.895 23.77 12.60 45.65 3.55
4925 7379 2.742372 AAGCCATGTCGCCGACAC 60.742 61.111 23.77 10.25 45.65 3.67
4926 7380 2.741985 CAAGCCATGTCGCCGACA 60.742 61.111 23.51 23.51 46.90 4.35
4927 7381 2.434185 TCAAGCCATGTCGCCGAC 60.434 61.111 10.96 10.96 0.00 4.79
4928 7382 2.434185 GTCAAGCCATGTCGCCGA 60.434 61.111 0.00 0.00 0.00 5.54
4929 7383 2.244436 CTTGTCAAGCCATGTCGCCG 62.244 60.000 0.00 0.00 0.00 6.46
4930 7384 1.237285 ACTTGTCAAGCCATGTCGCC 61.237 55.000 12.66 0.00 0.00 5.54
4931 7385 0.110056 CACTTGTCAAGCCATGTCGC 60.110 55.000 12.66 0.00 0.00 5.19
4932 7386 1.229428 ACACTTGTCAAGCCATGTCG 58.771 50.000 12.66 0.00 0.00 4.35
4933 7387 2.859806 GCAACACTTGTCAAGCCATGTC 60.860 50.000 12.66 2.73 0.00 3.06
4934 7388 1.067516 GCAACACTTGTCAAGCCATGT 59.932 47.619 12.66 6.97 0.00 3.21
4935 7389 1.338973 AGCAACACTTGTCAAGCCATG 59.661 47.619 12.66 9.57 0.00 3.66
4936 7390 1.338973 CAGCAACACTTGTCAAGCCAT 59.661 47.619 12.66 0.00 0.00 4.40
4937 7391 0.740149 CAGCAACACTTGTCAAGCCA 59.260 50.000 12.66 0.00 0.00 4.75
4938 7392 0.595825 GCAGCAACACTTGTCAAGCC 60.596 55.000 12.66 0.00 0.00 4.35
4939 7393 0.383231 AGCAGCAACACTTGTCAAGC 59.617 50.000 12.66 0.00 0.00 4.01
4940 7394 1.672363 TCAGCAGCAACACTTGTCAAG 59.328 47.619 11.17 11.17 0.00 3.02
4941 7395 1.672363 CTCAGCAGCAACACTTGTCAA 59.328 47.619 0.00 0.00 0.00 3.18
4942 7396 1.134431 TCTCAGCAGCAACACTTGTCA 60.134 47.619 0.00 0.00 0.00 3.58
4943 7397 1.586422 TCTCAGCAGCAACACTTGTC 58.414 50.000 0.00 0.00 0.00 3.18
4944 7398 1.672881 GTTCTCAGCAGCAACACTTGT 59.327 47.619 0.00 0.00 0.00 3.16
4945 7399 1.945394 AGTTCTCAGCAGCAACACTTG 59.055 47.619 0.00 0.00 0.00 3.16
4946 7400 2.338577 AGTTCTCAGCAGCAACACTT 57.661 45.000 0.00 0.00 0.00 3.16
4947 7401 2.366916 ACTAGTTCTCAGCAGCAACACT 59.633 45.455 0.00 0.00 0.00 3.55
4948 7402 2.478134 CACTAGTTCTCAGCAGCAACAC 59.522 50.000 0.00 0.00 0.00 3.32
4949 7403 2.103094 ACACTAGTTCTCAGCAGCAACA 59.897 45.455 0.00 0.00 0.00 3.33
4950 7404 2.734079 GACACTAGTTCTCAGCAGCAAC 59.266 50.000 0.00 0.00 0.00 4.17
4951 7405 2.608016 CGACACTAGTTCTCAGCAGCAA 60.608 50.000 0.00 0.00 0.00 3.91
4952 7406 1.068264 CGACACTAGTTCTCAGCAGCA 60.068 52.381 0.00 0.00 0.00 4.41
4953 7407 1.623359 CGACACTAGTTCTCAGCAGC 58.377 55.000 0.00 0.00 0.00 5.25
4954 7408 1.734047 GCCGACACTAGTTCTCAGCAG 60.734 57.143 0.00 0.00 0.00 4.24
4955 7409 0.243907 GCCGACACTAGTTCTCAGCA 59.756 55.000 0.00 0.00 0.00 4.41
4956 7410 0.798771 CGCCGACACTAGTTCTCAGC 60.799 60.000 0.00 0.00 0.00 4.26
4957 7411 0.803117 TCGCCGACACTAGTTCTCAG 59.197 55.000 0.00 0.00 0.00 3.35
4958 7412 0.803117 CTCGCCGACACTAGTTCTCA 59.197 55.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.