Multiple sequence alignment - TraesCS2A01G219200

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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 TraesCS2A01G219200 chr2A 100.000 5332 0 0 1 5332 206413916 206408585 0.000000e+00 9847.0
1 TraesCS2A01G219200 chr2A 93.648 551 35 0 4479 5029 100534272 100534822 0.000000e+00 824.0
2 TraesCS2A01G219200 chr2A 93.421 304 19 1 5029 5332 720052900 720053202 2.930000e-122 449.0
3 TraesCS2A01G219200 chr2B 94.887 1506 53 12 2033 3528 248659983 248658492 0.000000e+00 2333.0
4 TraesCS2A01G219200 chr2B 91.451 1392 62 27 660 2035 248661492 248660142 0.000000e+00 1858.0
5 TraesCS2A01G219200 chr2B 92.948 865 31 13 3639 4485 248658515 248657663 0.000000e+00 1232.0
6 TraesCS2A01G219200 chr2B 84.444 495 65 7 58 545 248662121 248661632 1.340000e-130 477.0
7 TraesCS2A01G219200 chr2B 78.495 186 25 7 486 659 90570440 90570622 2.030000e-19 108.0
8 TraesCS2A01G219200 chr2D 93.296 895 20 17 754 1635 191233825 191234692 0.000000e+00 1284.0
9 TraesCS2A01G219200 chr2D 92.486 905 54 9 2621 3522 191235484 191236377 0.000000e+00 1282.0
10 TraesCS2A01G219200 chr2D 92.784 873 23 16 3640 4485 191236361 191237220 0.000000e+00 1227.0
11 TraesCS2A01G219200 chr2D 92.914 748 36 10 1716 2449 191234718 191235462 0.000000e+00 1072.0
12 TraesCS2A01G219200 chr2D 92.763 304 22 0 5029 5332 58882112 58881809 1.760000e-119 440.0
13 TraesCS2A01G219200 chr2D 80.667 150 26 3 46 193 191232481 191232629 4.360000e-21 113.0
14 TraesCS2A01G219200 chr2D 79.798 99 20 0 535 633 14438950 14439048 7.410000e-09 73.1
15 TraesCS2A01G219200 chr4D 91.260 881 49 9 4479 5332 69233194 69234073 0.000000e+00 1175.0
16 TraesCS2A01G219200 chr4D 91.136 880 52 1 4479 5332 444213099 444213978 0.000000e+00 1170.0
17 TraesCS2A01G219200 chr6D 95.463 551 25 0 4479 5029 296760765 296760215 0.000000e+00 880.0
18 TraesCS2A01G219200 chr6D 92.763 304 22 0 5029 5332 296760189 296759886 1.760000e-119 440.0
19 TraesCS2A01G219200 chr6D 80.412 97 18 1 539 634 56907124 56907028 7.410000e-09 73.1
20 TraesCS2A01G219200 chr7D 94.374 551 31 0 4479 5029 632885432 632885982 0.000000e+00 846.0
21 TraesCS2A01G219200 chr7D 93.648 551 35 0 4479 5029 563629897 563629347 0.000000e+00 824.0
22 TraesCS2A01G219200 chr7D 76.216 185 33 5 483 658 112869167 112869349 2.650000e-13 87.9
23 TraesCS2A01G219200 chr3B 94.011 551 33 0 4479 5029 172765454 172764904 0.000000e+00 835.0
24 TraesCS2A01G219200 chr3B 79.845 129 21 4 536 659 100825423 100825295 7.360000e-14 89.8
25 TraesCS2A01G219200 chr5D 93.829 551 34 0 4479 5029 356851042 356850492 0.000000e+00 830.0
26 TraesCS2A01G219200 chr5D 77.564 156 27 4 484 632 334261733 334261579 2.650000e-13 87.9
27 TraesCS2A01G219200 chr5D 76.774 155 29 5 508 656 348477357 348477204 4.430000e-11 80.5
28 TraesCS2A01G219200 chr5D 92.500 40 2 1 588 627 353633820 353633858 7.460000e-04 56.5
29 TraesCS2A01G219200 chr5A 93.829 551 34 0 4479 5029 683941584 683942134 0.000000e+00 830.0
30 TraesCS2A01G219200 chr3D 93.688 301 18 1 5032 5332 253575354 253575055 2.930000e-122 449.0
31 TraesCS2A01G219200 chr3D 93.377 302 20 0 5031 5332 104783790 104783489 1.050000e-121 448.0
32 TraesCS2A01G219200 chr3D 83.206 131 15 5 535 659 2630534 2630405 4.360000e-21 113.0
33 TraesCS2A01G219200 chr3D 77.632 152 26 4 492 636 2455392 2455542 9.510000e-13 86.1
34 TraesCS2A01G219200 chr6A 92.763 304 22 0 5029 5332 61811476 61811173 1.760000e-119 440.0
35 TraesCS2A01G219200 chr6A 76.720 189 29 9 482 659 96717464 96717280 2.050000e-14 91.6
36 TraesCS2A01G219200 chr6A 76.647 167 29 4 499 657 560727382 560727546 3.420000e-12 84.2
37 TraesCS2A01G219200 chr1A 92.763 304 22 0 5029 5332 507565824 507565521 1.760000e-119 440.0
38 TraesCS2A01G219200 chr1A 92.763 304 22 0 5029 5332 580727118 580726815 1.760000e-119 440.0
39 TraesCS2A01G219200 chr1A 74.324 222 40 10 448 656 337980050 337980267 1.590000e-10 78.7
40 TraesCS2A01G219200 chrUn 77.473 182 25 9 490 656 402856023 402855843 1.580000e-15 95.3
41 TraesCS2A01G219200 chr7B 78.947 152 23 3 490 634 642294981 642294832 1.580000e-15 95.3
42 TraesCS2A01G219200 chr7A 77.473 182 25 9 490 656 5248899 5249079 1.580000e-15 95.3
43 TraesCS2A01G219200 chr7A 77.596 183 24 11 490 656 5261700 5261881 1.580000e-15 95.3
44 TraesCS2A01G219200 chr7A 77.473 182 25 9 490 656 5275482 5275662 1.580000e-15 95.3
45 TraesCS2A01G219200 chr7A 77.596 183 24 10 490 656 5304878 5305059 1.580000e-15 95.3
46 TraesCS2A01G219200 chr5B 77.778 135 25 3 502 634 248687089 248686958 1.590000e-10 78.7
47 TraesCS2A01G219200 chr5B 100.000 34 0 0 501 534 589379583 589379616 4.460000e-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 TraesCS2A01G219200 chr2A 206408585 206413916 5331 True 9847.0 9847 100.0000 1 5332 1 chr2A.!!$R1 5331
1 TraesCS2A01G219200 chr2A 100534272 100534822 550 False 824.0 824 93.6480 4479 5029 1 chr2A.!!$F1 550
2 TraesCS2A01G219200 chr2B 248657663 248662121 4458 True 1475.0 2333 90.9325 58 4485 4 chr2B.!!$R1 4427
3 TraesCS2A01G219200 chr2D 191232481 191237220 4739 False 995.6 1284 90.4294 46 4485 5 chr2D.!!$F2 4439
4 TraesCS2A01G219200 chr4D 69233194 69234073 879 False 1175.0 1175 91.2600 4479 5332 1 chr4D.!!$F1 853
5 TraesCS2A01G219200 chr4D 444213099 444213978 879 False 1170.0 1170 91.1360 4479 5332 1 chr4D.!!$F2 853
6 TraesCS2A01G219200 chr6D 296759886 296760765 879 True 660.0 880 94.1130 4479 5332 2 chr6D.!!$R2 853
7 TraesCS2A01G219200 chr7D 632885432 632885982 550 False 846.0 846 94.3740 4479 5029 1 chr7D.!!$F2 550
8 TraesCS2A01G219200 chr7D 563629347 563629897 550 True 824.0 824 93.6480 4479 5029 1 chr7D.!!$R1 550
9 TraesCS2A01G219200 chr3B 172764904 172765454 550 True 835.0 835 94.0110 4479 5029 1 chr3B.!!$R2 550
10 TraesCS2A01G219200 chr5D 356850492 356851042 550 True 830.0 830 93.8290 4479 5029 1 chr5D.!!$R3 550
11 TraesCS2A01G219200 chr5A 683941584 683942134 550 False 830.0 830 93.8290 4479 5029 1 chr5A.!!$F1 550

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
377 379 2.102588 GCTTTCGGGAGAGGCATAACTA 59.897 50.0 0.00 0.00 41.75 2.24 F
1168 1923 0.673644 CCAAGATGACGCGGTTCCTT 60.674 55.0 12.47 5.64 0.00 3.36 F
1295 2050 0.843343 TCTTCTTAGGCCCCGGGTTT 60.843 55.0 21.85 6.82 0.00 3.27 F
1699 2454 0.880278 GTTGTGCAGCGAGAGGACAA 60.880 55.0 5.44 5.44 43.53 3.18 F
2819 3764 0.941542 CGCCGAAACAAACAAGGAGA 59.058 50.0 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2752 1.065199 TCATTGCAGAGGCCTTAGTGG 60.065 52.381 6.77 0.00 40.13 4.00 R
3147 4092 1.699656 CGCTGCTTCCGGTCTCAATG 61.700 60.000 0.00 0.00 0.00 2.82 R
3186 4131 1.070134 CCTCGGCCGATTCCTTGAATA 59.930 52.381 31.19 0.52 31.89 1.75 R
3307 4253 1.021202 TGGCCATAATCTTTTCGCCG 58.979 50.000 0.00 0.00 39.30 6.46 R
4806 5784 0.693049 ATCGTCCCCTTGTCTTGCTT 59.307 50.000 0.00 0.00 0.00 3.91 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
30 31 3.863142 AAATGTGCTTTCATGAGAGGC 57.137 42.857 14.60 11.46 0.00 4.70
31 32 2.502142 ATGTGCTTTCATGAGAGGCA 57.498 45.000 14.60 13.67 33.92 4.75
32 33 2.275134 TGTGCTTTCATGAGAGGCAA 57.725 45.000 14.60 6.46 36.56 4.52
33 34 2.585330 TGTGCTTTCATGAGAGGCAAA 58.415 42.857 14.60 9.73 36.56 3.68
34 35 3.159472 TGTGCTTTCATGAGAGGCAAAT 58.841 40.909 14.60 0.00 36.56 2.32
35 36 3.575256 TGTGCTTTCATGAGAGGCAAATT 59.425 39.130 14.60 0.00 36.56 1.82
36 37 4.039488 TGTGCTTTCATGAGAGGCAAATTT 59.961 37.500 14.60 0.00 36.56 1.82
37 38 4.387862 GTGCTTTCATGAGAGGCAAATTTG 59.612 41.667 14.03 14.03 36.56 2.32
93 94 5.657474 AGAAATACGGATTTGCTTCTCGTA 58.343 37.500 11.16 0.00 39.95 3.43
94 95 6.103997 AGAAATACGGATTTGCTTCTCGTAA 58.896 36.000 11.16 0.00 39.27 3.18
124 125 7.269937 CACATATTTTCTTTCAAGAGAAGCACG 59.730 37.037 0.00 0.00 37.01 5.34
177 178 7.386059 TCTATGCTTTCACATGAAACACTCTA 58.614 34.615 0.00 0.00 38.94 2.43
186 187 6.206048 TCACATGAAACACTCTACTTCTCGTA 59.794 38.462 0.00 0.00 0.00 3.43
224 225 4.027572 TCTGCAAAAAGTACAGTTGTGC 57.972 40.909 14.52 14.52 33.12 4.57
236 237 6.322491 AGTACAGTTGTGCTTCTTGAAAAAC 58.678 36.000 0.00 0.00 37.74 2.43
239 240 5.988561 ACAGTTGTGCTTCTTGAAAAACAAA 59.011 32.000 10.23 0.00 38.08 2.83
240 241 6.650390 ACAGTTGTGCTTCTTGAAAAACAAAT 59.350 30.769 10.23 7.87 38.08 2.32
241 242 6.957077 CAGTTGTGCTTCTTGAAAAACAAATG 59.043 34.615 16.33 16.33 37.30 2.32
247 248 6.149142 TGCTTCTTGAAAAACAAATGTGCTTT 59.851 30.769 0.00 0.00 38.08 3.51
287 289 5.681337 GCTTCTTAAGGAGGCACATATTC 57.319 43.478 12.86 0.00 44.96 1.75
288 290 5.126067 GCTTCTTAAGGAGGCACATATTCA 58.874 41.667 12.86 0.00 44.96 2.57
315 317 2.348666 GCGAGTAGCATACCTGTGTTTG 59.651 50.000 0.00 0.00 44.47 2.93
317 319 3.994392 CGAGTAGCATACCTGTGTTTGTT 59.006 43.478 0.00 0.00 44.47 2.83
318 320 5.165676 CGAGTAGCATACCTGTGTTTGTTA 58.834 41.667 0.00 0.00 44.47 2.41
337 339 9.986833 GTTTGTTAGAATGAAAAATTGTGCTTT 57.013 25.926 0.00 0.00 0.00 3.51
339 341 8.060020 TGTTAGAATGAAAAATTGTGCTTTCG 57.940 30.769 0.00 0.00 34.84 3.46
377 379 2.102588 GCTTTCGGGAGAGGCATAACTA 59.897 50.000 0.00 0.00 41.75 2.24
391 393 8.475639 AGAGGCATAACTATACTTCTCGAAAAA 58.524 33.333 0.00 0.00 0.00 1.94
559 572 6.662865 AGATCTCGACATGAGTAATCCAAT 57.337 37.500 0.00 0.00 45.46 3.16
561 574 4.948847 TCTCGACATGAGTAATCCAATGG 58.051 43.478 0.00 0.00 45.46 3.16
575 588 9.308000 AGTAATCCAATGGTGAAAATAGTTCAA 57.692 29.630 0.00 0.00 0.00 2.69
580 593 9.487790 TCCAATGGTGAAAATAGTTCAAAATTC 57.512 29.630 0.00 0.00 0.00 2.17
581 594 9.492973 CCAATGGTGAAAATAGTTCAAAATTCT 57.507 29.630 0.00 0.00 0.00 2.40
593 606 7.393551 AGTTCAAAATTCTAACGCACAATTG 57.606 32.000 3.24 3.24 0.00 2.32
684 756 9.668497 GATAACTCTTAACTAGTGATTTTGGGT 57.332 33.333 0.00 0.00 0.00 4.51
686 758 8.762481 AACTCTTAACTAGTGATTTTGGGTTT 57.238 30.769 0.00 0.00 0.00 3.27
687 759 8.762481 ACTCTTAACTAGTGATTTTGGGTTTT 57.238 30.769 0.00 0.00 0.00 2.43
806 1544 2.287009 GCACAACAGTCAGCAGGTTTAC 60.287 50.000 0.00 0.00 0.00 2.01
807 1545 2.942376 CACAACAGTCAGCAGGTTTACA 59.058 45.455 0.00 0.00 0.00 2.41
810 1548 4.067896 CAACAGTCAGCAGGTTTACATCT 58.932 43.478 0.00 0.00 0.00 2.90
811 1549 3.931578 ACAGTCAGCAGGTTTACATCTC 58.068 45.455 0.00 0.00 0.00 2.75
812 1550 3.324846 ACAGTCAGCAGGTTTACATCTCA 59.675 43.478 0.00 0.00 0.00 3.27
813 1551 3.931468 CAGTCAGCAGGTTTACATCTCAG 59.069 47.826 0.00 0.00 0.00 3.35
814 1552 3.834813 AGTCAGCAGGTTTACATCTCAGA 59.165 43.478 0.00 0.00 0.00 3.27
815 1553 4.284490 AGTCAGCAGGTTTACATCTCAGAA 59.716 41.667 0.00 0.00 0.00 3.02
816 1554 4.997395 GTCAGCAGGTTTACATCTCAGAAA 59.003 41.667 0.00 0.00 0.00 2.52
817 1555 5.121454 GTCAGCAGGTTTACATCTCAGAAAG 59.879 44.000 0.00 0.00 0.00 2.62
878 1616 3.295228 GACGCACGCAATCGCTGTT 62.295 57.895 0.00 0.00 39.84 3.16
968 1706 6.891388 TGGTATAGTTATTTGGTTCCATCGT 58.109 36.000 0.00 0.00 0.00 3.73
1003 1741 1.056660 ACCACACCAGGACGATCTTT 58.943 50.000 0.00 0.00 0.00 2.52
1015 1753 2.412089 GACGATCTTTCCAAAGTCACCG 59.588 50.000 0.00 0.00 37.31 4.94
1021 1759 0.834612 TTCCAAAGTCACCGTCACCT 59.165 50.000 0.00 0.00 0.00 4.00
1066 1815 1.528309 CGCCTCTCTCCCTCTCTCC 60.528 68.421 0.00 0.00 0.00 3.71
1079 1828 2.370189 CCTCTCTCCCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
1104 1859 2.887152 ACAGGAAGCCAAGATGAACAAC 59.113 45.455 0.00 0.00 0.00 3.32
1158 1913 7.271511 ACAAGATAATCTCTGTCCAAGATGAC 58.728 38.462 0.00 0.00 33.78 3.06
1168 1923 0.673644 CCAAGATGACGCGGTTCCTT 60.674 55.000 12.47 5.64 0.00 3.36
1169 1924 1.156736 CAAGATGACGCGGTTCCTTT 58.843 50.000 12.47 0.00 0.00 3.11
1170 1925 1.535462 CAAGATGACGCGGTTCCTTTT 59.465 47.619 12.47 0.00 0.00 2.27
1171 1926 1.439679 AGATGACGCGGTTCCTTTTC 58.560 50.000 12.47 0.00 0.00 2.29
1175 1930 1.202604 TGACGCGGTTCCTTTTCTTCT 60.203 47.619 12.47 0.00 0.00 2.85
1251 2006 5.798434 TCAACGAATGTAGATACAGTTCGTG 59.202 40.000 25.71 21.55 46.51 4.35
1252 2007 4.103357 ACGAATGTAGATACAGTTCGTGC 58.897 43.478 25.08 5.00 46.08 5.34
1253 2008 3.486108 CGAATGTAGATACAGTTCGTGCC 59.514 47.826 18.72 0.01 39.47 5.01
1295 2050 0.843343 TCTTCTTAGGCCCCGGGTTT 60.843 55.000 21.85 6.82 0.00 3.27
1351 2106 8.589701 TTGGTTTCTACTAGTGTCATCATAGA 57.410 34.615 5.39 0.00 0.00 1.98
1397 2152 8.790718 CATAACCCTGATTGATTTCCAGATAAG 58.209 37.037 0.00 0.00 0.00 1.73
1404 2159 7.751732 TGATTGATTTCCAGATAAGTCAAACG 58.248 34.615 0.00 0.00 38.21 3.60
1448 2203 4.159693 GTCCAAATCCTATTGGTTGGAACC 59.840 45.833 16.36 1.24 44.78 3.62
1690 2445 1.280746 CAACCTCAGTTGTGCAGCG 59.719 57.895 0.00 0.00 46.88 5.18
1699 2454 0.880278 GTTGTGCAGCGAGAGGACAA 60.880 55.000 5.44 5.44 43.53 3.18
1741 2497 6.525578 ACTGTAGAAAATCATCGTCCTACA 57.474 37.500 0.00 0.00 36.22 2.74
1969 2735 2.270986 CCACCTGCAGGAAGCCAAC 61.271 63.158 39.19 0.00 44.83 3.77
1986 2752 2.160417 CCAACGAGGAGTCAAAATCAGC 59.840 50.000 0.00 0.00 41.22 4.26
2017 2783 4.301628 CCTCTGCAATGAAAGGTTTGAAC 58.698 43.478 0.00 0.00 0.00 3.18
2207 3136 5.619981 GCAAATGGACAGAAATGTACTGACC 60.620 44.000 0.00 0.00 45.28 4.02
2209 3138 2.028476 TGGACAGAAATGTACTGACCGG 60.028 50.000 0.00 0.00 46.94 5.28
2210 3139 2.000447 GACAGAAATGTACTGACCGGC 59.000 52.381 0.00 0.00 38.55 6.13
2218 3147 1.903860 TGTACTGACCGGCATTAACCT 59.096 47.619 0.00 0.00 0.00 3.50
2254 3184 3.686726 GCACCTGAATTCACCTGACTAAG 59.313 47.826 3.38 0.00 0.00 2.18
2256 3186 5.174395 CACCTGAATTCACCTGACTAAGAG 58.826 45.833 3.38 0.00 0.00 2.85
2587 3524 6.470278 GGCGGACCTATACCAGTTTAATAAT 58.530 40.000 0.00 0.00 0.00 1.28
2612 3549 6.772716 TGAGCTAGTCCTCTTGTTTCAAAAAT 59.227 34.615 0.00 0.00 33.02 1.82
2616 3553 9.744468 GCTAGTCCTCTTGTTTCAAAAATAAAA 57.256 29.630 0.00 0.00 0.00 1.52
2670 3613 6.349363 GGCTGTCAGGGAAAAGTTTAATGTAG 60.349 42.308 1.14 0.00 0.00 2.74
2726 3671 4.943093 TGCTAGCTTTTGATGATTGCAGTA 59.057 37.500 17.23 0.00 0.00 2.74
2809 3754 1.298157 CCATCTTCTGCGCCGAAACA 61.298 55.000 15.27 5.62 0.00 2.83
2819 3764 0.941542 CGCCGAAACAAACAAGGAGA 59.058 50.000 0.00 0.00 0.00 3.71
2947 3892 6.624352 ATTCTTAATGCATTATGCTCGTGT 57.376 33.333 19.51 1.91 45.31 4.49
2988 3933 4.823790 AAATCGTCTTGCTACCGTTTTT 57.176 36.364 0.00 0.00 0.00 1.94
3057 4002 2.532250 TGAGGTGAGGATGCTAGTCA 57.468 50.000 0.00 0.00 0.00 3.41
3060 4005 4.745351 TGAGGTGAGGATGCTAGTCATAT 58.255 43.478 0.00 0.00 35.05 1.78
3093 4038 8.254178 TGTACATGGAAAATGAAAAATGCATC 57.746 30.769 0.00 0.00 0.00 3.91
3147 4092 6.821388 ACATGACTAGGTGATTGATAACCTC 58.179 40.000 3.18 0.00 43.52 3.85
3186 4131 2.418471 CGAGCAGATCTTTGAGAAGGCT 60.418 50.000 0.00 0.00 33.59 4.58
3283 4229 4.925646 TGTTGTCGAGTCTGATGATTCTTG 59.074 41.667 0.00 0.00 0.00 3.02
3404 4350 7.177392 AGCTTCTAGAATTGCAACAGGTAATTT 59.823 33.333 16.48 0.00 41.16 1.82
3413 4359 3.740832 GCAACAGGTAATTTTTGGCAGAC 59.259 43.478 0.00 0.00 0.00 3.51
3419 4365 0.319813 AATTTTTGGCAGACTGCGCC 60.320 50.000 20.82 9.09 46.21 6.53
3443 4389 4.015872 TCCGTTTAGCTCTTGGTCAAAT 57.984 40.909 0.00 0.00 0.00 2.32
3472 4419 7.573968 AAACTTCAGAGAGCTTTGTTGTAAT 57.426 32.000 0.00 0.00 0.00 1.89
3473 4420 7.573968 AACTTCAGAGAGCTTTGTTGTAATT 57.426 32.000 0.00 0.00 0.00 1.40
3506 4453 6.153067 TGTCAATGTTCTTTGTTTGTCGTTT 58.847 32.000 0.00 0.00 0.00 3.60
3507 4454 6.642950 TGTCAATGTTCTTTGTTTGTCGTTTT 59.357 30.769 0.00 0.00 0.00 2.43
3508 4455 7.169982 TGTCAATGTTCTTTGTTTGTCGTTTTT 59.830 29.630 0.00 0.00 0.00 1.94
3509 4456 7.474025 GTCAATGTTCTTTGTTTGTCGTTTTTG 59.526 33.333 0.00 0.00 0.00 2.44
3510 4457 7.169982 TCAATGTTCTTTGTTTGTCGTTTTTGT 59.830 29.630 0.00 0.00 0.00 2.83
3511 4458 6.830114 TGTTCTTTGTTTGTCGTTTTTGTT 57.170 29.167 0.00 0.00 0.00 2.83
3512 4459 7.235430 TGTTCTTTGTTTGTCGTTTTTGTTT 57.765 28.000 0.00 0.00 0.00 2.83
3513 4460 7.338462 TGTTCTTTGTTTGTCGTTTTTGTTTC 58.662 30.769 0.00 0.00 0.00 2.78
3514 4461 6.129923 TCTTTGTTTGTCGTTTTTGTTTCG 57.870 33.333 0.00 0.00 0.00 3.46
3515 4462 4.887763 TTGTTTGTCGTTTTTGTTTCGG 57.112 36.364 0.00 0.00 0.00 4.30
3516 4463 3.898529 TGTTTGTCGTTTTTGTTTCGGT 58.101 36.364 0.00 0.00 0.00 4.69
3517 4464 4.296690 TGTTTGTCGTTTTTGTTTCGGTT 58.703 34.783 0.00 0.00 0.00 4.44
3518 4465 4.743644 TGTTTGTCGTTTTTGTTTCGGTTT 59.256 33.333 0.00 0.00 0.00 3.27
3519 4466 5.107951 TGTTTGTCGTTTTTGTTTCGGTTTC 60.108 36.000 0.00 0.00 0.00 2.78
3520 4467 4.422546 TGTCGTTTTTGTTTCGGTTTCT 57.577 36.364 0.00 0.00 0.00 2.52
3521 4468 4.796369 TGTCGTTTTTGTTTCGGTTTCTT 58.204 34.783 0.00 0.00 0.00 2.52
3522 4469 4.852650 TGTCGTTTTTGTTTCGGTTTCTTC 59.147 37.500 0.00 0.00 0.00 2.87
3523 4470 4.029069 GTCGTTTTTGTTTCGGTTTCTTCG 60.029 41.667 0.00 0.00 0.00 3.79
3524 4471 4.090034 CGTTTTTGTTTCGGTTTCTTCGA 58.910 39.130 0.00 0.00 34.62 3.71
3525 4472 4.731480 CGTTTTTGTTTCGGTTTCTTCGAT 59.269 37.500 0.00 0.00 36.49 3.59
3526 4473 5.108891 CGTTTTTGTTTCGGTTTCTTCGATC 60.109 40.000 0.00 0.00 36.49 3.69
3527 4474 5.744666 TTTTGTTTCGGTTTCTTCGATCT 57.255 34.783 0.00 0.00 36.49 2.75
3528 4475 5.744666 TTTGTTTCGGTTTCTTCGATCTT 57.255 34.783 0.00 0.00 36.49 2.40
3529 4476 5.744666 TTGTTTCGGTTTCTTCGATCTTT 57.255 34.783 0.00 0.00 36.49 2.52
3530 4477 5.744666 TGTTTCGGTTTCTTCGATCTTTT 57.255 34.783 0.00 0.00 36.49 2.27
3531 4478 6.126568 TGTTTCGGTTTCTTCGATCTTTTT 57.873 33.333 0.00 0.00 36.49 1.94
3573 4520 8.986991 AGTAATCAAGATATCAACTGAACCTCT 58.013 33.333 5.32 1.45 0.00 3.69
3577 4524 9.775854 ATCAAGATATCAACTGAACCTCTATTG 57.224 33.333 5.32 0.00 0.00 1.90
3578 4525 8.762645 TCAAGATATCAACTGAACCTCTATTGT 58.237 33.333 5.32 0.00 0.00 2.71
3579 4526 9.388506 CAAGATATCAACTGAACCTCTATTGTT 57.611 33.333 5.32 0.00 0.00 2.83
3580 4527 9.965902 AAGATATCAACTGAACCTCTATTGTTT 57.034 29.630 5.32 0.00 0.00 2.83
3581 4528 9.965902 AGATATCAACTGAACCTCTATTGTTTT 57.034 29.630 5.32 0.00 0.00 2.43
3583 4530 9.739276 ATATCAACTGAACCTCTATTGTTTTCA 57.261 29.630 0.00 0.00 0.00 2.69
3584 4531 7.259290 TCAACTGAACCTCTATTGTTTTCAC 57.741 36.000 0.00 0.00 0.00 3.18
3585 4532 6.826231 TCAACTGAACCTCTATTGTTTTCACA 59.174 34.615 0.00 0.00 0.00 3.58
3586 4533 7.502226 TCAACTGAACCTCTATTGTTTTCACAT 59.498 33.333 0.00 0.00 31.06 3.21
3587 4534 8.783093 CAACTGAACCTCTATTGTTTTCACATA 58.217 33.333 0.00 0.00 31.06 2.29
3588 4535 9.520515 AACTGAACCTCTATTGTTTTCACATAT 57.479 29.630 0.00 0.00 31.06 1.78
3589 4536 9.520515 ACTGAACCTCTATTGTTTTCACATATT 57.479 29.630 0.00 0.00 31.06 1.28
3590 4537 9.994432 CTGAACCTCTATTGTTTTCACATATTC 57.006 33.333 0.00 0.00 31.06 1.75
3591 4538 9.739276 TGAACCTCTATTGTTTTCACATATTCT 57.261 29.630 0.00 0.00 31.06 2.40
3594 4541 8.960591 ACCTCTATTGTTTTCACATATTCTTGG 58.039 33.333 0.00 0.00 31.06 3.61
3595 4542 8.960591 CCTCTATTGTTTTCACATATTCTTGGT 58.039 33.333 0.00 0.00 31.06 3.67
3596 4543 9.994432 CTCTATTGTTTTCACATATTCTTGGTC 57.006 33.333 0.00 0.00 31.06 4.02
3597 4544 9.513906 TCTATTGTTTTCACATATTCTTGGTCA 57.486 29.630 0.00 0.00 31.06 4.02
3601 4548 8.862325 TGTTTTCACATATTCTTGGTCATACT 57.138 30.769 0.00 0.00 0.00 2.12
3602 4549 9.295825 TGTTTTCACATATTCTTGGTCATACTT 57.704 29.630 0.00 0.00 0.00 2.24
3606 4553 8.958119 TCACATATTCTTGGTCATACTTTACC 57.042 34.615 0.00 0.00 36.24 2.85
3607 4554 8.544622 TCACATATTCTTGGTCATACTTTACCA 58.455 33.333 0.00 0.00 43.99 3.25
3618 4565 9.747898 TGGTCATACTTTACCAATGTTCTTTAT 57.252 29.630 0.00 0.00 42.74 1.40
3620 4567 9.916397 GTCATACTTTACCAATGTTCTTTATCG 57.084 33.333 0.00 0.00 0.00 2.92
3621 4568 9.104965 TCATACTTTACCAATGTTCTTTATCGG 57.895 33.333 0.00 0.00 0.00 4.18
3622 4569 8.889717 CATACTTTACCAATGTTCTTTATCGGT 58.110 33.333 0.00 0.00 0.00 4.69
3623 4570 7.754851 ACTTTACCAATGTTCTTTATCGGTT 57.245 32.000 0.00 0.00 0.00 4.44
3624 4571 8.173542 ACTTTACCAATGTTCTTTATCGGTTT 57.826 30.769 0.00 0.00 0.00 3.27
3625 4572 8.294577 ACTTTACCAATGTTCTTTATCGGTTTC 58.705 33.333 0.00 0.00 0.00 2.78
3626 4573 7.989416 TTACCAATGTTCTTTATCGGTTTCT 57.011 32.000 0.00 0.00 0.00 2.52
3627 4574 6.894339 ACCAATGTTCTTTATCGGTTTCTT 57.106 33.333 0.00 0.00 0.00 2.52
3628 4575 6.909909 ACCAATGTTCTTTATCGGTTTCTTC 58.090 36.000 0.00 0.00 0.00 2.87
3629 4576 6.021596 CCAATGTTCTTTATCGGTTTCTTCG 58.978 40.000 0.00 0.00 0.00 3.79
3630 4577 6.128391 CCAATGTTCTTTATCGGTTTCTTCGA 60.128 38.462 0.00 0.00 41.04 3.71
3631 4578 7.295201 CAATGTTCTTTATCGGTTTCTTCGAA 58.705 34.615 0.00 0.00 40.15 3.71
3632 4579 6.847956 TGTTCTTTATCGGTTTCTTCGAAA 57.152 33.333 0.00 0.00 40.15 3.46
3633 4580 7.249186 TGTTCTTTATCGGTTTCTTCGAAAA 57.751 32.000 0.00 0.00 40.15 2.29
3634 4581 7.695820 TGTTCTTTATCGGTTTCTTCGAAAAA 58.304 30.769 0.00 0.54 40.15 1.94
3635 4582 7.853929 TGTTCTTTATCGGTTTCTTCGAAAAAG 59.146 33.333 0.00 3.23 40.15 2.27
3636 4583 7.718272 TCTTTATCGGTTTCTTCGAAAAAGA 57.282 32.000 10.33 10.33 40.15 2.52
3637 4584 8.145316 TCTTTATCGGTTTCTTCGAAAAAGAA 57.855 30.769 11.47 4.14 40.15 2.52
3638 4585 8.780249 TCTTTATCGGTTTCTTCGAAAAAGAAT 58.220 29.630 11.47 6.59 40.15 2.40
3639 4586 9.394477 CTTTATCGGTTTCTTCGAAAAAGAATT 57.606 29.630 0.00 0.00 40.15 2.17
3640 4587 9.738832 TTTATCGGTTTCTTCGAAAAAGAATTT 57.261 25.926 0.00 0.00 40.15 1.82
3723 4671 5.278463 CGTTGGTCCAAAATCAAGACTTCAT 60.278 40.000 5.69 0.00 0.00 2.57
4086 5038 2.477825 CTTCTCATCATCGCGGTGATT 58.522 47.619 31.40 14.67 36.72 2.57
4102 5054 4.492570 CGGTGATTATCGTGCTTTCAGTTC 60.493 45.833 0.00 0.00 0.00 3.01
4155 5109 3.038280 GTGGGACGCATGTTGCAA 58.962 55.556 0.00 0.00 45.36 4.08
4156 5110 1.586028 GTGGGACGCATGTTGCAAT 59.414 52.632 0.59 0.00 45.36 3.56
4157 5111 0.038343 GTGGGACGCATGTTGCAATT 60.038 50.000 0.59 0.00 45.36 2.32
4158 5112 0.678395 TGGGACGCATGTTGCAATTT 59.322 45.000 0.59 0.00 45.36 1.82
4159 5113 1.070038 GGGACGCATGTTGCAATTTG 58.930 50.000 0.59 4.75 45.36 2.32
4160 5114 0.439600 GGACGCATGTTGCAATTTGC 59.560 50.000 20.56 20.56 45.36 3.68
4231 5187 9.398538 CTTTCTGATGTACTCCTACTACTTAGT 57.601 37.037 0.00 0.00 40.24 2.24
4293 5261 3.625764 GTGATACGTATGGTTTGGCATGT 59.374 43.478 13.97 0.00 0.00 3.21
4298 5266 2.227626 CGTATGGTTTGGCATGTGACAA 59.772 45.455 0.00 0.00 42.18 3.18
4387 5357 7.044181 TGATTACAAACAAATCTTGCCACAAA 58.956 30.769 0.00 0.00 34.95 2.83
4413 5383 7.308450 TGGAGACTCTTATATTGATGGAAGG 57.692 40.000 1.74 0.00 0.00 3.46
4414 5384 6.169800 GGAGACTCTTATATTGATGGAAGGC 58.830 44.000 1.74 0.00 0.00 4.35
4416 5386 7.385894 AGACTCTTATATTGATGGAAGGCTT 57.614 36.000 0.00 0.00 0.00 4.35
4417 5387 7.222872 AGACTCTTATATTGATGGAAGGCTTG 58.777 38.462 3.46 0.00 0.00 4.01
4438 5416 6.524586 GCTTGTTTGAGTTGACATACATAAGC 59.475 38.462 0.00 0.00 32.89 3.09
4591 5569 5.485708 AGAGGCTCCTTACACTTATTCAGTT 59.514 40.000 11.71 0.00 30.92 3.16
4687 5665 0.036858 AAAGAACTCCTGCGAGAGGC 60.037 55.000 7.62 0.09 42.47 4.70
4715 5693 0.322456 AGTGGGCATTGCGAGCTAAA 60.322 50.000 1.91 0.00 0.00 1.85
4736 5714 1.673920 GTTCGCAAAGTTGTCCAAGGA 59.326 47.619 0.00 0.00 0.00 3.36
4741 5719 2.561569 CAAAGTTGTCCAAGGAGACGT 58.438 47.619 0.00 0.00 39.77 4.34
4761 5739 7.576236 AGACGTTAACACTCAATTCTTTCATG 58.424 34.615 6.39 0.00 0.00 3.07
4774 5752 3.608796 TCTTTCATGTGATCGCCAATGA 58.391 40.909 3.31 4.56 0.00 2.57
4831 5809 4.575885 CAAGACAAGGGGACGATTTTAGA 58.424 43.478 0.00 0.00 0.00 2.10
4883 5861 2.638480 ACTACAAGCAGCTGTTTGGA 57.362 45.000 36.37 31.03 40.00 3.53
4989 5967 0.885196 CGCCCCATTTTCGGAGAAAA 59.115 50.000 9.90 9.90 45.90 2.29
4994 5972 4.083565 CCCCATTTTCGGAGAAAAAGGTA 58.916 43.478 20.76 0.00 45.90 3.08
5001 5979 8.699749 CATTTTCGGAGAAAAAGGTATTTGAAC 58.300 33.333 11.28 0.00 45.90 3.18
5021 5999 7.672983 TGAACCTATTTCACAGATGAAGAAC 57.327 36.000 0.00 0.00 45.54 3.01
5173 6178 5.869579 AGAAAACAGAGGCTGTGAGAATTA 58.130 37.500 19.57 0.00 44.62 1.40
5192 6197 1.195115 AAGCAGTTCAGGCCGATCTA 58.805 50.000 0.00 0.00 0.00 1.98
5293 6299 1.608590 CGTCCCAAACTGCTTTCATGT 59.391 47.619 0.00 0.00 0.00 3.21
5304 6310 5.068636 ACTGCTTTCATGTCAGACAGAAAT 58.931 37.500 19.78 9.34 30.70 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.502142 TGCCTCTCATGAAAGCACAT 57.498 45.000 9.29 0.00 29.85 3.21
13 14 2.275134 TTGCCTCTCATGAAAGCACA 57.725 45.000 12.17 0.48 33.17 4.57
14 15 3.863142 ATTTGCCTCTCATGAAAGCAC 57.137 42.857 12.17 0.00 33.17 4.40
15 16 4.562082 CAAATTTGCCTCTCATGAAAGCA 58.438 39.130 5.01 9.29 32.04 3.91
30 31 5.640218 TTTCTCTCGCAAAAGCAAATTTG 57.360 34.783 14.03 14.03 42.01 2.32
31 32 6.534793 TCTTTTTCTCTCGCAAAAGCAAATTT 59.465 30.769 0.00 0.00 39.08 1.82
32 33 6.042143 TCTTTTTCTCTCGCAAAAGCAAATT 58.958 32.000 0.00 0.00 39.08 1.82
33 34 5.591099 TCTTTTTCTCTCGCAAAAGCAAAT 58.409 33.333 0.00 0.00 39.08 2.32
34 35 4.992688 TCTTTTTCTCTCGCAAAAGCAAA 58.007 34.783 0.00 0.00 39.08 3.68
35 36 4.630894 TCTTTTTCTCTCGCAAAAGCAA 57.369 36.364 0.00 0.00 39.08 3.91
36 37 4.630894 TTCTTTTTCTCTCGCAAAAGCA 57.369 36.364 0.00 0.00 39.08 3.91
37 38 4.978580 ACATTCTTTTTCTCTCGCAAAAGC 59.021 37.500 0.00 0.00 39.08 3.51
38 39 8.733857 AATACATTCTTTTTCTCTCGCAAAAG 57.266 30.769 0.00 0.00 40.12 2.27
39 40 9.180678 GAAATACATTCTTTTTCTCTCGCAAAA 57.819 29.630 0.00 0.00 35.04 2.44
40 41 7.807907 GGAAATACATTCTTTTTCTCTCGCAAA 59.192 33.333 0.00 0.00 38.18 3.68
41 42 7.040755 TGGAAATACATTCTTTTTCTCTCGCAA 60.041 33.333 0.00 0.00 38.18 4.85
42 43 6.429692 TGGAAATACATTCTTTTTCTCTCGCA 59.570 34.615 0.00 0.00 38.18 5.10
43 44 6.842163 TGGAAATACATTCTTTTTCTCTCGC 58.158 36.000 0.00 0.00 38.18 5.03
44 45 8.668353 TCATGGAAATACATTCTTTTTCTCTCG 58.332 33.333 0.00 0.00 38.18 4.04
46 47 9.745018 TCTCATGGAAATACATTCTTTTTCTCT 57.255 29.630 0.00 0.00 38.18 3.10
79 80 3.188460 TGTGCCTTTACGAGAAGCAAATC 59.812 43.478 0.00 0.00 0.00 2.17
93 94 8.181904 TCTCTTGAAAGAAAATATGTGCCTTT 57.818 30.769 0.00 0.00 34.03 3.11
94 95 7.765695 TCTCTTGAAAGAAAATATGTGCCTT 57.234 32.000 0.00 0.00 34.03 4.35
177 178 2.814919 CACCTGTGTCTCTACGAGAAGT 59.185 50.000 0.00 0.00 40.59 3.01
200 201 4.500477 CACAACTGTACTTTTTGCAGAAGC 59.500 41.667 10.74 0.00 40.27 3.86
208 209 6.509418 TCAAGAAGCACAACTGTACTTTTT 57.491 33.333 0.00 0.00 32.16 1.94
218 219 6.737750 CACATTTGTTTTTCAAGAAGCACAAC 59.262 34.615 7.84 1.20 37.35 3.32
224 225 7.741198 TGAAAGCACATTTGTTTTTCAAGAAG 58.259 30.769 13.55 0.00 36.39 2.85
229 230 8.092521 TCTTTTGAAAGCACATTTGTTTTTCA 57.907 26.923 12.56 12.56 36.39 2.69
236 237 5.721876 TGCTTCTTTTGAAAGCACATTTG 57.278 34.783 6.45 0.00 37.52 2.32
273 275 3.887716 GCAGAAATGAATATGTGCCTCCT 59.112 43.478 0.00 0.00 0.00 3.69
305 307 9.097257 CAATTTTTCATTCTAACAAACACAGGT 57.903 29.630 0.00 0.00 0.00 4.00
306 308 9.097257 ACAATTTTTCATTCTAACAAACACAGG 57.903 29.630 0.00 0.00 0.00 4.00
337 339 3.135414 GCAAATATGTGCTTCTTGCGA 57.865 42.857 10.84 0.00 46.63 5.10
414 416 5.865085 AGAACCATAACTGTGCTTCTTGTA 58.135 37.500 0.00 0.00 0.00 2.41
559 572 9.672086 CGTTAGAATTTTGAACTATTTTCACCA 57.328 29.630 0.00 0.00 0.00 4.17
561 574 9.176181 TGCGTTAGAATTTTGAACTATTTTCAC 57.824 29.630 0.00 0.00 0.00 3.18
575 588 7.202016 TCTCTTCAATTGTGCGTTAGAATTT 57.798 32.000 5.13 0.00 30.52 1.82
578 591 7.899178 TTATCTCTTCAATTGTGCGTTAGAA 57.101 32.000 5.13 0.00 0.00 2.10
639 652 7.362662 AGTTATCGTCACTTGTCGTAACTAAA 58.637 34.615 15.03 0.00 34.98 1.85
694 766 1.403914 CCACCGCATAATGCAGCAAAA 60.404 47.619 0.00 0.00 45.36 2.44
721 793 1.246649 TACTCCCACGTTAACGCTCA 58.753 50.000 27.07 8.45 44.43 4.26
731 803 2.090524 GTCGCGGTTTACTCCCACG 61.091 63.158 6.13 0.00 0.00 4.94
806 1544 9.230932 GACTGTTTTTCTTTTCTTTCTGAGATG 57.769 33.333 0.00 0.00 33.49 2.90
807 1545 8.960591 TGACTGTTTTTCTTTTCTTTCTGAGAT 58.039 29.630 0.00 0.00 33.49 2.75
810 1548 7.312899 GGTGACTGTTTTTCTTTTCTTTCTGA 58.687 34.615 0.00 0.00 0.00 3.27
811 1549 6.251376 CGGTGACTGTTTTTCTTTTCTTTCTG 59.749 38.462 0.00 0.00 0.00 3.02
812 1550 6.072119 ACGGTGACTGTTTTTCTTTTCTTTCT 60.072 34.615 0.00 0.00 0.00 2.52
813 1551 6.033513 CACGGTGACTGTTTTTCTTTTCTTTC 59.966 38.462 0.74 0.00 0.00 2.62
814 1552 5.861787 CACGGTGACTGTTTTTCTTTTCTTT 59.138 36.000 0.74 0.00 0.00 2.52
815 1553 5.399013 CACGGTGACTGTTTTTCTTTTCTT 58.601 37.500 0.74 0.00 0.00 2.52
816 1554 4.142469 CCACGGTGACTGTTTTTCTTTTCT 60.142 41.667 10.28 0.00 0.00 2.52
817 1555 4.102649 CCACGGTGACTGTTTTTCTTTTC 58.897 43.478 10.28 0.00 0.00 2.29
878 1616 3.081409 GCTTGCCGTCTAGGGGGA 61.081 66.667 4.39 0.00 41.48 4.81
982 1720 0.832135 AGATCGTCCTGGTGTGGTGT 60.832 55.000 0.00 0.00 0.00 4.16
983 1721 0.321671 AAGATCGTCCTGGTGTGGTG 59.678 55.000 0.00 0.00 0.00 4.17
984 1722 1.002087 GAAAGATCGTCCTGGTGTGGT 59.998 52.381 0.00 0.00 0.00 4.16
985 1723 1.676014 GGAAAGATCGTCCTGGTGTGG 60.676 57.143 10.38 0.00 31.94 4.17
986 1724 1.001974 TGGAAAGATCGTCCTGGTGTG 59.998 52.381 16.62 0.00 36.03 3.82
1003 1741 0.391597 GAGGTGACGGTGACTTTGGA 59.608 55.000 0.00 0.00 0.00 3.53
1015 1753 6.111382 TGAGATGAAGAAATGATGAGGTGAC 58.889 40.000 0.00 0.00 0.00 3.67
1021 1759 7.803131 AGGAAGATGAGATGAAGAAATGATGA 58.197 34.615 0.00 0.00 0.00 2.92
1066 1815 2.368439 CTGTGTGGAGAGAGAGAGAGG 58.632 57.143 0.00 0.00 0.00 3.69
1079 1828 1.171308 CATCTTGGCTTCCTGTGTGG 58.829 55.000 0.00 0.00 37.10 4.17
1104 1859 6.961576 TGTAAAGAACATTACCGTCAAAAGG 58.038 36.000 0.00 0.00 35.38 3.11
1140 1895 2.736719 CGCGTCATCTTGGACAGAGATT 60.737 50.000 0.00 0.00 37.66 2.40
1158 1913 1.197036 GGAAGAAGAAAAGGAACCGCG 59.803 52.381 0.00 0.00 0.00 6.46
1168 1923 5.938125 AGCGCAAGTAATAAGGAAGAAGAAA 59.062 36.000 11.47 0.00 41.68 2.52
1169 1924 5.351465 CAGCGCAAGTAATAAGGAAGAAGAA 59.649 40.000 11.47 0.00 41.68 2.52
1170 1925 4.870426 CAGCGCAAGTAATAAGGAAGAAGA 59.130 41.667 11.47 0.00 41.68 2.87
1171 1926 4.494855 GCAGCGCAAGTAATAAGGAAGAAG 60.495 45.833 11.47 0.00 41.68 2.85
1175 1930 2.985896 AGCAGCGCAAGTAATAAGGAA 58.014 42.857 11.47 0.00 41.68 3.36
1295 2050 4.968259 TCTTTGTTCGAAAAGGAGGATGA 58.032 39.130 0.00 0.00 37.67 2.92
1351 2106 7.307989 GGTTATGCAGCACGTCTAATTATTGAT 60.308 37.037 0.00 0.00 0.00 2.57
1366 2121 2.804986 TCAATCAGGGTTATGCAGCA 57.195 45.000 0.00 0.00 0.00 4.41
1397 2152 5.086888 ACCGATTACTTTTCACGTTTGAC 57.913 39.130 0.00 0.00 0.00 3.18
1404 2159 5.005107 GGACGTATGACCGATTACTTTTCAC 59.995 44.000 0.00 0.00 0.00 3.18
1448 2203 4.321230 GCAAGTTCCACCCATTTACTGAAG 60.321 45.833 0.00 0.00 0.00 3.02
1626 2381 4.584743 TGATGCTCATGGACTAGATAACGT 59.415 41.667 0.00 0.00 0.00 3.99
1627 2382 5.126396 TGATGCTCATGGACTAGATAACG 57.874 43.478 0.00 0.00 0.00 3.18
1657 2412 5.126061 ACTGAGGTTGCCATCAAAATACATC 59.874 40.000 0.00 0.00 33.37 3.06
1690 2445 4.757149 AGCACTTACACAAATTGTCCTCTC 59.243 41.667 0.00 0.00 39.91 3.20
1699 2454 9.938280 TCTACAGTTAATAGCACTTACACAAAT 57.062 29.630 0.00 0.00 0.00 2.32
1881 2644 5.815581 AGGTGATGGCAAGATGTAACTAAA 58.184 37.500 0.00 0.00 0.00 1.85
1885 2648 5.186198 ACTAAGGTGATGGCAAGATGTAAC 58.814 41.667 0.00 0.00 0.00 2.50
1892 2655 3.902881 AGAGACTAAGGTGATGGCAAG 57.097 47.619 0.00 0.00 0.00 4.01
1969 2735 1.734465 GTGGCTGATTTTGACTCCTCG 59.266 52.381 0.00 0.00 0.00 4.63
1986 2752 1.065199 TCATTGCAGAGGCCTTAGTGG 60.065 52.381 6.77 0.00 40.13 4.00
2045 2972 6.032094 CACATTACCACTCAGAAATGCAATC 58.968 40.000 0.00 0.00 33.57 2.67
2207 3136 4.201822 GCTGAACTAGAAAGGTTAATGCCG 60.202 45.833 0.00 0.00 0.00 5.69
2209 3138 5.674820 GCTGCTGAACTAGAAAGGTTAATGC 60.675 44.000 0.00 0.00 0.00 3.56
2210 3139 5.412594 TGCTGCTGAACTAGAAAGGTTAATG 59.587 40.000 0.00 0.00 0.00 1.90
2218 3147 2.368548 TCAGGTGCTGCTGAACTAGAAA 59.631 45.455 0.00 0.00 0.00 2.52
2254 3184 4.214332 GGTGAGTGAAACCTGAACATTCTC 59.786 45.833 0.00 0.00 37.80 2.87
2256 3186 4.137543 AGGTGAGTGAAACCTGAACATTC 58.862 43.478 0.00 0.00 46.51 2.67
2484 3421 5.016831 GGTCATTGGAGGGTCAGTATTTTT 58.983 41.667 0.00 0.00 0.00 1.94
2587 3524 4.955811 TTGAAACAAGAGGACTAGCTCA 57.044 40.909 0.00 0.00 0.00 4.26
2645 3588 4.280929 ACATTAAACTTTTCCCTGACAGCC 59.719 41.667 0.00 0.00 0.00 4.85
2670 3613 4.667922 CGTTTTTGTTGGTGGAAAAAGCAC 60.668 41.667 0.00 0.00 32.98 4.40
2726 3671 5.552870 TCTTTAAGCCTCTTCTTCAGTGT 57.447 39.130 0.00 0.00 0.00 3.55
2988 3933 6.570764 GCGGTTCCAACATTTAGGTTTATCAA 60.571 38.462 0.00 0.00 0.00 2.57
3093 4038 6.962686 TGACACATTGAATTCAGAAAGACAG 58.037 36.000 8.41 0.00 0.00 3.51
3147 4092 1.699656 CGCTGCTTCCGGTCTCAATG 61.700 60.000 0.00 0.00 0.00 2.82
3177 4122 4.443457 CCGATTCCTTGAATAGCCTTCTCA 60.443 45.833 0.00 0.00 31.89 3.27
3186 4131 1.070134 CCTCGGCCGATTCCTTGAATA 59.930 52.381 31.19 0.52 31.89 1.75
3252 4198 3.824443 TCAGACTCGACAACATGAGGTTA 59.176 43.478 0.00 0.00 37.72 2.85
3307 4253 1.021202 TGGCCATAATCTTTTCGCCG 58.979 50.000 0.00 0.00 39.30 6.46
3413 4359 1.134694 GCTAAACGGAAAGGCGCAG 59.865 57.895 10.83 0.00 0.00 5.18
3419 4365 3.399330 TGACCAAGAGCTAAACGGAAAG 58.601 45.455 0.00 0.00 0.00 2.62
3443 4389 7.283127 ACAACAAAGCTCTCTGAAGTTTTGATA 59.717 33.333 22.50 0.00 45.13 2.15
3472 4419 9.921637 AACAAAGAACATTGACAAACTCTAAAA 57.078 25.926 0.00 0.00 34.38 1.52
3473 4420 9.921637 AAACAAAGAACATTGACAAACTCTAAA 57.078 25.926 0.00 0.00 34.38 1.85
3488 4435 6.830114 AACAAAAACGACAAACAAAGAACA 57.170 29.167 0.00 0.00 0.00 3.18
3489 4436 6.510307 CGAAACAAAAACGACAAACAAAGAAC 59.490 34.615 0.00 0.00 0.00 3.01
3490 4437 6.345882 CCGAAACAAAAACGACAAACAAAGAA 60.346 34.615 0.00 0.00 0.00 2.52
3491 4438 5.117287 CCGAAACAAAAACGACAAACAAAGA 59.883 36.000 0.00 0.00 0.00 2.52
3492 4439 5.107798 ACCGAAACAAAAACGACAAACAAAG 60.108 36.000 0.00 0.00 0.00 2.77
3493 4440 4.743644 ACCGAAACAAAAACGACAAACAAA 59.256 33.333 0.00 0.00 0.00 2.83
3494 4441 4.296690 ACCGAAACAAAAACGACAAACAA 58.703 34.783 0.00 0.00 0.00 2.83
3506 4453 5.744666 AAGATCGAAGAAACCGAAACAAA 57.255 34.783 0.00 0.00 43.58 2.83
3507 4454 5.744666 AAAGATCGAAGAAACCGAAACAA 57.255 34.783 0.00 0.00 43.58 2.83
3508 4455 5.744666 AAAAGATCGAAGAAACCGAAACA 57.255 34.783 0.00 0.00 43.58 2.83
3547 4494 8.986991 AGAGGTTCAGTTGATATCTTGATTACT 58.013 33.333 3.98 4.67 0.00 2.24
3551 4498 9.775854 CAATAGAGGTTCAGTTGATATCTTGAT 57.224 33.333 3.98 0.00 0.00 2.57
3552 4499 8.762645 ACAATAGAGGTTCAGTTGATATCTTGA 58.237 33.333 3.98 3.02 0.00 3.02
3553 4500 8.954950 ACAATAGAGGTTCAGTTGATATCTTG 57.045 34.615 3.98 0.66 0.00 3.02
3554 4501 9.965902 AAACAATAGAGGTTCAGTTGATATCTT 57.034 29.630 3.98 0.00 0.00 2.40
3555 4502 9.965902 AAAACAATAGAGGTTCAGTTGATATCT 57.034 29.630 3.98 0.00 0.00 1.98
3557 4504 9.739276 TGAAAACAATAGAGGTTCAGTTGATAT 57.261 29.630 0.00 0.00 0.00 1.63
3558 4505 8.999431 GTGAAAACAATAGAGGTTCAGTTGATA 58.001 33.333 0.00 0.00 0.00 2.15
3559 4506 7.502226 TGTGAAAACAATAGAGGTTCAGTTGAT 59.498 33.333 0.00 0.00 0.00 2.57
3560 4507 6.826231 TGTGAAAACAATAGAGGTTCAGTTGA 59.174 34.615 0.00 0.00 0.00 3.18
3561 4508 7.026631 TGTGAAAACAATAGAGGTTCAGTTG 57.973 36.000 0.00 0.00 0.00 3.16
3562 4509 7.823745 ATGTGAAAACAATAGAGGTTCAGTT 57.176 32.000 0.00 0.00 0.00 3.16
3563 4510 9.520515 AATATGTGAAAACAATAGAGGTTCAGT 57.479 29.630 0.00 0.00 0.00 3.41
3564 4511 9.994432 GAATATGTGAAAACAATAGAGGTTCAG 57.006 33.333 0.00 0.00 0.00 3.02
3565 4512 9.739276 AGAATATGTGAAAACAATAGAGGTTCA 57.261 29.630 0.00 0.00 0.00 3.18
3568 4515 8.960591 CCAAGAATATGTGAAAACAATAGAGGT 58.039 33.333 0.00 0.00 0.00 3.85
3569 4516 8.960591 ACCAAGAATATGTGAAAACAATAGAGG 58.039 33.333 0.00 0.00 0.00 3.69
3570 4517 9.994432 GACCAAGAATATGTGAAAACAATAGAG 57.006 33.333 0.00 0.00 0.00 2.43
3571 4518 9.513906 TGACCAAGAATATGTGAAAACAATAGA 57.486 29.630 0.00 0.00 0.00 1.98
3575 4522 9.295825 AGTATGACCAAGAATATGTGAAAACAA 57.704 29.630 0.00 0.00 0.00 2.83
3576 4523 8.862325 AGTATGACCAAGAATATGTGAAAACA 57.138 30.769 0.00 0.00 0.00 2.83
3580 4527 9.391006 GGTAAAGTATGACCAAGAATATGTGAA 57.609 33.333 0.00 0.00 35.65 3.18
3581 4528 8.544622 TGGTAAAGTATGACCAAGAATATGTGA 58.455 33.333 0.00 0.00 42.81 3.58
3582 4529 8.731275 TGGTAAAGTATGACCAAGAATATGTG 57.269 34.615 0.00 0.00 42.81 3.21
3592 4539 9.747898 ATAAAGAACATTGGTAAAGTATGACCA 57.252 29.630 0.00 0.00 44.08 4.02
3594 4541 9.916397 CGATAAAGAACATTGGTAAAGTATGAC 57.084 33.333 0.00 0.00 0.00 3.06
3595 4542 9.104965 CCGATAAAGAACATTGGTAAAGTATGA 57.895 33.333 0.00 0.00 0.00 2.15
3596 4543 8.889717 ACCGATAAAGAACATTGGTAAAGTATG 58.110 33.333 0.00 0.00 38.23 2.39
3597 4544 9.457436 AACCGATAAAGAACATTGGTAAAGTAT 57.543 29.630 0.00 0.00 38.94 2.12
3598 4545 8.851541 AACCGATAAAGAACATTGGTAAAGTA 57.148 30.769 0.00 0.00 38.94 2.24
3599 4546 7.754851 AACCGATAAAGAACATTGGTAAAGT 57.245 32.000 0.00 0.00 38.94 2.66
3600 4547 8.512138 AGAAACCGATAAAGAACATTGGTAAAG 58.488 33.333 0.00 0.00 38.94 1.85
3601 4548 8.398878 AGAAACCGATAAAGAACATTGGTAAA 57.601 30.769 0.00 0.00 38.94 2.01
3602 4549 7.989416 AGAAACCGATAAAGAACATTGGTAA 57.011 32.000 0.00 0.00 38.94 2.85
3603 4550 7.148540 CGAAGAAACCGATAAAGAACATTGGTA 60.149 37.037 0.00 0.00 38.94 3.25
3604 4551 6.348213 CGAAGAAACCGATAAAGAACATTGGT 60.348 38.462 0.00 0.00 41.20 3.67
3605 4552 6.021596 CGAAGAAACCGATAAAGAACATTGG 58.978 40.000 0.00 0.00 33.67 3.16
3606 4553 6.827641 TCGAAGAAACCGATAAAGAACATTG 58.172 36.000 0.00 0.00 0.00 2.82
3607 4554 7.429636 TTCGAAGAAACCGATAAAGAACATT 57.570 32.000 0.00 0.00 45.90 2.71
3608 4555 7.429636 TTTCGAAGAAACCGATAAAGAACAT 57.570 32.000 0.00 0.00 45.90 2.71
3609 4556 6.847956 TTTCGAAGAAACCGATAAAGAACA 57.152 33.333 0.00 0.00 45.90 3.18
3613 4560 8.950403 ATTCTTTTTCGAAGAAACCGATAAAG 57.050 30.769 16.47 16.47 46.41 1.85
3614 4561 9.738832 AAATTCTTTTTCGAAGAAACCGATAAA 57.261 25.926 2.50 0.00 45.90 1.40
3615 4562 9.738832 AAAATTCTTTTTCGAAGAAACCGATAA 57.261 25.926 2.50 0.00 45.90 1.75
3616 4563 9.738832 AAAAATTCTTTTTCGAAGAAACCGATA 57.261 25.926 2.50 0.00 45.90 2.92
3617 4564 8.539674 CAAAAATTCTTTTTCGAAGAAACCGAT 58.460 29.630 2.50 0.00 45.90 4.18
3618 4565 7.542824 ACAAAAATTCTTTTTCGAAGAAACCGA 59.457 29.630 2.50 0.00 45.90 4.69
3619 4566 7.671827 ACAAAAATTCTTTTTCGAAGAAACCG 58.328 30.769 2.50 0.00 45.90 4.44
3620 4567 9.820229 AAACAAAAATTCTTTTTCGAAGAAACC 57.180 25.926 2.50 0.00 45.90 3.27
3622 4569 9.734269 CGAAACAAAAATTCTTTTTCGAAGAAA 57.266 25.926 14.30 4.40 45.90 2.52
3623 4570 8.376942 CCGAAACAAAAATTCTTTTTCGAAGAA 58.623 29.630 18.35 4.21 45.90 2.52
3624 4571 7.542824 ACCGAAACAAAAATTCTTTTTCGAAGA 59.457 29.630 18.35 0.00 40.65 2.87
3625 4572 7.671827 ACCGAAACAAAAATTCTTTTTCGAAG 58.328 30.769 18.35 10.02 40.65 3.79
3626 4573 7.583860 ACCGAAACAAAAATTCTTTTTCGAA 57.416 28.000 18.35 0.00 40.65 3.71
3627 4574 7.583860 AACCGAAACAAAAATTCTTTTTCGA 57.416 28.000 18.35 0.00 40.65 3.71
3628 4575 8.166066 AGAAACCGAAACAAAAATTCTTTTTCG 58.834 29.630 13.24 13.24 40.65 3.46
3629 4576 9.820229 AAGAAACCGAAACAAAAATTCTTTTTC 57.180 25.926 0.00 0.00 40.65 2.29
3630 4577 9.820229 GAAGAAACCGAAACAAAAATTCTTTTT 57.180 25.926 0.00 0.00 43.20 1.94
3631 4578 8.166066 CGAAGAAACCGAAACAAAAATTCTTTT 58.834 29.630 0.00 0.00 36.20 2.27
3632 4579 7.201487 CCGAAGAAACCGAAACAAAAATTCTTT 60.201 33.333 0.00 0.00 36.20 2.52
3633 4580 6.254804 CCGAAGAAACCGAAACAAAAATTCTT 59.745 34.615 0.00 0.00 38.09 2.52
3634 4581 5.746721 CCGAAGAAACCGAAACAAAAATTCT 59.253 36.000 0.00 0.00 0.00 2.40
3635 4582 5.517411 ACCGAAGAAACCGAAACAAAAATTC 59.483 36.000 0.00 0.00 0.00 2.17
3636 4583 5.412640 ACCGAAGAAACCGAAACAAAAATT 58.587 33.333 0.00 0.00 0.00 1.82
3637 4584 5.001237 ACCGAAGAAACCGAAACAAAAAT 57.999 34.783 0.00 0.00 0.00 1.82
3638 4585 4.156373 AGACCGAAGAAACCGAAACAAAAA 59.844 37.500 0.00 0.00 0.00 1.94
3639 4586 3.690628 AGACCGAAGAAACCGAAACAAAA 59.309 39.130 0.00 0.00 0.00 2.44
3640 4587 3.064271 CAGACCGAAGAAACCGAAACAAA 59.936 43.478 0.00 0.00 0.00 2.83
3688 4636 5.621197 TTTGGACCAACGATCTAACATTG 57.379 39.130 6.36 0.00 0.00 2.82
3723 4671 1.073125 TGAAATCGCTGGAGGTTTGGA 59.927 47.619 0.00 0.00 0.00 3.53
3923 4875 3.770263 GCAGCAAGCATGAACATCTAA 57.230 42.857 0.00 0.00 44.79 2.10
4355 5325 7.096065 GCAAGATTTGTTTGTAATCAGGACAAC 60.096 37.037 0.00 0.00 36.55 3.32
4387 5357 8.381636 CCTTCCATCAATATAAGAGTCTCCATT 58.618 37.037 0.00 0.00 0.00 3.16
4413 5383 6.524586 GCTTATGTATGTCAACTCAAACAAGC 59.475 38.462 0.00 0.00 0.00 4.01
4414 5384 6.738200 CGCTTATGTATGTCAACTCAAACAAG 59.262 38.462 0.00 0.00 0.00 3.16
4416 5386 5.699001 ACGCTTATGTATGTCAACTCAAACA 59.301 36.000 0.00 0.00 0.00 2.83
4417 5387 6.165659 ACGCTTATGTATGTCAACTCAAAC 57.834 37.500 0.00 0.00 0.00 2.93
4520 5498 3.344137 ATGCTTAGCCCACCCACGG 62.344 63.158 0.29 0.00 0.00 4.94
4591 5569 4.468510 TGGACTCGGCTTTTAAATCTAGGA 59.531 41.667 0.00 0.00 0.00 2.94
4687 5665 1.994779 GCAATGCCCACTTCAATTTCG 59.005 47.619 0.00 0.00 0.00 3.46
4689 5667 1.617850 TCGCAATGCCCACTTCAATTT 59.382 42.857 0.00 0.00 0.00 1.82
4715 5693 1.676006 CCTTGGACAACTTTGCGAACT 59.324 47.619 0.00 0.00 0.00 3.01
4736 5714 7.226720 ACATGAAAGAATTGAGTGTTAACGTCT 59.773 33.333 0.00 2.02 0.00 4.18
4741 5719 8.229811 CGATCACATGAAAGAATTGAGTGTTAA 58.770 33.333 0.00 0.00 0.00 2.01
4761 5739 0.804364 TGCTTGTCATTGGCGATCAC 59.196 50.000 0.00 0.00 0.00 3.06
4774 5752 6.705863 AGATTCTTTTCTTTCTGTGCTTGT 57.294 33.333 0.00 0.00 0.00 3.16
4806 5784 0.693049 ATCGTCCCCTTGTCTTGCTT 59.307 50.000 0.00 0.00 0.00 3.91
5097 6102 1.939934 TGAAACAACTGAAGCTGTCCG 59.060 47.619 0.00 0.00 0.00 4.79
5173 6178 1.195115 TAGATCGGCCTGAACTGCTT 58.805 50.000 14.50 0.00 31.37 3.91
5263 6269 3.723097 TTTGGGACGGCTGCACCAA 62.723 57.895 15.45 15.45 40.94 3.67
5293 6299 7.358263 ACTCCTTCTAGGATATTTCTGTCTGA 58.642 38.462 0.00 0.00 44.81 3.27
5304 6310 4.016479 AGGACCACAACTCCTTCTAGGATA 60.016 45.833 0.00 0.00 44.81 2.59


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

AutoCloner maintained by Alex Coulton.