Multiple sequence alignment - TraesCS1B01G235200

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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 TraesCS1B01G235200 chr1B 100.000 5146 0 0 1 5146 421416745 421421890 0.000000e+00 9503.0
1 TraesCS1B01G235200 chr1B 87.234 517 61 5 70 582 22648284 22647769 7.430000e-163 584.0
2 TraesCS1B01G235200 chr1B 87.115 520 57 9 70 584 31537416 31537930 9.600000e-162 580.0
3 TraesCS1B01G235200 chr1B 87.205 508 59 6 80 582 8779680 8779174 1.610000e-159 573.0
4 TraesCS1B01G235200 chr1B 86.486 518 63 6 71 584 31560516 31561030 3.480000e-156 562.0
5 TraesCS1B01G235200 chr1B 90.678 354 24 7 4197 4546 421426247 421426595 3.630000e-126 462.0
6 TraesCS1B01G235200 chr1B 89.888 356 25 9 4197 4546 421458060 421458410 1.020000e-121 448.0
7 TraesCS1B01G235200 chr1B 89.607 356 26 9 4197 4546 421498215 421498565 4.730000e-120 442.0
8 TraesCS1B01G235200 chr1B 91.304 184 16 0 4738 4921 421498640 421498823 8.550000e-63 252.0
9 TraesCS1B01G235200 chr1B 90.217 184 18 0 4738 4921 421458485 421458668 1.850000e-59 241.0
10 TraesCS1B01G235200 chr1B 86.854 213 18 4 4738 4944 421426669 421426877 4.010000e-56 230.0
11 TraesCS1B01G235200 chr1B 87.970 133 9 5 1 128 543884000 543884130 3.210000e-32 150.0
12 TraesCS1B01G235200 chr1B 94.318 88 5 0 1 88 421416839 421416926 8.990000e-28 135.0
13 TraesCS1B01G235200 chr1B 85.714 133 12 4 1 128 689826526 689826656 3.230000e-27 134.0
14 TraesCS1B01G235200 chr1B 93.243 74 5 0 1 74 486820420 486820493 5.450000e-20 110.0
15 TraesCS1B01G235200 chr1B 89.873 79 4 1 4619 4697 421458408 421458482 1.180000e-16 99.0
16 TraesCS1B01G235200 chr1B 88.608 79 5 1 4619 4697 421498563 421498637 5.490000e-15 93.5
17 TraesCS1B01G235200 chr1B 97.368 38 0 1 4694 4731 421458500 421458536 4.300000e-06 63.9
18 TraesCS1B01G235200 chr1B 97.368 38 0 1 4694 4731 421498655 421498691 4.300000e-06 63.9
19 TraesCS1B01G235200 chr1D 93.049 2604 131 23 2002 4574 311681922 311684506 0.000000e+00 3760.0
20 TraesCS1B01G235200 chr1D 93.130 1412 69 5 600 2004 311680460 311681850 0.000000e+00 2045.0
21 TraesCS1B01G235200 chr1D 94.653 505 26 1 4642 5146 311684533 311685036 0.000000e+00 782.0
22 TraesCS1B01G235200 chr1D 87.625 501 51 9 80 573 36527457 36526961 5.780000e-159 571.0
23 TraesCS1B01G235200 chr1D 93.182 88 5 1 1 88 463580004 463580090 1.500000e-25 128.0
24 TraesCS1B01G235200 chr1A 93.100 2000 101 22 2558 4546 391672909 391674882 0.000000e+00 2894.0
25 TraesCS1B01G235200 chr1A 91.075 1423 87 18 600 2004 391669662 391671062 0.000000e+00 1888.0
26 TraesCS1B01G235200 chr1A 91.966 585 30 5 2002 2577 391671134 391671710 0.000000e+00 804.0
27 TraesCS1B01G235200 chr1A 91.268 355 22 7 4197 4546 391679924 391680274 4.660000e-130 475.0
28 TraesCS1B01G235200 chr1A 91.268 355 22 7 4197 4546 391765027 391765377 4.660000e-130 475.0
29 TraesCS1B01G235200 chr1A 90.986 355 23 7 4197 4546 391795490 391795840 2.170000e-128 470.0
30 TraesCS1B01G235200 chr1A 88.372 344 35 4 4807 5146 391675161 391675503 4.800000e-110 409.0
31 TraesCS1B01G235200 chr1A 86.387 191 14 5 4619 4808 391674880 391675059 1.130000e-46 198.0
32 TraesCS1B01G235200 chr1A 91.139 79 3 1 4619 4697 391680272 391680346 2.530000e-18 104.0
33 TraesCS1B01G235200 chr1A 91.139 79 3 1 4619 4697 391765375 391765449 2.530000e-18 104.0
34 TraesCS1B01G235200 chr1A 89.873 79 4 1 4619 4697 391795838 391795912 1.180000e-16 99.0
35 TraesCS1B01G235200 chr1A 97.368 38 0 1 4694 4731 391704651 391704687 4.300000e-06 63.9
36 TraesCS1B01G235200 chr1A 97.368 38 0 1 4694 4731 391795930 391795966 4.300000e-06 63.9
37 TraesCS1B01G235200 chr1A 100.000 31 0 0 4701 4731 391680370 391680400 2.000000e-04 58.4
38 TraesCS1B01G235200 chr1A 100.000 31 0 0 4701 4731 391765473 391765503 2.000000e-04 58.4
39 TraesCS1B01G235200 chr3D 87.578 483 57 3 91 570 485205565 485206047 1.620000e-154 556.0
40 TraesCS1B01G235200 chr2D 87.421 477 58 1 93 567 637607600 637608076 9.740000e-152 547.0
41 TraesCS1B01G235200 chr2D 92.045 88 7 0 1 88 196225636 196225723 1.950000e-24 124.0
42 TraesCS1B01G235200 chr2D 94.595 74 3 1 4548 4620 468866619 468866546 4.210000e-21 113.0
43 TraesCS1B01G235200 chr2D 98.182 55 1 0 1049 1103 480459831 480459777 4.240000e-16 97.1
44 TraesCS1B01G235200 chr5D 86.939 490 58 5 91 575 517675456 517675944 3.500000e-151 545.0
45 TraesCS1B01G235200 chr5D 86.694 496 57 5 91 582 473442147 473442637 4.530000e-150 542.0
46 TraesCS1B01G235200 chr5D 94.595 74 2 2 4549 4621 520412904 520412832 4.210000e-21 113.0
47 TraesCS1B01G235200 chr5D 90.110 91 2 4 4548 4632 370941366 370941277 1.510000e-20 111.0
48 TraesCS1B01G235200 chrUn 90.986 355 23 7 4197 4546 422087639 422087289 2.170000e-128 470.0
49 TraesCS1B01G235200 chrUn 83.704 135 17 3 1 131 12271666 12271533 7.000000e-24 122.0
50 TraesCS1B01G235200 chrUn 90.000 60 2 1 4619 4678 422087291 422087236 1.990000e-09 75.0
51 TraesCS1B01G235200 chrUn 93.182 44 2 1 4694 4737 375644722 375644680 4.300000e-06 63.9
52 TraesCS1B01G235200 chr7D 98.611 72 1 0 4549 4620 13036151 13036222 1.500000e-25 128.0
53 TraesCS1B01G235200 chr7D 92.683 82 5 1 4548 4628 5307737 5307656 3.260000e-22 117.0
54 TraesCS1B01G235200 chr7D 95.833 72 1 2 4549 4620 252560779 252560710 1.170000e-21 115.0
55 TraesCS1B01G235200 chr7D 94.521 73 4 0 4548 4620 184573431 184573359 4.210000e-21 113.0
56 TraesCS1B01G235200 chr2A 90.909 88 8 0 1 88 559104354 559104267 9.050000e-23 119.0
57 TraesCS1B01G235200 chr7A 94.595 74 3 1 4549 4622 7805383 7805311 4.210000e-21 113.0
58 TraesCS1B01G235200 chr7A 89.773 88 5 4 4540 4625 424298694 424298779 5.450000e-20 110.0
59 TraesCS1B01G235200 chr6A 85.882 85 11 1 2 86 485389094 485389011 7.100000e-14 89.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G235200 chr1B 421416745 421421890 5145 False 9503.000000 9503 100.000000 1 5146 1 chr1B.!!$F3 5145
1 TraesCS1B01G235200 chr1B 22647769 22648284 515 True 584.000000 584 87.234000 70 582 1 chr1B.!!$R2 512
2 TraesCS1B01G235200 chr1B 31537416 31537930 514 False 580.000000 580 87.115000 70 584 1 chr1B.!!$F1 514
3 TraesCS1B01G235200 chr1B 8779174 8779680 506 True 573.000000 573 87.205000 80 582 1 chr1B.!!$R1 502
4 TraesCS1B01G235200 chr1B 31560516 31561030 514 False 562.000000 562 86.486000 71 584 1 chr1B.!!$F2 513
5 TraesCS1B01G235200 chr1B 421426247 421426877 630 False 346.000000 462 88.766000 4197 4944 2 chr1B.!!$F8 747
6 TraesCS1B01G235200 chr1B 421458060 421458668 608 False 212.975000 448 91.836500 4197 4921 4 chr1B.!!$F9 724
7 TraesCS1B01G235200 chr1B 421498215 421498823 608 False 212.850000 442 91.721750 4197 4921 4 chr1B.!!$F10 724
8 TraesCS1B01G235200 chr1D 311680460 311685036 4576 False 2195.666667 3760 93.610667 600 5146 3 chr1D.!!$F2 4546
9 TraesCS1B01G235200 chr1A 391669662 391675503 5841 False 1238.600000 2894 90.180000 600 5146 5 chr1A.!!$F2 4546

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
593 602 0.040351 TTTGGGATCCGGCCAATGAA 59.960 50.000 12.17 0.0 0.00 2.57 F
1215 1229 0.033601 TATTCGCCTGGGTTTGCCAT 60.034 50.000 0.00 0.0 36.17 4.40 F
1744 1770 1.342374 GGATGCCCATGGTTTCCTTCT 60.342 52.381 11.73 0.0 0.00 2.85 F
3512 4870 0.322816 AAGGTCCATCTGCATTGCGT 60.323 50.000 3.84 0.0 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1642 0.459237 GTGGAGAGAGACCATGTGCG 60.459 60.000 0.00 0.0 39.69 5.34 R
2275 2375 1.482593 CCGCCAATACTGGAAGAGACT 59.517 52.381 0.00 0.0 46.92 3.24 R
3585 4943 0.958091 AAACAACAAGCGGCTATGCA 59.042 45.000 1.35 0.0 37.31 3.96 R
4911 6381 0.249953 TAATGGTTGTGCGTCGGTGT 60.250 50.000 0.00 0.0 0.00 4.16 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
41 42 3.993234 CGCTGGCTTATCGCGCAG 61.993 66.667 8.75 2.51 40.42 5.18
62 63 4.814294 GCCGACCGAATCCGCTGT 62.814 66.667 0.00 0.00 0.00 4.40
63 64 2.582498 CCGACCGAATCCGCTGTC 60.582 66.667 0.00 0.00 0.00 3.51
64 65 2.582498 CGACCGAATCCGCTGTCC 60.582 66.667 0.00 0.00 0.00 4.02
65 66 2.202892 GACCGAATCCGCTGTCCC 60.203 66.667 0.00 0.00 0.00 4.46
66 67 2.683933 ACCGAATCCGCTGTCCCT 60.684 61.111 0.00 0.00 0.00 4.20
67 68 1.380785 ACCGAATCCGCTGTCCCTA 60.381 57.895 0.00 0.00 0.00 3.53
68 69 1.067582 CCGAATCCGCTGTCCCTAC 59.932 63.158 0.00 0.00 0.00 3.18
182 184 4.269523 AAGGAACAGCGCTGGCCA 62.270 61.111 36.82 4.71 41.24 5.36
230 232 4.796231 CGCGACTGCTTACCGGCT 62.796 66.667 0.00 0.00 39.65 5.52
356 360 2.066999 GTGCGAGAGGAAGGGGGAT 61.067 63.158 0.00 0.00 0.00 3.85
368 372 0.935194 AGGGGGATAGGACGAGAAGT 59.065 55.000 0.00 0.00 0.00 3.01
374 378 3.318557 GGGATAGGACGAGAAGTTTCGAT 59.681 47.826 12.36 0.00 43.03 3.59
463 470 4.888823 GGAACTAACCCAAACAAACACCTA 59.111 41.667 0.00 0.00 0.00 3.08
536 545 7.610580 AACCTTCCTGTTTGGATATTTTTGA 57.389 32.000 0.00 0.00 45.68 2.69
570 579 8.983307 AGTCTAAACTAATCCAAACTAACTCG 57.017 34.615 0.00 0.00 32.59 4.18
573 582 9.635520 TCTAAACTAATCCAAACTAACTCGAAG 57.364 33.333 0.00 0.00 0.00 3.79
575 584 8.672823 AAACTAATCCAAACTAACTCGAAGTT 57.327 30.769 0.00 0.00 41.97 2.66
576 585 8.672823 AACTAATCCAAACTAACTCGAAGTTT 57.327 30.769 7.71 7.71 45.64 2.66
583 592 4.203654 ACTAACTCGAAGTTTGGGATCC 57.796 45.455 1.92 1.92 39.51 3.36
584 593 2.094762 AACTCGAAGTTTGGGATCCG 57.905 50.000 5.45 0.00 34.11 4.18
585 594 0.249398 ACTCGAAGTTTGGGATCCGG 59.751 55.000 5.45 0.00 0.00 5.14
586 595 1.078708 TCGAAGTTTGGGATCCGGC 60.079 57.895 5.45 0.00 0.00 6.13
587 596 2.112815 CGAAGTTTGGGATCCGGCC 61.113 63.158 5.45 0.00 0.00 6.13
588 597 1.001393 GAAGTTTGGGATCCGGCCA 60.001 57.895 5.45 0.00 0.00 5.36
589 598 0.610785 GAAGTTTGGGATCCGGCCAA 60.611 55.000 5.45 7.84 0.00 4.52
590 599 0.041090 AAGTTTGGGATCCGGCCAAT 59.959 50.000 12.17 0.00 0.00 3.16
591 600 0.684153 AGTTTGGGATCCGGCCAATG 60.684 55.000 12.17 0.00 0.00 2.82
592 601 0.682855 GTTTGGGATCCGGCCAATGA 60.683 55.000 12.17 0.00 0.00 2.57
593 602 0.040351 TTTGGGATCCGGCCAATGAA 59.960 50.000 12.17 0.00 0.00 2.57
594 603 0.395586 TTGGGATCCGGCCAATGAAG 60.396 55.000 5.45 0.00 0.00 3.02
595 604 2.196245 GGGATCCGGCCAATGAAGC 61.196 63.158 5.45 0.00 0.00 3.86
596 605 1.152881 GGATCCGGCCAATGAAGCT 60.153 57.895 2.24 0.00 0.00 3.74
597 606 1.169034 GGATCCGGCCAATGAAGCTC 61.169 60.000 2.24 0.00 0.00 4.09
598 607 1.502163 GATCCGGCCAATGAAGCTCG 61.502 60.000 2.24 0.00 0.00 5.03
602 611 2.115291 GGCCAATGAAGCTCGGTCC 61.115 63.158 0.00 0.00 0.00 4.46
607 616 1.135972 CAATGAAGCTCGGTCCGTTTG 60.136 52.381 11.88 4.35 0.00 2.93
671 684 0.878961 AACCTGACGCCGTCAACTTC 60.879 55.000 21.56 0.00 42.26 3.01
730 743 2.941025 CCCACAGACCACCCCCAT 60.941 66.667 0.00 0.00 0.00 4.00
758 771 3.062504 CGAATCTCAACGCATCATTGACA 59.937 43.478 0.00 0.00 32.67 3.58
778 791 1.595093 GGCTTGCATACGCCCAAGTT 61.595 55.000 10.21 0.00 40.34 2.66
851 864 1.335597 CCTCGTCGTCACTGTAAAGCA 60.336 52.381 0.00 0.00 0.00 3.91
922 936 0.810031 CGATTCCGGCGATCCAAACT 60.810 55.000 9.30 0.00 0.00 2.66
979 993 4.462280 GTTCGGATTCGGGGCGGT 62.462 66.667 0.00 0.00 36.95 5.68
991 1005 2.185608 GGCGGTGAAGAGGAGAGC 59.814 66.667 0.00 0.00 0.00 4.09
1176 1190 0.601311 AGCCGCTAAATCGAGGATGC 60.601 55.000 0.00 0.00 0.00 3.91
1215 1229 0.033601 TATTCGCCTGGGTTTGCCAT 60.034 50.000 0.00 0.00 36.17 4.40
1253 1267 4.238514 CAGGAGGACGGATAATTTCGATC 58.761 47.826 0.00 0.00 0.00 3.69
1264 1278 5.911280 GGATAATTTCGATCTGTGCATTGTG 59.089 40.000 0.00 0.00 0.00 3.33
1286 1300 8.610248 TGTGTTAGATTAATTCGTTTCCTTGA 57.390 30.769 0.00 0.00 0.00 3.02
1324 1339 1.740025 CCATCTTTGTCTTTCGAGGGC 59.260 52.381 0.00 0.00 0.00 5.19
1330 1345 2.859165 TGTCTTTCGAGGGCTTTCAT 57.141 45.000 0.00 0.00 0.00 2.57
1336 1351 1.821332 CGAGGGCTTTCATCTGGGC 60.821 63.158 0.00 0.00 0.00 5.36
1413 1428 5.411669 GTGTTGAAGTTCCTCGGTAATTGAT 59.588 40.000 0.00 0.00 0.00 2.57
1516 1541 5.462398 GGTAGTCGATTTATGTTAGGCTGTG 59.538 44.000 0.00 0.00 0.00 3.66
1548 1573 6.088016 TGAATATGCATTCACCTATTTGGC 57.912 37.500 3.54 0.00 44.44 4.52
1599 1625 8.861086 CAGTACCAATGTAGACAGGATAGTATT 58.139 37.037 0.00 0.00 0.00 1.89
1606 1632 7.182817 TGTAGACAGGATAGTATTTGCAAGT 57.817 36.000 0.00 0.00 0.00 3.16
1616 1642 7.433425 GGATAGTATTTGCAAGTTCTTGAATGC 59.567 37.037 15.52 10.45 39.22 3.56
1623 1649 2.624316 AGTTCTTGAATGCGCACATG 57.376 45.000 14.90 10.01 36.36 3.21
1646 1672 7.792364 TGGTCTCTCTCCACTTTATCTTTTA 57.208 36.000 0.00 0.00 0.00 1.52
1670 1696 6.663734 AGGCCATACTAAAGATGTTTAGCTT 58.336 36.000 19.40 6.97 46.40 3.74
1744 1770 1.342374 GGATGCCCATGGTTTCCTTCT 60.342 52.381 11.73 0.00 0.00 2.85
1765 1791 8.475639 CCTTCTTAGAGTTACAAATGGCTACTA 58.524 37.037 0.00 0.00 0.00 1.82
1780 1806 5.616270 TGGCTACTAATTGACACAACAGAA 58.384 37.500 0.00 0.00 0.00 3.02
1785 1811 7.798982 GCTACTAATTGACACAACAGAAGAAAC 59.201 37.037 0.00 0.00 0.00 2.78
1923 1949 8.450578 ACATGATTGTTAAGACTTTTGACTCA 57.549 30.769 0.00 0.00 29.55 3.41
2177 2277 2.821969 GCATCTCCCACTGTTTTGATGT 59.178 45.455 0.00 0.00 35.22 3.06
2182 2282 7.605449 CATCTCCCACTGTTTTGATGTTTTAT 58.395 34.615 0.00 0.00 0.00 1.40
2214 2314 4.078805 TCCAGACCCTGCTTATAGGTAAGA 60.079 45.833 0.00 0.00 39.77 2.10
2275 2375 7.828717 ACATTATGTACATGTTGAATCCAGTCA 59.171 33.333 18.81 0.00 30.22 3.41
2389 2496 9.453572 ACTATGTTGTAGCAAATATCCATATGG 57.546 33.333 16.25 16.25 0.00 2.74
2552 2661 9.381038 TCTAGTATGGATAGAAAATAGCAACCT 57.619 33.333 0.00 0.00 0.00 3.50
2556 2665 9.120538 GTATGGATAGAAAATAGCAACCTTTGA 57.879 33.333 0.00 0.00 0.00 2.69
2627 3955 7.210873 TGTGGTTGTGGTTTATTTACATTTCC 58.789 34.615 0.00 0.00 0.00 3.13
2646 3974 7.872483 ACATTTCCGATATTTTTGAAAGCTGTT 59.128 29.630 0.00 0.00 30.96 3.16
2691 4023 8.015658 CCATCTATAATTTTAAGGCGCTAACAC 58.984 37.037 7.64 0.00 0.00 3.32
2692 4024 8.556194 CATCTATAATTTTAAGGCGCTAACACA 58.444 33.333 7.64 0.00 0.00 3.72
2702 4034 1.302949 GCTAACACATGCCCCCTCA 59.697 57.895 0.00 0.00 0.00 3.86
2709 4041 0.706433 ACATGCCCCCTCAGTTTCAT 59.294 50.000 0.00 0.00 0.00 2.57
2711 4043 2.301346 CATGCCCCCTCAGTTTCATAC 58.699 52.381 0.00 0.00 0.00 2.39
2782 4121 3.317406 TGGTGACATGTCTATATGGCCT 58.683 45.455 25.55 0.00 35.11 5.19
2794 4133 7.378966 TGTCTATATGGCCTATCTCTTTTTCG 58.621 38.462 3.32 0.00 0.00 3.46
2925 4264 4.518970 GCATTGGAACTTTGGAAGTGTAGA 59.481 41.667 0.00 0.00 41.91 2.59
2926 4265 5.009610 GCATTGGAACTTTGGAAGTGTAGAA 59.990 40.000 0.00 0.00 41.91 2.10
2927 4266 6.672147 CATTGGAACTTTGGAAGTGTAGAAG 58.328 40.000 0.00 0.00 41.91 2.85
2933 4272 3.402628 TTGGAAGTGTAGAAGGACAGC 57.597 47.619 0.00 0.00 0.00 4.40
2970 4310 2.003301 GAGAGGCTAAAAGGACGCTTG 58.997 52.381 0.00 0.00 0.00 4.01
2974 4314 3.746940 AGGCTAAAAGGACGCTTGTTTA 58.253 40.909 0.00 0.00 0.00 2.01
2982 4322 1.869132 GGACGCTTGTTTAGAAACGGT 59.131 47.619 0.97 0.00 41.74 4.83
3023 4364 9.167311 ACCAAGACATACTCAGATAATGAAAAC 57.833 33.333 0.25 0.00 37.52 2.43
3025 4366 9.979270 CAAGACATACTCAGATAATGAAAACAC 57.021 33.333 0.25 0.00 37.52 3.32
3028 4369 9.926751 GACATACTCAGATAATGAAAACACATG 57.073 33.333 0.00 0.00 37.52 3.21
3051 4392 5.179452 ACTTACCAGTTATGCACCATCTT 57.821 39.130 0.00 0.00 0.00 2.40
3113 4454 2.025321 GGAGTAAATCTGGAAGGGGCAA 60.025 50.000 0.00 0.00 0.00 4.52
3155 4496 3.199677 TGTACAAGGTTTTGACGAGTGG 58.800 45.455 0.00 0.00 37.73 4.00
3246 4588 7.902920 AATGCTGGTTCCTTTATGTGATAAT 57.097 32.000 0.00 0.00 0.00 1.28
3258 4600 8.739039 CCTTTATGTGATAATCAAAAGTGTGGA 58.261 33.333 0.00 0.00 0.00 4.02
3346 4690 3.201290 CAGAATCATCCCGAAACTCTGG 58.799 50.000 0.00 0.00 30.65 3.86
3478 4836 8.062512 TTGGTAACCATGAGTCACATCTATGTG 61.063 40.741 15.47 15.47 45.45 3.21
3512 4870 0.322816 AAGGTCCATCTGCATTGCGT 60.323 50.000 3.84 0.00 0.00 5.24
3537 4895 5.352284 CAAGGCGTTACATGAGAGATTACT 58.648 41.667 0.00 0.00 0.00 2.24
3556 4914 2.158813 ACTTTGAGGGTCGTGTTCATGT 60.159 45.455 0.00 0.00 0.00 3.21
3585 4943 5.373854 ACTCTGGCTCCCCATCTTTTTATAT 59.626 40.000 0.00 0.00 41.21 0.86
3596 4954 5.124457 CCATCTTTTTATATGCATAGCCGCT 59.876 40.000 12.79 0.00 0.00 5.52
3597 4955 6.349611 CCATCTTTTTATATGCATAGCCGCTT 60.350 38.462 12.79 0.00 0.00 4.68
3598 4956 6.000891 TCTTTTTATATGCATAGCCGCTTG 57.999 37.500 12.79 0.00 0.00 4.01
3630 4988 5.815233 TCCTTTCTCTCTGTCTGATTGTT 57.185 39.130 0.00 0.00 0.00 2.83
3703 5061 5.491973 CACGTTGAAAAAGGCTGAAATTTG 58.508 37.500 0.00 0.00 0.00 2.32
3705 5063 4.517287 GTTGAAAAAGGCTGAAATTTGCG 58.483 39.130 0.00 0.00 0.00 4.85
3760 5119 3.202906 GTTTGCTGACCTGAGTACAACA 58.797 45.455 0.00 0.00 0.00 3.33
3762 5121 4.882842 TTGCTGACCTGAGTACAACATA 57.117 40.909 0.00 0.00 0.00 2.29
4073 5432 1.879380 TCAAAGGTCCATTTCACTGCG 59.121 47.619 0.00 0.00 0.00 5.18
4253 5615 3.258123 ACCAACTGTGTTGCTGAAAACTT 59.742 39.130 5.04 0.00 0.00 2.66
4480 5844 7.725844 GGGAGAAAAATAGATTATGGGTGTGAT 59.274 37.037 0.00 0.00 0.00 3.06
4514 5879 4.918201 GGCGGAGGGCTTCATCGG 62.918 72.222 0.00 0.00 42.94 4.18
4542 5907 2.874701 ACAGTGCTTGTGCTTTAGTCTG 59.125 45.455 0.00 0.00 38.99 3.51
4546 5911 4.058817 GTGCTTGTGCTTTAGTCTGTACT 58.941 43.478 0.00 0.00 40.48 2.73
4547 5912 4.150804 GTGCTTGTGCTTTAGTCTGTACTC 59.849 45.833 0.00 0.00 40.48 2.59
4548 5913 4.039245 TGCTTGTGCTTTAGTCTGTACTCT 59.961 41.667 0.00 0.00 40.48 3.24
4549 5914 5.243060 TGCTTGTGCTTTAGTCTGTACTCTA 59.757 40.000 0.00 0.00 40.48 2.43
4550 5915 5.573669 GCTTGTGCTTTAGTCTGTACTCTAC 59.426 44.000 0.00 0.00 35.19 2.59
4554 5919 4.948621 TGCTTTAGTCTGTACTCTACTCCC 59.051 45.833 0.00 0.00 37.15 4.30
4562 5927 0.842635 TACTCTACTCCCTCCGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
4574 5939 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4576 5941 4.712337 CCTCCGTCCCATAATATAAGAGCT 59.288 45.833 0.00 0.00 0.00 4.09
4577 5942 5.892119 CCTCCGTCCCATAATATAAGAGCTA 59.108 44.000 0.00 0.00 0.00 3.32
4578 5943 6.183360 CCTCCGTCCCATAATATAAGAGCTAC 60.183 46.154 0.00 0.00 0.00 3.58
4580 5945 7.636579 TCCGTCCCATAATATAAGAGCTACTA 58.363 38.462 0.00 0.00 0.00 1.82
4581 5946 7.774157 TCCGTCCCATAATATAAGAGCTACTAG 59.226 40.741 0.00 0.00 0.00 2.57
4582 5947 7.556996 CCGTCCCATAATATAAGAGCTACTAGT 59.443 40.741 0.00 0.00 0.00 2.57
4583 5948 8.399425 CGTCCCATAATATAAGAGCTACTAGTG 58.601 40.741 5.39 0.00 0.00 2.74
4584 5949 9.245481 GTCCCATAATATAAGAGCTACTAGTGT 57.755 37.037 5.39 0.00 0.00 3.55
4610 5975 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4611 5976 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
4612 5977 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
4613 5978 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4614 5979 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
4615 5980 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
4616 5981 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4617 5982 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4618 5983 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4619 5984 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4620 5985 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
4621 5986 0.928505 TATGGGACGGAGGGAGTACA 59.071 55.000 0.00 0.00 0.00 2.90
4622 5987 0.686769 ATGGGACGGAGGGAGTACAC 60.687 60.000 0.00 0.00 0.00 2.90
4637 6002 5.705905 GGGAGTACACTTTTGCTTGTTATCT 59.294 40.000 0.00 0.00 0.00 1.98
4638 6003 6.348540 GGGAGTACACTTTTGCTTGTTATCTG 60.349 42.308 0.00 0.00 0.00 2.90
4639 6004 6.426937 GGAGTACACTTTTGCTTGTTATCTGA 59.573 38.462 0.00 0.00 0.00 3.27
4640 6005 7.119846 GGAGTACACTTTTGCTTGTTATCTGAT 59.880 37.037 0.00 0.00 0.00 2.90
4764 6129 6.033725 CGTTGTAATTTTATTTTGGGCGGTAC 59.966 38.462 0.00 0.00 0.00 3.34
4773 6138 3.420300 TTTGGGCGGTACATGACTTTA 57.580 42.857 0.00 0.00 0.00 1.85
4785 6151 7.910162 CGGTACATGACTTTATTCATTCAAAGG 59.090 37.037 0.00 0.00 36.32 3.11
4856 6325 7.531871 GCATATTACAACAGATAATCAACGCAG 59.468 37.037 0.00 0.00 0.00 5.18
4899 6368 3.760684 CCTAGAGCTTGCAAACAGGAAAT 59.239 43.478 0.00 0.00 0.00 2.17
4911 6381 1.617850 ACAGGAAATTGCCGAAATGCA 59.382 42.857 0.00 0.00 40.07 3.96
5020 6496 2.257207 CCACCCATCACCTATACCGAT 58.743 52.381 0.00 0.00 0.00 4.18
5053 6529 1.296715 GCCGCTTCTCTTTCTCCCA 59.703 57.895 0.00 0.00 0.00 4.37
5066 6545 4.844085 TCTTTCTCCCAAGTGATAGGAACA 59.156 41.667 0.00 0.00 0.00 3.18
5077 6556 6.865834 AGTGATAGGAACAGAGATCAACTT 57.134 37.500 0.00 0.00 30.43 2.66
5116 6595 6.245890 AGATAATCAAGAGAACAGGGGAAG 57.754 41.667 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.582498 GACAGCGGATTCGGTCGG 60.582 66.667 0.00 0.00 46.01 4.79
47 48 2.582498 GGACAGCGGATTCGGTCG 60.582 66.667 0.00 0.00 46.01 4.79
48 49 1.389609 TAGGGACAGCGGATTCGGTC 61.390 60.000 0.00 0.00 46.01 4.79
50 51 1.067582 GTAGGGACAGCGGATTCGG 59.932 63.158 0.00 0.00 36.79 4.30
51 52 1.299165 CGTAGGGACAGCGGATTCG 60.299 63.158 0.00 0.00 39.81 3.34
52 53 1.591863 GCGTAGGGACAGCGGATTC 60.592 63.158 0.00 0.00 0.00 2.52
53 54 1.895020 TTGCGTAGGGACAGCGGATT 61.895 55.000 0.00 0.00 0.00 3.01
54 55 2.298158 CTTGCGTAGGGACAGCGGAT 62.298 60.000 0.00 0.00 0.00 4.18
55 56 2.992689 TTGCGTAGGGACAGCGGA 60.993 61.111 0.00 0.00 0.00 5.54
56 57 2.509336 CTTGCGTAGGGACAGCGG 60.509 66.667 0.00 0.00 0.00 5.52
57 58 2.501223 TTCCTTGCGTAGGGACAGCG 62.501 60.000 3.21 0.00 44.86 5.18
58 59 1.295423 TTCCTTGCGTAGGGACAGC 59.705 57.895 3.21 0.00 44.86 4.40
62 63 2.975536 CGGTTCCTTGCGTAGGGA 59.024 61.111 0.00 0.00 44.86 4.20
63 64 2.818274 GCGGTTCCTTGCGTAGGG 60.818 66.667 0.00 0.00 44.86 3.53
88 89 1.605058 CCAGGTGTGTCCCCGTCTAG 61.605 65.000 0.00 0.00 36.75 2.43
89 90 1.608336 CCAGGTGTGTCCCCGTCTA 60.608 63.158 0.00 0.00 36.75 2.59
182 184 3.470888 CCCGTCCTGATCGGCCTT 61.471 66.667 0.00 0.00 45.71 4.35
245 247 2.351276 CAACCCCCTTGTCTCCCG 59.649 66.667 0.00 0.00 0.00 5.14
348 350 1.291335 ACTTCTCGTCCTATCCCCCTT 59.709 52.381 0.00 0.00 0.00 3.95
356 360 4.458295 ACTTCATCGAAACTTCTCGTCCTA 59.542 41.667 0.00 0.00 39.84 2.94
368 372 0.618458 CCCTCCCCACTTCATCGAAA 59.382 55.000 0.00 0.00 0.00 3.46
374 378 1.651770 AGTAGATCCCTCCCCACTTCA 59.348 52.381 0.00 0.00 0.00 3.02
429 436 2.668625 GGTTAGTTCCCCTCGAGATCT 58.331 52.381 15.71 0.00 0.00 2.75
440 447 3.702548 AGGTGTTTGTTTGGGTTAGTTCC 59.297 43.478 0.00 0.00 0.00 3.62
496 505 7.184022 ACAGGAAGGTTAGTTTGGGTTAGATAT 59.816 37.037 0.00 0.00 0.00 1.63
497 506 6.502863 ACAGGAAGGTTAGTTTGGGTTAGATA 59.497 38.462 0.00 0.00 0.00 1.98
544 553 9.420551 CGAGTTAGTTTGGATTAGTTTAGACTT 57.579 33.333 0.00 0.00 37.33 3.01
549 558 9.768662 AACTTCGAGTTAGTTTGGATTAGTTTA 57.231 29.630 0.00 0.00 36.52 2.01
570 579 0.610785 TTGGCCGGATCCCAAACTTC 60.611 55.000 5.05 0.00 39.29 3.01
573 582 0.682855 TCATTGGCCGGATCCCAAAC 60.683 55.000 14.94 0.00 44.80 2.93
575 584 0.395586 CTTCATTGGCCGGATCCCAA 60.396 55.000 13.56 13.56 45.63 4.12
576 585 1.227102 CTTCATTGGCCGGATCCCA 59.773 57.895 5.05 0.00 0.00 4.37
577 586 2.196245 GCTTCATTGGCCGGATCCC 61.196 63.158 5.05 0.00 0.00 3.85
578 587 1.152881 AGCTTCATTGGCCGGATCC 60.153 57.895 5.05 0.00 0.00 3.36
579 588 1.502163 CGAGCTTCATTGGCCGGATC 61.502 60.000 5.05 0.00 0.00 3.36
580 589 1.524621 CGAGCTTCATTGGCCGGAT 60.525 57.895 5.05 0.00 0.00 4.18
581 590 2.125147 CGAGCTTCATTGGCCGGA 60.125 61.111 5.05 0.00 0.00 5.14
582 591 3.204827 CCGAGCTTCATTGGCCGG 61.205 66.667 0.00 0.00 37.26 6.13
583 592 2.436646 ACCGAGCTTCATTGGCCG 60.437 61.111 0.00 0.00 0.00 6.13
584 593 2.115291 GGACCGAGCTTCATTGGCC 61.115 63.158 0.00 0.00 0.00 5.36
585 594 2.464459 CGGACCGAGCTTCATTGGC 61.464 63.158 8.64 0.00 0.00 4.52
586 595 0.673644 AACGGACCGAGCTTCATTGG 60.674 55.000 23.38 0.00 0.00 3.16
587 596 1.135972 CAAACGGACCGAGCTTCATTG 60.136 52.381 23.38 9.47 0.00 2.82
588 597 1.156736 CAAACGGACCGAGCTTCATT 58.843 50.000 23.38 0.00 0.00 2.57
589 598 0.673644 CCAAACGGACCGAGCTTCAT 60.674 55.000 23.38 0.00 0.00 2.57
590 599 1.301401 CCAAACGGACCGAGCTTCA 60.301 57.895 23.38 0.00 0.00 3.02
591 600 1.301479 ACCAAACGGACCGAGCTTC 60.301 57.895 23.38 0.00 0.00 3.86
592 601 1.597027 CACCAAACGGACCGAGCTT 60.597 57.895 23.38 7.85 0.00 3.74
593 602 2.030562 CACCAAACGGACCGAGCT 59.969 61.111 23.38 0.95 0.00 4.09
594 603 3.047877 CCACCAAACGGACCGAGC 61.048 66.667 23.38 0.00 0.00 5.03
595 604 3.047877 GCCACCAAACGGACCGAG 61.048 66.667 23.38 9.78 0.00 4.63
596 605 4.629523 GGCCACCAAACGGACCGA 62.630 66.667 23.38 0.00 0.00 4.69
597 606 4.636435 AGGCCACCAAACGGACCG 62.636 66.667 13.61 13.61 28.17 4.79
598 607 2.671963 GAGGCCACCAAACGGACC 60.672 66.667 5.01 0.00 28.17 4.46
602 611 0.541863 ATAGAGGAGGCCACCAAACG 59.458 55.000 22.29 0.00 0.00 3.60
607 616 2.210711 CGGGATAGAGGAGGCCACC 61.211 68.421 11.96 11.96 0.00 4.61
730 743 0.032815 TGCGTTGAGATTCGTGACCA 59.967 50.000 0.00 0.00 0.00 4.02
778 791 1.736282 CTGTGCACGCGGTGTATGA 60.736 57.895 12.47 0.00 35.75 2.15
800 813 1.652563 CGGTGTCGCGGAGATATCA 59.347 57.895 6.13 0.00 0.00 2.15
851 864 3.505293 GCGACCTACCGGACTTTATCTAT 59.495 47.826 9.46 0.00 0.00 1.98
880 893 1.472376 GGAAGCGATGGAGTTGAGAGG 60.472 57.143 0.00 0.00 0.00 3.69
940 954 4.021925 AGTCCGCCTCAACCTGCC 62.022 66.667 0.00 0.00 0.00 4.85
941 955 2.743928 CAGTCCGCCTCAACCTGC 60.744 66.667 0.00 0.00 0.00 4.85
942 956 2.046892 CCAGTCCGCCTCAACCTG 60.047 66.667 0.00 0.00 0.00 4.00
943 957 3.322466 CCCAGTCCGCCTCAACCT 61.322 66.667 0.00 0.00 0.00 3.50
944 958 4.410400 CCCCAGTCCGCCTCAACC 62.410 72.222 0.00 0.00 0.00 3.77
945 959 4.410400 CCCCCAGTCCGCCTCAAC 62.410 72.222 0.00 0.00 0.00 3.18
946 960 4.974438 ACCCCCAGTCCGCCTCAA 62.974 66.667 0.00 0.00 0.00 3.02
947 961 4.974438 AACCCCCAGTCCGCCTCA 62.974 66.667 0.00 0.00 0.00 3.86
979 993 1.306482 CCCCCTGCTCTCCTCTTCA 60.306 63.158 0.00 0.00 0.00 3.02
991 1005 2.074948 CCTGGTCCATCTCCCCCTG 61.075 68.421 0.00 0.00 0.00 4.45
1176 1190 6.466413 CGAATAATCCTCGATTTAGTCTAGCG 59.534 42.308 0.00 0.00 38.61 4.26
1215 1229 0.760567 CCTGGACATCTCGGATCCCA 60.761 60.000 6.06 0.00 0.00 4.37
1239 1253 4.997905 ATGCACAGATCGAAATTATCCG 57.002 40.909 0.00 0.00 0.00 4.18
1253 1267 7.243487 ACGAATTAATCTAACACAATGCACAG 58.757 34.615 0.00 0.00 0.00 3.66
1264 1278 7.187480 GGCTCAAGGAAACGAATTAATCTAAC 58.813 38.462 0.00 0.00 0.00 2.34
1286 1300 0.250338 GGAATCCTATTTCCGCGGCT 60.250 55.000 23.51 10.28 36.12 5.52
1324 1339 1.386533 AGCAATCGCCCAGATGAAAG 58.613 50.000 0.00 0.00 40.02 2.62
1330 1345 1.485124 TCTAGAAGCAATCGCCCAGA 58.515 50.000 0.00 0.00 39.83 3.86
1403 1418 6.542370 ACCCAATCTAGTTGAATCAATTACCG 59.458 38.462 0.00 0.00 40.37 4.02
1413 1428 4.998672 CCGTGTAAACCCAATCTAGTTGAA 59.001 41.667 6.62 0.00 40.37 2.69
1538 1563 3.557898 CGCATGAGATAGGCCAAATAGGT 60.558 47.826 5.01 0.00 40.61 3.08
1545 1570 2.936919 AAATCGCATGAGATAGGCCA 57.063 45.000 12.62 0.00 30.89 5.36
1548 1573 7.041167 TGGAAACATTAAATCGCATGAGATAGG 60.041 37.037 12.62 1.79 33.40 2.57
1599 1625 1.066757 TGCGCATTCAAGAACTTGCAA 59.933 42.857 5.66 0.00 40.24 4.08
1606 1632 1.199789 GACCATGTGCGCATTCAAGAA 59.800 47.619 15.91 0.00 31.99 2.52
1616 1642 0.459237 GTGGAGAGAGACCATGTGCG 60.459 60.000 0.00 0.00 39.69 5.34
1623 1649 7.269316 CCTAAAAGATAAAGTGGAGAGAGACC 58.731 42.308 0.00 0.00 0.00 3.85
1646 1672 6.253946 AGCTAAACATCTTTAGTATGGCCT 57.746 37.500 3.32 0.00 40.73 5.19
1670 1696 7.686438 ATACACATGTAGCAAAGAAACATCA 57.314 32.000 0.00 0.00 31.60 3.07
1716 1742 1.134098 ACCATGGGCATCCTTCGTAAG 60.134 52.381 18.09 0.00 0.00 2.34
1717 1743 0.916086 ACCATGGGCATCCTTCGTAA 59.084 50.000 18.09 0.00 0.00 3.18
1720 1746 0.740737 GAAACCATGGGCATCCTTCG 59.259 55.000 18.09 0.00 0.00 3.79
1729 1755 4.576330 ACTCTAAGAAGGAAACCATGGG 57.424 45.455 18.09 0.00 0.00 4.00
1765 1791 7.396540 AAGAGTTTCTTCTGTTGTGTCAATT 57.603 32.000 0.00 0.00 28.99 2.32
1780 1806 8.041919 GCTATAGGAAAGTGGTTAAGAGTTTCT 58.958 37.037 1.04 4.62 34.47 2.52
1785 1811 9.482627 CTTATGCTATAGGAAAGTGGTTAAGAG 57.517 37.037 0.00 0.00 0.00 2.85
1830 1856 6.914757 GCATGAGCTGGAAACAATAATTACTC 59.085 38.462 0.00 0.00 42.06 2.59
1923 1949 5.066505 GCGTGTCTTTCATGGATTATTCCTT 59.933 40.000 5.31 0.00 43.07 3.36
1995 2021 2.546368 GCGGACATGTGTGTTTCTAACA 59.454 45.455 1.15 0.00 39.09 2.41
2004 2104 2.102438 ATCGCTGCGGACATGTGTG 61.102 57.895 23.03 0.00 0.00 3.82
2047 2147 5.012148 ACCTAACAGCAGAACATAACAGAGT 59.988 40.000 0.00 0.00 0.00 3.24
2140 2240 6.326323 TGGGAGATGCTTCACATAGTACATTA 59.674 38.462 2.07 0.00 39.84 1.90
2177 2277 6.071616 GCAGGGTCTGGAAATACAACATAAAA 60.072 38.462 0.00 0.00 31.21 1.52
2182 2282 2.375174 AGCAGGGTCTGGAAATACAACA 59.625 45.455 0.00 0.00 31.21 3.33
2214 2314 5.009410 GCTGGAAATGCATATAGAGCTTTGT 59.991 40.000 0.00 0.00 30.91 2.83
2262 2362 4.249661 GGAAGAGACTGACTGGATTCAAC 58.750 47.826 0.00 0.00 0.00 3.18
2275 2375 1.482593 CCGCCAATACTGGAAGAGACT 59.517 52.381 0.00 0.00 46.92 3.24
2635 3963 7.656412 TGCTCAATATTACAAACAGCTTTCAA 58.344 30.769 0.00 0.00 0.00 2.69
2646 3974 9.797642 ATAGATGGTCATTGCTCAATATTACAA 57.202 29.630 0.00 0.00 0.00 2.41
2691 4023 2.092212 AGTATGAAACTGAGGGGGCATG 60.092 50.000 0.00 0.00 36.93 4.06
2692 4024 2.208872 AGTATGAAACTGAGGGGGCAT 58.791 47.619 0.00 0.00 36.93 4.40
2741 4080 3.974401 CCAACACTCTAAATTTGTGTGCG 59.026 43.478 12.09 7.77 43.11 5.34
2782 4121 7.962964 ATGACTTTGTGACGAAAAAGAGATA 57.037 32.000 1.53 0.00 36.96 1.98
2794 4133 7.497925 AAGGAGAACTTAATGACTTTGTGAC 57.502 36.000 0.00 0.00 37.74 3.67
2925 4264 6.461509 CCAAGTTTGTCAAAATAGCTGTCCTT 60.462 38.462 0.00 0.00 0.00 3.36
2926 4265 5.010012 CCAAGTTTGTCAAAATAGCTGTCCT 59.990 40.000 0.00 0.00 0.00 3.85
2927 4266 5.009610 TCCAAGTTTGTCAAAATAGCTGTCC 59.990 40.000 0.00 0.00 0.00 4.02
2933 4272 5.474876 AGCCTCTCCAAGTTTGTCAAAATAG 59.525 40.000 0.00 0.00 0.00 1.73
2970 4310 4.886579 TCTTACTCCCACCGTTTCTAAAC 58.113 43.478 0.00 0.00 35.59 2.01
2974 4314 2.885616 TCTCTTACTCCCACCGTTTCT 58.114 47.619 0.00 0.00 0.00 2.52
2982 4322 4.410883 TGTCTTGGTTTTCTCTTACTCCCA 59.589 41.667 0.00 0.00 0.00 4.37
3023 4364 4.094887 GGTGCATAACTGGTAAGTCATGTG 59.905 45.833 0.00 0.00 34.84 3.21
3025 4366 4.260985 TGGTGCATAACTGGTAAGTCATG 58.739 43.478 0.00 0.00 35.40 3.07
3028 4369 4.770795 AGATGGTGCATAACTGGTAAGTC 58.229 43.478 0.00 0.00 34.77 3.01
3113 4454 6.220726 ACAGCTCCAAAAACTAACAAATGT 57.779 33.333 0.00 0.00 0.00 2.71
3155 4496 2.846371 CTGCAAGGCACCACTAGTC 58.154 57.895 0.00 0.00 33.79 2.59
3246 4588 8.253810 TGAACACAATTAAATCCACACTTTTGA 58.746 29.630 0.00 0.00 0.00 2.69
3478 4836 8.778358 CAGATGGACCTTTACTAGCATTATTTC 58.222 37.037 0.00 0.00 0.00 2.17
3481 4839 6.183361 TGCAGATGGACCTTTACTAGCATTAT 60.183 38.462 0.00 0.00 0.00 1.28
3494 4852 1.028330 CACGCAATGCAGATGGACCT 61.028 55.000 5.91 0.00 0.00 3.85
3512 4870 1.275010 TCTCTCATGTAACGCCTTGCA 59.725 47.619 0.00 0.00 0.00 4.08
3537 4895 2.631160 ACATGAACACGACCCTCAAA 57.369 45.000 0.00 0.00 0.00 2.69
3556 4914 2.119495 GATGGGGAGCCAGAGTAAGAA 58.881 52.381 0.00 0.00 0.00 2.52
3585 4943 0.958091 AAACAACAAGCGGCTATGCA 59.042 45.000 1.35 0.00 37.31 3.96
3596 4954 6.208599 ACAGAGAGAAAGGAACAAAACAACAA 59.791 34.615 0.00 0.00 0.00 2.83
3597 4955 5.710099 ACAGAGAGAAAGGAACAAAACAACA 59.290 36.000 0.00 0.00 0.00 3.33
3598 4956 6.094186 AGACAGAGAGAAAGGAACAAAACAAC 59.906 38.462 0.00 0.00 0.00 3.32
3682 5040 4.517287 GCAAATTTCAGCCTTTTTCAACG 58.483 39.130 0.00 0.00 0.00 4.10
3687 5045 4.379652 ACATCGCAAATTTCAGCCTTTTT 58.620 34.783 0.00 0.00 0.00 1.94
3703 5061 7.298122 TGAAGAAAAAGATCAGTAAACATCGC 58.702 34.615 0.00 0.00 0.00 4.58
3732 5091 5.483685 ACTCAGGTCAGCAAACATTAGTA 57.516 39.130 0.00 0.00 0.00 1.82
3738 5097 3.202906 GTTGTACTCAGGTCAGCAAACA 58.797 45.455 0.00 0.00 0.00 2.83
3760 5119 1.202698 GCTTCCCTGCGACCAAGATAT 60.203 52.381 0.00 0.00 0.00 1.63
3762 5121 1.078143 GCTTCCCTGCGACCAAGAT 60.078 57.895 0.00 0.00 0.00 2.40
3989 5348 2.905415 TGGTCTTCATGCCCTCAATT 57.095 45.000 0.00 0.00 0.00 2.32
3992 5351 0.329261 CCTTGGTCTTCATGCCCTCA 59.671 55.000 0.00 0.00 0.00 3.86
4073 5432 2.115291 GCGGGTCTTCTTCATGCCC 61.115 63.158 0.00 0.00 36.08 5.36
4253 5615 9.565090 CAAGATATAGAAAAAGTCATGGATGGA 57.435 33.333 0.00 0.00 0.00 3.41
4514 5879 0.595825 GCACAAGCACTGTTTGAGGC 60.596 55.000 12.14 10.74 41.58 4.70
4542 5907 1.476652 GGGACGGAGGGAGTAGAGTAC 60.477 61.905 0.00 0.00 0.00 2.73
4546 5911 1.526315 TATGGGACGGAGGGAGTAGA 58.474 55.000 0.00 0.00 0.00 2.59
4547 5912 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
4548 5913 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4549 5914 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4550 5915 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4554 5919 5.923733 AGCTCTTATATTATGGGACGGAG 57.076 43.478 0.00 0.00 0.00 4.63
4586 5951 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4587 5952 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4588 5953 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4589 5954 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4590 5955 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4591 5956 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4592 5957 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4593 5958 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4594 5959 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4595 5960 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4596 5961 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4597 5962 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4598 5963 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4599 5964 3.140707 TGTACTCCCTCCGTCCCATAATA 59.859 47.826 0.00 0.00 0.00 0.98
4600 5965 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
4601 5966 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
4602 5967 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
4603 5968 0.686769 GTGTACTCCCTCCGTCCCAT 60.687 60.000 0.00 0.00 0.00 4.00
4604 5969 1.304713 GTGTACTCCCTCCGTCCCA 60.305 63.158 0.00 0.00 0.00 4.37
4605 5970 0.614134 AAGTGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
4606 5971 1.264295 AAAGTGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
4607 5972 2.685100 CAAAAGTGTACTCCCTCCGTC 58.315 52.381 0.00 0.00 0.00 4.79
4608 5973 1.270678 GCAAAAGTGTACTCCCTCCGT 60.271 52.381 0.00 0.00 0.00 4.69
4609 5974 1.002087 AGCAAAAGTGTACTCCCTCCG 59.998 52.381 0.00 0.00 0.00 4.63
4610 5975 2.814336 CAAGCAAAAGTGTACTCCCTCC 59.186 50.000 0.00 0.00 0.00 4.30
4611 5976 3.477530 ACAAGCAAAAGTGTACTCCCTC 58.522 45.455 0.00 0.00 0.00 4.30
4612 5977 3.577805 ACAAGCAAAAGTGTACTCCCT 57.422 42.857 0.00 0.00 0.00 4.20
4613 5978 5.705905 AGATAACAAGCAAAAGTGTACTCCC 59.294 40.000 0.00 0.00 0.00 4.30
4614 5979 6.426937 TCAGATAACAAGCAAAAGTGTACTCC 59.573 38.462 0.00 0.00 0.00 3.85
4615 5980 7.421530 TCAGATAACAAGCAAAAGTGTACTC 57.578 36.000 0.00 0.00 0.00 2.59
4616 5981 7.986085 ATCAGATAACAAGCAAAAGTGTACT 57.014 32.000 0.00 0.00 0.00 2.73
4617 5982 8.289618 TCAATCAGATAACAAGCAAAAGTGTAC 58.710 33.333 0.00 0.00 0.00 2.90
4618 5983 8.389779 TCAATCAGATAACAAGCAAAAGTGTA 57.610 30.769 0.00 0.00 0.00 2.90
4619 5984 7.275888 TCAATCAGATAACAAGCAAAAGTGT 57.724 32.000 0.00 0.00 0.00 3.55
4620 5985 8.644619 CAATCAATCAGATAACAAGCAAAAGTG 58.355 33.333 0.00 0.00 35.39 3.16
4621 5986 8.579006 TCAATCAATCAGATAACAAGCAAAAGT 58.421 29.630 0.00 0.00 35.39 2.66
4622 5987 8.975410 TCAATCAATCAGATAACAAGCAAAAG 57.025 30.769 0.00 0.00 35.39 2.27
4637 6002 4.522722 TGTGCAAAGCATCAATCAATCA 57.477 36.364 0.00 0.00 41.91 2.57
4638 6003 4.687018 TGTTGTGCAAAGCATCAATCAATC 59.313 37.500 0.00 0.00 41.91 2.67
4639 6004 4.449743 GTGTTGTGCAAAGCATCAATCAAT 59.550 37.500 0.00 0.00 41.91 2.57
4640 6005 3.803231 GTGTTGTGCAAAGCATCAATCAA 59.197 39.130 0.00 0.00 41.91 2.57
4669 6034 2.926838 CAACAAACAAAACGGACAAGGG 59.073 45.455 0.00 0.00 0.00 3.95
4764 6129 7.829725 TCCACCTTTGAATGAATAAAGTCATG 58.170 34.615 0.00 0.00 38.28 3.07
4773 6138 5.126707 GCTCAAGATCCACCTTTGAATGAAT 59.873 40.000 0.00 0.00 0.00 2.57
4785 6151 4.479786 AGAACTAAGGCTCAAGATCCAC 57.520 45.455 4.02 0.00 0.00 4.02
4856 6325 5.246307 AGGTTTAGGCAGTTCATAGTGTTC 58.754 41.667 0.00 0.00 0.00 3.18
4899 6368 1.894282 TCGGTGTGCATTTCGGCAA 60.894 52.632 0.00 0.00 46.93 4.52
4911 6381 0.249953 TAATGGTTGTGCGTCGGTGT 60.250 50.000 0.00 0.00 0.00 4.16
4965 6441 2.810767 GCGAAAAGAGAGGGGAGTGTTT 60.811 50.000 0.00 0.00 0.00 2.83
4966 6442 1.270893 GCGAAAAGAGAGGGGAGTGTT 60.271 52.381 0.00 0.00 0.00 3.32
5020 6496 3.606662 GGCGGCCTCGATCTAGCA 61.607 66.667 12.87 0.00 39.00 3.49
5053 6529 6.865834 AGTTGATCTCTGTTCCTATCACTT 57.134 37.500 0.00 0.00 0.00 3.16
5066 6545 2.462456 TTGCGCTCAAGTTGATCTCT 57.538 45.000 9.73 0.00 0.00 3.10
5077 6556 4.560136 TTATCTTGTTTGTTTGCGCTCA 57.440 36.364 9.73 2.35 0.00 4.26
5116 6595 2.087646 GAAACCCAATCACTCCTCTGC 58.912 52.381 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.