Multiple sequence alignment - TraesCS1B01G225100

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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 TraesCS1B01G225100 chr1B 100.000 2702 0 0 1 2702 403975471 403978172 0.000000e+00 4990.0
1 TraesCS1B01G225100 chr1B 92.308 572 31 4 1 564 632682340 632681774 0.000000e+00 800.0
2 TraesCS1B01G225100 chr1B 92.683 82 5 1 2187 2267 675980558 675980639 1.700000e-22 117.0
3 TraesCS1B01G225100 chr1B 87.368 95 12 0 2180 2274 364125420 364125326 2.840000e-20 110.0
4 TraesCS1B01G225100 chr1D 92.759 1450 53 24 689 2124 299756856 299758267 0.000000e+00 2049.0
5 TraesCS1B01G225100 chr1D 85.294 306 27 13 2398 2699 299760904 299761195 1.570000e-77 300.0
6 TraesCS1B01G225100 chr1D 96.377 138 5 0 2266 2403 299758315 299758452 7.530000e-56 228.0
7 TraesCS1B01G225100 chr1D 92.683 82 5 1 2187 2267 209139280 209139361 1.700000e-22 117.0
8 TraesCS1B01G225100 chr1D 90.698 86 7 1 2187 2271 241268659 241268574 2.200000e-21 113.0
9 TraesCS1B01G225100 chr1D 91.463 82 6 1 2187 2267 42391722 42391803 7.910000e-21 111.0
10 TraesCS1B01G225100 chr1D 90.588 85 7 1 2185 2268 349811070 349811154 7.910000e-21 111.0
11 TraesCS1B01G225100 chr1D 88.421 95 8 2 2187 2280 469153998 469153906 7.910000e-21 111.0
12 TraesCS1B01G225100 chr1D 88.043 92 11 0 2180 2271 250421661 250421752 2.840000e-20 110.0
13 TraesCS1B01G225100 chr1A 91.246 891 45 12 1318 2183 374137257 374138139 0.000000e+00 1182.0
14 TraesCS1B01G225100 chr1A 95.113 532 17 4 689 1211 374136461 374136992 0.000000e+00 830.0
15 TraesCS1B01G225100 chr1A 90.960 177 13 2 2266 2441 374138139 374138313 4.500000e-58 235.0
16 TraesCS1B01G225100 chr1A 85.556 180 17 6 394 565 509040506 509040328 2.140000e-41 180.0
17 TraesCS1B01G225100 chr1A 84.302 172 23 3 394 564 466367732 466367900 5.980000e-37 165.0
18 TraesCS1B01G225100 chr1A 88.043 92 11 0 2180 2271 320485586 320485677 2.840000e-20 110.0
19 TraesCS1B01G225100 chr2B 92.657 572 29 6 1 564 776537055 776536489 0.000000e+00 811.0
20 TraesCS1B01G225100 chr2B 93.191 235 8 1 338 564 292857275 292857041 3.330000e-89 339.0
21 TraesCS1B01G225100 chr6D 92.281 570 30 3 3 564 76403301 76403864 0.000000e+00 797.0
22 TraesCS1B01G225100 chr6D 90.476 84 8 0 2185 2268 196357911 196357994 7.910000e-21 111.0
23 TraesCS1B01G225100 chr6D 89.655 87 8 1 2187 2272 403969126 403969212 2.840000e-20 110.0
24 TraesCS1B01G225100 chr6D 92.105 76 6 0 2193 2268 105560538 105560463 1.020000e-19 108.0
25 TraesCS1B01G225100 chr2D 92.014 576 28 7 1 564 66563491 66564060 0.000000e+00 793.0
26 TraesCS1B01G225100 chr2D 91.566 83 6 1 2187 2268 382455943 382456025 2.200000e-21 113.0
27 TraesCS1B01G225100 chr2D 87.500 96 11 1 2175 2269 518804201 518804296 2.840000e-20 110.0
28 TraesCS1B01G225100 chr5B 91.958 572 32 4 1 564 673032450 673033015 0.000000e+00 789.0
29 TraesCS1B01G225100 chr5A 91.826 575 30 7 1 564 495875797 495876365 0.000000e+00 785.0
30 TraesCS1B01G225100 chr5D 91.798 573 32 4 1 564 563313004 563313570 0.000000e+00 784.0
31 TraesCS1B01G225100 chr5D 91.908 173 12 1 394 564 72693792 72693964 9.670000e-60 241.0
32 TraesCS1B01G225100 chr5D 87.571 177 16 4 394 564 163001816 163001992 1.640000e-47 200.0
33 TraesCS1B01G225100 chr5D 85.859 99 14 0 2176 2274 302021535 302021437 3.680000e-19 106.0
34 TraesCS1B01G225100 chr3B 91.608 572 33 4 1 564 8683255 8683819 0.000000e+00 776.0
35 TraesCS1B01G225100 chr3D 91.259 572 33 5 1 564 40742807 40742245 0.000000e+00 763.0
36 TraesCS1B01G225100 chr3D 86.408 103 12 2 2166 2267 66523480 66523379 7.910000e-21 111.0
37 TraesCS1B01G225100 chr7B 90.796 565 32 10 1 564 669278167 669278712 0.000000e+00 737.0
38 TraesCS1B01G225100 chr7B 91.928 223 8 2 350 564 686890004 686889784 1.220000e-78 303.0
39 TraesCS1B01G225100 chr2A 86.932 176 21 2 394 568 42361062 42361236 2.120000e-46 196.0
40 TraesCS1B01G225100 chr2A 89.109 101 10 1 2171 2270 608910819 608910719 1.020000e-24 124.0
41 TraesCS1B01G225100 chr2A 93.750 80 5 0 2191 2270 473417512 473417591 1.310000e-23 121.0
42 TraesCS1B01G225100 chr7D 87.879 165 18 1 402 564 380149709 380149545 2.750000e-45 193.0
43 TraesCS1B01G225100 chr7D 90.588 85 7 1 2187 2270 540570427 540570511 7.910000e-21 111.0
44 TraesCS1B01G225100 chr4B 82.222 135 24 0 1535 1669 654728276 654728142 1.700000e-22 117.0
45 TraesCS1B01G225100 chr3A 89.362 94 8 2 2175 2267 427762646 427762738 1.700000e-22 117.0
46 TraesCS1B01G225100 chrUn 87.368 95 11 1 2174 2268 37028903 37028996 1.020000e-19 108.0
47 TraesCS1B01G225100 chrUn 89.412 85 8 1 2187 2270 77893544 77893460 3.680000e-19 106.0
48 TraesCS1B01G225100 chrUn 89.286 84 8 1 2187 2269 377707933 377707850 1.320000e-18 104.0
49 TraesCS1B01G225100 chrUn 90.000 80 7 1 2193 2271 29814041 29813962 4.760000e-18 102.0
50 TraesCS1B01G225100 chrUn 88.235 85 10 0 2185 2269 287061745 287061829 4.760000e-18 102.0
51 TraesCS1B01G225100 chrUn 88.095 84 9 1 2187 2269 348315191 348315108 6.160000e-17 99.0
52 TraesCS1B01G225100 chrUn 88.095 84 9 1 2187 2269 382593690 382593773 6.160000e-17 99.0
53 TraesCS1B01G225100 chrUn 88.095 84 9 1 2187 2269 427230616 427230699 6.160000e-17 99.0
54 TraesCS1B01G225100 chrUn 87.805 82 9 1 2187 2267 29813970 29814051 7.960000e-16 95.3
55 TraesCS1B01G225100 chrUn 84.043 94 15 0 2175 2268 29029294 29029201 1.030000e-14 91.6
56 TraesCS1B01G225100 chr4D 90.123 81 8 0 2186 2266 149997742 149997822 3.680000e-19 106.0
57 TraesCS1B01G225100 chr4D 86.957 92 12 0 2180 2271 18692705 18692614 1.320000e-18 104.0
58 TraesCS1B01G225100 chr4D 89.286 84 8 1 2187 2269 64347364 64347447 1.320000e-18 104.0
59 TraesCS1B01G225100 chr4D 89.286 84 8 1 2187 2269 245478341 245478424 1.320000e-18 104.0


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 TraesCS1B01G225100 chr1B 403975471 403978172 2701 False 4990 4990 100.000000 1 2702 1 chr1B.!!$F1 2701
1 TraesCS1B01G225100 chr1B 632681774 632682340 566 True 800 800 92.308000 1 564 1 chr1B.!!$R2 563
2 TraesCS1B01G225100 chr1D 299756856 299761195 4339 False 859 2049 91.476667 689 2699 3 chr1D.!!$F5 2010
3 TraesCS1B01G225100 chr1A 374136461 374138313 1852 False 749 1182 92.439667 689 2441 3 chr1A.!!$F3 1752
4 TraesCS1B01G225100 chr2B 776536489 776537055 566 True 811 811 92.657000 1 564 1 chr2B.!!$R2 563
5 TraesCS1B01G225100 chr6D 76403301 76403864 563 False 797 797 92.281000 3 564 1 chr6D.!!$F1 561
6 TraesCS1B01G225100 chr2D 66563491 66564060 569 False 793 793 92.014000 1 564 1 chr2D.!!$F1 563
7 TraesCS1B01G225100 chr5B 673032450 673033015 565 False 789 789 91.958000 1 564 1 chr5B.!!$F1 563
8 TraesCS1B01G225100 chr5A 495875797 495876365 568 False 785 785 91.826000 1 564 1 chr5A.!!$F1 563
9 TraesCS1B01G225100 chr5D 563313004 563313570 566 False 784 784 91.798000 1 564 1 chr5D.!!$F3 563
10 TraesCS1B01G225100 chr3B 8683255 8683819 564 False 776 776 91.608000 1 564 1 chr3B.!!$F1 563
11 TraesCS1B01G225100 chr3D 40742245 40742807 562 True 763 763 91.259000 1 564 1 chr3D.!!$R1 563
12 TraesCS1B01G225100 chr7B 669278167 669278712 545 False 737 737 90.796000 1 564 1 chr7B.!!$F1 563

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
633 650 0.108963 TTTGGGTGTTTCCGTCGGAT 59.891 50.0 16.23 0.0 37.0 4.18 F
1271 1297 0.106719 AGCGGTGGTGGGATAATTGG 60.107 55.0 0.00 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1822 0.396060 GGATGAGGCTGAGGTGGATC 59.604 60.000 0.0 0.0 0.0 3.36 R
2680 5353 2.660944 GTTCGATTCCGCACGATGA 58.339 52.632 0.0 0.0 38.3 2.92 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
42 43 3.267233 TTGGGCCAGGATGCAGGT 61.267 61.111 6.23 0.00 31.97 4.00
117 118 0.829990 GCCTGCTTAGAGAGGAGCTT 59.170 55.000 2.36 0.00 42.08 3.74
181 182 2.428890 CTCTCAACTAGCGAAGTGGGAT 59.571 50.000 0.00 0.00 38.88 3.85
198 199 3.894427 TGGGATTAAACATTGTGCACTGT 59.106 39.130 19.41 12.27 0.00 3.55
227 228 0.928229 CGCACCATCTTTAGTACCGC 59.072 55.000 0.00 0.00 0.00 5.68
349 357 5.221581 TGACTTCAACCTGTACTAAAGACCC 60.222 44.000 0.00 0.00 0.00 4.46
495 512 2.752903 GTTGGAACCGGCACTAATGATT 59.247 45.455 0.00 0.00 0.00 2.57
564 581 7.549488 CACATTAGACCCTTTTTCTACTAGTGG 59.451 40.741 5.39 1.87 0.00 4.00
565 582 7.456902 ACATTAGACCCTTTTTCTACTAGTGGA 59.543 37.037 4.58 4.58 0.00 4.02
566 583 8.487028 CATTAGACCCTTTTTCTACTAGTGGAT 58.513 37.037 10.02 0.00 0.00 3.41
567 584 6.954352 AGACCCTTTTTCTACTAGTGGATT 57.046 37.500 10.02 0.00 0.00 3.01
568 585 6.948589 AGACCCTTTTTCTACTAGTGGATTC 58.051 40.000 10.02 0.00 0.00 2.52
569 586 5.731591 ACCCTTTTTCTACTAGTGGATTCG 58.268 41.667 10.02 0.00 0.00 3.34
570 587 4.571176 CCCTTTTTCTACTAGTGGATTCGC 59.429 45.833 10.02 0.00 0.00 4.70
571 588 4.571176 CCTTTTTCTACTAGTGGATTCGCC 59.429 45.833 10.02 0.00 37.10 5.54
572 589 4.811969 TTTTCTACTAGTGGATTCGCCA 57.188 40.909 10.02 0.00 46.96 5.69
579 596 2.285368 TGGATTCGCCACCTCCCT 60.285 61.111 0.00 0.00 43.33 4.20
580 597 2.367202 TGGATTCGCCACCTCCCTC 61.367 63.158 0.00 0.00 43.33 4.30
581 598 2.506472 GATTCGCCACCTCCCTCC 59.494 66.667 0.00 0.00 0.00 4.30
582 599 3.090532 ATTCGCCACCTCCCTCCC 61.091 66.667 0.00 0.00 0.00 4.30
587 604 3.787001 CCACCTCCCTCCCGCTTC 61.787 72.222 0.00 0.00 0.00 3.86
588 605 2.685380 CACCTCCCTCCCGCTTCT 60.685 66.667 0.00 0.00 0.00 2.85
589 606 2.364448 ACCTCCCTCCCGCTTCTC 60.364 66.667 0.00 0.00 0.00 2.87
590 607 3.532155 CCTCCCTCCCGCTTCTCG 61.532 72.222 0.00 0.00 38.08 4.04
591 608 2.756283 CTCCCTCCCGCTTCTCGT 60.756 66.667 0.00 0.00 36.19 4.18
592 609 3.068691 TCCCTCCCGCTTCTCGTG 61.069 66.667 0.00 0.00 36.19 4.35
593 610 4.148825 CCCTCCCGCTTCTCGTGG 62.149 72.222 0.00 0.00 43.15 4.94
598 615 2.032071 CCGCTTCTCGTGGGGTTT 59.968 61.111 0.00 0.00 39.71 3.27
599 616 1.294138 CCGCTTCTCGTGGGGTTTA 59.706 57.895 0.00 0.00 39.71 2.01
600 617 0.320946 CCGCTTCTCGTGGGGTTTAA 60.321 55.000 0.00 0.00 39.71 1.52
601 618 1.076332 CGCTTCTCGTGGGGTTTAAG 58.924 55.000 0.00 0.00 0.00 1.85
602 619 1.450025 GCTTCTCGTGGGGTTTAAGG 58.550 55.000 0.00 0.00 0.00 2.69
603 620 1.450025 CTTCTCGTGGGGTTTAAGGC 58.550 55.000 0.00 0.00 0.00 4.35
604 621 1.003233 CTTCTCGTGGGGTTTAAGGCT 59.997 52.381 0.00 0.00 0.00 4.58
605 622 0.611714 TCTCGTGGGGTTTAAGGCTC 59.388 55.000 0.00 0.00 0.00 4.70
606 623 0.323629 CTCGTGGGGTTTAAGGCTCA 59.676 55.000 0.00 0.00 0.00 4.26
607 624 0.766131 TCGTGGGGTTTAAGGCTCAA 59.234 50.000 0.00 0.00 0.00 3.02
608 625 1.353022 TCGTGGGGTTTAAGGCTCAAT 59.647 47.619 0.00 0.00 0.00 2.57
609 626 1.743394 CGTGGGGTTTAAGGCTCAATC 59.257 52.381 0.00 0.00 0.00 2.67
610 627 2.802719 GTGGGGTTTAAGGCTCAATCA 58.197 47.619 0.00 0.00 0.00 2.57
611 628 3.161866 GTGGGGTTTAAGGCTCAATCAA 58.838 45.455 0.00 0.00 0.00 2.57
612 629 3.193479 GTGGGGTTTAAGGCTCAATCAAG 59.807 47.826 0.00 0.00 0.00 3.02
613 630 2.166459 GGGGTTTAAGGCTCAATCAAGC 59.834 50.000 0.00 0.00 41.73 4.01
614 631 3.092301 GGGTTTAAGGCTCAATCAAGCT 58.908 45.455 0.00 0.00 42.13 3.74
615 632 3.511540 GGGTTTAAGGCTCAATCAAGCTT 59.488 43.478 0.00 0.00 42.13 3.74
616 633 4.021104 GGGTTTAAGGCTCAATCAAGCTTT 60.021 41.667 0.00 0.00 43.20 3.51
617 634 4.925646 GGTTTAAGGCTCAATCAAGCTTTG 59.074 41.667 0.00 0.00 41.17 2.77
618 635 4.789012 TTAAGGCTCAATCAAGCTTTGG 57.211 40.909 0.00 0.00 41.17 3.28
619 636 1.553706 AGGCTCAATCAAGCTTTGGG 58.446 50.000 0.00 0.00 42.13 4.12
620 637 1.203100 AGGCTCAATCAAGCTTTGGGT 60.203 47.619 0.00 0.00 42.13 4.51
621 638 1.067354 GGCTCAATCAAGCTTTGGGTG 60.067 52.381 0.00 0.00 42.13 4.61
622 639 1.615392 GCTCAATCAAGCTTTGGGTGT 59.385 47.619 0.00 0.00 39.27 4.16
623 640 2.036346 GCTCAATCAAGCTTTGGGTGTT 59.964 45.455 0.00 0.00 39.27 3.32
624 641 3.493176 GCTCAATCAAGCTTTGGGTGTTT 60.493 43.478 0.00 0.00 39.27 2.83
625 642 4.301628 CTCAATCAAGCTTTGGGTGTTTC 58.698 43.478 0.00 0.00 0.00 2.78
626 643 3.069443 TCAATCAAGCTTTGGGTGTTTCC 59.931 43.478 0.00 0.00 0.00 3.13
627 644 1.028905 TCAAGCTTTGGGTGTTTCCG 58.971 50.000 0.00 0.00 37.00 4.30
628 645 0.744281 CAAGCTTTGGGTGTTTCCGT 59.256 50.000 0.00 0.00 37.00 4.69
629 646 1.029681 AAGCTTTGGGTGTTTCCGTC 58.970 50.000 0.00 0.00 37.00 4.79
630 647 1.164041 AGCTTTGGGTGTTTCCGTCG 61.164 55.000 0.00 0.00 37.00 5.12
631 648 1.946267 CTTTGGGTGTTTCCGTCGG 59.054 57.895 4.39 4.39 37.00 4.79
632 649 0.533308 CTTTGGGTGTTTCCGTCGGA 60.533 55.000 10.71 10.71 37.00 4.55
633 650 0.108963 TTTGGGTGTTTCCGTCGGAT 59.891 50.000 16.23 0.00 37.00 4.18
634 651 0.108963 TTGGGTGTTTCCGTCGGATT 59.891 50.000 16.23 0.00 37.00 3.01
635 652 0.604243 TGGGTGTTTCCGTCGGATTG 60.604 55.000 16.23 0.00 37.00 2.67
636 653 1.303091 GGGTGTTTCCGTCGGATTGG 61.303 60.000 16.23 0.00 37.00 3.16
637 654 0.320946 GGTGTTTCCGTCGGATTGGA 60.321 55.000 16.23 0.00 0.00 3.53
638 655 1.515081 GTGTTTCCGTCGGATTGGAA 58.485 50.000 16.23 3.10 42.35 3.53
639 656 1.463444 GTGTTTCCGTCGGATTGGAAG 59.537 52.381 16.23 0.00 44.58 3.46
640 657 1.345089 TGTTTCCGTCGGATTGGAAGA 59.655 47.619 16.23 1.68 44.58 2.87
641 658 2.000447 GTTTCCGTCGGATTGGAAGAG 59.000 52.381 16.23 0.00 44.58 2.85
642 659 1.552578 TTCCGTCGGATTGGAAGAGA 58.447 50.000 16.23 0.00 39.29 3.10
643 660 1.776662 TCCGTCGGATTGGAAGAGAT 58.223 50.000 10.71 0.00 0.00 2.75
644 661 1.681793 TCCGTCGGATTGGAAGAGATC 59.318 52.381 10.71 0.00 0.00 2.75
645 662 1.409064 CCGTCGGATTGGAAGAGATCA 59.591 52.381 4.91 0.00 0.00 2.92
646 663 2.036475 CCGTCGGATTGGAAGAGATCAT 59.964 50.000 4.91 0.00 0.00 2.45
647 664 3.255888 CCGTCGGATTGGAAGAGATCATA 59.744 47.826 4.91 0.00 0.00 2.15
648 665 4.480541 CGTCGGATTGGAAGAGATCATAG 58.519 47.826 0.00 0.00 0.00 2.23
649 666 4.617067 CGTCGGATTGGAAGAGATCATAGG 60.617 50.000 0.00 0.00 0.00 2.57
650 667 4.282195 GTCGGATTGGAAGAGATCATAGGT 59.718 45.833 0.00 0.00 0.00 3.08
651 668 4.901849 TCGGATTGGAAGAGATCATAGGTT 59.098 41.667 0.00 0.00 0.00 3.50
652 669 5.366768 TCGGATTGGAAGAGATCATAGGTTT 59.633 40.000 0.00 0.00 0.00 3.27
653 670 5.468072 CGGATTGGAAGAGATCATAGGTTTG 59.532 44.000 0.00 0.00 0.00 2.93
654 671 6.360618 GGATTGGAAGAGATCATAGGTTTGT 58.639 40.000 0.00 0.00 0.00 2.83
655 672 7.509546 GGATTGGAAGAGATCATAGGTTTGTA 58.490 38.462 0.00 0.00 0.00 2.41
656 673 7.442666 GGATTGGAAGAGATCATAGGTTTGTAC 59.557 40.741 0.00 0.00 0.00 2.90
657 674 6.235231 TGGAAGAGATCATAGGTTTGTACC 57.765 41.667 0.00 0.00 45.39 3.34
677 694 3.813443 CCTTAGGAGGTTGATGGATGTG 58.187 50.000 0.00 0.00 38.32 3.21
678 695 3.434167 CCTTAGGAGGTTGATGGATGTGG 60.434 52.174 0.00 0.00 38.32 4.17
679 696 1.971149 AGGAGGTTGATGGATGTGGA 58.029 50.000 0.00 0.00 0.00 4.02
680 697 2.496297 AGGAGGTTGATGGATGTGGAT 58.504 47.619 0.00 0.00 0.00 3.41
681 698 2.854967 AGGAGGTTGATGGATGTGGATT 59.145 45.455 0.00 0.00 0.00 3.01
682 699 4.047166 AGGAGGTTGATGGATGTGGATTA 58.953 43.478 0.00 0.00 0.00 1.75
683 700 4.103785 AGGAGGTTGATGGATGTGGATTAG 59.896 45.833 0.00 0.00 0.00 1.73
684 701 4.141390 GGAGGTTGATGGATGTGGATTAGT 60.141 45.833 0.00 0.00 0.00 2.24
685 702 5.440610 GAGGTTGATGGATGTGGATTAGTT 58.559 41.667 0.00 0.00 0.00 2.24
686 703 5.440610 AGGTTGATGGATGTGGATTAGTTC 58.559 41.667 0.00 0.00 0.00 3.01
687 704 5.044919 AGGTTGATGGATGTGGATTAGTTCA 60.045 40.000 0.00 0.00 0.00 3.18
691 708 3.270027 TGGATGTGGATTAGTTCAAGCG 58.730 45.455 0.00 0.00 0.00 4.68
697 714 5.483811 TGTGGATTAGTTCAAGCGATTACA 58.516 37.500 0.00 0.00 0.00 2.41
752 769 2.509336 CCGCTGTCACCCACGATC 60.509 66.667 0.00 0.00 0.00 3.69
778 803 0.746063 CAGTGCCTGCAACCAGAAAA 59.254 50.000 0.00 0.00 41.77 2.29
1025 1051 1.066430 GTCCAAGGTGTCGGCTTCATA 60.066 52.381 0.00 0.00 0.00 2.15
1060 1086 3.653836 TGCCCTTAACCTCCTCTTGTTTA 59.346 43.478 0.00 0.00 0.00 2.01
1155 1181 4.265056 GGTGGCGGTGGAAGTGGT 62.265 66.667 0.00 0.00 0.00 4.16
1162 1188 2.345991 GTGGAAGTGGTAGCGGCA 59.654 61.111 1.45 0.00 0.00 5.69
1164 1190 2.125106 GGAAGTGGTAGCGGCAGG 60.125 66.667 1.45 0.00 0.00 4.85
1257 1283 1.988406 GGGTGGAGGAAGTAGCGGT 60.988 63.158 0.00 0.00 0.00 5.68
1258 1284 1.218316 GGTGGAGGAAGTAGCGGTG 59.782 63.158 0.00 0.00 0.00 4.94
1259 1285 1.218316 GTGGAGGAAGTAGCGGTGG 59.782 63.158 0.00 0.00 0.00 4.61
1260 1286 1.229082 TGGAGGAAGTAGCGGTGGT 60.229 57.895 0.00 0.00 0.00 4.16
1261 1287 1.218316 GGAGGAAGTAGCGGTGGTG 59.782 63.158 0.00 0.00 0.00 4.17
1262 1288 1.218316 GAGGAAGTAGCGGTGGTGG 59.782 63.158 0.00 0.00 0.00 4.61
1263 1289 2.240162 GAGGAAGTAGCGGTGGTGGG 62.240 65.000 0.00 0.00 0.00 4.61
1264 1290 2.288025 GGAAGTAGCGGTGGTGGGA 61.288 63.158 0.00 0.00 0.00 4.37
1265 1291 1.623542 GGAAGTAGCGGTGGTGGGAT 61.624 60.000 0.00 0.00 0.00 3.85
1266 1292 1.117150 GAAGTAGCGGTGGTGGGATA 58.883 55.000 0.00 0.00 0.00 2.59
1267 1293 1.483415 GAAGTAGCGGTGGTGGGATAA 59.517 52.381 0.00 0.00 0.00 1.75
1268 1294 1.802553 AGTAGCGGTGGTGGGATAAT 58.197 50.000 0.00 0.00 0.00 1.28
1269 1295 2.124411 AGTAGCGGTGGTGGGATAATT 58.876 47.619 0.00 0.00 0.00 1.40
1270 1296 2.158813 AGTAGCGGTGGTGGGATAATTG 60.159 50.000 0.00 0.00 0.00 2.32
1271 1297 0.106719 AGCGGTGGTGGGATAATTGG 60.107 55.000 0.00 0.00 0.00 3.16
1272 1298 1.734388 GCGGTGGTGGGATAATTGGC 61.734 60.000 0.00 0.00 0.00 4.52
1273 1299 1.444119 CGGTGGTGGGATAATTGGCG 61.444 60.000 0.00 0.00 0.00 5.69
1274 1300 1.106944 GGTGGTGGGATAATTGGCGG 61.107 60.000 0.00 0.00 0.00 6.13
1275 1301 1.454847 TGGTGGGATAATTGGCGGC 60.455 57.895 0.00 0.00 0.00 6.53
1276 1302 2.551912 GGTGGGATAATTGGCGGCG 61.552 63.158 0.51 0.51 0.00 6.46
1277 1303 2.203280 TGGGATAATTGGCGGCGG 60.203 61.111 9.78 0.00 0.00 6.13
1278 1304 2.203294 GGGATAATTGGCGGCGGT 60.203 61.111 9.78 0.00 0.00 5.68
1279 1305 2.258726 GGGATAATTGGCGGCGGTC 61.259 63.158 9.78 0.00 0.00 4.79
1280 1306 2.258726 GGATAATTGGCGGCGGTCC 61.259 63.158 9.78 2.12 0.00 4.46
1281 1307 1.227853 GATAATTGGCGGCGGTCCT 60.228 57.895 9.78 0.00 0.00 3.85
1282 1308 1.507141 GATAATTGGCGGCGGTCCTG 61.507 60.000 9.78 0.00 0.00 3.86
1283 1309 2.958578 ATAATTGGCGGCGGTCCTGG 62.959 60.000 9.78 0.00 0.00 4.45
1326 1510 1.995066 AGGTGGTGGCATCATCGGA 60.995 57.895 2.60 0.00 0.00 4.55
1330 1514 2.443394 GGTGGCATCATCGGAGGGA 61.443 63.158 0.00 0.00 0.00 4.20
1335 1519 2.142761 CATCATCGGAGGGAGCCCA 61.143 63.158 8.53 0.00 38.92 5.36
1381 1565 2.194597 GTGGTGGTGGAAGTGGCA 59.805 61.111 0.00 0.00 0.00 4.92
1527 1717 2.746277 GGCGTGCCTCCGTTGAAT 60.746 61.111 2.98 0.00 0.00 2.57
1632 1822 1.097547 GCATCCACATCAACCTCCCG 61.098 60.000 0.00 0.00 0.00 5.14
1662 1852 2.027377 CAGCCTCATCCTCAACTTCTGT 60.027 50.000 0.00 0.00 0.00 3.41
1712 1902 1.900486 CCCTACCTAATCCCGGTGATC 59.100 57.143 0.00 0.00 35.98 2.92
1728 1920 3.187700 GTGATCCTATTGAGTTCGCGTT 58.812 45.455 5.77 0.00 0.00 4.84
1766 1964 0.110678 TGAGAGAGGTCACGTCCACT 59.889 55.000 0.00 0.00 0.00 4.00
1886 2085 5.483685 TTGAGTCATAGCTTGTGGTAGTT 57.516 39.130 0.00 0.00 0.00 2.24
1933 2132 1.880796 GTGGCCGTTTGTTGTTGGC 60.881 57.895 0.00 0.00 46.82 4.52
1938 2137 0.456995 CCGTTTGTTGTTGGCGTTGT 60.457 50.000 0.00 0.00 0.00 3.32
2055 2264 1.927174 GTGATTGTTGGATCCGAGTCG 59.073 52.381 7.39 5.29 0.00 4.18
2145 2354 7.121168 ACGAAAATCATAAGCCTCATCTTCAAA 59.879 33.333 0.00 0.00 0.00 2.69
2188 2400 8.956426 TGTCACATCATTTTTATAGTTCCTTCC 58.044 33.333 0.00 0.00 0.00 3.46
2189 2401 8.406297 GTCACATCATTTTTATAGTTCCTTCCC 58.594 37.037 0.00 0.00 0.00 3.97
2190 2402 7.559897 TCACATCATTTTTATAGTTCCTTCCCC 59.440 37.037 0.00 0.00 0.00 4.81
2191 2403 6.839134 ACATCATTTTTATAGTTCCTTCCCCC 59.161 38.462 0.00 0.00 0.00 5.40
2192 2404 5.442391 TCATTTTTATAGTTCCTTCCCCCG 58.558 41.667 0.00 0.00 0.00 5.73
2193 2405 4.932911 TTTTTATAGTTCCTTCCCCCGT 57.067 40.909 0.00 0.00 0.00 5.28
2194 2406 6.158344 TCATTTTTATAGTTCCTTCCCCCGTA 59.842 38.462 0.00 0.00 0.00 4.02
2195 2407 6.385766 TTTTTATAGTTCCTTCCCCCGTAA 57.614 37.500 0.00 0.00 0.00 3.18
2196 2408 6.385766 TTTTATAGTTCCTTCCCCCGTAAA 57.614 37.500 0.00 0.00 0.00 2.01
2197 2409 5.619132 TTATAGTTCCTTCCCCCGTAAAG 57.381 43.478 0.00 0.00 0.00 1.85
2198 2410 2.034436 AGTTCCTTCCCCCGTAAAGA 57.966 50.000 0.00 0.00 0.00 2.52
2199 2411 2.341695 AGTTCCTTCCCCCGTAAAGAA 58.658 47.619 0.00 0.00 0.00 2.52
2200 2412 2.712627 AGTTCCTTCCCCCGTAAAGAAA 59.287 45.455 0.00 0.00 0.00 2.52
2201 2413 3.332783 AGTTCCTTCCCCCGTAAAGAAAT 59.667 43.478 0.00 0.00 0.00 2.17
2202 2414 4.537288 AGTTCCTTCCCCCGTAAAGAAATA 59.463 41.667 0.00 0.00 0.00 1.40
2203 2415 5.193124 AGTTCCTTCCCCCGTAAAGAAATAT 59.807 40.000 0.00 0.00 0.00 1.28
2204 2416 6.387807 AGTTCCTTCCCCCGTAAAGAAATATA 59.612 38.462 0.00 0.00 0.00 0.86
2205 2417 6.828307 TCCTTCCCCCGTAAAGAAATATAA 57.172 37.500 0.00 0.00 0.00 0.98
2206 2418 6.834107 TCCTTCCCCCGTAAAGAAATATAAG 58.166 40.000 0.00 0.00 0.00 1.73
2207 2419 6.616548 TCCTTCCCCCGTAAAGAAATATAAGA 59.383 38.462 0.00 0.00 0.00 2.10
2208 2420 6.935208 CCTTCCCCCGTAAAGAAATATAAGAG 59.065 42.308 0.00 0.00 0.00 2.85
2209 2421 5.861727 TCCCCCGTAAAGAAATATAAGAGC 58.138 41.667 0.00 0.00 0.00 4.09
2210 2422 5.367352 TCCCCCGTAAAGAAATATAAGAGCA 59.633 40.000 0.00 0.00 0.00 4.26
2211 2423 6.043938 TCCCCCGTAAAGAAATATAAGAGCAT 59.956 38.462 0.00 0.00 0.00 3.79
2212 2424 6.715264 CCCCCGTAAAGAAATATAAGAGCATT 59.285 38.462 0.00 0.00 0.00 3.56
2213 2425 7.230712 CCCCCGTAAAGAAATATAAGAGCATTT 59.769 37.037 0.00 0.00 0.00 2.32
2214 2426 8.630037 CCCCGTAAAGAAATATAAGAGCATTTT 58.370 33.333 0.00 0.00 0.00 1.82
2215 2427 9.450807 CCCGTAAAGAAATATAAGAGCATTTTG 57.549 33.333 0.00 0.00 0.00 2.44
2262 2474 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
2263 2475 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
2264 2476 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
2275 2487 7.179966 TCTTTACAGAGGGAGTACAAGACATA 58.820 38.462 0.00 0.00 0.00 2.29
2393 2605 1.080093 CACTCGGGCGAACTAAGCA 60.080 57.895 0.00 0.00 36.08 3.91
2445 5115 4.371681 AGGATTTGTGGTAGTAGGGACAT 58.628 43.478 0.00 0.00 0.00 3.06
2539 5211 5.694674 TGTTTGCATTTTCGTGTTTCTTC 57.305 34.783 0.00 0.00 0.00 2.87
2543 5215 4.597079 TGCATTTTCGTGTTTCTTCTGAC 58.403 39.130 0.00 0.00 0.00 3.51
2544 5216 4.095632 TGCATTTTCGTGTTTCTTCTGACA 59.904 37.500 0.00 0.00 0.00 3.58
2552 5224 4.134563 GTGTTTCTTCTGACAAGGGCTTA 58.865 43.478 0.00 0.00 0.00 3.09
2563 5235 7.826690 TCTGACAAGGGCTTACAAATAAATTC 58.173 34.615 0.00 0.00 0.00 2.17
2569 5241 9.450807 CAAGGGCTTACAAATAAATTCTATTCG 57.549 33.333 0.00 0.00 0.00 3.34
2590 5263 8.955061 ATTCGATTACATCTTGTTGAGTTTTG 57.045 30.769 0.00 0.00 0.00 2.44
2598 5271 8.466086 ACATCTTGTTGAGTTTTGAAAACTTC 57.534 30.769 22.61 15.94 0.00 3.01
2614 5287 7.981142 TGAAAACTTCGATAACTTTCAACTGT 58.019 30.769 8.96 0.00 34.10 3.55
2616 5289 9.925268 GAAAACTTCGATAACTTTCAACTGTTA 57.075 29.630 0.00 0.00 33.87 2.41
2624 5297 8.953990 CGATAACTTTCAACTGTTAAAACTTGG 58.046 33.333 0.00 0.00 33.21 3.61
2628 5301 7.245604 ACTTTCAACTGTTAAAACTTGGTACG 58.754 34.615 0.00 0.00 0.00 3.67
2629 5302 6.981762 TTCAACTGTTAAAACTTGGTACGA 57.018 33.333 0.00 0.00 0.00 3.43
2630 5303 7.556733 TTCAACTGTTAAAACTTGGTACGAT 57.443 32.000 0.00 0.00 0.00 3.73
2631 5304 7.556733 TCAACTGTTAAAACTTGGTACGATT 57.443 32.000 0.00 0.00 0.00 3.34
2632 5305 7.411274 TCAACTGTTAAAACTTGGTACGATTG 58.589 34.615 0.00 0.00 0.00 2.67
2635 5308 8.161699 ACTGTTAAAACTTGGTACGATTGAAT 57.838 30.769 0.00 0.00 0.00 2.57
2636 5309 8.073768 ACTGTTAAAACTTGGTACGATTGAATG 58.926 33.333 0.00 0.00 0.00 2.67
2637 5310 8.155821 TGTTAAAACTTGGTACGATTGAATGA 57.844 30.769 0.00 0.00 0.00 2.57
2638 5311 8.071368 TGTTAAAACTTGGTACGATTGAATGAC 58.929 33.333 0.00 0.00 0.00 3.06
2639 5312 6.627395 AAAACTTGGTACGATTGAATGACA 57.373 33.333 0.00 0.00 0.00 3.58
2642 5315 6.627395 ACTTGGTACGATTGAATGACAAAA 57.373 33.333 0.00 0.00 42.03 2.44
2643 5316 7.214467 ACTTGGTACGATTGAATGACAAAAT 57.786 32.000 0.00 0.00 42.03 1.82
2644 5317 7.305474 ACTTGGTACGATTGAATGACAAAATC 58.695 34.615 0.00 0.00 42.03 2.17
2645 5318 6.809630 TGGTACGATTGAATGACAAAATCA 57.190 33.333 0.00 0.00 42.03 2.57
2680 5353 8.691661 AAACTAAGATGTTAAACATGGTGTCT 57.308 30.769 0.00 0.00 39.27 3.41
2688 5361 1.442769 AACATGGTGTCTCATCGTGC 58.557 50.000 0.00 0.00 35.12 5.34
2690 5363 1.153568 ATGGTGTCTCATCGTGCGG 60.154 57.895 0.00 0.00 0.00 5.69
2695 5368 0.525455 TGTCTCATCGTGCGGAATCG 60.525 55.000 0.00 0.00 39.81 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.207791 CATCCTGGCCCAACTAGAGT 58.792 55.000 0.00 0.00 0.00 3.24
42 43 2.440796 CCTACTGGGCCGTACGGA 60.441 66.667 37.62 16.31 37.50 4.69
62 63 0.397941 CAAGTCTTCTGCCCTGTGGA 59.602 55.000 0.00 0.00 0.00 4.02
181 182 3.027412 ACCCACAGTGCACAATGTTTAA 58.973 40.909 21.04 0.00 37.55 1.52
215 216 1.338389 GCCACCAAGCGGTACTAAAGA 60.338 52.381 0.00 0.00 46.94 2.52
262 263 2.169978 GGCTCCAACCGGTACTAAAGAT 59.830 50.000 8.00 0.00 0.00 2.40
327 332 4.041321 GGGGTCTTTAGTACAGGTTGAAGT 59.959 45.833 0.00 0.00 0.00 3.01
330 335 2.908351 GGGGGTCTTTAGTACAGGTTGA 59.092 50.000 0.00 0.00 0.00 3.18
495 512 3.127895 GCAATTGAACCGGCACTAATGTA 59.872 43.478 10.34 0.00 0.00 2.29
564 581 2.506472 GGAGGGAGGTGGCGAATC 59.494 66.667 0.00 0.00 0.00 2.52
565 582 3.090532 GGGAGGGAGGTGGCGAAT 61.091 66.667 0.00 0.00 0.00 3.34
570 587 3.787001 GAAGCGGGAGGGAGGTGG 61.787 72.222 0.00 0.00 0.00 4.61
571 588 2.685380 AGAAGCGGGAGGGAGGTG 60.685 66.667 0.00 0.00 0.00 4.00
572 589 2.364448 GAGAAGCGGGAGGGAGGT 60.364 66.667 0.00 0.00 0.00 3.85
573 590 3.532155 CGAGAAGCGGGAGGGAGG 61.532 72.222 0.00 0.00 36.03 4.30
574 591 2.756283 ACGAGAAGCGGGAGGGAG 60.756 66.667 0.00 0.00 46.49 4.30
580 597 2.175035 TAAACCCCACGAGAAGCGGG 62.175 60.000 0.00 0.00 46.49 6.13
581 598 0.320946 TTAAACCCCACGAGAAGCGG 60.321 55.000 0.00 0.00 46.49 5.52
583 600 1.450025 CCTTAAACCCCACGAGAAGC 58.550 55.000 0.00 0.00 0.00 3.86
584 601 1.003233 AGCCTTAAACCCCACGAGAAG 59.997 52.381 0.00 0.00 0.00 2.85
585 602 1.002773 GAGCCTTAAACCCCACGAGAA 59.997 52.381 0.00 0.00 0.00 2.87
586 603 0.611714 GAGCCTTAAACCCCACGAGA 59.388 55.000 0.00 0.00 0.00 4.04
587 604 0.323629 TGAGCCTTAAACCCCACGAG 59.676 55.000 0.00 0.00 0.00 4.18
588 605 0.766131 TTGAGCCTTAAACCCCACGA 59.234 50.000 0.00 0.00 0.00 4.35
589 606 1.743394 GATTGAGCCTTAAACCCCACG 59.257 52.381 0.00 0.00 0.00 4.94
590 607 2.802719 TGATTGAGCCTTAAACCCCAC 58.197 47.619 0.00 0.00 0.00 4.61
591 608 3.430453 CTTGATTGAGCCTTAAACCCCA 58.570 45.455 0.00 0.00 0.00 4.96
592 609 2.166459 GCTTGATTGAGCCTTAAACCCC 59.834 50.000 0.00 0.00 36.66 4.95
593 610 3.092301 AGCTTGATTGAGCCTTAAACCC 58.908 45.455 0.00 0.00 43.74 4.11
594 611 4.790765 AAGCTTGATTGAGCCTTAAACC 57.209 40.909 0.00 0.00 43.74 3.27
595 612 4.925646 CCAAAGCTTGATTGAGCCTTAAAC 59.074 41.667 0.00 0.00 43.74 2.01
596 613 4.021192 CCCAAAGCTTGATTGAGCCTTAAA 60.021 41.667 0.00 0.00 43.74 1.52
597 614 3.511146 CCCAAAGCTTGATTGAGCCTTAA 59.489 43.478 0.00 0.00 43.74 1.85
598 615 3.091545 CCCAAAGCTTGATTGAGCCTTA 58.908 45.455 0.00 0.00 43.74 2.69
599 616 1.897802 CCCAAAGCTTGATTGAGCCTT 59.102 47.619 0.00 0.00 43.74 4.35
600 617 1.203100 ACCCAAAGCTTGATTGAGCCT 60.203 47.619 0.00 0.00 43.74 4.58
601 618 1.067354 CACCCAAAGCTTGATTGAGCC 60.067 52.381 0.00 0.00 43.74 4.70
602 619 1.615392 ACACCCAAAGCTTGATTGAGC 59.385 47.619 0.00 0.00 43.02 4.26
603 620 4.301628 GAAACACCCAAAGCTTGATTGAG 58.698 43.478 0.00 0.00 0.00 3.02
604 621 3.069443 GGAAACACCCAAAGCTTGATTGA 59.931 43.478 0.00 0.00 0.00 2.57
605 622 3.392882 GGAAACACCCAAAGCTTGATTG 58.607 45.455 0.00 0.00 0.00 2.67
606 623 2.035832 CGGAAACACCCAAAGCTTGATT 59.964 45.455 0.00 0.00 34.64 2.57
607 624 1.613437 CGGAAACACCCAAAGCTTGAT 59.387 47.619 0.00 0.00 34.64 2.57
608 625 1.028905 CGGAAACACCCAAAGCTTGA 58.971 50.000 0.00 0.00 34.64 3.02
609 626 0.744281 ACGGAAACACCCAAAGCTTG 59.256 50.000 0.00 0.00 34.64 4.01
610 627 1.029681 GACGGAAACACCCAAAGCTT 58.970 50.000 0.00 0.00 34.64 3.74
611 628 1.164041 CGACGGAAACACCCAAAGCT 61.164 55.000 0.00 0.00 34.64 3.74
612 629 1.281656 CGACGGAAACACCCAAAGC 59.718 57.895 0.00 0.00 34.64 3.51
613 630 0.533308 TCCGACGGAAACACCCAAAG 60.533 55.000 15.79 0.00 34.64 2.77
614 631 0.108963 ATCCGACGGAAACACCCAAA 59.891 50.000 22.55 0.00 34.34 3.28
615 632 0.108963 AATCCGACGGAAACACCCAA 59.891 50.000 22.55 0.00 34.34 4.12
616 633 0.604243 CAATCCGACGGAAACACCCA 60.604 55.000 22.55 0.00 34.34 4.51
617 634 1.303091 CCAATCCGACGGAAACACCC 61.303 60.000 22.55 0.00 34.34 4.61
618 635 0.320946 TCCAATCCGACGGAAACACC 60.321 55.000 22.55 0.00 34.34 4.16
619 636 1.463444 CTTCCAATCCGACGGAAACAC 59.537 52.381 22.55 0.00 40.71 3.32
620 637 1.345089 TCTTCCAATCCGACGGAAACA 59.655 47.619 22.55 2.18 40.71 2.83
621 638 2.000447 CTCTTCCAATCCGACGGAAAC 59.000 52.381 22.55 0.00 40.71 2.78
622 639 1.897133 TCTCTTCCAATCCGACGGAAA 59.103 47.619 22.55 9.66 40.71 3.13
623 640 1.552578 TCTCTTCCAATCCGACGGAA 58.447 50.000 22.55 0.23 38.99 4.30
624 641 1.681793 GATCTCTTCCAATCCGACGGA 59.318 52.381 20.85 20.85 35.55 4.69
625 642 1.409064 TGATCTCTTCCAATCCGACGG 59.591 52.381 7.84 7.84 0.00 4.79
626 643 2.871182 TGATCTCTTCCAATCCGACG 57.129 50.000 0.00 0.00 0.00 5.12
627 644 4.282195 ACCTATGATCTCTTCCAATCCGAC 59.718 45.833 0.00 0.00 0.00 4.79
628 645 4.483950 ACCTATGATCTCTTCCAATCCGA 58.516 43.478 0.00 0.00 0.00 4.55
629 646 4.881019 ACCTATGATCTCTTCCAATCCG 57.119 45.455 0.00 0.00 0.00 4.18
630 647 6.360618 ACAAACCTATGATCTCTTCCAATCC 58.639 40.000 0.00 0.00 0.00 3.01
631 648 7.442666 GGTACAAACCTATGATCTCTTCCAATC 59.557 40.741 0.00 0.00 43.08 2.67
632 649 7.283329 GGTACAAACCTATGATCTCTTCCAAT 58.717 38.462 0.00 0.00 43.08 3.16
633 650 6.650120 GGTACAAACCTATGATCTCTTCCAA 58.350 40.000 0.00 0.00 43.08 3.53
634 651 6.235231 GGTACAAACCTATGATCTCTTCCA 57.765 41.667 0.00 0.00 43.08 3.53
657 674 3.455910 TCCACATCCATCAACCTCCTAAG 59.544 47.826 0.00 0.00 0.00 2.18
658 675 3.459828 TCCACATCCATCAACCTCCTAA 58.540 45.455 0.00 0.00 0.00 2.69
659 676 3.129262 TCCACATCCATCAACCTCCTA 57.871 47.619 0.00 0.00 0.00 2.94
660 677 1.971149 TCCACATCCATCAACCTCCT 58.029 50.000 0.00 0.00 0.00 3.69
661 678 3.303351 AATCCACATCCATCAACCTCC 57.697 47.619 0.00 0.00 0.00 4.30
662 679 5.041191 ACTAATCCACATCCATCAACCTC 57.959 43.478 0.00 0.00 0.00 3.85
663 680 5.044919 TGAACTAATCCACATCCATCAACCT 60.045 40.000 0.00 0.00 0.00 3.50
664 681 5.192927 TGAACTAATCCACATCCATCAACC 58.807 41.667 0.00 0.00 0.00 3.77
665 682 6.678900 GCTTGAACTAATCCACATCCATCAAC 60.679 42.308 0.00 0.00 0.00 3.18
666 683 5.357878 GCTTGAACTAATCCACATCCATCAA 59.642 40.000 0.00 0.00 0.00 2.57
667 684 4.883585 GCTTGAACTAATCCACATCCATCA 59.116 41.667 0.00 0.00 0.00 3.07
668 685 4.024556 CGCTTGAACTAATCCACATCCATC 60.025 45.833 0.00 0.00 0.00 3.51
669 686 3.879295 CGCTTGAACTAATCCACATCCAT 59.121 43.478 0.00 0.00 0.00 3.41
670 687 3.055458 TCGCTTGAACTAATCCACATCCA 60.055 43.478 0.00 0.00 0.00 3.41
671 688 3.531538 TCGCTTGAACTAATCCACATCC 58.468 45.455 0.00 0.00 0.00 3.51
672 689 5.741388 AATCGCTTGAACTAATCCACATC 57.259 39.130 0.00 0.00 0.00 3.06
673 690 6.037172 GTGTAATCGCTTGAACTAATCCACAT 59.963 38.462 0.00 0.00 0.00 3.21
674 691 5.350365 GTGTAATCGCTTGAACTAATCCACA 59.650 40.000 0.00 0.00 0.00 4.17
675 692 5.350365 TGTGTAATCGCTTGAACTAATCCAC 59.650 40.000 0.00 0.00 0.00 4.02
676 693 5.483811 TGTGTAATCGCTTGAACTAATCCA 58.516 37.500 0.00 0.00 0.00 3.41
677 694 6.480320 AGATGTGTAATCGCTTGAACTAATCC 59.520 38.462 0.00 0.00 0.00 3.01
678 695 7.470289 AGATGTGTAATCGCTTGAACTAATC 57.530 36.000 0.00 0.00 0.00 1.75
679 696 7.849804 AAGATGTGTAATCGCTTGAACTAAT 57.150 32.000 0.00 0.00 0.00 1.73
680 697 8.766000 TTAAGATGTGTAATCGCTTGAACTAA 57.234 30.769 0.00 0.00 0.00 2.24
681 698 8.942338 ATTAAGATGTGTAATCGCTTGAACTA 57.058 30.769 0.00 0.00 0.00 2.24
682 699 7.849804 ATTAAGATGTGTAATCGCTTGAACT 57.150 32.000 0.00 0.00 0.00 3.01
683 700 9.982291 TTAATTAAGATGTGTAATCGCTTGAAC 57.018 29.630 0.00 0.00 0.00 3.18
771 796 2.539476 GTGCACTGGTTTGTTTTCTGG 58.461 47.619 10.32 0.00 0.00 3.86
778 803 0.537371 GGCTAGGTGCACTGGTTTGT 60.537 55.000 17.98 0.00 45.15 2.83
1214 1240 1.374758 CTTCCGCCTCCATATCCGC 60.375 63.158 0.00 0.00 0.00 5.54
1215 1241 1.374758 GCTTCCGCCTCCATATCCG 60.375 63.158 0.00 0.00 0.00 4.18
1216 1242 1.374758 CGCTTCCGCCTCCATATCC 60.375 63.158 0.00 0.00 0.00 2.59
1257 1283 1.454847 GCCGCCAATTATCCCACCA 60.455 57.895 0.00 0.00 0.00 4.17
1258 1284 2.551912 CGCCGCCAATTATCCCACC 61.552 63.158 0.00 0.00 0.00 4.61
1259 1285 2.551912 CCGCCGCCAATTATCCCAC 61.552 63.158 0.00 0.00 0.00 4.61
1260 1286 2.203280 CCGCCGCCAATTATCCCA 60.203 61.111 0.00 0.00 0.00 4.37
1261 1287 2.203294 ACCGCCGCCAATTATCCC 60.203 61.111 0.00 0.00 0.00 3.85
1262 1288 2.258726 GGACCGCCGCCAATTATCC 61.259 63.158 0.00 0.00 0.00 2.59
1263 1289 1.227853 AGGACCGCCGCCAATTATC 60.228 57.895 0.00 0.00 39.96 1.75
1264 1290 1.525995 CAGGACCGCCGCCAATTAT 60.526 57.895 0.00 0.00 39.96 1.28
1265 1291 2.124901 CAGGACCGCCGCCAATTA 60.125 61.111 0.00 0.00 39.96 1.40
1275 1301 3.009115 ATCCCACCACCAGGACCG 61.009 66.667 0.00 0.00 38.69 4.79
1276 1302 1.281925 ATGATCCCACCACCAGGACC 61.282 60.000 0.00 0.00 38.69 4.46
1277 1303 0.625849 AATGATCCCACCACCAGGAC 59.374 55.000 0.00 0.00 38.69 3.85
1278 1304 0.625316 CAATGATCCCACCACCAGGA 59.375 55.000 0.00 0.00 38.69 3.86
1279 1305 0.396139 CCAATGATCCCACCACCAGG 60.396 60.000 0.00 0.00 42.21 4.45
1280 1306 1.039233 GCCAATGATCCCACCACCAG 61.039 60.000 0.00 0.00 0.00 4.00
1281 1307 1.000233 GCCAATGATCCCACCACCA 60.000 57.895 0.00 0.00 0.00 4.17
1282 1308 2.120909 CGCCAATGATCCCACCACC 61.121 63.158 0.00 0.00 0.00 4.61
1283 1309 2.120909 CCGCCAATGATCCCACCAC 61.121 63.158 0.00 0.00 0.00 4.16
1335 1519 3.550431 CCGATGATCCCGCCACCT 61.550 66.667 0.00 0.00 0.00 4.00
1392 1582 3.616721 CCTCCTCCATACCCGCCG 61.617 72.222 0.00 0.00 0.00 6.46
1632 1822 0.396060 GGATGAGGCTGAGGTGGATC 59.604 60.000 0.00 0.00 0.00 3.36
1712 1902 3.865745 AGATCAAACGCGAACTCAATAGG 59.134 43.478 15.93 0.00 0.00 2.57
1933 2132 7.267600 GGAAAAGATAATGTAACGACAACAACG 59.732 37.037 0.00 0.00 39.59 4.10
2055 2264 3.069443 TGCAGTTTGGTCAAATTTCCCTC 59.931 43.478 0.00 0.00 32.36 4.30
2125 2334 5.831525 TGCATTTGAAGATGAGGCTTATGAT 59.168 36.000 0.00 0.00 0.00 2.45
2126 2335 5.195185 TGCATTTGAAGATGAGGCTTATGA 58.805 37.500 0.00 0.00 0.00 2.15
2128 2337 5.198965 ACTGCATTTGAAGATGAGGCTTAT 58.801 37.500 0.00 0.00 0.00 1.73
2129 2338 4.592942 ACTGCATTTGAAGATGAGGCTTA 58.407 39.130 0.00 0.00 0.00 3.09
2133 2342 5.381174 TTGAACTGCATTTGAAGATGAGG 57.619 39.130 0.00 0.00 0.00 3.86
2145 2354 6.330004 TGTGACATTGTAATTGAACTGCAT 57.670 33.333 0.00 0.00 0.00 3.96
2176 2388 4.882559 TCTTTACGGGGGAAGGAACTATA 58.117 43.478 0.00 0.00 38.49 1.31
2182 2394 6.616548 TCTTATATTTCTTTACGGGGGAAGGA 59.383 38.462 0.00 0.00 0.00 3.36
2183 2395 6.834107 TCTTATATTTCTTTACGGGGGAAGG 58.166 40.000 0.00 0.00 0.00 3.46
2184 2396 6.427242 GCTCTTATATTTCTTTACGGGGGAAG 59.573 42.308 0.00 0.00 0.00 3.46
2185 2397 6.126710 TGCTCTTATATTTCTTTACGGGGGAA 60.127 38.462 0.00 0.00 0.00 3.97
2186 2398 5.367352 TGCTCTTATATTTCTTTACGGGGGA 59.633 40.000 0.00 0.00 0.00 4.81
2187 2399 5.617252 TGCTCTTATATTTCTTTACGGGGG 58.383 41.667 0.00 0.00 0.00 5.40
2188 2400 7.745620 AATGCTCTTATATTTCTTTACGGGG 57.254 36.000 0.00 0.00 0.00 5.73
2189 2401 9.450807 CAAAATGCTCTTATATTTCTTTACGGG 57.549 33.333 0.00 0.00 0.00 5.28
2236 2448 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
2237 2449 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
2238 2450 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
2239 2451 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
2245 2457 9.268282 TCTTGTACTCCCTCTGTAAAGAAATAT 57.732 33.333 0.00 0.00 0.00 1.28
2246 2458 8.529476 GTCTTGTACTCCCTCTGTAAAGAAATA 58.471 37.037 0.00 0.00 0.00 1.40
2247 2459 7.016268 TGTCTTGTACTCCCTCTGTAAAGAAAT 59.984 37.037 0.00 0.00 0.00 2.17
2248 2460 6.325545 TGTCTTGTACTCCCTCTGTAAAGAAA 59.674 38.462 0.00 0.00 0.00 2.52
2249 2461 5.836898 TGTCTTGTACTCCCTCTGTAAAGAA 59.163 40.000 0.00 0.00 0.00 2.52
2250 2462 5.391256 TGTCTTGTACTCCCTCTGTAAAGA 58.609 41.667 0.00 0.00 0.00 2.52
2251 2463 5.723672 TGTCTTGTACTCCCTCTGTAAAG 57.276 43.478 0.00 0.00 0.00 1.85
2252 2464 7.233962 TGTTATGTCTTGTACTCCCTCTGTAAA 59.766 37.037 0.00 0.00 0.00 2.01
2253 2465 6.722590 TGTTATGTCTTGTACTCCCTCTGTAA 59.277 38.462 0.00 0.00 0.00 2.41
2254 2466 6.250711 TGTTATGTCTTGTACTCCCTCTGTA 58.749 40.000 0.00 0.00 0.00 2.74
2255 2467 5.084519 TGTTATGTCTTGTACTCCCTCTGT 58.915 41.667 0.00 0.00 0.00 3.41
2256 2468 5.661056 TGTTATGTCTTGTACTCCCTCTG 57.339 43.478 0.00 0.00 0.00 3.35
2257 2469 5.958380 TCATGTTATGTCTTGTACTCCCTCT 59.042 40.000 0.00 0.00 0.00 3.69
2258 2470 6.222038 TCATGTTATGTCTTGTACTCCCTC 57.778 41.667 0.00 0.00 0.00 4.30
2259 2471 6.814954 ATCATGTTATGTCTTGTACTCCCT 57.185 37.500 0.00 0.00 0.00 4.20
2260 2472 7.727181 AGTATCATGTTATGTCTTGTACTCCC 58.273 38.462 0.00 0.00 0.00 4.30
2261 2473 9.035607 CAAGTATCATGTTATGTCTTGTACTCC 57.964 37.037 0.00 0.00 34.08 3.85
2262 2474 8.543774 GCAAGTATCATGTTATGTCTTGTACTC 58.456 37.037 11.37 0.00 37.15 2.59
2263 2475 8.260818 AGCAAGTATCATGTTATGTCTTGTACT 58.739 33.333 11.37 0.00 37.15 2.73
2264 2476 8.425577 AGCAAGTATCATGTTATGTCTTGTAC 57.574 34.615 11.37 0.00 37.15 2.90
2393 2605 7.275920 CACAAGAAACCTACCATCTAAGCTAT 58.724 38.462 0.00 0.00 0.00 2.97
2504 5176 9.483062 CGAAAATGCAAACAAAACTTAATTTGA 57.517 25.926 8.23 0.00 41.73 2.69
2517 5189 5.288232 CAGAAGAAACACGAAAATGCAAACA 59.712 36.000 0.00 0.00 0.00 2.83
2521 5193 4.095632 TGTCAGAAGAAACACGAAAATGCA 59.904 37.500 0.00 0.00 0.00 3.96
2539 5211 7.830739 AGAATTTATTTGTAAGCCCTTGTCAG 58.169 34.615 0.00 0.00 0.00 3.51
2543 5215 9.450807 CGAATAGAATTTATTTGTAAGCCCTTG 57.549 33.333 0.00 0.00 0.00 3.61
2544 5216 9.403583 TCGAATAGAATTTATTTGTAAGCCCTT 57.596 29.630 0.00 0.00 0.00 3.95
2584 5257 9.849166 TTGAAAGTTATCGAAGTTTTCAAAACT 57.151 25.926 9.89 9.89 38.14 2.66
2590 5263 8.836959 AACAGTTGAAAGTTATCGAAGTTTTC 57.163 30.769 0.00 0.00 38.14 2.29
2598 5271 8.953990 CCAAGTTTTAACAGTTGAAAGTTATCG 58.046 33.333 18.45 9.99 32.20 2.92
2614 5287 8.155821 TGTCATTCAATCGTACCAAGTTTTAA 57.844 30.769 0.00 0.00 0.00 1.52
2616 5289 6.627395 TGTCATTCAATCGTACCAAGTTTT 57.373 33.333 0.00 0.00 0.00 2.43
2624 5297 9.988350 ACTTATGATTTTGTCATTCAATCGTAC 57.012 29.630 0.00 0.00 45.25 3.67
2649 5322 9.612620 CCATGTTTAACATCTTAGTTTCTGAAC 57.387 33.333 7.71 0.00 36.53 3.18
2650 5323 9.349713 ACCATGTTTAACATCTTAGTTTCTGAA 57.650 29.630 7.71 0.00 36.53 3.02
2651 5324 8.783093 CACCATGTTTAACATCTTAGTTTCTGA 58.217 33.333 7.71 0.00 36.53 3.27
2652 5325 8.567948 ACACCATGTTTAACATCTTAGTTTCTG 58.432 33.333 7.71 0.00 36.53 3.02
2653 5326 8.691661 ACACCATGTTTAACATCTTAGTTTCT 57.308 30.769 7.71 0.00 36.53 2.52
2654 5327 8.784043 AGACACCATGTTTAACATCTTAGTTTC 58.216 33.333 7.71 6.42 36.53 2.78
2680 5353 2.660944 GTTCGATTCCGCACGATGA 58.339 52.632 0.00 0.00 38.30 2.92


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

AutoCloner maintained by Alex Coulton.