Multiple sequence alignment - TraesCS6D01G385000

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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 TraesCS6D01G385000 chr6D 100.000 2557 0 0 1 2557 463052982 463050426 0.000000e+00 4723.0
1 TraesCS6D01G385000 chr6D 83.918 827 108 11 1648 2458 462915740 462914923 0.000000e+00 767.0
2 TraesCS6D01G385000 chr6D 91.860 86 4 3 2468 2553 462884032 462883950 1.610000e-22 117.0
3 TraesCS6D01G385000 chr6A 85.936 1678 165 40 913 2551 609739198 609737553 0.000000e+00 1725.0
4 TraesCS6D01G385000 chr6A 83.448 1601 180 50 774 2338 609636915 609635364 0.000000e+00 1410.0
5 TraesCS6D01G385000 chr6A 80.071 1124 178 20 1260 2362 609821297 609820199 0.000000e+00 793.0
6 TraesCS6D01G385000 chr6A 89.172 157 7 4 541 689 609637075 609636921 1.210000e-43 187.0
7 TraesCS6D01G385000 chr6A 93.151 73 4 1 687 758 409445638 409445566 3.480000e-19 106.0
8 TraesCS6D01G385000 chr6A 92.754 69 2 1 765 830 609739319 609739251 2.090000e-16 97.1
9 TraesCS6D01G385000 chr6B 81.257 1750 214 55 774 2474 705999648 705997964 0.000000e+00 1310.0
10 TraesCS6D01G385000 chr6B 83.702 1356 158 32 1013 2338 706158952 706157630 0.000000e+00 1221.0
11 TraesCS6D01G385000 chr6B 84.929 1201 150 6 1193 2369 705927418 705926225 0.000000e+00 1186.0
12 TraesCS6D01G385000 chr6B 84.970 1171 140 12 1193 2338 705581136 705579977 0.000000e+00 1155.0
13 TraesCS6D01G385000 chr6B 84.682 1149 134 15 1215 2336 706132509 706131376 0.000000e+00 1109.0
14 TraesCS6D01G385000 chr6B 84.676 1142 138 16 1222 2338 705896910 705895781 0.000000e+00 1105.0
15 TraesCS6D01G385000 chr6B 84.582 1148 136 18 1215 2336 705796388 705795256 0.000000e+00 1101.0
16 TraesCS6D01G385000 chr6B 84.045 1147 139 16 1215 2336 705629412 705628285 0.000000e+00 1064.0
17 TraesCS6D01G385000 chr6B 80.594 1381 199 34 1199 2545 705873554 705872209 0.000000e+00 1002.0
18 TraesCS6D01G385000 chr6B 84.985 686 33 27 37 671 706189044 706188378 1.290000e-177 632.0
19 TraesCS6D01G385000 chr6B 82.916 439 50 7 1264 1696 705642375 705641956 3.110000e-99 372.0
20 TraesCS6D01G385000 chr6B 91.765 85 7 0 2468 2552 705926126 705926042 4.470000e-23 119.0
21 TraesCS6D01G385000 chr6B 75.096 261 30 20 774 1023 706188379 706188143 3.500000e-14 89.8
22 TraesCS6D01G385000 chr2D 88.372 129 15 0 269 397 393585479 393585607 3.410000e-34 156.0
23 TraesCS6D01G385000 chr2D 86.923 130 15 2 269 397 97614388 97614516 7.370000e-31 145.0
24 TraesCS6D01G385000 chr4A 88.800 125 12 2 269 392 618156233 618156356 4.410000e-33 152.0
25 TraesCS6D01G385000 chr4A 86.466 133 16 2 269 400 547311644 547311513 7.370000e-31 145.0
26 TraesCS6D01G385000 chr4B 87.121 132 17 0 269 400 357958190 357958059 1.580000e-32 150.0
27 TraesCS6D01G385000 chr1A 87.500 128 16 0 270 397 490778203 490778076 5.700000e-32 148.0
28 TraesCS6D01G385000 chr1A 91.358 81 6 1 693 772 1304852 1304932 2.690000e-20 110.0
29 TraesCS6D01G385000 chr2A 86.822 129 17 0 269 397 531599494 531599622 7.370000e-31 145.0
30 TraesCS6D01G385000 chr4D 86.154 130 16 2 269 397 40582273 40582401 3.430000e-29 139.0
31 TraesCS6D01G385000 chr7D 98.462 65 1 0 694 758 181847285 181847349 5.780000e-22 115.0
32 TraesCS6D01G385000 chr7B 96.970 66 2 0 693 758 104001933 104001868 7.480000e-21 111.0
33 TraesCS6D01G385000 chr5A 96.970 66 2 0 693 758 115244827 115244762 7.480000e-21 111.0
34 TraesCS6D01G385000 chr7A 98.387 62 1 0 697 758 57868227 57868166 2.690000e-20 110.0
35 TraesCS6D01G385000 chr3B 96.923 65 2 0 694 758 22525461 22525397 2.690000e-20 110.0
36 TraesCS6D01G385000 chr3B 96.825 63 2 0 696 758 167775405 167775343 3.480000e-19 106.0
37 TraesCS6D01G385000 chr1D 98.387 62 1 0 697 758 77665608 77665547 2.690000e-20 110.0


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 TraesCS6D01G385000 chr6D 463050426 463052982 2556 True 4723.00 4723 100.0000 1 2557 1 chr6D.!!$R3 2556
1 TraesCS6D01G385000 chr6D 462914923 462915740 817 True 767.00 767 83.9180 1648 2458 1 chr6D.!!$R2 810
2 TraesCS6D01G385000 chr6A 609737553 609739319 1766 True 911.05 1725 89.3450 765 2551 2 chr6A.!!$R4 1786
3 TraesCS6D01G385000 chr6A 609635364 609637075 1711 True 798.50 1410 86.3100 541 2338 2 chr6A.!!$R3 1797
4 TraesCS6D01G385000 chr6A 609820199 609821297 1098 True 793.00 793 80.0710 1260 2362 1 chr6A.!!$R2 1102
5 TraesCS6D01G385000 chr6B 705997964 705999648 1684 True 1310.00 1310 81.2570 774 2474 1 chr6B.!!$R7 1700
6 TraesCS6D01G385000 chr6B 706157630 706158952 1322 True 1221.00 1221 83.7020 1013 2338 1 chr6B.!!$R9 1325
7 TraesCS6D01G385000 chr6B 705579977 705581136 1159 True 1155.00 1155 84.9700 1193 2338 1 chr6B.!!$R1 1145
8 TraesCS6D01G385000 chr6B 706131376 706132509 1133 True 1109.00 1109 84.6820 1215 2336 1 chr6B.!!$R8 1121
9 TraesCS6D01G385000 chr6B 705895781 705896910 1129 True 1105.00 1105 84.6760 1222 2338 1 chr6B.!!$R6 1116
10 TraesCS6D01G385000 chr6B 705795256 705796388 1132 True 1101.00 1101 84.5820 1215 2336 1 chr6B.!!$R4 1121
11 TraesCS6D01G385000 chr6B 705628285 705629412 1127 True 1064.00 1064 84.0450 1215 2336 1 chr6B.!!$R2 1121
12 TraesCS6D01G385000 chr6B 705872209 705873554 1345 True 1002.00 1002 80.5940 1199 2545 1 chr6B.!!$R5 1346
13 TraesCS6D01G385000 chr6B 705926042 705927418 1376 True 652.50 1186 88.3470 1193 2552 2 chr6B.!!$R10 1359
14 TraesCS6D01G385000 chr6B 706188143 706189044 901 True 360.90 632 80.0405 37 1023 2 chr6B.!!$R11 986

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
928 1027 0.035725 CTCAACCAGCTGAGCATCCA 60.036 55.0 17.39 0.0 36.67 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2221 0.036388 TGGGAGATGACCTGCGAAAC 60.036 55.0 0.0 0.0 33.55 2.78 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
23 24 3.396260 AAGCTTGGTAGAACGCTTACA 57.604 42.857 0.00 0.00 40.59 2.41
24 25 3.396260 AGCTTGGTAGAACGCTTACAA 57.604 42.857 0.00 0.00 0.00 2.41
25 26 3.939066 AGCTTGGTAGAACGCTTACAAT 58.061 40.909 0.00 0.00 0.00 2.71
26 27 5.080969 AGCTTGGTAGAACGCTTACAATA 57.919 39.130 0.00 0.00 0.00 1.90
27 28 5.671493 AGCTTGGTAGAACGCTTACAATAT 58.329 37.500 0.00 0.00 0.00 1.28
28 29 6.113411 AGCTTGGTAGAACGCTTACAATATT 58.887 36.000 0.00 0.00 0.00 1.28
29 30 6.598064 AGCTTGGTAGAACGCTTACAATATTT 59.402 34.615 0.00 0.00 0.00 1.40
30 31 7.120726 AGCTTGGTAGAACGCTTACAATATTTT 59.879 33.333 0.00 0.00 0.00 1.82
31 32 7.753580 GCTTGGTAGAACGCTTACAATATTTTT 59.246 33.333 0.00 0.00 0.00 1.94
32 33 8.958175 TTGGTAGAACGCTTACAATATTTTTG 57.042 30.769 0.00 0.00 0.00 2.44
33 34 8.325421 TGGTAGAACGCTTACAATATTTTTGA 57.675 30.769 0.00 0.00 0.00 2.69
34 35 8.231837 TGGTAGAACGCTTACAATATTTTTGAC 58.768 33.333 0.00 0.00 0.00 3.18
35 36 7.424452 GGTAGAACGCTTACAATATTTTTGACG 59.576 37.037 0.00 0.00 0.00 4.35
36 37 5.793457 AGAACGCTTACAATATTTTTGACGC 59.207 36.000 0.00 0.00 0.00 5.19
37 38 4.085884 ACGCTTACAATATTTTTGACGCG 58.914 39.130 3.53 3.53 38.09 6.01
38 39 3.477090 CGCTTACAATATTTTTGACGCGG 59.523 43.478 12.47 0.00 33.34 6.46
39 40 3.789224 GCTTACAATATTTTTGACGCGGG 59.211 43.478 12.47 0.00 0.00 6.13
40 41 4.437659 GCTTACAATATTTTTGACGCGGGA 60.438 41.667 12.47 0.00 0.00 5.14
41 42 5.732247 GCTTACAATATTTTTGACGCGGGAT 60.732 40.000 12.47 0.00 0.00 3.85
46 47 0.035820 TTTTTGACGCGGGATAGCCT 60.036 50.000 12.47 0.00 0.00 4.58
67 68 0.308993 GTTCACACAACAGCCTCAGC 59.691 55.000 0.00 0.00 40.32 4.26
115 116 0.765510 AGGGGACTGGTGAGTTGTTC 59.234 55.000 0.00 0.00 41.13 3.18
145 146 2.555757 GTGGCAAAGACTTGATGCTCTT 59.444 45.455 10.82 0.00 39.94 2.85
174 175 6.428771 TCCATAACCTTAAAAACGTCTTCCAG 59.571 38.462 0.00 0.00 0.00 3.86
198 199 3.312736 TTTTCAGGTTTCCAAGGCTCT 57.687 42.857 0.00 0.00 0.00 4.09
199 200 2.276732 TTCAGGTTTCCAAGGCTCTG 57.723 50.000 0.00 0.00 0.00 3.35
200 201 1.140312 TCAGGTTTCCAAGGCTCTGT 58.860 50.000 0.00 0.00 0.00 3.41
307 312 4.556592 AATAACATTGGCTTGGCATTGT 57.443 36.364 15.59 15.59 0.00 2.71
379 402 6.607689 TGACTTTGGACAAAACTTATATGCG 58.392 36.000 0.00 0.00 0.00 4.73
389 412 9.274065 GACAAAACTTATATGCGGACTAAAAAG 57.726 33.333 0.00 0.00 0.00 2.27
393 416 6.053650 ACTTATATGCGGACTAAAAAGGACC 58.946 40.000 0.00 0.00 0.00 4.46
404 446 1.497309 AAAAGGACCGGATGGCCTCA 61.497 55.000 9.46 0.00 39.82 3.86
405 447 1.497309 AAAGGACCGGATGGCCTCAA 61.497 55.000 9.46 0.00 39.82 3.02
422 464 6.127647 TGGCCTCAAGCTTAATTAAAGACATG 60.128 38.462 3.32 0.00 43.05 3.21
423 465 6.095440 GGCCTCAAGCTTAATTAAAGACATGA 59.905 38.462 0.00 1.02 43.05 3.07
426 468 9.727627 CCTCAAGCTTAATTAAAGACATGAATC 57.272 33.333 0.00 0.00 37.38 2.52
432 474 9.674824 GCTTAATTAAAGACATGAATCAGGATG 57.325 33.333 0.58 0.00 37.38 3.51
438 480 9.695526 TTAAAGACATGAATCAGGATGTTTTTG 57.304 29.630 0.58 0.00 37.42 2.44
455 498 5.047943 TGTTTTTGTATATTTCACGGTGGGG 60.048 40.000 8.50 0.00 0.00 4.96
480 523 1.958715 CCCGACACGTGTGCATTCA 60.959 57.895 28.82 0.00 0.00 2.57
482 525 0.095245 CCGACACGTGTGCATTCATC 59.905 55.000 28.82 7.86 0.00 2.92
494 537 1.678728 GCATTCATCGTGTCCCTTCCA 60.679 52.381 0.00 0.00 0.00 3.53
528 571 1.002069 TCCAGGGTCAATTGGAGCAT 58.998 50.000 5.42 0.00 45.90 3.79
529 572 1.064463 TCCAGGGTCAATTGGAGCATC 60.064 52.381 5.42 0.00 45.90 3.91
530 573 1.019673 CAGGGTCAATTGGAGCATCG 58.980 55.000 5.42 0.00 45.90 3.84
531 574 0.620556 AGGGTCAATTGGAGCATCGT 59.379 50.000 5.42 0.00 45.90 3.73
532 575 1.837439 AGGGTCAATTGGAGCATCGTA 59.163 47.619 5.42 0.00 45.90 3.43
533 576 2.439507 AGGGTCAATTGGAGCATCGTAT 59.560 45.455 5.42 0.00 45.90 3.06
534 577 2.808543 GGGTCAATTGGAGCATCGTATC 59.191 50.000 5.42 0.00 45.90 2.24
535 578 3.466836 GGTCAATTGGAGCATCGTATCA 58.533 45.455 5.42 0.00 43.54 2.15
536 579 3.248602 GGTCAATTGGAGCATCGTATCAC 59.751 47.826 5.42 0.00 43.54 3.06
537 580 3.248602 GTCAATTGGAGCATCGTATCACC 59.751 47.826 5.42 0.00 34.37 4.02
538 581 3.134623 TCAATTGGAGCATCGTATCACCT 59.865 43.478 5.42 0.00 34.37 4.00
539 582 2.602257 TTGGAGCATCGTATCACCTG 57.398 50.000 0.00 0.00 34.37 4.00
567 610 1.665679 GTATCACCAGATGTGTTGCCG 59.334 52.381 0.00 0.00 45.61 5.69
609 652 4.343231 TGCAGCTGATTTTAATTCCTCCA 58.657 39.130 20.43 0.00 0.00 3.86
611 654 4.731773 GCAGCTGATTTTAATTCCTCCACG 60.732 45.833 20.43 0.00 0.00 4.94
612 655 4.396166 CAGCTGATTTTAATTCCTCCACGT 59.604 41.667 8.42 0.00 0.00 4.49
614 657 4.394920 GCTGATTTTAATTCCTCCACGTGA 59.605 41.667 19.30 2.03 0.00 4.35
615 658 5.066505 GCTGATTTTAATTCCTCCACGTGAT 59.933 40.000 19.30 0.00 0.00 3.06
616 659 6.435430 TGATTTTAATTCCTCCACGTGATG 57.565 37.500 19.30 8.96 0.00 3.07
637 686 1.618447 GCCCCCTCCTTCCTTGGTA 60.618 63.158 0.00 0.00 0.00 3.25
670 719 4.504916 CTCCGCGGAGACTGGCTG 62.505 72.222 45.28 20.53 44.53 4.85
674 723 4.459089 GCGGAGACTGGCTGGGTC 62.459 72.222 0.00 0.00 0.00 4.46
675 724 4.135153 CGGAGACTGGCTGGGTCG 62.135 72.222 0.00 0.00 38.58 4.79
676 725 4.459089 GGAGACTGGCTGGGTCGC 62.459 72.222 0.00 0.00 38.58 5.19
677 726 4.803426 GAGACTGGCTGGGTCGCG 62.803 72.222 0.00 0.00 38.58 5.87
694 743 3.479269 GTCGCGCGCTGCTAGTTT 61.479 61.111 30.48 0.00 43.27 2.66
695 744 3.179265 TCGCGCGCTGCTAGTTTC 61.179 61.111 30.48 0.00 43.27 2.78
696 745 3.181967 CGCGCGCTGCTAGTTTCT 61.182 61.111 30.48 0.00 43.27 2.52
697 746 1.872234 CGCGCGCTGCTAGTTTCTA 60.872 57.895 30.48 0.00 43.27 2.10
698 747 1.631595 GCGCGCTGCTAGTTTCTAC 59.368 57.895 26.67 0.00 41.73 2.59
699 748 0.802607 GCGCGCTGCTAGTTTCTACT 60.803 55.000 26.67 0.00 41.73 2.57
700 749 1.192793 CGCGCTGCTAGTTTCTACTC 58.807 55.000 5.56 0.00 35.78 2.59
701 750 1.562017 GCGCTGCTAGTTTCTACTCC 58.438 55.000 0.00 0.00 35.78 3.85
702 751 1.803252 GCGCTGCTAGTTTCTACTCCC 60.803 57.143 0.00 0.00 35.78 4.30
703 752 1.751924 CGCTGCTAGTTTCTACTCCCT 59.248 52.381 0.00 0.00 35.78 4.20
704 753 2.223618 CGCTGCTAGTTTCTACTCCCTC 60.224 54.545 0.00 0.00 35.78 4.30
705 754 2.101750 GCTGCTAGTTTCTACTCCCTCC 59.898 54.545 0.00 0.00 35.78 4.30
706 755 2.359531 CTGCTAGTTTCTACTCCCTCCG 59.640 54.545 0.00 0.00 35.78 4.63
707 756 2.291411 TGCTAGTTTCTACTCCCTCCGT 60.291 50.000 0.00 0.00 35.78 4.69
708 757 2.759535 GCTAGTTTCTACTCCCTCCGTT 59.240 50.000 0.00 0.00 35.78 4.44
709 758 3.195182 GCTAGTTTCTACTCCCTCCGTTT 59.805 47.826 0.00 0.00 35.78 3.60
710 759 3.957591 AGTTTCTACTCCCTCCGTTTC 57.042 47.619 0.00 0.00 0.00 2.78
711 760 3.508426 AGTTTCTACTCCCTCCGTTTCT 58.492 45.455 0.00 0.00 0.00 2.52
712 761 4.670765 AGTTTCTACTCCCTCCGTTTCTA 58.329 43.478 0.00 0.00 0.00 2.10
713 762 5.082425 AGTTTCTACTCCCTCCGTTTCTAA 58.918 41.667 0.00 0.00 0.00 2.10
714 763 5.541484 AGTTTCTACTCCCTCCGTTTCTAAA 59.459 40.000 0.00 0.00 0.00 1.85
715 764 6.212993 AGTTTCTACTCCCTCCGTTTCTAAAT 59.787 38.462 0.00 0.00 0.00 1.40
716 765 7.398332 AGTTTCTACTCCCTCCGTTTCTAAATA 59.602 37.037 0.00 0.00 0.00 1.40
717 766 6.705863 TCTACTCCCTCCGTTTCTAAATAC 57.294 41.667 0.00 0.00 0.00 1.89
718 767 6.430007 TCTACTCCCTCCGTTTCTAAATACT 58.570 40.000 0.00 0.00 0.00 2.12
719 768 6.894103 TCTACTCCCTCCGTTTCTAAATACTT 59.106 38.462 0.00 0.00 0.00 2.24
720 769 5.731591 ACTCCCTCCGTTTCTAAATACTTG 58.268 41.667 0.00 0.00 0.00 3.16
721 770 5.247792 ACTCCCTCCGTTTCTAAATACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
722 771 5.727434 TCCCTCCGTTTCTAAATACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
723 772 5.482878 TCCCTCCGTTTCTAAATACTTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
724 773 6.013984 TCCCTCCGTTTCTAAATACTTGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
725 774 6.653740 CCCTCCGTTTCTAAATACTTGTCTTT 59.346 38.462 0.00 0.00 0.00 2.52
726 775 7.174426 CCCTCCGTTTCTAAATACTTGTCTTTT 59.826 37.037 0.00 0.00 0.00 2.27
727 776 8.565416 CCTCCGTTTCTAAATACTTGTCTTTTT 58.435 33.333 0.00 0.00 0.00 1.94
730 779 9.821662 CCGTTTCTAAATACTTGTCTTTTTAGG 57.178 33.333 0.00 0.00 34.13 2.69
731 780 9.326339 CGTTTCTAAATACTTGTCTTTTTAGGC 57.674 33.333 0.00 0.00 34.13 3.93
742 791 9.313118 ACTTGTCTTTTTAGGCATTTTAACAAG 57.687 29.630 0.00 0.00 43.26 3.16
743 792 9.313118 CTTGTCTTTTTAGGCATTTTAACAAGT 57.687 29.630 0.00 0.00 36.66 3.16
744 793 8.641499 TGTCTTTTTAGGCATTTTAACAAGTG 57.359 30.769 0.00 0.00 0.00 3.16
745 794 8.470805 TGTCTTTTTAGGCATTTTAACAAGTGA 58.529 29.630 0.00 0.00 0.00 3.41
746 795 8.752254 GTCTTTTTAGGCATTTTAACAAGTGAC 58.248 33.333 0.00 0.00 0.00 3.67
747 796 8.691797 TCTTTTTAGGCATTTTAACAAGTGACT 58.308 29.630 0.00 0.00 40.91 3.41
748 797 9.959749 CTTTTTAGGCATTTTAACAAGTGACTA 57.040 29.630 0.00 0.00 38.82 2.59
749 798 9.738832 TTTTTAGGCATTTTAACAAGTGACTAC 57.261 29.630 0.00 0.00 39.37 2.73
750 799 8.453238 TTTAGGCATTTTAACAAGTGACTACA 57.547 30.769 0.00 0.00 39.37 2.74
751 800 8.630054 TTAGGCATTTTAACAAGTGACTACAT 57.370 30.769 0.00 0.00 39.37 2.29
752 801 9.727859 TTAGGCATTTTAACAAGTGACTACATA 57.272 29.630 0.00 0.00 39.37 2.29
753 802 8.040716 AGGCATTTTAACAAGTGACTACATAC 57.959 34.615 0.00 0.00 36.22 2.39
754 803 6.959311 GGCATTTTAACAAGTGACTACATACG 59.041 38.462 0.00 0.00 0.00 3.06
755 804 6.959311 GCATTTTAACAAGTGACTACATACGG 59.041 38.462 0.00 0.00 0.00 4.02
756 805 7.148540 GCATTTTAACAAGTGACTACATACGGA 60.149 37.037 0.00 0.00 0.00 4.69
757 806 7.878477 TTTTAACAAGTGACTACATACGGAG 57.122 36.000 0.00 0.00 0.00 4.63
758 807 4.451629 AACAAGTGACTACATACGGAGG 57.548 45.455 0.00 0.00 0.00 4.30
759 808 2.758979 ACAAGTGACTACATACGGAGGG 59.241 50.000 0.00 0.00 0.00 4.30
760 809 3.021695 CAAGTGACTACATACGGAGGGA 58.978 50.000 0.00 0.00 0.00 4.20
761 810 2.933573 AGTGACTACATACGGAGGGAG 58.066 52.381 0.00 0.00 0.00 4.30
762 811 2.241685 AGTGACTACATACGGAGGGAGT 59.758 50.000 0.00 0.00 0.00 3.85
763 812 3.457380 AGTGACTACATACGGAGGGAGTA 59.543 47.826 0.00 0.00 0.00 2.59
771 820 6.890979 ACATACGGAGGGAGTAGTATTTAC 57.109 41.667 0.00 0.00 0.00 2.01
830 906 0.974383 TTGAGGTCTTCCTTCCGGTC 59.026 55.000 0.00 0.00 45.24 4.79
831 907 0.178944 TGAGGTCTTCCTTCCGGTCA 60.179 55.000 0.00 0.00 45.24 4.02
837 924 1.550524 TCTTCCTTCCGGTCAGACATG 59.449 52.381 0.00 0.00 0.00 3.21
838 925 0.613260 TTCCTTCCGGTCAGACATGG 59.387 55.000 0.00 3.77 0.00 3.66
840 927 0.108138 CCTTCCGGTCAGACATGGTC 60.108 60.000 0.00 0.00 0.00 4.02
842 929 0.320374 TTCCGGTCAGACATGGTCAC 59.680 55.000 0.00 0.00 34.60 3.67
852 939 4.469586 TCAGACATGGTCACAAGGCTAATA 59.530 41.667 0.00 0.00 30.44 0.98
854 941 5.295292 CAGACATGGTCACAAGGCTAATAAG 59.705 44.000 0.00 0.00 30.44 1.73
855 942 5.045578 AGACATGGTCACAAGGCTAATAAGT 60.046 40.000 0.00 0.00 30.44 2.24
856 943 4.943705 ACATGGTCACAAGGCTAATAAGTG 59.056 41.667 0.00 0.00 0.00 3.16
857 944 4.634012 TGGTCACAAGGCTAATAAGTGT 57.366 40.909 0.00 0.00 0.00 3.55
858 945 4.323417 TGGTCACAAGGCTAATAAGTGTG 58.677 43.478 8.16 8.16 40.72 3.82
863 950 4.156008 CACAAGGCTAATAAGTGTGGGAAC 59.844 45.833 6.82 0.00 36.72 3.62
864 951 3.261981 AGGCTAATAAGTGTGGGAACG 57.738 47.619 0.00 0.00 0.00 3.95
865 952 1.669265 GGCTAATAAGTGTGGGAACGC 59.331 52.381 0.00 0.00 42.66 4.84
866 953 1.326548 GCTAATAAGTGTGGGAACGCG 59.673 52.381 3.53 3.53 46.31 6.01
921 1020 3.650950 GGGGCCTCAACCAGCTGA 61.651 66.667 17.39 0.00 0.00 4.26
922 1021 2.045536 GGGCCTCAACCAGCTGAG 60.046 66.667 17.39 8.04 42.19 3.35
923 1022 2.749441 GGCCTCAACCAGCTGAGC 60.749 66.667 17.39 7.71 41.36 4.26
924 1023 2.033141 GCCTCAACCAGCTGAGCA 59.967 61.111 17.39 0.00 41.36 4.26
925 1024 1.378250 GCCTCAACCAGCTGAGCAT 60.378 57.895 17.39 0.00 41.36 3.79
926 1025 1.375098 GCCTCAACCAGCTGAGCATC 61.375 60.000 17.39 0.00 41.36 3.91
927 1026 0.747283 CCTCAACCAGCTGAGCATCC 60.747 60.000 17.39 0.00 41.36 3.51
928 1027 0.035725 CTCAACCAGCTGAGCATCCA 60.036 55.000 17.39 0.00 36.67 3.41
929 1028 0.035725 TCAACCAGCTGAGCATCCAG 60.036 55.000 17.39 0.00 37.23 3.86
934 1033 0.035725 CAGCTGAGCATCCAGTCCAA 60.036 55.000 8.42 0.00 36.57 3.53
975 1078 2.281761 GGCACACACACCCCTCAG 60.282 66.667 0.00 0.00 0.00 3.35
977 1080 1.598130 GCACACACACCCCTCAGAC 60.598 63.158 0.00 0.00 0.00 3.51
1055 1158 3.432046 CCAAGCAAAGGTGTCCAAACATT 60.432 43.478 0.00 0.00 37.81 2.71
1084 1187 1.082104 CTTGCCGTCGGTTTTCTGC 60.082 57.895 13.94 0.00 0.00 4.26
1128 1242 7.611467 ACAAAATCAAACCTCTGTGCTATGATA 59.389 33.333 0.00 0.00 0.00 2.15
1183 1301 9.624697 TTTACATGCATGAGTTCTAATGTTTTC 57.375 29.630 32.75 0.00 31.19 2.29
1185 1303 7.310664 ACATGCATGAGTTCTAATGTTTTCTG 58.689 34.615 32.75 1.05 0.00 3.02
1191 1309 9.270576 CATGAGTTCTAATGTTTTCTGAATTCG 57.729 33.333 0.04 0.00 0.00 3.34
1196 1314 7.962964 TCTAATGTTTTCTGAATTCGTCACT 57.037 32.000 0.04 0.00 31.13 3.41
1238 1359 1.670083 GTGTACCAGTCAACCCGCC 60.670 63.158 0.00 0.00 0.00 6.13
1276 1397 0.951040 AAGTTACTGTCGCTGCTGCC 60.951 55.000 10.24 0.00 35.36 4.85
1485 1615 2.202987 GGCGAGTCATGGAGCTGG 60.203 66.667 0.00 0.00 0.00 4.85
1495 1625 0.908198 ATGGAGCTGGACCTTCACTC 59.092 55.000 0.00 0.00 0.00 3.51
1503 1633 0.389757 GGACCTTCACTCCCTATCGC 59.610 60.000 0.00 0.00 0.00 4.58
1549 1679 4.499357 CCTCGGGAATCTAACGTTCCTTAG 60.499 50.000 2.82 0.00 43.70 2.18
1550 1680 3.382546 TCGGGAATCTAACGTTCCTTAGG 59.617 47.826 2.82 0.00 43.70 2.69
1551 1681 3.382546 CGGGAATCTAACGTTCCTTAGGA 59.617 47.826 2.82 0.00 43.70 2.94
1552 1682 4.499357 CGGGAATCTAACGTTCCTTAGGAG 60.499 50.000 2.82 0.00 43.70 3.69
1553 1683 4.405036 GGGAATCTAACGTTCCTTAGGAGT 59.595 45.833 2.82 0.00 43.70 3.85
1688 1818 4.951715 TCCGGATACTCTTACAAACTGCTA 59.048 41.667 0.00 0.00 0.00 3.49
1726 1871 7.945109 GCAATTTACTAATAGGAGAAATCCCCT 59.055 37.037 0.00 0.00 36.60 4.79
1734 1879 6.882768 ATAGGAGAAATCCCCTGTGATATC 57.117 41.667 0.00 0.00 34.11 1.63
1758 1903 2.027745 CCGCCTATCCAATCTAGTGCAT 60.028 50.000 0.00 0.00 0.00 3.96
1765 1910 7.609532 GCCTATCCAATCTAGTGCATTTAGATT 59.390 37.037 21.49 21.49 44.58 2.40
1841 1987 1.396301 GCTTCAACTGATCTCGCTTGG 59.604 52.381 0.00 0.00 0.00 3.61
2079 2225 4.766375 TCGGATTGGAGGATAACAGTTTC 58.234 43.478 0.00 0.00 0.00 2.78
2081 2227 3.312697 GGATTGGAGGATAACAGTTTCGC 59.687 47.826 0.00 0.00 0.00 4.70
2100 2246 2.105128 GGTCATCTCCCAGCGTCG 59.895 66.667 0.00 0.00 0.00 5.12
2131 2277 7.227156 CAATATTTCAGGGCTAGAGTGGTTAT 58.773 38.462 0.00 0.00 0.00 1.89
2158 2304 6.378710 TGTCATTCAACAATTTCGTTGGTA 57.621 33.333 8.36 0.00 45.16 3.25
2172 2318 3.878699 TCGTTGGTAAAGTTCCAAGTTCC 59.121 43.478 0.00 0.00 44.21 3.62
2214 2360 3.832527 ACAACACCTAAACCTTCAGCAT 58.167 40.909 0.00 0.00 0.00 3.79
2223 2369 8.519526 CACCTAAACCTTCAGCATAACAATTTA 58.480 33.333 0.00 0.00 0.00 1.40
2240 2386 3.374042 TTTATCGGGCTTCATCCCAAA 57.626 42.857 0.00 0.00 46.92 3.28
2260 2406 2.675658 AGAGCTGGGTGGCTTAAAAA 57.324 45.000 0.00 0.00 43.20 1.94
2391 2566 1.271982 GGGGACTTCTTTGGAGGAACC 60.272 57.143 0.00 0.00 39.54 3.62
2407 2582 0.990374 AACCAAGGATCAGCTGCTCT 59.010 50.000 16.61 7.40 0.00 4.09
2418 2593 1.755959 CAGCTGCTCTCATGTCCTACT 59.244 52.381 0.00 0.00 0.00 2.57
2419 2594 2.954989 CAGCTGCTCTCATGTCCTACTA 59.045 50.000 0.00 0.00 0.00 1.82
2420 2595 3.573538 CAGCTGCTCTCATGTCCTACTAT 59.426 47.826 0.00 0.00 0.00 2.12
2421 2596 3.826157 AGCTGCTCTCATGTCCTACTATC 59.174 47.826 0.00 0.00 0.00 2.08
2422 2597 3.826157 GCTGCTCTCATGTCCTACTATCT 59.174 47.826 0.00 0.00 0.00 1.98
2431 2606 7.397761 TCTCATGTCCTACTATCTATCTCTCGA 59.602 40.741 0.00 0.00 0.00 4.04
2446 2621 9.542462 TCTATCTCTCGAAGAAAAGAAACAAAA 57.458 29.630 2.21 0.00 37.61 2.44
2534 2743 7.568349 AGATGTCAAGAGCAAACCTATCATTA 58.432 34.615 0.00 0.00 0.00 1.90
2535 2744 6.985188 TGTCAAGAGCAAACCTATCATTAC 57.015 37.500 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.484715 TGTAAGCGTTCTACCAAGCTTTAT 58.515 37.500 6.85 0.00 46.36 1.40
1 2 4.885413 TGTAAGCGTTCTACCAAGCTTTA 58.115 39.130 6.85 0.00 46.36 1.85
5 6 5.986004 ATATTGTAAGCGTTCTACCAAGC 57.014 39.130 0.00 0.00 0.00 4.01
6 7 9.061610 CAAAAATATTGTAAGCGTTCTACCAAG 57.938 33.333 0.00 0.00 0.00 3.61
7 8 8.784994 TCAAAAATATTGTAAGCGTTCTACCAA 58.215 29.630 0.00 0.00 0.00 3.67
8 9 8.231837 GTCAAAAATATTGTAAGCGTTCTACCA 58.768 33.333 0.00 0.00 0.00 3.25
9 10 7.424452 CGTCAAAAATATTGTAAGCGTTCTACC 59.576 37.037 0.00 0.00 0.00 3.18
10 11 7.045804 GCGTCAAAAATATTGTAAGCGTTCTAC 60.046 37.037 0.00 0.00 0.00 2.59
11 12 6.957077 GCGTCAAAAATATTGTAAGCGTTCTA 59.043 34.615 0.00 0.00 0.00 2.10
12 13 5.793457 GCGTCAAAAATATTGTAAGCGTTCT 59.207 36.000 0.00 0.00 0.00 3.01
13 14 5.274641 CGCGTCAAAAATATTGTAAGCGTTC 60.275 40.000 0.00 0.00 39.19 3.95
14 15 4.551892 CGCGTCAAAAATATTGTAAGCGTT 59.448 37.500 0.00 0.00 39.19 4.84
15 16 4.085884 CGCGTCAAAAATATTGTAAGCGT 58.914 39.130 0.00 0.00 39.19 5.07
16 17 3.477090 CCGCGTCAAAAATATTGTAAGCG 59.523 43.478 4.92 12.93 42.92 4.68
17 18 3.789224 CCCGCGTCAAAAATATTGTAAGC 59.211 43.478 4.92 0.00 0.00 3.09
18 19 5.224562 TCCCGCGTCAAAAATATTGTAAG 57.775 39.130 4.92 0.00 0.00 2.34
19 20 5.821516 ATCCCGCGTCAAAAATATTGTAA 57.178 34.783 4.92 0.00 0.00 2.41
20 21 5.049954 GCTATCCCGCGTCAAAAATATTGTA 60.050 40.000 4.92 0.00 0.00 2.41
21 22 4.261031 GCTATCCCGCGTCAAAAATATTGT 60.261 41.667 4.92 0.00 0.00 2.71
22 23 4.219033 GCTATCCCGCGTCAAAAATATTG 58.781 43.478 4.92 0.00 0.00 1.90
23 24 3.252458 GGCTATCCCGCGTCAAAAATATT 59.748 43.478 4.92 0.00 0.00 1.28
24 25 2.812011 GGCTATCCCGCGTCAAAAATAT 59.188 45.455 4.92 0.00 0.00 1.28
25 26 2.158871 AGGCTATCCCGCGTCAAAAATA 60.159 45.455 4.92 0.00 39.21 1.40
26 27 1.021968 GGCTATCCCGCGTCAAAAAT 58.978 50.000 4.92 0.00 0.00 1.82
27 28 0.035820 AGGCTATCCCGCGTCAAAAA 60.036 50.000 4.92 0.00 39.21 1.94
28 29 0.742990 CAGGCTATCCCGCGTCAAAA 60.743 55.000 4.92 0.00 39.21 2.44
29 30 1.153449 CAGGCTATCCCGCGTCAAA 60.153 57.895 4.92 0.00 39.21 2.69
30 31 2.499205 CAGGCTATCCCGCGTCAA 59.501 61.111 4.92 0.00 39.21 3.18
31 32 3.536917 CCAGGCTATCCCGCGTCA 61.537 66.667 4.92 0.00 39.21 4.35
32 33 2.973180 GAACCAGGCTATCCCGCGTC 62.973 65.000 4.92 0.00 39.21 5.19
33 34 3.081409 AACCAGGCTATCCCGCGT 61.081 61.111 4.92 0.00 39.21 6.01
34 35 2.280186 GAACCAGGCTATCCCGCG 60.280 66.667 0.00 0.00 39.21 6.46
35 36 1.523938 GTGAACCAGGCTATCCCGC 60.524 63.158 0.00 0.00 39.21 6.13
36 37 0.462047 GTGTGAACCAGGCTATCCCG 60.462 60.000 0.00 0.00 39.21 5.14
37 38 0.618458 TGTGTGAACCAGGCTATCCC 59.382 55.000 0.00 0.00 0.00 3.85
38 39 2.084546 GTTGTGTGAACCAGGCTATCC 58.915 52.381 0.00 0.00 0.00 2.59
39 40 2.744202 CTGTTGTGTGAACCAGGCTATC 59.256 50.000 0.00 0.00 0.00 2.08
40 41 2.783135 CTGTTGTGTGAACCAGGCTAT 58.217 47.619 0.00 0.00 0.00 2.97
41 42 1.813862 GCTGTTGTGTGAACCAGGCTA 60.814 52.381 0.00 0.00 0.00 3.93
46 47 0.254462 TGAGGCTGTTGTGTGAACCA 59.746 50.000 0.00 0.00 0.00 3.67
67 68 3.495193 CAAAAATGCGGACATCAGTGAG 58.505 45.455 0.00 0.00 34.62 3.51
73 74 2.155539 GTGTTGCAAAAATGCGGACATC 59.844 45.455 0.00 4.61 36.43 3.06
115 116 0.928229 GTCTTTGCCACGGCGTATAG 59.072 55.000 14.22 5.80 45.51 1.31
174 175 3.321968 AGCCTTGGAAACCTGAAAATCAC 59.678 43.478 0.00 0.00 0.00 3.06
198 199 2.167662 TGCACTCGAGTATCTTCCACA 58.832 47.619 19.57 3.92 0.00 4.17
199 200 2.941453 TGCACTCGAGTATCTTCCAC 57.059 50.000 19.57 1.32 0.00 4.02
200 201 2.101415 CCATGCACTCGAGTATCTTCCA 59.899 50.000 19.57 8.93 0.00 3.53
235 236 6.361433 TCCTTATGAAACCTTCAAACACTCA 58.639 36.000 0.00 0.00 43.95 3.41
296 301 3.029320 TCAACATTCACAATGCCAAGC 57.971 42.857 0.00 0.00 42.69 4.01
297 302 5.957798 AGTATCAACATTCACAATGCCAAG 58.042 37.500 0.00 0.00 42.69 3.61
352 358 9.255304 GCATATAAGTTTTGTCCAAAGTCAAAA 57.745 29.630 0.00 0.00 38.24 2.44
358 381 6.027749 GTCCGCATATAAGTTTTGTCCAAAG 58.972 40.000 0.00 0.00 0.00 2.77
361 384 4.839121 AGTCCGCATATAAGTTTTGTCCA 58.161 39.130 0.00 0.00 0.00 4.02
364 387 8.241367 CCTTTTTAGTCCGCATATAAGTTTTGT 58.759 33.333 0.00 0.00 0.00 2.83
379 402 2.640184 CCATCCGGTCCTTTTTAGTCC 58.360 52.381 0.00 0.00 0.00 3.85
389 412 2.190578 CTTGAGGCCATCCGGTCC 59.809 66.667 5.01 0.00 37.79 4.46
393 416 1.972872 ATTAAGCTTGAGGCCATCCG 58.027 50.000 9.86 0.00 43.05 4.18
404 446 9.466497 TCCTGATTCATGTCTTTAATTAAGCTT 57.534 29.630 3.48 3.48 33.66 3.74
405 447 9.638176 ATCCTGATTCATGTCTTTAATTAAGCT 57.362 29.630 0.00 0.00 33.66 3.74
423 465 9.787532 CGTGAAATATACAAAAACATCCTGATT 57.212 29.630 0.00 0.00 0.00 2.57
426 468 7.484641 CACCGTGAAATATACAAAAACATCCTG 59.515 37.037 0.00 0.00 0.00 3.86
432 474 5.404096 CCCCACCGTGAAATATACAAAAAC 58.596 41.667 0.00 0.00 0.00 2.43
438 480 2.809299 GCTCCCCCACCGTGAAATATAC 60.809 54.545 0.00 0.00 0.00 1.47
480 523 1.697432 TCTTGTTGGAAGGGACACGAT 59.303 47.619 0.00 0.00 0.00 3.73
482 525 2.076863 GATCTTGTTGGAAGGGACACG 58.923 52.381 0.00 0.00 0.00 4.49
494 537 2.504367 CCTGGACCGTTTGATCTTGTT 58.496 47.619 0.00 0.00 0.00 2.83
533 576 1.190643 TGATACGGCATCACAGGTGA 58.809 50.000 4.37 4.37 44.59 4.02
534 577 3.758715 TGATACGGCATCACAGGTG 57.241 52.632 0.00 0.00 38.79 4.00
567 610 2.568090 CGCATCTTGTGGTTGCCC 59.432 61.111 0.00 0.00 37.35 5.36
593 636 6.435430 CATCACGTGGAGGAATTAAAATCA 57.565 37.500 17.00 0.00 0.00 2.57
680 729 0.802607 AGTAGAAACTAGCAGCGCGC 60.803 55.000 26.66 26.66 42.91 6.86
681 730 1.192793 GAGTAGAAACTAGCAGCGCG 58.807 55.000 0.00 0.00 35.56 6.86
682 731 1.562017 GGAGTAGAAACTAGCAGCGC 58.438 55.000 0.00 0.00 35.56 5.92
683 732 1.751924 AGGGAGTAGAAACTAGCAGCG 59.248 52.381 0.00 0.00 35.56 5.18
684 733 2.101750 GGAGGGAGTAGAAACTAGCAGC 59.898 54.545 0.00 0.00 35.56 5.25
685 734 2.359531 CGGAGGGAGTAGAAACTAGCAG 59.640 54.545 0.00 0.00 35.56 4.24
686 735 2.291411 ACGGAGGGAGTAGAAACTAGCA 60.291 50.000 0.00 0.00 35.56 3.49
687 736 2.377073 ACGGAGGGAGTAGAAACTAGC 58.623 52.381 0.00 0.00 35.56 3.42
688 737 4.705991 AGAAACGGAGGGAGTAGAAACTAG 59.294 45.833 0.00 0.00 35.56 2.57
689 738 4.670765 AGAAACGGAGGGAGTAGAAACTA 58.329 43.478 0.00 0.00 35.56 2.24
690 739 3.508426 AGAAACGGAGGGAGTAGAAACT 58.492 45.455 0.00 0.00 39.21 2.66
691 740 3.957591 AGAAACGGAGGGAGTAGAAAC 57.042 47.619 0.00 0.00 0.00 2.78
692 741 6.616237 ATTTAGAAACGGAGGGAGTAGAAA 57.384 37.500 0.00 0.00 0.00 2.52
693 742 6.894103 AGTATTTAGAAACGGAGGGAGTAGAA 59.106 38.462 0.00 0.00 0.00 2.10
694 743 6.430007 AGTATTTAGAAACGGAGGGAGTAGA 58.570 40.000 0.00 0.00 0.00 2.59
695 744 6.712179 AGTATTTAGAAACGGAGGGAGTAG 57.288 41.667 0.00 0.00 0.00 2.57
696 745 6.438425 ACAAGTATTTAGAAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
697 746 5.247792 ACAAGTATTTAGAAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
698 747 5.731591 ACAAGTATTTAGAAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
699 748 5.482878 AGACAAGTATTTAGAAACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
700 749 5.731591 AGACAAGTATTTAGAAACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
701 750 7.668525 AAAGACAAGTATTTAGAAACGGAGG 57.331 36.000 0.00 0.00 0.00 4.30
704 753 9.821662 CCTAAAAAGACAAGTATTTAGAAACGG 57.178 33.333 5.87 0.00 37.48 4.44
705 754 9.326339 GCCTAAAAAGACAAGTATTTAGAAACG 57.674 33.333 5.87 0.00 37.48 3.60
716 765 9.313118 CTTGTTAAAATGCCTAAAAAGACAAGT 57.687 29.630 0.00 0.00 36.91 3.16
717 766 9.313118 ACTTGTTAAAATGCCTAAAAAGACAAG 57.687 29.630 0.00 0.00 43.36 3.16
718 767 9.092876 CACTTGTTAAAATGCCTAAAAAGACAA 57.907 29.630 0.62 0.00 30.93 3.18
719 768 8.470805 TCACTTGTTAAAATGCCTAAAAAGACA 58.529 29.630 0.62 0.00 30.93 3.41
720 769 8.752254 GTCACTTGTTAAAATGCCTAAAAAGAC 58.248 33.333 0.62 0.00 30.93 3.01
721 770 8.691797 AGTCACTTGTTAAAATGCCTAAAAAGA 58.308 29.630 0.62 0.00 30.93 2.52
722 771 8.871686 AGTCACTTGTTAAAATGCCTAAAAAG 57.128 30.769 0.00 0.00 32.14 2.27
723 772 9.738832 GTAGTCACTTGTTAAAATGCCTAAAAA 57.261 29.630 0.00 0.00 0.00 1.94
724 773 8.904834 TGTAGTCACTTGTTAAAATGCCTAAAA 58.095 29.630 0.00 0.00 0.00 1.52
725 774 8.453238 TGTAGTCACTTGTTAAAATGCCTAAA 57.547 30.769 0.00 0.00 0.00 1.85
726 775 8.630054 ATGTAGTCACTTGTTAAAATGCCTAA 57.370 30.769 0.00 0.00 0.00 2.69
727 776 9.158233 GTATGTAGTCACTTGTTAAAATGCCTA 57.842 33.333 0.00 0.00 0.00 3.93
728 777 7.148474 CGTATGTAGTCACTTGTTAAAATGCCT 60.148 37.037 0.00 0.00 0.00 4.75
729 778 6.959311 CGTATGTAGTCACTTGTTAAAATGCC 59.041 38.462 0.00 0.00 0.00 4.40
730 779 6.959311 CCGTATGTAGTCACTTGTTAAAATGC 59.041 38.462 0.00 0.00 0.00 3.56
731 780 8.246908 TCCGTATGTAGTCACTTGTTAAAATG 57.753 34.615 0.00 0.00 0.00 2.32
732 781 7.548075 CCTCCGTATGTAGTCACTTGTTAAAAT 59.452 37.037 0.00 0.00 0.00 1.82
733 782 6.869913 CCTCCGTATGTAGTCACTTGTTAAAA 59.130 38.462 0.00 0.00 0.00 1.52
734 783 6.392354 CCTCCGTATGTAGTCACTTGTTAAA 58.608 40.000 0.00 0.00 0.00 1.52
735 784 5.105635 CCCTCCGTATGTAGTCACTTGTTAA 60.106 44.000 0.00 0.00 0.00 2.01
736 785 4.400251 CCCTCCGTATGTAGTCACTTGTTA 59.600 45.833 0.00 0.00 0.00 2.41
737 786 3.194968 CCCTCCGTATGTAGTCACTTGTT 59.805 47.826 0.00 0.00 0.00 2.83
738 787 2.758979 CCCTCCGTATGTAGTCACTTGT 59.241 50.000 0.00 0.00 0.00 3.16
739 788 3.021695 TCCCTCCGTATGTAGTCACTTG 58.978 50.000 0.00 0.00 0.00 3.16
740 789 3.288964 CTCCCTCCGTATGTAGTCACTT 58.711 50.000 0.00 0.00 0.00 3.16
741 790 2.241685 ACTCCCTCCGTATGTAGTCACT 59.758 50.000 0.00 0.00 0.00 3.41
742 791 2.652590 ACTCCCTCCGTATGTAGTCAC 58.347 52.381 0.00 0.00 0.00 3.67
743 792 3.457380 ACTACTCCCTCCGTATGTAGTCA 59.543 47.826 0.00 0.00 39.37 3.41
744 793 4.084011 ACTACTCCCTCCGTATGTAGTC 57.916 50.000 0.00 0.00 39.37 2.59
745 794 5.839517 ATACTACTCCCTCCGTATGTAGT 57.160 43.478 0.00 0.00 43.85 2.73
746 795 7.882271 AGTAAATACTACTCCCTCCGTATGTAG 59.118 40.741 0.00 0.00 37.29 2.74
747 796 7.749666 AGTAAATACTACTCCCTCCGTATGTA 58.250 38.462 0.00 0.00 34.13 2.29
748 797 6.608922 AGTAAATACTACTCCCTCCGTATGT 58.391 40.000 0.00 0.00 34.13 2.29
749 798 7.230108 TCAAGTAAATACTACTCCCTCCGTATG 59.770 40.741 0.00 0.00 34.99 2.39
750 799 7.230309 GTCAAGTAAATACTACTCCCTCCGTAT 59.770 40.741 0.00 0.00 34.99 3.06
751 800 6.543831 GTCAAGTAAATACTACTCCCTCCGTA 59.456 42.308 0.00 0.00 34.99 4.02
752 801 5.359292 GTCAAGTAAATACTACTCCCTCCGT 59.641 44.000 0.00 0.00 34.99 4.69
753 802 5.221204 GGTCAAGTAAATACTACTCCCTCCG 60.221 48.000 0.00 0.00 34.99 4.63
754 803 5.221204 CGGTCAAGTAAATACTACTCCCTCC 60.221 48.000 0.00 0.00 34.99 4.30
755 804 5.221204 CCGGTCAAGTAAATACTACTCCCTC 60.221 48.000 0.00 0.00 34.99 4.30
756 805 4.648307 CCGGTCAAGTAAATACTACTCCCT 59.352 45.833 0.00 0.00 34.99 4.20
757 806 4.403752 ACCGGTCAAGTAAATACTACTCCC 59.596 45.833 0.00 0.00 34.99 4.30
758 807 5.346522 CACCGGTCAAGTAAATACTACTCC 58.653 45.833 2.59 0.00 34.99 3.85
759 808 5.105595 ACCACCGGTCAAGTAAATACTACTC 60.106 44.000 2.59 0.00 34.99 2.59
760 809 4.774200 ACCACCGGTCAAGTAAATACTACT 59.226 41.667 2.59 0.00 34.99 2.57
761 810 4.866486 CACCACCGGTCAAGTAAATACTAC 59.134 45.833 2.59 0.00 31.39 2.73
762 811 4.081531 CCACCACCGGTCAAGTAAATACTA 60.082 45.833 2.59 0.00 31.39 1.82
763 812 3.307199 CCACCACCGGTCAAGTAAATACT 60.307 47.826 2.59 0.00 33.31 2.12
771 820 0.884704 CAAGTCCACCACCGGTCAAG 60.885 60.000 2.59 0.00 31.02 3.02
823 899 0.320374 GTGACCATGTCTGACCGGAA 59.680 55.000 9.46 0.00 33.15 4.30
830 906 2.768253 TAGCCTTGTGACCATGTCTG 57.232 50.000 0.00 0.00 33.15 3.51
831 907 5.045578 ACTTATTAGCCTTGTGACCATGTCT 60.046 40.000 0.00 0.00 33.15 3.41
837 924 3.689649 CCACACTTATTAGCCTTGTGACC 59.310 47.826 1.64 0.00 40.02 4.02
838 925 3.689649 CCCACACTTATTAGCCTTGTGAC 59.310 47.826 1.64 0.00 40.02 3.67
840 927 3.950397 TCCCACACTTATTAGCCTTGTG 58.050 45.455 0.00 0.00 37.83 3.33
842 929 3.374058 CGTTCCCACACTTATTAGCCTTG 59.626 47.826 0.00 0.00 0.00 3.61
865 952 2.774951 CTTCTAACGTCACCGCGCG 61.775 63.158 25.67 25.67 37.70 6.86
866 953 1.403972 CTCTTCTAACGTCACCGCGC 61.404 60.000 0.00 0.00 37.70 6.86
869 956 3.555917 AAGACTCTTCTAACGTCACCG 57.444 47.619 0.00 0.00 40.83 4.94
870 957 7.704789 TTAAAAAGACTCTTCTAACGTCACC 57.295 36.000 0.00 0.00 0.00 4.02
871 958 8.060679 GGTTTAAAAAGACTCTTCTAACGTCAC 58.939 37.037 0.00 0.00 0.00 3.67
872 959 7.225341 GGGTTTAAAAAGACTCTTCTAACGTCA 59.775 37.037 0.00 0.00 0.00 4.35
873 960 7.307632 GGGGTTTAAAAAGACTCTTCTAACGTC 60.308 40.741 0.00 0.00 0.00 4.34
874 961 6.484643 GGGGTTTAAAAAGACTCTTCTAACGT 59.515 38.462 0.00 0.00 0.00 3.99
875 962 6.347160 CGGGGTTTAAAAAGACTCTTCTAACG 60.347 42.308 0.00 0.00 0.00 3.18
876 963 6.072838 CCGGGGTTTAAAAAGACTCTTCTAAC 60.073 42.308 0.00 0.00 0.00 2.34
877 964 5.999600 CCGGGGTTTAAAAAGACTCTTCTAA 59.000 40.000 0.00 0.00 0.00 2.10
878 965 5.554070 CCGGGGTTTAAAAAGACTCTTCTA 58.446 41.667 0.00 0.00 0.00 2.10
879 966 4.395625 CCGGGGTTTAAAAAGACTCTTCT 58.604 43.478 0.00 0.00 0.00 2.85
880 967 3.057736 GCCGGGGTTTAAAAAGACTCTTC 60.058 47.826 2.18 0.00 0.00 2.87
881 968 2.889045 GCCGGGGTTTAAAAAGACTCTT 59.111 45.455 2.18 0.00 0.00 2.85
882 969 2.511659 GCCGGGGTTTAAAAAGACTCT 58.488 47.619 2.18 0.00 0.00 3.24
883 970 1.542915 GGCCGGGGTTTAAAAAGACTC 59.457 52.381 2.18 0.00 0.00 3.36
884 971 1.624336 GGCCGGGGTTTAAAAAGACT 58.376 50.000 2.18 0.00 0.00 3.24
918 1017 0.036952 ACGTTGGACTGGATGCTCAG 60.037 55.000 0.00 0.00 40.40 3.35
919 1018 0.396435 AACGTTGGACTGGATGCTCA 59.604 50.000 0.00 0.00 0.00 4.26
920 1019 1.079503 GAACGTTGGACTGGATGCTC 58.920 55.000 5.00 0.00 0.00 4.26
921 1020 0.321653 GGAACGTTGGACTGGATGCT 60.322 55.000 5.00 0.00 0.00 3.79
922 1021 0.605319 TGGAACGTTGGACTGGATGC 60.605 55.000 5.00 0.00 0.00 3.91
923 1022 1.535462 GTTGGAACGTTGGACTGGATG 59.465 52.381 5.00 0.00 0.00 3.51
924 1023 1.420138 AGTTGGAACGTTGGACTGGAT 59.580 47.619 5.00 0.00 0.00 3.41
925 1024 0.834612 AGTTGGAACGTTGGACTGGA 59.165 50.000 5.00 0.00 0.00 3.86
926 1025 1.226746 GAGTTGGAACGTTGGACTGG 58.773 55.000 5.00 0.00 0.00 4.00
927 1026 1.948104 TGAGTTGGAACGTTGGACTG 58.052 50.000 5.00 0.00 0.00 3.51
928 1027 2.930826 ATGAGTTGGAACGTTGGACT 57.069 45.000 5.00 6.51 0.00 3.85
929 1028 2.415512 GCTATGAGTTGGAACGTTGGAC 59.584 50.000 5.00 0.97 0.00 4.02
934 1033 1.676014 GGCAGCTATGAGTTGGAACGT 60.676 52.381 0.00 0.00 0.00 3.99
975 1078 4.394712 CTGCCGGGTGGTGAGGTC 62.395 72.222 2.18 0.00 37.67 3.85
1037 1140 3.451141 TGAATGTTTGGACACCTTTGC 57.549 42.857 0.00 0.00 38.91 3.68
1055 1158 1.710013 GACGGCAAGACGAAAGATGA 58.290 50.000 0.66 0.00 37.61 2.92
1084 1187 4.582701 TTGTGAAATGGTTGGTAGCAAG 57.417 40.909 7.79 0.00 35.04 4.01
1183 1301 2.414481 CCTGCAAGAGTGACGAATTCAG 59.586 50.000 6.22 1.11 31.42 3.02
1185 1303 2.417719 ACCTGCAAGAGTGACGAATTC 58.582 47.619 0.00 0.00 34.07 2.17
1191 1309 1.623811 TCCCTTACCTGCAAGAGTGAC 59.376 52.381 0.00 0.00 34.07 3.67
1196 1314 1.203313 AGACCTCCCTTACCTGCAAGA 60.203 52.381 0.00 0.00 34.07 3.02
1238 1359 1.269958 TGAGGATGGTGGTGAGTCTG 58.730 55.000 0.00 0.00 0.00 3.51
1276 1397 0.240945 GCCGACTCCACAACAAATGG 59.759 55.000 0.00 0.00 38.71 3.16
1485 1615 1.067821 CAGCGATAGGGAGTGAAGGTC 59.932 57.143 0.00 0.00 0.00 3.85
1495 1625 1.227380 GTGCCTGACAGCGATAGGG 60.227 63.158 0.00 0.00 34.65 3.53
1503 1633 0.798776 GGTGAAATCGTGCCTGACAG 59.201 55.000 0.00 0.00 0.00 3.51
1549 1679 2.104170 CAGGTCCAGTCTCCTAACTCC 58.896 57.143 0.00 0.00 32.26 3.85
1550 1680 2.756207 GACAGGTCCAGTCTCCTAACTC 59.244 54.545 7.15 0.00 33.29 3.01
1551 1681 2.810164 GACAGGTCCAGTCTCCTAACT 58.190 52.381 7.15 0.00 33.29 2.24
1704 1849 7.626084 TCACAGGGGATTTCTCCTATTAGTAAA 59.374 37.037 0.00 0.00 41.74 2.01
1722 1867 2.343758 CGGCCGATATCACAGGGG 59.656 66.667 24.07 0.00 0.00 4.79
1726 1871 0.530744 GATAGGCGGCCGATATCACA 59.469 55.000 33.48 5.85 0.00 3.58
1734 1879 0.108615 CTAGATTGGATAGGCGGCCG 60.109 60.000 24.05 24.05 0.00 6.13
1765 1910 7.094162 TGTTCCGGTGAGATTATTTGCATAAAA 60.094 33.333 0.00 0.00 0.00 1.52
1769 1914 4.269183 TGTTCCGGTGAGATTATTTGCAT 58.731 39.130 0.00 0.00 0.00 3.96
1770 1915 3.680490 TGTTCCGGTGAGATTATTTGCA 58.320 40.909 0.00 0.00 0.00 4.08
1825 1971 2.084610 TCACCAAGCGAGATCAGTTG 57.915 50.000 0.00 0.00 0.00 3.16
1829 1975 4.991056 GCTTATTATCACCAAGCGAGATCA 59.009 41.667 0.00 0.00 35.75 2.92
1841 1987 3.808174 GGTTCCGGTGAGCTTATTATCAC 59.192 47.826 0.00 0.00 44.10 3.06
2075 2221 0.036388 TGGGAGATGACCTGCGAAAC 60.036 55.000 0.00 0.00 33.55 2.78
2079 2225 2.202987 GCTGGGAGATGACCTGCG 60.203 66.667 0.00 0.00 41.91 5.18
2081 2227 1.142748 GACGCTGGGAGATGACCTG 59.857 63.158 0.00 0.00 0.00 4.00
2100 2246 2.868899 AGCCCTGAAATATTGCCTAGC 58.131 47.619 0.00 0.00 0.00 3.42
2172 2318 7.012894 TGTTGTAACAGTCCAAGATTACCAAAG 59.987 37.037 0.00 0.00 34.30 2.77
2214 2360 4.825085 GGGATGAAGCCCGATAAATTGTTA 59.175 41.667 0.00 0.00 38.58 2.41
2240 2386 2.675658 TTTTAAGCCACCCAGCTCTT 57.324 45.000 0.00 0.00 44.11 2.85
2260 2406 2.838202 ACAGATCCACACGGGTAAGATT 59.162 45.455 4.17 0.00 38.11 2.40
2262 2408 1.822990 GACAGATCCACACGGGTAAGA 59.177 52.381 0.00 0.00 38.11 2.10
2265 2411 1.182667 CAGACAGATCCACACGGGTA 58.817 55.000 0.00 0.00 38.11 3.69
2272 2418 6.155827 GCAGACTATTATCAGACAGATCCAC 58.844 44.000 0.00 0.00 38.19 4.02
2391 2566 2.214347 CATGAGAGCAGCTGATCCTTG 58.786 52.381 27.52 20.63 0.00 3.61
2392 2567 1.838715 ACATGAGAGCAGCTGATCCTT 59.161 47.619 27.52 11.09 0.00 3.36
2393 2568 1.413445 GACATGAGAGCAGCTGATCCT 59.587 52.381 27.52 15.22 0.00 3.24
2396 2571 1.498264 AGGACATGAGAGCAGCTGAT 58.502 50.000 20.43 12.64 0.00 2.90
2397 2572 1.753649 GTAGGACATGAGAGCAGCTGA 59.246 52.381 20.43 0.00 0.00 4.26
2398 2573 1.755959 AGTAGGACATGAGAGCAGCTG 59.244 52.381 10.11 10.11 0.00 4.24
2407 2582 7.483580 TCGAGAGATAGATAGTAGGACATGA 57.516 40.000 0.00 0.00 33.31 3.07
2419 2594 9.712305 TTTGTTTCTTTTCTTCGAGAGATAGAT 57.288 29.630 0.00 0.00 41.60 1.98
2420 2595 9.542462 TTTTGTTTCTTTTCTTCGAGAGATAGA 57.458 29.630 0.00 0.00 41.60 1.98
2446 2621 8.847196 TGAGTGCTCTAATCAAATAGTACGTAT 58.153 33.333 0.00 0.00 29.08 3.06


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

AutoCloner maintained by Alex Coulton.