Multiple sequence alignment - TraesCS6A01G353900

Loading Multiple Alignment...

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 TraesCS6A01G353900 chr6A 100.000 4937 0 0 426 5362 585442649 585437713 0.000000e+00 9118
1 TraesCS6A01G353900 chr6A 100.000 108 0 0 1 108 585443074 585442967 3.280000e-47 200
2 TraesCS6A01G353900 chr6D 94.531 3639 147 28 1750 5362 437179140 437175528 0.000000e+00 5570
3 TraesCS6A01G353900 chr6D 89.359 780 54 15 802 1554 437180234 437179457 0.000000e+00 953
4 TraesCS6A01G353900 chr6D 93.421 152 8 1 1513 1662 437179458 437179307 1.940000e-54 224
5 TraesCS6A01G353900 chr6D 91.667 108 3 1 1 108 451667877 451667978 1.560000e-30 145
6 TraesCS6A01G353900 chr6D 91.781 73 3 2 1677 1749 437179245 437179176 1.230000e-16 99
7 TraesCS6A01G353900 chr6B 91.988 2696 163 24 1750 4423 661466510 661463846 0.000000e+00 3733
8 TraesCS6A01G353900 chr6B 92.652 939 46 13 741 1662 661467609 661466677 0.000000e+00 1330
9 TraesCS6A01G353900 chr6B 90.308 227 12 6 4457 4675 661463849 661463625 6.790000e-74 289
10 TraesCS6A01G353900 chr6B 88.496 226 23 3 4693 4916 661463366 661463142 2.460000e-68 270
11 TraesCS6A01G353900 chr6B 88.387 155 13 3 4952 5101 661463145 661462991 1.190000e-41 182
12 TraesCS6A01G353900 chr6B 91.781 73 3 2 1677 1749 661466615 661466546 1.230000e-16 99
13 TraesCS6A01G353900 chr4A 89.325 459 45 2 3890 4344 658750345 658749887 1.680000e-159 573
14 TraesCS6A01G353900 chr4A 89.107 459 46 2 3890 4344 658796853 658796395 7.790000e-158 568
15 TraesCS6A01G353900 chr4A 90.332 331 15 9 427 742 684298330 684298002 8.310000e-113 418
16 TraesCS6A01G353900 chr1A 91.541 331 13 6 427 744 420530625 420530953 4.930000e-120 442
17 TraesCS6A01G353900 chr1A 91.018 334 13 8 426 742 520128347 520128680 8.250000e-118 435
18 TraesCS6A01G353900 chr1A 94.074 270 11 3 483 749 18104094 18103827 6.470000e-109 405
19 TraesCS6A01G353900 chr1A 89.908 327 15 8 432 742 509010703 509011027 6.470000e-109 405
20 TraesCS6A01G353900 chr1A 92.593 108 2 2 1 108 509010564 509010665 3.350000e-32 150
21 TraesCS6A01G353900 chr1A 90.741 108 4 1 1 108 131255051 131255152 7.240000e-29 139
22 TraesCS6A01G353900 chr3A 94.757 267 11 2 483 746 32201218 32200952 3.860000e-111 412
23 TraesCS6A01G353900 chr5A 90.566 318 12 7 443 742 566145011 566145328 6.470000e-109 405
24 TraesCS6A01G353900 chr5A 93.985 266 10 3 483 747 491737759 491737499 1.080000e-106 398
25 TraesCS6A01G353900 chr7A 88.103 311 25 11 450 750 474515574 474515266 5.110000e-95 359
26 TraesCS6A01G353900 chr7A 92.593 108 2 3 1 108 90655762 90655661 3.350000e-32 150
27 TraesCS6A01G353900 chr5D 92.593 108 2 2 1 108 374627263 374627162 3.350000e-32 150
28 TraesCS6A01G353900 chr5D 92.593 108 2 2 1 108 423273317 423273216 3.350000e-32 150
29 TraesCS6A01G353900 chr3D 92.593 108 2 2 1 108 80219958 80220059 3.350000e-32 150
30 TraesCS6A01G353900 chr2D 92.593 108 2 2 1 108 453731134 453731235 3.350000e-32 150
31 TraesCS6A01G353900 chr4D 91.667 108 3 1 1 108 439874459 439874358 1.560000e-30 145


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 TraesCS6A01G353900 chr6A 585437713 585443074 5361 True 4659.000000 9118 100.000 1 5362 2 chr6A.!!$R1 5361
1 TraesCS6A01G353900 chr6D 437175528 437180234 4706 True 1711.500000 5570 92.273 802 5362 4 chr6D.!!$R1 4560
2 TraesCS6A01G353900 chr6B 661462991 661467609 4618 True 983.833333 3733 90.602 741 5101 6 chr6B.!!$R1 4360

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
639 640 0.026285 CAACTGCTTATACCGCACGC 59.974 55.000 0.00 0.00 33.19 5.34 F
736 737 0.391130 TTAGCGCGCCTGTTGAAGAT 60.391 50.000 30.33 7.53 0.00 2.40 F
1346 1372 0.752743 TGCCACTATGGATTGCCTGC 60.753 55.000 0.00 0.00 40.96 4.85 F
1664 1744 0.875908 GCGGTATTGAGAGCATGCGA 60.876 55.000 13.01 0.00 0.00 5.10 F
2047 2213 1.171308 CAGAACCATTGGAGCCACAG 58.829 55.000 10.37 0.00 0.00 3.66 F
2198 2364 1.195448 CGGTGAGTCATGCAACTTGAC 59.805 52.381 10.35 10.35 43.05 3.18 F
3488 3678 1.278985 TGGGATGATGAGTTGAAGCGT 59.721 47.619 0.00 0.00 0.00 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1751 1.000506 ACTTTCTTGCAGCAGCCAATG 59.999 47.619 0.00 0.0 41.13 2.82 R
1675 1755 1.200948 CCTTACTTTCTTGCAGCAGCC 59.799 52.381 0.00 0.0 41.13 4.85 R
3102 3292 0.954452 GCACAGTCCAAAGGGTTCAG 59.046 55.000 0.00 0.0 34.93 3.02 R
3562 3752 0.108186 ATCTTCGCCGCTCACATCAA 60.108 50.000 0.00 0.0 0.00 2.57 R
3897 4090 0.037697 TTCGTGCGGTGTATGCTTCT 60.038 50.000 0.00 0.0 0.00 2.85 R
3913 4106 0.451792 GCTGCGCTTCTTGTCTTTCG 60.452 55.000 9.73 0.0 0.00 3.46 R
4835 5323 0.179215 GCTTTGGATGCGTTCTGTCG 60.179 55.000 0.00 0.0 0.00 4.35 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 3.056328 GCCGCCAAGGTCAAGGTC 61.056 66.667 0.00 0.00 43.70 3.85
42 43 2.429930 CCGCCAAGGTCAAGGTCA 59.570 61.111 0.00 0.00 34.51 4.02
43 44 1.002134 CCGCCAAGGTCAAGGTCAT 60.002 57.895 0.00 0.00 34.51 3.06
44 45 1.026718 CCGCCAAGGTCAAGGTCATC 61.027 60.000 0.00 0.00 34.51 2.92
45 46 1.026718 CGCCAAGGTCAAGGTCATCC 61.027 60.000 0.00 0.00 0.00 3.51
46 47 1.026718 GCCAAGGTCAAGGTCATCCG 61.027 60.000 0.00 0.00 39.05 4.18
47 48 1.026718 CCAAGGTCAAGGTCATCCGC 61.027 60.000 0.00 0.00 39.05 5.54
48 49 1.079127 AAGGTCAAGGTCATCCGCG 60.079 57.895 0.00 0.00 39.05 6.46
49 50 2.511600 GGTCAAGGTCATCCGCGG 60.512 66.667 22.12 22.12 39.05 6.46
50 51 3.195698 GTCAAGGTCATCCGCGGC 61.196 66.667 23.51 6.01 39.05 6.53
51 52 4.812476 TCAAGGTCATCCGCGGCG 62.812 66.667 23.51 16.78 39.05 6.46
457 458 3.692406 GGGGGTCGCGGCTATAGG 61.692 72.222 11.94 0.00 0.00 2.57
458 459 2.599578 GGGGTCGCGGCTATAGGA 60.600 66.667 11.94 0.00 0.00 2.94
459 460 2.649614 GGGTCGCGGCTATAGGAC 59.350 66.667 11.94 0.00 0.00 3.85
465 466 4.828409 CGGCTATAGGACGGGGTA 57.172 61.111 1.04 0.00 43.88 3.69
466 467 3.040965 CGGCTATAGGACGGGGTAA 57.959 57.895 1.04 0.00 43.88 2.85
467 468 0.886563 CGGCTATAGGACGGGGTAAG 59.113 60.000 1.04 0.00 43.88 2.34
468 469 0.607112 GGCTATAGGACGGGGTAAGC 59.393 60.000 1.04 0.00 0.00 3.09
469 470 0.243095 GCTATAGGACGGGGTAAGCG 59.757 60.000 1.04 0.00 0.00 4.68
470 471 0.886563 CTATAGGACGGGGTAAGCGG 59.113 60.000 0.00 0.00 0.00 5.52
471 472 0.540365 TATAGGACGGGGTAAGCGGG 60.540 60.000 0.00 0.00 0.00 6.13
472 473 3.901313 TATAGGACGGGGTAAGCGGGG 62.901 61.905 0.00 0.00 0.00 5.73
474 475 4.462280 GACGGGGTAAGCGGGGTG 62.462 72.222 0.00 0.00 0.00 4.61
526 527 3.744155 GGGGCTTTGGAGGGGGAG 61.744 72.222 0.00 0.00 0.00 4.30
527 528 2.614013 GGGCTTTGGAGGGGGAGA 60.614 66.667 0.00 0.00 0.00 3.71
528 529 2.238701 GGGCTTTGGAGGGGGAGAA 61.239 63.158 0.00 0.00 0.00 2.87
529 530 1.304617 GGCTTTGGAGGGGGAGAAG 59.695 63.158 0.00 0.00 0.00 2.85
530 531 1.208165 GGCTTTGGAGGGGGAGAAGA 61.208 60.000 0.00 0.00 0.00 2.87
531 532 0.698818 GCTTTGGAGGGGGAGAAGAA 59.301 55.000 0.00 0.00 0.00 2.52
532 533 1.340502 GCTTTGGAGGGGGAGAAGAAG 60.341 57.143 0.00 0.00 0.00 2.85
533 534 2.269940 CTTTGGAGGGGGAGAAGAAGA 58.730 52.381 0.00 0.00 0.00 2.87
534 535 1.958288 TTGGAGGGGGAGAAGAAGAG 58.042 55.000 0.00 0.00 0.00 2.85
535 536 0.618968 TGGAGGGGGAGAAGAAGAGC 60.619 60.000 0.00 0.00 0.00 4.09
536 537 1.681486 GGAGGGGGAGAAGAAGAGCG 61.681 65.000 0.00 0.00 0.00 5.03
537 538 2.188207 GGGGGAGAAGAAGAGCGC 59.812 66.667 0.00 0.00 0.00 5.92
538 539 2.202810 GGGGAGAAGAAGAGCGCG 60.203 66.667 0.00 0.00 0.00 6.86
539 540 2.888051 GGGAGAAGAAGAGCGCGC 60.888 66.667 26.66 26.66 0.00 6.86
540 541 2.125912 GGAGAAGAAGAGCGCGCA 60.126 61.111 35.10 0.00 0.00 6.09
541 542 2.164026 GGAGAAGAAGAGCGCGCAG 61.164 63.158 35.10 0.72 0.00 5.18
589 590 2.483288 CGGGTGCCGCAAATACAC 59.517 61.111 0.00 0.00 41.17 2.90
591 592 2.483288 GGTGCCGCAAATACACCG 59.517 61.111 0.00 0.00 44.02 4.94
592 593 2.202427 GTGCCGCAAATACACCGC 60.202 61.111 0.00 0.00 0.00 5.68
597 598 2.021380 GCAAATACACCGCGCGAG 59.979 61.111 34.63 25.26 0.00 5.03
598 599 2.701006 CAAATACACCGCGCGAGG 59.299 61.111 34.63 28.09 37.30 4.63
600 601 0.802994 CAAATACACCGCGCGAGGTA 60.803 55.000 34.02 29.97 43.89 3.08
601 602 0.803380 AAATACACCGCGCGAGGTAC 60.803 55.000 34.02 1.73 43.89 3.34
602 603 2.618312 AATACACCGCGCGAGGTACC 62.618 60.000 34.02 2.73 43.89 3.34
609 610 3.446570 CGCGAGGTACCGGTTCCT 61.447 66.667 30.84 30.84 36.70 3.36
610 611 2.183555 GCGAGGTACCGGTTCCTG 59.816 66.667 34.74 25.43 33.83 3.86
611 612 2.183555 CGAGGTACCGGTTCCTGC 59.816 66.667 34.74 23.41 33.83 4.85
612 613 2.582978 GAGGTACCGGTTCCTGCC 59.417 66.667 34.74 18.90 33.83 4.85
629 630 3.047280 CGCGTGCCCAACTGCTTA 61.047 61.111 0.00 0.00 0.00 3.09
630 631 2.398554 CGCGTGCCCAACTGCTTAT 61.399 57.895 0.00 0.00 0.00 1.73
631 632 1.087202 CGCGTGCCCAACTGCTTATA 61.087 55.000 0.00 0.00 0.00 0.98
632 633 0.377203 GCGTGCCCAACTGCTTATAC 59.623 55.000 0.00 0.00 0.00 1.47
633 634 1.014352 CGTGCCCAACTGCTTATACC 58.986 55.000 0.00 0.00 0.00 2.73
634 635 1.014352 GTGCCCAACTGCTTATACCG 58.986 55.000 0.00 0.00 0.00 4.02
635 636 0.746563 TGCCCAACTGCTTATACCGC 60.747 55.000 0.00 0.00 0.00 5.68
636 637 0.746563 GCCCAACTGCTTATACCGCA 60.747 55.000 0.00 0.00 35.80 5.69
637 638 1.014352 CCCAACTGCTTATACCGCAC 58.986 55.000 0.00 0.00 33.19 5.34
638 639 0.650512 CCAACTGCTTATACCGCACG 59.349 55.000 0.00 0.00 33.19 5.34
639 640 0.026285 CAACTGCTTATACCGCACGC 59.974 55.000 0.00 0.00 33.19 5.34
640 641 1.418342 AACTGCTTATACCGCACGCG 61.418 55.000 3.53 3.53 39.44 6.01
641 642 3.210419 CTGCTTATACCGCACGCGC 62.210 63.158 5.73 0.00 38.24 6.86
696 697 2.507547 CGCGCGCTAAAGTGGGTA 60.508 61.111 30.48 0.00 40.13 3.69
697 698 1.881252 CGCGCGCTAAAGTGGGTAT 60.881 57.895 30.48 0.00 40.13 2.73
698 699 0.595567 CGCGCGCTAAAGTGGGTATA 60.596 55.000 30.48 0.00 40.13 1.47
699 700 1.792006 GCGCGCTAAAGTGGGTATAT 58.208 50.000 26.67 0.00 40.13 0.86
700 701 2.140717 GCGCGCTAAAGTGGGTATATT 58.859 47.619 26.67 0.00 40.13 1.28
701 702 2.546789 GCGCGCTAAAGTGGGTATATTT 59.453 45.455 26.67 0.00 40.13 1.40
702 703 3.742369 GCGCGCTAAAGTGGGTATATTTA 59.258 43.478 26.67 0.00 40.13 1.40
703 704 4.376717 GCGCGCTAAAGTGGGTATATTTAC 60.377 45.833 26.67 0.00 40.13 2.01
704 705 4.143473 CGCGCTAAAGTGGGTATATTTACG 60.143 45.833 5.56 0.00 34.35 3.18
705 706 4.151157 GCGCTAAAGTGGGTATATTTACGG 59.849 45.833 0.00 0.00 0.00 4.02
706 707 4.151157 CGCTAAAGTGGGTATATTTACGGC 59.849 45.833 0.00 0.00 0.00 5.68
707 708 4.151157 GCTAAAGTGGGTATATTTACGGCG 59.849 45.833 4.80 4.80 0.00 6.46
708 709 2.159327 AGTGGGTATATTTACGGCGC 57.841 50.000 6.90 0.00 0.00 6.53
709 710 0.785979 GTGGGTATATTTACGGCGCG 59.214 55.000 6.90 0.00 0.00 6.86
710 711 0.945265 TGGGTATATTTACGGCGCGC 60.945 55.000 25.94 25.94 0.00 6.86
711 712 1.413368 GGTATATTTACGGCGCGCG 59.587 57.895 28.44 28.44 0.00 6.86
712 713 1.225289 GTATATTTACGGCGCGCGC 60.225 57.895 44.40 44.40 41.06 6.86
728 729 4.166011 GCCTGTTTAGCGCGCCTG 62.166 66.667 30.33 15.84 0.00 4.85
729 730 2.742372 CCTGTTTAGCGCGCCTGT 60.742 61.111 30.33 12.78 0.00 4.00
730 731 2.325082 CCTGTTTAGCGCGCCTGTT 61.325 57.895 30.33 12.34 0.00 3.16
731 732 1.154413 CTGTTTAGCGCGCCTGTTG 60.154 57.895 30.33 10.42 0.00 3.33
732 733 1.565156 CTGTTTAGCGCGCCTGTTGA 61.565 55.000 30.33 2.19 0.00 3.18
733 734 1.160946 TGTTTAGCGCGCCTGTTGAA 61.161 50.000 30.33 9.55 0.00 2.69
734 735 0.452784 GTTTAGCGCGCCTGTTGAAG 60.453 55.000 30.33 0.00 0.00 3.02
735 736 0.601576 TTTAGCGCGCCTGTTGAAGA 60.602 50.000 30.33 0.33 0.00 2.87
736 737 0.391130 TTAGCGCGCCTGTTGAAGAT 60.391 50.000 30.33 7.53 0.00 2.40
737 738 1.083806 TAGCGCGCCTGTTGAAGATG 61.084 55.000 30.33 0.00 0.00 2.90
738 739 2.099062 CGCGCCTGTTGAAGATGC 59.901 61.111 0.00 0.00 0.00 3.91
739 740 2.393768 CGCGCCTGTTGAAGATGCT 61.394 57.895 0.00 0.00 0.00 3.79
779 780 4.936248 CGCGCGCTCTCTCTCTCG 62.936 72.222 30.48 5.07 0.00 4.04
780 781 4.605967 GCGCGCTCTCTCTCTCGG 62.606 72.222 26.67 0.00 0.00 4.63
781 782 4.605967 CGCGCTCTCTCTCTCGGC 62.606 72.222 5.56 0.00 0.00 5.54
806 808 1.951130 CGACCGAAGCGATGATGGG 60.951 63.158 0.00 0.00 0.00 4.00
818 820 1.410850 ATGATGGGCCCTAGTGTCCG 61.411 60.000 25.70 0.00 0.00 4.79
869 873 1.674651 GCCCGTGGACTTTTCCTCC 60.675 63.158 0.00 0.00 43.31 4.30
870 874 1.375523 CCCGTGGACTTTTCCTCCG 60.376 63.158 0.00 0.00 43.31 4.63
871 875 2.033194 CCGTGGACTTTTCCTCCGC 61.033 63.158 0.00 0.00 43.31 5.54
872 876 1.301401 CGTGGACTTTTCCTCCGCA 60.301 57.895 0.00 0.00 43.31 5.69
1003 1008 2.927856 TGGACCGGTGAGCCATGT 60.928 61.111 14.63 0.00 34.09 3.21
1008 1013 4.838152 CGGTGAGCCATGTCGGGG 62.838 72.222 0.00 0.00 34.06 5.73
1157 1162 3.081133 GCGTACGCATCTGTGTGG 58.919 61.111 33.90 0.00 40.16 4.17
1159 1164 2.452813 CGTACGCATCTGTGTGGGC 61.453 63.158 0.52 0.00 40.16 5.36
1209 1233 6.115446 CAGATTGCTGATTAACTAGTTCCCA 58.885 40.000 12.39 7.74 45.17 4.37
1242 1266 4.379263 TTCTTAGGGGTCCTAGGGATTT 57.621 45.455 9.46 0.00 37.42 2.17
1243 1267 5.508364 TTCTTAGGGGTCCTAGGGATTTA 57.492 43.478 9.46 0.00 37.42 1.40
1274 1300 0.876342 GGCATCCCTGATTCGTCGAC 60.876 60.000 5.18 5.18 0.00 4.20
1302 1328 2.832733 AGTAGGGAGCTAGTGGTTGTTC 59.167 50.000 0.00 0.00 0.00 3.18
1332 1358 4.265073 AGTAGAACCTGAATGATTGCCAC 58.735 43.478 0.00 0.00 0.00 5.01
1346 1372 0.752743 TGCCACTATGGATTGCCTGC 60.753 55.000 0.00 0.00 40.96 4.85
1365 1391 1.267806 GCTTGTGATGGGATTATGGCG 59.732 52.381 0.00 0.00 0.00 5.69
1439 1469 3.903467 AGGGATGTTCTATTTTGGGAGC 58.097 45.455 0.00 0.00 0.00 4.70
1570 1645 4.874970 AGCTCATTCATGTGTTGTTTTCC 58.125 39.130 0.00 0.00 0.00 3.13
1576 1651 5.604758 TTCATGTGTTGTTTTCCCATTGA 57.395 34.783 0.00 0.00 0.00 2.57
1662 1742 1.233019 ATGCGGTATTGAGAGCATGC 58.767 50.000 10.51 10.51 46.97 4.06
1664 1744 0.875908 GCGGTATTGAGAGCATGCGA 60.876 55.000 13.01 0.00 0.00 5.10
1666 1746 2.926586 GCGGTATTGAGAGCATGCGATA 60.927 50.000 13.01 4.57 0.00 2.92
1667 1747 3.515630 CGGTATTGAGAGCATGCGATAT 58.484 45.455 13.01 5.64 0.00 1.63
1668 1748 3.928992 CGGTATTGAGAGCATGCGATATT 59.071 43.478 13.01 0.00 0.00 1.28
1670 1750 5.625251 GGTATTGAGAGCATGCGATATTTG 58.375 41.667 13.01 0.00 0.00 2.32
1671 1751 3.614159 TTGAGAGCATGCGATATTTGC 57.386 42.857 13.01 0.00 36.63 3.68
1712 1839 4.775780 AGTAAGGCATGTACTGTGGAAGTA 59.224 41.667 0.00 0.00 40.56 2.24
1713 1840 3.895232 AGGCATGTACTGTGGAAGTAG 57.105 47.619 0.00 0.00 42.15 2.57
1726 1853 3.384146 GTGGAAGTAGTTAGTAGCTCCCC 59.616 52.174 0.00 0.00 0.00 4.81
1761 1923 6.006275 TCATTCCTTATCCCTTGGAGAAAG 57.994 41.667 0.00 0.00 32.27 2.62
2047 2213 1.171308 CAGAACCATTGGAGCCACAG 58.829 55.000 10.37 0.00 0.00 3.66
2119 2285 6.065976 TGGTATAATGGATGCATTCTAGGG 57.934 41.667 16.40 0.00 0.00 3.53
2198 2364 1.195448 CGGTGAGTCATGCAACTTGAC 59.805 52.381 10.35 10.35 43.05 3.18
2204 2370 3.873952 GAGTCATGCAACTTGACCTATCC 59.126 47.826 13.92 0.00 43.62 2.59
2243 2409 4.405358 TGTCTTTTGAATTGAACCAGCCTT 59.595 37.500 0.00 0.00 0.00 4.35
2244 2410 4.746611 GTCTTTTGAATTGAACCAGCCTTG 59.253 41.667 0.00 0.00 0.00 3.61
2277 2443 2.640826 CCACCAGAGTTAACCCCTTACA 59.359 50.000 0.88 0.00 0.00 2.41
2371 2539 8.520351 ACTTTGTAGTATGTATTCCTTTTTGCC 58.480 33.333 0.00 0.00 31.21 4.52
2424 2592 3.197766 CACTTCCACTAATGCTAGGACCA 59.802 47.826 0.00 0.00 0.00 4.02
2461 2629 5.709631 TGTTGAATAGCCTTTGACTATTGCA 59.290 36.000 0.99 0.00 39.77 4.08
2462 2630 5.818136 TGAATAGCCTTTGACTATTGCAC 57.182 39.130 0.99 0.00 39.77 4.57
2463 2631 5.252547 TGAATAGCCTTTGACTATTGCACA 58.747 37.500 0.99 0.00 39.77 4.57
2546 2726 7.414436 TGAATTTTAAACTCAACAGAAGTCCG 58.586 34.615 0.00 0.00 0.00 4.79
2591 2771 7.806487 GTCTAATGTGGACATGCATAATCAATG 59.194 37.037 0.00 0.00 36.56 2.82
2623 2803 3.005791 GCTGGGTTACAAAGCTGTTCATT 59.994 43.478 0.00 0.00 36.96 2.57
2654 2834 2.850833 TCCAAATCCCATCTCCTCAGT 58.149 47.619 0.00 0.00 0.00 3.41
2656 2836 3.969976 TCCAAATCCCATCTCCTCAGTAG 59.030 47.826 0.00 0.00 0.00 2.57
2848 3033 5.163499 GGACACCCAGAAATACACAACAAAA 60.163 40.000 0.00 0.00 0.00 2.44
2893 3080 1.425694 TACACAGGTGGGTTGCTACA 58.574 50.000 4.24 0.00 31.69 2.74
2931 3120 4.337555 CAGCCATAACTTTCTGCTGCTTAT 59.662 41.667 0.00 0.00 42.40 1.73
2932 3121 5.528690 CAGCCATAACTTTCTGCTGCTTATA 59.471 40.000 0.00 0.00 42.40 0.98
3170 3360 9.454859 TTGTTTTCACATTGAACCCTTTAAAAT 57.545 25.926 0.00 0.00 35.89 1.82
3257 3447 2.107950 TGTCCCTGTTTTCCTATGCG 57.892 50.000 0.00 0.00 0.00 4.73
3263 3453 4.007659 CCCTGTTTTCCTATGCGTTACTT 58.992 43.478 0.00 0.00 0.00 2.24
3367 3557 6.655003 GTGATTCCTACTTCATCCTTGAAACA 59.345 38.462 0.00 0.00 41.22 2.83
3488 3678 1.278985 TGGGATGATGAGTTGAAGCGT 59.721 47.619 0.00 0.00 0.00 5.07
3562 3752 7.527868 CGATTCCCTTTCTATCCCAGAATATGT 60.528 40.741 0.00 0.00 42.88 2.29
3689 3882 5.813157 CCGTTTGGAAACCACAAATTTAACT 59.187 36.000 0.00 0.00 39.68 2.24
3719 3912 1.413767 CGGAGACCGTGATCTTTGCG 61.414 60.000 1.80 0.00 42.73 4.85
3740 3933 3.654021 TGGGAACAGCACACCAGA 58.346 55.556 0.00 0.00 35.01 3.86
3845 4038 4.019681 CCAATCCCAGTCAAAGTACTACCA 60.020 45.833 0.00 0.00 0.00 3.25
3869 4062 2.027073 GCAATCACTCGACCACGCA 61.027 57.895 0.00 0.00 39.58 5.24
3875 4068 2.430921 CTCGACCACGCAGTCACC 60.431 66.667 6.28 0.00 41.61 4.02
3913 4106 1.425428 GCAGAAGCATACACCGCAC 59.575 57.895 0.00 0.00 41.58 5.34
3957 4150 4.103103 GGCAAAGGAAGCGCGACC 62.103 66.667 12.10 15.99 0.00 4.79
4109 4302 2.438434 CCATCGGGTCAGGCCAAC 60.438 66.667 5.01 1.87 39.65 3.77
4241 4434 2.607892 GGACAAGGCAGTGCACGAC 61.608 63.158 18.61 8.88 0.00 4.34
4364 4557 8.329203 AGAAGAAGTGGTTGAAATTCTGATAC 57.671 34.615 0.00 0.00 32.50 2.24
4423 4655 1.002544 GGAGCTCTGTTGTAGTTGGCT 59.997 52.381 14.64 0.00 33.38 4.75
4424 4656 2.072298 GAGCTCTGTTGTAGTTGGCTG 58.928 52.381 6.43 0.00 31.90 4.85
4425 4657 1.160137 GCTCTGTTGTAGTTGGCTGG 58.840 55.000 0.00 0.00 0.00 4.85
4426 4658 1.270839 GCTCTGTTGTAGTTGGCTGGA 60.271 52.381 0.00 0.00 0.00 3.86
4427 4659 2.616510 GCTCTGTTGTAGTTGGCTGGAT 60.617 50.000 0.00 0.00 0.00 3.41
4428 4660 3.005554 CTCTGTTGTAGTTGGCTGGATG 58.994 50.000 0.00 0.00 0.00 3.51
4429 4661 2.371841 TCTGTTGTAGTTGGCTGGATGT 59.628 45.455 0.00 0.00 0.00 3.06
4430 4662 2.485426 CTGTTGTAGTTGGCTGGATGTG 59.515 50.000 0.00 0.00 0.00 3.21
4431 4663 2.105649 TGTTGTAGTTGGCTGGATGTGA 59.894 45.455 0.00 0.00 0.00 3.58
4432 4664 3.244875 TGTTGTAGTTGGCTGGATGTGAT 60.245 43.478 0.00 0.00 0.00 3.06
4433 4665 4.019771 TGTTGTAGTTGGCTGGATGTGATA 60.020 41.667 0.00 0.00 0.00 2.15
4434 4666 5.126067 GTTGTAGTTGGCTGGATGTGATAT 58.874 41.667 0.00 0.00 0.00 1.63
4435 4667 4.960938 TGTAGTTGGCTGGATGTGATATC 58.039 43.478 0.00 0.00 0.00 1.63
4436 4668 4.655649 TGTAGTTGGCTGGATGTGATATCT 59.344 41.667 3.98 0.00 0.00 1.98
4437 4669 5.838521 TGTAGTTGGCTGGATGTGATATCTA 59.161 40.000 3.98 0.00 0.00 1.98
4438 4670 5.480642 AGTTGGCTGGATGTGATATCTAG 57.519 43.478 3.98 0.00 0.00 2.43
4439 4671 4.904251 AGTTGGCTGGATGTGATATCTAGT 59.096 41.667 3.98 0.00 0.00 2.57
4440 4672 5.367937 AGTTGGCTGGATGTGATATCTAGTT 59.632 40.000 3.98 0.00 0.00 2.24
4441 4673 6.554982 AGTTGGCTGGATGTGATATCTAGTTA 59.445 38.462 3.98 0.00 0.00 2.24
4442 4674 6.596309 TGGCTGGATGTGATATCTAGTTAG 57.404 41.667 3.98 0.00 0.00 2.34
4443 4675 6.314917 TGGCTGGATGTGATATCTAGTTAGA 58.685 40.000 3.98 0.00 36.65 2.10
4444 4676 6.435591 TGGCTGGATGTGATATCTAGTTAGAG 59.564 42.308 3.98 0.00 35.50 2.43
4445 4677 6.127479 GGCTGGATGTGATATCTAGTTAGAGG 60.127 46.154 3.98 0.00 35.50 3.69
4446 4678 6.127479 GCTGGATGTGATATCTAGTTAGAGGG 60.127 46.154 3.98 0.00 35.50 4.30
4447 4679 6.256819 TGGATGTGATATCTAGTTAGAGGGG 58.743 44.000 3.98 0.00 35.50 4.79
4448 4680 6.183361 TGGATGTGATATCTAGTTAGAGGGGT 60.183 42.308 3.98 0.00 35.50 4.95
4449 4681 6.726764 GGATGTGATATCTAGTTAGAGGGGTT 59.273 42.308 3.98 0.00 35.50 4.11
4450 4682 7.235812 GGATGTGATATCTAGTTAGAGGGGTTT 59.764 40.741 3.98 0.00 35.50 3.27
4451 4683 7.989947 TGTGATATCTAGTTAGAGGGGTTTT 57.010 36.000 3.98 0.00 35.50 2.43
4452 4684 8.019656 TGTGATATCTAGTTAGAGGGGTTTTC 57.980 38.462 3.98 0.00 35.50 2.29
4453 4685 7.146648 GTGATATCTAGTTAGAGGGGTTTTCG 58.853 42.308 3.98 0.00 35.50 3.46
4454 4686 6.837568 TGATATCTAGTTAGAGGGGTTTTCGT 59.162 38.462 3.98 0.00 35.50 3.85
4455 4687 8.000709 TGATATCTAGTTAGAGGGGTTTTCGTA 58.999 37.037 3.98 0.00 35.50 3.43
4456 4688 8.953223 ATATCTAGTTAGAGGGGTTTTCGTAT 57.047 34.615 0.00 0.00 35.50 3.06
4457 4689 6.461110 TCTAGTTAGAGGGGTTTTCGTATG 57.539 41.667 0.00 0.00 0.00 2.39
4458 4690 4.482952 AGTTAGAGGGGTTTTCGTATGG 57.517 45.455 0.00 0.00 0.00 2.74
4459 4691 2.941064 GTTAGAGGGGTTTTCGTATGGC 59.059 50.000 0.00 0.00 0.00 4.40
4466 4698 2.092807 GGGTTTTCGTATGGCCCTAGAA 60.093 50.000 0.00 0.00 36.49 2.10
4638 4872 6.811954 TGTTGACTAACAGTTGATGAGTACA 58.188 36.000 0.00 0.00 41.66 2.90
4675 4920 1.000843 TGCTTGTCTGCTTCGCTTAGA 59.999 47.619 0.00 0.00 0.00 2.10
4835 5323 2.100216 CACGCCGGCATAGCAAAC 59.900 61.111 28.98 0.00 0.00 2.93
4850 5338 0.865111 CAAACGACAGAACGCATCCA 59.135 50.000 0.00 0.00 36.70 3.41
4951 5439 5.865085 ACAATAGTTGGTTAGCACTTGAGA 58.135 37.500 0.00 0.00 34.12 3.27
4952 5440 5.701290 ACAATAGTTGGTTAGCACTTGAGAC 59.299 40.000 0.00 0.00 34.12 3.36
4953 5441 5.746990 ATAGTTGGTTAGCACTTGAGACT 57.253 39.130 0.00 0.00 0.00 3.24
4954 5442 4.423625 AGTTGGTTAGCACTTGAGACTT 57.576 40.909 0.00 0.00 0.00 3.01
4955 5443 4.130118 AGTTGGTTAGCACTTGAGACTTG 58.870 43.478 0.00 0.00 0.00 3.16
4956 5444 4.127171 GTTGGTTAGCACTTGAGACTTGA 58.873 43.478 0.00 0.00 0.00 3.02
4957 5445 3.995199 TGGTTAGCACTTGAGACTTGAG 58.005 45.455 0.00 0.00 0.00 3.02
4979 5472 1.556911 GGGAGGAAGAAGCATCTCACA 59.443 52.381 0.00 0.00 33.77 3.58
5150 5643 3.764160 CTCCTCCTGGATTGGCCGC 62.764 68.421 0.00 0.00 42.29 6.53
5151 5644 4.113815 CCTCCTGGATTGGCCGCA 62.114 66.667 0.00 0.00 40.66 5.69
5229 5722 0.977395 CTTCGGTCCTGTCCCTCTTT 59.023 55.000 0.00 0.00 0.00 2.52
5240 5733 3.565307 TGTCCCTCTTTGCAGACATTTT 58.435 40.909 0.44 0.00 34.44 1.82
5252 5745 2.552315 CAGACATTTTGCCGTGGTAAGT 59.448 45.455 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.056328 GACCTTGACCTTGGCGGC 61.056 66.667 0.00 0.00 35.61 6.53
25 26 1.002134 ATGACCTTGACCTTGGCGG 60.002 57.895 0.00 0.00 39.35 6.13
26 27 1.026718 GGATGACCTTGACCTTGGCG 61.027 60.000 0.00 0.00 0.00 5.69
27 28 1.026718 CGGATGACCTTGACCTTGGC 61.027 60.000 0.00 0.00 0.00 4.52
28 29 1.026718 GCGGATGACCTTGACCTTGG 61.027 60.000 0.00 0.00 0.00 3.61
29 30 1.361668 CGCGGATGACCTTGACCTTG 61.362 60.000 0.00 0.00 0.00 3.61
30 31 1.079127 CGCGGATGACCTTGACCTT 60.079 57.895 0.00 0.00 0.00 3.50
31 32 2.579201 CGCGGATGACCTTGACCT 59.421 61.111 0.00 0.00 0.00 3.85
32 33 2.511600 CCGCGGATGACCTTGACC 60.512 66.667 24.07 0.00 0.00 4.02
33 34 3.195698 GCCGCGGATGACCTTGAC 61.196 66.667 33.48 2.06 0.00 3.18
34 35 4.812476 CGCCGCGGATGACCTTGA 62.812 66.667 33.48 0.00 0.00 3.02
440 441 3.692406 CCTATAGCCGCGACCCCC 61.692 72.222 8.23 0.00 0.00 5.40
441 442 2.599578 TCCTATAGCCGCGACCCC 60.600 66.667 8.23 0.00 0.00 4.95
442 443 2.649614 GTCCTATAGCCGCGACCC 59.350 66.667 8.23 0.00 0.00 4.46
443 444 2.254651 CGTCCTATAGCCGCGACC 59.745 66.667 8.23 0.00 0.00 4.79
444 445 2.254651 CCGTCCTATAGCCGCGAC 59.745 66.667 8.23 0.00 0.00 5.19
445 446 2.981909 CCCGTCCTATAGCCGCGA 60.982 66.667 8.23 0.00 0.00 5.87
446 447 4.052229 CCCCGTCCTATAGCCGCG 62.052 72.222 0.00 0.00 0.00 6.46
447 448 1.181098 TTACCCCGTCCTATAGCCGC 61.181 60.000 0.00 0.00 0.00 6.53
448 449 0.886563 CTTACCCCGTCCTATAGCCG 59.113 60.000 0.00 0.00 0.00 5.52
449 450 0.607112 GCTTACCCCGTCCTATAGCC 59.393 60.000 0.00 0.00 0.00 3.93
450 451 0.243095 CGCTTACCCCGTCCTATAGC 59.757 60.000 0.00 0.00 0.00 2.97
451 452 0.886563 CCGCTTACCCCGTCCTATAG 59.113 60.000 0.00 0.00 0.00 1.31
452 453 0.540365 CCCGCTTACCCCGTCCTATA 60.540 60.000 0.00 0.00 0.00 1.31
453 454 1.835712 CCCGCTTACCCCGTCCTAT 60.836 63.158 0.00 0.00 0.00 2.57
454 455 2.442643 CCCGCTTACCCCGTCCTA 60.443 66.667 0.00 0.00 0.00 2.94
457 458 4.462280 CACCCCGCTTACCCCGTC 62.462 72.222 0.00 0.00 0.00 4.79
509 510 3.744155 CTCCCCCTCCAAAGCCCC 61.744 72.222 0.00 0.00 0.00 5.80
510 511 2.216782 CTTCTCCCCCTCCAAAGCCC 62.217 65.000 0.00 0.00 0.00 5.19
511 512 1.208165 TCTTCTCCCCCTCCAAAGCC 61.208 60.000 0.00 0.00 0.00 4.35
512 513 0.698818 TTCTTCTCCCCCTCCAAAGC 59.301 55.000 0.00 0.00 0.00 3.51
513 514 2.238395 CTCTTCTTCTCCCCCTCCAAAG 59.762 54.545 0.00 0.00 0.00 2.77
514 515 2.269940 CTCTTCTTCTCCCCCTCCAAA 58.730 52.381 0.00 0.00 0.00 3.28
515 516 1.958288 CTCTTCTTCTCCCCCTCCAA 58.042 55.000 0.00 0.00 0.00 3.53
516 517 0.618968 GCTCTTCTTCTCCCCCTCCA 60.619 60.000 0.00 0.00 0.00 3.86
517 518 1.681486 CGCTCTTCTTCTCCCCCTCC 61.681 65.000 0.00 0.00 0.00 4.30
518 519 1.819905 CGCTCTTCTTCTCCCCCTC 59.180 63.158 0.00 0.00 0.00 4.30
519 520 2.363172 GCGCTCTTCTTCTCCCCCT 61.363 63.158 0.00 0.00 0.00 4.79
520 521 2.188207 GCGCTCTTCTTCTCCCCC 59.812 66.667 0.00 0.00 0.00 5.40
521 522 2.202810 CGCGCTCTTCTTCTCCCC 60.203 66.667 5.56 0.00 0.00 4.81
522 523 2.888051 GCGCGCTCTTCTTCTCCC 60.888 66.667 26.67 0.00 0.00 4.30
523 524 2.125912 TGCGCGCTCTTCTTCTCC 60.126 61.111 33.29 0.00 0.00 3.71
524 525 2.797462 GCTGCGCGCTCTTCTTCTC 61.797 63.158 33.29 6.49 35.14 2.87
525 526 2.813042 GCTGCGCGCTCTTCTTCT 60.813 61.111 33.29 0.00 35.14 2.85
573 574 2.882132 GGTGTATTTGCGGCACCC 59.118 61.111 0.05 0.00 44.95 4.61
574 575 2.483288 CGGTGTATTTGCGGCACC 59.517 61.111 0.05 0.00 46.61 5.01
575 576 2.202427 GCGGTGTATTTGCGGCAC 60.202 61.111 0.05 0.00 0.00 5.01
580 581 2.021380 CTCGCGCGGTGTATTTGC 59.979 61.111 31.69 0.00 0.00 3.68
581 582 0.802994 TACCTCGCGCGGTGTATTTG 60.803 55.000 30.04 11.89 37.93 2.32
582 583 0.803380 GTACCTCGCGCGGTGTATTT 60.803 55.000 30.04 4.88 37.93 1.40
583 584 1.226773 GTACCTCGCGCGGTGTATT 60.227 57.895 30.04 5.68 37.93 1.89
584 585 2.410469 GTACCTCGCGCGGTGTAT 59.590 61.111 30.04 13.70 37.93 2.29
585 586 3.814268 GGTACCTCGCGCGGTGTA 61.814 66.667 30.04 26.13 37.93 2.90
592 593 3.446570 AGGAACCGGTACCTCGCG 61.447 66.667 8.00 0.00 0.00 5.87
593 594 2.183555 CAGGAACCGGTACCTCGC 59.816 66.667 8.00 0.00 33.91 5.03
594 595 2.183555 GCAGGAACCGGTACCTCG 59.816 66.667 8.00 2.07 33.91 4.63
595 596 2.582978 GGCAGGAACCGGTACCTC 59.417 66.667 8.00 0.63 33.91 3.85
612 613 1.087202 TATAAGCAGTTGGGCACGCG 61.087 55.000 3.53 3.53 35.83 6.01
613 614 0.377203 GTATAAGCAGTTGGGCACGC 59.623 55.000 0.00 0.00 35.83 5.34
614 615 1.014352 GGTATAAGCAGTTGGGCACG 58.986 55.000 0.00 0.00 35.83 5.34
615 616 1.014352 CGGTATAAGCAGTTGGGCAC 58.986 55.000 0.00 0.00 35.83 5.01
616 617 0.746563 GCGGTATAAGCAGTTGGGCA 60.747 55.000 0.00 0.00 35.83 5.36
617 618 0.746563 TGCGGTATAAGCAGTTGGGC 60.747 55.000 0.50 0.00 40.01 5.36
618 619 1.014352 GTGCGGTATAAGCAGTTGGG 58.986 55.000 4.58 0.00 46.10 4.12
619 620 0.650512 CGTGCGGTATAAGCAGTTGG 59.349 55.000 4.58 0.00 46.10 3.77
620 621 0.026285 GCGTGCGGTATAAGCAGTTG 59.974 55.000 4.58 0.77 46.10 3.16
621 622 1.418342 CGCGTGCGGTATAAGCAGTT 61.418 55.000 6.30 0.00 46.10 3.16
622 623 1.876714 CGCGTGCGGTATAAGCAGT 60.877 57.895 6.30 0.00 46.10 4.40
623 624 2.920869 CGCGTGCGGTATAAGCAG 59.079 61.111 6.30 1.95 46.10 4.24
624 625 3.259020 GCGCGTGCGGTATAAGCA 61.259 61.111 16.70 0.50 42.99 3.91
679 680 0.595567 TATACCCACTTTAGCGCGCG 60.596 55.000 28.44 28.44 0.00 6.86
680 681 1.792006 ATATACCCACTTTAGCGCGC 58.208 50.000 26.66 26.66 0.00 6.86
681 682 4.143473 CGTAAATATACCCACTTTAGCGCG 60.143 45.833 0.00 0.00 0.00 6.86
682 683 4.151157 CCGTAAATATACCCACTTTAGCGC 59.849 45.833 0.00 0.00 0.00 5.92
683 684 4.151157 GCCGTAAATATACCCACTTTAGCG 59.849 45.833 0.00 0.00 0.00 4.26
684 685 4.151157 CGCCGTAAATATACCCACTTTAGC 59.849 45.833 0.00 0.00 0.00 3.09
685 686 4.151157 GCGCCGTAAATATACCCACTTTAG 59.849 45.833 0.00 0.00 0.00 1.85
686 687 4.057432 GCGCCGTAAATATACCCACTTTA 58.943 43.478 0.00 0.00 0.00 1.85
687 688 2.874086 GCGCCGTAAATATACCCACTTT 59.126 45.455 0.00 0.00 0.00 2.66
688 689 2.486918 GCGCCGTAAATATACCCACTT 58.513 47.619 0.00 0.00 0.00 3.16
689 690 1.603678 CGCGCCGTAAATATACCCACT 60.604 52.381 0.00 0.00 0.00 4.00
690 691 0.785979 CGCGCCGTAAATATACCCAC 59.214 55.000 0.00 0.00 0.00 4.61
691 692 0.945265 GCGCGCCGTAAATATACCCA 60.945 55.000 23.24 0.00 0.00 4.51
692 693 1.783434 GCGCGCCGTAAATATACCC 59.217 57.895 23.24 0.00 0.00 3.69
693 694 1.413368 CGCGCGCCGTAAATATACC 59.587 57.895 27.72 0.00 0.00 2.73
694 695 1.225289 GCGCGCGCCGTAAATATAC 60.225 57.895 42.83 12.00 39.71 1.47
695 696 3.149092 GCGCGCGCCGTAAATATA 58.851 55.556 42.83 0.00 39.71 0.86
711 712 4.166011 CAGGCGCGCTAAACAGGC 62.166 66.667 32.29 11.63 0.00 4.85
712 713 2.325082 AACAGGCGCGCTAAACAGG 61.325 57.895 32.29 14.36 0.00 4.00
713 714 1.154413 CAACAGGCGCGCTAAACAG 60.154 57.895 32.29 13.50 0.00 3.16
714 715 1.160946 TTCAACAGGCGCGCTAAACA 61.161 50.000 32.29 8.11 0.00 2.83
715 716 0.452784 CTTCAACAGGCGCGCTAAAC 60.453 55.000 32.29 14.56 0.00 2.01
716 717 0.601576 TCTTCAACAGGCGCGCTAAA 60.602 50.000 32.29 14.38 0.00 1.85
717 718 0.391130 ATCTTCAACAGGCGCGCTAA 60.391 50.000 32.29 14.04 0.00 3.09
718 719 1.083806 CATCTTCAACAGGCGCGCTA 61.084 55.000 32.29 6.87 0.00 4.26
719 720 2.046892 ATCTTCAACAGGCGCGCT 60.047 55.556 32.29 14.46 0.00 5.92
720 721 2.099062 CATCTTCAACAGGCGCGC 59.901 61.111 25.94 25.94 0.00 6.86
721 722 2.099062 GCATCTTCAACAGGCGCG 59.901 61.111 0.00 0.00 0.00 6.86
722 723 1.427020 GAGCATCTTCAACAGGCGC 59.573 57.895 0.00 0.00 0.00 6.53
734 735 0.179097 GAACCCGACCTGAGAGCATC 60.179 60.000 0.00 0.00 0.00 3.91
735 736 1.617947 GGAACCCGACCTGAGAGCAT 61.618 60.000 0.00 0.00 0.00 3.79
736 737 2.283529 GGAACCCGACCTGAGAGCA 61.284 63.158 0.00 0.00 0.00 4.26
737 738 1.985116 AGGAACCCGACCTGAGAGC 60.985 63.158 0.00 0.00 36.30 4.09
738 739 4.443934 AGGAACCCGACCTGAGAG 57.556 61.111 0.00 0.00 36.30 3.20
767 768 4.605967 CGCGCCGAGAGAGAGAGC 62.606 72.222 0.00 0.00 0.00 4.09
771 772 3.812019 GGTTCGCGCCGAGAGAGA 61.812 66.667 0.00 0.00 37.14 3.10
923 927 1.122632 TGGGTGAAGAAGTGCCGGTA 61.123 55.000 1.90 0.00 0.00 4.02
959 963 0.382515 GTCGGTCGGGAGAAGAGATG 59.617 60.000 0.00 0.00 42.89 2.90
960 964 0.752376 GGTCGGTCGGGAGAAGAGAT 60.752 60.000 0.00 0.00 42.89 2.75
984 989 2.284625 ATGGCTCACCGGTCCAGA 60.285 61.111 17.60 6.31 39.70 3.86
1008 1013 3.742248 CTCGTCCTCCTCCCCCTCC 62.742 73.684 0.00 0.00 0.00 4.30
1117 1122 3.692406 GAGGAGGTCCGCGTTGGT 61.692 66.667 4.92 0.00 42.08 3.67
1157 1162 2.358737 CACGTTCAGGGACAGGCC 60.359 66.667 0.00 0.00 0.00 5.19
1159 1164 1.669115 CTGCACGTTCAGGGACAGG 60.669 63.158 7.37 0.00 0.00 4.00
1209 1233 2.433031 CCCTAAGAATCCCCATCCCTT 58.567 52.381 0.00 0.00 0.00 3.95
1242 1266 2.400467 GGATGCCCCCTAGAAGTCTA 57.600 55.000 0.00 0.00 0.00 2.59
1243 1267 3.249119 GGATGCCCCCTAGAAGTCT 57.751 57.895 0.00 0.00 0.00 3.24
1274 1300 1.152735 TAGCTCCCTACTCCCTGCG 60.153 63.158 0.00 0.00 0.00 5.18
1302 1328 5.950883 TCATTCAGGTTCTACTTGTACTCG 58.049 41.667 0.00 0.00 0.00 4.18
1332 1358 2.646930 TCACAAGCAGGCAATCCATAG 58.353 47.619 0.00 0.00 33.74 2.23
1346 1372 2.575532 ACGCCATAATCCCATCACAAG 58.424 47.619 0.00 0.00 0.00 3.16
1377 1403 6.373774 GCAACTATCAGCTAATAATCCAGCAT 59.626 38.462 0.00 0.00 40.36 3.79
1439 1469 2.486982 CCAAGACACCAATTGCTCTCAG 59.513 50.000 0.00 0.00 0.00 3.35
1492 1526 2.268076 ACTGGAACAATGCCACGCC 61.268 57.895 0.00 0.00 38.70 5.68
1570 1645 1.747709 AGCTTAGCTGCTGTCAATGG 58.252 50.000 13.43 0.00 42.33 3.16
1626 1706 5.178797 ACCGCATGCCAGTATAAATAGATC 58.821 41.667 13.15 0.00 0.00 2.75
1671 1751 1.000506 ACTTTCTTGCAGCAGCCAATG 59.999 47.619 0.00 0.00 41.13 2.82
1675 1755 1.200948 CCTTACTTTCTTGCAGCAGCC 59.799 52.381 0.00 0.00 41.13 4.85
1733 1860 3.887716 CCAAGGGATAAGGAATGAGCAAG 59.112 47.826 0.00 0.00 0.00 4.01
1734 1861 3.527253 TCCAAGGGATAAGGAATGAGCAA 59.473 43.478 0.00 0.00 0.00 3.91
1735 1862 3.122480 TCCAAGGGATAAGGAATGAGCA 58.878 45.455 0.00 0.00 0.00 4.26
1791 1953 6.979465 TGCAGATTTATGAAACATTGTGACA 58.021 32.000 0.00 0.00 0.00 3.58
2015 2181 3.159213 TGGTTCTGGCTCAACATCATT 57.841 42.857 2.30 0.00 0.00 2.57
2047 2213 7.454260 ACACTTTGATCCTACTGAAAATTCC 57.546 36.000 0.00 0.00 0.00 3.01
2119 2285 1.670967 GCATTGCCTGAACCTTCAAGC 60.671 52.381 0.00 2.21 43.25 4.01
2198 2364 9.014297 AGACAATCTTTGTGTAAAAAGGATAGG 57.986 33.333 0.00 0.00 45.52 2.57
2226 2392 4.038642 GGTAACAAGGCTGGTTCAATTCAA 59.961 41.667 11.33 0.00 0.00 2.69
2227 2393 3.572255 GGTAACAAGGCTGGTTCAATTCA 59.428 43.478 11.33 0.00 0.00 2.57
2277 2443 5.065613 ACCAATACCAACCATATCAGCAT 57.934 39.130 0.00 0.00 0.00 3.79
2371 2539 4.096984 AGCATATTTGAAGAAGGGAAAGCG 59.903 41.667 0.00 0.00 0.00 4.68
2424 2592 6.493458 AGGCTATTCAACAAAACAACCATACT 59.507 34.615 0.00 0.00 0.00 2.12
2445 2613 3.254166 CAGTTGTGCAATAGTCAAAGGCT 59.746 43.478 0.00 0.00 0.00 4.58
2546 2726 7.576750 TTAGACAATCGTATTCACAACAGAC 57.423 36.000 0.00 0.00 0.00 3.51
2623 2803 5.547276 AGATGGGATTTGGAAATCAAACCAA 59.453 36.000 12.90 0.00 46.72 3.67
2715 2900 5.055812 TGAGTATATGCGCATTTCACATGA 58.944 37.500 30.42 8.10 0.00 3.07
2765 2950 5.491982 ACGCTCAGGTTTTATCAAGAGAAT 58.508 37.500 0.00 0.00 0.00 2.40
2848 3033 2.026729 GCTCTAAGAGGGGTTTTCTGCT 60.027 50.000 0.00 0.00 0.00 4.24
2893 3080 1.705186 TGGCTGAAGGAAAGGTAGCTT 59.295 47.619 0.12 0.12 34.89 3.74
3102 3292 0.954452 GCACAGTCCAAAGGGTTCAG 59.046 55.000 0.00 0.00 34.93 3.02
3130 3320 5.047731 TGTGAAAACAAATGGACAAGACACA 60.048 36.000 0.00 0.00 0.00 3.72
3170 3360 5.018149 TGAATCCATTGAAGGAGCAATTCA 58.982 37.500 0.00 0.00 41.90 2.57
3239 3429 2.109425 ACGCATAGGAAAACAGGGAC 57.891 50.000 0.00 0.00 0.00 4.46
3287 3477 4.588899 TGCATACCACTTAGCATGAAAGT 58.411 39.130 0.00 2.13 37.67 2.66
3383 3573 3.050275 GCCAAGGACTGTCGCCAC 61.050 66.667 1.07 0.00 0.00 5.01
3434 3624 0.540923 CTCTCCTCCAAAGGCCAGAG 59.459 60.000 5.01 5.26 43.02 3.35
3488 3678 2.123589 TCTTGAAAGACCACCTGACCA 58.876 47.619 0.00 0.00 0.00 4.02
3536 3726 4.689612 TTCTGGGATAGAAAGGGAATCG 57.310 45.455 0.00 0.00 42.31 3.34
3562 3752 0.108186 ATCTTCGCCGCTCACATCAA 60.108 50.000 0.00 0.00 0.00 2.57
3689 3882 2.046938 GGTCTCCGACTGAACACCA 58.953 57.895 0.00 0.00 32.47 4.17
3701 3894 0.108804 TCGCAAAGATCACGGTCTCC 60.109 55.000 0.00 0.00 0.00 3.71
3719 3912 1.270550 CTGGTGTGCTGTTCCCATTTC 59.729 52.381 0.00 0.00 0.00 2.17
3845 4038 0.321653 GGTCGAGTGATTGCTTGGGT 60.322 55.000 0.00 0.00 0.00 4.51
3869 4062 2.508928 CCCGTGGTTGTGGTGACT 59.491 61.111 0.00 0.00 0.00 3.41
3875 4068 4.308458 TCCTCGCCCGTGGTTGTG 62.308 66.667 8.41 0.00 0.00 3.33
3897 4090 0.037697 TTCGTGCGGTGTATGCTTCT 60.038 50.000 0.00 0.00 0.00 2.85
3913 4106 0.451792 GCTGCGCTTCTTGTCTTTCG 60.452 55.000 9.73 0.00 0.00 3.46
3957 4150 2.680913 CCAGCTCCGCAAACTTCCG 61.681 63.158 0.00 0.00 0.00 4.30
4071 4264 1.270839 CGACTCTTTCCTGGCTTTGGA 60.271 52.381 0.00 0.00 0.00 3.53
4323 4516 2.383683 TCTTCTCCTTCTCCTTCCTGGA 59.616 50.000 0.00 0.00 43.86 3.86
4364 4557 4.046998 GCACACACAGACGTCGCG 62.047 66.667 10.46 0.00 0.00 5.87
4394 4587 4.749245 ACAACAGAGCTCCAATTAAACG 57.251 40.909 10.93 0.00 0.00 3.60
4423 4655 6.183361 ACCCCTCTAACTAGATATCACATCCA 60.183 42.308 5.32 0.00 0.00 3.41
4424 4656 6.257586 ACCCCTCTAACTAGATATCACATCC 58.742 44.000 5.32 0.00 0.00 3.51
4425 4657 7.784470 AACCCCTCTAACTAGATATCACATC 57.216 40.000 5.32 0.00 0.00 3.06
4426 4658 8.568617 AAAACCCCTCTAACTAGATATCACAT 57.431 34.615 5.32 0.00 0.00 3.21
4427 4659 7.201884 CGAAAACCCCTCTAACTAGATATCACA 60.202 40.741 5.32 0.00 0.00 3.58
4428 4660 7.146648 CGAAAACCCCTCTAACTAGATATCAC 58.853 42.308 5.32 0.00 0.00 3.06
4429 4661 6.837568 ACGAAAACCCCTCTAACTAGATATCA 59.162 38.462 5.32 0.00 0.00 2.15
4430 4662 7.287512 ACGAAAACCCCTCTAACTAGATATC 57.712 40.000 0.00 0.00 0.00 1.63
4431 4663 8.804204 CATACGAAAACCCCTCTAACTAGATAT 58.196 37.037 0.00 0.00 0.00 1.63
4432 4664 7.232127 CCATACGAAAACCCCTCTAACTAGATA 59.768 40.741 0.00 0.00 0.00 1.98
4433 4665 6.041751 CCATACGAAAACCCCTCTAACTAGAT 59.958 42.308 0.00 0.00 0.00 1.98
4434 4666 5.361857 CCATACGAAAACCCCTCTAACTAGA 59.638 44.000 0.00 0.00 0.00 2.43
4435 4667 5.598769 CCATACGAAAACCCCTCTAACTAG 58.401 45.833 0.00 0.00 0.00 2.57
4436 4668 4.141869 GCCATACGAAAACCCCTCTAACTA 60.142 45.833 0.00 0.00 0.00 2.24
4437 4669 3.370209 GCCATACGAAAACCCCTCTAACT 60.370 47.826 0.00 0.00 0.00 2.24
4438 4670 2.941064 GCCATACGAAAACCCCTCTAAC 59.059 50.000 0.00 0.00 0.00 2.34
4439 4671 2.092807 GGCCATACGAAAACCCCTCTAA 60.093 50.000 0.00 0.00 0.00 2.10
4440 4672 1.487558 GGCCATACGAAAACCCCTCTA 59.512 52.381 0.00 0.00 0.00 2.43
4441 4673 0.255033 GGCCATACGAAAACCCCTCT 59.745 55.000 0.00 0.00 0.00 3.69
4442 4674 0.750546 GGGCCATACGAAAACCCCTC 60.751 60.000 4.39 0.00 34.23 4.30
4443 4675 1.212250 AGGGCCATACGAAAACCCCT 61.212 55.000 6.18 0.00 41.86 4.79
4444 4676 0.547553 TAGGGCCATACGAAAACCCC 59.452 55.000 6.18 0.00 41.86 4.95
4445 4677 1.487558 TCTAGGGCCATACGAAAACCC 59.512 52.381 6.18 0.00 41.17 4.11
4446 4678 2.994186 TCTAGGGCCATACGAAAACC 57.006 50.000 6.18 0.00 0.00 3.27
4447 4679 3.870274 ACTTCTAGGGCCATACGAAAAC 58.130 45.455 6.18 0.00 0.00 2.43
4448 4680 4.957954 TCTACTTCTAGGGCCATACGAAAA 59.042 41.667 6.18 0.00 0.00 2.29
4449 4681 4.539726 TCTACTTCTAGGGCCATACGAAA 58.460 43.478 6.18 0.00 0.00 3.46
4450 4682 4.174704 TCTACTTCTAGGGCCATACGAA 57.825 45.455 6.18 7.08 0.00 3.85
4451 4683 3.870538 TCTACTTCTAGGGCCATACGA 57.129 47.619 6.18 0.00 0.00 3.43
4452 4684 3.005578 GGTTCTACTTCTAGGGCCATACG 59.994 52.174 6.18 0.00 0.00 3.06
4453 4685 3.965347 TGGTTCTACTTCTAGGGCCATAC 59.035 47.826 6.18 0.00 0.00 2.39
4454 4686 4.274794 TGGTTCTACTTCTAGGGCCATA 57.725 45.455 6.18 0.00 0.00 2.74
4455 4687 3.130734 TGGTTCTACTTCTAGGGCCAT 57.869 47.619 6.18 0.00 0.00 4.40
4456 4688 2.634639 TGGTTCTACTTCTAGGGCCA 57.365 50.000 6.18 0.00 0.00 5.36
4457 4689 3.181453 GGAATGGTTCTACTTCTAGGGCC 60.181 52.174 0.00 0.00 0.00 5.80
4458 4690 3.712218 AGGAATGGTTCTACTTCTAGGGC 59.288 47.826 0.00 0.00 0.00 5.19
4459 4691 4.717280 ACAGGAATGGTTCTACTTCTAGGG 59.283 45.833 0.00 0.00 0.00 3.53
4634 4868 3.955650 TCACCTTGGAAGCTACTGTAC 57.044 47.619 0.00 0.00 0.00 2.90
4635 4869 3.369471 GCATCACCTTGGAAGCTACTGTA 60.369 47.826 0.00 0.00 0.00 2.74
4636 4870 2.616510 GCATCACCTTGGAAGCTACTGT 60.617 50.000 0.00 0.00 0.00 3.55
4637 4871 2.012673 GCATCACCTTGGAAGCTACTG 58.987 52.381 0.00 0.00 0.00 2.74
4638 4872 1.912043 AGCATCACCTTGGAAGCTACT 59.088 47.619 0.00 0.00 39.80 2.57
4675 4920 5.647658 TCGAGTGAATTGATATTTTGCACCT 59.352 36.000 0.00 0.00 0.00 4.00
4766 5252 6.924913 ATCAAGCCACTAGAAGCTCATATA 57.075 37.500 10.89 0.00 38.74 0.86
4835 5323 0.179215 GCTTTGGATGCGTTCTGTCG 60.179 55.000 0.00 0.00 0.00 4.35
4931 5419 5.746990 AGTCTCAAGTGCTAACCAACTAT 57.253 39.130 0.00 0.00 0.00 2.12
4951 5439 1.905894 GCTTCTTCCTCCCTCTCAAGT 59.094 52.381 0.00 0.00 0.00 3.16
4952 5440 1.905215 TGCTTCTTCCTCCCTCTCAAG 59.095 52.381 0.00 0.00 0.00 3.02
4953 5441 2.030027 TGCTTCTTCCTCCCTCTCAA 57.970 50.000 0.00 0.00 0.00 3.02
4954 5442 2.114616 GATGCTTCTTCCTCCCTCTCA 58.885 52.381 0.00 0.00 0.00 3.27
4955 5443 2.365293 GAGATGCTTCTTCCTCCCTCTC 59.635 54.545 3.29 0.00 30.30 3.20
4956 5444 2.292785 TGAGATGCTTCTTCCTCCCTCT 60.293 50.000 3.29 0.00 30.30 3.69
4957 5445 2.114616 TGAGATGCTTCTTCCTCCCTC 58.885 52.381 3.29 0.00 30.30 4.30
5158 5651 1.678970 GGACCCAGCATCCCAACAC 60.679 63.158 0.00 0.00 0.00 3.32
5229 5722 1.106351 ACCACGGCAAAATGTCTGCA 61.106 50.000 0.00 0.00 41.78 4.41
5240 5733 2.563620 TCATCAGTTACTTACCACGGCA 59.436 45.455 0.00 0.00 0.00 5.69
5269 5762 4.567971 CTGAGCTCACATATTCCCATCTC 58.432 47.826 13.74 0.00 0.00 2.75
5316 5809 7.176690 GCAGGTATACATTAAACTTATGGGCAT 59.823 37.037 5.01 0.00 0.00 4.40
5339 5832 2.937469 TTCATAAATGGGTTGCGCAG 57.063 45.000 11.31 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.