Multiple sequence alignment - TraesCS7B01G103200

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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 TraesCS7B01G103200 chr7B 100.000 8135 0 0 1 8135 118812878 118821012 0.000000e+00 15023.0
1 TraesCS7B01G103200 chr7B 88.699 584 57 7 1 576 234202207 234201625 0.000000e+00 704.0
2 TraesCS7B01G103200 chr7B 87.040 571 66 8 1 567 460540452 460541018 8.900000e-179 638.0
3 TraesCS7B01G103200 chr7B 86.047 129 17 1 7901 8029 339254423 339254296 3.960000e-28 137.0
4 TraesCS7B01G103200 chr7B 96.970 66 1 1 7481 7545 519460207 519460272 8.630000e-20 110.0
5 TraesCS7B01G103200 chr7A 95.920 4779 126 22 1636 6359 211202833 211207597 0.000000e+00 7681.0
6 TraesCS7B01G103200 chr7A 92.994 1513 57 18 6359 7827 211207665 211209172 0.000000e+00 2161.0
7 TraesCS7B01G103200 chr7A 93.293 835 43 9 816 1638 211201921 211202754 0.000000e+00 1219.0
8 TraesCS7B01G103200 chr7A 91.641 323 16 2 7824 8135 211211307 211211629 3.490000e-118 436.0
9 TraesCS7B01G103200 chr7D 95.955 3634 95 19 2771 6363 156449556 156453178 0.000000e+00 5849.0
10 TraesCS7B01G103200 chr7D 94.397 1160 29 14 6359 7486 156453242 156454397 0.000000e+00 1749.0
11 TraesCS7B01G103200 chr7D 94.559 974 46 3 1739 2708 156448271 156449241 0.000000e+00 1498.0
12 TraesCS7B01G103200 chr7D 92.388 867 49 12 786 1636 156447007 156447872 0.000000e+00 1219.0
13 TraesCS7B01G103200 chr7D 91.181 601 30 7 7557 8135 156454396 156454995 0.000000e+00 795.0
14 TraesCS7B01G103200 chr7D 95.327 107 3 1 1638 1742 156447929 156448035 1.400000e-37 169.0
15 TraesCS7B01G103200 chr3D 88.562 577 58 6 3 576 6199990 6200561 0.000000e+00 693.0
16 TraesCS7B01G103200 chr6B 87.500 576 69 3 1 574 276239700 276240274 0.000000e+00 662.0
17 TraesCS7B01G103200 chr2A 87.024 578 60 14 1 572 535421899 535422467 8.900000e-179 638.0
18 TraesCS7B01G103200 chr2A 77.211 294 40 13 876 1143 71593406 71593114 6.580000e-31 147.0
19 TraesCS7B01G103200 chr2A 82.895 76 12 1 1521 1596 601710556 601710630 5.270000e-07 67.6
20 TraesCS7B01G103200 chr2B 87.002 577 57 17 1 567 11325311 11325879 1.150000e-177 634.0
21 TraesCS7B01G103200 chr2D 86.851 578 60 10 1 567 362487089 362487661 4.140000e-177 632.0
22 TraesCS7B01G103200 chr2D 82.558 86 15 0 1654 1739 535056859 535056774 8.750000e-10 76.8
23 TraesCS7B01G103200 chr2D 82.895 76 12 1 1521 1596 458159864 458159938 5.270000e-07 67.6
24 TraesCS7B01G103200 chr1D 86.783 575 66 9 2 571 367815907 367815338 4.140000e-177 632.0
25 TraesCS7B01G103200 chr1D 86.598 582 62 14 1 574 303214443 303213870 5.360000e-176 628.0
26 TraesCS7B01G103200 chr1D 86.260 131 15 3 7900 8029 12942941 12943069 1.100000e-28 139.0
27 TraesCS7B01G103200 chr1D 86.260 131 15 3 7900 8029 174272731 174272859 1.100000e-28 139.0
28 TraesCS7B01G103200 chr6A 86.260 131 15 3 7900 8029 463910228 463910100 1.100000e-28 139.0
29 TraesCS7B01G103200 chr5D 86.260 131 15 3 7900 8029 122866937 122866809 1.100000e-28 139.0
30 TraesCS7B01G103200 chr4D 86.260 131 15 3 7900 8029 37973422 37973294 1.100000e-28 139.0
31 TraesCS7B01G103200 chr4D 86.260 131 15 3 7900 8029 400771390 400771262 1.100000e-28 139.0
32 TraesCS7B01G103200 chr5B 98.438 64 1 0 7482 7545 25131187 25131124 6.670000e-21 113.0
33 TraesCS7B01G103200 chr5B 82.353 85 15 0 1654 1738 518102227 518102311 3.150000e-09 75.0
34 TraesCS7B01G103200 chr4B 98.387 62 1 0 7484 7545 50752054 50752115 8.630000e-20 110.0
35 TraesCS7B01G103200 chr4B 98.387 62 1 0 7484 7545 448958043 448957982 8.630000e-20 110.0
36 TraesCS7B01G103200 chr4B 98.387 62 1 0 7484 7545 459999605 459999666 8.630000e-20 110.0
37 TraesCS7B01G103200 chr1B 98.387 62 1 0 7484 7545 148289602 148289541 8.630000e-20 110.0
38 TraesCS7B01G103200 chr1B 98.387 62 1 0 7484 7545 472167858 472167797 8.630000e-20 110.0
39 TraesCS7B01G103200 chr1B 98.387 62 1 0 7484 7545 544910895 544910834 8.630000e-20 110.0
40 TraesCS7B01G103200 chr3B 92.958 71 5 0 7475 7545 651725134 651725064 4.020000e-18 104.0
41 TraesCS7B01G103200 chr4A 82.558 86 15 0 1654 1739 485998820 485998905 8.750000e-10 76.8
42 TraesCS7B01G103200 chr5A 88.679 53 4 2 1544 1594 230548175 230548123 6.820000e-06 63.9
43 TraesCS7B01G103200 chr5A 88.679 53 4 2 1544 1594 230549638 230549586 6.820000e-06 63.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G103200 chr7B 118812878 118821012 8134 False 15023.000000 15023 100.000000 1 8135 1 chr7B.!!$F1 8134
1 TraesCS7B01G103200 chr7B 234201625 234202207 582 True 704.000000 704 88.699000 1 576 1 chr7B.!!$R1 575
2 TraesCS7B01G103200 chr7B 460540452 460541018 566 False 638.000000 638 87.040000 1 567 1 chr7B.!!$F2 566
3 TraesCS7B01G103200 chr7A 211201921 211211629 9708 False 2874.250000 7681 93.462000 816 8135 4 chr7A.!!$F1 7319
4 TraesCS7B01G103200 chr7D 156447007 156454995 7988 False 1879.833333 5849 93.967833 786 8135 6 chr7D.!!$F1 7349
5 TraesCS7B01G103200 chr3D 6199990 6200561 571 False 693.000000 693 88.562000 3 576 1 chr3D.!!$F1 573
6 TraesCS7B01G103200 chr6B 276239700 276240274 574 False 662.000000 662 87.500000 1 574 1 chr6B.!!$F1 573
7 TraesCS7B01G103200 chr2A 535421899 535422467 568 False 638.000000 638 87.024000 1 572 1 chr2A.!!$F1 571
8 TraesCS7B01G103200 chr2B 11325311 11325879 568 False 634.000000 634 87.002000 1 567 1 chr2B.!!$F1 566
9 TraesCS7B01G103200 chr2D 362487089 362487661 572 False 632.000000 632 86.851000 1 567 1 chr2D.!!$F1 566
10 TraesCS7B01G103200 chr1D 367815338 367815907 569 True 632.000000 632 86.783000 2 571 1 chr1D.!!$R2 569
11 TraesCS7B01G103200 chr1D 303213870 303214443 573 True 628.000000 628 86.598000 1 574 1 chr1D.!!$R1 573

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
662 683 0.036952 CAGATGCCCTCTTCACACGT 60.037 55.000 0.00 0.00 29.16 4.49 F
724 745 0.040058 ATTGGCCAGCTGTCCAATCA 59.960 50.000 31.33 12.48 46.90 2.57 F
727 748 0.106819 GGCCAGCTGTCCAATCAGAT 60.107 55.000 9.40 0.00 37.61 2.90 F
1041 1068 0.109342 CTTCCATTCCAGCCGCCTAT 59.891 55.000 0.00 0.00 0.00 2.57 F
1454 1490 0.179004 TGGGAATGTGGCGAACAAGT 60.179 50.000 0.00 0.00 43.61 3.16 F
2559 2928 2.027837 CACTCCCTGACATCACATGTGA 60.028 50.000 29.67 29.67 45.03 3.58 F
3792 4423 0.657312 TATGGCGCGCATTCTTCAAG 59.343 50.000 34.42 0.00 0.00 3.02 F
4216 4848 1.202698 GGTATGAGAGGTGATGGGCAC 60.203 57.143 0.00 0.00 46.98 5.01 F
5623 6301 1.000896 AGTTTCCATCGGCCCCTTG 60.001 57.895 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1650 0.251608 ACACACCCAATACCCCAAGC 60.252 55.000 0.00 0.00 0.00 4.01 R
2637 3006 0.730840 ACACATGCATGCTGACATCG 59.269 50.000 26.53 7.39 32.87 3.84 R
2744 3124 5.768164 TCCTCCTCAAGTAACACAAATTTCC 59.232 40.000 0.00 0.00 0.00 3.13 R
2950 3571 3.200605 TGAGCCAAATAGAGAATGCCTCA 59.799 43.478 0.00 0.00 44.40 3.86 R
3425 4055 2.408565 TCCTCGCCCATCCTCTTTATT 58.591 47.619 0.00 0.00 0.00 1.40 R
4216 4848 2.376808 ATGCACCTTCAGAGTTCTCG 57.623 50.000 0.00 0.00 0.00 4.04 R
5084 5722 1.604593 GCACACAGATGGCCCAACT 60.605 57.895 0.00 0.00 0.00 3.16 R
6115 6796 2.225369 TGACATGTCAGGGGAGAAGAGA 60.225 50.000 24.56 0.00 34.14 3.10 R
7541 8325 0.523072 TTTTACTCCCTCCGTCGACG 59.477 55.000 30.33 30.33 39.44 5.12 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
115 116 1.082038 CGACGATCGAATCTCGGGG 60.082 63.158 24.34 0.00 43.74 5.73
147 148 2.036733 CCGACAGACAAAGGGAACTACA 59.963 50.000 0.00 0.00 42.68 2.74
181 184 9.098355 TCATAAAGGTTTGACTGATAAAGATCG 57.902 33.333 0.00 0.00 34.49 3.69
185 188 5.122396 AGGTTTGACTGATAAAGATCGTTGC 59.878 40.000 3.97 0.00 34.49 4.17
209 212 7.168219 GCAGAATATGTAGGAACCAATATGGA 58.832 38.462 2.85 0.00 40.96 3.41
354 359 1.946768 AGTTGGTGACCGAATGTTGTG 59.053 47.619 0.00 0.00 0.00 3.33
384 398 2.550180 CGAATGAGATGACGAGGAGCTA 59.450 50.000 0.00 0.00 0.00 3.32
385 399 3.190327 CGAATGAGATGACGAGGAGCTAT 59.810 47.826 0.00 0.00 0.00 2.97
389 403 2.487762 GAGATGACGAGGAGCTATGGAG 59.512 54.545 0.00 0.00 0.00 3.86
450 466 1.897133 TGATCTCCGGAAAGGTTTCGA 59.103 47.619 5.23 0.00 41.99 3.71
578 599 2.844839 GCGCCCTCTCCCTGGTAT 60.845 66.667 0.00 0.00 0.00 2.73
579 600 2.444256 GCGCCCTCTCCCTGGTATT 61.444 63.158 0.00 0.00 0.00 1.89
580 601 1.749033 CGCCCTCTCCCTGGTATTC 59.251 63.158 0.00 0.00 0.00 1.75
581 602 0.760945 CGCCCTCTCCCTGGTATTCT 60.761 60.000 0.00 0.00 0.00 2.40
582 603 1.512735 GCCCTCTCCCTGGTATTCTT 58.487 55.000 0.00 0.00 0.00 2.52
583 604 1.141858 GCCCTCTCCCTGGTATTCTTG 59.858 57.143 0.00 0.00 0.00 3.02
584 605 2.764269 CCCTCTCCCTGGTATTCTTGA 58.236 52.381 0.00 0.00 0.00 3.02
585 606 3.321950 CCCTCTCCCTGGTATTCTTGAT 58.678 50.000 0.00 0.00 0.00 2.57
586 607 4.493618 CCCTCTCCCTGGTATTCTTGATA 58.506 47.826 0.00 0.00 0.00 2.15
587 608 4.530161 CCCTCTCCCTGGTATTCTTGATAG 59.470 50.000 0.00 0.00 0.00 2.08
588 609 5.398236 CCTCTCCCTGGTATTCTTGATAGA 58.602 45.833 0.00 0.00 0.00 1.98
589 610 5.841237 CCTCTCCCTGGTATTCTTGATAGAA 59.159 44.000 0.00 0.00 44.16 2.10
590 611 6.327626 CCTCTCCCTGGTATTCTTGATAGAAA 59.672 42.308 0.00 0.00 43.32 2.52
591 612 7.147479 CCTCTCCCTGGTATTCTTGATAGAAAA 60.147 40.741 0.00 0.00 43.32 2.29
592 613 7.565680 TCTCCCTGGTATTCTTGATAGAAAAC 58.434 38.462 0.00 0.00 43.32 2.43
593 614 6.659824 TCCCTGGTATTCTTGATAGAAAACC 58.340 40.000 0.00 0.00 43.32 3.27
594 615 6.216662 TCCCTGGTATTCTTGATAGAAAACCA 59.783 38.462 0.00 0.00 43.32 3.67
595 616 7.062957 CCCTGGTATTCTTGATAGAAAACCAT 58.937 38.462 0.00 0.00 43.32 3.55
596 617 7.561356 CCCTGGTATTCTTGATAGAAAACCATT 59.439 37.037 0.00 0.00 43.32 3.16
597 618 8.624776 CCTGGTATTCTTGATAGAAAACCATTC 58.375 37.037 0.00 0.00 43.32 2.67
598 619 9.401058 CTGGTATTCTTGATAGAAAACCATTCT 57.599 33.333 0.00 0.00 43.32 2.40
603 624 9.667107 ATTCTTGATAGAAAACCATTCTACGAA 57.333 29.630 0.34 3.14 43.32 3.85
604 625 9.496873 TTCTTGATAGAAAACCATTCTACGAAA 57.503 29.630 0.34 0.00 37.45 3.46
605 626 9.667107 TCTTGATAGAAAACCATTCTACGAAAT 57.333 29.630 0.34 0.00 34.25 2.17
613 634 9.285770 GAAAACCATTCTACGAAATTACAATCC 57.714 33.333 0.00 0.00 0.00 3.01
614 635 6.598753 ACCATTCTACGAAATTACAATCCG 57.401 37.500 0.00 0.00 0.00 4.18
615 636 6.342906 ACCATTCTACGAAATTACAATCCGA 58.657 36.000 0.00 0.00 0.00 4.55
616 637 6.990349 ACCATTCTACGAAATTACAATCCGAT 59.010 34.615 0.00 0.00 0.00 4.18
617 638 7.497909 ACCATTCTACGAAATTACAATCCGATT 59.502 33.333 0.00 0.00 0.00 3.34
618 639 7.798516 CCATTCTACGAAATTACAATCCGATTG 59.201 37.037 17.88 17.88 45.59 2.67
628 649 1.331756 CAATCCGATTGTACAGCTGGC 59.668 52.381 19.93 11.09 35.57 4.85
629 650 0.179045 ATCCGATTGTACAGCTGGCC 60.179 55.000 19.93 8.34 0.00 5.36
630 651 1.078497 CCGATTGTACAGCTGGCCA 60.078 57.895 19.93 4.71 0.00 5.36
631 652 0.676466 CCGATTGTACAGCTGGCCAA 60.676 55.000 19.93 19.24 0.00 4.52
632 653 1.382522 CGATTGTACAGCTGGCCAAT 58.617 50.000 24.60 24.60 0.00 3.16
633 654 1.331756 CGATTGTACAGCTGGCCAATC 59.668 52.381 31.06 31.06 39.69 2.67
634 655 2.648059 GATTGTACAGCTGGCCAATCT 58.352 47.619 32.26 17.55 39.86 2.40
635 656 2.584835 TTGTACAGCTGGCCAATCTT 57.415 45.000 19.93 0.00 0.00 2.40
636 657 3.712016 TTGTACAGCTGGCCAATCTTA 57.288 42.857 19.93 0.00 0.00 2.10
637 658 3.931907 TGTACAGCTGGCCAATCTTAT 57.068 42.857 19.93 0.35 0.00 1.73
638 659 3.808728 TGTACAGCTGGCCAATCTTATC 58.191 45.455 19.93 0.56 0.00 1.75
639 660 2.355010 ACAGCTGGCCAATCTTATCC 57.645 50.000 19.93 0.00 0.00 2.59
640 661 1.233019 CAGCTGGCCAATCTTATCCG 58.767 55.000 7.01 0.00 0.00 4.18
641 662 0.109342 AGCTGGCCAATCTTATCCGG 59.891 55.000 7.01 0.00 0.00 5.14
642 663 0.890996 GCTGGCCAATCTTATCCGGG 60.891 60.000 7.01 0.00 0.00 5.73
643 664 0.890996 CTGGCCAATCTTATCCGGGC 60.891 60.000 7.01 0.00 44.05 6.13
644 665 1.150536 GGCCAATCTTATCCGGGCA 59.849 57.895 0.00 0.00 46.37 5.36
645 666 0.890996 GGCCAATCTTATCCGGGCAG 60.891 60.000 0.00 0.00 46.37 4.85
646 667 0.108585 GCCAATCTTATCCGGGCAGA 59.891 55.000 0.00 0.43 44.01 4.26
647 668 1.271597 GCCAATCTTATCCGGGCAGAT 60.272 52.381 0.00 3.19 44.01 2.90
648 669 2.430465 CCAATCTTATCCGGGCAGATG 58.570 52.381 0.00 2.08 0.00 2.90
649 670 1.808945 CAATCTTATCCGGGCAGATGC 59.191 52.381 0.00 0.00 41.14 3.91
660 681 2.475666 GCAGATGCCCTCTTCACAC 58.524 57.895 0.00 0.00 34.31 3.82
661 682 1.364626 GCAGATGCCCTCTTCACACG 61.365 60.000 0.00 0.00 34.31 4.49
662 683 0.036952 CAGATGCCCTCTTCACACGT 60.037 55.000 0.00 0.00 29.16 4.49
663 684 0.687354 AGATGCCCTCTTCACACGTT 59.313 50.000 0.00 0.00 0.00 3.99
664 685 0.798776 GATGCCCTCTTCACACGTTG 59.201 55.000 0.00 0.00 0.00 4.10
665 686 1.237285 ATGCCCTCTTCACACGTTGC 61.237 55.000 0.00 0.00 0.00 4.17
666 687 2.617274 GCCCTCTTCACACGTTGCC 61.617 63.158 0.00 0.00 0.00 4.52
667 688 2.317609 CCCTCTTCACACGTTGCCG 61.318 63.158 0.00 0.00 40.83 5.69
679 700 2.452006 CGTTGCCGTTTCATATCCAC 57.548 50.000 0.00 0.00 0.00 4.02
680 701 1.267334 CGTTGCCGTTTCATATCCACG 60.267 52.381 0.00 0.00 0.00 4.94
681 702 1.735571 GTTGCCGTTTCATATCCACGT 59.264 47.619 0.00 0.00 31.83 4.49
682 703 1.364721 TGCCGTTTCATATCCACGTG 58.635 50.000 9.08 9.08 31.83 4.49
683 704 1.338294 TGCCGTTTCATATCCACGTGT 60.338 47.619 15.65 0.00 31.83 4.49
684 705 1.062002 GCCGTTTCATATCCACGTGTG 59.938 52.381 15.65 6.16 31.83 3.82
685 706 2.612604 CCGTTTCATATCCACGTGTGA 58.387 47.619 15.65 11.79 31.83 3.58
686 707 2.997303 CCGTTTCATATCCACGTGTGAA 59.003 45.455 15.65 14.40 31.83 3.18
687 708 3.181524 CCGTTTCATATCCACGTGTGAAC 60.182 47.826 16.26 11.56 30.96 3.18
688 709 3.430556 CGTTTCATATCCACGTGTGAACA 59.569 43.478 16.26 7.68 30.96 3.18
689 710 4.092821 CGTTTCATATCCACGTGTGAACAT 59.907 41.667 16.26 8.15 30.96 2.71
690 711 5.289917 CGTTTCATATCCACGTGTGAACATA 59.710 40.000 16.26 2.99 30.96 2.29
691 712 6.019075 CGTTTCATATCCACGTGTGAACATAT 60.019 38.462 16.26 6.97 30.96 1.78
692 713 7.345192 GTTTCATATCCACGTGTGAACATATC 58.655 38.462 16.26 4.83 30.96 1.63
693 714 6.155475 TCATATCCACGTGTGAACATATCA 57.845 37.500 15.65 0.00 35.05 2.15
694 715 6.578023 TCATATCCACGTGTGAACATATCAA 58.422 36.000 15.65 0.00 40.50 2.57
695 716 6.478673 TCATATCCACGTGTGAACATATCAAC 59.521 38.462 15.65 0.00 40.50 3.18
696 717 2.990514 TCCACGTGTGAACATATCAACG 59.009 45.455 15.65 9.77 42.72 4.10
697 718 2.734606 CCACGTGTGAACATATCAACGT 59.265 45.455 15.65 10.66 46.61 3.99
699 720 2.734606 ACGTGTGAACATATCAACGTGG 59.265 45.455 13.71 0.00 45.33 4.94
700 721 2.990514 CGTGTGAACATATCAACGTGGA 59.009 45.455 0.00 0.00 40.50 4.02
701 722 3.616821 CGTGTGAACATATCAACGTGGAT 59.383 43.478 10.94 10.94 40.50 3.41
702 723 4.492409 CGTGTGAACATATCAACGTGGATG 60.492 45.833 16.00 3.74 40.50 3.51
703 724 4.629634 GTGTGAACATATCAACGTGGATGA 59.370 41.667 16.00 2.98 40.50 2.92
704 725 4.869861 TGTGAACATATCAACGTGGATGAG 59.130 41.667 16.00 9.93 40.50 2.90
705 726 5.109210 GTGAACATATCAACGTGGATGAGA 58.891 41.667 16.00 0.11 40.50 3.27
706 727 5.755375 GTGAACATATCAACGTGGATGAGAT 59.245 40.000 16.00 2.79 40.50 2.75
707 728 6.258727 GTGAACATATCAACGTGGATGAGATT 59.741 38.462 16.00 4.67 40.50 2.40
708 729 6.258507 TGAACATATCAACGTGGATGAGATTG 59.741 38.462 16.00 7.67 34.30 2.67
709 730 5.059161 ACATATCAACGTGGATGAGATTGG 58.941 41.667 16.00 0.00 0.00 3.16
710 731 1.737838 TCAACGTGGATGAGATTGGC 58.262 50.000 0.00 0.00 0.00 4.52
711 732 0.734889 CAACGTGGATGAGATTGGCC 59.265 55.000 0.00 0.00 0.00 5.36
712 733 0.327924 AACGTGGATGAGATTGGCCA 59.672 50.000 0.00 0.00 0.00 5.36
713 734 0.107508 ACGTGGATGAGATTGGCCAG 60.108 55.000 5.11 0.00 0.00 4.85
714 735 1.442526 CGTGGATGAGATTGGCCAGC 61.443 60.000 5.11 1.90 0.00 4.85
715 736 0.106819 GTGGATGAGATTGGCCAGCT 60.107 55.000 5.11 7.86 0.00 4.24
716 737 0.106868 TGGATGAGATTGGCCAGCTG 60.107 55.000 14.22 6.78 0.00 4.24
717 738 0.106819 GGATGAGATTGGCCAGCTGT 60.107 55.000 13.81 0.81 0.00 4.40
718 739 1.307097 GATGAGATTGGCCAGCTGTC 58.693 55.000 13.81 10.58 0.00 3.51
719 740 0.106819 ATGAGATTGGCCAGCTGTCC 60.107 55.000 13.81 10.52 0.00 4.02
720 741 1.300963 GAGATTGGCCAGCTGTCCA 59.699 57.895 13.62 13.62 0.00 4.02
721 742 0.322816 GAGATTGGCCAGCTGTCCAA 60.323 55.000 29.77 29.77 45.35 3.53
723 744 2.892025 ATTGGCCAGCTGTCCAATC 58.108 52.632 31.33 7.13 46.90 2.67
724 745 0.040058 ATTGGCCAGCTGTCCAATCA 59.960 50.000 31.33 12.48 46.90 2.57
725 746 0.609957 TTGGCCAGCTGTCCAATCAG 60.610 55.000 24.79 1.32 37.43 2.90
726 747 1.300963 GGCCAGCTGTCCAATCAGA 59.699 57.895 9.40 0.00 37.61 3.27
727 748 0.106819 GGCCAGCTGTCCAATCAGAT 60.107 55.000 9.40 0.00 37.61 2.90
728 749 1.684248 GGCCAGCTGTCCAATCAGATT 60.684 52.381 9.40 0.00 37.61 2.40
729 750 1.404391 GCCAGCTGTCCAATCAGATTG 59.596 52.381 15.40 15.40 37.61 2.67
730 751 2.719739 CCAGCTGTCCAATCAGATTGT 58.280 47.619 19.79 0.00 38.59 2.71
731 752 3.877559 CCAGCTGTCCAATCAGATTGTA 58.122 45.455 19.79 3.36 38.59 2.41
732 753 3.875727 CCAGCTGTCCAATCAGATTGTAG 59.124 47.826 19.79 15.36 38.59 2.74
733 754 4.511527 CAGCTGTCCAATCAGATTGTAGT 58.488 43.478 19.79 5.82 38.59 2.73
734 755 4.331992 CAGCTGTCCAATCAGATTGTAGTG 59.668 45.833 19.79 6.59 38.59 2.74
735 756 4.223700 AGCTGTCCAATCAGATTGTAGTGA 59.776 41.667 19.79 8.64 38.59 3.41
736 757 4.331168 GCTGTCCAATCAGATTGTAGTGAC 59.669 45.833 19.79 18.31 38.59 3.67
737 758 5.482006 CTGTCCAATCAGATTGTAGTGACA 58.518 41.667 21.90 21.90 38.59 3.58
738 759 7.512043 GCTGTCCAATCAGATTGTAGTGACAA 61.512 42.308 22.76 13.22 41.20 3.18
752 773 8.620116 TTGTAGTGACAATTCTTGATGAATGA 57.380 30.769 0.00 0.00 43.99 2.57
753 774 8.620116 TGTAGTGACAATTCTTGATGAATGAA 57.380 30.769 0.00 0.00 43.99 2.57
754 775 9.065798 TGTAGTGACAATTCTTGATGAATGAAA 57.934 29.630 0.00 0.00 43.99 2.69
755 776 9.334693 GTAGTGACAATTCTTGATGAATGAAAC 57.665 33.333 0.00 0.00 43.99 2.78
756 777 7.944061 AGTGACAATTCTTGATGAATGAAACA 58.056 30.769 0.00 0.00 43.99 2.83
757 778 7.864379 AGTGACAATTCTTGATGAATGAAACAC 59.136 33.333 0.00 0.00 43.99 3.32
758 779 7.115378 GTGACAATTCTTGATGAATGAAACACC 59.885 37.037 0.00 0.00 43.99 4.16
759 780 7.053316 ACAATTCTTGATGAATGAAACACCA 57.947 32.000 0.00 0.00 43.99 4.17
760 781 7.673180 ACAATTCTTGATGAATGAAACACCAT 58.327 30.769 0.00 0.00 43.99 3.55
761 782 8.152246 ACAATTCTTGATGAATGAAACACCATT 58.848 29.630 0.00 0.00 43.99 3.16
762 783 8.995220 CAATTCTTGATGAATGAAACACCATTT 58.005 29.630 0.00 0.00 43.99 2.32
763 784 9.563748 AATTCTTGATGAATGAAACACCATTTT 57.436 25.926 0.00 0.00 43.99 1.82
764 785 8.961294 TTCTTGATGAATGAAACACCATTTTT 57.039 26.923 0.00 0.00 36.93 1.94
1027 1054 0.972983 CCTCGCCTCTTCTCCTTCCA 60.973 60.000 0.00 0.00 0.00 3.53
1029 1056 1.484240 CTCGCCTCTTCTCCTTCCATT 59.516 52.381 0.00 0.00 0.00 3.16
1037 1064 1.821332 CTCCTTCCATTCCAGCCGC 60.821 63.158 0.00 0.00 0.00 6.53
1041 1068 0.109342 CTTCCATTCCAGCCGCCTAT 59.891 55.000 0.00 0.00 0.00 2.57
1134 1161 4.662961 TCAGCGACGCCTGTGGTG 62.663 66.667 17.79 7.22 39.41 4.17
1214 1250 4.101448 GGTGGCGGGCACAGAGAT 62.101 66.667 31.77 0.00 0.00 2.75
1290 1326 0.462047 CCCGTGGCCACAAGATACTC 60.462 60.000 34.16 5.35 0.00 2.59
1323 1359 3.717294 GTGCCCGATGACCCCACT 61.717 66.667 0.00 0.00 0.00 4.00
1409 1445 7.173218 TCCGCATTATTAGAACATCAATTCCTC 59.827 37.037 0.00 0.00 0.00 3.71
1435 1471 9.586435 CAAGTTTTAGTGGTTTCTGAGAAATTT 57.414 29.630 11.20 0.00 0.00 1.82
1454 1490 0.179004 TGGGAATGTGGCGAACAAGT 60.179 50.000 0.00 0.00 43.61 3.16
1500 1537 6.681729 AGTACTCCAGAAACACAGGAATAA 57.318 37.500 0.00 0.00 33.85 1.40
1540 1577 4.795469 TCATGTCATGGCATATTGAACCT 58.205 39.130 13.48 0.00 0.00 3.50
1603 1640 3.760738 TGGTTGCACCACATGAGAAATA 58.239 40.909 0.00 0.00 44.79 1.40
1613 1650 7.864379 GCACCACATGAGAAATATAGGAATTTG 59.136 37.037 0.00 0.00 0.00 2.32
1619 1656 7.587037 TGAGAAATATAGGAATTTGCTTGGG 57.413 36.000 0.00 0.00 0.00 4.12
1694 1815 3.891366 CCAGTCCCTCAAATCAAACAAGT 59.109 43.478 0.00 0.00 0.00 3.16
1786 2148 7.615582 TTCAGTCCATTAGCACAATTCTTAG 57.384 36.000 0.00 0.00 0.00 2.18
1804 2166 6.811253 TCTTAGCGTTATTTGTTGTCCATT 57.189 33.333 0.00 0.00 0.00 3.16
1850 2215 4.472691 TTCAATTTCTGAGTCGTTGCAG 57.527 40.909 0.00 0.00 34.81 4.41
1860 2225 4.878439 TGAGTCGTTGCAGTTGTAGTAAT 58.122 39.130 0.00 0.00 0.00 1.89
1863 2228 6.072342 TGAGTCGTTGCAGTTGTAGTAATAGA 60.072 38.462 0.00 0.00 0.00 1.98
1959 2324 6.932400 TGATGAAGTCCGTGTATTGTTACTTT 59.068 34.615 0.00 0.00 0.00 2.66
1960 2325 8.089597 TGATGAAGTCCGTGTATTGTTACTTTA 58.910 33.333 0.00 0.00 0.00 1.85
1961 2326 9.095065 GATGAAGTCCGTGTATTGTTACTTTAT 57.905 33.333 0.00 0.00 0.00 1.40
1975 2340 7.499200 TGTTACTTTATTAGGAACCTAGGCA 57.501 36.000 9.30 0.00 45.67 4.75
2309 2677 6.073058 TGTGATCTTTGTCACTTTGTGCTATC 60.073 38.462 8.31 0.00 46.70 2.08
2485 2854 4.065789 GGTCACTTAACCTCCTGAACTTG 58.934 47.826 0.00 0.00 36.32 3.16
2492 2861 3.801114 ACCTCCTGAACTTGTTTTTGC 57.199 42.857 0.00 0.00 0.00 3.68
2511 2880 6.374417 TTTGCTCTACTTAACTCCTGGAAT 57.626 37.500 0.00 0.00 0.00 3.01
2528 2897 7.751646 TCCTGGAATTTATAATAACGGGTCAT 58.248 34.615 0.00 0.00 0.00 3.06
2559 2928 2.027837 CACTCCCTGACATCACATGTGA 60.028 50.000 29.67 29.67 45.03 3.58
2637 3006 2.029380 GGCCCACCATGTTGTAGAAAAC 60.029 50.000 0.00 0.00 35.26 2.43
2702 3071 3.896854 GGGGGAGGGTGTATGAAAC 57.103 57.895 0.00 0.00 0.00 2.78
2709 3078 3.458189 GAGGGTGTATGAAACGATCTGG 58.542 50.000 0.00 0.00 0.00 3.86
2723 3092 9.878667 TGAAACGATCTGGTATTAGAATTACAA 57.121 29.630 0.00 0.00 0.00 2.41
2791 3412 4.503714 AGTGGACTTTTTCCTTGACTCA 57.496 40.909 0.00 0.00 46.10 3.41
2828 3449 2.176273 GCTATGAGGTGCCACGCAG 61.176 63.158 0.00 0.00 40.08 5.18
2950 3571 8.204160 TGGATTAGTGTATTTGAAGATGACGAT 58.796 33.333 0.00 0.00 0.00 3.73
2985 3606 2.189594 TGGCTCAATGAGGTCAGTTG 57.810 50.000 12.66 0.00 0.00 3.16
3055 3684 7.486551 TGTTTGTTTGTTACTGCAGTGATAAAC 59.513 33.333 36.00 36.00 42.03 2.01
3085 3714 5.835113 ACATTTAACCACATATCACTGCC 57.165 39.130 0.00 0.00 0.00 4.85
3094 3723 4.641541 CCACATATCACTGCCAATTCTCAA 59.358 41.667 0.00 0.00 0.00 3.02
3115 3744 9.983024 TCTCAAATTAATTTAACCCTGTCCATA 57.017 29.630 12.98 0.00 0.00 2.74
3180 3809 8.785329 TTAAAATCCCCAGAAAAATATGCAAC 57.215 30.769 0.00 0.00 0.00 4.17
3188 3817 6.369615 CCCAGAAAAATATGCAACTTTTCCAG 59.630 38.462 19.54 14.93 39.02 3.86
3249 3878 9.681692 TCTGTGTAATGAATTTGTGATTCTTTG 57.318 29.630 9.03 0.00 31.03 2.77
3295 3924 2.987046 CACGTTTCTTTTGAGAGGTGC 58.013 47.619 0.00 0.00 40.65 5.01
3470 4100 5.417580 TGATAATTTTTGGACTAGTGGTGCC 59.582 40.000 0.00 0.00 35.29 5.01
3792 4423 0.657312 TATGGCGCGCATTCTTCAAG 59.343 50.000 34.42 0.00 0.00 3.02
3833 4464 7.552050 TCCTTCAAATGGTCCATAACATTTT 57.448 32.000 4.33 0.00 42.78 1.82
3834 4465 7.610865 TCCTTCAAATGGTCCATAACATTTTC 58.389 34.615 4.33 0.00 42.78 2.29
4216 4848 1.202698 GGTATGAGAGGTGATGGGCAC 60.203 57.143 0.00 0.00 46.98 5.01
4276 4908 5.163405 TGAGACAGTAATTAGCCTTAGCAGG 60.163 44.000 0.00 0.00 43.56 4.85
4657 5295 4.023291 TCCCTGATACTGAATTTTTGGGC 58.977 43.478 0.00 0.00 32.62 5.36
4993 5631 2.369394 CAGGGAGCCAAGGTATGAAAC 58.631 52.381 0.00 0.00 0.00 2.78
5342 6020 7.617723 ACCTCAATTATCTAGTGTCTTCTCAGT 59.382 37.037 0.00 0.00 0.00 3.41
5387 6065 9.777297 ATATTACTGTTGCCTTGAAACAAAATT 57.223 25.926 0.00 0.00 37.10 1.82
5400 6078 7.227992 TGAAACAAAATTTTTGCCTCTAACG 57.772 32.000 19.29 0.00 0.00 3.18
5623 6301 1.000896 AGTTTCCATCGGCCCCTTG 60.001 57.895 0.00 0.00 0.00 3.61
5655 6333 7.918076 AGGAGTTACTGGAAATTGAATCACTA 58.082 34.615 0.00 0.00 0.00 2.74
6104 6784 5.221461 CGCTTAAGGTATGGTCCTACTCATT 60.221 44.000 4.29 0.00 36.74 2.57
6115 6796 5.116882 GGTCCTACTCATTGTAGCGATTTT 58.883 41.667 0.00 0.00 45.44 1.82
6121 6802 6.654793 ACTCATTGTAGCGATTTTCTCTTC 57.345 37.500 0.00 0.00 0.00 2.87
6216 6898 5.178996 TGTTCAAATGAATTTGGCATTTCCG 59.821 36.000 14.19 0.00 45.39 4.30
6294 6976 7.327214 TGTTACAGATGCACATACTACATTCA 58.673 34.615 0.00 0.00 0.00 2.57
6298 6980 8.962884 ACAGATGCACATACTACATTCATTAA 57.037 30.769 0.00 0.00 0.00 1.40
6300 6982 9.655769 CAGATGCACATACTACATTCATTAAAC 57.344 33.333 0.00 0.00 0.00 2.01
6374 7124 5.560966 AATTGTAAGCAATACCTTGTCCG 57.439 39.130 0.00 0.00 43.89 4.79
6402 7152 4.081642 GGGTAGTGTGATTAGAGAGTGCAA 60.082 45.833 0.00 0.00 0.00 4.08
6403 7153 5.105752 GGTAGTGTGATTAGAGAGTGCAAG 58.894 45.833 0.00 0.00 0.00 4.01
6446 7196 2.159667 GCCATTCAAAATTTCCTTGCGC 60.160 45.455 0.00 0.00 0.00 6.09
6458 7208 2.511373 TTGCGCCTGCCATAGACG 60.511 61.111 4.18 0.00 41.78 4.18
6677 7429 5.824624 CCTCATAATGTCAGGTAATTGCTGT 59.175 40.000 0.00 0.00 0.00 4.40
6726 7478 5.511363 ACTTACTGTACTGTCTATCTGGCT 58.489 41.667 8.85 0.00 0.00 4.75
6792 7561 6.267699 CCTCCCTCTCCTAAAAATTTGTGTTT 59.732 38.462 0.00 0.00 0.00 2.83
7299 8070 6.295916 CCTTGACTTCTTCCAAGTGGTATACT 60.296 42.308 2.25 0.00 42.89 2.12
7310 8081 1.881252 GGTATACTGCACCGTGGCG 60.881 63.158 2.25 0.00 36.28 5.69
7373 8150 4.525996 ACAGTTGCACATATATGCTGGAA 58.474 39.130 12.79 13.49 46.28 3.53
7433 8217 4.943705 GCAGGAATACAGAAACCATGAGAA 59.056 41.667 0.00 0.00 0.00 2.87
7490 8274 1.360820 GAAGCTTCGCAACTACTCCC 58.639 55.000 11.40 0.00 0.00 4.30
7493 8277 0.460459 GCTTCGCAACTACTCCCTCC 60.460 60.000 0.00 0.00 0.00 4.30
7504 8288 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
7510 8294 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
7512 8296 4.421948 CTCCGTCCCATAATATAAGACGC 58.578 47.826 14.86 0.00 46.66 5.19
7519 8303 6.856426 GTCCCATAATATAAGACGCTTTTTGC 59.144 38.462 0.00 0.00 38.57 3.68
7521 8305 6.238897 CCCATAATATAAGACGCTTTTTGCCA 60.239 38.462 0.00 0.00 38.78 4.92
7527 8311 3.396260 AGACGCTTTTTGCCACTAGTA 57.604 42.857 0.00 0.00 38.78 1.82
7604 8404 7.268199 TGATTTGCCATCTTTAGCTAATGAG 57.732 36.000 22.17 12.19 35.16 2.90
7626 8426 4.583073 AGCGAAAAGGACAAAGTTATGGTT 59.417 37.500 0.00 0.00 0.00 3.67
7627 8427 4.679654 GCGAAAAGGACAAAGTTATGGTTG 59.320 41.667 0.00 0.00 0.00 3.77
7654 8454 2.297315 CCCCTGTTTCTTTTTCCTCTGC 59.703 50.000 0.00 0.00 0.00 4.26
7747 8547 6.268847 TGGCCACTTGTTTATCAGGTTAAAAT 59.731 34.615 0.00 0.00 34.09 1.82
7749 8549 7.375053 GCCACTTGTTTATCAGGTTAAAATCA 58.625 34.615 0.00 0.00 34.09 2.57
7872 10820 9.593134 AACAAATTGCACTTTTGAACACTATTA 57.407 25.926 21.94 0.00 37.48 0.98
7973 10921 7.528996 TTTCATGAGAAGTTTCCATGACAAT 57.471 32.000 17.75 0.00 40.84 2.71
8031 10979 4.781775 TCAAGGTCAACCCTCACTTTTA 57.218 40.909 0.00 0.00 45.47 1.52
8050 11009 8.576442 CACTTTTATTTCCTTTGTATGTCCAGT 58.424 33.333 0.00 0.00 0.00 4.00
8065 11024 2.679837 GTCCAGTCCATGCACATAACAG 59.320 50.000 0.00 0.00 0.00 3.16
8072 11031 2.096980 CCATGCACATAACAGCTGTCAG 59.903 50.000 21.95 15.12 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 5.347907 CCTTTGTCTGTCGGTATGTTACTTC 59.652 44.000 0.00 0.00 0.00 3.01
147 148 8.862325 TCAGTCAAACCTTTATGACAACATAT 57.138 30.769 8.43 0.00 46.55 1.78
181 184 6.699575 ATTGGTTCCTACATATTCTGCAAC 57.300 37.500 0.00 0.00 0.00 4.17
185 188 8.156820 TGTCCATATTGGTTCCTACATATTCTG 58.843 37.037 0.00 0.00 39.03 3.02
209 212 0.469917 CAATAGCGGGACCTGGATGT 59.530 55.000 0.00 0.00 0.00 3.06
365 370 3.257873 CCATAGCTCCTCGTCATCTCATT 59.742 47.826 0.00 0.00 0.00 2.57
384 398 0.042131 TTACCTCCGGACCACTCCAT 59.958 55.000 0.00 0.00 36.12 3.41
385 399 0.178926 TTTACCTCCGGACCACTCCA 60.179 55.000 0.00 0.00 36.12 3.86
389 403 1.202382 CGATCTTTACCTCCGGACCAC 60.202 57.143 0.00 0.00 0.00 4.16
432 448 3.412237 TTTCGAAACCTTTCCGGAGAT 57.588 42.857 6.47 0.00 36.31 2.75
525 542 1.073284 GCTGGTGTGTTCCTTCCCTTA 59.927 52.381 0.00 0.00 0.00 2.69
531 551 1.152756 GTGGGCTGGTGTGTTCCTT 60.153 57.895 0.00 0.00 0.00 3.36
577 598 9.667107 TTCGTAGAATGGTTTTCTATCAAGAAT 57.333 29.630 0.00 0.00 45.90 2.40
578 599 9.496873 TTTCGTAGAATGGTTTTCTATCAAGAA 57.503 29.630 0.00 0.00 45.90 2.52
579 600 9.667107 ATTTCGTAGAATGGTTTTCTATCAAGA 57.333 29.630 0.00 0.00 45.90 3.02
587 608 9.285770 GGATTGTAATTTCGTAGAATGGTTTTC 57.714 33.333 0.00 0.00 45.90 2.29
588 609 7.966204 CGGATTGTAATTTCGTAGAATGGTTTT 59.034 33.333 0.00 0.00 45.90 2.43
589 610 7.334921 TCGGATTGTAATTTCGTAGAATGGTTT 59.665 33.333 0.00 0.00 45.90 3.27
590 611 6.819649 TCGGATTGTAATTTCGTAGAATGGTT 59.180 34.615 0.00 0.00 45.90 3.67
591 612 6.342906 TCGGATTGTAATTTCGTAGAATGGT 58.657 36.000 0.00 0.00 45.90 3.55
592 613 6.838198 TCGGATTGTAATTTCGTAGAATGG 57.162 37.500 0.00 0.00 45.90 3.16
593 614 8.699582 CAATCGGATTGTAATTTCGTAGAATG 57.300 34.615 20.07 0.00 37.29 2.67
608 629 1.331756 GCCAGCTGTACAATCGGATTG 59.668 52.381 25.13 25.13 45.59 2.67
609 630 1.668419 GCCAGCTGTACAATCGGATT 58.332 50.000 13.81 0.00 0.00 3.01
610 631 0.179045 GGCCAGCTGTACAATCGGAT 60.179 55.000 13.81 0.00 0.00 4.18
611 632 1.220749 GGCCAGCTGTACAATCGGA 59.779 57.895 13.81 0.00 0.00 4.55
612 633 0.676466 TTGGCCAGCTGTACAATCGG 60.676 55.000 13.81 0.00 0.00 4.18
613 634 1.331756 GATTGGCCAGCTGTACAATCG 59.668 52.381 29.16 10.92 39.58 3.34
614 635 2.648059 AGATTGGCCAGCTGTACAATC 58.352 47.619 32.38 32.38 45.80 2.67
615 636 2.814805 AGATTGGCCAGCTGTACAAT 57.185 45.000 24.60 24.60 36.35 2.71
616 637 2.584835 AAGATTGGCCAGCTGTACAA 57.415 45.000 18.77 18.77 0.00 2.41
617 638 3.433598 GGATAAGATTGGCCAGCTGTACA 60.434 47.826 13.81 8.26 0.00 2.90
618 639 3.142174 GGATAAGATTGGCCAGCTGTAC 58.858 50.000 13.81 5.41 0.00 2.90
619 640 2.224281 CGGATAAGATTGGCCAGCTGTA 60.224 50.000 13.81 0.00 0.00 2.74
620 641 1.475751 CGGATAAGATTGGCCAGCTGT 60.476 52.381 13.81 0.57 0.00 4.40
621 642 1.233019 CGGATAAGATTGGCCAGCTG 58.767 55.000 5.11 6.78 0.00 4.24
622 643 0.109342 CCGGATAAGATTGGCCAGCT 59.891 55.000 5.11 4.74 0.00 4.24
623 644 0.890996 CCCGGATAAGATTGGCCAGC 60.891 60.000 5.11 1.90 0.00 4.85
624 645 0.890996 GCCCGGATAAGATTGGCCAG 60.891 60.000 5.11 0.00 36.07 4.85
625 646 1.150536 GCCCGGATAAGATTGGCCA 59.849 57.895 0.00 0.00 36.07 5.36
626 647 0.890996 CTGCCCGGATAAGATTGGCC 60.891 60.000 0.73 0.00 41.46 5.36
627 648 0.108585 TCTGCCCGGATAAGATTGGC 59.891 55.000 0.73 0.00 42.49 4.52
628 649 2.430465 CATCTGCCCGGATAAGATTGG 58.570 52.381 0.73 0.00 0.00 3.16
629 650 1.808945 GCATCTGCCCGGATAAGATTG 59.191 52.381 0.73 4.85 34.31 2.67
630 651 2.191128 GCATCTGCCCGGATAAGATT 57.809 50.000 0.73 0.00 34.31 2.40
631 652 3.944476 GCATCTGCCCGGATAAGAT 57.056 52.632 0.73 5.26 34.31 2.40
642 663 1.364626 CGTGTGAAGAGGGCATCTGC 61.365 60.000 0.87 0.00 38.67 4.26
643 664 0.036952 ACGTGTGAAGAGGGCATCTG 60.037 55.000 0.87 0.00 38.67 2.90
644 665 0.687354 AACGTGTGAAGAGGGCATCT 59.313 50.000 0.00 0.00 41.27 2.90
645 666 0.798776 CAACGTGTGAAGAGGGCATC 59.201 55.000 0.00 0.00 0.00 3.91
646 667 1.237285 GCAACGTGTGAAGAGGGCAT 61.237 55.000 0.00 0.00 0.00 4.40
647 668 1.891919 GCAACGTGTGAAGAGGGCA 60.892 57.895 0.00 0.00 0.00 5.36
648 669 2.617274 GGCAACGTGTGAAGAGGGC 61.617 63.158 0.00 0.00 0.00 5.19
649 670 3.655481 GGCAACGTGTGAAGAGGG 58.345 61.111 0.00 0.00 0.00 4.30
661 682 1.735571 ACGTGGATATGAAACGGCAAC 59.264 47.619 0.00 0.00 41.50 4.17
662 683 1.735018 CACGTGGATATGAAACGGCAA 59.265 47.619 7.95 0.00 41.50 4.52
663 684 1.338294 ACACGTGGATATGAAACGGCA 60.338 47.619 21.57 0.00 41.50 5.69
664 685 1.062002 CACACGTGGATATGAAACGGC 59.938 52.381 21.57 0.00 41.50 5.68
665 686 2.612604 TCACACGTGGATATGAAACGG 58.387 47.619 21.57 0.00 41.50 4.44
666 687 3.430556 TGTTCACACGTGGATATGAAACG 59.569 43.478 21.57 0.00 42.82 3.60
667 688 5.545658 ATGTTCACACGTGGATATGAAAC 57.454 39.130 21.57 13.96 33.09 2.78
668 689 7.044798 TGATATGTTCACACGTGGATATGAAA 58.955 34.615 21.57 11.03 33.09 2.69
669 690 6.578023 TGATATGTTCACACGTGGATATGAA 58.422 36.000 21.57 16.94 0.00 2.57
670 691 6.155475 TGATATGTTCACACGTGGATATGA 57.845 37.500 21.57 11.53 0.00 2.15
671 692 6.562086 CGTTGATATGTTCACACGTGGATATG 60.562 42.308 21.57 9.10 35.75 1.78
672 693 5.462068 CGTTGATATGTTCACACGTGGATAT 59.538 40.000 21.57 12.16 35.75 1.63
673 694 4.801516 CGTTGATATGTTCACACGTGGATA 59.198 41.667 21.57 8.04 35.75 2.59
674 695 3.616821 CGTTGATATGTTCACACGTGGAT 59.383 43.478 21.57 6.06 35.75 3.41
675 696 2.990514 CGTTGATATGTTCACACGTGGA 59.009 45.455 21.57 11.48 35.75 4.02
676 697 2.734606 ACGTTGATATGTTCACACGTGG 59.265 45.455 21.57 9.11 43.65 4.94
678 699 2.734606 CCACGTTGATATGTTCACACGT 59.265 45.455 0.00 11.35 44.86 4.49
679 700 2.990514 TCCACGTTGATATGTTCACACG 59.009 45.455 0.00 0.00 40.98 4.49
680 701 4.629634 TCATCCACGTTGATATGTTCACAC 59.370 41.667 1.23 0.00 32.84 3.82
681 702 4.826556 TCATCCACGTTGATATGTTCACA 58.173 39.130 1.23 0.00 32.84 3.58
682 703 5.109210 TCTCATCCACGTTGATATGTTCAC 58.891 41.667 1.23 0.00 32.84 3.18
683 704 5.337578 TCTCATCCACGTTGATATGTTCA 57.662 39.130 1.23 0.00 0.00 3.18
684 705 6.293081 CCAATCTCATCCACGTTGATATGTTC 60.293 42.308 1.23 0.00 0.00 3.18
685 706 5.528690 CCAATCTCATCCACGTTGATATGTT 59.471 40.000 1.23 0.00 0.00 2.71
686 707 5.059161 CCAATCTCATCCACGTTGATATGT 58.941 41.667 1.23 0.00 0.00 2.29
687 708 4.083643 GCCAATCTCATCCACGTTGATATG 60.084 45.833 1.23 0.00 0.00 1.78
688 709 4.067896 GCCAATCTCATCCACGTTGATAT 58.932 43.478 1.23 0.00 0.00 1.63
689 710 3.466836 GCCAATCTCATCCACGTTGATA 58.533 45.455 1.23 0.00 0.00 2.15
690 711 2.292267 GCCAATCTCATCCACGTTGAT 58.708 47.619 0.00 0.00 0.00 2.57
691 712 1.678728 GGCCAATCTCATCCACGTTGA 60.679 52.381 0.00 0.00 0.00 3.18
692 713 0.734889 GGCCAATCTCATCCACGTTG 59.265 55.000 0.00 0.00 0.00 4.10
693 714 0.327924 TGGCCAATCTCATCCACGTT 59.672 50.000 0.61 0.00 0.00 3.99
694 715 0.107508 CTGGCCAATCTCATCCACGT 60.108 55.000 7.01 0.00 0.00 4.49
695 716 1.442526 GCTGGCCAATCTCATCCACG 61.443 60.000 7.01 0.00 0.00 4.94
696 717 0.106819 AGCTGGCCAATCTCATCCAC 60.107 55.000 7.01 0.00 0.00 4.02
697 718 0.106868 CAGCTGGCCAATCTCATCCA 60.107 55.000 7.01 0.00 0.00 3.41
698 719 0.106819 ACAGCTGGCCAATCTCATCC 60.107 55.000 19.93 0.00 0.00 3.51
699 720 1.307097 GACAGCTGGCCAATCTCATC 58.693 55.000 19.93 3.52 0.00 2.92
700 721 0.106819 GGACAGCTGGCCAATCTCAT 60.107 55.000 34.67 0.00 44.76 2.90
701 722 1.300963 GGACAGCTGGCCAATCTCA 59.699 57.895 34.67 0.00 44.76 3.27
702 723 4.232310 GGACAGCTGGCCAATCTC 57.768 61.111 34.67 11.80 44.76 2.75
708 729 0.106819 ATCTGATTGGACAGCTGGCC 60.107 55.000 33.16 33.16 45.93 5.36
709 730 1.404391 CAATCTGATTGGACAGCTGGC 59.596 52.381 19.93 16.59 37.75 4.85
710 731 2.719739 ACAATCTGATTGGACAGCTGG 58.280 47.619 28.41 6.25 44.42 4.85
711 732 4.331992 CACTACAATCTGATTGGACAGCTG 59.668 45.833 28.41 13.48 44.42 4.24
712 733 4.223700 TCACTACAATCTGATTGGACAGCT 59.776 41.667 28.41 12.99 44.42 4.24
713 734 4.331168 GTCACTACAATCTGATTGGACAGC 59.669 45.833 28.41 13.61 44.42 4.40
714 735 5.482006 TGTCACTACAATCTGATTGGACAG 58.518 41.667 28.41 23.15 44.42 3.51
715 736 5.482163 TGTCACTACAATCTGATTGGACA 57.518 39.130 28.41 25.90 44.42 4.02
735 756 8.152246 AATGGTGTTTCATTCATCAAGAATTGT 58.848 29.630 0.00 0.00 44.48 2.71
736 757 8.542497 AATGGTGTTTCATTCATCAAGAATTG 57.458 30.769 0.00 0.00 44.48 2.32
737 758 9.563748 AAAATGGTGTTTCATTCATCAAGAATT 57.436 25.926 0.00 0.00 44.48 2.17
739 760 8.961294 AAAAATGGTGTTTCATTCATCAAGAA 57.039 26.923 0.00 0.00 41.28 2.52
798 819 7.951347 AAAGAGATTATGGCTGTTCTCAAAT 57.049 32.000 0.00 0.00 37.63 2.32
831 852 3.196254 CCCAACAGATTATGGCTTTTGCT 59.804 43.478 0.00 0.00 46.54 3.91
833 854 4.220382 TCACCCAACAGATTATGGCTTTTG 59.780 41.667 0.00 0.00 35.28 2.44
836 857 3.737559 TCACCCAACAGATTATGGCTT 57.262 42.857 0.00 0.00 35.28 4.35
849 873 2.724454 TCGGTTTTCTGTTTCACCCAA 58.276 42.857 0.00 0.00 0.00 4.12
1027 1054 1.344953 TGTGGATAGGCGGCTGGAAT 61.345 55.000 23.55 7.16 0.00 3.01
1029 1056 2.364973 TGTGGATAGGCGGCTGGA 60.365 61.111 23.55 1.95 0.00 3.86
1037 1064 1.696336 CAGGGGAGATGTGTGGATAGG 59.304 57.143 0.00 0.00 0.00 2.57
1041 1068 2.659063 CGCAGGGGAGATGTGTGGA 61.659 63.158 0.00 0.00 0.00 4.02
1164 1191 0.179073 CTCCGGTCATTGTAGGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
1168 1195 0.174845 TTCGCTCCGGTCATTGTAGG 59.825 55.000 0.00 0.00 0.00 3.18
1170 1197 1.202486 GGATTCGCTCCGGTCATTGTA 60.202 52.381 0.00 0.00 33.29 2.41
1214 1250 2.125326 CCGCTCCACTCCGATGGTA 61.125 63.158 1.00 0.00 40.95 3.25
1409 1445 9.586435 AAATTTCTCAGAAACCACTAAAACTTG 57.414 29.630 0.68 0.00 0.00 3.16
1435 1471 0.179004 ACTTGTTCGCCACATTCCCA 60.179 50.000 0.00 0.00 34.43 4.37
1507 1544 6.106648 TGCCATGACATGAAATTGGTTAAA 57.893 33.333 17.24 0.00 0.00 1.52
1603 1640 4.901250 CCAATACCCCAAGCAAATTCCTAT 59.099 41.667 0.00 0.00 0.00 2.57
1613 1650 0.251608 ACACACCCAATACCCCAAGC 60.252 55.000 0.00 0.00 0.00 4.01
1619 1656 2.290641 TGGATGTCACACACCCAATACC 60.291 50.000 0.00 0.00 0.00 2.73
1643 1764 4.698780 ACAAGAAATTTTCCTACCCGCTAC 59.301 41.667 5.52 0.00 0.00 3.58
1725 1848 8.678199 GTCTTTGATTAGTAGGAATTTTGGAGG 58.322 37.037 0.00 0.00 0.00 4.30
1804 2166 8.911918 ATTGAACTGTAAACACCACTATTGTA 57.088 30.769 0.00 0.00 0.00 2.41
1814 2179 9.515020 TCAGAAATTGAATTGAACTGTAAACAC 57.485 29.630 14.62 0.00 31.34 3.32
1818 2183 8.282592 CGACTCAGAAATTGAATTGAACTGTAA 58.717 33.333 14.62 2.83 34.81 2.41
1850 2215 8.242739 ACGAAGTTCCTTCTCTATTACTACAAC 58.757 37.037 0.00 0.00 37.78 3.32
1875 2240 6.398918 AGTGTGTGTATCTAGGAACAATGAC 58.601 40.000 0.38 0.40 0.00 3.06
1905 2270 1.901591 ATCAAACAGGCACAGACTGG 58.098 50.000 7.51 0.00 44.18 4.00
1959 2324 5.469579 TGGTACATGCCTAGGTTCCTAATA 58.530 41.667 11.31 0.00 30.49 0.98
1960 2325 4.303794 TGGTACATGCCTAGGTTCCTAAT 58.696 43.478 11.31 0.00 30.49 1.73
1961 2326 3.726790 TGGTACATGCCTAGGTTCCTAA 58.273 45.455 11.31 0.00 30.49 2.69
1994 2359 5.623956 TTGTCCGTATACATTTCTGGGAT 57.376 39.130 3.32 0.00 0.00 3.85
2485 2854 5.995897 TCCAGGAGTTAAGTAGAGCAAAAAC 59.004 40.000 0.00 0.00 0.00 2.43
2511 2880 8.795842 ACAGTGAAATGACCCGTTATTATAAA 57.204 30.769 0.00 0.00 0.00 1.40
2521 2890 2.480419 GAGTGAACAGTGAAATGACCCG 59.520 50.000 0.00 0.00 0.00 5.28
2528 2897 2.503765 TGTCAGGGAGTGAACAGTGAAA 59.496 45.455 0.00 0.00 36.74 2.69
2559 2928 5.068636 CAGGTAGAAGATGGCATTAGCATT 58.931 41.667 0.00 0.00 44.61 3.56
2637 3006 0.730840 ACACATGCATGCTGACATCG 59.269 50.000 26.53 7.39 32.87 3.84
2744 3124 5.768164 TCCTCCTCAAGTAACACAAATTTCC 59.232 40.000 0.00 0.00 0.00 3.13
2791 3412 7.568349 TCATAGCATGTTCTAAAGATTCCACT 58.432 34.615 0.00 0.00 0.00 4.00
2950 3571 3.200605 TGAGCCAAATAGAGAATGCCTCA 59.799 43.478 0.00 0.00 44.40 3.86
3180 3809 7.762382 ACTAAAACTGAGTTGTTCTGGAAAAG 58.238 34.615 0.00 0.00 0.00 2.27
3295 3924 3.260475 TGATACCAAACACGATCCCTG 57.740 47.619 0.00 0.00 0.00 4.45
3362 3992 8.064814 GGAAGAAATTCGTTGCTATAAGCTTAG 58.935 37.037 12.54 1.85 42.97 2.18
3425 4055 2.408565 TCCTCGCCCATCCTCTTTATT 58.591 47.619 0.00 0.00 0.00 1.40
3792 4423 4.811024 TGAAGGATTGACGAGCATTACATC 59.189 41.667 0.00 0.00 0.00 3.06
3833 4464 9.448438 TGCAAAGTTAGATTATAGCTCAAAAGA 57.552 29.630 0.00 0.00 0.00 2.52
3834 4465 9.495754 GTGCAAAGTTAGATTATAGCTCAAAAG 57.504 33.333 0.00 0.00 0.00 2.27
3940 4572 6.912951 TCAGCTTTACTGTAGGAAACTAGT 57.087 37.500 0.00 0.00 45.49 2.57
4216 4848 2.376808 ATGCACCTTCAGAGTTCTCG 57.623 50.000 0.00 0.00 0.00 4.04
4276 4908 7.002250 TGATTCAACATCTGGATCTATCTCC 57.998 40.000 0.00 0.00 40.40 3.71
4657 5295 4.616835 GCTGTTGCAAAAAGGGACTCATAG 60.617 45.833 0.00 0.00 36.97 2.23
5073 5711 8.641541 CACAGATGGCCCAACTATTAATTATTT 58.358 33.333 0.00 0.00 0.00 1.40
5084 5722 1.604593 GCACACAGATGGCCCAACT 60.605 57.895 0.00 0.00 0.00 3.16
5269 5927 4.136796 TGATATTCATGCCAGTTACCAGC 58.863 43.478 0.00 0.00 0.00 4.85
5387 6065 3.407698 TGAGCATTCGTTAGAGGCAAAA 58.592 40.909 0.00 0.00 32.93 2.44
5400 6078 3.879892 GGTAACTTCCTGGATGAGCATTC 59.120 47.826 15.76 0.00 0.00 2.67
5623 6301 5.966742 ATTTCCAGTAACTCCTTTTCTGC 57.033 39.130 0.00 0.00 0.00 4.26
5655 6333 3.270877 GTCGCTAATCCATTGGTTCACT 58.729 45.455 1.86 0.00 0.00 3.41
5863 6543 6.166279 CAACTCTAACCTAGCAGAATTCACA 58.834 40.000 8.44 0.00 0.00 3.58
6104 6784 3.118738 GGGGAGAAGAGAAAATCGCTACA 60.119 47.826 0.00 0.00 0.00 2.74
6115 6796 2.225369 TGACATGTCAGGGGAGAAGAGA 60.225 50.000 24.56 0.00 34.14 3.10
6121 6802 5.688807 AGAAAATATGACATGTCAGGGGAG 58.311 41.667 30.63 0.00 43.61 4.30
6216 6898 4.033932 GTGGGTTTCAATGCACTTCAAAAC 59.966 41.667 0.00 0.00 0.00 2.43
6294 6976 5.351233 TTCGTCAAATCTGCACGTTTAAT 57.649 34.783 0.00 0.00 35.05 1.40
6298 6980 2.612212 AGTTTCGTCAAATCTGCACGTT 59.388 40.909 0.00 0.00 35.05 3.99
6300 6982 2.949714 AGTTTCGTCAAATCTGCACG 57.050 45.000 0.00 0.00 34.78 5.34
6374 7124 5.361285 ACTCTCTAATCACACTACCCACATC 59.639 44.000 0.00 0.00 0.00 3.06
6402 7152 2.802719 GGTCAACAGACCTCTCTCTCT 58.197 52.381 7.39 0.00 46.73 3.10
6446 7196 6.377327 AATAATTGAAACGTCTATGGCAGG 57.623 37.500 0.00 0.00 0.00 4.85
6458 7208 8.192774 TCATGCTCCATGAGAAATAATTGAAAC 58.807 33.333 3.91 0.00 44.60 2.78
6769 7522 7.125053 ACAAAACACAAATTTTTAGGAGAGGGA 59.875 33.333 0.00 0.00 29.17 4.20
6770 7523 7.272244 ACAAAACACAAATTTTTAGGAGAGGG 58.728 34.615 0.00 0.00 29.17 4.30
6785 7554 6.833041 TCAACTAGGATCCTACAAAACACAA 58.167 36.000 18.00 0.00 0.00 3.33
6792 7561 6.127054 CCATGTTCTCAACTAGGATCCTACAA 60.127 42.308 18.00 0.00 0.00 2.41
6852 7621 1.596934 GGTTCCCACGAGATGCTCA 59.403 57.895 0.00 0.00 0.00 4.26
7299 8070 4.228567 TTCACTCGCCACGGTGCA 62.229 61.111 1.68 0.00 33.91 4.57
7373 8150 5.594317 GCAAACTGGACCCAAATCTATGTAT 59.406 40.000 0.00 0.00 0.00 2.29
7437 8221 5.663456 ACAGCAACAACAAACATGAGATTT 58.337 33.333 0.00 0.00 0.00 2.17
7438 8222 5.266733 ACAGCAACAACAAACATGAGATT 57.733 34.783 0.00 0.00 0.00 2.40
7458 8242 2.504367 GAAGCTTCCAAACAGCCTACA 58.496 47.619 15.97 0.00 38.09 2.74
7490 8274 4.158025 AGCGTCTTATATTATGGGACGGAG 59.842 45.833 22.36 7.20 46.26 4.63
7541 8325 0.523072 TTTTACTCCCTCCGTCGACG 59.477 55.000 30.33 30.33 39.44 5.12
7542 8326 2.955477 ATTTTACTCCCTCCGTCGAC 57.045 50.000 5.18 5.18 0.00 4.20
7543 8327 3.355378 TGTATTTTACTCCCTCCGTCGA 58.645 45.455 0.00 0.00 0.00 4.20
7604 8404 4.499037 ACCATAACTTTGTCCTTTTCGC 57.501 40.909 0.00 0.00 0.00 4.70
7610 8410 6.415573 GGATCTACAACCATAACTTTGTCCT 58.584 40.000 0.00 0.00 37.19 3.85
7626 8426 5.074515 AGGAAAAAGAAACAGGGGATCTACA 59.925 40.000 0.00 0.00 0.00 2.74
7627 8427 5.571285 AGGAAAAAGAAACAGGGGATCTAC 58.429 41.667 0.00 0.00 0.00 2.59
7654 8454 2.795329 AGGCAGACACAACCCTTATTG 58.205 47.619 0.00 0.00 35.59 1.90
7872 10820 3.066621 AGTGCAATGTGAAAACGTGACAT 59.933 39.130 0.00 0.00 31.54 3.06
7988 10936 4.182693 ACATTTGTGTTCATGCTCATGG 57.817 40.909 9.69 0.00 39.24 3.66
8031 10979 5.255397 TGGACTGGACATACAAAGGAAAT 57.745 39.130 0.00 0.00 0.00 2.17
8050 11009 2.290197 TGACAGCTGTTATGTGCATGGA 60.290 45.455 22.65 0.00 0.00 3.41
8065 11024 6.090898 AGTGTATAATTCAAACGTCTGACAGC 59.909 38.462 8.73 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.