Multiple sequence alignment - TraesCS7D01G124800

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 TraesCS7D01G124800 chr7D 100.000 3148 0 0 378 3525 78206208 78209355 0.000000e+00 5814.0
1 TraesCS7D01G124800 chr7D 85.577 1040 98 28 2517 3525 78299846 78300864 0.000000e+00 1042.0
2 TraesCS7D01G124800 chr7D 87.337 845 92 6 2688 3525 78306634 78307470 0.000000e+00 953.0
3 TraesCS7D01G124800 chr7D 90.816 392 28 7 383 771 500220242 500220628 5.220000e-143 518.0
4 TraesCS7D01G124800 chr7D 100.000 98 0 0 1 98 78205831 78205928 7.770000e-42 182.0
5 TraesCS7D01G124800 chr7D 87.586 145 15 3 2790 2933 78306057 78306199 7.830000e-37 165.0
6 TraesCS7D01G124800 chr7D 92.647 68 3 2 712 777 579334149 579334082 2.900000e-16 97.1
7 TraesCS7D01G124800 chr7B 92.811 2782 103 49 793 3525 25627791 25630524 0.000000e+00 3940.0
8 TraesCS7D01G124800 chr7B 88.982 835 82 6 2693 3525 25653185 25654011 0.000000e+00 1024.0
9 TraesCS7D01G124800 chr7B 86.770 839 93 8 2688 3525 25888977 25888156 0.000000e+00 918.0
10 TraesCS7D01G124800 chr7B 88.550 655 75 0 2794 3448 25662822 25663476 0.000000e+00 795.0
11 TraesCS7D01G124800 chr7B 98.305 59 1 0 711 769 1399801 1399743 1.730000e-18 104.0
12 TraesCS7D01G124800 chr7A 95.770 2246 70 14 1302 3525 81638311 81640553 0.000000e+00 3598.0
13 TraesCS7D01G124800 chr7A 84.003 1194 136 28 2370 3525 81766974 81768150 0.000000e+00 1096.0
14 TraesCS7D01G124800 chr7A 89.218 742 73 4 2791 3525 81775605 81776346 0.000000e+00 920.0
15 TraesCS7D01G124800 chr7A 86.854 426 30 15 820 1238 81637580 81637986 1.490000e-123 453.0
16 TraesCS7D01G124800 chr2A 91.500 400 18 6 383 771 588261185 588260791 1.440000e-148 536.0
17 TraesCS7D01G124800 chr2D 90.777 412 19 8 380 779 527542798 527543202 1.860000e-147 532.0
18 TraesCS7D01G124800 chr2D 90.640 406 18 9 380 769 157143344 157143745 4.030000e-144 521.0
19 TraesCS7D01G124800 chr2D 90.123 405 22 7 383 773 121768393 121767993 8.730000e-141 510.0
20 TraesCS7D01G124800 chr2D 76.427 403 63 23 383 772 491815237 491814854 4.650000e-44 189.0
21 TraesCS7D01G124800 chr5D 91.250 400 18 12 383 769 473446127 473446522 2.410000e-146 529.0
22 TraesCS7D01G124800 chr5D 98.333 60 1 0 712 771 477027124 477027183 4.810000e-19 106.0
23 TraesCS7D01G124800 chr3D 90.955 398 21 9 386 772 509149066 509148673 4.030000e-144 521.0
24 TraesCS7D01G124800 chr3D 95.918 98 4 0 1 98 400272685 400272782 3.640000e-35 159.0
25 TraesCS7D01G124800 chr3D 87.952 83 7 3 692 774 278980858 278980937 1.040000e-15 95.3
26 TraesCS7D01G124800 chr6D 90.394 406 20 7 378 771 423799886 423799488 1.880000e-142 516.0
27 TraesCS7D01G124800 chr6D 96.842 95 3 0 4 98 464065892 464065798 3.640000e-35 159.0
28 TraesCS7D01G124800 chr6D 95.522 67 1 2 704 769 91075929 91075994 4.810000e-19 106.0
29 TraesCS7D01G124800 chr4A 90.657 396 22 6 383 767 127213030 127212639 2.430000e-141 512.0
30 TraesCS7D01G124800 chr4A 96.939 98 3 0 1 98 41037272 41037175 7.830000e-37 165.0
31 TraesCS7D01G124800 chr4A 95.833 96 4 0 3 98 59340175 59340080 4.710000e-34 156.0
32 TraesCS7D01G124800 chr1D 95.918 98 4 0 1 98 342175929 342176026 3.640000e-35 159.0
33 TraesCS7D01G124800 chr1D 95.918 98 4 0 1 98 356921466 356921369 3.640000e-35 159.0
34 TraesCS7D01G124800 chr6A 95.918 98 3 1 2 98 432568881 432568978 1.310000e-34 158.0
35 TraesCS7D01G124800 chr5A 95.918 98 3 1 2 98 636609481 636609384 1.310000e-34 158.0
36 TraesCS7D01G124800 chr4D 95.833 96 4 0 3 98 378452812 378452717 4.710000e-34 156.0
37 TraesCS7D01G124800 chr1A 98.276 58 1 0 712 769 369574591 369574648 6.230000e-18 102.0
38 TraesCS7D01G124800 chr1B 91.667 72 4 2 704 774 171183318 171183248 8.050000e-17 99.0


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 TraesCS7D01G124800 chr7D 78205831 78209355 3524 False 2998.0 5814 100.0000 1 3525 2 chr7D.!!$F3 3524
1 TraesCS7D01G124800 chr7D 78299846 78300864 1018 False 1042.0 1042 85.5770 2517 3525 1 chr7D.!!$F1 1008
2 TraesCS7D01G124800 chr7D 78306057 78307470 1413 False 559.0 953 87.4615 2688 3525 2 chr7D.!!$F4 837
3 TraesCS7D01G124800 chr7B 25627791 25630524 2733 False 3940.0 3940 92.8110 793 3525 1 chr7B.!!$F1 2732
4 TraesCS7D01G124800 chr7B 25653185 25654011 826 False 1024.0 1024 88.9820 2693 3525 1 chr7B.!!$F2 832
5 TraesCS7D01G124800 chr7B 25888156 25888977 821 True 918.0 918 86.7700 2688 3525 1 chr7B.!!$R2 837
6 TraesCS7D01G124800 chr7B 25662822 25663476 654 False 795.0 795 88.5500 2794 3448 1 chr7B.!!$F3 654
7 TraesCS7D01G124800 chr7A 81637580 81640553 2973 False 2025.5 3598 91.3120 820 3525 2 chr7A.!!$F3 2705
8 TraesCS7D01G124800 chr7A 81766974 81768150 1176 False 1096.0 1096 84.0030 2370 3525 1 chr7A.!!$F1 1155
9 TraesCS7D01G124800 chr7A 81775605 81776346 741 False 920.0 920 89.2180 2791 3525 1 chr7A.!!$F2 734

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
659 660 0.037046 CAAAATGGGTTCAGGCCAGC 60.037 55.0 5.01 0.0 0.00 4.85 F
745 746 0.040781 ACAAAATCGCCGTCCGTTTG 60.041 50.0 0.00 0.0 38.28 2.93 F
770 771 0.321298 GCCCGTTGGAGTTGCTCTTA 60.321 55.0 0.00 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 2703 0.179009 AATCAGCAGTGCACCAGTGT 60.179 50.000 19.2 0.0 37.16 3.55 R
2375 2707 1.401761 AAACAATCAGCAGTGCACCA 58.598 45.000 19.2 0.0 0.00 4.17 R
2593 2934 4.214119 TCCAGCAGTTTGAAGAAGAAATCG 59.786 41.667 0.0 0.0 0.00 3.34 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
17 18 3.089838 CCAGATCAGGGTGGCCAA 58.910 61.111 7.24 0.00 0.00 4.52
19 20 1.077212 CAGATCAGGGTGGCCAAGG 60.077 63.158 7.24 0.00 0.00 3.61
21 22 1.225704 GATCAGGGTGGCCAAGGAG 59.774 63.158 7.24 0.00 0.00 3.69
22 23 2.900671 GATCAGGGTGGCCAAGGAGC 62.901 65.000 7.24 1.26 0.00 4.70
61 62 4.560856 AGATGCTCGAGCGCGACC 62.561 66.667 30.75 17.37 45.83 4.79
62 63 4.560856 GATGCTCGAGCGCGACCT 62.561 66.667 30.75 11.91 45.83 3.85
63 64 4.560856 ATGCTCGAGCGCGACCTC 62.561 66.667 30.75 7.03 45.83 3.85
81 82 2.025441 GAGGTAGAGCAGCGCGAG 59.975 66.667 12.10 1.41 0.00 5.03
82 83 3.477224 GAGGTAGAGCAGCGCGAGG 62.477 68.421 12.10 0.41 0.00 4.63
399 400 4.498520 CCGACATGACGGCGCTCT 62.499 66.667 22.90 0.00 46.20 4.09
400 401 3.250323 CGACATGACGGCGCTCTG 61.250 66.667 6.90 4.00 0.00 3.35
401 402 2.887568 GACATGACGGCGCTCTGG 60.888 66.667 6.90 3.45 0.00 3.86
402 403 3.356639 GACATGACGGCGCTCTGGA 62.357 63.158 6.90 0.00 0.00 3.86
403 404 2.125552 CATGACGGCGCTCTGGAA 60.126 61.111 6.90 0.00 0.00 3.53
404 405 2.125512 ATGACGGCGCTCTGGAAC 60.126 61.111 6.90 0.00 0.00 3.62
405 406 2.942796 ATGACGGCGCTCTGGAACA 61.943 57.895 6.90 0.00 0.00 3.18
406 407 3.112709 GACGGCGCTCTGGAACAC 61.113 66.667 6.90 0.00 0.00 3.32
412 413 3.112709 GCTCTGGAACACGGCGTC 61.113 66.667 10.85 0.00 0.00 5.19
413 414 2.432628 CTCTGGAACACGGCGTCC 60.433 66.667 10.85 9.81 0.00 4.79
449 450 4.194720 GCCGACGCTCATCGACCT 62.195 66.667 3.74 0.00 45.13 3.85
450 451 2.024871 CCGACGCTCATCGACCTC 59.975 66.667 3.74 0.00 45.13 3.85
451 452 2.761195 CCGACGCTCATCGACCTCA 61.761 63.158 3.74 0.00 45.13 3.86
452 453 1.583967 CGACGCTCATCGACCTCAC 60.584 63.158 0.00 0.00 45.13 3.51
453 454 1.583967 GACGCTCATCGACCTCACG 60.584 63.158 0.00 0.00 41.67 4.35
454 455 1.978712 GACGCTCATCGACCTCACGA 61.979 60.000 0.00 0.00 46.04 4.35
455 456 1.136774 CGCTCATCGACCTCACGAA 59.863 57.895 0.00 0.00 45.16 3.85
456 457 1.134530 CGCTCATCGACCTCACGAAC 61.135 60.000 0.00 0.00 45.16 3.95
457 458 0.802607 GCTCATCGACCTCACGAACC 60.803 60.000 0.00 0.00 45.16 3.62
458 459 0.179134 CTCATCGACCTCACGAACCC 60.179 60.000 0.00 0.00 45.16 4.11
459 460 1.153628 CATCGACCTCACGAACCCC 60.154 63.158 0.00 0.00 45.16 4.95
460 461 2.707849 ATCGACCTCACGAACCCCG 61.708 63.158 0.00 0.00 45.16 5.73
461 462 3.367743 CGACCTCACGAACCCCGA 61.368 66.667 0.00 0.00 41.76 5.14
462 463 2.572284 GACCTCACGAACCCCGAG 59.428 66.667 0.00 0.00 41.76 4.63
465 466 2.572284 CTCACGAACCCCGAGGAC 59.428 66.667 0.00 0.00 41.76 3.85
466 467 3.338126 CTCACGAACCCCGAGGACG 62.338 68.421 0.00 0.00 41.76 4.79
467 468 3.367743 CACGAACCCCGAGGACGA 61.368 66.667 12.75 0.00 42.66 4.20
468 469 3.368571 ACGAACCCCGAGGACGAC 61.369 66.667 12.75 0.00 42.66 4.34
469 470 4.471726 CGAACCCCGAGGACGACG 62.472 72.222 0.00 0.00 42.66 5.12
470 471 3.058160 GAACCCCGAGGACGACGA 61.058 66.667 0.00 0.00 42.66 4.20
471 472 3.333898 GAACCCCGAGGACGACGAC 62.334 68.421 0.00 0.00 42.66 4.34
474 475 4.157958 CCCGAGGACGACGACGAC 62.158 72.222 15.32 7.84 42.66 4.34
475 476 4.495939 CCGAGGACGACGACGACG 62.496 72.222 17.60 17.60 42.66 5.12
476 477 3.473166 CGAGGACGACGACGACGA 61.473 66.667 25.15 0.00 41.06 4.20
477 478 2.856032 GAGGACGACGACGACGAA 59.144 61.111 25.15 0.00 42.66 3.85
478 479 1.225691 GAGGACGACGACGACGAAG 60.226 63.158 25.15 9.52 42.66 3.79
479 480 2.868787 GGACGACGACGACGAAGC 60.869 66.667 25.15 13.42 42.66 3.86
480 481 2.868787 GACGACGACGACGAAGCC 60.869 66.667 25.15 8.22 42.66 4.35
481 482 3.306134 GACGACGACGACGAAGCCT 62.306 63.158 25.15 3.08 42.66 4.58
482 483 1.959899 GACGACGACGACGAAGCCTA 61.960 60.000 25.15 0.00 42.66 3.93
483 484 1.133253 CGACGACGACGAAGCCTAA 59.867 57.895 15.32 0.00 42.66 2.69
484 485 0.856490 CGACGACGACGAAGCCTAAG 60.856 60.000 15.32 0.00 42.66 2.18
485 486 0.522915 GACGACGACGAAGCCTAAGG 60.523 60.000 15.32 0.00 42.66 2.69
486 487 1.872679 CGACGACGAAGCCTAAGGC 60.873 63.158 0.00 0.00 45.44 4.35
487 488 2.537792 CGACGACGAAGCCTAAGGCA 62.538 60.000 0.00 0.00 46.68 4.75
507 508 2.202650 GCGCCGCCTCGTAGTTTA 60.203 61.111 0.00 0.00 0.00 2.01
508 509 2.228914 GCGCCGCCTCGTAGTTTAG 61.229 63.158 0.00 0.00 0.00 1.85
509 510 1.588139 CGCCGCCTCGTAGTTTAGG 60.588 63.158 0.00 0.00 35.86 2.69
519 520 6.980051 CCTCGTAGTTTAGGCTGTTTTTAT 57.020 37.500 0.00 0.00 0.00 1.40
520 521 7.373778 CCTCGTAGTTTAGGCTGTTTTTATT 57.626 36.000 0.00 0.00 0.00 1.40
521 522 7.813645 CCTCGTAGTTTAGGCTGTTTTTATTT 58.186 34.615 0.00 0.00 0.00 1.40
522 523 8.294577 CCTCGTAGTTTAGGCTGTTTTTATTTT 58.705 33.333 0.00 0.00 0.00 1.82
523 524 9.673454 CTCGTAGTTTAGGCTGTTTTTATTTTT 57.327 29.630 0.00 0.00 0.00 1.94
543 544 4.981389 TTTTAAATGCAAATGTGGACGC 57.019 36.364 0.00 0.00 0.00 5.19
544 545 3.932545 TTAAATGCAAATGTGGACGCT 57.067 38.095 0.00 0.00 0.00 5.07
545 546 2.818130 AAATGCAAATGTGGACGCTT 57.182 40.000 0.00 0.00 0.00 4.68
546 547 2.068837 AATGCAAATGTGGACGCTTG 57.931 45.000 0.00 0.00 0.00 4.01
547 548 0.244450 ATGCAAATGTGGACGCTTGG 59.756 50.000 0.00 0.00 0.00 3.61
548 549 0.821301 TGCAAATGTGGACGCTTGGA 60.821 50.000 0.00 0.00 0.00 3.53
549 550 0.387239 GCAAATGTGGACGCTTGGAC 60.387 55.000 0.00 0.00 0.00 4.02
550 551 1.238439 CAAATGTGGACGCTTGGACT 58.762 50.000 0.00 0.00 0.00 3.85
551 552 1.197721 CAAATGTGGACGCTTGGACTC 59.802 52.381 0.00 0.00 0.00 3.36
552 553 0.687354 AATGTGGACGCTTGGACTCT 59.313 50.000 0.00 0.00 0.00 3.24
553 554 0.247736 ATGTGGACGCTTGGACTCTC 59.752 55.000 0.00 0.00 0.00 3.20
554 555 1.444553 GTGGACGCTTGGACTCTCG 60.445 63.158 0.00 0.00 0.00 4.04
555 556 2.507324 GGACGCTTGGACTCTCGC 60.507 66.667 0.00 0.00 0.00 5.03
556 557 2.507324 GACGCTTGGACTCTCGCC 60.507 66.667 0.00 0.00 0.00 5.54
557 558 4.421479 ACGCTTGGACTCTCGCCG 62.421 66.667 0.00 0.00 0.00 6.46
560 561 4.821589 CTTGGACTCTCGCCGGCC 62.822 72.222 23.46 4.99 0.00 6.13
563 564 4.516195 GGACTCTCGCCGGCCTTC 62.516 72.222 23.46 9.81 0.00 3.46
564 565 4.856607 GACTCTCGCCGGCCTTCG 62.857 72.222 23.46 6.82 38.88 3.79
576 577 2.348243 CCTTCGTGGCCGGGTTTA 59.652 61.111 2.18 0.00 33.95 2.01
577 578 1.302671 CCTTCGTGGCCGGGTTTAA 60.303 57.895 2.18 0.00 33.95 1.52
578 579 0.678684 CCTTCGTGGCCGGGTTTAAT 60.679 55.000 2.18 0.00 33.95 1.40
579 580 0.450184 CTTCGTGGCCGGGTTTAATG 59.550 55.000 2.18 0.00 33.95 1.90
580 581 0.250814 TTCGTGGCCGGGTTTAATGT 60.251 50.000 2.18 0.00 33.95 2.71
581 582 0.250814 TCGTGGCCGGGTTTAATGTT 60.251 50.000 2.18 0.00 33.95 2.71
582 583 0.599060 CGTGGCCGGGTTTAATGTTT 59.401 50.000 2.18 0.00 0.00 2.83
583 584 1.811359 CGTGGCCGGGTTTAATGTTTA 59.189 47.619 2.18 0.00 0.00 2.01
584 585 2.228343 CGTGGCCGGGTTTAATGTTTAA 59.772 45.455 2.18 0.00 0.00 1.52
585 586 3.119424 CGTGGCCGGGTTTAATGTTTAAT 60.119 43.478 2.18 0.00 0.00 1.40
586 587 4.618693 CGTGGCCGGGTTTAATGTTTAATT 60.619 41.667 2.18 0.00 0.00 1.40
587 588 5.392811 CGTGGCCGGGTTTAATGTTTAATTA 60.393 40.000 2.18 0.00 0.00 1.40
588 589 6.396450 GTGGCCGGGTTTAATGTTTAATTAA 58.604 36.000 2.18 0.00 0.00 1.40
589 590 7.042950 GTGGCCGGGTTTAATGTTTAATTAAT 58.957 34.615 2.18 0.00 0.00 1.40
590 591 7.010645 GTGGCCGGGTTTAATGTTTAATTAATG 59.989 37.037 2.18 0.00 0.00 1.90
591 592 6.018588 GGCCGGGTTTAATGTTTAATTAATGC 60.019 38.462 2.18 0.00 0.00 3.56
592 593 6.759356 GCCGGGTTTAATGTTTAATTAATGCT 59.241 34.615 2.18 0.00 0.00 3.79
593 594 7.254286 GCCGGGTTTAATGTTTAATTAATGCTG 60.254 37.037 2.18 0.00 0.00 4.41
594 595 7.762159 CCGGGTTTAATGTTTAATTAATGCTGT 59.238 33.333 0.00 0.00 0.00 4.40
595 596 9.145865 CGGGTTTAATGTTTAATTAATGCTGTT 57.854 29.630 0.00 0.00 0.00 3.16
644 645 3.694535 TTTTTCTAGCGCCGTTCAAAA 57.305 38.095 2.29 0.58 0.00 2.44
645 646 3.907894 TTTTCTAGCGCCGTTCAAAAT 57.092 38.095 2.29 0.00 0.00 1.82
646 647 2.892373 TTCTAGCGCCGTTCAAAATG 57.108 45.000 2.29 0.00 0.00 2.32
647 648 1.083489 TCTAGCGCCGTTCAAAATGG 58.917 50.000 2.29 0.00 40.68 3.16
648 649 0.098728 CTAGCGCCGTTCAAAATGGG 59.901 55.000 2.29 0.00 38.05 4.00
649 650 0.606944 TAGCGCCGTTCAAAATGGGT 60.607 50.000 2.29 0.00 38.05 4.51
650 651 1.006688 GCGCCGTTCAAAATGGGTT 60.007 52.632 0.00 0.00 38.05 4.11
651 652 1.006825 GCGCCGTTCAAAATGGGTTC 61.007 55.000 0.00 0.00 38.05 3.62
652 653 0.312416 CGCCGTTCAAAATGGGTTCA 59.688 50.000 0.41 0.00 38.05 3.18
653 654 1.665735 CGCCGTTCAAAATGGGTTCAG 60.666 52.381 0.41 0.00 38.05 3.02
654 655 1.336795 GCCGTTCAAAATGGGTTCAGG 60.337 52.381 0.41 0.00 38.05 3.86
655 656 1.336795 CCGTTCAAAATGGGTTCAGGC 60.337 52.381 0.00 0.00 33.75 4.85
656 657 1.336795 CGTTCAAAATGGGTTCAGGCC 60.337 52.381 0.00 0.00 0.00 5.19
657 658 1.691434 GTTCAAAATGGGTTCAGGCCA 59.309 47.619 5.01 0.00 0.00 5.36
658 659 1.631405 TCAAAATGGGTTCAGGCCAG 58.369 50.000 5.01 0.00 0.00 4.85
659 660 0.037046 CAAAATGGGTTCAGGCCAGC 60.037 55.000 5.01 0.00 0.00 4.85
660 661 1.535204 AAAATGGGTTCAGGCCAGCG 61.535 55.000 5.01 0.00 0.00 5.18
661 662 2.713531 AAATGGGTTCAGGCCAGCGT 62.714 55.000 5.01 0.00 0.00 5.07
662 663 2.713531 AATGGGTTCAGGCCAGCGTT 62.714 55.000 5.01 0.00 0.00 4.84
663 664 1.847798 ATGGGTTCAGGCCAGCGTTA 61.848 55.000 5.01 0.00 0.00 3.18
664 665 1.745489 GGGTTCAGGCCAGCGTTAG 60.745 63.158 5.01 0.00 0.00 2.34
665 666 1.745489 GGTTCAGGCCAGCGTTAGG 60.745 63.158 5.01 0.00 0.00 2.69
683 684 4.397090 CGCACGCGCCAATCCAAA 62.397 61.111 5.73 0.00 33.11 3.28
684 685 2.181525 GCACGCGCCAATCCAAAT 59.818 55.556 5.73 0.00 0.00 2.32
685 686 2.160221 GCACGCGCCAATCCAAATG 61.160 57.895 5.73 0.00 0.00 2.32
686 687 2.160221 CACGCGCCAATCCAAATGC 61.160 57.895 5.73 0.00 0.00 3.56
688 689 2.583045 GCGCCAATCCAAATGCGG 60.583 61.111 0.00 0.00 46.59 5.69
689 690 3.062500 GCGCCAATCCAAATGCGGA 62.063 57.895 0.00 0.00 46.59 5.54
690 691 1.510383 CGCCAATCCAAATGCGGAA 59.490 52.632 0.00 0.00 43.08 4.30
691 692 0.526096 CGCCAATCCAAATGCGGAAG 60.526 55.000 0.00 0.00 43.08 3.46
712 713 2.970639 ACATCCGTGTCCGTCTGG 59.029 61.111 0.00 0.00 31.41 3.86
713 714 2.509336 CATCCGTGTCCGTCTGGC 60.509 66.667 0.00 0.00 34.14 4.85
714 715 3.771160 ATCCGTGTCCGTCTGGCC 61.771 66.667 0.00 0.00 34.14 5.36
718 719 4.736896 GTGTCCGTCTGGCCGACC 62.737 72.222 18.07 8.23 39.56 4.79
722 723 4.323477 CCGTCTGGCCGACCCAAA 62.323 66.667 18.07 0.00 44.81 3.28
723 724 3.047877 CGTCTGGCCGACCCAAAC 61.048 66.667 18.07 0.34 44.81 2.93
724 725 3.047877 GTCTGGCCGACCCAAACG 61.048 66.667 14.46 0.00 44.81 3.60
733 734 2.325509 CGACCCAAACGGACAAAATC 57.674 50.000 0.00 0.00 34.64 2.17
734 735 1.399215 CGACCCAAACGGACAAAATCG 60.399 52.381 0.00 0.00 34.64 3.34
735 736 0.312729 ACCCAAACGGACAAAATCGC 59.687 50.000 0.00 0.00 34.64 4.58
736 737 0.388006 CCCAAACGGACAAAATCGCC 60.388 55.000 0.00 0.00 0.00 5.54
740 741 2.782615 CGGACAAAATCGCCGTCC 59.217 61.111 0.00 0.00 44.79 4.79
741 742 2.782615 GGACAAAATCGCCGTCCG 59.217 61.111 0.00 0.00 39.86 4.79
742 743 2.030958 GGACAAAATCGCCGTCCGT 61.031 57.895 0.00 0.00 39.86 4.69
743 744 1.571215 GGACAAAATCGCCGTCCGTT 61.571 55.000 0.00 0.00 39.86 4.44
744 745 0.236449 GACAAAATCGCCGTCCGTTT 59.764 50.000 0.00 0.00 38.35 3.60
745 746 0.040781 ACAAAATCGCCGTCCGTTTG 60.041 50.000 0.00 0.00 38.28 2.93
746 747 0.727793 CAAAATCGCCGTCCGTTTGG 60.728 55.000 0.00 0.00 38.35 3.28
747 748 1.858372 AAAATCGCCGTCCGTTTGGG 61.858 55.000 0.00 0.00 38.35 4.12
748 749 3.540367 AATCGCCGTCCGTTTGGGT 62.540 57.895 0.00 0.00 38.35 4.51
749 750 3.945304 ATCGCCGTCCGTTTGGGTC 62.945 63.158 0.00 0.00 38.35 4.46
763 764 4.324991 GGTCGGCCCGTTGGAGTT 62.325 66.667 1.63 0.00 0.00 3.01
764 765 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
767 768 3.056328 GGCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 0.00 4.26
768 769 2.032681 GCCCGTTGGAGTTGCTCT 59.967 61.111 0.00 0.00 0.00 4.09
769 770 1.600916 GCCCGTTGGAGTTGCTCTT 60.601 57.895 0.00 0.00 0.00 2.85
770 771 0.321298 GCCCGTTGGAGTTGCTCTTA 60.321 55.000 0.00 0.00 0.00 2.10
771 772 1.726853 CCCGTTGGAGTTGCTCTTAG 58.273 55.000 0.00 0.00 0.00 2.18
772 773 1.676014 CCCGTTGGAGTTGCTCTTAGG 60.676 57.143 0.00 0.00 0.00 2.69
773 774 1.079503 CGTTGGAGTTGCTCTTAGGC 58.920 55.000 0.00 0.00 0.00 3.93
774 775 1.338200 CGTTGGAGTTGCTCTTAGGCT 60.338 52.381 0.00 0.00 0.00 4.58
775 776 2.784347 GTTGGAGTTGCTCTTAGGCTT 58.216 47.619 0.00 0.00 0.00 4.35
776 777 2.479566 TGGAGTTGCTCTTAGGCTTG 57.520 50.000 0.00 0.00 0.00 4.01
777 778 1.977854 TGGAGTTGCTCTTAGGCTTGA 59.022 47.619 0.00 0.00 0.00 3.02
778 779 2.573462 TGGAGTTGCTCTTAGGCTTGAT 59.427 45.455 0.00 0.00 0.00 2.57
779 780 3.009473 TGGAGTTGCTCTTAGGCTTGATT 59.991 43.478 0.00 0.00 0.00 2.57
780 781 4.013050 GGAGTTGCTCTTAGGCTTGATTT 58.987 43.478 0.00 0.00 0.00 2.17
781 782 4.460731 GGAGTTGCTCTTAGGCTTGATTTT 59.539 41.667 0.00 0.00 0.00 1.82
782 783 5.047731 GGAGTTGCTCTTAGGCTTGATTTTT 60.048 40.000 0.00 0.00 0.00 1.94
783 784 5.776744 AGTTGCTCTTAGGCTTGATTTTTG 58.223 37.500 0.00 0.00 0.00 2.44
784 785 4.789012 TGCTCTTAGGCTTGATTTTTGG 57.211 40.909 0.00 0.00 0.00 3.28
785 786 4.151883 TGCTCTTAGGCTTGATTTTTGGT 58.848 39.130 0.00 0.00 0.00 3.67
786 787 5.321102 TGCTCTTAGGCTTGATTTTTGGTA 58.679 37.500 0.00 0.00 0.00 3.25
787 788 5.183140 TGCTCTTAGGCTTGATTTTTGGTAC 59.817 40.000 0.00 0.00 0.00 3.34
788 789 5.183140 GCTCTTAGGCTTGATTTTTGGTACA 59.817 40.000 0.00 0.00 0.00 2.90
865 866 5.298276 GTGAGGATAGGATAGGATTAGAGCG 59.702 48.000 0.00 0.00 0.00 5.03
888 889 1.297672 CTCGCGTCGATCGACATGT 60.298 57.895 38.62 0.00 44.77 3.21
893 894 1.141881 GTCGATCGACATGTGCCCT 59.858 57.895 36.61 0.00 44.02 5.19
919 927 3.630312 TGCCTAGTGGACTTTTGACAAAC 59.370 43.478 0.00 0.00 34.57 2.93
945 955 3.467226 GTCCCGATTGGCTCCCGA 61.467 66.667 0.00 0.00 0.00 5.14
946 956 3.154473 TCCCGATTGGCTCCCGAG 61.154 66.667 0.00 0.00 0.00 4.63
1042 1056 3.496131 CACCGGGCGAACGAATGG 61.496 66.667 6.32 0.00 35.47 3.16
1044 1058 2.184836 CCGGGCGAACGAATGGTA 59.815 61.111 0.00 0.00 35.47 3.25
1045 1059 2.169146 CCGGGCGAACGAATGGTAC 61.169 63.158 0.00 0.00 35.47 3.34
1047 1061 1.143969 CGGGCGAACGAATGGTACTC 61.144 60.000 0.00 0.00 35.47 2.59
1058 1072 5.288543 CGAATGGTACTCGTACTATACCC 57.711 47.826 6.51 0.61 36.44 3.69
1059 1073 4.154918 CGAATGGTACTCGTACTATACCCC 59.845 50.000 6.51 4.22 36.44 4.95
1060 1074 4.729552 ATGGTACTCGTACTATACCCCA 57.270 45.455 12.15 3.10 38.07 4.96
1061 1075 4.090761 TGGTACTCGTACTATACCCCAG 57.909 50.000 12.15 0.00 38.07 4.45
1063 1077 1.992538 ACTCGTACTATACCCCAGCC 58.007 55.000 0.00 0.00 0.00 4.85
1309 1602 3.519930 GTCCTCGACCTCCTCGGC 61.520 72.222 0.00 0.00 43.16 5.54
1310 1603 4.816984 TCCTCGACCTCCTCGGCC 62.817 72.222 0.00 0.00 43.16 6.13
1988 2320 4.166888 TCCTCCGCTGGCTCATGC 62.167 66.667 0.00 0.00 38.76 4.06
2161 2493 2.677003 CGTGACGTGCATTGGGACC 61.677 63.158 0.00 0.00 30.51 4.46
2375 2707 4.078516 GGACGCCGGCCTAACACT 62.079 66.667 23.46 0.00 0.00 3.55
2476 2811 9.920946 AGTATTCTGTTACATTGGGTTCATTAT 57.079 29.630 0.00 0.00 0.00 1.28
2551 2892 8.370493 ACCTACAATTCATGTTAGATTCGATG 57.630 34.615 0.00 0.00 43.63 3.84
2558 2899 7.637709 TTCATGTTAGATTCGATGTATTCCG 57.362 36.000 0.00 0.00 0.00 4.30
2572 2913 4.699637 TGTATTCCGGTTTGCTATCGATT 58.300 39.130 1.71 0.00 0.00 3.34
2573 2914 5.120399 TGTATTCCGGTTTGCTATCGATTT 58.880 37.500 1.71 0.00 0.00 2.17
2574 2915 6.282167 TGTATTCCGGTTTGCTATCGATTTA 58.718 36.000 1.71 0.00 0.00 1.40
2593 2934 8.088981 TCGATTTATTAGCTCCTAAGGATCAAC 58.911 37.037 0.00 0.00 29.02 3.18
2846 3350 2.158957 TGAAAGCAGAGTTTCGACCACT 60.159 45.455 0.00 0.00 38.99 4.00
2889 3393 3.449018 GCTCCTCTCTTCTTCCACACATA 59.551 47.826 0.00 0.00 0.00 2.29
2966 3470 4.641094 AGTCTATAGTCGACAAACTCCAGG 59.359 45.833 19.50 0.00 33.89 4.45
2975 3479 3.619733 CGACAAACTCCAGGATCCATGAA 60.620 47.826 15.82 0.00 0.00 2.57
3381 3885 5.410067 CAACTGCAATATTGTACCTTTGGG 58.590 41.667 16.61 1.78 38.88 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.077212 CCTTGGCCACCCTGATCTG 60.077 63.158 3.88 0.00 0.00 2.90
5 6 3.650950 GCTCCTTGGCCACCCTGA 61.651 66.667 3.88 0.00 0.00 3.86
61 62 2.025441 GCGCTGCTCTACCTCGAG 59.975 66.667 5.13 5.13 0.00 4.04
62 63 3.877357 CGCGCTGCTCTACCTCGA 61.877 66.667 5.56 0.00 0.00 4.04
63 64 3.798639 CTCGCGCTGCTCTACCTCG 62.799 68.421 5.56 0.00 0.00 4.63
64 65 2.025441 CTCGCGCTGCTCTACCTC 59.975 66.667 5.56 0.00 0.00 3.85
65 66 3.522731 CCTCGCGCTGCTCTACCT 61.523 66.667 5.56 0.00 0.00 3.08
383 384 3.250323 CAGAGCGCCGTCATGTCG 61.250 66.667 2.29 5.32 0.00 4.35
384 385 2.835701 TTCCAGAGCGCCGTCATGTC 62.836 60.000 2.29 0.00 0.00 3.06
385 386 2.942796 TTCCAGAGCGCCGTCATGT 61.943 57.895 2.29 0.00 0.00 3.21
386 387 2.125552 TTCCAGAGCGCCGTCATG 60.126 61.111 2.29 0.00 0.00 3.07
387 388 2.125512 GTTCCAGAGCGCCGTCAT 60.126 61.111 2.29 0.00 0.00 3.06
388 389 3.611674 TGTTCCAGAGCGCCGTCA 61.612 61.111 2.29 0.00 0.00 4.35
389 390 3.112709 GTGTTCCAGAGCGCCGTC 61.113 66.667 2.29 0.00 0.00 4.79
395 396 3.112709 GACGCCGTGTTCCAGAGC 61.113 66.667 0.00 0.00 0.00 4.09
396 397 2.432628 GGACGCCGTGTTCCAGAG 60.433 66.667 0.00 0.00 0.00 3.35
397 398 4.351938 CGGACGCCGTGTTCCAGA 62.352 66.667 0.00 0.00 42.73 3.86
432 433 4.194720 AGGTCGATGAGCGTCGGC 62.195 66.667 11.67 9.94 44.95 5.54
433 434 2.024871 GAGGTCGATGAGCGTCGG 59.975 66.667 11.67 0.00 41.74 4.79
434 435 1.583967 GTGAGGTCGATGAGCGTCG 60.584 63.158 5.78 5.78 42.74 5.12
435 436 1.583967 CGTGAGGTCGATGAGCGTC 60.584 63.158 0.00 0.00 41.80 5.19
436 437 1.583495 TTCGTGAGGTCGATGAGCGT 61.583 55.000 0.00 0.00 41.80 5.07
437 438 1.134530 GTTCGTGAGGTCGATGAGCG 61.135 60.000 0.00 0.00 39.57 5.03
438 439 0.802607 GGTTCGTGAGGTCGATGAGC 60.803 60.000 0.00 0.00 39.57 4.26
439 440 0.179134 GGGTTCGTGAGGTCGATGAG 60.179 60.000 0.00 0.00 39.57 2.90
440 441 1.601419 GGGGTTCGTGAGGTCGATGA 61.601 60.000 0.00 0.00 39.57 2.92
441 442 1.153628 GGGGTTCGTGAGGTCGATG 60.154 63.158 0.00 0.00 39.57 3.84
442 443 2.707849 CGGGGTTCGTGAGGTCGAT 61.708 63.158 0.00 0.00 39.57 3.59
443 444 3.367743 CGGGGTTCGTGAGGTCGA 61.368 66.667 0.00 0.00 38.08 4.20
444 445 3.338126 CTCGGGGTTCGTGAGGTCG 62.338 68.421 0.00 0.00 40.32 4.79
445 446 2.572284 CTCGGGGTTCGTGAGGTC 59.428 66.667 0.00 0.00 40.32 3.85
446 447 2.995574 CCTCGGGGTTCGTGAGGT 60.996 66.667 0.00 0.00 43.48 3.85
448 449 2.572284 GTCCTCGGGGTTCGTGAG 59.428 66.667 0.00 0.00 40.32 3.51
449 450 3.367743 CGTCCTCGGGGTTCGTGA 61.368 66.667 0.00 0.00 40.32 4.35
450 451 3.367743 TCGTCCTCGGGGTTCGTG 61.368 66.667 17.65 0.00 40.32 4.35
451 452 3.368571 GTCGTCCTCGGGGTTCGT 61.369 66.667 17.65 0.00 40.32 3.85
452 453 4.471726 CGTCGTCCTCGGGGTTCG 62.472 72.222 0.00 8.37 40.90 3.95
453 454 3.058160 TCGTCGTCCTCGGGGTTC 61.058 66.667 0.00 0.00 37.69 3.62
454 455 3.368571 GTCGTCGTCCTCGGGGTT 61.369 66.667 0.00 0.00 37.69 4.11
457 458 4.157958 GTCGTCGTCGTCCTCGGG 62.158 72.222 1.33 0.00 38.33 5.14
458 459 4.495939 CGTCGTCGTCGTCCTCGG 62.496 72.222 3.67 0.00 38.33 4.63
459 460 2.860421 CTTCGTCGTCGTCGTCCTCG 62.860 65.000 11.41 4.14 38.33 4.63
460 461 1.225691 CTTCGTCGTCGTCGTCCTC 60.226 63.158 11.41 0.00 38.33 3.71
461 462 2.858868 CTTCGTCGTCGTCGTCCT 59.141 61.111 11.41 0.00 38.33 3.85
462 463 2.868787 GCTTCGTCGTCGTCGTCC 60.869 66.667 11.41 0.00 38.33 4.79
463 464 1.959899 TAGGCTTCGTCGTCGTCGTC 61.960 60.000 11.41 0.00 38.33 4.20
464 465 1.568612 TTAGGCTTCGTCGTCGTCGT 61.569 55.000 11.41 0.00 38.33 4.34
465 466 0.856490 CTTAGGCTTCGTCGTCGTCG 60.856 60.000 5.50 5.50 38.33 5.12
466 467 0.522915 CCTTAGGCTTCGTCGTCGTC 60.523 60.000 1.33 0.00 38.33 4.20
467 468 1.505353 CCTTAGGCTTCGTCGTCGT 59.495 57.895 1.33 0.00 38.33 4.34
468 469 1.872679 GCCTTAGGCTTCGTCGTCG 60.873 63.158 17.16 0.00 46.69 5.12
469 470 4.089983 GCCTTAGGCTTCGTCGTC 57.910 61.111 17.16 0.00 46.69 4.20
490 491 2.202650 TAAACTACGAGGCGGCGC 60.203 61.111 26.17 26.17 33.86 6.53
491 492 1.588139 CCTAAACTACGAGGCGGCG 60.588 63.158 0.51 0.51 37.29 6.46
492 493 4.414732 CCTAAACTACGAGGCGGC 57.585 61.111 0.00 0.00 0.00 6.53
496 497 6.980051 ATAAAAACAGCCTAAACTACGAGG 57.020 37.500 0.00 0.00 35.78 4.63
497 498 9.673454 AAAAATAAAAACAGCCTAAACTACGAG 57.327 29.630 0.00 0.00 0.00 4.18
521 522 5.053145 AGCGTCCACATTTGCATTTAAAAA 58.947 33.333 0.00 0.00 0.00 1.94
522 523 4.626042 AGCGTCCACATTTGCATTTAAAA 58.374 34.783 0.00 0.00 0.00 1.52
523 524 4.250116 AGCGTCCACATTTGCATTTAAA 57.750 36.364 0.00 0.00 0.00 1.52
524 525 3.932545 AGCGTCCACATTTGCATTTAA 57.067 38.095 0.00 0.00 0.00 1.52
525 526 3.573598 CAAGCGTCCACATTTGCATTTA 58.426 40.909 0.00 0.00 0.00 1.40
526 527 2.406130 CAAGCGTCCACATTTGCATTT 58.594 42.857 0.00 0.00 0.00 2.32
527 528 1.337074 CCAAGCGTCCACATTTGCATT 60.337 47.619 0.00 0.00 0.00 3.56
528 529 0.244450 CCAAGCGTCCACATTTGCAT 59.756 50.000 0.00 0.00 0.00 3.96
529 530 0.821301 TCCAAGCGTCCACATTTGCA 60.821 50.000 0.00 0.00 0.00 4.08
530 531 0.387239 GTCCAAGCGTCCACATTTGC 60.387 55.000 0.00 0.00 0.00 3.68
531 532 1.197721 GAGTCCAAGCGTCCACATTTG 59.802 52.381 0.00 0.00 0.00 2.32
532 533 1.072331 AGAGTCCAAGCGTCCACATTT 59.928 47.619 0.00 0.00 0.00 2.32
533 534 0.687354 AGAGTCCAAGCGTCCACATT 59.313 50.000 0.00 0.00 0.00 2.71
534 535 0.247736 GAGAGTCCAAGCGTCCACAT 59.752 55.000 0.00 0.00 0.00 3.21
535 536 1.666011 GAGAGTCCAAGCGTCCACA 59.334 57.895 0.00 0.00 0.00 4.17
536 537 1.444553 CGAGAGTCCAAGCGTCCAC 60.445 63.158 0.00 0.00 0.00 4.02
537 538 2.962569 CGAGAGTCCAAGCGTCCA 59.037 61.111 0.00 0.00 0.00 4.02
538 539 2.507324 GCGAGAGTCCAAGCGTCC 60.507 66.667 0.00 0.00 0.00 4.79
539 540 2.507324 GGCGAGAGTCCAAGCGTC 60.507 66.667 0.00 0.00 0.00 5.19
540 541 4.421479 CGGCGAGAGTCCAAGCGT 62.421 66.667 0.00 0.00 0.00 5.07
543 544 4.821589 GGCCGGCGAGAGTCCAAG 62.822 72.222 22.54 0.00 0.00 3.61
546 547 4.516195 GAAGGCCGGCGAGAGTCC 62.516 72.222 22.54 4.09 0.00 3.85
547 548 4.856607 CGAAGGCCGGCGAGAGTC 62.857 72.222 22.54 11.59 33.91 3.36
559 560 0.678684 ATTAAACCCGGCCACGAAGG 60.679 55.000 2.24 0.00 44.60 3.46
560 561 0.450184 CATTAAACCCGGCCACGAAG 59.550 55.000 2.24 0.00 44.60 3.79
561 562 0.250814 ACATTAAACCCGGCCACGAA 60.251 50.000 2.24 0.00 44.60 3.85
562 563 0.250814 AACATTAAACCCGGCCACGA 60.251 50.000 2.24 0.00 44.60 4.35
563 564 0.599060 AAACATTAAACCCGGCCACG 59.401 50.000 2.24 0.00 40.55 4.94
564 565 3.938289 TTAAACATTAAACCCGGCCAC 57.062 42.857 2.24 0.00 0.00 5.01
565 566 6.600882 TTAATTAAACATTAAACCCGGCCA 57.399 33.333 2.24 0.00 0.00 5.36
566 567 6.018588 GCATTAATTAAACATTAAACCCGGCC 60.019 38.462 1.21 0.00 0.00 6.13
567 568 6.759356 AGCATTAATTAAACATTAAACCCGGC 59.241 34.615 1.21 0.00 0.00 6.13
568 569 7.762159 ACAGCATTAATTAAACATTAAACCCGG 59.238 33.333 1.21 0.00 0.00 5.73
569 570 8.696410 ACAGCATTAATTAAACATTAAACCCG 57.304 30.769 1.21 0.00 0.00 5.28
624 625 3.694535 TTTTGAACGGCGCTAGAAAAA 57.305 38.095 6.90 5.94 0.00 1.94
625 626 3.560503 CATTTTGAACGGCGCTAGAAAA 58.439 40.909 6.90 7.95 0.00 2.29
626 627 2.095466 CCATTTTGAACGGCGCTAGAAA 60.095 45.455 6.90 4.08 0.00 2.52
627 628 1.466950 CCATTTTGAACGGCGCTAGAA 59.533 47.619 6.90 0.00 0.00 2.10
628 629 1.083489 CCATTTTGAACGGCGCTAGA 58.917 50.000 6.90 0.00 0.00 2.43
629 630 0.098728 CCCATTTTGAACGGCGCTAG 59.901 55.000 6.90 4.36 0.00 3.42
630 631 0.606944 ACCCATTTTGAACGGCGCTA 60.607 50.000 6.90 0.00 0.00 4.26
631 632 1.460273 AACCCATTTTGAACGGCGCT 61.460 50.000 6.90 0.00 0.00 5.92
632 633 1.006688 AACCCATTTTGAACGGCGC 60.007 52.632 6.90 0.00 0.00 6.53
633 634 0.312416 TGAACCCATTTTGAACGGCG 59.688 50.000 4.80 4.80 0.00 6.46
634 635 1.336795 CCTGAACCCATTTTGAACGGC 60.337 52.381 0.00 0.00 0.00 5.68
635 636 1.336795 GCCTGAACCCATTTTGAACGG 60.337 52.381 0.00 0.00 0.00 4.44
636 637 1.336795 GGCCTGAACCCATTTTGAACG 60.337 52.381 0.00 0.00 0.00 3.95
637 638 1.691434 TGGCCTGAACCCATTTTGAAC 59.309 47.619 3.32 0.00 0.00 3.18
638 639 1.969923 CTGGCCTGAACCCATTTTGAA 59.030 47.619 3.32 0.00 0.00 2.69
639 640 1.631405 CTGGCCTGAACCCATTTTGA 58.369 50.000 3.32 0.00 0.00 2.69
640 641 0.037046 GCTGGCCTGAACCCATTTTG 60.037 55.000 14.77 0.00 0.00 2.44
641 642 1.535204 CGCTGGCCTGAACCCATTTT 61.535 55.000 14.77 0.00 0.00 1.82
642 643 1.978617 CGCTGGCCTGAACCCATTT 60.979 57.895 14.77 0.00 0.00 2.32
643 644 2.361610 CGCTGGCCTGAACCCATT 60.362 61.111 14.77 0.00 0.00 3.16
644 645 1.847798 TAACGCTGGCCTGAACCCAT 61.848 55.000 14.77 0.00 0.00 4.00
645 646 2.463589 CTAACGCTGGCCTGAACCCA 62.464 60.000 14.77 0.00 0.00 4.51
646 647 1.745489 CTAACGCTGGCCTGAACCC 60.745 63.158 14.77 0.00 0.00 4.11
647 648 1.745489 CCTAACGCTGGCCTGAACC 60.745 63.158 14.77 0.00 0.00 3.62
648 649 2.399356 GCCTAACGCTGGCCTGAAC 61.399 63.158 14.77 0.00 44.32 3.18
649 650 2.046314 GCCTAACGCTGGCCTGAA 60.046 61.111 14.77 0.00 44.32 3.02
666 667 3.681961 ATTTGGATTGGCGCGTGCG 62.682 57.895 15.81 10.36 44.10 5.34
667 668 2.160221 CATTTGGATTGGCGCGTGC 61.160 57.895 13.78 13.78 41.71 5.34
668 669 2.160221 GCATTTGGATTGGCGCGTG 61.160 57.895 8.43 0.00 0.00 5.34
669 670 2.181525 GCATTTGGATTGGCGCGT 59.818 55.556 8.43 0.00 0.00 6.01
670 671 2.950710 CGCATTTGGATTGGCGCG 60.951 61.111 0.00 0.00 43.14 6.86
673 674 0.807275 GCTTCCGCATTTGGATTGGC 60.807 55.000 0.00 0.00 38.00 4.52
674 675 0.526096 CGCTTCCGCATTTGGATTGG 60.526 55.000 0.00 0.00 38.00 3.16
675 676 0.526096 CCGCTTCCGCATTTGGATTG 60.526 55.000 0.00 0.00 38.00 2.67
676 677 0.679640 TCCGCTTCCGCATTTGGATT 60.680 50.000 0.00 0.00 38.00 3.01
677 678 1.077787 TCCGCTTCCGCATTTGGAT 60.078 52.632 0.00 0.00 38.00 3.41
678 679 2.038269 GTCCGCTTCCGCATTTGGA 61.038 57.895 0.00 0.00 35.83 3.53
679 680 1.656818 ATGTCCGCTTCCGCATTTGG 61.657 55.000 0.00 0.00 35.30 3.28
680 681 0.248215 GATGTCCGCTTCCGCATTTG 60.248 55.000 0.00 0.00 35.30 2.32
681 682 1.376609 GGATGTCCGCTTCCGCATTT 61.377 55.000 0.00 0.00 35.30 2.32
682 683 1.819632 GGATGTCCGCTTCCGCATT 60.820 57.895 0.00 0.00 35.30 3.56
683 684 2.203070 GGATGTCCGCTTCCGCAT 60.203 61.111 0.00 0.00 35.30 4.73
695 696 2.970639 CCAGACGGACACGGATGT 59.029 61.111 0.00 0.00 46.48 3.06
696 697 2.509336 GCCAGACGGACACGGATG 60.509 66.667 0.00 0.00 46.48 3.51
697 698 3.771160 GGCCAGACGGACACGGAT 61.771 66.667 0.00 0.00 46.48 4.18
708 709 4.323477 CCGTTTGGGTCGGCCAGA 62.323 66.667 9.07 0.00 41.48 3.86
709 710 4.323477 TCCGTTTGGGTCGGCCAG 62.323 66.667 9.07 0.00 46.49 4.85
710 711 4.629523 GTCCGTTTGGGTCGGCCA 62.630 66.667 9.07 0.00 46.49 5.36
711 712 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
712 713 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
714 715 1.399215 CGATTTTGTCCGTTTGGGTCG 60.399 52.381 0.00 0.00 37.00 4.79
715 716 1.664874 GCGATTTTGTCCGTTTGGGTC 60.665 52.381 0.00 0.00 37.00 4.46
716 717 0.312729 GCGATTTTGTCCGTTTGGGT 59.687 50.000 0.00 0.00 37.00 4.51
717 718 0.388006 GGCGATTTTGTCCGTTTGGG 60.388 55.000 0.00 0.00 35.24 4.12
718 719 0.727793 CGGCGATTTTGTCCGTTTGG 60.728 55.000 0.00 0.00 38.47 3.28
719 720 2.707192 CGGCGATTTTGTCCGTTTG 58.293 52.632 0.00 0.00 38.47 2.93
724 725 1.571215 AACGGACGGCGATTTTGTCC 61.571 55.000 16.62 8.05 46.91 4.02
725 726 0.236449 AAACGGACGGCGATTTTGTC 59.764 50.000 16.62 0.00 0.00 3.18
726 727 0.040781 CAAACGGACGGCGATTTTGT 60.041 50.000 16.62 1.09 0.00 2.83
727 728 0.727793 CCAAACGGACGGCGATTTTG 60.728 55.000 16.62 15.66 0.00 2.44
728 729 1.577421 CCAAACGGACGGCGATTTT 59.423 52.632 16.62 3.87 0.00 1.82
729 730 2.329614 CCCAAACGGACGGCGATTT 61.330 57.895 16.62 5.62 0.00 2.17
730 731 2.744709 CCCAAACGGACGGCGATT 60.745 61.111 16.62 0.00 0.00 3.34
731 732 3.945304 GACCCAAACGGACGGCGAT 62.945 63.158 16.62 0.00 34.64 4.58
732 733 4.668118 GACCCAAACGGACGGCGA 62.668 66.667 16.62 0.00 34.64 5.54
746 747 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
747 748 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
750 751 3.056328 GAGCAACTCCAACGGGCC 61.056 66.667 0.00 0.00 0.00 5.80
751 752 0.321298 TAAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
752 753 1.676014 CCTAAGAGCAACTCCAACGGG 60.676 57.143 0.00 0.00 0.00 5.28
753 754 1.726853 CCTAAGAGCAACTCCAACGG 58.273 55.000 0.00 0.00 0.00 4.44
754 755 1.079503 GCCTAAGAGCAACTCCAACG 58.920 55.000 0.00 0.00 0.00 4.10
755 756 2.481289 AGCCTAAGAGCAACTCCAAC 57.519 50.000 0.00 0.00 34.23 3.77
756 757 2.371841 TCAAGCCTAAGAGCAACTCCAA 59.628 45.455 0.00 0.00 34.23 3.53
757 758 1.977854 TCAAGCCTAAGAGCAACTCCA 59.022 47.619 0.00 0.00 34.23 3.86
758 759 2.770164 TCAAGCCTAAGAGCAACTCC 57.230 50.000 0.00 0.00 34.23 3.85
759 760 5.635417 AAAATCAAGCCTAAGAGCAACTC 57.365 39.130 0.00 0.00 34.23 3.01
760 761 5.279156 CCAAAAATCAAGCCTAAGAGCAACT 60.279 40.000 0.00 0.00 34.23 3.16
761 762 4.925646 CCAAAAATCAAGCCTAAGAGCAAC 59.074 41.667 0.00 0.00 34.23 4.17
762 763 4.588528 ACCAAAAATCAAGCCTAAGAGCAA 59.411 37.500 0.00 0.00 34.23 3.91
763 764 4.151883 ACCAAAAATCAAGCCTAAGAGCA 58.848 39.130 0.00 0.00 34.23 4.26
764 765 4.790765 ACCAAAAATCAAGCCTAAGAGC 57.209 40.909 0.00 0.00 0.00 4.09
765 766 6.817765 TGTACCAAAAATCAAGCCTAAGAG 57.182 37.500 0.00 0.00 0.00 2.85
766 767 7.589958 TTTGTACCAAAAATCAAGCCTAAGA 57.410 32.000 0.00 0.00 0.00 2.10
767 768 7.331687 CCATTTGTACCAAAAATCAAGCCTAAG 59.668 37.037 0.00 0.00 0.00 2.18
768 769 7.015682 TCCATTTGTACCAAAAATCAAGCCTAA 59.984 33.333 0.00 0.00 0.00 2.69
769 770 6.495181 TCCATTTGTACCAAAAATCAAGCCTA 59.505 34.615 0.00 0.00 0.00 3.93
770 771 5.306678 TCCATTTGTACCAAAAATCAAGCCT 59.693 36.000 0.00 0.00 0.00 4.58
771 772 5.546526 TCCATTTGTACCAAAAATCAAGCC 58.453 37.500 0.00 0.00 0.00 4.35
772 773 6.223120 ACTCCATTTGTACCAAAAATCAAGC 58.777 36.000 0.00 0.00 0.00 4.01
773 774 8.356657 TGTACTCCATTTGTACCAAAAATCAAG 58.643 33.333 0.00 0.00 39.42 3.02
774 775 8.239038 TGTACTCCATTTGTACCAAAAATCAA 57.761 30.769 0.00 0.00 39.42 2.57
775 776 7.825331 TGTACTCCATTTGTACCAAAAATCA 57.175 32.000 0.00 0.00 39.42 2.57
776 777 9.139174 CAATGTACTCCATTTGTACCAAAAATC 57.861 33.333 0.00 0.00 41.93 2.17
777 778 7.602265 GCAATGTACTCCATTTGTACCAAAAAT 59.398 33.333 0.00 0.00 41.93 1.82
778 779 6.926272 GCAATGTACTCCATTTGTACCAAAAA 59.074 34.615 0.00 0.00 41.93 1.94
779 780 6.451393 GCAATGTACTCCATTTGTACCAAAA 58.549 36.000 0.00 0.00 41.93 2.44
780 781 5.047660 GGCAATGTACTCCATTTGTACCAAA 60.048 40.000 0.00 0.00 41.93 3.28
781 782 4.461081 GGCAATGTACTCCATTTGTACCAA 59.539 41.667 0.00 0.00 41.93 3.67
782 783 4.013728 GGCAATGTACTCCATTTGTACCA 58.986 43.478 0.00 0.00 41.93 3.25
783 784 4.013728 TGGCAATGTACTCCATTTGTACC 58.986 43.478 0.00 0.00 41.93 3.34
784 785 5.835113 ATGGCAATGTACTCCATTTGTAC 57.165 39.130 0.00 0.00 41.93 2.90
790 791 2.951642 CGGAAATGGCAATGTACTCCAT 59.048 45.455 0.00 0.00 42.01 3.41
791 792 2.290641 ACGGAAATGGCAATGTACTCCA 60.291 45.455 0.00 0.00 0.00 3.86
797 798 1.102978 GCCTACGGAAATGGCAATGT 58.897 50.000 0.00 0.00 45.46 2.71
888 889 3.720601 CACTAGGCAGGCAGGGCA 61.721 66.667 0.00 0.00 35.46 5.36
893 894 0.771127 AAAAGTCCACTAGGCAGGCA 59.229 50.000 0.00 0.00 33.74 4.75
919 927 0.394352 CCAATCGGGACAAGAAGGGG 60.394 60.000 0.00 0.00 40.01 4.79
969 979 1.304464 GGAGGGTTGGAAAGGCTGG 60.304 63.158 0.00 0.00 0.00 4.85
970 980 0.178964 TTGGAGGGTTGGAAAGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
971 981 0.113190 CTTGGAGGGTTGGAAAGGCT 59.887 55.000 0.00 0.00 0.00 4.58
972 982 0.178961 ACTTGGAGGGTTGGAAAGGC 60.179 55.000 0.00 0.00 0.00 4.35
1042 1056 2.816672 GGCTGGGGTATAGTACGAGTAC 59.183 54.545 5.32 5.32 36.35 2.73
1044 1058 1.816961 CGGCTGGGGTATAGTACGAGT 60.817 57.143 0.00 0.00 0.00 4.18
1045 1059 0.879765 CGGCTGGGGTATAGTACGAG 59.120 60.000 0.00 0.00 0.00 4.18
1047 1061 1.177256 AGCGGCTGGGGTATAGTACG 61.177 60.000 0.00 0.00 0.00 3.67
1051 1065 0.251653 TCCTAGCGGCTGGGGTATAG 60.252 60.000 29.07 9.43 32.70 1.31
1052 1066 0.251653 CTCCTAGCGGCTGGGGTATA 60.252 60.000 29.07 11.44 32.70 1.47
1058 1072 2.521950 TAGGCTCCTAGCGGCTGG 60.522 66.667 13.86 9.99 43.62 4.85
1059 1073 2.569354 CCTAGGCTCCTAGCGGCTG 61.569 68.421 13.86 2.54 43.62 4.85
1060 1074 2.203567 CCTAGGCTCCTAGCGGCT 60.204 66.667 15.80 7.98 43.62 5.52
1061 1075 2.203509 TCCTAGGCTCCTAGCGGC 60.204 66.667 15.80 0.00 43.62 6.53
1063 1077 2.622011 CGCTCCTAGGCTCCTAGCG 61.622 68.421 22.64 22.64 43.62 4.26
2078 2410 2.851102 CCCCATCAGGCTCCGGAT 60.851 66.667 3.57 0.00 0.00 4.18
2161 2493 2.466982 ATTGTGGAGCATCGCGCAG 61.467 57.895 8.75 0.00 46.13 5.18
2371 2703 0.179009 AATCAGCAGTGCACCAGTGT 60.179 50.000 19.20 0.00 37.16 3.55
2375 2707 1.401761 AAACAATCAGCAGTGCACCA 58.598 45.000 19.20 0.00 0.00 4.17
2476 2811 4.766373 TGATTTATTGAGCAGCCAACAGAA 59.234 37.500 0.00 0.00 0.00 3.02
2551 2892 5.668558 AAATCGATAGCAAACCGGAATAC 57.331 39.130 9.46 0.00 0.00 1.89
2556 2897 5.408604 AGCTAATAAATCGATAGCAAACCGG 59.591 40.000 17.09 0.00 43.48 5.28
2558 2899 6.651225 AGGAGCTAATAAATCGATAGCAAACC 59.349 38.462 17.09 15.56 43.48 3.27
2572 2913 6.971726 TCGTTGATCCTTAGGAGCTAATAA 57.028 37.500 17.83 0.40 39.11 1.40
2573 2914 7.540474 AATCGTTGATCCTTAGGAGCTAATA 57.460 36.000 17.83 2.35 39.11 0.98
2574 2915 6.426646 AATCGTTGATCCTTAGGAGCTAAT 57.573 37.500 17.83 0.00 39.11 1.73
2593 2934 4.214119 TCCAGCAGTTTGAAGAAGAAATCG 59.786 41.667 0.00 0.00 0.00 3.34
2846 3350 0.391661 GAAGACCGAGCATGAGCCAA 60.392 55.000 0.00 0.00 43.56 4.52
2966 3470 3.436015 CAGGCGAAGATCATTCATGGATC 59.564 47.826 0.00 0.00 41.14 3.36
2975 3479 2.119801 AACTTGCAGGCGAAGATCAT 57.880 45.000 0.00 0.00 0.00 2.45
3284 3788 2.415090 GCATTGTGATGTCAAGCCAGAC 60.415 50.000 0.00 0.00 38.99 3.51
3381 3885 1.751927 CTCCTGTGCTCCAATGGGC 60.752 63.158 0.00 2.35 0.00 5.36


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

AutoCloner maintained by Alex Coulton.