Multiple sequence alignment - TraesCS2B01G141000

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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 TraesCS2B01G141000 chr2B 100.000 2952 0 0 1 2952 107567621 107570572 0.000000e+00 5452
1 TraesCS2B01G141000 chr2B 83.891 478 76 1 1 477 707977184 707976707 3.470000e-124 455
2 TraesCS2B01G141000 chr2B 81.688 557 81 15 850 1389 107793136 107793688 7.510000e-121 444
3 TraesCS2B01G141000 chr2B 82.353 510 64 19 2071 2563 107790253 107790753 1.270000e-113 420
4 TraesCS2B01G141000 chr2B 87.537 337 34 5 2231 2565 107578242 107578572 1.660000e-102 383
5 TraesCS2B01G141000 chr2B 77.447 705 98 38 850 1521 107576781 107577457 6.010000e-97 364
6 TraesCS2B01G141000 chr2B 78.616 318 62 3 1538 1849 107038568 107038251 3.860000e-49 206
7 TraesCS2B01G141000 chr2B 86.792 106 7 2 837 941 107789027 107789126 8.650000e-21 111
8 TraesCS2B01G141000 chr2D 95.589 2131 65 11 834 2952 71404523 71406636 0.000000e+00 3387
9 TraesCS2B01G141000 chr2D 82.161 1805 214 54 1182 2952 71455211 71456941 0.000000e+00 1450
10 TraesCS2B01G141000 chr2D 78.156 1616 229 66 1029 2565 71565745 71567315 0.000000e+00 915
11 TraesCS2B01G141000 chr2D 82.098 1039 137 22 1560 2565 71470721 71471743 0.000000e+00 843
12 TraesCS2B01G141000 chr2D 80.036 1122 168 36 850 1944 71598714 71599806 0.000000e+00 780
13 TraesCS2B01G141000 chr2D 83.992 481 69 7 1 477 570100567 570100091 3.470000e-124 455
14 TraesCS2B01G141000 chr2D 83.750 480 70 5 1 475 192667642 192667166 5.800000e-122 448
15 TraesCS2B01G141000 chr2D 87.798 336 25 8 2237 2565 71410170 71410496 2.150000e-101 379
16 TraesCS2B01G141000 chr2D 79.344 518 65 27 2069 2565 71595131 71595627 2.840000e-85 326
17 TraesCS2B01G141000 chr2D 76.889 450 55 25 1960 2365 71600086 71600530 2.980000e-50 209
18 TraesCS2B01G141000 chr2D 81.746 252 26 11 836 1079 71578176 71578415 3.000000e-45 193
19 TraesCS2B01G141000 chr2A 94.868 1890 62 10 834 2708 70284522 70282653 0.000000e+00 2920
20 TraesCS2B01G141000 chr2A 84.529 1422 152 32 1560 2952 70270805 70269423 0.000000e+00 1345
21 TraesCS2B01G141000 chr2A 78.193 1605 223 60 850 2365 70654910 70656476 0.000000e+00 907
22 TraesCS2B01G141000 chr2A 89.982 559 37 6 2394 2952 70282585 70282046 0.000000e+00 704
23 TraesCS2B01G141000 chr2A 81.413 807 102 26 1 774 329695510 329694719 1.500000e-172 616
24 TraesCS2B01G141000 chr2A 77.104 891 123 38 1535 2365 70155983 70155114 9.710000e-120 440
25 TraesCS2B01G141000 chr2A 80.389 617 89 25 845 1443 70649207 70649809 9.710000e-120 440
26 TraesCS2B01G141000 chr2A 76.796 724 85 43 842 1524 70235159 70234478 2.190000e-86 329
27 TraesCS2B01G141000 chr2A 82.591 247 26 9 850 1079 70643834 70644080 4.990000e-48 202
28 TraesCS2B01G141000 chr2A 81.193 218 26 10 894 1107 70273192 70272986 8.470000e-36 161
29 TraesCS2B01G141000 chr7B 81.338 777 118 18 1 762 521201931 521201167 9.050000e-170 606
30 TraesCS2B01G141000 chr1B 80.275 801 125 13 1 770 538462779 538463577 9.180000e-160 573
31 TraesCS2B01G141000 chr1D 80.488 656 98 13 1 627 62439984 62440638 2.660000e-130 475
32 TraesCS2B01G141000 chr7D 84.648 469 64 7 13 477 448518473 448518009 7.450000e-126 460
33 TraesCS2B01G141000 chr1A 83.682 478 76 2 1 477 153332135 153332611 1.610000e-122 449
34 TraesCS2B01G141000 chr3A 81.119 286 49 5 483 767 524295165 524295446 1.060000e-54 224


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 TraesCS2B01G141000 chr2B 107567621 107570572 2951 False 5452.000000 5452 100.000000 1 2952 1 chr2B.!!$F1 2951
1 TraesCS2B01G141000 chr2B 107576781 107578572 1791 False 373.500000 383 82.492000 850 2565 2 chr2B.!!$F2 1715
2 TraesCS2B01G141000 chr2B 107789027 107793688 4661 False 325.000000 444 83.611000 837 2563 3 chr2B.!!$F3 1726
3 TraesCS2B01G141000 chr2D 71404523 71410496 5973 False 1883.000000 3387 91.693500 834 2952 2 chr2D.!!$F5 2118
4 TraesCS2B01G141000 chr2D 71455211 71456941 1730 False 1450.000000 1450 82.161000 1182 2952 1 chr2D.!!$F1 1770
5 TraesCS2B01G141000 chr2D 71565745 71567315 1570 False 915.000000 915 78.156000 1029 2565 1 chr2D.!!$F3 1536
6 TraesCS2B01G141000 chr2D 71470721 71471743 1022 False 843.000000 843 82.098000 1560 2565 1 chr2D.!!$F2 1005
7 TraesCS2B01G141000 chr2D 71595131 71600530 5399 False 438.333333 780 78.756333 850 2565 3 chr2D.!!$F6 1715
8 TraesCS2B01G141000 chr2A 70282046 70284522 2476 True 1812.000000 2920 92.425000 834 2952 2 chr2A.!!$R5 2118
9 TraesCS2B01G141000 chr2A 70654910 70656476 1566 False 907.000000 907 78.193000 850 2365 1 chr2A.!!$F3 1515
10 TraesCS2B01G141000 chr2A 70269423 70273192 3769 True 753.000000 1345 82.861000 894 2952 2 chr2A.!!$R4 2058
11 TraesCS2B01G141000 chr2A 329694719 329695510 791 True 616.000000 616 81.413000 1 774 1 chr2A.!!$R3 773
12 TraesCS2B01G141000 chr2A 70155114 70155983 869 True 440.000000 440 77.104000 1535 2365 1 chr2A.!!$R1 830
13 TraesCS2B01G141000 chr2A 70649207 70649809 602 False 440.000000 440 80.389000 845 1443 1 chr2A.!!$F2 598
14 TraesCS2B01G141000 chr2A 70234478 70235159 681 True 329.000000 329 76.796000 842 1524 1 chr2A.!!$R2 682
15 TraesCS2B01G141000 chr7B 521201167 521201931 764 True 606.000000 606 81.338000 1 762 1 chr7B.!!$R1 761
16 TraesCS2B01G141000 chr1B 538462779 538463577 798 False 573.000000 573 80.275000 1 770 1 chr1B.!!$F1 769
17 TraesCS2B01G141000 chr1D 62439984 62440638 654 False 475.000000 475 80.488000 1 627 1 chr1D.!!$F1 626

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
475 478 0.101399 CTCGTCCCAAGACAGATCCG 59.899 60.0 0.0 0.0 43.73 4.18 F
579 582 0.102663 GCCTACTCTACCTTGTCGGC 59.897 60.0 0.0 0.0 37.75 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 6247 0.249911 AGGACAACCTGAAGCACGAC 60.250 55.0 0.0 0.0 45.92 4.34 R
1958 6977 1.881903 GAGCAAAGCAAAGGGGGAGC 61.882 60.0 0.0 0.0 0.00 4.70 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
35 36 1.380403 CGTCGACCCTGAGCTCATCT 61.380 60.000 18.63 1.90 0.00 2.90
103 105 2.765807 CAGGAGGAGGCCCGTCAT 60.766 66.667 0.00 0.00 37.58 3.06
215 218 1.303074 AGGTCGTGCGGTCTGTCTA 60.303 57.895 0.00 0.00 0.00 2.59
255 258 2.112297 GCACAACCCCTCCGTTGA 59.888 61.111 8.36 0.00 44.88 3.18
304 307 3.822192 CGTCCGACGAGGCCATGA 61.822 66.667 16.03 0.00 46.05 3.07
309 312 3.188786 GACGAGGCCATGACACGC 61.189 66.667 5.01 0.00 0.00 5.34
397 400 3.693245 CGGAGTCGCATTCTTCGG 58.307 61.111 0.00 0.00 31.12 4.30
423 426 3.469970 ATGGCGCATCAGTCCGGA 61.470 61.111 10.83 0.00 0.00 5.14
444 447 4.444024 CGCAACCGCATCGTGGTG 62.444 66.667 0.00 0.00 46.56 4.17
445 448 4.101790 GCAACCGCATCGTGGTGG 62.102 66.667 0.00 0.00 46.56 4.61
446 449 2.358125 CAACCGCATCGTGGTGGA 60.358 61.111 14.03 0.00 46.56 4.02
449 452 2.125147 CCGCATCGTGGTGGATGT 60.125 61.111 3.10 0.00 44.47 3.06
452 455 0.102300 CGCATCGTGGTGGATGTCTA 59.898 55.000 4.67 0.00 44.47 2.59
453 456 1.571919 GCATCGTGGTGGATGTCTAC 58.428 55.000 4.67 0.00 44.47 2.59
455 458 1.404035 CATCGTGGTGGATGTCTACGA 59.596 52.381 6.93 6.93 46.06 3.43
456 459 0.806868 TCGTGGTGGATGTCTACGAC 59.193 55.000 0.00 2.38 38.65 4.34
458 461 1.202154 CGTGGTGGATGTCTACGACTC 60.202 57.143 9.26 0.00 34.78 3.36
459 462 1.092348 TGGTGGATGTCTACGACTCG 58.908 55.000 0.00 0.00 33.15 4.18
460 463 1.093159 GGTGGATGTCTACGACTCGT 58.907 55.000 9.45 9.45 44.35 4.18
461 464 1.063764 GGTGGATGTCTACGACTCGTC 59.936 57.143 7.52 0.00 41.54 4.20
462 465 1.063764 GTGGATGTCTACGACTCGTCC 59.936 57.143 7.52 2.58 41.54 4.79
463 466 0.662085 GGATGTCTACGACTCGTCCC 59.338 60.000 7.52 0.00 41.54 4.46
464 467 1.376543 GATGTCTACGACTCGTCCCA 58.623 55.000 7.52 3.94 41.54 4.37
465 468 1.741706 GATGTCTACGACTCGTCCCAA 59.258 52.381 7.52 0.00 41.54 4.12
466 469 1.162698 TGTCTACGACTCGTCCCAAG 58.837 55.000 7.52 0.00 41.54 3.61
467 470 1.271001 TGTCTACGACTCGTCCCAAGA 60.271 52.381 7.52 2.45 41.54 3.02
468 471 1.130186 GTCTACGACTCGTCCCAAGAC 59.870 57.143 7.52 11.39 41.54 3.01
469 472 1.162698 CTACGACTCGTCCCAAGACA 58.837 55.000 7.52 0.00 43.73 3.41
470 473 1.130749 CTACGACTCGTCCCAAGACAG 59.869 57.143 7.52 0.00 43.73 3.51
471 474 0.536687 ACGACTCGTCCCAAGACAGA 60.537 55.000 0.00 0.00 43.73 3.41
473 476 1.202200 CGACTCGTCCCAAGACAGATC 60.202 57.143 0.00 0.00 43.73 2.75
474 477 1.135333 GACTCGTCCCAAGACAGATCC 59.865 57.143 0.00 0.00 43.73 3.36
475 478 0.101399 CTCGTCCCAAGACAGATCCG 59.899 60.000 0.00 0.00 43.73 4.18
476 479 0.611062 TCGTCCCAAGACAGATCCGT 60.611 55.000 0.00 0.00 43.73 4.69
477 480 0.246635 CGTCCCAAGACAGATCCGTT 59.753 55.000 0.00 0.00 43.73 4.44
478 481 1.736032 CGTCCCAAGACAGATCCGTTC 60.736 57.143 0.00 0.00 43.73 3.95
479 482 0.530744 TCCCAAGACAGATCCGTTCG 59.469 55.000 0.00 0.00 0.00 3.95
480 483 0.460284 CCCAAGACAGATCCGTTCGG 60.460 60.000 4.74 4.74 0.00 4.30
481 484 0.246635 CCAAGACAGATCCGTTCGGT 59.753 55.000 11.04 0.00 35.29 4.69
482 485 1.337823 CCAAGACAGATCCGTTCGGTT 60.338 52.381 11.04 2.76 32.52 4.44
483 486 2.413837 CAAGACAGATCCGTTCGGTTT 58.586 47.619 11.04 0.55 32.52 3.27
484 487 2.806244 CAAGACAGATCCGTTCGGTTTT 59.194 45.455 11.04 0.00 32.52 2.43
485 488 2.685100 AGACAGATCCGTTCGGTTTTC 58.315 47.619 11.04 7.18 32.52 2.29
486 489 1.389106 GACAGATCCGTTCGGTTTTCG 59.611 52.381 11.04 6.55 32.52 3.46
487 490 0.719465 CAGATCCGTTCGGTTTTCGG 59.281 55.000 11.04 0.00 44.76 4.30
488 491 0.390735 AGATCCGTTCGGTTTTCGGG 60.391 55.000 11.04 0.00 43.75 5.14
491 494 2.674084 CCGTTCGGTTTTCGGGCTC 61.674 63.158 2.82 0.00 40.49 4.70
492 495 2.674084 CGTTCGGTTTTCGGGCTCC 61.674 63.158 0.00 0.00 39.77 4.70
510 513 1.884235 CCGATGAGGAACAATAGGGC 58.116 55.000 0.00 0.00 45.00 5.19
511 514 1.140852 CCGATGAGGAACAATAGGGCA 59.859 52.381 0.00 0.00 45.00 5.36
512 515 2.224621 CCGATGAGGAACAATAGGGCAT 60.225 50.000 0.00 0.00 45.00 4.40
513 516 3.007940 CCGATGAGGAACAATAGGGCATA 59.992 47.826 0.00 0.00 45.00 3.14
515 518 4.583871 GATGAGGAACAATAGGGCATAGG 58.416 47.826 0.00 0.00 0.00 2.57
516 519 3.664320 TGAGGAACAATAGGGCATAGGA 58.336 45.455 0.00 0.00 0.00 2.94
517 520 3.648067 TGAGGAACAATAGGGCATAGGAG 59.352 47.826 0.00 0.00 0.00 3.69
520 523 3.496870 GGAACAATAGGGCATAGGAGGTG 60.497 52.174 0.00 0.00 0.00 4.00
521 524 2.057922 ACAATAGGGCATAGGAGGTGG 58.942 52.381 0.00 0.00 0.00 4.61
522 525 2.057922 CAATAGGGCATAGGAGGTGGT 58.942 52.381 0.00 0.00 0.00 4.16
523 526 1.734655 ATAGGGCATAGGAGGTGGTG 58.265 55.000 0.00 0.00 0.00 4.17
524 527 0.399949 TAGGGCATAGGAGGTGGTGG 60.400 60.000 0.00 0.00 0.00 4.61
525 528 2.001269 GGGCATAGGAGGTGGTGGT 61.001 63.158 0.00 0.00 0.00 4.16
526 529 1.224592 GGCATAGGAGGTGGTGGTG 59.775 63.158 0.00 0.00 0.00 4.17
528 531 1.224592 CATAGGAGGTGGTGGTGCC 59.775 63.158 0.00 0.00 37.90 5.01
529 532 1.082954 ATAGGAGGTGGTGGTGCCT 59.917 57.895 0.00 0.00 38.35 4.75
530 533 0.550147 ATAGGAGGTGGTGGTGCCTT 60.550 55.000 0.00 0.00 38.35 4.35
531 534 1.488705 TAGGAGGTGGTGGTGCCTTG 61.489 60.000 0.00 0.00 38.35 3.61
532 535 2.829384 GGAGGTGGTGGTGCCTTGA 61.829 63.158 0.00 0.00 38.35 3.02
533 536 1.302832 GAGGTGGTGGTGCCTTGAG 60.303 63.158 0.00 0.00 38.35 3.02
534 537 2.056906 GAGGTGGTGGTGCCTTGAGT 62.057 60.000 0.00 0.00 38.35 3.41
536 539 1.172812 GGTGGTGGTGCCTTGAGTTC 61.173 60.000 0.00 0.00 38.35 3.01
538 541 1.150536 GGTGGTGCCTTGAGTTCCA 59.849 57.895 0.00 0.00 0.00 3.53
539 542 0.251341 GGTGGTGCCTTGAGTTCCAT 60.251 55.000 0.00 0.00 0.00 3.41
540 543 0.883833 GTGGTGCCTTGAGTTCCATG 59.116 55.000 0.00 0.00 0.00 3.66
541 544 0.770499 TGGTGCCTTGAGTTCCATGA 59.230 50.000 0.00 0.00 0.00 3.07
542 545 1.144708 TGGTGCCTTGAGTTCCATGAA 59.855 47.619 0.00 0.00 0.00 2.57
543 546 1.541588 GGTGCCTTGAGTTCCATGAAC 59.458 52.381 0.00 0.00 42.25 3.18
545 548 2.227388 GTGCCTTGAGTTCCATGAACAG 59.773 50.000 9.42 0.00 44.11 3.16
546 549 1.815003 GCCTTGAGTTCCATGAACAGG 59.185 52.381 9.42 8.19 44.11 4.00
547 550 1.815003 CCTTGAGTTCCATGAACAGGC 59.185 52.381 9.42 0.05 44.11 4.85
548 551 2.553904 CCTTGAGTTCCATGAACAGGCT 60.554 50.000 9.42 0.00 44.11 4.58
551 554 2.158623 TGAGTTCCATGAACAGGCTTGT 60.159 45.455 9.42 0.00 44.11 3.16
552 555 2.227388 GAGTTCCATGAACAGGCTTGTG 59.773 50.000 0.65 0.00 44.11 3.33
553 556 1.956477 GTTCCATGAACAGGCTTGTGT 59.044 47.619 0.65 0.00 41.62 3.72
554 557 1.896220 TCCATGAACAGGCTTGTGTC 58.104 50.000 0.65 3.36 37.67 3.67
555 558 0.883833 CCATGAACAGGCTTGTGTCC 59.116 55.000 0.65 0.00 37.67 4.02
557 560 0.478072 ATGAACAGGCTTGTGTCCCA 59.522 50.000 0.65 0.00 37.67 4.37
559 562 0.883833 GAACAGGCTTGTGTCCCATG 59.116 55.000 0.65 0.00 37.67 3.66
560 563 0.540365 AACAGGCTTGTGTCCCATGG 60.540 55.000 4.14 4.14 37.67 3.66
561 564 2.036256 AGGCTTGTGTCCCATGGC 59.964 61.111 6.09 0.00 42.20 4.40
562 565 3.070576 GGCTTGTGTCCCATGGCC 61.071 66.667 6.09 0.00 37.69 5.36
563 566 2.036256 GCTTGTGTCCCATGGCCT 59.964 61.111 6.09 0.00 0.00 5.19
564 567 1.302949 GCTTGTGTCCCATGGCCTA 59.697 57.895 6.09 0.00 0.00 3.93
565 568 1.032114 GCTTGTGTCCCATGGCCTAC 61.032 60.000 6.09 4.66 0.00 3.18
566 569 0.620556 CTTGTGTCCCATGGCCTACT 59.379 55.000 6.09 0.00 0.00 2.57
568 571 0.252696 TGTGTCCCATGGCCTACTCT 60.253 55.000 6.09 0.00 0.00 3.24
569 572 1.007842 TGTGTCCCATGGCCTACTCTA 59.992 52.381 6.09 0.00 0.00 2.43
571 574 1.049402 GTCCCATGGCCTACTCTACC 58.951 60.000 6.09 0.00 0.00 3.18
573 576 1.294068 TCCCATGGCCTACTCTACCTT 59.706 52.381 6.09 0.00 0.00 3.50
574 577 1.417890 CCCATGGCCTACTCTACCTTG 59.582 57.143 6.09 0.00 0.00 3.61
575 578 2.119495 CCATGGCCTACTCTACCTTGT 58.881 52.381 3.32 0.00 0.00 3.16
576 579 2.103263 CCATGGCCTACTCTACCTTGTC 59.897 54.545 3.32 0.00 0.00 3.18
577 580 1.471119 TGGCCTACTCTACCTTGTCG 58.529 55.000 3.32 0.00 0.00 4.35
578 581 0.745468 GGCCTACTCTACCTTGTCGG 59.255 60.000 0.00 0.00 39.35 4.79
579 582 0.102663 GCCTACTCTACCTTGTCGGC 59.897 60.000 0.00 0.00 37.75 5.54
580 583 0.381089 CCTACTCTACCTTGTCGGCG 59.619 60.000 0.00 0.00 35.61 6.46
582 585 1.063764 CTACTCTACCTTGTCGGCGAC 59.936 57.143 31.68 31.68 35.61 5.19
583 586 1.139095 CTCTACCTTGTCGGCGACC 59.861 63.158 34.28 18.38 35.61 4.79
595 598 3.112709 GCGACCGGAGCAACACTC 61.113 66.667 9.46 0.00 45.45 3.51
596 599 2.651361 CGACCGGAGCAACACTCT 59.349 61.111 9.46 0.00 45.48 3.24
602 605 3.830679 GGAGCAACACTCTGAGGAG 57.169 57.895 9.85 3.81 45.48 3.69
603 606 0.390998 GGAGCAACACTCTGAGGAGC 60.391 60.000 9.85 7.14 45.48 4.70
604 607 0.735632 GAGCAACACTCTGAGGAGCG 60.736 60.000 9.85 0.00 42.98 5.03
605 608 1.005630 GCAACACTCTGAGGAGCGT 60.006 57.895 9.85 0.00 42.98 5.07
606 609 0.243907 GCAACACTCTGAGGAGCGTA 59.756 55.000 9.85 0.00 42.98 4.42
607 610 1.734047 GCAACACTCTGAGGAGCGTAG 60.734 57.143 9.85 0.00 42.98 3.51
629 632 3.770040 CCGCGGACATGACCAGGA 61.770 66.667 24.07 0.00 31.87 3.86
630 633 2.509336 CGCGGACATGACCAGGAC 60.509 66.667 14.61 0.00 0.00 3.85
631 634 2.509336 GCGGACATGACCAGGACG 60.509 66.667 14.61 1.10 0.00 4.79
632 635 2.184322 CGGACATGACCAGGACGG 59.816 66.667 14.61 0.00 42.50 4.79
633 636 2.348104 CGGACATGACCAGGACGGA 61.348 63.158 14.61 0.00 38.63 4.69
634 637 1.517832 GGACATGACCAGGACGGAG 59.482 63.158 9.48 0.00 38.63 4.63
635 638 1.153549 GACATGACCAGGACGGAGC 60.154 63.158 0.00 0.00 38.63 4.70
637 640 3.083997 ATGACCAGGACGGAGCCC 61.084 66.667 0.00 0.00 38.63 5.19
661 664 3.116531 CGGGAAGCGAAACCGGAC 61.117 66.667 9.46 0.00 43.69 4.79
664 667 1.167781 GGGAAGCGAAACCGGACAAA 61.168 55.000 9.46 0.00 0.00 2.83
665 668 0.237498 GGAAGCGAAACCGGACAAAG 59.763 55.000 9.46 0.00 0.00 2.77
666 669 0.385598 GAAGCGAAACCGGACAAAGC 60.386 55.000 9.46 7.04 0.00 3.51
667 670 0.818040 AAGCGAAACCGGACAAAGCT 60.818 50.000 9.46 9.53 34.70 3.74
668 671 0.818040 AGCGAAACCGGACAAAGCTT 60.818 50.000 9.46 0.00 0.00 3.74
670 673 0.110823 CGAAACCGGACAAAGCTTCG 60.111 55.000 9.46 6.89 0.00 3.79
671 674 0.385598 GAAACCGGACAAAGCTTCGC 60.386 55.000 9.46 0.00 0.00 4.70
673 676 1.228657 AACCGGACAAAGCTTCGCTC 61.229 55.000 9.46 0.00 38.25 5.03
675 678 1.227999 CCGGACAAAGCTTCGCTCAA 61.228 55.000 0.00 0.00 38.25 3.02
677 680 1.398960 CGGACAAAGCTTCGCTCAAAG 60.399 52.381 0.00 0.00 38.25 2.77
678 681 1.873591 GGACAAAGCTTCGCTCAAAGA 59.126 47.619 0.00 0.00 38.25 2.52
679 682 2.485814 GGACAAAGCTTCGCTCAAAGAT 59.514 45.455 0.00 0.00 38.25 2.40
680 683 3.425492 GGACAAAGCTTCGCTCAAAGATC 60.425 47.826 0.00 0.00 38.25 2.75
681 684 3.406764 ACAAAGCTTCGCTCAAAGATCT 58.593 40.909 0.00 0.00 38.25 2.75
682 685 3.434984 ACAAAGCTTCGCTCAAAGATCTC 59.565 43.478 0.00 0.00 38.25 2.75
684 687 2.891112 AGCTTCGCTCAAAGATCTCTG 58.109 47.619 0.00 0.00 30.62 3.35
685 688 1.327156 GCTTCGCTCAAAGATCTCTGC 59.673 52.381 0.00 0.00 0.00 4.26
686 689 1.587490 CTTCGCTCAAAGATCTCTGCG 59.413 52.381 18.81 18.81 43.95 5.18
687 690 0.528017 TCGCTCAAAGATCTCTGCGT 59.472 50.000 21.78 0.00 43.23 5.24
689 692 1.060266 CGCTCAAAGATCTCTGCGTTG 59.940 52.381 17.48 9.61 38.81 4.10
693 696 2.417586 TCAAAGATCTCTGCGTTGCATG 59.582 45.455 0.00 0.00 38.13 4.06
694 697 2.105006 AAGATCTCTGCGTTGCATGT 57.895 45.000 0.00 0.00 38.13 3.21
695 698 2.967599 AGATCTCTGCGTTGCATGTA 57.032 45.000 0.00 0.00 38.13 2.29
696 699 3.251479 AGATCTCTGCGTTGCATGTAA 57.749 42.857 0.00 0.00 38.13 2.41
700 703 5.994054 AGATCTCTGCGTTGCATGTAATAAT 59.006 36.000 0.00 0.00 38.13 1.28
703 706 7.120789 TCTCTGCGTTGCATGTAATAATATG 57.879 36.000 0.00 0.00 38.13 1.78
704 707 6.928492 TCTCTGCGTTGCATGTAATAATATGA 59.072 34.615 0.00 0.00 38.13 2.15
705 708 7.440856 TCTCTGCGTTGCATGTAATAATATGAA 59.559 33.333 0.00 0.00 38.13 2.57
706 709 8.098220 TCTGCGTTGCATGTAATAATATGAAT 57.902 30.769 0.00 0.00 38.13 2.57
707 710 8.567104 TCTGCGTTGCATGTAATAATATGAATT 58.433 29.630 0.00 0.00 38.13 2.17
708 711 8.726650 TGCGTTGCATGTAATAATATGAATTC 57.273 30.769 0.00 0.00 31.71 2.17
709 712 8.348507 TGCGTTGCATGTAATAATATGAATTCA 58.651 29.630 11.26 11.26 31.71 2.57
746 749 6.990798 TGAAGTATCCAAAATGTGAAATGCA 58.009 32.000 0.00 0.00 0.00 3.96
747 750 7.613585 TGAAGTATCCAAAATGTGAAATGCAT 58.386 30.769 0.00 0.00 0.00 3.96
748 751 7.546316 TGAAGTATCCAAAATGTGAAATGCATG 59.454 33.333 0.00 0.00 0.00 4.06
749 752 6.938507 AGTATCCAAAATGTGAAATGCATGT 58.061 32.000 0.00 0.00 0.00 3.21
750 753 7.388437 AGTATCCAAAATGTGAAATGCATGTT 58.612 30.769 0.00 0.00 0.00 2.71
751 754 7.879160 AGTATCCAAAATGTGAAATGCATGTTT 59.121 29.630 0.00 0.00 0.00 2.83
752 755 6.939132 TCCAAAATGTGAAATGCATGTTTT 57.061 29.167 0.00 0.00 0.00 2.43
753 756 6.726230 TCCAAAATGTGAAATGCATGTTTTG 58.274 32.000 0.00 10.79 40.06 2.44
755 758 6.853872 CCAAAATGTGAAATGCATGTTTTGAG 59.146 34.615 20.24 12.70 41.32 3.02
756 759 7.254829 CCAAAATGTGAAATGCATGTTTTGAGA 60.255 33.333 20.24 2.59 41.32 3.27
757 760 6.774354 AATGTGAAATGCATGTTTTGAGAC 57.226 33.333 0.00 0.00 0.00 3.36
758 761 4.289342 TGTGAAATGCATGTTTTGAGACG 58.711 39.130 0.00 0.00 0.00 4.18
760 763 4.146961 GTGAAATGCATGTTTTGAGACGTG 59.853 41.667 0.00 0.00 39.10 4.49
763 766 1.260297 TGCATGTTTTGAGACGTGACG 59.740 47.619 2.24 2.24 38.53 4.35
764 767 1.398451 GCATGTTTTGAGACGTGACGG 60.398 52.381 10.66 0.00 38.53 4.79
765 768 1.194547 CATGTTTTGAGACGTGACGGG 59.805 52.381 10.66 0.00 38.53 5.28
766 769 0.176219 TGTTTTGAGACGTGACGGGT 59.824 50.000 10.66 0.00 0.00 5.28
768 771 0.460722 TTTTGAGACGTGACGGGTCA 59.539 50.000 10.66 8.74 36.87 4.02
784 787 3.036084 CACCGTCAGTGGACACGC 61.036 66.667 0.00 0.00 44.54 5.34
785 788 3.533105 ACCGTCAGTGGACACGCA 61.533 61.111 0.00 0.00 44.54 5.24
786 789 2.734723 CCGTCAGTGGACACGCAG 60.735 66.667 0.00 0.00 44.54 5.18
788 791 2.016704 CGTCAGTGGACACGCAGAC 61.017 63.158 12.44 12.44 44.54 3.51
789 792 2.016704 GTCAGTGGACACGCAGACG 61.017 63.158 8.93 0.00 43.73 4.18
801 804 2.256158 CAGACGTGTCCGCGGTTA 59.744 61.111 27.15 12.81 37.70 2.85
802 805 1.800315 CAGACGTGTCCGCGGTTAG 60.800 63.158 27.15 17.10 37.70 2.34
804 807 1.138247 GACGTGTCCGCGGTTAGAT 59.862 57.895 27.15 9.51 37.70 1.98
805 808 1.138047 GACGTGTCCGCGGTTAGATG 61.138 60.000 27.15 13.37 37.70 2.90
806 809 2.514013 CGTGTCCGCGGTTAGATGC 61.514 63.158 27.15 8.61 0.00 3.91
815 818 0.597637 CGGTTAGATGCCGGCTGTAG 60.598 60.000 29.70 6.95 44.98 2.74
816 819 0.750850 GGTTAGATGCCGGCTGTAGA 59.249 55.000 29.70 7.00 0.00 2.59
817 820 1.344763 GGTTAGATGCCGGCTGTAGAT 59.655 52.381 29.70 12.62 0.00 1.98
818 821 2.408050 GTTAGATGCCGGCTGTAGATG 58.592 52.381 29.70 0.00 0.00 2.90
819 822 0.318441 TAGATGCCGGCTGTAGATGC 59.682 55.000 29.70 7.59 0.00 3.91
820 823 1.070445 GATGCCGGCTGTAGATGCT 59.930 57.895 29.70 0.26 0.00 3.79
821 824 0.948141 GATGCCGGCTGTAGATGCTC 60.948 60.000 29.70 6.41 0.00 4.26
822 825 1.406065 ATGCCGGCTGTAGATGCTCT 61.406 55.000 29.70 0.00 0.00 4.09
823 826 1.144936 GCCGGCTGTAGATGCTCTT 59.855 57.895 22.15 0.00 0.00 2.85
825 828 1.604185 GCCGGCTGTAGATGCTCTTAG 60.604 57.143 22.15 0.00 0.00 2.18
826 829 1.957177 CCGGCTGTAGATGCTCTTAGA 59.043 52.381 0.00 0.00 0.00 2.10
830 833 3.493524 GGCTGTAGATGCTCTTAGAACCC 60.494 52.174 0.00 0.00 0.00 4.11
832 835 2.693591 TGTAGATGCTCTTAGAACCCCG 59.306 50.000 0.00 0.00 0.00 5.73
1159 5747 4.337060 CGGTCGCGTGTGTCTCCA 62.337 66.667 5.77 0.00 0.00 3.86
1260 5849 2.204029 TACGGGGGCCTCAAGGTT 60.204 61.111 4.16 0.00 37.57 3.50
1427 6149 2.180017 CGGTCCAATTGCAGCAGC 59.820 61.111 0.00 0.00 42.57 5.25
1691 6660 1.476488 AGCCGCTTTCACACTTGTTTT 59.524 42.857 0.00 0.00 0.00 2.43
1782 6751 0.458543 CTGGTAGCAACGATGTCGCT 60.459 55.000 1.77 0.00 44.43 4.93
1958 6977 5.516696 CGATCACAGTGTTGTTGAGGTATAG 59.483 44.000 0.00 0.00 34.62 1.31
2067 7340 1.967319 TGAAAACAGTCCTCCAGTGC 58.033 50.000 0.00 0.00 0.00 4.40
2185 7505 3.317711 TGCATACTAAATTGGGATTGGCG 59.682 43.478 0.00 0.00 0.00 5.69
2226 7555 0.877071 AGCCAACGAATGCAGTTCTG 59.123 50.000 0.00 0.00 34.56 3.02
2250 7591 4.734854 CCATATGCGTTTGTTATGAAGTGC 59.265 41.667 0.00 0.00 0.00 4.40
2334 7687 6.701400 CCATCGTTCACTGTGATCATTGTATA 59.299 38.462 11.86 0.00 0.00 1.47
2478 7841 4.094294 TGAAGTTTTGGCTATGCATACGAC 59.906 41.667 1.16 2.26 0.00 4.34
2479 7842 3.873910 AGTTTTGGCTATGCATACGACT 58.126 40.909 1.16 0.00 0.00 4.18
2480 7843 4.261801 AGTTTTGGCTATGCATACGACTT 58.738 39.130 1.16 0.00 0.00 3.01
2481 7844 5.424757 AGTTTTGGCTATGCATACGACTTA 58.575 37.500 1.16 0.00 0.00 2.24
2482 7845 5.293569 AGTTTTGGCTATGCATACGACTTAC 59.706 40.000 1.16 0.00 0.00 2.34
2484 7847 2.619646 TGGCTATGCATACGACTTACGA 59.380 45.455 1.16 0.00 45.77 3.43
2587 7954 2.177394 TCAGGAGTACGCAAATTGCA 57.823 45.000 18.65 0.00 45.36 4.08
2596 7963 5.123227 AGTACGCAAATTGCATACCATAGT 58.877 37.500 18.76 8.09 42.36 2.12
2680 8819 5.180367 GCAAGAGCAAAGAGAAAACTCTT 57.820 39.130 6.66 6.66 45.98 2.85
2724 8863 5.440610 ACTCCTCACAGAAATGTTGAACTT 58.559 37.500 0.00 0.00 0.00 2.66
2809 9736 1.687123 GGATACCGTGTCATGCCTACT 59.313 52.381 0.00 0.00 0.00 2.57
2886 9818 4.041198 TCGAATCAAACCCTTTCCTGTACT 59.959 41.667 0.00 0.00 0.00 2.73
2932 10010 2.373169 AGCTCCACCAAGATTCAAGACA 59.627 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 2.765807 CATGACGGGCCTCCTCCT 60.766 66.667 0.84 0.00 0.00 3.69
103 105 1.806461 AAGAAGTCCGAGCGCAGTCA 61.806 55.000 11.47 0.00 0.00 3.41
215 218 3.812019 CCACTACGCTCGGACGCT 61.812 66.667 0.00 0.00 36.19 5.07
339 342 3.471244 GAGGGATGTCGTCGCCTCG 62.471 68.421 11.57 0.00 40.47 4.63
365 368 4.147449 CCGCCTCGCTGATGTCCA 62.147 66.667 0.00 0.00 0.00 4.02
405 408 3.274586 CCGGACTGATGCGCCATG 61.275 66.667 4.18 0.00 38.54 3.66
445 448 6.487354 GTCTTGGGACGAGTCGTAGACATC 62.487 54.167 28.73 14.11 45.91 3.06
446 449 4.727556 GTCTTGGGACGAGTCGTAGACAT 61.728 52.174 28.73 6.17 45.91 3.06
449 452 1.271001 TGTCTTGGGACGAGTCGTAGA 60.271 52.381 19.93 14.78 44.83 2.59
452 455 0.536687 TCTGTCTTGGGACGAGTCGT 60.537 55.000 20.02 20.02 44.83 4.34
453 456 0.811915 ATCTGTCTTGGGACGAGTCG 59.188 55.000 11.85 11.85 44.83 4.18
455 458 1.187087 GGATCTGTCTTGGGACGAGT 58.813 55.000 0.00 0.00 44.83 4.18
456 459 0.101399 CGGATCTGTCTTGGGACGAG 59.899 60.000 0.00 0.00 44.83 4.18
458 461 0.246635 AACGGATCTGTCTTGGGACG 59.753 55.000 7.86 0.00 44.83 4.79
459 462 1.736032 CGAACGGATCTGTCTTGGGAC 60.736 57.143 7.86 0.00 42.42 4.46
460 463 0.530744 CGAACGGATCTGTCTTGGGA 59.469 55.000 7.86 0.00 0.00 4.37
461 464 0.460284 CCGAACGGATCTGTCTTGGG 60.460 60.000 7.86 0.02 37.50 4.12
462 465 0.246635 ACCGAACGGATCTGTCTTGG 59.753 55.000 20.14 12.28 38.96 3.61
463 466 2.080286 AACCGAACGGATCTGTCTTG 57.920 50.000 20.14 1.83 38.96 3.02
464 467 2.833631 AAACCGAACGGATCTGTCTT 57.166 45.000 20.14 0.00 38.96 3.01
465 468 2.685100 GAAAACCGAACGGATCTGTCT 58.315 47.619 20.14 0.00 38.96 3.41
466 469 1.389106 CGAAAACCGAACGGATCTGTC 59.611 52.381 20.14 7.38 41.76 3.51
467 470 1.425412 CGAAAACCGAACGGATCTGT 58.575 50.000 20.14 0.00 41.76 3.41
473 476 2.667199 AGCCCGAAAACCGAACGG 60.667 61.111 11.83 11.83 45.24 4.44
474 477 2.674084 GGAGCCCGAAAACCGAACG 61.674 63.158 0.00 0.00 41.76 3.95
475 478 3.260931 GGAGCCCGAAAACCGAAC 58.739 61.111 0.00 0.00 41.76 3.95
486 489 0.181350 ATTGTTCCTCATCGGAGCCC 59.819 55.000 0.00 0.00 44.28 5.19
487 490 2.548920 CCTATTGTTCCTCATCGGAGCC 60.549 54.545 0.00 0.00 44.28 4.70
488 491 2.548920 CCCTATTGTTCCTCATCGGAGC 60.549 54.545 0.00 0.00 44.28 4.70
491 494 1.140852 TGCCCTATTGTTCCTCATCGG 59.859 52.381 0.00 0.00 0.00 4.18
492 495 2.620251 TGCCCTATTGTTCCTCATCG 57.380 50.000 0.00 0.00 0.00 3.84
493 496 4.287067 TCCTATGCCCTATTGTTCCTCATC 59.713 45.833 0.00 0.00 0.00 2.92
494 497 4.242811 TCCTATGCCCTATTGTTCCTCAT 58.757 43.478 0.00 0.00 0.00 2.90
495 498 3.648067 CTCCTATGCCCTATTGTTCCTCA 59.352 47.826 0.00 0.00 0.00 3.86
496 499 3.008485 CCTCCTATGCCCTATTGTTCCTC 59.992 52.174 0.00 0.00 0.00 3.71
497 500 2.982488 CCTCCTATGCCCTATTGTTCCT 59.018 50.000 0.00 0.00 0.00 3.36
498 501 2.711547 ACCTCCTATGCCCTATTGTTCC 59.288 50.000 0.00 0.00 0.00 3.62
499 502 3.496870 CCACCTCCTATGCCCTATTGTTC 60.497 52.174 0.00 0.00 0.00 3.18
500 503 2.443255 CCACCTCCTATGCCCTATTGTT 59.557 50.000 0.00 0.00 0.00 2.83
502 505 2.057922 ACCACCTCCTATGCCCTATTG 58.942 52.381 0.00 0.00 0.00 1.90
503 506 2.057922 CACCACCTCCTATGCCCTATT 58.942 52.381 0.00 0.00 0.00 1.73
504 507 1.734655 CACCACCTCCTATGCCCTAT 58.265 55.000 0.00 0.00 0.00 2.57
505 508 0.399949 CCACCACCTCCTATGCCCTA 60.400 60.000 0.00 0.00 0.00 3.53
507 510 2.001269 ACCACCACCTCCTATGCCC 61.001 63.158 0.00 0.00 0.00 5.36
508 511 1.224592 CACCACCACCTCCTATGCC 59.775 63.158 0.00 0.00 0.00 4.40
509 512 1.452108 GCACCACCACCTCCTATGC 60.452 63.158 0.00 0.00 0.00 3.14
510 513 1.224592 GGCACCACCACCTCCTATG 59.775 63.158 0.00 0.00 38.86 2.23
511 514 0.550147 AAGGCACCACCACCTCCTAT 60.550 55.000 0.00 0.00 43.14 2.57
512 515 1.151899 AAGGCACCACCACCTCCTA 60.152 57.895 0.00 0.00 43.14 2.94
513 516 2.450502 AAGGCACCACCACCTCCT 60.451 61.111 0.00 0.00 43.14 3.69
515 518 1.302832 CTCAAGGCACCACCACCTC 60.303 63.158 0.00 0.00 43.14 3.85
516 519 1.645402 AACTCAAGGCACCACCACCT 61.645 55.000 0.00 0.00 43.14 4.00
517 520 1.152756 AACTCAAGGCACCACCACC 60.153 57.895 0.00 0.00 43.14 4.61
520 523 0.251341 ATGGAACTCAAGGCACCACC 60.251 55.000 0.00 0.00 39.61 4.61
521 524 0.883833 CATGGAACTCAAGGCACCAC 59.116 55.000 0.00 0.00 33.38 4.16
522 525 0.770499 TCATGGAACTCAAGGCACCA 59.230 50.000 0.00 0.00 35.09 4.17
523 526 1.541588 GTTCATGGAACTCAAGGCACC 59.458 52.381 2.00 0.00 39.23 5.01
524 527 2.227388 CTGTTCATGGAACTCAAGGCAC 59.773 50.000 10.14 0.00 42.39 5.01
525 528 2.507484 CTGTTCATGGAACTCAAGGCA 58.493 47.619 10.14 0.00 42.39 4.75
526 529 1.815003 CCTGTTCATGGAACTCAAGGC 59.185 52.381 10.14 0.00 42.39 4.35
528 531 2.787994 AGCCTGTTCATGGAACTCAAG 58.212 47.619 10.14 0.46 42.39 3.02
529 532 2.886523 CAAGCCTGTTCATGGAACTCAA 59.113 45.455 10.14 0.00 42.39 3.02
530 533 2.158623 ACAAGCCTGTTCATGGAACTCA 60.159 45.455 10.14 0.00 42.39 3.41
531 534 2.227388 CACAAGCCTGTTCATGGAACTC 59.773 50.000 10.14 1.01 42.39 3.01
532 535 2.233271 CACAAGCCTGTTCATGGAACT 58.767 47.619 10.14 0.00 42.39 3.01
533 536 1.956477 ACACAAGCCTGTTCATGGAAC 59.044 47.619 2.25 2.25 42.26 3.62
534 537 2.229792 GACACAAGCCTGTTCATGGAA 58.770 47.619 0.00 0.00 31.64 3.53
536 539 0.883833 GGACACAAGCCTGTTCATGG 59.116 55.000 0.00 0.00 31.64 3.66
538 541 0.478072 TGGGACACAAGCCTGTTCAT 59.522 50.000 0.00 0.00 31.64 2.57
539 542 1.919012 TGGGACACAAGCCTGTTCA 59.081 52.632 0.00 0.00 31.64 3.18
540 543 4.898607 TGGGACACAAGCCTGTTC 57.101 55.556 0.00 0.00 31.64 3.18
552 555 1.049402 GGTAGAGTAGGCCATGGGAC 58.951 60.000 15.13 0.00 0.00 4.46
553 556 0.941963 AGGTAGAGTAGGCCATGGGA 59.058 55.000 15.13 0.00 0.00 4.37
554 557 1.417890 CAAGGTAGAGTAGGCCATGGG 59.582 57.143 15.13 0.00 0.00 4.00
555 558 2.103263 GACAAGGTAGAGTAGGCCATGG 59.897 54.545 7.63 7.63 0.00 3.66
557 560 2.032620 CGACAAGGTAGAGTAGGCCAT 58.967 52.381 5.01 0.00 0.00 4.40
559 562 0.745468 CCGACAAGGTAGAGTAGGCC 59.255 60.000 0.00 0.00 34.51 5.19
560 563 0.102663 GCCGACAAGGTAGAGTAGGC 59.897 60.000 0.00 0.00 46.45 3.93
561 564 0.381089 CGCCGACAAGGTAGAGTAGG 59.619 60.000 0.00 0.00 43.70 3.18
562 565 1.063764 GTCGCCGACAAGGTAGAGTAG 59.936 57.143 13.23 0.00 43.70 2.57
563 566 1.089920 GTCGCCGACAAGGTAGAGTA 58.910 55.000 13.23 0.00 43.70 2.59
564 567 1.593296 GGTCGCCGACAAGGTAGAGT 61.593 60.000 20.08 0.00 43.70 3.24
565 568 1.139095 GGTCGCCGACAAGGTAGAG 59.861 63.158 20.08 0.00 43.70 2.43
566 569 3.281240 GGTCGCCGACAAGGTAGA 58.719 61.111 20.08 0.00 43.70 2.59
577 580 4.681978 AGTGTTGCTCCGGTCGCC 62.682 66.667 14.26 2.84 0.00 5.54
578 581 3.112709 GAGTGTTGCTCCGGTCGC 61.113 66.667 0.00 6.43 38.27 5.19
579 582 1.734477 CAGAGTGTTGCTCCGGTCG 60.734 63.158 0.00 0.00 45.21 4.79
580 583 0.389166 CTCAGAGTGTTGCTCCGGTC 60.389 60.000 0.00 0.00 45.21 4.79
582 585 1.079543 CCTCAGAGTGTTGCTCCGG 60.080 63.158 0.00 0.00 45.21 5.14
583 586 0.108898 CTCCTCAGAGTGTTGCTCCG 60.109 60.000 0.00 0.00 45.21 4.63
584 587 0.390998 GCTCCTCAGAGTGTTGCTCC 60.391 60.000 0.00 0.00 45.21 4.70
585 588 0.735632 CGCTCCTCAGAGTGTTGCTC 60.736 60.000 0.00 0.00 44.19 4.26
586 589 1.291588 CGCTCCTCAGAGTGTTGCT 59.708 57.895 0.00 0.00 44.19 3.91
593 596 2.718731 CGGCTACGCTCCTCAGAG 59.281 66.667 0.00 0.00 43.57 3.35
595 598 4.577246 GCCGGCTACGCTCCTCAG 62.577 72.222 22.15 0.00 39.22 3.35
614 617 2.509336 CGTCCTGGTCATGTCCGC 60.509 66.667 4.48 0.00 0.00 5.54
615 618 2.184322 CCGTCCTGGTCATGTCCG 59.816 66.667 4.48 0.00 0.00 4.79
616 619 1.517832 CTCCGTCCTGGTCATGTCC 59.482 63.158 1.55 1.55 39.52 4.02
617 620 1.153549 GCTCCGTCCTGGTCATGTC 60.154 63.158 0.00 0.00 39.52 3.06
618 621 2.660064 GGCTCCGTCCTGGTCATGT 61.660 63.158 0.00 0.00 39.52 3.21
619 622 2.187946 GGCTCCGTCCTGGTCATG 59.812 66.667 0.00 0.00 39.52 3.07
620 623 3.083997 GGGCTCCGTCCTGGTCAT 61.084 66.667 0.00 0.00 39.52 3.06
641 644 3.488090 CGGTTTCGCTTCCCGCTC 61.488 66.667 0.00 0.00 34.62 5.03
644 647 3.116531 GTCCGGTTTCGCTTCCCG 61.117 66.667 0.00 0.00 41.37 5.14
645 648 1.167781 TTTGTCCGGTTTCGCTTCCC 61.168 55.000 0.00 0.00 34.56 3.97
646 649 0.237498 CTTTGTCCGGTTTCGCTTCC 59.763 55.000 0.00 0.00 34.56 3.46
648 651 0.818040 AGCTTTGTCCGGTTTCGCTT 60.818 50.000 0.00 0.00 34.56 4.68
649 652 0.818040 AAGCTTTGTCCGGTTTCGCT 60.818 50.000 0.00 1.51 34.56 4.93
650 653 0.385598 GAAGCTTTGTCCGGTTTCGC 60.386 55.000 0.00 0.00 34.56 4.70
651 654 0.110823 CGAAGCTTTGTCCGGTTTCG 60.111 55.000 0.00 3.84 39.04 3.46
652 655 3.748021 CGAAGCTTTGTCCGGTTTC 57.252 52.632 0.00 0.00 0.00 2.78
670 673 1.202009 GCAACGCAGAGATCTTTGAGC 60.202 52.381 17.06 10.22 0.00 4.26
671 674 2.071540 TGCAACGCAGAGATCTTTGAG 58.928 47.619 17.06 15.58 33.32 3.02
673 676 2.161012 ACATGCAACGCAGAGATCTTTG 59.839 45.455 8.88 8.88 43.65 2.77
675 678 2.105006 ACATGCAACGCAGAGATCTT 57.895 45.000 0.00 0.00 43.65 2.40
677 680 5.657470 TTATTACATGCAACGCAGAGATC 57.343 39.130 0.00 0.00 43.65 2.75
678 681 7.603784 TCATATTATTACATGCAACGCAGAGAT 59.396 33.333 0.00 0.00 43.65 2.75
679 682 6.928492 TCATATTATTACATGCAACGCAGAGA 59.072 34.615 0.00 0.00 43.65 3.10
680 683 7.120789 TCATATTATTACATGCAACGCAGAG 57.879 36.000 0.00 0.00 43.65 3.35
681 684 7.489574 TTCATATTATTACATGCAACGCAGA 57.510 32.000 0.00 0.00 43.65 4.26
682 685 8.732413 AATTCATATTATTACATGCAACGCAG 57.268 30.769 0.00 0.00 43.65 5.18
684 687 8.726650 TGAATTCATATTATTACATGCAACGC 57.273 30.769 3.38 0.00 0.00 4.84
719 722 8.938906 GCATTTCACATTTTGGATACTTCAAAT 58.061 29.630 0.00 0.00 34.58 2.32
720 723 7.930325 TGCATTTCACATTTTGGATACTTCAAA 59.070 29.630 0.00 0.00 37.61 2.69
721 724 7.440198 TGCATTTCACATTTTGGATACTTCAA 58.560 30.769 0.00 0.00 37.61 2.69
722 725 6.990798 TGCATTTCACATTTTGGATACTTCA 58.009 32.000 0.00 0.00 37.61 3.02
724 727 7.388437 ACATGCATTTCACATTTTGGATACTT 58.612 30.769 0.00 0.00 37.61 2.24
727 730 8.504815 CAAAACATGCATTTCACATTTTGGATA 58.495 29.630 0.00 0.00 38.22 2.59
728 731 7.228906 TCAAAACATGCATTTCACATTTTGGAT 59.771 29.630 17.25 0.00 40.15 3.41
729 732 6.541278 TCAAAACATGCATTTCACATTTTGGA 59.459 30.769 17.25 4.36 40.15 3.53
730 733 6.726230 TCAAAACATGCATTTCACATTTTGG 58.274 32.000 17.25 0.60 40.15 3.28
731 734 7.584847 GTCTCAAAACATGCATTTCACATTTTG 59.415 33.333 0.00 7.86 40.59 2.44
732 735 7.517101 CGTCTCAAAACATGCATTTCACATTTT 60.517 33.333 0.00 0.00 0.00 1.82
737 740 4.146961 CACGTCTCAAAACATGCATTTCAC 59.853 41.667 0.00 0.00 0.00 3.18
738 741 4.036144 TCACGTCTCAAAACATGCATTTCA 59.964 37.500 0.00 0.00 0.00 2.69
739 742 4.379793 GTCACGTCTCAAAACATGCATTTC 59.620 41.667 0.00 0.00 0.00 2.17
740 743 4.290155 GTCACGTCTCAAAACATGCATTT 58.710 39.130 0.00 0.00 0.00 2.32
741 744 3.606846 CGTCACGTCTCAAAACATGCATT 60.607 43.478 0.00 0.00 0.00 3.56
742 745 2.096268 CGTCACGTCTCAAAACATGCAT 60.096 45.455 0.00 0.00 0.00 3.96
743 746 1.260297 CGTCACGTCTCAAAACATGCA 59.740 47.619 0.00 0.00 0.00 3.96
744 747 1.398451 CCGTCACGTCTCAAAACATGC 60.398 52.381 0.00 0.00 0.00 4.06
746 749 1.202604 ACCCGTCACGTCTCAAAACAT 60.203 47.619 0.00 0.00 0.00 2.71
747 750 0.176219 ACCCGTCACGTCTCAAAACA 59.824 50.000 0.00 0.00 0.00 2.83
748 751 0.857287 GACCCGTCACGTCTCAAAAC 59.143 55.000 0.00 0.00 0.00 2.43
749 752 0.460722 TGACCCGTCACGTCTCAAAA 59.539 50.000 0.00 0.00 34.14 2.44
750 753 2.117257 TGACCCGTCACGTCTCAAA 58.883 52.632 0.00 0.00 34.14 2.69
751 754 3.844741 TGACCCGTCACGTCTCAA 58.155 55.556 0.00 0.00 34.14 3.02
768 771 3.499929 CTGCGTGTCCACTGACGGT 62.500 63.158 0.00 0.00 44.86 4.83
770 773 2.016704 GTCTGCGTGTCCACTGACG 61.017 63.158 0.00 0.00 44.86 4.35
771 774 2.016704 CGTCTGCGTGTCCACTGAC 61.017 63.158 0.00 1.57 42.12 3.51
784 787 1.800315 CTAACCGCGGACACGTCTG 60.800 63.158 35.90 8.61 43.45 3.51
785 788 1.310933 ATCTAACCGCGGACACGTCT 61.311 55.000 35.90 3.57 43.45 4.18
786 789 1.138047 CATCTAACCGCGGACACGTC 61.138 60.000 35.90 0.00 43.45 4.34
788 791 2.514013 GCATCTAACCGCGGACACG 61.514 63.158 35.90 16.75 44.63 4.49
789 792 2.171725 GGCATCTAACCGCGGACAC 61.172 63.158 35.90 13.07 0.00 3.67
790 793 2.185867 GGCATCTAACCGCGGACA 59.814 61.111 35.90 17.92 0.00 4.02
791 794 2.960129 CGGCATCTAACCGCGGAC 60.960 66.667 35.90 11.20 44.90 4.79
798 801 2.408050 CATCTACAGCCGGCATCTAAC 58.592 52.381 31.54 0.00 0.00 2.34
799 802 1.270305 GCATCTACAGCCGGCATCTAA 60.270 52.381 31.54 11.54 0.00 2.10
800 803 0.318441 GCATCTACAGCCGGCATCTA 59.682 55.000 31.54 13.24 0.00 1.98
801 804 1.070445 GCATCTACAGCCGGCATCT 59.930 57.895 31.54 12.74 0.00 2.90
802 805 0.948141 GAGCATCTACAGCCGGCATC 60.948 60.000 31.54 7.96 0.00 3.91
804 807 2.501128 GAGCATCTACAGCCGGCA 59.499 61.111 31.54 7.75 0.00 5.69
815 818 1.757699 ACTCGGGGTTCTAAGAGCATC 59.242 52.381 0.00 0.00 34.31 3.91
816 819 1.867363 ACTCGGGGTTCTAAGAGCAT 58.133 50.000 0.00 0.00 34.31 3.79
817 820 2.025605 TCTACTCGGGGTTCTAAGAGCA 60.026 50.000 0.00 0.00 34.31 4.26
818 821 2.652590 TCTACTCGGGGTTCTAAGAGC 58.347 52.381 0.00 0.00 34.31 4.09
819 822 4.705991 AGTTTCTACTCGGGGTTCTAAGAG 59.294 45.833 0.00 0.00 36.83 2.85
820 823 4.461781 CAGTTTCTACTCGGGGTTCTAAGA 59.538 45.833 0.00 0.00 30.26 2.10
821 824 4.461781 TCAGTTTCTACTCGGGGTTCTAAG 59.538 45.833 0.00 0.00 30.26 2.18
822 825 4.410099 TCAGTTTCTACTCGGGGTTCTAA 58.590 43.478 0.00 0.00 30.26 2.10
823 826 4.038271 TCAGTTTCTACTCGGGGTTCTA 57.962 45.455 0.00 0.00 30.26 2.10
825 828 3.324117 GTTCAGTTTCTACTCGGGGTTC 58.676 50.000 0.00 0.00 30.26 3.62
826 829 2.038164 GGTTCAGTTTCTACTCGGGGTT 59.962 50.000 0.00 0.00 30.26 4.11
830 833 1.992170 CGGGTTCAGTTTCTACTCGG 58.008 55.000 0.00 0.00 32.35 4.63
832 835 3.586892 CTTCCGGGTTCAGTTTCTACTC 58.413 50.000 0.00 0.00 30.26 2.59
941 3736 3.839432 CTCGAAGGGGGCGGAGTC 61.839 72.222 0.00 0.00 0.00 3.36
1260 5849 2.867855 AAGGACGCTGAGGACGCAA 61.868 57.895 0.00 0.00 0.00 4.85
1355 6076 6.201425 GCACGATACCTTATTGTATTCCGAAA 59.799 38.462 0.00 0.00 31.67 3.46
1427 6149 8.382030 TCATAATCATAACACTTGCCTATGTG 57.618 34.615 0.00 0.00 37.81 3.21
1502 6247 0.249911 AGGACAACCTGAAGCACGAC 60.250 55.000 0.00 0.00 45.92 4.34
1782 6751 2.313051 TTTCGAACCCTCCACGTGCA 62.313 55.000 10.91 0.00 0.00 4.57
1958 6977 1.881903 GAGCAAAGCAAAGGGGGAGC 61.882 60.000 0.00 0.00 0.00 4.70
2067 7340 7.174253 TCAACACCAGTAGGCAGTAATTAAAAG 59.826 37.037 0.00 0.00 39.06 2.27
2185 7505 5.960105 GCTACTTGCACAATTTAAGATCGAC 59.040 40.000 0.00 0.00 42.31 4.20
2226 7555 4.734854 CACTTCATAACAAACGCATATGGC 59.265 41.667 4.56 0.00 39.90 4.40
2250 7591 8.950961 CGTGCAACTGATCATTTTTATTATCAG 58.049 33.333 9.10 9.10 46.94 2.90
2334 7687 5.359756 TGTTATATCTCACTCGCTGCAAAT 58.640 37.500 0.00 0.00 0.00 2.32
2443 7805 4.457603 GCCAAAACTTCAAAACTTTGGGTT 59.542 37.500 12.88 5.75 45.24 4.11
2478 7841 6.252281 CAGCTAAGAAGTGTAGACTCGTAAG 58.748 44.000 0.00 0.00 0.00 2.34
2479 7842 5.391736 GCAGCTAAGAAGTGTAGACTCGTAA 60.392 44.000 0.00 0.00 0.00 3.18
2480 7843 4.094590 GCAGCTAAGAAGTGTAGACTCGTA 59.905 45.833 0.00 0.00 0.00 3.43
2481 7844 3.119779 GCAGCTAAGAAGTGTAGACTCGT 60.120 47.826 0.00 0.00 0.00 4.18
2482 7845 3.119814 TGCAGCTAAGAAGTGTAGACTCG 60.120 47.826 0.00 0.00 0.00 4.18
2483 7846 4.442375 TGCAGCTAAGAAGTGTAGACTC 57.558 45.455 0.00 0.00 0.00 3.36
2484 7847 5.413309 AATGCAGCTAAGAAGTGTAGACT 57.587 39.130 0.00 0.00 0.00 3.24
2587 7954 8.598041 CCTCTGCCTTCTATAAAACTATGGTAT 58.402 37.037 0.00 0.00 0.00 2.73
2596 7963 9.832445 CTACATTTACCTCTGCCTTCTATAAAA 57.168 33.333 0.00 0.00 0.00 1.52
2680 8819 7.897565 AGGAGTAGTGTATGGTTTTAGGAGTTA 59.102 37.037 0.00 0.00 0.00 2.24
2772 8920 4.263156 GGTATCCAAATGGGTATCGGCTTA 60.263 45.833 0.00 0.00 38.11 3.09
2778 8926 4.062991 GACACGGTATCCAAATGGGTATC 58.937 47.826 0.00 0.00 38.11 2.24
2788 8936 1.411246 GTAGGCATGACACGGTATCCA 59.589 52.381 0.00 0.00 0.00 3.41
2809 9736 3.438781 GCAATGGAATGGACGAGTGTTTA 59.561 43.478 0.00 0.00 0.00 2.01
2886 9818 7.877003 TCTAATCGCAAACACATTCCTAAAAA 58.123 30.769 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.