Multiple sequence alignment - TraesCS5D01G240400

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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 TraesCS5D01G240400 chr5D 100.000 5802 0 0 1 5802 348740802 348746603 0.000000e+00 10715.0
1 TraesCS5D01G240400 chr5D 87.209 86 10 1 482 566 40725691 40725606 4.790000e-16 97.1
2 TraesCS5D01G240400 chr5D 92.683 41 3 0 895 935 6979783 6979743 6.280000e-05 60.2
3 TraesCS5D01G240400 chr5B 95.595 4064 125 21 1771 5802 409056158 409060199 0.000000e+00 6464.0
4 TraesCS5D01G240400 chr5B 93.569 793 33 9 986 1771 409055330 409056111 0.000000e+00 1166.0
5 TraesCS5D01G240400 chr5B 90.509 432 30 6 56 485 409054293 409054715 1.410000e-155 560.0
6 TraesCS5D01G240400 chr5B 82.569 327 25 14 575 886 409054714 409055023 5.770000e-65 259.0
7 TraesCS5D01G240400 chr5B 94.595 37 0 2 602 637 188019571 188019606 8.120000e-04 56.5
8 TraesCS5D01G240400 chr5B 100.000 30 0 0 908 937 687331188 687331217 8.120000e-04 56.5
9 TraesCS5D01G240400 chr5A 93.929 3179 129 23 1771 4918 448831798 448834943 0.000000e+00 4743.0
10 TraesCS5D01G240400 chr5A 95.169 890 19 7 4923 5802 448834996 448835871 0.000000e+00 1384.0
11 TraesCS5D01G240400 chr5A 93.020 831 36 6 963 1774 448830942 448831769 0.000000e+00 1194.0
12 TraesCS5D01G240400 chr5A 87.056 479 57 2 1 479 448830125 448830598 2.380000e-148 536.0
13 TraesCS5D01G240400 chr5A 88.095 84 9 1 483 565 466949471 466949388 1.330000e-16 99.0
14 TraesCS5D01G240400 chr4A 86.022 93 10 3 475 565 89431050 89430959 4.790000e-16 97.1
15 TraesCS5D01G240400 chr7B 86.905 84 10 1 483 566 104044732 104044650 6.190000e-15 93.5
16 TraesCS5D01G240400 chr2D 86.905 84 10 1 483 565 71386572 71386489 6.190000e-15 93.5
17 TraesCS5D01G240400 chr2D 87.097 62 7 1 895 955 201435669 201435730 1.040000e-07 69.4
18 TraesCS5D01G240400 chr2D 91.304 46 3 1 891 935 638858024 638857979 1.750000e-05 62.1
19 TraesCS5D01G240400 chr1B 86.905 84 10 1 484 566 33097793 33097710 6.190000e-15 93.5
20 TraesCS5D01G240400 chr1B 97.368 38 0 1 602 638 282135775 282135812 4.850000e-06 63.9
21 TraesCS5D01G240400 chr1B 94.595 37 2 0 899 935 68725409 68725445 2.260000e-04 58.4
22 TraesCS5D01G240400 chr1B 83.077 65 7 2 609 671 48971158 48971096 8.120000e-04 56.5
23 TraesCS5D01G240400 chr1A 86.905 84 10 1 483 565 559234357 559234274 6.190000e-15 93.5
24 TraesCS5D01G240400 chr6D 86.747 83 10 1 484 565 418956987 418957069 2.230000e-14 91.6
25 TraesCS5D01G240400 chr6D 100.000 30 0 0 609 638 413078324 413078295 8.120000e-04 56.5
26 TraesCS5D01G240400 chr2A 83.871 93 14 1 483 574 306150569 306150477 2.880000e-13 87.9
27 TraesCS5D01G240400 chr7D 93.023 43 3 0 895 937 536309779 536309821 4.850000e-06 63.9
28 TraesCS5D01G240400 chr7D 92.308 39 2 1 600 638 265692658 265692621 3.000000e-03 54.7
29 TraesCS5D01G240400 chr7A 94.737 38 1 1 602 638 60731065 60731102 2.260000e-04 58.4
30 TraesCS5D01G240400 chr3D 94.595 37 1 1 603 639 406158323 406158358 8.120000e-04 56.5
31 TraesCS5D01G240400 chr1D 96.970 33 1 0 604 636 47710697 47710729 8.120000e-04 56.5
32 TraesCS5D01G240400 chr6A 96.970 33 0 1 603 634 499792864 499792896 3.000000e-03 54.7


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 TraesCS5D01G240400 chr5D 348740802 348746603 5801 False 10715.00 10715 100.0000 1 5802 1 chr5D.!!$F1 5801
1 TraesCS5D01G240400 chr5B 409054293 409060199 5906 False 2112.25 6464 90.5605 56 5802 4 chr5B.!!$F3 5746
2 TraesCS5D01G240400 chr5A 448830125 448835871 5746 False 1964.25 4743 92.2935 1 5802 4 chr5A.!!$F1 5801

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
518 519 0.655208 CAATGTAATGTGCCGCGCTA 59.345 50.000 5.56 0.0 0.00 4.26 F
530 531 0.803117 CCGCGCTATCCGAGATCTAA 59.197 55.000 5.56 0.0 39.21 2.10 F
769 785 0.947960 CGTGTGGGCATGTTGTTACA 59.052 50.000 0.00 0.0 38.95 2.41 F
930 986 1.065418 GGGATGGTTAGGTGGACAGTG 60.065 57.143 0.00 0.0 0.00 3.66 F
1194 1423 1.275291 CCACTTTCCAGTCCTCGCTTA 59.725 52.381 0.00 0.0 0.00 3.09 F
3001 3307 0.465097 CGCTGCTTGGAGGATTGGAT 60.465 55.000 0.00 0.0 0.00 3.41 F
4153 4468 0.681733 TGCTCAGGTGAGGTTCACTC 59.318 55.000 9.03 0.0 46.19 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1738 1.675801 CAGTTCCAGCAGCTCCTCA 59.324 57.895 0.00 0.0 0.00 3.86 R
2476 2771 1.846439 CCTCCAGCCCCTATGAAGAAA 59.154 52.381 0.00 0.0 0.00 2.52 R
2748 3054 8.556194 CGCCAATTACTAGTTAATAGATTGCAA 58.444 33.333 0.00 0.0 35.30 4.08 R
2770 3076 1.462616 ATGAAACTGCAATAGCGCCA 58.537 45.000 2.29 0.0 46.23 5.69 R
3094 3400 4.023291 GCCACCCTTCCATATCAAAGAAA 58.977 43.478 0.00 0.0 0.00 2.52 R
4447 4763 0.242017 AAGCGGTGAAAATGCTGCTC 59.758 50.000 0.00 0.0 45.55 4.26 R
5628 6023 0.167908 CGTGCGTGCAATGGTTATGT 59.832 50.000 0.00 0.0 0.00 2.29 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
30 31 2.046314 AACGTCGCATCCCCAAGG 60.046 61.111 0.00 0.00 0.00 3.61
50 51 0.763652 CCTGGCTGAGGAGTATGCAT 59.236 55.000 3.79 3.79 46.33 3.96
69 70 1.008538 GCAACCAAGCACGTCCTTG 60.009 57.895 12.46 12.46 41.40 3.61
112 113 5.346181 TCGTTCACCACCATACATATCAA 57.654 39.130 0.00 0.00 0.00 2.57
242 243 9.915629 TTGTTTTACAAGAGTACACAAATTTGT 57.084 25.926 18.13 18.13 35.96 2.83
267 268 9.713740 GTCATTAAATGTCAAATTTTTGCAACA 57.286 25.926 0.00 0.00 38.05 3.33
370 371 4.406326 TGGCCTTAGGAAACGATATACACA 59.594 41.667 3.32 0.00 0.00 3.72
372 373 6.268158 TGGCCTTAGGAAACGATATACACATA 59.732 38.462 3.32 0.00 0.00 2.29
394 395 7.554118 ACATAACCTATCATGTAGCAATATGCC 59.446 37.037 0.00 0.00 46.52 4.40
415 416 1.620819 AGTGATCACAACTCGAAGGCT 59.379 47.619 27.02 0.00 0.00 4.58
433 434 1.000270 TGTGTTGCCTGTTGGGTGT 60.000 52.632 0.00 0.00 37.43 4.16
446 447 2.936498 GTTGGGTGTAAGATCGGTCATG 59.064 50.000 0.00 0.00 0.00 3.07
447 448 1.134521 TGGGTGTAAGATCGGTCATGC 60.135 52.381 0.00 0.00 0.00 4.06
448 449 1.583054 GGTGTAAGATCGGTCATGCC 58.417 55.000 0.00 0.00 0.00 4.40
485 486 7.991084 ACCCTAGGAACAAACTAAAACATAC 57.009 36.000 11.48 0.00 0.00 2.39
486 487 7.752638 ACCCTAGGAACAAACTAAAACATACT 58.247 34.615 11.48 0.00 0.00 2.12
487 488 7.881751 ACCCTAGGAACAAACTAAAACATACTC 59.118 37.037 11.48 0.00 0.00 2.59
488 489 7.336176 CCCTAGGAACAAACTAAAACATACTCC 59.664 40.741 11.48 0.00 0.00 3.85
489 490 7.336176 CCTAGGAACAAACTAAAACATACTCCC 59.664 40.741 1.05 0.00 0.00 4.30
494 495 6.838382 ACAAACTAAAACATACTCCCTCTGT 58.162 36.000 0.00 0.00 0.00 3.41
495 496 7.287810 ACAAACTAAAACATACTCCCTCTGTT 58.712 34.615 0.00 0.00 34.71 3.16
496 497 7.778382 ACAAACTAAAACATACTCCCTCTGTTT 59.222 33.333 0.00 0.00 43.06 2.83
497 498 7.981102 AACTAAAACATACTCCCTCTGTTTC 57.019 36.000 0.89 0.00 41.03 2.78
498 499 7.074653 ACTAAAACATACTCCCTCTGTTTCA 57.925 36.000 0.89 0.00 41.03 2.69
499 500 6.935208 ACTAAAACATACTCCCTCTGTTTCAC 59.065 38.462 0.89 0.00 41.03 3.18
500 501 4.974645 AACATACTCCCTCTGTTTCACA 57.025 40.909 0.00 0.00 29.06 3.58
501 502 4.974645 ACATACTCCCTCTGTTTCACAA 57.025 40.909 0.00 0.00 0.00 3.33
502 503 5.505181 ACATACTCCCTCTGTTTCACAAT 57.495 39.130 0.00 0.00 0.00 2.71
503 504 5.248640 ACATACTCCCTCTGTTTCACAATG 58.751 41.667 0.00 0.00 0.00 2.82
504 505 3.864789 ACTCCCTCTGTTTCACAATGT 57.135 42.857 0.00 0.00 0.00 2.71
505 506 4.974645 ACTCCCTCTGTTTCACAATGTA 57.025 40.909 0.00 0.00 0.00 2.29
506 507 5.304686 ACTCCCTCTGTTTCACAATGTAA 57.695 39.130 0.00 0.00 0.00 2.41
507 508 5.880901 ACTCCCTCTGTTTCACAATGTAAT 58.119 37.500 0.00 0.00 0.00 1.89
508 509 5.707298 ACTCCCTCTGTTTCACAATGTAATG 59.293 40.000 0.00 0.00 0.00 1.90
509 510 5.630121 TCCCTCTGTTTCACAATGTAATGT 58.370 37.500 0.00 0.00 0.00 2.71
515 516 2.928801 CACAATGTAATGTGCCGCG 58.071 52.632 0.00 0.00 43.67 6.46
516 517 1.133363 CACAATGTAATGTGCCGCGC 61.133 55.000 0.00 0.00 43.67 6.86
517 518 1.305219 ACAATGTAATGTGCCGCGCT 61.305 50.000 5.56 0.00 30.82 5.92
518 519 0.655208 CAATGTAATGTGCCGCGCTA 59.345 50.000 5.56 0.00 0.00 4.26
519 520 1.264020 CAATGTAATGTGCCGCGCTAT 59.736 47.619 5.56 0.00 0.00 2.97
520 521 1.148310 ATGTAATGTGCCGCGCTATC 58.852 50.000 5.56 0.00 0.00 2.08
521 522 0.878523 TGTAATGTGCCGCGCTATCC 60.879 55.000 5.56 0.00 0.00 2.59
522 523 1.663388 TAATGTGCCGCGCTATCCG 60.663 57.895 5.56 0.00 40.75 4.18
523 524 2.077821 TAATGTGCCGCGCTATCCGA 62.078 55.000 5.56 0.00 40.02 4.55
524 525 3.848347 ATGTGCCGCGCTATCCGAG 62.848 63.158 5.56 0.00 40.02 4.63
525 526 4.266070 GTGCCGCGCTATCCGAGA 62.266 66.667 5.56 0.00 39.21 4.04
526 527 3.295273 TGCCGCGCTATCCGAGAT 61.295 61.111 5.56 0.00 39.21 2.75
527 528 2.505118 GCCGCGCTATCCGAGATC 60.505 66.667 5.56 0.00 39.21 2.75
528 529 2.983930 GCCGCGCTATCCGAGATCT 61.984 63.158 5.56 0.00 39.21 2.75
529 530 1.645704 GCCGCGCTATCCGAGATCTA 61.646 60.000 5.56 0.00 39.21 1.98
530 531 0.803117 CCGCGCTATCCGAGATCTAA 59.197 55.000 5.56 0.00 39.21 2.10
531 532 1.202087 CCGCGCTATCCGAGATCTAAG 60.202 57.143 5.56 0.00 39.21 2.18
532 533 1.465387 CGCGCTATCCGAGATCTAAGT 59.535 52.381 5.56 0.00 39.21 2.24
533 534 2.095668 CGCGCTATCCGAGATCTAAGTT 60.096 50.000 5.56 0.00 39.21 2.66
534 535 3.609644 CGCGCTATCCGAGATCTAAGTTT 60.610 47.826 5.56 0.00 39.21 2.66
535 536 3.670991 GCGCTATCCGAGATCTAAGTTTG 59.329 47.826 0.00 0.00 40.02 2.93
536 537 4.556898 GCGCTATCCGAGATCTAAGTTTGA 60.557 45.833 0.00 0.00 40.02 2.69
537 538 4.912766 CGCTATCCGAGATCTAAGTTTGAC 59.087 45.833 0.00 0.00 40.02 3.18
538 539 5.224135 GCTATCCGAGATCTAAGTTTGACC 58.776 45.833 0.00 0.00 0.00 4.02
539 540 5.221263 GCTATCCGAGATCTAAGTTTGACCA 60.221 44.000 0.00 0.00 0.00 4.02
540 541 5.878406 ATCCGAGATCTAAGTTTGACCAT 57.122 39.130 0.00 0.00 0.00 3.55
541 542 6.978674 ATCCGAGATCTAAGTTTGACCATA 57.021 37.500 0.00 0.00 0.00 2.74
542 543 6.785337 TCCGAGATCTAAGTTTGACCATAA 57.215 37.500 0.00 0.00 0.00 1.90
543 544 7.177832 TCCGAGATCTAAGTTTGACCATAAA 57.822 36.000 0.00 0.00 0.00 1.40
544 545 7.792032 TCCGAGATCTAAGTTTGACCATAAAT 58.208 34.615 0.00 0.00 0.00 1.40
545 546 8.265055 TCCGAGATCTAAGTTTGACCATAAATT 58.735 33.333 0.00 0.00 0.00 1.82
546 547 8.893727 CCGAGATCTAAGTTTGACCATAAATTT 58.106 33.333 0.00 0.00 0.00 1.82
556 557 9.965824 AGTTTGACCATAAATTTAGTCAACAAG 57.034 29.630 22.77 3.60 45.98 3.16
557 558 9.959749 GTTTGACCATAAATTTAGTCAACAAGA 57.040 29.630 22.77 12.18 45.98 3.02
558 559 9.959749 TTTGACCATAAATTTAGTCAACAAGAC 57.040 29.630 22.77 0.00 45.98 3.01
570 571 5.306532 GTCAACAAGACCGACTGTATAGA 57.693 43.478 0.00 0.00 41.56 1.98
571 572 5.333513 GTCAACAAGACCGACTGTATAGAG 58.666 45.833 0.00 0.00 41.56 2.43
572 573 5.123502 GTCAACAAGACCGACTGTATAGAGA 59.876 44.000 3.49 0.00 41.56 3.10
573 574 5.354513 TCAACAAGACCGACTGTATAGAGAG 59.645 44.000 3.49 0.00 0.00 3.20
574 575 4.846040 ACAAGACCGACTGTATAGAGAGT 58.154 43.478 3.49 0.00 0.00 3.24
575 576 5.987098 ACAAGACCGACTGTATAGAGAGTA 58.013 41.667 3.49 0.00 0.00 2.59
576 577 6.593807 ACAAGACCGACTGTATAGAGAGTAT 58.406 40.000 3.49 0.00 0.00 2.12
577 578 7.733969 ACAAGACCGACTGTATAGAGAGTATA 58.266 38.462 3.49 0.00 0.00 1.47
578 579 8.377034 ACAAGACCGACTGTATAGAGAGTATAT 58.623 37.037 3.49 0.00 0.00 0.86
579 580 9.872721 CAAGACCGACTGTATAGAGAGTATATA 57.127 37.037 3.49 0.00 0.00 0.86
625 626 4.676799 ATAGATACTCCCTCCGATCCAA 57.323 45.455 0.00 0.00 0.00 3.53
649 650 2.933495 ATTGTCGCTCGTGCTAAGTA 57.067 45.000 7.97 0.00 36.97 2.24
741 752 7.497925 AAGTTTATTCAGACTTGGAGTTGTC 57.502 36.000 0.00 0.00 34.96 3.18
746 757 3.206150 TCAGACTTGGAGTTGTCTTTGC 58.794 45.455 0.00 0.00 41.06 3.68
769 785 0.947960 CGTGTGGGCATGTTGTTACA 59.052 50.000 0.00 0.00 38.95 2.41
783 799 7.254286 GCATGTTGTTACAATTTTCGTCCTTTT 60.254 33.333 0.00 0.00 37.91 2.27
908 964 9.574516 AAAACTAATCTGGAATCAACTTGTAGT 57.425 29.630 0.00 0.00 0.00 2.73
909 965 9.574516 AAACTAATCTGGAATCAACTTGTAGTT 57.425 29.630 0.00 0.00 39.39 2.24
921 977 4.569719 ACTTGTAGTTGGGATGGTTAGG 57.430 45.455 0.00 0.00 0.00 2.69
923 979 3.992943 TGTAGTTGGGATGGTTAGGTG 57.007 47.619 0.00 0.00 0.00 4.00
924 980 2.574369 TGTAGTTGGGATGGTTAGGTGG 59.426 50.000 0.00 0.00 0.00 4.61
925 981 2.053747 AGTTGGGATGGTTAGGTGGA 57.946 50.000 0.00 0.00 0.00 4.02
926 982 1.633945 AGTTGGGATGGTTAGGTGGAC 59.366 52.381 0.00 0.00 0.00 4.02
927 983 1.353022 GTTGGGATGGTTAGGTGGACA 59.647 52.381 0.00 0.00 0.00 4.02
928 984 1.285280 TGGGATGGTTAGGTGGACAG 58.715 55.000 0.00 0.00 0.00 3.51
929 985 1.286248 GGGATGGTTAGGTGGACAGT 58.714 55.000 0.00 0.00 0.00 3.55
930 986 1.065418 GGGATGGTTAGGTGGACAGTG 60.065 57.143 0.00 0.00 0.00 3.66
932 988 2.505819 GGATGGTTAGGTGGACAGTGAT 59.494 50.000 0.00 0.00 0.00 3.06
933 989 3.709653 GGATGGTTAGGTGGACAGTGATA 59.290 47.826 0.00 0.00 0.00 2.15
936 992 5.353394 TGGTTAGGTGGACAGTGATATTC 57.647 43.478 0.00 0.00 0.00 1.75
937 993 4.142026 TGGTTAGGTGGACAGTGATATTCG 60.142 45.833 0.00 0.00 0.00 3.34
938 994 4.369182 GTTAGGTGGACAGTGATATTCGG 58.631 47.826 0.00 0.00 0.00 4.30
939 995 1.762957 AGGTGGACAGTGATATTCGGG 59.237 52.381 0.00 0.00 0.00 5.14
941 997 2.483188 GGTGGACAGTGATATTCGGGTC 60.483 54.545 0.00 0.00 0.00 4.46
942 998 1.760613 TGGACAGTGATATTCGGGTCC 59.239 52.381 0.00 0.00 43.88 4.46
943 999 1.760613 GGACAGTGATATTCGGGTCCA 59.239 52.381 0.00 0.00 43.27 4.02
947 1003 5.215252 ACAGTGATATTCGGGTCCATTAG 57.785 43.478 0.00 0.00 0.00 1.73
948 1004 4.040461 ACAGTGATATTCGGGTCCATTAGG 59.960 45.833 0.00 0.00 0.00 2.69
949 1005 3.583086 AGTGATATTCGGGTCCATTAGGG 59.417 47.826 0.00 0.00 34.83 3.53
952 1008 4.041198 TGATATTCGGGTCCATTAGGGTTC 59.959 45.833 0.00 0.00 38.11 3.62
953 1009 1.659022 TTCGGGTCCATTAGGGTTCA 58.341 50.000 0.00 0.00 38.11 3.18
954 1010 1.659022 TCGGGTCCATTAGGGTTCAA 58.341 50.000 0.00 0.00 38.11 2.69
955 1011 1.986631 TCGGGTCCATTAGGGTTCAAA 59.013 47.619 0.00 0.00 38.11 2.69
956 1012 2.375845 TCGGGTCCATTAGGGTTCAAAA 59.624 45.455 0.00 0.00 38.11 2.44
958 1014 3.767131 CGGGTCCATTAGGGTTCAAAAAT 59.233 43.478 0.00 0.00 38.11 1.82
959 1015 4.221924 CGGGTCCATTAGGGTTCAAAAATT 59.778 41.667 0.00 0.00 38.11 1.82
960 1016 5.623596 CGGGTCCATTAGGGTTCAAAAATTC 60.624 44.000 0.00 0.00 38.11 2.17
1170 1399 1.562672 AACCCTCCCATTCCTCACCG 61.563 60.000 0.00 0.00 0.00 4.94
1194 1423 1.275291 CCACTTTCCAGTCCTCGCTTA 59.725 52.381 0.00 0.00 0.00 3.09
1243 1472 4.554363 CTCGCTGACCTACGCCGG 62.554 72.222 0.00 0.00 0.00 6.13
1309 1538 4.463879 CAGGACTCAGGCTGCCCG 62.464 72.222 16.57 5.01 35.76 6.13
1326 1555 4.097361 GGTCCGTTCTCCCTGCCC 62.097 72.222 0.00 0.00 0.00 5.36
1373 1602 1.805945 CGCGGCAGAAGGTACTGTC 60.806 63.158 0.00 0.00 40.86 3.51
1380 1609 3.369157 GGCAGAAGGTACTGTCCGTAATT 60.369 47.826 0.00 0.00 40.86 1.40
1397 1631 4.336993 CGTAATTAAATTGGGGCTGTGCTA 59.663 41.667 0.00 0.00 0.00 3.49
1417 1654 4.201861 GCTATTGGCTTGAGCTCTTGTAAC 60.202 45.833 16.19 1.23 41.70 2.50
1497 1738 2.270205 CTGGAGCTTGCCACCGAT 59.730 61.111 0.00 0.00 33.52 4.18
1556 1797 2.125350 GTCTGGGGCTCGAGCTTG 60.125 66.667 34.46 21.38 41.70 4.01
1606 1854 8.783093 CACTGAGATAACTGATTGTTTGGTTTA 58.217 33.333 0.00 0.00 39.89 2.01
1623 1871 7.684317 TTGGTTTAGATCATAGTGATGGGTA 57.316 36.000 0.00 0.00 37.20 3.69
1640 1888 2.159226 GGGTATCACGAGACAGAGTTGG 60.159 54.545 0.00 0.00 0.00 3.77
1646 1894 1.887198 ACGAGACAGAGTTGGATTCGT 59.113 47.619 0.00 0.00 35.45 3.85
1648 1896 3.243771 ACGAGACAGAGTTGGATTCGTTT 60.244 43.478 0.00 0.00 36.22 3.60
1653 1901 5.007724 AGACAGAGTTGGATTCGTTTGTTTC 59.992 40.000 0.00 0.00 0.00 2.78
1728 1976 2.288457 GGAGTTTTTGGCTGCCTCTTTC 60.288 50.000 21.03 9.63 0.00 2.62
1823 2118 8.733092 ATTATGGACAAAGAGGATCAGATCTA 57.267 34.615 10.36 0.00 37.82 1.98
2133 2428 2.620251 AGCTGTGGCGCAATATCTAA 57.380 45.000 10.83 0.00 44.37 2.10
2158 2453 8.352137 ACTGTCATCATATTCCAATGTTTCAA 57.648 30.769 0.00 0.00 0.00 2.69
2261 2556 2.159626 CGAACACCGTTTCTGTTGTTGT 60.160 45.455 0.00 0.00 31.83 3.32
2384 2679 8.375506 CAAGTAGGCTTTTATCCCTGTATCATA 58.624 37.037 0.00 0.00 31.49 2.15
2476 2771 7.542534 TGAACGTTTTGTACTTGTACAATCT 57.457 32.000 21.99 9.09 39.39 2.40
2626 2921 9.709387 TCCTGGATGAATATTCGAGGTATATAA 57.291 33.333 10.80 0.00 39.40 0.98
2722 3018 3.819564 AACCAGATACGCTGCAATCTA 57.180 42.857 12.53 0.00 43.50 1.98
2723 3019 4.342862 AACCAGATACGCTGCAATCTAT 57.657 40.909 12.53 4.03 43.50 1.98
2848 3154 4.353777 ACCTATACTCTCTCTTTGCCACA 58.646 43.478 0.00 0.00 0.00 4.17
3001 3307 0.465097 CGCTGCTTGGAGGATTGGAT 60.465 55.000 0.00 0.00 0.00 3.41
3009 3315 2.287584 TGGAGGATTGGATCAAAGGGT 58.712 47.619 0.00 0.00 0.00 4.34
3012 3318 3.549794 GAGGATTGGATCAAAGGGTCTG 58.450 50.000 0.00 0.00 0.00 3.51
3045 3351 9.088987 ACATTCTTGAAGGTTATTTGTGGTTAT 57.911 29.630 0.00 0.00 0.00 1.89
3094 3400 9.612066 TTTCACTTCTTTGGCTAATTTCATTTT 57.388 25.926 0.00 0.00 0.00 1.82
3199 3506 8.200792 GGAAGATCAAATTCTGCTACTTCTAGA 58.799 37.037 0.00 0.00 33.22 2.43
3215 3525 4.652421 TCTAGACACAACACCGTTGTTA 57.348 40.909 9.69 0.66 44.57 2.41
3324 3634 5.742063 AGAACTTGTTAAGCAGGTATACCC 58.258 41.667 18.65 4.13 36.31 3.69
3349 3659 9.396938 CCATTTTAATTGATTCTTTTGGTTTGC 57.603 29.630 0.00 0.00 0.00 3.68
3366 3676 7.214467 TGGTTTGCTACTCCTGAATTTTTAG 57.786 36.000 0.00 0.00 0.00 1.85
3440 3750 6.546428 TGCCTAGTATAAGCTCTTGTTCTT 57.454 37.500 0.00 0.00 0.00 2.52
3490 3800 6.350110 GCAAAGCTTGATATTTAGACCAACCA 60.350 38.462 0.00 0.00 0.00 3.67
3872 4183 9.521841 TTACTTGGACCAATGTATGTTTATTCA 57.478 29.630 7.54 0.00 0.00 2.57
4153 4468 0.681733 TGCTCAGGTGAGGTTCACTC 59.318 55.000 9.03 0.00 46.19 3.51
4218 4534 3.010420 GCCTTTCTTACAGATTCGGCTT 58.990 45.455 0.00 0.00 32.17 4.35
4375 4691 1.068333 GTCGCAGTACTCCACGGTAAA 60.068 52.381 9.00 0.00 0.00 2.01
4447 4763 5.606348 AGGTAGCAAGGACAGATAAGAAG 57.394 43.478 0.00 0.00 0.00 2.85
4898 5230 0.320073 TTTCCCTCGCGACGTTCATT 60.320 50.000 3.71 0.00 0.00 2.57
5035 5415 3.964909 AGATGGTCGTGCAAAGTTTTTC 58.035 40.909 0.00 0.00 0.00 2.29
5091 5472 4.213270 TGTGCAAAGTTTCAATAGGAGACG 59.787 41.667 0.00 0.00 35.83 4.18
5101 5482 2.625314 CAATAGGAGACGAGAGCCATGA 59.375 50.000 0.00 0.00 0.00 3.07
5301 5686 2.506065 CCCGTCTTCTCTAGGGGTG 58.494 63.158 0.00 0.00 40.18 4.61
5303 5688 0.324460 CCGTCTTCTCTAGGGGTGGT 60.324 60.000 0.00 0.00 0.00 4.16
5628 6023 6.569035 CGTGTCATCGGTACATATAGGCTTTA 60.569 42.308 0.00 0.00 0.00 1.85
5709 6104 0.249531 TATGTGTGTCGTGCCGTGTT 60.250 50.000 0.00 0.00 0.00 3.32
5790 6185 2.681591 TCCTCCGTGGAGACCGAT 59.318 61.111 17.52 0.00 44.53 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.046314 CCTTGGGGATGCGACGTT 60.046 61.111 0.00 0.00 33.58 3.99
17 18 4.113815 CAGGCCTTGGGGATGCGA 62.114 66.667 0.00 0.00 33.58 5.10
30 31 1.227793 GCATACTCCTCAGCCAGGC 60.228 63.158 1.84 1.84 43.08 4.85
36 37 1.945394 GGTTGCATGCATACTCCTCAG 59.055 52.381 23.37 0.00 0.00 3.35
50 51 1.453015 AAGGACGTGCTTGGTTGCA 60.453 52.632 22.32 0.00 41.05 4.08
69 70 0.731855 GAGGTGGTGTTAGCGTCGTC 60.732 60.000 0.00 0.00 0.00 4.20
79 80 0.034896 GGTGAACGATGAGGTGGTGT 59.965 55.000 0.00 0.00 0.00 4.16
112 113 5.533154 CAGAGGTAGGAGTAGATCAATTCGT 59.467 44.000 0.00 0.00 0.00 3.85
218 219 9.562583 TGACAAATTTGTGTACTCTTGTAAAAC 57.437 29.630 27.85 8.32 42.43 2.43
307 308 8.957028 CACACTATGTTTTATGTGTTGTTCTTG 58.043 33.333 0.00 0.00 41.04 3.02
370 371 7.632861 TGGCATATTGCTACATGATAGGTTAT 58.367 34.615 0.00 0.00 44.28 1.89
372 373 5.879763 TGGCATATTGCTACATGATAGGTT 58.120 37.500 0.00 0.00 44.28 3.50
383 384 4.420522 TGTGATCACTGGCATATTGCTA 57.579 40.909 25.55 0.00 44.28 3.49
394 395 1.728971 GCCTTCGAGTTGTGATCACTG 59.271 52.381 25.55 10.93 0.00 3.66
415 416 0.256177 TACACCCAACAGGCAACACA 59.744 50.000 0.00 0.00 40.58 3.72
446 447 3.219198 GGTTGGCATCCATCCGGC 61.219 66.667 9.74 0.00 34.24 6.13
447 448 1.705002 TAGGGTTGGCATCCATCCGG 61.705 60.000 16.10 0.00 42.61 5.14
448 449 0.250467 CTAGGGTTGGCATCCATCCG 60.250 60.000 16.10 1.13 42.61 4.18
449 450 0.111253 CCTAGGGTTGGCATCCATCC 59.889 60.000 16.10 0.00 41.37 3.51
450 451 1.140312 TCCTAGGGTTGGCATCCATC 58.860 55.000 16.10 0.19 31.53 3.51
451 452 1.215423 GTTCCTAGGGTTGGCATCCAT 59.785 52.381 16.10 11.71 31.53 3.41
452 453 0.623723 GTTCCTAGGGTTGGCATCCA 59.376 55.000 16.10 0.00 0.00 3.41
498 499 1.136565 GCGCGGCACATTACATTGT 59.863 52.632 8.83 0.00 0.00 2.71
499 500 0.655208 TAGCGCGGCACATTACATTG 59.345 50.000 8.83 0.00 0.00 2.82
500 501 1.531149 GATAGCGCGGCACATTACATT 59.469 47.619 8.83 0.00 0.00 2.71
501 502 1.148310 GATAGCGCGGCACATTACAT 58.852 50.000 8.83 0.00 0.00 2.29
502 503 0.878523 GGATAGCGCGGCACATTACA 60.879 55.000 8.83 0.00 0.00 2.41
503 504 1.860078 GGATAGCGCGGCACATTAC 59.140 57.895 8.83 0.00 0.00 1.89
504 505 1.663388 CGGATAGCGCGGCACATTA 60.663 57.895 8.83 0.00 0.00 1.90
505 506 2.967076 CGGATAGCGCGGCACATT 60.967 61.111 8.83 0.00 0.00 2.71
506 507 3.848347 CTCGGATAGCGCGGCACAT 62.848 63.158 8.83 0.00 0.00 3.21
507 508 4.569023 CTCGGATAGCGCGGCACA 62.569 66.667 8.83 0.00 0.00 4.57
508 509 3.559657 ATCTCGGATAGCGCGGCAC 62.560 63.158 8.83 0.00 0.00 5.01
509 510 3.268965 GATCTCGGATAGCGCGGCA 62.269 63.158 8.83 0.00 0.00 5.69
510 511 1.645704 TAGATCTCGGATAGCGCGGC 61.646 60.000 8.83 0.00 0.00 6.53
511 512 0.803117 TTAGATCTCGGATAGCGCGG 59.197 55.000 8.83 0.00 0.00 6.46
512 513 1.465387 ACTTAGATCTCGGATAGCGCG 59.535 52.381 0.00 0.00 0.00 6.86
513 514 3.562567 AACTTAGATCTCGGATAGCGC 57.437 47.619 0.00 0.00 0.00 5.92
514 515 4.912766 GTCAAACTTAGATCTCGGATAGCG 59.087 45.833 0.00 0.00 0.00 4.26
515 516 5.221263 TGGTCAAACTTAGATCTCGGATAGC 60.221 44.000 0.00 0.00 0.00 2.97
516 517 6.392625 TGGTCAAACTTAGATCTCGGATAG 57.607 41.667 0.00 0.00 0.00 2.08
517 518 6.978674 ATGGTCAAACTTAGATCTCGGATA 57.021 37.500 0.00 0.00 0.00 2.59
518 519 5.878406 ATGGTCAAACTTAGATCTCGGAT 57.122 39.130 0.00 0.00 0.00 4.18
519 520 6.785337 TTATGGTCAAACTTAGATCTCGGA 57.215 37.500 0.00 0.00 0.00 4.55
520 521 8.438676 AATTTATGGTCAAACTTAGATCTCGG 57.561 34.615 0.00 0.00 0.00 4.63
530 531 9.965824 CTTGTTGACTAAATTTATGGTCAAACT 57.034 29.630 23.82 0.00 45.86 2.66
531 532 9.959749 TCTTGTTGACTAAATTTATGGTCAAAC 57.040 29.630 23.82 19.42 45.86 2.93
532 533 9.959749 GTCTTGTTGACTAAATTTATGGTCAAA 57.040 29.630 23.82 14.48 45.86 2.69
533 534 8.573035 GGTCTTGTTGACTAAATTTATGGTCAA 58.427 33.333 20.66 20.66 44.74 3.18
534 535 7.094975 CGGTCTTGTTGACTAAATTTATGGTCA 60.095 37.037 13.48 13.48 44.74 4.02
535 536 7.118680 TCGGTCTTGTTGACTAAATTTATGGTC 59.881 37.037 9.55 9.55 44.74 4.02
536 537 6.938030 TCGGTCTTGTTGACTAAATTTATGGT 59.062 34.615 0.00 0.00 44.74 3.55
537 538 7.119262 AGTCGGTCTTGTTGACTAAATTTATGG 59.881 37.037 0.00 0.00 44.74 2.74
538 539 7.957484 CAGTCGGTCTTGTTGACTAAATTTATG 59.043 37.037 0.00 0.00 44.74 1.90
539 540 7.660208 ACAGTCGGTCTTGTTGACTAAATTTAT 59.340 33.333 0.00 0.00 44.74 1.40
540 541 6.987992 ACAGTCGGTCTTGTTGACTAAATTTA 59.012 34.615 0.00 0.00 44.74 1.40
541 542 5.820947 ACAGTCGGTCTTGTTGACTAAATTT 59.179 36.000 0.00 0.00 44.74 1.82
542 543 5.365619 ACAGTCGGTCTTGTTGACTAAATT 58.634 37.500 0.00 0.00 44.74 1.82
543 544 4.957296 ACAGTCGGTCTTGTTGACTAAAT 58.043 39.130 0.00 0.00 44.74 1.40
544 545 4.395959 ACAGTCGGTCTTGTTGACTAAA 57.604 40.909 0.00 0.00 44.74 1.85
545 546 5.717078 ATACAGTCGGTCTTGTTGACTAA 57.283 39.130 0.00 0.00 44.74 2.24
546 547 6.175471 TCTATACAGTCGGTCTTGTTGACTA 58.825 40.000 0.00 0.00 44.74 2.59
547 548 5.008331 TCTATACAGTCGGTCTTGTTGACT 58.992 41.667 0.00 0.00 44.74 3.41
548 549 5.123502 TCTCTATACAGTCGGTCTTGTTGAC 59.876 44.000 0.00 0.00 44.63 3.18
549 550 5.250982 TCTCTATACAGTCGGTCTTGTTGA 58.749 41.667 0.00 0.00 0.00 3.18
550 551 5.124138 ACTCTCTATACAGTCGGTCTTGTTG 59.876 44.000 0.00 0.00 0.00 3.33
551 552 5.254901 ACTCTCTATACAGTCGGTCTTGTT 58.745 41.667 0.00 0.00 0.00 2.83
552 553 4.846040 ACTCTCTATACAGTCGGTCTTGT 58.154 43.478 0.00 0.00 0.00 3.16
553 554 8.780846 ATATACTCTCTATACAGTCGGTCTTG 57.219 38.462 0.00 0.00 0.00 3.02
563 564 9.800572 GGGCTCATGATATATACTCTCTATACA 57.199 37.037 0.00 0.00 0.00 2.29
564 565 9.800572 TGGGCTCATGATATATACTCTCTATAC 57.199 37.037 0.00 0.00 0.00 1.47
657 658 8.579850 AGCAACTCTGTTTGATCCATATTAAA 57.420 30.769 0.00 0.00 0.00 1.52
668 669 4.130118 GGAGAAAGAGCAACTCTGTTTGA 58.870 43.478 0.00 0.00 40.28 2.69
670 671 4.133078 CAGGAGAAAGAGCAACTCTGTTT 58.867 43.478 0.00 0.00 40.28 2.83
671 672 3.135530 ACAGGAGAAAGAGCAACTCTGTT 59.864 43.478 0.00 0.00 40.28 3.16
673 674 3.399440 ACAGGAGAAAGAGCAACTCTG 57.601 47.619 0.00 0.00 40.28 3.35
674 675 3.389329 TGAACAGGAGAAAGAGCAACTCT 59.611 43.478 0.00 0.00 43.37 3.24
679 680 2.430465 GCATGAACAGGAGAAAGAGCA 58.570 47.619 0.00 0.00 0.00 4.26
746 757 2.985282 AACATGCCCACACGCTGG 60.985 61.111 0.00 0.00 40.26 4.85
787 804 7.775561 AGAGGACTGCCAGGTTATTAATTTTAG 59.224 37.037 0.00 0.00 36.29 1.85
788 805 7.639378 AGAGGACTGCCAGGTTATTAATTTTA 58.361 34.615 0.00 0.00 36.29 1.52
789 806 6.494059 AGAGGACTGCCAGGTTATTAATTTT 58.506 36.000 0.00 0.00 36.29 1.82
900 956 3.914435 ACCTAACCATCCCAACTACAAGT 59.086 43.478 0.00 0.00 0.00 3.16
901 957 4.261801 CACCTAACCATCCCAACTACAAG 58.738 47.826 0.00 0.00 0.00 3.16
902 958 3.009695 CCACCTAACCATCCCAACTACAA 59.990 47.826 0.00 0.00 0.00 2.41
903 959 2.574369 CCACCTAACCATCCCAACTACA 59.426 50.000 0.00 0.00 0.00 2.74
904 960 2.841881 TCCACCTAACCATCCCAACTAC 59.158 50.000 0.00 0.00 0.00 2.73
905 961 2.841881 GTCCACCTAACCATCCCAACTA 59.158 50.000 0.00 0.00 0.00 2.24
906 962 1.633945 GTCCACCTAACCATCCCAACT 59.366 52.381 0.00 0.00 0.00 3.16
907 963 1.353022 TGTCCACCTAACCATCCCAAC 59.647 52.381 0.00 0.00 0.00 3.77
908 964 1.633432 CTGTCCACCTAACCATCCCAA 59.367 52.381 0.00 0.00 0.00 4.12
909 965 1.285280 CTGTCCACCTAACCATCCCA 58.715 55.000 0.00 0.00 0.00 4.37
910 966 1.065418 CACTGTCCACCTAACCATCCC 60.065 57.143 0.00 0.00 0.00 3.85
911 967 1.906574 TCACTGTCCACCTAACCATCC 59.093 52.381 0.00 0.00 0.00 3.51
912 968 3.914426 ATCACTGTCCACCTAACCATC 57.086 47.619 0.00 0.00 0.00 3.51
913 969 5.453339 CGAATATCACTGTCCACCTAACCAT 60.453 44.000 0.00 0.00 0.00 3.55
915 971 4.369182 CGAATATCACTGTCCACCTAACC 58.631 47.826 0.00 0.00 0.00 2.85
916 972 4.369182 CCGAATATCACTGTCCACCTAAC 58.631 47.826 0.00 0.00 0.00 2.34
920 976 1.485066 ACCCGAATATCACTGTCCACC 59.515 52.381 0.00 0.00 0.00 4.61
921 977 2.483188 GGACCCGAATATCACTGTCCAC 60.483 54.545 0.00 0.00 41.46 4.02
923 979 1.760613 TGGACCCGAATATCACTGTCC 59.239 52.381 0.00 0.00 42.03 4.02
924 980 3.753294 ATGGACCCGAATATCACTGTC 57.247 47.619 0.00 0.00 0.00 3.51
925 981 4.040461 CCTAATGGACCCGAATATCACTGT 59.960 45.833 0.00 0.00 34.57 3.55
926 982 4.563580 CCCTAATGGACCCGAATATCACTG 60.564 50.000 0.00 0.00 35.39 3.66
927 983 3.583086 CCCTAATGGACCCGAATATCACT 59.417 47.826 0.00 0.00 35.39 3.41
928 984 3.326880 ACCCTAATGGACCCGAATATCAC 59.673 47.826 0.00 0.00 38.00 3.06
929 985 3.593942 ACCCTAATGGACCCGAATATCA 58.406 45.455 0.00 0.00 38.00 2.15
930 986 4.041198 TGAACCCTAATGGACCCGAATATC 59.959 45.833 0.00 0.00 38.00 1.63
932 988 3.386063 TGAACCCTAATGGACCCGAATA 58.614 45.455 0.00 0.00 38.00 1.75
933 989 2.201830 TGAACCCTAATGGACCCGAAT 58.798 47.619 0.00 0.00 38.00 3.34
936 992 2.500392 TTTGAACCCTAATGGACCCG 57.500 50.000 0.00 0.00 38.00 5.28
937 993 5.483937 AGAATTTTTGAACCCTAATGGACCC 59.516 40.000 0.00 0.00 38.00 4.46
938 994 6.605471 AGAATTTTTGAACCCTAATGGACC 57.395 37.500 0.00 0.00 38.00 4.46
939 995 8.575649 TCTAGAATTTTTGAACCCTAATGGAC 57.424 34.615 0.00 0.00 38.00 4.02
979 1035 4.019174 CCCAGTTTCATGGCAAAGACTAT 58.981 43.478 0.00 0.00 39.17 2.12
1125 1354 4.812476 CGAGACGGCGGCCATTGA 62.812 66.667 20.71 0.00 0.00 2.57
1153 1382 2.911143 CGGTGAGGAATGGGAGGG 59.089 66.667 0.00 0.00 0.00 4.30
1170 1399 0.035915 GAGGACTGGAAAGTGGAGGC 60.036 60.000 0.00 0.00 0.00 4.70
1309 1538 4.097361 GGGCAGGGAGAACGGACC 62.097 72.222 0.00 0.00 0.00 4.46
1373 1602 3.736740 GCACAGCCCCAATTTAATTACGG 60.737 47.826 0.00 0.00 0.00 4.02
1380 1609 3.030291 CCAATAGCACAGCCCCAATTTA 58.970 45.455 0.00 0.00 0.00 1.40
1397 1631 3.755378 CAGTTACAAGAGCTCAAGCCAAT 59.245 43.478 17.77 0.00 43.38 3.16
1417 1654 6.857964 CCTTCAAAAGCATACAACTGTAACAG 59.142 38.462 0.00 0.00 37.52 3.16
1497 1738 1.675801 CAGTTCCAGCAGCTCCTCA 59.324 57.895 0.00 0.00 0.00 3.86
1556 1797 6.633784 GCTAAACAGCATTGGAACAATCAGC 61.634 44.000 0.00 0.00 38.05 4.26
1623 1871 3.428180 CGAATCCAACTCTGTCTCGTGAT 60.428 47.826 0.00 0.00 0.00 3.06
1640 1888 4.594136 ACCAAACTCGAAACAAACGAATC 58.406 39.130 0.00 0.00 39.23 2.52
1646 1894 7.911205 CACACTATTAACCAAACTCGAAACAAA 59.089 33.333 0.00 0.00 0.00 2.83
1648 1896 6.512091 GCACACTATTAACCAAACTCGAAACA 60.512 38.462 0.00 0.00 0.00 2.83
1653 1901 5.545658 ATGCACACTATTAACCAAACTCG 57.454 39.130 0.00 0.00 0.00 4.18
2133 2428 7.943079 TGAAACATTGGAATATGATGACAGT 57.057 32.000 0.00 0.00 0.00 3.55
2261 2556 6.071320 TCTCTCTCCTCGATATCATCCAAAA 58.929 40.000 3.12 0.00 0.00 2.44
2302 2597 3.697045 AGATACAAGAACCTCGACTCCAG 59.303 47.826 0.00 0.00 0.00 3.86
2410 2705 3.087781 AGGTCGACTTCTACAGGGTAAC 58.912 50.000 16.46 0.00 0.00 2.50
2476 2771 1.846439 CCTCCAGCCCCTATGAAGAAA 59.154 52.381 0.00 0.00 0.00 2.52
2748 3054 8.556194 CGCCAATTACTAGTTAATAGATTGCAA 58.444 33.333 0.00 0.00 35.30 4.08
2770 3076 1.462616 ATGAAACTGCAATAGCGCCA 58.537 45.000 2.29 0.00 46.23 5.69
2816 3122 9.984590 AAAGAGAGAGTATAGGTCTTAGAAGTT 57.015 33.333 0.00 0.00 0.00 2.66
3001 3307 4.993705 ATGTACTTTCCAGACCCTTTGA 57.006 40.909 0.00 0.00 0.00 2.69
3009 3315 6.187727 ACCTTCAAGAATGTACTTTCCAGA 57.812 37.500 15.75 11.82 0.00 3.86
3012 3318 9.626045 CAAATAACCTTCAAGAATGTACTTTCC 57.374 33.333 15.75 1.62 0.00 3.13
3067 3373 9.783081 AAATGAAATTAGCCAAAGAAGTGAAAT 57.217 25.926 0.00 0.00 33.67 2.17
3094 3400 4.023291 GCCACCCTTCCATATCAAAGAAA 58.977 43.478 0.00 0.00 0.00 2.52
3351 3661 8.576442 CCACACAATAACTAAAAATTCAGGAGT 58.424 33.333 0.00 0.00 0.00 3.85
3366 3676 3.001330 GCTAGCGATGACCACACAATAAC 59.999 47.826 0.00 0.00 0.00 1.89
3372 3682 2.517450 GCGCTAGCGATGACCACAC 61.517 63.158 39.52 15.25 42.83 3.82
3536 3846 5.546499 TGGTAAAGACATTACTTCTGGAGGT 59.454 40.000 1.01 0.00 42.93 3.85
3777 4088 5.105228 CCAAACCCTGCATACATTCAAGATT 60.105 40.000 0.00 0.00 0.00 2.40
3778 4089 4.403432 CCAAACCCTGCATACATTCAAGAT 59.597 41.667 0.00 0.00 0.00 2.40
3975 4286 3.737559 AATACTCCATGTGCAAAGGGA 57.262 42.857 10.45 10.45 0.00 4.20
4153 4468 6.214191 TGCTGAGACTAAACAAGGAGATAG 57.786 41.667 0.00 0.00 0.00 2.08
4218 4534 3.610040 TCTAGGTAACACGACCGAGTA 57.390 47.619 0.00 0.00 44.88 2.59
4418 4734 2.766263 CTGTCCTTGCTACCTACCATCA 59.234 50.000 0.00 0.00 0.00 3.07
4447 4763 0.242017 AAGCGGTGAAAATGCTGCTC 59.758 50.000 0.00 0.00 45.55 4.26
4930 5310 2.164422 GTCCTAAGCAAAACCAGCATCC 59.836 50.000 0.00 0.00 0.00 3.51
5035 5415 5.618561 GCGTTCTCACATGTAAAGTTTAGG 58.381 41.667 0.00 0.00 0.00 2.69
5091 5472 2.548904 GCTCATTCACATCATGGCTCTC 59.451 50.000 0.00 0.00 0.00 3.20
5101 5482 1.019673 GACATGGCGCTCATTCACAT 58.980 50.000 7.64 0.00 32.92 3.21
5301 5686 1.709147 CTTAGCAGCCATGTCGCACC 61.709 60.000 0.00 0.00 0.00 5.01
5303 5688 0.178767 ATCTTAGCAGCCATGTCGCA 59.821 50.000 0.00 0.00 0.00 5.10
5491 5881 3.236391 TGGAACGACCAGCACCTT 58.764 55.556 0.00 0.00 44.64 3.50
5620 6015 4.334203 CGTGCAATGGTTATGTAAAGCCTA 59.666 41.667 0.00 0.00 0.00 3.93
5628 6023 0.167908 CGTGCGTGCAATGGTTATGT 59.832 50.000 0.00 0.00 0.00 2.29
5656 6051 0.251608 TCCCCGTGACAGACTGATCA 60.252 55.000 10.08 6.55 0.00 2.92


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

AutoCloner maintained by Alex Coulton.