Multiple sequence alignment - TraesCS1D01G023100

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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 TraesCS1D01G023100 chr1D 100.000 4976 0 0 1 4976 9806837 9811812 0.000000e+00 9190
1 TraesCS1D01G023100 chr1D 85.335 3348 443 36 755 4080 9775830 9779151 0.000000e+00 3419
2 TraesCS1D01G023100 chr1D 93.803 468 27 2 1 467 42270606 42271072 0.000000e+00 702
3 TraesCS1D01G023100 chr1A 84.494 3160 454 31 928 4075 11630074 11633209 0.000000e+00 3088
4 TraesCS1D01G023100 chr1A 86.845 2615 300 25 755 3348 11581186 11583777 0.000000e+00 2883
5 TraesCS1D01G023100 chr1A 91.682 1647 96 11 3351 4976 11583822 11585448 0.000000e+00 2244
6 TraesCS1D01G023100 chr1A 84.762 420 54 9 4474 4888 11633652 11634066 3.580000e-111 412
7 TraesCS1D01G023100 chr1B 85.360 2903 364 41 1340 4206 14459604 14462481 0.000000e+00 2950
8 TraesCS1D01G023100 chr1B 81.705 3121 481 58 1136 4206 14652595 14655675 0.000000e+00 2518
9 TraesCS1D01G023100 chr1B 80.137 3071 543 57 1042 4080 14162701 14165736 0.000000e+00 2230
10 TraesCS1D01G023100 chr1B 80.017 2312 429 29 1133 3435 14565562 14567849 0.000000e+00 1679
11 TraesCS1D01G023100 chr1B 83.881 1551 234 12 2531 4076 14623856 14625395 0.000000e+00 1465
12 TraesCS1D01G023100 chr1B 82.848 1510 204 37 932 2430 14622392 14623857 0.000000e+00 1303
13 TraesCS1D01G023100 chr1B 78.140 1011 186 24 3223 4206 14541899 14542901 1.180000e-170 610
14 TraesCS1D01G023100 chr1B 82.240 625 106 4 2607 3229 14531667 14532288 7.330000e-148 534
15 TraesCS1D01G023100 chr1B 86.024 415 48 9 4475 4882 14569958 14570369 2.130000e-118 436
16 TraesCS1D01G023100 chr1B 87.469 399 23 15 720 1115 14451093 14451467 7.650000e-118 435
17 TraesCS1D01G023100 chr1B 80.996 542 77 12 3689 4206 14496555 14497094 1.670000e-109 407
18 TraesCS1D01G023100 chr1B 92.520 254 19 0 469 722 593448688 593448435 1.020000e-96 364
19 TraesCS1D01G023100 chr1B 90.551 254 24 0 469 722 256901472 256901219 2.220000e-88 337
20 TraesCS1D01G023100 chr1B 84.103 195 25 5 4698 4888 14626895 14627087 3.060000e-42 183
21 TraesCS1D01G023100 chr3D 94.658 468 24 1 1 467 319046750 319047217 0.000000e+00 725
22 TraesCS1D01G023100 chr3D 91.732 254 21 0 469 722 319047167 319047420 2.200000e-93 353
23 TraesCS1D01G023100 chr2D 94.231 468 26 1 1 467 387226090 387225623 0.000000e+00 713
24 TraesCS1D01G023100 chr2D 94.231 468 26 1 1 467 572375684 572376151 0.000000e+00 713
25 TraesCS1D01G023100 chr2D 94.017 468 27 1 1 467 44919283 44919750 0.000000e+00 708
26 TraesCS1D01G023100 chr7A 94.372 462 24 2 1 461 6170924 6171384 0.000000e+00 708
27 TraesCS1D01G023100 chr5A 94.017 468 27 1 1 467 645610399 645610866 0.000000e+00 708
28 TraesCS1D01G023100 chr4D 94.017 468 27 1 1 467 9244534 9244067 0.000000e+00 708
29 TraesCS1D01G023100 chr4D 91.270 252 22 0 469 720 9244117 9243866 1.330000e-90 344
30 TraesCS1D01G023100 chr4A 93.803 468 28 1 1 467 724778747 724779214 0.000000e+00 702
31 TraesCS1D01G023100 chr4B 92.126 254 19 1 469 722 260044656 260044908 1.700000e-94 357
32 TraesCS1D01G023100 chr7D 92.063 252 20 0 469 720 218051118 218051369 6.130000e-94 355
33 TraesCS1D01G023100 chr6D 91.339 254 22 0 469 722 415198724 415198977 1.030000e-91 348
34 TraesCS1D01G023100 chr5D 90.551 254 24 0 469 722 24776030 24776283 2.220000e-88 337
35 TraesCS1D01G023100 chr3B 90.551 254 24 0 469 722 11238171 11237918 2.220000e-88 337


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 TraesCS1D01G023100 chr1D 9806837 9811812 4975 False 9190.000000 9190 100.000000 1 4976 1 chr1D.!!$F2 4975
1 TraesCS1D01G023100 chr1D 9775830 9779151 3321 False 3419.000000 3419 85.335000 755 4080 1 chr1D.!!$F1 3325
2 TraesCS1D01G023100 chr1A 11581186 11585448 4262 False 2563.500000 2883 89.263500 755 4976 2 chr1A.!!$F1 4221
3 TraesCS1D01G023100 chr1A 11630074 11634066 3992 False 1750.000000 3088 84.628000 928 4888 2 chr1A.!!$F2 3960
4 TraesCS1D01G023100 chr1B 14459604 14462481 2877 False 2950.000000 2950 85.360000 1340 4206 1 chr1B.!!$F3 2866
5 TraesCS1D01G023100 chr1B 14652595 14655675 3080 False 2518.000000 2518 81.705000 1136 4206 1 chr1B.!!$F7 3070
6 TraesCS1D01G023100 chr1B 14162701 14165736 3035 False 2230.000000 2230 80.137000 1042 4080 1 chr1B.!!$F1 3038
7 TraesCS1D01G023100 chr1B 14565562 14570369 4807 False 1057.500000 1679 83.020500 1133 4882 2 chr1B.!!$F8 3749
8 TraesCS1D01G023100 chr1B 14622392 14627087 4695 False 983.666667 1465 83.610667 932 4888 3 chr1B.!!$F9 3956
9 TraesCS1D01G023100 chr1B 14541899 14542901 1002 False 610.000000 610 78.140000 3223 4206 1 chr1B.!!$F6 983
10 TraesCS1D01G023100 chr1B 14531667 14532288 621 False 534.000000 534 82.240000 2607 3229 1 chr1B.!!$F5 622
11 TraesCS1D01G023100 chr1B 14496555 14497094 539 False 407.000000 407 80.996000 3689 4206 1 chr1B.!!$F4 517
12 TraesCS1D01G023100 chr3D 319046750 319047420 670 False 539.000000 725 93.195000 1 722 2 chr3D.!!$F1 721
13 TraesCS1D01G023100 chr4D 9243866 9244534 668 True 526.000000 708 92.643500 1 720 2 chr4D.!!$R1 719

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
461 463 0.175073 GCTCCGGTGTCGTATCCTTT 59.825 55.000 0.00 0.00 33.95 3.11 F
753 755 0.248565 TGCAGTTTGTTTTGCTGGCA 59.751 45.000 0.00 0.00 40.87 4.92 F
1747 1780 0.539051 AGTGGCAGCTATCACCTCAC 59.461 55.000 13.07 3.11 34.67 3.51 F
1801 1834 1.352017 TCTTGCCTGGAATGAGCTTCA 59.648 47.619 0.00 0.00 35.41 3.02 F
2995 3031 0.911045 TCCTTGGCATGAGCTGGAGA 60.911 55.000 0.00 0.00 41.70 3.71 F
3348 3432 0.031449 GGACTGAGCGCCATCTAGAC 59.969 60.000 2.29 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 2463 0.465460 TGCTCTTTTCGTTGGCCACT 60.465 50.000 3.88 0.00 0.00 4.00 R
2664 2700 2.731976 GAGCTTCAACGACTGTAGTTGG 59.268 50.000 26.20 16.01 46.36 3.77 R
2944 2980 0.395312 GAAGGAACACCCACGAGGAA 59.605 55.000 0.00 0.00 39.89 3.36 R
3126 3162 1.695242 TGGAAAAACCGTCCAGCTCTA 59.305 47.619 0.00 0.00 40.33 2.43 R
3956 5103 0.177604 CTAGAGCTTGCTCCACCAGG 59.822 60.000 17.78 0.00 0.00 4.45 R
4294 5488 0.617413 ATGGAAGCACCTGGAGACTG 59.383 55.000 0.00 0.00 39.86 3.51 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
36 37 4.988716 AGCAGGACGGGTCGGTGA 62.989 66.667 4.51 0.00 0.00 4.02
113 114 2.434774 GGTGGGACCTTTCCGCTT 59.565 61.111 0.00 0.00 43.94 4.68
234 235 3.357079 GTCCGTGCCTTGGTGCTG 61.357 66.667 0.00 0.00 0.00 4.41
259 261 4.386951 CCATGGTCGTGTGGGCGA 62.387 66.667 2.57 0.00 38.68 5.54
301 303 2.258013 CGGTGGCGGTGAATGTTGT 61.258 57.895 0.00 0.00 0.00 3.32
415 417 4.029809 CGGCTCCGGGGGAAACTT 62.030 66.667 1.90 0.00 35.56 2.66
432 434 1.916181 ACTTTGATCCTTGGATCGGGT 59.084 47.619 20.69 16.21 34.46 5.28
456 458 2.890371 GGTGCTCCGGTGTCGTAT 59.110 61.111 0.00 0.00 33.95 3.06
457 459 1.226888 GGTGCTCCGGTGTCGTATC 60.227 63.158 0.00 0.00 33.95 2.24
458 460 1.226888 GTGCTCCGGTGTCGTATCC 60.227 63.158 0.00 0.00 33.95 2.59
459 461 1.379443 TGCTCCGGTGTCGTATCCT 60.379 57.895 0.00 0.00 33.95 3.24
460 462 0.968901 TGCTCCGGTGTCGTATCCTT 60.969 55.000 0.00 0.00 33.95 3.36
461 463 0.175073 GCTCCGGTGTCGTATCCTTT 59.825 55.000 0.00 0.00 33.95 3.11
462 464 1.801765 GCTCCGGTGTCGTATCCTTTC 60.802 57.143 0.00 0.00 33.95 2.62
463 465 1.749634 CTCCGGTGTCGTATCCTTTCT 59.250 52.381 0.00 0.00 33.95 2.52
464 466 1.475280 TCCGGTGTCGTATCCTTTCTG 59.525 52.381 0.00 0.00 33.95 3.02
465 467 1.475280 CCGGTGTCGTATCCTTTCTGA 59.525 52.381 0.00 0.00 33.95 3.27
466 468 2.094390 CCGGTGTCGTATCCTTTCTGAA 60.094 50.000 0.00 0.00 33.95 3.02
467 469 3.430374 CCGGTGTCGTATCCTTTCTGAAT 60.430 47.826 0.00 0.00 33.95 2.57
468 470 4.181578 CGGTGTCGTATCCTTTCTGAATT 58.818 43.478 0.00 0.00 0.00 2.17
469 471 4.032900 CGGTGTCGTATCCTTTCTGAATTG 59.967 45.833 0.00 0.00 0.00 2.32
470 472 5.175859 GGTGTCGTATCCTTTCTGAATTGA 58.824 41.667 0.00 0.00 0.00 2.57
471 473 5.817816 GGTGTCGTATCCTTTCTGAATTGAT 59.182 40.000 7.18 7.18 0.00 2.57
472 474 6.018669 GGTGTCGTATCCTTTCTGAATTGATC 60.019 42.308 5.70 0.00 0.00 2.92
473 475 6.018669 GTGTCGTATCCTTTCTGAATTGATCC 60.019 42.308 5.70 0.00 0.00 3.36
474 476 6.127054 TGTCGTATCCTTTCTGAATTGATCCT 60.127 38.462 5.70 0.00 0.00 3.24
475 477 6.763610 GTCGTATCCTTTCTGAATTGATCCTT 59.236 38.462 5.70 0.00 0.00 3.36
476 478 6.763135 TCGTATCCTTTCTGAATTGATCCTTG 59.237 38.462 5.70 0.00 0.00 3.61
477 479 6.017605 CGTATCCTTTCTGAATTGATCCTTGG 60.018 42.308 5.70 0.00 0.00 3.61
478 480 5.519183 TCCTTTCTGAATTGATCCTTGGA 57.481 39.130 0.00 0.00 0.00 3.53
479 481 6.083487 TCCTTTCTGAATTGATCCTTGGAT 57.917 37.500 1.18 1.18 0.00 3.41
480 482 6.125029 TCCTTTCTGAATTGATCCTTGGATC 58.875 40.000 19.70 19.70 0.00 3.36
481 483 5.008415 CCTTTCTGAATTGATCCTTGGATCG 59.992 44.000 20.69 8.74 34.46 3.69
482 484 4.077300 TCTGAATTGATCCTTGGATCGG 57.923 45.455 20.69 7.27 34.46 4.18
483 485 3.144506 CTGAATTGATCCTTGGATCGGG 58.855 50.000 20.69 6.92 34.46 5.14
484 486 2.509548 TGAATTGATCCTTGGATCGGGT 59.490 45.455 20.69 10.58 34.46 5.28
485 487 2.645838 ATTGATCCTTGGATCGGGTG 57.354 50.000 20.69 0.00 34.46 4.61
486 488 0.546122 TTGATCCTTGGATCGGGTGG 59.454 55.000 20.69 0.00 34.46 4.61
487 489 0.620410 TGATCCTTGGATCGGGTGGT 60.620 55.000 20.69 0.00 34.46 4.16
488 490 0.179045 GATCCTTGGATCGGGTGGTG 60.179 60.000 13.16 0.00 0.00 4.17
489 491 1.635817 ATCCTTGGATCGGGTGGTGG 61.636 60.000 0.00 0.00 0.00 4.61
490 492 2.438434 CTTGGATCGGGTGGTGGC 60.438 66.667 0.00 0.00 0.00 5.01
491 493 4.402528 TTGGATCGGGTGGTGGCG 62.403 66.667 0.00 0.00 0.00 5.69
513 515 0.175073 GCTCCGGTGTCGTATCCTTT 59.825 55.000 0.00 0.00 33.95 3.11
520 522 3.119602 CGGTGTCGTATCCTTTCTGAAGA 60.120 47.826 0.00 0.00 34.71 2.87
530 532 0.534203 TTTCTGAAGACGCCGCCTTT 60.534 50.000 0.00 0.00 0.00 3.11
549 551 1.921243 TGAGCGTATGGTTCGTCATG 58.079 50.000 0.00 0.00 0.00 3.07
598 600 3.204467 TAGGGGTGGTGTTGCTGCC 62.204 63.158 0.00 0.00 0.00 4.85
615 617 2.175878 GCCCTCAGCACCTATGTATG 57.824 55.000 0.00 0.00 42.97 2.39
641 643 2.403378 GGGTGTGTGCGTGTGTTGT 61.403 57.895 0.00 0.00 0.00 3.32
648 650 3.513438 GCGTGTGTTGTGGTGGCA 61.513 61.111 0.00 0.00 0.00 4.92
653 655 2.123554 TGTTGTGGTGGCATGGCA 60.124 55.556 19.43 19.43 0.00 4.92
678 680 2.685897 GTTTGTACTGGGTGCTTGTTGA 59.314 45.455 0.00 0.00 0.00 3.18
685 687 1.039856 GGGTGCTTGTTGATTGGTGT 58.960 50.000 0.00 0.00 0.00 4.16
726 728 4.328667 CGAAAGCCTTTTTCGGTATTACG 58.671 43.478 12.72 0.00 45.17 3.18
727 729 4.143052 CGAAAGCCTTTTTCGGTATTACGT 60.143 41.667 12.72 0.00 45.17 3.57
728 730 4.673534 AAGCCTTTTTCGGTATTACGTG 57.326 40.909 0.00 0.00 34.94 4.49
729 731 3.667360 AGCCTTTTTCGGTATTACGTGT 58.333 40.909 0.00 0.00 34.94 4.49
730 732 4.819769 AGCCTTTTTCGGTATTACGTGTA 58.180 39.130 0.00 0.00 34.94 2.90
731 733 4.627035 AGCCTTTTTCGGTATTACGTGTAC 59.373 41.667 0.00 0.98 34.94 2.90
732 734 4.627035 GCCTTTTTCGGTATTACGTGTACT 59.373 41.667 0.00 0.00 34.94 2.73
733 735 5.220284 GCCTTTTTCGGTATTACGTGTACTC 60.220 44.000 0.00 0.00 34.94 2.59
734 736 6.095377 CCTTTTTCGGTATTACGTGTACTCT 58.905 40.000 0.00 0.00 34.94 3.24
735 737 6.034256 CCTTTTTCGGTATTACGTGTACTCTG 59.966 42.308 0.00 0.00 34.94 3.35
736 738 3.680642 TCGGTATTACGTGTACTCTGC 57.319 47.619 0.00 0.00 34.94 4.26
737 739 3.009026 TCGGTATTACGTGTACTCTGCA 58.991 45.455 0.00 0.00 34.94 4.41
738 740 3.064408 TCGGTATTACGTGTACTCTGCAG 59.936 47.826 7.63 7.63 34.94 4.41
739 741 3.181503 CGGTATTACGTGTACTCTGCAGT 60.182 47.826 14.67 0.00 36.55 4.40
740 742 4.673580 CGGTATTACGTGTACTCTGCAGTT 60.674 45.833 14.67 4.66 33.62 3.16
741 743 5.166398 GGTATTACGTGTACTCTGCAGTTT 58.834 41.667 14.67 4.27 33.62 2.66
742 744 5.061808 GGTATTACGTGTACTCTGCAGTTTG 59.938 44.000 14.67 8.01 33.62 2.93
743 745 2.596904 ACGTGTACTCTGCAGTTTGT 57.403 45.000 14.67 13.35 33.62 2.83
744 746 2.901249 ACGTGTACTCTGCAGTTTGTT 58.099 42.857 14.67 0.00 33.62 2.83
745 747 3.267483 ACGTGTACTCTGCAGTTTGTTT 58.733 40.909 14.67 0.00 33.62 2.83
746 748 3.687698 ACGTGTACTCTGCAGTTTGTTTT 59.312 39.130 14.67 0.00 33.62 2.43
747 749 4.028383 CGTGTACTCTGCAGTTTGTTTTG 58.972 43.478 14.67 0.00 33.62 2.44
748 750 3.791353 GTGTACTCTGCAGTTTGTTTTGC 59.209 43.478 14.67 4.44 40.67 3.68
749 751 3.694072 TGTACTCTGCAGTTTGTTTTGCT 59.306 39.130 14.67 0.00 40.87 3.91
750 752 3.155093 ACTCTGCAGTTTGTTTTGCTG 57.845 42.857 14.67 0.00 40.87 4.41
751 753 2.159198 ACTCTGCAGTTTGTTTTGCTGG 60.159 45.455 14.67 0.00 40.87 4.85
752 754 0.932399 CTGCAGTTTGTTTTGCTGGC 59.068 50.000 5.25 0.00 40.87 4.85
753 755 0.248565 TGCAGTTTGTTTTGCTGGCA 59.751 45.000 0.00 0.00 40.87 4.92
771 773 6.183360 TGCTGGCATATTAATGGAACGAATTT 60.183 34.615 0.00 0.00 33.38 1.82
789 791 5.277345 CGAATTTCTTATGGATCCGTTGGTC 60.277 44.000 12.82 0.29 0.00 4.02
803 805 9.886132 GGATCCGTTGGTCATATTATTTATACT 57.114 33.333 0.00 0.00 0.00 2.12
870 872 7.566760 TGAAAGTAATCAAGCTTCTTGAACA 57.433 32.000 12.53 2.28 31.55 3.18
871 873 7.417612 TGAAAGTAATCAAGCTTCTTGAACAC 58.582 34.615 12.53 12.38 31.55 3.32
872 874 5.597813 AGTAATCAAGCTTCTTGAACACG 57.402 39.130 12.53 0.00 31.55 4.49
873 875 5.297547 AGTAATCAAGCTTCTTGAACACGA 58.702 37.500 12.53 0.00 31.55 4.35
874 876 5.934625 AGTAATCAAGCTTCTTGAACACGAT 59.065 36.000 12.53 0.00 31.55 3.73
876 878 5.695851 ATCAAGCTTCTTGAACACGATTT 57.304 34.783 12.53 0.00 31.55 2.17
877 879 6.801539 ATCAAGCTTCTTGAACACGATTTA 57.198 33.333 12.53 0.00 31.55 1.40
878 880 6.228273 TCAAGCTTCTTGAACACGATTTAG 57.772 37.500 6.78 0.00 0.00 1.85
879 881 5.179368 TCAAGCTTCTTGAACACGATTTAGG 59.821 40.000 6.78 0.00 0.00 2.69
880 882 4.642429 AGCTTCTTGAACACGATTTAGGT 58.358 39.130 0.00 0.00 0.00 3.08
886 888 5.995282 TCTTGAACACGATTTAGGTTGACAT 59.005 36.000 0.00 0.00 0.00 3.06
923 929 1.398390 CGGCTAGCTGTTGACCATTTC 59.602 52.381 15.85 0.00 0.00 2.17
930 936 3.370978 AGCTGTTGACCATTTCGATTACG 59.629 43.478 0.00 0.00 41.26 3.18
1005 1020 5.660117 CGTGAGACGGAAGCATATATGCAG 61.660 50.000 33.36 23.74 46.32 4.41
1024 1039 2.600420 CAGTTGGACGATGATCTGTTCG 59.400 50.000 10.40 10.40 41.04 3.95
1028 1043 1.482278 GACGATGATCTGTTCGGCTC 58.518 55.000 14.63 4.23 40.25 4.70
1034 1049 4.320861 CGATGATCTGTTCGGCTCTTATCT 60.321 45.833 0.00 0.00 0.00 1.98
1039 1054 1.134367 TGTTCGGCTCTTATCTCGTGG 59.866 52.381 0.00 0.00 0.00 4.94
1048 1063 4.202223 GCTCTTATCTCGTGGGTTGGAATA 60.202 45.833 0.00 0.00 0.00 1.75
1092 1107 1.485124 ACACACGAGCCATATCAGGA 58.515 50.000 0.00 0.00 0.00 3.86
1093 1108 1.137086 ACACACGAGCCATATCAGGAC 59.863 52.381 0.00 0.00 0.00 3.85
1129 1150 8.030106 AGACAATCCTTAAGTACGAAAGAGAAG 58.970 37.037 10.71 7.10 0.00 2.85
1288 1309 1.203287 GGCTCAAGGAAAAGCATGACC 59.797 52.381 0.00 0.00 40.36 4.02
1296 1317 2.162408 GGAAAAGCATGACCAGCTACAC 59.838 50.000 0.00 0.00 42.53 2.90
1304 1325 4.202161 GCATGACCAGCTACACTACTACAT 60.202 45.833 0.00 0.00 0.00 2.29
1361 1385 1.066605 GGAGTATCACGTGCGGTACAT 59.933 52.381 11.67 0.00 36.25 2.29
1509 1539 5.508657 GGCAAATTCTTATTGGCTCATCTCC 60.509 44.000 5.67 0.00 46.43 3.71
1621 1654 4.021981 CCCTCTATGCACTACATCAATCGA 60.022 45.833 0.00 0.00 40.38 3.59
1693 1726 1.688772 CATAGCCCTGCAATGCTTCT 58.311 50.000 14.15 0.83 39.00 2.85
1700 1733 3.813443 CCCTGCAATGCTTCTACTATGT 58.187 45.455 6.82 0.00 0.00 2.29
1747 1780 0.539051 AGTGGCAGCTATCACCTCAC 59.461 55.000 13.07 3.11 34.67 3.51
1798 1831 2.022754 GCATCTTGCCTGGAATGAGCT 61.023 52.381 0.00 0.00 37.42 4.09
1801 1834 1.352017 TCTTGCCTGGAATGAGCTTCA 59.648 47.619 0.00 0.00 35.41 3.02
1802 1835 2.025605 TCTTGCCTGGAATGAGCTTCAT 60.026 45.455 0.00 0.00 39.09 2.57
1803 1836 3.200605 TCTTGCCTGGAATGAGCTTCATA 59.799 43.478 0.00 0.00 35.76 2.15
1850 1883 2.551032 TCATCAGCAGCAAGTGTTCAAG 59.449 45.455 0.00 0.00 0.00 3.02
1903 1936 7.086376 TGAAGCATTTGAGAAATACTCTTTGC 58.914 34.615 0.00 0.00 45.13 3.68
2138 2171 4.377839 TTCTAAGAGGTTGCTCAGATCG 57.622 45.455 0.00 0.00 0.00 3.69
2253 2286 5.256474 CCTTCTTCCATTGGTTGTCTACAT 58.744 41.667 1.86 0.00 0.00 2.29
2256 2289 7.393234 CCTTCTTCCATTGGTTGTCTACATAAA 59.607 37.037 1.86 0.00 0.00 1.40
2263 2296 5.471556 TGGTTGTCTACATAAACTTCGGA 57.528 39.130 0.00 0.00 0.00 4.55
2430 2463 5.059161 CCTGTTTCTCATCTGACACAAGAA 58.941 41.667 0.00 0.00 0.00 2.52
2463 2496 5.796935 CGAAAAGAGCAATTTGATACACCTG 59.203 40.000 0.00 0.00 0.00 4.00
2473 2506 4.632327 TTGATACACCTGGACATGTCAA 57.368 40.909 26.47 15.68 0.00 3.18
2538 2571 4.774124 TGTCAAATCTGGAGGAGCTTATG 58.226 43.478 0.00 0.00 0.00 1.90
2628 2661 2.038952 TGAGGTCACAGGGACTCAAATG 59.961 50.000 1.94 0.00 46.16 2.32
2634 2667 5.888161 GGTCACAGGGACTCAAATGAAATAT 59.112 40.000 1.94 0.00 46.16 1.28
2664 2700 8.375465 CCGCAAAAGATATTTGAAGAAATGAAC 58.625 33.333 5.17 0.00 33.63 3.18
2665 2701 8.375465 CGCAAAAGATATTTGAAGAAATGAACC 58.625 33.333 5.17 0.00 33.63 3.62
2710 2746 8.369424 TCATTGACAACAAGGAATTGATTTCAT 58.631 29.630 0.00 0.00 42.46 2.57
2884 2920 4.908601 TTGGAGGAGCTTGATTTGTCTA 57.091 40.909 0.00 0.00 0.00 2.59
2895 2931 6.983307 AGCTTGATTTGTCTAGTACAGCTATG 59.017 38.462 0.00 0.00 39.87 2.23
2944 2980 7.399674 AATCTTCCCAAGCTTAGGAGATTAT 57.600 36.000 23.59 12.08 32.76 1.28
2995 3031 0.911045 TCCTTGGCATGAGCTGGAGA 60.911 55.000 0.00 0.00 41.70 3.71
3079 3115 5.874897 AGTTACCCAAGTGTGTGTTACTA 57.125 39.130 0.00 0.00 0.00 1.82
3084 3120 3.181448 CCCAAGTGTGTGTTACTAACCCT 60.181 47.826 0.00 0.00 0.00 4.34
3116 3152 2.959357 GCTTCCGTGACACTGCTGC 61.959 63.158 3.68 0.00 0.00 5.25
3117 3153 1.595109 CTTCCGTGACACTGCTGCA 60.595 57.895 0.88 0.88 0.00 4.41
3126 3162 3.499918 GTGACACTGCTGCAGATTTAGTT 59.500 43.478 34.28 8.77 35.18 2.24
3131 3167 4.033817 CACTGCTGCAGATTTAGTTAGAGC 59.966 45.833 34.28 0.00 35.18 4.09
3210 3252 2.039084 ACGGCAAGAAGATGAAGAAGGT 59.961 45.455 0.00 0.00 0.00 3.50
3213 3255 4.509600 CGGCAAGAAGATGAAGAAGGTATC 59.490 45.833 0.00 0.00 0.00 2.24
3220 3262 9.445973 AAGAAGATGAAGAAGGTATCCTAGATT 57.554 33.333 0.00 0.00 31.13 2.40
3277 3319 6.586344 ACATATGTGGATGTATATAGCAGCC 58.414 40.000 7.78 10.75 42.28 4.85
3296 3338 2.099756 GCCGCTTTGCAGAGGAAATTAT 59.900 45.455 6.36 0.00 42.60 1.28
3307 3349 6.088824 GCAGAGGAAATTATAATTGCATCGG 58.911 40.000 20.27 20.27 39.21 4.18
3343 3385 4.148825 ACCGGACTGAGCGCCATC 62.149 66.667 9.46 0.00 0.00 3.51
3348 3432 0.031449 GGACTGAGCGCCATCTAGAC 59.969 60.000 2.29 0.00 0.00 2.59
3355 3439 1.482182 AGCGCCATCTAGACATCACAA 59.518 47.619 2.29 0.00 0.00 3.33
3383 3467 6.413892 TGCAAGAGACACATGATGGTTTATA 58.586 36.000 0.00 0.00 0.00 0.98
3726 4873 4.718961 ACATCTTGTTCTGCTACAACCTT 58.281 39.130 0.00 0.00 34.50 3.50
3762 4909 6.482973 TCATCAGCAATTATACGCAAGATGAA 59.517 34.615 15.15 5.74 43.10 2.57
3764 4911 6.718388 TCAGCAATTATACGCAAGATGAAAG 58.282 36.000 0.00 0.00 43.62 2.62
3789 4936 2.346541 GCTCCCAAGCCTCCAAAGC 61.347 63.158 0.00 0.00 43.10 3.51
3795 4942 0.099436 CAAGCCTCCAAAGCATACGC 59.901 55.000 0.00 0.00 38.99 4.42
3956 5103 0.680061 AAGGTCAACGGTGAGAGGAC 59.320 55.000 1.63 0.00 33.27 3.85
3973 5120 1.835927 GACCTGGTGGAGCAAGCTCT 61.836 60.000 20.26 0.00 42.38 4.09
3985 5132 0.177604 CAAGCTCTAGTGGGGCTCAG 59.822 60.000 0.00 0.00 35.06 3.35
4017 5164 1.153549 CAGCTACGACCCCAAGCTC 60.154 63.158 0.00 0.00 44.58 4.09
4097 5267 4.198028 TCAATGCTCCATCCATCTATCG 57.802 45.455 0.00 0.00 0.00 2.92
4113 5283 6.486657 CCATCTATCGGTTGGTATGTGATTTT 59.513 38.462 0.00 0.00 31.83 1.82
4118 5288 4.865925 TCGGTTGGTATGTGATTTTACTCG 59.134 41.667 0.00 0.00 0.00 4.18
4143 5313 7.307989 CGGCATACTTATCCCTTTGTTCATTAG 60.308 40.741 0.00 0.00 0.00 1.73
4183 5373 8.794335 ATACCTTCCTAAACTCTAGCTTTTTG 57.206 34.615 0.00 0.00 0.00 2.44
4208 5401 1.812507 GTTCCACCATACGTCCGCC 60.813 63.158 0.00 0.00 0.00 6.13
4223 5416 2.974698 GCCTCAGCGCCGCATTAT 60.975 61.111 13.36 0.00 0.00 1.28
4294 5488 4.749099 CCTGCTCTGCAAGATGATACTTAC 59.251 45.833 0.00 0.00 45.62 2.34
4381 5888 2.336809 GAGCCTACGATGCCTCCG 59.663 66.667 0.00 0.00 0.00 4.63
4435 5944 2.633481 ACCAGAGTACCTTCCTCAACAC 59.367 50.000 0.00 0.00 0.00 3.32
4493 6048 7.009179 ACCATAGTGTCCATCCATAACATAG 57.991 40.000 0.00 0.00 0.00 2.23
4590 6711 7.153217 TCGAAATAAAAGTCCAATTTCCCTC 57.847 36.000 0.00 0.00 36.64 4.30
4634 6756 2.235402 TCTCCCGTGGAATCAGGTTTAC 59.765 50.000 0.00 0.00 0.00 2.01
4675 6797 7.277981 ACACATTTTATTCGAGTGTCCACTATC 59.722 37.037 0.00 0.00 42.66 2.08
4770 6937 4.530553 TGTCTCTGGACTTTAAGTGGCATA 59.469 41.667 0.93 0.00 42.54 3.14
4832 6999 3.195825 GTGTTGTACTCCTACCAGCATCT 59.804 47.826 0.00 0.00 0.00 2.90
4884 7053 7.232330 TCAATGTATGATTCAAGTTTTGTGGGA 59.768 33.333 0.00 0.00 31.50 4.37
4892 7061 8.869109 TGATTCAAGTTTTGTGGGAATTCTATT 58.131 29.630 5.23 0.00 0.00 1.73
4893 7062 9.143631 GATTCAAGTTTTGTGGGAATTCTATTG 57.856 33.333 5.23 0.00 0.00 1.90
4894 7063 6.991938 TCAAGTTTTGTGGGAATTCTATTGG 58.008 36.000 5.23 0.00 0.00 3.16
4895 7064 6.014669 TCAAGTTTTGTGGGAATTCTATTGGG 60.015 38.462 5.23 0.00 0.00 4.12
4963 7149 5.412594 CAGGTTAAGTTATGAAGCAGCTTGA 59.587 40.000 13.91 3.98 0.00 3.02
4966 7152 6.582672 GGTTAAGTTATGAAGCAGCTTGAAAC 59.417 38.462 13.91 13.18 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 0.534203 GCACCCCAACGAAAGAGACA 60.534 55.000 0.00 0.00 0.00 3.41
143 144 3.680786 CTCGACACCACCTCGCCA 61.681 66.667 0.00 0.00 0.00 5.69
146 147 1.524863 AAGACCTCGACACCACCTCG 61.525 60.000 0.00 0.00 0.00 4.63
187 188 4.373116 CACCGCGCTACCACCACT 62.373 66.667 5.56 0.00 0.00 4.00
234 235 4.388499 ACGACCATGGTGACCGGC 62.388 66.667 25.52 5.40 0.00 6.13
339 341 2.508439 GAACGATCTTCGCCGCCA 60.508 61.111 0.00 0.00 45.12 5.69
441 443 0.968901 AAGGATACGACACCGGAGCA 60.969 55.000 9.46 0.00 36.60 4.26
442 444 0.175073 AAAGGATACGACACCGGAGC 59.825 55.000 9.46 0.00 46.39 4.70
443 445 1.749634 AGAAAGGATACGACACCGGAG 59.250 52.381 9.46 1.26 46.39 4.63
444 446 1.475280 CAGAAAGGATACGACACCGGA 59.525 52.381 9.46 0.00 46.39 5.14
445 447 1.475280 TCAGAAAGGATACGACACCGG 59.525 52.381 0.00 0.00 46.39 5.28
446 448 2.933495 TCAGAAAGGATACGACACCG 57.067 50.000 0.00 0.00 46.39 4.94
447 449 5.175859 TCAATTCAGAAAGGATACGACACC 58.824 41.667 0.00 0.00 46.39 4.16
448 450 6.018669 GGATCAATTCAGAAAGGATACGACAC 60.019 42.308 0.00 0.00 46.39 3.67
449 451 6.049149 GGATCAATTCAGAAAGGATACGACA 58.951 40.000 0.00 0.00 46.39 4.35
450 452 6.284459 AGGATCAATTCAGAAAGGATACGAC 58.716 40.000 0.00 0.00 46.39 4.34
451 453 6.485830 AGGATCAATTCAGAAAGGATACGA 57.514 37.500 0.00 0.00 46.39 3.43
452 454 6.017605 CCAAGGATCAATTCAGAAAGGATACG 60.018 42.308 0.00 0.00 46.39 3.06
453 455 7.056635 TCCAAGGATCAATTCAGAAAGGATAC 58.943 38.462 0.00 2.65 0.00 2.24
454 456 7.211897 TCCAAGGATCAATTCAGAAAGGATA 57.788 36.000 0.00 0.00 0.00 2.59
455 457 6.083487 TCCAAGGATCAATTCAGAAAGGAT 57.917 37.500 0.00 0.70 0.00 3.24
456 458 5.519183 TCCAAGGATCAATTCAGAAAGGA 57.481 39.130 0.00 0.00 0.00 3.36
469 471 0.179045 CACCACCCGATCCAAGGATC 60.179 60.000 17.30 17.30 45.42 3.36
470 472 1.635817 CCACCACCCGATCCAAGGAT 61.636 60.000 0.16 0.16 37.59 3.24
471 473 2.297895 CCACCACCCGATCCAAGGA 61.298 63.158 0.00 0.00 0.00 3.36
472 474 2.272146 CCACCACCCGATCCAAGG 59.728 66.667 0.00 0.00 0.00 3.61
473 475 2.438434 GCCACCACCCGATCCAAG 60.438 66.667 0.00 0.00 0.00 3.61
474 476 4.402528 CGCCACCACCCGATCCAA 62.403 66.667 0.00 0.00 0.00 3.53
491 493 1.226888 GATACGACACCGGAGCACC 60.227 63.158 9.46 0.00 40.78 5.01
492 494 1.226888 GGATACGACACCGGAGCAC 60.227 63.158 9.46 0.00 36.60 4.40
493 495 0.968901 AAGGATACGACACCGGAGCA 60.969 55.000 9.46 0.00 36.60 4.26
513 515 1.667830 CAAAGGCGGCGTCTTCAGA 60.668 57.895 28.30 0.00 0.00 3.27
530 532 1.203758 ACATGACGAACCATACGCTCA 59.796 47.619 0.00 0.00 0.00 4.26
549 551 2.482142 CCCCGAAGAGATGAAGCTACAC 60.482 54.545 0.00 0.00 0.00 2.90
605 607 2.050144 CCCAGGACAGCATACATAGGT 58.950 52.381 0.00 0.00 0.00 3.08
615 617 2.980233 GCACACACCCAGGACAGC 60.980 66.667 0.00 0.00 0.00 4.40
641 643 1.120184 AAACACATGCCATGCCACCA 61.120 50.000 4.17 0.00 0.00 4.17
648 650 2.170166 CCCAGTACAAACACATGCCAT 58.830 47.619 0.00 0.00 0.00 4.40
653 655 2.622942 CAAGCACCCAGTACAAACACAT 59.377 45.455 0.00 0.00 0.00 3.21
678 680 8.585018 GCCCTGCTTTATATATAAAACACCAAT 58.415 33.333 16.69 0.00 32.39 3.16
685 687 7.590279 GCTTTCGCCCTGCTTTATATATAAAA 58.410 34.615 16.69 4.84 32.39 1.52
722 724 4.049546 ACAAACTGCAGAGTACACGTAA 57.950 40.909 23.35 0.00 0.00 3.18
723 725 3.720949 ACAAACTGCAGAGTACACGTA 57.279 42.857 23.35 0.00 0.00 3.57
724 726 2.596904 ACAAACTGCAGAGTACACGT 57.403 45.000 23.35 4.35 0.00 4.49
725 727 3.944422 AAACAAACTGCAGAGTACACG 57.056 42.857 23.35 3.70 0.00 4.49
726 728 3.791353 GCAAAACAAACTGCAGAGTACAC 59.209 43.478 23.35 3.51 38.48 2.90
727 729 3.694072 AGCAAAACAAACTGCAGAGTACA 59.306 39.130 23.35 0.00 41.17 2.90
728 730 4.037690 CAGCAAAACAAACTGCAGAGTAC 58.962 43.478 23.35 6.75 41.17 2.73
729 731 3.066621 CCAGCAAAACAAACTGCAGAGTA 59.933 43.478 23.35 0.00 41.17 2.59
730 732 2.159198 CCAGCAAAACAAACTGCAGAGT 60.159 45.455 23.35 12.91 41.17 3.24
731 733 2.466846 CCAGCAAAACAAACTGCAGAG 58.533 47.619 23.35 12.22 41.17 3.35
732 734 1.471327 GCCAGCAAAACAAACTGCAGA 60.471 47.619 23.35 0.00 41.17 4.26
733 735 0.932399 GCCAGCAAAACAAACTGCAG 59.068 50.000 13.48 13.48 41.17 4.41
734 736 0.248565 TGCCAGCAAAACAAACTGCA 59.751 45.000 0.00 0.00 41.17 4.41
735 737 1.585297 ATGCCAGCAAAACAAACTGC 58.415 45.000 0.00 0.00 38.91 4.40
736 738 7.413219 CCATTAATATGCCAGCAAAACAAACTG 60.413 37.037 0.00 0.00 0.00 3.16
737 739 6.594937 CCATTAATATGCCAGCAAAACAAACT 59.405 34.615 0.00 0.00 0.00 2.66
738 740 6.593382 TCCATTAATATGCCAGCAAAACAAAC 59.407 34.615 0.00 0.00 0.00 2.93
739 741 6.705302 TCCATTAATATGCCAGCAAAACAAA 58.295 32.000 0.00 0.00 0.00 2.83
740 742 6.291648 TCCATTAATATGCCAGCAAAACAA 57.708 33.333 0.00 0.00 0.00 2.83
741 743 5.929058 TCCATTAATATGCCAGCAAAACA 57.071 34.783 0.00 0.00 0.00 2.83
742 744 5.231991 CGTTCCATTAATATGCCAGCAAAAC 59.768 40.000 0.00 0.00 0.00 2.43
743 745 5.126222 TCGTTCCATTAATATGCCAGCAAAA 59.874 36.000 0.00 0.00 0.00 2.44
744 746 4.642437 TCGTTCCATTAATATGCCAGCAAA 59.358 37.500 0.00 0.00 0.00 3.68
745 747 4.203226 TCGTTCCATTAATATGCCAGCAA 58.797 39.130 0.00 0.00 0.00 3.91
746 748 3.814625 TCGTTCCATTAATATGCCAGCA 58.185 40.909 0.00 0.00 0.00 4.41
747 749 4.829064 TTCGTTCCATTAATATGCCAGC 57.171 40.909 0.00 0.00 0.00 4.85
748 750 7.651808 AGAAATTCGTTCCATTAATATGCCAG 58.348 34.615 0.00 0.00 36.86 4.85
749 751 7.581213 AGAAATTCGTTCCATTAATATGCCA 57.419 32.000 0.00 0.00 36.86 4.92
771 773 6.433847 AATATGACCAACGGATCCATAAGA 57.566 37.500 13.41 0.00 0.00 2.10
822 824 8.181573 TCAACCAATCTCTCGTATTAAATTTGC 58.818 33.333 0.00 0.00 0.00 3.68
826 828 9.449719 ACTTTCAACCAATCTCTCGTATTAAAT 57.550 29.630 0.00 0.00 0.00 1.40
830 832 9.099454 GATTACTTTCAACCAATCTCTCGTATT 57.901 33.333 0.00 0.00 0.00 1.89
834 836 6.968131 TGATTACTTTCAACCAATCTCTCG 57.032 37.500 0.00 0.00 0.00 4.04
850 852 5.297547 TCGTGTTCAAGAAGCTTGATTACT 58.702 37.500 2.10 0.00 0.00 2.24
862 864 5.361427 TGTCAACCTAAATCGTGTTCAAGA 58.639 37.500 0.00 0.00 0.00 3.02
865 867 7.604545 TCAATATGTCAACCTAAATCGTGTTCA 59.395 33.333 0.00 0.00 0.00 3.18
868 870 7.552687 ACATCAATATGTCAACCTAAATCGTGT 59.447 33.333 0.00 0.00 42.92 4.49
870 872 8.397906 CAACATCAATATGTCAACCTAAATCGT 58.602 33.333 0.00 0.00 45.79 3.73
871 873 7.857389 CCAACATCAATATGTCAACCTAAATCG 59.143 37.037 0.00 0.00 45.79 3.34
872 874 7.649306 GCCAACATCAATATGTCAACCTAAATC 59.351 37.037 0.00 0.00 45.79 2.17
873 875 7.417797 GGCCAACATCAATATGTCAACCTAAAT 60.418 37.037 0.00 0.00 45.79 1.40
874 876 6.127479 GGCCAACATCAATATGTCAACCTAAA 60.127 38.462 0.00 0.00 45.79 1.85
876 878 4.887071 GGCCAACATCAATATGTCAACCTA 59.113 41.667 0.00 0.00 45.79 3.08
877 879 3.701040 GGCCAACATCAATATGTCAACCT 59.299 43.478 0.00 0.00 45.79 3.50
878 880 3.446873 TGGCCAACATCAATATGTCAACC 59.553 43.478 0.61 0.00 45.79 3.77
879 881 4.675510 CTGGCCAACATCAATATGTCAAC 58.324 43.478 7.01 0.00 45.79 3.18
880 882 3.130869 GCTGGCCAACATCAATATGTCAA 59.869 43.478 7.01 0.00 45.79 3.18
886 888 0.751277 CCGGCTGGCCAACATCAATA 60.751 55.000 7.01 0.00 35.37 1.90
963 978 1.871039 CGGTATCCATTAAACCTGGCG 59.129 52.381 0.00 0.00 33.56 5.69
1002 1017 2.015736 ACAGATCATCGTCCAACTGC 57.984 50.000 0.00 0.00 0.00 4.40
1005 1020 1.927174 CCGAACAGATCATCGTCCAAC 59.073 52.381 12.54 0.00 37.36 3.77
1015 1030 3.003897 ACGAGATAAGAGCCGAACAGATC 59.996 47.826 0.00 0.00 0.00 2.75
1024 1039 1.473434 CCAACCCACGAGATAAGAGCC 60.473 57.143 0.00 0.00 0.00 4.70
1028 1043 5.470098 CCAATATTCCAACCCACGAGATAAG 59.530 44.000 0.00 0.00 0.00 1.73
1034 1049 1.064314 CCCCAATATTCCAACCCACGA 60.064 52.381 0.00 0.00 0.00 4.35
1039 1054 1.691163 CCCCACCCCAATATTCCAACC 60.691 57.143 0.00 0.00 0.00 3.77
1073 1088 1.137086 GTCCTGATATGGCTCGTGTGT 59.863 52.381 0.00 0.00 0.00 3.72
1092 1107 1.617947 GGATTGTCTCCTCGGCCAGT 61.618 60.000 2.24 0.00 41.29 4.00
1093 1108 1.144936 GGATTGTCTCCTCGGCCAG 59.855 63.158 2.24 0.00 41.29 4.85
1129 1150 3.810941 TCCACCTTTATCACGTGTTTGAC 59.189 43.478 16.51 0.00 0.00 3.18
1288 1309 4.213694 CCCGTAGATGTAGTAGTGTAGCTG 59.786 50.000 0.00 0.00 0.00 4.24
1296 1317 3.564644 CACAGGACCCGTAGATGTAGTAG 59.435 52.174 0.00 0.00 0.00 2.57
1304 1325 0.040646 ACCATCACAGGACCCGTAGA 59.959 55.000 0.00 0.00 0.00 2.59
1361 1385 6.720309 TGTTTGATGATCTGAGGAACCATAA 58.280 36.000 0.00 0.00 0.00 1.90
1482 1509 3.448301 TGAGCCAATAAGAATTTGCCCAG 59.552 43.478 0.00 0.00 34.96 4.45
1509 1539 2.414994 AGGCATCATGAGAAGTGGTG 57.585 50.000 0.09 0.00 0.00 4.17
1621 1654 3.925379 TCGTGTTGAATATGTGCTCTGT 58.075 40.909 0.00 0.00 0.00 3.41
1693 1726 4.976116 CGCAAAGATCGTCATGACATAGTA 59.024 41.667 24.93 5.59 0.00 1.82
1700 1733 1.660607 GCTTCGCAAAGATCGTCATGA 59.339 47.619 0.00 0.00 34.14 3.07
1747 1780 1.012086 CAATGGTGGATGAGCTCGTG 58.988 55.000 14.59 0.00 0.00 4.35
1791 1824 8.538701 TCTTCTTCTTCTTCTATGAAGCTCATT 58.461 33.333 4.35 0.00 42.15 2.57
1798 1831 9.495572 GGTTTCTTCTTCTTCTTCTTCTATGAA 57.504 33.333 0.00 0.00 0.00 2.57
1801 1834 7.606073 GCTGGTTTCTTCTTCTTCTTCTTCTAT 59.394 37.037 0.00 0.00 0.00 1.98
1802 1835 6.931840 GCTGGTTTCTTCTTCTTCTTCTTCTA 59.068 38.462 0.00 0.00 0.00 2.10
1803 1836 5.762711 GCTGGTTTCTTCTTCTTCTTCTTCT 59.237 40.000 0.00 0.00 0.00 2.85
1850 1883 2.213499 CCCTTCCAAGTCGATGCATAC 58.787 52.381 0.00 0.00 0.00 2.39
1903 1936 1.734465 CGGAGAAAAAGGTAGCTGCAG 59.266 52.381 10.11 10.11 0.00 4.41
2253 2286 4.537135 AAGTGAGAGCATCCGAAGTTTA 57.463 40.909 0.00 0.00 33.66 2.01
2256 2289 3.357203 TCTAAGTGAGAGCATCCGAAGT 58.643 45.455 0.00 0.00 33.66 3.01
2430 2463 0.465460 TGCTCTTTTCGTTGGCCACT 60.465 50.000 3.88 0.00 0.00 4.00
2440 2473 6.071952 TCCAGGTGTATCAAATTGCTCTTTTC 60.072 38.462 0.00 0.00 0.00 2.29
2628 2661 9.528018 TCAAATATCTTTTGCGGGAAATATTTC 57.472 29.630 18.22 18.22 36.46 2.17
2634 2667 6.582677 TCTTCAAATATCTTTTGCGGGAAA 57.417 33.333 0.00 0.00 0.00 3.13
2664 2700 2.731976 GAGCTTCAACGACTGTAGTTGG 59.268 50.000 26.20 16.01 46.36 3.77
2857 2893 4.313020 AATCAAGCTCCTCCAAATCACT 57.687 40.909 0.00 0.00 0.00 3.41
2895 2931 1.140804 GTCGGCAGAGAGCTCCTTC 59.859 63.158 10.93 1.96 44.79 3.46
2944 2980 0.395312 GAAGGAACACCCACGAGGAA 59.605 55.000 0.00 0.00 39.89 3.36
2995 3031 2.904434 AGTAAAACACATCCGGGAGTCT 59.096 45.455 0.00 0.00 0.00 3.24
3084 3120 3.132289 CACGGAAGCTATGGAAGAACCTA 59.868 47.826 0.00 0.00 39.86 3.08
3116 3152 4.142138 ACCGTCCAGCTCTAACTAAATCTG 60.142 45.833 0.00 0.00 0.00 2.90
3117 3153 4.024670 ACCGTCCAGCTCTAACTAAATCT 58.975 43.478 0.00 0.00 0.00 2.40
3126 3162 1.695242 TGGAAAAACCGTCCAGCTCTA 59.305 47.619 0.00 0.00 40.33 2.43
3131 3167 4.218417 AGAATGATTGGAAAAACCGTCCAG 59.782 41.667 0.00 0.00 45.79 3.86
3196 3232 7.602265 GCAATCTAGGATACCTTCTTCATCTTC 59.398 40.741 0.00 0.00 34.61 2.87
3277 3319 6.074676 GCAATTATAATTTCCTCTGCAAAGCG 60.075 38.462 8.01 0.00 0.00 4.68
3296 3338 3.550820 ACTGTAATGGCCGATGCAATTA 58.449 40.909 0.00 0.00 39.42 1.40
3307 3349 2.092323 GTGAAGGGGAACTGTAATGGC 58.908 52.381 0.00 0.00 0.00 4.40
3355 3439 3.542648 CATCATGTGTCTCTTGCATCCT 58.457 45.455 0.00 0.00 0.00 3.24
3383 3467 3.928727 TCGTGACGTTTAGAAGACCAT 57.071 42.857 4.40 0.00 0.00 3.55
3549 4692 6.263344 CCTTTTGAGATTACAGACATGCATG 58.737 40.000 25.09 25.09 0.00 4.06
3922 5069 2.677228 CTTCACCATCCCCGGCTT 59.323 61.111 0.00 0.00 0.00 4.35
3956 5103 0.177604 CTAGAGCTTGCTCCACCAGG 59.822 60.000 17.78 0.00 0.00 4.45
4097 5267 4.201881 GCCGAGTAAAATCACATACCAACC 60.202 45.833 0.00 0.00 0.00 3.77
4118 5288 6.715347 AATGAACAAAGGGATAAGTATGCC 57.285 37.500 0.75 0.75 43.72 4.40
4143 5313 4.816925 GGAAGGTATTCTGTAATGAGTGGC 59.183 45.833 0.00 0.00 35.63 5.01
4208 5401 1.783284 TTCTATAATGCGGCGCTGAG 58.217 50.000 33.26 20.43 0.00 3.35
4223 5416 9.263446 ACTGTAACAAGGGATAACTGTATTCTA 57.737 33.333 0.00 0.00 0.00 2.10
4294 5488 0.617413 ATGGAAGCACCTGGAGACTG 59.383 55.000 0.00 0.00 39.86 3.51
4381 5888 1.064685 ACTGTTAATAGGGCAGGCACC 60.065 52.381 4.12 0.00 34.79 5.01
4493 6048 1.451207 TATGCACGTGGGTGGCATC 60.451 57.895 18.88 0.00 44.54 3.91
4568 6689 6.920817 ACGAGGGAAATTGGACTTTTATTTC 58.079 36.000 0.00 0.00 37.48 2.17
4590 6711 1.710013 AGTGGCAGTCGACAATAACG 58.290 50.000 19.50 0.00 0.00 3.18
4675 6797 6.483307 CCTTACACATACATCACCAACATAGG 59.517 42.308 0.00 0.00 0.00 2.57
4787 6954 3.619929 ACTTGTAGTCAAACACAACGTCC 59.380 43.478 0.00 0.00 32.87 4.79
4832 6999 8.421249 AATGGATCTTGACAAATAAAACCAGA 57.579 30.769 0.00 0.00 0.00 3.86
4935 7121 6.490040 AGCTGCTTCATAACTTAACCTGAAAA 59.510 34.615 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.