Multiple sequence alignment - TraesCS5B01G255500

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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 TraesCS5B01G255500 chr5B 100.000 3875 0 0 1 3875 438166328 438170202 0.000000e+00 7156.0
1 TraesCS5B01G255500 chr5B 93.609 266 14 3 592 855 67901916 67902180 1.010000e-105 394.0
2 TraesCS5B01G255500 chr5A 95.164 2688 107 14 845 3523 471903981 471906654 0.000000e+00 4222.0
3 TraesCS5B01G255500 chr5A 82.664 473 64 13 2 465 471903347 471903810 1.680000e-108 403.0
4 TraesCS5B01G255500 chr5A 87.879 66 6 2 504 569 644927140 644927077 4.150000e-10 76.8
5 TraesCS5B01G255500 chr5A 84.932 73 9 2 503 574 477438437 477438366 5.370000e-09 73.1
6 TraesCS5B01G255500 chr5D 95.874 2036 78 4 883 2916 369377676 369379707 0.000000e+00 3290.0
7 TraesCS5B01G255500 chr5D 93.981 731 37 2 2911 3640 369379896 369380620 0.000000e+00 1099.0
8 TraesCS5B01G255500 chr5D 93.644 236 15 0 3640 3875 369380865 369381100 1.710000e-93 353.0
9 TraesCS5B01G255500 chr5D 87.500 64 6 2 510 572 175300009 175299947 5.370000e-09 73.1
10 TraesCS5B01G255500 chr2D 80.590 881 116 28 2538 3379 2197417 2198281 2.540000e-176 628.0
11 TraesCS5B01G255500 chr2D 86.055 545 56 6 1071 1604 2196337 2196872 5.620000e-158 568.0
12 TraesCS5B01G255500 chr2D 83.183 333 50 3 1645 1971 2196874 2197206 2.260000e-77 300.0
13 TraesCS5B01G255500 chr2D 84.507 71 9 2 504 574 600154236 600154168 6.950000e-08 69.4
14 TraesCS5B01G255500 chr4A 94.318 264 14 1 594 856 688909657 688909920 1.680000e-108 403.0
15 TraesCS5B01G255500 chr4A 88.060 67 8 0 521 587 725702104 725702038 3.210000e-11 80.5
16 TraesCS5B01G255500 chr7A 94.253 261 13 2 595 854 252742476 252742735 7.800000e-107 398.0
17 TraesCS5B01G255500 chr6D 93.939 264 14 2 592 854 26353977 26354239 7.800000e-107 398.0
18 TraesCS5B01G255500 chr6D 84.286 70 9 2 504 572 2956114 2956182 2.500000e-07 67.6
19 TraesCS5B01G255500 chr6D 83.333 72 10 2 504 574 134289002 134289072 8.990000e-07 65.8
20 TraesCS5B01G255500 chr6D 83.333 72 10 2 504 574 134694180 134694250 8.990000e-07 65.8
21 TraesCS5B01G255500 chr2B 93.609 266 16 1 590 854 119319700 119319435 2.810000e-106 396.0
22 TraesCS5B01G255500 chr6B 92.701 274 18 2 583 855 153521303 153521575 1.010000e-105 394.0
23 TraesCS5B01G255500 chr1A 93.309 269 15 3 593 858 377423890 377423622 1.010000e-105 394.0
24 TraesCS5B01G255500 chr3D 92.620 271 18 2 585 854 603703159 603703428 4.690000e-104 388.0
25 TraesCS5B01G255500 chr3D 92.029 276 21 1 580 854 83428811 83428536 1.690000e-103 387.0
26 TraesCS5B01G255500 chr6A 83.333 72 10 2 504 574 175653613 175653683 8.990000e-07 65.8


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 TraesCS5B01G255500 chr5B 438166328 438170202 3874 False 7156.000000 7156 100.000000 1 3875 1 chr5B.!!$F2 3874
1 TraesCS5B01G255500 chr5A 471903347 471906654 3307 False 2312.500000 4222 88.914000 2 3523 2 chr5A.!!$F1 3521
2 TraesCS5B01G255500 chr5D 369377676 369381100 3424 False 1580.666667 3290 94.499667 883 3875 3 chr5D.!!$F1 2992
3 TraesCS5B01G255500 chr2D 2196337 2198281 1944 False 498.666667 628 83.276000 1071 3379 3 chr2D.!!$F1 2308

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
939 957 0.102481 CTTGTCATACGGACCCCTCG 59.898 60.0 0.0 0.0 46.38 4.63 F
940 958 0.612732 TTGTCATACGGACCCCTCGT 60.613 55.0 0.0 0.0 46.38 4.18 F
2380 2418 0.685097 TAGTGGTCCACCTGTCTTGC 59.315 55.0 18.8 0.0 34.49 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2036 0.606673 AAACTGCTTCCTTCCCGAGC 60.607 55.000 0.0 0.0 36.95 5.03 R
2645 2683 1.907255 GGTACTGTAGGTTTGCCTCCT 59.093 52.381 0.0 0.0 45.64 3.69 R
3350 3624 0.971386 AGCAAAATCACCCAGCCTTG 59.029 50.000 0.0 0.0 0.00 3.61 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.052519 CGGCGGTTACTTGGTTGT 57.947 55.556 0.00 0.00 0.00 3.32
22 23 1.677052 GCGGTTACTTGGTTGTTTCCA 59.323 47.619 0.00 0.00 35.49 3.53
26 27 0.948678 TACTTGGTTGTTTCCAGCGC 59.051 50.000 0.00 0.00 38.80 5.92
33 34 2.813908 GTTTCCAGCGCCGTCGAT 60.814 61.111 2.29 0.00 38.10 3.59
35 36 4.847516 TTCCAGCGCCGTCGATCG 62.848 66.667 9.36 9.36 38.10 3.69
40 41 2.023741 GCGCCGTCGATCGACTAA 59.976 61.111 37.12 8.42 42.54 2.24
45 46 0.381089 CCGTCGATCGACTAAGGCTT 59.619 55.000 37.12 4.58 42.54 4.35
46 47 1.467875 CGTCGATCGACTAAGGCTTG 58.532 55.000 37.12 20.38 42.54 4.01
47 48 1.201343 GTCGATCGACTAAGGCTTGC 58.799 55.000 34.97 9.87 41.57 4.01
53 54 3.052455 TCGACTAAGGCTTGCAAATGA 57.948 42.857 10.69 0.00 0.00 2.57
54 55 2.742053 TCGACTAAGGCTTGCAAATGAC 59.258 45.455 10.69 0.00 0.00 3.06
60 61 1.508088 GCTTGCAAATGACCCTCCG 59.492 57.895 0.00 0.00 0.00 4.63
62 63 1.755179 CTTGCAAATGACCCTCCGAT 58.245 50.000 0.00 0.00 0.00 4.18
71 72 0.181350 GACCCTCCGATGCCATCTTT 59.819 55.000 2.75 0.00 0.00 2.52
112 113 1.004918 AGCGAAAAGGGACCTCACG 60.005 57.895 0.00 0.00 0.00 4.35
114 115 1.289800 GCGAAAAGGGACCTCACGAC 61.290 60.000 13.09 4.39 0.00 4.34
118 119 1.843368 AAAGGGACCTCACGACGATA 58.157 50.000 0.00 0.00 0.00 2.92
129 130 0.105593 ACGACGATAGGACGGAGCTA 59.894 55.000 0.00 0.00 42.34 3.32
130 131 0.512085 CGACGATAGGACGGAGCTAC 59.488 60.000 0.00 0.00 43.77 3.58
138 139 4.570663 ACGGAGCTACGCGATGGC 62.571 66.667 20.78 13.91 37.37 4.40
165 166 2.680577 ACGGGTAGTGAAAACGATGAC 58.319 47.619 0.00 0.00 0.00 3.06
171 172 3.594603 AGTGAAAACGATGACTCCGAT 57.405 42.857 0.00 0.00 0.00 4.18
172 173 3.254060 AGTGAAAACGATGACTCCGATG 58.746 45.455 0.00 0.00 0.00 3.84
174 175 0.999406 AAAACGATGACTCCGATGCG 59.001 50.000 0.00 0.00 0.00 4.73
200 201 0.749649 TGCGGCAGACCAAATTTGTT 59.250 45.000 16.73 2.17 34.57 2.83
245 246 3.869623 CCTGAGGGGTGAGATGTTG 57.130 57.895 0.00 0.00 0.00 3.33
259 260 6.152379 GTGAGATGTTGGGATTGAAAAGTTC 58.848 40.000 0.00 0.00 0.00 3.01
262 263 5.598005 AGATGTTGGGATTGAAAAGTTCACA 59.402 36.000 0.00 0.00 39.87 3.58
265 266 6.648192 TGTTGGGATTGAAAAGTTCACATTT 58.352 32.000 0.00 0.00 39.87 2.32
266 267 7.786030 TGTTGGGATTGAAAAGTTCACATTTA 58.214 30.769 0.00 0.00 39.87 1.40
304 310 4.324331 GGGTGGACTAGAAGGTGCTTAATT 60.324 45.833 0.00 0.00 0.00 1.40
305 311 4.876679 GGTGGACTAGAAGGTGCTTAATTC 59.123 45.833 0.00 0.00 0.00 2.17
308 314 6.314152 GTGGACTAGAAGGTGCTTAATTCTTC 59.686 42.308 0.00 0.00 35.09 2.87
309 315 6.013725 TGGACTAGAAGGTGCTTAATTCTTCA 60.014 38.462 0.00 0.00 38.35 3.02
310 316 7.051000 GGACTAGAAGGTGCTTAATTCTTCAT 58.949 38.462 0.00 0.00 38.35 2.57
312 318 8.950208 ACTAGAAGGTGCTTAATTCTTCATAC 57.050 34.615 0.00 0.00 38.35 2.39
313 319 8.763601 ACTAGAAGGTGCTTAATTCTTCATACT 58.236 33.333 0.00 0.00 38.35 2.12
355 361 5.796424 AATCTGATTTATGTGGAATGGGC 57.204 39.130 0.00 0.00 0.00 5.36
356 362 4.524802 TCTGATTTATGTGGAATGGGCT 57.475 40.909 0.00 0.00 0.00 5.19
357 363 5.645056 TCTGATTTATGTGGAATGGGCTA 57.355 39.130 0.00 0.00 0.00 3.93
385 391 2.236395 GGCCCTTGCTACTCTCTTAACA 59.764 50.000 0.00 0.00 37.74 2.41
387 393 4.518249 GCCCTTGCTACTCTCTTAACAAT 58.482 43.478 0.00 0.00 33.53 2.71
415 421 2.795175 TCGATCGAACTAGCCATTCC 57.205 50.000 16.99 0.00 0.00 3.01
416 422 1.340248 TCGATCGAACTAGCCATTCCC 59.660 52.381 16.99 0.00 0.00 3.97
419 425 3.741388 CGATCGAACTAGCCATTCCCTTT 60.741 47.826 10.26 0.00 0.00 3.11
420 426 3.713826 TCGAACTAGCCATTCCCTTTT 57.286 42.857 0.00 0.00 0.00 2.27
422 428 5.367945 TCGAACTAGCCATTCCCTTTTAT 57.632 39.130 0.00 0.00 0.00 1.40
424 430 4.261197 CGAACTAGCCATTCCCTTTTATGC 60.261 45.833 0.00 0.00 0.00 3.14
428 434 3.566351 AGCCATTCCCTTTTATGCTACC 58.434 45.455 0.00 0.00 0.00 3.18
429 435 3.205282 AGCCATTCCCTTTTATGCTACCT 59.795 43.478 0.00 0.00 0.00 3.08
432 438 3.553828 TTCCCTTTTATGCTACCTCCG 57.446 47.619 0.00 0.00 0.00 4.63
433 439 2.474112 TCCCTTTTATGCTACCTCCGT 58.526 47.619 0.00 0.00 0.00 4.69
434 440 2.841881 TCCCTTTTATGCTACCTCCGTT 59.158 45.455 0.00 0.00 0.00 4.44
435 441 3.118519 TCCCTTTTATGCTACCTCCGTTC 60.119 47.826 0.00 0.00 0.00 3.95
436 442 3.370103 CCCTTTTATGCTACCTCCGTTCA 60.370 47.826 0.00 0.00 0.00 3.18
442 452 7.925043 TTTATGCTACCTCCGTTCAAAATAA 57.075 32.000 0.00 0.00 0.00 1.40
444 454 6.827586 ATGCTACCTCCGTTCAAAATAAAA 57.172 33.333 0.00 0.00 0.00 1.52
445 455 6.827586 TGCTACCTCCGTTCAAAATAAAAT 57.172 33.333 0.00 0.00 0.00 1.82
446 456 7.222000 TGCTACCTCCGTTCAAAATAAAATT 57.778 32.000 0.00 0.00 0.00 1.82
449 459 6.779115 ACCTCCGTTCAAAATAAAATTTGC 57.221 33.333 0.00 0.00 39.57 3.68
453 463 8.983724 CCTCCGTTCAAAATAAAATTTGCTTTA 58.016 29.630 0.00 0.00 39.57 1.85
541 551 9.651718 CTAGAACTAAAATGAGTGAACAAACAC 57.348 33.333 0.00 0.00 40.60 3.32
549 559 9.651913 AAAATGAGTGAACAAACACACTAAAAT 57.348 25.926 0.00 0.00 45.54 1.82
603 616 6.786967 TTAACATCTTGTAGTACTCCCTCC 57.213 41.667 0.00 0.00 0.00 4.30
604 617 3.288964 ACATCTTGTAGTACTCCCTCCG 58.711 50.000 0.00 0.00 0.00 4.63
605 618 3.288964 CATCTTGTAGTACTCCCTCCGT 58.711 50.000 0.00 0.00 0.00 4.69
606 619 3.446442 TCTTGTAGTACTCCCTCCGTT 57.554 47.619 0.00 0.00 0.00 4.44
607 620 3.771216 TCTTGTAGTACTCCCTCCGTTT 58.229 45.455 0.00 0.00 0.00 3.60
608 621 3.760684 TCTTGTAGTACTCCCTCCGTTTC 59.239 47.826 0.00 0.00 0.00 2.78
609 622 3.446442 TGTAGTACTCCCTCCGTTTCT 57.554 47.619 0.00 0.00 0.00 2.52
610 623 3.771216 TGTAGTACTCCCTCCGTTTCTT 58.229 45.455 0.00 0.00 0.00 2.52
611 624 4.154942 TGTAGTACTCCCTCCGTTTCTTT 58.845 43.478 0.00 0.00 0.00 2.52
612 625 4.590222 TGTAGTACTCCCTCCGTTTCTTTT 59.410 41.667 0.00 0.00 0.00 2.27
613 626 4.701651 AGTACTCCCTCCGTTTCTTTTT 57.298 40.909 0.00 0.00 0.00 1.94
614 627 5.813513 AGTACTCCCTCCGTTTCTTTTTA 57.186 39.130 0.00 0.00 0.00 1.52
615 628 5.791666 AGTACTCCCTCCGTTTCTTTTTAG 58.208 41.667 0.00 0.00 0.00 1.85
616 629 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
617 630 4.639334 ACTCCCTCCGTTTCTTTTTAGTC 58.361 43.478 0.00 0.00 0.00 2.59
618 631 4.347292 ACTCCCTCCGTTTCTTTTTAGTCT 59.653 41.667 0.00 0.00 0.00 3.24
619 632 4.638304 TCCCTCCGTTTCTTTTTAGTCTG 58.362 43.478 0.00 0.00 0.00 3.51
620 633 3.188667 CCCTCCGTTTCTTTTTAGTCTGC 59.811 47.826 0.00 0.00 0.00 4.26
621 634 4.065789 CCTCCGTTTCTTTTTAGTCTGCT 58.934 43.478 0.00 0.00 0.00 4.24
622 635 5.235516 CCTCCGTTTCTTTTTAGTCTGCTA 58.764 41.667 0.00 0.00 0.00 3.49
623 636 5.875359 CCTCCGTTTCTTTTTAGTCTGCTAT 59.125 40.000 0.00 0.00 0.00 2.97
624 637 7.039882 CCTCCGTTTCTTTTTAGTCTGCTATA 58.960 38.462 0.00 0.00 0.00 1.31
625 638 7.548075 CCTCCGTTTCTTTTTAGTCTGCTATAA 59.452 37.037 0.00 0.00 0.00 0.98
626 639 8.475331 TCCGTTTCTTTTTAGTCTGCTATAAG 57.525 34.615 0.00 0.00 0.00 1.73
627 640 8.308931 TCCGTTTCTTTTTAGTCTGCTATAAGA 58.691 33.333 0.00 0.00 31.86 2.10
628 641 9.099454 CCGTTTCTTTTTAGTCTGCTATAAGAT 57.901 33.333 0.00 0.00 32.87 2.40
633 646 9.959721 TCTTTTTAGTCTGCTATAAGATTTGGT 57.040 29.630 0.00 0.00 30.28 3.67
635 648 9.733556 TTTTTAGTCTGCTATAAGATTTGGTCA 57.266 29.630 0.00 0.00 0.00 4.02
636 649 9.733556 TTTTAGTCTGCTATAAGATTTGGTCAA 57.266 29.630 0.00 0.00 0.00 3.18
637 650 9.733556 TTTAGTCTGCTATAAGATTTGGTCAAA 57.266 29.630 0.00 0.00 34.46 2.69
638 651 7.856145 AGTCTGCTATAAGATTTGGTCAAAG 57.144 36.000 2.55 0.00 33.32 2.77
639 652 7.398024 AGTCTGCTATAAGATTTGGTCAAAGT 58.602 34.615 2.55 0.00 33.32 2.66
640 653 7.550906 AGTCTGCTATAAGATTTGGTCAAAGTC 59.449 37.037 2.55 1.51 33.32 3.01
641 654 7.334421 GTCTGCTATAAGATTTGGTCAAAGTCA 59.666 37.037 2.55 0.00 33.32 3.41
642 655 7.882791 TCTGCTATAAGATTTGGTCAAAGTCAA 59.117 33.333 2.55 0.00 33.32 3.18
643 656 8.402798 TGCTATAAGATTTGGTCAAAGTCAAA 57.597 30.769 2.55 0.00 37.29 2.69
644 657 8.296713 TGCTATAAGATTTGGTCAAAGTCAAAC 58.703 33.333 2.55 0.00 35.97 2.93
645 658 8.515414 GCTATAAGATTTGGTCAAAGTCAAACT 58.485 33.333 2.55 0.00 35.97 2.66
648 661 7.639113 AAGATTTGGTCAAAGTCAAACTACA 57.361 32.000 2.55 0.00 35.97 2.74
649 662 7.027778 AGATTTGGTCAAAGTCAAACTACAC 57.972 36.000 2.55 0.00 35.97 2.90
650 663 6.601613 AGATTTGGTCAAAGTCAAACTACACA 59.398 34.615 2.55 0.00 35.97 3.72
651 664 6.576662 TTTGGTCAAAGTCAAACTACACAA 57.423 33.333 0.00 0.00 0.00 3.33
652 665 6.576662 TTGGTCAAAGTCAAACTACACAAA 57.423 33.333 0.00 0.00 0.00 2.83
653 666 6.576662 TGGTCAAAGTCAAACTACACAAAA 57.423 33.333 0.00 0.00 0.00 2.44
654 667 7.164230 TGGTCAAAGTCAAACTACACAAAAT 57.836 32.000 0.00 0.00 0.00 1.82
655 668 7.607250 TGGTCAAAGTCAAACTACACAAAATT 58.393 30.769 0.00 0.00 0.00 1.82
656 669 8.091449 TGGTCAAAGTCAAACTACACAAAATTT 58.909 29.630 0.00 0.00 0.00 1.82
657 670 8.379902 GGTCAAAGTCAAACTACACAAAATTTG 58.620 33.333 3.89 3.89 34.11 2.32
658 671 9.134734 GTCAAAGTCAAACTACACAAAATTTGA 57.865 29.630 13.19 0.00 38.42 2.69
738 751 9.669353 GAAAATACGTTTCATGATGCATCTAAT 57.331 29.630 26.32 10.77 44.42 1.73
803 816 3.477530 AGTTAGTCAAACTCAACCAGGC 58.522 45.455 0.00 0.00 45.64 4.85
804 817 3.136626 AGTTAGTCAAACTCAACCAGGCT 59.863 43.478 0.00 0.00 45.64 4.58
805 818 2.736670 AGTCAAACTCAACCAGGCTT 57.263 45.000 0.00 0.00 0.00 4.35
806 819 2.301346 AGTCAAACTCAACCAGGCTTG 58.699 47.619 0.00 0.00 0.00 4.01
807 820 2.092429 AGTCAAACTCAACCAGGCTTGA 60.092 45.455 0.00 4.87 0.00 3.02
808 821 2.033424 GTCAAACTCAACCAGGCTTGAC 59.967 50.000 0.00 0.00 39.75 3.18
809 822 2.092429 TCAAACTCAACCAGGCTTGACT 60.092 45.455 0.00 0.00 0.00 3.41
810 823 2.689983 CAAACTCAACCAGGCTTGACTT 59.310 45.455 0.00 0.00 0.00 3.01
811 824 2.736670 ACTCAACCAGGCTTGACTTT 57.263 45.000 0.00 0.00 0.00 2.66
812 825 2.301346 ACTCAACCAGGCTTGACTTTG 58.699 47.619 0.00 0.00 0.00 2.77
813 826 2.092429 ACTCAACCAGGCTTGACTTTGA 60.092 45.455 0.00 2.60 0.00 2.69
814 827 2.291741 CTCAACCAGGCTTGACTTTGAC 59.708 50.000 0.00 0.00 0.00 3.18
815 828 1.338020 CAACCAGGCTTGACTTTGACC 59.662 52.381 0.00 0.00 0.00 4.02
816 829 0.550914 ACCAGGCTTGACTTTGACCA 59.449 50.000 0.00 0.00 0.00 4.02
817 830 1.064017 ACCAGGCTTGACTTTGACCAA 60.064 47.619 0.00 0.00 0.00 3.67
818 831 2.031120 CCAGGCTTGACTTTGACCAAA 58.969 47.619 0.00 0.00 0.00 3.28
819 832 2.223805 CCAGGCTTGACTTTGACCAAAC 60.224 50.000 0.00 0.00 0.00 2.93
820 833 2.031870 AGGCTTGACTTTGACCAAACC 58.968 47.619 0.00 0.00 0.00 3.27
821 834 2.031870 GGCTTGACTTTGACCAAACCT 58.968 47.619 0.00 0.00 0.00 3.50
822 835 2.430694 GGCTTGACTTTGACCAAACCTT 59.569 45.455 0.00 0.00 0.00 3.50
823 836 3.634910 GGCTTGACTTTGACCAAACCTTA 59.365 43.478 0.00 0.00 0.00 2.69
824 837 4.280929 GGCTTGACTTTGACCAAACCTTAT 59.719 41.667 0.00 0.00 0.00 1.73
825 838 5.475564 GGCTTGACTTTGACCAAACCTTATA 59.524 40.000 0.00 0.00 0.00 0.98
826 839 6.152831 GGCTTGACTTTGACCAAACCTTATAT 59.847 38.462 0.00 0.00 0.00 0.86
827 840 7.029563 GCTTGACTTTGACCAAACCTTATATG 58.970 38.462 0.00 0.00 0.00 1.78
828 841 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
829 842 5.123186 TGACTTTGACCAAACCTTATATGCG 59.877 40.000 0.00 0.00 0.00 4.73
830 843 4.398044 ACTTTGACCAAACCTTATATGCGG 59.602 41.667 0.00 0.00 0.00 5.69
831 844 3.916359 TGACCAAACCTTATATGCGGA 57.084 42.857 0.00 0.00 0.00 5.54
832 845 3.804036 TGACCAAACCTTATATGCGGAG 58.196 45.455 0.00 0.00 0.00 4.63
833 846 3.199071 TGACCAAACCTTATATGCGGAGT 59.801 43.478 0.00 0.00 0.00 3.85
834 847 4.406326 TGACCAAACCTTATATGCGGAGTA 59.594 41.667 0.00 0.00 0.00 2.59
835 848 5.104859 TGACCAAACCTTATATGCGGAGTAA 60.105 40.000 0.00 0.00 0.00 2.24
836 849 5.747342 ACCAAACCTTATATGCGGAGTAAA 58.253 37.500 0.00 0.00 0.00 2.01
837 850 6.181908 ACCAAACCTTATATGCGGAGTAAAA 58.818 36.000 0.00 0.00 0.00 1.52
838 851 6.660094 ACCAAACCTTATATGCGGAGTAAAAA 59.340 34.615 0.00 0.00 0.00 1.94
867 880 3.871594 GAGGGAGTATTTGTGAACGGATG 59.128 47.826 0.00 0.00 0.00 3.51
870 883 3.871594 GGAGTATTTGTGAACGGATGGAG 59.128 47.826 0.00 0.00 0.00 3.86
880 893 5.929992 TGTGAACGGATGGAGTAGTAAAAAG 59.070 40.000 0.00 0.00 0.00 2.27
881 894 5.350640 GTGAACGGATGGAGTAGTAAAAAGG 59.649 44.000 0.00 0.00 0.00 3.11
882 895 5.246656 TGAACGGATGGAGTAGTAAAAAGGA 59.753 40.000 0.00 0.00 0.00 3.36
883 896 5.750352 ACGGATGGAGTAGTAAAAAGGAA 57.250 39.130 0.00 0.00 0.00 3.36
885 898 5.936372 ACGGATGGAGTAGTAAAAAGGAAAC 59.064 40.000 0.00 0.00 0.00 2.78
887 900 6.092259 CGGATGGAGTAGTAAAAAGGAAACTG 59.908 42.308 0.00 0.00 42.68 3.16
888 901 7.166167 GGATGGAGTAGTAAAAAGGAAACTGA 58.834 38.462 0.00 0.00 42.68 3.41
889 902 7.334671 GGATGGAGTAGTAAAAAGGAAACTGAG 59.665 40.741 0.00 0.00 42.68 3.35
891 904 7.798071 TGGAGTAGTAAAAAGGAAACTGAGAA 58.202 34.615 0.00 0.00 42.68 2.87
892 905 8.437575 TGGAGTAGTAAAAAGGAAACTGAGAAT 58.562 33.333 0.00 0.00 42.68 2.40
936 954 1.276989 TGTTCTTGTCATACGGACCCC 59.723 52.381 0.00 0.00 46.38 4.95
937 955 1.553704 GTTCTTGTCATACGGACCCCT 59.446 52.381 0.00 0.00 46.38 4.79
938 956 1.481871 TCTTGTCATACGGACCCCTC 58.518 55.000 0.00 0.00 46.38 4.30
939 957 0.102481 CTTGTCATACGGACCCCTCG 59.898 60.000 0.00 0.00 46.38 4.63
940 958 0.612732 TTGTCATACGGACCCCTCGT 60.613 55.000 0.00 0.00 46.38 4.18
981 1003 2.241880 AAAACGTCGGACACCTGCG 61.242 57.895 9.10 0.00 0.00 5.18
1049 1071 2.211806 CTACCTTCTCCTCTACCGACG 58.788 57.143 0.00 0.00 0.00 5.12
1330 1359 2.776072 CGCGGAATGTGTTCGACC 59.224 61.111 0.00 0.00 35.10 4.79
1400 1429 2.742372 GCAGAACGACATGCCGGT 60.742 61.111 6.33 0.00 36.41 5.28
1705 1738 1.912043 CAAGGAAGGGTGATGGAGAGT 59.088 52.381 0.00 0.00 0.00 3.24
1998 2036 3.119065 TCACAGCATTTGCACAATATGGG 60.119 43.478 5.20 0.00 45.16 4.00
2016 2054 1.003233 GCTCGGGAAGGAAGCAGTT 60.003 57.895 0.00 0.00 0.00 3.16
2040 2078 4.080129 TCCCATTTTGAGGAGATGAGGAAG 60.080 45.833 0.00 0.00 0.00 3.46
2160 2198 5.988310 TGAAGGAGTACGATTTAGAACCA 57.012 39.130 0.00 0.00 0.00 3.67
2340 2378 4.036567 GCAATTTGCAGCTGATCATGTA 57.963 40.909 20.43 0.00 44.26 2.29
2377 2415 2.623418 TGATAGTGGTCCACCTGTCT 57.377 50.000 18.80 2.01 34.49 3.41
2380 2418 0.685097 TAGTGGTCCACCTGTCTTGC 59.315 55.000 18.80 0.00 34.49 4.01
2403 2441 7.449247 TGCTGTATAACATATATGCTTCCACA 58.551 34.615 12.79 9.40 0.00 4.17
2435 2473 1.906253 CTGCAGCCAGAGTGAGGAT 59.094 57.895 0.00 0.00 41.77 3.24
2645 2683 6.475596 TCTGCATGTAGATGATCAAGAGAA 57.524 37.500 9.69 0.00 0.00 2.87
2736 2774 4.142271 GGGGCAACAATTCGTATCATGAAA 60.142 41.667 0.00 0.00 39.74 2.69
2900 2938 4.760878 TGCCAAGATGTAGTGCGTTTATA 58.239 39.130 0.00 0.00 0.00 0.98
2918 3150 6.262273 CGTTTATAAATCTACAAGGCCATGGT 59.738 38.462 14.67 6.05 0.00 3.55
2971 3203 6.773976 TTTATGGACTGATAAAGGGCAAAG 57.226 37.500 0.00 0.00 0.00 2.77
2973 3205 4.112634 TGGACTGATAAAGGGCAAAGTT 57.887 40.909 0.00 0.00 0.00 2.66
3070 3329 2.941720 GGATGAACTCCAGAAGACATGC 59.058 50.000 0.00 0.00 44.26 4.06
3071 3330 3.603532 GATGAACTCCAGAAGACATGCA 58.396 45.455 0.00 0.00 0.00 3.96
3083 3342 4.458295 AGAAGACATGCACTTTCATCCTTG 59.542 41.667 7.09 0.00 0.00 3.61
3273 3547 2.348362 TGCAAACGAATGATAGTCTGCG 59.652 45.455 0.00 0.00 0.00 5.18
3281 3555 4.636249 GAATGATAGTCTGCGGATTTCCT 58.364 43.478 0.00 0.00 0.00 3.36
3283 3557 2.103094 TGATAGTCTGCGGATTTCCTGG 59.897 50.000 0.00 0.00 0.00 4.45
3350 3624 9.472361 TTTAGATATCCGTAATTCTACAAGTGC 57.528 33.333 0.00 0.00 0.00 4.40
3385 3659 6.545298 TGATTTTGCTACATATGCATGGTGTA 59.455 34.615 19.41 19.41 40.34 2.90
3394 3668 6.121590 ACATATGCATGGTGTACATTTCAGA 58.878 36.000 10.16 0.00 37.84 3.27
3460 3734 3.582208 TGATTTTGCTAACCATTGCCCTT 59.418 39.130 0.00 0.00 0.00 3.95
3578 3852 1.601171 CAGAAGCCTCTGGGACTGG 59.399 63.158 4.26 0.00 44.72 4.00
3579 3853 1.614824 AGAAGCCTCTGGGACTGGG 60.615 63.158 0.00 0.00 33.58 4.45
3602 3876 1.568612 ATGCGTGGTTGTTCTGCTCG 61.569 55.000 0.00 0.00 0.00 5.03
3605 3879 2.281484 TGGTTGTTCTGCTCGGCC 60.281 61.111 0.00 0.00 0.00 6.13
3628 3902 2.816087 CTGGAGGTGATTGTCCAACAAG 59.184 50.000 0.00 0.00 41.94 3.16
3629 3903 2.162681 GGAGGTGATTGTCCAACAAGG 58.837 52.381 0.00 0.00 41.94 3.61
3714 4233 7.274603 AGATAAAGCTACTCCTAAACCTACG 57.725 40.000 0.00 0.00 0.00 3.51
3719 4238 5.749462 AGCTACTCCTAAACCTACGTAGAA 58.251 41.667 24.15 5.56 0.00 2.10
3758 4277 4.530710 AGACGCTCACAACATAAGGTTA 57.469 40.909 0.00 0.00 37.72 2.85
3765 4284 6.183360 CGCTCACAACATAAGGTTAGCAATTA 60.183 38.462 0.00 0.00 38.11 1.40
3782 4301 6.510536 AGCAATTATTTGGCTATCTTTGCTC 58.489 36.000 0.00 0.00 43.53 4.26
3795 4314 1.165907 TTTGCTCGTGTGGAAGGCAG 61.166 55.000 0.00 0.00 34.37 4.85
3807 4326 4.943705 TGTGGAAGGCAGAACTATGATTTC 59.056 41.667 0.00 0.00 0.00 2.17
3831 4350 3.775654 GTCTGGCCCTCCTCGTGG 61.776 72.222 0.00 0.00 0.00 4.94
3871 4390 7.736031 CAATGTTGATTGTAATGCTCTTCTG 57.264 36.000 0.00 0.00 35.19 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.664224 AAACAACCAAGTAACCGCCG 59.336 50.000 0.00 0.00 0.00 6.46
14 15 3.342627 CGACGGCGCTGGAAACAA 61.343 61.111 22.44 0.00 42.06 2.83
15 16 3.583276 ATCGACGGCGCTGGAAACA 62.583 57.895 22.44 0.00 37.46 2.83
17 18 2.508439 GATCGACGGCGCTGGAAA 60.508 61.111 22.44 5.08 37.46 3.13
33 34 2.742053 GTCATTTGCAAGCCTTAGTCGA 59.258 45.455 0.00 0.00 0.00 4.20
35 36 2.164422 GGGTCATTTGCAAGCCTTAGTC 59.836 50.000 0.00 0.00 0.00 2.59
36 37 2.171003 GGGTCATTTGCAAGCCTTAGT 58.829 47.619 0.00 0.00 0.00 2.24
40 41 0.613012 GGAGGGTCATTTGCAAGCCT 60.613 55.000 6.57 6.57 45.78 4.58
45 46 1.031571 GCATCGGAGGGTCATTTGCA 61.032 55.000 0.00 0.00 0.00 4.08
46 47 1.728490 GGCATCGGAGGGTCATTTGC 61.728 60.000 0.00 0.00 0.00 3.68
47 48 0.394216 TGGCATCGGAGGGTCATTTG 60.394 55.000 0.00 0.00 0.00 2.32
53 54 0.107017 CAAAGATGGCATCGGAGGGT 60.107 55.000 21.01 0.10 0.00 4.34
54 55 0.181114 TCAAAGATGGCATCGGAGGG 59.819 55.000 21.01 10.76 0.00 4.30
71 72 0.251916 AATCGAATCGGCCAACCTCA 59.748 50.000 2.24 0.00 0.00 3.86
101 102 0.465824 CCTATCGTCGTGAGGTCCCT 60.466 60.000 6.93 0.00 0.00 4.20
112 113 0.512085 CGTAGCTCCGTCCTATCGTC 59.488 60.000 0.00 0.00 0.00 4.20
138 139 2.718747 TTTCACTACCCGTGTGGCCG 62.719 60.000 0.00 0.00 44.16 6.13
139 140 0.535553 TTTTCACTACCCGTGTGGCC 60.536 55.000 0.00 0.00 44.16 5.36
146 147 2.921754 GAGTCATCGTTTTCACTACCCG 59.078 50.000 0.00 0.00 0.00 5.28
150 151 4.421058 CATCGGAGTCATCGTTTTCACTA 58.579 43.478 0.00 0.00 0.00 2.74
176 177 2.731691 ATTTGGTCTGCCGCACTCGT 62.732 55.000 0.00 0.00 37.67 4.18
183 184 2.293122 TCTCAACAAATTTGGTCTGCCG 59.707 45.455 21.74 3.75 37.67 5.69
186 187 6.199531 CACAACATCTCAACAAATTTGGTCTG 59.800 38.462 21.74 14.96 0.00 3.51
200 201 3.329386 GCTCTAGCAACACAACATCTCA 58.671 45.455 0.00 0.00 41.59 3.27
229 230 0.178876 TCCCAACATCTCACCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
244 245 9.672673 TTTTTAAATGTGAACTTTTCAATCCCA 57.327 25.926 0.00 0.00 42.15 4.37
272 273 4.081309 CCTTCTAGTCCACCCGTTTCATTA 60.081 45.833 0.00 0.00 0.00 1.90
273 274 3.307480 CCTTCTAGTCCACCCGTTTCATT 60.307 47.826 0.00 0.00 0.00 2.57
274 275 2.236395 CCTTCTAGTCCACCCGTTTCAT 59.764 50.000 0.00 0.00 0.00 2.57
275 276 1.621814 CCTTCTAGTCCACCCGTTTCA 59.378 52.381 0.00 0.00 0.00 2.69
276 277 1.622312 ACCTTCTAGTCCACCCGTTTC 59.378 52.381 0.00 0.00 0.00 2.78
278 279 0.974383 CACCTTCTAGTCCACCCGTT 59.026 55.000 0.00 0.00 0.00 4.44
279 280 1.542187 GCACCTTCTAGTCCACCCGT 61.542 60.000 0.00 0.00 0.00 5.28
280 281 1.218316 GCACCTTCTAGTCCACCCG 59.782 63.158 0.00 0.00 0.00 5.28
281 282 0.984995 AAGCACCTTCTAGTCCACCC 59.015 55.000 0.00 0.00 0.00 4.61
282 283 3.975168 TTAAGCACCTTCTAGTCCACC 57.025 47.619 0.00 0.00 0.00 4.61
283 284 5.735766 AGAATTAAGCACCTTCTAGTCCAC 58.264 41.667 0.00 0.00 0.00 4.02
336 342 7.397221 TCTATAGCCCATTCCACATAAATCAG 58.603 38.462 0.00 0.00 0.00 2.90
340 346 6.013379 CCTCTCTATAGCCCATTCCACATAAA 60.013 42.308 0.00 0.00 0.00 1.40
355 361 3.761752 GAGTAGCAAGGGCCTCTCTATAG 59.238 52.174 6.46 0.00 42.56 1.31
356 362 3.399644 AGAGTAGCAAGGGCCTCTCTATA 59.600 47.826 17.54 0.70 43.67 1.31
357 363 2.178984 AGAGTAGCAAGGGCCTCTCTAT 59.821 50.000 17.54 7.82 43.67 1.98
385 391 7.494625 TGGCTAGTTCGATCGATTTAGAAAATT 59.505 33.333 27.28 10.22 0.00 1.82
387 393 6.334989 TGGCTAGTTCGATCGATTTAGAAAA 58.665 36.000 27.28 15.40 0.00 2.29
395 401 2.028930 GGGAATGGCTAGTTCGATCGAT 60.029 50.000 20.18 7.62 0.00 3.59
402 408 4.889995 AGCATAAAAGGGAATGGCTAGTTC 59.110 41.667 0.00 0.00 0.00 3.01
405 411 4.762251 GGTAGCATAAAAGGGAATGGCTAG 59.238 45.833 0.00 0.00 0.00 3.42
415 421 3.869065 TGAACGGAGGTAGCATAAAAGG 58.131 45.455 0.00 0.00 0.00 3.11
416 422 5.873179 TTTGAACGGAGGTAGCATAAAAG 57.127 39.130 0.00 0.00 0.00 2.27
419 425 7.925043 TTTATTTTGAACGGAGGTAGCATAA 57.075 32.000 0.00 0.00 0.00 1.90
420 426 7.925043 TTTTATTTTGAACGGAGGTAGCATA 57.075 32.000 0.00 0.00 0.00 3.14
422 428 6.827586 ATTTTATTTTGAACGGAGGTAGCA 57.172 33.333 0.00 0.00 0.00 3.49
424 430 7.812669 AGCAAATTTTATTTTGAACGGAGGTAG 59.187 33.333 1.33 0.00 38.58 3.18
429 435 9.751542 TCTAAAGCAAATTTTATTTTGAACGGA 57.248 25.926 1.33 0.00 38.58 4.69
514 524 9.391006 TGTTTGTTCACTCATTTTAGTTCTAGT 57.609 29.630 0.00 0.00 0.00 2.57
515 525 9.651718 GTGTTTGTTCACTCATTTTAGTTCTAG 57.348 33.333 0.00 0.00 35.68 2.43
516 526 9.168451 TGTGTTTGTTCACTCATTTTAGTTCTA 57.832 29.630 0.00 0.00 38.90 2.10
517 527 7.968405 GTGTGTTTGTTCACTCATTTTAGTTCT 59.032 33.333 0.00 0.00 38.90 3.01
519 529 7.826690 AGTGTGTTTGTTCACTCATTTTAGTT 58.173 30.769 0.00 0.00 40.28 2.24
521 531 9.781834 TTTAGTGTGTTTGTTCACTCATTTTAG 57.218 29.630 1.08 0.00 42.77 1.85
523 533 9.651913 ATTTTAGTGTGTTTGTTCACTCATTTT 57.348 25.926 1.08 0.00 42.77 1.82
577 587 8.098912 GGAGGGAGTACTACAAGATGTTAAAAA 58.901 37.037 7.57 0.00 0.00 1.94
578 588 7.578189 CGGAGGGAGTACTACAAGATGTTAAAA 60.578 40.741 7.57 0.00 0.00 1.52
579 589 6.127535 CGGAGGGAGTACTACAAGATGTTAAA 60.128 42.308 7.57 0.00 0.00 1.52
580 590 5.359009 CGGAGGGAGTACTACAAGATGTTAA 59.641 44.000 7.57 0.00 0.00 2.01
581 591 4.885907 CGGAGGGAGTACTACAAGATGTTA 59.114 45.833 7.57 0.00 0.00 2.41
586 599 3.446442 AACGGAGGGAGTACTACAAGA 57.554 47.619 7.57 0.00 0.00 3.02
587 600 3.762823 AGAAACGGAGGGAGTACTACAAG 59.237 47.826 7.57 0.00 0.00 3.16
590 603 4.797800 AAAGAAACGGAGGGAGTACTAC 57.202 45.455 0.00 0.00 0.00 2.73
602 615 8.475331 TCTTATAGCAGACTAAAAAGAAACGG 57.525 34.615 0.00 0.00 34.23 4.44
607 620 9.959721 ACCAAATCTTATAGCAGACTAAAAAGA 57.040 29.630 0.00 0.00 38.13 2.52
609 622 9.733556 TGACCAAATCTTATAGCAGACTAAAAA 57.266 29.630 0.00 0.00 30.45 1.94
610 623 9.733556 TTGACCAAATCTTATAGCAGACTAAAA 57.266 29.630 0.00 0.00 30.45 1.52
611 624 9.733556 TTTGACCAAATCTTATAGCAGACTAAA 57.266 29.630 0.00 0.00 30.45 1.85
612 625 9.383519 CTTTGACCAAATCTTATAGCAGACTAA 57.616 33.333 0.00 0.00 30.45 2.24
613 626 8.540388 ACTTTGACCAAATCTTATAGCAGACTA 58.460 33.333 0.00 0.00 0.00 2.59
614 627 7.398024 ACTTTGACCAAATCTTATAGCAGACT 58.602 34.615 0.00 0.00 0.00 3.24
615 628 7.334421 TGACTTTGACCAAATCTTATAGCAGAC 59.666 37.037 0.00 0.00 0.00 3.51
616 629 7.394016 TGACTTTGACCAAATCTTATAGCAGA 58.606 34.615 0.00 0.00 0.00 4.26
617 630 7.615582 TGACTTTGACCAAATCTTATAGCAG 57.384 36.000 0.00 0.00 0.00 4.24
618 631 7.994425 TTGACTTTGACCAAATCTTATAGCA 57.006 32.000 0.00 0.00 0.00 3.49
619 632 8.515414 AGTTTGACTTTGACCAAATCTTATAGC 58.485 33.333 0.00 0.00 35.14 2.97
622 635 9.349713 TGTAGTTTGACTTTGACCAAATCTTAT 57.650 29.630 0.00 0.00 35.14 1.73
623 636 8.617809 GTGTAGTTTGACTTTGACCAAATCTTA 58.382 33.333 0.00 0.00 35.14 2.10
624 637 7.122055 TGTGTAGTTTGACTTTGACCAAATCTT 59.878 33.333 0.00 0.00 35.14 2.40
625 638 6.601613 TGTGTAGTTTGACTTTGACCAAATCT 59.398 34.615 0.00 0.00 35.14 2.40
626 639 6.791303 TGTGTAGTTTGACTTTGACCAAATC 58.209 36.000 0.00 0.00 35.14 2.17
627 640 6.767524 TGTGTAGTTTGACTTTGACCAAAT 57.232 33.333 0.00 0.00 35.14 2.32
628 641 6.576662 TTGTGTAGTTTGACTTTGACCAAA 57.423 33.333 0.00 0.00 0.00 3.28
629 642 6.576662 TTTGTGTAGTTTGACTTTGACCAA 57.423 33.333 0.00 0.00 0.00 3.67
630 643 6.576662 TTTTGTGTAGTTTGACTTTGACCA 57.423 33.333 0.00 0.00 0.00 4.02
631 644 8.379902 CAAATTTTGTGTAGTTTGACTTTGACC 58.620 33.333 0.78 0.00 34.38 4.02
632 645 9.134734 TCAAATTTTGTGTAGTTTGACTTTGAC 57.865 29.630 8.89 0.00 36.11 3.18
639 652 9.442047 AATTTGGTCAAATTTTGTGTAGTTTGA 57.558 25.926 13.92 0.00 45.67 2.69
712 725 9.669353 ATTAGATGCATCATGAAACGTATTTTC 57.331 29.630 27.81 0.00 43.63 2.29
776 789 9.449719 CCTGGTTGAGTTTGACTAACTTTATAT 57.550 33.333 3.78 0.00 47.00 0.86
777 790 7.389607 GCCTGGTTGAGTTTGACTAACTTTATA 59.610 37.037 3.78 0.00 47.00 0.98
778 791 6.206829 GCCTGGTTGAGTTTGACTAACTTTAT 59.793 38.462 3.78 0.00 47.00 1.40
779 792 5.529800 GCCTGGTTGAGTTTGACTAACTTTA 59.470 40.000 3.78 0.00 47.00 1.85
780 793 4.338400 GCCTGGTTGAGTTTGACTAACTTT 59.662 41.667 3.78 0.00 47.00 2.66
781 794 3.883489 GCCTGGTTGAGTTTGACTAACTT 59.117 43.478 3.78 0.00 47.00 2.66
783 796 3.477530 AGCCTGGTTGAGTTTGACTAAC 58.522 45.455 0.00 0.00 36.99 2.34
784 797 3.857157 AGCCTGGTTGAGTTTGACTAA 57.143 42.857 0.00 0.00 0.00 2.24
785 798 3.135712 TCAAGCCTGGTTGAGTTTGACTA 59.864 43.478 7.63 0.00 32.54 2.59
786 799 2.092429 TCAAGCCTGGTTGAGTTTGACT 60.092 45.455 7.63 0.00 32.54 3.41
787 800 2.033424 GTCAAGCCTGGTTGAGTTTGAC 59.967 50.000 11.71 4.40 37.12 3.18
788 801 2.092429 AGTCAAGCCTGGTTGAGTTTGA 60.092 45.455 11.71 0.00 36.85 2.69
789 802 2.301346 AGTCAAGCCTGGTTGAGTTTG 58.699 47.619 11.71 0.00 36.85 2.93
790 803 2.736670 AGTCAAGCCTGGTTGAGTTT 57.263 45.000 11.71 0.00 36.85 2.66
791 804 2.736670 AAGTCAAGCCTGGTTGAGTT 57.263 45.000 20.65 20.65 42.68 3.01
792 805 2.092429 TCAAAGTCAAGCCTGGTTGAGT 60.092 45.455 11.71 12.06 41.06 3.41
793 806 2.291741 GTCAAAGTCAAGCCTGGTTGAG 59.708 50.000 11.71 1.60 37.12 3.02
794 807 2.297701 GTCAAAGTCAAGCCTGGTTGA 58.702 47.619 7.63 7.63 33.95 3.18
795 808 1.338020 GGTCAAAGTCAAGCCTGGTTG 59.662 52.381 2.75 2.75 0.00 3.77
796 809 1.064017 TGGTCAAAGTCAAGCCTGGTT 60.064 47.619 0.00 0.00 0.00 3.67
797 810 0.550914 TGGTCAAAGTCAAGCCTGGT 59.449 50.000 0.00 0.00 0.00 4.00
798 811 1.691196 TTGGTCAAAGTCAAGCCTGG 58.309 50.000 0.00 0.00 0.00 4.45
799 812 2.223805 GGTTTGGTCAAAGTCAAGCCTG 60.224 50.000 0.00 0.00 39.90 4.85
800 813 2.031870 GGTTTGGTCAAAGTCAAGCCT 58.968 47.619 0.00 0.00 39.90 4.58
801 814 2.031870 AGGTTTGGTCAAAGTCAAGCC 58.968 47.619 0.00 0.00 42.22 4.35
802 815 3.801114 AAGGTTTGGTCAAAGTCAAGC 57.199 42.857 0.00 0.00 0.00 4.01
803 816 7.029563 GCATATAAGGTTTGGTCAAAGTCAAG 58.970 38.462 0.00 0.00 0.00 3.02
804 817 6.348950 CGCATATAAGGTTTGGTCAAAGTCAA 60.349 38.462 0.00 0.00 0.00 3.18
805 818 5.123186 CGCATATAAGGTTTGGTCAAAGTCA 59.877 40.000 0.00 0.00 0.00 3.41
806 819 5.448632 CCGCATATAAGGTTTGGTCAAAGTC 60.449 44.000 0.00 0.00 0.00 3.01
807 820 4.398044 CCGCATATAAGGTTTGGTCAAAGT 59.602 41.667 0.00 0.00 0.00 2.66
808 821 4.638421 TCCGCATATAAGGTTTGGTCAAAG 59.362 41.667 0.00 0.00 0.00 2.77
809 822 4.590918 TCCGCATATAAGGTTTGGTCAAA 58.409 39.130 0.00 0.00 0.00 2.69
810 823 4.196193 CTCCGCATATAAGGTTTGGTCAA 58.804 43.478 0.00 0.00 0.00 3.18
811 824 3.199071 ACTCCGCATATAAGGTTTGGTCA 59.801 43.478 0.00 0.00 0.00 4.02
812 825 3.805207 ACTCCGCATATAAGGTTTGGTC 58.195 45.455 0.00 0.00 0.00 4.02
813 826 3.926058 ACTCCGCATATAAGGTTTGGT 57.074 42.857 0.00 0.00 0.00 3.67
814 827 6.687081 TTTTACTCCGCATATAAGGTTTGG 57.313 37.500 0.00 0.00 0.00 3.28
839 852 5.240844 CGTTCACAAATACTCCCTCCTTTTT 59.759 40.000 0.00 0.00 0.00 1.94
840 853 4.760204 CGTTCACAAATACTCCCTCCTTTT 59.240 41.667 0.00 0.00 0.00 2.27
841 854 4.324267 CGTTCACAAATACTCCCTCCTTT 58.676 43.478 0.00 0.00 0.00 3.11
842 855 3.307480 CCGTTCACAAATACTCCCTCCTT 60.307 47.826 0.00 0.00 0.00 3.36
843 856 2.236395 CCGTTCACAAATACTCCCTCCT 59.764 50.000 0.00 0.00 0.00 3.69
849 862 4.504858 ACTCCATCCGTTCACAAATACTC 58.495 43.478 0.00 0.00 0.00 2.59
867 880 8.850007 ATTCTCAGTTTCCTTTTTACTACTCC 57.150 34.615 0.00 0.00 0.00 3.85
870 883 9.880064 GTTGATTCTCAGTTTCCTTTTTACTAC 57.120 33.333 0.00 0.00 0.00 2.73
891 904 9.520204 CAGCGAGAAAATATATTTTTGGTTGAT 57.480 29.630 21.39 11.16 39.86 2.57
892 905 8.519526 ACAGCGAGAAAATATATTTTTGGTTGA 58.480 29.630 21.39 0.00 39.86 3.18
895 908 8.739972 AGAACAGCGAGAAAATATATTTTTGGT 58.260 29.630 21.39 14.94 39.86 3.67
896 909 9.573133 AAGAACAGCGAGAAAATATATTTTTGG 57.427 29.630 21.39 15.06 39.86 3.28
923 941 0.101939 GAACGAGGGGTCCGTATGAC 59.898 60.000 0.00 0.00 43.67 3.06
936 954 0.528470 AGAAGGCGAGAAGGAACGAG 59.472 55.000 0.00 0.00 0.00 4.18
937 955 0.526662 GAGAAGGCGAGAAGGAACGA 59.473 55.000 0.00 0.00 0.00 3.85
938 956 0.798771 CGAGAAGGCGAGAAGGAACG 60.799 60.000 0.00 0.00 0.00 3.95
939 957 0.458716 CCGAGAAGGCGAGAAGGAAC 60.459 60.000 0.00 0.00 0.00 3.62
940 958 1.605058 CCCGAGAAGGCGAGAAGGAA 61.605 60.000 0.00 0.00 39.21 3.36
985 1007 1.612146 TCATGGAGGTGGCGAAGGA 60.612 57.895 0.00 0.00 0.00 3.36
987 1009 0.250234 TTCTCATGGAGGTGGCGAAG 59.750 55.000 0.00 0.00 0.00 3.79
1049 1071 1.192146 TGAGGTGTAGGGTCTGGTGC 61.192 60.000 0.00 0.00 0.00 5.01
1163 1189 0.739813 ACAGGCGGTTATGAACGAGC 60.740 55.000 0.00 0.00 35.77 5.03
1311 1340 3.474904 TCGAACACATTCCGCGCG 61.475 61.111 25.67 25.67 0.00 6.86
1320 1349 0.533085 TCCGCATTTGGTCGAACACA 60.533 50.000 0.44 0.00 0.00 3.72
1330 1359 2.159338 CCATGTCTTTCCTCCGCATTTG 60.159 50.000 0.00 0.00 0.00 2.32
1440 1469 0.741915 TGAACCCGTTTGGCTTGAAC 59.258 50.000 0.00 0.00 37.83 3.18
1508 1541 2.429058 CATGGATCTGCCTCCCGG 59.571 66.667 0.00 0.00 37.63 5.73
1705 1738 1.348696 TGCAAAGGTCATCAGAGCAGA 59.651 47.619 0.00 0.00 44.60 4.26
1998 2036 0.606673 AAACTGCTTCCTTCCCGAGC 60.607 55.000 0.00 0.00 36.95 5.03
2016 2054 3.851976 TCCTCATCTCCTCAAAATGGGAA 59.148 43.478 0.00 0.00 0.00 3.97
2040 2078 2.673368 CTGATTCAGGTAAACGCCAGAC 59.327 50.000 5.73 0.00 0.00 3.51
2160 2198 7.987458 ACAACCGTAACATAATGATCAATCTCT 59.013 33.333 0.00 0.00 0.00 3.10
2340 2378 6.600822 CACTATCATCTGGGTCAAGTTCAAAT 59.399 38.462 0.00 0.00 0.00 2.32
2377 2415 7.936301 TGTGGAAGCATATATGTTATACAGCAA 59.064 33.333 14.14 0.00 0.00 3.91
2380 2418 7.065085 GCCTGTGGAAGCATATATGTTATACAG 59.935 40.741 21.07 21.07 0.00 2.74
2403 2441 2.443390 GCAGCATCCCATTGGCCT 60.443 61.111 3.32 0.00 0.00 5.19
2435 2473 4.067192 CACACCAGTTGTCTTCATCATCA 58.933 43.478 0.00 0.00 35.67 3.07
2627 2665 5.011943 GCCTCCTTCTCTTGATCATCTACAT 59.988 44.000 0.00 0.00 0.00 2.29
2645 2683 1.907255 GGTACTGTAGGTTTGCCTCCT 59.093 52.381 0.00 0.00 45.64 3.69
2736 2774 6.897413 GGCAATCCCCACATATCCTAATATTT 59.103 38.462 0.00 0.00 0.00 1.40
2900 2938 4.415596 TCAAACCATGGCCTTGTAGATTT 58.584 39.130 20.92 9.05 0.00 2.17
2918 3150 4.278170 CCTGTTGGCTGTTACTGAATCAAA 59.722 41.667 0.00 0.00 0.00 2.69
2971 3203 5.825507 ACAGAGACAATCAAGCAGAAAAAC 58.174 37.500 0.00 0.00 0.00 2.43
2973 3205 5.589855 TCAACAGAGACAATCAAGCAGAAAA 59.410 36.000 0.00 0.00 0.00 2.29
3054 3297 3.498774 AAGTGCATGTCTTCTGGAGTT 57.501 42.857 0.00 0.00 0.00 3.01
3070 3329 2.076100 TGCGCTACAAGGATGAAAGTG 58.924 47.619 9.73 0.00 0.00 3.16
3071 3330 2.472695 TGCGCTACAAGGATGAAAGT 57.527 45.000 9.73 0.00 0.00 2.66
3083 3342 5.833400 CGAAATTTTAGTGATTGCGCTAC 57.167 39.130 9.73 2.58 36.88 3.58
3133 3392 4.934797 ACTTTTCTCCCAGGAATCATGA 57.065 40.909 0.00 0.00 0.00 3.07
3258 3532 3.430218 GGAAATCCGCAGACTATCATTCG 59.570 47.826 0.00 0.00 0.00 3.34
3273 3547 4.645136 GTGGAAATTAGGTCCAGGAAATCC 59.355 45.833 0.00 0.00 45.85 3.01
3281 3555 1.003812 CCGGTGTGGAAATTAGGTCCA 59.996 52.381 0.00 0.00 43.03 4.02
3283 3557 2.773993 TCCGGTGTGGAAATTAGGTC 57.226 50.000 0.00 0.00 46.38 3.85
3350 3624 0.971386 AGCAAAATCACCCAGCCTTG 59.029 50.000 0.00 0.00 0.00 3.61
3385 3659 6.479972 TGAACCCGATATACTCTGAAATGT 57.520 37.500 0.00 0.00 0.00 2.71
3394 3668 3.823873 CTCTGAGCTGAACCCGATATACT 59.176 47.826 0.00 0.00 0.00 2.12
3460 3734 1.588239 AGAGCCATCATCAGTCCCAA 58.412 50.000 0.00 0.00 0.00 4.12
3574 3848 1.004277 ACAACCACGCATATTCCCAGT 59.996 47.619 0.00 0.00 0.00 4.00
3575 3849 1.750193 ACAACCACGCATATTCCCAG 58.250 50.000 0.00 0.00 0.00 4.45
3576 3850 2.088423 GAACAACCACGCATATTCCCA 58.912 47.619 0.00 0.00 0.00 4.37
3577 3851 2.097466 CAGAACAACCACGCATATTCCC 59.903 50.000 0.00 0.00 0.00 3.97
3578 3852 2.477863 GCAGAACAACCACGCATATTCC 60.478 50.000 0.00 0.00 0.00 3.01
3579 3853 2.420022 AGCAGAACAACCACGCATATTC 59.580 45.455 0.00 0.00 0.00 1.75
3605 3879 3.998143 TTGTTGGACAATCACCTCCAGTG 60.998 47.826 0.00 0.00 39.46 3.66
3628 3902 2.019984 GACTGAATCAAGTGCATCCCC 58.980 52.381 0.00 0.00 0.00 4.81
3629 3903 2.681848 CAGACTGAATCAAGTGCATCCC 59.318 50.000 0.00 0.00 0.00 3.85
3657 4176 4.082136 AGGAAGAGTAAACCGATCTGTCAC 60.082 45.833 0.00 0.00 0.00 3.67
3719 4238 8.847196 TGAGCGTCTAACATGATTAATACTAGT 58.153 33.333 0.00 0.00 0.00 2.57
3729 4248 3.925379 TGTTGTGAGCGTCTAACATGAT 58.075 40.909 0.00 0.00 0.00 2.45
3731 4250 5.220472 CCTTATGTTGTGAGCGTCTAACATG 60.220 44.000 17.00 0.00 42.04 3.21
3734 4253 4.243270 ACCTTATGTTGTGAGCGTCTAAC 58.757 43.478 0.00 0.00 0.00 2.34
3758 4277 6.475596 AGCAAAGATAGCCAAATAATTGCT 57.524 33.333 4.02 4.02 45.17 3.91
3765 4284 3.127548 CACACGAGCAAAGATAGCCAAAT 59.872 43.478 0.00 0.00 0.00 2.32
3782 4301 2.002586 CATAGTTCTGCCTTCCACACG 58.997 52.381 0.00 0.00 0.00 4.49
3795 4314 4.985409 CAGACCCTAGCGAAATCATAGTTC 59.015 45.833 0.00 0.00 0.00 3.01
3831 4350 2.228822 ACATTGTTCAACTCAATCGGCC 59.771 45.455 0.00 0.00 33.92 6.13
3833 4352 5.107109 TCAACATTGTTCAACTCAATCGG 57.893 39.130 0.00 0.00 33.92 4.18


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

AutoCloner maintained by Alex Coulton.