Multiple sequence alignment - TraesCS4A01G116600

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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 TraesCS4A01G116600 chr4A 100.000 2285 0 0 1 2285 141130481 141128197 0.000000e+00 4220.0
1 TraesCS4A01G116600 chr4A 97.211 1291 32 3 995 2285 309375145 309376431 0.000000e+00 2182.0
2 TraesCS4A01G116600 chr5D 98.064 1291 24 1 995 2285 6236653 6237942 0.000000e+00 2244.0
3 TraesCS4A01G116600 chr5D 98.064 1291 24 1 995 2285 503330157 503328868 0.000000e+00 2244.0
4 TraesCS4A01G116600 chr5D 96.341 164 6 0 839 1002 503330348 503330185 1.040000e-68 270.0
5 TraesCS4A01G116600 chr1D 97.289 1291 33 2 995 2285 254476244 254474956 0.000000e+00 2189.0
6 TraesCS4A01G116600 chr1D 96.902 1291 38 2 995 2285 180357148 180358436 0.000000e+00 2161.0
7 TraesCS4A01G116600 chr1D 96.362 1292 42 3 995 2285 244767733 244766446 0.000000e+00 2121.0
8 TraesCS4A01G116600 chr1D 96.341 164 6 0 839 1002 254476435 254476272 1.040000e-68 270.0
9 TraesCS4A01G116600 chr1D 95.122 164 8 0 839 1002 290506605 290506442 2.250000e-65 259.0
10 TraesCS4A01G116600 chr2A 96.904 1292 37 3 995 2285 419795460 419794171 0.000000e+00 2161.0
11 TraesCS4A01G116600 chr2A 92.434 304 23 0 529 832 729555245 729554942 3.490000e-118 435.0
12 TraesCS4A01G116600 chr2A 92.105 304 22 2 529 832 459017004 459017305 5.830000e-116 427.0
13 TraesCS4A01G116600 chr2A 91.176 306 26 1 528 832 743327794 743327489 4.540000e-112 414.0
14 TraesCS4A01G116600 chr1A 98.124 1226 20 3 995 2220 554448699 554449921 0.000000e+00 2134.0
15 TraesCS4A01G116600 chr1A 96.341 164 6 0 839 1002 554448508 554448671 1.040000e-68 270.0
16 TraesCS4A01G116600 chr2D 98.042 1226 22 2 995 2220 33930461 33931684 0.000000e+00 2130.0
17 TraesCS4A01G116600 chr2D 94.579 535 15 8 1 529 407225960 407225434 0.000000e+00 815.0
18 TraesCS4A01G116600 chr2D 96.951 164 5 0 839 1002 33930270 33930433 2.240000e-70 276.0
19 TraesCS4A01G116600 chr2D 96.341 164 6 0 839 1002 648663866 648664029 1.040000e-68 270.0
20 TraesCS4A01G116600 chr4D 94.579 535 15 8 1 529 328998754 328999280 0.000000e+00 815.0
21 TraesCS4A01G116600 chr4D 91.722 302 25 0 529 830 226384948 226385249 9.760000e-114 420.0
22 TraesCS4A01G116600 chr1B 93.173 542 16 9 1 529 135962948 135962415 0.000000e+00 776.0
23 TraesCS4A01G116600 chr1B 90.879 307 28 0 528 834 537041593 537041287 1.630000e-111 412.0
24 TraesCS4A01G116600 chr4B 91.829 514 21 9 1 510 408951309 408951805 0.000000e+00 697.0
25 TraesCS4A01G116600 chr5B 91.830 306 24 1 527 832 229081975 229081671 2.100000e-115 425.0
26 TraesCS4A01G116600 chr6B 91.262 309 23 4 527 832 675396239 675395932 3.510000e-113 418.0
27 TraesCS4A01G116600 chr2B 91.503 306 23 3 529 832 131178489 131178185 3.510000e-113 418.0
28 TraesCS4A01G116600 chr3D 90.282 319 29 2 528 845 488120896 488121213 1.260000e-112 416.0
29 TraesCS4A01G116600 chrUn 96.951 164 5 0 839 1002 432823287 432823124 2.240000e-70 276.0
30 TraesCS4A01G116600 chr3B 96.951 164 5 0 839 1002 201492440 201492277 2.240000e-70 276.0
31 TraesCS4A01G116600 chr3B 95.312 64 3 0 2221 2284 405424838 405424901 4.020000e-18 102.0
32 TraesCS4A01G116600 chr3B 95.918 49 2 0 2237 2285 729906882 729906930 1.880000e-11 80.5
33 TraesCS4A01G116600 chr7D 96.341 164 5 1 839 1002 231565732 231565570 3.740000e-68 268.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G116600 chr4A 141128197 141130481 2284 True 4220.0 4220 100.0000 1 2285 1 chr4A.!!$R1 2284
1 TraesCS4A01G116600 chr4A 309375145 309376431 1286 False 2182.0 2182 97.2110 995 2285 1 chr4A.!!$F1 1290
2 TraesCS4A01G116600 chr5D 6236653 6237942 1289 False 2244.0 2244 98.0640 995 2285 1 chr5D.!!$F1 1290
3 TraesCS4A01G116600 chr5D 503328868 503330348 1480 True 1257.0 2244 97.2025 839 2285 2 chr5D.!!$R1 1446
4 TraesCS4A01G116600 chr1D 180357148 180358436 1288 False 2161.0 2161 96.9020 995 2285 1 chr1D.!!$F1 1290
5 TraesCS4A01G116600 chr1D 244766446 244767733 1287 True 2121.0 2121 96.3620 995 2285 1 chr1D.!!$R1 1290
6 TraesCS4A01G116600 chr1D 254474956 254476435 1479 True 1229.5 2189 96.8150 839 2285 2 chr1D.!!$R3 1446
7 TraesCS4A01G116600 chr2A 419794171 419795460 1289 True 2161.0 2161 96.9040 995 2285 1 chr2A.!!$R1 1290
8 TraesCS4A01G116600 chr1A 554448508 554449921 1413 False 1202.0 2134 97.2325 839 2220 2 chr1A.!!$F1 1381
9 TraesCS4A01G116600 chr2D 33930270 33931684 1414 False 1203.0 2130 97.4965 839 2220 2 chr2D.!!$F2 1381
10 TraesCS4A01G116600 chr2D 407225434 407225960 526 True 815.0 815 94.5790 1 529 1 chr2D.!!$R1 528
11 TraesCS4A01G116600 chr4D 328998754 328999280 526 False 815.0 815 94.5790 1 529 1 chr4D.!!$F2 528
12 TraesCS4A01G116600 chr1B 135962415 135962948 533 True 776.0 776 93.1730 1 529 1 chr1B.!!$R1 528

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
657 671 0.035152 AGCCGGCATGTCATCTTGAA 60.035 50.0 31.54 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2180 1.463056 TGTGCTAAGTAATGTGCGTGC 59.537 47.619 0.0 0.0 0.0 5.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.453762 GCTACTACGCCGAGGTGGAT 61.454 60.000 7.65 0.00 42.00 3.41
76 84 3.134127 GGGGCCGACATGAGCAAC 61.134 66.667 0.00 0.00 0.00 4.17
187 195 3.583276 CTCCAAGTACGGCGTGCCA 62.583 63.158 24.86 0.00 35.37 4.92
240 248 1.665916 CCCACACTGACACTGAGCG 60.666 63.158 0.00 0.00 0.00 5.03
293 304 2.296190 GGATTGTGGACAAGGGTTGTTC 59.704 50.000 0.00 0.00 45.52 3.18
306 317 8.066612 ACAAGGGTTGTTCATTTTATGGATAG 57.933 34.615 0.00 0.00 42.22 2.08
328 339 1.131126 AGGATCGGTTGTACGTACACG 59.869 52.381 27.36 25.81 46.33 4.49
329 340 1.538276 GATCGGTTGTACGTACACGG 58.462 55.000 27.36 22.63 44.95 4.94
330 341 0.881118 ATCGGTTGTACGTACACGGT 59.119 50.000 27.36 21.19 44.95 4.83
331 342 1.514003 TCGGTTGTACGTACACGGTA 58.486 50.000 27.36 10.79 44.95 4.02
332 343 1.195900 TCGGTTGTACGTACACGGTAC 59.804 52.381 27.36 21.18 44.95 3.34
333 344 1.069568 CGGTTGTACGTACACGGTACA 60.070 52.381 27.36 9.63 44.95 2.90
334 345 2.315901 GGTTGTACGTACACGGTACAC 58.684 52.381 27.36 20.16 44.95 2.90
355 366 8.765219 GTACACTGTTGTTGATGTATATCATCC 58.235 37.037 2.71 0.00 42.97 3.51
487 501 8.480643 ACTCAAATAGAACAGGATTTAAGACG 57.519 34.615 0.00 0.00 0.00 4.18
496 510 8.512138 AGAACAGGATTTAAGACGGTTTAATTG 58.488 33.333 0.00 0.00 0.00 2.32
498 512 5.737290 CAGGATTTAAGACGGTTTAATTGCG 59.263 40.000 0.00 0.00 0.00 4.85
529 543 9.034544 GTTGATCTTTTTGCTTGTGTTTATCTT 57.965 29.630 0.00 0.00 0.00 2.40
530 544 9.598517 TTGATCTTTTTGCTTGTGTTTATCTTT 57.401 25.926 0.00 0.00 0.00 2.52
531 545 9.598517 TGATCTTTTTGCTTGTGTTTATCTTTT 57.401 25.926 0.00 0.00 0.00 2.27
552 566 6.525121 TTTTTCTGAACATCAGTACAGACG 57.475 37.500 7.21 0.00 44.58 4.18
553 567 3.217599 TCTGAACATCAGTACAGACGC 57.782 47.619 7.21 0.00 44.58 5.19
554 568 2.556622 TCTGAACATCAGTACAGACGCA 59.443 45.455 7.21 0.00 44.58 5.24
555 569 3.005367 TCTGAACATCAGTACAGACGCAA 59.995 43.478 7.21 0.00 44.58 4.85
556 570 3.366121 CTGAACATCAGTACAGACGCAAG 59.634 47.826 0.00 0.00 39.58 4.01
557 571 1.714794 ACATCAGTACAGACGCAAGC 58.285 50.000 0.00 0.00 45.62 4.01
558 572 0.642291 CATCAGTACAGACGCAAGCG 59.358 55.000 13.50 13.50 46.03 4.68
559 573 1.078759 ATCAGTACAGACGCAAGCGC 61.079 55.000 15.09 0.00 44.19 5.92
560 574 1.734477 CAGTACAGACGCAAGCGCT 60.734 57.895 15.09 2.64 44.19 5.92
561 575 1.444553 AGTACAGACGCAAGCGCTC 60.445 57.895 12.06 11.06 44.19 5.03
562 576 1.733041 GTACAGACGCAAGCGCTCA 60.733 57.895 12.06 0.83 44.19 4.26
563 577 1.078759 GTACAGACGCAAGCGCTCAT 61.079 55.000 12.06 0.00 44.19 2.90
564 578 0.454196 TACAGACGCAAGCGCTCATA 59.546 50.000 12.06 5.16 44.19 2.15
565 579 1.078759 ACAGACGCAAGCGCTCATAC 61.079 55.000 12.06 1.58 44.19 2.39
566 580 1.078201 CAGACGCAAGCGCTCATACA 61.078 55.000 12.06 0.00 44.19 2.29
567 581 0.179100 AGACGCAAGCGCTCATACAT 60.179 50.000 12.06 0.00 44.19 2.29
568 582 1.067060 AGACGCAAGCGCTCATACATA 59.933 47.619 12.06 0.00 44.19 2.29
569 583 1.190323 GACGCAAGCGCTCATACATAC 59.810 52.381 12.06 0.00 44.19 2.39
570 584 0.159554 CGCAAGCGCTCATACATACG 59.840 55.000 12.06 0.00 35.30 3.06
574 588 3.916439 CGCTCATACATACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
575 589 2.434688 CGCTCATACATACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
576 590 1.613270 CGCTCATACATACGCGCATA 58.387 50.000 5.73 0.00 39.11 3.14
577 591 1.317611 CGCTCATACATACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
578 592 2.324860 GCTCATACATACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
579 593 2.090658 GCTCATACATACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
580 594 3.565516 CTCATACATACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
581 595 3.561503 TCATACATACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
582 596 3.003897 TCATACATACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
583 597 1.556564 ACATACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
584 598 0.852777 CATACGCGCATACACTCACC 59.147 55.000 5.73 0.00 0.00 4.02
585 599 0.744874 ATACGCGCATACACTCACCT 59.255 50.000 5.73 0.00 0.00 4.00
586 600 0.099968 TACGCGCATACACTCACCTC 59.900 55.000 5.73 0.00 0.00 3.85
587 601 1.139734 CGCGCATACACTCACCTCT 59.860 57.895 8.75 0.00 0.00 3.69
588 602 0.380733 CGCGCATACACTCACCTCTA 59.619 55.000 8.75 0.00 0.00 2.43
589 603 1.001268 CGCGCATACACTCACCTCTAT 60.001 52.381 8.75 0.00 0.00 1.98
590 604 2.398498 GCGCATACACTCACCTCTATG 58.602 52.381 0.30 0.00 0.00 2.23
591 605 2.034685 GCGCATACACTCACCTCTATGA 59.965 50.000 0.30 0.00 0.00 2.15
592 606 3.490933 GCGCATACACTCACCTCTATGAA 60.491 47.826 0.30 0.00 0.00 2.57
593 607 4.797604 GCGCATACACTCACCTCTATGAAT 60.798 45.833 0.30 0.00 0.00 2.57
594 608 4.683320 CGCATACACTCACCTCTATGAATG 59.317 45.833 0.00 0.00 32.12 2.67
595 609 4.450419 GCATACACTCACCTCTATGAATGC 59.550 45.833 0.00 0.00 34.00 3.56
596 610 5.604565 CATACACTCACCTCTATGAATGCA 58.395 41.667 0.00 0.00 28.78 3.96
597 611 3.866651 ACACTCACCTCTATGAATGCAC 58.133 45.455 0.00 0.00 28.78 4.57
598 612 3.261643 ACACTCACCTCTATGAATGCACA 59.738 43.478 0.00 0.00 28.78 4.57
599 613 3.620374 CACTCACCTCTATGAATGCACAC 59.380 47.826 0.00 0.00 0.00 3.82
600 614 3.261643 ACTCACCTCTATGAATGCACACA 59.738 43.478 0.00 0.00 0.00 3.72
601 615 3.599343 TCACCTCTATGAATGCACACAC 58.401 45.455 0.00 0.00 0.00 3.82
602 616 2.349580 CACCTCTATGAATGCACACACG 59.650 50.000 0.00 0.00 0.00 4.49
603 617 1.328680 CCTCTATGAATGCACACACGC 59.671 52.381 0.00 0.00 0.00 5.34
610 624 2.747022 TGCACACACGCATACCCT 59.253 55.556 0.00 0.00 36.86 4.34
611 625 1.976112 TGCACACACGCATACCCTA 59.024 52.632 0.00 0.00 36.86 3.53
612 626 0.390603 TGCACACACGCATACCCTAC 60.391 55.000 0.00 0.00 36.86 3.18
613 627 1.087771 GCACACACGCATACCCTACC 61.088 60.000 0.00 0.00 0.00 3.18
614 628 0.461339 CACACACGCATACCCTACCC 60.461 60.000 0.00 0.00 0.00 3.69
615 629 1.145377 CACACGCATACCCTACCCC 59.855 63.158 0.00 0.00 0.00 4.95
616 630 1.002533 ACACGCATACCCTACCCCT 59.997 57.895 0.00 0.00 0.00 4.79
617 631 0.262580 ACACGCATACCCTACCCCTA 59.737 55.000 0.00 0.00 0.00 3.53
618 632 1.132945 ACACGCATACCCTACCCCTAT 60.133 52.381 0.00 0.00 0.00 2.57
619 633 2.110543 ACACGCATACCCTACCCCTATA 59.889 50.000 0.00 0.00 0.00 1.31
620 634 3.167485 CACGCATACCCTACCCCTATAA 58.833 50.000 0.00 0.00 0.00 0.98
621 635 3.194968 CACGCATACCCTACCCCTATAAG 59.805 52.174 0.00 0.00 0.00 1.73
622 636 2.167900 CGCATACCCTACCCCTATAAGC 59.832 54.545 0.00 0.00 0.00 3.09
623 637 3.178865 GCATACCCTACCCCTATAAGCA 58.821 50.000 0.00 0.00 0.00 3.91
624 638 3.055312 GCATACCCTACCCCTATAAGCAC 60.055 52.174 0.00 0.00 0.00 4.40
625 639 2.113807 ACCCTACCCCTATAAGCACC 57.886 55.000 0.00 0.00 0.00 5.01
626 640 1.584105 ACCCTACCCCTATAAGCACCT 59.416 52.381 0.00 0.00 0.00 4.00
627 641 2.021341 ACCCTACCCCTATAAGCACCTT 60.021 50.000 0.00 0.00 0.00 3.50
628 642 2.638363 CCCTACCCCTATAAGCACCTTC 59.362 54.545 0.00 0.00 0.00 3.46
629 643 3.314693 CCTACCCCTATAAGCACCTTCA 58.685 50.000 0.00 0.00 0.00 3.02
630 644 3.910627 CCTACCCCTATAAGCACCTTCAT 59.089 47.826 0.00 0.00 0.00 2.57
631 645 3.864789 ACCCCTATAAGCACCTTCATG 57.135 47.619 0.00 0.00 0.00 3.07
632 646 3.393687 ACCCCTATAAGCACCTTCATGA 58.606 45.455 0.00 0.00 0.00 3.07
633 647 3.392616 ACCCCTATAAGCACCTTCATGAG 59.607 47.826 0.00 0.00 0.00 2.90
634 648 3.648067 CCCCTATAAGCACCTTCATGAGA 59.352 47.826 0.00 0.00 0.00 3.27
635 649 4.503991 CCCCTATAAGCACCTTCATGAGAC 60.504 50.000 0.00 0.00 0.00 3.36
636 650 4.346418 CCCTATAAGCACCTTCATGAGACT 59.654 45.833 0.00 0.00 0.00 3.24
637 651 5.295950 CCTATAAGCACCTTCATGAGACTG 58.704 45.833 0.00 0.00 0.00 3.51
638 652 5.069648 CCTATAAGCACCTTCATGAGACTGA 59.930 44.000 0.00 0.00 0.00 3.41
639 653 3.331478 AAGCACCTTCATGAGACTGAG 57.669 47.619 0.00 0.00 0.00 3.35
640 654 1.066286 AGCACCTTCATGAGACTGAGC 60.066 52.381 0.00 0.00 0.00 4.26
641 655 2.011046 GCACCTTCATGAGACTGAGCC 61.011 57.143 0.00 0.00 0.00 4.70
642 656 0.534412 ACCTTCATGAGACTGAGCCG 59.466 55.000 0.00 0.00 0.00 5.52
643 657 0.179089 CCTTCATGAGACTGAGCCGG 60.179 60.000 0.00 0.00 0.00 6.13
644 658 0.809241 CTTCATGAGACTGAGCCGGC 60.809 60.000 21.89 21.89 0.00 6.13
645 659 1.543944 TTCATGAGACTGAGCCGGCA 61.544 55.000 31.54 7.98 0.00 5.69
646 660 1.145598 CATGAGACTGAGCCGGCAT 59.854 57.895 31.54 14.28 0.00 4.40
647 661 1.145598 ATGAGACTGAGCCGGCATG 59.854 57.895 31.54 19.90 0.00 4.06
648 662 1.620739 ATGAGACTGAGCCGGCATGT 61.621 55.000 31.54 23.16 0.00 3.21
649 663 1.520342 GAGACTGAGCCGGCATGTC 60.520 63.158 31.54 29.08 0.00 3.06
650 664 2.230994 GAGACTGAGCCGGCATGTCA 62.231 60.000 32.41 25.37 0.00 3.58
651 665 1.153289 GACTGAGCCGGCATGTCAT 60.153 57.895 31.54 13.17 0.00 3.06
652 666 1.153289 ACTGAGCCGGCATGTCATC 60.153 57.895 31.54 16.99 0.00 2.92
653 667 1.145598 CTGAGCCGGCATGTCATCT 59.854 57.895 31.54 4.27 0.00 2.90
654 668 0.463295 CTGAGCCGGCATGTCATCTT 60.463 55.000 31.54 3.33 0.00 2.40
655 669 0.745486 TGAGCCGGCATGTCATCTTG 60.745 55.000 31.54 0.00 0.00 3.02
656 670 0.462581 GAGCCGGCATGTCATCTTGA 60.463 55.000 31.54 0.00 0.00 3.02
657 671 0.035152 AGCCGGCATGTCATCTTGAA 60.035 50.000 31.54 0.00 0.00 2.69
658 672 0.810648 GCCGGCATGTCATCTTGAAA 59.189 50.000 24.80 0.00 0.00 2.69
659 673 1.406539 GCCGGCATGTCATCTTGAAAT 59.593 47.619 24.80 0.00 0.00 2.17
660 674 2.159198 GCCGGCATGTCATCTTGAAATT 60.159 45.455 24.80 0.00 0.00 1.82
661 675 3.676873 GCCGGCATGTCATCTTGAAATTT 60.677 43.478 24.80 0.00 0.00 1.82
662 676 4.439974 GCCGGCATGTCATCTTGAAATTTA 60.440 41.667 24.80 0.00 0.00 1.40
663 677 5.036737 CCGGCATGTCATCTTGAAATTTAC 58.963 41.667 0.00 0.00 0.00 2.01
664 678 4.730042 CGGCATGTCATCTTGAAATTTACG 59.270 41.667 0.00 0.00 0.00 3.18
665 679 5.447144 CGGCATGTCATCTTGAAATTTACGA 60.447 40.000 0.00 0.00 0.00 3.43
666 680 6.321717 GGCATGTCATCTTGAAATTTACGAA 58.678 36.000 0.00 0.00 0.00 3.85
667 681 6.470235 GGCATGTCATCTTGAAATTTACGAAG 59.530 38.462 0.00 0.00 0.00 3.79
669 683 7.217070 GCATGTCATCTTGAAATTTACGAAGTC 59.783 37.037 0.00 0.00 43.93 3.01
670 684 7.722795 TGTCATCTTGAAATTTACGAAGTCA 57.277 32.000 0.00 0.00 43.93 3.41
671 685 7.572759 TGTCATCTTGAAATTTACGAAGTCAC 58.427 34.615 0.00 0.00 43.93 3.67
672 686 7.015877 GTCATCTTGAAATTTACGAAGTCACC 58.984 38.462 0.00 0.00 43.93 4.02
673 687 5.585500 TCTTGAAATTTACGAAGTCACCG 57.415 39.130 0.00 0.00 43.93 4.94
674 688 5.291178 TCTTGAAATTTACGAAGTCACCGA 58.709 37.500 0.00 0.00 43.93 4.69
675 689 5.754406 TCTTGAAATTTACGAAGTCACCGAA 59.246 36.000 0.00 0.00 43.93 4.30
676 690 5.585500 TGAAATTTACGAAGTCACCGAAG 57.415 39.130 0.00 0.00 43.93 3.79
688 702 4.052229 CCGAAGGCACCTCGTCGT 62.052 66.667 9.32 0.00 46.14 4.34
689 703 2.504244 CGAAGGCACCTCGTCGTC 60.504 66.667 3.16 0.00 34.79 4.20
690 704 2.504244 GAAGGCACCTCGTCGTCG 60.504 66.667 0.00 0.00 38.55 5.12
691 705 2.974489 GAAGGCACCTCGTCGTCGA 61.974 63.158 4.42 4.42 44.12 4.20
692 706 3.264866 AAGGCACCTCGTCGTCGAC 62.265 63.158 15.51 15.51 41.35 4.20
710 724 2.979649 GGGGACGTCTCCTTCCAC 59.020 66.667 27.83 0.17 36.68 4.02
711 725 1.609794 GGGGACGTCTCCTTCCACT 60.610 63.158 27.83 0.00 36.68 4.00
712 726 0.324091 GGGGACGTCTCCTTCCACTA 60.324 60.000 27.83 0.00 36.68 2.74
713 727 1.553706 GGGACGTCTCCTTCCACTAA 58.446 55.000 16.46 0.00 36.68 2.24
714 728 1.897802 GGGACGTCTCCTTCCACTAAA 59.102 52.381 16.46 0.00 36.68 1.85
715 729 2.301009 GGGACGTCTCCTTCCACTAAAA 59.699 50.000 16.46 0.00 36.68 1.52
716 730 3.586892 GGACGTCTCCTTCCACTAAAAG 58.413 50.000 16.46 0.00 33.07 2.27
717 731 2.994578 GACGTCTCCTTCCACTAAAAGC 59.005 50.000 8.70 0.00 0.00 3.51
718 732 1.993370 CGTCTCCTTCCACTAAAAGCG 59.007 52.381 0.00 0.00 0.00 4.68
719 733 1.732809 GTCTCCTTCCACTAAAAGCGC 59.267 52.381 0.00 0.00 0.00 5.92
720 734 1.346395 TCTCCTTCCACTAAAAGCGCA 59.654 47.619 11.47 0.00 0.00 6.09
721 735 2.027192 TCTCCTTCCACTAAAAGCGCAT 60.027 45.455 11.47 0.00 0.00 4.73
722 736 2.352960 CTCCTTCCACTAAAAGCGCATC 59.647 50.000 11.47 0.00 0.00 3.91
723 737 1.062587 CCTTCCACTAAAAGCGCATCG 59.937 52.381 11.47 0.00 0.00 3.84
737 751 3.673746 CGCATCGCCTGAAATTCTTAA 57.326 42.857 0.00 0.00 0.00 1.85
738 752 4.014847 CGCATCGCCTGAAATTCTTAAA 57.985 40.909 0.00 0.00 0.00 1.52
739 753 4.601019 CGCATCGCCTGAAATTCTTAAAT 58.399 39.130 0.00 0.00 0.00 1.40
740 754 5.747565 CGCATCGCCTGAAATTCTTAAATA 58.252 37.500 0.00 0.00 0.00 1.40
741 755 6.198687 CGCATCGCCTGAAATTCTTAAATAA 58.801 36.000 0.00 0.00 0.00 1.40
742 756 6.690957 CGCATCGCCTGAAATTCTTAAATAAA 59.309 34.615 0.00 0.00 0.00 1.40
743 757 7.379529 CGCATCGCCTGAAATTCTTAAATAAAT 59.620 33.333 0.00 0.00 0.00 1.40
744 758 8.694394 GCATCGCCTGAAATTCTTAAATAAATC 58.306 33.333 0.00 0.00 0.00 2.17
745 759 9.956720 CATCGCCTGAAATTCTTAAATAAATCT 57.043 29.630 0.00 0.00 0.00 2.40
748 762 9.884465 CGCCTGAAATTCTTAAATAAATCTAGG 57.116 33.333 0.00 0.00 0.00 3.02
761 775 8.621532 AAATAAATCTAGGAATAATGCGAGCA 57.378 30.769 0.00 0.00 0.00 4.26
762 776 5.931441 AAATCTAGGAATAATGCGAGCAC 57.069 39.130 0.00 0.00 0.00 4.40
763 777 3.386768 TCTAGGAATAATGCGAGCACC 57.613 47.619 0.00 0.00 0.00 5.01
764 778 2.698274 TCTAGGAATAATGCGAGCACCA 59.302 45.455 0.00 0.00 0.00 4.17
765 779 1.959042 AGGAATAATGCGAGCACCAG 58.041 50.000 0.00 0.00 0.00 4.00
766 780 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
767 781 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
768 782 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
769 783 2.645838 ATAATGCGAGCACCAGGATT 57.354 45.000 0.00 0.00 33.17 3.01
770 784 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
771 785 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
772 786 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.000 0.00 0.00 0.00 2.69
773 787 0.250684 TGCGAGCACCAGGATTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
774 788 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
775 789 0.804989 CGAGCACCAGGATTTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
776 790 1.177401 GAGCACCAGGATTTGAACCC 58.823 55.000 0.00 0.00 0.00 4.11
777 791 0.779997 AGCACCAGGATTTGAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
782 796 1.549203 CAGGATTTGAACCCTGGTGG 58.451 55.000 0.00 0.00 44.68 4.61
792 806 2.368192 CCTGGTGGGCTGGGGATA 60.368 66.667 0.00 0.00 0.00 2.59
793 807 2.757124 CCTGGTGGGCTGGGGATAC 61.757 68.421 0.00 0.00 0.00 2.24
809 823 3.232662 GGATACCACTCTCCCTCTAACC 58.767 54.545 0.00 0.00 0.00 2.85
810 824 3.373877 GGATACCACTCTCCCTCTAACCA 60.374 52.174 0.00 0.00 0.00 3.67
811 825 2.950990 ACCACTCTCCCTCTAACCAT 57.049 50.000 0.00 0.00 0.00 3.55
812 826 2.753247 ACCACTCTCCCTCTAACCATC 58.247 52.381 0.00 0.00 0.00 3.51
813 827 2.043227 CCACTCTCCCTCTAACCATCC 58.957 57.143 0.00 0.00 0.00 3.51
814 828 2.626950 CCACTCTCCCTCTAACCATCCA 60.627 54.545 0.00 0.00 0.00 3.41
815 829 3.107601 CACTCTCCCTCTAACCATCCAA 58.892 50.000 0.00 0.00 0.00 3.53
816 830 3.108376 ACTCTCCCTCTAACCATCCAAC 58.892 50.000 0.00 0.00 0.00 3.77
817 831 2.436173 CTCTCCCTCTAACCATCCAACC 59.564 54.545 0.00 0.00 0.00 3.77
818 832 2.196595 CTCCCTCTAACCATCCAACCA 58.803 52.381 0.00 0.00 0.00 3.67
819 833 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
820 834 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
821 835 2.356125 CCCTCTAACCATCCAACCACAG 60.356 54.545 0.00 0.00 0.00 3.66
822 836 2.356125 CCTCTAACCATCCAACCACAGG 60.356 54.545 0.00 0.00 0.00 4.00
823 837 2.305927 CTCTAACCATCCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
833 847 4.157607 CCACAGGTTGGTTCGCTT 57.842 55.556 0.00 0.00 41.10 4.68
834 848 1.654220 CCACAGGTTGGTTCGCTTG 59.346 57.895 0.00 0.00 41.10 4.01
835 849 1.008538 CACAGGTTGGTTCGCTTGC 60.009 57.895 0.00 0.00 0.00 4.01
836 850 1.152963 ACAGGTTGGTTCGCTTGCT 60.153 52.632 0.00 0.00 0.00 3.91
837 851 0.751643 ACAGGTTGGTTCGCTTGCTT 60.752 50.000 0.00 0.00 0.00 3.91
844 858 1.266718 TGGTTCGCTTGCTTGATCAAC 59.733 47.619 3.38 2.70 0.00 3.18
880 894 5.820947 CAGACCTAATTTTAACAGCCGGTAT 59.179 40.000 1.90 0.00 0.00 2.73
921 935 6.295405 GGCTCCCTCTTTAGTGAGATTATACC 60.295 46.154 0.00 0.00 36.23 2.73
944 958 5.180271 CAGCAAATGCCTGAACCAAAATAT 58.820 37.500 0.94 0.00 43.38 1.28
1037 1086 2.754375 CTGCCCACCTAAACCGGT 59.246 61.111 0.00 0.00 37.93 5.28
1107 1156 6.568869 AGAAATAGTTGAGGATCGAACTCTG 58.431 40.000 17.84 0.00 37.53 3.35
1453 1503 5.418840 GGTTCATAGATCTTTGGGCTTTGAA 59.581 40.000 12.51 0.00 30.72 2.69
1458 1508 2.151502 TCTTTGGGCTTTGAACACCA 57.848 45.000 0.00 0.00 0.00 4.17
1490 1540 7.231467 AGAGACTTTACAAATAAAAGCAGGGA 58.769 34.615 0.00 0.00 37.44 4.20
2125 2180 6.347859 AGTTCTCTACCAGGAACTTTGTAG 57.652 41.667 0.00 0.00 46.55 2.74
2127 2182 4.157246 TCTCTACCAGGAACTTTGTAGCA 58.843 43.478 0.00 0.00 39.62 3.49
2209 2264 2.983402 TATTCGTCGGAATAGCGGAG 57.017 50.000 0.00 0.00 42.71 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 130 2.818432 TCTCCACGGTGTACTTCTCTTC 59.182 50.000 7.45 0.00 0.00 2.87
187 195 1.076777 CAGCAACCCCGGGATGAAT 60.077 57.895 26.32 10.15 0.00 2.57
240 248 1.872679 CCGGACGAACGCTAGCTTC 60.873 63.158 13.93 13.78 0.00 3.86
253 261 1.757340 ATCTTCCTCGACCCCGGAC 60.757 63.158 0.73 0.00 36.24 4.79
255 263 2.797278 CCATCTTCCTCGACCCCGG 61.797 68.421 0.00 0.00 36.24 5.73
293 304 6.054860 ACCGATCCTCCTATCCATAAAATG 57.945 41.667 0.00 0.00 0.00 2.32
306 317 1.745087 TGTACGTACAACCGATCCTCC 59.255 52.381 25.54 0.00 32.40 4.30
328 339 8.662781 ATGATATACATCAACAACAGTGTACC 57.337 34.615 0.00 0.00 44.27 3.34
355 366 7.113704 TCTCACATATACTGTACGATACACG 57.886 40.000 0.00 0.00 41.45 4.49
487 501 5.640732 AGATCAACATGTCGCAATTAAACC 58.359 37.500 0.00 0.00 0.00 3.27
496 510 3.568538 AGCAAAAAGATCAACATGTCGC 58.431 40.909 0.00 0.00 0.00 5.19
498 512 5.750067 ACACAAGCAAAAAGATCAACATGTC 59.250 36.000 0.00 0.00 0.00 3.06
535 549 3.317150 CTTGCGTCTGTACTGATGTTCA 58.683 45.455 19.48 9.90 0.00 3.18
536 550 2.092838 GCTTGCGTCTGTACTGATGTTC 59.907 50.000 19.48 7.84 0.00 3.18
537 551 2.069273 GCTTGCGTCTGTACTGATGTT 58.931 47.619 19.48 0.00 0.00 2.71
538 552 1.714794 GCTTGCGTCTGTACTGATGT 58.285 50.000 19.48 0.00 0.00 3.06
539 553 0.642291 CGCTTGCGTCTGTACTGATG 59.358 55.000 15.57 15.57 0.00 3.07
540 554 1.078759 GCGCTTGCGTCTGTACTGAT 61.079 55.000 16.38 0.00 0.00 2.90
541 555 1.733041 GCGCTTGCGTCTGTACTGA 60.733 57.895 16.38 0.00 0.00 3.41
542 556 1.678269 GAGCGCTTGCGTCTGTACTG 61.678 60.000 13.26 0.00 45.69 2.74
543 557 1.444553 GAGCGCTTGCGTCTGTACT 60.445 57.895 13.26 3.73 45.69 2.73
544 558 1.078759 ATGAGCGCTTGCGTCTGTAC 61.079 55.000 13.26 0.00 45.69 2.90
545 559 0.454196 TATGAGCGCTTGCGTCTGTA 59.546 50.000 13.26 6.26 45.69 2.74
546 560 1.078759 GTATGAGCGCTTGCGTCTGT 61.079 55.000 13.26 7.66 45.69 3.41
547 561 1.078201 TGTATGAGCGCTTGCGTCTG 61.078 55.000 13.26 0.00 45.69 3.51
548 562 0.179100 ATGTATGAGCGCTTGCGTCT 60.179 50.000 13.26 13.17 45.69 4.18
549 563 1.190323 GTATGTATGAGCGCTTGCGTC 59.810 52.381 13.26 12.36 45.69 5.19
550 564 1.209128 GTATGTATGAGCGCTTGCGT 58.791 50.000 13.26 3.97 45.69 5.24
551 565 0.159554 CGTATGTATGAGCGCTTGCG 59.840 55.000 13.26 10.90 45.69 4.85
552 566 0.111089 GCGTATGTATGAGCGCTTGC 60.111 55.000 13.26 0.00 45.48 4.01
553 567 0.159554 CGCGTATGTATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
554 568 2.506544 CGCGTATGTATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
555 569 4.228451 CGCGTATGTATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
558 572 2.090658 GTGTATGCGCGTATGTATGAGC 59.909 50.000 20.45 0.00 38.31 4.26
559 573 3.565516 AGTGTATGCGCGTATGTATGAG 58.434 45.455 20.45 0.00 0.00 2.90
560 574 3.003897 TGAGTGTATGCGCGTATGTATGA 59.996 43.478 20.45 0.00 0.00 2.15
561 575 3.119628 GTGAGTGTATGCGCGTATGTATG 59.880 47.826 20.45 0.00 0.00 2.39
562 576 3.305964 GTGAGTGTATGCGCGTATGTAT 58.694 45.455 20.45 2.87 0.00 2.29
563 577 2.542205 GGTGAGTGTATGCGCGTATGTA 60.542 50.000 20.45 5.53 0.00 2.29
564 578 1.556564 GTGAGTGTATGCGCGTATGT 58.443 50.000 20.45 0.00 0.00 2.29
565 579 0.852777 GGTGAGTGTATGCGCGTATG 59.147 55.000 20.45 0.00 0.00 2.39
566 580 0.744874 AGGTGAGTGTATGCGCGTAT 59.255 50.000 15.52 15.52 0.00 3.06
567 581 0.099968 GAGGTGAGTGTATGCGCGTA 59.900 55.000 8.43 4.92 0.00 4.42
568 582 1.153823 GAGGTGAGTGTATGCGCGT 60.154 57.895 8.43 7.55 0.00 6.01
569 583 0.380733 TAGAGGTGAGTGTATGCGCG 59.619 55.000 0.00 0.00 0.00 6.86
570 584 2.034685 TCATAGAGGTGAGTGTATGCGC 59.965 50.000 0.00 0.00 0.00 6.09
571 585 3.990318 TCATAGAGGTGAGTGTATGCG 57.010 47.619 0.00 0.00 0.00 4.73
572 586 4.450419 GCATTCATAGAGGTGAGTGTATGC 59.550 45.833 0.00 0.00 37.92 3.14
573 587 5.464722 GTGCATTCATAGAGGTGAGTGTATG 59.535 44.000 0.00 0.00 37.92 2.39
574 588 5.129320 TGTGCATTCATAGAGGTGAGTGTAT 59.871 40.000 0.00 0.00 37.92 2.29
575 589 4.466015 TGTGCATTCATAGAGGTGAGTGTA 59.534 41.667 0.00 0.00 37.92 2.90
576 590 3.261643 TGTGCATTCATAGAGGTGAGTGT 59.738 43.478 0.00 0.00 37.92 3.55
577 591 3.620374 GTGTGCATTCATAGAGGTGAGTG 59.380 47.826 0.00 0.00 38.45 3.51
578 592 3.261643 TGTGTGCATTCATAGAGGTGAGT 59.738 43.478 0.00 0.00 0.00 3.41
579 593 3.620374 GTGTGTGCATTCATAGAGGTGAG 59.380 47.826 0.00 0.00 0.00 3.51
580 594 3.599343 GTGTGTGCATTCATAGAGGTGA 58.401 45.455 0.00 0.00 0.00 4.02
581 595 2.349580 CGTGTGTGCATTCATAGAGGTG 59.650 50.000 0.00 0.00 0.00 4.00
582 596 2.621338 CGTGTGTGCATTCATAGAGGT 58.379 47.619 0.00 0.00 0.00 3.85
583 597 1.328680 GCGTGTGTGCATTCATAGAGG 59.671 52.381 0.00 0.00 34.15 3.69
584 598 2.001872 TGCGTGTGTGCATTCATAGAG 58.998 47.619 0.00 0.00 40.62 2.43
585 599 2.091852 TGCGTGTGTGCATTCATAGA 57.908 45.000 0.00 0.00 40.62 1.98
594 608 1.087771 GGTAGGGTATGCGTGTGTGC 61.088 60.000 0.00 0.00 0.00 4.57
595 609 0.461339 GGGTAGGGTATGCGTGTGTG 60.461 60.000 0.00 0.00 0.00 3.82
596 610 1.619807 GGGGTAGGGTATGCGTGTGT 61.620 60.000 0.00 0.00 0.00 3.72
597 611 1.145377 GGGGTAGGGTATGCGTGTG 59.855 63.158 0.00 0.00 0.00 3.82
598 612 0.262580 TAGGGGTAGGGTATGCGTGT 59.737 55.000 0.00 0.00 0.00 4.49
599 613 1.640917 ATAGGGGTAGGGTATGCGTG 58.359 55.000 0.00 0.00 0.00 5.34
600 614 3.438183 CTTATAGGGGTAGGGTATGCGT 58.562 50.000 0.00 0.00 0.00 5.24
601 615 2.167900 GCTTATAGGGGTAGGGTATGCG 59.832 54.545 0.00 0.00 0.00 4.73
602 616 3.055312 GTGCTTATAGGGGTAGGGTATGC 60.055 52.174 0.00 0.00 0.00 3.14
603 617 3.518303 GGTGCTTATAGGGGTAGGGTATG 59.482 52.174 0.00 0.00 0.00 2.39
604 618 3.408586 AGGTGCTTATAGGGGTAGGGTAT 59.591 47.826 0.00 0.00 0.00 2.73
605 619 2.799576 AGGTGCTTATAGGGGTAGGGTA 59.200 50.000 0.00 0.00 0.00 3.69
606 620 1.584105 AGGTGCTTATAGGGGTAGGGT 59.416 52.381 0.00 0.00 0.00 4.34
607 621 2.417719 AGGTGCTTATAGGGGTAGGG 57.582 55.000 0.00 0.00 0.00 3.53
608 622 3.314693 TGAAGGTGCTTATAGGGGTAGG 58.685 50.000 0.00 0.00 0.00 3.18
609 623 4.593206 TCATGAAGGTGCTTATAGGGGTAG 59.407 45.833 0.00 0.00 0.00 3.18
610 624 4.562767 TCATGAAGGTGCTTATAGGGGTA 58.437 43.478 0.00 0.00 0.00 3.69
611 625 3.392616 CTCATGAAGGTGCTTATAGGGGT 59.607 47.826 0.00 0.00 0.00 4.95
612 626 3.648067 TCTCATGAAGGTGCTTATAGGGG 59.352 47.826 0.00 0.00 0.00 4.79
613 627 4.346418 AGTCTCATGAAGGTGCTTATAGGG 59.654 45.833 0.00 0.00 0.00 3.53
614 628 5.069648 TCAGTCTCATGAAGGTGCTTATAGG 59.930 44.000 0.00 0.00 0.00 2.57
615 629 6.154203 TCAGTCTCATGAAGGTGCTTATAG 57.846 41.667 0.00 0.00 0.00 1.31
616 630 5.452496 GCTCAGTCTCATGAAGGTGCTTATA 60.452 44.000 0.00 0.00 0.00 0.98
617 631 4.682859 GCTCAGTCTCATGAAGGTGCTTAT 60.683 45.833 0.00 0.00 0.00 1.73
618 632 3.368843 GCTCAGTCTCATGAAGGTGCTTA 60.369 47.826 0.00 0.00 0.00 3.09
619 633 2.614987 GCTCAGTCTCATGAAGGTGCTT 60.615 50.000 0.00 0.00 0.00 3.91
620 634 1.066286 GCTCAGTCTCATGAAGGTGCT 60.066 52.381 0.00 0.00 0.00 4.40
621 635 1.367659 GCTCAGTCTCATGAAGGTGC 58.632 55.000 0.00 0.00 0.00 5.01
622 636 1.738365 CGGCTCAGTCTCATGAAGGTG 60.738 57.143 0.00 0.00 0.00 4.00
623 637 0.534412 CGGCTCAGTCTCATGAAGGT 59.466 55.000 0.00 0.00 0.00 3.50
624 638 0.179089 CCGGCTCAGTCTCATGAAGG 60.179 60.000 0.00 0.00 0.00 3.46
625 639 0.809241 GCCGGCTCAGTCTCATGAAG 60.809 60.000 22.15 0.00 0.00 3.02
626 640 1.219124 GCCGGCTCAGTCTCATGAA 59.781 57.895 22.15 0.00 0.00 2.57
627 641 1.332889 ATGCCGGCTCAGTCTCATGA 61.333 55.000 29.70 1.81 0.00 3.07
628 642 1.145598 ATGCCGGCTCAGTCTCATG 59.854 57.895 29.70 0.00 0.00 3.07
629 643 1.145598 CATGCCGGCTCAGTCTCAT 59.854 57.895 29.70 6.94 0.00 2.90
630 644 2.230994 GACATGCCGGCTCAGTCTCA 62.231 60.000 29.70 4.25 0.00 3.27
631 645 1.520342 GACATGCCGGCTCAGTCTC 60.520 63.158 29.70 9.51 0.00 3.36
632 646 1.620739 ATGACATGCCGGCTCAGTCT 61.621 55.000 31.39 20.84 0.00 3.24
633 647 1.153289 ATGACATGCCGGCTCAGTC 60.153 57.895 29.70 28.59 0.00 3.51
634 648 1.153289 GATGACATGCCGGCTCAGT 60.153 57.895 29.70 22.43 0.00 3.41
635 649 0.463295 AAGATGACATGCCGGCTCAG 60.463 55.000 29.70 19.20 0.00 3.35
636 650 0.745486 CAAGATGACATGCCGGCTCA 60.745 55.000 29.70 23.34 0.00 4.26
637 651 0.462581 TCAAGATGACATGCCGGCTC 60.463 55.000 29.70 17.89 0.00 4.70
638 652 0.035152 TTCAAGATGACATGCCGGCT 60.035 50.000 29.70 7.33 0.00 5.52
639 653 0.810648 TTTCAAGATGACATGCCGGC 59.189 50.000 22.73 22.73 0.00 6.13
640 654 3.788333 AATTTCAAGATGACATGCCGG 57.212 42.857 0.00 0.00 0.00 6.13
641 655 4.730042 CGTAAATTTCAAGATGACATGCCG 59.270 41.667 0.00 0.00 0.00 5.69
642 656 5.879237 TCGTAAATTTCAAGATGACATGCC 58.121 37.500 0.00 0.00 0.00 4.40
643 657 7.023575 ACTTCGTAAATTTCAAGATGACATGC 58.976 34.615 0.00 0.00 0.00 4.06
644 658 8.229811 TGACTTCGTAAATTTCAAGATGACATG 58.770 33.333 0.00 0.00 0.00 3.21
645 659 8.230486 GTGACTTCGTAAATTTCAAGATGACAT 58.770 33.333 0.00 0.00 0.00 3.06
646 660 7.307751 GGTGACTTCGTAAATTTCAAGATGACA 60.308 37.037 0.00 0.26 0.00 3.58
647 661 7.015877 GGTGACTTCGTAAATTTCAAGATGAC 58.984 38.462 0.00 0.00 0.00 3.06
648 662 6.128661 CGGTGACTTCGTAAATTTCAAGATGA 60.129 38.462 0.00 0.00 0.00 2.92
649 663 6.015504 CGGTGACTTCGTAAATTTCAAGATG 58.984 40.000 0.00 0.00 0.00 2.90
650 664 5.929992 TCGGTGACTTCGTAAATTTCAAGAT 59.070 36.000 0.00 0.00 0.00 2.40
651 665 5.291178 TCGGTGACTTCGTAAATTTCAAGA 58.709 37.500 0.00 0.00 0.00 3.02
652 666 5.585500 TCGGTGACTTCGTAAATTTCAAG 57.415 39.130 0.00 0.00 0.00 3.02
653 667 5.049954 CCTTCGGTGACTTCGTAAATTTCAA 60.050 40.000 0.00 0.00 0.00 2.69
654 668 4.449743 CCTTCGGTGACTTCGTAAATTTCA 59.550 41.667 0.00 0.00 0.00 2.69
655 669 4.668431 GCCTTCGGTGACTTCGTAAATTTC 60.668 45.833 0.00 0.00 0.00 2.17
656 670 3.187842 GCCTTCGGTGACTTCGTAAATTT 59.812 43.478 0.00 0.00 0.00 1.82
657 671 2.740447 GCCTTCGGTGACTTCGTAAATT 59.260 45.455 0.00 0.00 0.00 1.82
658 672 2.289195 TGCCTTCGGTGACTTCGTAAAT 60.289 45.455 0.00 0.00 0.00 1.40
659 673 1.068895 TGCCTTCGGTGACTTCGTAAA 59.931 47.619 0.00 0.00 0.00 2.01
660 674 0.675083 TGCCTTCGGTGACTTCGTAA 59.325 50.000 0.00 0.00 0.00 3.18
661 675 0.038892 GTGCCTTCGGTGACTTCGTA 60.039 55.000 0.00 0.00 0.00 3.43
662 676 1.300697 GTGCCTTCGGTGACTTCGT 60.301 57.895 0.00 0.00 0.00 3.85
663 677 2.027625 GGTGCCTTCGGTGACTTCG 61.028 63.158 0.00 0.00 0.00 3.79
664 678 0.670854 GAGGTGCCTTCGGTGACTTC 60.671 60.000 0.00 0.00 0.00 3.01
665 679 1.371558 GAGGTGCCTTCGGTGACTT 59.628 57.895 0.00 0.00 0.00 3.01
666 680 2.932234 CGAGGTGCCTTCGGTGACT 61.932 63.158 0.00 0.00 0.00 3.41
667 681 2.432628 CGAGGTGCCTTCGGTGAC 60.433 66.667 0.00 0.00 0.00 3.67
668 682 2.915659 ACGAGGTGCCTTCGGTGA 60.916 61.111 10.49 0.00 0.00 4.02
669 683 2.432628 GACGAGGTGCCTTCGGTG 60.433 66.667 10.49 0.00 0.00 4.94
670 684 4.052229 CGACGAGGTGCCTTCGGT 62.052 66.667 10.49 3.62 0.00 4.69
671 685 3.966026 GACGACGAGGTGCCTTCGG 62.966 68.421 14.45 1.60 32.48 4.30
672 686 2.504244 GACGACGAGGTGCCTTCG 60.504 66.667 0.00 9.90 33.87 3.79
673 687 2.504244 CGACGACGAGGTGCCTTC 60.504 66.667 0.00 0.00 42.66 3.46
674 688 2.981909 TCGACGACGAGGTGCCTT 60.982 61.111 5.75 0.00 43.81 4.35
696 710 2.994578 GCTTTTAGTGGAAGGAGACGTC 59.005 50.000 7.70 7.70 38.20 4.34
697 711 2.609737 CGCTTTTAGTGGAAGGAGACGT 60.610 50.000 0.00 0.00 0.00 4.34
698 712 1.993370 CGCTTTTAGTGGAAGGAGACG 59.007 52.381 0.00 0.00 0.00 4.18
699 713 1.732809 GCGCTTTTAGTGGAAGGAGAC 59.267 52.381 0.00 0.00 0.00 3.36
700 714 1.346395 TGCGCTTTTAGTGGAAGGAGA 59.654 47.619 9.73 0.00 0.00 3.71
701 715 1.808411 TGCGCTTTTAGTGGAAGGAG 58.192 50.000 9.73 0.00 0.00 3.69
702 716 2.356135 GATGCGCTTTTAGTGGAAGGA 58.644 47.619 9.73 0.00 27.73 3.36
703 717 1.062587 CGATGCGCTTTTAGTGGAAGG 59.937 52.381 9.73 0.00 27.73 3.46
704 718 2.442189 CGATGCGCTTTTAGTGGAAG 57.558 50.000 9.73 0.00 27.73 3.46
717 731 3.673746 TTAAGAATTTCAGGCGATGCG 57.326 42.857 0.00 0.00 0.00 4.73
718 732 7.985634 TTTATTTAAGAATTTCAGGCGATGC 57.014 32.000 0.00 0.00 0.00 3.91
719 733 9.956720 AGATTTATTTAAGAATTTCAGGCGATG 57.043 29.630 0.00 0.00 0.00 3.84
722 736 9.884465 CCTAGATTTATTTAAGAATTTCAGGCG 57.116 33.333 0.00 0.00 0.00 5.52
735 749 9.719355 TGCTCGCATTATTCCTAGATTTATTTA 57.281 29.630 0.00 0.00 0.00 1.40
736 750 8.507249 GTGCTCGCATTATTCCTAGATTTATTT 58.493 33.333 0.00 0.00 0.00 1.40
737 751 7.119846 GGTGCTCGCATTATTCCTAGATTTATT 59.880 37.037 0.00 0.00 0.00 1.40
738 752 6.595716 GGTGCTCGCATTATTCCTAGATTTAT 59.404 38.462 0.00 0.00 0.00 1.40
739 753 5.932303 GGTGCTCGCATTATTCCTAGATTTA 59.068 40.000 0.00 0.00 0.00 1.40
740 754 4.757149 GGTGCTCGCATTATTCCTAGATTT 59.243 41.667 0.00 0.00 0.00 2.17
741 755 4.202357 TGGTGCTCGCATTATTCCTAGATT 60.202 41.667 0.00 0.00 0.00 2.40
742 756 3.324846 TGGTGCTCGCATTATTCCTAGAT 59.675 43.478 0.00 0.00 0.00 1.98
743 757 2.698274 TGGTGCTCGCATTATTCCTAGA 59.302 45.455 0.00 0.00 0.00 2.43
744 758 3.062763 CTGGTGCTCGCATTATTCCTAG 58.937 50.000 0.00 0.00 0.00 3.02
745 759 2.224281 CCTGGTGCTCGCATTATTCCTA 60.224 50.000 0.00 0.00 0.00 2.94
746 760 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
747 761 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
748 762 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
749 763 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
750 764 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
751 765 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
752 766 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
753 767 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
754 768 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
755 769 0.169009 GTTCAAATCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
756 770 0.804989 GGTTCAAATCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
757 771 1.177401 GGGTTCAAATCCTGGTGCTC 58.823 55.000 0.00 0.00 0.00 4.26
758 772 0.779997 AGGGTTCAAATCCTGGTGCT 59.220 50.000 0.00 0.00 38.36 4.40
759 773 3.363787 AGGGTTCAAATCCTGGTGC 57.636 52.632 0.00 0.00 38.36 5.01
775 789 2.368192 TATCCCCAGCCCACCAGG 60.368 66.667 0.00 0.00 39.47 4.45
776 790 2.757124 GGTATCCCCAGCCCACCAG 61.757 68.421 0.00 0.00 0.00 4.00
777 791 2.694616 GGTATCCCCAGCCCACCA 60.695 66.667 0.00 0.00 0.00 4.17
778 792 2.694616 TGGTATCCCCAGCCCACC 60.695 66.667 0.00 0.00 38.72 4.61
779 793 1.984288 GAGTGGTATCCCCAGCCCAC 61.984 65.000 0.00 0.00 46.45 4.61
780 794 1.692749 GAGTGGTATCCCCAGCCCA 60.693 63.158 0.00 0.00 46.45 5.36
781 795 1.384643 AGAGTGGTATCCCCAGCCC 60.385 63.158 0.00 0.00 46.45 5.19
782 796 1.411651 GGAGAGTGGTATCCCCAGCC 61.412 65.000 0.00 0.00 46.45 4.85
783 797 2.137692 GGAGAGTGGTATCCCCAGC 58.862 63.158 0.00 0.00 46.45 4.85
788 802 3.232662 GGTTAGAGGGAGAGTGGTATCC 58.767 54.545 0.00 0.00 32.72 2.59
789 803 3.912248 TGGTTAGAGGGAGAGTGGTATC 58.088 50.000 0.00 0.00 0.00 2.24
790 804 4.484912 GATGGTTAGAGGGAGAGTGGTAT 58.515 47.826 0.00 0.00 0.00 2.73
791 805 3.373877 GGATGGTTAGAGGGAGAGTGGTA 60.374 52.174 0.00 0.00 0.00 3.25
792 806 2.627217 GGATGGTTAGAGGGAGAGTGGT 60.627 54.545 0.00 0.00 0.00 4.16
793 807 2.043227 GGATGGTTAGAGGGAGAGTGG 58.957 57.143 0.00 0.00 0.00 4.00
794 808 2.752030 TGGATGGTTAGAGGGAGAGTG 58.248 52.381 0.00 0.00 0.00 3.51
795 809 3.108376 GTTGGATGGTTAGAGGGAGAGT 58.892 50.000 0.00 0.00 0.00 3.24
796 810 2.436173 GGTTGGATGGTTAGAGGGAGAG 59.564 54.545 0.00 0.00 0.00 3.20
797 811 2.225779 TGGTTGGATGGTTAGAGGGAGA 60.226 50.000 0.00 0.00 0.00 3.71
798 812 2.092914 GTGGTTGGATGGTTAGAGGGAG 60.093 54.545 0.00 0.00 0.00 4.30
799 813 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
800 814 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
801 815 2.356125 CCTGTGGTTGGATGGTTAGAGG 60.356 54.545 0.00 0.00 0.00 3.69
802 816 2.305927 ACCTGTGGTTGGATGGTTAGAG 59.694 50.000 0.00 0.00 27.29 2.43
803 817 2.344592 ACCTGTGGTTGGATGGTTAGA 58.655 47.619 0.00 0.00 27.29 2.10
804 818 2.879103 ACCTGTGGTTGGATGGTTAG 57.121 50.000 0.00 0.00 27.29 2.34
817 831 1.008538 GCAAGCGAACCAACCTGTG 60.009 57.895 0.00 0.00 0.00 3.66
818 832 0.751643 AAGCAAGCGAACCAACCTGT 60.752 50.000 0.00 0.00 0.00 4.00
819 833 0.318107 CAAGCAAGCGAACCAACCTG 60.318 55.000 0.00 0.00 0.00 4.00
820 834 0.465460 TCAAGCAAGCGAACCAACCT 60.465 50.000 0.00 0.00 0.00 3.50
821 835 0.598065 ATCAAGCAAGCGAACCAACC 59.402 50.000 0.00 0.00 0.00 3.77
822 836 1.266718 TGATCAAGCAAGCGAACCAAC 59.733 47.619 0.00 0.00 0.00 3.77
823 837 1.603456 TGATCAAGCAAGCGAACCAA 58.397 45.000 0.00 0.00 0.00 3.67
824 838 1.266718 GTTGATCAAGCAAGCGAACCA 59.733 47.619 8.80 0.00 0.00 3.67
825 839 1.537202 AGTTGATCAAGCAAGCGAACC 59.463 47.619 8.80 0.00 0.00 3.62
826 840 2.413371 GGAGTTGATCAAGCAAGCGAAC 60.413 50.000 8.80 0.00 0.00 3.95
827 841 1.806542 GGAGTTGATCAAGCAAGCGAA 59.193 47.619 8.80 0.00 0.00 4.70
828 842 1.002430 AGGAGTTGATCAAGCAAGCGA 59.998 47.619 8.80 0.00 0.00 4.93
829 843 1.446907 AGGAGTTGATCAAGCAAGCG 58.553 50.000 8.80 0.00 0.00 4.68
830 844 2.941720 CCTAGGAGTTGATCAAGCAAGC 59.058 50.000 8.80 0.00 0.00 4.01
831 845 2.941720 GCCTAGGAGTTGATCAAGCAAG 59.058 50.000 14.75 5.79 0.00 4.01
832 846 2.305635 TGCCTAGGAGTTGATCAAGCAA 59.694 45.455 14.75 0.00 0.00 3.91
833 847 1.908619 TGCCTAGGAGTTGATCAAGCA 59.091 47.619 14.75 10.17 0.00 3.91
834 848 2.698855 TGCCTAGGAGTTGATCAAGC 57.301 50.000 14.75 7.50 0.00 4.01
835 849 2.941720 GCTTGCCTAGGAGTTGATCAAG 59.058 50.000 14.75 14.95 34.32 3.02
836 850 2.305635 TGCTTGCCTAGGAGTTGATCAA 59.694 45.455 14.75 3.38 0.00 2.57
837 851 1.908619 TGCTTGCCTAGGAGTTGATCA 59.091 47.619 14.75 0.00 0.00 2.92
844 858 1.781786 TAGGTCTGCTTGCCTAGGAG 58.218 55.000 14.75 2.50 43.23 3.69
880 894 3.088532 GGAGCCATGTTCATTGTTACCA 58.911 45.455 0.00 0.00 0.00 3.25
893 907 3.191078 CTCACTAAAGAGGGAGCCATG 57.809 52.381 0.00 0.00 46.20 3.66
921 935 2.529780 TTTGGTTCAGGCATTTGCTG 57.470 45.000 2.12 0.00 41.70 4.41
1124 1173 6.062095 AGCTTGTGACTGGTAGTAAAACATT 58.938 36.000 0.00 0.00 0.00 2.71
1320 1370 3.815856 TGCAAGTTTGAAAGATTGCCA 57.184 38.095 19.17 9.21 45.76 4.92
1453 1503 6.681729 TGTAAAGTCTCTATTCCTTGGTGT 57.318 37.500 0.00 0.00 0.00 4.16
1988 2041 5.356470 GCTCAGTCTATCTGGAATGCTTTTT 59.644 40.000 0.00 0.00 43.76 1.94
2016 2069 5.457487 GGGGAATCCAAATGAAACCCTTTTT 60.457 40.000 0.09 0.00 40.26 1.94
2125 2180 1.463056 TGTGCTAAGTAATGTGCGTGC 59.537 47.619 0.00 0.00 0.00 5.34
2127 2182 3.399330 AGTTGTGCTAAGTAATGTGCGT 58.601 40.909 0.00 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.