Multiple sequence alignment - TraesCS7D01G360300

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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 TraesCS7D01G360300 chr7D 100.000 2966 0 0 1 2966 463255912 463258877 0.000000e+00 5478
1 TraesCS7D01G360300 chr7B 93.590 1560 56 16 679 2199 488419389 488417835 0.000000e+00 2287
2 TraesCS7D01G360300 chr7B 97.963 589 10 2 2379 2966 488417800 488417213 0.000000e+00 1020
3 TraesCS7D01G360300 chr7B 88.610 439 38 5 561 999 488703431 488703005 9.420000e-145 523
4 TraesCS7D01G360300 chr7A 90.244 1558 78 27 678 2196 536989503 536987981 0.000000e+00 1967
5 TraesCS7D01G360300 chr7A 93.594 562 30 2 1 561 115537479 115536923 0.000000e+00 833
6 TraesCS7D01G360300 chr7A 89.214 547 43 7 2297 2834 536987855 536987316 0.000000e+00 669
7 TraesCS7D01G360300 chr7A 100.000 40 0 0 2157 2196 536987982 536987943 1.140000e-09 75
8 TraesCS7D01G360300 chr3B 93.950 562 28 2 1 561 192887474 192888030 0.000000e+00 845
9 TraesCS7D01G360300 chr3B 73.884 605 130 24 1223 1825 260355336 260354758 1.790000e-52 217
10 TraesCS7D01G360300 chr6D 93.772 562 29 2 1 561 162289044 162288488 0.000000e+00 839
11 TraesCS7D01G360300 chr6D 93.594 562 30 2 1 561 433634916 433635472 0.000000e+00 833
12 TraesCS7D01G360300 chr6A 93.772 562 29 2 1 561 249152948 249153504 0.000000e+00 839
13 TraesCS7D01G360300 chr5D 93.594 562 30 2 1 561 324395470 324394914 0.000000e+00 833
14 TraesCS7D01G360300 chr3D 93.594 562 30 2 1 561 561720970 561720414 0.000000e+00 833
15 TraesCS7D01G360300 chr3D 93.451 565 30 3 1 564 42362167 42362725 0.000000e+00 832
16 TraesCS7D01G360300 chr1B 93.594 562 30 2 1 561 643595638 643595082 0.000000e+00 833


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 TraesCS7D01G360300 chr7D 463255912 463258877 2965 False 5478.000000 5478 100.000000 1 2966 1 chr7D.!!$F1 2965
1 TraesCS7D01G360300 chr7B 488417213 488419389 2176 True 1653.500000 2287 95.776500 679 2966 2 chr7B.!!$R2 2287
2 TraesCS7D01G360300 chr7A 536987316 536989503 2187 True 903.666667 1967 93.152667 678 2834 3 chr7A.!!$R2 2156
3 TraesCS7D01G360300 chr7A 115536923 115537479 556 True 833.000000 833 93.594000 1 561 1 chr7A.!!$R1 560
4 TraesCS7D01G360300 chr3B 192887474 192888030 556 False 845.000000 845 93.950000 1 561 1 chr3B.!!$F1 560
5 TraesCS7D01G360300 chr3B 260354758 260355336 578 True 217.000000 217 73.884000 1223 1825 1 chr3B.!!$R1 602
6 TraesCS7D01G360300 chr6D 162288488 162289044 556 True 839.000000 839 93.772000 1 561 1 chr6D.!!$R1 560
7 TraesCS7D01G360300 chr6D 433634916 433635472 556 False 833.000000 833 93.594000 1 561 1 chr6D.!!$F1 560
8 TraesCS7D01G360300 chr6A 249152948 249153504 556 False 839.000000 839 93.772000 1 561 1 chr6A.!!$F1 560
9 TraesCS7D01G360300 chr5D 324394914 324395470 556 True 833.000000 833 93.594000 1 561 1 chr5D.!!$R1 560
10 TraesCS7D01G360300 chr3D 561720414 561720970 556 True 833.000000 833 93.594000 1 561 1 chr3D.!!$R1 560
11 TraesCS7D01G360300 chr3D 42362167 42362725 558 False 832.000000 832 93.451000 1 564 1 chr3D.!!$F1 563
12 TraesCS7D01G360300 chr1B 643595082 643595638 556 True 833.000000 833 93.594000 1 561 1 chr1B.!!$R1 560

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
650 652 0.529119 GGCCGAACATCGAACCGTAT 60.529 55.0 0.58 0.0 43.74 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2294 0.036164 TGGTGGCTTTGTACTGCGAT 59.964 50.0 0.0 0.0 0.0 4.58 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
45 46 3.644966 ACCACTTCAGTTCCTTGAACA 57.355 42.857 9.42 0.00 44.11 3.18
145 146 2.279741 ACACGATGGTCACATATGTGC 58.720 47.619 27.71 21.74 45.25 4.57
256 257 1.825090 TTCGAATGGACAATGCTGCT 58.175 45.000 0.00 0.00 0.00 4.24
277 278 3.476552 TGAATTCTCCTCACGTGCTTTT 58.523 40.909 11.67 0.00 0.00 2.27
279 280 4.690748 TGAATTCTCCTCACGTGCTTTTAG 59.309 41.667 11.67 2.04 0.00 1.85
318 319 1.815003 GGGGATTGAAGTTCAGCACTG 59.185 52.381 5.56 0.00 35.12 3.66
367 368 6.397272 TGGTTTGGCTGAATCATTGATTAAC 58.603 36.000 11.79 10.81 31.89 2.01
369 370 7.043565 GGTTTGGCTGAATCATTGATTAACAT 58.956 34.615 11.79 0.00 31.89 2.71
417 418 2.035704 TGACGAATTGCAACTTGCCAAT 59.964 40.909 11.29 8.12 44.23 3.16
418 419 3.059166 GACGAATTGCAACTTGCCAATT 58.941 40.909 11.29 14.89 44.23 2.32
423 424 5.404968 CGAATTGCAACTTGCCAATTTCTTA 59.595 36.000 11.29 0.00 44.23 2.10
445 447 1.301423 GGGTCACGCTGTTTTACACA 58.699 50.000 0.00 0.00 0.00 3.72
451 453 2.542178 CACGCTGTTTTACACACTGCTA 59.458 45.455 0.00 0.00 37.05 3.49
475 477 5.815581 ACTTGATACAATTGAGGCCAACTA 58.184 37.500 13.59 0.00 34.72 2.24
476 478 5.648092 ACTTGATACAATTGAGGCCAACTAC 59.352 40.000 13.59 0.00 34.72 2.73
477 479 5.172687 TGATACAATTGAGGCCAACTACA 57.827 39.130 13.59 0.00 34.72 2.74
478 480 5.754782 TGATACAATTGAGGCCAACTACAT 58.245 37.500 13.59 0.00 34.72 2.29
479 481 6.894682 TGATACAATTGAGGCCAACTACATA 58.105 36.000 13.59 0.00 34.72 2.29
480 482 7.517320 TGATACAATTGAGGCCAACTACATAT 58.483 34.615 13.59 0.00 34.72 1.78
499 501 7.623999 ACATATCATATCACAGTTCTTCCCT 57.376 36.000 0.00 0.00 0.00 4.20
504 506 5.721480 TCATATCACAGTTCTTCCCTTCTGA 59.279 40.000 0.00 0.00 0.00 3.27
525 527 5.074115 TGAAATTGGTACGTGGAAATCCTT 58.926 37.500 0.00 0.00 36.82 3.36
527 529 4.569719 ATTGGTACGTGGAAATCCTTCT 57.430 40.909 0.00 0.00 36.82 2.85
535 537 5.010282 ACGTGGAAATCCTTCTAGCATTTT 58.990 37.500 0.44 0.00 36.82 1.82
561 563 1.076332 GCGTAAGTTCGGATGTGCTT 58.924 50.000 0.00 0.00 41.68 3.91
562 564 1.201921 GCGTAAGTTCGGATGTGCTTG 60.202 52.381 0.00 0.00 41.68 4.01
563 565 1.201921 CGTAAGTTCGGATGTGCTTGC 60.202 52.381 0.00 0.00 0.00 4.01
564 566 1.130561 GTAAGTTCGGATGTGCTTGCC 59.869 52.381 0.00 0.00 0.00 4.52
565 567 1.577328 AAGTTCGGATGTGCTTGCCG 61.577 55.000 0.00 0.00 46.08 5.69
576 578 3.052082 CTTGCCGAGCTGTGTGGG 61.052 66.667 0.00 0.00 0.00 4.61
577 579 3.832237 CTTGCCGAGCTGTGTGGGT 62.832 63.158 0.00 0.00 0.00 4.51
578 580 3.825160 TTGCCGAGCTGTGTGGGTC 62.825 63.158 0.00 0.00 0.00 4.46
581 583 4.363990 CGAGCTGTGTGGGTCGCT 62.364 66.667 0.00 0.00 47.00 4.93
582 584 2.740055 GAGCTGTGTGGGTCGCTG 60.740 66.667 0.00 0.00 31.96 5.18
583 585 4.996434 AGCTGTGTGGGTCGCTGC 62.996 66.667 0.00 0.00 46.73 5.25
585 587 4.624364 CTGTGTGGGTCGCTGCCA 62.624 66.667 0.00 0.00 0.00 4.92
586 588 4.624364 TGTGTGGGTCGCTGCCAG 62.624 66.667 0.00 0.00 0.00 4.85
600 602 2.360852 CCAGCCTGGCTCCACTTG 60.361 66.667 20.49 7.34 36.40 3.16
601 603 2.360852 CAGCCTGGCTCCACTTGG 60.361 66.667 20.49 1.27 36.40 3.61
602 604 2.530151 AGCCTGGCTCCACTTGGA 60.530 61.111 17.22 0.00 43.08 3.53
603 605 2.360475 GCCTGGCTCCACTTGGAC 60.360 66.667 12.43 0.00 39.78 4.02
604 606 2.046892 CCTGGCTCCACTTGGACG 60.047 66.667 0.00 0.00 39.78 4.79
605 607 2.743928 CTGGCTCCACTTGGACGC 60.744 66.667 9.84 9.84 39.78 5.19
606 608 3.241530 TGGCTCCACTTGGACGCT 61.242 61.111 15.12 0.00 39.78 5.07
607 609 2.032681 GGCTCCACTTGGACGCTT 59.967 61.111 15.12 0.00 39.78 4.68
608 610 2.035442 GGCTCCACTTGGACGCTTC 61.035 63.158 15.12 0.00 39.78 3.86
609 611 1.301716 GCTCCACTTGGACGCTTCA 60.302 57.895 10.66 0.00 39.78 3.02
610 612 0.884704 GCTCCACTTGGACGCTTCAA 60.885 55.000 10.66 0.00 39.78 2.69
611 613 1.813513 CTCCACTTGGACGCTTCAAT 58.186 50.000 0.00 0.00 39.78 2.57
612 614 2.154462 CTCCACTTGGACGCTTCAATT 58.846 47.619 0.00 0.00 39.78 2.32
613 615 2.554032 CTCCACTTGGACGCTTCAATTT 59.446 45.455 0.00 0.00 39.78 1.82
614 616 2.552315 TCCACTTGGACGCTTCAATTTC 59.448 45.455 0.00 0.00 39.78 2.17
615 617 2.574322 CACTTGGACGCTTCAATTTCG 58.426 47.619 0.00 0.00 0.00 3.46
616 618 2.032030 CACTTGGACGCTTCAATTTCGT 60.032 45.455 0.00 0.00 39.33 3.85
617 619 2.032030 ACTTGGACGCTTCAATTTCGTG 60.032 45.455 0.00 0.00 36.50 4.35
618 620 1.872388 TGGACGCTTCAATTTCGTGA 58.128 45.000 0.00 0.00 36.50 4.35
619 621 2.422597 TGGACGCTTCAATTTCGTGAT 58.577 42.857 0.00 0.00 36.50 3.06
620 622 2.811431 TGGACGCTTCAATTTCGTGATT 59.189 40.909 0.00 0.00 36.50 2.57
621 623 3.163594 GGACGCTTCAATTTCGTGATTG 58.836 45.455 7.03 7.03 38.16 2.67
622 624 3.163594 GACGCTTCAATTTCGTGATTGG 58.836 45.455 11.58 1.65 37.56 3.16
623 625 2.811431 ACGCTTCAATTTCGTGATTGGA 59.189 40.909 11.58 4.65 37.56 3.53
624 626 3.163594 CGCTTCAATTTCGTGATTGGAC 58.836 45.455 11.58 3.91 37.56 4.02
625 627 3.501950 GCTTCAATTTCGTGATTGGACC 58.498 45.455 11.58 0.00 37.56 4.46
626 628 3.747193 CTTCAATTTCGTGATTGGACCG 58.253 45.455 11.58 0.00 37.56 4.79
627 629 3.046968 TCAATTTCGTGATTGGACCGA 57.953 42.857 11.58 0.00 37.56 4.69
628 630 2.739913 TCAATTTCGTGATTGGACCGAC 59.260 45.455 11.58 0.00 37.56 4.79
629 631 2.465860 ATTTCGTGATTGGACCGACA 57.534 45.000 0.00 0.00 0.00 4.35
630 632 1.504359 TTTCGTGATTGGACCGACAC 58.496 50.000 5.73 5.73 0.00 3.67
631 633 3.459027 CGTGATTGGACCGACACG 58.541 61.111 18.21 18.21 46.78 4.49
641 643 3.186047 CCGACACGGCCGAACATC 61.186 66.667 35.90 20.79 41.17 3.06
642 644 3.541831 CGACACGGCCGAACATCG 61.542 66.667 35.90 27.64 40.07 3.84
643 645 2.126228 GACACGGCCGAACATCGA 60.126 61.111 35.90 0.00 43.74 3.59
644 646 1.735198 GACACGGCCGAACATCGAA 60.735 57.895 35.90 0.00 43.74 3.71
645 647 1.952266 GACACGGCCGAACATCGAAC 61.952 60.000 35.90 8.25 43.74 3.95
646 648 2.433664 ACGGCCGAACATCGAACC 60.434 61.111 35.90 1.91 43.74 3.62
647 649 3.550992 CGGCCGAACATCGAACCG 61.551 66.667 24.07 15.86 46.63 4.44
648 650 2.433664 GGCCGAACATCGAACCGT 60.434 61.111 0.58 0.00 43.74 4.83
649 651 1.153784 GGCCGAACATCGAACCGTA 60.154 57.895 0.58 0.00 43.74 4.02
650 652 0.529119 GGCCGAACATCGAACCGTAT 60.529 55.000 0.58 0.00 43.74 3.06
651 653 1.269206 GGCCGAACATCGAACCGTATA 60.269 52.381 0.58 0.00 43.74 1.47
652 654 1.783140 GCCGAACATCGAACCGTATAC 59.217 52.381 0.58 0.00 43.74 1.47
653 655 2.388121 CCGAACATCGAACCGTATACC 58.612 52.381 0.58 0.00 43.74 2.73
654 656 2.039085 CGAACATCGAACCGTATACCG 58.961 52.381 0.00 0.00 43.74 4.02
655 657 2.539547 CGAACATCGAACCGTATACCGT 60.540 50.000 0.00 0.00 43.74 4.83
656 658 3.303066 CGAACATCGAACCGTATACCGTA 60.303 47.826 0.00 0.00 43.74 4.02
657 659 4.611355 CGAACATCGAACCGTATACCGTAT 60.611 45.833 0.00 0.00 43.74 3.06
658 660 4.410492 ACATCGAACCGTATACCGTATC 57.590 45.455 0.00 0.00 33.66 2.24
659 661 3.120546 ACATCGAACCGTATACCGTATCG 60.121 47.826 15.51 15.51 41.35 2.92
660 662 2.749776 TCGAACCGTATACCGTATCGA 58.250 47.619 17.99 17.99 44.25 3.59
661 663 2.731451 TCGAACCGTATACCGTATCGAG 59.269 50.000 17.99 4.28 42.75 4.04
662 664 2.723010 CGAACCGTATACCGTATCGAGC 60.723 54.545 16.10 0.00 42.06 5.03
663 665 1.160137 ACCGTATACCGTATCGAGCC 58.840 55.000 0.00 0.00 33.66 4.70
664 666 1.159285 CCGTATACCGTATCGAGCCA 58.841 55.000 0.00 0.00 33.66 4.75
665 667 1.129998 CCGTATACCGTATCGAGCCAG 59.870 57.143 0.00 0.00 33.66 4.85
666 668 1.465354 CGTATACCGTATCGAGCCAGC 60.465 57.143 0.00 0.00 0.00 4.85
667 669 1.135460 GTATACCGTATCGAGCCAGCC 60.135 57.143 0.00 0.00 0.00 4.85
668 670 0.826256 ATACCGTATCGAGCCAGCCA 60.826 55.000 0.00 0.00 0.00 4.75
669 671 1.452953 TACCGTATCGAGCCAGCCAG 61.453 60.000 0.00 0.00 0.00 4.85
670 672 2.028190 CGTATCGAGCCAGCCAGG 59.972 66.667 0.00 0.00 41.84 4.45
671 673 2.786495 CGTATCGAGCCAGCCAGGT 61.786 63.158 0.00 0.00 40.61 4.00
672 674 1.452953 CGTATCGAGCCAGCCAGGTA 61.453 60.000 0.00 0.00 40.61 3.08
673 675 0.750850 GTATCGAGCCAGCCAGGTAA 59.249 55.000 0.00 0.00 40.61 2.85
674 676 0.750850 TATCGAGCCAGCCAGGTAAC 59.249 55.000 0.00 0.00 40.61 2.50
722 724 2.716244 CGTATCGGCAGCGAGACT 59.284 61.111 8.19 0.00 0.00 3.24
950 979 2.639926 CGATCGATCGCCGCAGAAC 61.640 63.158 32.34 0.00 43.84 3.01
951 980 1.588932 GATCGATCGCCGCAGAACA 60.589 57.895 11.09 0.00 38.37 3.18
952 981 0.941463 GATCGATCGCCGCAGAACAT 60.941 55.000 11.09 0.00 38.37 2.71
954 983 2.920964 CGATCGCCGCAGAACATCG 61.921 63.158 0.26 0.00 0.00 3.84
956 985 0.941463 GATCGCCGCAGAACATCGAT 60.941 55.000 0.00 0.00 41.79 3.59
957 986 0.941463 ATCGCCGCAGAACATCGATC 60.941 55.000 0.00 0.00 35.28 3.69
960 989 1.089481 GCCGCAGAACATCGATCCAA 61.089 55.000 0.00 0.00 0.00 3.53
962 991 1.645034 CGCAGAACATCGATCCAAGT 58.355 50.000 0.00 0.00 0.00 3.16
969 999 5.409520 CAGAACATCGATCCAAGTCAAAGAA 59.590 40.000 0.00 0.00 0.00 2.52
971 1001 4.899502 ACATCGATCCAAGTCAAAGAACT 58.100 39.130 0.00 0.00 0.00 3.01
1461 1495 1.448013 GAAGGCGTACCAGCAGACC 60.448 63.158 0.00 0.00 39.06 3.85
1809 1843 1.169661 TCACGCCGAAAAACATGGCT 61.170 50.000 0.00 0.00 46.67 4.75
1836 1870 4.166011 GCCAGCCAAGCTTACGCG 62.166 66.667 3.53 3.53 42.32 6.01
1872 1906 2.325082 GGACACGCCGTTCAGCATT 61.325 57.895 0.00 0.00 0.00 3.56
1996 2030 2.428890 AGCTACCTAGTGATGCAGTGAC 59.571 50.000 0.00 0.00 0.00 3.67
2199 2292 8.817100 GTTGGTTAAAGATTCTTTGGAAAACTG 58.183 33.333 19.60 0.00 34.90 3.16
2200 2293 8.299990 TGGTTAAAGATTCTTTGGAAAACTGA 57.700 30.769 19.60 6.39 34.90 3.41
2201 2294 8.754080 TGGTTAAAGATTCTTTGGAAAACTGAA 58.246 29.630 19.60 2.27 34.90 3.02
2202 2295 9.764363 GGTTAAAGATTCTTTGGAAAACTGAAT 57.236 29.630 19.60 0.00 34.90 2.57
2204 2297 9.677567 TTAAAGATTCTTTGGAAAACTGAATCG 57.322 29.630 19.60 0.00 44.28 3.34
2205 2298 5.703876 AGATTCTTTGGAAAACTGAATCGC 58.296 37.500 0.00 0.00 44.28 4.58
2206 2299 4.909696 TTCTTTGGAAAACTGAATCGCA 57.090 36.364 0.00 0.00 0.00 5.10
2207 2300 5.464168 ATTCTTTGGAAAACTGAATCGCAG 58.536 37.500 0.00 0.00 41.53 5.18
2209 2302 6.206634 ATTCTTTGGAAAACTGAATCGCAGTA 59.793 34.615 0.00 0.00 44.21 2.74
2218 2357 1.804151 TGAATCGCAGTACAAAGCCAC 59.196 47.619 0.00 0.00 0.00 5.01
2238 2377 5.008712 GCCACCATAAAACTACAGGATAAGC 59.991 44.000 0.00 0.00 0.00 3.09
2239 2378 6.357367 CCACCATAAAACTACAGGATAAGCT 58.643 40.000 0.00 0.00 0.00 3.74
2240 2379 6.260936 CCACCATAAAACTACAGGATAAGCTG 59.739 42.308 0.00 0.00 0.00 4.24
2242 2381 7.552687 CACCATAAAACTACAGGATAAGCTGAA 59.447 37.037 0.00 0.00 0.00 3.02
2244 2383 7.552687 CCATAAAACTACAGGATAAGCTGAACA 59.447 37.037 0.00 0.00 0.00 3.18
2246 2385 7.817418 AAAACTACAGGATAAGCTGAACAAA 57.183 32.000 0.00 0.00 0.00 2.83
2247 2386 6.803154 AACTACAGGATAAGCTGAACAAAC 57.197 37.500 0.00 0.00 0.00 2.93
2248 2387 5.865085 ACTACAGGATAAGCTGAACAAACA 58.135 37.500 0.00 0.00 0.00 2.83
2249 2388 5.701290 ACTACAGGATAAGCTGAACAAACAC 59.299 40.000 0.00 0.00 0.00 3.32
2250 2389 3.821033 ACAGGATAAGCTGAACAAACACC 59.179 43.478 0.00 0.00 0.00 4.16
2251 2390 4.074970 CAGGATAAGCTGAACAAACACCT 58.925 43.478 0.00 0.00 0.00 4.00
2252 2391 5.221843 ACAGGATAAGCTGAACAAACACCTA 60.222 40.000 0.00 0.00 0.00 3.08
2253 2392 5.352569 CAGGATAAGCTGAACAAACACCTAG 59.647 44.000 0.00 0.00 0.00 3.02
2254 2393 4.636206 GGATAAGCTGAACAAACACCTAGG 59.364 45.833 7.41 7.41 0.00 3.02
2255 2394 3.857157 AAGCTGAACAAACACCTAGGA 57.143 42.857 17.98 0.00 0.00 2.94
2256 2395 3.409026 AGCTGAACAAACACCTAGGAG 57.591 47.619 17.98 10.85 0.00 3.69
2257 2396 2.706190 AGCTGAACAAACACCTAGGAGT 59.294 45.455 17.98 11.68 0.00 3.85
2258 2397 3.901844 AGCTGAACAAACACCTAGGAGTA 59.098 43.478 17.98 0.00 0.00 2.59
2259 2398 4.021016 AGCTGAACAAACACCTAGGAGTAG 60.021 45.833 17.98 12.55 0.00 2.57
2260 2399 4.262506 GCTGAACAAACACCTAGGAGTAGT 60.263 45.833 17.98 13.21 0.00 2.73
2261 2400 5.464030 TGAACAAACACCTAGGAGTAGTC 57.536 43.478 17.98 9.70 0.00 2.59
2262 2401 4.897076 TGAACAAACACCTAGGAGTAGTCA 59.103 41.667 17.98 12.06 0.00 3.41
2263 2402 5.364446 TGAACAAACACCTAGGAGTAGTCAA 59.636 40.000 17.98 5.71 0.00 3.18
2264 2403 6.042781 TGAACAAACACCTAGGAGTAGTCAAT 59.957 38.462 17.98 1.81 0.00 2.57
2265 2404 7.233962 TGAACAAACACCTAGGAGTAGTCAATA 59.766 37.037 17.98 1.98 0.00 1.90
2266 2405 7.549147 ACAAACACCTAGGAGTAGTCAATAA 57.451 36.000 17.98 0.00 0.00 1.40
2267 2406 8.147244 ACAAACACCTAGGAGTAGTCAATAAT 57.853 34.615 17.98 0.00 0.00 1.28
2268 2407 9.263446 ACAAACACCTAGGAGTAGTCAATAATA 57.737 33.333 17.98 0.00 0.00 0.98
2271 2410 7.953752 ACACCTAGGAGTAGTCAATAATAAGC 58.046 38.462 17.98 0.00 0.00 3.09
2272 2411 7.563924 ACACCTAGGAGTAGTCAATAATAAGCA 59.436 37.037 17.98 0.00 0.00 3.91
2273 2412 7.868415 CACCTAGGAGTAGTCAATAATAAGCAC 59.132 40.741 17.98 0.00 0.00 4.40
2274 2413 7.015389 ACCTAGGAGTAGTCAATAATAAGCACC 59.985 40.741 17.98 0.00 0.00 5.01
2275 2414 6.176014 AGGAGTAGTCAATAATAAGCACCC 57.824 41.667 0.00 0.00 0.00 4.61
2276 2415 5.665812 AGGAGTAGTCAATAATAAGCACCCA 59.334 40.000 0.00 0.00 0.00 4.51
2277 2416 6.157994 AGGAGTAGTCAATAATAAGCACCCAA 59.842 38.462 0.00 0.00 0.00 4.12
2278 2417 6.826741 GGAGTAGTCAATAATAAGCACCCAAA 59.173 38.462 0.00 0.00 0.00 3.28
2279 2418 7.338449 GGAGTAGTCAATAATAAGCACCCAAAA 59.662 37.037 0.00 0.00 0.00 2.44
2280 2419 8.281212 AGTAGTCAATAATAAGCACCCAAAAG 57.719 34.615 0.00 0.00 0.00 2.27
2281 2420 5.965922 AGTCAATAATAAGCACCCAAAAGC 58.034 37.500 0.00 0.00 0.00 3.51
2282 2421 5.480073 AGTCAATAATAAGCACCCAAAAGCA 59.520 36.000 0.00 0.00 0.00 3.91
2283 2422 5.807011 GTCAATAATAAGCACCCAAAAGCAG 59.193 40.000 0.00 0.00 0.00 4.24
2284 2423 2.749280 AATAAGCACCCAAAAGCAGC 57.251 45.000 0.00 0.00 0.00 5.25
2285 2424 1.928868 ATAAGCACCCAAAAGCAGCT 58.071 45.000 0.00 0.00 37.08 4.24
2286 2425 2.577606 TAAGCACCCAAAAGCAGCTA 57.422 45.000 0.00 0.00 34.66 3.32
2287 2426 0.961753 AAGCACCCAAAAGCAGCTAC 59.038 50.000 0.00 0.00 34.66 3.58
2288 2427 1.210155 GCACCCAAAAGCAGCTACG 59.790 57.895 0.00 0.00 0.00 3.51
2289 2428 1.515521 GCACCCAAAAGCAGCTACGT 61.516 55.000 0.00 0.00 0.00 3.57
2290 2429 1.803334 CACCCAAAAGCAGCTACGTA 58.197 50.000 0.00 0.00 0.00 3.57
2291 2430 2.356135 CACCCAAAAGCAGCTACGTAT 58.644 47.619 0.00 0.00 0.00 3.06
2292 2431 2.747446 CACCCAAAAGCAGCTACGTATT 59.253 45.455 0.00 0.00 0.00 1.89
2293 2432 3.007635 ACCCAAAAGCAGCTACGTATTC 58.992 45.455 0.00 0.00 0.00 1.75
2294 2433 3.270877 CCCAAAAGCAGCTACGTATTCT 58.729 45.455 0.00 0.00 0.00 2.40
2295 2434 3.063997 CCCAAAAGCAGCTACGTATTCTG 59.936 47.826 16.30 16.30 0.00 3.02
2296 2435 3.063997 CCAAAAGCAGCTACGTATTCTGG 59.936 47.826 19.92 5.72 0.00 3.86
2297 2436 3.887621 AAAGCAGCTACGTATTCTGGA 57.112 42.857 19.92 0.00 0.00 3.86
2298 2437 3.444703 AAGCAGCTACGTATTCTGGAG 57.555 47.619 19.92 1.78 0.00 3.86
2299 2438 1.067821 AGCAGCTACGTATTCTGGAGC 59.932 52.381 19.92 10.61 0.00 4.70
2300 2439 1.202417 GCAGCTACGTATTCTGGAGCA 60.202 52.381 19.92 0.00 35.55 4.26
2301 2440 2.546795 GCAGCTACGTATTCTGGAGCAT 60.547 50.000 19.92 0.68 35.55 3.79
2302 2441 3.312828 CAGCTACGTATTCTGGAGCATC 58.687 50.000 13.98 0.00 35.55 3.91
2303 2442 2.030717 AGCTACGTATTCTGGAGCATCG 60.031 50.000 6.97 0.00 35.55 3.84
2304 2443 2.031069 GCTACGTATTCTGGAGCATCGA 60.031 50.000 0.00 0.00 34.37 3.59
2305 2444 2.783828 ACGTATTCTGGAGCATCGAG 57.216 50.000 0.00 0.00 42.88 4.04
2306 2445 1.269309 ACGTATTCTGGAGCATCGAGC 60.269 52.381 0.00 0.00 41.12 5.03
2351 2490 4.895668 AAAGGCACCATCATTTGTCAAT 57.104 36.364 0.00 0.00 0.00 2.57
2362 2501 5.375417 TCATTTGTCAATAACAGCCTGTG 57.625 39.130 0.00 0.00 39.58 3.66
2375 2514 2.706555 GCCTGTGCTGAAAGTAAACC 57.293 50.000 0.00 0.00 35.30 3.27
2443 2588 5.089970 TGAATAGTGATGAAGGGTGACAG 57.910 43.478 0.00 0.00 0.00 3.51
2541 2686 0.404040 GAATGGGTCCACCTTCCACA 59.596 55.000 0.00 0.00 41.11 4.17
2792 2940 3.963383 AAGCACACTTTGTAGAAACCG 57.037 42.857 0.00 0.00 29.41 4.44
2850 2998 8.029642 ACACATACAGCAACAAAGACTAATAC 57.970 34.615 0.00 0.00 0.00 1.89
2955 3103 5.019470 AGACTACCAGATGTCACTTCATCA 58.981 41.667 8.93 0.00 44.46 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 5.888161 GGACCACAAATGTCTCCTTGAATAT 59.112 40.000 0.00 0.00 33.22 1.28
140 141 1.134401 CCGTGTGGATAGAAGGCACAT 60.134 52.381 0.00 0.00 37.49 3.21
145 146 3.819564 TGATTCCGTGTGGATAGAAGG 57.180 47.619 0.00 0.00 45.91 3.46
163 164 5.221362 CCTCATTATCTTGGCAAATGCATGA 60.221 40.000 0.00 6.53 44.36 3.07
256 257 2.839486 AAGCACGTGAGGAGAATTCA 57.161 45.000 22.23 0.00 0.00 2.57
277 278 4.341806 CCCAAAGCCATGCAATAATCACTA 59.658 41.667 0.00 0.00 0.00 2.74
279 280 3.460103 CCCAAAGCCATGCAATAATCAC 58.540 45.455 0.00 0.00 0.00 3.06
318 319 6.751514 TTTGTGTATGGACATATGGAACAC 57.248 37.500 7.80 12.82 38.83 3.32
367 368 5.100259 GGTCTTGCAATGAGTTTGATCATG 58.900 41.667 0.00 0.00 39.84 3.07
369 370 4.401022 AGGTCTTGCAATGAGTTTGATCA 58.599 39.130 0.00 0.00 37.53 2.92
417 418 3.134574 ACAGCGTGACCCAATAAGAAA 57.865 42.857 0.00 0.00 0.00 2.52
418 419 2.851263 ACAGCGTGACCCAATAAGAA 57.149 45.000 0.00 0.00 0.00 2.52
423 424 2.292292 GTGTAAAACAGCGTGACCCAAT 59.708 45.455 0.00 0.00 0.00 3.16
445 447 5.355350 GCCTCAATTGTATCAAGTTAGCAGT 59.645 40.000 5.13 0.00 0.00 4.40
451 453 5.079643 AGTTGGCCTCAATTGTATCAAGTT 58.920 37.500 3.32 0.00 35.10 2.66
475 477 7.623999 AGGGAAGAACTGTGATATGATATGT 57.376 36.000 0.00 0.00 0.00 2.29
476 478 8.373981 AGAAGGGAAGAACTGTGATATGATATG 58.626 37.037 0.00 0.00 0.00 1.78
477 479 8.373981 CAGAAGGGAAGAACTGTGATATGATAT 58.626 37.037 0.00 0.00 0.00 1.63
478 480 7.565029 TCAGAAGGGAAGAACTGTGATATGATA 59.435 37.037 0.00 0.00 0.00 2.15
479 481 6.385176 TCAGAAGGGAAGAACTGTGATATGAT 59.615 38.462 0.00 0.00 0.00 2.45
480 482 5.721480 TCAGAAGGGAAGAACTGTGATATGA 59.279 40.000 0.00 0.00 0.00 2.15
499 501 5.182380 GGATTTCCACGTACCAATTTCAGAA 59.818 40.000 0.00 0.00 35.64 3.02
504 506 5.321927 AGAAGGATTTCCACGTACCAATTT 58.678 37.500 0.00 0.00 38.89 1.82
525 527 3.266510 ACGCAGATGGAAAATGCTAGA 57.733 42.857 0.00 0.00 37.81 2.43
527 529 4.513442 ACTTACGCAGATGGAAAATGCTA 58.487 39.130 0.00 0.00 37.81 3.49
535 537 1.179152 TCCGAACTTACGCAGATGGA 58.821 50.000 0.00 0.00 0.00 3.41
561 563 4.314440 GACCCACACAGCTCGGCA 62.314 66.667 0.00 0.00 0.00 5.69
564 566 4.363990 AGCGACCCACACAGCTCG 62.364 66.667 0.00 0.00 34.48 5.03
565 567 2.740055 CAGCGACCCACACAGCTC 60.740 66.667 0.00 0.00 37.94 4.09
566 568 4.996434 GCAGCGACCCACACAGCT 62.996 66.667 0.00 0.00 41.07 4.24
568 570 4.624364 TGGCAGCGACCCACACAG 62.624 66.667 0.00 0.00 0.00 3.66
569 571 4.624364 CTGGCAGCGACCCACACA 62.624 66.667 0.00 0.00 0.00 3.72
583 585 2.360852 CAAGTGGAGCCAGGCTGG 60.361 66.667 29.44 29.44 39.88 4.85
584 586 2.360852 CCAAGTGGAGCCAGGCTG 60.361 66.667 22.26 7.75 39.88 4.85
585 587 2.530151 TCCAAGTGGAGCCAGGCT 60.530 61.111 16.12 16.12 43.88 4.58
586 588 2.360475 GTCCAAGTGGAGCCAGGC 60.360 66.667 1.84 1.84 46.49 4.85
587 589 2.046892 CGTCCAAGTGGAGCCAGG 60.047 66.667 0.00 0.00 46.49 4.45
588 590 2.738213 AAGCGTCCAAGTGGAGCCAG 62.738 60.000 14.39 3.90 46.49 4.85
589 591 2.731691 GAAGCGTCCAAGTGGAGCCA 62.732 60.000 14.39 0.00 46.49 4.75
590 592 2.032681 AAGCGTCCAAGTGGAGCC 59.967 61.111 14.39 4.31 46.49 4.70
591 593 0.884704 TTGAAGCGTCCAAGTGGAGC 60.885 55.000 0.00 6.94 46.49 4.70
592 594 1.813513 ATTGAAGCGTCCAAGTGGAG 58.186 50.000 0.00 0.00 46.49 3.86
593 595 2.270352 AATTGAAGCGTCCAAGTGGA 57.730 45.000 0.00 0.00 43.08 4.02
594 596 2.665519 CGAAATTGAAGCGTCCAAGTGG 60.666 50.000 0.00 0.00 0.00 4.00
595 597 2.032030 ACGAAATTGAAGCGTCCAAGTG 60.032 45.455 0.00 0.00 31.98 3.16
596 598 2.032030 CACGAAATTGAAGCGTCCAAGT 60.032 45.455 0.00 0.00 35.90 3.16
597 599 2.223144 TCACGAAATTGAAGCGTCCAAG 59.777 45.455 0.00 0.00 35.90 3.61
598 600 2.214347 TCACGAAATTGAAGCGTCCAA 58.786 42.857 0.00 0.00 35.90 3.53
599 601 1.872388 TCACGAAATTGAAGCGTCCA 58.128 45.000 0.00 0.00 35.90 4.02
600 602 3.163594 CAATCACGAAATTGAAGCGTCC 58.836 45.455 8.26 0.00 38.64 4.79
601 603 3.120338 TCCAATCACGAAATTGAAGCGTC 60.120 43.478 13.59 0.00 38.64 5.19
602 604 2.811431 TCCAATCACGAAATTGAAGCGT 59.189 40.909 13.59 0.00 38.64 5.07
603 605 3.163594 GTCCAATCACGAAATTGAAGCG 58.836 45.455 13.59 0.00 38.64 4.68
604 606 3.501950 GGTCCAATCACGAAATTGAAGC 58.498 45.455 13.59 2.66 38.64 3.86
605 607 3.435327 TCGGTCCAATCACGAAATTGAAG 59.565 43.478 13.59 2.01 38.64 3.02
606 608 3.187637 GTCGGTCCAATCACGAAATTGAA 59.812 43.478 13.59 0.00 38.64 2.69
607 609 2.739913 GTCGGTCCAATCACGAAATTGA 59.260 45.455 13.59 0.00 38.64 2.57
608 610 2.482336 TGTCGGTCCAATCACGAAATTG 59.518 45.455 0.00 0.00 38.46 2.32
609 611 2.482721 GTGTCGGTCCAATCACGAAATT 59.517 45.455 0.00 0.00 38.46 1.82
610 612 2.073816 GTGTCGGTCCAATCACGAAAT 58.926 47.619 0.00 0.00 38.46 2.17
611 613 1.504359 GTGTCGGTCCAATCACGAAA 58.496 50.000 0.00 0.00 38.46 3.46
612 614 3.204505 GTGTCGGTCCAATCACGAA 57.795 52.632 0.00 0.00 38.46 3.85
613 615 4.979204 GTGTCGGTCCAATCACGA 57.021 55.556 0.00 0.00 0.00 4.35
614 616 3.459027 CGTGTCGGTCCAATCACG 58.541 61.111 13.34 13.34 45.10 4.35
615 617 3.870606 CCGTGTCGGTCCAATCAC 58.129 61.111 0.00 0.00 42.73 3.06
616 618 3.599285 GGCCGTGTCGGTCCAATCA 62.599 63.158 9.86 0.00 46.90 2.57
617 619 2.818274 GGCCGTGTCGGTCCAATC 60.818 66.667 9.86 0.00 46.90 2.67
625 627 3.541831 CGATGTTCGGCCGTGTCG 61.542 66.667 27.15 23.80 36.00 4.35
626 628 1.735198 TTCGATGTTCGGCCGTGTC 60.735 57.895 27.15 16.92 40.88 3.67
627 629 2.025418 GTTCGATGTTCGGCCGTGT 61.025 57.895 27.15 9.62 40.88 4.49
628 630 2.736682 GGTTCGATGTTCGGCCGTG 61.737 63.158 27.15 9.33 40.88 4.94
629 631 2.433664 GGTTCGATGTTCGGCCGT 60.434 61.111 27.15 5.04 40.88 5.68
630 632 3.550992 CGGTTCGATGTTCGGCCG 61.551 66.667 22.12 22.12 45.61 6.13
631 633 0.529119 ATACGGTTCGATGTTCGGCC 60.529 55.000 0.00 0.00 40.88 6.13
632 634 1.783140 GTATACGGTTCGATGTTCGGC 59.217 52.381 0.00 0.00 40.88 5.54
633 635 2.388121 GGTATACGGTTCGATGTTCGG 58.612 52.381 0.00 0.00 40.88 4.30
634 636 2.039085 CGGTATACGGTTCGATGTTCG 58.961 52.381 2.37 0.00 39.16 3.95
647 649 1.135460 GGCTGGCTCGATACGGTATAC 60.135 57.143 0.00 0.00 0.00 1.47
648 650 1.171308 GGCTGGCTCGATACGGTATA 58.829 55.000 0.00 0.00 0.00 1.47
649 651 0.826256 TGGCTGGCTCGATACGGTAT 60.826 55.000 0.00 0.00 0.00 2.73
650 652 1.452953 CTGGCTGGCTCGATACGGTA 61.453 60.000 2.00 0.00 0.00 4.02
651 653 2.758327 TGGCTGGCTCGATACGGT 60.758 61.111 2.00 0.00 0.00 4.83
652 654 2.028190 CTGGCTGGCTCGATACGG 59.972 66.667 2.00 0.00 0.00 4.02
653 655 1.452953 TACCTGGCTGGCTCGATACG 61.453 60.000 10.71 0.00 40.22 3.06
654 656 0.750850 TTACCTGGCTGGCTCGATAC 59.249 55.000 10.71 0.00 40.22 2.24
655 657 0.750850 GTTACCTGGCTGGCTCGATA 59.249 55.000 10.71 0.00 40.22 2.92
656 658 0.978146 AGTTACCTGGCTGGCTCGAT 60.978 55.000 10.71 0.00 40.22 3.59
657 659 1.192146 AAGTTACCTGGCTGGCTCGA 61.192 55.000 10.71 0.00 40.22 4.04
658 660 0.741221 GAAGTTACCTGGCTGGCTCG 60.741 60.000 10.71 0.00 40.22 5.03
659 661 0.324943 TGAAGTTACCTGGCTGGCTC 59.675 55.000 10.71 1.46 40.22 4.70
660 662 0.995024 ATGAAGTTACCTGGCTGGCT 59.005 50.000 10.71 0.00 40.22 4.75
661 663 1.340017 TGATGAAGTTACCTGGCTGGC 60.340 52.381 10.71 0.00 40.22 4.85
662 664 2.787473 TGATGAAGTTACCTGGCTGG 57.213 50.000 9.11 9.11 42.93 4.85
663 665 3.804325 CGTATGATGAAGTTACCTGGCTG 59.196 47.826 0.00 0.00 0.00 4.85
664 666 3.181465 CCGTATGATGAAGTTACCTGGCT 60.181 47.826 0.00 0.00 0.00 4.75
665 667 3.131396 CCGTATGATGAAGTTACCTGGC 58.869 50.000 0.00 0.00 0.00 4.85
666 668 4.402056 ACCGTATGATGAAGTTACCTGG 57.598 45.455 0.00 0.00 0.00 4.45
667 669 6.800408 CGTATACCGTATGATGAAGTTACCTG 59.200 42.308 0.98 0.00 0.00 4.00
668 670 6.712095 TCGTATACCGTATGATGAAGTTACCT 59.288 38.462 0.98 0.00 37.94 3.08
669 671 6.902341 TCGTATACCGTATGATGAAGTTACC 58.098 40.000 0.98 0.00 37.94 2.85
670 672 9.483062 GTATCGTATACCGTATGATGAAGTTAC 57.517 37.037 0.98 0.00 37.94 2.50
671 673 9.440773 AGTATCGTATACCGTATGATGAAGTTA 57.559 33.333 0.98 0.00 37.94 2.24
672 674 8.332996 AGTATCGTATACCGTATGATGAAGTT 57.667 34.615 0.98 0.00 37.94 2.66
673 675 7.065563 GGAGTATCGTATACCGTATGATGAAGT 59.934 40.741 0.98 0.00 37.94 3.01
674 676 7.280428 AGGAGTATCGTATACCGTATGATGAAG 59.720 40.741 0.98 0.00 37.94 3.02
675 677 7.108194 AGGAGTATCGTATACCGTATGATGAA 58.892 38.462 0.98 0.00 37.94 2.57
676 678 6.647229 AGGAGTATCGTATACCGTATGATGA 58.353 40.000 0.98 0.00 37.94 2.92
677 679 6.922247 AGGAGTATCGTATACCGTATGATG 57.078 41.667 0.98 0.00 37.94 3.07
720 722 2.653130 GTCGCGCGCCGTATAAGT 60.653 61.111 27.95 0.00 38.35 2.24
722 724 2.652813 CTGTCGCGCGCCGTATAA 60.653 61.111 27.95 2.03 38.35 0.98
754 770 2.644992 GCGGGAGTTGTTGGCTTG 59.355 61.111 0.00 0.00 0.00 4.01
853 871 1.073177 CTGATTACGCGTTCCGGTTT 58.927 50.000 20.78 0.00 42.52 3.27
945 974 4.931601 TCTTTGACTTGGATCGATGTTCTG 59.068 41.667 0.54 0.00 0.00 3.02
950 979 4.032217 CGAGTTCTTTGACTTGGATCGATG 59.968 45.833 0.54 0.00 0.00 3.84
951 980 4.082190 TCGAGTTCTTTGACTTGGATCGAT 60.082 41.667 0.00 0.00 32.83 3.59
952 981 3.254903 TCGAGTTCTTTGACTTGGATCGA 59.745 43.478 0.00 0.00 32.83 3.59
954 983 4.266502 CGATCGAGTTCTTTGACTTGGATC 59.733 45.833 10.26 0.00 36.99 3.36
956 985 3.254903 TCGATCGAGTTCTTTGACTTGGA 59.745 43.478 15.15 0.00 32.83 3.53
957 986 3.575630 TCGATCGAGTTCTTTGACTTGG 58.424 45.455 15.15 0.00 32.83 3.61
1686 1720 2.600769 ACGTCGCCTTCCTCCACT 60.601 61.111 0.00 0.00 0.00 4.00
1809 1843 0.745486 CTTGGCTGGCGATGATGTCA 60.745 55.000 0.00 0.00 0.00 3.58
1883 1917 2.283351 CCGATTTTATTCCGTCCGTGTC 59.717 50.000 0.00 0.00 0.00 3.67
1932 1966 2.930764 CGAGACTCGATGAAGGCGACT 61.931 57.143 20.25 0.00 43.74 4.18
1996 2030 2.959516 TGACAAGACCATGCTAACTCG 58.040 47.619 0.00 0.00 0.00 4.18
2199 2292 1.130561 GGTGGCTTTGTACTGCGATTC 59.869 52.381 0.00 0.00 0.00 2.52
2200 2293 1.165270 GGTGGCTTTGTACTGCGATT 58.835 50.000 0.00 0.00 0.00 3.34
2201 2294 0.036164 TGGTGGCTTTGTACTGCGAT 59.964 50.000 0.00 0.00 0.00 4.58
2202 2295 0.036164 ATGGTGGCTTTGTACTGCGA 59.964 50.000 0.00 0.00 0.00 5.10
2204 2297 4.022329 AGTTTTATGGTGGCTTTGTACTGC 60.022 41.667 0.00 0.00 0.00 4.40
2205 2298 5.705609 AGTTTTATGGTGGCTTTGTACTG 57.294 39.130 0.00 0.00 0.00 2.74
2206 2299 6.300703 TGTAGTTTTATGGTGGCTTTGTACT 58.699 36.000 0.00 0.00 0.00 2.73
2207 2300 6.349033 CCTGTAGTTTTATGGTGGCTTTGTAC 60.349 42.308 0.00 0.00 0.00 2.90
2209 2302 4.522789 CCTGTAGTTTTATGGTGGCTTTGT 59.477 41.667 0.00 0.00 0.00 2.83
2218 2357 7.552687 TGTTCAGCTTATCCTGTAGTTTTATGG 59.447 37.037 0.00 0.00 34.47 2.74
2238 2377 5.010719 TGACTACTCCTAGGTGTTTGTTCAG 59.989 44.000 20.98 13.36 0.00 3.02
2239 2378 4.897076 TGACTACTCCTAGGTGTTTGTTCA 59.103 41.667 20.98 14.51 0.00 3.18
2240 2379 5.464030 TGACTACTCCTAGGTGTTTGTTC 57.536 43.478 20.98 12.47 0.00 3.18
2242 2381 7.549147 TTATTGACTACTCCTAGGTGTTTGT 57.451 36.000 20.98 18.55 0.00 2.83
2246 2385 7.563924 TGCTTATTATTGACTACTCCTAGGTGT 59.436 37.037 19.80 19.80 0.00 4.16
2247 2386 7.868415 GTGCTTATTATTGACTACTCCTAGGTG 59.132 40.741 9.08 9.22 0.00 4.00
2248 2387 7.015389 GGTGCTTATTATTGACTACTCCTAGGT 59.985 40.741 9.08 0.00 0.00 3.08
2249 2388 7.379750 GGTGCTTATTATTGACTACTCCTAGG 58.620 42.308 0.82 0.82 0.00 3.02
2250 2389 7.015292 TGGGTGCTTATTATTGACTACTCCTAG 59.985 40.741 0.00 0.00 0.00 3.02
2251 2390 6.842280 TGGGTGCTTATTATTGACTACTCCTA 59.158 38.462 0.00 0.00 0.00 2.94
2252 2391 5.665812 TGGGTGCTTATTATTGACTACTCCT 59.334 40.000 0.00 0.00 0.00 3.69
2253 2392 5.925509 TGGGTGCTTATTATTGACTACTCC 58.074 41.667 0.00 0.00 0.00 3.85
2254 2393 7.859325 TTTGGGTGCTTATTATTGACTACTC 57.141 36.000 0.00 0.00 0.00 2.59
2255 2394 7.148069 GCTTTTGGGTGCTTATTATTGACTACT 60.148 37.037 0.00 0.00 0.00 2.57
2256 2395 6.972901 GCTTTTGGGTGCTTATTATTGACTAC 59.027 38.462 0.00 0.00 0.00 2.73
2257 2396 6.661377 TGCTTTTGGGTGCTTATTATTGACTA 59.339 34.615 0.00 0.00 0.00 2.59
2258 2397 5.480073 TGCTTTTGGGTGCTTATTATTGACT 59.520 36.000 0.00 0.00 0.00 3.41
2259 2398 5.719173 TGCTTTTGGGTGCTTATTATTGAC 58.281 37.500 0.00 0.00 0.00 3.18
2260 2399 5.624281 GCTGCTTTTGGGTGCTTATTATTGA 60.624 40.000 0.00 0.00 0.00 2.57
2261 2400 4.567959 GCTGCTTTTGGGTGCTTATTATTG 59.432 41.667 0.00 0.00 0.00 1.90
2262 2401 4.467438 AGCTGCTTTTGGGTGCTTATTATT 59.533 37.500 0.00 0.00 0.00 1.40
2263 2402 4.026052 AGCTGCTTTTGGGTGCTTATTAT 58.974 39.130 0.00 0.00 0.00 1.28
2264 2403 3.430453 AGCTGCTTTTGGGTGCTTATTA 58.570 40.909 0.00 0.00 0.00 0.98
2265 2404 2.250924 AGCTGCTTTTGGGTGCTTATT 58.749 42.857 0.00 0.00 0.00 1.40
2266 2405 1.928868 AGCTGCTTTTGGGTGCTTAT 58.071 45.000 0.00 0.00 0.00 1.73
2267 2406 2.159382 GTAGCTGCTTTTGGGTGCTTA 58.841 47.619 7.79 0.00 35.47 3.09
2268 2407 0.961753 GTAGCTGCTTTTGGGTGCTT 59.038 50.000 7.79 0.00 35.47 3.91
2269 2408 1.237285 CGTAGCTGCTTTTGGGTGCT 61.237 55.000 7.79 0.00 37.72 4.40
2270 2409 1.210155 CGTAGCTGCTTTTGGGTGC 59.790 57.895 7.79 0.00 0.00 5.01
2271 2410 1.803334 TACGTAGCTGCTTTTGGGTG 58.197 50.000 7.79 0.00 0.00 4.61
2272 2411 2.781681 ATACGTAGCTGCTTTTGGGT 57.218 45.000 7.79 1.87 0.00 4.51
2273 2412 3.063997 CAGAATACGTAGCTGCTTTTGGG 59.936 47.826 7.79 0.00 0.00 4.12
2274 2413 3.063997 CCAGAATACGTAGCTGCTTTTGG 59.936 47.826 7.79 10.54 0.00 3.28
2275 2414 3.932710 TCCAGAATACGTAGCTGCTTTTG 59.067 43.478 7.79 0.26 0.00 2.44
2276 2415 4.184629 CTCCAGAATACGTAGCTGCTTTT 58.815 43.478 7.79 0.00 0.00 2.27
2277 2416 3.786635 CTCCAGAATACGTAGCTGCTTT 58.213 45.455 7.79 0.00 0.00 3.51
2278 2417 2.482142 GCTCCAGAATACGTAGCTGCTT 60.482 50.000 7.79 1.00 0.00 3.91
2279 2418 1.067821 GCTCCAGAATACGTAGCTGCT 59.932 52.381 18.02 7.57 0.00 4.24
2280 2419 1.202417 TGCTCCAGAATACGTAGCTGC 60.202 52.381 18.02 10.63 34.28 5.25
2281 2420 2.871182 TGCTCCAGAATACGTAGCTG 57.129 50.000 16.99 16.99 34.28 4.24
2282 2421 2.030717 CGATGCTCCAGAATACGTAGCT 60.031 50.000 0.08 0.00 34.28 3.32
2283 2422 2.031069 TCGATGCTCCAGAATACGTAGC 60.031 50.000 0.08 0.00 0.00 3.58
2284 2423 3.816091 CTCGATGCTCCAGAATACGTAG 58.184 50.000 0.08 0.00 0.00 3.51
2285 2424 2.031069 GCTCGATGCTCCAGAATACGTA 60.031 50.000 0.00 0.00 38.95 3.57
2286 2425 1.269309 GCTCGATGCTCCAGAATACGT 60.269 52.381 0.00 0.00 38.95 3.57
2287 2426 1.269257 TGCTCGATGCTCCAGAATACG 60.269 52.381 8.07 0.00 43.37 3.06
2288 2427 2.131183 GTGCTCGATGCTCCAGAATAC 58.869 52.381 8.07 0.00 43.37 1.89
2289 2428 2.515926 GTGCTCGATGCTCCAGAATA 57.484 50.000 8.07 0.00 43.37 1.75
2290 2429 3.376218 GTGCTCGATGCTCCAGAAT 57.624 52.632 8.07 0.00 43.37 2.40
2291 2430 4.919653 GTGCTCGATGCTCCAGAA 57.080 55.556 8.07 0.00 43.37 3.02
2296 2435 4.521062 AGGCGGTGCTCGATGCTC 62.521 66.667 8.07 4.86 43.37 4.26
2297 2436 4.827087 CAGGCGGTGCTCGATGCT 62.827 66.667 8.07 0.00 43.37 3.79
2298 2437 4.819761 TCAGGCGGTGCTCGATGC 62.820 66.667 4.33 0.00 42.43 3.91
2299 2438 2.887568 GTCAGGCGGTGCTCGATG 60.888 66.667 4.33 2.72 42.43 3.84
2300 2439 4.498520 CGTCAGGCGGTGCTCGAT 62.499 66.667 4.33 0.00 42.43 3.59
2303 2442 3.112709 GAACGTCAGGCGGTGCTC 61.113 66.667 0.00 0.00 42.72 4.26
2304 2443 4.681978 GGAACGTCAGGCGGTGCT 62.682 66.667 0.00 0.00 45.44 4.40
2306 2445 2.432628 GAGGAACGTCAGGCGGTG 60.433 66.667 0.00 0.00 42.72 4.94
2371 2510 3.876309 TGAGGCTACTGGAAAAGGTTT 57.124 42.857 0.00 0.00 0.00 3.27
2374 2513 3.539604 CTGATGAGGCTACTGGAAAAGG 58.460 50.000 0.00 0.00 0.00 3.11
2375 2514 2.941720 GCTGATGAGGCTACTGGAAAAG 59.058 50.000 0.00 0.00 0.00 2.27
2443 2588 2.027192 TGGTGATGGTTCTTGGTAGCTC 60.027 50.000 0.00 0.00 0.00 4.09
2541 2686 1.194781 AGATTGGTGCCACGACTCCT 61.195 55.000 0.00 0.00 0.00 3.69
2581 2729 0.257039 AGGGTGATCCAGATTGTGCC 59.743 55.000 0.00 0.00 38.24 5.01
2792 2940 6.907206 TGTATGGCTTATAACGTGTTTACC 57.093 37.500 0.00 0.00 0.00 2.85
2867 3015 9.855021 TGTGCTTTATTTTCCTTAATCTTTAGC 57.145 29.630 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.