Multiple sequence alignment - TraesCS4B01G303700

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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 TraesCS4B01G303700 chr4B 100.000 3435 0 0 1 3435 591910453 591907019 0.000000e+00 6344
1 TraesCS4B01G303700 chr4B 93.342 1502 82 13 843 2342 591539901 591538416 0.000000e+00 2204
2 TraesCS4B01G303700 chr4B 90.753 1341 111 6 960 2298 592079737 592078408 0.000000e+00 1777
3 TraesCS4B01G303700 chr4B 90.165 1332 111 10 963 2294 592188170 592186859 0.000000e+00 1716
4 TraesCS4B01G303700 chr4B 90.403 1240 109 5 1044 2281 591955113 591953882 0.000000e+00 1622
5 TraesCS4B01G303700 chr4B 88.194 432 33 8 2338 2761 591538242 591537821 1.840000e-137 499
6 TraesCS4B01G303700 chr4B 86.957 414 37 8 2928 3339 591537646 591537248 1.880000e-122 449
7 TraesCS4B01G303700 chr4B 91.667 120 9 1 726 845 591540341 591540223 7.630000e-37 165
8 TraesCS4B01G303700 chr4D 92.911 1721 91 11 726 2429 470122213 470120507 0.000000e+00 2473
9 TraesCS4B01G303700 chr4D 90.559 1324 112 6 960 2281 470138498 470137186 0.000000e+00 1740
10 TraesCS4B01G303700 chr4D 87.560 627 40 16 2824 3434 470120060 470119456 0.000000e+00 691
11 TraesCS4B01G303700 chr4D 91.579 190 16 0 2435 2624 470120199 470120388 2.630000e-66 263
12 TraesCS4B01G303700 chr4D 94.872 117 6 0 2665 2781 470120388 470120504 2.110000e-42 183
13 TraesCS4B01G303700 chr4D 82.941 170 17 5 725 888 470130644 470130481 3.570000e-30 143
14 TraesCS4B01G303700 chr4A 92.063 1726 91 24 726 2429 677958884 677957183 0.000000e+00 2386
15 TraesCS4B01G303700 chr4A 90.187 1335 122 6 960 2294 677989004 677987679 0.000000e+00 1731
16 TraesCS4B01G303700 chr4A 89.197 1333 120 11 960 2282 677969653 677968335 0.000000e+00 1642
17 TraesCS4B01G303700 chr4A 86.757 589 37 18 2824 3398 677956631 677956070 4.870000e-173 617
18 TraesCS4B01G303700 chr4A 94.017 117 7 0 2665 2781 677956957 677957073 9.800000e-41 178
19 TraesCS4B01G303700 chr6A 85.781 647 84 7 5 646 608656003 608656646 0.000000e+00 678
20 TraesCS4B01G303700 chr6A 86.107 619 79 6 1 614 497996305 497996921 0.000000e+00 660
21 TraesCS4B01G303700 chr7D 86.054 631 84 4 3 630 635663672 635663043 0.000000e+00 675
22 TraesCS4B01G303700 chr2D 85.150 633 90 4 1 630 534163276 534162645 0.000000e+00 645
23 TraesCS4B01G303700 chr2D 85.227 616 82 7 1 612 131775659 131775049 2.910000e-175 625
24 TraesCS4B01G303700 chr5D 84.772 637 83 10 1 628 498465134 498464503 8.090000e-176 627
25 TraesCS4B01G303700 chr3B 84.615 637 91 4 1 630 821758092 821758728 8.090000e-176 627
26 TraesCS4B01G303700 chr3B 84.409 635 91 7 1 628 184958188 184957555 4.870000e-173 617
27 TraesCS4B01G303700 chr5B 84.543 634 90 5 1 630 668107795 668107166 3.770000e-174 621


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 TraesCS4B01G303700 chr4B 591907019 591910453 3434 True 6344.00 6344 100.0000 1 3435 1 chr4B.!!$R1 3434
1 TraesCS4B01G303700 chr4B 592078408 592079737 1329 True 1777.00 1777 90.7530 960 2298 1 chr4B.!!$R3 1338
2 TraesCS4B01G303700 chr4B 592186859 592188170 1311 True 1716.00 1716 90.1650 963 2294 1 chr4B.!!$R4 1331
3 TraesCS4B01G303700 chr4B 591953882 591955113 1231 True 1622.00 1622 90.4030 1044 2281 1 chr4B.!!$R2 1237
4 TraesCS4B01G303700 chr4B 591537248 591540341 3093 True 829.25 2204 90.0400 726 3339 4 chr4B.!!$R5 2613
5 TraesCS4B01G303700 chr4D 470137186 470138498 1312 True 1740.00 1740 90.5590 960 2281 1 chr4D.!!$R2 1321
6 TraesCS4B01G303700 chr4D 470119456 470122213 2757 True 1582.00 2473 90.2355 726 3434 2 chr4D.!!$R3 2708
7 TraesCS4B01G303700 chr4A 677987679 677989004 1325 True 1731.00 1731 90.1870 960 2294 1 chr4A.!!$R2 1334
8 TraesCS4B01G303700 chr4A 677968335 677969653 1318 True 1642.00 1642 89.1970 960 2282 1 chr4A.!!$R1 1322
9 TraesCS4B01G303700 chr4A 677956070 677958884 2814 True 1501.50 2386 89.4100 726 3398 2 chr4A.!!$R3 2672
10 TraesCS4B01G303700 chr6A 608656003 608656646 643 False 678.00 678 85.7810 5 646 1 chr6A.!!$F2 641
11 TraesCS4B01G303700 chr6A 497996305 497996921 616 False 660.00 660 86.1070 1 614 1 chr6A.!!$F1 613
12 TraesCS4B01G303700 chr7D 635663043 635663672 629 True 675.00 675 86.0540 3 630 1 chr7D.!!$R1 627
13 TraesCS4B01G303700 chr2D 534162645 534163276 631 True 645.00 645 85.1500 1 630 1 chr2D.!!$R2 629
14 TraesCS4B01G303700 chr2D 131775049 131775659 610 True 625.00 625 85.2270 1 612 1 chr2D.!!$R1 611
15 TraesCS4B01G303700 chr5D 498464503 498465134 631 True 627.00 627 84.7720 1 628 1 chr5D.!!$R1 627
16 TraesCS4B01G303700 chr3B 821758092 821758728 636 False 627.00 627 84.6150 1 630 1 chr3B.!!$F1 629
17 TraesCS4B01G303700 chr3B 184957555 184958188 633 True 617.00 617 84.4090 1 628 1 chr3B.!!$R1 627
18 TraesCS4B01G303700 chr5B 668107166 668107795 629 True 621.00 621 84.5430 1 630 1 chr5B.!!$R1 629

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
616 629 0.038159 CGACGGAAGGTGAAGAGCTT 60.038 55.0 0.0 0.0 42.73 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 3410 0.947244 CGCTCAGCTTTTCCACTGTT 59.053 50.0 0.0 0.0 35.37 3.16 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
23 24 4.876107 TGCGAGAAACTTCCAATCTATTCC 59.124 41.667 0.00 0.00 0.00 3.01
126 127 2.186384 CTGGAGCGAGCTGAAGGG 59.814 66.667 0.84 0.00 0.00 3.95
165 167 4.463879 CTCACCAGAGCCGGGCAG 62.464 72.222 23.09 10.42 34.61 4.85
179 181 1.809684 GGGCAGACCTTGTTGTAGTC 58.190 55.000 0.00 0.00 35.85 2.59
200 202 2.950433 GACAATTGGGAAGTCGTCGTA 58.050 47.619 10.83 0.00 0.00 3.43
208 214 1.742268 GGAAGTCGTCGTACTAAGGCT 59.258 52.381 0.00 0.00 0.00 4.58
215 221 2.877168 CGTCGTACTAAGGCTCCATAGT 59.123 50.000 8.61 8.61 35.15 2.12
251 257 3.505680 AGTAGCAAACATCGCCAATGAAA 59.494 39.130 0.97 0.00 38.83 2.69
278 284 5.654650 AGTCGTAGATCAGAAGGATGAAACT 59.345 40.000 0.00 0.00 40.67 2.66
300 307 5.244178 ACTTGTAAACACCCAAACAAAGACA 59.756 36.000 0.00 0.00 31.90 3.41
342 349 1.751924 GATCCACCGAAGACTAGCACT 59.248 52.381 0.00 0.00 0.00 4.40
358 365 2.417516 CTGACCGAATCCCGCGAT 59.582 61.111 8.23 0.00 36.84 4.58
365 372 0.100682 CGAATCCCGCGATATCCGAT 59.899 55.000 8.23 0.00 41.76 4.18
369 376 0.683179 TCCCGCGATATCCGATGGAT 60.683 55.000 8.23 3.49 45.40 3.41
373 381 2.541794 CCGCGATATCCGATGGATACAG 60.542 54.545 8.23 6.41 45.95 2.74
393 401 2.110899 AGACCTCCACATATCCTCCGAT 59.889 50.000 0.00 0.00 0.00 4.18
405 413 0.955178 CCTCCGATGATGCTAGACGT 59.045 55.000 0.00 0.00 0.00 4.34
408 416 2.548480 CTCCGATGATGCTAGACGTACA 59.452 50.000 0.00 0.00 0.00 2.90
410 418 3.043586 CCGATGATGCTAGACGTACAAC 58.956 50.000 0.00 0.00 0.00 3.32
416 424 2.937591 TGCTAGACGTACAACCGAAAG 58.062 47.619 0.00 0.00 0.00 2.62
444 455 4.819105 AGAACGTGGGAGACATTATTCA 57.181 40.909 0.00 0.00 0.00 2.57
483 496 2.430610 GCCACACAGCCCAACCAAA 61.431 57.895 0.00 0.00 0.00 3.28
495 508 2.607771 CCCAACCAAAACGCTGAATCTG 60.608 50.000 0.00 0.00 0.00 2.90
520 533 0.328258 AACAAGAATGGGGTCCCTCG 59.672 55.000 8.15 0.00 36.94 4.63
521 534 1.452108 CAAGAATGGGGTCCCTCGC 60.452 63.158 8.15 0.00 36.94 5.03
522 535 3.031417 AAGAATGGGGTCCCTCGCG 62.031 63.158 8.15 0.00 36.94 5.87
541 554 3.149038 GGTAGGGGGCCGAGATTC 58.851 66.667 0.00 0.00 0.00 2.52
542 555 1.459730 GGTAGGGGGCCGAGATTCT 60.460 63.158 0.00 0.00 0.00 2.40
543 556 1.473497 GGTAGGGGGCCGAGATTCTC 61.473 65.000 3.43 3.43 0.00 2.87
544 557 0.470268 GTAGGGGGCCGAGATTCTCT 60.470 60.000 11.75 0.00 0.00 3.10
545 558 0.470080 TAGGGGGCCGAGATTCTCTG 60.470 60.000 11.75 6.43 0.00 3.35
546 559 2.110006 GGGGCCGAGATTCTCTGC 59.890 66.667 18.62 18.62 39.42 4.26
547 560 2.735772 GGGGCCGAGATTCTCTGCA 61.736 63.158 25.27 0.00 41.37 4.41
548 561 1.522580 GGGCCGAGATTCTCTGCAC 60.523 63.158 25.27 20.74 41.37 4.57
549 562 1.522580 GGCCGAGATTCTCTGCACC 60.523 63.158 25.27 12.03 41.37 5.01
550 563 1.519719 GCCGAGATTCTCTGCACCT 59.480 57.895 21.02 0.00 39.80 4.00
551 564 0.747255 GCCGAGATTCTCTGCACCTA 59.253 55.000 21.02 0.00 39.80 3.08
552 565 1.537135 GCCGAGATTCTCTGCACCTAC 60.537 57.143 21.02 0.00 39.80 3.18
553 566 1.751351 CCGAGATTCTCTGCACCTACA 59.249 52.381 11.75 0.00 0.00 2.74
554 567 2.363680 CCGAGATTCTCTGCACCTACAT 59.636 50.000 11.75 0.00 0.00 2.29
555 568 3.379240 CGAGATTCTCTGCACCTACATG 58.621 50.000 11.75 0.00 0.00 3.21
556 569 3.726607 GAGATTCTCTGCACCTACATGG 58.273 50.000 6.42 0.00 42.93 3.66
557 570 2.158842 AGATTCTCTGCACCTACATGGC 60.159 50.000 0.00 0.00 40.22 4.40
558 571 0.253044 TTCTCTGCACCTACATGGCC 59.747 55.000 0.00 0.00 40.22 5.36
559 572 0.618680 TCTCTGCACCTACATGGCCT 60.619 55.000 3.32 0.00 40.22 5.19
560 573 1.123077 CTCTGCACCTACATGGCCTA 58.877 55.000 3.32 0.00 40.22 3.93
561 574 1.069823 CTCTGCACCTACATGGCCTAG 59.930 57.143 3.32 0.00 40.22 3.02
562 575 1.123077 CTGCACCTACATGGCCTAGA 58.877 55.000 3.32 0.00 40.22 2.43
563 576 1.486310 CTGCACCTACATGGCCTAGAA 59.514 52.381 3.32 0.00 40.22 2.10
564 577 1.486310 TGCACCTACATGGCCTAGAAG 59.514 52.381 3.32 0.00 40.22 2.85
565 578 1.811941 GCACCTACATGGCCTAGAAGC 60.812 57.143 3.32 1.56 40.22 3.86
575 588 2.829741 GCCTAGAAGCCATCGAAGAT 57.170 50.000 0.00 0.00 45.12 2.40
576 589 2.411904 GCCTAGAAGCCATCGAAGATG 58.588 52.381 3.21 3.21 45.12 2.90
577 590 2.869636 GCCTAGAAGCCATCGAAGATGG 60.870 54.545 21.26 21.26 45.12 3.51
578 591 2.289320 CCTAGAAGCCATCGAAGATGGG 60.289 54.545 25.10 11.03 45.12 4.00
579 592 0.471617 AGAAGCCATCGAAGATGGGG 59.528 55.000 25.10 6.61 45.12 4.96
580 593 0.181350 GAAGCCATCGAAGATGGGGT 59.819 55.000 25.10 12.26 45.12 4.95
581 594 1.416401 GAAGCCATCGAAGATGGGGTA 59.584 52.381 25.10 0.00 45.12 3.69
582 595 1.051812 AGCCATCGAAGATGGGGTAG 58.948 55.000 25.10 5.34 45.12 3.18
583 596 1.048601 GCCATCGAAGATGGGGTAGA 58.951 55.000 25.10 0.00 45.12 2.59
584 597 1.270358 GCCATCGAAGATGGGGTAGAC 60.270 57.143 25.10 8.31 45.12 2.59
585 598 1.344763 CCATCGAAGATGGGGTAGACC 59.655 57.143 18.63 0.00 45.12 3.85
586 599 1.000163 CATCGAAGATGGGGTAGACCG 60.000 57.143 2.29 0.00 45.12 4.79
587 600 0.754217 TCGAAGATGGGGTAGACCGG 60.754 60.000 0.00 0.00 41.60 5.28
588 601 1.446366 GAAGATGGGGTAGACCGGC 59.554 63.158 0.00 0.00 41.60 6.13
589 602 2.365095 GAAGATGGGGTAGACCGGCG 62.365 65.000 0.00 0.00 41.60 6.46
590 603 3.925090 GATGGGGTAGACCGGCGG 61.925 72.222 27.06 27.06 41.60 6.13
612 625 4.186136 ACCGACGGAAGGTGAAGA 57.814 55.556 23.38 0.00 41.10 2.87
613 626 1.965219 ACCGACGGAAGGTGAAGAG 59.035 57.895 23.38 0.00 41.10 2.85
614 627 1.446272 CCGACGGAAGGTGAAGAGC 60.446 63.158 8.64 0.00 0.00 4.09
615 628 1.587054 CGACGGAAGGTGAAGAGCT 59.413 57.895 0.00 0.00 0.00 4.09
616 629 0.038159 CGACGGAAGGTGAAGAGCTT 60.038 55.000 0.00 0.00 42.73 3.74
617 630 1.605712 CGACGGAAGGTGAAGAGCTTT 60.606 52.381 0.00 0.00 40.07 3.51
618 631 2.495084 GACGGAAGGTGAAGAGCTTTT 58.505 47.619 0.00 0.00 40.07 2.27
619 632 2.480802 GACGGAAGGTGAAGAGCTTTTC 59.519 50.000 10.00 10.00 40.07 2.29
620 633 2.104963 ACGGAAGGTGAAGAGCTTTTCT 59.895 45.455 17.07 0.00 40.07 2.52
622 635 3.058639 CGGAAGGTGAAGAGCTTTTCTTG 60.059 47.826 17.07 0.00 46.12 3.02
623 636 3.885901 GGAAGGTGAAGAGCTTTTCTTGT 59.114 43.478 17.07 1.46 46.12 3.16
624 637 4.261363 GGAAGGTGAAGAGCTTTTCTTGTG 60.261 45.833 17.07 0.00 46.12 3.33
625 638 3.217626 AGGTGAAGAGCTTTTCTTGTGG 58.782 45.455 17.07 0.00 46.12 4.17
626 639 3.117888 AGGTGAAGAGCTTTTCTTGTGGA 60.118 43.478 17.07 0.00 46.12 4.02
627 640 3.251972 GGTGAAGAGCTTTTCTTGTGGAG 59.748 47.826 17.07 0.00 46.12 3.86
628 641 3.251972 GTGAAGAGCTTTTCTTGTGGAGG 59.748 47.826 17.07 0.00 46.12 4.30
629 642 3.136443 TGAAGAGCTTTTCTTGTGGAGGA 59.864 43.478 17.07 0.00 46.12 3.71
630 643 3.864789 AGAGCTTTTCTTGTGGAGGAA 57.135 42.857 0.00 0.00 29.61 3.36
631 644 4.379302 AGAGCTTTTCTTGTGGAGGAAT 57.621 40.909 0.00 0.00 29.61 3.01
632 645 5.505181 AGAGCTTTTCTTGTGGAGGAATA 57.495 39.130 0.00 0.00 29.61 1.75
633 646 5.880901 AGAGCTTTTCTTGTGGAGGAATAA 58.119 37.500 0.00 0.00 29.61 1.40
634 647 6.306987 AGAGCTTTTCTTGTGGAGGAATAAA 58.693 36.000 0.00 0.00 29.61 1.40
635 648 6.207614 AGAGCTTTTCTTGTGGAGGAATAAAC 59.792 38.462 0.00 0.00 29.61 2.01
636 649 5.833131 AGCTTTTCTTGTGGAGGAATAAACA 59.167 36.000 0.00 0.00 0.00 2.83
637 650 6.323739 AGCTTTTCTTGTGGAGGAATAAACAA 59.676 34.615 0.00 0.00 0.00 2.83
638 651 6.983890 GCTTTTCTTGTGGAGGAATAAACAAA 59.016 34.615 0.00 0.00 32.50 2.83
639 652 7.657354 GCTTTTCTTGTGGAGGAATAAACAAAT 59.343 33.333 0.00 0.00 32.50 2.32
640 653 8.885494 TTTTCTTGTGGAGGAATAAACAAATG 57.115 30.769 0.00 0.00 32.50 2.32
641 654 7.831691 TTCTTGTGGAGGAATAAACAAATGA 57.168 32.000 0.00 0.00 32.50 2.57
642 655 7.831691 TCTTGTGGAGGAATAAACAAATGAA 57.168 32.000 0.00 0.00 32.50 2.57
643 656 8.421249 TCTTGTGGAGGAATAAACAAATGAAT 57.579 30.769 0.00 0.00 32.50 2.57
644 657 8.522830 TCTTGTGGAGGAATAAACAAATGAATC 58.477 33.333 0.00 0.00 32.50 2.52
645 658 8.421249 TTGTGGAGGAATAAACAAATGAATCT 57.579 30.769 0.00 0.00 29.96 2.40
646 659 8.421249 TGTGGAGGAATAAACAAATGAATCTT 57.579 30.769 0.00 0.00 0.00 2.40
647 660 8.869109 TGTGGAGGAATAAACAAATGAATCTTT 58.131 29.630 0.00 0.00 0.00 2.52
648 661 9.710900 GTGGAGGAATAAACAAATGAATCTTTT 57.289 29.630 0.00 0.00 0.00 2.27
672 685 3.666345 AGTAATGACTACTCCCTCCGT 57.334 47.619 0.00 0.00 35.90 4.69
673 686 3.553904 AGTAATGACTACTCCCTCCGTC 58.446 50.000 0.00 0.00 35.90 4.79
674 687 2.830651 AATGACTACTCCCTCCGTCT 57.169 50.000 0.00 0.00 0.00 4.18
675 688 3.947612 AATGACTACTCCCTCCGTCTA 57.052 47.619 0.00 0.00 0.00 2.59
676 689 3.495434 ATGACTACTCCCTCCGTCTAG 57.505 52.381 0.00 0.00 0.00 2.43
677 690 2.194859 TGACTACTCCCTCCGTCTAGT 58.805 52.381 0.00 0.00 0.00 2.57
678 691 2.093075 TGACTACTCCCTCCGTCTAGTG 60.093 54.545 0.00 0.00 0.00 2.74
679 692 1.914798 ACTACTCCCTCCGTCTAGTGT 59.085 52.381 0.00 0.00 0.00 3.55
680 693 2.093021 ACTACTCCCTCCGTCTAGTGTC 60.093 54.545 0.00 0.00 0.00 3.67
681 694 0.697079 ACTCCCTCCGTCTAGTGTCA 59.303 55.000 0.00 0.00 0.00 3.58
682 695 1.075050 ACTCCCTCCGTCTAGTGTCAA 59.925 52.381 0.00 0.00 0.00 3.18
683 696 2.168496 CTCCCTCCGTCTAGTGTCAAA 58.832 52.381 0.00 0.00 0.00 2.69
684 697 2.561419 CTCCCTCCGTCTAGTGTCAAAA 59.439 50.000 0.00 0.00 0.00 2.44
685 698 2.967201 TCCCTCCGTCTAGTGTCAAAAA 59.033 45.455 0.00 0.00 0.00 1.94
686 699 3.581332 TCCCTCCGTCTAGTGTCAAAAAT 59.419 43.478 0.00 0.00 0.00 1.82
687 700 4.041198 TCCCTCCGTCTAGTGTCAAAAATT 59.959 41.667 0.00 0.00 0.00 1.82
688 701 4.392138 CCCTCCGTCTAGTGTCAAAAATTC 59.608 45.833 0.00 0.00 0.00 2.17
689 702 5.238583 CCTCCGTCTAGTGTCAAAAATTCT 58.761 41.667 0.00 0.00 0.00 2.40
690 703 5.348997 CCTCCGTCTAGTGTCAAAAATTCTC 59.651 44.000 0.00 0.00 0.00 2.87
691 704 6.097915 TCCGTCTAGTGTCAAAAATTCTCT 57.902 37.500 0.00 0.00 0.00 3.10
692 705 6.522054 TCCGTCTAGTGTCAAAAATTCTCTT 58.478 36.000 0.00 0.00 0.00 2.85
693 706 7.663827 TCCGTCTAGTGTCAAAAATTCTCTTA 58.336 34.615 0.00 0.00 0.00 2.10
694 707 8.311836 TCCGTCTAGTGTCAAAAATTCTCTTAT 58.688 33.333 0.00 0.00 0.00 1.73
695 708 9.582431 CCGTCTAGTGTCAAAAATTCTCTTATA 57.418 33.333 0.00 0.00 0.00 0.98
712 725 9.902684 TTCTCTTATATTATAGGACGTAGGGAG 57.097 37.037 0.00 0.00 0.00 4.30
713 726 9.055689 TCTCTTATATTATAGGACGTAGGGAGT 57.944 37.037 0.00 0.00 0.00 3.85
724 737 6.932947 AGGACGTAGGGAGTAATAAATATGC 58.067 40.000 0.00 0.00 0.00 3.14
748 761 4.937620 TCAAGATGAATGCAAGTGGAGTAC 59.062 41.667 0.00 0.00 0.00 2.73
779 792 1.280746 CCATTATTGGCAGCGCTCG 59.719 57.895 7.13 4.46 35.85 5.03
822 835 9.469807 GAGTTGAGAACATAACATATAGACTGG 57.530 37.037 0.00 0.00 0.00 4.00
830 843 6.150307 ACATAACATATAGACTGGAGAGCTCG 59.850 42.308 8.37 0.00 0.00 5.03
887 1224 6.295916 CCTTCCTTTATGTTGACTGACCTACT 60.296 42.308 0.00 0.00 0.00 2.57
888 1225 7.093465 CCTTCCTTTATGTTGACTGACCTACTA 60.093 40.741 0.00 0.00 0.00 1.82
889 1226 7.786046 TCCTTTATGTTGACTGACCTACTAA 57.214 36.000 0.00 0.00 0.00 2.24
890 1227 8.375493 TCCTTTATGTTGACTGACCTACTAAT 57.625 34.615 0.00 0.00 0.00 1.73
908 1245 9.178427 CCTACTAATTAACTCATTAGTGTACGC 57.822 37.037 13.88 0.00 45.59 4.42
1077 1425 3.861113 TCGTAAGCCAAAGTAGCAATACG 59.139 43.478 12.12 12.12 43.58 3.06
1128 1477 6.927276 ATGGCAACCATAACTGCTAGTGCA 62.927 45.833 0.00 0.00 43.19 4.57
1389 1741 1.747924 CTGTGCATCTCTCTCTTCCGA 59.252 52.381 0.00 0.00 0.00 4.55
1476 1828 1.216977 CGGGTTCTACGCCATGTCA 59.783 57.895 0.00 0.00 0.00 3.58
1629 1981 1.519234 CGCCGTCTTGCTGCTCATA 60.519 57.895 0.00 0.00 0.00 2.15
1953 2311 3.621805 TTCGGGCTCGGCAAGACA 61.622 61.111 5.94 0.00 32.94 3.41
2266 2633 1.872653 GCAAAACGGAAGACCTCGAGT 60.873 52.381 12.31 0.00 0.00 4.18
2411 2972 8.964420 TTTTATGTAGCACAGACAAATTAAGC 57.036 30.769 0.00 0.00 0.00 3.09
2479 3312 1.089920 CTTGCCCATGAGCACAGTAC 58.910 55.000 0.00 0.00 43.97 2.73
2514 3347 3.858503 GCTGCTTTTGAAATGTGGGAGTC 60.859 47.826 0.00 0.00 0.00 3.36
2518 3351 4.787598 CTTTTGAAATGTGGGAGTCGAAG 58.212 43.478 0.00 0.00 0.00 3.79
2523 3356 3.771577 AATGTGGGAGTCGAAGTCTTT 57.228 42.857 0.00 0.00 0.00 2.52
2533 3366 2.866762 GTCGAAGTCTTTTGCTGACTGT 59.133 45.455 0.00 0.00 43.16 3.55
2541 3374 4.025313 GTCTTTTGCTGACTGTTGTCTCTC 60.025 45.833 0.00 0.00 43.29 3.20
2562 3395 5.247110 TCTCTGAACAGGATAGCAGAAGTTT 59.753 40.000 1.93 0.00 36.99 2.66
2577 3410 5.750067 GCAGAAGTTTTGCTGATTTCTTGAA 59.250 36.000 10.98 0.00 38.51 2.69
2615 3450 2.863739 CGCACTAGACATCGAACTTGA 58.136 47.619 0.00 0.00 0.00 3.02
2617 3452 3.859961 CGCACTAGACATCGAACTTGAAT 59.140 43.478 0.00 0.00 0.00 2.57
2619 3454 5.499334 CGCACTAGACATCGAACTTGAATTC 60.499 44.000 0.00 0.00 0.00 2.17
2632 3467 3.879295 ACTTGAATTCTGGTGTGTGTCTG 59.121 43.478 7.05 0.00 0.00 3.51
2641 3479 1.609061 GGTGTGTGTCTGACATCCCTG 60.609 57.143 14.37 0.00 36.78 4.45
2696 3534 7.339721 TCTCCATCGAAGAGTAAAGAGTAATGT 59.660 37.037 13.68 0.00 43.63 2.71
2698 3536 8.963725 TCCATCGAAGAGTAAAGAGTAATGTTA 58.036 33.333 0.00 0.00 43.63 2.41
2699 3537 9.751542 CCATCGAAGAGTAAAGAGTAATGTTAT 57.248 33.333 0.00 0.00 43.63 1.89
2761 3599 8.127327 CAGCAATACTTGTCCATTAGAATTCAG 58.873 37.037 8.44 0.00 0.00 3.02
2763 3601 8.677300 GCAATACTTGTCCATTAGAATTCAGAA 58.323 33.333 8.44 1.66 0.00 3.02
2766 3604 7.454260 ACTTGTCCATTAGAATTCAGAAACC 57.546 36.000 8.44 0.00 0.00 3.27
2768 3606 4.941263 TGTCCATTAGAATTCAGAAACCGG 59.059 41.667 8.44 0.00 0.00 5.28
2769 3607 3.945285 TCCATTAGAATTCAGAAACCGGC 59.055 43.478 8.44 0.00 0.00 6.13
2770 3608 3.066760 CCATTAGAATTCAGAAACCGGCC 59.933 47.826 8.44 0.00 0.00 6.13
2771 3609 2.413310 TAGAATTCAGAAACCGGCCC 57.587 50.000 8.44 0.00 0.00 5.80
2772 3610 0.404040 AGAATTCAGAAACCGGCCCA 59.596 50.000 8.44 0.00 0.00 5.36
2773 3611 1.203001 AGAATTCAGAAACCGGCCCAA 60.203 47.619 8.44 0.00 0.00 4.12
2775 3613 0.611896 ATTCAGAAACCGGCCCAAGG 60.612 55.000 0.00 0.00 0.00 3.61
2777 3615 1.228429 CAGAAACCGGCCCAAGGAA 60.228 57.895 0.00 0.00 0.00 3.36
2778 3616 1.074951 AGAAACCGGCCCAAGGAAG 59.925 57.895 0.00 0.00 0.00 3.46
2780 3618 1.524008 GAAACCGGCCCAAGGAAGTG 61.524 60.000 0.00 0.00 0.00 3.16
2783 3621 1.078426 CCGGCCCAAGGAAGTGTAG 60.078 63.158 0.00 0.00 0.00 2.74
2784 3622 1.745489 CGGCCCAAGGAAGTGTAGC 60.745 63.158 0.00 0.00 0.00 3.58
2785 3623 1.378762 GGCCCAAGGAAGTGTAGCA 59.621 57.895 0.00 0.00 0.00 3.49
2786 3624 0.960861 GGCCCAAGGAAGTGTAGCAC 60.961 60.000 0.00 0.00 34.10 4.40
2788 3626 1.813513 CCCAAGGAAGTGTAGCACAG 58.186 55.000 2.01 0.00 36.74 3.66
2789 3627 1.611673 CCCAAGGAAGTGTAGCACAGG 60.612 57.143 2.01 0.00 36.74 4.00
2791 3629 2.224523 CCAAGGAAGTGTAGCACAGGAA 60.225 50.000 2.01 0.00 36.74 3.36
2792 3630 2.808543 CAAGGAAGTGTAGCACAGGAAC 59.191 50.000 2.01 0.00 36.74 3.62
2794 3632 2.438021 AGGAAGTGTAGCACAGGAACAA 59.562 45.455 2.01 0.00 36.74 2.83
2795 3633 3.118038 AGGAAGTGTAGCACAGGAACAAA 60.118 43.478 2.01 0.00 36.74 2.83
2796 3634 3.821033 GGAAGTGTAGCACAGGAACAAAT 59.179 43.478 2.01 0.00 36.74 2.32
2797 3635 4.278419 GGAAGTGTAGCACAGGAACAAATT 59.722 41.667 2.01 0.00 36.74 1.82
2798 3636 5.221244 GGAAGTGTAGCACAGGAACAAATTT 60.221 40.000 2.01 0.00 36.74 1.82
2799 3637 5.852282 AGTGTAGCACAGGAACAAATTTT 57.148 34.783 2.01 0.00 36.74 1.82
2800 3638 6.220726 AGTGTAGCACAGGAACAAATTTTT 57.779 33.333 2.01 0.00 36.74 1.94
2801 3639 7.341445 AGTGTAGCACAGGAACAAATTTTTA 57.659 32.000 2.01 0.00 36.74 1.52
2802 3640 7.425606 AGTGTAGCACAGGAACAAATTTTTAG 58.574 34.615 2.01 0.00 36.74 1.85
2804 3642 7.704899 GTGTAGCACAGGAACAAATTTTTAGTT 59.295 33.333 0.00 0.00 34.08 2.24
2805 3643 8.904834 TGTAGCACAGGAACAAATTTTTAGTTA 58.095 29.630 0.00 0.00 0.00 2.24
2807 3645 8.007405 AGCACAGGAACAAATTTTTAGTTACT 57.993 30.769 0.00 0.00 36.90 2.24
2809 3647 7.918562 GCACAGGAACAAATTTTTAGTTACTCA 59.081 33.333 2.41 0.00 34.30 3.41
2811 3649 9.185680 ACAGGAACAAATTTTTAGTTACTCACT 57.814 29.630 2.41 0.00 34.30 3.41
2813 3651 9.403583 AGGAACAAATTTTTAGTTACTCACTCA 57.596 29.630 0.00 0.00 30.85 3.41
2814 3652 9.447040 GGAACAAATTTTTAGTTACTCACTCAC 57.553 33.333 0.00 0.00 36.88 3.51
2815 3653 9.997482 GAACAAATTTTTAGTTACTCACTCACA 57.003 29.630 0.00 0.00 36.88 3.58
2822 3660 8.683550 TTTTAGTTACTCACTCACATACATCG 57.316 34.615 0.00 0.00 36.88 3.84
2840 3678 9.127006 CATACATCGAGATTCTCTTACAAGATG 57.873 37.037 17.96 17.96 38.92 2.90
2917 3760 9.885934 GACATAGTACTGTCATACTGTAAGATG 57.114 37.037 5.39 0.00 44.03 2.90
2918 3761 9.409918 ACATAGTACTGTCATACTGTAAGATGT 57.590 33.333 5.39 13.51 36.46 3.06
2985 3831 8.134895 GGCGAATATAAATTTGACTCCATTCAA 58.865 33.333 0.00 0.00 32.32 2.69
2986 3832 9.683069 GCGAATATAAATTTGACTCCATTCAAT 57.317 29.630 0.00 0.00 35.42 2.57
3262 4112 9.742144 TTATAGATACTCCCTCTGTCTCATAAC 57.258 37.037 0.00 0.00 0.00 1.89
3267 4117 6.472686 ACTCCCTCTGTCTCATAACATAAC 57.527 41.667 0.00 0.00 0.00 1.89
3327 4177 8.901793 GTTATATTATAGGACGAAGGGAGTAGG 58.098 40.741 0.00 0.00 0.00 3.18
3333 4183 5.336491 AGGACGAAGGGAGTAGGTAATAT 57.664 43.478 0.00 0.00 0.00 1.28
3354 4210 5.862924 ATTACAAGAGAACATTCCACGTG 57.137 39.130 9.08 9.08 0.00 4.49
3355 4211 1.873591 ACAAGAGAACATTCCACGTGC 59.126 47.619 10.91 0.00 0.00 5.34
3356 4212 2.146342 CAAGAGAACATTCCACGTGCT 58.854 47.619 10.91 0.00 0.00 4.40
3357 4213 2.086054 AGAGAACATTCCACGTGCTC 57.914 50.000 10.91 9.43 39.08 4.26
3374 4230 6.422100 CACGTGCTCTTCTAACATAAGCATAT 59.578 38.462 0.82 0.00 44.07 1.78
3386 4247 2.346766 AAGCATATGTCGCATCCCAA 57.653 45.000 4.29 0.00 0.00 4.12
3414 4275 4.098807 GGTTTTGTGCCAGTTCTAGGAAAA 59.901 41.667 0.00 0.00 0.00 2.29
3415 4276 5.221441 GGTTTTGTGCCAGTTCTAGGAAAAT 60.221 40.000 0.00 0.00 0.00 1.82
3416 4277 6.015772 GGTTTTGTGCCAGTTCTAGGAAAATA 60.016 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.645067 TCTTTGTACTGCCATGATTGAAGAG 59.355 40.000 0.00 0.00 0.00 2.85
74 75 1.771565 CTAGGTGGTCCACGGACATA 58.228 55.000 17.72 3.63 46.20 2.29
186 188 2.086869 CCTTAGTACGACGACTTCCCA 58.913 52.381 0.00 0.00 0.00 4.37
200 202 2.966516 GCTGGTACTATGGAGCCTTAGT 59.033 50.000 16.37 16.37 39.31 2.24
208 214 0.973496 TGGTGCGCTGGTACTATGGA 60.973 55.000 9.73 0.00 0.00 3.41
215 221 1.945354 GCTACTCTGGTGCGCTGGTA 61.945 60.000 9.73 2.11 0.00 3.25
251 257 6.531503 TCATCCTTCTGATCTACGACTTTT 57.468 37.500 0.00 0.00 0.00 2.27
273 279 6.869388 TCTTTGTTTGGGTGTTTACAAGTTTC 59.131 34.615 0.00 0.00 32.67 2.78
278 284 5.723672 TGTCTTTGTTTGGGTGTTTACAA 57.276 34.783 0.00 0.00 0.00 2.41
300 307 3.292460 TGTTTGGATCCGGTCTTTGTTT 58.708 40.909 7.39 0.00 0.00 2.83
342 349 0.242825 GATATCGCGGGATTCGGTCA 59.757 55.000 20.86 1.25 39.69 4.02
358 365 3.075432 TGGAGGTCTGTATCCATCGGATA 59.925 47.826 0.00 0.00 41.16 2.59
365 372 4.140686 AGGATATGTGGAGGTCTGTATCCA 60.141 45.833 10.75 0.00 43.34 3.41
369 376 3.750922 CGGAGGATATGTGGAGGTCTGTA 60.751 52.174 0.00 0.00 0.00 2.74
373 381 1.996798 TCGGAGGATATGTGGAGGTC 58.003 55.000 0.00 0.00 0.00 3.85
383 391 3.010420 CGTCTAGCATCATCGGAGGATA 58.990 50.000 4.66 0.00 0.00 2.59
384 392 1.815613 CGTCTAGCATCATCGGAGGAT 59.184 52.381 0.00 0.00 0.00 3.24
393 401 2.086094 TCGGTTGTACGTCTAGCATCA 58.914 47.619 0.00 0.00 34.94 3.07
405 413 4.142315 CGTTCTATCCTCCTTTCGGTTGTA 60.142 45.833 0.00 0.00 0.00 2.41
408 416 2.830321 ACGTTCTATCCTCCTTTCGGTT 59.170 45.455 0.00 0.00 0.00 4.44
410 418 2.481449 CCACGTTCTATCCTCCTTTCGG 60.481 54.545 0.00 0.00 0.00 4.30
416 424 1.682323 GTCTCCCACGTTCTATCCTCC 59.318 57.143 0.00 0.00 0.00 4.30
444 455 1.692519 GGCGGTGATGTCCCTTAGTAT 59.307 52.381 0.00 0.00 0.00 2.12
483 496 3.466836 TGTTCTTGTCAGATTCAGCGTT 58.533 40.909 0.00 0.00 0.00 4.84
495 508 2.820197 GGACCCCATTCTTGTTCTTGTC 59.180 50.000 0.00 0.00 0.00 3.18
524 537 1.459730 AGAATCTCGGCCCCCTACC 60.460 63.158 0.00 0.00 0.00 3.18
525 538 2.051105 GAGAATCTCGGCCCCCTAC 58.949 63.158 0.00 0.00 0.00 3.18
526 539 4.621269 GAGAATCTCGGCCCCCTA 57.379 61.111 0.00 0.00 0.00 3.53
535 548 4.049376 GCCATGTAGGTGCAGAGAATCTC 61.049 52.174 1.19 1.19 42.10 2.75
536 549 2.158842 GCCATGTAGGTGCAGAGAATCT 60.159 50.000 0.00 0.00 44.27 2.40
537 550 2.216898 GCCATGTAGGTGCAGAGAATC 58.783 52.381 0.00 0.00 40.61 2.52
538 551 1.133976 GGCCATGTAGGTGCAGAGAAT 60.134 52.381 0.00 0.00 40.61 2.40
539 552 0.253044 GGCCATGTAGGTGCAGAGAA 59.747 55.000 0.00 0.00 40.61 2.87
540 553 0.618680 AGGCCATGTAGGTGCAGAGA 60.619 55.000 5.01 0.00 40.61 3.10
541 554 1.069823 CTAGGCCATGTAGGTGCAGAG 59.930 57.143 5.01 0.00 40.61 3.35
542 555 1.123077 CTAGGCCATGTAGGTGCAGA 58.877 55.000 5.01 0.00 40.61 4.26
543 556 1.123077 TCTAGGCCATGTAGGTGCAG 58.877 55.000 5.01 0.00 40.61 4.41
544 557 1.486310 CTTCTAGGCCATGTAGGTGCA 59.514 52.381 5.01 0.00 40.61 4.57
545 558 1.811941 GCTTCTAGGCCATGTAGGTGC 60.812 57.143 5.01 2.96 40.61 5.01
546 559 2.246719 GCTTCTAGGCCATGTAGGTG 57.753 55.000 5.01 0.00 40.61 4.00
556 569 2.411904 CATCTTCGATGGCTTCTAGGC 58.588 52.381 0.00 0.00 41.77 3.93
557 570 2.289320 CCCATCTTCGATGGCTTCTAGG 60.289 54.545 15.70 0.00 37.85 3.02
558 571 2.289320 CCCCATCTTCGATGGCTTCTAG 60.289 54.545 15.70 3.25 37.85 2.43
559 572 1.694150 CCCCATCTTCGATGGCTTCTA 59.306 52.381 15.70 0.00 37.85 2.10
560 573 0.471617 CCCCATCTTCGATGGCTTCT 59.528 55.000 15.70 0.00 37.85 2.85
561 574 0.181350 ACCCCATCTTCGATGGCTTC 59.819 55.000 15.70 0.00 37.85 3.86
562 575 1.417890 CTACCCCATCTTCGATGGCTT 59.582 52.381 15.70 8.10 37.85 4.35
563 576 1.051812 CTACCCCATCTTCGATGGCT 58.948 55.000 15.70 6.87 37.85 4.75
564 577 1.048601 TCTACCCCATCTTCGATGGC 58.951 55.000 15.70 0.00 37.85 4.40
565 578 1.344763 GGTCTACCCCATCTTCGATGG 59.655 57.143 14.48 14.48 38.88 3.51
566 579 1.000163 CGGTCTACCCCATCTTCGATG 60.000 57.143 0.00 0.00 0.00 3.84
567 580 1.329256 CGGTCTACCCCATCTTCGAT 58.671 55.000 0.00 0.00 0.00 3.59
568 581 0.754217 CCGGTCTACCCCATCTTCGA 60.754 60.000 0.00 0.00 0.00 3.71
569 582 1.740285 CCGGTCTACCCCATCTTCG 59.260 63.158 0.00 0.00 0.00 3.79
570 583 1.446366 GCCGGTCTACCCCATCTTC 59.554 63.158 1.90 0.00 0.00 2.87
571 584 2.432300 CGCCGGTCTACCCCATCTT 61.432 63.158 1.90 0.00 0.00 2.40
572 585 2.838225 CGCCGGTCTACCCCATCT 60.838 66.667 1.90 0.00 0.00 2.90
573 586 3.925090 CCGCCGGTCTACCCCATC 61.925 72.222 1.90 0.00 0.00 3.51
595 608 1.965219 CTCTTCACCTTCCGTCGGT 59.035 57.895 11.88 0.00 34.38 4.69
596 609 1.446272 GCTCTTCACCTTCCGTCGG 60.446 63.158 4.39 4.39 0.00 4.79
597 610 0.038159 AAGCTCTTCACCTTCCGTCG 60.038 55.000 0.00 0.00 0.00 5.12
598 611 2.171341 AAAGCTCTTCACCTTCCGTC 57.829 50.000 0.00 0.00 0.00 4.79
599 612 2.104963 AGAAAAGCTCTTCACCTTCCGT 59.895 45.455 1.97 0.00 0.00 4.69
600 613 2.772287 AGAAAAGCTCTTCACCTTCCG 58.228 47.619 1.97 0.00 0.00 4.30
601 614 3.885901 ACAAGAAAAGCTCTTCACCTTCC 59.114 43.478 1.97 0.00 42.84 3.46
602 615 4.261363 CCACAAGAAAAGCTCTTCACCTTC 60.261 45.833 1.97 0.00 42.84 3.46
603 616 3.633986 CCACAAGAAAAGCTCTTCACCTT 59.366 43.478 1.97 0.00 42.84 3.50
604 617 3.117888 TCCACAAGAAAAGCTCTTCACCT 60.118 43.478 1.97 0.00 42.84 4.00
605 618 3.214328 TCCACAAGAAAAGCTCTTCACC 58.786 45.455 1.97 0.00 42.84 4.02
606 619 3.251972 CCTCCACAAGAAAAGCTCTTCAC 59.748 47.826 1.97 0.00 42.84 3.18
607 620 3.136443 TCCTCCACAAGAAAAGCTCTTCA 59.864 43.478 1.97 0.00 42.84 3.02
608 621 3.744660 TCCTCCACAAGAAAAGCTCTTC 58.255 45.455 0.00 0.00 42.84 2.87
609 622 3.864789 TCCTCCACAAGAAAAGCTCTT 57.135 42.857 0.00 0.00 45.80 2.85
610 623 3.864789 TTCCTCCACAAGAAAAGCTCT 57.135 42.857 0.00 0.00 35.13 4.09
611 624 6.016276 TGTTTATTCCTCCACAAGAAAAGCTC 60.016 38.462 0.00 0.00 0.00 4.09
612 625 5.833131 TGTTTATTCCTCCACAAGAAAAGCT 59.167 36.000 0.00 0.00 0.00 3.74
613 626 6.084326 TGTTTATTCCTCCACAAGAAAAGC 57.916 37.500 0.00 0.00 0.00 3.51
614 627 8.981647 CATTTGTTTATTCCTCCACAAGAAAAG 58.018 33.333 0.00 0.00 31.00 2.27
615 628 8.700051 TCATTTGTTTATTCCTCCACAAGAAAA 58.300 29.630 0.00 0.00 31.00 2.29
616 629 8.243961 TCATTTGTTTATTCCTCCACAAGAAA 57.756 30.769 0.00 0.00 31.00 2.52
617 630 7.831691 TCATTTGTTTATTCCTCCACAAGAA 57.168 32.000 0.00 0.00 31.00 2.52
618 631 7.831691 TTCATTTGTTTATTCCTCCACAAGA 57.168 32.000 0.00 0.00 31.00 3.02
619 632 8.526147 AGATTCATTTGTTTATTCCTCCACAAG 58.474 33.333 0.00 0.00 31.00 3.16
620 633 8.421249 AGATTCATTTGTTTATTCCTCCACAA 57.579 30.769 0.00 0.00 0.00 3.33
621 634 8.421249 AAGATTCATTTGTTTATTCCTCCACA 57.579 30.769 0.00 0.00 0.00 4.17
622 635 9.710900 AAAAGATTCATTTGTTTATTCCTCCAC 57.289 29.630 0.00 0.00 0.00 4.02
652 665 3.202595 AGACGGAGGGAGTAGTCATTACT 59.797 47.826 0.00 0.00 45.32 2.24
653 666 3.553904 AGACGGAGGGAGTAGTCATTAC 58.446 50.000 0.00 0.00 36.18 1.89
654 667 3.947612 AGACGGAGGGAGTAGTCATTA 57.052 47.619 0.00 0.00 36.18 1.90
655 668 2.830651 AGACGGAGGGAGTAGTCATT 57.169 50.000 0.00 0.00 36.18 2.57
656 669 2.778850 ACTAGACGGAGGGAGTAGTCAT 59.221 50.000 0.00 0.00 36.18 3.06
657 670 2.093075 CACTAGACGGAGGGAGTAGTCA 60.093 54.545 0.00 0.00 36.18 3.41
658 671 2.093021 ACACTAGACGGAGGGAGTAGTC 60.093 54.545 0.00 0.00 0.00 2.59
659 672 1.914798 ACACTAGACGGAGGGAGTAGT 59.085 52.381 0.00 0.00 0.00 2.73
660 673 2.093075 TGACACTAGACGGAGGGAGTAG 60.093 54.545 0.00 0.00 0.00 2.57
661 674 1.911357 TGACACTAGACGGAGGGAGTA 59.089 52.381 0.00 0.00 0.00 2.59
662 675 0.697079 TGACACTAGACGGAGGGAGT 59.303 55.000 0.00 0.00 0.00 3.85
663 676 1.835494 TTGACACTAGACGGAGGGAG 58.165 55.000 0.00 0.00 0.00 4.30
664 677 2.297698 TTTGACACTAGACGGAGGGA 57.702 50.000 0.00 0.00 0.00 4.20
665 678 3.396260 TTTTTGACACTAGACGGAGGG 57.604 47.619 0.00 0.00 0.00 4.30
666 679 5.238583 AGAATTTTTGACACTAGACGGAGG 58.761 41.667 0.00 0.00 0.00 4.30
667 680 6.159988 AGAGAATTTTTGACACTAGACGGAG 58.840 40.000 0.00 0.00 0.00 4.63
668 681 6.097915 AGAGAATTTTTGACACTAGACGGA 57.902 37.500 0.00 0.00 0.00 4.69
669 682 6.787085 AAGAGAATTTTTGACACTAGACGG 57.213 37.500 0.00 0.00 0.00 4.79
686 699 9.902684 CTCCCTACGTCCTATAATATAAGAGAA 57.097 37.037 0.00 0.00 0.00 2.87
687 700 9.055689 ACTCCCTACGTCCTATAATATAAGAGA 57.944 37.037 0.00 0.00 0.00 3.10
698 711 8.693625 GCATATTTATTACTCCCTACGTCCTAT 58.306 37.037 0.00 0.00 0.00 2.57
699 712 7.892241 AGCATATTTATTACTCCCTACGTCCTA 59.108 37.037 0.00 0.00 0.00 2.94
700 713 6.724905 AGCATATTTATTACTCCCTACGTCCT 59.275 38.462 0.00 0.00 0.00 3.85
701 714 6.932947 AGCATATTTATTACTCCCTACGTCC 58.067 40.000 0.00 0.00 0.00 4.79
702 715 7.600065 TGAGCATATTTATTACTCCCTACGTC 58.400 38.462 0.00 0.00 0.00 4.34
703 716 7.534723 TGAGCATATTTATTACTCCCTACGT 57.465 36.000 0.00 0.00 0.00 3.57
704 717 8.304596 TCTTGAGCATATTTATTACTCCCTACG 58.695 37.037 0.00 0.00 0.00 3.51
707 720 8.884323 TCATCTTGAGCATATTTATTACTCCCT 58.116 33.333 0.00 0.00 0.00 4.20
708 721 9.507329 TTCATCTTGAGCATATTTATTACTCCC 57.493 33.333 0.00 0.00 0.00 4.30
714 727 9.692749 CTTGCATTCATCTTGAGCATATTTATT 57.307 29.630 0.00 0.00 29.53 1.40
715 728 8.857098 ACTTGCATTCATCTTGAGCATATTTAT 58.143 29.630 0.00 0.00 29.53 1.40
716 729 8.132995 CACTTGCATTCATCTTGAGCATATTTA 58.867 33.333 0.00 0.00 29.53 1.40
717 730 6.978659 CACTTGCATTCATCTTGAGCATATTT 59.021 34.615 0.00 0.00 29.53 1.40
718 731 6.461092 CCACTTGCATTCATCTTGAGCATATT 60.461 38.462 0.00 0.00 29.53 1.28
719 732 5.009710 CCACTTGCATTCATCTTGAGCATAT 59.990 40.000 0.00 0.00 29.53 1.78
720 733 4.337274 CCACTTGCATTCATCTTGAGCATA 59.663 41.667 0.00 0.00 29.53 3.14
721 734 3.130516 CCACTTGCATTCATCTTGAGCAT 59.869 43.478 0.00 0.00 29.53 3.79
722 735 2.490509 CCACTTGCATTCATCTTGAGCA 59.509 45.455 0.00 0.00 0.00 4.26
723 736 2.751259 TCCACTTGCATTCATCTTGAGC 59.249 45.455 0.00 0.00 0.00 4.26
724 737 4.008330 ACTCCACTTGCATTCATCTTGAG 58.992 43.478 0.00 0.00 0.00 3.02
748 761 5.947228 CCAATAATGGCAGTGGTATGTAG 57.053 43.478 0.00 0.00 40.58 2.74
779 792 7.509546 TCTCAACTCAAGATATATTTGTCCCC 58.490 38.462 0.00 0.00 0.00 4.81
822 835 4.088213 CGTAACAGTTAACAACGAGCTCTC 59.912 45.833 12.85 0.00 35.66 3.20
830 843 6.573617 AGTACACACGTAACAGTTAACAAC 57.426 37.500 8.61 0.00 0.00 3.32
887 1224 8.991243 AACTGCGTACACTAATGAGTTAATTA 57.009 30.769 0.00 0.00 31.73 1.40
888 1225 7.900782 AACTGCGTACACTAATGAGTTAATT 57.099 32.000 0.00 0.00 31.73 1.40
889 1226 8.991243 TTAACTGCGTACACTAATGAGTTAAT 57.009 30.769 0.00 0.00 32.31 1.40
890 1227 8.991243 ATTAACTGCGTACACTAATGAGTTAA 57.009 30.769 0.00 0.00 38.25 2.01
930 1267 4.625742 AGATGTTAACAATGAGTTCGACCG 59.374 41.667 13.23 0.00 41.64 4.79
1077 1425 2.894126 TCCTAGCCAGCTAGAAGTATGC 59.106 50.000 24.86 0.00 46.56 3.14
1128 1477 0.962356 CTTCTTGCATGGCCGGACTT 60.962 55.000 9.82 0.00 0.00 3.01
1471 1823 2.127251 CGCATACACGTAGCATGACAT 58.873 47.619 0.00 0.00 0.00 3.06
1476 1828 1.605457 CCCATCGCATACACGTAGCAT 60.605 52.381 0.00 0.00 0.00 3.79
1512 1864 3.285215 AGCGACGACGTGGACAGT 61.285 61.111 14.57 0.00 41.98 3.55
1953 2311 2.029290 CACGAGCACCAGGTAGTAGTTT 60.029 50.000 0.00 0.00 29.82 2.66
2266 2633 1.228552 GTCTTCAAGGGGCAGCCAA 60.229 57.895 15.19 0.00 0.00 4.52
2391 2952 4.062293 ACGCTTAATTTGTCTGTGCTACA 58.938 39.130 0.00 0.00 0.00 2.74
2447 3114 4.022068 TCATGGGCAAGAACTGAACATTTC 60.022 41.667 0.00 0.00 0.00 2.17
2492 3325 2.036346 ACTCCCACATTTCAAAAGCAGC 59.964 45.455 0.00 0.00 0.00 5.25
2514 3347 3.063997 ACAACAGTCAGCAAAAGACTTCG 59.936 43.478 0.00 0.00 43.47 3.79
2518 3351 3.873952 AGAGACAACAGTCAGCAAAAGAC 59.126 43.478 0.00 0.00 34.69 3.01
2523 3356 2.695147 TCAGAGAGACAACAGTCAGCAA 59.305 45.455 0.00 0.00 34.69 3.91
2533 3366 4.089361 TGCTATCCTGTTCAGAGAGACAA 58.911 43.478 1.00 0.00 0.00 3.18
2541 3374 5.618640 GCAAAACTTCTGCTATCCTGTTCAG 60.619 44.000 0.00 0.00 36.84 3.02
2562 3395 4.644234 TCCACTGTTTCAAGAAATCAGCAA 59.356 37.500 17.25 7.30 35.17 3.91
2577 3410 0.947244 CGCTCAGCTTTTCCACTGTT 59.053 50.000 0.00 0.00 35.37 3.16
2615 3450 3.558931 TGTCAGACACACACCAGAATT 57.441 42.857 0.00 0.00 0.00 2.17
2617 3452 2.224281 GGATGTCAGACACACACCAGAA 60.224 50.000 5.05 0.00 38.04 3.02
2619 3454 1.609061 GGGATGTCAGACACACACCAG 60.609 57.143 5.05 0.00 38.04 4.00
2721 3559 5.947443 AGTATTGCTGCTTCATTCTTTCAC 58.053 37.500 0.00 0.00 0.00 3.18
2761 3599 1.228459 ACTTCCTTGGGCCGGTTTC 60.228 57.895 1.90 0.00 0.00 2.78
2763 3601 1.420532 TACACTTCCTTGGGCCGGTT 61.421 55.000 1.90 0.00 0.00 4.44
2764 3602 1.838073 CTACACTTCCTTGGGCCGGT 61.838 60.000 1.90 0.00 0.00 5.28
2765 3603 1.078426 CTACACTTCCTTGGGCCGG 60.078 63.158 0.00 0.00 0.00 6.13
2766 3604 1.745489 GCTACACTTCCTTGGGCCG 60.745 63.158 0.00 0.00 0.00 6.13
2768 3606 0.250727 TGTGCTACACTTCCTTGGGC 60.251 55.000 0.00 0.00 35.11 5.36
2769 3607 1.611673 CCTGTGCTACACTTCCTTGGG 60.612 57.143 0.00 0.00 35.11 4.12
2770 3608 1.347707 TCCTGTGCTACACTTCCTTGG 59.652 52.381 0.00 0.00 35.11 3.61
2771 3609 2.808543 GTTCCTGTGCTACACTTCCTTG 59.191 50.000 0.00 0.00 35.11 3.61
2772 3610 2.438021 TGTTCCTGTGCTACACTTCCTT 59.562 45.455 0.00 0.00 35.11 3.36
2773 3611 2.047061 TGTTCCTGTGCTACACTTCCT 58.953 47.619 0.00 0.00 35.11 3.36
2775 3613 5.438761 AATTTGTTCCTGTGCTACACTTC 57.561 39.130 0.00 0.00 35.11 3.01
2777 3615 5.852282 AAAATTTGTTCCTGTGCTACACT 57.148 34.783 0.00 0.00 35.11 3.55
2778 3616 7.200455 ACTAAAAATTTGTTCCTGTGCTACAC 58.800 34.615 0.00 0.00 34.56 2.90
2780 3618 9.177304 GTAACTAAAAATTTGTTCCTGTGCTAC 57.823 33.333 0.00 0.00 0.00 3.58
2783 3621 7.918562 TGAGTAACTAAAAATTTGTTCCTGTGC 59.081 33.333 0.00 0.00 0.00 4.57
2784 3622 9.233232 GTGAGTAACTAAAAATTTGTTCCTGTG 57.767 33.333 0.00 0.00 0.00 3.66
2785 3623 9.185680 AGTGAGTAACTAAAAATTTGTTCCTGT 57.814 29.630 0.00 0.00 37.36 4.00
2786 3624 9.665264 GAGTGAGTAACTAAAAATTTGTTCCTG 57.335 33.333 0.00 0.00 40.07 3.86
2788 3626 9.447040 GTGAGTGAGTAACTAAAAATTTGTTCC 57.553 33.333 0.00 0.00 40.07 3.62
2789 3627 9.997482 TGTGAGTGAGTAACTAAAAATTTGTTC 57.003 29.630 0.00 0.00 40.07 3.18
2796 3634 9.135843 CGATGTATGTGAGTGAGTAACTAAAAA 57.864 33.333 0.00 0.00 40.07 1.94
2797 3635 8.517056 TCGATGTATGTGAGTGAGTAACTAAAA 58.483 33.333 0.00 0.00 40.07 1.52
2798 3636 8.047413 TCGATGTATGTGAGTGAGTAACTAAA 57.953 34.615 0.00 0.00 40.07 1.85
2799 3637 7.551617 TCTCGATGTATGTGAGTGAGTAACTAA 59.448 37.037 0.00 0.00 40.07 2.24
2800 3638 7.046033 TCTCGATGTATGTGAGTGAGTAACTA 58.954 38.462 0.00 0.00 40.07 2.24
2801 3639 5.880887 TCTCGATGTATGTGAGTGAGTAACT 59.119 40.000 0.00 0.00 43.85 2.24
2802 3640 6.120378 TCTCGATGTATGTGAGTGAGTAAC 57.880 41.667 0.00 0.00 0.00 2.50
2804 3642 6.768381 AGAATCTCGATGTATGTGAGTGAGTA 59.232 38.462 0.00 0.00 0.00 2.59
2805 3643 5.592282 AGAATCTCGATGTATGTGAGTGAGT 59.408 40.000 0.00 0.00 0.00 3.41
2807 3645 6.066054 GAGAATCTCGATGTATGTGAGTGA 57.934 41.667 0.00 0.00 0.00 3.41
2840 3678 2.627699 TGGAATGGGTTTGTTCTTCTGC 59.372 45.455 0.00 0.00 0.00 4.26
3130 3978 6.996509 ACAACAAAATCATACAGAATGGCTT 58.003 32.000 0.00 0.00 43.62 4.35
3247 4097 6.644347 ACAAGTTATGTTATGAGACAGAGGG 58.356 40.000 0.00 0.00 40.06 4.30
3301 4151 8.901793 CCTACTCCCTTCGTCCTATAATATAAC 58.098 40.741 0.00 0.00 0.00 1.89
3311 4161 3.684408 ATTACCTACTCCCTTCGTCCT 57.316 47.619 0.00 0.00 0.00 3.85
3317 4167 9.725206 TTCTCTTGTAATATTACCTACTCCCTT 57.275 33.333 20.35 0.00 32.72 3.95
3327 4177 9.095065 ACGTGGAATGTTCTCTTGTAATATTAC 57.905 33.333 17.18 17.18 25.44 1.89
3333 4183 3.496884 GCACGTGGAATGTTCTCTTGTAA 59.503 43.478 18.88 0.00 30.19 2.41
3354 4210 6.400515 GCGACATATGCTTATGTTAGAAGAGC 60.401 42.308 22.10 15.46 46.64 4.09
3355 4211 6.642540 TGCGACATATGCTTATGTTAGAAGAG 59.357 38.462 22.10 11.33 46.64 2.85
3356 4212 6.512297 TGCGACATATGCTTATGTTAGAAGA 58.488 36.000 22.10 8.36 46.64 2.87
3357 4213 6.769608 TGCGACATATGCTTATGTTAGAAG 57.230 37.500 22.10 13.87 46.64 2.85
3386 4247 5.418840 CCTAGAACTGGCACAAAACCAATAT 59.581 40.000 0.00 0.00 38.70 1.28
3395 4256 5.876357 ACTATTTTCCTAGAACTGGCACAA 58.124 37.500 0.00 0.00 38.70 3.33
3399 4260 9.174166 TCATTTTACTATTTTCCTAGAACTGGC 57.826 33.333 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.