Multiple sequence alignment - TraesCS7B01G017400

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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 TraesCS7B01G017400 chr7B 100.000 2411 0 0 1 2411 14979792 14982202 0.000000e+00 4453.0
1 TraesCS7B01G017400 chr7B 87.662 770 73 20 667 1425 14788831 14788073 0.000000e+00 876.0
2 TraesCS7B01G017400 chr7B 87.831 756 73 12 667 1412 14696737 14697483 0.000000e+00 869.0
3 TraesCS7B01G017400 chr7B 88.356 730 62 16 709 1425 14866736 14866017 0.000000e+00 856.0
4 TraesCS7B01G017400 chr7B 87.500 64 6 2 71 132 709085253 709085316 3.320000e-09 73.1
5 TraesCS7B01G017400 chrUn 93.054 763 51 2 651 1411 273471213 273470451 0.000000e+00 1114.0
6 TraesCS7B01G017400 chrUn 88.571 735 62 13 682 1412 84331403 84330687 0.000000e+00 872.0
7 TraesCS7B01G017400 chrUn 87.452 781 66 22 651 1421 82605400 82604642 0.000000e+00 870.0
8 TraesCS7B01G017400 chrUn 88.331 737 69 12 687 1412 84318111 84317381 0.000000e+00 869.0
9 TraesCS7B01G017400 chrUn 85.492 772 72 23 655 1412 82565610 82566355 0.000000e+00 769.0
10 TraesCS7B01G017400 chrUn 89.850 266 23 3 2144 2405 311108735 311108470 2.970000e-89 339.0
11 TraesCS7B01G017400 chr7D 93.054 763 51 2 651 1411 72128144 72128906 0.000000e+00 1114.0
12 TraesCS7B01G017400 chr7D 88.336 703 64 15 721 1412 71812295 71812990 0.000000e+00 828.0
13 TraesCS7B01G017400 chr7D 77.346 437 68 25 58 488 463710437 463710026 1.860000e-56 230.0
14 TraesCS7B01G017400 chr7D 91.228 57 3 2 78 132 615949150 615949206 2.570000e-10 76.8
15 TraesCS7B01G017400 chr7A 85.613 563 47 13 1852 2405 77151394 77151931 5.820000e-156 560.0
16 TraesCS7B01G017400 chr7A 82.134 403 39 16 1431 1812 77150995 77151385 5.000000e-82 315.0
17 TraesCS7B01G017400 chr7A 76.104 385 54 20 257 635 48298002 48298354 1.480000e-37 167.0
18 TraesCS7B01G017400 chr6B 77.960 549 79 27 40 576 702301606 702302124 3.010000e-79 305.0
19 TraesCS7B01G017400 chr3A 75.618 607 89 40 40 634 508538261 508537702 1.850000e-61 246.0
20 TraesCS7B01G017400 chr3A 77.099 393 62 25 72 457 701865680 701865309 4.060000e-48 202.0
21 TraesCS7B01G017400 chr3A 79.654 231 28 16 182 402 574253287 574253066 5.370000e-32 148.0
22 TraesCS7B01G017400 chr2A 76.709 468 75 25 170 630 85294433 85293993 1.860000e-56 230.0
23 TraesCS7B01G017400 chr5A 77.898 371 62 18 30 388 458495393 458495031 1.880000e-51 213.0
24 TraesCS7B01G017400 chr5A 77.871 357 66 11 237 584 503549294 503549646 2.430000e-50 209.0
25 TraesCS7B01G017400 chr3D 75.212 472 78 33 45 491 419390512 419390969 1.140000e-43 187.0
26 TraesCS7B01G017400 chr3D 85.217 115 10 4 500 609 387349773 387349661 7.050000e-21 111.0
27 TraesCS7B01G017400 chr5D 76.238 404 63 18 237 635 476752647 476752272 1.470000e-42 183.0
28 TraesCS7B01G017400 chr6A 78.545 275 44 14 219 487 77604911 77604646 1.480000e-37 167.0
29 TraesCS7B01G017400 chr2B 78.700 277 37 18 132 395 649212799 649213066 5.330000e-37 165.0
30 TraesCS7B01G017400 chr2D 77.419 310 44 21 181 476 59630352 59630055 6.900000e-36 161.0
31 TraesCS7B01G017400 chr1D 76.385 343 55 18 237 576 50285357 50285676 6.900000e-36 161.0
32 TraesCS7B01G017400 chr3B 74.342 304 41 28 309 608 504654614 504654884 7.100000e-16 95.3


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 TraesCS7B01G017400 chr7B 14979792 14982202 2410 False 4453.0 4453 100.0000 1 2411 1 chr7B.!!$F2 2410
1 TraesCS7B01G017400 chr7B 14788073 14788831 758 True 876.0 876 87.6620 667 1425 1 chr7B.!!$R1 758
2 TraesCS7B01G017400 chr7B 14696737 14697483 746 False 869.0 869 87.8310 667 1412 1 chr7B.!!$F1 745
3 TraesCS7B01G017400 chr7B 14866017 14866736 719 True 856.0 856 88.3560 709 1425 1 chr7B.!!$R2 716
4 TraesCS7B01G017400 chrUn 273470451 273471213 762 True 1114.0 1114 93.0540 651 1411 1 chrUn.!!$R4 760
5 TraesCS7B01G017400 chrUn 84330687 84331403 716 True 872.0 872 88.5710 682 1412 1 chrUn.!!$R3 730
6 TraesCS7B01G017400 chrUn 82604642 82605400 758 True 870.0 870 87.4520 651 1421 1 chrUn.!!$R1 770
7 TraesCS7B01G017400 chrUn 84317381 84318111 730 True 869.0 869 88.3310 687 1412 1 chrUn.!!$R2 725
8 TraesCS7B01G017400 chrUn 82565610 82566355 745 False 769.0 769 85.4920 655 1412 1 chrUn.!!$F1 757
9 TraesCS7B01G017400 chr7D 72128144 72128906 762 False 1114.0 1114 93.0540 651 1411 1 chr7D.!!$F2 760
10 TraesCS7B01G017400 chr7D 71812295 71812990 695 False 828.0 828 88.3360 721 1412 1 chr7D.!!$F1 691
11 TraesCS7B01G017400 chr7A 77150995 77151931 936 False 437.5 560 83.8735 1431 2405 2 chr7A.!!$F2 974
12 TraesCS7B01G017400 chr6B 702301606 702302124 518 False 305.0 305 77.9600 40 576 1 chr6B.!!$F1 536
13 TraesCS7B01G017400 chr3A 508537702 508538261 559 True 246.0 246 75.6180 40 634 1 chr3A.!!$R1 594

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
778 795 0.262876 AAATCCCAGCCCTCCATTCC 59.737 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2046 1.068121 AACTTTGCCAGAGGTAGCCT 58.932 50.0 0.0 0.0 36.03 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
22 23 5.913946 CCACCTTCTTCTTTCCCCTATAT 57.086 43.478 0.00 0.00 0.00 0.86
23 24 6.267492 CCACCTTCTTCTTTCCCCTATATT 57.733 41.667 0.00 0.00 0.00 1.28
24 25 7.388638 CCACCTTCTTCTTTCCCCTATATTA 57.611 40.000 0.00 0.00 0.00 0.98
25 26 7.990055 CCACCTTCTTCTTTCCCCTATATTAT 58.010 38.462 0.00 0.00 0.00 1.28
26 27 8.448816 CCACCTTCTTCTTTCCCCTATATTATT 58.551 37.037 0.00 0.00 0.00 1.40
27 28 9.508642 CACCTTCTTCTTTCCCCTATATTATTC 57.491 37.037 0.00 0.00 0.00 1.75
28 29 9.467030 ACCTTCTTCTTTCCCCTATATTATTCT 57.533 33.333 0.00 0.00 0.00 2.40
97 98 7.642669 AGAACGAATTAGTGGCATTGATATTG 58.357 34.615 0.00 0.00 0.00 1.90
247 255 8.992835 ACAAAGATTCATAAAAGAAGGAATGC 57.007 30.769 0.00 0.00 30.60 3.56
260 268 9.729281 AAAAGAAGGAATGCATTATTCACATTT 57.271 25.926 26.54 21.74 45.70 2.32
264 272 9.754382 GAAGGAATGCATTATTCACATTTGTAT 57.246 29.630 22.75 0.00 45.70 2.29
351 359 6.189859 AGGAAGAATGAATTAGTGGCATTGA 58.810 36.000 0.00 0.00 32.80 2.57
523 536 9.926751 TTTTGCACACAATATACAAACAAATTG 57.073 25.926 0.00 0.00 39.22 2.32
524 537 7.114882 TGCACACAATATACAAACAAATTGC 57.885 32.000 0.00 0.00 43.13 3.56
525 538 6.128982 TGCACACAATATACAAACAAATTGCG 60.129 34.615 0.00 0.00 43.13 4.85
526 539 6.128956 GCACACAATATACAAACAAATTGCGT 60.129 34.615 0.00 0.00 43.13 5.24
527 540 7.568497 GCACACAATATACAAACAAATTGCGTT 60.568 33.333 0.00 0.00 43.13 4.84
528 541 8.272176 CACACAATATACAAACAAATTGCGTTT 58.728 29.630 0.00 1.39 43.13 3.60
529 542 8.821894 ACACAATATACAAACAAATTGCGTTTT 58.178 25.926 4.02 0.00 43.13 2.43
530 543 9.643652 CACAATATACAAACAAATTGCGTTTTT 57.356 25.926 4.02 1.87 43.13 1.94
531 544 9.856803 ACAATATACAAACAAATTGCGTTTTTC 57.143 25.926 4.02 0.00 43.13 2.29
541 554 7.728895 ACAAATTGCGTTTTTCTATAATGTGC 58.271 30.769 0.00 0.00 0.00 4.57
542 555 7.383572 ACAAATTGCGTTTTTCTATAATGTGCA 59.616 29.630 0.00 0.00 0.00 4.57
543 556 7.881643 AATTGCGTTTTTCTATAATGTGCAA 57.118 28.000 0.00 0.00 43.01 4.08
544 557 6.926280 TTGCGTTTTTCTATAATGTGCAAG 57.074 33.333 0.00 0.00 35.17 4.01
545 558 6.247727 TGCGTTTTTCTATAATGTGCAAGA 57.752 33.333 0.00 0.00 0.00 3.02
546 559 6.673106 TGCGTTTTTCTATAATGTGCAAGAA 58.327 32.000 0.00 0.00 0.00 2.52
547 560 7.312154 TGCGTTTTTCTATAATGTGCAAGAAT 58.688 30.769 0.00 0.00 0.00 2.40
548 561 8.454894 TGCGTTTTTCTATAATGTGCAAGAATA 58.545 29.630 0.00 0.00 0.00 1.75
549 562 9.284594 GCGTTTTTCTATAATGTGCAAGAATAA 57.715 29.630 0.00 0.00 0.00 1.40
556 569 8.925700 TCTATAATGTGCAAGAATAAGCATACG 58.074 33.333 0.00 0.00 43.44 3.06
557 570 4.818534 ATGTGCAAGAATAAGCATACGG 57.181 40.909 0.00 0.00 43.44 4.02
558 571 2.354510 TGTGCAAGAATAAGCATACGGC 59.645 45.455 0.00 0.00 43.44 5.68
569 582 2.939460 GCATACGGCAGTGGAATTTT 57.061 45.000 0.00 0.00 43.97 1.82
570 583 2.797491 GCATACGGCAGTGGAATTTTC 58.203 47.619 0.00 0.00 43.97 2.29
571 584 2.163412 GCATACGGCAGTGGAATTTTCA 59.837 45.455 0.00 0.00 43.97 2.69
572 585 3.758300 CATACGGCAGTGGAATTTTCAC 58.242 45.455 0.00 0.00 35.51 3.18
573 586 1.686355 ACGGCAGTGGAATTTTCACA 58.314 45.000 10.42 0.00 37.58 3.58
574 587 2.028130 ACGGCAGTGGAATTTTCACAA 58.972 42.857 10.42 0.00 37.58 3.33
575 588 2.428890 ACGGCAGTGGAATTTTCACAAA 59.571 40.909 10.42 0.00 37.58 2.83
576 589 3.052036 CGGCAGTGGAATTTTCACAAAG 58.948 45.455 10.42 1.34 37.58 2.77
577 590 3.243367 CGGCAGTGGAATTTTCACAAAGA 60.243 43.478 10.42 0.00 37.58 2.52
578 591 4.692228 GGCAGTGGAATTTTCACAAAGAA 58.308 39.130 10.42 0.00 37.58 2.52
579 592 4.746611 GGCAGTGGAATTTTCACAAAGAAG 59.253 41.667 10.42 0.00 37.57 2.85
580 593 5.451798 GGCAGTGGAATTTTCACAAAGAAGA 60.452 40.000 10.42 0.00 37.57 2.87
581 594 6.042143 GCAGTGGAATTTTCACAAAGAAGAA 58.958 36.000 10.42 0.00 37.57 2.52
582 595 6.534793 GCAGTGGAATTTTCACAAAGAAGAAA 59.465 34.615 10.42 0.00 37.57 2.52
583 596 7.225341 GCAGTGGAATTTTCACAAAGAAGAAAT 59.775 33.333 10.42 0.00 37.57 2.17
584 597 9.748708 CAGTGGAATTTTCACAAAGAAGAAATA 57.251 29.630 10.42 0.00 37.57 1.40
594 607 7.861630 TCACAAAGAAGAAATAAGAAGGAACG 58.138 34.615 0.00 0.00 0.00 3.95
595 608 7.713507 TCACAAAGAAGAAATAAGAAGGAACGA 59.286 33.333 0.00 0.00 0.00 3.85
596 609 8.342634 CACAAAGAAGAAATAAGAAGGAACGAA 58.657 33.333 0.00 0.00 0.00 3.85
597 610 9.067986 ACAAAGAAGAAATAAGAAGGAACGAAT 57.932 29.630 0.00 0.00 0.00 3.34
598 611 9.899226 CAAAGAAGAAATAAGAAGGAACGAATT 57.101 29.630 0.00 0.00 0.00 2.17
600 613 9.899226 AAGAAGAAATAAGAAGGAACGAATTTG 57.101 29.630 0.00 0.00 0.00 2.32
601 614 9.067986 AGAAGAAATAAGAAGGAACGAATTTGT 57.932 29.630 0.00 0.00 0.00 2.83
602 615 9.118236 GAAGAAATAAGAAGGAACGAATTTGTG 57.882 33.333 0.00 0.00 0.00 3.33
603 616 7.593825 AGAAATAAGAAGGAACGAATTTGTGG 58.406 34.615 0.00 0.00 0.00 4.17
604 617 3.643159 AAGAAGGAACGAATTTGTGGC 57.357 42.857 0.00 0.00 0.00 5.01
605 618 2.582052 AGAAGGAACGAATTTGTGGCA 58.418 42.857 0.00 0.00 0.00 4.92
606 619 3.157087 AGAAGGAACGAATTTGTGGCAT 58.843 40.909 0.00 0.00 0.00 4.40
607 620 3.573967 AGAAGGAACGAATTTGTGGCATT 59.426 39.130 0.00 0.00 0.00 3.56
608 621 3.302365 AGGAACGAATTTGTGGCATTG 57.698 42.857 0.00 0.00 0.00 2.82
609 622 2.029110 AGGAACGAATTTGTGGCATTGG 60.029 45.455 0.00 0.00 0.00 3.16
610 623 2.336667 GAACGAATTTGTGGCATTGGG 58.663 47.619 0.00 0.00 0.00 4.12
611 624 1.626686 ACGAATTTGTGGCATTGGGA 58.373 45.000 0.00 0.00 0.00 4.37
612 625 2.178580 ACGAATTTGTGGCATTGGGAT 58.821 42.857 0.00 0.00 0.00 3.85
613 626 2.566724 ACGAATTTGTGGCATTGGGATT 59.433 40.909 0.00 0.00 0.00 3.01
614 627 3.766591 ACGAATTTGTGGCATTGGGATTA 59.233 39.130 0.00 0.00 0.00 1.75
615 628 4.111916 CGAATTTGTGGCATTGGGATTAC 58.888 43.478 0.00 0.00 0.00 1.89
616 629 4.441792 GAATTTGTGGCATTGGGATTACC 58.558 43.478 0.00 0.00 40.81 2.85
645 658 8.797266 AATGAAGAAATAAAAACTCGTTCACC 57.203 30.769 0.00 0.00 0.00 4.02
646 659 7.323049 TGAAGAAATAAAAACTCGTTCACCA 57.677 32.000 0.00 0.00 0.00 4.17
647 660 7.414436 TGAAGAAATAAAAACTCGTTCACCAG 58.586 34.615 0.00 0.00 0.00 4.00
648 661 5.758924 AGAAATAAAAACTCGTTCACCAGC 58.241 37.500 0.00 0.00 0.00 4.85
649 662 4.499037 AATAAAAACTCGTTCACCAGCC 57.501 40.909 0.00 0.00 0.00 4.85
650 663 2.052782 AAAAACTCGTTCACCAGCCT 57.947 45.000 0.00 0.00 0.00 4.58
651 664 1.308998 AAAACTCGTTCACCAGCCTG 58.691 50.000 0.00 0.00 0.00 4.85
652 665 1.166531 AAACTCGTTCACCAGCCTGC 61.167 55.000 0.00 0.00 0.00 4.85
653 666 2.743928 CTCGTTCACCAGCCTGCC 60.744 66.667 0.00 0.00 0.00 4.85
654 667 3.535629 CTCGTTCACCAGCCTGCCA 62.536 63.158 0.00 0.00 0.00 4.92
655 668 2.594303 CGTTCACCAGCCTGCCAA 60.594 61.111 0.00 0.00 0.00 4.52
656 669 2.192861 CGTTCACCAGCCTGCCAAA 61.193 57.895 0.00 0.00 0.00 3.28
657 670 1.733402 CGTTCACCAGCCTGCCAAAA 61.733 55.000 0.00 0.00 0.00 2.44
658 671 0.463620 GTTCACCAGCCTGCCAAAAA 59.536 50.000 0.00 0.00 0.00 1.94
778 795 0.262876 AAATCCCAGCCCTCCATTCC 59.737 55.000 0.00 0.00 0.00 3.01
815 832 4.181010 CATCCCACCCTCCGCTGG 62.181 72.222 0.00 0.00 0.00 4.85
910 943 4.782691 CCCCTTTAAAATCCACCTCCATTT 59.217 41.667 0.00 0.00 0.00 2.32
940 978 0.462225 TCACCACCGCGAAGTGAAAA 60.462 50.000 19.03 2.27 43.07 2.29
989 1032 4.172512 AGCCAGATCCGCAGCCAG 62.173 66.667 5.28 0.00 0.00 4.85
1242 1286 1.738099 CGCCCAGGACTTCAAGACG 60.738 63.158 0.00 0.00 0.00 4.18
1421 1494 2.202756 CGCCTAGGCTGTTCGTCC 60.203 66.667 30.55 0.00 39.32 4.79
1422 1495 2.202756 GCCTAGGCTGTTCGTCCG 60.203 66.667 27.17 0.00 38.26 4.79
1423 1496 2.494918 CCTAGGCTGTTCGTCCGG 59.505 66.667 0.00 0.00 0.00 5.14
1424 1497 2.202756 CTAGGCTGTTCGTCCGGC 60.203 66.667 0.00 0.00 0.00 6.13
1425 1498 3.718210 CTAGGCTGTTCGTCCGGCC 62.718 68.421 16.08 16.08 44.38 6.13
1448 1521 2.819595 CGCCACGGTTCCATCCTG 60.820 66.667 0.00 0.00 0.00 3.86
1504 1577 1.180456 TAGTCCACCCGTGCTTCGAA 61.180 55.000 0.00 0.00 42.86 3.71
1513 1586 3.255725 CCCGTGCTTCGAATTGTTACTA 58.744 45.455 0.00 0.00 42.86 1.82
1527 1600 9.500864 CGAATTGTTACTACTAGGTTCTAGTTC 57.499 37.037 12.11 1.64 0.00 3.01
1566 1639 5.127845 TGCTGTTGATTACCAGTTGGAAAAA 59.872 36.000 4.92 0.00 38.94 1.94
1568 1641 6.705825 GCTGTTGATTACCAGTTGGAAAAATT 59.294 34.615 4.92 0.00 38.94 1.82
1569 1642 7.307337 GCTGTTGATTACCAGTTGGAAAAATTG 60.307 37.037 4.92 0.00 38.94 2.32
1570 1643 6.989169 TGTTGATTACCAGTTGGAAAAATTGG 59.011 34.615 4.92 0.00 38.94 3.16
1572 1645 7.366847 TGATTACCAGTTGGAAAAATTGGAA 57.633 32.000 4.92 0.00 38.94 3.53
1573 1646 7.796054 TGATTACCAGTTGGAAAAATTGGAAA 58.204 30.769 4.92 0.00 38.94 3.13
1575 1648 5.034852 ACCAGTTGGAAAAATTGGAAAGG 57.965 39.130 4.92 0.00 38.94 3.11
1577 1650 5.190726 ACCAGTTGGAAAAATTGGAAAGGAA 59.809 36.000 4.92 0.00 38.94 3.36
1578 1651 5.759763 CCAGTTGGAAAAATTGGAAAGGAAG 59.240 40.000 0.00 0.00 37.39 3.46
1581 1654 6.156083 AGTTGGAAAAATTGGAAAGGAAGTGA 59.844 34.615 0.00 0.00 0.00 3.41
1613 1686 5.573380 TCCCCATTTCTGAGATCTTATGG 57.427 43.478 0.00 5.84 33.86 2.74
1616 1689 5.944599 CCCCATTTCTGAGATCTTATGGATG 59.055 44.000 16.73 10.65 35.63 3.51
1619 1692 6.654161 CCATTTCTGAGATCTTATGGATGGAC 59.346 42.308 16.99 0.00 35.63 4.02
1622 1695 7.443302 TTCTGAGATCTTATGGATGGACTTT 57.557 36.000 0.00 0.00 34.33 2.66
1623 1696 7.443302 TCTGAGATCTTATGGATGGACTTTT 57.557 36.000 0.00 0.00 34.33 2.27
1627 1700 5.591877 AGATCTTATGGATGGACTTTTGTGC 59.408 40.000 0.00 0.00 41.43 4.57
1639 1712 3.460103 ACTTTTGTGCTTGGATGCTTTG 58.540 40.909 0.00 0.00 0.00 2.77
1641 1714 4.099266 ACTTTTGTGCTTGGATGCTTTGTA 59.901 37.500 0.00 0.00 0.00 2.41
1642 1715 4.870123 TTTGTGCTTGGATGCTTTGTAT 57.130 36.364 0.00 0.00 0.00 2.29
1653 1726 5.532032 TGGATGCTTTGTATGGTGTATGATG 59.468 40.000 0.00 0.00 0.00 3.07
1654 1727 5.764686 GGATGCTTTGTATGGTGTATGATGA 59.235 40.000 0.00 0.00 0.00 2.92
1657 1730 5.008911 TGCTTTGTATGGTGTATGATGATGC 59.991 40.000 0.00 0.00 0.00 3.91
1659 1732 4.703379 TGTATGGTGTATGATGATGCCA 57.297 40.909 0.00 0.00 0.00 4.92
1660 1733 5.245584 TGTATGGTGTATGATGATGCCAT 57.754 39.130 0.00 0.00 39.66 4.40
1684 1757 3.176552 AGGAATGATTCTCGTGCTGAG 57.823 47.619 5.03 0.64 46.72 3.35
1751 1843 3.507162 TGTTCATGTTGGTGTGATCCT 57.493 42.857 0.00 0.00 0.00 3.24
1757 1849 4.764823 TCATGTTGGTGTGATCCTTTTACC 59.235 41.667 0.00 0.00 0.00 2.85
1758 1850 4.171878 TGTTGGTGTGATCCTTTTACCA 57.828 40.909 0.00 0.00 39.49 3.25
1765 1857 2.943033 GTGATCCTTTTACCACCATCCG 59.057 50.000 0.00 0.00 0.00 4.18
1774 1866 6.404293 CCTTTTACCACCATCCGTTTAATCTG 60.404 42.308 0.00 0.00 0.00 2.90
1782 1874 7.145323 CACCATCCGTTTAATCTGAAAAGTTT 58.855 34.615 0.00 0.00 0.00 2.66
1800 1893 8.967664 AAAAGTTTACAACAGTGGTACATAGA 57.032 30.769 0.00 0.00 44.52 1.98
1801 1894 8.603242 AAAGTTTACAACAGTGGTACATAGAG 57.397 34.615 0.00 0.00 44.52 2.43
1812 1905 6.929049 CAGTGGTACATAGAGAAACAAGTTCA 59.071 38.462 0.00 0.00 44.52 3.18
1813 1906 7.604164 CAGTGGTACATAGAGAAACAAGTTCAT 59.396 37.037 0.00 0.00 44.52 2.57
1815 1908 8.784043 GTGGTACATAGAGAAACAAGTTCATTT 58.216 33.333 0.00 0.00 44.52 2.32
1819 1912 8.045176 ACATAGAGAAACAAGTTCATTTAGGC 57.955 34.615 0.00 0.00 38.86 3.93
1820 1913 7.665559 ACATAGAGAAACAAGTTCATTTAGGCA 59.334 33.333 0.00 0.00 38.86 4.75
1821 1914 6.319141 AGAGAAACAAGTTCATTTAGGCAC 57.681 37.500 0.00 0.00 38.86 5.01
1822 1915 5.827797 AGAGAAACAAGTTCATTTAGGCACA 59.172 36.000 0.00 0.00 38.86 4.57
1823 1916 6.321181 AGAGAAACAAGTTCATTTAGGCACAA 59.679 34.615 0.00 0.00 38.86 3.33
1824 1917 6.273071 AGAAACAAGTTCATTTAGGCACAAC 58.727 36.000 0.00 0.00 38.86 3.32
1825 1918 5.852282 AACAAGTTCATTTAGGCACAACT 57.148 34.783 0.00 0.00 0.00 3.16
1826 1919 5.852282 ACAAGTTCATTTAGGCACAACTT 57.148 34.783 0.00 0.00 37.70 2.66
1827 1920 6.220726 ACAAGTTCATTTAGGCACAACTTT 57.779 33.333 0.00 0.00 35.57 2.66
1828 1921 6.273071 ACAAGTTCATTTAGGCACAACTTTC 58.727 36.000 0.00 0.00 35.57 2.62
1829 1922 5.453567 AGTTCATTTAGGCACAACTTTCC 57.546 39.130 0.00 0.00 0.00 3.13
1830 1923 4.280929 AGTTCATTTAGGCACAACTTTCCC 59.719 41.667 0.00 0.00 0.00 3.97
1831 1924 4.112634 TCATTTAGGCACAACTTTCCCT 57.887 40.909 0.00 0.00 0.00 4.20
1832 1925 4.479158 TCATTTAGGCACAACTTTCCCTT 58.521 39.130 0.00 0.00 0.00 3.95
1833 1926 5.636123 TCATTTAGGCACAACTTTCCCTTA 58.364 37.500 0.00 0.00 0.00 2.69
1834 1927 6.071984 TCATTTAGGCACAACTTTCCCTTAA 58.928 36.000 0.00 0.00 0.00 1.85
1835 1928 6.208599 TCATTTAGGCACAACTTTCCCTTAAG 59.791 38.462 0.00 0.00 0.00 1.85
1836 1929 3.876309 AGGCACAACTTTCCCTTAAGA 57.124 42.857 3.36 0.00 0.00 2.10
1837 1930 3.487372 AGGCACAACTTTCCCTTAAGAC 58.513 45.455 3.36 0.00 0.00 3.01
1838 1931 3.138468 AGGCACAACTTTCCCTTAAGACT 59.862 43.478 3.36 0.00 0.00 3.24
1839 1932 4.349930 AGGCACAACTTTCCCTTAAGACTA 59.650 41.667 3.36 0.00 0.00 2.59
1840 1933 5.014228 AGGCACAACTTTCCCTTAAGACTAT 59.986 40.000 3.36 0.00 0.00 2.12
1841 1934 5.710567 GGCACAACTTTCCCTTAAGACTATT 59.289 40.000 3.36 0.00 0.00 1.73
1842 1935 6.882678 GGCACAACTTTCCCTTAAGACTATTA 59.117 38.462 3.36 0.00 0.00 0.98
1843 1936 7.556635 GGCACAACTTTCCCTTAAGACTATTAT 59.443 37.037 3.36 0.00 0.00 1.28
1844 1937 8.957466 GCACAACTTTCCCTTAAGACTATTATT 58.043 33.333 3.36 0.00 0.00 1.40
1849 1942 9.819267 ACTTTCCCTTAAGACTATTATTTCTCG 57.181 33.333 3.36 0.00 0.00 4.04
1866 1959 9.599866 TTATTTCTCGATCATTTTTCTCTGCTA 57.400 29.630 0.00 0.00 0.00 3.49
1886 1979 9.733556 TCTGCTATTAACTGAAAGATTTGGTAA 57.266 29.630 0.00 0.00 37.43 2.85
1908 2006 3.295734 GCTGTCAGCAACACTCTCA 57.704 52.632 20.16 0.00 41.89 3.27
1929 2027 6.012658 TCAGAATAAACTTGTTGTGATGCC 57.987 37.500 0.00 0.00 29.13 4.40
1930 2028 5.769662 TCAGAATAAACTTGTTGTGATGCCT 59.230 36.000 0.00 0.00 29.13 4.75
1932 2030 2.514205 AAACTTGTTGTGATGCCTGC 57.486 45.000 0.00 0.00 0.00 4.85
1941 2039 1.338105 TGTGATGCCTGCTACTGTGAC 60.338 52.381 0.00 0.00 0.00 3.67
1942 2040 1.066573 GTGATGCCTGCTACTGTGACT 60.067 52.381 0.00 0.00 0.00 3.41
1943 2041 1.205655 TGATGCCTGCTACTGTGACTC 59.794 52.381 0.00 0.00 0.00 3.36
1944 2042 1.480137 GATGCCTGCTACTGTGACTCT 59.520 52.381 0.00 0.00 0.00 3.24
1945 2043 0.605083 TGCCTGCTACTGTGACTCTG 59.395 55.000 0.00 0.00 0.00 3.35
1946 2044 0.605589 GCCTGCTACTGTGACTCTGT 59.394 55.000 0.00 0.00 0.00 3.41
1947 2045 1.671261 GCCTGCTACTGTGACTCTGTG 60.671 57.143 0.00 0.00 0.00 3.66
1948 2046 1.889170 CCTGCTACTGTGACTCTGTGA 59.111 52.381 0.00 0.00 0.00 3.58
1984 2082 4.489679 AAGTTTTGAAAGATCTGTCGGC 57.510 40.909 8.41 0.00 0.00 5.54
1989 2087 2.028876 TGAAAGATCTGTCGGCGGATA 58.971 47.619 12.20 0.00 40.59 2.59
2020 2118 2.969238 CTCATCACCGCGGATGCC 60.969 66.667 35.90 0.00 43.44 4.40
2035 2133 3.488047 CGGATGCCAAGTATTTTCTGCAG 60.488 47.826 7.63 7.63 31.53 4.41
2036 2134 3.442100 GATGCCAAGTATTTTCTGCAGC 58.558 45.455 9.47 0.00 31.53 5.25
2039 2137 3.057315 TGCCAAGTATTTTCTGCAGCTTC 60.057 43.478 9.47 0.00 0.00 3.86
2072 2170 5.927115 GGATTCTATCCCAGTTCACGTAATC 59.073 44.000 0.00 0.00 43.88 1.75
2077 2175 1.369625 CCAGTTCACGTAATCCTGCC 58.630 55.000 0.00 0.00 0.00 4.85
2078 2176 0.999406 CAGTTCACGTAATCCTGCCG 59.001 55.000 0.00 0.00 0.00 5.69
2079 2177 0.108329 AGTTCACGTAATCCTGCCGG 60.108 55.000 0.00 0.00 0.00 6.13
2080 2178 1.448893 TTCACGTAATCCTGCCGGC 60.449 57.895 22.73 22.73 0.00 6.13
2082 2180 4.524318 ACGTAATCCTGCCGGCCG 62.524 66.667 26.77 21.04 0.00 6.13
2083 2181 4.524318 CGTAATCCTGCCGGCCGT 62.524 66.667 26.77 5.81 0.00 5.68
2084 2182 2.124860 GTAATCCTGCCGGCCGTT 60.125 61.111 26.77 15.35 0.00 4.44
2085 2183 2.124901 TAATCCTGCCGGCCGTTG 60.125 61.111 26.77 11.15 0.00 4.10
2139 2237 3.073798 TGTGATGGTCCAATTAGGTGTGT 59.926 43.478 0.00 0.00 39.02 3.72
2153 2251 4.584327 AGGTGTGTTCCTTGCAAATAAC 57.416 40.909 13.90 13.90 33.52 1.89
2172 2270 1.127701 CGCGACCACCAATTTGTTTG 58.872 50.000 0.00 0.00 34.93 2.93
2190 2288 1.153745 GCTGCAGTCTGGGAGTACG 60.154 63.158 16.64 0.00 0.00 3.67
2192 2290 1.460504 CTGCAGTCTGGGAGTACGTA 58.539 55.000 5.25 0.00 0.00 3.57
2198 2296 4.142315 GCAGTCTGGGAGTACGTACATTTA 60.142 45.833 26.55 9.97 0.00 1.40
2199 2297 5.622914 GCAGTCTGGGAGTACGTACATTTAA 60.623 44.000 26.55 8.01 0.00 1.52
2203 2301 5.813672 TCTGGGAGTACGTACATTTAAATGC 59.186 40.000 26.55 9.81 40.04 3.56
2259 2358 5.840149 AGCCCCATCAGATGCATTTTATTTA 59.160 36.000 0.00 0.00 0.00 1.40
2260 2359 6.499350 AGCCCCATCAGATGCATTTTATTTAT 59.501 34.615 0.00 0.00 0.00 1.40
2261 2360 6.815142 GCCCCATCAGATGCATTTTATTTATC 59.185 38.462 0.00 0.00 0.00 1.75
2262 2361 7.525859 GCCCCATCAGATGCATTTTATTTATCA 60.526 37.037 0.00 0.00 0.00 2.15
2263 2362 8.537016 CCCCATCAGATGCATTTTATTTATCAT 58.463 33.333 0.00 0.00 0.00 2.45
2295 2397 0.809385 CAGATTGGCAGGCTTCACAG 59.191 55.000 0.00 0.00 0.00 3.66
2337 2439 1.123077 ATGACCGATAGCCTCTGCAA 58.877 50.000 0.00 0.00 41.13 4.08
2339 2441 1.486310 TGACCGATAGCCTCTGCAAAT 59.514 47.619 0.00 0.00 41.13 2.32
2340 2442 2.092968 TGACCGATAGCCTCTGCAAATT 60.093 45.455 0.00 0.00 41.13 1.82
2347 2449 5.753438 CGATAGCCTCTGCAAATTACTACAA 59.247 40.000 0.00 0.00 41.13 2.41
2352 2454 6.763610 AGCCTCTGCAAATTACTACAAGTATC 59.236 38.462 0.00 0.00 41.13 2.24
2405 2507 6.036517 CAGGTTACATGTAGAACTGATTGCTC 59.963 42.308 19.83 1.58 0.00 4.26
2406 2508 6.070538 AGGTTACATGTAGAACTGATTGCTCT 60.071 38.462 5.56 0.00 0.00 4.09
2407 2509 6.256757 GGTTACATGTAGAACTGATTGCTCTC 59.743 42.308 5.56 0.00 0.00 3.20
2408 2510 5.674052 ACATGTAGAACTGATTGCTCTCT 57.326 39.130 0.00 0.00 0.00 3.10
2409 2511 6.782082 ACATGTAGAACTGATTGCTCTCTA 57.218 37.500 0.00 0.00 0.00 2.43
2410 2512 7.175347 ACATGTAGAACTGATTGCTCTCTAA 57.825 36.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.913946 ATATAGGGGAAAGAAGAAGGTGG 57.086 43.478 0.00 0.00 0.00 4.61
1 2 9.508642 GAATAATATAGGGGAAAGAAGAAGGTG 57.491 37.037 0.00 0.00 0.00 4.00
65 66 8.612619 CAATGCCACTAATTCGTTCTTTACTAT 58.387 33.333 0.00 0.00 0.00 2.12
69 70 7.624360 ATCAATGCCACTAATTCGTTCTTTA 57.376 32.000 0.00 0.00 0.00 1.85
70 71 5.957842 TCAATGCCACTAATTCGTTCTTT 57.042 34.783 0.00 0.00 0.00 2.52
165 166 9.123902 TCTTGCATATTACAAATAGCACATTCT 57.876 29.630 0.00 0.00 0.00 2.40
166 167 9.734620 TTCTTGCATATTACAAATAGCACATTC 57.265 29.630 0.00 0.00 0.00 2.67
172 173 9.897744 TGCTTATTCTTGCATATTACAAATAGC 57.102 29.630 0.00 0.00 33.94 2.97
223 231 8.991243 TGCATTCCTTCTTTTATGAATCTTTG 57.009 30.769 0.00 0.00 0.00 2.77
234 242 9.729281 AAATGTGAATAATGCATTCCTTCTTTT 57.271 25.926 24.10 19.27 42.17 2.27
235 243 9.158233 CAAATGTGAATAATGCATTCCTTCTTT 57.842 29.630 24.10 17.33 42.17 2.52
236 244 8.316214 ACAAATGTGAATAATGCATTCCTTCTT 58.684 29.630 24.10 14.11 42.17 2.52
332 340 9.846248 GGTAATATCAATGCCACTAATTCATTC 57.154 33.333 0.00 0.00 0.00 2.67
498 511 8.066595 GCAATTTGTTTGTATATTGTGTGCAAA 58.933 29.630 0.00 0.00 36.59 3.68
515 528 8.220434 GCACATTATAGAAAAACGCAATTTGTT 58.780 29.630 0.00 0.00 0.00 2.83
516 529 7.383572 TGCACATTATAGAAAAACGCAATTTGT 59.616 29.630 0.00 0.00 0.00 2.83
517 530 7.727955 TGCACATTATAGAAAAACGCAATTTG 58.272 30.769 0.00 0.00 0.00 2.32
518 531 7.881643 TGCACATTATAGAAAAACGCAATTT 57.118 28.000 0.00 0.00 0.00 1.82
519 532 7.812191 TCTTGCACATTATAGAAAAACGCAATT 59.188 29.630 0.00 0.00 36.38 2.32
520 533 7.312154 TCTTGCACATTATAGAAAAACGCAAT 58.688 30.769 0.00 0.00 36.38 3.56
521 534 6.673106 TCTTGCACATTATAGAAAAACGCAA 58.327 32.000 0.00 0.00 35.70 4.85
522 535 6.247727 TCTTGCACATTATAGAAAAACGCA 57.752 33.333 0.00 0.00 0.00 5.24
523 536 7.740519 ATTCTTGCACATTATAGAAAAACGC 57.259 32.000 0.66 0.00 31.11 4.84
530 543 8.925700 CGTATGCTTATTCTTGCACATTATAGA 58.074 33.333 0.00 0.00 42.26 1.98
531 544 8.171196 CCGTATGCTTATTCTTGCACATTATAG 58.829 37.037 0.00 0.00 42.26 1.31
532 545 7.360861 GCCGTATGCTTATTCTTGCACATTATA 60.361 37.037 0.00 0.00 42.26 0.98
533 546 6.568462 GCCGTATGCTTATTCTTGCACATTAT 60.568 38.462 0.00 0.00 42.26 1.28
534 547 5.277779 GCCGTATGCTTATTCTTGCACATTA 60.278 40.000 0.00 0.00 42.26 1.90
535 548 4.498009 GCCGTATGCTTATTCTTGCACATT 60.498 41.667 0.00 0.00 42.26 2.71
536 549 3.003689 GCCGTATGCTTATTCTTGCACAT 59.996 43.478 0.00 0.00 42.26 3.21
537 550 2.354510 GCCGTATGCTTATTCTTGCACA 59.645 45.455 0.00 0.00 42.26 4.57
538 551 2.354510 TGCCGTATGCTTATTCTTGCAC 59.645 45.455 0.00 0.00 42.26 4.57
539 552 2.613595 CTGCCGTATGCTTATTCTTGCA 59.386 45.455 0.00 0.00 43.67 4.08
540 553 2.614057 ACTGCCGTATGCTTATTCTTGC 59.386 45.455 0.00 0.00 42.00 4.01
541 554 3.002656 CCACTGCCGTATGCTTATTCTTG 59.997 47.826 0.00 0.00 42.00 3.02
542 555 3.118408 TCCACTGCCGTATGCTTATTCTT 60.118 43.478 0.00 0.00 42.00 2.52
543 556 2.434336 TCCACTGCCGTATGCTTATTCT 59.566 45.455 0.00 0.00 42.00 2.40
544 557 2.833794 TCCACTGCCGTATGCTTATTC 58.166 47.619 0.00 0.00 42.00 1.75
545 558 3.275617 TTCCACTGCCGTATGCTTATT 57.724 42.857 0.00 0.00 42.00 1.40
546 559 3.492102 ATTCCACTGCCGTATGCTTAT 57.508 42.857 0.00 0.00 42.00 1.73
547 560 3.275617 AATTCCACTGCCGTATGCTTA 57.724 42.857 0.00 0.00 42.00 3.09
548 561 2.128771 AATTCCACTGCCGTATGCTT 57.871 45.000 0.00 0.00 42.00 3.91
549 562 2.128771 AAATTCCACTGCCGTATGCT 57.871 45.000 0.00 0.00 42.00 3.79
550 563 2.163412 TGAAAATTCCACTGCCGTATGC 59.837 45.455 0.00 0.00 41.77 3.14
551 564 3.190327 TGTGAAAATTCCACTGCCGTATG 59.810 43.478 10.89 0.00 35.66 2.39
552 565 3.417101 TGTGAAAATTCCACTGCCGTAT 58.583 40.909 10.89 0.00 35.66 3.06
553 566 2.852449 TGTGAAAATTCCACTGCCGTA 58.148 42.857 10.89 0.00 35.66 4.02
554 567 1.686355 TGTGAAAATTCCACTGCCGT 58.314 45.000 10.89 0.00 35.66 5.68
555 568 2.791383 TTGTGAAAATTCCACTGCCG 57.209 45.000 10.89 0.00 35.66 5.69
556 569 4.320608 TCTTTGTGAAAATTCCACTGCC 57.679 40.909 10.89 0.00 35.66 4.85
557 570 5.591099 TCTTCTTTGTGAAAATTCCACTGC 58.409 37.500 10.89 0.00 35.66 4.40
558 571 8.652810 ATTTCTTCTTTGTGAAAATTCCACTG 57.347 30.769 10.89 3.98 36.06 3.66
568 581 8.342634 CGTTCCTTCTTATTTCTTCTTTGTGAA 58.657 33.333 0.00 0.00 0.00 3.18
569 582 7.713507 TCGTTCCTTCTTATTTCTTCTTTGTGA 59.286 33.333 0.00 0.00 0.00 3.58
570 583 7.861630 TCGTTCCTTCTTATTTCTTCTTTGTG 58.138 34.615 0.00 0.00 0.00 3.33
571 584 8.446599 TTCGTTCCTTCTTATTTCTTCTTTGT 57.553 30.769 0.00 0.00 0.00 2.83
572 585 9.899226 AATTCGTTCCTTCTTATTTCTTCTTTG 57.101 29.630 0.00 0.00 0.00 2.77
574 587 9.899226 CAAATTCGTTCCTTCTTATTTCTTCTT 57.101 29.630 0.00 0.00 0.00 2.52
575 588 9.067986 ACAAATTCGTTCCTTCTTATTTCTTCT 57.932 29.630 0.00 0.00 0.00 2.85
576 589 9.118236 CACAAATTCGTTCCTTCTTATTTCTTC 57.882 33.333 0.00 0.00 0.00 2.87
577 590 8.082242 CCACAAATTCGTTCCTTCTTATTTCTT 58.918 33.333 0.00 0.00 0.00 2.52
578 591 7.593825 CCACAAATTCGTTCCTTCTTATTTCT 58.406 34.615 0.00 0.00 0.00 2.52
579 592 6.308041 GCCACAAATTCGTTCCTTCTTATTTC 59.692 38.462 0.00 0.00 0.00 2.17
580 593 6.156519 GCCACAAATTCGTTCCTTCTTATTT 58.843 36.000 0.00 0.00 0.00 1.40
581 594 5.242838 TGCCACAAATTCGTTCCTTCTTATT 59.757 36.000 0.00 0.00 0.00 1.40
582 595 4.764823 TGCCACAAATTCGTTCCTTCTTAT 59.235 37.500 0.00 0.00 0.00 1.73
583 596 4.138290 TGCCACAAATTCGTTCCTTCTTA 58.862 39.130 0.00 0.00 0.00 2.10
584 597 2.955660 TGCCACAAATTCGTTCCTTCTT 59.044 40.909 0.00 0.00 0.00 2.52
585 598 2.582052 TGCCACAAATTCGTTCCTTCT 58.418 42.857 0.00 0.00 0.00 2.85
586 599 3.575965 ATGCCACAAATTCGTTCCTTC 57.424 42.857 0.00 0.00 0.00 3.46
587 600 3.554752 CCAATGCCACAAATTCGTTCCTT 60.555 43.478 0.00 0.00 0.00 3.36
588 601 2.029110 CCAATGCCACAAATTCGTTCCT 60.029 45.455 0.00 0.00 0.00 3.36
589 602 2.336667 CCAATGCCACAAATTCGTTCC 58.663 47.619 0.00 0.00 0.00 3.62
590 603 2.029470 TCCCAATGCCACAAATTCGTTC 60.029 45.455 0.00 0.00 0.00 3.95
591 604 1.967066 TCCCAATGCCACAAATTCGTT 59.033 42.857 0.00 0.00 0.00 3.85
592 605 1.626686 TCCCAATGCCACAAATTCGT 58.373 45.000 0.00 0.00 0.00 3.85
593 606 2.965572 ATCCCAATGCCACAAATTCG 57.034 45.000 0.00 0.00 0.00 3.34
594 607 4.081198 TGGTAATCCCAATGCCACAAATTC 60.081 41.667 0.00 0.00 41.50 2.17
595 608 3.843027 TGGTAATCCCAATGCCACAAATT 59.157 39.130 0.00 0.00 41.50 1.82
596 609 3.448934 TGGTAATCCCAATGCCACAAAT 58.551 40.909 0.00 0.00 41.50 2.32
597 610 2.894731 TGGTAATCCCAATGCCACAAA 58.105 42.857 0.00 0.00 41.50 2.83
598 611 2.612285 TGGTAATCCCAATGCCACAA 57.388 45.000 0.00 0.00 41.50 3.33
619 632 9.887406 GGTGAACGAGTTTTTATTTCTTCATTA 57.113 29.630 0.00 0.00 0.00 1.90
620 633 8.410141 TGGTGAACGAGTTTTTATTTCTTCATT 58.590 29.630 0.00 0.00 0.00 2.57
621 634 7.936584 TGGTGAACGAGTTTTTATTTCTTCAT 58.063 30.769 0.00 0.00 0.00 2.57
622 635 7.323049 TGGTGAACGAGTTTTTATTTCTTCA 57.677 32.000 0.00 0.00 0.00 3.02
623 636 6.359883 GCTGGTGAACGAGTTTTTATTTCTTC 59.640 38.462 0.00 0.00 0.00 2.87
624 637 6.206498 GCTGGTGAACGAGTTTTTATTTCTT 58.794 36.000 0.00 0.00 0.00 2.52
625 638 5.278315 GGCTGGTGAACGAGTTTTTATTTCT 60.278 40.000 0.00 0.00 0.00 2.52
626 639 4.915667 GGCTGGTGAACGAGTTTTTATTTC 59.084 41.667 0.00 0.00 0.00 2.17
627 640 4.583073 AGGCTGGTGAACGAGTTTTTATTT 59.417 37.500 0.00 0.00 0.00 1.40
628 641 4.023193 CAGGCTGGTGAACGAGTTTTTATT 60.023 41.667 6.61 0.00 0.00 1.40
629 642 3.502211 CAGGCTGGTGAACGAGTTTTTAT 59.498 43.478 6.61 0.00 0.00 1.40
630 643 2.875933 CAGGCTGGTGAACGAGTTTTTA 59.124 45.455 6.61 0.00 0.00 1.52
631 644 1.676006 CAGGCTGGTGAACGAGTTTTT 59.324 47.619 6.61 0.00 0.00 1.94
632 645 1.308998 CAGGCTGGTGAACGAGTTTT 58.691 50.000 6.61 0.00 0.00 2.43
633 646 1.166531 GCAGGCTGGTGAACGAGTTT 61.167 55.000 17.64 0.00 0.00 2.66
634 647 1.598130 GCAGGCTGGTGAACGAGTT 60.598 57.895 17.64 0.00 0.00 3.01
635 648 2.031163 GCAGGCTGGTGAACGAGT 59.969 61.111 17.64 0.00 0.00 4.18
636 649 2.743928 GGCAGGCTGGTGAACGAG 60.744 66.667 17.64 0.00 0.00 4.18
637 650 2.616797 TTTGGCAGGCTGGTGAACGA 62.617 55.000 17.64 0.00 0.00 3.85
638 651 1.733402 TTTTGGCAGGCTGGTGAACG 61.733 55.000 17.64 0.00 0.00 3.95
639 652 0.463620 TTTTTGGCAGGCTGGTGAAC 59.536 50.000 17.64 0.00 0.00 3.18
640 653 2.907703 TTTTTGGCAGGCTGGTGAA 58.092 47.368 17.64 0.00 0.00 3.18
641 654 4.695014 TTTTTGGCAGGCTGGTGA 57.305 50.000 17.64 0.00 0.00 4.02
655 668 5.118286 CAGGCTGGTGAACAAATTCTTTTT 58.882 37.500 6.61 0.00 35.69 1.94
656 669 4.696455 CAGGCTGGTGAACAAATTCTTTT 58.304 39.130 6.61 0.00 35.69 2.27
657 670 3.493176 GCAGGCTGGTGAACAAATTCTTT 60.493 43.478 17.64 0.00 35.69 2.52
658 671 2.036346 GCAGGCTGGTGAACAAATTCTT 59.964 45.455 17.64 0.00 35.69 2.52
659 672 1.615392 GCAGGCTGGTGAACAAATTCT 59.385 47.619 17.64 0.00 35.69 2.40
660 673 1.337167 GGCAGGCTGGTGAACAAATTC 60.337 52.381 17.64 0.00 35.18 2.17
661 674 0.681175 GGCAGGCTGGTGAACAAATT 59.319 50.000 17.64 0.00 0.00 1.82
662 675 0.469705 TGGCAGGCTGGTGAACAAAT 60.470 50.000 17.64 0.00 0.00 2.32
663 676 0.685785 TTGGCAGGCTGGTGAACAAA 60.686 50.000 17.64 0.00 0.00 2.83
664 677 0.685785 TTTGGCAGGCTGGTGAACAA 60.686 50.000 17.64 0.00 0.00 2.83
665 678 0.685785 TTTTGGCAGGCTGGTGAACA 60.686 50.000 17.64 0.00 0.00 3.18
749 765 1.376683 CTGGGATTTGGGTTCGCGA 60.377 57.895 3.71 3.71 0.00 5.87
844 863 3.018973 GCGCGCGATAATTTGGGA 58.981 55.556 37.18 0.00 0.00 4.37
910 943 0.036164 CGGTGGTGATTTGGTGGAGA 59.964 55.000 0.00 0.00 0.00 3.71
940 978 4.841422 CTCTGGTGTTTGGAGAATGAGAT 58.159 43.478 0.00 0.00 0.00 2.75
1242 1286 2.579738 GACTGGAAGCGGAGGTCC 59.420 66.667 0.00 0.00 37.06 4.46
1475 1548 2.764572 ACGGGTGGACTAGAATAACAGG 59.235 50.000 0.00 0.00 0.00 4.00
1513 1586 5.772169 ACCGTTACTTGAACTAGAACCTAGT 59.228 40.000 0.00 1.09 35.74 2.57
1527 1600 1.595794 ACAGCAAACGACCGTTACTTG 59.404 47.619 8.28 9.09 37.35 3.16
1529 1602 1.595794 CAACAGCAAACGACCGTTACT 59.404 47.619 8.28 6.58 37.35 2.24
1534 1607 2.412325 GGTAATCAACAGCAAACGACCG 60.412 50.000 0.00 0.00 0.00 4.79
1568 1641 7.998964 GGGATAAAATAGATCACTTCCTTTCCA 59.001 37.037 0.00 0.00 0.00 3.53
1569 1642 7.448777 GGGGATAAAATAGATCACTTCCTTTCC 59.551 40.741 0.00 0.00 0.00 3.13
1570 1643 7.998964 TGGGGATAAAATAGATCACTTCCTTTC 59.001 37.037 0.00 0.00 0.00 2.62
1572 1645 7.465900 TGGGGATAAAATAGATCACTTCCTT 57.534 36.000 0.00 0.00 0.00 3.36
1573 1646 7.654287 ATGGGGATAAAATAGATCACTTCCT 57.346 36.000 0.00 0.00 0.00 3.36
1575 1648 9.579932 AGAAATGGGGATAAAATAGATCACTTC 57.420 33.333 0.00 0.00 0.00 3.01
1577 1650 8.727149 TCAGAAATGGGGATAAAATAGATCACT 58.273 33.333 0.00 0.00 0.00 3.41
1578 1651 8.924511 TCAGAAATGGGGATAAAATAGATCAC 57.075 34.615 0.00 0.00 0.00 3.06
1581 1654 9.972106 GATCTCAGAAATGGGGATAAAATAGAT 57.028 33.333 0.00 0.00 0.00 1.98
1613 1686 3.841643 CATCCAAGCACAAAAGTCCATC 58.158 45.455 0.00 0.00 0.00 3.51
1616 1689 1.615392 AGCATCCAAGCACAAAAGTCC 59.385 47.619 0.00 0.00 36.85 3.85
1619 1692 3.460103 ACAAAGCATCCAAGCACAAAAG 58.540 40.909 0.00 0.00 36.85 2.27
1622 1695 3.056678 CCATACAAAGCATCCAAGCACAA 60.057 43.478 0.00 0.00 36.85 3.33
1623 1696 2.492881 CCATACAAAGCATCCAAGCACA 59.507 45.455 0.00 0.00 36.85 4.57
1627 1700 5.589855 TCATACACCATACAAAGCATCCAAG 59.410 40.000 0.00 0.00 0.00 3.61
1639 1712 5.808042 GATGGCATCATCATACACCATAC 57.192 43.478 22.23 0.00 46.74 2.39
1659 1732 6.793759 CTCAGCACGAGAATCATTCCTATGAT 60.794 42.308 0.00 0.00 45.45 2.45
1660 1733 4.342092 TCAGCACGAGAATCATTCCTATGA 59.658 41.667 0.00 0.00 44.52 2.15
1661 1734 4.625028 TCAGCACGAGAATCATTCCTATG 58.375 43.478 0.00 0.00 33.17 2.23
1662 1735 4.343526 ACTCAGCACGAGAATCATTCCTAT 59.656 41.667 9.90 0.00 45.45 2.57
1663 1736 3.701542 ACTCAGCACGAGAATCATTCCTA 59.298 43.478 9.90 0.00 45.45 2.94
1664 1737 2.499289 ACTCAGCACGAGAATCATTCCT 59.501 45.455 9.90 0.00 45.45 3.36
1665 1738 2.898705 ACTCAGCACGAGAATCATTCC 58.101 47.619 9.90 0.00 45.45 3.01
1666 1739 4.935885 AAACTCAGCACGAGAATCATTC 57.064 40.909 9.90 0.00 45.45 2.67
1667 1740 5.695851 AAAAACTCAGCACGAGAATCATT 57.304 34.783 9.90 0.00 45.45 2.57
1690 1763 9.219603 CAAGAGAATTTCTTATGTACAGACCAA 57.780 33.333 0.33 0.00 44.34 3.67
1694 1767 8.846943 TTGCAAGAGAATTTCTTATGTACAGA 57.153 30.769 0.33 0.00 44.34 3.41
1713 1786 8.336806 ACATGAACAACAAAATGTAATTGCAAG 58.663 29.630 4.94 0.00 36.10 4.01
1724 1816 5.728471 TCACACCAACATGAACAACAAAAT 58.272 33.333 0.00 0.00 0.00 1.82
1729 1821 3.569701 AGGATCACACCAACATGAACAAC 59.430 43.478 0.00 0.00 0.00 3.32
1751 1843 6.239396 TCAGATTAAACGGATGGTGGTAAAA 58.761 36.000 0.00 0.00 0.00 1.52
1757 1849 6.254281 ACTTTTCAGATTAAACGGATGGTG 57.746 37.500 0.00 0.00 0.00 4.17
1758 1850 6.894339 AACTTTTCAGATTAAACGGATGGT 57.106 33.333 0.00 0.00 0.00 3.55
1782 1874 7.292713 TGTTTCTCTATGTACCACTGTTGTA 57.707 36.000 0.00 0.00 0.00 2.41
1800 1893 6.096846 AGTTGTGCCTAAATGAACTTGTTTCT 59.903 34.615 0.00 0.00 34.97 2.52
1801 1894 6.273071 AGTTGTGCCTAAATGAACTTGTTTC 58.727 36.000 0.00 0.00 34.41 2.78
1812 1905 6.208797 GTCTTAAGGGAAAGTTGTGCCTAAAT 59.791 38.462 1.85 0.00 38.62 1.40
1813 1906 5.533528 GTCTTAAGGGAAAGTTGTGCCTAAA 59.466 40.000 1.85 0.00 38.62 1.85
1815 1908 4.349930 AGTCTTAAGGGAAAGTTGTGCCTA 59.650 41.667 1.85 0.00 38.62 3.93
1816 1909 3.138468 AGTCTTAAGGGAAAGTTGTGCCT 59.862 43.478 1.85 0.00 41.94 4.75
1817 1910 3.487372 AGTCTTAAGGGAAAGTTGTGCC 58.513 45.455 1.85 0.00 0.00 5.01
1818 1911 6.819397 AATAGTCTTAAGGGAAAGTTGTGC 57.181 37.500 1.85 0.00 0.00 4.57
1823 1916 9.819267 CGAGAAATAATAGTCTTAAGGGAAAGT 57.181 33.333 1.85 0.00 0.00 2.66
1827 1920 9.363401 TGATCGAGAAATAATAGTCTTAAGGGA 57.637 33.333 1.85 0.00 0.00 4.20
1839 1932 9.118300 AGCAGAGAAAAATGATCGAGAAATAAT 57.882 29.630 0.00 0.00 0.00 1.28
1840 1933 8.498054 AGCAGAGAAAAATGATCGAGAAATAA 57.502 30.769 0.00 0.00 0.00 1.40
1841 1934 9.770097 ATAGCAGAGAAAAATGATCGAGAAATA 57.230 29.630 0.00 0.00 0.00 1.40
1842 1935 6.998968 AGCAGAGAAAAATGATCGAGAAAT 57.001 33.333 0.00 0.00 0.00 2.17
1843 1936 8.498054 AATAGCAGAGAAAAATGATCGAGAAA 57.502 30.769 0.00 0.00 0.00 2.52
1844 1937 9.599866 TTAATAGCAGAGAAAAATGATCGAGAA 57.400 29.630 0.00 0.00 0.00 2.87
1845 1938 9.035607 GTTAATAGCAGAGAAAAATGATCGAGA 57.964 33.333 0.00 0.00 0.00 4.04
1846 1939 9.039870 AGTTAATAGCAGAGAAAAATGATCGAG 57.960 33.333 0.00 0.00 0.00 4.04
1847 1940 8.820933 CAGTTAATAGCAGAGAAAAATGATCGA 58.179 33.333 0.00 0.00 0.00 3.59
1848 1941 8.820933 TCAGTTAATAGCAGAGAAAAATGATCG 58.179 33.333 0.00 0.00 0.00 3.69
1859 1952 8.273780 ACCAAATCTTTCAGTTAATAGCAGAG 57.726 34.615 0.00 0.00 0.00 3.35
1891 1984 2.808523 TCTGAGAGTGTTGCTGACAG 57.191 50.000 0.00 0.00 39.39 3.51
1908 2006 5.565439 GCAGGCATCACAACAAGTTTATTCT 60.565 40.000 0.00 0.00 0.00 2.40
1929 2027 2.094803 CCTCACAGAGTCACAGTAGCAG 60.095 54.545 0.00 0.00 0.00 4.24
1930 2028 1.889170 CCTCACAGAGTCACAGTAGCA 59.111 52.381 0.00 0.00 0.00 3.49
1932 2030 2.166829 AGCCTCACAGAGTCACAGTAG 58.833 52.381 0.00 0.00 0.00 2.57
1948 2046 1.068121 AACTTTGCCAGAGGTAGCCT 58.932 50.000 0.00 0.00 36.03 4.58
1984 2082 2.490115 GAGTGGCTCCTACTCATATCCG 59.510 54.545 4.18 0.00 43.12 4.18
2020 2118 5.152097 CACAGAAGCTGCAGAAAATACTTG 58.848 41.667 20.43 6.44 34.37 3.16
2035 2133 1.760192 AGAATCCATGCCACAGAAGC 58.240 50.000 0.00 0.00 0.00 3.86
2062 2160 1.448893 GCCGGCAGGATTACGTGAA 60.449 57.895 24.80 0.00 41.02 3.18
2116 2214 4.078537 CACACCTAATTGGACCATCACAA 58.921 43.478 0.00 0.00 39.71 3.33
2127 2225 4.582701 TTGCAAGGAACACACCTAATTG 57.417 40.909 0.00 0.00 39.62 2.32
2129 2227 6.569610 CGTTATTTGCAAGGAACACACCTAAT 60.570 38.462 19.57 2.52 39.62 1.73
2139 2237 1.198178 GGTCGCGTTATTTGCAAGGAA 59.802 47.619 5.77 0.00 0.00 3.36
2153 2251 1.127701 CAAACAAATTGGTGGTCGCG 58.872 50.000 0.00 0.00 35.27 5.87
2172 2270 1.153745 CGTACTCCCAGACTGCAGC 60.154 63.158 15.27 6.85 0.00 5.25
2190 2288 5.728351 TCGGCTACAGCATTTAAATGTAC 57.272 39.130 25.15 12.50 44.36 2.90
2192 2290 5.238650 GGTATCGGCTACAGCATTTAAATGT 59.761 40.000 25.15 12.86 44.36 2.71
2198 2296 3.492102 ATGGTATCGGCTACAGCATTT 57.508 42.857 3.24 0.00 44.36 2.32
2199 2297 3.492102 AATGGTATCGGCTACAGCATT 57.508 42.857 3.24 0.00 44.36 3.56
2237 2336 7.898918 TGATAAATAAAATGCATCTGATGGGG 58.101 34.615 18.60 0.00 0.00 4.96
2259 2358 8.970020 TGCCAATCTGAAATTTAGTGTTATGAT 58.030 29.630 0.00 0.00 0.00 2.45
2260 2359 8.347004 TGCCAATCTGAAATTTAGTGTTATGA 57.653 30.769 0.00 0.00 0.00 2.15
2261 2360 7.703621 CCTGCCAATCTGAAATTTAGTGTTATG 59.296 37.037 0.00 0.00 0.00 1.90
2262 2361 7.631377 GCCTGCCAATCTGAAATTTAGTGTTAT 60.631 37.037 0.00 0.00 0.00 1.89
2263 2362 6.350110 GCCTGCCAATCTGAAATTTAGTGTTA 60.350 38.462 0.00 0.00 0.00 2.41
2272 2374 2.494870 GTGAAGCCTGCCAATCTGAAAT 59.505 45.455 0.00 0.00 0.00 2.17
2295 2397 3.733337 CCTCTACATCCATGTAACTGGC 58.267 50.000 1.19 0.00 42.20 4.85
2311 2413 1.257743 GGCTATCGGTCATGCCTCTA 58.742 55.000 0.00 0.00 41.92 2.43
2312 2414 2.053618 GGCTATCGGTCATGCCTCT 58.946 57.895 0.00 0.00 41.92 3.69
2339 2441 9.063615 TGCTTCTCATATCGATACTTGTAGTAA 57.936 33.333 7.41 0.00 33.89 2.24
2340 2442 8.617290 TGCTTCTCATATCGATACTTGTAGTA 57.383 34.615 7.41 0.38 34.82 1.82
2347 2449 8.147058 ACTTTGAATGCTTCTCATATCGATACT 58.853 33.333 7.41 0.00 34.33 2.12
2352 2454 9.773328 TTAAAACTTTGAATGCTTCTCATATCG 57.227 29.630 0.00 0.00 34.33 2.92
2376 2478 9.214957 CAATCAGTTCTACATGTAACCTGTTTA 57.785 33.333 18.32 6.99 0.00 2.01


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

AutoCloner maintained by Alex Coulton.