Multiple sequence alignment - TraesCS5D01G560400

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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 TraesCS5D01G560400 chr5D 100.000 2876 0 0 1 2876 561574072 561571197 0.000000e+00 5312
1 TraesCS5D01G560400 chr5D 89.587 1018 81 9 883 1880 556273708 556272696 0.000000e+00 1269
2 TraesCS5D01G560400 chr7B 92.404 1514 85 6 888 2392 1482182 1483674 0.000000e+00 2132
3 TraesCS5D01G560400 chr7B 90.415 1085 83 14 821 1890 1436825 1437903 0.000000e+00 1408
4 TraesCS5D01G560400 chr7B 87.640 267 14 1 2565 2831 1483697 1483944 2.800000e-75 292
5 TraesCS5D01G560400 chr5B 91.508 1472 80 21 999 2460 711268950 711267514 0.000000e+00 1984
6 TraesCS5D01G560400 chr5B 91.232 1015 78 10 881 1890 711281060 711280052 0.000000e+00 1371
7 TraesCS5D01G560400 chr5B 93.204 309 19 1 391 697 644259436 644259744 1.210000e-123 453
8 TraesCS5D01G560400 chr5B 86.705 346 10 10 2540 2872 711267372 711267050 4.560000e-93 351
9 TraesCS5D01G560400 chr5B 82.822 326 29 12 2194 2519 711279629 711279331 1.700000e-67 267
10 TraesCS5D01G560400 chr5B 79.412 204 16 9 1978 2158 711280033 711279833 1.400000e-23 121
11 TraesCS5D01G560400 chr4A 87.723 1629 111 32 884 2460 603666015 603667606 0.000000e+00 1818
12 TraesCS5D01G560400 chr4A 83.966 580 77 12 125 697 455532462 455533032 2.520000e-150 542
13 TraesCS5D01G560400 chr4A 83.621 580 81 11 125 697 341645713 341646285 1.520000e-147 532
14 TraesCS5D01G560400 chr4A 93.528 309 19 1 390 697 83641195 83641503 2.610000e-125 459
15 TraesCS5D01G560400 chr4A 87.162 148 13 5 2682 2824 603667812 603667958 2.290000e-36 163
16 TraesCS5D01G560400 chr4B 87.891 768 93 0 1070 1837 651514487 651515254 0.000000e+00 904
17 TraesCS5D01G560400 chr4B 92.880 309 20 1 391 697 130977330 130977022 5.650000e-122 448
18 TraesCS5D01G560400 chr4D 86.553 818 107 3 1020 1837 504597416 504598230 0.000000e+00 898
19 TraesCS5D01G560400 chr4D 92.949 312 18 2 390 697 299382548 299382859 4.370000e-123 451
20 TraesCS5D01G560400 chr4D 85.266 414 49 8 156 559 386842681 386842270 1.590000e-112 416
21 TraesCS5D01G560400 chr5A 86.308 818 109 3 1020 1837 689251882 689252696 0.000000e+00 887
22 TraesCS5D01G560400 chr3B 89.273 578 53 6 121 694 627980941 627981513 0.000000e+00 715
23 TraesCS5D01G560400 chr7A 84.083 578 79 10 125 697 495336539 495335970 1.950000e-151 545
24 TraesCS5D01G560400 chr2A 83.765 579 80 11 125 697 521239840 521239270 1.170000e-148 536
25 TraesCS5D01G560400 chr2A 84.600 500 66 8 125 621 183784920 183785411 1.200000e-133 486
26 TraesCS5D01G560400 chr2B 83.128 569 70 15 122 674 77204188 77203630 1.990000e-136 496
27 TraesCS5D01G560400 chr2B 93.204 309 19 1 391 697 130758548 130758856 1.210000e-123 453
28 TraesCS5D01G560400 chr2B 88.995 209 20 1 124 332 111168084 111167879 3.680000e-64 255
29 TraesCS5D01G560400 chr7D 93.226 310 20 1 389 697 462071751 462072060 3.380000e-124 455
30 TraesCS5D01G560400 chr3A 93.204 309 20 1 390 697 334565699 334565391 1.210000e-123 453
31 TraesCS5D01G560400 chr2D 93.950 281 14 1 122 402 561397713 561397990 3.430000e-114 422
32 TraesCS5D01G560400 chr6D 76.567 367 81 4 1261 1626 465011249 465010887 2.260000e-46 196


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 TraesCS5D01G560400 chr5D 561571197 561574072 2875 True 5312.000000 5312 100.000000 1 2876 1 chr5D.!!$R2 2875
1 TraesCS5D01G560400 chr5D 556272696 556273708 1012 True 1269.000000 1269 89.587000 883 1880 1 chr5D.!!$R1 997
2 TraesCS5D01G560400 chr7B 1436825 1437903 1078 False 1408.000000 1408 90.415000 821 1890 1 chr7B.!!$F1 1069
3 TraesCS5D01G560400 chr7B 1482182 1483944 1762 False 1212.000000 2132 90.022000 888 2831 2 chr7B.!!$F2 1943
4 TraesCS5D01G560400 chr5B 711267050 711268950 1900 True 1167.500000 1984 89.106500 999 2872 2 chr5B.!!$R1 1873
5 TraesCS5D01G560400 chr5B 711279331 711281060 1729 True 586.333333 1371 84.488667 881 2519 3 chr5B.!!$R2 1638
6 TraesCS5D01G560400 chr4A 603666015 603667958 1943 False 990.500000 1818 87.442500 884 2824 2 chr4A.!!$F4 1940
7 TraesCS5D01G560400 chr4A 455532462 455533032 570 False 542.000000 542 83.966000 125 697 1 chr4A.!!$F3 572
8 TraesCS5D01G560400 chr4A 341645713 341646285 572 False 532.000000 532 83.621000 125 697 1 chr4A.!!$F2 572
9 TraesCS5D01G560400 chr4B 651514487 651515254 767 False 904.000000 904 87.891000 1070 1837 1 chr4B.!!$F1 767
10 TraesCS5D01G560400 chr4D 504597416 504598230 814 False 898.000000 898 86.553000 1020 1837 1 chr4D.!!$F2 817
11 TraesCS5D01G560400 chr5A 689251882 689252696 814 False 887.000000 887 86.308000 1020 1837 1 chr5A.!!$F1 817
12 TraesCS5D01G560400 chr3B 627980941 627981513 572 False 715.000000 715 89.273000 121 694 1 chr3B.!!$F1 573
13 TraesCS5D01G560400 chr7A 495335970 495336539 569 True 545.000000 545 84.083000 125 697 1 chr7A.!!$R1 572
14 TraesCS5D01G560400 chr2A 521239270 521239840 570 True 536.000000 536 83.765000 125 697 1 chr2A.!!$R1 572
15 TraesCS5D01G560400 chr2B 77203630 77204188 558 True 496.000000 496 83.128000 122 674 1 chr2B.!!$R1 552

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
754 767 0.039527 AATCACTCCCGCAAAAACGC 60.04 50.0 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 2575 0.946221 GAACAGAGGTGGCGTGACAG 60.946 60.0 0.0 0.0 0.0 3.51 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
37 38 3.354771 CGTTTGTACGCAGTCTTCATC 57.645 47.619 0.00 0.00 43.93 2.92
38 39 2.729360 CGTTTGTACGCAGTCTTCATCA 59.271 45.455 0.00 0.00 43.93 3.07
39 40 3.183574 CGTTTGTACGCAGTCTTCATCAA 59.816 43.478 0.00 0.00 43.93 2.57
40 41 4.318475 CGTTTGTACGCAGTCTTCATCAAA 60.318 41.667 0.00 0.00 43.93 2.69
41 42 4.990543 TTGTACGCAGTCTTCATCAAAG 57.009 40.909 0.00 0.00 43.93 2.77
42 43 3.990092 TGTACGCAGTCTTCATCAAAGT 58.010 40.909 0.00 0.00 43.93 2.66
43 44 3.987868 TGTACGCAGTCTTCATCAAAGTC 59.012 43.478 0.00 0.00 43.93 3.01
44 45 3.111853 ACGCAGTCTTCATCAAAGTCA 57.888 42.857 0.00 0.00 29.74 3.41
45 46 3.668447 ACGCAGTCTTCATCAAAGTCAT 58.332 40.909 0.00 0.00 29.74 3.06
46 47 4.820897 ACGCAGTCTTCATCAAAGTCATA 58.179 39.130 0.00 0.00 29.74 2.15
47 48 4.867047 ACGCAGTCTTCATCAAAGTCATAG 59.133 41.667 0.00 0.00 29.74 2.23
48 49 4.260132 CGCAGTCTTCATCAAAGTCATAGC 60.260 45.833 0.00 0.00 36.31 2.97
49 50 4.874966 GCAGTCTTCATCAAAGTCATAGCT 59.125 41.667 0.00 0.00 36.31 3.32
50 51 6.045318 GCAGTCTTCATCAAAGTCATAGCTA 58.955 40.000 0.00 0.00 36.31 3.32
51 52 6.200665 GCAGTCTTCATCAAAGTCATAGCTAG 59.799 42.308 0.00 0.00 36.31 3.42
52 53 7.264221 CAGTCTTCATCAAAGTCATAGCTAGT 58.736 38.462 0.00 0.00 36.31 2.57
53 54 7.763528 CAGTCTTCATCAAAGTCATAGCTAGTT 59.236 37.037 0.00 0.00 36.31 2.24
54 55 8.972127 AGTCTTCATCAAAGTCATAGCTAGTTA 58.028 33.333 0.00 0.00 36.31 2.24
55 56 9.587772 GTCTTCATCAAAGTCATAGCTAGTTAA 57.412 33.333 0.00 0.00 36.31 2.01
91 92 9.554395 AAACAAATAATTACAAAAGGTTGGGAG 57.446 29.630 0.00 0.00 39.22 4.30
92 93 8.485578 ACAAATAATTACAAAAGGTTGGGAGA 57.514 30.769 0.00 0.00 39.22 3.71
93 94 9.100197 ACAAATAATTACAAAAGGTTGGGAGAT 57.900 29.630 0.00 0.00 39.22 2.75
96 97 9.762381 AATAATTACAAAAGGTTGGGAGATACA 57.238 29.630 0.00 0.00 39.22 2.29
97 98 9.762381 ATAATTACAAAAGGTTGGGAGATACAA 57.238 29.630 0.00 0.00 39.22 2.41
98 99 6.887626 TTACAAAAGGTTGGGAGATACAAC 57.112 37.500 0.00 0.00 45.60 3.32
105 106 4.820894 GTTGGGAGATACAACCTGTAGT 57.179 45.455 0.00 0.00 41.70 2.73
106 107 5.161943 GTTGGGAGATACAACCTGTAGTT 57.838 43.478 0.00 0.00 41.70 2.24
107 108 5.557866 GTTGGGAGATACAACCTGTAGTTT 58.442 41.667 0.00 0.00 41.70 2.66
108 109 5.836024 TGGGAGATACAACCTGTAGTTTT 57.164 39.130 0.00 0.00 36.14 2.43
109 110 5.801380 TGGGAGATACAACCTGTAGTTTTC 58.199 41.667 0.00 0.00 36.14 2.29
110 111 5.546499 TGGGAGATACAACCTGTAGTTTTCT 59.454 40.000 0.00 0.00 36.14 2.52
111 112 6.727231 TGGGAGATACAACCTGTAGTTTTCTA 59.273 38.462 0.00 0.00 36.14 2.10
112 113 7.402071 TGGGAGATACAACCTGTAGTTTTCTAT 59.598 37.037 0.00 0.00 36.14 1.98
113 114 8.265764 GGGAGATACAACCTGTAGTTTTCTATT 58.734 37.037 0.00 0.00 36.14 1.73
114 115 9.668497 GGAGATACAACCTGTAGTTTTCTATTT 57.332 33.333 0.00 0.00 36.14 1.40
189 190 8.950403 AACGAAATAATCTCAAAACACTTAGC 57.050 30.769 0.00 0.00 0.00 3.09
210 211 2.498481 CCACGGTACATTAACTCCCTCA 59.502 50.000 0.00 0.00 0.00 3.86
213 214 4.099573 CACGGTACATTAACTCCCTCATCT 59.900 45.833 0.00 0.00 0.00 2.90
321 322 4.039004 AGTGGTTAGTTCATTGCATGCAAA 59.961 37.500 34.84 18.59 39.55 3.68
357 358 8.547967 AGCAAAAAGACATTAAGTTATCTCGA 57.452 30.769 0.00 0.00 0.00 4.04
368 369 2.628657 AGTTATCTCGATTTCCCCTCCG 59.371 50.000 0.00 0.00 0.00 4.63
411 412 6.641474 ACCTAAAATGACTTAGACTAGCCAC 58.359 40.000 0.00 0.00 31.59 5.01
423 428 2.766828 GACTAGCCACAGTGGGAGTAAT 59.233 50.000 21.77 0.00 38.19 1.89
428 433 3.153919 GCCACAGTGGGAGTAATTTCAA 58.846 45.455 21.77 0.00 38.19 2.69
497 510 8.231692 TGAGTTAATGAGGAGAGAGATAGTTG 57.768 38.462 0.00 0.00 0.00 3.16
542 555 3.916761 ACATCACATGTTCCAATGCAAC 58.083 40.909 0.00 0.00 41.63 4.17
574 587 9.712305 TCTATAACCTAATAAATGAAGCTCTGC 57.288 33.333 0.00 0.00 0.00 4.26
575 588 9.494271 CTATAACCTAATAAATGAAGCTCTGCA 57.506 33.333 0.00 0.00 0.00 4.41
576 589 8.930846 ATAACCTAATAAATGAAGCTCTGCAT 57.069 30.769 0.00 0.00 0.00 3.96
577 590 6.874288 ACCTAATAAATGAAGCTCTGCATC 57.126 37.500 0.00 0.00 0.00 3.91
578 591 6.599445 ACCTAATAAATGAAGCTCTGCATCT 58.401 36.000 0.00 0.00 0.00 2.90
579 592 7.059156 ACCTAATAAATGAAGCTCTGCATCTT 58.941 34.615 0.00 0.00 0.00 2.40
580 593 8.213679 ACCTAATAAATGAAGCTCTGCATCTTA 58.786 33.333 0.00 0.00 0.00 2.10
581 594 8.502387 CCTAATAAATGAAGCTCTGCATCTTAC 58.498 37.037 0.00 0.00 0.00 2.34
582 595 6.874288 ATAAATGAAGCTCTGCATCTTACC 57.126 37.500 0.00 0.00 0.00 2.85
583 596 3.920231 ATGAAGCTCTGCATCTTACCA 57.080 42.857 0.00 0.00 0.00 3.25
584 597 2.977914 TGAAGCTCTGCATCTTACCAC 58.022 47.619 0.00 0.00 0.00 4.16
585 598 2.302733 TGAAGCTCTGCATCTTACCACA 59.697 45.455 0.00 0.00 0.00 4.17
586 599 2.393271 AGCTCTGCATCTTACCACAC 57.607 50.000 0.00 0.00 0.00 3.82
587 600 1.905215 AGCTCTGCATCTTACCACACT 59.095 47.619 0.00 0.00 0.00 3.55
588 601 2.304180 AGCTCTGCATCTTACCACACTT 59.696 45.455 0.00 0.00 0.00 3.16
589 602 3.515502 AGCTCTGCATCTTACCACACTTA 59.484 43.478 0.00 0.00 0.00 2.24
590 603 4.163078 AGCTCTGCATCTTACCACACTTAT 59.837 41.667 0.00 0.00 0.00 1.73
591 604 4.272018 GCTCTGCATCTTACCACACTTATG 59.728 45.833 0.00 0.00 0.00 1.90
592 605 5.420725 TCTGCATCTTACCACACTTATGT 57.579 39.130 0.00 0.00 40.80 2.29
593 606 5.804639 TCTGCATCTTACCACACTTATGTT 58.195 37.500 0.00 0.00 36.72 2.71
594 607 6.941857 TCTGCATCTTACCACACTTATGTTA 58.058 36.000 0.00 0.00 36.72 2.41
595 608 6.816640 TCTGCATCTTACCACACTTATGTTAC 59.183 38.462 0.00 0.00 36.72 2.50
596 609 6.707290 TGCATCTTACCACACTTATGTTACT 58.293 36.000 0.00 0.00 36.72 2.24
597 610 7.842982 TGCATCTTACCACACTTATGTTACTA 58.157 34.615 0.00 0.00 36.72 1.82
598 611 7.762615 TGCATCTTACCACACTTATGTTACTAC 59.237 37.037 0.00 0.00 36.72 2.73
599 612 7.224167 GCATCTTACCACACTTATGTTACTACC 59.776 40.741 0.00 0.00 36.72 3.18
600 613 7.174107 TCTTACCACACTTATGTTACTACCC 57.826 40.000 0.00 0.00 36.72 3.69
601 614 6.725369 TCTTACCACACTTATGTTACTACCCA 59.275 38.462 0.00 0.00 36.72 4.51
602 615 5.156608 ACCACACTTATGTTACTACCCAC 57.843 43.478 0.00 0.00 36.72 4.61
603 616 4.842380 ACCACACTTATGTTACTACCCACT 59.158 41.667 0.00 0.00 36.72 4.00
604 617 6.018469 ACCACACTTATGTTACTACCCACTA 58.982 40.000 0.00 0.00 36.72 2.74
605 618 6.670902 ACCACACTTATGTTACTACCCACTAT 59.329 38.462 0.00 0.00 36.72 2.12
606 619 6.984474 CCACACTTATGTTACTACCCACTATG 59.016 42.308 0.00 0.00 36.72 2.23
607 620 7.147794 CCACACTTATGTTACTACCCACTATGA 60.148 40.741 0.00 0.00 36.72 2.15
608 621 8.255206 CACACTTATGTTACTACCCACTATGAA 58.745 37.037 0.00 0.00 36.72 2.57
609 622 8.989131 ACACTTATGTTACTACCCACTATGAAT 58.011 33.333 0.00 0.00 34.46 2.57
610 623 9.261180 CACTTATGTTACTACCCACTATGAATG 57.739 37.037 0.00 0.00 0.00 2.67
611 624 8.989131 ACTTATGTTACTACCCACTATGAATGT 58.011 33.333 0.00 0.00 0.00 2.71
623 636 9.998106 ACCCACTATGAATGTAATAACATAGTC 57.002 33.333 13.37 0.00 45.14 2.59
667 680 8.988064 ACTAGTGTATGTTACTCTTCATTGTG 57.012 34.615 0.00 0.00 34.65 3.33
668 681 8.035394 ACTAGTGTATGTTACTCTTCATTGTGG 58.965 37.037 0.00 0.00 34.65 4.17
669 682 5.643777 AGTGTATGTTACTCTTCATTGTGGC 59.356 40.000 0.00 0.00 0.00 5.01
670 683 5.643777 GTGTATGTTACTCTTCATTGTGGCT 59.356 40.000 0.00 0.00 0.00 4.75
671 684 6.816640 GTGTATGTTACTCTTCATTGTGGCTA 59.183 38.462 0.00 0.00 0.00 3.93
672 685 7.010552 GTGTATGTTACTCTTCATTGTGGCTAG 59.989 40.741 0.00 0.00 0.00 3.42
673 686 5.483685 TGTTACTCTTCATTGTGGCTAGT 57.516 39.130 0.00 0.00 0.00 2.57
674 687 5.865085 TGTTACTCTTCATTGTGGCTAGTT 58.135 37.500 0.00 0.00 0.00 2.24
675 688 6.999950 TGTTACTCTTCATTGTGGCTAGTTA 58.000 36.000 0.00 0.00 0.00 2.24
676 689 7.620880 TGTTACTCTTCATTGTGGCTAGTTAT 58.379 34.615 0.00 0.00 0.00 1.89
677 690 8.755028 TGTTACTCTTCATTGTGGCTAGTTATA 58.245 33.333 0.00 0.00 0.00 0.98
678 691 9.032420 GTTACTCTTCATTGTGGCTAGTTATAC 57.968 37.037 0.00 0.00 0.00 1.47
679 692 7.182817 ACTCTTCATTGTGGCTAGTTATACA 57.817 36.000 0.00 0.00 0.00 2.29
680 693 7.042335 ACTCTTCATTGTGGCTAGTTATACAC 58.958 38.462 0.00 0.00 0.00 2.90
681 694 6.346096 TCTTCATTGTGGCTAGTTATACACC 58.654 40.000 0.00 0.00 33.07 4.16
682 695 5.950544 TCATTGTGGCTAGTTATACACCT 57.049 39.130 0.00 0.00 33.07 4.00
683 696 7.343574 TCTTCATTGTGGCTAGTTATACACCTA 59.656 37.037 0.00 0.00 33.07 3.08
684 697 7.050970 TCATTGTGGCTAGTTATACACCTAG 57.949 40.000 0.00 0.00 34.95 3.02
685 698 6.837048 TCATTGTGGCTAGTTATACACCTAGA 59.163 38.462 0.00 0.00 33.93 2.43
686 699 6.461110 TTGTGGCTAGTTATACACCTAGAC 57.539 41.667 0.00 0.00 39.36 2.59
687 700 4.577693 TGTGGCTAGTTATACACCTAGACG 59.422 45.833 0.00 0.00 41.39 4.18
688 701 4.023365 GTGGCTAGTTATACACCTAGACGG 60.023 50.000 0.00 0.00 41.39 4.79
689 702 4.141413 TGGCTAGTTATACACCTAGACGGA 60.141 45.833 0.00 0.00 41.39 4.69
690 703 4.455190 GGCTAGTTATACACCTAGACGGAG 59.545 50.000 0.00 0.00 33.93 4.63
691 704 4.455190 GCTAGTTATACACCTAGACGGAGG 59.545 50.000 0.00 0.00 42.89 4.30
692 705 3.830121 AGTTATACACCTAGACGGAGGG 58.170 50.000 5.42 0.00 41.36 4.30
693 706 3.461085 AGTTATACACCTAGACGGAGGGA 59.539 47.826 5.42 0.00 41.36 4.20
694 707 2.660670 ATACACCTAGACGGAGGGAG 57.339 55.000 5.42 0.78 41.36 4.30
695 708 1.293062 TACACCTAGACGGAGGGAGT 58.707 55.000 5.42 5.82 41.36 3.85
696 709 1.293062 ACACCTAGACGGAGGGAGTA 58.707 55.000 5.42 0.00 41.36 2.59
697 710 1.637553 ACACCTAGACGGAGGGAGTAA 59.362 52.381 5.42 0.00 41.36 2.24
698 711 2.299521 CACCTAGACGGAGGGAGTAAG 58.700 57.143 5.42 0.00 41.36 2.34
699 712 2.092538 CACCTAGACGGAGGGAGTAAGA 60.093 54.545 5.42 0.00 41.36 2.10
700 713 2.579860 ACCTAGACGGAGGGAGTAAGAA 59.420 50.000 5.42 0.00 41.36 2.52
701 714 3.011032 ACCTAGACGGAGGGAGTAAGAAA 59.989 47.826 5.42 0.00 41.36 2.52
702 715 4.021916 CCTAGACGGAGGGAGTAAGAAAA 58.978 47.826 0.00 0.00 32.39 2.29
703 716 4.650131 CCTAGACGGAGGGAGTAAGAAAAT 59.350 45.833 0.00 0.00 32.39 1.82
704 717 5.832060 CCTAGACGGAGGGAGTAAGAAAATA 59.168 44.000 0.00 0.00 32.39 1.40
705 718 6.323225 CCTAGACGGAGGGAGTAAGAAAATAA 59.677 42.308 0.00 0.00 32.39 1.40
706 719 6.809976 AGACGGAGGGAGTAAGAAAATAAT 57.190 37.500 0.00 0.00 0.00 1.28
707 720 7.196637 AGACGGAGGGAGTAAGAAAATAATT 57.803 36.000 0.00 0.00 0.00 1.40
708 721 8.315220 AGACGGAGGGAGTAAGAAAATAATTA 57.685 34.615 0.00 0.00 0.00 1.40
709 722 8.935741 AGACGGAGGGAGTAAGAAAATAATTAT 58.064 33.333 0.00 0.00 0.00 1.28
711 724 9.993454 ACGGAGGGAGTAAGAAAATAATTATAC 57.007 33.333 0.00 0.00 0.00 1.47
712 725 9.991906 CGGAGGGAGTAAGAAAATAATTATACA 57.008 33.333 0.00 0.00 0.00 2.29
743 756 9.167311 ACACATCTTTGTTAAGATAATCACTCC 57.833 33.333 0.46 0.00 46.83 3.85
744 757 8.616076 CACATCTTTGTTAAGATAATCACTCCC 58.384 37.037 0.46 0.00 46.83 4.30
745 758 7.495934 ACATCTTTGTTAAGATAATCACTCCCG 59.504 37.037 0.46 0.00 46.83 5.14
746 759 5.815740 TCTTTGTTAAGATAATCACTCCCGC 59.184 40.000 0.00 0.00 35.49 6.13
747 760 4.746535 TGTTAAGATAATCACTCCCGCA 57.253 40.909 0.00 0.00 0.00 5.69
748 761 5.092554 TGTTAAGATAATCACTCCCGCAA 57.907 39.130 0.00 0.00 0.00 4.85
749 762 5.492895 TGTTAAGATAATCACTCCCGCAAA 58.507 37.500 0.00 0.00 0.00 3.68
750 763 5.941058 TGTTAAGATAATCACTCCCGCAAAA 59.059 36.000 0.00 0.00 0.00 2.44
751 764 6.431543 TGTTAAGATAATCACTCCCGCAAAAA 59.568 34.615 0.00 0.00 0.00 1.94
752 765 4.965119 AGATAATCACTCCCGCAAAAAC 57.035 40.909 0.00 0.00 0.00 2.43
753 766 3.374058 AGATAATCACTCCCGCAAAAACG 59.626 43.478 0.00 0.00 0.00 3.60
754 767 0.039527 AATCACTCCCGCAAAAACGC 60.040 50.000 0.00 0.00 0.00 4.84
755 768 0.889186 ATCACTCCCGCAAAAACGCT 60.889 50.000 0.00 0.00 0.00 5.07
756 769 1.370414 CACTCCCGCAAAAACGCTG 60.370 57.895 0.00 0.00 0.00 5.18
757 770 2.429069 CTCCCGCAAAAACGCTGC 60.429 61.111 0.00 0.00 36.41 5.25
758 771 3.896863 CTCCCGCAAAAACGCTGCC 62.897 63.158 0.00 0.00 36.40 4.85
775 788 4.728095 CGCGCGCGGCACTAAAAA 62.728 61.111 43.28 0.00 43.84 1.94
803 816 5.911378 TGCATGGCATGTAAATCAGTAAA 57.089 34.783 26.94 0.00 31.71 2.01
804 817 6.468333 TGCATGGCATGTAAATCAGTAAAT 57.532 33.333 26.94 0.00 31.71 1.40
805 818 6.274579 TGCATGGCATGTAAATCAGTAAATG 58.725 36.000 26.94 0.00 31.71 2.32
806 819 5.693104 GCATGGCATGTAAATCAGTAAATGG 59.307 40.000 26.94 0.00 0.00 3.16
807 820 5.261209 TGGCATGTAAATCAGTAAATGGC 57.739 39.130 0.00 2.77 42.13 4.40
808 821 4.708909 TGGCATGTAAATCAGTAAATGGCA 59.291 37.500 7.36 7.36 46.52 4.92
809 822 5.043248 GGCATGTAAATCAGTAAATGGCAC 58.957 41.667 0.00 0.00 41.65 5.01
810 823 5.163519 GGCATGTAAATCAGTAAATGGCACT 60.164 40.000 0.00 0.00 41.65 4.40
811 824 6.332630 GCATGTAAATCAGTAAATGGCACTT 58.667 36.000 0.00 0.00 0.00 3.16
812 825 6.254157 GCATGTAAATCAGTAAATGGCACTTG 59.746 38.462 0.00 0.00 0.00 3.16
813 826 7.537715 CATGTAAATCAGTAAATGGCACTTGA 58.462 34.615 0.00 0.00 0.00 3.02
814 827 7.517614 TGTAAATCAGTAAATGGCACTTGAA 57.482 32.000 0.00 0.00 0.00 2.69
815 828 8.121305 TGTAAATCAGTAAATGGCACTTGAAT 57.879 30.769 0.00 0.00 0.00 2.57
816 829 8.243426 TGTAAATCAGTAAATGGCACTTGAATC 58.757 33.333 0.00 0.00 0.00 2.52
817 830 5.841957 ATCAGTAAATGGCACTTGAATCC 57.158 39.130 0.00 0.00 0.00 3.01
818 831 4.922206 TCAGTAAATGGCACTTGAATCCT 58.078 39.130 0.00 0.00 0.00 3.24
819 832 4.943705 TCAGTAAATGGCACTTGAATCCTC 59.056 41.667 0.00 0.00 0.00 3.71
820 833 4.701651 CAGTAAATGGCACTTGAATCCTCA 59.298 41.667 0.00 0.00 0.00 3.86
821 834 5.183713 CAGTAAATGGCACTTGAATCCTCAA 59.816 40.000 0.00 0.00 39.30 3.02
822 835 5.774690 AGTAAATGGCACTTGAATCCTCAAA 59.225 36.000 0.00 0.00 41.05 2.69
823 836 5.549742 AAATGGCACTTGAATCCTCAAAA 57.450 34.783 0.00 0.00 41.05 2.44
824 837 5.549742 AATGGCACTTGAATCCTCAAAAA 57.450 34.783 0.00 0.00 41.05 1.94
851 864 2.318578 CGGCACTCGTCGTAGTAAAAA 58.681 47.619 0.00 0.00 34.87 1.94
864 877 7.163520 CGTCGTAGTAAAAATATGCAAATGGTG 59.836 37.037 0.00 0.00 0.00 4.17
873 886 2.428902 CAAATGGTGCGTGCCACG 60.429 61.111 13.95 13.95 45.62 4.94
874 887 2.593148 AAATGGTGCGTGCCACGA 60.593 55.556 23.33 3.12 46.05 4.35
875 888 2.616330 AAATGGTGCGTGCCACGAG 61.616 57.895 23.33 0.00 46.05 4.18
876 889 3.529341 AATGGTGCGTGCCACGAGA 62.529 57.895 23.33 2.96 46.05 4.04
877 890 3.939837 ATGGTGCGTGCCACGAGAG 62.940 63.158 23.33 0.00 46.05 3.20
878 891 4.357947 GGTGCGTGCCACGAGAGA 62.358 66.667 23.33 0.00 46.05 3.10
879 892 2.355837 GTGCGTGCCACGAGAGAA 60.356 61.111 23.33 0.00 46.05 2.87
896 913 0.463654 GAACGGTGATGCTGGCCATA 60.464 55.000 5.51 0.00 33.29 2.74
986 1011 4.753516 TCCTTGATTAATCAGCCGAGAA 57.246 40.909 17.28 1.35 38.19 2.87
1362 1398 2.126031 GTGACGTTCGGCCTCCTC 60.126 66.667 0.00 0.00 0.00 3.71
1474 1510 2.913578 ACGGCGGTCACCACTACA 60.914 61.111 13.24 0.00 0.00 2.74
1743 1779 2.280321 GCCGTGGTGTACAACGGT 60.280 61.111 30.04 0.00 42.15 4.83
1897 1971 1.027357 ACTTCCATCCATTGATGCGC 58.973 50.000 0.00 0.00 45.86 6.09
1943 2017 8.083828 AGGTGAGATCCACATTATATATGGAC 57.916 38.462 13.95 2.12 45.15 4.02
2136 2302 3.149196 TGCTTGTGTTCTCCCTGAATTC 58.851 45.455 0.00 0.00 36.99 2.17
2198 2532 1.162698 GGGTTTTGGCTACGTTCCTC 58.837 55.000 0.00 0.00 0.00 3.71
2215 2549 1.606480 CCTCATCAGCAGTGTCACGTT 60.606 52.381 0.00 0.00 0.00 3.99
2217 2551 1.341209 TCATCAGCAGTGTCACGTTCT 59.659 47.619 0.00 0.00 0.00 3.01
2237 2575 7.382759 ACGTTCTCTACATGTTTTCTTTCTCTC 59.617 37.037 2.30 0.00 0.00 3.20
2529 2924 7.596749 AACTAATACATCAAGTGGTTTCTCG 57.403 36.000 0.00 0.00 0.00 4.04
2643 3076 5.534654 GCATGCCATACAGGGAGTAAAAATA 59.465 40.000 6.36 0.00 43.00 1.40
2674 3107 5.946298 CATGAATGGATGAAATATGGACCG 58.054 41.667 0.00 0.00 0.00 4.79
2680 3113 1.647346 TGAAATATGGACCGCACGAC 58.353 50.000 0.00 0.00 0.00 4.34
2831 3267 5.590530 TGGCGCCAAATAACTATGAATTT 57.409 34.783 30.74 0.00 0.00 1.82
2832 3268 5.347342 TGGCGCCAAATAACTATGAATTTG 58.653 37.500 30.74 0.00 40.94 2.32
2833 3269 5.126222 TGGCGCCAAATAACTATGAATTTGA 59.874 36.000 30.74 0.00 42.90 2.69
2834 3270 6.183360 TGGCGCCAAATAACTATGAATTTGAT 60.183 34.615 30.74 0.00 42.90 2.57
2835 3271 6.144402 GGCGCCAAATAACTATGAATTTGATG 59.856 38.462 24.80 3.28 42.90 3.07
2836 3272 6.697019 GCGCCAAATAACTATGAATTTGATGT 59.303 34.615 0.00 0.00 42.90 3.06
2837 3273 7.222611 GCGCCAAATAACTATGAATTTGATGTT 59.777 33.333 0.00 0.00 42.90 2.71
2838 3274 9.086336 CGCCAAATAACTATGAATTTGATGTTT 57.914 29.630 8.87 0.00 42.90 2.83
2873 3320 8.923683 CCTTTTTCACAGTTTACTACTACTAGC 58.076 37.037 0.00 0.00 34.56 3.42
2874 3321 8.511465 TTTTTCACAGTTTACTACTACTAGCG 57.489 34.615 0.00 0.00 34.56 4.26
2875 3322 5.227238 TCACAGTTTACTACTACTAGCGC 57.773 43.478 0.00 0.00 34.56 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.404137 CTTTGATGAAGACTGCGTACAAACGT 62.404 42.308 0.00 0.00 43.43 3.99
17 18 6.109908 CTTTGATGAAGACTGCGTACAAACG 61.110 44.000 0.00 0.00 43.93 3.60
18 19 4.725556 TTGATGAAGACTGCGTACAAAC 57.274 40.909 0.00 0.00 0.00 2.93
19 20 4.814234 ACTTTGATGAAGACTGCGTACAAA 59.186 37.500 0.00 0.00 38.77 2.83
20 21 4.377021 ACTTTGATGAAGACTGCGTACAA 58.623 39.130 0.00 0.00 38.77 2.41
21 22 3.987868 GACTTTGATGAAGACTGCGTACA 59.012 43.478 0.00 0.00 38.77 2.90
22 23 3.987868 TGACTTTGATGAAGACTGCGTAC 59.012 43.478 0.00 0.00 38.77 3.67
23 24 4.251543 TGACTTTGATGAAGACTGCGTA 57.748 40.909 0.00 0.00 38.77 4.42
24 25 3.111853 TGACTTTGATGAAGACTGCGT 57.888 42.857 0.00 0.00 38.77 5.24
25 26 4.260132 GCTATGACTTTGATGAAGACTGCG 60.260 45.833 0.00 0.00 38.77 5.18
26 27 4.874966 AGCTATGACTTTGATGAAGACTGC 59.125 41.667 0.00 0.00 38.77 4.40
27 28 7.264221 ACTAGCTATGACTTTGATGAAGACTG 58.736 38.462 0.00 0.00 38.77 3.51
28 29 7.416964 ACTAGCTATGACTTTGATGAAGACT 57.583 36.000 0.00 0.00 38.77 3.24
29 30 9.587772 TTAACTAGCTATGACTTTGATGAAGAC 57.412 33.333 0.00 0.00 38.77 3.01
65 66 9.554395 CTCCCAACCTTTTGTAATTATTTGTTT 57.446 29.630 0.00 0.00 0.00 2.83
66 67 8.929487 TCTCCCAACCTTTTGTAATTATTTGTT 58.071 29.630 0.00 0.00 0.00 2.83
67 68 8.485578 TCTCCCAACCTTTTGTAATTATTTGT 57.514 30.769 0.00 0.00 0.00 2.83
70 71 9.762381 TGTATCTCCCAACCTTTTGTAATTATT 57.238 29.630 0.00 0.00 0.00 1.40
71 72 9.762381 TTGTATCTCCCAACCTTTTGTAATTAT 57.238 29.630 0.00 0.00 0.00 1.28
72 73 9.016438 GTTGTATCTCCCAACCTTTTGTAATTA 57.984 33.333 0.00 0.00 36.94 1.40
73 74 7.892609 GTTGTATCTCCCAACCTTTTGTAATT 58.107 34.615 0.00 0.00 36.94 1.40
74 75 7.462571 GTTGTATCTCCCAACCTTTTGTAAT 57.537 36.000 0.00 0.00 36.94 1.89
75 76 6.887626 GTTGTATCTCCCAACCTTTTGTAA 57.112 37.500 0.00 0.00 36.94 2.41
84 85 4.820894 ACTACAGGTTGTATCTCCCAAC 57.179 45.455 0.00 0.00 41.11 3.77
85 86 5.836024 AAACTACAGGTTGTATCTCCCAA 57.164 39.130 0.00 0.00 38.29 4.12
86 87 5.546499 AGAAAACTACAGGTTGTATCTCCCA 59.454 40.000 0.00 0.00 38.29 4.37
87 88 6.051179 AGAAAACTACAGGTTGTATCTCCC 57.949 41.667 0.00 0.00 38.29 4.30
88 89 9.668497 AAATAGAAAACTACAGGTTGTATCTCC 57.332 33.333 5.85 0.00 38.29 3.71
97 98 9.892130 CCAAGATCTAAATAGAAAACTACAGGT 57.108 33.333 0.00 0.00 35.69 4.00
98 99 9.892130 ACCAAGATCTAAATAGAAAACTACAGG 57.108 33.333 0.00 0.00 35.69 4.00
104 105 9.327628 GGGAGTACCAAGATCTAAATAGAAAAC 57.672 37.037 0.00 0.00 39.85 2.43
105 106 9.280456 AGGGAGTACCAAGATCTAAATAGAAAA 57.720 33.333 0.00 0.00 43.89 2.29
106 107 8.855804 AGGGAGTACCAAGATCTAAATAGAAA 57.144 34.615 0.00 0.00 43.89 2.52
107 108 7.509659 GGAGGGAGTACCAAGATCTAAATAGAA 59.490 40.741 0.00 0.00 43.89 2.10
108 109 7.011382 GGAGGGAGTACCAAGATCTAAATAGA 58.989 42.308 0.00 0.00 43.89 1.98
109 110 6.071840 CGGAGGGAGTACCAAGATCTAAATAG 60.072 46.154 0.00 0.00 43.89 1.73
110 111 5.773680 CGGAGGGAGTACCAAGATCTAAATA 59.226 44.000 0.00 0.00 43.89 1.40
111 112 4.589374 CGGAGGGAGTACCAAGATCTAAAT 59.411 45.833 0.00 0.00 43.89 1.40
112 113 3.958798 CGGAGGGAGTACCAAGATCTAAA 59.041 47.826 0.00 0.00 43.89 1.85
113 114 3.053095 ACGGAGGGAGTACCAAGATCTAA 60.053 47.826 0.00 0.00 43.89 2.10
114 115 2.512896 ACGGAGGGAGTACCAAGATCTA 59.487 50.000 0.00 0.00 43.89 1.98
115 116 1.288335 ACGGAGGGAGTACCAAGATCT 59.712 52.381 0.00 0.00 43.89 2.75
116 117 1.682323 GACGGAGGGAGTACCAAGATC 59.318 57.143 0.00 0.00 43.89 2.75
117 118 1.288335 AGACGGAGGGAGTACCAAGAT 59.712 52.381 0.00 0.00 43.89 2.40
118 119 0.702902 AGACGGAGGGAGTACCAAGA 59.297 55.000 0.00 0.00 43.89 3.02
119 120 2.299521 CTAGACGGAGGGAGTACCAAG 58.700 57.143 0.00 0.00 43.89 3.61
157 158 9.932699 TGTTTTGAGATTATTTCGTTTTCGTAA 57.067 25.926 0.00 0.00 44.46 3.18
158 159 9.372541 GTGTTTTGAGATTATTTCGTTTTCGTA 57.627 29.630 0.00 0.00 44.46 3.43
159 160 8.126700 AGTGTTTTGAGATTATTTCGTTTTCGT 58.873 29.630 0.00 0.00 44.46 3.85
176 177 2.335316 ACCGTGGCTAAGTGTTTTGA 57.665 45.000 0.00 0.00 0.00 2.69
189 190 2.498481 TGAGGGAGTTAATGTACCGTGG 59.502 50.000 0.00 0.00 0.00 4.94
351 352 1.749033 GCGGAGGGGAAATCGAGAT 59.251 57.895 0.00 0.00 0.00 2.75
357 358 2.211468 GACCAAGGCGGAGGGGAAAT 62.211 60.000 0.00 0.00 38.63 2.17
368 369 3.660111 GTGCACCGTGACCAAGGC 61.660 66.667 5.22 0.00 32.98 4.35
393 394 4.081420 CCACTGTGGCTAGTCTAAGTCATT 60.081 45.833 14.87 0.00 32.82 2.57
411 412 6.485313 TGTTACTGTTGAAATTACTCCCACTG 59.515 38.462 0.00 0.00 0.00 3.66
423 428 4.951254 TGGACTCGATGTTACTGTTGAAA 58.049 39.130 0.00 0.00 0.00 2.69
428 433 4.175787 GAGTTGGACTCGATGTTACTGT 57.824 45.455 0.00 0.00 35.28 3.55
532 545 5.822519 GGTTATAGACTCATGTTGCATTGGA 59.177 40.000 0.00 0.00 0.00 3.53
571 584 6.818644 AGTAACATAAGTGTGGTAAGATGCAG 59.181 38.462 0.00 0.00 38.92 4.41
572 585 6.707290 AGTAACATAAGTGTGGTAAGATGCA 58.293 36.000 0.00 0.00 38.92 3.96
573 586 7.224167 GGTAGTAACATAAGTGTGGTAAGATGC 59.776 40.741 0.00 0.00 38.92 3.91
574 587 7.709613 GGGTAGTAACATAAGTGTGGTAAGATG 59.290 40.741 0.00 0.00 38.92 2.90
575 588 7.400915 TGGGTAGTAACATAAGTGTGGTAAGAT 59.599 37.037 0.00 0.00 38.92 2.40
576 589 6.725369 TGGGTAGTAACATAAGTGTGGTAAGA 59.275 38.462 0.00 0.00 38.92 2.10
577 590 6.815142 GTGGGTAGTAACATAAGTGTGGTAAG 59.185 42.308 0.00 0.00 38.92 2.34
578 591 6.497954 AGTGGGTAGTAACATAAGTGTGGTAA 59.502 38.462 0.00 0.00 38.92 2.85
579 592 6.018469 AGTGGGTAGTAACATAAGTGTGGTA 58.982 40.000 0.00 0.00 38.92 3.25
580 593 4.842380 AGTGGGTAGTAACATAAGTGTGGT 59.158 41.667 0.00 0.00 38.92 4.16
581 594 5.416271 AGTGGGTAGTAACATAAGTGTGG 57.584 43.478 0.00 0.00 38.92 4.17
582 595 7.778083 TCATAGTGGGTAGTAACATAAGTGTG 58.222 38.462 0.00 0.00 38.92 3.82
583 596 7.966339 TCATAGTGGGTAGTAACATAAGTGT 57.034 36.000 0.00 0.00 41.28 3.55
584 597 9.261180 CATTCATAGTGGGTAGTAACATAAGTG 57.739 37.037 0.00 0.00 0.00 3.16
585 598 8.989131 ACATTCATAGTGGGTAGTAACATAAGT 58.011 33.333 0.00 0.00 0.00 2.24
597 610 9.998106 GACTATGTTATTACATTCATAGTGGGT 57.002 33.333 17.43 0.00 46.89 4.51
642 655 8.035394 CCACAATGAAGAGTAACATACACTAGT 58.965 37.037 0.00 0.00 0.00 2.57
643 656 7.010552 GCCACAATGAAGAGTAACATACACTAG 59.989 40.741 0.00 0.00 0.00 2.57
644 657 6.816640 GCCACAATGAAGAGTAACATACACTA 59.183 38.462 0.00 0.00 0.00 2.74
645 658 5.643777 GCCACAATGAAGAGTAACATACACT 59.356 40.000 0.00 0.00 0.00 3.55
646 659 5.643777 AGCCACAATGAAGAGTAACATACAC 59.356 40.000 0.00 0.00 0.00 2.90
647 660 5.804639 AGCCACAATGAAGAGTAACATACA 58.195 37.500 0.00 0.00 0.00 2.29
648 661 7.042335 ACTAGCCACAATGAAGAGTAACATAC 58.958 38.462 0.00 0.00 0.00 2.39
649 662 7.182817 ACTAGCCACAATGAAGAGTAACATA 57.817 36.000 0.00 0.00 0.00 2.29
650 663 6.054860 ACTAGCCACAATGAAGAGTAACAT 57.945 37.500 0.00 0.00 0.00 2.71
651 664 5.483685 ACTAGCCACAATGAAGAGTAACA 57.516 39.130 0.00 0.00 0.00 2.41
652 665 9.032420 GTATAACTAGCCACAATGAAGAGTAAC 57.968 37.037 0.00 0.00 0.00 2.50
653 666 8.755028 TGTATAACTAGCCACAATGAAGAGTAA 58.245 33.333 0.00 0.00 0.00 2.24
654 667 8.195436 GTGTATAACTAGCCACAATGAAGAGTA 58.805 37.037 0.00 0.00 0.00 2.59
655 668 7.042335 GTGTATAACTAGCCACAATGAAGAGT 58.958 38.462 0.00 0.00 0.00 3.24
656 669 6.480320 GGTGTATAACTAGCCACAATGAAGAG 59.520 42.308 0.00 0.00 0.00 2.85
657 670 6.156256 AGGTGTATAACTAGCCACAATGAAGA 59.844 38.462 0.00 0.00 0.00 2.87
658 671 6.349300 AGGTGTATAACTAGCCACAATGAAG 58.651 40.000 0.00 0.00 0.00 3.02
659 672 6.308015 AGGTGTATAACTAGCCACAATGAA 57.692 37.500 0.00 0.00 0.00 2.57
660 673 5.950544 AGGTGTATAACTAGCCACAATGA 57.049 39.130 0.00 0.00 0.00 2.57
661 674 6.924060 GTCTAGGTGTATAACTAGCCACAATG 59.076 42.308 6.69 0.00 37.26 2.82
662 675 6.238953 CGTCTAGGTGTATAACTAGCCACAAT 60.239 42.308 6.69 0.00 37.26 2.71
663 676 5.066893 CGTCTAGGTGTATAACTAGCCACAA 59.933 44.000 6.69 0.00 37.26 3.33
664 677 4.577693 CGTCTAGGTGTATAACTAGCCACA 59.422 45.833 6.69 0.00 37.26 4.17
665 678 4.023365 CCGTCTAGGTGTATAACTAGCCAC 60.023 50.000 6.69 0.77 37.26 5.01
666 679 4.139786 CCGTCTAGGTGTATAACTAGCCA 58.860 47.826 6.69 0.00 37.26 4.75
667 680 4.392940 TCCGTCTAGGTGTATAACTAGCC 58.607 47.826 6.69 0.00 41.99 3.93
668 681 4.455190 CCTCCGTCTAGGTGTATAACTAGC 59.545 50.000 6.69 2.12 41.99 3.42
669 682 5.002516 CCCTCCGTCTAGGTGTATAACTAG 58.997 50.000 5.23 5.23 41.99 2.57
670 683 4.660303 TCCCTCCGTCTAGGTGTATAACTA 59.340 45.833 0.00 0.00 41.99 2.24
671 684 3.461085 TCCCTCCGTCTAGGTGTATAACT 59.539 47.826 0.00 0.00 41.99 2.24
672 685 3.819902 CTCCCTCCGTCTAGGTGTATAAC 59.180 52.174 0.00 0.00 41.99 1.89
673 686 3.461085 ACTCCCTCCGTCTAGGTGTATAA 59.539 47.826 0.00 0.00 41.99 0.98
674 687 3.051581 ACTCCCTCCGTCTAGGTGTATA 58.948 50.000 0.00 0.00 41.99 1.47
675 688 1.851653 ACTCCCTCCGTCTAGGTGTAT 59.148 52.381 0.00 0.00 41.99 2.29
676 689 1.293062 ACTCCCTCCGTCTAGGTGTA 58.707 55.000 0.00 0.00 41.99 2.90
677 690 1.293062 TACTCCCTCCGTCTAGGTGT 58.707 55.000 0.00 0.00 41.99 4.16
678 691 2.092538 TCTTACTCCCTCCGTCTAGGTG 60.093 54.545 0.00 0.00 41.99 4.00
679 692 2.203584 TCTTACTCCCTCCGTCTAGGT 58.796 52.381 0.00 0.00 41.99 3.08
680 693 3.294038 TTCTTACTCCCTCCGTCTAGG 57.706 52.381 0.00 0.00 42.97 3.02
681 694 5.855740 ATTTTCTTACTCCCTCCGTCTAG 57.144 43.478 0.00 0.00 0.00 2.43
682 695 7.909485 ATTATTTTCTTACTCCCTCCGTCTA 57.091 36.000 0.00 0.00 0.00 2.59
683 696 6.809976 ATTATTTTCTTACTCCCTCCGTCT 57.190 37.500 0.00 0.00 0.00 4.18
685 698 9.993454 GTATAATTATTTTCTTACTCCCTCCGT 57.007 33.333 2.68 0.00 0.00 4.69
686 699 9.991906 TGTATAATTATTTTCTTACTCCCTCCG 57.008 33.333 2.68 0.00 0.00 4.63
717 730 9.167311 GGAGTGATTATCTTAACAAAGATGTGT 57.833 33.333 10.20 0.00 40.46 3.72
718 731 8.616076 GGGAGTGATTATCTTAACAAAGATGTG 58.384 37.037 10.20 0.00 40.46 3.21
719 732 7.495934 CGGGAGTGATTATCTTAACAAAGATGT 59.504 37.037 10.20 0.61 43.14 3.06
720 733 7.519008 GCGGGAGTGATTATCTTAACAAAGATG 60.519 40.741 10.20 0.00 39.65 2.90
721 734 6.483640 GCGGGAGTGATTATCTTAACAAAGAT 59.516 38.462 5.96 5.96 41.92 2.40
722 735 5.815740 GCGGGAGTGATTATCTTAACAAAGA 59.184 40.000 0.00 0.00 0.00 2.52
723 736 5.584649 TGCGGGAGTGATTATCTTAACAAAG 59.415 40.000 0.00 0.00 0.00 2.77
724 737 5.492895 TGCGGGAGTGATTATCTTAACAAA 58.507 37.500 0.00 0.00 0.00 2.83
725 738 5.092554 TGCGGGAGTGATTATCTTAACAA 57.907 39.130 0.00 0.00 0.00 2.83
726 739 4.746535 TGCGGGAGTGATTATCTTAACA 57.253 40.909 0.00 0.00 0.00 2.41
727 740 6.431198 TTTTGCGGGAGTGATTATCTTAAC 57.569 37.500 0.00 0.00 0.00 2.01
728 741 6.402766 CGTTTTTGCGGGAGTGATTATCTTAA 60.403 38.462 0.00 0.00 0.00 1.85
729 742 5.064198 CGTTTTTGCGGGAGTGATTATCTTA 59.936 40.000 0.00 0.00 0.00 2.10
730 743 4.142687 CGTTTTTGCGGGAGTGATTATCTT 60.143 41.667 0.00 0.00 0.00 2.40
731 744 3.374058 CGTTTTTGCGGGAGTGATTATCT 59.626 43.478 0.00 0.00 0.00 1.98
732 745 3.680789 CGTTTTTGCGGGAGTGATTATC 58.319 45.455 0.00 0.00 0.00 1.75
733 746 2.159435 GCGTTTTTGCGGGAGTGATTAT 60.159 45.455 0.00 0.00 0.00 1.28
734 747 1.198178 GCGTTTTTGCGGGAGTGATTA 59.802 47.619 0.00 0.00 0.00 1.75
735 748 0.039527 GCGTTTTTGCGGGAGTGATT 60.040 50.000 0.00 0.00 0.00 2.57
736 749 0.889186 AGCGTTTTTGCGGGAGTGAT 60.889 50.000 0.00 0.00 40.67 3.06
737 750 1.525077 AGCGTTTTTGCGGGAGTGA 60.525 52.632 0.00 0.00 40.67 3.41
738 751 1.370414 CAGCGTTTTTGCGGGAGTG 60.370 57.895 0.00 0.00 40.67 3.51
739 752 3.030652 CAGCGTTTTTGCGGGAGT 58.969 55.556 0.00 0.00 40.67 3.85
740 753 2.429069 GCAGCGTTTTTGCGGGAG 60.429 61.111 0.00 0.00 40.67 4.30
741 754 3.972276 GGCAGCGTTTTTGCGGGA 61.972 61.111 0.00 0.00 42.42 5.14
758 771 4.728095 TTTTTAGTGCCGCGCGCG 62.728 61.111 43.73 43.73 44.45 6.86
781 794 5.911378 TTTACTGATTTACATGCCATGCA 57.089 34.783 4.17 0.00 44.86 3.96
782 795 5.693104 CCATTTACTGATTTACATGCCATGC 59.307 40.000 4.17 0.00 0.00 4.06
783 796 5.693104 GCCATTTACTGATTTACATGCCATG 59.307 40.000 2.40 2.40 0.00 3.66
784 797 5.363292 TGCCATTTACTGATTTACATGCCAT 59.637 36.000 0.00 0.00 0.00 4.40
785 798 4.708909 TGCCATTTACTGATTTACATGCCA 59.291 37.500 0.00 0.00 0.00 4.92
786 799 5.043248 GTGCCATTTACTGATTTACATGCC 58.957 41.667 0.00 0.00 0.00 4.40
787 800 5.894807 AGTGCCATTTACTGATTTACATGC 58.105 37.500 0.00 0.00 0.00 4.06
788 801 7.537715 TCAAGTGCCATTTACTGATTTACATG 58.462 34.615 0.00 0.00 0.00 3.21
789 802 7.701539 TCAAGTGCCATTTACTGATTTACAT 57.298 32.000 0.00 0.00 0.00 2.29
790 803 7.517614 TTCAAGTGCCATTTACTGATTTACA 57.482 32.000 0.00 0.00 0.00 2.41
791 804 7.702348 GGATTCAAGTGCCATTTACTGATTTAC 59.298 37.037 0.00 0.00 0.00 2.01
792 805 7.615365 AGGATTCAAGTGCCATTTACTGATTTA 59.385 33.333 0.00 0.00 0.00 1.40
793 806 6.438425 AGGATTCAAGTGCCATTTACTGATTT 59.562 34.615 0.00 0.00 0.00 2.17
794 807 5.954150 AGGATTCAAGTGCCATTTACTGATT 59.046 36.000 0.00 0.00 0.00 2.57
795 808 5.513233 AGGATTCAAGTGCCATTTACTGAT 58.487 37.500 0.00 0.00 0.00 2.90
796 809 4.922206 AGGATTCAAGTGCCATTTACTGA 58.078 39.130 0.00 0.00 0.00 3.41
797 810 4.701651 TGAGGATTCAAGTGCCATTTACTG 59.298 41.667 0.00 0.00 0.00 2.74
798 811 4.922206 TGAGGATTCAAGTGCCATTTACT 58.078 39.130 0.00 0.00 0.00 2.24
799 812 5.643379 TTGAGGATTCAAGTGCCATTTAC 57.357 39.130 0.00 0.00 38.37 2.01
800 813 6.662865 TTTTGAGGATTCAAGTGCCATTTA 57.337 33.333 0.00 0.00 43.76 1.40
801 814 5.549742 TTTTGAGGATTCAAGTGCCATTT 57.450 34.783 0.00 0.00 43.76 2.32
802 815 5.549742 TTTTTGAGGATTCAAGTGCCATT 57.450 34.783 0.00 0.00 43.76 3.16
831 844 1.967762 TTTTACTACGACGAGTGCCG 58.032 50.000 0.00 0.00 45.44 5.69
838 851 7.163520 CACCATTTGCATATTTTTACTACGACG 59.836 37.037 0.00 0.00 0.00 5.12
864 877 3.470567 CGTTCTCTCGTGGCACGC 61.471 66.667 33.59 17.93 42.21 5.34
869 882 1.078759 GCATCACCGTTCTCTCGTGG 61.079 60.000 0.00 0.00 0.00 4.94
873 886 1.086634 GCCAGCATCACCGTTCTCTC 61.087 60.000 0.00 0.00 0.00 3.20
874 887 1.078848 GCCAGCATCACCGTTCTCT 60.079 57.895 0.00 0.00 0.00 3.10
875 888 2.109126 GGCCAGCATCACCGTTCTC 61.109 63.158 0.00 0.00 0.00 2.87
876 889 2.045926 GGCCAGCATCACCGTTCT 60.046 61.111 0.00 0.00 0.00 3.01
877 890 0.463654 TATGGCCAGCATCACCGTTC 60.464 55.000 13.05 0.00 0.00 3.95
878 891 0.748005 GTATGGCCAGCATCACCGTT 60.748 55.000 13.05 0.00 0.00 4.44
879 892 1.153168 GTATGGCCAGCATCACCGT 60.153 57.895 13.05 0.00 0.00 4.83
925 942 3.189606 AGGAGATTGGGTGTCCATAACA 58.810 45.455 0.00 0.00 42.69 2.41
943 960 1.541015 CGATCGGCAATGATGGAAGGA 60.541 52.381 7.38 0.00 0.00 3.36
944 961 0.870393 CGATCGGCAATGATGGAAGG 59.130 55.000 7.38 0.00 0.00 3.46
945 962 1.869774 TCGATCGGCAATGATGGAAG 58.130 50.000 16.41 0.00 31.30 3.46
946 963 2.416747 GATCGATCGGCAATGATGGAA 58.583 47.619 16.41 0.00 36.80 3.53
986 1011 0.829602 AGGCATGATCGATCTCGGGT 60.830 55.000 25.02 5.74 40.29 5.28
1263 1299 4.215742 CCGAAGGCCCACGCGATA 62.216 66.667 15.93 0.00 46.14 2.92
1464 1500 0.800631 CGTAGAGCGTGTAGTGGTGA 59.199 55.000 0.00 0.00 35.54 4.02
1647 1683 3.204827 GCCATGAGCACGGCGAAT 61.205 61.111 16.62 0.00 42.97 3.34
1671 1707 2.363975 GGTGACGGGGATAGTGGCA 61.364 63.158 0.00 0.00 0.00 4.92
1692 1728 2.270850 GCTGGGTTGATGCCGGTA 59.729 61.111 1.90 0.00 0.00 4.02
1743 1779 1.691219 GTCATCCCAAGCCTTCCCA 59.309 57.895 0.00 0.00 0.00 4.37
2136 2302 3.865164 GGTTGCAAAGTCAAAGGTTTCAG 59.135 43.478 0.00 0.00 0.00 3.02
2198 2532 1.723542 GAGAACGTGACACTGCTGATG 59.276 52.381 3.68 0.00 0.00 3.07
2215 2549 7.957002 ACAGAGAGAAAGAAAACATGTAGAGA 58.043 34.615 0.00 0.00 0.00 3.10
2217 2551 7.653713 GTGACAGAGAGAAAGAAAACATGTAGA 59.346 37.037 0.00 0.00 0.00 2.59
2237 2575 0.946221 GAACAGAGGTGGCGTGACAG 60.946 60.000 0.00 0.00 0.00 3.51
2529 2924 6.620678 ACTGTTTGACATGTATATGGTTTGC 58.379 36.000 0.00 0.00 38.66 3.68
2611 3042 3.243501 CCCTGTATGGCATGCATGTAAAC 60.244 47.826 26.79 18.97 0.00 2.01
2613 3046 2.174424 TCCCTGTATGGCATGCATGTAA 59.826 45.455 26.79 16.09 0.00 2.41
2831 3267 8.690884 TGTGAAAAAGGAGAACATTAAACATCA 58.309 29.630 0.00 0.00 0.00 3.07
2832 3268 9.185192 CTGTGAAAAAGGAGAACATTAAACATC 57.815 33.333 0.00 0.00 0.00 3.06
2833 3269 8.695456 ACTGTGAAAAAGGAGAACATTAAACAT 58.305 29.630 0.00 0.00 0.00 2.71
2834 3270 8.062065 ACTGTGAAAAAGGAGAACATTAAACA 57.938 30.769 0.00 0.00 0.00 2.83
2835 3271 8.926715 AACTGTGAAAAAGGAGAACATTAAAC 57.073 30.769 0.00 0.00 0.00 2.01
2838 3274 9.403583 AGTAAACTGTGAAAAAGGAGAACATTA 57.596 29.630 0.00 0.00 0.00 1.90
2839 3275 8.293699 AGTAAACTGTGAAAAAGGAGAACATT 57.706 30.769 0.00 0.00 0.00 2.71
2840 3276 7.881775 AGTAAACTGTGAAAAAGGAGAACAT 57.118 32.000 0.00 0.00 0.00 2.71
2841 3277 8.044908 AGTAGTAAACTGTGAAAAAGGAGAACA 58.955 33.333 0.00 0.00 36.93 3.18
2850 3297 6.583806 GCGCTAGTAGTAGTAAACTGTGAAAA 59.416 38.462 0.00 0.00 39.39 2.29


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

AutoCloner maintained by Alex Coulton.