Multiple sequence alignment - TraesCS6B01G025200

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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 TraesCS6B01G025200 chr6B 100.000 3267 0 0 1 3267 15250499 15247233 0.000000e+00 6034.0
1 TraesCS6B01G025200 chr6B 82.640 2068 284 47 989 3018 670602195 670600165 0.000000e+00 1760.0
2 TraesCS6B01G025200 chr6B 83.553 1520 176 36 1782 3265 53075837 53074356 0.000000e+00 1354.0
3 TraesCS6B01G025200 chr6B 86.650 1206 152 6 956 2155 16237265 16238467 0.000000e+00 1327.0
4 TraesCS6B01G025200 chr6B 87.088 1092 134 5 1356 2442 16255614 16256703 0.000000e+00 1229.0
5 TraesCS6B01G025200 chr6B 82.806 1169 173 19 995 2156 15715201 15714054 0.000000e+00 1020.0
6 TraesCS6B01G025200 chr6B 81.910 691 72 24 2616 3265 53061128 53060450 4.800000e-148 534.0
7 TraesCS6B01G025200 chr6B 91.420 338 27 2 16 352 663118886 663119222 2.300000e-126 462.0
8 TraesCS6B01G025200 chr6B 90.476 231 22 0 3037 3267 52578439 52578209 4.100000e-79 305.0
9 TraesCS6B01G025200 chr6B 92.611 203 13 2 545 745 663127882 663128084 1.150000e-74 291.0
10 TraesCS6B01G025200 chr6B 87.248 149 15 4 3117 3263 670576486 670576340 2.020000e-37 167.0
11 TraesCS6B01G025200 chr6B 92.982 57 4 0 3209 3265 16259875 16259931 2.090000e-12 84.2
12 TraesCS6B01G025200 chr2B 89.474 2204 187 25 946 3121 89494565 89496751 0.000000e+00 2743.0
13 TraesCS6B01G025200 chr2B 82.095 1871 276 34 1263 3116 709487505 709485677 0.000000e+00 1544.0
14 TraesCS6B01G025200 chr2B 82.877 1168 176 12 995 2154 711161420 711162571 0.000000e+00 1027.0
15 TraesCS6B01G025200 chr2B 82.781 453 63 9 2006 2450 709454768 709454323 1.100000e-104 390.0
16 TraesCS6B01G025200 chr2B 77.778 540 66 34 2770 3263 800298958 800298427 1.920000e-72 283.0
17 TraesCS6B01G025200 chr6D 85.821 2137 241 40 997 3116 8578916 8576825 0.000000e+00 2211.0
18 TraesCS6B01G025200 chr6D 86.022 1209 153 12 953 2156 33895005 33896202 0.000000e+00 1282.0
19 TraesCS6B01G025200 chr6D 86.376 756 69 13 2538 3267 34019219 34019966 0.000000e+00 795.0
20 TraesCS6B01G025200 chr6D 91.946 149 12 0 3117 3265 8818100 8818248 3.300000e-50 209.0
21 TraesCS6B01G025200 chr6D 77.027 222 32 8 2878 3092 8804239 8804448 3.450000e-20 110.0
22 TraesCS6B01G025200 chr6D 77.103 214 29 12 2617 2816 7904277 7904484 4.460000e-19 106.0
23 TraesCS6B01G025200 chr6A 84.378 1229 171 17 997 2222 9350237 9351447 0.000000e+00 1186.0
24 TraesCS6B01G025200 chr6A 81.670 1042 184 6 1118 2156 9040184 9039147 0.000000e+00 859.0
25 TraesCS6B01G025200 chr6A 93.000 400 19 6 2724 3120 9366471 9366864 2.830000e-160 575.0
26 TraesCS6B01G025200 chr6A 92.992 371 22 4 2308 2675 9366103 9366472 3.710000e-149 538.0
27 TraesCS6B01G025200 chr6A 82.478 565 61 20 2717 3265 8993472 8992930 8.260000e-126 460.0
28 TraesCS6B01G025200 chr6A 94.314 299 16 1 372 669 117097002 117097300 1.070000e-124 457.0
29 TraesCS6B01G025200 chr6A 92.880 309 19 2 47 355 117096725 117097030 2.310000e-121 446.0
30 TraesCS6B01G025200 chr6A 77.929 367 54 16 2475 2820 7979720 7980080 1.540000e-48 204.0
31 TraesCS6B01G025200 chr6A 89.091 55 6 0 688 742 117097296 117097350 5.850000e-08 69.4
32 TraesCS6B01G025200 chr4A 90.629 747 42 9 1 741 168738009 168737285 0.000000e+00 966.0
33 TraesCS6B01G025200 chr5D 79.379 1416 235 35 1280 2675 42073883 42075261 0.000000e+00 944.0
34 TraesCS6B01G025200 chr5D 91.877 357 26 3 1 355 436608277 436608632 2.260000e-136 496.0
35 TraesCS6B01G025200 chr5D 83.273 550 47 19 2472 2993 499860920 499860388 6.380000e-127 464.0
36 TraesCS6B01G025200 chr5D 87.958 382 14 8 372 740 436608601 436608963 3.900000e-114 422.0
37 TraesCS6B01G025200 chrUn 78.731 1387 257 27 1231 2591 65790530 65789156 0.000000e+00 893.0
38 TraesCS6B01G025200 chrUn 96.939 98 3 0 2724 2821 65788964 65788867 7.250000e-37 165.0
39 TraesCS6B01G025200 chr2A 93.381 559 37 0 1 559 36637782 36638340 0.000000e+00 828.0
40 TraesCS6B01G025200 chr2A 96.053 76 3 0 1 76 583094802 583094877 1.230000e-24 124.0
41 TraesCS6B01G025200 chr5A 90.460 587 31 6 157 742 430501254 430501816 0.000000e+00 750.0
42 TraesCS6B01G025200 chr5A 92.979 470 29 4 1 468 430494689 430495156 0.000000e+00 682.0
43 TraesCS6B01G025200 chr5A 83.971 549 51 17 2472 2993 624201576 624201038 2.930000e-135 492.0
44 TraesCS6B01G025200 chr1B 96.765 371 12 0 372 742 677532380 677532750 1.290000e-173 619.0
45 TraesCS6B01G025200 chr1B 96.901 355 8 2 1 355 677532057 677532408 2.810000e-165 592.0
46 TraesCS6B01G025200 chr3D 88.668 503 27 14 18 519 710948 710475 1.310000e-163 586.0
47 TraesCS6B01G025200 chr3D 92.350 183 11 3 565 745 710482 710301 1.160000e-64 257.0
48 TraesCS6B01G025200 chr3D 93.651 63 4 0 680 742 30423344 30423406 9.650000e-16 95.3
49 TraesCS6B01G025200 chr7A 93.651 378 23 1 366 742 563849341 563849718 6.120000e-157 564.0
50 TraesCS6B01G025200 chr7A 94.051 353 18 2 3 355 563849026 563849375 1.730000e-147 532.0
51 TraesCS6B01G025200 chr3B 90.975 277 23 2 2167 2442 558530657 558530382 3.980000e-99 372.0
52 TraesCS6B01G025200 chr4B 93.289 149 10 0 599 747 642699853 642700001 1.530000e-53 220.0
53 TraesCS6B01G025200 chr5B 86.441 118 14 2 3117 3233 621233622 621233506 9.510000e-26 128.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G025200 chr6B 15247233 15250499 3266 True 6034.000000 6034 100.0000 1 3267 1 chr6B.!!$R1 3266
1 TraesCS6B01G025200 chr6B 670600165 670602195 2030 True 1760.000000 1760 82.6400 989 3018 1 chr6B.!!$R7 2029
2 TraesCS6B01G025200 chr6B 53074356 53075837 1481 True 1354.000000 1354 83.5530 1782 3265 1 chr6B.!!$R5 1483
3 TraesCS6B01G025200 chr6B 16237265 16238467 1202 False 1327.000000 1327 86.6500 956 2155 1 chr6B.!!$F1 1199
4 TraesCS6B01G025200 chr6B 15714054 15715201 1147 True 1020.000000 1020 82.8060 995 2156 1 chr6B.!!$R2 1161
5 TraesCS6B01G025200 chr6B 16255614 16259931 4317 False 656.600000 1229 90.0350 1356 3265 2 chr6B.!!$F4 1909
6 TraesCS6B01G025200 chr6B 53060450 53061128 678 True 534.000000 534 81.9100 2616 3265 1 chr6B.!!$R4 649
7 TraesCS6B01G025200 chr2B 89494565 89496751 2186 False 2743.000000 2743 89.4740 946 3121 1 chr2B.!!$F1 2175
8 TraesCS6B01G025200 chr2B 709485677 709487505 1828 True 1544.000000 1544 82.0950 1263 3116 1 chr2B.!!$R2 1853
9 TraesCS6B01G025200 chr2B 711161420 711162571 1151 False 1027.000000 1027 82.8770 995 2154 1 chr2B.!!$F2 1159
10 TraesCS6B01G025200 chr2B 800298427 800298958 531 True 283.000000 283 77.7780 2770 3263 1 chr2B.!!$R3 493
11 TraesCS6B01G025200 chr6D 8576825 8578916 2091 True 2211.000000 2211 85.8210 997 3116 1 chr6D.!!$R1 2119
12 TraesCS6B01G025200 chr6D 33895005 33896202 1197 False 1282.000000 1282 86.0220 953 2156 1 chr6D.!!$F4 1203
13 TraesCS6B01G025200 chr6D 34019219 34019966 747 False 795.000000 795 86.3760 2538 3267 1 chr6D.!!$F5 729
14 TraesCS6B01G025200 chr6A 9350237 9351447 1210 False 1186.000000 1186 84.3780 997 2222 1 chr6A.!!$F2 1225
15 TraesCS6B01G025200 chr6A 9039147 9040184 1037 True 859.000000 859 81.6700 1118 2156 1 chr6A.!!$R2 1038
16 TraesCS6B01G025200 chr6A 9366103 9366864 761 False 556.500000 575 92.9960 2308 3120 2 chr6A.!!$F3 812
17 TraesCS6B01G025200 chr6A 8992930 8993472 542 True 460.000000 460 82.4780 2717 3265 1 chr6A.!!$R1 548
18 TraesCS6B01G025200 chr6A 117096725 117097350 625 False 324.133333 457 92.0950 47 742 3 chr6A.!!$F4 695
19 TraesCS6B01G025200 chr4A 168737285 168738009 724 True 966.000000 966 90.6290 1 741 1 chr4A.!!$R1 740
20 TraesCS6B01G025200 chr5D 42073883 42075261 1378 False 944.000000 944 79.3790 1280 2675 1 chr5D.!!$F1 1395
21 TraesCS6B01G025200 chr5D 499860388 499860920 532 True 464.000000 464 83.2730 2472 2993 1 chr5D.!!$R1 521
22 TraesCS6B01G025200 chr5D 436608277 436608963 686 False 459.000000 496 89.9175 1 740 2 chr5D.!!$F2 739
23 TraesCS6B01G025200 chrUn 65788867 65790530 1663 True 529.000000 893 87.8350 1231 2821 2 chrUn.!!$R1 1590
24 TraesCS6B01G025200 chr2A 36637782 36638340 558 False 828.000000 828 93.3810 1 559 1 chr2A.!!$F1 558
25 TraesCS6B01G025200 chr5A 430501254 430501816 562 False 750.000000 750 90.4600 157 742 1 chr5A.!!$F2 585
26 TraesCS6B01G025200 chr5A 624201038 624201576 538 True 492.000000 492 83.9710 2472 2993 1 chr5A.!!$R1 521
27 TraesCS6B01G025200 chr1B 677532057 677532750 693 False 605.500000 619 96.8330 1 742 2 chr1B.!!$F1 741
28 TraesCS6B01G025200 chr3D 710301 710948 647 True 421.500000 586 90.5090 18 745 2 chr3D.!!$R1 727
29 TraesCS6B01G025200 chr7A 563849026 563849718 692 False 548.000000 564 93.8510 3 742 2 chr7A.!!$F1 739

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
689 696 0.032403 TTAATCGTGGTATCGGGCGG 59.968 55.0 0.0 0.0 0.0 6.13 F
851 858 0.036294 GGGCTGTACTTGGACCAGAC 60.036 60.0 0.0 0.0 33.3 3.51 F
852 859 0.036294 GGCTGTACTTGGACCAGACC 60.036 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2332 1.683385 CCATAGTCATCAGCGAGGTGA 59.317 52.381 7.46 7.46 0.00 4.02 R
2249 2507 4.841246 ACTCTCCTAGTTCCAAGATGTGTT 59.159 41.667 0.00 0.00 33.35 3.32 R
2314 2574 6.340962 ACAGAGTGTGCACAAATACTACTA 57.659 37.500 23.59 0.00 0.00 1.82 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
207 210 1.248785 GGTAGTCGTCTCCAGCACCA 61.249 60.000 0.00 0.00 0.00 4.17
368 371 3.488090 GGCTACGAACGGCAGCAC 61.488 66.667 18.88 9.17 37.02 4.40
370 373 2.261671 CTACGAACGGCAGCACCT 59.738 61.111 0.00 0.00 35.61 4.00
567 574 2.250939 TGCTTCAACCTTGGTCGCG 61.251 57.895 0.00 0.00 0.00 5.87
599 606 2.801162 CGTCAGACGTCGCTGTGG 60.801 66.667 15.21 0.00 36.74 4.17
600 607 3.106407 GTCAGACGTCGCTGTGGC 61.106 66.667 10.46 0.00 37.20 5.01
601 608 4.357947 TCAGACGTCGCTGTGGCC 62.358 66.667 10.46 0.00 37.20 5.36
609 616 4.041917 CGCTGTGGCCGTTGCAAT 62.042 61.111 0.59 0.00 40.13 3.56
610 617 2.339712 GCTGTGGCCGTTGCAATT 59.660 55.556 0.59 0.00 40.13 2.32
611 618 1.300853 GCTGTGGCCGTTGCAATTT 60.301 52.632 0.59 0.00 40.13 1.82
612 619 0.879839 GCTGTGGCCGTTGCAATTTT 60.880 50.000 0.59 0.00 40.13 1.82
613 620 0.860533 CTGTGGCCGTTGCAATTTTG 59.139 50.000 0.59 0.00 40.13 2.44
614 621 0.461548 TGTGGCCGTTGCAATTTTGA 59.538 45.000 0.59 0.00 40.13 2.69
615 622 1.069823 TGTGGCCGTTGCAATTTTGAT 59.930 42.857 0.59 0.00 40.13 2.57
616 623 1.726248 GTGGCCGTTGCAATTTTGATC 59.274 47.619 0.59 0.00 40.13 2.92
617 624 0.991344 GGCCGTTGCAATTTTGATCG 59.009 50.000 0.59 0.00 40.13 3.69
618 625 0.991344 GCCGTTGCAATTTTGATCGG 59.009 50.000 15.73 15.73 38.84 4.18
619 626 1.402194 GCCGTTGCAATTTTGATCGGA 60.402 47.619 22.15 0.00 38.46 4.55
620 627 2.518949 CCGTTGCAATTTTGATCGGAG 58.481 47.619 15.13 0.00 38.46 4.63
621 628 2.518949 CGTTGCAATTTTGATCGGAGG 58.481 47.619 0.59 0.00 0.00 4.30
622 629 2.731968 CGTTGCAATTTTGATCGGAGGG 60.732 50.000 0.59 0.00 0.00 4.30
623 630 1.473258 TGCAATTTTGATCGGAGGGG 58.527 50.000 0.00 0.00 0.00 4.79
624 631 1.005332 TGCAATTTTGATCGGAGGGGA 59.995 47.619 0.00 0.00 0.00 4.81
625 632 2.099405 GCAATTTTGATCGGAGGGGAA 58.901 47.619 0.00 0.00 0.00 3.97
626 633 2.159240 GCAATTTTGATCGGAGGGGAAC 60.159 50.000 0.00 0.00 0.00 3.62
627 634 3.088532 CAATTTTGATCGGAGGGGAACA 58.911 45.455 0.00 0.00 0.00 3.18
628 635 2.961531 TTTTGATCGGAGGGGAACAA 57.038 45.000 0.00 0.00 0.00 2.83
629 636 2.194201 TTTGATCGGAGGGGAACAAC 57.806 50.000 0.00 0.00 29.84 3.32
630 637 0.326927 TTGATCGGAGGGGAACAACC 59.673 55.000 0.00 0.00 38.08 3.77
631 638 0.838554 TGATCGGAGGGGAACAACCA 60.839 55.000 0.00 0.00 41.20 3.67
632 639 0.107654 GATCGGAGGGGAACAACCAG 60.108 60.000 0.00 0.00 41.20 4.00
633 640 1.562672 ATCGGAGGGGAACAACCAGG 61.563 60.000 0.00 0.00 41.20 4.45
634 641 2.221299 CGGAGGGGAACAACCAGGA 61.221 63.158 0.00 0.00 41.20 3.86
635 642 1.685820 GGAGGGGAACAACCAGGAG 59.314 63.158 0.00 0.00 41.20 3.69
636 643 1.685820 GAGGGGAACAACCAGGAGG 59.314 63.158 0.00 0.00 41.20 4.30
637 644 0.840722 GAGGGGAACAACCAGGAGGA 60.841 60.000 0.00 0.00 41.20 3.71
638 645 0.842467 AGGGGAACAACCAGGAGGAG 60.842 60.000 0.00 0.00 41.20 3.69
639 646 1.685820 GGGAACAACCAGGAGGAGG 59.314 63.158 0.00 0.00 41.20 4.30
640 647 0.840722 GGGAACAACCAGGAGGAGGA 60.841 60.000 0.00 0.00 41.20 3.71
641 648 0.325272 GGAACAACCAGGAGGAGGAC 59.675 60.000 0.00 0.00 38.69 3.85
642 649 0.037232 GAACAACCAGGAGGAGGACG 60.037 60.000 0.00 0.00 38.69 4.79
643 650 0.471211 AACAACCAGGAGGAGGACGA 60.471 55.000 0.00 0.00 38.69 4.20
644 651 0.471211 ACAACCAGGAGGAGGACGAA 60.471 55.000 0.00 0.00 38.69 3.85
645 652 0.247736 CAACCAGGAGGAGGACGAAG 59.752 60.000 0.00 0.00 38.69 3.79
646 653 1.545706 AACCAGGAGGAGGACGAAGC 61.546 60.000 0.00 0.00 38.69 3.86
647 654 1.984570 CCAGGAGGAGGACGAAGCA 60.985 63.158 0.00 0.00 36.89 3.91
648 655 1.544825 CCAGGAGGAGGACGAAGCAA 61.545 60.000 0.00 0.00 36.89 3.91
649 656 0.108424 CAGGAGGAGGACGAAGCAAG 60.108 60.000 0.00 0.00 0.00 4.01
650 657 1.219393 GGAGGAGGACGAAGCAAGG 59.781 63.158 0.00 0.00 0.00 3.61
651 658 1.219393 GAGGAGGACGAAGCAAGGG 59.781 63.158 0.00 0.00 0.00 3.95
652 659 2.245438 GAGGAGGACGAAGCAAGGGG 62.245 65.000 0.00 0.00 0.00 4.79
653 660 2.269241 GAGGACGAAGCAAGGGGG 59.731 66.667 0.00 0.00 0.00 5.40
654 661 2.529389 AGGACGAAGCAAGGGGGT 60.529 61.111 0.00 0.00 0.00 4.95
655 662 2.046217 GGACGAAGCAAGGGGGTC 60.046 66.667 0.00 0.00 0.00 4.46
656 663 2.747686 GACGAAGCAAGGGGGTCA 59.252 61.111 0.00 0.00 0.00 4.02
657 664 1.072505 GACGAAGCAAGGGGGTCAA 59.927 57.895 0.00 0.00 0.00 3.18
658 665 0.536460 GACGAAGCAAGGGGGTCAAA 60.536 55.000 0.00 0.00 0.00 2.69
659 666 0.112412 ACGAAGCAAGGGGGTCAAAT 59.888 50.000 0.00 0.00 0.00 2.32
660 667 0.811281 CGAAGCAAGGGGGTCAAATC 59.189 55.000 0.00 0.00 0.00 2.17
661 668 1.614317 CGAAGCAAGGGGGTCAAATCT 60.614 52.381 0.00 0.00 0.00 2.40
662 669 1.821136 GAAGCAAGGGGGTCAAATCTG 59.179 52.381 0.00 0.00 0.00 2.90
663 670 1.075601 AGCAAGGGGGTCAAATCTGA 58.924 50.000 0.00 0.00 0.00 3.27
675 682 5.396750 GTCAAATCTGACGGCTCTTAATC 57.603 43.478 0.00 0.00 42.54 1.75
676 683 4.026475 GTCAAATCTGACGGCTCTTAATCG 60.026 45.833 0.00 0.00 42.54 3.34
677 684 3.802948 AATCTGACGGCTCTTAATCGT 57.197 42.857 0.00 0.00 39.99 3.73
678 685 2.561733 TCTGACGGCTCTTAATCGTG 57.438 50.000 0.00 0.00 37.25 4.35
679 686 1.134367 TCTGACGGCTCTTAATCGTGG 59.866 52.381 0.00 0.00 37.25 4.94
680 687 0.892755 TGACGGCTCTTAATCGTGGT 59.107 50.000 0.00 0.00 37.25 4.16
681 688 2.093890 TGACGGCTCTTAATCGTGGTA 58.906 47.619 0.00 0.00 37.25 3.25
682 689 2.691526 TGACGGCTCTTAATCGTGGTAT 59.308 45.455 0.00 0.00 37.25 2.73
683 690 3.243301 TGACGGCTCTTAATCGTGGTATC 60.243 47.826 0.00 0.00 37.25 2.24
684 691 2.287427 ACGGCTCTTAATCGTGGTATCG 60.287 50.000 0.00 0.00 35.70 2.92
685 692 2.673833 GGCTCTTAATCGTGGTATCGG 58.326 52.381 0.00 0.00 0.00 4.18
686 693 2.609737 GGCTCTTAATCGTGGTATCGGG 60.610 54.545 0.00 0.00 0.00 5.14
687 694 2.673833 CTCTTAATCGTGGTATCGGGC 58.326 52.381 0.00 0.00 0.00 6.13
688 695 1.001048 TCTTAATCGTGGTATCGGGCG 60.001 52.381 0.00 0.00 0.00 6.13
689 696 0.032403 TTAATCGTGGTATCGGGCGG 59.968 55.000 0.00 0.00 0.00 6.13
690 697 2.424705 TAATCGTGGTATCGGGCGGC 62.425 60.000 0.00 0.00 0.00 6.53
693 700 4.910585 GTGGTATCGGGCGGCTGG 62.911 72.222 18.83 6.08 0.00 4.85
775 782 9.705290 AAAAACACTAAAAACTCAACTGAACAT 57.295 25.926 0.00 0.00 0.00 2.71
776 783 8.687824 AAACACTAAAAACTCAACTGAACATG 57.312 30.769 0.00 0.00 0.00 3.21
777 784 7.391148 ACACTAAAAACTCAACTGAACATGT 57.609 32.000 0.00 0.00 0.00 3.21
778 785 7.250569 ACACTAAAAACTCAACTGAACATGTG 58.749 34.615 0.00 0.00 0.00 3.21
779 786 7.094377 ACACTAAAAACTCAACTGAACATGTGT 60.094 33.333 0.00 0.00 0.00 3.72
780 787 7.429340 CACTAAAAACTCAACTGAACATGTGTC 59.571 37.037 0.00 0.00 0.00 3.67
781 788 5.895636 AAAACTCAACTGAACATGTGTCA 57.104 34.783 0.00 4.88 0.00 3.58
782 789 4.882671 AACTCAACTGAACATGTGTCAC 57.117 40.909 0.00 0.00 0.00 3.67
783 790 4.142609 ACTCAACTGAACATGTGTCACT 57.857 40.909 0.00 0.00 0.00 3.41
784 791 4.122776 ACTCAACTGAACATGTGTCACTC 58.877 43.478 0.00 0.00 0.00 3.51
785 792 4.141846 ACTCAACTGAACATGTGTCACTCT 60.142 41.667 0.00 0.00 0.00 3.24
786 793 5.069119 ACTCAACTGAACATGTGTCACTCTA 59.931 40.000 0.00 0.00 0.00 2.43
787 794 5.912892 TCAACTGAACATGTGTCACTCTAA 58.087 37.500 0.00 0.00 0.00 2.10
788 795 6.524734 TCAACTGAACATGTGTCACTCTAAT 58.475 36.000 0.00 0.00 0.00 1.73
789 796 6.646653 TCAACTGAACATGTGTCACTCTAATC 59.353 38.462 0.00 0.00 0.00 1.75
790 797 6.352016 ACTGAACATGTGTCACTCTAATCT 57.648 37.500 0.00 0.00 0.00 2.40
791 798 6.763355 ACTGAACATGTGTCACTCTAATCTT 58.237 36.000 0.00 0.00 0.00 2.40
792 799 6.648310 ACTGAACATGTGTCACTCTAATCTTG 59.352 38.462 0.00 0.00 0.00 3.02
793 800 6.524734 TGAACATGTGTCACTCTAATCTTGT 58.475 36.000 0.00 0.00 0.00 3.16
794 801 6.646653 TGAACATGTGTCACTCTAATCTTGTC 59.353 38.462 0.00 0.00 0.00 3.18
795 802 6.101650 ACATGTGTCACTCTAATCTTGTCA 57.898 37.500 0.00 0.00 0.00 3.58
796 803 6.524734 ACATGTGTCACTCTAATCTTGTCAA 58.475 36.000 0.00 0.00 0.00 3.18
797 804 7.164122 ACATGTGTCACTCTAATCTTGTCAAT 58.836 34.615 0.00 0.00 0.00 2.57
798 805 7.663081 ACATGTGTCACTCTAATCTTGTCAATT 59.337 33.333 0.00 0.00 0.00 2.32
799 806 8.509690 CATGTGTCACTCTAATCTTGTCAATTT 58.490 33.333 4.27 0.00 0.00 1.82
800 807 8.450578 TGTGTCACTCTAATCTTGTCAATTTT 57.549 30.769 4.27 0.00 0.00 1.82
801 808 9.554395 TGTGTCACTCTAATCTTGTCAATTTTA 57.446 29.630 4.27 0.00 0.00 1.52
804 811 9.495754 GTCACTCTAATCTTGTCAATTTTATGC 57.504 33.333 0.00 0.00 0.00 3.14
805 812 9.230122 TCACTCTAATCTTGTCAATTTTATGCA 57.770 29.630 0.00 0.00 0.00 3.96
806 813 9.844790 CACTCTAATCTTGTCAATTTTATGCAA 57.155 29.630 0.00 0.00 0.00 4.08
812 819 8.712285 ATCTTGTCAATTTTATGCAAGAATGG 57.288 30.769 8.95 0.00 41.81 3.16
813 820 7.098477 TCTTGTCAATTTTATGCAAGAATGGG 58.902 34.615 0.00 0.00 38.87 4.00
814 821 6.602410 TGTCAATTTTATGCAAGAATGGGA 57.398 33.333 0.00 0.00 0.00 4.37
815 822 6.632909 TGTCAATTTTATGCAAGAATGGGAG 58.367 36.000 0.00 0.00 0.00 4.30
816 823 5.521372 GTCAATTTTATGCAAGAATGGGAGC 59.479 40.000 0.00 0.00 0.00 4.70
817 824 4.677673 ATTTTATGCAAGAATGGGAGCC 57.322 40.909 0.00 0.00 0.00 4.70
818 825 2.824689 TTATGCAAGAATGGGAGCCA 57.175 45.000 0.00 0.00 38.19 4.75
819 826 2.057137 TATGCAAGAATGGGAGCCAC 57.943 50.000 0.00 0.00 35.80 5.01
820 827 0.333993 ATGCAAGAATGGGAGCCACT 59.666 50.000 0.00 0.00 35.80 4.00
821 828 0.112995 TGCAAGAATGGGAGCCACTT 59.887 50.000 0.00 0.00 35.80 3.16
822 829 0.529378 GCAAGAATGGGAGCCACTTG 59.471 55.000 0.00 0.00 39.26 3.16
823 830 1.180029 CAAGAATGGGAGCCACTTGG 58.820 55.000 0.00 0.00 35.38 3.61
824 831 0.040204 AAGAATGGGAGCCACTTGGG 59.960 55.000 0.00 0.00 35.80 4.12
840 847 4.803908 GGCTGGGCTGGGCTGTAC 62.804 72.222 0.00 0.00 0.00 2.90
841 848 3.721706 GCTGGGCTGGGCTGTACT 61.722 66.667 0.00 0.00 0.00 2.73
842 849 3.081554 CTGGGCTGGGCTGTACTT 58.918 61.111 0.00 0.00 0.00 2.24
843 850 1.377725 CTGGGCTGGGCTGTACTTG 60.378 63.158 0.00 0.00 0.00 3.16
844 851 2.044946 GGGCTGGGCTGTACTTGG 60.045 66.667 0.00 0.00 0.00 3.61
845 852 2.602676 GGGCTGGGCTGTACTTGGA 61.603 63.158 0.00 0.00 0.00 3.53
846 853 1.377333 GGCTGGGCTGTACTTGGAC 60.377 63.158 0.00 0.00 0.00 4.02
847 854 1.377333 GCTGGGCTGTACTTGGACC 60.377 63.158 0.00 0.00 0.00 4.46
848 855 2.066340 CTGGGCTGTACTTGGACCA 58.934 57.895 8.04 8.04 38.46 4.02
849 856 2.066340 TGGGCTGTACTTGGACCAG 58.934 57.895 4.87 0.00 35.41 4.00
850 857 0.472925 TGGGCTGTACTTGGACCAGA 60.473 55.000 4.87 0.00 35.41 3.86
851 858 0.036294 GGGCTGTACTTGGACCAGAC 60.036 60.000 0.00 0.00 33.30 3.51
852 859 0.036294 GGCTGTACTTGGACCAGACC 60.036 60.000 0.00 0.00 0.00 3.85
853 860 0.685097 GCTGTACTTGGACCAGACCA 59.315 55.000 0.00 0.00 38.24 4.02
854 861 1.608283 GCTGTACTTGGACCAGACCAC 60.608 57.143 0.00 0.00 39.85 4.16
855 862 1.002087 CTGTACTTGGACCAGACCACC 59.998 57.143 0.00 0.00 39.85 4.61
856 863 1.053424 GTACTTGGACCAGACCACCA 58.947 55.000 0.00 0.00 39.85 4.17
857 864 1.418637 GTACTTGGACCAGACCACCAA 59.581 52.381 0.00 0.00 39.85 3.67
858 865 0.923358 ACTTGGACCAGACCACCAAA 59.077 50.000 0.00 0.00 42.02 3.28
859 866 1.318576 CTTGGACCAGACCACCAAAC 58.681 55.000 0.00 0.00 42.02 2.93
860 867 0.106419 TTGGACCAGACCACCAAACC 60.106 55.000 0.00 0.00 40.12 3.27
861 868 1.282653 TGGACCAGACCACCAAACCA 61.283 55.000 0.00 0.00 34.77 3.67
862 869 0.106419 GGACCAGACCACCAAACCAA 60.106 55.000 0.00 0.00 0.00 3.67
863 870 1.029681 GACCAGACCACCAAACCAAC 58.970 55.000 0.00 0.00 0.00 3.77
864 871 0.396556 ACCAGACCACCAAACCAACC 60.397 55.000 0.00 0.00 0.00 3.77
865 872 0.396417 CCAGACCACCAAACCAACCA 60.396 55.000 0.00 0.00 0.00 3.67
866 873 0.744281 CAGACCACCAAACCAACCAC 59.256 55.000 0.00 0.00 0.00 4.16
867 874 0.750182 AGACCACCAAACCAACCACG 60.750 55.000 0.00 0.00 0.00 4.94
868 875 1.730451 GACCACCAAACCAACCACGG 61.730 60.000 0.00 0.00 0.00 4.94
869 876 1.454111 CCACCAAACCAACCACGGA 60.454 57.895 0.00 0.00 0.00 4.69
870 877 1.038130 CCACCAAACCAACCACGGAA 61.038 55.000 0.00 0.00 0.00 4.30
871 878 0.818296 CACCAAACCAACCACGGAAA 59.182 50.000 0.00 0.00 0.00 3.13
872 879 1.410882 CACCAAACCAACCACGGAAAT 59.589 47.619 0.00 0.00 0.00 2.17
873 880 1.684450 ACCAAACCAACCACGGAAATC 59.316 47.619 0.00 0.00 0.00 2.17
874 881 1.683917 CCAAACCAACCACGGAAATCA 59.316 47.619 0.00 0.00 0.00 2.57
875 882 2.298729 CCAAACCAACCACGGAAATCAT 59.701 45.455 0.00 0.00 0.00 2.45
876 883 3.574614 CAAACCAACCACGGAAATCATC 58.425 45.455 0.00 0.00 0.00 2.92
877 884 1.834188 ACCAACCACGGAAATCATCC 58.166 50.000 0.00 0.00 45.57 3.51
878 885 1.102978 CCAACCACGGAAATCATCCC 58.897 55.000 0.00 0.00 46.39 3.85
879 886 1.615651 CCAACCACGGAAATCATCCCA 60.616 52.381 0.00 0.00 46.39 4.37
880 887 2.378038 CAACCACGGAAATCATCCCAT 58.622 47.619 0.00 0.00 46.39 4.00
881 888 2.760092 CAACCACGGAAATCATCCCATT 59.240 45.455 0.00 0.00 46.39 3.16
882 889 2.654863 ACCACGGAAATCATCCCATTC 58.345 47.619 0.00 0.00 46.39 2.67
883 890 1.956477 CCACGGAAATCATCCCATTCC 59.044 52.381 0.00 0.00 46.39 3.01
884 891 2.653726 CACGGAAATCATCCCATTCCA 58.346 47.619 4.81 0.00 46.39 3.53
885 892 3.225104 CACGGAAATCATCCCATTCCAT 58.775 45.455 4.81 0.00 46.39 3.41
886 893 3.638160 CACGGAAATCATCCCATTCCATT 59.362 43.478 4.81 0.00 46.39 3.16
887 894 3.891366 ACGGAAATCATCCCATTCCATTC 59.109 43.478 4.81 0.00 46.39 2.67
888 895 3.058016 CGGAAATCATCCCATTCCATTCG 60.058 47.826 4.81 0.00 46.39 3.34
889 896 3.256631 GGAAATCATCCCATTCCATTCGG 59.743 47.826 0.00 0.00 43.00 4.30
890 897 2.592102 ATCATCCCATTCCATTCGGG 57.408 50.000 0.00 0.00 41.76 5.14
899 906 3.786656 TCCATTCGGGATCAAGCAG 57.213 52.632 0.00 0.00 42.15 4.24
900 907 0.464373 TCCATTCGGGATCAAGCAGC 60.464 55.000 0.00 0.00 42.15 5.25
901 908 1.450531 CCATTCGGGATCAAGCAGCC 61.451 60.000 0.00 0.00 40.01 4.85
902 909 0.749091 CATTCGGGATCAAGCAGCCA 60.749 55.000 0.00 0.00 0.00 4.75
903 910 0.184451 ATTCGGGATCAAGCAGCCAT 59.816 50.000 0.00 0.00 0.00 4.40
904 911 0.464373 TTCGGGATCAAGCAGCCATC 60.464 55.000 0.00 0.00 0.00 3.51
905 912 1.895707 CGGGATCAAGCAGCCATCC 60.896 63.158 6.99 6.99 36.14 3.51
906 913 1.895707 GGGATCAAGCAGCCATCCG 60.896 63.158 8.80 0.00 37.55 4.18
907 914 1.153086 GGATCAAGCAGCCATCCGT 60.153 57.895 0.00 0.00 0.00 4.69
908 915 0.749454 GGATCAAGCAGCCATCCGTT 60.749 55.000 0.00 0.00 0.00 4.44
909 916 1.098050 GATCAAGCAGCCATCCGTTT 58.902 50.000 0.00 0.00 0.00 3.60
910 917 1.474077 GATCAAGCAGCCATCCGTTTT 59.526 47.619 0.00 0.00 0.00 2.43
911 918 0.881118 TCAAGCAGCCATCCGTTTTC 59.119 50.000 0.00 0.00 0.00 2.29
912 919 0.109132 CAAGCAGCCATCCGTTTTCC 60.109 55.000 0.00 0.00 0.00 3.13
913 920 1.250840 AAGCAGCCATCCGTTTTCCC 61.251 55.000 0.00 0.00 0.00 3.97
914 921 2.710902 GCAGCCATCCGTTTTCCCC 61.711 63.158 0.00 0.00 0.00 4.81
915 922 1.304052 CAGCCATCCGTTTTCCCCA 60.304 57.895 0.00 0.00 0.00 4.96
916 923 0.684153 CAGCCATCCGTTTTCCCCAT 60.684 55.000 0.00 0.00 0.00 4.00
917 924 0.041090 AGCCATCCGTTTTCCCCATT 59.959 50.000 0.00 0.00 0.00 3.16
918 925 0.459899 GCCATCCGTTTTCCCCATTC 59.540 55.000 0.00 0.00 0.00 2.67
919 926 1.111277 CCATCCGTTTTCCCCATTCC 58.889 55.000 0.00 0.00 0.00 3.01
920 927 1.618345 CCATCCGTTTTCCCCATTCCA 60.618 52.381 0.00 0.00 0.00 3.53
921 928 2.387757 CATCCGTTTTCCCCATTCCAT 58.612 47.619 0.00 0.00 0.00 3.41
922 929 2.137810 TCCGTTTTCCCCATTCCATC 57.862 50.000 0.00 0.00 0.00 3.51
923 930 0.738389 CCGTTTTCCCCATTCCATCG 59.262 55.000 0.00 0.00 0.00 3.84
924 931 0.100503 CGTTTTCCCCATTCCATCGC 59.899 55.000 0.00 0.00 0.00 4.58
925 932 0.459899 GTTTTCCCCATTCCATCGCC 59.540 55.000 0.00 0.00 0.00 5.54
926 933 1.034838 TTTTCCCCATTCCATCGCCG 61.035 55.000 0.00 0.00 0.00 6.46
927 934 4.562425 TCCCCATTCCATCGCCGC 62.562 66.667 0.00 0.00 0.00 6.53
959 966 4.933064 CATCCTCGCGCCTCCGTC 62.933 72.222 0.00 0.00 36.67 4.79
1041 1049 1.149782 TCCTCACCCACCTCCTCTCT 61.150 60.000 0.00 0.00 0.00 3.10
1044 1052 1.552792 CTCACCCACCTCCTCTCTTTC 59.447 57.143 0.00 0.00 0.00 2.62
1047 1055 1.617947 CCCACCTCCTCTCTTTCCGG 61.618 65.000 0.00 0.00 0.00 5.14
1048 1056 1.617947 CCACCTCCTCTCTTTCCGGG 61.618 65.000 0.00 0.00 0.00 5.73
1188 1214 2.547595 CCTCAAGGCCTCCCCCAAA 61.548 63.158 5.23 0.00 0.00 3.28
1203 1229 1.144913 CCCAAACTCTCCCACCTCAAA 59.855 52.381 0.00 0.00 0.00 2.69
1296 1439 3.480133 GTAGCCAGGGACCCGCAT 61.480 66.667 12.40 0.07 0.00 4.73
1382 1527 1.153765 CGCCTTCTGAGATCGCACA 60.154 57.895 0.00 0.00 0.00 4.57
1450 1601 1.002430 CCAAGCTTGAGTACTGCCTGA 59.998 52.381 28.05 0.00 0.00 3.86
1480 1631 1.549170 GCTCCTCCGACAACCTCTTTA 59.451 52.381 0.00 0.00 0.00 1.85
1609 1769 3.304525 GCTCTACGTACTTATGCCATCGT 60.305 47.826 0.00 0.00 35.73 3.73
1631 1791 0.671472 CTCAGCATCAGCACGGAACA 60.671 55.000 0.00 0.00 45.49 3.18
1747 1916 2.305927 GAGGAGGAAATCACCACCAAGA 59.694 50.000 0.00 0.00 41.90 3.02
1944 2194 1.453379 CAGCTTGGAGGGCAGGATG 60.453 63.158 0.00 0.00 40.87 3.51
2082 2332 1.142465 CCTCATAAGGATGCTGCACCT 59.858 52.381 3.57 11.16 46.67 4.00
2164 2414 7.921786 TTCACATGAACCAAGACTAATAAGG 57.078 36.000 0.00 0.00 0.00 2.69
2249 2507 6.115446 GTCCTTCCTCATGTTGTCATATTGA 58.885 40.000 0.00 0.00 32.47 2.57
2314 2574 8.587608 TCTGCCAATTTCTTTGAAGTATCAATT 58.412 29.630 0.00 0.00 44.70 2.32
2889 3513 0.665369 GTGGGTCTTGTGTACCGTCG 60.665 60.000 0.00 0.00 37.93 5.12
2959 3588 2.398588 GGATGGGACCATGTAGTCTGA 58.601 52.381 8.88 0.00 36.70 3.27
3109 3741 2.331893 TGCGTGCGCTTAGGCAAAT 61.332 52.632 17.49 0.00 45.93 2.32
3260 6501 0.324645 AAAGTGGCTGGGCAATAGGG 60.325 55.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 196 4.056125 CGCTGGTGCTGGAGACGA 62.056 66.667 0.00 0.00 36.97 4.20
207 210 4.756458 GCTCTGCAGGCTGACGCT 62.756 66.667 20.86 0.00 36.09 5.07
211 214 1.221021 CTCATGCTCTGCAGGCTGA 59.779 57.895 20.86 20.14 43.65 4.26
213 216 2.124653 GCTCATGCTCTGCAGGCT 60.125 61.111 22.36 9.76 43.65 4.58
368 371 4.914420 CGCTCGTAGCCTCGCAGG 62.914 72.222 2.00 0.00 38.18 4.85
388 391 3.804193 CTCAAAAGCCTCGCCGCC 61.804 66.667 0.00 0.00 0.00 6.13
456 459 1.604593 GCTCCACCCATGCAACAGT 60.605 57.895 0.00 0.00 0.00 3.55
593 600 0.879839 AAAATTGCAACGGCCACAGC 60.880 50.000 0.00 3.00 40.13 4.40
598 605 0.991344 CGATCAAAATTGCAACGGCC 59.009 50.000 0.00 0.00 40.13 6.13
599 606 0.991344 CCGATCAAAATTGCAACGGC 59.009 50.000 0.00 0.00 41.68 5.68
600 607 2.518949 CTCCGATCAAAATTGCAACGG 58.481 47.619 14.32 14.32 38.29 4.44
601 608 2.518949 CCTCCGATCAAAATTGCAACG 58.481 47.619 0.00 0.00 0.00 4.10
602 609 2.417243 CCCCTCCGATCAAAATTGCAAC 60.417 50.000 0.00 0.00 0.00 4.17
603 610 1.824230 CCCCTCCGATCAAAATTGCAA 59.176 47.619 0.00 0.00 0.00 4.08
604 611 1.005332 TCCCCTCCGATCAAAATTGCA 59.995 47.619 0.00 0.00 0.00 4.08
605 612 1.762708 TCCCCTCCGATCAAAATTGC 58.237 50.000 0.00 0.00 0.00 3.56
606 613 3.088532 TGTTCCCCTCCGATCAAAATTG 58.911 45.455 0.00 0.00 0.00 2.32
607 614 3.449746 TGTTCCCCTCCGATCAAAATT 57.550 42.857 0.00 0.00 0.00 1.82
608 615 3.089284 GTTGTTCCCCTCCGATCAAAAT 58.911 45.455 0.00 0.00 0.00 1.82
609 616 2.510613 GTTGTTCCCCTCCGATCAAAA 58.489 47.619 0.00 0.00 0.00 2.44
610 617 1.271707 GGTTGTTCCCCTCCGATCAAA 60.272 52.381 0.00 0.00 0.00 2.69
611 618 0.326927 GGTTGTTCCCCTCCGATCAA 59.673 55.000 0.00 0.00 0.00 2.57
612 619 0.838554 TGGTTGTTCCCCTCCGATCA 60.839 55.000 0.00 0.00 34.77 2.92
613 620 0.107654 CTGGTTGTTCCCCTCCGATC 60.108 60.000 0.00 0.00 34.77 3.69
614 621 1.562672 CCTGGTTGTTCCCCTCCGAT 61.563 60.000 0.00 0.00 34.77 4.18
615 622 2.221299 CCTGGTTGTTCCCCTCCGA 61.221 63.158 0.00 0.00 34.77 4.55
616 623 2.185310 CTCCTGGTTGTTCCCCTCCG 62.185 65.000 0.00 0.00 34.77 4.63
617 624 1.685820 CTCCTGGTTGTTCCCCTCC 59.314 63.158 0.00 0.00 34.77 4.30
618 625 0.840722 TCCTCCTGGTTGTTCCCCTC 60.841 60.000 0.00 0.00 34.77 4.30
619 626 0.842467 CTCCTCCTGGTTGTTCCCCT 60.842 60.000 0.00 0.00 34.77 4.79
620 627 1.685820 CTCCTCCTGGTTGTTCCCC 59.314 63.158 0.00 0.00 34.77 4.81
621 628 0.840722 TCCTCCTCCTGGTTGTTCCC 60.841 60.000 0.00 0.00 34.77 3.97
622 629 0.325272 GTCCTCCTCCTGGTTGTTCC 59.675 60.000 0.00 0.00 34.23 3.62
623 630 0.037232 CGTCCTCCTCCTGGTTGTTC 60.037 60.000 0.00 0.00 34.23 3.18
624 631 0.471211 TCGTCCTCCTCCTGGTTGTT 60.471 55.000 0.00 0.00 34.23 2.83
625 632 0.471211 TTCGTCCTCCTCCTGGTTGT 60.471 55.000 0.00 0.00 34.23 3.32
626 633 0.247736 CTTCGTCCTCCTCCTGGTTG 59.752 60.000 0.00 0.00 34.23 3.77
627 634 1.545706 GCTTCGTCCTCCTCCTGGTT 61.546 60.000 0.00 0.00 34.23 3.67
628 635 1.985116 GCTTCGTCCTCCTCCTGGT 60.985 63.158 0.00 0.00 34.23 4.00
629 636 1.544825 TTGCTTCGTCCTCCTCCTGG 61.545 60.000 0.00 0.00 0.00 4.45
630 637 0.108424 CTTGCTTCGTCCTCCTCCTG 60.108 60.000 0.00 0.00 0.00 3.86
631 638 1.261238 CCTTGCTTCGTCCTCCTCCT 61.261 60.000 0.00 0.00 0.00 3.69
632 639 1.219393 CCTTGCTTCGTCCTCCTCC 59.781 63.158 0.00 0.00 0.00 4.30
633 640 1.219393 CCCTTGCTTCGTCCTCCTC 59.781 63.158 0.00 0.00 0.00 3.71
634 641 2.294078 CCCCTTGCTTCGTCCTCCT 61.294 63.158 0.00 0.00 0.00 3.69
635 642 2.269241 CCCCTTGCTTCGTCCTCC 59.731 66.667 0.00 0.00 0.00 4.30
636 643 2.269241 CCCCCTTGCTTCGTCCTC 59.731 66.667 0.00 0.00 0.00 3.71
637 644 2.529389 ACCCCCTTGCTTCGTCCT 60.529 61.111 0.00 0.00 0.00 3.85
638 645 2.046217 GACCCCCTTGCTTCGTCC 60.046 66.667 0.00 0.00 0.00 4.79
639 646 0.536460 TTTGACCCCCTTGCTTCGTC 60.536 55.000 0.00 0.00 0.00 4.20
640 647 0.112412 ATTTGACCCCCTTGCTTCGT 59.888 50.000 0.00 0.00 0.00 3.85
641 648 0.811281 GATTTGACCCCCTTGCTTCG 59.189 55.000 0.00 0.00 0.00 3.79
642 649 1.821136 CAGATTTGACCCCCTTGCTTC 59.179 52.381 0.00 0.00 0.00 3.86
643 650 1.428912 TCAGATTTGACCCCCTTGCTT 59.571 47.619 0.00 0.00 0.00 3.91
644 651 1.075601 TCAGATTTGACCCCCTTGCT 58.924 50.000 0.00 0.00 0.00 3.91
645 652 1.177401 GTCAGATTTGACCCCCTTGC 58.823 55.000 5.05 0.00 46.47 4.01
654 661 4.112634 CGATTAAGAGCCGTCAGATTTGA 58.887 43.478 0.00 0.00 0.00 2.69
655 662 3.865745 ACGATTAAGAGCCGTCAGATTTG 59.134 43.478 0.00 0.00 29.82 2.32
656 663 3.865745 CACGATTAAGAGCCGTCAGATTT 59.134 43.478 0.00 0.00 33.96 2.17
657 664 3.448686 CACGATTAAGAGCCGTCAGATT 58.551 45.455 0.00 0.00 33.96 2.40
658 665 2.223829 CCACGATTAAGAGCCGTCAGAT 60.224 50.000 0.00 0.00 33.96 2.90
659 666 1.134367 CCACGATTAAGAGCCGTCAGA 59.866 52.381 0.00 0.00 33.96 3.27
660 667 1.135083 ACCACGATTAAGAGCCGTCAG 60.135 52.381 0.00 0.00 33.96 3.51
661 668 0.892755 ACCACGATTAAGAGCCGTCA 59.107 50.000 0.00 0.00 33.96 4.35
662 669 2.857592 TACCACGATTAAGAGCCGTC 57.142 50.000 0.00 0.00 33.96 4.79
663 670 2.287427 CGATACCACGATTAAGAGCCGT 60.287 50.000 0.00 0.00 36.95 5.68
664 671 2.316792 CGATACCACGATTAAGAGCCG 58.683 52.381 0.00 0.00 35.09 5.52
665 672 2.609737 CCCGATACCACGATTAAGAGCC 60.610 54.545 0.00 0.00 35.09 4.70
666 673 2.673833 CCCGATACCACGATTAAGAGC 58.326 52.381 0.00 0.00 35.09 4.09
667 674 2.673833 GCCCGATACCACGATTAAGAG 58.326 52.381 0.00 0.00 35.09 2.85
668 675 1.001048 CGCCCGATACCACGATTAAGA 60.001 52.381 0.00 0.00 35.09 2.10
669 676 1.415374 CGCCCGATACCACGATTAAG 58.585 55.000 0.00 0.00 35.09 1.85
670 677 0.032403 CCGCCCGATACCACGATTAA 59.968 55.000 0.00 0.00 35.09 1.40
671 678 1.661480 CCGCCCGATACCACGATTA 59.339 57.895 0.00 0.00 35.09 1.75
672 679 2.420043 CCGCCCGATACCACGATT 59.580 61.111 0.00 0.00 35.09 3.34
673 680 4.295119 GCCGCCCGATACCACGAT 62.295 66.667 0.00 0.00 35.09 3.73
676 683 4.910585 CCAGCCGCCCGATACCAC 62.911 72.222 0.00 0.00 0.00 4.16
749 756 9.705290 ATGTTCAGTTGAGTTTTTAGTGTTTTT 57.295 25.926 0.00 0.00 0.00 1.94
750 757 9.139174 CATGTTCAGTTGAGTTTTTAGTGTTTT 57.861 29.630 0.00 0.00 0.00 2.43
751 758 8.303876 ACATGTTCAGTTGAGTTTTTAGTGTTT 58.696 29.630 0.00 0.00 0.00 2.83
752 759 7.754924 CACATGTTCAGTTGAGTTTTTAGTGTT 59.245 33.333 0.00 0.00 0.00 3.32
753 760 7.094377 ACACATGTTCAGTTGAGTTTTTAGTGT 60.094 33.333 0.00 0.00 0.00 3.55
754 761 7.250569 ACACATGTTCAGTTGAGTTTTTAGTG 58.749 34.615 0.00 0.00 0.00 2.74
755 762 7.120579 TGACACATGTTCAGTTGAGTTTTTAGT 59.879 33.333 0.00 0.00 0.00 2.24
756 763 7.429340 GTGACACATGTTCAGTTGAGTTTTTAG 59.571 37.037 0.00 0.00 0.00 1.85
757 764 7.120579 AGTGACACATGTTCAGTTGAGTTTTTA 59.879 33.333 8.59 0.00 0.00 1.52
758 765 6.071952 AGTGACACATGTTCAGTTGAGTTTTT 60.072 34.615 8.59 0.00 0.00 1.94
759 766 5.415701 AGTGACACATGTTCAGTTGAGTTTT 59.584 36.000 8.59 0.00 0.00 2.43
760 767 4.943705 AGTGACACATGTTCAGTTGAGTTT 59.056 37.500 8.59 0.00 0.00 2.66
761 768 4.517285 AGTGACACATGTTCAGTTGAGTT 58.483 39.130 8.59 0.00 0.00 3.01
762 769 4.122776 GAGTGACACATGTTCAGTTGAGT 58.877 43.478 8.59 1.42 0.00 3.41
763 770 4.375272 AGAGTGACACATGTTCAGTTGAG 58.625 43.478 8.59 0.00 0.00 3.02
764 771 4.406648 AGAGTGACACATGTTCAGTTGA 57.593 40.909 8.59 0.00 0.00 3.18
765 772 6.648310 AGATTAGAGTGACACATGTTCAGTTG 59.352 38.462 8.59 0.00 0.00 3.16
766 773 6.763355 AGATTAGAGTGACACATGTTCAGTT 58.237 36.000 8.59 7.03 0.00 3.16
767 774 6.352016 AGATTAGAGTGACACATGTTCAGT 57.648 37.500 8.59 14.37 0.00 3.41
768 775 6.648310 ACAAGATTAGAGTGACACATGTTCAG 59.352 38.462 8.59 0.00 0.00 3.02
769 776 6.524734 ACAAGATTAGAGTGACACATGTTCA 58.475 36.000 8.59 0.86 0.00 3.18
770 777 6.646653 TGACAAGATTAGAGTGACACATGTTC 59.353 38.462 8.59 0.00 0.00 3.18
771 778 6.524734 TGACAAGATTAGAGTGACACATGTT 58.475 36.000 8.59 0.00 0.00 2.71
772 779 6.101650 TGACAAGATTAGAGTGACACATGT 57.898 37.500 8.59 0.00 0.00 3.21
773 780 7.606858 ATTGACAAGATTAGAGTGACACATG 57.393 36.000 8.59 0.00 0.00 3.21
774 781 8.627208 AAATTGACAAGATTAGAGTGACACAT 57.373 30.769 8.59 0.00 0.00 3.21
775 782 8.450578 AAAATTGACAAGATTAGAGTGACACA 57.549 30.769 8.59 0.00 0.00 3.72
778 785 9.495754 GCATAAAATTGACAAGATTAGAGTGAC 57.504 33.333 0.00 0.00 0.00 3.67
779 786 9.230122 TGCATAAAATTGACAAGATTAGAGTGA 57.770 29.630 0.00 0.00 0.00 3.41
780 787 9.844790 TTGCATAAAATTGACAAGATTAGAGTG 57.155 29.630 0.00 0.00 0.00 3.51
786 793 9.158233 CCATTCTTGCATAAAATTGACAAGATT 57.842 29.630 4.74 0.00 44.36 2.40
787 794 7.767198 CCCATTCTTGCATAAAATTGACAAGAT 59.233 33.333 4.74 0.00 44.36 2.40
788 795 7.039152 TCCCATTCTTGCATAAAATTGACAAGA 60.039 33.333 0.00 0.00 43.57 3.02
789 796 7.098477 TCCCATTCTTGCATAAAATTGACAAG 58.902 34.615 0.00 0.00 39.22 3.16
790 797 7.002250 TCCCATTCTTGCATAAAATTGACAA 57.998 32.000 0.00 0.00 0.00 3.18
791 798 6.602410 TCCCATTCTTGCATAAAATTGACA 57.398 33.333 0.00 0.00 0.00 3.58
792 799 5.521372 GCTCCCATTCTTGCATAAAATTGAC 59.479 40.000 0.00 0.00 0.00 3.18
793 800 5.395546 GGCTCCCATTCTTGCATAAAATTGA 60.396 40.000 0.00 0.00 0.00 2.57
794 801 4.812626 GGCTCCCATTCTTGCATAAAATTG 59.187 41.667 0.00 0.00 0.00 2.32
795 802 4.470664 TGGCTCCCATTCTTGCATAAAATT 59.529 37.500 0.00 0.00 0.00 1.82
796 803 4.032310 TGGCTCCCATTCTTGCATAAAAT 58.968 39.130 0.00 0.00 0.00 1.82
797 804 3.195396 GTGGCTCCCATTCTTGCATAAAA 59.805 43.478 0.00 0.00 35.28 1.52
798 805 2.760092 GTGGCTCCCATTCTTGCATAAA 59.240 45.455 0.00 0.00 35.28 1.40
799 806 2.025037 AGTGGCTCCCATTCTTGCATAA 60.025 45.455 0.00 0.00 35.28 1.90
800 807 1.565759 AGTGGCTCCCATTCTTGCATA 59.434 47.619 0.00 0.00 35.28 3.14
801 808 0.333993 AGTGGCTCCCATTCTTGCAT 59.666 50.000 0.00 0.00 35.28 3.96
802 809 0.112995 AAGTGGCTCCCATTCTTGCA 59.887 50.000 0.00 0.00 35.28 4.08
803 810 0.529378 CAAGTGGCTCCCATTCTTGC 59.471 55.000 2.83 0.00 33.21 4.01
804 811 1.180029 CCAAGTGGCTCCCATTCTTG 58.820 55.000 7.33 7.33 37.36 3.02
805 812 0.040204 CCCAAGTGGCTCCCATTCTT 59.960 55.000 0.00 0.00 35.28 2.52
806 813 1.693640 CCCAAGTGGCTCCCATTCT 59.306 57.895 0.00 0.00 35.28 2.40
807 814 4.344237 CCCAAGTGGCTCCCATTC 57.656 61.111 0.00 0.00 35.28 2.67
823 830 4.803908 GTACAGCCCAGCCCAGCC 62.804 72.222 0.00 0.00 0.00 4.85
824 831 3.273788 AAGTACAGCCCAGCCCAGC 62.274 63.158 0.00 0.00 0.00 4.85
825 832 1.377725 CAAGTACAGCCCAGCCCAG 60.378 63.158 0.00 0.00 0.00 4.45
826 833 2.756400 CAAGTACAGCCCAGCCCA 59.244 61.111 0.00 0.00 0.00 5.36
827 834 2.044946 CCAAGTACAGCCCAGCCC 60.045 66.667 0.00 0.00 0.00 5.19
828 835 1.377333 GTCCAAGTACAGCCCAGCC 60.377 63.158 0.00 0.00 0.00 4.85
829 836 1.377333 GGTCCAAGTACAGCCCAGC 60.377 63.158 0.00 0.00 0.00 4.85
830 837 0.036010 CTGGTCCAAGTACAGCCCAG 60.036 60.000 0.00 0.00 34.10 4.45
831 838 0.472925 TCTGGTCCAAGTACAGCCCA 60.473 55.000 0.00 0.00 32.42 5.36
832 839 0.036294 GTCTGGTCCAAGTACAGCCC 60.036 60.000 0.00 0.00 32.42 5.19
833 840 0.036294 GGTCTGGTCCAAGTACAGCC 60.036 60.000 0.00 0.00 32.42 4.85
834 841 0.685097 TGGTCTGGTCCAAGTACAGC 59.315 55.000 0.00 0.00 34.24 4.40
835 842 1.002087 GGTGGTCTGGTCCAAGTACAG 59.998 57.143 0.00 0.00 39.34 2.74
836 843 1.053424 GGTGGTCTGGTCCAAGTACA 58.947 55.000 0.00 0.00 39.34 2.90
837 844 1.053424 TGGTGGTCTGGTCCAAGTAC 58.947 55.000 0.00 0.00 39.34 2.73
838 845 1.809133 TTGGTGGTCTGGTCCAAGTA 58.191 50.000 0.00 0.00 39.34 2.24
839 846 0.923358 TTTGGTGGTCTGGTCCAAGT 59.077 50.000 0.00 0.00 41.34 3.16
840 847 1.318576 GTTTGGTGGTCTGGTCCAAG 58.681 55.000 0.00 0.00 41.34 3.61
841 848 0.106419 GGTTTGGTGGTCTGGTCCAA 60.106 55.000 0.00 0.00 39.34 3.53
842 849 1.282653 TGGTTTGGTGGTCTGGTCCA 61.283 55.000 0.00 0.00 34.85 4.02
843 850 0.106419 TTGGTTTGGTGGTCTGGTCC 60.106 55.000 0.00 0.00 0.00 4.46
844 851 1.029681 GTTGGTTTGGTGGTCTGGTC 58.970 55.000 0.00 0.00 0.00 4.02
845 852 0.396556 GGTTGGTTTGGTGGTCTGGT 60.397 55.000 0.00 0.00 0.00 4.00
846 853 0.396417 TGGTTGGTTTGGTGGTCTGG 60.396 55.000 0.00 0.00 0.00 3.86
847 854 0.744281 GTGGTTGGTTTGGTGGTCTG 59.256 55.000 0.00 0.00 0.00 3.51
848 855 0.750182 CGTGGTTGGTTTGGTGGTCT 60.750 55.000 0.00 0.00 0.00 3.85
849 856 1.730451 CCGTGGTTGGTTTGGTGGTC 61.730 60.000 0.00 0.00 0.00 4.02
850 857 1.755008 CCGTGGTTGGTTTGGTGGT 60.755 57.895 0.00 0.00 0.00 4.16
851 858 1.038130 TTCCGTGGTTGGTTTGGTGG 61.038 55.000 0.00 0.00 0.00 4.61
852 859 0.818296 TTTCCGTGGTTGGTTTGGTG 59.182 50.000 0.00 0.00 0.00 4.17
853 860 1.684450 GATTTCCGTGGTTGGTTTGGT 59.316 47.619 0.00 0.00 0.00 3.67
854 861 1.683917 TGATTTCCGTGGTTGGTTTGG 59.316 47.619 0.00 0.00 0.00 3.28
855 862 3.574614 GATGATTTCCGTGGTTGGTTTG 58.425 45.455 0.00 0.00 0.00 2.93
856 863 2.560981 GGATGATTTCCGTGGTTGGTTT 59.439 45.455 0.00 0.00 33.93 3.27
857 864 2.167662 GGATGATTTCCGTGGTTGGTT 58.832 47.619 0.00 0.00 33.93 3.67
858 865 1.615919 GGGATGATTTCCGTGGTTGGT 60.616 52.381 0.00 0.00 46.52 3.67
859 866 1.102978 GGGATGATTTCCGTGGTTGG 58.897 55.000 0.00 0.00 46.52 3.77
860 867 1.832883 TGGGATGATTTCCGTGGTTG 58.167 50.000 0.00 0.00 46.52 3.77
861 868 2.826674 ATGGGATGATTTCCGTGGTT 57.173 45.000 0.00 0.00 46.52 3.67
862 869 2.654863 GAATGGGATGATTTCCGTGGT 58.345 47.619 0.00 0.00 46.52 4.16
863 870 1.956477 GGAATGGGATGATTTCCGTGG 59.044 52.381 0.00 0.00 46.52 4.94
864 871 2.653726 TGGAATGGGATGATTTCCGTG 58.346 47.619 0.00 0.00 46.52 4.94
865 872 3.600448 ATGGAATGGGATGATTTCCGT 57.400 42.857 0.00 0.00 46.52 4.69
866 873 3.058016 CGAATGGAATGGGATGATTTCCG 60.058 47.826 0.00 0.00 46.52 4.30
867 874 3.256631 CCGAATGGAATGGGATGATTTCC 59.743 47.826 0.00 0.00 40.06 3.13
868 875 3.256631 CCCGAATGGAATGGGATGATTTC 59.743 47.826 0.00 0.00 46.41 2.17
869 876 3.117169 TCCCGAATGGAATGGGATGATTT 60.117 43.478 0.00 0.00 46.96 2.17
870 877 2.446666 TCCCGAATGGAATGGGATGATT 59.553 45.455 0.00 0.00 46.96 2.57
871 878 2.065007 TCCCGAATGGAATGGGATGAT 58.935 47.619 0.00 0.00 46.96 2.45
872 879 1.517238 TCCCGAATGGAATGGGATGA 58.483 50.000 0.00 0.00 46.96 2.92
882 889 1.450531 GGCTGCTTGATCCCGAATGG 61.451 60.000 0.00 0.00 0.00 3.16
883 890 0.749091 TGGCTGCTTGATCCCGAATG 60.749 55.000 0.00 0.00 0.00 2.67
884 891 0.184451 ATGGCTGCTTGATCCCGAAT 59.816 50.000 0.00 0.00 0.00 3.34
885 892 0.464373 GATGGCTGCTTGATCCCGAA 60.464 55.000 0.00 0.00 0.00 4.30
886 893 1.146930 GATGGCTGCTTGATCCCGA 59.853 57.895 0.00 0.00 0.00 5.14
887 894 1.895707 GGATGGCTGCTTGATCCCG 60.896 63.158 12.18 0.00 31.01 5.14
888 895 1.895707 CGGATGGCTGCTTGATCCC 60.896 63.158 15.51 3.39 33.31 3.85
889 896 0.749454 AACGGATGGCTGCTTGATCC 60.749 55.000 12.85 12.85 33.53 3.36
890 897 1.098050 AAACGGATGGCTGCTTGATC 58.902 50.000 0.00 0.00 0.00 2.92
891 898 1.474077 GAAAACGGATGGCTGCTTGAT 59.526 47.619 0.00 0.00 0.00 2.57
892 899 0.881118 GAAAACGGATGGCTGCTTGA 59.119 50.000 0.00 0.00 0.00 3.02
893 900 0.109132 GGAAAACGGATGGCTGCTTG 60.109 55.000 0.00 0.00 0.00 4.01
894 901 1.250840 GGGAAAACGGATGGCTGCTT 61.251 55.000 0.00 0.00 0.00 3.91
895 902 1.678970 GGGAAAACGGATGGCTGCT 60.679 57.895 0.00 0.00 0.00 4.24
896 903 2.710902 GGGGAAAACGGATGGCTGC 61.711 63.158 0.00 0.00 0.00 5.25
897 904 0.684153 ATGGGGAAAACGGATGGCTG 60.684 55.000 0.00 0.00 0.00 4.85
898 905 0.041090 AATGGGGAAAACGGATGGCT 59.959 50.000 0.00 0.00 0.00 4.75
899 906 0.459899 GAATGGGGAAAACGGATGGC 59.540 55.000 0.00 0.00 0.00 4.40
900 907 1.111277 GGAATGGGGAAAACGGATGG 58.889 55.000 0.00 0.00 0.00 3.51
901 908 1.846007 TGGAATGGGGAAAACGGATG 58.154 50.000 0.00 0.00 0.00 3.51
902 909 2.666317 GATGGAATGGGGAAAACGGAT 58.334 47.619 0.00 0.00 0.00 4.18
903 910 1.680555 CGATGGAATGGGGAAAACGGA 60.681 52.381 0.00 0.00 0.00 4.69
904 911 0.738389 CGATGGAATGGGGAAAACGG 59.262 55.000 0.00 0.00 0.00 4.44
905 912 0.100503 GCGATGGAATGGGGAAAACG 59.899 55.000 0.00 0.00 0.00 3.60
906 913 0.459899 GGCGATGGAATGGGGAAAAC 59.540 55.000 0.00 0.00 0.00 2.43
907 914 1.034838 CGGCGATGGAATGGGGAAAA 61.035 55.000 0.00 0.00 0.00 2.29
908 915 1.453015 CGGCGATGGAATGGGGAAA 60.453 57.895 0.00 0.00 0.00 3.13
909 916 2.191908 CGGCGATGGAATGGGGAA 59.808 61.111 0.00 0.00 0.00 3.97
910 917 4.562425 GCGGCGATGGAATGGGGA 62.562 66.667 12.98 0.00 0.00 4.81
942 949 4.933064 GACGGAGGCGCGAGGATG 62.933 72.222 12.10 0.00 0.00 3.51
969 976 2.840102 AGAGGCCGGGGAGATTCG 60.840 66.667 2.18 0.00 0.00 3.34
970 977 2.512355 GGAGAGGCCGGGGAGATTC 61.512 68.421 2.18 0.00 0.00 2.52
1041 1049 3.327404 GGAGAGGTGGCCCGGAAA 61.327 66.667 0.73 0.00 35.12 3.13
1047 1055 2.508751 GGATACGGGAGAGGTGGCC 61.509 68.421 0.00 0.00 0.00 5.36
1048 1056 2.508751 GGGATACGGGAGAGGTGGC 61.509 68.421 0.00 0.00 37.60 5.01
1102 1128 2.579738 GAAGGCGGAGACAGGGTC 59.420 66.667 0.00 0.00 39.87 4.46
1188 1214 1.290134 GGGATTTGAGGTGGGAGAGT 58.710 55.000 0.00 0.00 0.00 3.24
1309 1452 0.322008 GCCAGGGTCTTCTCCACTTG 60.322 60.000 0.00 0.00 0.00 3.16
1382 1527 4.070552 GGCCAAGCGAGACGAGGT 62.071 66.667 0.00 0.00 0.00 3.85
1402 1547 1.203928 GATCTGCGACGGAATCTGTG 58.796 55.000 0.00 0.00 0.00 3.66
1480 1631 3.397906 GCCACTCTTGAGGGCTCT 58.602 61.111 17.13 0.00 44.32 4.09
1609 1769 2.507769 CGTGCTGATGCTGAGCGA 60.508 61.111 0.00 0.00 39.47 4.93
1631 1791 2.665000 CCACTGCTGTCCGGATGT 59.335 61.111 7.81 0.00 0.00 3.06
1747 1916 5.758296 TGAACGTTTTCTTCAAGTGCTCTAT 59.242 36.000 0.46 0.00 32.36 1.98
1944 2194 2.211806 ACAGCGTAGTATCGAGGTCTC 58.788 52.381 0.00 0.00 0.00 3.36
2082 2332 1.683385 CCATAGTCATCAGCGAGGTGA 59.317 52.381 7.46 7.46 0.00 4.02
2249 2507 4.841246 ACTCTCCTAGTTCCAAGATGTGTT 59.159 41.667 0.00 0.00 33.35 3.32
2314 2574 6.340962 ACAGAGTGTGCACAAATACTACTA 57.659 37.500 23.59 0.00 0.00 1.82
2854 3467 6.760440 AGACCCACTATACTACACTAGCTA 57.240 41.667 0.00 0.00 0.00 3.32
2855 3468 5.649970 AGACCCACTATACTACACTAGCT 57.350 43.478 0.00 0.00 0.00 3.32
2856 3469 5.593502 ACAAGACCCACTATACTACACTAGC 59.406 44.000 0.00 0.00 0.00 3.42
2857 3470 6.602406 ACACAAGACCCACTATACTACACTAG 59.398 42.308 0.00 0.00 0.00 2.57
2889 3513 8.593492 ACTTCCAGATAGAAATTTGCAAAAAC 57.407 30.769 17.19 10.33 0.00 2.43
3099 3731 3.117738 AGGGACCATCTCATTTGCCTAAG 60.118 47.826 0.00 0.00 0.00 2.18
3109 3741 1.079490 ACCAGAGAAGGGACCATCTCA 59.921 52.381 21.55 0.00 42.17 3.27


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

AutoCloner maintained by Alex Coulton.