Multiple sequence alignment - TraesCS7A01G533900

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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 TraesCS7A01G533900 chr7A 100.000 4051 0 0 1 4051 712306104 712310154 0.000000e+00 7481
1 TraesCS7A01G533900 chr7A 91.733 629 49 3 1 627 144166609 144167236 0.000000e+00 870
2 TraesCS7A01G533900 chr7A 85.169 681 74 19 993 1666 692056505 692055845 0.000000e+00 673
3 TraesCS7A01G533900 chr7A 78.063 702 112 31 1001 1667 116018884 116019578 4.880000e-109 405
4 TraesCS7A01G533900 chr7A 79.644 506 82 14 1165 1666 692130740 692130252 1.080000e-90 344
5 TraesCS7A01G533900 chr7A 89.573 211 13 3 875 1076 712254017 712254227 4.020000e-65 259
6 TraesCS7A01G533900 chr7B 93.867 3783 133 42 1 3745 713098492 713102213 0.000000e+00 5609
7 TraesCS7A01G533900 chr7B 84.080 402 52 12 993 1389 679684119 679683725 1.060000e-100 377
8 TraesCS7A01G533900 chr7B 92.683 164 11 1 3872 4035 713108365 713108527 6.770000e-58 235
9 TraesCS7A01G533900 chr7D 94.485 3427 82 22 1 3386 618678603 618681963 0.000000e+00 5182
10 TraesCS7A01G533900 chr7D 78.063 702 112 31 1001 1667 110890678 110891372 4.880000e-109 405
11 TraesCS7A01G533900 chr7D 80.594 505 79 14 1165 1666 599884613 599884125 4.940000e-99 372
12 TraesCS7A01G533900 chr7D 90.521 211 11 3 875 1076 618646907 618647117 1.860000e-68 270
13 TraesCS7A01G533900 chr7D 82.237 152 16 7 938 1087 599884875 599884733 1.980000e-23 121
14 TraesCS7A01G533900 chr3B 91.547 627 51 2 1 626 27514204 27513579 0.000000e+00 863
15 TraesCS7A01G533900 chr1A 91.080 639 54 3 2 639 491375914 491376550 0.000000e+00 861
16 TraesCS7A01G533900 chr1A 85.060 502 57 11 1164 1665 541895505 541895022 2.810000e-136 496
17 TraesCS7A01G533900 chr6A 91.626 621 51 1 1 620 590371511 590370891 0.000000e+00 857
18 TraesCS7A01G533900 chr4D 91.640 622 49 3 1 620 397696618 397697238 0.000000e+00 857
19 TraesCS7A01G533900 chr2A 91.360 625 53 1 1 624 138923001 138922377 0.000000e+00 854
20 TraesCS7A01G533900 chr2A 81.836 523 71 19 1165 1667 20365664 20366182 6.260000e-113 418
21 TraesCS7A01G533900 chr2A 86.538 104 12 2 1001 1104 17300138 17300239 3.310000e-21 113
22 TraesCS7A01G533900 chr3D 91.009 634 54 3 1 631 611593541 611594174 0.000000e+00 852
23 TraesCS7A01G533900 chr1B 82.743 678 81 24 995 1665 608996442 608995794 4.540000e-159 571
24 TraesCS7A01G533900 chr1D 84.615 507 54 13 1164 1665 445642521 445642034 2.190000e-132 483
25 TraesCS7A01G533900 chrUn 82.122 509 70 15 1176 1667 266170960 266170456 2.250000e-112 416
26 TraesCS7A01G533900 chrUn 78.200 711 105 37 1001 1667 233477197 233476493 3.770000e-110 409
27 TraesCS7A01G533900 chrUn 80.153 524 81 18 1165 1667 16444032 16443511 1.780000e-98 370
28 TraesCS7A01G533900 chrUn 88.194 144 15 1 2637 2780 16613640 16613781 1.940000e-38 171
29 TraesCS7A01G533900 chrUn 85.906 149 19 1 2637 2785 266169925 266169779 1.510000e-34 158
30 TraesCS7A01G533900 chrUn 85.906 149 19 1 2637 2785 379210447 379210301 1.510000e-34 158
31 TraesCS7A01G533900 chrUn 85.906 149 19 1 2637 2785 379233678 379233532 1.510000e-34 158
32 TraesCS7A01G533900 chrUn 87.500 96 11 1 1001 1096 266171183 266171089 4.280000e-20 110
33 TraesCS7A01G533900 chr2D 82.122 509 70 14 1176 1667 15228968 15229472 2.250000e-112 416
34 TraesCS7A01G533900 chr2D 85.065 154 23 0 2619 2772 15229985 15230138 1.510000e-34 158
35 TraesCS7A01G533900 chr2D 85.065 154 23 0 2619 2772 15250788 15250941 1.510000e-34 158
36 TraesCS7A01G533900 chr2D 85.065 154 23 0 2619 2772 15265696 15265849 1.510000e-34 158
37 TraesCS7A01G533900 chr2D 84.404 109 15 2 1001 1108 19849273 19849166 5.540000e-19 106


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 TraesCS7A01G533900 chr7A 712306104 712310154 4050 False 7481.0 7481 100.0000 1 4051 1 chr7A.!!$F4 4050
1 TraesCS7A01G533900 chr7A 144166609 144167236 627 False 870.0 870 91.7330 1 627 1 chr7A.!!$F2 626
2 TraesCS7A01G533900 chr7A 692055845 692056505 660 True 673.0 673 85.1690 993 1666 1 chr7A.!!$R1 673
3 TraesCS7A01G533900 chr7A 116018884 116019578 694 False 405.0 405 78.0630 1001 1667 1 chr7A.!!$F1 666
4 TraesCS7A01G533900 chr7B 713098492 713102213 3721 False 5609.0 5609 93.8670 1 3745 1 chr7B.!!$F1 3744
5 TraesCS7A01G533900 chr7D 618678603 618681963 3360 False 5182.0 5182 94.4850 1 3386 1 chr7D.!!$F3 3385
6 TraesCS7A01G533900 chr7D 110890678 110891372 694 False 405.0 405 78.0630 1001 1667 1 chr7D.!!$F1 666
7 TraesCS7A01G533900 chr7D 599884125 599884875 750 True 246.5 372 81.4155 938 1666 2 chr7D.!!$R1 728
8 TraesCS7A01G533900 chr3B 27513579 27514204 625 True 863.0 863 91.5470 1 626 1 chr3B.!!$R1 625
9 TraesCS7A01G533900 chr1A 491375914 491376550 636 False 861.0 861 91.0800 2 639 1 chr1A.!!$F1 637
10 TraesCS7A01G533900 chr6A 590370891 590371511 620 True 857.0 857 91.6260 1 620 1 chr6A.!!$R1 619
11 TraesCS7A01G533900 chr4D 397696618 397697238 620 False 857.0 857 91.6400 1 620 1 chr4D.!!$F1 619
12 TraesCS7A01G533900 chr2A 138922377 138923001 624 True 854.0 854 91.3600 1 624 1 chr2A.!!$R1 623
13 TraesCS7A01G533900 chr2A 20365664 20366182 518 False 418.0 418 81.8360 1165 1667 1 chr2A.!!$F2 502
14 TraesCS7A01G533900 chr3D 611593541 611594174 633 False 852.0 852 91.0090 1 631 1 chr3D.!!$F1 630
15 TraesCS7A01G533900 chr1B 608995794 608996442 648 True 571.0 571 82.7430 995 1665 1 chr1B.!!$R1 670
16 TraesCS7A01G533900 chrUn 233476493 233477197 704 True 409.0 409 78.2000 1001 1667 1 chrUn.!!$R2 666
17 TraesCS7A01G533900 chrUn 16443511 16444032 521 True 370.0 370 80.1530 1165 1667 1 chrUn.!!$R1 502
18 TraesCS7A01G533900 chrUn 266169779 266171183 1404 True 228.0 416 85.1760 1001 2785 3 chrUn.!!$R5 1784
19 TraesCS7A01G533900 chr2D 15228968 15230138 1170 False 287.0 416 83.5935 1176 2772 2 chr2D.!!$F3 1596

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
283 286 0.106918 TTTGGTCGGTGCTGGTCTTT 60.107 50.0 0.00 0.0 0.00 2.52 F
1598 1769 0.176680 ACGAGAAGCGCTCCATGATT 59.823 50.0 12.06 0.0 46.04 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2077 1.068121 ACTTGGGCCAAAGAGCTAGT 58.932 50.0 27.39 9.79 0.00 2.57 R
3404 3633 0.106708 ACAACTGAGCCTCGCAGAAA 59.893 50.0 4.65 0.00 34.97 2.52 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
64 67 4.421365 GCATTTGCCTGTGGAGGA 57.579 55.556 0.00 0.00 42.93 3.71
127 130 6.542005 TGTTCTCATTTTTGCTAGACTGAACA 59.458 34.615 0.00 0.00 38.04 3.18
283 286 0.106918 TTTGGTCGGTGCTGGTCTTT 60.107 50.000 0.00 0.00 0.00 2.52
452 455 3.805422 TGTCTACTACAACAAGGTTTGCG 59.195 43.478 0.00 0.00 34.29 4.85
479 483 0.617413 GATGATGGAGGGGCGATGAT 59.383 55.000 0.00 0.00 0.00 2.45
584 588 3.070878 TGTGTTCTCTGTACTGCCATGAA 59.929 43.478 0.00 0.00 0.00 2.57
594 598 7.281841 TCTGTACTGCCATGAATGATGAATAA 58.718 34.615 0.00 0.00 33.31 1.40
1011 1047 2.982130 AGCGAGATGGTTTCCGCT 59.018 55.556 0.00 0.00 44.30 5.52
1315 1436 1.182667 TCCTCGTCGTCACCATCAAT 58.817 50.000 0.00 0.00 0.00 2.57
1394 1515 1.065358 CAACAAGCGGGTACGTACTG 58.935 55.000 24.07 16.34 43.45 2.74
1553 1724 3.387091 ATGGTGGCCGTCGTGCTA 61.387 61.111 0.00 0.00 0.00 3.49
1598 1769 0.176680 ACGAGAAGCGCTCCATGATT 59.823 50.000 12.06 0.00 46.04 2.57
1687 1858 2.626950 CCTACACCCTCCTTCCTCATGA 60.627 54.545 0.00 0.00 0.00 3.07
1844 2018 1.537348 GCATGCCGTTCTGGTCGTATA 60.537 52.381 6.36 0.00 41.21 1.47
1861 2036 8.406297 TGGTCGTATAGAGTGATAATATGCATC 58.594 37.037 0.19 0.00 0.00 3.91
1902 2077 5.005740 GGTTAATCTGCATGCATGGATCTA 58.994 41.667 27.34 13.70 0.00 1.98
2024 2215 2.880443 AGATGTTGCCTTGTGGACATT 58.120 42.857 0.00 0.00 32.83 2.71
2083 2274 4.546570 GCTTCACACACCCAAGTTATTTC 58.453 43.478 0.00 0.00 0.00 2.17
2094 2285 5.183904 ACCCAAGTTATTTCAGAAGATGCAC 59.816 40.000 0.00 0.00 0.00 4.57
2095 2286 5.183713 CCCAAGTTATTTCAGAAGATGCACA 59.816 40.000 0.00 0.00 0.00 4.57
2097 2288 5.886960 AGTTATTTCAGAAGATGCACACC 57.113 39.130 0.00 0.00 0.00 4.16
2148 2339 7.121759 AGACATCCAAGTTATTTCACAAGATGG 59.878 37.037 0.00 0.00 0.00 3.51
2426 2617 3.808174 CGAGGATGCATGCATGGATATAG 59.192 47.826 36.73 19.06 39.04 1.31
2447 2638 1.675483 TGCGTGCATGTTCTCTTTTGT 59.325 42.857 7.93 0.00 0.00 2.83
2475 2666 3.149196 TGATCCTTCACTCTTGCCAAAC 58.851 45.455 0.00 0.00 0.00 2.93
2772 2987 2.417586 TCTACGTCACGGTCAGTACATG 59.582 50.000 0.35 0.00 0.00 3.21
2845 3060 8.316214 TCTCAAACAAGTATACCGATTAAACCT 58.684 33.333 0.00 0.00 0.00 3.50
2865 3080 5.606505 ACCTAGCTAGCTAGATTTTTCTGC 58.393 41.667 40.98 6.33 46.56 4.26
2886 3101 3.805108 GCCTCATCGATCTAACTGCCATT 60.805 47.826 0.00 0.00 0.00 3.16
2930 3149 2.125269 GGCGCTTTCTTCGGCCTA 60.125 61.111 7.64 0.00 45.13 3.93
3082 3301 3.039988 CAGCAGCAGCAGCAAACT 58.960 55.556 12.92 0.00 45.49 2.66
3103 3322 1.970917 GCCGTCGCCAAGTGATTCTG 61.971 60.000 0.00 0.00 0.00 3.02
3167 3386 6.214399 AGTAGTTAAATTCCGGATGATCGAC 58.786 40.000 4.15 0.29 0.00 4.20
3193 3412 1.953559 ACAAGTGTGGTGTGCTAGTG 58.046 50.000 0.00 0.00 0.00 2.74
3194 3413 1.229428 CAAGTGTGGTGTGCTAGTGG 58.771 55.000 0.00 0.00 0.00 4.00
3195 3414 0.837272 AAGTGTGGTGTGCTAGTGGT 59.163 50.000 0.00 0.00 0.00 4.16
3241 3470 1.275657 GAGTGTGCGTTTCGTGGTG 59.724 57.895 0.00 0.00 0.00 4.17
3255 3484 3.660111 GGTGTGCCCTCGTGCAAC 61.660 66.667 0.00 0.00 44.11 4.17
3270 3499 6.142480 CCTCGTGCAACTTAGAACTATATTCG 59.858 42.308 0.00 0.00 31.75 3.34
3275 3504 6.761242 TGCAACTTAGAACTATATTCGTGCAT 59.239 34.615 0.00 0.00 0.00 3.96
3276 3505 7.065894 GCAACTTAGAACTATATTCGTGCATG 58.934 38.462 0.00 0.00 0.00 4.06
3279 3508 4.955811 AGAACTATATTCGTGCATGGGA 57.044 40.909 5.98 0.00 0.00 4.37
3283 3512 1.888215 ATATTCGTGCATGGGAGCAG 58.112 50.000 5.98 0.00 46.69 4.24
3286 3515 2.046988 CGTGCATGGGAGCAGACA 60.047 61.111 0.00 0.00 46.69 3.41
3292 3521 0.325933 CATGGGAGCAGACAGGAACA 59.674 55.000 0.00 0.00 0.00 3.18
3308 3537 9.314133 AGACAGGAACATAATATATGTAGCTGA 57.686 33.333 0.00 0.00 0.00 4.26
3358 3587 3.734776 TGTCACGTATGTGTACTCTCG 57.265 47.619 14.63 0.91 46.49 4.04
3359 3588 3.328505 TGTCACGTATGTGTACTCTCGA 58.671 45.455 14.63 0.00 46.49 4.04
3360 3589 3.937079 TGTCACGTATGTGTACTCTCGAT 59.063 43.478 14.63 0.00 46.49 3.59
3361 3590 4.033702 TGTCACGTATGTGTACTCTCGATC 59.966 45.833 14.63 0.00 46.49 3.69
3362 3591 3.244579 TCACGTATGTGTACTCTCGATCG 59.755 47.826 14.63 9.36 46.49 3.69
3387 3616 7.027760 GGAATCTATTCTTACGCGATGATACA 58.972 38.462 15.93 0.00 37.00 2.29
3392 3621 9.503427 TCTATTCTTACGCGATGATACAATATG 57.497 33.333 15.93 0.00 0.00 1.78
3395 3624 7.940178 TCTTACGCGATGATACAATATGTTT 57.060 32.000 15.93 0.00 0.00 2.83
3415 3644 6.494842 TGTTTATGAATTATTTCTGCGAGGC 58.505 36.000 0.00 0.00 32.78 4.70
3417 3646 6.545504 TTATGAATTATTTCTGCGAGGCTC 57.454 37.500 3.87 3.87 32.78 4.70
3419 3648 3.873361 TGAATTATTTCTGCGAGGCTCAG 59.127 43.478 15.95 6.08 32.78 3.35
3423 3652 0.106708 TTTCTGCGAGGCTCAGTTGT 59.893 50.000 15.95 0.00 33.48 3.32
3428 3657 1.343142 TGCGAGGCTCAGTTGTTAAGA 59.657 47.619 15.95 0.00 0.00 2.10
3432 3663 1.692519 AGGCTCAGTTGTTAAGACCGT 59.307 47.619 0.00 0.00 0.00 4.83
3434 3665 2.479275 GGCTCAGTTGTTAAGACCGTTC 59.521 50.000 0.00 0.00 0.00 3.95
3438 3669 3.552699 TCAGTTGTTAAGACCGTTCGTTG 59.447 43.478 0.00 0.00 0.00 4.10
3464 3695 5.209977 GTGGAACCACATTTTTCTAACGTC 58.790 41.667 17.69 0.00 45.53 4.34
3465 3696 5.008316 GTGGAACCACATTTTTCTAACGTCT 59.992 40.000 17.69 0.00 45.53 4.18
3466 3697 5.008217 TGGAACCACATTTTTCTAACGTCTG 59.992 40.000 0.00 0.00 0.00 3.51
3470 3701 5.147162 CCACATTTTTCTAACGTCTGCTTC 58.853 41.667 0.00 0.00 0.00 3.86
3471 3702 5.147162 CACATTTTTCTAACGTCTGCTTCC 58.853 41.667 0.00 0.00 0.00 3.46
3473 3704 3.764237 TTTTCTAACGTCTGCTTCCCT 57.236 42.857 0.00 0.00 0.00 4.20
3474 3705 3.764237 TTTCTAACGTCTGCTTCCCTT 57.236 42.857 0.00 0.00 0.00 3.95
3475 3706 4.877378 TTTCTAACGTCTGCTTCCCTTA 57.123 40.909 0.00 0.00 0.00 2.69
3476 3707 4.877378 TTCTAACGTCTGCTTCCCTTAA 57.123 40.909 0.00 0.00 0.00 1.85
3493 3724 0.476338 TAACACCACCACCATGCTGT 59.524 50.000 0.00 0.00 0.00 4.40
3504 3735 0.606401 CCATGCTGTCTTGGGAACGT 60.606 55.000 0.00 0.00 34.75 3.99
3519 3750 3.041940 CGTGACGGCAACCCTGTC 61.042 66.667 0.00 0.00 36.13 3.51
3535 3766 0.459899 TGTCGCTGAGCCACGATAAT 59.540 50.000 0.00 0.00 40.90 1.28
3537 3768 1.032794 TCGCTGAGCCACGATAATCT 58.967 50.000 0.00 0.00 32.45 2.40
3614 3845 2.158608 AGAAAAAGTGCTACAGCCCTGT 60.159 45.455 6.17 6.17 46.87 4.00
3616 3847 0.036875 AAAGTGCTACAGCCCTGTCC 59.963 55.000 3.88 0.00 43.74 4.02
3621 3852 1.832912 CTACAGCCCTGTCCCCATC 59.167 63.158 3.88 0.00 43.74 3.51
3624 3855 1.077212 CAGCCCTGTCCCCATCTTG 60.077 63.158 0.00 0.00 0.00 3.02
3625 3856 1.542375 AGCCCTGTCCCCATCTTGT 60.542 57.895 0.00 0.00 0.00 3.16
3626 3857 0.253160 AGCCCTGTCCCCATCTTGTA 60.253 55.000 0.00 0.00 0.00 2.41
3627 3858 0.846693 GCCCTGTCCCCATCTTGTAT 59.153 55.000 0.00 0.00 0.00 2.29
3688 3922 2.223363 TGTGTGTGTACATTTTGTGCGG 60.223 45.455 0.00 0.00 39.39 5.69
3733 3967 7.930325 TGAATTTTGGTTGTCATTGCTCATTTA 59.070 29.630 0.00 0.00 0.00 1.40
3745 3979 8.668353 GTCATTGCTCATTTAGACAGACAAATA 58.332 33.333 0.00 0.00 0.00 1.40
3746 3980 8.668353 TCATTGCTCATTTAGACAGACAAATAC 58.332 33.333 0.00 0.00 0.00 1.89
3747 3981 6.985188 TGCTCATTTAGACAGACAAATACC 57.015 37.500 0.00 0.00 0.00 2.73
3748 3982 5.580691 TGCTCATTTAGACAGACAAATACCG 59.419 40.000 0.00 0.00 0.00 4.02
3749 3983 5.810587 GCTCATTTAGACAGACAAATACCGA 59.189 40.000 0.00 0.00 0.00 4.69
3750 3984 6.312918 GCTCATTTAGACAGACAAATACCGAA 59.687 38.462 0.00 0.00 0.00 4.30
3751 3985 7.011482 GCTCATTTAGACAGACAAATACCGAAT 59.989 37.037 0.00 0.00 0.00 3.34
3752 3986 8.196802 TCATTTAGACAGACAAATACCGAATG 57.803 34.615 0.00 0.00 0.00 2.67
3753 3987 6.417191 TTTAGACAGACAAATACCGAATGC 57.583 37.500 0.00 0.00 0.00 3.56
3754 3988 2.930040 AGACAGACAAATACCGAATGCG 59.070 45.455 0.00 0.00 37.24 4.73
3755 3989 2.671396 GACAGACAAATACCGAATGCGT 59.329 45.455 0.00 0.00 35.23 5.24
3756 3990 2.415168 ACAGACAAATACCGAATGCGTG 59.585 45.455 0.00 0.00 35.23 5.34
3757 3991 2.415168 CAGACAAATACCGAATGCGTGT 59.585 45.455 0.00 0.00 35.23 4.49
3758 3992 2.415168 AGACAAATACCGAATGCGTGTG 59.585 45.455 0.00 0.00 35.23 3.82
3759 3993 2.413796 GACAAATACCGAATGCGTGTGA 59.586 45.455 0.00 0.00 35.23 3.58
3760 3994 2.158841 ACAAATACCGAATGCGTGTGAC 59.841 45.455 0.00 0.00 35.23 3.67
3761 3995 0.996462 AATACCGAATGCGTGTGACG 59.004 50.000 0.00 0.00 45.88 4.35
3781 4015 3.118807 GCTCCTTTAGCGTTTAAGCAC 57.881 47.619 0.00 0.00 42.53 4.40
3782 4016 2.482721 GCTCCTTTAGCGTTTAAGCACA 59.517 45.455 0.00 0.00 42.53 4.57
3783 4017 3.058501 GCTCCTTTAGCGTTTAAGCACAA 60.059 43.478 0.00 0.00 42.53 3.33
3784 4018 4.555906 GCTCCTTTAGCGTTTAAGCACAAA 60.556 41.667 0.00 0.00 42.53 2.83
3785 4019 5.502153 TCCTTTAGCGTTTAAGCACAAAA 57.498 34.783 0.00 0.00 40.15 2.44
3786 4020 5.892568 TCCTTTAGCGTTTAAGCACAAAAA 58.107 33.333 0.00 0.00 40.15 1.94
3787 4021 5.744819 TCCTTTAGCGTTTAAGCACAAAAAC 59.255 36.000 0.00 0.00 40.15 2.43
3788 4022 5.051307 CCTTTAGCGTTTAAGCACAAAAACC 60.051 40.000 0.00 0.00 40.15 3.27
3789 4023 3.793797 AGCGTTTAAGCACAAAAACCT 57.206 38.095 0.00 0.00 40.15 3.50
3790 4024 4.904253 AGCGTTTAAGCACAAAAACCTA 57.096 36.364 0.00 0.00 40.15 3.08
3791 4025 4.855531 AGCGTTTAAGCACAAAAACCTAG 58.144 39.130 0.00 0.00 40.15 3.02
3792 4026 4.577283 AGCGTTTAAGCACAAAAACCTAGA 59.423 37.500 0.00 0.00 40.15 2.43
3793 4027 5.240844 AGCGTTTAAGCACAAAAACCTAGAT 59.759 36.000 0.00 0.00 40.15 1.98
3794 4028 5.918576 GCGTTTAAGCACAAAAACCTAGATT 59.081 36.000 0.00 0.00 37.05 2.40
3795 4029 6.129194 GCGTTTAAGCACAAAAACCTAGATTG 60.129 38.462 0.00 0.00 37.05 2.67
3796 4030 6.129194 CGTTTAAGCACAAAAACCTAGATTGC 60.129 38.462 0.00 0.00 33.05 3.56
3797 4031 3.942130 AGCACAAAAACCTAGATTGCC 57.058 42.857 0.00 0.00 0.00 4.52
3798 4032 3.500343 AGCACAAAAACCTAGATTGCCT 58.500 40.909 0.00 0.00 0.00 4.75
3799 4033 3.897505 AGCACAAAAACCTAGATTGCCTT 59.102 39.130 0.00 0.00 0.00 4.35
3800 4034 4.344968 AGCACAAAAACCTAGATTGCCTTT 59.655 37.500 0.00 0.00 0.00 3.11
3801 4035 5.056480 GCACAAAAACCTAGATTGCCTTTT 58.944 37.500 0.00 0.00 0.00 2.27
3802 4036 5.527214 GCACAAAAACCTAGATTGCCTTTTT 59.473 36.000 0.00 0.00 0.00 1.94
3823 4057 4.319139 TTTTAACCCCCAAAGCGTAAAC 57.681 40.909 0.00 0.00 0.00 2.01
3824 4058 2.653234 TAACCCCCAAAGCGTAAACA 57.347 45.000 0.00 0.00 0.00 2.83
3825 4059 1.777941 AACCCCCAAAGCGTAAACAA 58.222 45.000 0.00 0.00 0.00 2.83
3826 4060 2.003937 ACCCCCAAAGCGTAAACAAT 57.996 45.000 0.00 0.00 0.00 2.71
3827 4061 3.157750 ACCCCCAAAGCGTAAACAATA 57.842 42.857 0.00 0.00 0.00 1.90
3828 4062 3.086282 ACCCCCAAAGCGTAAACAATAG 58.914 45.455 0.00 0.00 0.00 1.73
3829 4063 2.159296 CCCCCAAAGCGTAAACAATAGC 60.159 50.000 0.00 0.00 0.00 2.97
3830 4064 2.752903 CCCCAAAGCGTAAACAATAGCT 59.247 45.455 0.00 0.00 42.35 3.32
3831 4065 3.181500 CCCCAAAGCGTAAACAATAGCTC 60.181 47.826 0.00 0.00 39.25 4.09
3832 4066 3.689649 CCCAAAGCGTAAACAATAGCTCT 59.310 43.478 0.00 0.00 39.25 4.09
3833 4067 4.873827 CCCAAAGCGTAAACAATAGCTCTA 59.126 41.667 0.00 0.00 39.25 2.43
3834 4068 5.353123 CCCAAAGCGTAAACAATAGCTCTAA 59.647 40.000 0.00 0.00 39.25 2.10
3835 4069 6.456988 CCCAAAGCGTAAACAATAGCTCTAAG 60.457 42.308 0.00 0.00 39.25 2.18
3836 4070 6.456988 CCAAAGCGTAAACAATAGCTCTAAGG 60.457 42.308 0.00 0.00 39.25 2.69
3837 4071 5.340439 AGCGTAAACAATAGCTCTAAGGT 57.660 39.130 0.00 0.00 34.48 3.50
3838 4072 6.461110 AGCGTAAACAATAGCTCTAAGGTA 57.539 37.500 0.00 0.00 34.48 3.08
3839 4073 7.052142 AGCGTAAACAATAGCTCTAAGGTAT 57.948 36.000 0.00 0.00 40.32 2.73
3840 4074 7.498443 AGCGTAAACAATAGCTCTAAGGTATT 58.502 34.615 5.76 5.76 46.35 1.89
3841 4075 7.985752 AGCGTAAACAATAGCTCTAAGGTATTT 59.014 33.333 8.31 0.37 43.92 1.40
3842 4076 8.610035 GCGTAAACAATAGCTCTAAGGTATTTT 58.390 33.333 8.31 5.34 43.92 1.82
3923 4157 9.559732 TGGTAACATATGAAGTAGGAATCATTG 57.440 33.333 10.38 0.00 46.17 2.82
3924 4158 9.561069 GGTAACATATGAAGTAGGAATCATTGT 57.439 33.333 10.38 0.00 37.46 2.71
3927 4161 9.553064 AACATATGAAGTAGGAATCATTGTCTC 57.447 33.333 10.38 0.00 37.46 3.36
3928 4162 8.932610 ACATATGAAGTAGGAATCATTGTCTCT 58.067 33.333 10.38 0.00 37.46 3.10
3929 4163 9.775854 CATATGAAGTAGGAATCATTGTCTCTT 57.224 33.333 0.00 0.00 37.46 2.85
3932 4166 9.606631 ATGAAGTAGGAATCATTGTCTCTTAAC 57.393 33.333 0.00 0.00 32.47 2.01
3933 4167 8.593679 TGAAGTAGGAATCATTGTCTCTTAACA 58.406 33.333 0.00 0.00 0.00 2.41
3934 4168 9.436957 GAAGTAGGAATCATTGTCTCTTAACAA 57.563 33.333 0.00 0.00 42.92 2.83
3935 4169 8.779354 AGTAGGAATCATTGTCTCTTAACAAC 57.221 34.615 0.00 0.00 41.65 3.32
3936 4170 8.375506 AGTAGGAATCATTGTCTCTTAACAACA 58.624 33.333 0.00 0.00 41.65 3.33
3937 4171 9.167311 GTAGGAATCATTGTCTCTTAACAACAT 57.833 33.333 0.00 0.00 41.65 2.71
3938 4172 8.273780 AGGAATCATTGTCTCTTAACAACATC 57.726 34.615 0.00 0.00 41.65 3.06
3939 4173 7.884877 AGGAATCATTGTCTCTTAACAACATCA 59.115 33.333 0.00 0.00 41.65 3.07
3940 4174 8.680903 GGAATCATTGTCTCTTAACAACATCAT 58.319 33.333 0.00 0.00 41.65 2.45
3946 4180 7.776933 TGTCTCTTAACAACATCATAGATGC 57.223 36.000 6.90 0.00 0.00 3.91
3947 4181 6.476706 TGTCTCTTAACAACATCATAGATGCG 59.523 38.462 6.90 1.91 0.00 4.73
3948 4182 6.477033 GTCTCTTAACAACATCATAGATGCGT 59.523 38.462 6.90 2.49 0.00 5.24
3949 4183 7.010552 GTCTCTTAACAACATCATAGATGCGTT 59.989 37.037 15.30 15.30 0.00 4.84
3950 4184 7.003939 TCTTAACAACATCATAGATGCGTTG 57.996 36.000 18.20 16.64 42.00 4.10
3951 4185 3.680642 ACAACATCATAGATGCGTTGC 57.319 42.857 17.52 0.00 40.98 4.17
3952 4186 3.009026 ACAACATCATAGATGCGTTGCA 58.991 40.909 17.52 0.00 44.86 4.08
3953 4187 3.439825 ACAACATCATAGATGCGTTGCAA 59.560 39.130 17.52 0.00 43.62 4.08
3954 4188 4.096833 ACAACATCATAGATGCGTTGCAAT 59.903 37.500 17.52 0.00 43.62 3.56
3955 4189 4.478843 ACATCATAGATGCGTTGCAATC 57.521 40.909 0.59 0.00 43.62 2.67
3956 4190 3.878699 ACATCATAGATGCGTTGCAATCA 59.121 39.130 0.59 4.48 43.62 2.57
3957 4191 4.024302 ACATCATAGATGCGTTGCAATCAG 60.024 41.667 0.59 0.00 43.62 2.90
3958 4192 3.795877 TCATAGATGCGTTGCAATCAGA 58.204 40.909 0.59 0.00 43.62 3.27
3959 4193 4.383173 TCATAGATGCGTTGCAATCAGAT 58.617 39.130 0.59 0.11 43.62 2.90
3960 4194 4.818005 TCATAGATGCGTTGCAATCAGATT 59.182 37.500 0.59 0.00 43.62 2.40
3961 4195 3.687572 AGATGCGTTGCAATCAGATTC 57.312 42.857 0.59 0.00 43.62 2.52
3962 4196 3.276857 AGATGCGTTGCAATCAGATTCT 58.723 40.909 0.59 1.81 43.62 2.40
3963 4197 2.905959 TGCGTTGCAATCAGATTCTG 57.094 45.000 0.59 7.38 34.76 3.02
3964 4198 2.425539 TGCGTTGCAATCAGATTCTGA 58.574 42.857 18.29 18.29 38.11 3.27
3965 4199 2.813172 TGCGTTGCAATCAGATTCTGAA 59.187 40.909 19.73 1.11 37.59 3.02
3966 4200 3.120095 TGCGTTGCAATCAGATTCTGAAG 60.120 43.478 19.73 15.65 37.59 3.02
3967 4201 3.125829 GCGTTGCAATCAGATTCTGAAGA 59.874 43.478 19.73 0.00 44.04 2.87
3968 4202 4.645956 CGTTGCAATCAGATTCTGAAGAC 58.354 43.478 19.73 12.07 44.04 3.01
3969 4203 4.391216 CGTTGCAATCAGATTCTGAAGACT 59.609 41.667 19.73 1.11 44.04 3.24
3970 4204 5.445673 CGTTGCAATCAGATTCTGAAGACTC 60.446 44.000 19.73 8.60 44.04 3.36
3971 4205 5.417754 TGCAATCAGATTCTGAAGACTCT 57.582 39.130 19.73 0.00 44.04 3.24
3972 4206 5.417811 TGCAATCAGATTCTGAAGACTCTC 58.582 41.667 19.73 6.50 44.04 3.20
3973 4207 5.046807 TGCAATCAGATTCTGAAGACTCTCA 60.047 40.000 19.73 8.64 44.04 3.27
3974 4208 5.521010 GCAATCAGATTCTGAAGACTCTCAG 59.479 44.000 19.73 7.81 44.04 3.35
3975 4209 4.717233 TCAGATTCTGAAGACTCTCAGC 57.283 45.455 13.96 0.00 42.25 4.26
3976 4210 4.085009 TCAGATTCTGAAGACTCTCAGCA 58.915 43.478 13.96 1.47 42.25 4.41
3977 4211 4.710865 TCAGATTCTGAAGACTCTCAGCAT 59.289 41.667 13.96 5.23 42.25 3.79
3978 4212 5.890419 TCAGATTCTGAAGACTCTCAGCATA 59.110 40.000 13.96 0.00 42.25 3.14
3979 4213 5.978919 CAGATTCTGAAGACTCTCAGCATAC 59.021 44.000 8.00 3.39 42.25 2.39
3980 4214 5.893255 AGATTCTGAAGACTCTCAGCATACT 59.107 40.000 0.00 4.87 42.25 2.12
3981 4215 5.991933 TTCTGAAGACTCTCAGCATACTT 57.008 39.130 8.81 0.00 42.25 2.24
3982 4216 5.574891 TCTGAAGACTCTCAGCATACTTC 57.425 43.478 0.00 0.00 42.25 3.01
3983 4217 5.012893 TCTGAAGACTCTCAGCATACTTCA 58.987 41.667 0.00 0.00 42.25 3.02
3984 4218 5.655974 TCTGAAGACTCTCAGCATACTTCAT 59.344 40.000 0.00 0.00 42.25 2.57
3985 4219 6.830838 TCTGAAGACTCTCAGCATACTTCATA 59.169 38.462 0.00 0.00 42.25 2.15
3986 4220 7.505248 TCTGAAGACTCTCAGCATACTTCATAT 59.495 37.037 0.00 0.00 42.25 1.78
3987 4221 8.016301 TGAAGACTCTCAGCATACTTCATATT 57.984 34.615 0.00 0.00 38.73 1.28
3988 4222 8.140628 TGAAGACTCTCAGCATACTTCATATTC 58.859 37.037 0.00 0.00 38.73 1.75
3989 4223 7.594351 AGACTCTCAGCATACTTCATATTCA 57.406 36.000 0.00 0.00 0.00 2.57
3990 4224 7.432869 AGACTCTCAGCATACTTCATATTCAC 58.567 38.462 0.00 0.00 0.00 3.18
3991 4225 7.287466 AGACTCTCAGCATACTTCATATTCACT 59.713 37.037 0.00 0.00 0.00 3.41
3992 4226 7.432869 ACTCTCAGCATACTTCATATTCACTC 58.567 38.462 0.00 0.00 0.00 3.51
3993 4227 6.442112 TCTCAGCATACTTCATATTCACTCG 58.558 40.000 0.00 0.00 0.00 4.18
3994 4228 6.263168 TCTCAGCATACTTCATATTCACTCGA 59.737 38.462 0.00 0.00 0.00 4.04
3995 4229 6.986250 TCAGCATACTTCATATTCACTCGAT 58.014 36.000 0.00 0.00 0.00 3.59
3996 4230 6.865205 TCAGCATACTTCATATTCACTCGATG 59.135 38.462 0.00 0.00 0.00 3.84
3997 4231 5.636965 AGCATACTTCATATTCACTCGATGC 59.363 40.000 0.00 0.00 36.95 3.91
3998 4232 5.163913 GCATACTTCATATTCACTCGATGCC 60.164 44.000 0.00 0.00 31.89 4.40
3999 4233 3.733337 ACTTCATATTCACTCGATGCCC 58.267 45.455 0.00 0.00 0.00 5.36
4000 4234 2.839486 TCATATTCACTCGATGCCCC 57.161 50.000 0.00 0.00 0.00 5.80
4001 4235 2.046292 TCATATTCACTCGATGCCCCA 58.954 47.619 0.00 0.00 0.00 4.96
4002 4236 2.146342 CATATTCACTCGATGCCCCAC 58.854 52.381 0.00 0.00 0.00 4.61
4003 4237 1.199615 TATTCACTCGATGCCCCACA 58.800 50.000 0.00 0.00 0.00 4.17
4004 4238 0.327924 ATTCACTCGATGCCCCACAA 59.672 50.000 0.00 0.00 0.00 3.33
4005 4239 0.321564 TTCACTCGATGCCCCACAAG 60.322 55.000 0.00 0.00 0.00 3.16
4006 4240 1.191489 TCACTCGATGCCCCACAAGA 61.191 55.000 0.00 0.00 0.00 3.02
4007 4241 0.742281 CACTCGATGCCCCACAAGAG 60.742 60.000 0.00 0.00 40.73 2.85
4008 4242 1.194781 ACTCGATGCCCCACAAGAGT 61.195 55.000 0.00 0.00 42.15 3.24
4009 4243 0.460987 CTCGATGCCCCACAAGAGTC 60.461 60.000 0.00 0.00 34.36 3.36
4010 4244 1.191489 TCGATGCCCCACAAGAGTCA 61.191 55.000 0.00 0.00 0.00 3.41
4011 4245 1.021390 CGATGCCCCACAAGAGTCAC 61.021 60.000 0.00 0.00 0.00 3.67
4012 4246 0.036732 GATGCCCCACAAGAGTCACA 59.963 55.000 0.00 0.00 0.00 3.58
4013 4247 0.700564 ATGCCCCACAAGAGTCACAT 59.299 50.000 0.00 0.00 0.00 3.21
4014 4248 1.357137 TGCCCCACAAGAGTCACATA 58.643 50.000 0.00 0.00 0.00 2.29
4015 4249 1.702401 TGCCCCACAAGAGTCACATAA 59.298 47.619 0.00 0.00 0.00 1.90
4016 4250 2.107378 TGCCCCACAAGAGTCACATAAA 59.893 45.455 0.00 0.00 0.00 1.40
4017 4251 3.153919 GCCCCACAAGAGTCACATAAAA 58.846 45.455 0.00 0.00 0.00 1.52
4018 4252 3.572255 GCCCCACAAGAGTCACATAAAAA 59.428 43.478 0.00 0.00 0.00 1.94
4036 4270 4.937201 AAAAAGAATTTCCAGGCGTTCT 57.063 36.364 0.00 0.00 37.28 3.01
4037 4271 4.505313 AAAAGAATTTCCAGGCGTTCTC 57.495 40.909 0.00 0.00 37.28 2.87
4038 4272 2.859165 AGAATTTCCAGGCGTTCTCA 57.141 45.000 0.00 0.00 0.00 3.27
4039 4273 3.356529 AGAATTTCCAGGCGTTCTCAT 57.643 42.857 0.00 0.00 0.00 2.90
4040 4274 3.690460 AGAATTTCCAGGCGTTCTCATT 58.310 40.909 0.00 0.00 0.00 2.57
4041 4275 4.082125 AGAATTTCCAGGCGTTCTCATTT 58.918 39.130 0.00 0.00 0.00 2.32
4042 4276 4.524328 AGAATTTCCAGGCGTTCTCATTTT 59.476 37.500 0.00 0.00 0.00 1.82
4043 4277 4.871933 ATTTCCAGGCGTTCTCATTTTT 57.128 36.364 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 67 3.483869 GGGCCAAGATCCTCCGCT 61.484 66.667 4.39 0.00 0.00 5.52
127 130 0.540365 CACACAGCCCCAACCAAGAT 60.540 55.000 0.00 0.00 0.00 2.40
452 455 2.356793 CTCCATCATCGGAGCCGC 60.357 66.667 3.59 0.00 45.95 6.53
859 886 1.132453 GGCTTCCCAAGTTATCGTTGC 59.868 52.381 0.00 0.00 0.00 4.17
1315 1436 2.443952 ATGACGAGCCCGATCCCA 60.444 61.111 0.00 0.00 39.50 4.37
1339 1460 5.725490 AGGAAGAAGATGATGAGGTAGGAT 58.275 41.667 0.00 0.00 0.00 3.24
1394 1515 4.336280 GGGATTAGATTTAGGGATGTGGC 58.664 47.826 0.00 0.00 0.00 5.01
1429 1577 7.646130 CCAGATCTTGTTCTATCTAGACGAAAC 59.354 40.741 0.00 0.27 31.25 2.78
1687 1858 1.852280 CATGCACACGTACGATCGATT 59.148 47.619 24.34 2.14 34.70 3.34
1844 2018 8.887036 TTGTAAACGATGCATATTATCACTCT 57.113 30.769 0.00 0.00 0.00 3.24
1861 2036 1.529438 ACCACGCATGTCTTGTAAACG 59.471 47.619 0.00 0.00 0.00 3.60
1867 2042 3.728864 GCAGATTAACCACGCATGTCTTG 60.729 47.826 0.00 0.00 0.00 3.02
1902 2077 1.068121 ACTTGGGCCAAAGAGCTAGT 58.932 50.000 27.39 9.79 0.00 2.57
2019 2210 7.816640 TCTAGCCACAAAATACAGAAAATGTC 58.183 34.615 0.00 0.00 42.70 3.06
2024 2215 7.360861 CGTGAATCTAGCCACAAAATACAGAAA 60.361 37.037 9.35 0.00 33.13 2.52
2083 2274 1.511850 TGAACGGTGTGCATCTTCTG 58.488 50.000 0.00 0.00 0.00 3.02
2094 2285 6.971184 AGTAGATCTACGTAAATTGAACGGTG 59.029 38.462 23.82 9.08 44.48 4.94
2095 2286 7.093322 AGTAGATCTACGTAAATTGAACGGT 57.907 36.000 23.82 2.01 44.48 4.83
2097 2288 8.610855 TGAAGTAGATCTACGTAAATTGAACG 57.389 34.615 23.82 11.00 45.64 3.95
2148 2339 3.181522 CCAAACATGTGCACACAAAACAC 60.182 43.478 24.37 0.00 45.41 3.32
2426 2617 2.046313 CAAAAGAGAACATGCACGCAC 58.954 47.619 0.00 0.00 0.00 5.34
2797 3012 9.590451 TGAGATGTGTATATGTATGCATGTATG 57.410 33.333 10.16 0.00 36.58 2.39
2799 3014 9.995003 TTTGAGATGTGTATATGTATGCATGTA 57.005 29.630 10.16 1.06 36.58 2.29
2800 3015 8.777413 GTTTGAGATGTGTATATGTATGCATGT 58.223 33.333 10.16 2.14 36.58 3.21
2801 3016 8.776470 TGTTTGAGATGTGTATATGTATGCATG 58.224 33.333 10.16 0.00 36.58 4.06
2802 3017 8.907222 TGTTTGAGATGTGTATATGTATGCAT 57.093 30.769 3.79 3.79 39.03 3.96
2803 3018 8.729805 TTGTTTGAGATGTGTATATGTATGCA 57.270 30.769 0.00 0.00 0.00 3.96
2804 3019 8.830580 ACTTGTTTGAGATGTGTATATGTATGC 58.169 33.333 0.00 0.00 0.00 3.14
2845 3060 5.363868 TGAGGCAGAAAAATCTAGCTAGCTA 59.636 40.000 22.85 22.85 0.00 3.32
2865 3080 3.674528 ATGGCAGTTAGATCGATGAGG 57.325 47.619 0.54 0.00 0.00 3.86
2886 3101 0.259356 TTGGGGATCTGCATGCATGA 59.741 50.000 30.64 19.98 0.00 3.07
2930 3149 1.069823 CCGTAGAGGATGAGCTGCATT 59.930 52.381 1.02 0.00 45.00 3.56
3073 3292 4.430423 CGACGGCGAGTTTGCTGC 62.430 66.667 16.62 0.00 45.31 5.25
3074 3293 4.430423 GCGACGGCGAGTTTGCTG 62.430 66.667 18.90 0.00 46.83 4.41
3077 3296 3.295228 CTTGGCGACGGCGAGTTTG 62.295 63.158 26.24 5.92 41.24 2.93
3078 3297 3.041940 CTTGGCGACGGCGAGTTT 61.042 61.111 26.24 0.00 41.24 2.66
3081 3300 3.989698 ATCACTTGGCGACGGCGAG 62.990 63.158 31.00 31.00 44.03 5.03
3082 3301 3.583276 AATCACTTGGCGACGGCGA 62.583 57.895 18.90 14.23 41.24 5.54
3167 3386 0.732571 ACACCACACTTGTTGAAGCG 59.267 50.000 0.00 0.00 31.68 4.68
3241 3470 0.320421 TCTAAGTTGCACGAGGGCAC 60.320 55.000 0.00 0.00 44.86 5.01
3255 3484 6.455647 TCCCATGCACGAATATAGTTCTAAG 58.544 40.000 0.00 0.00 0.00 2.18
3270 3499 1.748122 CCTGTCTGCTCCCATGCAC 60.748 63.158 0.00 0.00 38.12 4.57
3275 3504 1.951209 TATGTTCCTGTCTGCTCCCA 58.049 50.000 0.00 0.00 0.00 4.37
3276 3505 3.567478 ATTATGTTCCTGTCTGCTCCC 57.433 47.619 0.00 0.00 0.00 4.30
3279 3508 8.037758 GCTACATATATTATGTTCCTGTCTGCT 58.962 37.037 5.55 0.00 33.76 4.24
3283 3512 9.579768 CTCAGCTACATATATTATGTTCCTGTC 57.420 37.037 17.37 2.59 34.02 3.51
3286 3515 9.935241 CAACTCAGCTACATATATTATGTTCCT 57.065 33.333 5.55 1.14 33.76 3.36
3292 3521 7.396339 TCGGGACAACTCAGCTACATATATTAT 59.604 37.037 0.00 0.00 0.00 1.28
3308 3537 7.281549 GTGGTGTAATTATTATTCGGGACAACT 59.718 37.037 0.00 0.00 0.00 3.16
3358 3587 4.720090 TCGCGTAAGAATAGATTCCGATC 58.280 43.478 5.77 0.00 43.02 3.69
3359 3588 4.761235 TCGCGTAAGAATAGATTCCGAT 57.239 40.909 5.77 0.00 43.02 4.18
3360 3589 4.214758 TCATCGCGTAAGAATAGATTCCGA 59.785 41.667 5.77 1.68 43.02 4.55
3361 3590 4.473199 TCATCGCGTAAGAATAGATTCCG 58.527 43.478 5.77 0.00 43.02 4.30
3362 3591 7.027760 TGTATCATCGCGTAAGAATAGATTCC 58.972 38.462 5.77 0.00 43.02 3.01
3392 3621 6.729187 AGCCTCGCAGAAATAATTCATAAAC 58.271 36.000 0.00 0.00 38.06 2.01
3395 3624 5.610398 TGAGCCTCGCAGAAATAATTCATA 58.390 37.500 0.00 0.00 38.06 2.15
3404 3633 0.106708 ACAACTGAGCCTCGCAGAAA 59.893 50.000 4.65 0.00 34.97 2.52
3406 3635 0.966179 TAACAACTGAGCCTCGCAGA 59.034 50.000 4.65 0.00 34.97 4.26
3407 3636 1.728971 CTTAACAACTGAGCCTCGCAG 59.271 52.381 0.00 0.00 37.31 5.18
3408 3637 1.343142 TCTTAACAACTGAGCCTCGCA 59.657 47.619 0.00 0.00 0.00 5.10
3410 3639 2.338500 GGTCTTAACAACTGAGCCTCG 58.662 52.381 0.00 0.00 0.00 4.63
3412 3641 1.692519 ACGGTCTTAACAACTGAGCCT 59.307 47.619 0.00 0.00 0.00 4.58
3413 3642 2.165319 ACGGTCTTAACAACTGAGCC 57.835 50.000 0.00 0.00 0.00 4.70
3414 3643 2.155155 CGAACGGTCTTAACAACTGAGC 59.845 50.000 0.00 0.00 0.00 4.26
3415 3644 3.378339 ACGAACGGTCTTAACAACTGAG 58.622 45.455 0.00 0.00 0.00 3.35
3417 3646 3.307782 ACAACGAACGGTCTTAACAACTG 59.692 43.478 0.00 0.00 0.00 3.16
3419 3648 3.931285 ACAACGAACGGTCTTAACAAC 57.069 42.857 0.00 0.00 0.00 3.32
3423 3652 2.608546 CCACAACAACGAACGGTCTTAA 59.391 45.455 0.00 0.00 0.00 1.85
3428 3657 0.728542 GTTCCACAACAACGAACGGT 59.271 50.000 0.00 0.00 32.14 4.83
3432 3663 1.822506 TGTGGTTCCACAACAACGAA 58.177 45.000 20.47 0.00 42.99 3.85
3455 3686 4.039488 TGTTAAGGGAAGCAGACGTTAGAA 59.961 41.667 0.00 0.00 0.00 2.10
3459 3690 2.490991 GTGTTAAGGGAAGCAGACGTT 58.509 47.619 0.00 0.00 0.00 3.99
3460 3691 1.270678 GGTGTTAAGGGAAGCAGACGT 60.271 52.381 0.00 0.00 0.00 4.34
3464 3695 1.202879 TGGTGGTGTTAAGGGAAGCAG 60.203 52.381 0.00 0.00 0.00 4.24
3465 3696 0.847373 TGGTGGTGTTAAGGGAAGCA 59.153 50.000 0.00 0.00 0.00 3.91
3466 3697 1.244816 GTGGTGGTGTTAAGGGAAGC 58.755 55.000 0.00 0.00 0.00 3.86
3470 3701 1.544724 CATGGTGGTGGTGTTAAGGG 58.455 55.000 0.00 0.00 0.00 3.95
3471 3702 0.887933 GCATGGTGGTGGTGTTAAGG 59.112 55.000 0.00 0.00 0.00 2.69
3473 3704 1.614996 CAGCATGGTGGTGGTGTTAA 58.385 50.000 17.24 0.00 41.77 2.01
3474 3705 3.337834 CAGCATGGTGGTGGTGTTA 57.662 52.632 17.24 0.00 41.77 2.41
3475 3706 4.179361 CAGCATGGTGGTGGTGTT 57.821 55.556 17.24 0.00 41.77 3.32
3493 3724 2.029964 GCCGTCACGTTCCCAAGA 59.970 61.111 0.00 0.00 0.00 3.02
3504 3735 4.980805 GCGACAGGGTTGCCGTCA 62.981 66.667 0.00 0.00 36.99 4.35
3519 3750 1.135046 CAGATTATCGTGGCTCAGCG 58.865 55.000 0.00 0.00 0.00 5.18
3535 3766 4.031418 TGTAGACGTCGTTTTTCACAGA 57.969 40.909 10.46 0.00 0.00 3.41
3537 3768 4.175516 ACTTGTAGACGTCGTTTTTCACA 58.824 39.130 10.46 4.35 0.00 3.58
3601 3832 3.009115 GGGGACAGGGCTGTAGCA 61.009 66.667 6.18 0.00 45.05 3.49
3614 3845 6.315714 TGTTTTTGGTAATACAAGATGGGGA 58.684 36.000 0.00 0.00 0.00 4.81
3667 3901 2.223363 CCGCACAAAATGTACACACACA 60.223 45.455 0.00 0.00 37.54 3.72
3668 3902 2.032302 TCCGCACAAAATGTACACACAC 59.968 45.455 0.00 0.00 37.54 3.82
3669 3903 2.289565 TCCGCACAAAATGTACACACA 58.710 42.857 0.00 0.00 39.52 3.72
3672 3906 3.181510 GGAGATCCGCACAAAATGTACAC 60.182 47.826 0.00 0.00 0.00 2.90
3685 3919 3.798202 AGTACAAAATCAGGAGATCCGC 58.202 45.455 0.00 0.00 42.08 5.54
3733 3967 2.930040 CGCATTCGGTATTTGTCTGTCT 59.070 45.455 0.00 0.00 0.00 3.41
3753 3987 2.070861 GCTAAAGGAGCGTCACACG 58.929 57.895 0.00 0.00 42.62 4.49
3762 3996 4.742438 TTGTGCTTAAACGCTAAAGGAG 57.258 40.909 0.00 0.00 0.00 3.69
3763 3997 5.502153 TTTTGTGCTTAAACGCTAAAGGA 57.498 34.783 0.00 0.00 0.00 3.36
3764 3998 5.051307 GGTTTTTGTGCTTAAACGCTAAAGG 60.051 40.000 0.72 0.00 35.59 3.11
3765 3999 5.746721 AGGTTTTTGTGCTTAAACGCTAAAG 59.253 36.000 0.72 0.00 35.59 1.85
3766 4000 5.652518 AGGTTTTTGTGCTTAAACGCTAAA 58.347 33.333 0.00 0.00 35.59 1.85
3767 4001 5.251601 AGGTTTTTGTGCTTAAACGCTAA 57.748 34.783 0.00 0.00 35.59 3.09
3768 4002 4.904253 AGGTTTTTGTGCTTAAACGCTA 57.096 36.364 0.00 0.00 35.59 4.26
3769 4003 3.793797 AGGTTTTTGTGCTTAAACGCT 57.206 38.095 0.00 0.00 35.59 5.07
3770 4004 4.851010 TCTAGGTTTTTGTGCTTAAACGC 58.149 39.130 0.00 0.00 35.59 4.84
3771 4005 6.129194 GCAATCTAGGTTTTTGTGCTTAAACG 60.129 38.462 0.00 0.00 35.59 3.60
3772 4006 6.145534 GGCAATCTAGGTTTTTGTGCTTAAAC 59.854 38.462 0.00 0.00 34.34 2.01
3773 4007 6.041523 AGGCAATCTAGGTTTTTGTGCTTAAA 59.958 34.615 0.00 0.00 0.00 1.52
3774 4008 5.538433 AGGCAATCTAGGTTTTTGTGCTTAA 59.462 36.000 0.00 0.00 0.00 1.85
3775 4009 5.076873 AGGCAATCTAGGTTTTTGTGCTTA 58.923 37.500 0.00 0.00 0.00 3.09
3776 4010 3.897505 AGGCAATCTAGGTTTTTGTGCTT 59.102 39.130 0.00 0.00 0.00 3.91
3777 4011 3.500343 AGGCAATCTAGGTTTTTGTGCT 58.500 40.909 0.00 0.00 0.00 4.40
3778 4012 3.942130 AGGCAATCTAGGTTTTTGTGC 57.058 42.857 0.00 0.00 0.00 4.57
3801 4035 4.161001 TGTTTACGCTTTGGGGGTTAAAAA 59.839 37.500 0.00 0.00 41.43 1.94
3802 4036 3.703052 TGTTTACGCTTTGGGGGTTAAAA 59.297 39.130 0.00 0.00 41.43 1.52
3803 4037 3.294214 TGTTTACGCTTTGGGGGTTAAA 58.706 40.909 0.00 0.00 41.43 1.52
3804 4038 2.941480 TGTTTACGCTTTGGGGGTTAA 58.059 42.857 0.00 0.00 41.43 2.01
3805 4039 2.653234 TGTTTACGCTTTGGGGGTTA 57.347 45.000 0.00 0.00 41.43 2.85
3806 4040 1.777941 TTGTTTACGCTTTGGGGGTT 58.222 45.000 0.00 0.00 41.43 4.11
3807 4041 2.003937 ATTGTTTACGCTTTGGGGGT 57.996 45.000 0.00 0.00 43.60 4.95
3808 4042 2.159296 GCTATTGTTTACGCTTTGGGGG 60.159 50.000 0.00 0.00 0.00 5.40
3809 4043 2.752903 AGCTATTGTTTACGCTTTGGGG 59.247 45.455 0.00 0.00 0.00 4.96
3810 4044 3.689649 AGAGCTATTGTTTACGCTTTGGG 59.310 43.478 0.00 0.00 31.96 4.12
3811 4045 4.946784 AGAGCTATTGTTTACGCTTTGG 57.053 40.909 0.00 0.00 31.96 3.28
3812 4046 6.092259 ACCTTAGAGCTATTGTTTACGCTTTG 59.908 38.462 0.00 0.00 31.96 2.77
3813 4047 6.171213 ACCTTAGAGCTATTGTTTACGCTTT 58.829 36.000 0.00 0.00 31.96 3.51
3814 4048 5.731591 ACCTTAGAGCTATTGTTTACGCTT 58.268 37.500 0.00 0.00 31.96 4.68
3815 4049 5.340439 ACCTTAGAGCTATTGTTTACGCT 57.660 39.130 0.00 0.00 35.03 5.07
3816 4050 7.710766 AATACCTTAGAGCTATTGTTTACGC 57.289 36.000 0.00 0.00 0.00 4.42
3894 4128 9.967451 TGATTCCTACTTCATATGTTACCAAAA 57.033 29.630 1.90 0.00 0.00 2.44
3897 4131 9.559732 CAATGATTCCTACTTCATATGTTACCA 57.440 33.333 1.90 0.00 32.40 3.25
3898 4132 9.561069 ACAATGATTCCTACTTCATATGTTACC 57.439 33.333 1.90 0.00 32.40 2.85
3901 4135 9.553064 GAGACAATGATTCCTACTTCATATGTT 57.447 33.333 1.90 0.00 32.40 2.71
3902 4136 8.932610 AGAGACAATGATTCCTACTTCATATGT 58.067 33.333 1.90 0.00 32.40 2.29
3903 4137 9.775854 AAGAGACAATGATTCCTACTTCATATG 57.224 33.333 0.00 0.00 32.40 1.78
3906 4140 9.606631 GTTAAGAGACAATGATTCCTACTTCAT 57.393 33.333 0.00 0.00 34.08 2.57
3907 4141 8.593679 TGTTAAGAGACAATGATTCCTACTTCA 58.406 33.333 0.00 0.00 0.00 3.02
3908 4142 9.436957 TTGTTAAGAGACAATGATTCCTACTTC 57.563 33.333 0.00 0.00 34.77 3.01
3909 4143 9.220767 GTTGTTAAGAGACAATGATTCCTACTT 57.779 33.333 0.00 0.00 41.18 2.24
3910 4144 8.375506 TGTTGTTAAGAGACAATGATTCCTACT 58.624 33.333 0.00 0.00 41.18 2.57
3911 4145 8.547967 TGTTGTTAAGAGACAATGATTCCTAC 57.452 34.615 0.00 0.00 41.18 3.18
3912 4146 9.383519 GATGTTGTTAAGAGACAATGATTCCTA 57.616 33.333 0.00 0.00 41.18 2.94
3913 4147 7.884877 TGATGTTGTTAAGAGACAATGATTCCT 59.115 33.333 0.00 0.00 41.18 3.36
3914 4148 8.044060 TGATGTTGTTAAGAGACAATGATTCC 57.956 34.615 0.00 0.00 41.18 3.01
3920 4154 8.834465 GCATCTATGATGTTGTTAAGAGACAAT 58.166 33.333 8.98 0.00 41.18 2.71
3921 4155 7.010460 CGCATCTATGATGTTGTTAAGAGACAA 59.990 37.037 8.98 0.00 37.20 3.18
3922 4156 6.476706 CGCATCTATGATGTTGTTAAGAGACA 59.523 38.462 8.98 0.00 0.00 3.41
3923 4157 6.477033 ACGCATCTATGATGTTGTTAAGAGAC 59.523 38.462 8.98 0.00 0.00 3.36
3924 4158 6.573434 ACGCATCTATGATGTTGTTAAGAGA 58.427 36.000 8.98 0.00 0.00 3.10
3925 4159 6.834959 ACGCATCTATGATGTTGTTAAGAG 57.165 37.500 8.98 0.00 0.00 2.85
3926 4160 6.456853 GCAACGCATCTATGATGTTGTTAAGA 60.457 38.462 20.20 0.00 42.51 2.10
3927 4161 5.678483 GCAACGCATCTATGATGTTGTTAAG 59.322 40.000 20.20 8.80 42.51 1.85
3928 4162 5.123027 TGCAACGCATCTATGATGTTGTTAA 59.877 36.000 20.20 10.52 42.51 2.01
3929 4163 4.633565 TGCAACGCATCTATGATGTTGTTA 59.366 37.500 20.20 12.45 42.51 2.41
3930 4164 3.439825 TGCAACGCATCTATGATGTTGTT 59.560 39.130 20.20 13.96 42.51 2.83
3931 4165 3.009026 TGCAACGCATCTATGATGTTGT 58.991 40.909 20.20 10.39 42.51 3.32
3932 4166 3.678915 TGCAACGCATCTATGATGTTG 57.321 42.857 17.32 17.32 42.96 3.33
3933 4167 4.336153 TGATTGCAACGCATCTATGATGTT 59.664 37.500 0.00 0.00 38.76 2.71
3934 4168 3.878699 TGATTGCAACGCATCTATGATGT 59.121 39.130 0.00 0.00 38.76 3.06
3935 4169 4.212636 TCTGATTGCAACGCATCTATGATG 59.787 41.667 0.00 3.42 38.76 3.07
3936 4170 4.383173 TCTGATTGCAACGCATCTATGAT 58.617 39.130 0.00 0.00 38.76 2.45
3937 4171 3.795877 TCTGATTGCAACGCATCTATGA 58.204 40.909 0.00 0.00 38.76 2.15
3938 4172 4.744136 ATCTGATTGCAACGCATCTATG 57.256 40.909 0.00 0.00 38.76 2.23
3939 4173 5.049612 CAGAATCTGATTGCAACGCATCTAT 60.050 40.000 7.78 0.00 33.87 1.98
3940 4174 4.271776 CAGAATCTGATTGCAACGCATCTA 59.728 41.667 7.78 0.00 33.87 1.98
3941 4175 3.064958 CAGAATCTGATTGCAACGCATCT 59.935 43.478 7.78 0.72 33.87 2.90
3942 4176 3.064408 TCAGAATCTGATTGCAACGCATC 59.936 43.478 9.18 0.00 35.35 3.91
3943 4177 3.011818 TCAGAATCTGATTGCAACGCAT 58.988 40.909 9.18 0.00 35.35 4.73
3944 4178 2.425539 TCAGAATCTGATTGCAACGCA 58.574 42.857 9.18 2.02 35.39 5.24
3945 4179 3.125829 TCTTCAGAATCTGATTGCAACGC 59.874 43.478 14.31 0.00 40.39 4.84
3946 4180 4.391216 AGTCTTCAGAATCTGATTGCAACG 59.609 41.667 14.31 0.00 40.39 4.10
3947 4181 5.642919 AGAGTCTTCAGAATCTGATTGCAAC 59.357 40.000 14.31 8.04 46.25 4.17
3948 4182 5.802465 AGAGTCTTCAGAATCTGATTGCAA 58.198 37.500 14.31 0.00 46.25 4.08
3949 4183 5.417754 AGAGTCTTCAGAATCTGATTGCA 57.582 39.130 14.31 0.00 46.25 4.08
3957 4191 6.147864 AGTATGCTGAGAGTCTTCAGAATC 57.852 41.667 18.26 0.00 45.95 2.52
3958 4192 6.154192 TGAAGTATGCTGAGAGTCTTCAGAAT 59.846 38.462 18.26 16.11 45.95 2.40
3959 4193 5.478332 TGAAGTATGCTGAGAGTCTTCAGAA 59.522 40.000 18.26 11.44 45.95 3.02
3960 4194 5.012893 TGAAGTATGCTGAGAGTCTTCAGA 58.987 41.667 18.26 3.44 45.95 3.27
3961 4195 5.321959 TGAAGTATGCTGAGAGTCTTCAG 57.678 43.478 12.59 12.59 45.85 3.02
3962 4196 5.929058 ATGAAGTATGCTGAGAGTCTTCA 57.071 39.130 7.65 7.65 42.97 3.02
3963 4197 8.140628 TGAATATGAAGTATGCTGAGAGTCTTC 58.859 37.037 0.00 0.00 34.02 2.87
3964 4198 7.925483 GTGAATATGAAGTATGCTGAGAGTCTT 59.075 37.037 0.00 0.00 0.00 3.01
3965 4199 7.287466 AGTGAATATGAAGTATGCTGAGAGTCT 59.713 37.037 0.00 0.00 0.00 3.24
3966 4200 7.432869 AGTGAATATGAAGTATGCTGAGAGTC 58.567 38.462 0.00 0.00 0.00 3.36
3967 4201 7.358770 AGTGAATATGAAGTATGCTGAGAGT 57.641 36.000 0.00 0.00 0.00 3.24
3968 4202 6.581919 CGAGTGAATATGAAGTATGCTGAGAG 59.418 42.308 0.00 0.00 0.00 3.20
3969 4203 6.263168 TCGAGTGAATATGAAGTATGCTGAGA 59.737 38.462 0.00 0.00 0.00 3.27
3970 4204 6.442112 TCGAGTGAATATGAAGTATGCTGAG 58.558 40.000 0.00 0.00 0.00 3.35
3971 4205 6.391227 TCGAGTGAATATGAAGTATGCTGA 57.609 37.500 0.00 0.00 0.00 4.26
3972 4206 6.400834 GCATCGAGTGAATATGAAGTATGCTG 60.401 42.308 0.00 0.00 34.61 4.41
3973 4207 5.636965 GCATCGAGTGAATATGAAGTATGCT 59.363 40.000 0.00 0.00 34.61 3.79
3974 4208 5.163913 GGCATCGAGTGAATATGAAGTATGC 60.164 44.000 0.00 0.00 36.22 3.14
3975 4209 5.349817 GGGCATCGAGTGAATATGAAGTATG 59.650 44.000 0.00 0.00 0.00 2.39
3976 4210 5.482908 GGGCATCGAGTGAATATGAAGTAT 58.517 41.667 0.00 0.00 0.00 2.12
3977 4211 4.262463 GGGGCATCGAGTGAATATGAAGTA 60.262 45.833 0.00 0.00 0.00 2.24
3978 4212 3.495100 GGGGCATCGAGTGAATATGAAGT 60.495 47.826 0.00 0.00 0.00 3.01
3979 4213 3.070018 GGGGCATCGAGTGAATATGAAG 58.930 50.000 0.00 0.00 0.00 3.02
3980 4214 2.437651 TGGGGCATCGAGTGAATATGAA 59.562 45.455 0.00 0.00 0.00 2.57
3981 4215 2.046292 TGGGGCATCGAGTGAATATGA 58.954 47.619 0.00 0.00 0.00 2.15
3982 4216 2.146342 GTGGGGCATCGAGTGAATATG 58.854 52.381 0.00 0.00 0.00 1.78
3983 4217 1.768275 TGTGGGGCATCGAGTGAATAT 59.232 47.619 0.00 0.00 0.00 1.28
3984 4218 1.199615 TGTGGGGCATCGAGTGAATA 58.800 50.000 0.00 0.00 0.00 1.75
3985 4219 0.327924 TTGTGGGGCATCGAGTGAAT 59.672 50.000 0.00 0.00 0.00 2.57
3986 4220 0.321564 CTTGTGGGGCATCGAGTGAA 60.322 55.000 0.00 0.00 0.00 3.18
3987 4221 1.191489 TCTTGTGGGGCATCGAGTGA 61.191 55.000 0.00 0.00 0.00 3.41
3988 4222 0.742281 CTCTTGTGGGGCATCGAGTG 60.742 60.000 0.00 0.00 0.00 3.51
3989 4223 1.194781 ACTCTTGTGGGGCATCGAGT 61.195 55.000 0.00 0.00 35.08 4.18
3990 4224 0.460987 GACTCTTGTGGGGCATCGAG 60.461 60.000 0.00 0.00 33.74 4.04
3991 4225 1.191489 TGACTCTTGTGGGGCATCGA 61.191 55.000 0.00 0.00 0.00 3.59
3992 4226 1.021390 GTGACTCTTGTGGGGCATCG 61.021 60.000 0.00 0.00 0.00 3.84
3993 4227 0.036732 TGTGACTCTTGTGGGGCATC 59.963 55.000 0.00 0.00 0.00 3.91
3994 4228 0.700564 ATGTGACTCTTGTGGGGCAT 59.299 50.000 0.00 0.00 0.00 4.40
3995 4229 1.357137 TATGTGACTCTTGTGGGGCA 58.643 50.000 0.00 0.00 0.00 5.36
3996 4230 2.489938 TTATGTGACTCTTGTGGGGC 57.510 50.000 0.00 0.00 0.00 5.80
4015 4249 4.340950 TGAGAACGCCTGGAAATTCTTTTT 59.659 37.500 0.00 0.00 31.58 1.94
4016 4250 3.888930 TGAGAACGCCTGGAAATTCTTTT 59.111 39.130 0.00 0.00 31.58 2.27
4017 4251 3.486383 TGAGAACGCCTGGAAATTCTTT 58.514 40.909 0.00 0.00 31.58 2.52
4018 4252 3.140325 TGAGAACGCCTGGAAATTCTT 57.860 42.857 0.00 0.00 31.58 2.52
4019 4253 2.859165 TGAGAACGCCTGGAAATTCT 57.141 45.000 0.00 2.35 34.11 2.40
4020 4254 4.440839 AAATGAGAACGCCTGGAAATTC 57.559 40.909 0.00 0.00 0.00 2.17
4021 4255 4.871933 AAAATGAGAACGCCTGGAAATT 57.128 36.364 0.00 0.00 0.00 1.82
4022 4256 4.871933 AAAAATGAGAACGCCTGGAAAT 57.128 36.364 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.