Multiple sequence alignment - TraesCS1A01G365600

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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 TraesCS1A01G365600 chr1A 100.000 4632 0 0 1 4632 544589458 544584827 0.000000e+00 8554
1 TraesCS1A01G365600 chr1A 87.131 474 31 15 1 445 578546948 578547420 1.150000e-140 510
2 TraesCS1A01G365600 chr1D 92.579 3948 181 43 611 4501 449458187 449454295 0.000000e+00 5565
3 TraesCS1A01G365600 chr1D 91.184 397 23 5 109 499 236090469 236090079 3.170000e-146 529
4 TraesCS1A01G365600 chr1B 93.439 3780 180 36 506 4246 615113589 615109839 0.000000e+00 5544
5 TraesCS1A01G365600 chr1B 91.989 362 19 5 4281 4632 615021874 615021513 2.490000e-137 499
6 TraesCS1A01G365600 chr2A 88.046 527 32 15 1 498 588429072 588428548 3.090000e-166 595
7 TraesCS1A01G365600 chr5A 93.862 391 16 4 109 498 446425765 446426148 2.400000e-162 582
8 TraesCS1A01G365600 chr3D 88.469 503 24 18 1 470 358569593 358569092 1.120000e-160 577
9 TraesCS1A01G365600 chr3D 85.055 542 32 22 1 496 388514612 388515150 1.490000e-139 507
10 TraesCS1A01G365600 chr3D 79.800 401 62 16 979 1362 356827861 356827463 1.640000e-69 274
11 TraesCS1A01G365600 chr4D 86.778 537 35 19 1 502 451680808 451681343 2.420000e-157 566
12 TraesCS1A01G365600 chr7A 86.767 529 38 16 1 499 14302927 14302401 1.130000e-155 560
13 TraesCS1A01G365600 chr7A 86.973 522 37 19 1 496 65033214 65033730 4.050000e-155 558
14 TraesCS1A01G365600 chr7A 91.026 390 28 3 109 497 667481435 667481052 1.910000e-143 520
15 TraesCS1A01G365600 chr7A 90.537 391 29 3 109 498 273654759 273654376 1.150000e-140 510
16 TraesCS1A01G365600 chr5D 92.802 389 18 7 109 496 424819958 424820337 5.240000e-154 555
17 TraesCS1A01G365600 chr3A 92.288 389 20 5 109 496 717900774 717901153 1.130000e-150 544
18 TraesCS1A01G365600 chr3A 90.428 397 23 9 109 500 721253914 721254300 4.130000e-140 508
19 TraesCS1A01G365600 chr3A 84.791 526 36 19 1 498 743518036 743518545 5.390000e-134 488
20 TraesCS1A01G365600 chr3A 79.948 384 56 16 997 1362 475722319 475721939 3.550000e-66 263
21 TraesCS1A01G365600 chr3A 97.321 112 3 0 1 112 721253772 721253883 1.700000e-44 191
22 TraesCS1A01G365600 chr6A 91.560 391 26 4 109 498 562465105 562464721 2.450000e-147 532
23 TraesCS1A01G365600 chr3B 79.790 381 60 14 997 1362 457970957 457970579 1.280000e-65 261


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 TraesCS1A01G365600 chr1A 544584827 544589458 4631 True 8554.0 8554 100.0000 1 4632 1 chr1A.!!$R1 4631
1 TraesCS1A01G365600 chr1D 449454295 449458187 3892 True 5565.0 5565 92.5790 611 4501 1 chr1D.!!$R2 3890
2 TraesCS1A01G365600 chr1B 615109839 615113589 3750 True 5544.0 5544 93.4390 506 4246 1 chr1B.!!$R2 3740
3 TraesCS1A01G365600 chr2A 588428548 588429072 524 True 595.0 595 88.0460 1 498 1 chr2A.!!$R1 497
4 TraesCS1A01G365600 chr3D 358569092 358569593 501 True 577.0 577 88.4690 1 470 1 chr3D.!!$R2 469
5 TraesCS1A01G365600 chr3D 388514612 388515150 538 False 507.0 507 85.0550 1 496 1 chr3D.!!$F1 495
6 TraesCS1A01G365600 chr4D 451680808 451681343 535 False 566.0 566 86.7780 1 502 1 chr4D.!!$F1 501
7 TraesCS1A01G365600 chr7A 14302401 14302927 526 True 560.0 560 86.7670 1 499 1 chr7A.!!$R1 498
8 TraesCS1A01G365600 chr7A 65033214 65033730 516 False 558.0 558 86.9730 1 496 1 chr7A.!!$F1 495
9 TraesCS1A01G365600 chr3A 743518036 743518545 509 False 488.0 488 84.7910 1 498 1 chr3A.!!$F2 497
10 TraesCS1A01G365600 chr3A 721253772 721254300 528 False 349.5 508 93.8745 1 500 2 chr3A.!!$F3 499

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
786 858 0.179020 TCCAACCACTCCAGCACAAG 60.179 55.000 0.00 0.0 0.00 3.16 F
828 902 0.399233 CTCCGATCTCCCCTTCCCTT 60.399 60.000 0.00 0.0 0.00 3.95 F
1203 1283 1.002379 CTGAGCTCTGCCCTGCTTT 60.002 57.895 16.19 0.0 39.91 3.51 F
1546 1640 1.202710 TGGTATGTGGTGCGTTTCTGT 60.203 47.619 0.00 0.0 0.00 3.41 F
1557 1651 2.223144 TGCGTTTCTGTGTTACATGAGC 59.777 45.455 0.00 0.0 0.00 4.26 F
2850 2946 2.559668 CAAGTCCTGGCACACATTTGAT 59.440 45.455 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2546 2642 0.169009 CTTTAGTTGCTCGGCCTTGC 59.831 55.000 0.0 5.42 0.0 4.01 R
2807 2903 5.939447 TGGCATCTCATATGTCACCAAATA 58.061 37.500 1.9 0.00 0.0 1.40 R
3052 3148 3.568538 CGGTGCTGGAAATGAGAAAAAG 58.431 45.455 0.0 0.00 0.0 2.27 R
3329 3425 0.179045 CCGAGGTAATGCTGGGAAGG 60.179 60.000 0.0 0.00 0.0 3.46 R
3341 3437 0.611714 GGGTTGCTTCTTCCGAGGTA 59.388 55.000 0.0 0.00 0.0 3.08 R
3759 3861 0.992695 AAGGGTGGAGCTTTAGGGAC 59.007 55.000 0.0 0.00 0.0 4.46 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
120 155 0.250901 GGTGGTGAGACATGTGGCTT 60.251 55.000 1.15 0.00 30.09 4.35
132 167 0.824109 TGTGGCTTGATACCTCGGAG 59.176 55.000 0.00 0.00 0.00 4.63
133 168 0.824759 GTGGCTTGATACCTCGGAGT 59.175 55.000 4.02 0.00 0.00 3.85
197 238 1.404843 GACTGGGAGTAGGCTGTAGG 58.595 60.000 0.00 0.00 0.00 3.18
440 500 3.283684 CAAACCAGGCGAACGGCA 61.284 61.111 21.28 0.00 46.16 5.69
500 560 3.456280 GCTGTTGGAGATGCTCTAAGAG 58.544 50.000 11.58 11.58 42.30 2.85
514 574 0.317160 TAAGAGCCGCATATCCACCG 59.683 55.000 0.00 0.00 0.00 4.94
527 587 0.840617 TCCACCGCATATTTGGGCTA 59.159 50.000 0.00 0.00 34.59 3.93
528 588 1.202758 TCCACCGCATATTTGGGCTAG 60.203 52.381 0.00 0.00 34.59 3.42
530 590 2.571212 CACCGCATATTTGGGCTAGAA 58.429 47.619 0.00 0.00 34.59 2.10
532 592 3.569701 CACCGCATATTTGGGCTAGAAAT 59.430 43.478 0.00 0.00 34.59 2.17
536 596 4.756642 CGCATATTTGGGCTAGAAATGAGA 59.243 41.667 0.00 0.00 0.00 3.27
537 597 5.239306 CGCATATTTGGGCTAGAAATGAGAA 59.761 40.000 0.00 0.00 0.00 2.87
538 598 6.238731 CGCATATTTGGGCTAGAAATGAGAAA 60.239 38.462 0.00 0.00 0.00 2.52
545 605 2.287248 GCTAGAAATGAGAAATGCCGGC 60.287 50.000 22.73 22.73 0.00 6.13
549 609 0.323725 AATGAGAAATGCCGGCCAGT 60.324 50.000 26.77 9.89 0.00 4.00
551 611 2.044946 AGAAATGCCGGCCAGTCC 60.045 61.111 26.77 9.46 0.00 3.85
562 622 1.566018 GGCCAGTCCGAACGTTTGAG 61.566 60.000 17.38 7.32 0.00 3.02
563 623 0.599204 GCCAGTCCGAACGTTTGAGA 60.599 55.000 17.38 9.53 0.00 3.27
564 624 1.137513 CCAGTCCGAACGTTTGAGAC 58.862 55.000 17.38 19.44 0.00 3.36
565 625 1.269621 CCAGTCCGAACGTTTGAGACT 60.270 52.381 23.30 23.30 38.30 3.24
566 626 2.052157 CAGTCCGAACGTTTGAGACTC 58.948 52.381 24.92 9.87 35.67 3.36
574 634 4.438797 CGAACGTTTGAGACTCGTTTAAGA 59.561 41.667 10.16 0.00 45.48 2.10
597 657 3.663908 GTCTGTCTTGATCGCATTTTCG 58.336 45.455 0.00 0.00 0.00 3.46
598 658 2.672874 TCTGTCTTGATCGCATTTTCGG 59.327 45.455 0.00 0.00 0.00 4.30
599 659 2.416547 CTGTCTTGATCGCATTTTCGGT 59.583 45.455 0.00 0.00 0.00 4.69
600 660 2.159430 TGTCTTGATCGCATTTTCGGTG 59.841 45.455 0.00 0.00 0.00 4.94
601 661 2.415168 GTCTTGATCGCATTTTCGGTGA 59.585 45.455 0.00 0.00 0.00 4.02
602 662 2.415168 TCTTGATCGCATTTTCGGTGAC 59.585 45.455 0.00 0.00 0.00 3.67
603 663 1.083489 TGATCGCATTTTCGGTGACC 58.917 50.000 0.00 0.00 0.00 4.02
628 688 4.509737 GGGCGTCCGGCTGTAGAC 62.510 72.222 13.05 0.00 42.94 2.59
644 705 0.976641 AGACGCTCAACCTTGATCCA 59.023 50.000 0.00 0.00 36.46 3.41
645 706 1.556911 AGACGCTCAACCTTGATCCAT 59.443 47.619 0.00 0.00 36.46 3.41
685 750 5.521010 TCACACGTGTTACTCCTGTTAAAAG 59.479 40.000 20.79 1.54 0.00 2.27
686 751 5.521010 CACACGTGTTACTCCTGTTAAAAGA 59.479 40.000 20.79 0.00 0.00 2.52
687 752 5.521372 ACACGTGTTACTCCTGTTAAAAGAC 59.479 40.000 17.22 0.00 0.00 3.01
688 753 5.751990 CACGTGTTACTCCTGTTAAAAGACT 59.248 40.000 7.58 0.00 0.00 3.24
786 858 0.179020 TCCAACCACTCCAGCACAAG 60.179 55.000 0.00 0.00 0.00 3.16
823 897 2.840102 CGGCTCCGATCTCCCCTT 60.840 66.667 1.35 0.00 42.83 3.95
828 902 0.399233 CTCCGATCTCCCCTTCCCTT 60.399 60.000 0.00 0.00 0.00 3.95
834 908 1.082954 CTCCCCTTCCCTTCCCTCA 59.917 63.158 0.00 0.00 0.00 3.86
1132 1206 1.216710 CTGCTCGACAAGGAGGTCC 59.783 63.158 0.00 0.00 39.66 4.46
1136 1210 1.228337 TCGACAAGGAGGTCCGTGA 60.228 57.895 17.55 0.00 46.41 4.35
1141 1215 3.547787 AAGGAGGTCCGTGAGCCCT 62.548 63.158 0.35 4.24 42.08 5.19
1142 1216 3.462678 GGAGGTCCGTGAGCCCTC 61.463 72.222 0.00 0.00 43.35 4.30
1203 1283 1.002379 CTGAGCTCTGCCCTGCTTT 60.002 57.895 16.19 0.00 39.91 3.51
1365 1459 1.933041 CGCCTCGTCGATGTACGTG 60.933 63.158 4.21 0.00 43.31 4.49
1422 1516 1.290203 TAGCATTGCGAGCAAGTAGC 58.710 50.000 15.90 17.36 46.19 3.58
1454 1548 3.690475 TTCTGCTCATGTGATCTGTGT 57.310 42.857 0.00 0.00 0.00 3.72
1457 1551 2.671888 CTGCTCATGTGATCTGTGTGTC 59.328 50.000 0.00 0.00 0.00 3.67
1546 1640 1.202710 TGGTATGTGGTGCGTTTCTGT 60.203 47.619 0.00 0.00 0.00 3.41
1557 1651 2.223144 TGCGTTTCTGTGTTACATGAGC 59.777 45.455 0.00 0.00 0.00 4.26
1703 1797 3.701241 GACGATCCTGAGTGAGTTCATC 58.299 50.000 0.00 0.00 0.00 2.92
1790 1884 4.286320 CGGAGCGAGGGGATTCGG 62.286 72.222 0.00 0.00 40.79 4.30
1878 1972 5.874261 GGTTATGTGATGGGAAAATTGTTGG 59.126 40.000 0.00 0.00 0.00 3.77
1881 1975 3.006752 TGTGATGGGAAAATTGTTGGCTC 59.993 43.478 0.00 0.00 0.00 4.70
1940 2034 6.360681 GTGTCAACATTCTTGTCAATAGCAAC 59.639 38.462 0.00 0.00 34.06 4.17
2054 2148 8.458843 ACCACAAATTCACACTATGCTTATAAC 58.541 33.333 0.00 0.00 0.00 1.89
2064 2158 5.757320 CACTATGCTTATAACTCAGCTGCTT 59.243 40.000 9.47 5.25 36.92 3.91
2065 2159 5.757320 ACTATGCTTATAACTCAGCTGCTTG 59.243 40.000 9.47 4.21 36.92 4.01
2155 2249 5.942961 TCCAACACATTCCTGTAACCTTTA 58.057 37.500 0.00 0.00 33.14 1.85
2295 2391 7.988028 ACAAGCAGACTTTACTTAGTTCTCTTT 59.012 33.333 0.00 0.00 32.29 2.52
2401 2497 3.877508 CTGGTTTCGACTTCTGGTCTTTT 59.122 43.478 0.00 0.00 42.44 2.27
2409 2505 4.760204 CGACTTCTGGTCTTTTGGGTTAAT 59.240 41.667 0.00 0.00 42.44 1.40
2415 2511 3.117093 TGGTCTTTTGGGTTAATGGGTCA 60.117 43.478 0.00 0.00 0.00 4.02
2418 2514 5.510690 GGTCTTTTGGGTTAATGGGTCAAAG 60.511 44.000 0.00 0.00 0.00 2.77
2490 2586 5.694231 TGGCTGATATGCATGTATTTGTC 57.306 39.130 10.16 0.00 34.04 3.18
2546 2642 6.092670 TGAATGATAGAGTTCTTTTGGAAGCG 59.907 38.462 0.00 0.00 34.23 4.68
2807 2903 7.254628 TCCTTTGTGTTTTACAACCAGGAACT 61.255 38.462 9.58 0.00 46.14 3.01
2850 2946 2.559668 CAAGTCCTGGCACACATTTGAT 59.440 45.455 0.00 0.00 0.00 2.57
3052 3148 7.761409 TGAATGACCAACTTACATAGCATTTC 58.239 34.615 0.00 0.00 0.00 2.17
3114 3210 2.891580 AGTACCTGTACCCTATGATGCG 59.108 50.000 3.89 0.00 36.75 4.73
3236 3332 3.392616 GGTCCTGATCCAGTTCCATATGT 59.607 47.826 1.24 0.00 0.00 2.29
3323 3419 7.459795 TCAGGAATATATGTGTAGAGCAGAG 57.540 40.000 0.00 0.00 0.00 3.35
3329 3425 9.134734 GAATATATGTGTAGAGCAGAGTTTAGC 57.865 37.037 0.00 0.00 0.00 3.09
3341 3437 2.310052 AGAGTTTAGCCTTCCCAGCATT 59.690 45.455 0.00 0.00 0.00 3.56
3401 3497 6.920569 ATACGTGTGAAATTTGAGATACCC 57.079 37.500 0.00 0.00 0.00 3.69
3429 3525 2.224670 ACCGTTTCAGGCATTCAGGTAA 60.225 45.455 0.00 0.00 33.69 2.85
3456 3552 6.406288 CCATCAGCTCTTGTTGTAGATCTGTA 60.406 42.308 5.18 0.00 38.75 2.74
3459 3555 6.209589 TCAGCTCTTGTTGTAGATCTGTAACT 59.790 38.462 18.71 2.25 38.75 2.24
3462 3558 6.975772 GCTCTTGTTGTAGATCTGTAACTAGG 59.024 42.308 22.35 17.35 30.50 3.02
3468 3564 7.614583 TGTTGTAGATCTGTAACTAGGTAGCTT 59.385 37.037 18.71 0.00 0.00 3.74
3469 3565 8.468399 GTTGTAGATCTGTAACTAGGTAGCTTT 58.532 37.037 5.18 0.00 0.00 3.51
3470 3566 7.997482 TGTAGATCTGTAACTAGGTAGCTTTG 58.003 38.462 5.18 0.00 0.00 2.77
3484 3580 4.036852 GGTAGCTTTGCTCACAACTTTCTT 59.963 41.667 0.00 0.00 40.44 2.52
3515 3611 7.180946 AGTCTTGCATCCTGCTTATATACCATA 59.819 37.037 0.34 0.00 45.31 2.74
3516 3612 7.989741 GTCTTGCATCCTGCTTATATACCATAT 59.010 37.037 0.34 0.00 45.31 1.78
3517 3613 8.551440 TCTTGCATCCTGCTTATATACCATATT 58.449 33.333 0.34 0.00 45.31 1.28
3518 3614 8.737168 TTGCATCCTGCTTATATACCATATTC 57.263 34.615 0.34 0.00 45.31 1.75
3604 3700 2.949644 GGTTAGGTACATCACAATGGCC 59.050 50.000 0.00 0.00 37.19 5.36
3613 3709 1.745232 TCACAATGGCCGGTGAATAC 58.255 50.000 18.88 0.00 40.80 1.89
3759 3861 2.677875 GGCAGGTTGGGGCTCTTG 60.678 66.667 0.00 0.00 0.00 3.02
3831 3934 3.824443 ACCCATGTTTGCTGTAAGTTACC 59.176 43.478 10.51 0.00 35.30 2.85
3832 3935 3.823873 CCCATGTTTGCTGTAAGTTACCA 59.176 43.478 10.51 0.00 35.30 3.25
3833 3936 4.462483 CCCATGTTTGCTGTAAGTTACCAT 59.538 41.667 10.51 2.97 35.30 3.55
3835 3938 5.393027 CCATGTTTGCTGTAAGTTACCATCC 60.393 44.000 10.51 0.00 35.30 3.51
3836 3939 4.720046 TGTTTGCTGTAAGTTACCATCCA 58.280 39.130 10.51 0.18 35.30 3.41
3837 3940 4.517453 TGTTTGCTGTAAGTTACCATCCAC 59.483 41.667 10.51 3.32 35.30 4.02
3957 4060 1.751351 GCTTGGGCCCTGTTTCTAATC 59.249 52.381 25.70 0.00 0.00 1.75
3999 4102 8.902806 CAAGCTATTTTGATTGGAGGTGTATTA 58.097 33.333 0.00 0.00 30.62 0.98
4000 4103 9.646522 AAGCTATTTTGATTGGAGGTGTATTAT 57.353 29.630 0.00 0.00 0.00 1.28
4001 4104 9.646522 AGCTATTTTGATTGGAGGTGTATTATT 57.353 29.630 0.00 0.00 0.00 1.40
4017 4120 7.093421 GGTGTATTATTACCCTCTGATACCTCC 60.093 44.444 0.00 0.00 0.00 4.30
4020 4123 9.411189 GTATTATTACCCTCTGATACCTCCTAG 57.589 40.741 0.00 0.00 0.00 3.02
4021 4124 5.952161 ATTACCCTCTGATACCTCCTAGT 57.048 43.478 0.00 0.00 0.00 2.57
4077 4181 2.171237 CTGTATTCCCTGTGGAGCATCA 59.829 50.000 0.00 0.00 43.07 3.07
4078 4182 2.092968 TGTATTCCCTGTGGAGCATCAC 60.093 50.000 2.95 2.95 43.07 3.06
4080 4184 1.191489 TTCCCTGTGGAGCATCACGA 61.191 55.000 0.00 0.00 43.07 4.35
4094 4198 3.684788 GCATCACGAACTGTATTGACCTT 59.315 43.478 0.00 0.00 0.00 3.50
4132 4241 0.694771 ATGATGACCTGTGGTGCAGT 59.305 50.000 0.00 0.00 43.55 4.40
4134 4243 0.322975 GATGACCTGTGGTGCAGTCT 59.677 55.000 0.00 0.00 43.55 3.24
4149 4258 2.673610 GCAGTCTCCAGCAAGTCTACAG 60.674 54.545 0.00 0.00 0.00 2.74
4188 4297 3.693085 AGCGAGCAATCTGAAACAATCAT 59.307 39.130 0.00 0.00 37.44 2.45
4203 4312 6.380079 AACAATCATGAGTTTAGGAGGTCT 57.620 37.500 0.09 0.00 0.00 3.85
4246 4355 4.207891 TCTCATGGAGTTTCTTAGTGCC 57.792 45.455 0.00 0.00 0.00 5.01
4274 4384 1.134521 ACGGTTGTATCATGATGCCGT 60.135 47.619 27.22 27.22 44.88 5.68
4276 4386 2.288666 GGTTGTATCATGATGCCGTGT 58.711 47.619 18.72 0.00 0.00 4.49
4297 4407 4.744137 TGTTTGCTTATGTGACAACAATGC 59.256 37.500 0.00 0.00 40.46 3.56
4307 4417 3.758554 GTGACAACAATGCTCCTTATGGT 59.241 43.478 0.00 0.00 34.23 3.55
4325 4435 9.807921 CCTTATGGTAGGAATGTATTGGTTAAT 57.192 33.333 0.00 0.00 37.50 1.40
4359 4469 5.669848 GCTCATCATTCGTGAAGAACAGTTC 60.670 44.000 5.00 5.00 42.39 3.01
4377 4487 4.396166 CAGTTCTAGCACAAAATGGGTAGG 59.604 45.833 0.00 0.00 36.15 3.18
4378 4488 2.999331 TCTAGCACAAAATGGGTAGGC 58.001 47.619 0.00 0.00 36.15 3.93
4390 4500 0.172578 GGGTAGGCGCACCAAATTTC 59.827 55.000 17.73 0.00 40.65 2.17
4408 4524 7.436118 CAAATTTCTGATCTCCCAAACTGAAA 58.564 34.615 0.00 0.00 35.76 2.69
4413 4529 4.531854 TGATCTCCCAAACTGAAACACAA 58.468 39.130 0.00 0.00 0.00 3.33
4466 4594 1.746991 TGTTGCACACGAACCAGCA 60.747 52.632 0.00 0.00 34.79 4.41
4478 4606 4.507388 CACGAACCAGCACAAATCAAAATT 59.493 37.500 0.00 0.00 0.00 1.82
4482 4610 5.534207 ACCAGCACAAATCAAAATTGAGA 57.466 34.783 1.98 0.00 41.08 3.27
4486 4614 4.022935 AGCACAAATCAAAATTGAGAGCGA 60.023 37.500 1.98 0.00 41.08 4.93
4490 4618 4.691860 AATCAAAATTGAGAGCGACCTG 57.308 40.909 1.98 0.00 41.08 4.00
4491 4619 2.426522 TCAAAATTGAGAGCGACCTGG 58.573 47.619 0.00 0.00 32.50 4.45
4497 4625 1.332889 TGAGAGCGACCTGGCATCAT 61.333 55.000 0.00 0.00 34.64 2.45
4499 4627 1.596477 GAGCGACCTGGCATCATCC 60.596 63.158 0.00 0.00 34.64 3.51
4500 4628 2.190313 GCGACCTGGCATCATCCA 59.810 61.111 0.00 0.00 34.42 3.41
4507 4635 1.687563 CTGGCATCATCCAGCAATCA 58.312 50.000 0.00 0.00 46.11 2.57
4508 4636 2.028876 CTGGCATCATCCAGCAATCAA 58.971 47.619 0.00 0.00 46.11 2.57
4509 4637 2.429250 CTGGCATCATCCAGCAATCAAA 59.571 45.455 0.00 0.00 46.11 2.69
4510 4638 2.166870 TGGCATCATCCAGCAATCAAAC 59.833 45.455 0.00 0.00 0.00 2.93
4511 4639 2.429610 GGCATCATCCAGCAATCAAACT 59.570 45.455 0.00 0.00 0.00 2.66
4512 4640 3.490419 GGCATCATCCAGCAATCAAACTC 60.490 47.826 0.00 0.00 0.00 3.01
4513 4641 3.129813 GCATCATCCAGCAATCAAACTCA 59.870 43.478 0.00 0.00 0.00 3.41
4514 4642 4.381185 GCATCATCCAGCAATCAAACTCAA 60.381 41.667 0.00 0.00 0.00 3.02
4515 4643 5.681437 GCATCATCCAGCAATCAAACTCAAT 60.681 40.000 0.00 0.00 0.00 2.57
4516 4644 6.460537 GCATCATCCAGCAATCAAACTCAATA 60.461 38.462 0.00 0.00 0.00 1.90
4517 4645 7.658261 CATCATCCAGCAATCAAACTCAATAT 58.342 34.615 0.00 0.00 0.00 1.28
4518 4646 7.268199 TCATCCAGCAATCAAACTCAATATC 57.732 36.000 0.00 0.00 0.00 1.63
4519 4647 7.058525 TCATCCAGCAATCAAACTCAATATCT 58.941 34.615 0.00 0.00 0.00 1.98
4520 4648 7.558807 TCATCCAGCAATCAAACTCAATATCTT 59.441 33.333 0.00 0.00 0.00 2.40
4521 4649 7.092137 TCCAGCAATCAAACTCAATATCTTG 57.908 36.000 0.00 0.00 0.00 3.02
4522 4650 5.747197 CCAGCAATCAAACTCAATATCTTGC 59.253 40.000 0.00 0.00 38.35 4.01
4523 4651 5.747197 CAGCAATCAAACTCAATATCTTGCC 59.253 40.000 0.00 0.00 38.73 4.52
4524 4652 5.655532 AGCAATCAAACTCAATATCTTGCCT 59.344 36.000 0.00 0.00 38.73 4.75
4525 4653 6.154021 AGCAATCAAACTCAATATCTTGCCTT 59.846 34.615 0.00 0.00 38.73 4.35
4526 4654 6.815142 GCAATCAAACTCAATATCTTGCCTTT 59.185 34.615 0.00 0.00 33.44 3.11
4527 4655 7.009907 GCAATCAAACTCAATATCTTGCCTTTC 59.990 37.037 0.00 0.00 33.44 2.62
4528 4656 6.515272 TCAAACTCAATATCTTGCCTTTCC 57.485 37.500 0.00 0.00 32.11 3.13
4529 4657 6.248433 TCAAACTCAATATCTTGCCTTTCCT 58.752 36.000 0.00 0.00 32.11 3.36
4530 4658 7.402054 TCAAACTCAATATCTTGCCTTTCCTA 58.598 34.615 0.00 0.00 32.11 2.94
4531 4659 7.888021 TCAAACTCAATATCTTGCCTTTCCTAA 59.112 33.333 0.00 0.00 32.11 2.69
4532 4660 7.872113 AACTCAATATCTTGCCTTTCCTAAG 57.128 36.000 0.00 0.00 32.11 2.18
4545 4673 3.802948 TTCCTAAGGATCTTCGTCAGC 57.197 47.619 0.00 0.00 0.00 4.26
4546 4674 2.735151 TCCTAAGGATCTTCGTCAGCA 58.265 47.619 0.00 0.00 0.00 4.41
4547 4675 3.096852 TCCTAAGGATCTTCGTCAGCAA 58.903 45.455 0.00 0.00 0.00 3.91
4548 4676 3.513912 TCCTAAGGATCTTCGTCAGCAAA 59.486 43.478 0.00 0.00 0.00 3.68
4549 4677 3.619038 CCTAAGGATCTTCGTCAGCAAAC 59.381 47.826 0.00 0.00 0.00 2.93
4550 4678 3.409026 AAGGATCTTCGTCAGCAAACT 57.591 42.857 0.00 0.00 0.00 2.66
4551 4679 2.966050 AGGATCTTCGTCAGCAAACTC 58.034 47.619 0.00 0.00 0.00 3.01
4552 4680 2.300152 AGGATCTTCGTCAGCAAACTCA 59.700 45.455 0.00 0.00 0.00 3.41
4553 4681 3.067106 GGATCTTCGTCAGCAAACTCAA 58.933 45.455 0.00 0.00 0.00 3.02
4554 4682 3.686726 GGATCTTCGTCAGCAAACTCAAT 59.313 43.478 0.00 0.00 0.00 2.57
4555 4683 4.870426 GGATCTTCGTCAGCAAACTCAATA 59.130 41.667 0.00 0.00 0.00 1.90
4556 4684 5.525378 GGATCTTCGTCAGCAAACTCAATAT 59.475 40.000 0.00 0.00 0.00 1.28
4557 4685 6.292596 GGATCTTCGTCAGCAAACTCAATATC 60.293 42.308 0.00 0.00 0.00 1.63
4558 4686 5.724328 TCTTCGTCAGCAAACTCAATATCT 58.276 37.500 0.00 0.00 0.00 1.98
4559 4687 5.807520 TCTTCGTCAGCAAACTCAATATCTC 59.192 40.000 0.00 0.00 0.00 2.75
4560 4688 5.072040 TCGTCAGCAAACTCAATATCTCA 57.928 39.130 0.00 0.00 0.00 3.27
4561 4689 4.864806 TCGTCAGCAAACTCAATATCTCAC 59.135 41.667 0.00 0.00 0.00 3.51
4562 4690 4.033358 CGTCAGCAAACTCAATATCTCACC 59.967 45.833 0.00 0.00 0.00 4.02
4563 4691 4.937620 GTCAGCAAACTCAATATCTCACCA 59.062 41.667 0.00 0.00 0.00 4.17
4564 4692 5.587844 GTCAGCAAACTCAATATCTCACCAT 59.412 40.000 0.00 0.00 0.00 3.55
4565 4693 6.094603 GTCAGCAAACTCAATATCTCACCATT 59.905 38.462 0.00 0.00 0.00 3.16
4566 4694 6.317140 TCAGCAAACTCAATATCTCACCATTC 59.683 38.462 0.00 0.00 0.00 2.67
4567 4695 5.295292 AGCAAACTCAATATCTCACCATTCG 59.705 40.000 0.00 0.00 0.00 3.34
4568 4696 5.065218 GCAAACTCAATATCTCACCATTCGT 59.935 40.000 0.00 0.00 0.00 3.85
4569 4697 6.257849 GCAAACTCAATATCTCACCATTCGTA 59.742 38.462 0.00 0.00 0.00 3.43
4570 4698 7.201609 GCAAACTCAATATCTCACCATTCGTAA 60.202 37.037 0.00 0.00 0.00 3.18
4571 4699 8.331022 CAAACTCAATATCTCACCATTCGTAAG 58.669 37.037 0.00 0.00 0.00 2.34
4572 4700 6.516718 ACTCAATATCTCACCATTCGTAAGG 58.483 40.000 0.00 0.00 38.47 2.69
4573 4701 6.323996 ACTCAATATCTCACCATTCGTAAGGA 59.676 38.462 0.00 0.00 38.47 3.36
4574 4702 7.015682 ACTCAATATCTCACCATTCGTAAGGAT 59.984 37.037 0.00 0.00 34.11 3.24
4575 4703 7.378966 TCAATATCTCACCATTCGTAAGGATC 58.621 38.462 0.00 0.00 27.95 3.36
4576 4704 7.233553 TCAATATCTCACCATTCGTAAGGATCT 59.766 37.037 0.00 0.00 27.95 2.75
4577 4705 5.878406 ATCTCACCATTCGTAAGGATCTT 57.122 39.130 0.00 0.00 27.95 2.40
4578 4706 5.263968 TCTCACCATTCGTAAGGATCTTC 57.736 43.478 0.00 0.00 27.95 2.87
4579 4707 4.041740 TCACCATTCGTAAGGATCTTCG 57.958 45.455 0.00 0.00 27.95 3.79
4580 4708 3.697542 TCACCATTCGTAAGGATCTTCGA 59.302 43.478 0.00 0.00 27.95 3.71
4581 4709 4.341235 TCACCATTCGTAAGGATCTTCGAT 59.659 41.667 0.00 0.00 27.95 3.59
4582 4710 4.445718 CACCATTCGTAAGGATCTTCGATG 59.554 45.833 0.00 0.00 27.95 3.84
4583 4711 4.099573 ACCATTCGTAAGGATCTTCGATGT 59.900 41.667 0.00 0.00 27.95 3.06
4584 4712 4.681942 CCATTCGTAAGGATCTTCGATGTC 59.318 45.833 0.00 0.00 27.95 3.06
4585 4713 3.604065 TCGTAAGGATCTTCGATGTCG 57.396 47.619 0.00 0.00 38.36 4.35
4586 4714 2.289820 TCGTAAGGATCTTCGATGTCGG 59.710 50.000 2.25 0.00 37.79 4.79
4587 4715 2.033049 CGTAAGGATCTTCGATGTCGGT 59.967 50.000 2.25 0.00 40.29 4.69
4588 4716 2.586258 AAGGATCTTCGATGTCGGTG 57.414 50.000 2.25 0.00 40.29 4.94
4589 4717 1.763968 AGGATCTTCGATGTCGGTGA 58.236 50.000 2.25 2.20 40.29 4.02
4590 4718 2.100197 AGGATCTTCGATGTCGGTGAA 58.900 47.619 2.25 0.00 40.29 3.18
4591 4719 2.099921 AGGATCTTCGATGTCGGTGAAG 59.900 50.000 2.25 0.00 40.30 3.02
4593 4721 2.631418 TCTTCGATGTCGGTGAAGAC 57.369 50.000 2.25 0.00 42.21 3.01
4602 4730 4.126208 TGTCGGTGAAGACAAACTAACA 57.874 40.909 0.00 0.00 46.81 2.41
4603 4731 4.505808 TGTCGGTGAAGACAAACTAACAA 58.494 39.130 0.00 0.00 46.81 2.83
4604 4732 5.120399 TGTCGGTGAAGACAAACTAACAAT 58.880 37.500 0.00 0.00 46.81 2.71
4605 4733 5.007234 TGTCGGTGAAGACAAACTAACAATG 59.993 40.000 0.00 0.00 46.81 2.82
4606 4734 4.024387 TCGGTGAAGACAAACTAACAATGC 60.024 41.667 0.00 0.00 0.00 3.56
4607 4735 4.260990 CGGTGAAGACAAACTAACAATGCA 60.261 41.667 0.00 0.00 0.00 3.96
4608 4736 5.562696 CGGTGAAGACAAACTAACAATGCAT 60.563 40.000 0.00 0.00 0.00 3.96
4609 4737 5.858581 GGTGAAGACAAACTAACAATGCATC 59.141 40.000 0.00 0.00 0.00 3.91
4610 4738 6.294176 GGTGAAGACAAACTAACAATGCATCT 60.294 38.462 0.00 0.00 0.00 2.90
4611 4739 7.094805 GGTGAAGACAAACTAACAATGCATCTA 60.095 37.037 0.00 0.00 0.00 1.98
4612 4740 8.454106 GTGAAGACAAACTAACAATGCATCTAT 58.546 33.333 0.00 0.00 0.00 1.98
4613 4741 8.453320 TGAAGACAAACTAACAATGCATCTATG 58.547 33.333 0.00 0.00 0.00 2.23
4614 4742 7.928307 AGACAAACTAACAATGCATCTATGT 57.072 32.000 0.00 0.00 0.00 2.29
4615 4743 8.340618 AGACAAACTAACAATGCATCTATGTT 57.659 30.769 17.02 17.02 40.22 2.71
4616 4744 8.239314 AGACAAACTAACAATGCATCTATGTTG 58.761 33.333 20.48 14.16 37.78 3.33
4617 4745 7.885297 ACAAACTAACAATGCATCTATGTTGT 58.115 30.769 20.48 14.63 37.78 3.32
4618 4746 8.359642 ACAAACTAACAATGCATCTATGTTGTT 58.640 29.630 20.48 18.14 44.33 2.83
4619 4747 9.195411 CAAACTAACAATGCATCTATGTTGTTT 57.805 29.630 20.48 21.18 40.70 2.83
4620 4748 9.762933 AAACTAACAATGCATCTATGTTGTTTT 57.237 25.926 20.48 16.18 40.70 2.43
4621 4749 9.762933 AACTAACAATGCATCTATGTTGTTTTT 57.237 25.926 20.48 11.50 40.70 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.041922 ACTGGGATAGCGCCAGGA 60.042 61.111 16.62 0.00 37.01 3.86
120 155 2.748798 GCTGGTCTACTCCGAGGTATCA 60.749 54.545 0.00 0.00 0.00 2.15
132 167 1.068250 GCCATCCTCGCTGGTCTAC 59.932 63.158 0.00 0.00 36.10 2.59
133 168 2.490148 CGCCATCCTCGCTGGTCTA 61.490 63.158 0.00 0.00 36.10 2.59
151 186 2.037649 GTCATCGTCATCGTCATCGTC 58.962 52.381 0.00 0.00 38.33 4.20
152 187 1.594760 CGTCATCGTCATCGTCATCGT 60.595 52.381 0.00 0.00 38.33 3.73
153 188 1.037998 CGTCATCGTCATCGTCATCG 58.962 55.000 0.00 0.00 38.33 3.84
154 189 2.037649 GTCGTCATCGTCATCGTCATC 58.962 52.381 0.00 0.00 38.33 2.92
155 190 1.594760 CGTCGTCATCGTCATCGTCAT 60.595 52.381 0.00 0.00 38.33 3.06
156 191 0.247537 CGTCGTCATCGTCATCGTCA 60.248 55.000 0.00 0.00 38.33 4.35
197 238 9.032420 GGACATAGATAAAAACTACTAGTGCAC 57.968 37.037 9.40 9.40 0.00 4.57
325 382 3.003478 GCGCGCGCTAAATAGTGT 58.997 55.556 44.38 0.00 38.26 3.55
344 401 2.045340 AGCGGCCGCCTAAAATGT 60.045 55.556 44.47 22.83 43.17 2.71
383 443 1.082756 CCAGCAGACGCGTCAAAAC 60.083 57.895 37.85 23.77 45.49 2.43
440 500 0.387565 AAAAAGGTCATTTGCCGCGT 59.612 45.000 4.92 0.00 0.00 6.01
500 560 0.744414 ATATGCGGTGGATATGCGGC 60.744 55.000 0.00 0.00 0.00 6.53
501 561 1.737838 AATATGCGGTGGATATGCGG 58.262 50.000 0.00 0.00 0.00 5.69
503 563 2.164219 CCCAAATATGCGGTGGATATGC 59.836 50.000 0.00 0.00 34.05 3.14
504 564 2.164219 GCCCAAATATGCGGTGGATATG 59.836 50.000 0.00 0.00 34.05 1.78
514 574 6.639632 TTCTCATTTCTAGCCCAAATATGC 57.360 37.500 0.00 0.00 0.00 3.14
527 587 1.106285 GGCCGGCATTTCTCATTTCT 58.894 50.000 30.85 0.00 0.00 2.52
528 588 0.817013 TGGCCGGCATTTCTCATTTC 59.183 50.000 30.85 6.35 0.00 2.17
530 590 0.323725 ACTGGCCGGCATTTCTCATT 60.324 50.000 30.85 6.98 0.00 2.57
532 592 1.377202 GACTGGCCGGCATTTCTCA 60.377 57.895 30.85 14.92 0.00 3.27
545 605 1.137513 GTCTCAAACGTTCGGACTGG 58.862 55.000 0.00 0.00 0.00 4.00
549 609 0.664761 ACGAGTCTCAAACGTTCGGA 59.335 50.000 0.00 1.49 36.91 4.55
551 611 4.438797 TCTTAAACGAGTCTCAAACGTTCG 59.561 41.667 0.00 0.89 46.74 3.95
552 612 5.654616 GTCTTAAACGAGTCTCAAACGTTC 58.345 41.667 0.00 0.00 46.74 3.95
574 634 2.370281 AATGCGATCAAGACAGACGT 57.630 45.000 0.00 0.00 0.00 4.34
578 638 2.416547 ACCGAAAATGCGATCAAGACAG 59.583 45.455 0.00 0.00 0.00 3.51
579 639 2.159430 CACCGAAAATGCGATCAAGACA 59.841 45.455 0.00 0.00 0.00 3.41
584 644 1.083489 GGTCACCGAAAATGCGATCA 58.917 50.000 0.00 0.00 0.00 2.92
618 678 1.805945 GGTTGAGCGTCTACAGCCG 60.806 63.158 0.00 0.00 34.64 5.52
628 688 3.855689 AAAATGGATCAAGGTTGAGCG 57.144 42.857 2.09 0.00 44.10 5.03
651 712 2.099141 ACACGTGTGATTGATGAGGG 57.901 50.000 22.71 0.00 0.00 4.30
666 731 7.650903 AGTTAGTCTTTTAACAGGAGTAACACG 59.349 37.037 19.84 0.00 43.06 4.49
685 750 4.884458 GCTTTGCCAGGATTAGTTAGTC 57.116 45.455 0.00 0.00 0.00 2.59
764 833 0.036732 GTGCTGGAGTGGTTGGATCA 59.963 55.000 0.00 0.00 0.00 2.92
823 897 1.420138 GTGTTTGAGTGAGGGAAGGGA 59.580 52.381 0.00 0.00 0.00 4.20
828 902 1.070786 GCCGTGTTTGAGTGAGGGA 59.929 57.895 0.00 0.00 0.00 4.20
1023 1097 1.649664 CCTTGATGTCGAGCAGGAAG 58.350 55.000 0.00 0.00 0.00 3.46
1132 1206 4.787280 AGGGAGGGAGGGCTCACG 62.787 72.222 0.00 0.00 38.25 4.35
1136 1210 3.773154 GGAGAGGGAGGGAGGGCT 61.773 72.222 0.00 0.00 0.00 5.19
1141 1215 0.253868 TCTGAGAGGAGAGGGAGGGA 60.254 60.000 0.00 0.00 0.00 4.20
1142 1216 0.859760 ATCTGAGAGGAGAGGGAGGG 59.140 60.000 0.00 0.00 0.00 4.30
1181 1261 2.686835 AGGGCAGAGCTCAGACCC 60.687 66.667 26.46 25.16 41.17 4.46
1381 1475 4.144681 GAAGCACTGCTCGCTGCG 62.145 66.667 17.25 17.25 46.63 5.18
1454 1548 3.741830 TTGAACACCTGCGCCGACA 62.742 57.895 4.18 0.00 0.00 4.35
1457 1551 4.389576 GCTTGAACACCTGCGCCG 62.390 66.667 4.18 0.00 0.00 6.46
1546 1640 2.158534 ACCAAACCCAGCTCATGTAACA 60.159 45.455 0.00 0.00 0.00 2.41
1557 1651 3.023832 ACTCAAACTGAACCAAACCCAG 58.976 45.455 0.00 0.00 0.00 4.45
1703 1797 2.602257 TCCTGTATGCATCGGTCTTG 57.398 50.000 0.19 0.00 0.00 3.02
1790 1884 5.786401 ATCGCACTTCATTCTTCTTGTAC 57.214 39.130 0.00 0.00 0.00 2.90
1878 1972 0.736325 AACACCTGCGATACACGAGC 60.736 55.000 0.00 0.00 45.77 5.03
1881 1975 1.390123 CAAGAACACCTGCGATACACG 59.610 52.381 0.00 0.00 45.66 4.49
1940 2034 4.643733 GATCTCACGATCTGCCCG 57.356 61.111 0.00 0.00 42.25 6.13
2005 2099 7.093333 TGGTATGACTGTATGGGATGATATCAC 60.093 40.741 7.78 2.27 0.00 3.06
2054 2148 6.968131 TTTATTACTACACAAGCAGCTGAG 57.032 37.500 20.43 8.88 0.00 3.35
2155 2249 9.774413 AACTGCTACTACACAACTACTAATTTT 57.226 29.630 0.00 0.00 0.00 1.82
2163 2257 6.575267 TGTTTCAACTGCTACTACACAACTA 58.425 36.000 0.00 0.00 0.00 2.24
2166 2260 6.745159 TTTGTTTCAACTGCTACTACACAA 57.255 33.333 0.00 0.00 0.00 3.33
2295 2391 8.088365 CGGGTACAACTTGATGATATTATCTGA 58.912 37.037 8.76 0.00 0.00 3.27
2387 2483 5.048013 CCATTAACCCAAAAGACCAGAAGTC 60.048 44.000 0.00 0.00 46.71 3.01
2401 2497 7.064229 GGATAATACTTTGACCCATTAACCCA 58.936 38.462 0.00 0.00 0.00 4.51
2409 2505 6.325545 ACATAGTCGGATAATACTTTGACCCA 59.674 38.462 0.00 0.00 31.56 4.51
2415 2511 8.491958 AGGGAAAACATAGTCGGATAATACTTT 58.508 33.333 0.00 0.00 0.00 2.66
2418 2514 7.215085 ACAGGGAAAACATAGTCGGATAATAC 58.785 38.462 0.00 0.00 0.00 1.89
2490 2586 1.003355 ACTCGGGCATTCCACTGTG 60.003 57.895 0.00 0.00 34.36 3.66
2546 2642 0.169009 CTTTAGTTGCTCGGCCTTGC 59.831 55.000 0.00 5.42 0.00 4.01
2628 2724 9.802039 ACCCTAAAATGACTACTATGACAAAAA 57.198 29.630 0.00 0.00 0.00 1.94
2646 2742 9.777008 AAGGATTGGTCAATATAAACCCTAAAA 57.223 29.630 4.44 0.00 34.47 1.52
2807 2903 5.939447 TGGCATCTCATATGTCACCAAATA 58.061 37.500 1.90 0.00 0.00 1.40
2850 2946 7.395190 AAGCAAGATGTTTCATGCACTAATA 57.605 32.000 6.05 0.00 46.45 0.98
3052 3148 3.568538 CGGTGCTGGAAATGAGAAAAAG 58.431 45.455 0.00 0.00 0.00 2.27
3114 3210 7.696992 TGAAGTCCTTATATTTGGGTTTGTC 57.303 36.000 0.00 0.00 0.00 3.18
3223 3319 5.415701 AGCAAAAGTGTACATATGGAACTGG 59.584 40.000 7.80 3.22 0.00 4.00
3236 3332 5.476599 AGCATAACATGGAAGCAAAAGTGTA 59.523 36.000 0.00 0.00 0.00 2.90
3323 3419 2.688446 GGTAATGCTGGGAAGGCTAAAC 59.312 50.000 0.00 0.00 0.00 2.01
3329 3425 0.179045 CCGAGGTAATGCTGGGAAGG 60.179 60.000 0.00 0.00 0.00 3.46
3341 3437 0.611714 GGGTTGCTTCTTCCGAGGTA 59.388 55.000 0.00 0.00 0.00 3.08
3401 3497 6.189677 TGAATGCCTGAAACGGTAAAATAG 57.810 37.500 0.00 0.00 0.00 1.73
3410 3506 3.065371 GGATTACCTGAATGCCTGAAACG 59.935 47.826 0.00 0.00 29.85 3.60
3429 3525 5.366186 AGATCTACAACAAGAGCTGATGGAT 59.634 40.000 0.00 0.00 40.61 3.41
3456 3552 4.065789 GTTGTGAGCAAAGCTACCTAGTT 58.934 43.478 0.00 0.00 39.88 2.24
3459 3555 4.351874 AAGTTGTGAGCAAAGCTACCTA 57.648 40.909 0.00 0.00 39.88 3.08
3462 3558 4.820284 AGAAAGTTGTGAGCAAAGCTAC 57.180 40.909 0.00 0.00 39.88 3.58
3468 3564 2.495270 TGCCAAAGAAAGTTGTGAGCAA 59.505 40.909 0.00 0.00 0.00 3.91
3469 3565 2.098614 TGCCAAAGAAAGTTGTGAGCA 58.901 42.857 0.00 0.00 0.00 4.26
3470 3566 2.099756 ACTGCCAAAGAAAGTTGTGAGC 59.900 45.455 0.00 0.00 0.00 4.26
3515 3611 7.448748 AACGAACCTGCAAAAGTATAAGAAT 57.551 32.000 0.00 0.00 0.00 2.40
3516 3612 6.870971 AACGAACCTGCAAAAGTATAAGAA 57.129 33.333 0.00 0.00 0.00 2.52
3517 3613 8.038944 AGATAACGAACCTGCAAAAGTATAAGA 58.961 33.333 0.00 0.00 0.00 2.10
3518 3614 8.116753 CAGATAACGAACCTGCAAAAGTATAAG 58.883 37.037 0.00 0.00 0.00 1.73
3525 3621 5.298276 ACTTTCAGATAACGAACCTGCAAAA 59.702 36.000 0.00 0.00 0.00 2.44
3604 3700 0.872021 GCCTCAGCTCGTATTCACCG 60.872 60.000 0.00 0.00 35.50 4.94
3658 3754 4.345257 TCCTCAGACTCTAACAAACTGCTT 59.655 41.667 0.00 0.00 0.00 3.91
3759 3861 0.992695 AAGGGTGGAGCTTTAGGGAC 59.007 55.000 0.00 0.00 0.00 4.46
3831 3934 1.024579 GGCAACTGTACCGGTGGATG 61.025 60.000 19.93 12.92 0.00 3.51
3832 3935 1.298667 GGCAACTGTACCGGTGGAT 59.701 57.895 19.93 0.00 0.00 3.41
3833 3936 2.745037 GGCAACTGTACCGGTGGA 59.255 61.111 19.93 1.63 0.00 4.02
3999 4102 5.375956 TGACTAGGAGGTATCAGAGGGTAAT 59.624 44.000 0.00 0.00 0.00 1.89
4000 4103 4.730392 TGACTAGGAGGTATCAGAGGGTAA 59.270 45.833 0.00 0.00 0.00 2.85
4001 4104 4.313362 TGACTAGGAGGTATCAGAGGGTA 58.687 47.826 0.00 0.00 0.00 3.69
4077 4181 5.930569 GGTAAGAAAGGTCAATACAGTTCGT 59.069 40.000 0.00 0.00 0.00 3.85
4078 4182 5.929992 TGGTAAGAAAGGTCAATACAGTTCG 59.070 40.000 0.00 0.00 0.00 3.95
4080 4184 6.710744 CACTGGTAAGAAAGGTCAATACAGTT 59.289 38.462 0.00 0.00 0.00 3.16
4094 4198 7.549134 GTCATCATACATTCACACTGGTAAGAA 59.451 37.037 0.00 0.00 0.00 2.52
4132 4241 3.441500 TCTCTGTAGACTTGCTGGAGA 57.558 47.619 0.00 0.00 0.00 3.71
4134 4243 4.774726 AGATTTCTCTGTAGACTTGCTGGA 59.225 41.667 0.00 0.00 0.00 3.86
4149 4258 5.120830 TGCTCGCTTAAGTTGAAGATTTCTC 59.879 40.000 4.02 0.00 0.00 2.87
4166 4275 3.076621 TGATTGTTTCAGATTGCTCGCT 58.923 40.909 0.00 0.00 0.00 4.93
4188 4297 2.897969 GTCACCAGACCTCCTAAACTCA 59.102 50.000 0.00 0.00 38.89 3.41
4258 4367 3.427368 GCAAACACGGCATCATGATACAA 60.427 43.478 8.15 0.00 0.00 2.41
4274 4384 4.744137 GCATTGTTGTCACATAAGCAAACA 59.256 37.500 0.00 0.00 31.06 2.83
4276 4386 5.199024 AGCATTGTTGTCACATAAGCAAA 57.801 34.783 0.00 0.00 31.06 3.68
4297 4407 7.079451 ACCAATACATTCCTACCATAAGGAG 57.921 40.000 0.00 0.00 46.29 3.69
4307 4417 9.349713 GGTGATTGATTAACCAATACATTCCTA 57.650 33.333 0.00 0.00 36.93 2.94
4325 4435 3.200483 CGAATGATGAGCTGGTGATTGA 58.800 45.455 0.00 0.00 0.00 2.57
4326 4436 2.941064 ACGAATGATGAGCTGGTGATTG 59.059 45.455 0.00 0.00 0.00 2.67
4328 4438 2.169144 TCACGAATGATGAGCTGGTGAT 59.831 45.455 0.00 0.00 0.00 3.06
4359 4469 1.670811 CGCCTACCCATTTTGTGCTAG 59.329 52.381 0.00 0.00 0.00 3.42
4377 4487 2.478539 GGAGATCAGAAATTTGGTGCGC 60.479 50.000 0.00 0.00 0.00 6.09
4378 4488 2.098117 GGGAGATCAGAAATTTGGTGCG 59.902 50.000 0.00 0.00 0.00 5.34
4390 4500 4.136796 TGTGTTTCAGTTTGGGAGATCAG 58.863 43.478 0.00 0.00 0.00 2.90
4413 4529 3.198068 CCTCGCAGCAATACACTTATGT 58.802 45.455 0.00 0.00 43.30 2.29
4450 4575 1.308783 TTGTGCTGGTTCGTGTGCAA 61.309 50.000 0.00 0.00 37.17 4.08
4458 4583 5.984926 TCTCAATTTTGATTTGTGCTGGTTC 59.015 36.000 0.00 0.00 36.46 3.62
4466 4594 4.520492 AGGTCGCTCTCAATTTTGATTTGT 59.480 37.500 0.00 0.00 36.46 2.83
4478 4606 1.332889 ATGATGCCAGGTCGCTCTCA 61.333 55.000 0.00 0.00 0.00 3.27
4482 4610 2.369633 TGGATGATGCCAGGTCGCT 61.370 57.895 0.00 0.00 33.10 4.93
4490 4618 2.429610 AGTTTGATTGCTGGATGATGCC 59.570 45.455 0.00 0.00 0.00 4.40
4491 4619 3.129813 TGAGTTTGATTGCTGGATGATGC 59.870 43.478 0.00 0.00 0.00 3.91
4497 4625 6.405065 GCAAGATATTGAGTTTGATTGCTGGA 60.405 38.462 3.77 0.00 38.90 3.86
4499 4627 5.747197 GGCAAGATATTGAGTTTGATTGCTG 59.253 40.000 3.77 0.00 41.08 4.41
4500 4628 5.655532 AGGCAAGATATTGAGTTTGATTGCT 59.344 36.000 3.77 0.00 41.08 3.91
4501 4629 5.899299 AGGCAAGATATTGAGTTTGATTGC 58.101 37.500 3.77 0.00 40.70 3.56
4502 4630 7.490402 GGAAAGGCAAGATATTGAGTTTGATTG 59.510 37.037 3.77 0.00 0.00 2.67
4503 4631 7.398332 AGGAAAGGCAAGATATTGAGTTTGATT 59.602 33.333 3.77 0.00 0.00 2.57
4504 4632 6.894103 AGGAAAGGCAAGATATTGAGTTTGAT 59.106 34.615 3.77 0.00 0.00 2.57
4505 4633 6.248433 AGGAAAGGCAAGATATTGAGTTTGA 58.752 36.000 3.77 0.00 0.00 2.69
4506 4634 6.521151 AGGAAAGGCAAGATATTGAGTTTG 57.479 37.500 3.77 0.00 0.00 2.93
4507 4635 7.340487 CCTTAGGAAAGGCAAGATATTGAGTTT 59.660 37.037 3.77 2.17 45.78 2.66
4508 4636 6.830838 CCTTAGGAAAGGCAAGATATTGAGTT 59.169 38.462 3.77 0.00 45.78 3.01
4509 4637 6.360618 CCTTAGGAAAGGCAAGATATTGAGT 58.639 40.000 3.77 0.00 45.78 3.41
4510 4638 6.874288 CCTTAGGAAAGGCAAGATATTGAG 57.126 41.667 3.77 0.00 45.78 3.02
4523 4651 4.116238 GCTGACGAAGATCCTTAGGAAAG 58.884 47.826 4.56 0.00 34.34 2.62
4524 4652 3.513912 TGCTGACGAAGATCCTTAGGAAA 59.486 43.478 4.56 0.00 34.34 3.13
4525 4653 3.096852 TGCTGACGAAGATCCTTAGGAA 58.903 45.455 4.56 0.00 34.34 3.36
4526 4654 2.735151 TGCTGACGAAGATCCTTAGGA 58.265 47.619 2.37 2.37 35.55 2.94
4527 4655 3.526931 TTGCTGACGAAGATCCTTAGG 57.473 47.619 0.00 0.00 0.00 2.69
4528 4656 4.499183 AGTTTGCTGACGAAGATCCTTAG 58.501 43.478 0.00 0.00 0.00 2.18
4529 4657 4.021456 TGAGTTTGCTGACGAAGATCCTTA 60.021 41.667 0.00 0.00 0.00 2.69
4530 4658 3.244215 TGAGTTTGCTGACGAAGATCCTT 60.244 43.478 0.00 0.00 0.00 3.36
4531 4659 2.300152 TGAGTTTGCTGACGAAGATCCT 59.700 45.455 0.00 0.00 0.00 3.24
4532 4660 2.688507 TGAGTTTGCTGACGAAGATCC 58.311 47.619 0.00 0.00 0.00 3.36
4533 4661 4.935885 ATTGAGTTTGCTGACGAAGATC 57.064 40.909 0.00 0.00 0.00 2.75
4534 4662 6.344500 AGATATTGAGTTTGCTGACGAAGAT 58.656 36.000 0.00 0.00 0.00 2.40
4535 4663 5.724328 AGATATTGAGTTTGCTGACGAAGA 58.276 37.500 0.00 0.00 0.00 2.87
4536 4664 5.578336 TGAGATATTGAGTTTGCTGACGAAG 59.422 40.000 0.00 0.00 0.00 3.79
4537 4665 5.348724 GTGAGATATTGAGTTTGCTGACGAA 59.651 40.000 0.00 0.00 0.00 3.85
4538 4666 4.864806 GTGAGATATTGAGTTTGCTGACGA 59.135 41.667 0.00 0.00 0.00 4.20
4539 4667 4.033358 GGTGAGATATTGAGTTTGCTGACG 59.967 45.833 0.00 0.00 0.00 4.35
4540 4668 4.937620 TGGTGAGATATTGAGTTTGCTGAC 59.062 41.667 0.00 0.00 0.00 3.51
4541 4669 5.164620 TGGTGAGATATTGAGTTTGCTGA 57.835 39.130 0.00 0.00 0.00 4.26
4542 4670 6.446781 AATGGTGAGATATTGAGTTTGCTG 57.553 37.500 0.00 0.00 0.00 4.41
4543 4671 5.295292 CGAATGGTGAGATATTGAGTTTGCT 59.705 40.000 0.00 0.00 0.00 3.91
4544 4672 5.065218 ACGAATGGTGAGATATTGAGTTTGC 59.935 40.000 0.00 0.00 0.00 3.68
4545 4673 6.668541 ACGAATGGTGAGATATTGAGTTTG 57.331 37.500 0.00 0.00 0.00 2.93
4546 4674 7.495934 CCTTACGAATGGTGAGATATTGAGTTT 59.504 37.037 0.00 0.00 34.29 2.66
4547 4675 6.986817 CCTTACGAATGGTGAGATATTGAGTT 59.013 38.462 0.00 0.00 34.29 3.01
4548 4676 6.323996 TCCTTACGAATGGTGAGATATTGAGT 59.676 38.462 0.00 0.00 34.29 3.41
4549 4677 6.749139 TCCTTACGAATGGTGAGATATTGAG 58.251 40.000 0.00 0.00 34.29 3.02
4550 4678 6.724893 TCCTTACGAATGGTGAGATATTGA 57.275 37.500 0.00 0.00 34.29 2.57
4551 4679 7.382110 AGATCCTTACGAATGGTGAGATATTG 58.618 38.462 0.00 0.00 34.29 1.90
4552 4680 7.546250 AGATCCTTACGAATGGTGAGATATT 57.454 36.000 0.00 0.00 34.29 1.28
4553 4681 7.546250 AAGATCCTTACGAATGGTGAGATAT 57.454 36.000 0.00 0.00 34.29 1.63
4554 4682 6.294010 CGAAGATCCTTACGAATGGTGAGATA 60.294 42.308 0.00 0.00 34.29 1.98
4555 4683 5.508153 CGAAGATCCTTACGAATGGTGAGAT 60.508 44.000 0.00 0.00 34.29 2.75
4556 4684 4.202020 CGAAGATCCTTACGAATGGTGAGA 60.202 45.833 0.00 0.00 34.29 3.27
4557 4685 4.045104 CGAAGATCCTTACGAATGGTGAG 58.955 47.826 0.00 0.00 32.28 3.51
4558 4686 3.697542 TCGAAGATCCTTACGAATGGTGA 59.302 43.478 0.00 0.00 0.00 4.02
4559 4687 4.041740 TCGAAGATCCTTACGAATGGTG 57.958 45.455 0.00 0.00 0.00 4.17
4560 4688 4.099573 ACATCGAAGATCCTTACGAATGGT 59.900 41.667 0.00 0.00 45.12 3.55
4561 4689 4.621991 ACATCGAAGATCCTTACGAATGG 58.378 43.478 0.00 0.00 45.12 3.16
4562 4690 4.380087 CGACATCGAAGATCCTTACGAATG 59.620 45.833 0.00 0.00 45.12 2.67
4563 4691 4.537965 CGACATCGAAGATCCTTACGAAT 58.462 43.478 0.00 0.00 45.12 3.34
4564 4692 3.242969 CCGACATCGAAGATCCTTACGAA 60.243 47.826 2.09 0.00 45.12 3.85
4565 4693 2.289820 CCGACATCGAAGATCCTTACGA 59.710 50.000 2.09 0.00 45.12 3.43
4566 4694 2.033049 ACCGACATCGAAGATCCTTACG 59.967 50.000 2.09 0.00 45.12 3.18
4567 4695 3.066342 TCACCGACATCGAAGATCCTTAC 59.934 47.826 2.09 0.00 45.12 2.34
4568 4696 3.284617 TCACCGACATCGAAGATCCTTA 58.715 45.455 2.09 0.00 45.12 2.69
4569 4697 2.100197 TCACCGACATCGAAGATCCTT 58.900 47.619 2.09 0.00 45.12 3.36
4570 4698 1.763968 TCACCGACATCGAAGATCCT 58.236 50.000 2.09 0.00 45.12 3.24
4571 4699 2.099263 TCTTCACCGACATCGAAGATCC 59.901 50.000 2.09 0.00 45.12 3.36
4572 4700 3.109619 GTCTTCACCGACATCGAAGATC 58.890 50.000 2.09 0.00 44.98 2.75
4573 4701 2.492088 TGTCTTCACCGACATCGAAGAT 59.508 45.455 2.09 0.00 44.98 2.40
4574 4702 1.883926 TGTCTTCACCGACATCGAAGA 59.116 47.619 2.09 1.50 42.09 2.87
4575 4703 2.347697 TGTCTTCACCGACATCGAAG 57.652 50.000 2.09 0.00 43.02 3.79
4576 4704 2.798283 GTTTGTCTTCACCGACATCGAA 59.202 45.455 2.09 0.00 42.91 3.71
4577 4705 2.035449 AGTTTGTCTTCACCGACATCGA 59.965 45.455 2.09 0.00 42.91 3.59
4578 4706 2.404215 AGTTTGTCTTCACCGACATCG 58.596 47.619 0.00 0.00 42.91 3.84
4579 4707 4.748102 TGTTAGTTTGTCTTCACCGACATC 59.252 41.667 0.00 0.00 42.91 3.06
4580 4708 4.699637 TGTTAGTTTGTCTTCACCGACAT 58.300 39.130 0.00 0.00 42.91 3.06
4581 4709 4.126208 TGTTAGTTTGTCTTCACCGACA 57.874 40.909 0.00 0.00 41.82 4.35
4582 4710 5.440685 CATTGTTAGTTTGTCTTCACCGAC 58.559 41.667 0.00 0.00 34.52 4.79
4583 4711 4.024387 GCATTGTTAGTTTGTCTTCACCGA 60.024 41.667 0.00 0.00 0.00 4.69
4584 4712 4.219033 GCATTGTTAGTTTGTCTTCACCG 58.781 43.478 0.00 0.00 0.00 4.94
4585 4713 5.181690 TGCATTGTTAGTTTGTCTTCACC 57.818 39.130 0.00 0.00 0.00 4.02
4586 4714 6.672147 AGATGCATTGTTAGTTTGTCTTCAC 58.328 36.000 0.00 0.00 0.00 3.18
4587 4715 6.882610 AGATGCATTGTTAGTTTGTCTTCA 57.117 33.333 0.00 0.00 0.00 3.02
4588 4716 8.454106 ACATAGATGCATTGTTAGTTTGTCTTC 58.546 33.333 0.00 0.00 0.00 2.87
4589 4717 8.340618 ACATAGATGCATTGTTAGTTTGTCTT 57.659 30.769 0.00 0.00 0.00 3.01
4590 4718 7.928307 ACATAGATGCATTGTTAGTTTGTCT 57.072 32.000 0.00 0.00 0.00 3.41
4591 4719 8.023128 ACAACATAGATGCATTGTTAGTTTGTC 58.977 33.333 13.47 0.00 31.27 3.18
4592 4720 7.885297 ACAACATAGATGCATTGTTAGTTTGT 58.115 30.769 13.47 6.67 31.27 2.83
4593 4721 8.746922 AACAACATAGATGCATTGTTAGTTTG 57.253 30.769 13.47 6.13 42.06 2.93
4594 4722 9.762933 AAAACAACATAGATGCATTGTTAGTTT 57.237 25.926 21.65 21.65 42.82 2.66
4595 4723 9.762933 AAAAACAACATAGATGCATTGTTAGTT 57.237 25.926 13.47 15.22 42.82 2.24


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

AutoCloner maintained by Alex Coulton.