Multiple sequence alignment - TraesCS1B01G320800

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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 TraesCS1B01G320800 chr1B 100.000 4352 0 0 1 4352 545000060 544995709 0.000000e+00 8037
1 TraesCS1B01G320800 chr1B 88.956 661 70 1 2670 3330 473824102 473824759 0.000000e+00 813
2 TraesCS1B01G320800 chr1B 84.938 405 60 1 997 1400 473822304 473822708 4.050000e-110 409
3 TraesCS1B01G320800 chr1A 89.503 4468 262 96 2 4351 500566289 500561911 0.000000e+00 5461
4 TraesCS1B01G320800 chr1A 88.421 665 74 1 2670 3334 452020221 452020882 0.000000e+00 798
5 TraesCS1B01G320800 chr1D 90.511 3678 214 63 1 3591 405113805 405110176 0.000000e+00 4734
6 TraesCS1B01G320800 chr1D 88.671 662 70 3 2670 3330 351247234 351247891 0.000000e+00 802
7 TraesCS1B01G320800 chr1D 84.938 405 60 1 997 1400 351245578 351245982 4.050000e-110 409
8 TraesCS1B01G320800 chr1D 82.955 352 22 20 3795 4133 405110000 405109674 2.560000e-72 283
9 TraesCS1B01G320800 chr1D 83.060 183 15 7 4173 4352 405109675 405109506 7.540000e-33 152
10 TraesCS1B01G320800 chr2B 82.234 1576 206 46 814 2334 59178896 59180452 0.000000e+00 1291
11 TraesCS1B01G320800 chr2B 89.032 155 16 1 2129 2282 12700431 12700585 1.600000e-44 191
12 TraesCS1B01G320800 chr5A 89.021 674 68 2 2682 3352 691670159 691669489 0.000000e+00 830
13 TraesCS1B01G320800 chr4B 88.988 672 68 5 2682 3347 654036838 654036167 0.000000e+00 826
14 TraesCS1B01G320800 chrUn 88.338 686 77 2 2670 3352 126674860 126675545 0.000000e+00 821
15 TraesCS1B01G320800 chr5D 88.924 641 69 2 2668 3307 483698688 483699327 0.000000e+00 789
16 TraesCS1B01G320800 chr3B 85.408 699 79 13 699 1386 11656381 11657067 0.000000e+00 704
17 TraesCS1B01G320800 chr3B 83.090 686 88 18 1669 2334 265730833 265730156 2.240000e-167 599
18 TraesCS1B01G320800 chr3B 89.538 411 42 1 988 1397 575256237 575256647 1.790000e-143 520
19 TraesCS1B01G320800 chr3B 91.667 288 24 0 1882 2169 575257092 575257379 2.440000e-107 399
20 TraesCS1B01G320800 chr3B 88.034 117 13 1 2331 2447 265730130 265730015 2.110000e-28 137
21 TraesCS1B01G320800 chr4A 83.358 685 88 17 1669 2334 20575882 20575205 1.030000e-170 610
22 TraesCS1B01G320800 chr4A 88.034 117 13 1 2331 2447 20575179 20575064 2.110000e-28 137
23 TraesCS1B01G320800 chr3D 90.024 411 40 1 988 1397 438942159 438942569 8.290000e-147 531
24 TraesCS1B01G320800 chr3D 91.667 288 24 0 1882 2169 438943037 438943324 2.440000e-107 399
25 TraesCS1B01G320800 chr3A 89.951 408 40 1 998 1405 578873651 578874057 3.860000e-145 525
26 TraesCS1B01G320800 chr3A 90.278 288 28 0 1882 2169 578874488 578874775 1.140000e-100 377
27 TraesCS1B01G320800 chr7D 82.143 280 50 0 1892 2171 573692842 573693121 1.560000e-59 241


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 TraesCS1B01G320800 chr1B 544995709 545000060 4351 True 8037.0 8037 100.000000 1 4352 1 chr1B.!!$R1 4351
1 TraesCS1B01G320800 chr1B 473822304 473824759 2455 False 611.0 813 86.947000 997 3330 2 chr1B.!!$F1 2333
2 TraesCS1B01G320800 chr1A 500561911 500566289 4378 True 5461.0 5461 89.503000 2 4351 1 chr1A.!!$R1 4349
3 TraesCS1B01G320800 chr1A 452020221 452020882 661 False 798.0 798 88.421000 2670 3334 1 chr1A.!!$F1 664
4 TraesCS1B01G320800 chr1D 405109506 405113805 4299 True 1723.0 4734 85.508667 1 4352 3 chr1D.!!$R1 4351
5 TraesCS1B01G320800 chr1D 351245578 351247891 2313 False 605.5 802 86.804500 997 3330 2 chr1D.!!$F1 2333
6 TraesCS1B01G320800 chr2B 59178896 59180452 1556 False 1291.0 1291 82.234000 814 2334 1 chr2B.!!$F2 1520
7 TraesCS1B01G320800 chr5A 691669489 691670159 670 True 830.0 830 89.021000 2682 3352 1 chr5A.!!$R1 670
8 TraesCS1B01G320800 chr4B 654036167 654036838 671 True 826.0 826 88.988000 2682 3347 1 chr4B.!!$R1 665
9 TraesCS1B01G320800 chrUn 126674860 126675545 685 False 821.0 821 88.338000 2670 3352 1 chrUn.!!$F1 682
10 TraesCS1B01G320800 chr5D 483698688 483699327 639 False 789.0 789 88.924000 2668 3307 1 chr5D.!!$F1 639
11 TraesCS1B01G320800 chr3B 11656381 11657067 686 False 704.0 704 85.408000 699 1386 1 chr3B.!!$F1 687
12 TraesCS1B01G320800 chr3B 575256237 575257379 1142 False 459.5 520 90.602500 988 2169 2 chr3B.!!$F2 1181
13 TraesCS1B01G320800 chr3B 265730015 265730833 818 True 368.0 599 85.562000 1669 2447 2 chr3B.!!$R1 778
14 TraesCS1B01G320800 chr4A 20575064 20575882 818 True 373.5 610 85.696000 1669 2447 2 chr4A.!!$R1 778
15 TraesCS1B01G320800 chr3D 438942159 438943324 1165 False 465.0 531 90.845500 988 2169 2 chr3D.!!$F1 1181
16 TraesCS1B01G320800 chr3A 578873651 578874775 1124 False 451.0 525 90.114500 998 2169 2 chr3A.!!$F1 1171

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
711 730 0.179070 GCTAAGTCAGTAGGCCCTGC 60.179 60.000 0.00 0.0 32.32 4.85 F
735 761 1.008538 GCTTGGTTGCACCGTTCTG 60.009 57.895 0.00 0.0 42.58 3.02 F
968 1000 1.625315 TGCTGCAGTATGTGACTCCTT 59.375 47.619 16.64 0.0 39.31 3.36 F
2063 2367 2.164422 GCCTTACAATGCCACTCTTTCC 59.836 50.000 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2277 0.250467 GCATCATGCGGTCAGGGTAT 60.250 55.000 0.00 0.0 31.71 2.73 R
2036 2340 1.885887 GTGGCATTGTAAGGCTCAACA 59.114 47.619 1.15 0.0 35.75 3.33 R
2790 3842 1.971357 ACCATGAAGAAGTGGAGACGT 59.029 47.619 0.00 0.0 38.86 4.34 R
3639 4719 0.107703 TCCATCGAGGTGGCAATCAC 60.108 55.000 0.00 0.0 45.34 3.06 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
150 155 0.401395 ATATTTCTCCCTGCCCCCGA 60.401 55.000 0.00 0.00 0.00 5.14
185 190 4.548513 GCCCCACCCCACAACCAA 62.549 66.667 0.00 0.00 0.00 3.67
252 260 0.669625 GCTCGCCAACCGTAAGTTCT 60.670 55.000 0.00 0.00 36.18 3.01
253 261 1.792006 CTCGCCAACCGTAAGTTCTT 58.208 50.000 0.00 0.00 36.18 2.52
255 263 3.319755 CTCGCCAACCGTAAGTTCTTAA 58.680 45.455 0.00 0.00 36.18 1.85
256 264 3.319755 TCGCCAACCGTAAGTTCTTAAG 58.680 45.455 0.00 0.00 36.18 1.85
257 265 2.159747 CGCCAACCGTAAGTTCTTAAGC 60.160 50.000 0.00 0.00 36.18 3.09
258 266 2.161012 GCCAACCGTAAGTTCTTAAGCC 59.839 50.000 0.00 0.00 36.18 4.35
292 300 1.966762 CTTCCGCCAATGCCTTGTT 59.033 52.632 0.91 0.00 0.00 2.83
301 309 3.633525 GCCAATGCCTTGTTGATCTGATA 59.366 43.478 0.91 0.00 0.00 2.15
313 331 7.719778 TGTTGATCTGATATGTTGTATGAGC 57.280 36.000 0.00 0.00 0.00 4.26
314 332 6.421801 TGTTGATCTGATATGTTGTATGAGCG 59.578 38.462 0.00 0.00 0.00 5.03
316 334 3.653344 TCTGATATGTTGTATGAGCGGC 58.347 45.455 0.00 0.00 0.00 6.53
317 335 2.403259 TGATATGTTGTATGAGCGGCG 58.597 47.619 0.51 0.51 0.00 6.46
319 337 0.462375 TATGTTGTATGAGCGGCGGT 59.538 50.000 13.08 13.08 0.00 5.68
323 341 0.519519 TTGTATGAGCGGCGGTTTTG 59.480 50.000 14.71 0.00 0.00 2.44
324 342 0.604243 TGTATGAGCGGCGGTTTTGT 60.604 50.000 14.71 2.33 0.00 2.83
325 343 0.519961 GTATGAGCGGCGGTTTTGTT 59.480 50.000 14.71 0.00 0.00 2.83
326 344 1.068816 GTATGAGCGGCGGTTTTGTTT 60.069 47.619 14.71 0.00 0.00 2.83
331 349 0.248949 GCGGCGGTTTTGTTTGGTTA 60.249 50.000 9.78 0.00 0.00 2.85
447 465 0.669077 GGATGCGTCGATCTGGTAGT 59.331 55.000 0.00 0.00 0.00 2.73
461 479 4.523083 TCTGGTAGTTTTGTCTTGTGCTT 58.477 39.130 0.00 0.00 0.00 3.91
467 485 7.094118 TGGTAGTTTTGTCTTGTGCTTAAGTTT 60.094 33.333 4.02 0.00 0.00 2.66
468 486 7.220108 GGTAGTTTTGTCTTGTGCTTAAGTTTG 59.780 37.037 4.02 0.00 0.00 2.93
469 487 6.687604 AGTTTTGTCTTGTGCTTAAGTTTGT 58.312 32.000 4.02 0.00 0.00 2.83
470 488 7.822658 AGTTTTGTCTTGTGCTTAAGTTTGTA 58.177 30.769 4.02 0.00 0.00 2.41
471 489 8.466798 AGTTTTGTCTTGTGCTTAAGTTTGTAT 58.533 29.630 4.02 0.00 0.00 2.29
475 493 4.217550 TCTTGTGCTTAAGTTTGTATGGGC 59.782 41.667 4.02 0.00 0.00 5.36
503 521 3.577848 TGGATCTGTTTTGTGGGGATTTG 59.422 43.478 0.00 0.00 0.00 2.32
592 610 5.106157 CGCATCTAGGTTTGGAACAGATTTT 60.106 40.000 0.00 0.00 42.39 1.82
634 652 8.543839 TGGTTTCCCCACATTAGAGTATCTGC 62.544 46.154 0.00 0.00 42.55 4.26
654 672 1.129998 CAAGCCTGATTTCTGAGCACG 59.870 52.381 0.00 0.00 0.00 5.34
663 681 2.154854 TTCTGAGCACGTCCTCTTTG 57.845 50.000 8.21 0.00 33.02 2.77
693 711 4.344359 TTTGGGAAAATTAACCTGGTGC 57.656 40.909 0.00 0.00 0.00 5.01
697 715 4.770010 TGGGAAAATTAACCTGGTGCTAAG 59.230 41.667 0.00 0.00 0.00 2.18
699 717 5.105877 GGGAAAATTAACCTGGTGCTAAGTC 60.106 44.000 0.00 0.00 0.00 3.01
700 718 5.475564 GGAAAATTAACCTGGTGCTAAGTCA 59.524 40.000 0.00 0.00 0.00 3.41
707 726 0.902531 TGGTGCTAAGTCAGTAGGCC 59.097 55.000 0.00 0.00 0.00 5.19
710 729 1.134670 GTGCTAAGTCAGTAGGCCCTG 60.135 57.143 0.00 0.00 0.00 4.45
711 730 0.179070 GCTAAGTCAGTAGGCCCTGC 60.179 60.000 0.00 0.00 32.32 4.85
712 731 1.490574 CTAAGTCAGTAGGCCCTGCT 58.509 55.000 0.00 0.00 32.32 4.24
735 761 1.008538 GCTTGGTTGCACCGTTCTG 60.009 57.895 0.00 0.00 42.58 3.02
766 792 8.673711 TGAATTTACTGTGTAACCATATCTTGC 58.326 33.333 0.00 0.00 34.36 4.01
770 796 6.247229 ACTGTGTAACCATATCTTGCCATA 57.753 37.500 0.00 0.00 34.36 2.74
772 798 6.936900 ACTGTGTAACCATATCTTGCCATATC 59.063 38.462 0.00 0.00 34.36 1.63
773 799 6.836242 TGTGTAACCATATCTTGCCATATCA 58.164 36.000 0.00 0.00 34.36 2.15
777 803 8.629158 TGTAACCATATCTTGCCATATCAAAAC 58.371 33.333 0.00 0.00 0.00 2.43
778 804 7.902920 AACCATATCTTGCCATATCAAAACT 57.097 32.000 0.00 0.00 0.00 2.66
808 834 3.426159 GCACGTGAACATTTGGACTATGG 60.426 47.826 22.23 0.00 0.00 2.74
827 858 7.007116 ACTATGGTGCTAGTCATAGAGATTGA 58.993 38.462 23.72 0.00 43.14 2.57
942 974 2.488204 TCAATCATTTCCCACGCTGA 57.512 45.000 0.00 0.00 0.00 4.26
945 977 2.489329 CAATCATTTCCCACGCTGAACT 59.511 45.455 0.00 0.00 0.00 3.01
947 979 3.627395 TCATTTCCCACGCTGAACTAT 57.373 42.857 0.00 0.00 0.00 2.12
949 981 3.689161 TCATTTCCCACGCTGAACTATTG 59.311 43.478 0.00 0.00 0.00 1.90
963 995 4.631377 TGAACTATTGCTGCAGTATGTGAC 59.369 41.667 16.64 8.86 39.31 3.67
968 1000 1.625315 TGCTGCAGTATGTGACTCCTT 59.375 47.619 16.64 0.00 39.31 3.36
969 1001 2.831526 TGCTGCAGTATGTGACTCCTTA 59.168 45.455 16.64 0.00 39.31 2.69
970 1002 3.190874 GCTGCAGTATGTGACTCCTTAC 58.809 50.000 16.64 0.00 39.31 2.34
971 1003 3.786635 CTGCAGTATGTGACTCCTTACC 58.213 50.000 5.25 0.00 39.31 2.85
972 1004 3.441101 TGCAGTATGTGACTCCTTACCT 58.559 45.455 0.00 0.00 39.31 3.08
973 1005 3.838317 TGCAGTATGTGACTCCTTACCTT 59.162 43.478 0.00 0.00 39.31 3.50
1397 1432 2.639839 ACTGTGACTGCCTTCAAGGTAT 59.360 45.455 5.03 0.00 37.80 2.73
1635 1855 5.475564 GTGAATAAGGGCACTAGTTGGAAAA 59.524 40.000 0.00 0.00 32.44 2.29
1650 1870 3.153919 TGGAAAACCTGCATACTTGGAC 58.846 45.455 0.00 0.00 0.00 4.02
1663 1883 5.183140 GCATACTTGGACAACTTGGTGTATT 59.817 40.000 0.00 0.00 0.00 1.89
1692 1912 5.883673 AGAGTTAGTACTAGGTCTCTGCTTG 59.116 44.000 22.07 0.00 33.84 4.01
1812 2090 5.050644 TGCTGCTTTCATCTATTTGTGTG 57.949 39.130 0.00 0.00 0.00 3.82
1973 2277 6.829985 TTGATATCAAAGATCAGGGAGGAA 57.170 37.500 15.82 0.00 34.85 3.36
2036 2340 6.405953 CCTCACCGAAAGTATCTGATACTGTT 60.406 42.308 26.32 21.15 44.94 3.16
2063 2367 2.164422 GCCTTACAATGCCACTCTTTCC 59.836 50.000 0.00 0.00 0.00 3.13
2329 3183 6.908870 TCATAACTGAAGAATCGGAACATG 57.091 37.500 0.00 0.00 35.77 3.21
2340 3194 3.417069 TCGGAACATGATGTTTGTCCT 57.583 42.857 12.62 0.00 41.28 3.85
2383 3237 6.948309 AGTTTGGGTAATTCTTAGACATGCTT 59.052 34.615 0.00 0.00 0.00 3.91
2498 3549 5.877012 ACACTGTTATGATTCAGATGTGTCC 59.123 40.000 8.44 0.00 35.84 4.02
2532 3583 3.942829 TGCTTAAGTTGGATCTGTGAGG 58.057 45.455 4.02 0.00 0.00 3.86
2533 3584 3.582647 TGCTTAAGTTGGATCTGTGAGGA 59.417 43.478 4.02 0.00 0.00 3.71
2534 3585 4.225942 TGCTTAAGTTGGATCTGTGAGGAT 59.774 41.667 4.02 0.00 0.00 3.24
2535 3586 4.574013 GCTTAAGTTGGATCTGTGAGGATG 59.426 45.833 4.02 0.00 0.00 3.51
2652 3704 5.351233 TTGCTGTGTCTAACATTTAACCG 57.649 39.130 0.00 0.00 38.39 4.44
2790 3842 0.178846 TGAACCTGATCCCCTTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
3363 4421 4.273257 GAGTAGGGGCGAGCGAGC 62.273 72.222 0.00 0.00 0.00 5.03
3377 4435 1.444553 CGAGCGAGGTCTGTGTTCC 60.445 63.158 0.74 0.00 0.00 3.62
3380 4438 1.079750 GCGAGGTCTGTGTTCCTCC 60.080 63.158 5.76 0.00 45.12 4.30
3399 4457 2.804931 TGATCGTGTGCGTGCTCG 60.805 61.111 3.31 3.31 39.49 5.03
3429 4487 3.501445 GCTATTTCTGATGGCTCCATGTC 59.499 47.826 6.07 0.00 36.70 3.06
3495 4567 0.385390 GGGTTGTGGACTTGTTGCTG 59.615 55.000 0.00 0.00 0.00 4.41
3498 4570 1.476488 GTTGTGGACTTGTTGCTGGTT 59.524 47.619 0.00 0.00 0.00 3.67
3499 4571 1.102154 TGTGGACTTGTTGCTGGTTG 58.898 50.000 0.00 0.00 0.00 3.77
3500 4572 1.102978 GTGGACTTGTTGCTGGTTGT 58.897 50.000 0.00 0.00 0.00 3.32
3507 4579 3.128589 ACTTGTTGCTGGTTGTGTAGTTG 59.871 43.478 0.00 0.00 0.00 3.16
3546 4618 0.237498 GGTAGTCAGTTTGTTGCGCC 59.763 55.000 4.18 0.00 0.00 6.53
3555 4631 1.787057 TTTGTTGCGCCTTACGGTGG 61.787 55.000 4.18 0.00 43.93 4.61
3607 4687 3.282021 TGGCTCTGAATCCTAATGCAAC 58.718 45.455 0.00 0.00 0.00 4.17
3626 4706 3.840890 ACGTTTGCTGTTTCTTCACAA 57.159 38.095 0.00 0.00 0.00 3.33
3627 4707 4.370364 ACGTTTGCTGTTTCTTCACAAT 57.630 36.364 0.00 0.00 0.00 2.71
3629 4709 4.142491 ACGTTTGCTGTTTCTTCACAATGA 60.142 37.500 0.00 0.00 0.00 2.57
3630 4710 4.797868 CGTTTGCTGTTTCTTCACAATGAA 59.202 37.500 0.00 0.00 34.79 2.57
3631 4711 5.275881 CGTTTGCTGTTTCTTCACAATGAAC 60.276 40.000 0.00 0.00 32.21 3.18
3632 4712 4.979943 TGCTGTTTCTTCACAATGAACA 57.020 36.364 0.00 0.00 32.21 3.18
3633 4713 4.923893 TGCTGTTTCTTCACAATGAACAG 58.076 39.130 9.49 9.49 32.21 3.16
3634 4714 4.639755 TGCTGTTTCTTCACAATGAACAGA 59.360 37.500 16.16 0.00 32.21 3.41
3635 4715 5.210715 GCTGTTTCTTCACAATGAACAGAG 58.789 41.667 16.16 0.00 32.21 3.35
3637 4717 6.678900 GCTGTTTCTTCACAATGAACAGAGTT 60.679 38.462 16.16 0.00 32.21 3.01
3638 4718 7.156876 TGTTTCTTCACAATGAACAGAGTTT 57.843 32.000 0.00 0.00 32.21 2.66
3639 4719 7.028962 TGTTTCTTCACAATGAACAGAGTTTG 58.971 34.615 0.00 0.00 32.21 2.93
3646 4726 5.284079 ACAATGAACAGAGTTTGTGATTGC 58.716 37.500 14.24 0.00 40.65 3.56
3647 4727 3.988379 TGAACAGAGTTTGTGATTGCC 57.012 42.857 0.00 0.00 40.74 4.52
3648 4728 3.286353 TGAACAGAGTTTGTGATTGCCA 58.714 40.909 0.00 0.00 40.74 4.92
3650 4730 1.956477 ACAGAGTTTGTGATTGCCACC 59.044 47.619 0.00 0.00 45.09 4.61
3651 4731 2.233271 CAGAGTTTGTGATTGCCACCT 58.767 47.619 0.00 0.00 45.09 4.00
3652 4732 2.227388 CAGAGTTTGTGATTGCCACCTC 59.773 50.000 0.00 0.00 45.09 3.85
3653 4733 1.197721 GAGTTTGTGATTGCCACCTCG 59.802 52.381 0.00 0.00 45.09 4.63
3655 4735 1.812571 GTTTGTGATTGCCACCTCGAT 59.187 47.619 0.00 0.00 45.09 3.59
3656 4736 1.452110 TTGTGATTGCCACCTCGATG 58.548 50.000 0.00 0.00 45.09 3.84
3657 4737 0.392863 TGTGATTGCCACCTCGATGG 60.393 55.000 0.37 0.37 45.09 3.51
3658 4738 0.107703 GTGATTGCCACCTCGATGGA 60.108 55.000 9.29 0.00 43.02 3.41
3659 4739 0.107703 TGATTGCCACCTCGATGGAC 60.108 55.000 9.29 1.52 43.02 4.02
3660 4740 0.179000 GATTGCCACCTCGATGGACT 59.821 55.000 9.29 0.00 43.02 3.85
3661 4741 1.412710 GATTGCCACCTCGATGGACTA 59.587 52.381 9.29 0.00 43.02 2.59
3662 4742 0.824109 TTGCCACCTCGATGGACTAG 59.176 55.000 9.29 0.00 43.02 2.57
3680 4769 1.671054 GCCACGCTAGCTGAACCAA 60.671 57.895 13.93 0.00 0.00 3.67
3694 4783 1.474077 GAACCAATGGACTGGATGCAC 59.526 52.381 6.16 0.00 38.96 4.57
3695 4784 0.405198 ACCAATGGACTGGATGCACA 59.595 50.000 6.16 0.00 38.96 4.57
3696 4785 1.006281 ACCAATGGACTGGATGCACAT 59.994 47.619 6.16 0.00 38.96 3.21
3697 4786 2.241941 ACCAATGGACTGGATGCACATA 59.758 45.455 6.16 0.00 38.96 2.29
3699 4788 3.893200 CCAATGGACTGGATGCACATATT 59.107 43.478 0.00 0.00 38.96 1.28
3709 4798 2.948093 GCACATATTGCCGCAGTTG 58.052 52.632 0.00 0.00 46.63 3.16
3711 4800 0.526096 CACATATTGCCGCAGTTGCC 60.526 55.000 0.00 0.00 37.91 4.52
3714 4803 0.457035 ATATTGCCGCAGTTGCCTTG 59.543 50.000 0.00 0.00 37.91 3.61
3716 4805 2.146073 ATTGCCGCAGTTGCCTTGTC 62.146 55.000 0.00 0.00 37.91 3.18
3722 4811 1.228367 CAGTTGCCTTGTCCCTGCT 60.228 57.895 0.00 0.00 0.00 4.24
3731 4820 3.755628 GTCCCTGCTACGTCGCCA 61.756 66.667 9.82 0.00 0.00 5.69
3735 4824 2.261671 CTGCTACGTCGCCACCTT 59.738 61.111 9.82 0.00 0.00 3.50
3737 4826 2.813908 GCTACGTCGCCACCTTGG 60.814 66.667 0.00 0.00 41.55 3.61
3739 4828 1.885157 CTACGTCGCCACCTTGGTA 59.115 57.895 0.00 0.00 40.46 3.25
3742 4831 2.461110 CGTCGCCACCTTGGTATGC 61.461 63.158 0.00 0.00 40.46 3.14
3749 4838 1.066430 CCACCTTGGTATGCTACGTGT 60.066 52.381 0.00 0.00 31.35 4.49
3754 4843 1.934589 TGGTATGCTACGTGTCATGC 58.065 50.000 12.70 11.34 0.00 4.06
3755 4844 1.480545 TGGTATGCTACGTGTCATGCT 59.519 47.619 15.37 0.00 0.00 3.79
3756 4845 1.860950 GGTATGCTACGTGTCATGCTG 59.139 52.381 15.37 0.00 0.00 4.41
3757 4846 2.540515 GTATGCTACGTGTCATGCTGT 58.459 47.619 12.70 0.00 0.00 4.40
3758 4847 1.362768 ATGCTACGTGTCATGCTGTG 58.637 50.000 0.00 0.00 0.00 3.66
3759 4848 1.291184 TGCTACGTGTCATGCTGTGC 61.291 55.000 0.00 0.00 0.00 4.57
3760 4849 1.970917 GCTACGTGTCATGCTGTGCC 61.971 60.000 0.00 0.00 0.00 5.01
3761 4850 1.686566 CTACGTGTCATGCTGTGCCG 61.687 60.000 0.00 0.00 0.00 5.69
3767 4856 4.409218 CATGCTGTGCCGTGTGCC 62.409 66.667 0.00 0.00 40.16 5.01
3833 4944 3.081409 ACTTCAGCGGGCCGGTAT 61.081 61.111 31.94 13.77 35.27 2.73
3903 5032 1.225376 CCAAGCTACAACGACGGCAA 61.225 55.000 0.00 0.00 0.00 4.52
3931 5080 2.175069 ACTAGGCTGCTAGCTGGTAGTA 59.825 50.000 21.46 9.79 41.99 1.82
4016 5173 3.119316 AGCCTCGATTTATCTATCGCCTG 60.119 47.826 0.00 0.00 45.28 4.85
4063 5220 2.215465 TACGCACCGCCGAGATTTCA 62.215 55.000 0.00 0.00 0.00 2.69
4084 5241 1.933181 GTTGGTTCTGCCTTTTTGTGC 59.067 47.619 0.00 0.00 38.35 4.57
4090 5248 0.031178 CTGCCTTTTTGTGCGAGCTT 59.969 50.000 0.00 0.00 0.00 3.74
4091 5249 0.459489 TGCCTTTTTGTGCGAGCTTT 59.541 45.000 0.00 0.00 0.00 3.51
4092 5250 0.854705 GCCTTTTTGTGCGAGCTTTG 59.145 50.000 0.00 0.00 0.00 2.77
4139 5338 4.988598 CAACGTGAGGCGGCCTGT 62.989 66.667 29.31 15.86 46.52 4.00
4140 5339 4.681978 AACGTGAGGCGGCCTGTC 62.682 66.667 29.31 17.30 46.52 3.51
4143 5342 4.373116 GTGAGGCGGCCTGTCGAA 62.373 66.667 29.31 3.43 31.76 3.71
4144 5343 3.621805 TGAGGCGGCCTGTCGAAA 61.622 61.111 29.31 1.47 31.76 3.46
4145 5344 2.358247 GAGGCGGCCTGTCGAAAA 60.358 61.111 29.31 0.00 31.76 2.29
4146 5345 2.358737 AGGCGGCCTGTCGAAAAG 60.359 61.111 23.19 0.00 29.57 2.27
4147 5346 2.668550 GGCGGCCTGTCGAAAAGT 60.669 61.111 12.87 0.00 0.00 2.66
4148 5347 1.375013 GGCGGCCTGTCGAAAAGTA 60.375 57.895 12.87 0.00 0.00 2.24
4149 5348 1.359459 GGCGGCCTGTCGAAAAGTAG 61.359 60.000 12.87 0.00 0.00 2.57
4150 5349 1.967597 GCGGCCTGTCGAAAAGTAGC 61.968 60.000 0.00 0.00 0.00 3.58
4151 5350 0.669318 CGGCCTGTCGAAAAGTAGCA 60.669 55.000 0.00 0.00 0.00 3.49
4152 5351 1.739067 GGCCTGTCGAAAAGTAGCAT 58.261 50.000 0.00 0.00 0.00 3.79
4153 5352 1.666189 GGCCTGTCGAAAAGTAGCATC 59.334 52.381 0.00 0.00 0.00 3.91
4154 5353 1.324736 GCCTGTCGAAAAGTAGCATCG 59.675 52.381 0.00 0.00 37.90 3.84
4155 5354 1.324736 CCTGTCGAAAAGTAGCATCGC 59.675 52.381 0.00 0.00 36.56 4.58
4156 5355 0.989164 TGTCGAAAAGTAGCATCGCG 59.011 50.000 0.00 0.00 36.56 5.87
4157 5356 0.989890 GTCGAAAAGTAGCATCGCGT 59.010 50.000 5.77 0.00 36.56 6.01
4158 5357 0.989164 TCGAAAAGTAGCATCGCGTG 59.011 50.000 5.77 5.06 36.56 5.34
4167 5366 3.685592 CATCGCGTGCTCTCACTC 58.314 61.111 5.77 0.00 40.99 3.51
4168 5367 1.153958 CATCGCGTGCTCTCACTCA 60.154 57.895 5.77 0.00 40.99 3.41
4169 5368 0.733909 CATCGCGTGCTCTCACTCAA 60.734 55.000 5.77 0.00 40.99 3.02
4170 5369 0.734253 ATCGCGTGCTCTCACTCAAC 60.734 55.000 5.77 0.00 40.99 3.18
4171 5370 1.661509 CGCGTGCTCTCACTCAACA 60.662 57.895 0.00 0.00 40.99 3.33
4172 5371 1.612469 CGCGTGCTCTCACTCAACAG 61.612 60.000 0.00 0.00 40.99 3.16
4173 5372 1.895280 GCGTGCTCTCACTCAACAGC 61.895 60.000 0.00 0.00 40.99 4.40
4201 5400 2.413371 GGATCTCGCAAAGTCACAAAGC 60.413 50.000 0.00 0.00 0.00 3.51
4274 5473 4.089208 CGAGAAAGAAAGATCACACTCACG 59.911 45.833 0.00 0.00 0.00 4.35
4277 5476 3.111853 AGAAAGATCACACTCACGCAA 57.888 42.857 0.00 0.00 0.00 4.85
4279 5478 1.512926 AAGATCACACTCACGCAACC 58.487 50.000 0.00 0.00 0.00 3.77
4280 5479 0.392706 AGATCACACTCACGCAACCA 59.607 50.000 0.00 0.00 0.00 3.67
4289 5497 3.206246 ACGCAACCACACCAACGG 61.206 61.111 0.00 0.00 0.00 4.44
4310 5521 1.125270 GTTTAAACAAGGCGCCAACG 58.875 50.000 31.54 18.73 44.07 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 177 1.614317 GGAGAGATTGGTTGTGGGGTG 60.614 57.143 0.00 0.00 0.00 4.61
173 178 0.698818 GGAGAGATTGGTTGTGGGGT 59.301 55.000 0.00 0.00 0.00 4.95
185 190 3.532155 GTGGCGGCGAGGAGAGAT 61.532 66.667 12.98 0.00 0.00 2.75
241 249 1.274447 AGCGGCTTAAGAACTTACGGT 59.726 47.619 6.67 3.18 0.00 4.83
252 260 3.987220 GCAAATTCAAGAAAGCGGCTTAA 59.013 39.130 16.73 6.50 0.00 1.85
253 261 3.255642 AGCAAATTCAAGAAAGCGGCTTA 59.744 39.130 16.73 0.00 0.00 3.09
255 263 1.615392 AGCAAATTCAAGAAAGCGGCT 59.385 42.857 0.00 0.00 0.00 5.52
256 264 2.070262 AGCAAATTCAAGAAAGCGGC 57.930 45.000 0.00 0.00 0.00 6.53
257 265 2.989166 GGAAGCAAATTCAAGAAAGCGG 59.011 45.455 0.00 0.00 39.91 5.52
258 266 2.658325 CGGAAGCAAATTCAAGAAAGCG 59.342 45.455 0.00 0.00 39.91 4.68
292 300 5.473039 CCGCTCATACAACATATCAGATCA 58.527 41.667 0.00 0.00 0.00 2.92
301 309 0.392461 AACCGCCGCTCATACAACAT 60.392 50.000 0.00 0.00 0.00 2.71
313 331 1.065851 ACTAACCAAACAAAACCGCCG 59.934 47.619 0.00 0.00 0.00 6.46
314 332 2.875087 ACTAACCAAACAAAACCGCC 57.125 45.000 0.00 0.00 0.00 6.13
316 334 6.707599 TGAAAAACTAACCAAACAAAACCG 57.292 33.333 0.00 0.00 0.00 4.44
317 335 9.900710 AATTTGAAAAACTAACCAAACAAAACC 57.099 25.926 0.00 0.00 32.26 3.27
345 363 5.051973 CCAAAACGACCTCGATTTTTCAAAC 60.052 40.000 0.78 0.00 41.29 2.93
414 432 1.433064 CATCCCACGGCCAAAATCG 59.567 57.895 2.24 0.00 0.00 3.34
447 465 7.704472 CCATACAAACTTAAGCACAAGACAAAA 59.296 33.333 1.29 0.00 0.00 2.44
461 479 4.017958 TCCAATCTGGCCCATACAAACTTA 60.018 41.667 0.00 0.00 37.47 2.24
467 485 2.421725 AGATCCAATCTGGCCCATACA 58.578 47.619 0.00 0.00 38.44 2.29
503 521 2.202479 GGCGCAAAATCTGACGGC 60.202 61.111 10.83 0.00 40.67 5.68
571 589 8.164070 AGTACAAAATCTGTTCCAAACCTAGAT 58.836 33.333 0.00 0.00 39.64 1.98
592 610 1.897133 ACCACGGCATGAACTAGTACA 59.103 47.619 0.00 0.00 0.00 2.90
628 646 4.449131 CTCAGAAATCAGGCTTGCAGATA 58.551 43.478 0.00 0.00 0.00 1.98
634 652 1.129998 CGTGCTCAGAAATCAGGCTTG 59.870 52.381 0.00 0.00 0.00 4.01
663 681 7.334171 CAGGTTAATTTTCCCAAAATCACATCC 59.666 37.037 0.00 0.00 40.05 3.51
693 711 1.490574 AGCAGGGCCTACTGACTTAG 58.509 55.000 5.28 0.00 40.97 2.18
697 715 1.202698 CCAATAGCAGGGCCTACTGAC 60.203 57.143 16.88 4.66 40.97 3.51
699 717 0.536006 GCCAATAGCAGGGCCTACTG 60.536 60.000 16.88 3.20 44.53 2.74
700 718 1.839894 GCCAATAGCAGGGCCTACT 59.160 57.895 11.85 11.85 44.53 2.57
710 729 3.423848 GTGCAACCAAGCCAATAGC 57.576 52.632 0.00 0.00 44.25 2.97
766 792 5.335127 GTGCAAGCTACAGTTTTGATATGG 58.665 41.667 0.00 0.00 0.00 2.74
770 796 2.878406 ACGTGCAAGCTACAGTTTTGAT 59.122 40.909 0.00 0.00 0.00 2.57
772 798 2.031560 TCACGTGCAAGCTACAGTTTTG 59.968 45.455 11.67 0.00 0.00 2.44
773 799 2.285083 TCACGTGCAAGCTACAGTTTT 58.715 42.857 11.67 0.00 0.00 2.43
777 803 1.217001 TGTTCACGTGCAAGCTACAG 58.783 50.000 11.67 0.00 0.00 2.74
778 804 1.877637 ATGTTCACGTGCAAGCTACA 58.122 45.000 11.67 8.10 0.00 2.74
808 834 6.442952 ACGAATCAATCTCTATGACTAGCAC 58.557 40.000 0.00 0.00 0.00 4.40
827 858 8.990163 ACTATTTGGGGTTATTATGAACGAAT 57.010 30.769 0.00 0.00 0.00 3.34
942 974 4.836825 AGTCACATACTGCAGCAATAGTT 58.163 39.130 15.27 0.00 36.93 2.24
945 977 3.797039 GGAGTCACATACTGCAGCAATA 58.203 45.455 15.27 0.00 45.40 1.90
947 979 2.099141 GGAGTCACATACTGCAGCAA 57.901 50.000 15.27 2.03 45.40 3.91
1029 1063 2.586425 CCAATCTGGTTTCCACACTGT 58.414 47.619 0.00 0.00 31.35 3.55
1593 1795 5.781210 TTCACAAACAAGTAATCATGGCA 57.219 34.783 0.00 0.00 0.00 4.92
1635 1855 3.149196 CAAGTTGTCCAAGTATGCAGGT 58.851 45.455 0.00 0.00 0.00 4.00
1650 1870 9.436957 ACTAACTCTGAATAATACACCAAGTTG 57.563 33.333 0.00 0.00 0.00 3.16
1692 1912 6.592166 CCATGACAACAATACAAAACAATGC 58.408 36.000 0.00 0.00 0.00 3.56
1973 2277 0.250467 GCATCATGCGGTCAGGGTAT 60.250 55.000 0.00 0.00 31.71 2.73
2036 2340 1.885887 GTGGCATTGTAAGGCTCAACA 59.114 47.619 1.15 0.00 35.75 3.33
2197 2922 7.104290 ACATCATGCTCACAATCATCTATAGG 58.896 38.462 0.00 0.00 0.00 2.57
2268 3092 9.904647 GCATTAATGTTTGTGTTATTAAGCATG 57.095 29.630 16.61 0.00 31.92 4.06
2301 3125 7.224753 TGTTCCGATTCTTCAGTTATGAATAGC 59.775 37.037 0.00 0.00 44.32 2.97
2309 3133 6.406370 ACATCATGTTCCGATTCTTCAGTTA 58.594 36.000 0.00 0.00 0.00 2.24
2329 3183 9.436957 TCTAAAAGAATAGTCAGGACAAACATC 57.563 33.333 1.84 0.00 0.00 3.06
2340 3194 6.655003 CCCAAACTGCTCTAAAAGAATAGTCA 59.345 38.462 0.00 0.00 0.00 3.41
2383 3237 6.017109 GCACAAGAGTCCATTTAGAGTTTCAA 60.017 38.462 0.00 0.00 0.00 2.69
2468 3519 9.973450 ACATCTGAATCATAACAGTGTAGTATC 57.027 33.333 0.00 0.00 35.84 2.24
2498 3549 5.922544 CCAACTTAAGCAAAATCTCAACCAG 59.077 40.000 1.29 0.00 0.00 4.00
2652 3704 3.813529 ACTGCAGAAAATAACACGAGC 57.186 42.857 23.35 0.00 0.00 5.03
2790 3842 1.971357 ACCATGAAGAAGTGGAGACGT 59.029 47.619 0.00 0.00 38.86 4.34
3192 4244 2.598099 TCGCCCGTGTACCAGTGA 60.598 61.111 0.00 0.00 0.00 3.41
3365 4423 0.469331 TCACGGAGGAACACAGACCT 60.469 55.000 0.00 0.00 39.41 3.85
3366 4424 0.608640 ATCACGGAGGAACACAGACC 59.391 55.000 0.00 0.00 0.00 3.85
3377 4435 2.126463 ACGCACACGATCACGGAG 60.126 61.111 0.00 0.00 43.93 4.63
3380 4438 3.059472 GAGCACGCACACGATCACG 62.059 63.158 0.00 0.00 43.93 4.35
3399 4457 2.487986 CCATCAGAAATAGCCCCTGACC 60.488 54.545 0.00 0.00 39.43 4.02
3403 4461 1.423161 GAGCCATCAGAAATAGCCCCT 59.577 52.381 0.00 0.00 0.00 4.79
3429 4487 3.844657 CGAAACACACACTACTAGTAGCG 59.155 47.826 26.54 20.73 36.66 4.26
3477 4549 0.385390 CCAGCAACAAGTCCACAACC 59.615 55.000 0.00 0.00 0.00 3.77
3480 4552 1.102154 CAACCAGCAACAAGTCCACA 58.898 50.000 0.00 0.00 0.00 4.17
3495 4567 2.870411 GACACAGACCAACTACACAACC 59.130 50.000 0.00 0.00 0.00 3.77
3498 4570 1.067974 CCGACACAGACCAACTACACA 59.932 52.381 0.00 0.00 0.00 3.72
3499 4571 1.604693 CCCGACACAGACCAACTACAC 60.605 57.143 0.00 0.00 0.00 2.90
3500 4572 0.677288 CCCGACACAGACCAACTACA 59.323 55.000 0.00 0.00 0.00 2.74
3507 4579 1.997606 CGAATTAACCCGACACAGACC 59.002 52.381 0.00 0.00 0.00 3.85
3546 4618 4.457834 AAGATCTCAAGTCCACCGTAAG 57.542 45.455 0.00 0.00 0.00 2.34
3555 4631 5.845391 ACCTGCTACTAAGATCTCAAGTC 57.155 43.478 12.62 3.02 0.00 3.01
3607 4687 4.350346 TCATTGTGAAGAAACAGCAAACG 58.650 39.130 0.00 0.00 0.00 3.60
3626 4706 3.890756 TGGCAATCACAAACTCTGTTCAT 59.109 39.130 0.00 0.00 35.47 2.57
3627 4707 3.066621 GTGGCAATCACAAACTCTGTTCA 59.933 43.478 0.00 0.00 45.39 3.18
3629 4709 3.715628 GTGGCAATCACAAACTCTGTT 57.284 42.857 0.00 0.00 45.39 3.16
3639 4719 0.107703 TCCATCGAGGTGGCAATCAC 60.108 55.000 0.00 0.00 45.34 3.06
3642 4722 1.414181 CTAGTCCATCGAGGTGGCAAT 59.586 52.381 0.00 0.00 39.19 3.56
3643 4723 0.824109 CTAGTCCATCGAGGTGGCAA 59.176 55.000 0.00 0.00 39.19 4.52
3644 4724 1.676678 GCTAGTCCATCGAGGTGGCA 61.677 60.000 0.00 0.00 39.19 4.92
3645 4725 1.068250 GCTAGTCCATCGAGGTGGC 59.932 63.158 0.00 0.00 39.19 5.01
3646 4726 1.043116 TGGCTAGTCCATCGAGGTGG 61.043 60.000 0.00 0.00 40.72 4.61
3647 4727 2.504920 TGGCTAGTCCATCGAGGTG 58.495 57.895 0.00 0.00 40.72 4.00
3660 4740 1.254975 TGGTTCAGCTAGCGTGGCTA 61.255 55.000 9.55 0.00 40.44 3.93
3661 4741 2.111999 TTGGTTCAGCTAGCGTGGCT 62.112 55.000 9.55 0.00 43.41 4.75
3662 4742 1.026718 ATTGGTTCAGCTAGCGTGGC 61.027 55.000 9.55 1.47 0.00 5.01
3665 4745 0.613260 TCCATTGGTTCAGCTAGCGT 59.387 50.000 9.55 0.00 0.00 5.07
3668 4748 2.237143 TCCAGTCCATTGGTTCAGCTAG 59.763 50.000 1.86 0.00 39.35 3.42
3669 4749 2.265367 TCCAGTCCATTGGTTCAGCTA 58.735 47.619 1.86 0.00 39.35 3.32
3670 4750 1.067295 TCCAGTCCATTGGTTCAGCT 58.933 50.000 1.86 0.00 39.35 4.24
3673 4753 1.075212 TGCATCCAGTCCATTGGTTCA 59.925 47.619 1.86 0.00 39.35 3.18
3674 4754 1.474077 GTGCATCCAGTCCATTGGTTC 59.526 52.381 1.86 0.00 39.35 3.62
3675 4755 1.203038 TGTGCATCCAGTCCATTGGTT 60.203 47.619 1.86 0.00 39.35 3.67
3694 4783 4.715983 GGCAACTGCGGCAATATG 57.284 55.556 3.44 4.58 43.26 1.78
3706 4795 1.298859 CGTAGCAGGGACAAGGCAAC 61.299 60.000 0.00 0.00 0.00 4.17
3707 4796 1.003839 CGTAGCAGGGACAAGGCAA 60.004 57.895 0.00 0.00 0.00 4.52
3709 4798 1.448013 GACGTAGCAGGGACAAGGC 60.448 63.158 0.00 0.00 0.00 4.35
3711 4800 1.805945 GCGACGTAGCAGGGACAAG 60.806 63.158 16.21 0.00 37.05 3.16
3714 4803 3.755628 TGGCGACGTAGCAGGGAC 61.756 66.667 22.25 5.01 39.27 4.46
3716 4805 4.814294 GGTGGCGACGTAGCAGGG 62.814 72.222 22.25 0.00 39.27 4.45
3722 4811 0.173935 CATACCAAGGTGGCGACGTA 59.826 55.000 1.07 0.00 42.67 3.57
3731 4820 1.897133 TGACACGTAGCATACCAAGGT 59.103 47.619 0.00 0.00 38.71 3.50
3735 4824 1.480545 AGCATGACACGTAGCATACCA 59.519 47.619 0.00 0.00 38.71 3.25
3737 4826 2.282555 CACAGCATGACACGTAGCATAC 59.717 50.000 0.00 0.00 39.69 2.39
3739 4828 1.362768 CACAGCATGACACGTAGCAT 58.637 50.000 0.00 0.00 39.69 3.79
3742 4831 1.686566 CGGCACAGCATGACACGTAG 61.687 60.000 0.00 0.00 39.69 3.51
3749 4838 3.356267 GCACACGGCACAGCATGA 61.356 61.111 0.00 0.00 43.97 3.07
3767 4856 1.129809 GTGTCAAACGATGCCGACG 59.870 57.895 0.00 0.00 39.50 5.12
3833 4944 1.607148 CAGATACGATACCACTGCCGA 59.393 52.381 0.00 0.00 0.00 5.54
3865 4983 0.884704 GCTGGTTTTCTGCCTCACGA 60.885 55.000 0.00 0.00 34.72 4.35
3872 4990 1.068264 GTAGCTTGGCTGGTTTTCTGC 60.068 52.381 0.00 0.00 40.10 4.26
3903 5032 1.970092 CTAGCAGCCTAGTACGGTCT 58.030 55.000 0.00 0.00 36.99 3.85
4016 5173 1.195674 GACCTCGCTTTCAGTTTCAGC 59.804 52.381 0.00 0.00 0.00 4.26
4063 5220 2.418609 GCACAAAAAGGCAGAACCAACT 60.419 45.455 0.00 0.00 43.14 3.16
4084 5241 1.937846 GCGATGCATGCAAAGCTCG 60.938 57.895 30.94 29.70 36.46 5.03
4090 5248 1.138036 GCTGAAGCGATGCATGCAA 59.862 52.632 26.68 8.49 33.85 4.08
4091 5249 2.795973 GCTGAAGCGATGCATGCA 59.204 55.556 25.04 25.04 33.85 3.96
4133 5332 1.666189 GATGCTACTTTTCGACAGGCC 59.334 52.381 0.00 0.00 0.00 5.19
4134 5333 1.324736 CGATGCTACTTTTCGACAGGC 59.675 52.381 0.00 0.00 34.92 4.85
4135 5334 1.324736 GCGATGCTACTTTTCGACAGG 59.675 52.381 0.00 0.00 34.92 4.00
4136 5335 1.007011 CGCGATGCTACTTTTCGACAG 60.007 52.381 0.00 0.00 34.92 3.51
4137 5336 0.989164 CGCGATGCTACTTTTCGACA 59.011 50.000 0.00 0.00 34.92 4.35
4138 5337 0.989890 ACGCGATGCTACTTTTCGAC 59.010 50.000 15.93 0.00 34.92 4.20
4139 5338 0.989164 CACGCGATGCTACTTTTCGA 59.011 50.000 15.93 0.00 34.92 3.71
4140 5339 3.474823 CACGCGATGCTACTTTTCG 57.525 52.632 15.93 0.00 36.02 3.46
4156 5355 3.295734 TGCTGTTGAGTGAGAGCAC 57.704 52.632 0.00 0.00 40.52 4.40
4157 5356 0.250038 GGTGCTGTTGAGTGAGAGCA 60.250 55.000 0.00 0.00 42.80 4.26
4158 5357 1.287730 CGGTGCTGTTGAGTGAGAGC 61.288 60.000 0.00 0.00 36.54 4.09
4159 5358 1.287730 GCGGTGCTGTTGAGTGAGAG 61.288 60.000 0.00 0.00 0.00 3.20
4160 5359 1.300931 GCGGTGCTGTTGAGTGAGA 60.301 57.895 0.00 0.00 0.00 3.27
4161 5360 2.320587 GGCGGTGCTGTTGAGTGAG 61.321 63.158 0.00 0.00 0.00 3.51
4162 5361 2.280797 GGCGGTGCTGTTGAGTGA 60.281 61.111 0.00 0.00 0.00 3.41
4163 5362 3.716006 CGGCGGTGCTGTTGAGTG 61.716 66.667 0.00 0.00 0.00 3.51
4164 5363 4.988598 CCGGCGGTGCTGTTGAGT 62.989 66.667 19.97 0.00 32.22 3.41
4165 5364 3.958147 ATCCGGCGGTGCTGTTGAG 62.958 63.158 27.32 0.00 32.22 3.02
4166 5365 3.950794 GATCCGGCGGTGCTGTTGA 62.951 63.158 27.32 3.55 32.22 3.18
4167 5366 3.499737 GATCCGGCGGTGCTGTTG 61.500 66.667 27.32 0.00 32.22 3.33
4168 5367 3.665675 GAGATCCGGCGGTGCTGTT 62.666 63.158 27.32 6.83 32.22 3.16
4169 5368 4.148825 GAGATCCGGCGGTGCTGT 62.149 66.667 27.32 10.52 32.22 4.40
4173 5372 4.812476 TTGCGAGATCCGGCGGTG 62.812 66.667 27.32 12.61 39.04 4.94
4201 5400 4.150098 GTCAACTGTAGGCTTACTTTGTCG 59.850 45.833 7.57 0.00 31.17 4.35
4260 5459 1.202639 TGGTTGCGTGAGTGTGATCTT 60.203 47.619 0.00 0.00 0.00 2.40
4261 5460 0.392706 TGGTTGCGTGAGTGTGATCT 59.607 50.000 0.00 0.00 0.00 2.75
4262 5461 0.512952 GTGGTTGCGTGAGTGTGATC 59.487 55.000 0.00 0.00 0.00 2.92
4263 5462 0.179059 TGTGGTTGCGTGAGTGTGAT 60.179 50.000 0.00 0.00 0.00 3.06
4264 5463 1.087202 GTGTGGTTGCGTGAGTGTGA 61.087 55.000 0.00 0.00 0.00 3.58
4265 5464 1.351707 GTGTGGTTGCGTGAGTGTG 59.648 57.895 0.00 0.00 0.00 3.82
4266 5465 1.817941 GGTGTGGTTGCGTGAGTGT 60.818 57.895 0.00 0.00 0.00 3.55
4267 5466 1.372838 TTGGTGTGGTTGCGTGAGTG 61.373 55.000 0.00 0.00 0.00 3.51
4268 5467 1.078072 TTGGTGTGGTTGCGTGAGT 60.078 52.632 0.00 0.00 0.00 3.41
4269 5468 1.355210 GTTGGTGTGGTTGCGTGAG 59.645 57.895 0.00 0.00 0.00 3.51
4274 5473 1.381165 AACTCCGTTGGTGTGGTTGC 61.381 55.000 0.00 0.00 29.35 4.17
4277 5476 2.684374 GTTTAAACTCCGTTGGTGTGGT 59.316 45.455 11.18 0.00 29.35 4.16
4279 5478 4.347813 CTTGTTTAAACTCCGTTGGTGTG 58.652 43.478 18.72 0.00 29.35 3.82
4280 5479 3.379057 CCTTGTTTAAACTCCGTTGGTGT 59.621 43.478 18.72 0.00 0.00 4.16
4289 5497 2.390938 GTTGGCGCCTTGTTTAAACTC 58.609 47.619 29.70 0.00 0.00 3.01
4310 5521 2.731976 TGTTTTTGTGAACGTGGTTTGC 59.268 40.909 0.00 0.00 32.18 3.68


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

AutoCloner maintained by Alex Coulton.