Multiple sequence alignment - TraesCS3B01G530800

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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 TraesCS3B01G530800 chr3B 100.000 3868 0 0 1 3868 771667119 771663252 0.000000e+00 7143
1 TraesCS3B01G530800 chr3B 91.729 1342 97 6 1755 3085 771630702 771629364 0.000000e+00 1851
2 TraesCS3B01G530800 chr3B 84.989 1792 194 36 887 2647 771623852 771622105 0.000000e+00 1749
3 TraesCS3B01G530800 chr3B 85.906 894 93 13 887 1761 771634529 771633650 0.000000e+00 922
4 TraesCS3B01G530800 chr3B 90.580 414 34 5 3460 3868 29883701 29883288 9.450000e-151 544
5 TraesCS3B01G530800 chr3A 90.116 1983 166 15 875 2836 713964005 713962032 0.000000e+00 2549
6 TraesCS3B01G530800 chr3A 85.139 1191 126 22 1478 2647 713947023 713945863 0.000000e+00 1171
7 TraesCS3B01G530800 chr3A 94.553 257 10 2 2830 3085 713957136 713956883 1.010000e-105 394
8 TraesCS3B01G530800 chr3A 97.403 77 1 1 816 891 713964095 713964019 3.140000e-26 130
9 TraesCS3B01G530800 chr3D 86.047 1763 174 33 917 2647 578270354 578268632 0.000000e+00 1827
10 TraesCS3B01G530800 chr3D 80.864 1782 246 58 816 2539 578273737 578271993 0.000000e+00 1314
11 TraesCS3B01G530800 chr3D 92.457 411 26 5 3460 3865 121212952 121213362 2.000000e-162 582
12 TraesCS3B01G530800 chr3D 90.338 414 34 6 3460 3868 80255929 80255517 4.400000e-149 538
13 TraesCS3B01G530800 chr3D 84.367 371 53 4 3090 3456 121212246 121212615 3.670000e-95 359
14 TraesCS3B01G530800 chr5D 83.906 727 108 7 34 754 456587893 456588616 0.000000e+00 686
15 TraesCS3B01G530800 chr5D 91.727 411 29 5 3460 3865 386175236 386174826 2.020000e-157 566
16 TraesCS3B01G530800 chr5D 91.176 408 31 5 3460 3862 257155524 257155117 2.030000e-152 549
17 TraesCS3B01G530800 chr1D 82.580 752 116 10 11 754 91013831 91013087 0.000000e+00 649
18 TraesCS3B01G530800 chr2B 81.867 750 124 10 11 753 212568970 212569714 4.240000e-174 621
19 TraesCS3B01G530800 chr2B 85.714 364 50 2 3099 3461 791981003 791981365 2.180000e-102 383
20 TraesCS3B01G530800 chr2B 85.135 370 53 2 3093 3461 791960195 791960563 1.010000e-100 377
21 TraesCS3B01G530800 chr2B 85.135 370 53 2 3093 3461 792043599 792043967 1.010000e-100 377
22 TraesCS3B01G530800 chr2B 81.963 377 60 7 3085 3458 670988397 670988768 2.900000e-81 313
23 TraesCS3B01G530800 chr1A 82.591 718 104 13 49 754 587920775 587921483 7.100000e-172 614
24 TraesCS3B01G530800 chr2A 81.855 733 125 7 25 754 144917456 144916729 9.190000e-171 610
25 TraesCS3B01G530800 chr6D 82.213 714 111 12 52 758 57466046 57466750 5.530000e-168 601
26 TraesCS3B01G530800 chr6D 90.580 414 34 5 3460 3868 459081507 459081094 9.450000e-151 544
27 TraesCS3B01G530800 chr1B 81.383 752 124 13 13 754 513146212 513146957 1.990000e-167 599
28 TraesCS3B01G530800 chr1B 86.312 263 35 1 3097 3359 12065731 12065992 6.330000e-73 285
29 TraesCS3B01G530800 chr4A 81.564 716 121 9 50 758 627729984 627730695 7.200000e-162 580
30 TraesCS3B01G530800 chr4A 81.399 715 124 7 50 758 627623313 627624024 3.350000e-160 575
31 TraesCS3B01G530800 chr7D 91.787 414 29 5 3460 3868 595964216 595963803 4.340000e-159 571
32 TraesCS3B01G530800 chr7D 90.488 410 33 6 3462 3865 625229748 625230157 1.580000e-148 536
33 TraesCS3B01G530800 chr7D 87.302 315 38 2 3091 3404 97614167 97613854 3.670000e-95 359
34 TraesCS3B01G530800 chrUn 91.525 413 31 4 3460 3868 110645664 110645252 2.020000e-157 566
35 TraesCS3B01G530800 chr5A 85.526 380 53 2 3082 3459 132919019 132918640 2.800000e-106 396
36 TraesCS3B01G530800 chr4B 81.657 338 51 8 3085 3412 94521951 94521615 1.770000e-68 270


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 TraesCS3B01G530800 chr3B 771663252 771667119 3867 True 7143.0 7143 100.0000 1 3868 1 chr3B.!!$R3 3867
1 TraesCS3B01G530800 chr3B 771622105 771623852 1747 True 1749.0 1749 84.9890 887 2647 1 chr3B.!!$R2 1760
2 TraesCS3B01G530800 chr3B 771629364 771634529 5165 True 1386.5 1851 88.8175 887 3085 2 chr3B.!!$R4 2198
3 TraesCS3B01G530800 chr3A 713962032 713964095 2063 True 1339.5 2549 93.7595 816 2836 2 chr3A.!!$R3 2020
4 TraesCS3B01G530800 chr3A 713945863 713947023 1160 True 1171.0 1171 85.1390 1478 2647 1 chr3A.!!$R1 1169
5 TraesCS3B01G530800 chr3D 578268632 578273737 5105 True 1570.5 1827 83.4555 816 2647 2 chr3D.!!$R2 1831
6 TraesCS3B01G530800 chr3D 121212246 121213362 1116 False 470.5 582 88.4120 3090 3865 2 chr3D.!!$F1 775
7 TraesCS3B01G530800 chr5D 456587893 456588616 723 False 686.0 686 83.9060 34 754 1 chr5D.!!$F1 720
8 TraesCS3B01G530800 chr1D 91013087 91013831 744 True 649.0 649 82.5800 11 754 1 chr1D.!!$R1 743
9 TraesCS3B01G530800 chr2B 212568970 212569714 744 False 621.0 621 81.8670 11 753 1 chr2B.!!$F1 742
10 TraesCS3B01G530800 chr1A 587920775 587921483 708 False 614.0 614 82.5910 49 754 1 chr1A.!!$F1 705
11 TraesCS3B01G530800 chr2A 144916729 144917456 727 True 610.0 610 81.8550 25 754 1 chr2A.!!$R1 729
12 TraesCS3B01G530800 chr6D 57466046 57466750 704 False 601.0 601 82.2130 52 758 1 chr6D.!!$F1 706
13 TraesCS3B01G530800 chr1B 513146212 513146957 745 False 599.0 599 81.3830 13 754 1 chr1B.!!$F2 741
14 TraesCS3B01G530800 chr4A 627729984 627730695 711 False 580.0 580 81.5640 50 758 1 chr4A.!!$F2 708
15 TraesCS3B01G530800 chr4A 627623313 627624024 711 False 575.0 575 81.3990 50 758 1 chr4A.!!$F1 708

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
205 214 0.108138 CTTGGGTCCTACGAAGGCTG 60.108 60.0 0.00 0.00 43.31 4.85 F
721 760 0.392863 CAAGTCCGTGGATGGATGCA 60.393 55.0 0.00 0.00 40.91 3.96 F
1814 8130 0.320421 TGCTGCTTTGTCGAGGTACC 60.320 55.0 2.73 2.73 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 5078 0.179004 AACATCAGTGAACCCCGCAA 60.179 50.0 0.00 0.0 0.00 4.85 R
2162 8504 0.321671 TCCCTTCAGGTTGAGCGAAG 59.678 55.0 0.00 0.0 36.68 3.79 R
3266 9611 0.107268 ACCCATTTATACGCGGTCCC 59.893 55.0 12.47 0.0 0.00 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
111 114 2.985896 GCAGAAGCCAGGTATGTACAA 58.014 47.619 0.00 0.00 33.58 2.41
168 177 1.472376 GCCATCACCGAGGAGAAGAAG 60.472 57.143 0.00 0.00 0.00 2.85
204 213 1.900545 GCTTGGGTCCTACGAAGGCT 61.901 60.000 0.00 0.00 43.31 4.58
205 214 0.108138 CTTGGGTCCTACGAAGGCTG 60.108 60.000 0.00 0.00 43.31 4.85
234 243 1.295792 CAACACCTGCGTACACAACT 58.704 50.000 0.00 0.00 0.00 3.16
257 267 0.673956 GTCTTGCCCGGTTCTTCTCC 60.674 60.000 0.00 0.00 0.00 3.71
269 279 3.073209 GGTTCTTCTCCTTTGAGGACCTT 59.927 47.826 0.00 0.00 40.06 3.50
272 282 1.267121 TCTCCTTTGAGGACCTTCGG 58.733 55.000 0.00 0.00 40.06 4.30
367 380 2.047179 GTGAGTGACGGGGAAGCC 60.047 66.667 0.00 0.00 0.00 4.35
389 402 1.134995 GCCATCCTTTGCACTTAAGCC 60.135 52.381 1.29 0.00 0.00 4.35
397 410 5.045140 TCCTTTGCACTTAAGCCTATACCTT 60.045 40.000 1.29 0.00 0.00 3.50
400 413 5.174037 TGCACTTAAGCCTATACCTTTGT 57.826 39.130 1.29 0.00 0.00 2.83
403 416 5.741011 CACTTAAGCCTATACCTTTGTGGA 58.259 41.667 1.29 0.00 39.71 4.02
464 477 1.850755 AAAGGGATCCGTGGGTGGT 60.851 57.895 7.93 0.00 0.00 4.16
523 536 5.353938 GGACTAGCACCGTTGATGTAAATA 58.646 41.667 0.00 0.00 0.00 1.40
535 548 9.273016 CCGTTGATGTAAATATACTGAAATCCT 57.727 33.333 0.00 0.00 32.98 3.24
558 593 9.002600 TCCTTCATGTTTATATGAAATCCATCG 57.997 33.333 0.00 0.00 44.06 3.84
586 621 2.536761 TGAAATCCGGTCGAGTTTGT 57.463 45.000 0.00 0.00 0.00 2.83
590 625 3.880047 AATCCGGTCGAGTTTGTATGA 57.120 42.857 0.00 0.00 0.00 2.15
604 639 4.678509 TTGTATGAAATCCGCACTTGTC 57.321 40.909 0.00 0.00 0.00 3.18
625 660 3.380004 TCTGCACAAATTTCGTCTGGTTT 59.620 39.130 0.00 0.00 0.00 3.27
637 672 3.372822 TCGTCTGGTTTGTTTCAGTTGTC 59.627 43.478 0.00 0.00 33.13 3.18
651 686 6.612247 TTCAGTTGTCGTGAAAATGTATGT 57.388 33.333 0.00 0.00 30.89 2.29
653 688 4.612614 CAGTTGTCGTGAAAATGTATGTGC 59.387 41.667 0.00 0.00 0.00 4.57
681 716 3.576078 TGGATGATTGCCTTCCGTATT 57.424 42.857 0.00 0.00 40.86 1.89
699 736 1.678598 TTCGTGTCCGTGGACTGGTT 61.679 55.000 19.17 0.00 44.80 3.67
703 742 2.122769 TCCGTGGACTGGTTCCCA 60.123 61.111 0.00 0.00 45.17 4.37
704 743 1.766864 TCCGTGGACTGGTTCCCAA 60.767 57.895 0.00 0.00 45.17 4.12
721 760 0.392863 CAAGTCCGTGGATGGATGCA 60.393 55.000 0.00 0.00 40.91 3.96
754 794 0.610232 GGTTGCTGTTGGAGATGCCT 60.610 55.000 0.00 0.00 37.63 4.75
758 798 2.436417 TGCTGTTGGAGATGCCTTTAC 58.564 47.619 0.00 0.00 37.63 2.01
759 799 1.398390 GCTGTTGGAGATGCCTTTACG 59.602 52.381 0.00 0.00 37.63 3.18
760 800 2.009774 CTGTTGGAGATGCCTTTACGG 58.990 52.381 0.00 0.00 37.63 4.02
774 814 5.183014 CCTTTACGGCTTTTCAAGTTTCT 57.817 39.130 0.00 0.00 0.00 2.52
775 815 4.976116 CCTTTACGGCTTTTCAAGTTTCTG 59.024 41.667 0.00 0.00 0.00 3.02
776 816 2.492019 ACGGCTTTTCAAGTTTCTGC 57.508 45.000 0.00 0.00 0.00 4.26
777 817 1.067060 ACGGCTTTTCAAGTTTCTGCC 59.933 47.619 0.00 0.00 35.94 4.85
778 818 1.338020 CGGCTTTTCAAGTTTCTGCCT 59.662 47.619 0.00 0.00 37.01 4.75
779 819 2.223805 CGGCTTTTCAAGTTTCTGCCTT 60.224 45.455 0.00 0.00 37.01 4.35
780 820 3.004315 CGGCTTTTCAAGTTTCTGCCTTA 59.996 43.478 0.00 0.00 37.01 2.69
781 821 4.321230 CGGCTTTTCAAGTTTCTGCCTTAT 60.321 41.667 0.00 0.00 37.01 1.73
782 822 5.541845 GGCTTTTCAAGTTTCTGCCTTATT 58.458 37.500 0.00 0.00 36.32 1.40
783 823 5.991606 GGCTTTTCAAGTTTCTGCCTTATTT 59.008 36.000 0.00 0.00 36.32 1.40
784 824 6.483307 GGCTTTTCAAGTTTCTGCCTTATTTT 59.517 34.615 0.00 0.00 36.32 1.82
785 825 7.012327 GGCTTTTCAAGTTTCTGCCTTATTTTT 59.988 33.333 0.00 0.00 36.32 1.94
877 924 2.352519 GGTGAGGTCGGTACAAACTCTC 60.353 54.545 12.26 9.17 0.00 3.20
928 1005 6.362686 CGATCGTTGTCATCAGAAAAGAAAA 58.637 36.000 7.03 0.00 0.00 2.29
953 1030 3.129638 TCCTTTTCCCAAACAGAAACGTG 59.870 43.478 0.00 0.00 33.11 4.49
1001 1082 0.732880 CGTGTCTAGGCGGTTCACAG 60.733 60.000 0.00 0.00 0.00 3.66
1024 1112 1.575244 CGAGCAACGATGGATCACAT 58.425 50.000 0.00 0.00 45.77 3.21
1205 4543 1.880646 GCCAACTACAACGACCACCAT 60.881 52.381 0.00 0.00 0.00 3.55
1245 4589 2.583441 CCCTCCACTTCCTGCGTCA 61.583 63.158 0.00 0.00 0.00 4.35
1280 4624 0.400594 ACTTCCTGCCCAACTACACC 59.599 55.000 0.00 0.00 0.00 4.16
1405 4749 1.452110 CCTGGAACGCACAATGATGA 58.548 50.000 0.00 0.00 0.00 2.92
1484 4828 3.775316 TGTTCTTGATCCCTCCTAAGGAC 59.225 47.826 0.00 0.00 46.67 3.85
1490 4834 2.012168 TCCCTCCTAAGGACCTAGGT 57.988 55.000 16.26 16.26 46.67 3.08
1556 4900 3.195661 ACAGCTCGTCGAAGAAAACTTT 58.804 40.909 1.95 0.00 39.69 2.66
1573 4917 8.771766 AGAAAACTTTACGATAAGTTCAAGACC 58.228 33.333 16.04 6.36 45.13 3.85
1574 4918 8.672823 AAAACTTTACGATAAGTTCAAGACCT 57.327 30.769 16.04 1.72 45.13 3.85
1575 4919 7.886405 AACTTTACGATAAGTTCAAGACCTC 57.114 36.000 11.87 0.00 43.04 3.85
1617 4979 1.811266 CACTCGACGGAATGGCCAG 60.811 63.158 13.05 0.00 35.94 4.85
1656 5018 3.436704 GGACGTTTTCTCATCAAGCATGA 59.563 43.478 0.00 0.00 39.39 3.07
1716 5078 2.438411 CTACGAGGAGAGTGGTCAACT 58.562 52.381 0.00 0.00 43.85 3.16
1737 5099 1.305930 GCGGGGTTCACTGATGTTCC 61.306 60.000 0.00 0.00 0.00 3.62
1738 5100 0.324943 CGGGGTTCACTGATGTTCCT 59.675 55.000 0.00 0.00 0.00 3.36
1763 8079 0.911769 ATTGGGTGAGAAGATGGCGA 59.088 50.000 0.00 0.00 0.00 5.54
1779 8095 1.007271 CGATACAGCGCCTACTGGG 60.007 63.158 2.29 0.00 42.21 4.45
1808 8124 2.162319 TACATGTGCTGCTTTGTCGA 57.838 45.000 9.11 0.00 0.00 4.20
1814 8130 0.320421 TGCTGCTTTGTCGAGGTACC 60.320 55.000 2.73 2.73 0.00 3.34
1882 8213 6.737254 ATTCCCTTGTACTCGTATTGTTTG 57.263 37.500 0.00 0.00 0.00 2.93
1897 8228 6.305399 CGTATTGTTTGTTTGACATCACCATC 59.695 38.462 0.00 0.00 0.00 3.51
1898 8229 5.588958 TTGTTTGTTTGACATCACCATCA 57.411 34.783 0.00 0.00 0.00 3.07
1899 8230 5.588958 TGTTTGTTTGACATCACCATCAA 57.411 34.783 0.00 0.00 33.03 2.57
1900 8231 6.159299 TGTTTGTTTGACATCACCATCAAT 57.841 33.333 0.00 0.00 34.87 2.57
1901 8232 7.282332 TGTTTGTTTGACATCACCATCAATA 57.718 32.000 0.00 0.00 34.87 1.90
1902 8233 7.894708 TGTTTGTTTGACATCACCATCAATAT 58.105 30.769 0.00 0.00 34.87 1.28
1908 8246 9.060347 GTTTGACATCACCATCAATATCACTAT 57.940 33.333 0.00 0.00 34.87 2.12
1952 8294 3.316308 GGCGATCTTTGCAGGTTATCATT 59.684 43.478 0.00 0.00 0.00 2.57
2016 8358 4.437659 GCTAACGAACACAAAGTTGGACAA 60.438 41.667 0.00 0.00 41.51 3.18
2070 8412 3.120199 ACTTTGCAAATCTTCGTGATCGG 60.120 43.478 13.23 0.00 37.69 4.18
2075 8417 3.309682 GCAAATCTTCGTGATCGGATTCA 59.690 43.478 0.00 0.00 37.69 2.57
2083 8425 3.118775 TCGTGATCGGATTCAGATTTGGT 60.119 43.478 0.75 0.00 37.69 3.67
2086 8428 5.360591 GTGATCGGATTCAGATTTGGTACT 58.639 41.667 0.75 0.00 0.00 2.73
2090 8432 5.989477 TCGGATTCAGATTTGGTACTTGAT 58.011 37.500 0.00 0.00 0.00 2.57
2110 8452 6.757897 TGATTGAATCAAATGGTGAGGTAC 57.242 37.500 5.21 0.00 40.43 3.34
2174 8516 5.468072 CAGCAAATATATCTTCGCTCAACCT 59.532 40.000 0.00 0.00 0.00 3.50
2175 8517 5.468072 AGCAAATATATCTTCGCTCAACCTG 59.532 40.000 0.00 0.00 0.00 4.00
2187 8529 2.290577 GCTCAACCTGAAGGGAATCTGT 60.291 50.000 0.56 0.00 40.27 3.41
2230 8572 9.784531 ATGACGATCCTAATCTTGACAAATATT 57.215 29.630 0.00 0.00 0.00 1.28
2261 8603 5.409826 ACAAAAGGCTAGAGAAAGTGATTCG 59.590 40.000 0.00 0.00 43.15 3.34
2310 8652 2.571757 GATGAGTGTGGACGCCGA 59.428 61.111 0.00 0.00 0.00 5.54
2311 8653 1.141881 GATGAGTGTGGACGCCGAT 59.858 57.895 0.00 0.00 0.00 4.18
2338 8680 2.736721 CACTGTCCGTTACTTGGATGTG 59.263 50.000 4.57 4.57 37.93 3.21
2494 8836 3.040147 TGTCGGTTGATGAGTCCTTTC 57.960 47.619 0.00 0.00 0.00 2.62
2505 8847 3.381335 TGAGTCCTTTCTATACACCCCC 58.619 50.000 0.00 0.00 0.00 5.40
2542 8884 3.598299 CTTCCAGAGAAGGCTGAAAGAG 58.402 50.000 0.00 0.00 44.97 2.85
2549 8891 5.760253 CAGAGAAGGCTGAAAGAGTTAAACA 59.240 40.000 0.00 0.00 38.14 2.83
2551 8893 4.822350 AGAAGGCTGAAAGAGTTAAACACC 59.178 41.667 0.00 0.00 34.07 4.16
2555 8897 3.558418 GCTGAAAGAGTTAAACACCGACA 59.442 43.478 0.00 0.00 34.07 4.35
2558 8900 4.936411 TGAAAGAGTTAAACACCGACACAA 59.064 37.500 0.00 0.00 0.00 3.33
2567 8909 1.068417 ACCGACACAAACGCAGCTA 59.932 52.632 0.00 0.00 0.00 3.32
2574 8916 4.537015 GACACAAACGCAGCTAAAGATTT 58.463 39.130 0.00 0.00 0.00 2.17
2696 9041 3.034721 TCGAGCCGATAGTTTGTGTTT 57.965 42.857 0.00 0.00 0.00 2.83
2749 9094 2.558286 CCCCATGCATGGCTAAGCG 61.558 63.158 36.08 22.33 46.70 4.68
2769 9114 2.347452 CGTAATGCCTCGGTTGTGTAAG 59.653 50.000 0.00 0.00 0.00 2.34
2771 9116 2.094762 ATGCCTCGGTTGTGTAAGTC 57.905 50.000 0.00 0.00 0.00 3.01
2772 9117 0.034337 TGCCTCGGTTGTGTAAGTCC 59.966 55.000 0.00 0.00 0.00 3.85
2810 9155 5.983540 TCTTTTTGCAATTACAAAGGTGGT 58.016 33.333 17.17 0.00 40.43 4.16
2865 9210 6.070824 TCAGACATGCTTAAGATTGTGGAGTA 60.071 38.462 6.67 0.00 0.00 2.59
2886 9231 9.027129 GGAGTAAACTTTTATTGAACCACAAAC 57.973 33.333 0.00 0.00 42.03 2.93
2908 9253 9.309516 CAAACTTGTGAGTAAAAGTGAGTACTA 57.690 33.333 0.00 0.00 36.75 1.82
3006 9351 3.002791 CGAGTTCCAGCATTGCTCTTTA 58.997 45.455 8.54 0.00 36.40 1.85
3011 9356 4.492494 TCCAGCATTGCTCTTTATGAGA 57.508 40.909 8.54 0.00 45.39 3.27
3012 9357 5.045012 TCCAGCATTGCTCTTTATGAGAT 57.955 39.130 8.54 0.00 45.39 2.75
3013 9358 6.178607 TCCAGCATTGCTCTTTATGAGATA 57.821 37.500 8.54 0.00 45.39 1.98
3043 9388 5.172934 TGACTAATACGCTTTGGTTAGTGG 58.827 41.667 1.77 0.00 37.47 4.00
3085 9430 3.638627 CAGTTCTCCCTTTCCTGCTTTTT 59.361 43.478 0.00 0.00 0.00 1.94
3139 9484 2.488153 GTCCATGTACTCAGTTTTGCCC 59.512 50.000 0.00 0.00 0.00 5.36
3143 9488 3.126001 TGTACTCAGTTTTGCCCTCAG 57.874 47.619 0.00 0.00 0.00 3.35
3146 9491 2.301346 ACTCAGTTTTGCCCTCAGTTG 58.699 47.619 0.00 0.00 0.00 3.16
3164 9509 0.790207 TGCGAATCGTGCTCAGTTTC 59.210 50.000 4.07 0.00 0.00 2.78
3175 9520 1.187087 CTCAGTTTCGCCCCTAGTCT 58.813 55.000 0.00 0.00 0.00 3.24
3176 9521 0.895530 TCAGTTTCGCCCCTAGTCTG 59.104 55.000 0.00 0.00 0.00 3.51
3181 9526 3.760035 CGCCCCTAGTCTGTGCGT 61.760 66.667 0.00 0.00 40.33 5.24
3224 9569 3.054361 ACGGCCAGATTTAAGTCCATTCT 60.054 43.478 2.24 0.00 0.00 2.40
3225 9570 3.313526 CGGCCAGATTTAAGTCCATTCTG 59.686 47.826 2.24 0.00 34.86 3.02
3230 9575 6.409704 CCAGATTTAAGTCCATTCTGTCTGA 58.590 40.000 0.00 0.00 34.10 3.27
3231 9576 6.538021 CCAGATTTAAGTCCATTCTGTCTGAG 59.462 42.308 0.00 0.00 34.10 3.35
3232 9577 6.538021 CAGATTTAAGTCCATTCTGTCTGAGG 59.462 42.308 0.00 0.00 34.10 3.86
3235 9580 0.615331 GTCCATTCTGTCTGAGGGCA 59.385 55.000 0.00 0.00 0.00 5.36
3266 9611 1.445582 GGTCCGGAGCTTACACGTG 60.446 63.158 26.19 15.48 0.00 4.49
3280 9625 4.810730 CGTGGGACCGCGTATAAA 57.189 55.556 15.63 0.00 43.86 1.40
3288 9633 0.249573 ACCGCGTATAAATGGGTCCG 60.250 55.000 4.92 0.00 0.00 4.79
3293 9638 1.069513 CGTATAAATGGGTCCGGAGCA 59.930 52.381 32.94 20.02 0.00 4.26
3298 9643 1.140312 AATGGGTCCGGAGCATACAT 58.860 50.000 32.94 23.57 0.00 2.29
3307 9652 0.532862 GGAGCATACATGTGGGACCG 60.533 60.000 9.11 0.00 0.00 4.79
3308 9653 0.178068 GAGCATACATGTGGGACCGT 59.822 55.000 9.11 0.00 0.00 4.83
3313 9658 0.326595 TACATGTGGGACCGTGCAAT 59.673 50.000 9.11 0.00 0.00 3.56
3319 9664 1.669760 GGGACCGTGCAATGACGAA 60.670 57.895 6.76 0.00 42.10 3.85
3322 9667 1.002251 GGACCGTGCAATGACGAAAAA 60.002 47.619 6.76 0.00 42.10 1.94
3334 9679 3.592059 TGACGAAAAATCCTAGGGTTCG 58.408 45.455 23.97 23.97 44.93 3.95
3369 9714 1.282875 CGCCGATCTATCTCGTGCA 59.717 57.895 0.00 0.00 36.93 4.57
3370 9715 0.999228 CGCCGATCTATCTCGTGCAC 60.999 60.000 6.82 6.82 36.93 4.57
3404 9750 2.832661 GTGCCACCACCACTTGCA 60.833 61.111 0.00 0.00 35.92 4.08
3405 9751 2.832661 TGCCACCACCACTTGCAC 60.833 61.111 0.00 0.00 0.00 4.57
3406 9752 3.605664 GCCACCACCACTTGCACC 61.606 66.667 0.00 0.00 0.00 5.01
3407 9753 3.286751 CCACCACCACTTGCACCG 61.287 66.667 0.00 0.00 0.00 4.94
3408 9754 3.964875 CACCACCACTTGCACCGC 61.965 66.667 0.00 0.00 0.00 5.68
3411 9757 3.964875 CACCACTTGCACCGCCAC 61.965 66.667 0.00 0.00 0.00 5.01
3412 9758 4.189580 ACCACTTGCACCGCCACT 62.190 61.111 0.00 0.00 0.00 4.00
3413 9759 3.663176 CCACTTGCACCGCCACTG 61.663 66.667 0.00 0.00 0.00 3.66
3414 9760 2.591429 CACTTGCACCGCCACTGA 60.591 61.111 0.00 0.00 0.00 3.41
3436 9782 3.807538 GCTGTCGCGACCGTCCTA 61.808 66.667 34.34 15.26 35.54 2.94
3448 9796 2.893398 GTCCTACTCCACCGCCAG 59.107 66.667 0.00 0.00 0.00 4.85
3467 10163 2.360726 TGCTCCACCGCGTCTCTA 60.361 61.111 4.92 0.00 0.00 2.43
3491 10187 1.481871 TCGTGGGTTAGGATGGAGTC 58.518 55.000 0.00 0.00 0.00 3.36
3501 10197 1.741770 GATGGAGTCGCGGTTTGCT 60.742 57.895 6.13 0.00 43.27 3.91
3507 10203 1.002792 GAGTCGCGGTTTGCTTTCTTT 60.003 47.619 6.13 0.00 43.27 2.52
3526 10222 2.093306 TGTGCACATTAGAAGGGACG 57.907 50.000 17.42 0.00 0.00 4.79
3535 10232 3.393426 TTAGAAGGGACGGTACATCCT 57.607 47.619 13.51 3.21 42.39 3.24
3544 10241 3.006940 GACGGTACATCCTGAATGCAAA 58.993 45.455 0.00 0.00 39.12 3.68
3573 10270 6.656632 AGAAGAAATTTCAAGGAGGTTTCC 57.343 37.500 19.99 0.00 44.39 3.13
3574 10271 5.540337 AGAAGAAATTTCAAGGAGGTTTCCC 59.460 40.000 19.99 0.00 45.24 3.97
3584 10282 3.532102 AGGAGGTTTCCCTTATCTGTGT 58.468 45.455 0.00 0.00 45.24 3.72
3606 10304 5.048083 TGTCAATGGCTTGTAATTGGAGTTC 60.048 40.000 0.00 0.00 35.04 3.01
3607 10305 5.183904 GTCAATGGCTTGTAATTGGAGTTCT 59.816 40.000 0.00 0.00 35.04 3.01
3631 10329 4.222810 AGACAATTTGGGGAGGTAATTTGC 59.777 41.667 0.78 0.00 0.00 3.68
3652 10350 3.909732 CAGCCAATATCCTTGGGGTTTA 58.090 45.455 6.16 0.00 39.90 2.01
3657 10355 5.515106 CCAATATCCTTGGGGTTTACTTGA 58.485 41.667 0.00 0.00 35.96 3.02
3698 10396 6.008696 ACTACGATGGGGAAAATAAATGGA 57.991 37.500 0.00 0.00 0.00 3.41
3748 10446 5.277974 CGCTACCATGTTTGCTAAGCATAAT 60.278 40.000 0.00 0.00 38.76 1.28
3774 10472 5.771666 AGAAAGAGAATTTTCATGTGAGGCA 59.228 36.000 0.00 0.00 39.08 4.75
3775 10473 5.640189 AAGAGAATTTTCATGTGAGGCAG 57.360 39.130 0.00 0.00 0.00 4.85
3804 10502 4.085876 GCTTGAGCAGGCTTTGGA 57.914 55.556 0.00 0.00 41.59 3.53
3807 10507 1.613836 CTTGAGCAGGCTTTGGACTT 58.386 50.000 0.00 0.00 0.00 3.01
3822 10522 3.136123 CTTGGATGGCGGGTGCAG 61.136 66.667 0.00 0.00 45.35 4.41
3831 10531 4.379243 CGGGTGCAGCTTCTCGGT 62.379 66.667 16.65 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.589492 GGAGGCGCGATTGTCGATG 61.589 63.158 12.10 0.00 43.74 3.84
1 2 2.279517 GGAGGCGCGATTGTCGAT 60.280 61.111 12.10 0.00 43.74 3.59
2 3 4.508128 GGGAGGCGCGATTGTCGA 62.508 66.667 12.10 0.00 43.74 4.20
104 107 1.614385 CGACTCGTCGCTTTGTACAT 58.386 50.000 6.52 0.00 46.50 2.29
182 191 0.608640 CTTCGTAGGACCCAAGCAGT 59.391 55.000 0.00 0.00 0.00 4.40
184 193 1.980052 CCTTCGTAGGACCCAAGCA 59.020 57.895 0.98 0.00 45.05 3.91
234 243 1.990160 AAGAACCGGGCAAGACACCA 61.990 55.000 6.32 0.00 0.00 4.17
287 297 2.125106 GCCTCCGCTTCCGTGAAT 60.125 61.111 0.00 0.00 0.00 2.57
350 363 2.047179 GGCTTCCCCGTCACTCAC 60.047 66.667 0.00 0.00 0.00 3.51
357 370 4.115199 GATGGCTGGCTTCCCCGT 62.115 66.667 2.00 0.00 35.87 5.28
367 380 2.416431 GCTTAAGTGCAAAGGATGGCTG 60.416 50.000 4.02 0.00 0.00 4.85
389 402 3.386726 TGTCGGGATCCACAAAGGTATAG 59.613 47.826 15.23 0.00 39.02 1.31
397 410 1.884075 CGGACTGTCGGGATCCACAA 61.884 60.000 15.23 0.00 32.35 3.33
400 413 2.758327 CCGGACTGTCGGGATCCA 60.758 66.667 25.28 0.00 45.78 3.41
535 548 9.119418 ACACGATGGATTTCATATAAACATGAA 57.881 29.630 0.00 0.00 41.90 2.57
558 593 3.680937 TCGACCGGATTTCATACAAACAC 59.319 43.478 9.46 0.00 0.00 3.32
586 621 2.677836 GCAGACAAGTGCGGATTTCATA 59.322 45.455 0.00 0.00 32.74 2.15
604 639 3.354089 AACCAGACGAAATTTGTGCAG 57.646 42.857 0.00 0.00 0.00 4.41
625 660 5.303747 ACATTTTCACGACAACTGAAACA 57.696 34.783 0.00 0.00 37.36 2.83
637 672 3.544048 CGCTAGGCACATACATTTTCACG 60.544 47.826 0.00 0.00 0.00 4.35
651 686 1.667236 CAATCATCCAACGCTAGGCA 58.333 50.000 0.00 0.00 0.00 4.75
653 688 0.947244 GGCAATCATCCAACGCTAGG 59.053 55.000 0.00 0.00 0.00 3.02
681 716 2.079020 GAACCAGTCCACGGACACGA 62.079 60.000 18.21 0.00 46.76 4.35
699 736 0.620410 ATCCATCCACGGACTTGGGA 60.620 55.000 5.99 3.64 38.07 4.37
703 742 0.107508 CTGCATCCATCCACGGACTT 60.108 55.000 0.00 0.00 38.07 3.01
704 743 1.524002 CTGCATCCATCCACGGACT 59.476 57.895 0.00 0.00 38.07 3.85
721 760 1.073199 CAACCCGCAGAAACCTCCT 59.927 57.895 0.00 0.00 0.00 3.69
788 828 7.468631 ACAATATTGTACGGATTGAAATCCAGC 60.469 37.037 19.51 10.39 46.20 4.85
789 829 7.930217 ACAATATTGTACGGATTGAAATCCAG 58.070 34.615 19.51 14.57 46.20 3.86
790 830 7.873719 ACAATATTGTACGGATTGAAATCCA 57.126 32.000 19.51 2.80 46.20 3.41
791 831 9.878599 CTTACAATATTGTACGGATTGAAATCC 57.121 33.333 24.60 11.43 43.91 3.01
795 835 9.661563 ACTTCTTACAATATTGTACGGATTGAA 57.338 29.630 24.60 18.52 42.84 2.69
796 836 9.309516 GACTTCTTACAATATTGTACGGATTGA 57.690 33.333 24.60 13.97 42.84 2.57
797 837 9.093970 TGACTTCTTACAATATTGTACGGATTG 57.906 33.333 24.60 19.99 42.84 2.67
798 838 9.095065 GTGACTTCTTACAATATTGTACGGATT 57.905 33.333 24.60 13.83 42.84 3.01
799 839 8.255206 TGTGACTTCTTACAATATTGTACGGAT 58.745 33.333 24.60 13.26 42.84 4.18
800 840 7.604549 TGTGACTTCTTACAATATTGTACGGA 58.395 34.615 24.60 21.19 42.84 4.69
801 841 7.821595 TGTGACTTCTTACAATATTGTACGG 57.178 36.000 24.60 19.63 42.84 4.02
802 842 9.083080 TCATGTGACTTCTTACAATATTGTACG 57.917 33.333 24.60 22.44 42.84 3.67
804 844 9.599866 CCTCATGTGACTTCTTACAATATTGTA 57.400 33.333 21.73 21.73 42.35 2.41
805 845 8.103305 ACCTCATGTGACTTCTTACAATATTGT 58.897 33.333 23.80 23.80 44.86 2.71
806 846 8.498054 ACCTCATGTGACTTCTTACAATATTG 57.502 34.615 14.01 14.01 0.00 1.90
807 847 7.492669 CGACCTCATGTGACTTCTTACAATATT 59.507 37.037 0.00 0.00 0.00 1.28
808 848 6.980978 CGACCTCATGTGACTTCTTACAATAT 59.019 38.462 0.00 0.00 0.00 1.28
809 849 6.330278 CGACCTCATGTGACTTCTTACAATA 58.670 40.000 0.00 0.00 0.00 1.90
810 850 5.171476 CGACCTCATGTGACTTCTTACAAT 58.829 41.667 0.00 0.00 0.00 2.71
811 851 4.556233 CGACCTCATGTGACTTCTTACAA 58.444 43.478 0.00 0.00 0.00 2.41
812 852 3.056821 CCGACCTCATGTGACTTCTTACA 60.057 47.826 0.00 0.00 0.00 2.41
813 853 3.056749 ACCGACCTCATGTGACTTCTTAC 60.057 47.826 0.00 0.00 0.00 2.34
814 854 3.162666 ACCGACCTCATGTGACTTCTTA 58.837 45.455 0.00 0.00 0.00 2.10
877 924 5.945191 TGGTATGATGCAACATATACATGGG 59.055 40.000 18.32 0.00 36.39 4.00
928 1005 5.105106 ACGTTTCTGTTTGGGAAAAGGAAAT 60.105 36.000 0.00 0.00 36.81 2.17
953 1030 3.580731 GCTTATATTGAGCCGGACTCTC 58.419 50.000 21.36 12.63 46.41 3.20
976 1057 2.401766 CCGCCTAGACACGTACGGT 61.402 63.158 21.06 14.36 35.99 4.83
1001 1082 2.098842 GATCCATCGTTGCTCGCTGC 62.099 60.000 0.00 0.00 43.25 5.25
1010 1091 1.475751 GCCTCCATGTGATCCATCGTT 60.476 52.381 0.00 0.00 0.00 3.85
1245 4589 2.203294 GTGGAGGTTGCCGTGGTT 60.203 61.111 0.00 0.00 0.00 3.67
1280 4624 1.630148 CGACCTTTCTGTAGCCTTCG 58.370 55.000 0.00 0.00 0.00 3.79
1296 4640 2.742372 ATTGCAGTGGTCCGCGAC 60.742 61.111 8.23 3.56 0.00 5.19
1317 4661 0.179134 GTGTCGCCGTAGAGCAAGAT 60.179 55.000 0.00 0.00 0.00 2.40
1320 4664 2.126618 CGTGTCGCCGTAGAGCAA 60.127 61.111 0.00 0.00 0.00 3.91
1392 4736 1.402968 GCATTCCTCATCATTGTGCGT 59.597 47.619 0.00 0.00 0.00 5.24
1398 4742 2.715749 TCACGGCATTCCTCATCATT 57.284 45.000 0.00 0.00 0.00 2.57
1405 4749 0.839946 ATAGGCTTCACGGCATTCCT 59.160 50.000 0.00 0.00 41.46 3.36
1454 4798 3.170717 AGGGATCAAGAACACCTCGTAA 58.829 45.455 0.00 0.00 0.00 3.18
1484 4828 2.478031 CGTCACATCGAACAGACCTAGG 60.478 54.545 7.41 7.41 0.00 3.02
1490 4834 1.068541 CAGTCCGTCACATCGAACAGA 60.069 52.381 0.00 0.00 0.00 3.41
1556 4900 5.105877 CCACTGAGGTCTTGAACTTATCGTA 60.106 44.000 0.00 0.00 0.00 3.43
1617 4979 4.439472 CAGCGTAAACACGGCCGC 62.439 66.667 28.58 8.56 46.07 6.53
1656 5018 0.902516 GACCTCTCCTGCCACTGTCT 60.903 60.000 0.00 0.00 0.00 3.41
1661 5023 0.951040 CAAACGACCTCTCCTGCCAC 60.951 60.000 0.00 0.00 0.00 5.01
1716 5078 0.179004 AACATCAGTGAACCCCGCAA 60.179 50.000 0.00 0.00 0.00 4.85
1763 8079 1.075525 TCCCCAGTAGGCGCTGTAT 60.076 57.895 7.64 0.00 34.84 2.29
1814 8130 5.947228 ATGATGTGTACCTTGTGACAAAG 57.053 39.130 0.00 0.00 0.00 2.77
1848 8164 7.879160 ACGAGTACAAGGGAATTTAACATTACA 59.121 33.333 0.00 0.00 0.00 2.41
1870 8186 5.851177 GGTGATGTCAAACAAACAATACGAG 59.149 40.000 0.00 0.00 0.00 4.18
1882 8213 7.325660 AGTGATATTGATGGTGATGTCAAAC 57.674 36.000 0.00 0.00 37.82 2.93
1921 8259 4.037208 CCTGCAAAGATCGCCATAAAGATT 59.963 41.667 0.00 0.00 0.00 2.40
1932 8270 5.295292 AGACAATGATAACCTGCAAAGATCG 59.705 40.000 0.00 0.00 0.00 3.69
1933 8271 6.690194 AGACAATGATAACCTGCAAAGATC 57.310 37.500 0.00 0.00 0.00 2.75
2016 8358 2.366916 CTCGGAGCTCCCAAGATAATGT 59.633 50.000 27.20 0.00 34.14 2.71
2046 8388 5.220662 CCGATCACGAAGATTTGCAAAGTAT 60.221 40.000 18.19 5.58 42.66 2.12
2070 8412 9.727627 GATTCAATCAAGTACCAAATCTGAATC 57.272 33.333 13.73 13.73 39.32 2.52
2086 8428 6.718912 TGTACCTCACCATTTGATTCAATCAA 59.281 34.615 8.85 8.85 46.77 2.57
2090 8432 6.071447 CCATTGTACCTCACCATTTGATTCAA 60.071 38.462 0.00 0.00 32.17 2.69
2110 8452 5.587388 ATGCTATTCTTCAACACCCATTG 57.413 39.130 0.00 0.00 0.00 2.82
2162 8504 0.321671 TCCCTTCAGGTTGAGCGAAG 59.678 55.000 0.00 0.00 36.68 3.79
2174 8516 3.519510 CCAAGGTCTACAGATTCCCTTCA 59.480 47.826 0.00 0.00 33.31 3.02
2175 8517 3.775316 TCCAAGGTCTACAGATTCCCTTC 59.225 47.826 0.00 0.00 33.31 3.46
2187 8529 4.709886 TCGTCATCAAAGATCCAAGGTCTA 59.290 41.667 0.00 0.00 0.00 2.59
2230 8572 6.490040 ACTTTCTCTAGCCTTTTGTTATTGCA 59.510 34.615 0.00 0.00 0.00 4.08
2261 8603 3.889815 TCATCATCCCAGTTCCAATCAC 58.110 45.455 0.00 0.00 0.00 3.06
2536 8878 5.473796 TTGTGTCGGTGTTTAACTCTTTC 57.526 39.130 0.00 0.00 0.00 2.62
2542 8884 2.103388 GCGTTTGTGTCGGTGTTTAAC 58.897 47.619 0.00 0.00 0.00 2.01
2549 8891 0.531090 TTAGCTGCGTTTGTGTCGGT 60.531 50.000 0.00 0.00 0.00 4.69
2551 8893 1.525197 TCTTTAGCTGCGTTTGTGTCG 59.475 47.619 0.00 0.00 0.00 4.35
2555 8897 7.200455 AGTTTAAAATCTTTAGCTGCGTTTGT 58.800 30.769 0.00 0.00 0.00 2.83
2558 8900 7.200455 ACAAGTTTAAAATCTTTAGCTGCGTT 58.800 30.769 0.00 0.00 0.00 4.84
2574 8916 5.633655 TGGGAGTCCTACAACAAGTTTAA 57.366 39.130 9.58 0.00 0.00 1.52
2588 8930 6.590234 AAACAAGTATTTTGATGGGAGTCC 57.410 37.500 0.00 0.00 0.00 3.85
2696 9041 7.781324 AAGAAAAGGAGAAATAAGGATGCAA 57.219 32.000 0.00 0.00 0.00 4.08
2742 9087 0.529992 ACCGAGGCATTACGCTTAGC 60.530 55.000 0.00 0.00 41.91 3.09
2749 9094 3.332034 ACTTACACAACCGAGGCATTAC 58.668 45.455 0.00 0.00 0.00 1.89
2769 9114 7.382488 GCAAAAAGAAAAGAAGATACCAAGGAC 59.618 37.037 0.00 0.00 0.00 3.85
2771 9116 7.209475 TGCAAAAAGAAAAGAAGATACCAAGG 58.791 34.615 0.00 0.00 0.00 3.61
2772 9117 8.647143 TTGCAAAAAGAAAAGAAGATACCAAG 57.353 30.769 0.00 0.00 0.00 3.61
2810 9155 3.608941 CGTGGTGTGTGTACGTGTATACA 60.609 47.826 0.08 0.08 35.31 2.29
2865 9210 8.840833 ACAAGTTTGTGGTTCAATAAAAGTTT 57.159 26.923 0.00 0.00 40.49 2.66
2886 9231 9.862371 ATCATAGTACTCACTTTTACTCACAAG 57.138 33.333 0.00 0.00 36.14 3.16
2908 9253 6.094048 CCACCATAGTTCGAACTTCAAATCAT 59.906 38.462 33.82 17.49 40.37 2.45
2921 9266 0.108329 ACTTCGCCCACCATAGTTCG 60.108 55.000 0.00 0.00 0.00 3.95
3011 9356 9.998106 ACCAAAGCGTATTAGTCAGATTATTAT 57.002 29.630 0.00 0.00 0.00 1.28
3012 9357 9.826574 AACCAAAGCGTATTAGTCAGATTATTA 57.173 29.630 0.00 0.00 0.00 0.98
3013 9358 8.732746 AACCAAAGCGTATTAGTCAGATTATT 57.267 30.769 0.00 0.00 0.00 1.40
3019 9364 5.291128 CCACTAACCAAAGCGTATTAGTCAG 59.709 44.000 0.00 0.00 36.06 3.51
3036 9381 3.202829 TGGGTTGAGTTCACCACTAAC 57.797 47.619 0.00 0.00 35.01 2.34
3043 9388 7.770897 AGAACTGATATAATGGGTTGAGTTCAC 59.229 37.037 0.00 0.00 40.23 3.18
3085 9430 5.365314 GGGCAAAAGGATAATCAACCCATAA 59.635 40.000 0.00 0.00 34.82 1.90
3086 9431 4.898861 GGGCAAAAGGATAATCAACCCATA 59.101 41.667 0.00 0.00 34.82 2.74
3087 9432 3.711190 GGGCAAAAGGATAATCAACCCAT 59.289 43.478 0.00 0.00 34.82 4.00
3088 9433 3.103742 GGGCAAAAGGATAATCAACCCA 58.896 45.455 0.00 0.00 34.82 4.51
3089 9434 3.374764 AGGGCAAAAGGATAATCAACCC 58.625 45.455 0.00 0.00 34.91 4.11
3090 9435 4.023291 TGAGGGCAAAAGGATAATCAACC 58.977 43.478 0.00 0.00 0.00 3.77
3091 9436 4.706962 ACTGAGGGCAAAAGGATAATCAAC 59.293 41.667 0.00 0.00 0.00 3.18
3092 9437 4.706476 CACTGAGGGCAAAAGGATAATCAA 59.294 41.667 0.00 0.00 0.00 2.57
3093 9438 4.272489 CACTGAGGGCAAAAGGATAATCA 58.728 43.478 0.00 0.00 0.00 2.57
3094 9439 3.633986 CCACTGAGGGCAAAAGGATAATC 59.366 47.826 0.00 0.00 0.00 1.75
3095 9440 3.011708 ACCACTGAGGGCAAAAGGATAAT 59.988 43.478 0.00 0.00 43.89 1.28
3096 9441 2.378547 ACCACTGAGGGCAAAAGGATAA 59.621 45.455 0.00 0.00 43.89 1.75
3097 9442 1.992557 ACCACTGAGGGCAAAAGGATA 59.007 47.619 0.00 0.00 43.89 2.59
3098 9443 0.779997 ACCACTGAGGGCAAAAGGAT 59.220 50.000 0.00 0.00 43.89 3.24
3099 9444 0.178992 CACCACTGAGGGCAAAAGGA 60.179 55.000 0.00 0.00 43.89 3.36
3139 9484 0.368227 GAGCACGATTCGCAACTGAG 59.632 55.000 5.86 0.00 0.00 3.35
3143 9488 0.512952 AACTGAGCACGATTCGCAAC 59.487 50.000 5.86 0.00 0.00 4.17
3146 9491 0.246912 CGAAACTGAGCACGATTCGC 60.247 55.000 5.86 0.00 36.81 4.70
3175 9520 2.282407 TCGTCATAGTAGCTACGCACA 58.718 47.619 17.99 5.70 35.40 4.57
3176 9521 2.349627 CCTCGTCATAGTAGCTACGCAC 60.350 54.545 17.99 11.71 35.40 5.34
3181 9526 2.651382 TGGCCTCGTCATAGTAGCTA 57.349 50.000 3.32 0.00 0.00 3.32
3214 9559 1.280421 GCCCTCAGACAGAATGGACTT 59.720 52.381 0.00 0.00 43.62 3.01
3224 9569 1.656587 ACCACTAATGCCCTCAGACA 58.343 50.000 0.00 0.00 0.00 3.41
3225 9570 2.766828 ACTACCACTAATGCCCTCAGAC 59.233 50.000 0.00 0.00 0.00 3.51
3230 9575 1.213296 CCCACTACCACTAATGCCCT 58.787 55.000 0.00 0.00 0.00 5.19
3231 9576 0.916809 ACCCACTACCACTAATGCCC 59.083 55.000 0.00 0.00 0.00 5.36
3232 9577 1.134189 GGACCCACTACCACTAATGCC 60.134 57.143 0.00 0.00 0.00 4.40
3235 9580 1.007479 TCCGGACCCACTACCACTAAT 59.993 52.381 0.00 0.00 0.00 1.73
3266 9611 0.107268 ACCCATTTATACGCGGTCCC 59.893 55.000 12.47 0.00 0.00 4.46
3274 9619 2.922740 TGCTCCGGACCCATTTATAC 57.077 50.000 0.00 0.00 0.00 1.47
3276 9621 2.708861 TGTATGCTCCGGACCCATTTAT 59.291 45.455 15.80 0.00 0.00 1.40
3277 9622 2.120312 TGTATGCTCCGGACCCATTTA 58.880 47.619 15.80 5.53 0.00 1.40
3280 9625 0.397941 CATGTATGCTCCGGACCCAT 59.602 55.000 15.14 15.14 0.00 4.00
3288 9633 0.532862 CGGTCCCACATGTATGCTCC 60.533 60.000 0.00 0.00 0.00 4.70
3293 9638 0.326595 TTGCACGGTCCCACATGTAT 59.673 50.000 0.00 0.00 0.00 2.29
3298 9643 1.599518 GTCATTGCACGGTCCCACA 60.600 57.895 0.00 0.00 0.00 4.17
3307 9652 4.438744 CCCTAGGATTTTTCGTCATTGCAC 60.439 45.833 11.48 0.00 0.00 4.57
3308 9653 3.694072 CCCTAGGATTTTTCGTCATTGCA 59.306 43.478 11.48 0.00 0.00 4.08
3313 9658 3.258872 TCGAACCCTAGGATTTTTCGTCA 59.741 43.478 22.87 10.82 39.95 4.35
3319 9664 2.355412 CCGGTTCGAACCCTAGGATTTT 60.355 50.000 35.50 0.00 46.53 1.82
3322 9667 1.047034 CCCGGTTCGAACCCTAGGAT 61.047 60.000 35.50 0.00 46.53 3.24
3348 9693 0.110147 CACGAGATAGATCGGCGTCC 60.110 60.000 6.85 0.00 46.91 4.79
3388 9734 2.832661 GTGCAAGTGGTGGTGGCA 60.833 61.111 0.00 0.00 0.00 4.92
3399 9745 2.281070 AGTCAGTGGCGGTGCAAG 60.281 61.111 0.00 0.00 0.00 4.01
3400 9746 2.591429 CAGTCAGTGGCGGTGCAA 60.591 61.111 0.00 0.00 0.00 4.08
3407 9753 3.418068 GACAGCGCAGTCAGTGGC 61.418 66.667 25.88 4.99 38.40 5.01
3408 9754 3.108289 CGACAGCGCAGTCAGTGG 61.108 66.667 28.96 11.74 38.43 4.00
3423 9769 2.821366 GGAGTAGGACGGTCGCGA 60.821 66.667 3.71 3.71 0.00 5.87
3428 9774 3.066814 GCGGTGGAGTAGGACGGT 61.067 66.667 0.00 0.00 0.00 4.83
3431 9777 2.893398 CTGGCGGTGGAGTAGGAC 59.107 66.667 0.00 0.00 0.00 3.85
3467 10163 4.263771 ACTCCATCCTAACCCACGAAAAAT 60.264 41.667 0.00 0.00 0.00 1.82
3501 10197 5.009610 GTCCCTTCTAATGTGCACAAAGAAA 59.990 40.000 31.41 21.81 34.03 2.52
3507 10203 1.338674 CCGTCCCTTCTAATGTGCACA 60.339 52.381 24.08 24.08 0.00 4.57
3526 10222 5.841957 ATTCTTTGCATTCAGGATGTACC 57.158 39.130 0.00 0.00 38.07 3.34
3544 10241 9.593565 AACCTCCTTGAAATTTCTTCTTATTCT 57.406 29.630 18.64 0.00 0.00 2.40
3572 10269 3.287867 AGCCATTGACACAGATAAGGG 57.712 47.619 0.00 0.00 0.00 3.95
3573 10270 4.012374 ACAAGCCATTGACACAGATAAGG 58.988 43.478 0.00 0.00 38.83 2.69
3574 10271 6.741992 TTACAAGCCATTGACACAGATAAG 57.258 37.500 0.00 0.00 38.83 1.73
3584 10282 5.324409 AGAACTCCAATTACAAGCCATTGA 58.676 37.500 0.00 0.00 38.83 2.57
3606 10304 6.405842 GCAAATTACCTCCCCAAATTGTCTAG 60.406 42.308 0.00 0.00 0.00 2.43
3607 10305 5.420739 GCAAATTACCTCCCCAAATTGTCTA 59.579 40.000 0.00 0.00 0.00 2.59
3631 10329 2.459555 AACCCCAAGGATATTGGCTG 57.540 50.000 0.95 0.00 38.23 4.85
3657 10355 9.261180 CATCGTAGTATTTGTATTCCACTTCAT 57.739 33.333 0.00 0.00 0.00 2.57
3679 10377 5.301551 TGTCATCCATTTATTTTCCCCATCG 59.698 40.000 0.00 0.00 0.00 3.84
3698 10396 7.790027 AGCTCTTCATCATTACTAACTGTCAT 58.210 34.615 0.00 0.00 0.00 3.06
3748 10446 6.072286 GCCTCACATGAAAATTCTCTTTCTCA 60.072 38.462 0.00 0.00 36.46 3.27
3795 10493 0.613012 GCCATCCAAGTCCAAAGCCT 60.613 55.000 0.00 0.00 0.00 4.58
3799 10497 1.304052 CCCGCCATCCAAGTCCAAA 60.304 57.895 0.00 0.00 0.00 3.28
3802 10500 2.438434 CACCCGCCATCCAAGTCC 60.438 66.667 0.00 0.00 0.00 3.85
3804 10502 3.925630 CTGCACCCGCCATCCAAGT 62.926 63.158 0.00 0.00 37.32 3.16
3831 10531 3.735820 GCCATTACGACGACATGGTTCTA 60.736 47.826 22.58 0.00 39.88 2.10


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

AutoCloner maintained by Alex Coulton.