Multiple sequence alignment - TraesCS7A01G476700

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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 TraesCS7A01G476700 chr7A 100.000 5450 0 0 1 5450 670826149 670820700 0.000000e+00 10065.0
1 TraesCS7A01G476700 chr7A 99.894 939 1 0 4512 5450 670762196 670763134 0.000000e+00 1729.0
2 TraesCS7A01G476700 chr7D 92.614 3493 207 22 931 4403 578497425 578493964 0.000000e+00 4974.0
3 TraesCS7A01G476700 chr7D 91.720 157 12 1 589 745 578497719 578497564 3.310000e-52 217.0
4 TraesCS7A01G476700 chr7D 90.816 98 9 0 3763 3860 579051871 579051968 1.230000e-26 132.0
5 TraesCS7A01G476700 chr7D 79.167 120 17 7 3628 3743 535513649 535513534 5.850000e-10 76.8
6 TraesCS7A01G476700 chr7B 91.029 3578 276 25 811 4358 642285340 642281778 0.000000e+00 4787.0
7 TraesCS7A01G476700 chr7B 83.421 573 78 11 5 566 29380555 29381121 2.910000e-142 516.0
8 TraesCS7A01G476700 chr7B 98.561 139 2 0 4512 4650 595172773 595172635 4.220000e-61 246.0
9 TraesCS7A01G476700 chr7B 87.417 151 18 1 587 737 642285503 642285354 7.260000e-39 172.0
10 TraesCS7A01G476700 chr7B 84.000 100 14 2 469 567 101320930 101321028 1.620000e-15 95.3
11 TraesCS7A01G476700 chr7B 79.167 120 17 7 3628 3743 577204193 577204078 5.850000e-10 76.8
12 TraesCS7A01G476700 chrUn 99.894 939 1 0 4512 5450 384849949 384850887 0.000000e+00 1729.0
13 TraesCS7A01G476700 chr1A 87.500 536 60 5 6 536 391749257 391749790 3.610000e-171 612.0
14 TraesCS7A01G476700 chr1A 87.500 536 60 5 6 536 391838373 391838906 3.610000e-171 612.0
15 TraesCS7A01G476700 chr5B 84.929 564 79 5 6 566 473652388 473651828 2.850000e-157 566.0
16 TraesCS7A01G476700 chr4A 84.672 548 79 5 26 571 415857326 415856782 4.800000e-150 542.0
17 TraesCS7A01G476700 chr6D 83.938 579 75 10 4 567 451860517 451861092 6.210000e-149 538.0
18 TraesCS7A01G476700 chr4B 84.043 564 84 5 6 566 207106153 207105593 6.210000e-149 538.0
19 TraesCS7A01G476700 chr2D 85.827 508 67 5 5 507 175304089 175304596 8.040000e-148 534.0
20 TraesCS7A01G476700 chr6B 83.480 569 88 5 5 568 699801078 699800511 4.840000e-145 525.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G476700 chr7A 670820700 670826149 5449 True 10065.0 10065 100.000 1 5450 1 chr7A.!!$R1 5449
1 TraesCS7A01G476700 chr7A 670762196 670763134 938 False 1729.0 1729 99.894 4512 5450 1 chr7A.!!$F1 938
2 TraesCS7A01G476700 chr7D 578493964 578497719 3755 True 2595.5 4974 92.167 589 4403 2 chr7D.!!$R2 3814
3 TraesCS7A01G476700 chr7B 642281778 642285503 3725 True 2479.5 4787 89.223 587 4358 2 chr7B.!!$R3 3771
4 TraesCS7A01G476700 chr7B 29380555 29381121 566 False 516.0 516 83.421 5 566 1 chr7B.!!$F1 561
5 TraesCS7A01G476700 chrUn 384849949 384850887 938 False 1729.0 1729 99.894 4512 5450 1 chrUn.!!$F1 938
6 TraesCS7A01G476700 chr1A 391749257 391749790 533 False 612.0 612 87.500 6 536 1 chr1A.!!$F1 530
7 TraesCS7A01G476700 chr1A 391838373 391838906 533 False 612.0 612 87.500 6 536 1 chr1A.!!$F2 530
8 TraesCS7A01G476700 chr5B 473651828 473652388 560 True 566.0 566 84.929 6 566 1 chr5B.!!$R1 560
9 TraesCS7A01G476700 chr4A 415856782 415857326 544 True 542.0 542 84.672 26 571 1 chr4A.!!$R1 545
10 TraesCS7A01G476700 chr6D 451860517 451861092 575 False 538.0 538 83.938 4 567 1 chr6D.!!$F1 563
11 TraesCS7A01G476700 chr4B 207105593 207106153 560 True 538.0 538 84.043 6 566 1 chr4B.!!$R1 560
12 TraesCS7A01G476700 chr2D 175304089 175304596 507 False 534.0 534 85.827 5 507 1 chr2D.!!$F1 502
13 TraesCS7A01G476700 chr6B 699800511 699801078 567 True 525.0 525 83.480 5 568 1 chr6B.!!$R1 563

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
544 564 0.102120 CAGATGCAGAGTCCGAGGAC 59.898 60.0 14.1 14.1 44.86 3.85 F
1639 1712 0.108615 AACCTCAAGTCGATCCAGCG 60.109 55.0 0.0 0.0 0.00 5.18 F
2393 2466 0.752009 TTAGCCTCGACCTCAGCGAT 60.752 55.0 0.0 0.0 37.13 4.58 F
2744 2817 0.326522 TGAAGGGGCTCAGGATGCTA 60.327 55.0 0.0 0.0 34.76 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2011 0.031178 GTGAAGCTGTTGTTGGCCAG 59.969 55.0 5.11 0.0 0.00 4.85 R
2715 2788 0.251077 AGCCCCTTCAACTTGCTCAG 60.251 55.0 0.00 0.0 0.00 3.35 R
3491 3564 0.716108 GCATGAAGTCGAACACGAGG 59.284 55.0 0.00 0.0 36.72 4.63 R
4509 4585 0.249657 GACTGCACCGGAGATGGATC 60.250 60.0 9.46 0.0 0.00 3.36 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
53 58 3.879295 CGTCATTCTTGGAGGTATGCATT 59.121 43.478 3.54 0.00 0.00 3.56
88 93 1.079127 GGACGACATCTGTGGTGGG 60.079 63.158 2.56 0.00 37.11 4.61
172 177 0.108851 CGACGGGTGTGTGATGATGA 60.109 55.000 0.00 0.00 0.00 2.92
177 182 1.155889 GGTGTGTGATGATGAACGCA 58.844 50.000 0.00 0.00 34.57 5.24
180 185 0.519175 GTGTGATGATGAACGCACGC 60.519 55.000 0.00 0.00 37.67 5.34
181 186 1.296145 GTGATGATGAACGCACGCG 60.296 57.895 10.36 10.36 46.03 6.01
201 206 1.545651 GGGGAGAAGTTGTTGTCTGGG 60.546 57.143 0.00 0.00 0.00 4.45
244 250 1.220206 CTGGCAAGGTCGATGCTCT 59.780 57.895 9.20 0.00 43.34 4.09
274 280 4.741837 GCTCTGAAGATGGATCGATGGAAA 60.742 45.833 0.54 0.00 0.00 3.13
303 313 2.846039 ACGACCTAAGTGCGTCATAG 57.154 50.000 0.00 0.00 31.98 2.23
332 346 1.689273 GCCTCAGACCTAGTATGTGGG 59.311 57.143 11.20 6.29 38.39 4.61
341 355 2.574369 CCTAGTATGTGGGTTGGTTGGA 59.426 50.000 0.00 0.00 0.00 3.53
348 362 1.379146 GGGTTGGTTGGAGTCTCCC 59.621 63.158 16.60 1.42 35.03 4.30
362 376 2.832129 AGTCTCCCGCTTCAGATGTTAA 59.168 45.455 0.00 0.00 0.00 2.01
373 387 5.643777 GCTTCAGATGTTAAGCTTAGGTGAA 59.356 40.000 6.24 10.76 43.77 3.18
390 404 4.141018 AGGTGAAAGGTTTGGGTATTCAGT 60.141 41.667 0.00 0.00 31.24 3.41
411 425 0.670162 CACACTTTCTGCACCCCTTG 59.330 55.000 0.00 0.00 0.00 3.61
424 438 3.181440 GCACCCCTTGATCAATGGATAGA 60.181 47.826 26.19 0.00 32.67 1.98
442 456 3.944055 AGAAGTAGCGACAGATGTTGT 57.056 42.857 0.00 0.00 44.55 3.32
457 472 2.665165 TGTTGTCAAGATGGTGGCTTT 58.335 42.857 0.00 0.00 0.00 3.51
460 475 3.071874 TGTCAAGATGGTGGCTTTAGG 57.928 47.619 0.00 0.00 0.00 2.69
540 560 0.820226 CTTCCAGATGCAGAGTCCGA 59.180 55.000 0.00 0.00 0.00 4.55
543 563 1.039785 CCAGATGCAGAGTCCGAGGA 61.040 60.000 0.00 0.00 0.00 3.71
544 564 0.102120 CAGATGCAGAGTCCGAGGAC 59.898 60.000 14.10 14.10 44.86 3.85
594 614 5.004726 GCAAAAGCGAATAATGGTTAGCAAG 59.995 40.000 0.00 0.00 32.95 4.01
597 617 4.513442 AGCGAATAATGGTTAGCAAGACA 58.487 39.130 0.00 0.00 32.95 3.41
600 620 5.739161 GCGAATAATGGTTAGCAAGACAAAG 59.261 40.000 0.00 0.00 31.19 2.77
608 628 7.435068 TGGTTAGCAAGACAAAGAATAGTTC 57.565 36.000 0.00 0.00 0.00 3.01
614 635 7.624549 AGCAAGACAAAGAATAGTTCTATGGA 58.375 34.615 0.00 0.00 39.61 3.41
617 638 8.877779 CAAGACAAAGAATAGTTCTATGGACAG 58.122 37.037 0.00 0.00 39.61 3.51
637 658 4.940046 ACAGTTATTCCAGCTGACATTCTG 59.060 41.667 17.39 16.96 37.67 3.02
646 667 4.392445 CCAGCTGACATTCTGAAGAAAGAG 59.608 45.833 17.39 0.00 37.61 2.85
652 673 7.251704 TGACATTCTGAAGAAAGAGACAAAC 57.748 36.000 2.51 0.00 37.61 2.93
721 742 3.007074 TCAACCAAGTGCCTAACGATGTA 59.993 43.478 0.00 0.00 0.00 2.29
745 766 6.291377 ACTGGCACGATCATTAGTTCATTAT 58.709 36.000 0.00 0.00 0.00 1.28
746 767 6.767902 ACTGGCACGATCATTAGTTCATTATT 59.232 34.615 0.00 0.00 0.00 1.40
748 769 8.083462 TGGCACGATCATTAGTTCATTATTAC 57.917 34.615 0.00 0.00 0.00 1.89
749 770 7.095816 TGGCACGATCATTAGTTCATTATTACG 60.096 37.037 0.00 0.00 0.00 3.18
751 772 7.945178 GCACGATCATTAGTTCATTATTACGAC 59.055 37.037 0.00 0.00 0.00 4.34
752 773 9.181805 CACGATCATTAGTTCATTATTACGACT 57.818 33.333 0.00 0.00 0.00 4.18
757 778 9.678941 TCATTAGTTCATTATTACGACTAGCTG 57.321 33.333 0.00 0.00 0.00 4.24
758 779 9.678941 CATTAGTTCATTATTACGACTAGCTGA 57.321 33.333 0.00 0.00 0.00 4.26
761 782 8.804688 AGTTCATTATTACGACTAGCTGAATC 57.195 34.615 0.00 0.00 0.00 2.52
762 783 7.591795 AGTTCATTATTACGACTAGCTGAATCG 59.408 37.037 12.78 12.78 41.60 3.34
763 784 5.856986 TCATTATTACGACTAGCTGAATCGC 59.143 40.000 13.91 0.00 39.47 4.58
764 785 3.710326 ATTACGACTAGCTGAATCGCA 57.290 42.857 13.91 1.36 39.47 5.10
765 786 3.497297 TTACGACTAGCTGAATCGCAA 57.503 42.857 13.91 6.78 39.47 4.85
766 787 2.363788 ACGACTAGCTGAATCGCAAA 57.636 45.000 13.91 0.00 39.47 3.68
767 788 2.893637 ACGACTAGCTGAATCGCAAAT 58.106 42.857 13.91 0.00 39.47 2.32
770 791 3.182572 CGACTAGCTGAATCGCAAATACC 59.817 47.826 0.00 0.00 0.00 2.73
781 802 4.112716 TCGCAAATACCATGTCGAACTA 57.887 40.909 0.00 0.00 0.00 2.24
782 803 4.109766 TCGCAAATACCATGTCGAACTAG 58.890 43.478 0.00 0.00 0.00 2.57
784 805 4.328983 CGCAAATACCATGTCGAACTAGTT 59.671 41.667 8.13 8.13 0.00 2.24
785 806 5.560148 GCAAATACCATGTCGAACTAGTTG 58.440 41.667 14.14 5.81 0.00 3.16
786 807 5.350365 GCAAATACCATGTCGAACTAGTTGA 59.650 40.000 14.14 8.16 0.00 3.18
787 808 6.037172 GCAAATACCATGTCGAACTAGTTGAT 59.963 38.462 14.14 0.00 0.00 2.57
788 809 7.414098 GCAAATACCATGTCGAACTAGTTGATT 60.414 37.037 14.14 0.00 0.00 2.57
789 810 9.093970 CAAATACCATGTCGAACTAGTTGATTA 57.906 33.333 14.14 5.41 0.00 1.75
790 811 9.661563 AAATACCATGTCGAACTAGTTGATTAA 57.338 29.630 14.14 2.55 0.00 1.40
791 812 6.963049 ACCATGTCGAACTAGTTGATTAAC 57.037 37.500 14.14 4.41 37.06 2.01
792 813 5.575606 ACCATGTCGAACTAGTTGATTAACG 59.424 40.000 14.14 9.27 41.71 3.18
793 814 5.005394 CCATGTCGAACTAGTTGATTAACGG 59.995 44.000 14.14 1.65 41.71 4.44
794 815 5.375417 TGTCGAACTAGTTGATTAACGGA 57.625 39.130 14.14 0.00 41.71 4.69
795 816 5.771469 TGTCGAACTAGTTGATTAACGGAA 58.229 37.500 14.14 0.00 41.71 4.30
796 817 6.392354 TGTCGAACTAGTTGATTAACGGAAT 58.608 36.000 14.14 0.00 41.71 3.01
797 818 6.309494 TGTCGAACTAGTTGATTAACGGAATG 59.691 38.462 14.14 0.00 41.71 2.67
843 871 2.414293 CGTGTTCTCTTGACCTACGAGG 60.414 54.545 0.00 0.00 42.49 4.63
846 874 1.735386 TCTCTTGACCTACGAGGACG 58.265 55.000 7.76 0.00 37.67 4.79
851 879 1.446907 TGACCTACGAGGACGAAGAC 58.553 55.000 7.76 0.00 37.67 3.01
854 882 0.651551 CCTACGAGGACGAAGACGAG 59.348 60.000 0.00 0.00 37.67 4.18
869 897 0.742281 ACGAGGTCAGTGCATGCATC 60.742 55.000 25.64 17.07 0.00 3.91
893 921 0.179111 ATCGTACCACCATCAGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
894 922 2.452813 CGTACCACCATCAGCGTGC 61.453 63.158 0.00 0.00 0.00 5.34
895 923 2.125713 TACCACCATCAGCGTGCG 60.126 61.111 0.00 0.00 0.00 5.34
908 945 1.133946 GCGTGCGTTACCTACCGTAC 61.134 60.000 0.00 0.00 36.52 3.67
909 946 0.167908 CGTGCGTTACCTACCGTACA 59.832 55.000 0.00 0.00 39.23 2.90
910 947 1.791555 CGTGCGTTACCTACCGTACAG 60.792 57.143 0.00 0.00 39.23 2.74
911 948 1.200020 GTGCGTTACCTACCGTACAGT 59.800 52.381 0.00 0.00 39.12 3.55
912 949 1.199789 TGCGTTACCTACCGTACAGTG 59.800 52.381 0.00 0.00 0.00 3.66
913 950 1.900237 CGTTACCTACCGTACAGTGC 58.100 55.000 0.00 0.00 0.00 4.40
914 951 1.791555 CGTTACCTACCGTACAGTGCG 60.792 57.143 3.71 3.71 0.00 5.34
915 952 1.200020 GTTACCTACCGTACAGTGCGT 59.800 52.381 10.34 1.30 0.00 5.24
916 953 0.804364 TACCTACCGTACAGTGCGTG 59.196 55.000 10.34 4.35 0.00 5.34
917 954 1.804326 CCTACCGTACAGTGCGTGC 60.804 63.158 10.34 0.00 0.00 5.34
922 959 4.409588 GTACAGTGCGTGCGTGCG 62.410 66.667 0.00 0.00 37.81 5.34
923 960 4.934942 TACAGTGCGTGCGTGCGT 62.935 61.111 0.00 0.00 37.81 5.24
924 961 3.539560 TACAGTGCGTGCGTGCGTA 62.540 57.895 0.00 0.00 37.81 4.42
925 962 4.409588 CAGTGCGTGCGTGCGTAC 62.410 66.667 12.15 12.15 45.36 3.67
927 964 4.117372 GTGCGTGCGTGCGTACTC 62.117 66.667 10.65 3.83 42.58 2.59
928 965 4.632458 TGCGTGCGTGCGTACTCA 62.632 61.111 10.65 6.35 37.81 3.41
929 966 4.117372 GCGTGCGTGCGTACTCAC 62.117 66.667 15.60 15.60 38.76 3.51
933 970 3.170585 GCGTGCGTACTCACCGTC 61.171 66.667 10.28 0.00 33.57 4.79
969 1006 6.372659 CACTTGCACAACAGATTAGATTACCT 59.627 38.462 0.00 0.00 0.00 3.08
970 1007 6.372659 ACTTGCACAACAGATTAGATTACCTG 59.627 38.462 0.00 0.00 0.00 4.00
993 1059 3.536917 TATGCGCTAGCCAGCCGT 61.537 61.111 9.73 2.32 45.64 5.68
999 1065 1.811679 GCTAGCCAGCCGTGACTTC 60.812 63.158 2.29 0.00 42.37 3.01
1013 1081 0.593773 GACTTCATCGCTCGAGCTCC 60.594 60.000 32.88 7.16 39.32 4.70
1022 1090 1.517242 GCTCGAGCTCCCCATTTATG 58.483 55.000 29.88 0.00 38.21 1.90
1026 1094 1.613836 GAGCTCCCCATTTATGCAGG 58.386 55.000 0.87 0.00 0.00 4.85
1054 1126 4.040068 GCAGACCTGATCGGCATC 57.960 61.111 0.47 0.00 46.73 3.91
1125 1198 0.969917 TCTGCTCCTGCTCTCCTGTC 60.970 60.000 0.00 0.00 40.48 3.51
1222 1295 2.204461 TCCGGTCTTGGAGCAACGA 61.204 57.895 0.00 0.00 33.05 3.85
1223 1296 1.079127 CCGGTCTTGGAGCAACGAT 60.079 57.895 0.00 0.00 0.00 3.73
1225 1298 1.560923 CGGTCTTGGAGCAACGATAG 58.439 55.000 0.00 0.00 46.19 2.08
1227 1300 1.291132 GTCTTGGAGCAACGATAGGC 58.709 55.000 0.00 0.00 43.77 3.93
1373 1446 1.885388 CAACCTCACCGACAACGCA 60.885 57.895 0.00 0.00 38.29 5.24
1377 1450 0.670546 CCTCACCGACAACGCATTCT 60.671 55.000 0.00 0.00 38.29 2.40
1379 1452 0.669318 TCACCGACAACGCATTCTCC 60.669 55.000 0.00 0.00 38.29 3.71
1382 1455 2.785258 GACAACGCATTCTCCGGC 59.215 61.111 0.00 0.00 0.00 6.13
1383 1456 1.741770 GACAACGCATTCTCCGGCT 60.742 57.895 0.00 0.00 0.00 5.52
1388 1461 1.958205 CGCATTCTCCGGCTCCATC 60.958 63.158 0.00 0.00 0.00 3.51
1463 1536 3.447025 CTTCACCGGCGAGATCCCC 62.447 68.421 9.30 0.00 0.00 4.81
1528 1601 4.025401 CAACAACCTCACCGGCGC 62.025 66.667 0.00 0.00 35.61 6.53
1573 1646 2.355837 GTCGCTCACGGTGCTGAA 60.356 61.111 2.51 0.00 40.63 3.02
1629 1702 2.357517 CGCTCGGCAACCTCAAGT 60.358 61.111 0.00 0.00 0.00 3.16
1639 1712 0.108615 AACCTCAAGTCGATCCAGCG 60.109 55.000 0.00 0.00 0.00 5.18
1691 1764 4.804420 ATCCCTGAGGGCCTCGCA 62.804 66.667 27.58 11.86 43.94 5.10
1711 1784 2.818132 CCTCCCGATGCTCCAGTC 59.182 66.667 0.00 0.00 0.00 3.51
1712 1785 2.415010 CTCCCGATGCTCCAGTCG 59.585 66.667 0.00 0.00 37.58 4.18
1767 1840 3.431725 CGCCCGGCTTCTTCAACC 61.432 66.667 8.05 0.00 0.00 3.77
1775 1848 1.270358 GGCTTCTTCAACCTGTCGTCT 60.270 52.381 0.00 0.00 0.00 4.18
1779 1852 2.307768 TCTTCAACCTGTCGTCTCTGT 58.692 47.619 0.00 0.00 0.00 3.41
1780 1853 2.034685 TCTTCAACCTGTCGTCTCTGTG 59.965 50.000 0.00 0.00 0.00 3.66
1811 1884 3.959975 GCCAACAACGCGCTCCAA 61.960 61.111 5.73 0.00 0.00 3.53
1814 1887 3.660111 AACAACGCGCTCCAAGGC 61.660 61.111 5.73 0.00 0.00 4.35
1864 1937 1.592400 CCGAACCTCGTGCACCTCTA 61.592 60.000 12.15 0.00 38.40 2.43
1868 1941 0.966370 ACCTCGTGCACCTCTACCTC 60.966 60.000 12.15 0.00 0.00 3.85
1878 1951 3.718210 CTCTACCTCGGCGGCAACC 62.718 68.421 10.53 0.00 35.61 3.77
1941 2014 1.376942 CTGCAGTTCCTCAGCCTGG 60.377 63.158 5.25 0.00 0.00 4.45
1963 2036 3.726517 CAACAGCTTCACCGGCCG 61.727 66.667 21.04 21.04 0.00 6.13
2015 2088 2.037136 GTCGCTGCAGCTGTCCAAT 61.037 57.895 34.22 0.00 39.32 3.16
2114 2187 2.556287 CTCGGCGGCAACAAGTTC 59.444 61.111 10.53 0.00 0.00 3.01
2152 2225 4.990389 CATCGCGCGCCTCTCGAT 62.990 66.667 27.95 18.83 42.82 3.59
2393 2466 0.752009 TTAGCCTCGACCTCAGCGAT 60.752 55.000 0.00 0.00 37.13 4.58
2519 2592 2.636412 CGGCCTCTCGTCCTTGTCA 61.636 63.158 0.00 0.00 0.00 3.58
2694 2767 1.980765 ACCTGGACAGCAATCTCTTCA 59.019 47.619 0.00 0.00 0.00 3.02
2715 2788 4.179579 GAAGCATCCCGCCGTTGC 62.180 66.667 0.00 0.00 44.04 4.17
2744 2817 0.326522 TGAAGGGGCTCAGGATGCTA 60.327 55.000 0.00 0.00 34.76 3.49
2810 2883 2.046023 CAGATGACGGGGCTGCAA 60.046 61.111 0.50 0.00 0.00 4.08
2813 2886 0.539438 AGATGACGGGGCTGCAAAAA 60.539 50.000 0.50 0.00 0.00 1.94
2870 2943 1.488812 CCCGTGGGATTGGAGAACATA 59.511 52.381 0.00 0.00 37.50 2.29
2880 2953 2.629336 GGAGAACATAAGCTCCCTGG 57.371 55.000 0.00 0.00 43.91 4.45
2886 2959 0.537188 CATAAGCTCCCTGGTCGTGT 59.463 55.000 0.00 0.00 0.00 4.49
2911 2984 3.723348 GTCCGGCAACAACCTCGC 61.723 66.667 0.00 0.00 0.00 5.03
2969 3042 3.140814 GGGTTCAAGATGGCCGGC 61.141 66.667 21.18 21.18 0.00 6.13
2974 3047 0.825425 TTCAAGATGGCCGGCAACAA 60.825 50.000 30.85 11.08 0.00 2.83
3035 3108 2.165301 CCGGACACTCGCGAATTCC 61.165 63.158 11.33 14.73 0.00 3.01
3036 3109 1.445410 CGGACACTCGCGAATTCCA 60.445 57.895 23.02 0.00 0.00 3.53
3037 3110 1.683790 CGGACACTCGCGAATTCCAC 61.684 60.000 23.02 9.24 0.00 4.02
3111 3184 2.802667 CTGTGCATCGCCGTACTGC 61.803 63.158 0.00 0.00 36.45 4.40
3116 3189 2.102357 ATCGCCGTACTGCTCACG 59.898 61.111 7.70 0.00 39.10 4.35
3307 3380 1.239968 GGCAACCTGGCACTGAAGAG 61.240 60.000 0.00 0.00 43.14 2.85
3317 3390 2.554462 GGCACTGAAGAGGAAAGGAAAC 59.446 50.000 0.00 0.00 0.00 2.78
3516 3589 1.234821 GTTCGACTTCATGCCCAACA 58.765 50.000 0.00 0.00 0.00 3.33
3677 3753 2.743928 CACTGCGACCTCAAGCCC 60.744 66.667 0.00 0.00 0.00 5.19
3831 3907 1.880819 GCCGGGTACGTTTCTCTCCA 61.881 60.000 2.18 0.00 38.78 3.86
3862 3938 0.323633 TTCCACCATGGCATGTCAGG 60.324 55.000 24.80 21.27 37.47 3.86
3870 3946 2.034879 GGCATGTCAGGTGTCACGG 61.035 63.158 0.00 0.00 0.00 4.94
3894 3970 4.572389 TCACTTGTCTGAAGAAACTCTTGC 59.428 41.667 0.00 0.00 36.73 4.01
3897 3973 1.867233 GTCTGAAGAAACTCTTGCGCA 59.133 47.619 5.66 5.66 36.73 6.09
3942 4018 2.432628 GACGGGAAGCGTGTCCAG 60.433 66.667 8.52 6.92 39.70 3.86
3970 4046 2.103736 GCGTACAGCTACGGGGTC 59.896 66.667 10.82 0.00 45.06 4.46
3973 4049 1.138247 GTACAGCTACGGGGTCACG 59.862 63.158 0.00 0.00 40.31 4.35
3985 4061 1.142748 GGTCACGCTCCTGGAGATG 59.857 63.158 27.53 21.91 0.00 2.90
4110 4186 4.559063 CCTGCTGCCGATGGAGGG 62.559 72.222 0.00 0.00 39.04 4.30
4117 4193 3.554342 CCGATGGAGGGGCTGGAG 61.554 72.222 0.00 0.00 0.00 3.86
4360 4436 0.107831 ACAAGCCTGTGGTTTAGCGA 59.892 50.000 0.00 0.00 33.30 4.93
4361 4437 0.798776 CAAGCCTGTGGTTTAGCGAG 59.201 55.000 0.00 0.00 0.00 5.03
4362 4438 0.955919 AAGCCTGTGGTTTAGCGAGC 60.956 55.000 0.00 0.00 0.00 5.03
4363 4439 2.740714 GCCTGTGGTTTAGCGAGCG 61.741 63.158 0.00 0.00 0.00 5.03
4385 4461 2.570582 CTTCCTCTGACAGCCGGAGC 62.571 65.000 5.05 0.00 45.05 4.70
4392 4468 2.919856 ACAGCCGGAGCAGTGAGT 60.920 61.111 5.05 0.00 43.56 3.41
4397 4473 1.513158 CCGGAGCAGTGAGTTCGAT 59.487 57.895 0.00 0.00 0.00 3.59
4443 4519 6.870971 TTTTGCGGGGAATATACTTGATAC 57.129 37.500 0.00 0.00 0.00 2.24
4444 4520 5.818678 TTGCGGGGAATATACTTGATACT 57.181 39.130 0.00 0.00 0.00 2.12
4445 4521 6.921486 TTGCGGGGAATATACTTGATACTA 57.079 37.500 0.00 0.00 0.00 1.82
4446 4522 6.276832 TGCGGGGAATATACTTGATACTAC 57.723 41.667 0.00 0.00 0.00 2.73
4447 4523 6.014647 TGCGGGGAATATACTTGATACTACT 58.985 40.000 0.00 0.00 0.00 2.57
4448 4524 6.495872 TGCGGGGAATATACTTGATACTACTT 59.504 38.462 0.00 0.00 0.00 2.24
4449 4525 6.812160 GCGGGGAATATACTTGATACTACTTG 59.188 42.308 0.00 0.00 0.00 3.16
4450 4526 7.309621 GCGGGGAATATACTTGATACTACTTGA 60.310 40.741 0.00 0.00 0.00 3.02
4451 4527 8.750298 CGGGGAATATACTTGATACTACTTGAT 58.250 37.037 0.00 0.00 0.00 2.57
4461 4537 9.134055 ACTTGATACTACTTGATTAGTACTCCC 57.866 37.037 0.00 0.00 37.38 4.30
4462 4538 9.357161 CTTGATACTACTTGATTAGTACTCCCT 57.643 37.037 0.00 0.00 37.38 4.20
4464 4540 9.790344 TGATACTACTTGATTAGTACTCCCTAC 57.210 37.037 0.00 0.00 37.38 3.18
4466 4542 9.796180 ATACTACTTGATTAGTACTCCCTACTG 57.204 37.037 0.00 0.00 37.38 2.74
4467 4543 7.641249 ACTACTTGATTAGTACTCCCTACTGT 58.359 38.462 0.00 0.00 36.29 3.55
4468 4544 8.776119 ACTACTTGATTAGTACTCCCTACTGTA 58.224 37.037 0.00 0.00 36.29 2.74
4469 4545 9.796180 CTACTTGATTAGTACTCCCTACTGTAT 57.204 37.037 0.00 0.00 36.29 2.29
4479 4555 9.406113 AGTACTCCCTACTGTATAAAGTTAGTG 57.594 37.037 0.00 0.00 34.08 2.74
4480 4556 7.110043 ACTCCCTACTGTATAAAGTTAGTGC 57.890 40.000 0.00 0.00 0.00 4.40
4481 4557 6.666546 ACTCCCTACTGTATAAAGTTAGTGCA 59.333 38.462 0.00 0.00 0.00 4.57
4482 4558 7.179694 ACTCCCTACTGTATAAAGTTAGTGCAA 59.820 37.037 0.00 0.00 0.00 4.08
4483 4559 8.086143 TCCCTACTGTATAAAGTTAGTGCAAT 57.914 34.615 0.00 0.00 0.00 3.56
4484 4560 7.985184 TCCCTACTGTATAAAGTTAGTGCAATG 59.015 37.037 0.00 0.00 0.00 2.82
4485 4561 7.769044 CCCTACTGTATAAAGTTAGTGCAATGT 59.231 37.037 0.00 0.00 0.00 2.71
4486 4562 9.162764 CCTACTGTATAAAGTTAGTGCAATGTT 57.837 33.333 0.00 0.00 0.00 2.71
4487 4563 9.973246 CTACTGTATAAAGTTAGTGCAATGTTG 57.027 33.333 0.00 0.00 0.00 3.33
4488 4564 8.615878 ACTGTATAAAGTTAGTGCAATGTTGA 57.384 30.769 0.00 0.00 0.00 3.18
4489 4565 8.721478 ACTGTATAAAGTTAGTGCAATGTTGAG 58.279 33.333 0.00 0.00 0.00 3.02
4490 4566 8.615878 TGTATAAAGTTAGTGCAATGTTGAGT 57.384 30.769 0.00 0.00 0.00 3.41
4491 4567 8.717821 TGTATAAAGTTAGTGCAATGTTGAGTC 58.282 33.333 0.00 0.00 0.00 3.36
4492 4568 7.744087 ATAAAGTTAGTGCAATGTTGAGTCA 57.256 32.000 0.00 0.00 0.00 3.41
4493 4569 6.639632 AAAGTTAGTGCAATGTTGAGTCAT 57.360 33.333 0.00 0.00 0.00 3.06
4494 4570 6.639632 AAGTTAGTGCAATGTTGAGTCATT 57.360 33.333 0.00 0.00 38.38 2.57
4495 4571 6.639632 AGTTAGTGCAATGTTGAGTCATTT 57.360 33.333 0.00 0.00 36.10 2.32
4496 4572 7.744087 AGTTAGTGCAATGTTGAGTCATTTA 57.256 32.000 0.00 0.00 36.10 1.40
4497 4573 8.340618 AGTTAGTGCAATGTTGAGTCATTTAT 57.659 30.769 0.00 0.00 36.10 1.40
4498 4574 8.796475 AGTTAGTGCAATGTTGAGTCATTTATT 58.204 29.630 0.00 0.00 36.10 1.40
4499 4575 9.410556 GTTAGTGCAATGTTGAGTCATTTATTT 57.589 29.630 0.00 0.00 36.10 1.40
4500 4576 9.979578 TTAGTGCAATGTTGAGTCATTTATTTT 57.020 25.926 0.00 0.00 36.10 1.82
4501 4577 8.301730 AGTGCAATGTTGAGTCATTTATTTTG 57.698 30.769 0.00 0.00 36.10 2.44
4502 4578 7.385752 AGTGCAATGTTGAGTCATTTATTTTGG 59.614 33.333 0.00 0.00 36.10 3.28
4503 4579 7.384660 GTGCAATGTTGAGTCATTTATTTTGGA 59.615 33.333 0.00 0.00 36.10 3.53
4504 4580 7.930325 TGCAATGTTGAGTCATTTATTTTGGAA 59.070 29.630 0.00 0.00 36.10 3.53
4505 4581 8.223100 GCAATGTTGAGTCATTTATTTTGGAAC 58.777 33.333 0.00 0.00 36.10 3.62
4506 4582 8.427012 CAATGTTGAGTCATTTATTTTGGAACG 58.573 33.333 0.00 0.00 36.10 3.95
4507 4583 6.442952 TGTTGAGTCATTTATTTTGGAACGG 58.557 36.000 0.00 0.00 0.00 4.44
4508 4584 6.263392 TGTTGAGTCATTTATTTTGGAACGGA 59.737 34.615 0.00 0.00 0.00 4.69
4509 4585 6.494893 TGAGTCATTTATTTTGGAACGGAG 57.505 37.500 0.00 0.00 0.00 4.63
4510 4586 6.234920 TGAGTCATTTATTTTGGAACGGAGA 58.765 36.000 0.00 0.00 0.00 3.71
5392 5468 4.979197 CGAGCCACTTAAGATGATGTACTC 59.021 45.833 10.09 5.48 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.609459 GGGATACGACACAAGAGCAATG 59.391 50.000 0.00 0.00 37.60 2.82
1 2 2.501723 AGGGATACGACACAAGAGCAAT 59.498 45.455 0.00 0.00 37.60 3.56
2 3 1.899814 AGGGATACGACACAAGAGCAA 59.100 47.619 0.00 0.00 37.60 3.91
53 58 2.997315 CACTGGTCCCTCGAGCCA 60.997 66.667 6.99 8.53 35.55 4.75
88 93 3.799755 GTCACATGGAACGCCGCC 61.800 66.667 0.00 0.00 36.79 6.13
159 164 1.462378 CGTGCGTTCATCATCACACAC 60.462 52.381 0.00 0.00 0.00 3.82
177 182 1.597027 CAACAACTTCTCCCCGCGT 60.597 57.895 4.92 0.00 0.00 6.01
180 185 1.512926 CAGACAACAACTTCTCCCCG 58.487 55.000 0.00 0.00 0.00 5.73
181 186 1.545651 CCCAGACAACAACTTCTCCCC 60.546 57.143 0.00 0.00 0.00 4.81
187 192 1.528309 CGGCCCCAGACAACAACTT 60.528 57.895 0.00 0.00 0.00 2.66
190 195 2.203280 CACGGCCCCAGACAACAA 60.203 61.111 0.00 0.00 0.00 2.83
244 250 5.052481 CGATCCATCTTCAGAGCAAATACA 58.948 41.667 0.00 0.00 0.00 2.29
301 311 0.320421 GTCTGAGGCACAAACCGCTA 60.320 55.000 0.00 0.00 33.69 4.26
303 313 2.617274 GGTCTGAGGCACAAACCGC 61.617 63.158 0.00 0.00 29.47 5.68
332 346 1.671379 GCGGGAGACTCCAACCAAC 60.671 63.158 23.06 3.57 38.64 3.77
341 355 1.270907 AACATCTGAAGCGGGAGACT 58.729 50.000 0.00 0.00 0.00 3.24
362 376 2.177016 ACCCAAACCTTTCACCTAAGCT 59.823 45.455 0.00 0.00 0.00 3.74
373 387 4.583073 GTGTGAACTGAATACCCAAACCTT 59.417 41.667 0.00 0.00 0.00 3.50
390 404 0.550914 AGGGGTGCAGAAAGTGTGAA 59.449 50.000 0.00 0.00 0.00 3.18
411 425 5.773575 TGTCGCTACTTCTATCCATTGATC 58.226 41.667 0.00 0.00 32.18 2.92
442 456 1.354031 TGCCTAAAGCCACCATCTTGA 59.646 47.619 0.00 0.00 42.71 3.02
451 465 9.532494 AATAATACATCAATATGCCTAAAGCCA 57.468 29.630 0.00 0.00 42.71 4.75
492 507 9.329913 GCATGTAGCCACTTTATTAATTATTCG 57.670 33.333 0.00 0.00 37.23 3.34
567 587 5.230097 GCTAACCATTATTCGCTTTTGCTTC 59.770 40.000 0.00 0.00 44.80 3.86
569 589 4.157656 TGCTAACCATTATTCGCTTTTGCT 59.842 37.500 0.00 0.00 44.80 3.91
570 590 4.420168 TGCTAACCATTATTCGCTTTTGC 58.580 39.130 0.00 0.00 43.23 3.68
571 591 6.251376 GTCTTGCTAACCATTATTCGCTTTTG 59.749 38.462 0.00 0.00 0.00 2.44
572 592 6.072175 TGTCTTGCTAACCATTATTCGCTTTT 60.072 34.615 0.00 0.00 0.00 2.27
573 593 5.414454 TGTCTTGCTAACCATTATTCGCTTT 59.586 36.000 0.00 0.00 0.00 3.51
574 594 4.941263 TGTCTTGCTAACCATTATTCGCTT 59.059 37.500 0.00 0.00 0.00 4.68
575 595 4.513442 TGTCTTGCTAACCATTATTCGCT 58.487 39.130 0.00 0.00 0.00 4.93
576 596 4.875544 TGTCTTGCTAACCATTATTCGC 57.124 40.909 0.00 0.00 0.00 4.70
577 597 7.072177 TCTTTGTCTTGCTAACCATTATTCG 57.928 36.000 0.00 0.00 0.00 3.34
580 600 9.686683 ACTATTCTTTGTCTTGCTAACCATTAT 57.313 29.630 0.00 0.00 0.00 1.28
581 601 9.515226 AACTATTCTTTGTCTTGCTAACCATTA 57.485 29.630 0.00 0.00 0.00 1.90
582 602 8.409358 AACTATTCTTTGTCTTGCTAACCATT 57.591 30.769 0.00 0.00 0.00 3.16
583 603 7.885399 AGAACTATTCTTTGTCTTGCTAACCAT 59.115 33.333 0.00 0.00 36.36 3.55
584 604 7.224297 AGAACTATTCTTTGTCTTGCTAACCA 58.776 34.615 0.00 0.00 36.36 3.67
585 605 7.674471 AGAACTATTCTTTGTCTTGCTAACC 57.326 36.000 0.00 0.00 36.36 2.85
594 614 8.779354 AACTGTCCATAGAACTATTCTTTGTC 57.221 34.615 7.82 3.11 41.14 3.18
600 620 9.482627 CTGGAATAACTGTCCATAGAACTATTC 57.517 37.037 0.00 0.00 44.19 1.75
608 628 5.053145 GTCAGCTGGAATAACTGTCCATAG 58.947 45.833 15.13 0.00 44.19 2.23
614 635 4.940046 CAGAATGTCAGCTGGAATAACTGT 59.060 41.667 15.13 0.00 33.12 3.55
617 638 5.877012 TCTTCAGAATGTCAGCTGGAATAAC 59.123 40.000 15.13 4.58 37.40 1.89
637 658 7.095565 GCTAACCTAGTGTTTGTCTCTTTCTTC 60.096 40.741 2.53 0.00 38.42 2.87
646 667 2.742589 GGCTGCTAACCTAGTGTTTGTC 59.257 50.000 0.00 0.23 38.42 3.18
652 673 2.744202 CAAAGTGGCTGCTAACCTAGTG 59.256 50.000 0.00 0.00 0.00 2.74
686 707 3.443681 ACTTGGTTGAGATTATTTGGGCG 59.556 43.478 0.00 0.00 0.00 6.13
721 742 3.610040 TGAACTAATGATCGTGCCAGT 57.390 42.857 0.00 0.00 0.00 4.00
745 766 3.497297 TTGCGATTCAGCTAGTCGTAA 57.503 42.857 11.85 11.85 37.57 3.18
746 767 3.497297 TTTGCGATTCAGCTAGTCGTA 57.503 42.857 13.73 8.33 37.66 3.43
748 769 3.182572 GGTATTTGCGATTCAGCTAGTCG 59.817 47.826 9.45 9.45 38.13 4.18
749 770 4.119862 TGGTATTTGCGATTCAGCTAGTC 58.880 43.478 0.00 0.00 38.13 2.59
751 772 4.512944 ACATGGTATTTGCGATTCAGCTAG 59.487 41.667 0.00 0.00 38.13 3.42
752 773 4.450976 ACATGGTATTTGCGATTCAGCTA 58.549 39.130 0.00 0.00 38.13 3.32
753 774 3.282021 ACATGGTATTTGCGATTCAGCT 58.718 40.909 0.00 0.00 38.13 4.24
754 775 3.621794 GACATGGTATTTGCGATTCAGC 58.378 45.455 0.00 0.00 37.71 4.26
755 776 3.555547 TCGACATGGTATTTGCGATTCAG 59.444 43.478 0.00 0.00 0.00 3.02
756 777 3.526534 TCGACATGGTATTTGCGATTCA 58.473 40.909 0.00 0.00 0.00 2.57
757 778 4.034048 AGTTCGACATGGTATTTGCGATTC 59.966 41.667 0.00 0.00 0.00 2.52
758 779 3.938963 AGTTCGACATGGTATTTGCGATT 59.061 39.130 0.00 0.00 0.00 3.34
759 780 3.531538 AGTTCGACATGGTATTTGCGAT 58.468 40.909 0.00 0.00 0.00 4.58
760 781 2.967362 AGTTCGACATGGTATTTGCGA 58.033 42.857 0.00 0.00 0.00 5.10
761 782 3.863424 ACTAGTTCGACATGGTATTTGCG 59.137 43.478 0.00 0.00 0.00 4.85
762 783 5.350365 TCAACTAGTTCGACATGGTATTTGC 59.650 40.000 4.77 0.00 0.00 3.68
763 784 6.961359 TCAACTAGTTCGACATGGTATTTG 57.039 37.500 4.77 0.00 0.00 2.32
764 785 9.661563 TTAATCAACTAGTTCGACATGGTATTT 57.338 29.630 4.77 0.00 0.00 1.40
765 786 9.095065 GTTAATCAACTAGTTCGACATGGTATT 57.905 33.333 4.77 0.44 0.00 1.89
766 787 7.434307 CGTTAATCAACTAGTTCGACATGGTAT 59.566 37.037 4.77 0.00 32.09 2.73
767 788 6.748658 CGTTAATCAACTAGTTCGACATGGTA 59.251 38.462 4.77 0.00 32.09 3.25
770 791 5.803461 TCCGTTAATCAACTAGTTCGACATG 59.197 40.000 4.77 0.00 32.09 3.21
789 810 9.709495 TGTTAGTGTACTTTTATACATTCCGTT 57.291 29.630 0.00 0.00 37.40 4.44
790 811 9.709495 TTGTTAGTGTACTTTTATACATTCCGT 57.291 29.630 0.00 0.00 37.40 4.69
791 812 9.962759 GTTGTTAGTGTACTTTTATACATTCCG 57.037 33.333 0.00 0.00 37.40 4.30
796 817 9.480053 GACAGGTTGTTAGTGTACTTTTATACA 57.520 33.333 0.00 0.00 32.57 2.29
797 818 8.642020 CGACAGGTTGTTAGTGTACTTTTATAC 58.358 37.037 0.00 0.00 0.00 1.47
802 823 4.807304 CACGACAGGTTGTTAGTGTACTTT 59.193 41.667 0.00 0.00 35.82 2.66
808 829 3.454375 AGAACACGACAGGTTGTTAGTG 58.546 45.455 13.40 13.40 41.59 2.74
843 871 0.729816 GCACTGACCTCGTCTTCGTC 60.730 60.000 0.00 0.00 38.33 4.20
846 874 1.354040 CATGCACTGACCTCGTCTTC 58.646 55.000 0.00 0.00 33.15 2.87
851 879 1.759293 CGATGCATGCACTGACCTCG 61.759 60.000 25.37 22.53 0.00 4.63
854 882 1.020861 TGTCGATGCATGCACTGACC 61.021 55.000 33.82 23.01 34.50 4.02
869 897 2.193447 CTGATGGTGGTACGATTGTCG 58.807 52.381 0.00 0.00 46.93 4.35
893 921 1.900237 CACTGTACGGTAGGTAACGC 58.100 55.000 7.11 0.00 46.39 4.84
894 922 1.791555 CGCACTGTACGGTAGGTAACG 60.792 57.143 7.11 1.54 46.39 3.18
895 923 1.200020 ACGCACTGTACGGTAGGTAAC 59.800 52.381 7.11 0.00 31.61 2.50
908 945 4.409588 GTACGCACGCACGCACTG 62.410 66.667 0.00 0.00 36.19 3.66
909 946 4.640855 AGTACGCACGCACGCACT 62.641 61.111 0.00 0.00 34.87 4.40
910 947 4.117372 GAGTACGCACGCACGCAC 62.117 66.667 0.00 0.00 36.19 5.34
911 948 4.632458 TGAGTACGCACGCACGCA 62.632 61.111 0.00 0.00 36.19 5.24
912 949 4.117372 GTGAGTACGCACGCACGC 62.117 66.667 14.10 0.00 43.96 5.34
915 952 3.884581 GACGGTGAGTACGCACGCA 62.885 63.158 21.23 0.00 39.66 5.24
916 953 2.244436 TAGACGGTGAGTACGCACGC 62.244 60.000 21.23 13.94 39.66 5.34
917 954 0.519999 GTAGACGGTGAGTACGCACG 60.520 60.000 21.23 18.15 39.66 5.34
918 955 0.801251 AGTAGACGGTGAGTACGCAC 59.199 55.000 20.14 20.14 38.05 5.34
919 956 1.081892 GAGTAGACGGTGAGTACGCA 58.918 55.000 0.00 0.00 34.00 5.24
920 957 0.026027 CGAGTAGACGGTGAGTACGC 59.974 60.000 0.00 0.00 34.00 4.42
921 958 0.649475 CCGAGTAGACGGTGAGTACG 59.351 60.000 0.00 0.00 46.70 3.67
933 970 1.269723 TGTGCAAGTGAGACCGAGTAG 59.730 52.381 0.00 0.00 0.00 2.57
969 1006 1.326951 TGGCTAGCGCATACAGGTCA 61.327 55.000 11.47 0.00 38.10 4.02
970 1007 0.598680 CTGGCTAGCGCATACAGGTC 60.599 60.000 11.47 0.00 38.10 3.85
993 1059 4.794164 GCTCGAGCGATGAAGTCA 57.206 55.556 23.61 0.00 0.00 3.41
1063 1135 4.467084 CCATGGTGGTCCGTCCGG 62.467 72.222 2.57 0.00 39.52 5.14
1211 1284 1.813753 GCGCCTATCGTTGCTCCAA 60.814 57.895 0.00 0.00 41.07 3.53
1373 1446 2.511452 CGGGATGGAGCCGGAGAAT 61.511 63.158 5.05 0.00 0.00 2.40
1424 1497 2.047844 TTGTCGCAGAGGCTGAGC 60.048 61.111 0.00 0.00 36.95 4.26
1478 1551 2.435059 GTGCTGAGGTTCCCGAGC 60.435 66.667 0.00 0.00 35.42 5.03
1492 1565 3.475774 CGTTGAGGTACGCGGTGC 61.476 66.667 12.47 0.00 34.45 5.01
1557 1630 2.049156 CTTCAGCACCGTGAGCGA 60.049 61.111 1.65 0.00 41.33 4.93
1558 1631 3.782244 GCTTCAGCACCGTGAGCG 61.782 66.667 1.65 0.00 41.59 5.03
1573 1646 2.431601 GCGAGTTCGTGCTGAGCT 60.432 61.111 5.83 0.00 41.35 4.09
1618 1691 1.363744 CTGGATCGACTTGAGGTTGC 58.636 55.000 0.00 0.00 0.00 4.17
1639 1712 3.057547 TTCTCTGCGAGCTCGAGCC 62.058 63.158 38.74 21.64 43.38 4.70
1652 1725 1.594310 GCCTTCGAGCAGGTTCTCT 59.406 57.895 5.09 0.00 36.15 3.10
1712 1785 1.145803 GGTTCTGGTACACGCTGAAC 58.854 55.000 10.07 10.07 37.04 3.18
1754 1827 0.600255 ACGACAGGTTGAAGAAGCCG 60.600 55.000 0.00 0.00 0.00 5.52
1757 1830 3.243569 ACAGAGACGACAGGTTGAAGAAG 60.244 47.826 0.00 0.00 0.00 2.85
1767 1840 2.262915 GCCCCACAGAGACGACAG 59.737 66.667 0.00 0.00 0.00 3.51
1806 1879 4.521062 CGGGAGCTCGCCTTGGAG 62.521 72.222 23.61 5.99 37.11 3.86
1842 1915 4.980805 GTGCACGAGGTTCGGCCA 62.981 66.667 2.24 0.00 45.59 5.36
1847 1920 0.108756 GGTAGAGGTGCACGAGGTTC 60.109 60.000 11.45 3.49 0.00 3.62
1854 1927 2.184579 GCCGAGGTAGAGGTGCAC 59.815 66.667 8.80 8.80 0.00 4.57
1857 1930 4.208686 GCCGCCGAGGTAGAGGTG 62.209 72.222 0.00 0.00 43.70 4.00
1938 2011 0.031178 GTGAAGCTGTTGTTGGCCAG 59.969 55.000 5.11 0.00 0.00 4.85
1941 2014 1.008538 CGGTGAAGCTGTTGTTGGC 60.009 57.895 0.00 0.00 0.00 4.52
2015 2088 2.260434 GTCGCCGTGAGCTGGTTA 59.740 61.111 0.00 0.00 40.39 2.85
2085 2158 1.810412 GCCGCCGAGGAATATTTCAGT 60.810 52.381 0.00 0.00 45.00 3.41
2152 2225 1.148273 AAACTCAACGCCTGGAGCA 59.852 52.632 0.00 0.00 44.04 4.26
2273 2346 1.305623 CAGCTTGCCAATCCCCTCT 59.694 57.895 0.00 0.00 0.00 3.69
2349 2422 3.499737 CGTGAGGTCGCCAATGGC 61.500 66.667 15.52 15.52 46.75 4.40
2393 2466 0.950836 TCGACCCGTTCAACGAGTTA 59.049 50.000 12.68 0.00 46.05 2.24
2491 2564 1.878656 CGAGAGGCCGAACAGTTCCT 61.879 60.000 7.76 0.00 0.00 3.36
2519 2592 1.226974 CGACAAGTCCATCGCCGAT 60.227 57.895 0.00 0.00 0.00 4.18
2715 2788 0.251077 AGCCCCTTCAACTTGCTCAG 60.251 55.000 0.00 0.00 0.00 3.35
2810 2883 1.004918 CCGCGAGAGGTCCAGTTTT 60.005 57.895 8.23 0.00 0.00 2.43
2813 2886 2.282958 TTCCGCGAGAGGTCCAGT 60.283 61.111 8.23 0.00 0.00 4.00
2854 2927 3.117888 GGAGCTTATGTTCTCCAATCCCA 60.118 47.826 3.60 0.00 46.24 4.37
2870 2943 1.371558 GAACACGACCAGGGAGCTT 59.628 57.895 0.00 0.00 0.00 3.74
2886 2959 2.659244 GTTGCCGGACACGTCGAA 60.659 61.111 5.05 0.00 38.78 3.71
3030 3103 0.329596 GAGCCTCTGGTGGTGGAATT 59.670 55.000 0.00 0.00 0.00 2.17
3035 3108 1.294780 GTGAGAGCCTCTGGTGGTG 59.705 63.158 0.00 0.00 0.00 4.17
3036 3109 1.915769 GGTGAGAGCCTCTGGTGGT 60.916 63.158 0.00 0.00 0.00 4.16
3037 3110 1.611851 AGGTGAGAGCCTCTGGTGG 60.612 63.158 0.00 0.00 32.39 4.61
3078 3151 2.423446 CAGAGCGGCCCCTATGAC 59.577 66.667 6.14 0.00 0.00 3.06
3111 3184 2.973899 CCACAGGAGGACCGTGAG 59.026 66.667 0.00 0.00 40.40 3.51
3292 3365 1.072965 CTTTCCTCTTCAGTGCCAGGT 59.927 52.381 0.00 0.00 0.00 4.00
3307 3380 1.901464 TGCGCCAGGTTTCCTTTCC 60.901 57.895 4.18 0.00 0.00 3.13
3491 3564 0.716108 GCATGAAGTCGAACACGAGG 59.284 55.000 0.00 0.00 36.72 4.63
3594 3670 2.202932 GATGTCCACGGCGATGCT 60.203 61.111 16.62 0.00 0.00 3.79
3677 3753 3.726517 CCAAGGAGCACGTTGCCG 61.727 66.667 10.57 0.00 46.52 5.69
3761 3837 2.343758 GTGCTCTCGGTGCCTTCA 59.656 61.111 0.00 0.00 0.00 3.02
3762 3838 2.435059 GGTGCTCTCGGTGCCTTC 60.435 66.667 0.00 0.00 0.00 3.46
3763 3839 2.527951 GATGGTGCTCTCGGTGCCTT 62.528 60.000 0.00 0.00 0.00 4.35
3823 3899 5.045651 TGGAAAAGTAGCATGATGGAGAGAA 60.046 40.000 0.00 0.00 0.00 2.87
3862 3938 1.202371 TCAGACAAGTGACCGTGACAC 60.202 52.381 0.00 0.00 38.38 3.67
3870 3946 5.503194 GCAAGAGTTTCTTCAGACAAGTGAC 60.503 44.000 0.00 0.00 33.78 3.67
3946 4022 4.183686 TAGCTGTACGCGTCGCCC 62.184 66.667 18.63 3.01 45.59 6.13
3970 4046 1.521010 CAGCATCTCCAGGAGCGTG 60.521 63.158 12.26 13.55 0.00 5.34
3973 4049 2.203181 GCCAGCATCTCCAGGAGC 60.203 66.667 12.26 0.72 0.00 4.70
4342 4418 0.798776 CTCGCTAAACCACAGGCTTG 59.201 55.000 0.00 0.00 0.00 4.01
4360 4436 1.291588 CTGTCAGAGGAAGCACGCT 59.708 57.895 0.00 0.00 0.00 5.07
4361 4437 2.386660 GCTGTCAGAGGAAGCACGC 61.387 63.158 3.32 0.00 36.91 5.34
4362 4438 1.739562 GGCTGTCAGAGGAAGCACG 60.740 63.158 3.32 0.00 38.73 5.34
4363 4439 1.739562 CGGCTGTCAGAGGAAGCAC 60.740 63.158 3.32 0.00 38.73 4.40
4385 4461 8.779303 AGTATCAAGTATCTATCGAACTCACTG 58.221 37.037 0.00 0.00 0.00 3.66
4419 4495 7.057894 AGTATCAAGTATATTCCCCGCAAAAA 58.942 34.615 0.00 0.00 0.00 1.94
4420 4496 6.597562 AGTATCAAGTATATTCCCCGCAAAA 58.402 36.000 0.00 0.00 0.00 2.44
4421 4497 6.182507 AGTATCAAGTATATTCCCCGCAAA 57.817 37.500 0.00 0.00 0.00 3.68
4422 4498 5.818678 AGTATCAAGTATATTCCCCGCAA 57.181 39.130 0.00 0.00 0.00 4.85
4423 4499 6.014647 AGTAGTATCAAGTATATTCCCCGCA 58.985 40.000 0.00 0.00 0.00 5.69
4424 4500 6.527057 AGTAGTATCAAGTATATTCCCCGC 57.473 41.667 0.00 0.00 0.00 6.13
4425 4501 8.118976 TCAAGTAGTATCAAGTATATTCCCCG 57.881 38.462 0.00 0.00 0.00 5.73
4435 4511 9.134055 GGGAGTACTAATCAAGTAGTATCAAGT 57.866 37.037 0.00 0.00 43.17 3.16
4436 4512 9.357161 AGGGAGTACTAATCAAGTAGTATCAAG 57.643 37.037 0.00 0.00 43.17 3.02
4438 4514 9.790344 GTAGGGAGTACTAATCAAGTAGTATCA 57.210 37.037 0.00 0.00 43.17 2.15
4440 4516 9.796180 CAGTAGGGAGTACTAATCAAGTAGTAT 57.204 37.037 0.00 0.00 43.17 2.12
4441 4517 8.776119 ACAGTAGGGAGTACTAATCAAGTAGTA 58.224 37.037 0.00 0.00 43.17 1.82
4442 4518 7.641249 ACAGTAGGGAGTACTAATCAAGTAGT 58.359 38.462 0.00 0.00 45.33 2.73
4443 4519 9.796180 ATACAGTAGGGAGTACTAATCAAGTAG 57.204 37.037 0.00 0.00 41.42 2.57
4453 4529 9.406113 CACTAACTTTATACAGTAGGGAGTACT 57.594 37.037 0.00 0.00 43.31 2.73
4454 4530 8.134261 GCACTAACTTTATACAGTAGGGAGTAC 58.866 40.741 0.00 0.00 0.00 2.73
4455 4531 7.835682 TGCACTAACTTTATACAGTAGGGAGTA 59.164 37.037 0.00 0.00 0.00 2.59
4456 4532 6.666546 TGCACTAACTTTATACAGTAGGGAGT 59.333 38.462 0.00 0.00 0.00 3.85
4457 4533 7.108841 TGCACTAACTTTATACAGTAGGGAG 57.891 40.000 0.00 0.00 0.00 4.30
4458 4534 7.484993 TTGCACTAACTTTATACAGTAGGGA 57.515 36.000 0.00 0.00 0.00 4.20
4459 4535 7.769044 ACATTGCACTAACTTTATACAGTAGGG 59.231 37.037 0.00 0.00 0.00 3.53
4460 4536 8.718102 ACATTGCACTAACTTTATACAGTAGG 57.282 34.615 0.00 0.00 0.00 3.18
4461 4537 9.973246 CAACATTGCACTAACTTTATACAGTAG 57.027 33.333 0.00 0.00 0.00 2.57
4462 4538 9.713713 TCAACATTGCACTAACTTTATACAGTA 57.286 29.630 0.00 0.00 0.00 2.74
4463 4539 8.615878 TCAACATTGCACTAACTTTATACAGT 57.384 30.769 0.00 0.00 0.00 3.55
4464 4540 8.721478 ACTCAACATTGCACTAACTTTATACAG 58.279 33.333 0.00 0.00 0.00 2.74
4465 4541 8.615878 ACTCAACATTGCACTAACTTTATACA 57.384 30.769 0.00 0.00 0.00 2.29
4466 4542 8.717821 TGACTCAACATTGCACTAACTTTATAC 58.282 33.333 0.00 0.00 0.00 1.47
4467 4543 8.840833 TGACTCAACATTGCACTAACTTTATA 57.159 30.769 0.00 0.00 0.00 0.98
4468 4544 7.744087 TGACTCAACATTGCACTAACTTTAT 57.256 32.000 0.00 0.00 0.00 1.40
4469 4545 7.744087 ATGACTCAACATTGCACTAACTTTA 57.256 32.000 0.00 0.00 0.00 1.85
4470 4546 6.639632 ATGACTCAACATTGCACTAACTTT 57.360 33.333 0.00 0.00 0.00 2.66
4471 4547 6.639632 AATGACTCAACATTGCACTAACTT 57.360 33.333 0.00 0.00 38.76 2.66
4472 4548 6.639632 AAATGACTCAACATTGCACTAACT 57.360 33.333 0.00 0.00 39.88 2.24
4473 4549 8.970691 AATAAATGACTCAACATTGCACTAAC 57.029 30.769 0.00 0.00 39.88 2.34
4474 4550 9.979578 AAAATAAATGACTCAACATTGCACTAA 57.020 25.926 0.00 0.00 39.88 2.24
4475 4551 9.409312 CAAAATAAATGACTCAACATTGCACTA 57.591 29.630 0.00 0.00 39.88 2.74
4476 4552 7.385752 CCAAAATAAATGACTCAACATTGCACT 59.614 33.333 0.00 0.00 39.88 4.40
4477 4553 7.384660 TCCAAAATAAATGACTCAACATTGCAC 59.615 33.333 0.00 0.00 39.88 4.57
4478 4554 7.440198 TCCAAAATAAATGACTCAACATTGCA 58.560 30.769 0.00 0.00 39.88 4.08
4479 4555 7.887996 TCCAAAATAAATGACTCAACATTGC 57.112 32.000 0.00 0.00 39.88 3.56
4480 4556 8.427012 CGTTCCAAAATAAATGACTCAACATTG 58.573 33.333 0.00 0.00 39.88 2.82
4481 4557 7.598493 CCGTTCCAAAATAAATGACTCAACATT 59.402 33.333 0.00 0.00 41.43 2.71
4482 4558 7.040062 TCCGTTCCAAAATAAATGACTCAACAT 60.040 33.333 0.00 0.00 0.00 2.71
4483 4559 6.263392 TCCGTTCCAAAATAAATGACTCAACA 59.737 34.615 0.00 0.00 0.00 3.33
4484 4560 6.674066 TCCGTTCCAAAATAAATGACTCAAC 58.326 36.000 0.00 0.00 0.00 3.18
4485 4561 6.712998 TCTCCGTTCCAAAATAAATGACTCAA 59.287 34.615 0.00 0.00 0.00 3.02
4486 4562 6.234920 TCTCCGTTCCAAAATAAATGACTCA 58.765 36.000 0.00 0.00 0.00 3.41
4487 4563 6.737254 TCTCCGTTCCAAAATAAATGACTC 57.263 37.500 0.00 0.00 0.00 3.36
4488 4564 6.318900 GGATCTCCGTTCCAAAATAAATGACT 59.681 38.462 0.00 0.00 33.21 3.41
4489 4565 6.094881 TGGATCTCCGTTCCAAAATAAATGAC 59.905 38.462 0.00 0.00 40.29 3.06
4490 4566 6.184068 TGGATCTCCGTTCCAAAATAAATGA 58.816 36.000 0.00 0.00 40.29 2.57
4491 4567 6.449635 TGGATCTCCGTTCCAAAATAAATG 57.550 37.500 0.00 0.00 40.29 2.32
4492 4568 7.062957 AGATGGATCTCCGTTCCAAAATAAAT 58.937 34.615 0.00 0.00 45.99 1.40
4493 4569 6.423182 AGATGGATCTCCGTTCCAAAATAAA 58.577 36.000 0.00 0.00 45.99 1.40
4494 4570 6.001449 AGATGGATCTCCGTTCCAAAATAA 57.999 37.500 0.00 0.00 45.99 1.40
4495 4571 5.611374 GAGATGGATCTCCGTTCCAAAATA 58.389 41.667 5.45 0.00 45.99 1.40
4496 4572 4.455606 GAGATGGATCTCCGTTCCAAAAT 58.544 43.478 5.45 0.00 45.99 1.82
4497 4573 3.873910 GAGATGGATCTCCGTTCCAAAA 58.126 45.455 5.45 0.00 45.99 2.44
4498 4574 3.543680 GAGATGGATCTCCGTTCCAAA 57.456 47.619 5.45 0.00 45.99 3.28
4508 4584 0.689080 ACTGCACCGGAGATGGATCT 60.689 55.000 9.46 0.00 40.50 2.75
4509 4585 0.249657 GACTGCACCGGAGATGGATC 60.250 60.000 9.46 0.00 0.00 3.36
4510 4586 0.977627 TGACTGCACCGGAGATGGAT 60.978 55.000 9.46 0.00 0.00 3.41
5392 5468 7.939039 ACATTTGTACTAGAATCACATATGGGG 59.061 37.037 4.82 0.00 36.52 4.96


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

AutoCloner maintained by Alex Coulton.