Multiple sequence alignment - TraesCS3D01G399000

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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 TraesCS3D01G399000 chr3D 100.000 4645 0 0 1 4645 513894866 513890222 0.000000e+00 8578
1 TraesCS3D01G399000 chr3D 88.018 676 65 9 1 666 505321040 505320371 0.000000e+00 785
2 TraesCS3D01G399000 chr3D 88.083 193 17 2 935 1127 160295431 160295245 1.680000e-54 224
3 TraesCS3D01G399000 chr3D 90.299 134 11 2 535 667 451156857 451156989 1.720000e-39 174
4 TraesCS3D01G399000 chr3A 90.313 2075 134 37 761 2800 648865863 648863821 0.000000e+00 2656
5 TraesCS3D01G399000 chr3A 91.740 908 43 10 3538 4433 648862929 648862042 0.000000e+00 1232
6 TraesCS3D01G399000 chr3A 85.403 781 70 19 2787 3534 648863797 648863028 0.000000e+00 771
7 TraesCS3D01G399000 chr3A 92.056 214 6 4 4432 4645 648861991 648861789 1.630000e-74 291
8 TraesCS3D01G399000 chr3B 88.555 2132 158 46 717 2800 676217810 676215717 0.000000e+00 2507
9 TraesCS3D01G399000 chr3B 85.392 1020 75 34 2787 3762 676215693 676214704 0.000000e+00 990
10 TraesCS3D01G399000 chr3B 88.793 696 41 9 3763 4433 676214624 676213941 0.000000e+00 819
11 TraesCS3D01G399000 chr3B 88.764 267 21 3 1960 2226 762577018 762577275 7.500000e-83 318
12 TraesCS3D01G399000 chr3B 92.991 214 11 2 4432 4645 676213889 676213680 4.510000e-80 309
13 TraesCS3D01G399000 chr4B 91.716 676 45 5 1 667 70727423 70726750 0.000000e+00 928
14 TraesCS3D01G399000 chr4B 89.387 669 63 6 1 667 618406985 618407647 0.000000e+00 835
15 TraesCS3D01G399000 chr4B 89.150 682 55 10 1 668 286321295 286321971 0.000000e+00 832
16 TraesCS3D01G399000 chr4B 88.401 319 24 5 935 1248 219274322 219274012 5.680000e-99 372
17 TraesCS3D01G399000 chr4B 84.197 386 47 8 1343 1719 653845821 653846201 3.420000e-96 363
18 TraesCS3D01G399000 chr7A 88.710 682 58 10 1 668 679842786 679843462 0.000000e+00 815
19 TraesCS3D01G399000 chr2A 87.647 680 59 16 1 665 683220593 683219924 0.000000e+00 767
20 TraesCS3D01G399000 chr2A 75.403 683 135 21 7 666 561014309 561013637 2.720000e-77 300
21 TraesCS3D01G399000 chr4D 87.353 680 55 10 1 666 404668211 404667549 0.000000e+00 750
22 TraesCS3D01G399000 chr6A 86.519 675 50 13 1 663 3682398 3683043 0.000000e+00 704
23 TraesCS3D01G399000 chr2B 81.738 679 100 16 7 666 77908706 77908033 3.160000e-151 545
24 TraesCS3D01G399000 chr2B 86.869 297 26 4 957 1248 320515697 320515409 2.090000e-83 320
25 TraesCS3D01G399000 chr7D 86.815 493 47 10 190 666 40836990 40836500 6.840000e-148 534
26 TraesCS3D01G399000 chr7D 89.744 195 14 1 1 195 40846324 40846136 1.290000e-60 244
27 TraesCS3D01G399000 chr5B 86.462 325 30 9 929 1248 37321452 37321767 1.240000e-90 344
28 TraesCS3D01G399000 chr2D 86.164 318 22 9 935 1247 38519996 38519696 1.610000e-84 324
29 TraesCS3D01G399000 chr1B 87.732 269 24 3 1958 2226 126507329 126507588 5.840000e-79 305
30 TraesCS3D01G399000 chr6B 86.765 204 18 3 2023 2226 440455406 440455600 7.830000e-53 219


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 TraesCS3D01G399000 chr3D 513890222 513894866 4644 True 8578.00 8578 100.00000 1 4645 1 chr3D.!!$R3 4644
1 TraesCS3D01G399000 chr3D 505320371 505321040 669 True 785.00 785 88.01800 1 666 1 chr3D.!!$R2 665
2 TraesCS3D01G399000 chr3A 648861789 648865863 4074 True 1237.50 2656 89.87800 761 4645 4 chr3A.!!$R1 3884
3 TraesCS3D01G399000 chr3B 676213680 676217810 4130 True 1156.25 2507 88.93275 717 4645 4 chr3B.!!$R1 3928
4 TraesCS3D01G399000 chr4B 70726750 70727423 673 True 928.00 928 91.71600 1 667 1 chr4B.!!$R1 666
5 TraesCS3D01G399000 chr4B 618406985 618407647 662 False 835.00 835 89.38700 1 667 1 chr4B.!!$F2 666
6 TraesCS3D01G399000 chr4B 286321295 286321971 676 False 832.00 832 89.15000 1 668 1 chr4B.!!$F1 667
7 TraesCS3D01G399000 chr7A 679842786 679843462 676 False 815.00 815 88.71000 1 668 1 chr7A.!!$F1 667
8 TraesCS3D01G399000 chr2A 683219924 683220593 669 True 767.00 767 87.64700 1 665 1 chr2A.!!$R2 664
9 TraesCS3D01G399000 chr2A 561013637 561014309 672 True 300.00 300 75.40300 7 666 1 chr2A.!!$R1 659
10 TraesCS3D01G399000 chr4D 404667549 404668211 662 True 750.00 750 87.35300 1 666 1 chr4D.!!$R1 665
11 TraesCS3D01G399000 chr6A 3682398 3683043 645 False 704.00 704 86.51900 1 663 1 chr6A.!!$F1 662
12 TraesCS3D01G399000 chr2B 77908033 77908706 673 True 545.00 545 81.73800 7 666 1 chr2B.!!$R1 659

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
462 481 0.035820 GACCGCTCCATTGTGGGTTA 60.036 55.0 0.00 0.00 41.59 2.85 F
1272 1325 0.107945 GCTGTACTGAGGCCTTCCTG 60.108 60.0 6.77 1.07 44.46 3.86 F
1432 1490 0.514691 GTGAGCTCTTTTGGCTGACG 59.485 55.0 16.19 0.00 40.40 4.35 F
1630 1688 0.535335 TCTGTGTATTGCTCCGGGTC 59.465 55.0 0.00 0.00 0.00 4.46 F
3092 3270 0.244721 GGAATTCTGGCTGTGCAACC 59.755 55.0 5.23 0.00 34.36 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1911 0.036952 AGCAGCATAACTCACAGCGT 60.037 50.0 0.00 0.00 0.00 5.07 R
3069 3227 0.109597 GCACAGCCAGAATTCCGTTG 60.110 55.0 0.65 3.77 0.00 4.10 R
3073 3231 0.244721 GGTTGCACAGCCAGAATTCC 59.755 55.0 0.65 0.00 0.00 3.01 R
3422 3638 0.898320 ATCGTCAGTGACCTCAAGGG 59.102 55.0 17.57 1.85 40.27 3.95 R
4602 5075 0.744414 GAGCGGCTGCCAATGAACTA 60.744 55.0 20.29 0.00 44.31 2.24 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
37 38 0.531753 GAGGCTCGGAATTCTGCTCC 60.532 60.000 9.58 12.00 0.00 4.70
128 129 6.409524 TTCCAGCATCTTTTCAAAACTCAT 57.590 33.333 0.00 0.00 0.00 2.90
129 130 6.017400 TCCAGCATCTTTTCAAAACTCATC 57.983 37.500 0.00 0.00 0.00 2.92
130 131 5.047802 TCCAGCATCTTTTCAAAACTCATCC 60.048 40.000 0.00 0.00 0.00 3.51
182 186 2.184020 CTCATTGGTCTCCGCCACCA 62.184 60.000 0.00 0.00 42.48 4.17
187 191 2.662596 GTCTCCGCCACCACATGA 59.337 61.111 0.00 0.00 0.00 3.07
238 244 4.689549 TGGACCGGGGCTCTTCGA 62.690 66.667 6.32 0.00 0.00 3.71
247 253 0.178068 GGGCTCTTCGACAATAGGCA 59.822 55.000 10.05 0.00 34.05 4.75
301 310 0.183492 TGCTGCTTCAGAACCCTTGT 59.817 50.000 0.00 0.00 32.44 3.16
462 481 0.035820 GACCGCTCCATTGTGGGTTA 60.036 55.000 0.00 0.00 41.59 2.85
534 553 2.097954 TCAAGCATGTTCATCGGCAATC 59.902 45.455 0.00 0.00 0.00 2.67
682 719 3.446310 AAAAGGTGGCAAGTTTAACGG 57.554 42.857 0.00 0.00 0.00 4.44
683 720 1.324383 AAGGTGGCAAGTTTAACGGG 58.676 50.000 0.00 0.00 0.00 5.28
684 721 1.176619 AGGTGGCAAGTTTAACGGGC 61.177 55.000 8.79 8.79 0.00 6.13
685 722 1.457009 GGTGGCAAGTTTAACGGGCA 61.457 55.000 12.99 12.99 32.48 5.36
686 723 0.386113 GTGGCAAGTTTAACGGGCAA 59.614 50.000 17.03 4.25 35.47 4.52
687 724 1.112113 TGGCAAGTTTAACGGGCAAA 58.888 45.000 14.18 1.97 32.13 3.68
688 725 1.202428 TGGCAAGTTTAACGGGCAAAC 60.202 47.619 14.18 0.00 36.37 2.93
689 726 1.202428 GGCAAGTTTAACGGGCAAACA 60.202 47.619 13.87 0.00 38.16 2.83
690 727 2.547007 GGCAAGTTTAACGGGCAAACAT 60.547 45.455 13.87 0.00 38.16 2.71
691 728 2.474735 GCAAGTTTAACGGGCAAACATG 59.525 45.455 8.64 9.40 38.16 3.21
692 729 3.056304 CAAGTTTAACGGGCAAACATGG 58.944 45.455 0.00 0.00 38.16 3.66
693 730 1.000394 AGTTTAACGGGCAAACATGGC 60.000 47.619 0.00 0.00 38.16 4.40
694 731 1.040646 TTTAACGGGCAAACATGGCA 58.959 45.000 0.00 0.00 35.93 4.92
695 732 1.040646 TTAACGGGCAAACATGGCAA 58.959 45.000 0.00 0.00 35.93 4.52
696 733 1.261480 TAACGGGCAAACATGGCAAT 58.739 45.000 0.00 0.00 35.93 3.56
697 734 0.396060 AACGGGCAAACATGGCAATT 59.604 45.000 0.00 0.00 35.93 2.32
698 735 0.396060 ACGGGCAAACATGGCAATTT 59.604 45.000 0.00 0.00 35.93 1.82
699 736 1.202746 ACGGGCAAACATGGCAATTTT 60.203 42.857 0.00 0.00 35.93 1.82
700 737 1.464219 CGGGCAAACATGGCAATTTTC 59.536 47.619 0.00 0.00 35.93 2.29
701 738 2.502295 GGGCAAACATGGCAATTTTCA 58.498 42.857 0.00 0.00 35.93 2.69
702 739 2.226200 GGGCAAACATGGCAATTTTCAC 59.774 45.455 0.00 0.00 35.93 3.18
703 740 2.877168 GGCAAACATGGCAATTTTCACA 59.123 40.909 0.00 0.00 0.00 3.58
704 741 3.314635 GGCAAACATGGCAATTTTCACAA 59.685 39.130 0.00 0.00 0.00 3.33
705 742 4.201990 GGCAAACATGGCAATTTTCACAAA 60.202 37.500 0.00 0.00 0.00 2.83
706 743 5.338365 GCAAACATGGCAATTTTCACAAAA 58.662 33.333 0.00 0.00 34.41 2.44
707 744 5.978322 GCAAACATGGCAATTTTCACAAAAT 59.022 32.000 0.00 0.00 42.62 1.82
709 746 7.010275 GCAAACATGGCAATTTTCACAAAATTT 59.990 29.630 0.00 0.00 46.01 1.82
710 747 7.988904 AACATGGCAATTTTCACAAAATTTG 57.011 28.000 3.89 3.89 46.01 2.32
711 748 7.330900 ACATGGCAATTTTCACAAAATTTGA 57.669 28.000 13.19 0.00 46.01 2.69
712 749 7.194962 ACATGGCAATTTTCACAAAATTTGAC 58.805 30.769 13.19 3.90 46.01 3.18
713 750 5.804173 TGGCAATTTTCACAAAATTTGACG 58.196 33.333 13.19 3.33 46.01 4.35
714 751 5.352569 TGGCAATTTTCACAAAATTTGACGT 59.647 32.000 13.19 0.00 46.01 4.34
715 752 6.128172 TGGCAATTTTCACAAAATTTGACGTT 60.128 30.769 13.19 0.00 46.01 3.99
734 774 9.493206 TTGACGTTCAAAACTAAGACAATAAAC 57.507 29.630 0.00 0.00 32.71 2.01
735 775 8.666573 TGACGTTCAAAACTAAGACAATAAACA 58.333 29.630 0.00 0.00 0.00 2.83
737 777 9.281075 ACGTTCAAAACTAAGACAATAAACAAC 57.719 29.630 0.00 0.00 0.00 3.32
757 797 6.223120 ACAACAAAAGAAAAGAGCAGTTGTT 58.777 32.000 0.00 0.00 43.87 2.83
759 799 5.170748 ACAAAAGAAAAGAGCAGTTGTTGG 58.829 37.500 0.00 0.00 0.00 3.77
767 809 6.899393 AAAGAGCAGTTGTTGGATAATTGA 57.101 33.333 0.00 0.00 0.00 2.57
795 837 0.734942 ACTTATGACCCGTTGACGCG 60.735 55.000 3.53 3.53 38.18 6.01
894 936 2.358247 CACCCCACTTCCGTTCCG 60.358 66.667 0.00 0.00 0.00 4.30
979 1021 1.308216 CCTCTCCCTCCCATTGGGT 60.308 63.158 21.31 0.00 44.74 4.51
1029 1071 2.664081 CCTCTGCCTCCACCTCCAC 61.664 68.421 0.00 0.00 0.00 4.02
1138 1186 1.379527 CCTGCGGATTGGTAAAGGAC 58.620 55.000 0.00 0.00 0.00 3.85
1139 1187 1.065418 CCTGCGGATTGGTAAAGGACT 60.065 52.381 0.00 0.00 0.00 3.85
1174 1222 2.934083 GCCAATCGCCTCTAATCCC 58.066 57.895 0.00 0.00 0.00 3.85
1203 1256 3.866582 GCCCCTGGAGCTGCGTAT 61.867 66.667 0.00 0.00 0.00 3.06
1208 1261 1.718757 CCTGGAGCTGCGTATTTGCC 61.719 60.000 0.00 0.00 0.00 4.52
1213 1266 2.709475 CTGCGTATTTGCCGGAGC 59.291 61.111 5.05 0.00 36.98 4.70
1254 1307 1.091771 TTCTTATCCGCTGCTGCTGC 61.092 55.000 19.94 19.94 36.97 5.25
1255 1308 1.523258 CTTATCCGCTGCTGCTGCT 60.523 57.895 25.43 12.33 40.48 4.24
1256 1309 1.773054 CTTATCCGCTGCTGCTGCTG 61.773 60.000 25.43 20.27 40.48 4.41
1272 1325 0.107945 GCTGTACTGAGGCCTTCCTG 60.108 60.000 6.77 1.07 44.46 3.86
1423 1477 2.775890 CCTGTGTGATGTGAGCTCTTT 58.224 47.619 16.19 0.00 0.00 2.52
1426 1484 2.880268 TGTGTGATGTGAGCTCTTTTGG 59.120 45.455 16.19 0.00 0.00 3.28
1432 1490 0.514691 GTGAGCTCTTTTGGCTGACG 59.485 55.000 16.19 0.00 40.40 4.35
1446 1504 1.797025 CTGACGGAGGGTTCTGTTTC 58.203 55.000 0.00 0.00 42.99 2.78
1488 1546 1.745864 GAGAGGAGCGTCTCGGTGA 60.746 63.158 4.66 0.00 37.83 4.02
1530 1588 3.463704 AGGGAAGAGAATGGGGGTATTTC 59.536 47.826 0.00 0.00 0.00 2.17
1531 1589 3.463704 GGGAAGAGAATGGGGGTATTTCT 59.536 47.826 0.00 0.00 0.00 2.52
1532 1590 4.446455 GGGAAGAGAATGGGGGTATTTCTC 60.446 50.000 4.19 4.19 0.00 2.87
1533 1591 4.413851 GGAAGAGAATGGGGGTATTTCTCT 59.586 45.833 8.26 8.26 34.95 3.10
1535 1593 6.101296 GGAAGAGAATGGGGGTATTTCTCTTA 59.899 42.308 20.88 0.00 41.38 2.10
1536 1594 7.202232 GGAAGAGAATGGGGGTATTTCTCTTAT 60.202 40.741 20.88 6.51 41.38 1.73
1537 1595 7.323052 AGAGAATGGGGGTATTTCTCTTATC 57.677 40.000 8.26 0.00 29.93 1.75
1538 1596 7.085601 AGAGAATGGGGGTATTTCTCTTATCT 58.914 38.462 8.26 0.00 29.93 1.98
1539 1597 7.236640 AGAGAATGGGGGTATTTCTCTTATCTC 59.763 40.741 8.26 0.00 29.93 2.75
1540 1598 6.851836 AGAATGGGGGTATTTCTCTTATCTCA 59.148 38.462 0.00 0.00 0.00 3.27
1571 1629 3.399330 TCCAAACTTAGCTTCCACGAAG 58.601 45.455 0.00 0.00 42.03 3.79
1630 1688 0.535335 TCTGTGTATTGCTCCGGGTC 59.465 55.000 0.00 0.00 0.00 4.46
1751 1809 7.408132 TCGTGCTATAAGTGAAGATAAATGC 57.592 36.000 0.00 0.00 0.00 3.56
1768 1826 9.236006 AGATAAATGCAGTGTACAAGAGATTTT 57.764 29.630 0.00 0.00 0.00 1.82
1769 1827 9.282247 GATAAATGCAGTGTACAAGAGATTTTG 57.718 33.333 0.00 0.00 0.00 2.44
1773 1831 9.448438 AATGCAGTGTACAAGAGATTTTGTATA 57.552 29.630 0.00 0.00 43.27 1.47
1862 1926 8.942338 ATCAATTTTAGATACGCTGTGAGTTA 57.058 30.769 0.00 0.00 0.00 2.24
1872 1936 2.354259 GCTGTGAGTTATGCTGCTTCT 58.646 47.619 0.00 0.00 0.00 2.85
1873 1937 2.095532 GCTGTGAGTTATGCTGCTTCTG 59.904 50.000 0.00 0.00 0.00 3.02
1878 1942 5.814188 TGTGAGTTATGCTGCTTCTGAATAG 59.186 40.000 0.00 0.00 0.00 1.73
1879 1943 5.814705 GTGAGTTATGCTGCTTCTGAATAGT 59.185 40.000 0.00 0.00 0.00 2.12
1884 1948 8.669243 AGTTATGCTGCTTCTGAATAGTTTTAC 58.331 33.333 0.00 0.00 0.00 2.01
1939 2003 8.906867 CAGTGGATGATGAATGTACCTAAATTT 58.093 33.333 0.00 0.00 0.00 1.82
1941 2005 9.125026 GTGGATGATGAATGTACCTAAATTTCT 57.875 33.333 0.00 0.00 0.00 2.52
1947 2011 9.566432 GATGAATGTACCTAAATTTCTCTCCAT 57.434 33.333 0.00 0.00 0.00 3.41
2031 2096 3.084786 GCACAGGTTCATTTCCTTAGCT 58.915 45.455 0.00 0.00 32.79 3.32
2039 2104 7.065204 CAGGTTCATTTCCTTAGCTTAGAACTC 59.935 40.741 0.16 0.00 35.65 3.01
2041 2106 7.390718 GGTTCATTTCCTTAGCTTAGAACTCAA 59.609 37.037 0.16 0.00 35.65 3.02
2044 2109 9.823647 TCATTTCCTTAGCTTAGAACTCAATAG 57.176 33.333 0.16 0.00 0.00 1.73
2062 2127 5.127519 TCAATAGTTCCCTGATTTGGCAATG 59.872 40.000 0.00 0.00 0.00 2.82
2067 2132 3.443052 TCCCTGATTTGGCAATGTCATT 58.557 40.909 13.90 0.00 0.00 2.57
2068 2133 4.608269 TCCCTGATTTGGCAATGTCATTA 58.392 39.130 13.90 0.00 0.00 1.90
2069 2134 5.210430 TCCCTGATTTGGCAATGTCATTAT 58.790 37.500 13.90 0.00 0.00 1.28
2070 2135 5.069383 TCCCTGATTTGGCAATGTCATTATG 59.931 40.000 13.90 5.25 0.00 1.90
2071 2136 5.163385 CCCTGATTTGGCAATGTCATTATGT 60.163 40.000 13.90 0.00 0.00 2.29
2072 2137 5.981315 CCTGATTTGGCAATGTCATTATGTC 59.019 40.000 13.90 0.00 0.00 3.06
2073 2138 5.904941 TGATTTGGCAATGTCATTATGTCC 58.095 37.500 0.00 0.00 0.00 4.02
2074 2139 4.734398 TTTGGCAATGTCATTATGTCCC 57.266 40.909 0.00 0.00 0.00 4.46
2200 2265 5.160607 TGTATTTGAAGGTTCGTCTGGAT 57.839 39.130 0.00 0.00 0.00 3.41
2201 2266 5.175859 TGTATTTGAAGGTTCGTCTGGATC 58.824 41.667 0.00 0.00 0.00 3.36
2222 2287 7.684529 GGATCCATCCTATACTCATTGTCTTT 58.315 38.462 6.95 0.00 43.73 2.52
2260 2326 6.944290 TCTACCTAGCATCTACGCCTTATTAA 59.056 38.462 0.00 0.00 0.00 1.40
2269 2335 9.946165 GCATCTACGCCTTATTAAAATTAAGTT 57.054 29.630 0.00 0.00 0.00 2.66
2307 2373 4.946478 AGAATGATACAGTACAGCCTCC 57.054 45.455 0.00 0.00 0.00 4.30
2325 2391 4.680708 GCCTCCGAGTAAGATGTTCATCAA 60.681 45.833 14.05 0.75 0.00 2.57
2327 2393 6.051717 CCTCCGAGTAAGATGTTCATCAATT 58.948 40.000 14.05 4.57 0.00 2.32
2432 2498 7.558444 TGTTTTTAATGGACTTCAGGTTAGTGT 59.442 33.333 0.00 0.00 0.00 3.55
2438 2504 3.261137 GGACTTCAGGTTAGTGTTAGCCT 59.739 47.826 0.00 0.00 40.75 4.58
2441 2507 5.085219 ACTTCAGGTTAGTGTTAGCCTACT 58.915 41.667 0.00 0.00 38.32 2.57
2443 2509 5.401531 TCAGGTTAGTGTTAGCCTACTTG 57.598 43.478 0.00 0.00 38.32 3.16
2445 2511 5.306160 TCAGGTTAGTGTTAGCCTACTTGTT 59.694 40.000 0.00 0.00 38.32 2.83
2446 2512 6.494491 TCAGGTTAGTGTTAGCCTACTTGTTA 59.506 38.462 0.00 0.00 38.32 2.41
2447 2513 6.812160 CAGGTTAGTGTTAGCCTACTTGTTAG 59.188 42.308 0.00 0.00 38.32 2.34
2466 2537 3.715628 AGGTTGCTTGCTTTTGTACAG 57.284 42.857 0.00 0.00 0.00 2.74
2468 2539 2.127251 GTTGCTTGCTTTTGTACAGCC 58.873 47.619 0.00 0.00 36.33 4.85
2470 2541 1.066908 TGCTTGCTTTTGTACAGCCAC 59.933 47.619 0.00 0.00 36.33 5.01
2472 2543 2.731217 CTTGCTTTTGTACAGCCACAC 58.269 47.619 0.00 0.00 36.33 3.82
2473 2544 1.756430 TGCTTTTGTACAGCCACACA 58.244 45.000 0.00 0.00 36.33 3.72
2483 2558 3.325293 ACAGCCACACAGTATCTTCAG 57.675 47.619 0.00 0.00 0.00 3.02
2484 2559 2.899900 ACAGCCACACAGTATCTTCAGA 59.100 45.455 0.00 0.00 0.00 3.27
2492 2567 7.094805 GCCACACAGTATCTTCAGAATTTGTAA 60.095 37.037 0.00 0.00 0.00 2.41
2542 2618 5.008811 GCAGGAAATTGATGGAGATTCAGAG 59.991 44.000 0.00 0.00 0.00 3.35
2593 2669 4.444022 CCCTTGGTATCCTCTGAAGATGTG 60.444 50.000 0.00 0.00 0.00 3.21
2616 2692 8.383175 TGTGAAAAAGGTTACCTTCTATGATCT 58.617 33.333 17.77 0.00 43.92 2.75
2620 2696 6.673839 AAGGTTACCTTCTATGATCTAGCC 57.326 41.667 11.39 0.00 40.17 3.93
2637 2713 9.222098 TGATCTAGCCTGAATTATCCATCATAT 57.778 33.333 0.00 0.00 0.00 1.78
2642 2718 5.877012 GCCTGAATTATCCATCATATCGTGT 59.123 40.000 0.00 0.00 0.00 4.49
2660 2736 5.838529 TCGTGTCTTGTAAGATGTTCTTGA 58.161 37.500 0.00 0.00 37.29 3.02
2669 2745 9.956720 CTTGTAAGATGTTCTTGAATCTGTTTT 57.043 29.630 0.07 0.00 37.29 2.43
2696 2778 8.415950 TTTCTATAAAGGGAATTCTTGCACAA 57.584 30.769 5.23 0.00 0.00 3.33
2724 2807 6.289064 TCAACTAACAGAAAACTCTCCCTTC 58.711 40.000 0.00 0.00 0.00 3.46
2731 2814 5.070047 ACAGAAAACTCTCCCTTCGAAGTTA 59.930 40.000 23.03 10.08 0.00 2.24
2735 2818 4.950205 ACTCTCCCTTCGAAGTTACAAA 57.050 40.909 23.03 3.65 0.00 2.83
2782 2866 7.959175 ACATGCATGATAAATTATCTGGCTTT 58.041 30.769 32.75 0.57 36.54 3.51
2800 2956 6.539173 TGGCTTTGAACTTACTTAATCCTGA 58.461 36.000 0.00 0.00 0.00 3.86
2832 2988 9.616156 TGGTATTTCACAGTAACTTTGTAAAGA 57.384 29.630 11.07 0.00 39.31 2.52
2864 3020 9.586435 AAGTAATATTTGTAAAATCTTGCAGGC 57.414 29.630 0.00 0.00 0.00 4.85
2865 3021 8.971073 AGTAATATTTGTAAAATCTTGCAGGCT 58.029 29.630 0.00 0.00 0.00 4.58
2873 3029 0.680280 ATCTTGCAGGCTGCTCAAGG 60.680 55.000 36.50 19.46 45.31 3.61
2948 3104 1.312815 GAGCAGCTGTTCTTGGTGTT 58.687 50.000 21.96 0.00 35.60 3.32
2975 3131 6.640518 TGTCAAAGCTACTATAAAGGAGGTG 58.359 40.000 0.00 0.00 43.87 4.00
2990 3146 5.615925 AGGAGGTGACTGTTTATACATCC 57.384 43.478 0.00 0.00 44.43 3.51
2991 3147 4.409247 AGGAGGTGACTGTTTATACATCCC 59.591 45.833 12.26 0.00 43.07 3.85
3033 3191 4.004644 AGCTTGCAAAGATCCTTGGTCAA 61.005 43.478 0.00 2.38 38.98 3.18
3034 3192 6.059406 AGCTTGCAAAGATCCTTGGTCAAC 62.059 45.833 0.00 0.00 38.98 3.18
3035 3193 3.228188 TGCAAAGATCCTTGGTCAACT 57.772 42.857 6.20 0.00 0.00 3.16
3036 3194 3.565307 TGCAAAGATCCTTGGTCAACTT 58.435 40.909 6.20 0.00 0.00 2.66
3038 3196 3.365364 GCAAAGATCCTTGGTCAACTTCG 60.365 47.826 6.20 0.00 0.00 3.79
3040 3198 3.601443 AGATCCTTGGTCAACTTCGAG 57.399 47.619 0.00 0.00 0.00 4.04
3041 3199 3.165875 AGATCCTTGGTCAACTTCGAGA 58.834 45.455 0.00 0.00 0.00 4.04
3042 3200 3.772025 AGATCCTTGGTCAACTTCGAGAT 59.228 43.478 0.00 0.00 0.00 2.75
3045 3203 5.263968 TCCTTGGTCAACTTCGAGATATC 57.736 43.478 0.00 0.00 0.00 1.63
3046 3204 4.956700 TCCTTGGTCAACTTCGAGATATCT 59.043 41.667 4.47 4.47 0.00 1.98
3047 3205 6.127101 TCCTTGGTCAACTTCGAGATATCTA 58.873 40.000 4.89 0.00 0.00 1.98
3050 3208 8.577296 CCTTGGTCAACTTCGAGATATCTAATA 58.423 37.037 4.89 0.00 0.00 0.98
3051 3209 9.967346 CTTGGTCAACTTCGAGATATCTAATAA 57.033 33.333 4.89 0.00 0.00 1.40
3081 3259 5.639757 TGCATAAATGACAACGGAATTCTG 58.360 37.500 12.91 12.91 0.00 3.02
3092 3270 0.244721 GGAATTCTGGCTGTGCAACC 59.755 55.000 5.23 0.00 34.36 3.77
3093 3271 0.961019 GAATTCTGGCTGTGCAACCA 59.039 50.000 0.00 4.46 34.36 3.67
3104 3282 3.209410 CTGTGCAACCATAATCCTCTCC 58.791 50.000 0.00 0.00 34.36 3.71
3106 3284 1.494721 TGCAACCATAATCCTCTCCCC 59.505 52.381 0.00 0.00 0.00 4.81
3107 3285 1.202940 GCAACCATAATCCTCTCCCCC 60.203 57.143 0.00 0.00 0.00 5.40
3126 3304 0.622665 CCTTCTGTCTCCAGGCCAAT 59.377 55.000 5.01 0.00 39.31 3.16
3132 3310 0.530870 GTCTCCAGGCCAATAGCGAC 60.531 60.000 5.01 0.00 45.17 5.19
3135 3313 1.592669 CCAGGCCAATAGCGACTCG 60.593 63.158 5.01 0.00 45.17 4.18
3138 3316 0.249398 AGGCCAATAGCGACTCGTTT 59.751 50.000 5.01 0.00 45.17 3.60
3153 3331 6.029209 GACTCGTTTGTCGTAAAAACTCTT 57.971 37.500 8.11 0.00 40.80 2.85
3193 3371 3.191371 GGAAATGCAAACTCCACAGGTAG 59.809 47.826 7.11 0.00 0.00 3.18
3195 3373 4.634012 AATGCAAACTCCACAGGTAGTA 57.366 40.909 0.00 0.00 0.00 1.82
3196 3374 4.844349 ATGCAAACTCCACAGGTAGTAT 57.156 40.909 0.00 0.00 0.00 2.12
3198 3376 4.323417 TGCAAACTCCACAGGTAGTATTG 58.677 43.478 0.00 0.00 0.00 1.90
3199 3377 3.127030 GCAAACTCCACAGGTAGTATTGC 59.873 47.826 0.00 0.00 35.12 3.56
3200 3378 3.629142 AACTCCACAGGTAGTATTGCC 57.371 47.619 0.00 0.00 0.00 4.52
3201 3379 2.834113 ACTCCACAGGTAGTATTGCCT 58.166 47.619 0.00 0.00 40.43 4.75
3204 3386 2.766263 TCCACAGGTAGTATTGCCTCTG 59.234 50.000 0.00 0.00 37.30 3.35
3208 3390 5.109903 CACAGGTAGTATTGCCTCTGTAAC 58.890 45.833 0.00 0.00 37.30 2.50
3229 3411 9.247126 TGTAACAAGAACATTTCATGATTTGTG 57.753 29.630 10.75 4.32 34.54 3.33
3235 3417 7.499292 AGAACATTTCATGATTTGTGTTTCCA 58.501 30.769 10.75 0.00 30.70 3.53
3236 3418 8.152246 AGAACATTTCATGATTTGTGTTTCCAT 58.848 29.630 10.75 0.00 30.70 3.41
3238 3420 8.680039 ACATTTCATGATTTGTGTTTCCATTT 57.320 26.923 9.55 0.00 0.00 2.32
3239 3421 8.776470 ACATTTCATGATTTGTGTTTCCATTTC 58.224 29.630 9.55 0.00 0.00 2.17
3241 3423 6.416631 TCATGATTTGTGTTTCCATTTCCA 57.583 33.333 0.00 0.00 0.00 3.53
3242 3424 7.006865 TCATGATTTGTGTTTCCATTTCCAT 57.993 32.000 0.00 0.00 0.00 3.41
3271 3461 4.030216 TGTGGGCAGAACAGATATGACTA 58.970 43.478 0.00 0.00 0.00 2.59
3278 3468 6.426328 GGCAGAACAGATATGACTAGGAAATG 59.574 42.308 0.00 0.00 0.00 2.32
3304 3494 4.589908 ACTGATTGTAGGTGATGAAACCC 58.410 43.478 0.00 0.00 41.54 4.11
3315 3505 4.240096 GTGATGAAACCCAATTTGCTCAG 58.760 43.478 0.00 0.00 0.00 3.35
3316 3506 3.258872 TGATGAAACCCAATTTGCTCAGG 59.741 43.478 0.00 0.00 0.00 3.86
3337 3527 3.504520 GGGATGGTTTCGAGCTTGTTAAA 59.495 43.478 0.00 0.00 0.00 1.52
3338 3528 4.473199 GGATGGTTTCGAGCTTGTTAAAC 58.527 43.478 8.97 8.97 0.00 2.01
3346 3536 2.159747 CGAGCTTGTTAAACGGTTAGCC 60.160 50.000 4.51 0.00 0.00 3.93
3361 3554 4.177026 GGTTAGCCGATCACAGCATATAG 58.823 47.826 0.00 0.00 0.00 1.31
3372 3582 6.332735 TCACAGCATATAGTCCACTGATAC 57.667 41.667 0.00 0.00 32.67 2.24
3385 3595 5.992217 GTCCACTGATACACTAATTCCCATC 59.008 44.000 0.00 0.00 0.00 3.51
3389 3605 7.151308 CACTGATACACTAATTCCCATCTCTC 58.849 42.308 0.00 0.00 0.00 3.20
3398 3614 1.198713 TCCCATCTCTCCTTGCTGAC 58.801 55.000 0.00 0.00 0.00 3.51
3405 3621 4.792521 TCTCTCCTTGCTGACTAAACTC 57.207 45.455 0.00 0.00 0.00 3.01
3413 3629 1.989165 GCTGACTAAACTCTGCACTCG 59.011 52.381 0.00 0.00 35.70 4.18
3438 3654 0.326264 ATGCCCTTGAGGTCACTGAC 59.674 55.000 0.00 0.00 38.26 3.51
3526 3742 9.060347 ACATCAAGGTATCATGTTAGCTATTTG 57.940 33.333 14.27 13.29 30.06 2.32
3536 3847 8.932945 TCATGTTAGCTATTTGAACTAGTCTG 57.067 34.615 0.00 0.00 0.00 3.51
3545 3856 7.148557 GCTATTTGAACTAGTCTGTTCTGAACC 60.149 40.741 17.26 2.90 44.63 3.62
3546 3857 4.238761 TGAACTAGTCTGTTCTGAACCG 57.761 45.455 17.26 11.46 44.63 4.44
3559 3870 7.711772 TCTGTTCTGAACCGTTAAGTTTGAATA 59.288 33.333 17.26 0.00 30.75 1.75
3615 3926 2.697751 ACTACTCCTGATGACATGCTCC 59.302 50.000 0.00 0.00 0.00 4.70
3649 3960 3.659786 TGATGAACGATAAATAGGGCCG 58.340 45.455 0.00 0.00 0.00 6.13
3702 4013 5.414454 GGCACCTGTATGAATTTGTCAGTAA 59.586 40.000 0.00 0.00 40.43 2.24
3705 4016 7.066284 GCACCTGTATGAATTTGTCAGTAAGAT 59.934 37.037 0.00 0.00 40.43 2.40
3770 4161 8.440833 AGAAAAATAAACATGTACGTAGCTCAC 58.559 33.333 0.00 0.00 0.00 3.51
3785 4176 5.388994 CGTAGCTCACACACGAGATAGATAG 60.389 48.000 0.00 0.00 34.71 2.08
3870 4268 0.737804 TGACACAACGCAGCAAATGT 59.262 45.000 0.00 0.00 0.00 2.71
3912 4310 4.805219 AGTTTGGTAATAAAAAGGCGCTG 58.195 39.130 7.64 0.00 0.00 5.18
4049 4463 3.276857 GCATGATGATGGCCCTGTATAG 58.723 50.000 0.00 0.00 0.00 1.31
4050 4464 3.276857 CATGATGATGGCCCTGTATAGC 58.723 50.000 0.00 0.00 0.00 2.97
4051 4465 2.337849 TGATGATGGCCCTGTATAGCA 58.662 47.619 0.00 0.00 0.00 3.49
4052 4466 2.303890 TGATGATGGCCCTGTATAGCAG 59.696 50.000 0.00 0.00 44.63 4.24
4053 4467 1.806496 TGATGGCCCTGTATAGCAGT 58.194 50.000 0.00 0.00 43.55 4.40
4054 4468 2.970987 TGATGGCCCTGTATAGCAGTA 58.029 47.619 0.00 0.00 43.55 2.74
4055 4469 3.520696 TGATGGCCCTGTATAGCAGTAT 58.479 45.455 0.00 0.00 43.55 2.12
4056 4470 4.683643 TGATGGCCCTGTATAGCAGTATA 58.316 43.478 0.00 0.00 43.55 1.47
4057 4471 4.711846 TGATGGCCCTGTATAGCAGTATAG 59.288 45.833 0.00 0.00 43.55 1.31
4142 4556 5.120208 GCATGCCATGAAATCATAAGCAATC 59.880 40.000 18.51 12.09 43.43 2.67
4321 4739 2.319844 TCAGAGTTCAGCCAAGACTCA 58.680 47.619 5.64 0.00 0.00 3.41
4331 4749 3.503748 CAGCCAAGACTCAAAACTTAGGG 59.496 47.826 0.00 0.00 0.00 3.53
4492 4965 5.599999 ACTAGTTATTGCTGGAACTCGAT 57.400 39.130 0.00 0.00 37.16 3.59
4538 5011 6.169419 TGCGATCTGTATTGTTCTTTTCTG 57.831 37.500 0.00 0.00 0.00 3.02
4555 5028 6.929049 TCTTTTCTGAACGAACAGACATGTAT 59.071 34.615 13.62 0.00 44.94 2.29
4579 5052 1.610038 CAGCTGGACACTGATTTGCAA 59.390 47.619 5.57 0.00 37.32 4.08
4580 5053 1.884579 AGCTGGACACTGATTTGCAAG 59.115 47.619 0.00 0.00 0.00 4.01
4581 5054 1.881973 GCTGGACACTGATTTGCAAGA 59.118 47.619 0.00 0.00 0.00 3.02
4582 5055 2.294233 GCTGGACACTGATTTGCAAGAA 59.706 45.455 0.00 0.00 0.00 2.52
4583 5056 3.243501 GCTGGACACTGATTTGCAAGAAA 60.244 43.478 0.00 0.00 0.00 2.52
4602 5075 1.867363 AGAATACCTTGGAGGCTCGT 58.133 50.000 8.69 3.15 39.63 4.18
4611 5084 2.672961 TGGAGGCTCGTAGTTCATTG 57.327 50.000 8.69 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.187694 GAGAGGAGCAACAGGTTCATTAG 58.812 47.826 0.00 0.00 0.00 1.73
128 129 0.322546 TCTCACGTCTAGCAGCAGGA 60.323 55.000 0.00 0.00 0.00 3.86
129 130 0.179150 GTCTCACGTCTAGCAGCAGG 60.179 60.000 0.00 0.00 0.00 4.85
130 131 0.179150 GGTCTCACGTCTAGCAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
182 186 4.292186 AGACACCAGCAAAGTATCATGT 57.708 40.909 0.00 0.00 0.00 3.21
187 191 4.080919 TGCATCTAGACACCAGCAAAGTAT 60.081 41.667 0.00 0.00 0.00 2.12
238 244 3.202818 TCCTGAATCACCATGCCTATTGT 59.797 43.478 0.00 0.00 0.00 2.71
301 310 0.901114 TCCGAGGATGAAACACCCGA 60.901 55.000 0.00 0.00 0.00 5.14
374 383 9.053840 GGATTGGAAGATCACATGCATATATAG 57.946 37.037 0.00 0.00 0.00 1.31
375 384 7.712205 CGGATTGGAAGATCACATGCATATATA 59.288 37.037 0.00 0.00 0.00 0.86
376 385 6.541278 CGGATTGGAAGATCACATGCATATAT 59.459 38.462 0.00 0.00 0.00 0.86
462 481 6.256539 CGCCAACTTGATATCAGCGATTATAT 59.743 38.462 24.14 0.00 44.51 0.86
498 517 2.866156 TGCTTGAAAGTCACAGAAGACG 59.134 45.455 0.00 0.00 43.24 4.18
557 588 8.682936 AAAATACAAAGACTCACTGAGTTCAT 57.317 30.769 13.06 0.51 43.53 2.57
668 705 1.112113 TTTGCCCGTTAAACTTGCCA 58.888 45.000 0.00 0.00 0.00 4.92
669 706 1.202428 TGTTTGCCCGTTAAACTTGCC 60.202 47.619 0.00 0.00 38.50 4.52
670 707 2.211353 TGTTTGCCCGTTAAACTTGC 57.789 45.000 0.00 0.00 38.50 4.01
671 708 3.056304 CCATGTTTGCCCGTTAAACTTG 58.944 45.455 0.00 0.00 40.23 3.16
672 709 2.547007 GCCATGTTTGCCCGTTAAACTT 60.547 45.455 0.00 0.00 38.50 2.66
673 710 1.000394 GCCATGTTTGCCCGTTAAACT 60.000 47.619 0.00 0.00 38.50 2.66
674 711 1.269831 TGCCATGTTTGCCCGTTAAAC 60.270 47.619 0.00 0.00 38.26 2.01
675 712 1.040646 TGCCATGTTTGCCCGTTAAA 58.959 45.000 0.00 0.00 0.00 1.52
676 713 1.040646 TTGCCATGTTTGCCCGTTAA 58.959 45.000 0.00 0.00 0.00 2.01
677 714 1.261480 ATTGCCATGTTTGCCCGTTA 58.739 45.000 0.00 0.00 0.00 3.18
678 715 0.396060 AATTGCCATGTTTGCCCGTT 59.604 45.000 0.00 0.00 0.00 4.44
679 716 0.396060 AAATTGCCATGTTTGCCCGT 59.604 45.000 0.00 0.00 0.00 5.28
680 717 1.464219 GAAAATTGCCATGTTTGCCCG 59.536 47.619 0.00 0.00 0.00 6.13
681 718 2.226200 GTGAAAATTGCCATGTTTGCCC 59.774 45.455 0.00 0.00 0.00 5.36
682 719 2.877168 TGTGAAAATTGCCATGTTTGCC 59.123 40.909 0.00 0.00 0.00 4.52
683 720 4.548991 TTGTGAAAATTGCCATGTTTGC 57.451 36.364 0.00 0.00 0.00 3.68
684 721 7.988904 AATTTTGTGAAAATTGCCATGTTTG 57.011 28.000 6.29 0.00 46.30 2.93
695 732 9.323963 GTTTTGAACGTCAAATTTTGTGAAAAT 57.676 25.926 8.89 0.00 44.75 1.82
696 733 8.552034 AGTTTTGAACGTCAAATTTTGTGAAAA 58.448 25.926 8.89 1.05 44.75 2.29
697 734 8.077836 AGTTTTGAACGTCAAATTTTGTGAAA 57.922 26.923 8.89 0.00 44.75 2.69
698 735 7.644986 AGTTTTGAACGTCAAATTTTGTGAA 57.355 28.000 8.89 0.00 44.75 3.18
699 736 8.744008 TTAGTTTTGAACGTCAAATTTTGTGA 57.256 26.923 8.89 0.00 44.75 3.58
700 737 8.855279 TCTTAGTTTTGAACGTCAAATTTTGTG 58.145 29.630 8.89 5.95 44.75 3.33
701 738 8.856247 GTCTTAGTTTTGAACGTCAAATTTTGT 58.144 29.630 8.89 0.00 44.75 2.83
702 739 8.855279 TGTCTTAGTTTTGAACGTCAAATTTTG 58.145 29.630 11.98 2.59 44.75 2.44
703 740 8.973835 TGTCTTAGTTTTGAACGTCAAATTTT 57.026 26.923 11.98 5.94 44.75 1.82
704 741 8.973835 TTGTCTTAGTTTTGAACGTCAAATTT 57.026 26.923 11.98 7.66 44.75 1.82
708 745 9.493206 GTTTATTGTCTTAGTTTTGAACGTCAA 57.507 29.630 0.00 0.00 34.03 3.18
709 746 8.666573 TGTTTATTGTCTTAGTTTTGAACGTCA 58.333 29.630 0.00 0.00 36.23 4.35
710 747 9.493206 TTGTTTATTGTCTTAGTTTTGAACGTC 57.507 29.630 0.00 0.00 36.23 4.34
711 748 9.281075 GTTGTTTATTGTCTTAGTTTTGAACGT 57.719 29.630 0.00 0.00 36.23 3.99
712 749 9.279904 TGTTGTTTATTGTCTTAGTTTTGAACG 57.720 29.630 0.00 0.00 36.23 3.95
727 764 8.872845 ACTGCTCTTTTCTTTTGTTGTTTATTG 58.127 29.630 0.00 0.00 0.00 1.90
734 774 6.401367 CCAACAACTGCTCTTTTCTTTTGTTG 60.401 38.462 14.44 14.44 46.08 3.33
735 775 5.639082 CCAACAACTGCTCTTTTCTTTTGTT 59.361 36.000 0.00 0.00 36.41 2.83
737 777 5.410067 TCCAACAACTGCTCTTTTCTTTTG 58.590 37.500 0.00 0.00 0.00 2.44
740 780 6.959639 TTATCCAACAACTGCTCTTTTCTT 57.040 33.333 0.00 0.00 0.00 2.52
742 782 7.370383 TCAATTATCCAACAACTGCTCTTTTC 58.630 34.615 0.00 0.00 0.00 2.29
757 797 9.540538 TCATAAGTTCCCTTTTTCAATTATCCA 57.459 29.630 0.00 0.00 31.89 3.41
759 799 9.803315 GGTCATAAGTTCCCTTTTTCAATTATC 57.197 33.333 0.00 0.00 31.89 1.75
767 809 4.108501 ACGGGTCATAAGTTCCCTTTTT 57.891 40.909 0.00 0.00 39.10 1.94
778 820 4.172346 CGCGTCAACGGGTCATAA 57.828 55.556 11.00 0.00 45.50 1.90
795 837 3.378427 GTGCAAGGGATGTCTACCATTTC 59.622 47.826 0.00 0.00 32.56 2.17
1138 1186 4.298009 CTGGAGCAACAGGAGCAG 57.702 61.111 0.10 0.00 34.84 4.24
1174 1222 2.983592 AGGGGCGCCAAAACGAAG 60.984 61.111 30.85 0.00 34.06 3.79
1201 1254 0.178068 GACTGGAGCTCCGGCAAATA 59.822 55.000 36.86 13.70 46.43 1.40
1203 1256 2.347490 GACTGGAGCTCCGGCAAA 59.653 61.111 36.86 15.19 46.43 3.68
1213 1266 3.868757 TTACAGACAATCGGACTGGAG 57.131 47.619 0.00 0.00 36.17 3.86
1254 1307 1.270907 ACAGGAAGGCCTCAGTACAG 58.729 55.000 5.23 0.00 44.80 2.74
1255 1308 1.729586 AACAGGAAGGCCTCAGTACA 58.270 50.000 5.23 0.00 44.80 2.90
1256 1309 2.861147 AAACAGGAAGGCCTCAGTAC 57.139 50.000 5.23 0.00 44.80 2.73
1423 1477 1.841556 AGAACCCTCCGTCAGCCAA 60.842 57.895 0.00 0.00 0.00 4.52
1426 1484 0.250338 AAACAGAACCCTCCGTCAGC 60.250 55.000 0.00 0.00 0.00 4.26
1432 1490 0.955919 CTGGCGAAACAGAACCCTCC 60.956 60.000 0.00 0.00 40.97 4.30
1530 1588 6.038997 TGGAGCATGATGATGAGATAAGAG 57.961 41.667 0.00 0.00 0.00 2.85
1531 1589 6.429521 TTGGAGCATGATGATGAGATAAGA 57.570 37.500 0.00 0.00 0.00 2.10
1532 1590 6.711194 AGTTTGGAGCATGATGATGAGATAAG 59.289 38.462 0.00 0.00 0.00 1.73
1533 1591 6.598503 AGTTTGGAGCATGATGATGAGATAA 58.401 36.000 0.00 0.00 0.00 1.75
1535 1593 5.050126 AGTTTGGAGCATGATGATGAGAT 57.950 39.130 0.00 0.00 0.00 2.75
1536 1594 4.498894 AGTTTGGAGCATGATGATGAGA 57.501 40.909 0.00 0.00 0.00 3.27
1537 1595 5.277876 GCTAAGTTTGGAGCATGATGATGAG 60.278 44.000 0.00 0.00 38.62 2.90
1538 1596 4.577693 GCTAAGTTTGGAGCATGATGATGA 59.422 41.667 0.00 0.00 38.62 2.92
1539 1597 4.579340 AGCTAAGTTTGGAGCATGATGATG 59.421 41.667 0.00 0.00 41.36 3.07
1540 1598 4.789807 AGCTAAGTTTGGAGCATGATGAT 58.210 39.130 0.00 0.00 41.36 2.45
1571 1629 2.017049 ACACTTGAGAACAACAGCCAC 58.983 47.619 0.00 0.00 32.27 5.01
1850 1911 0.036952 AGCAGCATAACTCACAGCGT 60.037 50.000 0.00 0.00 0.00 5.07
1851 1912 1.061711 GAAGCAGCATAACTCACAGCG 59.938 52.381 0.00 0.00 0.00 5.18
1862 1926 8.970859 ATAGTAAAACTATTCAGAAGCAGCAT 57.029 30.769 0.00 0.00 38.17 3.79
1939 2003 4.565652 GGCCTGTTACAAAAGATGGAGAGA 60.566 45.833 0.00 0.00 0.00 3.10
1941 2005 3.073798 TGGCCTGTTACAAAAGATGGAGA 59.926 43.478 3.32 0.00 0.00 3.71
1947 2011 5.323371 GCATATTGGCCTGTTACAAAAGA 57.677 39.130 3.32 0.00 0.00 2.52
2001 2065 0.953727 TGAACCTGTGCAGTGCAATC 59.046 50.000 21.67 9.26 41.47 2.67
2039 2104 5.105228 ACATTGCCAAATCAGGGAACTATTG 60.105 40.000 0.00 0.00 42.01 1.90
2041 2106 4.613437 ACATTGCCAAATCAGGGAACTAT 58.387 39.130 0.00 0.00 42.01 2.12
2044 2109 2.562298 TGACATTGCCAAATCAGGGAAC 59.438 45.455 0.00 0.00 42.01 3.62
2070 2135 2.906354 AGTATTTCATGTCTGCGGGAC 58.094 47.619 0.00 0.00 44.70 4.46
2071 2136 3.627395 AAGTATTTCATGTCTGCGGGA 57.373 42.857 0.00 0.00 0.00 5.14
2072 2137 4.188462 TGTAAGTATTTCATGTCTGCGGG 58.812 43.478 0.00 0.00 0.00 6.13
2073 2138 5.991328 ATGTAAGTATTTCATGTCTGCGG 57.009 39.130 0.00 0.00 34.67 5.69
2074 2139 7.688372 AGAAATGTAAGTATTTCATGTCTGCG 58.312 34.615 12.19 0.00 45.23 5.18
2200 2265 8.783660 AGTAAAGACAATGAGTATAGGATGGA 57.216 34.615 0.00 0.00 0.00 3.41
2228 2293 6.072064 GGCGTAGATGCTAGGTAGATAAAAGA 60.072 42.308 0.00 0.00 34.52 2.52
2229 2295 6.071840 AGGCGTAGATGCTAGGTAGATAAAAG 60.072 42.308 0.00 0.00 34.52 2.27
2236 2302 5.646577 AATAAGGCGTAGATGCTAGGTAG 57.353 43.478 0.00 0.00 34.52 3.18
2237 2303 7.528996 TTTAATAAGGCGTAGATGCTAGGTA 57.471 36.000 0.00 0.00 34.52 3.08
2239 2305 7.907214 ATTTTAATAAGGCGTAGATGCTAGG 57.093 36.000 0.00 0.00 34.52 3.02
2269 2335 9.371136 GTATCATTCTTCAAATGTAGTCACAGA 57.629 33.333 0.00 0.00 38.30 3.41
2277 2343 9.098355 GCTGTACTGTATCATTCTTCAAATGTA 57.902 33.333 1.46 0.00 0.00 2.29
2279 2345 7.281774 AGGCTGTACTGTATCATTCTTCAAATG 59.718 37.037 1.46 0.00 0.00 2.32
2284 2350 5.293560 GGAGGCTGTACTGTATCATTCTTC 58.706 45.833 0.00 0.00 0.00 2.87
2307 2373 8.873830 ACAGTTAATTGATGAACATCTTACTCG 58.126 33.333 14.50 8.47 38.60 4.18
2337 2403 4.702612 TGCAAGTTTTCAACAGAACCTGTA 59.297 37.500 0.00 0.00 44.62 2.74
2438 2504 5.126384 ACAAAAGCAAGCAACCTAACAAGTA 59.874 36.000 0.00 0.00 0.00 2.24
2441 2507 4.464069 ACAAAAGCAAGCAACCTAACAA 57.536 36.364 0.00 0.00 0.00 2.83
2443 2509 4.927422 TGTACAAAAGCAAGCAACCTAAC 58.073 39.130 0.00 0.00 0.00 2.34
2445 2511 3.004315 GCTGTACAAAAGCAAGCAACCTA 59.996 43.478 0.00 0.00 40.52 3.08
2446 2512 2.223805 GCTGTACAAAAGCAAGCAACCT 60.224 45.455 0.00 0.00 40.52 3.50
2447 2513 2.127251 GCTGTACAAAAGCAAGCAACC 58.873 47.619 0.00 0.00 40.52 3.77
2449 2515 1.753649 TGGCTGTACAAAAGCAAGCAA 59.246 42.857 7.75 0.00 42.69 3.91
2451 2517 1.066908 TGTGGCTGTACAAAAGCAAGC 59.933 47.619 7.75 0.65 42.69 4.01
2452 2518 2.098934 TGTGTGGCTGTACAAAAGCAAG 59.901 45.455 7.75 0.00 42.69 4.01
2466 2537 5.182001 ACAAATTCTGAAGATACTGTGTGGC 59.818 40.000 0.00 0.00 0.00 5.01
2518 2594 4.885907 TCTGAATCTCCATCAATTTCCTGC 59.114 41.667 0.00 0.00 0.00 4.85
2542 2618 4.232221 CAGAATCATGGACACAAACAAGC 58.768 43.478 0.00 0.00 0.00 4.01
2593 2669 9.047371 GCTAGATCATAGAAGGTAACCTTTTTC 57.953 37.037 0.00 0.00 44.82 2.29
2616 2692 7.093333 ACACGATATGATGGATAATTCAGGCTA 60.093 37.037 0.00 0.00 0.00 3.93
2620 2696 8.654215 CAAGACACGATATGATGGATAATTCAG 58.346 37.037 0.00 0.00 0.00 3.02
2637 2713 5.838529 TCAAGAACATCTTACAAGACACGA 58.161 37.500 0.00 0.00 37.98 4.35
2642 2718 8.908786 AACAGATTCAAGAACATCTTACAAGA 57.091 30.769 0.00 0.00 33.78 3.02
2669 2745 8.865090 TGTGCAAGAATTCCCTTTATAGAAAAA 58.135 29.630 0.65 0.00 0.00 1.94
2674 2750 7.999679 TGATTGTGCAAGAATTCCCTTTATAG 58.000 34.615 0.65 0.00 25.38 1.31
2676 2752 6.855763 TGATTGTGCAAGAATTCCCTTTAT 57.144 33.333 0.65 0.00 25.38 1.40
2678 2754 5.246656 TGATGATTGTGCAAGAATTCCCTTT 59.753 36.000 0.65 0.00 25.38 3.11
2679 2755 4.773674 TGATGATTGTGCAAGAATTCCCTT 59.226 37.500 0.65 0.00 25.38 3.95
2680 2756 4.346730 TGATGATTGTGCAAGAATTCCCT 58.653 39.130 0.65 0.00 25.38 4.20
2681 2757 4.724074 TGATGATTGTGCAAGAATTCCC 57.276 40.909 0.65 0.00 25.38 3.97
2682 2758 5.717119 AGTTGATGATTGTGCAAGAATTCC 58.283 37.500 0.65 0.00 25.38 3.01
2696 2778 6.881602 GGGAGAGTTTTCTGTTAGTTGATGAT 59.118 38.462 0.00 0.00 32.53 2.45
2771 2855 9.174166 GGATTAAGTAAGTTCAAAGCCAGATAA 57.826 33.333 0.00 0.00 0.00 1.75
2782 2866 7.121168 CCAAAGCATCAGGATTAAGTAAGTTCA 59.879 37.037 0.00 0.00 0.00 3.18
2790 2946 7.917505 GTGAAATACCAAAGCATCAGGATTAAG 59.082 37.037 0.00 0.00 0.00 1.85
2800 2956 7.524717 AAGTTACTGTGAAATACCAAAGCAT 57.475 32.000 0.00 0.00 0.00 3.79
2839 2995 8.971073 AGCCTGCAAGATTTTACAAATATTACT 58.029 29.630 0.00 0.00 34.07 2.24
2864 3020 8.469200 TCAAAACCAATATTATTCCTTGAGCAG 58.531 33.333 0.00 0.00 0.00 4.24
2865 3021 8.359875 TCAAAACCAATATTATTCCTTGAGCA 57.640 30.769 0.00 0.00 0.00 4.26
2894 3050 5.359576 AGCATCTTCTAAGACCTAGTCAGTG 59.640 44.000 0.00 0.00 37.98 3.66
2948 3104 6.098409 CCTCCTTTATAGTAGCTTTGACAGGA 59.902 42.308 0.00 0.00 0.00 3.86
2975 3131 9.088512 GATGAATATCGGGATGTATAAACAGTC 57.911 37.037 0.00 0.00 39.49 3.51
3053 3211 9.248291 GAATTCCGTTGTCATTTATGCATTATT 57.752 29.630 3.54 0.00 0.00 1.40
3054 3212 8.632679 AGAATTCCGTTGTCATTTATGCATTAT 58.367 29.630 3.54 0.00 0.00 1.28
3055 3213 7.914871 CAGAATTCCGTTGTCATTTATGCATTA 59.085 33.333 3.54 0.00 0.00 1.90
3056 3214 6.753279 CAGAATTCCGTTGTCATTTATGCATT 59.247 34.615 3.54 0.00 0.00 3.56
3057 3215 6.267817 CAGAATTCCGTTGTCATTTATGCAT 58.732 36.000 3.79 3.79 0.00 3.96
3058 3216 5.392919 CCAGAATTCCGTTGTCATTTATGCA 60.393 40.000 0.65 0.00 0.00 3.96
3059 3217 5.036737 CCAGAATTCCGTTGTCATTTATGC 58.963 41.667 0.65 0.00 0.00 3.14
3060 3218 5.036737 GCCAGAATTCCGTTGTCATTTATG 58.963 41.667 0.65 0.00 0.00 1.90
3061 3219 4.949856 AGCCAGAATTCCGTTGTCATTTAT 59.050 37.500 0.65 0.00 0.00 1.40
3062 3220 4.155826 CAGCCAGAATTCCGTTGTCATTTA 59.844 41.667 0.65 0.00 0.00 1.40
3063 3221 3.057315 CAGCCAGAATTCCGTTGTCATTT 60.057 43.478 0.65 0.00 0.00 2.32
3064 3222 2.489329 CAGCCAGAATTCCGTTGTCATT 59.511 45.455 0.65 0.00 0.00 2.57
3065 3223 2.086869 CAGCCAGAATTCCGTTGTCAT 58.913 47.619 0.65 0.00 0.00 3.06
3066 3224 1.202758 ACAGCCAGAATTCCGTTGTCA 60.203 47.619 0.65 0.00 0.00 3.58
3067 3225 1.197721 CACAGCCAGAATTCCGTTGTC 59.802 52.381 0.65 0.00 0.00 3.18
3068 3226 1.238439 CACAGCCAGAATTCCGTTGT 58.762 50.000 0.65 4.41 0.00 3.32
3069 3227 0.109597 GCACAGCCAGAATTCCGTTG 60.110 55.000 0.65 3.77 0.00 4.10
3070 3228 0.537143 TGCACAGCCAGAATTCCGTT 60.537 50.000 0.65 0.00 0.00 4.44
3073 3231 0.244721 GGTTGCACAGCCAGAATTCC 59.755 55.000 0.65 0.00 0.00 3.01
3075 3233 1.636148 ATGGTTGCACAGCCAGAATT 58.364 45.000 11.94 0.00 44.90 2.17
3081 3259 1.678101 GAGGATTATGGTTGCACAGCC 59.322 52.381 0.00 0.00 0.00 4.85
3132 3310 6.028040 TCAAGAGTTTTTACGACAAACGAG 57.972 37.500 0.00 0.00 45.77 4.18
3135 3313 8.080083 TCCTATCAAGAGTTTTTACGACAAAC 57.920 34.615 0.00 0.00 34.80 2.93
3138 3316 8.553696 GTTTTCCTATCAAGAGTTTTTACGACA 58.446 33.333 0.00 0.00 0.00 4.35
3174 3352 3.508845 ACTACCTGTGGAGTTTGCATT 57.491 42.857 0.00 0.00 0.00 3.56
3193 3371 6.743575 ATGTTCTTGTTACAGAGGCAATAC 57.256 37.500 0.00 0.00 0.00 1.89
3195 3373 6.265196 TGAAATGTTCTTGTTACAGAGGCAAT 59.735 34.615 0.00 0.00 0.00 3.56
3196 3374 5.592282 TGAAATGTTCTTGTTACAGAGGCAA 59.408 36.000 0.00 0.00 0.00 4.52
3198 3376 5.689383 TGAAATGTTCTTGTTACAGAGGC 57.311 39.130 0.00 0.00 0.00 4.70
3199 3377 7.439157 TCATGAAATGTTCTTGTTACAGAGG 57.561 36.000 0.00 0.00 46.80 3.69
3200 3378 9.903682 AAATCATGAAATGTTCTTGTTACAGAG 57.096 29.630 0.00 0.00 46.80 3.35
3201 3379 9.681692 CAAATCATGAAATGTTCTTGTTACAGA 57.318 29.630 0.00 0.00 46.80 3.41
3204 3386 9.248291 ACACAAATCATGAAATGTTCTTGTTAC 57.752 29.630 12.58 0.00 46.80 2.50
3208 3390 8.277713 GGAAACACAAATCATGAAATGTTCTTG 58.722 33.333 12.58 6.12 46.80 3.02
3271 3461 8.319057 TCACCTACAATCAGTATACATTTCCT 57.681 34.615 5.50 0.00 30.93 3.36
3278 3468 7.441458 GGGTTTCATCACCTACAATCAGTATAC 59.559 40.741 0.00 0.00 36.97 1.47
3282 3472 4.042809 TGGGTTTCATCACCTACAATCAGT 59.957 41.667 0.00 0.00 36.97 3.41
3304 3494 3.674138 CGAAACCATCCCTGAGCAAATTG 60.674 47.826 0.00 0.00 0.00 2.32
3315 3505 1.534729 AACAAGCTCGAAACCATCCC 58.465 50.000 0.00 0.00 0.00 3.85
3316 3506 4.473199 GTTTAACAAGCTCGAAACCATCC 58.527 43.478 0.00 0.00 0.00 3.51
3346 3536 4.022849 TCAGTGGACTATATGCTGTGATCG 60.023 45.833 0.00 0.00 0.00 3.69
3348 3538 6.494835 TGTATCAGTGGACTATATGCTGTGAT 59.505 38.462 0.00 0.00 0.00 3.06
3349 3539 5.833131 TGTATCAGTGGACTATATGCTGTGA 59.167 40.000 0.00 0.00 0.00 3.58
3350 3540 5.923114 GTGTATCAGTGGACTATATGCTGTG 59.077 44.000 0.00 0.00 0.00 3.66
3351 3541 5.835819 AGTGTATCAGTGGACTATATGCTGT 59.164 40.000 0.00 0.00 0.00 4.40
3352 3542 6.338214 AGTGTATCAGTGGACTATATGCTG 57.662 41.667 0.00 0.00 0.00 4.41
3354 3544 9.360093 GAATTAGTGTATCAGTGGACTATATGC 57.640 37.037 0.00 0.00 0.00 3.14
3361 3554 5.353394 TGGGAATTAGTGTATCAGTGGAC 57.647 43.478 0.00 0.00 0.00 4.02
3372 3582 4.133078 GCAAGGAGAGATGGGAATTAGTG 58.867 47.826 0.00 0.00 0.00 2.74
3385 3595 4.493547 CAGAGTTTAGTCAGCAAGGAGAG 58.506 47.826 0.00 0.00 0.00 3.20
3389 3605 2.481952 GTGCAGAGTTTAGTCAGCAAGG 59.518 50.000 6.27 0.00 40.25 3.61
3422 3638 0.898320 ATCGTCAGTGACCTCAAGGG 59.102 55.000 17.57 1.85 40.27 3.95
3483 3699 4.693283 TGATGTTTGTATAAGAGCCCTCG 58.307 43.478 0.00 0.00 34.09 4.63
3526 3742 4.240175 ACGGTTCAGAACAGACTAGTTC 57.760 45.455 19.03 8.76 46.35 3.01
3534 3845 5.728351 TCAAACTTAACGGTTCAGAACAG 57.272 39.130 15.36 13.38 0.00 3.16
3536 3847 8.950961 GTTTATTCAAACTTAACGGTTCAGAAC 58.049 33.333 8.94 4.52 40.78 3.01
3559 3870 8.695456 ACAAGTTCACATTTTAAGGATCAGTTT 58.305 29.630 0.00 0.00 0.00 2.66
3566 3877 6.214191 TGCAACAAGTTCACATTTTAAGGA 57.786 33.333 0.00 0.00 0.00 3.36
3570 3881 5.126222 TCACCTGCAACAAGTTCACATTTTA 59.874 36.000 0.00 0.00 0.00 1.52
3615 3926 3.648179 GTTCATCAAACGCTCAGCTAG 57.352 47.619 0.00 0.00 0.00 3.42
3702 4013 4.079558 ACTGTGGAAAGGCAATGGATATCT 60.080 41.667 2.05 0.00 0.00 1.98
3705 4016 3.737559 ACTGTGGAAAGGCAATGGATA 57.262 42.857 0.00 0.00 0.00 2.59
3770 4161 5.182190 ACATACAGGCTATCTATCTCGTGTG 59.818 44.000 0.00 0.00 0.00 3.82
3785 4176 2.364632 TGGCACATGTTACATACAGGC 58.635 47.619 0.00 4.21 42.15 4.85
3870 4268 7.971168 CCAAACTACTTTTCACATTTGTGTGTA 59.029 33.333 10.30 8.65 45.76 2.90
3912 4310 9.651718 CAAATTGGATCTACTTTTAAGCGATAC 57.348 33.333 0.00 0.00 0.00 2.24
3996 4403 2.095919 GTCGCACACCATTGTAACCTTC 60.096 50.000 0.00 0.00 33.30 3.46
4049 4463 2.101582 CACAGGGTCTGTCCTATACTGC 59.898 54.545 0.00 0.00 43.43 4.40
4050 4464 3.366396 ACACAGGGTCTGTCCTATACTG 58.634 50.000 0.00 0.00 43.43 2.74
4051 4465 3.759815 ACACAGGGTCTGTCCTATACT 57.240 47.619 0.00 0.00 43.43 2.12
4052 4466 4.894114 ACATACACAGGGTCTGTCCTATAC 59.106 45.833 0.00 0.00 43.43 1.47
4053 4467 5.138758 ACATACACAGGGTCTGTCCTATA 57.861 43.478 0.00 0.00 43.43 1.31
4054 4468 3.995636 ACATACACAGGGTCTGTCCTAT 58.004 45.455 0.00 0.00 43.43 2.57
4055 4469 3.468071 ACATACACAGGGTCTGTCCTA 57.532 47.619 0.00 0.00 43.43 2.94
4056 4470 2.327325 ACATACACAGGGTCTGTCCT 57.673 50.000 0.00 0.00 43.43 3.85
4057 4471 3.418684 AAACATACACAGGGTCTGTCC 57.581 47.619 0.00 0.00 43.43 4.02
4092 4506 1.959282 GAGCTTATGCCCAATTCCCTG 59.041 52.381 0.00 0.00 40.80 4.45
4094 4508 1.332195 GGAGCTTATGCCCAATTCCC 58.668 55.000 0.00 0.00 40.80 3.97
4135 4549 1.251251 GCCAAGGTGTCTGATTGCTT 58.749 50.000 0.00 0.00 0.00 3.91
4142 4556 1.149174 ACAGGTGCCAAGGTGTCTG 59.851 57.895 0.00 0.00 0.00 3.51
4169 4583 6.321181 GCCCCTTTACAATGTTATCATCTTCA 59.679 38.462 0.00 0.00 32.56 3.02
4321 4739 2.719705 TCCCCATCACACCCTAAGTTTT 59.280 45.455 0.00 0.00 0.00 2.43
4331 4749 4.261741 GCATTGTCATATTCCCCATCACAC 60.262 45.833 0.00 0.00 0.00 3.82
4430 4850 3.538634 GGTACCCAAGCTTAGGTGTAG 57.461 52.381 24.74 7.00 36.88 2.74
4451 4924 2.026822 AGTTATGTCACCCAGCTTCCAG 60.027 50.000 0.00 0.00 0.00 3.86
4457 4930 5.007724 GCAATAACTAGTTATGTCACCCAGC 59.992 44.000 25.21 15.57 36.04 4.85
4511 4984 3.534554 AGAACAATACAGATCGCATGCA 58.465 40.909 19.57 5.34 0.00 3.96
4538 5011 5.220416 GCTGGTTATACATGTCTGTTCGTTC 60.220 44.000 0.00 0.00 36.79 3.95
4555 5028 3.411446 CAAATCAGTGTCCAGCTGGTTA 58.589 45.455 31.58 18.92 36.39 2.85
4579 5052 3.118592 CGAGCCTCCAAGGTATTCTTTCT 60.119 47.826 0.00 0.00 37.80 2.52
4580 5053 3.198872 CGAGCCTCCAAGGTATTCTTTC 58.801 50.000 0.00 0.00 37.80 2.62
4581 5054 2.572104 ACGAGCCTCCAAGGTATTCTTT 59.428 45.455 0.00 0.00 37.80 2.52
4582 5055 2.188817 ACGAGCCTCCAAGGTATTCTT 58.811 47.619 0.00 0.00 37.80 2.52
4583 5056 1.867363 ACGAGCCTCCAAGGTATTCT 58.133 50.000 0.00 0.00 37.80 2.40
4602 5075 0.744414 GAGCGGCTGCCAATGAACTA 60.744 55.000 20.29 0.00 44.31 2.24


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

AutoCloner maintained by Alex Coulton.