Multiple sequence alignment - TraesCS7A01G495800

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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 TraesCS7A01G495800 chr7A 100.000 4655 0 0 1 4655 686023144 686018490 0.000000e+00 8597.0
1 TraesCS7A01G495800 chr7D 91.266 4717 263 63 11 4655 593240226 593235587 0.000000e+00 6290.0
2 TraesCS7A01G495800 chr7D 80.412 485 43 19 3879 4317 597515266 597515744 5.810000e-84 322.0
3 TraesCS7A01G495800 chr7D 80.000 485 45 17 3879 4317 27354046 27354524 1.260000e-80 311.0
4 TraesCS7A01G495800 chr7D 86.054 294 27 8 3879 4163 39862787 39862499 2.100000e-78 303.0
5 TraesCS7A01G495800 chr7D 79.630 486 46 18 3879 4317 228136915 228137394 2.720000e-77 300.0
6 TraesCS7A01G495800 chr7D 86.127 173 7 9 4495 4655 27354601 27354768 2.230000e-38 171.0
7 TraesCS7A01G495800 chr7D 85.465 172 8 9 4496 4655 228137470 228137636 3.730000e-36 163.0
8 TraesCS7A01G495800 chr7B 87.868 4212 282 110 11 4099 667745911 667750016 0.000000e+00 4735.0
9 TraesCS7A01G495800 chr7B 84.830 323 34 8 4104 4411 667750338 667750660 1.260000e-80 311.0
10 TraesCS7A01G495800 chr7B 91.667 168 8 3 4494 4655 667752670 667752837 1.300000e-55 228.0
11 TraesCS7A01G495800 chr7B 93.571 140 5 4 4337 4472 667752547 667752686 6.110000e-49 206.0
12 TraesCS7A01G495800 chr6A 84.694 294 30 9 3879 4163 325084231 325084518 3.550000e-71 279.0
13 TraesCS7A01G495800 chr6A 82.184 174 13 10 4495 4655 325084756 325084924 2.920000e-27 134.0
14 TraesCS7A01G495800 chr1A 86.585 164 14 6 3879 4034 55285190 55285027 1.720000e-39 174.0
15 TraesCS7A01G495800 chr1A 84.971 173 9 9 4495 4655 55284925 55284758 4.820000e-35 159.0
16 TraesCS7A01G495800 chr4B 86.127 173 7 9 4495 4655 20347930 20348097 2.230000e-38 171.0
17 TraesCS7A01G495800 chr4B 88.991 109 12 0 3034 3142 578227123 578227231 8.120000e-28 135.0
18 TraesCS7A01G495800 chr4A 84.971 173 6 10 4495 4655 592505381 592505217 1.730000e-34 158.0
19 TraesCS7A01G495800 chr4A 84.971 173 6 10 4495 4655 593071761 593071597 1.730000e-34 158.0
20 TraesCS7A01G495800 chr4A 84.393 173 7 10 4495 4655 592784202 592784038 8.070000e-33 152.0
21 TraesCS7A01G495800 chr4A 88.991 109 12 0 3034 3142 6635059 6634951 8.120000e-28 135.0
22 TraesCS7A01G495800 chr4A 86.885 61 7 1 2310 2370 6635983 6635924 3.010000e-07 67.6
23 TraesCS7A01G495800 chr4D 88.991 109 12 0 3034 3142 462744650 462744542 8.120000e-28 135.0
24 TraesCS7A01G495800 chr4D 86.885 61 7 1 2310 2370 462745671 462745612 3.010000e-07 67.6
25 TraesCS7A01G495800 chr5A 81.250 160 24 3 41 195 624754032 624753874 1.760000e-24 124.0
26 TraesCS7A01G495800 chr1D 84.821 112 13 4 32 141 17232246 17232137 4.920000e-20 110.0
27 TraesCS7A01G495800 chr3D 84.694 98 15 0 39 136 92375534 92375437 1.070000e-16 99.0
28 TraesCS7A01G495800 chr3D 100.000 28 0 0 1786 1813 442971817 442971844 8.000000e-03 52.8
29 TraesCS7A01G495800 chr3B 100.000 30 0 0 1784 1813 580782988 580783017 6.510000e-04 56.5


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 TraesCS7A01G495800 chr7A 686018490 686023144 4654 True 8597.0 8597 100.0000 1 4655 1 chr7A.!!$R1 4654
1 TraesCS7A01G495800 chr7D 593235587 593240226 4639 True 6290.0 6290 91.2660 11 4655 1 chr7D.!!$R2 4644
2 TraesCS7A01G495800 chr7D 27354046 27354768 722 False 241.0 311 83.0635 3879 4655 2 chr7D.!!$F2 776
3 TraesCS7A01G495800 chr7D 228136915 228137636 721 False 231.5 300 82.5475 3879 4655 2 chr7D.!!$F3 776
4 TraesCS7A01G495800 chr7B 667745911 667752837 6926 False 1370.0 4735 89.4840 11 4655 4 chr7B.!!$F1 4644
5 TraesCS7A01G495800 chr6A 325084231 325084924 693 False 206.5 279 83.4390 3879 4655 2 chr6A.!!$F1 776

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
765 782 0.179150 CGTGTGCAGGCTCTCTACTC 60.179 60.0 0.00 0.00 0.00 2.59 F
1669 1724 0.107066 ATTGCATGCACCGGATCAGA 60.107 50.0 22.58 1.96 0.00 3.27 F
2227 2299 0.249911 GGTGAGTGACCGACTTTGCT 60.250 55.0 0.00 0.00 33.83 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1815 0.106708 ACCGGTGCCTGCATACATAG 59.893 55.0 6.12 0.00 0.00 2.23 R
3123 3245 0.316032 GGATGCTCTCGACGTCGTAC 60.316 60.0 34.40 22.32 40.80 3.67 R
3838 3990 0.255033 TCTCCGCTACAGCCTACAGA 59.745 55.0 0.00 0.00 37.91 3.41 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
48 49 4.386424 GGGGCCTTTTAACAGACTGGATAT 60.386 45.833 7.51 0.00 0.00 1.63
62 63 1.301423 GGATATTTGCCCGTGCGTTA 58.699 50.000 0.00 0.00 41.78 3.18
108 113 6.299141 AGTATGTTAGCCCATGATTACCTTG 58.701 40.000 0.00 0.00 0.00 3.61
156 162 7.254227 AGTTGTTTAAAGTTATGCTCGTGAA 57.746 32.000 0.00 0.00 0.00 3.18
158 164 8.015658 AGTTGTTTAAAGTTATGCTCGTGAATC 58.984 33.333 0.00 0.00 0.00 2.52
162 168 5.395325 AAAGTTATGCTCGTGAATCATCG 57.605 39.130 0.00 0.00 0.00 3.84
176 182 7.923878 TCGTGAATCATCGACCTAAATGAATTA 59.076 33.333 4.36 0.00 35.64 1.40
262 269 2.056577 GTGAACGACAGAACCTTACGG 58.943 52.381 0.00 0.00 0.00 4.02
321 328 5.048224 TCAGTCTTGTACACTAGCAGTAACC 60.048 44.000 0.00 0.00 0.00 2.85
335 346 3.411446 CAGTAACCAAGCAATGAGACCA 58.589 45.455 0.00 0.00 0.00 4.02
337 348 4.460382 CAGTAACCAAGCAATGAGACCATT 59.540 41.667 0.00 0.00 43.37 3.16
339 350 6.150976 CAGTAACCAAGCAATGAGACCATTTA 59.849 38.462 0.00 0.00 40.81 1.40
341 352 5.841957 ACCAAGCAATGAGACCATTTATC 57.158 39.130 0.00 0.00 40.81 1.75
348 359 6.604396 AGCAATGAGACCATTTATCACATCAA 59.396 34.615 0.00 0.00 40.81 2.57
384 395 1.817099 GTGAGAAGCGCCATGGAGG 60.817 63.158 18.40 7.48 41.84 4.30
395 406 1.680249 GCCATGGAGGAGGAGTGAAAC 60.680 57.143 18.40 0.00 41.22 2.78
498 510 1.344438 GCAAACAAAAAGGGAGAGGGG 59.656 52.381 0.00 0.00 0.00 4.79
510 522 2.557676 GGGAGAGGGGGAAAAGAAAAGG 60.558 54.545 0.00 0.00 0.00 3.11
511 523 2.171840 GAGAGGGGGAAAAGAAAAGGC 58.828 52.381 0.00 0.00 0.00 4.35
512 524 0.888619 GAGGGGGAAAAGAAAAGGCG 59.111 55.000 0.00 0.00 0.00 5.52
513 525 1.185618 AGGGGGAAAAGAAAAGGCGC 61.186 55.000 0.00 0.00 0.00 6.53
514 526 1.080772 GGGGAAAAGAAAAGGCGCG 60.081 57.895 0.00 0.00 0.00 6.86
665 680 2.038813 CCCGGCCCCTTTGGATTT 59.961 61.111 0.00 0.00 35.39 2.17
703 718 4.515567 GCTACCATGCATTAAACTACTCCC 59.484 45.833 0.00 0.00 0.00 4.30
714 729 4.302559 AAACTACTCCCCAAATCACTCC 57.697 45.455 0.00 0.00 0.00 3.85
715 730 2.197465 ACTACTCCCCAAATCACTCCC 58.803 52.381 0.00 0.00 0.00 4.30
716 731 2.225908 ACTACTCCCCAAATCACTCCCT 60.226 50.000 0.00 0.00 0.00 4.20
717 732 1.290134 ACTCCCCAAATCACTCCCTC 58.710 55.000 0.00 0.00 0.00 4.30
718 733 1.203492 ACTCCCCAAATCACTCCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
719 734 1.488393 CTCCCCAAATCACTCCCTCTC 59.512 57.143 0.00 0.00 0.00 3.20
754 771 4.641645 TCCTTGGCCCGTGTGCAG 62.642 66.667 0.00 0.00 0.00 4.41
763 780 1.153745 CCGTGTGCAGGCTCTCTAC 60.154 63.158 0.00 0.00 0.00 2.59
764 781 1.599606 CCGTGTGCAGGCTCTCTACT 61.600 60.000 0.00 0.00 0.00 2.57
765 782 0.179150 CGTGTGCAGGCTCTCTACTC 60.179 60.000 0.00 0.00 0.00 2.59
766 783 1.181786 GTGTGCAGGCTCTCTACTCT 58.818 55.000 0.00 0.00 0.00 3.24
767 784 1.135141 GTGTGCAGGCTCTCTACTCTG 60.135 57.143 0.00 0.00 0.00 3.35
857 874 3.181493 ACAGTTCAAACAAGCAAGCTCAG 60.181 43.478 0.00 0.00 0.00 3.35
859 876 1.321474 TCAAACAAGCAAGCTCAGGG 58.679 50.000 0.00 0.00 0.00 4.45
919 948 3.107402 TGACTATTCCCTGCAGAGAGT 57.893 47.619 17.39 8.20 0.00 3.24
920 949 3.027412 TGACTATTCCCTGCAGAGAGTC 58.973 50.000 17.39 17.37 33.96 3.36
921 950 3.027412 GACTATTCCCTGCAGAGAGTCA 58.973 50.000 17.39 0.00 33.74 3.41
922 951 3.030291 ACTATTCCCTGCAGAGAGTCAG 58.970 50.000 17.39 8.18 0.00 3.51
990 1019 1.084370 ACTTCTATCAAGGCACGCGC 61.084 55.000 5.73 0.00 37.44 6.86
991 1020 2.082437 CTTCTATCAAGGCACGCGCG 62.082 60.000 30.96 30.96 39.92 6.86
992 1021 4.285149 CTATCAAGGCACGCGCGC 62.285 66.667 32.58 23.91 39.92 6.86
1134 1163 1.067582 CCAGATCGCCGGTAAGGAC 59.932 63.158 1.90 0.00 45.00 3.85
1148 1177 1.838073 AAGGACGCCAACACCCCTAG 61.838 60.000 0.00 0.00 0.00 3.02
1149 1178 2.436115 GACGCCAACACCCCTAGC 60.436 66.667 0.00 0.00 0.00 3.42
1151 1180 1.610554 GACGCCAACACCCCTAGCTA 61.611 60.000 0.00 0.00 0.00 3.32
1154 1183 0.108774 GCCAACACCCCTAGCTATCC 59.891 60.000 0.00 0.00 0.00 2.59
1199 1230 1.537638 CGAGCTAGCTACACATCCGAT 59.462 52.381 19.38 0.00 0.00 4.18
1200 1231 2.742589 CGAGCTAGCTACACATCCGATA 59.257 50.000 19.38 0.00 0.00 2.92
1202 1233 4.667262 GAGCTAGCTACACATCCGATATG 58.333 47.826 19.38 0.00 0.00 1.78
1203 1234 3.445450 AGCTAGCTACACATCCGATATGG 59.555 47.826 17.69 0.00 40.09 2.74
1213 1251 1.040646 TCCGATATGGACTGTGGCTC 58.959 55.000 0.00 0.00 43.74 4.70
1237 1279 2.796593 GGTGCATGTTTTCTTGTGCTTC 59.203 45.455 0.00 0.00 38.37 3.86
1240 1282 2.473984 GCATGTTTTCTTGTGCTTCTGC 59.526 45.455 0.00 0.00 40.20 4.26
1252 1294 2.285668 TTCTGCAGGGGAGGAGGG 60.286 66.667 15.13 0.00 0.00 4.30
1254 1296 4.421554 CTGCAGGGGAGGAGGGGA 62.422 72.222 5.57 0.00 0.00 4.81
1300 1342 2.742372 CTTCCTTGGCGGTGTCGG 60.742 66.667 0.00 0.00 36.79 4.79
1529 1580 2.682494 GGCGTCACCAGGTAGGGA 60.682 66.667 0.00 0.00 43.89 4.20
1530 1581 2.064581 GGCGTCACCAGGTAGGGAT 61.065 63.158 0.00 0.00 43.89 3.85
1560 1611 3.219281 TGCTAATCACATGCATGCATCT 58.781 40.909 30.07 16.91 33.90 2.90
1586 1637 3.838317 TCTTCCCATCGAGAGGAAAGAAA 59.162 43.478 17.08 4.20 41.54 2.52
1591 1642 4.702131 CCCATCGAGAGGAAAGAAAAACAT 59.298 41.667 8.19 0.00 0.00 2.71
1592 1643 5.880332 CCCATCGAGAGGAAAGAAAAACATA 59.120 40.000 8.19 0.00 0.00 2.29
1593 1644 6.183360 CCCATCGAGAGGAAAGAAAAACATAC 60.183 42.308 8.19 0.00 0.00 2.39
1606 1657 8.919777 AAGAAAAACATACCACTAGCTAGTTT 57.080 30.769 23.94 15.68 33.46 2.66
1629 1680 8.669243 GTTTGGTAGGATGATTCTTACTTCTTG 58.331 37.037 0.00 0.00 35.39 3.02
1665 1720 2.156917 CATCTATTGCATGCACCGGAT 58.843 47.619 22.58 19.25 0.00 4.18
1666 1721 1.882912 TCTATTGCATGCACCGGATC 58.117 50.000 22.58 0.00 0.00 3.36
1667 1722 1.140652 TCTATTGCATGCACCGGATCA 59.859 47.619 22.58 3.73 0.00 2.92
1668 1723 1.534163 CTATTGCATGCACCGGATCAG 59.466 52.381 22.58 5.95 0.00 2.90
1669 1724 0.107066 ATTGCATGCACCGGATCAGA 60.107 50.000 22.58 1.96 0.00 3.27
1737 1792 0.385974 GCATCTCGTGGTGTTTGTGC 60.386 55.000 0.00 0.00 0.00 4.57
1745 1800 4.065789 TCGTGGTGTTTGTGCATGTAATA 58.934 39.130 0.00 0.00 0.00 0.98
1746 1801 4.515567 TCGTGGTGTTTGTGCATGTAATAA 59.484 37.500 0.00 0.00 0.00 1.40
1747 1802 5.182190 TCGTGGTGTTTGTGCATGTAATAAT 59.818 36.000 0.00 0.00 0.00 1.28
1748 1803 5.285845 CGTGGTGTTTGTGCATGTAATAATG 59.714 40.000 0.00 0.00 0.00 1.90
1749 1804 6.155827 GTGGTGTTTGTGCATGTAATAATGT 58.844 36.000 0.00 0.00 0.00 2.71
1753 1808 8.187480 GGTGTTTGTGCATGTAATAATGTATGA 58.813 33.333 0.00 0.00 0.00 2.15
1754 1809 9.734620 GTGTTTGTGCATGTAATAATGTATGAT 57.265 29.630 0.00 0.00 0.00 2.45
1758 1813 9.747293 TTGTGCATGTAATAATGTATGATTTGG 57.253 29.630 0.00 0.00 0.00 3.28
1759 1814 7.866898 TGTGCATGTAATAATGTATGATTTGGC 59.133 33.333 0.00 0.00 0.00 4.52
1760 1815 7.329226 GTGCATGTAATAATGTATGATTTGGCC 59.671 37.037 0.00 0.00 0.00 5.36
1761 1816 7.233144 TGCATGTAATAATGTATGATTTGGCCT 59.767 33.333 3.32 0.00 0.00 5.19
1762 1817 8.739039 GCATGTAATAATGTATGATTTGGCCTA 58.261 33.333 3.32 0.00 0.00 3.93
1899 1956 6.798482 TGCTCAATAATCCTGCAAATACAAG 58.202 36.000 0.00 0.00 0.00 3.16
1901 1958 7.122501 TGCTCAATAATCCTGCAAATACAAGAA 59.877 33.333 0.00 0.00 0.00 2.52
1930 1992 7.801547 AAATTCTGATCGCTAACATGTTTTG 57.198 32.000 17.78 11.26 0.00 2.44
1931 1993 4.340894 TCTGATCGCTAACATGTTTTGC 57.659 40.909 17.78 19.04 0.00 3.68
1932 1994 4.002982 TCTGATCGCTAACATGTTTTGCT 58.997 39.130 17.78 7.01 0.00 3.91
1933 1995 4.082274 TGATCGCTAACATGTTTTGCTG 57.918 40.909 17.78 15.85 0.00 4.41
1934 1996 2.330231 TCGCTAACATGTTTTGCTGC 57.670 45.000 17.78 12.11 0.00 5.25
1935 1997 1.068610 TCGCTAACATGTTTTGCTGCC 60.069 47.619 17.78 0.00 0.00 4.85
1936 1998 1.068333 CGCTAACATGTTTTGCTGCCT 60.068 47.619 17.78 0.00 0.00 4.75
1937 1999 2.607771 CGCTAACATGTTTTGCTGCCTT 60.608 45.455 17.78 0.00 0.00 4.35
1942 2007 2.435437 ACATGTTTTGCTGCCTTTTCCT 59.565 40.909 0.00 0.00 0.00 3.36
1950 2015 2.297033 TGCTGCCTTTTCCTCACAAATC 59.703 45.455 0.00 0.00 0.00 2.17
1954 2019 3.822735 TGCCTTTTCCTCACAAATCTCTG 59.177 43.478 0.00 0.00 0.00 3.35
1958 2023 5.048434 CCTTTTCCTCACAAATCTCTGAACC 60.048 44.000 0.00 0.00 0.00 3.62
1961 2026 2.746362 CCTCACAAATCTCTGAACCTGC 59.254 50.000 0.00 0.00 0.00 4.85
1962 2027 2.746362 CTCACAAATCTCTGAACCTGCC 59.254 50.000 0.00 0.00 0.00 4.85
1964 2029 1.347707 ACAAATCTCTGAACCTGCCGA 59.652 47.619 0.00 0.00 0.00 5.54
1979 2044 2.585330 TGCCGATGCATTGGTGATAAT 58.415 42.857 29.87 0.00 44.23 1.28
1980 2045 2.293955 TGCCGATGCATTGGTGATAATG 59.706 45.455 29.87 6.52 44.23 1.90
2023 2093 5.327616 TGTTAATTGCATTCCACATCCAG 57.672 39.130 0.00 0.00 0.00 3.86
2024 2094 2.973694 AATTGCATTCCACATCCAGC 57.026 45.000 0.00 0.00 0.00 4.85
2025 2095 2.154567 ATTGCATTCCACATCCAGCT 57.845 45.000 0.00 0.00 0.00 4.24
2027 2097 2.804986 TGCATTCCACATCCAGCTAA 57.195 45.000 0.00 0.00 0.00 3.09
2032 2102 5.834742 TGCATTCCACATCCAGCTAATTTAT 59.165 36.000 0.00 0.00 0.00 1.40
2033 2103 6.016024 TGCATTCCACATCCAGCTAATTTATC 60.016 38.462 0.00 0.00 0.00 1.75
2039 2109 7.237471 TCCACATCCAGCTAATTTATCCATCTA 59.763 37.037 0.00 0.00 0.00 1.98
2040 2110 8.051535 CCACATCCAGCTAATTTATCCATCTAT 58.948 37.037 0.00 0.00 0.00 1.98
2041 2111 9.107177 CACATCCAGCTAATTTATCCATCTATC 57.893 37.037 0.00 0.00 0.00 2.08
2043 2113 9.902684 CATCCAGCTAATTTATCCATCTATCTT 57.097 33.333 0.00 0.00 0.00 2.40
2051 2121 8.945195 AATTTATCCATCTATCTTCATTGCCA 57.055 30.769 0.00 0.00 0.00 4.92
2052 2122 9.543231 AATTTATCCATCTATCTTCATTGCCAT 57.457 29.630 0.00 0.00 0.00 4.40
2053 2123 7.933215 TTATCCATCTATCTTCATTGCCATG 57.067 36.000 0.00 0.00 0.00 3.66
2054 2124 5.314718 TCCATCTATCTTCATTGCCATGT 57.685 39.130 0.00 0.00 0.00 3.21
2056 2126 4.217767 CCATCTATCTTCATTGCCATGTGG 59.782 45.833 0.00 0.00 38.53 4.17
2059 2129 1.838112 TCTTCATTGCCATGTGGTCC 58.162 50.000 0.35 0.00 37.57 4.46
2060 2130 1.075212 TCTTCATTGCCATGTGGTCCA 59.925 47.619 0.35 0.00 37.57 4.02
2061 2131 2.104967 CTTCATTGCCATGTGGTCCAT 58.895 47.619 0.00 0.00 37.57 3.41
2075 2145 4.704540 TGTGGTCCATGTATGATTTGGAAC 59.295 41.667 0.00 0.00 45.63 3.62
2098 2168 5.010012 ACAAGAAATGTTTGAGGGCTTACAG 59.990 40.000 0.00 0.00 40.06 2.74
2133 2205 3.370840 AATGCAGGAGGCTATGACAAA 57.629 42.857 3.50 0.00 45.15 2.83
2142 2214 4.080863 GGAGGCTATGACAAAGAGGAGAAA 60.081 45.833 0.00 0.00 0.00 2.52
2145 2217 3.625313 GCTATGACAAAGAGGAGAAAGCC 59.375 47.826 0.00 0.00 0.00 4.35
2169 2241 3.264897 GCCTACGACATGGCTGCG 61.265 66.667 0.00 0.00 45.26 5.18
2172 2244 2.202743 TACGACATGGCTGCGCTC 60.203 61.111 9.73 0.00 0.00 5.03
2187 2259 2.602676 GCTCAAGTACTGGGGCCCA 61.603 63.158 26.87 26.87 0.00 5.36
2226 2298 2.235546 GGTGAGTGACCGACTTTGC 58.764 57.895 0.00 0.00 33.83 3.68
2227 2299 0.249911 GGTGAGTGACCGACTTTGCT 60.250 55.000 0.00 0.00 33.83 3.91
2242 2314 5.289675 CGACTTTGCTAAGAGATCGACATTT 59.710 40.000 14.98 0.00 32.30 2.32
2243 2315 6.414408 ACTTTGCTAAGAGATCGACATTTG 57.586 37.500 14.98 0.00 35.30 2.32
2247 2320 5.478407 TGCTAAGAGATCGACATTTGTTGA 58.522 37.500 3.19 3.19 42.20 3.18
2268 2341 8.267183 TGTTGACAACTCCATATACATCAGAAT 58.733 33.333 18.73 0.00 0.00 2.40
2312 2389 4.412199 TGCTATCTAAAGGTGGCCAACTAT 59.588 41.667 27.18 16.70 0.00 2.12
2363 2440 2.185350 CGGCAGGAGTTCATCGCT 59.815 61.111 0.00 0.00 0.00 4.93
2366 2443 0.391661 GGCAGGAGTTCATCGCTTCA 60.392 55.000 0.00 0.00 0.00 3.02
2416 2493 1.396653 CCCAGATTGCCAGATTCACC 58.603 55.000 0.00 0.00 0.00 4.02
2432 2509 0.392998 CACCGGGCTTGCTGACTTAT 60.393 55.000 6.32 0.00 0.00 1.73
2467 2544 0.677288 TCTCCACGTACACACCTTGG 59.323 55.000 0.00 0.00 0.00 3.61
2473 2550 1.339235 CGTACACACCTTGGCGTACG 61.339 60.000 11.84 11.84 42.70 3.67
2474 2551 1.373246 TACACACCTTGGCGTACGC 60.373 57.895 31.54 31.54 41.06 4.42
2475 2552 2.085042 TACACACCTTGGCGTACGCA 62.085 55.000 37.99 22.91 44.11 5.24
2476 2553 2.663852 ACACCTTGGCGTACGCAC 60.664 61.111 37.99 27.39 44.11 5.34
2533 2610 3.273434 TGCATGTGATCTGCTTTACTCC 58.727 45.455 6.93 0.00 40.34 3.85
2556 2633 1.541147 CCGAGTTCCAACACATGCATT 59.459 47.619 0.00 0.00 0.00 3.56
2667 2745 5.382618 AATTGTTTCACCTGAATGAGCTC 57.617 39.130 6.82 6.82 33.54 4.09
2688 2766 2.797719 CGCCAAAACAAAATGTGGTACC 59.202 45.455 4.43 4.43 33.43 3.34
2723 2801 6.844696 TGAATATATGAAGAAGGAACACGC 57.155 37.500 0.00 0.00 0.00 5.34
2950 3046 4.641989 AGGGCTCAGTGCATTACTAATTTG 59.358 41.667 0.00 0.00 45.15 2.32
3087 3209 3.564027 GCGGCGATCAAGTTCCGG 61.564 66.667 12.98 0.00 41.96 5.14
3093 3215 1.303282 GATCAAGTTCCGGGGGCTT 59.697 57.895 0.00 0.44 0.00 4.35
3123 3245 1.361668 CCAACTTCGACATGAGCCGG 61.362 60.000 0.00 0.00 0.00 6.13
3168 3290 4.101448 GACCTGCCCATCGGTGCT 62.101 66.667 0.00 0.00 32.62 4.40
3198 3320 2.668212 CGCGCCTCCAAGTTCCAA 60.668 61.111 0.00 0.00 0.00 3.53
3201 3323 2.325082 CGCCTCCAAGTTCCAACCG 61.325 63.158 0.00 0.00 0.00 4.44
3219 3341 2.353607 GACGTCCTATCGCTGCCG 60.354 66.667 3.51 0.00 0.00 5.69
3237 3359 4.147322 GCACCGAACGTGGCATCG 62.147 66.667 2.10 2.10 43.24 3.84
3252 3374 3.333899 ATCGCCAGACATGCTGCCA 62.334 57.895 10.54 0.00 43.50 4.92
3294 3416 1.750930 CCTCCTCGCCATGCACTAT 59.249 57.895 0.00 0.00 0.00 2.12
3312 3434 0.965866 ATCAGCAGCAGCAGCAACAT 60.966 50.000 12.92 0.00 45.49 2.71
3336 3458 2.033757 CAGCAGCAGCAGTTCCCT 59.966 61.111 3.17 0.00 45.49 4.20
3354 3476 4.983090 GCATCGGCATTTGAGACG 57.017 55.556 0.00 0.00 40.72 4.18
3384 3506 1.149361 GCGTGAACGTGGACTTCACA 61.149 55.000 15.49 0.00 45.31 3.58
3490 3615 0.036577 CAGGCAGAGCAACAGCTACT 60.037 55.000 0.00 0.00 39.10 2.57
3522 3647 2.846206 TCCTTATGCTTCCATGGTGTCT 59.154 45.455 12.58 0.00 32.85 3.41
3539 3664 3.362399 CTGGATCAGCGGCGTCAGT 62.362 63.158 9.37 0.00 0.00 3.41
3927 4081 2.557056 TCTGGTGTGTCAGCTACAGTAC 59.443 50.000 0.00 0.00 39.29 2.73
4076 4236 7.720957 TCAGGTGAATGAGAAGAAGAATTTTCA 59.279 33.333 0.00 0.00 0.00 2.69
4127 4605 5.449304 GTTGTAAAATCTTGGGAACGACTG 58.551 41.667 0.00 0.00 0.00 3.51
4183 4674 2.071778 ACCTGCACAGAAACATTGGT 57.928 45.000 0.00 0.00 0.00 3.67
4250 4766 3.551846 ACGGAAGACCAAGAAACATGTT 58.448 40.909 4.92 4.92 35.59 2.71
4251 4767 3.951680 ACGGAAGACCAAGAAACATGTTT 59.048 39.130 23.49 23.49 35.59 2.83
4252 4768 4.036380 ACGGAAGACCAAGAAACATGTTTC 59.964 41.667 34.21 34.21 41.49 2.78
4594 7118 4.020662 AGCCTCAAAGGACTCTTAGTCTTG 60.021 45.833 6.99 5.19 44.46 3.02
4642 7166 7.596248 GCCAAATTGCCAATACTATATTCACAG 59.404 37.037 0.00 0.00 0.00 3.66
4649 7173 8.582437 TGCCAATACTATATTCACAGTACTACC 58.418 37.037 0.00 0.00 30.36 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.250569 CAACTGCCAAGATATAACGAATTTGT 58.749 34.615 0.00 0.00 0.00 2.83
1 2 6.692681 CCAACTGCCAAGATATAACGAATTTG 59.307 38.462 0.00 0.00 0.00 2.32
2 3 6.183360 CCCAACTGCCAAGATATAACGAATTT 60.183 38.462 0.00 0.00 0.00 1.82
3 4 5.299279 CCCAACTGCCAAGATATAACGAATT 59.701 40.000 0.00 0.00 0.00 2.17
4 5 4.821805 CCCAACTGCCAAGATATAACGAAT 59.178 41.667 0.00 0.00 0.00 3.34
5 6 4.196193 CCCAACTGCCAAGATATAACGAA 58.804 43.478 0.00 0.00 0.00 3.85
6 7 3.433031 CCCCAACTGCCAAGATATAACGA 60.433 47.826 0.00 0.00 0.00 3.85
7 8 2.878406 CCCCAACTGCCAAGATATAACG 59.122 50.000 0.00 0.00 0.00 3.18
8 9 2.623416 GCCCCAACTGCCAAGATATAAC 59.377 50.000 0.00 0.00 0.00 1.89
9 10 2.944129 GCCCCAACTGCCAAGATATAA 58.056 47.619 0.00 0.00 0.00 0.98
48 49 0.591741 CGTTTTAACGCACGGGCAAA 60.592 50.000 11.77 0.00 46.06 3.68
133 138 7.801315 TGATTCACGAGCATAACTTTAAACAAC 59.199 33.333 0.00 0.00 0.00 3.32
143 148 4.361926 GTCGATGATTCACGAGCATAAC 57.638 45.455 10.28 0.00 39.16 1.89
150 155 5.257082 TCATTTAGGTCGATGATTCACGA 57.743 39.130 7.08 7.08 36.18 4.35
321 328 6.198650 TGTGATAAATGGTCTCATTGCTTG 57.801 37.500 0.00 0.00 42.29 4.01
339 350 7.915397 GCGTGGATTAATTTACTTTGATGTGAT 59.085 33.333 0.00 0.00 0.00 3.06
341 352 6.194508 CGCGTGGATTAATTTACTTTGATGTG 59.805 38.462 0.00 0.00 0.00 3.21
348 359 5.172934 TCTCACGCGTGGATTAATTTACTT 58.827 37.500 36.41 0.00 0.00 2.24
384 395 5.184096 TCTGATGAGTAGTGTTTCACTCCTC 59.816 44.000 13.10 13.10 44.24 3.71
439 451 2.110757 GAGCATAGCTGGAGGAGGGC 62.111 65.000 0.00 0.00 39.88 5.19
498 510 1.275471 GCACGCGCCTTTTCTTTTCC 61.275 55.000 5.73 0.00 0.00 3.13
511 523 2.279451 TAGCTAGCCATGCACGCG 60.279 61.111 12.13 3.53 32.80 6.01
512 524 2.602322 GCTAGCTAGCCATGCACGC 61.602 63.158 31.67 7.26 43.39 5.34
513 525 2.305853 CGCTAGCTAGCCATGCACG 61.306 63.158 34.27 18.04 46.34 5.34
514 526 2.602322 GCGCTAGCTAGCCATGCAC 61.602 63.158 34.27 16.35 46.34 4.57
651 663 1.218047 GCGAAAATCCAAAGGGGCC 59.782 57.895 0.00 0.00 36.21 5.80
703 718 5.885449 ATTAGAGAGAGGGAGTGATTTGG 57.115 43.478 0.00 0.00 0.00 3.28
714 729 4.770010 AGGGCGAGATTAATTAGAGAGAGG 59.230 45.833 0.00 0.00 0.00 3.69
715 730 5.105917 GGAGGGCGAGATTAATTAGAGAGAG 60.106 48.000 0.00 0.00 0.00 3.20
716 731 4.767928 GGAGGGCGAGATTAATTAGAGAGA 59.232 45.833 0.00 0.00 0.00 3.10
717 732 4.770010 AGGAGGGCGAGATTAATTAGAGAG 59.230 45.833 0.00 0.00 0.00 3.20
718 733 4.742012 AGGAGGGCGAGATTAATTAGAGA 58.258 43.478 0.00 0.00 0.00 3.10
719 734 5.233988 CAAGGAGGGCGAGATTAATTAGAG 58.766 45.833 0.00 0.00 0.00 2.43
754 771 1.136110 GTCCAAGCAGAGTAGAGAGCC 59.864 57.143 0.00 0.00 0.00 4.70
763 780 2.046892 CCACCCGTCCAAGCAGAG 60.047 66.667 0.00 0.00 0.00 3.35
764 781 1.990160 AAACCACCCGTCCAAGCAGA 61.990 55.000 0.00 0.00 0.00 4.26
765 782 1.515521 GAAACCACCCGTCCAAGCAG 61.516 60.000 0.00 0.00 0.00 4.24
766 783 1.527380 GAAACCACCCGTCCAAGCA 60.527 57.895 0.00 0.00 0.00 3.91
767 784 2.265904 GGAAACCACCCGTCCAAGC 61.266 63.158 0.00 0.00 0.00 4.01
819 836 0.378257 CTGTGCACTGTTCACACACC 59.622 55.000 19.41 0.00 39.29 4.16
875 892 5.708877 AGTCCGGTATAAATAGAGAGTGC 57.291 43.478 0.00 0.00 0.00 4.40
876 893 7.648510 GTCAAAGTCCGGTATAAATAGAGAGTG 59.351 40.741 0.00 0.00 0.00 3.51
877 894 7.560626 AGTCAAAGTCCGGTATAAATAGAGAGT 59.439 37.037 0.00 0.00 0.00 3.24
878 895 7.942990 AGTCAAAGTCCGGTATAAATAGAGAG 58.057 38.462 0.00 0.00 0.00 3.20
919 948 0.121197 AAGGAGGGGAATGGGACTGA 59.879 55.000 0.00 0.00 0.00 3.41
920 949 0.257039 CAAGGAGGGGAATGGGACTG 59.743 60.000 0.00 0.00 0.00 3.51
921 950 1.575447 GCAAGGAGGGGAATGGGACT 61.575 60.000 0.00 0.00 0.00 3.85
922 951 1.076705 GCAAGGAGGGGAATGGGAC 60.077 63.158 0.00 0.00 0.00 4.46
947 976 7.056006 GTCTAAGCTAGAAGAAGGGTAGTAGT 58.944 42.308 0.00 0.00 36.40 2.73
948 977 7.284820 AGTCTAAGCTAGAAGAAGGGTAGTAG 58.715 42.308 0.00 0.00 36.40 2.57
949 978 7.210618 AGTCTAAGCTAGAAGAAGGGTAGTA 57.789 40.000 0.00 0.00 36.40 1.82
950 979 6.082228 AGTCTAAGCTAGAAGAAGGGTAGT 57.918 41.667 0.00 0.00 36.40 2.73
991 1020 3.434319 CATATCCATGGCGGCCGC 61.434 66.667 41.63 41.63 41.06 6.53
992 1021 2.747460 CCATATCCATGGCGGCCG 60.747 66.667 24.05 24.05 45.29 6.13
1134 1163 0.249911 GATAGCTAGGGGTGTTGGCG 60.250 60.000 0.00 0.00 0.00 5.69
1148 1177 7.753309 AGTACATGATCGATATAGGGATAGC 57.247 40.000 0.00 0.00 0.00 2.97
1151 1180 8.495260 TCACTAGTACATGATCGATATAGGGAT 58.505 37.037 0.00 0.00 0.00 3.85
1154 1183 7.517575 CGCTCACTAGTACATGATCGATATAGG 60.518 44.444 0.00 0.00 36.77 2.57
1199 1230 0.902984 ACCGTGAGCCACAGTCCATA 60.903 55.000 6.21 0.00 33.40 2.74
1200 1231 2.217038 ACCGTGAGCCACAGTCCAT 61.217 57.895 6.21 0.00 33.40 3.41
1202 1233 2.357517 CACCGTGAGCCACAGTCC 60.358 66.667 0.00 0.00 33.40 3.85
1203 1234 3.044305 GCACCGTGAGCCACAGTC 61.044 66.667 1.65 0.00 33.40 3.51
1204 1235 3.182590 ATGCACCGTGAGCCACAGT 62.183 57.895 1.65 0.00 33.40 3.55
1205 1236 2.359107 ATGCACCGTGAGCCACAG 60.359 61.111 1.65 0.00 33.40 3.66
1213 1251 2.118683 CACAAGAAAACATGCACCGTG 58.881 47.619 0.00 0.00 0.00 4.94
1237 1279 4.421554 TCCCCTCCTCCCCTGCAG 62.422 72.222 6.78 6.78 0.00 4.41
1244 1286 4.393778 TCCACCGTCCCCTCCTCC 62.394 72.222 0.00 0.00 0.00 4.30
1314 1356 4.735132 CACCACGGCCGTCGATGT 62.735 66.667 31.80 20.05 42.43 3.06
1448 1499 2.279120 GCCTGATCGGACTCAGCG 60.279 66.667 2.08 6.69 41.12 5.18
1451 1502 2.121538 CCTCGCCTGATCGGACTCA 61.122 63.158 2.08 0.00 33.16 3.41
1499 1550 4.203076 ACGCCGCGGTAGATGGAC 62.203 66.667 28.70 5.98 0.00 4.02
1530 1581 8.453320 GCATGCATGTGATTAGCAAGTATATAA 58.547 33.333 26.79 0.00 42.15 0.98
1560 1611 3.101643 TCCTCTCGATGGGAAGAAGAA 57.898 47.619 4.32 0.00 0.00 2.52
1586 1637 6.123045 ACCAAACTAGCTAGTGGTATGTTT 57.877 37.500 26.65 14.47 36.50 2.83
1591 1642 5.197224 TCCTACCAAACTAGCTAGTGGTA 57.803 43.478 28.47 28.47 35.17 3.25
1592 1643 4.057063 TCCTACCAAACTAGCTAGTGGT 57.943 45.455 29.09 29.09 36.76 4.16
1593 1644 4.649674 TCATCCTACCAAACTAGCTAGTGG 59.350 45.833 26.70 24.42 36.50 4.00
1606 1657 6.443849 ACCAAGAAGTAAGAATCATCCTACCA 59.556 38.462 0.00 0.00 0.00 3.25
1629 1680 8.358148 TGCAATAGATGTTTAGCTAGTAGTACC 58.642 37.037 0.00 0.00 0.00 3.34
1665 1720 2.598565 AGTACCAGCAGTTCACTCTGA 58.401 47.619 7.56 0.00 37.61 3.27
1666 1721 3.393089 AAGTACCAGCAGTTCACTCTG 57.607 47.619 0.00 0.00 38.35 3.35
1667 1722 4.101741 AGAAAAGTACCAGCAGTTCACTCT 59.898 41.667 0.00 0.00 0.00 3.24
1668 1723 4.212214 CAGAAAAGTACCAGCAGTTCACTC 59.788 45.833 0.00 0.00 0.00 3.51
1669 1724 4.130118 CAGAAAAGTACCAGCAGTTCACT 58.870 43.478 0.00 0.00 0.00 3.41
1713 1768 3.188460 ACAAACACCACGAGATGCATTAC 59.812 43.478 0.00 0.00 0.00 1.89
1745 1800 6.720748 TGCATACATAGGCCAAATCATACATT 59.279 34.615 5.01 0.00 30.87 2.71
1746 1801 6.247676 TGCATACATAGGCCAAATCATACAT 58.752 36.000 5.01 0.00 30.87 2.29
1747 1802 5.629125 TGCATACATAGGCCAAATCATACA 58.371 37.500 5.01 0.00 30.87 2.29
1748 1803 5.124457 CCTGCATACATAGGCCAAATCATAC 59.876 44.000 5.01 0.00 30.87 2.39
1749 1804 5.255687 CCTGCATACATAGGCCAAATCATA 58.744 41.667 5.01 0.00 30.87 2.15
1759 1814 0.603707 CCGGTGCCTGCATACATAGG 60.604 60.000 0.00 0.00 37.14 2.57
1760 1815 0.106708 ACCGGTGCCTGCATACATAG 59.893 55.000 6.12 0.00 0.00 2.23
1761 1816 0.179059 CACCGGTGCCTGCATACATA 60.179 55.000 24.02 0.00 0.00 2.29
1762 1817 1.451927 CACCGGTGCCTGCATACAT 60.452 57.895 24.02 0.00 0.00 2.29
1763 1818 2.046411 CACCGGTGCCTGCATACA 60.046 61.111 24.02 0.00 0.00 2.29
1764 1819 2.824041 CCACCGGTGCCTGCATAC 60.824 66.667 29.75 0.00 0.00 2.39
1917 1979 2.730550 AGGCAGCAAAACATGTTAGC 57.269 45.000 21.81 21.81 0.00 3.09
1930 1992 2.560105 AGATTTGTGAGGAAAAGGCAGC 59.440 45.455 0.00 0.00 0.00 5.25
1931 1993 4.077822 AGAGATTTGTGAGGAAAAGGCAG 58.922 43.478 0.00 0.00 0.00 4.85
1932 1994 3.822735 CAGAGATTTGTGAGGAAAAGGCA 59.177 43.478 0.00 0.00 0.00 4.75
1933 1995 4.074970 TCAGAGATTTGTGAGGAAAAGGC 58.925 43.478 0.00 0.00 0.00 4.35
1934 1996 5.048434 GGTTCAGAGATTTGTGAGGAAAAGG 60.048 44.000 0.00 0.00 0.00 3.11
1935 1997 5.767168 AGGTTCAGAGATTTGTGAGGAAAAG 59.233 40.000 0.00 0.00 0.00 2.27
1936 1998 5.532406 CAGGTTCAGAGATTTGTGAGGAAAA 59.468 40.000 0.00 0.00 0.00 2.29
1937 1999 5.065914 CAGGTTCAGAGATTTGTGAGGAAA 58.934 41.667 0.00 0.00 0.00 3.13
1942 2007 2.783135 GGCAGGTTCAGAGATTTGTGA 58.217 47.619 0.00 0.00 0.00 3.58
1950 2015 3.805267 GCATCGGCAGGTTCAGAG 58.195 61.111 0.00 0.00 40.72 3.35
1958 2023 8.750403 GATCATTATCACCAATGCATCGGCAG 62.750 46.154 2.74 0.00 41.84 4.85
1961 2026 4.456566 TGATCATTATCACCAATGCATCGG 59.543 41.667 0.88 0.88 37.20 4.18
1962 2027 5.616488 TGATCATTATCACCAATGCATCG 57.384 39.130 0.00 0.00 37.20 3.84
1964 2029 6.719829 ACTGATGATCATTATCACCAATGCAT 59.280 34.615 10.14 0.00 44.79 3.96
1990 2059 9.688091 TGGAATGCAATTAACATACCTAAGTAA 57.312 29.630 0.00 0.00 36.07 2.24
1993 2062 7.995289 TGTGGAATGCAATTAACATACCTAAG 58.005 34.615 0.00 0.00 36.07 2.18
2004 2073 3.634504 AGCTGGATGTGGAATGCAATTA 58.365 40.909 0.00 0.00 36.07 1.40
2008 2077 2.804986 TTAGCTGGATGTGGAATGCA 57.195 45.000 0.00 0.00 0.00 3.96
2012 2081 6.012337 TGGATAAATTAGCTGGATGTGGAA 57.988 37.500 0.00 0.00 0.00 3.53
2013 2083 5.645056 TGGATAAATTAGCTGGATGTGGA 57.355 39.130 0.00 0.00 0.00 4.02
2027 2097 8.967918 CATGGCAATGAAGATAGATGGATAAAT 58.032 33.333 0.00 0.00 35.67 1.40
2032 2102 5.067954 CACATGGCAATGAAGATAGATGGA 58.932 41.667 8.45 0.00 37.24 3.41
2033 2103 4.217767 CCACATGGCAATGAAGATAGATGG 59.782 45.833 8.45 0.00 37.24 3.51
2039 2109 2.291735 TGGACCACATGGCAATGAAGAT 60.292 45.455 8.45 0.00 39.32 2.40
2040 2110 1.075212 TGGACCACATGGCAATGAAGA 59.925 47.619 8.45 0.00 39.32 2.87
2041 2111 1.548081 TGGACCACATGGCAATGAAG 58.452 50.000 8.45 0.56 39.32 3.02
2051 2121 5.128033 TCCAAATCATACATGGACCACAT 57.872 39.130 0.00 0.00 38.30 3.21
2052 2122 4.582973 TCCAAATCATACATGGACCACA 57.417 40.909 0.00 0.00 38.30 4.17
2053 2123 4.704540 TGTTCCAAATCATACATGGACCAC 59.295 41.667 0.00 0.00 42.71 4.16
2054 2124 4.928263 TGTTCCAAATCATACATGGACCA 58.072 39.130 0.00 0.00 42.71 4.02
2056 2126 6.757897 TCTTGTTCCAAATCATACATGGAC 57.242 37.500 0.00 0.00 42.71 4.02
2059 2129 8.991243 ACATTTCTTGTTCCAAATCATACATG 57.009 30.769 0.00 0.00 33.74 3.21
2075 2145 5.010012 ACTGTAAGCCCTCAAACATTTCTTG 59.990 40.000 0.00 0.00 37.60 3.02
2076 2146 5.140454 ACTGTAAGCCCTCAAACATTTCTT 58.860 37.500 0.00 0.00 37.60 2.52
2078 2148 5.938125 TCTACTGTAAGCCCTCAAACATTTC 59.062 40.000 0.00 0.00 37.60 2.17
2081 2151 5.499004 TTCTACTGTAAGCCCTCAAACAT 57.501 39.130 0.00 0.00 37.60 2.71
2082 2152 4.967084 TTCTACTGTAAGCCCTCAAACA 57.033 40.909 0.00 0.00 37.60 2.83
2083 2153 6.349363 CCAATTTCTACTGTAAGCCCTCAAAC 60.349 42.308 0.00 0.00 37.60 2.93
2090 2160 3.053917 TCCCCCAATTTCTACTGTAAGCC 60.054 47.826 0.00 0.00 37.60 4.35
2091 2161 4.230745 TCCCCCAATTTCTACTGTAAGC 57.769 45.455 0.00 0.00 37.60 3.09
2098 2168 3.132824 CCTGCATTTCCCCCAATTTCTAC 59.867 47.826 0.00 0.00 0.00 2.59
2133 2205 2.716017 CCTCGCGGCTTTCTCCTCT 61.716 63.158 6.13 0.00 0.00 3.69
2145 2217 3.900892 ATGTCGTAGGCCCTCGCG 61.901 66.667 0.00 0.00 35.02 5.87
2166 2238 2.662596 CCCCAGTACTTGAGCGCA 59.337 61.111 11.47 0.00 0.00 6.09
2169 2241 2.137177 TTGGGCCCCAGTACTTGAGC 62.137 60.000 22.27 0.00 33.81 4.26
2172 2244 1.304134 GGTTGGGCCCCAGTACTTG 60.304 63.158 22.27 0.00 33.81 3.16
2187 2259 0.531311 GGAAGTTCGTCGTGGTGGTT 60.531 55.000 0.00 0.00 0.00 3.67
2199 2271 0.320508 GGTCACTCACCGGGAAGTTC 60.321 60.000 6.32 4.37 34.56 3.01
2223 2295 5.931724 TCAACAAATGTCGATCTCTTAGCAA 59.068 36.000 0.00 0.00 0.00 3.91
2224 2296 5.348724 GTCAACAAATGTCGATCTCTTAGCA 59.651 40.000 0.00 0.00 0.00 3.49
2226 2298 6.951256 TGTCAACAAATGTCGATCTCTTAG 57.049 37.500 0.00 0.00 0.00 2.18
2227 2299 6.929049 AGTTGTCAACAAATGTCGATCTCTTA 59.071 34.615 17.78 0.00 37.63 2.10
2242 2314 7.181569 TCTGATGTATATGGAGTTGTCAACA 57.818 36.000 17.78 0.00 0.00 3.33
2243 2315 8.554528 CATTCTGATGTATATGGAGTTGTCAAC 58.445 37.037 7.68 7.68 0.00 3.18
2247 2320 6.709397 CAGCATTCTGATGTATATGGAGTTGT 59.291 38.462 0.00 0.00 42.95 3.32
2268 2341 1.479730 AGAACTCAGCGATGATCAGCA 59.520 47.619 12.15 0.00 35.48 4.41
2312 2389 0.707024 TCTCCTCCAGCTCCTTCTCA 59.293 55.000 0.00 0.00 0.00 3.27
2363 2440 0.880278 GTGCTCACCTGCGAAGTGAA 60.880 55.000 5.02 0.00 43.36 3.18
2366 2443 0.882042 CAAGTGCTCACCTGCGAAGT 60.882 55.000 0.00 0.00 35.36 3.01
2396 2473 0.743097 GTGAATCTGGCAATCTGGGC 59.257 55.000 0.00 0.00 0.00 5.36
2416 2493 1.723870 GCATAAGTCAGCAAGCCCG 59.276 57.895 0.00 0.00 0.00 6.13
2432 2509 0.881118 GAGAAAATGAACAGGGCGCA 59.119 50.000 10.83 0.00 0.00 6.09
2533 2610 1.671054 ATGTGTTGGAACTCGGCCG 60.671 57.895 22.12 22.12 0.00 6.13
2544 2621 3.979948 TGAGGTCAAAATGCATGTGTTG 58.020 40.909 0.00 5.82 0.00 3.33
2545 2622 4.669206 TTGAGGTCAAAATGCATGTGTT 57.331 36.364 0.00 0.00 32.11 3.32
2556 2633 1.606668 GGAACACGCATTGAGGTCAAA 59.393 47.619 0.00 0.00 39.55 2.69
2644 2721 5.122239 CGAGCTCATTCAGGTGAAACAATTA 59.878 40.000 15.40 0.00 39.98 1.40
2667 2745 2.797719 GGTACCACATTTTGTTTTGGCG 59.202 45.455 7.15 0.00 31.76 5.69
2716 2794 2.032799 TGAAGACATTTGTGGCGTGTTC 59.967 45.455 0.00 0.00 34.48 3.18
2717 2795 2.020720 TGAAGACATTTGTGGCGTGTT 58.979 42.857 0.00 0.00 0.00 3.32
2719 2797 2.485426 AGATGAAGACATTTGTGGCGTG 59.515 45.455 0.00 0.00 36.82 5.34
2721 2799 3.837213 AAGATGAAGACATTTGTGGCG 57.163 42.857 0.00 0.00 36.82 5.69
2723 2801 7.874940 TGACTAAAAGATGAAGACATTTGTGG 58.125 34.615 0.00 0.00 36.82 4.17
2790 2871 1.450848 CCGTGCTGATGATGCCTGT 60.451 57.895 0.00 0.00 0.00 4.00
2979 3097 6.118852 ACCACATTGTTTGTTTTTGCCTAAT 58.881 32.000 0.00 0.00 36.00 1.73
2982 3100 3.949132 ACCACATTGTTTGTTTTTGCCT 58.051 36.364 0.00 0.00 36.00 4.75
3093 3215 0.940519 CGAAGTTGGTCACGGCGTTA 60.941 55.000 11.19 0.00 0.00 3.18
3123 3245 0.316032 GGATGCTCTCGACGTCGTAC 60.316 60.000 34.40 22.32 40.80 3.67
3198 3320 2.124403 AGCGATAGGACGTCCGGT 60.124 61.111 28.26 20.59 42.08 5.28
3201 3323 2.027751 GGCAGCGATAGGACGTCC 59.972 66.667 27.67 27.67 35.59 4.79
3219 3341 3.799755 GATGCCACGTTCGGTGCC 61.800 66.667 0.00 0.00 45.62 5.01
3252 3374 2.050934 GTAGTCCTTCTCCGCCGGT 61.051 63.158 1.63 0.00 0.00 5.28
3294 3416 1.583495 GATGTTGCTGCTGCTGCTGA 61.583 55.000 27.67 16.03 40.01 4.26
3339 3461 1.556564 CGTACGTCTCAAATGCCGAT 58.443 50.000 7.22 0.00 0.00 4.18
3354 3476 4.424566 TTCACGCCGGAGCCGTAC 62.425 66.667 5.05 0.00 37.81 3.67
3384 3506 3.142838 GTGCCGCTCATGCCCATT 61.143 61.111 0.00 0.00 35.36 3.16
3448 3570 3.041940 GTCGCCGTGTCCTGTTGG 61.042 66.667 0.00 0.00 0.00 3.77
3490 3615 3.370840 AGCATAAGGAATGTTGCTGGA 57.629 42.857 0.00 0.00 43.44 3.86
3522 3647 3.356639 GACTGACGCCGCTGATCCA 62.357 63.158 0.00 0.00 0.00 3.41
3539 3664 2.123597 CCTCGTATCCCCCACCGA 60.124 66.667 0.00 0.00 0.00 4.69
3543 3668 2.122989 GAGCCCTCGTATCCCCCA 60.123 66.667 0.00 0.00 0.00 4.96
3549 3674 2.838225 CCGGTGGAGCCCTCGTAT 60.838 66.667 0.00 0.00 0.00 3.06
3823 3975 3.325135 CCTACAGAACCTTGTCAGGAAGT 59.675 47.826 0.00 0.00 44.19 3.01
3838 3990 0.255033 TCTCCGCTACAGCCTACAGA 59.745 55.000 0.00 0.00 37.91 3.41
3927 4081 5.288712 ACATACAGTACTTTTCGAATGCTCG 59.711 40.000 0.00 0.00 46.87 5.03
4076 4236 6.466885 AGTATGTACTCTACCGCATTTTCT 57.533 37.500 0.00 0.00 0.00 2.52
4127 4605 0.447801 AATTCCAATGCTCGCGTGTC 59.552 50.000 5.77 0.50 0.00 3.67
4183 4674 7.458397 ACTTCCATGTTATTTTAGACTGACCA 58.542 34.615 0.00 0.00 0.00 4.02
4594 7118 5.162075 GCATAATATACACCTGAGTCGGAC 58.838 45.833 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.