Multiple sequence alignment - TraesCS7A01G084700

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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 TraesCS7A01G084700 chr7A 100.000 3109 0 0 1 3109 49161721 49158613 0.000000e+00 5742.0
1 TraesCS7A01G084700 chr7A 97.421 1241 32 0 1869 3109 49141558 49140318 0.000000e+00 2115.0
2 TraesCS7A01G084700 chr4A 90.404 1313 82 21 1233 2530 661021837 661020554 0.000000e+00 1687.0
3 TraesCS7A01G084700 chr4A 88.861 404 34 3 2520 2913 661020188 661019786 1.300000e-133 486.0
4 TraesCS7A01G084700 chr4A 83.051 354 58 1 882 1233 75951001 75951354 1.390000e-83 320.0
5 TraesCS7A01G084700 chr4A 97.297 37 1 0 2945 2981 661019679 661019643 2.590000e-06 63.9
6 TraesCS7A01G084700 chr5A 94.379 765 41 2 123 886 529961842 529962605 0.000000e+00 1173.0
7 TraesCS7A01G084700 chr5A 94.393 749 39 3 139 886 425605112 425605858 0.000000e+00 1147.0
8 TraesCS7A01G084700 chr5A 94.055 757 43 2 131 886 425617661 425618416 0.000000e+00 1147.0
9 TraesCS7A01G084700 chr5A 93.595 765 47 2 123 886 529949259 529950022 0.000000e+00 1140.0
10 TraesCS7A01G084700 chr5A 84.438 347 54 0 889 1235 639215537 639215191 2.970000e-90 342.0
11 TraesCS7A01G084700 chr5A 95.349 129 6 0 1 129 70876454 70876582 4.060000e-49 206.0
12 TraesCS7A01G084700 chr2A 94.256 766 43 1 123 887 64179724 64180489 0.000000e+00 1170.0
13 TraesCS7A01G084700 chr2A 93.725 765 45 3 123 886 753923732 753922970 0.000000e+00 1144.0
14 TraesCS7A01G084700 chr2A 93.676 759 46 2 123 880 704654166 704654923 0.000000e+00 1134.0
15 TraesCS7A01G084700 chr2A 93.333 765 48 3 123 886 753902852 753902090 0.000000e+00 1127.0
16 TraesCS7A01G084700 chr2A 86.217 341 45 2 1233 1572 639695364 639695703 4.900000e-98 368.0
17 TraesCS7A01G084700 chr3A 93.676 759 41 5 128 886 724162400 724163151 0.000000e+00 1129.0
18 TraesCS7A01G084700 chr3A 82.428 552 88 2 1575 2125 649953978 649954521 1.010000e-129 473.0
19 TraesCS7A01G084700 chr3A 85.920 348 49 0 888 1235 674070745 674070398 3.790000e-99 372.0
20 TraesCS7A01G084700 chr3A 95.349 129 6 0 1 129 74232667 74232795 4.060000e-49 206.0
21 TraesCS7A01G084700 chr3A 94.074 135 8 0 1 135 235682631 235682497 4.060000e-49 206.0
22 TraesCS7A01G084700 chr3A 94.074 135 8 0 1 135 238029057 238028923 4.060000e-49 206.0
23 TraesCS7A01G084700 chr3A 94.074 135 8 0 1 135 289556409 289556275 4.060000e-49 206.0
24 TraesCS7A01G084700 chr3A 94.074 135 8 0 1 135 297599818 297599684 4.060000e-49 206.0
25 TraesCS7A01G084700 chr7D 93.643 645 39 2 1238 1881 46909817 46909174 0.000000e+00 963.0
26 TraesCS7A01G084700 chr7D 86.391 338 46 0 887 1224 562383688 562384025 1.360000e-98 370.0
27 TraesCS7A01G084700 chr7D 95.200 125 6 0 2982 3106 55693787 55693663 6.800000e-47 198.0
28 TraesCS7A01G084700 chr5B 85.152 559 69 7 1575 2130 330430355 330430902 7.530000e-156 560.0
29 TraesCS7A01G084700 chr5B 84.767 558 73 5 1575 2130 330120753 330121300 1.630000e-152 549.0
30 TraesCS7A01G084700 chr6B 84.353 556 75 5 1578 2131 95236495 95235950 4.560000e-148 534.0
31 TraesCS7A01G084700 chr6B 83.060 549 82 5 1575 2121 159703641 159704180 3.600000e-134 488.0
32 TraesCS7A01G084700 chr6B 87.353 340 43 0 1233 1572 95236997 95236658 1.050000e-104 390.0
33 TraesCS7A01G084700 chr6B 85.380 342 46 4 1233 1572 665161690 665161351 4.930000e-93 351.0
34 TraesCS7A01G084700 chr6B 82.143 420 66 5 1575 1993 665416485 665416074 4.930000e-93 351.0
35 TraesCS7A01G084700 chr6D 83.818 550 77 6 1575 2121 84085390 84085930 2.140000e-141 512.0
36 TraesCS7A01G084700 chr6D 85.673 342 45 4 1233 1572 440014655 440014316 1.060000e-94 357.0
37 TraesCS7A01G084700 chr6D 85.380 342 46 4 1233 1572 439921466 439921127 4.930000e-93 351.0
38 TraesCS7A01G084700 chr6A 83.333 558 83 3 1575 2131 52466294 52466842 9.950000e-140 507.0
39 TraesCS7A01G084700 chr6A 87.834 337 41 0 1233 1569 52406440 52406776 2.250000e-106 396.0
40 TraesCS7A01G084700 chr6A 95.349 129 6 0 1 129 112560396 112560524 4.060000e-49 206.0
41 TraesCS7A01G084700 chr6A 94.074 135 8 0 1 135 358436809 358436675 4.060000e-49 206.0
42 TraesCS7A01G084700 chr6A 93.893 131 6 1 2981 3109 459078001 459078131 2.450000e-46 196.0
43 TraesCS7A01G084700 chr1D 88.000 350 40 2 887 1235 191511331 191510983 2.230000e-111 412.0
44 TraesCS7A01G084700 chr1D 85.014 347 50 1 882 1226 481988857 481989203 4.930000e-93 351.0
45 TraesCS7A01G084700 chr3D 86.246 349 48 0 887 1235 427207864 427208212 2.260000e-101 379.0
46 TraesCS7A01G084700 chr3D 94.531 128 7 0 2981 3108 410999001 410998874 6.800000e-47 198.0
47 TraesCS7A01G084700 chr1A 86.726 339 44 1 887 1225 571642527 571642190 2.930000e-100 375.0
48 TraesCS7A01G084700 chr1A 94.074 135 8 0 1 135 395709321 395709187 4.060000e-49 206.0
49 TraesCS7A01G084700 chr1A 93.284 134 9 0 2975 3108 494822589 494822722 6.800000e-47 198.0
50 TraesCS7A01G084700 chr2D 86.217 341 45 2 1233 1572 493882695 493882356 4.900000e-98 368.0
51 TraesCS7A01G084700 chr2D 85.100 349 51 1 887 1235 598726798 598726451 3.810000e-94 355.0
52 TraesCS7A01G084700 chr2D 94.531 128 7 0 2982 3109 21755753 21755880 6.800000e-47 198.0
53 TraesCS7A01G084700 chr2D 94.574 129 6 1 2981 3108 32523152 32523280 6.800000e-47 198.0
54 TraesCS7A01G084700 chr2B 94.488 127 7 0 2979 3105 528830264 528830390 2.450000e-46 196.0
55 TraesCS7A01G084700 chr1B 93.333 135 6 2 2978 3109 102843690 102843556 2.450000e-46 196.0


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 TraesCS7A01G084700 chr7A 49158613 49161721 3108 True 5742.000000 5742 100.000000 1 3109 1 chr7A.!!$R2 3108
1 TraesCS7A01G084700 chr7A 49140318 49141558 1240 True 2115.000000 2115 97.421000 1869 3109 1 chr7A.!!$R1 1240
2 TraesCS7A01G084700 chr4A 661019643 661021837 2194 True 745.633333 1687 92.187333 1233 2981 3 chr4A.!!$R1 1748
3 TraesCS7A01G084700 chr5A 529961842 529962605 763 False 1173.000000 1173 94.379000 123 886 1 chr5A.!!$F5 763
4 TraesCS7A01G084700 chr5A 425605112 425605858 746 False 1147.000000 1147 94.393000 139 886 1 chr5A.!!$F2 747
5 TraesCS7A01G084700 chr5A 425617661 425618416 755 False 1147.000000 1147 94.055000 131 886 1 chr5A.!!$F3 755
6 TraesCS7A01G084700 chr5A 529949259 529950022 763 False 1140.000000 1140 93.595000 123 886 1 chr5A.!!$F4 763
7 TraesCS7A01G084700 chr2A 64179724 64180489 765 False 1170.000000 1170 94.256000 123 887 1 chr2A.!!$F1 764
8 TraesCS7A01G084700 chr2A 753922970 753923732 762 True 1144.000000 1144 93.725000 123 886 1 chr2A.!!$R2 763
9 TraesCS7A01G084700 chr2A 704654166 704654923 757 False 1134.000000 1134 93.676000 123 880 1 chr2A.!!$F3 757
10 TraesCS7A01G084700 chr2A 753902090 753902852 762 True 1127.000000 1127 93.333000 123 886 1 chr2A.!!$R1 763
11 TraesCS7A01G084700 chr3A 724162400 724163151 751 False 1129.000000 1129 93.676000 128 886 1 chr3A.!!$F3 758
12 TraesCS7A01G084700 chr3A 649953978 649954521 543 False 473.000000 473 82.428000 1575 2125 1 chr3A.!!$F2 550
13 TraesCS7A01G084700 chr7D 46909174 46909817 643 True 963.000000 963 93.643000 1238 1881 1 chr7D.!!$R1 643
14 TraesCS7A01G084700 chr5B 330430355 330430902 547 False 560.000000 560 85.152000 1575 2130 1 chr5B.!!$F2 555
15 TraesCS7A01G084700 chr5B 330120753 330121300 547 False 549.000000 549 84.767000 1575 2130 1 chr5B.!!$F1 555
16 TraesCS7A01G084700 chr6B 159703641 159704180 539 False 488.000000 488 83.060000 1575 2121 1 chr6B.!!$F1 546
17 TraesCS7A01G084700 chr6B 95235950 95236997 1047 True 462.000000 534 85.853000 1233 2131 2 chr6B.!!$R3 898
18 TraesCS7A01G084700 chr6D 84085390 84085930 540 False 512.000000 512 83.818000 1575 2121 1 chr6D.!!$F1 546
19 TraesCS7A01G084700 chr6A 52466294 52466842 548 False 507.000000 507 83.333000 1575 2131 1 chr6A.!!$F2 556

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
40 41 0.034896 AATGGTAATCCGGCTAGGCG 59.965 55.0 30.07 30.07 40.77 5.52 F
75 76 0.179026 TATGTCTACGCTCTCCGGCT 60.179 55.0 0.00 0.00 42.52 5.52 F
79 80 0.179702 TCTACGCTCTCCGGCTTCTA 59.820 55.0 0.00 0.00 42.52 2.10 F
1149 1152 0.033366 GGTTGTTCCCATGGTTGCAC 59.967 55.0 11.73 2.01 0.00 4.57 F
1150 1153 0.033366 GTTGTTCCCATGGTTGCACC 59.967 55.0 11.73 0.00 39.22 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1120 1123 0.250770 GGGAACAACCTCAGGGTGAC 60.251 60.000 18.43 9.02 46.67 3.67 R
1122 1125 0.405585 ATGGGAACAACCTCAGGGTG 59.594 55.000 7.41 7.41 46.67 4.61 R
1883 2053 0.506932 ATCGCACAAAGTTGTCGTCG 59.493 50.000 12.44 8.71 39.91 5.12 R
1967 2137 1.893808 GTCACCACAGTGCCCACAG 60.894 63.158 0.00 0.00 44.16 3.66 R
2473 2647 2.607750 ATGGCTGGTGGTCGAGGT 60.608 61.111 0.00 0.00 0.00 3.85 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
26 27 3.018805 CCCCGGGGGTACAATGGT 61.019 66.667 34.01 0.00 38.25 3.55
27 28 1.693458 CCCCGGGGGTACAATGGTA 60.693 63.158 34.01 0.00 38.25 3.25
28 29 1.280473 CCCCGGGGGTACAATGGTAA 61.280 60.000 34.01 0.00 38.25 2.85
29 30 0.848053 CCCGGGGGTACAATGGTAAT 59.152 55.000 14.71 0.00 0.00 1.89
30 31 1.202842 CCCGGGGGTACAATGGTAATC 60.203 57.143 14.71 0.00 0.00 1.75
31 32 1.202842 CCGGGGGTACAATGGTAATCC 60.203 57.143 0.00 0.00 0.00 3.01
32 33 1.541670 CGGGGGTACAATGGTAATCCG 60.542 57.143 0.00 3.71 34.59 4.18
33 34 1.202842 GGGGGTACAATGGTAATCCGG 60.203 57.143 0.00 0.00 36.30 5.14
34 35 1.601166 GGGTACAATGGTAATCCGGC 58.399 55.000 0.00 0.00 36.30 6.13
35 36 1.142262 GGGTACAATGGTAATCCGGCT 59.858 52.381 0.00 0.00 36.30 5.52
36 37 2.369532 GGGTACAATGGTAATCCGGCTA 59.630 50.000 0.00 0.00 36.30 3.93
37 38 3.556423 GGGTACAATGGTAATCCGGCTAG 60.556 52.174 0.00 0.00 36.30 3.42
38 39 2.930826 ACAATGGTAATCCGGCTAGG 57.069 50.000 0.00 0.00 42.97 3.02
39 40 1.202770 ACAATGGTAATCCGGCTAGGC 60.203 52.381 6.15 6.15 40.77 3.93
40 41 0.034896 AATGGTAATCCGGCTAGGCG 59.965 55.000 30.07 30.07 40.77 5.52
41 42 1.119574 ATGGTAATCCGGCTAGGCGT 61.120 55.000 33.14 19.84 40.77 5.68
42 43 1.300697 GGTAATCCGGCTAGGCGTG 60.301 63.158 33.14 24.69 40.77 5.34
43 44 1.300697 GTAATCCGGCTAGGCGTGG 60.301 63.158 33.14 20.97 40.77 4.94
44 45 2.504274 TAATCCGGCTAGGCGTGGG 61.504 63.158 33.14 20.29 40.77 4.61
56 57 4.003788 CGTGGGGCCAAGTCGTCT 62.004 66.667 4.39 0.00 0.00 4.18
57 58 2.642254 CGTGGGGCCAAGTCGTCTA 61.642 63.158 4.39 0.00 0.00 2.59
58 59 1.905512 GTGGGGCCAAGTCGTCTAT 59.094 57.895 4.39 0.00 0.00 1.98
59 60 0.462047 GTGGGGCCAAGTCGTCTATG 60.462 60.000 4.39 0.00 0.00 2.23
60 61 0.907704 TGGGGCCAAGTCGTCTATGT 60.908 55.000 4.39 0.00 0.00 2.29
61 62 0.179081 GGGGCCAAGTCGTCTATGTC 60.179 60.000 4.39 0.00 0.00 3.06
62 63 0.824759 GGGCCAAGTCGTCTATGTCT 59.175 55.000 4.39 0.00 0.00 3.41
63 64 2.029623 GGGCCAAGTCGTCTATGTCTA 58.970 52.381 4.39 0.00 0.00 2.59
64 65 2.223758 GGGCCAAGTCGTCTATGTCTAC 60.224 54.545 4.39 0.00 0.00 2.59
65 66 2.541178 GGCCAAGTCGTCTATGTCTACG 60.541 54.545 0.00 0.00 40.40 3.51
66 67 2.717530 CCAAGTCGTCTATGTCTACGC 58.282 52.381 0.00 0.00 38.94 4.42
67 68 2.355132 CCAAGTCGTCTATGTCTACGCT 59.645 50.000 0.00 0.00 38.94 5.07
68 69 3.546417 CCAAGTCGTCTATGTCTACGCTC 60.546 52.174 0.00 0.00 38.94 5.03
69 70 3.182341 AGTCGTCTATGTCTACGCTCT 57.818 47.619 0.00 0.00 38.94 4.09
70 71 3.125316 AGTCGTCTATGTCTACGCTCTC 58.875 50.000 0.00 0.00 38.94 3.20
71 72 2.221517 GTCGTCTATGTCTACGCTCTCC 59.778 54.545 0.00 0.00 38.94 3.71
72 73 1.192757 CGTCTATGTCTACGCTCTCCG 59.807 57.143 0.00 0.00 44.21 4.63
73 74 1.532007 GTCTATGTCTACGCTCTCCGG 59.468 57.143 0.00 0.00 42.52 5.14
74 75 0.238817 CTATGTCTACGCTCTCCGGC 59.761 60.000 0.00 0.00 42.52 6.13
75 76 0.179026 TATGTCTACGCTCTCCGGCT 60.179 55.000 0.00 0.00 42.52 5.52
76 77 1.038130 ATGTCTACGCTCTCCGGCTT 61.038 55.000 0.00 0.00 42.52 4.35
77 78 1.064458 GTCTACGCTCTCCGGCTTC 59.936 63.158 0.00 0.00 42.52 3.86
78 79 1.077644 TCTACGCTCTCCGGCTTCT 60.078 57.895 0.00 0.00 42.52 2.85
79 80 0.179702 TCTACGCTCTCCGGCTTCTA 59.820 55.000 0.00 0.00 42.52 2.10
80 81 0.308376 CTACGCTCTCCGGCTTCTAC 59.692 60.000 0.00 0.00 42.52 2.59
81 82 1.434622 TACGCTCTCCGGCTTCTACG 61.435 60.000 0.00 0.00 42.52 3.51
82 83 2.278923 GCTCTCCGGCTTCTACGC 60.279 66.667 0.00 0.00 0.00 4.42
83 84 2.413765 CTCTCCGGCTTCTACGCC 59.586 66.667 0.00 0.00 46.68 5.68
90 91 4.821589 GCTTCTACGCCGGCTGCT 62.822 66.667 26.68 9.23 38.05 4.24
91 92 2.887568 CTTCTACGCCGGCTGCTG 60.888 66.667 26.68 11.62 38.05 4.41
92 93 4.451150 TTCTACGCCGGCTGCTGG 62.451 66.667 26.68 23.28 38.05 4.85
220 222 4.722700 CTGGTCGGGGGCTGGTTG 62.723 72.222 0.00 0.00 0.00 3.77
230 232 2.253452 GCTGGTTGCTGTTGCTCG 59.747 61.111 0.00 0.00 40.48 5.03
248 250 3.083997 ATCCTGGTGACGAGGGCC 61.084 66.667 13.84 0.00 31.80 5.80
343 345 1.961180 AATGGGGCGTCTCCTTCGAG 61.961 60.000 0.00 0.00 37.48 4.04
648 651 1.337541 GGGTACGGTCTTGACCACTTC 60.338 57.143 18.51 6.23 34.73 3.01
735 738 3.864921 GCTTTCTTCACGAGGGCTAAAGA 60.865 47.826 0.00 0.00 0.00 2.52
747 750 1.376812 CTAAAGACGGGCCGCCTTT 60.377 57.895 35.95 35.95 41.75 3.11
821 824 0.617535 TTCTTGAGAGCCGGATGGGA 60.618 55.000 5.05 0.00 38.47 4.37
887 890 2.572191 TGGCTATTTACTCCGACACG 57.428 50.000 0.00 0.00 0.00 4.49
899 902 4.736896 GACACGGCCCCTCACGAC 62.737 72.222 0.00 0.00 0.00 4.34
928 931 4.193334 CGTCAGCCCGCTCATCGA 62.193 66.667 0.00 0.00 41.67 3.59
929 932 2.583593 GTCAGCCCGCTCATCGAC 60.584 66.667 0.00 0.00 41.67 4.20
930 933 3.838271 TCAGCCCGCTCATCGACC 61.838 66.667 0.00 0.00 41.67 4.79
931 934 3.842923 CAGCCCGCTCATCGACCT 61.843 66.667 0.00 0.00 41.67 3.85
932 935 2.123854 AGCCCGCTCATCGACCTA 60.124 61.111 0.00 0.00 41.67 3.08
933 936 2.027751 GCCCGCTCATCGACCTAC 59.972 66.667 0.00 0.00 41.67 3.18
934 937 2.331805 CCCGCTCATCGACCTACG 59.668 66.667 0.00 0.00 41.67 3.51
935 938 2.478890 CCCGCTCATCGACCTACGT 61.479 63.158 0.00 0.00 43.13 3.57
936 939 1.009900 CCGCTCATCGACCTACGTC 60.010 63.158 0.00 0.00 43.13 4.34
944 947 3.271014 GACCTACGTCGGCTGTCA 58.729 61.111 5.94 0.00 0.00 3.58
945 948 1.154073 GACCTACGTCGGCTGTCAC 60.154 63.158 5.94 0.00 0.00 3.67
946 949 2.181021 CCTACGTCGGCTGTCACC 59.819 66.667 0.00 0.00 0.00 4.02
956 959 4.394712 CTGTCACCGCCCTGTCCC 62.395 72.222 0.00 0.00 0.00 4.46
963 966 4.452733 CGCCCTGTCCCCGAGTTC 62.453 72.222 0.00 0.00 0.00 3.01
964 967 3.319198 GCCCTGTCCCCGAGTTCA 61.319 66.667 0.00 0.00 0.00 3.18
965 968 2.982130 CCCTGTCCCCGAGTTCAG 59.018 66.667 0.00 0.00 0.00 3.02
966 969 2.266055 CCTGTCCCCGAGTTCAGC 59.734 66.667 0.00 0.00 0.00 4.26
967 970 2.583441 CCTGTCCCCGAGTTCAGCA 61.583 63.158 0.00 0.00 0.00 4.41
968 971 1.374758 CTGTCCCCGAGTTCAGCAC 60.375 63.158 0.00 0.00 0.00 4.40
969 972 2.432628 GTCCCCGAGTTCAGCACG 60.433 66.667 0.00 0.00 0.00 5.34
970 973 4.373116 TCCCCGAGTTCAGCACGC 62.373 66.667 0.00 0.00 0.00 5.34
974 977 4.379243 CGAGTTCAGCACGCCCCT 62.379 66.667 0.00 0.00 0.00 4.79
975 978 2.435059 GAGTTCAGCACGCCCCTC 60.435 66.667 0.00 0.00 0.00 4.30
976 979 3.959991 GAGTTCAGCACGCCCCTCC 62.960 68.421 0.00 0.00 0.00 4.30
977 980 4.329545 GTTCAGCACGCCCCTCCA 62.330 66.667 0.00 0.00 0.00 3.86
978 981 4.329545 TTCAGCACGCCCCTCCAC 62.330 66.667 0.00 0.00 0.00 4.02
982 985 4.101448 GCACGCCCCTCCACTGAT 62.101 66.667 0.00 0.00 0.00 2.90
983 986 2.124983 CACGCCCCTCCACTGATG 60.125 66.667 0.00 0.00 0.00 3.07
993 996 3.895025 CACTGATGGAGCAACGGG 58.105 61.111 0.00 0.00 0.00 5.28
994 997 2.045926 ACTGATGGAGCAACGGGC 60.046 61.111 0.00 0.00 45.30 6.13
1004 1007 3.803082 CAACGGGCTGCCGATGTG 61.803 66.667 13.40 4.28 36.94 3.21
1005 1008 4.329545 AACGGGCTGCCGATGTGT 62.330 61.111 13.40 3.02 36.94 3.72
1006 1009 4.760047 ACGGGCTGCCGATGTGTC 62.760 66.667 13.40 0.00 36.94 3.67
1013 1016 4.856801 GCCGATGTGTCGCCCCAT 62.857 66.667 0.00 0.00 46.32 4.00
1014 1017 2.588877 CCGATGTGTCGCCCCATC 60.589 66.667 0.00 0.00 46.32 3.51
1016 1019 2.588877 GATGTGTCGCCCCATCGG 60.589 66.667 0.00 0.00 0.00 4.18
1043 1046 4.473520 CCGCCGCCCAGTGATTCT 62.474 66.667 0.00 0.00 0.00 2.40
1044 1047 2.892425 CGCCGCCCAGTGATTCTC 60.892 66.667 0.00 0.00 0.00 2.87
1045 1048 2.514824 GCCGCCCAGTGATTCTCC 60.515 66.667 0.00 0.00 0.00 3.71
1046 1049 2.190578 CCGCCCAGTGATTCTCCC 59.809 66.667 0.00 0.00 0.00 4.30
1047 1050 2.370445 CCGCCCAGTGATTCTCCCT 61.370 63.158 0.00 0.00 0.00 4.20
1048 1051 1.153289 CGCCCAGTGATTCTCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
1049 1052 1.903877 CGCCCAGTGATTCTCCCTGT 61.904 60.000 0.00 0.00 0.00 4.00
1050 1053 0.393537 GCCCAGTGATTCTCCCTGTG 60.394 60.000 0.00 0.00 0.00 3.66
1051 1054 0.254178 CCCAGTGATTCTCCCTGTGG 59.746 60.000 0.00 0.00 0.00 4.17
1052 1055 0.393537 CCAGTGATTCTCCCTGTGGC 60.394 60.000 0.00 0.00 0.00 5.01
1053 1056 0.617413 CAGTGATTCTCCCTGTGGCT 59.383 55.000 0.00 0.00 0.00 4.75
1054 1057 0.617413 AGTGATTCTCCCTGTGGCTG 59.383 55.000 0.00 0.00 0.00 4.85
1055 1058 1.028868 GTGATTCTCCCTGTGGCTGC 61.029 60.000 0.00 0.00 0.00 5.25
1056 1059 1.300963 GATTCTCCCTGTGGCTGCA 59.699 57.895 0.50 0.00 0.00 4.41
1057 1060 1.001641 ATTCTCCCTGTGGCTGCAC 60.002 57.895 0.50 0.00 0.00 4.57
1058 1061 1.495579 ATTCTCCCTGTGGCTGCACT 61.496 55.000 0.50 0.00 0.00 4.40
1059 1062 2.359602 CTCCCTGTGGCTGCACTG 60.360 66.667 0.50 2.41 0.00 3.66
1060 1063 2.848679 TCCCTGTGGCTGCACTGA 60.849 61.111 0.50 0.00 0.00 3.41
1061 1064 2.194388 CTCCCTGTGGCTGCACTGAT 62.194 60.000 0.50 0.00 0.00 2.90
1062 1065 1.303888 CCCTGTGGCTGCACTGATT 60.304 57.895 0.50 0.00 0.00 2.57
1063 1066 1.310933 CCCTGTGGCTGCACTGATTC 61.311 60.000 0.50 0.00 0.00 2.52
1064 1067 0.607217 CCTGTGGCTGCACTGATTCA 60.607 55.000 0.50 0.00 0.00 2.57
1065 1068 0.520404 CTGTGGCTGCACTGATTCAC 59.480 55.000 0.50 0.00 0.00 3.18
1066 1069 1.229975 TGTGGCTGCACTGATTCACG 61.230 55.000 0.50 0.00 0.00 4.35
1067 1070 2.327343 TGGCTGCACTGATTCACGC 61.327 57.895 0.50 0.00 0.00 5.34
1068 1071 2.037136 GGCTGCACTGATTCACGCT 61.037 57.895 0.50 0.00 0.00 5.07
1069 1072 1.134075 GCTGCACTGATTCACGCTG 59.866 57.895 0.00 5.68 0.00 5.18
1070 1073 1.572085 GCTGCACTGATTCACGCTGT 61.572 55.000 0.00 0.00 0.00 4.40
1071 1074 0.441533 CTGCACTGATTCACGCTGTC 59.558 55.000 5.25 0.00 0.00 3.51
1072 1075 1.284297 TGCACTGATTCACGCTGTCG 61.284 55.000 5.25 0.00 42.43 4.35
1073 1076 1.417592 CACTGATTCACGCTGTCGC 59.582 57.895 0.00 0.00 39.84 5.19
1074 1077 1.010935 CACTGATTCACGCTGTCGCT 61.011 55.000 0.00 0.00 39.84 4.93
1075 1078 1.010935 ACTGATTCACGCTGTCGCTG 61.011 55.000 0.00 0.00 39.84 5.18
1076 1079 2.288926 CTGATTCACGCTGTCGCTGC 62.289 60.000 0.00 0.00 39.84 5.25
1077 1080 2.357396 ATTCACGCTGTCGCTGCA 60.357 55.556 0.00 0.00 39.84 4.41
1078 1081 1.699656 GATTCACGCTGTCGCTGCAT 61.700 55.000 0.00 0.00 39.84 3.96
1079 1082 1.699656 ATTCACGCTGTCGCTGCATC 61.700 55.000 0.00 0.00 39.84 3.91
1080 1083 4.200851 CACGCTGTCGCTGCATCG 62.201 66.667 2.97 2.97 39.84 3.84
1087 1090 4.838152 TCGCTGCATCGCCCCTTC 62.838 66.667 4.79 0.00 0.00 3.46
1098 1101 4.626081 CCCCTTCGGGCCATAGCG 62.626 72.222 4.39 0.00 44.50 4.26
1099 1102 3.861797 CCCTTCGGGCCATAGCGT 61.862 66.667 4.39 0.00 41.24 5.07
1100 1103 2.280186 CCTTCGGGCCATAGCGTC 60.280 66.667 4.39 0.00 41.24 5.19
1101 1104 2.658593 CTTCGGGCCATAGCGTCG 60.659 66.667 4.39 0.00 41.24 5.12
1102 1105 4.884257 TTCGGGCCATAGCGTCGC 62.884 66.667 9.80 9.80 41.24 5.19
1106 1109 4.865761 GGCCATAGCGTCGCGACA 62.866 66.667 35.71 19.52 41.24 4.35
1107 1110 3.617538 GCCATAGCGTCGCGACAC 61.618 66.667 35.71 28.01 0.00 3.67
1108 1111 3.312504 CCATAGCGTCGCGACACG 61.313 66.667 35.71 25.68 42.95 4.49
1109 1112 2.576053 CATAGCGTCGCGACACGT 60.576 61.111 35.71 22.31 44.19 4.49
1110 1113 2.576053 ATAGCGTCGCGACACGTG 60.576 61.111 35.71 21.74 44.19 4.49
1111 1114 4.746951 TAGCGTCGCGACACGTGG 62.747 66.667 35.71 21.38 44.19 4.94
1142 1145 3.271250 CCCTGAGGTTGTTCCCATG 57.729 57.895 0.00 0.00 36.75 3.66
1143 1146 0.323725 CCCTGAGGTTGTTCCCATGG 60.324 60.000 4.14 4.14 36.75 3.66
1144 1147 0.405585 CCTGAGGTTGTTCCCATGGT 59.594 55.000 11.73 0.00 36.75 3.55
1145 1148 1.203050 CCTGAGGTTGTTCCCATGGTT 60.203 52.381 11.73 0.00 36.75 3.67
1146 1149 1.888512 CTGAGGTTGTTCCCATGGTTG 59.111 52.381 11.73 0.00 36.75 3.77
1147 1150 0.603065 GAGGTTGTTCCCATGGTTGC 59.397 55.000 11.73 0.17 36.75 4.17
1148 1151 0.105760 AGGTTGTTCCCATGGTTGCA 60.106 50.000 11.73 3.07 36.75 4.08
1149 1152 0.033366 GGTTGTTCCCATGGTTGCAC 59.967 55.000 11.73 2.01 0.00 4.57
1150 1153 0.033366 GTTGTTCCCATGGTTGCACC 59.967 55.000 11.73 0.00 39.22 5.01
1158 1161 3.743208 TGGTTGCACCACATCACG 58.257 55.556 4.16 0.00 44.79 4.35
1159 1162 2.255252 GGTTGCACCACATCACGC 59.745 61.111 0.00 0.00 38.42 5.34
1160 1163 2.127270 GTTGCACCACATCACGCG 60.127 61.111 3.53 3.53 0.00 6.01
1161 1164 4.024143 TTGCACCACATCACGCGC 62.024 61.111 5.73 0.00 0.00 6.86
1162 1165 4.986645 TGCACCACATCACGCGCT 62.987 61.111 5.73 0.00 0.00 5.92
1163 1166 4.450122 GCACCACATCACGCGCTG 62.450 66.667 5.73 3.87 0.00 5.18
1164 1167 4.450122 CACCACATCACGCGCTGC 62.450 66.667 5.73 0.00 0.00 5.25
1169 1172 4.799473 CATCACGCGCTGCCGTTG 62.799 66.667 5.73 7.06 39.83 4.10
1178 1181 2.972505 CTGCCGTTGCGTCACCTT 60.973 61.111 0.00 0.00 41.78 3.50
1179 1182 2.515057 TGCCGTTGCGTCACCTTT 60.515 55.556 0.00 0.00 41.78 3.11
1180 1183 2.058829 CTGCCGTTGCGTCACCTTTT 62.059 55.000 0.00 0.00 41.78 2.27
1181 1184 1.370051 GCCGTTGCGTCACCTTTTC 60.370 57.895 0.00 0.00 0.00 2.29
1182 1185 1.083015 CCGTTGCGTCACCTTTTCG 60.083 57.895 0.00 0.00 0.00 3.46
1183 1186 1.083015 CGTTGCGTCACCTTTTCGG 60.083 57.895 0.00 0.00 39.35 4.30
1184 1187 1.281656 GTTGCGTCACCTTTTCGGG 59.718 57.895 0.00 0.00 36.97 5.14
1185 1188 2.548295 TTGCGTCACCTTTTCGGGC 61.548 57.895 0.00 0.00 36.97 6.13
1186 1189 3.733960 GCGTCACCTTTTCGGGCC 61.734 66.667 0.00 0.00 36.97 5.80
1187 1190 3.419759 CGTCACCTTTTCGGGCCG 61.420 66.667 22.51 22.51 36.97 6.13
1188 1191 2.281276 GTCACCTTTTCGGGCCGT 60.281 61.111 27.32 1.27 36.97 5.68
1189 1192 1.004679 GTCACCTTTTCGGGCCGTA 60.005 57.895 27.32 14.78 36.97 4.02
1190 1193 1.017701 GTCACCTTTTCGGGCCGTAG 61.018 60.000 27.32 20.03 36.97 3.51
1191 1194 1.004200 CACCTTTTCGGGCCGTAGT 60.004 57.895 27.32 13.90 36.97 2.73
1192 1195 1.004200 ACCTTTTCGGGCCGTAGTG 60.004 57.895 27.32 14.45 36.97 2.74
1193 1196 2.396157 CCTTTTCGGGCCGTAGTGC 61.396 63.158 27.32 0.00 0.00 4.40
1221 1224 2.506962 GGTCAACCACCACACCGA 59.493 61.111 0.00 0.00 45.98 4.69
1222 1225 1.597027 GGTCAACCACCACACCGAG 60.597 63.158 0.00 0.00 45.98 4.63
1223 1226 1.597027 GTCAACCACCACACCGAGG 60.597 63.158 0.00 0.00 0.00 4.63
1224 1227 2.978010 CAACCACCACACCGAGGC 60.978 66.667 0.00 0.00 0.00 4.70
1225 1228 4.265056 AACCACCACACCGAGGCC 62.265 66.667 0.00 0.00 0.00 5.19
1227 1230 4.033776 CCACCACACCGAGGCCAT 62.034 66.667 5.01 0.00 0.00 4.40
1228 1231 2.436646 CACCACACCGAGGCCATC 60.437 66.667 5.01 0.00 0.00 3.51
1229 1232 2.607750 ACCACACCGAGGCCATCT 60.608 61.111 5.01 0.00 0.00 2.90
1230 1233 2.124983 CCACACCGAGGCCATCTG 60.125 66.667 5.01 0.00 0.00 2.90
1231 1234 2.821366 CACACCGAGGCCATCTGC 60.821 66.667 5.01 0.00 40.16 4.26
1395 1398 2.173782 TCTGCCAAAACTCCAACAGGTA 59.826 45.455 0.00 0.00 0.00 3.08
1439 1442 9.565090 CTCTTATGAAGATCCCATGTATTTTGA 57.435 33.333 8.09 0.00 36.82 2.69
1462 1465 3.951775 TTGTGCCACAACTTTCAAAGT 57.048 38.095 6.08 0.00 45.46 2.66
1499 1502 0.603065 GGCTCCCGTTTGCAAAAGAT 59.397 50.000 24.13 0.00 0.00 2.40
1519 1522 5.715070 AGATCCTTGAGTTAAGTCAGTTCG 58.285 41.667 12.62 4.17 34.45 3.95
1554 1557 4.464244 CCTTCCATAAGCGATCTCCATCTA 59.536 45.833 0.00 0.00 0.00 1.98
1568 1571 8.572185 CGATCTCCATCTAGATTTTAGAAGTGA 58.428 37.037 1.33 0.00 36.33 3.41
1640 1801 6.389830 TCAGCAAACTACAACATGTGAATT 57.610 33.333 0.00 0.00 0.00 2.17
1649 1810 7.541162 ACTACAACATGTGAATTTGGATCATG 58.459 34.615 0.00 0.00 40.80 3.07
1708 1869 1.719063 TTGAAGCTGCACCCTCCCTT 61.719 55.000 0.00 0.00 0.00 3.95
1715 1876 1.630878 CTGCACCCTCCCTTAAAGAGT 59.369 52.381 0.00 0.00 0.00 3.24
1740 1902 6.486941 TGTGCATCACATATGGGATCATTAT 58.513 36.000 17.83 0.00 39.62 1.28
1769 1931 2.031012 CACAGGCGCAGAGTTCCA 59.969 61.111 10.83 0.00 0.00 3.53
1770 1932 1.597854 CACAGGCGCAGAGTTCCAA 60.598 57.895 10.83 0.00 0.00 3.53
1800 1962 0.593128 GTTTGTGCGACAAGGCAGAT 59.407 50.000 0.00 0.00 44.93 2.90
1844 2006 3.318839 CCTGGTTTCAAGCACAAGAATCA 59.681 43.478 0.00 0.00 32.29 2.57
1882 2052 4.821589 GCTTCCAGCCCGACGAGG 62.822 72.222 0.00 0.00 34.48 4.63
2271 2443 9.330063 CTAATATCAAGTCAAAAGGTATCTGCA 57.670 33.333 0.00 0.00 0.00 4.41
2473 2647 4.777896 GTGGCCTATAATGAGATCACCCTA 59.222 45.833 3.32 0.00 0.00 3.53
2532 3092 1.619654 CTCAGTTTGGTTGGGATGCA 58.380 50.000 0.00 0.00 0.00 3.96
2617 3177 2.765785 CGCGTCGTTCTTCTGCTG 59.234 61.111 0.00 0.00 0.00 4.41
2802 3371 4.184649 ACCTTTCCTGTTCCACAAAGAT 57.815 40.909 0.00 0.00 0.00 2.40
2847 3416 2.568956 AGCTTATCAGTTGAGCACCTCA 59.431 45.455 0.00 0.00 38.87 3.86
3031 3676 7.692460 TCTCAAAATGTAGCATCAAAGTCAT 57.308 32.000 0.00 0.00 0.00 3.06
3056 3701 5.116180 CAAAGCATTAAGAGTATCACCCGA 58.884 41.667 0.00 0.00 37.82 5.14
3068 3713 1.496060 TCACCCGACCTCTGCATAAT 58.504 50.000 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.848053 ATTACCATTGTACCCCCGGG 59.152 55.000 15.80 15.80 42.03 5.73
11 12 1.202842 GGATTACCATTGTACCCCCGG 60.203 57.143 0.00 0.00 35.97 5.73
12 13 1.541670 CGGATTACCATTGTACCCCCG 60.542 57.143 0.00 0.00 35.59 5.73
13 14 1.202842 CCGGATTACCATTGTACCCCC 60.203 57.143 0.00 0.00 35.59 5.40
14 15 1.816572 GCCGGATTACCATTGTACCCC 60.817 57.143 5.05 0.00 35.59 4.95
15 16 1.142262 AGCCGGATTACCATTGTACCC 59.858 52.381 5.05 0.00 35.59 3.69
16 17 2.632987 AGCCGGATTACCATTGTACC 57.367 50.000 5.05 0.00 35.59 3.34
17 18 3.660865 CCTAGCCGGATTACCATTGTAC 58.339 50.000 5.05 0.00 35.59 2.90
18 19 2.038033 GCCTAGCCGGATTACCATTGTA 59.962 50.000 5.05 0.00 35.59 2.41
19 20 1.202770 GCCTAGCCGGATTACCATTGT 60.203 52.381 5.05 0.00 35.59 2.71
20 21 1.523758 GCCTAGCCGGATTACCATTG 58.476 55.000 5.05 0.00 35.59 2.82
21 22 0.034896 CGCCTAGCCGGATTACCATT 59.965 55.000 5.05 0.00 35.59 3.16
22 23 1.119574 ACGCCTAGCCGGATTACCAT 61.120 55.000 5.05 0.00 35.59 3.55
23 24 1.759299 ACGCCTAGCCGGATTACCA 60.759 57.895 5.05 0.00 35.59 3.25
24 25 1.300697 CACGCCTAGCCGGATTACC 60.301 63.158 5.05 0.00 33.16 2.85
25 26 1.300697 CCACGCCTAGCCGGATTAC 60.301 63.158 5.05 0.00 33.16 1.89
26 27 2.504274 CCCACGCCTAGCCGGATTA 61.504 63.158 5.05 0.00 33.16 1.75
27 28 3.861797 CCCACGCCTAGCCGGATT 61.862 66.667 5.05 0.00 33.16 3.01
39 40 1.956629 ATAGACGACTTGGCCCCACG 61.957 60.000 0.00 3.54 0.00 4.94
40 41 0.462047 CATAGACGACTTGGCCCCAC 60.462 60.000 0.00 0.00 0.00 4.61
41 42 0.907704 ACATAGACGACTTGGCCCCA 60.908 55.000 0.00 0.00 0.00 4.96
42 43 0.179081 GACATAGACGACTTGGCCCC 60.179 60.000 0.00 0.00 0.00 5.80
43 44 0.824759 AGACATAGACGACTTGGCCC 59.175 55.000 0.00 0.00 0.00 5.80
44 45 2.541178 CGTAGACATAGACGACTTGGCC 60.541 54.545 0.00 0.00 41.60 5.36
45 46 2.717530 CGTAGACATAGACGACTTGGC 58.282 52.381 0.00 0.00 41.60 4.52
46 47 2.355132 AGCGTAGACATAGACGACTTGG 59.645 50.000 0.00 0.00 41.60 3.61
47 48 3.310227 AGAGCGTAGACATAGACGACTTG 59.690 47.826 0.00 0.00 41.60 3.16
48 49 3.533547 AGAGCGTAGACATAGACGACTT 58.466 45.455 0.00 0.00 41.60 3.01
49 50 3.125316 GAGAGCGTAGACATAGACGACT 58.875 50.000 0.00 0.00 41.60 4.18
50 51 2.221517 GGAGAGCGTAGACATAGACGAC 59.778 54.545 0.00 0.00 41.60 4.34
51 52 2.481854 GGAGAGCGTAGACATAGACGA 58.518 52.381 0.00 0.00 41.60 4.20
52 53 1.192757 CGGAGAGCGTAGACATAGACG 59.807 57.143 0.00 0.00 41.97 4.18
53 54 1.532007 CCGGAGAGCGTAGACATAGAC 59.468 57.143 0.00 0.00 0.00 2.59
54 55 1.880271 CCGGAGAGCGTAGACATAGA 58.120 55.000 0.00 0.00 0.00 1.98
55 56 0.238817 GCCGGAGAGCGTAGACATAG 59.761 60.000 5.05 0.00 0.00 2.23
56 57 0.179026 AGCCGGAGAGCGTAGACATA 60.179 55.000 5.05 0.00 38.01 2.29
57 58 1.038130 AAGCCGGAGAGCGTAGACAT 61.038 55.000 5.05 0.00 38.01 3.06
58 59 1.654954 GAAGCCGGAGAGCGTAGACA 61.655 60.000 5.05 0.00 38.01 3.41
59 60 1.064458 GAAGCCGGAGAGCGTAGAC 59.936 63.158 5.05 0.00 38.01 2.59
60 61 0.179702 TAGAAGCCGGAGAGCGTAGA 59.820 55.000 5.05 0.00 38.01 2.59
61 62 0.308376 GTAGAAGCCGGAGAGCGTAG 59.692 60.000 5.05 0.00 38.01 3.51
62 63 1.434622 CGTAGAAGCCGGAGAGCGTA 61.435 60.000 5.05 0.00 38.01 4.42
63 64 2.762234 CGTAGAAGCCGGAGAGCGT 61.762 63.158 5.05 0.00 38.01 5.07
64 65 2.024871 CGTAGAAGCCGGAGAGCG 59.975 66.667 5.05 0.00 38.01 5.03
65 66 2.278923 GCGTAGAAGCCGGAGAGC 60.279 66.667 5.05 0.00 0.00 4.09
220 222 1.078848 ACCAGGATCGAGCAACAGC 60.079 57.895 1.84 0.00 0.00 4.40
230 232 2.501610 GCCCTCGTCACCAGGATC 59.498 66.667 0.00 0.00 31.91 3.36
248 250 1.360551 CCATGCCTACCTCGACGAG 59.639 63.158 18.08 18.08 0.00 4.18
290 292 1.299468 GGTGAGGCTACAGCGATCG 60.299 63.158 11.69 11.69 43.26 3.69
295 297 1.884926 GATGCGGTGAGGCTACAGC 60.885 63.158 10.51 10.51 41.27 4.40
418 421 3.318191 CCCCTTCAGGCAGAGAGG 58.682 66.667 0.00 0.00 0.00 3.69
648 651 4.394712 AAGAAGCCGGCTCCCACG 62.395 66.667 32.93 0.00 0.00 4.94
735 738 3.441011 CTATCGAAAGGCGGCCCGT 62.441 63.158 17.02 3.02 41.33 5.28
747 750 4.533124 TCCCAGGCCGGCTATCGA 62.533 66.667 28.56 14.34 42.43 3.59
911 914 4.193334 TCGATGAGCGGGCTGACG 62.193 66.667 0.00 1.32 41.33 4.35
912 915 2.583593 GTCGATGAGCGGGCTGAC 60.584 66.667 0.00 0.00 41.33 3.51
913 916 2.904178 TAGGTCGATGAGCGGGCTGA 62.904 60.000 0.00 0.00 41.33 4.26
914 917 2.490148 TAGGTCGATGAGCGGGCTG 61.490 63.158 0.00 0.00 41.33 4.85
915 918 2.123854 TAGGTCGATGAGCGGGCT 60.124 61.111 0.00 0.00 41.33 5.19
916 919 2.027751 GTAGGTCGATGAGCGGGC 59.972 66.667 0.00 0.00 41.33 6.13
917 920 2.331805 CGTAGGTCGATGAGCGGG 59.668 66.667 0.00 0.00 42.86 6.13
918 921 1.009900 GACGTAGGTCGATGAGCGG 60.010 63.158 0.00 0.00 42.86 5.52
919 922 4.591852 GACGTAGGTCGATGAGCG 57.408 61.111 0.00 0.00 42.86 5.03
927 930 1.154073 GTGACAGCCGACGTAGGTC 60.154 63.158 16.51 8.61 39.89 3.85
928 931 2.633509 GGTGACAGCCGACGTAGGT 61.634 63.158 16.51 0.00 0.00 3.08
929 932 2.181021 GGTGACAGCCGACGTAGG 59.819 66.667 10.78 10.78 0.00 3.18
939 942 4.394712 GGGACAGGGCGGTGACAG 62.395 72.222 0.00 0.00 0.00 3.51
946 949 4.452733 GAACTCGGGGACAGGGCG 62.453 72.222 0.00 0.00 0.00 6.13
947 950 3.316573 CTGAACTCGGGGACAGGGC 62.317 68.421 3.55 0.00 0.00 5.19
948 951 2.982130 CTGAACTCGGGGACAGGG 59.018 66.667 3.55 0.00 0.00 4.45
949 952 2.266055 GCTGAACTCGGGGACAGG 59.734 66.667 11.75 0.00 0.00 4.00
950 953 1.374758 GTGCTGAACTCGGGGACAG 60.375 63.158 6.62 6.62 0.00 3.51
951 954 2.741092 GTGCTGAACTCGGGGACA 59.259 61.111 0.00 0.00 0.00 4.02
952 955 2.432628 CGTGCTGAACTCGGGGAC 60.433 66.667 0.00 0.00 0.00 4.46
953 956 4.373116 GCGTGCTGAACTCGGGGA 62.373 66.667 0.00 0.00 35.83 4.81
957 960 4.379243 AGGGGCGTGCTGAACTCG 62.379 66.667 0.00 0.00 38.28 4.18
958 961 2.435059 GAGGGGCGTGCTGAACTC 60.435 66.667 0.00 0.00 0.00 3.01
959 962 4.021925 GGAGGGGCGTGCTGAACT 62.022 66.667 0.00 0.00 0.00 3.01
960 963 4.329545 TGGAGGGGCGTGCTGAAC 62.330 66.667 0.00 0.00 0.00 3.18
961 964 4.329545 GTGGAGGGGCGTGCTGAA 62.330 66.667 0.00 0.00 0.00 3.02
965 968 4.101448 ATCAGTGGAGGGGCGTGC 62.101 66.667 0.00 0.00 0.00 5.34
966 969 2.124983 CATCAGTGGAGGGGCGTG 60.125 66.667 0.00 0.00 0.00 5.34
976 979 2.401766 GCCCGTTGCTCCATCAGTG 61.402 63.158 0.00 0.00 36.87 3.66
977 980 2.045926 GCCCGTTGCTCCATCAGT 60.046 61.111 0.00 0.00 36.87 3.41
1026 1029 4.473520 AGAATCACTGGGCGGCGG 62.474 66.667 9.78 0.34 0.00 6.13
1027 1030 2.892425 GAGAATCACTGGGCGGCG 60.892 66.667 0.51 0.51 33.17 6.46
1028 1031 2.514824 GGAGAATCACTGGGCGGC 60.515 66.667 0.00 0.00 36.25 6.53
1029 1032 2.190578 GGGAGAATCACTGGGCGG 59.809 66.667 0.00 0.00 33.91 6.13
1036 1039 1.028868 GCAGCCACAGGGAGAATCAC 61.029 60.000 0.00 0.00 40.51 3.06
1037 1040 1.300963 GCAGCCACAGGGAGAATCA 59.699 57.895 0.00 0.00 36.25 2.57
1038 1041 1.028868 GTGCAGCCACAGGGAGAATC 61.029 60.000 0.00 0.00 41.67 2.52
1039 1042 1.001641 GTGCAGCCACAGGGAGAAT 60.002 57.895 0.00 0.00 41.67 2.40
1040 1043 2.149383 AGTGCAGCCACAGGGAGAA 61.149 57.895 0.00 0.00 44.53 2.87
1041 1044 2.527624 AGTGCAGCCACAGGGAGA 60.528 61.111 0.00 0.00 44.53 3.71
1042 1045 2.194388 ATCAGTGCAGCCACAGGGAG 62.194 60.000 0.00 0.00 44.53 4.30
1043 1046 1.782201 AATCAGTGCAGCCACAGGGA 61.782 55.000 0.00 0.00 44.53 4.20
1044 1047 1.303888 AATCAGTGCAGCCACAGGG 60.304 57.895 0.00 0.00 44.53 4.45
1045 1048 0.607217 TGAATCAGTGCAGCCACAGG 60.607 55.000 0.00 0.00 44.53 4.00
1046 1049 0.520404 GTGAATCAGTGCAGCCACAG 59.480 55.000 0.00 0.00 44.53 3.66
1047 1050 1.229975 CGTGAATCAGTGCAGCCACA 61.230 55.000 0.00 0.00 44.53 4.17
1048 1051 1.499056 CGTGAATCAGTGCAGCCAC 59.501 57.895 0.00 0.00 42.39 5.01
1049 1052 2.327343 GCGTGAATCAGTGCAGCCA 61.327 57.895 2.92 0.00 0.00 4.75
1050 1053 2.037136 AGCGTGAATCAGTGCAGCC 61.037 57.895 9.61 0.00 0.00 4.85
1051 1054 1.134075 CAGCGTGAATCAGTGCAGC 59.866 57.895 9.61 0.00 0.00 5.25
1052 1055 0.441533 GACAGCGTGAATCAGTGCAG 59.558 55.000 9.61 4.59 0.00 4.41
1053 1056 1.284297 CGACAGCGTGAATCAGTGCA 61.284 55.000 9.61 0.00 0.00 4.57
1054 1057 1.417592 CGACAGCGTGAATCAGTGC 59.582 57.895 0.00 0.00 0.00 4.40
1055 1058 1.417592 GCGACAGCGTGAATCAGTG 59.582 57.895 0.00 0.00 40.36 3.66
1056 1059 3.862124 GCGACAGCGTGAATCAGT 58.138 55.556 0.00 0.00 40.36 3.41
1070 1073 4.838152 GAAGGGGCGATGCAGCGA 62.838 66.667 30.90 0.00 38.18 4.93
1084 1087 2.658593 CGACGCTATGGCCCGAAG 60.659 66.667 0.00 0.00 34.53 3.79
1085 1088 4.884257 GCGACGCTATGGCCCGAA 62.884 66.667 13.73 0.00 34.53 4.30
1089 1092 4.865761 TGTCGCGACGCTATGGCC 62.866 66.667 31.88 7.69 34.44 5.36
1090 1093 3.617538 GTGTCGCGACGCTATGGC 61.618 66.667 37.89 17.00 38.69 4.40
1091 1094 3.312504 CGTGTCGCGACGCTATGG 61.313 66.667 39.77 25.79 44.77 2.74
1092 1095 2.576053 ACGTGTCGCGACGCTATG 60.576 61.111 39.77 29.82 43.33 2.23
1093 1096 2.576053 CACGTGTCGCGACGCTAT 60.576 61.111 39.77 28.92 43.33 2.97
1094 1097 4.746951 CCACGTGTCGCGACGCTA 62.747 66.667 39.77 20.83 43.33 4.26
1116 1119 4.003788 AACCTCAGGGTGACGGCG 62.004 66.667 4.80 4.80 46.67 6.46
1117 1120 2.358737 CAACCTCAGGGTGACGGC 60.359 66.667 0.71 0.00 46.67 5.68
1118 1121 0.602905 GAACAACCTCAGGGTGACGG 60.603 60.000 18.43 0.00 46.67 4.79
1119 1122 0.602905 GGAACAACCTCAGGGTGACG 60.603 60.000 18.43 0.00 46.67 4.35
1120 1123 0.250770 GGGAACAACCTCAGGGTGAC 60.251 60.000 18.43 9.02 46.67 3.67
1121 1124 0.696143 TGGGAACAACCTCAGGGTGA 60.696 55.000 18.43 0.00 46.67 4.02
1122 1125 0.405585 ATGGGAACAACCTCAGGGTG 59.594 55.000 7.41 7.41 46.67 4.61
1143 1146 2.127270 CGCGTGATGTGGTGCAAC 60.127 61.111 0.00 0.00 0.00 4.17
1144 1147 4.024143 GCGCGTGATGTGGTGCAA 62.024 61.111 8.43 0.00 39.38 4.08
1145 1148 4.986645 AGCGCGTGATGTGGTGCA 62.987 61.111 8.43 0.00 41.92 4.57
1152 1155 4.799473 CAACGGCAGCGCGTGATG 62.799 66.667 10.41 10.41 33.68 3.07
1162 1165 2.054140 GAAAAGGTGACGCAACGGCA 62.054 55.000 0.00 0.00 45.13 5.69
1163 1166 1.370051 GAAAAGGTGACGCAACGGC 60.370 57.895 0.00 0.00 34.27 5.68
1164 1167 1.083015 CGAAAAGGTGACGCAACGG 60.083 57.895 0.00 0.00 0.00 4.44
1165 1168 1.083015 CCGAAAAGGTGACGCAACG 60.083 57.895 0.00 0.00 34.51 4.10
1166 1169 1.281656 CCCGAAAAGGTGACGCAAC 59.718 57.895 0.00 0.00 38.74 4.17
1167 1170 2.548295 GCCCGAAAAGGTGACGCAA 61.548 57.895 0.00 0.00 38.74 4.85
1168 1171 2.975799 GCCCGAAAAGGTGACGCA 60.976 61.111 0.00 0.00 38.74 5.24
1169 1172 3.733960 GGCCCGAAAAGGTGACGC 61.734 66.667 0.00 0.00 38.74 5.19
1170 1173 2.768503 TACGGCCCGAAAAGGTGACG 62.769 60.000 11.71 0.00 44.11 4.35
1171 1174 1.004679 TACGGCCCGAAAAGGTGAC 60.005 57.895 11.71 0.00 38.74 3.67
1172 1175 1.294138 CTACGGCCCGAAAAGGTGA 59.706 57.895 11.71 0.00 38.74 4.02
1173 1176 1.004200 ACTACGGCCCGAAAAGGTG 60.004 57.895 11.71 0.00 38.74 4.00
1174 1177 1.004200 CACTACGGCCCGAAAAGGT 60.004 57.895 11.71 0.00 38.74 3.50
1175 1178 2.396157 GCACTACGGCCCGAAAAGG 61.396 63.158 11.71 0.00 40.63 3.11
1176 1179 3.174788 GCACTACGGCCCGAAAAG 58.825 61.111 11.71 6.76 0.00 2.27
1204 1207 1.597027 CTCGGTGTGGTGGTTGACC 60.597 63.158 0.00 0.00 46.37 4.02
1205 1208 1.597027 CCTCGGTGTGGTGGTTGAC 60.597 63.158 0.00 0.00 0.00 3.18
1206 1209 2.825982 CCTCGGTGTGGTGGTTGA 59.174 61.111 0.00 0.00 0.00 3.18
1207 1210 2.978010 GCCTCGGTGTGGTGGTTG 60.978 66.667 0.00 0.00 0.00 3.77
1208 1211 4.265056 GGCCTCGGTGTGGTGGTT 62.265 66.667 0.00 0.00 0.00 3.67
1210 1213 3.976701 GATGGCCTCGGTGTGGTGG 62.977 68.421 3.32 0.00 0.00 4.61
1211 1214 2.436646 GATGGCCTCGGTGTGGTG 60.437 66.667 3.32 0.00 0.00 4.17
1212 1215 2.607750 AGATGGCCTCGGTGTGGT 60.608 61.111 3.32 0.00 0.00 4.16
1213 1216 2.124983 CAGATGGCCTCGGTGTGG 60.125 66.667 3.32 0.00 0.00 4.17
1214 1217 2.821366 GCAGATGGCCTCGGTGTG 60.821 66.667 3.32 0.00 36.11 3.82
1215 1218 3.005539 AGCAGATGGCCTCGGTGT 61.006 61.111 3.32 0.00 46.50 4.16
1216 1219 2.202987 GAGCAGATGGCCTCGGTG 60.203 66.667 3.32 0.00 46.50 4.94
1217 1220 3.474570 GGAGCAGATGGCCTCGGT 61.475 66.667 3.32 1.78 46.50 4.69
1218 1221 3.160047 AGGAGCAGATGGCCTCGG 61.160 66.667 3.32 0.86 46.50 4.63
1219 1222 2.108566 CAGGAGCAGATGGCCTCG 59.891 66.667 3.32 0.00 46.50 4.63
1220 1223 1.446791 CTCAGGAGCAGATGGCCTC 59.553 63.158 3.32 0.00 46.50 4.70
1221 1224 3.644719 CTCAGGAGCAGATGGCCT 58.355 61.111 3.32 0.00 46.50 5.19
1231 1234 0.605860 AGCTTGCAAGTGCTCAGGAG 60.606 55.000 26.55 0.00 42.66 3.69
1409 1412 6.566079 ACATGGGATCTTCATAAGAGAACA 57.434 37.500 0.00 0.00 41.61 3.18
1439 1442 5.244755 ACTTTGAAAGTTGTGGCACAAAAT 58.755 33.333 32.60 21.75 38.13 1.82
1499 1502 4.931661 ACGAACTGACTTAACTCAAGGA 57.068 40.909 0.00 0.00 38.70 3.36
1519 1522 6.027749 CGCTTATGGAAGGAACATTAACAAC 58.972 40.000 0.00 0.00 32.84 3.32
1640 1801 1.912731 TCCTTCGGGAACATGATCCAA 59.087 47.619 22.18 9.08 41.89 3.53
1715 1876 5.141910 AATGATCCCATATGTGATGCACAA 58.858 37.500 5.33 0.00 38.84 3.33
1740 1902 0.522626 CGCCTGTGAACATGATGCAA 59.477 50.000 0.00 0.00 0.00 4.08
1769 1931 3.868661 GTCGCACAAACCATTTTCCTTTT 59.131 39.130 0.00 0.00 0.00 2.27
1770 1932 3.118956 TGTCGCACAAACCATTTTCCTTT 60.119 39.130 0.00 0.00 0.00 3.11
1800 1962 2.421952 GGCATATGGCTTCCACTTCAGA 60.422 50.000 21.32 0.00 44.01 3.27
1844 2006 4.696479 CCATAGATGGTGAGCTTAACCT 57.304 45.455 17.62 0.00 43.05 3.50
1881 2051 1.368850 GCACAAAGTTGTCGTCGCC 60.369 57.895 0.00 0.00 39.91 5.54
1882 2052 1.717728 CGCACAAAGTTGTCGTCGC 60.718 57.895 0.00 0.00 39.91 5.19
1883 2053 0.506932 ATCGCACAAAGTTGTCGTCG 59.493 50.000 12.44 8.71 39.91 5.12
1884 2054 2.473609 TGTATCGCACAAAGTTGTCGTC 59.526 45.455 12.44 7.83 39.91 4.20
1885 2055 2.475818 TGTATCGCACAAAGTTGTCGT 58.524 42.857 12.44 6.33 39.91 4.34
1886 2056 3.122780 TCATGTATCGCACAAAGTTGTCG 59.877 43.478 0.00 2.32 41.55 4.35
1967 2137 1.893808 GTCACCACAGTGCCCACAG 60.894 63.158 0.00 0.00 44.16 3.66
2473 2647 2.607750 ATGGCTGGTGGTCGAGGT 60.608 61.111 0.00 0.00 0.00 3.85
2532 3092 2.856000 AGAACCACAGCCTGGCCT 60.856 61.111 16.57 0.00 45.32 5.19
2802 3371 4.669866 TCTACTACTCCCAGAGGTGAAA 57.330 45.455 0.00 0.00 33.35 2.69
2847 3416 4.036498 ACAGTCTATTCATACGTAAGCGCT 59.964 41.667 2.64 2.64 42.83 5.92
3031 3676 6.046593 CGGGTGATACTCTTAATGCTTTGTA 58.953 40.000 0.00 0.00 0.00 2.41
3068 3713 3.814625 TGTTTGACTGTGTGCATCCTAA 58.185 40.909 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.