Multiple sequence alignment - TraesCS7B01G134900

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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 TraesCS7B01G134900 chr7B 100.000 4717 0 0 912 5628 164973871 164978587 0.000000e+00 8711.0
1 TraesCS7B01G134900 chr7B 100.000 638 0 0 1 638 164972960 164973597 0.000000e+00 1179.0
2 TraesCS7B01G134900 chr7A 94.156 3696 160 29 1318 4976 211808221 211811897 0.000000e+00 5578.0
3 TraesCS7B01G134900 chr7A 89.796 784 45 11 948 1725 211807880 211808634 0.000000e+00 972.0
4 TraesCS7B01G134900 chr7A 87.611 452 29 13 5185 5626 211812012 211812446 3.030000e-137 499.0
5 TraesCS7B01G134900 chr7A 84.109 258 18 15 385 637 211807567 211807806 1.580000e-55 228.0
6 TraesCS7B01G134900 chr7A 95.556 45 2 0 2139 2183 667231746 667231790 7.820000e-09 73.1
7 TraesCS7B01G134900 chr7A 95.122 41 2 0 2145 2185 78450323 78450363 1.310000e-06 65.8
8 TraesCS7B01G134900 chr7A 85.714 63 8 1 2123 2184 458990869 458990931 1.310000e-06 65.8
9 TraesCS7B01G134900 chr7D 92.360 3992 182 50 912 4832 199914303 199918242 0.000000e+00 5568.0
10 TraesCS7B01G134900 chr7D 86.636 434 29 16 5198 5628 199918724 199919131 2.390000e-123 453.0
11 TraesCS7B01G134900 chr7D 85.635 362 18 10 310 637 199913931 199914292 3.230000e-92 350.0
12 TraesCS7B01G134900 chr7D 91.304 184 10 4 147 324 199910369 199910552 4.350000e-61 246.0
13 TraesCS7B01G134900 chr7D 86.792 159 14 4 2 160 199910204 199910355 2.700000e-38 171.0
14 TraesCS7B01G134900 chr7D 94.118 102 3 3 5084 5185 481573849 481573751 9.770000e-33 152.0
15 TraesCS7B01G134900 chr5A 81.324 589 106 4 3533 4119 471916749 471917335 5.100000e-130 475.0
16 TraesCS7B01G134900 chr5A 96.296 54 2 0 2135 2188 56731891 56731838 7.770000e-14 89.8
17 TraesCS7B01G134900 chr5B 80.815 589 109 4 3533 4119 438220048 438220634 5.140000e-125 459.0
18 TraesCS7B01G134900 chr5D 80.862 580 108 3 3533 4111 369388712 369389289 2.390000e-123 453.0
19 TraesCS7B01G134900 chr5D 98.876 89 1 0 5095 5183 29115604 29115692 5.840000e-35 159.0
20 TraesCS7B01G134900 chr5D 96.000 50 1 1 2135 2183 518875200 518875249 4.670000e-11 80.5
21 TraesCS7B01G134900 chr2B 95.050 101 5 0 5086 5186 36422943 36423043 5.840000e-35 159.0
22 TraesCS7B01G134900 chr2B 95.833 96 3 1 5090 5185 5009047 5009141 2.720000e-33 154.0
23 TraesCS7B01G134900 chr3B 96.809 94 3 0 5094 5187 719780151 719780244 2.100000e-34 158.0
24 TraesCS7B01G134900 chr1D 96.809 94 3 0 5092 5185 467803505 467803598 2.100000e-34 158.0
25 TraesCS7B01G134900 chr1D 96.774 93 3 0 5093 5185 211632332 211632424 7.550000e-34 156.0
26 TraesCS7B01G134900 chr2A 94.898 98 5 0 5097 5194 48468095 48467998 2.720000e-33 154.0
27 TraesCS7B01G134900 chr1A 93.204 103 4 3 5079 5181 313905838 313905937 1.260000e-31 148.0
28 TraesCS7B01G134900 chr1A 87.755 49 6 0 2135 2183 29250872 29250824 2.190000e-04 58.4
29 TraesCS7B01G134900 chr4A 93.878 49 3 0 2135 2183 98595153 98595201 2.170000e-09 75.0
30 TraesCS7B01G134900 chr4A 97.436 39 1 0 3799 3837 161172148 161172110 3.640000e-07 67.6
31 TraesCS7B01G134900 chr4B 89.091 55 4 2 449 502 634172188 634172241 3.640000e-07 67.6


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 TraesCS7B01G134900 chr7B 164972960 164978587 5627 False 4945.00 8711 100.0000 1 5628 2 chr7B.!!$F1 5627
1 TraesCS7B01G134900 chr7A 211807567 211812446 4879 False 1819.25 5578 88.9180 385 5626 4 chr7A.!!$F4 5241
2 TraesCS7B01G134900 chr7D 199910204 199919131 8927 False 1357.60 5568 88.5454 2 5628 5 chr7D.!!$F1 5626
3 TraesCS7B01G134900 chr5A 471916749 471917335 586 False 475.00 475 81.3240 3533 4119 1 chr5A.!!$F1 586
4 TraesCS7B01G134900 chr5B 438220048 438220634 586 False 459.00 459 80.8150 3533 4119 1 chr5B.!!$F1 586
5 TraesCS7B01G134900 chr5D 369388712 369389289 577 False 453.00 453 80.8620 3533 4111 1 chr5D.!!$F2 578

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
44 45 0.037975 TTCCGTTCGCTAGGACAACC 60.038 55.000 0.00 0.0 36.06 3.77 F
1226 4715 0.037326 TGGTGATCTTCGCAGTGACC 60.037 55.000 0.00 0.0 0.00 4.02 F
1272 4761 0.248458 CAATTTGGTATGGCCGCGTC 60.248 55.000 4.92 0.0 41.21 5.19 F
1361 4850 0.685097 ACTGAAGCTTTGCGGTCCTA 59.315 50.000 0.00 0.0 0.00 2.94 F
2185 5710 1.263356 TTGGAACGGAGGGAGTACTG 58.737 55.000 0.00 0.0 0.00 2.74 F
2772 6300 1.403514 GGACCAGTTGAGAAGAGCGAG 60.404 57.143 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1322 4811 0.037232 CGACCTCCGAAAGCCTTTCT 60.037 55.000 14.82 0.0 41.76 2.52 R
3176 6705 0.976641 TTAGCTGCTACCTGTGCTGT 59.023 50.000 9.27 0.0 37.02 4.40 R
3270 6799 6.212888 ACTTGTCTTGATATGGAAAATGCC 57.787 37.500 0.00 0.0 0.00 4.40 R
3314 6843 8.743085 ACATTGTCAGAGAATAATGCATAGTT 57.257 30.769 0.00 0.0 34.69 2.24 R
3610 7141 0.996583 AGCTTTAACCGGGGGATTCA 59.003 50.000 6.32 0.0 0.00 2.57 R
4763 8320 0.698238 ATTCCACAAGGCCTGCTACA 59.302 50.000 5.69 0.0 33.74 2.74 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
24 25 4.344102 AGGGAGGATCAATTTATCGAACGA 59.656 41.667 0.00 0.00 36.25 3.85
27 28 6.128526 GGGAGGATCAATTTATCGAACGATTC 60.129 42.308 14.61 4.93 36.25 2.52
40 41 2.869354 CGATTCCGTTCGCTAGGAC 58.131 57.895 0.00 0.00 36.06 3.85
42 43 1.468565 CGATTCCGTTCGCTAGGACAA 60.469 52.381 0.00 0.00 36.06 3.18
44 45 0.037975 TTCCGTTCGCTAGGACAACC 60.038 55.000 0.00 0.00 36.06 3.77
54 55 2.202756 GGACAACCTCCTAGCGCG 60.203 66.667 0.00 0.00 35.89 6.86
55 56 2.886124 GACAACCTCCTAGCGCGC 60.886 66.667 26.66 26.66 0.00 6.86
56 57 4.796231 ACAACCTCCTAGCGCGCG 62.796 66.667 28.44 28.44 0.00 6.86
122 123 1.202065 CCCAACGTCATCATTGCGAAG 60.202 52.381 0.00 0.00 0.00 3.79
127 128 2.413112 ACGTCATCATTGCGAAGAACAG 59.587 45.455 0.00 0.00 0.00 3.16
180 206 5.401531 TGGTGACTACTAACAAGCCTTAG 57.598 43.478 0.00 0.00 0.00 2.18
181 207 4.182339 GGTGACTACTAACAAGCCTTAGC 58.818 47.826 0.00 0.00 40.32 3.09
204 230 4.507157 CCCTGGAATTTGGGCTTGATTTTT 60.507 41.667 0.00 0.00 36.61 1.94
205 231 4.696877 CCTGGAATTTGGGCTTGATTTTTC 59.303 41.667 0.00 0.00 0.00 2.29
242 273 7.117285 TGCCAAATATGTAAATACAATGCCA 57.883 32.000 0.00 0.00 39.99 4.92
324 356 3.181475 ACGAGCAGACCATACCAGTTATG 60.181 47.826 0.00 0.00 37.86 1.90
325 357 3.068165 CGAGCAGACCATACCAGTTATGA 59.932 47.826 0.00 0.00 40.27 2.15
326 358 4.441495 CGAGCAGACCATACCAGTTATGAA 60.441 45.833 0.00 0.00 40.27 2.57
327 359 5.428253 GAGCAGACCATACCAGTTATGAAA 58.572 41.667 0.00 0.00 40.27 2.69
328 360 5.186198 AGCAGACCATACCAGTTATGAAAC 58.814 41.667 0.00 0.00 40.27 2.78
359 3784 9.680315 AAAATGCCAATAATTGAAAAACACATG 57.320 25.926 0.00 0.00 0.00 3.21
362 3787 7.166851 TGCCAATAATTGAAAAACACATGGAT 58.833 30.769 0.00 0.00 0.00 3.41
518 3949 8.351495 TGCTTTGTTCAACAATTTTCTATGTC 57.649 30.769 3.17 0.00 38.00 3.06
614 4074 1.789576 ATCCCGCCCCAAACAGAACT 61.790 55.000 0.00 0.00 0.00 3.01
637 4097 0.893727 GGAACGTGGCAACCCTGATT 60.894 55.000 0.00 0.00 0.00 2.57
957 4444 2.701780 GCGGAGGTCTCAGAAGCGA 61.702 63.158 2.43 0.00 0.00 4.93
1144 4631 4.446413 CCGCCCGTACGCCTCTTT 62.446 66.667 10.49 0.00 0.00 2.52
1148 4635 2.186125 CCGTACGCCTCTTTCCCC 59.814 66.667 10.49 0.00 0.00 4.81
1149 4636 2.652095 CCGTACGCCTCTTTCCCCA 61.652 63.158 10.49 0.00 0.00 4.96
1150 4637 1.294138 CGTACGCCTCTTTCCCCAA 59.706 57.895 0.52 0.00 0.00 4.12
1151 4638 0.320946 CGTACGCCTCTTTCCCCAAA 60.321 55.000 0.52 0.00 0.00 3.28
1156 4643 0.900182 GCCTCTTTCCCCAAACCCTG 60.900 60.000 0.00 0.00 0.00 4.45
1164 4651 4.383602 CCAAACCCTGCGTTCGCG 62.384 66.667 12.35 0.00 44.73 5.87
1193 4681 2.284405 ACCGAACCCGTCCCTGAT 60.284 61.111 0.00 0.00 0.00 2.90
1226 4715 0.037326 TGGTGATCTTCGCAGTGACC 60.037 55.000 0.00 0.00 0.00 4.02
1272 4761 0.248458 CAATTTGGTATGGCCGCGTC 60.248 55.000 4.92 0.00 41.21 5.19
1294 4783 4.219070 TCTGGGAATTTCTGCATGTTTCAG 59.781 41.667 0.00 0.00 0.00 3.02
1295 4784 4.151121 TGGGAATTTCTGCATGTTTCAGA 58.849 39.130 0.00 0.00 38.67 3.27
1296 4785 4.588106 TGGGAATTTCTGCATGTTTCAGAA 59.412 37.500 9.41 9.41 45.62 3.02
1300 4789 3.648339 TTCTGCATGTTTCAGAAAGGC 57.352 42.857 10.67 1.75 44.70 4.35
1301 4790 2.867624 TCTGCATGTTTCAGAAAGGCT 58.132 42.857 12.77 0.00 37.61 4.58
1302 4791 3.225104 TCTGCATGTTTCAGAAAGGCTT 58.775 40.909 12.77 0.00 37.61 4.35
1303 4792 3.638160 TCTGCATGTTTCAGAAAGGCTTT 59.362 39.130 13.25 13.25 37.61 3.51
1304 4793 4.099881 TCTGCATGTTTCAGAAAGGCTTTT 59.900 37.500 14.66 0.00 37.61 2.27
1305 4794 4.768583 TGCATGTTTCAGAAAGGCTTTTT 58.231 34.783 14.66 5.44 0.00 1.94
1361 4850 0.685097 ACTGAAGCTTTGCGGTCCTA 59.315 50.000 0.00 0.00 0.00 2.94
1374 4863 1.804601 GGTCCTAACGTGTTTCCCTG 58.195 55.000 0.00 0.00 0.00 4.45
1387 4876 4.995487 GTGTTTCCCTGTTCGTAGATTTCT 59.005 41.667 0.00 0.00 35.04 2.52
1464 4962 4.576463 AGATATGCGTCCATTTGTTCTTCC 59.424 41.667 0.00 0.00 32.85 3.46
1499 4997 4.574599 AAGGTTGTCATCTGAAGTTTGC 57.425 40.909 0.00 0.00 0.00 3.68
1537 5035 5.277250 TCCTAGGACACATTTGATCCTGTA 58.723 41.667 7.62 0.74 42.95 2.74
1573 5071 3.490249 CGGATACAGGAGCGAACAATGTA 60.490 47.826 0.00 0.00 0.00 2.29
1646 5144 5.353678 GTCATGGGAAGCAATATAGAGATGC 59.646 44.000 0.00 0.00 40.34 3.91
1678 5176 2.054453 GGGTAGTAAGGACGGCGGT 61.054 63.158 13.24 0.00 0.00 5.68
1730 5255 6.885247 TCGTCACATGATACGAGTATTACTC 58.115 40.000 18.63 12.94 42.74 2.59
1753 5278 2.289532 GGAGGGTGCTCAGCTCACT 61.290 63.158 2.25 2.25 38.55 3.41
1861 5386 6.385649 TTGGACAAGGTAATGACTGTTTTC 57.614 37.500 0.00 0.00 0.00 2.29
1911 5436 7.093322 ACATTCCTGCTCATCAAGTAAAATC 57.907 36.000 0.00 0.00 0.00 2.17
2044 5569 5.067153 CACTAACAGAGTCATCCTAGGTCAG 59.933 48.000 9.08 0.00 35.64 3.51
2074 5599 3.473147 CAGTTCCTGCTATGCTGCT 57.527 52.632 0.00 0.00 0.00 4.24
2129 5654 9.483916 TTTTCGTCATGACTAATCTCAAAGTAA 57.516 29.630 22.95 4.47 0.00 2.24
2135 5660 8.772250 TCATGACTAATCTCAAAGTAATCCCTT 58.228 33.333 0.00 0.00 0.00 3.95
2157 5682 6.200097 CCTTCAAATTTGAACTAAAACCACGG 59.800 38.462 26.01 18.05 41.88 4.94
2185 5710 1.263356 TTGGAACGGAGGGAGTACTG 58.737 55.000 0.00 0.00 0.00 2.74
2204 5729 5.132897 ACTGTTTGTTTCACTTCTTTGCA 57.867 34.783 0.00 0.00 0.00 4.08
2227 5752 6.582672 GCAGTTCTTATGTTTGTTAGCTTTCC 59.417 38.462 0.00 0.00 0.00 3.13
2228 5753 7.522236 GCAGTTCTTATGTTTGTTAGCTTTCCT 60.522 37.037 0.00 0.00 0.00 3.36
2229 5754 8.352942 CAGTTCTTATGTTTGTTAGCTTTCCTT 58.647 33.333 0.00 0.00 0.00 3.36
2233 5758 8.567948 TCTTATGTTTGTTAGCTTTCCTTCTTG 58.432 33.333 0.00 0.00 0.00 3.02
2235 5760 7.817418 ATGTTTGTTAGCTTTCCTTCTTGTA 57.183 32.000 0.00 0.00 0.00 2.41
2280 5805 5.083122 TCCTTTCCATTTATTGAGGCAACA 58.917 37.500 0.00 0.00 41.41 3.33
2342 5867 6.787085 AGAAACACTAATTGAAGAGAACCG 57.213 37.500 0.00 0.00 0.00 4.44
2346 5871 2.304761 ACTAATTGAAGAGAACCGGCCA 59.695 45.455 0.00 0.00 0.00 5.36
2357 5882 1.487558 GAACCGGCCATTTACTCCCTA 59.512 52.381 0.00 0.00 0.00 3.53
2455 5980 2.355310 CCAGCGGTGGTGTATTTTAGGA 60.355 50.000 25.51 0.00 39.30 2.94
2737 6265 4.844085 TCCCCAACTTCTTCAGATAAGACA 59.156 41.667 1.01 0.00 0.00 3.41
2738 6266 5.046304 TCCCCAACTTCTTCAGATAAGACAG 60.046 44.000 1.01 0.00 0.00 3.51
2749 6277 8.861086 TCTTCAGATAAGACAGTACTTGTTCTT 58.139 33.333 13.23 13.23 41.05 2.52
2772 6300 1.403514 GGACCAGTTGAGAAGAGCGAG 60.404 57.143 0.00 0.00 0.00 5.03
2953 6481 2.565046 TGGTGTTGAGTGATGATGCA 57.435 45.000 0.00 0.00 0.00 3.96
3265 6794 7.727578 TGAGTACTATACATCCAGTTCCAAA 57.272 36.000 0.00 0.00 0.00 3.28
3305 6834 2.100605 AGACAAGTTGGAAGATCCGC 57.899 50.000 7.96 0.00 40.17 5.54
3314 6843 4.161565 AGTTGGAAGATCCGCAACTACATA 59.838 41.667 0.00 0.00 40.17 2.29
3437 6966 7.169308 CACGTATAACTAATTAGGTGCTTCTGG 59.831 40.741 13.50 0.00 0.00 3.86
3610 7141 3.244181 GCAATGAGGATGTGGTTTTTGGT 60.244 43.478 0.00 0.00 0.00 3.67
3722 7253 1.398390 GCGTCCCAGTTCATGATCAAC 59.602 52.381 0.00 0.00 0.00 3.18
3803 7334 6.128172 CCAAGTACCTGTCAATTCTCAATCAC 60.128 42.308 0.00 0.00 0.00 3.06
4195 7730 3.558418 TGAGCTCCGACAACAAGTAAAAC 59.442 43.478 12.15 0.00 0.00 2.43
4288 7844 6.299805 TGAACTATGTTGGAGCTGAGTATT 57.700 37.500 0.00 0.00 0.00 1.89
4343 7900 1.806542 CCACCAAGGACATGTTTCTCG 59.193 52.381 0.00 0.00 41.22 4.04
4422 7979 4.385825 GTGACATTCTGGAACAACACCTA 58.614 43.478 0.00 0.00 38.70 3.08
4456 8013 1.006281 TCATGGCATCTCTTGGGCTTT 59.994 47.619 0.00 0.00 0.00 3.51
4519 8076 2.559231 TGCAGTCATACACTACAACGGA 59.441 45.455 0.00 0.00 32.21 4.69
4613 8170 0.739462 CGCGTTCATAAGGGAGTGCA 60.739 55.000 0.00 0.00 0.00 4.57
4674 8231 2.504585 AGGCTGCTGAGATGATTTCAGA 59.495 45.455 16.22 1.98 43.75 3.27
4736 8293 8.229253 TCTACATTATCTAGAGCGTTGGTTTA 57.771 34.615 0.00 0.00 0.00 2.01
4740 8297 3.587797 TCTAGAGCGTTGGTTTACTGG 57.412 47.619 0.00 0.00 0.00 4.00
4763 8320 3.806625 AAATCACAGTGCAAGCAAGTT 57.193 38.095 0.00 0.00 0.00 2.66
4775 8332 0.111253 AGCAAGTTGTAGCAGGCCTT 59.889 50.000 0.00 0.00 0.00 4.35
4776 8333 0.242017 GCAAGTTGTAGCAGGCCTTG 59.758 55.000 0.00 0.00 36.47 3.61
4805 8362 4.826274 AAATGTGCAGTAGAGGCTAGAA 57.174 40.909 0.00 0.00 0.00 2.10
4933 8490 2.037251 TCTGTGTCAACCCTAGTTCTGC 59.963 50.000 0.00 0.00 32.45 4.26
4956 8513 2.705127 TGGTCTGGTCAGCATGCATATA 59.295 45.455 21.98 0.00 34.76 0.86
4957 8514 3.328637 TGGTCTGGTCAGCATGCATATAT 59.671 43.478 21.98 0.00 34.76 0.86
4966 8523 6.118170 GTCAGCATGCATATATCTTACCCAT 58.882 40.000 21.98 0.00 34.76 4.00
4976 8533 9.667107 GCATATATCTTACCCATTTAAGTAGCA 57.333 33.333 0.00 0.00 31.87 3.49
4979 8536 6.944234 ATCTTACCCATTTAAGTAGCAAGC 57.056 37.500 0.00 0.00 31.87 4.01
4981 8538 3.449746 ACCCATTTAAGTAGCAAGCCA 57.550 42.857 0.00 0.00 0.00 4.75
4983 8540 3.763897 ACCCATTTAAGTAGCAAGCCAAG 59.236 43.478 0.00 0.00 0.00 3.61
4984 8541 3.429410 CCCATTTAAGTAGCAAGCCAAGC 60.429 47.826 0.00 0.00 0.00 4.01
4985 8542 3.429085 CATTTAAGTAGCAAGCCAAGCG 58.571 45.455 0.00 0.00 37.01 4.68
4986 8543 0.802494 TTAAGTAGCAAGCCAAGCGC 59.198 50.000 0.00 0.00 37.01 5.92
4988 8545 0.962356 AAGTAGCAAGCCAAGCGCAT 60.962 50.000 11.47 0.00 41.38 4.73
4989 8546 1.226491 GTAGCAAGCCAAGCGCATG 60.226 57.895 11.47 8.27 41.38 4.06
4999 8557 2.875485 AGCGCATGAGCTTGCTTG 59.125 55.556 19.02 0.00 46.80 4.01
5000 8558 1.673337 AGCGCATGAGCTTGCTTGA 60.673 52.632 19.02 0.00 46.80 3.02
5006 8564 2.097142 GCATGAGCTTGCTTGAGGTAAG 59.903 50.000 3.04 0.00 39.57 2.34
5015 8573 3.466836 TGCTTGAGGTAAGTTCACACTG 58.533 45.455 0.00 0.00 38.70 3.66
5016 8574 2.224314 GCTTGAGGTAAGTTCACACTGC 59.776 50.000 0.00 0.00 38.70 4.40
5019 8577 5.482908 CTTGAGGTAAGTTCACACTGCTAT 58.517 41.667 0.00 0.00 31.60 2.97
5020 8578 5.483685 TGAGGTAAGTTCACACTGCTATT 57.516 39.130 0.00 0.00 31.60 1.73
5022 8580 6.296026 TGAGGTAAGTTCACACTGCTATTTT 58.704 36.000 0.00 0.00 31.60 1.82
5023 8581 6.426937 TGAGGTAAGTTCACACTGCTATTTTC 59.573 38.462 0.00 0.00 31.60 2.29
5024 8582 6.296026 AGGTAAGTTCACACTGCTATTTTCA 58.704 36.000 0.00 0.00 31.60 2.69
5026 8584 7.284489 AGGTAAGTTCACACTGCTATTTTCAAA 59.716 33.333 0.00 0.00 31.60 2.69
5027 8585 7.918562 GGTAAGTTCACACTGCTATTTTCAAAA 59.081 33.333 0.00 0.00 31.60 2.44
5028 8586 9.296400 GTAAGTTCACACTGCTATTTTCAAAAA 57.704 29.630 0.00 0.00 31.60 1.94
5099 8858 9.305555 TGTCTAACAGACCTAAACATTAGTACT 57.694 33.333 0.00 0.00 44.44 2.73
5100 8859 9.786105 GTCTAACAGACCTAAACATTAGTACTC 57.214 37.037 0.00 0.00 39.28 2.59
5101 8860 8.964772 TCTAACAGACCTAAACATTAGTACTCC 58.035 37.037 0.00 0.00 0.00 3.85
5103 8862 6.262207 ACAGACCTAAACATTAGTACTCCCT 58.738 40.000 0.00 0.00 0.00 4.20
5104 8863 6.380560 ACAGACCTAAACATTAGTACTCCCTC 59.619 42.308 0.00 0.00 0.00 4.30
5105 8864 5.898397 AGACCTAAACATTAGTACTCCCTCC 59.102 44.000 0.00 0.00 0.00 4.30
5106 8865 4.648307 ACCTAAACATTAGTACTCCCTCCG 59.352 45.833 0.00 0.00 0.00 4.63
5107 8866 4.648307 CCTAAACATTAGTACTCCCTCCGT 59.352 45.833 0.00 0.00 0.00 4.69
5108 8867 5.829924 CCTAAACATTAGTACTCCCTCCGTA 59.170 44.000 0.00 0.00 0.00 4.02
5110 8869 6.610075 AAACATTAGTACTCCCTCCGTAAA 57.390 37.500 0.00 0.00 0.00 2.01
5111 8870 5.588958 ACATTAGTACTCCCTCCGTAAAC 57.411 43.478 0.00 0.00 0.00 2.01
5114 8873 6.891908 ACATTAGTACTCCCTCCGTAAACTAA 59.108 38.462 0.00 0.00 0.00 2.24
5116 8875 9.071276 CATTAGTACTCCCTCCGTAAACTAATA 57.929 37.037 0.00 0.00 0.00 0.98
5117 8876 9.819754 ATTAGTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
5120 8879 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
5121 8880 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
5122 8881 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5123 8882 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5124 8883 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
5125 8884 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
5126 8885 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
5127 8886 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
5175 8934 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
5176 8935 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
5177 8936 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
5178 8937 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
5179 8938 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
5186 8945 5.893897 AGTTTACAGAGGGAGTAGTTACG 57.106 43.478 0.00 0.00 0.00 3.18
5191 8950 3.952967 ACAGAGGGAGTAGTTACGATTCC 59.047 47.826 0.00 0.00 0.00 3.01
5254 9013 3.346315 TCAATACGAGTAACGGAGTCCA 58.654 45.455 10.49 0.00 45.00 4.02
5261 9020 0.531200 GTAACGGAGTCCAGGGAGTG 59.469 60.000 10.49 0.00 45.00 3.51
5277 9036 0.520404 AGTGATCGACAGCGTTACGT 59.480 50.000 6.63 0.00 38.98 3.57
5311 9078 1.287730 CTGCAAGCGAGACACAGACC 61.288 60.000 0.00 0.00 0.00 3.85
5314 9081 2.932234 AAGCGAGACACAGACCCCG 61.932 63.158 0.00 0.00 0.00 5.73
5331 9098 2.093658 CCCCGTGCTCTACAAATACTGT 60.094 50.000 0.00 0.00 42.47 3.55
5334 9101 4.110482 CCGTGCTCTACAAATACTGTACC 58.890 47.826 0.00 0.00 39.64 3.34
5336 9103 4.437794 CGTGCTCTACAAATACTGTACCGA 60.438 45.833 0.00 0.00 39.64 4.69
5341 9108 6.683974 TCTACAAATACTGTACCGAGTACC 57.316 41.667 10.45 0.00 38.14 3.34
5345 9112 5.945784 ACAAATACTGTACCGAGTACCACTA 59.054 40.000 10.45 0.90 38.14 2.74
5346 9113 6.094603 ACAAATACTGTACCGAGTACCACTAG 59.905 42.308 10.45 0.00 38.14 2.57
5347 9114 3.710209 ACTGTACCGAGTACCACTAGT 57.290 47.619 10.45 0.00 38.14 2.57
5407 9174 0.525761 GTACGTACAACCGCCACCTA 59.474 55.000 20.67 0.00 0.00 3.08
5477 9244 2.203167 TCCCGATCCTCCTCGTCG 60.203 66.667 0.00 0.00 36.93 5.12
5483 9250 0.248134 GATCCTCCTCGTCGTTGTCG 60.248 60.000 0.00 0.00 38.55 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.057149 CGTTCGATAAATTGATCCTCCCTT 58.943 41.667 0.00 0.00 0.00 3.95
24 25 1.405121 GGTTGTCCTAGCGAACGGAAT 60.405 52.381 0.00 0.00 0.00 3.01
27 28 0.458025 GAGGTTGTCCTAGCGAACGG 60.458 60.000 0.00 0.00 45.24 4.44
65 66 0.322187 TAAAGTCTTGGCCGGCCTTC 60.322 55.000 43.34 28.74 36.94 3.46
71 72 1.135112 GCCCAATTAAAGTCTTGGCCG 60.135 52.381 0.00 0.00 40.51 6.13
103 104 1.731709 TCTTCGCAATGATGACGTTGG 59.268 47.619 0.00 0.00 41.65 3.77
144 145 3.242011 AGTCACCATGAAAATTGGCCTT 58.758 40.909 3.32 0.00 37.81 4.35
145 146 2.893424 AGTCACCATGAAAATTGGCCT 58.107 42.857 3.32 0.00 37.81 5.19
160 186 4.182339 GGCTAAGGCTTGTTAGTAGTCAC 58.818 47.826 10.69 0.00 38.73 3.67
219 245 7.871973 TGATGGCATTGTATTTACATATTTGGC 59.128 33.333 0.00 1.97 35.89 4.52
220 246 9.932207 ATGATGGCATTGTATTTACATATTTGG 57.068 29.630 0.00 0.00 35.89 3.28
225 251 9.129532 TGAACATGATGGCATTGTATTTACATA 57.870 29.630 0.00 0.00 35.89 2.29
226 252 8.009622 TGAACATGATGGCATTGTATTTACAT 57.990 30.769 0.00 0.00 35.89 2.29
227 253 7.401955 TGAACATGATGGCATTGTATTTACA 57.598 32.000 0.00 0.00 30.68 2.41
228 254 8.757789 CATTGAACATGATGGCATTGTATTTAC 58.242 33.333 0.00 0.00 30.68 2.01
237 268 6.072649 TCTAATCCATTGAACATGATGGCAT 58.927 36.000 0.00 0.00 42.05 4.40
238 269 5.447757 TCTAATCCATTGAACATGATGGCA 58.552 37.500 0.00 0.00 42.05 4.92
338 3763 7.333921 TCATCCATGTGTTTTTCAATTATTGGC 59.666 33.333 5.02 0.00 0.00 4.52
345 3770 8.735692 AGTTTTTCATCCATGTGTTTTTCAAT 57.264 26.923 0.00 0.00 0.00 2.57
359 3784 8.921670 ACGCATAAATTTGTAAGTTTTTCATCC 58.078 29.630 0.00 0.00 0.00 3.51
362 3787 8.858003 TGACGCATAAATTTGTAAGTTTTTCA 57.142 26.923 0.00 0.00 0.00 2.69
526 3957 8.506168 TCGCATAGAAAATTGTTTCCTCTAAT 57.494 30.769 0.00 0.00 43.65 1.73
527 3958 7.915293 TCGCATAGAAAATTGTTTCCTCTAA 57.085 32.000 0.00 0.00 43.65 2.10
528 3959 9.607988 TTATCGCATAGAAAATTGTTTCCTCTA 57.392 29.630 0.00 0.00 43.65 2.43
529 3960 8.506168 TTATCGCATAGAAAATTGTTTCCTCT 57.494 30.769 0.00 0.00 43.65 3.69
530 3961 9.567848 TTTTATCGCATAGAAAATTGTTTCCTC 57.432 29.630 0.00 0.00 43.65 3.71
531 3962 9.573133 CTTTTATCGCATAGAAAATTGTTTCCT 57.427 29.630 0.00 0.00 43.65 3.36
532 3963 9.353999 ACTTTTATCGCATAGAAAATTGTTTCC 57.646 29.630 0.00 0.00 43.65 3.13
537 3968 9.573133 AGGAAACTTTTATCGCATAGAAAATTG 57.427 29.630 0.00 0.00 37.44 2.32
538 3969 9.788960 GAGGAAACTTTTATCGCATAGAAAATT 57.211 29.630 0.00 0.00 44.43 1.82
540 3971 8.561738 AGAGGAAACTTTTATCGCATAGAAAA 57.438 30.769 0.00 0.00 44.43 2.29
541 3972 9.661563 TTAGAGGAAACTTTTATCGCATAGAAA 57.338 29.630 0.00 0.00 44.43 2.52
614 4074 2.030862 GGTTGCCACGTTCCGGTA 59.969 61.111 0.00 0.00 0.00 4.02
957 4444 0.172803 GACGTGGTGATTAGAGCCGT 59.827 55.000 0.00 0.00 0.00 5.68
1144 4631 2.114411 GAACGCAGGGTTTGGGGA 59.886 61.111 4.05 0.00 43.60 4.81
1148 4635 3.342627 TCGCGAACGCAGGGTTTG 61.343 61.111 18.69 12.40 39.50 2.93
1149 4636 3.343421 GTCGCGAACGCAGGGTTT 61.343 61.111 12.06 0.00 39.50 3.27
1150 4637 4.595538 TGTCGCGAACGCAGGGTT 62.596 61.111 12.06 1.73 42.96 4.11
1156 4643 4.122515 GCACTCTGTCGCGAACGC 62.123 66.667 12.06 9.20 39.84 4.84
1164 4651 1.668151 GTTCGGTGGGCACTCTGTC 60.668 63.158 0.00 0.00 0.00 3.51
1193 4681 0.105778 TCACCAAGATCACACACGCA 59.894 50.000 0.00 0.00 0.00 5.24
1240 4729 1.340991 CCAAATTGGAGGGATCACGGT 60.341 52.381 6.04 0.00 40.96 4.83
1272 4761 4.219070 TCTGAAACATGCAGAAATTCCCAG 59.781 41.667 0.00 0.00 39.29 4.45
1304 4793 3.284793 TCTGAAACGAGTCCCCAAAAA 57.715 42.857 0.00 0.00 0.00 1.94
1305 4794 3.284793 TTCTGAAACGAGTCCCCAAAA 57.715 42.857 0.00 0.00 0.00 2.44
1306 4795 3.211045 CTTTCTGAAACGAGTCCCCAAA 58.789 45.455 0.00 0.00 0.00 3.28
1307 4796 2.486548 CCTTTCTGAAACGAGTCCCCAA 60.487 50.000 0.00 0.00 0.00 4.12
1308 4797 1.071699 CCTTTCTGAAACGAGTCCCCA 59.928 52.381 0.00 0.00 0.00 4.96
1309 4798 1.809684 CCTTTCTGAAACGAGTCCCC 58.190 55.000 0.00 0.00 0.00 4.81
1310 4799 1.157585 GCCTTTCTGAAACGAGTCCC 58.842 55.000 0.00 0.00 0.00 4.46
1311 4800 2.171341 AGCCTTTCTGAAACGAGTCC 57.829 50.000 0.00 0.00 0.00 3.85
1312 4801 3.363084 CGAAAGCCTTTCTGAAACGAGTC 60.363 47.826 14.82 0.00 37.52 3.36
1313 4802 2.544267 CGAAAGCCTTTCTGAAACGAGT 59.456 45.455 14.82 0.00 37.52 4.18
1314 4803 2.096218 CCGAAAGCCTTTCTGAAACGAG 60.096 50.000 14.82 0.00 37.52 4.18
1315 4804 1.871039 CCGAAAGCCTTTCTGAAACGA 59.129 47.619 14.82 0.00 37.52 3.85
1316 4805 1.871039 TCCGAAAGCCTTTCTGAAACG 59.129 47.619 14.82 1.58 37.52 3.60
1317 4806 2.226674 CCTCCGAAAGCCTTTCTGAAAC 59.773 50.000 14.82 0.00 37.52 2.78
1318 4807 2.158667 ACCTCCGAAAGCCTTTCTGAAA 60.159 45.455 14.82 2.44 37.52 2.69
1319 4808 1.420138 ACCTCCGAAAGCCTTTCTGAA 59.580 47.619 14.82 0.17 37.52 3.02
1320 4809 1.002087 GACCTCCGAAAGCCTTTCTGA 59.998 52.381 14.82 12.48 37.52 3.27
1321 4810 1.443802 GACCTCCGAAAGCCTTTCTG 58.556 55.000 14.82 8.78 37.52 3.02
1322 4811 0.037232 CGACCTCCGAAAGCCTTTCT 60.037 55.000 14.82 0.00 41.76 2.52
1361 4850 2.101249 TCTACGAACAGGGAAACACGTT 59.899 45.455 0.00 0.00 35.66 3.99
1374 4863 4.740695 CCTCATTCCGAGAAATCTACGAAC 59.259 45.833 0.00 0.00 45.45 3.95
1387 4876 2.685743 TTCCCCGCCTCATTCCGA 60.686 61.111 0.00 0.00 0.00 4.55
1464 4962 5.518812 TGACAACCTTTCACATTCATTTCG 58.481 37.500 0.00 0.00 0.00 3.46
1499 4997 6.870965 GTGTCCTAGGAATATATTCAGCACTG 59.129 42.308 23.54 9.30 38.53 3.66
1573 5071 2.293318 TTGAGTGCCCTGATCGCCT 61.293 57.895 0.00 0.00 0.00 5.52
1603 5101 1.608590 ACAACTTGCTGAATTCCACCG 59.391 47.619 2.27 0.00 0.00 4.94
1678 5176 0.038251 CCTCTTCTACACTGCGCACA 60.038 55.000 5.66 0.00 0.00 4.57
1686 5184 1.272769 ACACCTTCGCCTCTTCTACAC 59.727 52.381 0.00 0.00 0.00 2.90
1730 5255 3.465403 CTGAGCACCCTCCTCCGG 61.465 72.222 0.00 0.00 37.29 5.14
1753 5278 1.429930 TGGTCAGGCCACTCTGTTTA 58.570 50.000 5.01 0.00 43.61 2.01
1941 5466 9.807649 GGATTTTGTCTGCTCACATAATTTATT 57.192 29.630 6.00 0.00 30.72 1.40
1942 5467 9.193806 AGGATTTTGTCTGCTCACATAATTTAT 57.806 29.630 6.00 0.00 30.72 1.40
1944 5469 7.472334 AGGATTTTGTCTGCTCACATAATTT 57.528 32.000 6.00 0.00 30.72 1.82
1955 5480 7.573968 ATCCAGTAATAAGGATTTTGTCTGC 57.426 36.000 0.00 0.00 41.80 4.26
2129 5654 7.931407 GTGGTTTTAGTTCAAATTTGAAGGGAT 59.069 33.333 29.34 18.85 46.80 3.85
2135 5660 5.044558 GCCGTGGTTTTAGTTCAAATTTGA 58.955 37.500 16.91 16.91 34.92 2.69
2157 5682 2.163613 CCCTCCGTTCCAAAATACTTGC 59.836 50.000 0.00 0.00 0.00 4.01
2185 5710 5.863935 AGAACTGCAAAGAAGTGAAACAAAC 59.136 36.000 0.00 0.00 41.43 2.93
2204 5729 8.465273 AAGGAAAGCTAACAAACATAAGAACT 57.535 30.769 0.00 0.00 0.00 3.01
2233 5758 9.747293 GGAGATGAACCTACAATTAGTTACTAC 57.253 37.037 0.00 0.00 0.00 2.73
2235 5760 8.611051 AGGAGATGAACCTACAATTAGTTACT 57.389 34.615 0.00 0.00 35.84 2.24
2280 5805 6.716284 TGGAAGAACAAAACCAAAAGGATTT 58.284 32.000 0.00 0.00 42.41 2.17
2342 5867 3.117663 TCCACAATAGGGAGTAAATGGCC 60.118 47.826 0.00 0.00 0.00 5.36
2346 5871 5.193679 GCAAGTCCACAATAGGGAGTAAAT 58.806 41.667 0.00 0.00 37.09 1.40
2357 5882 5.829924 CCTAAATGATAGGCAAGTCCACAAT 59.170 40.000 0.00 0.00 37.29 2.71
2478 6003 7.620394 GCTTCTCTCAAAAAGTGACTCGTAATC 60.620 40.741 0.00 0.00 31.13 1.75
2737 6265 6.099269 TCAACTGGTCCTTAAGAACAAGTACT 59.901 38.462 1.80 0.00 43.24 2.73
2738 6266 6.285990 TCAACTGGTCCTTAAGAACAAGTAC 58.714 40.000 1.80 0.00 43.24 2.73
2749 6277 2.231478 CGCTCTTCTCAACTGGTCCTTA 59.769 50.000 0.00 0.00 0.00 2.69
2875 6403 4.504858 ACTTCTTTGGTAACTGCCTATCG 58.495 43.478 0.00 0.00 37.61 2.92
2953 6481 3.097614 AGAGTAACCGAACAGCAGGTAT 58.902 45.455 0.00 0.00 40.37 2.73
2965 6493 6.812160 AGTCACTTGCTATAAAAGAGTAACCG 59.188 38.462 2.61 0.00 0.00 4.44
3176 6705 0.976641 TTAGCTGCTACCTGTGCTGT 59.023 50.000 9.27 0.00 37.02 4.40
3265 6794 8.537728 TGTCTTGATATGGAAAATGCCTATTT 57.462 30.769 0.00 0.00 38.11 1.40
3270 6799 6.212888 ACTTGTCTTGATATGGAAAATGCC 57.787 37.500 0.00 0.00 0.00 4.40
3314 6843 8.743085 ACATTGTCAGAGAATAATGCATAGTT 57.257 30.769 0.00 0.00 34.69 2.24
3437 6966 6.473455 GCACCATAAGTTTACTTGCAATGATC 59.527 38.462 0.00 0.00 37.40 2.92
3610 7141 0.996583 AGCTTTAACCGGGGGATTCA 59.003 50.000 6.32 0.00 0.00 2.57
3722 7253 7.589958 ATTCTGTGGAGTATGGAAGTAGTAG 57.410 40.000 0.00 0.00 0.00 2.57
3803 7334 5.683876 TCTCAGGAAGATAAAACCTCAGG 57.316 43.478 0.00 0.00 31.06 3.86
4258 7794 7.168219 TCAGCTCCAACATAGTTCAATACTTT 58.832 34.615 0.00 0.00 38.33 2.66
4288 7844 7.589954 GCAAGAGTAGAACAAAATAGCGAAAAA 59.410 33.333 0.00 0.00 0.00 1.94
4300 7856 7.715249 GTGGAATATATGGCAAGAGTAGAACAA 59.285 37.037 0.00 0.00 0.00 2.83
4343 7900 5.641209 ACAGTCTATGTTCATTCTGCAGAAC 59.359 40.000 30.66 19.21 39.96 3.01
4422 7979 1.459455 CCATGAGCGATCGAGAGGGT 61.459 60.000 21.57 0.00 0.00 4.34
4456 8013 3.006940 GTTGACATTCCGCTTGTATCCA 58.993 45.455 0.00 0.00 0.00 3.41
4519 8076 3.575687 CCTCAAGCCAAGGTTTCAGATTT 59.424 43.478 0.00 0.00 0.00 2.17
4613 8170 3.379372 GCAGCAACTCATGGATGTATGTT 59.621 43.478 0.00 0.00 0.00 2.71
4736 8293 2.566833 TGCACTGTGATTTAGCCAGT 57.433 45.000 12.86 0.00 39.93 4.00
4740 8297 2.995466 TGCTTGCACTGTGATTTAGC 57.005 45.000 12.86 13.17 0.00 3.09
4763 8320 0.698238 ATTCCACAAGGCCTGCTACA 59.302 50.000 5.69 0.00 33.74 2.74
4775 8332 5.647658 CCTCTACTGCACATTTTATTCCACA 59.352 40.000 0.00 0.00 0.00 4.17
4776 8333 5.449177 GCCTCTACTGCACATTTTATTCCAC 60.449 44.000 0.00 0.00 0.00 4.02
4902 8459 4.702131 AGGGTTGACACAGAAATGCTAATC 59.298 41.667 0.00 0.00 0.00 1.75
4909 8466 5.308825 CAGAACTAGGGTTGACACAGAAAT 58.691 41.667 0.00 0.00 35.58 2.17
4913 8470 2.037772 AGCAGAACTAGGGTTGACACAG 59.962 50.000 0.00 0.00 35.58 3.66
4915 8472 2.808543 CAAGCAGAACTAGGGTTGACAC 59.191 50.000 0.00 0.00 43.25 3.67
4933 8490 0.607217 TGCATGCTGACCAGACCAAG 60.607 55.000 20.33 0.00 0.00 3.61
4956 8513 5.828328 GGCTTGCTACTTAAATGGGTAAGAT 59.172 40.000 0.00 0.00 35.45 2.40
4957 8514 5.190677 GGCTTGCTACTTAAATGGGTAAGA 58.809 41.667 0.00 0.00 35.45 2.10
4966 8523 1.199097 GCGCTTGGCTTGCTACTTAAA 59.801 47.619 0.00 0.00 39.11 1.52
4976 8533 2.360852 AGCTCATGCGCTTGGCTT 60.361 55.556 23.83 13.78 45.42 4.35
4985 8542 1.742761 TACCTCAAGCAAGCTCATGC 58.257 50.000 1.95 1.95 46.78 4.06
4986 8543 3.341823 ACTTACCTCAAGCAAGCTCATG 58.658 45.455 0.00 0.00 37.83 3.07
4988 8545 3.181455 TGAACTTACCTCAAGCAAGCTCA 60.181 43.478 0.00 0.00 37.83 4.26
4989 8546 3.187432 GTGAACTTACCTCAAGCAAGCTC 59.813 47.826 0.00 0.00 37.83 4.09
4999 8557 6.426937 TGAAAATAGCAGTGTGAACTTACCTC 59.573 38.462 0.00 0.00 0.00 3.85
5000 8558 6.296026 TGAAAATAGCAGTGTGAACTTACCT 58.704 36.000 0.00 0.00 0.00 3.08
5030 8588 3.731867 CGCTTGAGCAGTGTGAACTTTTT 60.732 43.478 3.65 0.00 42.21 1.94
5031 8589 2.223340 CGCTTGAGCAGTGTGAACTTTT 60.223 45.455 3.65 0.00 42.21 2.27
5033 8591 0.940126 CGCTTGAGCAGTGTGAACTT 59.060 50.000 3.65 0.00 42.21 2.66
5035 8593 1.151668 ATCGCTTGAGCAGTGTGAAC 58.848 50.000 3.65 0.00 42.21 3.18
5038 8596 4.115516 ACTAATATCGCTTGAGCAGTGTG 58.884 43.478 3.65 0.00 42.21 3.82
5039 8597 4.392921 ACTAATATCGCTTGAGCAGTGT 57.607 40.909 3.65 0.00 42.21 3.55
5040 8598 6.624710 GATACTAATATCGCTTGAGCAGTG 57.375 41.667 3.65 0.00 42.21 3.66
5084 8843 4.648307 ACGGAGGGAGTACTAATGTTTAGG 59.352 45.833 0.00 0.00 0.00 2.69
5087 8846 6.212187 AGTTTACGGAGGGAGTACTAATGTTT 59.788 38.462 0.00 0.00 0.00 2.83
5088 8847 5.718607 AGTTTACGGAGGGAGTACTAATGTT 59.281 40.000 0.00 0.00 0.00 2.71
5089 8848 5.267587 AGTTTACGGAGGGAGTACTAATGT 58.732 41.667 0.00 0.00 0.00 2.71
5090 8849 5.848833 AGTTTACGGAGGGAGTACTAATG 57.151 43.478 0.00 0.00 0.00 1.90
5094 8853 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
5095 8854 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
5096 8855 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
5099 8858 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
5100 8859 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
5101 8860 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
5149 8908 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
5150 8909 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
5151 8910 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
5152 8911 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
5153 8912 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
5160 8919 9.113838 CGTAACTACTCCCTCTGTAAACTAATA 57.886 37.037 0.00 0.00 0.00 0.98
5161 8920 7.831193 TCGTAACTACTCCCTCTGTAAACTAAT 59.169 37.037 0.00 0.00 0.00 1.73
5162 8921 7.168219 TCGTAACTACTCCCTCTGTAAACTAA 58.832 38.462 0.00 0.00 0.00 2.24
5163 8922 6.711277 TCGTAACTACTCCCTCTGTAAACTA 58.289 40.000 0.00 0.00 0.00 2.24
5164 8923 5.564550 TCGTAACTACTCCCTCTGTAAACT 58.435 41.667 0.00 0.00 0.00 2.66
5165 8924 5.886960 TCGTAACTACTCCCTCTGTAAAC 57.113 43.478 0.00 0.00 0.00 2.01
5166 8925 6.096001 GGAATCGTAACTACTCCCTCTGTAAA 59.904 42.308 0.00 0.00 0.00 2.01
5167 8926 5.591877 GGAATCGTAACTACTCCCTCTGTAA 59.408 44.000 0.00 0.00 0.00 2.41
5168 8927 5.128919 GGAATCGTAACTACTCCCTCTGTA 58.871 45.833 0.00 0.00 0.00 2.74
5169 8928 3.952967 GGAATCGTAACTACTCCCTCTGT 59.047 47.826 0.00 0.00 0.00 3.41
5170 8929 3.952323 TGGAATCGTAACTACTCCCTCTG 59.048 47.826 0.00 0.00 0.00 3.35
5171 8930 4.246712 TGGAATCGTAACTACTCCCTCT 57.753 45.455 0.00 0.00 0.00 3.69
5172 8931 4.996788 TTGGAATCGTAACTACTCCCTC 57.003 45.455 0.00 0.00 0.00 4.30
5173 8932 5.247792 AGTTTTGGAATCGTAACTACTCCCT 59.752 40.000 0.00 0.00 0.00 4.20
5174 8933 5.485620 AGTTTTGGAATCGTAACTACTCCC 58.514 41.667 0.00 0.00 0.00 4.30
5175 8934 6.396450 AGAGTTTTGGAATCGTAACTACTCC 58.604 40.000 0.00 0.00 31.41 3.85
5176 8935 6.530887 GGAGAGTTTTGGAATCGTAACTACTC 59.469 42.308 0.00 0.00 31.41 2.59
5177 8936 6.014840 TGGAGAGTTTTGGAATCGTAACTACT 60.015 38.462 0.00 0.00 31.41 2.57
5178 8937 6.090493 GTGGAGAGTTTTGGAATCGTAACTAC 59.910 42.308 0.00 0.00 31.41 2.73
5179 8938 6.161381 GTGGAGAGTTTTGGAATCGTAACTA 58.839 40.000 0.00 0.00 31.41 2.24
5180 8939 4.995487 GTGGAGAGTTTTGGAATCGTAACT 59.005 41.667 0.00 0.00 33.78 2.24
5181 8940 4.153655 GGTGGAGAGTTTTGGAATCGTAAC 59.846 45.833 0.00 0.00 0.00 2.50
5182 8941 4.202377 TGGTGGAGAGTTTTGGAATCGTAA 60.202 41.667 0.00 0.00 0.00 3.18
5183 8942 3.325425 TGGTGGAGAGTTTTGGAATCGTA 59.675 43.478 0.00 0.00 0.00 3.43
5186 8945 3.445096 CCATGGTGGAGAGTTTTGGAATC 59.555 47.826 2.57 0.00 40.96 2.52
5191 8950 0.890683 GGCCATGGTGGAGAGTTTTG 59.109 55.000 14.67 0.00 40.96 2.44
5221 8980 7.253354 CGTTACTCGTATTGAAGCTGTCTTTAG 60.253 40.741 0.00 0.00 31.62 1.85
5254 9013 1.251527 AACGCTGTCGATCACTCCCT 61.252 55.000 0.00 0.00 39.41 4.20
5261 9020 1.740043 GCCACGTAACGCTGTCGATC 61.740 60.000 0.00 0.00 39.41 3.69
5277 9036 2.719531 TGCAGATTATAAACCGGCCA 57.280 45.000 0.00 0.00 0.00 5.36
5311 9078 3.247006 ACAGTATTTGTAGAGCACGGG 57.753 47.619 0.00 0.00 38.56 5.28
5314 9081 4.990257 TCGGTACAGTATTTGTAGAGCAC 58.010 43.478 0.00 0.00 42.75 4.40
5341 9108 3.622828 CTGTGCGATGCTAGTACTAGTG 58.377 50.000 26.76 16.75 35.65 2.74
5345 9112 0.817654 TGCTGTGCGATGCTAGTACT 59.182 50.000 0.00 0.00 0.00 2.73
5346 9113 1.203928 CTGCTGTGCGATGCTAGTAC 58.796 55.000 0.00 0.00 0.00 2.73
5347 9114 0.528466 GCTGCTGTGCGATGCTAGTA 60.528 55.000 0.00 0.00 0.00 1.82
5350 9117 0.745486 AATGCTGCTGTGCGATGCTA 60.745 50.000 0.00 0.00 35.36 3.49
5351 9118 2.044555 AATGCTGCTGTGCGATGCT 61.045 52.632 0.00 0.00 35.36 3.79
5352 9119 1.872234 CAATGCTGCTGTGCGATGC 60.872 57.895 0.00 0.00 35.36 3.91
5353 9120 1.872234 GCAATGCTGCTGTGCGATG 60.872 57.895 11.32 0.00 45.74 3.84
5354 9121 2.488355 GCAATGCTGCTGTGCGAT 59.512 55.556 11.32 0.00 45.74 4.58
5433 9200 2.507324 GGAGGAACGAGCACGAGC 60.507 66.667 11.40 0.00 42.66 5.03
5444 9211 2.351276 GAGGCAAAGGCGGAGGAA 59.649 61.111 0.00 0.00 42.47 3.36


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

AutoCloner maintained by Alex Coulton.