Multiple sequence alignment - TraesCS2A01G527200

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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 TraesCS2A01G527200 chr2A 100.000 3952 0 0 803 4754 746935125 746939076 0.000000e+00 7299.0
1 TraesCS2A01G527200 chr2A 85.697 804 51 24 3065 3834 746952750 746953523 0.000000e+00 789.0
2 TraesCS2A01G527200 chr2A 100.000 426 0 0 1 426 746934323 746934748 0.000000e+00 787.0
3 TraesCS2A01G527200 chr2A 79.381 388 51 20 3396 3764 746963611 746963988 3.670000e-61 246.0
4 TraesCS2A01G527200 chr2A 84.028 144 16 3 1887 2030 746944008 746944144 1.070000e-26 132.0
5 TraesCS2A01G527200 chr2B 88.498 3095 222 69 812 3834 752405231 752408263 0.000000e+00 3620.0
6 TraesCS2A01G527200 chr2B 84.713 1727 167 55 2179 3834 752477042 752478742 0.000000e+00 1637.0
7 TraesCS2A01G527200 chr2B 85.994 714 63 21 1361 2061 752476064 752476753 0.000000e+00 730.0
8 TraesCS2A01G527200 chr2B 90.000 410 29 7 992 1389 752475468 752475877 1.960000e-143 520.0
9 TraesCS2A01G527200 chr2B 85.548 429 34 18 10 424 752404834 752405248 1.580000e-114 424.0
10 TraesCS2A01G527200 chr2B 79.494 356 43 8 2218 2564 752485457 752485791 4.790000e-55 226.0
11 TraesCS2A01G527200 chr2B 84.058 207 24 5 1411 1612 752475865 752476067 1.750000e-44 191.0
12 TraesCS2A01G527200 chr2B 88.596 114 12 1 4576 4688 752479538 752479651 2.310000e-28 137.0
13 TraesCS2A01G527200 chr2B 87.059 85 9 2 2672 2755 752415359 752415442 1.410000e-15 95.3
14 TraesCS2A01G527200 chr2B 80.342 117 17 4 3926 4037 752486193 752486308 3.050000e-12 84.2
15 TraesCS2A01G527200 chrUn 87.529 2566 187 50 1336 3834 9574210 9576709 0.000000e+00 2843.0
16 TraesCS2A01G527200 chrUn 93.056 72 3 2 4684 4753 9577458 9577529 2.340000e-18 104.0
17 TraesCS2A01G527200 chr5B 87.392 1959 149 54 1887 3769 61390138 61392074 0.000000e+00 2159.0
18 TraesCS2A01G527200 chr2D 93.087 839 48 7 2194 3026 616939834 616940668 0.000000e+00 1219.0
19 TraesCS2A01G527200 chr2D 83.649 1266 109 45 870 2104 616938033 616939231 0.000000e+00 1101.0
20 TraesCS2A01G527200 chr2D 84.835 1121 94 32 3163 4221 616940857 616941963 0.000000e+00 1059.0
21 TraesCS2A01G527200 chr2D 89.398 415 18 13 15 424 616937625 616938018 2.550000e-137 499.0
22 TraesCS2A01G527200 chr2D 98.450 129 1 1 4627 4754 616942301 616942429 4.790000e-55 226.0
23 TraesCS2A01G527200 chr2D 85.135 148 14 4 3396 3538 616947764 616947908 1.380000e-30 145.0
24 TraesCS2A01G527200 chr2D 87.273 55 7 0 812 866 616938001 616938055 3.970000e-06 63.9
25 TraesCS2A01G527200 chr6B 82.734 695 95 22 2361 3045 710289728 710289049 3.170000e-166 595.0
26 TraesCS2A01G527200 chr6B 86.062 452 56 6 2361 2809 42368332 42368779 3.330000e-131 479.0
27 TraesCS2A01G527200 chr7B 83.630 617 84 15 2361 2973 532036030 532036633 8.930000e-157 564.0
28 TraesCS2A01G527200 chr3B 86.504 452 54 6 2361 2809 773725719 773725272 1.540000e-134 490.0


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 TraesCS2A01G527200 chr2A 746934323 746939076 4753 False 4043.00 7299 100.000000 1 4754 2 chr2A.!!$F4 4753
1 TraesCS2A01G527200 chr2A 746952750 746953523 773 False 789.00 789 85.697000 3065 3834 1 chr2A.!!$F2 769
2 TraesCS2A01G527200 chr2B 752404834 752408263 3429 False 2022.00 3620 87.023000 10 3834 2 chr2B.!!$F2 3824
3 TraesCS2A01G527200 chr2B 752475468 752479651 4183 False 643.00 1637 86.672200 992 4688 5 chr2B.!!$F3 3696
4 TraesCS2A01G527200 chrUn 9574210 9577529 3319 False 1473.50 2843 90.292500 1336 4753 2 chrUn.!!$F1 3417
5 TraesCS2A01G527200 chr5B 61390138 61392074 1936 False 2159.00 2159 87.392000 1887 3769 1 chr5B.!!$F1 1882
6 TraesCS2A01G527200 chr2D 616937625 616942429 4804 False 694.65 1219 89.448667 15 4754 6 chr2D.!!$F2 4739
7 TraesCS2A01G527200 chr6B 710289049 710289728 679 True 595.00 595 82.734000 2361 3045 1 chr6B.!!$R1 684
8 TraesCS2A01G527200 chr7B 532036030 532036633 603 False 564.00 564 83.630000 2361 2973 1 chr7B.!!$F1 612

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
293 315 0.110486 ATTGGTGGTTCCTTGCTCGT 59.890 50.0 0.00 0.00 37.07 4.18 F
1266 1341 0.108138 CTCTTTCTGTACCCCCGCTG 60.108 60.0 0.00 0.00 0.00 5.18 F
1589 1914 0.101939 GTCCCGGACACGAGGTAATC 59.898 60.0 13.05 0.00 44.60 1.75 F
1758 2093 0.532862 CGGCCAATGTAGGATCGCTT 60.533 55.0 2.24 0.00 0.00 4.68 F
3615 4692 0.036952 AATGCACGACAGACTCTGGG 60.037 55.0 10.86 4.66 35.51 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1896 0.323633 TGATTACCTCGTGTCCGGGA 60.324 55.000 0.0 0.0 36.35 5.14 R
3004 3936 0.742281 CTCCAGCCATGTGTTCTCCG 60.742 60.000 0.0 0.0 0.00 4.63 R
3563 4622 2.025605 TCAGGATGCCAATTCTCAGCTT 60.026 45.455 0.0 0.0 34.76 3.74 R
3636 4743 0.460311 CAAGGGACGAGAAGGCGTAT 59.540 55.000 0.0 0.0 45.72 3.06 R
4457 5666 0.039618 GGGGAAGGAGCAACAATCCA 59.960 55.000 0.0 0.0 39.47 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 2.439156 GTGAGCATGTGGCCCTCC 60.439 66.667 0.00 0.00 46.50 4.30
134 135 1.900351 CTCCTGAGGACGCCATTGA 59.100 57.895 0.00 0.00 0.00 2.57
142 143 1.812571 AGGACGCCATTGACAATGTTC 59.187 47.619 23.27 16.48 37.18 3.18
149 154 2.474526 CCATTGACAATGTTCGTCTCGC 60.475 50.000 23.27 0.00 37.18 5.03
156 161 0.457509 ATGTTCGTCTCGCTGCTCAG 60.458 55.000 0.00 0.00 0.00 3.35
176 181 1.369091 GGCACCTGTACTTGATGCCG 61.369 60.000 8.66 0.00 45.85 5.69
177 182 1.369091 GCACCTGTACTTGATGCCGG 61.369 60.000 0.00 0.00 0.00 6.13
182 187 1.220749 GTACTTGATGCCGGCCTGA 59.779 57.895 26.77 5.00 0.00 3.86
184 189 0.179048 TACTTGATGCCGGCCTGATG 60.179 55.000 26.77 13.38 0.00 3.07
193 198 2.842058 GGCCTGATGGATGGGAGG 59.158 66.667 0.00 0.00 34.57 4.30
204 209 0.461961 GATGGGAGGTTCAGAGGACG 59.538 60.000 0.00 0.00 0.00 4.79
237 242 1.421346 TATGCAGGGGAGCTGGATGG 61.421 60.000 0.00 0.00 34.74 3.51
287 309 1.269012 CATGGCATTGGTGGTTCCTT 58.731 50.000 0.00 0.00 37.07 3.36
288 310 1.066716 CATGGCATTGGTGGTTCCTTG 60.067 52.381 0.00 0.00 37.07 3.61
289 311 1.293179 GGCATTGGTGGTTCCTTGC 59.707 57.895 0.00 0.00 41.71 4.01
290 312 1.187567 GGCATTGGTGGTTCCTTGCT 61.188 55.000 10.35 0.00 41.93 3.91
291 313 0.244721 GCATTGGTGGTTCCTTGCTC 59.755 55.000 0.00 0.00 40.38 4.26
292 314 0.523072 CATTGGTGGTTCCTTGCTCG 59.477 55.000 0.00 0.00 37.07 5.03
293 315 0.110486 ATTGGTGGTTCCTTGCTCGT 59.890 50.000 0.00 0.00 37.07 4.18
294 316 0.817634 TTGGTGGTTCCTTGCTCGTG 60.818 55.000 0.00 0.00 37.07 4.35
295 317 1.070786 GGTGGTTCCTTGCTCGTGA 59.929 57.895 0.00 0.00 0.00 4.35
296 318 1.228657 GGTGGTTCCTTGCTCGTGAC 61.229 60.000 0.00 0.00 0.00 3.67
297 319 1.070786 TGGTTCCTTGCTCGTGACC 59.929 57.895 0.00 0.00 0.00 4.02
298 320 1.070786 GGTTCCTTGCTCGTGACCA 59.929 57.895 0.00 0.00 0.00 4.02
299 321 0.321653 GGTTCCTTGCTCGTGACCAT 60.322 55.000 0.00 0.00 0.00 3.55
300 322 0.798776 GTTCCTTGCTCGTGACCATG 59.201 55.000 0.00 0.00 0.00 3.66
301 323 0.955428 TTCCTTGCTCGTGACCATGC 60.955 55.000 0.00 0.00 0.00 4.06
302 324 1.376424 CCTTGCTCGTGACCATGCT 60.376 57.895 0.00 0.00 0.00 3.79
313 335 1.480545 TGACCATGCTTCGCTTAGCTA 59.519 47.619 1.76 0.00 41.76 3.32
317 339 2.874701 CCATGCTTCGCTTAGCTACATT 59.125 45.455 1.76 0.00 41.76 2.71
321 343 5.907197 TGCTTCGCTTAGCTACATTAATC 57.093 39.130 1.76 0.00 41.76 1.75
322 344 5.601662 TGCTTCGCTTAGCTACATTAATCT 58.398 37.500 1.76 0.00 41.76 2.40
323 345 6.745116 TGCTTCGCTTAGCTACATTAATCTA 58.255 36.000 1.76 0.00 41.76 1.98
822 866 3.733443 TTTTTGAGGGAAGCTTGAAGC 57.267 42.857 9.59 9.59 42.84 3.86
823 867 2.363306 TTTGAGGGAAGCTTGAAGCA 57.637 45.000 20.45 0.00 45.56 3.91
824 868 2.592102 TTGAGGGAAGCTTGAAGCAT 57.408 45.000 20.45 7.41 45.56 3.79
825 869 2.119801 TGAGGGAAGCTTGAAGCATC 57.880 50.000 20.45 16.82 45.56 3.91
826 870 1.352017 TGAGGGAAGCTTGAAGCATCA 59.648 47.619 21.82 13.04 45.56 3.07
827 871 1.742268 GAGGGAAGCTTGAAGCATCAC 59.258 52.381 21.82 19.17 45.56 3.06
828 872 0.813821 GGGAAGCTTGAAGCATCACC 59.186 55.000 21.82 16.46 45.56 4.02
845 889 2.642311 TCACCCTAAATGCCAGAACTGA 59.358 45.455 3.19 0.00 0.00 3.41
848 892 2.019984 CCTAAATGCCAGAACTGAGCC 58.980 52.381 3.19 0.00 0.00 4.70
855 899 2.038975 AGAACTGAGCCGGGCCTA 59.961 61.111 17.02 3.79 0.00 3.93
856 900 1.383248 AGAACTGAGCCGGGCCTAT 60.383 57.895 17.02 0.00 0.00 2.57
862 906 2.690881 AGCCGGGCCTATGTGGAA 60.691 61.111 17.02 0.00 38.35 3.53
863 907 2.056906 GAGCCGGGCCTATGTGGAAT 62.057 60.000 17.02 0.00 38.35 3.01
868 912 0.751643 GGGCCTATGTGGAATGCGTT 60.752 55.000 0.84 0.00 38.35 4.84
875 919 3.369400 TGGAATGCGTTTGGGCCG 61.369 61.111 0.00 0.00 0.00 6.13
924 977 0.827925 TGGGAGACGAGAACTGCAGT 60.828 55.000 15.25 15.25 0.00 4.40
927 980 0.315568 GAGACGAGAACTGCAGTGGT 59.684 55.000 22.49 15.86 0.00 4.16
990 1053 4.947147 GCGGGTGGGTTGCTGTCA 62.947 66.667 0.00 0.00 0.00 3.58
1232 1305 4.807039 CGCTCCCCACGTAACCCG 62.807 72.222 0.00 0.00 44.03 5.28
1237 1312 1.980772 CCCCACGTAACCCGAGACT 60.981 63.158 0.00 0.00 40.70 3.24
1255 1330 3.605749 TTCCGCCCCGCTCTTTCTG 62.606 63.158 0.00 0.00 0.00 3.02
1266 1341 0.108138 CTCTTTCTGTACCCCCGCTG 60.108 60.000 0.00 0.00 0.00 5.18
1270 1360 4.162690 CTGTACCCCCGCTGCCTC 62.163 72.222 0.00 0.00 0.00 4.70
1279 1369 4.834453 CGCTGCCTCCTGCTCCTG 62.834 72.222 0.00 0.00 42.00 3.86
1281 1371 3.400928 CTGCCTCCTGCTCCTGCT 61.401 66.667 0.00 0.00 42.00 4.24
1282 1372 3.388703 CTGCCTCCTGCTCCTGCTC 62.389 68.421 0.00 0.00 42.00 4.26
1283 1373 4.173924 GCCTCCTGCTCCTGCTCC 62.174 72.222 0.00 0.00 40.48 4.70
1439 1747 3.793888 CCCAGGTTCCCCCGCTAC 61.794 72.222 0.00 0.00 38.74 3.58
1455 1763 1.331756 GCTACTCCACATTCCATTGCG 59.668 52.381 0.00 0.00 0.00 4.85
1461 1769 2.342650 ACATTCCATTGCGGCGCTT 61.343 52.632 33.26 17.70 33.14 4.68
1489 1814 2.088423 CTGAGCTCCTAGTGACGAACT 58.912 52.381 12.15 0.00 43.40 3.01
1490 1815 1.813178 TGAGCTCCTAGTGACGAACTG 59.187 52.381 12.15 0.00 40.26 3.16
1491 1816 2.085320 GAGCTCCTAGTGACGAACTGA 58.915 52.381 0.87 0.00 40.26 3.41
1492 1817 2.488545 GAGCTCCTAGTGACGAACTGAA 59.511 50.000 0.87 0.00 40.26 3.02
1495 1820 3.671164 GCTCCTAGTGACGAACTGAACTC 60.671 52.174 5.89 0.00 40.26 3.01
1496 1821 3.752665 TCCTAGTGACGAACTGAACTCT 58.247 45.455 5.89 0.00 40.26 3.24
1497 1822 4.142790 TCCTAGTGACGAACTGAACTCTT 58.857 43.478 5.89 0.00 40.26 2.85
1498 1823 4.215827 TCCTAGTGACGAACTGAACTCTTC 59.784 45.833 5.89 0.00 40.26 2.87
1499 1824 4.216687 CCTAGTGACGAACTGAACTCTTCT 59.783 45.833 5.89 0.00 40.26 2.85
1500 1825 4.657436 AGTGACGAACTGAACTCTTCTT 57.343 40.909 0.00 0.00 37.88 2.52
1501 1826 4.612943 AGTGACGAACTGAACTCTTCTTC 58.387 43.478 0.00 0.00 37.88 2.87
1502 1827 4.339814 AGTGACGAACTGAACTCTTCTTCT 59.660 41.667 0.00 0.00 37.88 2.85
1503 1828 5.044558 GTGACGAACTGAACTCTTCTTCTT 58.955 41.667 0.00 0.00 0.00 2.52
1504 1829 5.043903 TGACGAACTGAACTCTTCTTCTTG 58.956 41.667 0.00 0.00 0.00 3.02
1505 1830 3.804873 ACGAACTGAACTCTTCTTCTTGC 59.195 43.478 0.00 0.00 0.00 4.01
1506 1831 4.054671 CGAACTGAACTCTTCTTCTTGCT 58.945 43.478 0.00 0.00 0.00 3.91
1507 1832 4.149747 CGAACTGAACTCTTCTTCTTGCTC 59.850 45.833 0.00 0.00 0.00 4.26
1508 1833 4.953940 ACTGAACTCTTCTTCTTGCTCT 57.046 40.909 0.00 0.00 0.00 4.09
1589 1914 0.101939 GTCCCGGACACGAGGTAATC 59.898 60.000 13.05 0.00 44.60 1.75
1600 1925 5.357257 ACACGAGGTAATCAATATGGACAC 58.643 41.667 0.00 0.00 0.00 3.67
1623 1948 2.100087 ACTGAACCGAAACGCCAAATTT 59.900 40.909 0.00 0.00 0.00 1.82
1646 1971 1.299541 CGTTGTTTCTGCTGGACTGT 58.700 50.000 0.00 0.00 0.00 3.55
1654 1979 1.615883 TCTGCTGGACTGTGAGAACTC 59.384 52.381 0.00 0.00 0.00 3.01
1758 2093 0.532862 CGGCCAATGTAGGATCGCTT 60.533 55.000 2.24 0.00 0.00 4.68
1776 2111 4.039488 TCGCTTAAGGACTTTGGAGTTACA 59.961 41.667 4.29 0.00 35.88 2.41
1798 2133 1.446272 CGAGAAGTTCCGGTGAGCC 60.446 63.158 0.00 0.00 0.00 4.70
1839 2180 8.356657 AGATATCTGCTACTCTGTGTTACATTC 58.643 37.037 3.89 0.00 0.00 2.67
1840 2181 5.722021 TCTGCTACTCTGTGTTACATTCA 57.278 39.130 0.00 0.00 0.00 2.57
1841 2182 6.096673 TCTGCTACTCTGTGTTACATTCAA 57.903 37.500 0.00 0.00 0.00 2.69
1879 2220 2.221169 TGTGTTACTTTGCCTCTGCTG 58.779 47.619 0.00 0.00 38.71 4.41
1880 2221 2.222027 GTGTTACTTTGCCTCTGCTGT 58.778 47.619 0.00 0.00 38.71 4.40
1968 2315 2.233566 TGGCCTTGACTGGGATGCT 61.234 57.895 3.32 0.00 0.00 3.79
2073 2420 3.169099 AGCTGATATCCGTAGAGCCATT 58.831 45.455 8.05 0.00 0.00 3.16
2128 2481 2.856760 TGAGGGGAGCAGAGTATTCT 57.143 50.000 0.00 0.00 0.00 2.40
2129 2482 2.672098 TGAGGGGAGCAGAGTATTCTC 58.328 52.381 0.00 0.00 40.70 2.87
2177 2530 8.374464 GTACTGTGTAGTACGTACTGAAATTC 57.626 38.462 33.23 18.56 46.91 2.17
2192 3052 6.888105 ACTGAAATTCTTCATGTTTTGGGTT 58.112 32.000 0.00 0.00 40.78 4.11
2195 3061 6.765512 TGAAATTCTTCATGTTTTGGGTTTCC 59.234 34.615 0.00 0.00 36.62 3.13
2260 3126 4.323417 TGCTACGGTGAATTTGTTGAGAT 58.677 39.130 0.00 0.00 0.00 2.75
2294 3160 3.627395 ATGGTGGTATGTTCACGATGT 57.373 42.857 0.00 0.00 33.45 3.06
2345 3244 7.445402 AGTCTTACCTAATTGCGCATTTCATAT 59.555 33.333 19.84 2.24 0.00 1.78
3004 3936 7.272731 GGTACTCTTCCAATGTTTAAATTTCGC 59.727 37.037 0.00 0.00 0.00 4.70
3021 3953 2.401766 GCGGAGAACACATGGCTGG 61.402 63.158 0.00 0.00 0.00 4.85
3026 3958 2.356535 GGAGAACACATGGCTGGAGAAT 60.357 50.000 0.00 0.00 0.00 2.40
3051 3987 8.021898 TCCCTCAAATTCAAAGTTTGATCTTT 57.978 30.769 18.69 16.84 42.68 2.52
3416 4472 5.349543 TGATGCTATGTTATTGCTATCTGCG 59.650 40.000 0.00 0.00 46.63 5.18
3425 4482 3.887621 TTGCTATCTGCGTAGTTTCCT 57.112 42.857 0.00 0.00 46.63 3.36
3430 4487 5.106712 TGCTATCTGCGTAGTTTCCTTTTTG 60.107 40.000 0.00 0.00 46.63 2.44
3563 4622 1.617322 ACGCTGTCTTCTGTCAGGTA 58.383 50.000 0.00 0.00 31.60 3.08
3566 4625 2.342179 GCTGTCTTCTGTCAGGTAAGC 58.658 52.381 0.00 0.00 31.60 3.09
3613 4690 1.923204 GCTAATGCACGACAGACTCTG 59.077 52.381 4.36 4.36 39.41 3.35
3614 4691 2.534298 CTAATGCACGACAGACTCTGG 58.466 52.381 10.86 0.00 35.51 3.86
3615 4692 0.036952 AATGCACGACAGACTCTGGG 60.037 55.000 10.86 4.66 35.51 4.45
3618 4695 1.290324 CACGACAGACTCTGGGTGG 59.710 63.158 18.15 5.81 36.83 4.61
3619 4696 1.908793 ACGACAGACTCTGGGTGGG 60.909 63.158 10.86 0.00 35.51 4.61
3620 4697 2.650116 CGACAGACTCTGGGTGGGG 61.650 68.421 10.86 0.00 35.51 4.96
3621 4698 1.229209 GACAGACTCTGGGTGGGGA 60.229 63.158 10.86 0.00 35.51 4.81
3622 4699 1.229336 ACAGACTCTGGGTGGGGAG 60.229 63.158 10.86 0.00 35.51 4.30
3648 4755 1.261619 GGCATCAAATACGCCTTCTCG 59.738 52.381 0.00 0.00 42.78 4.04
3665 4772 1.003355 CGTCCCTTGCACTGATGGT 60.003 57.895 0.00 0.00 0.00 3.55
3714 4821 1.234821 GAGGAACGCATTGGACACAA 58.765 50.000 0.00 0.00 41.59 3.33
3798 4907 2.472695 TTTCTGGAATGGAGGTCACG 57.527 50.000 0.00 0.00 0.00 4.35
3811 4920 3.592059 GAGGTCACGTAGCCATTTGTTA 58.408 45.455 9.77 0.00 0.00 2.41
3813 4922 3.938963 AGGTCACGTAGCCATTTGTTATG 59.061 43.478 9.77 0.00 0.00 1.90
3814 4923 3.687698 GGTCACGTAGCCATTTGTTATGT 59.312 43.478 0.00 0.00 0.00 2.29
3815 4924 4.155280 GGTCACGTAGCCATTTGTTATGTT 59.845 41.667 0.00 0.00 0.00 2.71
3826 4935 7.015195 AGCCATTTGTTATGTTACCAAAAGACT 59.985 33.333 0.00 0.00 32.39 3.24
3828 4937 9.191995 CCATTTGTTATGTTACCAAAAGACTTC 57.808 33.333 0.00 0.00 32.39 3.01
3830 4939 7.883391 TTGTTATGTTACCAAAAGACTTCCA 57.117 32.000 0.00 0.00 0.00 3.53
3831 4940 8.472007 TTGTTATGTTACCAAAAGACTTCCAT 57.528 30.769 0.00 0.00 0.00 3.41
3896 5058 5.916661 AATCTTTTCTCATTGATGCTGCT 57.083 34.783 0.00 0.00 0.00 4.24
3958 5128 1.117150 AATGCAGGAACCATCATGGC 58.883 50.000 2.52 0.00 42.67 4.40
3962 5132 0.323633 CAGGAACCATCATGGCCACA 60.324 55.000 8.16 0.00 42.67 4.17
4020 5226 2.949447 ACAGGTTTCAAGGCTGTGAAT 58.051 42.857 11.19 0.00 37.36 2.57
4086 5295 1.134007 TGAAGCCGGAGCATCATTGAT 60.134 47.619 5.05 0.00 41.55 2.57
4087 5296 1.952296 GAAGCCGGAGCATCATTGATT 59.048 47.619 5.05 0.00 43.56 2.57
4102 5311 8.086522 GCATCATTGATTTTGGATAGCTTATGT 58.913 33.333 0.00 0.00 0.00 2.29
4107 5316 8.750515 TTGATTTTGGATAGCTTATGTGATCA 57.249 30.769 0.00 0.00 0.00 2.92
4128 5337 3.914426 ACTCGGCAGTTGATTAGGATT 57.086 42.857 0.00 0.00 0.00 3.01
4169 5378 5.048013 AGTGGGTTAGTTAGAAATGCTTTGC 60.048 40.000 0.00 0.00 0.00 3.68
4175 5384 4.874970 AGTTAGAAATGCTTTGCAAGTGG 58.125 39.130 0.00 0.00 43.62 4.00
4176 5385 4.342092 AGTTAGAAATGCTTTGCAAGTGGT 59.658 37.500 0.00 0.00 43.62 4.16
4181 5390 0.173029 TGCTTTGCAAGTGGTGTGTG 59.827 50.000 0.00 0.00 34.76 3.82
4191 5400 1.974957 AGTGGTGTGTGCCATGTACTA 59.025 47.619 0.00 0.00 41.08 1.82
4195 5404 2.355716 GGTGTGTGCCATGTACTACCAT 60.356 50.000 13.92 0.00 31.26 3.55
4237 5446 8.557864 CATTCATTCAACAAGAGATAGATGACC 58.442 37.037 0.00 0.00 0.00 4.02
4261 5470 2.624838 CACAGCACTTCATTTTGGAGGT 59.375 45.455 0.00 0.00 0.00 3.85
4264 5473 4.162131 ACAGCACTTCATTTTGGAGGTTTT 59.838 37.500 0.00 0.00 0.00 2.43
4307 5516 2.418368 TGCTGAATTGTTAGGGCGAT 57.582 45.000 0.00 0.00 0.00 4.58
4432 5641 6.318144 CCTGAACATCTGCTCTATGAACAAAT 59.682 38.462 0.00 0.00 0.00 2.32
4443 5652 8.959548 TGCTCTATGAACAAATTTGTGATGTAT 58.040 29.630 23.93 15.09 41.31 2.29
4444 5653 9.443283 GCTCTATGAACAAATTTGTGATGTATC 57.557 33.333 23.93 16.21 41.31 2.24
4459 5668 4.344968 TGATGTATCACCCTGTCATAGTGG 59.655 45.833 3.32 0.00 32.29 4.00
4460 5669 3.989056 TGTATCACCCTGTCATAGTGGA 58.011 45.455 3.32 0.00 32.29 4.02
4461 5670 4.556697 TGTATCACCCTGTCATAGTGGAT 58.443 43.478 3.32 0.00 32.29 3.41
4463 5672 3.912496 TCACCCTGTCATAGTGGATTG 57.088 47.619 3.32 0.00 32.29 2.67
4464 5673 3.181329 TCACCCTGTCATAGTGGATTGT 58.819 45.455 3.32 0.00 32.29 2.71
4465 5674 3.587061 TCACCCTGTCATAGTGGATTGTT 59.413 43.478 3.32 0.00 32.29 2.83
4466 5675 3.691118 CACCCTGTCATAGTGGATTGTTG 59.309 47.826 0.00 0.00 0.00 3.33
4467 5676 2.684881 CCCTGTCATAGTGGATTGTTGC 59.315 50.000 0.00 0.00 0.00 4.17
4468 5677 3.614092 CCTGTCATAGTGGATTGTTGCT 58.386 45.455 0.00 0.00 0.00 3.91
4470 5679 3.609853 TGTCATAGTGGATTGTTGCTCC 58.390 45.455 0.00 0.00 0.00 4.70
4471 5680 3.264193 TGTCATAGTGGATTGTTGCTCCT 59.736 43.478 0.00 0.00 33.69 3.69
4472 5681 4.263462 TGTCATAGTGGATTGTTGCTCCTT 60.263 41.667 0.00 0.00 33.69 3.36
4473 5682 4.333926 GTCATAGTGGATTGTTGCTCCTTC 59.666 45.833 0.00 0.00 33.69 3.46
4474 5683 2.206576 AGTGGATTGTTGCTCCTTCC 57.793 50.000 0.00 0.00 33.69 3.46
4475 5684 1.177401 GTGGATTGTTGCTCCTTCCC 58.823 55.000 0.00 0.00 33.69 3.97
4476 5685 0.039618 TGGATTGTTGCTCCTTCCCC 59.960 55.000 0.00 0.00 33.69 4.81
4477 5686 0.039618 GGATTGTTGCTCCTTCCCCA 59.960 55.000 0.00 0.00 0.00 4.96
4478 5687 1.342374 GGATTGTTGCTCCTTCCCCAT 60.342 52.381 0.00 0.00 0.00 4.00
4479 5688 2.027385 GATTGTTGCTCCTTCCCCATC 58.973 52.381 0.00 0.00 0.00 3.51
4480 5689 0.776810 TTGTTGCTCCTTCCCCATCA 59.223 50.000 0.00 0.00 0.00 3.07
4481 5690 1.002069 TGTTGCTCCTTCCCCATCAT 58.998 50.000 0.00 0.00 0.00 2.45
4482 5691 1.341285 TGTTGCTCCTTCCCCATCATG 60.341 52.381 0.00 0.00 0.00 3.07
4483 5692 0.396139 TTGCTCCTTCCCCATCATGC 60.396 55.000 0.00 0.00 0.00 4.06
4492 5720 1.701292 TCCCCATCATGCTCATAGTGG 59.299 52.381 0.00 5.99 0.00 4.00
4494 5722 2.639347 CCCCATCATGCTCATAGTGGTA 59.361 50.000 10.07 0.00 0.00 3.25
4522 5766 2.357034 CCGGACACCTTCACGTGG 60.357 66.667 17.00 1.58 38.11 4.94
4562 5810 3.682858 ACGATGGTGTAAATTTCCTGACG 59.317 43.478 0.00 1.32 0.00 4.35
4589 5979 6.348132 GGGTGCCATTTTTACATTTTACAAGC 60.348 38.462 0.00 0.00 0.00 4.01
4599 5989 5.338614 ACATTTTACAAGCACGTACTGTC 57.661 39.130 0.00 0.00 0.00 3.51
4602 5992 3.994204 TTACAAGCACGTACTGTCTGA 57.006 42.857 0.00 0.00 0.00 3.27
4615 6005 5.508573 CGTACTGTCTGACTTTTGACTATCG 59.491 44.000 9.51 0.00 34.57 2.92
4619 6009 3.927142 GTCTGACTTTTGACTATCGGGTG 59.073 47.826 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.112580 CGCACAGGTAAAAACAACTTGG 58.887 45.455 0.00 0.00 0.00 3.61
1 2 4.022464 TCGCACAGGTAAAAACAACTTG 57.978 40.909 0.00 0.00 0.00 3.16
2 3 4.578928 AGATCGCACAGGTAAAAACAACTT 59.421 37.500 0.00 0.00 0.00 2.66
3 4 4.024048 CAGATCGCACAGGTAAAAACAACT 60.024 41.667 0.00 0.00 0.00 3.16
4 5 4.219033 CAGATCGCACAGGTAAAAACAAC 58.781 43.478 0.00 0.00 0.00 3.32
5 6 3.252215 CCAGATCGCACAGGTAAAAACAA 59.748 43.478 0.00 0.00 0.00 2.83
6 7 2.811431 CCAGATCGCACAGGTAAAAACA 59.189 45.455 0.00 0.00 0.00 2.83
7 8 2.414161 GCCAGATCGCACAGGTAAAAAC 60.414 50.000 0.00 0.00 0.00 2.43
8 9 1.810151 GCCAGATCGCACAGGTAAAAA 59.190 47.619 0.00 0.00 0.00 1.94
134 135 0.319900 AGCAGCGAGACGAACATTGT 60.320 50.000 0.00 0.00 0.00 2.71
156 161 2.482326 GCATCAAGTACAGGTGCCC 58.518 57.895 11.32 0.00 0.00 5.36
159 164 1.369091 GCCGGCATCAAGTACAGGTG 61.369 60.000 24.80 0.00 0.00 4.00
162 167 1.091771 CAGGCCGGCATCAAGTACAG 61.092 60.000 30.85 1.86 0.00 2.74
163 168 1.078497 CAGGCCGGCATCAAGTACA 60.078 57.895 30.85 0.00 0.00 2.90
164 169 0.179045 ATCAGGCCGGCATCAAGTAC 60.179 55.000 30.85 8.01 0.00 2.73
165 170 0.179048 CATCAGGCCGGCATCAAGTA 60.179 55.000 30.85 6.01 0.00 2.24
166 171 1.452651 CATCAGGCCGGCATCAAGT 60.453 57.895 30.85 5.54 0.00 3.16
167 172 2.191513 CCATCAGGCCGGCATCAAG 61.192 63.158 30.85 14.55 0.00 3.02
168 173 1.998444 ATCCATCAGGCCGGCATCAA 61.998 55.000 30.85 12.50 33.74 2.57
169 174 2.454688 ATCCATCAGGCCGGCATCA 61.455 57.895 30.85 8.56 33.74 3.07
170 175 1.970114 CATCCATCAGGCCGGCATC 60.970 63.158 30.85 12.35 33.74 3.91
171 176 2.114625 CATCCATCAGGCCGGCAT 59.885 61.111 30.85 21.35 33.74 4.40
172 177 4.193893 CCATCCATCAGGCCGGCA 62.194 66.667 30.85 8.42 33.74 5.69
173 178 4.962836 CCCATCCATCAGGCCGGC 62.963 72.222 21.18 21.18 33.74 6.13
174 179 3.170672 TCCCATCCATCAGGCCGG 61.171 66.667 0.00 0.00 33.74 6.13
175 180 2.429058 CTCCCATCCATCAGGCCG 59.571 66.667 0.00 0.00 33.74 6.13
176 181 1.649271 AACCTCCCATCCATCAGGCC 61.649 60.000 0.00 0.00 33.74 5.19
177 182 0.179006 GAACCTCCCATCCATCAGGC 60.179 60.000 0.00 0.00 33.74 4.85
182 187 1.010046 TCCTCTGAACCTCCCATCCAT 59.990 52.381 0.00 0.00 0.00 3.41
184 189 0.833949 GTCCTCTGAACCTCCCATCC 59.166 60.000 0.00 0.00 0.00 3.51
193 198 1.153349 GCCATCCCGTCCTCTGAAC 60.153 63.158 0.00 0.00 0.00 3.18
204 209 2.684881 CCTGCATATAAATCGCCATCCC 59.315 50.000 0.00 0.00 0.00 3.85
237 242 4.717313 AAACCTCGCCGCCTTCCC 62.717 66.667 0.00 0.00 0.00 3.97
287 309 1.737735 CGAAGCATGGTCACGAGCA 60.738 57.895 15.80 0.79 43.48 4.26
288 310 3.084579 CGAAGCATGGTCACGAGC 58.915 61.111 15.80 0.00 0.00 5.03
301 323 7.327275 CCACTAGATTAATGTAGCTAAGCGAAG 59.673 40.741 17.27 0.00 0.00 3.79
302 324 7.145985 CCACTAGATTAATGTAGCTAAGCGAA 58.854 38.462 17.27 0.00 0.00 4.70
313 335 6.539173 TGAACCACAACCACTAGATTAATGT 58.461 36.000 0.00 0.00 0.00 2.71
317 339 5.512404 CCACTGAACCACAACCACTAGATTA 60.512 44.000 0.00 0.00 0.00 1.75
321 343 2.104111 TCCACTGAACCACAACCACTAG 59.896 50.000 0.00 0.00 0.00 2.57
322 344 2.120312 TCCACTGAACCACAACCACTA 58.880 47.619 0.00 0.00 0.00 2.74
323 345 0.916086 TCCACTGAACCACAACCACT 59.084 50.000 0.00 0.00 0.00 4.00
802 846 3.030291 TGCTTCAAGCTTCCCTCAAAAA 58.970 40.909 11.57 0.00 42.97 1.94
803 847 2.665165 TGCTTCAAGCTTCCCTCAAAA 58.335 42.857 11.57 0.00 42.97 2.44
804 848 2.363306 TGCTTCAAGCTTCCCTCAAA 57.637 45.000 11.57 0.00 42.97 2.69
805 849 2.224843 TGATGCTTCAAGCTTCCCTCAA 60.225 45.455 19.73 1.22 42.66 3.02
806 850 1.352017 TGATGCTTCAAGCTTCCCTCA 59.648 47.619 19.73 8.44 42.66 3.86
807 851 1.742268 GTGATGCTTCAAGCTTCCCTC 59.258 52.381 19.73 8.89 42.66 4.30
808 852 1.615384 GGTGATGCTTCAAGCTTCCCT 60.615 52.381 19.73 0.00 42.66 4.20
809 853 0.813821 GGTGATGCTTCAAGCTTCCC 59.186 55.000 19.73 16.30 42.66 3.97
810 854 0.813821 GGGTGATGCTTCAAGCTTCC 59.186 55.000 19.73 12.16 42.66 3.46
811 855 1.831580 AGGGTGATGCTTCAAGCTTC 58.168 50.000 16.61 16.61 42.97 3.86
812 856 3.439857 TTAGGGTGATGCTTCAAGCTT 57.560 42.857 11.57 3.78 42.97 3.74
813 857 3.439857 TTTAGGGTGATGCTTCAAGCT 57.560 42.857 11.57 0.00 42.97 3.74
814 858 3.736126 GCATTTAGGGTGATGCTTCAAGC 60.736 47.826 1.04 1.04 43.98 4.01
815 859 3.181483 GGCATTTAGGGTGATGCTTCAAG 60.181 47.826 3.51 0.00 46.01 3.02
816 860 2.760092 GGCATTTAGGGTGATGCTTCAA 59.240 45.455 3.51 0.00 46.01 2.69
817 861 2.291475 TGGCATTTAGGGTGATGCTTCA 60.291 45.455 8.06 0.00 46.01 3.02
818 862 2.360165 CTGGCATTTAGGGTGATGCTTC 59.640 50.000 8.06 0.00 46.01 3.86
819 863 2.025037 TCTGGCATTTAGGGTGATGCTT 60.025 45.455 8.06 0.00 46.01 3.91
820 864 1.565759 TCTGGCATTTAGGGTGATGCT 59.434 47.619 8.06 0.00 46.01 3.79
821 865 2.057137 TCTGGCATTTAGGGTGATGC 57.943 50.000 0.00 0.00 46.03 3.91
822 866 3.379372 CAGTTCTGGCATTTAGGGTGATG 59.621 47.826 0.00 0.00 0.00 3.07
823 867 3.266772 TCAGTTCTGGCATTTAGGGTGAT 59.733 43.478 0.00 0.00 0.00 3.06
824 868 2.642311 TCAGTTCTGGCATTTAGGGTGA 59.358 45.455 0.00 0.00 0.00 4.02
825 869 3.012518 CTCAGTTCTGGCATTTAGGGTG 58.987 50.000 0.00 0.00 0.00 4.61
826 870 2.619074 GCTCAGTTCTGGCATTTAGGGT 60.619 50.000 0.00 0.00 0.00 4.34
827 871 2.019984 GCTCAGTTCTGGCATTTAGGG 58.980 52.381 0.00 0.00 0.00 3.53
828 872 2.019984 GGCTCAGTTCTGGCATTTAGG 58.980 52.381 12.54 0.00 0.00 2.69
845 889 2.078665 ATTCCACATAGGCCCGGCT 61.079 57.895 9.86 0.34 37.29 5.52
848 892 2.253758 CGCATTCCACATAGGCCCG 61.254 63.158 0.00 0.00 37.29 6.13
855 899 1.591183 GCCCAAACGCATTCCACAT 59.409 52.632 0.00 0.00 0.00 3.21
856 900 2.569354 GGCCCAAACGCATTCCACA 61.569 57.895 0.00 0.00 0.00 4.17
875 919 2.203209 CGCATTCCACCTAGGCCC 60.203 66.667 9.30 0.00 37.29 5.80
881 925 2.676471 GCCCAACGCATTCCACCT 60.676 61.111 0.00 0.00 37.47 4.00
916 969 1.893808 CCGCTTCACCACTGCAGTT 60.894 57.895 18.94 0.00 0.00 3.16
1218 1291 1.978617 GTCTCGGGTTACGTGGGGA 60.979 63.158 0.00 0.00 44.69 4.81
1232 1305 4.516195 GAGCGGGGCGGAAGTCTC 62.516 72.222 0.00 0.00 34.89 3.36
1237 1312 3.319198 AGAAAGAGCGGGGCGGAA 61.319 61.111 0.00 0.00 0.00 4.30
1266 1341 4.173924 GGAGCAGGAGCAGGAGGC 62.174 72.222 0.00 0.00 45.49 4.70
1270 1360 2.686470 TCAGGGAGCAGGAGCAGG 60.686 66.667 0.00 0.00 45.49 4.85
1294 1384 2.179547 CAGTTCACACACAGGCGCA 61.180 57.895 10.83 0.00 0.00 6.09
1430 1736 1.146263 GAATGTGGAGTAGCGGGGG 59.854 63.158 0.00 0.00 0.00 5.40
1435 1741 1.331756 CGCAATGGAATGTGGAGTAGC 59.668 52.381 0.00 0.00 0.00 3.58
1478 1803 5.531659 AGAAGAAGAGTTCAGTTCGTCACTA 59.468 40.000 0.00 0.00 34.69 2.74
1489 1814 4.818546 CCAAAGAGCAAGAAGAAGAGTTCA 59.181 41.667 0.00 0.00 0.00 3.18
1490 1815 4.819088 ACCAAAGAGCAAGAAGAAGAGTTC 59.181 41.667 0.00 0.00 0.00 3.01
1491 1816 4.786425 ACCAAAGAGCAAGAAGAAGAGTT 58.214 39.130 0.00 0.00 0.00 3.01
1492 1817 4.429854 ACCAAAGAGCAAGAAGAAGAGT 57.570 40.909 0.00 0.00 0.00 3.24
1495 1820 4.047142 GCAAACCAAAGAGCAAGAAGAAG 58.953 43.478 0.00 0.00 0.00 2.85
1496 1821 3.181476 GGCAAACCAAAGAGCAAGAAGAA 60.181 43.478 0.00 0.00 35.26 2.52
1497 1822 2.362077 GGCAAACCAAAGAGCAAGAAGA 59.638 45.455 0.00 0.00 35.26 2.87
1498 1823 2.101249 TGGCAAACCAAAGAGCAAGAAG 59.899 45.455 0.00 0.00 45.37 2.85
1499 1824 2.106566 TGGCAAACCAAAGAGCAAGAA 58.893 42.857 0.00 0.00 45.37 2.52
1500 1825 1.774110 TGGCAAACCAAAGAGCAAGA 58.226 45.000 0.00 0.00 45.37 3.02
1571 1896 0.323633 TGATTACCTCGTGTCCGGGA 60.324 55.000 0.00 0.00 36.35 5.14
1574 1899 3.987868 CCATATTGATTACCTCGTGTCCG 59.012 47.826 0.00 0.00 0.00 4.79
1589 1914 2.603110 CGGTTCAGTCGTGTCCATATTG 59.397 50.000 0.00 0.00 0.00 1.90
1600 1925 1.492319 TTGGCGTTTCGGTTCAGTCG 61.492 55.000 0.00 0.00 0.00 4.18
1623 1948 0.749818 TCCAGCAGAAACAACGCCAA 60.750 50.000 0.00 0.00 0.00 4.52
1628 1953 2.288666 TCACAGTCCAGCAGAAACAAC 58.711 47.619 0.00 0.00 0.00 3.32
1646 1971 4.262207 GGAGTTGTCTGTCATGAGTTCTCA 60.262 45.833 0.00 4.96 0.00 3.27
1654 1979 3.257393 GCAGTAGGAGTTGTCTGTCATG 58.743 50.000 0.00 0.00 0.00 3.07
1701 2036 2.109229 CCTCCTCCAGGGTGTCATAT 57.891 55.000 0.00 0.00 38.91 1.78
1758 2093 5.716228 TCGGTATGTAACTCCAAAGTCCTTA 59.284 40.000 0.00 0.00 33.48 2.69
1798 2133 5.683509 GCAGATATCTGGAGGGGAATAATCG 60.684 48.000 29.43 3.44 43.94 3.34
1839 2180 5.466728 ACACAGAGTAGCACAATGTAACTTG 59.533 40.000 0.00 0.00 0.00 3.16
1840 2181 5.611374 ACACAGAGTAGCACAATGTAACTT 58.389 37.500 0.00 0.00 0.00 2.66
1841 2182 5.215252 ACACAGAGTAGCACAATGTAACT 57.785 39.130 0.00 0.00 0.00 2.24
1879 2220 3.315191 AGCACAATGTAACACACCAGAAC 59.685 43.478 0.00 0.00 0.00 3.01
1880 2221 3.550820 AGCACAATGTAACACACCAGAA 58.449 40.909 0.00 0.00 0.00 3.02
2073 2420 9.577222 TGATATAATCTTGCCTTGATCAAATCA 57.423 29.630 9.88 8.06 37.55 2.57
2160 2513 9.701098 AAACATGAAGAATTTCAGTACGTACTA 57.299 29.630 26.95 13.25 45.89 1.82
2165 2518 6.582295 CCCAAAACATGAAGAATTTCAGTACG 59.418 38.462 0.00 0.00 45.89 3.67
2192 3052 3.777087 TGGATTTTGCATCTGAAGGGAA 58.223 40.909 0.00 0.00 0.00 3.97
2195 3061 4.927425 CAGTTTGGATTTTGCATCTGAAGG 59.073 41.667 0.00 0.00 0.00 3.46
2294 3160 7.729116 TGCTCTGTTACTCATATGATGATGAA 58.271 34.615 5.72 0.00 38.85 2.57
2345 3244 1.140452 GCAATCAGATCTGCTCCCTGA 59.860 52.381 18.36 0.00 40.68 3.86
2966 3896 5.674525 TGGAAGAGTACCATCATTCATCAC 58.325 41.667 0.00 0.00 32.03 3.06
3004 3936 0.742281 CTCCAGCCATGTGTTCTCCG 60.742 60.000 0.00 0.00 0.00 4.63
3021 3953 7.661040 TCAAACTTTGAATTTGAGGGATTCTC 58.339 34.615 1.47 0.00 40.32 2.87
3026 3958 7.601705 AAGATCAAACTTTGAATTTGAGGGA 57.398 32.000 8.28 0.00 46.33 4.20
3051 3987 5.426689 AAGAGATTGCTTGACCATCTGTA 57.573 39.130 0.00 0.00 0.00 2.74
3057 3993 7.707624 ATGATTTAAAGAGATTGCTTGACCA 57.292 32.000 0.00 0.00 0.00 4.02
3339 4368 9.730420 AATAAACTGCCGTCAAATATATTGTTC 57.270 29.630 0.00 0.00 0.00 3.18
3342 4371 8.349245 TGGAATAAACTGCCGTCAAATATATTG 58.651 33.333 0.00 0.00 0.00 1.90
3354 4384 7.259290 AGTAAATACATGGAATAAACTGCCG 57.741 36.000 0.00 0.00 0.00 5.69
3384 4414 7.730084 AGCAATAACATAGCATCAGTTAGAGA 58.270 34.615 0.00 0.00 31.96 3.10
3563 4622 2.025605 TCAGGATGCCAATTCTCAGCTT 60.026 45.455 0.00 0.00 34.76 3.74
3566 4625 5.374921 AGTAATCAGGATGCCAATTCTCAG 58.625 41.667 0.00 0.00 34.76 3.35
3636 4743 0.460311 CAAGGGACGAGAAGGCGTAT 59.540 55.000 0.00 0.00 45.72 3.06
3648 4755 1.168714 GAACCATCAGTGCAAGGGAC 58.831 55.000 0.00 0.00 0.00 4.46
3665 4772 4.219070 TCGATACGTTTCAAGGGAGAAGAA 59.781 41.667 6.81 0.00 0.00 2.52
3714 4821 1.542375 ACCCAGGACAAGAGCCCAT 60.542 57.895 0.00 0.00 0.00 4.00
3797 4906 5.804692 TGGTAACATAACAAATGGCTACG 57.195 39.130 0.00 0.00 46.17 3.51
3869 5021 6.095860 CAGCATCAATGAGAAAAGATTACCCA 59.904 38.462 0.00 0.00 0.00 4.51
3870 5022 6.501781 CAGCATCAATGAGAAAAGATTACCC 58.498 40.000 0.00 0.00 0.00 3.69
3896 5058 1.472878 GTCAGCACCGTGTCAGATCTA 59.527 52.381 0.00 0.00 0.00 1.98
4049 5258 4.006319 GCTTCAACTTACTCTGGCAATCT 58.994 43.478 0.00 0.00 0.00 2.40
4086 5295 7.011389 CGAGTTGATCACATAAGCTATCCAAAA 59.989 37.037 0.00 0.00 0.00 2.44
4087 5296 6.479990 CGAGTTGATCACATAAGCTATCCAAA 59.520 38.462 0.00 0.00 0.00 3.28
4107 5316 3.914426 ATCCTAATCAACTGCCGAGTT 57.086 42.857 0.00 0.00 43.63 3.01
4128 5337 2.635915 CCACTACAGTTTAGGGTGTGGA 59.364 50.000 0.00 0.00 44.21 4.02
4175 5384 8.754461 ATACAAATGGTAGTACATGGCACACAC 61.754 40.741 2.06 0.00 36.75 3.82
4176 5385 6.802103 ATACAAATGGTAGTACATGGCACACA 60.802 38.462 2.06 0.00 36.75 3.72
4181 5390 5.689383 CCATACAAATGGTAGTACATGGC 57.311 43.478 2.06 0.00 46.68 4.40
4203 5412 3.399440 TGTTGAATGAATGGGCAAACC 57.601 42.857 0.00 0.00 40.81 3.27
4217 5426 5.185056 TGACGGTCATCTATCTCTTGTTGAA 59.815 40.000 6.76 0.00 0.00 2.69
4219 5428 4.800993 GTGACGGTCATCTATCTCTTGTTG 59.199 45.833 14.78 0.00 0.00 3.33
4220 5429 4.462834 TGTGACGGTCATCTATCTCTTGTT 59.537 41.667 14.78 0.00 0.00 2.83
4221 5430 4.017126 TGTGACGGTCATCTATCTCTTGT 58.983 43.478 14.78 0.00 0.00 3.16
4222 5431 4.605968 CTGTGACGGTCATCTATCTCTTG 58.394 47.826 14.78 0.00 0.00 3.02
4237 5446 2.290367 TCCAAAATGAAGTGCTGTGACG 59.710 45.455 0.00 0.00 0.00 4.35
4261 5470 3.936453 AGATCCGCTGTACGCAAATAAAA 59.064 39.130 9.69 0.00 41.76 1.52
4264 5473 2.469826 CAGATCCGCTGTACGCAAATA 58.530 47.619 9.69 0.00 41.76 1.40
4284 5493 2.543641 GCCCTAACAATTCAGCAATGC 58.456 47.619 0.00 0.00 0.00 3.56
4352 5561 3.051327 CGCTCTGCACTATCAAGATCTG 58.949 50.000 0.00 0.00 0.00 2.90
4401 5610 1.484240 GAGCAGATGTTCAGGCCTAGT 59.516 52.381 3.98 0.00 0.00 2.57
4405 5614 2.103771 TCATAGAGCAGATGTTCAGGCC 59.896 50.000 0.00 0.00 0.00 5.19
4443 5652 3.181329 ACAATCCACTATGACAGGGTGA 58.819 45.455 10.85 0.90 33.32 4.02
4444 5653 3.634397 ACAATCCACTATGACAGGGTG 57.366 47.619 4.25 4.25 0.00 4.61
4445 5654 3.873801 GCAACAATCCACTATGACAGGGT 60.874 47.826 0.00 0.00 0.00 4.34
4446 5655 2.684881 GCAACAATCCACTATGACAGGG 59.315 50.000 0.00 0.00 0.00 4.45
4447 5656 3.614092 AGCAACAATCCACTATGACAGG 58.386 45.455 0.00 0.00 0.00 4.00
4448 5657 3.624861 GGAGCAACAATCCACTATGACAG 59.375 47.826 0.00 0.00 36.79 3.51
4449 5658 3.264193 AGGAGCAACAATCCACTATGACA 59.736 43.478 0.00 0.00 39.47 3.58
4450 5659 3.878778 AGGAGCAACAATCCACTATGAC 58.121 45.455 0.00 0.00 39.47 3.06
4457 5666 0.039618 GGGGAAGGAGCAACAATCCA 59.960 55.000 0.00 0.00 39.47 3.41
4459 5668 2.027385 GATGGGGAAGGAGCAACAATC 58.973 52.381 0.00 0.00 0.00 2.67
4460 5669 1.358787 TGATGGGGAAGGAGCAACAAT 59.641 47.619 0.00 0.00 0.00 2.71
4461 5670 0.776810 TGATGGGGAAGGAGCAACAA 59.223 50.000 0.00 0.00 0.00 2.83
4463 5672 1.396653 CATGATGGGGAAGGAGCAAC 58.603 55.000 0.00 0.00 0.00 4.17
4464 5673 0.396139 GCATGATGGGGAAGGAGCAA 60.396 55.000 0.00 0.00 0.00 3.91
4465 5674 1.228228 GCATGATGGGGAAGGAGCA 59.772 57.895 0.00 0.00 0.00 4.26
4466 5675 0.536915 GAGCATGATGGGGAAGGAGC 60.537 60.000 0.00 0.00 0.00 4.70
4467 5676 0.841961 TGAGCATGATGGGGAAGGAG 59.158 55.000 0.00 0.00 0.00 3.69
4468 5677 1.526315 ATGAGCATGATGGGGAAGGA 58.474 50.000 0.00 0.00 0.00 3.36
4470 5679 3.409570 CACTATGAGCATGATGGGGAAG 58.590 50.000 0.00 0.00 0.00 3.46
4471 5680 2.107031 CCACTATGAGCATGATGGGGAA 59.893 50.000 0.00 0.00 0.00 3.97
4472 5681 1.701292 CCACTATGAGCATGATGGGGA 59.299 52.381 0.00 0.00 0.00 4.81
4473 5682 1.422781 ACCACTATGAGCATGATGGGG 59.577 52.381 15.18 8.76 0.00 4.96
4474 5683 2.945080 ACCACTATGAGCATGATGGG 57.055 50.000 15.18 5.67 0.00 4.00
4475 5684 4.067896 GGTTACCACTATGAGCATGATGG 58.932 47.826 0.00 11.23 0.00 3.51
4476 5685 4.965814 AGGTTACCACTATGAGCATGATG 58.034 43.478 3.51 0.00 0.00 3.07
4477 5686 4.904251 AGAGGTTACCACTATGAGCATGAT 59.096 41.667 3.51 0.00 0.00 2.45
4478 5687 4.290093 AGAGGTTACCACTATGAGCATGA 58.710 43.478 3.51 0.00 0.00 3.07
4479 5688 4.679373 AGAGGTTACCACTATGAGCATG 57.321 45.455 3.51 0.00 0.00 4.06
4480 5689 4.684485 GCAAGAGGTTACCACTATGAGCAT 60.684 45.833 3.51 0.00 0.00 3.79
4481 5690 3.369471 GCAAGAGGTTACCACTATGAGCA 60.369 47.826 3.51 0.00 0.00 4.26
4482 5691 3.198872 GCAAGAGGTTACCACTATGAGC 58.801 50.000 3.51 2.28 0.00 4.26
4483 5692 3.432326 GGGCAAGAGGTTACCACTATGAG 60.432 52.174 3.51 0.00 0.00 2.90
4492 5720 1.078637 GTCCGGGGCAAGAGGTTAC 60.079 63.158 0.00 0.00 0.00 2.50
4494 5722 2.852075 TGTCCGGGGCAAGAGGTT 60.852 61.111 0.00 0.00 0.00 3.50
4562 5810 5.992217 TGTAAAATGTAAAAATGGCACCCAC 59.008 36.000 0.00 0.00 35.80 4.61
4589 5979 4.360563 AGTCAAAAGTCAGACAGTACGTG 58.639 43.478 2.66 0.00 37.23 4.49
4599 5989 2.673368 GCACCCGATAGTCAAAAGTCAG 59.327 50.000 0.00 0.00 0.00 3.51
4602 5992 2.109425 GGCACCCGATAGTCAAAAGT 57.891 50.000 0.00 0.00 0.00 2.66
4619 6009 2.025699 TGTGGGTCAGGTAATTAAGGGC 60.026 50.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.