Multiple sequence alignment - TraesCS4B01G322700

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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 TraesCS4B01G322700 chr4B 100.000 4925 0 0 1 4925 613161877 613156953 0.000000e+00 9095.0
1 TraesCS4B01G322700 chr4B 85.973 442 52 7 2917 3348 612872609 612873050 9.660000e-127 464.0
2 TraesCS4B01G322700 chr4B 86.935 199 24 1 1332 1530 612855909 612856105 6.420000e-54 222.0
3 TraesCS4B01G322700 chr4B 89.759 166 15 2 2097 2261 612856657 612856821 1.390000e-50 211.0
4 TraesCS4B01G322700 chr4B 86.316 190 24 2 4438 4627 135218033 135218220 6.460000e-49 206.0
5 TraesCS4B01G322700 chr4B 88.976 127 14 0 1694 1820 612856293 612856419 1.840000e-34 158.0
6 TraesCS4B01G322700 chr4D 92.431 3382 165 55 1132 4456 483068324 483064977 0.000000e+00 4743.0
7 TraesCS4B01G322700 chr4D 96.089 358 10 4 1 357 483069396 483069042 9.190000e-162 580.0
8 TraesCS4B01G322700 chr4D 89.835 364 11 8 765 1111 483068751 483068397 1.260000e-120 444.0
9 TraesCS4B01G322700 chr4D 92.258 310 17 3 4616 4925 483064978 483064676 2.720000e-117 433.0
10 TraesCS4B01G322700 chr4D 84.163 442 59 7 2917 3348 483036078 483036518 7.620000e-113 418.0
11 TraesCS4B01G322700 chr4D 80.380 474 74 12 2892 3348 482967145 482967616 4.720000e-90 342.0
12 TraesCS4B01G322700 chr4D 90.964 166 14 1 4455 4620 401422748 401422912 6.420000e-54 222.0
13 TraesCS4B01G322700 chr4D 90.964 166 13 2 2097 2261 483035338 483035502 6.420000e-54 222.0
14 TraesCS4B01G322700 chr4D 92.357 157 11 1 589 744 483068893 483068737 6.420000e-54 222.0
15 TraesCS4B01G322700 chr4D 90.058 171 16 1 4452 4622 334164388 334164557 2.310000e-53 220.0
16 TraesCS4B01G322700 chr4D 88.827 179 20 0 1356 1534 483034564 483034742 2.310000e-53 220.0
17 TraesCS4B01G322700 chr4D 84.659 176 19 5 347 521 36603041 36603209 8.480000e-38 169.0
18 TraesCS4B01G322700 chr4D 88.976 127 14 0 1694 1820 483034962 483035088 1.840000e-34 158.0
19 TraesCS4B01G322700 chr4D 91.398 93 8 0 2385 2477 482966583 482966675 1.440000e-25 128.0
20 TraesCS4B01G322700 chr4D 88.776 98 11 0 1694 1791 482960040 482960137 2.410000e-23 121.0
21 TraesCS4B01G322700 chr5A 91.984 1784 103 26 2698 4456 663216936 663215168 0.000000e+00 2466.0
22 TraesCS4B01G322700 chr5A 90.012 861 51 17 1854 2699 663217804 663216964 0.000000e+00 1081.0
23 TraesCS4B01G322700 chr5A 80.925 1038 91 44 603 1580 663219076 663218086 0.000000e+00 721.0
24 TraesCS4B01G322700 chr5A 96.452 310 9 1 4616 4925 663215169 663214862 1.220000e-140 510.0
25 TraesCS4B01G322700 chr5A 84.580 441 56 9 2917 3348 663173144 663173581 1.270000e-115 427.0
26 TraesCS4B01G322700 chr5A 80.508 472 73 12 2894 3348 659527825 659527356 1.310000e-90 344.0
27 TraesCS4B01G322700 chr5A 92.718 206 14 1 1633 1837 663218060 663217855 3.730000e-76 296.0
28 TraesCS4B01G322700 chr5A 90.761 184 10 3 1 180 663219952 663219772 6.370000e-59 239.0
29 TraesCS4B01G322700 chr5A 86.070 201 26 1 1332 1530 663160433 663160633 1.070000e-51 215.0
30 TraesCS4B01G322700 chr5A 90.741 162 13 2 2097 2257 663172454 663172614 1.070000e-51 215.0
31 TraesCS4B01G322700 chr5A 86.628 172 21 2 1356 1526 659529641 659529471 6.510000e-44 189.0
32 TraesCS4B01G322700 chr5A 87.970 133 14 1 1694 1826 659529247 659529117 6.600000e-34 156.0
33 TraesCS4B01G322700 chr5A 88.235 136 5 5 215 349 663219266 663219141 8.540000e-33 152.0
34 TraesCS4B01G322700 chr5A 85.156 128 17 2 1694 1820 663160839 663160965 4.000000e-26 130.0
35 TraesCS4B01G322700 chr5A 91.566 83 7 0 2394 2476 663172613 663172695 1.120000e-21 115.0
36 TraesCS4B01G322700 chr5A 95.122 41 0 2 2074 2114 663217866 663217828 4.120000e-06 63.9
37 TraesCS4B01G322700 chr6D 92.025 163 12 1 4455 4617 145462624 145462463 1.380000e-55 228.0
38 TraesCS4B01G322700 chr6D 91.411 163 12 2 4455 4617 431160668 431160828 6.420000e-54 222.0
39 TraesCS4B01G322700 chr6D 85.380 171 17 5 352 521 298453568 298453731 2.360000e-38 171.0
40 TraesCS4B01G322700 chr5B 91.515 165 11 3 4454 4617 144586312 144586474 1.780000e-54 224.0
41 TraesCS4B01G322700 chr5B 89.855 138 13 1 353 489 36481758 36481895 5.070000e-40 176.0
42 TraesCS4B01G322700 chr5B 84.118 170 23 3 353 520 455291477 455291644 1.420000e-35 161.0
43 TraesCS4B01G322700 chr3B 90.533 169 14 2 4451 4619 529407786 529407952 6.420000e-54 222.0
44 TraesCS4B01G322700 chr3B 86.391 169 16 4 354 521 761137360 761137198 1.410000e-40 178.0
45 TraesCS4B01G322700 chr7A 90.909 165 14 1 4454 4618 494786991 494786828 2.310000e-53 220.0
46 TraesCS4B01G322700 chr2D 88.525 183 18 3 4441 4621 134301665 134301484 8.300000e-53 219.0
47 TraesCS4B01G322700 chr2B 85.882 170 22 2 353 521 766565303 766565471 3.920000e-41 180.0
48 TraesCS4B01G322700 chr2B 84.971 173 18 5 349 520 512624084 512624249 8.480000e-38 169.0
49 TraesCS4B01G322700 chr1A 85.380 171 18 4 351 520 209495102 209494938 2.360000e-38 171.0
50 TraesCS4B01G322700 chr5D 84.884 172 18 5 350 520 53583074 53583238 3.050000e-37 167.0


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 TraesCS4B01G322700 chr4B 613156953 613161877 4924 True 9095.000000 9095 100.000000 1 4925 1 chr4B.!!$R1 4924
1 TraesCS4B01G322700 chr4D 483064676 483069396 4720 True 1284.400000 4743 92.594000 1 4925 5 chr4D.!!$R1 4924
2 TraesCS4B01G322700 chr4D 483034564 483036518 1954 False 254.500000 418 88.232500 1356 3348 4 chr4D.!!$F6 1992
3 TraesCS4B01G322700 chr4D 482966583 482967616 1033 False 235.000000 342 85.889000 2385 3348 2 chr4D.!!$F5 963
4 TraesCS4B01G322700 chr5A 663214862 663219952 5090 True 691.112500 2466 90.776125 1 4925 8 chr5A.!!$R2 4924
5 TraesCS4B01G322700 chr5A 663172454 663173581 1127 False 252.333333 427 88.962333 2097 3348 3 chr5A.!!$F2 1251
6 TraesCS4B01G322700 chr5A 659527356 659529641 2285 True 229.666667 344 85.035333 1356 3348 3 chr5A.!!$R1 1992

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
737 1231 0.249398 AACCTCGCGCTAGGAAACAT 59.751 50.0 32.51 8.6 39.15 2.71 F
1281 1862 0.107654 GCTCGGCCATGTAAGTTCCT 60.108 55.0 2.24 0.0 0.00 3.36 F
1932 2689 0.251354 TCCTGCTGCAGATGAGAACC 59.749 55.0 30.10 0.0 32.44 3.62 F
3177 4592 0.323360 GGGATGCAAGGCACCAAGTA 60.323 55.0 0.00 0.0 43.04 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 3841 0.250295 CGCAAGGAAGACCAACAGGA 60.250 55.000 0.0 0.00 38.94 3.86 R
2591 3846 1.347707 AGATCACGCAAGGAAGACCAA 59.652 47.619 0.0 0.00 46.39 3.67 R
3802 5232 0.038166 AGGAAAAATCTGCGCTGGGA 59.962 50.000 14.7 7.56 0.00 4.37 R
4675 6117 1.470494 TCTGATGCTCTCTCGTGTGTC 59.530 52.381 0.0 0.00 0.00 3.67 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
19 20 0.319211 TCGCGTCATTTTCTCCACGT 60.319 50.000 5.77 0.00 34.69 4.49
105 107 1.724623 CCGACGTCACACAATTCGATT 59.275 47.619 17.16 0.00 0.00 3.34
253 730 1.961277 CGTCGGCTTTTGTCCTGCT 60.961 57.895 0.00 0.00 0.00 4.24
367 856 4.701651 AAAAACTACTCCCTCCGTTTCT 57.298 40.909 0.00 0.00 0.00 2.52
370 859 5.813513 AAACTACTCCCTCCGTTTCTAAA 57.186 39.130 0.00 0.00 0.00 1.85
373 862 7.672122 AACTACTCCCTCCGTTTCTAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
374 863 8.773033 AACTACTCCCTCCGTTTCTAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
375 864 8.773033 ACTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
378 867 8.087303 ACTCCCTCCGTTTCTAAATATAAGTT 57.913 34.615 0.00 0.00 0.00 2.66
379 868 8.546322 ACTCCCTCCGTTTCTAAATATAAGTTT 58.454 33.333 0.00 0.00 0.00 2.66
380 869 9.392259 CTCCCTCCGTTTCTAAATATAAGTTTT 57.608 33.333 0.00 0.00 0.00 2.43
381 870 9.743581 TCCCTCCGTTTCTAAATATAAGTTTTT 57.256 29.630 0.00 0.00 0.00 1.94
382 871 9.999009 CCCTCCGTTTCTAAATATAAGTTTTTC 57.001 33.333 0.00 0.00 0.00 2.29
452 941 8.464770 TTTAAGTGCATATTCACTCATTTTGC 57.535 30.769 8.51 0.00 45.77 3.68
453 942 5.909621 AGTGCATATTCACTCATTTTGCT 57.090 34.783 1.81 0.00 43.28 3.91
454 943 5.888105 AGTGCATATTCACTCATTTTGCTC 58.112 37.500 1.81 0.00 43.28 4.26
455 944 5.651139 AGTGCATATTCACTCATTTTGCTCT 59.349 36.000 1.81 0.00 43.28 4.09
456 945 5.742453 GTGCATATTCACTCATTTTGCTCTG 59.258 40.000 0.00 0.00 34.29 3.35
457 946 5.416639 TGCATATTCACTCATTTTGCTCTGT 59.583 36.000 0.00 0.00 0.00 3.41
458 947 6.598850 TGCATATTCACTCATTTTGCTCTGTA 59.401 34.615 0.00 0.00 0.00 2.74
459 948 7.283807 TGCATATTCACTCATTTTGCTCTGTAT 59.716 33.333 0.00 0.00 0.00 2.29
460 949 7.590322 GCATATTCACTCATTTTGCTCTGTATG 59.410 37.037 0.00 0.00 0.00 2.39
461 950 8.618677 CATATTCACTCATTTTGCTCTGTATGT 58.381 33.333 0.00 0.00 0.00 2.29
462 951 9.836864 ATATTCACTCATTTTGCTCTGTATGTA 57.163 29.630 0.00 0.00 0.00 2.29
463 952 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
464 953 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
465 954 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
466 955 6.815641 CACTCATTTTGCTCTGTATGTAGTCT 59.184 38.462 0.00 0.00 0.00 3.24
467 956 7.332926 CACTCATTTTGCTCTGTATGTAGTCTT 59.667 37.037 0.00 0.00 0.00 3.01
468 957 7.880195 ACTCATTTTGCTCTGTATGTAGTCTTT 59.120 33.333 0.00 0.00 0.00 2.52
469 958 8.621532 TCATTTTGCTCTGTATGTAGTCTTTT 57.378 30.769 0.00 0.00 0.00 2.27
470 959 8.506437 TCATTTTGCTCTGTATGTAGTCTTTTG 58.494 33.333 0.00 0.00 0.00 2.44
471 960 7.801716 TTTTGCTCTGTATGTAGTCTTTTGT 57.198 32.000 0.00 0.00 0.00 2.83
472 961 7.801716 TTTGCTCTGTATGTAGTCTTTTGTT 57.198 32.000 0.00 0.00 0.00 2.83
473 962 6.785488 TGCTCTGTATGTAGTCTTTTGTTG 57.215 37.500 0.00 0.00 0.00 3.33
474 963 5.700832 TGCTCTGTATGTAGTCTTTTGTTGG 59.299 40.000 0.00 0.00 0.00 3.77
475 964 5.932303 GCTCTGTATGTAGTCTTTTGTTGGA 59.068 40.000 0.00 0.00 0.00 3.53
476 965 6.426937 GCTCTGTATGTAGTCTTTTGTTGGAA 59.573 38.462 0.00 0.00 0.00 3.53
477 966 7.119846 GCTCTGTATGTAGTCTTTTGTTGGAAT 59.880 37.037 0.00 0.00 0.00 3.01
478 967 8.547967 TCTGTATGTAGTCTTTTGTTGGAATC 57.452 34.615 0.00 0.00 0.00 2.52
479 968 8.375506 TCTGTATGTAGTCTTTTGTTGGAATCT 58.624 33.333 0.00 0.00 0.00 2.40
480 969 8.547967 TGTATGTAGTCTTTTGTTGGAATCTC 57.452 34.615 0.00 0.00 0.00 2.75
481 970 8.375506 TGTATGTAGTCTTTTGTTGGAATCTCT 58.624 33.333 0.00 0.00 0.00 3.10
482 971 9.871238 GTATGTAGTCTTTTGTTGGAATCTCTA 57.129 33.333 0.00 0.00 0.00 2.43
484 973 9.793259 ATGTAGTCTTTTGTTGGAATCTCTAAA 57.207 29.630 0.00 0.00 0.00 1.85
485 974 9.621629 TGTAGTCTTTTGTTGGAATCTCTAAAA 57.378 29.630 0.00 0.00 0.00 1.52
488 977 9.408648 AGTCTTTTGTTGGAATCTCTAAAAAGA 57.591 29.630 0.00 0.00 38.90 2.52
528 1017 4.468153 GGAACAGAGGGAGTAGTCAAGAAT 59.532 45.833 0.00 0.00 0.00 2.40
550 1039 8.813951 AGAATAATACTACGGATTCCCTAAAGG 58.186 37.037 0.00 0.00 0.00 3.11
616 1105 6.830873 ATACTACAAGTAAAGTGACCGTCT 57.169 37.500 0.00 0.00 33.89 4.18
618 1107 4.826183 ACTACAAGTAAAGTGACCGTCTCT 59.174 41.667 0.00 0.00 0.00 3.10
731 1225 2.202756 GTCCAACCTCGCGCTAGG 60.203 66.667 25.27 25.27 42.82 3.02
732 1226 2.361992 TCCAACCTCGCGCTAGGA 60.362 61.111 32.51 14.12 39.15 2.94
733 1227 1.980232 TCCAACCTCGCGCTAGGAA 60.980 57.895 32.51 12.92 39.15 3.36
734 1228 1.079405 CCAACCTCGCGCTAGGAAA 60.079 57.895 32.51 0.00 39.15 3.13
735 1229 1.359459 CCAACCTCGCGCTAGGAAAC 61.359 60.000 32.51 0.00 39.15 2.78
736 1230 0.669318 CAACCTCGCGCTAGGAAACA 60.669 55.000 32.51 0.00 39.15 2.83
737 1231 0.249398 AACCTCGCGCTAGGAAACAT 59.751 50.000 32.51 8.60 39.15 2.71
738 1232 1.108776 ACCTCGCGCTAGGAAACATA 58.891 50.000 32.51 0.00 39.15 2.29
739 1233 1.067212 ACCTCGCGCTAGGAAACATAG 59.933 52.381 32.51 5.55 39.15 2.23
740 1234 1.132588 CTCGCGCTAGGAAACATAGC 58.867 55.000 5.56 5.53 41.83 2.97
741 1235 0.744874 TCGCGCTAGGAAACATAGCT 59.255 50.000 5.56 0.00 42.84 3.32
742 1236 1.132588 CGCGCTAGGAAACATAGCTC 58.867 55.000 5.56 4.97 42.84 4.09
743 1237 1.132588 GCGCTAGGAAACATAGCTCG 58.867 55.000 0.00 1.35 42.84 5.03
744 1238 1.269102 GCGCTAGGAAACATAGCTCGA 60.269 52.381 0.00 0.00 42.84 4.04
745 1239 2.608261 GCGCTAGGAAACATAGCTCGAT 60.608 50.000 0.00 0.00 42.84 3.59
746 1240 3.238441 CGCTAGGAAACATAGCTCGATC 58.762 50.000 12.25 0.00 42.84 3.69
747 1241 3.580731 GCTAGGAAACATAGCTCGATCC 58.419 50.000 7.93 0.00 41.96 3.36
748 1242 3.615351 GCTAGGAAACATAGCTCGATCCC 60.615 52.174 7.93 0.00 41.96 3.85
749 1243 2.683768 AGGAAACATAGCTCGATCCCT 58.316 47.619 0.00 0.00 0.00 4.20
750 1244 2.630580 AGGAAACATAGCTCGATCCCTC 59.369 50.000 0.00 0.00 0.00 4.30
751 1245 2.365617 GGAAACATAGCTCGATCCCTCA 59.634 50.000 0.00 0.00 0.00 3.86
752 1246 3.181465 GGAAACATAGCTCGATCCCTCAA 60.181 47.826 0.00 0.00 0.00 3.02
753 1247 4.442706 GAAACATAGCTCGATCCCTCAAA 58.557 43.478 0.00 0.00 0.00 2.69
754 1248 3.460857 ACATAGCTCGATCCCTCAAAC 57.539 47.619 0.00 0.00 0.00 2.93
755 1249 2.766263 ACATAGCTCGATCCCTCAAACA 59.234 45.455 0.00 0.00 0.00 2.83
756 1250 3.197766 ACATAGCTCGATCCCTCAAACAA 59.802 43.478 0.00 0.00 0.00 2.83
757 1251 2.859165 AGCTCGATCCCTCAAACAAA 57.141 45.000 0.00 0.00 0.00 2.83
758 1252 3.140325 AGCTCGATCCCTCAAACAAAA 57.860 42.857 0.00 0.00 0.00 2.44
759 1253 3.486383 AGCTCGATCCCTCAAACAAAAA 58.514 40.909 0.00 0.00 0.00 1.94
1060 1590 2.094854 CGGCCACGTAGAATAGATACCC 60.095 54.545 2.24 0.00 34.81 3.69
1092 1622 1.444553 CCTCGTTGGCTCAGACGAC 60.445 63.158 0.00 0.00 42.67 4.34
1281 1862 0.107654 GCTCGGCCATGTAAGTTCCT 60.108 55.000 2.24 0.00 0.00 3.36
1284 1865 1.065709 TCGGCCATGTAAGTTCCTTCC 60.066 52.381 2.24 0.00 0.00 3.46
1286 1867 1.379527 GCCATGTAAGTTCCTTCCCG 58.620 55.000 0.00 0.00 0.00 5.14
1287 1868 2.017113 GCCATGTAAGTTCCTTCCCGG 61.017 57.143 0.00 0.00 0.00 5.73
1288 1869 1.557832 CCATGTAAGTTCCTTCCCGGA 59.442 52.381 0.73 0.00 41.06 5.14
1301 1882 5.007682 TCCTTCCCGGAAAAAGTAAATGAG 58.992 41.667 0.73 0.00 39.40 2.90
1302 1883 4.765339 CCTTCCCGGAAAAAGTAAATGAGT 59.235 41.667 0.73 0.00 33.16 3.41
1304 1885 4.721132 TCCCGGAAAAAGTAAATGAGTGT 58.279 39.130 0.73 0.00 0.00 3.55
1305 1886 4.758165 TCCCGGAAAAAGTAAATGAGTGTC 59.242 41.667 0.73 0.00 0.00 3.67
1306 1887 4.760204 CCCGGAAAAAGTAAATGAGTGTCT 59.240 41.667 0.73 0.00 0.00 3.41
1307 1888 5.334879 CCCGGAAAAAGTAAATGAGTGTCTG 60.335 44.000 0.73 0.00 0.00 3.51
1308 1889 5.147162 CGGAAAAAGTAAATGAGTGTCTGC 58.853 41.667 0.00 0.00 0.00 4.26
1311 1892 2.789409 AGTAAATGAGTGTCTGCCCC 57.211 50.000 0.00 0.00 0.00 5.80
1312 1893 1.985159 AGTAAATGAGTGTCTGCCCCA 59.015 47.619 0.00 0.00 0.00 4.96
1313 1894 2.026822 AGTAAATGAGTGTCTGCCCCAG 60.027 50.000 0.00 0.00 0.00 4.45
1314 1895 0.773644 AAATGAGTGTCTGCCCCAGT 59.226 50.000 0.00 0.00 32.61 4.00
1341 1931 2.791170 GCTCATGGCTTCCTCCTTG 58.209 57.895 0.00 0.00 38.06 3.61
1346 1939 0.613012 ATGGCTTCCTCCTTGTTGGC 60.613 55.000 0.00 0.00 35.26 4.52
1348 1941 1.600916 GCTTCCTCCTTGTTGGCGT 60.601 57.895 0.00 0.00 35.26 5.68
1593 2266 3.386237 AGGTGAGCCTGTCGGAGC 61.386 66.667 0.00 0.00 45.05 4.70
1613 2301 2.737252 GCCGGAACAAAAACACAAACAA 59.263 40.909 5.05 0.00 0.00 2.83
1643 2334 1.266989 GGCCGGAGTTTCTTCTTGTTG 59.733 52.381 5.05 0.00 0.00 3.33
1644 2335 1.947456 GCCGGAGTTTCTTCTTGTTGT 59.053 47.619 5.05 0.00 0.00 3.32
1646 2337 3.181490 GCCGGAGTTTCTTCTTGTTGTTT 60.181 43.478 5.05 0.00 0.00 2.83
1647 2338 4.676986 GCCGGAGTTTCTTCTTGTTGTTTT 60.677 41.667 5.05 0.00 0.00 2.43
1679 2374 1.228429 TTGGCCTAACTGGTGTGGC 60.228 57.895 3.32 3.41 44.22 5.01
1682 2377 3.118454 CCTAACTGGTGTGGCGCG 61.118 66.667 0.00 0.00 0.00 6.86
1841 2541 7.340487 TGAGCCTTTCTTTCTTTCTTTCTTTCT 59.660 33.333 0.00 0.00 0.00 2.52
1842 2542 8.072321 AGCCTTTCTTTCTTTCTTTCTTTCTT 57.928 30.769 0.00 0.00 0.00 2.52
1859 2559 4.030821 TTTTTACCGCGCGTCTGT 57.969 50.000 29.95 21.48 0.00 3.41
1860 2560 1.854664 TTTTTACCGCGCGTCTGTC 59.145 52.632 29.95 0.00 0.00 3.51
1867 2567 3.807538 GCGCGTCTGTCCTCGGTA 61.808 66.667 8.43 0.00 0.00 4.02
1868 2568 2.872557 CGCGTCTGTCCTCGGTAA 59.127 61.111 0.00 0.00 0.00 2.85
1871 2571 1.066136 GCGTCTGTCCTCGGTAAAAC 58.934 55.000 0.00 0.00 0.00 2.43
1872 2572 1.336609 GCGTCTGTCCTCGGTAAAACT 60.337 52.381 0.00 0.00 0.00 2.66
1873 2573 2.325761 CGTCTGTCCTCGGTAAAACTG 58.674 52.381 0.00 0.00 0.00 3.16
1876 2606 3.057033 GTCTGTCCTCGGTAAAACTGCTA 60.057 47.826 0.00 0.00 0.00 3.49
1878 2608 2.028748 TGTCCTCGGTAAAACTGCTACC 60.029 50.000 0.00 0.00 36.27 3.18
1882 2612 1.002315 TCGGTAAAACTGCTACCACCC 59.998 52.381 0.61 0.00 39.08 4.61
1896 2626 0.395724 CCACCCATCCTTAACCTGCC 60.396 60.000 0.00 0.00 0.00 4.85
1932 2689 0.251354 TCCTGCTGCAGATGAGAACC 59.749 55.000 30.10 0.00 32.44 3.62
2005 2762 3.505680 TGGTCAGACAATTTCCGAAATGG 59.494 43.478 7.13 6.89 40.09 3.16
2068 2847 4.681744 GATCAGAGGAGTGAACTGATGAC 58.318 47.826 12.51 0.00 46.75 3.06
2268 3397 2.229543 AGGCTTCATCAACGTACGTACA 59.770 45.455 23.12 11.59 0.00 2.90
2272 3401 3.639716 TCATCAACGTACGTACAACCA 57.360 42.857 23.12 6.69 0.00 3.67
2302 3431 0.395862 CCCTCCTTCTAGCTCCGTCA 60.396 60.000 0.00 0.00 0.00 4.35
2317 3446 4.695993 TCAGCCATTGCCGCGACA 62.696 61.111 8.23 0.00 38.69 4.35
2333 3462 4.804139 CCGCGACACTTCTGAAATAAGTAT 59.196 41.667 8.23 0.00 35.44 2.12
2334 3463 5.975344 CCGCGACACTTCTGAAATAAGTATA 59.025 40.000 8.23 0.00 35.44 1.47
2335 3464 6.641314 CCGCGACACTTCTGAAATAAGTATAT 59.359 38.462 8.23 0.00 35.44 0.86
2377 3506 3.926616 TGTCTTCTCTTTCCACGATTCC 58.073 45.455 0.00 0.00 0.00 3.01
2477 3606 1.421410 CGTCGTTGGCATCAGGTAGC 61.421 60.000 0.00 0.00 0.00 3.58
2483 3612 3.343617 GTTGGCATCAGGTAGCTTACAA 58.656 45.455 0.00 0.00 0.00 2.41
2484 3613 2.985896 TGGCATCAGGTAGCTTACAAC 58.014 47.619 0.00 0.00 0.00 3.32
2497 3752 6.204882 GGTAGCTTACAACATTCCATGGATAC 59.795 42.308 17.06 9.98 33.60 2.24
2538 3793 6.182627 CCAGGCTCCATATGATATTGCTTAA 58.817 40.000 3.65 0.00 0.00 1.85
2586 3841 1.580845 GCTGCGTCATGGTCTTTGCT 61.581 55.000 0.00 0.00 0.00 3.91
2591 3846 1.609061 CGTCATGGTCTTTGCTCCTGT 60.609 52.381 0.00 0.00 0.00 4.00
2679 3934 1.645710 TCCTCACCCTCTTCCTTGAC 58.354 55.000 0.00 0.00 0.00 3.18
2750 4132 5.240844 CCACCGTTCATTTTCTAACCTTTCT 59.759 40.000 0.00 0.00 0.00 2.52
2822 4204 1.743958 CATCCCTCTCGTCGTAAGTGT 59.256 52.381 0.00 0.00 39.48 3.55
2904 4298 6.183360 CCTTAATTGAAAATGCCATTGTCTGC 60.183 38.462 8.98 0.00 0.00 4.26
3086 4493 4.014406 TCTTCTTCATACACCTGACGCTA 58.986 43.478 0.00 0.00 0.00 4.26
3177 4592 0.323360 GGGATGCAAGGCACCAAGTA 60.323 55.000 0.00 0.00 43.04 2.24
3178 4593 1.098050 GGATGCAAGGCACCAAGTAG 58.902 55.000 0.00 0.00 43.04 2.57
3216 4644 4.235360 CTGACGGAGATTTACTTGTTCGT 58.765 43.478 0.00 0.00 0.00 3.85
3671 5101 3.147595 CCGACGATCCCCAGAGCA 61.148 66.667 0.00 0.00 0.00 4.26
3676 5106 3.785859 GATCCCCAGAGCACGCCA 61.786 66.667 0.00 0.00 0.00 5.69
3736 5166 2.983030 GTTGTGGTGGCGCATCCA 60.983 61.111 16.80 16.80 44.18 3.41
3778 5208 0.961358 ACAGGAGAAGGTCGGTCTCG 60.961 60.000 0.00 0.00 42.13 4.04
3802 5232 3.050703 GGCACTCGATGTCGACATT 57.949 52.632 30.46 13.35 44.22 2.71
4051 5483 3.639561 TCTTCAGCCCCAAAAAGGTAAAC 59.360 43.478 0.00 0.00 34.66 2.01
4074 5506 4.206404 CGAGTGCCACTAATGTAATACACG 59.794 45.833 0.00 0.00 32.22 4.49
4364 5804 4.518211 AGGAAAGAGACATGAGTTGCAAAG 59.482 41.667 0.00 0.00 0.00 2.77
4365 5805 3.911661 AAGAGACATGAGTTGCAAAGC 57.088 42.857 0.00 0.00 0.00 3.51
4366 5806 2.854963 AGAGACATGAGTTGCAAAGCA 58.145 42.857 0.00 2.34 36.47 3.91
4412 5852 4.516698 ACAGTCAATTGTAAGGCACAGAAG 59.483 41.667 5.13 0.00 38.72 2.85
4444 5884 4.039852 TCATCCATGTGCCGCTAAATACTA 59.960 41.667 0.00 0.00 0.00 1.82
4454 5894 7.148154 TGTGCCGCTAAATACTACATTGAAAAT 60.148 33.333 0.00 0.00 0.00 1.82
4455 5895 8.339714 GTGCCGCTAAATACTACATTGAAAATA 58.660 33.333 0.00 0.00 0.00 1.40
4456 5896 8.339714 TGCCGCTAAATACTACATTGAAAATAC 58.660 33.333 0.00 0.00 0.00 1.89
4457 5897 8.557029 GCCGCTAAATACTACATTGAAAATACT 58.443 33.333 0.00 0.00 0.00 2.12
4467 5907 9.167311 ACTACATTGAAAATACTCACTCCATTC 57.833 33.333 0.00 0.00 0.00 2.67
4468 5908 7.396540 ACATTGAAAATACTCACTCCATTCC 57.603 36.000 0.00 0.00 0.00 3.01
4469 5909 7.177878 ACATTGAAAATACTCACTCCATTCCT 58.822 34.615 0.00 0.00 0.00 3.36
4470 5910 8.328758 ACATTGAAAATACTCACTCCATTCCTA 58.671 33.333 0.00 0.00 0.00 2.94
4471 5911 9.177608 CATTGAAAATACTCACTCCATTCCTAA 57.822 33.333 0.00 0.00 0.00 2.69
4472 5912 9.753674 ATTGAAAATACTCACTCCATTCCTAAA 57.246 29.630 0.00 0.00 0.00 1.85
4473 5913 9.753674 TTGAAAATACTCACTCCATTCCTAAAT 57.246 29.630 0.00 0.00 0.00 1.40
4481 5921 9.440761 ACTCACTCCATTCCTAAATATAAGTCT 57.559 33.333 0.00 0.00 0.00 3.24
4517 5957 8.721133 TCCAATATAGACTACATAAAGGAGCA 57.279 34.615 0.00 0.00 0.00 4.26
4518 5958 9.154632 TCCAATATAGACTACATAAAGGAGCAA 57.845 33.333 0.00 0.00 0.00 3.91
4519 5959 9.778741 CCAATATAGACTACATAAAGGAGCAAA 57.221 33.333 0.00 0.00 0.00 3.68
4526 5966 9.167311 AGACTACATAAAGGAGCAAAATAAGTG 57.833 33.333 0.00 0.00 0.00 3.16
4527 5967 9.162764 GACTACATAAAGGAGCAAAATAAGTGA 57.837 33.333 0.00 0.00 0.00 3.41
4528 5968 9.515226 ACTACATAAAGGAGCAAAATAAGTGAA 57.485 29.630 0.00 0.00 0.00 3.18
4531 5971 9.247861 ACATAAAGGAGCAAAATAAGTGAATCT 57.752 29.630 0.00 0.00 0.00 2.40
4532 5972 9.512435 CATAAAGGAGCAAAATAAGTGAATCTG 57.488 33.333 0.00 0.00 0.00 2.90
4533 5973 5.573337 AGGAGCAAAATAAGTGAATCTGC 57.427 39.130 0.00 0.00 0.00 4.26
4534 5974 5.012239 AGGAGCAAAATAAGTGAATCTGCA 58.988 37.500 0.00 0.00 0.00 4.41
4535 5975 5.098211 GGAGCAAAATAAGTGAATCTGCAC 58.902 41.667 0.00 0.00 39.05 4.57
4559 5999 8.653036 ACTCTAAAGTGGGTCTATATACATCC 57.347 38.462 0.00 0.00 33.32 3.51
4560 6000 7.393796 ACTCTAAAGTGGGTCTATATACATCCG 59.606 40.741 0.00 0.00 33.32 4.18
4561 6001 7.236529 TCTAAAGTGGGTCTATATACATCCGT 58.763 38.462 0.00 0.00 0.00 4.69
4562 6002 8.385491 TCTAAAGTGGGTCTATATACATCCGTA 58.615 37.037 0.00 0.00 0.00 4.02
4563 6003 9.186837 CTAAAGTGGGTCTATATACATCCGTAT 57.813 37.037 0.00 0.00 41.34 3.06
4564 6004 7.406031 AAGTGGGTCTATATACATCCGTATG 57.594 40.000 0.00 0.00 38.79 2.39
4577 6017 6.381481 ACATCCGTATGTAGTTCGTATTGA 57.619 37.500 0.00 0.00 44.66 2.57
4578 6018 6.798482 ACATCCGTATGTAGTTCGTATTGAA 58.202 36.000 0.00 0.00 44.66 2.69
4579 6019 7.259882 ACATCCGTATGTAGTTCGTATTGAAA 58.740 34.615 0.00 0.00 44.66 2.69
4580 6020 7.924412 ACATCCGTATGTAGTTCGTATTGAAAT 59.076 33.333 0.00 0.00 44.66 2.17
4581 6021 7.919313 TCCGTATGTAGTTCGTATTGAAATC 57.081 36.000 0.00 0.00 38.60 2.17
4582 6022 7.709947 TCCGTATGTAGTTCGTATTGAAATCT 58.290 34.615 0.00 0.00 38.60 2.40
4583 6023 7.859377 TCCGTATGTAGTTCGTATTGAAATCTC 59.141 37.037 0.00 0.00 38.60 2.75
4584 6024 7.861372 CCGTATGTAGTTCGTATTGAAATCTCT 59.139 37.037 0.00 0.00 38.60 3.10
4585 6025 9.874215 CGTATGTAGTTCGTATTGAAATCTCTA 57.126 33.333 0.00 0.00 38.60 2.43
4592 6032 9.152595 AGTTCGTATTGAAATCTCTAAAAGGAC 57.847 33.333 0.00 0.00 38.60 3.85
4593 6033 9.152595 GTTCGTATTGAAATCTCTAAAAGGACT 57.847 33.333 0.00 0.00 38.60 3.85
4594 6034 9.720769 TTCGTATTGAAATCTCTAAAAGGACTT 57.279 29.630 0.00 0.00 32.37 3.01
4610 6050 8.959705 AAAAGGACTTATATTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
4611 6051 6.667558 AGGACTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
4612 6052 6.379579 AGGACTTATATTTAGGAACGGAGGA 58.620 40.000 0.00 0.00 0.00 3.71
4613 6053 6.842807 AGGACTTATATTTAGGAACGGAGGAA 59.157 38.462 0.00 0.00 0.00 3.36
4614 6054 7.015389 AGGACTTATATTTAGGAACGGAGGAAG 59.985 40.741 0.00 0.00 0.00 3.46
4631 6073 5.418840 GGAGGAAGTAGAATGCATGGAAAAA 59.581 40.000 0.00 0.00 0.00 1.94
4675 6117 0.877071 AGTTCCAACAGCAGCATTCG 59.123 50.000 0.00 0.00 0.00 3.34
4794 6236 7.093354 ACTGGATATGCATAAACATCTCTACG 58.907 38.462 11.13 2.34 0.00 3.51
4801 6243 5.536538 TGCATAAACATCTCTACGAGATCCT 59.463 40.000 3.50 0.00 45.03 3.24
4842 6286 2.363038 CGGTCGTCCCATAGGTATTCAA 59.637 50.000 0.00 0.00 0.00 2.69
4843 6287 3.181473 CGGTCGTCCCATAGGTATTCAAA 60.181 47.826 0.00 0.00 0.00 2.69
4912 6356 2.275880 GCATAGGCCAAGCACCAAA 58.724 52.632 5.01 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.041135 CCGTTCGCGCCAAAGTTTTA 60.041 50.000 0.00 0.00 39.70 1.52
241 718 5.552178 ACTCCTAGTTAAGCAGGACAAAAG 58.448 41.667 1.54 0.00 35.99 2.27
279 757 1.344114 AGTTTTGTCCCGCGTAGGTAA 59.656 47.619 4.92 0.00 38.74 2.85
349 827 7.672122 ATATTTAGAAACGGAGGGAGTAGTT 57.328 36.000 0.00 0.00 0.00 2.24
350 828 8.773033 TTATATTTAGAAACGGAGGGAGTAGT 57.227 34.615 0.00 0.00 0.00 2.73
351 829 8.858094 ACTTATATTTAGAAACGGAGGGAGTAG 58.142 37.037 0.00 0.00 0.00 2.57
432 921 5.742453 CAGAGCAAAATGAGTGAATATGCAC 59.258 40.000 5.60 5.60 39.05 4.57
434 923 5.888105 ACAGAGCAAAATGAGTGAATATGC 58.112 37.500 0.00 0.00 0.00 3.14
435 924 8.618677 ACATACAGAGCAAAATGAGTGAATATG 58.381 33.333 0.00 0.00 0.00 1.78
437 926 9.317936 CTACATACAGAGCAAAATGAGTGAATA 57.682 33.333 0.00 0.00 0.00 1.75
440 929 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
443 932 7.840342 AAGACTACATACAGAGCAAAATGAG 57.160 36.000 0.00 0.00 0.00 2.90
444 933 8.506437 CAAAAGACTACATACAGAGCAAAATGA 58.494 33.333 0.00 0.00 0.00 2.57
450 939 5.700832 CCAACAAAAGACTACATACAGAGCA 59.299 40.000 0.00 0.00 0.00 4.26
451 940 5.932303 TCCAACAAAAGACTACATACAGAGC 59.068 40.000 0.00 0.00 0.00 4.09
452 941 7.962964 TTCCAACAAAAGACTACATACAGAG 57.037 36.000 0.00 0.00 0.00 3.35
453 942 8.375506 AGATTCCAACAAAAGACTACATACAGA 58.624 33.333 0.00 0.00 0.00 3.41
454 943 8.553459 AGATTCCAACAAAAGACTACATACAG 57.447 34.615 0.00 0.00 0.00 2.74
455 944 8.375506 AGAGATTCCAACAAAAGACTACATACA 58.624 33.333 0.00 0.00 0.00 2.29
456 945 8.779354 AGAGATTCCAACAAAAGACTACATAC 57.221 34.615 0.00 0.00 0.00 2.39
458 947 9.793259 TTTAGAGATTCCAACAAAAGACTACAT 57.207 29.630 0.00 0.00 0.00 2.29
459 948 9.621629 TTTTAGAGATTCCAACAAAAGACTACA 57.378 29.630 0.00 0.00 0.00 2.74
462 951 9.408648 TCTTTTTAGAGATTCCAACAAAAGACT 57.591 29.630 0.00 0.00 35.09 3.24
489 978 9.327731 CCCTCTGTTCCTAAATACTCCTATATT 57.672 37.037 0.00 0.00 0.00 1.28
490 979 8.689054 TCCCTCTGTTCCTAAATACTCCTATAT 58.311 37.037 0.00 0.00 0.00 0.86
491 980 8.065385 TCCCTCTGTTCCTAAATACTCCTATA 57.935 38.462 0.00 0.00 0.00 1.31
492 981 6.935036 TCCCTCTGTTCCTAAATACTCCTAT 58.065 40.000 0.00 0.00 0.00 2.57
493 982 6.068379 ACTCCCTCTGTTCCTAAATACTCCTA 60.068 42.308 0.00 0.00 0.00 2.94
495 984 4.963628 ACTCCCTCTGTTCCTAAATACTCC 59.036 45.833 0.00 0.00 0.00 3.85
501 990 5.006896 TGACTACTCCCTCTGTTCCTAAA 57.993 43.478 0.00 0.00 0.00 1.85
504 993 3.076182 TCTTGACTACTCCCTCTGTTCCT 59.924 47.826 0.00 0.00 0.00 3.36
506 995 5.669164 ATTCTTGACTACTCCCTCTGTTC 57.331 43.478 0.00 0.00 0.00 3.18
510 999 9.577222 GTAGTATTATTCTTGACTACTCCCTCT 57.423 37.037 4.24 0.00 40.63 3.69
590 1079 8.964772 AGACGGTCACTTTACTTGTAGTATTAT 58.035 33.333 11.27 0.00 29.64 1.28
593 1082 6.658391 AGAGACGGTCACTTTACTTGTAGTAT 59.342 38.462 11.27 0.00 29.64 2.12
599 1088 3.978687 ACAGAGACGGTCACTTTACTTG 58.021 45.455 11.27 0.23 0.00 3.16
600 1089 3.635373 TGACAGAGACGGTCACTTTACTT 59.365 43.478 11.27 0.00 40.16 2.24
690 1184 0.697658 TGGTTGATCCAGTGATGGCA 59.302 50.000 0.00 0.00 41.93 4.92
731 1225 3.735237 TGAGGGATCGAGCTATGTTTC 57.265 47.619 0.00 0.00 0.00 2.78
732 1226 4.192317 GTTTGAGGGATCGAGCTATGTTT 58.808 43.478 0.00 0.00 0.00 2.83
733 1227 3.197766 TGTTTGAGGGATCGAGCTATGTT 59.802 43.478 0.00 0.00 0.00 2.71
734 1228 2.766263 TGTTTGAGGGATCGAGCTATGT 59.234 45.455 0.00 0.00 0.00 2.29
735 1229 3.459232 TGTTTGAGGGATCGAGCTATG 57.541 47.619 0.00 0.00 0.00 2.23
736 1230 4.487714 TTTGTTTGAGGGATCGAGCTAT 57.512 40.909 0.00 0.00 0.00 2.97
737 1231 3.973206 TTTGTTTGAGGGATCGAGCTA 57.027 42.857 0.00 0.00 0.00 3.32
738 1232 2.859165 TTTGTTTGAGGGATCGAGCT 57.141 45.000 0.00 0.00 0.00 4.09
739 1233 3.915437 TTTTTGTTTGAGGGATCGAGC 57.085 42.857 0.00 0.00 0.00 5.03
760 1254 6.183360 GCTGATACGAGCTATGTTTCCTTTTT 60.183 38.462 0.00 0.00 35.95 1.94
761 1255 5.294552 GCTGATACGAGCTATGTTTCCTTTT 59.705 40.000 0.00 0.00 35.95 2.27
762 1256 4.811557 GCTGATACGAGCTATGTTTCCTTT 59.188 41.667 0.00 0.00 35.95 3.11
763 1257 4.372656 GCTGATACGAGCTATGTTTCCTT 58.627 43.478 0.00 0.00 35.95 3.36
764 1258 3.243907 GGCTGATACGAGCTATGTTTCCT 60.244 47.826 0.00 0.00 39.11 3.36
765 1259 3.060602 GGCTGATACGAGCTATGTTTCC 58.939 50.000 0.00 0.00 39.11 3.13
775 1269 0.870307 CGGGTTTCGGCTGATACGAG 60.870 60.000 9.63 3.24 41.81 4.18
915 1424 4.293626 CCTTTTATCGGCGCGGCG 62.294 66.667 44.16 44.16 0.00 6.46
916 1425 4.607606 GCCTTTTATCGGCGCGGC 62.608 66.667 24.49 24.49 37.87 6.53
1015 1541 1.177401 GCCGGAGCAAGAAAGGAAAT 58.823 50.000 5.05 0.00 39.53 2.17
1099 1629 1.192146 TTCCTTGTCCGGAGACCCAG 61.192 60.000 3.06 0.00 42.81 4.45
1104 1634 1.267121 CCTCTTTCCTTGTCCGGAGA 58.733 55.000 3.06 0.00 33.89 3.71
1111 1680 0.179018 AGCGCAACCTCTTTCCTTGT 60.179 50.000 11.47 0.00 0.00 3.16
1139 1720 4.170062 TCGTCGTCGTCCGCCATC 62.170 66.667 1.33 0.00 38.33 3.51
1259 1840 2.419574 GGAACTTACATGGCCGAGCTTA 60.420 50.000 0.00 0.00 0.00 3.09
1281 1862 5.134661 ACACTCATTTACTTTTTCCGGGAA 58.865 37.500 5.09 5.09 0.00 3.97
1284 1865 5.689819 CAGACACTCATTTACTTTTTCCGG 58.310 41.667 0.00 0.00 0.00 5.14
1286 1867 5.461526 GGCAGACACTCATTTACTTTTTCC 58.538 41.667 0.00 0.00 0.00 3.13
1287 1868 5.461526 GGGCAGACACTCATTTACTTTTTC 58.538 41.667 0.00 0.00 0.00 2.29
1288 1869 4.280929 GGGGCAGACACTCATTTACTTTTT 59.719 41.667 0.00 0.00 0.00 1.94
1289 1870 3.826729 GGGGCAGACACTCATTTACTTTT 59.173 43.478 0.00 0.00 0.00 2.27
1290 1871 3.181434 TGGGGCAGACACTCATTTACTTT 60.181 43.478 0.00 0.00 0.00 2.66
1291 1872 2.375174 TGGGGCAGACACTCATTTACTT 59.625 45.455 0.00 0.00 0.00 2.24
1293 1874 2.290323 ACTGGGGCAGACACTCATTTAC 60.290 50.000 0.00 0.00 35.18 2.01
1294 1875 1.985159 ACTGGGGCAGACACTCATTTA 59.015 47.619 0.00 0.00 35.18 1.40
1297 1878 0.837691 TGACTGGGGCAGACACTCAT 60.838 55.000 0.00 0.00 32.09 2.90
1298 1879 1.459348 TGACTGGGGCAGACACTCA 60.459 57.895 0.00 0.00 32.09 3.41
1299 1880 1.188219 TCTGACTGGGGCAGACACTC 61.188 60.000 0.00 0.00 37.46 3.51
1301 1882 3.471620 TCTGACTGGGGCAGACAC 58.528 61.111 0.00 0.00 37.46 3.67
1304 1885 0.902048 CTGAGTCTGACTGGGGCAGA 60.902 60.000 16.28 0.00 39.90 4.26
1305 1886 1.595882 CTGAGTCTGACTGGGGCAG 59.404 63.158 16.28 11.98 37.52 4.85
1306 1887 2.587247 GCTGAGTCTGACTGGGGCA 61.587 63.158 16.28 5.91 0.00 5.36
1307 1888 2.237534 GAGCTGAGTCTGACTGGGGC 62.238 65.000 16.28 15.07 0.00 5.80
1308 1889 0.902048 TGAGCTGAGTCTGACTGGGG 60.902 60.000 16.28 6.02 0.00 4.96
1311 1892 1.739707 GCCATGAGCTGAGTCTGACTG 60.740 57.143 16.28 2.73 38.99 3.51
1312 1893 0.536260 GCCATGAGCTGAGTCTGACT 59.464 55.000 10.66 10.66 38.99 3.41
1313 1894 3.062585 GCCATGAGCTGAGTCTGAC 57.937 57.895 0.00 0.00 38.99 3.51
1338 1928 0.660488 TGCTTACACACGCCAACAAG 59.340 50.000 0.00 0.00 0.00 3.16
1339 1929 0.660488 CTGCTTACACACGCCAACAA 59.340 50.000 0.00 0.00 0.00 2.83
1340 1930 0.462937 ACTGCTTACACACGCCAACA 60.463 50.000 0.00 0.00 0.00 3.33
1341 1931 0.041312 CACTGCTTACACACGCCAAC 60.041 55.000 0.00 0.00 0.00 3.77
1346 1939 0.865769 GGAACCACTGCTTACACACG 59.134 55.000 0.00 0.00 0.00 4.49
1348 1941 1.210722 TGTGGAACCACTGCTTACACA 59.789 47.619 21.98 1.98 46.30 3.72
1588 2261 0.317519 GTGTTTTTGTTCCGGCTCCG 60.318 55.000 0.00 0.48 39.44 4.63
1590 2263 2.570442 TTGTGTTTTTGTTCCGGCTC 57.430 45.000 0.00 0.00 0.00 4.70
1592 2265 2.338500 TGTTTGTGTTTTTGTTCCGGC 58.662 42.857 0.00 0.00 0.00 6.13
1593 2266 4.992381 TTTGTTTGTGTTTTTGTTCCGG 57.008 36.364 0.00 0.00 0.00 5.14
1596 2269 6.018542 CCGGAATTTGTTTGTGTTTTTGTTC 58.981 36.000 0.00 0.00 0.00 3.18
1597 2270 5.617973 GCCGGAATTTGTTTGTGTTTTTGTT 60.618 36.000 5.05 0.00 0.00 2.83
1598 2271 4.142795 GCCGGAATTTGTTTGTGTTTTTGT 60.143 37.500 5.05 0.00 0.00 2.83
1643 2334 3.862264 GCCAAGCCAATCAGGAAGAAAAC 60.862 47.826 0.00 0.00 41.22 2.43
1644 2335 2.299867 GCCAAGCCAATCAGGAAGAAAA 59.700 45.455 0.00 0.00 41.22 2.29
1646 2337 1.549203 GCCAAGCCAATCAGGAAGAA 58.451 50.000 0.00 0.00 41.22 2.52
1647 2338 3.271250 GCCAAGCCAATCAGGAAGA 57.729 52.632 0.00 0.00 41.22 2.87
1679 2374 2.127118 CTGCCAGAAAAGCACGCG 60.127 61.111 3.53 3.53 36.01 6.01
1682 2377 1.747325 TTGCCCTGCCAGAAAAGCAC 61.747 55.000 0.00 0.00 36.01 4.40
1685 2380 0.829182 ACCTTGCCCTGCCAGAAAAG 60.829 55.000 0.00 0.00 0.00 2.27
1842 2542 1.559149 GGACAGACGCGCGGTAAAAA 61.559 55.000 35.22 0.00 0.00 1.94
1845 2545 3.332493 GAGGACAGACGCGCGGTAA 62.332 63.158 35.22 0.00 0.00 2.85
1850 2550 2.807631 TTTACCGAGGACAGACGCGC 62.808 60.000 5.73 0.00 0.00 6.86
1856 2556 2.457366 AGCAGTTTTACCGAGGACAG 57.543 50.000 0.00 0.00 0.00 3.51
1857 2557 2.028748 GGTAGCAGTTTTACCGAGGACA 60.029 50.000 0.00 0.00 31.96 4.02
1859 2559 2.028748 GTGGTAGCAGTTTTACCGAGGA 60.029 50.000 0.00 0.00 42.85 3.71
1860 2560 2.344025 GTGGTAGCAGTTTTACCGAGG 58.656 52.381 0.00 0.00 42.85 4.63
1864 2564 2.572209 TGGGTGGTAGCAGTTTTACC 57.428 50.000 0.00 0.00 40.80 2.85
1866 2566 2.916934 AGGATGGGTGGTAGCAGTTTTA 59.083 45.455 0.00 0.00 0.00 1.52
1867 2567 1.710809 AGGATGGGTGGTAGCAGTTTT 59.289 47.619 0.00 0.00 0.00 2.43
1868 2568 1.372501 AGGATGGGTGGTAGCAGTTT 58.627 50.000 0.00 0.00 0.00 2.66
1871 2571 2.421529 GGTTAAGGATGGGTGGTAGCAG 60.422 54.545 0.00 0.00 0.00 4.24
1872 2572 1.562475 GGTTAAGGATGGGTGGTAGCA 59.438 52.381 0.00 0.00 0.00 3.49
1873 2573 1.844497 AGGTTAAGGATGGGTGGTAGC 59.156 52.381 0.00 0.00 0.00 3.58
1876 2606 0.331616 GCAGGTTAAGGATGGGTGGT 59.668 55.000 0.00 0.00 0.00 4.16
1878 2608 0.395724 GGGCAGGTTAAGGATGGGTG 60.396 60.000 0.00 0.00 0.00 4.61
1882 2612 1.152963 CCGGGGCAGGTTAAGGATG 60.153 63.158 0.00 0.00 0.00 3.51
1896 2626 0.459759 GGAAAGAAGAGTACGCCGGG 60.460 60.000 2.18 0.00 0.00 5.73
1902 2632 2.999355 CTGCAGCAGGAAAGAAGAGTAC 59.001 50.000 15.35 0.00 0.00 2.73
1932 2689 3.517100 TCTCTGTCTCCCATTTCTTCCAG 59.483 47.826 0.00 0.00 0.00 3.86
2005 2762 6.033831 CGTTTGTAAATGCATCAATCAGGTTC 59.966 38.462 0.00 0.00 0.00 3.62
2068 2847 4.153117 CACGGGAAAGAGAGAGAAAACATG 59.847 45.833 0.00 0.00 0.00 3.21
2284 3413 1.028905 CTGACGGAGCTAGAAGGAGG 58.971 60.000 0.00 0.00 0.00 4.30
2302 3431 4.704833 AGTGTCGCGGCAATGGCT 62.705 61.111 18.26 5.06 40.87 4.75
2333 3462 5.351948 TGAGATCATTGGTGTCGGAAATA 57.648 39.130 0.00 0.00 0.00 1.40
2334 3463 4.220693 TGAGATCATTGGTGTCGGAAAT 57.779 40.909 0.00 0.00 0.00 2.17
2335 3464 3.694043 TGAGATCATTGGTGTCGGAAA 57.306 42.857 0.00 0.00 0.00 3.13
2477 3606 6.049149 AGTCGTATCCATGGAATGTTGTAAG 58.951 40.000 20.67 7.91 44.81 2.34
2483 3612 6.911250 TGTATAGTCGTATCCATGGAATGT 57.089 37.500 20.67 4.84 44.81 2.71
2484 3613 8.659491 CAATTGTATAGTCGTATCCATGGAATG 58.341 37.037 20.67 13.32 46.21 2.67
2497 3752 1.526887 CTGGCGGCAATTGTATAGTCG 59.473 52.381 14.48 0.00 0.00 4.18
2538 3793 8.928448 ACTGATAGTATTGTATCATGTGGAACT 58.072 33.333 0.00 0.00 38.47 3.01
2586 3841 0.250295 CGCAAGGAAGACCAACAGGA 60.250 55.000 0.00 0.00 38.94 3.86
2591 3846 1.347707 AGATCACGCAAGGAAGACCAA 59.652 47.619 0.00 0.00 46.39 3.67
2750 4132 2.597455 CCAGCAGAAAGAAGGGGAAAA 58.403 47.619 0.00 0.00 0.00 2.29
2822 4204 2.761559 TGCTTTCGACGGAGAAATTCA 58.238 42.857 7.78 6.85 39.13 2.57
3086 4493 2.163818 TCTGAAACGCGTTCTGGAAT 57.836 45.000 26.77 8.34 37.13 3.01
3496 4926 3.284449 GCCGTGTTCCGCCAGTTT 61.284 61.111 0.00 0.00 34.38 2.66
3622 5052 0.820891 CCTTGTGAAGCAGGTGCACT 60.821 55.000 17.98 0.00 45.16 4.40
3736 5166 2.304180 AGCAGGATTTAGTCTGTGCACT 59.696 45.455 19.41 0.00 38.47 4.40
3764 5194 1.297456 GACGACGAGACCGACCTTCT 61.297 60.000 0.00 0.00 39.50 2.85
3766 5196 2.675056 CGACGACGAGACCGACCTT 61.675 63.158 0.00 0.00 42.66 3.50
3795 5225 1.960040 ATCTGCGCTGGGAATGTCGA 61.960 55.000 14.70 0.00 0.00 4.20
3802 5232 0.038166 AGGAAAAATCTGCGCTGGGA 59.962 50.000 14.70 7.56 0.00 4.37
4040 5472 3.284617 AGTGGCACTCGTTTACCTTTTT 58.715 40.909 15.88 0.00 0.00 1.94
4051 5483 4.206404 CGTGTATTACATTAGTGGCACTCG 59.794 45.833 25.80 16.11 0.00 4.18
4074 5506 3.198872 GTGCCTTCCAGTAGCTTGATAC 58.801 50.000 0.00 0.00 0.00 2.24
4102 5534 6.542821 TGGTTAGATTTCCAGTTGAGTCAAT 58.457 36.000 9.18 0.00 0.00 2.57
4300 5732 3.004734 GGCCAATATGTGTCACTTATGGC 59.995 47.826 24.95 24.95 34.97 4.40
4364 5804 2.755103 CTCTTATTGTCCCCACCTTTGC 59.245 50.000 0.00 0.00 0.00 3.68
4365 5805 2.755103 GCTCTTATTGTCCCCACCTTTG 59.245 50.000 0.00 0.00 0.00 2.77
4366 5806 2.378547 TGCTCTTATTGTCCCCACCTTT 59.621 45.455 0.00 0.00 0.00 3.11
4412 5852 2.559440 GCACATGGATGAGACTTCCTC 58.441 52.381 0.00 0.00 42.30 3.71
4444 5884 7.177878 AGGAATGGAGTGAGTATTTTCAATGT 58.822 34.615 0.00 0.00 0.00 2.71
4455 5895 9.440761 AGACTTATATTTAGGAATGGAGTGAGT 57.559 33.333 0.00 0.00 0.00 3.41
4491 5931 9.154632 TGCTCCTTTATGTAGTCTATATTGGAA 57.845 33.333 0.00 0.00 0.00 3.53
4492 5932 8.721133 TGCTCCTTTATGTAGTCTATATTGGA 57.279 34.615 0.00 1.43 0.00 3.53
4493 5933 9.778741 TTTGCTCCTTTATGTAGTCTATATTGG 57.221 33.333 0.00 0.00 0.00 3.16
4500 5940 9.167311 CACTTATTTTGCTCCTTTATGTAGTCT 57.833 33.333 0.00 0.00 0.00 3.24
4501 5941 9.162764 TCACTTATTTTGCTCCTTTATGTAGTC 57.837 33.333 0.00 0.00 0.00 2.59
4502 5942 9.515226 TTCACTTATTTTGCTCCTTTATGTAGT 57.485 29.630 0.00 0.00 0.00 2.73
4505 5945 9.247861 AGATTCACTTATTTTGCTCCTTTATGT 57.752 29.630 0.00 0.00 0.00 2.29
4506 5946 9.512435 CAGATTCACTTATTTTGCTCCTTTATG 57.488 33.333 0.00 0.00 0.00 1.90
4507 5947 8.193438 GCAGATTCACTTATTTTGCTCCTTTAT 58.807 33.333 0.00 0.00 0.00 1.40
4508 5948 7.176515 TGCAGATTCACTTATTTTGCTCCTTTA 59.823 33.333 0.00 0.00 0.00 1.85
4509 5949 6.015180 TGCAGATTCACTTATTTTGCTCCTTT 60.015 34.615 0.00 0.00 0.00 3.11
4510 5950 5.477984 TGCAGATTCACTTATTTTGCTCCTT 59.522 36.000 0.00 0.00 0.00 3.36
4511 5951 5.012239 TGCAGATTCACTTATTTTGCTCCT 58.988 37.500 0.00 0.00 0.00 3.69
4512 5952 5.098211 GTGCAGATTCACTTATTTTGCTCC 58.902 41.667 0.00 0.00 34.29 4.70
4513 5953 5.947443 AGTGCAGATTCACTTATTTTGCTC 58.053 37.500 0.00 0.00 44.26 4.26
4514 5954 5.709164 AGAGTGCAGATTCACTTATTTTGCT 59.291 36.000 0.00 0.00 46.40 3.91
4515 5955 5.947443 AGAGTGCAGATTCACTTATTTTGC 58.053 37.500 0.00 0.00 46.40 3.68
4516 5956 9.552114 CTTTAGAGTGCAGATTCACTTATTTTG 57.448 33.333 0.00 0.00 46.40 2.44
4517 5957 9.289782 ACTTTAGAGTGCAGATTCACTTATTTT 57.710 29.630 0.00 0.00 46.40 1.82
4518 5958 8.725148 CACTTTAGAGTGCAGATTCACTTATTT 58.275 33.333 0.00 0.00 46.40 1.40
4519 5959 8.261492 CACTTTAGAGTGCAGATTCACTTATT 57.739 34.615 0.00 0.00 46.40 1.40
4520 5960 7.840342 CACTTTAGAGTGCAGATTCACTTAT 57.160 36.000 0.00 0.00 46.40 1.73
4534 5974 7.393796 CGGATGTATATAGACCCACTTTAGAGT 59.606 40.741 0.00 0.00 36.25 3.24
4535 5975 7.393796 ACGGATGTATATAGACCCACTTTAGAG 59.606 40.741 0.00 0.00 0.00 2.43
4536 5976 7.236529 ACGGATGTATATAGACCCACTTTAGA 58.763 38.462 0.00 0.00 0.00 2.10
4537 5977 7.463961 ACGGATGTATATAGACCCACTTTAG 57.536 40.000 0.00 0.00 0.00 1.85
4538 5978 8.963725 CATACGGATGTATATAGACCCACTTTA 58.036 37.037 0.00 0.00 39.28 1.85
4539 5979 7.453752 ACATACGGATGTATATAGACCCACTTT 59.546 37.037 12.79 0.00 44.77 2.66
4540 5980 6.952358 ACATACGGATGTATATAGACCCACTT 59.048 38.462 12.79 0.00 44.77 3.16
4541 5981 6.491383 ACATACGGATGTATATAGACCCACT 58.509 40.000 12.79 0.00 44.77 4.00
4542 5982 6.770746 ACATACGGATGTATATAGACCCAC 57.229 41.667 12.79 0.00 44.77 4.61
4543 5983 7.636579 ACTACATACGGATGTATATAGACCCA 58.363 38.462 20.64 0.00 45.42 4.51
4544 5984 8.517062 AACTACATACGGATGTATATAGACCC 57.483 38.462 20.64 0.00 45.42 4.46
4545 5985 8.333908 CGAACTACATACGGATGTATATAGACC 58.666 40.741 20.64 7.52 45.42 3.85
4546 5986 8.877779 ACGAACTACATACGGATGTATATAGAC 58.122 37.037 20.64 9.63 45.42 2.59
4550 5990 9.999009 CAATACGAACTACATACGGATGTATAT 57.001 33.333 20.64 12.07 45.42 0.86
4551 5991 9.218440 TCAATACGAACTACATACGGATGTATA 57.782 33.333 20.64 10.32 45.42 1.47
4552 5992 8.102800 TCAATACGAACTACATACGGATGTAT 57.897 34.615 20.64 7.28 45.42 2.29
4553 5993 7.495135 TCAATACGAACTACATACGGATGTA 57.505 36.000 19.32 19.32 44.77 2.29
4554 5994 7.259882 TTTCAATACGAACTACATACGGATGT 58.740 34.615 19.12 19.12 40.55 3.06
4555 5995 7.688478 TTTCAATACGAACTACATACGGATG 57.312 36.000 5.94 5.94 34.47 3.51
4556 5996 8.358148 AGATTTCAATACGAACTACATACGGAT 58.642 33.333 0.00 0.00 31.73 4.18
4557 5997 7.709947 AGATTTCAATACGAACTACATACGGA 58.290 34.615 0.00 0.00 31.73 4.69
4558 5998 7.861372 AGAGATTTCAATACGAACTACATACGG 59.139 37.037 0.00 0.00 31.73 4.02
4559 5999 8.783999 AGAGATTTCAATACGAACTACATACG 57.216 34.615 0.00 0.00 31.73 3.06
4566 6006 9.152595 GTCCTTTTAGAGATTTCAATACGAACT 57.847 33.333 0.00 0.00 31.73 3.01
4567 6007 9.152595 AGTCCTTTTAGAGATTTCAATACGAAC 57.847 33.333 0.00 0.00 31.73 3.95
4568 6008 9.720769 AAGTCCTTTTAGAGATTTCAATACGAA 57.279 29.630 0.00 0.00 0.00 3.85
4585 6025 7.991460 CCTCCGTTCCTAAATATAAGTCCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4586 6026 7.346436 TCCTCCGTTCCTAAATATAAGTCCTTT 59.654 37.037 0.00 0.00 0.00 3.11
4587 6027 6.842807 TCCTCCGTTCCTAAATATAAGTCCTT 59.157 38.462 0.00 0.00 0.00 3.36
4588 6028 6.379579 TCCTCCGTTCCTAAATATAAGTCCT 58.620 40.000 0.00 0.00 0.00 3.85
4589 6029 6.661304 TCCTCCGTTCCTAAATATAAGTCC 57.339 41.667 0.00 0.00 0.00 3.85
4590 6030 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
4591 6031 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
4592 6032 9.075678 TCTACTTCCTCCGTTCCTAAATATAAG 57.924 37.037 0.00 0.00 0.00 1.73
4593 6033 9.425248 TTCTACTTCCTCCGTTCCTAAATATAA 57.575 33.333 0.00 0.00 0.00 0.98
4594 6034 9.597681 ATTCTACTTCCTCCGTTCCTAAATATA 57.402 33.333 0.00 0.00 0.00 0.86
4595 6035 7.909485 TTCTACTTCCTCCGTTCCTAAATAT 57.091 36.000 0.00 0.00 0.00 1.28
4596 6036 7.686127 GCATTCTACTTCCTCCGTTCCTAAATA 60.686 40.741 0.00 0.00 0.00 1.40
4597 6037 6.583562 CATTCTACTTCCTCCGTTCCTAAAT 58.416 40.000 0.00 0.00 0.00 1.40
4598 6038 5.626116 GCATTCTACTTCCTCCGTTCCTAAA 60.626 44.000 0.00 0.00 0.00 1.85
4599 6039 4.142004 GCATTCTACTTCCTCCGTTCCTAA 60.142 45.833 0.00 0.00 0.00 2.69
4600 6040 3.383825 GCATTCTACTTCCTCCGTTCCTA 59.616 47.826 0.00 0.00 0.00 2.94
4601 6041 2.168728 GCATTCTACTTCCTCCGTTCCT 59.831 50.000 0.00 0.00 0.00 3.36
4602 6042 2.093658 TGCATTCTACTTCCTCCGTTCC 60.094 50.000 0.00 0.00 0.00 3.62
4603 6043 3.247006 TGCATTCTACTTCCTCCGTTC 57.753 47.619 0.00 0.00 0.00 3.95
4604 6044 3.535561 CATGCATTCTACTTCCTCCGTT 58.464 45.455 0.00 0.00 0.00 4.44
4605 6045 2.158900 CCATGCATTCTACTTCCTCCGT 60.159 50.000 0.00 0.00 0.00 4.69
4606 6046 2.103094 TCCATGCATTCTACTTCCTCCG 59.897 50.000 0.00 0.00 0.00 4.63
4607 6047 3.845781 TCCATGCATTCTACTTCCTCC 57.154 47.619 0.00 0.00 0.00 4.30
4608 6048 6.515272 TTTTTCCATGCATTCTACTTCCTC 57.485 37.500 0.00 0.00 0.00 3.71
4631 6073 7.233855 AGTCTATATTACCACCCCCATTTTT 57.766 36.000 0.00 0.00 0.00 1.94
4632 6074 6.858792 AGTCTATATTACCACCCCCATTTT 57.141 37.500 0.00 0.00 0.00 1.82
4633 6075 7.086920 ACTAGTCTATATTACCACCCCCATTT 58.913 38.462 0.00 0.00 0.00 2.32
4634 6076 6.640925 ACTAGTCTATATTACCACCCCCATT 58.359 40.000 0.00 0.00 0.00 3.16
4675 6117 1.470494 TCTGATGCTCTCTCGTGTGTC 59.530 52.381 0.00 0.00 0.00 3.67
4720 6162 4.096682 GCTCGTGGACTAACTATTCAGAGT 59.903 45.833 0.00 0.00 0.00 3.24
4794 6236 6.148948 CGAGTATCATGAAAGACAGGATCTC 58.851 44.000 0.00 0.00 45.08 2.75
4801 6243 3.181490 CCGGACGAGTATCATGAAAGACA 60.181 47.826 0.00 0.00 33.17 3.41
4843 6287 8.652290 AGGTAAAGATACTGACTCTGACTTTTT 58.348 33.333 0.00 0.00 32.36 1.94
4851 6295 4.353777 TGGCAGGTAAAGATACTGACTCT 58.646 43.478 0.00 0.00 32.36 3.24
4852 6296 4.737855 TGGCAGGTAAAGATACTGACTC 57.262 45.455 0.00 0.00 32.36 3.36


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

AutoCloner maintained by Alex Coulton.