Multiple sequence alignment - TraesCS4D01G228600

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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 TraesCS4D01G228600 chr4D 100.000 4915 0 0 1 4915 388125392 388120478 0.000000e+00 9077.0
1 TraesCS4D01G228600 chr4B 94.438 1852 68 16 2580 4408 476360039 476358200 0.000000e+00 2817.0
2 TraesCS4D01G228600 chr4B 89.970 2024 101 43 518 2497 476362003 476360038 0.000000e+00 2519.0
3 TraesCS4D01G228600 chr4B 95.427 503 11 5 5 496 476362493 476361992 0.000000e+00 791.0
4 TraesCS4D01G228600 chr4B 82.806 506 43 19 4422 4909 476358112 476357633 3.540000e-111 412.0
5 TraesCS4D01G228600 chr4B 82.292 96 10 7 2496 2588 106975942 106975851 5.280000e-10 76.8
6 TraesCS4D01G228600 chr4A 94.131 1806 52 13 2583 4361 69318699 69316921 0.000000e+00 2699.0
7 TraesCS4D01G228600 chr4A 90.293 1844 100 34 703 2496 69320512 69318698 0.000000e+00 2340.0
8 TraesCS4D01G228600 chr4A 92.335 561 36 6 4360 4915 69316827 69316269 0.000000e+00 791.0
9 TraesCS4D01G228600 chr4A 91.139 474 11 6 5 472 69321090 69320642 9.040000e-172 614.0
10 TraesCS4D01G228600 chr4A 98.039 102 2 0 547 648 69320612 69320511 1.410000e-40 178.0
11 TraesCS4D01G228600 chr4A 86.364 88 10 2 134 221 614871662 614871747 1.460000e-15 95.3
12 TraesCS4D01G228600 chr2B 92.045 88 4 2 2495 2581 14834410 14834325 2.400000e-23 121.0
13 TraesCS4D01G228600 chr5D 89.011 91 7 2 132 222 288588511 288588424 5.200000e-20 110.0
14 TraesCS4D01G228600 chr5D 87.356 87 8 2 2496 2581 430065185 430065269 4.050000e-16 97.1
15 TraesCS4D01G228600 chr3D 87.912 91 8 2 131 221 418394890 418394803 2.420000e-18 104.0
16 TraesCS4D01G228600 chr3D 86.364 88 8 3 2496 2581 589758943 589759028 5.240000e-15 93.5
17 TraesCS4D01G228600 chr3D 82.105 95 12 5 2496 2588 570848668 570848759 5.280000e-10 76.8
18 TraesCS4D01G228600 chr7D 88.506 87 7 2 2496 2581 595026477 595026561 8.700000e-18 102.0
19 TraesCS4D01G228600 chr3A 91.026 78 4 2 2505 2581 86601828 86601753 8.700000e-18 102.0
20 TraesCS4D01G228600 chr3A 92.958 71 2 2 2497 2566 12955961 12956029 3.130000e-17 100.0
21 TraesCS4D01G228600 chr5B 85.263 95 11 2 2496 2589 431070539 431070447 1.460000e-15 95.3
22 TraesCS4D01G228600 chr6D 85.714 91 10 2 131 221 78352686 78352773 5.240000e-15 93.5
23 TraesCS4D01G228600 chr1B 87.805 82 7 2 134 215 85441708 85441630 5.240000e-15 93.5
24 TraesCS4D01G228600 chr1B 92.157 51 4 0 1067 1117 369190572 369190622 6.820000e-09 73.1
25 TraesCS4D01G228600 chr5A 85.393 89 10 2 133 221 19105078 19104993 6.780000e-14 89.8
26 TraesCS4D01G228600 chr3B 83.696 92 13 2 131 221 778340622 778340712 8.770000e-13 86.1
27 TraesCS4D01G228600 chr1D 95.556 45 2 0 1073 1117 237334627 237334583 6.820000e-09 73.1
28 TraesCS4D01G228600 chr1A 92.157 51 4 0 1067 1117 308202949 308202999 6.820000e-09 73.1


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 TraesCS4D01G228600 chr4D 388120478 388125392 4914 True 9077.00 9077 100.00000 1 4915 1 chr4D.!!$R1 4914
1 TraesCS4D01G228600 chr4B 476357633 476362493 4860 True 1634.75 2817 90.66025 5 4909 4 chr4B.!!$R2 4904
2 TraesCS4D01G228600 chr4A 69316269 69321090 4821 True 1324.40 2699 93.18740 5 4915 5 chr4A.!!$R1 4910

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
956 1002 0.313672 CTGCTCTCGTGATCTAGCCC 59.686 60.0 0.0 0.0 33.99 5.19 F
1638 1706 0.036164 TGCTGTGGCAATTACGGACT 59.964 50.0 0.0 0.0 46.36 3.85 F
1737 1806 0.320050 TTGTCCTGCTATGCGTCACA 59.680 50.0 0.0 0.0 0.00 3.58 F
2364 2444 0.591170 GCTACAAAGCTTGCCGTTCA 59.409 50.0 0.0 0.0 45.85 3.18 F
3111 3203 0.322975 TCACAGAGAGCTTTCCTGGC 59.677 55.0 0.0 0.0 32.52 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 2647 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.0 0.0 0.0 0.00 4.00 R
2565 2648 0.613853 CAACTACTCCCTCCGTCCCA 60.614 60.0 0.0 0.0 0.00 4.37 R
2566 2649 0.614134 ACAACTACTCCCTCCGTCCC 60.614 60.0 0.0 0.0 0.00 4.46 R
3751 3846 0.688487 CGGTGGGAGGTTCCTTTGTA 59.312 55.0 0.0 0.0 36.57 2.41 R
4089 4184 0.872021 GGAGTCGCCACTAGCAATCG 60.872 60.0 0.0 0.0 44.04 3.34 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
126 129 4.225267 TGAGGGGTTTTGGTAGAGATCTTC 59.775 45.833 0.00 0.00 0.00 2.87
224 232 8.688747 ATATTTAGTTACGGAGCTAGTACAGT 57.311 34.615 0.00 0.00 0.00 3.55
394 405 2.253758 GCGTGTGTGTGATGCAGGT 61.254 57.895 0.00 0.00 0.00 4.00
484 507 1.403814 CCGAGCTCCCAGTATCAGAA 58.596 55.000 8.47 0.00 0.00 3.02
485 508 1.967066 CCGAGCTCCCAGTATCAGAAT 59.033 52.381 8.47 0.00 0.00 2.40
486 509 2.029470 CCGAGCTCCCAGTATCAGAATC 60.029 54.545 8.47 0.00 0.00 2.52
487 510 2.625314 CGAGCTCCCAGTATCAGAATCA 59.375 50.000 8.47 0.00 0.00 2.57
488 511 3.305267 CGAGCTCCCAGTATCAGAATCAG 60.305 52.174 8.47 0.00 0.00 2.90
489 512 3.894427 GAGCTCCCAGTATCAGAATCAGA 59.106 47.826 0.87 0.00 0.00 3.27
490 513 4.293494 AGCTCCCAGTATCAGAATCAGAA 58.707 43.478 0.00 0.00 0.00 3.02
491 514 4.906664 AGCTCCCAGTATCAGAATCAGAAT 59.093 41.667 0.00 0.00 0.00 2.40
492 515 5.011943 AGCTCCCAGTATCAGAATCAGAATC 59.988 44.000 0.00 0.00 0.00 2.52
493 516 5.221601 GCTCCCAGTATCAGAATCAGAATCA 60.222 44.000 0.00 0.00 0.00 2.57
494 517 6.416631 TCCCAGTATCAGAATCAGAATCAG 57.583 41.667 0.00 0.00 0.00 2.90
495 518 6.138967 TCCCAGTATCAGAATCAGAATCAGA 58.861 40.000 0.00 0.00 0.00 3.27
496 519 6.041409 TCCCAGTATCAGAATCAGAATCAGAC 59.959 42.308 0.00 0.00 0.00 3.51
497 520 6.041865 CCCAGTATCAGAATCAGAATCAGACT 59.958 42.308 0.00 0.00 0.00 3.24
498 521 7.418827 CCCAGTATCAGAATCAGAATCAGACTT 60.419 40.741 0.00 0.00 0.00 3.01
499 522 7.652909 CCAGTATCAGAATCAGAATCAGACTTC 59.347 40.741 0.00 0.00 0.00 3.01
500 523 7.379262 CAGTATCAGAATCAGAATCAGACTTCG 59.621 40.741 0.00 0.00 0.00 3.79
501 524 5.651387 TCAGAATCAGAATCAGACTTCGT 57.349 39.130 0.00 0.00 0.00 3.85
502 525 6.030548 TCAGAATCAGAATCAGACTTCGTT 57.969 37.500 0.00 0.00 0.00 3.85
503 526 6.096036 TCAGAATCAGAATCAGACTTCGTTC 58.904 40.000 0.00 0.00 0.00 3.95
504 527 5.866092 CAGAATCAGAATCAGACTTCGTTCA 59.134 40.000 0.00 0.00 0.00 3.18
505 528 6.367149 CAGAATCAGAATCAGACTTCGTTCAA 59.633 38.462 0.00 0.00 0.00 2.69
506 529 6.931281 AGAATCAGAATCAGACTTCGTTCAAA 59.069 34.615 0.00 0.00 0.00 2.69
507 530 7.442364 AGAATCAGAATCAGACTTCGTTCAAAA 59.558 33.333 0.00 0.00 0.00 2.44
508 531 6.918892 TCAGAATCAGACTTCGTTCAAAAA 57.081 33.333 0.00 0.00 0.00 1.94
545 568 0.820871 AGACGCTCCCAATCTGACTC 59.179 55.000 0.00 0.00 0.00 3.36
613 636 2.476320 GCCAAGAGGATCCAAGCGC 61.476 63.158 15.82 0.00 36.89 5.92
649 672 0.373716 GGTCAATCCTGCGCGTAAAG 59.626 55.000 8.43 3.06 0.00 1.85
656 679 0.713883 CCTGCGCGTAAAGTGTGTAG 59.286 55.000 8.43 0.00 0.00 2.74
658 681 2.587956 CTGCGCGTAAAGTGTGTAGTA 58.412 47.619 8.43 0.00 0.00 1.82
659 682 2.318578 TGCGCGTAAAGTGTGTAGTAC 58.681 47.619 8.43 0.00 0.00 2.73
660 683 2.030893 TGCGCGTAAAGTGTGTAGTACT 60.031 45.455 8.43 0.00 0.00 2.73
661 684 2.982470 GCGCGTAAAGTGTGTAGTACTT 59.018 45.455 8.43 0.00 39.92 2.24
662 685 3.181546 GCGCGTAAAGTGTGTAGTACTTG 60.182 47.826 8.43 0.00 38.32 3.16
663 686 3.181546 CGCGTAAAGTGTGTAGTACTTGC 60.182 47.826 0.00 0.00 38.32 4.01
664 687 3.985925 GCGTAAAGTGTGTAGTACTTGCT 59.014 43.478 0.00 0.00 38.32 3.91
665 688 4.446719 GCGTAAAGTGTGTAGTACTTGCTT 59.553 41.667 0.00 0.67 38.32 3.91
666 689 5.611844 GCGTAAAGTGTGTAGTACTTGCTTG 60.612 44.000 0.00 0.00 38.32 4.01
667 690 5.461078 CGTAAAGTGTGTAGTACTTGCTTGT 59.539 40.000 0.00 0.00 38.32 3.16
668 691 6.638063 CGTAAAGTGTGTAGTACTTGCTTGTA 59.362 38.462 0.00 0.00 38.32 2.41
669 692 6.839820 AAAGTGTGTAGTACTTGCTTGTAC 57.160 37.500 0.00 10.43 42.09 2.90
670 693 4.543692 AGTGTGTAGTACTTGCTTGTACG 58.456 43.478 0.00 0.00 45.23 3.67
671 694 4.276678 AGTGTGTAGTACTTGCTTGTACGA 59.723 41.667 0.00 6.42 45.23 3.43
678 701 4.758674 AGTACTTGCTTGTACGAGTAGTCA 59.241 41.667 17.92 4.27 45.23 3.41
778 808 4.796231 AGCATCGACCGACACGCC 62.796 66.667 0.00 0.00 0.00 5.68
780 810 2.431771 CATCGACCGACACGCCAA 60.432 61.111 0.00 0.00 0.00 4.52
781 811 2.024868 CATCGACCGACACGCCAAA 61.025 57.895 0.00 0.00 0.00 3.28
938 984 2.813908 GTTCGAATCGCGCCCACT 60.814 61.111 0.00 0.00 40.61 4.00
956 1002 0.313672 CTGCTCTCGTGATCTAGCCC 59.686 60.000 0.00 0.00 33.99 5.19
958 1004 1.811645 GCTCTCGTGATCTAGCCCCC 61.812 65.000 0.00 0.00 0.00 5.40
959 1005 1.519751 CTCTCGTGATCTAGCCCCCG 61.520 65.000 0.00 0.00 0.00 5.73
960 1006 2.520982 TCGTGATCTAGCCCCCGG 60.521 66.667 0.00 0.00 0.00 5.73
980 1026 3.507009 CGTCTCGTCGAGGGGGTC 61.507 72.222 21.63 7.18 0.00 4.46
1137 1193 2.782222 GCGCCTCCCGTCTGTGATA 61.782 63.158 0.00 0.00 39.71 2.15
1138 1194 1.065928 CGCCTCCCGTCTGTGATAC 59.934 63.158 0.00 0.00 0.00 2.24
1140 1196 1.065928 CCTCCCGTCTGTGATACGC 59.934 63.158 0.00 0.00 39.00 4.42
1142 1198 1.663379 CTCCCGTCTGTGATACGCCA 61.663 60.000 0.00 0.00 39.00 5.69
1143 1199 1.216977 CCCGTCTGTGATACGCCAA 59.783 57.895 0.00 0.00 39.00 4.52
1145 1201 0.108804 CCGTCTGTGATACGCCAACT 60.109 55.000 0.00 0.00 39.00 3.16
1146 1202 1.269166 CGTCTGTGATACGCCAACTC 58.731 55.000 0.00 0.00 33.04 3.01
1147 1203 1.269166 GTCTGTGATACGCCAACTCG 58.731 55.000 0.00 0.00 0.00 4.18
1153 1210 0.638746 GATACGCCAACTCGTGAACG 59.361 55.000 0.00 0.00 43.21 3.95
1160 1217 1.001048 CCAACTCGTGAACGTCTGGTA 60.001 52.381 2.37 0.00 40.80 3.25
1168 1225 1.005394 AACGTCTGGTAGTTGGCGG 60.005 57.895 0.00 0.00 0.00 6.13
1172 1229 0.249398 GTCTGGTAGTTGGCGGATGT 59.751 55.000 0.00 0.00 0.00 3.06
1187 1244 1.202580 GGATGTCGTGAGATTGGGAGG 60.203 57.143 0.00 0.00 45.19 4.30
1189 1246 1.866015 TGTCGTGAGATTGGGAGGAT 58.134 50.000 0.00 0.00 45.19 3.24
1195 1252 3.005261 CGTGAGATTGGGAGGATGTAGAG 59.995 52.174 0.00 0.00 0.00 2.43
1213 1270 4.457834 AGAGTAGGCATGTGTTACTGAC 57.542 45.455 9.60 0.03 0.00 3.51
1214 1271 3.119459 AGAGTAGGCATGTGTTACTGACG 60.119 47.826 9.60 0.00 0.00 4.35
1215 1272 2.823747 AGTAGGCATGTGTTACTGACGA 59.176 45.455 0.00 0.00 0.00 4.20
1216 1273 2.080286 AGGCATGTGTTACTGACGAC 57.920 50.000 0.00 0.00 0.00 4.34
1217 1274 1.618837 AGGCATGTGTTACTGACGACT 59.381 47.619 0.00 0.00 0.00 4.18
1218 1275 2.037251 AGGCATGTGTTACTGACGACTT 59.963 45.455 0.00 0.00 0.00 3.01
1219 1276 2.806244 GGCATGTGTTACTGACGACTTT 59.194 45.455 0.00 0.00 0.00 2.66
1220 1277 3.363970 GGCATGTGTTACTGACGACTTTG 60.364 47.826 0.00 0.00 0.00 2.77
1221 1278 3.493129 GCATGTGTTACTGACGACTTTGA 59.507 43.478 0.00 0.00 0.00 2.69
1222 1279 4.152402 GCATGTGTTACTGACGACTTTGAT 59.848 41.667 0.00 0.00 0.00 2.57
1223 1280 5.611919 CATGTGTTACTGACGACTTTGATG 58.388 41.667 0.00 0.00 0.00 3.07
1262 1319 2.826128 TGAGAGCCTATTCGTCAGTGTT 59.174 45.455 0.00 0.00 0.00 3.32
1291 1354 0.179134 CTTCGTCCTCGGATCACACC 60.179 60.000 0.00 0.00 37.69 4.16
1326 1390 4.098960 TCGAGTACAGAAAGGAGTGTTGTT 59.901 41.667 0.00 0.00 0.00 2.83
1409 1474 1.075601 AGCCAAATGGAGTGGGAGAA 58.924 50.000 2.98 0.00 36.58 2.87
1579 1647 5.918576 CACATATGCCTCAATGCACTTAATG 59.081 40.000 1.58 0.00 45.48 1.90
1587 1655 5.184864 CCTCAATGCACTTAATGTTTGGGTA 59.815 40.000 0.00 0.00 0.00 3.69
1591 1659 6.849085 ATGCACTTAATGTTTGGGTATTGA 57.151 33.333 0.00 0.00 0.00 2.57
1603 1671 6.068498 TGTTTGGGTATTGAAGGGGAGATAAT 60.068 38.462 0.00 0.00 0.00 1.28
1609 1677 5.859205 ATTGAAGGGGAGATAATTGCAAC 57.141 39.130 0.00 0.00 0.00 4.17
1638 1706 0.036164 TGCTGTGGCAATTACGGACT 59.964 50.000 0.00 0.00 46.36 3.85
1639 1707 1.276705 TGCTGTGGCAATTACGGACTA 59.723 47.619 0.00 0.00 46.36 2.59
1737 1806 0.320050 TTGTCCTGCTATGCGTCACA 59.680 50.000 0.00 0.00 0.00 3.58
1858 1927 7.112122 TGCATTCGCCATCCTTAGAAATATAT 58.888 34.615 0.00 0.00 37.32 0.86
1860 1929 9.277783 GCATTCGCCATCCTTAGAAATATATAT 57.722 33.333 0.00 0.00 0.00 0.86
1979 2048 1.300931 TATGCGCCTGAGAATCGGC 60.301 57.895 4.18 0.00 46.39 5.54
2013 2082 2.489329 ACACCATAGTTGCATGCTGTTC 59.511 45.455 20.33 6.57 0.00 3.18
2109 2188 3.776969 TGGTGCATCTCATCTTAGAAGGT 59.223 43.478 0.00 0.00 0.00 3.50
2185 2264 0.947660 TGCTCTCGCTCTGTGCTTTG 60.948 55.000 0.00 0.00 40.11 2.77
2204 2283 0.890683 GCCAGCTTGTACCATTTGCT 59.109 50.000 0.00 0.00 0.00 3.91
2271 2351 3.808218 TTGTGGAAGTGCAGGGGGC 62.808 63.158 0.00 0.00 45.13 5.80
2364 2444 0.591170 GCTACAAAGCTTGCCGTTCA 59.409 50.000 0.00 0.00 45.85 3.18
2376 2456 4.728608 GCTTGCCGTTCAATTTTCTATACG 59.271 41.667 0.00 0.00 33.57 3.06
2444 2524 1.889545 GCTCTCTGCACCTTTGAACT 58.110 50.000 0.00 0.00 42.31 3.01
2448 2531 2.170397 TCTCTGCACCTTTGAACTCACA 59.830 45.455 0.00 0.00 0.00 3.58
2468 2551 7.397761 ACTCACAGCCTATCTTTAGTAGTTTCT 59.602 37.037 0.00 0.00 0.00 2.52
2495 2578 8.517062 ACTTTATGAGCAAGCTGATCTATTTT 57.483 30.769 0.00 0.00 33.24 1.82
2496 2579 9.618890 ACTTTATGAGCAAGCTGATCTATTTTA 57.381 29.630 0.00 0.00 33.24 1.52
2497 2580 9.875675 CTTTATGAGCAAGCTGATCTATTTTAC 57.124 33.333 0.00 0.00 33.24 2.01
2498 2581 9.618890 TTTATGAGCAAGCTGATCTATTTTACT 57.381 29.630 0.00 0.00 33.24 2.24
2499 2582 7.727331 ATGAGCAAGCTGATCTATTTTACTC 57.273 36.000 0.00 0.00 33.24 2.59
2500 2583 6.051717 TGAGCAAGCTGATCTATTTTACTCC 58.948 40.000 0.00 0.00 33.24 3.85
2501 2584 5.372373 AGCAAGCTGATCTATTTTACTCCC 58.628 41.667 0.00 0.00 0.00 4.30
2502 2585 5.131809 AGCAAGCTGATCTATTTTACTCCCT 59.868 40.000 0.00 0.00 0.00 4.20
2503 2586 5.468409 GCAAGCTGATCTATTTTACTCCCTC 59.532 44.000 0.00 0.00 0.00 4.30
2504 2587 5.816955 AGCTGATCTATTTTACTCCCTCC 57.183 43.478 0.00 0.00 0.00 4.30
2505 2588 4.282195 AGCTGATCTATTTTACTCCCTCCG 59.718 45.833 0.00 0.00 0.00 4.63
2506 2589 4.039366 GCTGATCTATTTTACTCCCTCCGT 59.961 45.833 0.00 0.00 0.00 4.69
2507 2590 5.774630 CTGATCTATTTTACTCCCTCCGTC 58.225 45.833 0.00 0.00 0.00 4.79
2508 2591 4.587684 TGATCTATTTTACTCCCTCCGTCC 59.412 45.833 0.00 0.00 0.00 4.79
2509 2592 3.985127 TCTATTTTACTCCCTCCGTCCA 58.015 45.455 0.00 0.00 0.00 4.02
2510 2593 4.553678 TCTATTTTACTCCCTCCGTCCAT 58.446 43.478 0.00 0.00 0.00 3.41
2511 2594 5.708544 TCTATTTTACTCCCTCCGTCCATA 58.291 41.667 0.00 0.00 0.00 2.74
2512 2595 6.138263 TCTATTTTACTCCCTCCGTCCATAA 58.862 40.000 0.00 0.00 0.00 1.90
2513 2596 5.906772 ATTTTACTCCCTCCGTCCATAAT 57.093 39.130 0.00 0.00 0.00 1.28
2514 2597 7.951806 TCTATTTTACTCCCTCCGTCCATAATA 59.048 37.037 0.00 0.00 0.00 0.98
2515 2598 7.569599 ATTTTACTCCCTCCGTCCATAATAT 57.430 36.000 0.00 0.00 0.00 1.28
2516 2599 8.674925 ATTTTACTCCCTCCGTCCATAATATA 57.325 34.615 0.00 0.00 0.00 0.86
2517 2600 8.495160 TTTTACTCCCTCCGTCCATAATATAA 57.505 34.615 0.00 0.00 0.00 0.98
2518 2601 7.713734 TTACTCCCTCCGTCCATAATATAAG 57.286 40.000 0.00 0.00 0.00 1.73
2519 2602 5.900437 ACTCCCTCCGTCCATAATATAAGA 58.100 41.667 0.00 0.00 0.00 2.10
2520 2603 6.503944 ACTCCCTCCGTCCATAATATAAGAT 58.496 40.000 0.00 0.00 0.00 2.40
2521 2604 6.608002 ACTCCCTCCGTCCATAATATAAGATC 59.392 42.308 0.00 0.00 0.00 2.75
2522 2605 6.499436 TCCCTCCGTCCATAATATAAGATCA 58.501 40.000 0.00 0.00 0.00 2.92
2523 2606 7.132805 TCCCTCCGTCCATAATATAAGATCAT 58.867 38.462 0.00 0.00 0.00 2.45
2524 2607 7.623677 TCCCTCCGTCCATAATATAAGATCATT 59.376 37.037 0.00 0.00 0.00 2.57
2525 2608 8.267894 CCCTCCGTCCATAATATAAGATCATTT 58.732 37.037 0.00 0.00 0.00 2.32
2526 2609 9.672673 CCTCCGTCCATAATATAAGATCATTTT 57.327 33.333 0.00 0.00 0.00 1.82
2548 2631 7.891183 TTTTTGTAAGTTGTTTTAGCTTGCA 57.109 28.000 0.00 0.00 39.63 4.08
2549 2632 7.891183 TTTTGTAAGTTGTTTTAGCTTGCAA 57.109 28.000 0.00 0.00 45.32 4.08
2551 2634 7.891183 TTGTAAGTTGTTTTAGCTTGCAAAA 57.109 28.000 0.00 0.00 44.54 2.44
2552 2635 7.284518 TGTAAGTTGTTTTAGCTTGCAAAAC 57.715 32.000 13.93 13.93 38.76 2.43
2553 2636 5.448926 AAGTTGTTTTAGCTTGCAAAACG 57.551 34.783 15.21 0.00 44.91 3.60
2554 2637 4.739195 AGTTGTTTTAGCTTGCAAAACGA 58.261 34.783 15.21 12.02 44.91 3.85
2555 2638 5.348164 AGTTGTTTTAGCTTGCAAAACGAT 58.652 33.333 13.76 3.83 44.91 3.73
2556 2639 5.458779 AGTTGTTTTAGCTTGCAAAACGATC 59.541 36.000 13.76 9.27 44.91 3.69
2557 2640 5.181690 TGTTTTAGCTTGCAAAACGATCT 57.818 34.783 15.21 0.00 44.91 2.75
2558 2641 5.587289 TGTTTTAGCTTGCAAAACGATCTT 58.413 33.333 15.21 0.00 44.91 2.40
2559 2642 6.039616 TGTTTTAGCTTGCAAAACGATCTTT 58.960 32.000 15.21 0.00 44.91 2.52
2560 2643 6.533367 TGTTTTAGCTTGCAAAACGATCTTTT 59.467 30.769 15.21 0.00 44.91 2.27
2561 2644 7.702772 TGTTTTAGCTTGCAAAACGATCTTTTA 59.297 29.630 15.21 0.00 44.91 1.52
2562 2645 8.699749 GTTTTAGCTTGCAAAACGATCTTTTAT 58.300 29.630 0.00 0.00 36.47 1.40
2563 2646 8.810652 TTTAGCTTGCAAAACGATCTTTTATT 57.189 26.923 0.00 0.00 0.00 1.40
2564 2647 9.900710 TTTAGCTTGCAAAACGATCTTTTATTA 57.099 25.926 0.00 0.00 0.00 0.98
2566 2649 8.398491 AGCTTGCAAAACGATCTTTTATTATG 57.602 30.769 0.00 0.00 0.00 1.90
2567 2650 7.489113 AGCTTGCAAAACGATCTTTTATTATGG 59.511 33.333 0.00 0.00 0.00 2.74
2568 2651 7.254084 GCTTGCAAAACGATCTTTTATTATGGG 60.254 37.037 0.00 0.00 0.00 4.00
2569 2652 7.397892 TGCAAAACGATCTTTTATTATGGGA 57.602 32.000 0.00 0.00 0.00 4.37
2570 2653 7.254852 TGCAAAACGATCTTTTATTATGGGAC 58.745 34.615 0.00 0.00 0.00 4.46
2571 2654 6.413818 GCAAAACGATCTTTTATTATGGGACG 59.586 38.462 0.00 0.00 0.00 4.79
2572 2655 6.613755 AAACGATCTTTTATTATGGGACGG 57.386 37.500 0.00 0.00 0.00 4.79
2573 2656 5.540400 ACGATCTTTTATTATGGGACGGA 57.460 39.130 0.00 0.00 0.00 4.69
2574 2657 5.539048 ACGATCTTTTATTATGGGACGGAG 58.461 41.667 0.00 0.00 0.00 4.63
2575 2658 4.929808 CGATCTTTTATTATGGGACGGAGG 59.070 45.833 0.00 0.00 0.00 4.30
2576 2659 4.699925 TCTTTTATTATGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
2577 2660 4.300345 TCTTTTATTATGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
2578 2661 4.347000 TCTTTTATTATGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
2602 2685 8.301252 AGTAGTTGTTATTTGACCCAAAAACT 57.699 30.769 10.26 10.26 36.90 2.66
2603 2686 8.194769 AGTAGTTGTTATTTGACCCAAAAACTG 58.805 33.333 13.27 0.00 36.90 3.16
2604 2687 5.815222 AGTTGTTATTTGACCCAAAAACTGC 59.185 36.000 6.49 0.00 36.90 4.40
2610 2693 1.408702 TGACCCAAAAACTGCTCAAGC 59.591 47.619 0.00 0.00 42.50 4.01
2629 2712 9.170584 GCTCAAGCGAAGGATTTATTTTTATAC 57.829 33.333 0.00 0.00 0.00 1.47
2745 2837 6.159988 AGAAACACTCGTCCTTCTTTAGATG 58.840 40.000 0.00 0.00 0.00 2.90
2919 3011 1.683385 GAAACAGGCACCTTTTCAGCT 59.317 47.619 14.31 0.00 30.91 4.24
2920 3012 1.780503 AACAGGCACCTTTTCAGCTT 58.219 45.000 0.00 0.00 0.00 3.74
3039 3131 3.126858 GCGGAAGTATTGTTGATCTTGCA 59.873 43.478 0.00 0.00 0.00 4.08
3049 3141 0.804364 TGATCTTGCACGTCAATGGC 59.196 50.000 0.00 0.00 33.57 4.40
3073 3165 0.771755 AAAGCGGGGTCTTCTTCCTT 59.228 50.000 0.00 0.00 0.00 3.36
3111 3203 0.322975 TCACAGAGAGCTTTCCTGGC 59.677 55.000 0.00 0.00 32.52 4.85
3480 3574 4.406003 TCTTACTCCAAGGGAAGATAGCAC 59.594 45.833 0.00 0.00 34.76 4.40
3487 3581 3.688553 GGAAGATAGCACCCTTCCG 57.311 57.895 12.97 0.00 45.99 4.30
3508 3602 2.000447 GTAGTGACCCGCAAAGATGAC 59.000 52.381 0.00 0.00 0.00 3.06
3511 3605 0.396435 TGACCCGCAAAGATGACACT 59.604 50.000 0.00 0.00 0.00 3.55
3751 3846 3.633116 GGTACCACCACTGCCGGT 61.633 66.667 7.15 0.00 41.07 5.28
3770 3865 0.688487 TACAAAGGAACCTCCCACCG 59.312 55.000 0.00 0.00 37.19 4.94
3812 3907 1.264288 CTGCCGGTGTTTTCTTCAGAC 59.736 52.381 1.90 0.00 0.00 3.51
4012 4107 2.684881 GTGTTGGATTCCAGCTGGTATG 59.315 50.000 31.58 7.03 35.72 2.39
4089 4184 1.486211 TGTTGGCCTAGTCTCTAGCC 58.514 55.000 3.32 0.00 45.96 3.93
4230 4325 0.251077 AGCAAAAGAGCAGGGGACAG 60.251 55.000 0.00 0.00 36.85 3.51
4318 4432 2.154567 ATTGAAGTGGGCTGATGCAT 57.845 45.000 0.00 0.00 41.91 3.96
4384 4594 2.791383 TGTTTGAATGTTTCCTGGCG 57.209 45.000 0.00 0.00 0.00 5.69
4393 4603 3.050354 TTTCCTGGCGTGTGGTGGT 62.050 57.895 0.00 0.00 0.00 4.16
4463 4749 7.215789 TGCATTGTTTGTTGATTACCTGATTT 58.784 30.769 0.00 0.00 0.00 2.17
4464 4750 7.171167 TGCATTGTTTGTTGATTACCTGATTTG 59.829 33.333 0.00 0.00 0.00 2.32
4533 4820 1.798283 ATTAAAGGCGTGTGCGTGTA 58.202 45.000 0.00 0.00 44.10 2.90
4644 4938 5.402997 TTCATAATGCCACAAGAATGCAA 57.597 34.783 0.00 0.00 38.69 4.08
4645 4939 5.001237 TCATAATGCCACAAGAATGCAAG 57.999 39.130 0.00 0.00 38.69 4.01
4646 4940 2.088950 AATGCCACAAGAATGCAAGC 57.911 45.000 0.00 0.00 38.69 4.01
4651 4945 2.715046 CCACAAGAATGCAAGCCTCTA 58.285 47.619 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.473007 TCTATCTCATCTTCTTCTTCTTCTTCA 57.527 33.333 0.00 0.00 0.00 3.02
3 4 9.699410 TCTTCTATCTCATCTTCTTCTTCTTCT 57.301 33.333 0.00 0.00 0.00 2.85
7 8 9.480053 CCATTCTTCTATCTCATCTTCTTCTTC 57.520 37.037 0.00 0.00 0.00 2.87
8 9 8.991275 ACCATTCTTCTATCTCATCTTCTTCTT 58.009 33.333 0.00 0.00 0.00 2.52
9 10 8.551682 ACCATTCTTCTATCTCATCTTCTTCT 57.448 34.615 0.00 0.00 0.00 2.85
126 129 7.611079 ACTTAGTTACAGAGGTAGTAGTTCCTG 59.389 40.741 0.00 0.00 33.83 3.86
221 229 9.525007 GTAATTCTGACGTTTTACATGTTACTG 57.475 33.333 2.30 0.60 0.00 2.74
224 232 8.836268 AGGTAATTCTGACGTTTTACATGTTA 57.164 30.769 2.30 0.00 0.00 2.41
394 405 3.273434 GCACTGATTGATGTTAGGCTCA 58.727 45.455 0.00 0.00 0.00 4.26
444 455 4.501400 CGGGATTTTTCTTTCCTTTGCACT 60.501 41.667 0.00 0.00 32.34 4.40
484 507 7.496529 TTTTTGAACGAAGTCTGATTCTGAT 57.503 32.000 0.00 0.00 45.00 2.90
485 508 6.918892 TTTTTGAACGAAGTCTGATTCTGA 57.081 33.333 0.00 0.00 45.00 3.27
510 533 5.123027 GGAGCGTCTGATTCTGATTCTTTTT 59.877 40.000 0.00 0.00 0.00 1.94
511 534 4.633565 GGAGCGTCTGATTCTGATTCTTTT 59.366 41.667 0.00 0.00 0.00 2.27
512 535 4.187694 GGAGCGTCTGATTCTGATTCTTT 58.812 43.478 0.00 0.00 0.00 2.52
513 536 3.431486 GGGAGCGTCTGATTCTGATTCTT 60.431 47.826 0.00 0.00 0.00 2.52
514 537 2.102252 GGGAGCGTCTGATTCTGATTCT 59.898 50.000 0.00 0.00 0.00 2.40
515 538 2.159043 TGGGAGCGTCTGATTCTGATTC 60.159 50.000 0.00 0.00 0.00 2.52
516 539 1.833630 TGGGAGCGTCTGATTCTGATT 59.166 47.619 0.00 0.00 0.00 2.57
517 540 1.489481 TGGGAGCGTCTGATTCTGAT 58.511 50.000 0.00 0.00 0.00 2.90
529 552 1.880340 GCGAGTCAGATTGGGAGCG 60.880 63.158 0.00 0.00 0.00 5.03
545 568 2.100418 TCAACATCTGAGATCTCCTGCG 59.900 50.000 20.03 8.74 0.00 5.18
613 636 4.963276 TGACCTTGGATTAAAGAATGCG 57.037 40.909 0.00 0.00 36.23 4.73
649 672 4.539870 TCGTACAAGCAAGTACTACACAC 58.460 43.478 14.28 0.00 41.65 3.82
656 679 4.850470 GTGACTACTCGTACAAGCAAGTAC 59.150 45.833 8.24 8.24 40.68 2.73
658 681 3.305199 GGTGACTACTCGTACAAGCAAGT 60.305 47.826 0.00 0.00 0.00 3.16
659 682 3.057456 AGGTGACTACTCGTACAAGCAAG 60.057 47.826 0.00 0.00 40.61 4.01
660 683 2.889045 AGGTGACTACTCGTACAAGCAA 59.111 45.455 0.00 0.00 40.61 3.91
661 684 2.511659 AGGTGACTACTCGTACAAGCA 58.488 47.619 0.00 0.00 40.61 3.91
662 685 3.243336 CAAGGTGACTACTCGTACAAGC 58.757 50.000 0.00 0.00 42.68 4.01
663 686 3.504906 TCCAAGGTGACTACTCGTACAAG 59.495 47.826 0.00 0.00 42.68 3.16
664 687 3.489355 TCCAAGGTGACTACTCGTACAA 58.511 45.455 0.00 0.00 42.68 2.41
665 688 3.144657 TCCAAGGTGACTACTCGTACA 57.855 47.619 0.00 0.00 42.68 2.90
666 689 3.693085 TGATCCAAGGTGACTACTCGTAC 59.307 47.826 0.00 0.00 42.68 3.67
667 690 3.959293 TGATCCAAGGTGACTACTCGTA 58.041 45.455 0.00 0.00 42.68 3.43
668 691 2.803956 TGATCCAAGGTGACTACTCGT 58.196 47.619 0.00 0.00 42.68 4.18
669 692 3.868757 TTGATCCAAGGTGACTACTCG 57.131 47.619 0.00 0.00 42.68 4.18
670 693 3.927142 CGTTTGATCCAAGGTGACTACTC 59.073 47.826 0.00 0.00 42.68 2.59
671 694 3.576982 TCGTTTGATCCAAGGTGACTACT 59.423 43.478 0.00 0.00 42.68 2.57
678 701 2.814336 GCTCTTTCGTTTGATCCAAGGT 59.186 45.455 0.00 0.00 0.00 3.50
778 808 0.242825 TGACGGGAGAGTAGCGTTTG 59.757 55.000 0.00 0.00 0.00 2.93
779 809 0.526662 CTGACGGGAGAGTAGCGTTT 59.473 55.000 0.00 0.00 0.00 3.60
780 810 1.935327 GCTGACGGGAGAGTAGCGTT 61.935 60.000 0.00 0.00 0.00 4.84
781 811 2.408241 GCTGACGGGAGAGTAGCGT 61.408 63.158 0.00 0.00 0.00 5.07
783 813 2.325666 GACGCTGACGGGAGAGTAGC 62.326 65.000 0.00 0.00 46.04 3.58
784 814 1.025113 TGACGCTGACGGGAGAGTAG 61.025 60.000 0.00 0.00 46.04 2.57
785 815 1.002990 TGACGCTGACGGGAGAGTA 60.003 57.895 0.00 0.00 46.04 2.59
830 872 1.549950 GCATTCCAGTTTTCAGGGGGA 60.550 52.381 0.00 0.00 0.00 4.81
938 984 1.109920 GGGGCTAGATCACGAGAGCA 61.110 60.000 0.03 0.00 36.63 4.26
963 1009 3.507009 GACCCCCTCGACGAGACG 61.507 72.222 26.11 14.64 0.00 4.18
964 1010 3.139469 GGACCCCCTCGACGAGAC 61.139 72.222 26.11 10.95 0.00 3.36
965 1011 4.437587 GGGACCCCCTCGACGAGA 62.438 72.222 26.11 0.00 41.34 4.04
1131 1187 0.599060 TCACGAGTTGGCGTATCACA 59.401 50.000 0.00 0.00 43.59 3.58
1132 1188 1.389106 GTTCACGAGTTGGCGTATCAC 59.611 52.381 0.00 0.00 43.59 3.06
1133 1189 1.705256 GTTCACGAGTTGGCGTATCA 58.295 50.000 0.00 0.00 43.59 2.15
1134 1190 0.638746 CGTTCACGAGTTGGCGTATC 59.361 55.000 0.00 0.00 43.59 2.24
1135 1191 0.038892 ACGTTCACGAGTTGGCGTAT 60.039 50.000 6.30 0.00 43.59 3.06
1137 1193 1.947642 GACGTTCACGAGTTGGCGT 60.948 57.895 6.30 0.00 46.88 5.68
1138 1194 1.660575 AGACGTTCACGAGTTGGCG 60.661 57.895 6.30 0.00 43.02 5.69
1140 1196 0.249322 ACCAGACGTTCACGAGTTGG 60.249 55.000 6.30 12.02 43.02 3.77
1142 1198 1.952296 ACTACCAGACGTTCACGAGTT 59.048 47.619 6.30 0.00 43.02 3.01
1143 1199 1.602311 ACTACCAGACGTTCACGAGT 58.398 50.000 6.30 0.00 43.02 4.18
1145 1201 1.001048 CCAACTACCAGACGTTCACGA 60.001 52.381 6.30 0.00 43.02 4.35
1146 1202 1.415374 CCAACTACCAGACGTTCACG 58.585 55.000 0.00 0.00 46.33 4.35
1147 1203 1.145803 GCCAACTACCAGACGTTCAC 58.854 55.000 0.00 0.00 0.00 3.18
1153 1210 0.249398 ACATCCGCCAACTACCAGAC 59.751 55.000 0.00 0.00 0.00 3.51
1160 1217 1.079819 CTCACGACATCCGCCAACT 60.080 57.895 0.00 0.00 43.32 3.16
1168 1225 1.757118 TCCTCCCAATCTCACGACATC 59.243 52.381 0.00 0.00 0.00 3.06
1172 1229 1.866015 ACATCCTCCCAATCTCACGA 58.134 50.000 0.00 0.00 0.00 4.35
1187 1244 5.980116 CAGTAACACATGCCTACTCTACATC 59.020 44.000 0.00 0.00 0.00 3.06
1189 1246 5.014202 TCAGTAACACATGCCTACTCTACA 58.986 41.667 0.00 0.00 0.00 2.74
1195 1252 2.921754 GTCGTCAGTAACACATGCCTAC 59.078 50.000 0.00 0.00 0.00 3.18
1213 1270 4.581493 CAATTCACGATCCATCAAAGTCG 58.419 43.478 0.00 0.00 39.78 4.18
1214 1271 4.346129 GCAATTCACGATCCATCAAAGTC 58.654 43.478 0.00 0.00 0.00 3.01
1215 1272 3.129287 GGCAATTCACGATCCATCAAAGT 59.871 43.478 0.00 0.00 0.00 2.66
1216 1273 3.379372 AGGCAATTCACGATCCATCAAAG 59.621 43.478 0.00 0.00 0.00 2.77
1217 1274 3.355378 AGGCAATTCACGATCCATCAAA 58.645 40.909 0.00 0.00 0.00 2.69
1218 1275 3.003394 AGGCAATTCACGATCCATCAA 57.997 42.857 0.00 0.00 0.00 2.57
1219 1276 2.715749 AGGCAATTCACGATCCATCA 57.284 45.000 0.00 0.00 0.00 3.07
1220 1277 4.756642 TCAATAGGCAATTCACGATCCATC 59.243 41.667 0.00 0.00 0.00 3.51
1221 1278 4.717877 TCAATAGGCAATTCACGATCCAT 58.282 39.130 0.00 0.00 0.00 3.41
1222 1279 4.129380 CTCAATAGGCAATTCACGATCCA 58.871 43.478 0.00 0.00 0.00 3.41
1223 1280 4.380531 TCTCAATAGGCAATTCACGATCC 58.619 43.478 0.00 0.00 0.00 3.36
1262 1319 4.060038 GGACGAAGGCGGAACCGA 62.060 66.667 17.63 0.00 46.52 4.69
1291 1354 4.556233 TCTGTACTCGATTTGTTCACCAG 58.444 43.478 0.00 0.00 0.00 4.00
1326 1390 1.549037 GCCATTGTCCCAACCCAACTA 60.549 52.381 0.00 0.00 0.00 2.24
1346 1411 4.321527 GCAGGAAAAGTTCAGAAAGATGGG 60.322 45.833 0.00 0.00 0.00 4.00
1409 1474 2.375146 ACAAGGGCAAAAAGACGAGTT 58.625 42.857 0.00 0.00 0.00 3.01
1456 1521 6.183360 TGGCGTGCTTACTAGTAAATGATTTG 60.183 38.462 15.95 4.42 0.00 2.32
1457 1522 5.878116 TGGCGTGCTTACTAGTAAATGATTT 59.122 36.000 15.95 0.00 0.00 2.17
1458 1523 5.424757 TGGCGTGCTTACTAGTAAATGATT 58.575 37.500 15.95 0.00 0.00 2.57
1460 1525 4.459390 TGGCGTGCTTACTAGTAAATGA 57.541 40.909 15.95 0.98 0.00 2.57
1461 1526 5.293324 TGATTGGCGTGCTTACTAGTAAATG 59.707 40.000 15.95 9.02 0.00 2.32
1463 1528 4.823157 TGATTGGCGTGCTTACTAGTAAA 58.177 39.130 15.95 0.00 0.00 2.01
1464 1529 4.459390 TGATTGGCGTGCTTACTAGTAA 57.541 40.909 14.52 14.52 0.00 2.24
1466 1531 3.328382 TTGATTGGCGTGCTTACTAGT 57.672 42.857 0.00 0.00 0.00 2.57
1467 1532 4.882671 AATTGATTGGCGTGCTTACTAG 57.117 40.909 0.00 0.00 0.00 2.57
1579 1647 3.732048 TCTCCCCTTCAATACCCAAAC 57.268 47.619 0.00 0.00 0.00 2.93
1587 1655 5.271598 TGTTGCAATTATCTCCCCTTCAAT 58.728 37.500 0.59 0.00 0.00 2.57
1591 1659 3.628257 CCCTGTTGCAATTATCTCCCCTT 60.628 47.826 0.59 0.00 0.00 3.95
1609 1677 1.662044 GCCACAGCAAAACTCCCTG 59.338 57.895 0.00 0.00 39.53 4.45
1638 1706 9.910267 TTCTATACCACTGAATACGGCTATATA 57.090 33.333 0.00 0.00 0.00 0.86
1639 1707 8.818622 TTCTATACCACTGAATACGGCTATAT 57.181 34.615 0.00 0.00 0.00 0.86
1703 1772 3.737266 CAGGACAACATCACAAATTGCAC 59.263 43.478 0.00 0.00 0.00 4.57
2000 2069 3.999663 AGAAGAGTAGAACAGCATGCAAC 59.000 43.478 21.98 7.84 42.53 4.17
2109 2188 2.299993 CTGGTCGAGCAATAGCAGAA 57.700 50.000 19.16 0.00 45.49 3.02
2358 2438 6.964370 TGATTTGCGTATAGAAAATTGAACGG 59.036 34.615 0.00 0.00 38.20 4.44
2376 2456 6.704512 AAACGTCATTTACCATTGATTTGC 57.295 33.333 0.00 0.00 0.00 3.68
2435 2515 4.213564 AGATAGGCTGTGAGTTCAAAGG 57.786 45.455 0.00 0.00 31.81 3.11
2441 2521 7.483580 AACTACTAAAGATAGGCTGTGAGTT 57.516 36.000 0.00 0.00 33.15 3.01
2444 2524 7.719871 AGAAACTACTAAAGATAGGCTGTGA 57.280 36.000 0.00 0.00 33.15 3.58
2468 2551 9.618890 AAATAGATCAGCTTGCTCATAAAGTAA 57.381 29.630 0.00 0.00 0.00 2.24
2473 2556 9.265901 GAGTAAAATAGATCAGCTTGCTCATAA 57.734 33.333 0.00 0.00 31.47 1.90
2495 2578 7.036154 TCTTATATTATGGACGGAGGGAGTA 57.964 40.000 0.00 0.00 0.00 2.59
2496 2579 5.900437 TCTTATATTATGGACGGAGGGAGT 58.100 41.667 0.00 0.00 0.00 3.85
2497 2580 6.607600 TGATCTTATATTATGGACGGAGGGAG 59.392 42.308 0.00 0.00 0.00 4.30
2498 2581 6.499436 TGATCTTATATTATGGACGGAGGGA 58.501 40.000 0.00 0.00 0.00 4.20
2499 2582 6.791867 TGATCTTATATTATGGACGGAGGG 57.208 41.667 0.00 0.00 0.00 4.30
2500 2583 9.672673 AAAATGATCTTATATTATGGACGGAGG 57.327 33.333 0.00 0.00 0.00 4.30
2524 2607 7.891183 TGCAAGCTAAAACAACTTACAAAAA 57.109 28.000 0.00 0.00 0.00 1.94
2525 2608 7.891183 TTGCAAGCTAAAACAACTTACAAAA 57.109 28.000 0.00 0.00 0.00 2.44
2526 2609 7.891183 TTTGCAAGCTAAAACAACTTACAAA 57.109 28.000 0.00 0.00 35.40 2.83
2527 2610 7.410942 CGTTTTGCAAGCTAAAACAACTTACAA 60.411 33.333 18.63 0.00 44.28 2.41
2528 2611 6.034044 CGTTTTGCAAGCTAAAACAACTTACA 59.966 34.615 18.63 0.00 44.28 2.41
2529 2612 6.251801 TCGTTTTGCAAGCTAAAACAACTTAC 59.748 34.615 18.63 5.92 44.28 2.34
2530 2613 6.323266 TCGTTTTGCAAGCTAAAACAACTTA 58.677 32.000 18.63 1.79 44.28 2.24
2531 2614 5.164954 TCGTTTTGCAAGCTAAAACAACTT 58.835 33.333 18.63 0.00 44.28 2.66
2532 2615 4.739195 TCGTTTTGCAAGCTAAAACAACT 58.261 34.783 18.63 0.00 44.28 3.16
2533 2616 5.458779 AGATCGTTTTGCAAGCTAAAACAAC 59.541 36.000 18.63 11.15 44.28 3.32
2534 2617 5.587289 AGATCGTTTTGCAAGCTAAAACAA 58.413 33.333 18.63 5.54 44.28 2.83
2535 2618 5.181690 AGATCGTTTTGCAAGCTAAAACA 57.818 34.783 18.63 9.57 44.28 2.83
2536 2619 6.510746 AAAGATCGTTTTGCAAGCTAAAAC 57.489 33.333 11.65 11.65 41.97 2.43
2537 2620 8.810652 ATAAAAGATCGTTTTGCAAGCTAAAA 57.189 26.923 11.90 1.77 0.00 1.52
2538 2621 8.810652 AATAAAAGATCGTTTTGCAAGCTAAA 57.189 26.923 11.90 0.00 0.00 1.85
2540 2623 9.502145 CATAATAAAAGATCGTTTTGCAAGCTA 57.498 29.630 11.90 0.00 0.00 3.32
2541 2624 7.489113 CCATAATAAAAGATCGTTTTGCAAGCT 59.511 33.333 11.90 0.00 0.00 3.74
2542 2625 7.254084 CCCATAATAAAAGATCGTTTTGCAAGC 60.254 37.037 11.90 0.00 0.00 4.01
2543 2626 7.973388 TCCCATAATAAAAGATCGTTTTGCAAG 59.027 33.333 11.90 1.33 0.00 4.01
2544 2627 7.757624 GTCCCATAATAAAAGATCGTTTTGCAA 59.242 33.333 11.90 0.00 0.00 4.08
2545 2628 7.254852 GTCCCATAATAAAAGATCGTTTTGCA 58.745 34.615 11.90 0.00 0.00 4.08
2546 2629 6.413818 CGTCCCATAATAAAAGATCGTTTTGC 59.586 38.462 11.90 0.00 0.00 3.68
2547 2630 6.910433 CCGTCCCATAATAAAAGATCGTTTTG 59.090 38.462 11.90 4.53 0.00 2.44
2548 2631 6.824704 TCCGTCCCATAATAAAAGATCGTTTT 59.175 34.615 11.90 9.40 0.00 2.43
2549 2632 6.350906 TCCGTCCCATAATAAAAGATCGTTT 58.649 36.000 11.40 11.40 0.00 3.60
2550 2633 5.920903 TCCGTCCCATAATAAAAGATCGTT 58.079 37.500 0.00 0.00 0.00 3.85
2551 2634 5.510861 CCTCCGTCCCATAATAAAAGATCGT 60.511 44.000 0.00 0.00 0.00 3.73
2552 2635 4.929808 CCTCCGTCCCATAATAAAAGATCG 59.070 45.833 0.00 0.00 0.00 3.69
2553 2636 5.012768 TCCCTCCGTCCCATAATAAAAGATC 59.987 44.000 0.00 0.00 0.00 2.75
2554 2637 4.911522 TCCCTCCGTCCCATAATAAAAGAT 59.088 41.667 0.00 0.00 0.00 2.40
2555 2638 4.300345 TCCCTCCGTCCCATAATAAAAGA 58.700 43.478 0.00 0.00 0.00 2.52
2556 2639 4.102681 ACTCCCTCCGTCCCATAATAAAAG 59.897 45.833 0.00 0.00 0.00 2.27
2557 2640 4.042174 ACTCCCTCCGTCCCATAATAAAA 58.958 43.478 0.00 0.00 0.00 1.52
2558 2641 3.660959 ACTCCCTCCGTCCCATAATAAA 58.339 45.455 0.00 0.00 0.00 1.40
2559 2642 3.339713 ACTCCCTCCGTCCCATAATAA 57.660 47.619 0.00 0.00 0.00 1.40
2560 2643 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2561 2644 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2562 2645 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2563 2646 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2564 2647 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2565 2648 0.613853 CAACTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2566 2649 0.614134 ACAACTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
2567 2650 1.264295 AACAACTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
2568 2651 4.732672 AATAACAACTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
2569 2652 4.529377 TCAAATAACAACTACTCCCTCCGT 59.471 41.667 0.00 0.00 0.00 4.69
2570 2653 4.868734 GTCAAATAACAACTACTCCCTCCG 59.131 45.833 0.00 0.00 0.00 4.63
2571 2654 5.183969 GGTCAAATAACAACTACTCCCTCC 58.816 45.833 0.00 0.00 0.00 4.30
2572 2655 5.183969 GGGTCAAATAACAACTACTCCCTC 58.816 45.833 0.00 0.00 0.00 4.30
2573 2656 4.600111 TGGGTCAAATAACAACTACTCCCT 59.400 41.667 0.00 0.00 33.15 4.20
2574 2657 4.913784 TGGGTCAAATAACAACTACTCCC 58.086 43.478 0.00 0.00 0.00 4.30
2575 2658 6.887626 TTTGGGTCAAATAACAACTACTCC 57.112 37.500 0.00 0.00 0.00 3.85
2576 2659 8.410912 AGTTTTTGGGTCAAATAACAACTACTC 58.589 33.333 14.39 0.00 32.50 2.59
2577 2660 8.194769 CAGTTTTTGGGTCAAATAACAACTACT 58.805 33.333 14.39 0.00 32.50 2.57
2578 2661 7.042992 GCAGTTTTTGGGTCAAATAACAACTAC 60.043 37.037 14.39 6.05 32.50 2.73
2602 2685 5.643379 AAAATAAATCCTTCGCTTGAGCA 57.357 34.783 3.65 0.00 42.21 4.26
2603 2686 9.170584 GTATAAAAATAAATCCTTCGCTTGAGC 57.829 33.333 0.00 0.00 37.78 4.26
2610 2693 8.958043 GCTGCAAGTATAAAAATAAATCCTTCG 58.042 33.333 0.00 0.00 35.30 3.79
2629 2712 1.671979 TAGGCATTAGCAGCTGCAAG 58.328 50.000 38.24 24.61 45.16 4.01
2919 3011 2.983192 TGGTCCACCAGATCCAAGTAAA 59.017 45.455 0.00 0.00 42.01 2.01
2920 3012 2.626785 TGGTCCACCAGATCCAAGTAA 58.373 47.619 0.00 0.00 42.01 2.24
3049 3141 1.897560 AGAAGACCCCGCTTTTCAAG 58.102 50.000 0.00 0.00 0.00 3.02
3073 3165 2.170397 TGAGTGGAAGTTCTTCACTGCA 59.830 45.455 16.57 12.06 41.24 4.41
3111 3203 1.821753 ACCGAGATGAGACCAGAGTTG 59.178 52.381 0.00 0.00 0.00 3.16
3207 3299 6.319399 ACTGAAACGACAAAGAACGAAAAAT 58.681 32.000 0.00 0.00 0.00 1.82
3240 3332 6.071447 TGCAATCAAAGGTTAGCATGTTATGT 60.071 34.615 0.00 0.00 0.00 2.29
3487 3581 1.066430 TCATCTTTGCGGGTCACTACC 60.066 52.381 0.00 0.00 45.97 3.18
3508 3602 6.015940 ACCTTTTCCTTTGAAAGCTATCAGTG 60.016 38.462 0.00 0.00 41.31 3.66
3511 3605 6.068010 TCACCTTTTCCTTTGAAAGCTATCA 58.932 36.000 0.00 0.00 41.31 2.15
3559 3653 2.348472 TCTTTGAGTGGGGGAGTTGAT 58.652 47.619 0.00 0.00 0.00 2.57
3751 3846 0.688487 CGGTGGGAGGTTCCTTTGTA 59.312 55.000 0.00 0.00 36.57 2.41
3770 3865 2.047179 GGGTCGAGAGTTGGTGGC 60.047 66.667 0.00 0.00 0.00 5.01
3812 3907 7.950512 AGGAGAATCTGTGATATCTGTAGTTG 58.049 38.462 3.98 0.00 33.73 3.16
3920 4015 3.831911 CCCTTTAAGCCTTTTGACATCCA 59.168 43.478 0.00 0.00 0.00 3.41
3974 4069 3.371063 CCACCAAGGCAGCAGCAG 61.371 66.667 2.65 0.00 44.61 4.24
3975 4070 4.208403 ACCACCAAGGCAGCAGCA 62.208 61.111 2.65 0.00 44.61 4.41
3976 4071 3.677648 CACCACCAAGGCAGCAGC 61.678 66.667 0.00 0.00 43.14 5.25
4012 4107 2.883386 GGAAGGCATCAGATGGTTCATC 59.117 50.000 12.54 0.00 40.80 2.92
4089 4184 0.872021 GGAGTCGCCACTAGCAATCG 60.872 60.000 0.00 0.00 44.04 3.34
4303 4401 2.154567 AATCATGCATCAGCCCACTT 57.845 45.000 0.00 0.00 41.13 3.16
4318 4432 8.770010 TTTCCTGTTCCTACCTTTTAAAATCA 57.230 30.769 0.09 0.00 0.00 2.57
4358 4472 6.873076 GCCAGGAAACATTCAAACAATGATAA 59.127 34.615 1.36 0.00 38.03 1.75
4363 4477 3.069443 ACGCCAGGAAACATTCAAACAAT 59.931 39.130 0.00 0.00 0.00 2.71
4384 4594 2.740826 ATACGCGCACCACCACAC 60.741 61.111 5.73 0.00 0.00 3.82
4436 4721 6.389091 TCAGGTAATCAACAAACAATGCATC 58.611 36.000 0.00 0.00 0.00 3.91
4463 4749 2.938451 CTCAAAGTGCTATTGCGGATCA 59.062 45.455 0.00 0.00 43.34 2.92
4464 4750 2.939103 ACTCAAAGTGCTATTGCGGATC 59.061 45.455 0.00 0.00 43.34 3.36
4533 4820 5.651612 TCATGTGGATTGAAGGATGGTAT 57.348 39.130 0.00 0.00 0.00 2.73
4596 4883 1.065551 GTTGGGAGCACACACAGAAAC 59.934 52.381 0.00 0.00 0.00 2.78
4644 4938 1.557371 GGCCTTCTCAGTTTAGAGGCT 59.443 52.381 11.92 0.00 38.64 4.58
4645 4939 1.407575 GGGCCTTCTCAGTTTAGAGGC 60.408 57.143 0.84 4.16 38.25 4.70
4646 4940 1.134670 CGGGCCTTCTCAGTTTAGAGG 60.135 57.143 0.84 0.00 36.30 3.69
4651 4945 1.600916 GCACGGGCCTTCTCAGTTT 60.601 57.895 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.