Multiple sequence alignment - TraesCS7B01G160700

Loading Multiple Alignment...

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 TraesCS7B01G160700 chr7B 100.000 3615 0 0 1 3615 219497478 219493864 0.000000e+00 6676.0
1 TraesCS7B01G160700 chr7D 88.880 1223 63 25 1668 2853 244154085 244152899 0.000000e+00 1437.0
2 TraesCS7B01G160700 chr7D 91.291 976 48 23 666 1612 244155053 244154086 0.000000e+00 1297.0
3 TraesCS7B01G160700 chr7D 91.441 666 49 7 1 660 616465491 616464828 0.000000e+00 907.0
4 TraesCS7B01G160700 chr7D 91.337 658 50 6 1 653 164761763 164761108 0.000000e+00 893.0
5 TraesCS7B01G160700 chr7D 90.855 667 53 6 1 661 145919631 145918967 0.000000e+00 887.0
6 TraesCS7B01G160700 chr7D 83.707 491 49 20 3143 3615 244152499 244152022 5.540000e-118 435.0
7 TraesCS7B01G160700 chr7A 91.168 1053 51 18 754 1779 259574747 259573710 0.000000e+00 1391.0
8 TraesCS7B01G160700 chr7A 89.015 883 40 20 1992 2853 259573711 259572865 0.000000e+00 1040.0
9 TraesCS7B01G160700 chr7A 85.714 112 16 0 3496 3607 259571505 259571394 6.340000e-23 119.0
10 TraesCS7B01G160700 chr7A 93.443 61 4 0 3143 3203 259572222 259572162 1.380000e-14 91.6
11 TraesCS7B01G160700 chr2D 91.766 668 47 8 1 662 276936330 276935665 0.000000e+00 922.0
12 TraesCS7B01G160700 chr6D 91.933 657 48 5 1 654 446133709 446133055 0.000000e+00 915.0
13 TraesCS7B01G160700 chr6D 91.502 659 49 7 1 655 464696485 464697140 0.000000e+00 900.0
14 TraesCS7B01G160700 chr6B 91.590 654 49 6 1 653 626809827 626809179 0.000000e+00 898.0
15 TraesCS7B01G160700 chr5D 90.964 664 54 6 1 661 432174068 432173408 0.000000e+00 889.0
16 TraesCS7B01G160700 chr2B 90.964 664 54 6 1 661 24843691 24844351 0.000000e+00 889.0
17 TraesCS7B01G160700 chr2A 89.655 87 8 1 3407 3493 758718087 758718172 3.820000e-20 110.0


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 TraesCS7B01G160700 chr7B 219493864 219497478 3614 True 6676.000000 6676 100.000000 1 3615 1 chr7B.!!$R1 3614
1 TraesCS7B01G160700 chr7D 244152022 244155053 3031 True 1056.333333 1437 87.959333 666 3615 3 chr7D.!!$R4 2949
2 TraesCS7B01G160700 chr7D 616464828 616465491 663 True 907.000000 907 91.441000 1 660 1 chr7D.!!$R3 659
3 TraesCS7B01G160700 chr7D 164761108 164761763 655 True 893.000000 893 91.337000 1 653 1 chr7D.!!$R2 652
4 TraesCS7B01G160700 chr7D 145918967 145919631 664 True 887.000000 887 90.855000 1 661 1 chr7D.!!$R1 660
5 TraesCS7B01G160700 chr7A 259571394 259574747 3353 True 660.400000 1391 89.835000 754 3607 4 chr7A.!!$R1 2853
6 TraesCS7B01G160700 chr2D 276935665 276936330 665 True 922.000000 922 91.766000 1 662 1 chr2D.!!$R1 661
7 TraesCS7B01G160700 chr6D 446133055 446133709 654 True 915.000000 915 91.933000 1 654 1 chr6D.!!$R1 653
8 TraesCS7B01G160700 chr6D 464696485 464697140 655 False 900.000000 900 91.502000 1 655 1 chr6D.!!$F1 654
9 TraesCS7B01G160700 chr6B 626809179 626809827 648 True 898.000000 898 91.590000 1 653 1 chr6B.!!$R1 652
10 TraesCS7B01G160700 chr5D 432173408 432174068 660 True 889.000000 889 90.964000 1 661 1 chr5D.!!$R1 660
11 TraesCS7B01G160700 chr2B 24843691 24844351 660 False 889.000000 889 90.964000 1 661 1 chr2B.!!$F1 660

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
847 869 0.035725 CTCCCGGTCCAAGTTTACCC 60.036 60.0 0.0 0.0 31.68 3.69 F
1416 1461 0.096976 CGGTTCGGCTATGTTGCAAG 59.903 55.0 0.0 0.0 34.04 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2676 0.249238 GAGACGCCCTACTGCATCTG 60.249 60.0 0.00 0.00 33.28 2.90 R
3383 3969 0.104120 CCATCATTGTCGGCCGTCTA 59.896 55.0 27.15 17.58 0.00 2.59 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
101 102 8.956426 CATGTATGGTCTGGTTTACAATAGTTT 58.044 33.333 0.00 0.00 0.00 2.66
137 138 4.057063 ACTTAGGAGTTGCCACCTACTA 57.943 45.455 0.00 0.00 38.31 1.82
143 144 3.072211 GAGTTGCCACCTACTAAACACC 58.928 50.000 0.00 0.00 0.00 4.16
154 155 3.012934 ACTAAACACCAGGCAGTTGTT 57.987 42.857 0.00 0.00 0.00 2.83
180 182 2.157668 AGCGCTACAAAAAGACATGACG 59.842 45.455 8.99 0.00 0.00 4.35
190 193 6.811170 ACAAAAAGACATGACGAAACAACATT 59.189 30.769 0.00 0.00 0.00 2.71
332 342 1.003118 CAAGCACACTAGGGGCAGTTA 59.997 52.381 7.99 0.00 0.00 2.24
389 400 1.304217 GGTGTGGGAGAGGAGACGA 60.304 63.158 0.00 0.00 0.00 4.20
391 402 0.609681 GTGTGGGAGAGGAGACGAGT 60.610 60.000 0.00 0.00 0.00 4.18
437 448 2.360350 ATCAGCCCTTGTGCGTGG 60.360 61.111 0.00 0.00 36.02 4.94
445 456 0.673437 CCTTGTGCGTGGGTGAAAAT 59.327 50.000 0.00 0.00 0.00 1.82
456 468 1.622811 GGGTGAAAATTGGCATGTGGA 59.377 47.619 0.00 0.00 0.00 4.02
475 487 0.321298 ACGAACTGCTAAACGCCCAT 60.321 50.000 0.00 0.00 38.05 4.00
503 515 2.677902 GCCTCTCCGTGTGATGAAATGA 60.678 50.000 0.00 0.00 0.00 2.57
559 573 0.465705 CCAGTCCTACGTGGCATCAT 59.534 55.000 0.00 0.00 35.26 2.45
629 645 2.713967 GGCAGATGCAAACGCCCAT 61.714 57.895 11.52 0.00 44.36 4.00
631 647 0.670162 GCAGATGCAAACGCCCATAT 59.330 50.000 0.00 0.00 41.59 1.78
632 648 1.067516 GCAGATGCAAACGCCCATATT 59.932 47.619 0.00 0.00 41.59 1.28
685 701 7.142680 AGGGAACAACATAAAACAAATACGTG 58.857 34.615 0.00 0.00 0.00 4.49
691 707 9.445786 ACAACATAAAACAAATACGTGAAAGAG 57.554 29.630 0.00 0.00 0.00 2.85
713 729 3.765257 TTGGGTTGGGGCAAGGTGG 62.765 63.158 0.00 0.00 0.00 4.61
734 750 1.520666 CGTTACGATGGAAGGCCCT 59.479 57.895 0.00 0.00 35.38 5.19
735 751 0.748450 CGTTACGATGGAAGGCCCTA 59.252 55.000 0.00 0.00 35.38 3.53
736 752 1.137479 CGTTACGATGGAAGGCCCTAA 59.863 52.381 0.00 0.00 35.38 2.69
737 753 2.802057 CGTTACGATGGAAGGCCCTAAG 60.802 54.545 0.00 0.00 35.38 2.18
738 754 2.433239 GTTACGATGGAAGGCCCTAAGA 59.567 50.000 0.00 0.00 35.38 2.10
739 755 1.807814 ACGATGGAAGGCCCTAAGAT 58.192 50.000 0.00 0.00 35.38 2.40
740 756 2.127708 ACGATGGAAGGCCCTAAGATT 58.872 47.619 0.00 0.00 35.38 2.40
741 757 3.314693 ACGATGGAAGGCCCTAAGATTA 58.685 45.455 0.00 0.00 35.38 1.75
742 758 3.910627 ACGATGGAAGGCCCTAAGATTAT 59.089 43.478 0.00 0.00 35.38 1.28
743 759 5.091552 ACGATGGAAGGCCCTAAGATTATA 58.908 41.667 0.00 0.00 35.38 0.98
744 760 5.726793 ACGATGGAAGGCCCTAAGATTATAT 59.273 40.000 0.00 0.00 35.38 0.86
746 762 7.569111 ACGATGGAAGGCCCTAAGATTATATAT 59.431 37.037 0.00 0.00 35.38 0.86
764 785 9.642343 ATTATATATGTAGTCGGATCCTTGCTA 57.358 33.333 10.75 6.46 0.00 3.49
765 786 9.642343 TTATATATGTAGTCGGATCCTTGCTAT 57.358 33.333 10.75 0.22 0.00 2.97
766 787 4.792521 ATGTAGTCGGATCCTTGCTATC 57.207 45.455 10.75 5.36 0.00 2.08
767 788 2.891580 TGTAGTCGGATCCTTGCTATCC 59.108 50.000 10.75 0.00 39.71 2.59
847 869 0.035725 CTCCCGGTCCAAGTTTACCC 60.036 60.000 0.00 0.00 31.68 3.69
854 876 3.293337 GGTCCAAGTTTACCCAAAGTGT 58.707 45.455 0.00 0.00 0.00 3.55
861 883 2.621526 GTTTACCCAAAGTGTGACCCAG 59.378 50.000 0.00 0.00 0.00 4.45
886 909 1.219935 CGCCTAACCTTACCCGCTT 59.780 57.895 0.00 0.00 0.00 4.68
929 952 1.131638 CTCAGATCCCCCAATTCGGA 58.868 55.000 0.00 0.00 36.56 4.55
956 982 4.763793 TCTCCTTCTCCAAGCAAAAATCAG 59.236 41.667 0.00 0.00 0.00 2.90
1065 1092 3.633986 GGGAGCTCCTTTATGTTGATTGG 59.366 47.826 31.36 0.00 35.95 3.16
1226 1253 4.148825 GCGGATCCGTGGACAGCT 62.149 66.667 33.33 0.00 42.09 4.24
1298 1325 1.065854 GGTGGTGGAGTGGATCTGAAG 60.066 57.143 0.00 0.00 0.00 3.02
1316 1343 5.046950 TCTGAAGTTTCTCTTAGAGGAAGCC 60.047 44.000 9.58 0.00 36.40 4.35
1334 1361 3.657448 CTGCGGGCGGTGTGATGTA 62.657 63.158 0.00 0.00 0.00 2.29
1357 1384 3.010420 GTGGAAGGCTGTGGTCTAATTC 58.990 50.000 0.00 0.00 0.00 2.17
1363 1390 2.872858 GGCTGTGGTCTAATTCGGATTC 59.127 50.000 0.00 0.00 0.00 2.52
1364 1391 2.540101 GCTGTGGTCTAATTCGGATTCG 59.460 50.000 0.00 0.00 37.82 3.34
1365 1392 3.737047 GCTGTGGTCTAATTCGGATTCGA 60.737 47.826 0.00 0.00 44.44 3.71
1366 1393 4.621991 CTGTGGTCTAATTCGGATTCGAT 58.378 43.478 0.00 0.00 45.51 3.59
1393 1438 6.183360 TGGTGATGCTTGTTAAGTTTTGGATT 60.183 34.615 0.00 0.00 0.00 3.01
1416 1461 0.096976 CGGTTCGGCTATGTTGCAAG 59.903 55.000 0.00 0.00 34.04 4.01
1482 1530 8.152898 AGAGGTAAAATAGTTCAACGGTTAAGT 58.847 33.333 0.00 0.00 0.00 2.24
1513 1561 4.553547 GCATTGGAACTATTTGCTAGCGAG 60.554 45.833 10.77 7.19 0.00 5.03
1553 1601 2.093181 ACTATTGCGGTTATGTGCCAGA 60.093 45.455 0.00 0.00 0.00 3.86
1554 1602 1.094785 ATTGCGGTTATGTGCCAGAC 58.905 50.000 0.00 0.00 0.00 3.51
1600 1648 2.637947 GTCTGATCTTTGGCCCTCTTC 58.362 52.381 0.00 0.00 0.00 2.87
1603 1651 4.080863 GTCTGATCTTTGGCCCTCTTCTTA 60.081 45.833 0.00 0.00 0.00 2.10
1622 1670 4.283467 TCTTACTGCAGATACCACAACTGT 59.717 41.667 23.35 0.00 34.60 3.55
1636 1684 9.693739 ATACCACAACTGTTATGATTTATTGGA 57.306 29.630 0.00 0.00 0.00 3.53
1639 1687 9.304731 CCACAACTGTTATGATTTATTGGATTG 57.695 33.333 0.00 0.00 0.00 2.67
1700 1750 4.478206 CTGAGGAAGTCAGCCTTTATGA 57.522 45.455 0.00 0.00 46.41 2.15
1714 1764 9.453572 TCAGCCTTTATGATTCATATATGTTCC 57.546 33.333 12.42 3.88 0.00 3.62
1717 1767 7.679638 GCCTTTATGATTCATATATGTTCCGGC 60.680 40.741 12.42 7.01 0.00 6.13
1725 1775 2.831685 ATATGTTCCGGCGCTCATTA 57.168 45.000 7.64 0.00 0.00 1.90
1730 1780 1.091537 TTCCGGCGCTCATTAAAAGG 58.908 50.000 7.64 0.00 0.00 3.11
1795 1845 5.520376 AGCTTTGTTGTGAACTTGCTATT 57.480 34.783 0.00 0.00 33.11 1.73
1796 1846 5.906073 AGCTTTGTTGTGAACTTGCTATTT 58.094 33.333 0.00 0.00 33.11 1.40
1806 1856 6.206438 TGTGAACTTGCTATTTGCTTATGTCA 59.794 34.615 0.00 0.00 43.37 3.58
1821 1871 5.636543 GCTTATGTCAATTTGCTTTGCTTCT 59.363 36.000 0.00 0.00 0.00 2.85
1823 1873 4.389890 TGTCAATTTGCTTTGCTTCTGT 57.610 36.364 0.00 0.00 0.00 3.41
1837 1887 2.229784 GCTTCTGTTTTCCCTCATGGTG 59.770 50.000 0.00 0.00 34.77 4.17
1842 1892 1.478105 GTTTTCCCTCATGGTGCATCC 59.522 52.381 0.00 0.00 34.77 3.51
1909 1978 1.792949 CTCGTTCCACAGCACTGTAAC 59.207 52.381 2.38 4.83 42.83 2.50
1922 1991 9.935682 CACAGCACTGTAACCTTAATATATTTG 57.064 33.333 2.68 0.00 42.83 2.32
1946 2015 0.758734 GGGAAAAAGCTGCACCCTTT 59.241 50.000 1.02 0.96 37.75 3.11
2034 2103 5.599242 TCCCATTGCACATATTGATCACATT 59.401 36.000 0.00 0.00 0.00 2.71
2048 2117 6.729391 TGATCACATTTTTGCATCCAAATG 57.271 33.333 18.26 18.26 43.31 2.32
2077 2146 3.751621 CGATCATCCTTTGTGTCAAAGC 58.248 45.455 14.40 2.40 0.00 3.51
2160 2230 4.125703 CCTGAGCTTGTCCATTAGATCAC 58.874 47.826 0.00 0.00 33.63 3.06
2163 2233 2.093500 AGCTTGTCCATTAGATCACGCA 60.093 45.455 0.00 0.00 0.00 5.24
2183 2253 5.474532 ACGCATTATAACTACATACCCTCGA 59.525 40.000 0.00 0.00 0.00 4.04
2184 2254 5.798934 CGCATTATAACTACATACCCTCGAC 59.201 44.000 0.00 0.00 0.00 4.20
2186 2256 6.628185 CATTATAACTACATACCCTCGACCC 58.372 44.000 0.00 0.00 0.00 4.46
2187 2257 2.537633 AACTACATACCCTCGACCCA 57.462 50.000 0.00 0.00 0.00 4.51
2188 2258 2.769602 ACTACATACCCTCGACCCAT 57.230 50.000 0.00 0.00 0.00 4.00
2189 2259 2.595238 ACTACATACCCTCGACCCATC 58.405 52.381 0.00 0.00 0.00 3.51
2190 2260 2.177233 ACTACATACCCTCGACCCATCT 59.823 50.000 0.00 0.00 0.00 2.90
2191 2261 1.414158 ACATACCCTCGACCCATCTG 58.586 55.000 0.00 0.00 0.00 2.90
2192 2262 1.063190 ACATACCCTCGACCCATCTGA 60.063 52.381 0.00 0.00 0.00 3.27
2193 2263 2.039418 CATACCCTCGACCCATCTGAA 58.961 52.381 0.00 0.00 0.00 3.02
2194 2264 2.471815 TACCCTCGACCCATCTGAAT 57.528 50.000 0.00 0.00 0.00 2.57
2195 2265 1.584724 ACCCTCGACCCATCTGAATT 58.415 50.000 0.00 0.00 0.00 2.17
2196 2266 1.486726 ACCCTCGACCCATCTGAATTC 59.513 52.381 0.00 0.00 0.00 2.17
2197 2267 1.486310 CCCTCGACCCATCTGAATTCA 59.514 52.381 8.12 8.12 0.00 2.57
2198 2268 2.555199 CCTCGACCCATCTGAATTCAC 58.445 52.381 3.38 0.00 0.00 3.18
2199 2269 2.555199 CTCGACCCATCTGAATTCACC 58.445 52.381 3.38 0.00 0.00 4.02
2200 2270 1.209504 TCGACCCATCTGAATTCACCC 59.790 52.381 3.38 0.00 0.00 4.61
2201 2271 1.065491 CGACCCATCTGAATTCACCCA 60.065 52.381 3.38 0.00 0.00 4.51
2202 2272 2.421952 CGACCCATCTGAATTCACCCAT 60.422 50.000 3.38 0.00 0.00 4.00
2203 2273 3.635591 GACCCATCTGAATTCACCCATT 58.364 45.455 3.38 0.00 0.00 3.16
2204 2274 4.685848 CGACCCATCTGAATTCACCCATTA 60.686 45.833 3.38 0.00 0.00 1.90
2205 2275 5.388654 GACCCATCTGAATTCACCCATTAT 58.611 41.667 3.38 0.00 0.00 1.28
2206 2276 5.142639 ACCCATCTGAATTCACCCATTATG 58.857 41.667 3.38 2.37 0.00 1.90
2207 2277 5.142639 CCCATCTGAATTCACCCATTATGT 58.857 41.667 3.38 0.00 0.00 2.29
2208 2278 5.010314 CCCATCTGAATTCACCCATTATGTG 59.990 44.000 3.38 0.00 35.01 3.21
2239 2309 4.764308 TCATCCGTGTCCATTTCAATTTCA 59.236 37.500 0.00 0.00 0.00 2.69
2298 2369 5.904984 AGCCCCACAACTATATGTTCATA 57.095 39.130 0.00 0.00 36.63 2.15
2365 2437 5.484173 TTTTGAGTTGTTCTAGTGTGCTG 57.516 39.130 0.00 0.00 0.00 4.41
2391 2464 5.766174 TGTTGGTTATCTTTGTAACTGGGTC 59.234 40.000 0.00 0.00 35.43 4.46
2392 2465 5.570205 TGGTTATCTTTGTAACTGGGTCA 57.430 39.130 0.00 0.00 35.43 4.02
2447 2520 2.678836 CAGCAAGAGAAGCAGAAGATGG 59.321 50.000 0.00 0.00 0.00 3.51
2471 2544 4.532126 TGATGAGTGAGATGGTAACCAAGT 59.468 41.667 0.00 0.00 36.95 3.16
2476 2549 4.102524 AGTGAGATGGTAACCAAGTTGACA 59.897 41.667 3.87 0.00 36.95 3.58
2500 2573 0.889994 TGTGCTGGGACAAATGCATC 59.110 50.000 0.00 0.00 39.17 3.91
2557 2630 1.705186 ACTACCTGCCTGACCAATTGT 59.295 47.619 4.43 0.00 0.00 2.71
2569 2642 3.264193 TGACCAATTGTGCTCAGAGGTAT 59.736 43.478 4.43 0.00 0.00 2.73
2582 2655 4.026052 TCAGAGGTATCTTGACATGAGCA 58.974 43.478 0.00 0.00 31.64 4.26
2602 2675 4.274459 AGCATGATAATTGCGAAGAGGTTC 59.726 41.667 0.00 0.00 44.82 3.62
2603 2676 4.555511 GCATGATAATTGCGAAGAGGTTCC 60.556 45.833 0.00 0.00 0.00 3.62
2625 2698 1.680522 ATGCAGTAGGGCGTCTCCAG 61.681 60.000 0.00 0.00 36.21 3.86
2628 2701 2.055042 AGTAGGGCGTCTCCAGCTG 61.055 63.158 6.78 6.78 36.21 4.24
2731 2818 3.311106 TCTGTCGTAAACGCTTGGTTAG 58.689 45.455 0.00 0.00 38.08 2.34
2732 2819 3.054878 CTGTCGTAAACGCTTGGTTAGT 58.945 45.455 0.00 0.00 38.08 2.24
2733 2820 4.023279 TCTGTCGTAAACGCTTGGTTAGTA 60.023 41.667 0.00 0.00 38.08 1.82
2734 2821 3.980775 TGTCGTAAACGCTTGGTTAGTAC 59.019 43.478 0.00 0.00 38.08 2.73
2735 2822 4.229876 GTCGTAAACGCTTGGTTAGTACT 58.770 43.478 0.00 0.00 38.08 2.73
2736 2823 4.322009 GTCGTAAACGCTTGGTTAGTACTC 59.678 45.833 0.00 0.00 38.08 2.59
2737 2824 4.023279 TCGTAAACGCTTGGTTAGTACTCA 60.023 41.667 0.00 0.00 38.08 3.41
2738 2825 4.322804 CGTAAACGCTTGGTTAGTACTCAG 59.677 45.833 0.00 0.00 38.08 3.35
2739 2826 4.332428 AAACGCTTGGTTAGTACTCAGT 57.668 40.909 0.00 0.00 38.08 3.41
2747 2834 5.130292 TGGTTAGTACTCAGTGTAGTTGC 57.870 43.478 0.00 0.00 36.33 4.17
2766 2857 1.270550 GCATCTGTGGTGAACCTTTGG 59.729 52.381 0.37 0.00 36.82 3.28
2796 2887 6.942532 TTCTTGTGAAGCTACTGTCATTTT 57.057 33.333 0.00 0.00 0.00 1.82
2803 2894 7.334421 TGTGAAGCTACTGTCATTTTATTCTCC 59.666 37.037 0.00 0.00 0.00 3.71
2804 2895 7.334421 GTGAAGCTACTGTCATTTTATTCTCCA 59.666 37.037 0.00 0.00 0.00 3.86
2849 2940 8.654230 TTCAAGTCAATCTATATGAAGTCTGC 57.346 34.615 0.00 0.00 0.00 4.26
2865 3258 4.082125 AGTCTGCCAAATTTTCAGTAGGG 58.918 43.478 13.77 1.72 0.00 3.53
2892 3286 6.013725 TGGTACAGGACAATTAACATCTGTCT 60.014 38.462 0.00 0.00 39.53 3.41
2893 3287 6.879458 GGTACAGGACAATTAACATCTGTCTT 59.121 38.462 0.00 0.00 39.53 3.01
2894 3288 7.390718 GGTACAGGACAATTAACATCTGTCTTT 59.609 37.037 0.00 0.00 39.53 2.52
2928 3414 3.391626 TGGTTGGACATGTACAGTGGTTA 59.608 43.478 11.40 0.00 0.00 2.85
2929 3415 4.042311 TGGTTGGACATGTACAGTGGTTAT 59.958 41.667 11.40 0.00 0.00 1.89
2940 3426 7.174107 TGTACAGTGGTTATTAAGGTAGTCC 57.826 40.000 0.00 0.00 0.00 3.85
2943 3429 5.046087 ACAGTGGTTATTAAGGTAGTCCCAC 60.046 44.000 0.00 0.00 41.05 4.61
2962 3459 9.280456 AGTCCCACCTTATAATTAAGAGAAGAA 57.720 33.333 0.00 0.00 37.59 2.52
2993 3492 0.252197 ATTGCCTCCGTACAGGGTTC 59.748 55.000 1.69 0.00 41.52 3.62
2997 3496 1.543871 GCCTCCGTACAGGGTTCAAAA 60.544 52.381 1.69 0.00 41.52 2.44
3035 3534 0.748367 TGCTGCCGTACCAAACACAA 60.748 50.000 0.00 0.00 0.00 3.33
3037 3536 1.599419 GCTGCCGTACCAAACACAAAG 60.599 52.381 0.00 0.00 0.00 2.77
3038 3537 1.001815 CTGCCGTACCAAACACAAAGG 60.002 52.381 0.00 0.00 0.00 3.11
3039 3538 0.318360 GCCGTACCAAACACAAAGGC 60.318 55.000 0.00 0.00 36.32 4.35
3041 3540 1.314730 CGTACCAAACACAAAGGCCT 58.685 50.000 0.00 0.00 0.00 5.19
3042 3541 1.001815 CGTACCAAACACAAAGGCCTG 60.002 52.381 5.69 0.00 0.00 4.85
3043 3542 1.036707 TACCAAACACAAAGGCCTGC 58.963 50.000 5.69 0.00 0.00 4.85
3044 3543 0.975040 ACCAAACACAAAGGCCTGCA 60.975 50.000 5.69 0.00 0.00 4.41
3045 3544 0.177604 CCAAACACAAAGGCCTGCAA 59.822 50.000 5.69 0.00 0.00 4.08
3046 3545 1.406614 CCAAACACAAAGGCCTGCAAA 60.407 47.619 5.69 0.00 0.00 3.68
3047 3546 2.354259 CAAACACAAAGGCCTGCAAAA 58.646 42.857 5.69 0.00 0.00 2.44
3048 3547 2.944349 CAAACACAAAGGCCTGCAAAAT 59.056 40.909 5.69 0.00 0.00 1.82
3049 3548 2.531522 ACACAAAGGCCTGCAAAATC 57.468 45.000 5.69 0.00 0.00 2.17
3050 3549 1.761784 ACACAAAGGCCTGCAAAATCA 59.238 42.857 5.69 0.00 0.00 2.57
3051 3550 2.170187 ACACAAAGGCCTGCAAAATCAA 59.830 40.909 5.69 0.00 0.00 2.57
3052 3551 2.545106 CACAAAGGCCTGCAAAATCAAC 59.455 45.455 5.69 0.00 0.00 3.18
3053 3552 2.145536 CAAAGGCCTGCAAAATCAACC 58.854 47.619 5.69 0.00 0.00 3.77
3054 3553 1.720781 AAGGCCTGCAAAATCAACCT 58.279 45.000 5.69 0.00 0.00 3.50
3055 3554 1.720781 AGGCCTGCAAAATCAACCTT 58.279 45.000 3.11 0.00 0.00 3.50
3056 3555 2.049372 AGGCCTGCAAAATCAACCTTT 58.951 42.857 3.11 0.00 0.00 3.11
3057 3556 2.037641 AGGCCTGCAAAATCAACCTTTC 59.962 45.455 3.11 0.00 0.00 2.62
3058 3557 2.224257 GGCCTGCAAAATCAACCTTTCA 60.224 45.455 0.00 0.00 0.00 2.69
3059 3558 3.557686 GGCCTGCAAAATCAACCTTTCAT 60.558 43.478 0.00 0.00 0.00 2.57
3060 3559 3.434299 GCCTGCAAAATCAACCTTTCATG 59.566 43.478 0.00 0.00 0.00 3.07
3061 3560 3.434299 CCTGCAAAATCAACCTTTCATGC 59.566 43.478 0.00 0.00 0.00 4.06
3062 3561 3.401182 TGCAAAATCAACCTTTCATGCC 58.599 40.909 0.00 0.00 0.00 4.40
3063 3562 3.181457 TGCAAAATCAACCTTTCATGCCA 60.181 39.130 0.00 0.00 0.00 4.92
3074 3573 6.212888 ACCTTTCATGCCAAACATATCTTC 57.787 37.500 0.00 0.00 36.64 2.87
3088 3587 2.486472 ATCTTCAGCACCACAAGAGG 57.514 50.000 0.00 0.00 29.78 3.69
3098 3597 1.203262 ACCACAAGAGGCCTACCACTA 60.203 52.381 4.42 0.00 35.58 2.74
3101 3600 3.322254 CCACAAGAGGCCTACCACTATAG 59.678 52.174 4.42 0.00 35.58 1.31
3102 3601 3.961408 CACAAGAGGCCTACCACTATAGT 59.039 47.826 4.42 0.00 35.58 2.12
3103 3602 4.406003 CACAAGAGGCCTACCACTATAGTT 59.594 45.833 4.42 0.00 35.58 2.24
3104 3603 5.597182 CACAAGAGGCCTACCACTATAGTTA 59.403 44.000 4.42 0.00 35.58 2.24
3164 3733 0.400213 ACAAAGCCCCGAAGATGACA 59.600 50.000 0.00 0.00 0.00 3.58
3165 3734 0.804989 CAAAGCCCCGAAGATGACAC 59.195 55.000 0.00 0.00 0.00 3.67
3171 3740 2.108168 CCCCGAAGATGACACCTTCTA 58.892 52.381 7.96 0.00 38.23 2.10
3216 3785 3.944087 TCGAGAGAGACTGATCAGAACA 58.056 45.455 29.27 2.76 34.84 3.18
3217 3786 4.522114 TCGAGAGAGACTGATCAGAACAT 58.478 43.478 29.27 11.84 34.84 2.71
3225 3794 4.687948 AGACTGATCAGAACATTGTCAACG 59.312 41.667 29.27 0.00 0.00 4.10
3248 3817 3.243068 ACGAAGCAAGAACCATTGTGTTC 60.243 43.478 8.93 8.93 43.95 3.18
3258 3827 9.079833 CAAGAACCATTGTGTTCATGATTATTC 57.920 33.333 15.69 0.00 43.20 1.75
3269 3838 8.892723 GTGTTCATGATTATTCTGAATACCACA 58.107 33.333 9.54 10.12 35.94 4.17
3293 3862 8.157476 ACAACTATCCAACATATGAATCCCTAC 58.843 37.037 10.38 0.00 0.00 3.18
3294 3863 7.259088 ACTATCCAACATATGAATCCCTACC 57.741 40.000 10.38 0.00 0.00 3.18
3297 3866 4.074970 CCAACATATGAATCCCTACCTGC 58.925 47.826 10.38 0.00 0.00 4.85
3298 3867 3.685139 ACATATGAATCCCTACCTGCG 57.315 47.619 10.38 0.00 0.00 5.18
3299 3868 2.972713 ACATATGAATCCCTACCTGCGT 59.027 45.455 10.38 0.00 0.00 5.24
3301 3870 0.389391 ATGAATCCCTACCTGCGTCG 59.611 55.000 0.00 0.00 0.00 5.12
3302 3871 1.591863 GAATCCCTACCTGCGTCGC 60.592 63.158 11.10 11.10 0.00 5.19
3303 3872 2.292794 GAATCCCTACCTGCGTCGCA 62.293 60.000 20.44 20.44 36.92 5.10
3304 3873 1.686325 AATCCCTACCTGCGTCGCAT 61.686 55.000 22.03 9.67 38.13 4.73
3306 3875 2.586079 CCTACCTGCGTCGCATGG 60.586 66.667 22.03 23.81 38.13 3.66
3307 3876 2.586079 CTACCTGCGTCGCATGGG 60.586 66.667 27.83 24.66 38.13 4.00
3308 3877 3.371097 CTACCTGCGTCGCATGGGT 62.371 63.158 27.80 27.80 39.74 4.51
3309 3878 3.657448 TACCTGCGTCGCATGGGTG 62.657 63.158 30.85 16.55 37.59 4.61
3310 3879 4.758251 CCTGCGTCGCATGGGTGA 62.758 66.667 22.03 0.00 38.13 4.02
3331 3916 1.151450 CAGGAGGCACACAAACCCT 59.849 57.895 0.00 0.00 0.00 4.34
3333 3918 0.693049 AGGAGGCACACAAACCCTAG 59.307 55.000 0.00 0.00 0.00 3.02
3335 3920 0.960861 GAGGCACACAAACCCTAGCC 60.961 60.000 0.00 0.00 42.31 3.93
3336 3921 1.228429 GGCACACAAACCCTAGCCA 60.228 57.895 0.00 0.00 41.63 4.75
3337 3922 1.524008 GGCACACAAACCCTAGCCAC 61.524 60.000 0.00 0.00 41.63 5.01
3338 3923 0.537371 GCACACAAACCCTAGCCACT 60.537 55.000 0.00 0.00 0.00 4.00
3361 3947 3.124088 CTCCTCCCTTCCTCCCCT 58.876 66.667 0.00 0.00 0.00 4.79
3362 3948 1.398234 CTCCTCCCTTCCTCCCCTT 59.602 63.158 0.00 0.00 0.00 3.95
3371 3957 4.016706 CCTCCCCTTCGTTGCCGT 62.017 66.667 0.00 0.00 35.01 5.68
3372 3958 2.032071 CTCCCCTTCGTTGCCGTT 59.968 61.111 0.00 0.00 35.01 4.44
3387 3973 1.653151 CCGTTGGGCTAAGCTTAGAC 58.347 55.000 32.88 30.71 38.09 2.59
3388 3974 1.278238 CGTTGGGCTAAGCTTAGACG 58.722 55.000 32.88 27.33 39.77 4.18
3389 3975 1.653151 GTTGGGCTAAGCTTAGACGG 58.347 55.000 32.88 11.44 39.77 4.79
3390 3976 0.107848 TTGGGCTAAGCTTAGACGGC 60.108 55.000 32.88 20.39 39.77 5.68
3391 3977 1.227586 GGGCTAAGCTTAGACGGCC 60.228 63.158 32.88 26.42 39.77 6.13
3392 3978 1.591863 GGCTAAGCTTAGACGGCCG 60.592 63.158 32.88 26.86 32.47 6.13
3394 3980 0.870735 GCTAAGCTTAGACGGCCGAC 60.871 60.000 35.90 27.70 32.47 4.79
3398 3984 0.460284 AGCTTAGACGGCCGACAATG 60.460 55.000 35.90 19.39 0.00 2.82
3399 3985 0.459585 GCTTAGACGGCCGACAATGA 60.460 55.000 35.90 9.88 0.00 2.57
3401 3987 1.860950 CTTAGACGGCCGACAATGATG 59.139 52.381 35.90 10.75 0.00 3.07
3402 3988 0.104120 TAGACGGCCGACAATGATGG 59.896 55.000 35.90 0.00 0.00 3.51
3403 3989 1.449601 GACGGCCGACAATGATGGT 60.450 57.895 35.90 4.22 0.00 3.55
3404 3990 1.705337 GACGGCCGACAATGATGGTG 61.705 60.000 35.90 0.00 0.00 4.17
3405 3991 1.449423 CGGCCGACAATGATGGTGA 60.449 57.895 24.07 0.00 0.00 4.02
3414 4165 0.262580 AATGATGGTGATGGTGGGGG 59.737 55.000 0.00 0.00 0.00 5.40
3492 4499 0.177141 GTCCCCGATTTGATCCACGA 59.823 55.000 0.00 0.00 0.00 4.35
3494 4501 0.178068 CCCCGATTTGATCCACGACT 59.822 55.000 0.00 0.00 0.00 4.18
3511 4518 2.187685 TGCATGGCAGCTACTCCG 59.812 61.111 9.68 0.00 33.32 4.63
3513 4520 3.094062 GCATGGCAGCTACTCCGGA 62.094 63.158 2.93 2.93 0.00 5.14
3514 4521 1.750930 CATGGCAGCTACTCCGGAT 59.249 57.895 3.57 0.00 0.00 4.18
3526 4533 4.776322 CCGGATGGAGGCGCACAA 62.776 66.667 10.83 0.00 37.49 3.33
3574 4581 2.885676 GCGGCATGTATGTGGAGCG 61.886 63.158 0.00 0.00 0.00 5.03
3589 4596 3.161450 GCGGTGGAGGGCTGGATA 61.161 66.667 0.00 0.00 0.00 2.59
3594 4601 1.204146 GTGGAGGGCTGGATAGTGAA 58.796 55.000 0.00 0.00 0.00 3.18
3600 4607 1.432270 GGCTGGATAGTGAAGCGTGC 61.432 60.000 0.00 0.00 37.83 5.34
3607 4614 2.209064 TAGTGAAGCGTGCCGACCTC 62.209 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 8.359642 CAACTCCTAAGTTTTTCAAATCATGGA 58.640 33.333 0.00 0.00 43.28 3.41
143 144 0.235665 CGCTACACAACAACTGCCTG 59.764 55.000 0.00 0.00 0.00 4.85
154 155 3.459145 TGTCTTTTTGTAGCGCTACACA 58.541 40.909 41.78 34.86 44.81 3.72
180 182 7.703197 TCTCTTTTTACCCGAAAATGTTGTTTC 59.297 33.333 0.00 0.00 36.89 2.78
190 193 5.430007 TGACAACTCTCTTTTTACCCGAAA 58.570 37.500 0.00 0.00 0.00 3.46
291 301 6.360370 TTGTAAGCAGATGGTAACTCTCTT 57.640 37.500 0.00 0.00 37.61 2.85
323 333 1.280998 AGTGTACATGGTAACTGCCCC 59.719 52.381 0.00 0.00 37.61 5.80
332 342 6.312399 CATGTGTTTTGTAGTGTACATGGT 57.688 37.500 0.00 0.00 40.80 3.55
389 400 2.665000 CCATCTCGCCCACACACT 59.335 61.111 0.00 0.00 0.00 3.55
391 402 2.689035 TTTGCCATCTCGCCCACACA 62.689 55.000 0.00 0.00 0.00 3.72
413 424 0.250858 CACAAGGGCTGATGTGTGGA 60.251 55.000 8.87 0.00 41.51 4.02
437 448 2.687370 GTCCACATGCCAATTTTCACC 58.313 47.619 0.00 0.00 0.00 4.02
445 456 1.514678 GCAGTTCGTCCACATGCCAA 61.515 55.000 0.00 0.00 0.00 4.52
485 497 2.993220 CGTTCATTTCATCACACGGAGA 59.007 45.455 0.00 0.00 0.00 3.71
559 573 4.381825 GGTGCATGAATCTTGGCATGTTTA 60.382 41.667 0.00 0.00 42.86 2.01
600 614 4.314440 ATCTGCCCACACGCGTGT 62.314 61.111 37.52 37.52 46.17 4.49
629 645 3.502979 GGAAACACTAACGCCCACAAATA 59.497 43.478 0.00 0.00 0.00 1.40
631 647 1.677052 GGAAACACTAACGCCCACAAA 59.323 47.619 0.00 0.00 0.00 2.83
632 648 1.310904 GGAAACACTAACGCCCACAA 58.689 50.000 0.00 0.00 0.00 3.33
661 677 7.140048 TCACGTATTTGTTTTATGTTGTTCCC 58.860 34.615 0.00 0.00 0.00 3.97
662 678 8.563289 TTCACGTATTTGTTTTATGTTGTTCC 57.437 30.769 0.00 0.00 0.00 3.62
664 680 9.790389 TCTTTCACGTATTTGTTTTATGTTGTT 57.210 25.926 0.00 0.00 0.00 2.83
685 701 2.028112 GCCCCAACCCAATTTCTCTTTC 60.028 50.000 0.00 0.00 0.00 2.62
691 707 0.324614 CCTTGCCCCAACCCAATTTC 59.675 55.000 0.00 0.00 0.00 2.17
713 729 2.178235 GCCTTCCATCGTAACGGGC 61.178 63.158 0.00 0.00 0.00 6.13
721 737 2.938956 AATCTTAGGGCCTTCCATCG 57.061 50.000 13.45 0.00 38.24 3.84
736 752 8.634444 GCAAGGATCCGACTACATATATAATCT 58.366 37.037 5.98 0.00 0.00 2.40
737 753 8.634444 AGCAAGGATCCGACTACATATATAATC 58.366 37.037 5.98 0.00 0.00 1.75
738 754 8.540507 AGCAAGGATCCGACTACATATATAAT 57.459 34.615 5.98 0.00 0.00 1.28
739 755 7.956328 AGCAAGGATCCGACTACATATATAA 57.044 36.000 5.98 0.00 0.00 0.98
740 756 9.286170 GATAGCAAGGATCCGACTACATATATA 57.714 37.037 5.98 0.00 0.00 0.86
741 757 7.231722 GGATAGCAAGGATCCGACTACATATAT 59.768 40.741 5.98 0.00 33.85 0.86
742 758 6.546403 GGATAGCAAGGATCCGACTACATATA 59.454 42.308 5.98 0.00 33.85 0.86
743 759 5.361285 GGATAGCAAGGATCCGACTACATAT 59.639 44.000 5.98 0.18 33.85 1.78
744 760 4.705507 GGATAGCAAGGATCCGACTACATA 59.294 45.833 5.98 0.00 33.85 2.29
746 762 2.891580 GGATAGCAAGGATCCGACTACA 59.108 50.000 5.98 0.00 33.85 2.74
847 869 1.174712 CCTGGCTGGGTCACACTTTG 61.175 60.000 1.84 0.00 0.00 2.77
861 883 0.461516 GTAAGGTTAGGCGTCCTGGC 60.462 60.000 8.44 2.00 45.27 4.85
886 909 1.070105 GCCGCCGGGTTATGTATGA 59.930 57.895 4.77 0.00 34.97 2.15
913 936 1.596496 ACTTCCGAATTGGGGGATCT 58.404 50.000 6.66 0.00 38.76 2.75
929 952 3.864789 TTGCTTGGAGAAGGAGAACTT 57.135 42.857 0.00 0.00 43.65 2.66
956 982 4.221482 TCGTTCTAGAACCCTAAAACCCTC 59.779 45.833 26.12 1.02 38.03 4.30
1065 1092 5.925969 CACACAAACCCAAAATACCAGATTC 59.074 40.000 0.00 0.00 0.00 2.52
1162 1189 4.901849 AGATACAGCAGACCCTAAGCAATA 59.098 41.667 0.00 0.00 0.00 1.90
1226 1253 2.036098 TAACCCGCGTCCTCCTCA 59.964 61.111 4.92 0.00 0.00 3.86
1298 1325 3.266636 GCAGGCTTCCTCTAAGAGAAAC 58.733 50.000 0.00 0.00 37.38 2.78
1316 1343 3.657448 TACATCACACCGCCCGCAG 62.657 63.158 0.00 0.00 0.00 5.18
1334 1361 0.178903 TAGACCACAGCCTTCCACCT 60.179 55.000 0.00 0.00 0.00 4.00
1357 1384 1.942657 AGCATCACCAAATCGAATCCG 59.057 47.619 0.00 0.00 37.07 4.18
1363 1390 5.046910 ACTTAACAAGCATCACCAAATCG 57.953 39.130 0.00 0.00 0.00 3.34
1364 1391 7.307337 CCAAAACTTAACAAGCATCACCAAATC 60.307 37.037 0.00 0.00 0.00 2.17
1365 1392 6.482973 CCAAAACTTAACAAGCATCACCAAAT 59.517 34.615 0.00 0.00 0.00 2.32
1366 1393 5.814705 CCAAAACTTAACAAGCATCACCAAA 59.185 36.000 0.00 0.00 0.00 3.28
1393 1438 1.434555 CAACATAGCCGAACCGAACA 58.565 50.000 0.00 0.00 0.00 3.18
1416 1461 6.708054 ACCTGCATCTAGCTTCATAATACAAC 59.292 38.462 0.00 0.00 45.94 3.32
1482 1530 0.693622 TAGTTCCAATGCACCGGGAA 59.306 50.000 6.32 10.58 38.33 3.97
1513 1561 2.623416 AGTTCCTTGCAAACTAACAGCC 59.377 45.455 16.20 0.00 35.25 4.85
1553 1601 7.840342 TGACAAACAAATGCAAAAATAGTGT 57.160 28.000 0.00 0.00 0.00 3.55
1554 1602 7.736880 CGATGACAAACAAATGCAAAAATAGTG 59.263 33.333 0.00 0.00 0.00 2.74
1563 1611 3.563390 TCAGACGATGACAAACAAATGCA 59.437 39.130 0.00 0.00 31.12 3.96
1565 1613 6.174451 AGATCAGACGATGACAAACAAATG 57.826 37.500 0.00 0.00 41.91 2.32
1600 1648 4.569943 ACAGTTGTGGTATCTGCAGTAAG 58.430 43.478 14.67 0.00 33.12 2.34
1603 1651 3.492102 AACAGTTGTGGTATCTGCAGT 57.508 42.857 14.67 3.75 33.12 4.40
1698 1748 3.000041 GCGCCGGAACATATATGAATCA 59.000 45.455 19.63 0.00 0.00 2.57
1700 1750 3.262420 GAGCGCCGGAACATATATGAAT 58.738 45.455 19.63 7.54 0.00 2.57
1714 1764 1.651987 TCTCCTTTTAATGAGCGCCG 58.348 50.000 2.29 0.00 0.00 6.46
1755 1805 7.716612 ACAAAGCTAGCAAGAAACAATTAAGT 58.283 30.769 18.83 0.00 0.00 2.24
1795 1845 5.299148 AGCAAAGCAAATTGACATAAGCAA 58.701 33.333 0.00 0.00 31.84 3.91
1796 1846 4.885413 AGCAAAGCAAATTGACATAAGCA 58.115 34.783 0.00 0.00 31.84 3.91
1806 1856 4.576053 GGGAAAACAGAAGCAAAGCAAATT 59.424 37.500 0.00 0.00 0.00 1.82
1821 1871 2.170166 GATGCACCATGAGGGAAAACA 58.830 47.619 0.00 0.00 41.15 2.83
1823 1873 1.076841 TGGATGCACCATGAGGGAAAA 59.923 47.619 0.00 0.00 44.64 2.29
1837 1887 3.243301 CCAGCTTGTGATATTGTGGATGC 60.243 47.826 0.00 0.00 0.00 3.91
1842 1892 3.853831 TTGCCAGCTTGTGATATTGTG 57.146 42.857 0.00 0.00 0.00 3.33
1878 1928 5.169295 GCTGTGGAACGAGTACTTTATTCT 58.831 41.667 0.00 0.00 42.39 2.40
1879 1929 4.927425 TGCTGTGGAACGAGTACTTTATTC 59.073 41.667 0.00 1.60 42.39 1.75
1880 1930 4.689345 GTGCTGTGGAACGAGTACTTTATT 59.311 41.667 0.00 0.00 42.39 1.40
1882 1932 3.319972 AGTGCTGTGGAACGAGTACTTTA 59.680 43.478 0.00 0.00 42.39 1.85
1883 1933 2.102588 AGTGCTGTGGAACGAGTACTTT 59.897 45.455 0.00 0.00 42.39 2.66
1884 1934 1.687123 AGTGCTGTGGAACGAGTACTT 59.313 47.619 0.00 0.00 42.39 2.24
1885 1935 1.000163 CAGTGCTGTGGAACGAGTACT 60.000 52.381 0.00 0.00 42.39 2.73
1922 1991 1.272490 GGTGCAGCTTTTTCCCCTAAC 59.728 52.381 9.07 0.00 0.00 2.34
1946 2015 7.335924 GCTTTTCAGTATCATTGTAGGTAACCA 59.664 37.037 0.00 0.00 37.17 3.67
1990 2059 7.493499 TGGGATTTTCCATTAACATGTGAAT 57.507 32.000 2.22 2.22 38.64 2.57
2048 2117 1.098050 AAAGGATGATCGCCTTGCAC 58.902 50.000 17.47 0.00 44.72 4.57
2077 2146 6.500684 AGTAGATTACAACACCAATTGCTG 57.499 37.500 0.00 0.00 32.47 4.41
2127 2197 4.202151 GGACAAGCTCAGGAATTTGTGTTT 60.202 41.667 0.00 0.00 34.18 2.83
2160 2230 5.798934 GTCGAGGGTATGTAGTTATAATGCG 59.201 44.000 0.00 0.00 0.00 4.73
2163 2233 6.317312 TGGGTCGAGGGTATGTAGTTATAAT 58.683 40.000 0.00 0.00 0.00 1.28
2183 2253 3.763557 AATGGGTGAATTCAGATGGGT 57.236 42.857 8.80 0.00 0.00 4.51
2184 2254 5.010314 CACATAATGGGTGAATTCAGATGGG 59.990 44.000 8.80 3.70 38.54 4.00
2186 2256 6.080648 CCACATAATGGGTGAATTCAGATG 57.919 41.667 8.80 8.27 45.95 2.90
2200 2270 7.035004 ACACGGATGAAAATTTCCACATAATG 58.965 34.615 3.00 1.59 31.99 1.90
2201 2271 7.169158 ACACGGATGAAAATTTCCACATAAT 57.831 32.000 3.00 0.00 31.99 1.28
2202 2272 6.349777 GGACACGGATGAAAATTTCCACATAA 60.350 38.462 3.00 0.00 31.99 1.90
2203 2273 5.124776 GGACACGGATGAAAATTTCCACATA 59.875 40.000 3.00 0.00 31.99 2.29
2204 2274 4.082245 GGACACGGATGAAAATTTCCACAT 60.082 41.667 3.00 0.00 31.99 3.21
2205 2275 3.254657 GGACACGGATGAAAATTTCCACA 59.745 43.478 3.00 0.00 31.99 4.17
2206 2276 3.254657 TGGACACGGATGAAAATTTCCAC 59.745 43.478 3.00 0.00 31.99 4.02
2207 2277 3.491342 TGGACACGGATGAAAATTTCCA 58.509 40.909 3.00 0.00 31.99 3.53
2208 2278 4.718940 ATGGACACGGATGAAAATTTCC 57.281 40.909 3.00 0.00 0.00 3.13
2211 2281 5.720371 TGAAATGGACACGGATGAAAATT 57.280 34.783 0.00 0.00 0.00 1.82
2239 2309 3.380320 GGGCAAACTTACGGATGCTAAAT 59.620 43.478 0.00 0.00 38.79 1.40
2298 2369 5.738909 AGCATAGTCATCAGCTGTAAAAGT 58.261 37.500 14.67 3.92 35.72 2.66
2341 2413 6.204688 CCAGCACACTAGAACAACTCAAAATA 59.795 38.462 0.00 0.00 0.00 1.40
2365 2437 5.048294 CCCAGTTACAAAGATAACCAACACC 60.048 44.000 0.00 0.00 35.95 4.16
2391 2464 7.205297 AGAAATTCACATGAGTCCTGTTTTTG 58.795 34.615 0.00 0.00 0.00 2.44
2392 2465 7.352079 AGAAATTCACATGAGTCCTGTTTTT 57.648 32.000 0.00 0.57 0.00 1.94
2440 2513 4.141756 ACCATCTCACTCATCACCATCTTC 60.142 45.833 0.00 0.00 0.00 2.87
2447 2520 4.471904 TGGTTACCATCTCACTCATCAC 57.528 45.455 0.00 0.00 0.00 3.06
2471 2544 1.680735 GTCCCAGCACACATTTGTCAA 59.319 47.619 0.00 0.00 31.66 3.18
2476 2549 2.548493 GCATTTGTCCCAGCACACATTT 60.548 45.455 0.00 0.00 0.00 2.32
2500 2573 2.034687 CTTCCTGGGGTGCTGGTG 59.965 66.667 0.00 0.00 0.00 4.17
2557 2630 4.026052 TCATGTCAAGATACCTCTGAGCA 58.974 43.478 0.00 0.00 0.00 4.26
2569 2642 5.277634 CGCAATTATCATGCTCATGTCAAGA 60.278 40.000 9.41 0.00 41.64 3.02
2582 2655 4.780815 TGGAACCTCTTCGCAATTATCAT 58.219 39.130 0.00 0.00 0.00 2.45
2602 2675 1.227380 GACGCCCTACTGCATCTGG 60.227 63.158 0.00 0.00 0.00 3.86
2603 2676 0.249238 GAGACGCCCTACTGCATCTG 60.249 60.000 0.00 0.00 33.28 2.90
2625 2698 4.395583 GACGCAACCAGCTGCAGC 62.396 66.667 31.53 31.53 42.77 5.25
2628 2701 1.855213 TTGATGACGCAACCAGCTGC 61.855 55.000 8.66 0.00 42.61 5.25
2651 2727 3.896888 TGGCATGTTCAGAGTTTGGAATT 59.103 39.130 0.00 0.00 0.00 2.17
2652 2728 3.499338 TGGCATGTTCAGAGTTTGGAAT 58.501 40.909 0.00 0.00 0.00 3.01
2731 2818 4.623167 CACAGATGCAACTACACTGAGTAC 59.377 45.833 0.00 0.00 33.53 2.73
2732 2819 4.321974 CCACAGATGCAACTACACTGAGTA 60.322 45.833 0.00 0.00 33.53 2.59
2733 2820 3.555795 CCACAGATGCAACTACACTGAGT 60.556 47.826 0.00 0.00 33.53 3.41
2734 2821 2.998670 CCACAGATGCAACTACACTGAG 59.001 50.000 0.00 0.00 33.53 3.35
2735 2822 2.368548 ACCACAGATGCAACTACACTGA 59.631 45.455 0.00 0.00 33.53 3.41
2736 2823 2.481568 CACCACAGATGCAACTACACTG 59.518 50.000 0.00 0.00 35.14 3.66
2737 2824 2.368548 TCACCACAGATGCAACTACACT 59.631 45.455 0.00 0.00 0.00 3.55
2738 2825 2.766313 TCACCACAGATGCAACTACAC 58.234 47.619 0.00 0.00 0.00 2.90
2739 2826 3.138304 GTTCACCACAGATGCAACTACA 58.862 45.455 0.00 0.00 0.00 2.74
2747 2834 2.586425 ACCAAAGGTTCACCACAGATG 58.414 47.619 0.00 0.00 38.89 2.90
2766 2857 5.467063 ACAGTAGCTTCACAAGAAAGCTAAC 59.533 40.000 16.63 11.86 39.68 2.34
2803 2894 6.491394 TGAAACGAAACCAACTAAGTGATTG 58.509 36.000 0.00 0.00 0.00 2.67
2804 2895 6.687081 TGAAACGAAACCAACTAAGTGATT 57.313 33.333 0.00 0.00 0.00 2.57
2849 2940 3.506398 ACCACCCCTACTGAAAATTTGG 58.494 45.455 0.00 0.00 0.00 3.28
2865 3258 5.354234 CAGATGTTAATTGTCCTGTACCACC 59.646 44.000 0.00 0.00 0.00 4.61
2907 3301 2.561478 ACCACTGTACATGTCCAACC 57.439 50.000 0.00 0.00 0.00 3.77
2997 3496 5.065235 CAGCAATTGTTCTTCCCCATTTTT 58.935 37.500 7.40 0.00 0.00 1.94
3014 3513 0.596082 GTGTTTGGTACGGCAGCAAT 59.404 50.000 4.99 0.00 43.82 3.56
3035 3534 1.720781 AGGTTGATTTTGCAGGCCTT 58.279 45.000 0.00 0.00 0.00 4.35
3037 3536 2.224257 TGAAAGGTTGATTTTGCAGGCC 60.224 45.455 0.00 0.00 0.00 5.19
3038 3537 3.110447 TGAAAGGTTGATTTTGCAGGC 57.890 42.857 0.00 0.00 0.00 4.85
3039 3538 3.434299 GCATGAAAGGTTGATTTTGCAGG 59.566 43.478 0.00 0.00 0.00 4.85
3041 3540 3.181457 TGGCATGAAAGGTTGATTTTGCA 60.181 39.130 0.00 0.00 0.00 4.08
3042 3541 3.401182 TGGCATGAAAGGTTGATTTTGC 58.599 40.909 0.00 0.00 0.00 3.68
3043 3542 5.296283 TGTTTGGCATGAAAGGTTGATTTTG 59.704 36.000 0.00 0.00 0.00 2.44
3044 3543 5.435291 TGTTTGGCATGAAAGGTTGATTTT 58.565 33.333 0.00 0.00 0.00 1.82
3045 3544 5.033589 TGTTTGGCATGAAAGGTTGATTT 57.966 34.783 0.00 0.00 0.00 2.17
3046 3545 4.686191 TGTTTGGCATGAAAGGTTGATT 57.314 36.364 0.00 0.00 0.00 2.57
3047 3546 4.895668 ATGTTTGGCATGAAAGGTTGAT 57.104 36.364 0.00 0.00 36.26 2.57
3048 3547 5.716228 AGATATGTTTGGCATGAAAGGTTGA 59.284 36.000 0.00 0.00 38.47 3.18
3049 3548 5.969423 AGATATGTTTGGCATGAAAGGTTG 58.031 37.500 0.00 0.00 38.47 3.77
3050 3549 6.211184 TGAAGATATGTTTGGCATGAAAGGTT 59.789 34.615 0.00 0.00 38.47 3.50
3051 3550 5.716228 TGAAGATATGTTTGGCATGAAAGGT 59.284 36.000 0.00 0.00 38.47 3.50
3052 3551 6.211587 TGAAGATATGTTTGGCATGAAAGG 57.788 37.500 0.00 0.00 38.47 3.11
3053 3552 5.747197 GCTGAAGATATGTTTGGCATGAAAG 59.253 40.000 0.00 0.00 38.47 2.62
3054 3553 5.185442 TGCTGAAGATATGTTTGGCATGAAA 59.815 36.000 0.00 0.00 38.47 2.69
3055 3554 4.705991 TGCTGAAGATATGTTTGGCATGAA 59.294 37.500 0.00 0.00 38.47 2.57
3056 3555 4.096833 GTGCTGAAGATATGTTTGGCATGA 59.903 41.667 13.45 0.00 38.47 3.07
3057 3556 4.357142 GTGCTGAAGATATGTTTGGCATG 58.643 43.478 13.45 0.00 38.47 4.06
3058 3557 3.382546 GGTGCTGAAGATATGTTTGGCAT 59.617 43.478 13.45 0.00 41.42 4.40
3059 3558 2.754552 GGTGCTGAAGATATGTTTGGCA 59.245 45.455 8.56 8.56 0.00 4.92
3060 3559 2.754552 TGGTGCTGAAGATATGTTTGGC 59.245 45.455 4.56 4.56 0.00 4.52
3061 3560 3.758023 TGTGGTGCTGAAGATATGTTTGG 59.242 43.478 0.00 0.00 0.00 3.28
3062 3561 5.181811 TCTTGTGGTGCTGAAGATATGTTTG 59.818 40.000 0.00 0.00 0.00 2.93
3063 3562 5.316167 TCTTGTGGTGCTGAAGATATGTTT 58.684 37.500 0.00 0.00 0.00 2.83
3074 3573 0.674895 GTAGGCCTCTTGTGGTGCTG 60.675 60.000 9.68 0.00 0.00 4.41
3088 3587 7.614583 TCTCATGGTATAACTATAGTGGTAGGC 59.385 40.741 6.06 0.00 0.00 3.93
3164 3733 2.239907 GTGCCCATTCTCCTTAGAAGGT 59.760 50.000 8.17 0.00 44.79 3.50
3165 3734 2.507471 AGTGCCCATTCTCCTTAGAAGG 59.493 50.000 1.53 1.53 44.79 3.46
3203 3772 4.686091 TCGTTGACAATGTTCTGATCAGTC 59.314 41.667 21.92 15.99 0.00 3.51
3204 3773 4.449068 GTCGTTGACAATGTTCTGATCAGT 59.551 41.667 21.92 1.67 32.09 3.41
3205 3774 4.433413 CGTCGTTGACAATGTTCTGATCAG 60.433 45.833 17.07 17.07 32.09 2.90
3206 3775 3.428534 CGTCGTTGACAATGTTCTGATCA 59.571 43.478 7.27 0.00 32.09 2.92
3207 3776 3.673338 TCGTCGTTGACAATGTTCTGATC 59.327 43.478 7.27 0.00 32.09 2.92
3208 3777 3.649073 TCGTCGTTGACAATGTTCTGAT 58.351 40.909 7.27 0.00 32.09 2.90
3209 3778 3.086818 TCGTCGTTGACAATGTTCTGA 57.913 42.857 7.27 0.00 32.09 3.27
3210 3779 3.787826 CTTCGTCGTTGACAATGTTCTG 58.212 45.455 7.27 0.00 32.09 3.02
3212 3781 2.033236 TGCTTCGTCGTTGACAATGTTC 60.033 45.455 7.27 2.22 32.09 3.18
3213 3782 1.937223 TGCTTCGTCGTTGACAATGTT 59.063 42.857 7.27 0.00 32.09 2.71
3214 3783 1.577468 TGCTTCGTCGTTGACAATGT 58.423 45.000 7.27 0.00 32.09 2.71
3216 3785 2.479837 TCTTGCTTCGTCGTTGACAAT 58.520 42.857 0.00 0.00 32.09 2.71
3217 3786 1.929230 TCTTGCTTCGTCGTTGACAA 58.071 45.000 0.00 0.00 32.09 3.18
3225 3794 2.290641 ACACAATGGTTCTTGCTTCGTC 59.709 45.455 0.00 0.00 0.00 4.20
3258 3827 8.777413 CATATGTTGGATAGTTGTGGTATTCAG 58.223 37.037 0.00 0.00 0.00 3.02
3269 3838 7.517604 AGGTAGGGATTCATATGTTGGATAGTT 59.482 37.037 1.90 0.00 0.00 2.24
3293 3862 4.758251 TCACCCATGCGACGCAGG 62.758 66.667 28.10 27.19 43.65 4.85
3294 3863 3.490759 GTCACCCATGCGACGCAG 61.491 66.667 28.10 16.77 43.65 5.18
3297 3866 1.807165 CTGAGTCACCCATGCGACG 60.807 63.158 0.00 0.00 37.23 5.12
3298 3867 1.448540 CCTGAGTCACCCATGCGAC 60.449 63.158 0.00 0.00 0.00 5.19
3299 3868 1.607801 CTCCTGAGTCACCCATGCGA 61.608 60.000 0.00 0.00 0.00 5.10
3301 3870 1.222936 CCTCCTGAGTCACCCATGC 59.777 63.158 0.00 0.00 0.00 4.06
3302 3871 1.222936 GCCTCCTGAGTCACCCATG 59.777 63.158 0.00 0.00 0.00 3.66
3303 3872 1.229625 TGCCTCCTGAGTCACCCAT 60.230 57.895 0.00 0.00 0.00 4.00
3304 3873 2.204034 TGCCTCCTGAGTCACCCA 59.796 61.111 0.00 0.00 0.00 4.51
3306 3875 1.004440 GTGTGCCTCCTGAGTCACC 60.004 63.158 5.94 0.00 0.00 4.02
3307 3876 0.106708 TTGTGTGCCTCCTGAGTCAC 59.893 55.000 1.54 1.54 0.00 3.67
3308 3877 0.836606 TTTGTGTGCCTCCTGAGTCA 59.163 50.000 0.00 0.00 0.00 3.41
3309 3878 1.230324 GTTTGTGTGCCTCCTGAGTC 58.770 55.000 0.00 0.00 0.00 3.36
3310 3879 0.179018 GGTTTGTGTGCCTCCTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
3311 3880 0.890996 GGGTTTGTGTGCCTCCTGAG 60.891 60.000 0.00 0.00 0.00 3.35
3312 3881 1.150536 GGGTTTGTGTGCCTCCTGA 59.849 57.895 0.00 0.00 0.00 3.86
3313 3882 0.400213 TAGGGTTTGTGTGCCTCCTG 59.600 55.000 0.00 0.00 0.00 3.86
3314 3883 0.693049 CTAGGGTTTGTGTGCCTCCT 59.307 55.000 0.00 0.00 0.00 3.69
3337 3922 4.214327 GAAGGGAGGAGCGGCGAG 62.214 72.222 12.98 0.00 0.00 5.03
3371 3957 0.107848 GCCGTCTAAGCTTAGCCCAA 60.108 55.000 25.83 8.43 0.00 4.12
3372 3958 1.520666 GCCGTCTAAGCTTAGCCCA 59.479 57.895 25.83 8.78 0.00 5.36
3382 3968 1.472552 CCATCATTGTCGGCCGTCTAA 60.473 52.381 27.15 18.41 0.00 2.10
3383 3969 0.104120 CCATCATTGTCGGCCGTCTA 59.896 55.000 27.15 17.58 0.00 2.59
3385 3971 1.449601 ACCATCATTGTCGGCCGTC 60.450 57.895 27.15 21.30 0.00 4.79
3386 3972 1.745115 CACCATCATTGTCGGCCGT 60.745 57.895 27.15 1.49 0.00 5.68
3387 3973 0.815213 ATCACCATCATTGTCGGCCG 60.815 55.000 22.12 22.12 0.00 6.13
3388 3974 0.664761 CATCACCATCATTGTCGGCC 59.335 55.000 0.00 0.00 0.00 6.13
3389 3975 0.664761 CCATCACCATCATTGTCGGC 59.335 55.000 0.00 0.00 0.00 5.54
3390 3976 1.672363 CACCATCACCATCATTGTCGG 59.328 52.381 0.00 0.00 0.00 4.79
3391 3977 1.672363 CCACCATCACCATCATTGTCG 59.328 52.381 0.00 0.00 0.00 4.35
3392 3978 2.026641 CCCACCATCACCATCATTGTC 58.973 52.381 0.00 0.00 0.00 3.18
3394 3980 1.405872 CCCCACCATCACCATCATTG 58.594 55.000 0.00 0.00 0.00 2.82
3398 3984 0.111253 GATCCCCCACCATCACCATC 59.889 60.000 0.00 0.00 0.00 3.51
3399 3985 0.627170 TGATCCCCCACCATCACCAT 60.627 55.000 0.00 0.00 0.00 3.55
3401 3987 1.227383 GTGATCCCCCACCATCACC 59.773 63.158 1.30 0.00 42.11 4.02
3402 3988 4.986467 GTGATCCCCCACCATCAC 57.014 61.111 0.00 0.00 41.56 3.06
3414 4165 1.969923 CTCCATGAGAGGGAGGTGATC 59.030 57.143 0.00 0.00 46.65 2.92
3473 4480 0.177141 TCGTGGATCAAATCGGGGAC 59.823 55.000 0.00 0.00 0.00 4.46
3494 4501 2.187685 CGGAGTAGCTGCCATGCA 59.812 61.111 0.00 0.00 36.92 3.96
3511 4518 3.499737 CGTTGTGCGCCTCCATCC 61.500 66.667 4.18 0.00 0.00 3.51
3524 4531 2.670934 AGCTCCAAGCAGCCGTTG 60.671 61.111 1.29 0.00 45.56 4.10
3525 4532 2.475371 ATCAGCTCCAAGCAGCCGTT 62.475 55.000 1.29 0.00 45.56 4.44
3526 4533 2.964310 ATCAGCTCCAAGCAGCCGT 61.964 57.895 1.29 0.00 45.56 5.68
3561 4568 0.465705 CTCCACCGCTCCACATACAT 59.534 55.000 0.00 0.00 0.00 2.29
3574 4581 0.691078 TCACTATCCAGCCCTCCACC 60.691 60.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.