Multiple sequence alignment - TraesCS3D01G393200

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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 TraesCS3D01G393200 chr3D 100.000 5430 0 0 1 5430 508387993 508382564 0.000000e+00 10028.0
1 TraesCS3D01G393200 chr3D 100.000 33 0 0 5339 5371 23075924 23075892 1.630000e-05 62.1
2 TraesCS3D01G393200 chr3B 90.142 2749 169 50 1 2710 671022172 671019487 0.000000e+00 3482.0
3 TraesCS3D01G393200 chr3B 92.263 1732 115 11 2818 4544 671019483 671017766 0.000000e+00 2438.0
4 TraesCS3D01G393200 chr3B 90.429 815 56 12 4541 5344 671017715 671016912 0.000000e+00 1053.0
5 TraesCS3D01G393200 chr3B 94.175 103 4 2 2702 2804 26656528 26656428 7.280000e-34 156.0
6 TraesCS3D01G393200 chr3B 100.000 30 0 0 5376 5405 606575178 606575207 7.600000e-04 56.5
7 TraesCS3D01G393200 chr3A 87.988 2764 194 68 10 2704 646132414 646129720 0.000000e+00 3138.0
8 TraesCS3D01G393200 chr3A 93.664 2115 90 21 2786 4881 646129722 646127633 0.000000e+00 3123.0
9 TraesCS3D01G393200 chr3A 92.327 404 26 3 4929 5330 646127633 646127233 2.190000e-158 569.0
10 TraesCS3D01G393200 chr3A 91.429 105 8 1 2703 2807 488042632 488042529 5.670000e-30 143.0
11 TraesCS3D01G393200 chr3A 100.000 31 0 0 5400 5430 646127224 646127194 2.110000e-04 58.4
12 TraesCS3D01G393200 chr1D 97.778 90 2 0 2703 2792 192809918 192810007 7.280000e-34 156.0
13 TraesCS3D01G393200 chr1D 100.000 29 0 0 5374 5402 57502437 57502409 3.000000e-03 54.7
14 TraesCS3D01G393200 chr7D 96.739 92 3 0 2700 2791 509603005 509603096 2.620000e-33 154.0
15 TraesCS3D01G393200 chr7D 96.629 89 3 0 2702 2790 542092354 542092266 1.220000e-31 148.0
16 TraesCS3D01G393200 chr4D 95.789 95 4 0 2694 2788 164649550 164649456 2.620000e-33 154.0
17 TraesCS3D01G393200 chrUn 95.745 94 4 0 2695 2788 279936308 279936215 9.420000e-33 152.0
18 TraesCS3D01G393200 chrUn 95.745 94 4 0 2695 2788 395541695 395541602 9.420000e-33 152.0
19 TraesCS3D01G393200 chr4A 90.000 110 10 1 2690 2798 4151957 4152066 2.040000e-29 141.0
20 TraesCS3D01G393200 chr5A 89.394 66 2 2 5342 5402 23817526 23817591 1.620000e-10 78.7
21 TraesCS3D01G393200 chr1A 82.759 87 5 4 5332 5410 60284389 60284305 9.760000e-08 69.4
22 TraesCS3D01G393200 chr1A 100.000 29 0 0 5374 5402 56623295 56623267 3.000000e-03 54.7
23 TraesCS3D01G393200 chr1B 87.097 62 3 2 5350 5406 652293978 652294039 1.260000e-06 65.8
24 TraesCS3D01G393200 chr5D 94.444 36 2 0 5374 5409 52247617 52247582 7.600000e-04 56.5
25 TraesCS3D01G393200 chr7B 100.000 29 0 0 5374 5402 746315374 746315402 3.000000e-03 54.7
26 TraesCS3D01G393200 chr2A 94.444 36 1 1 5374 5409 55567913 55567879 3.000000e-03 54.7


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 TraesCS3D01G393200 chr3D 508382564 508387993 5429 True 10028.000000 10028 100.000000 1 5430 1 chr3D.!!$R2 5429
1 TraesCS3D01G393200 chr3B 671016912 671022172 5260 True 2324.333333 3482 90.944667 1 5344 3 chr3B.!!$R2 5343
2 TraesCS3D01G393200 chr3A 646127194 646132414 5220 True 1722.100000 3138 93.494750 10 5430 4 chr3A.!!$R2 5420

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
417 447 0.249322 TGGAATTCTACGGCTAGCGC 60.249 55.0 9.00 0.0 0.00 5.92 F
430 460 0.307146 CTAGCGCGTACCACTAGTCC 59.693 60.0 8.43 0.0 30.86 3.85 F
1148 1214 0.846427 ATTCCCACTTCCCCAGCTCA 60.846 55.0 0.00 0.0 0.00 4.26 F
2717 2821 0.115745 AAGGTACTCCCTCCGTTCCA 59.884 55.0 0.00 0.0 45.47 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1671 0.899717 TCAAGCAAACCAGCCCATCC 60.900 55.0 0.00 0.00 34.23 3.51 R
1611 1698 1.303309 GACAAGGCATCGCAGCTAAT 58.697 50.0 0.00 0.00 34.17 1.73 R
2775 2879 0.039911 AGTGAGCTACTCCCTCCGTT 59.960 55.0 0.00 0.00 33.17 4.44 R
4709 4879 0.997932 GTGATCTCTGTTGCGCTGAG 59.002 55.0 9.73 11.11 42.40 3.35 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
36 37 8.801882 TTTTTCTACCAGAATTATGTAGTGGG 57.198 34.615 0.00 0.00 33.67 4.61
41 42 8.429641 TCTACCAGAATTATGTAGTGGGATTTC 58.570 37.037 0.00 0.00 34.83 2.17
52 53 8.738645 ATGTAGTGGGATTTCTAATTGACTTC 57.261 34.615 0.00 0.00 0.00 3.01
113 116 6.119144 TCACTGAAAACAAGCTGTTAGTTC 57.881 37.500 0.00 0.00 40.14 3.01
184 188 7.208064 ACCCAACCTGTAATGACAAGTATAT 57.792 36.000 0.00 0.00 34.35 0.86
185 189 7.639378 ACCCAACCTGTAATGACAAGTATATT 58.361 34.615 0.00 0.00 34.35 1.28
186 190 7.556275 ACCCAACCTGTAATGACAAGTATATTG 59.444 37.037 0.00 0.00 34.35 1.90
187 191 7.417612 CCAACCTGTAATGACAAGTATATTGC 58.582 38.462 0.00 0.00 34.35 3.56
188 192 7.283127 CCAACCTGTAATGACAAGTATATTGCT 59.717 37.037 0.00 0.00 34.35 3.91
270 293 2.830104 TGCATGCACATAGTAGCAGAG 58.170 47.619 18.46 0.00 44.94 3.35
414 444 1.868519 GCGGTGGAATTCTACGGCTAG 60.869 57.143 32.96 16.60 45.45 3.42
415 445 1.867166 GGTGGAATTCTACGGCTAGC 58.133 55.000 14.89 6.04 0.00 3.42
416 446 1.488527 GTGGAATTCTACGGCTAGCG 58.511 55.000 9.00 6.83 0.00 4.26
417 447 0.249322 TGGAATTCTACGGCTAGCGC 60.249 55.000 9.00 0.00 0.00 5.92
418 448 1.276145 GGAATTCTACGGCTAGCGCG 61.276 60.000 19.72 19.72 36.88 6.86
419 449 0.594284 GAATTCTACGGCTAGCGCGT 60.594 55.000 26.62 26.62 36.88 6.01
420 450 0.664761 AATTCTACGGCTAGCGCGTA 59.335 50.000 26.17 26.17 36.88 4.42
422 452 2.051525 CTACGGCTAGCGCGTACC 60.052 66.667 25.00 3.29 36.88 3.34
424 454 2.978598 CTACGGCTAGCGCGTACCAC 62.979 65.000 25.00 4.27 36.88 4.16
426 456 2.827051 CGGCTAGCGCGTACCACTA 61.827 63.158 8.43 0.00 36.88 2.74
427 457 1.008767 GGCTAGCGCGTACCACTAG 60.009 63.158 8.43 10.59 37.13 2.57
428 458 1.722636 GGCTAGCGCGTACCACTAGT 61.723 60.000 8.43 0.00 36.57 2.57
429 459 0.316854 GCTAGCGCGTACCACTAGTC 60.317 60.000 8.43 2.65 36.57 2.59
430 460 0.307146 CTAGCGCGTACCACTAGTCC 59.693 60.000 8.43 0.00 30.86 3.85
431 461 1.431488 TAGCGCGTACCACTAGTCCG 61.431 60.000 8.43 0.00 0.00 4.79
432 462 3.044059 GCGCGTACCACTAGTCCGT 62.044 63.158 8.43 0.00 0.00 4.69
433 463 1.061570 CGCGTACCACTAGTCCGTC 59.938 63.158 0.00 0.00 0.00 4.79
434 464 1.431036 GCGTACCACTAGTCCGTCC 59.569 63.158 0.00 0.00 0.00 4.79
535 565 1.783264 CGTCGACAAAAGCGCGAAC 60.783 57.895 17.16 0.00 35.66 3.95
804 847 1.543802 GAATCCACGAAAATGCCACCA 59.456 47.619 0.00 0.00 0.00 4.17
824 867 1.757306 GCTCCCATCACCCGATCAT 59.243 57.895 0.00 0.00 0.00 2.45
861 918 2.490991 GAGGGGCATTACCGTGAATAC 58.509 52.381 0.00 0.00 40.62 1.89
1040 1103 4.379243 CGACCGCCAGCTCCAGTT 62.379 66.667 0.00 0.00 0.00 3.16
1041 1104 2.435059 GACCGCCAGCTCCAGTTC 60.435 66.667 0.00 0.00 0.00 3.01
1042 1105 3.959991 GACCGCCAGCTCCAGTTCC 62.960 68.421 0.00 0.00 0.00 3.62
1043 1106 4.020617 CCGCCAGCTCCAGTTCCA 62.021 66.667 0.00 0.00 0.00 3.53
1044 1107 2.435586 CGCCAGCTCCAGTTCCAG 60.436 66.667 0.00 0.00 0.00 3.86
1045 1108 2.749441 GCCAGCTCCAGTTCCAGC 60.749 66.667 0.00 0.00 35.73 4.85
1047 1110 1.078567 CCAGCTCCAGTTCCAGCTC 60.079 63.158 0.00 0.00 44.47 4.09
1048 1111 1.078567 CAGCTCCAGTTCCAGCTCC 60.079 63.158 0.00 0.00 44.47 4.70
1083 1146 2.407210 CTCTCGTCGCTGCTCCTC 59.593 66.667 0.00 0.00 0.00 3.71
1095 1158 4.507916 CTCCTCCTCGCCTCCGGA 62.508 72.222 2.93 2.93 34.56 5.14
1130 1193 3.488363 AGGAGCGATTCGAAGGTAGTAT 58.512 45.455 10.88 0.00 0.00 2.12
1142 1208 2.772930 AGGTAGTATTCCCACTTCCCC 58.227 52.381 0.00 0.00 36.83 4.81
1143 1209 2.046729 AGGTAGTATTCCCACTTCCCCA 59.953 50.000 0.00 0.00 36.83 4.96
1144 1210 2.438392 GGTAGTATTCCCACTTCCCCAG 59.562 54.545 0.00 0.00 31.59 4.45
1145 1211 0.919710 AGTATTCCCACTTCCCCAGC 59.080 55.000 0.00 0.00 0.00 4.85
1146 1212 0.919710 GTATTCCCACTTCCCCAGCT 59.080 55.000 0.00 0.00 0.00 4.24
1147 1213 1.134068 GTATTCCCACTTCCCCAGCTC 60.134 57.143 0.00 0.00 0.00 4.09
1148 1214 0.846427 ATTCCCACTTCCCCAGCTCA 60.846 55.000 0.00 0.00 0.00 4.26
1149 1215 1.492133 TTCCCACTTCCCCAGCTCAG 61.492 60.000 0.00 0.00 0.00 3.35
1150 1216 2.227036 CCCACTTCCCCAGCTCAGT 61.227 63.158 0.00 0.00 0.00 3.41
1151 1217 1.298014 CCACTTCCCCAGCTCAGTC 59.702 63.158 0.00 0.00 0.00 3.51
1152 1218 1.197430 CCACTTCCCCAGCTCAGTCT 61.197 60.000 0.00 0.00 0.00 3.24
1153 1219 1.561643 CACTTCCCCAGCTCAGTCTA 58.438 55.000 0.00 0.00 0.00 2.59
1154 1220 1.480137 CACTTCCCCAGCTCAGTCTAG 59.520 57.143 0.00 0.00 0.00 2.43
1183 1251 4.515567 ACTTGCTGCTTAGTTACCAGTTTC 59.484 41.667 0.00 0.00 0.00 2.78
1207 1275 2.962253 GCCTGCGTGCTCCGTATC 60.962 66.667 0.00 0.00 39.32 2.24
1210 1278 4.865761 TGCGTGCTCCGTATCGCC 62.866 66.667 5.98 0.00 46.57 5.54
1265 1333 2.203126 CTGGATTCGCTGCTCCCC 60.203 66.667 4.21 0.00 0.00 4.81
1266 1334 3.764160 CTGGATTCGCTGCTCCCCC 62.764 68.421 4.21 0.00 0.00 5.40
1307 1375 1.410153 GATTGATGGGCGCCTGAAAAT 59.590 47.619 28.56 20.29 0.00 1.82
1350 1418 6.493115 TGGATTGACCACTATTTTGTTCATGT 59.507 34.615 0.00 0.00 44.64 3.21
1368 1436 2.517959 TGTCCTTGGGAATTTCTGCTG 58.482 47.619 0.00 0.00 31.38 4.41
1404 1472 4.561735 TTTTCGGTTCACAAAGGATGTC 57.438 40.909 0.00 0.00 41.46 3.06
1418 1486 4.351874 AGGATGTCGACTTCCTTTGAAA 57.648 40.909 35.41 7.22 45.08 2.69
1423 1491 3.118555 TGTCGACTTCCTTTGAAAGACCA 60.119 43.478 17.92 0.00 32.79 4.02
1427 1495 3.885901 GACTTCCTTTGAAAGACCAAGCT 59.114 43.478 6.49 0.00 0.00 3.74
1436 1504 4.985538 TGAAAGACCAAGCTAGGAATTGT 58.014 39.130 0.00 0.00 0.00 2.71
1443 1511 4.202524 ACCAAGCTAGGAATTGTGTGGTTA 60.203 41.667 0.00 0.00 34.49 2.85
1451 1519 3.751698 GGAATTGTGTGGTTAGAGGTGAC 59.248 47.826 0.00 0.00 0.00 3.67
1471 1539 6.351033 GGTGACTGATGTAGTGATGTTTCCTA 60.351 42.308 0.00 0.00 40.53 2.94
1591 1671 1.503542 GAGTGGCCAGTGAATTGCG 59.496 57.895 20.47 0.00 0.00 4.85
1611 1698 0.968405 GATGGGCTGGTTTGCTTGAA 59.032 50.000 0.00 0.00 0.00 2.69
1646 1733 4.380867 GCCTTGTCCAATACATGAGTTTGG 60.381 45.833 15.41 15.41 38.10 3.28
1669 1756 5.121925 GGTTAAGTTACTGCTGGTTTCTAGC 59.878 44.000 0.00 0.00 41.49 3.42
1680 1767 5.598417 TGCTGGTTTCTAGCTGTCTCATATA 59.402 40.000 0.00 0.00 41.66 0.86
1685 1772 6.422400 GGTTTCTAGCTGTCTCATATAGTTGC 59.578 42.308 0.00 0.00 0.00 4.17
1812 1899 4.405358 TCCTGATGACAAAGGTTTGCTTTT 59.595 37.500 2.27 0.00 41.79 2.27
1819 1906 5.096443 ACAAAGGTTTGCTTTTTCATCCA 57.904 34.783 2.27 0.00 41.79 3.41
1825 1912 6.870769 AGGTTTGCTTTTTCATCCATCATAG 58.129 36.000 0.00 0.00 0.00 2.23
1873 1964 3.365969 GGTTTGGTCGCAGGTCAAATAAG 60.366 47.826 0.00 0.00 34.08 1.73
1900 1991 2.609459 GCTTGCGCTAGCTTAATTCTGA 59.391 45.455 31.95 0.00 45.42 3.27
1932 2023 6.650807 TCTGATCCTTGTGTTCTATTTGTGTC 59.349 38.462 0.00 0.00 0.00 3.67
1936 2027 4.455877 CCTTGTGTTCTATTTGTGTCCTCC 59.544 45.833 0.00 0.00 0.00 4.30
1943 2034 4.037222 TCTATTTGTGTCCTCCAGGCATA 58.963 43.478 0.00 0.00 34.44 3.14
1952 2043 1.468520 CCTCCAGGCATACAAACAACG 59.531 52.381 0.00 0.00 0.00 4.10
2010 2101 2.224523 CCTGAGTTCAGTAACAAGGGCA 60.225 50.000 8.23 0.00 42.27 5.36
2063 2154 2.231964 TGAGCAGGAAATTGAATGTGGC 59.768 45.455 0.00 0.00 0.00 5.01
2160 2251 1.002502 GCCTACTTCTGCCCCGTTT 60.003 57.895 0.00 0.00 0.00 3.60
2204 2295 2.095853 CCACCATTGCTGTTAGTAAGCG 59.904 50.000 0.00 0.00 43.88 4.68
2211 2302 2.494471 TGCTGTTAGTAAGCGCCTAAGA 59.506 45.455 2.29 2.53 43.88 2.10
2213 2304 3.930848 GCTGTTAGTAAGCGCCTAAGAAA 59.069 43.478 2.29 0.00 0.00 2.52
2216 2307 5.544650 TGTTAGTAAGCGCCTAAGAAAACT 58.455 37.500 2.29 0.00 0.00 2.66
2230 2321 7.012044 GCCTAAGAAAACTCTGTCACTGTTTTA 59.988 37.037 9.73 0.00 41.89 1.52
2241 2332 6.017192 TCTGTCACTGTTTTAACCATGTGATG 60.017 38.462 12.65 10.27 36.16 3.07
2249 2340 7.495901 TGTTTTAACCATGTGATGTGAATGTT 58.504 30.769 0.00 0.00 0.00 2.71
2270 2361 7.977789 TGTTTGTATAGTTGATGAGCAAAGA 57.022 32.000 0.00 0.00 38.44 2.52
2272 2363 8.453320 TGTTTGTATAGTTGATGAGCAAAGATG 58.547 33.333 0.00 0.00 38.44 2.90
2273 2364 8.668353 GTTTGTATAGTTGATGAGCAAAGATGA 58.332 33.333 0.00 0.00 38.44 2.92
2274 2365 8.969260 TTGTATAGTTGATGAGCAAAGATGAT 57.031 30.769 0.00 0.00 38.44 2.45
2275 2366 8.969260 TGTATAGTTGATGAGCAAAGATGATT 57.031 30.769 0.00 0.00 38.44 2.57
2342 2446 1.470098 AGCTTGCGAATGTCCATTCAC 59.530 47.619 17.54 10.11 45.60 3.18
2360 2464 4.857871 TCACGATTAAGGCGAAATGAAG 57.142 40.909 7.42 0.00 0.00 3.02
2538 2642 7.925483 CAGAACTACCCTATCAAGAAAGATCTG 59.075 40.741 0.00 0.00 35.59 2.90
2583 2687 6.370166 TGACGCATGTTTACACATTCATTCTA 59.630 34.615 0.00 0.00 41.16 2.10
2610 2714 4.680110 CCCGACGCATCTTATAGTTTACTG 59.320 45.833 0.00 0.00 0.00 2.74
2710 2814 2.579410 TGCCAAAAAGGTACTCCCTC 57.421 50.000 0.00 0.00 45.47 4.30
2711 2815 1.074889 TGCCAAAAAGGTACTCCCTCC 59.925 52.381 0.00 0.00 45.47 4.30
2712 2816 1.949079 GCCAAAAAGGTACTCCCTCCG 60.949 57.143 0.00 0.00 45.47 4.63
2713 2817 1.350019 CCAAAAAGGTACTCCCTCCGT 59.650 52.381 0.00 0.00 45.47 4.69
2714 2818 2.224695 CCAAAAAGGTACTCCCTCCGTT 60.225 50.000 0.00 0.00 45.47 4.44
2715 2819 3.072211 CAAAAAGGTACTCCCTCCGTTC 58.928 50.000 0.00 0.00 45.47 3.95
2716 2820 1.273759 AAAGGTACTCCCTCCGTTCC 58.726 55.000 0.00 0.00 45.47 3.62
2717 2821 0.115745 AAGGTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 45.47 3.53
2718 2822 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53
2719 2823 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
2720 2824 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
2721 2825 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
2722 2826 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
2723 2827 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2724 2828 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2725 2829 3.055312 ACTCCCTCCGTTCCAAAATAGAC 60.055 47.826 0.00 0.00 0.00 2.59
2726 2830 2.093869 TCCCTCCGTTCCAAAATAGACG 60.094 50.000 0.00 0.00 35.44 4.18
2727 2831 2.093869 CCCTCCGTTCCAAAATAGACGA 60.094 50.000 0.00 0.00 37.69 4.20
2728 2832 2.928116 CCTCCGTTCCAAAATAGACGAC 59.072 50.000 0.00 0.00 37.69 4.34
2729 2833 3.368116 CCTCCGTTCCAAAATAGACGACT 60.368 47.826 0.00 0.00 37.69 4.18
2730 2834 3.841643 TCCGTTCCAAAATAGACGACTC 58.158 45.455 0.00 0.00 37.69 3.36
2731 2835 3.256383 TCCGTTCCAAAATAGACGACTCA 59.744 43.478 0.00 0.00 37.69 3.41
2732 2836 3.991773 CCGTTCCAAAATAGACGACTCAA 59.008 43.478 0.00 0.00 37.69 3.02
2733 2837 4.143179 CCGTTCCAAAATAGACGACTCAAC 60.143 45.833 0.00 0.00 37.69 3.18
2734 2838 4.684703 CGTTCCAAAATAGACGACTCAACT 59.315 41.667 0.00 0.00 37.69 3.16
2735 2839 5.176958 CGTTCCAAAATAGACGACTCAACTT 59.823 40.000 0.00 0.00 37.69 2.66
2736 2840 6.292703 CGTTCCAAAATAGACGACTCAACTTT 60.293 38.462 0.00 0.00 37.69 2.66
2737 2841 6.539649 TCCAAAATAGACGACTCAACTTTG 57.460 37.500 0.00 0.00 0.00 2.77
2738 2842 6.053005 TCCAAAATAGACGACTCAACTTTGT 58.947 36.000 0.00 0.00 0.00 2.83
2739 2843 7.211573 TCCAAAATAGACGACTCAACTTTGTA 58.788 34.615 0.00 0.00 0.00 2.41
2740 2844 7.170320 TCCAAAATAGACGACTCAACTTTGTAC 59.830 37.037 0.00 0.00 0.00 2.90
2741 2845 7.170998 CCAAAATAGACGACTCAACTTTGTACT 59.829 37.037 0.00 0.00 0.00 2.73
2742 2846 9.188588 CAAAATAGACGACTCAACTTTGTACTA 57.811 33.333 0.00 0.00 0.00 1.82
2743 2847 9.754382 AAAATAGACGACTCAACTTTGTACTAA 57.246 29.630 0.00 0.00 0.00 2.24
2744 2848 9.754382 AAATAGACGACTCAACTTTGTACTAAA 57.246 29.630 0.00 0.00 0.00 1.85
2745 2849 8.967552 ATAGACGACTCAACTTTGTACTAAAG 57.032 34.615 13.08 13.08 0.00 1.85
2746 2850 6.803642 AGACGACTCAACTTTGTACTAAAGT 58.196 36.000 14.04 14.04 41.82 2.66
2772 2876 8.918202 TGGTACAAAGTTGAGTCATCTATTTT 57.082 30.769 4.14 0.00 31.92 1.82
2773 2877 8.783093 TGGTACAAAGTTGAGTCATCTATTTTG 58.217 33.333 4.14 8.00 40.82 2.44
2774 2878 8.237267 GGTACAAAGTTGAGTCATCTATTTTGG 58.763 37.037 14.35 0.00 40.00 3.28
2775 2879 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2776 2880 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2777 2881 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2778 2882 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2779 2883 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2780 2884 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2781 2885 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2782 2886 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2783 2887 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2784 2888 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2785 2889 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2786 2890 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2787 2891 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2830 2934 7.350744 TGGAACTGTACTACAACTAGAAACA 57.649 36.000 0.00 0.00 0.00 2.83
2836 2940 9.909644 ACTGTACTACAACTAGAAACATTACAG 57.090 33.333 15.43 15.43 38.96 2.74
2840 2944 8.813643 ACTACAACTAGAAACATTACAGTGAC 57.186 34.615 0.00 0.00 0.00 3.67
2852 2956 9.896645 AAACATTACAGTGACAGAATCATCTAT 57.103 29.630 0.00 0.00 40.28 1.98
2853 2957 9.896645 AACATTACAGTGACAGAATCATCTATT 57.103 29.630 0.00 0.00 40.28 1.73
2854 2958 9.896645 ACATTACAGTGACAGAATCATCTATTT 57.103 29.630 0.00 0.00 40.28 1.40
2860 2964 9.538508 CAGTGACAGAATCATCTATTTGACATA 57.461 33.333 0.00 0.00 40.28 2.29
2946 3050 0.599558 CTGAGGTTTGTGTGCCCATG 59.400 55.000 0.00 0.00 0.00 3.66
3000 3109 4.817464 TGTAGCAAATTGTTCTGTAACGGT 59.183 37.500 0.00 0.00 38.53 4.83
3071 3180 5.420739 TGACCCAAAGGATAAAAAGGTATGC 59.579 40.000 0.00 0.00 36.73 3.14
3074 3183 6.070824 ACCCAAAGGATAAAAAGGTATGCAAG 60.071 38.462 0.00 0.00 36.73 4.01
3091 3200 8.778358 GGTATGCAAGTTCCTATCTTAATGAAG 58.222 37.037 0.00 0.00 0.00 3.02
3114 3223 7.516198 AGCTCAAGACATCAAACATTAAGTT 57.484 32.000 0.00 0.00 43.89 2.66
3128 3237 9.329913 CAAACATTAAGTTACTGCACTTCATAC 57.670 33.333 0.41 0.00 40.26 2.39
3131 3240 7.275779 ACATTAAGTTACTGCACTTCATACTCG 59.724 37.037 0.41 0.00 38.07 4.18
3181 3290 6.257849 TCGGTAATGCATCATTCAGTTCTAAC 59.742 38.462 0.00 0.00 35.54 2.34
3195 3304 8.948631 TTCAGTTCTAACTTATTAGCATGAGG 57.051 34.615 0.00 0.00 38.18 3.86
3208 3317 3.356290 AGCATGAGGTTGACCCATTTAC 58.644 45.455 0.00 0.00 36.42 2.01
3226 3335 6.409234 CCATTTACCCACTTATCTGGCTCTAA 60.409 42.308 0.00 0.00 0.00 2.10
3236 3345 9.125026 CACTTATCTGGCTCTAAATATTTGGTT 57.875 33.333 11.05 0.00 0.00 3.67
3346 3457 5.171476 TGATGAAGCTCTGTACAACTAAGC 58.829 41.667 0.00 4.18 0.00 3.09
3382 3493 8.861033 ATGACAAATATATGCATGTTGTGTTC 57.139 30.769 18.62 9.46 0.00 3.18
3399 3510 1.659098 GTTCTTAATCAGCCCGACACG 59.341 52.381 0.00 0.00 0.00 4.49
4407 4520 8.043710 CACCCTAGAACTCTTTGAAGTATCAAT 58.956 37.037 0.00 0.00 44.70 2.57
4420 4533 9.739276 TTTGAAGTATCAATTTCTGACTACCAT 57.261 29.630 0.00 0.00 44.70 3.55
4421 4534 8.948631 TGAAGTATCAATTTCTGACTACCATC 57.051 34.615 0.00 0.00 36.69 3.51
4422 4535 7.987458 TGAAGTATCAATTTCTGACTACCATCC 59.013 37.037 0.00 0.00 36.69 3.51
4423 4536 7.437713 AGTATCAATTTCTGACTACCATCCA 57.562 36.000 0.00 0.00 36.69 3.41
4424 4537 8.038862 AGTATCAATTTCTGACTACCATCCAT 57.961 34.615 0.00 0.00 36.69 3.41
4433 4546 4.223953 TGACTACCATCCATCCTAGAACC 58.776 47.826 0.00 0.00 0.00 3.62
4469 4584 2.301870 TCGCTGATTCCCTTAACACACT 59.698 45.455 0.00 0.00 0.00 3.55
4478 4593 8.598916 TGATTCCCTTAACACACTTATTGACTA 58.401 33.333 0.00 0.00 0.00 2.59
4515 4630 9.832445 TCAACATATTACAAAATCCTAGTCCTC 57.168 33.333 0.00 0.00 0.00 3.71
4516 4631 9.613428 CAACATATTACAAAATCCTAGTCCTCA 57.387 33.333 0.00 0.00 0.00 3.86
4605 4774 0.526096 GTGTGTTGCCTTGTGCTGTG 60.526 55.000 0.00 0.00 42.00 3.66
4626 4795 7.442364 GCTGTGGTGTCATATACAAATGTATCT 59.558 37.037 9.24 0.00 40.63 1.98
4627 4796 9.981114 CTGTGGTGTCATATACAAATGTATCTA 57.019 33.333 9.24 0.00 40.63 1.98
4648 4817 2.744787 CTGTGAAACTGTGACTGTGC 57.255 50.000 0.00 0.00 38.04 4.57
4650 4819 2.419673 CTGTGAAACTGTGACTGTGCAA 59.580 45.455 0.00 0.00 38.04 4.08
4651 4820 2.419673 TGTGAAACTGTGACTGTGCAAG 59.580 45.455 0.00 0.00 38.04 4.01
4652 4821 2.677836 GTGAAACTGTGACTGTGCAAGA 59.322 45.455 0.00 0.00 0.00 3.02
4653 4822 2.677836 TGAAACTGTGACTGTGCAAGAC 59.322 45.455 0.00 0.00 0.00 3.01
4654 4823 2.401583 AACTGTGACTGTGCAAGACA 57.598 45.000 0.00 0.00 0.00 3.41
4655 4824 2.627515 ACTGTGACTGTGCAAGACAT 57.372 45.000 0.00 0.00 33.13 3.06
4697 4867 7.654568 TGAATGCATGATTATTGACATCCTTC 58.345 34.615 0.00 0.00 0.00 3.46
4699 4869 6.872628 TGCATGATTATTGACATCCTTCTC 57.127 37.500 0.00 0.00 0.00 2.87
4709 4879 3.246619 GACATCCTTCTCGTCTTGTGTC 58.753 50.000 0.00 0.00 0.00 3.67
4760 4935 6.286758 ACTACCATGTAAGAAGCATCTCATG 58.713 40.000 11.66 11.66 37.52 3.07
4887 5064 3.397618 TCATTCCAAAGGAGAAACTGGGA 59.602 43.478 0.00 0.00 31.21 4.37
4896 5073 2.484264 GGAGAAACTGGGATTTGACACG 59.516 50.000 0.00 0.00 0.00 4.49
4917 5094 4.391830 ACGGACATTGTGTTATAGTTGCTG 59.608 41.667 0.00 0.00 0.00 4.41
4978 5155 3.758554 AGGGAAACTGATTGAATTGACCG 59.241 43.478 0.00 0.00 0.00 4.79
5009 5187 1.134580 CCTATGTGACAGCAGGACAGG 60.135 57.143 9.75 0.00 0.00 4.00
5031 5209 5.960202 AGGCAATTCCACTTATCCTCAAAAT 59.040 36.000 0.00 0.00 37.29 1.82
5033 5211 6.758416 GGCAATTCCACTTATCCTCAAAATTC 59.242 38.462 0.00 0.00 34.01 2.17
5050 5229 4.769345 AATTCAAAAACTTGGCCTTGGA 57.231 36.364 3.32 0.00 0.00 3.53
5076 5255 4.035675 TGAAATGTGATGTTGTGCGTGTAA 59.964 37.500 0.00 0.00 0.00 2.41
5170 5350 9.248291 GGTTCCATATTTATTGCATAACACAAG 57.752 33.333 0.00 0.00 0.00 3.16
5182 5362 5.163612 TGCATAACACAAGCAACTGTTGTTA 60.164 36.000 20.57 11.66 35.93 2.41
5282 5462 7.821846 AGAATTTAGCTTCTCAGGTAGTGAAAG 59.178 37.037 0.00 0.00 34.44 2.62
5299 5480 2.519771 AAGGAAAGCATGCATCCAGA 57.480 45.000 31.95 0.00 35.62 3.86
5338 5519 6.816640 AGCGTTTCTTTCATGCACTATAAGTA 59.183 34.615 0.00 0.00 0.00 2.24
5339 5520 7.333423 AGCGTTTCTTTCATGCACTATAAGTAA 59.667 33.333 0.00 0.00 0.00 2.24
5341 5522 9.988350 CGTTTCTTTCATGCACTATAAGTAAAT 57.012 29.630 0.00 0.00 0.00 1.40
5347 5528 9.555727 TTTCATGCACTATAAGTAAATACTCCC 57.444 33.333 0.00 0.00 34.99 4.30
5348 5529 8.492415 TCATGCACTATAAGTAAATACTCCCT 57.508 34.615 0.00 0.00 34.99 4.20
5349 5530 8.585881 TCATGCACTATAAGTAAATACTCCCTC 58.414 37.037 0.00 0.00 34.99 4.30
5350 5531 6.978338 TGCACTATAAGTAAATACTCCCTCG 58.022 40.000 0.00 0.00 34.99 4.63
5351 5532 6.548622 TGCACTATAAGTAAATACTCCCTCGT 59.451 38.462 0.00 0.00 34.99 4.18
5352 5533 6.862090 GCACTATAAGTAAATACTCCCTCGTG 59.138 42.308 0.00 0.00 34.99 4.35
5353 5534 7.255381 GCACTATAAGTAAATACTCCCTCGTGA 60.255 40.741 11.05 0.00 34.99 4.35
5354 5535 8.627403 CACTATAAGTAAATACTCCCTCGTGAA 58.373 37.037 0.00 0.00 34.99 3.18
5355 5536 8.848182 ACTATAAGTAAATACTCCCTCGTGAAG 58.152 37.037 0.00 0.00 34.99 3.02
5356 5537 7.893124 ATAAGTAAATACTCCCTCGTGAAGA 57.107 36.000 0.00 0.00 34.99 2.87
5357 5538 6.600882 AAGTAAATACTCCCTCGTGAAGAA 57.399 37.500 0.00 0.00 34.99 2.52
5358 5539 6.600882 AGTAAATACTCCCTCGTGAAGAAA 57.399 37.500 0.00 0.00 0.00 2.52
5359 5540 7.184067 AGTAAATACTCCCTCGTGAAGAAAT 57.816 36.000 0.00 0.00 0.00 2.17
5360 5541 8.302515 AGTAAATACTCCCTCGTGAAGAAATA 57.697 34.615 0.00 0.00 0.00 1.40
5361 5542 8.925338 AGTAAATACTCCCTCGTGAAGAAATAT 58.075 33.333 0.00 0.00 0.00 1.28
5364 5545 9.765795 AAATACTCCCTCGTGAAGAAATATAAG 57.234 33.333 0.00 0.00 0.00 1.73
5365 5546 8.707796 ATACTCCCTCGTGAAGAAATATAAGA 57.292 34.615 0.00 0.00 0.00 2.10
5366 5547 7.045126 ACTCCCTCGTGAAGAAATATAAGAG 57.955 40.000 0.00 0.00 0.00 2.85
5367 5548 6.608002 ACTCCCTCGTGAAGAAATATAAGAGT 59.392 38.462 0.00 0.00 0.00 3.24
5368 5549 6.806751 TCCCTCGTGAAGAAATATAAGAGTG 58.193 40.000 0.00 0.00 0.00 3.51
5369 5550 6.380274 TCCCTCGTGAAGAAATATAAGAGTGT 59.620 38.462 0.00 0.00 0.00 3.55
5370 5551 7.042335 CCCTCGTGAAGAAATATAAGAGTGTT 58.958 38.462 0.00 0.00 0.00 3.32
5371 5552 7.549488 CCCTCGTGAAGAAATATAAGAGTGTTT 59.451 37.037 0.00 0.00 0.00 2.83
5372 5553 9.582431 CCTCGTGAAGAAATATAAGAGTGTTTA 57.418 33.333 0.00 0.00 0.00 2.01
5374 5555 9.084164 TCGTGAAGAAATATAAGAGTGTTTAGC 57.916 33.333 0.00 0.00 0.00 3.09
5375 5556 9.088512 CGTGAAGAAATATAAGAGTGTTTAGCT 57.911 33.333 0.00 0.00 0.00 3.32
5396 5577 7.309770 AGCTCTTATATTCCTTTACAGAGGG 57.690 40.000 0.00 0.00 37.41 4.30
5397 5578 7.076446 AGCTCTTATATTCCTTTACAGAGGGA 58.924 38.462 0.00 0.00 37.41 4.20
5398 5579 7.234577 AGCTCTTATATTCCTTTACAGAGGGAG 59.765 40.741 0.00 0.00 37.41 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.799106 ATTAGAAATCCCACTACATAATTCTGG 57.201 33.333 0.00 0.00 0.00 3.86
36 37 9.565213 CTCATGGTTTGAAGTCAATTAGAAATC 57.435 33.333 0.00 0.00 35.55 2.17
41 42 6.506500 AGCTCATGGTTTGAAGTCAATTAG 57.493 37.500 0.00 0.00 35.55 1.73
52 53 2.703416 TCTGCACTAGCTCATGGTTTG 58.297 47.619 0.00 0.00 42.74 2.93
113 116 6.758254 AGGATGGGTTTCAAACAGTTTATTG 58.242 36.000 1.93 0.00 0.00 1.90
388 418 0.108041 TAGAATTCCACCGCGGTTCC 60.108 55.000 32.11 13.74 35.57 3.62
414 444 2.277756 CGGACTAGTGGTACGCGC 60.278 66.667 5.73 0.00 45.76 6.86
418 448 0.455005 GCTGGACGGACTAGTGGTAC 59.545 60.000 0.00 0.00 0.00 3.34
419 449 0.038599 TGCTGGACGGACTAGTGGTA 59.961 55.000 0.00 0.00 0.00 3.25
420 450 1.228769 TGCTGGACGGACTAGTGGT 60.229 57.895 0.00 0.00 0.00 4.16
422 452 1.215647 GGTGCTGGACGGACTAGTG 59.784 63.158 0.00 0.00 33.95 2.74
424 454 1.215647 GTGGTGCTGGACGGACTAG 59.784 63.158 0.00 0.00 33.95 2.57
426 456 3.991051 CGTGGTGCTGGACGGACT 61.991 66.667 0.00 0.00 33.95 3.85
427 457 3.916392 CTCGTGGTGCTGGACGGAC 62.916 68.421 0.00 0.00 36.23 4.79
428 458 3.680786 CTCGTGGTGCTGGACGGA 61.681 66.667 0.00 0.00 36.23 4.69
429 459 3.916392 GACTCGTGGTGCTGGACGG 62.916 68.421 0.00 0.00 36.23 4.79
430 460 2.430921 GACTCGTGGTGCTGGACG 60.431 66.667 0.00 0.00 36.91 4.79
431 461 2.430921 CGACTCGTGGTGCTGGAC 60.431 66.667 0.00 0.00 0.00 4.02
432 462 4.357947 GCGACTCGTGGTGCTGGA 62.358 66.667 0.00 0.00 0.00 3.86
434 464 4.700365 TCGCGACTCGTGGTGCTG 62.700 66.667 3.71 0.00 37.97 4.41
581 611 2.527951 AAATGAAGCTCGGCGAGGCT 62.528 55.000 35.03 28.02 40.85 4.58
584 614 1.061570 GCAAATGAAGCTCGGCGAG 59.938 57.895 31.40 31.40 0.00 5.03
586 616 1.226211 CAGCAAATGAAGCTCGGCG 60.226 57.895 0.00 0.00 41.14 6.46
788 831 1.081509 CGTGGTGGCATTTTCGTGG 60.082 57.895 0.00 0.00 0.00 4.94
804 847 2.764128 ATCGGGTGATGGGAGCGT 60.764 61.111 0.00 0.00 32.21 5.07
824 867 4.958897 CCGGCCCGACCAACCAAA 62.959 66.667 3.71 0.00 39.03 3.28
928 985 2.046120 AGGCTGCTGCTTCTGCTC 60.046 61.111 15.64 0.00 40.48 4.26
962 1019 1.458777 ACGAGGAAGTGGTGGTGGA 60.459 57.895 0.00 0.00 0.00 4.02
998 1055 4.175337 GGCGGCTGCTACCCATCA 62.175 66.667 18.85 0.00 42.25 3.07
1037 1100 2.753029 GGTGCAGGAGCTGGAACT 59.247 61.111 0.00 0.00 36.59 3.01
1038 1101 2.743928 CGGTGCAGGAGCTGGAAC 60.744 66.667 0.00 0.00 42.74 3.62
1039 1102 4.704833 GCGGTGCAGGAGCTGGAA 62.705 66.667 0.00 0.00 42.74 3.53
1045 1108 4.154347 GAGGAGGCGGTGCAGGAG 62.154 72.222 0.00 0.00 0.00 3.69
1095 1158 1.398692 GCTCCTCGAAGATGACCTCT 58.601 55.000 0.00 0.00 33.89 3.69
1130 1193 1.463214 TGAGCTGGGGAAGTGGGAA 60.463 57.895 0.00 0.00 0.00 3.97
1150 1216 5.502079 ACTAAGCAGCAAGTCTACTCTAGA 58.498 41.667 0.00 0.00 0.00 2.43
1151 1217 5.828299 ACTAAGCAGCAAGTCTACTCTAG 57.172 43.478 0.00 0.00 0.00 2.43
1152 1218 6.095160 GGTAACTAAGCAGCAAGTCTACTCTA 59.905 42.308 0.00 0.00 0.00 2.43
1153 1219 5.105675 GGTAACTAAGCAGCAAGTCTACTCT 60.106 44.000 0.00 0.00 0.00 3.24
1154 1220 5.103687 GGTAACTAAGCAGCAAGTCTACTC 58.896 45.833 0.00 0.00 0.00 2.59
1172 1240 1.154197 GCACCTCCGAAACTGGTAAC 58.846 55.000 0.00 0.00 32.13 2.50
1209 1277 1.386533 CACAGAAATAGCAGCAGGGG 58.613 55.000 0.00 0.00 0.00 4.79
1210 1278 0.737219 GCACAGAAATAGCAGCAGGG 59.263 55.000 0.00 0.00 0.00 4.45
1336 1404 6.588719 TTCCCAAGGACATGAACAAAATAG 57.411 37.500 0.00 0.00 0.00 1.73
1350 1418 1.549203 GCAGCAGAAATTCCCAAGGA 58.451 50.000 0.00 0.00 0.00 3.36
1368 1436 1.336795 CGAAAAACCATGAACAGGGGC 60.337 52.381 10.18 0.00 36.39 5.80
1404 1472 3.304057 GCTTGGTCTTTCAAAGGAAGTCG 60.304 47.826 0.00 0.00 33.82 4.18
1418 1486 3.560025 CCACACAATTCCTAGCTTGGTCT 60.560 47.826 14.12 0.00 0.00 3.85
1423 1491 5.491982 CTCTAACCACACAATTCCTAGCTT 58.508 41.667 0.00 0.00 0.00 3.74
1427 1495 4.841813 TCACCTCTAACCACACAATTCCTA 59.158 41.667 0.00 0.00 0.00 2.94
1436 1504 3.239449 ACATCAGTCACCTCTAACCACA 58.761 45.455 0.00 0.00 0.00 4.17
1443 1511 4.348486 ACATCACTACATCAGTCACCTCT 58.652 43.478 0.00 0.00 34.26 3.69
1451 1519 8.722480 TTCAATAGGAAACATCACTACATCAG 57.278 34.615 0.00 0.00 30.98 2.90
1471 1539 5.338463 GGCTGAGGGAACTAGTTACTTCAAT 60.338 44.000 27.22 6.87 44.43 2.57
1591 1671 0.899717 TCAAGCAAACCAGCCCATCC 60.900 55.000 0.00 0.00 34.23 3.51
1611 1698 1.303309 GACAAGGCATCGCAGCTAAT 58.697 50.000 0.00 0.00 34.17 1.73
1646 1733 5.932883 AGCTAGAAACCAGCAGTAACTTAAC 59.067 40.000 0.00 0.00 41.66 2.01
1669 1756 7.493645 TCTGAAACATGCAACTATATGAGACAG 59.506 37.037 0.00 0.00 0.00 3.51
1680 1767 3.006110 CCAACCATCTGAAACATGCAACT 59.994 43.478 0.00 0.00 0.00 3.16
1685 1772 3.441572 GTCTCCCAACCATCTGAAACATG 59.558 47.826 0.00 0.00 0.00 3.21
1900 1991 6.365970 AGAACACAAGGATCAGACAGTATT 57.634 37.500 0.00 0.00 0.00 1.89
1932 2023 1.468520 CGTTGTTTGTATGCCTGGAGG 59.531 52.381 0.00 0.00 38.53 4.30
1936 2027 5.741425 CATCTATCGTTGTTTGTATGCCTG 58.259 41.667 0.00 0.00 0.00 4.85
1943 2034 3.871594 GCCTAGCATCTATCGTTGTTTGT 59.128 43.478 0.00 0.00 0.00 2.83
1991 2082 2.224523 CCTGCCCTTGTTACTGAACTCA 60.225 50.000 0.00 0.00 36.45 3.41
2063 2154 2.363788 TCAGCTTAATATAGCCGCCG 57.636 50.000 0.00 0.00 42.20 6.46
2081 2172 3.266510 TGGTTGACATAGCCAGACATC 57.733 47.619 0.00 0.00 34.38 3.06
2160 2251 8.956426 GTGGATCTTTGTAAGAACATGGAATTA 58.044 33.333 0.00 0.00 41.63 1.40
2204 2295 4.381411 ACAGTGACAGAGTTTTCTTAGGC 58.619 43.478 0.00 0.00 0.00 3.93
2211 2302 6.827586 TGGTTAAAACAGTGACAGAGTTTT 57.172 33.333 17.20 17.20 44.72 2.43
2213 2304 5.885912 ACATGGTTAAAACAGTGACAGAGTT 59.114 36.000 0.00 0.00 0.00 3.01
2216 2307 5.432645 TCACATGGTTAAAACAGTGACAGA 58.567 37.500 0.00 1.44 34.29 3.41
2230 2321 5.534207 ACAAACATTCACATCACATGGTT 57.466 34.783 0.00 0.00 33.60 3.67
2241 2332 7.751732 TGCTCATCAACTATACAAACATTCAC 58.248 34.615 0.00 0.00 0.00 3.18
2249 2340 8.969260 ATCATCTTTGCTCATCAACTATACAA 57.031 30.769 0.00 0.00 33.73 2.41
2383 2487 7.527568 ACTCAGCAGTAGACTAGTAAAACTT 57.472 36.000 0.00 0.00 0.00 2.66
2538 2642 1.154225 CCTGTCGGTTTCGCATTGC 60.154 57.895 0.00 0.00 36.13 3.56
2583 2687 1.000955 CTATAAGATGCGTCGGGCCTT 59.999 52.381 0.84 0.00 42.61 4.35
2637 2741 3.244875 TGTCCCAATCAGTGTACATGCTT 60.245 43.478 0.00 0.00 0.00 3.91
2704 2808 3.532542 GTCTATTTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2705 2809 2.093869 CGTCTATTTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2706 2810 2.093869 TCGTCTATTTTGGAACGGAGGG 60.094 50.000 0.00 0.00 0.00 4.30
2707 2811 2.928116 GTCGTCTATTTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2708 2812 3.846360 AGTCGTCTATTTTGGAACGGAG 58.154 45.455 0.00 0.00 0.00 4.63
2709 2813 3.256383 TGAGTCGTCTATTTTGGAACGGA 59.744 43.478 0.00 0.00 0.00 4.69
2710 2814 3.581755 TGAGTCGTCTATTTTGGAACGG 58.418 45.455 0.00 0.00 0.00 4.44
2711 2815 4.684703 AGTTGAGTCGTCTATTTTGGAACG 59.315 41.667 0.00 0.00 0.00 3.95
2712 2816 6.541111 AAGTTGAGTCGTCTATTTTGGAAC 57.459 37.500 0.00 0.00 0.00 3.62
2713 2817 6.540914 ACAAAGTTGAGTCGTCTATTTTGGAA 59.459 34.615 0.00 0.00 38.53 3.53
2714 2818 6.053005 ACAAAGTTGAGTCGTCTATTTTGGA 58.947 36.000 0.00 0.00 38.53 3.53
2715 2819 6.300354 ACAAAGTTGAGTCGTCTATTTTGG 57.700 37.500 0.00 0.00 38.53 3.28
2716 2820 8.073355 AGTACAAAGTTGAGTCGTCTATTTTG 57.927 34.615 0.00 4.77 39.42 2.44
2717 2821 9.754382 TTAGTACAAAGTTGAGTCGTCTATTTT 57.246 29.630 0.00 0.00 0.00 1.82
2718 2822 9.754382 TTTAGTACAAAGTTGAGTCGTCTATTT 57.246 29.630 0.00 0.00 0.00 1.40
2719 2823 9.408069 CTTTAGTACAAAGTTGAGTCGTCTATT 57.592 33.333 0.00 0.00 0.00 1.73
2720 2824 8.574737 ACTTTAGTACAAAGTTGAGTCGTCTAT 58.425 33.333 14.04 0.00 37.18 1.98
2721 2825 7.934457 ACTTTAGTACAAAGTTGAGTCGTCTA 58.066 34.615 14.04 0.00 37.18 2.59
2722 2826 6.803642 ACTTTAGTACAAAGTTGAGTCGTCT 58.196 36.000 14.04 0.00 37.18 4.18
2723 2827 7.460751 AACTTTAGTACAAAGTTGAGTCGTC 57.539 36.000 23.48 0.00 45.58 4.20
2736 2840 8.042515 ACTCAACTTTGTACCAACTTTAGTACA 58.957 33.333 0.00 0.00 45.29 2.90
2737 2841 8.429493 ACTCAACTTTGTACCAACTTTAGTAC 57.571 34.615 0.00 0.00 39.44 2.73
2738 2842 8.259411 TGACTCAACTTTGTACCAACTTTAGTA 58.741 33.333 0.00 0.00 0.00 1.82
2739 2843 7.107542 TGACTCAACTTTGTACCAACTTTAGT 58.892 34.615 0.00 0.00 0.00 2.24
2740 2844 7.548196 TGACTCAACTTTGTACCAACTTTAG 57.452 36.000 0.00 0.00 0.00 1.85
2741 2845 7.990886 AGATGACTCAACTTTGTACCAACTTTA 59.009 33.333 0.00 0.00 0.00 1.85
2742 2846 6.828785 AGATGACTCAACTTTGTACCAACTTT 59.171 34.615 0.00 0.00 0.00 2.66
2743 2847 6.357367 AGATGACTCAACTTTGTACCAACTT 58.643 36.000 0.00 0.00 0.00 2.66
2744 2848 5.930135 AGATGACTCAACTTTGTACCAACT 58.070 37.500 0.00 0.00 0.00 3.16
2745 2849 7.907214 ATAGATGACTCAACTTTGTACCAAC 57.093 36.000 0.00 0.00 0.00 3.77
2746 2850 8.918202 AAATAGATGACTCAACTTTGTACCAA 57.082 30.769 0.00 0.00 0.00 3.67
2747 2851 8.783093 CAAAATAGATGACTCAACTTTGTACCA 58.217 33.333 0.00 0.00 0.00 3.25
2748 2852 8.237267 CCAAAATAGATGACTCAACTTTGTACC 58.763 37.037 0.00 0.00 0.00 3.34
2749 2853 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2750 2854 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2751 2855 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2752 2856 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2753 2857 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2754 2858 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2755 2859 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2756 2860 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2757 2861 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2758 2862 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2759 2863 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2760 2864 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2761 2865 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2762 2866 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2763 2867 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2764 2868 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2765 2869 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2766 2870 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2767 2871 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
2768 2872 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
2769 2873 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
2770 2874 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2771 2875 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2772 2876 0.683504 GAGCTACTCCCTCCGTTCCA 60.684 60.000 0.00 0.00 0.00 3.53
2773 2877 0.683504 TGAGCTACTCCCTCCGTTCC 60.684 60.000 0.00 0.00 0.00 3.62
2774 2878 0.456628 GTGAGCTACTCCCTCCGTTC 59.543 60.000 0.00 0.00 0.00 3.95
2775 2879 0.039911 AGTGAGCTACTCCCTCCGTT 59.960 55.000 0.00 0.00 33.17 4.44
2776 2880 0.039911 AAGTGAGCTACTCCCTCCGT 59.960 55.000 0.00 0.00 39.18 4.69
2777 2881 1.187087 AAAGTGAGCTACTCCCTCCG 58.813 55.000 0.00 0.00 39.18 4.63
2778 2882 3.704800 AAAAAGTGAGCTACTCCCTCC 57.295 47.619 0.00 0.00 39.18 4.30
2816 2920 8.812147 TGTCACTGTAATGTTTCTAGTTGTAG 57.188 34.615 0.00 0.00 0.00 2.74
2865 2969 2.167075 CCAATCCTTAGGCTGCAAAAGG 59.833 50.000 20.31 20.31 41.00 3.11
2866 2970 2.167075 CCCAATCCTTAGGCTGCAAAAG 59.833 50.000 0.50 4.12 0.00 2.27
2991 3100 4.181578 CCAAGGTAGATGAACCGTTACAG 58.818 47.826 0.00 0.00 44.77 2.74
3000 3109 0.918983 CCCTGGCCAAGGTAGATGAA 59.081 55.000 12.76 0.00 45.78 2.57
3020 3129 9.874205 GGAATCTCTCTTGGAATAGAATCATAG 57.126 37.037 0.00 0.00 0.00 2.23
3071 3180 8.498054 TTGAGCTTCATTAAGATAGGAACTTG 57.502 34.615 0.00 0.00 35.57 3.16
3074 3183 7.766278 TGTCTTGAGCTTCATTAAGATAGGAAC 59.234 37.037 0.00 0.00 34.37 3.62
3091 3200 8.507249 AGTAACTTAATGTTTGATGTCTTGAGC 58.493 33.333 0.00 0.00 39.89 4.26
3146 3255 5.056480 TGATGCATTACCGAATAAGTCAGG 58.944 41.667 0.00 0.00 0.00 3.86
3147 3256 6.791887 ATGATGCATTACCGAATAAGTCAG 57.208 37.500 0.00 0.00 0.00 3.51
3157 3266 6.258727 AGTTAGAACTGAATGATGCATTACCG 59.741 38.462 0.00 0.00 37.98 4.02
3181 3290 4.780815 TGGGTCAACCTCATGCTAATAAG 58.219 43.478 0.00 0.00 41.11 1.73
3194 3303 2.597578 AGTGGGTAAATGGGTCAACC 57.402 50.000 0.00 0.00 40.81 3.77
3195 3304 5.357032 CAGATAAGTGGGTAAATGGGTCAAC 59.643 44.000 0.00 0.00 0.00 3.18
3208 3317 7.175641 CCAAATATTTAGAGCCAGATAAGTGGG 59.824 40.741 0.00 0.00 38.14 4.61
3295 3406 6.313905 AGAATGTTTCTTTAGATGTGCTACGG 59.686 38.462 0.00 0.00 36.36 4.02
3323 3434 5.171476 GCTTAGTTGTACAGAGCTTCATCA 58.829 41.667 12.51 0.00 0.00 3.07
3324 3435 5.062809 GTGCTTAGTTGTACAGAGCTTCATC 59.937 44.000 17.58 5.89 32.08 2.92
3334 3445 3.545366 TGTGGTGTGCTTAGTTGTACA 57.455 42.857 0.00 0.00 0.00 2.90
3346 3457 6.859508 GCATATATTTGTCATCATGTGGTGTG 59.140 38.462 0.00 0.00 0.00 3.82
3382 3493 0.999406 CACGTGTCGGGCTGATTAAG 59.001 55.000 7.58 0.00 0.00 1.85
3399 3510 2.420642 CCATCATCATCATCGTCCCAC 58.579 52.381 0.00 0.00 0.00 4.61
3973 4085 2.006805 TTGCACCCCATGTTTCATCA 57.993 45.000 0.00 0.00 0.00 3.07
4407 4520 5.777449 TCTAGGATGGATGGTAGTCAGAAA 58.223 41.667 0.00 0.00 0.00 2.52
4420 4533 4.175962 ACTTCAAAGGGTTCTAGGATGGA 58.824 43.478 0.00 0.00 0.00 3.41
4421 4534 4.226168 AGACTTCAAAGGGTTCTAGGATGG 59.774 45.833 0.00 0.00 0.00 3.51
4422 4535 5.428184 AGACTTCAAAGGGTTCTAGGATG 57.572 43.478 0.00 0.00 0.00 3.51
4423 4536 7.757242 ATAAGACTTCAAAGGGTTCTAGGAT 57.243 36.000 0.00 0.00 0.00 3.24
4424 4537 7.569599 AATAAGACTTCAAAGGGTTCTAGGA 57.430 36.000 0.00 0.00 0.00 2.94
4433 4546 6.428385 AATCAGCGAATAAGACTTCAAAGG 57.572 37.500 0.00 0.00 0.00 3.11
4505 4620 3.445008 AGCAATGTCTTGAGGACTAGGA 58.555 45.455 0.00 0.00 44.74 2.94
4508 4623 7.071196 ACCATATTAGCAATGTCTTGAGGACTA 59.929 37.037 0.00 0.00 44.74 2.59
4515 4630 9.507280 CTTGTTTACCATATTAGCAATGTCTTG 57.493 33.333 0.00 0.00 35.36 3.02
4516 4631 9.243105 ACTTGTTTACCATATTAGCAATGTCTT 57.757 29.630 0.00 0.00 0.00 3.01
4626 4795 3.621268 GCACAGTCACAGTTTCACAGTTA 59.379 43.478 0.00 0.00 0.00 2.24
4627 4796 2.420022 GCACAGTCACAGTTTCACAGTT 59.580 45.455 0.00 0.00 0.00 3.16
4630 4799 2.106477 TGCACAGTCACAGTTTCACA 57.894 45.000 0.00 0.00 0.00 3.58
4686 4856 3.069586 ACACAAGACGAGAAGGATGTCAA 59.930 43.478 0.00 0.00 35.09 3.18
4697 4867 1.340657 GCGCTGAGACACAAGACGAG 61.341 60.000 0.00 0.00 0.00 4.18
4699 4869 1.215014 TTGCGCTGAGACACAAGACG 61.215 55.000 9.73 0.00 0.00 4.18
4709 4879 0.997932 GTGATCTCTGTTGCGCTGAG 59.002 55.000 9.73 11.11 42.40 3.35
4822 4998 5.771666 TCAAAGCTCATCCTGAACAAGAAAT 59.228 36.000 0.00 0.00 0.00 2.17
4866 5043 3.766545 TCCCAGTTTCTCCTTTGGAATG 58.233 45.455 0.00 0.00 32.34 2.67
4867 5044 4.682021 ATCCCAGTTTCTCCTTTGGAAT 57.318 40.909 0.00 0.00 32.34 3.01
4887 5064 5.957842 ATAACACAATGTCCGTGTCAAAT 57.042 34.783 0.00 0.00 46.65 2.32
4896 5073 4.155826 TGCAGCAACTATAACACAATGTCC 59.844 41.667 0.00 0.00 0.00 4.02
4978 5155 3.982475 TGTCACATAGGATGATCTTCGC 58.018 45.455 2.77 0.00 0.00 4.70
5009 5187 7.322664 TGAATTTTGAGGATAAGTGGAATTGC 58.677 34.615 0.00 0.00 0.00 3.56
5031 5209 2.169561 GGTCCAAGGCCAAGTTTTTGAA 59.830 45.455 5.01 0.00 36.36 2.69
5033 5211 1.762370 AGGTCCAAGGCCAAGTTTTTG 59.238 47.619 5.01 0.00 0.00 2.44
5050 5229 2.030893 CGCACAACATCACATTTCAGGT 60.031 45.455 0.00 0.00 0.00 4.00
5170 5350 3.467803 ACTCCTCAGTAACAACAGTTGC 58.532 45.455 13.56 0.00 0.00 4.17
5206 5386 8.353423 ACAGGAGCAACATAGAATTTTGTATT 57.647 30.769 0.00 0.00 0.00 1.89
5214 5394 5.762218 GCTGATTACAGGAGCAACATAGAAT 59.238 40.000 0.00 0.00 43.62 2.40
5217 5397 4.445453 TGCTGATTACAGGAGCAACATAG 58.555 43.478 0.00 0.00 43.62 2.23
5282 5462 2.372264 TCTTCTGGATGCATGCTTTCC 58.628 47.619 24.87 24.87 0.00 3.13
5299 5480 9.109393 TGAAAGAAACGCTAATATATGCTTCTT 57.891 29.630 9.37 9.37 36.17 2.52
5338 5519 9.765795 CTTATATTTCTTCACGAGGGAGTATTT 57.234 33.333 0.00 0.00 0.00 1.40
5339 5520 9.144298 TCTTATATTTCTTCACGAGGGAGTATT 57.856 33.333 0.00 0.00 0.00 1.89
5341 5522 7.778853 ACTCTTATATTTCTTCACGAGGGAGTA 59.221 37.037 0.00 0.00 0.00 2.59
5342 5523 6.608002 ACTCTTATATTTCTTCACGAGGGAGT 59.392 38.462 0.00 0.00 0.00 3.85
5343 5524 6.920758 CACTCTTATATTTCTTCACGAGGGAG 59.079 42.308 0.00 0.00 0.00 4.30
5344 5525 6.380274 ACACTCTTATATTTCTTCACGAGGGA 59.620 38.462 0.00 0.00 0.00 4.20
5345 5526 6.574350 ACACTCTTATATTTCTTCACGAGGG 58.426 40.000 0.00 0.00 0.00 4.30
5346 5527 8.480643 AAACACTCTTATATTTCTTCACGAGG 57.519 34.615 0.00 0.00 0.00 4.63
5348 5529 9.084164 GCTAAACACTCTTATATTTCTTCACGA 57.916 33.333 0.00 0.00 0.00 4.35
5349 5530 9.088512 AGCTAAACACTCTTATATTTCTTCACG 57.911 33.333 0.00 0.00 0.00 4.35
5370 5551 8.871125 CCCTCTGTAAAGGAATATAAGAGCTAA 58.129 37.037 0.00 0.00 38.87 3.09
5371 5552 8.232412 TCCCTCTGTAAAGGAATATAAGAGCTA 58.768 37.037 0.00 0.00 38.87 3.32
5372 5553 7.076446 TCCCTCTGTAAAGGAATATAAGAGCT 58.924 38.462 0.00 0.00 38.87 4.09
5373 5554 7.015779 ACTCCCTCTGTAAAGGAATATAAGAGC 59.984 40.741 0.00 0.00 38.87 4.09
5374 5555 8.485578 ACTCCCTCTGTAAAGGAATATAAGAG 57.514 38.462 0.00 0.00 38.87 2.85
5375 5556 9.364653 GTACTCCCTCTGTAAAGGAATATAAGA 57.635 37.037 0.00 0.00 38.87 2.10
5376 5557 9.144298 TGTACTCCCTCTGTAAAGGAATATAAG 57.856 37.037 0.00 0.00 38.87 1.73
5377 5558 9.670442 ATGTACTCCCTCTGTAAAGGAATATAA 57.330 33.333 0.00 0.00 38.87 0.98
5379 5560 9.845214 ATATGTACTCCCTCTGTAAAGGAATAT 57.155 33.333 0.00 0.00 38.87 1.28
5380 5561 9.310449 GATATGTACTCCCTCTGTAAAGGAATA 57.690 37.037 0.00 0.00 38.87 1.75
5381 5562 8.013667 AGATATGTACTCCCTCTGTAAAGGAAT 58.986 37.037 0.00 0.00 38.87 3.01
5382 5563 7.363031 AGATATGTACTCCCTCTGTAAAGGAA 58.637 38.462 0.00 0.00 38.87 3.36
5383 5564 6.923670 AGATATGTACTCCCTCTGTAAAGGA 58.076 40.000 0.00 0.00 38.87 3.36
5384 5565 8.887264 ATAGATATGTACTCCCTCTGTAAAGG 57.113 38.462 0.00 0.00 36.08 3.11
5388 5569 9.961264 CAAGTATAGATATGTACTCCCTCTGTA 57.039 37.037 0.00 0.00 31.10 2.74
5389 5570 7.891183 CCAAGTATAGATATGTACTCCCTCTGT 59.109 40.741 0.00 0.00 31.10 3.41
5390 5571 8.110271 TCCAAGTATAGATATGTACTCCCTCTG 58.890 40.741 0.00 0.00 31.10 3.35
5391 5572 8.233349 TCCAAGTATAGATATGTACTCCCTCT 57.767 38.462 0.00 0.00 31.10 3.69
5392 5573 8.741841 GTTCCAAGTATAGATATGTACTCCCTC 58.258 40.741 0.00 0.00 31.10 4.30
5393 5574 8.457757 AGTTCCAAGTATAGATATGTACTCCCT 58.542 37.037 0.00 0.00 31.10 4.20
5394 5575 8.653036 AGTTCCAAGTATAGATATGTACTCCC 57.347 38.462 0.00 0.00 31.10 4.30
5397 5578 9.884814 AGGAAGTTCCAAGTATAGATATGTACT 57.115 33.333 23.87 0.00 39.61 2.73


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

AutoCloner maintained by Alex Coulton.