Multiple sequence alignment - TraesCS3A01G180200

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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 TraesCS3A01G180200 chr3A 100.000 3566 0 0 1 3566 208220264 208223829 0.000000e+00 6586.0
1 TraesCS3A01G180200 chr3A 89.233 873 72 15 1702 2564 208086395 208085535 0.000000e+00 1072.0
2 TraesCS3A01G180200 chr3A 89.715 632 56 4 1977 2607 208089570 208088947 0.000000e+00 798.0
3 TraesCS3A01G180200 chr3A 82.283 587 65 28 669 1244 208087308 208086750 4.170000e-129 472.0
4 TraesCS3A01G180200 chr3A 88.889 306 26 7 930 1234 208090577 208090279 1.560000e-98 370.0
5 TraesCS3A01G180200 chr3A 87.619 210 26 0 1695 1904 208089883 208089674 9.890000e-61 244.0
6 TraesCS3A01G180200 chr3D 90.756 1785 69 41 1245 2980 170659069 170660806 0.000000e+00 2294.0
7 TraesCS3A01G180200 chr3D 89.992 1259 78 31 3 1244 170657691 170658918 0.000000e+00 1583.0
8 TraesCS3A01G180200 chr3D 89.862 868 68 17 1702 2564 170558159 170557307 0.000000e+00 1098.0
9 TraesCS3A01G180200 chr3D 88.712 629 64 3 1977 2605 170564231 170563610 0.000000e+00 761.0
10 TraesCS3A01G180200 chr3D 93.950 281 17 0 964 1244 170558813 170558533 3.290000e-115 425.0
11 TraesCS3A01G180200 chr3D 90.312 320 21 8 927 1245 170565233 170564923 9.210000e-111 411.0
12 TraesCS3A01G180200 chr3D 88.571 210 24 0 1695 1904 170564546 170564337 4.570000e-64 255.0
13 TraesCS3A01G180200 chr3B 90.954 1227 50 25 1945 3128 246129306 246130514 0.000000e+00 1594.0
14 TraesCS3A01G180200 chr3B 89.631 868 70 14 1702 2564 245964145 245963293 0.000000e+00 1086.0
15 TraesCS3A01G180200 chr3B 90.725 841 39 12 432 1244 246127350 246128179 0.000000e+00 1085.0
16 TraesCS3A01G180200 chr3B 92.188 704 24 13 1245 1939 246128335 246129016 0.000000e+00 966.0
17 TraesCS3A01G180200 chr3B 88.133 632 66 6 1977 2607 245969581 245968958 0.000000e+00 743.0
18 TraesCS3A01G180200 chr3B 88.144 582 69 0 1977 2558 246146565 246147146 0.000000e+00 693.0
19 TraesCS3A01G180200 chr3B 83.656 569 48 32 705 1244 245965036 245964484 8.890000e-136 494.0
20 TraesCS3A01G180200 chr3B 87.042 355 27 10 1 341 246119017 246119366 2.010000e-102 383.0
21 TraesCS3A01G180200 chr3B 87.220 313 30 8 927 1234 245970586 245970279 7.330000e-92 348.0
22 TraesCS3A01G180200 chr3B 88.889 216 24 0 1689 1904 245969902 245969687 2.110000e-67 267.0
23 TraesCS3A01G180200 chr3B 88.298 94 5 2 337 430 246127149 246127236 1.350000e-19 108.0
24 TraesCS3A01G180200 chr3B 98.113 53 1 0 3152 3204 246130594 246130646 3.790000e-15 93.5
25 TraesCS3A01G180200 chr2A 91.603 262 17 4 3258 3514 699241115 699240854 1.220000e-94 357.0
26 TraesCS3A01G180200 chr2A 90.566 265 19 5 3258 3518 24651011 24650749 2.640000e-91 346.0
27 TraesCS3A01G180200 chr2A 90.566 265 19 5 3258 3518 24679078 24678816 2.640000e-91 346.0
28 TraesCS3A01G180200 chr2A 90.566 265 19 5 3258 3518 25657833 25658095 2.640000e-91 346.0
29 TraesCS3A01G180200 chr2A 90.189 265 20 5 3258 3518 24692826 24692564 1.230000e-89 340.0
30 TraesCS3A01G180200 chr2A 90.189 265 21 4 3258 3518 24706255 24705992 1.230000e-89 340.0
31 TraesCS3A01G180200 chr5A 91.538 260 18 4 3259 3514 603918575 603918316 4.380000e-94 355.0
32 TraesCS3A01G180200 chr6A 91.406 256 17 5 3259 3509 36403866 36403611 2.640000e-91 346.0
33 TraesCS3A01G180200 chr7A 90.458 262 21 4 3259 3516 515222311 515222572 3.410000e-90 342.0
34 TraesCS3A01G180200 chr6B 89.691 97 8 2 1788 1883 147056480 147056575 4.830000e-24 122.0


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 TraesCS3A01G180200 chr3A 208220264 208223829 3565 False 6586.000000 6586 100.000000 1 3566 1 chr3A.!!$F1 3565
1 TraesCS3A01G180200 chr3A 208085535 208090577 5042 True 591.200000 1072 87.547800 669 2607 5 chr3A.!!$R1 1938
2 TraesCS3A01G180200 chr3D 170657691 170660806 3115 False 1938.500000 2294 90.374000 3 2980 2 chr3D.!!$F1 2977
3 TraesCS3A01G180200 chr3D 170557307 170558813 1506 True 761.500000 1098 91.906000 964 2564 2 chr3D.!!$R1 1600
4 TraesCS3A01G180200 chr3D 170563610 170565233 1623 True 475.666667 761 89.198333 927 2605 3 chr3D.!!$R2 1678
5 TraesCS3A01G180200 chr3B 246127149 246130646 3497 False 769.300000 1594 92.055600 337 3204 5 chr3B.!!$F3 2867
6 TraesCS3A01G180200 chr3B 246146565 246147146 581 False 693.000000 693 88.144000 1977 2558 1 chr3B.!!$F2 581
7 TraesCS3A01G180200 chr3B 245963293 245970586 7293 True 587.600000 1086 87.505800 705 2607 5 chr3B.!!$R1 1902

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
906 6249 0.314302 ACTCCGTGTTCACCTCTTCG 59.686 55.0 0.00 0.0 0.00 3.79 F
1598 7211 0.037697 TAACTCGACGCATGTGCCTT 60.038 50.0 6.08 0.0 37.91 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 7547 0.733150 GGCGGGAATAGAACTGTTGC 59.267 55.0 0.0 0.0 0.0 4.17 R
3155 9182 0.251787 ATGAAGTGGTGGGGCTTTCC 60.252 55.0 0.0 0.0 0.0 3.13 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
69 70 3.551485 TGTACATCTCACATCAAATCGCG 59.449 43.478 0.00 0.00 0.00 5.87
74 75 3.325870 TCTCACATCAAATCGCGTTTCT 58.674 40.909 5.77 0.00 0.00 2.52
75 76 4.490743 TCTCACATCAAATCGCGTTTCTA 58.509 39.130 5.77 0.00 0.00 2.10
77 78 3.062099 TCACATCAAATCGCGTTTCTAGC 59.938 43.478 5.77 0.00 0.00 3.42
78 79 3.000041 ACATCAAATCGCGTTTCTAGCA 59.000 40.909 5.77 0.00 34.19 3.49
79 80 3.181520 ACATCAAATCGCGTTTCTAGCAC 60.182 43.478 5.77 0.00 34.19 4.40
81 82 3.000041 TCAAATCGCGTTTCTAGCACAT 59.000 40.909 5.77 0.00 34.19 3.21
82 83 3.093574 CAAATCGCGTTTCTAGCACATG 58.906 45.455 5.77 0.00 34.19 3.21
84 85 1.067693 TCGCGTTTCTAGCACATGTG 58.932 50.000 21.83 21.83 34.19 3.21
142 147 0.948678 CGAAGCCCGAGAACCAAAAA 59.051 50.000 0.00 0.00 41.76 1.94
143 148 1.539827 CGAAGCCCGAGAACCAAAAAT 59.460 47.619 0.00 0.00 41.76 1.82
176 182 6.918022 GCTGCTTGTCACTTGTTACTTTTATT 59.082 34.615 0.00 0.00 0.00 1.40
177 183 8.073768 GCTGCTTGTCACTTGTTACTTTTATTA 58.926 33.333 0.00 0.00 0.00 0.98
178 184 9.599322 CTGCTTGTCACTTGTTACTTTTATTAG 57.401 33.333 0.00 0.00 0.00 1.73
179 185 9.116067 TGCTTGTCACTTGTTACTTTTATTAGT 57.884 29.630 0.00 0.00 0.00 2.24
199 205 1.148949 TGCATGTGTGTCTGCCTGT 59.851 52.632 0.00 0.00 37.59 4.00
200 206 0.466007 TGCATGTGTGTCTGCCTGTT 60.466 50.000 0.00 0.00 37.59 3.16
203 209 1.265095 CATGTGTGTCTGCCTGTTGTC 59.735 52.381 0.00 0.00 0.00 3.18
239 245 8.678798 AGTTAAAAGGCAATATGGATATACCCT 58.321 33.333 0.00 0.00 38.00 4.34
243 249 3.555966 GCAATATGGATATACCCTGGGC 58.444 50.000 14.08 0.00 38.00 5.36
248 254 1.133104 TGGATATACCCTGGGCGTACA 60.133 52.381 14.08 0.00 38.00 2.90
264 270 6.481976 TGGGCGTACAAAAGTATAATCATGAG 59.518 38.462 0.09 0.00 0.00 2.90
308 314 7.167635 GTGATGATTCTACGATAAGAGCGAAAA 59.832 37.037 0.00 0.00 0.00 2.29
312 318 6.627690 TTCTACGATAAGAGCGAAAACAAG 57.372 37.500 0.00 0.00 0.00 3.16
313 319 3.724295 ACGATAAGAGCGAAAACAAGC 57.276 42.857 0.00 0.00 0.00 4.01
314 320 2.092211 ACGATAAGAGCGAAAACAAGCG 59.908 45.455 0.00 0.00 38.61 4.68
316 322 2.941891 TAAGAGCGAAAACAAGCGTG 57.058 45.000 0.00 0.00 38.61 5.34
318 324 2.052237 AGCGAAAACAAGCGTGCG 60.052 55.556 0.00 0.00 38.61 5.34
319 325 2.351888 GCGAAAACAAGCGTGCGT 60.352 55.556 0.00 0.00 0.00 5.24
320 326 1.937362 GCGAAAACAAGCGTGCGTT 60.937 52.632 0.00 0.00 0.00 4.84
330 336 1.372582 AGCGTGCGTTGAATGATGAT 58.627 45.000 0.00 0.00 0.00 2.45
331 337 1.739466 AGCGTGCGTTGAATGATGATT 59.261 42.857 0.00 0.00 0.00 2.57
332 338 2.935849 AGCGTGCGTTGAATGATGATTA 59.064 40.909 0.00 0.00 0.00 1.75
334 340 4.749598 AGCGTGCGTTGAATGATGATTATA 59.250 37.500 0.00 0.00 0.00 0.98
335 341 4.840772 GCGTGCGTTGAATGATGATTATAC 59.159 41.667 0.00 0.00 0.00 1.47
375 381 0.994247 TGTGTTGGATGATGGCTCCT 59.006 50.000 0.00 0.00 33.69 3.69
376 382 1.065199 TGTGTTGGATGATGGCTCCTC 60.065 52.381 0.00 0.00 33.69 3.71
377 383 0.548031 TGTTGGATGATGGCTCCTCC 59.452 55.000 0.00 0.00 36.88 4.30
482 600 8.801882 TGATATGTGGTATATATCGTCACTCA 57.198 34.615 11.65 6.82 39.34 3.41
483 601 8.674607 TGATATGTGGTATATATCGTCACTCAC 58.325 37.037 11.65 0.00 39.34 3.51
505 623 2.273179 ACGTGTTGCTCGAGGCCTA 61.273 57.895 15.58 0.00 40.92 3.93
531 649 3.890250 TTGGCCCGGGGGTTAAAGC 62.890 63.158 25.28 4.27 37.65 3.51
535 653 2.124860 CCGGGGGTTAAAGCGAGG 60.125 66.667 0.00 0.00 0.00 4.63
556 674 4.338400 AGGCATGTGATGAAATGACAGATG 59.662 41.667 0.00 0.00 45.46 2.90
643 765 1.627864 TGCACACTGGCAGAGTAGTA 58.372 50.000 23.66 10.81 39.25 1.82
648 770 4.011023 CACACTGGCAGAGTAGTAGTAGT 58.989 47.826 23.66 0.88 31.73 2.73
811 6135 1.407936 CATCTCACCATCCGTCCTCT 58.592 55.000 0.00 0.00 0.00 3.69
892 6235 3.306780 CCCTGCTATATAAACCCACTCCG 60.307 52.174 0.00 0.00 0.00 4.63
906 6249 0.314302 ACTCCGTGTTCACCTCTTCG 59.686 55.000 0.00 0.00 0.00 3.79
1114 6478 0.038892 GTTCCCGCAGTTCTACGACA 60.039 55.000 0.00 0.00 0.00 4.35
1274 6857 4.033932 TGTGCATTTTATGTGCTACTAGCG 59.966 41.667 3.59 0.00 46.26 4.26
1293 6877 2.735762 GCGCTCTTACCTCTTCGAACAT 60.736 50.000 0.00 0.00 0.00 2.71
1404 6988 3.342926 ACTCTAGGAGCATGGAGGAAT 57.657 47.619 0.00 0.00 32.04 3.01
1405 6989 3.238597 ACTCTAGGAGCATGGAGGAATC 58.761 50.000 0.00 0.00 32.04 2.52
1441 7031 4.298332 GCAAACTGTTTAACCAGTGATGG 58.702 43.478 6.41 0.00 44.74 3.51
1443 7033 3.154827 ACTGTTTAACCAGTGATGGGG 57.845 47.619 4.67 0.00 43.86 4.96
1459 7049 1.343069 GGGGTGAGATAGCCTACCTG 58.657 60.000 1.86 0.00 46.40 4.00
1513 7106 2.969238 GGTGGCGGCATGATCGAG 60.969 66.667 17.19 0.00 0.00 4.04
1514 7107 2.202932 GTGGCGGCATGATCGAGT 60.203 61.111 17.19 0.00 0.00 4.18
1517 7110 1.953138 GGCGGCATGATCGAGTCAG 60.953 63.158 3.07 0.00 40.92 3.51
1598 7211 0.037697 TAACTCGACGCATGTGCCTT 60.038 50.000 6.08 0.00 37.91 4.35
1599 7212 1.291877 AACTCGACGCATGTGCCTTC 61.292 55.000 6.08 0.00 37.91 3.46
1600 7213 1.446792 CTCGACGCATGTGCCTTCT 60.447 57.895 6.08 0.00 37.91 2.85
1602 7215 2.456119 CGACGCATGTGCCTTCTCC 61.456 63.158 6.08 0.00 37.91 3.71
1603 7216 2.045926 ACGCATGTGCCTTCTCCC 60.046 61.111 6.08 0.00 37.91 4.30
1604 7217 2.270205 CGCATGTGCCTTCTCCCT 59.730 61.111 0.00 0.00 37.91 4.20
1605 7218 1.264749 ACGCATGTGCCTTCTCCCTA 61.265 55.000 6.08 0.00 37.91 3.53
1606 7219 0.811616 CGCATGTGCCTTCTCCCTAC 60.812 60.000 0.00 0.00 37.91 3.18
1607 7220 0.543749 GCATGTGCCTTCTCCCTACT 59.456 55.000 0.00 0.00 34.31 2.57
1652 7265 2.697431 TTTTCATGTGTGCGCCTAAC 57.303 45.000 4.18 0.31 0.00 2.34
1653 7266 0.878416 TTTCATGTGTGCGCCTAACC 59.122 50.000 4.18 0.00 0.00 2.85
1655 7268 0.953471 TCATGTGTGCGCCTAACCAC 60.953 55.000 4.18 4.62 0.00 4.16
1780 7401 1.850345 TCCAACCCCAACAAGAACTCT 59.150 47.619 0.00 0.00 0.00 3.24
1908 7529 2.418197 CCATCCTCGTATGTCACCGTTT 60.418 50.000 0.00 0.00 0.00 3.60
1909 7530 2.642139 TCCTCGTATGTCACCGTTTC 57.358 50.000 0.00 0.00 0.00 2.78
1910 7531 1.203052 TCCTCGTATGTCACCGTTTCC 59.797 52.381 0.00 0.00 0.00 3.13
1923 7547 1.877443 CCGTTTCCTAAACACCACCAG 59.123 52.381 3.68 0.00 41.44 4.00
1941 7565 1.398390 CAGCAACAGTTCTATTCCCGC 59.602 52.381 0.00 0.00 0.00 6.13
2560 8513 1.544314 GCAGGAGGCTCAACAACTTCT 60.544 52.381 17.69 0.00 40.25 2.85
2584 8537 9.840427 TCTACTAATTAAGTTGCTGAAAAATGC 57.160 29.630 0.00 0.00 39.80 3.56
2594 8552 3.177487 GCTGAAAAATGCTAGCTGCTTC 58.823 45.455 17.23 13.08 43.37 3.86
2605 8563 3.304928 GCTAGCTGCTTCATTTGTGTGTT 60.305 43.478 7.79 0.00 38.95 3.32
2606 8564 3.088194 AGCTGCTTCATTTGTGTGTTG 57.912 42.857 0.00 0.00 0.00 3.33
2608 8566 2.129607 CTGCTTCATTTGTGTGTTGCC 58.870 47.619 0.00 0.00 0.00 4.52
2610 8568 2.168106 TGCTTCATTTGTGTGTTGCCTT 59.832 40.909 0.00 0.00 0.00 4.35
2611 8569 2.540931 GCTTCATTTGTGTGTTGCCTTG 59.459 45.455 0.00 0.00 0.00 3.61
2612 8570 3.737663 GCTTCATTTGTGTGTTGCCTTGA 60.738 43.478 0.00 0.00 0.00 3.02
2613 8571 4.624015 CTTCATTTGTGTGTTGCCTTGAT 58.376 39.130 0.00 0.00 0.00 2.57
2714 8691 5.535333 CCCCAACTTCATAATTGATCATGC 58.465 41.667 0.00 0.00 0.00 4.06
2756 8733 5.290386 ACAAGAATCGATCGGATCTTAACC 58.710 41.667 25.40 2.21 33.02 2.85
2758 8735 6.264744 ACAAGAATCGATCGGATCTTAACCTA 59.735 38.462 25.40 2.31 33.02 3.08
2829 8820 1.669440 GACTACCGTGGCAGTTGGA 59.331 57.895 7.30 0.00 0.00 3.53
2969 8980 7.508687 AGCATATGTGTCATCATGGTTAGTAA 58.491 34.615 4.29 0.00 0.00 2.24
3021 9032 2.356382 TCGTTTGTTTGCTGGTTAGGTG 59.644 45.455 0.00 0.00 0.00 4.00
3035 9046 2.051334 TAGGTGGGTAACATGCATGC 57.949 50.000 26.53 11.82 39.74 4.06
3036 9047 0.039472 AGGTGGGTAACATGCATGCA 59.961 50.000 26.53 25.04 39.74 3.96
3037 9048 1.113788 GGTGGGTAACATGCATGCAT 58.886 50.000 27.46 27.46 37.08 3.96
3089 9100 4.222847 GCCGGCCGGTCTTCCTAG 62.223 72.222 42.53 16.82 37.65 3.02
3090 9101 3.537874 CCGGCCGGTCTTCCTAGG 61.538 72.222 36.64 6.12 0.00 3.02
3091 9102 2.758737 CGGCCGGTCTTCCTAGGT 60.759 66.667 20.10 0.00 0.00 3.08
3092 9103 2.783288 CGGCCGGTCTTCCTAGGTC 61.783 68.421 20.10 0.00 0.00 3.85
3112 9123 3.125316 GTCGGTCAAGGTAGCAATCAAAG 59.875 47.826 0.00 0.00 0.00 2.77
3115 9126 4.215399 CGGTCAAGGTAGCAATCAAAGAAA 59.785 41.667 0.00 0.00 0.00 2.52
3124 9135 5.368256 AGCAATCAAAGAAACTAGTGCTG 57.632 39.130 0.00 0.00 39.50 4.41
3132 9159 3.996480 AGAAACTAGTGCTGAGGTGAAC 58.004 45.455 0.00 0.00 0.00 3.18
3155 9182 3.337889 CGTGCCGACCACACACAG 61.338 66.667 6.91 0.00 44.91 3.66
3204 9271 2.365617 ACTGATCGGACCCACATGATAC 59.634 50.000 9.00 0.00 0.00 2.24
3205 9272 2.630098 CTGATCGGACCCACATGATACT 59.370 50.000 0.00 0.00 0.00 2.12
3206 9273 2.628178 TGATCGGACCCACATGATACTC 59.372 50.000 0.00 0.00 0.00 2.59
3207 9274 2.454336 TCGGACCCACATGATACTCT 57.546 50.000 0.00 0.00 0.00 3.24
3208 9275 2.747177 TCGGACCCACATGATACTCTT 58.253 47.619 0.00 0.00 0.00 2.85
3209 9276 3.104512 TCGGACCCACATGATACTCTTT 58.895 45.455 0.00 0.00 0.00 2.52
3210 9277 3.517901 TCGGACCCACATGATACTCTTTT 59.482 43.478 0.00 0.00 0.00 2.27
3211 9278 3.623060 CGGACCCACATGATACTCTTTTG 59.377 47.826 0.00 0.00 0.00 2.44
3212 9279 3.378427 GGACCCACATGATACTCTTTTGC 59.622 47.826 0.00 0.00 0.00 3.68
3213 9280 4.009675 GACCCACATGATACTCTTTTGCA 58.990 43.478 0.00 0.00 0.00 4.08
3214 9281 4.603131 ACCCACATGATACTCTTTTGCAT 58.397 39.130 0.00 0.00 0.00 3.96
3215 9282 4.400251 ACCCACATGATACTCTTTTGCATG 59.600 41.667 0.00 0.00 41.44 4.06
3216 9283 4.357142 CCACATGATACTCTTTTGCATGC 58.643 43.478 11.82 11.82 39.82 4.06
3217 9284 4.142337 CCACATGATACTCTTTTGCATGCA 60.142 41.667 18.46 18.46 39.82 3.96
3218 9285 5.034797 CACATGATACTCTTTTGCATGCAG 58.965 41.667 21.50 11.44 39.82 4.41
3219 9286 4.945543 ACATGATACTCTTTTGCATGCAGA 59.054 37.500 21.50 14.47 39.82 4.26
3220 9287 5.416639 ACATGATACTCTTTTGCATGCAGAA 59.583 36.000 21.50 21.29 39.82 3.02
3221 9288 5.963176 TGATACTCTTTTGCATGCAGAAA 57.037 34.783 22.39 20.86 0.00 2.52
3222 9289 5.946298 TGATACTCTTTTGCATGCAGAAAG 58.054 37.500 29.64 29.64 0.00 2.62
3223 9290 3.655276 ACTCTTTTGCATGCAGAAAGG 57.345 42.857 31.86 27.17 32.62 3.11
3224 9291 3.225104 ACTCTTTTGCATGCAGAAAGGA 58.775 40.909 31.86 24.59 32.62 3.36
3225 9292 3.638160 ACTCTTTTGCATGCAGAAAGGAA 59.362 39.130 31.86 22.25 32.62 3.36
3226 9293 4.099881 ACTCTTTTGCATGCAGAAAGGAAA 59.900 37.500 31.86 23.64 32.62 3.13
3227 9294 5.021033 TCTTTTGCATGCAGAAAGGAAAA 57.979 34.783 31.86 23.14 32.62 2.29
3228 9295 5.426504 TCTTTTGCATGCAGAAAGGAAAAA 58.573 33.333 31.86 22.64 33.32 1.94
3229 9296 5.524646 TCTTTTGCATGCAGAAAGGAAAAAG 59.475 36.000 31.86 27.70 33.32 2.27
3230 9297 3.389925 TGCATGCAGAAAGGAAAAAGG 57.610 42.857 18.46 0.00 0.00 3.11
3231 9298 2.964464 TGCATGCAGAAAGGAAAAAGGA 59.036 40.909 18.46 0.00 0.00 3.36
3232 9299 3.006110 TGCATGCAGAAAGGAAAAAGGAG 59.994 43.478 18.46 0.00 0.00 3.69
3233 9300 3.006217 GCATGCAGAAAGGAAAAAGGAGT 59.994 43.478 14.21 0.00 0.00 3.85
3234 9301 4.218417 GCATGCAGAAAGGAAAAAGGAGTA 59.782 41.667 14.21 0.00 0.00 2.59
3235 9302 5.703876 CATGCAGAAAGGAAAAAGGAGTAC 58.296 41.667 0.00 0.00 0.00 2.73
3236 9303 4.142038 TGCAGAAAGGAAAAAGGAGTACC 58.858 43.478 0.00 0.00 0.00 3.34
3237 9304 4.142038 GCAGAAAGGAAAAAGGAGTACCA 58.858 43.478 0.00 0.00 38.94 3.25
3238 9305 4.767409 GCAGAAAGGAAAAAGGAGTACCAT 59.233 41.667 0.00 0.00 38.94 3.55
3239 9306 5.335976 GCAGAAAGGAAAAAGGAGTACCATG 60.336 44.000 0.00 0.00 38.94 3.66
3240 9307 4.767409 AGAAAGGAAAAAGGAGTACCATGC 59.233 41.667 0.00 0.00 38.94 4.06
3241 9308 3.806949 AGGAAAAAGGAGTACCATGCA 57.193 42.857 0.00 0.00 38.94 3.96
3242 9309 4.322057 AGGAAAAAGGAGTACCATGCAT 57.678 40.909 0.00 0.00 38.94 3.96
3243 9310 4.677182 AGGAAAAAGGAGTACCATGCATT 58.323 39.130 0.00 0.00 38.94 3.56
3244 9311 5.086621 AGGAAAAAGGAGTACCATGCATTT 58.913 37.500 0.00 0.00 38.94 2.32
3245 9312 6.252995 AGGAAAAAGGAGTACCATGCATTTA 58.747 36.000 0.00 0.00 38.94 1.40
3246 9313 6.723977 AGGAAAAAGGAGTACCATGCATTTAA 59.276 34.615 0.00 0.00 38.94 1.52
3247 9314 6.811665 GGAAAAAGGAGTACCATGCATTTAAC 59.188 38.462 0.00 0.00 38.94 2.01
3248 9315 6.909550 AAAAGGAGTACCATGCATTTAACA 57.090 33.333 0.00 0.00 38.94 2.41
3249 9316 6.909550 AAAGGAGTACCATGCATTTAACAA 57.090 33.333 0.00 0.00 38.94 2.83
3250 9317 6.515272 AAGGAGTACCATGCATTTAACAAG 57.485 37.500 0.00 0.00 38.94 3.16
3251 9318 4.399303 AGGAGTACCATGCATTTAACAAGC 59.601 41.667 0.00 0.00 38.94 4.01
3252 9319 4.157656 GGAGTACCATGCATTTAACAAGCA 59.842 41.667 0.00 0.00 43.14 3.91
3253 9320 5.059404 AGTACCATGCATTTAACAAGCAC 57.941 39.130 0.00 0.00 41.60 4.40
3254 9321 4.766891 AGTACCATGCATTTAACAAGCACT 59.233 37.500 0.00 0.00 41.60 4.40
3255 9322 5.943416 AGTACCATGCATTTAACAAGCACTA 59.057 36.000 0.00 0.00 41.60 2.74
3256 9323 5.314923 ACCATGCATTTAACAAGCACTAG 57.685 39.130 0.00 0.00 41.60 2.57
3257 9324 4.158394 ACCATGCATTTAACAAGCACTAGG 59.842 41.667 0.00 0.00 41.60 3.02
3258 9325 4.158394 CCATGCATTTAACAAGCACTAGGT 59.842 41.667 0.00 0.00 41.60 3.08
3259 9326 5.356751 CCATGCATTTAACAAGCACTAGGTA 59.643 40.000 0.00 0.00 41.60 3.08
3260 9327 5.873179 TGCATTTAACAAGCACTAGGTAC 57.127 39.130 0.00 0.00 32.55 3.34
3261 9328 5.556915 TGCATTTAACAAGCACTAGGTACT 58.443 37.500 0.00 0.00 36.31 2.73
3262 9329 5.642063 TGCATTTAACAAGCACTAGGTACTC 59.358 40.000 0.00 0.00 34.49 2.59
3263 9330 5.064834 GCATTTAACAAGCACTAGGTACTCC 59.935 44.000 0.00 0.00 41.75 3.85
3264 9331 4.813750 TTAACAAGCACTAGGTACTCCC 57.186 45.455 0.00 0.00 41.75 4.30
3266 9333 2.458620 ACAAGCACTAGGTACTCCCTC 58.541 52.381 0.00 0.00 44.81 4.30
3267 9334 1.757699 CAAGCACTAGGTACTCCCTCC 59.242 57.143 0.00 0.00 44.81 4.30
3268 9335 0.106619 AGCACTAGGTACTCCCTCCG 60.107 60.000 0.00 0.00 44.81 4.63
3269 9336 0.395448 GCACTAGGTACTCCCTCCGT 60.395 60.000 0.00 0.00 44.81 4.69
3270 9337 1.959028 GCACTAGGTACTCCCTCCGTT 60.959 57.143 0.00 0.00 44.81 4.44
3271 9338 2.454538 CACTAGGTACTCCCTCCGTTT 58.545 52.381 0.00 0.00 44.81 3.60
3272 9339 2.830321 CACTAGGTACTCCCTCCGTTTT 59.170 50.000 0.00 0.00 44.81 2.43
3273 9340 3.260128 CACTAGGTACTCCCTCCGTTTTT 59.740 47.826 0.00 0.00 44.81 1.94
3295 9362 6.909550 TTTTGTCCATGTATTAGCTTTGGT 57.090 33.333 0.00 0.00 0.00 3.67
3296 9363 6.509418 TTTGTCCATGTATTAGCTTTGGTC 57.491 37.500 0.00 0.00 0.00 4.02
3297 9364 5.172687 TGTCCATGTATTAGCTTTGGTCA 57.827 39.130 0.00 0.00 0.00 4.02
3298 9365 5.565509 TGTCCATGTATTAGCTTTGGTCAA 58.434 37.500 0.00 0.00 0.00 3.18
3299 9366 6.007076 TGTCCATGTATTAGCTTTGGTCAAA 58.993 36.000 0.00 0.00 0.00 2.69
3458 9525 9.589111 TTTTTCATAAACTTGGTCAAACCTTAC 57.411 29.630 0.00 0.00 39.58 2.34
3459 9526 6.548441 TCATAAACTTGGTCAAACCTTACG 57.452 37.500 0.00 0.00 39.58 3.18
3460 9527 6.289834 TCATAAACTTGGTCAAACCTTACGA 58.710 36.000 0.00 0.00 39.58 3.43
3461 9528 6.766944 TCATAAACTTGGTCAAACCTTACGAA 59.233 34.615 0.00 0.00 39.58 3.85
3462 9529 5.494632 AAACTTGGTCAAACCTTACGAAG 57.505 39.130 0.00 0.00 39.58 3.79
3463 9530 4.146745 ACTTGGTCAAACCTTACGAAGT 57.853 40.909 0.00 0.00 41.92 3.01
3464 9531 4.520179 ACTTGGTCAAACCTTACGAAGTT 58.480 39.130 0.00 0.00 40.39 2.66
3465 9532 4.945543 ACTTGGTCAAACCTTACGAAGTTT 59.054 37.500 0.00 0.00 40.39 2.66
3466 9533 4.886247 TGGTCAAACCTTACGAAGTTTG 57.114 40.909 8.87 8.87 40.06 2.93
3467 9534 4.515361 TGGTCAAACCTTACGAAGTTTGA 58.485 39.130 12.83 12.83 40.06 2.69
3523 9590 8.874744 AAAAACGAAGGAAGTAGATAGATAGC 57.125 34.615 0.00 0.00 0.00 2.97
3524 9591 6.578163 AACGAAGGAAGTAGATAGATAGCC 57.422 41.667 0.00 0.00 0.00 3.93
3525 9592 5.632118 ACGAAGGAAGTAGATAGATAGCCA 58.368 41.667 0.00 0.00 0.00 4.75
3526 9593 6.069331 ACGAAGGAAGTAGATAGATAGCCAA 58.931 40.000 0.00 0.00 0.00 4.52
3527 9594 6.016108 ACGAAGGAAGTAGATAGATAGCCAAC 60.016 42.308 0.00 0.00 0.00 3.77
3528 9595 6.207810 CGAAGGAAGTAGATAGATAGCCAACT 59.792 42.308 0.00 0.00 0.00 3.16
3529 9596 7.255660 CGAAGGAAGTAGATAGATAGCCAACTT 60.256 40.741 0.00 0.00 0.00 2.66
3530 9597 9.080097 GAAGGAAGTAGATAGATAGCCAACTTA 57.920 37.037 0.00 0.00 0.00 2.24
3531 9598 9.608718 AAGGAAGTAGATAGATAGCCAACTTAT 57.391 33.333 0.00 0.00 0.00 1.73
3532 9599 9.608718 AGGAAGTAGATAGATAGCCAACTTATT 57.391 33.333 0.00 0.00 0.00 1.40
3533 9600 9.646427 GGAAGTAGATAGATAGCCAACTTATTG 57.354 37.037 0.00 0.00 35.40 1.90
3534 9601 9.145865 GAAGTAGATAGATAGCCAACTTATTGC 57.854 37.037 0.00 0.00 34.17 3.56
3535 9602 8.195165 AGTAGATAGATAGCCAACTTATTGCA 57.805 34.615 0.00 0.00 34.17 4.08
3536 9603 8.651389 AGTAGATAGATAGCCAACTTATTGCAA 58.349 33.333 0.00 0.00 34.17 4.08
3537 9604 7.976135 AGATAGATAGCCAACTTATTGCAAG 57.024 36.000 4.94 0.00 34.17 4.01
3538 9605 6.939163 AGATAGATAGCCAACTTATTGCAAGG 59.061 38.462 4.94 0.00 34.17 3.61
3539 9606 4.210331 AGATAGCCAACTTATTGCAAGGG 58.790 43.478 4.94 0.00 34.17 3.95
3540 9607 2.309136 AGCCAACTTATTGCAAGGGT 57.691 45.000 4.94 1.79 34.17 4.34
3541 9608 1.895131 AGCCAACTTATTGCAAGGGTG 59.105 47.619 4.94 6.60 34.17 4.61
3542 9609 1.892474 GCCAACTTATTGCAAGGGTGA 59.108 47.619 4.94 0.00 34.17 4.02
3543 9610 2.094545 GCCAACTTATTGCAAGGGTGAG 60.095 50.000 4.94 0.00 34.17 3.51
3544 9611 2.094545 CCAACTTATTGCAAGGGTGAGC 60.095 50.000 4.94 0.00 34.17 4.26
3545 9612 2.557924 CAACTTATTGCAAGGGTGAGCA 59.442 45.455 4.94 0.00 39.32 4.26
3549 9616 3.435846 TTGCAAGGGTGAGCAATCA 57.564 47.368 0.00 0.00 44.98 2.57
3550 9617 1.927487 TTGCAAGGGTGAGCAATCAT 58.073 45.000 0.00 0.00 44.98 2.45
3551 9618 2.804986 TGCAAGGGTGAGCAATCATA 57.195 45.000 0.00 0.00 37.90 2.15
3552 9619 2.368439 TGCAAGGGTGAGCAATCATAC 58.632 47.619 0.00 0.00 37.90 2.39
3553 9620 1.678101 GCAAGGGTGAGCAATCATACC 59.322 52.381 0.00 0.00 0.00 2.73
3554 9621 2.684927 GCAAGGGTGAGCAATCATACCT 60.685 50.000 0.00 0.00 33.33 3.08
3555 9622 3.624777 CAAGGGTGAGCAATCATACCTT 58.375 45.455 9.87 9.87 39.06 3.50
3556 9623 3.567478 AGGGTGAGCAATCATACCTTC 57.433 47.619 0.00 0.00 33.71 3.46
3557 9624 3.118531 AGGGTGAGCAATCATACCTTCT 58.881 45.455 0.00 0.00 33.71 2.85
3558 9625 3.135530 AGGGTGAGCAATCATACCTTCTC 59.864 47.826 0.00 0.00 33.71 2.87
3559 9626 3.118261 GGGTGAGCAATCATACCTTCTCA 60.118 47.826 0.00 0.00 33.71 3.27
3560 9627 4.445448 GGGTGAGCAATCATACCTTCTCAT 60.445 45.833 0.00 0.00 33.80 2.90
3561 9628 4.514441 GGTGAGCAATCATACCTTCTCATG 59.486 45.833 0.00 0.00 33.80 3.07
3562 9629 4.024218 GTGAGCAATCATACCTTCTCATGC 60.024 45.833 0.00 0.00 33.80 4.06
3563 9630 4.132336 GAGCAATCATACCTTCTCATGCA 58.868 43.478 0.00 0.00 35.11 3.96
3564 9631 4.726583 AGCAATCATACCTTCTCATGCAT 58.273 39.130 0.00 0.00 35.11 3.96
3565 9632 4.760715 AGCAATCATACCTTCTCATGCATC 59.239 41.667 0.00 0.00 35.11 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.107601 AGTGAATAGGGCAAGTGCTAGA 58.892 45.455 2.85 0.00 41.70 2.43
1 2 3.550437 AGTGAATAGGGCAAGTGCTAG 57.450 47.619 2.85 0.00 41.70 3.42
105 110 1.173913 CGAGGAAGCCCCGAATTTTT 58.826 50.000 0.00 0.00 40.87 1.94
142 147 1.203441 TGACAAGCAGCAGGGAGGAT 61.203 55.000 0.00 0.00 0.00 3.24
143 148 1.842920 TGACAAGCAGCAGGGAGGA 60.843 57.895 0.00 0.00 0.00 3.71
176 182 1.511850 GCAGACACACATGCACACTA 58.488 50.000 0.00 0.00 42.11 2.74
177 183 1.168407 GGCAGACACACATGCACACT 61.168 55.000 0.00 0.00 44.37 3.55
178 184 1.168407 AGGCAGACACACATGCACAC 61.168 55.000 0.00 0.00 44.37 3.82
179 185 1.148949 AGGCAGACACACATGCACA 59.851 52.632 0.00 0.00 44.37 4.57
181 187 0.466007 AACAGGCAGACACACATGCA 60.466 50.000 0.00 0.00 44.37 3.96
182 188 0.039798 CAACAGGCAGACACACATGC 60.040 55.000 0.00 0.00 41.80 4.06
199 205 5.810074 GCCTTTTAACTTTCTTGCTTGACAA 59.190 36.000 0.00 0.00 36.62 3.18
200 206 5.105554 TGCCTTTTAACTTTCTTGCTTGACA 60.106 36.000 0.00 0.00 0.00 3.58
203 209 6.849588 ATTGCCTTTTAACTTTCTTGCTTG 57.150 33.333 0.00 0.00 0.00 4.01
239 245 6.350103 TCATGATTATACTTTTGTACGCCCA 58.650 36.000 0.00 0.00 37.78 5.36
243 249 6.073222 GGGGCTCATGATTATACTTTTGTACG 60.073 42.308 0.00 0.00 37.78 3.67
248 254 4.104102 TCCGGGGCTCATGATTATACTTTT 59.896 41.667 0.00 0.00 0.00 2.27
264 270 0.463116 ACAATTCGTGTATCCGGGGC 60.463 55.000 0.00 0.00 39.29 5.80
308 314 0.874390 ATCATTCAACGCACGCTTGT 59.126 45.000 0.00 0.00 0.00 3.16
312 318 2.178474 AATCATCATTCAACGCACGC 57.822 45.000 0.00 0.00 0.00 5.34
313 319 6.215477 AGTATAATCATCATTCAACGCACG 57.785 37.500 0.00 0.00 0.00 5.34
316 322 9.887189 CGTATAAGTATAATCATCATTCAACGC 57.113 33.333 0.00 0.00 0.00 4.84
334 340 7.941238 ACACATACTACTGGGATACGTATAAGT 59.059 37.037 8.34 14.18 37.60 2.24
335 341 8.332996 ACACATACTACTGGGATACGTATAAG 57.667 38.462 8.34 9.16 37.60 1.73
375 381 1.302431 CATGGTGCGTTCCTGTGGA 60.302 57.895 0.00 0.00 0.00 4.02
376 382 2.981560 GCATGGTGCGTTCCTGTGG 61.982 63.158 0.00 0.00 31.71 4.17
377 383 2.562912 GCATGGTGCGTTCCTGTG 59.437 61.111 0.00 1.34 31.71 3.66
482 600 1.657487 CTCGAGCAACACGTGACGT 60.657 57.895 25.01 4.10 42.36 4.34
483 601 2.365068 CCTCGAGCAACACGTGACG 61.365 63.158 25.01 17.69 0.00 4.35
484 602 2.658707 GCCTCGAGCAACACGTGAC 61.659 63.158 25.01 11.19 42.97 3.67
505 623 2.603171 CCCGGGCCAACCATGTTT 60.603 61.111 8.08 0.00 40.22 2.83
524 642 2.677836 TCATCACATGCCTCGCTTTAAC 59.322 45.455 0.00 0.00 0.00 2.01
531 649 2.679336 TGTCATTTCATCACATGCCTCG 59.321 45.455 0.00 0.00 0.00 4.63
535 653 5.494632 TCATCTGTCATTTCATCACATGC 57.505 39.130 0.00 0.00 0.00 4.06
556 674 5.793952 CAGCTTCGATAATTGCAATATGCTC 59.206 40.000 13.39 6.40 45.31 4.26
643 765 6.824704 CCTAAAGAGTACAGAGTGCTACTACT 59.175 42.308 0.00 0.00 0.00 2.57
648 770 3.700038 GGCCTAAAGAGTACAGAGTGCTA 59.300 47.826 0.00 0.00 0.00 3.49
811 6135 2.356330 GGTTTCGAGAGAGAGGAGAGGA 60.356 54.545 0.00 0.00 43.69 3.71
892 6235 0.531974 TGGTGCGAAGAGGTGAACAC 60.532 55.000 0.00 0.00 0.00 3.32
906 6249 3.591835 CCGTGTTGTGGGTGGTGC 61.592 66.667 0.00 0.00 0.00 5.01
1268 6848 1.671845 CGAAGAGGTAAGAGCGCTAGT 59.328 52.381 11.50 3.13 0.00 2.57
1269 6849 1.941294 TCGAAGAGGTAAGAGCGCTAG 59.059 52.381 11.50 0.00 0.00 3.42
1274 6857 7.427214 AGTTATATGTTCGAAGAGGTAAGAGC 58.573 38.462 0.00 0.00 38.43 4.09
1293 6877 7.197071 AGAACATTTTGCACGTTGAGTTATA 57.803 32.000 0.00 0.00 0.00 0.98
1404 6988 6.420913 ACAGTTTGCCTAGAAAACTAGAGA 57.579 37.500 17.83 0.00 44.11 3.10
1405 6989 7.497925 AAACAGTTTGCCTAGAAAACTAGAG 57.502 36.000 17.83 11.47 44.11 2.43
1441 7031 0.682292 GCAGGTAGGCTATCTCACCC 59.318 60.000 3.79 0.00 0.00 4.61
1443 7033 3.397482 CAATGCAGGTAGGCTATCTCAC 58.603 50.000 3.79 0.73 34.04 3.51
1459 7049 2.103538 CGCTCACATGGGCAATGC 59.896 61.111 0.56 0.00 40.22 3.56
1513 7106 4.155462 TCAATCACGGTACTGACTACTGAC 59.845 45.833 9.17 0.00 35.49 3.51
1514 7107 4.329392 TCAATCACGGTACTGACTACTGA 58.671 43.478 9.17 1.26 35.49 3.41
1517 7110 6.474751 GGTTAATCAATCACGGTACTGACTAC 59.525 42.308 9.17 0.00 0.00 2.73
1598 7211 3.722627 AGTAGCACATAGGAGTAGGGAGA 59.277 47.826 0.00 0.00 0.00 3.71
1599 7212 3.823873 CAGTAGCACATAGGAGTAGGGAG 59.176 52.174 0.00 0.00 0.00 4.30
1600 7213 3.204606 ACAGTAGCACATAGGAGTAGGGA 59.795 47.826 0.00 0.00 0.00 4.20
1602 7215 6.320494 CTAACAGTAGCACATAGGAGTAGG 57.680 45.833 0.00 0.00 0.00 3.18
1652 7265 8.488651 AAGTTTATTTAGATTACGTGGAGTGG 57.511 34.615 0.00 0.00 0.00 4.00
1780 7401 1.682684 GACCTCGAAGCCCCTGAGA 60.683 63.158 0.00 0.00 31.31 3.27
1908 7529 1.213182 TGTTGCTGGTGGTGTTTAGGA 59.787 47.619 0.00 0.00 0.00 2.94
1909 7530 1.608590 CTGTTGCTGGTGGTGTTTAGG 59.391 52.381 0.00 0.00 0.00 2.69
1910 7531 2.297701 ACTGTTGCTGGTGGTGTTTAG 58.702 47.619 0.00 0.00 0.00 1.85
1923 7547 0.733150 GGCGGGAATAGAACTGTTGC 59.267 55.000 0.00 0.00 0.00 4.17
1941 7565 7.761249 GGTTCATTTCCATGTCAAATTAAGAGG 59.239 37.037 0.00 0.00 0.00 3.69
2583 8536 2.227388 ACACACAAATGAAGCAGCTAGC 59.773 45.455 6.62 6.62 46.19 3.42
2584 8537 4.224433 CAACACACAAATGAAGCAGCTAG 58.776 43.478 0.00 0.00 0.00 3.42
2594 8552 5.738118 AAAATCAAGGCAACACACAAATG 57.262 34.783 0.00 0.00 41.41 2.32
2605 8563 6.484364 AGAAAGGAAAGAAAAATCAAGGCA 57.516 33.333 0.00 0.00 0.00 4.75
2606 8564 7.280876 ACAAAGAAAGGAAAGAAAAATCAAGGC 59.719 33.333 0.00 0.00 0.00 4.35
2737 8714 6.094061 CCTTAGGTTAAGATCCGATCGATTC 58.906 44.000 18.66 12.66 38.02 2.52
2776 8753 1.614903 CCCTGACACAACAATGCATGT 59.385 47.619 0.00 0.00 46.82 3.21
2777 8754 1.887854 TCCCTGACACAACAATGCATG 59.112 47.619 0.00 0.00 0.00 4.06
2778 8755 2.291209 TCCCTGACACAACAATGCAT 57.709 45.000 0.00 0.00 0.00 3.96
2779 8756 2.064434 TTCCCTGACACAACAATGCA 57.936 45.000 0.00 0.00 0.00 3.96
2780 8757 4.989279 ATATTCCCTGACACAACAATGC 57.011 40.909 0.00 0.00 0.00 3.56
2845 8836 4.085733 CACCACCATCAAAATTACTCCCA 58.914 43.478 0.00 0.00 0.00 4.37
2969 8980 0.391263 GCCTGCCGCAGTAGTAGTTT 60.391 55.000 18.98 0.00 37.47 2.66
3035 9046 4.412933 CGTACTACGGCCCACATG 57.587 61.111 0.00 0.00 38.08 3.21
3089 9100 1.066430 TGATTGCTACCTTGACCGACC 60.066 52.381 0.00 0.00 0.00 4.79
3090 9101 2.380084 TGATTGCTACCTTGACCGAC 57.620 50.000 0.00 0.00 0.00 4.79
3091 9102 3.007506 TCTTTGATTGCTACCTTGACCGA 59.992 43.478 0.00 0.00 0.00 4.69
3092 9103 3.334691 TCTTTGATTGCTACCTTGACCG 58.665 45.455 0.00 0.00 0.00 4.79
3112 9123 3.067833 GGTTCACCTCAGCACTAGTTTC 58.932 50.000 0.00 0.00 0.00 2.78
3115 9126 1.717032 TGGTTCACCTCAGCACTAGT 58.283 50.000 0.00 0.00 36.82 2.57
3124 9135 2.690778 GCACGCCATGGTTCACCTC 61.691 63.158 14.67 0.00 36.82 3.85
3155 9182 0.251787 ATGAAGTGGTGGGGCTTTCC 60.252 55.000 0.00 0.00 0.00 3.13
3204 9271 3.928727 TCCTTTCTGCATGCAAAAGAG 57.071 42.857 33.25 26.84 32.89 2.85
3205 9272 4.669206 TTTCCTTTCTGCATGCAAAAGA 57.331 36.364 33.25 22.89 32.89 2.52
3206 9273 5.277634 CCTTTTTCCTTTCTGCATGCAAAAG 60.278 40.000 29.11 29.11 32.26 2.27
3207 9274 4.575645 CCTTTTTCCTTTCTGCATGCAAAA 59.424 37.500 22.88 20.90 0.00 2.44
3208 9275 4.128643 CCTTTTTCCTTTCTGCATGCAAA 58.871 39.130 22.88 13.16 0.00 3.68
3209 9276 3.387374 TCCTTTTTCCTTTCTGCATGCAA 59.613 39.130 22.88 10.06 0.00 4.08
3210 9277 2.964464 TCCTTTTTCCTTTCTGCATGCA 59.036 40.909 21.29 21.29 0.00 3.96
3211 9278 3.006217 ACTCCTTTTTCCTTTCTGCATGC 59.994 43.478 11.82 11.82 0.00 4.06
3212 9279 4.861102 ACTCCTTTTTCCTTTCTGCATG 57.139 40.909 0.00 0.00 0.00 4.06
3213 9280 4.767409 GGTACTCCTTTTTCCTTTCTGCAT 59.233 41.667 0.00 0.00 0.00 3.96
3214 9281 4.142038 GGTACTCCTTTTTCCTTTCTGCA 58.858 43.478 0.00 0.00 0.00 4.41
3215 9282 4.142038 TGGTACTCCTTTTTCCTTTCTGC 58.858 43.478 0.00 0.00 34.23 4.26
3216 9283 5.335976 GCATGGTACTCCTTTTTCCTTTCTG 60.336 44.000 0.00 0.00 34.23 3.02
3217 9284 4.767409 GCATGGTACTCCTTTTTCCTTTCT 59.233 41.667 0.00 0.00 34.23 2.52
3218 9285 4.522789 TGCATGGTACTCCTTTTTCCTTTC 59.477 41.667 0.00 0.00 34.23 2.62
3219 9286 4.479158 TGCATGGTACTCCTTTTTCCTTT 58.521 39.130 0.00 0.00 34.23 3.11
3220 9287 4.112634 TGCATGGTACTCCTTTTTCCTT 57.887 40.909 0.00 0.00 34.23 3.36
3221 9288 3.806949 TGCATGGTACTCCTTTTTCCT 57.193 42.857 0.00 0.00 34.23 3.36
3222 9289 5.405935 AAATGCATGGTACTCCTTTTTCC 57.594 39.130 0.00 0.00 34.23 3.13
3223 9290 7.375053 TGTTAAATGCATGGTACTCCTTTTTC 58.625 34.615 0.00 0.00 34.23 2.29
3224 9291 7.296628 TGTTAAATGCATGGTACTCCTTTTT 57.703 32.000 0.00 0.00 34.23 1.94
3225 9292 6.909550 TGTTAAATGCATGGTACTCCTTTT 57.090 33.333 0.00 0.00 34.23 2.27
3226 9293 6.572314 GCTTGTTAAATGCATGGTACTCCTTT 60.572 38.462 0.00 0.00 34.23 3.11
3227 9294 5.105756 GCTTGTTAAATGCATGGTACTCCTT 60.106 40.000 0.00 0.00 34.23 3.36
3228 9295 4.399303 GCTTGTTAAATGCATGGTACTCCT 59.601 41.667 0.00 0.00 34.23 3.69
3229 9296 4.157656 TGCTTGTTAAATGCATGGTACTCC 59.842 41.667 0.00 0.00 0.00 3.85
3230 9297 5.095490 GTGCTTGTTAAATGCATGGTACTC 58.905 41.667 0.00 0.00 39.00 2.59
3231 9298 4.766891 AGTGCTTGTTAAATGCATGGTACT 59.233 37.500 0.00 0.00 39.00 2.73
3232 9299 5.059404 AGTGCTTGTTAAATGCATGGTAC 57.941 39.130 0.00 0.00 39.00 3.34
3233 9300 5.356751 CCTAGTGCTTGTTAAATGCATGGTA 59.643 40.000 0.00 0.00 39.00 3.25
3234 9301 4.158394 CCTAGTGCTTGTTAAATGCATGGT 59.842 41.667 0.00 0.00 39.00 3.55
3235 9302 4.158394 ACCTAGTGCTTGTTAAATGCATGG 59.842 41.667 0.00 0.00 39.00 3.66
3236 9303 5.314923 ACCTAGTGCTTGTTAAATGCATG 57.685 39.130 0.00 0.00 39.00 4.06
3237 9304 6.180472 AGTACCTAGTGCTTGTTAAATGCAT 58.820 36.000 0.00 0.00 39.00 3.96
3238 9305 5.556915 AGTACCTAGTGCTTGTTAAATGCA 58.443 37.500 0.00 0.00 0.00 3.96
3239 9306 5.064834 GGAGTACCTAGTGCTTGTTAAATGC 59.935 44.000 0.00 0.00 0.00 3.56
3240 9307 5.585047 GGGAGTACCTAGTGCTTGTTAAATG 59.415 44.000 0.00 0.00 35.85 2.32
3241 9308 5.742063 GGGAGTACCTAGTGCTTGTTAAAT 58.258 41.667 0.00 0.00 35.85 1.40
3242 9309 5.156608 GGGAGTACCTAGTGCTTGTTAAA 57.843 43.478 0.00 0.00 35.85 1.52
3243 9310 4.813750 GGGAGTACCTAGTGCTTGTTAA 57.186 45.455 0.00 0.00 35.85 2.01
3271 9338 7.014711 TGACCAAAGCTAATACATGGACAAAAA 59.985 33.333 0.00 0.00 33.95 1.94
3272 9339 6.491745 TGACCAAAGCTAATACATGGACAAAA 59.508 34.615 0.00 0.00 33.95 2.44
3273 9340 6.007076 TGACCAAAGCTAATACATGGACAAA 58.993 36.000 0.00 0.00 33.95 2.83
3274 9341 5.565509 TGACCAAAGCTAATACATGGACAA 58.434 37.500 0.00 0.00 33.95 3.18
3275 9342 5.172687 TGACCAAAGCTAATACATGGACA 57.827 39.130 0.00 0.00 34.36 4.02
3276 9343 6.509418 TTTGACCAAAGCTAATACATGGAC 57.491 37.500 0.00 0.00 35.16 4.02
3277 9344 6.757897 CTTTGACCAAAGCTAATACATGGA 57.242 37.500 9.25 0.00 40.94 3.41
3432 9499 9.589111 GTAAGGTTTGACCAAGTTTATGAAAAA 57.411 29.630 0.00 0.00 41.95 1.94
3433 9500 7.916450 CGTAAGGTTTGACCAAGTTTATGAAAA 59.084 33.333 0.00 0.00 41.95 2.29
3434 9501 7.282675 TCGTAAGGTTTGACCAAGTTTATGAAA 59.717 33.333 0.00 0.00 41.95 2.69
3435 9502 6.766944 TCGTAAGGTTTGACCAAGTTTATGAA 59.233 34.615 0.00 0.00 41.95 2.57
3436 9503 6.289834 TCGTAAGGTTTGACCAAGTTTATGA 58.710 36.000 0.00 0.00 41.95 2.15
3437 9504 6.548441 TCGTAAGGTTTGACCAAGTTTATG 57.452 37.500 0.00 0.00 41.95 1.90
3438 9505 6.769341 ACTTCGTAAGGTTTGACCAAGTTTAT 59.231 34.615 0.00 0.00 41.95 1.40
3439 9506 6.114767 ACTTCGTAAGGTTTGACCAAGTTTA 58.885 36.000 0.00 0.00 41.95 2.01
3440 9507 4.945543 ACTTCGTAAGGTTTGACCAAGTTT 59.054 37.500 0.00 0.00 41.95 2.66
3441 9508 4.520179 ACTTCGTAAGGTTTGACCAAGTT 58.480 39.130 0.00 0.00 41.95 2.66
3442 9509 4.146745 ACTTCGTAAGGTTTGACCAAGT 57.853 40.909 0.00 0.00 41.95 3.16
3443 9510 5.494632 AAACTTCGTAAGGTTTGACCAAG 57.505 39.130 0.00 0.00 41.95 3.61
3497 9564 9.962783 GCTATCTATCTACTTCCTTCGTTTTTA 57.037 33.333 0.00 0.00 0.00 1.52
3498 9565 7.927092 GGCTATCTATCTACTTCCTTCGTTTTT 59.073 37.037 0.00 0.00 0.00 1.94
3499 9566 7.069578 TGGCTATCTATCTACTTCCTTCGTTTT 59.930 37.037 0.00 0.00 0.00 2.43
3500 9567 6.550108 TGGCTATCTATCTACTTCCTTCGTTT 59.450 38.462 0.00 0.00 0.00 3.60
3501 9568 6.069331 TGGCTATCTATCTACTTCCTTCGTT 58.931 40.000 0.00 0.00 0.00 3.85
3502 9569 5.632118 TGGCTATCTATCTACTTCCTTCGT 58.368 41.667 0.00 0.00 0.00 3.85
3503 9570 6.207810 AGTTGGCTATCTATCTACTTCCTTCG 59.792 42.308 0.00 0.00 0.00 3.79
3504 9571 7.533289 AGTTGGCTATCTATCTACTTCCTTC 57.467 40.000 0.00 0.00 0.00 3.46
3505 9572 7.922699 AAGTTGGCTATCTATCTACTTCCTT 57.077 36.000 0.00 0.00 0.00 3.36
3506 9573 9.608718 AATAAGTTGGCTATCTATCTACTTCCT 57.391 33.333 0.00 0.00 0.00 3.36
3507 9574 9.646427 CAATAAGTTGGCTATCTATCTACTTCC 57.354 37.037 0.00 0.00 0.00 3.46
3508 9575 9.145865 GCAATAAGTTGGCTATCTATCTACTTC 57.854 37.037 0.00 0.00 35.83 3.01
3509 9576 8.651389 TGCAATAAGTTGGCTATCTATCTACTT 58.349 33.333 0.00 0.00 35.83 2.24
3510 9577 8.195165 TGCAATAAGTTGGCTATCTATCTACT 57.805 34.615 0.00 0.00 35.83 2.57
3511 9578 8.833231 TTGCAATAAGTTGGCTATCTATCTAC 57.167 34.615 0.00 0.00 35.83 2.59
3512 9579 8.097038 CCTTGCAATAAGTTGGCTATCTATCTA 58.903 37.037 0.00 0.00 35.83 1.98
3513 9580 6.939163 CCTTGCAATAAGTTGGCTATCTATCT 59.061 38.462 0.00 0.00 35.83 1.98
3514 9581 6.150140 CCCTTGCAATAAGTTGGCTATCTATC 59.850 42.308 0.00 0.00 35.83 2.08
3515 9582 6.006449 CCCTTGCAATAAGTTGGCTATCTAT 58.994 40.000 0.00 0.00 35.83 1.98
3516 9583 5.104109 ACCCTTGCAATAAGTTGGCTATCTA 60.104 40.000 0.00 0.00 35.83 1.98
3517 9584 4.210331 CCCTTGCAATAAGTTGGCTATCT 58.790 43.478 0.00 0.00 35.83 1.98
3518 9585 3.954258 ACCCTTGCAATAAGTTGGCTATC 59.046 43.478 0.00 0.00 35.83 2.08
3519 9586 3.701040 CACCCTTGCAATAAGTTGGCTAT 59.299 43.478 0.00 0.00 35.83 2.97
3520 9587 3.088532 CACCCTTGCAATAAGTTGGCTA 58.911 45.455 0.00 0.00 35.83 3.93
3521 9588 1.895131 CACCCTTGCAATAAGTTGGCT 59.105 47.619 0.00 0.00 35.83 4.75
3522 9589 1.892474 TCACCCTTGCAATAAGTTGGC 59.108 47.619 0.00 0.00 35.83 4.52
3523 9590 2.094545 GCTCACCCTTGCAATAAGTTGG 60.095 50.000 0.00 0.00 35.83 3.77
3524 9591 2.557924 TGCTCACCCTTGCAATAAGTTG 59.442 45.455 0.00 0.00 36.15 3.16
3525 9592 2.875296 TGCTCACCCTTGCAATAAGTT 58.125 42.857 0.00 0.00 36.15 2.66
3526 9593 2.584835 TGCTCACCCTTGCAATAAGT 57.415 45.000 0.00 0.00 36.15 2.24
3532 9599 2.368439 GTATGATTGCTCACCCTTGCA 58.632 47.619 0.00 0.00 37.42 4.08
3533 9600 1.678101 GGTATGATTGCTCACCCTTGC 59.322 52.381 0.00 0.00 33.22 4.01
3534 9601 3.287867 AGGTATGATTGCTCACCCTTG 57.712 47.619 0.00 0.00 34.10 3.61
3535 9602 3.525199 AGAAGGTATGATTGCTCACCCTT 59.475 43.478 7.92 7.92 43.60 3.95
3536 9603 3.118531 AGAAGGTATGATTGCTCACCCT 58.881 45.455 0.00 0.00 37.58 4.34
3537 9604 3.118261 TGAGAAGGTATGATTGCTCACCC 60.118 47.826 0.00 0.00 33.22 4.61
3538 9605 4.142609 TGAGAAGGTATGATTGCTCACC 57.857 45.455 0.00 0.00 33.22 4.02
3539 9606 4.024218 GCATGAGAAGGTATGATTGCTCAC 60.024 45.833 0.00 0.00 35.49 3.51
3540 9607 4.132336 GCATGAGAAGGTATGATTGCTCA 58.868 43.478 0.00 0.00 36.88 4.26
3541 9608 4.132336 TGCATGAGAAGGTATGATTGCTC 58.868 43.478 0.00 0.00 0.00 4.26
3542 9609 4.160642 TGCATGAGAAGGTATGATTGCT 57.839 40.909 0.00 0.00 0.00 3.91
3543 9610 5.044428 GATGCATGAGAAGGTATGATTGC 57.956 43.478 2.46 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.