Multiple sequence alignment - TraesCS4D01G254200

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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 TraesCS4D01G254200 chr4D 100.000 3806 0 0 3908 7713 423379038 423382843 0.000000e+00 7029.0
1 TraesCS4D01G254200 chr4D 100.000 1702 0 0 1 1702 423375131 423376832 0.000000e+00 3144.0
2 TraesCS4D01G254200 chr4D 100.000 1631 0 0 2066 3696 423377196 423378826 0.000000e+00 3013.0
3 TraesCS4D01G254200 chr4D 89.873 79 8 0 2651 2729 369261455 369261533 1.370000e-17 102.0
4 TraesCS4D01G254200 chr4B 96.200 3263 83 11 3908 7150 519791877 519795118 0.000000e+00 5301.0
5 TraesCS4D01G254200 chr4B 89.288 1671 125 26 49 1701 519788405 519790039 0.000000e+00 2045.0
6 TraesCS4D01G254200 chr4B 94.729 1328 38 9 2371 3696 519790534 519791831 0.000000e+00 2036.0
7 TraesCS4D01G254200 chr4B 91.837 392 22 7 7330 7713 519795286 519795675 8.810000e-149 538.0
8 TraesCS4D01G254200 chr4B 82.875 327 26 9 2066 2373 519790186 519790501 4.590000e-67 267.0
9 TraesCS4D01G254200 chr4A 96.289 2883 77 12 3925 6790 40881237 40878368 0.000000e+00 4704.0
10 TraesCS4D01G254200 chr4A 96.196 1288 39 4 2371 3656 40882706 40881427 0.000000e+00 2098.0
11 TraesCS4D01G254200 chr4A 84.451 656 49 20 1067 1701 40883828 40883205 1.430000e-166 597.0
12 TraesCS4D01G254200 chr4A 90.557 413 17 9 6751 7150 40878366 40877963 1.910000e-145 527.0
13 TraesCS4D01G254200 chr4A 91.700 253 16 3 7312 7561 40877439 40877189 5.730000e-91 346.0
14 TraesCS4D01G254200 chr4A 84.709 327 30 8 2066 2373 40883064 40882739 7.520000e-80 309.0
15 TraesCS4D01G254200 chr4A 93.548 124 6 1 7146 7267 40877937 40877814 4.750000e-42 183.0
16 TraesCS4D01G254200 chr4A 93.388 121 6 2 7595 7713 40877191 40877071 2.210000e-40 178.0
17 TraesCS4D01G254200 chr3A 81.212 165 18 8 2603 2756 611709587 611709749 3.780000e-23 121.0
18 TraesCS4D01G254200 chr1B 85.567 97 13 1 2602 2697 435413319 435413223 4.930000e-17 100.0
19 TraesCS4D01G254200 chr2D 82.979 94 15 1 2679 2771 593157638 593157731 4.960000e-12 84.2
20 TraesCS4D01G254200 chr5D 78.462 130 15 5 2645 2761 454112540 454112669 1.070000e-08 73.1
21 TraesCS4D01G254200 chr3B 92.157 51 4 0 2674 2724 215610128 215610178 1.070000e-08 73.1
22 TraesCS4D01G254200 chr3B 89.583 48 4 1 2693 2739 217997001 217996954 8.360000e-05 60.2
23 TraesCS4D01G254200 chr7D 96.970 33 1 0 2678 2710 566550141 566550173 1.000000e-03 56.5


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 TraesCS4D01G254200 chr4D 423375131 423382843 7712 False 4395.333333 7029 100.00000 1 7713 3 chr4D.!!$F2 7712
1 TraesCS4D01G254200 chr4B 519788405 519795675 7270 False 2037.400000 5301 90.98580 49 7713 5 chr4B.!!$F1 7664
2 TraesCS4D01G254200 chr4A 40877071 40883828 6757 True 1117.750000 4704 91.35475 1067 7713 8 chr4A.!!$R1 6646

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
487 500 0.321564 CACACCTCTTCCATCGCCAA 60.322 55.000 0.00 0.00 0.00 4.52 F
488 501 0.321653 ACACCTCTTCCATCGCCAAC 60.322 55.000 0.00 0.00 0.00 3.77 F
953 967 0.526524 TTGTTTGCCCTTTTCGCACG 60.527 50.000 0.00 0.00 35.56 5.34 F
2281 2319 0.762418 TGTCCCACGAATGTTCTGGT 59.238 50.000 0.00 0.00 0.00 4.00 F
3945 4039 1.463444 GCACCACGTCATTCCTGTAAC 59.537 52.381 0.00 0.00 0.00 2.50 F
4512 4619 3.365472 TGCCTCTGCTACTGATAAGTCA 58.635 45.455 0.00 0.00 38.71 3.41 F
5907 6017 0.106519 AAACCTGCCAGCAGTGTTCT 60.107 50.000 17.86 9.57 42.15 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2185 0.179084 TTCCCTCGAATCATGGCGAC 60.179 55.000 0.00 0.00 32.51 5.19 R
2406 2497 1.002069 AACTTCATCTGGATGCCCCA 58.998 50.000 5.77 0.00 44.25 4.96 R
2844 2936 0.810031 CCCCTTGCAACGGATCTACG 60.810 60.000 15.24 0.00 40.31 3.51 R
3958 4052 0.183492 TGGAGCTTTGCAACACCTCT 59.817 50.000 15.63 3.42 0.00 3.69 R
5725 5835 2.288666 GGCGAACCAGAATGATTGCTA 58.711 47.619 0.00 0.00 39.69 3.49 R
6496 6615 1.230635 CCGTTGACAGGTTCCAGCAG 61.231 60.000 0.00 0.00 0.00 4.24 R
6887 7048 0.179032 CATAGCATAACCCACGGGCA 60.179 55.000 0.69 0.00 39.32 5.36 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
22 23 5.499004 ACCAAACAAGATAGCTAGTTCCA 57.501 39.130 0.00 0.00 0.00 3.53
23 24 5.491982 ACCAAACAAGATAGCTAGTTCCAG 58.508 41.667 0.00 0.00 0.00 3.86
24 25 4.333926 CCAAACAAGATAGCTAGTTCCAGC 59.666 45.833 0.00 0.00 42.12 4.85
25 26 4.826274 AACAAGATAGCTAGTTCCAGCA 57.174 40.909 0.00 0.00 44.35 4.41
26 27 4.826274 ACAAGATAGCTAGTTCCAGCAA 57.174 40.909 0.00 0.00 44.35 3.91
27 28 5.165961 ACAAGATAGCTAGTTCCAGCAAA 57.834 39.130 0.00 0.00 44.35 3.68
28 29 5.560724 ACAAGATAGCTAGTTCCAGCAAAA 58.439 37.500 0.00 0.00 44.35 2.44
29 30 6.003950 ACAAGATAGCTAGTTCCAGCAAAAA 58.996 36.000 0.00 0.00 44.35 1.94
46 47 2.745515 AAAACGTAGCAGGGAGACTC 57.254 50.000 0.00 0.00 0.00 3.36
47 48 0.896226 AAACGTAGCAGGGAGACTCC 59.104 55.000 13.60 13.60 35.23 3.85
54 55 0.687354 GCAGGGAGACTCCAGTTCAA 59.313 55.000 23.06 0.00 38.64 2.69
63 64 6.264518 GGGAGACTCCAGTTCAAACAAAATAA 59.735 38.462 23.06 0.00 38.64 1.40
68 69 8.474006 ACTCCAGTTCAAACAAAATAAAACAC 57.526 30.769 0.00 0.00 0.00 3.32
79 80 6.702329 ACAAAATAAAACACTGGTTCCAACA 58.298 32.000 0.00 0.00 35.82 3.33
135 136 0.736636 ACACATCGCATGGCTGATTG 59.263 50.000 0.00 0.00 33.60 2.67
142 143 1.269569 CGCATGGCTGATTGCATCATT 60.270 47.619 0.00 0.00 45.15 2.57
182 183 2.728846 CGAAATGGTTGGTCGATTGCAG 60.729 50.000 0.00 0.00 36.92 4.41
185 186 1.236616 TGGTTGGTCGATTGCAGCAG 61.237 55.000 0.00 0.00 0.00 4.24
196 197 1.527034 TTGCAGCAGAGGATGTTGTC 58.473 50.000 0.00 0.00 41.82 3.18
204 205 1.697432 AGAGGATGTTGTCGGTTCCAA 59.303 47.619 0.00 0.00 0.00 3.53
215 216 1.011333 CGGTTCCAACACAAAGTCGT 58.989 50.000 0.00 0.00 0.00 4.34
216 217 1.399089 CGGTTCCAACACAAAGTCGTT 59.601 47.619 0.00 0.00 0.00 3.85
238 239 5.290493 TGTAGTTGTTGTCCATCTTCACT 57.710 39.130 0.00 0.00 0.00 3.41
246 247 2.094700 TGTCCATCTTCACTACGCAGAC 60.095 50.000 0.00 0.00 0.00 3.51
252 253 1.255667 TTCACTACGCAGACCCCTCC 61.256 60.000 0.00 0.00 0.00 4.30
290 291 2.339712 CTTTTGGCTGGCCGGTTG 59.660 61.111 14.55 0.00 39.42 3.77
291 292 3.864160 CTTTTGGCTGGCCGGTTGC 62.864 63.158 14.55 7.37 39.42 4.17
338 351 3.542969 AACCTTAGCAAACCATCCCTT 57.457 42.857 0.00 0.00 0.00 3.95
345 358 1.201414 GCAAACCATCCCTTACCGTTG 59.799 52.381 0.00 0.00 0.00 4.10
378 391 2.585247 CTAGGTTGCCGCCGTAGC 60.585 66.667 0.00 0.00 0.00 3.58
398 411 3.785859 GGAGCATCGCACCTCCCA 61.786 66.667 4.35 0.00 41.42 4.37
420 433 2.029073 CCGACAGTTGTGCTCCGT 59.971 61.111 0.00 0.00 0.00 4.69
422 435 2.939022 GACAGTTGTGCTCCGTGC 59.061 61.111 0.00 0.00 43.25 5.34
467 480 1.215647 GGTGGTCACTAGCTCACCG 59.784 63.158 4.43 0.00 39.97 4.94
479 492 1.374758 CTCACCGCACACCTCTTCC 60.375 63.158 0.00 0.00 0.00 3.46
481 494 1.003355 CACCGCACACCTCTTCCAT 60.003 57.895 0.00 0.00 0.00 3.41
482 495 1.021390 CACCGCACACCTCTTCCATC 61.021 60.000 0.00 0.00 0.00 3.51
483 496 1.811266 CCGCACACCTCTTCCATCG 60.811 63.158 0.00 0.00 0.00 3.84
484 497 2.456119 CGCACACCTCTTCCATCGC 61.456 63.158 0.00 0.00 0.00 4.58
485 498 2.109126 GCACACCTCTTCCATCGCC 61.109 63.158 0.00 0.00 0.00 5.54
486 499 1.296392 CACACCTCTTCCATCGCCA 59.704 57.895 0.00 0.00 0.00 5.69
487 500 0.321564 CACACCTCTTCCATCGCCAA 60.322 55.000 0.00 0.00 0.00 4.52
488 501 0.321653 ACACCTCTTCCATCGCCAAC 60.322 55.000 0.00 0.00 0.00 3.77
500 513 2.393768 CGCCAACGAGCTGCTGATT 61.394 57.895 7.01 0.00 43.93 2.57
514 527 2.019156 GCTGATTTGGAGGTAGGCCAC 61.019 57.143 5.01 0.31 34.56 5.01
529 542 1.376037 CCACAGGGGAGAGAAACGC 60.376 63.158 0.00 0.00 40.01 4.84
530 543 1.371183 CACAGGGGAGAGAAACGCA 59.629 57.895 0.00 0.00 0.00 5.24
547 560 2.284995 AGAGGAGTGGCTGGGGAC 60.285 66.667 0.00 0.00 0.00 4.46
568 581 1.191535 CACACGAGGGGTATGAGGAA 58.808 55.000 0.00 0.00 0.00 3.36
569 582 1.137086 CACACGAGGGGTATGAGGAAG 59.863 57.143 0.00 0.00 0.00 3.46
603 616 0.756294 TGGCGTGAGGAGACAAGAAA 59.244 50.000 0.00 0.00 0.00 2.52
631 644 1.069935 GGTGAGAGGATAAGGCCGC 59.930 63.158 0.00 0.00 0.00 6.53
632 645 1.686325 GGTGAGAGGATAAGGCCGCA 61.686 60.000 0.00 0.00 0.00 5.69
659 672 1.325640 CCACACGATCTGCTTCGATTG 59.674 52.381 10.47 4.61 41.62 2.67
663 676 1.920574 ACGATCTGCTTCGATTGAACG 59.079 47.619 10.47 0.00 41.62 3.95
671 684 0.713883 TTCGATTGAACGAAGAGCGC 59.286 50.000 0.00 0.00 45.21 5.92
702 715 4.641645 CGGTCAGCCAACCAGCCA 62.642 66.667 5.99 0.00 39.43 4.75
731 744 7.786464 AGGGATCATTTGCCTAAAAGATAATGT 59.214 33.333 0.00 0.00 45.88 2.71
737 750 9.722056 CATTTGCCTAAAAGATAATGTACAGAC 57.278 33.333 0.33 0.00 0.00 3.51
740 753 9.461312 TTGCCTAAAAGATAATGTACAGACAAT 57.539 29.630 0.33 0.00 39.59 2.71
755 768 6.822667 ACAGACAATGAAAGCATATGTTGA 57.177 33.333 4.29 0.00 33.44 3.18
773 786 3.777106 TGAGGACTGCACTCAAAAGAT 57.223 42.857 3.17 0.00 41.66 2.40
774 787 4.890158 TGAGGACTGCACTCAAAAGATA 57.110 40.909 3.17 0.00 41.66 1.98
775 788 4.569943 TGAGGACTGCACTCAAAAGATAC 58.430 43.478 3.17 0.00 41.66 2.24
776 789 4.040339 TGAGGACTGCACTCAAAAGATACA 59.960 41.667 3.17 0.00 41.66 2.29
781 794 6.417930 GGACTGCACTCAAAAGATACAAAAAC 59.582 38.462 0.00 0.00 0.00 2.43
785 798 8.539770 TGCACTCAAAAGATACAAAAACAAAA 57.460 26.923 0.00 0.00 0.00 2.44
786 799 8.655092 TGCACTCAAAAGATACAAAAACAAAAG 58.345 29.630 0.00 0.00 0.00 2.27
787 800 7.635973 GCACTCAAAAGATACAAAAACAAAAGC 59.364 33.333 0.00 0.00 0.00 3.51
788 801 8.655092 CACTCAAAAGATACAAAAACAAAAGCA 58.345 29.630 0.00 0.00 0.00 3.91
789 802 8.655970 ACTCAAAAGATACAAAAACAAAAGCAC 58.344 29.630 0.00 0.00 0.00 4.40
794 807 6.503524 AGATACAAAAACAAAAGCACGTGAT 58.496 32.000 22.23 11.27 0.00 3.06
800 813 1.002468 ACAAAAGCACGTGATGAGCAC 60.002 47.619 22.23 0.00 44.21 4.40
810 823 2.046892 ATGAGCACTCACACGGGC 60.047 61.111 1.71 0.00 43.11 6.13
857 870 8.753175 CCGTGCTAGTAGTCATTTATTAAGTTC 58.247 37.037 0.00 0.00 0.00 3.01
874 887 7.933728 TTAAGTTCGCTATAAATATGACGCA 57.066 32.000 0.00 0.00 0.00 5.24
884 897 2.287393 ATATGACGCACACAACGCTA 57.713 45.000 0.00 0.00 0.00 4.26
885 898 2.287393 TATGACGCACACAACGCTAT 57.713 45.000 0.00 0.00 0.00 2.97
887 900 1.225745 GACGCACACAACGCTATGC 60.226 57.895 0.00 0.00 34.66 3.14
896 909 3.173599 CACAACGCTATGCTGGAAAATG 58.826 45.455 0.00 0.00 0.00 2.32
907 920 7.168135 GCTATGCTGGAAAATGCTTATTACAAC 59.832 37.037 0.00 0.00 0.00 3.32
923 936 1.214424 ACAACTGGGCTTGTGTAAGGT 59.786 47.619 0.00 0.00 32.95 3.50
927 940 0.770557 TGGGCTTGTGTAAGGTCCCT 60.771 55.000 0.00 0.00 37.21 4.20
946 959 0.908198 TTGCCACTTGTTTGCCCTTT 59.092 45.000 0.00 0.00 0.00 3.11
953 967 0.526524 TTGTTTGCCCTTTTCGCACG 60.527 50.000 0.00 0.00 35.56 5.34
1002 1016 4.450053 GAGAGAGGAAAAGGATCACCATG 58.550 47.826 0.00 0.00 38.94 3.66
1019 1033 2.126424 GGACGGCGAGACACACTC 60.126 66.667 16.62 0.00 41.79 3.51
1061 1075 4.459089 AGGCTTCCTCTTCGGCGC 62.459 66.667 0.00 0.00 0.00 6.53
1116 1130 1.530323 CTTCCGGTAAGGGGTTTGTG 58.470 55.000 0.00 0.00 41.52 3.33
1196 1210 8.525290 TTTTCAATCTTGTTTCCTCTTCTCTT 57.475 30.769 0.00 0.00 0.00 2.85
1234 1248 4.869297 TGCAAAACACACTCCATGAAAAAG 59.131 37.500 0.00 0.00 0.00 2.27
1308 1343 7.119387 CCAAAACCCTATAGTCCAGATTCTTT 58.881 38.462 0.00 0.00 0.00 2.52
1309 1344 8.272173 CCAAAACCCTATAGTCCAGATTCTTTA 58.728 37.037 0.00 0.00 0.00 1.85
1310 1345 9.853177 CAAAACCCTATAGTCCAGATTCTTTAT 57.147 33.333 0.00 0.00 0.00 1.40
1400 1435 1.888018 CCGTCGGACAGCTTTCCTA 59.112 57.895 16.72 2.98 32.88 2.94
1474 1509 4.035102 GCACCGCCTCCTTCCCTT 62.035 66.667 0.00 0.00 0.00 3.95
1547 1583 1.592669 GCTGTGCTCATATCGGCGT 60.593 57.895 6.85 0.00 0.00 5.68
1591 1627 4.141482 GGGGAGCATTGATTAGGACTGTAA 60.141 45.833 0.00 0.00 0.00 2.41
1643 1680 3.611766 ATTCACCGACTTGAACCCTAG 57.388 47.619 0.00 0.00 38.31 3.02
1701 1738 2.041265 ACTCCTGGGCGGATTCCT 59.959 61.111 0.30 0.00 42.12 3.36
2148 2185 2.268298 CCCATAGTCGGTGAGTTTTCG 58.732 52.381 0.00 0.00 0.00 3.46
2154 2191 1.952133 CGGTGAGTTTTCGTCGCCA 60.952 57.895 3.75 0.00 43.68 5.69
2161 2198 1.393539 AGTTTTCGTCGCCATGATTCG 59.606 47.619 0.00 0.00 0.00 3.34
2163 2200 1.277326 TTTCGTCGCCATGATTCGAG 58.723 50.000 0.00 0.00 35.21 4.04
2201 2238 5.339008 TCGTTGGTATCTTGCAGATTAGT 57.661 39.130 4.35 0.00 36.20 2.24
2205 2242 4.445453 TGGTATCTTGCAGATTAGTGCTG 58.555 43.478 4.35 0.00 44.32 4.41
2208 2245 6.049149 GGTATCTTGCAGATTAGTGCTGTTA 58.951 40.000 4.35 0.00 44.32 2.41
2211 2248 5.118990 TCTTGCAGATTAGTGCTGTTATCC 58.881 41.667 0.00 0.00 44.32 2.59
2224 2262 2.288666 TGTTATCCGCTGATTTGAGGC 58.711 47.619 0.00 0.00 32.18 4.70
2236 2274 5.216566 TGATTTGAGGCGATTTCGTTTAG 57.783 39.130 1.55 0.00 42.22 1.85
2239 2277 4.657075 TTGAGGCGATTTCGTTTAGTTC 57.343 40.909 1.55 0.00 42.22 3.01
2241 2279 3.678072 TGAGGCGATTTCGTTTAGTTCTG 59.322 43.478 1.55 0.00 42.22 3.02
2249 2287 4.961438 TTCGTTTAGTTCTGGTAGGGTT 57.039 40.909 0.00 0.00 0.00 4.11
2263 2301 2.645192 GGGTTGGGTTGGGCGAATG 61.645 63.158 0.00 0.00 0.00 2.67
2264 2302 1.906333 GGTTGGGTTGGGCGAATGT 60.906 57.895 0.00 0.00 0.00 2.71
2265 2303 1.584495 GTTGGGTTGGGCGAATGTC 59.416 57.895 0.00 0.00 0.00 3.06
2266 2304 1.605165 TTGGGTTGGGCGAATGTCC 60.605 57.895 0.00 0.00 41.64 4.02
2267 2305 2.754254 GGGTTGGGCGAATGTCCC 60.754 66.667 0.00 0.00 40.01 4.46
2272 2310 2.046700 GGGCGAATGTCCCACGAA 60.047 61.111 0.00 0.00 43.37 3.85
2273 2311 1.451387 GGGCGAATGTCCCACGAAT 60.451 57.895 0.00 0.00 43.37 3.34
2274 2312 1.714899 GGGCGAATGTCCCACGAATG 61.715 60.000 0.00 0.00 43.37 2.67
2275 2313 1.024579 GGCGAATGTCCCACGAATGT 61.025 55.000 0.00 0.00 0.00 2.71
2277 2315 1.202031 GCGAATGTCCCACGAATGTTC 60.202 52.381 0.00 0.00 0.00 3.18
2279 2317 2.094258 CGAATGTCCCACGAATGTTCTG 59.906 50.000 0.00 0.00 0.00 3.02
2281 2319 0.762418 TGTCCCACGAATGTTCTGGT 59.238 50.000 0.00 0.00 0.00 4.00
2282 2320 1.972075 TGTCCCACGAATGTTCTGGTA 59.028 47.619 0.00 0.00 0.00 3.25
2283 2321 2.028476 TGTCCCACGAATGTTCTGGTAG 60.028 50.000 0.00 0.00 0.00 3.18
2284 2322 1.553248 TCCCACGAATGTTCTGGTAGG 59.447 52.381 0.00 0.00 0.00 3.18
2288 2326 3.000727 CACGAATGTTCTGGTAGGGTTC 58.999 50.000 0.00 0.00 0.00 3.62
2290 2328 3.262420 CGAATGTTCTGGTAGGGTTCTG 58.738 50.000 0.00 0.00 0.00 3.02
2291 2329 3.056107 CGAATGTTCTGGTAGGGTTCTGA 60.056 47.826 0.00 0.00 0.00 3.27
2292 2330 4.383118 CGAATGTTCTGGTAGGGTTCTGAT 60.383 45.833 0.00 0.00 0.00 2.90
2293 2331 5.501156 GAATGTTCTGGTAGGGTTCTGATT 58.499 41.667 0.00 0.00 0.00 2.57
2294 2332 4.993705 TGTTCTGGTAGGGTTCTGATTT 57.006 40.909 0.00 0.00 0.00 2.17
2297 2353 4.826274 TCTGGTAGGGTTCTGATTTGAG 57.174 45.455 0.00 0.00 0.00 3.02
2318 2374 2.608506 GGTAATTTCGGTGTTTGGGTGC 60.609 50.000 0.00 0.00 0.00 5.01
2406 2497 4.995487 GTCTTTCAGACTTCCGGTGTTATT 59.005 41.667 0.00 0.00 41.88 1.40
2408 2499 3.328382 TCAGACTTCCGGTGTTATTGG 57.672 47.619 0.00 0.00 0.00 3.16
2481 2572 6.315642 TGCAAATGTAAATTTGTGCATATGGG 59.684 34.615 17.71 0.00 42.02 4.00
2482 2573 6.538021 GCAAATGTAAATTTGTGCATATGGGA 59.462 34.615 17.71 0.00 42.02 4.37
2483 2574 7.227116 GCAAATGTAAATTTGTGCATATGGGAT 59.773 33.333 17.71 0.00 42.02 3.85
2484 2575 9.761504 CAAATGTAAATTTGTGCATATGGGATA 57.238 29.630 9.85 0.00 36.91 2.59
2486 2577 9.932207 AATGTAAATTTGTGCATATGGGATATG 57.068 29.630 4.56 0.00 44.25 1.78
2487 2578 8.476064 TGTAAATTTGTGCATATGGGATATGT 57.524 30.769 4.56 0.00 43.52 2.29
2527 2619 5.400066 ACAAGTGTTTGGCTTACAGTTTT 57.600 34.783 9.06 2.73 37.12 2.43
2550 2642 1.549203 ATGGCCAGTTTAGCAACCTG 58.451 50.000 13.05 0.00 32.70 4.00
2573 2665 3.181524 CCTTATTGCTACGGTTGTGTTCG 60.182 47.826 0.00 0.00 0.00 3.95
2592 2684 9.790389 TGTGTTCGTTTACTGTTTTTATTGATT 57.210 25.926 0.00 0.00 0.00 2.57
2793 2885 9.814899 TTTTGCTCTTCATTTTGTTTGAGAATA 57.185 25.926 0.00 0.00 0.00 1.75
3541 3635 2.580470 CGCATGCATCGTCTCCGTC 61.580 63.158 19.57 0.00 35.01 4.79
3572 3666 4.459390 AGTGCTGCATTTATTGATTGCA 57.541 36.364 5.27 0.00 41.05 4.08
3606 3700 5.743117 ACAAATCTGAAGAGGAGAGATTGG 58.257 41.667 0.00 0.00 36.71 3.16
3620 3714 5.163499 GGAGAGATTGGTATCGTTTCTCTGT 60.163 44.000 5.55 0.00 42.33 3.41
3661 3755 7.255451 CCACGATAATTGGGCAACAGTATTAAT 60.255 37.037 0.00 0.00 39.74 1.40
3662 3756 8.134895 CACGATAATTGGGCAACAGTATTAATT 58.865 33.333 0.00 0.00 39.74 1.40
3945 4039 1.463444 GCACCACGTCATTCCTGTAAC 59.537 52.381 0.00 0.00 0.00 2.50
3951 4045 4.809426 CCACGTCATTCCTGTAACCTAATC 59.191 45.833 0.00 0.00 0.00 1.75
3956 4050 5.998363 GTCATTCCTGTAACCTAATCCCATC 59.002 44.000 0.00 0.00 0.00 3.51
3957 4051 5.911178 TCATTCCTGTAACCTAATCCCATCT 59.089 40.000 0.00 0.00 0.00 2.90
3958 4052 7.016268 GTCATTCCTGTAACCTAATCCCATCTA 59.984 40.741 0.00 0.00 0.00 1.98
3959 4053 6.996180 TTCCTGTAACCTAATCCCATCTAG 57.004 41.667 0.00 0.00 0.00 2.43
4024 4131 7.962918 CGGTGAAACACAATTAATTAGAGGAAG 59.037 37.037 0.00 0.00 39.98 3.46
4034 4141 9.817365 CAATTAATTAGAGGAAGATTATGTGCG 57.183 33.333 0.00 0.00 0.00 5.34
4099 4206 3.613671 CGCTACAGCCTTGATATGAGAGG 60.614 52.174 0.00 0.00 37.91 3.69
4110 4217 7.336931 GCCTTGATATGAGAGGTTTGAAAGTTA 59.663 37.037 0.00 0.00 33.03 2.24
4211 4318 3.807622 TGTGAATCGTTCAGGTGAGAAAC 59.192 43.478 1.43 0.00 41.01 2.78
4213 4320 3.807622 TGAATCGTTCAGGTGAGAAACAC 59.192 43.478 0.00 0.00 40.60 3.32
4512 4619 3.365472 TGCCTCTGCTACTGATAAGTCA 58.635 45.455 0.00 0.00 38.71 3.41
5483 5590 7.910162 TGACGATTCTTTTCTTGTTTTTCTCAG 59.090 33.333 0.00 0.00 0.00 3.35
5484 5591 7.762382 ACGATTCTTTTCTTGTTTTTCTCAGT 58.238 30.769 0.00 0.00 0.00 3.41
5485 5592 8.244113 ACGATTCTTTTCTTGTTTTTCTCAGTT 58.756 29.630 0.00 0.00 0.00 3.16
5635 5745 4.019501 AGTGATTTTGAGGACTCAGCAGAT 60.020 41.667 1.92 0.00 41.13 2.90
5725 5835 6.430007 AGTAAGCTCATCAAAATTGGAGGAT 58.570 36.000 0.00 0.00 0.00 3.24
5743 5853 4.384056 AGGATAGCAATCATTCTGGTTCG 58.616 43.478 0.00 0.00 33.41 3.95
5864 5974 2.033675 CAGCAGTGTCTCATTTTGTGCA 59.966 45.455 0.00 0.00 31.75 4.57
5906 6016 0.312102 GAAACCTGCCAGCAGTGTTC 59.688 55.000 17.86 15.38 42.15 3.18
5907 6017 0.106519 AAACCTGCCAGCAGTGTTCT 60.107 50.000 17.86 9.57 42.15 3.01
5911 6021 1.269413 CCTGCCAGCAGTGTTCTTTTG 60.269 52.381 17.86 0.00 42.15 2.44
5956 6066 8.757982 ACCTGCAGAATATCTCAAATAATTGT 57.242 30.769 17.39 0.00 37.79 2.71
5961 6071 8.133627 GCAGAATATCTCAAATAATTGTGCACT 58.866 33.333 19.41 0.00 37.93 4.40
6083 6197 5.479306 ACATGGAGTTATACACACACACTC 58.521 41.667 0.00 0.00 34.31 3.51
6084 6198 5.246203 ACATGGAGTTATACACACACACTCT 59.754 40.000 0.00 0.00 35.25 3.24
6086 6200 4.021456 TGGAGTTATACACACACACTCTGG 60.021 45.833 0.00 0.00 35.25 3.86
6087 6201 4.495422 GAGTTATACACACACACTCTGGG 58.505 47.826 0.00 0.00 32.64 4.45
6089 6203 4.591498 AGTTATACACACACACTCTGGGAA 59.409 41.667 0.00 0.00 0.00 3.97
6090 6204 5.071250 AGTTATACACACACACTCTGGGAAA 59.929 40.000 0.00 0.00 0.00 3.13
6181 6295 5.455056 TCGTAGCCAGGAATAGAATCTTC 57.545 43.478 0.00 0.00 0.00 2.87
6214 6328 3.189287 CCTTCTGACGTTTGCTTAATGCT 59.811 43.478 0.00 0.00 43.37 3.79
6222 6336 3.801594 CGTTTGCTTAATGCTTTTGTGGT 59.198 39.130 0.00 0.00 43.37 4.16
6276 6395 5.692115 ACATTCTTGGTTTTGTTTCCCTT 57.308 34.783 0.00 0.00 0.00 3.95
6384 6503 1.542915 GAGATGCAGCAGGCTGAAAAA 59.457 47.619 24.46 7.10 46.30 1.94
6496 6615 1.139095 GCCAAGATCAAGCAGCAGC 59.861 57.895 0.00 0.00 42.56 5.25
6649 6769 1.440938 CGAAAACAACGGTGAGGGCA 61.441 55.000 7.88 0.00 0.00 5.36
6852 7013 8.012241 GCTTAATTCCTTTATGCTTGTAGATCG 58.988 37.037 0.00 0.00 37.75 3.69
6857 7018 5.580691 TCCTTTATGCTTGTAGATCGTTGTG 59.419 40.000 0.00 0.00 0.00 3.33
6883 7044 4.226113 AGTCTCGGTTGATATCGTTAGC 57.774 45.455 0.00 0.00 0.00 3.09
6887 7048 4.097437 TCTCGGTTGATATCGTTAGCTTGT 59.903 41.667 0.00 0.00 0.00 3.16
6892 7053 1.792949 GATATCGTTAGCTTGTGCCCG 59.207 52.381 0.00 0.00 40.80 6.13
7150 7326 2.646719 CGTGCAATGCAAGCCAGT 59.353 55.556 10.44 0.00 41.47 4.00
7151 7327 1.875262 CGTGCAATGCAAGCCAGTA 59.125 52.632 10.44 0.00 41.47 2.74
7153 7329 0.454957 GTGCAATGCAAGCCAGTACG 60.455 55.000 10.44 0.00 41.47 3.67
7259 7470 7.016153 TGGTACATCCAAATCTTAGTCTTGT 57.984 36.000 0.00 0.00 44.12 3.16
7402 7952 0.744771 GCCCTTTGAGCCCTTCTACG 60.745 60.000 0.00 0.00 0.00 3.51
7403 7953 0.613777 CCCTTTGAGCCCTTCTACGT 59.386 55.000 0.00 0.00 0.00 3.57
7406 7956 1.275291 CTTTGAGCCCTTCTACGTCCA 59.725 52.381 0.00 0.00 0.00 4.02
7481 8031 4.019321 ACCGGATGCCAGTATAATAATGCT 60.019 41.667 9.46 0.00 0.00 3.79
7507 8057 5.748630 GCATGGCCACTTTTAGTAAATTAGC 59.251 40.000 8.16 0.00 0.00 3.09
7529 8082 6.249192 AGCAGTACCATCTGACTATAGCATA 58.751 40.000 0.00 0.00 37.61 3.14
7611 8164 2.870411 GGATACTGGGATACGTGCAAAC 59.130 50.000 0.00 0.00 37.60 2.93
7699 8256 2.686405 CCTGCTTGCTTGCTAATCATGA 59.314 45.455 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.491982 CTGGAACTAGCTATCTTGTTTGGT 58.508 41.667 0.00 0.00 38.15 3.67
1 2 4.333926 GCTGGAACTAGCTATCTTGTTTGG 59.666 45.833 0.00 0.00 38.15 3.28
2 3 4.937620 TGCTGGAACTAGCTATCTTGTTTG 59.062 41.667 11.06 0.00 44.01 2.93
3 4 5.165961 TGCTGGAACTAGCTATCTTGTTT 57.834 39.130 11.06 0.00 44.01 2.83
4 5 4.826274 TGCTGGAACTAGCTATCTTGTT 57.174 40.909 11.06 0.00 44.01 2.83
5 6 4.826274 TTGCTGGAACTAGCTATCTTGT 57.174 40.909 11.06 0.00 44.01 3.16
6 7 6.500684 TTTTTGCTGGAACTAGCTATCTTG 57.499 37.500 11.06 0.00 44.01 3.02
26 27 2.289506 GGAGTCTCCCTGCTACGTTTTT 60.290 50.000 7.78 0.00 0.00 1.94
27 28 1.275573 GGAGTCTCCCTGCTACGTTTT 59.724 52.381 7.78 0.00 0.00 2.43
28 29 0.896226 GGAGTCTCCCTGCTACGTTT 59.104 55.000 7.78 0.00 0.00 3.60
29 30 0.251653 TGGAGTCTCCCTGCTACGTT 60.252 55.000 16.60 0.00 35.03 3.99
30 31 0.681564 CTGGAGTCTCCCTGCTACGT 60.682 60.000 16.60 0.00 35.03 3.57
31 32 0.681564 ACTGGAGTCTCCCTGCTACG 60.682 60.000 16.60 0.00 35.03 3.51
32 33 1.478916 GAACTGGAGTCTCCCTGCTAC 59.521 57.143 16.60 0.00 35.03 3.58
33 34 1.077169 TGAACTGGAGTCTCCCTGCTA 59.923 52.381 16.60 0.00 35.03 3.49
34 35 0.178921 TGAACTGGAGTCTCCCTGCT 60.179 55.000 16.60 0.67 35.03 4.24
35 36 0.687354 TTGAACTGGAGTCTCCCTGC 59.313 55.000 16.60 0.64 35.03 4.85
36 37 2.104792 TGTTTGAACTGGAGTCTCCCTG 59.895 50.000 16.60 11.36 35.03 4.45
37 38 2.408565 TGTTTGAACTGGAGTCTCCCT 58.591 47.619 16.60 0.57 35.03 4.20
38 39 2.930826 TGTTTGAACTGGAGTCTCCC 57.069 50.000 16.60 1.16 35.03 4.30
39 40 5.774498 ATTTTGTTTGAACTGGAGTCTCC 57.226 39.130 12.40 12.40 36.96 3.71
40 41 9.020813 GTTTTATTTTGTTTGAACTGGAGTCTC 57.979 33.333 0.00 0.00 0.00 3.36
41 42 8.527810 TGTTTTATTTTGTTTGAACTGGAGTCT 58.472 29.630 0.00 0.00 0.00 3.24
42 43 8.592155 GTGTTTTATTTTGTTTGAACTGGAGTC 58.408 33.333 0.00 0.00 0.00 3.36
43 44 8.311109 AGTGTTTTATTTTGTTTGAACTGGAGT 58.689 29.630 0.00 0.00 0.00 3.85
44 45 8.594687 CAGTGTTTTATTTTGTTTGAACTGGAG 58.405 33.333 0.00 0.00 0.00 3.86
45 46 8.472683 CAGTGTTTTATTTTGTTTGAACTGGA 57.527 30.769 0.00 0.00 0.00 3.86
46 47 7.683746 CCAGTGTTTTATTTTGTTTGAACTGG 58.316 34.615 0.00 0.00 43.42 4.00
47 48 8.250538 ACCAGTGTTTTATTTTGTTTGAACTG 57.749 30.769 0.00 0.00 0.00 3.16
54 55 7.162082 TGTTGGAACCAGTGTTTTATTTTGTT 58.838 30.769 0.00 0.00 33.97 2.83
109 110 0.171007 CCATGCGATGTGTTGGAACC 59.829 55.000 0.00 0.00 0.00 3.62
160 161 1.895051 CAATCGACCAACCATTTCGC 58.105 50.000 0.00 0.00 32.70 4.70
182 183 1.079503 GAACCGACAACATCCTCTGC 58.920 55.000 0.00 0.00 0.00 4.26
185 186 1.804748 GTTGGAACCGACAACATCCTC 59.195 52.381 6.37 0.00 45.62 3.71
196 197 1.011333 ACGACTTTGTGTTGGAACCG 58.989 50.000 0.00 0.00 34.36 4.44
215 216 5.680619 AGTGAAGATGGACAACAACTACAA 58.319 37.500 0.00 0.00 31.22 2.41
216 217 5.290493 AGTGAAGATGGACAACAACTACA 57.710 39.130 0.00 0.00 31.22 2.74
252 253 2.499685 GAATCGGTGACCCTCGGG 59.500 66.667 0.00 0.00 42.03 5.14
280 281 2.641439 TTTTTGCTGCAACCGGCCAG 62.641 55.000 15.72 7.23 42.87 4.85
282 283 2.107953 TTTTTGCTGCAACCGGCC 59.892 55.556 15.72 0.00 42.87 6.13
338 351 1.079405 GCAGGCTGCTACAACGGTA 60.079 57.895 31.37 0.00 40.96 4.02
345 358 1.363744 CTAGTGTTGCAGGCTGCTAC 58.636 55.000 36.12 36.12 46.54 3.58
378 391 2.202987 GAGGTGCGATGCTCCCAG 60.203 66.667 6.29 0.00 42.42 4.45
396 409 4.619227 ACAACTGTCGGCGGGTGG 62.619 66.667 19.82 2.04 42.86 4.61
420 433 0.666274 CACGAAGTAGCGAAGGTGCA 60.666 55.000 0.00 0.00 44.68 4.57
422 435 1.060713 CACACGAAGTAGCGAAGGTG 58.939 55.000 0.00 0.00 41.61 4.00
426 439 0.942410 GGCACACACGAAGTAGCGAA 60.942 55.000 0.00 0.00 41.61 4.70
431 444 2.745037 GGGGGCACACACGAAGTA 59.255 61.111 0.00 0.00 41.61 2.24
467 480 2.109126 GGCGATGGAAGAGGTGTGC 61.109 63.158 0.00 0.00 0.00 4.57
479 492 2.816958 AGCAGCTCGTTGGCGATG 60.817 61.111 0.00 0.00 46.80 3.84
481 494 2.786539 AATCAGCAGCTCGTTGGCGA 62.787 55.000 0.00 0.00 45.79 5.54
482 495 1.915614 AAATCAGCAGCTCGTTGGCG 61.916 55.000 0.00 0.00 37.29 5.69
483 496 0.455633 CAAATCAGCAGCTCGTTGGC 60.456 55.000 0.00 0.00 0.00 4.52
484 497 0.169672 CCAAATCAGCAGCTCGTTGG 59.830 55.000 12.00 12.00 0.00 3.77
485 498 1.129998 CTCCAAATCAGCAGCTCGTTG 59.870 52.381 0.00 0.00 0.00 4.10
486 499 1.446907 CTCCAAATCAGCAGCTCGTT 58.553 50.000 0.00 0.00 0.00 3.85
487 500 0.392193 CCTCCAAATCAGCAGCTCGT 60.392 55.000 0.00 0.00 0.00 4.18
488 501 0.392193 ACCTCCAAATCAGCAGCTCG 60.392 55.000 0.00 0.00 0.00 5.03
500 513 1.923395 CCCTGTGGCCTACCTCCAA 60.923 63.158 3.32 0.00 35.01 3.53
514 527 0.108424 CTCTGCGTTTCTCTCCCCTG 60.108 60.000 0.00 0.00 0.00 4.45
529 542 2.284921 TCCCCAGCCACTCCTCTG 60.285 66.667 0.00 0.00 0.00 3.35
530 543 2.284995 GTCCCCAGCCACTCCTCT 60.285 66.667 0.00 0.00 0.00 3.69
547 560 1.226974 CTCATACCCCTCGTGTGCG 60.227 63.158 0.00 0.00 33.79 5.34
553 566 3.906720 TTTTCTTCCTCATACCCCTCG 57.093 47.619 0.00 0.00 0.00 4.63
581 594 1.081892 CTTGTCTCCTCACGCCAATG 58.918 55.000 0.00 0.00 0.00 2.82
603 616 2.452114 CTCTCACCCCCACCCTCT 59.548 66.667 0.00 0.00 0.00 3.69
631 644 1.078214 AGATCGTGTGGCCCATGTG 60.078 57.895 0.00 0.00 0.00 3.21
632 645 1.078214 CAGATCGTGTGGCCCATGT 60.078 57.895 0.00 0.00 0.00 3.21
659 672 4.179570 GTCGCGCGCTCTTCGTTC 62.180 66.667 30.48 7.25 41.07 3.95
663 676 4.135493 GTTGGTCGCGCGCTCTTC 62.135 66.667 30.48 15.79 0.00 2.87
686 699 0.323360 TTATGGCTGGTTGGCTGACC 60.323 55.000 4.01 4.01 42.34 4.02
687 700 1.098050 CTTATGGCTGGTTGGCTGAC 58.902 55.000 0.00 0.00 42.34 3.51
690 703 1.214305 TCCCTTATGGCTGGTTGGCT 61.214 55.000 0.00 0.00 42.34 4.75
691 704 0.106015 ATCCCTTATGGCTGGTTGGC 60.106 55.000 0.00 0.00 42.18 4.52
695 708 3.569491 CAAATGATCCCTTATGGCTGGT 58.431 45.455 0.00 0.00 0.00 4.00
702 715 9.881773 TTATCTTTTAGGCAAATGATCCCTTAT 57.118 29.630 11.28 0.00 38.65 1.73
731 744 7.066163 CCTCAACATATGCTTTCATTGTCTGTA 59.934 37.037 1.58 0.00 34.22 2.74
735 748 6.094603 AGTCCTCAACATATGCTTTCATTGTC 59.905 38.462 1.58 0.00 34.22 3.18
737 750 6.263344 CAGTCCTCAACATATGCTTTCATTG 58.737 40.000 1.58 0.00 34.22 2.82
740 753 3.691118 GCAGTCCTCAACATATGCTTTCA 59.309 43.478 1.58 0.00 0.00 2.69
743 756 3.012518 GTGCAGTCCTCAACATATGCTT 58.987 45.455 1.58 0.00 34.80 3.91
755 768 4.623932 TGTATCTTTTGAGTGCAGTCCT 57.376 40.909 18.82 0.00 0.00 3.85
771 784 6.416455 TCATCACGTGCTTTTGTTTTTGTATC 59.584 34.615 11.67 0.00 0.00 2.24
772 785 6.269315 TCATCACGTGCTTTTGTTTTTGTAT 58.731 32.000 11.67 0.00 0.00 2.29
773 786 5.641709 TCATCACGTGCTTTTGTTTTTGTA 58.358 33.333 11.67 0.00 0.00 2.41
774 787 4.489810 TCATCACGTGCTTTTGTTTTTGT 58.510 34.783 11.67 0.00 0.00 2.83
775 788 4.548726 GCTCATCACGTGCTTTTGTTTTTG 60.549 41.667 11.67 0.00 0.00 2.44
776 789 3.551485 GCTCATCACGTGCTTTTGTTTTT 59.449 39.130 11.67 0.00 0.00 1.94
781 794 1.678360 GTGCTCATCACGTGCTTTTG 58.322 50.000 11.67 6.01 35.76 2.44
794 807 4.662961 CGCCCGTGTGAGTGCTCA 62.663 66.667 0.00 0.00 37.24 4.26
823 836 1.146358 CTACTAGCACGGGAAAGCGC 61.146 60.000 0.00 0.00 35.48 5.92
829 842 5.864418 AATAAATGACTACTAGCACGGGA 57.136 39.130 0.00 0.00 0.00 5.14
833 846 8.267367 GCGAACTTAATAAATGACTACTAGCAC 58.733 37.037 0.00 0.00 0.00 4.40
857 870 4.965042 TGTGTGCGTCATATTTATAGCG 57.035 40.909 0.00 0.00 0.00 4.26
872 885 1.135315 CCAGCATAGCGTTGTGTGC 59.865 57.895 0.00 0.00 37.84 4.57
874 887 1.890876 TTTCCAGCATAGCGTTGTGT 58.109 45.000 0.00 0.00 0.00 3.72
884 897 7.037438 CAGTTGTAATAAGCATTTTCCAGCAT 58.963 34.615 0.00 0.00 0.00 3.79
885 898 6.389091 CAGTTGTAATAAGCATTTTCCAGCA 58.611 36.000 0.00 0.00 0.00 4.41
887 900 6.332630 CCCAGTTGTAATAAGCATTTTCCAG 58.667 40.000 0.00 0.00 0.00 3.86
896 909 3.506067 ACACAAGCCCAGTTGTAATAAGC 59.494 43.478 0.00 0.00 38.65 3.09
907 920 0.322546 GGGACCTTACACAAGCCCAG 60.323 60.000 0.00 0.00 35.30 4.45
923 936 1.398958 GGCAAACAAGTGGCAAGGGA 61.399 55.000 0.00 0.00 43.33 4.20
927 940 0.908198 AAAGGGCAAACAAGTGGCAA 59.092 45.000 0.00 0.00 45.56 4.52
976 990 3.445805 GTGATCCTTTTCCTCTCTCGAGT 59.554 47.826 13.13 0.00 35.43 4.18
992 1006 2.588877 CGCCGTCCATGGTGATCC 60.589 66.667 12.58 0.00 42.25 3.36
1002 1016 2.126424 GAGTGTGTCTCGCCGTCC 60.126 66.667 0.00 0.00 33.25 4.79
1019 1033 3.181514 CGGCTTACCCACGACATTAAAAG 60.182 47.826 0.00 0.00 0.00 2.27
1151 1165 2.046023 CACATCAAGCCCTCGCCA 60.046 61.111 0.00 0.00 34.57 5.69
1196 1210 7.010923 GTGTGTTTTGCAAATTAAAGATCCACA 59.989 33.333 13.65 7.28 0.00 4.17
1234 1248 1.133869 CGGCCGGTCGTTGATTTTC 59.866 57.895 22.93 0.00 0.00 2.29
1334 1369 3.497884 GAAGATGGGGATGGCCGGG 62.498 68.421 2.18 0.00 33.83 5.73
1465 1500 1.003118 CGTGGAATGTCAAGGGAAGGA 59.997 52.381 0.00 0.00 0.00 3.36
1469 1504 1.002624 GGCGTGGAATGTCAAGGGA 60.003 57.895 0.00 0.00 0.00 4.20
1564 1600 2.092429 TCCTAATCAATGCTCCCCACAC 60.092 50.000 0.00 0.00 0.00 3.82
1591 1627 6.465894 GCAACCTGATGTTAATACCCTCCTAT 60.466 42.308 0.00 0.00 34.69 2.57
2148 2185 0.179084 TTCCCTCGAATCATGGCGAC 60.179 55.000 0.00 0.00 32.51 5.19
2154 2191 2.509548 TCACCCAATTCCCTCGAATCAT 59.490 45.455 0.00 0.00 37.76 2.45
2161 2198 3.089284 ACGAATTTCACCCAATTCCCTC 58.911 45.455 0.00 0.00 39.20 4.30
2163 2200 3.584834 CAACGAATTTCACCCAATTCCC 58.415 45.455 0.00 0.00 39.20 3.97
2201 2238 2.938451 CTCAAATCAGCGGATAACAGCA 59.062 45.455 0.00 0.00 39.53 4.41
2205 2242 1.261619 CGCCTCAAATCAGCGGATAAC 59.738 52.381 0.00 0.00 45.88 1.89
2208 2245 4.131376 CGCCTCAAATCAGCGGAT 57.869 55.556 0.00 0.00 45.88 4.18
2224 2262 4.565564 CCCTACCAGAACTAAACGAAATCG 59.434 45.833 0.48 0.48 46.33 3.34
2236 2274 1.546998 CCAACCCAACCCTACCAGAAC 60.547 57.143 0.00 0.00 0.00 3.01
2239 2277 1.382629 CCCAACCCAACCCTACCAG 59.617 63.158 0.00 0.00 0.00 4.00
2241 2279 2.036731 GCCCAACCCAACCCTACC 59.963 66.667 0.00 0.00 0.00 3.18
2249 2287 2.034999 GGACATTCGCCCAACCCA 59.965 61.111 0.00 0.00 0.00 4.51
2263 2301 2.618053 CTACCAGAACATTCGTGGGAC 58.382 52.381 12.05 0.00 35.48 4.46
2264 2302 1.553248 CCTACCAGAACATTCGTGGGA 59.447 52.381 12.05 5.47 35.48 4.37
2265 2303 1.406887 CCCTACCAGAACATTCGTGGG 60.407 57.143 12.05 5.53 35.48 4.61
2266 2304 1.278127 ACCCTACCAGAACATTCGTGG 59.722 52.381 7.95 7.95 37.38 4.94
2267 2305 2.762535 ACCCTACCAGAACATTCGTG 57.237 50.000 0.00 0.00 0.00 4.35
2268 2306 2.904434 AGAACCCTACCAGAACATTCGT 59.096 45.455 0.00 0.00 0.00 3.85
2269 2307 3.056107 TCAGAACCCTACCAGAACATTCG 60.056 47.826 0.00 0.00 0.00 3.34
2271 2309 5.520748 AATCAGAACCCTACCAGAACATT 57.479 39.130 0.00 0.00 0.00 2.71
2272 2310 5.014123 TCAAATCAGAACCCTACCAGAACAT 59.986 40.000 0.00 0.00 0.00 2.71
2273 2311 4.349636 TCAAATCAGAACCCTACCAGAACA 59.650 41.667 0.00 0.00 0.00 3.18
2274 2312 4.906618 TCAAATCAGAACCCTACCAGAAC 58.093 43.478 0.00 0.00 0.00 3.01
2275 2313 4.019321 CCTCAAATCAGAACCCTACCAGAA 60.019 45.833 0.00 0.00 0.00 3.02
2277 2315 3.264450 ACCTCAAATCAGAACCCTACCAG 59.736 47.826 0.00 0.00 0.00 4.00
2279 2317 5.431179 TTACCTCAAATCAGAACCCTACC 57.569 43.478 0.00 0.00 0.00 3.18
2281 2319 6.821665 CGAAATTACCTCAAATCAGAACCCTA 59.178 38.462 0.00 0.00 0.00 3.53
2282 2320 5.648092 CGAAATTACCTCAAATCAGAACCCT 59.352 40.000 0.00 0.00 0.00 4.34
2283 2321 5.163652 CCGAAATTACCTCAAATCAGAACCC 60.164 44.000 0.00 0.00 0.00 4.11
2284 2322 5.414765 ACCGAAATTACCTCAAATCAGAACC 59.585 40.000 0.00 0.00 0.00 3.62
2288 2326 5.880054 ACACCGAAATTACCTCAAATCAG 57.120 39.130 0.00 0.00 0.00 2.90
2290 2328 5.861787 CCAAACACCGAAATTACCTCAAATC 59.138 40.000 0.00 0.00 0.00 2.17
2291 2329 5.279256 CCCAAACACCGAAATTACCTCAAAT 60.279 40.000 0.00 0.00 0.00 2.32
2292 2330 4.038162 CCCAAACACCGAAATTACCTCAAA 59.962 41.667 0.00 0.00 0.00 2.69
2293 2331 3.570550 CCCAAACACCGAAATTACCTCAA 59.429 43.478 0.00 0.00 0.00 3.02
2294 2332 3.150767 CCCAAACACCGAAATTACCTCA 58.849 45.455 0.00 0.00 0.00 3.86
2297 2353 2.608506 GCACCCAAACACCGAAATTACC 60.609 50.000 0.00 0.00 0.00 2.85
2406 2497 1.002069 AACTTCATCTGGATGCCCCA 58.998 50.000 5.77 0.00 44.25 4.96
2408 2499 2.425143 TCAACTTCATCTGGATGCCC 57.575 50.000 5.77 0.00 38.65 5.36
2484 2575 8.695456 ACTTGTAGAGTTTTTCCAAATTGACAT 58.305 29.630 0.00 0.00 33.92 3.06
2485 2576 7.973388 CACTTGTAGAGTTTTTCCAAATTGACA 59.027 33.333 0.00 0.00 36.10 3.58
2486 2577 7.973944 ACACTTGTAGAGTTTTTCCAAATTGAC 59.026 33.333 0.00 0.00 36.10 3.18
2487 2578 8.062065 ACACTTGTAGAGTTTTTCCAAATTGA 57.938 30.769 0.00 0.00 36.10 2.57
2527 2619 1.892474 GTTGCTAAACTGGCCATTCCA 59.108 47.619 5.51 0.00 44.18 3.53
2550 2642 2.081462 ACACAACCGTAGCAATAAGGC 58.919 47.619 0.00 0.00 0.00 4.35
2647 2739 2.806244 GCGTTTTGCTTTCACCTAGAGA 59.194 45.455 0.00 0.00 41.73 3.10
2770 2862 8.394971 TCTATTCTCAAACAAAATGAAGAGCA 57.605 30.769 0.00 0.00 0.00 4.26
2844 2936 0.810031 CCCCTTGCAACGGATCTACG 60.810 60.000 15.24 0.00 40.31 3.51
3572 3666 3.686227 TCAGATTTGTAATGCCCCCAT 57.314 42.857 0.00 0.00 0.00 4.00
3606 3700 3.050619 CGGGCATACAGAGAAACGATAC 58.949 50.000 0.00 0.00 0.00 2.24
3620 3714 0.246360 CGTGGCTCATATCGGGCATA 59.754 55.000 4.44 0.00 40.00 3.14
3678 3772 4.364817 TTCCGTAACAACTGCCCG 57.635 55.556 0.00 0.00 0.00 6.13
3907 4001 4.754618 TGGTGCCATTCGATTGTATATCAC 59.245 41.667 6.56 6.14 0.00 3.06
3908 4002 4.754618 GTGGTGCCATTCGATTGTATATCA 59.245 41.667 6.56 0.00 0.00 2.15
3909 4003 4.143115 CGTGGTGCCATTCGATTGTATATC 60.143 45.833 6.56 0.00 0.00 1.63
3945 4039 4.503991 GCAACACCTCTAGATGGGATTAGG 60.504 50.000 4.07 0.00 0.00 2.69
3951 4045 2.787473 TTGCAACACCTCTAGATGGG 57.213 50.000 0.00 4.69 0.00 4.00
3956 4050 2.079925 GGAGCTTTGCAACACCTCTAG 58.920 52.381 15.63 4.42 0.00 2.43
3957 4051 1.419762 TGGAGCTTTGCAACACCTCTA 59.580 47.619 15.63 9.84 0.00 2.43
3958 4052 0.183492 TGGAGCTTTGCAACACCTCT 59.817 50.000 15.63 3.42 0.00 3.69
3959 4053 0.312102 GTGGAGCTTTGCAACACCTC 59.688 55.000 0.00 5.14 33.57 3.85
4024 4131 1.548986 GCCAACAAGCGCACATAATC 58.451 50.000 11.47 0.00 0.00 1.75
4034 4141 0.383949 TTCAGTTTCGGCCAACAAGC 59.616 50.000 2.24 0.00 0.00 4.01
4099 4206 7.598869 CCAGATTTTTAGGGCTAACTTTCAAAC 59.401 37.037 0.00 0.00 0.00 2.93
4110 4217 3.117360 CCTCCATCCAGATTTTTAGGGCT 60.117 47.826 0.00 0.00 0.00 5.19
4512 4619 3.297134 ACCACATTCCAAAGTGTCAGT 57.703 42.857 0.00 0.00 33.99 3.41
5024 5131 7.756722 ACTTGCTTTCATAGTCATTATTGTTGC 59.243 33.333 0.00 0.00 0.00 4.17
5483 5590 8.812329 TGTGTATGCTTTCATTTTACAAACAAC 58.188 29.630 0.00 0.00 34.22 3.32
5484 5591 8.812329 GTGTGTATGCTTTCATTTTACAAACAA 58.188 29.630 0.00 0.00 31.67 2.83
5485 5592 7.976175 TGTGTGTATGCTTTCATTTTACAAACA 59.024 29.630 0.00 0.00 35.84 2.83
5566 5676 5.106038 TGTTTCAACATCAATCTCTGCATCC 60.106 40.000 0.00 0.00 33.17 3.51
5635 5745 3.036819 AGCAGGCAAGTAGATGATCTCA 58.963 45.455 0.00 0.00 0.00 3.27
5725 5835 2.288666 GGCGAACCAGAATGATTGCTA 58.711 47.619 0.00 0.00 39.69 3.49
5838 5948 5.237127 CACAAAATGAGACACTGCTGAAGTA 59.763 40.000 0.00 0.00 36.83 2.24
5906 6016 6.734104 TTTGTGTTTGATGGGAAACAAAAG 57.266 33.333 0.00 0.00 45.13 2.27
5907 6017 7.363431 GTTTTTGTGTTTGATGGGAAACAAAA 58.637 30.769 7.26 7.26 45.13 2.44
5911 6021 5.064579 CAGGTTTTTGTGTTTGATGGGAAAC 59.935 40.000 0.00 0.00 36.53 2.78
5977 6087 8.650143 AAATGAAGACCAACTTATGTTACCAT 57.350 30.769 0.00 0.00 39.13 3.55
5978 6088 8.472007 AAAATGAAGACCAACTTATGTTACCA 57.528 30.769 0.00 0.00 39.13 3.25
5979 6089 9.836076 GTAAAATGAAGACCAACTTATGTTACC 57.164 33.333 0.00 0.00 39.13 2.85
6129 6243 7.704789 TCATCATTCATCAATACGAGTTCAG 57.295 36.000 0.00 0.00 0.00 3.02
6135 6249 8.863049 CGATTACATCATCATTCATCAATACGA 58.137 33.333 0.00 0.00 0.00 3.43
6181 6295 2.943033 ACGTCAGAAGGTTCAGGTTTTG 59.057 45.455 0.00 0.00 0.00 2.44
6214 6328 8.472007 AGGATGATAACAGTTAAACCACAAAA 57.528 30.769 0.00 0.00 0.00 2.44
6222 6336 8.713708 TTTTGGGAAGGATGATAACAGTTAAA 57.286 30.769 0.00 0.00 0.00 1.52
6276 6395 3.243805 CCATGGAATTGTCAACAACTGCA 60.244 43.478 5.56 1.16 37.77 4.41
6384 6503 5.319043 TCTTTATGGGTGGTTTCTTCACT 57.681 39.130 0.00 0.00 35.61 3.41
6496 6615 1.230635 CCGTTGACAGGTTCCAGCAG 61.231 60.000 0.00 0.00 0.00 4.24
6649 6769 7.232552 ACATAGGTGATAGCCCTATCTCTAT 57.767 40.000 14.46 15.75 42.19 1.98
6805 6966 3.877508 GCTTAACCATGGTCCATACTGAC 59.122 47.826 20.07 0.00 34.42 3.51
6843 7004 6.092955 AGACTTAACCACAACGATCTACAA 57.907 37.500 0.00 0.00 0.00 2.41
6852 7013 3.460103 TCAACCGAGACTTAACCACAAC 58.540 45.455 0.00 0.00 0.00 3.32
6857 7018 4.929781 ACGATATCAACCGAGACTTAACC 58.070 43.478 3.12 0.00 0.00 2.85
6883 7044 1.933115 GCATAACCCACGGGCACAAG 61.933 60.000 0.69 0.00 39.32 3.16
6887 7048 0.179032 CATAGCATAACCCACGGGCA 60.179 55.000 0.69 0.00 39.32 5.36
6892 7053 2.938956 AGGCTCATAGCATAACCCAC 57.061 50.000 0.78 0.00 44.75 4.61
7150 7326 9.457110 TTTACTATTTCGTTTTGTACAGTCGTA 57.543 29.630 13.16 4.72 0.00 3.43
7151 7327 7.928908 TTACTATTTCGTTTTGTACAGTCGT 57.071 32.000 13.16 1.90 0.00 4.34
7153 7329 7.473411 CGCTTTACTATTTCGTTTTGTACAGTC 59.527 37.037 0.00 0.00 0.00 3.51
7301 7512 9.823098 CCTTGATTAGTACGTACACATAGTATC 57.177 37.037 26.55 16.24 34.67 2.24
7302 7513 8.790718 CCCTTGATTAGTACGTACACATAGTAT 58.209 37.037 26.55 6.77 34.67 2.12
7303 7514 7.992608 TCCCTTGATTAGTACGTACACATAGTA 59.007 37.037 26.55 7.21 0.00 1.82
7304 7515 6.830324 TCCCTTGATTAGTACGTACACATAGT 59.170 38.462 26.55 8.17 0.00 2.12
7305 7516 7.013083 ACTCCCTTGATTAGTACGTACACATAG 59.987 40.741 26.55 14.70 0.00 2.23
7306 7517 6.830324 ACTCCCTTGATTAGTACGTACACATA 59.170 38.462 26.55 8.65 0.00 2.29
7310 7859 6.418101 ACTACTCCCTTGATTAGTACGTACA 58.582 40.000 26.55 8.35 35.78 2.90
7315 7864 9.722184 AAAAAGAACTACTCCCTTGATTAGTAC 57.278 33.333 0.00 0.00 36.33 2.73
7354 7903 2.304180 ACCTGGGAGTCAATCAGAGTTG 59.696 50.000 0.00 0.00 0.00 3.16
7488 8038 7.120138 TGGTACTGCTAATTTACTAAAAGTGGC 59.880 37.037 0.00 0.60 44.41 5.01
7506 8056 4.855715 TGCTATAGTCAGATGGTACTGC 57.144 45.455 0.84 0.00 37.75 4.40
7507 8057 7.316640 GGTTATGCTATAGTCAGATGGTACTG 58.683 42.308 0.84 0.00 39.02 2.74
7525 8078 2.689983 CAGTGATCCCTTTGGGTTATGC 59.310 50.000 2.25 0.00 44.74 3.14
7529 8082 3.852578 AGATACAGTGATCCCTTTGGGTT 59.147 43.478 0.00 0.00 44.74 4.11


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

AutoCloner maintained by Alex Coulton.