Multiple sequence alignment - TraesCS3A01G387300

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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 TraesCS3A01G387300 chr3A 100.000 3525 0 0 1 3525 636539636 636536112 0.000000e+00 6510.0
1 TraesCS3A01G387300 chr3A 82.793 1296 178 25 729 2011 702953067 702951804 0.000000e+00 1116.0
2 TraesCS3A01G387300 chr3A 84.760 853 113 12 1188 2029 702589749 702588903 0.000000e+00 839.0
3 TraesCS3A01G387300 chr3A 86.427 641 58 13 1307 1944 655894626 655894012 0.000000e+00 675.0
4 TraesCS3A01G387300 chr3A 84.918 610 66 16 649 1248 655895219 655894626 8.430000e-166 593.0
5 TraesCS3A01G387300 chr3A 80.519 462 85 5 2181 2641 702587532 702587075 2.010000e-92 350.0
6 TraesCS3A01G387300 chr3A 84.706 340 30 3 2202 2541 655894011 655893694 1.580000e-83 320.0
7 TraesCS3A01G387300 chr3A 89.243 251 19 7 3277 3525 636400971 636400727 1.230000e-79 307.0
8 TraesCS3A01G387300 chr3A 83.333 246 23 12 3277 3518 636393803 636393572 9.910000e-51 211.0
9 TraesCS3A01G387300 chr3A 86.702 188 19 4 3337 3520 636159042 636158857 1.660000e-48 204.0
10 TraesCS3A01G387300 chr3A 85.417 192 25 3 25 215 655895533 655895344 2.780000e-46 196.0
11 TraesCS3A01G387300 chr3A 84.444 180 27 1 20 198 655630582 655630761 3.620000e-40 176.0
12 TraesCS3A01G387300 chr3A 94.444 90 3 2 2026 2115 23375510 23375423 1.710000e-28 137.0
13 TraesCS3A01G387300 chr3A 83.212 137 21 2 2169 2304 655629860 655629995 1.330000e-24 124.0
14 TraesCS3A01G387300 chr3A 87.368 95 12 0 1089 1183 702594477 702594383 3.720000e-20 110.0
15 TraesCS3A01G387300 chr3D 91.534 1512 104 12 528 2030 497867127 497868623 0.000000e+00 2061.0
16 TraesCS3A01G387300 chr3D 92.870 547 38 1 2119 2664 497868613 497869159 0.000000e+00 793.0
17 TraesCS3A01G387300 chr3D 84.887 622 81 10 946 1559 567848347 567848963 1.800000e-172 616.0
18 TraesCS3A01G387300 chr3D 83.837 563 58 19 156 688 520320677 520320118 4.060000e-139 505.0
19 TraesCS3A01G387300 chr3D 74.434 1060 219 44 992 2014 520319253 520318209 3.280000e-110 409.0
20 TraesCS3A01G387300 chr3D 88.000 350 35 6 3180 3525 497869377 497869723 1.180000e-109 407.0
21 TraesCS3A01G387300 chr3D 84.141 227 27 7 3300 3525 498096180 498096398 9.910000e-51 211.0
22 TraesCS3A01G387300 chr3D 82.819 227 27 9 3297 3520 497958879 497959096 3.590000e-45 193.0
23 TraesCS3A01G387300 chr3D 84.962 133 20 0 2172 2304 520321493 520321361 6.140000e-28 135.0
24 TraesCS3A01G387300 chr3D 97.143 35 1 0 2648 2682 497869208 497869174 3.800000e-05 60.2
25 TraesCS3A01G387300 chr3B 94.212 1313 66 8 720 2030 658489665 658490969 0.000000e+00 1995.0
26 TraesCS3A01G387300 chr3B 84.666 1226 152 23 817 2029 756687003 756685801 0.000000e+00 1190.0
27 TraesCS3A01G387300 chr3B 92.740 551 40 0 2115 2665 658490955 658491505 0.000000e+00 797.0
28 TraesCS3A01G387300 chr3B 87.656 640 62 7 1307 1944 684765206 684765830 0.000000e+00 728.0
29 TraesCS3A01G387300 chr3B 85.057 609 72 15 649 1248 684764608 684765206 1.400000e-168 603.0
30 TraesCS3A01G387300 chr3B 82.353 748 62 32 2813 3525 658491865 658492577 1.410000e-163 586.0
31 TraesCS3A01G387300 chr3B 84.979 466 51 2 2202 2667 684765831 684766277 4.150000e-124 455.0
32 TraesCS3A01G387300 chr3B 85.039 381 54 3 2158 2536 756685744 756685365 5.520000e-103 385.0
33 TraesCS3A01G387300 chr3B 86.726 339 31 11 3189 3520 659067879 659068210 7.190000e-97 364.0
34 TraesCS3A01G387300 chr3B 73.367 995 227 29 958 1940 756824209 756823241 5.640000e-88 335.0
35 TraesCS3A01G387300 chr3B 73.065 995 229 30 958 1940 756709077 756708110 2.040000e-82 316.0
36 TraesCS3A01G387300 chr3B 78.558 541 67 25 193 722 658489049 658489551 9.500000e-81 311.0
37 TraesCS3A01G387300 chr3B 88.945 199 18 4 2 197 658488772 658488969 3.520000e-60 243.0
38 TraesCS3A01G387300 chr3B 86.243 189 18 6 3337 3520 659000891 659001076 7.720000e-47 198.0
39 TraesCS3A01G387300 chr3B 84.896 192 25 4 25 215 684764295 684764483 1.290000e-44 191.0
40 TraesCS3A01G387300 chr3B 90.551 127 7 2 2677 2798 658491550 658491676 2.820000e-36 163.0
41 TraesCS3A01G387300 chr3B 96.471 85 1 2 2026 2110 691355146 691355064 4.740000e-29 139.0
42 TraesCS3A01G387300 chr3B 82.353 136 23 1 2169 2304 684763764 684763898 2.220000e-22 117.0
43 TraesCS3A01G387300 chr3B 100.000 31 0 0 2648 2678 658491553 658491523 1.370000e-04 58.4
44 TraesCS3A01G387300 chr5A 75.025 1013 206 26 941 1920 401317709 401316711 3.250000e-115 425.0
45 TraesCS3A01G387300 chr5D 74.950 1010 199 33 941 1917 297736826 297737814 7.040000e-112 414.0
46 TraesCS3A01G387300 chr5D 84.768 151 12 6 855 1003 297751139 297751280 1.320000e-29 141.0
47 TraesCS3A01G387300 chr7B 96.471 85 3 0 2026 2110 223611500 223611584 1.320000e-29 141.0
48 TraesCS3A01G387300 chr1B 95.506 89 2 2 2025 2113 137131848 137131934 1.320000e-29 141.0
49 TraesCS3A01G387300 chr1B 93.478 92 4 2 2021 2110 670233084 670233175 6.140000e-28 135.0
50 TraesCS3A01G387300 chr4B 94.505 91 3 2 2026 2115 496551591 496551680 4.740000e-29 139.0
51 TraesCS3A01G387300 chr2B 93.684 95 3 3 2021 2115 690214201 690214292 4.740000e-29 139.0
52 TraesCS3A01G387300 chr6D 92.553 94 5 2 2017 2110 114160417 114160326 2.210000e-27 134.0
53 TraesCS3A01G387300 chr1D 91.919 99 3 4 2019 2115 202541178 202541083 2.210000e-27 134.0


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 TraesCS3A01G387300 chr3A 636536112 636539636 3524 True 6510.000000 6510 100.000000 1 3525 1 chr3A.!!$R5 3524
1 TraesCS3A01G387300 chr3A 702951804 702953067 1263 True 1116.000000 1116 82.793000 729 2011 1 chr3A.!!$R7 1282
2 TraesCS3A01G387300 chr3A 702587075 702589749 2674 True 594.500000 839 82.639500 1188 2641 2 chr3A.!!$R9 1453
3 TraesCS3A01G387300 chr3A 655893694 655895533 1839 True 446.000000 675 85.367000 25 2541 4 chr3A.!!$R8 2516
4 TraesCS3A01G387300 chr3D 497867127 497869723 2596 False 1087.000000 2061 90.801333 528 3525 3 chr3D.!!$F4 2997
5 TraesCS3A01G387300 chr3D 567848347 567848963 616 False 616.000000 616 84.887000 946 1559 1 chr3D.!!$F3 613
6 TraesCS3A01G387300 chr3D 520318209 520321493 3284 True 349.666667 505 81.077667 156 2304 3 chr3D.!!$R2 2148
7 TraesCS3A01G387300 chr3B 756685365 756687003 1638 True 787.500000 1190 84.852500 817 2536 2 chr3B.!!$R5 1719
8 TraesCS3A01G387300 chr3B 658488772 658492577 3805 False 682.500000 1995 87.893167 2 3525 6 chr3B.!!$F3 3523
9 TraesCS3A01G387300 chr3B 684763764 684766277 2513 False 418.800000 728 84.988200 25 2667 5 chr3B.!!$F4 2642
10 TraesCS3A01G387300 chr3B 756823241 756824209 968 True 335.000000 335 73.367000 958 1940 1 chr3B.!!$R4 982
11 TraesCS3A01G387300 chr3B 756708110 756709077 967 True 316.000000 316 73.065000 958 1940 1 chr3B.!!$R3 982
12 TraesCS3A01G387300 chr5A 401316711 401317709 998 True 425.000000 425 75.025000 941 1920 1 chr5A.!!$R1 979
13 TraesCS3A01G387300 chr5D 297736826 297737814 988 False 414.000000 414 74.950000 941 1917 1 chr5D.!!$F1 976

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
258 1047 0.252197 GGTTTACAGGACCGCCAGAT 59.748 55.0 0.0 0.0 36.29 2.90 F
1378 2912 0.620556 ACGGGAAGATGGTGATTGCT 59.379 50.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 3645 0.036448 TCCGTCAATTAACCGGGCAA 59.964 50.0 6.32 0.0 41.98 4.52 R
2768 5694 0.031716 CCAGGAGAGATGGGTCCAGA 60.032 60.0 0.00 0.0 35.02 3.86 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
96 99 6.539103 GTGTTTGTATCTTCCCCTTATCTGAC 59.461 42.308 0.00 0.00 0.00 3.51
100 103 6.830912 TGTATCTTCCCCTTATCTGACAATG 58.169 40.000 0.00 0.00 0.00 2.82
131 135 7.498900 TGAGTTTAATATTGATGTTCCGCTGAT 59.501 33.333 0.00 0.00 0.00 2.90
216 1003 2.770802 ACAGAACATGCCATCTCTAGCT 59.229 45.455 0.00 0.00 0.00 3.32
247 1036 1.086696 CCATCAGTGGCGGTTTACAG 58.913 55.000 0.00 0.00 39.01 2.74
248 1037 1.086696 CATCAGTGGCGGTTTACAGG 58.913 55.000 0.00 0.00 0.00 4.00
258 1047 0.252197 GGTTTACAGGACCGCCAGAT 59.748 55.000 0.00 0.00 36.29 2.90
292 1086 2.497675 GTCAGTCCATCAGAGGCAGTTA 59.502 50.000 0.00 0.00 0.00 2.24
293 1087 2.497675 TCAGTCCATCAGAGGCAGTTAC 59.502 50.000 0.00 0.00 0.00 2.50
295 1089 1.555075 GTCCATCAGAGGCAGTTACCA 59.445 52.381 0.00 0.00 0.00 3.25
297 1091 2.027192 TCCATCAGAGGCAGTTACCAAC 60.027 50.000 0.00 0.00 0.00 3.77
298 1092 2.359900 CATCAGAGGCAGTTACCAACC 58.640 52.381 0.00 0.00 0.00 3.77
303 1097 3.263941 GCAGTTACCAACCGCCTG 58.736 61.111 0.00 0.00 0.00 4.85
331 1129 5.419542 GACAATATGTGAGCACTCCAGTTA 58.580 41.667 1.99 0.00 0.00 2.24
332 1130 5.423015 ACAATATGTGAGCACTCCAGTTAG 58.577 41.667 1.99 0.00 0.00 2.34
334 1132 6.154534 ACAATATGTGAGCACTCCAGTTAGTA 59.845 38.462 1.99 0.00 0.00 1.82
335 1133 6.985653 ATATGTGAGCACTCCAGTTAGTAT 57.014 37.500 1.99 0.00 0.00 2.12
336 1134 4.720649 TGTGAGCACTCCAGTTAGTATC 57.279 45.455 1.99 0.00 0.00 2.24
338 1136 4.158579 TGTGAGCACTCCAGTTAGTATCTG 59.841 45.833 1.99 1.76 0.00 2.90
339 1137 4.399618 GTGAGCACTCCAGTTAGTATCTGA 59.600 45.833 9.42 0.00 35.20 3.27
341 1139 5.658634 TGAGCACTCCAGTTAGTATCTGATT 59.341 40.000 9.42 0.00 35.20 2.57
342 1140 5.911752 AGCACTCCAGTTAGTATCTGATTG 58.088 41.667 9.42 5.10 35.20 2.67
344 1142 6.607600 AGCACTCCAGTTAGTATCTGATTGTA 59.392 38.462 9.42 0.00 35.20 2.41
345 1143 7.288852 AGCACTCCAGTTAGTATCTGATTGTAT 59.711 37.037 9.42 0.00 35.20 2.29
346 1144 8.577296 GCACTCCAGTTAGTATCTGATTGTATA 58.423 37.037 9.42 0.00 35.20 1.47
373 1174 6.260714 TCAATATGGTGCTTGTGTAATGCTAG 59.739 38.462 0.00 0.00 0.00 3.42
380 1181 6.250819 GTGCTTGTGTAATGCTAGTATTGTG 58.749 40.000 15.50 1.93 0.00 3.33
433 1242 7.519008 GCCGGAAATTCAGTTAGTATCTGATTG 60.519 40.741 5.05 0.00 40.83 2.67
487 1296 4.843728 ACCATGTCAAATAACGATCCTGT 58.156 39.130 0.00 0.00 0.00 4.00
538 1347 7.133891 AGTGACAGATTGTTTTTCTTATCCG 57.866 36.000 0.00 0.00 0.00 4.18
543 1352 9.278734 GACAGATTGTTTTTCTTATCCGAATTC 57.721 33.333 0.00 0.00 0.00 2.17
554 1363 5.361857 TCTTATCCGAATTCGACCCTTTAGT 59.638 40.000 28.76 6.32 43.02 2.24
563 1372 4.715527 TCGACCCTTTAGTCTTTCTAGC 57.284 45.455 0.00 0.00 34.46 3.42
580 1392 3.860681 CTGGCCCAAACAGCAGTT 58.139 55.556 0.00 0.00 40.40 3.16
623 1435 4.829968 CACATTGACCATTTTATTGCCCA 58.170 39.130 0.00 0.00 0.00 5.36
655 1471 1.271054 ACAGTCATCCCTGTTGAGCAC 60.271 52.381 0.00 0.00 42.99 4.40
658 1476 1.059098 TCATCCCTGTTGAGCACTGT 58.941 50.000 0.00 0.00 0.00 3.55
668 1486 6.461509 CCCTGTTGAGCACTGTAAAAGAAAAT 60.462 38.462 0.00 0.00 0.00 1.82
682 1500 8.257306 TGTAAAAGAAAATTTGAACTTCCAGCT 58.743 29.630 0.00 0.00 0.00 4.24
919 2403 3.119316 AGAGCTGAACTTCCAGTACATCG 60.119 47.826 0.00 0.00 36.57 3.84
920 2404 2.563179 AGCTGAACTTCCAGTACATCGT 59.437 45.455 0.00 0.00 36.57 3.73
921 2405 3.006967 AGCTGAACTTCCAGTACATCGTT 59.993 43.478 0.00 0.00 36.57 3.85
923 2407 3.064207 TGAACTTCCAGTACATCGTTGC 58.936 45.455 0.00 0.00 0.00 4.17
924 2408 2.094762 ACTTCCAGTACATCGTTGCC 57.905 50.000 0.00 0.00 0.00 4.52
925 2409 1.346395 ACTTCCAGTACATCGTTGCCA 59.654 47.619 0.00 0.00 0.00 4.92
926 2410 2.224426 ACTTCCAGTACATCGTTGCCAA 60.224 45.455 0.00 0.00 0.00 4.52
933 2417 1.227999 ACATCGTTGCCAACTCACCG 61.228 55.000 5.96 0.00 0.00 4.94
934 2418 2.325082 ATCGTTGCCAACTCACCGC 61.325 57.895 5.96 0.00 0.00 5.68
937 2421 2.594303 TTGCCAACTCACCGCCTG 60.594 61.111 0.00 0.00 0.00 4.85
1032 2523 6.239204 CCAAACAGATGGTGCATATGAATCAT 60.239 38.462 9.38 9.38 35.38 2.45
1378 2912 0.620556 ACGGGAAGATGGTGATTGCT 59.379 50.000 0.00 0.00 0.00 3.91
1457 2991 1.402787 CACCCACAGCCACTTTCTTT 58.597 50.000 0.00 0.00 0.00 2.52
1601 3143 1.303561 GCTGTGCCAGGGTCATTCA 60.304 57.895 4.65 0.00 31.21 2.57
1617 3159 3.779183 TCATTCAATGAGAGGCTCTTCCT 59.221 43.478 19.80 3.50 40.55 3.36
1669 3211 3.372206 CCAACAGTCTTTATTGGCTCTCG 59.628 47.826 0.00 0.00 36.72 4.04
1860 3419 4.855388 CAGCAATTCAGGAAAGATTTCACG 59.145 41.667 7.56 0.00 38.92 4.35
1922 3481 0.953471 CGGATGGTTGTTTCGCTCCA 60.953 55.000 0.00 0.00 0.00 3.86
2053 3613 8.419076 TTTTCTTATGAAACAAGGCAAAAGAC 57.581 30.769 3.41 0.00 41.34 3.01
2054 3614 6.959639 TCTTATGAAACAAGGCAAAAGACT 57.040 33.333 0.00 0.00 0.00 3.24
2055 3615 7.346751 TCTTATGAAACAAGGCAAAAGACTT 57.653 32.000 0.00 0.00 0.00 3.01
2057 3617 3.520569 TGAAACAAGGCAAAAGACTTGC 58.479 40.909 10.80 0.78 46.03 4.01
2067 3627 5.678132 GCAAAAGACTTGCCATTTTCATT 57.322 34.783 0.00 0.00 39.38 2.57
2068 3628 5.445845 GCAAAAGACTTGCCATTTTCATTG 58.554 37.500 0.00 0.00 39.38 2.82
2069 3629 5.236911 GCAAAAGACTTGCCATTTTCATTGA 59.763 36.000 0.00 0.00 39.38 2.57
2070 3630 6.072893 GCAAAAGACTTGCCATTTTCATTGAT 60.073 34.615 0.00 0.00 39.38 2.57
2071 3631 7.520937 GCAAAAGACTTGCCATTTTCATTGATT 60.521 33.333 0.00 0.00 39.38 2.57
2072 3632 8.991026 CAAAAGACTTGCCATTTTCATTGATTA 58.009 29.630 0.00 0.00 0.00 1.75
2073 3633 9.558396 AAAAGACTTGCCATTTTCATTGATTAA 57.442 25.926 0.00 0.00 0.00 1.40
2074 3634 8.767478 AAGACTTGCCATTTTCATTGATTAAG 57.233 30.769 0.00 0.00 0.00 1.85
2075 3635 8.125978 AGACTTGCCATTTTCATTGATTAAGA 57.874 30.769 0.00 0.00 0.00 2.10
2076 3636 8.587608 AGACTTGCCATTTTCATTGATTAAGAA 58.412 29.630 0.00 0.00 0.00 2.52
2077 3637 8.767478 ACTTGCCATTTTCATTGATTAAGAAG 57.233 30.769 0.00 0.00 0.00 2.85
2078 3638 8.587608 ACTTGCCATTTTCATTGATTAAGAAGA 58.412 29.630 0.00 0.00 0.00 2.87
2079 3639 9.426837 CTTGCCATTTTCATTGATTAAGAAGAA 57.573 29.630 0.00 0.00 0.00 2.52
2080 3640 8.991243 TGCCATTTTCATTGATTAAGAAGAAG 57.009 30.769 0.00 0.00 0.00 2.85
2081 3641 8.805175 TGCCATTTTCATTGATTAAGAAGAAGA 58.195 29.630 0.00 0.00 0.00 2.87
2082 3642 9.298774 GCCATTTTCATTGATTAAGAAGAAGAG 57.701 33.333 0.00 0.00 0.00 2.85
2089 3649 8.680903 TCATTGATTAAGAAGAAGAGAATTGCC 58.319 33.333 0.00 0.00 0.00 4.52
2090 3650 7.396540 TTGATTAAGAAGAAGAGAATTGCCC 57.603 36.000 0.00 0.00 0.00 5.36
2091 3651 5.586243 TGATTAAGAAGAAGAGAATTGCCCG 59.414 40.000 0.00 0.00 0.00 6.13
2092 3652 2.409948 AGAAGAAGAGAATTGCCCGG 57.590 50.000 0.00 0.00 0.00 5.73
2093 3653 1.630878 AGAAGAAGAGAATTGCCCGGT 59.369 47.619 0.00 0.00 0.00 5.28
2094 3654 2.040412 AGAAGAAGAGAATTGCCCGGTT 59.960 45.455 0.00 0.00 0.00 4.44
2095 3655 3.263425 AGAAGAAGAGAATTGCCCGGTTA 59.737 43.478 0.00 0.00 0.00 2.85
2096 3656 3.713826 AGAAGAGAATTGCCCGGTTAA 57.286 42.857 0.00 0.00 0.00 2.01
2097 3657 4.236527 AGAAGAGAATTGCCCGGTTAAT 57.763 40.909 0.00 0.00 0.00 1.40
2098 3658 4.600062 AGAAGAGAATTGCCCGGTTAATT 58.400 39.130 11.61 11.61 0.00 1.40
2099 3659 4.399303 AGAAGAGAATTGCCCGGTTAATTG 59.601 41.667 15.42 0.00 0.00 2.32
2100 3660 3.963129 AGAGAATTGCCCGGTTAATTGA 58.037 40.909 15.42 0.00 0.00 2.57
2101 3661 3.694566 AGAGAATTGCCCGGTTAATTGAC 59.305 43.478 15.42 10.04 0.00 3.18
2102 3662 2.422127 AGAATTGCCCGGTTAATTGACG 59.578 45.455 15.42 0.00 0.00 4.35
2103 3663 1.099689 ATTGCCCGGTTAATTGACGG 58.900 50.000 0.00 9.49 46.79 4.79
2110 3670 3.900388 CGGTTAATTGACGGAAAACCA 57.100 42.857 2.16 0.00 39.66 3.67
2111 3671 4.226113 CGGTTAATTGACGGAAAACCAA 57.774 40.909 2.16 0.00 39.66 3.67
2112 3672 4.223659 CGGTTAATTGACGGAAAACCAAG 58.776 43.478 2.16 0.00 39.66 3.61
2113 3673 4.552355 GGTTAATTGACGGAAAACCAAGG 58.448 43.478 0.00 0.00 39.51 3.61
2114 3674 2.812358 AATTGACGGAAAACCAAGGC 57.188 45.000 0.00 0.00 0.00 4.35
2115 3675 1.698506 ATTGACGGAAAACCAAGGCA 58.301 45.000 0.00 0.00 0.00 4.75
2116 3676 1.475403 TTGACGGAAAACCAAGGCAA 58.525 45.000 0.00 0.00 0.00 4.52
2117 3677 1.028905 TGACGGAAAACCAAGGCAAG 58.971 50.000 0.00 0.00 0.00 4.01
2118 3678 0.318699 GACGGAAAACCAAGGCAAGC 60.319 55.000 0.00 0.00 0.00 4.01
2119 3679 0.755327 ACGGAAAACCAAGGCAAGCT 60.755 50.000 0.00 0.00 0.00 3.74
2120 3680 0.389025 CGGAAAACCAAGGCAAGCTT 59.611 50.000 0.00 0.00 0.00 3.74
2121 3681 1.202521 CGGAAAACCAAGGCAAGCTTT 60.203 47.619 0.00 0.00 0.00 3.51
2122 3682 2.035321 CGGAAAACCAAGGCAAGCTTTA 59.965 45.455 0.00 0.00 0.00 1.85
2123 3683 3.390135 GGAAAACCAAGGCAAGCTTTAC 58.610 45.455 0.00 0.00 0.00 2.01
2124 3684 3.069586 GGAAAACCAAGGCAAGCTTTACT 59.930 43.478 0.00 0.00 0.00 2.24
2125 3685 4.442893 GGAAAACCAAGGCAAGCTTTACTT 60.443 41.667 0.00 0.83 40.05 2.24
2126 3686 4.753516 AAACCAAGGCAAGCTTTACTTT 57.246 36.364 9.15 0.00 36.04 2.66
2127 3687 4.753516 AACCAAGGCAAGCTTTACTTTT 57.246 36.364 9.15 1.69 36.04 2.27
2128 3688 4.058721 ACCAAGGCAAGCTTTACTTTTG 57.941 40.909 9.15 7.00 36.04 2.44
2194 5082 5.659463 CAGGGTGTGATTGACAAAGAAAAA 58.341 37.500 0.00 0.00 35.91 1.94
2233 5121 1.745489 GGTGCATGGACCTTCCGAC 60.745 63.158 27.66 0.28 40.17 4.79
2342 5230 1.303643 CTCCTCACCCCAAACAGGC 60.304 63.158 0.00 0.00 35.39 4.85
2350 5238 1.463553 CCCCAAACAGGCTGGTGAAC 61.464 60.000 20.34 0.00 35.39 3.18
2401 5289 0.034186 TCCAGCATTTTGGATCGCCT 60.034 50.000 0.00 0.00 42.24 5.52
2529 5417 1.100510 CTCACCAAGGCATGACATGG 58.899 55.000 21.34 21.34 38.91 3.66
2541 5429 0.240678 TGACATGGCAATTGACGTGC 59.759 50.000 29.63 22.32 43.83 5.34
2577 5465 4.042809 TCTGTATCCCTCACCAATTTGTGT 59.957 41.667 9.30 0.00 37.51 3.72
2582 5470 2.353011 CCCTCACCAATTTGTGTCATGC 60.353 50.000 9.30 0.00 37.51 4.06
2587 5475 2.036217 ACCAATTTGTGTCATGCCTGTG 59.964 45.455 0.00 0.00 0.00 3.66
2600 5488 1.262950 TGCCTGTGAAATTCAACGTCG 59.737 47.619 0.00 0.00 0.00 5.12
2608 5496 6.186785 TGTGAAATTCAACGTCGAACTTAAC 58.813 36.000 0.00 0.00 0.00 2.01
2628 5516 1.630148 CGGATTTGTGAGAGACGGAC 58.370 55.000 0.00 0.00 0.00 4.79
2671 5559 9.793252 GAAATTGCATTGTGAGACATATACTTT 57.207 29.630 0.00 0.00 0.00 2.66
2672 5560 9.577110 AAATTGCATTGTGAGACATATACTTTG 57.423 29.630 0.00 0.00 0.00 2.77
2675 5563 6.183360 TGCATTGTGAGACATATACTTTGCTG 60.183 38.462 0.00 0.00 0.00 4.41
2715 5636 4.396166 AGTTCTGCAAAGGTACATACATGC 59.604 41.667 6.07 6.07 34.52 4.06
2768 5694 8.816894 TCTCATAAGAATTAGTGTTGTTCTCCT 58.183 33.333 0.00 0.00 31.76 3.69
2815 5915 5.954150 TCATCTATGCTATCAGTGAGGCATA 59.046 40.000 27.18 27.18 43.74 3.14
2846 5946 5.962433 CAGATTTTGGAATGCAGAAGATGT 58.038 37.500 0.00 0.00 0.00 3.06
2849 5949 7.066645 CAGATTTTGGAATGCAGAAGATGTCTA 59.933 37.037 0.00 0.00 33.56 2.59
2850 5950 6.748333 TTTTGGAATGCAGAAGATGTCTAG 57.252 37.500 0.00 0.00 33.56 2.43
2852 5952 5.682234 TGGAATGCAGAAGATGTCTAGAA 57.318 39.130 0.00 0.00 33.56 2.10
2854 5954 6.656902 TGGAATGCAGAAGATGTCTAGAAAT 58.343 36.000 0.00 0.00 33.56 2.17
2860 5960 3.643792 AGAAGATGTCTAGAAATCCCCCG 59.356 47.826 17.83 0.00 33.56 5.73
2864 5964 1.007963 TGTCTAGAAATCCCCCGGAGT 59.992 52.381 0.73 0.00 34.05 3.85
2889 5989 2.258286 GCATGTCAAACCGGTGGC 59.742 61.111 8.52 0.00 0.00 5.01
2942 6042 2.378084 GGACCGCGTTTCCTCGTTC 61.378 63.158 15.09 0.00 0.00 3.95
2943 6043 2.356673 ACCGCGTTTCCTCGTTCC 60.357 61.111 4.92 0.00 0.00 3.62
2944 6044 3.116531 CCGCGTTTCCTCGTTCCC 61.117 66.667 4.92 0.00 0.00 3.97
2945 6045 3.475774 CGCGTTTCCTCGTTCCCG 61.476 66.667 0.00 0.00 0.00 5.14
2946 6046 2.356673 GCGTTTCCTCGTTCCCGT 60.357 61.111 0.00 0.00 35.01 5.28
2947 6047 1.080569 GCGTTTCCTCGTTCCCGTA 60.081 57.895 0.00 0.00 35.01 4.02
2948 6048 1.074872 GCGTTTCCTCGTTCCCGTAG 61.075 60.000 0.00 0.00 35.01 3.51
2949 6049 1.074872 CGTTTCCTCGTTCCCGTAGC 61.075 60.000 0.00 0.00 35.01 3.58
2950 6050 0.037975 GTTTCCTCGTTCCCGTAGCA 60.038 55.000 0.00 0.00 35.01 3.49
2951 6051 0.037975 TTTCCTCGTTCCCGTAGCAC 60.038 55.000 0.00 0.00 35.01 4.40
2963 6063 1.988406 GTAGCACCCCGTTCTCCCT 60.988 63.158 0.00 0.00 0.00 4.20
2969 6069 1.995626 CCCCGTTCTCCCTGGTCAT 60.996 63.158 0.00 0.00 0.00 3.06
2988 6088 3.512516 GCCGCCTTGCCATCTCAC 61.513 66.667 0.00 0.00 0.00 3.51
2991 6091 1.817099 CGCCTTGCCATCTCACCTC 60.817 63.158 0.00 0.00 0.00 3.85
2992 6092 1.452833 GCCTTGCCATCTCACCTCC 60.453 63.158 0.00 0.00 0.00 4.30
3037 6137 0.621082 CTGTTTCCCCCTTCCCTCTC 59.379 60.000 0.00 0.00 0.00 3.20
3058 6181 3.125573 CTCCGACGCCGTCAGAGA 61.126 66.667 22.71 12.16 38.84 3.10
3066 6189 2.584418 CCGTCAGAGAGCGCCATG 60.584 66.667 2.29 0.00 0.00 3.66
3123 6246 0.329596 GTGGCCTCTCCCAACTGATT 59.670 55.000 3.32 0.00 36.46 2.57
3124 6247 0.329261 TGGCCTCTCCCAACTGATTG 59.671 55.000 3.32 0.00 35.40 2.67
3125 6248 0.620556 GGCCTCTCCCAACTGATTGA 59.379 55.000 0.00 0.00 38.15 2.57
3126 6249 1.213926 GGCCTCTCCCAACTGATTGAT 59.786 52.381 0.00 0.00 38.15 2.57
3127 6250 2.570135 GCCTCTCCCAACTGATTGATC 58.430 52.381 0.00 0.00 38.15 2.92
3128 6251 2.747799 GCCTCTCCCAACTGATTGATCC 60.748 54.545 0.00 0.00 38.15 3.36
3129 6252 2.776536 CCTCTCCCAACTGATTGATCCT 59.223 50.000 0.00 0.00 38.15 3.24
3141 6268 0.036388 TTGATCCTCAACCAGACCGC 60.036 55.000 0.00 0.00 30.26 5.68
3151 6281 3.955551 TCAACCAGACCGCAGTATATACA 59.044 43.478 15.18 0.00 0.00 2.29
3164 6294 5.271625 CAGTATATACAGCGACGTGAACTT 58.728 41.667 15.18 0.00 0.00 2.66
3165 6295 5.742453 CAGTATATACAGCGACGTGAACTTT 59.258 40.000 15.18 0.00 0.00 2.66
3166 6296 6.908820 CAGTATATACAGCGACGTGAACTTTA 59.091 38.462 15.18 0.00 0.00 1.85
3168 6298 2.503920 ACAGCGACGTGAACTTTACT 57.496 45.000 0.00 0.00 0.00 2.24
3169 6299 2.124903 ACAGCGACGTGAACTTTACTG 58.875 47.619 0.00 0.00 0.00 2.74
3170 6300 1.455786 CAGCGACGTGAACTTTACTGG 59.544 52.381 0.00 0.00 0.00 4.00
3171 6301 1.338973 AGCGACGTGAACTTTACTGGA 59.661 47.619 0.00 0.00 0.00 3.86
3172 6302 2.129607 GCGACGTGAACTTTACTGGAA 58.870 47.619 0.00 0.00 0.00 3.53
3173 6303 2.540931 GCGACGTGAACTTTACTGGAAA 59.459 45.455 0.00 0.00 0.00 3.13
3174 6304 3.001533 GCGACGTGAACTTTACTGGAAAA 59.998 43.478 0.00 0.00 0.00 2.29
3175 6305 4.511734 CGACGTGAACTTTACTGGAAAAC 58.488 43.478 0.00 0.00 0.00 2.43
3176 6306 4.033129 CGACGTGAACTTTACTGGAAAACA 59.967 41.667 0.00 0.00 0.00 2.83
3187 6317 1.880027 CTGGAAAACAGTACACAGCCC 59.120 52.381 0.00 0.00 42.42 5.19
3255 6385 2.922740 TAAACTGGAGCGTCTTGGTT 57.077 45.000 0.00 0.00 0.00 3.67
3289 6419 3.130516 GGCCATCCATCATATTCATGCAG 59.869 47.826 0.00 0.00 31.73 4.41
3366 6499 4.760047 CACCGTGGGGGCTCGAAG 62.760 72.222 0.00 0.00 40.62 3.79
3436 6570 3.682377 CGGGCTGTCTTGTTTTTGTTTTT 59.318 39.130 0.00 0.00 0.00 1.94
3440 6574 7.406553 GGGCTGTCTTGTTTTTGTTTTTATTC 58.593 34.615 0.00 0.00 0.00 1.75
3477 6611 0.320421 GCTCCACGCACAGAAGGTAA 60.320 55.000 0.00 0.00 38.92 2.85
3496 6630 3.715648 AATCAGTCCATCCTACTCCCT 57.284 47.619 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.370593 TGTCTCTTCAATTTTACGAACATGC 58.629 36.000 0.00 0.00 0.00 4.06
14 15 9.273016 CAGGTACTTATCTTTTTGTCTCTTCAA 57.727 33.333 0.00 0.00 34.60 2.69
67 70 4.993705 AGGGGAAGATACAAACACTTGA 57.006 40.909 0.00 0.00 36.33 3.02
81 84 6.240549 ACTACATTGTCAGATAAGGGGAAG 57.759 41.667 0.00 0.00 0.00 3.46
100 103 9.916397 CGGAACATCAATATTAAACTCAACTAC 57.084 33.333 0.00 0.00 0.00 2.73
125 129 4.899502 AGGGAATTTCCTATACATCAGCG 58.100 43.478 14.95 0.00 36.57 5.18
131 135 7.265599 TGAACAGAAGGGAATTTCCTATACA 57.734 36.000 5.46 0.00 36.57 2.29
173 876 7.567994 TCTGTACTAGTGAGGAGTCCTATTCTA 59.432 40.741 12.99 13.25 31.76 2.10
175 878 6.593807 TCTGTACTAGTGAGGAGTCCTATTC 58.406 44.000 12.99 5.66 31.76 1.75
247 1036 2.105128 CTGACGATCTGGCGGTCC 59.895 66.667 0.00 0.00 35.12 4.46
248 1037 1.517257 CACTGACGATCTGGCGGTC 60.517 63.158 2.38 0.00 35.12 4.79
258 1047 2.290705 TGGACTGACCTATCACTGACGA 60.291 50.000 0.00 0.00 39.86 4.20
292 1086 1.228154 GTCCTTTCAGGCGGTTGGT 60.228 57.895 0.00 0.00 34.61 3.67
293 1087 0.821711 TTGTCCTTTCAGGCGGTTGG 60.822 55.000 0.00 0.00 34.61 3.77
295 1089 2.871096 TATTGTCCTTTCAGGCGGTT 57.129 45.000 0.00 0.00 34.61 4.44
297 1091 2.355756 CACATATTGTCCTTTCAGGCGG 59.644 50.000 0.00 0.00 34.61 6.13
298 1092 3.270027 TCACATATTGTCCTTTCAGGCG 58.730 45.455 0.00 0.00 34.61 5.52
301 1095 4.940046 AGTGCTCACATATTGTCCTTTCAG 59.060 41.667 2.63 0.00 0.00 3.02
302 1096 4.910195 AGTGCTCACATATTGTCCTTTCA 58.090 39.130 2.63 0.00 0.00 2.69
303 1097 4.333926 GGAGTGCTCACATATTGTCCTTTC 59.666 45.833 2.63 0.00 0.00 2.62
334 1132 9.970553 AGCACCATATTGAATATACAATCAGAT 57.029 29.630 0.00 0.00 40.36 2.90
335 1133 9.797642 AAGCACCATATTGAATATACAATCAGA 57.202 29.630 0.00 0.00 40.36 3.27
336 1134 9.836076 CAAGCACCATATTGAATATACAATCAG 57.164 33.333 0.00 0.00 40.36 2.90
338 1136 9.616634 CACAAGCACCATATTGAATATACAATC 57.383 33.333 0.00 0.00 40.36 2.67
339 1137 9.135189 ACACAAGCACCATATTGAATATACAAT 57.865 29.630 0.00 0.00 42.17 2.71
341 1139 9.620259 TTACACAAGCACCATATTGAATATACA 57.380 29.630 0.00 0.00 0.00 2.29
344 1142 8.084073 GCATTACACAAGCACCATATTGAATAT 58.916 33.333 0.00 0.00 0.00 1.28
345 1143 7.285172 AGCATTACACAAGCACCATATTGAATA 59.715 33.333 0.00 0.00 0.00 1.75
346 1144 6.097270 AGCATTACACAAGCACCATATTGAAT 59.903 34.615 0.00 0.00 0.00 2.57
348 1146 4.949238 AGCATTACACAAGCACCATATTGA 59.051 37.500 0.00 0.00 0.00 2.57
349 1147 5.252969 AGCATTACACAAGCACCATATTG 57.747 39.130 0.00 0.00 0.00 1.90
351 1149 5.684704 ACTAGCATTACACAAGCACCATAT 58.315 37.500 0.00 0.00 0.00 1.78
352 1150 5.097742 ACTAGCATTACACAAGCACCATA 57.902 39.130 0.00 0.00 0.00 2.74
407 1216 5.357257 TCAGATACTAACTGAATTTCCGGC 58.643 41.667 0.00 0.00 40.70 6.13
487 1296 8.822805 ACTACAGAGGATATTTGTTTAGACCAA 58.177 33.333 0.00 0.00 0.00 3.67
522 1331 7.248437 GGTCGAATTCGGATAAGAAAAACAAT 58.752 34.615 26.47 0.00 40.29 2.71
524 1333 5.122711 GGGTCGAATTCGGATAAGAAAAACA 59.877 40.000 26.47 0.41 40.29 2.83
538 1347 6.256104 GCTAGAAAGACTAAAGGGTCGAATTC 59.744 42.308 0.00 0.00 40.76 2.17
543 1352 4.425520 CAGCTAGAAAGACTAAAGGGTCG 58.574 47.826 0.00 0.00 40.76 4.79
554 1363 1.423541 TGTTTGGGCCAGCTAGAAAGA 59.576 47.619 6.23 0.00 0.00 2.52
563 1372 0.598065 GTAACTGCTGTTTGGGCCAG 59.402 55.000 14.54 0.00 37.59 4.85
580 1392 7.977789 TGTGCTTCTCAATCTGTTATTTGTA 57.022 32.000 0.00 0.00 0.00 2.41
623 1435 2.157738 GATGACTGTTCTGGCTGCTTT 58.842 47.619 0.00 0.00 0.00 3.51
655 1471 8.542953 GCTGGAAGTTCAAATTTTCTTTTACAG 58.457 33.333 5.01 8.88 35.30 2.74
658 1476 8.871686 GAGCTGGAAGTTCAAATTTTCTTTTA 57.128 30.769 5.01 0.00 44.36 1.52
682 1500 2.751436 GGCCATTGCTCCGCTTGA 60.751 61.111 0.00 0.00 37.74 3.02
693 1511 4.402474 GCTACCTGTTATTTTGAGGCCATT 59.598 41.667 5.01 0.00 0.00 3.16
919 2403 2.594592 AGGCGGTGAGTTGGCAAC 60.595 61.111 22.48 22.48 0.00 4.17
920 2404 2.594303 CAGGCGGTGAGTTGGCAA 60.594 61.111 0.00 0.00 0.00 4.52
923 2407 2.281761 AAGCAGGCGGTGAGTTGG 60.282 61.111 0.00 0.00 0.00 3.77
924 2408 2.328099 GGAAGCAGGCGGTGAGTTG 61.328 63.158 0.00 0.00 0.00 3.16
925 2409 1.192146 TAGGAAGCAGGCGGTGAGTT 61.192 55.000 0.00 0.00 0.00 3.01
926 2410 1.192146 TTAGGAAGCAGGCGGTGAGT 61.192 55.000 0.00 0.00 0.00 3.41
933 2417 1.946081 GAGCAAGATTAGGAAGCAGGC 59.054 52.381 0.00 0.00 0.00 4.85
934 2418 3.134442 AGAGAGCAAGATTAGGAAGCAGG 59.866 47.826 0.00 0.00 0.00 4.85
937 2421 4.370917 CTGAGAGAGCAAGATTAGGAAGC 58.629 47.826 0.00 0.00 0.00 3.86
1032 2523 0.685097 AGCTAGTTTCGCCTTGTCCA 59.315 50.000 0.00 0.00 0.00 4.02
1378 2912 2.149383 ACAGGAGCAGCCCAAGTCA 61.149 57.895 3.08 0.00 37.37 3.41
1623 3165 1.813513 ACAGAAAAGATGCACGGAGG 58.186 50.000 0.00 0.00 0.00 4.30
1654 3196 5.362717 TCATACCTTCGAGAGCCAATAAAGA 59.637 40.000 0.00 0.00 0.00 2.52
1658 3200 4.215908 ACTCATACCTTCGAGAGCCAATA 58.784 43.478 0.00 0.00 33.33 1.90
1669 3211 5.298276 TGGTGTCAAACAAACTCATACCTTC 59.702 40.000 0.00 0.00 0.00 3.46
1860 3419 0.803740 CTCTCAGCTGCAGGAAAAGC 59.196 55.000 17.12 0.00 39.82 3.51
1922 3481 1.306141 TCATCAGAACGCCTCCCCT 60.306 57.895 0.00 0.00 0.00 4.79
2030 3590 7.346751 AGTCTTTTGCCTTGTTTCATAAGAA 57.653 32.000 0.00 0.00 34.03 2.52
2031 3591 6.959639 AGTCTTTTGCCTTGTTTCATAAGA 57.040 33.333 0.00 0.00 31.25 2.10
2032 3592 6.074142 GCAAGTCTTTTGCCTTGTTTCATAAG 60.074 38.462 0.54 0.00 40.13 1.73
2033 3593 5.752955 GCAAGTCTTTTGCCTTGTTTCATAA 59.247 36.000 0.54 0.00 40.13 1.90
2034 3594 5.288804 GCAAGTCTTTTGCCTTGTTTCATA 58.711 37.500 0.54 0.00 40.13 2.15
2035 3595 4.122046 GCAAGTCTTTTGCCTTGTTTCAT 58.878 39.130 0.54 0.00 40.13 2.57
2036 3596 3.520569 GCAAGTCTTTTGCCTTGTTTCA 58.479 40.909 0.54 0.00 40.13 2.69
2045 3605 5.236911 TCAATGAAAATGGCAAGTCTTTTGC 59.763 36.000 1.54 3.39 44.22 3.68
2046 3606 6.847956 TCAATGAAAATGGCAAGTCTTTTG 57.152 33.333 1.54 4.22 0.00 2.44
2047 3607 9.558396 TTAATCAATGAAAATGGCAAGTCTTTT 57.442 25.926 0.00 0.00 0.00 2.27
2048 3608 9.211485 CTTAATCAATGAAAATGGCAAGTCTTT 57.789 29.630 0.00 0.00 0.00 2.52
2049 3609 8.587608 TCTTAATCAATGAAAATGGCAAGTCTT 58.412 29.630 0.00 0.00 0.00 3.01
2050 3610 8.125978 TCTTAATCAATGAAAATGGCAAGTCT 57.874 30.769 0.00 0.00 0.00 3.24
2051 3611 8.761575 TTCTTAATCAATGAAAATGGCAAGTC 57.238 30.769 0.00 0.00 0.00 3.01
2052 3612 8.587608 TCTTCTTAATCAATGAAAATGGCAAGT 58.412 29.630 0.00 0.00 0.00 3.16
2053 3613 8.991243 TCTTCTTAATCAATGAAAATGGCAAG 57.009 30.769 0.00 0.00 0.00 4.01
2054 3614 9.426837 CTTCTTCTTAATCAATGAAAATGGCAA 57.573 29.630 0.00 0.00 0.00 4.52
2055 3615 8.805175 TCTTCTTCTTAATCAATGAAAATGGCA 58.195 29.630 0.00 0.00 0.00 4.92
2056 3616 9.298774 CTCTTCTTCTTAATCAATGAAAATGGC 57.701 33.333 0.00 0.00 0.00 4.40
2063 3623 8.680903 GGCAATTCTCTTCTTCTTAATCAATGA 58.319 33.333 0.00 0.00 0.00 2.57
2064 3624 7.919621 GGGCAATTCTCTTCTTCTTAATCAATG 59.080 37.037 0.00 0.00 0.00 2.82
2065 3625 7.201767 CGGGCAATTCTCTTCTTCTTAATCAAT 60.202 37.037 0.00 0.00 0.00 2.57
2066 3626 6.094048 CGGGCAATTCTCTTCTTCTTAATCAA 59.906 38.462 0.00 0.00 0.00 2.57
2067 3627 5.586243 CGGGCAATTCTCTTCTTCTTAATCA 59.414 40.000 0.00 0.00 0.00 2.57
2068 3628 5.008118 CCGGGCAATTCTCTTCTTCTTAATC 59.992 44.000 0.00 0.00 0.00 1.75
2069 3629 4.884164 CCGGGCAATTCTCTTCTTCTTAAT 59.116 41.667 0.00 0.00 0.00 1.40
2070 3630 4.261801 CCGGGCAATTCTCTTCTTCTTAA 58.738 43.478 0.00 0.00 0.00 1.85
2071 3631 3.263425 ACCGGGCAATTCTCTTCTTCTTA 59.737 43.478 6.32 0.00 0.00 2.10
2072 3632 2.040412 ACCGGGCAATTCTCTTCTTCTT 59.960 45.455 6.32 0.00 0.00 2.52
2073 3633 1.630878 ACCGGGCAATTCTCTTCTTCT 59.369 47.619 6.32 0.00 0.00 2.85
2074 3634 2.115343 ACCGGGCAATTCTCTTCTTC 57.885 50.000 6.32 0.00 0.00 2.87
2075 3635 2.586648 AACCGGGCAATTCTCTTCTT 57.413 45.000 6.32 0.00 0.00 2.52
2076 3636 3.713826 TTAACCGGGCAATTCTCTTCT 57.286 42.857 6.32 0.00 0.00 2.85
2077 3637 4.398044 TCAATTAACCGGGCAATTCTCTTC 59.602 41.667 6.32 0.00 0.00 2.87
2078 3638 4.157840 GTCAATTAACCGGGCAATTCTCTT 59.842 41.667 6.32 0.00 0.00 2.85
2079 3639 3.694566 GTCAATTAACCGGGCAATTCTCT 59.305 43.478 6.32 0.00 0.00 3.10
2080 3640 3.486875 CGTCAATTAACCGGGCAATTCTC 60.487 47.826 6.32 5.39 0.00 2.87
2081 3641 2.422127 CGTCAATTAACCGGGCAATTCT 59.578 45.455 6.32 0.00 0.00 2.40
2082 3642 2.478879 CCGTCAATTAACCGGGCAATTC 60.479 50.000 6.32 0.00 38.09 2.17
2083 3643 1.474879 CCGTCAATTAACCGGGCAATT 59.525 47.619 6.32 8.10 38.09 2.32
2084 3644 1.099689 CCGTCAATTAACCGGGCAAT 58.900 50.000 6.32 0.96 38.09 3.56
2085 3645 0.036448 TCCGTCAATTAACCGGGCAA 59.964 50.000 6.32 0.00 41.98 4.52
2086 3646 0.036448 TTCCGTCAATTAACCGGGCA 59.964 50.000 6.32 0.00 41.98 5.36
2087 3647 1.166989 TTTCCGTCAATTAACCGGGC 58.833 50.000 6.32 0.00 41.98 6.13
2088 3648 2.095110 GGTTTTCCGTCAATTAACCGGG 60.095 50.000 6.32 0.00 41.98 5.73
2089 3649 2.553172 TGGTTTTCCGTCAATTAACCGG 59.447 45.455 0.00 0.00 44.36 5.28
2090 3650 3.900388 TGGTTTTCCGTCAATTAACCG 57.100 42.857 0.00 0.00 44.36 4.44
2091 3651 4.552355 CCTTGGTTTTCCGTCAATTAACC 58.448 43.478 0.00 0.00 44.36 2.85
2092 3652 3.985279 GCCTTGGTTTTCCGTCAATTAAC 59.015 43.478 0.00 0.00 44.36 2.01
2093 3653 3.637229 TGCCTTGGTTTTCCGTCAATTAA 59.363 39.130 0.00 0.00 44.36 1.40
2094 3654 3.223435 TGCCTTGGTTTTCCGTCAATTA 58.777 40.909 0.00 0.00 44.36 1.40
2095 3655 2.035632 TGCCTTGGTTTTCCGTCAATT 58.964 42.857 0.00 0.00 44.36 2.32
2096 3656 1.698506 TGCCTTGGTTTTCCGTCAAT 58.301 45.000 0.00 0.00 44.36 2.57
2097 3657 1.407258 CTTGCCTTGGTTTTCCGTCAA 59.593 47.619 0.00 0.00 44.36 3.18
2098 3658 1.028905 CTTGCCTTGGTTTTCCGTCA 58.971 50.000 0.00 0.00 44.36 4.35
2099 3659 0.318699 GCTTGCCTTGGTTTTCCGTC 60.319 55.000 0.00 0.00 44.36 4.79
2100 3660 0.755327 AGCTTGCCTTGGTTTTCCGT 60.755 50.000 0.00 0.00 44.36 4.69
2101 3661 0.389025 AAGCTTGCCTTGGTTTTCCG 59.611 50.000 0.00 0.00 44.36 4.30
2102 3662 2.620251 AAAGCTTGCCTTGGTTTTCC 57.380 45.000 0.00 0.00 41.14 3.13
2103 3663 4.322080 AGTAAAGCTTGCCTTGGTTTTC 57.678 40.909 0.00 0.00 36.65 2.29
2104 3664 4.753516 AAGTAAAGCTTGCCTTGGTTTT 57.246 36.364 0.00 0.00 36.65 2.43
2105 3665 4.753516 AAAGTAAAGCTTGCCTTGGTTT 57.246 36.364 0.00 0.00 37.52 3.27
2106 3666 4.161377 TCAAAAGTAAAGCTTGCCTTGGTT 59.839 37.500 0.00 0.00 37.52 3.67
2107 3667 3.704061 TCAAAAGTAAAGCTTGCCTTGGT 59.296 39.130 0.00 0.00 37.52 3.67
2108 3668 4.320608 TCAAAAGTAAAGCTTGCCTTGG 57.679 40.909 0.00 2.34 37.52 3.61
2109 3669 4.507756 GGTTCAAAAGTAAAGCTTGCCTTG 59.492 41.667 0.00 3.91 37.52 3.61
2110 3670 4.161377 TGGTTCAAAAGTAAAGCTTGCCTT 59.839 37.500 0.00 2.05 37.52 4.35
2111 3671 3.704061 TGGTTCAAAAGTAAAGCTTGCCT 59.296 39.130 0.00 0.00 37.52 4.75
2112 3672 4.053469 TGGTTCAAAAGTAAAGCTTGCC 57.947 40.909 0.00 0.00 37.52 4.52
2113 3673 5.049828 ACATGGTTCAAAAGTAAAGCTTGC 58.950 37.500 0.00 0.00 37.52 4.01
2114 3674 6.534793 ACAACATGGTTCAAAAGTAAAGCTTG 59.465 34.615 0.00 0.00 37.52 4.01
2115 3675 6.639563 ACAACATGGTTCAAAAGTAAAGCTT 58.360 32.000 0.00 0.00 39.52 3.74
2116 3676 6.127479 TGACAACATGGTTCAAAAGTAAAGCT 60.127 34.615 0.00 0.00 0.00 3.74
2117 3677 6.039616 TGACAACATGGTTCAAAAGTAAAGC 58.960 36.000 0.00 0.00 0.00 3.51
2118 3678 8.647143 AATGACAACATGGTTCAAAAGTAAAG 57.353 30.769 0.00 0.00 36.79 1.85
2119 3679 8.877779 CAAATGACAACATGGTTCAAAAGTAAA 58.122 29.630 0.00 0.00 36.79 2.01
2120 3680 7.010923 GCAAATGACAACATGGTTCAAAAGTAA 59.989 33.333 0.00 0.00 36.79 2.24
2121 3681 6.478344 GCAAATGACAACATGGTTCAAAAGTA 59.522 34.615 0.00 0.00 36.79 2.24
2122 3682 5.294060 GCAAATGACAACATGGTTCAAAAGT 59.706 36.000 0.00 0.00 36.79 2.66
2123 3683 5.524646 AGCAAATGACAACATGGTTCAAAAG 59.475 36.000 0.00 0.00 36.79 2.27
2124 3684 5.426504 AGCAAATGACAACATGGTTCAAAA 58.573 33.333 0.00 0.00 36.79 2.44
2125 3685 5.021033 AGCAAATGACAACATGGTTCAAA 57.979 34.783 0.00 0.00 36.79 2.69
2126 3686 4.669206 AGCAAATGACAACATGGTTCAA 57.331 36.364 0.00 0.00 36.79 2.69
2127 3687 5.781210 TTAGCAAATGACAACATGGTTCA 57.219 34.783 0.00 0.00 36.79 3.18
2128 3688 6.389091 TCATTAGCAAATGACAACATGGTTC 58.611 36.000 0.00 0.00 45.17 3.62
2170 5058 2.229792 TCTTTGTCAATCACACCCTGC 58.770 47.619 0.00 0.00 33.41 4.85
2194 5082 5.642063 CACCGGTATGTACAAAGAATCAAGT 59.358 40.000 6.87 0.00 0.00 3.16
2233 5121 3.058016 GGATGATCTCTCTCAGCTCTTCG 60.058 52.174 0.00 0.00 32.23 3.79
2350 5238 1.067985 TCGAAAGCAGCTCTCAGACTG 60.068 52.381 0.00 0.00 36.96 3.51
2401 5289 4.346127 ACGAATTCATCCATGATCTCTCCA 59.654 41.667 6.22 0.00 36.56 3.86
2467 5355 1.282875 GTTTCTGGCGTGCTTGACC 59.717 57.895 0.00 0.00 0.00 4.02
2529 5417 2.084681 GCAGCAGCACGTCAATTGC 61.085 57.895 0.00 0.00 41.58 3.56
2541 5429 2.545532 GGATACAGACTAGCAGCAGCAG 60.546 54.545 3.17 1.45 45.49 4.24
2577 5465 2.884012 ACGTTGAATTTCACAGGCATGA 59.116 40.909 4.84 0.00 0.00 3.07
2582 5470 3.247648 AGTTCGACGTTGAATTTCACAGG 59.752 43.478 20.81 0.23 0.00 4.00
2587 5475 4.837050 CGGTTAAGTTCGACGTTGAATTTC 59.163 41.667 24.61 14.16 31.37 2.17
2600 5488 5.120363 GTCTCTCACAAATCCGGTTAAGTTC 59.880 44.000 0.00 0.00 0.00 3.01
2608 5496 0.530744 TCCGTCTCTCACAAATCCGG 59.469 55.000 0.00 0.00 35.41 5.14
2628 5516 5.006358 GCAATTTCAGCAGATATTTGCCTTG 59.994 40.000 14.23 7.73 45.18 3.61
2671 5559 7.609146 AGAACTTCAATATCACTCAATTCAGCA 59.391 33.333 0.00 0.00 0.00 4.41
2672 5560 7.909121 CAGAACTTCAATATCACTCAATTCAGC 59.091 37.037 0.00 0.00 0.00 4.26
2675 5563 7.755591 TGCAGAACTTCAATATCACTCAATTC 58.244 34.615 0.00 0.00 0.00 2.17
2768 5694 0.031716 CCAGGAGAGATGGGTCCAGA 60.032 60.000 0.00 0.00 35.02 3.86
2815 5915 2.397044 TTCCAAAATCTGGCCAAGGT 57.603 45.000 7.01 0.00 45.98 3.50
2821 5921 3.194116 TCTTCTGCATTCCAAAATCTGGC 59.806 43.478 0.00 0.00 45.98 4.85
2825 5925 6.205101 AGACATCTTCTGCATTCCAAAATC 57.795 37.500 0.00 0.00 31.12 2.17
2836 5936 4.384940 GGGGATTTCTAGACATCTTCTGC 58.615 47.826 16.49 2.17 35.55 4.26
2846 5946 1.789523 CACTCCGGGGGATTTCTAGA 58.210 55.000 6.13 0.00 0.00 2.43
2849 5949 2.998949 GCACTCCGGGGGATTTCT 59.001 61.111 6.13 0.00 0.00 2.52
2850 5950 2.513897 CGCACTCCGGGGGATTTC 60.514 66.667 6.13 0.00 0.00 2.17
2852 5952 2.902457 AAACGCACTCCGGGGGATT 61.902 57.895 6.13 0.00 42.52 3.01
2854 5954 4.323477 CAAACGCACTCCGGGGGA 62.323 66.667 6.13 0.00 42.52 4.81
2939 6039 3.244281 AACGGGGTGCTACGGGAAC 62.244 63.158 0.00 0.00 0.00 3.62
2942 6042 3.366739 GAGAACGGGGTGCTACGGG 62.367 68.421 0.00 0.00 0.00 5.28
2943 6043 2.183555 GAGAACGGGGTGCTACGG 59.816 66.667 0.00 0.00 0.00 4.02
2944 6044 2.183555 GGAGAACGGGGTGCTACG 59.816 66.667 0.00 0.00 0.00 3.51
2945 6045 1.988406 AGGGAGAACGGGGTGCTAC 60.988 63.158 0.00 0.00 0.00 3.58
2946 6046 1.987855 CAGGGAGAACGGGGTGCTA 60.988 63.158 0.00 0.00 0.00 3.49
2947 6047 3.322466 CAGGGAGAACGGGGTGCT 61.322 66.667 0.00 0.00 0.00 4.40
2948 6048 4.410400 CCAGGGAGAACGGGGTGC 62.410 72.222 0.00 0.00 0.00 5.01
2949 6049 2.928396 ACCAGGGAGAACGGGGTG 60.928 66.667 0.00 0.00 0.00 4.61
2950 6050 2.606826 GACCAGGGAGAACGGGGT 60.607 66.667 0.00 0.00 33.78 4.95
2951 6051 1.995626 ATGACCAGGGAGAACGGGG 60.996 63.158 0.00 0.00 0.00 5.73
2991 6091 4.143333 CTAGGTGGCGTCACGGGG 62.143 72.222 14.98 2.20 44.50 5.73
2992 6092 4.814294 GCTAGGTGGCGTCACGGG 62.814 72.222 14.98 7.63 44.50 5.28
3019 6119 0.196118 AGAGAGGGAAGGGGGAAACA 59.804 55.000 0.00 0.00 0.00 2.83
3058 6181 4.172512 CTCTGAGGCCATGGCGCT 62.173 66.667 29.90 26.07 43.06 5.92
3066 6189 3.023949 ATGTGCGACCTCTGAGGCC 62.024 63.158 23.43 12.07 39.63 5.19
3098 6221 1.544825 TTGGGAGAGGCCACTTCGAG 61.545 60.000 5.01 0.00 38.95 4.04
3106 6229 0.620556 TCAATCAGTTGGGAGAGGCC 59.379 55.000 0.00 0.00 35.99 5.19
3110 6233 3.453868 TGAGGATCAATCAGTTGGGAGA 58.546 45.455 0.00 0.00 45.97 3.71
3124 6247 0.460987 CTGCGGTCTGGTTGAGGATC 60.461 60.000 0.00 0.00 0.00 3.36
3125 6248 1.194781 ACTGCGGTCTGGTTGAGGAT 61.195 55.000 0.00 0.00 0.00 3.24
3126 6249 0.541063 TACTGCGGTCTGGTTGAGGA 60.541 55.000 0.00 0.00 0.00 3.71
3127 6250 0.537188 ATACTGCGGTCTGGTTGAGG 59.463 55.000 0.00 0.00 0.00 3.86
3128 6251 3.735237 ATATACTGCGGTCTGGTTGAG 57.265 47.619 0.00 0.00 0.00 3.02
3129 6252 3.955551 TGTATATACTGCGGTCTGGTTGA 59.044 43.478 13.89 0.00 0.00 3.18
3141 6268 4.845387 AGTTCACGTCGCTGTATATACTG 58.155 43.478 13.89 13.84 0.00 2.74
3151 6281 1.338973 TCCAGTAAAGTTCACGTCGCT 59.661 47.619 0.00 0.00 0.00 4.93
3168 6298 1.812324 CGGGCTGTGTACTGTTTTCCA 60.812 52.381 0.00 0.00 0.00 3.53
3169 6299 0.872388 CGGGCTGTGTACTGTTTTCC 59.128 55.000 0.00 0.00 0.00 3.13
3170 6300 1.798813 CTCGGGCTGTGTACTGTTTTC 59.201 52.381 0.00 0.00 0.00 2.29
3171 6301 1.878953 CTCGGGCTGTGTACTGTTTT 58.121 50.000 0.00 0.00 0.00 2.43
3172 6302 0.602905 GCTCGGGCTGTGTACTGTTT 60.603 55.000 0.00 0.00 35.22 2.83
3173 6303 1.004918 GCTCGGGCTGTGTACTGTT 60.005 57.895 0.00 0.00 35.22 3.16
3174 6304 1.754380 TTGCTCGGGCTGTGTACTGT 61.754 55.000 9.62 0.00 39.59 3.55
3175 6305 0.602638 TTTGCTCGGGCTGTGTACTG 60.603 55.000 9.62 0.00 39.59 2.74
3176 6306 0.107831 TTTTGCTCGGGCTGTGTACT 59.892 50.000 9.62 0.00 39.59 2.73
3177 6307 0.517316 CTTTTGCTCGGGCTGTGTAC 59.483 55.000 9.62 0.00 39.59 2.90
3178 6308 0.605319 CCTTTTGCTCGGGCTGTGTA 60.605 55.000 9.62 0.00 39.59 2.90
3187 6317 2.256461 GCACTGGCCTTTTGCTCG 59.744 61.111 14.40 0.00 40.92 5.03
3289 6419 5.290158 CAGGAATCAATTTGCATGCAAGTAC 59.710 40.000 30.25 11.84 37.24 2.73
3436 6570 5.663106 AGCATGGAAGAGTTAGTGAGGAATA 59.337 40.000 0.00 0.00 0.00 1.75
3440 6574 3.431486 GGAGCATGGAAGAGTTAGTGAGG 60.431 52.174 0.00 0.00 0.00 3.86
3477 6611 3.730059 ACTAGGGAGTAGGATGGACTGAT 59.270 47.826 0.00 0.00 32.65 2.90


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

AutoCloner maintained by Alex Coulton.