Multiple sequence alignment - TraesCS5D01G534100

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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 TraesCS5D01G534100 chr5D 100.000 8240 0 0 1 8240 548361425 548369664 0.000000e+00 15217.0
1 TraesCS5D01G534100 chr5D 88.864 898 87 8 2764 3652 539962695 539961802 0.000000e+00 1092.0
2 TraesCS5D01G534100 chr5D 92.857 322 20 1 6655 6973 548367995 548368316 1.620000e-126 464.0
3 TraesCS5D01G534100 chr5D 92.857 322 20 1 6571 6892 548368079 548368397 1.620000e-126 464.0
4 TraesCS5D01G534100 chr5D 90.763 249 23 0 3693 3941 539961791 539961543 4.770000e-87 333.0
5 TraesCS5D01G534100 chr5D 88.259 247 24 3 6566 6811 548368155 548368397 2.910000e-74 291.0
6 TraesCS5D01G534100 chr5D 87.727 220 23 3 3939 4158 539961501 539961286 3.820000e-63 254.0
7 TraesCS5D01G534100 chr5D 84.153 183 22 3 6988 7163 548374710 548374892 3.950000e-38 171.0
8 TraesCS5D01G534100 chr5D 97.368 38 1 0 7120 7157 548461298 548461335 1.920000e-06 65.8
9 TraesCS5D01G534100 chr5D 89.130 46 5 0 7271 7316 548374941 548374986 3.210000e-04 58.4
10 TraesCS5D01G534100 chr5B 95.126 4247 128 36 3939 8149 692632613 692636816 0.000000e+00 6623.0
11 TraesCS5D01G534100 chr5B 92.971 2632 126 27 1335 3941 692629985 692632582 0.000000e+00 3781.0
12 TraesCS5D01G534100 chr5B 86.795 886 95 15 3009 3888 682169291 682168422 0.000000e+00 968.0
13 TraesCS5D01G534100 chr5B 84.412 834 73 32 6 823 692606377 692607169 0.000000e+00 767.0
14 TraesCS5D01G534100 chr5B 81.967 976 46 34 368 1281 692629066 692629973 0.000000e+00 708.0
15 TraesCS5D01G534100 chr5B 91.925 322 23 1 6571 6892 692635326 692635644 1.630000e-121 448.0
16 TraesCS5D01G534100 chr5B 91.304 322 25 1 6655 6973 692635242 692635563 3.530000e-118 436.0
17 TraesCS5D01G534100 chr5B 88.889 351 30 6 3939 4288 682168348 682168006 2.750000e-114 424.0
18 TraesCS5D01G534100 chr5B 90.840 262 20 3 2764 3024 682169721 682169463 1.700000e-91 348.0
19 TraesCS5D01G534100 chr5B 85.799 338 31 9 501 823 692626278 692626613 7.920000e-90 342.0
20 TraesCS5D01G534100 chr5B 89.474 247 21 3 6731 6973 692635237 692635482 2.890000e-79 307.0
21 TraesCS5D01G534100 chr5B 84.420 276 32 6 6988 7254 692649147 692649420 2.280000e-65 261.0
22 TraesCS5D01G534100 chr5B 96.591 88 3 0 8148 8235 692636858 692636945 6.660000e-31 147.0
23 TraesCS5D01G534100 chr5B 89.320 103 8 2 1494 1593 692630254 692630356 8.680000e-25 126.0
24 TraesCS5D01G534100 chr5B 97.368 38 1 0 7120 7157 692679444 692679481 1.920000e-06 65.8
25 TraesCS5D01G534100 chr4A 93.829 4132 160 46 3972 8078 619281525 619285586 0.000000e+00 6130.0
26 TraesCS5D01G534100 chr4A 93.605 1642 78 11 2326 3945 619279732 619281368 0.000000e+00 2425.0
27 TraesCS5D01G534100 chr4A 86.443 1549 98 40 672 2176 619278248 619279728 0.000000e+00 1594.0
28 TraesCS5D01G534100 chr4A 87.396 1198 104 22 2764 3945 627776974 627775808 0.000000e+00 1332.0
29 TraesCS5D01G534100 chr4A 91.615 322 24 1 6655 6973 619284092 619284413 7.590000e-120 442.0
30 TraesCS5D01G534100 chr4A 91.331 323 23 3 6571 6892 619284176 619284494 3.530000e-118 436.0
31 TraesCS5D01G534100 chr4A 89.091 220 22 2 3939 4158 627775769 627775552 1.050000e-68 272.0
32 TraesCS5D01G534100 chr4A 90.426 94 6 2 1602 1692 619279054 619279147 4.040000e-23 121.0
33 TraesCS5D01G534100 chr4A 97.826 46 1 0 7120 7165 619334423 619334468 6.860000e-11 80.5
34 TraesCS5D01G534100 chr4A 75.897 195 16 13 6988 7165 619313004 619313184 4.130000e-08 71.3
35 TraesCS5D01G534100 chr4A 100.000 35 0 0 3939 3973 619281408 619281442 1.920000e-06 65.8


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 TraesCS5D01G534100 chr5D 548361425 548369664 8239 False 4109.000000 15217 93.493250 1 8240 4 chr5D.!!$F2 8239
1 TraesCS5D01G534100 chr5D 539961286 539962695 1409 True 559.666667 1092 89.118000 2764 4158 3 chr5D.!!$R1 1394
2 TraesCS5D01G534100 chr5B 692626278 692636945 10667 False 1435.333333 6623 90.497444 368 8235 9 chr5B.!!$F4 7867
3 TraesCS5D01G534100 chr5B 692606377 692607169 792 False 767.000000 767 84.412000 6 823 1 chr5B.!!$F1 817
4 TraesCS5D01G534100 chr5B 682168006 682169721 1715 True 580.000000 968 88.841333 2764 4288 3 chr5B.!!$R1 1524
5 TraesCS5D01G534100 chr4A 619278248 619285586 7338 False 1601.971429 6130 92.464143 672 8078 7 chr4A.!!$F3 7406
6 TraesCS5D01G534100 chr4A 627775552 627776974 1422 True 802.000000 1332 88.243500 2764 4158 2 chr4A.!!$R1 1394

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
581 3020 0.044397 AACCCTACTTCCTCCCTCCC 59.956 60.000 0.00 0.0 0.00 4.30 F
1112 3587 0.035056 AAACATCCCCTCTTGCTCCG 60.035 55.000 0.00 0.0 0.00 4.63 F
1140 3615 0.815213 TCCATTAGCCTGCATCGCAC 60.815 55.000 8.47 0.0 33.79 5.34 F
1277 3782 0.884704 GCAGCGTTTCAGTCCCTTGA 60.885 55.000 0.00 0.0 0.00 3.02 F
1977 4501 1.066143 GTATGTGTCCTGGTCCTGGTG 60.066 57.143 14.11 0.0 0.00 4.17 F
2626 5156 1.171308 CTGTCCATGCTTGTTCCCTG 58.829 55.000 0.00 0.0 0.00 4.45 F
3557 6316 0.526662 AGGGACGAGCGTTGACTTAG 59.473 55.000 0.00 0.0 0.00 2.18 F
5379 8284 1.614413 AGTCAAAGTCACGAGACCTCC 59.386 52.381 9.50 0.0 46.15 4.30 F
6816 9721 0.469144 GGCTTCGAGATCCTCTCCCT 60.469 60.000 0.00 0.0 40.34 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 4217 1.320507 CTAGTAAGCCTCCCGAGTCC 58.679 60.000 0.00 0.0 0.00 3.85 R
2607 5137 1.171308 CAGGGAACAAGCATGGACAG 58.829 55.000 0.00 0.0 0.00 3.51 R
2626 5156 3.507622 AGACCAAGCAAATTGTTCCTAGC 59.492 43.478 0.00 0.0 37.17 3.42 R
3259 6006 5.623551 AGGGAGGTCCAGATATGATTCTA 57.376 43.478 0.00 0.0 38.24 2.10 R
3431 6190 3.448093 TTATGGAATGTGAGGGTTGCA 57.552 42.857 0.00 0.0 0.00 4.08 R
3628 6388 4.114794 GGCAAAAACATAATGCTAGCCAG 58.885 43.478 13.29 0.0 39.94 4.85 R
5508 8413 2.074124 CTTCGAAGCAACGGAGAGC 58.926 57.895 13.09 0.0 40.88 4.09 R
6917 9822 0.391395 CTGAGCCTCCTTGCTGACAG 60.391 60.000 0.00 0.0 42.95 3.51 R
7871 10820 0.038343 CCTGGGCAAAAACACCATCG 60.038 55.000 0.00 0.0 33.07 3.84 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
27 28 3.861840 ACAACACTAATGACCCAGATCG 58.138 45.455 0.00 0.00 0.00 3.69
45 46 2.441410 TCGCCATTCTTTATTGCACCA 58.559 42.857 0.00 0.00 0.00 4.17
75 76 3.062763 GGCATCCATGTCTCGAGTAATG 58.937 50.000 13.13 16.01 0.00 1.90
87 88 7.406553 TGTCTCGAGTAATGAAACACAAAAAG 58.593 34.615 13.13 0.00 0.00 2.27
89 90 8.120465 GTCTCGAGTAATGAAACACAAAAAGAA 58.880 33.333 13.13 0.00 0.00 2.52
90 91 8.670135 TCTCGAGTAATGAAACACAAAAAGAAA 58.330 29.630 13.13 0.00 0.00 2.52
91 92 9.450807 CTCGAGTAATGAAACACAAAAAGAAAT 57.549 29.630 3.62 0.00 0.00 2.17
92 93 9.445786 TCGAGTAATGAAACACAAAAAGAAATC 57.554 29.630 0.00 0.00 0.00 2.17
94 95 9.750125 GAGTAATGAAACACAAAAAGAAATCCT 57.250 29.630 0.00 0.00 0.00 3.24
95 96 9.750125 AGTAATGAAACACAAAAAGAAATCCTC 57.250 29.630 0.00 0.00 0.00 3.71
96 97 7.698836 AATGAAACACAAAAAGAAATCCTCG 57.301 32.000 0.00 0.00 0.00 4.63
151 153 4.539509 ACTTATGACGCGACAAAAACAA 57.460 36.364 15.93 3.12 0.00 2.83
155 157 4.690731 ATGACGCGACAAAAACAAAATG 57.309 36.364 15.93 0.00 0.00 2.32
156 158 3.502920 TGACGCGACAAAAACAAAATGT 58.497 36.364 15.93 0.00 0.00 2.71
157 159 3.544285 TGACGCGACAAAAACAAAATGTC 59.456 39.130 15.93 0.00 39.98 3.06
173 175 9.581099 AACAAAATGTCGAAACTCACTTAAAAT 57.419 25.926 0.00 0.00 0.00 1.82
189 191 8.271458 TCACTTAAAATCATGAGCCTACCAATA 58.729 33.333 0.09 0.00 0.00 1.90
199 201 8.393259 TCATGAGCCTACCAATATGGAATTATT 58.607 33.333 2.85 0.00 40.96 1.40
203 205 9.343539 GAGCCTACCAATATGGAATTATTATCC 57.656 37.037 2.85 0.00 40.96 2.59
209 211 9.088987 ACCAATATGGAATTATTATCCCAACAC 57.911 33.333 2.85 0.00 40.96 3.32
210 212 9.087871 CCAATATGGAATTATTATCCCAACACA 57.912 33.333 0.00 0.00 40.96 3.72
226 228 4.391216 CCAACACAGCAACAATGAAACAAA 59.609 37.500 0.00 0.00 0.00 2.83
234 236 6.246125 CAGCAACAATGAAACAAAACGAAAAC 59.754 34.615 0.00 0.00 0.00 2.43
250 252 2.704725 AAACGAATGCATCACCACAC 57.295 45.000 0.00 0.00 0.00 3.82
257 259 3.598019 ATGCATCACCACACATTTTCC 57.402 42.857 0.00 0.00 0.00 3.13
313 323 8.582096 GTGTAGTACTCTACTTGTATTTTTCGC 58.418 37.037 0.00 0.00 44.74 4.70
354 364 7.791029 ACTACTTGTACTAGGAGTAGGAGTAC 58.209 42.308 19.14 4.79 44.43 2.73
386 2808 1.227263 CCATAGGTTCGGTCTGGCG 60.227 63.158 0.00 0.00 0.00 5.69
432 2854 4.360405 CCCCGGACCCAACCCAAG 62.360 72.222 0.73 0.00 0.00 3.61
437 2859 1.908299 GGACCCAACCCAAGCCAAG 60.908 63.158 0.00 0.00 0.00 3.61
443 2865 2.510551 AACCCAAGCCAAGCCAAGC 61.511 57.895 0.00 0.00 0.00 4.01
463 2893 0.898320 AGACCAGATGTGTCCCGAAG 59.102 55.000 0.00 0.00 33.09 3.79
543 2982 1.668101 CCTTCGTCTTCCTCCCTCGG 61.668 65.000 0.00 0.00 0.00 4.63
581 3020 0.044397 AACCCTACTTCCTCCCTCCC 59.956 60.000 0.00 0.00 0.00 4.30
582 3021 0.860901 ACCCTACTTCCTCCCTCCCT 60.861 60.000 0.00 0.00 0.00 4.20
583 3022 0.105401 CCCTACTTCCTCCCTCCCTC 60.105 65.000 0.00 0.00 0.00 4.30
584 3023 0.105401 CCTACTTCCTCCCTCCCTCC 60.105 65.000 0.00 0.00 0.00 4.30
864 3319 4.385405 GCGACCACTGAGCCTGCT 62.385 66.667 0.00 0.00 0.00 4.24
865 3320 2.125753 CGACCACTGAGCCTGCTC 60.126 66.667 12.18 12.18 43.01 4.26
897 3352 0.106217 GAGAGGAGGAGGAGGAGGTG 60.106 65.000 0.00 0.00 0.00 4.00
929 3384 3.878667 GGCGGAGGGGGAGGATTG 61.879 72.222 0.00 0.00 0.00 2.67
930 3385 2.768344 GCGGAGGGGGAGGATTGA 60.768 66.667 0.00 0.00 0.00 2.57
931 3386 2.812619 GCGGAGGGGGAGGATTGAG 61.813 68.421 0.00 0.00 0.00 3.02
932 3387 2.143419 CGGAGGGGGAGGATTGAGG 61.143 68.421 0.00 0.00 0.00 3.86
936 3391 2.768344 GGGGAGGATTGAGGCGGA 60.768 66.667 0.00 0.00 0.00 5.54
962 3417 1.302832 GGCTCTGGTCTTGGTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
965 3420 1.385347 TCTGGTCTTGGTGGTGGGT 60.385 57.895 0.00 0.00 0.00 4.51
1094 3551 1.593196 CTGCTCGACAAGGTGGAAAA 58.407 50.000 0.00 0.00 0.00 2.29
1112 3587 0.035056 AAACATCCCCTCTTGCTCCG 60.035 55.000 0.00 0.00 0.00 4.63
1116 3591 4.148825 CCCCTCTTGCTCCGTCCG 62.149 72.222 0.00 0.00 0.00 4.79
1128 3603 1.299165 CCGTCCGTCGCTCCATTAG 60.299 63.158 0.00 0.00 38.35 1.73
1138 3613 1.849976 GCTCCATTAGCCTGCATCGC 61.850 60.000 0.00 0.00 46.25 4.58
1140 3615 0.815213 TCCATTAGCCTGCATCGCAC 60.815 55.000 8.47 0.00 33.79 5.34
1141 3616 1.277739 CATTAGCCTGCATCGCACG 59.722 57.895 8.47 0.00 33.79 5.34
1151 3645 1.087202 GCATCGCACGGGACATTGTA 61.087 55.000 0.00 0.00 0.00 2.41
1162 3656 2.328989 CATTGTATGCCGCCGCTG 59.671 61.111 0.00 0.00 35.36 5.18
1166 3660 2.100216 GTATGCCGCCGCTGTTTG 59.900 61.111 0.00 0.00 35.36 2.93
1167 3661 2.359354 TATGCCGCCGCTGTTTGT 60.359 55.556 0.00 0.00 35.36 2.83
1186 3685 6.429385 TGTTTGTTTGGTTGCAGAATTTCTTT 59.571 30.769 0.00 0.00 0.00 2.52
1187 3686 7.604164 TGTTTGTTTGGTTGCAGAATTTCTTTA 59.396 29.630 0.00 0.00 0.00 1.85
1188 3687 8.447053 GTTTGTTTGGTTGCAGAATTTCTTTAA 58.553 29.630 0.00 0.00 0.00 1.52
1208 3713 2.457366 AACCAGACCTTTAGCTCACG 57.543 50.000 0.00 0.00 0.00 4.35
1219 3724 4.495422 CTTTAGCTCACGTATCTGTGGTT 58.505 43.478 0.00 0.00 40.31 3.67
1244 3749 1.011968 TAGTTGCTTACGGCTGTGCG 61.012 55.000 8.92 0.00 42.39 5.34
1268 3773 4.093408 GTGATGAATCTTAGCAGCGTTTCA 59.907 41.667 0.00 0.00 0.00 2.69
1277 3782 0.884704 GCAGCGTTTCAGTCCCTTGA 60.885 55.000 0.00 0.00 0.00 3.02
1281 3786 1.947456 GCGTTTCAGTCCCTTGAGTTT 59.053 47.619 0.00 0.00 0.00 2.66
1294 3799 2.724977 TGAGTTTAGGTCACTCGCAG 57.275 50.000 0.00 0.00 43.26 5.18
1296 3801 1.272769 GAGTTTAGGTCACTCGCAGGT 59.727 52.381 0.00 0.00 31.69 4.00
1299 3804 2.167398 TTAGGTCACTCGCAGGTGCC 62.167 60.000 0.00 6.37 37.16 5.01
1300 3805 4.314440 GGTCACTCGCAGGTGCCA 62.314 66.667 0.00 0.00 37.16 4.92
1301 3806 2.280797 GTCACTCGCAGGTGCCAA 60.281 61.111 0.00 0.00 37.16 4.52
1302 3807 1.891919 GTCACTCGCAGGTGCCAAA 60.892 57.895 0.00 0.00 37.16 3.28
1303 3808 1.153066 TCACTCGCAGGTGCCAAAA 60.153 52.632 0.00 0.00 37.16 2.44
1304 3809 1.165907 TCACTCGCAGGTGCCAAAAG 61.166 55.000 0.00 0.00 37.16 2.27
1305 3810 2.256461 CTCGCAGGTGCCAAAAGC 59.744 61.111 0.00 0.00 44.14 3.51
1314 3819 4.418337 GCCAAAAGCGCTGTGTTT 57.582 50.000 12.58 4.94 0.00 2.83
1315 3820 3.560826 GCCAAAAGCGCTGTGTTTA 57.439 47.368 12.58 0.00 0.00 2.01
1316 3821 2.064573 GCCAAAAGCGCTGTGTTTAT 57.935 45.000 12.58 0.00 0.00 1.40
1323 3828 2.643551 AGCGCTGTGTTTATTATGCCT 58.356 42.857 10.39 0.00 0.00 4.75
1330 3835 4.421131 TGTGTTTATTATGCCTGGGGTTT 58.579 39.130 0.00 0.00 0.00 3.27
1331 3836 4.464597 TGTGTTTATTATGCCTGGGGTTTC 59.535 41.667 0.00 0.00 0.00 2.78
1332 3837 4.027437 TGTTTATTATGCCTGGGGTTTCC 58.973 43.478 0.00 0.00 0.00 3.13
1336 3841 2.525105 TATGCCTGGGGTTTCCTTTC 57.475 50.000 0.00 0.00 36.20 2.62
1373 3881 8.779354 ATTGGTAGAAAAGCTAGAGTACAAAG 57.221 34.615 0.00 0.00 0.00 2.77
1375 3883 8.413309 TGGTAGAAAAGCTAGAGTACAAAGTA 57.587 34.615 0.00 0.00 0.00 2.24
1385 3898 3.056749 AGAGTACAAAGTAGGCTGAACCG 60.057 47.826 0.00 0.00 46.52 4.44
1499 4015 1.284785 GGGTGGATCAATGGGAGAACA 59.715 52.381 0.00 0.00 0.00 3.18
1518 4034 2.166870 ACAGATGCGGGTTTATGTCGTA 59.833 45.455 0.00 0.00 0.00 3.43
1543 4059 5.237344 ACTCATTGATTATTGTCGCTTAGGC 59.763 40.000 0.00 0.00 0.00 3.93
1559 4078 1.080298 GGCCTTGCATGCTTCACAC 60.080 57.895 20.33 3.43 0.00 3.82
1577 4096 7.361713 GCTTCACACAAGTGTATTATAGGCAAA 60.362 37.037 5.41 0.00 46.01 3.68
1695 4217 3.944422 AAAGCGCATTTAGTATGTCGG 57.056 42.857 11.47 0.00 0.00 4.79
1849 4371 3.555966 CAGGAGTTTCCTTTGTCCTGTT 58.444 45.455 8.77 0.00 46.91 3.16
1977 4501 1.066143 GTATGTGTCCTGGTCCTGGTG 60.066 57.143 14.11 0.00 0.00 4.17
1979 4503 2.147387 GTGTCCTGGTCCTGGTGGT 61.147 63.158 14.11 0.00 34.23 4.16
2002 4526 5.514274 AGTTACCATCAGTTTTTGGTGTG 57.486 39.130 4.89 0.00 45.68 3.82
2049 4573 5.807520 CGTGCAAGTATGAATCACTTAGTCT 59.192 40.000 0.00 0.00 34.50 3.24
2053 4577 6.644347 CAAGTATGAATCACTTAGTCTGGGT 58.356 40.000 0.00 0.00 34.50 4.51
2059 4583 5.778241 TGAATCACTTAGTCTGGGTAAGTCA 59.222 40.000 0.00 0.00 38.42 3.41
2062 4586 6.282199 TCACTTAGTCTGGGTAAGTCAATC 57.718 41.667 0.00 0.00 38.42 2.67
2103 4627 3.426787 TTTCCTAATTGCCGGTCTCAA 57.573 42.857 1.90 0.00 0.00 3.02
2141 4665 7.670605 AATAAGTGGTACCTATGCTGTCTAA 57.329 36.000 14.36 0.00 0.00 2.10
2166 4690 4.733165 CATACAGGATGGTGGATTGGATT 58.267 43.478 0.00 0.00 43.62 3.01
2290 4819 7.141100 TCTAAAGGCTGTTATTGCTTGTTAC 57.859 36.000 0.00 0.00 0.00 2.50
2299 4828 6.296026 TGTTATTGCTTGTTACTCCTTCTGT 58.704 36.000 0.00 0.00 0.00 3.41
2314 4843 8.152023 ACTCCTTCTGTTAGGAAACTGATTAT 57.848 34.615 0.00 0.00 43.57 1.28
2323 4852 8.736244 TGTTAGGAAACTGATTATGCTTTAACC 58.264 33.333 0.00 0.00 43.88 2.85
2405 4934 5.072055 TGTGCCCCTATAACAATCATCATG 58.928 41.667 0.00 0.00 0.00 3.07
2505 5035 9.443323 AAAAGAGAGCCTCTATTTTTAGAGAAC 57.557 33.333 18.73 4.02 43.03 3.01
2506 5036 7.726033 AGAGAGCCTCTATTTTTAGAGAACA 57.274 36.000 10.81 0.00 44.79 3.18
2607 5137 7.743838 GCATCTTGCTAAATGATCGTCTTTATC 59.256 37.037 0.00 0.00 40.96 1.75
2617 5147 4.100035 TGATCGTCTTTATCTGTCCATGCT 59.900 41.667 0.00 0.00 0.00 3.79
2626 5156 1.171308 CTGTCCATGCTTGTTCCCTG 58.829 55.000 0.00 0.00 0.00 4.45
2842 5385 6.166279 TCCTGTGATTGATAGACTGTCAAAC 58.834 40.000 17.26 15.08 38.89 2.93
2911 5455 3.508845 TTCTTCTGTTCCAGGGGAAAG 57.491 47.619 0.00 0.98 43.86 2.62
2999 5544 5.291858 GCAGTTTAAAGGGCAATAGCATTTC 59.708 40.000 6.23 0.00 44.61 2.17
3335 6090 5.181690 TGTTTTGGTAACTGAACTCATGC 57.818 39.130 0.00 0.00 34.54 4.06
3431 6190 8.043710 CGAGAGGGGAATTAAGAATTATGCTAT 58.956 37.037 0.00 0.00 0.00 2.97
3440 6199 7.510549 TTAAGAATTATGCTATGCAACCCTC 57.489 36.000 0.00 0.00 43.62 4.30
3446 6205 2.368439 TGCTATGCAACCCTCACATTC 58.632 47.619 0.00 0.00 34.76 2.67
3557 6316 0.526662 AGGGACGAGCGTTGACTTAG 59.473 55.000 0.00 0.00 0.00 2.18
3628 6388 5.419542 TGTGTGTGCTCTAATGAACCTATC 58.580 41.667 0.00 0.00 0.00 2.08
4249 7151 2.290260 TGATTTCTGCAACCGATGGTCT 60.290 45.455 0.00 0.00 33.12 3.85
4531 7434 7.190335 ACTGTATGCCATTTAGGTAGTGTTA 57.810 36.000 0.00 0.00 40.61 2.41
4532 7435 7.802117 ACTGTATGCCATTTAGGTAGTGTTAT 58.198 34.615 0.00 0.00 40.61 1.89
4653 7556 8.099364 TCTGGTAGATCAACAAACTCATTTTC 57.901 34.615 0.00 0.00 0.00 2.29
5032 7937 7.121907 AGCAGGAAATCTGAAGAAATTAAGGAC 59.878 37.037 0.00 0.00 46.18 3.85
5314 8219 2.746362 CCTCAACAGTTCATCTCAAGGC 59.254 50.000 0.00 0.00 0.00 4.35
5335 8240 2.474816 GGCTCTGATGGCTTTAGTACG 58.525 52.381 0.00 0.00 0.00 3.67
5379 8284 1.614413 AGTCAAAGTCACGAGACCTCC 59.386 52.381 9.50 0.00 46.15 4.30
5508 8413 3.495753 GCAAAGAAAGAAATTGGCACCAG 59.504 43.478 0.00 0.00 0.00 4.00
5728 8633 2.159156 GGTTCGGCCAACTGAAAACTTT 60.159 45.455 2.24 0.00 42.79 2.66
5737 8642 5.817296 GCCAACTGAAAACTTTTCCATTTCT 59.183 36.000 11.03 0.00 34.84 2.52
5742 8647 7.203218 ACTGAAAACTTTTCCATTTCTGCTAC 58.797 34.615 11.03 0.00 36.22 3.58
5808 8713 0.681243 GGACCAGGTGGAAGAATGCC 60.681 60.000 0.00 0.00 38.94 4.40
5939 8844 8.868522 TGATCAGAAACAGGTTGATTCTAAAT 57.131 30.769 0.00 0.53 37.39 1.40
6241 9146 0.759959 CTCCTCCAGCTGATGATGCT 59.240 55.000 17.39 0.00 42.06 3.79
6256 9161 7.308450 TGATGATGCTAAAGTTATCCTAGCT 57.692 36.000 6.01 0.00 39.06 3.32
6347 9252 7.849804 TTGCTTTTTATTTTGCACTTACCAA 57.150 28.000 0.00 0.00 35.01 3.67
6374 9279 5.419542 TGCATAGTCTTGTAGAACACCATC 58.580 41.667 0.00 0.00 0.00 3.51
6816 9721 0.469144 GGCTTCGAGATCCTCTCCCT 60.469 60.000 0.00 0.00 40.34 4.20
6962 9867 4.243008 TGCGGTCGTTTCAGGGCA 62.243 61.111 0.00 0.00 0.00 5.36
7012 9920 1.153549 GCACCTGCTAGGAAGTCGG 60.154 63.158 8.91 0.00 37.67 4.79
7083 9991 1.537776 CCTCAGATCATGGAGTGCGAC 60.538 57.143 0.00 0.00 0.00 5.19
7244 10152 3.782046 ACGTCATTCCTTTCTGATACGG 58.218 45.455 0.00 0.00 0.00 4.02
7246 10154 3.551890 CGTCATTCCTTTCTGATACGGTG 59.448 47.826 0.00 0.00 0.00 4.94
7248 10156 3.197766 TCATTCCTTTCTGATACGGTGCT 59.802 43.478 0.00 0.00 0.00 4.40
7249 10157 2.961526 TCCTTTCTGATACGGTGCTC 57.038 50.000 0.00 0.00 0.00 4.26
7272 10188 4.187694 CCTGAACTACTGAGCAAAGATCC 58.812 47.826 0.00 0.00 0.00 3.36
7279 10195 4.298103 ACTGAGCAAAGATCCTGTGAAT 57.702 40.909 0.00 0.00 0.00 2.57
7487 10410 3.873026 GACGAGTGCTGTGCTGCCT 62.873 63.158 0.00 0.00 0.00 4.75
7519 10442 2.087646 GAAGAGAAGGCATTGGTGTCC 58.912 52.381 0.00 0.00 0.00 4.02
7676 10600 3.909732 ACATTAGAGAGACAGAGGAGGG 58.090 50.000 0.00 0.00 0.00 4.30
7678 10602 1.988539 TAGAGAGACAGAGGAGGGGT 58.011 55.000 0.00 0.00 0.00 4.95
7701 10634 0.689412 GGACTGGAGAGGGAGGAAGG 60.689 65.000 0.00 0.00 0.00 3.46
7777 10710 1.236628 CATAATCTGCTGCTCCTGCC 58.763 55.000 0.00 0.00 38.71 4.85
7866 10803 7.803131 ACTCTCTCCTTTTTAGTGGTTTTACT 58.197 34.615 0.00 0.00 34.71 2.24
7871 10820 9.551734 TCTCCTTTTTAGTGGTTTTACTTAGAC 57.448 33.333 0.00 0.00 32.19 2.59
7887 10836 0.958822 AGACGATGGTGTTTTTGCCC 59.041 50.000 0.00 0.00 0.00 5.36
7911 10860 1.937278 TTTGTAACGAACGCCACTCA 58.063 45.000 0.00 0.00 0.00 3.41
7918 10867 0.865111 CGAACGCCACTCATGTTGAA 59.135 50.000 0.00 0.00 0.00 2.69
7933 10882 1.876156 GTTGAAAGAGTCACTGCAGGG 59.124 52.381 19.93 15.69 35.39 4.45
7934 10883 1.131638 TGAAAGAGTCACTGCAGGGT 58.868 50.000 17.28 0.00 0.00 4.34
7943 10892 1.198713 CACTGCAGGGTATGAGGAGT 58.801 55.000 19.93 0.00 0.00 3.85
8008 10959 3.445096 GGGCATGATACTTTTCTGCTTGT 59.555 43.478 0.00 0.00 33.43 3.16
8041 10993 4.357325 TCTAGAAGAGAGTTTGGGATGCT 58.643 43.478 0.00 0.00 0.00 3.79
8083 11035 3.322514 TTTTTCAGGGGTGCTCGAG 57.677 52.632 8.45 8.45 0.00 4.04
8084 11036 0.889186 TTTTTCAGGGGTGCTCGAGC 60.889 55.000 30.42 30.42 42.50 5.03
8085 11037 2.748058 TTTTCAGGGGTGCTCGAGCC 62.748 60.000 33.23 23.41 42.09 4.70
8090 11042 4.681978 GGGTGCTCGAGCCGTTGT 62.682 66.667 33.23 0.00 41.18 3.32
8091 11043 2.665185 GGTGCTCGAGCCGTTGTT 60.665 61.111 33.23 0.00 41.18 2.83
8092 11044 2.251642 GGTGCTCGAGCCGTTGTTT 61.252 57.895 33.23 0.00 41.18 2.83
8109 11061 5.287274 CGTTGTTTTTGTTGCAACATGTAGA 59.713 36.000 31.48 14.73 41.60 2.59
8122 11074 5.455525 GCAACATGTAGACAAAGTTGTTGAC 59.544 40.000 22.12 13.64 41.76 3.18
8131 11083 6.899114 AGACAAAGTTGTTGACGAATAATCC 58.101 36.000 0.00 0.00 42.43 3.01
8136 11088 4.153475 AGTTGTTGACGAATAATCCCAACG 59.847 41.667 0.00 0.00 37.93 4.10
8210 11205 4.607293 AACTGACACTAGATGCAGAACA 57.393 40.909 14.25 0.00 36.51 3.18
8217 11212 3.369147 CACTAGATGCAGAACAAGGAACG 59.631 47.826 0.00 0.00 0.00 3.95
8235 11230 1.740025 ACGGCTAAGAAAAGCATGAGC 59.260 47.619 0.00 0.00 44.64 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.265737 TGGGTCATTAGTGTTGTAGCCAT 59.734 43.478 0.00 0.00 30.07 4.40
1 2 2.640332 TGGGTCATTAGTGTTGTAGCCA 59.360 45.455 0.00 0.00 32.45 4.75
4 5 5.043903 CGATCTGGGTCATTAGTGTTGTAG 58.956 45.833 0.00 0.00 0.00 2.74
14 15 1.492176 AGAATGGCGATCTGGGTCATT 59.508 47.619 0.00 0.00 0.00 2.57
19 20 3.304928 GCAATAAAGAATGGCGATCTGGG 60.305 47.826 0.00 0.00 0.00 4.45
20 21 3.316029 TGCAATAAAGAATGGCGATCTGG 59.684 43.478 0.00 0.00 37.33 3.86
27 28 3.514645 CACTGGTGCAATAAAGAATGGC 58.485 45.455 0.00 0.00 34.77 4.40
75 76 9.065871 CATATCGAGGATTTCTTTTTGTGTTTC 57.934 33.333 0.00 0.00 0.00 2.78
87 88 7.331026 TCCCACAATATCATATCGAGGATTTC 58.669 38.462 2.84 0.00 0.00 2.17
89 90 6.874278 TCCCACAATATCATATCGAGGATT 57.126 37.500 2.84 0.00 0.00 3.01
90 91 6.352222 GGTTCCCACAATATCATATCGAGGAT 60.352 42.308 0.00 0.00 0.00 3.24
91 92 5.046591 GGTTCCCACAATATCATATCGAGGA 60.047 44.000 0.00 0.00 0.00 3.71
92 93 5.178797 GGTTCCCACAATATCATATCGAGG 58.821 45.833 0.00 0.00 0.00 4.63
94 95 4.595350 TGGGTTCCCACAATATCATATCGA 59.405 41.667 6.46 0.00 0.00 3.59
95 96 4.905429 TGGGTTCCCACAATATCATATCG 58.095 43.478 6.46 0.00 0.00 2.92
96 97 6.294731 GCTTTGGGTTCCCACAATATCATATC 60.295 42.308 10.41 0.00 35.60 1.63
109 110 0.536460 TCGTCTTGCTTTGGGTTCCC 60.536 55.000 0.12 0.12 0.00 3.97
124 125 1.980844 TGTCGCGTCATAAGTTTCGTC 59.019 47.619 5.77 0.00 0.00 4.20
126 127 3.427516 TTTGTCGCGTCATAAGTTTCG 57.572 42.857 6.92 0.00 0.00 3.46
127 128 4.965158 TGTTTTTGTCGCGTCATAAGTTTC 59.035 37.500 6.92 2.60 0.00 2.78
151 153 9.398170 CATGATTTTAAGTGAGTTTCGACATTT 57.602 29.630 0.00 0.00 0.00 2.32
155 157 6.738649 GCTCATGATTTTAAGTGAGTTTCGAC 59.261 38.462 0.00 0.00 40.08 4.20
156 158 6.128282 GGCTCATGATTTTAAGTGAGTTTCGA 60.128 38.462 0.00 0.00 40.08 3.71
157 159 6.024049 GGCTCATGATTTTAAGTGAGTTTCG 58.976 40.000 0.00 0.00 40.08 3.46
158 160 7.150783 AGGCTCATGATTTTAAGTGAGTTTC 57.849 36.000 0.00 0.00 40.08 2.78
173 175 5.848286 ATTCCATATTGGTAGGCTCATGA 57.152 39.130 0.00 0.00 39.03 3.07
189 191 6.135454 TGCTGTGTTGGGATAATAATTCCAT 58.865 36.000 0.00 0.00 40.71 3.41
199 201 3.760738 TCATTGTTGCTGTGTTGGGATA 58.239 40.909 0.00 0.00 0.00 2.59
201 203 2.064434 TCATTGTTGCTGTGTTGGGA 57.936 45.000 0.00 0.00 0.00 4.37
203 205 3.519579 TGTTTCATTGTTGCTGTGTTGG 58.480 40.909 0.00 0.00 0.00 3.77
207 209 4.325741 TCGTTTTGTTTCATTGTTGCTGTG 59.674 37.500 0.00 0.00 0.00 3.66
209 211 5.447478 TTCGTTTTGTTTCATTGTTGCTG 57.553 34.783 0.00 0.00 0.00 4.41
210 212 6.303370 GTTTTCGTTTTGTTTCATTGTTGCT 58.697 32.000 0.00 0.00 0.00 3.91
226 228 2.292016 TGGTGATGCATTCGTTTTCGTT 59.708 40.909 0.00 0.00 44.46 3.85
234 236 2.925578 AATGTGTGGTGATGCATTCG 57.074 45.000 0.00 0.00 0.00 3.34
329 339 6.889595 ACTCCTACTCCTAGTACAAGTAGT 57.110 41.667 16.71 8.97 40.46 2.73
354 364 5.799936 CGAACCTATGGTTTGCTATTTGTTG 59.200 40.000 3.34 0.00 46.95 3.33
355 365 5.105917 CCGAACCTATGGTTTGCTATTTGTT 60.106 40.000 10.42 0.00 46.95 2.83
432 2854 2.598394 TGGTCTGCTTGGCTTGGC 60.598 61.111 0.00 0.00 0.00 4.52
437 2859 0.607489 ACACATCTGGTCTGCTTGGC 60.607 55.000 0.00 0.00 0.00 4.52
443 2865 0.608130 TTCGGGACACATCTGGTCTG 59.392 55.000 0.00 0.00 35.61 3.51
469 2899 6.936749 TATATATAGCCCCACCACCCCCAC 62.937 54.167 0.00 0.00 0.00 4.61
470 2900 2.292776 ATATAGCCCCACCACCCCCA 62.293 60.000 0.00 0.00 0.00 4.96
471 2901 0.178855 TATATAGCCCCACCACCCCC 60.179 60.000 0.00 0.00 0.00 5.40
581 3020 1.392589 CGGGTTGGATTTGGATGGAG 58.607 55.000 0.00 0.00 0.00 3.86
582 3021 0.033601 CCGGGTTGGATTTGGATGGA 60.034 55.000 0.00 0.00 42.00 3.41
583 3022 1.675720 GCCGGGTTGGATTTGGATGG 61.676 60.000 2.18 0.00 42.00 3.51
584 3023 0.969917 TGCCGGGTTGGATTTGGATG 60.970 55.000 2.18 0.00 42.00 3.51
848 3300 2.125753 GAGCAGGCTCAGTGGTCG 60.126 66.667 16.03 0.00 42.31 4.79
850 3302 2.527624 TGGAGCAGGCTCAGTGGT 60.528 61.111 21.63 0.00 44.40 4.16
853 3305 4.079850 CGCTGGAGCAGGCTCAGT 62.080 66.667 21.63 0.00 44.40 3.41
864 3319 1.380515 CTCTCTTCCTCCCGCTGGA 60.381 63.158 0.00 0.00 38.75 3.86
865 3320 2.430610 CCTCTCTTCCTCCCGCTGG 61.431 68.421 0.00 0.00 0.00 4.85
877 3332 0.254107 ACCTCCTCCTCCTCCTCTCT 60.254 60.000 0.00 0.00 0.00 3.10
913 3368 2.768344 TCAATCCTCCCCCTCCGC 60.768 66.667 0.00 0.00 0.00 5.54
914 3369 2.143419 CCTCAATCCTCCCCCTCCG 61.143 68.421 0.00 0.00 0.00 4.63
915 3370 2.456443 GCCTCAATCCTCCCCCTCC 61.456 68.421 0.00 0.00 0.00 4.30
916 3371 2.812619 CGCCTCAATCCTCCCCCTC 61.813 68.421 0.00 0.00 0.00 4.30
917 3372 2.770048 CGCCTCAATCCTCCCCCT 60.770 66.667 0.00 0.00 0.00 4.79
918 3373 3.878667 CCGCCTCAATCCTCCCCC 61.879 72.222 0.00 0.00 0.00 5.40
919 3374 2.768344 TCCGCCTCAATCCTCCCC 60.768 66.667 0.00 0.00 0.00 4.81
920 3375 2.812619 CCTCCGCCTCAATCCTCCC 61.813 68.421 0.00 0.00 0.00 4.30
921 3376 1.753368 CTCCTCCGCCTCAATCCTCC 61.753 65.000 0.00 0.00 0.00 4.30
922 3377 1.745264 CTCCTCCGCCTCAATCCTC 59.255 63.158 0.00 0.00 0.00 3.71
923 3378 1.764054 CCTCCTCCGCCTCAATCCT 60.764 63.158 0.00 0.00 0.00 3.24
924 3379 1.753368 CTCCTCCTCCGCCTCAATCC 61.753 65.000 0.00 0.00 0.00 3.01
925 3380 1.745264 CTCCTCCTCCGCCTCAATC 59.255 63.158 0.00 0.00 0.00 2.67
926 3381 1.764054 CCTCCTCCTCCGCCTCAAT 60.764 63.158 0.00 0.00 0.00 2.57
927 3382 2.364317 CCTCCTCCTCCGCCTCAA 60.364 66.667 0.00 0.00 0.00 3.02
928 3383 4.465446 CCCTCCTCCTCCGCCTCA 62.465 72.222 0.00 0.00 0.00 3.86
932 3387 4.851214 AGAGCCCTCCTCCTCCGC 62.851 72.222 0.00 0.00 41.74 5.54
936 3391 1.820866 AAGACCAGAGCCCTCCTCCT 61.821 60.000 0.00 0.00 41.74 3.69
1094 3551 1.201429 ACGGAGCAAGAGGGGATGTT 61.201 55.000 0.00 0.00 0.00 2.71
1112 3587 4.014065 GCTAATGGAGCGACGGAC 57.986 61.111 0.00 0.00 42.62 4.79
1129 3604 4.758251 TGTCCCGTGCGATGCAGG 62.758 66.667 4.60 4.60 40.08 4.85
1131 3606 2.046411 AATGTCCCGTGCGATGCA 60.046 55.556 0.00 0.00 35.60 3.96
1132 3607 1.087202 TACAATGTCCCGTGCGATGC 61.087 55.000 0.00 0.00 0.00 3.91
1134 3609 1.581934 CATACAATGTCCCGTGCGAT 58.418 50.000 0.00 0.00 0.00 4.58
1135 3610 1.087202 GCATACAATGTCCCGTGCGA 61.087 55.000 0.00 0.00 0.00 5.10
1136 3611 1.351707 GCATACAATGTCCCGTGCG 59.648 57.895 0.00 0.00 0.00 5.34
1138 3613 2.013807 CGGCATACAATGTCCCGTG 58.986 57.895 10.53 0.00 0.00 4.94
1140 3615 2.542907 GGCGGCATACAATGTCCCG 61.543 63.158 3.07 13.32 0.00 5.14
1141 3616 2.542907 CGGCGGCATACAATGTCCC 61.543 63.158 10.53 0.00 0.00 4.46
1151 3645 2.855514 AAACAAACAGCGGCGGCAT 61.856 52.632 19.21 2.96 43.41 4.40
1162 3656 6.421377 AAGAAATTCTGCAACCAAACAAAC 57.579 33.333 0.00 0.00 0.00 2.93
1166 3660 7.908082 GGTTTTAAAGAAATTCTGCAACCAAAC 59.092 33.333 15.38 10.49 0.00 2.93
1167 3661 7.607991 TGGTTTTAAAGAAATTCTGCAACCAAA 59.392 29.630 18.43 4.92 0.00 3.28
1186 3685 4.202284 ACGTGAGCTAAAGGTCTGGTTTTA 60.202 41.667 10.28 0.00 42.60 1.52
1187 3686 3.139077 CGTGAGCTAAAGGTCTGGTTTT 58.861 45.455 10.28 0.00 42.60 2.43
1188 3687 2.104281 ACGTGAGCTAAAGGTCTGGTTT 59.896 45.455 10.28 0.00 42.60 3.27
1208 3713 5.127356 AGCAACTAGTCCTAACCACAGATAC 59.873 44.000 0.00 0.00 0.00 2.24
1244 3749 2.555199 ACGCTGCTAAGATTCATCACC 58.445 47.619 0.00 0.00 0.00 4.02
1268 3773 3.579151 GAGTGACCTAAACTCAAGGGACT 59.421 47.826 0.00 0.00 42.98 3.85
1277 3782 1.000955 CACCTGCGAGTGACCTAAACT 59.999 52.381 0.00 0.00 40.34 2.66
1281 3786 2.646175 GGCACCTGCGAGTGACCTA 61.646 63.158 9.91 0.00 40.11 3.08
1294 3799 2.355009 CACAGCGCTTTTGGCACC 60.355 61.111 7.50 0.00 41.91 5.01
1296 3801 0.741326 TAAACACAGCGCTTTTGGCA 59.259 45.000 7.50 0.00 41.91 4.92
1299 3804 4.031652 GGCATAATAAACACAGCGCTTTTG 59.968 41.667 7.50 11.16 0.00 2.44
1300 3805 4.082245 AGGCATAATAAACACAGCGCTTTT 60.082 37.500 7.50 9.24 0.00 2.27
1301 3806 3.443681 AGGCATAATAAACACAGCGCTTT 59.556 39.130 7.50 0.00 0.00 3.51
1302 3807 3.016736 AGGCATAATAAACACAGCGCTT 58.983 40.909 7.50 0.00 0.00 4.68
1303 3808 2.355756 CAGGCATAATAAACACAGCGCT 59.644 45.455 2.64 2.64 0.00 5.92
1304 3809 2.541588 CCAGGCATAATAAACACAGCGC 60.542 50.000 0.00 0.00 0.00 5.92
1305 3810 2.033299 CCCAGGCATAATAAACACAGCG 59.967 50.000 0.00 0.00 0.00 5.18
1306 3811 2.362077 CCCCAGGCATAATAAACACAGC 59.638 50.000 0.00 0.00 0.00 4.40
1307 3812 3.631250 ACCCCAGGCATAATAAACACAG 58.369 45.455 0.00 0.00 0.00 3.66
1308 3813 3.748645 ACCCCAGGCATAATAAACACA 57.251 42.857 0.00 0.00 0.00 3.72
1309 3814 4.142026 GGAAACCCCAGGCATAATAAACAC 60.142 45.833 0.00 0.00 34.14 3.32
1310 3815 4.027437 GGAAACCCCAGGCATAATAAACA 58.973 43.478 0.00 0.00 34.14 2.83
1311 3816 4.286707 AGGAAACCCCAGGCATAATAAAC 58.713 43.478 0.00 0.00 37.41 2.01
1312 3817 4.618378 AGGAAACCCCAGGCATAATAAA 57.382 40.909 0.00 0.00 37.41 1.40
1313 3818 4.618378 AAGGAAACCCCAGGCATAATAA 57.382 40.909 0.00 0.00 37.41 1.40
1314 3819 4.231890 AGAAAGGAAACCCCAGGCATAATA 59.768 41.667 0.00 0.00 37.41 0.98
1315 3820 3.012844 AGAAAGGAAACCCCAGGCATAAT 59.987 43.478 0.00 0.00 37.41 1.28
1316 3821 2.381961 AGAAAGGAAACCCCAGGCATAA 59.618 45.455 0.00 0.00 37.41 1.90
1323 3828 1.133294 GGTGGAAGAAAGGAAACCCCA 60.133 52.381 0.00 0.00 37.41 4.96
1330 3835 3.498481 CCAATCAGTGGTGGAAGAAAGGA 60.498 47.826 7.77 0.00 43.20 3.36
1331 3836 2.821969 CCAATCAGTGGTGGAAGAAAGG 59.178 50.000 7.77 0.00 43.20 3.11
1357 3865 5.480772 TCAGCCTACTTTGTACTCTAGCTTT 59.519 40.000 0.00 0.00 0.00 3.51
1373 3881 2.007608 GAAACCATCGGTTCAGCCTAC 58.992 52.381 0.00 0.00 46.20 3.18
1375 3883 0.322546 GGAAACCATCGGTTCAGCCT 60.323 55.000 0.00 0.00 46.20 4.58
1385 3898 2.633488 AGCGCTCTTTAGGAAACCATC 58.367 47.619 2.64 0.00 0.00 3.51
1499 4015 3.118884 AGTTACGACATAAACCCGCATCT 60.119 43.478 0.00 0.00 0.00 2.90
1518 4034 6.238484 GCCTAAGCGACAATAATCAATGAGTT 60.238 38.462 0.00 0.00 0.00 3.01
1543 4059 1.338973 ACTTGTGTGAAGCATGCAAGG 59.661 47.619 21.98 1.83 40.35 3.61
1559 4078 7.320443 TCTGCTTTTGCCTATAATACACTTG 57.680 36.000 0.00 0.00 46.87 3.16
1577 4096 4.626042 CCGCTCTCATACTAAATCTGCTT 58.374 43.478 0.00 0.00 0.00 3.91
1695 4217 1.320507 CTAGTAAGCCTCCCGAGTCC 58.679 60.000 0.00 0.00 0.00 3.85
1849 4371 8.486210 AGGATATTTGCAGAAAGTAGTCATGTA 58.514 33.333 0.00 0.00 0.00 2.29
2002 4526 4.202151 GGATGGACAACTTTATGCCAATCC 60.202 45.833 0.00 0.00 32.74 3.01
2049 4573 2.708861 AGTGTGGTGATTGACTTACCCA 59.291 45.455 0.00 0.00 33.51 4.51
2053 4577 5.482163 TCATCAGTGTGGTGATTGACTTA 57.518 39.130 0.00 0.00 31.53 2.24
2059 4583 5.850557 TTTGTTTCATCAGTGTGGTGATT 57.149 34.783 0.00 0.00 37.35 2.57
2062 4586 6.018832 GGAAATTTTGTTTCATCAGTGTGGTG 60.019 38.462 0.00 0.00 0.00 4.17
2103 4627 7.446319 GGTACCACTTATTTAGAACACCTTGTT 59.554 37.037 7.15 0.00 44.37 2.83
2166 4690 9.733556 AATGTTTACAGTACAAATCCTACATCA 57.266 29.630 0.00 0.00 0.00 3.07
2207 4731 9.944376 ACAACTAACTGCTCTGAGATAAATAAA 57.056 29.630 9.28 0.00 0.00 1.40
2208 4732 9.944376 AACAACTAACTGCTCTGAGATAAATAA 57.056 29.630 9.28 0.00 0.00 1.40
2213 4737 8.531982 ACATAAACAACTAACTGCTCTGAGATA 58.468 33.333 9.28 0.00 0.00 1.98
2221 4745 7.568199 AGTTTCACATAAACAACTAACTGCT 57.432 32.000 3.70 0.00 32.81 4.24
2251 4778 9.023962 ACAGCCTTTAGATCACAAAAATATTGA 57.976 29.630 0.00 0.00 0.00 2.57
2259 4786 6.434028 AGCAATAACAGCCTTTAGATCACAAA 59.566 34.615 0.00 0.00 0.00 2.83
2290 4819 7.011857 GCATAATCAGTTTCCTAACAGAAGGAG 59.988 40.741 0.00 0.00 46.29 3.69
2314 4843 8.911918 TGTAACAAGAAATCTAGGTTAAAGCA 57.088 30.769 8.37 2.94 31.87 3.91
2505 5035 6.764308 TTCCCATCTTTCTCATAAGCTTTG 57.236 37.500 3.20 3.18 0.00 2.77
2506 5036 6.323225 CCATTCCCATCTTTCTCATAAGCTTT 59.677 38.462 3.20 0.00 0.00 3.51
2607 5137 1.171308 CAGGGAACAAGCATGGACAG 58.829 55.000 0.00 0.00 0.00 3.51
2626 5156 3.507622 AGACCAAGCAAATTGTTCCTAGC 59.492 43.478 0.00 0.00 37.17 3.42
2804 5347 7.171653 TCAATCACAGGAACACCAACATATAA 58.828 34.615 0.00 0.00 0.00 0.98
2842 5385 8.915871 AATCATGAAATGTCATTTTAGTTCGG 57.084 30.769 12.04 0.06 46.80 4.30
3099 5836 9.492730 AGTTTTCATGTATGGGGAAAAGATATT 57.507 29.630 0.00 0.00 40.13 1.28
3112 5849 6.293626 GGCTATGCTACCAGTTTTCATGTATG 60.294 42.308 0.00 0.00 0.00 2.39
3196 5936 7.286508 GTCACAATAATGAATACATCTGCTCG 58.713 38.462 0.00 0.00 35.50 5.03
3259 6006 5.623551 AGGGAGGTCCAGATATGATTCTA 57.376 43.478 0.00 0.00 38.24 2.10
3431 6190 3.448093 TTATGGAATGTGAGGGTTGCA 57.552 42.857 0.00 0.00 0.00 4.08
3557 6316 6.037830 TGACAGCTAAAACTAACAAAGACCAC 59.962 38.462 0.00 0.00 0.00 4.16
3628 6388 4.114794 GGCAAAAACATAATGCTAGCCAG 58.885 43.478 13.29 0.00 39.94 4.85
3838 6600 4.202151 GGGTTAATTCATGAACATCTGCCC 60.202 45.833 11.07 13.40 0.00 5.36
4120 7022 7.996644 AGGAAACAAACTAAGTCTAAATCACCA 59.003 33.333 0.00 0.00 0.00 4.17
4386 7289 7.307101 GCTTCTCTGATTGCAGCTTATACTTAC 60.307 40.741 0.00 0.00 42.01 2.34
4493 7396 6.894682 TGGCATACAGTATTCCAGATTTGTA 58.105 36.000 7.79 0.00 28.17 2.41
4532 7435 9.890629 AGAAACTACAATGAGCAGTGAATATTA 57.109 29.630 4.83 0.00 0.00 0.98
4894 7799 5.490139 TCTTGTCTTTGTGCTTCTCTTTG 57.510 39.130 0.00 0.00 0.00 2.77
5122 8027 4.046462 CACTAAAACCTTCACGACTTCGA 58.954 43.478 5.47 0.00 43.02 3.71
5314 8219 2.474816 GTACTAAAGCCATCAGAGCCG 58.525 52.381 0.00 0.00 0.00 5.52
5379 8284 4.753233 CACAGAATCAGTAGAGTTGGAGG 58.247 47.826 0.00 0.00 0.00 4.30
5508 8413 2.074124 CTTCGAAGCAACGGAGAGC 58.926 57.895 13.09 0.00 40.88 4.09
5939 8844 1.075601 ATTTTCTCCACAGCTGGGGA 58.924 50.000 35.16 35.16 46.44 4.81
6241 9146 8.548877 AGGTTTTCATCAGCTAGGATAACTTTA 58.451 33.333 11.58 0.00 32.55 1.85
6256 9161 3.738982 TCGCTTCTTCAGGTTTTCATCA 58.261 40.909 0.00 0.00 0.00 3.07
6347 9252 7.564793 TGGTGTTCTACAAGACTATGCAATAT 58.435 34.615 0.00 0.00 0.00 1.28
6752 9657 2.886523 TGAGCTTCCTTGTTGACATTGG 59.113 45.455 0.00 0.00 0.00 3.16
6793 9698 2.510664 GAGGATCTCGAAGCCCTGT 58.489 57.895 4.15 0.00 0.00 4.00
6816 9721 5.148502 ACAGTCACCTTCTCTTCCTTCTTA 58.851 41.667 0.00 0.00 0.00 2.10
6915 9820 0.898320 GAGCCTCCTTGCTGACAGTA 59.102 55.000 3.99 0.00 42.95 2.74
6917 9822 0.391395 CTGAGCCTCCTTGCTGACAG 60.391 60.000 0.00 0.00 42.95 3.51
6962 9867 2.121781 ATGCCCCAGGATCCCGAT 60.122 61.111 8.55 0.00 0.00 4.18
7012 9920 2.396590 TACTTGAAATCCGGGTGAGC 57.603 50.000 0.00 0.00 0.00 4.26
7083 9991 2.490217 CAGTCCTGGTCGCCGTAG 59.510 66.667 0.00 0.00 0.00 3.51
7244 10152 2.663826 CTCAGTAGTTCAGGGAGCAC 57.336 55.000 0.00 0.00 0.00 4.40
7246 10154 3.750828 GCTCAGTAGTTCAGGGAGC 57.249 57.895 0.00 0.00 43.41 4.70
7248 10156 3.239449 TCTTTGCTCAGTAGTTCAGGGA 58.761 45.455 0.00 0.00 0.00 4.20
7249 10157 3.685139 TCTTTGCTCAGTAGTTCAGGG 57.315 47.619 0.00 0.00 0.00 4.45
7487 10410 3.513515 GCCTTCTCTTCTCTTCTTCTCCA 59.486 47.826 0.00 0.00 0.00 3.86
7676 10600 1.687493 CCCTCTCCAGTCCTCCACC 60.687 68.421 0.00 0.00 0.00 4.61
7678 10602 1.700368 CTCCCTCTCCAGTCCTCCA 59.300 63.158 0.00 0.00 0.00 3.86
7701 10634 4.060038 TGTCTCACTCACTCAAAAGTCC 57.940 45.455 0.00 0.00 31.71 3.85
7705 10638 7.572523 AAATGAATGTCTCACTCACTCAAAA 57.427 32.000 0.00 0.00 36.69 2.44
7787 10720 1.312815 AGAATAAATCAGGCAGCGGC 58.687 50.000 0.00 0.00 40.13 6.53
7788 10721 2.684881 ACAAGAATAAATCAGGCAGCGG 59.315 45.455 0.00 0.00 0.00 5.52
7789 10722 4.346129 GAACAAGAATAAATCAGGCAGCG 58.654 43.478 0.00 0.00 0.00 5.18
7866 10803 2.554893 GGGCAAAAACACCATCGTCTAA 59.445 45.455 0.00 0.00 0.00 2.10
7871 10820 0.038343 CCTGGGCAAAAACACCATCG 60.038 55.000 0.00 0.00 33.07 3.84
7887 10836 1.331138 TGGCGTTCGTTACAAAACCTG 59.669 47.619 0.00 0.00 31.46 4.00
7911 10860 3.144506 CCTGCAGTGACTCTTTCAACAT 58.855 45.455 13.81 0.00 35.39 2.71
7918 10867 2.499289 CTCATACCCTGCAGTGACTCTT 59.501 50.000 13.81 0.00 0.00 2.85
7933 10882 6.334102 ACTTCCGATGATAACTCCTCATAC 57.666 41.667 0.00 0.00 33.56 2.39
7934 10883 6.978674 AACTTCCGATGATAACTCCTCATA 57.021 37.500 0.00 0.00 33.56 2.15
7943 10892 8.062065 AGCCAATTTTTAACTTCCGATGATAA 57.938 30.769 0.00 0.00 0.00 1.75
8008 10959 2.027100 TCTCTTCTAGAGCCAGTCGACA 60.027 50.000 19.50 0.00 42.04 4.35
8079 11031 1.795889 GCAACAAAAACAACGGCTCGA 60.796 47.619 1.50 0.00 0.00 4.04
8080 11032 0.570272 GCAACAAAAACAACGGCTCG 59.430 50.000 0.00 0.00 0.00 5.03
8081 11033 1.634702 TGCAACAAAAACAACGGCTC 58.365 45.000 0.00 0.00 0.00 4.70
8082 11034 1.729517 GTTGCAACAAAAACAACGGCT 59.270 42.857 24.52 0.00 34.89 5.52
8083 11035 1.461127 TGTTGCAACAAAAACAACGGC 59.539 42.857 29.36 0.00 45.18 5.68
8084 11036 3.124297 ACATGTTGCAACAAAAACAACGG 59.876 39.130 34.06 16.86 45.18 4.44
8085 11037 4.319235 ACATGTTGCAACAAAAACAACG 57.681 36.364 34.06 17.03 45.18 4.10
8086 11038 6.090088 TGTCTACATGTTGCAACAAAAACAAC 59.910 34.615 34.06 25.05 43.03 3.32
8087 11039 6.159293 TGTCTACATGTTGCAACAAAAACAA 58.841 32.000 34.06 16.29 43.03 2.83
8088 11040 5.714047 TGTCTACATGTTGCAACAAAAACA 58.286 33.333 34.06 26.74 43.03 2.83
8089 11041 6.639671 TTGTCTACATGTTGCAACAAAAAC 57.360 33.333 34.06 24.88 43.03 2.43
8090 11042 6.870965 ACTTTGTCTACATGTTGCAACAAAAA 59.129 30.769 34.06 20.52 43.03 1.94
8091 11043 6.393990 ACTTTGTCTACATGTTGCAACAAAA 58.606 32.000 34.06 24.55 43.03 2.44
8092 11044 5.960113 ACTTTGTCTACATGTTGCAACAAA 58.040 33.333 34.06 19.63 43.03 2.83
8109 11061 5.533154 TGGGATTATTCGTCAACAACTTTGT 59.467 36.000 0.00 0.00 44.72 2.83
8122 11074 1.261619 GCAGAGCGTTGGGATTATTCG 59.738 52.381 0.00 0.00 0.00 3.34
8131 11083 2.826428 ACATACATAGCAGAGCGTTGG 58.174 47.619 0.00 0.00 0.00 3.77
8136 11088 8.072567 CCTAATTTCAAACATACATAGCAGAGC 58.927 37.037 0.00 0.00 0.00 4.09
8197 11192 2.932614 CCGTTCCTTGTTCTGCATCTAG 59.067 50.000 0.00 0.00 0.00 2.43
8210 11205 2.858745 TGCTTTTCTTAGCCGTTCCTT 58.141 42.857 0.00 0.00 40.49 3.36
8217 11212 1.740025 ACGCTCATGCTTTTCTTAGCC 59.260 47.619 0.00 0.00 40.49 3.93


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

AutoCloner maintained by Alex Coulton.