Multiple sequence alignment - TraesCS2D01G292500

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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 TraesCS2D01G292500 chr2D 100.000 4886 0 0 1 4886 375029555 375034440 0.000000e+00 9023.0
1 TraesCS2D01G292500 chr2D 100.000 43 0 0 4274 4316 375033785 375033827 4.050000e-11 80.5
2 TraesCS2D01G292500 chr2D 100.000 43 0 0 4231 4273 375033828 375033870 4.050000e-11 80.5
3 TraesCS2D01G292500 chr2D 82.143 84 11 2 2265 2344 346088811 346088894 8.780000e-08 69.4
4 TraesCS2D01G292500 chr2D 94.444 36 2 0 4675 4710 122700497 122700532 6.830000e-04 56.5
5 TraesCS2D01G292500 chr2A 92.218 2236 103 33 2349 4560 507388659 507390847 0.000000e+00 3099.0
6 TraesCS2D01G292500 chr2A 85.591 1159 70 36 36 1123 507386239 507387371 0.000000e+00 1125.0
7 TraesCS2D01G292500 chr2A 92.842 475 26 3 1528 1997 507387881 507388352 0.000000e+00 682.0
8 TraesCS2D01G292500 chr2A 89.270 233 18 4 2106 2331 507388356 507388588 8.000000e-73 285.0
9 TraesCS2D01G292500 chr2A 90.541 74 7 0 4600 4673 507390861 507390934 1.120000e-16 99.0
10 TraesCS2D01G292500 chr2A 96.429 56 2 0 4679 4734 263462959 263463014 5.210000e-15 93.5
11 TraesCS2D01G292500 chr2B 94.364 1934 71 14 2349 4273 445176183 445178087 0.000000e+00 2933.0
12 TraesCS2D01G292500 chr2B 89.860 1075 47 22 74 1125 445173946 445174981 0.000000e+00 1325.0
13 TraesCS2D01G292500 chr2B 90.434 899 55 14 1118 1997 445175006 445175892 0.000000e+00 1155.0
14 TraesCS2D01G292500 chr2B 85.233 623 79 11 4274 4886 445178045 445178664 3.210000e-176 628.0
15 TraesCS2D01G292500 chr2B 89.474 247 18 5 2106 2347 445175896 445176139 6.140000e-79 305.0
16 TraesCS2D01G292500 chr2B 89.062 64 6 1 4662 4724 510625539 510625602 1.460000e-10 78.7
17 TraesCS2D01G292500 chr2B 87.273 55 7 0 4496 4550 166747786 166747840 4.080000e-06 63.9
18 TraesCS2D01G292500 chr3D 86.446 996 131 3 2626 3617 349642863 349641868 0.000000e+00 1088.0
19 TraesCS2D01G292500 chr3D 93.443 122 7 1 1986 2107 336616925 336616805 3.890000e-41 180.0
20 TraesCS2D01G292500 chr3D 89.362 47 5 0 4498 4544 252847454 252847500 5.280000e-05 60.2
21 TraesCS2D01G292500 chr3A 86.249 989 133 2 2632 3617 467878393 467877405 0.000000e+00 1070.0
22 TraesCS2D01G292500 chr3B 85.440 989 141 2 2632 3617 448577928 448576940 0.000000e+00 1026.0
23 TraesCS2D01G292500 chr7B 98.165 109 2 0 1996 2104 711431811 711431703 1.800000e-44 191.0
24 TraesCS2D01G292500 chr7B 92.857 126 8 1 1979 2104 523681958 523682082 1.080000e-41 182.0
25 TraesCS2D01G292500 chr4D 95.763 118 5 0 1997 2114 311845778 311845661 1.800000e-44 191.0
26 TraesCS2D01G292500 chr4D 92.800 125 8 1 1983 2107 60634340 60634463 3.890000e-41 180.0
27 TraesCS2D01G292500 chr4D 78.947 209 35 5 4678 4884 93822494 93822293 3.070000e-27 134.0
28 TraesCS2D01G292500 chr5D 92.969 128 7 2 1977 2104 391377005 391376880 8.350000e-43 185.0
29 TraesCS2D01G292500 chr5D 92.800 125 8 1 1983 2107 293988687 293988810 3.890000e-41 180.0
30 TraesCS2D01G292500 chr1B 94.915 118 6 0 1995 2112 145360869 145360986 8.350000e-43 185.0
31 TraesCS2D01G292500 chrUn 87.333 150 14 5 1966 2111 50839276 50839424 3.030000e-37 167.0
32 TraesCS2D01G292500 chr1D 86.486 111 15 0 4602 4712 101096826 101096936 6.640000e-24 122.0
33 TraesCS2D01G292500 chr5A 90.164 61 5 1 4671 4731 522999760 522999701 1.460000e-10 78.7
34 TraesCS2D01G292500 chr4B 82.022 89 9 6 4678 4765 195458985 195458903 8.780000e-08 69.4
35 TraesCS2D01G292500 chr4B 100.000 32 0 0 4496 4527 609310979 609310948 5.280000e-05 60.2
36 TraesCS2D01G292500 chr5B 91.837 49 2 2 4682 4730 625214772 625214726 3.160000e-07 67.6


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 TraesCS2D01G292500 chr2D 375029555 375034440 4885 False 3061.333333 9023 100.0000 1 4886 3 chr2D.!!$F3 4885
1 TraesCS2D01G292500 chr2A 507386239 507390934 4695 False 1058.000000 3099 90.0924 36 4673 5 chr2A.!!$F2 4637
2 TraesCS2D01G292500 chr2B 445173946 445178664 4718 False 1269.200000 2933 89.8730 74 4886 5 chr2B.!!$F3 4812
3 TraesCS2D01G292500 chr3D 349641868 349642863 995 True 1088.000000 1088 86.4460 2626 3617 1 chr3D.!!$R2 991
4 TraesCS2D01G292500 chr3A 467877405 467878393 988 True 1070.000000 1070 86.2490 2632 3617 1 chr3A.!!$R1 985
5 TraesCS2D01G292500 chr3B 448576940 448577928 988 True 1026.000000 1026 85.4400 2632 3617 1 chr3B.!!$R1 985

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
756 828 0.035458 ACAAAACCCTCGCTCCAGAG 59.965 55.0 0.00 0.0 37.97 3.35 F
795 875 0.386476 AACGGCTGTAACTGTCGTCA 59.614 50.0 0.00 0.0 42.19 4.35 F
1971 2279 0.034186 GTGGCCATTGGATGACTGGA 60.034 55.0 9.72 0.0 31.38 3.86 F
1972 2280 0.256752 TGGCCATTGGATGACTGGAG 59.743 55.0 0.00 0.0 31.38 3.86 F
2027 2335 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.0 6.13 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1997 0.252421 TGAGGGACCATGTGAGCTCT 60.252 55.000 16.19 0.0 0.00 4.09 R
2008 2316 0.527113 TCCGCGACAAGTAATTCCGA 59.473 50.000 8.23 0.0 0.00 4.55 R
3423 3807 0.179000 CTATCCTCCGCAGCAGGTTT 59.821 55.000 0.00 0.0 36.37 3.27 R
3732 4125 1.402456 GCCGTCTCGTAAAGAGCAAGA 60.402 52.381 0.00 0.0 46.44 3.02 R
3928 4326 2.574006 TGCTCAGGCTCAACATCTTT 57.426 45.000 0.00 0.0 39.59 2.52 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 5.534365 GTCCGTCGTGTTAACAAAATTTG 57.466 39.130 10.51 3.89 0.00 2.32
23 24 5.264712 GTCCGTCGTGTTAACAAAATTTGA 58.735 37.500 13.19 0.63 0.00 2.69
24 25 5.738225 GTCCGTCGTGTTAACAAAATTTGAA 59.262 36.000 13.19 0.00 0.00 2.69
25 26 5.966503 TCCGTCGTGTTAACAAAATTTGAAG 59.033 36.000 13.19 4.47 0.00 3.02
26 27 5.740099 CCGTCGTGTTAACAAAATTTGAAGT 59.260 36.000 13.19 0.09 0.00 3.01
27 28 6.290851 CCGTCGTGTTAACAAAATTTGAAGTG 60.291 38.462 13.19 0.00 0.00 3.16
28 29 6.249682 CGTCGTGTTAACAAAATTTGAAGTGT 59.750 34.615 13.19 0.00 0.00 3.55
29 30 7.425882 CGTCGTGTTAACAAAATTTGAAGTGTA 59.574 33.333 13.19 0.00 0.00 2.90
30 31 8.730427 GTCGTGTTAACAAAATTTGAAGTGTAG 58.270 33.333 13.19 0.00 0.00 2.74
31 32 8.666573 TCGTGTTAACAAAATTTGAAGTGTAGA 58.333 29.630 13.19 2.04 0.00 2.59
32 33 8.943925 CGTGTTAACAAAATTTGAAGTGTAGAG 58.056 33.333 13.19 0.00 0.00 2.43
33 34 8.743099 GTGTTAACAAAATTTGAAGTGTAGAGC 58.257 33.333 13.19 0.00 0.00 4.09
34 35 8.682710 TGTTAACAAAATTTGAAGTGTAGAGCT 58.317 29.630 13.19 0.00 0.00 4.09
58 59 2.486982 ACGAGTTGCTACGACTGTATGT 59.513 45.455 0.00 0.00 0.00 2.29
72 73 0.248215 GTATGTGGCAATGTCGCAGC 60.248 55.000 7.30 0.00 29.10 5.25
328 356 3.499157 CGTTTGGGAGAAACCGTTCATTA 59.501 43.478 0.00 0.00 40.11 1.90
401 438 2.032528 CCTCGCCTGAAACCTGCA 59.967 61.111 0.00 0.00 0.00 4.41
402 439 2.037136 CCTCGCCTGAAACCTGCAG 61.037 63.158 6.78 6.78 0.00 4.41
403 440 2.669569 TCGCCTGAAACCTGCAGC 60.670 61.111 8.66 0.00 32.06 5.25
404 441 3.741476 CGCCTGAAACCTGCAGCC 61.741 66.667 8.66 0.00 32.06 4.85
405 442 2.598394 GCCTGAAACCTGCAGCCA 60.598 61.111 8.66 2.25 32.06 4.75
448 491 1.933853 CTATTTTCGTCTGGGGAAGCG 59.066 52.381 0.00 0.00 0.00 4.68
466 509 0.803768 CGCCTCTGATCTCACCAACG 60.804 60.000 0.00 0.00 0.00 4.10
687 753 0.531090 CACACTCGTTTCCGTCCCAA 60.531 55.000 0.00 0.00 35.01 4.12
697 763 2.269241 CGTCCCAAGCTCTTCCCC 59.731 66.667 0.00 0.00 0.00 4.81
729 799 3.793144 CCTCGCGCTTTCCTGCAC 61.793 66.667 5.56 0.00 0.00 4.57
749 821 2.193536 AGGCACACAAAACCCTCGC 61.194 57.895 0.00 0.00 0.00 5.03
756 828 0.035458 ACAAAACCCTCGCTCCAGAG 59.965 55.000 0.00 0.00 37.97 3.35
767 839 2.031012 TCCAGAGGCACACGCAAG 59.969 61.111 0.00 0.00 41.24 4.01
795 875 0.386476 AACGGCTGTAACTGTCGTCA 59.614 50.000 0.00 0.00 42.19 4.35
834 916 3.320826 CCGCCCCTTAAATATCCCAAAAG 59.679 47.826 0.00 0.00 0.00 2.27
900 998 2.053465 CGTCCACACAAACACGCG 60.053 61.111 3.53 3.53 0.00 6.01
901 999 2.518312 CGTCCACACAAACACGCGA 61.518 57.895 15.93 0.00 0.00 5.87
1030 1133 2.032681 AGCCGTCAAGAACAGGGC 59.967 61.111 0.00 0.00 44.07 5.19
1168 1333 0.679640 TTTTGCGGGGCATACAGAGG 60.680 55.000 0.00 0.00 38.76 3.69
1171 1336 2.505982 CGGGGCATACAGAGGGTG 59.494 66.667 0.00 0.00 0.00 4.61
1182 1347 3.715648 ACAGAGGGTGGGATTAGAGAT 57.284 47.619 0.00 0.00 0.00 2.75
1225 1391 1.339055 TGATGCTCCAAAGGACCTTCG 60.339 52.381 7.34 0.00 0.00 3.79
1234 1400 3.308530 CAAAGGACCTTCGAATTTGTGC 58.691 45.455 7.34 8.78 0.00 4.57
1281 1457 1.528076 TTTGGGCTCAAAGCTGCGA 60.528 52.632 7.92 0.00 41.99 5.10
1288 1475 1.467035 GCTCAAAGCTGCGATCCTTTG 60.467 52.381 13.13 13.13 45.68 2.77
1295 1482 1.541588 GCTGCGATCCTTTGTTTTCCT 59.458 47.619 0.00 0.00 0.00 3.36
1296 1483 2.029918 GCTGCGATCCTTTGTTTTCCTT 60.030 45.455 0.00 0.00 0.00 3.36
1297 1484 3.568538 CTGCGATCCTTTGTTTTCCTTG 58.431 45.455 0.00 0.00 0.00 3.61
1298 1485 2.955660 TGCGATCCTTTGTTTTCCTTGT 59.044 40.909 0.00 0.00 0.00 3.16
1299 1486 4.138290 TGCGATCCTTTGTTTTCCTTGTA 58.862 39.130 0.00 0.00 0.00 2.41
1330 1517 4.057432 GCTTTACATGCCATTTGTGTTGT 58.943 39.130 0.00 0.00 0.00 3.32
1333 1520 3.281341 ACATGCCATTTGTGTTGTACG 57.719 42.857 0.00 0.00 0.00 3.67
1336 1523 2.495084 TGCCATTTGTGTTGTACGCTA 58.505 42.857 0.00 0.00 0.00 4.26
1345 1542 2.599082 GTGTTGTACGCTAGCTGATGTC 59.401 50.000 13.93 0.29 0.00 3.06
1348 1545 4.338400 TGTTGTACGCTAGCTGATGTCTAT 59.662 41.667 13.93 0.00 0.00 1.98
1349 1546 5.163550 TGTTGTACGCTAGCTGATGTCTATT 60.164 40.000 13.93 0.00 0.00 1.73
1379 1576 9.904198 TTCCATTGTCATCTATCAAACTTATCA 57.096 29.630 0.00 0.00 0.00 2.15
1383 1580 9.671279 ATTGTCATCTATCAAACTTATCACACA 57.329 29.630 0.00 0.00 0.00 3.72
1398 1595 8.403236 ACTTATCACACAACATCATTGATCATG 58.597 33.333 0.00 1.80 0.00 3.07
1403 1600 3.314357 ACAACATCATTGATCATGGAGCG 59.686 43.478 0.00 0.00 33.07 5.03
1521 1824 7.823745 TTGCTCTCCTTTTTAGTCTCAAAAT 57.176 32.000 0.00 0.00 0.00 1.82
1581 1884 3.628032 GCTGCCTGATTTCCCTTAAGTAC 59.372 47.826 0.97 0.00 0.00 2.73
1660 1967 9.781834 GAGATTATCTTATCACTTATCTGGACG 57.218 37.037 0.00 0.00 0.00 4.79
1661 1968 9.303116 AGATTATCTTATCACTTATCTGGACGT 57.697 33.333 0.00 0.00 0.00 4.34
1752 2060 1.466856 CTGCCCACTACGTACCACTA 58.533 55.000 0.00 0.00 0.00 2.74
1870 2178 0.391661 GAGCTGCGATGACTTTCCCA 60.392 55.000 0.00 0.00 0.00 4.37
1892 2200 5.427481 CCAGTAAAGTATCTCCCAAAGGGTA 59.573 44.000 1.36 0.00 44.74 3.69
1908 2216 0.960861 GGTACCCAAGTGGCTTGCTC 60.961 60.000 0.00 0.00 39.85 4.26
1959 2267 0.611618 TTTGGATCGCTTGTGGCCAT 60.612 50.000 9.72 0.00 37.74 4.40
1971 2279 0.034186 GTGGCCATTGGATGACTGGA 60.034 55.000 9.72 0.00 31.38 3.86
1972 2280 0.256752 TGGCCATTGGATGACTGGAG 59.743 55.000 0.00 0.00 31.38 3.86
1984 2292 3.624326 TGACTGGAGCAAAATGAAACG 57.376 42.857 0.00 0.00 0.00 3.60
1997 2305 6.639279 GCAAAATGAAACGCTCTAAAAAGGTA 59.361 34.615 0.00 0.00 0.00 3.08
1998 2306 7.358105 GCAAAATGAAACGCTCTAAAAAGGTAC 60.358 37.037 0.00 0.00 0.00 3.34
2000 2308 6.723131 ATGAAACGCTCTAAAAAGGTACTC 57.277 37.500 0.00 0.00 38.49 2.59
2001 2309 4.992951 TGAAACGCTCTAAAAAGGTACTCC 59.007 41.667 0.00 0.00 38.49 3.85
2002 2310 3.606595 ACGCTCTAAAAAGGTACTCCC 57.393 47.619 0.00 0.00 38.49 4.30
2004 2312 3.195182 ACGCTCTAAAAAGGTACTCCCTC 59.805 47.826 0.00 0.00 45.47 4.30
2005 2313 3.430513 CGCTCTAAAAAGGTACTCCCTCC 60.431 52.174 0.00 0.00 45.47 4.30
2006 2314 3.430513 GCTCTAAAAAGGTACTCCCTCCG 60.431 52.174 0.00 0.00 45.47 4.63
2007 2315 3.768215 CTCTAAAAAGGTACTCCCTCCGT 59.232 47.826 0.00 0.00 45.47 4.69
2008 2316 4.162651 TCTAAAAAGGTACTCCCTCCGTT 58.837 43.478 0.00 0.00 45.47 4.44
2009 2317 3.413846 AAAAAGGTACTCCCTCCGTTC 57.586 47.619 0.00 0.00 45.47 3.95
2010 2318 0.893447 AAAGGTACTCCCTCCGTTCG 59.107 55.000 0.00 0.00 45.47 3.95
2011 2319 0.969409 AAGGTACTCCCTCCGTTCGG 60.969 60.000 4.74 4.74 45.47 4.30
2012 2320 1.379044 GGTACTCCCTCCGTTCGGA 60.379 63.158 13.34 13.34 0.00 4.55
2013 2321 0.967380 GGTACTCCCTCCGTTCGGAA 60.967 60.000 14.79 0.04 33.41 4.30
2014 2322 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2015 2323 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2016 2324 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2017 2325 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2018 2326 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2019 2327 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2020 2328 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2021 2329 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2022 2330 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2023 2331 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2024 2332 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2025 2333 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
2026 2334 1.060122 GTTCGGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 0.00 6.46
2027 2335 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.00 0.00 5.54
2028 2336 1.067706 TCGGAATTACTTGTCGCGGAA 60.068 47.619 6.13 0.00 0.00 4.30
2029 2337 1.727880 CGGAATTACTTGTCGCGGAAA 59.272 47.619 6.13 0.00 0.00 3.13
2030 2338 2.350498 CGGAATTACTTGTCGCGGAAAT 59.650 45.455 6.13 0.00 0.00 2.17
2031 2339 3.680789 GGAATTACTTGTCGCGGAAATG 58.319 45.455 6.13 0.00 0.00 2.32
2032 2340 3.372822 GGAATTACTTGTCGCGGAAATGA 59.627 43.478 6.13 0.00 0.00 2.57
2033 2341 4.142773 GGAATTACTTGTCGCGGAAATGAA 60.143 41.667 6.13 0.00 0.00 2.57
2034 2342 5.448632 GGAATTACTTGTCGCGGAAATGAAT 60.449 40.000 6.13 0.00 0.00 2.57
2035 2343 2.900122 ACTTGTCGCGGAAATGAATG 57.100 45.000 6.13 0.00 0.00 2.67
2036 2344 2.151202 ACTTGTCGCGGAAATGAATGT 58.849 42.857 6.13 0.00 0.00 2.71
2037 2345 3.331150 ACTTGTCGCGGAAATGAATGTA 58.669 40.909 6.13 0.00 0.00 2.29
2038 2346 3.938963 ACTTGTCGCGGAAATGAATGTAT 59.061 39.130 6.13 0.00 0.00 2.29
2039 2347 4.034048 ACTTGTCGCGGAAATGAATGTATC 59.966 41.667 6.13 0.00 0.00 2.24
2040 2348 3.792401 TGTCGCGGAAATGAATGTATCT 58.208 40.909 6.13 0.00 0.00 1.98
2041 2349 4.939271 TGTCGCGGAAATGAATGTATCTA 58.061 39.130 6.13 0.00 0.00 1.98
2042 2350 4.982295 TGTCGCGGAAATGAATGTATCTAG 59.018 41.667 6.13 0.00 0.00 2.43
2043 2351 5.220381 GTCGCGGAAATGAATGTATCTAGA 58.780 41.667 6.13 0.00 0.00 2.43
2044 2352 5.117287 GTCGCGGAAATGAATGTATCTAGAC 59.883 44.000 6.13 0.00 0.00 2.59
2045 2353 4.088638 CGCGGAAATGAATGTATCTAGACG 59.911 45.833 0.00 0.00 0.00 4.18
2046 2354 4.982916 GCGGAAATGAATGTATCTAGACGT 59.017 41.667 0.00 0.00 0.00 4.34
2047 2355 6.147581 GCGGAAATGAATGTATCTAGACGTA 58.852 40.000 0.00 0.00 0.00 3.57
2048 2356 6.807230 GCGGAAATGAATGTATCTAGACGTAT 59.193 38.462 0.00 0.00 0.00 3.06
2049 2357 7.328737 GCGGAAATGAATGTATCTAGACGTATT 59.671 37.037 0.00 0.00 0.00 1.89
2050 2358 9.193133 CGGAAATGAATGTATCTAGACGTATTT 57.807 33.333 0.00 0.00 0.00 1.40
2089 2397 9.289303 CATCCATTTTTAAGACAAGTAATTCCG 57.711 33.333 0.00 0.00 0.00 4.30
2090 2398 8.624367 TCCATTTTTAAGACAAGTAATTCCGA 57.376 30.769 0.00 0.00 0.00 4.55
2091 2399 9.069082 TCCATTTTTAAGACAAGTAATTCCGAA 57.931 29.630 0.00 0.00 0.00 4.30
2092 2400 9.124807 CCATTTTTAAGACAAGTAATTCCGAAC 57.875 33.333 0.00 0.00 0.00 3.95
2093 2401 8.837059 CATTTTTAAGACAAGTAATTCCGAACG 58.163 33.333 0.00 0.00 0.00 3.95
2094 2402 6.470557 TTTAAGACAAGTAATTCCGAACGG 57.529 37.500 6.94 6.94 0.00 4.44
2095 2403 3.947910 AGACAAGTAATTCCGAACGGA 57.052 42.857 12.04 12.04 43.52 4.69
2096 2404 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2097 2405 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2098 2406 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2099 2407 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2100 2408 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2101 2409 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2102 2410 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2103 2411 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
2104 2412 1.396653 TTCCGAACGGAGGGAGTATC 58.603 55.000 15.34 0.00 46.06 2.24
2156 2464 0.918983 TTCTTGGTAGGATGCCCCAG 59.081 55.000 0.00 0.00 41.90 4.45
2198 2506 3.197766 TGGATCCGAGCTTTCACTGTATT 59.802 43.478 7.39 0.00 0.00 1.89
2279 2590 7.192913 TGTAGACATGTTTTGATGTGTTTGTC 58.807 34.615 0.00 0.00 36.67 3.18
2282 2593 5.108517 ACATGTTTTGATGTGTTTGTCCAC 58.891 37.500 0.00 0.00 35.17 4.02
2294 2606 4.576463 GTGTTTGTCCACTCATTTCAGTCT 59.424 41.667 0.00 0.00 32.50 3.24
2295 2607 5.066505 GTGTTTGTCCACTCATTTCAGTCTT 59.933 40.000 0.00 0.00 32.50 3.01
2370 2738 4.568152 ATTTTGAACCTTTGAGGACGTG 57.432 40.909 0.00 0.00 37.67 4.49
2393 2761 5.241506 TGTCTCCAGTTGGACAAAATTGATC 59.758 40.000 0.00 0.00 39.78 2.92
2396 2764 4.215399 TCCAGTTGGACAAAATTGATCGAC 59.785 41.667 0.00 2.34 39.78 4.20
2402 2770 4.273724 TGGACAAAATTGATCGACGTTTCA 59.726 37.500 0.00 0.00 0.00 2.69
2408 2776 8.714179 ACAAAATTGATCGACGTTTCATACTAA 58.286 29.630 0.00 0.00 0.00 2.24
2409 2777 9.702726 CAAAATTGATCGACGTTTCATACTAAT 57.297 29.630 0.00 0.00 0.00 1.73
2444 2815 9.667989 CAAGCGATCATAATCAAATTAATCACA 57.332 29.630 0.00 0.00 31.76 3.58
2490 2863 2.995939 GTGAGCATTGTCGTCAAGATCA 59.004 45.455 0.97 5.27 36.97 2.92
2505 2881 6.199908 CGTCAAGATCACCAATTAGTCATCTC 59.800 42.308 0.00 0.00 0.00 2.75
2534 2910 1.510623 CTGTGCGCGAAATGCAGTC 60.511 57.895 12.10 0.00 46.97 3.51
2545 2921 3.657634 GAAATGCAGTCTCTGTCTGTGA 58.342 45.455 0.00 0.00 35.60 3.58
2546 2922 3.758755 AATGCAGTCTCTGTCTGTGAA 57.241 42.857 0.00 0.00 35.60 3.18
2548 2924 3.103447 TGCAGTCTCTGTCTGTGAAAG 57.897 47.619 0.00 0.00 35.60 2.62
2751 3132 1.028330 TCTACGACGCCGACCAGAAT 61.028 55.000 0.00 0.00 39.50 2.40
2778 3159 4.353437 GCGTTCCTCGACACGGGT 62.353 66.667 0.00 0.00 42.86 5.28
3423 3807 2.265904 CGCCGGGATCTACATCGGA 61.266 63.158 2.18 0.00 44.69 4.55
3646 4030 3.751246 CCACGCGGACGGTAAGGA 61.751 66.667 12.47 0.00 46.04 3.36
3650 4038 2.493501 GCGGACGGTAAGGACCTC 59.506 66.667 0.00 0.00 44.46 3.85
3665 4053 1.455959 CCTCCGGGATCCGTCTTCT 60.456 63.158 5.45 0.00 46.80 2.85
3732 4125 3.518590 GTCGTCCGAGAATATTTGGTGT 58.481 45.455 0.00 0.00 0.00 4.16
3765 4159 4.848685 ACGGCACTGTCGTCTTTT 57.151 50.000 1.98 0.00 40.97 2.27
3790 4184 5.334414 GCATTTCTACTTTGTGTGAGACCTG 60.334 44.000 0.00 0.00 0.00 4.00
3928 4326 0.318441 AGACTGCAGTAAAGCGAGCA 59.682 50.000 21.73 0.00 37.31 4.26
3939 4337 3.549299 AAAGCGAGCAAAGATGTTGAG 57.451 42.857 0.00 0.00 0.00 3.02
3950 4348 1.838715 AGATGTTGAGCCTGAGCATCT 59.161 47.619 4.76 4.76 43.56 2.90
3951 4349 2.239150 AGATGTTGAGCCTGAGCATCTT 59.761 45.455 4.76 0.00 42.22 2.40
3999 4397 2.408271 TGCTGCTAGGGATTTCACTG 57.592 50.000 0.00 0.00 0.00 3.66
4001 4399 1.065126 GCTGCTAGGGATTTCACTGGT 60.065 52.381 0.00 0.00 29.73 4.00
4008 4406 4.762289 AGGGATTTCACTGGTAGATCAC 57.238 45.455 0.00 0.00 0.00 3.06
4020 4418 5.071788 ACTGGTAGATCACAAGGTGAGAAAA 59.928 40.000 5.25 0.00 46.04 2.29
4021 4419 5.305585 TGGTAGATCACAAGGTGAGAAAAC 58.694 41.667 5.25 1.49 46.04 2.43
4024 4422 5.296151 AGATCACAAGGTGAGAAAACTGA 57.704 39.130 5.25 0.00 46.04 3.41
4057 4455 2.145536 CTTTTGGGAATTGCTTGTGGC 58.854 47.619 0.00 0.00 42.22 5.01
4063 4461 2.298729 GGGAATTGCTTGTGGCTAACAA 59.701 45.455 0.00 5.58 46.66 2.83
4248 4647 9.588096 ACTCCATACATACATACATACTGAGAA 57.412 33.333 0.00 0.00 0.00 2.87
4266 4665 8.089115 ACTGAGAATGAAGTTTAACTAACTGC 57.911 34.615 0.00 0.00 46.34 4.40
4267 4666 7.934120 ACTGAGAATGAAGTTTAACTAACTGCT 59.066 33.333 0.00 0.00 46.34 4.24
4268 4667 8.677148 TGAGAATGAAGTTTAACTAACTGCTT 57.323 30.769 0.00 0.00 46.34 3.91
4269 4668 8.559536 TGAGAATGAAGTTTAACTAACTGCTTG 58.440 33.333 0.00 0.00 46.34 4.01
4270 4669 7.875971 AGAATGAAGTTTAACTAACTGCTTGG 58.124 34.615 0.00 0.00 46.34 3.61
4271 4670 6.575162 ATGAAGTTTAACTAACTGCTTGGG 57.425 37.500 0.00 0.00 46.34 4.12
4272 4671 4.277423 TGAAGTTTAACTAACTGCTTGGGC 59.723 41.667 0.00 0.00 46.34 5.36
4383 4782 5.530543 GGATTCCTCTTGATTCATTCTGGAC 59.469 44.000 0.00 0.00 0.00 4.02
4507 4906 4.083271 ACTTCTTAAAAGCATCTCCAACGC 60.083 41.667 0.00 0.00 0.00 4.84
4515 4914 2.291043 ATCTCCAACGCCGACCCTT 61.291 57.895 0.00 0.00 0.00 3.95
4570 4984 3.452627 GTCTGGACACTGATATGGGAGTT 59.547 47.826 0.00 0.00 0.00 3.01
4572 4986 4.895889 TCTGGACACTGATATGGGAGTTAG 59.104 45.833 0.00 0.00 0.00 2.34
4577 4991 4.413520 ACACTGATATGGGAGTTAGCCATT 59.586 41.667 0.00 0.00 0.00 3.16
4578 4992 5.103940 ACACTGATATGGGAGTTAGCCATTT 60.104 40.000 0.00 0.00 0.00 2.32
4583 4997 7.582719 TGATATGGGAGTTAGCCATTTAAAGT 58.417 34.615 0.00 0.00 0.00 2.66
4585 4999 8.838649 ATATGGGAGTTAGCCATTTAAAGTTT 57.161 30.769 0.00 0.00 0.00 2.66
4587 5001 5.168569 GGGAGTTAGCCATTTAAAGTTTGC 58.831 41.667 0.00 0.00 0.00 3.68
4588 5002 5.168569 GGAGTTAGCCATTTAAAGTTTGCC 58.831 41.667 0.00 0.00 0.00 4.52
4591 5005 1.618343 AGCCATTTAAAGTTTGCCGCT 59.382 42.857 0.00 0.00 0.00 5.52
4593 5007 3.447229 AGCCATTTAAAGTTTGCCGCTAT 59.553 39.130 0.00 0.00 0.00 2.97
4595 5009 4.440112 GCCATTTAAAGTTTGCCGCTATCT 60.440 41.667 0.00 0.00 0.00 1.98
4600 5014 0.462047 AGTTTGCCGCTATCTTCCGG 60.462 55.000 0.00 0.00 46.94 5.14
4643 5057 9.495572 TTTAAACAAACTTGACAACTTCCATTT 57.504 25.926 0.00 0.00 0.00 2.32
4706 5121 5.680619 TCTAAACCGGAGCACATTCATTAT 58.319 37.500 9.46 0.00 0.00 1.28
4712 5127 6.970484 ACCGGAGCACATTCATTATATTTTC 58.030 36.000 9.46 0.00 0.00 2.29
4737 5152 8.228464 TCGACATATCTCAACTAAACTATAGCG 58.772 37.037 0.00 0.00 0.00 4.26
4742 5157 6.374565 TCTCAACTAAACTATAGCGGACTC 57.625 41.667 0.00 0.00 0.00 3.36
4743 5158 5.007430 TCTCAACTAAACTATAGCGGACTCG 59.993 44.000 0.00 0.00 39.81 4.18
4747 5162 2.267174 AACTATAGCGGACTCGGCTA 57.733 50.000 17.82 17.82 46.12 3.93
4751 5166 3.416253 TAGCGGACTCGGCTATTCT 57.584 52.632 12.95 0.00 41.80 2.40
4752 5167 0.952280 TAGCGGACTCGGCTATTCTG 59.048 55.000 12.95 0.00 41.80 3.02
4761 5176 3.117813 ACTCGGCTATTCTGACCTAGTCT 60.118 47.826 0.00 0.00 33.15 3.24
4771 5186 5.502153 TCTGACCTAGTCTAAAAGATCGC 57.498 43.478 0.00 0.00 33.15 4.58
4775 5190 2.395654 CTAGTCTAAAAGATCGCCGGC 58.604 52.381 19.07 19.07 0.00 6.13
4776 5191 0.179081 AGTCTAAAAGATCGCCGGCC 60.179 55.000 23.46 7.02 0.00 6.13
4797 5212 2.877691 GCCATGCCCGTTTCTCAC 59.122 61.111 0.00 0.00 0.00 3.51
4816 5231 1.293924 CGACATGTCTTCCTCATGGC 58.706 55.000 22.95 6.32 44.93 4.40
4817 5232 1.134580 CGACATGTCTTCCTCATGGCT 60.135 52.381 22.95 0.00 45.84 4.75
4818 5233 2.286872 GACATGTCTTCCTCATGGCTG 58.713 52.381 18.83 0.00 44.95 4.85
4836 5251 1.952263 GGCAACAAGCTCACTGGAC 59.048 57.895 0.00 0.00 44.79 4.02
4837 5252 1.571460 GCAACAAGCTCACTGGACG 59.429 57.895 0.00 0.00 41.15 4.79
4839 5254 1.598130 AACAAGCTCACTGGACGGC 60.598 57.895 0.00 0.00 0.00 5.68
4841 5256 4.021925 AAGCTCACTGGACGGCCC 62.022 66.667 3.83 0.00 0.00 5.80
4851 5266 4.577246 GACGGCCCTGAGCGCTAG 62.577 72.222 11.50 8.45 45.17 3.42
4854 5269 2.584608 GGCCCTGAGCGCTAGAAA 59.415 61.111 11.50 0.00 45.17 2.52
4857 5272 0.659957 GCCCTGAGCGCTAGAAAATG 59.340 55.000 11.50 0.00 0.00 2.32
4860 5275 2.611292 CCCTGAGCGCTAGAAAATGAAG 59.389 50.000 11.50 0.00 0.00 3.02
4865 5280 3.338249 AGCGCTAGAAAATGAAGCTTCA 58.662 40.909 30.23 30.23 42.14 3.02
4868 5283 4.613622 GCGCTAGAAAATGAAGCTTCAACA 60.614 41.667 31.55 11.09 41.13 3.33
4872 5287 5.702349 AGAAAATGAAGCTTCAACAGGAG 57.298 39.130 31.55 0.00 41.13 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.264712 TCAAATTTTGTTAACACGACGGAC 58.735 37.500 8.07 0.00 0.00 4.79
1 2 5.481200 TCAAATTTTGTTAACACGACGGA 57.519 34.783 8.07 0.00 0.00 4.69
2 3 5.740099 ACTTCAAATTTTGTTAACACGACGG 59.260 36.000 8.07 0.00 0.00 4.79
3 4 6.249682 ACACTTCAAATTTTGTTAACACGACG 59.750 34.615 8.07 0.00 0.00 5.12
4 5 7.500807 ACACTTCAAATTTTGTTAACACGAC 57.499 32.000 8.07 0.00 0.00 4.34
5 6 8.666573 TCTACACTTCAAATTTTGTTAACACGA 58.333 29.630 8.07 0.00 0.00 4.35
7 8 8.743099 GCTCTACACTTCAAATTTTGTTAACAC 58.257 33.333 8.07 0.00 0.00 3.32
8 9 8.682710 AGCTCTACACTTCAAATTTTGTTAACA 58.317 29.630 3.59 3.59 0.00 2.41
12 13 9.516314 GTTTAGCTCTACACTTCAAATTTTGTT 57.484 29.630 8.89 0.00 0.00 2.83
13 14 7.855904 CGTTTAGCTCTACACTTCAAATTTTGT 59.144 33.333 8.89 0.00 0.00 2.83
14 15 8.067784 TCGTTTAGCTCTACACTTCAAATTTTG 58.932 33.333 2.59 2.59 0.00 2.44
15 16 8.149973 TCGTTTAGCTCTACACTTCAAATTTT 57.850 30.769 0.00 0.00 0.00 1.82
16 17 7.441458 ACTCGTTTAGCTCTACACTTCAAATTT 59.559 33.333 0.00 0.00 0.00 1.82
17 18 6.929606 ACTCGTTTAGCTCTACACTTCAAATT 59.070 34.615 0.00 0.00 0.00 1.82
18 19 6.456501 ACTCGTTTAGCTCTACACTTCAAAT 58.543 36.000 0.00 0.00 0.00 2.32
19 20 5.839621 ACTCGTTTAGCTCTACACTTCAAA 58.160 37.500 0.00 0.00 0.00 2.69
20 21 5.449107 ACTCGTTTAGCTCTACACTTCAA 57.551 39.130 0.00 0.00 0.00 2.69
21 22 5.220381 CAACTCGTTTAGCTCTACACTTCA 58.780 41.667 0.00 0.00 0.00 3.02
22 23 4.090210 GCAACTCGTTTAGCTCTACACTTC 59.910 45.833 0.00 0.00 0.00 3.01
23 24 3.988517 GCAACTCGTTTAGCTCTACACTT 59.011 43.478 0.00 0.00 0.00 3.16
24 25 3.256136 AGCAACTCGTTTAGCTCTACACT 59.744 43.478 0.00 0.00 30.05 3.55
25 26 3.576648 AGCAACTCGTTTAGCTCTACAC 58.423 45.455 0.00 0.00 30.05 2.90
26 27 3.936372 AGCAACTCGTTTAGCTCTACA 57.064 42.857 0.00 0.00 30.05 2.74
27 28 3.784994 CGTAGCAACTCGTTTAGCTCTAC 59.215 47.826 0.00 0.00 38.47 2.59
28 29 3.686241 TCGTAGCAACTCGTTTAGCTCTA 59.314 43.478 0.00 0.00 38.47 2.43
29 30 2.486982 TCGTAGCAACTCGTTTAGCTCT 59.513 45.455 0.00 0.00 38.47 4.09
30 31 2.593336 GTCGTAGCAACTCGTTTAGCTC 59.407 50.000 0.00 0.00 38.47 4.09
31 32 2.228343 AGTCGTAGCAACTCGTTTAGCT 59.772 45.455 0.00 0.00 40.92 3.32
32 33 2.341760 CAGTCGTAGCAACTCGTTTAGC 59.658 50.000 0.00 0.00 0.00 3.09
33 34 3.562505 ACAGTCGTAGCAACTCGTTTAG 58.437 45.455 0.00 0.00 0.00 1.85
34 35 3.631145 ACAGTCGTAGCAACTCGTTTA 57.369 42.857 0.00 0.00 0.00 2.01
58 59 3.120385 CGAGCTGCGACATTGCCA 61.120 61.111 0.00 0.00 44.57 4.92
72 73 4.735132 TTCCTTGTCCGCGCCGAG 62.735 66.667 0.00 2.08 0.00 4.63
79 80 1.078848 CTGCCTCCTTCCTTGTCCG 60.079 63.158 0.00 0.00 0.00 4.79
87 88 3.706373 TCACGGGCTGCCTCCTTC 61.706 66.667 19.68 0.00 0.00 3.46
321 349 3.160777 ACTGGACGTCCGATAATGAAC 57.839 47.619 28.70 2.12 39.43 3.18
328 356 3.259064 CATTTTGTACTGGACGTCCGAT 58.741 45.455 28.70 21.09 39.43 4.18
401 438 3.121030 GCACGAATCACGCTGGCT 61.121 61.111 0.00 0.00 46.94 4.75
402 439 4.166011 GGCACGAATCACGCTGGC 62.166 66.667 0.00 0.00 46.94 4.85
423 460 1.134788 CCCCAGACGAAAATAGACGCT 60.135 52.381 0.00 0.00 0.00 5.07
448 491 0.460987 CCGTTGGTGAGATCAGAGGC 60.461 60.000 0.00 0.00 0.00 4.70
478 531 3.154473 TCTCGGCCCAATCCTCCG 61.154 66.667 0.00 0.00 44.16 4.63
560 620 0.107897 CGACCATTCCATGTTCGGGA 60.108 55.000 0.00 0.00 40.83 5.14
687 753 3.394836 GCGAGGTGGGGAAGAGCT 61.395 66.667 0.00 0.00 0.00 4.09
697 763 2.043450 AGGAGGGAGAGCGAGGTG 60.043 66.667 0.00 0.00 0.00 4.00
729 799 1.795170 CGAGGGTTTTGTGTGCCTGG 61.795 60.000 0.00 0.00 0.00 4.45
749 821 2.031012 TTGCGTGTGCCTCTGGAG 59.969 61.111 0.00 0.00 41.78 3.86
756 828 2.671619 TTAGGCCTTGCGTGTGCC 60.672 61.111 12.58 0.00 45.70 5.01
795 875 1.227556 GGCAACAGTGGTGACGACT 60.228 57.895 13.73 0.00 0.00 4.18
834 916 1.051556 TTTTTGGGCTTGGGGTGGTC 61.052 55.000 0.00 0.00 0.00 4.02
918 1017 1.272092 TGGGGAAATGCTTGACCTCTG 60.272 52.381 0.00 0.00 0.00 3.35
1168 1333 5.353394 TGTACACAATCTCTAATCCCACC 57.647 43.478 0.00 0.00 0.00 4.61
1171 1336 7.445121 TGATCATGTACACAATCTCTAATCCC 58.555 38.462 16.27 0.00 0.00 3.85
1219 1385 2.293399 GGTGAAGCACAAATTCGAAGGT 59.707 45.455 3.35 0.00 35.86 3.50
1225 1391 0.958822 ACCGGGTGAAGCACAAATTC 59.041 50.000 6.32 0.00 35.86 2.17
1234 1400 2.099427 GAGTTAGCTCTACCGGGTGAAG 59.901 54.545 10.66 8.06 38.66 3.02
1260 1436 1.747325 GCAGCTTTGAGCCCAAACCA 61.747 55.000 0.00 0.00 43.77 3.67
1313 1500 2.606795 GCGTACAACACAAATGGCATGT 60.607 45.455 0.00 0.00 0.00 3.21
1330 1517 6.879276 ACTAAATAGACATCAGCTAGCGTA 57.121 37.500 9.55 1.26 0.00 4.42
1333 1520 6.516718 TGGAACTAAATAGACATCAGCTAGC 58.483 40.000 6.62 6.62 0.00 3.42
1336 1523 7.341805 ACAATGGAACTAAATAGACATCAGCT 58.658 34.615 0.00 0.00 0.00 4.24
1348 1545 9.739276 AGTTTGATAGATGACAATGGAACTAAA 57.261 29.630 0.00 0.00 0.00 1.85
1349 1546 9.739276 AAGTTTGATAGATGACAATGGAACTAA 57.261 29.630 0.00 0.00 0.00 2.24
1378 1575 5.570234 TCCATGATCAATGATGTTGTGTG 57.430 39.130 0.00 0.00 38.72 3.82
1379 1576 4.097437 GCTCCATGATCAATGATGTTGTGT 59.903 41.667 0.00 0.00 38.72 3.72
1383 1580 3.812262 TCGCTCCATGATCAATGATGTT 58.188 40.909 0.00 0.00 38.72 2.71
1398 1595 2.100605 ATGAAAGACCACTTCGCTCC 57.899 50.000 0.00 0.00 35.05 4.70
1403 1600 6.697455 GGAAACAAGAAATGAAAGACCACTTC 59.303 38.462 0.00 0.00 35.05 3.01
1471 1773 7.657336 AGATTGCACTCCGAAAAGAATTAAAA 58.343 30.769 0.00 0.00 0.00 1.52
1581 1884 2.235845 AGATCGTCATGTCATGCTGG 57.764 50.000 8.03 0.17 0.00 4.85
1689 1997 0.252421 TGAGGGACCATGTGAGCTCT 60.252 55.000 16.19 0.00 0.00 4.09
1908 2216 6.128172 CCAGGTTTAGCTCAAGAACTGTAATG 60.128 42.308 0.00 0.00 0.00 1.90
1959 2267 3.765381 TCATTTTGCTCCAGTCATCCAA 58.235 40.909 0.00 0.00 0.00 3.53
1971 2279 5.691754 CCTTTTTAGAGCGTTTCATTTTGCT 59.308 36.000 0.00 0.00 41.11 3.91
1972 2280 5.462068 ACCTTTTTAGAGCGTTTCATTTTGC 59.538 36.000 0.00 0.00 0.00 3.68
1997 2305 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1998 2306 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2000 2308 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2001 2309 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2002 2310 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2003 2311 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2004 2312 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2005 2313 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
2006 2314 1.060122 CCGCGACAAGTAATTCCGAAC 59.940 52.381 8.23 0.00 0.00 3.95
2007 2315 1.067706 TCCGCGACAAGTAATTCCGAA 60.068 47.619 8.23 0.00 0.00 4.30
2008 2316 0.527113 TCCGCGACAAGTAATTCCGA 59.473 50.000 8.23 0.00 0.00 4.55
2009 2317 1.352114 TTCCGCGACAAGTAATTCCG 58.648 50.000 8.23 0.00 0.00 4.30
2010 2318 3.372822 TCATTTCCGCGACAAGTAATTCC 59.627 43.478 8.23 0.00 0.00 3.01
2011 2319 4.593597 TCATTTCCGCGACAAGTAATTC 57.406 40.909 8.23 0.00 0.00 2.17
2012 2320 5.106317 ACATTCATTTCCGCGACAAGTAATT 60.106 36.000 8.23 0.00 0.00 1.40
2013 2321 4.394920 ACATTCATTTCCGCGACAAGTAAT 59.605 37.500 8.23 1.19 0.00 1.89
2014 2322 3.749088 ACATTCATTTCCGCGACAAGTAA 59.251 39.130 8.23 0.00 0.00 2.24
2015 2323 3.331150 ACATTCATTTCCGCGACAAGTA 58.669 40.909 8.23 0.00 0.00 2.24
2016 2324 2.151202 ACATTCATTTCCGCGACAAGT 58.849 42.857 8.23 0.00 0.00 3.16
2017 2325 2.900122 ACATTCATTTCCGCGACAAG 57.100 45.000 8.23 0.00 0.00 3.16
2018 2326 4.188462 AGATACATTCATTTCCGCGACAA 58.812 39.130 8.23 0.00 0.00 3.18
2019 2327 3.792401 AGATACATTCATTTCCGCGACA 58.208 40.909 8.23 0.00 0.00 4.35
2020 2328 5.117287 GTCTAGATACATTCATTTCCGCGAC 59.883 44.000 8.23 0.00 0.00 5.19
2021 2329 5.220381 GTCTAGATACATTCATTTCCGCGA 58.780 41.667 8.23 0.00 0.00 5.87
2022 2330 4.088638 CGTCTAGATACATTCATTTCCGCG 59.911 45.833 0.00 0.00 0.00 6.46
2023 2331 4.982916 ACGTCTAGATACATTCATTTCCGC 59.017 41.667 0.00 0.00 0.00 5.54
2024 2332 8.744008 AATACGTCTAGATACATTCATTTCCG 57.256 34.615 0.00 0.00 0.00 4.30
2063 2371 9.289303 CGGAATTACTTGTCTTAAAAATGGATG 57.711 33.333 0.00 0.00 0.00 3.51
2064 2372 9.238368 TCGGAATTACTTGTCTTAAAAATGGAT 57.762 29.630 0.00 0.00 0.00 3.41
2065 2373 8.624367 TCGGAATTACTTGTCTTAAAAATGGA 57.376 30.769 0.00 0.00 0.00 3.41
2066 2374 9.124807 GTTCGGAATTACTTGTCTTAAAAATGG 57.875 33.333 0.00 0.00 0.00 3.16
2067 2375 8.837059 CGTTCGGAATTACTTGTCTTAAAAATG 58.163 33.333 0.00 0.00 0.00 2.32
2068 2376 8.019094 CCGTTCGGAATTACTTGTCTTAAAAAT 58.981 33.333 5.19 0.00 0.00 1.82
2069 2377 7.226325 TCCGTTCGGAATTACTTGTCTTAAAAA 59.774 33.333 11.66 0.00 0.00 1.94
2070 2378 6.705381 TCCGTTCGGAATTACTTGTCTTAAAA 59.295 34.615 11.66 0.00 0.00 1.52
2071 2379 6.222389 TCCGTTCGGAATTACTTGTCTTAAA 58.778 36.000 11.66 0.00 0.00 1.52
2072 2380 5.782047 TCCGTTCGGAATTACTTGTCTTAA 58.218 37.500 11.66 0.00 0.00 1.85
2073 2381 5.389859 TCCGTTCGGAATTACTTGTCTTA 57.610 39.130 11.66 0.00 0.00 2.10
2074 2382 4.243270 CTCCGTTCGGAATTACTTGTCTT 58.757 43.478 14.79 0.00 33.41 3.01
2075 2383 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2076 2384 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2077 2385 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2078 2386 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2079 2387 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2080 2388 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2081 2389 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2082 2390 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2083 2391 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2084 2392 1.962100 GATACTCCCTCCGTTCGGAAT 59.038 52.381 14.79 4.68 33.41 3.01
2085 2393 1.064166 AGATACTCCCTCCGTTCGGAA 60.064 52.381 14.79 0.00 33.41 4.30
2086 2394 0.549950 AGATACTCCCTCCGTTCGGA 59.450 55.000 13.34 13.34 0.00 4.55
2087 2395 0.669077 CAGATACTCCCTCCGTTCGG 59.331 60.000 4.74 4.74 0.00 4.30
2088 2396 1.334243 GTCAGATACTCCCTCCGTTCG 59.666 57.143 0.00 0.00 0.00 3.95
2089 2397 2.376109 TGTCAGATACTCCCTCCGTTC 58.624 52.381 0.00 0.00 0.00 3.95
2090 2398 2.496470 GTTGTCAGATACTCCCTCCGTT 59.504 50.000 0.00 0.00 0.00 4.44
2091 2399 2.100989 GTTGTCAGATACTCCCTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
2092 2400 1.065701 CGTTGTCAGATACTCCCTCCG 59.934 57.143 0.00 0.00 0.00 4.63
2093 2401 2.100989 ACGTTGTCAGATACTCCCTCC 58.899 52.381 0.00 0.00 0.00 4.30
2094 2402 3.242673 CGTACGTTGTCAGATACTCCCTC 60.243 52.174 7.22 0.00 0.00 4.30
2095 2403 2.681848 CGTACGTTGTCAGATACTCCCT 59.318 50.000 7.22 0.00 0.00 4.20
2096 2404 2.421424 ACGTACGTTGTCAGATACTCCC 59.579 50.000 16.72 0.00 0.00 4.30
2097 2405 3.423571 CACGTACGTTGTCAGATACTCC 58.576 50.000 20.23 0.00 0.00 3.85
2098 2406 3.120060 ACCACGTACGTTGTCAGATACTC 60.120 47.826 20.23 0.00 0.00 2.59
2099 2407 2.816087 ACCACGTACGTTGTCAGATACT 59.184 45.455 20.23 0.00 0.00 2.12
2100 2408 3.120060 AGACCACGTACGTTGTCAGATAC 60.120 47.826 38.11 21.15 41.47 2.24
2101 2409 3.076621 AGACCACGTACGTTGTCAGATA 58.923 45.455 38.11 0.00 41.47 1.98
2102 2410 1.884579 AGACCACGTACGTTGTCAGAT 59.115 47.619 38.11 23.90 41.47 2.90
2103 2411 1.311859 AGACCACGTACGTTGTCAGA 58.688 50.000 38.11 0.00 41.47 3.27
2104 2412 2.129823 AAGACCACGTACGTTGTCAG 57.870 50.000 38.11 21.23 41.47 3.51
2180 2488 3.325870 CACAATACAGTGAAAGCTCGGA 58.674 45.455 0.00 0.00 42.05 4.55
2198 2506 5.240623 CAGGGAGTACTTGTTTAATTGCACA 59.759 40.000 0.00 0.00 0.00 4.57
2262 2573 4.460731 TGAGTGGACAAACACATCAAAACA 59.539 37.500 0.00 0.00 43.72 2.83
2263 2574 4.992688 TGAGTGGACAAACACATCAAAAC 58.007 39.130 0.00 0.00 43.72 2.43
2279 2590 8.553459 AACTACATAAAGACTGAAATGAGTGG 57.447 34.615 0.00 0.00 0.00 4.00
2338 2658 6.836527 TCAAAGGTTCAAAATACTTTCCTCCA 59.163 34.615 0.00 0.00 31.31 3.86
2370 2738 5.617751 CGATCAATTTTGTCCAACTGGAGAC 60.618 44.000 0.00 0.00 46.49 3.36
2393 2761 9.783256 TGGATCATATATTAGTATGAAACGTCG 57.217 33.333 0.00 0.00 42.54 5.12
2455 2826 9.626045 CGACAATGCTCACTATATTCATTACTA 57.374 33.333 0.00 0.00 0.00 1.82
2456 2827 8.144478 ACGACAATGCTCACTATATTCATTACT 58.856 33.333 0.00 0.00 0.00 2.24
2457 2828 8.299262 ACGACAATGCTCACTATATTCATTAC 57.701 34.615 0.00 0.00 0.00 1.89
2458 2829 8.141268 TGACGACAATGCTCACTATATTCATTA 58.859 33.333 0.00 0.00 0.00 1.90
2473 2846 2.076100 TGGTGATCTTGACGACAATGC 58.924 47.619 0.00 0.00 35.37 3.56
2475 2848 6.173339 ACTAATTGGTGATCTTGACGACAAT 58.827 36.000 0.00 0.00 35.37 2.71
2490 2863 2.478292 ACGGGGAGATGACTAATTGGT 58.522 47.619 0.00 0.00 0.00 3.67
2505 2881 4.341502 CGCACAGGCAAAACGGGG 62.342 66.667 0.00 0.00 41.24 5.73
2534 2910 5.525012 TCAACATCAACTTTCACAGACAGAG 59.475 40.000 0.00 0.00 0.00 3.35
2545 2921 4.260139 TGCATGCATCAACATCAACTTT 57.740 36.364 18.46 0.00 0.00 2.66
2546 2922 3.945981 TGCATGCATCAACATCAACTT 57.054 38.095 18.46 0.00 0.00 2.66
2724 3105 1.507174 GGCGTCGTAGAGCTTCACT 59.493 57.895 0.00 0.00 36.95 3.41
2778 3159 1.080093 GCCGATGACGAACTCCACA 60.080 57.895 0.00 0.00 42.66 4.17
3096 3480 3.792053 GAGCGGCTGGATGTACGGG 62.792 68.421 7.50 0.00 0.00 5.28
3255 3639 3.059884 CAGCATGTTGTCGTAGTTGAGT 58.940 45.455 0.65 0.00 0.00 3.41
3423 3807 0.179000 CTATCCTCCGCAGCAGGTTT 59.821 55.000 0.00 0.00 36.37 3.27
3732 4125 1.402456 GCCGTCTCGTAAAGAGCAAGA 60.402 52.381 0.00 0.00 46.44 3.02
3765 4159 4.515191 GGTCTCACACAAAGTAGAAATGCA 59.485 41.667 0.00 0.00 0.00 3.96
3790 4184 2.731691 TTTCCAGGCACGTCAGGCTC 62.732 60.000 0.00 0.00 43.24 4.70
3928 4326 2.574006 TGCTCAGGCTCAACATCTTT 57.426 45.000 0.00 0.00 39.59 2.52
3939 4337 4.096532 GGGTTTAACTAAAGATGCTCAGGC 59.903 45.833 0.00 0.00 39.26 4.85
3950 4348 3.822167 CTCGGGCTTTGGGTTTAACTAAA 59.178 43.478 0.00 0.00 0.00 1.85
3951 4349 3.414269 CTCGGGCTTTGGGTTTAACTAA 58.586 45.455 0.00 0.00 0.00 2.24
3999 4397 5.409826 CAGTTTTCTCACCTTGTGATCTACC 59.590 44.000 0.00 0.00 41.94 3.18
4001 4399 6.042093 AGTCAGTTTTCTCACCTTGTGATCTA 59.958 38.462 0.00 0.00 41.94 1.98
4008 4406 5.818136 TTTCAGTCAGTTTTCTCACCTTG 57.182 39.130 0.00 0.00 0.00 3.61
4020 4418 4.381932 CCAAAAGCAGGTTTTTCAGTCAGT 60.382 41.667 7.62 0.00 36.11 3.41
4021 4419 4.114794 CCAAAAGCAGGTTTTTCAGTCAG 58.885 43.478 7.62 0.00 36.11 3.51
4024 4422 3.103742 TCCCAAAAGCAGGTTTTTCAGT 58.896 40.909 7.62 0.00 36.11 3.41
4057 4455 5.403466 GGTGAAAAGAAGCTGCAATTGTTAG 59.597 40.000 7.40 7.33 0.00 2.34
4063 4461 2.318908 TGGGTGAAAAGAAGCTGCAAT 58.681 42.857 1.02 0.00 0.00 3.56
4068 4466 2.071778 TGCTTGGGTGAAAAGAAGCT 57.928 45.000 0.00 0.00 41.19 3.74
4243 4642 8.559536 CAAGCAGTTAGTTAAACTTCATTCTCA 58.440 33.333 0.00 0.00 46.61 3.27
4244 4643 8.017946 CCAAGCAGTTAGTTAAACTTCATTCTC 58.982 37.037 0.00 0.00 46.61 2.87
4246 4645 7.084486 CCCAAGCAGTTAGTTAAACTTCATTC 58.916 38.462 0.00 0.00 46.61 2.67
4248 4647 5.048013 GCCCAAGCAGTTAGTTAAACTTCAT 60.048 40.000 0.00 0.00 46.61 2.57
4249 4648 4.277423 GCCCAAGCAGTTAGTTAAACTTCA 59.723 41.667 0.00 0.00 46.61 3.02
4250 4649 4.795268 GCCCAAGCAGTTAGTTAAACTTC 58.205 43.478 0.00 0.00 46.61 3.01
4253 4652 2.888414 TGGCCCAAGCAGTTAGTTAAAC 59.112 45.455 0.00 0.00 42.56 2.01
4254 4653 3.231207 TGGCCCAAGCAGTTAGTTAAA 57.769 42.857 0.00 0.00 42.56 1.52
4255 4654 2.961531 TGGCCCAAGCAGTTAGTTAA 57.038 45.000 0.00 0.00 42.56 2.01
4258 4657 1.633432 TGTATGGCCCAAGCAGTTAGT 59.367 47.619 0.00 0.00 42.56 2.24
4259 4658 2.418368 TGTATGGCCCAAGCAGTTAG 57.582 50.000 0.00 0.00 42.56 2.34
4262 4661 1.563879 TGTATGTATGGCCCAAGCAGT 59.436 47.619 0.00 0.00 42.56 4.40
4263 4662 2.346766 TGTATGTATGGCCCAAGCAG 57.653 50.000 0.00 0.00 42.56 4.24
4264 4663 3.394274 AGTATGTATGTATGGCCCAAGCA 59.606 43.478 0.00 0.00 42.56 3.91
4265 4664 3.753272 CAGTATGTATGTATGGCCCAAGC 59.247 47.826 0.00 0.00 38.76 4.01
4266 4665 5.012046 TCTCAGTATGTATGTATGGCCCAAG 59.988 44.000 0.00 0.00 37.40 3.61
4267 4666 4.904853 TCTCAGTATGTATGTATGGCCCAA 59.095 41.667 0.00 0.00 37.40 4.12
4268 4667 4.488770 TCTCAGTATGTATGTATGGCCCA 58.511 43.478 0.00 0.00 37.40 5.36
4269 4668 5.483685 TTCTCAGTATGTATGTATGGCCC 57.516 43.478 0.00 0.00 37.40 5.80
4270 4669 6.701340 TCATTCTCAGTATGTATGTATGGCC 58.299 40.000 0.00 0.00 37.40 5.36
4271 4670 7.875041 ACTTCATTCTCAGTATGTATGTATGGC 59.125 37.037 0.00 0.00 37.40 4.40
4272 4671 9.770097 AACTTCATTCTCAGTATGTATGTATGG 57.230 33.333 0.00 0.00 37.40 2.74
4355 4754 7.943447 CCAGAATGAATCAAGAGGAATCCTATT 59.057 37.037 0.00 1.46 39.69 1.73
4383 4782 7.208777 ACAGCTTCATGTACAGAGAAGATATG 58.791 38.462 30.20 25.84 40.85 1.78
4570 4984 2.823154 AGCGGCAAACTTTAAATGGCTA 59.177 40.909 1.45 0.00 37.47 3.93
4572 4986 2.078849 AGCGGCAAACTTTAAATGGC 57.921 45.000 1.45 4.25 36.39 4.40
4577 4991 3.372822 CGGAAGATAGCGGCAAACTTTAA 59.627 43.478 1.45 0.00 0.00 1.52
4578 4992 2.933906 CGGAAGATAGCGGCAAACTTTA 59.066 45.455 1.45 0.00 0.00 1.85
4583 4997 1.817941 GCCGGAAGATAGCGGCAAA 60.818 57.895 5.05 0.00 45.77 3.68
4587 5001 2.280186 GTGGCCGGAAGATAGCGG 60.280 66.667 5.05 0.00 0.00 5.52
4588 5002 0.532862 AATGTGGCCGGAAGATAGCG 60.533 55.000 5.05 0.00 0.00 4.26
4591 5005 3.213506 CATCAAATGTGGCCGGAAGATA 58.786 45.455 5.05 0.00 0.00 1.98
4593 5007 1.271871 ACATCAAATGTGGCCGGAAGA 60.272 47.619 5.05 0.00 43.01 2.87
4595 5009 2.498644 TACATCAAATGTGGCCGGAA 57.501 45.000 5.05 0.00 44.60 4.30
4655 5069 6.524101 AACCAACCGCTTATATGTGAAAAT 57.476 33.333 0.93 0.00 0.00 1.82
4660 5074 5.303747 TGAAAACCAACCGCTTATATGTG 57.696 39.130 0.00 0.00 0.00 3.21
4661 5075 5.885912 AGATGAAAACCAACCGCTTATATGT 59.114 36.000 0.00 0.00 0.00 2.29
4712 5127 7.482113 CCGCTATAGTTTAGTTGAGATATGTCG 59.518 40.741 0.84 0.00 0.00 4.35
4720 5135 5.206299 CGAGTCCGCTATAGTTTAGTTGAG 58.794 45.833 0.84 0.00 0.00 3.02
4737 5152 1.404843 AGGTCAGAATAGCCGAGTCC 58.595 55.000 0.00 0.00 0.00 3.85
4742 5157 5.769484 TTTAGACTAGGTCAGAATAGCCG 57.231 43.478 0.00 0.00 34.60 5.52
4743 5158 7.349412 TCTTTTAGACTAGGTCAGAATAGCC 57.651 40.000 0.00 0.00 34.60 3.93
4747 5162 6.461788 GGCGATCTTTTAGACTAGGTCAGAAT 60.462 42.308 0.00 0.00 34.60 2.40
4749 5164 4.338682 GGCGATCTTTTAGACTAGGTCAGA 59.661 45.833 0.00 0.00 34.60 3.27
4750 5165 4.612943 GGCGATCTTTTAGACTAGGTCAG 58.387 47.826 0.00 0.00 34.60 3.51
4751 5166 3.066342 CGGCGATCTTTTAGACTAGGTCA 59.934 47.826 0.00 0.00 34.60 4.02
4752 5167 3.550436 CCGGCGATCTTTTAGACTAGGTC 60.550 52.174 9.30 0.00 0.00 3.85
4761 5176 2.893404 GCGGCCGGCGATCTTTTA 60.893 61.111 29.38 0.00 0.00 1.52
4794 5209 2.094026 CCATGAGGAAGACATGTCGTGA 60.094 50.000 19.32 0.79 42.16 4.35
4797 5212 1.134580 AGCCATGAGGAAGACATGTCG 60.135 52.381 19.85 3.87 42.16 4.35
4816 5231 0.535780 TCCAGTGAGCTTGTTGCCAG 60.536 55.000 0.00 0.00 44.23 4.85
4817 5232 0.819259 GTCCAGTGAGCTTGTTGCCA 60.819 55.000 0.00 0.00 44.23 4.92
4818 5233 1.845809 CGTCCAGTGAGCTTGTTGCC 61.846 60.000 0.00 0.00 44.23 4.52
4836 5251 2.852495 TTTTCTAGCGCTCAGGGCCG 62.852 60.000 16.34 1.94 42.59 6.13
4837 5252 0.464554 ATTTTCTAGCGCTCAGGGCC 60.465 55.000 16.34 0.00 42.59 5.80
4839 5254 2.315925 TCATTTTCTAGCGCTCAGGG 57.684 50.000 16.34 2.88 0.00 4.45
4841 5256 2.935201 AGCTTCATTTTCTAGCGCTCAG 59.065 45.455 16.34 10.49 39.82 3.35
4847 5262 5.182001 TCCTGTTGAAGCTTCATTTTCTAGC 59.818 40.000 28.89 8.62 37.00 3.42
4849 5264 5.707298 CCTCCTGTTGAAGCTTCATTTTCTA 59.293 40.000 28.89 11.01 37.00 2.10
4850 5265 4.522022 CCTCCTGTTGAAGCTTCATTTTCT 59.478 41.667 28.89 0.00 37.00 2.52
4851 5266 4.321527 CCCTCCTGTTGAAGCTTCATTTTC 60.322 45.833 28.89 18.67 37.00 2.29
4854 5269 2.556114 CCCCTCCTGTTGAAGCTTCATT 60.556 50.000 28.89 0.00 37.00 2.57
4857 5272 0.693049 TCCCCTCCTGTTGAAGCTTC 59.307 55.000 19.89 19.89 0.00 3.86
4860 5275 0.693049 TCTTCCCCTCCTGTTGAAGC 59.307 55.000 0.00 0.00 35.35 3.86
4865 5280 1.574263 GCTACTCTTCCCCTCCTGTT 58.426 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.