Multiple sequence alignment - TraesCS4A01G176900

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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 TraesCS4A01G176900 chr4A 100.000 2624 0 0 1 2624 448260205 448257582 0.000000e+00 4846.0
1 TraesCS4A01G176900 chr4A 96.358 302 11 0 2117 2418 448253069 448252768 5.040000e-137 497.0
2 TraesCS4A01G176900 chr4A 96.000 75 3 0 2043 2117 448252149 448252075 3.550000e-24 122.0
3 TraesCS4A01G176900 chr4B 93.683 1298 52 14 506 1803 185786835 185788102 0.000000e+00 1916.0
4 TraesCS4A01G176900 chr4B 94.314 299 17 0 2117 2415 602659818 602659520 2.380000e-125 459.0
5 TraesCS4A01G176900 chr4B 94.444 234 13 0 2391 2624 602673324 602673091 6.900000e-96 361.0
6 TraesCS4A01G176900 chr4D 96.649 955 27 2 691 1640 122246504 122247458 0.000000e+00 1581.0
7 TraesCS4A01G176900 chr4D 92.955 582 39 2 5 585 122215823 122216403 0.000000e+00 846.0
8 TraesCS4A01G176900 chr4D 85.286 367 46 5 6 370 456091385 456091025 3.190000e-99 372.0
9 TraesCS4A01G176900 chr4D 93.467 199 12 1 2116 2313 477499062 477499260 7.100000e-76 294.0
10 TraesCS4A01G176900 chr4D 85.714 175 8 4 1632 1806 122247612 122247769 4.490000e-38 169.0
11 TraesCS4A01G176900 chr4D 96.552 58 2 0 1862 1919 122247770 122247827 2.150000e-16 97.1
12 TraesCS4A01G176900 chrUn 93.768 353 20 2 2272 2624 284685591 284685241 1.790000e-146 529.0
13 TraesCS4A01G176900 chrUn 94.631 149 5 3 2272 2419 268331057 268330911 7.310000e-56 228.0
14 TraesCS4A01G176900 chr3D 81.495 535 61 28 2112 2624 28478346 28477828 3.140000e-109 405.0
15 TraesCS4A01G176900 chr3D 84.916 358 50 3 7 364 359957550 359957903 2.480000e-95 359.0
16 TraesCS4A01G176900 chr3D 93.939 198 11 1 2117 2313 28462341 28462144 5.490000e-77 298.0
17 TraesCS4A01G176900 chr3D 79.699 133 24 3 484 615 590521879 590521749 2.780000e-15 93.5
18 TraesCS4A01G176900 chr3D 84.091 88 11 3 2117 2203 199117539 199117624 6.020000e-12 82.4
19 TraesCS4A01G176900 chr5D 86.427 361 41 7 6 364 238377081 238377435 3.170000e-104 388.0
20 TraesCS4A01G176900 chr5D 80.907 529 64 27 2117 2624 124391945 124392457 1.470000e-102 383.0
21 TraesCS4A01G176900 chr5D 85.873 361 46 4 6 364 354830898 354831255 1.910000e-101 379.0
22 TraesCS4A01G176900 chr5D 93.434 198 12 1 2117 2313 124397005 124397202 2.550000e-75 292.0
23 TraesCS4A01G176900 chr2B 85.515 359 45 5 7 364 422518214 422518566 4.130000e-98 368.0
24 TraesCS4A01G176900 chr2D 85.475 358 44 5 8 365 154141038 154141387 1.480000e-97 366.0
25 TraesCS4A01G176900 chr2D 80.420 143 20 7 473 611 591139269 591139131 4.620000e-18 102.0
26 TraesCS4A01G176900 chr1D 85.359 362 43 8 6 364 331503956 331504310 1.480000e-97 366.0
27 TraesCS4A01G176900 chr1D 87.037 216 24 4 2117 2330 153027518 153027305 9.380000e-60 241.0
28 TraesCS4A01G176900 chr5A 84.874 357 47 5 11 366 316427573 316427223 1.160000e-93 353.0
29 TraesCS4A01G176900 chr6A 81.994 361 51 9 2274 2624 61446187 61446543 7.100000e-76 294.0
30 TraesCS4A01G176900 chr6A 92.308 143 11 0 2274 2416 61451242 61451384 1.230000e-48 204.0
31 TraesCS4A01G176900 chr6B 83.916 143 23 0 473 615 259070303 259070161 1.270000e-28 137.0
32 TraesCS4A01G176900 chr3A 80.882 136 25 1 480 615 507756428 507756294 3.570000e-19 106.0


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 TraesCS4A01G176900 chr4A 448257582 448260205 2623 True 4846.0 4846 100.000000 1 2624 1 chr4A.!!$R1 2623
1 TraesCS4A01G176900 chr4A 448252075 448253069 994 True 309.5 497 96.179000 2043 2418 2 chr4A.!!$R2 375
2 TraesCS4A01G176900 chr4B 185786835 185788102 1267 False 1916.0 1916 93.683000 506 1803 1 chr4B.!!$F1 1297
3 TraesCS4A01G176900 chr4D 122215823 122216403 580 False 846.0 846 92.955000 5 585 1 chr4D.!!$F1 580
4 TraesCS4A01G176900 chr4D 122246504 122247827 1323 False 615.7 1581 92.971667 691 1919 3 chr4D.!!$F3 1228
5 TraesCS4A01G176900 chr3D 28477828 28478346 518 True 405.0 405 81.495000 2112 2624 1 chr3D.!!$R2 512
6 TraesCS4A01G176900 chr5D 124391945 124392457 512 False 383.0 383 80.907000 2117 2624 1 chr5D.!!$F1 507

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
476 478 0.674895 CACAGTCAAGCCCTAGTGCC 60.675 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2164 0.033011 AGCCTGTCCGTAGAGGTCAT 60.033 55.0 0.0 0.0 38.45 3.06 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
80 82 7.205515 ACCATGTATCCAATCTTCTCTCTTT 57.794 36.000 0.00 0.00 0.00 2.52
129 131 7.984422 ACATGAATGTTCACACAATCTTCTA 57.016 32.000 0.00 0.00 40.49 2.10
174 176 4.449068 GGCTCAACACTAATATGACCGATG 59.551 45.833 0.00 0.00 0.00 3.84
185 187 8.208224 ACTAATATGACCGATGTTTGGATTACA 58.792 33.333 0.00 0.00 0.00 2.41
202 204 6.608405 TGGATTACACCTCGAATAGAACCTTA 59.392 38.462 0.00 0.00 0.00 2.69
215 217 8.339714 CGAATAGAACCTTAGTCAACACAAAAA 58.660 33.333 0.00 0.00 0.00 1.94
296 298 6.963322 AGCCCTTCAAATCTATAACTCAAGT 58.037 36.000 0.00 0.00 0.00 3.16
348 350 8.722622 TTAATTACCAAAACCAAACATAGGGA 57.277 30.769 0.00 0.00 0.00 4.20
368 370 4.079253 GGAAACCAAGCTCCTTCACATAA 58.921 43.478 0.00 0.00 0.00 1.90
376 378 4.973168 AGCTCCTTCACATAAAGTCAACA 58.027 39.130 0.00 0.00 0.00 3.33
382 384 6.770303 TCCTTCACATAAAGTCAACAACATCA 59.230 34.615 0.00 0.00 0.00 3.07
396 398 5.376854 ACAACATCACCACAAAGATAAGC 57.623 39.130 0.00 0.00 0.00 3.09
412 414 3.724494 GCCAGAATAGGCGACAGC 58.276 61.111 0.00 0.00 46.12 4.40
463 465 2.574399 GTCGAGGGCCTCACAGTC 59.426 66.667 31.69 13.31 0.00 3.51
464 466 2.117423 TCGAGGGCCTCACAGTCA 59.883 61.111 31.69 6.30 0.00 3.41
465 467 1.533033 TCGAGGGCCTCACAGTCAA 60.533 57.895 31.69 6.14 0.00 3.18
470 472 2.753029 GCCTCACAGTCAAGCCCT 59.247 61.111 0.00 0.00 0.00 5.19
476 478 0.674895 CACAGTCAAGCCCTAGTGCC 60.675 60.000 0.00 0.00 0.00 5.01
478 480 2.820037 GTCAAGCCCTAGTGCCGC 60.820 66.667 0.00 0.00 0.00 6.53
479 481 4.096003 TCAAGCCCTAGTGCCGCC 62.096 66.667 0.00 0.00 0.00 6.13
493 495 1.137282 TGCCGCCGTACATGAGAATAA 59.863 47.619 0.00 0.00 0.00 1.40
494 496 1.792949 GCCGCCGTACATGAGAATAAG 59.207 52.381 0.00 0.00 0.00 1.73
497 499 4.617530 GCCGCCGTACATGAGAATAAGATA 60.618 45.833 0.00 0.00 0.00 1.98
499 501 6.679638 GCCGCCGTACATGAGAATAAGATATA 60.680 42.308 0.00 0.00 0.00 0.86
526 528 4.508128 CTCCGGTACCGCGCACAT 62.508 66.667 29.15 0.00 38.24 3.21
606 608 3.246226 GCAATCTCATAGTAGTTGCCACG 59.754 47.826 0.00 0.00 39.27 4.94
683 685 4.081752 TGTTCCAAACAGCTGTGTTGATTT 60.082 37.500 28.28 15.40 46.68 2.17
685 687 5.843673 TCCAAACAGCTGTGTTGATTTTA 57.156 34.783 28.28 14.21 46.68 1.52
738 740 2.162681 CCTGCGATTTTCCCTTGTTCT 58.837 47.619 0.00 0.00 0.00 3.01
780 782 3.831911 AGGAAGGACTAGAGATGCTATGC 59.168 47.826 0.00 0.00 0.00 3.14
784 786 2.352225 GGACTAGAGATGCTATGCGGTG 60.352 54.545 0.00 0.00 0.00 4.94
787 789 2.452295 AGAGATGCTATGCGGTGATG 57.548 50.000 0.00 0.00 0.00 3.07
851 853 3.064820 TCGCAAGTCACAAAAGTTCTTCC 59.935 43.478 0.00 0.00 39.48 3.46
884 886 2.200373 AGCATAACGAGGCCTTGTTT 57.800 45.000 37.43 23.81 38.16 2.83
900 908 4.499040 CCTTGTTTCATCACGTGAACAAAC 59.501 41.667 30.52 30.52 46.14 2.93
1099 1107 1.202211 GGACACAAACAACAACCGTCC 60.202 52.381 0.00 0.00 35.13 4.79
1110 1118 1.918800 AACCGTCCTAGGCAAGGCT 60.919 57.895 2.96 0.72 46.10 4.58
1190 1198 1.595993 TTCCTCTCGCCGACCTTCAG 61.596 60.000 0.00 0.00 0.00 3.02
1398 1406 1.108132 GGGACGAGAGATACCGGCTT 61.108 60.000 0.00 0.00 33.63 4.35
1569 1577 2.665603 GGGAGCTTCCTGTTCGCT 59.334 61.111 2.76 0.00 36.57 4.93
1665 1835 1.327303 AACAATTCGCACACCACCAT 58.673 45.000 0.00 0.00 0.00 3.55
1690 1860 2.225491 CACCGAGAAATTTCCGCTTCAA 59.775 45.455 14.61 0.00 0.00 2.69
1706 1876 5.147162 CGCTTCAATTGGTGTTAGTTTCTC 58.853 41.667 5.42 0.00 0.00 2.87
1768 1938 7.950684 ACATATTACCAGGAAGTGAGAGCTATA 59.049 37.037 0.00 0.00 0.00 1.31
1806 1976 6.318648 TCTTCCGGTCTTAATTCCATTTGATG 59.681 38.462 0.00 0.00 0.00 3.07
1821 1991 6.978343 CATTTGATGGAAAAATGATGTGCT 57.022 33.333 3.36 0.00 44.30 4.40
1823 1993 8.481974 CATTTGATGGAAAAATGATGTGCTAA 57.518 30.769 3.36 0.00 44.30 3.09
1824 1994 7.887996 TTTGATGGAAAAATGATGTGCTAAC 57.112 32.000 0.00 0.00 0.00 2.34
1825 1995 6.839124 TGATGGAAAAATGATGTGCTAACT 57.161 33.333 0.00 0.00 0.00 2.24
1826 1996 6.623486 TGATGGAAAAATGATGTGCTAACTG 58.377 36.000 0.00 0.00 0.00 3.16
1827 1997 5.389859 TGGAAAAATGATGTGCTAACTGG 57.610 39.130 0.00 0.00 0.00 4.00
1828 1998 5.076182 TGGAAAAATGATGTGCTAACTGGA 58.924 37.500 0.00 0.00 0.00 3.86
1829 1999 5.716228 TGGAAAAATGATGTGCTAACTGGAT 59.284 36.000 0.00 0.00 0.00 3.41
1830 2000 6.889177 TGGAAAAATGATGTGCTAACTGGATA 59.111 34.615 0.00 0.00 0.00 2.59
1831 2001 7.148086 TGGAAAAATGATGTGCTAACTGGATAC 60.148 37.037 0.00 0.00 0.00 2.24
1847 2017 4.954092 GGATACAAGAACAAGCAAGGAG 57.046 45.455 0.00 0.00 0.00 3.69
1848 2018 3.691609 GGATACAAGAACAAGCAAGGAGG 59.308 47.826 0.00 0.00 0.00 4.30
1849 2019 1.986882 ACAAGAACAAGCAAGGAGGG 58.013 50.000 0.00 0.00 0.00 4.30
1850 2020 1.251251 CAAGAACAAGCAAGGAGGGG 58.749 55.000 0.00 0.00 0.00 4.79
1851 2021 1.149101 AAGAACAAGCAAGGAGGGGA 58.851 50.000 0.00 0.00 0.00 4.81
1852 2022 1.149101 AGAACAAGCAAGGAGGGGAA 58.851 50.000 0.00 0.00 0.00 3.97
1853 2023 1.202940 AGAACAAGCAAGGAGGGGAAC 60.203 52.381 0.00 0.00 0.00 3.62
1854 2024 0.537371 AACAAGCAAGGAGGGGAACG 60.537 55.000 0.00 0.00 0.00 3.95
1855 2025 1.073199 CAAGCAAGGAGGGGAACGT 59.927 57.895 0.00 0.00 0.00 3.99
1856 2026 1.073199 AAGCAAGGAGGGGAACGTG 59.927 57.895 0.00 0.00 0.00 4.49
1857 2027 2.359975 GCAAGGAGGGGAACGTGG 60.360 66.667 0.00 0.00 0.00 4.94
1858 2028 2.890766 GCAAGGAGGGGAACGTGGA 61.891 63.158 0.00 0.00 0.00 4.02
1859 2029 1.758592 CAAGGAGGGGAACGTGGAA 59.241 57.895 0.00 0.00 0.00 3.53
1860 2030 0.605589 CAAGGAGGGGAACGTGGAAC 60.606 60.000 0.00 0.00 0.00 3.62
1881 2051 2.040278 CCAAAGGTGGGAGAGAATGTCA 59.960 50.000 0.00 0.00 41.77 3.58
1889 2059 3.263425 TGGGAGAGAATGTCACTAAACCC 59.737 47.826 0.00 0.00 29.96 4.11
1919 2089 8.797266 ACAAGTGGAGAAAATAAACGAAATTC 57.203 30.769 0.00 0.00 0.00 2.17
1920 2090 7.865889 ACAAGTGGAGAAAATAAACGAAATTCC 59.134 33.333 0.00 0.00 0.00 3.01
1921 2091 6.608610 AGTGGAGAAAATAAACGAAATTCCG 58.391 36.000 0.00 0.00 0.00 4.30
1922 2092 6.428771 AGTGGAGAAAATAAACGAAATTCCGA 59.571 34.615 0.00 0.00 0.00 4.55
1923 2093 7.040961 AGTGGAGAAAATAAACGAAATTCCGAA 60.041 33.333 0.00 0.00 0.00 4.30
1924 2094 7.753580 GTGGAGAAAATAAACGAAATTCCGAAT 59.246 33.333 0.00 0.00 0.00 3.34
1925 2095 8.948145 TGGAGAAAATAAACGAAATTCCGAATA 58.052 29.630 0.00 0.00 0.00 1.75
1926 2096 9.946165 GGAGAAAATAAACGAAATTCCGAATAT 57.054 29.630 0.00 0.00 0.00 1.28
1930 2100 7.908193 AATAAACGAAATTCCGAATATGTGC 57.092 32.000 0.00 0.00 0.00 4.57
1931 2101 3.963383 ACGAAATTCCGAATATGTGCC 57.037 42.857 0.00 0.00 0.00 5.01
1932 2102 3.541632 ACGAAATTCCGAATATGTGCCT 58.458 40.909 0.00 0.00 0.00 4.75
1933 2103 4.699637 ACGAAATTCCGAATATGTGCCTA 58.300 39.130 0.00 0.00 0.00 3.93
1934 2104 4.750098 ACGAAATTCCGAATATGTGCCTAG 59.250 41.667 0.00 0.00 0.00 3.02
1935 2105 4.377431 CGAAATTCCGAATATGTGCCTAGC 60.377 45.833 0.00 0.00 0.00 3.42
1936 2106 2.148916 TTCCGAATATGTGCCTAGCG 57.851 50.000 0.00 0.00 0.00 4.26
1937 2107 1.037493 TCCGAATATGTGCCTAGCGT 58.963 50.000 0.00 0.00 0.00 5.07
1938 2108 1.139989 CCGAATATGTGCCTAGCGTG 58.860 55.000 0.00 0.00 0.00 5.34
1939 2109 1.538204 CCGAATATGTGCCTAGCGTGT 60.538 52.381 0.00 0.00 0.00 4.49
1940 2110 1.522676 CGAATATGTGCCTAGCGTGTG 59.477 52.381 0.00 0.00 0.00 3.82
1941 2111 2.798145 CGAATATGTGCCTAGCGTGTGA 60.798 50.000 0.00 0.00 0.00 3.58
1942 2112 3.393800 GAATATGTGCCTAGCGTGTGAT 58.606 45.455 0.00 0.00 0.00 3.06
1943 2113 4.556233 GAATATGTGCCTAGCGTGTGATA 58.444 43.478 0.00 0.00 0.00 2.15
1944 2114 2.225068 ATGTGCCTAGCGTGTGATAC 57.775 50.000 0.00 0.00 0.00 2.24
1945 2115 0.892063 TGTGCCTAGCGTGTGATACA 59.108 50.000 0.00 0.00 0.00 2.29
1946 2116 1.480545 TGTGCCTAGCGTGTGATACAT 59.519 47.619 0.00 0.00 0.00 2.29
1947 2117 2.691011 TGTGCCTAGCGTGTGATACATA 59.309 45.455 0.00 0.00 0.00 2.29
1948 2118 3.243401 TGTGCCTAGCGTGTGATACATAG 60.243 47.826 0.00 0.00 0.00 2.23
1949 2119 2.288213 TGCCTAGCGTGTGATACATAGC 60.288 50.000 0.00 0.00 35.73 2.97
1950 2120 2.585845 CCTAGCGTGTGATACATAGCG 58.414 52.381 0.00 0.00 38.81 4.26
1951 2121 2.225727 CCTAGCGTGTGATACATAGCGA 59.774 50.000 0.00 0.00 38.81 4.93
1952 2122 3.119814 CCTAGCGTGTGATACATAGCGAT 60.120 47.826 0.00 0.00 38.81 4.58
1953 2123 2.666026 AGCGTGTGATACATAGCGATG 58.334 47.619 5.14 5.14 38.81 3.84
1954 2124 1.721389 GCGTGTGATACATAGCGATGG 59.279 52.381 11.70 0.00 37.39 3.51
1955 2125 2.328473 CGTGTGATACATAGCGATGGG 58.672 52.381 11.70 0.00 37.39 4.00
1956 2126 2.288213 CGTGTGATACATAGCGATGGGT 60.288 50.000 11.70 0.00 37.39 4.51
1957 2127 3.057806 CGTGTGATACATAGCGATGGGTA 60.058 47.826 11.70 0.00 37.39 3.69
1958 2128 4.486090 GTGTGATACATAGCGATGGGTAG 58.514 47.826 11.70 0.00 37.39 3.18
1959 2129 4.217767 GTGTGATACATAGCGATGGGTAGA 59.782 45.833 11.70 0.00 37.39 2.59
1960 2130 4.217767 TGTGATACATAGCGATGGGTAGAC 59.782 45.833 11.70 2.31 37.39 2.59
1961 2131 3.439129 TGATACATAGCGATGGGTAGACG 59.561 47.826 11.70 0.00 37.39 4.18
1970 2140 2.315925 ATGGGTAGACGCATCACTTG 57.684 50.000 6.40 0.00 44.79 3.16
1971 2141 0.249120 TGGGTAGACGCATCACTTGG 59.751 55.000 0.00 0.00 33.68 3.61
1972 2142 1.090052 GGGTAGACGCATCACTTGGC 61.090 60.000 0.00 0.00 0.00 4.52
1973 2143 0.391130 GGTAGACGCATCACTTGGCA 60.391 55.000 0.00 0.00 0.00 4.92
1974 2144 1.438651 GTAGACGCATCACTTGGCAA 58.561 50.000 0.00 0.00 0.00 4.52
1975 2145 1.394917 GTAGACGCATCACTTGGCAAG 59.605 52.381 25.06 25.06 0.00 4.01
1976 2146 1.154150 GACGCATCACTTGGCAAGC 60.154 57.895 26.45 12.47 0.00 4.01
1977 2147 1.580845 GACGCATCACTTGGCAAGCT 61.581 55.000 26.45 11.42 0.00 3.74
1978 2148 1.136147 CGCATCACTTGGCAAGCTC 59.864 57.895 26.45 10.28 0.00 4.09
1979 2149 1.509923 GCATCACTTGGCAAGCTCC 59.490 57.895 26.45 7.57 0.00 4.70
1980 2150 1.798735 CATCACTTGGCAAGCTCCG 59.201 57.895 26.45 12.85 0.00 4.63
1981 2151 0.674581 CATCACTTGGCAAGCTCCGA 60.675 55.000 26.45 17.41 0.00 4.55
1982 2152 0.392193 ATCACTTGGCAAGCTCCGAG 60.392 55.000 26.45 10.03 42.27 4.63
1983 2153 1.004560 CACTTGGCAAGCTCCGAGA 60.005 57.895 26.45 0.00 39.53 4.04
1984 2154 1.004440 ACTTGGCAAGCTCCGAGAC 60.004 57.895 26.45 0.00 39.53 3.36
1985 2155 1.294780 CTTGGCAAGCTCCGAGACT 59.705 57.895 15.25 0.00 39.53 3.24
1986 2156 0.739112 CTTGGCAAGCTCCGAGACTC 60.739 60.000 15.25 0.00 39.53 3.36
1987 2157 1.471829 TTGGCAAGCTCCGAGACTCA 61.472 55.000 2.82 0.00 0.00 3.41
1988 2158 1.293498 GGCAAGCTCCGAGACTCAA 59.707 57.895 2.82 0.00 0.00 3.02
1989 2159 0.107945 GGCAAGCTCCGAGACTCAAT 60.108 55.000 2.82 0.00 0.00 2.57
1990 2160 1.137086 GGCAAGCTCCGAGACTCAATA 59.863 52.381 2.82 0.00 0.00 1.90
1991 2161 2.418746 GGCAAGCTCCGAGACTCAATAA 60.419 50.000 2.82 0.00 0.00 1.40
1992 2162 3.262420 GCAAGCTCCGAGACTCAATAAA 58.738 45.455 2.82 0.00 0.00 1.40
1993 2163 3.684788 GCAAGCTCCGAGACTCAATAAAA 59.315 43.478 2.82 0.00 0.00 1.52
1994 2164 4.154195 GCAAGCTCCGAGACTCAATAAAAA 59.846 41.667 2.82 0.00 0.00 1.94
1995 2165 5.163713 GCAAGCTCCGAGACTCAATAAAAAT 60.164 40.000 2.82 0.00 0.00 1.82
1996 2166 6.253746 CAAGCTCCGAGACTCAATAAAAATG 58.746 40.000 2.82 0.00 0.00 2.32
1997 2167 5.734720 AGCTCCGAGACTCAATAAAAATGA 58.265 37.500 2.82 0.00 0.00 2.57
1998 2168 5.582665 AGCTCCGAGACTCAATAAAAATGAC 59.417 40.000 2.82 0.00 0.00 3.06
1999 2169 5.220681 GCTCCGAGACTCAATAAAAATGACC 60.221 44.000 2.82 0.00 0.00 4.02
2000 2170 6.049955 TCCGAGACTCAATAAAAATGACCT 57.950 37.500 2.82 0.00 0.00 3.85
2001 2171 6.106673 TCCGAGACTCAATAAAAATGACCTC 58.893 40.000 2.82 0.00 0.00 3.85
2002 2172 6.070767 TCCGAGACTCAATAAAAATGACCTCT 60.071 38.462 2.82 0.00 0.00 3.69
2003 2173 7.123697 TCCGAGACTCAATAAAAATGACCTCTA 59.876 37.037 2.82 0.00 0.00 2.43
2004 2174 7.222999 CCGAGACTCAATAAAAATGACCTCTAC 59.777 40.741 2.82 0.00 0.00 2.59
2005 2175 7.043986 CGAGACTCAATAAAAATGACCTCTACG 60.044 40.741 2.82 0.00 0.00 3.51
2006 2176 7.042335 AGACTCAATAAAAATGACCTCTACGG 58.958 38.462 0.00 0.00 39.35 4.02
2007 2177 6.942976 ACTCAATAAAAATGACCTCTACGGA 58.057 36.000 0.00 0.00 36.31 4.69
2008 2178 6.817140 ACTCAATAAAAATGACCTCTACGGAC 59.183 38.462 0.00 0.00 36.31 4.79
2009 2179 6.703319 TCAATAAAAATGACCTCTACGGACA 58.297 36.000 0.00 0.00 41.58 4.02
2010 2180 6.816640 TCAATAAAAATGACCTCTACGGACAG 59.183 38.462 0.00 0.00 40.69 3.51
2011 2181 3.611766 AAAATGACCTCTACGGACAGG 57.388 47.619 0.00 0.00 40.69 4.00
2012 2182 0.824759 AATGACCTCTACGGACAGGC 59.175 55.000 0.00 0.00 40.69 4.85
2013 2183 0.033011 ATGACCTCTACGGACAGGCT 60.033 55.000 0.00 0.00 40.69 4.58
2014 2184 0.251653 TGACCTCTACGGACAGGCTT 60.252 55.000 0.00 0.00 32.44 4.35
2015 2185 0.173708 GACCTCTACGGACAGGCTTG 59.826 60.000 0.00 0.00 36.31 4.01
2016 2186 1.258445 ACCTCTACGGACAGGCTTGG 61.258 60.000 0.00 0.00 36.31 3.61
2017 2187 1.517832 CTCTACGGACAGGCTTGGG 59.482 63.158 0.00 0.00 0.00 4.12
2018 2188 0.970937 CTCTACGGACAGGCTTGGGA 60.971 60.000 0.00 0.00 0.00 4.37
2019 2189 0.325296 TCTACGGACAGGCTTGGGAT 60.325 55.000 0.00 0.00 0.00 3.85
2020 2190 0.541863 CTACGGACAGGCTTGGGATT 59.458 55.000 0.00 0.00 0.00 3.01
2021 2191 1.760613 CTACGGACAGGCTTGGGATTA 59.239 52.381 0.00 0.00 0.00 1.75
2022 2192 0.252197 ACGGACAGGCTTGGGATTAC 59.748 55.000 0.00 0.00 0.00 1.89
2023 2193 0.541863 CGGACAGGCTTGGGATTACT 59.458 55.000 0.00 0.00 0.00 2.24
2024 2194 1.473434 CGGACAGGCTTGGGATTACTC 60.473 57.143 0.00 0.00 0.00 2.59
2025 2195 1.473434 GGACAGGCTTGGGATTACTCG 60.473 57.143 0.00 0.00 0.00 4.18
2026 2196 1.207329 GACAGGCTTGGGATTACTCGT 59.793 52.381 0.00 0.00 0.00 4.18
2027 2197 1.628846 ACAGGCTTGGGATTACTCGTT 59.371 47.619 0.00 0.00 0.00 3.85
2028 2198 2.280628 CAGGCTTGGGATTACTCGTTC 58.719 52.381 0.00 0.00 0.00 3.95
2029 2199 1.209747 AGGCTTGGGATTACTCGTTCC 59.790 52.381 0.00 0.00 0.00 3.62
2032 2202 4.432859 GGGATTACTCGTTCCCGC 57.567 61.111 0.00 0.00 42.18 6.13
2033 2203 1.590792 GGGATTACTCGTTCCCGCG 60.591 63.158 0.00 0.00 42.18 6.46
2034 2204 1.140375 GGATTACTCGTTCCCGCGT 59.860 57.895 4.92 0.00 35.88 6.01
2035 2205 0.381801 GGATTACTCGTTCCCGCGTA 59.618 55.000 4.92 0.00 33.44 4.42
2036 2206 1.598924 GGATTACTCGTTCCCGCGTAG 60.599 57.143 4.92 0.00 35.86 3.51
2049 2219 3.121030 CGTAGCACCTGCACCTGC 61.121 66.667 0.00 3.06 45.16 4.85
2064 2234 2.674796 CCTGCACTACCAGGTCTTAC 57.325 55.000 0.00 0.00 45.87 2.34
2065 2235 1.135083 CCTGCACTACCAGGTCTTACG 60.135 57.143 0.00 0.00 45.87 3.18
2066 2236 0.892755 TGCACTACCAGGTCTTACGG 59.107 55.000 0.00 0.00 0.00 4.02
2067 2237 0.459759 GCACTACCAGGTCTTACGGC 60.460 60.000 0.00 0.00 0.00 5.68
2068 2238 0.892755 CACTACCAGGTCTTACGGCA 59.107 55.000 0.00 0.00 0.00 5.69
2069 2239 1.135083 CACTACCAGGTCTTACGGCAG 60.135 57.143 0.00 0.00 0.00 4.85
2070 2240 0.460311 CTACCAGGTCTTACGGCAGG 59.540 60.000 0.00 0.00 0.00 4.85
2071 2241 0.251922 TACCAGGTCTTACGGCAGGT 60.252 55.000 0.00 0.00 0.00 4.00
2072 2242 1.125711 ACCAGGTCTTACGGCAGGTT 61.126 55.000 0.00 0.00 0.00 3.50
2073 2243 0.673644 CCAGGTCTTACGGCAGGTTG 60.674 60.000 0.00 0.00 0.00 3.77
2074 2244 0.034896 CAGGTCTTACGGCAGGTTGT 59.965 55.000 0.00 0.00 0.00 3.32
2075 2245 1.274167 CAGGTCTTACGGCAGGTTGTA 59.726 52.381 0.00 0.00 0.00 2.41
2076 2246 1.274447 AGGTCTTACGGCAGGTTGTAC 59.726 52.381 0.00 0.00 0.00 2.90
2077 2247 1.343506 GTCTTACGGCAGGTTGTACG 58.656 55.000 0.00 0.00 0.00 3.67
2078 2248 0.961019 TCTTACGGCAGGTTGTACGT 59.039 50.000 0.00 0.00 42.71 3.57
2079 2249 1.340889 TCTTACGGCAGGTTGTACGTT 59.659 47.619 0.00 0.00 40.38 3.99
2080 2250 2.137523 CTTACGGCAGGTTGTACGTTT 58.862 47.619 0.00 0.00 40.38 3.60
2081 2251 2.237393 TACGGCAGGTTGTACGTTTT 57.763 45.000 0.00 0.00 40.38 2.43
2082 2252 2.237393 ACGGCAGGTTGTACGTTTTA 57.763 45.000 0.00 0.00 35.90 1.52
2083 2253 1.866601 ACGGCAGGTTGTACGTTTTAC 59.133 47.619 0.00 0.00 35.90 2.01
2084 2254 1.865970 CGGCAGGTTGTACGTTTTACA 59.134 47.619 0.00 0.00 0.00 2.41
2085 2255 2.481185 CGGCAGGTTGTACGTTTTACAT 59.519 45.455 0.00 0.00 0.00 2.29
2086 2256 3.058777 CGGCAGGTTGTACGTTTTACATT 60.059 43.478 0.00 0.00 0.00 2.71
2087 2257 4.469552 GGCAGGTTGTACGTTTTACATTC 58.530 43.478 0.00 0.00 0.00 2.67
2088 2258 4.469552 GCAGGTTGTACGTTTTACATTCC 58.530 43.478 0.00 0.00 0.00 3.01
2089 2259 4.023878 GCAGGTTGTACGTTTTACATTCCA 60.024 41.667 0.00 0.00 0.00 3.53
2090 2260 5.505985 GCAGGTTGTACGTTTTACATTCCAA 60.506 40.000 0.00 0.00 0.00 3.53
2091 2261 6.496571 CAGGTTGTACGTTTTACATTCCAAA 58.503 36.000 0.00 0.00 0.00 3.28
2092 2262 6.973474 CAGGTTGTACGTTTTACATTCCAAAA 59.027 34.615 0.00 0.00 0.00 2.44
2093 2263 7.488471 CAGGTTGTACGTTTTACATTCCAAAAA 59.512 33.333 0.00 0.00 0.00 1.94
2113 2283 6.569179 AAAAATCGTAGCAGGTTGTATGTT 57.431 33.333 0.00 0.00 0.00 2.71
2114 2284 5.796350 AAATCGTAGCAGGTTGTATGTTC 57.204 39.130 0.00 0.00 0.00 3.18
2115 2285 4.737855 ATCGTAGCAGGTTGTATGTTCT 57.262 40.909 0.00 0.00 0.00 3.01
2154 2324 1.016130 GTCACTACCGACGAGACCGA 61.016 60.000 0.00 0.00 39.50 4.69
2236 2406 4.382320 GCGGACGGCAACTGGGTA 62.382 66.667 0.00 0.00 42.87 3.69
2264 2434 9.914834 AGTCCTATATTAGTCTATCCTGTCATC 57.085 37.037 0.00 0.00 0.00 2.92
2352 2523 5.873712 AGCAAATACATCACAGACTTGAGAG 59.126 40.000 0.00 0.00 0.00 3.20
2374 2545 2.263077 GAATACGAGATGCCGCCATAG 58.737 52.381 0.00 0.00 0.00 2.23
2428 2709 7.682787 AGATCCTAACAATTGGTACTCAGAT 57.317 36.000 10.83 5.49 0.00 2.90
2431 2712 5.130477 TCCTAACAATTGGTACTCAGATCCC 59.870 44.000 10.83 0.00 0.00 3.85
2450 2883 2.324541 CCAAAATTCCCACCCACTTCA 58.675 47.619 0.00 0.00 0.00 3.02
2451 2884 2.037121 CCAAAATTCCCACCCACTTCAC 59.963 50.000 0.00 0.00 0.00 3.18
2458 2891 1.003355 CACCCACTTCACGCTGGAT 60.003 57.895 0.00 0.00 0.00 3.41
2460 2893 1.296392 CCCACTTCACGCTGGATCA 59.704 57.895 0.00 0.00 0.00 2.92
2462 2895 0.320683 CCACTTCACGCTGGATCACA 60.321 55.000 0.00 0.00 0.00 3.58
2470 2903 4.509756 CTGGATCACAGCCACGAG 57.490 61.111 0.00 0.00 40.97 4.18
2527 2960 4.536316 CTCATGGAGCACCTGAGC 57.464 61.111 13.57 0.00 35.97 4.26
2528 2961 1.521010 CTCATGGAGCACCTGAGCG 60.521 63.158 13.57 0.00 40.15 5.03
2548 2981 2.797278 CGAGGGCAAGGCGGTCTAT 61.797 63.158 0.00 0.00 0.00 1.98
2587 3171 3.537874 GAGGCGGCCCATCTACGT 61.538 66.667 17.02 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.419673 TGATCAATACACAAAGCGCTGG 59.580 45.455 12.58 9.61 0.00 4.85
2 3 3.745332 TGATCAATACACAAAGCGCTG 57.255 42.857 12.58 1.84 0.00 5.18
3 4 3.753272 AGTTGATCAATACACAAAGCGCT 59.247 39.130 12.12 2.64 0.00 5.92
80 82 8.999431 GTTTACCTTCAAGACATCATCTTTACA 58.001 33.333 0.00 0.00 46.05 2.41
146 148 6.346096 GGTCATATTAGTGTTGAGCCTGTTA 58.654 40.000 0.00 0.00 33.02 2.41
150 152 3.704566 TCGGTCATATTAGTGTTGAGCCT 59.295 43.478 0.00 0.00 35.10 4.58
174 176 6.036844 GGTTCTATTCGAGGTGTAATCCAAAC 59.963 42.308 0.00 0.00 0.00 2.93
185 187 5.479375 TGTTGACTAAGGTTCTATTCGAGGT 59.521 40.000 0.00 0.00 0.00 3.85
202 204 8.697507 ATTAGAAGGAGATTTTTGTGTTGACT 57.302 30.769 0.00 0.00 0.00 3.41
215 217 7.928873 TGGTTTCAAGGTTATTAGAAGGAGAT 58.071 34.615 0.00 0.00 0.00 2.75
256 258 0.465460 GGCTCGTCCATGGGCATTAA 60.465 55.000 18.31 0.00 34.01 1.40
296 298 7.128109 TGACAATCCCTATGGACTAATGGTTAA 59.872 37.037 0.00 0.00 45.58 2.01
306 308 7.942341 TGGTAATTAATGACAATCCCTATGGAC 59.058 37.037 5.29 0.00 45.58 4.02
324 326 8.722622 TTCCCTATGTTTGGTTTTGGTAATTA 57.277 30.769 0.00 0.00 0.00 1.40
345 347 1.248486 GTGAAGGAGCTTGGTTTCCC 58.752 55.000 0.00 0.00 33.83 3.97
346 348 1.981256 TGTGAAGGAGCTTGGTTTCC 58.019 50.000 0.00 0.00 0.00 3.13
348 350 5.140454 ACTTTATGTGAAGGAGCTTGGTTT 58.860 37.500 0.00 0.00 0.00 3.27
354 356 4.973168 TGTTGACTTTATGTGAAGGAGCT 58.027 39.130 0.00 0.00 0.00 4.09
368 370 4.704540 TCTTTGTGGTGATGTTGTTGACTT 59.295 37.500 0.00 0.00 0.00 3.01
376 378 4.406456 TGGCTTATCTTTGTGGTGATGTT 58.594 39.130 0.00 0.00 0.00 2.71
382 384 5.440610 CCTATTCTGGCTTATCTTTGTGGT 58.559 41.667 0.00 0.00 0.00 4.16
396 398 1.293924 CAAGCTGTCGCCTATTCTGG 58.706 55.000 0.00 0.00 36.60 3.86
412 414 0.539051 CCAGACCAGAGCTACCCAAG 59.461 60.000 0.00 0.00 0.00 3.61
449 451 1.376553 GCTTGACTGTGAGGCCCTC 60.377 63.158 2.98 2.98 0.00 4.30
454 456 1.066573 CACTAGGGCTTGACTGTGAGG 60.067 57.143 0.00 0.00 0.00 3.86
458 460 1.679898 GGCACTAGGGCTTGACTGT 59.320 57.895 18.29 0.00 39.42 3.55
470 472 1.033202 TCTCATGTACGGCGGCACTA 61.033 55.000 13.24 1.07 0.00 2.74
476 478 7.968956 ACTTATATCTTATTCTCATGTACGGCG 59.031 37.037 4.80 4.80 0.00 6.46
478 480 9.790389 GGACTTATATCTTATTCTCATGTACGG 57.210 37.037 0.00 0.00 0.00 4.02
493 495 5.846528 ACCGGAGACTAGGACTTATATCT 57.153 43.478 9.46 0.00 0.00 1.98
494 496 5.879777 GGTACCGGAGACTAGGACTTATATC 59.120 48.000 9.46 0.00 0.00 1.63
497 499 3.495806 CGGTACCGGAGACTAGGACTTAT 60.496 52.174 27.00 0.00 35.56 1.73
499 501 1.407989 CGGTACCGGAGACTAGGACTT 60.408 57.143 27.00 0.00 35.56 3.01
606 608 3.187022 GTGGCTGTCAATTGGAATTTTGC 59.813 43.478 5.42 1.44 0.00 3.68
692 694 8.463930 AATTTTGCAGGATCGAATTCCTATTA 57.536 30.769 7.26 0.00 44.54 0.98
710 712 2.672874 GGGAAAATCGCAGGAATTTTGC 59.327 45.455 5.96 5.96 35.71 3.68
738 740 1.360185 TGGAACTTAGGCCCCGTTTA 58.640 50.000 0.00 0.00 0.00 2.01
780 782 0.457035 CTTGGGATTTGGCATCACCG 59.543 55.000 0.00 0.00 43.94 4.94
784 786 1.478105 GGTGACTTGGGATTTGGCATC 59.522 52.381 0.00 0.00 0.00 3.91
787 789 1.273327 CTTGGTGACTTGGGATTTGGC 59.727 52.381 0.00 0.00 0.00 4.52
851 853 3.120199 CGTTATGCTTGGACTGAACAAGG 60.120 47.826 14.38 2.01 44.16 3.61
884 886 3.879892 TGGAATGTTTGTTCACGTGATGA 59.120 39.130 20.80 5.97 34.65 2.92
900 908 3.731565 CGTACCATGTGTGCAATGGAATG 60.732 47.826 20.37 7.12 38.75 2.67
1099 1107 0.179078 CTGCTCAGAGCCTTGCCTAG 60.179 60.000 20.16 4.64 41.51 3.02
1125 1133 3.991536 GAGGTGCTTCGCGAGGTCC 62.992 68.421 19.98 20.15 0.00 4.46
1648 1818 1.202177 GCTATGGTGGTGTGCGAATTG 60.202 52.381 0.00 0.00 0.00 2.32
1665 1835 2.010043 GCGGAAATTTCTCGGTGGCTA 61.010 52.381 22.16 0.00 0.00 3.93
1690 1860 8.793592 GGAAAATGTAGAGAAACTAACACCAAT 58.206 33.333 0.00 0.00 32.49 3.16
1706 1876 9.696917 AAGCACAAATTTTAGAGGAAAATGTAG 57.303 29.630 0.00 0.00 45.21 2.74
1768 1938 2.970640 ACCGGAAGAGGTAAGACAAAGT 59.029 45.455 9.46 0.00 43.89 2.66
1806 1976 5.643379 TCCAGTTAGCACATCATTTTTCC 57.357 39.130 0.00 0.00 0.00 3.13
1807 1977 7.761409 TGTATCCAGTTAGCACATCATTTTTC 58.239 34.615 0.00 0.00 0.00 2.29
1808 1978 7.701539 TGTATCCAGTTAGCACATCATTTTT 57.298 32.000 0.00 0.00 0.00 1.94
1809 1979 7.611467 TCTTGTATCCAGTTAGCACATCATTTT 59.389 33.333 0.00 0.00 0.00 1.82
1810 1980 7.112122 TCTTGTATCCAGTTAGCACATCATTT 58.888 34.615 0.00 0.00 0.00 2.32
1811 1981 6.653020 TCTTGTATCCAGTTAGCACATCATT 58.347 36.000 0.00 0.00 0.00 2.57
1812 1982 6.239217 TCTTGTATCCAGTTAGCACATCAT 57.761 37.500 0.00 0.00 0.00 2.45
1813 1983 5.675684 TCTTGTATCCAGTTAGCACATCA 57.324 39.130 0.00 0.00 0.00 3.07
1814 1984 5.874810 TGTTCTTGTATCCAGTTAGCACATC 59.125 40.000 0.00 0.00 0.00 3.06
1815 1985 5.804639 TGTTCTTGTATCCAGTTAGCACAT 58.195 37.500 0.00 0.00 0.00 3.21
1816 1986 5.222079 TGTTCTTGTATCCAGTTAGCACA 57.778 39.130 0.00 0.00 0.00 4.57
1817 1987 5.390991 GCTTGTTCTTGTATCCAGTTAGCAC 60.391 44.000 0.00 0.00 0.00 4.40
1818 1988 4.695455 GCTTGTTCTTGTATCCAGTTAGCA 59.305 41.667 0.00 0.00 0.00 3.49
1819 1989 4.695455 TGCTTGTTCTTGTATCCAGTTAGC 59.305 41.667 0.00 0.00 0.00 3.09
1820 1990 6.128172 CCTTGCTTGTTCTTGTATCCAGTTAG 60.128 42.308 0.00 0.00 0.00 2.34
1821 1991 5.705441 CCTTGCTTGTTCTTGTATCCAGTTA 59.295 40.000 0.00 0.00 0.00 2.24
1822 1992 4.520492 CCTTGCTTGTTCTTGTATCCAGTT 59.480 41.667 0.00 0.00 0.00 3.16
1823 1993 4.074970 CCTTGCTTGTTCTTGTATCCAGT 58.925 43.478 0.00 0.00 0.00 4.00
1824 1994 4.326826 TCCTTGCTTGTTCTTGTATCCAG 58.673 43.478 0.00 0.00 0.00 3.86
1825 1995 4.326826 CTCCTTGCTTGTTCTTGTATCCA 58.673 43.478 0.00 0.00 0.00 3.41
1826 1996 3.691609 CCTCCTTGCTTGTTCTTGTATCC 59.308 47.826 0.00 0.00 0.00 2.59
1827 1997 3.691609 CCCTCCTTGCTTGTTCTTGTATC 59.308 47.826 0.00 0.00 0.00 2.24
1828 1998 3.562176 CCCCTCCTTGCTTGTTCTTGTAT 60.562 47.826 0.00 0.00 0.00 2.29
1829 1999 2.224769 CCCCTCCTTGCTTGTTCTTGTA 60.225 50.000 0.00 0.00 0.00 2.41
1830 2000 1.479389 CCCCTCCTTGCTTGTTCTTGT 60.479 52.381 0.00 0.00 0.00 3.16
1831 2001 1.202927 TCCCCTCCTTGCTTGTTCTTG 60.203 52.381 0.00 0.00 0.00 3.02
1832 2002 1.149101 TCCCCTCCTTGCTTGTTCTT 58.851 50.000 0.00 0.00 0.00 2.52
1833 2003 1.149101 TTCCCCTCCTTGCTTGTTCT 58.851 50.000 0.00 0.00 0.00 3.01
1834 2004 1.248486 GTTCCCCTCCTTGCTTGTTC 58.752 55.000 0.00 0.00 0.00 3.18
1835 2005 0.537371 CGTTCCCCTCCTTGCTTGTT 60.537 55.000 0.00 0.00 0.00 2.83
1836 2006 1.073199 CGTTCCCCTCCTTGCTTGT 59.927 57.895 0.00 0.00 0.00 3.16
1837 2007 1.073199 ACGTTCCCCTCCTTGCTTG 59.927 57.895 0.00 0.00 0.00 4.01
1838 2008 1.073199 CACGTTCCCCTCCTTGCTT 59.927 57.895 0.00 0.00 0.00 3.91
1839 2009 2.750350 CACGTTCCCCTCCTTGCT 59.250 61.111 0.00 0.00 0.00 3.91
1840 2010 2.359975 CCACGTTCCCCTCCTTGC 60.360 66.667 0.00 0.00 0.00 4.01
1841 2011 0.605589 GTTCCACGTTCCCCTCCTTG 60.606 60.000 0.00 0.00 0.00 3.61
1842 2012 1.759236 GTTCCACGTTCCCCTCCTT 59.241 57.895 0.00 0.00 0.00 3.36
1843 2013 2.222013 GGTTCCACGTTCCCCTCCT 61.222 63.158 0.00 0.00 0.00 3.69
1844 2014 2.059345 TTGGTTCCACGTTCCCCTCC 62.059 60.000 0.00 0.00 0.00 4.30
1845 2015 0.179012 TTTGGTTCCACGTTCCCCTC 60.179 55.000 0.00 0.00 0.00 4.30
1846 2016 0.179001 CTTTGGTTCCACGTTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
1847 2017 1.176619 CCTTTGGTTCCACGTTCCCC 61.177 60.000 0.00 0.00 0.00 4.81
1848 2018 0.466739 ACCTTTGGTTCCACGTTCCC 60.467 55.000 0.00 0.00 27.29 3.97
1849 2019 0.666374 CACCTTTGGTTCCACGTTCC 59.334 55.000 0.00 0.00 31.02 3.62
1850 2020 0.666374 CCACCTTTGGTTCCACGTTC 59.334 55.000 0.00 0.00 38.23 3.95
1851 2021 0.753848 CCCACCTTTGGTTCCACGTT 60.754 55.000 0.00 0.00 42.10 3.99
1852 2022 1.152839 CCCACCTTTGGTTCCACGT 60.153 57.895 0.00 0.00 42.10 4.49
1853 2023 0.889186 CTCCCACCTTTGGTTCCACG 60.889 60.000 0.00 0.00 42.10 4.94
1854 2024 0.476771 TCTCCCACCTTTGGTTCCAC 59.523 55.000 0.00 0.00 42.10 4.02
1855 2025 0.771127 CTCTCCCACCTTTGGTTCCA 59.229 55.000 0.00 0.00 42.10 3.53
1856 2026 1.064825 TCTCTCCCACCTTTGGTTCC 58.935 55.000 0.00 0.00 42.10 3.62
1857 2027 2.951229 TTCTCTCCCACCTTTGGTTC 57.049 50.000 0.00 0.00 42.10 3.62
1858 2028 2.447047 ACATTCTCTCCCACCTTTGGTT 59.553 45.455 0.00 0.00 42.10 3.67
1859 2029 2.040412 GACATTCTCTCCCACCTTTGGT 59.960 50.000 0.00 0.00 42.10 3.67
1860 2030 2.040278 TGACATTCTCTCCCACCTTTGG 59.960 50.000 0.00 0.00 43.50 3.28
1881 2051 3.881089 CTCCACTTGTTTTCGGGTTTAGT 59.119 43.478 0.00 0.00 0.00 2.24
1889 2059 6.908284 TCGTTTATTTTCTCCACTTGTTTTCG 59.092 34.615 0.00 0.00 0.00 3.46
1919 2089 1.139989 CACGCTAGGCACATATTCGG 58.860 55.000 0.00 0.00 0.00 4.30
1920 2090 1.522676 CACACGCTAGGCACATATTCG 59.477 52.381 0.00 0.00 0.00 3.34
1921 2091 2.821546 TCACACGCTAGGCACATATTC 58.178 47.619 0.00 0.00 0.00 1.75
1922 2092 2.979814 TCACACGCTAGGCACATATT 57.020 45.000 0.00 0.00 0.00 1.28
1923 2093 3.320826 TGTATCACACGCTAGGCACATAT 59.679 43.478 0.00 0.00 0.00 1.78
1924 2094 2.691011 TGTATCACACGCTAGGCACATA 59.309 45.455 0.00 0.00 0.00 2.29
1925 2095 1.480545 TGTATCACACGCTAGGCACAT 59.519 47.619 0.00 0.00 0.00 3.21
1926 2096 0.892063 TGTATCACACGCTAGGCACA 59.108 50.000 0.00 0.00 0.00 4.57
1927 2097 2.225068 ATGTATCACACGCTAGGCAC 57.775 50.000 0.00 0.00 0.00 5.01
1928 2098 2.288213 GCTATGTATCACACGCTAGGCA 60.288 50.000 0.00 0.00 0.00 4.75
1929 2099 2.329379 GCTATGTATCACACGCTAGGC 58.671 52.381 0.00 0.00 0.00 3.93
1930 2100 2.225727 TCGCTATGTATCACACGCTAGG 59.774 50.000 0.00 0.00 0.00 3.02
1931 2101 3.537793 TCGCTATGTATCACACGCTAG 57.462 47.619 0.00 0.00 0.00 3.42
1932 2102 3.365969 CCATCGCTATGTATCACACGCTA 60.366 47.826 0.00 0.00 0.00 4.26
1933 2103 2.608016 CCATCGCTATGTATCACACGCT 60.608 50.000 0.00 0.00 0.00 5.07
1934 2104 1.721389 CCATCGCTATGTATCACACGC 59.279 52.381 0.00 0.00 0.00 5.34
1935 2105 2.288213 ACCCATCGCTATGTATCACACG 60.288 50.000 0.00 0.00 0.00 4.49
1936 2106 3.386768 ACCCATCGCTATGTATCACAC 57.613 47.619 0.00 0.00 0.00 3.82
1937 2107 4.217767 GTCTACCCATCGCTATGTATCACA 59.782 45.833 0.00 0.00 0.00 3.58
1938 2108 4.672024 CGTCTACCCATCGCTATGTATCAC 60.672 50.000 0.00 0.00 0.00 3.06
1939 2109 3.439129 CGTCTACCCATCGCTATGTATCA 59.561 47.826 0.00 0.00 0.00 2.15
1940 2110 3.731264 GCGTCTACCCATCGCTATGTATC 60.731 52.174 0.00 0.00 45.29 2.24
1941 2111 2.163815 GCGTCTACCCATCGCTATGTAT 59.836 50.000 0.00 0.00 45.29 2.29
1942 2112 1.538512 GCGTCTACCCATCGCTATGTA 59.461 52.381 0.00 0.00 45.29 2.29
1943 2113 0.314302 GCGTCTACCCATCGCTATGT 59.686 55.000 0.00 0.00 45.29 2.29
1944 2114 3.108521 GCGTCTACCCATCGCTATG 57.891 57.895 0.00 0.00 45.29 2.23
1949 2119 0.385751 AGTGATGCGTCTACCCATCG 59.614 55.000 7.58 0.00 40.48 3.84
1950 2120 2.205074 CAAGTGATGCGTCTACCCATC 58.795 52.381 7.58 1.59 38.60 3.51
1951 2121 1.134401 CCAAGTGATGCGTCTACCCAT 60.134 52.381 7.58 0.00 0.00 4.00
1952 2122 0.249120 CCAAGTGATGCGTCTACCCA 59.751 55.000 7.58 0.00 0.00 4.51
1953 2123 1.090052 GCCAAGTGATGCGTCTACCC 61.090 60.000 7.58 0.00 0.00 3.69
1954 2124 0.391130 TGCCAAGTGATGCGTCTACC 60.391 55.000 7.58 0.00 0.00 3.18
1955 2125 1.394917 CTTGCCAAGTGATGCGTCTAC 59.605 52.381 7.58 4.11 0.00 2.59
1956 2126 1.725641 CTTGCCAAGTGATGCGTCTA 58.274 50.000 7.58 0.00 0.00 2.59
1957 2127 1.580845 GCTTGCCAAGTGATGCGTCT 61.581 55.000 6.28 0.00 0.00 4.18
1958 2128 1.154150 GCTTGCCAAGTGATGCGTC 60.154 57.895 6.28 0.00 0.00 5.19
1959 2129 1.580845 GAGCTTGCCAAGTGATGCGT 61.581 55.000 6.28 0.00 0.00 5.24
1960 2130 1.136147 GAGCTTGCCAAGTGATGCG 59.864 57.895 6.28 0.00 0.00 4.73
1961 2131 1.509923 GGAGCTTGCCAAGTGATGC 59.490 57.895 6.28 0.00 0.00 3.91
1962 2132 0.674581 TCGGAGCTTGCCAAGTGATG 60.675 55.000 6.28 0.00 0.00 3.07
1963 2133 0.392193 CTCGGAGCTTGCCAAGTGAT 60.392 55.000 6.28 0.00 0.00 3.06
1964 2134 1.004560 CTCGGAGCTTGCCAAGTGA 60.005 57.895 6.28 0.00 0.00 3.41
1965 2135 1.004560 TCTCGGAGCTTGCCAAGTG 60.005 57.895 6.28 0.00 0.00 3.16
1966 2136 1.004440 GTCTCGGAGCTTGCCAAGT 60.004 57.895 6.28 0.00 0.00 3.16
1967 2137 0.739112 GAGTCTCGGAGCTTGCCAAG 60.739 60.000 0.00 0.00 0.00 3.61
1968 2138 1.293498 GAGTCTCGGAGCTTGCCAA 59.707 57.895 0.00 0.00 0.00 4.52
1969 2139 1.471829 TTGAGTCTCGGAGCTTGCCA 61.472 55.000 0.00 0.00 0.00 4.92
1970 2140 0.107945 ATTGAGTCTCGGAGCTTGCC 60.108 55.000 0.00 0.00 0.00 4.52
1971 2141 2.586258 TATTGAGTCTCGGAGCTTGC 57.414 50.000 0.00 0.00 0.00 4.01
1972 2142 5.862924 TTTTTATTGAGTCTCGGAGCTTG 57.137 39.130 0.00 0.00 0.00 4.01
1973 2143 6.092807 GTCATTTTTATTGAGTCTCGGAGCTT 59.907 38.462 0.00 0.00 0.00 3.74
1974 2144 5.582665 GTCATTTTTATTGAGTCTCGGAGCT 59.417 40.000 0.00 0.75 0.00 4.09
1975 2145 5.220681 GGTCATTTTTATTGAGTCTCGGAGC 60.221 44.000 0.00 0.00 0.00 4.70
1976 2146 6.109359 AGGTCATTTTTATTGAGTCTCGGAG 58.891 40.000 0.00 0.00 0.00 4.63
1977 2147 6.049955 AGGTCATTTTTATTGAGTCTCGGA 57.950 37.500 0.00 0.00 0.00 4.55
1978 2148 6.109359 AGAGGTCATTTTTATTGAGTCTCGG 58.891 40.000 0.00 0.00 33.42 4.63
1979 2149 7.043986 CGTAGAGGTCATTTTTATTGAGTCTCG 60.044 40.741 0.00 0.00 33.42 4.04
1980 2150 7.222999 CCGTAGAGGTCATTTTTATTGAGTCTC 59.777 40.741 0.00 0.00 34.51 3.36
1981 2151 7.042335 CCGTAGAGGTCATTTTTATTGAGTCT 58.958 38.462 0.00 0.00 34.51 3.24
1982 2152 7.010275 GTCCGTAGAGGTCATTTTTATTGAGTC 59.990 40.741 0.00 0.00 41.99 3.36
1983 2153 6.817140 GTCCGTAGAGGTCATTTTTATTGAGT 59.183 38.462 0.00 0.00 41.99 3.41
1984 2154 6.816640 TGTCCGTAGAGGTCATTTTTATTGAG 59.183 38.462 0.00 0.00 41.99 3.02
1985 2155 6.703319 TGTCCGTAGAGGTCATTTTTATTGA 58.297 36.000 0.00 0.00 41.99 2.57
1986 2156 6.037172 CCTGTCCGTAGAGGTCATTTTTATTG 59.963 42.308 0.00 0.00 41.99 1.90
1987 2157 6.113411 CCTGTCCGTAGAGGTCATTTTTATT 58.887 40.000 0.00 0.00 41.99 1.40
1988 2158 5.671493 CCTGTCCGTAGAGGTCATTTTTAT 58.329 41.667 0.00 0.00 41.99 1.40
1989 2159 4.622220 GCCTGTCCGTAGAGGTCATTTTTA 60.622 45.833 0.00 0.00 38.45 1.52
1990 2160 3.868754 GCCTGTCCGTAGAGGTCATTTTT 60.869 47.826 0.00 0.00 38.45 1.94
1991 2161 2.354805 GCCTGTCCGTAGAGGTCATTTT 60.355 50.000 0.00 0.00 38.45 1.82
1992 2162 1.207329 GCCTGTCCGTAGAGGTCATTT 59.793 52.381 0.00 0.00 38.45 2.32
1993 2163 0.824759 GCCTGTCCGTAGAGGTCATT 59.175 55.000 0.00 0.00 38.45 2.57
1994 2164 0.033011 AGCCTGTCCGTAGAGGTCAT 60.033 55.000 0.00 0.00 38.45 3.06
1995 2165 0.251653 AAGCCTGTCCGTAGAGGTCA 60.252 55.000 0.00 0.00 38.45 4.02
1996 2166 0.173708 CAAGCCTGTCCGTAGAGGTC 59.826 60.000 0.00 0.00 38.45 3.85
1997 2167 1.258445 CCAAGCCTGTCCGTAGAGGT 61.258 60.000 0.00 0.00 38.45 3.85
1998 2168 1.517832 CCAAGCCTGTCCGTAGAGG 59.482 63.158 0.00 0.00 39.23 3.69
1999 2169 0.970937 TCCCAAGCCTGTCCGTAGAG 60.971 60.000 0.00 0.00 0.00 2.43
2000 2170 0.325296 ATCCCAAGCCTGTCCGTAGA 60.325 55.000 0.00 0.00 0.00 2.59
2001 2171 0.541863 AATCCCAAGCCTGTCCGTAG 59.458 55.000 0.00 0.00 0.00 3.51
2002 2172 1.483415 GTAATCCCAAGCCTGTCCGTA 59.517 52.381 0.00 0.00 0.00 4.02
2003 2173 0.252197 GTAATCCCAAGCCTGTCCGT 59.748 55.000 0.00 0.00 0.00 4.69
2004 2174 0.541863 AGTAATCCCAAGCCTGTCCG 59.458 55.000 0.00 0.00 0.00 4.79
2005 2175 1.473434 CGAGTAATCCCAAGCCTGTCC 60.473 57.143 0.00 0.00 0.00 4.02
2006 2176 1.207329 ACGAGTAATCCCAAGCCTGTC 59.793 52.381 0.00 0.00 0.00 3.51
2007 2177 1.276622 ACGAGTAATCCCAAGCCTGT 58.723 50.000 0.00 0.00 0.00 4.00
2008 2178 2.280628 GAACGAGTAATCCCAAGCCTG 58.719 52.381 0.00 0.00 0.00 4.85
2009 2179 1.209747 GGAACGAGTAATCCCAAGCCT 59.790 52.381 0.00 0.00 0.00 4.58
2010 2180 1.664873 GGAACGAGTAATCCCAAGCC 58.335 55.000 0.00 0.00 0.00 4.35
2025 2195 2.813908 CAGGTGCTACGCGGGAAC 60.814 66.667 12.47 7.55 0.00 3.62
2026 2196 4.752879 GCAGGTGCTACGCGGGAA 62.753 66.667 12.47 0.00 38.21 3.97
2030 2200 4.742201 AGGTGCAGGTGCTACGCG 62.742 66.667 3.53 3.53 42.66 6.01
2031 2201 3.121030 CAGGTGCAGGTGCTACGC 61.121 66.667 3.18 0.00 42.66 4.42
2032 2202 3.121030 GCAGGTGCAGGTGCTACG 61.121 66.667 12.09 0.00 42.66 3.51
2045 2215 1.135083 CGTAAGACCTGGTAGTGCAGG 60.135 57.143 0.00 0.00 43.91 4.85
2046 2216 1.135083 CCGTAAGACCTGGTAGTGCAG 60.135 57.143 0.00 0.00 43.02 4.41
2047 2217 0.892755 CCGTAAGACCTGGTAGTGCA 59.107 55.000 0.00 0.00 43.02 4.57
2048 2218 0.459759 GCCGTAAGACCTGGTAGTGC 60.460 60.000 0.00 0.00 43.02 4.40
2049 2219 0.892755 TGCCGTAAGACCTGGTAGTG 59.107 55.000 0.00 0.00 43.02 2.74
2050 2220 1.183549 CTGCCGTAAGACCTGGTAGT 58.816 55.000 0.00 0.00 43.02 2.73
2051 2221 0.460311 CCTGCCGTAAGACCTGGTAG 59.540 60.000 0.00 0.00 43.02 3.18
2052 2222 0.251922 ACCTGCCGTAAGACCTGGTA 60.252 55.000 0.00 0.00 38.32 3.25
2053 2223 1.125711 AACCTGCCGTAAGACCTGGT 61.126 55.000 0.00 0.00 40.43 4.00
2054 2224 0.673644 CAACCTGCCGTAAGACCTGG 60.674 60.000 0.00 0.00 43.02 4.45
2055 2225 0.034896 ACAACCTGCCGTAAGACCTG 59.965 55.000 0.00 0.00 43.02 4.00
2056 2226 1.274447 GTACAACCTGCCGTAAGACCT 59.726 52.381 0.00 0.00 43.02 3.85
2057 2227 1.718396 GTACAACCTGCCGTAAGACC 58.282 55.000 0.00 0.00 43.02 3.85
2058 2228 1.336240 ACGTACAACCTGCCGTAAGAC 60.336 52.381 0.00 0.00 43.02 3.01
2059 2229 0.961019 ACGTACAACCTGCCGTAAGA 59.039 50.000 0.00 0.00 43.02 2.10
2060 2230 1.787012 AACGTACAACCTGCCGTAAG 58.213 50.000 0.00 0.00 29.94 2.34
2061 2231 2.237393 AAACGTACAACCTGCCGTAA 57.763 45.000 0.00 0.00 29.94 3.18
2062 2232 2.237393 AAAACGTACAACCTGCCGTA 57.763 45.000 0.00 0.00 29.94 4.02
2063 2233 1.866601 GTAAAACGTACAACCTGCCGT 59.133 47.619 0.00 0.00 31.07 5.68
2064 2234 1.865970 TGTAAAACGTACAACCTGCCG 59.134 47.619 0.00 0.00 0.00 5.69
2065 2235 4.469552 GAATGTAAAACGTACAACCTGCC 58.530 43.478 0.00 0.00 0.00 4.85
2066 2236 4.023878 TGGAATGTAAAACGTACAACCTGC 60.024 41.667 13.64 2.01 32.93 4.85
2067 2237 5.676532 TGGAATGTAAAACGTACAACCTG 57.323 39.130 13.64 0.00 32.93 4.00
2068 2238 6.696441 TTTGGAATGTAAAACGTACAACCT 57.304 33.333 13.64 0.00 32.93 3.50
2069 2239 7.752557 TTTTTGGAATGTAAAACGTACAACC 57.247 32.000 0.00 0.00 0.00 3.77
2090 2260 6.430000 AGAACATACAACCTGCTACGATTTTT 59.570 34.615 0.00 0.00 0.00 1.94
2091 2261 5.938125 AGAACATACAACCTGCTACGATTTT 59.062 36.000 0.00 0.00 0.00 1.82
2092 2262 5.488341 AGAACATACAACCTGCTACGATTT 58.512 37.500 0.00 0.00 0.00 2.17
2093 2263 5.086104 AGAACATACAACCTGCTACGATT 57.914 39.130 0.00 0.00 0.00 3.34
2094 2264 4.737855 AGAACATACAACCTGCTACGAT 57.262 40.909 0.00 0.00 0.00 3.73
2095 2265 4.242475 CAAGAACATACAACCTGCTACGA 58.758 43.478 0.00 0.00 0.00 3.43
2096 2266 3.994392 ACAAGAACATACAACCTGCTACG 59.006 43.478 0.00 0.00 0.00 3.51
2097 2267 5.941948 AACAAGAACATACAACCTGCTAC 57.058 39.130 0.00 0.00 0.00 3.58
2098 2268 6.993308 TGTTAACAAGAACATACAACCTGCTA 59.007 34.615 5.64 0.00 34.40 3.49
2099 2269 5.825679 TGTTAACAAGAACATACAACCTGCT 59.174 36.000 5.64 0.00 34.40 4.24
2100 2270 5.912955 GTGTTAACAAGAACATACAACCTGC 59.087 40.000 10.51 0.00 41.21 4.85
2101 2271 7.132213 CAGTGTTAACAAGAACATACAACCTG 58.868 38.462 10.51 4.87 41.21 4.00
2102 2272 6.262273 CCAGTGTTAACAAGAACATACAACCT 59.738 38.462 10.51 0.00 41.21 3.50
2103 2273 6.435428 CCAGTGTTAACAAGAACATACAACC 58.565 40.000 10.51 0.00 41.21 3.77
2104 2274 6.435428 CCCAGTGTTAACAAGAACATACAAC 58.565 40.000 10.51 0.00 41.21 3.32
2105 2275 5.009210 GCCCAGTGTTAACAAGAACATACAA 59.991 40.000 10.51 0.00 41.21 2.41
2106 2276 4.517453 GCCCAGTGTTAACAAGAACATACA 59.483 41.667 10.51 0.00 41.21 2.29
2107 2277 4.082949 GGCCCAGTGTTAACAAGAACATAC 60.083 45.833 10.51 0.00 41.21 2.39
2108 2278 4.076394 GGCCCAGTGTTAACAAGAACATA 58.924 43.478 10.51 0.00 41.21 2.29
2109 2279 2.890945 GGCCCAGTGTTAACAAGAACAT 59.109 45.455 10.51 0.00 41.21 2.71
2110 2280 2.092103 AGGCCCAGTGTTAACAAGAACA 60.092 45.455 10.51 0.00 36.98 3.18
2111 2281 2.583143 AGGCCCAGTGTTAACAAGAAC 58.417 47.619 10.51 0.00 0.00 3.01
2112 2282 3.393278 ACTAGGCCCAGTGTTAACAAGAA 59.607 43.478 10.51 0.00 0.00 2.52
2113 2283 2.976882 ACTAGGCCCAGTGTTAACAAGA 59.023 45.455 10.51 0.00 0.00 3.02
2114 2284 3.074412 CACTAGGCCCAGTGTTAACAAG 58.926 50.000 21.81 6.11 40.89 3.16
2115 2285 3.134574 CACTAGGCCCAGTGTTAACAA 57.865 47.619 21.81 0.00 40.89 2.83
2136 2306 0.107993 ATCGGTCTCGTCGGTAGTGA 60.108 55.000 0.00 0.00 37.69 3.41
2154 2324 2.236146 TCCTTGGTGATGAAGCGTACAT 59.764 45.455 0.00 0.00 0.00 2.29
2264 2434 1.081509 CAATTCGCCACCCAACACG 60.082 57.895 0.00 0.00 0.00 4.49
2306 2477 7.577303 TGCTTACAGAGGAAGGATTGATTTAT 58.423 34.615 0.00 0.00 0.00 1.40
2352 2523 0.529773 TGGCGGCATCTCGTATTCAC 60.530 55.000 7.97 0.00 0.00 3.18
2374 2545 2.971901 TGGAGAAGGAAGGGGAAAAC 57.028 50.000 0.00 0.00 0.00 2.43
2428 2709 0.863956 AGTGGGTGGGAATTTTGGGA 59.136 50.000 0.00 0.00 0.00 4.37
2431 2712 2.288152 CGTGAAGTGGGTGGGAATTTTG 60.288 50.000 0.00 0.00 0.00 2.44
2458 2891 4.700365 CGCGTCTCGTGGCTGTGA 62.700 66.667 0.00 0.00 33.47 3.58
2530 2963 2.797278 ATAGACCGCCTTGCCCTCG 61.797 63.158 0.00 0.00 0.00 4.63
2543 2976 3.244249 GCCTGGGTTATGGTCTCATAGAC 60.244 52.174 0.00 0.00 44.32 2.59
2548 2981 1.281867 CTTGCCTGGGTTATGGTCTCA 59.718 52.381 0.00 0.00 0.00 3.27
2554 2987 1.097547 CCTCGCTTGCCTGGGTTATG 61.098 60.000 0.00 0.00 0.00 1.90
2555 2988 1.224592 CCTCGCTTGCCTGGGTTAT 59.775 57.895 0.00 0.00 0.00 1.89
2582 3166 1.133407 GAGCTCCTTCTGGTGACGTAG 59.867 57.143 0.87 0.00 34.23 3.51
2583 3167 1.174783 GAGCTCCTTCTGGTGACGTA 58.825 55.000 0.87 0.00 34.23 3.57
2584 3168 1.867919 CGAGCTCCTTCTGGTGACGT 61.868 60.000 8.47 0.00 34.23 4.34
2587 3171 1.587043 CGTCGAGCTCCTTCTGGTGA 61.587 60.000 8.47 0.00 34.23 4.02


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

AutoCloner maintained by Alex Coulton.