Multiple sequence alignment - TraesCS4B01G157200

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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 TraesCS4B01G157200 chr4B 100.000 2282 0 0 1 2282 295124584 295122303 0.000000e+00 4215
1 TraesCS4B01G157200 chr4B 88.446 753 80 5 3 748 510388433 510389185 0.000000e+00 902
2 TraesCS4B01G157200 chr4B 87.040 679 74 12 741 1414 510389129 510389798 0.000000e+00 754
3 TraesCS4B01G157200 chr4B 78.717 343 65 8 1927 2267 641298521 641298857 2.950000e-54 222
4 TraesCS4B01G157200 chr5A 89.026 1950 175 30 3 1933 671875967 671874038 0.000000e+00 2379
5 TraesCS4B01G157200 chr5A 89.219 1920 176 24 3 1904 547532902 547534808 0.000000e+00 2370
6 TraesCS4B01G157200 chr5A 87.856 914 96 11 507 1417 181455576 181456477 0.000000e+00 1059
7 TraesCS4B01G157200 chr6A 89.111 1901 174 26 3 1881 83359951 83361840 0.000000e+00 2333
8 TraesCS4B01G157200 chr1A 88.462 1924 170 29 3 1904 75741314 75739421 0.000000e+00 2276
9 TraesCS4B01G157200 chr2B 88.592 1420 153 8 3 1417 551156833 551158248 0.000000e+00 1716
10 TraesCS4B01G157200 chr2B 89.590 634 57 8 1305 1931 47064050 47063419 0.000000e+00 797
11 TraesCS4B01G157200 chr5D 87.295 913 100 9 507 1417 177305676 177306574 0.000000e+00 1029
12 TraesCS4B01G157200 chr3A 92.068 706 55 1 1130 1834 671626027 671626732 0.000000e+00 992
13 TraesCS4B01G157200 chr6B 88.712 753 80 4 2 749 129396279 129397031 0.000000e+00 915
14 TraesCS4B01G157200 chr2D 87.947 755 84 4 2 749 52067234 52067988 0.000000e+00 883
15 TraesCS4B01G157200 chr3D 87.931 754 84 4 3 749 537328159 537327406 0.000000e+00 881
16 TraesCS4B01G157200 chr7B 86.892 679 74 11 741 1414 72302822 72302154 0.000000e+00 747
17 TraesCS4B01G157200 chr1B 88.985 463 50 1 1467 1928 152825484 152825946 2.540000e-159 571
18 TraesCS4B01G157200 chr1B 80.580 345 59 8 1927 2268 179835724 179836063 2.250000e-65 259
19 TraesCS4B01G157200 chr6D 83.008 359 53 6 1927 2282 105474255 105473902 3.660000e-83 318
20 TraesCS4B01G157200 chr6D 79.330 358 64 10 1930 2282 162403258 162403610 2.260000e-60 243
21 TraesCS4B01G157200 chr6D 85.165 182 24 3 1927 2107 342313994 342313815 1.390000e-42 183
22 TraesCS4B01G157200 chr2A 82.865 356 51 8 1933 2282 505173917 505174268 6.120000e-81 311
23 TraesCS4B01G157200 chr2A 80.447 358 61 9 1930 2282 675463938 675464291 4.830000e-67 265
24 TraesCS4B01G157200 chr2A 79.944 359 63 7 1927 2282 334824035 334823683 2.910000e-64 255
25 TraesCS4B01G157200 chr2A 82.000 150 20 4 2120 2266 742921595 742921740 1.110000e-23 121
26 TraesCS4B01G157200 chr4A 84.586 266 31 7 2022 2282 232247548 232247808 2.910000e-64 255
27 TraesCS4B01G157200 chr7D 79.501 361 64 7 1927 2282 172754697 172754342 4.870000e-62 248


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 TraesCS4B01G157200 chr4B 295122303 295124584 2281 True 4215 4215 100.000 1 2282 1 chr4B.!!$R1 2281
1 TraesCS4B01G157200 chr4B 510388433 510389798 1365 False 828 902 87.743 3 1414 2 chr4B.!!$F2 1411
2 TraesCS4B01G157200 chr5A 671874038 671875967 1929 True 2379 2379 89.026 3 1933 1 chr5A.!!$R1 1930
3 TraesCS4B01G157200 chr5A 547532902 547534808 1906 False 2370 2370 89.219 3 1904 1 chr5A.!!$F2 1901
4 TraesCS4B01G157200 chr5A 181455576 181456477 901 False 1059 1059 87.856 507 1417 1 chr5A.!!$F1 910
5 TraesCS4B01G157200 chr6A 83359951 83361840 1889 False 2333 2333 89.111 3 1881 1 chr6A.!!$F1 1878
6 TraesCS4B01G157200 chr1A 75739421 75741314 1893 True 2276 2276 88.462 3 1904 1 chr1A.!!$R1 1901
7 TraesCS4B01G157200 chr2B 551156833 551158248 1415 False 1716 1716 88.592 3 1417 1 chr2B.!!$F1 1414
8 TraesCS4B01G157200 chr2B 47063419 47064050 631 True 797 797 89.590 1305 1931 1 chr2B.!!$R1 626
9 TraesCS4B01G157200 chr5D 177305676 177306574 898 False 1029 1029 87.295 507 1417 1 chr5D.!!$F1 910
10 TraesCS4B01G157200 chr3A 671626027 671626732 705 False 992 992 92.068 1130 1834 1 chr3A.!!$F1 704
11 TraesCS4B01G157200 chr6B 129396279 129397031 752 False 915 915 88.712 2 749 1 chr6B.!!$F1 747
12 TraesCS4B01G157200 chr2D 52067234 52067988 754 False 883 883 87.947 2 749 1 chr2D.!!$F1 747
13 TraesCS4B01G157200 chr3D 537327406 537328159 753 True 881 881 87.931 3 749 1 chr3D.!!$R1 746
14 TraesCS4B01G157200 chr7B 72302154 72302822 668 True 747 747 86.892 741 1414 1 chr7B.!!$R1 673

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
20 21 0.033642 TCATGCGTTGTTCGGGTGTA 59.966 50.0 0.0 0.0 40.26 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1738 0.035317 CACAGGCACTAGGTTCTGCA 59.965 55.0 5.53 0.0 36.02 4.41 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
20 21 0.033642 TCATGCGTTGTTCGGGTGTA 59.966 50.000 0.00 0.00 40.26 2.90
55 57 8.318412 AGTTGGAAAGATTTGTAAAAGTTGGTT 58.682 29.630 0.00 0.00 0.00 3.67
103 105 5.205056 AGGTTGAGTGGTTTTGAATGGTTA 58.795 37.500 0.00 0.00 0.00 2.85
111 113 6.605594 AGTGGTTTTGAATGGTTACAAGAGAA 59.394 34.615 0.00 0.00 0.00 2.87
141 144 5.248640 CACACCAGGAGAGACATAACAATT 58.751 41.667 0.00 0.00 0.00 2.32
190 193 3.058293 TGATCTTCACGACAAATTGGTGC 60.058 43.478 0.00 0.00 0.00 5.01
309 320 0.871722 CCGTTTCAAACATGGAGCGA 59.128 50.000 0.22 0.00 0.00 4.93
313 324 4.201910 CCGTTTCAAACATGGAGCGAATAT 60.202 41.667 0.22 0.00 0.00 1.28
318 329 6.161855 TCAAACATGGAGCGAATATAGTCT 57.838 37.500 0.00 0.00 0.00 3.24
328 340 6.388435 AGCGAATATAGTCTCCGTAAGTTT 57.612 37.500 0.00 0.00 0.00 2.66
331 343 6.142002 GCGAATATAGTCTCCGTAAGTTTCAC 59.858 42.308 0.00 0.00 0.00 3.18
363 375 4.216902 ACAATGTGTGGTCAAGATGTCATG 59.783 41.667 0.00 0.00 0.00 3.07
376 388 7.761704 GTCAAGATGTCATGTCACTACATTAGT 59.238 37.037 0.00 0.00 44.07 2.24
412 424 5.700722 ATTTTCGCATCATGCATGATAGT 57.299 34.783 35.47 17.63 45.23 2.12
415 427 5.789710 TTCGCATCATGCATGATAGTATG 57.210 39.130 35.47 26.66 45.23 2.39
425 437 3.120286 GCATGATAGTATGAAGCGTGACG 59.880 47.826 0.00 0.00 0.00 4.35
449 461 6.939163 CGAAAGGGATTATCCTCATCTCAAAT 59.061 38.462 11.40 0.00 36.57 2.32
479 491 6.104877 ATTGGTGCAATAGATGGGACACATT 61.105 40.000 0.00 0.00 34.43 2.71
495 507 6.122964 GGACACATTTTAGGGCTTCTATTCT 58.877 40.000 0.00 0.00 0.00 2.40
549 561 2.936919 TCAGGTGCAACAACTCAGAT 57.063 45.000 3.64 0.00 39.98 2.90
588 600 6.209192 TGTGACTTTGATATGCATTTCACCTT 59.791 34.615 18.00 6.35 32.79 3.50
651 663 5.512788 GTGTGTTATTCCATGCAATCGAAAG 59.487 40.000 0.00 0.00 0.00 2.62
677 689 1.039233 GGCCACATTCCCACATCCTG 61.039 60.000 0.00 0.00 0.00 3.86
682 694 2.299582 CACATTCCCACATCCTGCAAAA 59.700 45.455 0.00 0.00 0.00 2.44
705 717 6.396829 AGGTTAGCATTTCTTGATATTGCC 57.603 37.500 0.00 0.00 33.85 4.52
725 786 7.921786 TTGCCACTTATGTAATATATCCTGC 57.078 36.000 0.00 0.00 0.00 4.85
726 787 7.014988 TGCCACTTATGTAATATATCCTGCA 57.985 36.000 0.00 0.00 0.00 4.41
727 788 7.457561 TGCCACTTATGTAATATATCCTGCAA 58.542 34.615 0.00 0.00 0.00 4.08
728 789 8.108999 TGCCACTTATGTAATATATCCTGCAAT 58.891 33.333 0.00 0.00 0.00 3.56
729 790 8.960591 GCCACTTATGTAATATATCCTGCAATT 58.039 33.333 0.00 0.00 0.00 2.32
736 797 7.819644 TGTAATATATCCTGCAATTCACATGC 58.180 34.615 0.00 0.00 44.08 4.06
756 817 5.401033 TGCATGTTTATTGTTGTTGCAAC 57.599 34.783 22.83 22.83 35.85 4.17
761 822 7.741216 GCATGTTTATTGTTGTTGCAACTTATG 59.259 33.333 28.61 16.73 0.00 1.90
764 825 9.973450 TGTTTATTGTTGTTGCAACTTATGTAT 57.027 25.926 28.61 16.29 0.00 2.29
773 834 7.984391 TGTTGCAACTTATGTATCATAACCTG 58.016 34.615 28.61 1.73 0.00 4.00
774 835 7.826744 TGTTGCAACTTATGTATCATAACCTGA 59.173 33.333 28.61 0.00 38.53 3.86
796 857 7.920151 CCTGAAACTCACAATCATGTTTGTTTA 59.080 33.333 17.54 9.48 39.95 2.01
879 940 2.301870 AGCACCATACAAAGGAGAACGA 59.698 45.455 0.00 0.00 0.00 3.85
901 962 1.374252 CACGTCCCCGACTTCCAAG 60.374 63.158 0.00 0.00 37.88 3.61
906 967 2.269241 CCCGACTTCCAAGGAGGC 59.731 66.667 0.00 0.00 37.29 4.70
907 968 2.294078 CCCGACTTCCAAGGAGGCT 61.294 63.158 0.00 0.00 37.29 4.58
908 969 1.078848 CCGACTTCCAAGGAGGCTG 60.079 63.158 0.00 0.00 37.29 4.85
957 1019 0.546747 ACCGGATCCACTCCTCCAAA 60.547 55.000 9.46 0.00 42.47 3.28
958 1020 0.179000 CCGGATCCACTCCTCCAAAG 59.821 60.000 13.41 0.00 42.47 2.77
959 1021 0.462759 CGGATCCACTCCTCCAAAGC 60.463 60.000 13.41 0.00 42.47 3.51
960 1022 0.462759 GGATCCACTCCTCCAAAGCG 60.463 60.000 6.95 0.00 41.29 4.68
961 1023 1.078143 ATCCACTCCTCCAAAGCGC 60.078 57.895 0.00 0.00 0.00 5.92
963 1025 1.600636 CCACTCCTCCAAAGCGCAA 60.601 57.895 11.47 0.00 0.00 4.85
964 1026 1.576421 CACTCCTCCAAAGCGCAAC 59.424 57.895 11.47 0.00 0.00 4.17
969 1031 1.283793 CTCCAAAGCGCAACACCAG 59.716 57.895 11.47 0.00 0.00 4.00
978 1040 1.873903 GCGCAACACCAGAGAGAGAAA 60.874 52.381 0.30 0.00 0.00 2.52
1011 1074 9.835389 TGTTTGGAAGATGAAATGAAAATCTTT 57.165 25.926 0.00 0.00 40.01 2.52
1038 1101 4.184629 AGATGCCAAACTACTCGATCAAC 58.815 43.478 0.00 0.00 0.00 3.18
1066 1148 2.283298 AGATGATTGTTGCGGCTACTG 58.717 47.619 15.15 0.00 0.00 2.74
1073 1155 0.878523 GTTGCGGCTACTGTGACACA 60.879 55.000 8.26 8.26 0.00 3.72
1134 1216 3.056465 ACTTTCTTCGATGTGAGAGGGAC 60.056 47.826 9.43 0.00 0.00 4.46
1214 1296 0.249120 TCGGATGCTTCAACATCGGT 59.751 50.000 10.58 0.00 46.11 4.69
1385 1468 7.179410 GCAAAGGACAAAACTTGTTGTTATTG 58.821 34.615 0.00 0.00 45.52 1.90
1422 1506 7.913789 ACTTGTCTTAACTGGGATAACATGTA 58.086 34.615 0.00 0.00 0.00 2.29
1423 1507 8.041323 ACTTGTCTTAACTGGGATAACATGTAG 58.959 37.037 0.00 0.00 0.00 2.74
1458 1552 6.479006 TGACTACTTTGTACTCTGCCTACTA 58.521 40.000 0.00 0.00 0.00 1.82
1469 1563 7.830697 TGTACTCTGCCTACTACTATAACACAA 59.169 37.037 0.00 0.00 0.00 3.33
1525 1621 3.117701 TGTTTTGGACTCACCCAGAATCA 60.118 43.478 0.00 0.00 37.53 2.57
1526 1622 4.082125 GTTTTGGACTCACCCAGAATCAT 58.918 43.478 0.00 0.00 37.53 2.45
1533 1629 5.046014 GGACTCACCCAGAATCATGCTATAT 60.046 44.000 0.00 0.00 0.00 0.86
1534 1630 6.445451 ACTCACCCAGAATCATGCTATATT 57.555 37.500 0.00 0.00 0.00 1.28
1542 1638 8.753133 CCCAGAATCATGCTATATTAGAGTACA 58.247 37.037 0.00 0.00 0.00 2.90
1572 1668 9.745880 TTGTAGGATAATTGATAAACTCGACTC 57.254 33.333 0.00 0.00 0.00 3.36
1574 1670 9.400638 GTAGGATAATTGATAAACTCGACTCAG 57.599 37.037 0.00 0.00 0.00 3.35
1617 1714 2.238144 ACTGCATGCCTCTCTGTACATT 59.762 45.455 16.68 0.00 0.00 2.71
1716 1820 2.474112 CTACTACAGCCCAACCCCTTA 58.526 52.381 0.00 0.00 0.00 2.69
1738 1843 7.993183 CCTTATATCTCTAAAAACCAAGCCAGA 59.007 37.037 0.00 0.00 0.00 3.86
1788 1893 2.840651 AGCTATAGACAAACAGGCCAGT 59.159 45.455 5.01 0.00 0.00 4.00
1834 1940 1.135024 GGGATAACCTACGACGTGCAA 60.135 52.381 11.56 0.00 35.85 4.08
1849 1955 2.281234 CGTGCAAAACGCTTCACAAATT 59.719 40.909 0.00 0.00 46.99 1.82
1907 2014 7.881775 ACTTTGAGAAGTTTTGGAAGTACAT 57.118 32.000 0.00 0.00 43.48 2.29
1916 2023 6.574350 AGTTTTGGAAGTACATAGGAGATCG 58.426 40.000 0.00 0.00 0.00 3.69
1922 2029 5.068723 GGAAGTACATAGGAGATCGGAACAA 59.931 44.000 0.00 0.00 0.00 2.83
1933 2040 5.513267 GGAGATCGGAACAAGCCCTAAATAT 60.513 44.000 0.00 0.00 0.00 1.28
1934 2041 5.941788 AGATCGGAACAAGCCCTAAATATT 58.058 37.500 0.00 0.00 0.00 1.28
1935 2042 6.365520 AGATCGGAACAAGCCCTAAATATTT 58.634 36.000 5.89 5.89 0.00 1.40
1936 2043 6.486993 AGATCGGAACAAGCCCTAAATATTTC 59.513 38.462 3.39 0.00 0.00 2.17
1937 2044 5.751586 TCGGAACAAGCCCTAAATATTTCT 58.248 37.500 3.39 0.00 0.00 2.52
1938 2045 6.184789 TCGGAACAAGCCCTAAATATTTCTT 58.815 36.000 3.39 0.00 0.00 2.52
1939 2046 6.094881 TCGGAACAAGCCCTAAATATTTCTTG 59.905 38.462 18.68 18.68 37.51 3.02
1940 2047 6.094881 CGGAACAAGCCCTAAATATTTCTTGA 59.905 38.462 23.69 2.33 35.97 3.02
1941 2048 7.201821 CGGAACAAGCCCTAAATATTTCTTGAT 60.202 37.037 23.69 16.60 35.97 2.57
1942 2049 8.138074 GGAACAAGCCCTAAATATTTCTTGATC 58.862 37.037 23.69 21.24 35.97 2.92
1943 2050 8.593945 AACAAGCCCTAAATATTTCTTGATCA 57.406 30.769 23.69 0.00 35.97 2.92
1944 2051 8.230472 ACAAGCCCTAAATATTTCTTGATCAG 57.770 34.615 23.69 8.81 35.97 2.90
1945 2052 7.836183 ACAAGCCCTAAATATTTCTTGATCAGT 59.164 33.333 23.69 7.95 35.97 3.41
1946 2053 8.689972 CAAGCCCTAAATATTTCTTGATCAGTT 58.310 33.333 16.68 0.00 34.49 3.16
1947 2054 9.920946 AAGCCCTAAATATTTCTTGATCAGTTA 57.079 29.630 3.39 0.00 0.00 2.24
1956 2063 6.834168 TTTCTTGATCAGTTATCCAAACCC 57.166 37.500 0.00 0.00 33.22 4.11
1957 2064 4.855340 TCTTGATCAGTTATCCAAACCCC 58.145 43.478 0.00 0.00 33.22 4.95
1958 2065 4.290985 TCTTGATCAGTTATCCAAACCCCA 59.709 41.667 0.00 0.00 33.22 4.96
1959 2066 4.879295 TGATCAGTTATCCAAACCCCAT 57.121 40.909 0.00 0.00 33.22 4.00
1960 2067 5.205517 TGATCAGTTATCCAAACCCCATT 57.794 39.130 0.00 0.00 33.22 3.16
1961 2068 5.588845 TGATCAGTTATCCAAACCCCATTT 58.411 37.500 0.00 0.00 33.22 2.32
1962 2069 6.022315 TGATCAGTTATCCAAACCCCATTTT 58.978 36.000 0.00 0.00 33.22 1.82
1963 2070 7.185565 TGATCAGTTATCCAAACCCCATTTTA 58.814 34.615 0.00 0.00 33.22 1.52
1964 2071 7.843760 TGATCAGTTATCCAAACCCCATTTTAT 59.156 33.333 0.00 0.00 33.22 1.40
1965 2072 7.416964 TCAGTTATCCAAACCCCATTTTATG 57.583 36.000 0.00 0.00 0.00 1.90
1980 2087 7.358770 CCATTTTATGGGTAAACATCATGGA 57.641 36.000 0.00 0.00 46.86 3.41
1981 2088 7.790027 CCATTTTATGGGTAAACATCATGGAA 58.210 34.615 0.00 0.00 46.86 3.53
1982 2089 8.431222 CCATTTTATGGGTAAACATCATGGAAT 58.569 33.333 0.00 0.00 46.86 3.01
1983 2090 9.835389 CATTTTATGGGTAAACATCATGGAATT 57.165 29.630 0.00 0.00 32.39 2.17
1985 2092 7.595819 TTATGGGTAAACATCATGGAATTCC 57.404 36.000 18.17 18.17 32.39 3.01
1986 2093 5.205517 TGGGTAAACATCATGGAATTCCT 57.794 39.130 24.73 8.22 36.82 3.36
1987 2094 5.588845 TGGGTAAACATCATGGAATTCCTT 58.411 37.500 24.73 16.20 36.82 3.36
1988 2095 5.421693 TGGGTAAACATCATGGAATTCCTTG 59.578 40.000 26.93 26.93 41.16 3.61
1989 2096 5.351458 GGTAAACATCATGGAATTCCTTGC 58.649 41.667 27.67 14.96 40.03 4.01
1990 2097 4.476628 AAACATCATGGAATTCCTTGCC 57.523 40.909 27.67 4.50 40.03 4.52
1991 2098 2.391678 ACATCATGGAATTCCTTGCCC 58.608 47.619 27.67 3.81 40.03 5.36
1992 2099 2.292389 ACATCATGGAATTCCTTGCCCA 60.292 45.455 27.67 15.98 40.03 5.36
1993 2100 2.619697 TCATGGAATTCCTTGCCCAA 57.380 45.000 27.67 13.39 40.03 4.12
1994 2101 2.899975 TCATGGAATTCCTTGCCCAAA 58.100 42.857 27.67 13.08 40.03 3.28
1995 2102 3.452878 TCATGGAATTCCTTGCCCAAAT 58.547 40.909 27.67 9.19 40.03 2.32
1996 2103 4.618635 TCATGGAATTCCTTGCCCAAATA 58.381 39.130 27.67 11.90 40.03 1.40
1997 2104 5.218179 TCATGGAATTCCTTGCCCAAATAT 58.782 37.500 27.67 7.90 40.03 1.28
1998 2105 5.305128 TCATGGAATTCCTTGCCCAAATATC 59.695 40.000 27.67 0.00 40.03 1.63
1999 2106 3.966665 TGGAATTCCTTGCCCAAATATCC 59.033 43.478 24.73 0.00 36.82 2.59
2000 2107 3.966665 GGAATTCCTTGCCCAAATATCCA 59.033 43.478 17.73 0.00 0.00 3.41
2001 2108 4.594491 GGAATTCCTTGCCCAAATATCCAT 59.406 41.667 17.73 0.00 0.00 3.41
2002 2109 5.779771 GGAATTCCTTGCCCAAATATCCATA 59.220 40.000 17.73 0.00 0.00 2.74
2003 2110 6.441604 GGAATTCCTTGCCCAAATATCCATAT 59.558 38.462 17.73 0.00 0.00 1.78
2004 2111 6.862469 ATTCCTTGCCCAAATATCCATATG 57.138 37.500 0.00 0.00 0.00 1.78
2005 2112 4.676109 TCCTTGCCCAAATATCCATATGG 58.324 43.478 16.25 16.25 0.00 2.74
2020 2127 5.234752 TCCATATGGATACGTACATGTTGC 58.765 41.667 20.98 0.00 41.91 4.17
2021 2128 4.391830 CCATATGGATACGTACATGTTGCC 59.608 45.833 17.49 0.00 41.91 4.52
2022 2129 3.552132 ATGGATACGTACATGTTGCCA 57.448 42.857 2.30 3.66 42.51 4.92
2023 2130 3.552132 TGGATACGTACATGTTGCCAT 57.448 42.857 2.30 0.00 42.51 4.40
2036 2143 6.563222 CATGTTGCCATGTCATGTATATCA 57.437 37.500 11.84 5.10 42.92 2.15
2037 2144 7.153217 CATGTTGCCATGTCATGTATATCAT 57.847 36.000 11.84 6.91 42.92 2.45
2038 2145 7.027161 CATGTTGCCATGTCATGTATATCATG 58.973 38.462 11.84 13.55 44.96 3.07
2039 2146 8.311091 CATGTTGCCATGTCATGTATATCATGC 61.311 40.741 11.84 5.89 44.27 4.06
2049 2156 6.872628 CATGTATATCATGCTCCACTTGTT 57.127 37.500 0.00 0.00 45.69 2.83
2050 2157 6.895898 CATGTATATCATGCTCCACTTGTTC 58.104 40.000 0.00 0.00 45.69 3.18
2051 2158 6.239217 TGTATATCATGCTCCACTTGTTCT 57.761 37.500 0.00 0.00 0.00 3.01
2052 2159 6.653020 TGTATATCATGCTCCACTTGTTCTT 58.347 36.000 0.00 0.00 0.00 2.52
2053 2160 6.539826 TGTATATCATGCTCCACTTGTTCTTG 59.460 38.462 0.00 0.00 0.00 3.02
2054 2161 2.507484 TCATGCTCCACTTGTTCTTGG 58.493 47.619 0.00 0.00 0.00 3.61
2055 2162 1.542915 CATGCTCCACTTGTTCTTGGG 59.457 52.381 0.00 0.00 33.25 4.12
2056 2163 0.843309 TGCTCCACTTGTTCTTGGGA 59.157 50.000 0.00 0.00 33.25 4.37
2057 2164 1.214175 TGCTCCACTTGTTCTTGGGAA 59.786 47.619 0.00 0.00 33.25 3.97
2058 2165 1.882623 GCTCCACTTGTTCTTGGGAAG 59.117 52.381 0.00 0.00 33.25 3.46
2059 2166 2.508526 CTCCACTTGTTCTTGGGAAGG 58.491 52.381 0.00 0.00 33.25 3.46
2060 2167 2.106511 CTCCACTTGTTCTTGGGAAGGA 59.893 50.000 0.00 0.00 33.25 3.36
2061 2168 2.716424 TCCACTTGTTCTTGGGAAGGAT 59.284 45.455 0.00 0.00 33.25 3.24
2062 2169 3.913799 TCCACTTGTTCTTGGGAAGGATA 59.086 43.478 0.00 0.00 33.25 2.59
2063 2170 4.540099 TCCACTTGTTCTTGGGAAGGATAT 59.460 41.667 0.00 0.00 33.25 1.63
2064 2171 5.729229 TCCACTTGTTCTTGGGAAGGATATA 59.271 40.000 0.00 0.00 33.25 0.86
2065 2172 5.823045 CCACTTGTTCTTGGGAAGGATATAC 59.177 44.000 0.00 0.00 31.46 1.47
2066 2173 6.353082 CCACTTGTTCTTGGGAAGGATATACT 60.353 42.308 0.00 0.00 31.46 2.12
2067 2174 6.763610 CACTTGTTCTTGGGAAGGATATACTC 59.236 42.308 0.00 0.00 31.46 2.59
2068 2175 5.888982 TGTTCTTGGGAAGGATATACTCC 57.111 43.478 0.00 0.00 45.33 3.85
2100 2207 9.573133 CTCATGTATAAACACATTTTCCTTTCC 57.427 33.333 0.00 0.00 38.78 3.13
2101 2208 9.083422 TCATGTATAAACACATTTTCCTTTCCA 57.917 29.630 0.00 0.00 38.78 3.53
2102 2209 9.874205 CATGTATAAACACATTTTCCTTTCCAT 57.126 29.630 0.00 0.00 38.78 3.41
2104 2211 9.703892 TGTATAAACACATTTTCCTTTCCATTG 57.296 29.630 0.00 0.00 0.00 2.82
2105 2212 9.150348 GTATAAACACATTTTCCTTTCCATTGG 57.850 33.333 0.00 0.00 0.00 3.16
2106 2213 5.628797 AACACATTTTCCTTTCCATTGGT 57.371 34.783 1.86 0.00 0.00 3.67
2107 2214 5.213891 ACACATTTTCCTTTCCATTGGTC 57.786 39.130 1.86 0.00 0.00 4.02
2108 2215 4.901250 ACACATTTTCCTTTCCATTGGTCT 59.099 37.500 1.86 0.00 0.00 3.85
2109 2216 6.074648 ACACATTTTCCTTTCCATTGGTCTA 58.925 36.000 1.86 0.00 0.00 2.59
2110 2217 6.725834 ACACATTTTCCTTTCCATTGGTCTAT 59.274 34.615 1.86 0.00 0.00 1.98
2111 2218 7.235399 ACACATTTTCCTTTCCATTGGTCTATT 59.765 33.333 1.86 0.00 0.00 1.73
2112 2219 8.096414 CACATTTTCCTTTCCATTGGTCTATTT 58.904 33.333 1.86 0.00 0.00 1.40
2113 2220 9.320295 ACATTTTCCTTTCCATTGGTCTATTTA 57.680 29.630 1.86 0.00 0.00 1.40
2117 2224 9.540538 TTTCCTTTCCATTGGTCTATTTAATCA 57.459 29.630 1.86 0.00 0.00 2.57
2118 2225 9.540538 TTCCTTTCCATTGGTCTATTTAATCAA 57.459 29.630 1.86 0.00 0.00 2.57
2119 2226 9.540538 TCCTTTCCATTGGTCTATTTAATCAAA 57.459 29.630 1.86 0.00 0.00 2.69
2146 2253 8.750515 AATGACATTTTCCTTTCCATTGTTTT 57.249 26.923 0.00 0.00 0.00 2.43
2147 2254 8.750515 ATGACATTTTCCTTTCCATTGTTTTT 57.249 26.923 0.00 0.00 0.00 1.94
2209 2316 9.908152 AAAAACATTCTAGCTTATGTAAACACC 57.092 29.630 0.00 0.00 34.04 4.16
2210 2317 8.863872 AAACATTCTAGCTTATGTAAACACCT 57.136 30.769 0.00 0.00 34.04 4.00
2211 2318 8.494016 AACATTCTAGCTTATGTAAACACCTC 57.506 34.615 0.00 0.00 34.04 3.85
2212 2319 6.757010 ACATTCTAGCTTATGTAAACACCTCG 59.243 38.462 0.00 0.00 33.42 4.63
2213 2320 5.258456 TCTAGCTTATGTAAACACCTCGG 57.742 43.478 0.00 0.00 0.00 4.63
2214 2321 3.975168 AGCTTATGTAAACACCTCGGT 57.025 42.857 0.00 0.00 0.00 4.69
2232 2339 3.756933 GGTGTACAACCCTGTCAGTAA 57.243 47.619 0.00 0.00 44.02 2.24
2233 2340 3.660865 GGTGTACAACCCTGTCAGTAAG 58.339 50.000 0.00 0.00 44.02 2.34
2234 2341 3.322828 GGTGTACAACCCTGTCAGTAAGA 59.677 47.826 0.00 0.00 44.02 2.10
2235 2342 4.020485 GGTGTACAACCCTGTCAGTAAGAT 60.020 45.833 0.00 0.00 44.02 2.40
2236 2343 5.169295 GTGTACAACCCTGTCAGTAAGATC 58.831 45.833 0.00 0.00 36.96 2.75
2237 2344 3.983044 ACAACCCTGTCAGTAAGATCC 57.017 47.619 0.00 0.00 0.00 3.36
2238 2345 3.521727 ACAACCCTGTCAGTAAGATCCT 58.478 45.455 0.00 0.00 0.00 3.24
2239 2346 3.261897 ACAACCCTGTCAGTAAGATCCTG 59.738 47.826 0.00 0.00 0.00 3.86
2240 2347 3.474798 ACCCTGTCAGTAAGATCCTGA 57.525 47.619 0.00 0.00 36.63 3.86
2241 2348 4.000928 ACCCTGTCAGTAAGATCCTGAT 57.999 45.455 3.84 0.00 40.79 2.90
2242 2349 5.144159 ACCCTGTCAGTAAGATCCTGATA 57.856 43.478 3.84 1.21 40.79 2.15
2243 2350 4.896482 ACCCTGTCAGTAAGATCCTGATAC 59.104 45.833 3.84 0.00 40.79 2.24
2244 2351 5.144100 CCCTGTCAGTAAGATCCTGATACT 58.856 45.833 3.84 0.00 40.79 2.12
2245 2352 6.126156 ACCCTGTCAGTAAGATCCTGATACTA 60.126 42.308 3.84 0.00 40.79 1.82
2246 2353 6.951198 CCCTGTCAGTAAGATCCTGATACTAT 59.049 42.308 3.84 0.00 40.79 2.12
2247 2354 7.453126 CCCTGTCAGTAAGATCCTGATACTATT 59.547 40.741 3.84 0.00 40.79 1.73
2248 2355 8.303156 CCTGTCAGTAAGATCCTGATACTATTG 58.697 40.741 3.84 0.00 40.79 1.90
2249 2356 8.768501 TGTCAGTAAGATCCTGATACTATTGT 57.231 34.615 3.84 0.00 40.79 2.71
2250 2357 9.201989 TGTCAGTAAGATCCTGATACTATTGTT 57.798 33.333 3.84 0.00 40.79 2.83
2251 2358 9.469807 GTCAGTAAGATCCTGATACTATTGTTG 57.530 37.037 3.84 0.00 40.79 3.33
2252 2359 9.201989 TCAGTAAGATCCTGATACTATTGTTGT 57.798 33.333 0.00 0.00 34.12 3.32
2253 2360 9.823647 CAGTAAGATCCTGATACTATTGTTGTT 57.176 33.333 0.00 0.00 31.38 2.83
2261 2368 9.391006 TCCTGATACTATTGTTGTTAACATTCC 57.609 33.333 9.56 1.49 41.79 3.01
2262 2369 8.335356 CCTGATACTATTGTTGTTAACATTCCG 58.665 37.037 9.56 0.00 41.79 4.30
2263 2370 8.203937 TGATACTATTGTTGTTAACATTCCGG 57.796 34.615 9.56 0.00 41.79 5.14
2264 2371 7.825270 TGATACTATTGTTGTTAACATTCCGGT 59.175 33.333 9.56 7.35 41.79 5.28
2265 2372 9.316730 GATACTATTGTTGTTAACATTCCGGTA 57.683 33.333 9.56 9.13 41.79 4.02
2266 2373 7.982761 ACTATTGTTGTTAACATTCCGGTAA 57.017 32.000 9.56 0.00 41.79 2.85
2267 2374 7.809665 ACTATTGTTGTTAACATTCCGGTAAC 58.190 34.615 9.56 2.92 41.79 2.50
2268 2375 6.887626 ATTGTTGTTAACATTCCGGTAACT 57.112 33.333 9.56 0.00 41.79 2.24
2269 2376 7.982761 ATTGTTGTTAACATTCCGGTAACTA 57.017 32.000 9.56 0.00 41.79 2.24
2270 2377 6.783892 TGTTGTTAACATTCCGGTAACTAC 57.216 37.500 9.56 14.97 36.25 2.73
2271 2378 5.700373 TGTTGTTAACATTCCGGTAACTACC 59.300 40.000 9.56 0.00 38.57 3.18
2272 2379 5.743636 TGTTAACATTCCGGTAACTACCT 57.256 39.130 3.59 0.00 44.25 3.08
2273 2380 5.481105 TGTTAACATTCCGGTAACTACCTG 58.519 41.667 3.59 0.00 44.25 4.00
2274 2381 5.011943 TGTTAACATTCCGGTAACTACCTGT 59.988 40.000 3.59 0.00 44.25 4.00
2275 2382 3.604875 ACATTCCGGTAACTACCTGTG 57.395 47.619 0.00 1.17 44.25 3.66
2276 2383 2.235402 ACATTCCGGTAACTACCTGTGG 59.765 50.000 0.00 0.00 44.25 4.17
2277 2384 2.307496 TTCCGGTAACTACCTGTGGA 57.693 50.000 0.00 1.34 44.25 4.02
2278 2385 1.549203 TCCGGTAACTACCTGTGGAC 58.451 55.000 0.00 0.00 44.25 4.02
2279 2386 0.171903 CCGGTAACTACCTGTGGACG 59.828 60.000 4.45 0.00 44.25 4.79
2280 2387 1.167851 CGGTAACTACCTGTGGACGA 58.832 55.000 4.45 0.00 44.25 4.20
2281 2388 1.131883 CGGTAACTACCTGTGGACGAG 59.868 57.143 4.45 0.00 44.25 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.206578 CACCCGAACAACGCATGAC 59.793 57.895 0.00 0.00 41.07 3.06
35 36 9.981114 CCTCATAACCAACTTTTACAAATCTTT 57.019 29.630 0.00 0.00 0.00 2.52
39 40 6.295632 GGCCCTCATAACCAACTTTTACAAAT 60.296 38.462 0.00 0.00 0.00 2.32
40 41 5.011227 GGCCCTCATAACCAACTTTTACAAA 59.989 40.000 0.00 0.00 0.00 2.83
72 74 5.071788 TCAAAACCACTCAACCTAGATGTCT 59.928 40.000 0.00 0.00 0.00 3.41
103 105 4.012374 CTGGTGTGCCAATATTCTCTTGT 58.988 43.478 0.00 0.00 45.51 3.16
111 113 2.171448 GTCTCTCCTGGTGTGCCAATAT 59.829 50.000 0.00 0.00 45.51 1.28
124 126 8.954350 CATTCTCAAAATTGTTATGTCTCTCCT 58.046 33.333 0.00 0.00 0.00 3.69
163 166 6.697019 ACCAATTTGTCGTGAAGATCAAAAAG 59.303 34.615 0.00 0.00 35.32 2.27
177 180 1.234615 ACTCCCGCACCAATTTGTCG 61.235 55.000 0.00 0.00 0.00 4.35
190 193 0.830648 TCTTTGAGGCCATACTCCCG 59.169 55.000 5.01 0.00 36.66 5.14
309 320 7.325660 TCGTGAAACTTACGGAGACTATATT 57.674 36.000 0.00 0.00 41.58 1.28
313 324 3.438087 CCTCGTGAAACTTACGGAGACTA 59.562 47.826 0.00 0.00 41.58 2.59
318 329 2.624838 AGAACCTCGTGAAACTTACGGA 59.375 45.455 0.00 0.00 41.58 4.69
328 340 3.554129 CCACACATTGTAGAACCTCGTGA 60.554 47.826 0.00 0.00 0.00 4.35
331 343 2.993899 GACCACACATTGTAGAACCTCG 59.006 50.000 0.00 0.00 0.00 4.63
363 375 5.394333 GGGTCTTGAGGACTAATGTAGTGAC 60.394 48.000 0.00 0.00 43.97 3.67
376 388 3.008594 TGCGAAAATTAGGGTCTTGAGGA 59.991 43.478 0.00 0.00 0.00 3.71
412 424 1.546923 TCCCTTTCGTCACGCTTCATA 59.453 47.619 0.00 0.00 0.00 2.15
415 427 1.439679 AATCCCTTTCGTCACGCTTC 58.560 50.000 0.00 0.00 0.00 3.86
425 437 9.972106 ATATTTGAGATGAGGATAATCCCTTTC 57.028 33.333 0.00 0.00 37.19 2.62
512 524 7.147391 TGCACCTGATCTTCCAATATACCTTAA 60.147 37.037 0.00 0.00 0.00 1.85
530 542 2.880268 CAATCTGAGTTGTTGCACCTGA 59.120 45.455 0.00 0.00 0.00 3.86
549 561 3.701205 AGTCACATACTGCCATCACAA 57.299 42.857 0.00 0.00 36.93 3.33
588 600 1.339610 CCGGTTGTCCAATTGAAGCAA 59.660 47.619 7.12 6.14 0.00 3.91
651 663 0.539438 TGGGAATGTGGCCTTGTCAC 60.539 55.000 3.32 0.00 38.79 3.67
677 689 8.598075 CAATATCAAGAAATGCTAACCTTTTGC 58.402 33.333 0.00 0.00 0.00 3.68
682 694 5.893255 TGGCAATATCAAGAAATGCTAACCT 59.107 36.000 0.00 0.00 37.20 3.50
724 785 6.411630 ACAATAAACATGCATGTGAATTGC 57.588 33.333 37.33 0.00 42.01 3.56
725 786 7.798801 ACAACAATAAACATGCATGTGAATTG 58.201 30.769 36.60 36.60 42.89 2.32
726 787 7.966246 ACAACAATAAACATGCATGTGAATT 57.034 28.000 31.98 27.22 41.61 2.17
727 788 7.571613 GCAACAACAATAAACATGCATGTGAAT 60.572 33.333 31.98 23.62 41.61 2.57
728 789 6.292757 GCAACAACAATAAACATGCATGTGAA 60.293 34.615 31.98 22.50 41.61 3.18
729 790 5.177142 GCAACAACAATAAACATGCATGTGA 59.823 36.000 31.98 22.75 41.61 3.58
730 791 5.050295 TGCAACAACAATAAACATGCATGTG 60.050 36.000 31.98 20.88 41.61 3.21
731 792 5.055144 TGCAACAACAATAAACATGCATGT 58.945 33.333 26.61 26.61 44.20 3.21
732 793 5.593183 TGCAACAACAATAAACATGCATG 57.407 34.783 25.09 25.09 37.40 4.06
733 794 5.759273 AGTTGCAACAACAATAAACATGCAT 59.241 32.000 30.11 0.00 41.38 3.96
734 795 5.114780 AGTTGCAACAACAATAAACATGCA 58.885 33.333 30.11 0.00 40.22 3.96
735 796 5.655893 AGTTGCAACAACAATAAACATGC 57.344 34.783 30.11 0.00 0.00 4.06
736 797 8.763356 ACATAAGTTGCAACAACAATAAACATG 58.237 29.630 30.11 17.32 0.00 3.21
737 798 8.885494 ACATAAGTTGCAACAACAATAAACAT 57.115 26.923 30.11 3.00 0.00 2.71
738 799 9.973450 ATACATAAGTTGCAACAACAATAAACA 57.027 25.926 30.11 6.73 0.00 2.83
756 817 9.599866 TGTGAGTTTCAGGTTATGATACATAAG 57.400 33.333 4.72 0.00 41.00 1.73
761 822 8.492673 TGATTGTGAGTTTCAGGTTATGATAC 57.507 34.615 0.00 0.00 39.42 2.24
764 825 6.942005 ACATGATTGTGAGTTTCAGGTTATGA 59.058 34.615 0.00 0.00 30.95 2.15
768 829 6.127366 ACAAACATGATTGTGAGTTTCAGGTT 60.127 34.615 19.31 0.00 43.72 3.50
769 830 5.360714 ACAAACATGATTGTGAGTTTCAGGT 59.639 36.000 19.31 0.00 41.78 4.00
906 967 0.905357 CAGGAGTAGTTGGGGGTCAG 59.095 60.000 0.00 0.00 0.00 3.51
907 968 0.192566 ACAGGAGTAGTTGGGGGTCA 59.807 55.000 0.00 0.00 0.00 4.02
908 969 2.108970 CTACAGGAGTAGTTGGGGGTC 58.891 57.143 0.00 0.00 42.25 4.46
957 1019 1.181741 TCTCTCTCTGGTGTTGCGCT 61.182 55.000 9.73 0.00 0.00 5.92
958 1020 0.319900 TTCTCTCTCTGGTGTTGCGC 60.320 55.000 0.00 0.00 0.00 6.09
959 1021 2.154854 TTTCTCTCTCTGGTGTTGCG 57.845 50.000 0.00 0.00 0.00 4.85
960 1022 5.218139 CAAAATTTCTCTCTCTGGTGTTGC 58.782 41.667 0.00 0.00 0.00 4.17
961 1023 5.300286 ACCAAAATTTCTCTCTCTGGTGTTG 59.700 40.000 7.50 0.00 34.46 3.33
963 1025 4.823989 CACCAAAATTTCTCTCTCTGGTGT 59.176 41.667 20.54 0.00 44.69 4.16
964 1026 5.368256 CACCAAAATTTCTCTCTCTGGTG 57.632 43.478 17.21 17.21 44.46 4.17
969 1031 6.391227 TCCAAACACCAAAATTTCTCTCTC 57.609 37.500 0.00 0.00 0.00 3.20
978 1040 7.507829 TCATTTCATCTTCCAAACACCAAAAT 58.492 30.769 0.00 0.00 0.00 1.82
1011 1074 5.654603 TCGAGTAGTTTGGCATCTTAAGA 57.345 39.130 7.82 7.82 0.00 2.10
1038 1101 3.426191 CCGCAACAATCATCTTTTGTGTG 59.574 43.478 0.00 0.00 37.38 3.82
1134 1216 4.760204 GGAATAGTTGGAACATAATCCGGG 59.240 45.833 0.00 0.00 42.76 5.73
1192 1274 2.286595 CCGATGTTGAAGCATCCGATTG 60.287 50.000 2.08 0.00 41.49 2.67
1193 1275 1.942657 CCGATGTTGAAGCATCCGATT 59.057 47.619 2.08 0.00 41.49 3.34
1214 1296 8.778059 ACAAATCCATATTAGGACTACTTTCCA 58.222 33.333 0.00 0.00 41.30 3.53
1418 1502 9.909644 CAAAGTAGTCAGTACAAGTTACTACAT 57.090 33.333 17.69 9.06 43.11 2.29
1422 1506 9.129532 AGTACAAAGTAGTCAGTACAAGTTACT 57.870 33.333 12.41 0.00 39.33 2.24
1423 1507 9.392021 GAGTACAAAGTAGTCAGTACAAGTTAC 57.608 37.037 12.41 0.00 39.33 2.50
1469 1563 9.475620 TCTATCCATTATCCTACAATCACGTAT 57.524 33.333 0.00 0.00 0.00 3.06
1571 1667 4.994852 CGATTCTGGGTGAGTAAAAACTGA 59.005 41.667 0.00 0.00 0.00 3.41
1572 1668 4.154195 CCGATTCTGGGTGAGTAAAAACTG 59.846 45.833 0.00 0.00 0.00 3.16
1574 1670 4.153655 GTCCGATTCTGGGTGAGTAAAAAC 59.846 45.833 0.00 0.00 0.00 2.43
1635 1736 1.352352 ACAGGCACTAGGTTCTGCAAT 59.648 47.619 5.53 0.00 36.02 3.56
1637 1738 0.035317 CACAGGCACTAGGTTCTGCA 59.965 55.000 5.53 0.00 36.02 4.41
1701 1804 2.711547 GAGATATAAGGGGTTGGGCTGT 59.288 50.000 0.00 0.00 0.00 4.40
1716 1820 6.122964 GGTCTGGCTTGGTTTTTAGAGATAT 58.877 40.000 0.00 0.00 0.00 1.63
1752 1857 2.601367 GCTTGGGCTGGCTGGAAA 60.601 61.111 0.00 0.00 35.22 3.13
1798 1904 4.265282 CCAACAATTTGGCCTGCG 57.735 55.556 3.32 0.00 46.09 5.18
1810 1916 2.094597 CACGTCGTAGGTTATCCCAACA 60.095 50.000 0.00 0.00 34.66 3.33
1812 1918 1.135024 GCACGTCGTAGGTTATCCCAA 60.135 52.381 0.00 0.00 34.66 4.12
1818 1924 1.786004 CGTTTTGCACGTCGTAGGTTA 59.214 47.619 0.00 0.00 44.49 2.85
1834 1940 3.317993 ACCTAGCAATTTGTGAAGCGTTT 59.682 39.130 0.00 0.00 0.00 3.60
1849 1955 2.534042 AGCTTCTACTCCACCTAGCA 57.466 50.000 0.00 0.00 0.00 3.49
1884 1991 8.507249 CCTATGTACTTCCAAAACTTCTCAAAG 58.493 37.037 0.00 0.00 38.54 2.77
1904 2011 2.103263 GGCTTGTTCCGATCTCCTATGT 59.897 50.000 0.00 0.00 0.00 2.29
1907 2014 1.120530 GGGCTTGTTCCGATCTCCTA 58.879 55.000 0.00 0.00 0.00 2.94
1916 2023 7.404671 TCAAGAAATATTTAGGGCTTGTTCC 57.595 36.000 19.12 0.00 35.49 3.62
1933 2040 5.714806 GGGGTTTGGATAACTGATCAAGAAA 59.285 40.000 0.00 0.00 36.12 2.52
1934 2041 5.222233 TGGGGTTTGGATAACTGATCAAGAA 60.222 40.000 0.00 0.00 36.12 2.52
1935 2042 4.290985 TGGGGTTTGGATAACTGATCAAGA 59.709 41.667 0.00 0.00 36.12 3.02
1936 2043 4.599041 TGGGGTTTGGATAACTGATCAAG 58.401 43.478 0.00 0.00 36.12 3.02
1937 2044 4.666412 TGGGGTTTGGATAACTGATCAA 57.334 40.909 0.00 0.00 36.12 2.57
1938 2045 4.879295 ATGGGGTTTGGATAACTGATCA 57.121 40.909 0.00 0.00 36.12 2.92
1939 2046 6.544928 AAAATGGGGTTTGGATAACTGATC 57.455 37.500 0.00 0.00 0.00 2.92
1940 2047 7.071071 CCATAAAATGGGGTTTGGATAACTGAT 59.929 37.037 0.00 0.00 46.86 2.90
1941 2048 6.382570 CCATAAAATGGGGTTTGGATAACTGA 59.617 38.462 0.00 0.00 46.86 3.41
1942 2049 6.581712 CCATAAAATGGGGTTTGGATAACTG 58.418 40.000 0.00 0.00 46.86 3.16
1943 2050 6.806668 CCATAAAATGGGGTTTGGATAACT 57.193 37.500 0.00 0.00 46.86 2.24
1957 2064 9.835389 AATTCCATGATGTTTACCCATAAAATG 57.165 29.630 0.00 0.00 32.04 2.32
1959 2066 8.482128 GGAATTCCATGATGTTTACCCATAAAA 58.518 33.333 20.04 0.00 32.24 1.52
1960 2067 7.843760 AGGAATTCCATGATGTTTACCCATAAA 59.156 33.333 26.22 0.00 38.89 1.40
1961 2068 7.361438 AGGAATTCCATGATGTTTACCCATAA 58.639 34.615 26.22 0.00 38.89 1.90
1962 2069 6.921412 AGGAATTCCATGATGTTTACCCATA 58.079 36.000 26.22 0.00 38.89 2.74
1963 2070 5.780731 AGGAATTCCATGATGTTTACCCAT 58.219 37.500 26.22 0.00 38.89 4.00
1964 2071 5.205517 AGGAATTCCATGATGTTTACCCA 57.794 39.130 26.22 0.00 38.89 4.51
1965 2072 5.682212 GCAAGGAATTCCATGATGTTTACCC 60.682 44.000 29.26 7.92 36.89 3.69
1966 2073 5.351458 GCAAGGAATTCCATGATGTTTACC 58.649 41.667 29.26 8.56 36.89 2.85
1967 2074 5.351458 GGCAAGGAATTCCATGATGTTTAC 58.649 41.667 29.26 12.05 36.89 2.01
1968 2075 4.405358 GGGCAAGGAATTCCATGATGTTTA 59.595 41.667 29.26 0.00 36.89 2.01
1969 2076 3.198417 GGGCAAGGAATTCCATGATGTTT 59.802 43.478 29.26 10.10 36.89 2.83
1970 2077 2.767960 GGGCAAGGAATTCCATGATGTT 59.232 45.455 29.26 10.80 36.89 2.71
1971 2078 2.292389 TGGGCAAGGAATTCCATGATGT 60.292 45.455 29.26 4.89 36.89 3.06
1972 2079 2.390696 TGGGCAAGGAATTCCATGATG 58.609 47.619 29.26 20.18 36.89 3.07
1973 2080 2.852714 TGGGCAAGGAATTCCATGAT 57.147 45.000 29.26 9.67 36.89 2.45
1974 2081 2.619697 TTGGGCAAGGAATTCCATGA 57.380 45.000 29.26 9.37 36.89 3.07
1975 2082 3.918294 ATTTGGGCAAGGAATTCCATG 57.082 42.857 26.22 24.31 37.74 3.66
1976 2083 4.594491 GGATATTTGGGCAAGGAATTCCAT 59.406 41.667 26.22 12.25 38.89 3.41
1977 2084 3.966665 GGATATTTGGGCAAGGAATTCCA 59.033 43.478 26.22 1.92 38.89 3.53
1978 2085 3.966665 TGGATATTTGGGCAAGGAATTCC 59.033 43.478 17.31 17.31 0.00 3.01
1979 2086 5.813513 ATGGATATTTGGGCAAGGAATTC 57.186 39.130 0.00 0.00 0.00 2.17
1980 2087 6.214005 CCATATGGATATTTGGGCAAGGAATT 59.786 38.462 17.49 0.00 37.39 2.17
1981 2088 5.722923 CCATATGGATATTTGGGCAAGGAAT 59.277 40.000 17.49 0.00 37.39 3.01
1982 2089 5.085920 CCATATGGATATTTGGGCAAGGAA 58.914 41.667 17.49 0.00 37.39 3.36
1983 2090 4.356492 TCCATATGGATATTTGGGCAAGGA 59.644 41.667 20.98 0.00 39.78 3.36
1984 2091 4.676109 TCCATATGGATATTTGGGCAAGG 58.324 43.478 20.98 0.00 39.78 3.61
1997 2104 8.148107 TGGCAACATGTACGTATCCATATGGA 62.148 42.308 26.49 26.49 46.76 3.41
1998 2105 4.391830 GGCAACATGTACGTATCCATATGG 59.608 45.833 16.25 16.25 0.00 2.74
1999 2106 4.994217 TGGCAACATGTACGTATCCATATG 59.006 41.667 0.00 0.00 46.17 1.78
2000 2107 5.222079 TGGCAACATGTACGTATCCATAT 57.778 39.130 0.00 0.00 46.17 1.78
2001 2108 4.674281 TGGCAACATGTACGTATCCATA 57.326 40.909 0.00 0.00 46.17 2.74
2002 2109 3.552132 TGGCAACATGTACGTATCCAT 57.448 42.857 0.00 0.00 46.17 3.41
2027 2134 6.835174 AGAACAAGTGGAGCATGATATACAT 58.165 36.000 0.00 0.00 40.17 2.29
2028 2135 6.239217 AGAACAAGTGGAGCATGATATACA 57.761 37.500 0.00 0.00 0.00 2.29
2029 2136 6.017605 CCAAGAACAAGTGGAGCATGATATAC 60.018 42.308 0.00 0.00 37.03 1.47
2030 2137 6.057533 CCAAGAACAAGTGGAGCATGATATA 58.942 40.000 0.00 0.00 37.03 0.86
2031 2138 4.885907 CCAAGAACAAGTGGAGCATGATAT 59.114 41.667 0.00 0.00 37.03 1.63
2032 2139 4.264253 CCAAGAACAAGTGGAGCATGATA 58.736 43.478 0.00 0.00 37.03 2.15
2033 2140 3.087031 CCAAGAACAAGTGGAGCATGAT 58.913 45.455 0.00 0.00 37.03 2.45
2034 2141 2.507484 CCAAGAACAAGTGGAGCATGA 58.493 47.619 0.00 0.00 37.03 3.07
2035 2142 1.542915 CCCAAGAACAAGTGGAGCATG 59.457 52.381 0.00 0.00 37.03 4.06
2036 2143 1.425066 TCCCAAGAACAAGTGGAGCAT 59.575 47.619 0.00 0.00 37.03 3.79
2037 2144 0.843309 TCCCAAGAACAAGTGGAGCA 59.157 50.000 0.00 0.00 37.03 4.26
2038 2145 1.882623 CTTCCCAAGAACAAGTGGAGC 59.117 52.381 0.00 0.00 37.03 4.70
2039 2146 2.106511 TCCTTCCCAAGAACAAGTGGAG 59.893 50.000 0.00 0.00 37.03 3.86
2040 2147 2.131854 TCCTTCCCAAGAACAAGTGGA 58.868 47.619 0.00 0.00 37.03 4.02
2041 2148 2.656947 TCCTTCCCAAGAACAAGTGG 57.343 50.000 0.00 0.00 34.44 4.00
2042 2149 6.653989 AGTATATCCTTCCCAAGAACAAGTG 58.346 40.000 0.00 0.00 0.00 3.16
2043 2150 6.126739 GGAGTATATCCTTCCCAAGAACAAGT 60.127 42.308 0.00 0.00 45.64 3.16
2044 2151 6.292150 GGAGTATATCCTTCCCAAGAACAAG 58.708 44.000 0.00 0.00 45.64 3.16
2045 2152 6.248569 GGAGTATATCCTTCCCAAGAACAA 57.751 41.667 0.00 0.00 45.64 2.83
2046 2153 5.888982 GGAGTATATCCTTCCCAAGAACA 57.111 43.478 0.00 0.00 45.64 3.18
2074 2181 9.573133 GGAAAGGAAAATGTGTTTATACATGAG 57.427 33.333 0.00 0.00 40.24 2.90
2075 2182 9.083422 TGGAAAGGAAAATGTGTTTATACATGA 57.917 29.630 0.00 0.00 40.24 3.07
2076 2183 9.874205 ATGGAAAGGAAAATGTGTTTATACATG 57.126 29.630 0.00 0.00 40.24 3.21
2078 2185 9.703892 CAATGGAAAGGAAAATGTGTTTATACA 57.296 29.630 0.00 0.00 34.63 2.29
2079 2186 9.150348 CCAATGGAAAGGAAAATGTGTTTATAC 57.850 33.333 0.00 0.00 0.00 1.47
2080 2187 8.875168 ACCAATGGAAAGGAAAATGTGTTTATA 58.125 29.630 6.16 0.00 0.00 0.98
2081 2188 7.744733 ACCAATGGAAAGGAAAATGTGTTTAT 58.255 30.769 6.16 0.00 0.00 1.40
2082 2189 7.070571 AGACCAATGGAAAGGAAAATGTGTTTA 59.929 33.333 6.16 0.00 0.00 2.01
2083 2190 6.000246 ACCAATGGAAAGGAAAATGTGTTT 58.000 33.333 6.16 0.00 0.00 2.83
2084 2191 5.366477 AGACCAATGGAAAGGAAAATGTGTT 59.634 36.000 6.16 0.00 0.00 3.32
2085 2192 4.901250 AGACCAATGGAAAGGAAAATGTGT 59.099 37.500 6.16 0.00 0.00 3.72
2086 2193 5.473066 AGACCAATGGAAAGGAAAATGTG 57.527 39.130 6.16 0.00 0.00 3.21
2087 2194 7.797121 AATAGACCAATGGAAAGGAAAATGT 57.203 32.000 6.16 0.00 0.00 2.71
2091 2198 9.540538 TGATTAAATAGACCAATGGAAAGGAAA 57.459 29.630 6.16 0.00 0.00 3.13
2092 2199 9.540538 TTGATTAAATAGACCAATGGAAAGGAA 57.459 29.630 6.16 0.00 0.00 3.36
2093 2200 9.540538 TTTGATTAAATAGACCAATGGAAAGGA 57.459 29.630 6.16 0.00 0.00 3.36
2120 2227 9.844257 AAAACAATGGAAAGGAAAATGTCATTA 57.156 25.926 0.00 0.00 27.90 1.90
2121 2228 8.750515 AAAACAATGGAAAGGAAAATGTCATT 57.249 26.923 0.00 0.00 0.00 2.57
2122 2229 8.750515 AAAAACAATGGAAAGGAAAATGTCAT 57.249 26.923 0.00 0.00 0.00 3.06
2183 2290 9.908152 GGTGTTTACATAAGCTAGAATGTTTTT 57.092 29.630 12.80 0.00 37.50 1.94
2184 2291 9.297037 AGGTGTTTACATAAGCTAGAATGTTTT 57.703 29.630 12.80 0.00 37.50 2.43
2185 2292 8.863872 AGGTGTTTACATAAGCTAGAATGTTT 57.136 30.769 12.80 0.00 37.50 2.83
2186 2293 7.277981 CGAGGTGTTTACATAAGCTAGAATGTT 59.722 37.037 12.80 0.00 37.50 2.71
2187 2294 6.757010 CGAGGTGTTTACATAAGCTAGAATGT 59.243 38.462 12.34 12.34 39.56 2.71
2188 2295 6.201044 CCGAGGTGTTTACATAAGCTAGAATG 59.799 42.308 0.00 0.00 0.00 2.67
2189 2296 6.127140 ACCGAGGTGTTTACATAAGCTAGAAT 60.127 38.462 0.00 0.00 0.00 2.40
2190 2297 5.186409 ACCGAGGTGTTTACATAAGCTAGAA 59.814 40.000 0.00 0.00 0.00 2.10
2191 2298 4.708421 ACCGAGGTGTTTACATAAGCTAGA 59.292 41.667 0.00 0.00 0.00 2.43
2192 2299 4.804139 CACCGAGGTGTTTACATAAGCTAG 59.196 45.833 13.82 0.00 40.91 3.42
2193 2300 4.751060 CACCGAGGTGTTTACATAAGCTA 58.249 43.478 13.82 0.00 40.91 3.32
2194 2301 3.596214 CACCGAGGTGTTTACATAAGCT 58.404 45.455 13.82 0.00 40.91 3.74
2212 2319 3.322828 TCTTACTGACAGGGTTGTACACC 59.677 47.826 7.51 0.02 46.46 4.16
2213 2320 4.595762 TCTTACTGACAGGGTTGTACAC 57.404 45.455 7.51 0.00 37.76 2.90
2214 2321 4.222145 GGATCTTACTGACAGGGTTGTACA 59.778 45.833 7.51 0.00 37.76 2.90
2215 2322 4.466726 AGGATCTTACTGACAGGGTTGTAC 59.533 45.833 7.51 0.00 37.76 2.90
2216 2323 4.466370 CAGGATCTTACTGACAGGGTTGTA 59.534 45.833 7.51 0.00 37.76 2.41
2217 2324 3.261897 CAGGATCTTACTGACAGGGTTGT 59.738 47.826 7.51 0.00 41.18 3.32
2218 2325 3.515502 TCAGGATCTTACTGACAGGGTTG 59.484 47.826 7.51 0.00 39.87 3.77
2219 2326 3.791320 TCAGGATCTTACTGACAGGGTT 58.209 45.455 7.51 0.00 39.87 4.11
2220 2327 3.474798 TCAGGATCTTACTGACAGGGT 57.525 47.619 7.51 0.00 39.87 4.34
2221 2328 5.144100 AGTATCAGGATCTTACTGACAGGG 58.856 45.833 7.51 0.00 46.67 4.45
2222 2329 8.303156 CAATAGTATCAGGATCTTACTGACAGG 58.697 40.741 7.51 0.00 46.67 4.00
2223 2330 8.855110 ACAATAGTATCAGGATCTTACTGACAG 58.145 37.037 0.00 0.00 46.67 3.51
2224 2331 8.768501 ACAATAGTATCAGGATCTTACTGACA 57.231 34.615 2.70 0.00 46.67 3.58
2225 2332 9.469807 CAACAATAGTATCAGGATCTTACTGAC 57.530 37.037 2.70 0.00 46.67 3.51
2227 2334 9.823647 AACAACAATAGTATCAGGATCTTACTG 57.176 33.333 0.00 0.00 37.30 2.74
2235 2342 9.391006 GGAATGTTAACAACAATAGTATCAGGA 57.609 33.333 13.23 0.00 45.86 3.86
2236 2343 8.335356 CGGAATGTTAACAACAATAGTATCAGG 58.665 37.037 13.23 0.00 45.86 3.86
2237 2344 8.335356 CCGGAATGTTAACAACAATAGTATCAG 58.665 37.037 13.23 1.84 45.86 2.90
2238 2345 7.825270 ACCGGAATGTTAACAACAATAGTATCA 59.175 33.333 13.23 0.00 45.86 2.15
2239 2346 8.205131 ACCGGAATGTTAACAACAATAGTATC 57.795 34.615 13.23 0.81 45.86 2.24
2240 2347 9.669887 TTACCGGAATGTTAACAACAATAGTAT 57.330 29.630 13.23 0.00 45.86 2.12
2241 2348 8.934825 GTTACCGGAATGTTAACAACAATAGTA 58.065 33.333 13.23 7.82 45.86 1.82
2242 2349 7.662669 AGTTACCGGAATGTTAACAACAATAGT 59.337 33.333 13.23 8.75 45.86 2.12
2243 2350 8.036273 AGTTACCGGAATGTTAACAACAATAG 57.964 34.615 13.23 3.12 45.86 1.73
2244 2351 7.982761 AGTTACCGGAATGTTAACAACAATA 57.017 32.000 13.23 0.00 45.86 1.90
2245 2352 6.887626 AGTTACCGGAATGTTAACAACAAT 57.112 33.333 13.23 0.00 45.86 2.71
2246 2353 6.204495 GGTAGTTACCGGAATGTTAACAACAA 59.796 38.462 13.23 0.00 39.77 2.83
2247 2354 5.700373 GGTAGTTACCGGAATGTTAACAACA 59.300 40.000 13.23 0.00 40.28 3.33
2248 2355 6.169419 GGTAGTTACCGGAATGTTAACAAC 57.831 41.667 13.23 9.72 36.50 3.32
2262 2369 2.935481 CTCGTCCACAGGTAGTTACC 57.065 55.000 0.00 0.00 46.82 2.85


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

AutoCloner maintained by Alex Coulton.