Multiple sequence alignment - TraesCS7B01G067200

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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 TraesCS7B01G067200 chr7B 100.000 3856 0 0 1 3856 72510927 72514782 0.000000e+00 7121.0
1 TraesCS7B01G067200 chr7B 85.831 1468 116 39 86 1496 72435291 72436723 0.000000e+00 1474.0
2 TraesCS7B01G067200 chr7B 92.486 865 52 6 2140 2992 72436982 72437845 0.000000e+00 1225.0
3 TraesCS7B01G067200 chr7B 88.000 300 36 0 3555 3854 105941044 105940745 4.740000e-94 355.0
4 TraesCS7B01G067200 chr7B 84.492 187 15 5 3388 3566 105941944 105941764 5.120000e-39 172.0
5 TraesCS7B01G067200 chr7A 86.420 1458 131 30 218 1631 118201713 118203147 0.000000e+00 1533.0
6 TraesCS7B01G067200 chr7A 83.980 799 92 26 2548 3320 118208275 118209063 0.000000e+00 734.0
7 TraesCS7B01G067200 chr7A 85.684 468 50 7 1617 2072 118207773 118208235 9.690000e-131 477.0
8 TraesCS7B01G067200 chr7A 91.875 160 12 1 10 168 118194620 118194779 5.010000e-54 222.0
9 TraesCS7B01G067200 chr7D 85.275 1365 125 28 1658 2992 112948519 112949837 0.000000e+00 1338.0
10 TraesCS7B01G067200 chr7D 91.055 872 67 7 2139 3000 112947620 112948490 0.000000e+00 1168.0
11 TraesCS7B01G067200 chr7D 91.803 793 53 10 2207 2992 113153598 113154385 0.000000e+00 1094.0
12 TraesCS7B01G067200 chr7D 88.915 848 70 10 2124 2971 113016044 113016867 0.000000e+00 1024.0
13 TraesCS7B01G067200 chr7D 88.591 859 59 18 2139 2991 112951631 112952456 0.000000e+00 1007.0
14 TraesCS7B01G067200 chr7D 82.149 1210 141 49 318 1496 112946257 112947422 0.000000e+00 968.0
15 TraesCS7B01G067200 chr7D 83.811 976 95 34 549 1496 112866641 112867581 0.000000e+00 869.0
16 TraesCS7B01G067200 chr7D 84.689 627 64 20 892 1496 113131865 113132481 7.130000e-167 597.0
17 TraesCS7B01G067200 chr7D 90.118 425 41 1 2139 2563 112867914 112868337 5.630000e-153 551.0
18 TraesCS7B01G067200 chr7D 84.615 559 48 19 3335 3856 420418065 420418622 4.410000e-144 521.0
19 TraesCS7B01G067200 chr7D 82.803 471 45 11 417 874 113131371 113131818 4.670000e-104 388.0
20 TraesCS7B01G067200 chr7D 87.291 299 23 6 1 287 112866156 112866451 1.030000e-85 327.0
21 TraesCS7B01G067200 chr7D 84.946 279 15 11 2737 2992 112868338 112868612 1.370000e-64 257.0
22 TraesCS7B01G067200 chr7D 90.667 75 4 2 213 287 113126072 113126143 3.170000e-16 97.1
23 TraesCS7B01G067200 chr7D 85.556 90 10 2 1634 1723 112947422 112947508 1.480000e-14 91.6
24 TraesCS7B01G067200 chr4B 87.242 533 52 10 3338 3856 665387484 665386954 9.220000e-166 593.0
25 TraesCS7B01G067200 chr4B 85.742 519 58 10 3352 3856 665432907 665433423 5.670000e-148 534.0
26 TraesCS7B01G067200 chr4B 90.789 304 28 0 3553 3856 146560825 146561128 1.290000e-109 407.0
27 TraesCS7B01G067200 chr4B 88.444 225 17 2 3331 3546 69293771 69293547 2.950000e-66 263.0
28 TraesCS7B01G067200 chr4B 87.037 216 21 4 3333 3546 559414142 559413932 1.790000e-58 237.0
29 TraesCS7B01G067200 chr4B 86.747 83 2 2 3449 3522 5410716 5410798 2.470000e-12 84.2
30 TraesCS7B01G067200 chr3D 87.194 531 56 7 3338 3856 550192765 550192235 9.220000e-166 593.0
31 TraesCS7B01G067200 chr3D 80.741 405 58 11 1485 1878 447574068 447573673 8.100000e-77 298.0
32 TraesCS7B01G067200 chr2D 80.000 670 103 22 2233 2876 413353538 413354202 2.100000e-127 466.0
33 TraesCS7B01G067200 chr2D 86.207 58 4 2 3493 3546 513541830 513541773 4.160000e-05 60.2
34 TraesCS7B01G067200 chr2A 79.970 669 103 21 2234 2876 580384923 580385586 7.550000e-127 464.0
35 TraesCS7B01G067200 chr2A 84.000 275 22 11 3334 3594 592344161 592344427 1.070000e-60 244.0
36 TraesCS7B01G067200 chr2A 92.982 57 4 0 764 820 580252235 580252291 2.470000e-12 84.2
37 TraesCS7B01G067200 chr2A 90.741 54 5 0 764 817 580322586 580322639 5.340000e-09 73.1
38 TraesCS7B01G067200 chr2B 79.701 670 105 22 2233 2876 486843651 486844315 4.540000e-124 455.0
39 TraesCS7B01G067200 chr2B 95.918 49 2 0 764 812 486585034 486585082 3.190000e-11 80.5
40 TraesCS7B01G067200 chr2B 90.741 54 5 0 764 817 486768920 486768973 5.340000e-09 73.1
41 TraesCS7B01G067200 chr6D 91.803 305 25 0 3552 3856 9533592 9533288 3.560000e-115 425.0
42 TraesCS7B01G067200 chr1B 96.761 247 8 0 1016 1262 60392265 60392019 2.770000e-111 412.0
43 TraesCS7B01G067200 chr1B 89.145 304 29 4 3555 3856 17248215 17248516 3.640000e-100 375.0
44 TraesCS7B01G067200 chr6B 88.158 304 36 0 3553 3856 716733541 716733844 2.830000e-96 363.0
45 TraesCS7B01G067200 chr3B 88.496 226 15 4 3338 3553 753516144 753515920 2.950000e-66 263.0
46 TraesCS7B01G067200 chr3B 86.842 228 15 6 3335 3553 761817965 761818186 1.380000e-59 241.0
47 TraesCS7B01G067200 chr5A 86.878 221 19 5 3334 3545 692158971 692158752 4.980000e-59 239.0
48 TraesCS7B01G067200 chr5D 76.829 164 23 9 1970 2123 351799541 351799383 1.150000e-10 78.7
49 TraesCS7B01G067200 chr3A 85.714 70 7 3 3477 3546 502084828 502084762 1.920000e-08 71.3
50 TraesCS7B01G067200 chr1A 95.238 42 2 0 1973 2014 449841675 449841634 2.490000e-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 TraesCS7B01G067200 chr7B 72510927 72514782 3855 False 7121.00 7121 100.0000 1 3856 1 chr7B.!!$F1 3855
1 TraesCS7B01G067200 chr7B 72435291 72437845 2554 False 1349.50 1474 89.1585 86 2992 2 chr7B.!!$F2 2906
2 TraesCS7B01G067200 chr7B 105940745 105941944 1199 True 263.50 355 86.2460 3388 3854 2 chr7B.!!$R1 466
3 TraesCS7B01G067200 chr7A 118201713 118203147 1434 False 1533.00 1533 86.4200 218 1631 1 chr7A.!!$F2 1413
4 TraesCS7B01G067200 chr7A 118207773 118209063 1290 False 605.50 734 84.8320 1617 3320 2 chr7A.!!$F3 1703
5 TraesCS7B01G067200 chr7D 113153598 113154385 787 False 1094.00 1094 91.8030 2207 2992 1 chr7D.!!$F3 785
6 TraesCS7B01G067200 chr7D 113016044 113016867 823 False 1024.00 1024 88.9150 2124 2971 1 chr7D.!!$F1 847
7 TraesCS7B01G067200 chr7D 112946257 112952456 6199 False 914.52 1338 86.5252 318 3000 5 chr7D.!!$F6 2682
8 TraesCS7B01G067200 chr7D 420418065 420418622 557 False 521.00 521 84.6150 3335 3856 1 chr7D.!!$F4 521
9 TraesCS7B01G067200 chr7D 112866156 112868612 2456 False 501.00 869 86.5415 1 2992 4 chr7D.!!$F5 2991
10 TraesCS7B01G067200 chr7D 113131371 113132481 1110 False 492.50 597 83.7460 417 1496 2 chr7D.!!$F7 1079
11 TraesCS7B01G067200 chr4B 665386954 665387484 530 True 593.00 593 87.2420 3338 3856 1 chr4B.!!$R3 518
12 TraesCS7B01G067200 chr4B 665432907 665433423 516 False 534.00 534 85.7420 3352 3856 1 chr4B.!!$F3 504
13 TraesCS7B01G067200 chr3D 550192235 550192765 530 True 593.00 593 87.1940 3338 3856 1 chr3D.!!$R2 518
14 TraesCS7B01G067200 chr2D 413353538 413354202 664 False 466.00 466 80.0000 2233 2876 1 chr2D.!!$F1 643
15 TraesCS7B01G067200 chr2A 580384923 580385586 663 False 464.00 464 79.9700 2234 2876 1 chr2A.!!$F3 642
16 TraesCS7B01G067200 chr2B 486843651 486844315 664 False 455.00 455 79.7010 2233 2876 1 chr2B.!!$F3 643

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
248 266 0.390603 TGGCCTCACGTATTTGGTCG 60.391 55.0 3.32 0.0 0.00 4.79 F
249 267 0.390735 GGCCTCACGTATTTGGTCGT 60.391 55.0 0.00 0.0 40.99 4.34 F
1530 1792 0.911769 TGGGGCTGAGATAACACAGG 59.088 55.0 0.00 0.0 35.75 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1792 0.250513 AATCCTCTGGAGTTGCGGTC 59.749 55.0 0.0 0.0 34.05 4.79 R
2036 2324 0.456653 AAAATTGCACGGATCGCAGC 60.457 50.0 0.0 0.0 41.18 5.25 R
3319 7728 0.036765 TATCAGTCACCCACAACCGC 60.037 55.0 0.0 0.0 0.00 5.68 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
34 36 3.134458 GAGATTCCGGAGTATTGGCTTG 58.866 50.000 3.34 0.00 0.00 4.01
35 37 2.158755 AGATTCCGGAGTATTGGCTTGG 60.159 50.000 3.34 0.00 0.00 3.61
43 45 4.137543 GGAGTATTGGCTTGGTATCCTTG 58.862 47.826 0.00 0.00 0.00 3.61
102 104 1.165907 TGCTGCGGAGGTTTGTCTTG 61.166 55.000 5.93 0.00 0.00 3.02
184 200 4.736165 CAGCAGGTTTGTTGGTGC 57.264 55.556 0.00 0.00 37.26 5.01
209 227 2.387445 TGCGTGCATTGCTACCGAC 61.387 57.895 10.49 0.00 0.00 4.79
211 229 2.798501 CGTGCATTGCTACCGACGG 61.799 63.158 13.61 13.61 0.00 4.79
246 264 1.280710 TGATGGCCTCACGTATTTGGT 59.719 47.619 3.32 0.00 0.00 3.67
248 266 0.390603 TGGCCTCACGTATTTGGTCG 60.391 55.000 3.32 0.00 0.00 4.79
249 267 0.390735 GGCCTCACGTATTTGGTCGT 60.391 55.000 0.00 0.00 40.99 4.34
250 268 0.997196 GCCTCACGTATTTGGTCGTC 59.003 55.000 0.00 0.00 38.23 4.20
251 269 1.265568 CCTCACGTATTTGGTCGTCG 58.734 55.000 0.00 0.00 38.23 5.12
337 425 3.005554 CACTGATCTGGCAAAACGAGAT 58.994 45.455 4.49 0.00 45.56 2.75
374 466 3.423154 CCAGCTTCGTCCGTTGGC 61.423 66.667 0.00 0.00 0.00 4.52
376 468 2.357517 AGCTTCGTCCGTTGGCTG 60.358 61.111 0.00 0.00 31.68 4.85
442 537 1.146358 GAAGCTAGCGTACGGCCAAG 61.146 60.000 18.39 10.48 45.17 3.61
547 663 5.068636 CACTTTATATCTGCCTGCCTTCAT 58.931 41.667 0.00 0.00 0.00 2.57
574 693 5.177511 CCGTATGTATAACCATCAAGCAGTG 59.822 44.000 0.00 0.00 0.00 3.66
596 743 1.223211 GCCCCTTCTTCCAGCTCTC 59.777 63.158 0.00 0.00 0.00 3.20
646 796 5.565509 TGTGGAAAATAGATACACCTTGCA 58.434 37.500 0.00 0.00 0.00 4.08
749 902 2.341101 GCGGAGAGGAAGACCGTCA 61.341 63.158 0.00 0.00 46.95 4.35
846 999 1.676746 CCCGACTCGAGAGGTAATGA 58.323 55.000 21.68 0.00 0.00 2.57
847 1000 2.231529 CCCGACTCGAGAGGTAATGAT 58.768 52.381 21.68 0.00 0.00 2.45
848 1001 3.409570 CCCGACTCGAGAGGTAATGATA 58.590 50.000 21.68 0.00 0.00 2.15
849 1002 4.011023 CCCGACTCGAGAGGTAATGATAT 58.989 47.826 21.68 0.00 0.00 1.63
853 1006 7.041916 CCCGACTCGAGAGGTAATGATATATAC 60.042 44.444 21.68 0.00 0.00 1.47
897 1079 1.487142 TCCAAAAGGTCGTGGTTCTCA 59.513 47.619 0.00 0.00 36.23 3.27
1048 1258 8.244113 CCTCTTGTTTCTTTTCTTAACACAACT 58.756 33.333 0.00 0.00 32.00 3.16
1075 1307 5.813080 TTAATTCTTCTTCTTTAGCCGCC 57.187 39.130 0.00 0.00 0.00 6.13
1269 1509 1.207329 GCACGGTAGGTCCAAGAGAAT 59.793 52.381 0.00 0.00 35.57 2.40
1270 1510 2.354805 GCACGGTAGGTCCAAGAGAATT 60.355 50.000 0.00 0.00 35.57 2.17
1317 1572 2.543861 GCGACCGATCATCTTTCTGCTA 60.544 50.000 0.00 0.00 0.00 3.49
1334 1589 3.450904 TGCTATGGTTCTCTAGGTGGTT 58.549 45.455 0.00 0.00 0.00 3.67
1355 1610 1.594833 CGGGGATTCGACAAGGTCA 59.405 57.895 0.00 0.00 32.09 4.02
1370 1625 3.290776 GTCATATGGACGGTGGAGC 57.709 57.895 2.13 0.00 36.65 4.70
1406 1664 1.915078 CGGCTCCCCCTTCATCACTT 61.915 60.000 0.00 0.00 0.00 3.16
1503 1765 7.714813 TCATCGAGAGGAAATTGCATAAATACA 59.285 33.333 0.00 0.00 0.00 2.29
1505 1767 6.821160 TCGAGAGGAAATTGCATAAATACACA 59.179 34.615 0.00 0.00 0.00 3.72
1507 1769 7.641411 CGAGAGGAAATTGCATAAATACACAAG 59.359 37.037 0.00 0.00 0.00 3.16
1520 1782 1.402787 ACACAAGTTTTGGGGCTGAG 58.597 50.000 0.00 0.00 38.76 3.35
1526 1788 3.806949 AGTTTTGGGGCTGAGATAACA 57.193 42.857 0.00 0.00 0.00 2.41
1530 1792 0.911769 TGGGGCTGAGATAACACAGG 59.088 55.000 0.00 0.00 35.75 4.00
1534 1796 1.471676 GGCTGAGATAACACAGGACCG 60.472 57.143 0.00 0.00 35.75 4.79
1569 1831 8.528044 AGGATTTTAACAGAAAACCACAACTA 57.472 30.769 0.00 0.00 34.82 2.24
1574 1836 2.092807 ACAGAAAACCACAACTACGGGT 60.093 45.455 0.00 0.00 36.19 5.28
1595 1857 4.084380 GGTCTAACCGGTTACAGAAAAACG 60.084 45.833 23.17 10.20 39.27 3.60
1599 1861 2.619646 ACCGGTTACAGAAAAACGCAAT 59.380 40.909 0.00 0.00 38.23 3.56
1601 1863 3.666797 CCGGTTACAGAAAAACGCAATTC 59.333 43.478 0.00 0.00 38.23 2.17
1608 1870 5.796279 CAGAAAAACGCAATTCTGTTCTC 57.204 39.130 13.54 0.00 44.72 2.87
1615 1877 3.673809 ACGCAATTCTGTTCTCGTTAGTC 59.326 43.478 0.00 0.00 0.00 2.59
1636 1898 9.871238 TTAGTCAGTTAAGGAGAATTATGACAC 57.129 33.333 0.00 0.00 38.57 3.67
1666 1928 7.554118 GGTTCAGTCTTAAATGATCAATCTGGA 59.446 37.037 0.00 0.00 0.00 3.86
1668 1930 8.728337 TCAGTCTTAAATGATCAATCTGGAAG 57.272 34.615 0.00 0.00 0.00 3.46
1709 1972 5.532779 GGCCAACCATTTAAAATTTGGACAA 59.467 36.000 21.43 0.00 43.80 3.18
1710 1973 6.208402 GGCCAACCATTTAAAATTTGGACAAT 59.792 34.615 21.43 3.07 43.80 2.71
1711 1974 7.255766 GGCCAACCATTTAAAATTTGGACAATT 60.256 33.333 21.43 3.29 43.80 2.32
1712 1975 8.140628 GCCAACCATTTAAAATTTGGACAATTT 58.859 29.630 21.43 3.01 39.33 1.82
1748 2011 8.757164 ATCGGTCAAATTTTGTTAAAGAATCC 57.243 30.769 8.89 0.38 0.00 3.01
1751 2014 8.821894 CGGTCAAATTTTGTTAAAGAATCCAAA 58.178 29.630 8.89 0.00 0.00 3.28
1794 2071 8.641499 TCTGAAAAACATGTTAAATGGTCAAC 57.359 30.769 12.39 0.00 0.00 3.18
1795 2072 8.253810 TCTGAAAAACATGTTAAATGGTCAACA 58.746 29.630 12.39 1.01 38.89 3.33
1802 2079 5.461032 TGTTAAATGGTCAACATGGGAAC 57.539 39.130 0.00 0.00 40.44 3.62
1823 2100 3.645687 ACTTTTCAGCCAATTTAGCCCAA 59.354 39.130 0.00 0.00 0.00 4.12
1836 2113 7.361971 CCAATTTAGCCCAACCATTTGAAATTC 60.362 37.037 0.00 0.00 34.24 2.17
1847 2124 5.752955 ACCATTTGAAATTCGGACAGTTTTG 59.247 36.000 1.74 0.00 0.00 2.44
1859 2147 6.161381 TCGGACAGTTTTGGTAAGATAGAAC 58.839 40.000 0.00 0.00 0.00 3.01
1862 2150 7.159372 GGACAGTTTTGGTAAGATAGAACTGA 58.841 38.462 17.74 0.00 43.95 3.41
1872 2160 9.529325 TGGTAAGATAGAACTGATTAATTCGTG 57.471 33.333 0.00 0.00 0.00 4.35
1900 2188 5.825593 ACTGATTAGTCCTGGAGTTTTGA 57.174 39.130 9.76 0.00 28.79 2.69
1927 2215 6.062258 TCTGTTAAAATCCCCTAGAGTTGG 57.938 41.667 0.00 0.00 31.94 3.77
1945 2233 1.133730 TGGGGTTTGGTGTTACCTCAC 60.134 52.381 0.00 0.00 39.96 3.51
1950 2238 2.105993 GTTTGGTGTTACCTCACTCCCT 59.894 50.000 0.00 0.00 39.58 4.20
1951 2239 1.348064 TGGTGTTACCTCACTCCCTG 58.652 55.000 0.00 0.00 39.58 4.45
1952 2240 1.349067 GGTGTTACCTCACTCCCTGT 58.651 55.000 0.00 0.00 38.28 4.00
1962 2250 3.769844 CCTCACTCCCTGTAGTTGTGTAT 59.230 47.826 0.00 0.00 0.00 2.29
1963 2251 4.223032 CCTCACTCCCTGTAGTTGTGTATT 59.777 45.833 0.00 0.00 0.00 1.89
1964 2252 5.280011 CCTCACTCCCTGTAGTTGTGTATTT 60.280 44.000 0.00 0.00 0.00 1.40
1965 2253 5.547465 TCACTCCCTGTAGTTGTGTATTTG 58.453 41.667 0.00 0.00 0.00 2.32
1966 2254 5.071250 TCACTCCCTGTAGTTGTGTATTTGT 59.929 40.000 0.00 0.00 0.00 2.83
1967 2255 5.179368 CACTCCCTGTAGTTGTGTATTTGTG 59.821 44.000 0.00 0.00 0.00 3.33
1968 2256 4.069304 TCCCTGTAGTTGTGTATTTGTGC 58.931 43.478 0.00 0.00 0.00 4.57
1969 2257 3.818210 CCCTGTAGTTGTGTATTTGTGCA 59.182 43.478 0.00 0.00 0.00 4.57
1970 2258 4.277174 CCCTGTAGTTGTGTATTTGTGCAA 59.723 41.667 0.00 0.00 0.00 4.08
1971 2259 5.212194 CCTGTAGTTGTGTATTTGTGCAAC 58.788 41.667 0.00 0.00 40.83 4.17
1986 2274 5.261209 TGTGCAACAGTTTTGCTAAATCT 57.739 34.783 14.69 0.00 45.67 2.40
1987 2275 5.280945 TGTGCAACAGTTTTGCTAAATCTC 58.719 37.500 14.69 0.00 45.67 2.75
1988 2276 5.163571 TGTGCAACAGTTTTGCTAAATCTCA 60.164 36.000 14.69 1.64 45.67 3.27
1989 2277 5.400485 GTGCAACAGTTTTGCTAAATCTCAG 59.600 40.000 14.69 0.00 45.13 3.35
1990 2278 5.067674 TGCAACAGTTTTGCTAAATCTCAGT 59.932 36.000 14.69 0.00 45.13 3.41
1991 2279 5.626955 GCAACAGTTTTGCTAAATCTCAGTC 59.373 40.000 6.75 0.00 41.87 3.51
1992 2280 5.597813 ACAGTTTTGCTAAATCTCAGTCG 57.402 39.130 0.00 0.00 0.00 4.18
1993 2281 5.297547 ACAGTTTTGCTAAATCTCAGTCGA 58.702 37.500 0.00 0.00 0.00 4.20
1994 2282 5.177696 ACAGTTTTGCTAAATCTCAGTCGAC 59.822 40.000 7.70 7.70 0.00 4.20
1995 2283 4.691216 AGTTTTGCTAAATCTCAGTCGACC 59.309 41.667 13.01 0.00 0.00 4.79
1996 2284 2.561733 TGCTAAATCTCAGTCGACCG 57.438 50.000 13.01 1.05 0.00 4.79
1997 2285 2.089201 TGCTAAATCTCAGTCGACCGA 58.911 47.619 13.01 6.63 0.00 4.69
1998 2286 2.097629 TGCTAAATCTCAGTCGACCGAG 59.902 50.000 20.59 20.59 0.00 4.63
1999 2287 2.355132 GCTAAATCTCAGTCGACCGAGA 59.645 50.000 28.64 28.64 42.25 4.04
2000 2288 2.923605 AAATCTCAGTCGACCGAGAC 57.076 50.000 28.97 0.00 40.92 3.36
2022 2310 4.631813 ACTTCATTAAGTCTCGGTTGATGC 59.368 41.667 0.00 0.00 42.42 3.91
2023 2311 4.200838 TCATTAAGTCTCGGTTGATGCA 57.799 40.909 0.00 0.00 0.00 3.96
2024 2312 4.574892 TCATTAAGTCTCGGTTGATGCAA 58.425 39.130 0.00 0.00 0.00 4.08
2025 2313 5.185454 TCATTAAGTCTCGGTTGATGCAAT 58.815 37.500 0.00 0.00 0.00 3.56
2026 2314 4.944962 TTAAGTCTCGGTTGATGCAATG 57.055 40.909 0.00 0.00 0.00 2.82
2027 2315 2.768253 AGTCTCGGTTGATGCAATGA 57.232 45.000 0.00 0.00 0.00 2.57
2028 2316 2.625737 AGTCTCGGTTGATGCAATGAG 58.374 47.619 0.00 0.00 33.26 2.90
2029 2317 2.234661 AGTCTCGGTTGATGCAATGAGA 59.765 45.455 0.00 9.53 36.29 3.27
2030 2318 3.118482 AGTCTCGGTTGATGCAATGAGAT 60.118 43.478 14.06 5.60 38.73 2.75
2031 2319 3.247173 GTCTCGGTTGATGCAATGAGATC 59.753 47.826 14.06 0.00 38.73 2.75
2032 2320 3.133542 TCTCGGTTGATGCAATGAGATCT 59.866 43.478 0.00 0.00 34.90 2.75
2033 2321 3.875727 CTCGGTTGATGCAATGAGATCTT 59.124 43.478 0.00 0.00 33.56 2.40
2034 2322 5.022282 TCGGTTGATGCAATGAGATCTTA 57.978 39.130 0.00 0.00 0.00 2.10
2035 2323 5.614308 TCGGTTGATGCAATGAGATCTTAT 58.386 37.500 0.00 0.00 0.00 1.73
2036 2324 5.467735 TCGGTTGATGCAATGAGATCTTATG 59.532 40.000 0.00 0.22 0.00 1.90
2037 2325 5.458891 GGTTGATGCAATGAGATCTTATGC 58.541 41.667 16.84 16.84 0.00 3.14
2038 2326 5.241064 GGTTGATGCAATGAGATCTTATGCT 59.759 40.000 21.43 11.91 0.00 3.79
2039 2327 5.941948 TGATGCAATGAGATCTTATGCTG 57.058 39.130 21.43 10.79 0.00 4.41
2040 2328 4.215613 TGATGCAATGAGATCTTATGCTGC 59.784 41.667 21.43 18.08 0.00 5.25
2041 2329 2.546789 TGCAATGAGATCTTATGCTGCG 59.453 45.455 21.43 4.29 0.00 5.18
2042 2330 2.804527 GCAATGAGATCTTATGCTGCGA 59.195 45.455 16.56 0.00 0.00 5.10
2043 2331 3.436015 GCAATGAGATCTTATGCTGCGAT 59.564 43.478 16.56 0.00 0.00 4.58
2044 2332 4.435784 GCAATGAGATCTTATGCTGCGATC 60.436 45.833 16.56 7.03 35.06 3.69
2045 2333 3.309961 TGAGATCTTATGCTGCGATCC 57.690 47.619 10.38 4.97 35.34 3.36
2046 2334 2.257894 GAGATCTTATGCTGCGATCCG 58.742 52.381 10.38 0.00 35.34 4.18
2047 2335 1.615883 AGATCTTATGCTGCGATCCGT 59.384 47.619 10.38 0.00 35.34 4.69
2048 2336 1.723542 GATCTTATGCTGCGATCCGTG 59.276 52.381 4.51 0.00 0.00 4.94
2049 2337 0.875908 TCTTATGCTGCGATCCGTGC 60.876 55.000 0.00 0.00 0.00 5.34
2050 2338 1.153469 TTATGCTGCGATCCGTGCA 60.153 52.632 10.22 10.22 40.68 4.57
2051 2339 0.742635 TTATGCTGCGATCCGTGCAA 60.743 50.000 11.36 0.00 42.70 4.08
2052 2340 0.532640 TATGCTGCGATCCGTGCAAT 60.533 50.000 11.36 0.00 42.70 3.56
2053 2341 1.378882 ATGCTGCGATCCGTGCAATT 61.379 50.000 11.36 0.00 42.70 2.32
2054 2342 1.137404 GCTGCGATCCGTGCAATTT 59.863 52.632 0.00 0.00 42.70 1.82
2055 2343 0.456653 GCTGCGATCCGTGCAATTTT 60.457 50.000 0.00 0.00 42.70 1.82
2056 2344 1.981254 CTGCGATCCGTGCAATTTTT 58.019 45.000 0.00 0.00 42.70 1.94
2111 2399 7.823745 ATTTGTCACTTTATTGAGACTTGGT 57.176 32.000 0.00 0.00 32.41 3.67
2112 2400 7.639113 TTTGTCACTTTATTGAGACTTGGTT 57.361 32.000 0.00 0.00 32.41 3.67
2113 2401 8.740123 TTTGTCACTTTATTGAGACTTGGTTA 57.260 30.769 0.00 0.00 32.41 2.85
2114 2402 8.740123 TTGTCACTTTATTGAGACTTGGTTAA 57.260 30.769 0.00 0.00 32.41 2.01
2115 2403 8.740123 TGTCACTTTATTGAGACTTGGTTAAA 57.260 30.769 0.00 0.00 32.41 1.52
2116 2404 8.617809 TGTCACTTTATTGAGACTTGGTTAAAC 58.382 33.333 0.00 0.00 32.41 2.01
2117 2405 8.074370 GTCACTTTATTGAGACTTGGTTAAACC 58.926 37.037 0.00 0.00 39.22 3.27
2118 2406 7.996644 TCACTTTATTGAGACTTGGTTAAACCT 59.003 33.333 0.00 0.00 39.58 3.50
2119 2407 8.290325 CACTTTATTGAGACTTGGTTAAACCTC 58.710 37.037 0.00 0.00 39.58 3.85
2120 2408 7.996644 ACTTTATTGAGACTTGGTTAAACCTCA 59.003 33.333 0.00 0.00 39.58 3.86
2121 2409 7.979444 TTATTGAGACTTGGTTAAACCTCAG 57.021 36.000 0.00 0.00 39.58 3.35
2122 2410 5.367945 TTGAGACTTGGTTAAACCTCAGT 57.632 39.130 0.00 0.00 39.58 3.41
2126 2414 4.163458 AGACTTGGTTAAACCTCAGTGACA 59.837 41.667 0.00 0.00 39.58 3.58
2135 2423 2.191400 ACCTCAGTGACATAGCCACAT 58.809 47.619 0.00 0.00 37.01 3.21
2137 2425 2.433604 CCTCAGTGACATAGCCACATCT 59.566 50.000 0.00 0.00 37.01 2.90
2319 2608 3.864686 GCATGAACGCGACGGCAT 61.865 61.111 15.93 7.54 39.92 4.40
2371 2660 0.824109 CATGCCTACTGGAACCTCGA 59.176 55.000 0.00 0.00 34.57 4.04
2573 4262 5.357257 GTCAATGGGTACGACATCAACTAT 58.643 41.667 2.63 0.00 0.00 2.12
2588 6898 1.216977 CTATGTTGTGGACGGCGGA 59.783 57.895 13.24 0.00 0.00 5.54
2753 7070 4.074526 GCGCTCTGCCTGGAGACA 62.075 66.667 0.00 0.00 37.76 3.41
2909 7258 1.146041 TCAGGCAACACAGTCGCTT 59.854 52.632 0.00 0.00 41.41 4.68
3065 7428 3.334583 TGCACTATGGGTCACTCTTTC 57.665 47.619 0.00 0.00 0.00 2.62
3066 7429 2.637382 TGCACTATGGGTCACTCTTTCA 59.363 45.455 0.00 0.00 0.00 2.69
3067 7430 3.072330 TGCACTATGGGTCACTCTTTCAA 59.928 43.478 0.00 0.00 0.00 2.69
3068 7431 4.072131 GCACTATGGGTCACTCTTTCAAA 58.928 43.478 0.00 0.00 0.00 2.69
3069 7432 4.518970 GCACTATGGGTCACTCTTTCAAAA 59.481 41.667 0.00 0.00 0.00 2.44
3070 7433 5.009610 GCACTATGGGTCACTCTTTCAAAAA 59.990 40.000 0.00 0.00 0.00 1.94
3111 7517 2.751166 ACTGCACTATGTGTCACTCC 57.249 50.000 4.27 0.00 35.75 3.85
3112 7518 1.067565 ACTGCACTATGTGTCACTCCG 60.068 52.381 4.27 0.00 35.75 4.63
3121 7529 1.965930 TGTCACTCCGGCATGCAAC 60.966 57.895 21.36 1.35 0.00 4.17
3135 7543 0.867746 TGCAACATCGTCACTGCTTC 59.132 50.000 0.00 0.00 35.78 3.86
3137 7545 1.136141 GCAACATCGTCACTGCTTCAG 60.136 52.381 0.00 0.00 37.52 3.02
3151 7559 1.228094 TTCAGCAACCACGGCATGA 60.228 52.632 0.00 0.00 0.00 3.07
3152 7560 0.608856 TTCAGCAACCACGGCATGAT 60.609 50.000 0.00 0.00 0.00 2.45
3199 7607 2.527624 AGGACCACCTCTGCTGCA 60.528 61.111 0.88 0.88 44.13 4.41
3201 7609 1.001641 GGACCACCTCTGCTGCAAT 60.002 57.895 3.02 0.00 0.00 3.56
3202 7610 0.610232 GGACCACCTCTGCTGCAATT 60.610 55.000 3.02 0.00 0.00 2.32
3207 7615 1.000521 CCTCTGCTGCAATTCCCCA 60.001 57.895 3.02 0.00 0.00 4.96
3209 7617 1.481871 CTCTGCTGCAATTCCCCATT 58.518 50.000 3.02 0.00 0.00 3.16
3222 7630 4.465512 CCATTGTCGCAGCACCGC 62.466 66.667 0.00 0.00 0.00 5.68
3223 7631 4.465512 CATTGTCGCAGCACCGCC 62.466 66.667 0.00 0.00 0.00 6.13
3247 7655 0.235665 CTGCAAGCGACGTTTGTGAT 59.764 50.000 22.71 0.00 0.00 3.06
3253 7661 1.154672 CGACGTTTGTGATGGTGCG 60.155 57.895 0.00 0.00 0.00 5.34
3254 7662 1.206578 GACGTTTGTGATGGTGCGG 59.793 57.895 0.00 0.00 0.00 5.69
3270 7678 1.747367 CGGCCATCAACGCCCTTTA 60.747 57.895 2.24 0.00 43.98 1.85
3292 7701 2.195567 AGTGCCGTTGTGCTGCAAT 61.196 52.632 2.77 0.00 38.99 3.56
3293 7702 2.017783 GTGCCGTTGTGCTGCAATG 61.018 57.895 2.77 0.00 38.99 2.82
3294 7703 2.192187 TGCCGTTGTGCTGCAATGA 61.192 52.632 2.77 0.00 44.68 2.57
3316 7725 3.159984 GCGAGGTGCGACAAGAAG 58.840 61.111 0.00 0.00 44.57 2.85
3317 7726 3.016474 GCGAGGTGCGACAAGAAGC 62.016 63.158 0.00 0.00 44.57 3.86
3318 7727 1.373497 CGAGGTGCGACAAGAAGCT 60.373 57.895 0.00 0.00 44.57 3.74
3319 7728 1.621301 CGAGGTGCGACAAGAAGCTG 61.621 60.000 0.00 0.00 44.57 4.24
3320 7729 1.905922 GAGGTGCGACAAGAAGCTGC 61.906 60.000 0.00 0.00 36.08 5.25
3321 7730 2.171940 GTGCGACAAGAAGCTGCG 59.828 61.111 0.00 0.00 0.00 5.18
3322 7731 3.043713 TGCGACAAGAAGCTGCGG 61.044 61.111 0.00 0.00 0.00 5.69
3323 7732 3.044305 GCGACAAGAAGCTGCGGT 61.044 61.111 0.00 0.00 0.00 5.68
3324 7733 2.607892 GCGACAAGAAGCTGCGGTT 61.608 57.895 0.00 0.00 0.00 4.44
3325 7734 1.205064 CGACAAGAAGCTGCGGTTG 59.795 57.895 9.24 9.24 0.00 3.77
3326 7735 1.498865 CGACAAGAAGCTGCGGTTGT 61.499 55.000 14.37 14.37 35.84 3.32
3327 7736 0.040958 GACAAGAAGCTGCGGTTGTG 60.041 55.000 17.86 6.87 33.30 3.33
3328 7737 1.283793 CAAGAAGCTGCGGTTGTGG 59.716 57.895 0.00 0.00 0.00 4.17
3329 7738 1.898574 AAGAAGCTGCGGTTGTGGG 60.899 57.895 0.00 0.00 0.00 4.61
3330 7739 2.594592 GAAGCTGCGGTTGTGGGT 60.595 61.111 0.00 0.00 0.00 4.51
3331 7740 2.906897 AAGCTGCGGTTGTGGGTG 60.907 61.111 0.00 0.00 0.00 4.61
3332 7741 3.414136 AAGCTGCGGTTGTGGGTGA 62.414 57.895 0.00 0.00 0.00 4.02
3333 7742 3.660111 GCTGCGGTTGTGGGTGAC 61.660 66.667 0.00 0.00 0.00 3.67
3336 7745 2.110213 GCGGTTGTGGGTGACTGA 59.890 61.111 0.00 0.00 0.00 3.41
3359 7768 7.500992 TGATAGACTATTCCTTGGATCACAAC 58.499 38.462 0.00 0.00 34.76 3.32
3377 7786 3.640029 ACAACTTTCCTAGTCCAAGTCGA 59.360 43.478 0.33 0.00 35.54 4.20
3546 7966 3.839432 GCCCGGCTACTTCGAGCT 61.839 66.667 0.71 0.00 42.43 4.09
3581 8757 0.038599 ATCAGTGCCTCACATGCCAA 59.961 50.000 0.00 0.00 36.74 4.52
3687 8864 0.033011 ATCTATAGGCCGCCCTCGAT 60.033 55.000 5.55 0.52 41.75 3.59
3715 8892 3.691342 CCTCCTTCGACACCGCCA 61.691 66.667 0.00 0.00 35.37 5.69
3749 8927 4.504916 CGGCTCCGAGTGCTCCAG 62.505 72.222 1.35 0.00 42.83 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.721021 ACTCCGGAATCTCCTTTTCCTA 58.279 45.455 5.23 0.00 40.46 2.94
18 20 1.868713 TACCAAGCCAATACTCCGGA 58.131 50.000 2.93 2.93 0.00 5.14
20 22 2.368875 AGGATACCAAGCCAATACTCCG 59.631 50.000 0.00 0.00 31.71 4.63
34 36 6.894339 TTCTTTTGAAACCTCAAGGATACC 57.106 37.500 2.30 0.00 42.48 2.73
35 37 9.249457 CTTTTTCTTTTGAAACCTCAAGGATAC 57.751 33.333 2.30 0.00 46.80 2.24
43 45 8.317891 TGGTTTTCTTTTTCTTTTGAAACCTC 57.682 30.769 14.04 0.00 46.80 3.85
121 123 1.139163 GTTTTTGTTGGATGCAGGCG 58.861 50.000 0.00 0.00 0.00 5.52
184 200 2.369629 GCAATGCACGCACAAGCTG 61.370 57.895 0.00 0.00 39.10 4.24
209 227 1.210931 CAGGCAAAGCATGTGACCG 59.789 57.895 0.00 0.00 22.06 4.79
211 229 1.135199 CCATCAGGCAAAGCATGTGAC 60.135 52.381 3.51 0.00 41.32 3.67
246 264 2.035449 AGACAAAGGATGTGAACGACGA 59.965 45.455 0.00 0.00 44.12 4.20
248 266 3.131396 ACAGACAAAGGATGTGAACGAC 58.869 45.455 0.00 0.00 44.12 4.34
249 267 3.469008 ACAGACAAAGGATGTGAACGA 57.531 42.857 0.00 0.00 44.12 3.85
250 268 3.058914 GGAACAGACAAAGGATGTGAACG 60.059 47.826 0.00 0.00 44.12 3.95
251 269 3.058914 CGGAACAGACAAAGGATGTGAAC 60.059 47.826 0.00 0.00 44.12 3.18
337 425 4.030216 TGGTCTGGATTGTAGCTCATGTA 58.970 43.478 0.00 0.00 0.00 2.29
374 466 2.712057 CAGCCTTACTTTGGTTGCAG 57.288 50.000 0.00 0.00 0.00 4.41
401 493 2.311688 CTTCGCCGGTGCCTATCCTT 62.312 60.000 11.05 0.00 0.00 3.36
442 537 2.791396 TACTCCTCGTGACGCGCAAC 62.791 60.000 5.73 3.36 41.07 4.17
547 663 5.163395 TGCTTGATGGTTATACATACGGACA 60.163 40.000 0.00 0.00 0.00 4.02
574 693 2.356667 CTGGAAGAAGGGGCCACC 59.643 66.667 0.00 0.57 34.07 4.61
596 743 0.036732 TGTCACCTTAGCAGCCAAGG 59.963 55.000 17.34 17.34 46.74 3.61
629 776 9.590451 CATTTTCATTGCAAGGTGTATCTATTT 57.410 29.630 11.36 0.00 0.00 1.40
730 883 2.035940 ACGGTCTTCCTCTCCGCT 59.964 61.111 2.72 0.00 46.92 5.52
733 886 0.528470 CACTGACGGTCTTCCTCTCC 59.472 60.000 9.88 0.00 0.00 3.71
749 902 2.545952 CCTTGTTGAGCTCGTACACACT 60.546 50.000 17.99 0.00 0.00 3.55
846 999 6.807230 GGAAGAAGCGTGTCATTCGTATATAT 59.193 38.462 0.00 0.00 0.00 0.86
847 1000 6.016527 AGGAAGAAGCGTGTCATTCGTATATA 60.017 38.462 0.00 0.00 0.00 0.86
848 1001 4.982916 GGAAGAAGCGTGTCATTCGTATAT 59.017 41.667 0.00 0.00 0.00 0.86
849 1002 4.097437 AGGAAGAAGCGTGTCATTCGTATA 59.903 41.667 0.00 0.00 0.00 1.47
853 1006 1.714794 AGGAAGAAGCGTGTCATTCG 58.285 50.000 0.00 0.00 0.00 3.34
914 1103 3.960102 AGAAGAGTGAGATCCCAGATCAC 59.040 47.826 7.30 4.32 42.91 3.06
965 1162 1.496060 ATCGTAGCCCAGGATCACAA 58.504 50.000 0.00 0.00 0.00 3.33
1048 1258 7.590279 CGGCTAAAGAAGAAGAATTAAACCAA 58.410 34.615 0.00 0.00 0.00 3.67
1075 1307 5.541008 CAAAAGCAGAAACAAACTTTGTCG 58.459 37.500 7.62 0.00 44.59 4.35
1108 1340 1.840630 GCACATGCACAGTACGCACA 61.841 55.000 0.00 0.00 43.35 4.57
1219 1455 2.734755 TGCCATCATTAGGAACCAGG 57.265 50.000 0.00 0.00 0.00 4.45
1228 1464 3.243035 GCAGCGTGTTATTGCCATCATTA 60.243 43.478 0.00 0.00 31.79 1.90
1231 1467 0.451383 GCAGCGTGTTATTGCCATCA 59.549 50.000 0.00 0.00 31.79 3.07
1270 1510 5.513267 GCTCTTAGGAACCAGGAGAGAAAAA 60.513 44.000 16.41 0.00 36.77 1.94
1284 1530 0.963856 TCGGTCGCAGCTCTTAGGAA 60.964 55.000 0.00 0.00 0.00 3.36
1317 1572 2.764572 CGGTAACCACCTAGAGAACCAT 59.235 50.000 0.00 0.00 43.33 3.55
1334 1589 0.615544 ACCTTGTCGAATCCCCGGTA 60.616 55.000 0.00 0.00 0.00 4.02
1355 1610 1.337384 TGCTGCTCCACCGTCCATAT 61.337 55.000 0.00 0.00 0.00 1.78
1388 1646 0.332972 AAAGTGATGAAGGGGGAGCC 59.667 55.000 0.00 0.00 0.00 4.70
1406 1664 3.562973 CCGTCGAAGCTATGGTAGTAGAA 59.437 47.826 0.00 0.00 0.00 2.10
1503 1765 2.683211 ATCTCAGCCCCAAAACTTGT 57.317 45.000 0.00 0.00 0.00 3.16
1505 1767 3.826729 GTGTTATCTCAGCCCCAAAACTT 59.173 43.478 0.00 0.00 0.00 2.66
1507 1769 3.153919 TGTGTTATCTCAGCCCCAAAAC 58.846 45.455 0.00 0.00 0.00 2.43
1520 1782 2.000447 GAGTTGCGGTCCTGTGTTATC 59.000 52.381 0.00 0.00 0.00 1.75
1526 1788 1.821061 CTCTGGAGTTGCGGTCCTGT 61.821 60.000 0.99 0.00 35.19 4.00
1530 1792 0.250513 AATCCTCTGGAGTTGCGGTC 59.749 55.000 0.00 0.00 34.05 4.79
1534 1796 5.003804 TCTGTTAAAATCCTCTGGAGTTGC 58.996 41.667 0.00 0.00 39.17 4.17
1569 1831 0.890683 CTGTAACCGGTTAGACCCGT 59.109 55.000 27.20 1.24 46.66 5.28
1574 1836 3.494251 GCGTTTTTCTGTAACCGGTTAGA 59.506 43.478 27.20 24.27 0.00 2.10
1588 1850 4.279659 ACGAGAACAGAATTGCGTTTTTC 58.720 39.130 0.00 0.00 0.00 2.29
1595 1857 4.686554 ACTGACTAACGAGAACAGAATTGC 59.313 41.667 0.00 0.00 35.88 3.56
1599 1861 6.263842 TCCTTAACTGACTAACGAGAACAGAA 59.736 38.462 0.00 0.00 35.88 3.02
1601 1863 6.010294 TCCTTAACTGACTAACGAGAACAG 57.990 41.667 0.00 0.00 37.00 3.16
1608 1870 9.021863 GTCATAATTCTCCTTAACTGACTAACG 57.978 37.037 0.00 0.00 31.42 3.18
1615 1877 6.036083 CCACGTGTCATAATTCTCCTTAACTG 59.964 42.308 15.65 0.00 0.00 3.16
1636 1898 4.935205 TGATCATTTAAGACTGAACCCACG 59.065 41.667 0.00 0.00 0.00 4.94
1712 1975 9.372369 ACAAAATTTGACCGATTCTTACAAAAA 57.628 25.926 13.19 0.00 34.86 1.94
1768 2031 9.260002 GTTGACCATTTAACATGTTTTTCAGAT 57.740 29.630 17.78 0.00 0.00 2.90
1769 2032 8.253810 TGTTGACCATTTAACATGTTTTTCAGA 58.746 29.630 17.78 0.00 32.30 3.27
1770 2033 8.417780 TGTTGACCATTTAACATGTTTTTCAG 57.582 30.769 17.78 6.26 32.30 3.02
1771 2034 8.954950 ATGTTGACCATTTAACATGTTTTTCA 57.045 26.923 17.78 7.71 43.66 2.69
1782 2059 6.739331 AAAGTTCCCATGTTGACCATTTAA 57.261 33.333 0.00 0.00 0.00 1.52
1789 2066 3.552890 GGCTGAAAAGTTCCCATGTTGAC 60.553 47.826 0.00 0.00 0.00 3.18
1794 2071 3.967332 ATTGGCTGAAAAGTTCCCATG 57.033 42.857 0.00 0.00 0.00 3.66
1795 2072 4.980339 AAATTGGCTGAAAAGTTCCCAT 57.020 36.364 0.00 0.00 0.00 4.00
1800 2077 3.645687 TGGGCTAAATTGGCTGAAAAGTT 59.354 39.130 0.56 0.00 0.00 2.66
1802 2079 3.959535 TGGGCTAAATTGGCTGAAAAG 57.040 42.857 0.56 0.00 0.00 2.27
1823 2100 5.529581 AAACTGTCCGAATTTCAAATGGT 57.470 34.783 0.00 0.00 0.00 3.55
1836 2113 6.090898 CAGTTCTATCTTACCAAAACTGTCCG 59.909 42.308 0.00 0.00 39.00 4.79
1847 2124 9.530633 ACACGAATTAATCAGTTCTATCTTACC 57.469 33.333 0.00 0.00 0.00 2.85
1865 2153 8.504005 CAGGACTAATCAGTAAAAACACGAATT 58.496 33.333 0.00 0.00 34.21 2.17
1866 2154 7.119262 CCAGGACTAATCAGTAAAAACACGAAT 59.881 37.037 0.00 0.00 34.21 3.34
1867 2155 6.425721 CCAGGACTAATCAGTAAAAACACGAA 59.574 38.462 0.00 0.00 34.21 3.85
1868 2156 5.929992 CCAGGACTAATCAGTAAAAACACGA 59.070 40.000 0.00 0.00 34.21 4.35
1869 2157 5.929992 TCCAGGACTAATCAGTAAAAACACG 59.070 40.000 0.00 0.00 34.21 4.49
1870 2158 6.935208 ACTCCAGGACTAATCAGTAAAAACAC 59.065 38.462 0.00 0.00 34.21 3.32
1871 2159 7.074653 ACTCCAGGACTAATCAGTAAAAACA 57.925 36.000 0.00 0.00 34.21 2.83
1872 2160 7.981102 AACTCCAGGACTAATCAGTAAAAAC 57.019 36.000 0.00 0.00 34.21 2.43
1900 2188 9.025041 CAACTCTAGGGGATTTTAACAGAAAAT 57.975 33.333 0.00 0.00 32.98 1.82
1927 2215 2.501261 GAGTGAGGTAACACCAAACCC 58.499 52.381 0.00 0.00 41.95 4.11
1933 2221 1.349067 ACAGGGAGTGAGGTAACACC 58.651 55.000 0.00 0.00 41.12 4.16
1945 2233 4.154195 GCACAAATACACAACTACAGGGAG 59.846 45.833 0.00 0.00 0.00 4.30
1950 2238 5.355630 ACTGTTGCACAAATACACAACTACA 59.644 36.000 6.32 0.00 42.22 2.74
1951 2239 5.816919 ACTGTTGCACAAATACACAACTAC 58.183 37.500 6.32 0.00 42.22 2.73
1952 2240 6.443934 AACTGTTGCACAAATACACAACTA 57.556 33.333 6.32 0.00 42.22 2.24
1967 2255 5.523369 ACTGAGATTTAGCAAAACTGTTGC 58.477 37.500 2.85 2.85 45.22 4.17
1968 2256 5.848036 CGACTGAGATTTAGCAAAACTGTTG 59.152 40.000 0.00 0.00 0.00 3.33
1969 2257 5.758296 TCGACTGAGATTTAGCAAAACTGTT 59.242 36.000 0.00 0.00 0.00 3.16
1970 2258 5.177696 GTCGACTGAGATTTAGCAAAACTGT 59.822 40.000 8.70 0.00 0.00 3.55
1971 2259 5.389935 GGTCGACTGAGATTTAGCAAAACTG 60.390 44.000 16.46 0.00 0.00 3.16
1972 2260 4.691216 GGTCGACTGAGATTTAGCAAAACT 59.309 41.667 16.46 0.00 0.00 2.66
1973 2261 4.434330 CGGTCGACTGAGATTTAGCAAAAC 60.434 45.833 20.01 0.00 0.00 2.43
1974 2262 3.678072 CGGTCGACTGAGATTTAGCAAAA 59.322 43.478 20.01 0.00 0.00 2.44
1975 2263 3.057104 TCGGTCGACTGAGATTTAGCAAA 60.057 43.478 23.11 0.00 0.00 3.68
1976 2264 2.490509 TCGGTCGACTGAGATTTAGCAA 59.509 45.455 23.11 0.00 0.00 3.91
1977 2265 2.089201 TCGGTCGACTGAGATTTAGCA 58.911 47.619 23.11 0.00 0.00 3.49
1978 2266 2.846039 TCGGTCGACTGAGATTTAGC 57.154 50.000 23.11 0.00 0.00 3.09
1985 2273 8.269095 ACTTAATGAAGTCTCGGTCGACTGAG 62.269 46.154 37.85 37.85 42.50 3.35
1986 2274 1.822506 ATGAAGTCTCGGTCGACTGA 58.177 50.000 25.02 25.02 43.14 3.41
1987 2275 2.638556 AATGAAGTCTCGGTCGACTG 57.361 50.000 18.66 18.66 43.14 3.51
1988 2276 3.757493 ACTTAATGAAGTCTCGGTCGACT 59.243 43.478 16.46 0.00 42.50 4.18
1989 2277 4.094090 ACTTAATGAAGTCTCGGTCGAC 57.906 45.455 7.13 7.13 42.50 4.20
2000 2288 4.631377 TGCATCAACCGAGACTTAATGAAG 59.369 41.667 0.00 0.00 38.76 3.02
2001 2289 4.574892 TGCATCAACCGAGACTTAATGAA 58.425 39.130 0.00 0.00 0.00 2.57
2002 2290 4.200838 TGCATCAACCGAGACTTAATGA 57.799 40.909 0.00 0.00 0.00 2.57
2003 2291 4.944962 TTGCATCAACCGAGACTTAATG 57.055 40.909 0.00 0.00 0.00 1.90
2004 2292 5.185454 TCATTGCATCAACCGAGACTTAAT 58.815 37.500 0.00 0.00 0.00 1.40
2005 2293 4.574892 TCATTGCATCAACCGAGACTTAA 58.425 39.130 0.00 0.00 0.00 1.85
2006 2294 4.081697 TCTCATTGCATCAACCGAGACTTA 60.082 41.667 0.00 0.00 33.33 2.24
2007 2295 3.005554 CTCATTGCATCAACCGAGACTT 58.994 45.455 0.00 0.00 31.74 3.01
2008 2296 2.234661 TCTCATTGCATCAACCGAGACT 59.765 45.455 0.00 0.00 33.33 3.24
2009 2297 2.621338 TCTCATTGCATCAACCGAGAC 58.379 47.619 0.00 0.00 33.33 3.36
2010 2298 3.133542 AGATCTCATTGCATCAACCGAGA 59.866 43.478 10.84 10.84 38.61 4.04
2011 2299 3.464907 AGATCTCATTGCATCAACCGAG 58.535 45.455 0.00 0.00 31.51 4.63
2012 2300 3.548745 AGATCTCATTGCATCAACCGA 57.451 42.857 0.00 0.00 0.00 4.69
2013 2301 5.686834 CATAAGATCTCATTGCATCAACCG 58.313 41.667 0.00 0.00 0.00 4.44
2014 2302 5.241064 AGCATAAGATCTCATTGCATCAACC 59.759 40.000 20.23 0.00 35.79 3.77
2015 2303 6.143496 CAGCATAAGATCTCATTGCATCAAC 58.857 40.000 20.23 0.00 35.79 3.18
2016 2304 5.278315 GCAGCATAAGATCTCATTGCATCAA 60.278 40.000 20.23 0.00 35.79 2.57
2017 2305 4.215613 GCAGCATAAGATCTCATTGCATCA 59.784 41.667 20.23 0.00 35.79 3.07
2018 2306 4.669453 CGCAGCATAAGATCTCATTGCATC 60.669 45.833 20.23 12.82 35.79 3.91
2019 2307 3.188667 CGCAGCATAAGATCTCATTGCAT 59.811 43.478 20.23 8.14 35.79 3.96
2020 2308 2.546789 CGCAGCATAAGATCTCATTGCA 59.453 45.455 20.23 0.00 35.79 4.08
2021 2309 2.804527 TCGCAGCATAAGATCTCATTGC 59.195 45.455 13.71 13.71 0.00 3.56
2022 2310 4.093115 GGATCGCAGCATAAGATCTCATTG 59.907 45.833 0.00 0.00 40.28 2.82
2023 2311 4.252073 GGATCGCAGCATAAGATCTCATT 58.748 43.478 0.00 0.00 40.28 2.57
2024 2312 3.675502 CGGATCGCAGCATAAGATCTCAT 60.676 47.826 0.00 0.00 40.28 2.90
2025 2313 2.352127 CGGATCGCAGCATAAGATCTCA 60.352 50.000 0.00 0.00 40.28 3.27
2026 2314 2.257894 CGGATCGCAGCATAAGATCTC 58.742 52.381 0.00 0.00 40.28 2.75
2027 2315 1.615883 ACGGATCGCAGCATAAGATCT 59.384 47.619 7.65 0.00 40.28 2.75
2028 2316 1.723542 CACGGATCGCAGCATAAGATC 59.276 52.381 0.00 0.00 39.84 2.75
2029 2317 1.788258 CACGGATCGCAGCATAAGAT 58.212 50.000 0.00 0.00 0.00 2.40
2030 2318 0.875908 GCACGGATCGCAGCATAAGA 60.876 55.000 0.00 0.00 32.86 2.10
2031 2319 1.153597 TGCACGGATCGCAGCATAAG 61.154 55.000 0.00 0.00 36.58 1.73
2032 2320 0.742635 TTGCACGGATCGCAGCATAA 60.743 50.000 8.38 0.00 41.18 1.90
2033 2321 0.532640 ATTGCACGGATCGCAGCATA 60.533 50.000 8.38 2.51 41.18 3.14
2034 2322 1.378882 AATTGCACGGATCGCAGCAT 61.379 50.000 8.38 0.00 41.18 3.79
2035 2323 1.585267 AAATTGCACGGATCGCAGCA 61.585 50.000 0.00 4.41 41.18 4.41
2036 2324 0.456653 AAAATTGCACGGATCGCAGC 60.457 50.000 0.00 0.00 41.18 5.25
2037 2325 1.981254 AAAAATTGCACGGATCGCAG 58.019 45.000 0.00 0.00 41.18 5.18
2085 2373 9.520515 ACCAAGTCTCAATAAAGTGACAAATAT 57.479 29.630 0.00 0.00 35.17 1.28
2086 2374 8.918202 ACCAAGTCTCAATAAAGTGACAAATA 57.082 30.769 0.00 0.00 35.17 1.40
2087 2375 7.823745 ACCAAGTCTCAATAAAGTGACAAAT 57.176 32.000 0.00 0.00 35.17 2.32
2088 2376 7.639113 AACCAAGTCTCAATAAAGTGACAAA 57.361 32.000 0.00 0.00 35.17 2.83
2089 2377 8.740123 TTAACCAAGTCTCAATAAAGTGACAA 57.260 30.769 0.00 0.00 35.17 3.18
2090 2378 8.617809 GTTTAACCAAGTCTCAATAAAGTGACA 58.382 33.333 0.00 0.00 35.17 3.58
2091 2379 8.074370 GGTTTAACCAAGTCTCAATAAAGTGAC 58.926 37.037 9.56 0.00 38.42 3.67
2092 2380 7.996644 AGGTTTAACCAAGTCTCAATAAAGTGA 59.003 33.333 17.10 0.00 41.95 3.41
2093 2381 8.166422 AGGTTTAACCAAGTCTCAATAAAGTG 57.834 34.615 17.10 0.00 41.95 3.16
2094 2382 7.996644 TGAGGTTTAACCAAGTCTCAATAAAGT 59.003 33.333 17.10 0.00 41.95 2.66
2095 2383 8.391075 TGAGGTTTAACCAAGTCTCAATAAAG 57.609 34.615 17.10 0.00 41.95 1.85
2096 2384 7.996644 ACTGAGGTTTAACCAAGTCTCAATAAA 59.003 33.333 17.10 0.00 41.95 1.40
2097 2385 7.444183 CACTGAGGTTTAACCAAGTCTCAATAA 59.556 37.037 17.10 0.00 41.95 1.40
2098 2386 6.934645 CACTGAGGTTTAACCAAGTCTCAATA 59.065 38.462 17.10 0.00 41.95 1.90
2099 2387 5.765182 CACTGAGGTTTAACCAAGTCTCAAT 59.235 40.000 17.10 0.00 41.95 2.57
2100 2388 5.104693 TCACTGAGGTTTAACCAAGTCTCAA 60.105 40.000 17.10 2.81 41.95 3.02
2101 2389 4.407621 TCACTGAGGTTTAACCAAGTCTCA 59.592 41.667 17.10 9.55 41.95 3.27
2102 2390 4.750598 GTCACTGAGGTTTAACCAAGTCTC 59.249 45.833 17.10 5.20 41.95 3.36
2103 2391 4.163458 TGTCACTGAGGTTTAACCAAGTCT 59.837 41.667 17.10 0.00 41.95 3.24
2104 2392 4.448210 TGTCACTGAGGTTTAACCAAGTC 58.552 43.478 17.10 5.94 41.95 3.01
2105 2393 4.497291 TGTCACTGAGGTTTAACCAAGT 57.503 40.909 17.10 15.46 41.95 3.16
2106 2394 5.122396 GCTATGTCACTGAGGTTTAACCAAG 59.878 44.000 17.10 14.84 41.95 3.61
2107 2395 5.001232 GCTATGTCACTGAGGTTTAACCAA 58.999 41.667 17.10 3.18 41.95 3.67
2108 2396 4.564821 GGCTATGTCACTGAGGTTTAACCA 60.565 45.833 17.10 0.00 41.95 3.67
2109 2397 3.939592 GGCTATGTCACTGAGGTTTAACC 59.060 47.826 5.91 5.91 38.99 2.85
2110 2398 4.392138 GTGGCTATGTCACTGAGGTTTAAC 59.608 45.833 0.00 0.00 35.05 2.01
2111 2399 4.041075 TGTGGCTATGTCACTGAGGTTTAA 59.959 41.667 3.97 0.00 39.12 1.52
2112 2400 3.580895 TGTGGCTATGTCACTGAGGTTTA 59.419 43.478 3.97 0.00 39.12 2.01
2113 2401 2.371841 TGTGGCTATGTCACTGAGGTTT 59.628 45.455 3.97 0.00 39.12 3.27
2114 2402 1.977854 TGTGGCTATGTCACTGAGGTT 59.022 47.619 3.97 0.00 39.12 3.50
2115 2403 1.644509 TGTGGCTATGTCACTGAGGT 58.355 50.000 3.97 0.00 39.12 3.85
2116 2404 2.433604 AGATGTGGCTATGTCACTGAGG 59.566 50.000 3.97 0.00 39.12 3.86
2117 2405 3.815856 AGATGTGGCTATGTCACTGAG 57.184 47.619 3.97 0.00 39.12 3.35
2118 2406 4.558226 AAAGATGTGGCTATGTCACTGA 57.442 40.909 3.97 0.00 39.12 3.41
2119 2407 4.456911 ACAAAAGATGTGGCTATGTCACTG 59.543 41.667 3.97 0.00 41.93 3.66
2120 2408 4.655963 ACAAAAGATGTGGCTATGTCACT 58.344 39.130 3.97 0.00 41.93 3.41
2135 2423 8.944029 TGATGAAAAAGAAAATTGCACAAAAGA 58.056 25.926 0.00 0.00 0.00 2.52
2137 2425 9.903682 TTTGATGAAAAAGAAAATTGCACAAAA 57.096 22.222 0.00 0.00 0.00 2.44
2150 2438 6.718454 AGAGCTCCTCAATTTGATGAAAAAGA 59.282 34.615 10.93 0.00 32.06 2.52
2153 2441 6.348786 CGAAGAGCTCCTCAATTTGATGAAAA 60.349 38.462 10.93 0.00 32.06 2.29
2214 2503 4.380531 CCTGTTCAAGTTCAGCTACTTCA 58.619 43.478 0.00 0.00 36.24 3.02
2292 2581 2.555782 GTTCATGCGCACGCTCAA 59.444 55.556 14.90 0.00 42.51 3.02
2354 2643 1.592400 CGTCGAGGTTCCAGTAGGCA 61.592 60.000 0.00 0.00 33.74 4.75
2426 2715 4.807039 GCGTCCACGGGCGTGTAT 62.807 66.667 12.28 0.00 44.02 2.29
2573 4262 4.308458 CCTCCGCCGTCCACAACA 62.308 66.667 0.00 0.00 0.00 3.33
2635 6951 4.100084 CCGCCCACAGCTCCATCA 62.100 66.667 0.00 0.00 40.39 3.07
2909 7258 6.561737 TTCAGACACTACACAAAACACAAA 57.438 33.333 0.00 0.00 0.00 2.83
3028 7391 8.461222 CCATAGTGCATTTTACTCTTCAATCAA 58.539 33.333 0.00 0.00 0.00 2.57
3029 7392 7.067372 CCCATAGTGCATTTTACTCTTCAATCA 59.933 37.037 0.00 0.00 0.00 2.57
3030 7393 7.067494 ACCCATAGTGCATTTTACTCTTCAATC 59.933 37.037 0.00 0.00 0.00 2.67
3088 7494 4.275936 GGAGTGACACATAGTGCAGTTTTT 59.724 41.667 8.59 0.00 36.98 1.94
3093 7499 1.633561 CGGAGTGACACATAGTGCAG 58.366 55.000 8.59 0.00 36.98 4.41
3100 7506 1.746615 GCATGCCGGAGTGACACAT 60.747 57.895 5.05 0.00 0.00 3.21
3103 7509 1.965930 GTTGCATGCCGGAGTGACA 60.966 57.895 16.68 2.64 0.00 3.58
3104 7510 1.308069 ATGTTGCATGCCGGAGTGAC 61.308 55.000 16.68 3.25 0.00 3.67
3111 7517 1.226101 GTGACGATGTTGCATGCCG 60.226 57.895 16.68 13.45 0.00 5.69
3112 7518 0.179181 CAGTGACGATGTTGCATGCC 60.179 55.000 16.68 0.28 0.00 4.40
3135 7543 0.457166 CAATCATGCCGTGGTTGCTG 60.457 55.000 0.00 0.00 41.68 4.41
3137 7545 4.481870 CAATCATGCCGTGGTTGC 57.518 55.556 0.00 0.00 41.68 4.17
3151 7559 1.678970 GTTCCCTCCGGCTTGCAAT 60.679 57.895 0.00 0.00 0.00 3.56
3152 7560 2.282180 GTTCCCTCCGGCTTGCAA 60.282 61.111 0.00 0.00 0.00 4.08
3166 7574 2.158959 CCTCATCGTCACGCGGTTC 61.159 63.158 12.47 0.00 41.72 3.62
3167 7575 2.126071 CCTCATCGTCACGCGGTT 60.126 61.111 12.47 0.00 41.72 4.44
3168 7576 3.060000 TCCTCATCGTCACGCGGT 61.060 61.111 12.47 0.00 41.72 5.68
3173 7581 2.277858 AGGTGGTCCTCATCGTCAC 58.722 57.895 0.00 0.00 40.58 3.67
3185 7593 0.610232 GGAATTGCAGCAGAGGTGGT 60.610 55.000 0.00 0.00 33.53 4.16
3199 7607 0.611618 TGCTGCGACAATGGGGAATT 60.612 50.000 0.00 0.00 0.00 2.17
3201 7609 1.971167 GTGCTGCGACAATGGGGAA 60.971 57.895 0.00 0.00 0.00 3.97
3202 7610 2.359850 GTGCTGCGACAATGGGGA 60.360 61.111 0.00 0.00 0.00 4.81
3228 7636 0.235665 ATCACAAACGTCGCTTGCAG 59.764 50.000 8.25 2.22 0.00 4.41
3238 7646 2.126888 GCCGCACCATCACAAACG 60.127 61.111 0.00 0.00 0.00 3.60
3240 7648 2.203408 TGGCCGCACCATCACAAA 60.203 55.556 0.00 0.00 46.36 2.83
3254 7662 1.427819 CGTAAAGGGCGTTGATGGC 59.572 57.895 0.00 0.00 0.00 4.40
3257 7665 0.321298 ACTGCGTAAAGGGCGTTGAT 60.321 50.000 0.00 0.00 0.00 2.57
3292 7701 3.989787 TCGCACCTCGCTGCTTCA 61.990 61.111 0.00 0.00 39.08 3.02
3293 7702 3.482783 GTCGCACCTCGCTGCTTC 61.483 66.667 0.00 0.00 39.08 3.86
3294 7703 3.807631 TTGTCGCACCTCGCTGCTT 62.808 57.895 0.00 0.00 39.08 3.91
3299 7708 3.016474 GCTTCTTGTCGCACCTCGC 62.016 63.158 0.00 0.00 38.27 5.03
3302 7711 1.963338 GCAGCTTCTTGTCGCACCT 60.963 57.895 0.00 0.00 0.00 4.00
3312 7721 2.281761 CCCACAACCGCAGCTTCT 60.282 61.111 0.00 0.00 0.00 2.85
3313 7722 2.594592 ACCCACAACCGCAGCTTC 60.595 61.111 0.00 0.00 0.00 3.86
3314 7723 2.906897 CACCCACAACCGCAGCTT 60.907 61.111 0.00 0.00 0.00 3.74
3315 7724 3.872603 TCACCCACAACCGCAGCT 61.873 61.111 0.00 0.00 0.00 4.24
3316 7725 3.660111 GTCACCCACAACCGCAGC 61.660 66.667 0.00 0.00 0.00 5.25
3317 7726 2.111043 AGTCACCCACAACCGCAG 59.889 61.111 0.00 0.00 0.00 5.18
3318 7727 2.050836 ATCAGTCACCCACAACCGCA 62.051 55.000 0.00 0.00 0.00 5.69
3319 7728 0.036765 TATCAGTCACCCACAACCGC 60.037 55.000 0.00 0.00 0.00 5.68
3320 7729 1.548719 TCTATCAGTCACCCACAACCG 59.451 52.381 0.00 0.00 0.00 4.44
3321 7730 2.567615 AGTCTATCAGTCACCCACAACC 59.432 50.000 0.00 0.00 0.00 3.77
3322 7731 3.963428 AGTCTATCAGTCACCCACAAC 57.037 47.619 0.00 0.00 0.00 3.32
3323 7732 5.128827 GGAATAGTCTATCAGTCACCCACAA 59.871 44.000 0.00 0.00 0.00 3.33
3324 7733 4.649674 GGAATAGTCTATCAGTCACCCACA 59.350 45.833 0.00 0.00 0.00 4.17
3325 7734 4.896482 AGGAATAGTCTATCAGTCACCCAC 59.104 45.833 0.00 0.00 0.00 4.61
3326 7735 5.144159 AGGAATAGTCTATCAGTCACCCA 57.856 43.478 0.00 0.00 0.00 4.51
3327 7736 5.221541 CCAAGGAATAGTCTATCAGTCACCC 60.222 48.000 0.00 0.00 0.00 4.61
3328 7737 5.598830 TCCAAGGAATAGTCTATCAGTCACC 59.401 44.000 0.00 0.00 0.00 4.02
3329 7738 6.716934 TCCAAGGAATAGTCTATCAGTCAC 57.283 41.667 0.00 0.00 0.00 3.67
3330 7739 7.014711 GTGATCCAAGGAATAGTCTATCAGTCA 59.985 40.741 0.00 0.00 0.00 3.41
3331 7740 7.014711 TGTGATCCAAGGAATAGTCTATCAGTC 59.985 40.741 0.00 0.00 0.00 3.51
3332 7741 6.841229 TGTGATCCAAGGAATAGTCTATCAGT 59.159 38.462 0.00 0.00 0.00 3.41
3333 7742 7.295322 TGTGATCCAAGGAATAGTCTATCAG 57.705 40.000 0.00 0.00 0.00 2.90
3336 7745 7.682787 AGTTGTGATCCAAGGAATAGTCTAT 57.317 36.000 0.00 0.00 32.51 1.98
3359 7768 5.238583 ACAAATCGACTTGGACTAGGAAAG 58.761 41.667 11.74 0.00 0.00 2.62
3636 8812 2.055299 CGGTAGTTGTGACTGGGGT 58.945 57.895 0.00 0.00 36.60 4.95
3645 8821 0.029700 GTTTTTGCCGCGGTAGTTGT 59.970 50.000 28.70 0.00 0.00 3.32
3715 8892 2.597510 GGCGCAGGGTTTGAAGGT 60.598 61.111 10.83 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.