Multiple sequence alignment - TraesCS3B01G584000

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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 TraesCS3B01G584000 chr3B 100.000 3420 0 0 1 3420 811154411 811150992 0.000000e+00 6316.0
1 TraesCS3B01G584000 chr3B 83.961 2070 267 38 393 2415 811141686 811139635 0.000000e+00 1923.0
2 TraesCS3B01G584000 chr3B 81.884 1943 278 41 549 2433 811079183 811081109 0.000000e+00 1570.0
3 TraesCS3B01G584000 chr3B 80.821 1851 293 31 688 2498 810948009 810949837 0.000000e+00 1395.0
4 TraesCS3B01G584000 chr3B 80.021 1872 320 31 648 2479 810970261 810972118 0.000000e+00 1336.0
5 TraesCS3B01G584000 chr3B 82.055 1538 241 18 920 2434 810952670 810954195 0.000000e+00 1279.0
6 TraesCS3B01G584000 chr3B 81.138 1617 242 31 901 2479 811040916 811042507 0.000000e+00 1238.0
7 TraesCS3B01G584000 chr3B 94.643 224 8 1 2 225 811163526 811163307 9.090000e-91 344.0
8 TraesCS3B01G584000 chr3B 84.321 287 43 2 2193 2479 810979404 810979688 2.600000e-71 279.0
9 TraesCS3B01G584000 chr3B 75.989 354 45 19 2830 3177 811179925 811179606 2.750000e-31 147.0
10 TraesCS3B01G584000 chr3B 78.448 232 30 5 434 653 811135757 811135534 2.140000e-27 134.0
11 TraesCS3B01G584000 chr3B 87.619 105 13 0 2772 2876 811126750 811126646 4.630000e-24 122.0
12 TraesCS3B01G584000 chr3D 94.602 3242 140 18 1 3232 604260007 604256791 0.000000e+00 4985.0
13 TraesCS3B01G584000 chr3D 83.962 2014 270 28 445 2415 604253253 604251250 0.000000e+00 1881.0
14 TraesCS3B01G584000 chr3D 81.235 2089 304 48 397 2429 603962356 603964412 0.000000e+00 1605.0
15 TraesCS3B01G584000 chr3D 80.917 1876 274 43 654 2479 603943475 603945316 0.000000e+00 1404.0
16 TraesCS3B01G584000 chr3D 80.159 1890 302 37 648 2479 602781708 602779834 0.000000e+00 1345.0
17 TraesCS3B01G584000 chr3D 81.883 1540 242 24 923 2437 602799078 602797551 0.000000e+00 1264.0
18 TraesCS3B01G584000 chr3D 94.545 110 6 0 3310 3419 604255219 604255110 1.630000e-38 171.0
19 TraesCS3B01G584000 chr3D 81.410 156 21 4 498 653 604237318 604237171 1.670000e-23 121.0
20 TraesCS3B01G584000 chr3D 85.849 106 14 1 2772 2876 604135725 604135620 1.000000e-20 111.0
21 TraesCS3B01G584000 chr3A 83.854 2081 268 32 393 2415 733726376 733724306 0.000000e+00 1919.0
22 TraesCS3B01G584000 chr3A 82.123 2120 287 43 397 2433 733860667 733858557 0.000000e+00 1731.0
23 TraesCS3B01G584000 chr3A 81.748 2071 284 51 416 2433 733917935 733915906 0.000000e+00 1644.0
24 TraesCS3B01G584000 chr3A 80.878 1867 276 44 662 2479 733465300 733467134 0.000000e+00 1395.0
25 TraesCS3B01G584000 chr3A 79.723 1874 300 37 648 2468 733411367 733413213 0.000000e+00 1282.0
26 TraesCS3B01G584000 chr3A 79.680 1875 301 36 648 2468 733436162 733438010 0.000000e+00 1279.0
27 TraesCS3B01G584000 chr3A 81.687 1589 240 26 749 2292 733732452 733730870 0.000000e+00 1275.0
28 TraesCS3B01G584000 chr3A 80.129 1706 289 34 757 2429 733637995 733636307 0.000000e+00 1227.0
29 TraesCS3B01G584000 chr3A 82.652 1199 195 4 920 2111 733043900 733045092 0.000000e+00 1050.0
30 TraesCS3B01G584000 chr3A 81.909 503 69 15 2447 2935 733699458 733698964 4.110000e-109 405.0
31 TraesCS3B01G584000 chr3A 83.721 258 36 6 3004 3259 733858088 733857835 4.410000e-59 239.0
32 TraesCS3B01G584000 chr3A 79.370 349 52 9 393 727 733676951 733676609 9.550000e-56 228.0
33 TraesCS3B01G584000 chr3A 86.029 136 15 4 2741 2875 733636035 733635903 3.560000e-30 143.0
34 TraesCS3B01G584000 chr3A 87.963 108 12 1 2751 2857 733724033 733723926 3.580000e-25 126.0
35 TraesCS3B01G584000 chr3A 81.410 156 21 4 498 653 733709682 733709535 1.670000e-23 121.0
36 TraesCS3B01G584000 chr1B 84.259 108 14 2 2751 2857 491067087 491067192 6.040000e-18 102.0
37 TraesCS3B01G584000 chr1B 96.078 51 2 0 3369 3419 684220993 684220943 2.190000e-12 84.2
38 TraesCS3B01G584000 chr7A 98.039 51 1 0 3369 3419 527978066 527978016 4.700000e-14 89.8
39 TraesCS3B01G584000 chr7A 93.878 49 3 0 3371 3419 102563366 102563318 1.320000e-09 75.0
40 TraesCS3B01G584000 chr7A 92.157 51 4 0 3369 3419 556314699 556314749 4.730000e-09 73.1
41 TraesCS3B01G584000 chr1A 96.078 51 2 0 3369 3419 589674370 589674420 2.190000e-12 84.2
42 TraesCS3B01G584000 chr7D 90.196 51 5 0 3369 3419 489120495 489120545 2.200000e-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 TraesCS3B01G584000 chr3B 811150992 811154411 3419 True 6316.000000 6316 100.000000 1 3420 1 chr3B.!!$R2 3419
1 TraesCS3B01G584000 chr3B 811079183 811081109 1926 False 1570.000000 1570 81.884000 549 2433 1 chr3B.!!$F4 1884
2 TraesCS3B01G584000 chr3B 810948009 810954195 6186 False 1337.000000 1395 81.438000 688 2498 2 chr3B.!!$F5 1810
3 TraesCS3B01G584000 chr3B 810970261 810972118 1857 False 1336.000000 1336 80.021000 648 2479 1 chr3B.!!$F1 1831
4 TraesCS3B01G584000 chr3B 811040916 811042507 1591 False 1238.000000 1238 81.138000 901 2479 1 chr3B.!!$F3 1578
5 TraesCS3B01G584000 chr3B 811135534 811141686 6152 True 1028.500000 1923 81.204500 393 2415 2 chr3B.!!$R5 2022
6 TraesCS3B01G584000 chr3D 604251250 604260007 8757 True 2345.666667 4985 91.036333 1 3419 3 chr3D.!!$R5 3418
7 TraesCS3B01G584000 chr3D 603962356 603964412 2056 False 1605.000000 1605 81.235000 397 2429 1 chr3D.!!$F2 2032
8 TraesCS3B01G584000 chr3D 603943475 603945316 1841 False 1404.000000 1404 80.917000 654 2479 1 chr3D.!!$F1 1825
9 TraesCS3B01G584000 chr3D 602779834 602781708 1874 True 1345.000000 1345 80.159000 648 2479 1 chr3D.!!$R1 1831
10 TraesCS3B01G584000 chr3D 602797551 602799078 1527 True 1264.000000 1264 81.883000 923 2437 1 chr3D.!!$R2 1514
11 TraesCS3B01G584000 chr3A 733915906 733917935 2029 True 1644.000000 1644 81.748000 416 2433 1 chr3A.!!$R5 2017
12 TraesCS3B01G584000 chr3A 733465300 733467134 1834 False 1395.000000 1395 80.878000 662 2479 1 chr3A.!!$F4 1817
13 TraesCS3B01G584000 chr3A 733411367 733413213 1846 False 1282.000000 1282 79.723000 648 2468 1 chr3A.!!$F2 1820
14 TraesCS3B01G584000 chr3A 733436162 733438010 1848 False 1279.000000 1279 79.680000 648 2468 1 chr3A.!!$F3 1820
15 TraesCS3B01G584000 chr3A 733730870 733732452 1582 True 1275.000000 1275 81.687000 749 2292 1 chr3A.!!$R4 1543
16 TraesCS3B01G584000 chr3A 733043900 733045092 1192 False 1050.000000 1050 82.652000 920 2111 1 chr3A.!!$F1 1191
17 TraesCS3B01G584000 chr3A 733723926 733726376 2450 True 1022.500000 1919 85.908500 393 2857 2 chr3A.!!$R7 2464
18 TraesCS3B01G584000 chr3A 733857835 733860667 2832 True 985.000000 1731 82.922000 397 3259 2 chr3A.!!$R8 2862
19 TraesCS3B01G584000 chr3A 733635903 733637995 2092 True 685.000000 1227 83.079000 757 2875 2 chr3A.!!$R6 2118

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
566 597 0.809385 CGTTGAGAGCCTCTCGGTTA 59.191 55.0 16.6 0.0 46.25 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 9078 0.238553 GCTTCAGAAAACGGACTGCC 59.761 55.0 0.0 0.0 34.57 4.85 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
89 90 4.521130 TGACGACTAGCAAGATTCAGTT 57.479 40.909 0.00 0.00 0.00 3.16
133 134 4.216902 TGTTTCTGTCCTTGCATTCATCTG 59.783 41.667 0.00 0.00 0.00 2.90
144 145 6.317140 CCTTGCATTCATCTGTTACAGTACAT 59.683 38.462 12.41 0.00 32.61 2.29
184 185 2.754658 GGAGAGGAACGCCCGAGA 60.755 66.667 0.00 0.00 40.87 4.04
195 196 2.948720 GCCCGAGAGTCAAGGCACT 61.949 63.158 11.92 0.00 45.07 4.40
226 227 4.282703 TGGGCGTTAGAGATCCTAAATACC 59.717 45.833 5.54 7.92 38.94 2.73
274 275 9.214957 CATGGACAGTACAAATACAGTTTAAGA 57.785 33.333 0.00 0.00 31.65 2.10
300 301 7.331687 ACATATGCTTGTTTAGATTTTGTTGCC 59.668 33.333 1.58 0.00 0.00 4.52
319 320 6.719370 TGTTGCCTAATTGAATCCACTTTAGT 59.281 34.615 0.00 0.00 0.00 2.24
356 357 6.832804 ACGTTGCTTCTTTTTATTCTCTAGC 58.167 36.000 0.00 0.00 0.00 3.42
373 374 8.709386 TTCTCTAGCTTTCTAGTGCTAATTTG 57.291 34.615 0.00 0.00 42.28 2.32
377 378 6.487689 AGCTTTCTAGTGCTAATTTGTCAC 57.512 37.500 6.01 6.42 37.81 3.67
521 544 3.608316 ATTGACTCTCTGTCCTGAAGC 57.392 47.619 0.00 0.00 44.75 3.86
565 596 1.179814 ACGTTGAGAGCCTCTCGGTT 61.180 55.000 16.60 0.00 46.25 4.44
566 597 0.809385 CGTTGAGAGCCTCTCGGTTA 59.191 55.000 16.60 0.00 46.25 2.85
576 607 4.544683 AGCCTCTCGGTTATATATACCCC 58.455 47.826 1.00 0.18 31.75 4.95
660 709 1.199789 TCTTCAAATGACCGCACATGC 59.800 47.619 0.00 0.00 37.78 4.06
811 7182 7.365741 CCGAGTTCAGTTCTGTTAGTAGTAAA 58.634 38.462 0.00 0.00 0.00 2.01
877 7281 7.341445 TGTTTTGTTATGAACAGGCTACTTT 57.659 32.000 0.00 0.00 43.27 2.66
879 7283 7.067615 TGTTTTGTTATGAACAGGCTACTTTCA 59.932 33.333 7.57 7.57 43.27 2.69
882 7286 7.843490 TGTTATGAACAGGCTACTTTCATAC 57.157 36.000 18.12 14.84 40.34 2.39
883 7287 6.821665 TGTTATGAACAGGCTACTTTCATACC 59.178 38.462 18.12 14.34 40.34 2.73
885 7289 2.981859 ACAGGCTACTTTCATACCGG 57.018 50.000 0.00 0.00 0.00 5.28
1073 7495 1.400142 CAGACTGAGCTGTCTACCTCG 59.600 57.143 6.40 0.00 44.56 4.63
1089 7511 1.681793 CCTCGAGAGATAAAGGGCGAA 59.318 52.381 15.71 0.00 40.84 4.70
1107 7529 3.181496 GCGAAATCCTCTCCCATTTGAAC 60.181 47.826 0.00 0.00 0.00 3.18
1120 7542 4.321156 CCCATTTGAACATCGAAGAAGCAA 60.321 41.667 0.00 0.00 43.58 3.91
1145 7567 8.728596 ATTAGGACTAGCACCTTATCAAGTAT 57.271 34.615 13.17 0.00 38.76 2.12
1169 7595 2.289945 GGAGGGATGCATGGACTGATAC 60.290 54.545 2.46 0.00 0.00 2.24
1201 7627 7.917505 AGATATTTCTGCGTGATGGAAATTTTC 59.082 33.333 0.24 0.24 39.44 2.29
1220 7646 6.702716 TTTTCCAAGAACCAAGTTCGTTAT 57.297 33.333 2.04 0.00 45.96 1.89
1230 7656 3.495377 CCAAGTTCGTTATGTTGGTCGAA 59.505 43.478 0.00 0.00 39.41 3.71
1405 7831 2.795231 TCCCTCATGCCTCTTTTCTG 57.205 50.000 0.00 0.00 0.00 3.02
1425 7851 4.282957 TCTGTTGCTGATCTGAAGTCTCTT 59.717 41.667 3.42 0.00 0.00 2.85
1460 7886 1.352622 ATTATCAGCTTGCCCCGGGA 61.353 55.000 26.32 0.00 0.00 5.14
1491 7917 5.073280 AGGTTTCAAGAGCCTAACTTACCTT 59.927 40.000 0.00 0.00 33.01 3.50
1531 7957 4.103785 CCTCCACAGACAGGGATATTCAAT 59.896 45.833 0.00 0.00 31.57 2.57
1574 8000 9.319143 CCCTGTACTGACTAATTTGAGATTAAG 57.681 37.037 0.60 0.00 0.00 1.85
1587 8013 5.740290 TGAGATTAAGTTCTTTCGAGGGT 57.260 39.130 0.00 0.00 0.00 4.34
1631 8057 7.492669 TCAAGCTCCTAAACTGAAATATCTTCG 59.507 37.037 0.00 0.00 0.00 3.79
1651 8077 5.168647 TCGTGTTAATGGGGACTTTGTAT 57.831 39.130 0.00 0.00 0.00 2.29
1671 8097 9.480861 TTTGTATACATTAAATTGGATGTCCCA 57.519 29.630 6.36 4.37 44.93 4.37
1699 8125 3.574354 AATGGGCCATTCTCTCTCTTC 57.426 47.619 25.94 0.00 26.27 2.87
1737 8163 7.035840 AGCATATCAATCTGTTCCAATTGTC 57.964 36.000 4.43 0.00 35.02 3.18
1756 8182 4.517285 TGTCCATGACAAGGAAAGCTATC 58.483 43.478 0.00 0.00 39.78 2.08
1872 8312 6.173339 CCTTGTTCTGCCTTCTAACTAATCA 58.827 40.000 0.00 0.00 0.00 2.57
1953 8408 1.660575 CCTGTCGTGTTTCGTCGCT 60.661 57.895 0.00 0.00 40.80 4.93
1972 8427 6.346919 CGTCGCTTGGAGAATATTTATCTTGG 60.347 42.308 0.00 0.00 0.00 3.61
1973 8428 5.470098 TCGCTTGGAGAATATTTATCTTGGC 59.530 40.000 0.00 0.00 0.00 4.52
1991 8446 1.830477 GGCATATGCTTTTGGGACCAA 59.170 47.619 26.12 0.00 41.70 3.67
1994 8449 3.524541 CATATGCTTTTGGGACCAAAGC 58.475 45.455 18.14 18.14 45.15 3.51
1995 8450 0.318120 ATGCTTTTGGGACCAAAGCG 59.682 50.000 19.14 16.22 45.15 4.68
2002 8457 0.034896 TGGGACCAAAGCGAAGTCTC 59.965 55.000 0.00 0.00 0.00 3.36
2027 8482 4.805192 GCTGCTTGTTCATTGTTTCAGAAA 59.195 37.500 0.00 0.00 0.00 2.52
2037 8492 2.871453 TGTTTCAGAAAGCCCCTAACC 58.129 47.619 0.00 0.00 0.00 2.85
2044 8499 4.788617 TCAGAAAGCCCCTAACCTAAAGAT 59.211 41.667 0.00 0.00 0.00 2.40
2052 8507 3.879892 CCCTAACCTAAAGATGCTTGAGC 59.120 47.826 0.00 0.00 42.50 4.26
2061 8516 4.348863 AAGATGCTTGAGCTATGGGTAG 57.651 45.455 4.44 0.00 42.66 3.18
2066 8521 4.747583 TGCTTGAGCTATGGGTAGGTATA 58.252 43.478 4.44 0.00 38.70 1.47
2092 8549 0.903236 GTAAACCCTCTCCCTCGCTT 59.097 55.000 0.00 0.00 0.00 4.68
2135 8604 4.955925 TCATTGTGTTTACGGCTAATGG 57.044 40.909 0.00 0.00 0.00 3.16
2137 8606 2.863132 TGTGTTTACGGCTAATGGGT 57.137 45.000 0.00 0.00 0.00 4.51
2200 8705 5.012561 GGATCAGGATCAGGTAAGCATTACT 59.987 44.000 11.12 0.00 43.85 2.24
2287 8798 3.665745 ATCAATTTCGTGGCAAAGCTT 57.334 38.095 0.00 0.00 0.00 3.74
2320 8831 4.696455 CACCAGCTTTGGAAAAACTGAAT 58.304 39.130 0.00 0.00 0.00 2.57
2332 8843 9.974980 TTGGAAAAACTGAATATAAAGTGGAAC 57.025 29.630 0.00 0.00 0.00 3.62
2352 8863 3.777925 CGAAACGGACTGCGGCAG 61.778 66.667 27.43 27.43 37.52 4.85
2406 8917 3.256960 TCCCAGGGCCAAGGTCAC 61.257 66.667 6.18 0.00 0.00 3.67
2416 8927 2.488153 GGCCAAGGTCACTGTTACATTC 59.512 50.000 0.00 0.00 0.00 2.67
2444 8955 2.352814 GCATGCACCCCTATAGTCTACG 60.353 54.545 14.21 0.00 0.00 3.51
2445 8956 2.742428 TGCACCCCTATAGTCTACGT 57.258 50.000 0.00 0.00 0.00 3.57
2481 8992 4.685628 CACTTTGCCGATTTAATTTGCTGT 59.314 37.500 0.00 0.00 0.00 4.40
2506 9017 7.605410 TGGGTAGAATTATTTCGTCTTTGTC 57.395 36.000 0.00 0.00 36.93 3.18
2507 9018 6.596497 TGGGTAGAATTATTTCGTCTTTGTCC 59.404 38.462 0.00 0.00 36.93 4.02
2508 9019 6.822170 GGGTAGAATTATTTCGTCTTTGTCCT 59.178 38.462 0.00 0.00 36.93 3.85
2512 9023 6.431234 AGAATTATTTCGTCTTTGTCCTTGCT 59.569 34.615 0.00 0.00 36.93 3.91
2514 9025 0.944386 TTCGTCTTTGTCCTTGCTGC 59.056 50.000 0.00 0.00 0.00 5.25
2517 9028 0.595095 GTCTTTGTCCTTGCTGCTGG 59.405 55.000 0.00 3.48 0.00 4.85
2520 9040 2.158682 TCTTTGTCCTTGCTGCTGGTTA 60.159 45.455 0.00 0.00 0.00 2.85
2527 9057 5.764686 TGTCCTTGCTGCTGGTTAATATATG 59.235 40.000 0.00 0.00 0.00 1.78
2537 9067 7.223584 TGCTGGTTAATATATGTATGTGTGCT 58.776 34.615 0.00 0.00 0.00 4.40
2539 9069 8.230486 GCTGGTTAATATATGTATGTGTGCTTC 58.770 37.037 0.00 0.00 0.00 3.86
2540 9070 9.271828 CTGGTTAATATATGTATGTGTGCTTCA 57.728 33.333 0.00 0.00 0.00 3.02
2542 9072 8.721478 GGTTAATATATGTATGTGTGCTTCAGG 58.279 37.037 0.00 0.00 0.00 3.86
2543 9073 8.721478 GTTAATATATGTATGTGTGCTTCAGGG 58.279 37.037 0.00 0.00 0.00 4.45
2544 9074 4.778213 ATATGTATGTGTGCTTCAGGGT 57.222 40.909 0.00 0.00 0.00 4.34
2545 9075 2.949177 TGTATGTGTGCTTCAGGGTT 57.051 45.000 0.00 0.00 0.00 4.11
2546 9076 2.503331 TGTATGTGTGCTTCAGGGTTG 58.497 47.619 0.00 0.00 0.00 3.77
2548 9078 1.901591 ATGTGTGCTTCAGGGTTGAG 58.098 50.000 0.00 0.00 34.15 3.02
2549 9079 0.179020 TGTGTGCTTCAGGGTTGAGG 60.179 55.000 0.00 0.00 34.15 3.86
2554 9084 3.239861 CTTCAGGGTTGAGGCAGTC 57.760 57.895 0.00 0.00 34.15 3.51
2555 9085 0.322008 CTTCAGGGTTGAGGCAGTCC 60.322 60.000 0.00 0.00 34.15 3.85
2558 9088 2.147387 AGGGTTGAGGCAGTCCGTT 61.147 57.895 0.00 0.00 37.47 4.44
2559 9089 1.228154 GGGTTGAGGCAGTCCGTTT 60.228 57.895 0.00 0.00 37.47 3.60
2560 9090 0.822121 GGGTTGAGGCAGTCCGTTTT 60.822 55.000 0.00 0.00 37.47 2.43
2563 9093 1.264288 GTTGAGGCAGTCCGTTTTCTG 59.736 52.381 0.00 0.00 37.47 3.02
2565 9095 1.140052 TGAGGCAGTCCGTTTTCTGAA 59.860 47.619 0.00 0.00 37.47 3.02
2566 9096 1.801178 GAGGCAGTCCGTTTTCTGAAG 59.199 52.381 0.00 0.00 37.47 3.02
2567 9097 0.238553 GGCAGTCCGTTTTCTGAAGC 59.761 55.000 0.00 0.00 34.02 3.86
2606 9160 6.778834 TCAGCACATTGTTTTCCATATGAT 57.221 33.333 3.65 0.00 0.00 2.45
2613 9167 8.415553 CACATTGTTTTCCATATGATACACCAT 58.584 33.333 3.65 0.00 0.00 3.55
2614 9168 8.980596 ACATTGTTTTCCATATGATACACCATT 58.019 29.630 3.65 0.00 0.00 3.16
2615 9169 9.467258 CATTGTTTTCCATATGATACACCATTC 57.533 33.333 3.65 0.00 0.00 2.67
2616 9170 7.258022 TGTTTTCCATATGATACACCATTCG 57.742 36.000 3.65 0.00 0.00 3.34
2617 9171 7.051000 TGTTTTCCATATGATACACCATTCGA 58.949 34.615 3.65 0.00 0.00 3.71
2622 9176 7.223584 TCCATATGATACACCATTCGACATTT 58.776 34.615 3.65 0.00 0.00 2.32
2623 9177 7.387673 TCCATATGATACACCATTCGACATTTC 59.612 37.037 3.65 0.00 0.00 2.17
2624 9178 7.388776 CCATATGATACACCATTCGACATTTCT 59.611 37.037 3.65 0.00 0.00 2.52
2625 9179 8.777413 CATATGATACACCATTCGACATTTCTT 58.223 33.333 0.00 0.00 0.00 2.52
2626 9180 7.630242 ATGATACACCATTCGACATTTCTTT 57.370 32.000 0.00 0.00 0.00 2.52
2628 9182 6.429692 TGATACACCATTCGACATTTCTTTGT 59.570 34.615 0.00 0.00 0.00 2.83
2629 9183 4.858935 ACACCATTCGACATTTCTTTGTG 58.141 39.130 0.00 0.00 0.00 3.33
2631 9185 3.317711 ACCATTCGACATTTCTTTGTGCA 59.682 39.130 0.00 0.00 0.00 4.57
2632 9186 4.202101 ACCATTCGACATTTCTTTGTGCAA 60.202 37.500 0.00 0.00 0.00 4.08
2633 9187 4.925054 CCATTCGACATTTCTTTGTGCAAT 59.075 37.500 0.00 0.00 0.00 3.56
2634 9188 5.164031 CCATTCGACATTTCTTTGTGCAATG 60.164 40.000 0.00 0.00 34.60 2.82
2635 9189 3.899734 TCGACATTTCTTTGTGCAATGG 58.100 40.909 0.00 0.00 33.00 3.16
2636 9190 2.988493 CGACATTTCTTTGTGCAATGGG 59.012 45.455 0.00 0.00 33.00 4.00
2637 9191 3.552684 CGACATTTCTTTGTGCAATGGGT 60.553 43.478 0.00 0.00 33.00 4.51
2638 9192 3.731089 ACATTTCTTTGTGCAATGGGTG 58.269 40.909 0.00 0.00 33.00 4.61
2639 9193 3.387374 ACATTTCTTTGTGCAATGGGTGA 59.613 39.130 0.00 0.00 33.00 4.02
2640 9194 3.451141 TTTCTTTGTGCAATGGGTGAC 57.549 42.857 0.00 0.00 0.00 3.67
2641 9195 2.064434 TCTTTGTGCAATGGGTGACA 57.936 45.000 0.00 0.00 0.00 3.58
2642 9196 1.680735 TCTTTGTGCAATGGGTGACAC 59.319 47.619 0.00 0.00 35.84 3.67
2643 9197 1.408340 CTTTGTGCAATGGGTGACACA 59.592 47.619 8.08 0.00 40.31 3.72
2644 9198 1.031235 TTGTGCAATGGGTGACACAG 58.969 50.000 8.08 0.00 41.80 3.66
2645 9199 0.106769 TGTGCAATGGGTGACACAGT 60.107 50.000 8.08 0.00 38.50 3.55
2646 9200 0.311790 GTGCAATGGGTGACACAGTG 59.688 55.000 11.38 11.38 37.03 3.66
2647 9201 0.182299 TGCAATGGGTGACACAGTGA 59.818 50.000 20.35 1.30 36.11 3.41
2648 9202 0.877071 GCAATGGGTGACACAGTGAG 59.123 55.000 20.35 0.00 36.11 3.51
2649 9203 1.543208 GCAATGGGTGACACAGTGAGA 60.543 52.381 20.35 0.00 36.11 3.27
2662 9216 2.821685 TGAGACACACAAGCCGCT 59.178 55.556 0.00 0.00 0.00 5.52
2665 9219 1.004918 AGACACACAAGCCGCTACC 60.005 57.895 0.00 0.00 0.00 3.18
2669 9223 3.490759 CACAAGCCGCTACCGCTG 61.491 66.667 0.00 0.00 0.00 5.18
2673 9227 4.796231 AGCCGCTACCGCTGTTCG 62.796 66.667 0.00 0.00 38.08 3.95
2678 9232 2.092882 GCTACCGCTGTTCGTCCAC 61.093 63.158 0.00 0.00 36.19 4.02
2679 9233 1.585006 CTACCGCTGTTCGTCCACT 59.415 57.895 0.00 0.00 36.19 4.00
2680 9234 0.038526 CTACCGCTGTTCGTCCACTT 60.039 55.000 0.00 0.00 36.19 3.16
2683 9237 1.956170 CGCTGTTCGTCCACTTGCT 60.956 57.895 0.00 0.00 0.00 3.91
2692 9246 1.967535 TCCACTTGCTGGAGACTCG 59.032 57.895 0.00 0.00 44.99 4.18
2722 9296 1.270625 CCACGCTTCCTTGTCCTGTTA 60.271 52.381 0.00 0.00 0.00 2.41
2724 9298 2.673368 CACGCTTCCTTGTCCTGTTATC 59.327 50.000 0.00 0.00 0.00 1.75
2736 9311 4.262617 GTCCTGTTATCTCCCTTTGTTCC 58.737 47.826 0.00 0.00 0.00 3.62
2739 9314 2.039216 TGTTATCTCCCTTTGTTCCGCA 59.961 45.455 0.00 0.00 0.00 5.69
2749 9327 4.340950 CCCTTTGTTCCGCATATGGTAAAT 59.659 41.667 4.56 0.00 0.00 1.40
2761 9339 6.507023 GCATATGGTAAATTTCCTGGTTCTG 58.493 40.000 4.56 0.00 0.00 3.02
2790 9368 8.484641 AATATATGTGTCCATAAGAAGCGATG 57.515 34.615 0.00 0.00 37.12 3.84
2795 9373 5.163457 TGTGTCCATAAGAAGCGATGACATA 60.163 40.000 0.00 0.00 0.00 2.29
2797 9375 5.928264 TGTCCATAAGAAGCGATGACATATG 59.072 40.000 0.00 0.00 0.00 1.78
2863 9442 8.408601 AGACATCAAATTGTACCTTCATATTGC 58.591 33.333 0.00 0.00 0.00 3.56
2902 9483 9.368416 AGTAGACATATGAAGCCTGAAGTAATA 57.632 33.333 10.38 0.00 0.00 0.98
2913 9494 6.657875 AGCCTGAAGTAATAAGATCAAAGCT 58.342 36.000 0.00 0.00 30.77 3.74
2916 9497 6.238593 CCTGAAGTAATAAGATCAAAGCTGCC 60.239 42.308 0.00 0.00 0.00 4.85
2925 9506 2.118951 AAAGCTGCCCATGCCTGT 59.881 55.556 0.00 0.00 36.33 4.00
2935 9516 2.838736 CCCATGCCTGTATCAGTGTAC 58.161 52.381 0.00 0.00 0.00 2.90
2939 9520 4.572389 CCATGCCTGTATCAGTGTACTTTC 59.428 45.833 0.00 0.00 0.00 2.62
2941 9522 4.820897 TGCCTGTATCAGTGTACTTTCAG 58.179 43.478 0.00 0.00 0.00 3.02
2942 9523 4.184629 GCCTGTATCAGTGTACTTTCAGG 58.815 47.826 0.00 0.00 42.54 3.86
2943 9524 4.081642 GCCTGTATCAGTGTACTTTCAGGA 60.082 45.833 17.62 0.61 42.33 3.86
2970 9569 8.231692 TCAGATTTGTTTACATTGGTTTCAGA 57.768 30.769 0.00 0.00 0.00 3.27
2974 9573 8.606040 ATTTGTTTACATTGGTTTCAGATTGG 57.394 30.769 0.00 0.00 0.00 3.16
2982 9581 7.101054 ACATTGGTTTCAGATTGGAATGAATG 58.899 34.615 0.00 0.00 35.47 2.67
2983 9582 6.669125 TTGGTTTCAGATTGGAATGAATGT 57.331 33.333 0.00 0.00 35.47 2.71
2984 9583 6.669125 TGGTTTCAGATTGGAATGAATGTT 57.331 33.333 0.00 0.00 35.47 2.71
2994 9593 6.602410 TTGGAATGAATGTTTAATGCTCCA 57.398 33.333 0.00 0.00 0.00 3.86
2995 9594 6.211587 TGGAATGAATGTTTAATGCTCCAG 57.788 37.500 0.00 0.00 0.00 3.86
3012 9611 5.999721 GCTCCAGCATCTCATATTCTTTTC 58.000 41.667 0.00 0.00 41.59 2.29
3019 9618 7.701078 CAGCATCTCATATTCTTTTCTTGTTGG 59.299 37.037 0.00 0.00 0.00 3.77
3022 9621 9.994432 CATCTCATATTCTTTTCTTGTTGGTAC 57.006 33.333 0.00 0.00 0.00 3.34
3037 9636 7.550196 TCTTGTTGGTACGGGAAATATTTCTAC 59.450 37.037 23.85 18.27 37.35 2.59
3041 9642 6.218019 TGGTACGGGAAATATTTCTACATCG 58.782 40.000 23.85 20.04 37.35 3.84
3047 9648 4.151867 GGAAATATTTCTACATCGCCGTCC 59.848 45.833 23.85 3.59 37.35 4.79
3113 9720 9.125026 GTGAGGTGAATATGATCCAGTTTTTAT 57.875 33.333 0.00 0.00 0.00 1.40
3124 9731 5.705609 TCCAGTTTTTATCTCAAACAGCC 57.294 39.130 0.00 0.00 36.71 4.85
3134 9742 5.841957 ATCTCAAACAGCCCACATAATTC 57.158 39.130 0.00 0.00 0.00 2.17
3147 9755 7.667219 AGCCCACATAATTCAGAGGTATTTATG 59.333 37.037 0.00 0.00 0.00 1.90
3151 9759 9.060347 CACATAATTCAGAGGTATTTATGCAGT 57.940 33.333 0.00 0.00 0.00 4.40
3156 9764 7.759489 TTCAGAGGTATTTATGCAGTTGTTT 57.241 32.000 0.00 0.00 0.00 2.83
3161 9769 9.632638 AGAGGTATTTATGCAGTTGTTTATCAT 57.367 29.630 0.00 0.00 0.00 2.45
3170 9779 5.123820 TGCAGTTGTTTATCATACTTGCTCC 59.876 40.000 0.00 0.00 0.00 4.70
3171 9780 5.449177 GCAGTTGTTTATCATACTTGCTCCC 60.449 44.000 0.00 0.00 0.00 4.30
3180 9789 1.568504 TACTTGCTCCCGGAATGAGT 58.431 50.000 0.73 2.70 32.31 3.41
3217 10224 8.482429 CAGCATTATTCTCACAGTTTTTGTTTC 58.518 33.333 0.00 0.00 38.16 2.78
3248 10255 9.841295 ATAACCATATACGTTTTGACCAATACT 57.159 29.630 0.00 0.00 0.00 2.12
3252 10259 8.282592 CCATATACGTTTTGACCAATACTCATG 58.717 37.037 0.00 0.00 0.00 3.07
3256 10263 5.763204 ACGTTTTGACCAATACTCATGTTCT 59.237 36.000 0.00 0.00 0.00 3.01
3258 10265 7.606456 ACGTTTTGACCAATACTCATGTTCTAT 59.394 33.333 0.00 0.00 0.00 1.98
3259 10266 8.450964 CGTTTTGACCAATACTCATGTTCTATT 58.549 33.333 0.00 0.00 0.00 1.73
3264 10271 9.513906 TGACCAATACTCATGTTCTATTTTTGA 57.486 29.630 0.00 0.00 0.00 2.69
3265 10272 9.774742 GACCAATACTCATGTTCTATTTTTGAC 57.225 33.333 0.00 0.00 0.00 3.18
3266 10273 8.450964 ACCAATACTCATGTTCTATTTTTGACG 58.549 33.333 0.00 0.00 0.00 4.35
3267 10274 7.429340 CCAATACTCATGTTCTATTTTTGACGC 59.571 37.037 0.00 0.00 0.00 5.19
3268 10275 7.849804 ATACTCATGTTCTATTTTTGACGCT 57.150 32.000 0.00 0.00 0.00 5.07
3269 10276 5.931532 ACTCATGTTCTATTTTTGACGCTG 58.068 37.500 0.00 0.00 0.00 5.18
3272 10279 3.884169 TGTTCTATTTTTGACGCTGCAC 58.116 40.909 0.00 0.00 0.00 4.57
3273 10280 3.563808 TGTTCTATTTTTGACGCTGCACT 59.436 39.130 0.00 0.00 0.00 4.40
3274 10281 3.811722 TCTATTTTTGACGCTGCACTG 57.188 42.857 0.00 0.00 0.00 3.66
3275 10282 2.095768 TCTATTTTTGACGCTGCACTGC 60.096 45.455 0.00 0.00 0.00 4.40
3276 10283 0.318955 ATTTTTGACGCTGCACTGCC 60.319 50.000 0.00 0.00 0.00 4.85
3277 10284 1.383456 TTTTTGACGCTGCACTGCCT 61.383 50.000 0.00 0.00 0.00 4.75
3278 10285 0.533978 TTTTGACGCTGCACTGCCTA 60.534 50.000 0.00 0.00 0.00 3.93
3288 10696 2.740981 CTGCACTGCCTATGCTTATAGC 59.259 50.000 0.00 0.00 43.77 2.97
3293 10701 1.980765 TGCCTATGCTTATAGCCAGCT 59.019 47.619 0.00 0.00 41.51 4.24
3294 10702 2.373169 TGCCTATGCTTATAGCCAGCTT 59.627 45.455 0.00 0.00 41.51 3.74
3295 10703 3.006247 GCCTATGCTTATAGCCAGCTTC 58.994 50.000 0.00 0.00 41.51 3.86
3297 10705 1.517242 ATGCTTATAGCCAGCTTCGC 58.483 50.000 0.00 0.00 41.51 4.70
3298 10706 0.465705 TGCTTATAGCCAGCTTCGCT 59.534 50.000 9.87 9.87 41.51 4.93
3300 10708 1.943340 GCTTATAGCCAGCTTCGCTTT 59.057 47.619 10.23 5.69 36.40 3.51
3301 10709 2.356069 GCTTATAGCCAGCTTCGCTTTT 59.644 45.455 10.23 2.48 36.40 2.27
3302 10710 3.181496 GCTTATAGCCAGCTTCGCTTTTT 60.181 43.478 10.23 0.30 36.40 1.94
3326 10734 2.880879 CAGGACATGACGCGACCG 60.881 66.667 15.93 2.87 41.14 4.79
3337 10985 2.726274 GCGACCGTCCCGTATGAT 59.274 61.111 0.00 0.00 0.00 2.45
3367 11015 3.758023 TCACTAACCATTCATGCACCAAG 59.242 43.478 0.00 0.00 0.00 3.61
3370 11018 1.999648 ACCATTCATGCACCAAGTGT 58.000 45.000 0.00 0.00 35.75 3.55
3406 12314 1.562942 AGCAGAGATCTTGGCCATCAA 59.437 47.619 6.09 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 6.737720 ACATTCTCTCCAACTATATGAGCA 57.262 37.500 0.00 0.00 0.00 4.26
91 92 9.258826 CAGAAACATTCTCTCCAACTATATGAG 57.741 37.037 0.00 0.00 38.11 2.90
96 97 6.214412 AGGACAGAAACATTCTCTCCAACTAT 59.786 38.462 14.30 0.00 44.52 2.12
144 145 4.381612 CCTCTCTCGTTGTACATAAGGCAA 60.382 45.833 0.00 0.00 0.00 4.52
180 181 0.108898 CCTGAGTGCCTTGACTCTCG 60.109 60.000 0.00 0.00 42.58 4.04
181 182 0.390998 GCCTGAGTGCCTTGACTCTC 60.391 60.000 0.00 0.00 42.58 3.20
182 183 1.676384 GCCTGAGTGCCTTGACTCT 59.324 57.895 0.00 0.00 42.58 3.24
202 203 3.814005 TTTAGGATCTCTAACGCCCAC 57.186 47.619 0.00 0.00 37.65 4.61
204 205 4.282703 TGGTATTTAGGATCTCTAACGCCC 59.717 45.833 0.00 0.36 37.65 6.13
226 227 6.590234 TGTATGTACCATGTATAGCTCCTG 57.410 41.667 0.00 0.00 0.00 3.86
274 275 7.331687 GGCAACAAAATCTAAACAAGCATATGT 59.668 33.333 4.29 0.00 34.24 2.29
293 294 6.418057 AAAGTGGATTCAATTAGGCAACAA 57.582 33.333 0.00 0.00 31.13 2.83
300 301 7.770897 ACAGGCTACTAAAGTGGATTCAATTAG 59.229 37.037 6.36 6.36 33.92 1.73
319 320 5.484715 AGAAGCAACGTAAATAACAGGCTA 58.515 37.500 0.00 0.00 30.74 3.93
356 357 6.706055 TCGTGACAAATTAGCACTAGAAAG 57.294 37.500 0.00 0.00 0.00 2.62
521 544 4.328983 GGCAAATGATGAAATGCAACTCTG 59.671 41.667 0.00 0.00 40.51 3.35
660 709 4.341366 AAGGGGTTTCTTTTGCTGAATG 57.659 40.909 0.00 0.00 0.00 2.67
811 7182 6.072199 AGAGATGCAGTTTAGGGAAAGAAT 57.928 37.500 0.00 0.00 0.00 2.40
824 7210 1.610522 GCAACAACCAAGAGATGCAGT 59.389 47.619 0.00 0.00 34.10 4.40
825 7211 1.884579 AGCAACAACCAAGAGATGCAG 59.115 47.619 0.00 0.00 36.30 4.41
826 7212 1.985473 AGCAACAACCAAGAGATGCA 58.015 45.000 0.00 0.00 36.30 3.96
827 7213 4.708726 ATAAGCAACAACCAAGAGATGC 57.291 40.909 0.00 0.00 0.00 3.91
877 7281 5.298276 GCAGAAATTAAATGGTCCGGTATGA 59.702 40.000 0.00 0.00 0.00 2.15
879 7283 5.197451 TGCAGAAATTAAATGGTCCGGTAT 58.803 37.500 0.00 0.00 0.00 2.73
882 7286 4.142182 ACATGCAGAAATTAAATGGTCCGG 60.142 41.667 0.00 0.00 0.00 5.14
883 7287 4.997565 ACATGCAGAAATTAAATGGTCCG 58.002 39.130 0.00 0.00 0.00 4.79
918 7331 3.713288 GTGCAGTCTACCGCATATAACA 58.287 45.455 0.00 0.00 40.89 2.41
988 7410 5.815581 ACAGGTACTCATTGCTCCAAAATA 58.184 37.500 0.00 0.00 34.60 1.40
992 7414 4.901197 TTACAGGTACTCATTGCTCCAA 57.099 40.909 0.00 0.00 34.60 3.53
995 7417 5.392057 GCCTTTTTACAGGTACTCATTGCTC 60.392 44.000 0.00 0.00 34.60 4.26
1063 7485 4.462133 CCCTTTATCTCTCGAGGTAGACA 58.538 47.826 13.56 0.00 0.00 3.41
1073 7495 4.039852 AGAGGATTTCGCCCTTTATCTCTC 59.960 45.833 0.00 0.00 33.36 3.20
1089 7511 4.080356 TCGATGTTCAAATGGGAGAGGATT 60.080 41.667 0.00 0.00 0.00 3.01
1107 7529 5.176590 GCTAGTCCTAATTGCTTCTTCGATG 59.823 44.000 0.00 0.00 0.00 3.84
1120 7542 8.728596 ATACTTGATAAGGTGCTAGTCCTAAT 57.271 34.615 8.60 0.00 34.56 1.73
1145 7567 1.002069 AGTCCATGCATCCCTCCAAA 58.998 50.000 0.00 0.00 0.00 3.28
1169 7595 2.351418 TCACGCAGAAATATCTTTGGCG 59.649 45.455 13.96 13.96 44.21 5.69
1201 7627 5.212194 CAACATAACGAACTTGGTTCTTGG 58.788 41.667 8.46 0.00 40.05 3.61
1220 7646 2.552599 TAGCACCATTTCGACCAACA 57.447 45.000 0.00 0.00 0.00 3.33
1230 7656 3.614092 CTTGTGGAGTGATAGCACCATT 58.386 45.455 7.66 0.00 46.32 3.16
1282 7708 5.292101 CGAACTCATCATGGTAACTTCCTTC 59.708 44.000 0.00 0.00 37.61 3.46
1359 7785 2.380064 ACCTTGGCCATGAGTTCAAA 57.620 45.000 19.85 0.00 0.00 2.69
1369 7795 2.062636 GGGAATCCTATACCTTGGCCA 58.937 52.381 0.00 0.00 0.00 5.36
1405 7831 3.611986 CGAAGAGACTTCAGATCAGCAAC 59.388 47.826 11.20 0.00 0.00 4.17
1425 7851 2.192664 TAATGCAGTTTTCCAGGCGA 57.807 45.000 0.00 0.00 0.00 5.54
1460 7886 3.756117 AGGCTCTTGAAACCTTCGAATT 58.244 40.909 0.00 0.00 0.00 2.17
1491 7917 3.587061 TGGAGGAGAAAATGTTCAGGCTA 59.413 43.478 0.00 0.00 36.09 3.93
1531 7957 2.239654 CAGGGCAAAAGGAGACCAGATA 59.760 50.000 0.00 0.00 0.00 1.98
1587 8013 8.082852 GGAGCTTGAATATTTAGACAGTCGATA 58.917 37.037 0.00 0.00 0.00 2.92
1591 8017 9.601217 TTTAGGAGCTTGAATATTTAGACAGTC 57.399 33.333 0.00 0.00 0.00 3.51
1631 8057 7.875327 ATGTATACAAAGTCCCCATTAACAC 57.125 36.000 10.14 0.00 0.00 3.32
1671 8097 4.617593 AGAGAATGGCCCATTTCAGATTT 58.382 39.130 10.97 0.00 33.90 2.17
1699 8125 5.696260 TGATATGCTTTAACTTCGTGACG 57.304 39.130 0.00 0.00 0.00 4.35
1709 8135 9.806203 CAATTGGAACAGATTGATATGCTTTAA 57.194 29.630 0.00 0.00 42.39 1.52
1737 8163 4.774124 TGAGATAGCTTTCCTTGTCATGG 58.226 43.478 0.00 0.00 0.00 3.66
1756 8182 1.471684 GCTTCCCAATGACTGCTTGAG 59.528 52.381 0.00 0.00 0.00 3.02
1827 8253 3.691609 GGCCATGCTGGAGCTAATAATAC 59.308 47.826 0.00 0.00 40.96 1.89
1852 8284 6.166982 ACACTGATTAGTTAGAAGGCAGAAC 58.833 40.000 0.00 0.00 34.07 3.01
1913 8368 0.946528 GCTTCGTATGCATGCATCCA 59.053 50.000 35.35 17.74 37.82 3.41
1953 8408 8.742777 GCATATGCCAAGATAAATATTCTCCAA 58.257 33.333 17.26 0.00 34.31 3.53
1972 8427 3.524541 CTTTGGTCCCAAAAGCATATGC 58.475 45.455 20.36 20.36 44.07 3.14
1973 8428 3.524541 GCTTTGGTCCCAAAAGCATATG 58.475 45.455 17.66 0.00 44.07 1.78
1991 8446 2.433318 GCAGCCGAGACTTCGCTT 60.433 61.111 0.00 0.00 45.38 4.68
1994 8449 0.946221 AACAAGCAGCCGAGACTTCG 60.946 55.000 0.00 0.00 46.29 3.79
1995 8450 0.793250 GAACAAGCAGCCGAGACTTC 59.207 55.000 0.00 0.00 0.00 3.01
2002 8457 2.053627 GAAACAATGAACAAGCAGCCG 58.946 47.619 0.00 0.00 0.00 5.52
2027 8482 2.493091 AGCATCTTTAGGTTAGGGGCT 58.507 47.619 0.00 0.00 0.00 5.19
2037 8492 4.712476 ACCCATAGCTCAAGCATCTTTAG 58.288 43.478 4.59 0.00 45.16 1.85
2044 8499 1.879575 ACCTACCCATAGCTCAAGCA 58.120 50.000 4.59 0.00 45.16 3.91
2061 8516 5.083122 GAGAGGGTTTACTAGGGGTATACC 58.917 50.000 13.99 13.99 45.54 2.73
2066 8521 1.009306 GGGAGAGGGTTTACTAGGGGT 59.991 57.143 0.00 0.00 0.00 4.95
2069 8524 2.308690 CGAGGGAGAGGGTTTACTAGG 58.691 57.143 0.00 0.00 0.00 3.02
2092 8549 6.661777 TGAATGAACATGGATCAGGTGATTA 58.338 36.000 9.03 0.00 34.37 1.75
2148 8620 2.493278 CCCAAAGGGTAACTCTGCATTG 59.507 50.000 0.00 0.00 38.25 2.82
2171 8646 1.407936 ACCTGATCCTGATCCGACAG 58.592 55.000 4.76 0.00 37.02 3.51
2173 8648 2.288518 GCTTACCTGATCCTGATCCGAC 60.289 54.545 4.76 0.00 37.02 4.79
2312 8823 5.163794 CGCCGTTCCACTTTATATTCAGTTT 60.164 40.000 0.00 0.00 0.00 2.66
2320 8831 2.667481 CGTTTCGCCGTTCCACTTTATA 59.333 45.455 0.00 0.00 0.00 0.98
2352 8863 2.359214 GCTAATAGCTTGGCAAGAACCC 59.641 50.000 30.45 12.62 38.62 4.11
2374 8885 4.459089 GGAGACACCCTCGGCAGC 62.459 72.222 0.00 0.00 42.89 5.25
2406 8917 6.197276 GTGCATGCTTATCAGAATGTAACAG 58.803 40.000 20.33 0.00 38.29 3.16
2416 8927 2.936919 TAGGGGTGCATGCTTATCAG 57.063 50.000 20.33 0.00 0.00 2.90
2444 8955 2.301346 CAAAGTGATGGGGGATGCTAC 58.699 52.381 0.00 0.00 0.00 3.58
2445 8956 1.410083 GCAAAGTGATGGGGGATGCTA 60.410 52.381 0.00 0.00 0.00 3.49
2481 8992 7.120138 GGACAAAGACGAAATAATTCTACCCAA 59.880 37.037 0.00 0.00 33.17 4.12
2506 9017 7.391554 ACATACATATATTAACCAGCAGCAAGG 59.608 37.037 0.00 0.00 0.00 3.61
2507 9018 8.232513 CACATACATATATTAACCAGCAGCAAG 58.767 37.037 0.00 0.00 0.00 4.01
2508 9019 7.719193 ACACATACATATATTAACCAGCAGCAA 59.281 33.333 0.00 0.00 0.00 3.91
2512 9023 7.223584 AGCACACATACATATATTAACCAGCA 58.776 34.615 0.00 0.00 0.00 4.41
2514 9025 9.271828 TGAAGCACACATACATATATTAACCAG 57.728 33.333 0.00 0.00 0.00 4.00
2517 9028 8.721478 CCCTGAAGCACACATACATATATTAAC 58.279 37.037 0.00 0.00 0.00 2.01
2520 9040 6.841601 ACCCTGAAGCACACATACATATATT 58.158 36.000 0.00 0.00 0.00 1.28
2527 9057 2.744202 CTCAACCCTGAAGCACACATAC 59.256 50.000 0.00 0.00 0.00 2.39
2537 9067 1.761174 GGACTGCCTCAACCCTGAA 59.239 57.895 0.00 0.00 0.00 3.02
2539 9069 2.046892 CGGACTGCCTCAACCCTG 60.047 66.667 0.00 0.00 0.00 4.45
2540 9070 1.705997 AAACGGACTGCCTCAACCCT 61.706 55.000 0.00 0.00 0.00 4.34
2542 9072 0.591659 GAAAACGGACTGCCTCAACC 59.408 55.000 0.00 0.00 0.00 3.77
2543 9073 1.264288 CAGAAAACGGACTGCCTCAAC 59.736 52.381 0.00 0.00 0.00 3.18
2544 9074 1.140052 TCAGAAAACGGACTGCCTCAA 59.860 47.619 0.00 0.00 34.57 3.02
2545 9075 0.756294 TCAGAAAACGGACTGCCTCA 59.244 50.000 0.00 0.00 34.57 3.86
2546 9076 1.801178 CTTCAGAAAACGGACTGCCTC 59.199 52.381 0.00 0.00 34.57 4.70
2548 9078 0.238553 GCTTCAGAAAACGGACTGCC 59.761 55.000 0.00 0.00 34.57 4.85
2549 9079 0.238553 GGCTTCAGAAAACGGACTGC 59.761 55.000 0.00 0.00 34.57 4.40
2552 9082 3.041508 AGTAGGCTTCAGAAAACGGAC 57.958 47.619 0.00 0.00 0.00 4.79
2553 9083 3.764237 AAGTAGGCTTCAGAAAACGGA 57.236 42.857 0.00 0.00 0.00 4.69
2554 9084 5.411669 ACATTAAGTAGGCTTCAGAAAACGG 59.588 40.000 0.00 0.00 36.22 4.44
2555 9085 6.307155 CACATTAAGTAGGCTTCAGAAAACG 58.693 40.000 0.00 0.00 36.22 3.60
2558 9088 5.560724 AGCACATTAAGTAGGCTTCAGAAA 58.439 37.500 0.00 0.00 36.22 2.52
2559 9089 5.165961 AGCACATTAAGTAGGCTTCAGAA 57.834 39.130 0.00 0.00 36.22 3.02
2560 9090 4.826274 AGCACATTAAGTAGGCTTCAGA 57.174 40.909 0.00 0.00 36.22 3.27
2563 9093 5.178438 GCTGATAGCACATTAAGTAGGCTTC 59.822 44.000 0.00 0.00 41.89 3.86
2565 9095 4.636249 GCTGATAGCACATTAAGTAGGCT 58.364 43.478 0.00 0.00 41.89 4.58
2566 9096 4.999751 GCTGATAGCACATTAAGTAGGC 57.000 45.455 0.00 0.00 41.89 3.93
2589 9143 9.467258 GAATGGTGTATCATATGGAAAACAATG 57.533 33.333 2.13 0.00 30.18 2.82
2590 9144 8.352201 CGAATGGTGTATCATATGGAAAACAAT 58.648 33.333 2.13 0.00 30.18 2.71
2606 9160 5.561919 GCACAAAGAAATGTCGAATGGTGTA 60.562 40.000 0.00 0.00 0.00 2.90
2613 9167 4.297510 CCATTGCACAAAGAAATGTCGAA 58.702 39.130 0.00 0.00 30.84 3.71
2614 9168 3.305267 CCCATTGCACAAAGAAATGTCGA 60.305 43.478 0.00 0.00 30.84 4.20
2615 9169 2.988493 CCCATTGCACAAAGAAATGTCG 59.012 45.455 0.00 0.00 30.84 4.35
2616 9170 3.742369 CACCCATTGCACAAAGAAATGTC 59.258 43.478 0.00 0.00 30.84 3.06
2617 9171 3.387374 TCACCCATTGCACAAAGAAATGT 59.613 39.130 0.00 0.00 30.84 2.71
2622 9176 1.680735 GTGTCACCCATTGCACAAAGA 59.319 47.619 0.00 0.00 34.33 2.52
2623 9177 1.408340 TGTGTCACCCATTGCACAAAG 59.592 47.619 0.00 0.00 38.49 2.77
2624 9178 1.408340 CTGTGTCACCCATTGCACAAA 59.592 47.619 0.00 0.00 39.89 2.83
2625 9179 1.031235 CTGTGTCACCCATTGCACAA 58.969 50.000 0.00 0.00 39.89 3.33
2626 9180 0.106769 ACTGTGTCACCCATTGCACA 60.107 50.000 0.00 0.00 38.86 4.57
2628 9182 0.182299 TCACTGTGTCACCCATTGCA 59.818 50.000 7.79 0.00 0.00 4.08
2629 9183 0.877071 CTCACTGTGTCACCCATTGC 59.123 55.000 7.79 0.00 0.00 3.56
2631 9185 1.768275 TGTCTCACTGTGTCACCCATT 59.232 47.619 7.79 0.00 0.00 3.16
2632 9186 1.070758 GTGTCTCACTGTGTCACCCAT 59.929 52.381 7.79 0.00 0.00 4.00
2633 9187 0.464036 GTGTCTCACTGTGTCACCCA 59.536 55.000 7.79 0.00 0.00 4.51
2634 9188 0.464036 TGTGTCTCACTGTGTCACCC 59.536 55.000 20.51 8.36 35.11 4.61
2635 9189 1.134818 TGTGTGTCTCACTGTGTCACC 60.135 52.381 20.51 15.41 46.27 4.02
2636 9190 2.293677 TGTGTGTCTCACTGTGTCAC 57.706 50.000 18.37 18.37 46.27 3.67
2637 9191 2.892374 CTTGTGTGTCTCACTGTGTCA 58.108 47.619 7.79 3.68 46.27 3.58
2638 9192 1.594862 GCTTGTGTGTCTCACTGTGTC 59.405 52.381 7.79 1.15 46.27 3.67
2639 9193 1.656652 GCTTGTGTGTCTCACTGTGT 58.343 50.000 7.79 0.00 46.27 3.72
2640 9194 0.940126 GGCTTGTGTGTCTCACTGTG 59.060 55.000 0.17 0.17 46.27 3.66
2641 9195 0.530650 CGGCTTGTGTGTCTCACTGT 60.531 55.000 6.60 0.00 46.27 3.55
2642 9196 1.835483 GCGGCTTGTGTGTCTCACTG 61.835 60.000 6.60 1.58 46.27 3.66
2643 9197 1.595382 GCGGCTTGTGTGTCTCACT 60.595 57.895 6.60 0.00 46.27 3.41
2644 9198 0.319555 TAGCGGCTTGTGTGTCTCAC 60.320 55.000 8.26 0.00 46.31 3.51
2645 9199 0.319555 GTAGCGGCTTGTGTGTCTCA 60.320 55.000 8.26 0.00 0.00 3.27
2646 9200 1.014564 GGTAGCGGCTTGTGTGTCTC 61.015 60.000 8.26 0.00 0.00 3.36
2647 9201 1.004918 GGTAGCGGCTTGTGTGTCT 60.005 57.895 8.26 0.00 0.00 3.41
2648 9202 2.380410 CGGTAGCGGCTTGTGTGTC 61.380 63.158 8.26 0.00 0.00 3.67
2649 9203 2.357034 CGGTAGCGGCTTGTGTGT 60.357 61.111 8.26 0.00 0.00 3.72
2662 9216 0.319211 CAAGTGGACGAACAGCGGTA 60.319 55.000 0.00 0.00 46.49 4.02
2678 9232 1.005748 TGTGCGAGTCTCCAGCAAG 60.006 57.895 4.24 0.00 42.93 4.01
2679 9233 1.300931 GTGTGCGAGTCTCCAGCAA 60.301 57.895 4.24 0.00 42.93 3.91
2680 9234 2.340078 GTGTGCGAGTCTCCAGCA 59.660 61.111 0.00 0.00 38.71 4.41
2683 9237 4.357947 GCGGTGTGCGAGTCTCCA 62.358 66.667 0.00 0.00 0.00 3.86
2702 9256 0.535102 AACAGGACAAGGAAGCGTGG 60.535 55.000 0.00 0.00 0.00 4.94
2703 9257 2.163818 TAACAGGACAAGGAAGCGTG 57.836 50.000 0.00 0.00 0.00 5.34
2704 9258 2.567615 AGATAACAGGACAAGGAAGCGT 59.432 45.455 0.00 0.00 0.00 5.07
2705 9259 3.190874 GAGATAACAGGACAAGGAAGCG 58.809 50.000 0.00 0.00 0.00 4.68
2706 9260 3.536570 GGAGATAACAGGACAAGGAAGC 58.463 50.000 0.00 0.00 0.00 3.86
2708 9262 3.803340 AGGGAGATAACAGGACAAGGAA 58.197 45.455 0.00 0.00 0.00 3.36
2710 9264 4.263506 ACAAAGGGAGATAACAGGACAAGG 60.264 45.833 0.00 0.00 0.00 3.61
2722 9296 3.480470 CATATGCGGAACAAAGGGAGAT 58.520 45.455 0.00 0.00 0.00 2.75
2724 9298 1.949525 CCATATGCGGAACAAAGGGAG 59.050 52.381 0.00 0.00 0.00 4.30
2736 9311 5.299279 AGAACCAGGAAATTTACCATATGCG 59.701 40.000 0.00 0.00 0.00 4.73
2739 9314 5.598417 GCCAGAACCAGGAAATTTACCATAT 59.402 40.000 0.00 0.00 0.00 1.78
2749 9327 6.096705 CACATATATTTGCCAGAACCAGGAAA 59.903 38.462 0.00 0.00 0.00 3.13
2761 9339 7.308435 GCTTCTTATGGACACATATATTTGCC 58.692 38.462 0.00 2.86 39.22 4.52
2863 9442 6.982724 TCATATGTCTACTCATGCAGAAAGTG 59.017 38.462 1.90 0.00 0.00 3.16
2876 9457 7.661536 TTACTTCAGGCTTCATATGTCTACT 57.338 36.000 1.90 0.00 0.00 2.57
2877 9458 9.982651 TTATTACTTCAGGCTTCATATGTCTAC 57.017 33.333 1.90 0.00 0.00 2.59
2879 9460 8.928448 TCTTATTACTTCAGGCTTCATATGTCT 58.072 33.333 1.90 0.00 0.00 3.41
2880 9461 9.717942 ATCTTATTACTTCAGGCTTCATATGTC 57.282 33.333 1.90 0.00 0.00 3.06
2902 9483 0.822164 GCATGGGCAGCTTTGATCTT 59.178 50.000 0.00 0.00 40.72 2.40
2913 9494 0.107066 CACTGATACAGGCATGGGCA 60.107 55.000 2.31 0.00 43.71 5.36
2916 9497 3.827008 AGTACACTGATACAGGCATGG 57.173 47.619 2.31 0.00 35.51 3.66
2925 9506 7.718334 TCTGATTCCTGAAAGTACACTGATA 57.282 36.000 0.00 0.00 0.00 2.15
2935 9516 9.918630 AATGTAAACAAATCTGATTCCTGAAAG 57.081 29.630 2.92 0.00 0.00 2.62
2939 9520 7.605449 ACCAATGTAAACAAATCTGATTCCTG 58.395 34.615 2.92 2.10 0.00 3.86
2941 9522 8.831715 AAACCAATGTAAACAAATCTGATTCC 57.168 30.769 2.92 0.00 0.00 3.01
2942 9523 9.474920 TGAAACCAATGTAAACAAATCTGATTC 57.525 29.630 2.92 0.00 0.00 2.52
2943 9524 9.480053 CTGAAACCAATGTAAACAAATCTGATT 57.520 29.630 0.00 0.00 0.00 2.57
2970 9569 7.185318 TGGAGCATTAAACATTCATTCCAAT 57.815 32.000 0.00 0.00 29.86 3.16
2994 9593 7.395489 ACCAACAAGAAAAGAATATGAGATGCT 59.605 33.333 0.00 0.00 0.00 3.79
2995 9594 7.542025 ACCAACAAGAAAAGAATATGAGATGC 58.458 34.615 0.00 0.00 0.00 3.91
3000 9599 6.373216 CCCGTACCAACAAGAAAAGAATATGA 59.627 38.462 0.00 0.00 0.00 2.15
3002 9601 6.478129 TCCCGTACCAACAAGAAAAGAATAT 58.522 36.000 0.00 0.00 0.00 1.28
3006 9605 3.842007 TCCCGTACCAACAAGAAAAGA 57.158 42.857 0.00 0.00 0.00 2.52
3007 9606 4.904253 TTTCCCGTACCAACAAGAAAAG 57.096 40.909 0.00 0.00 0.00 2.27
3012 9611 6.753107 AGAAATATTTCCCGTACCAACAAG 57.247 37.500 21.86 0.00 37.92 3.16
3019 9618 5.119743 GGCGATGTAGAAATATTTCCCGTAC 59.880 44.000 21.86 17.75 37.92 3.67
3022 9621 3.122948 CGGCGATGTAGAAATATTTCCCG 59.877 47.826 21.86 20.10 37.92 5.14
3037 9636 3.775661 ATTTTAAAAGGGACGGCGATG 57.224 42.857 16.62 0.00 0.00 3.84
3041 9642 3.056821 AGCTGAATTTTAAAAGGGACGGC 60.057 43.478 6.79 12.49 0.00 5.68
3087 9688 7.396540 AAAAACTGGATCATATTCACCTCAC 57.603 36.000 0.00 0.00 0.00 3.51
3099 9706 6.071952 GGCTGTTTGAGATAAAAACTGGATCA 60.072 38.462 0.00 0.00 38.17 2.92
3113 9720 4.661222 TGAATTATGTGGGCTGTTTGAGA 58.339 39.130 0.00 0.00 0.00 3.27
3122 9729 7.575720 GCATAAATACCTCTGAATTATGTGGGC 60.576 40.741 0.00 0.00 36.69 5.36
3124 9731 8.394971 TGCATAAATACCTCTGAATTATGTGG 57.605 34.615 0.00 0.00 36.69 4.17
3134 9742 8.892723 TGATAAACAACTGCATAAATACCTCTG 58.107 33.333 0.00 0.00 0.00 3.35
3147 9755 5.449177 GGGAGCAAGTATGATAAACAACTGC 60.449 44.000 0.00 0.00 0.00 4.40
3151 9759 4.080807 TCCGGGAGCAAGTATGATAAACAA 60.081 41.667 0.00 0.00 0.00 2.83
3156 9764 3.901222 TCATTCCGGGAGCAAGTATGATA 59.099 43.478 0.00 0.00 0.00 2.15
3161 9769 1.568504 ACTCATTCCGGGAGCAAGTA 58.431 50.000 0.00 0.00 35.79 2.24
3170 9779 5.068234 TGAGTAGTTGTAACTCATTCCGG 57.932 43.478 0.00 0.00 46.38 5.14
3180 9789 8.311109 TGTGAGAATAATGCTGAGTAGTTGTAA 58.689 33.333 0.00 0.00 0.00 2.41
3192 9801 8.416329 AGAAACAAAAACTGTGAGAATAATGCT 58.584 29.630 0.00 0.00 38.67 3.79
3217 10224 8.670135 TGGTCAAAACGTATATGGTTATTTGAG 58.330 33.333 6.53 0.00 29.59 3.02
3232 10239 5.763204 AGAACATGAGTATTGGTCAAAACGT 59.237 36.000 0.00 0.00 33.09 3.99
3233 10240 6.241207 AGAACATGAGTATTGGTCAAAACG 57.759 37.500 0.00 0.00 33.09 3.60
3248 10255 4.215185 TGCAGCGTCAAAAATAGAACATGA 59.785 37.500 0.00 0.00 0.00 3.07
3252 10259 3.908382 CAGTGCAGCGTCAAAAATAGAAC 59.092 43.478 0.00 0.00 0.00 3.01
3256 10263 1.068610 GGCAGTGCAGCGTCAAAAATA 60.069 47.619 18.61 0.00 34.64 1.40
3258 10265 1.065600 GGCAGTGCAGCGTCAAAAA 59.934 52.632 18.61 0.00 34.64 1.94
3259 10266 0.533978 TAGGCAGTGCAGCGTCAAAA 60.534 50.000 18.61 0.00 34.11 2.44
3261 10268 1.020861 CATAGGCAGTGCAGCGTCAA 61.021 55.000 18.61 0.00 34.11 3.18
3262 10269 1.448365 CATAGGCAGTGCAGCGTCA 60.448 57.895 18.61 0.00 34.11 4.35
3263 10270 2.817423 GCATAGGCAGTGCAGCGTC 61.817 63.158 18.61 0.00 42.08 5.19
3264 10271 2.809861 AAGCATAGGCAGTGCAGCGT 62.810 55.000 18.61 10.25 44.87 5.07
3265 10272 0.811219 TAAGCATAGGCAGTGCAGCG 60.811 55.000 18.61 3.01 44.87 5.18
3266 10273 1.602311 ATAAGCATAGGCAGTGCAGC 58.398 50.000 18.61 14.49 44.87 5.25
3267 10274 2.740981 GCTATAAGCATAGGCAGTGCAG 59.259 50.000 18.61 4.59 44.87 4.41
3268 10275 2.771089 GCTATAAGCATAGGCAGTGCA 58.229 47.619 18.61 0.00 44.87 4.57
3275 10282 3.257393 CGAAGCTGGCTATAAGCATAGG 58.743 50.000 0.78 0.00 44.75 2.57
3308 10716 2.571757 GGTCGCGTCATGTCCTGA 59.428 61.111 5.77 0.00 0.00 3.86
3309 10717 2.880879 CGGTCGCGTCATGTCCTG 60.881 66.667 5.77 0.00 0.00 3.86
3310 10718 3.338126 GACGGTCGCGTCATGTCCT 62.338 63.158 5.77 0.00 38.62 3.85
3311 10719 2.879462 GACGGTCGCGTCATGTCC 60.879 66.667 5.77 0.00 38.62 4.02
3312 10720 2.879462 GGACGGTCGCGTCATGTC 60.879 66.667 15.74 12.34 40.34 3.06
3313 10721 4.430765 GGGACGGTCGCGTCATGT 62.431 66.667 15.74 2.70 40.34 3.21
3326 10734 2.294979 GAACCCCAAATCATACGGGAC 58.705 52.381 0.00 0.00 43.21 4.46
3327 10735 1.916874 TGAACCCCAAATCATACGGGA 59.083 47.619 0.00 0.00 43.21 5.14
3328 10736 2.021457 GTGAACCCCAAATCATACGGG 58.979 52.381 0.00 0.00 41.71 5.28
3329 10737 2.999331 AGTGAACCCCAAATCATACGG 58.001 47.619 0.00 0.00 0.00 4.02
3380 11028 2.421107 GGCCAAGATCTCTGCTGAATCA 60.421 50.000 14.09 0.00 0.00 2.57
3381 11029 2.220313 GGCCAAGATCTCTGCTGAATC 58.780 52.381 14.09 1.95 0.00 2.52


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

AutoCloner maintained by Alex Coulton.