Multiple sequence alignment - TraesCS3D01G369300

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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 TraesCS3D01G369300 chr3D 100.000 9178 0 0 1 9178 482255208 482246031 0.000000e+00 16949.0
1 TraesCS3D01G369300 chr3D 83.119 2174 262 57 1251 3377 61358572 61356457 0.000000e+00 1884.0
2 TraesCS3D01G369300 chr3D 81.390 2187 290 75 7050 9178 61333839 61331712 0.000000e+00 1676.0
3 TraesCS3D01G369300 chr3D 83.333 792 106 17 6158 6937 61334626 61333849 0.000000e+00 708.0
4 TraesCS3D01G369300 chr3D 88.043 184 21 1 3495 3677 61346622 61346439 5.580000e-52 217.0
5 TraesCS3D01G369300 chr3D 94.286 35 2 0 4665 4699 61345837 61345803 5.000000e-03 54.7
6 TraesCS3D01G369300 chr3A 93.608 5210 263 33 3485 8647 625321941 625316755 0.000000e+00 7712.0
7 TraesCS3D01G369300 chr3A 94.312 1547 60 10 1212 2750 625324981 625323455 0.000000e+00 2344.0
8 TraesCS3D01G369300 chr3A 93.645 1133 52 10 3 1119 625326111 625324983 0.000000e+00 1676.0
9 TraesCS3D01G369300 chr3A 80.159 2016 297 63 7210 9175 742286036 742287998 0.000000e+00 1411.0
10 TraesCS3D01G369300 chr3A 94.511 747 36 4 2743 3488 625322983 625322241 0.000000e+00 1147.0
11 TraesCS3D01G369300 chr3A 81.638 1062 151 31 5893 6937 742284883 742285917 0.000000e+00 841.0
12 TraesCS3D01G369300 chr3A 93.494 538 35 0 8641 9178 625316735 625316198 0.000000e+00 800.0
13 TraesCS3D01G369300 chr3A 79.437 462 80 14 27 476 631267934 631268392 6.920000e-81 313.0
14 TraesCS3D01G369300 chr3A 85.052 194 27 2 3486 3677 742282272 742282465 7.270000e-46 196.0
15 TraesCS3D01G369300 chr3A 88.636 88 10 0 4149 4236 742282744 742282831 3.500000e-19 108.0
16 TraesCS3D01G369300 chr3B 89.667 5797 412 78 3485 9178 644503085 644497373 0.000000e+00 7214.0
17 TraesCS3D01G369300 chr3B 82.321 2042 270 52 1348 3349 793090211 793092201 0.000000e+00 1687.0
18 TraesCS3D01G369300 chr3B 83.533 1002 118 18 1251 2242 434652848 434653812 0.000000e+00 893.0
19 TraesCS3D01G369300 chr3B 83.162 778 103 20 6172 6937 434659277 434660038 0.000000e+00 686.0
20 TraesCS3D01G369300 chr1D 84.296 3063 333 74 5764 8752 64377909 64374921 0.000000e+00 2856.0
21 TraesCS3D01G369300 chr1D 83.172 1753 211 43 1251 2966 461058780 461060485 0.000000e+00 1526.0
22 TraesCS3D01G369300 chr1D 81.101 2016 279 63 7210 9175 461072675 461074638 0.000000e+00 1519.0
23 TraesCS3D01G369300 chr1D 79.554 538 76 22 3723 4237 461061493 461062019 4.080000e-93 353.0
24 TraesCS3D01G369300 chr5D 84.496 2193 266 43 1251 3405 441320172 441318016 0.000000e+00 2098.0
25 TraesCS3D01G369300 chr5D 81.727 2189 281 84 7050 9178 441313522 441311393 0.000000e+00 1716.0
26 TraesCS3D01G369300 chr5D 81.740 1276 171 30 5679 6937 441314762 441313532 0.000000e+00 1009.0
27 TraesCS3D01G369300 chr5D 75.993 554 110 20 70 609 529160840 529161384 1.970000e-66 265.0
28 TraesCS3D01G369300 chr5D 87.629 194 23 1 3485 3677 441317558 441317365 3.340000e-54 224.0
29 TraesCS3D01G369300 chr5A 84.392 2172 241 50 1251 3377 474626957 474624839 0.000000e+00 2043.0
30 TraesCS3D01G369300 chr5A 82.406 1006 142 20 5675 6661 474621376 474620387 0.000000e+00 845.0
31 TraesCS3D01G369300 chr5A 82.817 774 102 25 3485 4245 474624360 474623605 0.000000e+00 664.0
32 TraesCS3D01G369300 chr5A 81.055 834 114 30 7050 7867 474618838 474618033 7.820000e-175 625.0
33 TraesCS3D01G369300 chr5A 80.242 825 109 19 4552 5356 474623529 474622739 1.030000e-158 571.0
34 TraesCS3D01G369300 chr4B 84.347 1891 230 38 1251 3107 101047879 101049737 0.000000e+00 1792.0
35 TraesCS3D01G369300 chr2B 81.914 2173 287 57 1251 3377 726076235 726074123 0.000000e+00 1738.0
36 TraesCS3D01G369300 chr2B 81.120 2018 280 59 7210 9178 175483827 175481862 0.000000e+00 1522.0
37 TraesCS3D01G369300 chr2B 85.988 1356 113 34 1508 2854 535269363 535270650 0.000000e+00 1380.0
38 TraesCS3D01G369300 chr2B 81.884 1391 190 37 2019 3369 175493259 175491891 0.000000e+00 1116.0
39 TraesCS3D01G369300 chr2B 86.057 875 84 28 3494 4359 535289450 535290295 0.000000e+00 905.0
40 TraesCS3D01G369300 chr2B 88.873 719 72 8 1242 1955 26861450 26862165 0.000000e+00 878.0
41 TraesCS3D01G369300 chr2B 89.169 397 36 5 3095 3490 535288756 535289146 1.070000e-133 488.0
42 TraesCS3D01G369300 chr2B 89.340 197 20 1 2903 3099 535270922 535271117 7.120000e-61 246.0
43 TraesCS3D01G369300 chr2B 85.593 118 17 0 4728 4845 175490750 175490633 3.480000e-24 124.0
44 TraesCS3D01G369300 chr2B 71.667 360 67 28 80 419 63265775 63266119 5.950000e-07 67.6
45 TraesCS3D01G369300 chr2B 73.488 215 41 14 236 440 150402701 150402493 5.950000e-07 67.6
46 TraesCS3D01G369300 chr6B 81.112 2176 310 63 7055 9178 662459682 662457556 0.000000e+00 1648.0
47 TraesCS3D01G369300 chr6B 81.400 1086 140 36 2321 3377 662478396 662477344 0.000000e+00 830.0
48 TraesCS3D01G369300 chr6B 82.500 760 97 21 6194 6940 662460434 662459698 1.300000e-177 634.0
49 TraesCS3D01G369300 chr6B 80.224 536 79 19 3721 4235 662476665 662476136 2.420000e-100 377.0
50 TraesCS3D01G369300 chr6B 81.658 398 59 7 4728 5112 662476029 662475633 1.490000e-82 318.0
51 TraesCS3D01G369300 chr6B 78.363 342 57 14 3 336 169483328 169482996 1.210000e-48 206.0
52 TraesCS3D01G369300 chr6B 76.684 193 38 7 367 554 30452454 30452644 5.860000e-17 100.0
53 TraesCS3D01G369300 chr4A 80.384 2187 309 82 7055 9178 650263535 650261406 0.000000e+00 1552.0
54 TraesCS3D01G369300 chr4A 81.967 1403 190 37 2019 3377 650288348 650286965 0.000000e+00 1131.0
55 TraesCS3D01G369300 chr6A 82.841 1795 216 56 1630 3377 456008339 456006590 0.000000e+00 1524.0
56 TraesCS3D01G369300 chr6A 80.118 2203 305 82 7050 9178 456002826 456000683 0.000000e+00 1519.0
57 TraesCS3D01G369300 chr6A 79.783 2211 309 78 7050 9178 26580537 26578383 0.000000e+00 1480.0
58 TraesCS3D01G369300 chr6A 82.864 782 108 19 6171 6940 26581310 26580543 0.000000e+00 678.0
59 TraesCS3D01G369300 chr6A 83.299 491 59 12 6459 6940 456003311 456002835 1.830000e-116 431.0
60 TraesCS3D01G369300 chr6A 82.451 359 46 9 4728 5072 26583855 26583500 1.940000e-76 298.0
61 TraesCS3D01G369300 chr6A 77.273 572 87 32 10 553 600531317 600530761 6.970000e-76 296.0
62 TraesCS3D01G369300 chr6A 84.615 195 28 2 3485 3677 26584521 26584327 9.400000e-45 193.0
63 TraesCS3D01G369300 chr7D 80.748 2005 296 54 7210 9172 423313990 423315946 0.000000e+00 1482.0
64 TraesCS3D01G369300 chr7D 80.669 538 77 17 3721 4237 423309796 423310327 8.640000e-105 392.0
65 TraesCS3D01G369300 chr7D 81.443 97 13 3 185 278 35870988 35871082 3.550000e-09 75.0
66 TraesCS3D01G369300 chr7D 74.157 178 36 8 231 401 22334760 22334934 2.140000e-06 65.8
67 TraesCS3D01G369300 chr5B 81.189 1951 272 56 7050 8952 441546963 441545060 0.000000e+00 1482.0
68 TraesCS3D01G369300 chr5B 83.231 1306 168 32 5658 6937 441548252 441546972 0.000000e+00 1151.0
69 TraesCS3D01G369300 chr5B 84.540 1119 119 25 2291 3377 441552788 441551692 0.000000e+00 1059.0
70 TraesCS3D01G369300 chr5B 87.090 945 109 8 1251 2184 441553792 441552850 0.000000e+00 1057.0
71 TraesCS3D01G369300 chr5B 83.846 780 85 28 3485 4248 441551213 441550459 0.000000e+00 704.0
72 TraesCS3D01G369300 chr5B 80.485 743 100 17 4552 5278 441550383 441549670 2.270000e-145 527.0
73 TraesCS3D01G369300 chr7A 82.924 978 133 24 5976 6937 450664258 450663299 0.000000e+00 850.0
74 TraesCS3D01G369300 chr7A 82.805 884 111 22 8317 9175 450662166 450661299 0.000000e+00 752.0
75 TraesCS3D01G369300 chr7A 82.292 672 92 23 5916 6578 75234739 75235392 2.900000e-154 556.0
76 TraesCS3D01G369300 chr7A 79.160 619 79 22 4754 5356 75232776 75233360 5.200000e-102 383.0
77 TraesCS3D01G369300 chr7A 83.417 398 52 7 4728 5112 450666287 450665891 3.150000e-94 357.0
78 TraesCS3D01G369300 chr7A 85.128 195 27 2 3485 3677 450666950 450666756 2.020000e-46 198.0
79 TraesCS3D01G369300 chr7A 94.595 37 2 0 4665 4701 450666325 450666289 3.580000e-04 58.4
80 TraesCS3D01G369300 chr1B 79.248 665 95 28 3 633 311736670 311736015 3.060000e-114 424.0
81 TraesCS3D01G369300 chr7B 77.407 540 95 24 25 550 705785973 705785447 6.970000e-76 296.0
82 TraesCS3D01G369300 chr1A 76.776 577 100 24 78 633 540632506 540631943 9.010000e-75 292.0
83 TraesCS3D01G369300 chr2D 77.987 477 89 12 570 1034 413277621 413277149 1.510000e-72 285.0
84 TraesCS3D01G369300 chrUn 74.963 679 133 26 76 732 384867719 384868382 2.520000e-70 278.0
85 TraesCS3D01G369300 chr6D 73.684 456 88 24 183 622 41530481 41530920 2.060000e-31 148.0
86 TraesCS3D01G369300 chr6D 85.321 109 16 0 10 118 454312170 454312062 7.530000e-21 113.0
87 TraesCS3D01G369300 chr2A 77.124 153 29 6 293 442 97559414 97559265 5.910000e-12 84.2


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 TraesCS3D01G369300 chr3D 482246031 482255208 9177 True 16949.000000 16949 100.000000 1 9178 1 chr3D.!!$R2 9177
1 TraesCS3D01G369300 chr3D 61356457 61358572 2115 True 1884.000000 1884 83.119000 1251 3377 1 chr3D.!!$R1 2126
2 TraesCS3D01G369300 chr3D 61331712 61334626 2914 True 1192.000000 1676 82.361500 6158 9178 2 chr3D.!!$R3 3020
3 TraesCS3D01G369300 chr3A 625316198 625326111 9913 True 2735.800000 7712 93.914000 3 9178 5 chr3A.!!$R1 9175
4 TraesCS3D01G369300 chr3A 742282272 742287998 5726 False 639.000000 1411 83.871250 3486 9175 4 chr3A.!!$F2 5689
5 TraesCS3D01G369300 chr3B 644497373 644503085 5712 True 7214.000000 7214 89.667000 3485 9178 1 chr3B.!!$R1 5693
6 TraesCS3D01G369300 chr3B 793090211 793092201 1990 False 1687.000000 1687 82.321000 1348 3349 1 chr3B.!!$F3 2001
7 TraesCS3D01G369300 chr3B 434652848 434653812 964 False 893.000000 893 83.533000 1251 2242 1 chr3B.!!$F1 991
8 TraesCS3D01G369300 chr3B 434659277 434660038 761 False 686.000000 686 83.162000 6172 6937 1 chr3B.!!$F2 765
9 TraesCS3D01G369300 chr1D 64374921 64377909 2988 True 2856.000000 2856 84.296000 5764 8752 1 chr1D.!!$R1 2988
10 TraesCS3D01G369300 chr1D 461072675 461074638 1963 False 1519.000000 1519 81.101000 7210 9175 1 chr1D.!!$F1 1965
11 TraesCS3D01G369300 chr1D 461058780 461062019 3239 False 939.500000 1526 81.363000 1251 4237 2 chr1D.!!$F2 2986
12 TraesCS3D01G369300 chr5D 441311393 441320172 8779 True 1261.750000 2098 83.898000 1251 9178 4 chr5D.!!$R1 7927
13 TraesCS3D01G369300 chr5D 529160840 529161384 544 False 265.000000 265 75.993000 70 609 1 chr5D.!!$F1 539
14 TraesCS3D01G369300 chr5A 474618033 474626957 8924 True 949.600000 2043 82.182400 1251 7867 5 chr5A.!!$R1 6616
15 TraesCS3D01G369300 chr4B 101047879 101049737 1858 False 1792.000000 1792 84.347000 1251 3107 1 chr4B.!!$F1 1856
16 TraesCS3D01G369300 chr2B 726074123 726076235 2112 True 1738.000000 1738 81.914000 1251 3377 1 chr2B.!!$R3 2126
17 TraesCS3D01G369300 chr2B 175481862 175483827 1965 True 1522.000000 1522 81.120000 7210 9178 1 chr2B.!!$R2 1968
18 TraesCS3D01G369300 chr2B 26861450 26862165 715 False 878.000000 878 88.873000 1242 1955 1 chr2B.!!$F1 713
19 TraesCS3D01G369300 chr2B 535269363 535271117 1754 False 813.000000 1380 87.664000 1508 3099 2 chr2B.!!$F3 1591
20 TraesCS3D01G369300 chr2B 535288756 535290295 1539 False 696.500000 905 87.613000 3095 4359 2 chr2B.!!$F4 1264
21 TraesCS3D01G369300 chr2B 175490633 175493259 2626 True 620.000000 1116 83.738500 2019 4845 2 chr2B.!!$R4 2826
22 TraesCS3D01G369300 chr6B 662457556 662460434 2878 True 1141.000000 1648 81.806000 6194 9178 2 chr6B.!!$R2 2984
23 TraesCS3D01G369300 chr6B 662475633 662478396 2763 True 508.333333 830 81.094000 2321 5112 3 chr6B.!!$R3 2791
24 TraesCS3D01G369300 chr4A 650261406 650263535 2129 True 1552.000000 1552 80.384000 7055 9178 1 chr4A.!!$R1 2123
25 TraesCS3D01G369300 chr4A 650286965 650288348 1383 True 1131.000000 1131 81.967000 2019 3377 1 chr4A.!!$R2 1358
26 TraesCS3D01G369300 chr6A 456000683 456008339 7656 True 1158.000000 1524 82.086000 1630 9178 3 chr6A.!!$R3 7548
27 TraesCS3D01G369300 chr6A 26578383 26584521 6138 True 662.250000 1480 82.428250 3485 9178 4 chr6A.!!$R2 5693
28 TraesCS3D01G369300 chr6A 600530761 600531317 556 True 296.000000 296 77.273000 10 553 1 chr6A.!!$R1 543
29 TraesCS3D01G369300 chr7D 423309796 423315946 6150 False 937.000000 1482 80.708500 3721 9172 2 chr7D.!!$F3 5451
30 TraesCS3D01G369300 chr5B 441545060 441553792 8732 True 996.666667 1482 83.396833 1251 8952 6 chr5B.!!$R1 7701
31 TraesCS3D01G369300 chr7A 75232776 75235392 2616 False 469.500000 556 80.726000 4754 6578 2 chr7A.!!$F1 1824
32 TraesCS3D01G369300 chr7A 450661299 450666950 5651 True 443.080000 850 85.773800 3485 9175 5 chr7A.!!$R1 5690
33 TraesCS3D01G369300 chr1B 311736015 311736670 655 True 424.000000 424 79.248000 3 633 1 chr1B.!!$R1 630
34 TraesCS3D01G369300 chr7B 705785447 705785973 526 True 296.000000 296 77.407000 25 550 1 chr7B.!!$R1 525
35 TraesCS3D01G369300 chr1A 540631943 540632506 563 True 292.000000 292 76.776000 78 633 1 chr1A.!!$R1 555
36 TraesCS3D01G369300 chrUn 384867719 384868382 663 False 278.000000 278 74.963000 76 732 1 chrUn.!!$F1 656

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
762 813 1.382522 AGCGGTATGGAATGTGCAAG 58.617 50.000 0.00 0.00 0.00 4.01 F
1177 1234 0.105593 ACGATTCTGCGCCATGAGAT 59.894 50.000 4.18 0.00 33.86 2.75 F
1188 1245 0.730834 CCATGAGATCGCGATCGGAC 60.731 60.000 35.89 29.78 42.48 4.79 F
1198 1255 0.731514 GCGATCGGACGACAACAAGA 60.732 55.000 18.30 0.00 35.09 3.02 F
1602 1685 0.807667 CTTCGGGAGATCAAGTGCGG 60.808 60.000 0.00 0.00 39.57 5.69 F
3124 4017 1.662446 TCGGTCGGTTTTCGTCTGC 60.662 57.895 0.00 0.00 40.32 4.26 F
3887 5511 1.110442 CAGGTCACCCAGCAAACAAA 58.890 50.000 0.00 0.00 0.00 2.83 F
5264 6990 0.455410 TGTTGCAGCAACTGGTGTTC 59.545 50.000 32.99 10.06 43.85 3.18 F
5567 8235 0.478072 TGGCCTGAACCAGTGATGTT 59.522 50.000 3.32 0.00 33.75 2.71 F
6398 9479 0.108207 GCAGTGCCATGCCTAGATCT 59.892 55.000 2.85 0.00 40.43 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2557 2686 1.192090 CGCCAAACAAGCAAAAATCGG 59.808 47.619 0.00 0.00 0.00 4.18 R
3124 4017 2.576832 CCAAGCAGGCCAACCAAGG 61.577 63.158 5.01 0.00 39.06 3.61 R
3223 4116 9.573133 CCATATTGTGAGTACCAAAAGAAATTC 57.427 33.333 0.00 0.00 0.00 2.17 R
3432 4334 2.345991 GTTCACTGCCCCGCTACA 59.654 61.111 0.00 0.00 0.00 2.74 R
3582 5183 2.859992 GTGGAATGACCTCACCAGC 58.140 57.895 0.00 0.00 39.86 4.85 R
4968 6657 0.326264 AGAAGTGATGGTGGCCACTC 59.674 55.000 33.91 24.67 42.25 3.51 R
5996 8862 3.193056 TCATACACCCGAACACAACGATA 59.807 43.478 0.00 0.00 0.00 2.92 R
6311 9392 0.455633 GGCTTTGACAATGCTCTGCG 60.456 55.000 21.33 0.00 0.00 5.18 R
7755 12225 1.341383 GGTCATGGGTGAAAGCAGGAT 60.341 52.381 0.00 0.00 35.80 3.24 R
8522 13054 2.024588 CAAGCGCAACTGCACGTT 59.975 55.556 11.47 0.00 42.21 3.99 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
167 180 6.262193 AGAATTTTACCGTGGGTACATTTG 57.738 37.500 0.00 0.00 37.97 2.32
237 264 7.671302 AGTCAGGTCTGCGATTTGTATATTAT 58.329 34.615 0.00 0.00 0.00 1.28
410 451 6.954944 TCAACAACTATTTTCTTCGGTTCAG 58.045 36.000 0.00 0.00 0.00 3.02
532 577 3.254657 CCCTCGGTTCAAAGTTATTGCAA 59.745 43.478 0.00 0.00 0.00 4.08
607 653 8.697846 TTTTACAGAAGTTATCGGAGTATGTG 57.302 34.615 0.00 0.00 0.00 3.21
625 671 8.902540 AGTATGTGTCAACAACTATTTCTTCA 57.097 30.769 0.00 0.00 40.46 3.02
646 696 6.417191 TCAAGTCAAAGTTACAGTTGTGTC 57.583 37.500 0.00 0.00 38.19 3.67
746 797 7.858052 AAAACTTTTTGATCTATGTGAAGCG 57.142 32.000 0.00 0.00 0.00 4.68
755 806 4.955811 TCTATGTGAAGCGGTATGGAAT 57.044 40.909 0.00 0.00 0.00 3.01
762 813 1.382522 AGCGGTATGGAATGTGCAAG 58.617 50.000 0.00 0.00 0.00 4.01
882 933 3.064820 GTGTGTACCTTGTGACAAACCAG 59.935 47.826 0.00 0.00 28.97 4.00
905 956 6.007703 AGCAAATTAGCCTAGTTGGTTGTTA 58.992 36.000 0.00 0.00 38.35 2.41
908 959 6.920569 AATTAGCCTAGTTGGTTGTTATCG 57.079 37.500 0.00 0.00 38.35 2.92
955 1006 2.695359 TCGATTCCCTGCTACAACAAC 58.305 47.619 0.00 0.00 0.00 3.32
1040 1093 5.621197 TTAAAGTGTCATCAATTCCACGG 57.379 39.130 0.00 0.00 30.42 4.94
1051 1104 1.727511 ATTCCACGGCGCATGATTGG 61.728 55.000 10.83 6.16 0.00 3.16
1066 1119 7.143340 CGCATGATTGGAAAGTCATTAATCAT 58.857 34.615 0.00 0.00 44.72 2.45
1088 1141 1.750778 ACCGCAGAAAATTAGGCATGG 59.249 47.619 0.00 0.00 0.00 3.66
1160 1217 9.463443 AAAAAGGATCTCATTAAAACAAGAACG 57.537 29.630 0.00 0.00 0.00 3.95
1161 1218 7.979444 AAGGATCTCATTAAAACAAGAACGA 57.021 32.000 0.00 0.00 0.00 3.85
1162 1219 8.567285 AAGGATCTCATTAAAACAAGAACGAT 57.433 30.769 0.00 0.00 0.00 3.73
1163 1220 8.567285 AGGATCTCATTAAAACAAGAACGATT 57.433 30.769 0.00 0.00 0.00 3.34
1164 1221 8.669243 AGGATCTCATTAAAACAAGAACGATTC 58.331 33.333 0.00 0.00 0.00 2.52
1165 1222 8.669243 GGATCTCATTAAAACAAGAACGATTCT 58.331 33.333 0.00 0.00 43.15 2.40
1166 1223 9.483062 GATCTCATTAAAACAAGAACGATTCTG 57.517 33.333 0.00 0.00 40.59 3.02
1167 1224 7.298122 TCTCATTAAAACAAGAACGATTCTGC 58.702 34.615 0.00 0.00 40.59 4.26
1168 1225 6.077197 TCATTAAAACAAGAACGATTCTGCG 58.923 36.000 0.00 0.00 40.59 5.18
1169 1226 2.316119 AAACAAGAACGATTCTGCGC 57.684 45.000 0.00 0.00 40.59 6.09
1170 1227 0.517316 AACAAGAACGATTCTGCGCC 59.483 50.000 4.18 0.00 40.59 6.53
1171 1228 0.602638 ACAAGAACGATTCTGCGCCA 60.603 50.000 4.18 0.00 40.59 5.69
1172 1229 0.729116 CAAGAACGATTCTGCGCCAT 59.271 50.000 4.18 0.00 40.59 4.40
1173 1230 0.729116 AAGAACGATTCTGCGCCATG 59.271 50.000 4.18 0.00 40.59 3.66
1174 1231 0.108186 AGAACGATTCTGCGCCATGA 60.108 50.000 4.18 0.00 38.91 3.07
1175 1232 0.302890 GAACGATTCTGCGCCATGAG 59.697 55.000 4.18 0.00 33.86 2.90
1176 1233 0.108186 AACGATTCTGCGCCATGAGA 60.108 50.000 4.18 0.00 33.86 3.27
1177 1234 0.105593 ACGATTCTGCGCCATGAGAT 59.894 50.000 4.18 0.00 33.86 2.75
1178 1235 0.788995 CGATTCTGCGCCATGAGATC 59.211 55.000 4.18 6.20 0.00 2.75
1179 1236 0.788995 GATTCTGCGCCATGAGATCG 59.211 55.000 4.18 0.00 0.00 3.69
1185 1242 3.456798 GCCATGAGATCGCGATCG 58.543 61.111 35.89 24.90 42.48 3.69
1186 1243 2.091112 GCCATGAGATCGCGATCGG 61.091 63.158 35.89 31.01 42.48 4.18
1187 1244 1.581447 CCATGAGATCGCGATCGGA 59.419 57.895 35.89 28.00 42.48 4.55
1188 1245 0.730834 CCATGAGATCGCGATCGGAC 60.731 60.000 35.89 29.78 42.48 4.79
1189 1246 1.062336 CATGAGATCGCGATCGGACG 61.062 60.000 35.89 24.44 42.48 4.79
1190 1247 1.228657 ATGAGATCGCGATCGGACGA 61.229 55.000 35.89 22.12 42.48 4.20
1191 1248 1.439037 GAGATCGCGATCGGACGAC 60.439 63.158 35.89 22.09 41.76 4.34
1192 1249 2.102394 GAGATCGCGATCGGACGACA 62.102 60.000 35.89 0.93 41.76 4.35
1193 1250 1.298116 GATCGCGATCGGACGACAA 60.298 57.895 31.24 0.00 41.76 3.18
1194 1251 1.529883 GATCGCGATCGGACGACAAC 61.530 60.000 31.24 7.33 41.76 3.32
1195 1252 2.261172 ATCGCGATCGGACGACAACA 62.261 55.000 17.62 0.00 41.76 3.33
1196 1253 2.084101 CGCGATCGGACGACAACAA 61.084 57.895 18.30 0.00 35.09 2.83
1197 1254 1.702299 GCGATCGGACGACAACAAG 59.298 57.895 18.30 0.00 35.09 3.16
1198 1255 0.731514 GCGATCGGACGACAACAAGA 60.732 55.000 18.30 0.00 35.09 3.02
1199 1256 1.909376 CGATCGGACGACAACAAGAT 58.091 50.000 7.38 0.00 35.09 2.40
1200 1257 1.846782 CGATCGGACGACAACAAGATC 59.153 52.381 7.38 0.00 35.09 2.75
1201 1258 1.846782 GATCGGACGACAACAAGATCG 59.153 52.381 0.00 0.00 43.97 3.69
1207 1264 1.693467 CGACAACAAGATCGTTCGGA 58.307 50.000 0.00 0.00 33.63 4.55
1208 1265 2.259618 CGACAACAAGATCGTTCGGAT 58.740 47.619 0.00 0.00 38.35 4.18
1223 1280 4.568359 CGTTCGGATCTGATCACAAAATCT 59.432 41.667 18.64 0.00 0.00 2.40
1224 1281 5.501413 CGTTCGGATCTGATCACAAAATCTG 60.501 44.000 18.64 0.00 0.00 2.90
1230 1287 6.039493 GGATCTGATCACAAAATCTGAATGCT 59.961 38.462 18.64 0.00 37.23 3.79
1366 1431 7.031226 TCAATTCACCTTTCTCAACTCTTTG 57.969 36.000 0.00 0.00 0.00 2.77
1432 1512 1.153958 GATGCCAAGGAAGCGCAAC 60.154 57.895 11.47 2.10 35.85 4.17
1492 1573 3.011517 AAGCGCCCTCCACCTCAT 61.012 61.111 2.29 0.00 0.00 2.90
1533 1614 3.882888 TCACTTTTGACTGCCTGTAAAGG 59.117 43.478 0.00 0.00 31.74 3.11
1602 1685 0.807667 CTTCGGGAGATCAAGTGCGG 60.808 60.000 0.00 0.00 39.57 5.69
1884 1971 7.148188 TGTCAATATTGATGAGAAGTTCAAGCC 60.148 37.037 20.65 3.47 39.77 4.35
1885 1972 6.885918 TCAATATTGATGAGAAGTTCAAGCCA 59.114 34.615 14.23 0.00 39.77 4.75
2002 2093 7.087409 CATACTTGCTCATTTTGTATGGTGA 57.913 36.000 0.00 0.00 37.72 4.02
2011 2103 9.503427 GCTCATTTTGTATGGTGATAACTTTAC 57.497 33.333 0.00 0.00 0.00 2.01
2224 2321 7.817418 TGCCTTCTTTTCTACAATGTAAGTT 57.183 32.000 0.00 0.00 0.00 2.66
2307 2421 7.169140 CCTTTTTACCAGCTTTTGTACATTGAC 59.831 37.037 0.00 0.00 0.00 3.18
2557 2686 2.022240 TTGAAACCCCAGTTTGGCGC 62.022 55.000 0.00 0.00 46.25 6.53
2646 2779 1.813092 GCAGTGATGAGGTATGCTGGG 60.813 57.143 0.00 0.00 34.10 4.45
2696 2840 8.773404 TCTAGTAATTGTAGCTCCTTTTGTTC 57.227 34.615 0.00 0.00 0.00 3.18
2850 3482 2.341846 TTGTGGTTGTTCTCCCTGAC 57.658 50.000 0.00 0.00 0.00 3.51
2866 3518 3.496331 CCTGACAACCCATGTTTTACCT 58.504 45.455 0.00 0.00 44.12 3.08
2900 3559 5.585500 TTACTGTCGATAACTTGTGTTGC 57.415 39.130 0.00 0.00 37.59 4.17
2997 3885 5.462405 TCTTGGTTTGTGTGTTTTGTGTAC 58.538 37.500 0.00 0.00 0.00 2.90
3013 3901 8.968242 GTTTTGTGTACTTCATGATCCTTTTTC 58.032 33.333 0.00 0.00 0.00 2.29
3033 3922 6.983474 TTTCGCATCTGAAAATCATGTCTA 57.017 33.333 0.00 0.00 35.04 2.59
3124 4017 1.662446 TCGGTCGGTTTTCGTCTGC 60.662 57.895 0.00 0.00 40.32 4.26
3223 4116 2.885894 GACTAGACACGGATCTTAGGGG 59.114 54.545 0.00 0.00 0.00 4.79
3432 4334 2.239907 GGCCATACTGGTTCTTCTTCCT 59.760 50.000 0.00 0.00 40.46 3.36
3434 4336 3.307762 GCCATACTGGTTCTTCTTCCTGT 60.308 47.826 0.00 0.00 40.46 4.00
3582 5183 3.357079 GTGTGGCTGACAAGGGCG 61.357 66.667 0.00 0.00 35.91 6.13
3887 5511 1.110442 CAGGTCACCCAGCAAACAAA 58.890 50.000 0.00 0.00 0.00 2.83
4009 5641 9.806203 TTGCATAATAGATGAATTCCAAGTTTG 57.194 29.630 2.27 0.00 0.00 2.93
4017 5652 8.877808 AGATGAATTCCAAGTTTGTTTTCTTC 57.122 30.769 2.27 0.00 0.00 2.87
4220 5884 5.988561 CCTGATAACTTGCAACTATCTCCTC 59.011 44.000 18.20 1.98 0.00 3.71
4524 6194 9.812347 TCCGTATAATCTATTCTTACCTGGTTA 57.188 33.333 3.84 0.00 0.00 2.85
4788 6465 2.029290 GGTGCGGTTTCTCAAGACTAGA 60.029 50.000 0.00 0.00 0.00 2.43
4830 6507 1.899814 ACATCTTCACAGCCGGTAGAA 59.100 47.619 1.90 1.52 0.00 2.10
4863 6552 3.952811 GGTGACGTCTCCTGTTGC 58.047 61.111 25.66 1.93 0.00 4.17
4968 6657 5.830912 TGAATCTGTAAAACAACTTGCTGG 58.169 37.500 0.00 0.00 0.00 4.85
5105 6810 8.948631 ACTCTGATGTTAAACATACATACCTG 57.051 34.615 0.00 0.00 39.27 4.00
5264 6990 0.455410 TGTTGCAGCAACTGGTGTTC 59.545 50.000 32.99 10.06 43.85 3.18
5307 7075 6.051074 CAGGTAATCATGCACTGTTCTGATA 58.949 40.000 0.00 0.00 0.00 2.15
5340 7110 7.482169 AGAATAGTCTGATGGTAACTTCACA 57.518 36.000 0.00 0.00 44.96 3.58
5438 8090 2.439507 CCCTGATAACCTGTGCCACTAT 59.560 50.000 0.00 0.00 0.00 2.12
5531 8199 1.852309 TGTGCCCCTGATCAATACCAT 59.148 47.619 0.00 0.00 0.00 3.55
5567 8235 0.478072 TGGCCTGAACCAGTGATGTT 59.522 50.000 3.32 0.00 33.75 2.71
6102 8970 1.202568 AGCCAAAGGAAAAGCTGTTGC 60.203 47.619 0.00 0.00 40.05 4.17
6173 9041 6.936335 TGATGCACTATATAAATGTCACCTGG 59.064 38.462 0.00 0.00 0.00 4.45
6205 9259 4.709886 GCCCCCATTGTTGATAAGTTACTT 59.290 41.667 2.32 2.32 0.00 2.24
6290 9350 8.421249 TCTGTTTATCATCACCAATCCTTTTT 57.579 30.769 0.00 0.00 0.00 1.94
6303 9363 6.267699 ACCAATCCTTTTTCTAAACCCTTCAG 59.732 38.462 0.00 0.00 0.00 3.02
6311 9392 9.249457 CTTTTTCTAAACCCTTCAGAATGTTTC 57.751 33.333 12.07 0.00 37.40 2.78
6398 9479 0.108207 GCAGTGCCATGCCTAGATCT 59.892 55.000 2.85 0.00 40.43 2.75
6469 9555 1.434188 TATTCGGCACTCATCCCCAT 58.566 50.000 0.00 0.00 0.00 4.00
6476 9562 2.295885 GCACTCATCCCCATCAAAGAG 58.704 52.381 0.00 0.00 0.00 2.85
6631 9728 5.224441 TGCTTTCCCCCTAGTATCATAGTT 58.776 41.667 0.00 0.00 0.00 2.24
6640 9737 7.399478 CCCCCTAGTATCATAGTTTTAGGGTAG 59.601 44.444 12.13 1.79 43.76 3.18
6747 11111 1.601903 TGCATGTCCGTGTTCTTCAAC 59.398 47.619 0.00 0.00 0.00 3.18
6827 11192 7.214467 TGTTGGAGACTTCAAATGTAAATCC 57.786 36.000 0.00 0.00 0.00 3.01
6876 11241 2.799126 TTACATTCCGAGCCACCAAT 57.201 45.000 0.00 0.00 0.00 3.16
6890 11256 3.883489 GCCACCAATATGAGGTACTTTCC 59.117 47.826 0.12 0.00 41.55 3.13
7058 11433 9.342308 CTATTCTCATAATTTCCCAGTGCTTTA 57.658 33.333 0.00 0.00 0.00 1.85
7141 11556 9.866655 AAATTGAGCATCCAAGGTCTAATAATA 57.133 29.630 0.00 0.00 36.97 0.98
7145 11560 9.507329 TGAGCATCCAAGGTCTAATAATATTTC 57.493 33.333 0.00 0.00 36.97 2.17
7334 11785 6.447162 CCTTCCTTTTTCTGTTCATGTTACC 58.553 40.000 0.00 0.00 0.00 2.85
7379 11836 0.521735 CTACAAAAGTTGGGAGCGGC 59.478 55.000 0.00 0.00 34.12 6.53
7452 11909 4.872691 CGATTTGAGGTGCTAGATTCACTT 59.127 41.667 0.00 0.00 34.97 3.16
7752 12222 5.898120 TCTGGAGTTATGGAATGGGAAAAA 58.102 37.500 0.00 0.00 0.00 1.94
7755 12225 8.119246 TCTGGAGTTATGGAATGGGAAAAATAA 58.881 33.333 0.00 0.00 0.00 1.40
7847 12319 5.301551 ACTCATAACAAATGCAAACAGTGGA 59.698 36.000 0.00 0.00 0.00 4.02
7892 12364 9.671279 ACAATTCATGAAGTATCAACTGACATA 57.329 29.630 14.54 0.00 39.49 2.29
8464 12994 4.858692 CGGCAAACAAATGGAGATAAGTTG 59.141 41.667 0.00 0.00 0.00 3.16
8680 13248 1.001181 GCCATGTGGTTGCTTGAATGT 59.999 47.619 0.35 0.00 37.57 2.71
8681 13249 2.679450 CCATGTGGTTGCTTGAATGTG 58.321 47.619 0.00 0.00 0.00 3.21
8718 13286 3.861840 ACGCTAGCTTGTATTGTCACAT 58.138 40.909 13.93 0.00 0.00 3.21
8735 13303 2.296752 CACATGGATGCTTGTTTGTCCA 59.703 45.455 2.83 0.00 44.22 4.02
8868 13437 4.585162 GGAACGATCCTCTATCTTCTTCCA 59.415 45.833 4.14 0.00 42.93 3.53
8893 13462 2.423947 CCCTTCTGGCCTTCTTATGCAT 60.424 50.000 3.32 3.79 0.00 3.96
8920 13489 5.888691 TTTGTTAGCGCATCCATTTCTTA 57.111 34.783 11.47 0.00 0.00 2.10
8939 13508 9.686683 ATTTCTTACTTGAAAGCATATAGGTGT 57.313 29.630 0.00 0.00 39.01 4.16
9096 13665 9.346725 GTTCAAAATTAGGCTTGATTAGTTCTG 57.653 33.333 0.00 0.00 31.85 3.02
9111 13680 2.376518 AGTTCTGCTTCCTGATCCCAAA 59.623 45.455 0.00 0.00 0.00 3.28
9175 13744 2.554462 CGATCTGGTCCATCACTCGTAT 59.446 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 159 6.651975 TTCAAATGTACCCACGGTAAAATT 57.348 33.333 0.00 0.00 40.12 1.82
148 161 6.461110 TTTTCAAATGTACCCACGGTAAAA 57.539 33.333 0.00 0.00 40.12 1.52
410 451 7.330208 ACTTACGTACAAACATCATGGTAACTC 59.670 37.037 0.00 0.00 37.61 3.01
477 519 0.251033 AAAACTTACCCCGGCCACTC 60.251 55.000 2.24 0.00 0.00 3.51
607 653 9.226345 CTTTGACTTGAAGAAATAGTTGTTGAC 57.774 33.333 0.00 0.00 0.00 3.18
625 671 6.422776 CAGACACAACTGTAACTTTGACTT 57.577 37.500 0.00 0.00 33.73 3.01
646 696 4.111375 AGACCTGATTACTTGCGTACAG 57.889 45.455 0.00 0.00 0.00 2.74
746 797 5.964758 TCATTTTCTTGCACATTCCATACC 58.035 37.500 0.00 0.00 0.00 2.73
755 806 5.291178 CAAGTTCCATCATTTTCTTGCACA 58.709 37.500 0.00 0.00 0.00 4.57
762 813 4.866486 GTGCATCCAAGTTCCATCATTTTC 59.134 41.667 0.00 0.00 0.00 2.29
882 933 4.783764 ACAACCAACTAGGCTAATTTGC 57.216 40.909 3.03 3.03 43.14 3.68
905 956 5.566826 CGACCTCATATGTTAATCCCACGAT 60.567 44.000 1.90 0.00 0.00 3.73
908 959 4.750098 CACGACCTCATATGTTAATCCCAC 59.250 45.833 1.90 0.00 0.00 4.61
1015 1068 6.128035 CCGTGGAATTGATGACACTTTAATGA 60.128 38.462 0.00 0.00 0.00 2.57
1040 1093 2.857592 ATGACTTTCCAATCATGCGC 57.142 45.000 0.00 0.00 34.23 6.09
1066 1119 2.192664 TGCCTAATTTTCTGCGGTCA 57.807 45.000 0.00 0.00 0.00 4.02
1071 1124 3.638160 TGATCCCATGCCTAATTTTCTGC 59.362 43.478 0.00 0.00 0.00 4.26
1134 1191 9.463443 CGTTCTTGTTTTAATGAGATCCTTTTT 57.537 29.630 0.00 0.00 0.00 1.94
1135 1192 8.846211 TCGTTCTTGTTTTAATGAGATCCTTTT 58.154 29.630 0.00 0.00 0.00 2.27
1136 1193 8.391075 TCGTTCTTGTTTTAATGAGATCCTTT 57.609 30.769 0.00 0.00 0.00 3.11
1137 1194 7.979444 TCGTTCTTGTTTTAATGAGATCCTT 57.021 32.000 0.00 0.00 0.00 3.36
1138 1195 8.567285 AATCGTTCTTGTTTTAATGAGATCCT 57.433 30.769 0.00 0.00 0.00 3.24
1139 1196 8.669243 AGAATCGTTCTTGTTTTAATGAGATCC 58.331 33.333 0.00 0.00 36.36 3.36
1140 1197 9.483062 CAGAATCGTTCTTGTTTTAATGAGATC 57.517 33.333 0.00 0.00 38.11 2.75
1141 1198 7.965107 GCAGAATCGTTCTTGTTTTAATGAGAT 59.035 33.333 0.00 0.00 38.11 2.75
1142 1199 7.298122 GCAGAATCGTTCTTGTTTTAATGAGA 58.702 34.615 0.00 0.00 38.11 3.27
1143 1200 6.247165 CGCAGAATCGTTCTTGTTTTAATGAG 59.753 38.462 0.00 0.00 38.11 2.90
1144 1201 6.077197 CGCAGAATCGTTCTTGTTTTAATGA 58.923 36.000 0.00 0.00 38.11 2.57
1145 1202 5.219841 GCGCAGAATCGTTCTTGTTTTAATG 60.220 40.000 0.30 0.00 38.11 1.90
1146 1203 4.851558 GCGCAGAATCGTTCTTGTTTTAAT 59.148 37.500 0.30 0.00 38.11 1.40
1147 1204 4.215965 GCGCAGAATCGTTCTTGTTTTAA 58.784 39.130 0.30 0.00 38.11 1.52
1148 1205 3.364565 GGCGCAGAATCGTTCTTGTTTTA 60.365 43.478 10.83 0.00 38.11 1.52
1149 1206 2.604614 GGCGCAGAATCGTTCTTGTTTT 60.605 45.455 10.83 0.00 38.11 2.43
1150 1207 1.069227 GGCGCAGAATCGTTCTTGTTT 60.069 47.619 10.83 0.00 38.11 2.83
1151 1208 0.517316 GGCGCAGAATCGTTCTTGTT 59.483 50.000 10.83 0.00 38.11 2.83
1152 1209 0.602638 TGGCGCAGAATCGTTCTTGT 60.603 50.000 10.83 0.00 38.11 3.16
1153 1210 0.729116 ATGGCGCAGAATCGTTCTTG 59.271 50.000 10.83 0.00 38.11 3.02
1154 1211 0.729116 CATGGCGCAGAATCGTTCTT 59.271 50.000 10.83 0.00 38.11 2.52
1155 1212 0.108186 TCATGGCGCAGAATCGTTCT 60.108 50.000 10.83 0.00 41.70 3.01
1156 1213 0.302890 CTCATGGCGCAGAATCGTTC 59.697 55.000 10.83 0.00 0.00 3.95
1157 1214 0.108186 TCTCATGGCGCAGAATCGTT 60.108 50.000 10.83 0.00 0.00 3.85
1158 1215 0.105593 ATCTCATGGCGCAGAATCGT 59.894 50.000 10.83 0.00 0.00 3.73
1159 1216 0.788995 GATCTCATGGCGCAGAATCG 59.211 55.000 10.83 0.00 0.00 3.34
1160 1217 0.788995 CGATCTCATGGCGCAGAATC 59.211 55.000 10.83 8.74 0.00 2.52
1161 1218 2.910205 CGATCTCATGGCGCAGAAT 58.090 52.632 10.83 0.00 0.00 2.40
1162 1219 4.425578 CGATCTCATGGCGCAGAA 57.574 55.556 10.83 0.00 0.00 3.02
1168 1225 2.091112 CCGATCGCGATCTCATGGC 61.091 63.158 37.76 17.63 40.82 4.40
1169 1226 0.730834 GTCCGATCGCGATCTCATGG 60.731 60.000 37.76 31.52 40.82 3.66
1170 1227 1.062336 CGTCCGATCGCGATCTCATG 61.062 60.000 37.76 26.86 40.82 3.07
1171 1228 1.207848 CGTCCGATCGCGATCTCAT 59.792 57.895 37.76 13.33 40.82 2.90
1172 1229 1.885850 TCGTCCGATCGCGATCTCA 60.886 57.895 37.76 25.10 40.82 3.27
1173 1230 1.439037 GTCGTCCGATCGCGATCTC 60.439 63.158 37.76 27.39 40.82 2.75
1174 1231 1.712018 TTGTCGTCCGATCGCGATCT 61.712 55.000 37.76 14.94 40.82 2.75
1175 1232 1.298116 TTGTCGTCCGATCGCGATC 60.298 57.895 33.93 33.93 40.82 3.69
1176 1233 1.585521 GTTGTCGTCCGATCGCGAT 60.586 57.895 23.97 23.97 40.82 4.58
1177 1234 2.202388 GTTGTCGTCCGATCGCGA 60.202 61.111 13.09 13.09 40.82 5.87
1178 1235 1.998550 CTTGTTGTCGTCCGATCGCG 61.999 60.000 10.32 9.31 37.24 5.87
1179 1236 0.731514 TCTTGTTGTCGTCCGATCGC 60.732 55.000 10.32 0.00 0.00 4.58
1180 1237 1.846782 GATCTTGTTGTCGTCCGATCG 59.153 52.381 8.51 8.51 0.00 3.69
1181 1238 1.846782 CGATCTTGTTGTCGTCCGATC 59.153 52.381 0.00 0.00 33.42 3.69
1182 1239 1.909376 CGATCTTGTTGTCGTCCGAT 58.091 50.000 0.00 0.00 33.42 4.18
1183 1240 3.394800 CGATCTTGTTGTCGTCCGA 57.605 52.632 0.00 0.00 33.42 4.55
1188 1245 1.693467 TCCGAACGATCTTGTTGTCG 58.307 50.000 0.00 0.00 43.13 4.35
1189 1246 3.909019 GATCCGAACGATCTTGTTGTC 57.091 47.619 0.00 0.00 43.65 3.18
1197 1254 3.355626 TGTGATCAGATCCGAACGATC 57.644 47.619 8.00 0.00 46.86 3.69
1198 1255 3.801114 TTGTGATCAGATCCGAACGAT 57.199 42.857 8.00 0.00 0.00 3.73
1199 1256 3.586100 TTTGTGATCAGATCCGAACGA 57.414 42.857 8.00 0.00 0.00 3.85
1200 1257 4.568359 AGATTTTGTGATCAGATCCGAACG 59.432 41.667 8.00 0.00 0.00 3.95
1201 1258 5.582269 TCAGATTTTGTGATCAGATCCGAAC 59.418 40.000 8.00 0.45 0.00 3.95
1202 1259 5.733676 TCAGATTTTGTGATCAGATCCGAA 58.266 37.500 8.00 3.23 0.00 4.30
1203 1260 5.343307 TCAGATTTTGTGATCAGATCCGA 57.657 39.130 8.00 0.00 0.00 4.55
1204 1261 6.427974 CATTCAGATTTTGTGATCAGATCCG 58.572 40.000 8.00 0.00 0.00 4.18
1205 1262 6.039493 AGCATTCAGATTTTGTGATCAGATCC 59.961 38.462 8.00 0.39 0.00 3.36
1206 1263 7.028926 AGCATTCAGATTTTGTGATCAGATC 57.971 36.000 3.11 3.11 0.00 2.75
1207 1264 6.238402 CGAGCATTCAGATTTTGTGATCAGAT 60.238 38.462 0.00 0.00 0.00 2.90
1208 1265 5.064325 CGAGCATTCAGATTTTGTGATCAGA 59.936 40.000 0.00 0.00 0.00 3.27
1209 1266 5.263948 CGAGCATTCAGATTTTGTGATCAG 58.736 41.667 0.00 0.00 0.00 2.90
1210 1267 4.095334 CCGAGCATTCAGATTTTGTGATCA 59.905 41.667 0.00 0.00 0.00 2.92
1223 1280 5.879777 TGACAATCTAATTTCCGAGCATTCA 59.120 36.000 0.00 0.00 0.00 2.57
1224 1281 6.363577 TGACAATCTAATTTCCGAGCATTC 57.636 37.500 0.00 0.00 0.00 2.67
1230 1287 9.496873 TTTCTTAGTTGACAATCTAATTTCCGA 57.503 29.630 9.30 3.44 0.00 4.55
1264 1321 4.693283 TGGTAATCAGAACTTATCAGCCG 58.307 43.478 0.00 0.00 0.00 5.52
1366 1431 8.871686 AACAAAACAATTAAGGACTGACAATC 57.128 30.769 0.00 0.00 0.00 2.67
1492 1573 2.193993 GAGTTAGGGGAAGCCCTGTTA 58.806 52.381 0.00 0.00 44.66 2.41
1533 1614 5.863935 GCATTTTTCCTACCATCAGACAAAC 59.136 40.000 0.00 0.00 0.00 2.93
1602 1685 1.632589 AAGGAAACTGAATGGGTGGC 58.367 50.000 0.00 0.00 42.68 5.01
1865 1952 5.479375 ACATTGGCTTGAACTTCTCATCAAT 59.521 36.000 0.00 0.00 35.20 2.57
2002 2093 4.890088 TCAGCCACAAGACGTAAAGTTAT 58.110 39.130 0.00 0.00 0.00 1.89
2011 2103 2.159653 GCAAGTTATCAGCCACAAGACG 60.160 50.000 0.00 0.00 0.00 4.18
2242 2354 9.766277 GAATACACAATCAAAACAAAAGCAAAA 57.234 25.926 0.00 0.00 0.00 2.44
2246 2358 8.268738 GTCAGAATACACAATCAAAACAAAAGC 58.731 33.333 0.00 0.00 0.00 3.51
2307 2421 3.085443 AGACCAGTAAGATCAATCGCG 57.915 47.619 0.00 0.00 0.00 5.87
2517 2646 2.936498 ACTGGCGAATTATTGAGAACGG 59.064 45.455 0.00 0.00 0.00 4.44
2557 2686 1.192090 CGCCAAACAAGCAAAAATCGG 59.808 47.619 0.00 0.00 0.00 4.18
2696 2840 8.816640 AAGTTACCATGTAAATGCAAGAAAAG 57.183 30.769 0.00 0.00 0.00 2.27
2766 3395 9.724839 ACAACATATGTTAACAGTGTGTAAAAC 57.275 29.630 20.39 0.47 40.06 2.43
2850 3482 7.645058 ATTCAGATAGGTAAAACATGGGTTG 57.355 36.000 0.00 0.00 37.30 3.77
2885 3544 3.249799 TCCAAGTGCAACACAAGTTATCG 59.750 43.478 0.00 0.00 41.43 2.92
2900 3559 4.095483 GCAACAGAAGATACCATCCAAGTG 59.905 45.833 0.00 0.00 0.00 3.16
2997 3885 5.065602 TCAGATGCGAAAAAGGATCATGAAG 59.934 40.000 0.00 0.00 40.76 3.02
3013 3901 5.980698 ACTAGACATGATTTTCAGATGCG 57.019 39.130 0.00 0.00 0.00 4.73
3033 3922 7.827729 AGAACACAAGGAACACTTTTAGTTACT 59.172 33.333 0.00 0.00 41.82 2.24
3107 4000 2.664436 GGCAGACGAAAACCGACCG 61.664 63.158 0.00 0.00 41.76 4.79
3124 4017 2.576832 CCAAGCAGGCCAACCAAGG 61.577 63.158 5.01 0.00 39.06 3.61
3223 4116 9.573133 CCATATTGTGAGTACCAAAAGAAATTC 57.427 33.333 0.00 0.00 0.00 2.17
3432 4334 2.345991 GTTCACTGCCCCGCTACA 59.654 61.111 0.00 0.00 0.00 2.74
3434 4336 3.307906 ACGTTCACTGCCCCGCTA 61.308 61.111 0.00 0.00 0.00 4.26
3582 5183 2.859992 GTGGAATGACCTCACCAGC 58.140 57.895 0.00 0.00 39.86 4.85
3887 5511 1.346395 TGACGCCTCAAGTGTACCAAT 59.654 47.619 0.00 0.00 40.03 3.16
4009 5641 8.515414 AGTAGCATTATGAAACCTGAAGAAAAC 58.485 33.333 0.00 0.00 0.00 2.43
4087 5723 5.349543 ACGACGAATAATCAACCAGGTAAAC 59.650 40.000 0.00 0.00 0.00 2.01
4196 5860 5.923204 AGGAGATAGTTGCAAGTTATCAGG 58.077 41.667 23.00 0.00 0.00 3.86
4290 5955 2.747446 GTTTGTCGGGTGCACTGAATAT 59.253 45.455 17.98 0.00 35.91 1.28
4404 6070 9.806203 CTTGGAAATTCATCTATTATGCAACAA 57.194 29.630 0.00 0.00 0.00 2.83
4524 6194 6.674066 ACAAAAATGACCACGACGAATAATT 58.326 32.000 0.00 0.00 0.00 1.40
4532 6202 8.953990 GCATATATTAACAAAAATGACCACGAC 58.046 33.333 0.00 0.00 0.00 4.34
4788 6465 3.892284 TGCTCTTAGTCGAGGAGAAGAT 58.108 45.455 8.27 0.00 0.00 2.40
4830 6507 1.691976 TCACCGTCAAGATCCACAACT 59.308 47.619 0.00 0.00 0.00 3.16
4919 6608 1.882912 TCAGATGCAACTTCGCAAGT 58.117 45.000 0.00 0.00 46.87 3.16
4968 6657 0.326264 AGAAGTGATGGTGGCCACTC 59.674 55.000 33.91 24.67 42.25 3.51
5070 6761 7.548097 TGTTTAACATCAGAGTAGTGATCCTC 58.452 38.462 0.00 0.00 34.81 3.71
5438 8090 4.164796 AGAACATATTGTGGCATGAGAGGA 59.835 41.667 0.00 0.00 0.00 3.71
5567 8235 3.568007 GCCAAACAATGACACTTACCAGA 59.432 43.478 0.00 0.00 0.00 3.86
5996 8862 3.193056 TCATACACCCGAACACAACGATA 59.807 43.478 0.00 0.00 0.00 2.92
6173 9041 3.070302 TCAACAATGGGGGCAAAAGTTAC 59.930 43.478 0.00 0.00 0.00 2.50
6290 9350 4.454504 GCGAAACATTCTGAAGGGTTTAGA 59.545 41.667 22.42 0.00 33.92 2.10
6303 9363 3.166657 GACAATGCTCTGCGAAACATTC 58.833 45.455 0.00 0.00 30.54 2.67
6311 9392 0.455633 GGCTTTGACAATGCTCTGCG 60.456 55.000 21.33 0.00 0.00 5.18
6398 9479 8.235905 CGGGTAACAATAACTTTCCGAATTAAA 58.764 33.333 0.00 0.00 38.64 1.52
6469 9555 3.795688 AAACAGCCTCATCCTCTTTGA 57.204 42.857 0.00 0.00 0.00 2.69
6476 9562 5.128919 ACTTCATCATAAACAGCCTCATCC 58.871 41.667 0.00 0.00 0.00 3.51
6583 9671 6.063404 ACTCAACAAATGGAATGGCAATTTT 58.937 32.000 0.00 0.00 0.00 1.82
6586 9674 4.895668 ACTCAACAAATGGAATGGCAAT 57.104 36.364 0.00 0.00 0.00 3.56
6654 9751 3.148084 CCGAGTGTGACCCACCTT 58.852 61.111 0.00 0.00 45.74 3.50
6827 11192 2.348498 CCGTCGGAAATGATGCATTACG 60.348 50.000 4.91 0.00 36.45 3.18
6876 11241 6.597562 ACAACAAACTGGAAAGTACCTCATA 58.402 36.000 0.00 0.00 0.00 2.15
6890 11256 9.729023 TTAACATGTAAGAATGACAACAAACTG 57.271 29.630 0.00 0.00 29.49 3.16
6926 11294 7.491048 ACGCTAAATTGGCAATAAAAATGTAGG 59.509 33.333 14.05 0.00 0.00 3.18
7047 11418 7.338800 AGTTATCATGAAATAAAGCACTGGG 57.661 36.000 0.00 0.00 0.00 4.45
7087 11481 8.342634 CCATACCAGAAAAATACAAAGATACCG 58.657 37.037 0.00 0.00 0.00 4.02
7141 11556 9.480053 CACCATGAAAACACAAAAGATAGAAAT 57.520 29.630 0.00 0.00 0.00 2.17
7145 11560 5.634859 GCCACCATGAAAACACAAAAGATAG 59.365 40.000 0.00 0.00 0.00 2.08
7147 11562 4.101430 AGCCACCATGAAAACACAAAAGAT 59.899 37.500 0.00 0.00 0.00 2.40
7203 11642 7.645340 GCAAAGCAATCAAGTTATCATACGATT 59.355 33.333 0.00 0.00 32.73 3.34
7206 11645 6.257423 TGCAAAGCAATCAAGTTATCATACG 58.743 36.000 0.00 0.00 34.76 3.06
7334 11785 7.390027 AGCAGGGAATAGTAGCTACAATAATG 58.610 38.462 25.28 14.71 33.06 1.90
7379 11836 2.507484 ACCAATGACTGTCATGTGGTG 58.493 47.619 32.74 23.92 41.82 4.17
7752 12222 4.210331 GTCATGGGTGAAAGCAGGATTAT 58.790 43.478 0.00 0.00 35.80 1.28
7755 12225 1.341383 GGTCATGGGTGAAAGCAGGAT 60.341 52.381 0.00 0.00 35.80 3.24
7900 12377 4.152402 CACTGGAATTACTCTCACAAACGG 59.848 45.833 0.00 0.00 0.00 4.44
8011 12495 3.503748 GGTCCTTGATTTTCTCTGTGTGG 59.496 47.826 0.00 0.00 0.00 4.17
8283 12804 3.389002 TGATACTGTGGGACATCATCAGG 59.611 47.826 0.00 0.00 44.52 3.86
8432 12959 6.770303 TCTCCATTTGTTTGCCGATCATTATA 59.230 34.615 0.00 0.00 0.00 0.98
8442 12969 5.634859 CACAACTTATCTCCATTTGTTTGCC 59.365 40.000 0.00 0.00 0.00 4.52
8464 12994 4.688879 TCGTCACTACAAATGAATGGACAC 59.311 41.667 0.00 0.00 0.00 3.67
8522 13054 2.024588 CAAGCGCAACTGCACGTT 59.975 55.556 11.47 0.00 42.21 3.99
8718 13286 1.955778 CACTGGACAAACAAGCATCCA 59.044 47.619 0.00 0.00 38.94 3.41
8893 13462 1.543358 TGGATGCGCTAACAAAATGCA 59.457 42.857 9.73 0.00 40.23 3.96
8920 13489 9.167311 CTAGAAAACACCTATATGCTTTCAAGT 57.833 33.333 4.90 0.00 37.21 3.16
8957 13526 5.045012 ACACTTGCCTCACATATGATGAT 57.955 39.130 10.38 0.00 33.22 2.45
8965 13534 1.901591 CAAGGACACTTGCCTCACAT 58.098 50.000 0.00 0.00 46.67 3.21
9096 13665 2.442236 TGGATTTGGGATCAGGAAGC 57.558 50.000 0.00 0.00 0.00 3.86
9146 13715 0.031515 TGGACCAGATCGGGGTGTAT 60.032 55.000 16.73 0.00 39.19 2.29


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

AutoCloner maintained by Alex Coulton.