Multiple sequence alignment - TraesCS5A01G039100

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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 TraesCS5A01G039100 chr5A 100.000 3458 0 0 1 3458 36019315 36022772 0.000000e+00 6386.0
1 TraesCS5A01G039100 chr5A 88.642 854 96 1 1593 2446 36049283 36050135 0.000000e+00 1038.0
2 TraesCS5A01G039100 chr5A 88.642 854 96 1 1593 2446 36076056 36076908 0.000000e+00 1038.0
3 TraesCS5A01G039100 chr5A 88.525 854 97 1 1593 2446 36166397 36167249 0.000000e+00 1033.0
4 TraesCS5A01G039100 chr5A 88.525 854 97 1 1593 2446 36195430 36196282 0.000000e+00 1033.0
5 TraesCS5A01G039100 chr5A 88.861 404 44 1 1593 1996 36104217 36104619 2.400000e-136 496.0
6 TraesCS5A01G039100 chr5A 88.732 355 39 1 1593 1947 36132746 36133099 1.910000e-117 433.0
7 TraesCS5A01G039100 chr5A 89.274 317 34 0 2130 2446 36133093 36133409 6.950000e-107 398.0
8 TraesCS5A01G039100 chr5A 91.513 271 23 0 2176 2446 36104616 36104886 1.170000e-99 374.0
9 TraesCS5A01G039100 chr5A 88.194 288 18 8 933 1206 36074182 36074467 2.570000e-86 329.0
10 TraesCS5A01G039100 chr5A 88.194 288 18 8 933 1206 36193558 36193843 2.570000e-86 329.0
11 TraesCS5A01G039100 chr5A 87.847 288 19 8 933 1206 36102344 36102629 1.200000e-84 324.0
12 TraesCS5A01G039100 chr5A 87.847 288 19 8 933 1206 36130873 36131158 1.200000e-84 324.0
13 TraesCS5A01G039100 chr5A 87.847 288 19 8 933 1206 36164521 36164806 1.200000e-84 324.0
14 TraesCS5A01G039100 chr5B 87.420 1558 148 31 1602 3136 45241982 45243514 0.000000e+00 1748.0
15 TraesCS5A01G039100 chr5B 84.752 505 57 12 6 493 45239803 45240304 4.010000e-134 488.0
16 TraesCS5A01G039100 chr5B 86.691 278 27 8 933 1207 45240940 45241210 2.020000e-77 300.0
17 TraesCS5A01G039100 chr5B 82.105 380 23 22 569 914 45240428 45240796 2.030000e-72 283.0
18 TraesCS5A01G039100 chr5D 91.980 985 69 2 1597 2574 45213630 45214611 0.000000e+00 1373.0
19 TraesCS5A01G039100 chr5D 90.646 727 37 12 2742 3458 45249266 45249971 0.000000e+00 937.0
20 TraesCS5A01G039100 chr5D 88.092 655 29 26 596 1207 45212364 45213012 0.000000e+00 732.0
21 TraesCS5A01G039100 chr5D 87.003 377 30 8 126 493 45211853 45212219 1.160000e-109 407.0
22 TraesCS5A01G039100 chr5D 94.697 132 7 0 2573 2704 45249134 45249265 4.520000e-49 206.0
23 TraesCS5A01G039100 chrUn 87.907 430 52 0 1666 2095 476253799 476254228 1.110000e-139 507.0
24 TraesCS5A01G039100 chrUn 95.556 45 1 1 541 584 332381385 332381341 1.720000e-08 71.3
25 TraesCS5A01G039100 chr1D 76.338 841 172 21 1617 2440 62767979 62768809 3.190000e-115 425.0
26 TraesCS5A01G039100 chr1D 77.448 337 54 16 2735 3057 33857576 33857248 7.620000e-42 182.0
27 TraesCS5A01G039100 chr3D 81.381 333 49 8 2737 3062 487229270 487228944 3.420000e-65 259.0
28 TraesCS5A01G039100 chr3D 77.811 338 59 13 2732 3062 545256464 545256792 9.790000e-46 195.0
29 TraesCS5A01G039100 chr6A 77.246 334 61 10 2735 3061 606095894 606095569 7.620000e-42 182.0
30 TraesCS5A01G039100 chr2D 77.313 335 58 13 2735 3061 564704134 564703810 7.620000e-42 182.0
31 TraesCS5A01G039100 chr3A 76.316 342 58 16 2734 3062 492043715 492044046 9.930000e-36 161.0
32 TraesCS5A01G039100 chr3A 82.178 101 14 2 3192 3290 40840443 40840541 2.210000e-12 84.2
33 TraesCS5A01G039100 chr3A 100.000 41 0 0 543 583 642160696 642160656 3.700000e-10 76.8
34 TraesCS5A01G039100 chr6D 76.106 339 60 14 2735 3062 392525099 392524771 1.280000e-34 158.0
35 TraesCS5A01G039100 chr4A 91.045 67 2 1 514 580 642640029 642639967 1.710000e-13 87.9
36 TraesCS5A01G039100 chr3B 100.000 43 0 0 541 583 159560868 159560910 2.860000e-11 80.5
37 TraesCS5A01G039100 chr3B 92.157 51 3 1 535 584 88409495 88409545 1.720000e-08 71.3
38 TraesCS5A01G039100 chr4B 100.000 41 0 0 540 580 652274571 652274531 3.700000e-10 76.8
39 TraesCS5A01G039100 chr4B 100.000 28 0 0 512 539 524708515 524708488 6.000000e-03 52.8
40 TraesCS5A01G039100 chr6B 95.745 47 1 1 536 582 713937550 713937505 1.330000e-09 75.0
41 TraesCS5A01G039100 chr6B 89.831 59 4 2 524 582 713960580 713960524 1.330000e-09 75.0
42 TraesCS5A01G039100 chr2A 88.136 59 4 3 524 582 591749039 591749094 2.230000e-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 TraesCS5A01G039100 chr5A 36019315 36022772 3457 False 6386.000000 6386 100.000000 1 3458 1 chr5A.!!$F1 3457
1 TraesCS5A01G039100 chr5A 36049283 36050135 852 False 1038.000000 1038 88.642000 1593 2446 1 chr5A.!!$F2 853
2 TraesCS5A01G039100 chr5A 36074182 36076908 2726 False 683.500000 1038 88.418000 933 2446 2 chr5A.!!$F3 1513
3 TraesCS5A01G039100 chr5A 36193558 36196282 2724 False 681.000000 1033 88.359500 933 2446 2 chr5A.!!$F7 1513
4 TraesCS5A01G039100 chr5A 36164521 36167249 2728 False 678.500000 1033 88.186000 933 2446 2 chr5A.!!$F6 1513
5 TraesCS5A01G039100 chr5A 36102344 36104886 2542 False 398.000000 496 89.407000 933 2446 3 chr5A.!!$F4 1513
6 TraesCS5A01G039100 chr5A 36130873 36133409 2536 False 385.000000 433 88.617667 933 2446 3 chr5A.!!$F5 1513
7 TraesCS5A01G039100 chr5B 45239803 45243514 3711 False 704.750000 1748 85.242000 6 3136 4 chr5B.!!$F1 3130
8 TraesCS5A01G039100 chr5D 45211853 45214611 2758 False 837.333333 1373 89.025000 126 2574 3 chr5D.!!$F1 2448
9 TraesCS5A01G039100 chr5D 45249134 45249971 837 False 571.500000 937 92.671500 2573 3458 2 chr5D.!!$F2 885
10 TraesCS5A01G039100 chr1D 62767979 62768809 830 False 425.000000 425 76.338000 1617 2440 1 chr1D.!!$F1 823

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
350 364 0.179086 TATGTGGCGTGTGCGATGAT 60.179 50.0 0.00 0.00 44.10 2.45 F
1324 1661 0.382873 AGTGCCATGCATGCGTAATG 59.617 50.0 21.69 10.73 41.91 1.90 F
1409 1852 0.032540 GAATGGGATTGGCGGATTGC 59.967 55.0 0.00 0.00 45.38 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 1833 0.032540 GCAATCCGCCAATCCCATTC 59.967 55.0 0.00 0.0 32.94 2.67 R
2247 4486 0.250467 TGAAGAGCACCCTGTTCTGC 60.250 55.0 2.91 0.0 40.84 4.26 R
2942 5212 0.331278 ATCAAATCTGGGTGCCCGAA 59.669 50.0 2.44 0.0 39.42 4.30 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
163 169 8.800370 TTTAATAGACATGTATGCACCTTTCA 57.200 30.769 2.50 0.00 0.00 2.69
259 266 2.083774 ACATGTGTTATGGTTGCCTCG 58.916 47.619 0.00 0.00 0.00 4.63
293 300 8.581057 TTTGCGTTATTGTCATACACATTTTT 57.419 26.923 0.00 0.00 33.90 1.94
317 331 2.595954 ATTGTGTGCAACCCACCCCA 62.596 55.000 3.73 0.00 44.01 4.96
318 332 2.203625 GTGTGCAACCCACCCCAT 60.204 61.111 0.00 0.00 44.01 4.00
335 349 2.418471 CCCATTGGCACGCATTTTATGT 60.418 45.455 0.00 0.00 0.00 2.29
336 350 2.604011 CCATTGGCACGCATTTTATGTG 59.396 45.455 0.00 0.00 45.88 3.21
350 364 0.179086 TATGTGGCGTGTGCGATGAT 60.179 50.000 0.00 0.00 44.10 2.45
353 367 4.241999 GGCGTGTGCGATGATGCC 62.242 66.667 0.00 0.00 44.10 4.40
396 411 4.499023 CGCGCCGATGGTTCGTTG 62.499 66.667 0.00 0.00 43.97 4.10
460 479 3.126001 TGTCCAAGTCAGACATGTTCC 57.874 47.619 0.00 0.00 39.29 3.62
493 512 1.418264 GCCTAATCCCTCCTCCAGTTC 59.582 57.143 0.00 0.00 0.00 3.01
590 664 2.431057 CAGAGGGAGTAATAGGCAACGT 59.569 50.000 0.00 0.00 46.39 3.99
593 667 2.364647 AGGGAGTAATAGGCAACGTAGC 59.635 50.000 0.00 0.00 46.39 3.58
608 682 6.724502 CAACGTAGCTGCAGATATATATCG 57.275 41.667 20.43 17.03 37.76 2.92
646 720 1.002366 CAACATGGCAGCGACTACTC 58.998 55.000 0.00 0.00 0.00 2.59
825 914 1.828979 GGCCTGTATTTCCGGTCAAA 58.171 50.000 0.00 0.00 0.00 2.69
855 962 0.599558 GCATCCAGCAGCAAGAACAA 59.400 50.000 0.00 0.00 44.79 2.83
871 978 5.014808 AGAACAAATAATGCCATCTTGCC 57.985 39.130 0.00 0.00 0.00 4.52
872 979 3.441496 ACAAATAATGCCATCTTGCCG 57.559 42.857 0.00 0.00 0.00 5.69
873 980 3.023119 ACAAATAATGCCATCTTGCCGA 58.977 40.909 0.00 0.00 0.00 5.54
874 981 3.638160 ACAAATAATGCCATCTTGCCGAT 59.362 39.130 0.00 0.00 0.00 4.18
914 1021 3.244009 TGCAAGCTAAGCATAGGAGCTAG 60.244 47.826 9.48 0.00 45.74 3.42
915 1022 3.006323 GCAAGCTAAGCATAGGAGCTAGA 59.994 47.826 6.22 0.00 45.74 2.43
916 1023 4.808558 CAAGCTAAGCATAGGAGCTAGAG 58.191 47.826 0.00 0.00 45.74 2.43
917 1024 4.112634 AGCTAAGCATAGGAGCTAGAGT 57.887 45.455 0.00 0.00 45.89 3.24
918 1025 5.249780 AGCTAAGCATAGGAGCTAGAGTA 57.750 43.478 0.00 0.00 45.89 2.59
927 1160 9.130661 AGCATAGGAGCTAGAGTATTATACATG 57.869 37.037 5.11 0.00 44.50 3.21
928 1161 9.126151 GCATAGGAGCTAGAGTATTATACATGA 57.874 37.037 0.00 0.00 0.00 3.07
931 1164 8.445275 AGGAGCTAGAGTATTATACATGATCG 57.555 38.462 0.00 0.00 0.00 3.69
934 1167 7.911343 AGCTAGAGTATTATACATGATCGTCG 58.089 38.462 0.00 0.00 0.00 5.12
948 1181 4.135306 TGATCGTCGACCTTAAGCTATCT 58.865 43.478 10.58 0.00 0.00 1.98
949 1182 5.303165 TGATCGTCGACCTTAAGCTATCTA 58.697 41.667 10.58 0.00 0.00 1.98
988 1221 5.416952 ACAGCAGCAGTTTATCTTAGCAAAT 59.583 36.000 0.00 0.00 0.00 2.32
993 1241 7.293745 CAGCAGTTTATCTTAGCAAATATCGG 58.706 38.462 0.00 0.00 0.00 4.18
1045 1293 2.031616 TGCTGTCTCTGTGCCTGC 59.968 61.111 0.00 0.00 0.00 4.85
1062 1310 3.429141 CTGCTGGCCTGTTCTGCG 61.429 66.667 11.69 0.00 32.79 5.18
1188 1436 1.668151 GTTCCACGACTGCTGGGTC 60.668 63.158 0.00 0.00 0.00 4.46
1230 1547 3.119849 AGTTGATCGCCTAATTTGTGTGC 60.120 43.478 0.00 0.00 0.00 4.57
1233 1550 1.164411 TCGCCTAATTTGTGTGCCTG 58.836 50.000 0.00 0.00 0.00 4.85
1236 1553 2.486203 CGCCTAATTTGTGTGCCTGTTA 59.514 45.455 0.00 0.00 0.00 2.41
1237 1554 3.669557 CGCCTAATTTGTGTGCCTGTTAC 60.670 47.826 0.00 0.00 0.00 2.50
1241 1558 6.127730 GCCTAATTTGTGTGCCTGTTACTATT 60.128 38.462 0.00 0.00 0.00 1.73
1242 1559 7.250569 CCTAATTTGTGTGCCTGTTACTATTG 58.749 38.462 0.00 0.00 0.00 1.90
1243 1560 4.497473 TTTGTGTGCCTGTTACTATTGC 57.503 40.909 0.00 0.00 0.00 3.56
1246 1563 2.678336 GTGTGCCTGTTACTATTGCCTC 59.322 50.000 0.00 0.00 0.00 4.70
1247 1564 2.304470 TGTGCCTGTTACTATTGCCTCA 59.696 45.455 0.00 0.00 0.00 3.86
1251 1568 4.398988 TGCCTGTTACTATTGCCTCATTTG 59.601 41.667 0.00 0.00 0.00 2.32
1253 1570 5.300286 GCCTGTTACTATTGCCTCATTTGAT 59.700 40.000 0.00 0.00 0.00 2.57
1254 1571 6.732154 CCTGTTACTATTGCCTCATTTGATG 58.268 40.000 0.00 0.00 0.00 3.07
1256 1573 7.067372 CCTGTTACTATTGCCTCATTTGATGAA 59.933 37.037 0.00 0.00 39.11 2.57
1257 1574 8.347004 TGTTACTATTGCCTCATTTGATGAAA 57.653 30.769 0.00 0.00 39.11 2.69
1263 1580 7.707624 ATTGCCTCATTTGATGAAAGAGTAA 57.292 32.000 0.00 0.00 39.11 2.24
1297 1614 8.429641 ACTAAATCAGTGACGGGTAATATGAAT 58.570 33.333 0.00 0.00 35.62 2.57
1298 1615 7.496529 AAATCAGTGACGGGTAATATGAATG 57.503 36.000 0.00 0.00 0.00 2.67
1299 1616 4.956085 TCAGTGACGGGTAATATGAATGG 58.044 43.478 0.00 0.00 0.00 3.16
1300 1617 4.651962 TCAGTGACGGGTAATATGAATGGA 59.348 41.667 0.00 0.00 0.00 3.41
1303 1620 4.755123 GTGACGGGTAATATGAATGGAAGG 59.245 45.833 0.00 0.00 0.00 3.46
1304 1621 4.202419 TGACGGGTAATATGAATGGAAGGG 60.202 45.833 0.00 0.00 0.00 3.95
1305 1622 3.977999 ACGGGTAATATGAATGGAAGGGA 59.022 43.478 0.00 0.00 0.00 4.20
1306 1623 4.041691 ACGGGTAATATGAATGGAAGGGAG 59.958 45.833 0.00 0.00 0.00 4.30
1307 1624 4.041691 CGGGTAATATGAATGGAAGGGAGT 59.958 45.833 0.00 0.00 0.00 3.85
1308 1625 5.316987 GGGTAATATGAATGGAAGGGAGTG 58.683 45.833 0.00 0.00 0.00 3.51
1309 1626 4.762251 GGTAATATGAATGGAAGGGAGTGC 59.238 45.833 0.00 0.00 0.00 4.40
1312 1629 1.002069 TGAATGGAAGGGAGTGCCAT 58.998 50.000 2.50 0.00 43.95 4.40
1313 1630 1.341285 TGAATGGAAGGGAGTGCCATG 60.341 52.381 2.50 0.00 41.36 3.66
1314 1631 0.685458 AATGGAAGGGAGTGCCATGC 60.685 55.000 2.50 0.00 41.36 4.06
1315 1632 1.866483 ATGGAAGGGAGTGCCATGCA 61.866 55.000 2.04 2.04 40.72 3.96
1317 1634 1.389609 GGAAGGGAGTGCCATGCATG 61.390 60.000 20.19 20.19 41.91 4.06
1318 1635 2.012902 GAAGGGAGTGCCATGCATGC 62.013 60.000 21.69 11.82 41.91 4.06
1323 1660 0.664761 GAGTGCCATGCATGCGTAAT 59.335 50.000 21.69 12.83 41.91 1.89
1324 1661 0.382873 AGTGCCATGCATGCGTAATG 59.617 50.000 21.69 10.73 41.91 1.90
1339 1676 4.728534 GCGTAATGCATCCACTTTAAACA 58.271 39.130 0.00 0.00 45.45 2.83
1340 1677 5.339990 GCGTAATGCATCCACTTTAAACAT 58.660 37.500 0.00 0.00 45.45 2.71
1343 1680 7.195646 CGTAATGCATCCACTTTAAACATCAT 58.804 34.615 0.00 0.00 0.00 2.45
1346 1683 6.343716 TGCATCCACTTTAAACATCATGTT 57.656 33.333 0.00 0.00 43.41 2.71
1348 1685 7.312154 TGCATCCACTTTAAACATCATGTTAC 58.688 34.615 2.67 0.00 40.14 2.50
1350 1687 7.273381 GCATCCACTTTAAACATCATGTTACAC 59.727 37.037 2.67 0.00 40.14 2.90
1351 1688 7.209471 TCCACTTTAAACATCATGTTACACC 57.791 36.000 2.67 0.00 40.14 4.16
1353 1690 7.504238 TCCACTTTAAACATCATGTTACACCTT 59.496 33.333 2.67 0.00 40.14 3.50
1354 1691 7.594758 CCACTTTAAACATCATGTTACACCTTG 59.405 37.037 2.67 0.00 40.14 3.61
1355 1692 8.349245 CACTTTAAACATCATGTTACACCTTGA 58.651 33.333 2.67 0.00 40.14 3.02
1357 1694 9.743057 CTTTAAACATCATGTTACACCTTGAAA 57.257 29.630 2.67 0.00 40.14 2.69
1360 1803 6.899393 ACATCATGTTACACCTTGAAACAT 57.101 33.333 0.00 0.00 42.91 2.71
1371 1814 9.575783 TTACACCTTGAAACATGTAAAGAAAAC 57.424 29.630 14.33 0.00 35.23 2.43
1374 1817 9.796120 CACCTTGAAACATGTAAAGAAAACTAA 57.204 29.630 14.33 0.00 0.00 2.24
1400 1843 9.927668 ATGTAACACTTTAAAAGAATGGGATTG 57.072 29.630 0.00 0.00 0.00 2.67
1401 1844 8.364142 TGTAACACTTTAAAAGAATGGGATTGG 58.636 33.333 0.00 0.00 0.00 3.16
1402 1845 5.793817 ACACTTTAAAAGAATGGGATTGGC 58.206 37.500 0.00 0.00 0.00 4.52
1403 1846 4.864247 CACTTTAAAAGAATGGGATTGGCG 59.136 41.667 0.00 0.00 0.00 5.69
1404 1847 4.081697 ACTTTAAAAGAATGGGATTGGCGG 60.082 41.667 0.00 0.00 0.00 6.13
1405 1848 2.230130 AAAAGAATGGGATTGGCGGA 57.770 45.000 0.00 0.00 0.00 5.54
1406 1849 2.459555 AAAGAATGGGATTGGCGGAT 57.540 45.000 0.00 0.00 0.00 4.18
1407 1850 2.459555 AAGAATGGGATTGGCGGATT 57.540 45.000 0.00 0.00 0.00 3.01
1408 1851 1.696063 AGAATGGGATTGGCGGATTG 58.304 50.000 0.00 0.00 0.00 2.67
1409 1852 0.032540 GAATGGGATTGGCGGATTGC 59.967 55.000 0.00 0.00 45.38 3.56
1410 1853 0.397535 AATGGGATTGGCGGATTGCT 60.398 50.000 0.00 0.00 45.43 3.91
1411 1854 0.478072 ATGGGATTGGCGGATTGCTA 59.522 50.000 0.00 0.00 45.43 3.49
1418 1861 2.708216 TGGCGGATTGCTAAATCTCA 57.292 45.000 0.00 0.00 45.43 3.27
1419 1862 2.564771 TGGCGGATTGCTAAATCTCAG 58.435 47.619 0.00 0.00 45.43 3.35
1420 1863 2.092968 TGGCGGATTGCTAAATCTCAGT 60.093 45.455 0.00 0.00 45.43 3.41
1421 1864 2.289002 GGCGGATTGCTAAATCTCAGTG 59.711 50.000 0.00 0.00 45.43 3.66
1427 1870 3.920231 TGCTAAATCTCAGTGGATGCT 57.080 42.857 0.00 0.00 0.00 3.79
1429 1872 5.557576 TGCTAAATCTCAGTGGATGCTAT 57.442 39.130 0.00 0.00 0.00 2.97
1430 1873 6.670695 TGCTAAATCTCAGTGGATGCTATA 57.329 37.500 0.00 0.00 0.00 1.31
1434 1877 8.449397 GCTAAATCTCAGTGGATGCTATATTTG 58.551 37.037 0.00 0.00 0.00 2.32
1438 1881 9.499479 AATCTCAGTGGATGCTATATTTGTTAG 57.501 33.333 0.00 0.00 0.00 2.34
1440 1883 8.874156 TCTCAGTGGATGCTATATTTGTTAGAT 58.126 33.333 0.00 0.00 0.00 1.98
1441 1884 9.499479 CTCAGTGGATGCTATATTTGTTAGATT 57.501 33.333 0.00 0.00 0.00 2.40
1442 1885 9.851686 TCAGTGGATGCTATATTTGTTAGATTT 57.148 29.630 0.00 0.00 0.00 2.17
1451 1894 9.651718 GCTATATTTGTTAGATTTTTCGTGGAG 57.348 33.333 0.00 0.00 0.00 3.86
1470 1913 9.751542 TCGTGGAGATTATAATTTTCTCTTCTC 57.248 33.333 12.22 7.06 36.85 2.87
1471 1914 8.983724 CGTGGAGATTATAATTTTCTCTTCTCC 58.016 37.037 15.87 15.87 45.30 3.71
1485 1928 8.703604 TTTCTCTTCTCCTTTATTGTATGTCG 57.296 34.615 0.00 0.00 0.00 4.35
1491 1934 8.867112 TTCTCCTTTATTGTATGTCGTATCAC 57.133 34.615 0.00 0.00 0.00 3.06
1492 1935 8.234136 TCTCCTTTATTGTATGTCGTATCACT 57.766 34.615 0.00 0.00 0.00 3.41
1493 1936 9.346005 TCTCCTTTATTGTATGTCGTATCACTA 57.654 33.333 0.00 0.00 0.00 2.74
1494 1937 9.613957 CTCCTTTATTGTATGTCGTATCACTAG 57.386 37.037 0.00 0.00 0.00 2.57
1495 1938 9.346005 TCCTTTATTGTATGTCGTATCACTAGA 57.654 33.333 0.00 0.00 0.00 2.43
1508 2250 9.469807 GTCGTATCACTAGAATGAGATTTGATT 57.530 33.333 0.00 0.00 30.46 2.57
1548 2399 7.698506 ATCTCAAAATCAGAATCTCAAAGCA 57.301 32.000 0.00 0.00 0.00 3.91
1550 2401 8.118976 TCTCAAAATCAGAATCTCAAAGCAAT 57.881 30.769 0.00 0.00 0.00 3.56
1551 2402 8.027189 TCTCAAAATCAGAATCTCAAAGCAATG 58.973 33.333 0.00 0.00 0.00 2.82
1552 2403 7.094631 TCAAAATCAGAATCTCAAAGCAATGG 58.905 34.615 0.00 0.00 0.00 3.16
1554 2405 5.831702 ATCAGAATCTCAAAGCAATGGAC 57.168 39.130 0.00 0.00 0.00 4.02
1555 2406 4.654915 TCAGAATCTCAAAGCAATGGACA 58.345 39.130 0.00 0.00 0.00 4.02
1556 2407 4.698780 TCAGAATCTCAAAGCAATGGACAG 59.301 41.667 0.00 0.00 0.00 3.51
1558 2409 4.458295 AGAATCTCAAAGCAATGGACAGTG 59.542 41.667 0.00 0.00 0.00 3.66
1559 2410 2.507484 TCTCAAAGCAATGGACAGTGG 58.493 47.619 1.79 0.00 0.00 4.00
1560 2411 2.106338 TCTCAAAGCAATGGACAGTGGA 59.894 45.455 1.79 0.00 0.00 4.02
1561 2412 3.087031 CTCAAAGCAATGGACAGTGGAT 58.913 45.455 1.79 0.00 0.00 3.41
1563 3325 2.134789 AAGCAATGGACAGTGGATCC 57.865 50.000 4.20 4.20 36.70 3.36
1574 3336 2.690326 GTGGATCCATGCACGGTAC 58.310 57.895 19.62 0.00 39.29 3.34
1575 3337 0.107897 GTGGATCCATGCACGGTACA 60.108 55.000 19.62 0.00 39.29 2.90
1580 3342 3.306710 GGATCCATGCACGGTACATATCA 60.307 47.826 6.95 0.00 0.00 2.15
1581 3343 3.828875 TCCATGCACGGTACATATCAA 57.171 42.857 0.00 0.00 0.00 2.57
1583 3345 4.713553 TCCATGCACGGTACATATCAATT 58.286 39.130 0.00 0.00 0.00 2.32
1586 3348 5.239306 CCATGCACGGTACATATCAATTCTT 59.761 40.000 0.00 0.00 0.00 2.52
1588 3350 5.423886 TGCACGGTACATATCAATTCTTCA 58.576 37.500 0.00 0.00 0.00 3.02
1590 3352 6.542005 TGCACGGTACATATCAATTCTTCATT 59.458 34.615 0.00 0.00 0.00 2.57
1591 3353 7.072030 GCACGGTACATATCAATTCTTCATTC 58.928 38.462 0.00 0.00 0.00 2.67
1592 3354 7.041780 GCACGGTACATATCAATTCTTCATTCT 60.042 37.037 0.00 0.00 0.00 2.40
1593 3355 8.278408 CACGGTACATATCAATTCTTCATTCTG 58.722 37.037 0.00 0.00 0.00 3.02
1594 3356 8.204160 ACGGTACATATCAATTCTTCATTCTGA 58.796 33.333 0.00 0.00 0.00 3.27
1595 3357 8.491152 CGGTACATATCAATTCTTCATTCTGAC 58.509 37.037 0.00 0.00 0.00 3.51
1596 3358 9.330063 GGTACATATCAATTCTTCATTCTGACA 57.670 33.333 0.00 0.00 0.00 3.58
1753 3806 1.374252 AAGTACAAGCTGGGCGACG 60.374 57.895 0.00 0.00 0.00 5.12
1812 3865 3.391382 GCGGCCAGGTACCTGAGT 61.391 66.667 38.35 4.26 46.30 3.41
1813 3866 2.056223 GCGGCCAGGTACCTGAGTA 61.056 63.158 38.35 0.00 46.30 2.59
1814 3867 1.610554 GCGGCCAGGTACCTGAGTAA 61.611 60.000 38.35 0.00 46.30 2.24
1815 3868 1.120530 CGGCCAGGTACCTGAGTAAT 58.879 55.000 38.35 2.15 46.30 1.89
1821 3874 3.535561 CAGGTACCTGAGTAATGGCAAG 58.464 50.000 34.54 4.30 46.30 4.01
1862 3915 3.430862 GCGCAAGGACGGCATCAA 61.431 61.111 0.30 0.00 38.28 2.57
1937 3990 0.318699 CAGCTCGTGGACAACTTCGA 60.319 55.000 0.00 0.00 0.00 3.71
1955 4008 2.143925 CGACAAGAAGAAGTTCACCCC 58.856 52.381 5.50 0.00 34.82 4.95
1958 4011 2.224305 ACAAGAAGAAGTTCACCCCGAG 60.224 50.000 5.50 0.00 34.82 4.63
2001 4054 2.278206 CACTCCATCGGCGTCTCG 60.278 66.667 6.85 0.00 0.00 4.04
2019 4072 1.671742 GCACCTCTCGTCCTTCCAA 59.328 57.895 0.00 0.00 0.00 3.53
2032 4085 0.250295 CTTCCAAGACCGCCTCAACA 60.250 55.000 0.00 0.00 0.00 3.33
2034 4087 0.181587 TCCAAGACCGCCTCAACAAA 59.818 50.000 0.00 0.00 0.00 2.83
2115 4168 4.335416 CCCAGAAGAAGAGCCAAAATACA 58.665 43.478 0.00 0.00 0.00 2.29
2118 4171 4.761739 CAGAAGAAGAGCCAAAATACACCA 59.238 41.667 0.00 0.00 0.00 4.17
2247 4486 0.739813 GCTACTACCACGCCAACCTG 60.740 60.000 0.00 0.00 0.00 4.00
2328 4573 1.276421 GCTATGGCCGAGTACATGGAT 59.724 52.381 7.53 0.00 0.00 3.41
2427 4672 5.392811 CCGTTACGAGATAAGGAAGAACTGT 60.393 44.000 6.24 0.00 31.46 3.55
2535 4791 5.125417 GCTCTGTTCCATGCCTAATTTGTAA 59.875 40.000 0.00 0.00 0.00 2.41
2563 4819 8.367156 ACCACAATACTCACTGCAAAATAAAAT 58.633 29.630 0.00 0.00 0.00 1.82
2627 4887 7.173562 TCTCGTCCTAGATTTCTAGTTAGATGC 59.826 40.741 12.42 0.00 43.34 3.91
2662 4922 2.830370 GAAAGATGCAGGGGGCCG 60.830 66.667 0.00 0.00 43.89 6.13
2691 4952 5.929992 CGTTAAATACACAGGAGTTCTTGGA 59.070 40.000 0.00 0.00 0.00 3.53
2705 4966 2.791493 TGGATGCTCCACCCCCTA 59.209 61.111 1.25 0.00 42.67 3.53
2714 4977 3.330701 TGCTCCACCCCCTAATGAATATC 59.669 47.826 0.00 0.00 0.00 1.63
2760 5023 3.274288 GAGGATCTCAAACATGGGTGTC 58.726 50.000 0.00 0.00 37.67 3.67
2788 5051 2.404923 TCCCGTGTGAAGTTTTGTGA 57.595 45.000 0.00 0.00 0.00 3.58
2793 5060 4.326009 CCCGTGTGAAGTTTTGTGAAAAAG 59.674 41.667 0.00 0.00 31.13 2.27
2799 5066 9.783256 GTGTGAAGTTTTGTGAAAAAGTACTAT 57.217 29.630 0.00 0.00 31.13 2.12
2829 5096 5.859205 ATCCATGGCAAAGAAAATAGTCC 57.141 39.130 6.96 0.00 0.00 3.85
2837 5104 4.933400 GCAAAGAAAATAGTCCGACCTACA 59.067 41.667 0.00 0.00 0.00 2.74
2844 5111 6.989155 AAATAGTCCGACCTACAATCCATA 57.011 37.500 0.00 0.00 0.00 2.74
2852 5119 5.175859 CGACCTACAATCCATACAAACAGT 58.824 41.667 0.00 0.00 0.00 3.55
2864 5131 5.989168 CCATACAAACAGTTTTTCCCTTTCC 59.011 40.000 0.00 0.00 0.00 3.13
2912 5179 8.463930 TTTTTGTGAGAATACATTTCCTGAGT 57.536 30.769 0.00 0.00 0.00 3.41
2913 5180 8.463930 TTTTGTGAGAATACATTTCCTGAGTT 57.536 30.769 0.00 0.00 0.00 3.01
2914 5181 9.567776 TTTTGTGAGAATACATTTCCTGAGTTA 57.432 29.630 0.00 0.00 0.00 2.24
2934 5204 9.658475 TGAGTTATTTTTATGAAACTTCACACG 57.342 29.630 0.00 0.00 40.49 4.49
2942 5212 2.696707 TGAAACTTCACACGGGAGTAGT 59.303 45.455 0.00 0.00 34.62 2.73
3030 5302 8.548877 TCTGAATTTAATACTCATATAGGGGGC 58.451 37.037 0.00 0.00 0.00 5.80
3031 5303 7.335627 TGAATTTAATACTCATATAGGGGGCG 58.664 38.462 0.00 0.00 0.00 6.13
3033 5305 3.484953 AATACTCATATAGGGGGCGGA 57.515 47.619 0.00 0.00 0.00 5.54
3034 5306 2.526888 TACTCATATAGGGGGCGGAG 57.473 55.000 0.00 0.00 0.00 4.63
3083 5357 7.367285 TCCACAAATATCTTGTTACTTTGCAC 58.633 34.615 0.00 0.00 31.59 4.57
3165 5439 9.831737 GGTGCAGTTATACATGAAATATCAATC 57.168 33.333 0.00 0.00 39.49 2.67
3166 5440 9.831737 GTGCAGTTATACATGAAATATCAATCC 57.168 33.333 0.00 0.00 39.49 3.01
3167 5441 9.571816 TGCAGTTATACATGAAATATCAATCCA 57.428 29.630 0.00 0.00 39.49 3.41
3188 5469 7.227049 TCCAGTTTCCATTTCCTGTAATTTC 57.773 36.000 0.00 0.00 0.00 2.17
3261 5542 1.840635 CTCTAGCTTTAGGGGTTGGCT 59.159 52.381 0.00 0.00 37.08 4.75
3301 5582 1.581447 CTGGAAACCTTGCCTTCGC 59.419 57.895 0.00 0.00 0.00 4.70
3310 5591 2.947938 CTTGCCTTCGCCCCGATCAT 62.948 60.000 0.00 0.00 35.23 2.45
3318 5599 2.263741 GCCCCGATCATGGTGATGC 61.264 63.158 0.00 0.00 37.20 3.91
3347 5628 9.595823 GAGTAATAGAGTTTGCATGTTTACCTA 57.404 33.333 0.00 0.00 0.00 3.08
3387 5668 5.105752 GCACAATAACCTTGAAACAACACA 58.894 37.500 0.00 0.00 0.00 3.72
3391 5672 8.663911 CACAATAACCTTGAAACAACACAAATT 58.336 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.252967 TGTGCACTAAACATTTATCAGGTG 57.747 37.500 19.41 0.00 0.00 4.00
2 3 6.092748 GGTTGTGCACTAAACATTTATCAGG 58.907 40.000 19.41 0.00 0.00 3.86
3 4 6.676950 TGGTTGTGCACTAAACATTTATCAG 58.323 36.000 19.41 0.00 0.00 2.90
17 18 8.643752 GTGTATATAAAAATGTTGGTTGTGCAC 58.356 33.333 10.75 10.75 0.00 4.57
131 137 9.840427 GTGCATACATGTCTATTAAAAACTGTT 57.160 29.630 0.00 0.00 0.00 3.16
132 138 8.458843 GGTGCATACATGTCTATTAAAAACTGT 58.541 33.333 0.00 0.00 0.00 3.55
135 141 9.855021 AAAGGTGCATACATGTCTATTAAAAAC 57.145 29.630 0.00 0.00 0.00 2.43
155 161 7.864108 TGGTCATGTATATTTCTGAAAGGTG 57.136 36.000 8.95 2.05 0.00 4.00
203 209 1.224075 CATCGCTTCTAGCCATGTGG 58.776 55.000 0.00 0.00 35.52 4.17
267 274 8.755696 AAAATGTGTATGACAATAACGCAAAT 57.244 26.923 6.36 0.00 38.36 2.32
268 275 8.581057 AAAAATGTGTATGACAATAACGCAAA 57.419 26.923 6.36 0.00 38.36 3.68
293 300 3.432326 GGGTGGGTTGCACACAATTAAAA 60.432 43.478 8.07 0.00 40.54 1.52
317 331 2.891112 CCACATAAAATGCGTGCCAAT 58.109 42.857 0.00 0.00 0.00 3.16
318 332 1.671261 GCCACATAAAATGCGTGCCAA 60.671 47.619 0.00 0.00 0.00 4.52
335 349 3.498834 GCATCATCGCACACGCCA 61.499 61.111 0.00 0.00 39.84 5.69
336 350 4.241999 GGCATCATCGCACACGCC 62.242 66.667 0.00 0.00 39.84 5.68
364 379 2.709475 GCGGGTTGATGTGCGATC 59.291 61.111 0.00 0.00 0.00 3.69
394 409 1.628340 AGGTCATCATCCACGGTTCAA 59.372 47.619 0.00 0.00 0.00 2.69
396 411 3.536956 TTAGGTCATCATCCACGGTTC 57.463 47.619 0.00 0.00 0.00 3.62
459 478 4.401837 GGGATTAGGCTAGTTAGGTATCGG 59.598 50.000 0.00 0.00 0.00 4.18
460 479 5.262804 AGGGATTAGGCTAGTTAGGTATCG 58.737 45.833 0.00 0.00 0.00 2.92
549 586 8.943002 CCCTCTGTAAACAAATATAAGAACGTT 58.057 33.333 0.00 0.00 0.00 3.99
552 589 9.668497 ACTCCCTCTGTAAACAAATATAAGAAC 57.332 33.333 0.00 0.00 0.00 3.01
564 631 5.609533 TGCCTATTACTCCCTCTGTAAAC 57.390 43.478 0.00 0.00 34.20 2.01
565 632 5.394883 CGTTGCCTATTACTCCCTCTGTAAA 60.395 44.000 0.00 0.00 34.20 2.01
566 633 4.098960 CGTTGCCTATTACTCCCTCTGTAA 59.901 45.833 0.00 0.00 34.87 2.41
567 634 3.635373 CGTTGCCTATTACTCCCTCTGTA 59.365 47.826 0.00 0.00 0.00 2.74
570 637 2.748388 ACGTTGCCTATTACTCCCTCT 58.252 47.619 0.00 0.00 0.00 3.69
590 664 6.357367 TGAGTCCGATATATATCTGCAGCTA 58.643 40.000 18.39 3.80 0.00 3.32
593 667 6.691754 ACTGAGTCCGATATATATCTGCAG 57.308 41.667 18.39 7.63 0.00 4.41
596 670 9.995957 CAACTAACTGAGTCCGATATATATCTG 57.004 37.037 18.39 13.09 37.44 2.90
598 672 7.916450 GGCAACTAACTGAGTCCGATATATATC 59.084 40.741 12.07 12.07 37.44 1.63
600 674 7.154435 GGCAACTAACTGAGTCCGATATATA 57.846 40.000 0.00 0.00 37.44 0.86
601 675 6.026947 GGCAACTAACTGAGTCCGATATAT 57.973 41.667 0.00 0.00 37.44 0.86
602 676 5.449107 GGCAACTAACTGAGTCCGATATA 57.551 43.478 0.00 0.00 37.44 0.86
603 677 4.323553 GGCAACTAACTGAGTCCGATAT 57.676 45.455 0.00 0.00 37.44 1.63
604 678 3.795623 GGCAACTAACTGAGTCCGATA 57.204 47.619 0.00 0.00 37.44 2.92
605 679 2.674796 GGCAACTAACTGAGTCCGAT 57.325 50.000 0.00 0.00 37.44 4.18
850 953 3.798337 CGGCAAGATGGCATTATTTGTTC 59.202 43.478 0.00 4.24 43.94 3.18
855 962 2.485426 CGATCGGCAAGATGGCATTATT 59.515 45.455 7.38 0.00 43.94 1.40
871 978 3.632855 TCCACTCATGAAGATCGATCG 57.367 47.619 19.33 9.36 0.00 3.69
872 979 3.679025 GCATCCACTCATGAAGATCGATC 59.321 47.826 17.91 17.91 0.00 3.69
873 980 3.070590 TGCATCCACTCATGAAGATCGAT 59.929 43.478 0.00 0.00 0.00 3.59
874 981 2.431782 TGCATCCACTCATGAAGATCGA 59.568 45.455 0.00 0.00 0.00 3.59
914 1021 7.074507 AGGTCGACGATCATGTATAATACTC 57.925 40.000 11.33 0.00 0.00 2.59
915 1022 7.450124 AAGGTCGACGATCATGTATAATACT 57.550 36.000 11.33 0.00 0.00 2.12
916 1023 9.275231 CTTAAGGTCGACGATCATGTATAATAC 57.725 37.037 11.33 0.00 0.00 1.89
917 1024 7.966753 GCTTAAGGTCGACGATCATGTATAATA 59.033 37.037 11.33 0.00 0.00 0.98
918 1025 6.807230 GCTTAAGGTCGACGATCATGTATAAT 59.193 38.462 11.33 0.00 0.00 1.28
924 1157 3.085443 AGCTTAAGGTCGACGATCATG 57.915 47.619 11.33 0.00 0.00 3.07
927 1160 4.752661 AGATAGCTTAAGGTCGACGATC 57.247 45.455 11.11 8.23 0.00 3.69
928 1161 7.414319 GCTTATAGATAGCTTAAGGTCGACGAT 60.414 40.741 11.11 3.06 35.74 3.73
931 1164 6.802834 GTGCTTATAGATAGCTTAAGGTCGAC 59.197 42.308 11.11 7.13 39.38 4.20
934 1167 6.583050 CGTGTGCTTATAGATAGCTTAAGGTC 59.417 42.308 11.11 0.00 39.38 3.85
948 1181 1.720805 CTGTGGTGCGTGTGCTTATA 58.279 50.000 0.00 0.00 43.34 0.98
949 1182 1.577328 GCTGTGGTGCGTGTGCTTAT 61.577 55.000 0.00 0.00 43.34 1.73
988 1221 3.650942 ACCTTGGCCATCTTAATCCGATA 59.349 43.478 6.09 0.00 0.00 2.92
993 1241 4.497507 GCGTTAACCTTGGCCATCTTAATC 60.498 45.833 6.09 2.30 0.00 1.75
1030 1278 2.033755 GCAGCAGGCACAGAGACAG 61.034 63.158 0.00 0.00 43.97 3.51
1045 1293 3.429141 CGCAGAACAGGCCAGCAG 61.429 66.667 5.01 0.00 0.00 4.24
1188 1436 6.700960 TCAACTTTTGATGGCAACTTACATTG 59.299 34.615 0.00 0.00 34.08 2.82
1230 1547 6.543465 TCATCAAATGAGGCAATAGTAACAGG 59.457 38.462 0.00 0.00 33.59 4.00
1233 1550 8.677300 TCTTTCATCAAATGAGGCAATAGTAAC 58.323 33.333 0.00 0.00 40.94 2.50
1236 1553 6.888632 ACTCTTTCATCAAATGAGGCAATAGT 59.111 34.615 0.00 0.00 41.31 2.12
1237 1554 7.330900 ACTCTTTCATCAAATGAGGCAATAG 57.669 36.000 0.00 0.00 41.31 1.73
1241 1558 7.707624 ATTTACTCTTTCATCAAATGAGGCA 57.292 32.000 0.00 0.00 41.31 4.75
1242 1559 8.992835 AAATTTACTCTTTCATCAAATGAGGC 57.007 30.769 0.00 0.00 41.31 4.70
1270 1587 8.467963 TCATATTACCCGTCACTGATTTAGTA 57.532 34.615 0.00 0.00 37.60 1.82
1278 1595 4.956085 TCCATTCATATTACCCGTCACTG 58.044 43.478 0.00 0.00 0.00 3.66
1279 1596 5.454755 CCTTCCATTCATATTACCCGTCACT 60.455 44.000 0.00 0.00 0.00 3.41
1282 1599 4.041198 TCCCTTCCATTCATATTACCCGTC 59.959 45.833 0.00 0.00 0.00 4.79
1283 1600 3.977999 TCCCTTCCATTCATATTACCCGT 59.022 43.478 0.00 0.00 0.00 5.28
1284 1601 4.041691 ACTCCCTTCCATTCATATTACCCG 59.958 45.833 0.00 0.00 0.00 5.28
1286 1603 4.762251 GCACTCCCTTCCATTCATATTACC 59.238 45.833 0.00 0.00 0.00 2.85
1287 1604 4.762251 GGCACTCCCTTCCATTCATATTAC 59.238 45.833 0.00 0.00 0.00 1.89
1297 1614 1.866483 ATGCATGGCACTCCCTTCCA 61.866 55.000 0.00 0.00 43.04 3.53
1298 1615 1.076485 ATGCATGGCACTCCCTTCC 60.076 57.895 0.00 0.00 43.04 3.46
1299 1616 2.012902 GCATGCATGGCACTCCCTTC 62.013 60.000 27.34 3.43 43.04 3.46
1300 1617 2.056223 GCATGCATGGCACTCCCTT 61.056 57.895 27.34 0.00 43.04 3.95
1303 1620 1.375853 TTACGCATGCATGGCACTCC 61.376 55.000 27.34 9.08 43.04 3.85
1304 1621 0.664761 ATTACGCATGCATGGCACTC 59.335 50.000 27.34 9.80 43.04 3.51
1305 1622 0.382873 CATTACGCATGCATGGCACT 59.617 50.000 27.34 10.24 43.04 4.40
1306 1623 2.876052 CATTACGCATGCATGGCAC 58.124 52.632 27.34 10.54 43.04 5.01
1317 1634 4.728534 TGTTTAAAGTGGATGCATTACGC 58.271 39.130 0.00 4.11 42.89 4.42
1318 1635 6.550843 TGATGTTTAAAGTGGATGCATTACG 58.449 36.000 0.00 0.00 0.00 3.18
1323 1660 5.981088 ACATGATGTTTAAAGTGGATGCA 57.019 34.783 0.00 0.00 0.00 3.96
1324 1661 7.273381 GTGTAACATGATGTTTAAAGTGGATGC 59.727 37.037 16.75 0.00 41.45 3.91
1328 1665 7.214467 AGGTGTAACATGATGTTTAAAGTGG 57.786 36.000 16.75 0.00 41.45 4.00
1329 1666 8.349245 TCAAGGTGTAACATGATGTTTAAAGTG 58.651 33.333 16.75 8.33 41.45 3.16
1331 1668 9.743057 TTTCAAGGTGTAACATGATGTTTAAAG 57.257 29.630 16.75 1.49 41.45 1.85
1343 1680 7.867305 TCTTTACATGTTTCAAGGTGTAACA 57.133 32.000 2.30 3.40 40.85 2.41
1346 1683 8.962679 AGTTTTCTTTACATGTTTCAAGGTGTA 58.037 29.630 2.30 0.00 0.00 2.90
1348 1685 9.796120 TTAGTTTTCTTTACATGTTTCAAGGTG 57.204 29.630 2.30 0.00 0.00 4.00
1374 1817 9.927668 CAATCCCATTCTTTTAAAGTGTTACAT 57.072 29.630 4.53 0.00 0.00 2.29
1379 1822 5.566627 CGCCAATCCCATTCTTTTAAAGTGT 60.567 40.000 4.53 0.00 0.00 3.55
1380 1823 4.864247 CGCCAATCCCATTCTTTTAAAGTG 59.136 41.667 4.53 0.00 0.00 3.16
1387 1830 2.431782 CAATCCGCCAATCCCATTCTTT 59.568 45.455 0.00 0.00 0.00 2.52
1388 1831 2.034124 CAATCCGCCAATCCCATTCTT 58.966 47.619 0.00 0.00 0.00 2.52
1390 1833 0.032540 GCAATCCGCCAATCCCATTC 59.967 55.000 0.00 0.00 32.94 2.67
1391 1834 0.397535 AGCAATCCGCCAATCCCATT 60.398 50.000 0.00 0.00 44.04 3.16
1393 1836 0.257328 TTAGCAATCCGCCAATCCCA 59.743 50.000 0.00 0.00 44.04 4.37
1394 1837 1.398692 TTTAGCAATCCGCCAATCCC 58.601 50.000 0.00 0.00 44.04 3.85
1395 1838 2.887152 AGATTTAGCAATCCGCCAATCC 59.113 45.455 0.00 0.00 44.04 3.01
1396 1839 3.565482 TGAGATTTAGCAATCCGCCAATC 59.435 43.478 0.00 0.00 44.04 2.67
1397 1840 3.554934 TGAGATTTAGCAATCCGCCAAT 58.445 40.909 0.00 0.00 44.04 3.16
1398 1841 2.945008 CTGAGATTTAGCAATCCGCCAA 59.055 45.455 0.00 0.00 44.04 4.52
1399 1842 2.092968 ACTGAGATTTAGCAATCCGCCA 60.093 45.455 0.00 0.00 44.04 5.69
1400 1843 2.289002 CACTGAGATTTAGCAATCCGCC 59.711 50.000 0.00 0.00 44.04 6.13
1401 1844 2.289002 CCACTGAGATTTAGCAATCCGC 59.711 50.000 0.00 0.00 39.95 5.54
1402 1845 3.797039 TCCACTGAGATTTAGCAATCCG 58.203 45.455 0.00 0.00 39.95 4.18
1403 1846 4.023365 GCATCCACTGAGATTTAGCAATCC 60.023 45.833 0.00 0.00 39.95 3.01
1404 1847 4.820716 AGCATCCACTGAGATTTAGCAATC 59.179 41.667 0.00 0.00 39.45 2.67
1405 1848 4.789807 AGCATCCACTGAGATTTAGCAAT 58.210 39.130 0.00 0.00 0.00 3.56
1406 1849 4.226427 AGCATCCACTGAGATTTAGCAA 57.774 40.909 0.00 0.00 0.00 3.91
1407 1850 3.920231 AGCATCCACTGAGATTTAGCA 57.080 42.857 0.00 0.00 0.00 3.49
1408 1851 8.449397 CAAATATAGCATCCACTGAGATTTAGC 58.551 37.037 0.00 0.00 0.00 3.09
1409 1852 9.499479 ACAAATATAGCATCCACTGAGATTTAG 57.501 33.333 0.00 0.00 0.00 1.85
1410 1853 9.851686 AACAAATATAGCATCCACTGAGATTTA 57.148 29.630 0.00 0.00 0.00 1.40
1411 1854 8.757982 AACAAATATAGCATCCACTGAGATTT 57.242 30.769 0.00 0.00 0.00 2.17
1412 1855 9.499479 CTAACAAATATAGCATCCACTGAGATT 57.501 33.333 0.00 0.00 0.00 2.40
1413 1856 8.874156 TCTAACAAATATAGCATCCACTGAGAT 58.126 33.333 0.00 0.00 0.00 2.75
1414 1857 8.250143 TCTAACAAATATAGCATCCACTGAGA 57.750 34.615 0.00 0.00 0.00 3.27
1415 1858 9.499479 AATCTAACAAATATAGCATCCACTGAG 57.501 33.333 0.00 0.00 0.00 3.35
1416 1859 9.851686 AAATCTAACAAATATAGCATCCACTGA 57.148 29.630 0.00 0.00 0.00 3.41
1444 1887 9.751542 GAGAAGAGAAAATTATAATCTCCACGA 57.248 33.333 9.85 0.00 40.34 4.35
1459 1902 9.151471 CGACATACAATAAAGGAGAAGAGAAAA 57.849 33.333 0.00 0.00 0.00 2.29
1460 1903 8.311836 ACGACATACAATAAAGGAGAAGAGAAA 58.688 33.333 0.00 0.00 0.00 2.52
1462 1905 7.406031 ACGACATACAATAAAGGAGAAGAGA 57.594 36.000 0.00 0.00 0.00 3.10
1463 1906 9.400638 GATACGACATACAATAAAGGAGAAGAG 57.599 37.037 0.00 0.00 0.00 2.85
1464 1907 8.909923 TGATACGACATACAATAAAGGAGAAGA 58.090 33.333 0.00 0.00 0.00 2.87
1465 1908 8.969267 GTGATACGACATACAATAAAGGAGAAG 58.031 37.037 0.00 0.00 0.00 2.85
1466 1909 8.692710 AGTGATACGACATACAATAAAGGAGAA 58.307 33.333 0.00 0.00 0.00 2.87
1468 1911 9.613957 CTAGTGATACGACATACAATAAAGGAG 57.386 37.037 0.00 0.00 0.00 3.69
1469 1912 9.346005 TCTAGTGATACGACATACAATAAAGGA 57.654 33.333 0.00 0.00 0.00 3.36
1470 1913 9.961265 TTCTAGTGATACGACATACAATAAAGG 57.039 33.333 0.00 0.00 0.00 3.11
1476 1919 8.446599 TCTCATTCTAGTGATACGACATACAA 57.553 34.615 0.00 0.00 0.00 2.41
1477 1920 8.622948 ATCTCATTCTAGTGATACGACATACA 57.377 34.615 0.00 0.00 0.00 2.29
1478 1921 9.900710 AAATCTCATTCTAGTGATACGACATAC 57.099 33.333 0.00 0.00 0.00 2.39
1480 1923 8.633561 TCAAATCTCATTCTAGTGATACGACAT 58.366 33.333 0.00 0.00 0.00 3.06
1481 1924 7.996385 TCAAATCTCATTCTAGTGATACGACA 58.004 34.615 0.00 0.00 0.00 4.35
1482 1925 9.469807 AATCAAATCTCATTCTAGTGATACGAC 57.530 33.333 0.00 0.00 0.00 4.34
1526 2377 7.275779 CCATTGCTTTGAGATTCTGATTTTGAG 59.724 37.037 0.00 0.00 0.00 3.02
1528 2379 7.063074 GTCCATTGCTTTGAGATTCTGATTTTG 59.937 37.037 0.00 0.00 0.00 2.44
1536 2387 4.380233 CCACTGTCCATTGCTTTGAGATTC 60.380 45.833 0.00 0.00 0.00 2.52
1539 2390 2.106338 TCCACTGTCCATTGCTTTGAGA 59.894 45.455 0.00 0.00 0.00 3.27
1540 2391 2.507484 TCCACTGTCCATTGCTTTGAG 58.493 47.619 0.00 0.00 0.00 3.02
1542 2393 2.165030 GGATCCACTGTCCATTGCTTTG 59.835 50.000 6.95 0.00 35.76 2.77
1545 2396 0.994247 TGGATCCACTGTCCATTGCT 59.006 50.000 11.44 0.00 40.72 3.91
1551 2402 1.091771 CGTGCATGGATCCACTGTCC 61.092 60.000 18.99 9.97 36.26 4.02
1552 2403 1.091771 CCGTGCATGGATCCACTGTC 61.092 60.000 21.08 12.47 0.00 3.51
1554 2405 0.177836 TACCGTGCATGGATCCACTG 59.822 55.000 31.74 16.94 0.00 3.66
1555 2406 0.178068 GTACCGTGCATGGATCCACT 59.822 55.000 31.74 10.36 0.00 4.00
1556 2407 0.107897 TGTACCGTGCATGGATCCAC 60.108 55.000 31.74 20.65 0.00 4.02
1558 2409 2.831685 TATGTACCGTGCATGGATCC 57.168 50.000 31.74 17.34 0.00 3.36
1559 2410 3.925379 TGATATGTACCGTGCATGGATC 58.075 45.455 31.74 21.56 0.00 3.36
1560 2411 4.350368 TTGATATGTACCGTGCATGGAT 57.650 40.909 31.74 16.60 0.00 3.41
1561 2412 3.828875 TTGATATGTACCGTGCATGGA 57.171 42.857 31.74 9.82 0.00 3.41
1563 3325 5.929697 AGAATTGATATGTACCGTGCATG 57.070 39.130 11.94 0.00 0.00 4.06
1569 3331 8.593492 TCAGAATGAAGAATTGATATGTACCG 57.407 34.615 0.00 0.00 45.97 4.02
1580 3342 8.372031 CATGCATGCATGTCAGAATGAAGAATT 61.372 37.037 40.30 11.70 43.14 2.17
1581 3343 6.956371 CATGCATGCATGTCAGAATGAAGAAT 60.956 38.462 40.30 12.04 43.14 2.40
1583 3345 4.202010 CATGCATGCATGTCAGAATGAAGA 60.202 41.667 40.30 8.95 43.14 2.87
1586 3348 3.708563 CATGCATGCATGTCAGAATGA 57.291 42.857 40.30 10.25 46.20 2.57
1670 3723 1.291877 CGCCTTCTTCTCGGTGTTGG 61.292 60.000 0.00 0.00 0.00 3.77
1791 3844 2.365635 AGGTACCTGGCCGCATCT 60.366 61.111 15.42 0.00 0.00 2.90
1794 3847 2.791613 TACTCAGGTACCTGGCCGCA 62.792 60.000 35.94 19.08 43.75 5.69
1803 3856 4.051922 CGATCTTGCCATTACTCAGGTAC 58.948 47.826 0.00 0.00 0.00 3.34
1937 3990 1.766496 TCGGGGTGAACTTCTTCTTGT 59.234 47.619 0.00 0.00 0.00 3.16
1947 4000 3.003763 AGCTCCCTCGGGGTGAAC 61.004 66.667 0.00 0.00 44.74 3.18
1958 4011 1.460273 GGAGAGGATGACGAGCTCCC 61.460 65.000 8.47 2.68 39.33 4.30
2001 4054 0.390472 CTTGGAAGGACGAGAGGTGC 60.390 60.000 0.00 0.00 37.22 5.01
2019 4072 1.880027 GTTGATTTGTTGAGGCGGTCT 59.120 47.619 0.00 0.00 0.00 3.85
2032 4085 2.530958 ATCGGGGTCGCGGTTGATTT 62.531 55.000 6.13 0.00 36.13 2.17
2034 4087 3.441011 GATCGGGGTCGCGGTTGAT 62.441 63.158 6.13 2.96 36.13 2.57
2115 4168 3.515502 TGTTCTTCTCAATCGGATCTGGT 59.484 43.478 0.62 0.00 0.00 4.00
2118 4171 5.152623 TGTTGTTCTTCTCAATCGGATCT 57.847 39.130 0.00 0.00 0.00 2.75
2163 4216 4.682334 TACCCGGCGGTGGTCTGA 62.682 66.667 26.32 0.00 44.40 3.27
2208 4447 4.659172 TTGTCCAGGGCGCCCTTG 62.659 66.667 45.58 40.04 45.70 3.61
2247 4486 0.250467 TGAAGAGCACCCTGTTCTGC 60.250 55.000 2.91 0.00 40.84 4.26
2309 4554 4.495422 GTTATCCATGTACTCGGCCATAG 58.505 47.826 2.24 1.22 0.00 2.23
2395 4640 5.059833 CCTTATCTCGTAACGGGTACTACT 58.940 45.833 1.19 0.00 0.00 2.57
2427 4672 4.737578 AGTAGTTCTGGTTGGTGACTCTA 58.262 43.478 0.00 0.00 0.00 2.43
2535 4791 8.574251 TTATTTTGCAGTGAGTATTGTGGTAT 57.426 30.769 0.00 0.00 0.00 2.73
2627 4887 4.219507 TCTTTCTCAGCAGGAGTAGAACAG 59.780 45.833 5.46 0.00 44.40 3.16
2662 4922 9.530633 AAGAACTCCTGTGTATTTAACGATATC 57.469 33.333 0.00 0.00 0.00 1.63
2691 4952 1.607225 TTCATTAGGGGGTGGAGCAT 58.393 50.000 0.00 0.00 0.00 3.79
2724 4987 6.425735 TGAGATCCTCAAATTCCATGCTTAA 58.574 36.000 0.00 0.00 37.57 1.85
2725 4988 6.005066 TGAGATCCTCAAATTCCATGCTTA 57.995 37.500 0.00 0.00 37.57 3.09
2745 5008 3.424703 AGATTGGACACCCATGTTTGAG 58.575 45.455 0.00 0.00 43.12 3.02
2757 5020 2.835156 TCACACGGGAATAGATTGGACA 59.165 45.455 0.00 0.00 0.00 4.02
2760 5023 3.873910 ACTTCACACGGGAATAGATTGG 58.126 45.455 0.00 0.00 0.00 3.16
2829 5096 5.175859 ACTGTTTGTATGGATTGTAGGTCG 58.824 41.667 0.00 0.00 0.00 4.79
2837 5104 6.994421 AGGGAAAAACTGTTTGTATGGATT 57.006 33.333 6.53 0.00 0.00 3.01
2844 5111 5.692115 ATGGAAAGGGAAAAACTGTTTGT 57.308 34.783 6.53 0.14 0.00 2.83
2891 5158 9.739276 AAATAACTCAGGAAATGTATTCTCACA 57.261 29.630 0.00 0.00 0.00 3.58
2912 5179 8.167605 TCCCGTGTGAAGTTTCATAAAAATAA 57.832 30.769 0.00 0.00 39.73 1.40
2913 5180 7.446013 ACTCCCGTGTGAAGTTTCATAAAAATA 59.554 33.333 0.00 0.00 39.73 1.40
2914 5181 6.264518 ACTCCCGTGTGAAGTTTCATAAAAAT 59.735 34.615 0.00 0.00 39.73 1.82
2934 5204 2.582978 GGTGCCCGAACTACTCCC 59.417 66.667 0.00 0.00 0.00 4.30
2942 5212 0.331278 ATCAAATCTGGGTGCCCGAA 59.669 50.000 2.44 0.00 39.42 4.30
3035 5307 1.026718 GGATTTGGAGCACTCGGGTG 61.027 60.000 12.23 12.23 45.53 4.61
3036 5308 1.201429 AGGATTTGGAGCACTCGGGT 61.201 55.000 0.00 0.00 0.00 5.28
3161 5435 6.588719 TTACAGGAAATGGAAACTGGATTG 57.411 37.500 0.00 0.00 35.34 2.67
3165 5439 6.398095 GGAAATTACAGGAAATGGAAACTGG 58.602 40.000 0.00 0.00 34.61 4.00
3166 5440 6.092748 CGGAAATTACAGGAAATGGAAACTG 58.907 40.000 0.00 0.00 34.61 3.16
3167 5441 5.773176 ACGGAAATTACAGGAAATGGAAACT 59.227 36.000 0.00 0.00 34.61 2.66
3172 5453 5.356751 TCATGACGGAAATTACAGGAAATGG 59.643 40.000 0.00 0.00 0.00 3.16
3188 5469 3.056107 TCAAGGTCCTAAACTCATGACGG 60.056 47.826 0.00 0.00 0.00 4.79
3261 5542 1.112950 TGACCTAACCACACGTGACA 58.887 50.000 25.01 5.03 0.00 3.58
3301 5582 1.601759 GGCATCACCATGATCGGGG 60.602 63.158 8.00 4.72 34.28 5.73
3310 5591 4.290093 ACTCTATTACTCAGGCATCACCA 58.710 43.478 0.00 0.00 43.14 4.17
3318 5599 6.992063 AACATGCAAACTCTATTACTCAGG 57.008 37.500 0.00 0.00 0.00 3.86
3387 5668 9.372369 TCACCGTTTATTCTTTTGTCAAAATTT 57.628 25.926 11.09 2.75 0.00 1.82
3391 5672 7.323049 TCTCACCGTTTATTCTTTTGTCAAA 57.677 32.000 0.00 0.00 0.00 2.69
3408 5689 9.893305 AAATTGTAGAAGTAAATTTTCTCACCG 57.107 29.630 0.00 0.00 36.38 4.94


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

AutoCloner maintained by Alex Coulton.