Multiple sequence alignment - TraesCS5A01G514900

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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 TraesCS5A01G514900 chr5A 100.000 5341 0 0 1 5341 678263467 678268807 0.000000e+00 9864.0
1 TraesCS5A01G514900 chr5A 87.940 398 38 9 80 475 109965149 109965538 1.360000e-125 460.0
2 TraesCS5A01G514900 chr5A 81.928 581 61 20 3 557 620737431 620736869 8.160000e-123 451.0
3 TraesCS5A01G514900 chr5A 88.421 95 8 3 2881 2974 6156614 6156706 1.570000e-20 111.0
4 TraesCS5A01G514900 chr4B 92.733 4211 226 38 723 4898 639842657 639846822 0.000000e+00 6008.0
5 TraesCS5A01G514900 chr4B 92.405 395 18 6 4934 5319 639846822 639847213 2.170000e-153 553.0
6 TraesCS5A01G514900 chr4D 94.520 2865 117 20 2494 5331 497941836 497944687 0.000000e+00 4385.0
7 TraesCS5A01G514900 chr4D 89.973 1117 77 18 558 1665 497940756 497941846 0.000000e+00 1410.0
8 TraesCS5A01G514900 chr6D 93.277 476 22 8 1 475 448624912 448625378 0.000000e+00 693.0
9 TraesCS5A01G514900 chr6D 92.693 479 24 9 1 475 422220715 422221186 0.000000e+00 680.0
10 TraesCS5A01G514900 chr1D 92.259 478 21 14 4 475 301250931 301250464 0.000000e+00 664.0
11 TraesCS5A01G514900 chr7D 88.348 575 36 18 1 553 420911871 420912436 0.000000e+00 662.0
12 TraesCS5A01G514900 chr3A 92.034 477 29 8 1 475 585062122 585062591 0.000000e+00 662.0
13 TraesCS5A01G514900 chr3A 91.892 481 27 10 1 475 742377794 742378268 0.000000e+00 662.0
14 TraesCS5A01G514900 chr3A 87.522 561 54 10 1 552 661603835 661604388 7.550000e-178 634.0
15 TraesCS5A01G514900 chr2D 92.067 479 24 10 4 475 119370550 119370079 0.000000e+00 662.0
16 TraesCS5A01G514900 chr2D 90.619 501 31 10 1 493 161895591 161895099 0.000000e+00 651.0
17 TraesCS5A01G514900 chr6A 85.492 579 36 23 1 552 611518597 611519154 1.300000e-155 560.0
18 TraesCS5A01G514900 chrUn 88.211 475 38 14 1 472 407260280 407260739 7.820000e-153 551.0
19 TraesCS5A01G514900 chr7A 86.774 499 51 9 1 493 69532904 69532415 4.710000e-150 542.0
20 TraesCS5A01G514900 chr7A 80.287 487 63 19 13 493 589284892 589284433 2.380000e-88 337.0
21 TraesCS5A01G514900 chr5B 80.153 131 21 3 424 553 593937118 593936992 5.700000e-15 93.5


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 TraesCS5A01G514900 chr5A 678263467 678268807 5340 False 9864.0 9864 100.0000 1 5341 1 chr5A.!!$F3 5340
1 TraesCS5A01G514900 chr5A 620736869 620737431 562 True 451.0 451 81.9280 3 557 1 chr5A.!!$R1 554
2 TraesCS5A01G514900 chr4B 639842657 639847213 4556 False 3280.5 6008 92.5690 723 5319 2 chr4B.!!$F1 4596
3 TraesCS5A01G514900 chr4D 497940756 497944687 3931 False 2897.5 4385 92.2465 558 5331 2 chr4D.!!$F1 4773
4 TraesCS5A01G514900 chr7D 420911871 420912436 565 False 662.0 662 88.3480 1 553 1 chr7D.!!$F1 552
5 TraesCS5A01G514900 chr3A 661603835 661604388 553 False 634.0 634 87.5220 1 552 1 chr3A.!!$F2 551
6 TraesCS5A01G514900 chr6A 611518597 611519154 557 False 560.0 560 85.4920 1 552 1 chr6A.!!$F1 551

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
707 761 0.033504 GACGTGGCCTTCAGTTCTGA 59.966 55.000 3.32 0.0 0.00 3.27 F
1754 1827 0.035881 TGCTTCTCAGAACCAGGCAG 59.964 55.000 0.00 0.0 0.00 4.85 F
1810 1889 0.469917 TCGATCCAGATTTCAGGGGC 59.530 55.000 0.00 0.0 0.00 5.80 F
1907 1988 0.671781 CTGGCTGTGGTAGTGTGCTC 60.672 60.000 0.00 0.0 0.00 4.26 F
2677 2759 0.682292 TGTTCAGTGGACCATGCGTA 59.318 50.000 0.00 0.0 0.00 4.42 F
2938 3022 2.101415 GTGCTTTTGCCCTGAAGTTTCT 59.899 45.455 0.00 0.0 46.87 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2469 2550 0.037975 CAAAATGCTGGGTCTGCCAC 60.038 55.000 0.0 0.0 36.17 5.01 R
3457 3543 0.107654 AATCAGAAGGGCAGCGGTAC 60.108 55.000 0.0 0.0 0.00 3.34 R
3768 3857 0.326264 TCTGGGAAGCCTCTGAAAGC 59.674 55.000 0.0 0.0 0.00 3.51 R
3933 4022 1.683917 AGGTCACGAGCAGATATGGAC 59.316 52.381 0.0 0.0 0.00 4.02 R
3950 4039 0.839946 AGCAGGGCGATTCATTAGGT 59.160 50.000 0.0 0.0 0.00 3.08 R
4753 4846 0.107017 AGCCAAGTTCACACACAGCT 60.107 50.000 0.0 0.0 0.00 4.24 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
232 242 1.429463 GTTGTGATTTCGCGAGAGGT 58.571 50.000 9.59 0.00 43.69 3.85
350 363 5.995282 AGTTCGTCAAAACCTATCAACATGA 59.005 36.000 0.00 0.00 0.00 3.07
394 407 2.032549 CGCGAGGAATCCAATGATGAAC 60.033 50.000 0.00 0.00 0.00 3.18
421 434 1.717194 GAGATTTGGACGCACGGTTA 58.283 50.000 0.00 0.00 0.00 2.85
501 554 2.942376 TGATAAATGACGCACATGACCC 59.058 45.455 0.00 0.00 39.39 4.46
534 587 7.645340 GTGAAGTGTTCTTTGTAACGAGTACTA 59.355 37.037 0.00 0.00 33.64 1.82
535 588 8.355169 TGAAGTGTTCTTTGTAACGAGTACTAT 58.645 33.333 0.00 0.00 33.64 2.12
561 614 9.781834 TTTAATTAGTGATTTCGGCTAATTGTG 57.218 29.630 19.23 0.00 42.14 3.33
571 624 6.913873 TTCGGCTAATTGTGGTATTAACTC 57.086 37.500 0.00 0.00 0.00 3.01
613 666 0.670546 CGCTTTGTCGTCCACCAGAT 60.671 55.000 0.00 0.00 0.00 2.90
665 718 2.565391 TGTGATCAGGCCGAACTTTCTA 59.435 45.455 0.00 0.00 0.00 2.10
667 720 3.371285 GTGATCAGGCCGAACTTTCTAAC 59.629 47.826 0.00 0.00 0.00 2.34
668 721 2.074547 TCAGGCCGAACTTTCTAACG 57.925 50.000 0.00 0.00 0.00 3.18
669 722 1.076332 CAGGCCGAACTTTCTAACGG 58.924 55.000 0.00 0.00 46.74 4.44
670 723 0.971386 AGGCCGAACTTTCTAACGGA 59.029 50.000 0.00 0.00 46.94 4.69
671 724 1.345415 AGGCCGAACTTTCTAACGGAA 59.655 47.619 0.00 0.00 46.94 4.30
672 725 1.462283 GGCCGAACTTTCTAACGGAAC 59.538 52.381 0.00 0.00 46.94 3.62
673 726 2.137523 GCCGAACTTTCTAACGGAACA 58.862 47.619 0.00 0.00 46.94 3.18
674 727 2.545106 GCCGAACTTTCTAACGGAACAA 59.455 45.455 0.00 0.00 46.94 2.83
677 730 5.144359 CCGAACTTTCTAACGGAACAATTG 58.856 41.667 3.24 3.24 46.94 2.32
678 731 5.277634 CCGAACTTTCTAACGGAACAATTGT 60.278 40.000 4.92 4.92 46.94 2.71
681 735 7.219344 CGAACTTTCTAACGGAACAATTGTTTT 59.781 33.333 24.02 16.63 38.56 2.43
700 754 3.793775 TTTCGCGACGTGGCCTTCA 62.794 57.895 17.27 0.00 0.00 3.02
701 755 4.717629 TCGCGACGTGGCCTTCAG 62.718 66.667 17.27 2.44 0.00 3.02
707 761 0.033504 GACGTGGCCTTCAGTTCTGA 59.966 55.000 3.32 0.00 0.00 3.27
708 762 0.468226 ACGTGGCCTTCAGTTCTGAA 59.532 50.000 3.32 13.50 0.00 3.02
739 793 3.583882 CTGGGCCCGTTGAATGGGT 62.584 63.158 22.77 0.00 46.50 4.51
904 966 4.364686 GTCCCCTCCCCCTTCCCA 62.365 72.222 0.00 0.00 0.00 4.37
992 1054 3.793144 CGGAAGCAAGCAGGCGAC 61.793 66.667 0.00 0.00 39.27 5.19
993 1055 2.359230 GGAAGCAAGCAGGCGACT 60.359 61.111 0.00 0.00 46.44 4.18
1101 1163 3.470888 ATCCAGGCCGACTTCCCG 61.471 66.667 0.00 0.00 0.00 5.14
1110 1172 1.067635 GCCGACTTCCCGTGTAAGTAA 60.068 52.381 0.00 0.00 37.31 2.24
1113 1175 4.248058 CCGACTTCCCGTGTAAGTAAAAT 58.752 43.478 0.00 0.00 37.31 1.82
1122 1184 3.362304 CGTGTAAGTAAAATATCGCCGGC 60.362 47.826 19.07 19.07 0.00 6.13
1254 1321 0.248949 GGTGGTAAGCGATCCTCGAC 60.249 60.000 0.00 0.00 43.74 4.20
1260 1327 3.524606 GCGATCCTCGACCCCGAA 61.525 66.667 0.00 0.00 43.74 4.30
1262 1329 2.813200 GATCCTCGACCCCGAACC 59.187 66.667 0.00 0.00 45.04 3.62
1264 1331 3.312989 ATCCTCGACCCCGAACCCT 62.313 63.158 0.00 0.00 45.04 4.34
1266 1333 2.995574 CTCGACCCCGAACCCTGT 60.996 66.667 0.00 0.00 45.04 4.00
1269 1336 4.717313 GACCCCGAACCCTGTGCC 62.717 72.222 0.00 0.00 0.00 5.01
1271 1338 4.047125 CCCCGAACCCTGTGCCAT 62.047 66.667 0.00 0.00 0.00 4.40
1284 1351 1.106285 GTGCCATCCATTTCAGGGTC 58.894 55.000 0.00 0.00 0.00 4.46
1286 1353 1.064463 TGCCATCCATTTCAGGGTCTC 60.064 52.381 0.00 0.00 0.00 3.36
1288 1355 2.357569 GCCATCCATTTCAGGGTCTCTT 60.358 50.000 0.00 0.00 0.00 2.85
1289 1356 3.879321 GCCATCCATTTCAGGGTCTCTTT 60.879 47.826 0.00 0.00 0.00 2.52
1290 1357 4.347607 CCATCCATTTCAGGGTCTCTTTT 58.652 43.478 0.00 0.00 0.00 2.27
1291 1358 4.774200 CCATCCATTTCAGGGTCTCTTTTT 59.226 41.667 0.00 0.00 0.00 1.94
1293 1360 4.151883 TCCATTTCAGGGTCTCTTTTTGG 58.848 43.478 0.00 0.00 0.00 3.28
1294 1361 4.141041 TCCATTTCAGGGTCTCTTTTTGGA 60.141 41.667 0.00 0.00 0.00 3.53
1300 1367 0.608308 GGTCTCTTTTTGGACCCCCG 60.608 60.000 0.00 0.00 44.35 5.73
1336 1403 1.681825 GACGAATTGCCCGTGTTTTC 58.318 50.000 0.00 0.00 40.67 2.29
1358 1425 2.748532 CGCGAATTGGGTTAGGGTTTAA 59.251 45.455 0.00 0.00 0.00 1.52
1363 1430 1.385014 TGGGTTAGGGTTTAAGGGGG 58.615 55.000 0.00 0.00 0.00 5.40
1368 1435 3.076484 GGTTAGGGTTTAAGGGGGTTTCT 59.924 47.826 0.00 0.00 0.00 2.52
1465 1535 2.403252 ACTAGGTGGCAGTTATGTGC 57.597 50.000 0.00 0.00 43.19 4.57
1496 1569 1.730501 ACGATCGACGACCTCTTGTA 58.269 50.000 24.34 0.00 45.77 2.41
1552 1625 2.778299 TCCCGTCTCATGGTTTTTGAG 58.222 47.619 0.00 0.00 41.61 3.02
1575 1648 2.490903 CACCCTTTTCTGCTTGATCTGG 59.509 50.000 0.00 0.00 0.00 3.86
1601 1674 2.810028 TTGTCCGTGTTTTCGTGAAC 57.190 45.000 0.00 0.00 0.00 3.18
1603 1676 1.661617 TGTCCGTGTTTTCGTGAACTG 59.338 47.619 5.53 0.00 0.00 3.16
1626 1699 4.505918 GGGTTGGGTTTAAGGGAATTTTGG 60.506 45.833 0.00 0.00 0.00 3.28
1629 1702 3.913163 TGGGTTTAAGGGAATTTTGGCAT 59.087 39.130 0.00 0.00 0.00 4.40
1635 1708 8.482943 GGTTTAAGGGAATTTTGGCATAATACT 58.517 33.333 3.57 1.15 0.00 2.12
1662 1735 4.297299 ACTCTGTTTGTTCTGCATTGTG 57.703 40.909 0.00 0.00 0.00 3.33
1696 1769 3.829026 ACTAGCGATCATGAAGATGCCTA 59.171 43.478 0.00 0.00 37.00 3.93
1701 1774 4.329528 GCGATCATGAAGATGCCTAGATTC 59.670 45.833 0.00 0.00 37.00 2.52
1728 1801 3.299340 ACTAGCAGTTACCAGTTGACG 57.701 47.619 0.00 0.00 0.00 4.35
1729 1802 2.889045 ACTAGCAGTTACCAGTTGACGA 59.111 45.455 0.00 0.00 0.00 4.20
1754 1827 0.035881 TGCTTCTCAGAACCAGGCAG 59.964 55.000 0.00 0.00 0.00 4.85
1795 1874 2.369394 GTTTGGGCCTCTGAAATCGAT 58.631 47.619 4.53 0.00 0.00 3.59
1800 1879 1.414181 GGCCTCTGAAATCGATCCAGA 59.586 52.381 21.67 21.67 35.81 3.86
1809 1888 3.498774 AATCGATCCAGATTTCAGGGG 57.501 47.619 0.00 0.00 37.56 4.79
1810 1889 0.469917 TCGATCCAGATTTCAGGGGC 59.530 55.000 0.00 0.00 0.00 5.80
1820 1901 6.070656 CCAGATTTCAGGGGCTATGAATAAA 58.929 40.000 5.90 0.00 36.60 1.40
1827 1908 7.346751 TCAGGGGCTATGAATAAAACATTTC 57.653 36.000 0.00 0.00 0.00 2.17
1828 1909 6.323739 TCAGGGGCTATGAATAAAACATTTCC 59.676 38.462 0.00 0.00 0.00 3.13
1829 1910 5.301805 AGGGGCTATGAATAAAACATTTCCG 59.698 40.000 0.00 0.00 0.00 4.30
1830 1911 5.300792 GGGGCTATGAATAAAACATTTCCGA 59.699 40.000 0.00 0.00 0.00 4.55
1831 1912 6.015434 GGGGCTATGAATAAAACATTTCCGAT 60.015 38.462 0.00 0.00 0.00 4.18
1832 1913 7.175990 GGGGCTATGAATAAAACATTTCCGATA 59.824 37.037 0.00 0.00 0.00 2.92
1833 1914 8.739972 GGGCTATGAATAAAACATTTCCGATAT 58.260 33.333 0.00 0.00 0.00 1.63
1834 1915 9.559958 GGCTATGAATAAAACATTTCCGATATG 57.440 33.333 0.00 0.00 0.00 1.78
1838 1919 9.965824 ATGAATAAAACATTTCCGATATGAACC 57.034 29.630 5.90 0.00 0.00 3.62
1839 1920 9.184523 TGAATAAAACATTTCCGATATGAACCT 57.815 29.630 5.90 0.00 0.00 3.50
1887 1968 3.134458 GCGGTCCTCTTATCATTTCAGG 58.866 50.000 0.00 0.00 0.00 3.86
1888 1969 3.134458 CGGTCCTCTTATCATTTCAGGC 58.866 50.000 0.00 0.00 0.00 4.85
1891 1972 4.133078 GTCCTCTTATCATTTCAGGCTGG 58.867 47.826 15.73 0.00 0.00 4.85
1896 1977 1.471119 ATCATTTCAGGCTGGCTGTG 58.529 50.000 27.51 19.55 0.00 3.66
1907 1988 0.671781 CTGGCTGTGGTAGTGTGCTC 60.672 60.000 0.00 0.00 0.00 4.26
1914 1995 2.035961 TGTGGTAGTGTGCTCTCAGTTC 59.964 50.000 0.00 0.00 0.00 3.01
1921 2002 2.355756 GTGTGCTCTCAGTTCTTTTGCA 59.644 45.455 0.00 0.00 0.00 4.08
1923 2004 3.633525 TGTGCTCTCAGTTCTTTTGCATT 59.366 39.130 0.00 0.00 0.00 3.56
1979 2060 8.712285 TTCGTAAAATAGTAAGACCCAGAATG 57.288 34.615 0.00 0.00 0.00 2.67
1989 2070 7.231467 AGTAAGACCCAGAATGTTACATTTGT 58.769 34.615 12.13 7.46 29.34 2.83
2006 2087 6.518493 ACATTTGTCATTCTTTGAAGCACAT 58.482 32.000 0.00 0.00 35.70 3.21
2007 2088 6.987992 ACATTTGTCATTCTTTGAAGCACATT 59.012 30.769 0.00 0.00 35.70 2.71
2008 2089 6.831727 TTTGTCATTCTTTGAAGCACATTG 57.168 33.333 0.00 0.00 35.70 2.82
2009 2090 4.300803 TGTCATTCTTTGAAGCACATTGC 58.699 39.130 0.00 0.00 45.46 3.56
2032 2113 5.523916 GCAATTAGAACAGTCGGTGATACAT 59.476 40.000 0.00 0.00 0.00 2.29
2049 2130 2.511659 ACATGAGAGTTGCAACAGCAT 58.488 42.857 30.11 24.03 38.23 3.79
2051 2132 1.241165 TGAGAGTTGCAACAGCATGG 58.759 50.000 30.11 0.00 43.62 3.66
2062 2143 3.491447 GCAACAGCATGGAAAGTGAAGTT 60.491 43.478 0.00 0.00 43.62 2.66
2088 2169 3.569194 TGCACAGGGACTAAAACTGAA 57.431 42.857 0.00 0.00 36.02 3.02
2095 2176 6.591834 CACAGGGACTAAAACTGAAGTATGAG 59.408 42.308 0.00 0.00 36.02 2.90
2127 2208 6.173427 ACCACCTCAACTGCATTAATTTTT 57.827 33.333 0.00 0.00 0.00 1.94
2160 2241 6.148150 AGCTGCAATGTGATTTACAAATTTGG 59.852 34.615 21.74 4.79 43.77 3.28
2164 2245 6.650390 GCAATGTGATTTACAAATTTGGAGGT 59.350 34.615 21.74 6.25 43.77 3.85
2227 2308 5.356470 CCCAGTAGTTACTACTAGTCCACAC 59.644 48.000 22.66 0.00 44.37 3.82
2321 2402 6.513806 TGTTCATTTCCTGTCCAATGTATG 57.486 37.500 0.00 0.00 32.96 2.39
2322 2403 6.009589 TGTTCATTTCCTGTCCAATGTATGT 58.990 36.000 0.00 0.00 32.96 2.29
2323 2404 6.493115 TGTTCATTTCCTGTCCAATGTATGTT 59.507 34.615 0.00 0.00 32.96 2.71
2324 2405 7.015098 TGTTCATTTCCTGTCCAATGTATGTTT 59.985 33.333 0.00 0.00 32.96 2.83
2325 2406 6.923012 TCATTTCCTGTCCAATGTATGTTTG 58.077 36.000 0.00 0.00 32.96 2.93
2326 2407 6.493115 TCATTTCCTGTCCAATGTATGTTTGT 59.507 34.615 0.00 0.00 32.96 2.83
2327 2408 7.667635 TCATTTCCTGTCCAATGTATGTTTGTA 59.332 33.333 0.00 0.00 32.96 2.41
2328 2409 7.825331 TTTCCTGTCCAATGTATGTTTGTAA 57.175 32.000 0.00 0.00 0.00 2.41
2329 2410 7.447374 TTCCTGTCCAATGTATGTTTGTAAG 57.553 36.000 0.00 0.00 0.00 2.34
2330 2411 6.539173 TCCTGTCCAATGTATGTTTGTAAGT 58.461 36.000 0.00 0.00 0.00 2.24
2331 2412 7.001674 TCCTGTCCAATGTATGTTTGTAAGTT 58.998 34.615 0.00 0.00 0.00 2.66
2332 2413 7.504238 TCCTGTCCAATGTATGTTTGTAAGTTT 59.496 33.333 0.00 0.00 0.00 2.66
2333 2414 8.788806 CCTGTCCAATGTATGTTTGTAAGTTTA 58.211 33.333 0.00 0.00 0.00 2.01
2359 2440 9.941664 ATTATTGATTTTCTAGTCAAGCAATCG 57.058 29.630 17.59 0.00 39.23 3.34
2368 2449 3.950397 AGTCAAGCAATCGTATTGGGAA 58.050 40.909 8.86 0.00 0.00 3.97
2422 2503 8.636213 CAAGCAATCATATTGGGAAGTTTATCT 58.364 33.333 2.11 0.00 0.00 1.98
2469 2550 9.294030 GCAATCATGTTAGGAAGTTTTATCTTG 57.706 33.333 0.00 0.00 0.00 3.02
2480 2561 3.153919 GTTTTATCTTGTGGCAGACCCA 58.846 45.455 0.00 0.00 42.79 4.51
2668 2750 3.582647 TCCTCTATTTGCTGTTCAGTGGA 59.417 43.478 1.78 0.00 0.00 4.02
2677 2759 0.682292 TGTTCAGTGGACCATGCGTA 59.318 50.000 0.00 0.00 0.00 4.42
2938 3022 2.101415 GTGCTTTTGCCCTGAAGTTTCT 59.899 45.455 0.00 0.00 46.87 2.52
2989 3074 8.003629 TGATTTTGATGTGGTTGGATCCATATA 58.996 33.333 17.06 4.20 38.95 0.86
3030 3115 8.890410 TCTTACTGTACCTGTCCTAACTTATT 57.110 34.615 0.00 0.00 0.00 1.40
3031 3116 9.317827 TCTTACTGTACCTGTCCTAACTTATTT 57.682 33.333 0.00 0.00 0.00 1.40
3050 3135 5.913137 ATTTTCTTGATGCGGTTGGATTA 57.087 34.783 0.00 0.00 0.00 1.75
3062 3147 5.008514 TGCGGTTGGATTACATATTGACATG 59.991 40.000 0.00 0.00 0.00 3.21
3144 3229 3.001330 GCAGTATTCTGTACCGATTGTGC 59.999 47.826 1.02 0.00 43.05 4.57
3307 3392 4.201990 GCTTGAGATGGGTCAAATAAGCAG 60.202 45.833 0.00 0.00 39.14 4.24
3659 3748 5.368256 CAGATTTCTTTCTGTGGTTCCTG 57.632 43.478 0.00 0.00 38.64 3.86
3687 3776 7.973048 ACAATTCTCTACTGAATACCACCTA 57.027 36.000 0.00 0.00 35.82 3.08
3768 3857 4.437239 CTGCTATTGTTGGTAGTGAGGAG 58.563 47.826 0.00 0.00 0.00 3.69
3882 3971 6.982141 CACAATAAGCCTGCAATGTTGATAAT 59.018 34.615 9.99 0.00 0.00 1.28
3893 3982 5.638657 GCAATGTTGATAATCTTTTGCCACA 59.361 36.000 0.00 0.00 0.00 4.17
3949 4038 3.560902 ATACGTCCATATCTGCTCGTG 57.439 47.619 0.00 0.00 34.14 4.35
3950 4039 1.389555 ACGTCCATATCTGCTCGTGA 58.610 50.000 0.00 0.00 32.18 4.35
4064 4153 2.075355 ATGGGAAGTTCGGGCCACAA 62.075 55.000 4.39 0.00 0.00 3.33
4119 4208 0.249784 CATCGATCAGCCTGTCCCTG 60.250 60.000 0.00 0.00 0.00 4.45
4384 4473 0.951558 ATTCGTTGGTGAGGCAACAC 59.048 50.000 0.00 6.34 39.70 3.32
4513 4603 1.132977 TCCTCTGGGTGGTGAACTGTA 60.133 52.381 0.00 0.00 0.00 2.74
4561 4653 3.940852 TCAACTATGAACTGCATCGCATT 59.059 39.130 0.00 0.00 38.44 3.56
4620 4712 4.184629 GCATTCCGAGTATGTTGTTCTCT 58.815 43.478 0.00 0.00 0.00 3.10
4676 4768 2.781945 CTTGCAGTGTTGGAAGGTTC 57.218 50.000 1.41 0.00 45.76 3.62
4694 4787 5.831103 AGGTTCCATCTAATTTGGTGATGT 58.169 37.500 1.40 0.00 36.72 3.06
4695 4788 5.888161 AGGTTCCATCTAATTTGGTGATGTC 59.112 40.000 1.40 0.00 36.72 3.06
4696 4789 5.652014 GGTTCCATCTAATTTGGTGATGTCA 59.348 40.000 1.40 0.00 36.72 3.58
4699 4792 7.572523 TCCATCTAATTTGGTGATGTCATTC 57.427 36.000 1.40 0.00 36.72 2.67
4701 4794 8.493607 TCCATCTAATTTGGTGATGTCATTCTA 58.506 33.333 1.40 0.00 36.72 2.10
4706 4799 3.912496 TGGTGATGTCATTCTAGGTGG 57.088 47.619 0.00 0.00 0.00 4.61
4729 4822 8.515414 GTGGAGATTTTTGCTTGTTTCTAGTAT 58.485 33.333 0.00 0.00 0.00 2.12
4731 4824 7.486232 GGAGATTTTTGCTTGTTTCTAGTATGC 59.514 37.037 0.00 0.00 0.00 3.14
4736 4829 3.259064 GCTTGTTTCTAGTATGCGGTCA 58.741 45.455 0.00 0.00 0.00 4.02
4753 4846 3.243367 CGGTCAGCAATTTGAACCTGAAA 60.243 43.478 0.00 0.00 36.23 2.69
4768 4861 2.684881 CCTGAAAGCTGTGTGTGAACTT 59.315 45.455 0.00 0.00 0.00 2.66
4796 4889 1.852965 CCCTGATATTTGACCCTGGGT 59.147 52.381 20.72 20.72 39.44 4.51
4808 4901 0.836606 CCCTGGGTTTTGGCTTTTGT 59.163 50.000 3.97 0.00 0.00 2.83
4850 4943 7.360101 GGCCTACAGTTTGCATAACTATAATCG 60.360 40.741 12.06 4.44 0.00 3.34
4855 4948 5.820423 AGTTTGCATAACTATAATCGGCACA 59.180 36.000 11.11 0.00 0.00 4.57
4864 4957 2.620251 TAATCGGCACAATAGCTGCT 57.380 45.000 7.57 7.57 40.71 4.24
4885 4978 4.760715 GCTTAGATGATGAGGATGCACAAT 59.239 41.667 0.00 0.00 0.00 2.71
5046 5148 0.802494 GATACAACAAGGCCCACACG 59.198 55.000 0.00 0.00 0.00 4.49
5110 5213 4.094294 ACCGTTGAATGTTATCACCGATTG 59.906 41.667 0.00 0.00 37.41 2.67
5112 5215 5.292345 CCGTTGAATGTTATCACCGATTGTA 59.708 40.000 0.00 0.00 37.41 2.41
5113 5216 6.410845 CGTTGAATGTTATCACCGATTGTAG 58.589 40.000 0.00 0.00 37.41 2.74
5157 5263 4.887071 TGAAACAAAACAGCTATGGACAGT 59.113 37.500 0.00 0.00 0.00 3.55
5206 5312 1.806542 GAGGTGCGCATCTCTTTTTCA 59.193 47.619 37.33 0.00 35.71 2.69
5233 5339 1.651240 TTCGAGACGCCGTAGAAGGG 61.651 60.000 0.00 0.00 0.00 3.95
5240 5346 4.857251 CCGTAGAAGGGCATGGAC 57.143 61.111 0.00 0.00 0.00 4.02
5255 5363 4.943705 GGCATGGACCGATCAATATACATT 59.056 41.667 0.00 0.00 0.00 2.71
5264 5372 8.389779 ACCGATCAATATACATTTATGCACAA 57.610 30.769 0.00 0.00 0.00 3.33
5283 5391 5.117592 GCACAAGAATGAATTTTTGGAGACG 59.882 40.000 10.11 0.00 36.51 4.18
5305 5413 1.942677 TGTACGTTCACCCACAACAG 58.057 50.000 0.00 0.00 0.00 3.16
5320 5428 4.864247 CCACAACAGAAAAACCACAAGAAG 59.136 41.667 0.00 0.00 0.00 2.85
5321 5429 5.336372 CCACAACAGAAAAACCACAAGAAGA 60.336 40.000 0.00 0.00 0.00 2.87
5324 5432 7.331687 CACAACAGAAAAACCACAAGAAGATTT 59.668 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 0.657368 GCAAAACCGTGACTCTTGCG 60.657 55.000 0.00 0.00 33.74 4.85
66 67 0.663153 AGCAAAACCGTGACTCTTGC 59.337 50.000 0.00 0.00 42.10 4.01
67 68 3.363178 GAAAGCAAAACCGTGACTCTTG 58.637 45.455 0.00 0.00 0.00 3.02
68 69 2.031683 CGAAAGCAAAACCGTGACTCTT 59.968 45.455 0.00 0.00 0.00 2.85
107 113 1.588082 GCCGTGACTCCCGTAAAGA 59.412 57.895 0.00 0.00 0.00 2.52
232 242 2.987125 GAAAGAGGCAGGCCCGTA 59.013 61.111 6.70 0.00 39.21 4.02
239 249 0.324943 TCCCTTTCCGAAAGAGGCAG 59.675 55.000 20.43 5.05 41.02 4.85
350 363 6.491394 CGTCGAGATCTTCAAAACTAGATCT 58.509 40.000 12.93 12.93 46.88 2.75
394 407 0.713883 CGTCCAAATCTCGAACCGTG 59.286 55.000 0.00 0.00 0.00 4.94
475 489 7.362662 GGTCATGTGCGTCATTTATCATAAAT 58.637 34.615 0.00 0.00 34.09 1.40
476 490 6.238621 GGGTCATGTGCGTCATTTATCATAAA 60.239 38.462 0.00 0.00 34.09 1.40
479 493 3.565482 GGGTCATGTGCGTCATTTATCAT 59.435 43.478 0.00 0.00 34.09 2.45
480 494 2.942376 GGGTCATGTGCGTCATTTATCA 59.058 45.455 0.00 0.00 34.09 2.15
483 497 1.364721 CGGGTCATGTGCGTCATTTA 58.635 50.000 0.00 0.00 34.09 1.40
501 554 2.256117 AAGAACACTTCACTTCCCCG 57.744 50.000 0.00 0.00 0.00 5.73
505 558 6.035758 ACTCGTTACAAAGAACACTTCACTTC 59.964 38.462 0.00 0.00 0.00 3.01
535 588 9.781834 CACAATTAGCCGAAATCACTAATTAAA 57.218 29.630 13.68 0.00 42.05 1.52
650 703 1.076332 CCGTTAGAAAGTTCGGCCTG 58.924 55.000 0.00 0.00 36.68 4.85
651 704 0.971386 TCCGTTAGAAAGTTCGGCCT 59.029 50.000 0.00 0.00 42.28 5.19
656 709 7.980742 AAACAATTGTTCCGTTAGAAAGTTC 57.019 32.000 23.47 0.00 37.25 3.01
681 735 2.589442 AAGGCCACGTCGCGAAAA 60.589 55.556 12.06 0.00 0.00 2.29
700 754 2.735134 GCCGTACGATGTTTTCAGAACT 59.265 45.455 18.76 0.00 0.00 3.01
701 755 2.735134 AGCCGTACGATGTTTTCAGAAC 59.265 45.455 18.76 0.00 0.00 3.01
707 761 1.303091 GCCCAGCCGTACGATGTTTT 61.303 55.000 18.76 0.00 0.00 2.43
708 762 1.743995 GCCCAGCCGTACGATGTTT 60.744 57.895 18.76 0.00 0.00 2.83
1101 1163 3.362304 CGCCGGCGATATTTTACTTACAC 60.362 47.826 44.86 0.00 42.83 2.90
1159 1223 1.066587 CCAGGAGGAATCGACGAGC 59.933 63.158 3.01 0.00 36.89 5.03
1247 1314 3.988678 AGGGTTCGGGGTCGAGGA 61.989 66.667 0.00 0.00 46.75 3.71
1266 1333 1.002069 AGACCCTGAAATGGATGGCA 58.998 50.000 0.00 0.00 0.00 4.92
1269 1336 5.337009 CCAAAAAGAGACCCTGAAATGGATG 60.337 44.000 0.00 0.00 0.00 3.51
1270 1337 4.774200 CCAAAAAGAGACCCTGAAATGGAT 59.226 41.667 0.00 0.00 0.00 3.41
1271 1338 4.141041 TCCAAAAAGAGACCCTGAAATGGA 60.141 41.667 0.00 0.00 0.00 3.41
1284 1351 0.400594 AGACGGGGGTCCAAAAAGAG 59.599 55.000 0.00 0.00 0.00 2.85
1286 1353 0.608308 GGAGACGGGGGTCCAAAAAG 60.608 60.000 0.00 0.00 32.55 2.27
1288 1355 3.163503 GGAGACGGGGGTCCAAAA 58.836 61.111 0.00 0.00 32.55 2.44
1319 1386 0.727793 CGGAAAACACGGGCAATTCG 60.728 55.000 0.00 0.00 0.00 3.34
1320 1387 1.006825 GCGGAAAACACGGGCAATTC 61.007 55.000 0.00 0.00 0.00 2.17
1323 1390 3.955101 CGCGGAAAACACGGGCAA 61.955 61.111 0.00 0.00 37.46 4.52
1336 1403 0.678684 AACCCTAACCCAATTCGCGG 60.679 55.000 6.13 0.00 0.00 6.46
1358 1425 1.467920 CGTACTCGTAGAAACCCCCT 58.532 55.000 0.00 0.00 34.09 4.79
1363 1430 1.899115 CGCGCGTACTCGTAGAAAC 59.101 57.895 24.19 0.00 39.49 2.78
1481 1554 1.471287 CACCATACAAGAGGTCGTCGA 59.529 52.381 0.00 0.00 35.52 4.20
1496 1569 0.469917 CAGGGATCGCTTACCACCAT 59.530 55.000 10.01 0.00 0.00 3.55
1552 1625 1.203287 GATCAAGCAGAAAAGGGTGGC 59.797 52.381 0.00 0.00 0.00 5.01
1575 1648 3.058501 ACGAAAACACGGACAATTCATCC 60.059 43.478 0.00 0.00 37.61 3.51
1601 1674 2.687003 TTCCCTTAAACCCAACCCAG 57.313 50.000 0.00 0.00 0.00 4.45
1603 1676 4.505918 CCAAAATTCCCTTAAACCCAACCC 60.506 45.833 0.00 0.00 0.00 4.11
1626 1699 4.323553 ACAGAGTTCCCGAGTATTATGC 57.676 45.455 0.00 0.00 0.00 3.14
1629 1702 5.733620 ACAAACAGAGTTCCCGAGTATTA 57.266 39.130 0.00 0.00 0.00 0.98
1635 1708 2.833794 CAGAACAAACAGAGTTCCCGA 58.166 47.619 0.00 0.00 44.91 5.14
1662 1735 3.916172 TGATCGCTAGTAACGTCAACAAC 59.084 43.478 0.00 0.00 0.00 3.32
1696 1769 6.600822 TGGTAACTGCTAGTAAGTACGAATCT 59.399 38.462 0.00 0.00 37.61 2.40
1701 1774 5.557891 ACTGGTAACTGCTAGTAAGTACG 57.442 43.478 1.26 0.00 39.52 3.67
1728 1801 3.149196 TGGTTCTGAGAAGCAATTGGTC 58.851 45.455 23.14 4.92 0.00 4.02
1729 1802 3.152341 CTGGTTCTGAGAAGCAATTGGT 58.848 45.455 24.89 3.82 0.00 3.67
1754 1827 2.618053 CGGTCACAGAATAACCAGTCC 58.382 52.381 0.00 0.00 32.35 3.85
1795 1874 2.775418 TCATAGCCCCTGAAATCTGGA 58.225 47.619 7.82 0.00 37.15 3.86
1800 1879 7.919385 ATGTTTTATTCATAGCCCCTGAAAT 57.081 32.000 0.00 0.00 36.30 2.17
1804 1883 6.515832 GGAAATGTTTTATTCATAGCCCCTG 58.484 40.000 0.00 0.00 0.00 4.45
1808 1887 9.559958 CATATCGGAAATGTTTTATTCATAGCC 57.440 33.333 0.00 0.00 0.00 3.93
1820 1901 4.510340 GCGTAGGTTCATATCGGAAATGTT 59.490 41.667 0.00 0.00 0.00 2.71
1827 1908 2.519377 TTGGCGTAGGTTCATATCGG 57.481 50.000 0.00 0.00 0.00 4.18
1828 1909 2.221055 GCTTTGGCGTAGGTTCATATCG 59.779 50.000 0.00 0.00 0.00 2.92
1829 1910 3.202906 TGCTTTGGCGTAGGTTCATATC 58.797 45.455 0.00 0.00 42.25 1.63
1830 1911 3.275617 TGCTTTGGCGTAGGTTCATAT 57.724 42.857 0.00 0.00 42.25 1.78
1831 1912 2.772077 TGCTTTGGCGTAGGTTCATA 57.228 45.000 0.00 0.00 42.25 2.15
1832 1913 1.745087 CATGCTTTGGCGTAGGTTCAT 59.255 47.619 0.00 0.00 42.25 2.57
1833 1914 1.164411 CATGCTTTGGCGTAGGTTCA 58.836 50.000 0.00 0.00 42.25 3.18
1834 1915 0.179163 GCATGCTTTGGCGTAGGTTC 60.179 55.000 11.37 0.00 42.25 3.62
1835 1916 0.893270 TGCATGCTTTGGCGTAGGTT 60.893 50.000 20.33 0.00 42.25 3.50
1836 1917 0.680921 ATGCATGCTTTGGCGTAGGT 60.681 50.000 20.33 0.00 42.25 3.08
1837 1918 0.248743 CATGCATGCTTTGGCGTAGG 60.249 55.000 20.33 0.00 42.25 3.18
1838 1919 0.452987 ACATGCATGCTTTGGCGTAG 59.547 50.000 26.53 1.32 42.25 3.51
1839 1920 0.170784 CACATGCATGCTTTGGCGTA 59.829 50.000 26.53 0.00 42.25 4.42
1887 1968 2.328099 GCACACTACCACAGCCAGC 61.328 63.158 0.00 0.00 0.00 4.85
1888 1969 0.671781 GAGCACACTACCACAGCCAG 60.672 60.000 0.00 0.00 0.00 4.85
1891 1972 0.318441 TGAGAGCACACTACCACAGC 59.682 55.000 0.00 0.00 0.00 4.40
1896 1977 3.669251 AAGAACTGAGAGCACACTACC 57.331 47.619 0.00 0.00 0.00 3.18
1907 1988 6.309712 TCTTCTGAATGCAAAAGAACTGAG 57.690 37.500 0.00 0.00 0.00 3.35
1923 2004 8.830915 ACTCTACTTGATTAGGATTCTTCTGA 57.169 34.615 0.00 0.00 0.00 3.27
1953 2034 9.326413 CATTCTGGGTCTTACTATTTTACGAAT 57.674 33.333 0.00 0.00 0.00 3.34
1962 2043 9.396022 CAAATGTAACATTCTGGGTCTTACTAT 57.604 33.333 0.00 0.00 0.00 2.12
1979 2060 7.434897 TGTGCTTCAAAGAATGACAAATGTAAC 59.565 33.333 0.00 0.00 37.92 2.50
1983 2064 7.287950 CAATGTGCTTCAAAGAATGACAAATG 58.712 34.615 0.00 0.00 37.92 2.32
1989 2070 4.587584 TGCAATGTGCTTCAAAGAATGA 57.412 36.364 1.43 0.00 45.31 2.57
2001 2082 3.848019 CGACTGTTCTAATTGCAATGTGC 59.152 43.478 13.82 3.02 45.29 4.57
2006 2087 3.734463 TCACCGACTGTTCTAATTGCAA 58.266 40.909 0.00 0.00 0.00 4.08
2007 2088 3.394674 TCACCGACTGTTCTAATTGCA 57.605 42.857 0.00 0.00 0.00 4.08
2008 2089 4.868171 TGTATCACCGACTGTTCTAATTGC 59.132 41.667 0.00 0.00 0.00 3.56
2009 2090 6.756542 TCATGTATCACCGACTGTTCTAATTG 59.243 38.462 0.00 0.00 0.00 2.32
2010 2091 6.873997 TCATGTATCACCGACTGTTCTAATT 58.126 36.000 0.00 0.00 0.00 1.40
2015 2096 4.142359 ACTCTCATGTATCACCGACTGTTC 60.142 45.833 0.00 0.00 0.00 3.18
2049 2130 5.592282 TGTGCAAGAATAACTTCACTTTCCA 59.408 36.000 0.00 0.00 37.44 3.53
2051 2132 6.145535 CCTGTGCAAGAATAACTTCACTTTC 58.854 40.000 0.00 0.00 37.44 2.62
2062 2143 5.705441 CAGTTTTAGTCCCTGTGCAAGAATA 59.295 40.000 0.00 0.00 0.00 1.75
2088 2169 5.958380 TGAGGTGGTAATTGACTCTCATACT 59.042 40.000 0.00 0.00 30.49 2.12
2095 2176 3.437049 GCAGTTGAGGTGGTAATTGACTC 59.563 47.826 0.00 0.00 0.00 3.36
2136 2217 6.147492 TCCAAATTTGTAAATCACATTGCAGC 59.853 34.615 16.73 0.00 36.90 5.25
2160 2241 5.189180 AGCAGATCCAGTTAAATTGACCTC 58.811 41.667 0.00 0.00 0.00 3.85
2164 2245 9.162764 GTAAACTAGCAGATCCAGTTAAATTGA 57.837 33.333 0.00 0.00 32.35 2.57
2227 2308 3.388308 TGGCAAAATTCATTTGGTGTCG 58.612 40.909 3.41 0.00 46.93 4.35
2270 2351 4.642885 TCACCAAGAAACCAACACTAAAGG 59.357 41.667 0.00 0.00 0.00 3.11
2276 2357 3.859411 TGTTCACCAAGAAACCAACAC 57.141 42.857 0.00 0.00 38.13 3.32
2283 2364 6.760770 GGAAATGAACATTGTTCACCAAGAAA 59.239 34.615 29.29 8.99 38.13 2.52
2285 2366 5.598005 AGGAAATGAACATTGTTCACCAAGA 59.402 36.000 29.29 10.31 36.25 3.02
2333 2414 9.941664 CGATTGCTTGACTAGAAAATCAATAAT 57.058 29.630 0.00 0.76 34.43 1.28
2334 2415 8.946085 ACGATTGCTTGACTAGAAAATCAATAA 58.054 29.630 0.00 0.00 34.43 1.40
2335 2416 8.492673 ACGATTGCTTGACTAGAAAATCAATA 57.507 30.769 0.00 0.00 34.43 1.90
2336 2417 7.383102 ACGATTGCTTGACTAGAAAATCAAT 57.617 32.000 0.00 4.05 34.43 2.57
2337 2418 6.801539 ACGATTGCTTGACTAGAAAATCAA 57.198 33.333 0.00 0.00 32.29 2.57
2338 2419 8.390354 CAATACGATTGCTTGACTAGAAAATCA 58.610 33.333 0.00 0.00 32.29 2.57
2339 2420 7.852945 CCAATACGATTGCTTGACTAGAAAATC 59.147 37.037 0.00 0.00 0.00 2.17
2380 2461 9.926158 ATGATTGCTTGATTAGATACTCTACAG 57.074 33.333 0.00 0.00 0.00 2.74
2469 2550 0.037975 CAAAATGCTGGGTCTGCCAC 60.038 55.000 0.00 0.00 36.17 5.01
2645 2727 3.937706 CCACTGAACAGCAAATAGAGGAG 59.062 47.826 1.46 0.00 0.00 3.69
2668 2750 3.407424 AGCATGTATGATACGCATGGT 57.593 42.857 5.50 4.20 43.64 3.55
2677 2759 4.275936 GCCCTTTTACGAAGCATGTATGAT 59.724 41.667 0.00 0.00 0.00 2.45
2747 2829 2.334838 GACGCTTCTAACCGTGACAAT 58.665 47.619 0.00 0.00 37.87 2.71
2786 2870 0.909610 AGAAGCACGGAGGGGATCAA 60.910 55.000 0.00 0.00 0.00 2.57
2938 3022 6.901300 TCAGCTAAGAGAGGTATAGTGAGAA 58.099 40.000 0.00 0.00 33.44 2.87
2989 3074 4.641094 CAGTAAGAGGGAACTGATACGTCT 59.359 45.833 0.00 0.00 44.79 4.18
3030 3115 4.075682 TGTAATCCAACCGCATCAAGAAA 58.924 39.130 0.00 0.00 0.00 2.52
3031 3116 3.680490 TGTAATCCAACCGCATCAAGAA 58.320 40.909 0.00 0.00 0.00 2.52
3062 3147 8.948631 TCAGATCCACATGAAAACTATTAGAC 57.051 34.615 0.00 0.00 0.00 2.59
3144 3229 5.642063 TGAGCCTAGAAATACAAAAACTCCG 59.358 40.000 0.00 0.00 0.00 4.63
3457 3543 0.107654 AATCAGAAGGGCAGCGGTAC 60.108 55.000 0.00 0.00 0.00 3.34
3459 3545 0.618458 TAAATCAGAAGGGCAGCGGT 59.382 50.000 0.00 0.00 0.00 5.68
3512 3601 1.536709 CCAAAGCACAGAAACACCTGC 60.537 52.381 0.00 0.00 37.68 4.85
3659 3748 8.880750 GGTGGTATTCAGTAGAGAATTGTAAAC 58.119 37.037 0.00 0.00 38.97 2.01
3687 3776 5.648092 GCAGAACATGAAACCCTGTAGTAAT 59.352 40.000 0.00 0.00 0.00 1.89
3756 3845 2.828520 CTCTGAAAGCTCCTCACTACCA 59.171 50.000 0.00 0.00 0.00 3.25
3768 3857 0.326264 TCTGGGAAGCCTCTGAAAGC 59.674 55.000 0.00 0.00 0.00 3.51
3933 4022 1.683917 AGGTCACGAGCAGATATGGAC 59.316 52.381 0.00 0.00 0.00 4.02
3934 4023 2.073252 AGGTCACGAGCAGATATGGA 57.927 50.000 0.00 0.00 0.00 3.41
3949 4038 1.202698 AGCAGGGCGATTCATTAGGTC 60.203 52.381 0.00 0.00 0.00 3.85
3950 4039 0.839946 AGCAGGGCGATTCATTAGGT 59.160 50.000 0.00 0.00 0.00 3.08
4064 4153 2.036256 GGAGGCACTTGCATGGGT 59.964 61.111 3.52 0.00 41.55 4.51
4384 4473 7.202016 ACTGTTTACATGTTCACCATACTTG 57.798 36.000 2.30 0.00 30.71 3.16
4513 4603 2.649312 TGACCACCCAGAAGAAATCCAT 59.351 45.455 0.00 0.00 0.00 3.41
4561 4653 5.633655 TTTAACACCCAGAGGAACTACAA 57.366 39.130 0.00 0.00 41.55 2.41
4620 4712 4.574421 CACACCACCGCTCATATTTATTCA 59.426 41.667 0.00 0.00 0.00 2.57
4676 4768 7.578310 AGAATGACATCACCAAATTAGATGG 57.422 36.000 0.00 4.59 42.55 3.51
4684 4776 4.288366 TCCACCTAGAATGACATCACCAAA 59.712 41.667 0.00 0.00 0.00 3.28
4686 4778 3.449918 TCCACCTAGAATGACATCACCA 58.550 45.455 0.00 0.00 0.00 4.17
4687 4779 3.706594 TCTCCACCTAGAATGACATCACC 59.293 47.826 0.00 0.00 0.00 4.02
4694 4787 5.819991 AGCAAAAATCTCCACCTAGAATGA 58.180 37.500 0.00 0.00 0.00 2.57
4695 4788 6.071728 ACAAGCAAAAATCTCCACCTAGAATG 60.072 38.462 0.00 0.00 0.00 2.67
4696 4789 6.012745 ACAAGCAAAAATCTCCACCTAGAAT 58.987 36.000 0.00 0.00 0.00 2.40
4699 4792 5.712152 AACAAGCAAAAATCTCCACCTAG 57.288 39.130 0.00 0.00 0.00 3.02
4701 4794 4.651045 AGAAACAAGCAAAAATCTCCACCT 59.349 37.500 0.00 0.00 0.00 4.00
4706 4799 7.217070 CGCATACTAGAAACAAGCAAAAATCTC 59.783 37.037 0.00 0.00 0.00 2.75
4731 4824 1.879380 TCAGGTTCAAATTGCTGACCG 59.121 47.619 7.14 4.24 0.00 4.79
4736 4829 3.385755 ACAGCTTTCAGGTTCAAATTGCT 59.614 39.130 0.00 0.00 0.00 3.91
4743 4836 2.016318 CACACACAGCTTTCAGGTTCA 58.984 47.619 0.00 0.00 0.00 3.18
4746 4839 2.017049 GTTCACACACAGCTTTCAGGT 58.983 47.619 0.00 0.00 0.00 4.00
4753 4846 0.107017 AGCCAAGTTCACACACAGCT 60.107 50.000 0.00 0.00 0.00 4.24
4768 4861 4.532834 GGTCAAATATCAGGGTAAAGCCA 58.467 43.478 0.36 0.00 39.65 4.75
4796 4889 3.520569 GTGCAAGAGACAAAAGCCAAAA 58.479 40.909 0.00 0.00 0.00 2.44
4808 4901 0.324943 GGCCTTACTGGTGCAAGAGA 59.675 55.000 0.00 0.00 38.35 3.10
4850 4943 3.470709 TCATCTAAGCAGCTATTGTGCC 58.529 45.455 0.00 0.00 42.24 5.01
4855 4948 6.408035 CATCCTCATCATCTAAGCAGCTATT 58.592 40.000 0.00 0.00 0.00 1.73
4885 4978 8.364894 GGTCTCAACCACATACACACATATATA 58.635 37.037 0.00 0.00 45.68 0.86
4924 5023 4.020039 TCCCAGACTTTTCCAGCGTATAAA 60.020 41.667 0.00 0.00 0.00 1.40
4929 5028 0.250338 GTCCCAGACTTTTCCAGCGT 60.250 55.000 0.00 0.00 0.00 5.07
5046 5148 0.744771 GGAACGGAATCTCCAGTGCC 60.745 60.000 0.00 0.00 35.91 5.01
5052 5154 1.134401 TGATGCAGGAACGGAATCTCC 60.134 52.381 0.00 0.00 0.00 3.71
5110 5213 7.334421 TCAACTTTCAAAGGATGCTACATCTAC 59.666 37.037 1.31 0.00 0.00 2.59
5112 5215 6.240894 TCAACTTTCAAAGGATGCTACATCT 58.759 36.000 1.31 0.00 0.00 2.90
5113 5216 6.500684 TCAACTTTCAAAGGATGCTACATC 57.499 37.500 1.31 0.00 0.00 3.06
5206 5312 0.806102 CGGCGTCTCGAATGACCAAT 60.806 55.000 0.00 0.00 33.70 3.16
5233 5339 6.500684 AAATGTATATTGATCGGTCCATGC 57.499 37.500 0.00 0.00 0.00 4.06
5240 5346 8.720562 TCTTGTGCATAAATGTATATTGATCGG 58.279 33.333 0.00 0.00 0.00 4.18
5255 5363 8.366401 TCTCCAAAAATTCATTCTTGTGCATAA 58.634 29.630 0.00 0.00 0.00 1.90
5264 5372 7.687941 ACATACGTCTCCAAAAATTCATTCT 57.312 32.000 0.00 0.00 0.00 2.40
5283 5391 3.391965 TGTTGTGGGTGAACGTACATAC 58.608 45.455 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.