Multiple sequence alignment - TraesCS2B01G519400

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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 TraesCS2B01G519400 chr2B 100.000 2791 0 0 1 2791 714468916 714466126 0.000000e+00 5155.0
1 TraesCS2B01G519400 chr2B 96.660 479 15 1 33 511 140512792 140512315 0.000000e+00 795.0
2 TraesCS2B01G519400 chr2B 95.533 291 9 1 507 797 140506794 140506508 1.960000e-126 462.0
3 TraesCS2B01G519400 chr2B 93.950 281 17 0 2238 2518 714271921 714271641 2.570000e-115 425.0
4 TraesCS2B01G519400 chr2B 93.950 281 16 1 2238 2518 714328790 714328511 9.240000e-115 424.0
5 TraesCS2B01G519400 chr2B 88.502 287 11 9 2506 2791 714328485 714328220 7.450000e-86 327.0
6 TraesCS2B01G519400 chr2B 87.805 287 13 9 2506 2791 714271615 714271350 1.610000e-82 316.0
7 TraesCS2B01G519400 chr2B 85.492 193 28 0 1121 1313 714322203 714322011 4.710000e-48 202.0
8 TraesCS2B01G519400 chr2B 100.000 44 0 0 839 882 104852364 104852407 6.410000e-12 82.4
9 TraesCS2B01G519400 chr2B 88.889 63 4 3 777 838 731717400 731717460 1.070000e-09 75.0
10 TraesCS2B01G519400 chr4B 97.020 839 16 5 1 839 637400256 637401085 0.000000e+00 1402.0
11 TraesCS2B01G519400 chr4B 96.305 839 26 3 3 841 336213270 336212437 0.000000e+00 1373.0
12 TraesCS2B01G519400 chr2D 91.901 852 43 13 881 1719 590036521 590035683 0.000000e+00 1168.0
13 TraesCS2B01G519400 chr2D 95.406 283 13 0 2236 2518 390368689 390368971 4.240000e-123 451.0
14 TraesCS2B01G519400 chr2D 90.055 181 17 1 2057 2237 585899699 585899520 1.670000e-57 233.0
15 TraesCS2B01G519400 chr2D 90.116 172 12 4 2623 2791 240651193 240651024 4.680000e-53 219.0
16 TraesCS2B01G519400 chr2D 78.095 315 62 6 1121 1430 590032724 590032412 2.840000e-45 193.0
17 TraesCS2B01G519400 chr2D 91.538 130 10 1 2506 2634 390369000 390369129 7.940000e-41 178.0
18 TraesCS2B01G519400 chr2A 90.015 651 35 6 881 1531 724361741 724361121 0.000000e+00 815.0
19 TraesCS2B01G519400 chr5B 83.793 870 71 26 1 841 665504258 665505086 0.000000e+00 761.0
20 TraesCS2B01G519400 chr5B 88.264 409 36 8 2238 2634 646616698 646616290 1.940000e-131 479.0
21 TraesCS2B01G519400 chr5B 88.235 68 8 0 778 845 642566840 642566907 6.410000e-12 82.4
22 TraesCS2B01G519400 chr5B 97.778 45 1 0 839 883 693173406 693173362 8.290000e-11 78.7
23 TraesCS2B01G519400 chr5B 88.525 61 6 1 778 837 664206680 664206620 3.860000e-09 73.1
24 TraesCS2B01G519400 chr1D 85.413 569 57 23 2237 2791 152503466 152502910 4.030000e-158 568.0
25 TraesCS2B01G519400 chr1D 85.062 569 59 22 2237 2791 152515024 152514468 8.730000e-155 556.0
26 TraesCS2B01G519400 chr1D 88.095 420 27 8 2238 2634 152374708 152374289 6.990000e-131 477.0
27 TraesCS2B01G519400 chr1D 88.462 130 14 1 2506 2634 152514714 152514585 3.720000e-34 156.0
28 TraesCS2B01G519400 chr4D 90.571 403 37 1 2233 2634 464277244 464277646 1.470000e-147 532.0
29 TraesCS2B01G519400 chr4D 92.171 281 22 0 2238 2518 464293656 464293936 5.600000e-107 398.0
30 TraesCS2B01G519400 chr4D 89.552 134 13 1 2502 2634 464293958 464294091 4.780000e-38 169.0
31 TraesCS2B01G519400 chr3A 82.578 419 45 22 2375 2781 322655491 322655893 7.400000e-91 344.0
32 TraesCS2B01G519400 chr3A 93.671 158 6 2 2624 2781 322648643 322648796 1.670000e-57 233.0
33 TraesCS2B01G519400 chr3A 90.323 62 6 0 777 838 19092608 19092669 6.410000e-12 82.4
34 TraesCS2B01G519400 chr3A 90.164 61 6 0 777 837 64822733 64822673 2.300000e-11 80.5
35 TraesCS2B01G519400 chr7D 83.641 379 19 13 1 359 102781886 102782241 1.610000e-82 316.0
36 TraesCS2B01G519400 chr7D 91.589 107 4 3 691 797 102782725 102782826 2.900000e-30 143.0
37 TraesCS2B01G519400 chr3D 90.000 180 17 1 2058 2237 489529334 489529156 6.010000e-57 231.0
38 TraesCS2B01G519400 chr7B 91.566 166 12 2 2622 2786 252580299 252580463 7.780000e-56 228.0
39 TraesCS2B01G519400 chr7B 92.025 163 12 1 2624 2786 252587968 252588129 7.780000e-56 228.0
40 TraesCS2B01G519400 chr7B 87.845 181 21 1 2057 2237 162991189 162991010 7.830000e-51 211.0
41 TraesCS2B01G519400 chr7B 90.244 82 8 0 2055 2136 74836685 74836604 1.060000e-19 108.0
42 TraesCS2B01G519400 chr7B 87.097 62 6 1 777 838 688821330 688821271 4.990000e-08 69.4
43 TraesCS2B01G519400 chr1A 92.258 155 11 1 2080 2234 512857938 512858091 4.680000e-53 219.0
44 TraesCS2B01G519400 chr1A 83.133 83 10 3 759 838 516313187 516313268 3.860000e-09 73.1
45 TraesCS2B01G519400 chr5D 88.415 164 16 3 2081 2244 308627445 308627605 7.890000e-46 195.0
46 TraesCS2B01G519400 chr5A 87.117 163 19 2 2052 2213 494378541 494378380 1.710000e-42 183.0
47 TraesCS2B01G519400 chr5A 77.206 136 25 5 1 130 15125516 15125381 1.070000e-09 75.0
48 TraesCS2B01G519400 chr5A 87.500 64 6 2 779 841 196391033 196390971 3.860000e-09 73.1
49 TraesCS2B01G519400 chr5A 88.333 60 7 0 778 837 447658228 447658169 3.860000e-09 73.1
50 TraesCS2B01G519400 chr5A 85.246 61 7 2 779 838 622301765 622301824 8.350000e-06 62.1
51 TraesCS2B01G519400 chr6B 81.553 103 14 5 31 130 68417739 68417639 2.300000e-11 80.5
52 TraesCS2B01G519400 chr6B 97.727 44 0 1 795 837 661046528 661046485 1.070000e-09 75.0
53 TraesCS2B01G519400 chr4A 97.872 47 0 1 839 884 734912854 734912900 2.300000e-11 80.5
54 TraesCS2B01G519400 chr3B 97.727 44 1 0 839 882 113481434 113481477 2.980000e-10 76.8


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 TraesCS2B01G519400 chr2B 714466126 714468916 2790 True 5155.0 5155 100.0000 1 2791 1 chr2B.!!$R4 2790
1 TraesCS2B01G519400 chr2B 714328220 714328790 570 True 375.5 424 91.2260 2238 2791 2 chr2B.!!$R6 553
2 TraesCS2B01G519400 chr2B 714271350 714271921 571 True 370.5 425 90.8775 2238 2791 2 chr2B.!!$R5 553
3 TraesCS2B01G519400 chr4B 637400256 637401085 829 False 1402.0 1402 97.0200 1 839 1 chr4B.!!$F1 838
4 TraesCS2B01G519400 chr4B 336212437 336213270 833 True 1373.0 1373 96.3050 3 841 1 chr4B.!!$R1 838
5 TraesCS2B01G519400 chr2D 590032412 590036521 4109 True 680.5 1168 84.9980 881 1719 2 chr2D.!!$R3 838
6 TraesCS2B01G519400 chr2A 724361121 724361741 620 True 815.0 815 90.0150 881 1531 1 chr2A.!!$R1 650
7 TraesCS2B01G519400 chr5B 665504258 665505086 828 False 761.0 761 83.7930 1 841 1 chr5B.!!$F2 840
8 TraesCS2B01G519400 chr1D 152502910 152503466 556 True 568.0 568 85.4130 2237 2791 1 chr1D.!!$R2 554
9 TraesCS2B01G519400 chr1D 152514468 152515024 556 True 356.0 556 86.7620 2237 2791 2 chr1D.!!$R3 554
10 TraesCS2B01G519400 chr7D 102781886 102782826 940 False 229.5 316 87.6150 1 797 2 chr7D.!!$F1 796

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
977 1220 0.248949 GGCTCGTCCGATACCAACTC 60.249 60.0 4.55 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2987 0.035152 TGCTCCGCATCAAATGTCCT 60.035 50.0 0.0 0.0 31.71 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
498 526 6.150474 ACACTATTTGTAATTGTGTACCTGCC 59.850 38.462 14.77 0.00 39.65 4.85
841 1084 3.965539 CTGTCTCCGCCCCTGCTTG 62.966 68.421 0.00 0.00 34.43 4.01
847 1090 3.830192 CGCCCCTGCTTGCCATTC 61.830 66.667 0.00 0.00 34.43 2.67
848 1091 2.363406 GCCCCTGCTTGCCATTCT 60.363 61.111 0.00 0.00 33.53 2.40
849 1092 2.718073 GCCCCTGCTTGCCATTCTG 61.718 63.158 0.00 0.00 33.53 3.02
850 1093 1.304713 CCCCTGCTTGCCATTCTGT 60.305 57.895 0.00 0.00 0.00 3.41
851 1094 1.601419 CCCCTGCTTGCCATTCTGTG 61.601 60.000 0.00 0.00 0.00 3.66
852 1095 0.609957 CCCTGCTTGCCATTCTGTGA 60.610 55.000 0.00 0.00 0.00 3.58
853 1096 0.809385 CCTGCTTGCCATTCTGTGAG 59.191 55.000 0.00 0.00 0.00 3.51
854 1097 1.612462 CCTGCTTGCCATTCTGTGAGA 60.612 52.381 0.00 0.00 0.00 3.27
855 1098 2.156917 CTGCTTGCCATTCTGTGAGAA 58.843 47.619 0.00 0.00 38.78 2.87
856 1099 2.555325 CTGCTTGCCATTCTGTGAGAAA 59.445 45.455 0.00 0.00 37.82 2.52
857 1100 3.159472 TGCTTGCCATTCTGTGAGAAAT 58.841 40.909 0.00 0.00 37.82 2.17
858 1101 4.334552 TGCTTGCCATTCTGTGAGAAATA 58.665 39.130 0.00 0.00 37.82 1.40
859 1102 4.766373 TGCTTGCCATTCTGTGAGAAATAA 59.234 37.500 0.00 0.00 37.82 1.40
860 1103 5.243507 TGCTTGCCATTCTGTGAGAAATAAA 59.756 36.000 0.00 0.00 37.82 1.40
861 1104 5.803967 GCTTGCCATTCTGTGAGAAATAAAG 59.196 40.000 0.00 0.00 37.82 1.85
862 1105 5.902613 TGCCATTCTGTGAGAAATAAAGG 57.097 39.130 0.00 0.00 37.82 3.11
863 1106 5.324409 TGCCATTCTGTGAGAAATAAAGGT 58.676 37.500 0.00 0.00 37.82 3.50
864 1107 5.774690 TGCCATTCTGTGAGAAATAAAGGTT 59.225 36.000 0.00 0.00 37.82 3.50
865 1108 6.267471 TGCCATTCTGTGAGAAATAAAGGTTT 59.733 34.615 0.00 0.00 37.82 3.27
866 1109 7.450014 TGCCATTCTGTGAGAAATAAAGGTTTA 59.550 33.333 0.00 0.00 37.82 2.01
867 1110 7.755373 GCCATTCTGTGAGAAATAAAGGTTTAC 59.245 37.037 0.00 0.00 37.82 2.01
868 1111 8.244113 CCATTCTGTGAGAAATAAAGGTTTACC 58.756 37.037 0.00 0.00 37.82 2.85
869 1112 9.014297 CATTCTGTGAGAAATAAAGGTTTACCT 57.986 33.333 0.00 0.00 42.43 3.08
870 1113 8.391075 TTCTGTGAGAAATAAAGGTTTACCTG 57.609 34.615 1.41 0.00 37.61 4.00
871 1114 8.215050 TTCTGTGAGAAATAAAGGTTTACCTGA 58.785 33.333 1.41 0.00 37.61 3.86
976 1219 1.814527 GGCTCGTCCGATACCAACT 59.185 57.895 4.55 0.00 0.00 3.16
977 1220 0.248949 GGCTCGTCCGATACCAACTC 60.249 60.000 4.55 0.00 0.00 3.01
978 1221 0.248949 GCTCGTCCGATACCAACTCC 60.249 60.000 0.00 0.00 0.00 3.85
979 1222 1.100510 CTCGTCCGATACCAACTCCA 58.899 55.000 0.00 0.00 0.00 3.86
993 1236 1.813513 ACTCCATCCAAACAGAAGCG 58.186 50.000 0.00 0.00 0.00 4.68
1012 1255 1.499049 GCGAGGCCTATAAAAGACGG 58.501 55.000 4.42 0.00 0.00 4.79
1037 1280 3.476419 GCCCTGCCGTAAGCCCTA 61.476 66.667 0.00 0.00 42.71 3.53
1057 1300 4.020573 CCTATGTGGTTGTGTCTACAAGGA 60.021 45.833 0.00 0.00 46.75 3.36
1068 1315 0.460284 CTACAAGGATCAAGCGGCGT 60.460 55.000 9.37 0.00 0.00 5.68
1085 1335 4.617645 GCGGCGTTTATCTATCTTGTAGAG 59.382 45.833 9.37 0.00 0.00 2.43
1136 1386 4.899239 GAGAGGACATGGCGGCCG 62.899 72.222 24.05 24.05 0.00 6.13
1162 1412 4.390556 AGACAGCGGGAGGAGGCT 62.391 66.667 0.00 0.00 40.90 4.58
1212 1462 2.033424 GCAAAGACTTCAAGGTGTCCAC 59.967 50.000 0.00 0.00 34.02 4.02
1241 1491 2.107750 CCATGCTCATCGCGGTCT 59.892 61.111 6.13 0.00 43.27 3.85
1327 1577 3.952675 CAGTGCGCGGTGCTGTTT 61.953 61.111 15.31 0.00 46.63 2.83
1405 1669 4.972875 CCCAAGAGGCCTGATGTC 57.027 61.111 12.00 0.00 0.00 3.06
1406 1670 1.153289 CCCAAGAGGCCTGATGTCG 60.153 63.158 12.00 0.00 0.00 4.35
1407 1671 1.617018 CCCAAGAGGCCTGATGTCGA 61.617 60.000 12.00 0.00 0.00 4.20
1408 1672 0.250234 CCAAGAGGCCTGATGTCGAA 59.750 55.000 12.00 0.00 0.00 3.71
1409 1673 1.649664 CAAGAGGCCTGATGTCGAAG 58.350 55.000 12.00 0.00 0.00 3.79
1410 1674 0.539051 AAGAGGCCTGATGTCGAAGG 59.461 55.000 12.00 0.00 36.58 3.46
1414 1678 4.528674 CCTGATGTCGAAGGCCAG 57.471 61.111 5.01 0.00 0.00 4.85
1446 1710 3.902881 AGACAAGCCAGATCTCGAAAT 57.097 42.857 0.00 0.00 0.00 2.17
1500 1764 1.877443 TCGTTTCTGCCCAGTTTAAGC 59.123 47.619 0.00 0.00 0.00 3.09
1536 1800 5.304614 TGTTGCTAGTCTTCTGTTAGGAGTT 59.695 40.000 0.00 0.00 0.00 3.01
1537 1801 5.646577 TGCTAGTCTTCTGTTAGGAGTTC 57.353 43.478 0.00 0.00 0.00 3.01
1538 1802 5.326069 TGCTAGTCTTCTGTTAGGAGTTCT 58.674 41.667 0.00 0.00 0.00 3.01
1539 1803 5.184096 TGCTAGTCTTCTGTTAGGAGTTCTG 59.816 44.000 0.00 0.00 0.00 3.02
1541 1805 6.374894 GCTAGTCTTCTGTTAGGAGTTCTGTA 59.625 42.308 0.00 0.00 0.00 2.74
1543 1807 6.983984 AGTCTTCTGTTAGGAGTTCTGTAAC 58.016 40.000 0.00 0.00 35.72 2.50
1544 1808 6.550108 AGTCTTCTGTTAGGAGTTCTGTAACA 59.450 38.462 0.00 0.00 38.12 2.41
1570 1835 3.134458 GGTCTTGTGTTTGAGAGGTCAG 58.866 50.000 0.00 0.00 32.98 3.51
1588 1853 3.812053 GTCAGCAAGTGATGTGTCTTCTT 59.188 43.478 0.00 0.00 37.56 2.52
1589 1854 4.060900 TCAGCAAGTGATGTGTCTTCTTC 58.939 43.478 0.00 0.00 32.47 2.87
1590 1855 4.063689 CAGCAAGTGATGTGTCTTCTTCT 58.936 43.478 0.00 0.00 0.00 2.85
1591 1856 5.011023 TCAGCAAGTGATGTGTCTTCTTCTA 59.989 40.000 0.00 0.00 32.47 2.10
1634 1899 3.011517 AAGCCCAGCTCGGTGGAT 61.012 61.111 16.22 2.24 40.44 3.41
1642 1907 0.613292 AGCTCGGTGGATGAGACACT 60.613 55.000 0.00 0.00 38.83 3.55
1675 1945 4.791163 CGTTTCTGCGTTTATTATGTTGGG 59.209 41.667 0.00 0.00 0.00 4.12
1679 1949 3.687125 TGCGTTTATTATGTTGGGTCCA 58.313 40.909 0.00 0.00 0.00 4.02
1704 1974 8.251026 CAGGCGTCCAAGATGAACTAATATATA 58.749 37.037 0.00 0.00 0.00 0.86
1706 1976 9.035607 GGCGTCCAAGATGAACTAATATATATG 57.964 37.037 0.00 0.00 0.00 1.78
1707 1977 9.587772 GCGTCCAAGATGAACTAATATATATGT 57.412 33.333 0.00 0.00 0.00 2.29
1723 1993 8.987599 ATATATATGTTCGCAAACTTGAAACG 57.012 30.769 0.00 0.00 36.30 3.60
1724 1994 3.684103 ATGTTCGCAAACTTGAAACGA 57.316 38.095 0.00 0.00 36.30 3.85
1725 1995 3.684103 TGTTCGCAAACTTGAAACGAT 57.316 38.095 0.00 0.00 36.30 3.73
1726 1996 4.022464 TGTTCGCAAACTTGAAACGATT 57.978 36.364 0.00 0.00 36.30 3.34
1727 1997 5.158101 TGTTCGCAAACTTGAAACGATTA 57.842 34.783 0.00 0.00 36.30 1.75
1728 1998 5.753744 TGTTCGCAAACTTGAAACGATTAT 58.246 33.333 0.00 0.00 36.30 1.28
1729 1999 5.849081 TGTTCGCAAACTTGAAACGATTATC 59.151 36.000 0.00 0.00 36.30 1.75
1730 2000 5.856126 TCGCAAACTTGAAACGATTATCT 57.144 34.783 0.00 0.00 0.00 1.98
1731 2001 5.854157 TCGCAAACTTGAAACGATTATCTC 58.146 37.500 0.00 0.00 0.00 2.75
1734 2004 6.024049 GCAAACTTGAAACGATTATCTCCTG 58.976 40.000 0.00 0.00 0.00 3.86
1754 2024 9.584008 TCTCCTGGTTTCGAGTAATATATTAGT 57.416 33.333 11.83 11.83 0.00 2.24
1790 2060 8.831715 ATATATGTTATGTTTCACATCTCGCA 57.168 30.769 0.00 0.00 39.88 5.10
1791 2061 5.878332 ATGTTATGTTTCACATCTCGCAA 57.122 34.783 0.00 0.00 39.88 4.85
1792 2062 5.681337 TGTTATGTTTCACATCTCGCAAA 57.319 34.783 0.00 0.00 39.88 3.68
1793 2063 6.066054 TGTTATGTTTCACATCTCGCAAAA 57.934 33.333 0.00 0.00 39.88 2.44
1794 2064 6.499172 TGTTATGTTTCACATCTCGCAAAAA 58.501 32.000 0.00 0.00 39.88 1.94
1829 2099 9.915629 TTTGTTTAGACTAGTTTTTCTTTTGCA 57.084 25.926 0.00 0.00 0.00 4.08
1830 2100 9.915629 TTGTTTAGACTAGTTTTTCTTTTGCAA 57.084 25.926 0.00 0.00 0.00 4.08
1831 2101 9.915629 TGTTTAGACTAGTTTTTCTTTTGCAAA 57.084 25.926 8.05 8.05 0.00 3.68
1860 2130 5.880054 TTTGTTTAGACTAGAATGGCTGC 57.120 39.130 0.00 0.00 0.00 5.25
1862 2132 3.056107 TGTTTAGACTAGAATGGCTGCGT 60.056 43.478 0.00 0.00 0.00 5.24
1890 2165 2.158769 ACATGGGCAGAATAGCGATCAA 60.159 45.455 0.00 0.00 34.64 2.57
1911 2186 1.584483 GCGCAACATTCTCGCCATG 60.584 57.895 0.30 0.00 42.71 3.66
1919 2194 2.627699 ACATTCTCGCCATGTGGTTTTT 59.372 40.909 0.35 0.00 33.42 1.94
1920 2195 3.244976 CATTCTCGCCATGTGGTTTTTC 58.755 45.455 0.35 0.00 37.57 2.29
1929 2204 5.410924 GCCATGTGGTTTTTCTCTTATTCC 58.589 41.667 0.35 0.00 37.57 3.01
1930 2205 5.640732 CCATGTGGTTTTTCTCTTATTCCG 58.359 41.667 0.00 0.00 0.00 4.30
1931 2206 5.414454 CCATGTGGTTTTTCTCTTATTCCGA 59.586 40.000 0.00 0.00 0.00 4.55
1955 2230 1.460504 TTGATGAGTCGGTCGCTACT 58.539 50.000 0.00 0.00 0.00 2.57
1964 2239 0.241749 CGGTCGCTACTGTACCAACA 59.758 55.000 0.00 0.00 32.55 3.33
1974 2249 0.391130 TGTACCAACAGCTCGGATGC 60.391 55.000 0.36 0.00 0.00 3.91
1982 2257 2.894387 GCTCGGATGCACCTCAGC 60.894 66.667 0.00 0.00 35.88 4.26
1997 2273 0.323725 TCAGCAAATCCCTTCCCAGC 60.324 55.000 0.00 0.00 0.00 4.85
2008 2284 2.698797 CCCTTCCCAGCTTCGATACTTA 59.301 50.000 0.00 0.00 0.00 2.24
2009 2285 3.134081 CCCTTCCCAGCTTCGATACTTAA 59.866 47.826 0.00 0.00 0.00 1.85
2010 2286 4.383770 CCCTTCCCAGCTTCGATACTTAAA 60.384 45.833 0.00 0.00 0.00 1.52
2011 2287 5.183228 CCTTCCCAGCTTCGATACTTAAAA 58.817 41.667 0.00 0.00 0.00 1.52
2012 2288 5.646360 CCTTCCCAGCTTCGATACTTAAAAA 59.354 40.000 0.00 0.00 0.00 1.94
2013 2289 6.183360 CCTTCCCAGCTTCGATACTTAAAAAG 60.183 42.308 0.00 0.00 0.00 2.27
2014 2290 6.045072 TCCCAGCTTCGATACTTAAAAAGA 57.955 37.500 0.00 0.00 0.00 2.52
2015 2291 6.469410 TCCCAGCTTCGATACTTAAAAAGAA 58.531 36.000 0.00 0.00 0.00 2.52
2016 2292 6.594159 TCCCAGCTTCGATACTTAAAAAGAAG 59.406 38.462 0.00 0.00 38.37 2.85
2017 2293 6.594159 CCCAGCTTCGATACTTAAAAAGAAGA 59.406 38.462 7.13 0.00 37.78 2.87
2018 2294 7.119262 CCCAGCTTCGATACTTAAAAAGAAGAA 59.881 37.037 7.13 0.00 37.78 2.52
2019 2295 8.669243 CCAGCTTCGATACTTAAAAAGAAGAAT 58.331 33.333 7.13 0.00 37.78 2.40
2066 2342 9.927668 AAATGTTAAATTGGTTGTTGGATAGAG 57.072 29.630 0.00 0.00 0.00 2.43
2067 2343 7.461182 TGTTAAATTGGTTGTTGGATAGAGG 57.539 36.000 0.00 0.00 0.00 3.69
2068 2344 6.071616 TGTTAAATTGGTTGTTGGATAGAGGC 60.072 38.462 0.00 0.00 0.00 4.70
2069 2345 2.107950 TTGGTTGTTGGATAGAGGCG 57.892 50.000 0.00 0.00 0.00 5.52
2071 2347 1.207089 TGGTTGTTGGATAGAGGCGAG 59.793 52.381 0.00 0.00 0.00 5.03
2072 2348 1.473434 GGTTGTTGGATAGAGGCGAGG 60.473 57.143 0.00 0.00 0.00 4.63
2073 2349 1.480954 GTTGTTGGATAGAGGCGAGGA 59.519 52.381 0.00 0.00 0.00 3.71
2075 2351 1.688735 TGTTGGATAGAGGCGAGGATG 59.311 52.381 0.00 0.00 0.00 3.51
2076 2352 1.001406 GTTGGATAGAGGCGAGGATGG 59.999 57.143 0.00 0.00 0.00 3.51
2078 2354 0.892063 GGATAGAGGCGAGGATGGTC 59.108 60.000 0.00 0.00 0.00 4.02
2079 2355 1.621992 GATAGAGGCGAGGATGGTCA 58.378 55.000 0.00 0.00 0.00 4.02
2080 2356 2.175202 GATAGAGGCGAGGATGGTCAT 58.825 52.381 0.00 0.00 0.00 3.06
2081 2357 1.621992 TAGAGGCGAGGATGGTCATC 58.378 55.000 2.52 2.52 37.11 2.92
2091 2367 3.859411 GGATGGTCATCCGATCTACTC 57.141 52.381 13.49 0.00 46.84 2.59
2092 2368 3.157881 GGATGGTCATCCGATCTACTCA 58.842 50.000 13.49 0.00 46.84 3.41
2093 2369 3.766591 GGATGGTCATCCGATCTACTCAT 59.233 47.826 13.49 0.00 46.84 2.90
2095 2371 3.157881 TGGTCATCCGATCTACTCATCC 58.842 50.000 0.00 0.00 36.30 3.51
2096 2372 3.157881 GGTCATCCGATCTACTCATCCA 58.842 50.000 0.00 0.00 0.00 3.41
2097 2373 3.057174 GGTCATCCGATCTACTCATCCAC 60.057 52.174 0.00 0.00 0.00 4.02
2098 2374 2.814336 TCATCCGATCTACTCATCCACG 59.186 50.000 0.00 0.00 0.00 4.94
2099 2375 2.343484 TCCGATCTACTCATCCACGT 57.657 50.000 0.00 0.00 0.00 4.49
2100 2376 1.947456 TCCGATCTACTCATCCACGTG 59.053 52.381 9.08 9.08 0.00 4.49
2101 2377 1.600663 CCGATCTACTCATCCACGTGC 60.601 57.143 10.91 0.00 0.00 5.34
2104 2380 2.654749 TCTACTCATCCACGTGCTTG 57.345 50.000 10.91 9.79 0.00 4.01
2106 2382 2.094700 TCTACTCATCCACGTGCTTGAC 60.095 50.000 10.91 0.00 0.00 3.18
2107 2383 0.320771 ACTCATCCACGTGCTTGACC 60.321 55.000 10.91 0.00 0.00 4.02
2108 2384 0.036952 CTCATCCACGTGCTTGACCT 60.037 55.000 10.91 0.00 0.00 3.85
2110 2386 0.798776 CATCCACGTGCTTGACCTTC 59.201 55.000 10.91 0.00 0.00 3.46
2120 2396 1.408702 GCTTGACCTTCCTTGCAACAA 59.591 47.619 0.00 0.00 0.00 2.83
2121 2397 2.544486 GCTTGACCTTCCTTGCAACAAG 60.544 50.000 15.59 15.59 37.09 3.16
2124 2882 1.268079 GACCTTCCTTGCAACAAGAGC 59.732 52.381 12.99 3.55 0.00 4.09
2128 2886 1.165907 TCCTTGCAACAAGAGCGGTG 61.166 55.000 8.87 0.00 33.85 4.94
2129 2887 1.447317 CCTTGCAACAAGAGCGGTGT 61.447 55.000 8.87 0.00 33.85 4.16
2134 2892 0.317269 CAACAAGAGCGGTGTTGCAG 60.317 55.000 22.66 12.44 46.63 4.41
2138 2896 1.267806 CAAGAGCGGTGTTGCAGAAAT 59.732 47.619 11.74 0.00 37.31 2.17
2143 2901 4.941263 AGAGCGGTGTTGCAGAAATATTTA 59.059 37.500 0.00 0.00 37.31 1.40
2144 2902 5.590259 AGAGCGGTGTTGCAGAAATATTTAT 59.410 36.000 0.00 0.00 37.31 1.40
2146 2904 7.282224 AGAGCGGTGTTGCAGAAATATTTATAA 59.718 33.333 0.00 0.00 37.31 0.98
2147 2905 7.193595 AGCGGTGTTGCAGAAATATTTATAAC 58.806 34.615 0.00 1.48 37.31 1.89
2156 2914 8.020819 TGCAGAAATATTTATAACAATAGCCGC 58.979 33.333 0.00 0.00 0.00 6.53
2157 2915 7.484959 GCAGAAATATTTATAACAATAGCCGCC 59.515 37.037 0.00 0.00 0.00 6.13
2158 2916 7.968405 CAGAAATATTTATAACAATAGCCGCCC 59.032 37.037 0.00 0.00 0.00 6.13
2159 2917 6.431198 AATATTTATAACAATAGCCGCCCG 57.569 37.500 0.00 0.00 0.00 6.13
2160 2918 3.472283 TTTATAACAATAGCCGCCCGA 57.528 42.857 0.00 0.00 0.00 5.14
2162 2920 2.094762 ATAACAATAGCCGCCCGATC 57.905 50.000 0.00 0.00 0.00 3.69
2164 2922 1.045407 AACAATAGCCGCCCGATCTA 58.955 50.000 0.00 0.00 0.00 1.98
2165 2923 0.317479 ACAATAGCCGCCCGATCTAC 59.683 55.000 0.00 0.00 0.00 2.59
2166 2924 0.389948 CAATAGCCGCCCGATCTACC 60.390 60.000 0.00 0.00 0.00 3.18
2167 2925 1.874345 AATAGCCGCCCGATCTACCG 61.874 60.000 0.00 0.00 0.00 4.02
2169 2927 4.642542 GCCGCCCGATCTACCGTC 62.643 72.222 0.00 0.00 0.00 4.79
2170 2928 3.974757 CCGCCCGATCTACCGTCC 61.975 72.222 0.00 0.00 0.00 4.79
2171 2929 3.974757 CGCCCGATCTACCGTCCC 61.975 72.222 0.00 0.00 0.00 4.46
2172 2930 2.836360 GCCCGATCTACCGTCCCA 60.836 66.667 0.00 0.00 0.00 4.37
2174 2932 2.728817 CCGATCTACCGTCCCAGC 59.271 66.667 0.00 0.00 0.00 4.85
2175 2933 1.828660 CCGATCTACCGTCCCAGCT 60.829 63.158 0.00 0.00 0.00 4.24
2176 2934 0.536687 CCGATCTACCGTCCCAGCTA 60.537 60.000 0.00 0.00 0.00 3.32
2177 2935 0.875728 CGATCTACCGTCCCAGCTAG 59.124 60.000 0.00 0.00 0.00 3.42
2178 2936 1.814634 CGATCTACCGTCCCAGCTAGT 60.815 57.143 0.00 0.00 0.00 2.57
2180 2938 1.471119 TCTACCGTCCCAGCTAGTTG 58.529 55.000 0.00 0.00 0.00 3.16
2181 2939 1.005097 TCTACCGTCCCAGCTAGTTGA 59.995 52.381 8.34 0.00 0.00 3.18
2182 2940 1.405821 CTACCGTCCCAGCTAGTTGAG 59.594 57.143 8.34 0.00 0.00 3.02
2183 2941 1.258445 ACCGTCCCAGCTAGTTGAGG 61.258 60.000 8.34 7.84 0.00 3.86
2184 2942 0.970937 CCGTCCCAGCTAGTTGAGGA 60.971 60.000 8.34 10.02 0.00 3.71
2185 2943 0.173708 CGTCCCAGCTAGTTGAGGAC 59.826 60.000 24.56 24.56 42.94 3.85
2186 2944 0.537653 GTCCCAGCTAGTTGAGGACC 59.462 60.000 24.26 13.63 40.97 4.46
2189 2947 1.630878 CCCAGCTAGTTGAGGACCTTT 59.369 52.381 8.34 0.00 0.00 3.11
2191 2949 2.079925 CAGCTAGTTGAGGACCTTTGC 58.920 52.381 0.00 0.00 0.00 3.68
2192 2950 1.699634 AGCTAGTTGAGGACCTTTGCA 59.300 47.619 0.00 0.00 0.00 4.08
2196 2954 2.733956 AGTTGAGGACCTTTGCAACAA 58.266 42.857 20.75 7.04 42.16 2.83
2197 2955 2.427095 AGTTGAGGACCTTTGCAACAAC 59.573 45.455 20.75 16.42 42.16 3.32
2198 2956 2.427095 GTTGAGGACCTTTGCAACAACT 59.573 45.455 16.08 4.38 40.11 3.16
2199 2957 3.569194 TGAGGACCTTTGCAACAACTA 57.431 42.857 0.00 0.00 0.00 2.24
2200 2958 3.211045 TGAGGACCTTTGCAACAACTAC 58.789 45.455 0.00 0.00 0.00 2.73
2201 2959 2.552743 GAGGACCTTTGCAACAACTACC 59.447 50.000 0.00 0.00 0.00 3.18
2204 2962 3.243401 GGACCTTTGCAACAACTACCTTG 60.243 47.826 0.00 0.00 35.77 3.61
2217 2975 3.751518 ACTACCTTGTTGCACTTTAGGG 58.248 45.455 7.89 0.00 0.00 3.53
2219 2977 1.256812 CCTTGTTGCACTTTAGGGGG 58.743 55.000 0.00 0.00 0.00 5.40
2222 2980 2.463047 TGTTGCACTTTAGGGGGTTT 57.537 45.000 0.00 0.00 0.00 3.27
2223 2981 2.035632 TGTTGCACTTTAGGGGGTTTG 58.964 47.619 0.00 0.00 0.00 2.93
2224 2982 1.044611 TTGCACTTTAGGGGGTTTGC 58.955 50.000 0.00 0.00 0.00 3.68
2225 2983 0.105964 TGCACTTTAGGGGGTTTGCA 60.106 50.000 0.00 0.00 37.63 4.08
2227 2985 1.270094 GCACTTTAGGGGGTTTGCAAC 60.270 52.381 0.00 0.00 0.00 4.17
2228 2986 2.035632 CACTTTAGGGGGTTTGCAACA 58.964 47.619 0.00 0.00 0.00 3.33
2229 2987 2.432510 CACTTTAGGGGGTTTGCAACAA 59.567 45.455 0.00 0.00 0.00 2.83
2230 2988 2.698274 ACTTTAGGGGGTTTGCAACAAG 59.302 45.455 0.00 0.00 0.00 3.16
2232 2990 0.854218 TAGGGGGTTTGCAACAAGGA 59.146 50.000 0.00 0.00 0.00 3.36
2233 2991 0.759060 AGGGGGTTTGCAACAAGGAC 60.759 55.000 0.00 0.00 0.00 3.85
2234 2992 1.045911 GGGGGTTTGCAACAAGGACA 61.046 55.000 0.00 0.00 0.00 4.02
2320 3368 1.807165 CCATGACACGAGCACGAGG 60.807 63.158 11.40 4.47 42.66 4.63
2401 5210 6.313519 TGAGAAATGGCTACTACCTCAATT 57.686 37.500 0.00 0.00 0.00 2.32
2436 5245 1.276989 TGCTTAGGTACCAAGGAACCG 59.723 52.381 15.94 0.00 40.88 4.44
2586 5436 2.760799 CATGACCCGGGTCCCGTA 60.761 66.667 43.35 29.26 46.80 4.02
2587 5437 2.761213 ATGACCCGGGTCCCGTAC 60.761 66.667 43.35 24.13 46.80 3.67
2588 5438 3.307089 ATGACCCGGGTCCCGTACT 62.307 63.158 43.35 21.95 46.80 2.73
2589 5439 1.936767 ATGACCCGGGTCCCGTACTA 61.937 60.000 43.35 27.47 46.80 1.82
2590 5440 2.043953 ACCCGGGTCCCGTACTAC 60.044 66.667 28.39 0.00 46.80 2.73
2591 5441 2.834968 CCCGGGTCCCGTACTACC 60.835 72.222 28.39 0.00 46.80 3.18
2592 5442 3.211963 CCGGGTCCCGTACTACCG 61.212 72.222 28.39 7.83 46.80 4.02
2593 5443 3.892581 CGGGTCCCGTACTACCGC 61.893 72.222 23.02 0.00 42.73 5.68
2594 5444 3.531207 GGGTCCCGTACTACCGCC 61.531 72.222 0.00 0.00 36.57 6.13
2595 5445 2.755469 GGTCCCGTACTACCGCCA 60.755 66.667 0.00 0.00 0.00 5.69
2596 5446 2.779033 GGTCCCGTACTACCGCCAG 61.779 68.421 0.00 0.00 0.00 4.85
2597 5447 3.142838 TCCCGTACTACCGCCAGC 61.143 66.667 0.00 0.00 0.00 4.85
2598 5448 4.217159 CCCGTACTACCGCCAGCC 62.217 72.222 0.00 0.00 0.00 4.85
2599 5449 4.217159 CCGTACTACCGCCAGCCC 62.217 72.222 0.00 0.00 0.00 5.19
2600 5450 3.454573 CGTACTACCGCCAGCCCA 61.455 66.667 0.00 0.00 0.00 5.36
2601 5451 2.983791 GTACTACCGCCAGCCCAA 59.016 61.111 0.00 0.00 0.00 4.12
2602 5452 1.153429 GTACTACCGCCAGCCCAAG 60.153 63.158 0.00 0.00 0.00 3.61
2603 5453 3.026431 TACTACCGCCAGCCCAAGC 62.026 63.158 0.00 0.00 40.32 4.01
2621 5471 4.840168 GGCACTACCGCCGATAAA 57.160 55.556 0.00 0.00 43.52 1.40
2622 5472 3.300711 GGCACTACCGCCGATAAAT 57.699 52.632 0.00 0.00 43.52 1.40
2783 5655 8.280084 GGACATAGACTATATATACTCCCCACA 58.720 40.741 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
498 526 8.700051 CCATATATTCCAAGACTAGGGATACAG 58.300 40.741 0.00 0.00 29.46 2.74
841 1084 5.904362 ACCTTTATTTCTCACAGAATGGC 57.096 39.130 0.00 0.00 43.62 4.40
842 1085 8.244113 GGTAAACCTTTATTTCTCACAGAATGG 58.756 37.037 0.00 0.00 43.62 3.16
843 1086 9.014297 AGGTAAACCTTTATTTCTCACAGAATG 57.986 33.333 0.00 0.00 46.09 2.67
844 1087 9.014297 CAGGTAAACCTTTATTTCTCACAGAAT 57.986 33.333 0.00 0.00 46.09 2.40
845 1088 8.215050 TCAGGTAAACCTTTATTTCTCACAGAA 58.785 33.333 0.00 0.00 46.09 3.02
846 1089 7.741785 TCAGGTAAACCTTTATTTCTCACAGA 58.258 34.615 0.00 0.00 46.09 3.41
847 1090 7.979444 TCAGGTAAACCTTTATTTCTCACAG 57.021 36.000 0.00 0.00 46.09 3.66
879 1122 1.098712 TGTCGCTTCGCCAGGTTTTT 61.099 50.000 0.00 0.00 0.00 1.94
883 1126 1.961277 CTTTGTCGCTTCGCCAGGT 60.961 57.895 0.00 0.00 0.00 4.00
943 1186 1.552348 GAGCCGAATCCGATTGCGAG 61.552 60.000 0.00 0.00 40.82 5.03
944 1187 1.591594 GAGCCGAATCCGATTGCGA 60.592 57.895 0.00 0.00 40.82 5.10
945 1188 2.931386 GAGCCGAATCCGATTGCG 59.069 61.111 0.00 2.65 38.22 4.85
946 1189 1.822250 GACGAGCCGAATCCGATTGC 61.822 60.000 0.00 0.00 38.22 3.56
947 1190 1.215655 GGACGAGCCGAATCCGATTG 61.216 60.000 0.00 0.00 38.22 2.67
974 1217 1.813513 CGCTTCTGTTTGGATGGAGT 58.186 50.000 0.00 0.00 0.00 3.85
976 1219 1.298157 CGCGCTTCTGTTTGGATGGA 61.298 55.000 5.56 0.00 0.00 3.41
977 1220 1.135315 CGCGCTTCTGTTTGGATGG 59.865 57.895 5.56 0.00 0.00 3.51
978 1221 0.095935 CTCGCGCTTCTGTTTGGATG 59.904 55.000 5.56 0.00 0.00 3.51
979 1222 1.021390 CCTCGCGCTTCTGTTTGGAT 61.021 55.000 5.56 0.00 0.00 3.41
993 1236 1.499049 CCGTCTTTTATAGGCCTCGC 58.501 55.000 9.68 0.00 0.00 5.03
1037 1280 4.041567 TGATCCTTGTAGACACAACCACAT 59.958 41.667 0.00 0.00 39.75 3.21
1057 1300 4.258702 AGATAGATAAACGCCGCTTGAT 57.741 40.909 0.00 0.00 0.00 2.57
1068 1315 4.321008 CGCCGCCTCTACAAGATAGATAAA 60.321 45.833 0.00 0.00 0.00 1.40
1136 1386 4.838486 CCGCTGTCTCTCGCCGTC 62.838 72.222 0.00 0.00 0.00 4.79
1162 1412 1.381928 CGTACTTGGCGAGCTCCCTA 61.382 60.000 18.49 12.11 0.00 3.53
1212 1462 0.941463 GAGCATGGCGATCAGGTACG 60.941 60.000 0.00 0.00 0.00 3.67
1241 1491 2.144078 TGACCAGGAACGCCAAGGA 61.144 57.895 0.00 0.00 36.01 3.36
1324 1574 0.039527 ACGCGGCATCAAGGAAAAAC 60.040 50.000 12.47 0.00 0.00 2.43
1327 1577 1.873165 GAACGCGGCATCAAGGAAA 59.127 52.632 12.47 0.00 0.00 3.13
1401 1665 4.115199 GGGGCTGGCCTTCGACAT 62.115 66.667 20.47 0.00 36.10 3.06
1410 1674 4.785453 CTTCTCCACGGGGCTGGC 62.785 72.222 0.00 0.00 0.00 4.85
1411 1675 3.003173 TCTTCTCCACGGGGCTGG 61.003 66.667 0.00 0.00 0.00 4.85
1412 1676 2.111999 TTGTCTTCTCCACGGGGCTG 62.112 60.000 0.00 0.00 0.00 4.85
1413 1677 1.831652 CTTGTCTTCTCCACGGGGCT 61.832 60.000 0.00 0.00 0.00 5.19
1414 1678 1.376037 CTTGTCTTCTCCACGGGGC 60.376 63.158 0.00 0.00 0.00 5.80
1500 1764 3.740115 ACTAGCAACAATATAAGCCGGG 58.260 45.455 2.18 0.00 0.00 5.73
1536 1800 3.572682 ACACAAGACCGATCTGTTACAGA 59.427 43.478 17.87 17.87 44.99 3.41
1537 1801 3.914312 ACACAAGACCGATCTGTTACAG 58.086 45.455 5.94 5.94 34.48 2.74
1538 1802 4.330944 AACACAAGACCGATCTGTTACA 57.669 40.909 0.00 0.00 34.48 2.41
1539 1803 4.748102 TCAAACACAAGACCGATCTGTTAC 59.252 41.667 0.00 0.00 34.48 2.50
1541 1805 3.804036 TCAAACACAAGACCGATCTGTT 58.196 40.909 0.00 0.00 34.48 3.16
1543 1807 3.653344 TCTCAAACACAAGACCGATCTG 58.347 45.455 0.00 0.00 34.48 2.90
1544 1808 3.306364 CCTCTCAAACACAAGACCGATCT 60.306 47.826 0.00 0.00 36.42 2.75
1545 1809 2.996621 CCTCTCAAACACAAGACCGATC 59.003 50.000 0.00 0.00 0.00 3.69
1546 1810 2.368875 ACCTCTCAAACACAAGACCGAT 59.631 45.455 0.00 0.00 0.00 4.18
1547 1811 1.760613 ACCTCTCAAACACAAGACCGA 59.239 47.619 0.00 0.00 0.00 4.69
1570 1835 6.035866 CAGATAGAAGAAGACACATCACTTGC 59.964 42.308 0.00 0.00 0.00 4.01
1588 1853 3.067320 CAGGAGACACGATTGCAGATAGA 59.933 47.826 0.00 0.00 0.00 1.98
1589 1854 3.067320 TCAGGAGACACGATTGCAGATAG 59.933 47.826 0.00 0.00 0.00 2.08
1590 1855 3.023832 TCAGGAGACACGATTGCAGATA 58.976 45.455 0.00 0.00 0.00 1.98
1591 1856 1.827344 TCAGGAGACACGATTGCAGAT 59.173 47.619 0.00 0.00 0.00 2.90
1634 1899 1.216444 GATCAGCGCCAGTGTCTCA 59.784 57.895 2.29 0.00 0.00 3.27
1642 1907 2.390599 GCAGAAACGATCAGCGCCA 61.391 57.895 2.29 0.00 46.04 5.69
1663 1928 2.240160 ACGCCTGGACCCAACATAATAA 59.760 45.455 0.00 0.00 0.00 1.40
1675 1945 0.036388 TTCATCTTGGACGCCTGGAC 60.036 55.000 0.00 0.00 0.00 4.02
1679 1949 3.914426 ATTAGTTCATCTTGGACGCCT 57.086 42.857 0.00 0.00 0.00 5.52
1704 1974 3.684103 TCGTTTCAAGTTTGCGAACAT 57.316 38.095 19.01 3.95 38.26 2.71
1706 1976 6.077838 AGATAATCGTTTCAAGTTTGCGAAC 58.922 36.000 8.93 8.93 35.20 3.95
1707 1977 6.236017 AGATAATCGTTTCAAGTTTGCGAA 57.764 33.333 0.00 0.00 35.20 4.70
1708 1978 5.163893 GGAGATAATCGTTTCAAGTTTGCGA 60.164 40.000 0.00 0.00 36.02 5.10
1710 1980 6.024049 CAGGAGATAATCGTTTCAAGTTTGC 58.976 40.000 0.00 0.00 0.00 3.68
1711 1981 6.149474 ACCAGGAGATAATCGTTTCAAGTTTG 59.851 38.462 0.00 0.00 0.00 2.93
1713 1983 5.805728 ACCAGGAGATAATCGTTTCAAGTT 58.194 37.500 0.00 0.00 0.00 2.66
1714 1984 5.422214 ACCAGGAGATAATCGTTTCAAGT 57.578 39.130 0.00 0.00 0.00 3.16
1715 1985 6.455646 CGAAACCAGGAGATAATCGTTTCAAG 60.456 42.308 10.14 0.00 36.42 3.02
1716 1986 5.350365 CGAAACCAGGAGATAATCGTTTCAA 59.650 40.000 10.14 0.00 36.42 2.69
1717 1987 4.868171 CGAAACCAGGAGATAATCGTTTCA 59.132 41.667 10.14 0.00 36.42 2.69
1718 1988 5.107133 TCGAAACCAGGAGATAATCGTTTC 58.893 41.667 0.00 0.00 34.78 2.78
1719 1989 5.080969 TCGAAACCAGGAGATAATCGTTT 57.919 39.130 0.00 0.00 0.00 3.60
1720 1990 4.159879 ACTCGAAACCAGGAGATAATCGTT 59.840 41.667 0.00 0.00 34.40 3.85
1721 1991 3.700038 ACTCGAAACCAGGAGATAATCGT 59.300 43.478 0.00 0.00 34.40 3.73
1722 1992 4.308899 ACTCGAAACCAGGAGATAATCG 57.691 45.455 0.00 0.00 34.40 3.34
1728 1998 9.584008 ACTAATATATTACTCGAAACCAGGAGA 57.416 33.333 0.81 0.00 34.40 3.71
1803 2073 9.915629 TGCAAAAGAAAAACTAGTCTAAACAAA 57.084 25.926 0.00 0.00 0.00 2.83
1804 2074 9.915629 TTGCAAAAGAAAAACTAGTCTAAACAA 57.084 25.926 0.00 0.00 0.00 2.83
1805 2075 9.915629 TTTGCAAAAGAAAAACTAGTCTAAACA 57.084 25.926 10.02 0.00 0.00 2.83
1834 2104 8.458843 GCAGCCATTCTAGTCTAAACAAAATAA 58.541 33.333 0.00 0.00 0.00 1.40
1835 2105 7.201609 CGCAGCCATTCTAGTCTAAACAAAATA 60.202 37.037 0.00 0.00 0.00 1.40
1836 2106 6.403636 CGCAGCCATTCTAGTCTAAACAAAAT 60.404 38.462 0.00 0.00 0.00 1.82
1837 2107 5.106712 CGCAGCCATTCTAGTCTAAACAAAA 60.107 40.000 0.00 0.00 0.00 2.44
1860 2130 1.372004 CTGCCCATGTTGCAACACG 60.372 57.895 33.29 25.88 42.51 4.49
1862 2132 1.340088 ATTCTGCCCATGTTGCAACA 58.660 45.000 32.78 32.78 44.06 3.33
1870 2140 2.174363 TGATCGCTATTCTGCCCATG 57.826 50.000 0.00 0.00 0.00 3.66
1871 2141 2.880890 GTTTGATCGCTATTCTGCCCAT 59.119 45.455 0.00 0.00 0.00 4.00
1890 2165 2.173382 GCGAGAATGTTGCGCGTT 59.827 55.556 8.43 0.00 41.37 4.84
1894 2169 0.521867 CACATGGCGAGAATGTTGCG 60.522 55.000 0.00 0.00 36.10 4.85
1896 2171 1.167851 ACCACATGGCGAGAATGTTG 58.832 50.000 0.00 0.00 36.10 3.33
1899 2174 3.057315 AGAAAAACCACATGGCGAGAATG 60.057 43.478 0.00 0.00 39.32 2.67
1911 2186 8.812147 AAAAATCGGAATAAGAGAAAAACCAC 57.188 30.769 0.00 0.00 0.00 4.16
1937 2212 0.733150 CAGTAGCGACCGACTCATCA 59.267 55.000 0.00 0.00 0.00 3.07
1945 2220 0.241749 TGTTGGTACAGTAGCGACCG 59.758 55.000 22.32 0.00 42.39 4.79
1955 2230 0.391130 GCATCCGAGCTGTTGGTACA 60.391 55.000 0.00 0.00 0.00 2.90
1964 2239 2.898738 CTGAGGTGCATCCGAGCT 59.101 61.111 0.00 0.00 41.99 4.09
1974 2249 1.467920 GGAAGGGATTTGCTGAGGTG 58.532 55.000 0.00 0.00 0.00 4.00
1982 2257 1.098050 CGAAGCTGGGAAGGGATTTG 58.902 55.000 0.00 0.00 0.00 2.32
2056 2332 1.001406 CCATCCTCGCCTCTATCCAAC 59.999 57.143 0.00 0.00 0.00 3.77
2057 2333 1.342074 CCATCCTCGCCTCTATCCAA 58.658 55.000 0.00 0.00 0.00 3.53
2058 2334 0.188587 ACCATCCTCGCCTCTATCCA 59.811 55.000 0.00 0.00 0.00 3.41
2060 2336 1.621992 TGACCATCCTCGCCTCTATC 58.378 55.000 0.00 0.00 0.00 2.08
2072 2348 4.142271 GGATGAGTAGATCGGATGACCATC 60.142 50.000 0.00 8.32 37.11 3.51
2073 2349 3.766591 GGATGAGTAGATCGGATGACCAT 59.233 47.826 0.00 0.29 35.59 3.55
2075 2351 3.057174 GTGGATGAGTAGATCGGATGACC 60.057 52.174 0.00 0.00 0.00 4.02
2076 2352 3.365465 CGTGGATGAGTAGATCGGATGAC 60.365 52.174 0.00 0.00 0.00 3.06
2078 2354 2.554462 ACGTGGATGAGTAGATCGGATG 59.446 50.000 0.00 0.00 0.00 3.51
2079 2355 2.554462 CACGTGGATGAGTAGATCGGAT 59.446 50.000 7.95 0.00 0.00 4.18
2080 2356 1.947456 CACGTGGATGAGTAGATCGGA 59.053 52.381 7.95 0.00 0.00 4.55
2081 2357 1.600663 GCACGTGGATGAGTAGATCGG 60.601 57.143 18.88 0.00 0.00 4.18
2082 2358 1.335182 AGCACGTGGATGAGTAGATCG 59.665 52.381 18.88 0.00 0.00 3.69
2083 2359 3.119291 CAAGCACGTGGATGAGTAGATC 58.881 50.000 18.88 0.00 0.00 2.75
2084 2360 2.760650 TCAAGCACGTGGATGAGTAGAT 59.239 45.455 18.88 0.00 0.00 1.98
2085 2361 2.094700 GTCAAGCACGTGGATGAGTAGA 60.095 50.000 18.88 0.00 0.00 2.59
2086 2362 2.263077 GTCAAGCACGTGGATGAGTAG 58.737 52.381 18.88 0.00 0.00 2.57
2087 2363 1.067142 GGTCAAGCACGTGGATGAGTA 60.067 52.381 18.88 0.00 0.00 2.59
2089 2365 0.036952 AGGTCAAGCACGTGGATGAG 60.037 55.000 18.88 0.00 0.00 2.90
2091 2367 0.798776 GAAGGTCAAGCACGTGGATG 59.201 55.000 18.88 1.88 0.00 3.51
2092 2368 0.321653 GGAAGGTCAAGCACGTGGAT 60.322 55.000 18.88 0.00 0.00 3.41
2093 2369 1.070786 GGAAGGTCAAGCACGTGGA 59.929 57.895 18.88 2.95 0.00 4.02
2095 2371 0.588252 CAAGGAAGGTCAAGCACGTG 59.412 55.000 12.28 12.28 0.00 4.49
2096 2372 1.166531 GCAAGGAAGGTCAAGCACGT 61.167 55.000 0.00 0.00 0.00 4.49
2097 2373 1.165907 TGCAAGGAAGGTCAAGCACG 61.166 55.000 0.00 0.00 0.00 5.34
2098 2374 1.032014 TTGCAAGGAAGGTCAAGCAC 58.968 50.000 0.00 0.00 0.00 4.40
2099 2375 1.032014 GTTGCAAGGAAGGTCAAGCA 58.968 50.000 0.00 0.00 0.00 3.91
2100 2376 1.032014 TGTTGCAAGGAAGGTCAAGC 58.968 50.000 0.00 0.00 0.00 4.01
2101 2377 2.951642 TCTTGTTGCAAGGAAGGTCAAG 59.048 45.455 14.34 14.34 34.19 3.02
2104 2380 1.268079 GCTCTTGTTGCAAGGAAGGTC 59.732 52.381 15.07 6.57 0.00 3.85
2106 2382 0.239347 CGCTCTTGTTGCAAGGAAGG 59.761 55.000 15.07 9.07 0.00 3.46
2107 2383 0.239347 CCGCTCTTGTTGCAAGGAAG 59.761 55.000 0.00 5.55 0.00 3.46
2108 2384 0.465460 ACCGCTCTTGTTGCAAGGAA 60.465 50.000 0.00 0.00 0.00 3.36
2110 2386 1.283793 CACCGCTCTTGTTGCAAGG 59.716 57.895 0.00 0.00 0.00 3.61
2120 2396 2.472695 TATTTCTGCAACACCGCTCT 57.527 45.000 0.00 0.00 0.00 4.09
2121 2397 3.764885 AATATTTCTGCAACACCGCTC 57.235 42.857 0.00 0.00 0.00 5.03
2124 2882 8.903570 TTGTTATAAATATTTCTGCAACACCG 57.096 30.769 3.39 0.00 0.00 4.94
2129 2887 9.891828 CGGCTATTGTTATAAATATTTCTGCAA 57.108 29.630 3.39 6.86 0.00 4.08
2131 2889 7.484959 GGCGGCTATTGTTATAAATATTTCTGC 59.515 37.037 3.39 3.07 0.00 4.26
2134 2892 6.964934 CGGGCGGCTATTGTTATAAATATTTC 59.035 38.462 9.56 0.00 0.00 2.17
2138 2896 5.149973 TCGGGCGGCTATTGTTATAAATA 57.850 39.130 9.56 0.00 0.00 1.40
2143 2901 1.623811 AGATCGGGCGGCTATTGTTAT 59.376 47.619 9.56 0.00 0.00 1.89
2144 2902 1.045407 AGATCGGGCGGCTATTGTTA 58.955 50.000 9.56 0.00 0.00 2.41
2146 2904 0.317479 GTAGATCGGGCGGCTATTGT 59.683 55.000 9.56 0.00 0.00 2.71
2147 2905 0.389948 GGTAGATCGGGCGGCTATTG 60.390 60.000 9.56 0.00 0.00 1.90
2152 2910 4.642542 GACGGTAGATCGGGCGGC 62.643 72.222 0.00 0.00 0.00 6.53
2153 2911 3.974757 GGACGGTAGATCGGGCGG 61.975 72.222 0.00 0.00 0.00 6.13
2154 2912 3.974757 GGGACGGTAGATCGGGCG 61.975 72.222 0.00 0.00 0.00 6.13
2156 2914 2.857744 GCTGGGACGGTAGATCGGG 61.858 68.421 0.00 0.00 36.83 5.14
2157 2915 0.536687 TAGCTGGGACGGTAGATCGG 60.537 60.000 0.00 0.00 36.83 4.18
2158 2916 0.875728 CTAGCTGGGACGGTAGATCG 59.124 60.000 0.00 0.00 35.93 3.69
2159 2917 1.984066 ACTAGCTGGGACGGTAGATC 58.016 55.000 0.85 0.00 36.80 2.75
2160 2918 2.032620 CAACTAGCTGGGACGGTAGAT 58.967 52.381 0.85 0.00 36.80 1.98
2162 2920 1.405821 CTCAACTAGCTGGGACGGTAG 59.594 57.143 0.85 0.00 38.29 3.18
2164 2922 1.258445 CCTCAACTAGCTGGGACGGT 61.258 60.000 0.85 0.00 36.83 4.83
2165 2923 0.970937 TCCTCAACTAGCTGGGACGG 60.971 60.000 0.85 0.00 38.10 4.79
2166 2924 0.173708 GTCCTCAACTAGCTGGGACG 59.826 60.000 14.24 0.00 37.34 4.79
2167 2925 0.537653 GGTCCTCAACTAGCTGGGAC 59.462 60.000 18.33 18.33 43.86 4.46
2169 2927 1.280457 AAGGTCCTCAACTAGCTGGG 58.720 55.000 0.85 0.00 0.00 4.45
2170 2928 2.704572 CAAAGGTCCTCAACTAGCTGG 58.295 52.381 0.00 0.00 0.00 4.85
2171 2929 2.079925 GCAAAGGTCCTCAACTAGCTG 58.920 52.381 0.00 0.00 0.00 4.24
2172 2930 1.699634 TGCAAAGGTCCTCAACTAGCT 59.300 47.619 0.00 0.00 0.00 3.32
2174 2932 3.476552 TGTTGCAAAGGTCCTCAACTAG 58.523 45.455 18.08 0.00 39.44 2.57
2175 2933 3.569194 TGTTGCAAAGGTCCTCAACTA 57.431 42.857 18.08 6.69 39.44 2.24
2176 2934 2.427095 GTTGTTGCAAAGGTCCTCAACT 59.573 45.455 18.08 0.00 39.44 3.16
2177 2935 2.427095 AGTTGTTGCAAAGGTCCTCAAC 59.573 45.455 15.29 15.29 39.23 3.18
2178 2936 2.733956 AGTTGTTGCAAAGGTCCTCAA 58.266 42.857 0.00 0.00 0.00 3.02
2180 2938 2.552743 GGTAGTTGTTGCAAAGGTCCTC 59.447 50.000 0.00 0.00 0.00 3.71
2181 2939 2.174854 AGGTAGTTGTTGCAAAGGTCCT 59.825 45.455 0.00 2.03 0.00 3.85
2182 2940 2.583143 AGGTAGTTGTTGCAAAGGTCC 58.417 47.619 0.00 0.00 0.00 4.46
2183 2941 3.964909 CAAGGTAGTTGTTGCAAAGGTC 58.035 45.455 0.00 0.00 0.00 3.85
2196 2954 3.497942 CCCCTAAAGTGCAACAAGGTAGT 60.498 47.826 0.00 0.00 41.43 2.73
2197 2955 3.081804 CCCCTAAAGTGCAACAAGGTAG 58.918 50.000 0.00 0.00 41.43 3.18
2198 2956 2.224917 CCCCCTAAAGTGCAACAAGGTA 60.225 50.000 0.00 0.00 41.43 3.08
2199 2957 1.480498 CCCCCTAAAGTGCAACAAGGT 60.480 52.381 0.00 0.00 41.43 3.50
2200 2958 1.256812 CCCCCTAAAGTGCAACAAGG 58.743 55.000 0.00 0.00 41.43 3.61
2201 2959 1.995376 ACCCCCTAAAGTGCAACAAG 58.005 50.000 0.00 0.00 41.43 3.16
2204 2962 1.270094 GCAAACCCCCTAAAGTGCAAC 60.270 52.381 0.00 0.00 32.29 4.17
2207 2965 1.044611 TTGCAAACCCCCTAAAGTGC 58.955 50.000 0.00 0.00 0.00 4.40
2208 2966 2.812358 GTTGCAAACCCCCTAAAGTG 57.188 50.000 0.00 0.00 42.21 3.16
2219 2977 7.511450 CGCATCAAATGTCCTTGTTGCAAAC 62.511 44.000 0.00 0.00 45.82 2.93
2222 2980 2.607526 CGCATCAAATGTCCTTGTTGCA 60.608 45.455 15.68 0.00 45.82 4.08
2223 2981 1.987770 CGCATCAAATGTCCTTGTTGC 59.012 47.619 8.60 8.60 43.70 4.17
2224 2982 2.228582 TCCGCATCAAATGTCCTTGTTG 59.771 45.455 0.00 0.00 0.00 3.33
2225 2983 2.489329 CTCCGCATCAAATGTCCTTGTT 59.511 45.455 0.00 0.00 0.00 2.83
2227 2985 1.202222 GCTCCGCATCAAATGTCCTTG 60.202 52.381 0.00 0.00 0.00 3.61
2228 2986 1.098050 GCTCCGCATCAAATGTCCTT 58.902 50.000 0.00 0.00 0.00 3.36
2229 2987 0.035152 TGCTCCGCATCAAATGTCCT 60.035 50.000 0.00 0.00 31.71 3.85
2230 2988 2.481212 TGCTCCGCATCAAATGTCC 58.519 52.632 0.00 0.00 31.71 4.02
2320 3368 2.750712 ACCTTGTTCTCGAGAGCTCTAC 59.249 50.000 26.58 17.10 0.00 2.59
2401 5210 1.985473 AAGCACACAAAGCATCTCCA 58.015 45.000 0.00 0.00 0.00 3.86
2436 5245 0.756070 ACCGTAGCTTCTCCTAGGCC 60.756 60.000 2.96 0.00 0.00 5.19
2488 5297 4.069232 CTCGTTCTGGAGCGGGCA 62.069 66.667 6.96 0.00 35.70 5.36
2584 5434 1.153429 CTTGGGCTGGCGGTAGTAC 60.153 63.158 0.00 0.00 0.00 2.73
2585 5435 3.026431 GCTTGGGCTGGCGGTAGTA 62.026 63.158 0.00 0.00 35.22 1.82
2586 5436 4.410400 GCTTGGGCTGGCGGTAGT 62.410 66.667 0.00 0.00 35.22 2.73
2605 5455 0.865769 CCATTTATCGGCGGTAGTGC 59.134 55.000 7.21 0.00 0.00 4.40
2606 5456 2.234300 ACCATTTATCGGCGGTAGTG 57.766 50.000 7.21 7.35 0.00 2.74
2607 5457 2.961062 AGTACCATTTATCGGCGGTAGT 59.039 45.455 7.21 0.43 34.72 2.73
2608 5458 3.655276 AGTACCATTTATCGGCGGTAG 57.345 47.619 7.21 0.00 34.72 3.18
2609 5459 3.255642 GGTAGTACCATTTATCGGCGGTA 59.744 47.826 14.82 0.00 38.42 4.02
2610 5460 2.036346 GGTAGTACCATTTATCGGCGGT 59.964 50.000 14.82 0.65 38.42 5.68
2611 5461 2.680577 GGTAGTACCATTTATCGGCGG 58.319 52.381 14.82 0.00 38.42 6.13
2612 5462 2.322161 CGGTAGTACCATTTATCGGCG 58.678 52.381 19.41 0.00 38.47 6.46
2613 5463 2.064014 GCGGTAGTACCATTTATCGGC 58.936 52.381 19.41 7.86 38.47 5.54
2614 5464 3.005050 TGAGCGGTAGTACCATTTATCGG 59.995 47.826 19.41 1.45 38.47 4.18
2615 5465 4.227538 CTGAGCGGTAGTACCATTTATCG 58.772 47.826 19.41 4.49 38.47 2.92
2616 5466 5.197682 ACTGAGCGGTAGTACCATTTATC 57.802 43.478 19.41 9.16 38.47 1.75
2617 5467 4.038883 GGACTGAGCGGTAGTACCATTTAT 59.961 45.833 19.41 0.00 38.47 1.40
2618 5468 3.382546 GGACTGAGCGGTAGTACCATTTA 59.617 47.826 19.41 2.68 38.47 1.40
2619 5469 2.167900 GGACTGAGCGGTAGTACCATTT 59.832 50.000 19.41 3.65 38.47 2.32
2620 5470 1.755380 GGACTGAGCGGTAGTACCATT 59.245 52.381 19.41 6.22 38.47 3.16
2621 5471 1.341679 TGGACTGAGCGGTAGTACCAT 60.342 52.381 19.41 6.94 38.47 3.55
2622 5472 0.038599 TGGACTGAGCGGTAGTACCA 59.961 55.000 19.41 0.00 38.47 3.25


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

AutoCloner maintained by Alex Coulton.