Multiple sequence alignment - TraesCS1D01G242900

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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 TraesCS1D01G242900 chr1D 100.000 3765 0 0 1 3765 333006407 333002643 0.000000e+00 6953
1 TraesCS1D01G242900 chr1D 87.069 116 8 4 1699 1814 135931057 135930949 1.420000e-24 124
2 TraesCS1D01G242900 chr1D 85.000 100 15 0 3270 3369 435745135 435745234 6.650000e-18 102
3 TraesCS1D01G242900 chr1A 90.319 1911 106 41 1810 3674 430625392 430623515 0.000000e+00 2431
4 TraesCS1D01G242900 chr1A 92.670 955 48 8 769 1712 430626338 430625395 0.000000e+00 1356
5 TraesCS1D01G242900 chr1A 93.243 74 3 1 3692 3765 430623530 430623459 1.430000e-19 108
6 TraesCS1D01G242900 chr1B 94.218 1470 67 11 1811 3274 448534408 448532951 0.000000e+00 2228
7 TraesCS1D01G242900 chr1B 91.759 813 45 14 769 1575 448535409 448534613 0.000000e+00 1110
8 TraesCS1D01G242900 chr1B 82.482 411 37 20 3289 3674 448532764 448532364 1.010000e-85 327
9 TraesCS1D01G242900 chr1B 93.548 155 10 0 1558 1712 448534566 448534412 8.130000e-57 231
10 TraesCS1D01G242900 chr1B 98.649 74 0 1 3692 3765 448532379 448532307 3.050000e-26 130
11 TraesCS1D01G242900 chr7B 91.553 734 36 8 1 722 413976428 413975709 0.000000e+00 989
12 TraesCS1D01G242900 chr7B 89.563 709 46 14 1 683 590526290 590526996 0.000000e+00 874
13 TraesCS1D01G242900 chr7B 87.500 112 13 1 1702 1812 40192262 40192373 1.100000e-25 128
14 TraesCS1D01G242900 chr7D 91.129 744 38 15 1 718 607958001 607958742 0.000000e+00 983
15 TraesCS1D01G242900 chr7D 96.386 166 6 0 553 718 607958836 607959001 1.330000e-69 274
16 TraesCS1D01G242900 chr2D 90.318 723 43 9 1 712 460622690 460621984 0.000000e+00 922
17 TraesCS1D01G242900 chr2D 89.091 110 8 1 1710 1819 382198152 382198257 2.360000e-27 134
18 TraesCS1D01G242900 chr2D 89.091 110 7 2 1712 1821 643762841 643762737 8.490000e-27 132
19 TraesCS1D01G242900 chr2D 84.298 121 18 1 3261 3380 596995190 596995310 2.380000e-22 117
20 TraesCS1D01G242900 chr2D 84.956 113 15 2 3253 3364 101902036 101902147 3.070000e-21 113
21 TraesCS1D01G242900 chr2B 92.544 456 23 4 9 456 157262296 157262748 0.000000e+00 643
22 TraesCS1D01G242900 chr2B 85.185 162 20 2 561 722 655763324 655763481 3.010000e-36 163
23 TraesCS1D01G242900 chr2B 88.889 108 8 1 1705 1812 230532416 230532519 3.050000e-26 130
24 TraesCS1D01G242900 chr3D 90.476 105 9 1 3277 3380 548706924 548706820 1.820000e-28 137
25 TraesCS1D01G242900 chr3D 85.345 116 15 1 3267 3380 129022013 129022128 6.610000e-23 119
26 TraesCS1D01G242900 chr3B 90.476 105 9 1 3277 3380 727743353 727743249 1.820000e-28 137
27 TraesCS1D01G242900 chr7A 85.827 127 18 0 3254 3380 136346165 136346039 6.560000e-28 135
28 TraesCS1D01G242900 chr7A 85.366 123 13 3 1696 1818 238526328 238526211 5.110000e-24 122
29 TraesCS1D01G242900 chr4D 89.720 107 5 4 1707 1813 15316025 15316125 8.490000e-27 132
30 TraesCS1D01G242900 chr4D 90.196 102 6 2 1712 1813 93339453 93339356 3.050000e-26 130
31 TraesCS1D01G242900 chr4A 89.524 105 7 3 1711 1815 238389339 238389239 3.050000e-26 130
32 TraesCS1D01G242900 chr6D 86.325 117 14 2 3254 3369 156450515 156450400 3.950000e-25 126
33 TraesCS1D01G242900 chr6B 84.483 116 16 1 3254 3369 279050124 279050011 3.070000e-21 113


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 TraesCS1D01G242900 chr1D 333002643 333006407 3764 True 6953.000000 6953 100.000000 1 3765 1 chr1D.!!$R2 3764
1 TraesCS1D01G242900 chr1A 430623459 430626338 2879 True 1298.333333 2431 92.077333 769 3765 3 chr1A.!!$R1 2996
2 TraesCS1D01G242900 chr1B 448532307 448535409 3102 True 805.200000 2228 92.131200 769 3765 5 chr1B.!!$R1 2996
3 TraesCS1D01G242900 chr7B 413975709 413976428 719 True 989.000000 989 91.553000 1 722 1 chr7B.!!$R1 721
4 TraesCS1D01G242900 chr7B 590526290 590526996 706 False 874.000000 874 89.563000 1 683 1 chr7B.!!$F2 682
5 TraesCS1D01G242900 chr7D 607958001 607959001 1000 False 628.500000 983 93.757500 1 718 2 chr7D.!!$F1 717
6 TraesCS1D01G242900 chr2D 460621984 460622690 706 True 922.000000 922 90.318000 1 712 1 chr2D.!!$R1 711

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
767 1075 0.112995 TGGGCAAAGATGTGAAGGCT 59.887 50.0 0.0 0.0 0.0 4.58 F
1636 2020 0.625683 ATCTGATGGGTCCTGGGCTT 60.626 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 2760 0.253044 TCAGCTTCGCCTAGGCAAAT 59.747 50.0 32.47 11.09 42.06 2.32 R
3506 4105 0.109504 GGAGCGAGTGTCTCAGTGTC 60.110 60.0 0.00 0.00 32.38 3.67 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
108 112 4.826274 TGAAGTAAGTTCTGGAGATGGG 57.174 45.455 0.00 0.00 35.99 4.00
264 282 3.407424 AGCTCACATGCTGAAGTGTTA 57.593 42.857 0.00 0.00 42.33 2.41
559 608 2.069273 CCACGAGCGAAGTCAAAGAAT 58.931 47.619 0.00 0.00 0.00 2.40
635 943 6.706270 AGAATGAAACAGCTAGAAAGAACGAA 59.294 34.615 0.00 0.00 0.00 3.85
692 1000 2.389143 GCGCCGAAACTCGTTACG 59.611 61.111 0.00 0.00 38.40 3.18
722 1030 2.438795 GCCGACGAGGAGGTCTCT 60.439 66.667 0.00 0.00 45.00 3.10
723 1031 2.766400 GCCGACGAGGAGGTCTCTG 61.766 68.421 0.00 0.00 45.00 3.35
724 1032 2.766400 CCGACGAGGAGGTCTCTGC 61.766 68.421 0.00 0.00 45.00 4.26
725 1033 2.766400 CGACGAGGAGGTCTCTGCC 61.766 68.421 0.00 0.00 40.30 4.85
726 1034 2.752238 ACGAGGAGGTCTCTGCCG 60.752 66.667 0.00 2.73 40.30 5.69
727 1035 4.200283 CGAGGAGGTCTCTGCCGC 62.200 72.222 0.00 0.00 40.30 6.53
741 1049 3.925090 CCGCCCGGCCTACCTTAG 61.925 72.222 3.10 0.00 0.00 2.18
742 1050 2.836360 CGCCCGGCCTACCTTAGA 60.836 66.667 3.10 0.00 0.00 2.10
743 1051 2.428925 CGCCCGGCCTACCTTAGAA 61.429 63.158 3.10 0.00 0.00 2.10
744 1052 1.909975 GCCCGGCCTACCTTAGAAA 59.090 57.895 0.00 0.00 0.00 2.52
745 1053 0.253894 GCCCGGCCTACCTTAGAAAA 59.746 55.000 0.00 0.00 0.00 2.29
746 1054 1.133884 GCCCGGCCTACCTTAGAAAAT 60.134 52.381 0.00 0.00 0.00 1.82
747 1055 2.572290 CCCGGCCTACCTTAGAAAATG 58.428 52.381 0.00 0.00 0.00 2.32
748 1056 2.092592 CCCGGCCTACCTTAGAAAATGT 60.093 50.000 0.00 0.00 0.00 2.71
749 1057 2.943033 CCGGCCTACCTTAGAAAATGTG 59.057 50.000 0.00 0.00 0.00 3.21
750 1058 2.943033 CGGCCTACCTTAGAAAATGTGG 59.057 50.000 0.00 0.00 0.00 4.17
751 1059 3.288092 GGCCTACCTTAGAAAATGTGGG 58.712 50.000 0.00 0.00 35.72 4.61
752 1060 2.688446 GCCTACCTTAGAAAATGTGGGC 59.312 50.000 5.46 5.46 45.57 5.36
753 1061 3.963129 CCTACCTTAGAAAATGTGGGCA 58.037 45.455 0.00 0.00 28.05 5.36
754 1062 4.340617 CCTACCTTAGAAAATGTGGGCAA 58.659 43.478 0.00 0.00 28.05 4.52
755 1063 4.770010 CCTACCTTAGAAAATGTGGGCAAA 59.230 41.667 0.00 0.00 28.05 3.68
756 1064 4.871933 ACCTTAGAAAATGTGGGCAAAG 57.128 40.909 0.00 0.00 0.00 2.77
757 1065 4.479158 ACCTTAGAAAATGTGGGCAAAGA 58.521 39.130 0.00 0.00 0.00 2.52
758 1066 5.086621 ACCTTAGAAAATGTGGGCAAAGAT 58.913 37.500 0.00 0.00 0.00 2.40
759 1067 5.047092 ACCTTAGAAAATGTGGGCAAAGATG 60.047 40.000 0.00 0.00 0.00 2.90
760 1068 5.047092 CCTTAGAAAATGTGGGCAAAGATGT 60.047 40.000 0.00 0.00 0.00 3.06
761 1069 4.261578 AGAAAATGTGGGCAAAGATGTG 57.738 40.909 0.00 0.00 0.00 3.21
762 1070 3.896888 AGAAAATGTGGGCAAAGATGTGA 59.103 39.130 0.00 0.00 0.00 3.58
763 1071 4.344679 AGAAAATGTGGGCAAAGATGTGAA 59.655 37.500 0.00 0.00 0.00 3.18
764 1072 3.947910 AATGTGGGCAAAGATGTGAAG 57.052 42.857 0.00 0.00 0.00 3.02
765 1073 1.619654 TGTGGGCAAAGATGTGAAGG 58.380 50.000 0.00 0.00 0.00 3.46
766 1074 0.244721 GTGGGCAAAGATGTGAAGGC 59.755 55.000 0.00 0.00 0.00 4.35
767 1075 0.112995 TGGGCAAAGATGTGAAGGCT 59.887 50.000 0.00 0.00 0.00 4.58
776 1084 1.782201 ATGTGAAGGCTGCTGACCCA 61.782 55.000 0.00 0.00 0.00 4.51
796 1104 3.445096 CCAAAAACTCTCTATTGGGCCTG 59.555 47.826 4.53 0.00 38.89 4.85
799 1107 1.799933 ACTCTCTATTGGGCCTGGAG 58.200 55.000 4.53 2.00 0.00 3.86
801 1109 2.090267 ACTCTCTATTGGGCCTGGAGAT 60.090 50.000 4.53 0.00 33.44 2.75
802 1110 3.142977 ACTCTCTATTGGGCCTGGAGATA 59.857 47.826 4.53 0.00 33.44 1.98
803 1111 4.163427 CTCTCTATTGGGCCTGGAGATAA 58.837 47.826 4.53 0.00 33.44 1.75
804 1112 4.566837 TCTCTATTGGGCCTGGAGATAAA 58.433 43.478 4.53 0.00 0.00 1.40
805 1113 4.594920 TCTCTATTGGGCCTGGAGATAAAG 59.405 45.833 4.53 0.00 0.00 1.85
847 1162 1.374252 CAGTTCGCCCGTTAGCACT 60.374 57.895 0.00 0.00 0.00 4.40
848 1163 1.080025 AGTTCGCCCGTTAGCACTC 60.080 57.895 0.00 0.00 0.00 3.51
849 1164 1.080025 GTTCGCCCGTTAGCACTCT 60.080 57.895 0.00 0.00 0.00 3.24
850 1165 1.077089 GTTCGCCCGTTAGCACTCTC 61.077 60.000 0.00 0.00 0.00 3.20
851 1166 1.248785 TTCGCCCGTTAGCACTCTCT 61.249 55.000 0.00 0.00 0.00 3.10
852 1167 1.517257 CGCCCGTTAGCACTCTCTG 60.517 63.158 0.00 0.00 0.00 3.35
860 1175 2.505118 GCACTCTCTGCCGTCGAC 60.505 66.667 5.18 5.18 40.42 4.20
862 1177 3.432588 ACTCTCTGCCGTCGACCG 61.433 66.667 10.58 4.53 0.00 4.79
954 1269 4.070552 GCCCTTCTCGTCGCCACT 62.071 66.667 0.00 0.00 0.00 4.00
960 1275 1.236616 TTCTCGTCGCCACTTACCGA 61.237 55.000 0.00 0.00 0.00 4.69
1040 1355 2.284995 GCTCCTCCCCTCAGGTGT 60.285 66.667 0.00 0.00 36.75 4.16
1136 1451 0.820871 GGTTCGAGCTCCTGACTCAT 59.179 55.000 8.47 0.00 33.58 2.90
1146 1461 1.425066 TCCTGACTCATGGGTTTTGCT 59.575 47.619 0.00 0.00 0.00 3.91
1198 1513 2.050985 GTGCTTGTGCGAACTGGC 60.051 61.111 0.00 0.00 43.34 4.85
1280 1595 2.992114 AAGGAGCTCGTCGGCACT 60.992 61.111 9.78 0.00 34.17 4.40
1386 1701 2.535984 AGTTTCTTTAGATCGATGCGCG 59.464 45.455 0.54 0.00 42.69 6.86
1387 1702 0.852777 TTCTTTAGATCGATGCGCGC 59.147 50.000 27.26 27.26 40.61 6.86
1396 1711 2.202878 GATGCGCGCCAGGTCTTA 60.203 61.111 30.77 7.41 0.00 2.10
1434 1749 6.486993 GGGTGAAGTCTGTCTTATTTTGAGTT 59.513 38.462 0.00 0.00 36.40 3.01
1571 1955 1.312815 GCACCAGATTAGCATGACCC 58.687 55.000 0.00 0.00 0.00 4.46
1636 2020 0.625683 ATCTGATGGGTCCTGGGCTT 60.626 55.000 0.00 0.00 0.00 4.35
1654 2038 3.179048 GCTTGTTGGAGTTTGTGTGTTC 58.821 45.455 0.00 0.00 0.00 3.18
1656 2040 2.096248 TGTTGGAGTTTGTGTGTTCCC 58.904 47.619 0.00 0.00 0.00 3.97
1712 2096 8.633561 CCTCACTATCAGTGTTGATACTTGATA 58.366 37.037 6.23 0.00 46.03 2.15
1714 2098 9.190317 TCACTATCAGTGTTGATACTTGATACT 57.810 33.333 6.23 0.00 46.03 2.12
1715 2099 9.457110 CACTATCAGTGTTGATACTTGATACTC 57.543 37.037 0.00 0.00 42.21 2.59
1716 2100 8.634444 ACTATCAGTGTTGATACTTGATACTCC 58.366 37.037 0.00 0.00 42.21 3.85
1717 2101 6.222038 TCAGTGTTGATACTTGATACTCCC 57.778 41.667 0.00 0.00 0.00 4.30
1718 2102 5.958380 TCAGTGTTGATACTTGATACTCCCT 59.042 40.000 0.00 0.00 0.00 4.20
1719 2103 6.096987 TCAGTGTTGATACTTGATACTCCCTC 59.903 42.308 0.00 0.00 0.00 4.30
1720 2104 6.097554 CAGTGTTGATACTTGATACTCCCTCT 59.902 42.308 0.00 0.00 0.00 3.69
1721 2105 6.097554 AGTGTTGATACTTGATACTCCCTCTG 59.902 42.308 0.00 0.00 0.00 3.35
1722 2106 5.958380 TGTTGATACTTGATACTCCCTCTGT 59.042 40.000 0.00 0.00 0.00 3.41
1723 2107 6.096987 TGTTGATACTTGATACTCCCTCTGTC 59.903 42.308 0.00 0.00 0.00 3.51
1724 2108 5.141182 TGATACTTGATACTCCCTCTGTCC 58.859 45.833 0.00 0.00 0.00 4.02
1725 2109 2.753247 ACTTGATACTCCCTCTGTCCC 58.247 52.381 0.00 0.00 0.00 4.46
1726 2110 2.044492 ACTTGATACTCCCTCTGTCCCA 59.956 50.000 0.00 0.00 0.00 4.37
1727 2111 2.940514 TGATACTCCCTCTGTCCCAA 57.059 50.000 0.00 0.00 0.00 4.12
1728 2112 3.199442 TGATACTCCCTCTGTCCCAAA 57.801 47.619 0.00 0.00 0.00 3.28
1729 2113 3.107601 TGATACTCCCTCTGTCCCAAAG 58.892 50.000 0.00 0.00 0.00 2.77
1730 2114 2.715763 TACTCCCTCTGTCCCAAAGT 57.284 50.000 0.00 0.00 0.00 2.66
1731 2115 2.715763 ACTCCCTCTGTCCCAAAGTA 57.284 50.000 0.00 0.00 0.00 2.24
1732 2116 2.986050 ACTCCCTCTGTCCCAAAGTAA 58.014 47.619 0.00 0.00 0.00 2.24
1733 2117 2.907042 ACTCCCTCTGTCCCAAAGTAAG 59.093 50.000 0.00 0.00 0.00 2.34
1734 2118 2.907042 CTCCCTCTGTCCCAAAGTAAGT 59.093 50.000 0.00 0.00 0.00 2.24
1735 2119 2.637872 TCCCTCTGTCCCAAAGTAAGTG 59.362 50.000 0.00 0.00 0.00 3.16
1736 2120 2.372172 CCCTCTGTCCCAAAGTAAGTGT 59.628 50.000 0.00 0.00 0.00 3.55
1737 2121 3.557264 CCCTCTGTCCCAAAGTAAGTGTC 60.557 52.174 0.00 0.00 0.00 3.67
1738 2122 3.325135 CCTCTGTCCCAAAGTAAGTGTCT 59.675 47.826 0.00 0.00 0.00 3.41
1739 2123 4.561105 CTCTGTCCCAAAGTAAGTGTCTC 58.439 47.826 0.00 0.00 0.00 3.36
1740 2124 3.964688 TCTGTCCCAAAGTAAGTGTCTCA 59.035 43.478 0.00 0.00 0.00 3.27
1741 2125 4.058817 CTGTCCCAAAGTAAGTGTCTCAC 58.941 47.826 0.00 0.00 34.10 3.51
1743 2127 4.202223 TGTCCCAAAGTAAGTGTCTCACTC 60.202 45.833 2.86 0.00 44.62 3.51
1744 2128 3.964688 TCCCAAAGTAAGTGTCTCACTCA 59.035 43.478 2.86 0.00 44.62 3.41
1745 2129 4.407621 TCCCAAAGTAAGTGTCTCACTCAA 59.592 41.667 2.86 0.00 44.62 3.02
1746 2130 4.511826 CCCAAAGTAAGTGTCTCACTCAAC 59.488 45.833 2.86 5.36 44.62 3.18
1747 2131 5.360591 CCAAAGTAAGTGTCTCACTCAACT 58.639 41.667 2.86 7.27 44.62 3.16
1748 2132 5.817816 CCAAAGTAAGTGTCTCACTCAACTT 59.182 40.000 17.14 17.14 44.62 2.66
1750 2134 6.910536 AAGTAAGTGTCTCACTCAACTTTG 57.089 37.500 17.14 0.00 44.62 2.77
1751 2135 5.978814 AGTAAGTGTCTCACTCAACTTTGT 58.021 37.500 2.86 0.00 44.62 2.83
1752 2136 7.108841 AGTAAGTGTCTCACTCAACTTTGTA 57.891 36.000 2.86 0.00 44.62 2.41
1753 2137 6.979238 AGTAAGTGTCTCACTCAACTTTGTAC 59.021 38.462 2.86 0.77 44.62 2.90
1754 2138 5.599999 AGTGTCTCACTCAACTTTGTACT 57.400 39.130 0.00 0.00 41.21 2.73
1755 2139 6.710597 AGTGTCTCACTCAACTTTGTACTA 57.289 37.500 0.00 0.00 41.21 1.82
1756 2140 7.108841 AGTGTCTCACTCAACTTTGTACTAA 57.891 36.000 0.00 0.00 41.21 2.24
1757 2141 6.979238 AGTGTCTCACTCAACTTTGTACTAAC 59.021 38.462 0.00 0.00 41.21 2.34
1758 2142 6.979238 GTGTCTCACTCAACTTTGTACTAACT 59.021 38.462 0.00 0.00 0.00 2.24
1759 2143 7.167801 GTGTCTCACTCAACTTTGTACTAACTC 59.832 40.741 0.00 0.00 0.00 3.01
1760 2144 7.068348 TGTCTCACTCAACTTTGTACTAACTCT 59.932 37.037 0.00 0.00 0.00 3.24
1761 2145 8.566260 GTCTCACTCAACTTTGTACTAACTCTA 58.434 37.037 0.00 0.00 0.00 2.43
1762 2146 8.784994 TCTCACTCAACTTTGTACTAACTCTAG 58.215 37.037 0.00 0.00 0.00 2.43
1763 2147 8.461249 TCACTCAACTTTGTACTAACTCTAGT 57.539 34.615 0.00 0.00 41.43 2.57
1764 2148 9.565090 TCACTCAACTTTGTACTAACTCTAGTA 57.435 33.333 0.00 0.00 39.23 1.82
1789 2173 7.971455 ACAAAGTTGTACTAAAGTTGAGACAC 58.029 34.615 0.00 0.00 40.16 3.67
1790 2174 7.822822 ACAAAGTTGTACTAAAGTTGAGACACT 59.177 33.333 0.00 0.00 40.16 3.55
1791 2175 8.665685 CAAAGTTGTACTAAAGTTGAGACACTT 58.334 33.333 0.00 0.00 38.74 3.16
1792 2176 9.880157 AAAGTTGTACTAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
1800 2184 9.832445 ACTAAAGTTGAGACACTTATTTTCTGA 57.168 29.630 0.00 0.00 35.87 3.27
1802 2186 8.506168 AAAGTTGAGACACTTATTTTCTGACA 57.494 30.769 0.00 0.00 35.87 3.58
1803 2187 7.721286 AGTTGAGACACTTATTTTCTGACAG 57.279 36.000 0.00 0.00 0.00 3.51
1804 2188 7.500992 AGTTGAGACACTTATTTTCTGACAGA 58.499 34.615 0.00 0.00 0.00 3.41
1805 2189 7.655328 AGTTGAGACACTTATTTTCTGACAGAG 59.345 37.037 5.10 0.00 0.00 3.35
1806 2190 6.459066 TGAGACACTTATTTTCTGACAGAGG 58.541 40.000 5.10 0.00 0.00 3.69
1807 2191 5.799213 AGACACTTATTTTCTGACAGAGGG 58.201 41.667 5.10 0.00 0.00 4.30
1808 2192 5.544176 AGACACTTATTTTCTGACAGAGGGA 59.456 40.000 5.10 0.00 0.00 4.20
1842 2226 9.953565 ACAAGGTTGCTGTAGTAGATATAAAAA 57.046 29.630 0.00 0.00 0.00 1.94
1878 2262 3.496130 GCTGGTGCATATGTATCTCACAC 59.504 47.826 5.62 2.70 38.48 3.82
1919 2303 4.095483 CCAAAGATCACAACACAGCTATCC 59.905 45.833 0.00 0.00 0.00 2.59
1933 2317 6.313905 ACACAGCTATCCGTTTTCTGATTTAG 59.686 38.462 0.00 0.00 0.00 1.85
1942 2326 5.920273 CCGTTTTCTGATTTAGCATTGTGTT 59.080 36.000 0.00 0.00 0.00 3.32
1950 2334 8.525316 TCTGATTTAGCATTGTGTTTCATGATT 58.475 29.630 0.00 0.00 0.00 2.57
2349 2734 7.062956 TGACGCATAATTGAGTATATTTAGCGG 59.937 37.037 0.00 0.00 39.33 5.52
2389 2774 1.280710 TCTTCCATTTGCCTAGGCGAA 59.719 47.619 33.74 33.74 46.98 4.70
2433 2818 3.961408 TCTAGGTAGTCAATCTGGAAGCC 59.039 47.826 0.00 0.00 0.00 4.35
2457 2842 7.816995 GCCCATTACTTCAAAATGATGTTTACA 59.183 33.333 4.51 0.00 36.38 2.41
2564 2951 5.333263 CGGTTCAATTTTCCTTTGCATGTTC 60.333 40.000 0.00 0.00 0.00 3.18
2673 3060 3.896648 ACATTCGAACACCAACATCAC 57.103 42.857 0.00 0.00 0.00 3.06
2691 3078 6.336566 ACATCACTATCTGACTGTGCTAAAG 58.663 40.000 6.91 0.00 0.00 1.85
2694 3081 5.126222 TCACTATCTGACTGTGCTAAAGGAG 59.874 44.000 6.91 0.00 0.00 3.69
2813 3200 0.315886 TTGAGGCTAAACGAGACGCA 59.684 50.000 0.00 0.00 41.99 5.24
2900 3290 3.402628 TGGAACCTACTGAGCTGAAAC 57.597 47.619 0.00 0.00 0.00 2.78
2984 3374 7.801716 TGTCTCTAGTTGCTGTTTATGTTTT 57.198 32.000 0.00 0.00 0.00 2.43
3001 3391 5.886715 TGTTTTTCATTCTGCAATGTTCG 57.113 34.783 0.00 0.00 40.47 3.95
3023 3413 0.801872 CGGACGATTGCAATTGTGGA 59.198 50.000 32.30 0.00 33.21 4.02
3038 3428 8.584157 TGCAATTGTGGAGTTACTGAAATTATT 58.416 29.630 7.40 0.00 0.00 1.40
3057 3448 9.787435 AAATTATTATAGGTAGGCGATTTGTCA 57.213 29.630 0.00 0.00 0.00 3.58
3064 3455 4.161565 AGGTAGGCGATTTGTCATAGTGAA 59.838 41.667 0.00 0.00 0.00 3.18
3065 3456 5.057149 GGTAGGCGATTTGTCATAGTGAAT 58.943 41.667 0.00 0.00 0.00 2.57
3076 3467 3.327757 GTCATAGTGAATATGGGGGCTGA 59.672 47.826 0.00 0.00 41.51 4.26
3123 3514 7.786178 AAGCCTTTTGGTTCATTACTTTTTC 57.214 32.000 0.00 0.00 42.99 2.29
3144 3539 9.834628 TTTTTCTAAACTCAACAAACACTACAG 57.165 29.630 0.00 0.00 0.00 2.74
3189 3584 5.340403 CGCATCAATACAAAACAGTGAACAG 59.660 40.000 0.00 0.00 0.00 3.16
3194 3589 6.372937 TCAATACAAAACAGTGAACAGACACA 59.627 34.615 0.00 0.00 42.45 3.72
3195 3590 4.419522 ACAAAACAGTGAACAGACACAC 57.580 40.909 0.00 0.00 42.45 3.82
3196 3591 4.072131 ACAAAACAGTGAACAGACACACT 58.928 39.130 0.00 0.00 46.32 3.55
3197 3592 5.242434 ACAAAACAGTGAACAGACACACTA 58.758 37.500 0.00 0.00 44.07 2.74
3198 3593 5.703592 ACAAAACAGTGAACAGACACACTAA 59.296 36.000 0.00 0.00 44.07 2.24
3199 3594 6.205853 ACAAAACAGTGAACAGACACACTAAA 59.794 34.615 0.00 0.00 44.07 1.85
3200 3595 6.811253 AAACAGTGAACAGACACACTAAAA 57.189 33.333 0.00 0.00 44.07 1.52
3201 3596 7.391148 AAACAGTGAACAGACACACTAAAAT 57.609 32.000 0.00 0.00 44.07 1.82
3202 3597 6.363577 ACAGTGAACAGACACACTAAAATG 57.636 37.500 0.00 0.00 44.07 2.32
3203 3598 5.880332 ACAGTGAACAGACACACTAAAATGT 59.120 36.000 0.00 0.00 44.07 2.71
3211 3606 3.559238 CACACTAAAATGTGGCCTGTC 57.441 47.619 3.32 0.00 45.21 3.51
3212 3607 2.884012 CACACTAAAATGTGGCCTGTCA 59.116 45.455 3.32 0.74 45.21 3.58
3213 3608 3.507233 CACACTAAAATGTGGCCTGTCAT 59.493 43.478 3.32 3.44 45.21 3.06
3214 3609 3.507233 ACACTAAAATGTGGCCTGTCATG 59.493 43.478 3.32 0.00 41.84 3.07
3215 3610 3.507233 CACTAAAATGTGGCCTGTCATGT 59.493 43.478 3.32 0.00 34.56 3.21
3216 3611 4.022068 CACTAAAATGTGGCCTGTCATGTT 60.022 41.667 3.32 10.12 34.56 2.71
3220 3615 5.743636 AAATGTGGCCTGTCATGTTATTT 57.256 34.783 3.32 0.00 0.00 1.40
3257 3669 9.646427 TTTTTAAACATTTGTATGGGCATACTC 57.354 29.630 0.00 0.00 43.04 2.59
3266 3678 0.264657 TGGGCATACTCCCTCTGCTA 59.735 55.000 0.12 0.00 46.67 3.49
3268 3680 1.768870 GGGCATACTCCCTCTGCTAAA 59.231 52.381 0.00 0.00 43.13 1.85
3320 3852 9.991388 GATATAGACTACATACGGACTGAAATC 57.009 37.037 0.00 0.00 0.00 2.17
3321 3853 7.818997 ATAGACTACATACGGACTGAAATCA 57.181 36.000 0.00 0.00 0.00 2.57
3322 3854 6.525578 AGACTACATACGGACTGAAATCAA 57.474 37.500 0.00 0.00 0.00 2.57
3342 3926 8.994429 AATCAATGAACAAACACACTAAAACA 57.006 26.923 0.00 0.00 0.00 2.83
3375 3959 8.731275 ATACATCCGATTCACAAAATGTTAGA 57.269 30.769 0.00 0.00 0.00 2.10
3377 3961 7.305474 ACATCCGATTCACAAAATGTTAGAAC 58.695 34.615 0.00 0.00 0.00 3.01
3378 3962 6.869315 TCCGATTCACAAAATGTTAGAACA 57.131 33.333 0.00 0.00 44.06 3.18
3406 4004 5.007724 CGGAGGGAGTATTTGTAAAATCAGC 59.992 44.000 0.00 0.00 0.00 4.26
3407 4005 5.299531 GGAGGGAGTATTTGTAAAATCAGCC 59.700 44.000 0.00 0.00 0.00 4.85
3430 4028 6.308282 GCCGATAATCAGTTAATTCTCTACCG 59.692 42.308 0.00 0.00 0.00 4.02
3431 4029 7.591165 CCGATAATCAGTTAATTCTCTACCGA 58.409 38.462 0.00 0.00 0.00 4.69
3432 4030 7.751348 CCGATAATCAGTTAATTCTCTACCGAG 59.249 40.741 0.00 0.00 38.67 4.63
3433 4031 8.291032 CGATAATCAGTTAATTCTCTACCGAGT 58.709 37.037 0.00 0.00 38.45 4.18
3434 4032 9.400638 GATAATCAGTTAATTCTCTACCGAGTG 57.599 37.037 0.00 0.00 38.45 3.51
3445 4044 5.817988 TCTCTACCGAGTGACAATATTTCG 58.182 41.667 0.48 0.48 38.45 3.46
3518 4136 4.743151 TGTAAATCAACGACACTGAGACAC 59.257 41.667 0.00 0.00 0.00 3.67
3519 4137 3.735237 AATCAACGACACTGAGACACT 57.265 42.857 0.00 0.00 0.00 3.55
3521 4139 1.002792 TCAACGACACTGAGACACTCG 60.003 52.381 0.00 0.00 32.35 4.18
3522 4140 0.317938 AACGACACTGAGACACTCGC 60.318 55.000 0.00 0.00 32.35 5.03
3528 4146 0.600557 ACTGAGACACTCGCTCCTTG 59.399 55.000 0.00 0.00 32.35 3.61
3529 4147 0.735632 CTGAGACACTCGCTCCTTGC 60.736 60.000 0.00 0.00 32.35 4.01
3584 4202 5.612725 AATTGATGGTTCAACTTTGGTGT 57.387 34.783 0.00 0.00 44.36 4.16
3654 4272 1.674441 CTGTACTCCATTGCATGCCTG 59.326 52.381 16.68 12.62 0.00 4.85
3659 4277 0.259356 TCCATTGCATGCCTGATCCA 59.741 50.000 16.68 0.00 0.00 3.41
3660 4278 1.116308 CCATTGCATGCCTGATCCAA 58.884 50.000 16.68 0.34 0.00 3.53
3661 4279 1.483004 CCATTGCATGCCTGATCCAAA 59.517 47.619 16.68 0.00 0.00 3.28
3662 4280 2.483013 CCATTGCATGCCTGATCCAAAG 60.483 50.000 16.68 0.00 0.00 2.77
3663 4281 2.219080 TTGCATGCCTGATCCAAAGA 57.781 45.000 16.68 0.00 0.00 2.52
3664 4282 2.447408 TGCATGCCTGATCCAAAGAT 57.553 45.000 16.68 0.00 34.57 2.40
3665 4283 2.028876 TGCATGCCTGATCCAAAGATG 58.971 47.619 16.68 0.00 30.90 2.90
3666 4284 2.304092 GCATGCCTGATCCAAAGATGA 58.696 47.619 6.36 0.00 30.90 2.92
3667 4285 2.691526 GCATGCCTGATCCAAAGATGAA 59.308 45.455 6.36 0.00 30.90 2.57
3668 4286 3.321111 GCATGCCTGATCCAAAGATGAAT 59.679 43.478 6.36 0.00 30.90 2.57
3669 4287 4.202223 GCATGCCTGATCCAAAGATGAATT 60.202 41.667 6.36 0.00 30.90 2.17
3670 4288 4.994907 TGCCTGATCCAAAGATGAATTG 57.005 40.909 0.00 0.00 30.90 2.32
3671 4289 3.131577 TGCCTGATCCAAAGATGAATTGC 59.868 43.478 0.00 0.00 30.90 3.56
3672 4290 3.492137 GCCTGATCCAAAGATGAATTGCC 60.492 47.826 0.00 0.00 30.90 4.52
3673 4291 3.958798 CCTGATCCAAAGATGAATTGCCT 59.041 43.478 0.00 0.00 30.90 4.75
3674 4292 4.404715 CCTGATCCAAAGATGAATTGCCTT 59.595 41.667 0.00 0.00 30.90 4.35
3675 4293 5.333299 TGATCCAAAGATGAATTGCCTTG 57.667 39.130 0.00 0.00 30.90 3.61
3676 4294 4.773674 TGATCCAAAGATGAATTGCCTTGT 59.226 37.500 0.00 0.00 30.90 3.16
3677 4295 5.246656 TGATCCAAAGATGAATTGCCTTGTT 59.753 36.000 0.00 0.00 30.90 2.83
3678 4296 5.138125 TCCAAAGATGAATTGCCTTGTTC 57.862 39.130 0.00 0.00 0.00 3.18
3679 4297 4.021192 TCCAAAGATGAATTGCCTTGTTCC 60.021 41.667 0.00 0.00 0.00 3.62
3680 4298 4.248058 CAAAGATGAATTGCCTTGTTCCC 58.752 43.478 0.00 0.00 0.00 3.97
3681 4299 2.094675 AGATGAATTGCCTTGTTCCCG 58.905 47.619 0.00 0.00 0.00 5.14
3682 4300 0.532115 ATGAATTGCCTTGTTCCCGC 59.468 50.000 0.00 0.00 0.00 6.13
3683 4301 0.825425 TGAATTGCCTTGTTCCCGCA 60.825 50.000 0.00 0.00 0.00 5.69
3684 4302 0.316841 GAATTGCCTTGTTCCCGCAA 59.683 50.000 0.00 0.00 45.77 4.85
3685 4303 0.755686 AATTGCCTTGTTCCCGCAAA 59.244 45.000 0.00 0.00 44.94 3.68
3686 4304 0.755686 ATTGCCTTGTTCCCGCAAAA 59.244 45.000 0.00 0.00 44.94 2.44
3687 4305 0.537188 TTGCCTTGTTCCCGCAAAAA 59.463 45.000 0.00 0.00 39.43 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 229 7.338800 AGCACGATGATCCTATTGAATTTTT 57.661 32.000 0.00 0.00 0.00 1.94
220 230 6.949352 AGCACGATGATCCTATTGAATTTT 57.051 33.333 0.00 0.00 0.00 1.82
221 231 6.148480 GCTAGCACGATGATCCTATTGAATTT 59.852 38.462 10.63 0.00 0.00 1.82
222 232 5.641209 GCTAGCACGATGATCCTATTGAATT 59.359 40.000 10.63 0.00 0.00 2.17
223 233 5.046735 AGCTAGCACGATGATCCTATTGAAT 60.047 40.000 18.83 0.00 0.00 2.57
229 247 2.554462 GTGAGCTAGCACGATGATCCTA 59.446 50.000 18.83 0.00 0.00 2.94
264 282 8.164070 GGTCTTATATTACATTGGAGTGGGAAT 58.836 37.037 0.00 0.00 0.00 3.01
559 608 0.036483 TGGATGCTGTCGCTGCTTTA 60.036 50.000 0.00 0.00 36.97 1.85
635 943 0.899720 CTGCATTGTTGGAAGCCCAT 59.100 50.000 0.00 0.00 43.12 4.00
724 1032 3.925090 CTAAGGTAGGCCGGGCGG 61.925 72.222 23.81 0.00 40.50 6.13
725 1033 1.963464 TTTCTAAGGTAGGCCGGGCG 61.963 60.000 23.81 6.41 40.50 6.13
726 1034 0.253894 TTTTCTAAGGTAGGCCGGGC 59.746 55.000 22.67 22.67 40.50 6.13
727 1035 2.092592 ACATTTTCTAAGGTAGGCCGGG 60.093 50.000 2.18 0.00 40.50 5.73
728 1036 2.943033 CACATTTTCTAAGGTAGGCCGG 59.057 50.000 0.00 0.00 40.50 6.13
729 1037 2.943033 CCACATTTTCTAAGGTAGGCCG 59.057 50.000 0.00 0.00 40.50 6.13
730 1038 3.288092 CCCACATTTTCTAAGGTAGGCC 58.712 50.000 0.00 0.00 0.00 5.19
731 1039 2.688446 GCCCACATTTTCTAAGGTAGGC 59.312 50.000 0.00 0.00 43.43 3.93
732 1040 3.963129 TGCCCACATTTTCTAAGGTAGG 58.037 45.455 0.00 0.00 31.29 3.18
733 1041 5.710099 TCTTTGCCCACATTTTCTAAGGTAG 59.290 40.000 0.00 0.00 0.00 3.18
734 1042 5.636123 TCTTTGCCCACATTTTCTAAGGTA 58.364 37.500 0.00 0.00 0.00 3.08
735 1043 4.479158 TCTTTGCCCACATTTTCTAAGGT 58.521 39.130 0.00 0.00 0.00 3.50
736 1044 5.047092 ACATCTTTGCCCACATTTTCTAAGG 60.047 40.000 0.00 0.00 0.00 2.69
737 1045 5.865552 CACATCTTTGCCCACATTTTCTAAG 59.134 40.000 0.00 0.00 0.00 2.18
738 1046 5.538053 TCACATCTTTGCCCACATTTTCTAA 59.462 36.000 0.00 0.00 0.00 2.10
739 1047 5.076182 TCACATCTTTGCCCACATTTTCTA 58.924 37.500 0.00 0.00 0.00 2.10
740 1048 3.896888 TCACATCTTTGCCCACATTTTCT 59.103 39.130 0.00 0.00 0.00 2.52
741 1049 4.255833 TCACATCTTTGCCCACATTTTC 57.744 40.909 0.00 0.00 0.00 2.29
742 1050 4.503643 CCTTCACATCTTTGCCCACATTTT 60.504 41.667 0.00 0.00 0.00 1.82
743 1051 3.007182 CCTTCACATCTTTGCCCACATTT 59.993 43.478 0.00 0.00 0.00 2.32
744 1052 2.564062 CCTTCACATCTTTGCCCACATT 59.436 45.455 0.00 0.00 0.00 2.71
745 1053 2.173519 CCTTCACATCTTTGCCCACAT 58.826 47.619 0.00 0.00 0.00 3.21
746 1054 1.619654 CCTTCACATCTTTGCCCACA 58.380 50.000 0.00 0.00 0.00 4.17
747 1055 0.244721 GCCTTCACATCTTTGCCCAC 59.755 55.000 0.00 0.00 0.00 4.61
748 1056 0.112995 AGCCTTCACATCTTTGCCCA 59.887 50.000 0.00 0.00 0.00 5.36
749 1057 0.529378 CAGCCTTCACATCTTTGCCC 59.471 55.000 0.00 0.00 0.00 5.36
750 1058 0.108945 GCAGCCTTCACATCTTTGCC 60.109 55.000 0.00 0.00 0.00 4.52
751 1059 0.886563 AGCAGCCTTCACATCTTTGC 59.113 50.000 0.00 0.00 0.00 3.68
752 1060 2.095364 GTCAGCAGCCTTCACATCTTTG 60.095 50.000 0.00 0.00 0.00 2.77
753 1061 2.157738 GTCAGCAGCCTTCACATCTTT 58.842 47.619 0.00 0.00 0.00 2.52
754 1062 1.612726 GGTCAGCAGCCTTCACATCTT 60.613 52.381 0.00 0.00 0.00 2.40
755 1063 0.035630 GGTCAGCAGCCTTCACATCT 60.036 55.000 0.00 0.00 0.00 2.90
756 1064 1.028868 GGGTCAGCAGCCTTCACATC 61.029 60.000 0.00 0.00 37.19 3.06
757 1065 1.001641 GGGTCAGCAGCCTTCACAT 60.002 57.895 0.00 0.00 37.19 3.21
758 1066 1.993701 TTGGGTCAGCAGCCTTCACA 61.994 55.000 0.00 0.00 41.28 3.58
759 1067 0.823356 TTTGGGTCAGCAGCCTTCAC 60.823 55.000 0.00 0.00 41.28 3.18
760 1068 0.106268 TTTTGGGTCAGCAGCCTTCA 60.106 50.000 0.00 0.00 41.28 3.02
761 1069 1.039856 TTTTTGGGTCAGCAGCCTTC 58.960 50.000 0.00 0.00 41.28 3.46
762 1070 0.752658 GTTTTTGGGTCAGCAGCCTT 59.247 50.000 0.00 0.00 41.28 4.35
763 1071 0.106015 AGTTTTTGGGTCAGCAGCCT 60.106 50.000 0.00 0.00 41.28 4.58
764 1072 0.315251 GAGTTTTTGGGTCAGCAGCC 59.685 55.000 0.00 0.00 41.06 4.85
765 1073 1.268079 GAGAGTTTTTGGGTCAGCAGC 59.732 52.381 0.00 0.00 0.00 5.25
766 1074 2.856222 AGAGAGTTTTTGGGTCAGCAG 58.144 47.619 0.00 0.00 0.00 4.24
767 1075 4.640771 ATAGAGAGTTTTTGGGTCAGCA 57.359 40.909 0.00 0.00 0.00 4.41
776 1084 3.333680 TCCAGGCCCAATAGAGAGTTTTT 59.666 43.478 0.00 0.00 0.00 1.94
796 1104 2.014857 GTTTCGGCCCACTTTATCTCC 58.985 52.381 0.00 0.00 0.00 3.71
799 1107 0.730840 CGGTTTCGGCCCACTTTATC 59.269 55.000 0.00 0.00 0.00 1.75
801 1109 4.382788 CGGTTTCGGCCCACTTTA 57.617 55.556 0.00 0.00 0.00 1.85
860 1175 3.541093 TTTTGCTTCTGCGCTGCGG 62.541 57.895 24.61 8.13 43.34 5.69
862 1177 2.370393 GCTTTTGCTTCTGCGCTGC 61.370 57.895 9.73 8.62 43.34 5.25
954 1269 1.751927 GGGAGCTCGAGGTCGGTAA 60.752 63.158 31.81 0.00 43.03 2.85
1136 1451 3.678529 GCACAGAAAAGAAGCAAAACCCA 60.679 43.478 0.00 0.00 0.00 4.51
1146 1461 0.303493 GACACGCGCACAGAAAAGAA 59.697 50.000 5.73 0.00 0.00 2.52
1198 1513 3.748071 ATCAGCTCTGCTCGTCGCG 62.748 63.158 0.00 0.00 43.27 5.87
1205 1520 2.780094 CCGGTCGATCAGCTCTGCT 61.780 63.158 0.00 0.00 40.77 4.24
1280 1595 2.974489 GACGTCGAACCCGCAGAGA 61.974 63.158 0.00 0.00 35.37 3.10
1328 1643 0.530744 TGGGCTGCACTTACTACTCG 59.469 55.000 2.50 0.00 0.00 4.18
1396 1711 2.447047 ACTTCACCCAAGATTCCAGGTT 59.553 45.455 0.00 0.00 35.82 3.50
1571 1955 3.122948 CGTTAATTGACGTGAACTCCTGG 59.877 47.826 14.09 0.00 38.19 4.45
1636 2020 2.096248 GGGAACACACAAACTCCAACA 58.904 47.619 0.00 0.00 0.00 3.33
1654 2038 5.374921 TCTACTCCGTATAAGACAAGAGGG 58.625 45.833 0.00 0.00 34.01 4.30
1656 2040 7.228906 TCCAATCTACTCCGTATAAGACAAGAG 59.771 40.741 0.00 0.00 35.26 2.85
1712 2096 2.715763 TACTTTGGGACAGAGGGAGT 57.284 50.000 0.00 0.00 45.63 3.85
1714 2098 2.637872 CACTTACTTTGGGACAGAGGGA 59.362 50.000 0.00 0.00 45.63 4.20
1715 2099 2.372172 ACACTTACTTTGGGACAGAGGG 59.628 50.000 0.00 0.00 45.63 4.30
1716 2100 3.325135 AGACACTTACTTTGGGACAGAGG 59.675 47.826 0.00 0.00 45.63 3.69
1717 2101 4.039245 TGAGACACTTACTTTGGGACAGAG 59.961 45.833 0.00 0.00 46.85 3.35
1718 2102 3.964688 TGAGACACTTACTTTGGGACAGA 59.035 43.478 0.00 0.00 42.39 3.41
1719 2103 4.058817 GTGAGACACTTACTTTGGGACAG 58.941 47.826 0.00 0.00 42.39 3.51
1720 2104 3.709653 AGTGAGACACTTACTTTGGGACA 59.290 43.478 0.00 0.00 42.59 4.02
1721 2105 4.202223 TGAGTGAGACACTTACTTTGGGAC 60.202 45.833 5.88 0.00 45.44 4.46
1722 2106 3.964688 TGAGTGAGACACTTACTTTGGGA 59.035 43.478 5.88 0.00 45.44 4.37
1723 2107 4.336889 TGAGTGAGACACTTACTTTGGG 57.663 45.455 5.88 0.00 45.44 4.12
1724 2108 5.360591 AGTTGAGTGAGACACTTACTTTGG 58.639 41.667 5.88 0.00 45.44 3.28
1725 2109 6.910536 AAGTTGAGTGAGACACTTACTTTG 57.089 37.500 18.35 0.00 45.44 2.77
1726 2110 6.879458 ACAAAGTTGAGTGAGACACTTACTTT 59.121 34.615 23.65 23.65 46.97 2.66
1727 2111 6.407202 ACAAAGTTGAGTGAGACACTTACTT 58.593 36.000 18.35 18.35 45.44 2.24
1728 2112 5.978814 ACAAAGTTGAGTGAGACACTTACT 58.021 37.500 5.88 9.45 45.44 2.24
1729 2113 6.979238 AGTACAAAGTTGAGTGAGACACTTAC 59.021 38.462 5.88 7.63 45.44 2.34
1730 2114 7.108841 AGTACAAAGTTGAGTGAGACACTTA 57.891 36.000 5.88 0.00 45.44 2.24
1731 2115 5.978814 AGTACAAAGTTGAGTGAGACACTT 58.021 37.500 5.88 0.00 45.44 3.16
1733 2117 6.979238 AGTTAGTACAAAGTTGAGTGAGACAC 59.021 38.462 0.00 0.00 34.10 3.67
1734 2118 7.068348 AGAGTTAGTACAAAGTTGAGTGAGACA 59.932 37.037 0.00 0.00 0.00 3.41
1735 2119 7.427214 AGAGTTAGTACAAAGTTGAGTGAGAC 58.573 38.462 0.00 0.00 0.00 3.36
1736 2120 7.584122 AGAGTTAGTACAAAGTTGAGTGAGA 57.416 36.000 0.00 0.00 0.00 3.27
1737 2121 8.569641 ACTAGAGTTAGTACAAAGTTGAGTGAG 58.430 37.037 0.00 0.00 38.35 3.51
1738 2122 8.461249 ACTAGAGTTAGTACAAAGTTGAGTGA 57.539 34.615 0.00 0.00 38.35 3.41
1763 2147 9.090692 GTGTCTCAACTTTAGTACAACTTTGTA 57.909 33.333 0.00 0.00 42.35 2.41
1764 2148 7.822822 AGTGTCTCAACTTTAGTACAACTTTGT 59.177 33.333 0.00 0.00 44.86 2.83
1765 2149 8.197988 AGTGTCTCAACTTTAGTACAACTTTG 57.802 34.615 0.00 0.00 0.00 2.77
1766 2150 8.788325 AAGTGTCTCAACTTTAGTACAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
1774 2158 9.832445 TCAGAAAATAAGTGTCTCAACTTTAGT 57.168 29.630 0.00 0.00 40.77 2.24
1776 2160 9.607988 TGTCAGAAAATAAGTGTCTCAACTTTA 57.392 29.630 0.00 0.00 40.77 1.85
1777 2161 8.506168 TGTCAGAAAATAAGTGTCTCAACTTT 57.494 30.769 0.00 0.00 40.77 2.66
1778 2162 7.987458 TCTGTCAGAAAATAAGTGTCTCAACTT 59.013 33.333 0.00 0.00 42.89 2.66
1779 2163 7.500992 TCTGTCAGAAAATAAGTGTCTCAACT 58.499 34.615 0.00 0.00 0.00 3.16
1780 2164 7.095439 CCTCTGTCAGAAAATAAGTGTCTCAAC 60.095 40.741 3.67 0.00 0.00 3.18
1781 2165 6.931281 CCTCTGTCAGAAAATAAGTGTCTCAA 59.069 38.462 3.67 0.00 0.00 3.02
1782 2166 6.459066 CCTCTGTCAGAAAATAAGTGTCTCA 58.541 40.000 3.67 0.00 0.00 3.27
1783 2167 5.872070 CCCTCTGTCAGAAAATAAGTGTCTC 59.128 44.000 3.67 0.00 0.00 3.36
1784 2168 5.544176 TCCCTCTGTCAGAAAATAAGTGTCT 59.456 40.000 3.67 0.00 0.00 3.41
1785 2169 5.794894 TCCCTCTGTCAGAAAATAAGTGTC 58.205 41.667 3.67 0.00 0.00 3.67
1786 2170 5.308237 ACTCCCTCTGTCAGAAAATAAGTGT 59.692 40.000 3.67 0.00 0.00 3.55
1787 2171 5.799213 ACTCCCTCTGTCAGAAAATAAGTG 58.201 41.667 3.67 0.00 0.00 3.16
1788 2172 6.497259 TGTACTCCCTCTGTCAGAAAATAAGT 59.503 38.462 3.67 6.22 0.00 2.24
1789 2173 6.936279 TGTACTCCCTCTGTCAGAAAATAAG 58.064 40.000 3.67 0.76 0.00 1.73
1790 2174 6.928348 TGTACTCCCTCTGTCAGAAAATAA 57.072 37.500 3.67 0.00 0.00 1.40
1791 2175 6.269077 TGTTGTACTCCCTCTGTCAGAAAATA 59.731 38.462 3.67 0.00 0.00 1.40
1792 2176 5.071788 TGTTGTACTCCCTCTGTCAGAAAAT 59.928 40.000 3.67 0.00 0.00 1.82
1793 2177 4.407621 TGTTGTACTCCCTCTGTCAGAAAA 59.592 41.667 3.67 0.00 0.00 2.29
1794 2178 3.964688 TGTTGTACTCCCTCTGTCAGAAA 59.035 43.478 3.67 0.00 0.00 2.52
1795 2179 3.321111 GTGTTGTACTCCCTCTGTCAGAA 59.679 47.826 3.67 0.00 0.00 3.02
1796 2180 2.891580 GTGTTGTACTCCCTCTGTCAGA 59.108 50.000 1.78 1.78 0.00 3.27
1797 2181 2.628178 TGTGTTGTACTCCCTCTGTCAG 59.372 50.000 0.00 0.00 0.00 3.51
1798 2182 2.673258 TGTGTTGTACTCCCTCTGTCA 58.327 47.619 0.00 0.00 0.00 3.58
1799 2183 3.555168 CCTTGTGTTGTACTCCCTCTGTC 60.555 52.174 0.00 0.00 0.00 3.51
1800 2184 2.368875 CCTTGTGTTGTACTCCCTCTGT 59.631 50.000 0.00 0.00 0.00 3.41
1801 2185 2.368875 ACCTTGTGTTGTACTCCCTCTG 59.631 50.000 0.00 0.00 0.00 3.35
1802 2186 2.690840 ACCTTGTGTTGTACTCCCTCT 58.309 47.619 0.00 0.00 0.00 3.69
1803 2187 3.487120 AACCTTGTGTTGTACTCCCTC 57.513 47.619 0.00 0.00 35.31 4.30
1878 2262 2.564771 TGGAAGTCAAGCAAGTGTCAG 58.435 47.619 0.00 0.00 0.00 3.51
1919 2303 6.991485 AACACAATGCTAAATCAGAAAACG 57.009 33.333 0.00 0.00 0.00 3.60
1933 2317 4.687018 TCAGCAAATCATGAAACACAATGC 59.313 37.500 0.00 3.27 0.00 3.56
2349 2734 6.095160 GGAAGATCCATCAATATCCAGCATTC 59.905 42.308 0.00 0.00 36.28 2.67
2375 2760 0.253044 TCAGCTTCGCCTAGGCAAAT 59.747 50.000 32.47 11.09 42.06 2.32
2381 2766 2.803451 CAACTACTCAGCTTCGCCTAG 58.197 52.381 0.00 0.00 0.00 3.02
2457 2842 6.826741 TGTAAGAAGCCAACAAAGAACTACTT 59.173 34.615 0.00 0.00 40.98 2.24
2691 3078 4.082026 ACAAAAATGTTATCAGCCTGCTCC 60.082 41.667 0.00 0.00 0.00 4.70
2694 3081 6.544038 AAAACAAAAATGTTATCAGCCTGC 57.456 33.333 0.00 0.00 0.00 4.85
2813 3200 5.760253 CACAATACAAGGTTCAGACTTCACT 59.240 40.000 0.00 0.00 0.00 3.41
2900 3290 1.226575 CAGCAATCGCAGGTGCATG 60.227 57.895 2.33 0.00 40.52 4.06
2943 3333 7.826252 ACTAGAGACATGTCACAATTAGCATTT 59.174 33.333 27.02 1.76 0.00 2.32
2984 3374 2.159430 CGGACGAACATTGCAGAATGAA 59.841 45.455 5.39 0.00 41.49 2.57
3001 3391 0.802494 ACAATTGCAATCGTCCGGAC 59.198 50.000 25.28 25.28 0.00 4.79
3023 3413 9.924650 CGCCTACCTATAATAATTTCAGTAACT 57.075 33.333 0.00 0.00 0.00 2.24
3038 3428 6.717997 TCACTATGACAAATCGCCTACCTATA 59.282 38.462 0.00 0.00 0.00 1.31
3039 3429 5.538813 TCACTATGACAAATCGCCTACCTAT 59.461 40.000 0.00 0.00 0.00 2.57
3040 3430 4.891168 TCACTATGACAAATCGCCTACCTA 59.109 41.667 0.00 0.00 0.00 3.08
3057 3448 3.602608 AGTCAGCCCCCATATTCACTAT 58.397 45.455 0.00 0.00 0.00 2.12
3064 3455 5.669798 ATTTTAGAAGTCAGCCCCCATAT 57.330 39.130 0.00 0.00 0.00 1.78
3065 3456 6.584471 TTATTTTAGAAGTCAGCCCCCATA 57.416 37.500 0.00 0.00 0.00 2.74
3076 3467 4.788617 TCCTCCCCAGCTTATTTTAGAAGT 59.211 41.667 0.00 0.00 0.00 3.01
3117 3508 9.834628 TGTAGTGTTTGTTGAGTTTAGAAAAAG 57.165 29.630 0.00 0.00 0.00 2.27
3123 3514 9.620660 AAAAACTGTAGTGTTTGTTGAGTTTAG 57.379 29.630 0.00 0.00 39.71 1.85
3166 3561 6.360681 GTCTGTTCACTGTTTTGTATTGATGC 59.639 38.462 0.00 0.00 0.00 3.91
3189 3584 2.884639 ACAGGCCACATTTTAGTGTGTC 59.115 45.455 5.01 0.00 46.21 3.67
3194 3589 3.766545 ACATGACAGGCCACATTTTAGT 58.233 40.909 5.01 0.00 0.00 2.24
3195 3590 4.789012 AACATGACAGGCCACATTTTAG 57.211 40.909 5.01 0.00 0.00 1.85
3196 3591 6.849085 AATAACATGACAGGCCACATTTTA 57.151 33.333 5.01 11.37 0.00 1.52
3197 3592 5.743636 AATAACATGACAGGCCACATTTT 57.256 34.783 5.01 9.54 0.00 1.82
3198 3593 5.743636 AAATAACATGACAGGCCACATTT 57.256 34.783 5.01 7.62 0.00 2.32
3199 3594 5.743636 AAAATAACATGACAGGCCACATT 57.256 34.783 5.01 0.00 0.00 2.71
3200 3595 5.743636 AAAAATAACATGACAGGCCACAT 57.256 34.783 5.01 4.77 0.00 3.21
3233 3645 7.777095 GGAGTATGCCCATACAAATGTTTAAA 58.223 34.615 17.82 0.00 44.58 1.52
3236 3648 5.852282 GGAGTATGCCCATACAAATGTTT 57.148 39.130 17.82 0.00 44.58 2.83
3294 3826 9.991388 GATTTCAGTCCGTATGTAGTCTATATC 57.009 37.037 0.00 0.00 0.00 1.63
3299 3831 6.525578 TTGATTTCAGTCCGTATGTAGTCT 57.474 37.500 0.00 0.00 0.00 3.24
3310 3842 6.198966 GTGTGTTTGTTCATTGATTTCAGTCC 59.801 38.462 0.00 0.00 0.00 3.85
3320 3852 8.183830 ACATGTTTTAGTGTGTTTGTTCATTG 57.816 30.769 0.00 0.00 0.00 2.82
3321 3853 8.770438 AACATGTTTTAGTGTGTTTGTTCATT 57.230 26.923 4.92 0.00 31.20 2.57
3322 3854 8.770438 AAACATGTTTTAGTGTGTTTGTTCAT 57.230 26.923 18.13 0.00 41.64 2.57
3350 3934 8.731275 TCTAACATTTTGTGAATCGGATGTAT 57.269 30.769 0.00 0.00 0.00 2.29
3367 3951 5.189145 ACTCCCTCCGTTATGTTCTAACATT 59.811 40.000 13.18 0.00 46.95 2.71
3369 3953 4.091549 ACTCCCTCCGTTATGTTCTAACA 58.908 43.478 0.00 0.00 44.06 2.41
3370 3954 4.732672 ACTCCCTCCGTTATGTTCTAAC 57.267 45.455 0.00 0.00 0.00 2.34
3371 3955 7.093201 ACAAATACTCCCTCCGTTATGTTCTAA 60.093 37.037 0.00 0.00 0.00 2.10
3373 3957 5.189145 ACAAATACTCCCTCCGTTATGTTCT 59.811 40.000 0.00 0.00 0.00 3.01
3375 3959 5.431179 ACAAATACTCCCTCCGTTATGTT 57.569 39.130 0.00 0.00 0.00 2.71
3377 3961 7.852971 TTTTACAAATACTCCCTCCGTTATG 57.147 36.000 0.00 0.00 0.00 1.90
3378 3962 8.269317 TGATTTTACAAATACTCCCTCCGTTAT 58.731 33.333 0.00 0.00 0.00 1.89
3379 3963 7.622713 TGATTTTACAAATACTCCCTCCGTTA 58.377 34.615 0.00 0.00 0.00 3.18
3380 3964 6.478129 TGATTTTACAAATACTCCCTCCGTT 58.522 36.000 0.00 0.00 0.00 4.44
3382 3966 5.007724 GCTGATTTTACAAATACTCCCTCCG 59.992 44.000 0.00 0.00 0.00 4.63
3383 3967 5.299531 GGCTGATTTTACAAATACTCCCTCC 59.700 44.000 0.00 0.00 0.00 4.30
3406 4004 7.591165 TCGGTAGAGAATTAACTGATTATCGG 58.409 38.462 0.00 0.00 33.60 4.18
3488 4087 9.825972 CTCAGTGTCGTTGATTTACAAAATTAT 57.174 29.630 0.00 0.00 40.36 1.28
3506 4105 0.109504 GGAGCGAGTGTCTCAGTGTC 60.110 60.000 0.00 0.00 32.38 3.67
3507 4106 0.538516 AGGAGCGAGTGTCTCAGTGT 60.539 55.000 0.00 0.00 32.38 3.55
3508 4107 0.600557 AAGGAGCGAGTGTCTCAGTG 59.399 55.000 0.00 0.00 32.38 3.66
3521 4139 4.026293 GCTCATTAGAAAAGCAAGGAGC 57.974 45.455 5.38 5.38 46.99 4.70
3522 4140 5.638783 CAAGCTCATTAGAAAAGCAAGGAG 58.361 41.667 0.00 0.00 38.51 3.69
3528 4146 4.431661 ACTGCAAGCTCATTAGAAAAGC 57.568 40.909 0.00 0.00 37.60 3.51
3529 4147 8.801715 TTTAAACTGCAAGCTCATTAGAAAAG 57.198 30.769 0.00 0.00 37.60 2.27
3584 4202 8.485578 AATTTCCCAACTTCATTAGGTTACAA 57.514 30.769 0.00 0.00 0.00 2.41
3654 4272 5.334724 ACAAGGCAATTCATCTTTGGATC 57.665 39.130 0.00 0.00 0.00 3.36
3659 4277 3.056607 CGGGAACAAGGCAATTCATCTTT 60.057 43.478 0.00 0.00 0.00 2.52
3660 4278 2.493278 CGGGAACAAGGCAATTCATCTT 59.507 45.455 0.00 0.00 0.00 2.40
3661 4279 2.094675 CGGGAACAAGGCAATTCATCT 58.905 47.619 0.00 0.00 0.00 2.90
3662 4280 1.469767 GCGGGAACAAGGCAATTCATC 60.470 52.381 0.00 0.00 0.00 2.92
3663 4281 0.532115 GCGGGAACAAGGCAATTCAT 59.468 50.000 0.00 0.00 0.00 2.57
3664 4282 0.825425 TGCGGGAACAAGGCAATTCA 60.825 50.000 0.00 0.00 33.01 2.57
3665 4283 0.316841 TTGCGGGAACAAGGCAATTC 59.683 50.000 0.00 0.00 41.34 2.17
3666 4284 0.755686 TTTGCGGGAACAAGGCAATT 59.244 45.000 0.00 0.00 45.09 2.32
3667 4285 0.755686 TTTTGCGGGAACAAGGCAAT 59.244 45.000 0.00 0.00 45.09 3.56
3668 4286 0.537188 TTTTTGCGGGAACAAGGCAA 59.463 45.000 0.00 0.00 44.20 4.52
3669 4287 2.202866 TTTTTGCGGGAACAAGGCA 58.797 47.368 0.00 0.00 34.35 4.75
3689 4307 6.550854 TCTGGTTCAGGACAATTCATCTTTTT 59.449 34.615 0.00 0.00 31.51 1.94
3690 4308 6.070656 TCTGGTTCAGGACAATTCATCTTTT 58.929 36.000 0.00 0.00 31.51 2.27


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

AutoCloner maintained by Alex Coulton.