Multiple sequence alignment - TraesCS6A01G007900

Loading Multiple Alignment...

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 TraesCS6A01G007900 chr6A 100.000 2412 0 0 1 2412 3237032 3239443 0.000000e+00 4455.0
1 TraesCS6A01G007900 chr6A 96.071 840 31 2 1 839 3205219 3206057 0.000000e+00 1367.0
2 TraesCS6A01G007900 chr6A 87.596 653 54 2 1143 1780 3206379 3207019 0.000000e+00 732.0
3 TraesCS6A01G007900 chr6A 95.252 337 11 2 766 1098 3206055 3206390 1.640000e-146 529.0
4 TraesCS6A01G007900 chr6B 94.013 1186 40 10 798 1968 8428541 8429710 0.000000e+00 1768.0
5 TraesCS6A01G007900 chr6B 92.941 85 6 0 377 461 617177288 617177204 9.050000e-25 124.0
6 TraesCS6A01G007900 chr7A 87.640 445 52 3 1967 2410 91672158 91671716 4.600000e-142 514.0
7 TraesCS6A01G007900 chr7A 89.855 69 6 1 1 68 690573460 690573392 1.190000e-13 87.9
8 TraesCS6A01G007900 chr3D 87.444 446 55 1 1967 2411 43563935 43563490 1.650000e-141 512.0
9 TraesCS6A01G007900 chr3D 85.746 449 58 6 1967 2412 532955225 532954780 1.010000e-128 470.0
10 TraesCS6A01G007900 chr3D 91.667 84 7 0 377 460 603938856 603938939 1.520000e-22 117.0
11 TraesCS6A01G007900 chr3D 94.444 72 3 1 1 72 602225653 602225723 2.540000e-20 110.0
12 TraesCS6A01G007900 chr3D 91.429 70 3 3 1 68 538905779 538905711 2.550000e-15 93.5
13 TraesCS6A01G007900 chr3D 91.111 45 4 0 474 518 609494980 609495024 7.200000e-06 62.1
14 TraesCS6A01G007900 chrUn 86.323 446 56 5 1967 2409 108525676 108526119 4.660000e-132 481.0
15 TraesCS6A01G007900 chrUn 85.235 447 52 6 1967 2410 70433331 70433766 4.730000e-122 448.0
16 TraesCS6A01G007900 chrUn 89.175 194 21 0 72 265 96392999 96393192 2.400000e-60 243.0
17 TraesCS6A01G007900 chr1A 84.354 441 65 3 1974 2411 264393015 264392576 1.710000e-116 429.0
18 TraesCS6A01G007900 chr1A 88.265 196 23 0 70 265 5769329 5769524 4.010000e-58 235.0
19 TraesCS6A01G007900 chr5A 84.055 439 67 3 1974 2411 221095409 221094973 1.030000e-113 420.0
20 TraesCS6A01G007900 chr2B 83.945 436 67 3 1979 2412 134382915 134382481 4.800000e-112 414.0
21 TraesCS6A01G007900 chr2B 87.685 203 25 0 70 272 14986347 14986145 1.110000e-58 237.0
22 TraesCS6A01G007900 chr2B 79.021 143 28 2 1974 2115 202921964 202922105 1.970000e-16 97.1
23 TraesCS6A01G007900 chr2B 90.476 63 4 1 459 521 719561189 719561129 5.530000e-12 82.4
24 TraesCS6A01G007900 chr5B 82.944 428 68 5 1967 2391 577131069 577131494 4.870000e-102 381.0
25 TraesCS6A01G007900 chr5B 87.000 200 24 2 70 268 48728509 48728311 8.680000e-55 224.0
26 TraesCS6A01G007900 chr5B 90.698 86 8 0 377 462 285935650 285935735 5.450000e-22 115.0
27 TraesCS6A01G007900 chr5B 92.754 69 2 3 2 68 122203570 122203503 1.970000e-16 97.1
28 TraesCS6A01G007900 chr5D 85.153 229 33 1 37 265 316323814 316324041 1.440000e-57 233.0
29 TraesCS6A01G007900 chr5D 90.526 95 6 2 377 468 52889694 52889600 3.260000e-24 122.0
30 TraesCS6A01G007900 chr5D 91.176 68 6 0 1 68 19744396 19744463 2.550000e-15 93.5
31 TraesCS6A01G007900 chr1D 87.692 195 23 1 72 265 237089201 237089395 2.410000e-55 226.0
32 TraesCS6A01G007900 chr1D 90.217 92 6 2 377 465 341527489 341527580 1.520000e-22 117.0
33 TraesCS6A01G007900 chr1B 86.667 195 25 1 72 265 342464499 342464693 5.220000e-52 215.0
34 TraesCS6A01G007900 chr2D 81.304 230 41 2 37 265 632772950 632773178 4.090000e-43 185.0
35 TraesCS6A01G007900 chr2D 89.855 69 5 2 1 68 82970401 82970334 1.190000e-13 87.9
36 TraesCS6A01G007900 chr7D 94.048 84 5 0 377 460 81911037 81910954 7.000000e-26 128.0
37 TraesCS6A01G007900 chr7B 91.011 89 8 0 377 465 213903153 213903241 1.170000e-23 121.0
38 TraesCS6A01G007900 chr4B 89.888 89 9 0 377 465 432817375 432817287 5.450000e-22 115.0
39 TraesCS6A01G007900 chr3B 91.667 72 5 1 1 72 809406981 809407051 5.490000e-17 99.0
40 TraesCS6A01G007900 chr3B 92.308 65 5 0 1 65 501969950 501970014 2.550000e-15 93.5
41 TraesCS6A01G007900 chr2A 96.970 33 1 0 489 521 286457726 286457694 3.350000e-04 56.5


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 TraesCS6A01G007900 chr6A 3237032 3239443 2411 False 4455 4455 100.000 1 2412 1 chr6A.!!$F1 2411
1 TraesCS6A01G007900 chr6A 3205219 3207019 1800 False 876 1367 92.973 1 1780 3 chr6A.!!$F2 1779
2 TraesCS6A01G007900 chr6B 8428541 8429710 1169 False 1768 1768 94.013 798 1968 1 chr6B.!!$F1 1170

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
225 226 0.460109 GTACCGGGCCGTAAACGAAT 60.46 55.0 26.32 1.97 43.02 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2380 0.028505 CTTCGCATTGATTCCTGCCG 59.971 55.0 3.54 0.0 34.89 5.69 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
35 36 8.787818 TGAAGGGTTTATATAGGGATGTCTTTT 58.212 33.333 0.00 0.00 0.00 2.27
100 101 2.743179 GCTAGCCTACCACCACCCC 61.743 68.421 2.29 0.00 0.00 4.95
141 142 2.173519 CAAACCGGGACTAGAGGTACA 58.826 52.381 6.32 0.00 37.26 2.90
146 147 1.101331 GGGACTAGAGGTACACCACG 58.899 60.000 0.00 0.00 38.89 4.94
164 165 2.104967 ACGAACCGGGACTAATGATGA 58.895 47.619 6.32 0.00 0.00 2.92
167 168 0.750850 ACCGGGACTAATGATGACCG 59.249 55.000 6.32 0.00 40.89 4.79
178 179 4.547905 ATGACCGCGCCGTAGACG 62.548 66.667 0.00 0.00 39.44 4.18
201 202 3.189606 TGGAACAGGGACTAATGGTCAT 58.810 45.455 0.00 0.00 46.16 3.06
206 207 7.162082 GGAACAGGGACTAATGGTCATATTAG 58.838 42.308 0.00 0.00 46.16 1.73
213 214 6.600882 ACTAATGGTCATATTAGTACCGGG 57.399 41.667 6.32 0.00 46.59 5.73
225 226 0.460109 GTACCGGGCCGTAAACGAAT 60.460 55.000 26.32 1.97 43.02 3.34
265 266 5.705609 ACGTAAGGTCGGTTTTCTACTAA 57.294 39.130 0.00 0.00 46.39 2.24
287 288 1.597461 CCCGACTCTTCCCCAAGAC 59.403 63.158 0.00 0.00 34.71 3.01
304 305 1.421268 AGACCTCAATCACCAGCACAA 59.579 47.619 0.00 0.00 0.00 3.33
412 413 7.119262 CCCAAAATAAGTGACTCGACTTTGTAT 59.881 37.037 0.00 0.00 37.38 2.29
603 604 3.085533 TCCCAAACATTGATTACCACGG 58.914 45.455 0.00 0.00 0.00 4.94
605 606 3.699038 CCCAAACATTGATTACCACGGAT 59.301 43.478 0.00 0.00 0.00 4.18
746 748 7.857456 AGGATATGTAACAATTAGTGTGTGGA 58.143 34.615 0.00 0.00 40.60 4.02
865 942 3.128375 CACAACTTGGTGGTGGCC 58.872 61.111 0.00 0.00 37.78 5.36
949 1026 4.097286 CAGGGCAAGTAGAAGTACTCTCTC 59.903 50.000 9.83 0.00 38.66 3.20
976 1053 4.989875 AGTATGGCAATCCTCAATAGCT 57.010 40.909 0.00 0.00 0.00 3.32
987 1064 5.707242 TCCTCAATAGCTATACAAGGACG 57.293 43.478 20.04 5.40 0.00 4.79
1042 1119 2.799412 GTCATGATGATGTCCTCTTCGC 59.201 50.000 0.00 0.00 32.09 4.70
1087 1224 4.406456 TGAAGGTATGCAACAATGTCCTT 58.594 39.130 2.00 2.00 36.67 3.36
1088 1225 4.218200 TGAAGGTATGCAACAATGTCCTTG 59.782 41.667 6.53 0.00 40.90 3.61
1100 1237 6.780706 ACAATGTCCTTGTTTTACTCTACG 57.219 37.500 0.00 0.00 45.98 3.51
1101 1238 6.518493 ACAATGTCCTTGTTTTACTCTACGA 58.482 36.000 0.00 0.00 45.98 3.43
1102 1239 7.159372 ACAATGTCCTTGTTTTACTCTACGAT 58.841 34.615 0.00 0.00 45.98 3.73
1103 1240 7.660208 ACAATGTCCTTGTTTTACTCTACGATT 59.340 33.333 0.00 0.00 45.98 3.34
1104 1241 8.504005 CAATGTCCTTGTTTTACTCTACGATTT 58.496 33.333 0.00 0.00 0.00 2.17
1105 1242 7.647907 TGTCCTTGTTTTACTCTACGATTTC 57.352 36.000 0.00 0.00 0.00 2.17
1106 1243 6.647895 TGTCCTTGTTTTACTCTACGATTTCC 59.352 38.462 0.00 0.00 0.00 3.13
1107 1244 6.647895 GTCCTTGTTTTACTCTACGATTTCCA 59.352 38.462 0.00 0.00 0.00 3.53
1108 1245 7.172019 GTCCTTGTTTTACTCTACGATTTCCAA 59.828 37.037 0.00 0.00 0.00 3.53
1109 1246 7.716123 TCCTTGTTTTACTCTACGATTTCCAAA 59.284 33.333 0.00 0.00 0.00 3.28
1110 1247 7.801783 CCTTGTTTTACTCTACGATTTCCAAAC 59.198 37.037 0.00 0.00 0.00 2.93
1111 1248 7.789273 TGTTTTACTCTACGATTTCCAAACA 57.211 32.000 0.00 0.00 31.04 2.83
1112 1249 8.385898 TGTTTTACTCTACGATTTCCAAACAT 57.614 30.769 0.00 0.00 29.08 2.71
1113 1250 8.286800 TGTTTTACTCTACGATTTCCAAACATG 58.713 33.333 0.00 0.00 29.08 3.21
1114 1251 6.978343 TTACTCTACGATTTCCAAACATGG 57.022 37.500 0.00 0.00 0.00 3.66
1115 1252 5.160607 ACTCTACGATTTCCAAACATGGA 57.839 39.130 0.00 0.00 35.93 3.41
1116 1253 5.556915 ACTCTACGATTTCCAAACATGGAA 58.443 37.500 6.20 6.20 45.37 3.53
1128 1265 8.572855 TTCCAAACATGGAAAAACAAAAATCT 57.427 26.923 7.80 0.00 44.21 2.40
1129 1266 9.672673 TTCCAAACATGGAAAAACAAAAATCTA 57.327 25.926 7.80 0.00 44.21 1.98
1130 1267 9.323985 TCCAAACATGGAAAAACAAAAATCTAG 57.676 29.630 0.00 0.00 34.56 2.43
1131 1268 8.069574 CCAAACATGGAAAAACAAAAATCTAGC 58.930 33.333 0.00 0.00 0.00 3.42
1132 1269 8.829612 CAAACATGGAAAAACAAAAATCTAGCT 58.170 29.630 0.00 0.00 0.00 3.32
1134 1271 9.696917 AACATGGAAAAACAAAAATCTAGCTAG 57.303 29.630 15.01 15.01 0.00 3.42
1135 1272 7.814587 ACATGGAAAAACAAAAATCTAGCTAGC 59.185 33.333 16.35 6.62 0.00 3.42
1136 1273 7.524717 TGGAAAAACAAAAATCTAGCTAGCT 57.475 32.000 23.12 23.12 0.00 3.32
1137 1274 8.630054 TGGAAAAACAAAAATCTAGCTAGCTA 57.370 30.769 22.85 22.85 0.00 3.32
1138 1275 9.243105 TGGAAAAACAAAAATCTAGCTAGCTAT 57.757 29.630 24.36 9.59 0.00 2.97
1231 1371 0.240945 GTTGGGAGTGCCGTCAATTG 59.759 55.000 0.00 0.00 33.83 2.32
1248 1388 2.976350 GCTGCACTGCACTGCTCA 60.976 61.111 17.53 0.00 38.07 4.26
1249 1389 2.549198 GCTGCACTGCACTGCTCAA 61.549 57.895 17.53 0.00 38.07 3.02
1294 1434 5.068591 AGTTTTAAAACATGGTGGAGGTCAC 59.931 40.000 28.03 1.25 42.07 3.67
1423 1578 3.787785 TGGTGCATGAAATCATTGCATC 58.212 40.909 17.32 17.15 40.06 3.91
1517 1672 6.908825 TCATACATACTCCAAGCAAACAAAC 58.091 36.000 0.00 0.00 0.00 2.93
1568 1723 7.442969 TGTTCGACACCTGATTAACAATACTTT 59.557 33.333 0.00 0.00 0.00 2.66
1608 1764 4.228824 TGAAGTTATTAGGCCTATCGGGT 58.771 43.478 14.74 0.00 37.43 5.28
1659 1815 1.580059 ATCTGGGAGCGAAACCCTAA 58.420 50.000 11.97 2.73 46.82 2.69
1716 1872 4.752879 GGCCGTTGGTCTGCGCTA 62.753 66.667 9.73 0.00 0.00 4.26
1737 1893 2.034687 AGCAAAGACCGCATGGCT 59.965 55.556 0.00 0.00 39.70 4.75
1739 1895 1.153958 GCAAAGACCGCATGGCTTC 60.154 57.895 0.00 0.00 39.70 3.86
1830 1986 5.140454 AGTTTCTTGGCTGGTTGATAAGTT 58.860 37.500 0.00 0.00 0.00 2.66
1847 2003 3.587797 AGTTGCTTGAATGCCTGAATG 57.412 42.857 0.00 0.00 0.00 2.67
1858 2015 1.447838 CCTGAATGACCACCGACGG 60.448 63.158 13.61 13.61 0.00 4.79
1894 2051 4.973168 AGAAGCCATCTGTTTTGTCTGTA 58.027 39.130 0.00 0.00 36.88 2.74
1902 2059 6.441274 CATCTGTTTTGTCTGTAGTGCAAAT 58.559 36.000 0.00 0.00 33.00 2.32
1929 2086 3.052944 CCCCAATGACCAATCTTCCCTTA 60.053 47.826 0.00 0.00 0.00 2.69
1950 2107 9.284968 CCCTTATACTGTTCAATAAACCTATGG 57.715 37.037 0.00 0.00 37.03 2.74
1964 2121 8.897872 ATAAACCTATGGTCCAAAGTATAACG 57.102 34.615 0.00 0.00 33.12 3.18
1968 2125 7.850193 ACCTATGGTCCAAAGTATAACGTTTA 58.150 34.615 5.91 0.00 0.00 2.01
1969 2126 8.488668 ACCTATGGTCCAAAGTATAACGTTTAT 58.511 33.333 5.91 0.73 0.00 1.40
1970 2127 9.985730 CCTATGGTCCAAAGTATAACGTTTATA 57.014 33.333 5.91 0.00 0.00 0.98
1982 2139 8.738106 AGTATAACGTTTATAGTATCTCCAGCC 58.262 37.037 5.91 0.00 0.00 4.85
1983 2140 4.500603 ACGTTTATAGTATCTCCAGCCG 57.499 45.455 0.00 0.00 0.00 5.52
1984 2141 3.243336 CGTTTATAGTATCTCCAGCCGC 58.757 50.000 0.00 0.00 0.00 6.53
1985 2142 3.243336 GTTTATAGTATCTCCAGCCGCG 58.757 50.000 0.00 0.00 0.00 6.46
1986 2143 2.195741 TATAGTATCTCCAGCCGCGT 57.804 50.000 4.92 0.00 0.00 6.01
1987 2144 0.882474 ATAGTATCTCCAGCCGCGTC 59.118 55.000 4.92 0.00 0.00 5.19
1988 2145 1.170919 TAGTATCTCCAGCCGCGTCC 61.171 60.000 4.92 0.00 0.00 4.79
1989 2146 2.123854 TATCTCCAGCCGCGTCCT 60.124 61.111 4.92 0.00 0.00 3.85
1990 2147 2.194212 TATCTCCAGCCGCGTCCTC 61.194 63.158 4.92 0.00 0.00 3.71
1991 2148 2.904178 TATCTCCAGCCGCGTCCTCA 62.904 60.000 4.92 0.00 0.00 3.86
1992 2149 4.069232 CTCCAGCCGCGTCCTCAA 62.069 66.667 4.92 0.00 0.00 3.02
1993 2150 4.373116 TCCAGCCGCGTCCTCAAC 62.373 66.667 4.92 0.00 0.00 3.18
1994 2151 4.680237 CCAGCCGCGTCCTCAACA 62.680 66.667 4.92 0.00 0.00 3.33
1995 2152 3.114616 CAGCCGCGTCCTCAACAG 61.115 66.667 4.92 0.00 0.00 3.16
1996 2153 4.379243 AGCCGCGTCCTCAACAGG 62.379 66.667 4.92 0.00 42.01 4.00
2000 2157 4.021925 GCGTCCTCAACAGGCCCT 62.022 66.667 0.00 0.00 40.12 5.19
2001 2158 2.266055 CGTCCTCAACAGGCCCTC 59.734 66.667 0.00 0.00 40.12 4.30
2002 2159 2.671682 GTCCTCAACAGGCCCTCC 59.328 66.667 0.00 0.00 40.12 4.30
2003 2160 2.610859 TCCTCAACAGGCCCTCCC 60.611 66.667 0.00 0.00 40.12 4.30
2004 2161 3.732849 CCTCAACAGGCCCTCCCC 61.733 72.222 0.00 0.00 30.98 4.81
2005 2162 2.935481 CTCAACAGGCCCTCCCCA 60.935 66.667 0.00 0.00 0.00 4.96
2006 2163 2.935481 TCAACAGGCCCTCCCCAG 60.935 66.667 0.00 0.00 0.00 4.45
2007 2164 2.935481 CAACAGGCCCTCCCCAGA 60.935 66.667 0.00 0.00 0.00 3.86
2008 2165 2.936032 AACAGGCCCTCCCCAGAC 60.936 66.667 0.00 0.00 0.00 3.51
2011 2168 4.658786 AGGCCCTCCCCAGACGTT 62.659 66.667 0.00 0.00 0.00 3.99
2012 2169 3.647771 GGCCCTCCCCAGACGTTT 61.648 66.667 0.00 0.00 0.00 3.60
2013 2170 2.434774 GCCCTCCCCAGACGTTTT 59.565 61.111 0.00 0.00 0.00 2.43
2014 2171 1.228459 GCCCTCCCCAGACGTTTTT 60.228 57.895 0.00 0.00 0.00 1.94
2015 2172 1.241990 GCCCTCCCCAGACGTTTTTC 61.242 60.000 0.00 0.00 0.00 2.29
2016 2173 0.400594 CCCTCCCCAGACGTTTTTCT 59.599 55.000 0.00 0.00 0.00 2.52
2017 2174 1.610886 CCCTCCCCAGACGTTTTTCTC 60.611 57.143 0.00 0.00 0.00 2.87
2018 2175 1.429463 CTCCCCAGACGTTTTTCTCG 58.571 55.000 0.00 0.00 0.00 4.04
2019 2176 0.601841 TCCCCAGACGTTTTTCTCGC 60.602 55.000 0.00 0.00 0.00 5.03
2020 2177 1.491563 CCCAGACGTTTTTCTCGCG 59.508 57.895 0.00 0.00 0.00 5.87
2021 2178 1.154654 CCAGACGTTTTTCTCGCGC 60.155 57.895 0.00 0.00 0.00 6.86
2022 2179 1.154654 CAGACGTTTTTCTCGCGCC 60.155 57.895 0.00 0.00 0.00 6.53
2023 2180 2.202008 GACGTTTTTCTCGCGCCG 60.202 61.111 0.00 0.00 0.00 6.46
2024 2181 3.624831 GACGTTTTTCTCGCGCCGG 62.625 63.158 0.00 0.00 0.00 6.13
2026 2183 4.020378 GTTTTTCTCGCGCCGGCA 62.020 61.111 28.98 5.90 39.92 5.69
2027 2184 3.053291 TTTTTCTCGCGCCGGCAT 61.053 55.556 28.98 0.00 39.92 4.40
2028 2185 3.034370 TTTTTCTCGCGCCGGCATC 62.034 57.895 28.98 16.58 39.92 3.91
2034 2191 4.412270 CGCGCCGGCATCCAAAAA 62.412 61.111 28.98 0.00 39.92 1.94
2035 2192 2.184066 GCGCCGGCATCCAAAAAT 59.816 55.556 28.98 0.00 39.62 1.82
2036 2193 1.878069 GCGCCGGCATCCAAAAATC 60.878 57.895 28.98 0.00 39.62 2.17
2037 2194 1.586042 CGCCGGCATCCAAAAATCG 60.586 57.895 28.98 0.37 0.00 3.34
2038 2195 1.226945 GCCGGCATCCAAAAATCGG 60.227 57.895 24.80 0.00 40.33 4.18
2039 2196 1.226945 CCGGCATCCAAAAATCGGC 60.227 57.895 0.00 0.00 0.00 5.54
2040 2197 1.226945 CGGCATCCAAAAATCGGCC 60.227 57.895 0.00 0.00 38.04 6.13
2041 2198 1.143838 GGCATCCAAAAATCGGCCC 59.856 57.895 0.00 0.00 35.42 5.80
2042 2199 1.612395 GGCATCCAAAAATCGGCCCA 61.612 55.000 0.00 0.00 35.42 5.36
2043 2200 0.460109 GCATCCAAAAATCGGCCCAC 60.460 55.000 0.00 0.00 0.00 4.61
2044 2201 1.185315 CATCCAAAAATCGGCCCACT 58.815 50.000 0.00 0.00 0.00 4.00
2045 2202 1.134946 CATCCAAAAATCGGCCCACTC 59.865 52.381 0.00 0.00 0.00 3.51
2046 2203 0.958382 TCCAAAAATCGGCCCACTCG 60.958 55.000 0.00 0.00 0.00 4.18
2047 2204 1.154035 CAAAAATCGGCCCACTCGC 60.154 57.895 0.00 0.00 0.00 5.03
2048 2205 2.686816 AAAAATCGGCCCACTCGCG 61.687 57.895 0.00 0.00 0.00 5.87
2049 2206 3.894547 AAAATCGGCCCACTCGCGT 62.895 57.895 5.77 0.00 0.00 6.01
2050 2207 4.814294 AATCGGCCCACTCGCGTC 62.814 66.667 5.77 0.00 0.00 5.19
2055 2212 4.803426 GCCCACTCGCGTCTCCAG 62.803 72.222 5.77 0.00 0.00 3.86
2056 2213 4.135153 CCCACTCGCGTCTCCAGG 62.135 72.222 5.77 0.78 0.00 4.45
2057 2214 3.062466 CCACTCGCGTCTCCAGGA 61.062 66.667 5.77 0.00 0.00 3.86
2058 2215 2.487428 CACTCGCGTCTCCAGGAG 59.513 66.667 10.70 10.70 0.00 3.69
2059 2216 3.444805 ACTCGCGTCTCCAGGAGC 61.445 66.667 12.26 6.22 0.00 4.70
2060 2217 4.200283 CTCGCGTCTCCAGGAGCC 62.200 72.222 12.26 0.00 0.00 4.70
2064 2221 3.382832 CGTCTCCAGGAGCCCGTT 61.383 66.667 12.26 0.00 0.00 4.44
2065 2222 2.943978 CGTCTCCAGGAGCCCGTTT 61.944 63.158 12.26 0.00 0.00 3.60
2066 2223 1.375326 GTCTCCAGGAGCCCGTTTT 59.625 57.895 12.26 0.00 0.00 2.43
2067 2224 0.250770 GTCTCCAGGAGCCCGTTTTT 60.251 55.000 12.26 0.00 0.00 1.94
2068 2225 0.250727 TCTCCAGGAGCCCGTTTTTG 60.251 55.000 12.26 0.00 0.00 2.44
2069 2226 0.250727 CTCCAGGAGCCCGTTTTTGA 60.251 55.000 2.60 0.00 0.00 2.69
2070 2227 0.536460 TCCAGGAGCCCGTTTTTGAC 60.536 55.000 0.00 0.00 0.00 3.18
2071 2228 1.524008 CCAGGAGCCCGTTTTTGACC 61.524 60.000 0.00 0.00 0.00 4.02
2072 2229 1.599797 AGGAGCCCGTTTTTGACCG 60.600 57.895 0.00 0.00 0.00 4.79
2073 2230 2.622962 GGAGCCCGTTTTTGACCGG 61.623 63.158 0.00 0.00 43.82 5.28
2075 2232 3.292159 GCCCGTTTTTGACCGGCT 61.292 61.111 0.00 0.00 45.63 5.52
2076 2233 2.852180 GCCCGTTTTTGACCGGCTT 61.852 57.895 0.00 0.00 45.63 4.35
2077 2234 1.007849 CCCGTTTTTGACCGGCTTG 60.008 57.895 0.00 0.00 42.87 4.01
2078 2235 1.007849 CCGTTTTTGACCGGCTTGG 60.008 57.895 0.00 0.00 46.41 3.61
2079 2236 1.007849 CGTTTTTGACCGGCTTGGG 60.008 57.895 0.00 0.00 44.64 4.12
2080 2237 1.365999 GTTTTTGACCGGCTTGGGG 59.634 57.895 0.00 0.00 44.64 4.96
2081 2238 2.503382 TTTTTGACCGGCTTGGGGC 61.503 57.895 0.00 0.00 44.64 5.80
2089 2246 2.578664 GGCTTGGGGCGAAATTGG 59.421 61.111 0.00 0.00 42.94 3.16
2090 2247 2.125552 GCTTGGGGCGAAATTGGC 60.126 61.111 0.00 0.00 0.00 4.52
2091 2248 2.181525 CTTGGGGCGAAATTGGCG 59.818 61.111 0.00 0.00 34.76 5.69
2098 2255 4.474846 CGAAATTGGCGCCGGTGG 62.475 66.667 23.90 4.68 0.00 4.61
2099 2256 3.059386 GAAATTGGCGCCGGTGGA 61.059 61.111 23.90 0.00 0.00 4.02
2100 2257 3.336715 GAAATTGGCGCCGGTGGAC 62.337 63.158 23.90 5.19 0.00 4.02
2109 2266 3.943691 CCGGTGGACCCAAACGGA 61.944 66.667 21.63 0.00 45.46 4.69
2110 2267 2.111460 CGGTGGACCCAAACGGAA 59.889 61.111 6.53 0.00 34.64 4.30
2111 2268 2.255881 CGGTGGACCCAAACGGAAC 61.256 63.158 6.53 0.00 34.64 3.62
2112 2269 1.900016 GGTGGACCCAAACGGAACC 60.900 63.158 0.00 0.00 34.64 3.62
2113 2270 1.900016 GTGGACCCAAACGGAACCC 60.900 63.158 0.00 0.00 34.64 4.11
2155 2312 2.750237 GCCGGGGCGAGACATTTT 60.750 61.111 2.18 0.00 0.00 1.82
2156 2313 3.051392 GCCGGGGCGAGACATTTTG 62.051 63.158 2.18 0.00 0.00 2.44
2157 2314 2.406616 CCGGGGCGAGACATTTTGG 61.407 63.158 0.00 0.00 0.00 3.28
2158 2315 2.885113 GGGGCGAGACATTTTGGC 59.115 61.111 0.00 0.00 0.00 4.52
2159 2316 2.485122 GGGCGAGACATTTTGGCG 59.515 61.111 0.00 0.00 0.00 5.69
2160 2317 2.202479 GGCGAGACATTTTGGCGC 60.202 61.111 0.00 0.00 46.20 6.53
2164 2321 3.765349 GAGACATTTTGGCGCGAAA 57.235 47.368 13.91 13.91 0.00 3.46
2165 2322 1.606606 GAGACATTTTGGCGCGAAAG 58.393 50.000 17.08 9.77 0.00 2.62
2177 2334 2.504032 CGAAAGCGGATGGGCCTA 59.496 61.111 4.53 0.00 0.00 3.93
2178 2335 1.887707 CGAAAGCGGATGGGCCTAC 60.888 63.158 4.53 0.00 0.00 3.18
2179 2336 1.526225 GAAAGCGGATGGGCCTACC 60.526 63.158 4.53 7.32 40.81 3.18
2184 2341 3.557290 GGATGGGCCTACCGGGTC 61.557 72.222 6.32 0.00 44.64 4.46
2185 2342 2.766651 GATGGGCCTACCGGGTCA 60.767 66.667 6.32 0.00 42.62 4.02
2186 2343 2.768344 ATGGGCCTACCGGGTCAG 60.768 66.667 6.32 0.00 42.62 3.51
2190 2347 4.509737 GCCTACCGGGTCAGCGAC 62.510 72.222 6.32 0.79 37.43 5.19
2191 2348 3.066190 CCTACCGGGTCAGCGACA 61.066 66.667 6.32 0.00 33.68 4.35
2192 2349 2.181021 CTACCGGGTCAGCGACAC 59.819 66.667 6.32 6.05 33.68 3.67
2205 2362 3.173240 GACACGCCGCTTCGTCTC 61.173 66.667 0.00 0.00 41.21 3.36
2206 2363 4.719369 ACACGCCGCTTCGTCTCC 62.719 66.667 0.00 0.00 41.21 3.71
2209 2366 4.856607 CGCCGCTTCGTCTCCCTC 62.857 72.222 0.00 0.00 0.00 4.30
2210 2367 3.760035 GCCGCTTCGTCTCCCTCA 61.760 66.667 0.00 0.00 0.00 3.86
2211 2368 3.082579 GCCGCTTCGTCTCCCTCAT 62.083 63.158 0.00 0.00 0.00 2.90
2212 2369 1.066587 CCGCTTCGTCTCCCTCATC 59.933 63.158 0.00 0.00 0.00 2.92
2213 2370 1.298713 CGCTTCGTCTCCCTCATCG 60.299 63.158 0.00 0.00 0.00 3.84
2214 2371 1.590259 GCTTCGTCTCCCTCATCGC 60.590 63.158 0.00 0.00 0.00 4.58
2215 2372 1.066587 CTTCGTCTCCCTCATCGCC 59.933 63.158 0.00 0.00 0.00 5.54
2216 2373 1.379977 TTCGTCTCCCTCATCGCCT 60.380 57.895 0.00 0.00 0.00 5.52
2217 2374 1.384989 TTCGTCTCCCTCATCGCCTC 61.385 60.000 0.00 0.00 0.00 4.70
2218 2375 2.725008 GTCTCCCTCATCGCCTCG 59.275 66.667 0.00 0.00 0.00 4.63
2219 2376 2.519541 TCTCCCTCATCGCCTCGG 60.520 66.667 0.00 0.00 0.00 4.63
2220 2377 2.835431 CTCCCTCATCGCCTCGGT 60.835 66.667 0.00 0.00 0.00 4.69
2221 2378 2.363795 TCCCTCATCGCCTCGGTT 60.364 61.111 0.00 0.00 0.00 4.44
2222 2379 2.107141 CCCTCATCGCCTCGGTTC 59.893 66.667 0.00 0.00 0.00 3.62
2223 2380 2.107141 CCTCATCGCCTCGGTTCC 59.893 66.667 0.00 0.00 0.00 3.62
2224 2381 2.278857 CTCATCGCCTCGGTTCCG 60.279 66.667 4.74 4.74 0.00 4.30
2225 2382 3.774959 CTCATCGCCTCGGTTCCGG 62.775 68.421 11.37 0.00 0.00 5.14
2238 2395 4.240881 TCCGGCAGGAATCAATGC 57.759 55.556 1.89 1.61 45.12 3.56
2239 2396 1.819208 TCCGGCAGGAATCAATGCG 60.819 57.895 1.89 0.89 45.12 4.73
2240 2397 1.819208 CCGGCAGGAATCAATGCGA 60.819 57.895 0.00 0.00 43.49 5.10
2241 2398 1.375853 CCGGCAGGAATCAATGCGAA 61.376 55.000 0.00 0.00 43.49 4.70
2242 2399 0.028505 CGGCAGGAATCAATGCGAAG 59.971 55.000 4.06 0.00 43.49 3.79
2243 2400 0.383231 GGCAGGAATCAATGCGAAGG 59.617 55.000 4.06 0.00 43.49 3.46
2244 2401 0.248784 GCAGGAATCAATGCGAAGGC 60.249 55.000 0.00 0.00 40.52 4.35
2245 2402 1.386533 CAGGAATCAATGCGAAGGCT 58.613 50.000 0.00 0.00 40.82 4.58
2246 2403 2.564771 CAGGAATCAATGCGAAGGCTA 58.435 47.619 0.00 0.00 40.82 3.93
2247 2404 2.289002 CAGGAATCAATGCGAAGGCTAC 59.711 50.000 0.00 0.00 40.82 3.58
2248 2405 1.604278 GGAATCAATGCGAAGGCTACC 59.396 52.381 0.00 0.00 40.82 3.18
2249 2406 2.288666 GAATCAATGCGAAGGCTACCA 58.711 47.619 0.00 0.00 40.82 3.25
2250 2407 1.668419 ATCAATGCGAAGGCTACCAC 58.332 50.000 0.00 0.00 40.82 4.16
2251 2408 0.739462 TCAATGCGAAGGCTACCACG 60.739 55.000 0.00 0.00 40.82 4.94
2252 2409 2.106683 AATGCGAAGGCTACCACGC 61.107 57.895 16.91 16.91 45.61 5.34
2253 2410 2.521958 AATGCGAAGGCTACCACGCT 62.522 55.000 21.56 10.14 45.61 5.07
2254 2411 3.188786 GCGAAGGCTACCACGCTG 61.189 66.667 16.63 0.00 43.58 5.18
2255 2412 3.188786 CGAAGGCTACCACGCTGC 61.189 66.667 0.00 0.00 0.00 5.25
2256 2413 2.820037 GAAGGCTACCACGCTGCC 60.820 66.667 0.00 0.00 46.42 4.85
2273 2430 4.680237 CGTGCCGGTCAGCCTCAA 62.680 66.667 1.90 0.00 0.00 3.02
2274 2431 2.045926 GTGCCGGTCAGCCTCAAT 60.046 61.111 1.90 0.00 0.00 2.57
2275 2432 1.675641 GTGCCGGTCAGCCTCAATT 60.676 57.895 1.90 0.00 0.00 2.32
2276 2433 1.675310 TGCCGGTCAGCCTCAATTG 60.675 57.895 1.90 0.00 0.00 2.32
2277 2434 1.377202 GCCGGTCAGCCTCAATTGA 60.377 57.895 8.12 8.12 0.00 2.57
2278 2435 0.749454 GCCGGTCAGCCTCAATTGAT 60.749 55.000 8.96 0.00 0.00 2.57
2279 2436 1.019673 CCGGTCAGCCTCAATTGATG 58.980 55.000 8.96 7.52 0.00 3.07
2280 2437 1.019673 CGGTCAGCCTCAATTGATGG 58.980 55.000 8.96 13.15 0.00 3.51
2281 2438 0.743097 GGTCAGCCTCAATTGATGGC 59.257 55.000 27.77 27.77 46.42 4.40
2286 2443 0.379669 GCCTCAATTGATGGCTCACG 59.620 55.000 27.75 9.81 43.05 4.35
2287 2444 1.019673 CCTCAATTGATGGCTCACGG 58.980 55.000 8.96 0.00 0.00 4.94
2288 2445 1.019673 CTCAATTGATGGCTCACGGG 58.980 55.000 8.96 0.00 0.00 5.28
2289 2446 1.031571 TCAATTGATGGCTCACGGGC 61.032 55.000 3.38 0.00 41.27 6.13
2362 2519 4.944372 CCGACGCCGCCCATCTAC 62.944 72.222 0.00 0.00 0.00 2.59
2368 2525 3.377656 CCGCCCATCTACGGCTAT 58.622 61.111 0.00 0.00 44.73 2.97
2369 2526 2.575108 CCGCCCATCTACGGCTATA 58.425 57.895 0.00 0.00 44.73 1.31
2370 2527 0.892755 CCGCCCATCTACGGCTATAA 59.107 55.000 0.00 0.00 44.73 0.98
2371 2528 1.274167 CCGCCCATCTACGGCTATAAA 59.726 52.381 0.00 0.00 44.73 1.40
2372 2529 2.289195 CCGCCCATCTACGGCTATAAAA 60.289 50.000 0.00 0.00 44.73 1.52
2373 2530 2.993899 CGCCCATCTACGGCTATAAAAG 59.006 50.000 0.00 0.00 44.73 2.27
2374 2531 3.335579 GCCCATCTACGGCTATAAAAGG 58.664 50.000 0.00 0.00 43.48 3.11
2382 2539 1.880271 GGCTATAAAAGGCGACCTCC 58.120 55.000 0.00 0.00 41.50 4.30
2383 2540 1.542767 GGCTATAAAAGGCGACCTCCC 60.543 57.143 0.00 0.00 41.50 4.30
2384 2541 1.542767 GCTATAAAAGGCGACCTCCCC 60.543 57.143 0.00 0.00 30.89 4.81
2385 2542 0.754472 TATAAAAGGCGACCTCCCCG 59.246 55.000 0.00 0.00 30.89 5.73
2407 2564 2.917227 TGGACGCCACAGCTCTCA 60.917 61.111 0.00 0.00 36.60 3.27
2408 2565 2.285773 TGGACGCCACAGCTCTCAT 61.286 57.895 0.00 0.00 36.60 2.90
2409 2566 1.078848 GGACGCCACAGCTCTCATT 60.079 57.895 0.00 0.00 36.60 2.57
2410 2567 0.674895 GGACGCCACAGCTCTCATTT 60.675 55.000 0.00 0.00 36.60 2.32
2411 2568 1.160137 GACGCCACAGCTCTCATTTT 58.840 50.000 0.00 0.00 36.60 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.400120 GGTTTGTATAACCAACTGGGACA 58.600 43.478 0.00 0.00 40.03 4.02
41 42 3.328637 AGTCCCGGTTTGTATAACCAACT 59.671 43.478 0.00 4.59 40.28 3.16
84 85 0.178855 AAAGGGGTGGTGGTAGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
100 101 4.196193 TGTGTCACAAACCAGGACTAAAG 58.804 43.478 2.31 0.00 32.84 1.85
127 128 1.101331 CGTGGTGTACCTCTAGTCCC 58.899 60.000 2.32 0.00 36.82 4.46
141 142 0.248289 CATTAGTCCCGGTTCGTGGT 59.752 55.000 0.00 0.00 0.00 4.16
146 147 2.802057 CGGTCATCATTAGTCCCGGTTC 60.802 54.545 0.00 0.00 0.00 3.62
167 168 2.431260 TTCCAACGTCTACGGCGC 60.431 61.111 6.90 0.00 44.95 6.53
178 179 3.244770 TGACCATTAGTCCCTGTTCCAAC 60.245 47.826 0.00 0.00 45.68 3.77
201 202 2.034053 CGTTTACGGCCCGGTACTAATA 59.966 50.000 8.57 0.00 35.37 0.98
206 207 0.460109 ATTCGTTTACGGCCCGGTAC 60.460 55.000 8.57 0.89 40.29 3.34
212 213 1.153588 TCCCGATTCGTTTACGGCC 60.154 57.895 5.20 0.00 44.45 6.13
213 214 0.459063 AGTCCCGATTCGTTTACGGC 60.459 55.000 5.20 0.00 44.45 5.68
225 226 1.475280 CGTTCACCTCATTAGTCCCGA 59.525 52.381 0.00 0.00 0.00 5.14
253 254 2.941064 GTCGGGGCATTAGTAGAAAACC 59.059 50.000 0.00 0.00 0.00 3.27
254 255 3.869832 GAGTCGGGGCATTAGTAGAAAAC 59.130 47.826 0.00 0.00 0.00 2.43
265 266 3.090532 GGGGAAGAGTCGGGGCAT 61.091 66.667 0.00 0.00 0.00 4.40
287 288 0.883833 GGTTGTGCTGGTGATTGAGG 59.116 55.000 0.00 0.00 0.00 3.86
361 362 2.500098 GTGGGAGCTGGACAATACTACA 59.500 50.000 0.00 0.00 0.00 2.74
374 375 1.789576 ATTTTGGGACGGTGGGAGCT 61.790 55.000 0.00 0.00 0.00 4.09
375 376 0.034863 TATTTTGGGACGGTGGGAGC 60.035 55.000 0.00 0.00 0.00 4.70
412 413 7.335924 AGTGACTCAACTTTGCACTAACTTTAA 59.664 33.333 0.00 0.00 37.98 1.52
585 586 8.925161 AAAATATCCGTGGTAATCAATGTTTG 57.075 30.769 0.00 0.00 0.00 2.93
742 744 5.389516 CCGCGTATCTAGCATTTATTTCCAC 60.390 44.000 4.92 0.00 34.19 4.02
746 748 4.389077 GCTCCGCGTATCTAGCATTTATTT 59.611 41.667 4.92 0.00 35.05 1.40
749 751 2.352421 GGCTCCGCGTATCTAGCATTTA 60.352 50.000 4.92 0.00 36.68 1.40
774 776 9.528018 ACATTAAATAACACACAAAAGTCTTGG 57.472 29.630 0.00 0.00 0.00 3.61
865 942 7.341805 AGCTCCATTGCTGGTATTTATATAGG 58.658 38.462 0.00 0.00 43.61 2.57
949 1026 4.422073 TGAGGATTGCCATACTACAAGG 57.578 45.455 0.00 0.00 36.29 3.61
976 1053 5.653330 TGGTGTAGACAATCGTCCTTGTATA 59.347 40.000 0.00 1.25 43.73 1.47
987 1064 1.299541 CCGCCATGGTGTAGACAATC 58.700 55.000 23.44 0.00 0.00 2.67
1042 1119 2.422479 CAGTTCCATGACAAGATGGCAG 59.578 50.000 0.00 0.00 39.76 4.85
1087 1224 7.789273 TGTTTGGAAATCGTAGAGTAAAACA 57.211 32.000 0.00 0.00 43.63 2.83
1088 1225 7.749126 CCATGTTTGGAAATCGTAGAGTAAAAC 59.251 37.037 0.00 0.00 46.92 2.43
1089 1226 7.812648 CCATGTTTGGAAATCGTAGAGTAAAA 58.187 34.615 0.00 0.00 46.92 1.52
1090 1227 7.372451 CCATGTTTGGAAATCGTAGAGTAAA 57.628 36.000 0.00 0.00 46.92 2.01
1091 1228 6.978343 CCATGTTTGGAAATCGTAGAGTAA 57.022 37.500 0.00 0.00 46.92 2.24
1105 1242 8.069574 GCTAGATTTTTGTTTTTCCATGTTTGG 58.930 33.333 0.00 0.00 45.15 3.28
1106 1243 8.829612 AGCTAGATTTTTGTTTTTCCATGTTTG 58.170 29.630 0.00 0.00 0.00 2.93
1107 1244 8.962884 AGCTAGATTTTTGTTTTTCCATGTTT 57.037 26.923 0.00 0.00 0.00 2.83
1108 1245 9.696917 CTAGCTAGATTTTTGTTTTTCCATGTT 57.303 29.630 16.15 0.00 0.00 2.71
1109 1246 7.814587 GCTAGCTAGATTTTTGTTTTTCCATGT 59.185 33.333 25.15 0.00 0.00 3.21
1110 1247 8.031277 AGCTAGCTAGATTTTTGTTTTTCCATG 58.969 33.333 25.15 0.00 0.00 3.66
1111 1248 8.127150 AGCTAGCTAGATTTTTGTTTTTCCAT 57.873 30.769 25.15 0.00 0.00 3.41
1112 1249 7.524717 AGCTAGCTAGATTTTTGTTTTTCCA 57.475 32.000 25.15 0.00 0.00 3.53
1119 1256 9.757227 CAAGAGTATAGCTAGCTAGATTTTTGT 57.243 33.333 27.42 12.21 31.45 2.83
1120 1257 9.757227 ACAAGAGTATAGCTAGCTAGATTTTTG 57.243 33.333 28.34 28.34 32.22 2.44
1231 1371 2.459421 CTTGAGCAGTGCAGTGCAGC 62.459 60.000 39.87 31.58 46.60 5.25
1248 1388 1.635487 TGCAATAAGAGAGGCACCCTT 59.365 47.619 0.00 0.00 31.76 3.95
1249 1389 1.289160 TGCAATAAGAGAGGCACCCT 58.711 50.000 0.00 0.00 36.03 4.34
1294 1434 5.741425 CATTTGGACATGATACTGTAAGCG 58.259 41.667 0.00 0.00 37.60 4.68
1413 1568 6.338146 CAGGTTCATCAAAAGATGCAATGAT 58.662 36.000 0.00 0.00 32.94 2.45
1416 1571 4.020928 TGCAGGTTCATCAAAAGATGCAAT 60.021 37.500 0.00 0.00 39.29 3.56
1423 1578 2.095567 CCGACTGCAGGTTCATCAAAAG 60.096 50.000 19.93 0.00 0.00 2.27
1568 1723 5.481200 CTTCATACGAGGAAGTTCTACGA 57.519 43.478 21.55 10.68 37.55 3.43
1641 1797 0.611714 GTTAGGGTTTCGCTCCCAGA 59.388 55.000 10.93 0.00 46.82 3.86
1659 1815 1.075151 GGGGAGCCTAGCCAGTAGT 60.075 63.158 0.00 0.00 0.00 2.73
1716 1872 2.034879 CATGCGGTCTTTGCTCGGT 61.035 57.895 0.00 0.00 0.00 4.69
1758 1914 3.249189 GTGAGGGTGGGAGTGCCA 61.249 66.667 0.00 0.00 35.15 4.92
1830 1986 1.820519 GGTCATTCAGGCATTCAAGCA 59.179 47.619 0.00 0.00 35.83 3.91
1847 2003 1.226888 GATAGTGCCGTCGGTGGTC 60.227 63.158 13.94 0.00 0.00 4.02
1858 2015 1.872313 GGCTTCTCTGCATGATAGTGC 59.128 52.381 0.00 0.00 45.25 4.40
1894 2051 4.388485 GTCATTGGGGAAAAATTTGCACT 58.612 39.130 1.38 0.00 32.64 4.40
1902 2059 4.285775 GGAAGATTGGTCATTGGGGAAAAA 59.714 41.667 0.00 0.00 0.00 1.94
1929 2086 7.867921 TGGACCATAGGTTTATTGAACAGTAT 58.132 34.615 0.00 0.00 40.13 2.12
1964 2121 3.243336 CGCGGCTGGAGATACTATAAAC 58.757 50.000 0.00 0.00 0.00 2.01
1968 2125 0.882474 GACGCGGCTGGAGATACTAT 59.118 55.000 12.47 0.00 0.00 2.12
1969 2126 1.170919 GGACGCGGCTGGAGATACTA 61.171 60.000 13.91 0.00 0.00 1.82
1970 2127 2.491022 GGACGCGGCTGGAGATACT 61.491 63.158 13.91 0.00 0.00 2.12
1971 2128 2.027751 GGACGCGGCTGGAGATAC 59.972 66.667 13.91 0.00 0.00 2.24
1972 2129 2.123854 AGGACGCGGCTGGAGATA 60.124 61.111 13.91 0.00 0.00 1.98
1973 2130 3.532155 GAGGACGCGGCTGGAGAT 61.532 66.667 13.91 0.00 0.00 2.75
1975 2132 4.069232 TTGAGGACGCGGCTGGAG 62.069 66.667 13.91 0.00 0.00 3.86
1976 2133 4.373116 GTTGAGGACGCGGCTGGA 62.373 66.667 13.91 0.00 0.00 3.86
1977 2134 4.680237 TGTTGAGGACGCGGCTGG 62.680 66.667 13.91 0.00 0.00 4.85
1978 2135 3.114616 CTGTTGAGGACGCGGCTG 61.115 66.667 13.91 0.00 0.00 4.85
1979 2136 4.379243 CCTGTTGAGGACGCGGCT 62.379 66.667 13.91 0.00 42.93 5.52
1986 2143 2.610859 GGGAGGGCCTGTTGAGGA 60.611 66.667 12.95 0.00 42.93 3.71
1987 2144 3.732849 GGGGAGGGCCTGTTGAGG 61.733 72.222 12.95 0.00 43.19 3.86
1988 2145 2.935481 TGGGGAGGGCCTGTTGAG 60.935 66.667 12.95 0.00 0.00 3.02
1989 2146 2.935481 CTGGGGAGGGCCTGTTGA 60.935 66.667 12.95 0.00 0.00 3.18
1990 2147 2.935481 TCTGGGGAGGGCCTGTTG 60.935 66.667 12.95 0.00 0.00 3.33
1991 2148 2.936032 GTCTGGGGAGGGCCTGTT 60.936 66.667 12.95 0.00 0.00 3.16
1994 2151 4.658786 AACGTCTGGGGAGGGCCT 62.659 66.667 5.25 5.25 0.00 5.19
1995 2152 2.708593 AAAAACGTCTGGGGAGGGCC 62.709 60.000 0.00 0.00 0.00 5.80
1996 2153 1.228459 AAAAACGTCTGGGGAGGGC 60.228 57.895 0.00 0.00 0.00 5.19
1997 2154 0.400594 AGAAAAACGTCTGGGGAGGG 59.599 55.000 0.00 0.00 0.00 4.30
1998 2155 1.809684 GAGAAAAACGTCTGGGGAGG 58.190 55.000 0.00 0.00 0.00 4.30
1999 2156 1.429463 CGAGAAAAACGTCTGGGGAG 58.571 55.000 0.00 0.00 0.00 4.30
2000 2157 0.601841 GCGAGAAAAACGTCTGGGGA 60.602 55.000 0.00 0.00 0.00 4.81
2001 2158 1.866925 GCGAGAAAAACGTCTGGGG 59.133 57.895 0.00 0.00 0.00 4.96
2002 2159 1.491563 CGCGAGAAAAACGTCTGGG 59.508 57.895 0.00 0.00 0.00 4.45
2003 2160 1.154654 GCGCGAGAAAAACGTCTGG 60.155 57.895 12.10 0.00 0.00 3.86
2004 2161 1.154654 GGCGCGAGAAAAACGTCTG 60.155 57.895 12.10 0.00 0.00 3.51
2005 2162 2.654912 CGGCGCGAGAAAAACGTCT 61.655 57.895 12.10 0.00 0.00 4.18
2006 2163 2.202008 CGGCGCGAGAAAAACGTC 60.202 61.111 12.10 0.00 0.00 4.34
2007 2164 3.708734 CCGGCGCGAGAAAAACGT 61.709 61.111 12.10 0.00 0.00 3.99
2009 2166 3.322706 ATGCCGGCGCGAGAAAAAC 62.323 57.895 23.90 0.00 38.08 2.43
2010 2167 3.034370 GATGCCGGCGCGAGAAAAA 62.034 57.895 23.90 0.00 38.08 1.94
2011 2168 3.496131 GATGCCGGCGCGAGAAAA 61.496 61.111 23.90 0.49 38.08 2.29
2017 2174 3.698309 ATTTTTGGATGCCGGCGCG 62.698 57.895 23.90 0.00 38.08 6.86
2018 2175 1.878069 GATTTTTGGATGCCGGCGC 60.878 57.895 23.90 16.59 0.00 6.53
2019 2176 1.586042 CGATTTTTGGATGCCGGCG 60.586 57.895 23.90 0.00 0.00 6.46
2020 2177 1.226945 CCGATTTTTGGATGCCGGC 60.227 57.895 22.73 22.73 0.00 6.13
2021 2178 1.226945 GCCGATTTTTGGATGCCGG 60.227 57.895 0.00 0.00 39.88 6.13
2022 2179 1.226945 GGCCGATTTTTGGATGCCG 60.227 57.895 0.00 0.00 0.00 5.69
2023 2180 1.143838 GGGCCGATTTTTGGATGCC 59.856 57.895 0.00 0.00 38.16 4.40
2024 2181 0.460109 GTGGGCCGATTTTTGGATGC 60.460 55.000 0.00 0.00 0.00 3.91
2025 2182 1.134946 GAGTGGGCCGATTTTTGGATG 59.865 52.381 0.00 0.00 0.00 3.51
2026 2183 1.474330 GAGTGGGCCGATTTTTGGAT 58.526 50.000 0.00 0.00 0.00 3.41
2027 2184 0.958382 CGAGTGGGCCGATTTTTGGA 60.958 55.000 0.00 0.00 0.00 3.53
2028 2185 1.506262 CGAGTGGGCCGATTTTTGG 59.494 57.895 0.00 0.00 0.00 3.28
2029 2186 1.154035 GCGAGTGGGCCGATTTTTG 60.154 57.895 0.00 0.00 0.00 2.44
2030 2187 2.686816 CGCGAGTGGGCCGATTTTT 61.687 57.895 0.00 0.00 0.00 1.94
2031 2188 3.124921 CGCGAGTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
2032 2189 4.388499 ACGCGAGTGGGCCGATTT 62.388 61.111 15.93 0.00 46.97 2.17
2043 2200 4.200283 GGCTCCTGGAGACGCGAG 62.200 72.222 27.53 0.00 0.00 5.03
2047 2204 2.450479 AAAACGGGCTCCTGGAGACG 62.450 60.000 27.53 27.88 38.87 4.18
2048 2205 0.250770 AAAAACGGGCTCCTGGAGAC 60.251 55.000 27.53 24.79 36.87 3.36
2049 2206 0.250727 CAAAAACGGGCTCCTGGAGA 60.251 55.000 27.53 0.00 0.00 3.71
2050 2207 0.250727 TCAAAAACGGGCTCCTGGAG 60.251 55.000 19.55 19.55 0.00 3.86
2051 2208 0.536460 GTCAAAAACGGGCTCCTGGA 60.536 55.000 0.00 0.00 0.00 3.86
2052 2209 1.524008 GGTCAAAAACGGGCTCCTGG 61.524 60.000 0.00 0.00 0.00 4.45
2053 2210 1.852067 CGGTCAAAAACGGGCTCCTG 61.852 60.000 0.00 0.00 0.00 3.86
2054 2211 1.599797 CGGTCAAAAACGGGCTCCT 60.600 57.895 0.00 0.00 0.00 3.69
2055 2212 2.622962 CCGGTCAAAAACGGGCTCC 61.623 63.158 0.00 0.00 46.08 4.70
2056 2213 2.951458 CCGGTCAAAAACGGGCTC 59.049 61.111 0.00 0.00 46.08 4.70
2061 2218 1.007849 CCCAAGCCGGTCAAAAACG 60.008 57.895 1.90 0.00 0.00 3.60
2062 2219 1.365999 CCCCAAGCCGGTCAAAAAC 59.634 57.895 1.90 0.00 0.00 2.43
2063 2220 2.503382 GCCCCAAGCCGGTCAAAAA 61.503 57.895 1.90 0.00 34.35 1.94
2064 2221 2.915137 GCCCCAAGCCGGTCAAAA 60.915 61.111 1.90 0.00 34.35 2.44
2069 2226 3.879180 AATTTCGCCCCAAGCCGGT 62.879 57.895 1.90 0.00 38.78 5.28
2070 2227 3.068064 AATTTCGCCCCAAGCCGG 61.068 61.111 0.00 0.00 38.78 6.13
2071 2228 2.181525 CAATTTCGCCCCAAGCCG 59.818 61.111 0.00 0.00 38.78 5.52
2072 2229 2.578664 CCAATTTCGCCCCAAGCC 59.421 61.111 0.00 0.00 38.78 4.35
2073 2230 2.125552 GCCAATTTCGCCCCAAGC 60.126 61.111 0.00 0.00 38.52 4.01
2074 2231 2.181525 CGCCAATTTCGCCCCAAG 59.818 61.111 0.00 0.00 0.00 3.61
2075 2232 4.062656 GCGCCAATTTCGCCCCAA 62.063 61.111 9.93 0.00 46.18 4.12
2081 2238 4.474846 CCACCGGCGCCAATTTCG 62.475 66.667 28.98 11.16 0.00 3.46
2082 2239 3.059386 TCCACCGGCGCCAATTTC 61.059 61.111 28.98 0.00 0.00 2.17
2083 2240 3.370231 GTCCACCGGCGCCAATTT 61.370 61.111 28.98 3.35 0.00 1.82
2092 2249 3.479127 TTCCGTTTGGGTCCACCGG 62.479 63.158 16.71 16.71 44.64 5.28
2093 2250 2.111460 TTCCGTTTGGGTCCACCG 59.889 61.111 0.00 0.00 44.64 4.94
2094 2251 1.900016 GGTTCCGTTTGGGTCCACC 60.900 63.158 0.00 0.00 40.81 4.61
2095 2252 1.900016 GGGTTCCGTTTGGGTCCAC 60.900 63.158 0.00 0.00 37.00 4.02
2096 2253 2.516909 GGGTTCCGTTTGGGTCCA 59.483 61.111 0.00 0.00 37.00 4.02
2097 2254 2.670592 CGGGTTCCGTTTGGGTCC 60.671 66.667 0.00 0.00 42.73 4.46
2138 2295 2.750237 AAAATGTCTCGCCCCGGC 60.750 61.111 0.00 0.00 37.85 6.13
2139 2296 2.406616 CCAAAATGTCTCGCCCCGG 61.407 63.158 0.00 0.00 0.00 5.73
2140 2297 3.051392 GCCAAAATGTCTCGCCCCG 62.051 63.158 0.00 0.00 0.00 5.73
2141 2298 2.885113 GCCAAAATGTCTCGCCCC 59.115 61.111 0.00 0.00 0.00 5.80
2142 2299 2.485122 CGCCAAAATGTCTCGCCC 59.515 61.111 0.00 0.00 0.00 6.13
2143 2300 2.202479 GCGCCAAAATGTCTCGCC 60.202 61.111 0.00 0.00 39.91 5.54
2144 2301 2.507322 TTCGCGCCAAAATGTCTCGC 62.507 55.000 0.00 0.00 42.05 5.03
2145 2302 0.110419 TTTCGCGCCAAAATGTCTCG 60.110 50.000 0.00 0.00 0.00 4.04
2146 2303 1.606606 CTTTCGCGCCAAAATGTCTC 58.393 50.000 0.00 0.00 0.00 3.36
2147 2304 0.387239 GCTTTCGCGCCAAAATGTCT 60.387 50.000 0.00 0.00 0.00 3.41
2148 2305 2.061977 GCTTTCGCGCCAAAATGTC 58.938 52.632 0.00 0.00 0.00 3.06
2149 2306 4.243383 GCTTTCGCGCCAAAATGT 57.757 50.000 0.00 0.00 0.00 2.71
2159 2316 3.750373 TAGGCCCATCCGCTTTCGC 62.750 63.158 0.00 0.00 40.77 4.70
2160 2317 1.887707 GTAGGCCCATCCGCTTTCG 60.888 63.158 0.00 0.00 40.77 3.46
2161 2318 1.526225 GGTAGGCCCATCCGCTTTC 60.526 63.158 0.00 0.00 40.77 2.62
2162 2319 2.595655 GGTAGGCCCATCCGCTTT 59.404 61.111 0.00 0.00 40.77 3.51
2163 2320 3.861797 CGGTAGGCCCATCCGCTT 61.862 66.667 15.86 0.00 40.77 4.68
2167 2324 3.557290 GACCCGGTAGGCCCATCC 61.557 72.222 0.00 0.00 40.58 3.51
2168 2325 2.766651 TGACCCGGTAGGCCCATC 60.767 66.667 0.00 0.00 40.58 3.51
2169 2326 2.768344 CTGACCCGGTAGGCCCAT 60.768 66.667 0.00 0.00 40.58 4.00
2173 2330 4.509737 GTCGCTGACCCGGTAGGC 62.510 72.222 0.00 0.00 40.58 3.93
2174 2331 3.066190 TGTCGCTGACCCGGTAGG 61.066 66.667 0.00 0.00 43.78 3.18
2175 2332 2.181021 GTGTCGCTGACCCGGTAG 59.819 66.667 0.00 0.00 0.00 3.18
2176 2333 3.740397 CGTGTCGCTGACCCGGTA 61.740 66.667 0.00 0.00 30.46 4.02
2188 2345 3.173240 GAGACGAAGCGGCGTGTC 61.173 66.667 9.37 12.72 45.72 3.67
2189 2346 4.719369 GGAGACGAAGCGGCGTGT 62.719 66.667 9.37 7.64 45.72 4.49
2192 2349 4.856607 GAGGGAGACGAAGCGGCG 62.857 72.222 0.51 0.51 41.28 6.46
2193 2350 2.962697 GATGAGGGAGACGAAGCGGC 62.963 65.000 0.00 0.00 33.59 6.53
2194 2351 1.066587 GATGAGGGAGACGAAGCGG 59.933 63.158 0.00 0.00 0.00 5.52
2195 2352 1.298713 CGATGAGGGAGACGAAGCG 60.299 63.158 0.00 0.00 0.00 4.68
2196 2353 1.590259 GCGATGAGGGAGACGAAGC 60.590 63.158 0.00 0.00 0.00 3.86
2197 2354 1.066587 GGCGATGAGGGAGACGAAG 59.933 63.158 0.00 0.00 0.00 3.79
2198 2355 1.379977 AGGCGATGAGGGAGACGAA 60.380 57.895 0.00 0.00 0.00 3.85
2199 2356 1.824329 GAGGCGATGAGGGAGACGA 60.824 63.158 0.00 0.00 0.00 4.20
2200 2357 2.725008 GAGGCGATGAGGGAGACG 59.275 66.667 0.00 0.00 0.00 4.18
2201 2358 2.725008 CGAGGCGATGAGGGAGAC 59.275 66.667 0.00 0.00 0.00 3.36
2202 2359 2.519541 CCGAGGCGATGAGGGAGA 60.520 66.667 0.00 0.00 0.00 3.71
2203 2360 2.356818 GAACCGAGGCGATGAGGGAG 62.357 65.000 0.00 0.00 0.00 4.30
2204 2361 2.363795 AACCGAGGCGATGAGGGA 60.364 61.111 0.00 0.00 0.00 4.20
2205 2362 2.107141 GAACCGAGGCGATGAGGG 59.893 66.667 0.00 0.00 0.00 4.30
2206 2363 2.107141 GGAACCGAGGCGATGAGG 59.893 66.667 0.00 0.00 0.00 3.86
2207 2364 2.278857 CGGAACCGAGGCGATGAG 60.279 66.667 7.53 0.00 42.83 2.90
2208 2365 3.833645 CCGGAACCGAGGCGATGA 61.834 66.667 15.07 0.00 42.83 2.92
2214 2371 3.702048 TTCCTGCCGGAACCGAGG 61.702 66.667 15.07 13.75 44.28 4.63
2221 2378 1.819208 CGCATTGATTCCTGCCGGA 60.819 57.895 5.05 0.00 37.60 5.14
2222 2379 1.375853 TTCGCATTGATTCCTGCCGG 61.376 55.000 0.00 0.00 34.89 6.13
2223 2380 0.028505 CTTCGCATTGATTCCTGCCG 59.971 55.000 3.54 0.00 34.89 5.69
2224 2381 0.383231 CCTTCGCATTGATTCCTGCC 59.617 55.000 3.54 0.00 34.89 4.85
2225 2382 0.248784 GCCTTCGCATTGATTCCTGC 60.249 55.000 0.00 0.00 35.02 4.85
2226 2383 1.386533 AGCCTTCGCATTGATTCCTG 58.613 50.000 0.00 0.00 37.52 3.86
2227 2384 2.565841 GTAGCCTTCGCATTGATTCCT 58.434 47.619 0.00 0.00 37.52 3.36
2228 2385 1.604278 GGTAGCCTTCGCATTGATTCC 59.396 52.381 0.00 0.00 37.52 3.01
2229 2386 2.032178 GTGGTAGCCTTCGCATTGATTC 59.968 50.000 0.00 0.00 37.52 2.52
2230 2387 2.017049 GTGGTAGCCTTCGCATTGATT 58.983 47.619 0.00 0.00 37.52 2.57
2231 2388 1.668419 GTGGTAGCCTTCGCATTGAT 58.332 50.000 0.00 0.00 37.52 2.57
2232 2389 0.739462 CGTGGTAGCCTTCGCATTGA 60.739 55.000 0.00 0.00 37.52 2.57
2233 2390 1.715585 CGTGGTAGCCTTCGCATTG 59.284 57.895 0.00 0.00 37.52 2.82
2234 2391 2.106683 GCGTGGTAGCCTTCGCATT 61.107 57.895 16.81 0.00 42.74 3.56
2235 2392 2.511600 GCGTGGTAGCCTTCGCAT 60.512 61.111 16.81 0.00 42.74 4.73
2236 2393 3.691342 AGCGTGGTAGCCTTCGCA 61.691 61.111 21.24 0.00 44.33 5.10
2237 2394 3.188786 CAGCGTGGTAGCCTTCGC 61.189 66.667 14.89 14.89 43.18 4.70
2238 2395 3.188786 GCAGCGTGGTAGCCTTCG 61.189 66.667 0.00 0.00 38.01 3.79
2239 2396 2.820037 GGCAGCGTGGTAGCCTTC 60.820 66.667 0.00 0.00 44.92 3.46
2240 2397 4.760047 CGGCAGCGTGGTAGCCTT 62.760 66.667 0.00 0.00 46.14 4.35
2257 2414 1.675641 AATTGAGGCTGACCGGCAC 60.676 57.895 0.00 0.00 42.76 5.01
2258 2415 1.675310 CAATTGAGGCTGACCGGCA 60.675 57.895 0.00 0.00 42.76 5.69
2259 2416 0.749454 ATCAATTGAGGCTGACCGGC 60.749 55.000 14.54 0.00 42.76 6.13
2260 2417 1.019673 CATCAATTGAGGCTGACCGG 58.980 55.000 14.54 0.00 42.76 5.28
2261 2418 1.019673 CCATCAATTGAGGCTGACCG 58.980 55.000 14.55 0.00 42.76 4.79
2262 2419 0.743097 GCCATCAATTGAGGCTGACC 59.257 55.000 27.75 10.24 44.92 4.02
2268 2425 1.019673 CCGTGAGCCATCAATTGAGG 58.980 55.000 14.54 13.81 37.14 3.86
2269 2426 1.019673 CCCGTGAGCCATCAATTGAG 58.980 55.000 14.54 2.24 37.14 3.02
2270 2427 1.031571 GCCCGTGAGCCATCAATTGA 61.032 55.000 11.26 11.26 37.14 2.57
2271 2428 1.314534 TGCCCGTGAGCCATCAATTG 61.315 55.000 0.00 0.00 37.14 2.32
2272 2429 1.001020 TGCCCGTGAGCCATCAATT 60.001 52.632 0.00 0.00 37.14 2.32
2273 2430 1.452651 CTGCCCGTGAGCCATCAAT 60.453 57.895 0.00 0.00 37.14 2.57
2274 2431 2.046023 CTGCCCGTGAGCCATCAA 60.046 61.111 0.00 0.00 37.14 2.57
2275 2432 4.783621 GCTGCCCGTGAGCCATCA 62.784 66.667 0.00 0.00 0.00 3.07
2345 2502 4.944372 GTAGATGGGCGGCGTCGG 62.944 72.222 13.05 0.00 36.79 4.79
2347 2504 4.944372 CCGTAGATGGGCGGCGTC 62.944 72.222 9.37 5.57 41.53 5.19
2354 2511 3.335579 GCCTTTTATAGCCGTAGATGGG 58.664 50.000 0.00 0.00 0.00 4.00
2355 2512 2.993899 CGCCTTTTATAGCCGTAGATGG 59.006 50.000 0.00 0.00 0.00 3.51
2356 2513 3.673809 GTCGCCTTTTATAGCCGTAGATG 59.326 47.826 0.00 0.00 0.00 2.90
2357 2514 3.305881 GGTCGCCTTTTATAGCCGTAGAT 60.306 47.826 0.00 0.00 0.00 1.98
2358 2515 2.035066 GGTCGCCTTTTATAGCCGTAGA 59.965 50.000 0.00 0.00 0.00 2.59
2359 2516 2.035576 AGGTCGCCTTTTATAGCCGTAG 59.964 50.000 0.00 0.00 0.00 3.51
2360 2517 2.034124 AGGTCGCCTTTTATAGCCGTA 58.966 47.619 0.00 0.00 0.00 4.02
2361 2518 0.828677 AGGTCGCCTTTTATAGCCGT 59.171 50.000 0.00 0.00 0.00 5.68
2362 2519 1.499049 GAGGTCGCCTTTTATAGCCG 58.501 55.000 0.00 0.00 31.76 5.52
2363 2520 1.542767 GGGAGGTCGCCTTTTATAGCC 60.543 57.143 0.00 0.00 31.76 3.93
2364 2521 1.542767 GGGGAGGTCGCCTTTTATAGC 60.543 57.143 5.84 0.00 44.66 2.97
2365 2522 1.270147 CGGGGAGGTCGCCTTTTATAG 60.270 57.143 11.02 0.00 45.75 1.31
2366 2523 0.754472 CGGGGAGGTCGCCTTTTATA 59.246 55.000 11.02 0.00 45.75 0.98
2367 2524 1.525442 CGGGGAGGTCGCCTTTTAT 59.475 57.895 11.02 0.00 45.75 1.40
2368 2525 2.983791 CGGGGAGGTCGCCTTTTA 59.016 61.111 11.02 0.00 45.75 1.52
2369 2526 4.717313 GCGGGGAGGTCGCCTTTT 62.717 66.667 11.02 0.00 46.55 2.27
2390 2547 1.830587 AATGAGAGCTGTGGCGTCCA 61.831 55.000 0.00 0.00 44.37 4.02
2391 2548 0.674895 AAATGAGAGCTGTGGCGTCC 60.675 55.000 0.00 0.00 44.37 4.79
2392 2549 1.160137 AAAATGAGAGCTGTGGCGTC 58.840 50.000 0.00 0.00 44.37 5.19
2393 2550 3.329300 AAAATGAGAGCTGTGGCGT 57.671 47.368 0.00 0.00 44.37 5.68


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

AutoCloner maintained by Alex Coulton.