Multiple sequence alignment - TraesCS3A01G275700

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 TraesCS3A01G275700 chr3A 100.000 7411 0 0 1 7411 505225573 505232983 0.000000e+00 13686.0
1 TraesCS3A01G275700 chr3A 93.333 90 4 2 5837 5925 726840693 726840781 1.680000e-26 132.0
2 TraesCS3A01G275700 chr3A 89.157 83 9 0 478 560 514316252 514316334 3.660000e-18 104.0
3 TraesCS3A01G275700 chr3A 87.500 64 5 1 39 102 359363081 359363021 3.710000e-08 71.3
4 TraesCS3A01G275700 chr3B 94.779 4942 159 48 943 5835 498052613 498057504 0.000000e+00 7605.0
5 TraesCS3A01G275700 chr3B 94.559 1507 56 3 5916 7396 498057502 498059008 0.000000e+00 2305.0
6 TraesCS3A01G275700 chr3B 88.437 934 62 35 1 911 497713960 497714870 0.000000e+00 1085.0
7 TraesCS3A01G275700 chr3B 87.952 83 10 0 478 560 519062332 519062414 1.700000e-16 99.0
8 TraesCS3A01G275700 chr3D 93.172 4965 224 62 917 5835 382097756 382102651 0.000000e+00 7184.0
9 TraesCS3A01G275700 chr3D 93.799 1516 61 5 5919 7411 382102649 382104154 0.000000e+00 2248.0
10 TraesCS3A01G275700 chr3D 92.403 1053 68 8 5924 6971 382497955 382499000 0.000000e+00 1491.0
11 TraesCS3A01G275700 chr3D 90.595 925 56 22 1 902 381994499 381995415 0.000000e+00 1197.0
12 TraesCS3A01G275700 chr3D 88.340 506 35 10 6921 7411 382499000 382499496 2.980000e-163 586.0
13 TraesCS3A01G275700 chr3D 89.506 162 10 3 5569 5730 382496416 382496570 1.630000e-46 198.0
14 TraesCS3A01G275700 chr3D 89.157 83 9 0 478 560 394931983 394932065 3.660000e-18 104.0
15 TraesCS3A01G275700 chr1D 93.750 96 6 0 1 96 125070587 125070682 2.160000e-30 145.0
16 TraesCS3A01G275700 chr1B 93.750 96 6 0 1 96 189325574 189325669 2.160000e-30 145.0
17 TraesCS3A01G275700 chr1B 91.579 95 8 0 5828 5922 474683016 474683110 1.680000e-26 132.0
18 TraesCS3A01G275700 chr1B 92.308 91 7 0 5830 5920 164770455 164770365 6.030000e-26 130.0
19 TraesCS3A01G275700 chr1B 90.526 95 9 0 5830 5924 312230175 312230081 7.810000e-25 126.0
20 TraesCS3A01G275700 chr1A 93.750 96 6 0 1 96 138228022 138228117 2.160000e-30 145.0
21 TraesCS3A01G275700 chr1A 95.181 83 4 0 5837 5919 511621886 511621804 1.680000e-26 132.0
22 TraesCS3A01G275700 chr5D 93.333 90 6 0 5830 5919 297738431 297738342 4.660000e-27 134.0
23 TraesCS3A01G275700 chr5D 91.398 93 8 0 5831 5923 514202603 514202511 2.170000e-25 128.0
24 TraesCS3A01G275700 chr7B 91.489 94 6 2 5837 5929 254488488 254488580 2.170000e-25 128.0
25 TraesCS3A01G275700 chr7A 91.111 90 8 0 5837 5926 15007530 15007441 1.010000e-23 122.0
26 TraesCS3A01G275700 chr4B 90.625 64 3 2 39 102 65595652 65595712 1.710000e-11 82.4
27 TraesCS3A01G275700 chr6A 93.878 49 3 0 54 102 384876094 384876046 2.870000e-09 75.0
28 TraesCS3A01G275700 chr2A 87.500 64 5 1 39 102 723641372 723641432 3.710000e-08 71.3


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 TraesCS3A01G275700 chr3A 505225573 505232983 7410 False 13686.000000 13686 100.0000 1 7411 1 chr3A.!!$F1 7410
1 TraesCS3A01G275700 chr3B 498052613 498059008 6395 False 4955.000000 7605 94.6690 943 7396 2 chr3B.!!$F3 6453
2 TraesCS3A01G275700 chr3B 497713960 497714870 910 False 1085.000000 1085 88.4370 1 911 1 chr3B.!!$F1 910
3 TraesCS3A01G275700 chr3D 382097756 382104154 6398 False 4716.000000 7184 93.4855 917 7411 2 chr3D.!!$F3 6494
4 TraesCS3A01G275700 chr3D 381994499 381995415 916 False 1197.000000 1197 90.5950 1 902 1 chr3D.!!$F1 901
5 TraesCS3A01G275700 chr3D 382496416 382499496 3080 False 758.333333 1491 90.0830 5569 7411 3 chr3D.!!$F4 1842

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
187 211 0.039472 AGAGAGCTGAGCTGACCTGA 59.961 55.0 13.71 0.00 39.88 3.86 F
1031 1081 0.043334 CCTCCTCCTTCCTTCCTCCA 59.957 60.0 0.00 0.00 0.00 3.86 F
1165 1224 0.114560 TTCTTCCCACCCTCTCTCGT 59.885 55.0 0.00 0.00 0.00 4.18 F
1543 1606 0.517316 GGACGACGCTGCTTTGAATT 59.483 50.0 0.00 0.00 0.00 2.17 F
3239 3328 0.390492 AGCTCCAAGGTTTGCTTTGC 59.610 50.0 0.00 0.00 31.27 3.68 F
3622 3717 0.454957 CGCCTTTGCAATTCAGGACG 60.455 55.0 18.04 15.69 37.32 4.79 F
4731 4837 2.093869 TGAGCGAAGGGTGTTATGTACC 60.094 50.0 0.00 0.00 37.48 3.34 F
5851 7246 0.268869 AGTGCTCCCTCCATCCCATA 59.731 55.0 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1618 0.541392 ACACTCTCCGGCATTGCATA 59.459 50.000 11.39 0.0 0.00 3.14 R
2662 2728 0.774276 TGTTGTAGGGTGGCCATGAA 59.226 50.000 9.72 0.0 0.00 2.57 R
2943 3028 4.679654 GCATTAACACTGCTTGGTTAACAC 59.320 41.667 8.10 0.0 40.92 3.32 R
3273 3362 3.107601 AGCACCAGAAAGCTATCCACTA 58.892 45.455 0.00 0.0 39.78 2.74 R
4127 4231 2.479566 ACGTGATGGAAGTTGCAGAT 57.520 45.000 2.75 0.0 0.00 2.90 R
5305 5414 0.336737 GTGAGAGGGGGAAGGAGAGA 59.663 60.000 0.00 0.0 0.00 3.10 R
6156 7555 0.615827 GAAGCTTTCCCTGCCCCATT 60.616 55.000 0.00 0.0 0.00 3.16 R
6653 8078 2.240414 TGTGGATGATGCCATTCAGACT 59.760 45.455 0.00 0.0 38.89 3.24 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.757868 GAGCTTGTAGAAGAGCCTCTCA 59.242 50.000 3.33 0.00 39.71 3.27
87 88 4.224818 AGCTTGTAGAAGAGCCTCTCATTT 59.775 41.667 3.33 0.00 39.71 2.32
109 110 4.067896 TCTCTCCTGCAAACAAACAGATC 58.932 43.478 0.00 0.00 35.90 2.75
116 117 2.923605 GCAAACAAACAGATCAGCGCAT 60.924 45.455 11.47 0.00 0.00 4.73
117 118 2.907910 AACAAACAGATCAGCGCATC 57.092 45.000 11.47 4.62 0.00 3.91
118 119 1.812235 ACAAACAGATCAGCGCATCA 58.188 45.000 11.47 0.00 0.00 3.07
121 122 0.723414 AACAGATCAGCGCATCAACG 59.277 50.000 11.47 0.36 0.00 4.10
129 130 3.055719 CGCATCAACGCCAAGGGT 61.056 61.111 0.00 0.00 0.00 4.34
136 137 1.202879 TCAACGCCAAGGGTGAAAGAT 60.203 47.619 2.32 0.00 36.58 2.40
137 138 1.068333 CAACGCCAAGGGTGAAAGATG 60.068 52.381 2.32 0.00 36.58 2.90
138 139 0.400213 ACGCCAAGGGTGAAAGATGA 59.600 50.000 2.32 0.00 36.58 2.92
139 140 0.804989 CGCCAAGGGTGAAAGATGAC 59.195 55.000 0.00 0.00 34.74 3.06
140 141 1.881925 CGCCAAGGGTGAAAGATGACA 60.882 52.381 0.00 0.00 34.74 3.58
141 142 2.450476 GCCAAGGGTGAAAGATGACAT 58.550 47.619 0.00 0.00 0.00 3.06
142 143 2.165030 GCCAAGGGTGAAAGATGACATG 59.835 50.000 0.00 0.00 0.00 3.21
143 144 2.165030 CCAAGGGTGAAAGATGACATGC 59.835 50.000 0.00 0.00 0.00 4.06
144 145 2.134789 AGGGTGAAAGATGACATGCC 57.865 50.000 0.00 0.00 0.00 4.40
155 179 2.627515 TGACATGCCTAAGAGGATGC 57.372 50.000 0.00 0.00 37.67 3.91
156 180 1.839354 TGACATGCCTAAGAGGATGCA 59.161 47.619 0.00 0.00 37.67 3.96
158 182 1.224075 CATGCCTAAGAGGATGCACG 58.776 55.000 0.00 0.00 37.67 5.34
159 183 0.533755 ATGCCTAAGAGGATGCACGC 60.534 55.000 0.00 0.00 37.67 5.34
160 184 1.153369 GCCTAAGAGGATGCACGCA 60.153 57.895 0.00 0.00 37.67 5.24
161 185 0.533755 GCCTAAGAGGATGCACGCAT 60.534 55.000 3.71 3.71 37.67 4.73
162 186 1.224075 CCTAAGAGGATGCACGCATG 58.776 55.000 9.70 0.00 37.67 4.06
163 187 1.473965 CCTAAGAGGATGCACGCATGT 60.474 52.381 9.70 0.00 37.67 3.21
164 188 1.863454 CTAAGAGGATGCACGCATGTC 59.137 52.381 9.70 6.09 36.70 3.06
165 189 0.745845 AAGAGGATGCACGCATGTCC 60.746 55.000 9.70 6.40 36.70 4.02
166 190 2.512286 AGGATGCACGCATGTCCG 60.512 61.111 9.70 0.00 36.70 4.79
167 191 3.576356 GGATGCACGCATGTCCGG 61.576 66.667 9.70 0.00 36.70 5.14
168 192 2.511373 GATGCACGCATGTCCGGA 60.511 61.111 9.70 0.00 36.70 5.14
169 193 2.512286 ATGCACGCATGTCCGGAG 60.512 61.111 3.06 0.00 35.03 4.63
170 194 2.906182 GATGCACGCATGTCCGGAGA 62.906 60.000 3.06 2.85 36.70 3.71
171 195 2.887568 GCACGCATGTCCGGAGAG 60.888 66.667 3.06 0.00 0.00 3.20
172 196 2.885113 CACGCATGTCCGGAGAGA 59.115 61.111 3.06 0.00 0.00 3.10
173 197 1.226802 CACGCATGTCCGGAGAGAG 60.227 63.158 3.06 1.12 0.00 3.20
174 198 2.279120 CGCATGTCCGGAGAGAGC 60.279 66.667 3.06 11.84 0.00 4.09
175 199 2.780094 CGCATGTCCGGAGAGAGCT 61.780 63.158 21.34 0.00 0.00 4.09
180 204 1.752694 GTCCGGAGAGAGCTGAGCT 60.753 63.158 6.69 6.69 43.88 4.09
187 211 0.039472 AGAGAGCTGAGCTGACCTGA 59.961 55.000 13.71 0.00 39.88 3.86
389 415 2.177950 GAGTGGCCACTGCAGATTG 58.822 57.895 42.40 9.25 42.66 2.67
409 435 9.319143 CAGATTGATTAACCAAGTTCTAGGTAG 57.681 37.037 0.00 0.00 37.07 3.18
465 496 3.887335 GAACAAGGTGGCCGCCGTA 62.887 63.158 29.37 0.00 0.00 4.02
857 906 3.736482 GAGAGGCCGCGACACGTAG 62.736 68.421 8.23 0.00 41.42 3.51
929 978 3.131850 CCTGGAAAAACACAGGCCT 57.868 52.632 0.00 0.00 46.78 5.19
934 983 1.760029 GGAAAAACACAGGCCTTTCCA 59.240 47.619 21.80 0.00 44.14 3.53
1017 1067 2.757917 GCGGCACTCTCTCCTCCT 60.758 66.667 0.00 0.00 0.00 3.69
1025 1075 2.007636 ACTCTCTCCTCCTCCTTCCTT 58.992 52.381 0.00 0.00 0.00 3.36
1027 1077 1.289530 TCTCTCCTCCTCCTTCCTTCC 59.710 57.143 0.00 0.00 0.00 3.46
1031 1081 0.043334 CCTCCTCCTTCCTTCCTCCA 59.957 60.000 0.00 0.00 0.00 3.86
1032 1082 1.344906 CCTCCTCCTTCCTTCCTCCAT 60.345 57.143 0.00 0.00 0.00 3.41
1033 1083 2.046292 CTCCTCCTTCCTTCCTCCATC 58.954 57.143 0.00 0.00 0.00 3.51
1034 1084 1.135960 CCTCCTTCCTTCCTCCATCC 58.864 60.000 0.00 0.00 0.00 3.51
1035 1085 0.755686 CTCCTTCCTTCCTCCATCCG 59.244 60.000 0.00 0.00 0.00 4.18
1037 1087 0.691078 CCTTCCTTCCTCCATCCGGA 60.691 60.000 6.61 6.61 39.79 5.14
1072 1122 1.214853 CGAAGCAGAGCAGAGCAGA 59.785 57.895 0.00 0.00 0.00 4.26
1074 1124 0.531657 GAAGCAGAGCAGAGCAGAGA 59.468 55.000 0.00 0.00 0.00 3.10
1136 1195 4.908877 GCCTCTCCTCGCGTACGC 62.909 72.222 29.83 29.83 39.84 4.42
1147 1206 4.831307 CGTACGCGCGCTCTCCTT 62.831 66.667 32.58 11.38 0.00 3.36
1151 1210 2.594119 TACGCGCGCTCTCCTTCTTC 62.594 60.000 32.58 0.00 0.00 2.87
1152 1211 2.888051 GCGCGCTCTCCTTCTTCC 60.888 66.667 26.67 0.00 0.00 3.46
1153 1212 2.202810 CGCGCTCTCCTTCTTCCC 60.203 66.667 5.56 0.00 0.00 3.97
1154 1213 2.982130 GCGCTCTCCTTCTTCCCA 59.018 61.111 0.00 0.00 0.00 4.37
1155 1214 1.448717 GCGCTCTCCTTCTTCCCAC 60.449 63.158 0.00 0.00 0.00 4.61
1157 1216 1.604915 GCTCTCCTTCTTCCCACCC 59.395 63.158 0.00 0.00 0.00 4.61
1158 1217 0.912006 GCTCTCCTTCTTCCCACCCT 60.912 60.000 0.00 0.00 0.00 4.34
1159 1218 1.199615 CTCTCCTTCTTCCCACCCTC 58.800 60.000 0.00 0.00 0.00 4.30
1160 1219 0.793617 TCTCCTTCTTCCCACCCTCT 59.206 55.000 0.00 0.00 0.00 3.69
1162 1221 0.793617 TCCTTCTTCCCACCCTCTCT 59.206 55.000 0.00 0.00 0.00 3.10
1163 1222 1.199615 CCTTCTTCCCACCCTCTCTC 58.800 60.000 0.00 0.00 0.00 3.20
1164 1223 0.820871 CTTCTTCCCACCCTCTCTCG 59.179 60.000 0.00 0.00 0.00 4.04
1165 1224 0.114560 TTCTTCCCACCCTCTCTCGT 59.885 55.000 0.00 0.00 0.00 4.18
1170 1230 4.803426 CACCCTCTCTCGTGCGCC 62.803 72.222 4.18 0.00 0.00 6.53
1503 1566 0.522626 CACGTGATTGCCTGCATTCA 59.477 50.000 10.90 11.50 35.01 2.57
1504 1567 1.068402 CACGTGATTGCCTGCATTCAA 60.068 47.619 10.90 3.67 37.83 2.69
1541 1604 2.307309 CGGACGACGCTGCTTTGAA 61.307 57.895 0.00 0.00 34.82 2.69
1543 1606 0.517316 GGACGACGCTGCTTTGAATT 59.483 50.000 0.00 0.00 0.00 2.17
1544 1607 1.595609 GACGACGCTGCTTTGAATTG 58.404 50.000 0.00 0.00 0.00 2.32
1545 1608 0.944386 ACGACGCTGCTTTGAATTGT 59.056 45.000 0.00 0.00 0.00 2.71
1546 1609 1.321016 CGACGCTGCTTTGAATTGTG 58.679 50.000 0.00 0.00 0.00 3.33
1547 1610 1.069973 CGACGCTGCTTTGAATTGTGA 60.070 47.619 0.00 0.00 0.00 3.58
1548 1611 2.601979 CGACGCTGCTTTGAATTGTGAA 60.602 45.455 0.00 0.00 0.00 3.18
1549 1612 3.568538 GACGCTGCTTTGAATTGTGAAT 58.431 40.909 0.00 0.00 0.00 2.57
1550 1613 3.311106 ACGCTGCTTTGAATTGTGAATG 58.689 40.909 0.00 0.00 0.00 2.67
1551 1614 2.091588 CGCTGCTTTGAATTGTGAATGC 59.908 45.455 0.00 0.00 0.00 3.56
1552 1615 3.061322 GCTGCTTTGAATTGTGAATGCA 58.939 40.909 0.00 0.00 32.93 3.96
1553 1616 3.495377 GCTGCTTTGAATTGTGAATGCAA 59.505 39.130 0.00 0.00 34.59 4.08
1554 1617 4.024725 GCTGCTTTGAATTGTGAATGCAAA 60.025 37.500 0.00 3.07 42.68 3.68
1555 1618 5.334569 GCTGCTTTGAATTGTGAATGCAAAT 60.335 36.000 3.44 0.00 43.61 2.32
1593 1656 2.639286 CTTCAGTTGTGCACCGCC 59.361 61.111 15.69 1.57 0.00 6.13
1714 1777 2.010145 GCCGACTGCAATCTACTTCA 57.990 50.000 0.00 0.00 40.77 3.02
1723 1786 4.081406 TGCAATCTACTTCATGCAAACCT 58.919 39.130 0.00 0.00 45.04 3.50
1729 1792 6.109156 TCTACTTCATGCAAACCTTACAGA 57.891 37.500 0.00 0.00 0.00 3.41
1759 1823 0.612732 TTTGGATGGAGCAAGCTGGG 60.613 55.000 0.00 0.00 0.00 4.45
1760 1824 1.792757 TTGGATGGAGCAAGCTGGGT 61.793 55.000 0.00 0.00 0.00 4.51
1797 1861 2.558359 CACTTCACTTTTCATCCCACCC 59.442 50.000 0.00 0.00 0.00 4.61
1844 1908 3.735746 GGTTTTCTGTGCTTAACATGTGC 59.264 43.478 0.00 0.00 38.39 4.57
1845 1909 4.358851 GTTTTCTGTGCTTAACATGTGCA 58.641 39.130 0.00 1.38 38.39 4.57
1904 1968 3.924144 TGTTCAATAAGCCAATGCCAAC 58.076 40.909 0.00 0.00 38.69 3.77
1967 2031 9.851686 ATGGCATTATTCATTCACTACTAAGAA 57.148 29.630 0.00 0.00 0.00 2.52
1975 2039 8.792830 TTCATTCACTACTAAGAAATCCCTTG 57.207 34.615 0.00 0.00 0.00 3.61
2002 2066 6.283694 AGTTTTGCAAAGAAAGGGAATTCTC 58.716 36.000 12.41 0.00 38.69 2.87
2386 2452 7.228507 TGTTCTATCAAACTGTATTGCAAGTGT 59.771 33.333 4.94 0.00 0.00 3.55
2444 2510 8.767478 ATTATCAAAGCAATCAAACCAGAAAG 57.233 30.769 0.00 0.00 0.00 2.62
2482 2548 4.693532 CGCAAGGCTGGTTCAGTA 57.306 55.556 0.00 0.00 33.43 2.74
2492 2558 5.625150 AGGCTGGTTCAGTAATGATATTCC 58.375 41.667 0.00 0.00 33.43 3.01
2850 2935 3.885297 ACACAAGCTACAACTGCAAGATT 59.115 39.130 0.00 0.00 37.43 2.40
2908 2993 9.482627 CTAATCAGACAATATGAAGTACTTCCC 57.517 37.037 28.43 9.92 38.77 3.97
2909 2994 7.682787 ATCAGACAATATGAAGTACTTCCCT 57.317 36.000 28.43 19.35 38.77 4.20
2910 2995 7.496346 TCAGACAATATGAAGTACTTCCCTT 57.504 36.000 28.43 17.45 38.77 3.95
2911 2996 8.603898 TCAGACAATATGAAGTACTTCCCTTA 57.396 34.615 28.43 18.67 38.77 2.69
2912 2997 8.475639 TCAGACAATATGAAGTACTTCCCTTAC 58.524 37.037 28.43 15.36 38.77 2.34
2913 2998 8.258007 CAGACAATATGAAGTACTTCCCTTACA 58.742 37.037 28.43 13.04 38.77 2.41
2914 2999 8.478877 AGACAATATGAAGTACTTCCCTTACAG 58.521 37.037 28.43 16.16 38.77 2.74
2943 3028 5.645497 AGAAGTATAAAAAGCACAGCCTCTG 59.355 40.000 0.00 0.00 37.52 3.35
3231 3320 2.659428 GGCATTGATAGCTCCAAGGTT 58.341 47.619 12.79 0.00 0.00 3.50
3239 3328 0.390492 AGCTCCAAGGTTTGCTTTGC 59.610 50.000 0.00 0.00 31.27 3.68
3247 3336 3.308438 AGGTTTGCTTTGCATGCTTAG 57.692 42.857 20.33 16.19 38.76 2.18
3273 3362 2.301346 CTCTGTTTTGGTGTTCCTGCT 58.699 47.619 0.00 0.00 34.23 4.24
3490 3579 6.935167 TGATAGCTTCACTGTCAACTTATGA 58.065 36.000 0.00 0.00 42.86 2.15
3531 3626 8.442632 TCATCATAGTGCAGAAGGAATTTTAG 57.557 34.615 0.00 0.00 0.00 1.85
3539 3634 7.833183 AGTGCAGAAGGAATTTTAGAAGATGAT 59.167 33.333 0.00 0.00 0.00 2.45
3604 3699 8.548721 AGATTATTTGGTAGTCGAAAAATAGCG 58.451 33.333 0.00 0.00 0.00 4.26
3622 3717 0.454957 CGCCTTTGCAATTCAGGACG 60.455 55.000 18.04 15.69 37.32 4.79
3642 3737 4.632153 ACGGATATGAATAACCTGCAGTC 58.368 43.478 13.81 3.48 0.00 3.51
3724 3819 5.241403 TCCTACTGAGCAATGAAAGGAAA 57.759 39.130 0.00 0.00 0.00 3.13
3727 3822 3.160269 ACTGAGCAATGAAAGGAAAGGG 58.840 45.455 0.00 0.00 0.00 3.95
3990 4087 9.632969 CTTATAATTCTTTATCACGTGTTTCGG 57.367 33.333 16.51 4.97 35.37 4.30
3993 4090 5.738118 TTCTTTATCACGTGTTTCGGTTT 57.262 34.783 16.51 0.00 44.69 3.27
4006 4103 6.565060 CGTGTTTCGGTTTGTCATCAAGATTA 60.565 38.462 0.00 0.00 33.92 1.75
4030 4134 6.617879 ACACACCAAAGTTTTTCTGTACTTC 58.382 36.000 0.00 0.00 33.66 3.01
4052 4156 6.476243 TCGTCAAAATTGTTAGTTCTAGCC 57.524 37.500 0.00 0.00 0.00 3.93
4127 4231 2.183478 ATGCATGTCAAACGAGTCCA 57.817 45.000 0.00 0.00 0.00 4.02
4335 4440 9.433153 GTTATGTTAGTCCTAGTGTAAAAGCTT 57.567 33.333 0.00 0.00 0.00 3.74
4552 4657 4.411013 AGAAATTGGGAGGGTGAGAAAAG 58.589 43.478 0.00 0.00 0.00 2.27
4563 4669 7.057264 GGAGGGTGAGAAAAGCTAAATATTCT 58.943 38.462 0.00 0.00 34.96 2.40
4652 4758 3.951680 AGGCGGTTCATTATTTAAGGTGG 59.048 43.478 0.00 0.00 0.00 4.61
4656 4762 4.703093 CGGTTCATTATTTAAGGTGGGTGT 59.297 41.667 0.00 0.00 0.00 4.16
4657 4763 5.881443 CGGTTCATTATTTAAGGTGGGTGTA 59.119 40.000 0.00 0.00 0.00 2.90
4658 4764 6.037830 CGGTTCATTATTTAAGGTGGGTGTAG 59.962 42.308 0.00 0.00 0.00 2.74
4659 4765 6.888088 GGTTCATTATTTAAGGTGGGTGTAGT 59.112 38.462 0.00 0.00 0.00 2.73
4660 4766 7.066645 GGTTCATTATTTAAGGTGGGTGTAGTC 59.933 40.741 0.00 0.00 0.00 2.59
4661 4767 7.260387 TCATTATTTAAGGTGGGTGTAGTCA 57.740 36.000 0.00 0.00 0.00 3.41
4662 4768 7.691213 TCATTATTTAAGGTGGGTGTAGTCAA 58.309 34.615 0.00 0.00 0.00 3.18
4731 4837 2.093869 TGAGCGAAGGGTGTTATGTACC 60.094 50.000 0.00 0.00 37.48 3.34
4822 4928 3.375299 GTGTGATGTCCTTAACTGATGGC 59.625 47.826 0.00 0.00 0.00 4.40
4983 5092 6.351711 ACATAGTATTTGCAGAGCTGATTCA 58.648 36.000 0.85 0.00 0.00 2.57
5061 5170 9.302345 CGTACTACTGACATTCTGTTTATTGAT 57.698 33.333 0.00 0.00 31.00 2.57
5091 5200 2.828520 TCGAAGTCTGCTCCTTCAGATT 59.171 45.455 9.96 0.00 44.04 2.40
5213 5322 9.776158 CGTGTTTATGTTTATAGGTTTATGCAA 57.224 29.630 0.00 0.00 0.00 4.08
5299 5408 2.997315 TGACTCGCTCCCTGGGTG 60.997 66.667 13.56 11.90 0.00 4.61
5305 5414 2.283529 CGCTCCCTGGGTGTGTAGT 61.284 63.158 17.99 0.00 0.00 2.73
5335 5444 1.089920 CCCTCTCACCGCAATTTGAG 58.910 55.000 0.00 0.00 40.65 3.02
5340 5449 4.142816 CCTCTCACCGCAATTTGAGTTAAG 60.143 45.833 0.00 0.00 40.25 1.85
5478 5589 6.097356 GGAAAAACGAAAGAGGTCACTTTTT 58.903 36.000 0.00 0.00 39.71 1.94
5522 5633 2.106338 TCAGCCAGAACATGAAACAGGA 59.894 45.455 0.00 0.00 0.00 3.86
5625 5739 2.485479 CCAAGATATGAACTGGGGGACG 60.485 54.545 0.00 0.00 0.00 4.79
5633 5747 1.350310 AACTGGGGGACGTTCAAGGT 61.350 55.000 0.00 0.00 0.00 3.50
5694 5808 9.703892 CCTATTCAGGTCTGATAATCTTTAGTG 57.296 37.037 1.16 0.00 39.64 2.74
5817 7212 7.807977 AAGAAATTAATACAGTCCGCATCAT 57.192 32.000 0.00 0.00 0.00 2.45
5835 7230 3.011818 TCATGCATCAGCCACTAAAGTG 58.988 45.455 0.00 3.02 45.23 3.16
5836 7231 1.167851 TGCATCAGCCACTAAAGTGC 58.832 50.000 4.53 1.15 44.34 4.40
5837 7232 1.271543 TGCATCAGCCACTAAAGTGCT 60.272 47.619 4.53 3.36 44.34 4.40
5838 7233 1.399791 GCATCAGCCACTAAAGTGCTC 59.600 52.381 4.53 0.00 44.34 4.26
5839 7234 2.012673 CATCAGCCACTAAAGTGCTCC 58.987 52.381 4.53 0.00 44.34 4.70
5840 7235 0.324943 TCAGCCACTAAAGTGCTCCC 59.675 55.000 4.53 0.00 44.34 4.30
5841 7236 0.326264 CAGCCACTAAAGTGCTCCCT 59.674 55.000 4.53 0.00 44.34 4.20
5842 7237 0.615850 AGCCACTAAAGTGCTCCCTC 59.384 55.000 4.53 0.00 44.34 4.30
5843 7238 0.393132 GCCACTAAAGTGCTCCCTCC 60.393 60.000 4.53 0.00 44.34 4.30
5844 7239 0.984230 CCACTAAAGTGCTCCCTCCA 59.016 55.000 4.53 0.00 44.34 3.86
5845 7240 1.561542 CCACTAAAGTGCTCCCTCCAT 59.438 52.381 4.53 0.00 44.34 3.41
5846 7241 2.420687 CCACTAAAGTGCTCCCTCCATC 60.421 54.545 4.53 0.00 44.34 3.51
5847 7242 1.840635 ACTAAAGTGCTCCCTCCATCC 59.159 52.381 0.00 0.00 0.00 3.51
5848 7243 1.141858 CTAAAGTGCTCCCTCCATCCC 59.858 57.143 0.00 0.00 0.00 3.85
5849 7244 0.846427 AAAGTGCTCCCTCCATCCCA 60.846 55.000 0.00 0.00 0.00 4.37
5850 7245 0.625683 AAGTGCTCCCTCCATCCCAT 60.626 55.000 0.00 0.00 0.00 4.00
5851 7246 0.268869 AGTGCTCCCTCCATCCCATA 59.731 55.000 0.00 0.00 0.00 2.74
5852 7247 1.140312 GTGCTCCCTCCATCCCATAA 58.860 55.000 0.00 0.00 0.00 1.90
5853 7248 1.707427 GTGCTCCCTCCATCCCATAAT 59.293 52.381 0.00 0.00 0.00 1.28
5854 7249 1.706866 TGCTCCCTCCATCCCATAATG 59.293 52.381 0.00 0.00 0.00 1.90
5855 7250 1.707427 GCTCCCTCCATCCCATAATGT 59.293 52.381 0.00 0.00 0.00 2.71
5856 7251 2.912956 GCTCCCTCCATCCCATAATGTA 59.087 50.000 0.00 0.00 0.00 2.29
5857 7252 3.330701 GCTCCCTCCATCCCATAATGTAA 59.669 47.826 0.00 0.00 0.00 2.41
5858 7253 4.566488 GCTCCCTCCATCCCATAATGTAAG 60.566 50.000 0.00 0.00 0.00 2.34
5859 7254 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
5860 7255 5.424068 TCCCTCCATCCCATAATGTAAGAT 58.576 41.667 0.00 0.00 0.00 2.40
5861 7256 5.251468 TCCCTCCATCCCATAATGTAAGATG 59.749 44.000 0.00 0.00 35.24 2.90
5862 7257 5.014544 CCCTCCATCCCATAATGTAAGATGT 59.985 44.000 0.00 0.00 33.95 3.06
5863 7258 6.467775 CCCTCCATCCCATAATGTAAGATGTT 60.468 42.308 0.00 0.00 33.95 2.71
5864 7259 7.006509 CCTCCATCCCATAATGTAAGATGTTT 58.993 38.462 0.00 0.00 33.95 2.83
5865 7260 7.506938 CCTCCATCCCATAATGTAAGATGTTTT 59.493 37.037 0.00 0.00 33.95 2.43
5866 7261 8.837099 TCCATCCCATAATGTAAGATGTTTTT 57.163 30.769 0.00 0.00 33.95 1.94
5895 7290 7.958053 ACTACATTAGTGTTAAAAAGCGTCT 57.042 32.000 0.00 0.00 39.77 4.18
5896 7291 8.374327 ACTACATTAGTGTTAAAAAGCGTCTT 57.626 30.769 0.00 0.00 39.77 3.01
5897 7292 9.480053 ACTACATTAGTGTTAAAAAGCGTCTTA 57.520 29.630 0.00 0.00 39.77 2.10
5898 7293 9.737025 CTACATTAGTGTTAAAAAGCGTCTTAC 57.263 33.333 0.00 0.00 39.77 2.34
5899 7294 8.145316 ACATTAGTGTTAAAAAGCGTCTTACA 57.855 30.769 0.00 0.00 34.01 2.41
5900 7295 8.780249 ACATTAGTGTTAAAAAGCGTCTTACAT 58.220 29.630 0.00 0.00 34.01 2.29
5901 7296 9.607285 CATTAGTGTTAAAAAGCGTCTTACATT 57.393 29.630 0.00 0.00 0.00 2.71
5905 7300 8.234546 AGTGTTAAAAAGCGTCTTACATTATGG 58.765 33.333 0.00 0.00 0.00 2.74
5906 7301 7.483691 GTGTTAAAAAGCGTCTTACATTATGGG 59.516 37.037 0.00 0.00 0.00 4.00
5907 7302 7.390996 TGTTAAAAAGCGTCTTACATTATGGGA 59.609 33.333 0.00 0.00 0.00 4.37
5908 7303 8.403236 GTTAAAAAGCGTCTTACATTATGGGAT 58.597 33.333 0.00 0.00 0.00 3.85
5909 7304 6.377327 AAAAGCGTCTTACATTATGGGATG 57.623 37.500 0.00 0.00 0.00 3.51
5910 7305 4.008074 AGCGTCTTACATTATGGGATGG 57.992 45.455 0.00 0.00 0.00 3.51
5911 7306 3.646162 AGCGTCTTACATTATGGGATGGA 59.354 43.478 0.00 0.00 0.00 3.41
5912 7307 3.997021 GCGTCTTACATTATGGGATGGAG 59.003 47.826 0.00 0.00 0.00 3.86
5913 7308 4.569943 CGTCTTACATTATGGGATGGAGG 58.430 47.826 0.00 0.00 0.00 4.30
5914 7309 4.563580 CGTCTTACATTATGGGATGGAGGG 60.564 50.000 0.00 0.00 0.00 4.30
5973 7372 1.153369 ACGGATGCGAAGATGTGGG 60.153 57.895 15.49 0.00 0.00 4.61
6145 7544 5.222027 TGTCTGATCCAGGTTATTTGGACAA 60.222 40.000 0.00 0.00 46.85 3.18
6156 7555 6.719370 AGGTTATTTGGACAATGTTCTGCTAA 59.281 34.615 0.00 0.00 0.00 3.09
6313 7735 6.276847 CCTTTCTGCTAGTGGTACTGATAAG 58.723 44.000 0.00 0.00 0.00 1.73
6315 7737 3.315470 TCTGCTAGTGGTACTGATAAGCG 59.685 47.826 0.00 0.00 30.72 4.68
6356 7779 5.014202 GGATTAGCCTTTTGTTCCTGGTTA 58.986 41.667 0.00 0.00 0.00 2.85
6435 7858 7.557719 CCAAATACCATCTCTGGACAACTTTAT 59.442 37.037 0.00 0.00 46.37 1.40
6436 7859 8.400947 CAAATACCATCTCTGGACAACTTTATG 58.599 37.037 0.00 0.00 46.37 1.90
6484 7907 6.878923 TGTGGTTATGGTGATATAGCTTATGC 59.121 38.462 0.00 0.00 40.05 3.14
6506 7931 5.047872 TGCATGAAACATTTGCAGACTGTAT 60.048 36.000 3.99 0.00 41.18 2.29
6523 7948 4.063689 CTGTATGCTCCCTGCTAATTGAG 58.936 47.826 0.00 0.00 43.37 3.02
6639 8064 1.255667 TTGCCAGGACTCGGAGGTAC 61.256 60.000 10.23 0.00 0.00 3.34
6653 8078 3.314080 CGGAGGTACTTGTTTTCTTTGCA 59.686 43.478 0.00 0.00 41.55 4.08
6728 8153 5.505181 ACAGTGAAGGTCCATAAATCTGT 57.495 39.130 0.00 0.00 0.00 3.41
6753 8178 5.795441 GTGATTTCTTTTCCGTAAGCATGAC 59.205 40.000 0.00 0.00 0.00 3.06
6776 8201 4.408694 GGTATGTAATGAACCAACAACGC 58.591 43.478 0.00 0.00 33.28 4.84
6900 8325 5.129485 TCATTCAGATCTCTTACCCTCAACC 59.871 44.000 0.00 0.00 0.00 3.77
6951 8376 3.624861 CCATGTTTGCAGAGCCTAGTTAG 59.375 47.826 0.00 0.00 0.00 2.34
6981 8456 5.710099 TGAACTTAGAAAGCAAGGGGTTATG 59.290 40.000 0.00 0.00 33.60 1.90
7006 8496 3.011566 TGACCCAACAACAACAGACAT 57.988 42.857 0.00 0.00 0.00 3.06
7399 8889 2.162681 AGTGGGCTTATGCAAGTGTTC 58.837 47.619 2.72 0.00 41.91 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 4.889409 TCTGTTTGTTTGCAGGAGAGAAAT 59.111 37.500 0.00 0.00 33.81 2.17
87 88 3.558931 TCTGTTTGTTTGCAGGAGAGA 57.441 42.857 0.00 0.00 33.81 3.10
116 117 0.181587 TCTTTCACCCTTGGCGTTGA 59.818 50.000 0.00 0.00 0.00 3.18
117 118 1.068333 CATCTTTCACCCTTGGCGTTG 60.068 52.381 0.00 0.00 0.00 4.10
118 119 1.202879 TCATCTTTCACCCTTGGCGTT 60.203 47.619 0.00 0.00 0.00 4.84
121 122 1.909700 TGTCATCTTTCACCCTTGGC 58.090 50.000 0.00 0.00 0.00 4.52
122 123 2.165030 GCATGTCATCTTTCACCCTTGG 59.835 50.000 0.00 0.00 0.00 3.61
123 124 2.165030 GGCATGTCATCTTTCACCCTTG 59.835 50.000 0.00 0.00 0.00 3.61
124 125 2.042162 AGGCATGTCATCTTTCACCCTT 59.958 45.455 0.00 0.00 0.00 3.95
125 126 1.637553 AGGCATGTCATCTTTCACCCT 59.362 47.619 0.00 0.00 0.00 4.34
127 128 4.517285 TCTTAGGCATGTCATCTTTCACC 58.483 43.478 0.00 0.00 0.00 4.02
128 129 4.574013 CCTCTTAGGCATGTCATCTTTCAC 59.426 45.833 0.00 0.00 0.00 3.18
129 130 4.471025 TCCTCTTAGGCATGTCATCTTTCA 59.529 41.667 0.00 0.00 34.61 2.69
136 137 1.839354 TGCATCCTCTTAGGCATGTCA 59.161 47.619 0.00 0.00 34.61 3.58
137 138 2.216898 GTGCATCCTCTTAGGCATGTC 58.783 52.381 0.00 0.00 38.57 3.06
138 139 1.473965 CGTGCATCCTCTTAGGCATGT 60.474 52.381 0.00 0.00 38.57 3.21
139 140 1.224075 CGTGCATCCTCTTAGGCATG 58.776 55.000 0.00 0.00 38.57 4.06
140 141 0.533755 GCGTGCATCCTCTTAGGCAT 60.534 55.000 0.00 0.00 38.57 4.40
141 142 1.153369 GCGTGCATCCTCTTAGGCA 60.153 57.895 0.00 0.00 34.61 4.75
142 143 0.533755 ATGCGTGCATCCTCTTAGGC 60.534 55.000 0.51 0.00 34.61 3.93
143 144 1.224075 CATGCGTGCATCCTCTTAGG 58.776 55.000 3.96 0.00 33.90 2.69
144 145 1.863454 GACATGCGTGCATCCTCTTAG 59.137 52.381 5.64 0.00 33.90 2.18
155 179 1.226802 CTCTCTCCGGACATGCGTG 60.227 63.158 0.00 3.82 0.00 5.34
156 180 3.069980 GCTCTCTCCGGACATGCGT 62.070 63.158 0.00 0.00 0.00 5.24
158 182 1.227205 CAGCTCTCTCCGGACATGC 60.227 63.158 0.00 2.67 0.00 4.06
159 183 0.385029 CTCAGCTCTCTCCGGACATG 59.615 60.000 0.00 0.00 0.00 3.21
160 184 1.391157 GCTCAGCTCTCTCCGGACAT 61.391 60.000 0.00 0.00 0.00 3.06
161 185 2.049185 GCTCAGCTCTCTCCGGACA 61.049 63.158 0.00 0.00 0.00 4.02
162 186 1.752694 AGCTCAGCTCTCTCCGGAC 60.753 63.158 0.00 0.00 30.62 4.79
163 187 1.752310 CAGCTCAGCTCTCTCCGGA 60.752 63.158 2.93 2.93 36.40 5.14
164 188 1.752310 TCAGCTCAGCTCTCTCCGG 60.752 63.158 0.00 0.00 36.40 5.14
165 189 1.433064 GTCAGCTCAGCTCTCTCCG 59.567 63.158 0.00 0.00 36.40 4.63
166 190 0.684153 AGGTCAGCTCAGCTCTCTCC 60.684 60.000 0.00 0.00 36.40 3.71
167 191 0.457035 CAGGTCAGCTCAGCTCTCTC 59.543 60.000 0.00 0.00 36.40 3.20
168 192 0.039472 TCAGGTCAGCTCAGCTCTCT 59.961 55.000 0.00 0.00 36.40 3.10
169 193 0.894141 TTCAGGTCAGCTCAGCTCTC 59.106 55.000 0.00 0.00 36.40 3.20
170 194 0.896923 CTTCAGGTCAGCTCAGCTCT 59.103 55.000 0.00 0.00 36.40 4.09
171 195 0.108233 CCTTCAGGTCAGCTCAGCTC 60.108 60.000 0.00 0.00 36.40 4.09
172 196 1.981636 CCTTCAGGTCAGCTCAGCT 59.018 57.895 0.00 0.00 40.77 4.24
173 197 4.613929 CCTTCAGGTCAGCTCAGC 57.386 61.111 0.00 0.00 0.00 4.26
187 211 4.262635 CGCTATATGTTCCTCATGGACCTT 60.263 45.833 0.00 0.00 43.06 3.50
409 435 2.215812 GCCGTCGATCGTTGATTCTTAC 59.784 50.000 15.94 1.24 37.94 2.34
413 439 0.864377 TCGCCGTCGATCGTTGATTC 60.864 55.000 15.94 0.35 40.21 2.52
433 459 0.961019 TTGTTCCATTGGTGCTCTGC 59.039 50.000 1.86 0.00 0.00 4.26
465 496 0.529773 CGCCAGGTACATACACGCAT 60.530 55.000 0.00 0.00 0.00 4.73
469 500 1.217882 GCATCGCCAGGTACATACAC 58.782 55.000 0.00 0.00 0.00 2.90
474 512 1.218047 GTCTGCATCGCCAGGTACA 59.782 57.895 0.00 0.00 33.64 2.90
752 793 0.687354 TGGTGCTTCTCCAGTTCTCC 59.313 55.000 0.00 0.00 0.00 3.71
753 794 2.091852 CTGGTGCTTCTCCAGTTCTC 57.908 55.000 6.74 0.00 45.09 2.87
788 829 2.989253 TCTTCGCTGTCCTCCGCA 60.989 61.111 0.00 0.00 0.00 5.69
789 830 2.507324 GTCTTCGCTGTCCTCCGC 60.507 66.667 0.00 0.00 0.00 5.54
790 831 1.444553 GTGTCTTCGCTGTCCTCCG 60.445 63.158 0.00 0.00 0.00 4.63
791 832 1.079750 GGTGTCTTCGCTGTCCTCC 60.080 63.158 0.00 0.00 0.00 4.30
792 833 1.444553 CGGTGTCTTCGCTGTCCTC 60.445 63.158 0.00 0.00 0.00 3.71
793 834 2.201022 ACGGTGTCTTCGCTGTCCT 61.201 57.895 0.00 0.00 39.12 3.85
912 961 2.224042 GGAAAGGCCTGTGTTTTTCCAG 60.224 50.000 21.80 0.00 44.98 3.86
913 962 1.760029 GGAAAGGCCTGTGTTTTTCCA 59.240 47.619 21.80 0.00 44.98 3.53
914 963 1.760029 TGGAAAGGCCTGTGTTTTTCC 59.240 47.619 20.47 20.47 45.54 3.13
915 964 3.457234 CTTGGAAAGGCCTGTGTTTTTC 58.543 45.455 5.69 4.81 41.27 2.29
955 1004 2.092914 GGTTTTGAGATGGGGATCGAGT 60.093 50.000 0.00 0.00 0.00 4.18
960 1009 2.559705 GGTTGGGTTTTGAGATGGGGAT 60.560 50.000 0.00 0.00 0.00 3.85
1005 1055 1.693799 AGGAAGGAGGAGGAGAGAGT 58.306 55.000 0.00 0.00 0.00 3.24
1007 1057 1.289530 GGAAGGAAGGAGGAGGAGAGA 59.710 57.143 0.00 0.00 0.00 3.10
1017 1067 0.691078 CCGGATGGAGGAAGGAAGGA 60.691 60.000 0.00 0.00 37.49 3.36
1040 1090 3.723364 CTTCGGATTTGGCTGCGCG 62.723 63.158 0.00 0.00 0.00 6.86
1041 1091 2.100991 CTTCGGATTTGGCTGCGC 59.899 61.111 0.00 0.00 0.00 6.09
1042 1092 2.100991 GCTTCGGATTTGGCTGCG 59.899 61.111 0.00 0.00 0.00 5.18
1136 1195 2.202810 GGGAAGAAGGAGAGCGCG 60.203 66.667 0.00 0.00 0.00 6.86
1139 1198 0.912006 AGGGTGGGAAGAAGGAGAGC 60.912 60.000 0.00 0.00 0.00 4.09
1147 1206 0.612174 CACGAGAGAGGGTGGGAAGA 60.612 60.000 0.00 0.00 0.00 2.87
1151 1210 4.135153 CGCACGAGAGAGGGTGGG 62.135 72.222 0.00 0.00 40.06 4.61
1152 1211 4.803426 GCGCACGAGAGAGGGTGG 62.803 72.222 0.30 0.00 37.00 4.61
1153 1212 4.803426 GGCGCACGAGAGAGGGTG 62.803 72.222 10.83 0.00 37.00 4.61
1157 1216 2.994671 TTCAGGGCGCACGAGAGAG 61.995 63.158 10.83 0.00 0.00 3.20
1158 1217 2.989253 TTCAGGGCGCACGAGAGA 60.989 61.111 10.83 0.62 0.00 3.10
1159 1218 2.811317 GTTCAGGGCGCACGAGAG 60.811 66.667 10.83 0.00 0.00 3.20
1160 1219 4.717629 CGTTCAGGGCGCACGAGA 62.718 66.667 10.83 6.76 35.93 4.04
1213 1276 1.219664 CCAAACGGCGGGAGACATA 59.780 57.895 13.24 0.00 38.29 2.29
1503 1566 2.611224 CGCGTAACCTAACCTCCAACTT 60.611 50.000 0.00 0.00 0.00 2.66
1504 1567 1.067354 CGCGTAACCTAACCTCCAACT 60.067 52.381 0.00 0.00 0.00 3.16
1551 1614 2.620115 ACTCTCCGGCATTGCATATTTG 59.380 45.455 11.39 0.00 0.00 2.32
1552 1615 2.620115 CACTCTCCGGCATTGCATATTT 59.380 45.455 11.39 0.00 0.00 1.40
1553 1616 2.224606 CACTCTCCGGCATTGCATATT 58.775 47.619 11.39 0.00 0.00 1.28
1554 1617 1.141657 ACACTCTCCGGCATTGCATAT 59.858 47.619 11.39 0.00 0.00 1.78
1555 1618 0.541392 ACACTCTCCGGCATTGCATA 59.459 50.000 11.39 0.00 0.00 3.14
1565 1628 1.143305 CAACTGAAGCACACTCTCCG 58.857 55.000 0.00 0.00 0.00 4.63
1593 1656 1.085893 TAGCATTGCATCACACACCG 58.914 50.000 11.91 0.00 0.00 4.94
1618 1681 4.523943 GGAAAGGCATGCATTGGTATATCA 59.476 41.667 19.57 0.00 0.00 2.15
1686 1749 2.956987 GCAGTCGGCAACAGCAAT 59.043 55.556 0.00 0.00 43.97 3.56
1714 1777 5.882557 CAGGTATTCTCTGTAAGGTTTGCAT 59.117 40.000 0.00 0.00 0.00 3.96
1723 1786 6.884295 CCATCCAAAACAGGTATTCTCTGTAA 59.116 38.462 0.00 0.00 43.82 2.41
1729 1792 4.263905 TGCTCCATCCAAAACAGGTATTCT 60.264 41.667 0.00 0.00 0.00 2.40
1759 1823 5.811100 GTGAAGTGAAGCCTAACTGGTATAC 59.189 44.000 0.00 0.00 38.35 1.47
1760 1824 5.720041 AGTGAAGTGAAGCCTAACTGGTATA 59.280 40.000 0.00 0.00 38.35 1.47
1797 1861 7.699391 CCAAATGATTACTGCAACAATGAGTAG 59.301 37.037 0.00 0.00 0.00 2.57
1904 1968 3.313526 ACAGTGCTGCTTAGTGTGAAAAG 59.686 43.478 0.00 0.00 30.87 2.27
1967 2031 6.478512 TCTTTGCAAAACTTACAAGGGATT 57.521 33.333 13.84 0.00 0.00 3.01
1975 2039 7.710907 AGAATTCCCTTTCTTTGCAAAACTTAC 59.289 33.333 13.84 0.00 31.94 2.34
2013 2077 7.037586 CCAATAGGGGAAGTGGTATATACACAT 60.038 40.741 14.70 4.46 41.21 3.21
2386 2452 6.116806 TGAGACACTAACAGTAAAGCCAAAA 58.883 36.000 0.00 0.00 0.00 2.44
2444 2510 8.676454 TTGCGGTTACATTGTTTGATTAATAC 57.324 30.769 0.00 0.00 0.00 1.89
2482 2548 6.776887 AGATGAAGGTGGAGGAATATCATT 57.223 37.500 0.00 0.00 0.00 2.57
2492 2558 5.867903 ATCTCAACTAGATGAAGGTGGAG 57.132 43.478 4.11 0.00 43.62 3.86
2662 2728 0.774276 TGTTGTAGGGTGGCCATGAA 59.226 50.000 9.72 0.00 0.00 2.57
2850 2935 5.042463 TGAACCTCAGGTATCACACAAAA 57.958 39.130 0.00 0.00 33.12 2.44
2910 2995 9.767228 TGTGCTTTTTATACTTCTTGTACTGTA 57.233 29.630 0.00 0.00 33.45 2.74
2911 2996 8.671384 TGTGCTTTTTATACTTCTTGTACTGT 57.329 30.769 0.00 0.00 33.45 3.55
2912 2997 7.746475 GCTGTGCTTTTTATACTTCTTGTACTG 59.254 37.037 0.00 0.00 33.45 2.74
2913 2998 7.094762 GGCTGTGCTTTTTATACTTCTTGTACT 60.095 37.037 0.00 0.00 33.45 2.73
2914 2999 7.021790 GGCTGTGCTTTTTATACTTCTTGTAC 58.978 38.462 0.00 0.00 33.45 2.90
2943 3028 4.679654 GCATTAACACTGCTTGGTTAACAC 59.320 41.667 8.10 0.00 40.92 3.32
3231 3320 4.175516 GCATAACTAAGCATGCAAAGCAA 58.824 39.130 21.98 8.35 45.51 3.91
3239 3328 6.032094 CCAAAACAGAGCATAACTAAGCATG 58.968 40.000 0.00 0.00 0.00 4.06
3247 3336 4.278419 AGGAACACCAAAACAGAGCATAAC 59.722 41.667 0.00 0.00 0.00 1.89
3273 3362 3.107601 AGCACCAGAAAGCTATCCACTA 58.892 45.455 0.00 0.00 39.78 2.74
3466 3555 6.935167 TCATAAGTTGACAGTGAAGCTATCA 58.065 36.000 0.00 0.00 35.05 2.15
3539 3634 8.902540 AACATGTCTATTTGTGAAGTGAACTA 57.097 30.769 0.00 0.00 0.00 2.24
3604 3699 0.109132 CCGTCCTGAATTGCAAAGGC 60.109 55.000 1.71 1.90 41.68 4.35
3622 3717 6.942532 TTTGACTGCAGGTTATTCATATCC 57.057 37.500 19.93 0.00 0.00 2.59
3649 3744 9.797642 TCAATGCATATTATTGGTGTAGAGATT 57.202 29.630 0.00 0.00 36.44 2.40
3990 4087 6.312399 TGGTGTGTAATCTTGATGACAAAC 57.688 37.500 11.33 11.33 35.49 2.93
3993 4090 6.061441 ACTTTGGTGTGTAATCTTGATGACA 58.939 36.000 0.00 0.00 0.00 3.58
4006 4103 6.584185 AAGTACAGAAAAACTTTGGTGTGT 57.416 33.333 0.00 0.00 32.00 3.72
4030 4134 6.481954 AGGCTAGAACTAACAATTTTGACG 57.518 37.500 0.00 0.00 0.00 4.35
4127 4231 2.479566 ACGTGATGGAAGTTGCAGAT 57.520 45.000 2.75 0.00 0.00 2.90
4552 4657 8.335356 TCGCAAAAGATGTACAGAATATTTAGC 58.665 33.333 0.33 4.86 0.00 3.09
4563 4669 4.827692 ACTGGTATCGCAAAAGATGTACA 58.172 39.130 0.00 0.00 32.39 2.90
4652 4758 3.782046 ACGCATGACTATTGACTACACC 58.218 45.455 0.00 0.00 0.00 4.16
4656 4762 5.570234 TGTGTACGCATGACTATTGACTA 57.430 39.130 4.65 0.00 0.00 2.59
4657 4763 4.450082 TGTGTACGCATGACTATTGACT 57.550 40.909 4.65 0.00 0.00 3.41
4658 4764 4.025730 CCATGTGTACGCATGACTATTGAC 60.026 45.833 38.55 7.48 46.65 3.18
4659 4765 4.119136 CCATGTGTACGCATGACTATTGA 58.881 43.478 38.55 4.72 46.65 2.57
4660 4766 3.871006 ACCATGTGTACGCATGACTATTG 59.129 43.478 38.55 26.47 46.65 1.90
4661 4767 4.137116 ACCATGTGTACGCATGACTATT 57.863 40.909 38.55 20.33 46.65 1.73
4662 4768 3.819564 ACCATGTGTACGCATGACTAT 57.180 42.857 38.55 23.12 46.65 2.12
4731 4837 4.820173 ACCCAGAAAGTTCCGTAAGAAAAG 59.180 41.667 0.00 0.00 43.02 2.27
4916 5025 9.747898 ACATCTAGACTAGCAGTATAATAAGCT 57.252 33.333 4.47 0.00 40.92 3.74
5061 5170 3.316588 GGAGCAGACTTCGACATCTATCA 59.683 47.826 0.00 0.00 0.00 2.15
5091 5200 4.451096 GTCAAGAAGGTTAATGCGAGACAA 59.549 41.667 0.00 0.00 0.00 3.18
5222 5331 6.569418 GCAAAGCGTCAGAGATCTATCAGATA 60.569 42.308 0.00 0.00 34.53 1.98
5223 5332 5.771469 CAAAGCGTCAGAGATCTATCAGAT 58.229 41.667 0.00 0.00 37.73 2.90
5299 5408 1.007359 AGGGGGAAGGAGAGACTACAC 59.993 57.143 0.00 0.00 0.00 2.90
5305 5414 0.336737 GTGAGAGGGGGAAGGAGAGA 59.663 60.000 0.00 0.00 0.00 3.10
5478 5589 4.080919 AGCAGGTGTACTATTCAAGCATGA 60.081 41.667 0.00 0.00 0.00 3.07
5522 5633 2.840038 TGTTGGTCTATGTGCAGGAGAT 59.160 45.455 0.00 0.00 0.00 2.75
5694 5808 4.275689 TGAACATGATCAGACCACACAAAC 59.724 41.667 0.83 0.00 0.00 2.93
5738 7132 2.811873 GCCTGCATCCCTAGTACAATGG 60.812 54.545 0.00 0.00 0.00 3.16
5817 7212 1.167851 GCACTTTAGTGGCTGATGCA 58.832 50.000 11.55 0.00 45.72 3.96
5835 7230 1.707427 ACATTATGGGATGGAGGGAGC 59.293 52.381 0.00 0.00 0.00 4.70
5836 7231 4.846367 TCTTACATTATGGGATGGAGGGAG 59.154 45.833 0.00 0.00 0.00 4.30
5837 7232 4.838403 TCTTACATTATGGGATGGAGGGA 58.162 43.478 0.00 0.00 0.00 4.20
5838 7233 5.014544 ACATCTTACATTATGGGATGGAGGG 59.985 44.000 19.96 4.96 38.33 4.30
5839 7234 6.131972 ACATCTTACATTATGGGATGGAGG 57.868 41.667 19.96 7.52 38.33 4.30
5840 7235 8.469309 AAAACATCTTACATTATGGGATGGAG 57.531 34.615 19.96 5.43 38.33 3.86
5841 7236 8.837099 AAAAACATCTTACATTATGGGATGGA 57.163 30.769 19.96 4.87 38.33 3.41
5871 7266 7.958053 AGACGCTTTTTAACACTAATGTAGT 57.042 32.000 0.00 0.00 38.45 2.73
5872 7267 9.737025 GTAAGACGCTTTTTAACACTAATGTAG 57.263 33.333 0.00 0.00 38.45 2.74
5873 7268 9.258826 TGTAAGACGCTTTTTAACACTAATGTA 57.741 29.630 0.00 0.00 38.45 2.29
5874 7269 8.145316 TGTAAGACGCTTTTTAACACTAATGT 57.855 30.769 0.00 0.00 42.46 2.71
5875 7270 9.607285 AATGTAAGACGCTTTTTAACACTAATG 57.393 29.630 0.00 0.00 0.00 1.90
5879 7274 8.234546 CCATAATGTAAGACGCTTTTTAACACT 58.765 33.333 0.00 0.00 0.00 3.55
5880 7275 7.483691 CCCATAATGTAAGACGCTTTTTAACAC 59.516 37.037 0.00 0.00 0.00 3.32
5881 7276 7.390996 TCCCATAATGTAAGACGCTTTTTAACA 59.609 33.333 0.00 0.00 0.00 2.41
5882 7277 7.754625 TCCCATAATGTAAGACGCTTTTTAAC 58.245 34.615 0.00 0.00 0.00 2.01
5883 7278 7.925043 TCCCATAATGTAAGACGCTTTTTAA 57.075 32.000 0.00 0.00 0.00 1.52
5884 7279 7.012894 CCATCCCATAATGTAAGACGCTTTTTA 59.987 37.037 0.00 0.00 0.00 1.52
5885 7280 6.183360 CCATCCCATAATGTAAGACGCTTTTT 60.183 38.462 0.00 0.00 0.00 1.94
5886 7281 5.299279 CCATCCCATAATGTAAGACGCTTTT 59.701 40.000 0.00 0.00 0.00 2.27
5887 7282 4.821805 CCATCCCATAATGTAAGACGCTTT 59.178 41.667 0.00 0.00 0.00 3.51
5888 7283 4.102524 TCCATCCCATAATGTAAGACGCTT 59.897 41.667 0.00 0.00 0.00 4.68
5889 7284 3.646162 TCCATCCCATAATGTAAGACGCT 59.354 43.478 0.00 0.00 0.00 5.07
5890 7285 3.997021 CTCCATCCCATAATGTAAGACGC 59.003 47.826 0.00 0.00 0.00 5.19
5891 7286 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
5892 7287 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
5893 7288 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
5894 7289 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
5895 7290 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
5896 7291 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
5897 7292 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
5898 7293 4.171234 ACTACTCCCTCCATCCCATAATG 58.829 47.826 0.00 0.00 0.00 1.90
5899 7294 4.510303 ACTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
5900 7295 5.162760 ACATACTACTCCCTCCATCCCATAA 60.163 44.000 0.00 0.00 0.00 1.90
5901 7296 4.360140 ACATACTACTCCCTCCATCCCATA 59.640 45.833 0.00 0.00 0.00 2.74
5902 7297 3.144894 ACATACTACTCCCTCCATCCCAT 59.855 47.826 0.00 0.00 0.00 4.00
5903 7298 2.522705 ACATACTACTCCCTCCATCCCA 59.477 50.000 0.00 0.00 0.00 4.37
5904 7299 3.261818 ACATACTACTCCCTCCATCCC 57.738 52.381 0.00 0.00 0.00 3.85
5905 7300 3.757493 CGTACATACTACTCCCTCCATCC 59.243 52.174 0.00 0.00 0.00 3.51
5906 7301 4.215827 CACGTACATACTACTCCCTCCATC 59.784 50.000 0.00 0.00 0.00 3.51
5907 7302 4.142790 CACGTACATACTACTCCCTCCAT 58.857 47.826 0.00 0.00 0.00 3.41
5908 7303 3.548770 CACGTACATACTACTCCCTCCA 58.451 50.000 0.00 0.00 0.00 3.86
5909 7304 2.292845 GCACGTACATACTACTCCCTCC 59.707 54.545 0.00 0.00 0.00 4.30
5910 7305 3.212685 AGCACGTACATACTACTCCCTC 58.787 50.000 0.00 0.00 0.00 4.30
5911 7306 3.294038 AGCACGTACATACTACTCCCT 57.706 47.619 0.00 0.00 0.00 4.20
5912 7307 4.382345 AAAGCACGTACATACTACTCCC 57.618 45.455 0.00 0.00 0.00 4.30
5913 7308 6.129053 ACTAAAGCACGTACATACTACTCC 57.871 41.667 0.00 0.00 0.00 3.85
5914 7309 9.727627 ATTAACTAAAGCACGTACATACTACTC 57.272 33.333 0.00 0.00 0.00 2.59
6145 7544 2.530460 TGCCCCATTTAGCAGAACAT 57.470 45.000 0.00 0.00 33.08 2.71
6156 7555 0.615827 GAAGCTTTCCCTGCCCCATT 60.616 55.000 0.00 0.00 0.00 3.16
6275 7697 1.830477 AGAAAGGCCAACAAGTGCAAA 59.170 42.857 5.01 0.00 0.00 3.68
6313 7735 4.233789 TCCAAGCATATCAAACAAAACGC 58.766 39.130 0.00 0.00 0.00 4.84
6315 7737 7.010460 GGCTAATCCAAGCATATCAAACAAAAC 59.990 37.037 0.00 0.00 44.64 2.43
6435 7858 8.908903 ACACATGTAACTTTGAGAAAATAACCA 58.091 29.630 0.00 0.00 0.00 3.67
6436 7859 9.180678 CACACATGTAACTTTGAGAAAATAACC 57.819 33.333 0.00 0.00 0.00 2.85
6484 7907 5.287752 GCATACAGTCTGCAAATGTTTCATG 59.712 40.000 6.05 6.75 39.46 3.07
6523 7948 2.880890 TGAAGCTTTTTCCTCTGCTGAC 59.119 45.455 0.00 0.00 35.79 3.51
6639 8064 5.461078 CCATTCAGACTGCAAAGAAAACAAG 59.539 40.000 0.00 0.00 0.00 3.16
6653 8078 2.240414 TGTGGATGATGCCATTCAGACT 59.760 45.455 0.00 0.00 38.89 3.24
6728 8153 5.471797 TCATGCTTACGGAAAAGAAATCACA 59.528 36.000 0.00 0.00 0.00 3.58
6753 8178 4.643953 CGTTGTTGGTTCATTACATACCG 58.356 43.478 0.00 0.00 34.62 4.02
6776 8201 3.733727 GCTGTTGTGGTTTCGGTAAAATG 59.266 43.478 0.00 0.00 0.00 2.32
6951 8376 5.397326 CCTTGCTTTCTAAGTTCATCTTGC 58.603 41.667 0.00 0.00 37.56 4.01
6981 8456 4.213482 GTCTGTTGTTGTTGGGTCATAGTC 59.787 45.833 0.00 0.00 0.00 2.59
7006 8496 6.013379 AGTGGATTCTGAACTTCAGGTATTGA 60.013 38.462 17.12 0.00 44.39 2.57
7061 8551 2.940514 TATCTCCCCTCCACAAGTCA 57.059 50.000 0.00 0.00 0.00 3.41
7121 8611 2.818432 CTCTCTTTTGCAGAATGGTGCT 59.182 45.455 0.00 0.00 44.32 4.40
7240 8730 3.679389 AGCTTGAGGTAACATGTCCTTG 58.321 45.455 7.49 3.56 41.41 3.61
7368 8858 2.381752 AAGCCCACTAGCCAAAACTT 57.618 45.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.