Multiple sequence alignment - TraesCS1D01G049400

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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 TraesCS1D01G049400 chr1D 100.000 3145 0 0 1 3145 29484686 29481542 0.000000e+00 5808.0
1 TraesCS1D01G049400 chr1D 85.507 621 52 12 1004 1595 28289597 28290208 5.760000e-172 614.0
2 TraesCS1D01G049400 chr1D 92.788 208 13 2 1597 1803 28290255 28290461 1.830000e-77 300.0
3 TraesCS1D01G049400 chr1D 100.000 28 0 0 1932 1959 28290536 28290563 6.000000e-03 52.8
4 TraesCS1D01G049400 chr1B 86.247 1127 92 29 977 2057 46883491 46884600 0.000000e+00 1164.0
5 TraesCS1D01G049400 chr1B 88.314 599 69 1 244 841 409699202 409699800 0.000000e+00 717.0
6 TraesCS1D01G049400 chr1B 83.794 253 32 7 1 247 46883255 46883504 6.780000e-57 231.0
7 TraesCS1D01G049400 chr3D 87.757 972 88 16 2175 3145 147469764 147470705 0.000000e+00 1107.0
8 TraesCS1D01G049400 chr3D 87.140 972 99 13 2174 3145 61667939 61668884 0.000000e+00 1079.0
9 TraesCS1D01G049400 chr3D 89.145 737 74 3 247 977 460951538 460950802 0.000000e+00 913.0
10 TraesCS1D01G049400 chr7D 87.667 973 88 17 2176 3145 399828400 399827457 0.000000e+00 1103.0
11 TraesCS1D01G049400 chr7D 87.333 971 95 14 2177 3145 636813495 636812551 0.000000e+00 1086.0
12 TraesCS1D01G049400 chr7D 86.279 962 106 12 2185 3145 626447298 626448234 0.000000e+00 1022.0
13 TraesCS1D01G049400 chr7D 88.692 734 75 5 247 975 550639762 550639032 0.000000e+00 889.0
14 TraesCS1D01G049400 chr1A 85.370 1121 91 27 977 2050 29279835 29280929 0.000000e+00 1094.0
15 TraesCS1D01G049400 chr6D 87.762 956 87 15 2176 3129 20125823 20126750 0.000000e+00 1090.0
16 TraesCS1D01G049400 chr6D 86.694 977 99 15 2175 3145 467999701 467998750 0.000000e+00 1055.0
17 TraesCS1D01G049400 chr2D 86.934 972 100 18 2175 3145 81979495 81980440 0.000000e+00 1066.0
18 TraesCS1D01G049400 chr2D 87.915 662 75 4 244 904 478114146 478114803 0.000000e+00 774.0
19 TraesCS1D01G049400 chr2B 85.729 974 107 15 2173 3145 763039656 763038714 0.000000e+00 1000.0
20 TraesCS1D01G049400 chr2B 88.904 739 76 3 244 977 619965619 619966356 0.000000e+00 905.0
21 TraesCS1D01G049400 chr3A 88.108 740 82 3 244 977 53189611 53190350 0.000000e+00 874.0
22 TraesCS1D01G049400 chr7A 86.622 740 85 4 244 977 654212510 654213241 0.000000e+00 806.0
23 TraesCS1D01G049400 chr4D 86.413 736 86 7 247 977 51454654 51455380 0.000000e+00 793.0
24 TraesCS1D01G049400 chr7B 89.136 359 39 0 247 605 689234221 689233863 6.190000e-122 448.0
25 TraesCS1D01G049400 chr5D 87.427 342 37 3 642 977 68209831 68209490 3.800000e-104 388.0
26 TraesCS1D01G049400 chr6A 89.272 261 23 2 722 977 517660352 517660092 3.910000e-84 322.0


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 TraesCS1D01G049400 chr1D 29481542 29484686 3144 True 5808.000000 5808 100.0000 1 3145 1 chr1D.!!$R1 3144
1 TraesCS1D01G049400 chr1D 28289597 28290563 966 False 322.266667 614 92.7650 1004 1959 3 chr1D.!!$F1 955
2 TraesCS1D01G049400 chr1B 409699202 409699800 598 False 717.000000 717 88.3140 244 841 1 chr1B.!!$F1 597
3 TraesCS1D01G049400 chr1B 46883255 46884600 1345 False 697.500000 1164 85.0205 1 2057 2 chr1B.!!$F2 2056
4 TraesCS1D01G049400 chr3D 147469764 147470705 941 False 1107.000000 1107 87.7570 2175 3145 1 chr3D.!!$F2 970
5 TraesCS1D01G049400 chr3D 61667939 61668884 945 False 1079.000000 1079 87.1400 2174 3145 1 chr3D.!!$F1 971
6 TraesCS1D01G049400 chr3D 460950802 460951538 736 True 913.000000 913 89.1450 247 977 1 chr3D.!!$R1 730
7 TraesCS1D01G049400 chr7D 399827457 399828400 943 True 1103.000000 1103 87.6670 2176 3145 1 chr7D.!!$R1 969
8 TraesCS1D01G049400 chr7D 636812551 636813495 944 True 1086.000000 1086 87.3330 2177 3145 1 chr7D.!!$R3 968
9 TraesCS1D01G049400 chr7D 626447298 626448234 936 False 1022.000000 1022 86.2790 2185 3145 1 chr7D.!!$F1 960
10 TraesCS1D01G049400 chr7D 550639032 550639762 730 True 889.000000 889 88.6920 247 975 1 chr7D.!!$R2 728
11 TraesCS1D01G049400 chr1A 29279835 29280929 1094 False 1094.000000 1094 85.3700 977 2050 1 chr1A.!!$F1 1073
12 TraesCS1D01G049400 chr6D 20125823 20126750 927 False 1090.000000 1090 87.7620 2176 3129 1 chr6D.!!$F1 953
13 TraesCS1D01G049400 chr6D 467998750 467999701 951 True 1055.000000 1055 86.6940 2175 3145 1 chr6D.!!$R1 970
14 TraesCS1D01G049400 chr2D 81979495 81980440 945 False 1066.000000 1066 86.9340 2175 3145 1 chr2D.!!$F1 970
15 TraesCS1D01G049400 chr2D 478114146 478114803 657 False 774.000000 774 87.9150 244 904 1 chr2D.!!$F2 660
16 TraesCS1D01G049400 chr2B 763038714 763039656 942 True 1000.000000 1000 85.7290 2173 3145 1 chr2B.!!$R1 972
17 TraesCS1D01G049400 chr2B 619965619 619966356 737 False 905.000000 905 88.9040 244 977 1 chr2B.!!$F1 733
18 TraesCS1D01G049400 chr3A 53189611 53190350 739 False 874.000000 874 88.1080 244 977 1 chr3A.!!$F1 733
19 TraesCS1D01G049400 chr7A 654212510 654213241 731 False 806.000000 806 86.6220 244 977 1 chr7A.!!$F1 733
20 TraesCS1D01G049400 chr4D 51454654 51455380 726 False 793.000000 793 86.4130 247 977 1 chr4D.!!$F1 730

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
182 184 0.032952 TCCAACGGTTCTGGAGTTCG 59.967 55.0 0.0 0.0 38.07 3.95 F
673 686 0.035458 CAACTGAGGGGTTTCTCGCT 59.965 55.0 0.0 0.0 36.61 4.93 F
2114 2254 0.395312 ATATTTGGTACTCCGGGCGG 59.605 55.0 0.0 0.0 36.30 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2259 0.101579 CTTTTGGTTTGTCGGGCGTT 59.898 50.000 0.00 0.0 0.0 4.84 R
2121 2261 0.382515 TTCTTTTGGTTTGTCGGGCG 59.617 50.000 0.00 0.0 0.0 6.13 R
2925 3072 1.135888 GGCTTTCGGTAAAAATCGCGT 60.136 47.619 5.77 0.0 0.0 6.01 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
17 18 3.142393 CCTCCTACCCTCGCATGG 58.858 66.667 0.00 0.00 0.00 3.66
39 40 2.740055 CTCTGGCTGTGGTGCGAC 60.740 66.667 0.00 0.00 0.00 5.19
40 41 3.519973 CTCTGGCTGTGGTGCGACA 62.520 63.158 0.00 0.00 0.00 4.35
41 42 2.591429 CTGGCTGTGGTGCGACAA 60.591 61.111 0.00 0.00 0.00 3.18
42 43 1.968017 CTGGCTGTGGTGCGACAAT 60.968 57.895 0.00 0.00 0.00 2.71
43 44 0.673333 CTGGCTGTGGTGCGACAATA 60.673 55.000 0.00 0.00 0.00 1.90
56 57 4.894896 CAATACCCCTGGGCGCCC 62.895 72.222 39.40 39.40 39.32 6.13
101 102 4.651516 GGCGGGGGCCTAGGGATA 62.652 72.222 11.72 0.00 0.00 2.59
102 103 3.320014 GCGGGGGCCTAGGGATAC 61.320 72.222 11.72 0.00 0.00 2.24
133 135 1.911357 TGTGCAGAAGTCCAGATCCAT 59.089 47.619 0.00 0.00 0.00 3.41
137 139 2.836262 CAGAAGTCCAGATCCATCAGC 58.164 52.381 0.00 0.00 0.00 4.26
142 144 1.344114 GTCCAGATCCATCAGCTCTCC 59.656 57.143 0.00 0.00 0.00 3.71
149 151 0.252479 CCATCAGCTCTCCAACTGCT 59.748 55.000 0.00 0.00 37.56 4.24
159 161 4.543692 CTCTCCAACTGCTGTTTGATTTG 58.456 43.478 6.20 0.00 33.52 2.32
174 176 4.286297 TGATTTGAGATCCAACGGTTCT 57.714 40.909 0.00 0.00 34.79 3.01
181 183 2.028020 AGATCCAACGGTTCTGGAGTTC 60.028 50.000 7.55 2.04 46.04 3.01
182 184 0.032952 TCCAACGGTTCTGGAGTTCG 59.967 55.000 0.00 0.00 38.07 3.95
191 194 1.100510 TCTGGAGTTCGTATCACGGG 58.899 55.000 0.00 0.00 42.81 5.28
196 199 0.456221 AGTTCGTATCACGGGAGCAG 59.544 55.000 0.00 0.00 42.81 4.24
197 200 1.141019 TTCGTATCACGGGAGCAGC 59.859 57.895 0.00 0.00 42.81 5.25
198 201 1.320344 TTCGTATCACGGGAGCAGCT 61.320 55.000 0.00 0.00 42.81 4.24
204 207 3.382832 ACGGGAGCAGCTAAGCGT 61.383 61.111 0.00 0.00 40.15 5.07
213 216 1.374758 AGCTAAGCGTGTGGAGCAC 60.375 57.895 0.00 0.00 44.36 4.40
220 223 1.084370 GCGTGTGGAGCACCTGATAC 61.084 60.000 0.71 0.00 44.97 2.24
226 229 1.559682 TGGAGCACCTGATACTTTCCC 59.440 52.381 0.71 0.00 37.04 3.97
227 230 1.840635 GGAGCACCTGATACTTTCCCT 59.159 52.381 0.00 0.00 0.00 4.20
228 231 2.158885 GGAGCACCTGATACTTTCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
229 232 1.840635 AGCACCTGATACTTTCCCTCC 59.159 52.381 0.00 0.00 0.00 4.30
230 233 1.840635 GCACCTGATACTTTCCCTCCT 59.159 52.381 0.00 0.00 0.00 3.69
231 234 2.239907 GCACCTGATACTTTCCCTCCTT 59.760 50.000 0.00 0.00 0.00 3.36
232 235 3.878778 CACCTGATACTTTCCCTCCTTG 58.121 50.000 0.00 0.00 0.00 3.61
233 236 3.519510 CACCTGATACTTTCCCTCCTTGA 59.480 47.826 0.00 0.00 0.00 3.02
234 237 4.164988 CACCTGATACTTTCCCTCCTTGAT 59.835 45.833 0.00 0.00 0.00 2.57
235 238 4.164988 ACCTGATACTTTCCCTCCTTGATG 59.835 45.833 0.00 0.00 0.00 3.07
236 239 4.410228 CCTGATACTTTCCCTCCTTGATGA 59.590 45.833 0.00 0.00 0.00 2.92
237 240 5.359194 TGATACTTTCCCTCCTTGATGAC 57.641 43.478 0.00 0.00 0.00 3.06
238 241 4.782691 TGATACTTTCCCTCCTTGATGACA 59.217 41.667 0.00 0.00 0.00 3.58
239 242 3.425162 ACTTTCCCTCCTTGATGACAC 57.575 47.619 0.00 0.00 0.00 3.67
240 243 2.982488 ACTTTCCCTCCTTGATGACACT 59.018 45.455 0.00 0.00 0.00 3.55
241 244 3.008485 ACTTTCCCTCCTTGATGACACTC 59.992 47.826 0.00 0.00 0.00 3.51
242 245 2.630889 TCCCTCCTTGATGACACTCT 57.369 50.000 0.00 0.00 0.00 3.24
245 248 3.011821 TCCCTCCTTGATGACACTCTACT 59.988 47.826 0.00 0.00 0.00 2.57
267 270 1.825474 CATGGTCCCGAGACTTAGTGT 59.175 52.381 0.00 0.00 43.05 3.55
271 274 3.834732 CCCGAGACTTAGTGTTGGG 57.165 57.895 18.89 18.89 42.88 4.12
307 311 2.345641 CGACGGAACAATGTCAGATCAC 59.654 50.000 0.00 0.00 34.78 3.06
337 341 1.597195 GCATGCAATATGGTCGTCGAA 59.403 47.619 14.21 0.00 0.00 3.71
356 360 2.015736 AGAATCGCTGGACACATGAC 57.984 50.000 0.00 0.00 0.00 3.06
364 368 0.891904 TGGACACATGACGAGGACGA 60.892 55.000 0.00 0.00 42.66 4.20
377 381 4.628074 ACGAGGACGAATATAACCCAATG 58.372 43.478 0.00 0.00 42.66 2.82
397 401 2.435059 GGCAGTCAAGAGGGCGAC 60.435 66.667 0.00 0.00 0.00 5.19
424 428 2.117865 CCTGGCTCTCTTGGATCTTCT 58.882 52.381 0.00 0.00 0.00 2.85
425 429 2.504996 CCTGGCTCTCTTGGATCTTCTT 59.495 50.000 0.00 0.00 0.00 2.52
433 437 6.183360 GCTCTCTTGGATCTTCTTGGAGATAA 60.183 42.308 0.00 0.00 36.54 1.75
478 482 4.309950 GCGACCACCGGAACCTGT 62.310 66.667 9.46 0.00 39.04 4.00
504 508 7.175990 TCTGGGTTAAAATTAACACTGATGGAC 59.824 37.037 18.29 1.21 44.61 4.02
542 554 2.279408 GTAGGAGGAGGAGGCGGT 59.721 66.667 0.00 0.00 0.00 5.68
605 618 1.344087 CCCCTACCTGGTACCACTGAT 60.344 57.143 11.60 0.00 0.00 2.90
610 623 4.341520 CCTACCTGGTACCACTGATACTTC 59.658 50.000 11.60 0.00 0.00 3.01
628 641 1.412079 TCCATTGCCAAAGTGCTTGT 58.588 45.000 0.00 0.00 32.65 3.16
673 686 0.035458 CAACTGAGGGGTTTCTCGCT 59.965 55.000 0.00 0.00 36.61 4.93
715 729 6.488769 TTGTTTAGAGTGGTGAACCTCTAA 57.511 37.500 4.11 5.75 39.71 2.10
718 732 5.723672 TTAGAGTGGTGAACCTCTAACTG 57.276 43.478 4.11 0.00 39.71 3.16
719 733 2.300437 AGAGTGGTGAACCTCTAACTGC 59.700 50.000 4.11 0.00 39.71 4.40
740 754 3.121944 GCCGCGTCATAATACAAGATCTG 59.878 47.826 4.92 0.00 0.00 2.90
793 807 5.635417 AGAGAGCTGTAAATTTTGCTTCC 57.365 39.130 12.18 8.57 35.76 3.46
824 838 2.872245 CAACATGTTAGTAGGGATGCCG 59.128 50.000 11.53 0.00 0.00 5.69
827 841 1.855295 TGTTAGTAGGGATGCCGACA 58.145 50.000 18.33 7.22 0.00 4.35
847 861 2.827604 CACGGTCGATCTTTGTGCT 58.172 52.632 0.00 0.00 0.00 4.40
861 875 7.201522 CGATCTTTGTGCTAAACATGCTACTTA 60.202 37.037 0.00 0.00 38.99 2.24
862 876 7.364522 TCTTTGTGCTAAACATGCTACTTAG 57.635 36.000 0.00 0.00 38.99 2.18
863 877 7.158697 TCTTTGTGCTAAACATGCTACTTAGA 58.841 34.615 0.00 0.00 38.99 2.10
864 878 6.968131 TTGTGCTAAACATGCTACTTAGAG 57.032 37.500 0.00 0.00 38.99 2.43
865 879 5.419542 TGTGCTAAACATGCTACTTAGAGG 58.580 41.667 0.00 0.00 32.36 3.69
866 880 5.046591 TGTGCTAAACATGCTACTTAGAGGT 60.047 40.000 0.00 0.00 32.36 3.85
867 881 6.153851 TGTGCTAAACATGCTACTTAGAGGTA 59.846 38.462 0.00 0.00 32.36 3.08
868 882 7.147724 TGTGCTAAACATGCTACTTAGAGGTAT 60.148 37.037 0.00 0.00 32.36 2.73
869 883 7.382759 GTGCTAAACATGCTACTTAGAGGTATC 59.617 40.741 0.00 0.00 0.00 2.24
870 884 6.869388 GCTAAACATGCTACTTAGAGGTATCC 59.131 42.308 0.00 0.00 0.00 2.59
871 885 5.455056 AACATGCTACTTAGAGGTATCCG 57.545 43.478 0.00 0.00 0.00 4.18
872 886 4.726583 ACATGCTACTTAGAGGTATCCGA 58.273 43.478 0.00 0.00 0.00 4.55
875 889 4.135306 TGCTACTTAGAGGTATCCGAGTG 58.865 47.826 0.00 0.00 0.00 3.51
883 905 2.693591 GAGGTATCCGAGTGTTGGATGA 59.306 50.000 6.01 0.00 45.70 2.92
887 909 5.544176 AGGTATCCGAGTGTTGGATGAATAT 59.456 40.000 6.01 0.00 45.70 1.28
895 917 6.128035 CGAGTGTTGGATGAATATTTGTCCAA 60.128 38.462 22.00 22.00 45.68 3.53
931 953 2.295253 CCTTAGGGCTGAGTGTAACG 57.705 55.000 0.00 0.00 45.86 3.18
966 988 7.022979 TCATGCAATAAAACTCTCATGTTTCG 58.977 34.615 0.00 0.00 38.98 3.46
1039 1061 2.274232 TTAGACACGTCCATCCGGCG 62.274 60.000 0.00 0.00 37.68 6.46
1141 1174 4.143194 TCTAGAAGTTCTTCACGTGTCG 57.857 45.455 16.51 7.94 0.00 4.35
1145 1178 1.965083 AGTTCTTCACGTGTCGATCG 58.035 50.000 16.51 9.36 0.00 3.69
1148 1181 1.443702 CTTCACGTGTCGATCGGCA 60.444 57.895 20.25 20.25 0.00 5.69
1149 1182 1.006825 CTTCACGTGTCGATCGGCAA 61.007 55.000 26.02 5.73 0.00 4.52
1151 1184 1.006825 TCACGTGTCGATCGGCAAAG 61.007 55.000 26.02 22.63 0.00 2.77
1168 1201 3.491652 GGCGCCGCAGTTCTTCTC 61.492 66.667 12.58 0.00 0.00 2.87
1183 1216 7.308109 GCAGTTCTTCTCGCACTACTATAGTAT 60.308 40.741 12.98 1.68 37.23 2.12
1189 1233 5.636965 TCTCGCACTACTATAGTATCCGTTC 59.363 44.000 12.98 2.37 37.23 3.95
1193 1237 5.639506 GCACTACTATAGTATCCGTTCCGTA 59.360 44.000 12.98 0.00 37.23 4.02
1230 1274 0.759346 ATAGCATCCTCCACCGAACC 59.241 55.000 0.00 0.00 0.00 3.62
1231 1275 1.672854 TAGCATCCTCCACCGAACCG 61.673 60.000 0.00 0.00 0.00 4.44
1232 1276 3.014085 GCATCCTCCACCGAACCGA 62.014 63.158 0.00 0.00 0.00 4.69
1296 1340 2.539338 CGACCACCACCACCAAACG 61.539 63.158 0.00 0.00 0.00 3.60
1368 1412 2.362503 ACCATCGTCCTCCTCGCA 60.363 61.111 0.00 0.00 0.00 5.10
1410 1454 4.717629 TTCCTGCTGTCGTCGCCG 62.718 66.667 0.00 0.00 0.00 6.46
1527 1589 2.666862 CGCACGTGGGCCAAACTA 60.667 61.111 20.24 0.00 0.00 2.24
1542 1604 3.120199 CCAAACTAACGTGGATGAAGCTG 60.120 47.826 0.00 0.00 37.03 4.24
1565 1627 2.106938 GCCGCACTCCGATGATCA 59.893 61.111 0.00 0.00 40.02 2.92
1595 1657 7.962964 ACGTATTATTATGTTCCTGATGTGG 57.037 36.000 0.00 0.00 0.00 4.17
1596 1658 7.732025 ACGTATTATTATGTTCCTGATGTGGA 58.268 34.615 0.00 0.00 0.00 4.02
1597 1659 7.872993 ACGTATTATTATGTTCCTGATGTGGAG 59.127 37.037 0.00 0.00 37.43 3.86
1598 1660 7.872993 CGTATTATTATGTTCCTGATGTGGAGT 59.127 37.037 0.00 0.00 37.43 3.85
1601 1663 6.814954 ATTATGTTCCTGATGTGGAGTACT 57.185 37.500 0.00 0.00 37.43 2.73
1602 1664 7.914427 ATTATGTTCCTGATGTGGAGTACTA 57.086 36.000 0.00 0.00 37.43 1.82
1798 1905 3.206211 CTCCTCCGATGCCGAGCTC 62.206 68.421 2.73 2.73 38.22 4.09
1914 2025 4.461198 TCTGGGTCCTGTCTTTCTTTTTC 58.539 43.478 0.00 0.00 0.00 2.29
1915 2026 4.166144 TCTGGGTCCTGTCTTTCTTTTTCT 59.834 41.667 0.00 0.00 0.00 2.52
1917 2028 5.269189 TGGGTCCTGTCTTTCTTTTTCTTT 58.731 37.500 0.00 0.00 0.00 2.52
1918 2029 5.719563 TGGGTCCTGTCTTTCTTTTTCTTTT 59.280 36.000 0.00 0.00 0.00 2.27
1919 2030 6.127451 TGGGTCCTGTCTTTCTTTTTCTTTTC 60.127 38.462 0.00 0.00 0.00 2.29
1920 2031 6.096987 GGGTCCTGTCTTTCTTTTTCTTTTCT 59.903 38.462 0.00 0.00 0.00 2.52
1924 2035 9.996554 TCCTGTCTTTCTTTTTCTTTTCTTTTT 57.003 25.926 0.00 0.00 0.00 1.94
1980 2120 7.495934 GCTGAAGTTCCACATGTATATTGTACT 59.504 37.037 0.00 0.00 0.00 2.73
1982 2122 9.811995 TGAAGTTCCACATGTATATTGTACTAC 57.188 33.333 0.00 0.00 0.00 2.73
2002 2142 4.592485 ACGACAGAAAGTGAACAGAGAT 57.408 40.909 0.00 0.00 0.00 2.75
2028 2168 4.676471 GTGTTATGCGGCATAATCACAATG 59.324 41.667 33.52 0.00 38.37 2.82
2059 2199 9.852091 AAAACTTGATCATAAGAAGAGAAATGC 57.148 29.630 0.00 0.00 0.00 3.56
2060 2200 8.571461 AACTTGATCATAAGAAGAGAAATGCA 57.429 30.769 0.00 0.00 0.00 3.96
2061 2201 8.749026 ACTTGATCATAAGAAGAGAAATGCAT 57.251 30.769 0.00 0.00 0.00 3.96
2062 2202 8.622157 ACTTGATCATAAGAAGAGAAATGCATG 58.378 33.333 0.00 0.00 0.00 4.06
2063 2203 8.741603 TTGATCATAAGAAGAGAAATGCATGA 57.258 30.769 0.00 0.00 0.00 3.07
2064 2204 8.919777 TGATCATAAGAAGAGAAATGCATGAT 57.080 30.769 0.00 0.00 35.24 2.45
2073 2213 8.449397 AGAAGAGAAATGCATGATATAAATCGC 58.551 33.333 0.00 0.00 34.60 4.58
2074 2214 7.677454 AGAGAAATGCATGATATAAATCGCA 57.323 32.000 0.00 0.00 34.37 5.10
2075 2215 8.277490 AGAGAAATGCATGATATAAATCGCAT 57.723 30.769 0.00 0.00 39.45 4.73
2076 2216 8.396390 AGAGAAATGCATGATATAAATCGCATC 58.604 33.333 0.00 0.00 37.87 3.91
2077 2217 8.047413 AGAAATGCATGATATAAATCGCATCA 57.953 30.769 0.00 0.00 37.87 3.07
2078 2218 7.966753 AGAAATGCATGATATAAATCGCATCAC 59.033 33.333 0.00 0.00 37.87 3.06
2079 2219 5.550232 TGCATGATATAAATCGCATCACC 57.450 39.130 0.00 0.00 34.60 4.02
2080 2220 5.002516 TGCATGATATAAATCGCATCACCA 58.997 37.500 0.00 0.00 34.60 4.17
2081 2221 5.106594 TGCATGATATAAATCGCATCACCAC 60.107 40.000 0.00 0.00 34.60 4.16
2082 2222 5.106594 GCATGATATAAATCGCATCACCACA 60.107 40.000 0.00 0.00 34.60 4.17
2083 2223 6.568271 GCATGATATAAATCGCATCACCACAA 60.568 38.462 0.00 0.00 34.60 3.33
2084 2224 6.544038 TGATATAAATCGCATCACCACAAG 57.456 37.500 0.00 0.00 34.60 3.16
2085 2225 6.287525 TGATATAAATCGCATCACCACAAGA 58.712 36.000 0.00 0.00 34.60 3.02
2086 2226 6.765512 TGATATAAATCGCATCACCACAAGAA 59.234 34.615 0.00 0.00 34.60 2.52
2087 2227 3.559238 AAATCGCATCACCACAAGAAC 57.441 42.857 0.00 0.00 0.00 3.01
2088 2228 2.479566 ATCGCATCACCACAAGAACT 57.520 45.000 0.00 0.00 0.00 3.01
2089 2229 3.610040 ATCGCATCACCACAAGAACTA 57.390 42.857 0.00 0.00 0.00 2.24
2090 2230 2.683968 TCGCATCACCACAAGAACTAC 58.316 47.619 0.00 0.00 0.00 2.73
2091 2231 2.036604 TCGCATCACCACAAGAACTACA 59.963 45.455 0.00 0.00 0.00 2.74
2092 2232 2.157668 CGCATCACCACAAGAACTACAC 59.842 50.000 0.00 0.00 0.00 2.90
2093 2233 3.138304 GCATCACCACAAGAACTACACA 58.862 45.455 0.00 0.00 0.00 3.72
2094 2234 3.187227 GCATCACCACAAGAACTACACAG 59.813 47.826 0.00 0.00 0.00 3.66
2095 2235 4.631131 CATCACCACAAGAACTACACAGA 58.369 43.478 0.00 0.00 0.00 3.41
2096 2236 4.955811 TCACCACAAGAACTACACAGAT 57.044 40.909 0.00 0.00 0.00 2.90
2097 2237 6.398095 CATCACCACAAGAACTACACAGATA 58.602 40.000 0.00 0.00 0.00 1.98
2098 2238 6.605471 TCACCACAAGAACTACACAGATAT 57.395 37.500 0.00 0.00 0.00 1.63
2099 2239 7.004555 TCACCACAAGAACTACACAGATATT 57.995 36.000 0.00 0.00 0.00 1.28
2100 2240 7.450074 TCACCACAAGAACTACACAGATATTT 58.550 34.615 0.00 0.00 0.00 1.40
2101 2241 7.387673 TCACCACAAGAACTACACAGATATTTG 59.612 37.037 0.00 0.00 0.00 2.32
2102 2242 6.655003 ACCACAAGAACTACACAGATATTTGG 59.345 38.462 0.00 0.00 0.00 3.28
2103 2243 6.655003 CCACAAGAACTACACAGATATTTGGT 59.345 38.462 0.00 0.00 0.00 3.67
2104 2244 7.822334 CCACAAGAACTACACAGATATTTGGTA 59.178 37.037 0.00 0.00 0.00 3.25
2105 2245 8.656849 CACAAGAACTACACAGATATTTGGTAC 58.343 37.037 0.00 0.00 0.00 3.34
2106 2246 8.594550 ACAAGAACTACACAGATATTTGGTACT 58.405 33.333 0.00 0.00 0.00 2.73
2107 2247 9.088512 CAAGAACTACACAGATATTTGGTACTC 57.911 37.037 0.00 0.00 0.00 2.59
2108 2248 7.783042 AGAACTACACAGATATTTGGTACTCC 58.217 38.462 0.00 0.00 0.00 3.85
2109 2249 6.145338 ACTACACAGATATTTGGTACTCCG 57.855 41.667 0.00 0.00 36.30 4.63
2110 2250 4.402056 ACACAGATATTTGGTACTCCGG 57.598 45.455 0.00 0.00 36.30 5.14
2111 2251 3.134081 ACACAGATATTTGGTACTCCGGG 59.866 47.826 0.00 0.00 36.30 5.73
2112 2252 2.104281 ACAGATATTTGGTACTCCGGGC 59.896 50.000 0.00 0.00 36.30 6.13
2113 2253 1.343465 AGATATTTGGTACTCCGGGCG 59.657 52.381 0.00 0.00 36.30 6.13
2114 2254 0.395312 ATATTTGGTACTCCGGGCGG 59.605 55.000 0.00 0.00 36.30 6.13
2115 2255 0.687098 TATTTGGTACTCCGGGCGGA 60.687 55.000 0.00 0.00 42.90 5.54
2116 2256 1.555477 ATTTGGTACTCCGGGCGGAA 61.555 55.000 0.00 0.00 44.66 4.30
2117 2257 2.453379 TTTGGTACTCCGGGCGGAAC 62.453 60.000 0.00 0.00 44.66 3.62
2118 2258 3.073101 GGTACTCCGGGCGGAACT 61.073 66.667 0.00 0.00 44.66 3.01
2119 2259 1.754234 GGTACTCCGGGCGGAACTA 60.754 63.158 0.00 0.00 44.66 2.24
2120 2260 1.322538 GGTACTCCGGGCGGAACTAA 61.323 60.000 0.00 0.00 44.66 2.24
2121 2261 0.179127 GTACTCCGGGCGGAACTAAC 60.179 60.000 0.00 0.00 44.66 2.34
2122 2262 1.656818 TACTCCGGGCGGAACTAACG 61.657 60.000 0.00 0.00 44.66 3.18
2129 2269 2.259204 CGGAACTAACGCCCGACA 59.741 61.111 0.00 0.00 45.58 4.35
2130 2270 1.373246 CGGAACTAACGCCCGACAA 60.373 57.895 0.00 0.00 45.58 3.18
2131 2271 0.945265 CGGAACTAACGCCCGACAAA 60.945 55.000 0.00 0.00 45.58 2.83
2132 2272 0.514255 GGAACTAACGCCCGACAAAC 59.486 55.000 0.00 0.00 0.00 2.93
2133 2273 0.514255 GAACTAACGCCCGACAAACC 59.486 55.000 0.00 0.00 0.00 3.27
2134 2274 0.179051 AACTAACGCCCGACAAACCA 60.179 50.000 0.00 0.00 0.00 3.67
2135 2275 0.179051 ACTAACGCCCGACAAACCAA 60.179 50.000 0.00 0.00 0.00 3.67
2136 2276 0.945813 CTAACGCCCGACAAACCAAA 59.054 50.000 0.00 0.00 0.00 3.28
2137 2277 1.334243 CTAACGCCCGACAAACCAAAA 59.666 47.619 0.00 0.00 0.00 2.44
2138 2278 0.101579 AACGCCCGACAAACCAAAAG 59.898 50.000 0.00 0.00 0.00 2.27
2139 2279 0.748729 ACGCCCGACAAACCAAAAGA 60.749 50.000 0.00 0.00 0.00 2.52
2140 2280 0.382515 CGCCCGACAAACCAAAAGAA 59.617 50.000 0.00 0.00 0.00 2.52
2141 2281 1.000717 CGCCCGACAAACCAAAAGAAT 60.001 47.619 0.00 0.00 0.00 2.40
2142 2282 2.226912 CGCCCGACAAACCAAAAGAATA 59.773 45.455 0.00 0.00 0.00 1.75
2143 2283 3.304794 CGCCCGACAAACCAAAAGAATAA 60.305 43.478 0.00 0.00 0.00 1.40
2144 2284 4.623002 GCCCGACAAACCAAAAGAATAAA 58.377 39.130 0.00 0.00 0.00 1.40
2145 2285 5.051153 GCCCGACAAACCAAAAGAATAAAA 58.949 37.500 0.00 0.00 0.00 1.52
2146 2286 5.176774 GCCCGACAAACCAAAAGAATAAAAG 59.823 40.000 0.00 0.00 0.00 2.27
2147 2287 6.277605 CCCGACAAACCAAAAGAATAAAAGT 58.722 36.000 0.00 0.00 0.00 2.66
2148 2288 6.200097 CCCGACAAACCAAAAGAATAAAAGTG 59.800 38.462 0.00 0.00 0.00 3.16
2149 2289 6.292114 CCGACAAACCAAAAGAATAAAAGTGC 60.292 38.462 0.00 0.00 0.00 4.40
2150 2290 6.475402 CGACAAACCAAAAGAATAAAAGTGCT 59.525 34.615 0.00 0.00 0.00 4.40
2151 2291 7.646130 CGACAAACCAAAAGAATAAAAGTGCTA 59.354 33.333 0.00 0.00 0.00 3.49
2152 2292 9.476202 GACAAACCAAAAGAATAAAAGTGCTAT 57.524 29.630 0.00 0.00 0.00 2.97
2166 2306 9.982651 ATAAAAGTGCTATATATGACGAACAGT 57.017 29.630 0.00 0.00 0.00 3.55
2167 2307 8.718102 AAAAGTGCTATATATGACGAACAGTT 57.282 30.769 0.00 0.00 0.00 3.16
2168 2308 9.811995 AAAAGTGCTATATATGACGAACAGTTA 57.188 29.630 0.00 0.00 0.00 2.24
2169 2309 9.982651 AAAGTGCTATATATGACGAACAGTTAT 57.017 29.630 0.00 0.00 33.36 1.89
2170 2310 8.972262 AGTGCTATATATGACGAACAGTTATG 57.028 34.615 0.00 0.00 31.12 1.90
2171 2311 8.793592 AGTGCTATATATGACGAACAGTTATGA 58.206 33.333 0.00 0.00 31.12 2.15
2172 2312 9.406828 GTGCTATATATGACGAACAGTTATGAA 57.593 33.333 0.00 0.00 31.12 2.57
2173 2313 9.406828 TGCTATATATGACGAACAGTTATGAAC 57.593 33.333 0.00 0.00 31.12 3.18
2174 2314 9.627395 GCTATATATGACGAACAGTTATGAACT 57.373 33.333 0.00 0.00 44.06 3.01
2179 2319 7.730364 ATGACGAACAGTTATGAACTTTTCT 57.270 32.000 13.48 4.36 42.93 2.52
2180 2320 7.548196 TGACGAACAGTTATGAACTTTTCTT 57.452 32.000 13.48 6.76 42.93 2.52
2219 2359 2.580815 CGCCTCTGCATCTGGACA 59.419 61.111 4.26 0.00 37.32 4.02
2362 2507 0.733150 GTTGATGAAGGGGCGCTAAC 59.267 55.000 7.64 1.17 0.00 2.34
2366 2511 0.392998 ATGAAGGGGCGCTAACAGTG 60.393 55.000 7.64 0.00 0.00 3.66
2389 2534 2.651455 GGCCTAATACCAAACAGACCC 58.349 52.381 0.00 0.00 0.00 4.46
2413 2558 4.021544 TGCAGCCAAACCTAACATTTAAGG 60.022 41.667 0.00 0.00 38.93 2.69
2417 2562 4.707934 GCCAAACCTAACATTTAAGGCCTA 59.292 41.667 5.16 0.00 36.24 3.93
2439 2584 1.458777 TCCCAACCAGGACGTCTGT 60.459 57.895 16.46 7.77 41.83 3.41
2448 2594 1.226888 GGACGTCTGTCGGGTATGC 60.227 63.158 16.46 0.00 46.49 3.14
2459 2605 4.234019 GGTATGCGCACCCATCAA 57.766 55.556 14.90 0.00 31.91 2.57
2509 2655 4.849310 GGTATGAGGCCGCCGCAA 62.849 66.667 20.38 6.90 36.81 4.85
2542 2688 4.411540 ACCAATCCATCTTCAGAGCTGTAT 59.588 41.667 0.00 0.00 0.00 2.29
2554 2700 4.124970 CAGAGCTGTATTGCTGCATCTAA 58.875 43.478 1.84 0.00 44.17 2.10
2560 2706 4.264253 TGTATTGCTGCATCTAACTTGCT 58.736 39.130 1.84 0.00 40.77 3.91
2562 2708 2.775911 TGCTGCATCTAACTTGCTCT 57.224 45.000 0.00 0.00 40.77 4.09
2563 2709 3.893326 TGCTGCATCTAACTTGCTCTA 57.107 42.857 0.00 0.00 40.77 2.43
2694 2840 1.605710 CCGTCATCAATGGGCAAGATC 59.394 52.381 0.00 0.00 0.00 2.75
2711 2857 1.139853 GATCAATCACCGCTCCTCCTT 59.860 52.381 0.00 0.00 0.00 3.36
2750 2896 0.883833 CTTGCTCCAAAACGATGCCT 59.116 50.000 0.00 0.00 0.00 4.75
2870 3017 3.499737 CCTGCAACGACGATGCCC 61.500 66.667 24.68 2.03 43.16 5.36
2888 3035 3.300711 CCAAGAAGGGAACGACGTT 57.699 52.632 14.11 14.11 0.00 3.99
2904 3051 4.508128 TTCGAGACGCCGCCATCC 62.508 66.667 0.00 0.00 0.00 3.51
2925 3072 2.343758 GCCAAGACCGCAGTCAGA 59.656 61.111 2.32 0.00 46.15 3.27
2949 3096 2.247637 GATTTTTACCGAAAGCCACGC 58.752 47.619 0.00 0.00 0.00 5.34
3124 3274 2.257409 GACACCAGATCCACGGCCAT 62.257 60.000 2.24 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.953471 GTATTGTCGCACCACAGCCA 60.953 55.000 0.00 0.00 0.00 4.75
34 35 2.994699 CCCAGGGGTATTGTCGCA 59.005 61.111 0.00 0.00 0.00 5.10
37 38 2.516225 GCGCCCAGGGGTATTGTC 60.516 66.667 7.91 0.00 37.65 3.18
39 40 4.894896 GGGCGCCCAGGGGTATTG 62.895 72.222 40.73 0.00 37.65 1.90
92 93 2.408565 TCCTTTGCTGGTATCCCTAGG 58.591 52.381 0.06 0.06 0.00 3.02
94 95 3.136443 CACATCCTTTGCTGGTATCCCTA 59.864 47.826 0.00 0.00 0.00 3.53
99 100 2.025981 TCTGCACATCCTTTGCTGGTAT 60.026 45.455 0.00 0.00 40.86 2.73
100 101 1.350684 TCTGCACATCCTTTGCTGGTA 59.649 47.619 0.00 0.00 40.86 3.25
101 102 0.111061 TCTGCACATCCTTTGCTGGT 59.889 50.000 0.00 0.00 40.86 4.00
102 103 1.201647 CTTCTGCACATCCTTTGCTGG 59.798 52.381 0.00 0.00 40.86 4.85
104 105 2.157738 GACTTCTGCACATCCTTTGCT 58.842 47.619 0.00 0.00 40.86 3.91
106 107 2.486982 CTGGACTTCTGCACATCCTTTG 59.513 50.000 0.00 0.00 32.06 2.77
107 108 2.373169 TCTGGACTTCTGCACATCCTTT 59.627 45.455 0.00 0.00 32.06 3.11
112 114 1.911357 TGGATCTGGACTTCTGCACAT 59.089 47.619 0.00 0.00 0.00 3.21
137 139 4.276678 TCAAATCAAACAGCAGTTGGAGAG 59.723 41.667 5.24 0.00 40.88 3.20
142 144 5.159209 GGATCTCAAATCAAACAGCAGTTG 58.841 41.667 0.00 0.00 38.17 3.16
149 151 4.141287 ACCGTTGGATCTCAAATCAAACA 58.859 39.130 6.21 0.00 37.08 2.83
159 161 1.550976 ACTCCAGAACCGTTGGATCTC 59.449 52.381 0.00 0.00 43.46 2.75
174 176 1.100510 CTCCCGTGATACGAACTCCA 58.899 55.000 2.52 0.00 46.05 3.86
181 183 0.384309 TTAGCTGCTCCCGTGATACG 59.616 55.000 4.91 0.00 42.11 3.06
182 184 1.870167 GCTTAGCTGCTCCCGTGATAC 60.870 57.143 4.91 0.00 0.00 2.24
191 194 1.079819 TCCACACGCTTAGCTGCTC 60.080 57.895 4.91 0.00 0.00 4.26
196 199 3.169198 GTGCTCCACACGCTTAGC 58.831 61.111 0.00 0.00 40.07 3.09
204 207 2.027192 GGAAAGTATCAGGTGCTCCACA 60.027 50.000 7.70 0.00 35.86 4.17
213 216 4.410228 TCATCAAGGAGGGAAAGTATCAGG 59.590 45.833 0.00 0.00 0.00 3.86
220 223 3.262915 AGAGTGTCATCAAGGAGGGAAAG 59.737 47.826 0.00 0.00 0.00 2.62
226 229 6.460814 CCATGTAGTAGAGTGTCATCAAGGAG 60.461 46.154 0.00 0.00 0.00 3.69
227 230 5.360999 CCATGTAGTAGAGTGTCATCAAGGA 59.639 44.000 0.00 0.00 0.00 3.36
228 231 5.127845 ACCATGTAGTAGAGTGTCATCAAGG 59.872 44.000 0.00 0.00 0.00 3.61
229 232 6.214191 ACCATGTAGTAGAGTGTCATCAAG 57.786 41.667 0.00 0.00 0.00 3.02
230 233 5.127194 GGACCATGTAGTAGAGTGTCATCAA 59.873 44.000 0.00 0.00 0.00 2.57
231 234 4.645136 GGACCATGTAGTAGAGTGTCATCA 59.355 45.833 0.00 0.00 0.00 3.07
232 235 4.038162 GGGACCATGTAGTAGAGTGTCATC 59.962 50.000 0.00 0.00 0.00 2.92
233 236 3.961408 GGGACCATGTAGTAGAGTGTCAT 59.039 47.826 0.00 0.00 0.00 3.06
234 237 3.362706 GGGACCATGTAGTAGAGTGTCA 58.637 50.000 0.00 0.00 0.00 3.58
235 238 2.358267 CGGGACCATGTAGTAGAGTGTC 59.642 54.545 0.00 0.00 0.00 3.67
236 239 2.025605 TCGGGACCATGTAGTAGAGTGT 60.026 50.000 0.00 0.00 0.00 3.55
237 240 2.619177 CTCGGGACCATGTAGTAGAGTG 59.381 54.545 0.00 0.00 0.00 3.51
238 241 2.508716 TCTCGGGACCATGTAGTAGAGT 59.491 50.000 0.00 0.00 0.00 3.24
239 242 2.879646 GTCTCGGGACCATGTAGTAGAG 59.120 54.545 3.28 0.00 36.53 2.43
240 243 2.508716 AGTCTCGGGACCATGTAGTAGA 59.491 50.000 12.98 0.00 43.05 2.59
241 244 2.933573 AGTCTCGGGACCATGTAGTAG 58.066 52.381 12.98 0.00 43.05 2.57
242 245 3.377253 AAGTCTCGGGACCATGTAGTA 57.623 47.619 12.98 0.00 43.05 1.82
245 248 3.021695 CACTAAGTCTCGGGACCATGTA 58.978 50.000 12.98 0.00 43.05 2.29
267 270 2.092538 TCGTGGAAAACCTTGTACCCAA 60.093 45.455 0.00 0.00 0.00 4.12
271 274 1.528161 CCGTCGTGGAAAACCTTGTAC 59.472 52.381 0.00 0.00 42.00 2.90
307 311 3.498082 CATATTGCATGCATGATCGTGG 58.502 45.455 30.64 10.74 0.00 4.94
337 341 1.737029 CGTCATGTGTCCAGCGATTCT 60.737 52.381 0.00 0.00 0.00 2.40
350 354 4.261909 GGGTTATATTCGTCCTCGTCATGT 60.262 45.833 0.00 0.00 38.33 3.21
356 360 3.432252 GCATTGGGTTATATTCGTCCTCG 59.568 47.826 0.00 0.00 38.55 4.63
364 368 3.891366 GACTGCCTGCATTGGGTTATATT 59.109 43.478 0.00 0.00 0.00 1.28
377 381 2.749441 GCCCTCTTGACTGCCTGC 60.749 66.667 0.00 0.00 0.00 4.85
397 401 1.684049 AAGAGAGCCAGGTCCTCCG 60.684 63.158 6.61 0.00 39.05 4.63
424 428 5.425217 TCATGAGTGCTAGGTTTATCTCCAA 59.575 40.000 0.00 0.00 0.00 3.53
425 429 4.962362 TCATGAGTGCTAGGTTTATCTCCA 59.038 41.667 0.00 0.00 0.00 3.86
433 437 2.906389 TGACCTTCATGAGTGCTAGGTT 59.094 45.455 15.56 2.34 39.02 3.50
478 482 7.175990 GTCCATCAGTGTTAATTTTAACCCAGA 59.824 37.037 9.96 2.90 41.72 3.86
504 508 1.314534 TGCATCAAAGCATCCACCGG 61.315 55.000 0.00 0.00 40.11 5.28
542 554 3.277211 GAGGTGCGACCGTGCTACA 62.277 63.158 0.00 0.00 44.90 2.74
605 618 2.875296 AGCACTTTGGCAATGGAAGTA 58.125 42.857 16.35 0.00 32.69 2.24
610 623 1.202557 ACACAAGCACTTTGGCAATGG 60.203 47.619 16.35 8.33 41.25 3.16
628 641 4.955811 AATATGACTCCCTCGCATAACA 57.044 40.909 0.00 0.00 0.00 2.41
673 686 0.683179 ATCGACCTCCATCACCACGA 60.683 55.000 0.00 0.00 0.00 4.35
715 729 2.159156 TCTTGTATTATGACGCGGCAGT 60.159 45.455 23.88 11.96 0.00 4.40
718 732 3.121944 CAGATCTTGTATTATGACGCGGC 59.878 47.826 12.47 8.67 0.00 6.53
719 733 4.299155 ACAGATCTTGTATTATGACGCGG 58.701 43.478 12.47 0.00 38.56 6.46
740 754 2.186076 CTCGAAGATAGGCGTCACAAC 58.814 52.381 0.00 0.00 33.89 3.32
793 807 6.250819 CCTACTAACATGTTGCATCGAAAAG 58.749 40.000 21.42 9.27 0.00 2.27
824 838 0.716108 CAAAGATCGACCGTGCTGTC 59.284 55.000 0.00 0.00 0.00 3.51
827 841 2.827604 CACAAAGATCGACCGTGCT 58.172 52.632 0.00 0.00 0.00 4.40
834 848 4.002982 AGCATGTTTAGCACAAAGATCGA 58.997 39.130 0.00 0.00 39.50 3.59
847 861 6.774170 TCGGATACCTCTAAGTAGCATGTTTA 59.226 38.462 0.00 0.00 30.13 2.01
861 875 2.526888 TCCAACACTCGGATACCTCT 57.473 50.000 0.00 0.00 0.00 3.69
862 876 2.693591 TCATCCAACACTCGGATACCTC 59.306 50.000 0.00 0.00 41.48 3.85
863 877 2.747177 TCATCCAACACTCGGATACCT 58.253 47.619 0.00 0.00 41.48 3.08
864 878 3.536956 TTCATCCAACACTCGGATACC 57.463 47.619 0.00 0.00 41.48 2.73
865 879 7.226720 ACAAATATTCATCCAACACTCGGATAC 59.773 37.037 0.00 0.00 41.48 2.24
866 880 7.279615 ACAAATATTCATCCAACACTCGGATA 58.720 34.615 0.00 0.00 41.48 2.59
867 881 6.122277 ACAAATATTCATCCAACACTCGGAT 58.878 36.000 0.00 0.00 44.35 4.18
868 882 5.496556 ACAAATATTCATCCAACACTCGGA 58.503 37.500 0.00 0.00 36.84 4.55
869 883 5.220854 GGACAAATATTCATCCAACACTCGG 60.221 44.000 11.41 0.00 0.00 4.63
870 884 5.353956 TGGACAAATATTCATCCAACACTCG 59.646 40.000 15.14 0.00 38.30 4.18
871 885 6.757897 TGGACAAATATTCATCCAACACTC 57.242 37.500 15.14 0.00 38.30 3.51
883 905 8.034804 GCTTACAATGAAGGTTGGACAAATATT 58.965 33.333 0.00 0.00 33.40 1.28
887 909 4.646945 TGCTTACAATGAAGGTTGGACAAA 59.353 37.500 0.00 0.00 33.40 2.83
895 917 2.887151 AGGCTGCTTACAATGAAGGT 57.113 45.000 0.00 0.00 0.00 3.50
982 1004 1.123077 TTGCGGGTGAGATAGCAGAT 58.877 50.000 0.00 0.00 40.90 2.90
986 1008 2.356135 TCTTTTTGCGGGTGAGATAGC 58.644 47.619 0.00 0.00 0.00 2.97
990 1012 3.798548 GCAATTTCTTTTTGCGGGTGAGA 60.799 43.478 0.00 0.00 39.98 3.27
991 1013 2.476241 GCAATTTCTTTTTGCGGGTGAG 59.524 45.455 0.00 0.00 39.98 3.51
1017 1039 2.201732 CCGGATGGACGTGTCTAATTG 58.798 52.381 0.00 0.00 37.49 2.32
1020 1042 1.514087 GCCGGATGGACGTGTCTAA 59.486 57.895 5.05 0.00 37.49 2.10
1078 1111 2.910479 AGACGTGTCGGGCTCACA 60.910 61.111 0.00 0.00 35.79 3.58
1148 1181 2.594592 AAGAACTGCGGCGCCTTT 60.595 55.556 30.82 21.80 0.00 3.11
1149 1182 3.050275 GAAGAACTGCGGCGCCTT 61.050 61.111 30.82 23.99 0.00 4.35
1151 1184 3.491652 GAGAAGAACTGCGGCGCC 61.492 66.667 30.82 19.07 0.00 6.53
1162 1195 5.868258 CGGATACTATAGTAGTGCGAGAAGA 59.132 44.000 20.74 0.00 39.81 2.87
1168 1201 4.967437 GGAACGGATACTATAGTAGTGCG 58.033 47.826 22.25 22.25 39.81 5.34
1230 1274 4.470170 TCCGCCATGTCGTCGTCG 62.470 66.667 0.00 0.00 38.55 5.12
1231 1275 2.879462 GTCCGCCATGTCGTCGTC 60.879 66.667 0.00 0.00 0.00 4.20
1232 1276 4.771356 CGTCCGCCATGTCGTCGT 62.771 66.667 0.00 0.00 0.00 4.34
1338 1382 3.329386 GACGATGGTGATGGATATGGTG 58.671 50.000 0.00 0.00 0.00 4.17
1527 1589 1.580845 GCTGCAGCTTCATCCACGTT 61.581 55.000 31.33 0.00 38.21 3.99
1565 1627 8.114331 TCAGGAACATAATAATACGTACCGAT 57.886 34.615 0.00 0.00 0.00 4.18
1595 1657 6.035435 CACATCATGCTCACAAAGTAGTACTC 59.965 42.308 2.58 0.00 0.00 2.59
1596 1658 5.871524 CACATCATGCTCACAAAGTAGTACT 59.128 40.000 0.00 0.00 0.00 2.73
1597 1659 5.869344 TCACATCATGCTCACAAAGTAGTAC 59.131 40.000 0.00 0.00 0.00 2.73
1598 1660 6.036577 TCACATCATGCTCACAAAGTAGTA 57.963 37.500 0.00 0.00 0.00 1.82
1599 1661 4.898320 TCACATCATGCTCACAAAGTAGT 58.102 39.130 0.00 0.00 0.00 2.73
1600 1662 6.315642 AGAATCACATCATGCTCACAAAGTAG 59.684 38.462 0.00 0.00 0.00 2.57
1601 1663 6.093082 CAGAATCACATCATGCTCACAAAGTA 59.907 38.462 0.00 0.00 0.00 2.24
1602 1664 5.008331 AGAATCACATCATGCTCACAAAGT 58.992 37.500 0.00 0.00 0.00 2.66
1685 1791 1.134159 CCCATCTCCAGGCTCTTCTTG 60.134 57.143 0.00 0.00 0.00 3.02
1747 1853 1.071471 CTTCACGTGTCCTTGGCCT 59.929 57.895 16.51 0.00 0.00 5.19
1781 1888 3.219928 GAGCTCGGCATCGGAGGA 61.220 66.667 0.00 0.00 36.95 3.71
1782 1889 3.222855 AGAGCTCGGCATCGGAGG 61.223 66.667 8.37 0.00 36.95 4.30
1792 1899 4.985409 AGTAAAACTTCTGTTCAGAGCTCG 59.015 41.667 8.37 3.55 34.96 5.03
1798 1905 4.913924 GCATGCAGTAAAACTTCTGTTCAG 59.086 41.667 14.21 0.00 34.96 3.02
1924 2035 3.889815 CTCAGGCACCCAGAATCATTAA 58.110 45.455 0.00 0.00 0.00 1.40
1980 2120 5.707242 ATCTCTGTTCACTTTCTGTCGTA 57.293 39.130 0.00 0.00 0.00 3.43
1981 2121 4.592485 ATCTCTGTTCACTTTCTGTCGT 57.408 40.909 0.00 0.00 0.00 4.34
1982 2122 6.034363 CACATATCTCTGTTCACTTTCTGTCG 59.966 42.308 0.00 0.00 0.00 4.35
2002 2142 5.059833 TGTGATTATGCCGCATAACACATA 58.940 37.500 31.43 25.42 39.80 2.29
2057 2197 5.002516 TGGTGATGCGATTTATATCATGCA 58.997 37.500 0.00 0.00 33.82 3.96
2058 2198 5.106594 TGTGGTGATGCGATTTATATCATGC 60.107 40.000 0.00 0.00 33.82 4.06
2059 2199 6.484818 TGTGGTGATGCGATTTATATCATG 57.515 37.500 0.00 0.00 33.82 3.07
2060 2200 6.936335 TCTTGTGGTGATGCGATTTATATCAT 59.064 34.615 0.00 0.00 33.82 2.45
2061 2201 6.287525 TCTTGTGGTGATGCGATTTATATCA 58.712 36.000 0.00 0.00 0.00 2.15
2062 2202 6.785488 TCTTGTGGTGATGCGATTTATATC 57.215 37.500 0.00 0.00 0.00 1.63
2063 2203 6.767902 AGTTCTTGTGGTGATGCGATTTATAT 59.232 34.615 0.00 0.00 0.00 0.86
2064 2204 6.112734 AGTTCTTGTGGTGATGCGATTTATA 58.887 36.000 0.00 0.00 0.00 0.98
2065 2205 4.943705 AGTTCTTGTGGTGATGCGATTTAT 59.056 37.500 0.00 0.00 0.00 1.40
2066 2206 4.323417 AGTTCTTGTGGTGATGCGATTTA 58.677 39.130 0.00 0.00 0.00 1.40
2067 2207 3.149196 AGTTCTTGTGGTGATGCGATTT 58.851 40.909 0.00 0.00 0.00 2.17
2068 2208 2.783135 AGTTCTTGTGGTGATGCGATT 58.217 42.857 0.00 0.00 0.00 3.34
2069 2209 2.479566 AGTTCTTGTGGTGATGCGAT 57.520 45.000 0.00 0.00 0.00 4.58
2070 2210 2.036604 TGTAGTTCTTGTGGTGATGCGA 59.963 45.455 0.00 0.00 0.00 5.10
2071 2211 2.157668 GTGTAGTTCTTGTGGTGATGCG 59.842 50.000 0.00 0.00 0.00 4.73
2072 2212 3.138304 TGTGTAGTTCTTGTGGTGATGC 58.862 45.455 0.00 0.00 0.00 3.91
2073 2213 4.631131 TCTGTGTAGTTCTTGTGGTGATG 58.369 43.478 0.00 0.00 0.00 3.07
2074 2214 4.955811 TCTGTGTAGTTCTTGTGGTGAT 57.044 40.909 0.00 0.00 0.00 3.06
2075 2215 4.955811 ATCTGTGTAGTTCTTGTGGTGA 57.044 40.909 0.00 0.00 0.00 4.02
2076 2216 7.361201 CCAAATATCTGTGTAGTTCTTGTGGTG 60.361 40.741 0.00 0.00 0.00 4.17
2077 2217 6.655003 CCAAATATCTGTGTAGTTCTTGTGGT 59.345 38.462 0.00 0.00 0.00 4.16
2078 2218 6.655003 ACCAAATATCTGTGTAGTTCTTGTGG 59.345 38.462 0.00 0.00 0.00 4.17
2079 2219 7.672983 ACCAAATATCTGTGTAGTTCTTGTG 57.327 36.000 0.00 0.00 0.00 3.33
2080 2220 8.594550 AGTACCAAATATCTGTGTAGTTCTTGT 58.405 33.333 0.00 0.00 0.00 3.16
2081 2221 9.088512 GAGTACCAAATATCTGTGTAGTTCTTG 57.911 37.037 0.00 0.00 0.00 3.02
2082 2222 8.258708 GGAGTACCAAATATCTGTGTAGTTCTT 58.741 37.037 0.00 0.00 35.97 2.52
2083 2223 7.416438 CGGAGTACCAAATATCTGTGTAGTTCT 60.416 40.741 0.00 0.00 35.59 3.01
2084 2224 6.696148 CGGAGTACCAAATATCTGTGTAGTTC 59.304 42.308 0.00 0.00 35.59 3.01
2085 2225 6.406624 CCGGAGTACCAAATATCTGTGTAGTT 60.407 42.308 0.00 0.00 35.59 2.24
2086 2226 5.068723 CCGGAGTACCAAATATCTGTGTAGT 59.931 44.000 0.00 0.00 35.59 2.73
2087 2227 5.509163 CCCGGAGTACCAAATATCTGTGTAG 60.509 48.000 0.73 0.00 35.59 2.74
2088 2228 4.342951 CCCGGAGTACCAAATATCTGTGTA 59.657 45.833 0.73 0.00 35.59 2.90
2089 2229 3.134081 CCCGGAGTACCAAATATCTGTGT 59.866 47.826 0.73 0.00 35.59 3.72
2090 2230 3.728845 CCCGGAGTACCAAATATCTGTG 58.271 50.000 0.73 0.00 35.59 3.66
2091 2231 2.104281 GCCCGGAGTACCAAATATCTGT 59.896 50.000 0.73 0.00 35.59 3.41
2092 2232 2.767505 GCCCGGAGTACCAAATATCTG 58.232 52.381 0.73 0.00 35.59 2.90
2093 2233 1.343465 CGCCCGGAGTACCAAATATCT 59.657 52.381 0.73 0.00 35.59 1.98
2094 2234 1.607251 CCGCCCGGAGTACCAAATATC 60.607 57.143 0.73 0.00 37.50 1.63
2095 2235 0.395312 CCGCCCGGAGTACCAAATAT 59.605 55.000 0.73 0.00 37.50 1.28
2096 2236 0.687098 TCCGCCCGGAGTACCAAATA 60.687 55.000 0.73 0.00 39.76 1.40
2097 2237 1.555477 TTCCGCCCGGAGTACCAAAT 61.555 55.000 0.73 0.00 46.06 2.32
2098 2238 2.215625 TTCCGCCCGGAGTACCAAA 61.216 57.895 0.73 0.00 46.06 3.28
2099 2239 2.604079 TTCCGCCCGGAGTACCAA 60.604 61.111 0.73 0.00 46.06 3.67
2100 2240 2.497792 TAGTTCCGCCCGGAGTACCA 62.498 60.000 0.73 0.00 46.06 3.25
2101 2241 1.322538 TTAGTTCCGCCCGGAGTACC 61.323 60.000 0.73 0.41 46.06 3.34
2102 2242 0.179127 GTTAGTTCCGCCCGGAGTAC 60.179 60.000 0.73 6.48 46.06 2.73
2103 2243 1.656818 CGTTAGTTCCGCCCGGAGTA 61.657 60.000 0.73 3.49 46.06 2.59
2104 2244 2.976356 GTTAGTTCCGCCCGGAGT 59.024 61.111 0.73 4.43 46.06 3.85
2105 2245 2.202703 CGTTAGTTCCGCCCGGAG 60.203 66.667 0.73 0.00 46.06 4.63
2106 2246 4.440127 GCGTTAGTTCCGCCCGGA 62.440 66.667 0.73 5.12 45.20 5.14
2112 2252 0.945265 TTTGTCGGGCGTTAGTTCCG 60.945 55.000 0.00 0.00 44.59 4.30
2113 2253 0.514255 GTTTGTCGGGCGTTAGTTCC 59.486 55.000 0.00 0.00 0.00 3.62
2114 2254 0.514255 GGTTTGTCGGGCGTTAGTTC 59.486 55.000 0.00 0.00 0.00 3.01
2115 2255 0.179051 TGGTTTGTCGGGCGTTAGTT 60.179 50.000 0.00 0.00 0.00 2.24
2116 2256 0.179051 TTGGTTTGTCGGGCGTTAGT 60.179 50.000 0.00 0.00 0.00 2.24
2117 2257 0.945813 TTTGGTTTGTCGGGCGTTAG 59.054 50.000 0.00 0.00 0.00 2.34
2118 2258 1.334243 CTTTTGGTTTGTCGGGCGTTA 59.666 47.619 0.00 0.00 0.00 3.18
2119 2259 0.101579 CTTTTGGTTTGTCGGGCGTT 59.898 50.000 0.00 0.00 0.00 4.84
2120 2260 0.748729 TCTTTTGGTTTGTCGGGCGT 60.749 50.000 0.00 0.00 0.00 5.68
2121 2261 0.382515 TTCTTTTGGTTTGTCGGGCG 59.617 50.000 0.00 0.00 0.00 6.13
2122 2262 2.812358 ATTCTTTTGGTTTGTCGGGC 57.188 45.000 0.00 0.00 0.00 6.13
2123 2263 6.200097 CACTTTTATTCTTTTGGTTTGTCGGG 59.800 38.462 0.00 0.00 0.00 5.14
2124 2264 6.292114 GCACTTTTATTCTTTTGGTTTGTCGG 60.292 38.462 0.00 0.00 0.00 4.79
2125 2265 6.475402 AGCACTTTTATTCTTTTGGTTTGTCG 59.525 34.615 0.00 0.00 0.00 4.35
2126 2266 7.770801 AGCACTTTTATTCTTTTGGTTTGTC 57.229 32.000 0.00 0.00 0.00 3.18
2140 2280 9.982651 ACTGTTCGTCATATATAGCACTTTTAT 57.017 29.630 0.00 0.00 0.00 1.40
2141 2281 9.811995 AACTGTTCGTCATATATAGCACTTTTA 57.188 29.630 0.00 0.00 0.00 1.52
2142 2282 8.718102 AACTGTTCGTCATATATAGCACTTTT 57.282 30.769 0.00 0.00 0.00 2.27
2143 2283 9.982651 ATAACTGTTCGTCATATATAGCACTTT 57.017 29.630 0.00 0.00 0.00 2.66
2144 2284 9.411801 CATAACTGTTCGTCATATATAGCACTT 57.588 33.333 0.00 0.00 0.00 3.16
2145 2285 8.793592 TCATAACTGTTCGTCATATATAGCACT 58.206 33.333 0.00 0.00 0.00 4.40
2146 2286 8.965986 TCATAACTGTTCGTCATATATAGCAC 57.034 34.615 0.00 0.00 0.00 4.40
2147 2287 9.406828 GTTCATAACTGTTCGTCATATATAGCA 57.593 33.333 0.00 0.00 0.00 3.49
2148 2288 9.627395 AGTTCATAACTGTTCGTCATATATAGC 57.373 33.333 0.00 0.00 41.01 2.97
2173 2313 9.126151 AGGTCTTCCTCTTTTTCTAAAGAAAAG 57.874 33.333 15.38 9.98 46.72 2.27
2201 2341 2.894387 GTCCAGATGCAGAGGCGC 60.894 66.667 0.00 0.00 45.35 6.53
2202 2342 0.463295 ATTGTCCAGATGCAGAGGCG 60.463 55.000 0.00 0.00 45.35 5.52
2285 2426 9.577110 CGGTGACTTAGTGTCTTGTATTAATAA 57.423 33.333 0.00 0.00 45.54 1.40
2286 2427 8.742777 ACGGTGACTTAGTGTCTTGTATTAATA 58.257 33.333 0.00 0.00 45.54 0.98
2287 2428 7.609056 ACGGTGACTTAGTGTCTTGTATTAAT 58.391 34.615 0.00 0.00 45.54 1.40
2288 2429 6.985117 ACGGTGACTTAGTGTCTTGTATTAA 58.015 36.000 0.00 0.00 45.54 1.40
2289 2430 6.432162 AGACGGTGACTTAGTGTCTTGTATTA 59.568 38.462 0.00 0.00 45.54 0.98
2290 2431 5.243283 AGACGGTGACTTAGTGTCTTGTATT 59.757 40.000 0.00 0.00 45.54 1.89
2291 2432 4.765856 AGACGGTGACTTAGTGTCTTGTAT 59.234 41.667 0.00 0.00 45.54 2.29
2292 2433 4.139786 AGACGGTGACTTAGTGTCTTGTA 58.860 43.478 0.00 0.00 45.54 2.41
2293 2434 2.957006 AGACGGTGACTTAGTGTCTTGT 59.043 45.455 0.00 0.00 45.54 3.16
2294 2435 3.644884 AGACGGTGACTTAGTGTCTTG 57.355 47.619 0.00 0.00 45.54 3.02
2295 2436 5.779529 TTTAGACGGTGACTTAGTGTCTT 57.220 39.130 8.10 0.00 45.54 3.01
2296 2437 5.475909 TCATTTAGACGGTGACTTAGTGTCT 59.524 40.000 7.93 7.93 45.54 3.41
2297 2438 5.572126 GTCATTTAGACGGTGACTTAGTGTC 59.428 44.000 0.00 0.00 40.68 3.67
2298 2439 5.467705 GTCATTTAGACGGTGACTTAGTGT 58.532 41.667 0.00 0.00 39.24 3.55
2318 2459 6.805713 TGAATAGAAATAGCGACAGATGTCA 58.194 36.000 13.09 0.00 44.99 3.58
2319 2460 6.920758 ACTGAATAGAAATAGCGACAGATGTC 59.079 38.462 2.78 2.78 41.47 3.06
2335 2480 3.432186 CGCCCCTTCATCAACTGAATAGA 60.432 47.826 0.00 0.00 42.87 1.98
2340 2485 1.377202 GCGCCCCTTCATCAACTGA 60.377 57.895 0.00 0.00 0.00 3.41
2362 2507 2.752903 GTTTGGTATTAGGCCCACACTG 59.247 50.000 0.00 0.00 30.46 3.66
2366 2511 3.014623 GTCTGTTTGGTATTAGGCCCAC 58.985 50.000 0.00 0.00 0.00 4.61
2389 2534 3.665745 AAATGTTAGGTTTGGCTGCAG 57.334 42.857 10.11 10.11 0.00 4.41
2413 2558 1.205460 TCCTGGTTGGGACCTTAGGC 61.205 60.000 0.00 0.00 46.66 3.93
2448 2594 3.585990 GCCGGATTGATGGGTGCG 61.586 66.667 5.05 0.00 0.00 5.34
2459 2605 1.153086 GTTGAGGAGCATGCCGGAT 60.153 57.895 15.66 0.00 0.00 4.18
2509 2655 1.004745 GATGGATTGGTGACAGGTGGT 59.995 52.381 0.00 0.00 44.54 4.16
2542 2688 3.063510 AGAGCAAGTTAGATGCAGCAA 57.936 42.857 4.07 0.00 46.22 3.91
2554 2700 1.339610 CGGCAGCTAGATAGAGCAAGT 59.660 52.381 0.00 0.00 45.43 3.16
2576 2722 4.595538 GGCGTCGTGGTGGTGTCA 62.596 66.667 0.00 0.00 0.00 3.58
2603 2749 1.681327 GGACTCACGCAGGAGGGTA 60.681 63.158 6.57 0.00 39.11 3.69
2640 2786 3.749064 GGCGCAGTGGAGACTCGA 61.749 66.667 10.83 0.00 0.00 4.04
2694 2840 1.470098 CAAAAGGAGGAGCGGTGATTG 59.530 52.381 0.00 0.00 0.00 2.67
2711 2857 0.776810 TGCTGATTGGAGGGGACAAA 59.223 50.000 0.00 0.00 0.00 2.83
2870 3017 1.145803 GAACGTCGTTCCCTTCTTGG 58.854 55.000 24.47 0.00 36.65 3.61
2904 3051 4.379243 ACTGCGGTCTTGGCGGAG 62.379 66.667 0.00 0.00 40.04 4.63
2925 3072 1.135888 GGCTTTCGGTAAAAATCGCGT 60.136 47.619 5.77 0.00 0.00 6.01
3097 3247 2.933287 ATCTGGTGTCCCGGCCAA 60.933 61.111 2.24 0.00 37.01 4.52


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

AutoCloner maintained by Alex Coulton.