Multiple sequence alignment - TraesCS5A01G541400

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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 TraesCS5A01G541400 chr5A 100.000 9092 0 0 1 9092 698207572 698216663 0.000000e+00 16790.0
1 TraesCS5A01G541400 chr5A 89.594 788 62 8 29 797 460464300 460465086 0.000000e+00 983.0
2 TraesCS5A01G541400 chr5A 90.357 280 26 1 7944 8222 698228601 698228880 5.190000e-97 366.0
3 TraesCS5A01G541400 chr5A 85.119 168 19 4 8300 8464 698228873 698229037 5.650000e-37 167.0
4 TraesCS5A01G541400 chr5A 96.000 75 3 0 6079 6153 698228516 698228590 1.240000e-23 122.0
5 TraesCS5A01G541400 chr4D 95.772 4281 132 20 4581 8828 509368629 509372893 0.000000e+00 6857.0
6 TraesCS5A01G541400 chr4D 94.926 3370 112 31 1251 4572 509364162 509367520 0.000000e+00 5221.0
7 TraesCS5A01G541400 chr4D 88.127 379 15 11 788 1144 509363320 509363690 3.030000e-114 424.0
8 TraesCS5A01G541400 chr4D 85.171 263 25 5 8785 9047 509383158 509383406 3.260000e-64 257.0
9 TraesCS5A01G541400 chr4D 83.390 295 24 11 8226 8517 509382645 509382917 5.450000e-62 250.0
10 TraesCS5A01G541400 chr4D 94.366 142 4 2 8955 9092 509373121 509373262 1.990000e-51 215.0
11 TraesCS5A01G541400 chr4D 96.396 111 4 0 8807 8917 509373013 509373123 5.610000e-42 183.0
12 TraesCS5A01G541400 chr4D 100.000 28 0 0 1 28 42241834 42241861 1.600000e-02 52.8
13 TraesCS5A01G541400 chr4B 95.684 3383 86 13 2988 6362 657472063 657468733 0.000000e+00 5384.0
14 TraesCS5A01G541400 chr4B 94.225 1870 102 5 6358 8222 657468647 657466779 0.000000e+00 2850.0
15 TraesCS5A01G541400 chr4B 89.222 1633 91 30 1304 2899 657473996 657472412 0.000000e+00 1962.0
16 TraesCS5A01G541400 chr4B 90.649 770 60 5 29 795 562442944 562442184 0.000000e+00 1013.0
17 TraesCS5A01G541400 chr4B 89.213 788 61 5 29 793 31515115 31515901 0.000000e+00 963.0
18 TraesCS5A01G541400 chr4B 88.724 807 55 10 29 800 5185926 5185121 0.000000e+00 953.0
19 TraesCS5A01G541400 chr4B 89.189 407 18 10 787 1174 657474915 657474516 1.370000e-132 484.0
20 TraesCS5A01G541400 chr4B 78.423 241 22 12 8807 9047 657460715 657460505 7.410000e-26 130.0
21 TraesCS5A01G541400 chr5B 89.763 801 48 14 29 795 22072233 22071433 0.000000e+00 994.0
22 TraesCS5A01G541400 chr5B 88.648 784 65 15 29 795 472219131 472218355 0.000000e+00 933.0
23 TraesCS5A01G541400 chr5B 83.166 796 103 19 29 797 546543444 546544235 0.000000e+00 699.0
24 TraesCS5A01G541400 chr1A 89.388 801 49 16 29 795 329181324 329180526 0.000000e+00 976.0
25 TraesCS5A01G541400 chr1A 100.000 28 0 0 1 28 329182174 329182147 1.600000e-02 52.8
26 TraesCS5A01G541400 chr1D 89.012 810 51 17 29 801 299759251 299758443 0.000000e+00 968.0
27 TraesCS5A01G541400 chr1D 100.000 28 0 0 1 28 150954299 150954326 1.600000e-02 52.8
28 TraesCS5A01G541400 chr1D 100.000 28 0 0 1 28 282134403 282134376 1.600000e-02 52.8
29 TraesCS5A01G541400 chr1D 100.000 28 0 0 1 28 299760101 299760074 1.600000e-02 52.8
30 TraesCS5A01G541400 chr1D 100.000 28 0 0 1 28 365896725 365896752 1.600000e-02 52.8
31 TraesCS5A01G541400 chr1B 88.971 807 55 10 29 801 45356975 45357781 0.000000e+00 966.0
32 TraesCS5A01G541400 chr1B 87.195 820 55 23 29 799 633308409 633309227 0.000000e+00 887.0
33 TraesCS5A01G541400 chr6D 88.533 811 57 17 29 803 417528384 417527574 0.000000e+00 950.0
34 TraesCS5A01G541400 chr6D 88.104 269 17 5 543 797 422032838 422032571 1.150000e-78 305.0
35 TraesCS5A01G541400 chr6D 100.000 28 0 0 1 28 417529234 417529207 1.600000e-02 52.8
36 TraesCS5A01G541400 chr6D 100.000 28 0 0 1 28 422033047 422033020 1.600000e-02 52.8
37 TraesCS5A01G541400 chr6D 100.000 28 0 0 1 28 472983224 472983197 1.600000e-02 52.8
38 TraesCS5A01G541400 chr7D 90.332 693 42 6 126 795 429072161 429071471 0.000000e+00 885.0
39 TraesCS5A01G541400 chr7D 86.691 819 59 16 29 797 77496881 77497699 0.000000e+00 863.0
40 TraesCS5A01G541400 chr7D 88.539 445 36 6 356 797 604332129 604332561 8.090000e-145 525.0
41 TraesCS5A01G541400 chr7D 83.673 98 14 2 8418 8514 31365590 31365686 3.500000e-14 91.6
42 TraesCS5A01G541400 chr2A 86.139 808 68 12 29 795 737051435 737052239 0.000000e+00 832.0
43 TraesCS5A01G541400 chr2A 90.000 220 19 3 581 797 455482761 455482980 1.930000e-71 281.0
44 TraesCS5A01G541400 chr6B 87.349 743 53 13 29 743 563053034 563052305 0.000000e+00 813.0
45 TraesCS5A01G541400 chr6A 87.481 647 62 8 167 795 555306854 555306209 0.000000e+00 728.0
46 TraesCS5A01G541400 chr3B 84.060 596 54 18 239 794 201869003 201869597 3.740000e-148 536.0
47 TraesCS5A01G541400 chr3A 79.658 644 96 22 182 796 442897510 442898147 1.810000e-116 431.0
48 TraesCS5A01G541400 chr3A 86.957 345 34 6 462 795 686614184 686614528 2.400000e-100 377.0
49 TraesCS5A01G541400 chr3A 84.831 356 34 12 462 797 738820482 738820127 3.140000e-89 340.0


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 TraesCS5A01G541400 chr5A 698207572 698216663 9091 False 16790.000000 16790 100.0000 1 9092 1 chr5A.!!$F2 9091
1 TraesCS5A01G541400 chr5A 460464300 460465086 786 False 983.000000 983 89.5940 29 797 1 chr5A.!!$F1 768
2 TraesCS5A01G541400 chr5A 698228516 698229037 521 False 218.333333 366 90.4920 6079 8464 3 chr5A.!!$F3 2385
3 TraesCS5A01G541400 chr4D 509363320 509373262 9942 False 2580.000000 6857 93.9174 788 9092 5 chr4D.!!$F2 8304
4 TraesCS5A01G541400 chr4D 509382645 509383406 761 False 253.500000 257 84.2805 8226 9047 2 chr4D.!!$F3 821
5 TraesCS5A01G541400 chr4B 657466779 657474915 8136 True 2670.000000 5384 92.0800 787 8222 4 chr4B.!!$R4 7435
6 TraesCS5A01G541400 chr4B 562442184 562442944 760 True 1013.000000 1013 90.6490 29 795 1 chr4B.!!$R2 766
7 TraesCS5A01G541400 chr4B 31515115 31515901 786 False 963.000000 963 89.2130 29 793 1 chr4B.!!$F1 764
8 TraesCS5A01G541400 chr4B 5185121 5185926 805 True 953.000000 953 88.7240 29 800 1 chr4B.!!$R1 771
9 TraesCS5A01G541400 chr5B 22071433 22072233 800 True 994.000000 994 89.7630 29 795 1 chr5B.!!$R1 766
10 TraesCS5A01G541400 chr5B 472218355 472219131 776 True 933.000000 933 88.6480 29 795 1 chr5B.!!$R2 766
11 TraesCS5A01G541400 chr5B 546543444 546544235 791 False 699.000000 699 83.1660 29 797 1 chr5B.!!$F1 768
12 TraesCS5A01G541400 chr1A 329180526 329182174 1648 True 514.400000 976 94.6940 1 795 2 chr1A.!!$R1 794
13 TraesCS5A01G541400 chr1D 299758443 299760101 1658 True 510.400000 968 94.5060 1 801 2 chr1D.!!$R2 800
14 TraesCS5A01G541400 chr1B 45356975 45357781 806 False 966.000000 966 88.9710 29 801 1 chr1B.!!$F1 772
15 TraesCS5A01G541400 chr1B 633308409 633309227 818 False 887.000000 887 87.1950 29 799 1 chr1B.!!$F2 770
16 TraesCS5A01G541400 chr6D 417527574 417529234 1660 True 501.400000 950 94.2665 1 803 2 chr6D.!!$R2 802
17 TraesCS5A01G541400 chr7D 429071471 429072161 690 True 885.000000 885 90.3320 126 795 1 chr7D.!!$R1 669
18 TraesCS5A01G541400 chr7D 77496881 77497699 818 False 863.000000 863 86.6910 29 797 1 chr7D.!!$F2 768
19 TraesCS5A01G541400 chr2A 737051435 737052239 804 False 832.000000 832 86.1390 29 795 1 chr2A.!!$F2 766
20 TraesCS5A01G541400 chr6B 563052305 563053034 729 True 813.000000 813 87.3490 29 743 1 chr6B.!!$R1 714
21 TraesCS5A01G541400 chr6A 555306209 555306854 645 True 728.000000 728 87.4810 167 795 1 chr6A.!!$R1 628
22 TraesCS5A01G541400 chr3B 201869003 201869597 594 False 536.000000 536 84.0600 239 794 1 chr3B.!!$F1 555
23 TraesCS5A01G541400 chr3A 442897510 442898147 637 False 431.000000 431 79.6580 182 796 1 chr3A.!!$F1 614

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
966 1902 0.033109 CCCCACCTCCATTTCCCTTC 60.033 60.000 0.00 0.00 0.00 3.46 F
1584 2937 0.245539 CGTTCCGTGTGTACTCCCAT 59.754 55.000 0.00 0.00 0.00 4.00 F
1587 2940 0.251877 TCCGTGTGTACTCCCATCCA 60.252 55.000 0.00 0.00 0.00 3.41 F
2639 4019 1.128507 CGGACATGTCGATGTGTTTGG 59.871 52.381 19.33 0.00 43.22 3.28 F
2830 4210 1.657181 CCGTTGAAAAGCGGTGCAC 60.657 57.895 8.80 8.80 42.73 4.57 F
2930 4328 2.094182 ACGCAGTTGTCTGGTATAGTGG 60.094 50.000 0.00 0.00 37.78 4.00 F
5149 7902 0.096281 ATTTGGTATCGCAACGCACG 59.904 50.000 0.00 0.00 0.00 5.34 F
6415 9258 1.102978 TATGCTCGCTGTACTGCTCA 58.897 50.000 20.65 15.49 0.00 4.26 F
7272 10129 0.321298 GAAGCCAACTGTAGCCGGAA 60.321 55.000 5.05 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2823 4203 0.521291 ATGTTTTCCGATGTGCACCG 59.479 50.000 15.69 11.55 0.00 4.94 R
3561 5205 0.252696 TGCCAGAGGTACCATCCTGT 60.253 55.000 15.94 0.00 38.02 4.00 R
3841 5486 5.108254 GCAAAGCGAATGAACTGTAAAACTG 60.108 40.000 0.00 0.00 0.00 3.16 R
4616 7368 3.826157 TCCTGTTTAAAGGATGGTGCAAG 59.174 43.478 0.00 0.00 41.60 4.01 R
5149 7902 5.994668 AGTCAGAGTTTTGACCTCTTCAATC 59.005 40.000 2.76 0.00 46.81 2.67 R
5202 7955 4.379302 AAGAGAAAAGGTCAGGAGCAAT 57.621 40.909 0.97 0.00 0.00 3.56 R
6788 9642 0.400213 CCCCTACAGTGGACTTGCAA 59.600 55.000 0.00 0.00 0.00 4.08 R
7876 10736 0.033503 TACCACTCTGATCGCTGGGA 60.034 55.000 0.00 0.00 0.00 4.37 R
8963 12025 0.396435 ACGGCAGTCATCTGGAACAA 59.604 50.000 0.00 0.00 41.57 2.83 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
37 861 2.700897 CCTCTTTCGTGGTGGGATCTAT 59.299 50.000 0.00 0.00 0.00 1.98
69 893 0.534203 ACATTCGTCAAGCCGGTTGT 60.534 50.000 1.90 0.00 37.43 3.32
186 1015 0.940126 GCTATTGTGCGAGGACCATG 59.060 55.000 0.00 0.00 0.00 3.66
387 1220 5.094812 CAGCGAGATTAGAGATAGTGATGC 58.905 45.833 0.00 0.00 0.00 3.91
439 1274 1.153588 GCATTGGAAACGGCATGGG 60.154 57.895 0.00 0.00 30.61 4.00
648 1555 4.026052 GGACCATGAATTTGGACCATCTT 58.974 43.478 11.42 0.00 46.78 2.40
809 1724 6.458232 AGATGCTCTAACTAGTGATTTCGT 57.542 37.500 0.00 0.00 0.00 3.85
833 1748 0.178068 TCCTATTGCTCTTGCCGGTC 59.822 55.000 1.90 0.00 38.71 4.79
834 1749 1.154205 CCTATTGCTCTTGCCGGTCG 61.154 60.000 1.90 0.00 38.71 4.79
835 1750 1.766143 CTATTGCTCTTGCCGGTCGC 61.766 60.000 1.90 0.00 38.71 5.19
850 1777 4.760047 CGCACAAGGGAGGGGACG 62.760 72.222 0.00 0.00 0.00 4.79
862 1789 2.776913 GGGGACGCCTCGAGAGAAG 61.777 68.421 15.71 4.45 41.32 2.85
868 1795 3.144193 CCTCGAGAGAAGCGGGCT 61.144 66.667 15.71 0.00 41.32 5.19
872 1799 2.202676 GAGAGAAGCGGGCTGACG 60.203 66.667 0.00 0.00 0.00 4.35
908 1835 3.560278 GGCCGTATCCAACACGCG 61.560 66.667 3.53 3.53 38.07 6.01
965 1901 0.479589 TCCCCACCTCCATTTCCCTT 60.480 55.000 0.00 0.00 0.00 3.95
966 1902 0.033109 CCCCACCTCCATTTCCCTTC 60.033 60.000 0.00 0.00 0.00 3.46
971 1907 3.903714 CCACCTCCATTTCCCTTCTTTTT 59.096 43.478 0.00 0.00 0.00 1.94
994 1930 4.698625 ACGAGTTCCCGCCCCTCT 62.699 66.667 0.00 0.00 0.00 3.69
1060 1996 3.999297 GACCTCGTCCTCTCCGCCT 62.999 68.421 0.00 0.00 0.00 5.52
1075 2011 3.708210 CCTACGGCAAGTCCCAGA 58.292 61.111 0.00 0.00 0.00 3.86
1176 2112 4.849329 CGCTACCACCTCGGCGTC 62.849 72.222 6.85 0.00 42.23 5.19
1177 2113 3.755628 GCTACCACCTCGGCGTCA 61.756 66.667 6.85 0.00 39.03 4.35
1178 2114 2.967397 CTACCACCTCGGCGTCAA 59.033 61.111 6.85 0.00 39.03 3.18
1179 2115 1.445582 CTACCACCTCGGCGTCAAC 60.446 63.158 6.85 0.00 39.03 3.18
1180 2116 3.271706 TACCACCTCGGCGTCAACG 62.272 63.158 6.85 0.00 39.03 4.10
1181 2117 4.657824 CCACCTCGGCGTCAACGT 62.658 66.667 6.85 0.00 42.22 3.99
1182 2118 3.103911 CACCTCGGCGTCAACGTC 61.104 66.667 6.85 0.06 42.22 4.34
1183 2119 4.353437 ACCTCGGCGTCAACGTCC 62.353 66.667 6.85 4.04 41.58 4.79
1184 2120 4.052229 CCTCGGCGTCAACGTCCT 62.052 66.667 6.85 0.00 41.58 3.85
1185 2121 2.805353 CTCGGCGTCAACGTCCTG 60.805 66.667 6.85 2.65 41.58 3.86
1188 2124 3.112709 GGCGTCAACGTCCTGCTC 61.113 66.667 4.29 0.00 42.22 4.26
1189 2125 3.470567 GCGTCAACGTCCTGCTCG 61.471 66.667 4.29 0.00 42.22 5.03
1190 2126 2.805353 CGTCAACGTCCTGCTCGG 60.805 66.667 0.00 0.00 34.11 4.63
1191 2127 2.338984 GTCAACGTCCTGCTCGGT 59.661 61.111 0.00 0.00 0.00 4.69
1192 2128 1.733399 GTCAACGTCCTGCTCGGTC 60.733 63.158 0.00 0.00 0.00 4.79
1193 2129 2.432628 CAACGTCCTGCTCGGTCC 60.433 66.667 0.00 0.00 0.00 4.46
1194 2130 4.052229 AACGTCCTGCTCGGTCCG 62.052 66.667 4.39 4.39 35.39 4.79
1212 2148 3.151022 CACCCGCTCCTCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
1213 2149 4.467107 ACCCGCTCCTCCTCCTCC 62.467 72.222 0.00 0.00 0.00 4.30
1214 2150 4.150454 CCCGCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1215 2151 2.042435 CCGCTCCTCCTCCTCCTT 60.042 66.667 0.00 0.00 0.00 3.36
1216 2152 2.131067 CCGCTCCTCCTCCTCCTTC 61.131 68.421 0.00 0.00 0.00 3.46
1217 2153 2.131067 CGCTCCTCCTCCTCCTTCC 61.131 68.421 0.00 0.00 0.00 3.46
1218 2154 1.764454 GCTCCTCCTCCTCCTTCCC 60.764 68.421 0.00 0.00 0.00 3.97
1219 2155 1.074850 CTCCTCCTCCTCCTTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
1220 2156 2.444895 CCTCCTCCTCCTTCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
1221 2157 3.157949 CTCCTCCTCCTTCCCCGC 61.158 72.222 0.00 0.00 0.00 6.13
1222 2158 3.684628 TCCTCCTCCTTCCCCGCT 61.685 66.667 0.00 0.00 0.00 5.52
1223 2159 3.474570 CCTCCTCCTTCCCCGCTG 61.475 72.222 0.00 0.00 0.00 5.18
1224 2160 4.168291 CTCCTCCTTCCCCGCTGC 62.168 72.222 0.00 0.00 0.00 5.25
1234 2170 4.821589 CCCGCTGCCCGACTTCTC 62.822 72.222 0.00 0.00 40.02 2.87
1235 2171 4.821589 CCGCTGCCCGACTTCTCC 62.822 72.222 0.00 0.00 40.02 3.71
1236 2172 3.764466 CGCTGCCCGACTTCTCCT 61.764 66.667 0.00 0.00 40.02 3.69
1237 2173 2.185608 GCTGCCCGACTTCTCCTC 59.814 66.667 0.00 0.00 0.00 3.71
1238 2174 2.355193 GCTGCCCGACTTCTCCTCT 61.355 63.158 0.00 0.00 0.00 3.69
1239 2175 1.813192 CTGCCCGACTTCTCCTCTC 59.187 63.158 0.00 0.00 0.00 3.20
1240 2176 1.671901 CTGCCCGACTTCTCCTCTCC 61.672 65.000 0.00 0.00 0.00 3.71
1241 2177 2.428085 GCCCGACTTCTCCTCTCCC 61.428 68.421 0.00 0.00 0.00 4.30
1242 2178 1.758906 CCCGACTTCTCCTCTCCCC 60.759 68.421 0.00 0.00 0.00 4.81
1243 2179 1.758906 CCGACTTCTCCTCTCCCCC 60.759 68.421 0.00 0.00 0.00 5.40
1257 2558 3.129976 CCCCCTCCCCTACCTCTT 58.870 66.667 0.00 0.00 0.00 2.85
1334 2661 3.785859 GGCGATGAGGTGAGCCCA 61.786 66.667 0.00 0.00 43.54 5.36
1354 2681 2.125106 GATTCCGGCCGCACTTCT 60.125 61.111 22.85 0.00 0.00 2.85
1359 2686 3.188786 CGGCCGCACTTCTGTAGC 61.189 66.667 14.67 0.00 0.00 3.58
1408 2735 1.080366 CGATTCGACCACCAACGGA 60.080 57.895 0.00 0.00 0.00 4.69
1425 2752 4.927782 AGGCTGCGGCGTGTTGAA 62.928 61.111 12.82 0.00 39.81 2.69
1426 2753 3.959975 GGCTGCGGCGTGTTGAAA 61.960 61.111 12.29 0.00 39.81 2.69
1427 2754 2.255252 GCTGCGGCGTGTTGAAAT 59.745 55.556 9.37 0.00 0.00 2.17
1428 2755 1.797537 GCTGCGGCGTGTTGAAATC 60.798 57.895 9.37 0.00 0.00 2.17
1429 2756 1.154225 CTGCGGCGTGTTGAAATCC 60.154 57.895 9.37 0.00 0.00 3.01
1430 2757 2.202298 GCGGCGTGTTGAAATCCG 60.202 61.111 9.37 0.00 42.68 4.18
1431 2758 2.478746 CGGCGTGTTGAAATCCGG 59.521 61.111 0.00 0.00 36.73 5.14
1464 2805 3.243636 ACTTTCAGAGCCACATTTTGCTG 60.244 43.478 0.00 0.00 38.11 4.41
1563 2916 3.093835 AAATCCATCGCCCCCGGA 61.094 61.111 0.73 0.00 34.56 5.14
1581 2934 0.387750 GACCGTTCCGTGTGTACTCC 60.388 60.000 0.00 0.00 0.00 3.85
1582 2935 1.080298 CCGTTCCGTGTGTACTCCC 60.080 63.158 0.00 0.00 0.00 4.30
1583 2936 1.661480 CGTTCCGTGTGTACTCCCA 59.339 57.895 0.00 0.00 0.00 4.37
1584 2937 0.245539 CGTTCCGTGTGTACTCCCAT 59.754 55.000 0.00 0.00 0.00 4.00
1585 2938 1.734707 CGTTCCGTGTGTACTCCCATC 60.735 57.143 0.00 0.00 0.00 3.51
1586 2939 0.899720 TTCCGTGTGTACTCCCATCC 59.100 55.000 0.00 0.00 0.00 3.51
1587 2940 0.251877 TCCGTGTGTACTCCCATCCA 60.252 55.000 0.00 0.00 0.00 3.41
1591 2944 2.677836 CGTGTGTACTCCCATCCATTTG 59.322 50.000 0.00 0.00 0.00 2.32
1592 2945 3.686016 GTGTGTACTCCCATCCATTTGT 58.314 45.455 0.00 0.00 0.00 2.83
1593 2946 3.689649 GTGTGTACTCCCATCCATTTGTC 59.310 47.826 0.00 0.00 0.00 3.18
1596 2949 4.396166 GTGTACTCCCATCCATTTGTCAAG 59.604 45.833 0.00 0.00 0.00 3.02
1597 2950 2.450476 ACTCCCATCCATTTGTCAAGC 58.550 47.619 0.00 0.00 0.00 4.01
1599 2952 3.094572 CTCCCATCCATTTGTCAAGCTT 58.905 45.455 0.00 0.00 0.00 3.74
1630 3001 3.011119 ACCGCGCTATTGTTTCCATTTA 58.989 40.909 5.56 0.00 0.00 1.40
1644 3015 9.983024 TTGTTTCCATTTAATCTCATAAGGGTA 57.017 29.630 0.00 0.00 0.00 3.69
1647 3018 9.586732 TTTCCATTTAATCTCATAAGGGTATGG 57.413 33.333 0.00 0.00 38.15 2.74
1748 3119 2.717639 AGGTCATCCAGTATGTTGGC 57.282 50.000 0.00 0.00 38.16 4.52
1815 3186 7.600065 AGATGTCCAAAAATCTTCACATTCAG 58.400 34.615 0.00 0.00 28.51 3.02
1835 3206 4.892345 TCAGATGTATGCTGCTCTCTTACT 59.108 41.667 0.00 0.00 33.45 2.24
1902 3273 8.830915 ACAACACCCATTGGATGTTATATTTA 57.169 30.769 15.25 0.00 35.49 1.40
1962 3333 4.867608 GTCCTAGAGCATTGTTTCTCACTC 59.132 45.833 0.00 0.00 0.00 3.51
1995 3366 4.895297 AGGAATTTTGGTACATGGCCTATG 59.105 41.667 3.32 8.98 39.30 2.23
2091 3462 7.708322 GCCTTAATGGATCAAGATTTTCTTTCC 59.292 37.037 0.00 2.38 35.14 3.13
2095 3466 6.594788 TGGATCAAGATTTTCTTTCCCAAG 57.405 37.500 0.00 0.00 34.16 3.61
2204 3575 1.576356 GAGTTGCGGGCTCTGATTAG 58.424 55.000 0.00 0.00 0.00 1.73
2364 3738 3.385755 ACTTCTGCATGCCTTCAGTTTTT 59.614 39.130 16.68 0.00 0.00 1.94
2459 3834 7.226918 TGTTATAGAGTGATTCGTAGGTGAGAG 59.773 40.741 0.00 0.00 0.00 3.20
2473 3848 5.104259 AGGTGAGAGTTTTTGTTCTGTCT 57.896 39.130 0.00 0.00 0.00 3.41
2523 3903 4.898861 TGAGCACCATATACCTCATGTACA 59.101 41.667 0.00 0.00 30.62 2.90
2524 3904 5.011023 TGAGCACCATATACCTCATGTACAG 59.989 44.000 0.33 0.00 30.62 2.74
2525 3905 4.901849 AGCACCATATACCTCATGTACAGT 59.098 41.667 0.33 0.00 30.62 3.55
2526 3906 6.075315 AGCACCATATACCTCATGTACAGTA 58.925 40.000 0.33 0.00 30.62 2.74
2527 3907 6.015350 AGCACCATATACCTCATGTACAGTAC 60.015 42.308 0.33 3.49 30.62 2.73
2583 3963 5.300539 ACCTTGTGTGCAAACATATGTGTAA 59.699 36.000 11.33 0.00 37.67 2.41
2639 4019 1.128507 CGGACATGTCGATGTGTTTGG 59.871 52.381 19.33 0.00 43.22 3.28
2660 4040 9.069078 GTTTGGTAAAAACTGTTACTCTTTCAC 57.931 33.333 0.00 0.00 34.88 3.18
2710 4090 7.440523 ACACAGAAAATCAGAATGTACCTTC 57.559 36.000 2.91 2.91 37.40 3.46
2751 4131 2.880443 AGACAGTGGTTTGATTGGCAT 58.120 42.857 0.00 0.00 0.00 4.40
2767 4147 1.876156 GGCATTCCTCTCTTTATGGCG 59.124 52.381 0.00 0.00 34.54 5.69
2823 4203 5.600908 TTATCACAGTACCGTTGAAAAGC 57.399 39.130 0.00 0.00 0.00 3.51
2830 4210 1.657181 CCGTTGAAAAGCGGTGCAC 60.657 57.895 8.80 8.80 42.73 4.57
2852 4232 6.238621 GCACATCGGAAAACATATCCAATGTA 60.239 38.462 0.00 0.00 41.52 2.29
2911 4309 9.038803 CATTAGATGATATTGGATATGGTGACG 57.961 37.037 0.00 0.00 0.00 4.35
2929 4327 3.232213 ACGCAGTTGTCTGGTATAGTG 57.768 47.619 0.00 0.00 37.78 2.74
2930 4328 2.094182 ACGCAGTTGTCTGGTATAGTGG 60.094 50.000 0.00 0.00 37.78 4.00
2932 4330 3.129813 CGCAGTTGTCTGGTATAGTGGTA 59.870 47.826 0.00 0.00 41.57 3.25
2934 4332 5.009310 CGCAGTTGTCTGGTATAGTGGTATA 59.991 44.000 0.00 0.00 41.57 1.47
2935 4333 6.448006 GCAGTTGTCTGGTATAGTGGTATAG 58.552 44.000 0.00 0.00 41.57 1.31
2936 4334 6.040616 GCAGTTGTCTGGTATAGTGGTATAGT 59.959 42.308 0.00 0.00 41.57 2.12
2937 4335 7.649973 CAGTTGTCTGGTATAGTGGTATAGTC 58.350 42.308 0.00 0.00 37.97 2.59
2941 4339 7.295340 TGTCTGGTATAGTGGTATAGTCATGT 58.705 38.462 0.00 0.00 0.00 3.21
2942 4340 7.783119 TGTCTGGTATAGTGGTATAGTCATGTT 59.217 37.037 0.00 0.00 0.00 2.71
2943 4341 9.293404 GTCTGGTATAGTGGTATAGTCATGTTA 57.707 37.037 0.00 0.00 0.00 2.41
2944 4342 9.871175 TCTGGTATAGTGGTATAGTCATGTTAA 57.129 33.333 0.00 0.00 0.00 2.01
2946 4344 9.085645 TGGTATAGTGGTATAGTCATGTTAAGG 57.914 37.037 0.00 0.00 0.00 2.69
2947 4345 8.529476 GGTATAGTGGTATAGTCATGTTAAGGG 58.471 40.741 0.00 0.00 0.00 3.95
3020 4660 6.739331 TTCCACAAGAATAACCCAAACAAT 57.261 33.333 0.00 0.00 0.00 2.71
3128 4768 6.546395 CCAACCAGTTCTTTCTAATCATTCG 58.454 40.000 0.00 0.00 0.00 3.34
3212 4852 4.186926 TGAGATCTTCACATAAGCACAGC 58.813 43.478 0.00 0.00 0.00 4.40
3736 5381 7.847096 TCTTGTATCTATTTACAGCTCCACAA 58.153 34.615 0.00 0.00 33.81 3.33
3841 5486 3.308595 GGTTGTTTGTTTTTAGCTGGCAC 59.691 43.478 0.00 0.00 0.00 5.01
4188 5838 8.548877 AGAGGCTCTGTATAAATTTAAGTTCCA 58.451 33.333 17.96 0.00 0.00 3.53
4399 6051 2.133520 AGAGGGACTATACAGACCGGA 58.866 52.381 9.46 0.00 41.55 5.14
4403 6055 2.557490 GGGACTATACAGACCGGATGTC 59.443 54.545 18.15 1.31 44.82 3.06
4546 6198 2.352127 GCTGGACATTCTGCAGGTTTTC 60.352 50.000 15.13 5.85 38.76 2.29
4601 7353 2.908688 TTCTCTTATGGCTGCGCATA 57.091 45.000 12.24 0.00 0.00 3.14
4616 7368 6.524586 GGCTGCGCATATGTAAATAATTTCTC 59.475 38.462 12.24 0.00 0.00 2.87
4855 7607 7.875041 GGTGCTGATACTGTGAGTATAATTCAT 59.125 37.037 0.00 0.00 41.21 2.57
5149 7902 0.096281 ATTTGGTATCGCAACGCACG 59.904 50.000 0.00 0.00 0.00 5.34
5202 7955 9.146984 CGATGTACCAGTACTTTCTTGATTAAA 57.853 33.333 9.24 0.00 37.00 1.52
5323 8076 2.621407 GGATGCAACTGATGGGAAAGGA 60.621 50.000 0.00 0.00 0.00 3.36
5326 8079 3.509442 TGCAACTGATGGGAAAGGAAAT 58.491 40.909 0.00 0.00 0.00 2.17
5392 8145 1.697082 TACACCAGTTTGACCCCGCA 61.697 55.000 0.00 0.00 0.00 5.69
6164 8917 5.874810 GTGCAGTTGTGTAGATAATTCTGGA 59.125 40.000 0.00 0.00 33.17 3.86
6303 9056 5.957771 TCAGCTAGATGGTTGGTTCTTAT 57.042 39.130 8.37 0.00 0.00 1.73
6384 9227 5.603596 TGAATGCCTGAAAATATCATTGGC 58.396 37.500 0.00 0.00 45.29 4.52
6403 9246 3.809279 TGGCACTGATGTTTATATGCTCG 59.191 43.478 0.00 0.00 33.57 5.03
6415 9258 1.102978 TATGCTCGCTGTACTGCTCA 58.897 50.000 20.65 15.49 0.00 4.26
6430 9273 3.693085 ACTGCTCACATTGATGATGAACC 59.307 43.478 0.00 0.00 39.15 3.62
6439 9282 7.336679 TCACATTGATGATGAACCGTTATCTTT 59.663 33.333 0.00 0.00 39.15 2.52
6680 9531 6.035435 GCAGTATTGCTGTCCATAATAGATCG 59.965 42.308 2.45 0.00 46.95 3.69
6683 9534 3.653344 TGCTGTCCATAATAGATCGCAC 58.347 45.455 0.00 0.00 0.00 5.34
6761 9615 3.713858 TGTTCAGCACCTTTTCATGTG 57.286 42.857 0.00 0.00 35.58 3.21
6776 9630 2.005451 CATGTGTAGCAGTTCTGGCTC 58.995 52.381 1.97 0.00 42.62 4.70
6788 9642 4.520492 CAGTTCTGGCTCATTTGGTTACTT 59.480 41.667 0.00 0.00 0.00 2.24
6852 9706 8.696043 TGATACATTCCTGCAAAAGCTATATT 57.304 30.769 0.00 0.00 0.00 1.28
7031 9885 6.528072 GCTTGGTATCTAAAGTGCATTGAAAC 59.472 38.462 0.00 0.00 0.00 2.78
7072 9926 9.915629 AAAAATATGCCTTTTACGATGTTTGTA 57.084 25.926 0.00 0.00 0.00 2.41
7076 9930 5.694816 TGCCTTTTACGATGTTTGTACATG 58.305 37.500 0.00 0.00 44.90 3.21
7092 9946 5.555966 TGTACATGTATGGAAGCTTCAACA 58.444 37.500 27.02 24.55 0.00 3.33
7146 10001 6.482308 TCCACAGTTACTTGAGCTAGTTTTTC 59.518 38.462 0.00 0.00 0.00 2.29
7153 10008 8.613482 GTTACTTGAGCTAGTTTTTCTTTCACT 58.387 33.333 0.00 0.00 0.00 3.41
7173 10030 4.832266 CACTGCCTCTGTATCCTCTAGAAT 59.168 45.833 0.00 0.00 0.00 2.40
7272 10129 0.321298 GAAGCCAACTGTAGCCGGAA 60.321 55.000 5.05 0.00 0.00 4.30
7279 10136 2.109425 ACTGTAGCCGGAATTTGGAC 57.891 50.000 5.05 0.00 0.00 4.02
7419 10276 1.134995 TGCTCAGCGTTCTGGTATCAG 60.135 52.381 0.00 0.00 40.69 2.90
7429 10286 5.623824 GCGTTCTGGTATCAGTTCCTTCTTA 60.624 44.000 2.20 0.00 41.59 2.10
7431 10288 6.531948 CGTTCTGGTATCAGTTCCTTCTTAAG 59.468 42.308 2.20 0.00 41.59 1.85
7537 10396 9.278734 GCTGTTAGCATCTTAAATAGTTTGAAC 57.721 33.333 0.00 0.00 41.89 3.18
7627 10486 3.057736 CAGCTCAATTCAGTTGGACCAAG 60.058 47.826 7.31 0.00 38.39 3.61
7696 10555 8.413229 ACCAATAATTACAGCATATTTGTGTCC 58.587 33.333 0.00 0.00 0.00 4.02
7697 10556 7.591057 CCAATAATTACAGCATATTTGTGTCCG 59.409 37.037 0.00 0.00 0.00 4.79
7709 10568 7.480542 GCATATTTGTGTCCGTTAACTACTTTG 59.519 37.037 3.71 0.00 0.00 2.77
7744 10603 7.560368 AGCAGTAACAAGCTCTACATTATCTT 58.440 34.615 0.00 0.00 36.00 2.40
7782 10642 7.490079 CCACATCTGTATTTTCCAATGTGATTG 59.510 37.037 13.30 0.00 44.11 2.67
7876 10736 0.674895 GATTGGTCAGCGAAGTGGCT 60.675 55.000 0.00 0.00 46.13 4.75
7979 10839 5.053811 TGCGACAGTCTCACTTCAATTTTA 58.946 37.500 0.00 0.00 0.00 1.52
8100 10961 5.396213 GCCAGACTCAGATTAATCCTTGTCT 60.396 44.000 20.02 20.02 33.41 3.41
8105 10967 8.160106 AGACTCAGATTAATCCTTGTCTGTTTT 58.840 33.333 22.74 8.48 39.22 2.43
8107 10969 9.793259 ACTCAGATTAATCCTTGTCTGTTTTAA 57.207 29.630 11.92 0.00 39.22 1.52
8124 10986 5.221561 TGTTTTAACACTCAGCCTAGCTACA 60.222 40.000 0.00 0.00 33.13 2.74
8153 11015 4.505566 CCATGTATGTAGGGATGTTCCTGG 60.506 50.000 0.00 0.00 37.75 4.45
8173 11035 2.816689 GTGTAACCTGGCCACAAAAAC 58.183 47.619 0.00 0.00 0.00 2.43
8348 11210 3.954258 ACCTTTAACTTCAGTTTGCAGCT 59.046 39.130 0.00 0.00 39.31 4.24
8367 11229 6.080406 GCAGCTGTTGTTGTTTCTCTATAAC 58.920 40.000 16.64 0.00 0.00 1.89
8551 11456 2.687935 ACCAGACCATTGTGTTTGTGAC 59.312 45.455 0.00 0.00 0.00 3.67
8670 11579 2.095969 TCGTGTTTGGTCGATGCAAATC 60.096 45.455 0.00 0.00 0.00 2.17
8671 11580 2.350293 CGTGTTTGGTCGATGCAAATCA 60.350 45.455 0.00 0.00 0.00 2.57
8718 11627 3.096852 CAGGTACCTCACTGTGTATCCA 58.903 50.000 12.84 0.00 0.00 3.41
8733 11642 6.403049 TGTGTATCCATTAGTTAGTGGTGTG 58.597 40.000 1.29 0.00 34.93 3.82
8758 11667 8.639761 TGTCAGTTAAGAGTTTCTAGCTAGTTT 58.360 33.333 20.10 8.93 0.00 2.66
8759 11668 9.478768 GTCAGTTAAGAGTTTCTAGCTAGTTTT 57.521 33.333 20.10 5.51 0.00 2.43
8962 12024 1.631898 ACTAAAACCGCATACCCAGGT 59.368 47.619 0.00 0.00 40.50 4.00
8965 12027 2.955609 AACCGCATACCCAGGTTTG 58.044 52.632 0.00 0.00 45.04 2.93
8966 12028 0.111639 AACCGCATACCCAGGTTTGT 59.888 50.000 8.74 0.00 45.04 2.83
8979 12041 2.227388 CAGGTTTGTTCCAGATGACTGC 59.773 50.000 0.00 0.00 42.25 4.40
9048 12110 3.597255 TGGCGTGTACGGAAAATATTCA 58.403 40.909 6.55 0.00 40.23 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 861 1.100510 CGAATGTACTCCACCTCGGA 58.899 55.000 0.00 0.00 43.61 4.55
69 893 8.780249 CAAGTTCTTTCTTACCTTCGGATTTTA 58.220 33.333 0.00 0.00 0.00 1.52
297 1129 5.064325 GGGTTAACACGAATGTCTATCAACC 59.936 44.000 8.10 0.00 38.45 3.77
304 1136 3.343617 CATGGGGTTAACACGAATGTCT 58.656 45.455 8.10 0.00 38.45 3.41
387 1220 1.466167 CTTTCTGGAGTTGGTCATGCG 59.534 52.381 0.00 0.00 0.00 4.73
760 1675 8.208718 CCAATAGATGGTCTAAATTTTGACGA 57.791 34.615 21.20 19.06 44.85 4.20
809 1724 2.487762 CGGCAAGAGCAATAGGAAAACA 59.512 45.455 0.00 0.00 44.61 2.83
833 1748 4.760047 CGTCCCCTCCCTTGTGCG 62.760 72.222 0.00 0.00 0.00 5.34
835 1750 4.410400 GGCGTCCCCTCCCTTGTG 62.410 72.222 0.00 0.00 0.00 3.33
850 1777 4.882396 GCCCGCTTCTCTCGAGGC 62.882 72.222 13.56 6.97 38.75 4.70
887 1814 2.684294 TGTTGGATACGGCCCGGA 60.684 61.111 8.57 0.00 42.51 5.14
908 1835 1.893919 AAGAGACGAGAAGGCTGCCC 61.894 60.000 16.57 0.02 39.26 5.36
971 1907 1.167781 GGGCGGGAACTCGTGAAAAA 61.168 55.000 0.00 0.00 0.00 1.94
972 1908 1.598685 GGGCGGGAACTCGTGAAAA 60.599 57.895 0.00 0.00 0.00 2.29
1060 1996 1.335132 GGGATCTGGGACTTGCCGTA 61.335 60.000 0.00 0.00 37.63 4.02
1065 2001 2.911143 CGGGGGATCTGGGACTTG 59.089 66.667 0.00 0.00 0.00 3.16
1075 2011 4.565850 GGAGGAGAGGCGGGGGAT 62.566 72.222 0.00 0.00 0.00 3.85
1174 2110 1.733399 GACCGAGCAGGACGTTGAC 60.733 63.158 5.19 0.00 45.00 3.18
1175 2111 2.649034 GACCGAGCAGGACGTTGA 59.351 61.111 5.19 0.00 45.00 3.18
1176 2112 2.432628 GGACCGAGCAGGACGTTG 60.433 66.667 5.19 0.00 45.00 4.10
1177 2113 4.052229 CGGACCGAGCAGGACGTT 62.052 66.667 8.64 0.00 45.00 3.99
1195 2131 3.151022 GAGGAGGAGGAGCGGGTG 61.151 72.222 0.00 0.00 0.00 4.61
1196 2132 4.467107 GGAGGAGGAGGAGCGGGT 62.467 72.222 0.00 0.00 0.00 5.28
1197 2133 3.687828 AAGGAGGAGGAGGAGCGGG 62.688 68.421 0.00 0.00 0.00 6.13
1198 2134 2.042435 AAGGAGGAGGAGGAGCGG 60.042 66.667 0.00 0.00 0.00 5.52
1199 2135 2.131067 GGAAGGAGGAGGAGGAGCG 61.131 68.421 0.00 0.00 0.00 5.03
1200 2136 1.764454 GGGAAGGAGGAGGAGGAGC 60.764 68.421 0.00 0.00 0.00 4.70
1201 2137 1.074850 GGGGAAGGAGGAGGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
1202 2138 3.010226 CGGGGAAGGAGGAGGAGGA 62.010 68.421 0.00 0.00 0.00 3.71
1203 2139 2.444895 CGGGGAAGGAGGAGGAGG 60.445 72.222 0.00 0.00 0.00 4.30
1204 2140 3.157949 GCGGGGAAGGAGGAGGAG 61.158 72.222 0.00 0.00 0.00 3.69
1205 2141 3.684628 AGCGGGGAAGGAGGAGGA 61.685 66.667 0.00 0.00 0.00 3.71
1206 2142 3.474570 CAGCGGGGAAGGAGGAGG 61.475 72.222 0.00 0.00 0.00 4.30
1207 2143 4.168291 GCAGCGGGGAAGGAGGAG 62.168 72.222 0.00 0.00 0.00 3.69
1217 2153 4.821589 GAGAAGTCGGGCAGCGGG 62.822 72.222 0.00 0.00 0.00 6.13
1218 2154 4.821589 GGAGAAGTCGGGCAGCGG 62.822 72.222 0.00 0.00 0.00 5.52
1219 2155 3.708220 GAGGAGAAGTCGGGCAGCG 62.708 68.421 0.00 0.00 0.00 5.18
1220 2156 2.185608 GAGGAGAAGTCGGGCAGC 59.814 66.667 0.00 0.00 0.00 5.25
1221 2157 1.671901 GGAGAGGAGAAGTCGGGCAG 61.672 65.000 0.00 0.00 0.00 4.85
1222 2158 1.682684 GGAGAGGAGAAGTCGGGCA 60.683 63.158 0.00 0.00 0.00 5.36
1223 2159 2.428085 GGGAGAGGAGAAGTCGGGC 61.428 68.421 0.00 0.00 0.00 6.13
1224 2160 1.758906 GGGGAGAGGAGAAGTCGGG 60.759 68.421 0.00 0.00 0.00 5.14
1225 2161 1.758906 GGGGGAGAGGAGAAGTCGG 60.759 68.421 0.00 0.00 0.00 4.79
1226 2162 3.942601 GGGGGAGAGGAGAAGTCG 58.057 66.667 0.00 0.00 0.00 4.18
1240 2176 0.191314 CTAAGAGGTAGGGGAGGGGG 59.809 65.000 0.00 0.00 0.00 5.40
1241 2177 0.472161 GCTAAGAGGTAGGGGAGGGG 60.472 65.000 0.00 0.00 0.00 4.79
1242 2178 0.563672 AGCTAAGAGGTAGGGGAGGG 59.436 60.000 0.00 0.00 0.00 4.30
1243 2179 2.090999 AGAAGCTAAGAGGTAGGGGAGG 60.091 54.545 0.00 0.00 0.00 4.30
1244 2180 3.227614 GAGAAGCTAAGAGGTAGGGGAG 58.772 54.545 0.00 0.00 0.00 4.30
1245 2181 2.091222 GGAGAAGCTAAGAGGTAGGGGA 60.091 54.545 0.00 0.00 0.00 4.81
1246 2182 2.090999 AGGAGAAGCTAAGAGGTAGGGG 60.091 54.545 0.00 0.00 0.00 4.79
1247 2183 3.322191 AGGAGAAGCTAAGAGGTAGGG 57.678 52.381 0.00 0.00 0.00 3.53
1248 2184 4.282496 TCAAGGAGAAGCTAAGAGGTAGG 58.718 47.826 0.00 0.00 0.00 3.18
1249 2185 4.202111 GCTCAAGGAGAAGCTAAGAGGTAG 60.202 50.000 0.00 0.00 0.00 3.18
1257 2558 2.423892 CGTAGTGCTCAAGGAGAAGCTA 59.576 50.000 0.00 0.00 0.00 3.32
1334 2661 1.376609 GAAGTGCGGCCGGAATCAAT 61.377 55.000 29.38 12.83 0.00 2.57
1354 2681 0.031917 TCCCCAGGTAATCGGCTACA 60.032 55.000 0.00 0.00 0.00 2.74
1359 2686 2.803817 CCCGTCCCCAGGTAATCGG 61.804 68.421 0.00 0.00 38.05 4.18
1397 2724 4.643387 GCAGCCTCCGTTGGTGGT 62.643 66.667 5.88 0.00 38.49 4.16
1408 2735 4.927782 TTCAACACGCCGCAGCCT 62.928 61.111 0.00 0.00 34.57 4.58
1415 2742 2.178273 GCCGGATTTCAACACGCC 59.822 61.111 5.05 0.00 0.00 5.68
1416 2743 2.202298 CGCCGGATTTCAACACGC 60.202 61.111 5.05 0.00 0.00 5.34
1417 2744 2.202298 GCGCCGGATTTCAACACG 60.202 61.111 5.05 0.00 0.00 4.49
1418 2745 1.154225 CAGCGCCGGATTTCAACAC 60.154 57.895 5.05 0.00 0.00 3.32
1419 2746 2.976840 GCAGCGCCGGATTTCAACA 61.977 57.895 5.05 0.00 0.00 3.33
1420 2747 1.366111 TAGCAGCGCCGGATTTCAAC 61.366 55.000 5.05 0.00 0.00 3.18
1421 2748 0.675208 TTAGCAGCGCCGGATTTCAA 60.675 50.000 5.05 0.00 0.00 2.69
1422 2749 1.078778 TTAGCAGCGCCGGATTTCA 60.079 52.632 5.05 0.00 0.00 2.69
1423 2750 1.352056 GTTAGCAGCGCCGGATTTC 59.648 57.895 5.05 0.00 0.00 2.17
1424 2751 1.376683 TGTTAGCAGCGCCGGATTT 60.377 52.632 5.05 0.00 0.00 2.17
1425 2752 2.106683 GTGTTAGCAGCGCCGGATT 61.107 57.895 5.05 0.00 0.00 3.01
1426 2753 2.511600 GTGTTAGCAGCGCCGGAT 60.512 61.111 5.05 0.00 0.00 4.18
1427 2754 2.725203 AAAGTGTTAGCAGCGCCGGA 62.725 55.000 5.05 0.00 0.00 5.14
1428 2755 2.240612 GAAAGTGTTAGCAGCGCCGG 62.241 60.000 2.29 0.00 0.00 6.13
1429 2756 1.132640 GAAAGTGTTAGCAGCGCCG 59.867 57.895 2.29 0.00 0.00 6.46
1430 2757 0.166814 CTGAAAGTGTTAGCAGCGCC 59.833 55.000 2.29 0.00 0.00 6.53
1431 2758 1.127582 CTCTGAAAGTGTTAGCAGCGC 59.872 52.381 0.00 0.00 33.76 5.92
1464 2805 4.158394 ACATTATGGTCAGGCACAAACATC 59.842 41.667 0.00 0.00 0.00 3.06
1609 2980 4.705746 TGGAAACAATAGCGCGGT 57.294 50.000 17.70 17.70 37.44 5.68
1630 3001 9.547279 AAAGAAAAACCATACCCTTATGAGATT 57.453 29.630 0.00 0.00 37.86 2.40
1644 3015 5.675684 AACACCACTGAAAGAAAAACCAT 57.324 34.783 0.00 0.00 37.43 3.55
1647 3018 5.462068 GGCATAACACCACTGAAAGAAAAAC 59.538 40.000 0.00 0.00 37.43 2.43
1815 3186 6.325919 ACTAGTAAGAGAGCAGCATACATC 57.674 41.667 0.00 0.00 0.00 3.06
1835 3206 9.826574 AGATTTAGACACAAAGTACACAAACTA 57.173 29.630 0.00 0.00 0.00 2.24
1962 3333 8.883731 CATGTACCAAAATTCCTACAGAAGTAG 58.116 37.037 0.00 0.00 45.90 2.57
2095 3466 2.027192 TCACCACATAGAGCCAAGGAAC 60.027 50.000 0.00 0.00 0.00 3.62
2204 3575 4.865365 GCAGAACTAGTGTCATACAACTCC 59.135 45.833 0.00 0.00 0.00 3.85
2364 3738 2.502745 AGAAATTCATCTAGGGGCCCA 58.497 47.619 27.72 10.10 0.00 5.36
2430 3804 8.692710 TCACCTACGAATCACTCTATAACATTT 58.307 33.333 0.00 0.00 0.00 2.32
2459 3834 7.542130 AGATGTTGTTTCAGACAGAACAAAAAC 59.458 33.333 3.57 0.00 39.94 2.43
2473 3848 5.771469 CCAAGTTGCATAGATGTTGTTTCA 58.229 37.500 0.00 0.00 0.00 2.69
2523 3903 8.918202 TGAAAAACATTAATCTCAGTGGTACT 57.082 30.769 0.00 0.00 0.00 2.73
2557 3937 6.898603 ACACATATGTTTGCACACAAGGTGT 61.899 40.000 23.49 23.49 42.56 4.16
2627 4007 5.821516 ACAGTTTTTACCAAACACATCGA 57.178 34.783 0.00 0.00 32.81 3.59
2639 4019 9.233232 CATTGGTGAAAGAGTAACAGTTTTTAC 57.767 33.333 0.00 0.00 32.88 2.01
2681 4061 6.233430 ACATTCTGATTTTCTGTGTTCTCG 57.767 37.500 0.00 0.00 0.00 4.04
2751 4131 2.097036 TCGTCGCCATAAAGAGAGGAA 58.903 47.619 0.00 0.00 0.00 3.36
2767 4147 7.845617 TGTAAAAGCACAAATACATTTCGTC 57.154 32.000 0.00 0.00 0.00 4.20
2823 4203 0.521291 ATGTTTTCCGATGTGCACCG 59.479 50.000 15.69 11.55 0.00 4.94
2911 4309 3.611766 ACCACTATACCAGACAACTGC 57.388 47.619 0.00 0.00 42.25 4.40
2929 4327 6.229936 TGTGACCCTTAACATGACTATACC 57.770 41.667 0.00 0.00 0.00 2.73
2930 4328 7.101054 TGTTGTGACCCTTAACATGACTATAC 58.899 38.462 0.00 0.00 30.06 1.47
2932 4330 6.121776 TGTTGTGACCCTTAACATGACTAT 57.878 37.500 0.00 0.00 30.06 2.12
2934 4332 4.431416 TGTTGTGACCCTTAACATGACT 57.569 40.909 0.00 0.00 30.06 3.41
2935 4333 5.163602 TGTTTGTTGTGACCCTTAACATGAC 60.164 40.000 0.00 0.00 34.63 3.06
2936 4334 4.950475 TGTTTGTTGTGACCCTTAACATGA 59.050 37.500 0.00 0.00 34.63 3.07
2937 4335 5.255710 TGTTTGTTGTGACCCTTAACATG 57.744 39.130 0.00 0.00 34.63 3.21
2941 4339 6.433404 TGTTACTTGTTTGTTGTGACCCTTAA 59.567 34.615 0.00 0.00 0.00 1.85
2942 4340 5.944599 TGTTACTTGTTTGTTGTGACCCTTA 59.055 36.000 0.00 0.00 0.00 2.69
2943 4341 4.767928 TGTTACTTGTTTGTTGTGACCCTT 59.232 37.500 0.00 0.00 0.00 3.95
2944 4342 4.337145 TGTTACTTGTTTGTTGTGACCCT 58.663 39.130 0.00 0.00 0.00 4.34
2945 4343 4.705337 TGTTACTTGTTTGTTGTGACCC 57.295 40.909 0.00 0.00 0.00 4.46
2946 4344 5.705902 ACTTGTTACTTGTTTGTTGTGACC 58.294 37.500 0.00 0.00 0.00 4.02
2947 4345 6.858993 TGAACTTGTTACTTGTTTGTTGTGAC 59.141 34.615 0.00 0.00 0.00 3.67
3128 4768 3.140325 TGATGTGGGAAGAACTGGTTC 57.860 47.619 5.43 5.43 39.78 3.62
3246 4889 3.464907 TGGTGCATGTTCACATTTTTGG 58.535 40.909 5.92 0.00 38.66 3.28
3290 4933 7.875327 ACCAAAAGAAGCTGACTTAAAACTA 57.125 32.000 6.81 0.00 35.82 2.24
3561 5205 0.252696 TGCCAGAGGTACCATCCTGT 60.253 55.000 15.94 0.00 38.02 4.00
3841 5486 5.108254 GCAAAGCGAATGAACTGTAAAACTG 60.108 40.000 0.00 0.00 0.00 3.16
4054 5700 9.220767 GGAATGAACTAACTACTCTGAACAAAT 57.779 33.333 0.00 0.00 0.00 2.32
4188 5838 6.265196 TGATAGGAGTTGCAAAAACAAGACAT 59.735 34.615 0.00 0.00 0.00 3.06
4593 7345 9.110617 CAAGAGAAATTATTTACATATGCGCAG 57.889 33.333 18.32 4.62 0.00 5.18
4601 7353 8.416329 GGATGGTGCAAGAGAAATTATTTACAT 58.584 33.333 0.00 0.00 0.00 2.29
4616 7368 3.826157 TCCTGTTTAAAGGATGGTGCAAG 59.174 43.478 0.00 0.00 41.60 4.01
5149 7902 5.994668 AGTCAGAGTTTTGACCTCTTCAATC 59.005 40.000 2.76 0.00 46.81 2.67
5202 7955 4.379302 AAGAGAAAAGGTCAGGAGCAAT 57.621 40.909 0.97 0.00 0.00 3.56
5266 8019 9.639601 AAAATATTGTGGCTAAGCTTAAGTTTC 57.360 29.630 7.93 0.00 0.00 2.78
5323 8076 6.916360 TTAGCTTCATTTCCCAAGTCATTT 57.084 33.333 0.00 0.00 0.00 2.32
5326 8079 5.415701 GTCATTAGCTTCATTTCCCAAGTCA 59.584 40.000 0.00 0.00 0.00 3.41
5392 8145 2.472695 TTGTTTCCGCAGCTGTATCT 57.527 45.000 16.64 0.00 0.00 1.98
5404 8157 5.006386 AGTGTCTCCTCATTGATTGTTTCC 58.994 41.667 0.00 0.00 0.00 3.13
5819 8572 1.645710 AGTTGGACGGATCCTGAGTT 58.354 50.000 10.75 0.00 46.43 3.01
6164 8917 1.381867 TTCCTCCATGACCCCATGTT 58.618 50.000 0.00 0.00 46.68 2.71
6384 9227 4.509230 ACAGCGAGCATATAAACATCAGTG 59.491 41.667 0.00 0.00 0.00 3.66
6403 9246 3.264947 TCATCAATGTGAGCAGTACAGC 58.735 45.455 1.29 1.29 0.00 4.40
6415 9258 7.554118 AGAAAGATAACGGTTCATCATCAATGT 59.446 33.333 0.00 0.00 36.68 2.71
6430 9273 5.175859 TGCCAAGGTTAGAGAAAGATAACG 58.824 41.667 0.00 0.00 33.57 3.18
6439 9282 4.362677 AGTAATCCTGCCAAGGTTAGAGA 58.637 43.478 0.00 0.00 44.82 3.10
6579 9422 3.231736 AACGAGTCCACGGGCTGT 61.232 61.111 0.00 0.00 37.61 4.40
6660 9511 4.692625 GTGCGATCTATTATGGACAGCAAT 59.307 41.667 10.24 0.00 33.03 3.56
6680 9531 5.121768 ACGTGAAATTGGTAACTAGATGTGC 59.878 40.000 0.00 0.00 37.61 4.57
6683 9534 6.533723 TGCTACGTGAAATTGGTAACTAGATG 59.466 38.462 0.00 0.00 37.61 2.90
6733 9587 5.302568 TGAAAAGGTGCTGAACATGATTCTT 59.697 36.000 0.00 0.00 0.00 2.52
6761 9615 2.421424 CCAAATGAGCCAGAACTGCTAC 59.579 50.000 0.00 0.00 39.69 3.58
6788 9642 0.400213 CCCCTACAGTGGACTTGCAA 59.600 55.000 0.00 0.00 0.00 4.08
6953 9807 5.437289 TGCAAATGAACGAACTCAGATTT 57.563 34.783 0.00 0.00 0.00 2.17
7052 9906 5.950758 TGTACAAACATCGTAAAAGGCAT 57.049 34.783 0.00 0.00 0.00 4.40
7063 9917 6.683974 AGCTTCCATACATGTACAAACATC 57.316 37.500 7.96 0.00 44.70 3.06
7072 9926 5.255687 TGATGTTGAAGCTTCCATACATGT 58.744 37.500 28.73 16.17 0.00 3.21
7076 9930 5.182001 ACACTTGATGTTGAAGCTTCCATAC 59.818 40.000 23.42 17.68 38.98 2.39
7146 10001 3.450457 AGAGGATACAGAGGCAGTGAAAG 59.550 47.826 0.00 0.00 41.41 2.62
7153 10008 6.839134 TGTAAATTCTAGAGGATACAGAGGCA 59.161 38.462 8.62 0.00 41.41 4.75
7272 10129 1.134098 CCCATAGAGGTGCGTCCAAAT 60.134 52.381 0.75 0.00 39.02 2.32
7536 10395 2.751259 TGTCTTGCTACGGAGTAATCGT 59.249 45.455 0.00 0.00 45.13 3.73
7537 10396 3.416119 TGTCTTGCTACGGAGTAATCG 57.584 47.619 0.00 0.00 45.13 3.34
7604 10463 2.106338 TGGTCCAACTGAATTGAGCTGA 59.894 45.455 0.00 0.00 41.23 4.26
7627 10486 5.525378 CCACCTCATGAGCTACTGAATAAAC 59.475 44.000 17.76 0.00 0.00 2.01
7693 10552 5.963594 AGAGGATCAAAGTAGTTAACGGAC 58.036 41.667 0.00 2.86 37.82 4.79
7709 10568 3.620821 GCTTGTTACTGCTTGAGAGGATC 59.379 47.826 0.00 0.00 0.00 3.36
7750 10609 5.324409 TGGAAAATACAGATGTGGAGCTTT 58.676 37.500 0.00 0.00 0.00 3.51
7753 10612 5.126061 ACATTGGAAAATACAGATGTGGAGC 59.874 40.000 0.00 0.00 0.00 4.70
7762 10621 8.048534 AGACTCAATCACATTGGAAAATACAG 57.951 34.615 0.00 0.00 40.61 2.74
7782 10642 7.197703 GTGAGCCTGATAAACTAACTAGACTC 58.802 42.308 0.00 0.00 0.00 3.36
7801 10661 3.254903 ACGGAAACAAATTAAGGTGAGCC 59.745 43.478 0.00 0.00 0.00 4.70
7876 10736 0.033503 TACCACTCTGATCGCTGGGA 60.034 55.000 0.00 0.00 0.00 4.37
8100 10961 4.351874 AGCTAGGCTGAGTGTTAAAACA 57.648 40.909 0.00 0.00 37.57 2.83
8105 10967 4.023980 ACATGTAGCTAGGCTGAGTGTTA 58.976 43.478 0.00 0.00 40.10 2.41
8107 10969 2.461695 ACATGTAGCTAGGCTGAGTGT 58.538 47.619 0.00 1.85 40.10 3.55
8124 10986 4.846367 ACATCCCTACATACATGGCTACAT 59.154 41.667 0.00 0.00 37.99 2.29
8132 10994 4.103153 CACCAGGAACATCCCTACATACAT 59.897 45.833 0.00 0.00 37.19 2.29
8153 11015 2.166664 TGTTTTTGTGGCCAGGTTACAC 59.833 45.455 5.11 0.00 35.75 2.90
8170 11032 3.245730 ACATCCATGGTCCCTGATTGTTT 60.246 43.478 12.58 0.00 0.00 2.83
8173 11035 2.742428 ACATCCATGGTCCCTGATTG 57.258 50.000 12.58 1.10 0.00 2.67
8348 11210 5.333798 GCTGCGTTATAGAGAAACAACAACA 60.334 40.000 0.00 0.00 0.00 3.33
8367 11229 4.628333 AGGAAATGAAAAATGAATGCTGCG 59.372 37.500 0.00 0.00 0.00 5.18
8670 11579 3.302286 CGCGAGAAACATCACATCATCTG 60.302 47.826 0.00 0.00 0.00 2.90
8671 11580 2.862536 CGCGAGAAACATCACATCATCT 59.137 45.455 0.00 0.00 0.00 2.90
8718 11627 7.959175 TCTTAACTGACACACCACTAACTAAT 58.041 34.615 0.00 0.00 0.00 1.73
8733 11642 9.478768 AAAACTAGCTAGAAACTCTTAACTGAC 57.521 33.333 27.45 0.00 0.00 3.51
8783 11704 6.208988 AGCTAGTATGAACAAGTCGATCAA 57.791 37.500 0.00 0.00 29.18 2.57
8917 11979 9.745323 GTTTTGATTATTTATTTTCTGCAGTGC 57.255 29.630 14.67 8.58 0.00 4.40
8949 12011 0.808755 GAACAAACCTGGGTATGCGG 59.191 55.000 0.00 0.00 0.00 5.69
8950 12012 0.808755 GGAACAAACCTGGGTATGCG 59.191 55.000 0.00 0.00 0.00 4.73
8955 12017 1.780309 TCATCTGGAACAAACCTGGGT 59.220 47.619 0.00 0.00 38.70 4.51
8962 12024 1.202758 ACGGCAGTCATCTGGAACAAA 60.203 47.619 0.00 0.00 41.57 2.83
8963 12025 0.396435 ACGGCAGTCATCTGGAACAA 59.604 50.000 0.00 0.00 41.57 2.83
8964 12026 0.396435 AACGGCAGTCATCTGGAACA 59.604 50.000 0.00 0.00 41.57 3.18
8965 12027 2.380084 TAACGGCAGTCATCTGGAAC 57.620 50.000 0.00 0.00 41.57 3.62
8966 12028 4.746535 TTATAACGGCAGTCATCTGGAA 57.253 40.909 0.00 0.00 41.57 3.53
8979 12041 9.134734 AGCAACAACAAATGTAATTTATAACGG 57.865 29.630 0.00 0.00 46.64 4.44
9048 12110 7.012421 GGCTTCAGATCTACCGAACAAAATTAT 59.988 37.037 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.