Multiple sequence alignment - TraesCS7B01G000700

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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 TraesCS7B01G000700 chr7B 100.000 3293 0 0 1 3293 227976 231268 0.000000e+00 6082.0
1 TraesCS7B01G000700 chr7B 87.997 1158 124 7 1047 2197 128462 129611 0.000000e+00 1354.0
2 TraesCS7B01G000700 chr7B 85.082 1153 148 12 1048 2197 1020506 1021637 0.000000e+00 1155.0
3 TraesCS7B01G000700 chr7B 85.069 1152 150 11 1048 2197 1154139 1155270 0.000000e+00 1155.0
4 TraesCS7B01G000700 chr5D 95.976 994 38 1 1 994 238781524 238780533 0.000000e+00 1613.0
5 TraesCS7B01G000700 chr5D 93.177 1026 42 9 1363 2383 562414457 562413455 0.000000e+00 1482.0
6 TraesCS7B01G000700 chr5D 88.083 1158 123 7 1047 2197 562488329 562487180 0.000000e+00 1360.0
7 TraesCS7B01G000700 chr5D 88.083 1158 123 7 1047 2197 562531174 562530025 0.000000e+00 1360.0
8 TraesCS7B01G000700 chr5D 85.776 1153 140 12 1048 2197 561804202 561803071 0.000000e+00 1199.0
9 TraesCS7B01G000700 chr5D 93.955 579 16 7 2491 3057 562413182 562412611 0.000000e+00 857.0
10 TraesCS7B01G000700 chr5D 93.361 241 10 2 3053 3293 562412582 562412348 5.230000e-93 351.0
11 TraesCS7B01G000700 chr5D 82.991 341 49 8 2719 3054 562429770 562429434 1.920000e-77 300.0
12 TraesCS7B01G000700 chr5D 82.530 166 17 9 2214 2368 561802960 561802796 5.730000e-28 135.0
13 TraesCS7B01G000700 chr6D 95.762 991 42 0 1 991 412442654 412443644 0.000000e+00 1598.0
14 TraesCS7B01G000700 chr6D 94.753 991 48 3 1 990 68726066 68725079 0.000000e+00 1539.0
15 TraesCS7B01G000700 chr3D 95.482 996 45 0 1 996 360566098 360567093 0.000000e+00 1591.0
16 TraesCS7B01G000700 chr3D 95.391 998 46 0 1 998 461600979 461601976 0.000000e+00 1589.0
17 TraesCS7B01G000700 chr2D 95.377 995 46 0 1 995 222183723 222184717 0.000000e+00 1583.0
18 TraesCS7B01G000700 chr2D 82.609 115 8 9 2384 2487 591031673 591031786 1.260000e-14 91.6
19 TraesCS7B01G000700 chr4D 95.276 995 47 0 1 995 509444605 509443611 0.000000e+00 1578.0
20 TraesCS7B01G000700 chr4D 94.118 1003 55 2 1 999 373877747 373876745 0.000000e+00 1522.0
21 TraesCS7B01G000700 chr7D 94.283 997 54 3 1 996 618057957 618056963 0.000000e+00 1522.0
22 TraesCS7B01G000700 chr5B 85.823 1185 130 16 1047 2222 712890281 712889126 0.000000e+00 1223.0
23 TraesCS7B01G000700 chr5B 85.108 1155 146 13 1048 2197 711715573 711714440 0.000000e+00 1157.0
24 TraesCS7B01G000700 chr5B 86.799 553 28 15 2539 3057 712873973 712873432 2.850000e-160 575.0
25 TraesCS7B01G000700 chr5B 91.803 244 11 5 3053 3293 712873403 712873166 6.810000e-87 331.0
26 TraesCS7B01G000700 chr5B 82.530 166 17 9 2214 2368 711714329 711714165 5.730000e-28 135.0


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 TraesCS7B01G000700 chr7B 227976 231268 3292 False 6082.000000 6082 100.000000 1 3293 1 chr7B.!!$F2 3292
1 TraesCS7B01G000700 chr7B 128462 129611 1149 False 1354.000000 1354 87.997000 1047 2197 1 chr7B.!!$F1 1150
2 TraesCS7B01G000700 chr7B 1020506 1021637 1131 False 1155.000000 1155 85.082000 1048 2197 1 chr7B.!!$F3 1149
3 TraesCS7B01G000700 chr7B 1154139 1155270 1131 False 1155.000000 1155 85.069000 1048 2197 1 chr7B.!!$F4 1149
4 TraesCS7B01G000700 chr5D 238780533 238781524 991 True 1613.000000 1613 95.976000 1 994 1 chr5D.!!$R1 993
5 TraesCS7B01G000700 chr5D 562487180 562488329 1149 True 1360.000000 1360 88.083000 1047 2197 1 chr5D.!!$R3 1150
6 TraesCS7B01G000700 chr5D 562530025 562531174 1149 True 1360.000000 1360 88.083000 1047 2197 1 chr5D.!!$R4 1150
7 TraesCS7B01G000700 chr5D 562412348 562414457 2109 True 896.666667 1482 93.497667 1363 3293 3 chr5D.!!$R6 1930
8 TraesCS7B01G000700 chr5D 561802796 561804202 1406 True 667.000000 1199 84.153000 1048 2368 2 chr5D.!!$R5 1320
9 TraesCS7B01G000700 chr6D 412442654 412443644 990 False 1598.000000 1598 95.762000 1 991 1 chr6D.!!$F1 990
10 TraesCS7B01G000700 chr6D 68725079 68726066 987 True 1539.000000 1539 94.753000 1 990 1 chr6D.!!$R1 989
11 TraesCS7B01G000700 chr3D 360566098 360567093 995 False 1591.000000 1591 95.482000 1 996 1 chr3D.!!$F1 995
12 TraesCS7B01G000700 chr3D 461600979 461601976 997 False 1589.000000 1589 95.391000 1 998 1 chr3D.!!$F2 997
13 TraesCS7B01G000700 chr2D 222183723 222184717 994 False 1583.000000 1583 95.377000 1 995 1 chr2D.!!$F1 994
14 TraesCS7B01G000700 chr4D 509443611 509444605 994 True 1578.000000 1578 95.276000 1 995 1 chr4D.!!$R2 994
15 TraesCS7B01G000700 chr4D 373876745 373877747 1002 True 1522.000000 1522 94.118000 1 999 1 chr4D.!!$R1 998
16 TraesCS7B01G000700 chr7D 618056963 618057957 994 True 1522.000000 1522 94.283000 1 996 1 chr7D.!!$R1 995
17 TraesCS7B01G000700 chr5B 712889126 712890281 1155 True 1223.000000 1223 85.823000 1047 2222 1 chr5B.!!$R1 1175
18 TraesCS7B01G000700 chr5B 711714165 711715573 1408 True 646.000000 1157 83.819000 1048 2368 2 chr5B.!!$R2 1320
19 TraesCS7B01G000700 chr5B 712873166 712873973 807 True 453.000000 575 89.301000 2539 3293 2 chr5B.!!$R3 754

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
397 398 0.104144 CCCCCTATGTGATACCCCCA 60.104 60.0 0.00 0.00 0.0 4.96 F
1031 1039 0.033366 AAATCAAGTTTGGCCGGCAC 59.967 50.0 30.85 18.58 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1491 0.037303 CAGCATGGTGAGGTTCTGGT 59.963 55.0 20.2 0.0 0.0 4.00 R
2488 2735 0.034059 AGCAAACCTCACCTCAGACG 59.966 55.0 0.0 0.0 0.0 4.18 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
42 43 5.491982 GTCCCTACAATCTCAGTTCAACAT 58.508 41.667 0.00 0.00 0.00 2.71
69 70 0.902984 TTGACTTAGGGCTCCTCGCA 60.903 55.000 0.00 0.00 41.67 5.10
135 136 5.942236 TGAGCTTCTTGATTGTATTGCTCTT 59.058 36.000 11.90 0.00 43.95 2.85
141 142 7.926674 TCTTGATTGTATTGCTCTTCATGAA 57.073 32.000 8.12 8.12 0.00 2.57
144 145 5.357878 TGATTGTATTGCTCTTCATGAACCC 59.642 40.000 3.38 0.00 0.00 4.11
187 188 4.314440 TTCGCTGGCGCCTTGAGT 62.314 61.111 29.70 0.00 39.59 3.41
290 291 1.135112 CATTCGCCTGCCCCTTAAAAC 60.135 52.381 0.00 0.00 0.00 2.43
297 298 1.213430 CTGCCCCTTAAAACCCGGATA 59.787 52.381 0.73 0.00 0.00 2.59
318 319 0.255604 TCATGTGGCAATGGATCCGT 59.744 50.000 7.39 3.27 0.00 4.69
397 398 0.104144 CCCCCTATGTGATACCCCCA 60.104 60.000 0.00 0.00 0.00 4.96
504 505 0.115745 ACTCCAACTTCCCCGACCTA 59.884 55.000 0.00 0.00 0.00 3.08
516 517 1.065928 CGACCTATTCGCCGAGCTT 59.934 57.895 0.00 0.00 41.87 3.74
679 680 2.111999 TTACTTGCAGCTCTGGCGGT 62.112 55.000 0.00 0.00 44.37 5.68
888 892 2.904131 GCCCTCAGCAGTACCTCC 59.096 66.667 0.00 0.00 42.97 4.30
890 894 1.379977 CCCTCAGCAGTACCTCCGA 60.380 63.158 0.00 0.00 0.00 4.55
892 896 0.173708 CCTCAGCAGTACCTCCGAAC 59.826 60.000 0.00 0.00 0.00 3.95
904 908 4.081322 ACCTCCGAACTTATTGTTGTGT 57.919 40.909 0.00 0.00 39.30 3.72
912 920 5.007234 CGAACTTATTGTTGTGTGACTTGGA 59.993 40.000 0.00 0.00 39.30 3.53
944 952 6.041637 TGTTCTGAACTAGTCCTTGTATGTGT 59.958 38.462 20.18 0.00 0.00 3.72
983 991 2.695127 TTATAAAGCGGGGCGAAAGA 57.305 45.000 0.00 0.00 0.00 2.52
1001 1009 7.304066 CGAAAGACTTTTTCGGTAATTTCAC 57.696 36.000 12.72 0.00 45.17 3.18
1002 1010 7.130269 CGAAAGACTTTTTCGGTAATTTCACT 58.870 34.615 12.72 0.00 45.17 3.41
1003 1011 7.320560 CGAAAGACTTTTTCGGTAATTTCACTC 59.679 37.037 12.72 0.00 45.17 3.51
1004 1012 6.224420 AGACTTTTTCGGTAATTTCACTCG 57.776 37.500 0.00 0.00 0.00 4.18
1005 1013 5.987347 AGACTTTTTCGGTAATTTCACTCGA 59.013 36.000 0.00 0.00 0.00 4.04
1006 1014 6.145696 AGACTTTTTCGGTAATTTCACTCGAG 59.854 38.462 11.84 11.84 0.00 4.04
1007 1015 5.987347 ACTTTTTCGGTAATTTCACTCGAGA 59.013 36.000 21.68 0.00 0.00 4.04
1008 1016 6.145696 ACTTTTTCGGTAATTTCACTCGAGAG 59.854 38.462 21.68 12.21 0.00 3.20
1009 1017 4.778534 TTCGGTAATTTCACTCGAGAGT 57.221 40.909 21.68 0.00 43.61 3.24
1010 1018 4.352600 TCGGTAATTTCACTCGAGAGTC 57.647 45.455 21.68 0.52 40.20 3.36
1011 1019 3.754850 TCGGTAATTTCACTCGAGAGTCA 59.245 43.478 21.68 2.72 40.20 3.41
1012 1020 4.216902 TCGGTAATTTCACTCGAGAGTCAA 59.783 41.667 21.68 9.38 40.20 3.18
1013 1021 4.921515 CGGTAATTTCACTCGAGAGTCAAA 59.078 41.667 21.68 9.22 40.20 2.69
1014 1022 5.404366 CGGTAATTTCACTCGAGAGTCAAAA 59.596 40.000 21.68 8.48 35.13 2.44
1015 1023 6.090898 CGGTAATTTCACTCGAGAGTCAAAAT 59.909 38.462 21.68 10.45 35.13 1.82
1016 1024 7.457060 GGTAATTTCACTCGAGAGTCAAAATC 58.543 38.462 21.68 3.17 35.13 2.17
1017 1025 7.117812 GGTAATTTCACTCGAGAGTCAAAATCA 59.882 37.037 21.68 0.00 35.13 2.57
1018 1026 7.496529 AATTTCACTCGAGAGTCAAAATCAA 57.503 32.000 21.68 0.00 35.13 2.57
1019 1027 6.530913 TTTCACTCGAGAGTCAAAATCAAG 57.469 37.500 21.68 0.00 40.20 3.02
1020 1028 5.201713 TCACTCGAGAGTCAAAATCAAGT 57.798 39.130 21.68 0.00 40.20 3.16
1021 1029 5.601662 TCACTCGAGAGTCAAAATCAAGTT 58.398 37.500 21.68 0.00 40.20 2.66
1022 1030 6.049149 TCACTCGAGAGTCAAAATCAAGTTT 58.951 36.000 21.68 0.00 40.20 2.66
1023 1031 6.018751 TCACTCGAGAGTCAAAATCAAGTTTG 60.019 38.462 21.68 0.07 40.20 2.93
1024 1032 5.237344 ACTCGAGAGTCAAAATCAAGTTTGG 59.763 40.000 21.68 0.00 36.92 3.28
1025 1033 4.024048 TCGAGAGTCAAAATCAAGTTTGGC 60.024 41.667 0.00 0.00 42.25 4.52
1026 1034 4.550422 GAGAGTCAAAATCAAGTTTGGCC 58.450 43.478 0.00 0.00 42.80 5.36
1027 1035 3.004734 AGAGTCAAAATCAAGTTTGGCCG 59.995 43.478 0.00 0.00 42.80 6.13
1028 1036 2.035832 AGTCAAAATCAAGTTTGGCCGG 59.964 45.455 0.00 0.00 42.80 6.13
1029 1037 1.147473 CAAAATCAAGTTTGGCCGGC 58.853 50.000 21.18 21.18 35.29 6.13
1030 1038 0.755686 AAAATCAAGTTTGGCCGGCA 59.244 45.000 30.85 12.04 0.00 5.69
1031 1039 0.033366 AAATCAAGTTTGGCCGGCAC 59.967 50.000 30.85 18.58 0.00 5.01
1032 1040 0.827507 AATCAAGTTTGGCCGGCACT 60.828 50.000 30.85 20.79 0.00 4.40
1033 1041 0.827507 ATCAAGTTTGGCCGGCACTT 60.828 50.000 30.85 25.45 0.00 3.16
1034 1042 0.179015 TCAAGTTTGGCCGGCACTTA 60.179 50.000 30.85 14.30 0.00 2.24
1035 1043 0.039527 CAAGTTTGGCCGGCACTTAC 60.040 55.000 30.85 19.34 0.00 2.34
1036 1044 0.179001 AAGTTTGGCCGGCACTTACT 60.179 50.000 30.85 21.28 0.00 2.24
1037 1045 0.179001 AGTTTGGCCGGCACTTACTT 60.179 50.000 30.85 3.83 0.00 2.24
1038 1046 0.039527 GTTTGGCCGGCACTTACTTG 60.040 55.000 30.85 0.00 0.00 3.16
1039 1047 0.179015 TTTGGCCGGCACTTACTTGA 60.179 50.000 30.85 0.00 0.00 3.02
1040 1048 0.179015 TTGGCCGGCACTTACTTGAA 60.179 50.000 30.85 3.24 0.00 2.69
1041 1049 0.605319 TGGCCGGCACTTACTTGAAG 60.605 55.000 30.85 0.00 41.37 3.02
1058 1066 0.995024 AAGTAGGCATCACCCAAGCT 59.005 50.000 0.00 0.00 40.58 3.74
1094 1102 1.907936 AGAGAGAGCACTTGCCAATCT 59.092 47.619 0.00 0.00 43.38 2.40
1107 1116 2.025155 GCCAATCTCTCACTCGACCTA 58.975 52.381 0.00 0.00 0.00 3.08
1108 1117 2.034053 GCCAATCTCTCACTCGACCTAG 59.966 54.545 0.00 0.00 0.00 3.02
1109 1118 2.034053 CCAATCTCTCACTCGACCTAGC 59.966 54.545 0.00 0.00 0.00 3.42
1110 1119 2.948979 CAATCTCTCACTCGACCTAGCT 59.051 50.000 0.00 0.00 0.00 3.32
1111 1120 2.319136 TCTCTCACTCGACCTAGCTC 57.681 55.000 0.00 0.00 0.00 4.09
1112 1121 1.555533 TCTCTCACTCGACCTAGCTCA 59.444 52.381 0.00 0.00 0.00 4.26
1113 1122 1.939934 CTCTCACTCGACCTAGCTCAG 59.060 57.143 0.00 0.00 0.00 3.35
1116 1125 0.179150 CACTCGACCTAGCTCAGTGC 60.179 60.000 0.00 0.00 43.29 4.40
1150 1159 2.063378 GCTGCCTACTGCTCCTCCT 61.063 63.158 0.00 0.00 42.00 3.69
1152 1161 1.381872 TGCCTACTGCTCCTCCTCC 60.382 63.158 0.00 0.00 42.00 4.30
1158 1167 0.682855 ACTGCTCCTCCTCCTCTTCG 60.683 60.000 0.00 0.00 0.00 3.79
1159 1168 1.380515 TGCTCCTCCTCCTCTTCGG 60.381 63.158 0.00 0.00 0.00 4.30
1171 1186 1.002544 CCTCTTCGGGTTTCTCTTGCT 59.997 52.381 0.00 0.00 0.00 3.91
1231 1249 1.251251 GGATTGCAGGACTTTGCTGT 58.749 50.000 0.00 0.00 44.38 4.40
1239 1257 0.957888 GGACTTTGCTGTGAGCCTCC 60.958 60.000 0.00 0.00 41.51 4.30
1267 1285 1.639635 GGTGTCCTCCTCCATGCCAT 61.640 60.000 0.00 0.00 0.00 4.40
1268 1286 0.257039 GTGTCCTCCTCCATGCCATT 59.743 55.000 0.00 0.00 0.00 3.16
1279 1297 0.108709 CATGCCATTTGGTTCGGTGG 60.109 55.000 0.00 0.00 37.57 4.61
1401 1419 2.185310 CTCCCTTGTAGGCCTTGCGT 62.185 60.000 12.58 0.00 32.73 5.24
1472 1490 1.468520 GTGCTCACAATATTGCGTGGT 59.531 47.619 15.48 0.00 33.83 4.16
1473 1491 2.675844 GTGCTCACAATATTGCGTGGTA 59.324 45.455 15.48 0.89 33.83 3.25
1549 1568 3.257375 CCGACGATGGTATTATTGGAGGA 59.743 47.826 0.00 0.00 0.00 3.71
1652 1671 1.144708 TGGAGGTGCTTGATTTGTCCA 59.855 47.619 0.00 0.00 0.00 4.02
1720 1739 3.074538 ACCACCTTTGCTACTTGGATCTT 59.925 43.478 0.00 0.00 0.00 2.40
1731 1751 7.725251 TGCTACTTGGATCTTTCAAACAATTT 58.275 30.769 0.00 0.00 0.00 1.82
1853 1873 5.179368 GTGAAGCATAACAGAAGCACACTTA 59.821 40.000 0.00 0.00 35.82 2.24
1928 1948 4.009675 GACATCAGGGAGCAACAATGTTA 58.990 43.478 0.00 0.00 0.00 2.41
1935 1955 4.102524 AGGGAGCAACAATGTTATATCCGA 59.897 41.667 13.65 0.00 0.00 4.55
1980 2000 3.370103 GGGGATGAAAACACCGTATCTGA 60.370 47.826 0.00 0.00 0.00 3.27
2029 2049 7.537596 TGAAAACATTGTATCAGGGAACAAT 57.462 32.000 0.00 0.00 44.94 2.71
2107 2131 0.388294 GAGGTAGTGTGGTATCCGGC 59.612 60.000 0.00 0.00 0.00 6.13
2108 2132 1.047034 AGGTAGTGTGGTATCCGGCC 61.047 60.000 0.00 0.00 0.00 6.13
2109 2133 1.066918 GTAGTGTGGTATCCGGCCG 59.933 63.158 21.04 21.04 0.00 6.13
2110 2134 2.129146 TAGTGTGGTATCCGGCCGG 61.129 63.158 39.13 39.13 0.00 6.13
2124 2148 1.037030 GGCCGGATTCAAGAATGGCA 61.037 55.000 19.59 0.00 39.98 4.92
2169 2193 1.732259 CTGGGAGCAACAACATCGTAC 59.268 52.381 0.00 0.00 0.00 3.67
2176 2200 2.939640 GCAACAACATCGTACCTGGGAT 60.940 50.000 0.00 0.00 0.00 3.85
2177 2201 2.677836 CAACAACATCGTACCTGGGATG 59.322 50.000 9.14 9.14 44.34 3.51
2181 2205 1.485066 ACATCGTACCTGGGATGAACC 59.515 52.381 15.52 0.00 42.00 3.62
2184 2208 3.035055 TCGTACCTGGGATGAACCATA 57.965 47.619 0.00 0.00 40.36 2.74
2250 2369 9.929180 GATATGATGTTGAGCCTTTGTAGTATA 57.071 33.333 0.00 0.00 0.00 1.47
2293 2413 5.106791 GGCCATGAGATGATGTTCGATAAAG 60.107 44.000 0.00 0.00 0.00 1.85
2297 2424 8.867935 CCATGAGATGATGTTCGATAAAGATAC 58.132 37.037 0.00 0.00 0.00 2.24
2414 2542 1.002857 AAAAGGAGGATGACCCCCTG 58.997 55.000 0.00 0.00 36.23 4.45
2415 2543 1.575447 AAAGGAGGATGACCCCCTGC 61.575 60.000 0.00 0.00 41.76 4.85
2416 2544 2.692368 GGAGGATGACCCCCTGCA 60.692 66.667 0.00 0.00 41.19 4.41
2418 2546 1.453669 GAGGATGACCCCCTGCATC 59.546 63.158 0.00 0.00 40.05 3.91
2420 2548 1.150081 GGATGACCCCCTGCATCTG 59.850 63.158 0.00 0.00 40.49 2.90
2422 2550 0.548031 GATGACCCCCTGCATCTGAA 59.452 55.000 0.00 0.00 38.25 3.02
2452 2699 9.562408 TGCATGCATCCATTTTATTGATTATTT 57.438 25.926 18.46 0.00 0.00 1.40
2523 2818 7.437862 TGAGGTTTGCTTTTATACTTTGCTTTG 59.562 33.333 0.00 0.00 0.00 2.77
2534 2829 8.537728 TTATACTTTGCTTTGATCCATCCATT 57.462 30.769 0.00 0.00 0.00 3.16
2535 2830 9.639563 TTATACTTTGCTTTGATCCATCCATTA 57.360 29.630 0.00 0.00 0.00 1.90
2536 2831 6.461110 ACTTTGCTTTGATCCATCCATTAG 57.539 37.500 0.00 0.00 0.00 1.73
2537 2832 6.189859 ACTTTGCTTTGATCCATCCATTAGA 58.810 36.000 0.00 0.00 0.00 2.10
2546 2841 6.962182 TGATCCATCCATTAGATATTCCACC 58.038 40.000 0.00 0.00 32.37 4.61
2607 2905 6.214399 CAAACCGGTAGATAGATCCAAGTAC 58.786 44.000 8.00 0.00 0.00 2.73
2608 2906 5.057843 ACCGGTAGATAGATCCAAGTACA 57.942 43.478 4.49 0.00 0.00 2.90
2989 3327 3.305773 CGCTTCTACGACGCGCTC 61.306 66.667 5.73 1.80 42.61 5.03
3085 3456 2.922503 TGGCACTCCTTCTCCGCA 60.923 61.111 0.00 0.00 0.00 5.69
3132 3503 1.377366 CGCCTGGAGCTCGTCTTCTA 61.377 60.000 7.83 0.00 40.39 2.10
3153 3524 1.444553 GCGTCCGGTTCAGAGTCAG 60.445 63.158 0.00 0.00 0.00 3.51
3164 3535 0.319383 CAGAGTCAGCAGCGTGTTCT 60.319 55.000 0.00 0.00 0.00 3.01
3168 3539 1.341531 AGTCAGCAGCGTGTTCTACTT 59.658 47.619 0.00 0.00 0.00 2.24
3169 3540 1.721926 GTCAGCAGCGTGTTCTACTTC 59.278 52.381 0.00 0.00 0.00 3.01
3170 3541 1.071605 CAGCAGCGTGTTCTACTTCC 58.928 55.000 0.00 0.00 0.00 3.46
3171 3542 0.679505 AGCAGCGTGTTCTACTTCCA 59.320 50.000 0.00 0.00 0.00 3.53
3172 3543 0.790814 GCAGCGTGTTCTACTTCCAC 59.209 55.000 0.00 0.00 0.00 4.02
3173 3544 1.605712 GCAGCGTGTTCTACTTCCACT 60.606 52.381 0.00 0.00 0.00 4.00
3174 3545 2.329379 CAGCGTGTTCTACTTCCACTC 58.671 52.381 0.00 0.00 0.00 3.51
3175 3546 1.272769 AGCGTGTTCTACTTCCACTCC 59.727 52.381 0.00 0.00 0.00 3.85
3214 3585 2.356313 AAGTGCGACCTGCTCGTG 60.356 61.111 0.00 0.00 44.92 4.35
3236 3607 4.680237 CCGACGGCAACCTGCTCA 62.680 66.667 0.00 0.00 44.28 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.678684 TGTAGGGACGACAGCGATGA 60.679 55.000 8.12 0.00 39.46 2.92
69 70 1.076044 CCCAAATGGCCTCCGGAAT 60.076 57.895 5.23 0.00 0.00 3.01
135 136 1.675714 GCATCGACAGTGGGTTCATGA 60.676 52.381 0.00 0.00 0.00 3.07
141 142 2.665000 CCAGCATCGACAGTGGGT 59.335 61.111 0.00 0.00 0.00 4.51
144 145 2.821366 GGGCCAGCATCGACAGTG 60.821 66.667 4.39 0.00 0.00 3.66
174 175 2.097038 CGAAGACTCAAGGCGCCAG 61.097 63.158 31.54 20.31 0.00 4.85
187 188 1.278127 GGTGGAGAATTGACCCGAAGA 59.722 52.381 0.00 0.00 0.00 2.87
290 291 1.979855 TTGCCACATGAATATCCGGG 58.020 50.000 0.00 0.00 0.00 5.73
297 298 1.958579 CGGATCCATTGCCACATGAAT 59.041 47.619 13.41 0.00 0.00 2.57
397 398 6.702329 AGAAGAATATGTGGTTCGAGTCTTT 58.298 36.000 0.00 0.00 0.00 2.52
504 505 2.512515 GCCTGAAGCTCGGCGAAT 60.513 61.111 12.13 0.00 38.99 3.34
836 840 4.113354 GCCCAAAACACACACGAAATAAA 58.887 39.130 0.00 0.00 0.00 1.40
888 892 5.007234 TCCAAGTCACACAACAATAAGTTCG 59.993 40.000 0.00 0.00 38.74 3.95
890 894 6.321181 ACATCCAAGTCACACAACAATAAGTT 59.679 34.615 0.00 0.00 42.42 2.66
892 896 6.144854 CACATCCAAGTCACACAACAATAAG 58.855 40.000 0.00 0.00 0.00 1.73
904 908 3.118445 TCAGAACACACACATCCAAGTCA 60.118 43.478 0.00 0.00 0.00 3.41
912 920 4.345257 AGGACTAGTTCAGAACACACACAT 59.655 41.667 15.85 0.00 0.00 3.21
944 952 4.329462 AAATAAAGCAAACCGCCAAGAA 57.671 36.364 0.00 0.00 44.04 2.52
983 991 5.987347 TCTCGAGTGAAATTACCGAAAAAGT 59.013 36.000 13.13 0.00 0.00 2.66
999 1007 5.914085 AACTTGATTTTGACTCTCGAGTG 57.086 39.130 13.13 12.94 42.66 3.51
1000 1008 5.237344 CCAAACTTGATTTTGACTCTCGAGT 59.763 40.000 13.13 0.00 45.84 4.18
1001 1009 5.683859 CCAAACTTGATTTTGACTCTCGAG 58.316 41.667 5.93 5.93 38.54 4.04
1002 1010 4.024048 GCCAAACTTGATTTTGACTCTCGA 60.024 41.667 0.00 0.00 38.54 4.04
1003 1011 4.222114 GCCAAACTTGATTTTGACTCTCG 58.778 43.478 0.00 0.00 38.54 4.04
1004 1012 4.550422 GGCCAAACTTGATTTTGACTCTC 58.450 43.478 0.00 0.00 38.54 3.20
1005 1013 3.004734 CGGCCAAACTTGATTTTGACTCT 59.995 43.478 2.24 0.00 38.54 3.24
1006 1014 3.308530 CGGCCAAACTTGATTTTGACTC 58.691 45.455 2.24 0.00 38.54 3.36
1007 1015 2.035832 CCGGCCAAACTTGATTTTGACT 59.964 45.455 2.24 0.00 38.54 3.41
1008 1016 2.403259 CCGGCCAAACTTGATTTTGAC 58.597 47.619 2.24 0.00 38.54 3.18
1009 1017 1.270041 GCCGGCCAAACTTGATTTTGA 60.270 47.619 18.11 0.00 38.54 2.69
1010 1018 1.147473 GCCGGCCAAACTTGATTTTG 58.853 50.000 18.11 0.00 36.40 2.44
1011 1019 0.755686 TGCCGGCCAAACTTGATTTT 59.244 45.000 26.77 0.00 0.00 1.82
1012 1020 0.033366 GTGCCGGCCAAACTTGATTT 59.967 50.000 26.77 0.00 0.00 2.17
1013 1021 0.827507 AGTGCCGGCCAAACTTGATT 60.828 50.000 26.77 0.00 0.00 2.57
1014 1022 0.827507 AAGTGCCGGCCAAACTTGAT 60.828 50.000 25.07 6.12 33.01 2.57
1015 1023 0.179015 TAAGTGCCGGCCAAACTTGA 60.179 50.000 30.62 17.07 35.77 3.02
1016 1024 0.039527 GTAAGTGCCGGCCAAACTTG 60.040 55.000 30.62 0.00 35.77 3.16
1017 1025 0.179001 AGTAAGTGCCGGCCAAACTT 60.179 50.000 27.55 27.55 37.82 2.66
1018 1026 0.179001 AAGTAAGTGCCGGCCAAACT 60.179 50.000 26.77 18.66 0.00 2.66
1019 1027 0.039527 CAAGTAAGTGCCGGCCAAAC 60.040 55.000 26.77 16.33 0.00 2.93
1020 1028 0.179015 TCAAGTAAGTGCCGGCCAAA 60.179 50.000 26.77 1.08 0.00 3.28
1021 1029 0.179015 TTCAAGTAAGTGCCGGCCAA 60.179 50.000 26.77 2.06 0.00 4.52
1022 1030 0.605319 CTTCAAGTAAGTGCCGGCCA 60.605 55.000 26.77 9.53 0.00 5.36
1023 1031 0.605589 ACTTCAAGTAAGTGCCGGCC 60.606 55.000 26.77 15.80 46.90 6.13
1024 1032 2.928416 ACTTCAAGTAAGTGCCGGC 58.072 52.632 22.73 22.73 46.90 6.13
1031 1039 4.192317 GGGTGATGCCTACTTCAAGTAAG 58.808 47.826 0.00 0.00 38.10 2.34
1032 1040 3.585289 TGGGTGATGCCTACTTCAAGTAA 59.415 43.478 0.00 0.00 37.43 2.24
1033 1041 3.178046 TGGGTGATGCCTACTTCAAGTA 58.822 45.455 0.00 0.00 37.43 2.24
1034 1042 1.985159 TGGGTGATGCCTACTTCAAGT 59.015 47.619 0.00 0.00 37.43 3.16
1035 1043 2.787473 TGGGTGATGCCTACTTCAAG 57.213 50.000 0.00 0.00 37.43 3.02
1036 1044 2.879756 GCTTGGGTGATGCCTACTTCAA 60.880 50.000 0.00 0.00 37.43 2.69
1037 1045 1.340017 GCTTGGGTGATGCCTACTTCA 60.340 52.381 0.00 0.00 37.43 3.02
1038 1046 1.065126 AGCTTGGGTGATGCCTACTTC 60.065 52.381 0.00 0.00 37.43 3.01
1039 1047 0.995024 AGCTTGGGTGATGCCTACTT 59.005 50.000 0.00 0.00 37.43 2.24
1040 1048 0.254178 CAGCTTGGGTGATGCCTACT 59.746 55.000 0.00 0.00 37.43 2.57
1041 1049 0.035056 ACAGCTTGGGTGATGCCTAC 60.035 55.000 3.72 0.00 37.43 3.18
1042 1050 0.698238 AACAGCTTGGGTGATGCCTA 59.302 50.000 3.72 0.00 37.43 3.93
1043 1051 0.178953 AAACAGCTTGGGTGATGCCT 60.179 50.000 3.72 0.00 37.43 4.75
1044 1052 0.037975 CAAACAGCTTGGGTGATGCC 60.038 55.000 3.72 0.00 34.87 4.40
1045 1053 0.675633 ACAAACAGCTTGGGTGATGC 59.324 50.000 3.72 0.00 39.56 3.91
1058 1066 5.092554 TCTCTCTTGGTGTTGTACAAACA 57.907 39.130 10.51 8.21 0.00 2.83
1094 1102 1.279558 ACTGAGCTAGGTCGAGTGAGA 59.720 52.381 19.47 2.08 0.00 3.27
1107 1116 1.226542 CCATGGGATGCACTGAGCT 59.773 57.895 2.85 0.00 45.94 4.09
1108 1117 2.487532 GCCATGGGATGCACTGAGC 61.488 63.158 15.13 0.00 45.96 4.26
1109 1118 1.826921 GGCCATGGGATGCACTGAG 60.827 63.158 15.13 0.00 0.00 3.35
1110 1119 2.152602 TTGGCCATGGGATGCACTGA 62.153 55.000 15.13 0.00 0.00 3.41
1111 1120 1.259142 TTTGGCCATGGGATGCACTG 61.259 55.000 15.13 0.00 0.00 3.66
1112 1121 0.325860 ATTTGGCCATGGGATGCACT 60.326 50.000 15.13 0.00 0.00 4.40
1113 1122 0.179067 CATTTGGCCATGGGATGCAC 60.179 55.000 15.13 0.00 0.00 4.57
1116 1125 0.105964 CAGCATTTGGCCATGGGATG 59.894 55.000 15.13 10.26 46.50 3.51
1150 1159 1.002087 GCAAGAGAAACCCGAAGAGGA 59.998 52.381 0.00 0.00 45.00 3.71
1152 1161 2.342179 GAGCAAGAGAAACCCGAAGAG 58.658 52.381 0.00 0.00 0.00 2.85
1158 1167 1.021920 GCCTCGAGCAAGAGAAACCC 61.022 60.000 6.99 0.00 42.97 4.11
1159 1168 1.355066 CGCCTCGAGCAAGAGAAACC 61.355 60.000 6.99 0.00 44.04 3.27
1185 1200 3.670377 GTCGGGGTGGCACAAAGC 61.670 66.667 20.82 1.05 44.16 3.51
1211 1229 0.169672 CAGCAAAGTCCTGCAATCCG 59.830 55.000 0.00 0.00 45.18 4.18
1213 1231 1.881973 TCACAGCAAAGTCCTGCAATC 59.118 47.619 0.00 0.00 45.18 2.67
1215 1233 1.311859 CTCACAGCAAAGTCCTGCAA 58.688 50.000 0.00 0.00 45.18 4.08
1267 1285 2.037053 CATGTGCCACCGAACCAAA 58.963 52.632 0.00 0.00 0.00 3.28
1268 1286 2.560119 GCATGTGCCACCGAACCAA 61.560 57.895 0.00 0.00 34.31 3.67
1305 1323 3.549150 GCTAGCAGCGTCACAGCG 61.549 66.667 10.63 0.00 43.00 5.18
1316 1334 4.735132 GTGACACGGCCGCTAGCA 62.735 66.667 28.58 15.93 46.50 3.49
1472 1490 1.278985 CAGCATGGTGAGGTTCTGGTA 59.721 52.381 20.20 0.00 0.00 3.25
1473 1491 0.037303 CAGCATGGTGAGGTTCTGGT 59.963 55.000 20.20 0.00 0.00 4.00
1549 1568 0.107945 GCACCTCGAGGCTCTTGAAT 60.108 55.000 31.56 6.22 39.32 2.57
1720 1739 6.415280 CGTCGTCAACCAATAAATTGTTTGAA 59.585 34.615 14.74 1.61 46.08 2.69
1731 1751 0.319083 AGGTGCGTCGTCAACCAATA 59.681 50.000 13.85 0.00 0.00 1.90
1740 1760 1.604693 CCAAACTCTTAGGTGCGTCGT 60.605 52.381 0.00 0.00 0.00 4.34
1853 1873 2.792599 CTCGCTAAGTCGCCGTCT 59.207 61.111 0.00 0.00 0.00 4.18
1928 1948 5.344743 ACAGTGTTGTCATTCTCGGATAT 57.655 39.130 0.00 0.00 29.46 1.63
1980 2000 3.476552 CCATATACGGCATGGTTGTTCT 58.523 45.455 0.00 0.00 38.53 3.01
2029 2049 1.775385 TGCTCCCAGATACGACATGA 58.225 50.000 0.00 0.00 0.00 3.07
2107 2131 4.155462 CAGATATGCCATTCTTGAATCCGG 59.845 45.833 0.00 0.00 0.00 5.14
2108 2132 4.155462 CCAGATATGCCATTCTTGAATCCG 59.845 45.833 0.00 0.00 0.00 4.18
2109 2133 5.319453 TCCAGATATGCCATTCTTGAATCC 58.681 41.667 0.00 0.00 0.00 3.01
2110 2134 6.889301 TTCCAGATATGCCATTCTTGAATC 57.111 37.500 0.00 0.00 0.00 2.52
2111 2135 7.008332 TGATTCCAGATATGCCATTCTTGAAT 58.992 34.615 12.01 12.01 37.17 2.57
2124 2148 5.296151 ACGACATGGTTGATTCCAGATAT 57.704 39.130 0.00 0.00 41.05 1.63
2169 2193 5.942236 CAGATACAATATGGTTCATCCCAGG 59.058 44.000 0.00 0.00 38.07 4.45
2176 2200 6.320434 TGTTCCCAGATACAATATGGTTCA 57.680 37.500 0.00 0.00 40.00 3.18
2177 2201 6.601613 TGTTGTTCCCAGATACAATATGGTTC 59.398 38.462 0.00 0.00 40.00 3.62
2181 2205 8.055279 ACTTTGTTGTTCCCAGATACAATATG 57.945 34.615 0.00 0.00 36.72 1.78
2184 2208 6.976934 AACTTTGTTGTTCCCAGATACAAT 57.023 33.333 0.00 0.00 36.72 2.71
2293 2413 1.588404 CATCTCGTGTGGCAACGTATC 59.412 52.381 17.30 0.00 43.96 2.24
2297 2424 1.626654 GGACATCTCGTGTGGCAACG 61.627 60.000 13.53 13.53 42.36 4.10
2400 2528 1.059006 AGATGCAGGGGGTCATCCTC 61.059 60.000 0.00 0.00 39.79 3.71
2402 2530 1.150081 CAGATGCAGGGGGTCATCC 59.850 63.158 0.00 0.00 39.79 3.51
2403 2531 0.548031 TTCAGATGCAGGGGGTCATC 59.452 55.000 0.00 0.00 39.38 2.92
2406 2534 0.620556 TCTTTCAGATGCAGGGGGTC 59.379 55.000 0.00 0.00 0.00 4.46
2408 2536 1.688772 CATCTTTCAGATGCAGGGGG 58.311 55.000 0.84 0.00 44.69 5.40
2425 2672 9.733556 AATAATCAATAAAATGGATGCATGCAT 57.266 25.926 32.66 32.66 40.77 3.96
2466 2713 7.769044 AGACGTGGCATATTATTGTTCTACTTT 59.231 33.333 0.00 0.00 0.00 2.66
2467 2714 7.224753 CAGACGTGGCATATTATTGTTCTACTT 59.775 37.037 0.00 0.00 0.00 2.24
2468 2715 6.701841 CAGACGTGGCATATTATTGTTCTACT 59.298 38.462 0.00 0.00 0.00 2.57
2469 2716 6.700081 TCAGACGTGGCATATTATTGTTCTAC 59.300 38.462 0.00 0.00 0.00 2.59
2470 2717 6.811954 TCAGACGTGGCATATTATTGTTCTA 58.188 36.000 0.00 0.00 0.00 2.10
2472 2719 5.050091 CCTCAGACGTGGCATATTATTGTTC 60.050 44.000 0.00 0.00 0.00 3.18
2473 2720 4.816385 CCTCAGACGTGGCATATTATTGTT 59.184 41.667 0.00 0.00 0.00 2.83
2474 2721 4.141711 ACCTCAGACGTGGCATATTATTGT 60.142 41.667 0.00 0.00 0.00 2.71
2476 2723 4.100963 TCACCTCAGACGTGGCATATTATT 59.899 41.667 0.00 0.00 0.00 1.40
2477 2724 3.641436 TCACCTCAGACGTGGCATATTAT 59.359 43.478 0.00 0.00 0.00 1.28
2478 2725 3.028130 TCACCTCAGACGTGGCATATTA 58.972 45.455 0.00 0.00 0.00 0.98
2479 2726 1.831106 TCACCTCAGACGTGGCATATT 59.169 47.619 0.00 0.00 0.00 1.28
2480 2727 1.410517 CTCACCTCAGACGTGGCATAT 59.589 52.381 0.00 0.00 0.00 1.78
2481 2728 0.817654 CTCACCTCAGACGTGGCATA 59.182 55.000 0.00 0.00 0.00 3.14
2482 2729 1.593787 CTCACCTCAGACGTGGCAT 59.406 57.895 0.00 0.00 0.00 4.40
2483 2730 2.574018 CCTCACCTCAGACGTGGCA 61.574 63.158 0.00 0.00 0.00 4.92
2485 2732 0.393077 AAACCTCACCTCAGACGTGG 59.607 55.000 0.00 0.00 0.00 4.94
2486 2733 1.502231 CAAACCTCACCTCAGACGTG 58.498 55.000 0.00 0.00 0.00 4.49
2487 2734 0.249911 GCAAACCTCACCTCAGACGT 60.250 55.000 0.00 0.00 0.00 4.34
2488 2735 0.034059 AGCAAACCTCACCTCAGACG 59.966 55.000 0.00 0.00 0.00 4.18
2489 2736 2.262423 AAGCAAACCTCACCTCAGAC 57.738 50.000 0.00 0.00 0.00 3.51
2523 2818 7.205515 AGGTGGAATATCTAATGGATGGATC 57.794 40.000 0.00 0.00 35.98 3.36
2534 2829 4.180377 AGACGTGGAGGTGGAATATCTA 57.820 45.455 0.00 0.00 0.00 1.98
2535 2830 3.033659 AGACGTGGAGGTGGAATATCT 57.966 47.619 0.00 0.00 0.00 1.98
2536 2831 3.821421 AAGACGTGGAGGTGGAATATC 57.179 47.619 0.00 0.00 0.00 1.63
2537 2832 5.687166 TTTAAGACGTGGAGGTGGAATAT 57.313 39.130 0.00 0.00 0.00 1.28
2546 2841 8.934507 AGAAGAAGAATATTTAAGACGTGGAG 57.065 34.615 0.00 0.00 0.00 3.86
2815 3135 4.443266 AGCCAGGCGACGAAGAGC 62.443 66.667 5.55 0.00 0.00 4.09
2962 3300 2.058595 GTAGAAGCGGAGGGAGGCA 61.059 63.158 0.00 0.00 0.00 4.75
3067 3438 2.125350 GCGGAGAAGGAGTGCCAG 60.125 66.667 0.00 0.00 36.29 4.85
3132 3503 2.156051 GACTCTGAACCGGACGCCTT 62.156 60.000 9.46 0.00 0.00 4.35
3153 3524 0.790814 GTGGAAGTAGAACACGCTGC 59.209 55.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.