Multiple sequence alignment - TraesCS4B01G195700

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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 TraesCS4B01G195700 chr4B 100.000 3976 0 0 1 3976 421860276 421856301 0.000000e+00 7343.0
1 TraesCS4B01G195700 chr4B 93.119 1555 76 11 1126 2672 149035424 149033893 0.000000e+00 2250.0
2 TraesCS4B01G195700 chr4B 92.990 1555 79 10 1126 2672 148999200 148997668 0.000000e+00 2241.0
3 TraesCS4B01G195700 chr4B 96.429 952 30 4 1 952 149000123 148999176 0.000000e+00 1567.0
4 TraesCS4B01G195700 chr4B 96.429 952 30 4 1 952 149036347 149035400 0.000000e+00 1567.0
5 TraesCS4B01G195700 chr4B 96.667 210 1 4 923 1132 429720310 429720107 1.060000e-90 344.0
6 TraesCS4B01G195700 chr6D 95.247 1557 53 11 1125 2672 16117416 16118960 0.000000e+00 2446.0
7 TraesCS4B01G195700 chr6D 95.397 956 31 5 1 952 16116495 16117441 0.000000e+00 1509.0
8 TraesCS4B01G195700 chr6D 86.550 171 13 5 3772 3933 296688215 296688046 3.160000e-41 180.0
9 TraesCS4B01G195700 chr1A 94.926 1557 59 12 1126 2672 176410068 176411614 0.000000e+00 2420.0
10 TraesCS4B01G195700 chr1A 92.437 952 36 7 1 952 176409177 176410092 0.000000e+00 1327.0
11 TraesCS4B01G195700 chr3A 94.923 1556 60 10 1126 2672 296899843 296901388 0.000000e+00 2418.0
12 TraesCS4B01G195700 chr3A 92.138 725 27 5 228 952 296899173 296899867 0.000000e+00 996.0
13 TraesCS4B01G195700 chr3A 100.000 184 0 0 949 1132 38034030 38033847 1.370000e-89 340.0
14 TraesCS4B01G195700 chr5B 97.258 1313 25 4 2666 3976 392492810 392494113 0.000000e+00 2215.0
15 TraesCS4B01G195700 chr5B 95.833 216 6 3 919 1132 407489299 407489085 2.940000e-91 346.0
16 TraesCS4B01G195700 chr5B 94.196 224 7 5 920 1139 287781214 287780993 1.770000e-88 337.0
17 TraesCS4B01G195700 chr5B 92.308 104 8 0 4 107 700063133 700063030 8.900000e-32 148.0
18 TraesCS4B01G195700 chr7D 96.575 1314 35 4 2666 3976 534868779 534867473 0.000000e+00 2169.0
19 TraesCS4B01G195700 chr7B 95.050 1313 55 6 2666 3976 186766724 186768028 0.000000e+00 2056.0
20 TraesCS4B01G195700 chr7B 94.170 223 7 5 914 1132 491581483 491581703 6.370000e-88 335.0
21 TraesCS4B01G195700 chr3B 97.498 1159 21 2 2819 3976 284563950 284562799 0.000000e+00 1973.0
22 TraesCS4B01G195700 chr3B 98.216 953 12 4 1 952 286888617 286887669 0.000000e+00 1661.0
23 TraesCS4B01G195700 chr3B 96.099 564 18 3 1126 1685 286887693 286887130 0.000000e+00 917.0
24 TraesCS4B01G195700 chr3B 95.833 216 5 4 919 1132 157236430 157236643 2.940000e-91 346.0
25 TraesCS4B01G195700 chr3B 94.483 145 5 2 2666 2810 284564257 284564116 1.860000e-53 220.0
26 TraesCS4B01G195700 chr1B 93.832 1297 60 9 1382 2672 538915656 538916938 0.000000e+00 1934.0
27 TraesCS4B01G195700 chr1B 93.138 1297 67 11 1382 2672 117567862 117569142 0.000000e+00 1882.0
28 TraesCS4B01G195700 chr1B 94.545 220 9 3 919 1135 567190984 567190765 1.770000e-88 337.0
29 TraesCS4B01G195700 chrUn 93.359 1295 70 8 1382 2670 286669929 286671213 0.000000e+00 1901.0
30 TraesCS4B01G195700 chrUn 93.205 1295 72 8 1382 2670 286677286 286676002 0.000000e+00 1890.0
31 TraesCS4B01G195700 chrUn 93.051 993 56 5 1382 2371 316389957 316390939 0.000000e+00 1439.0
32 TraesCS4B01G195700 chr6B 95.278 953 42 3 1 952 328338677 328339627 0.000000e+00 1507.0
33 TraesCS4B01G195700 chr6B 92.035 1017 64 10 1126 2136 328339603 328340608 0.000000e+00 1413.0
34 TraesCS4B01G195700 chr6B 86.854 213 20 6 3772 3976 460502961 460503173 8.590000e-57 231.0
35 TraesCS4B01G195700 chr7A 94.797 788 34 5 1126 1907 629779436 629778650 0.000000e+00 1221.0
36 TraesCS4B01G195700 chr7A 95.646 735 22 4 1904 2636 629778593 629777867 0.000000e+00 1171.0
37 TraesCS4B01G195700 chr7A 96.737 613 18 2 340 952 629780022 629779412 0.000000e+00 1020.0
38 TraesCS4B01G195700 chr7A 95.894 341 14 0 1 341 629780456 629780116 1.610000e-153 553.0
39 TraesCS4B01G195700 chr5A 95.349 215 8 2 919 1132 133519191 133519404 1.370000e-89 340.0
40 TraesCS4B01G195700 chr4A 94.570 221 8 4 919 1135 365637431 365637211 4.920000e-89 339.0
41 TraesCS4B01G195700 chr6A 86.916 214 15 6 3772 3976 423312264 423312055 1.110000e-55 228.0
42 TraesCS4B01G195700 chr5D 84.211 190 12 9 1161 1332 65007507 65007696 6.830000e-38 169.0
43 TraesCS4B01G195700 chr5D 77.844 167 15 11 783 946 65007131 65007278 2.550000e-12 84.2
44 TraesCS4B01G195700 chr2A 92.157 102 8 0 6 107 722812976 722812875 1.150000e-30 145.0


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 TraesCS4B01G195700 chr4B 421856301 421860276 3975 True 7343.00 7343 100.0000 1 3976 1 chr4B.!!$R1 3975
1 TraesCS4B01G195700 chr4B 149033893 149036347 2454 True 1908.50 2250 94.7740 1 2672 2 chr4B.!!$R4 2671
2 TraesCS4B01G195700 chr4B 148997668 149000123 2455 True 1904.00 2241 94.7095 1 2672 2 chr4B.!!$R3 2671
3 TraesCS4B01G195700 chr6D 16116495 16118960 2465 False 1977.50 2446 95.3220 1 2672 2 chr6D.!!$F1 2671
4 TraesCS4B01G195700 chr1A 176409177 176411614 2437 False 1873.50 2420 93.6815 1 2672 2 chr1A.!!$F1 2671
5 TraesCS4B01G195700 chr3A 296899173 296901388 2215 False 1707.00 2418 93.5305 228 2672 2 chr3A.!!$F1 2444
6 TraesCS4B01G195700 chr5B 392492810 392494113 1303 False 2215.00 2215 97.2580 2666 3976 1 chr5B.!!$F1 1310
7 TraesCS4B01G195700 chr7D 534867473 534868779 1306 True 2169.00 2169 96.5750 2666 3976 1 chr7D.!!$R1 1310
8 TraesCS4B01G195700 chr7B 186766724 186768028 1304 False 2056.00 2056 95.0500 2666 3976 1 chr7B.!!$F1 1310
9 TraesCS4B01G195700 chr3B 286887130 286888617 1487 True 1289.00 1661 97.1575 1 1685 2 chr3B.!!$R2 1684
10 TraesCS4B01G195700 chr3B 284562799 284564257 1458 True 1096.50 1973 95.9905 2666 3976 2 chr3B.!!$R1 1310
11 TraesCS4B01G195700 chr1B 538915656 538916938 1282 False 1934.00 1934 93.8320 1382 2672 1 chr1B.!!$F2 1290
12 TraesCS4B01G195700 chr1B 117567862 117569142 1280 False 1882.00 1882 93.1380 1382 2672 1 chr1B.!!$F1 1290
13 TraesCS4B01G195700 chrUn 286669929 286671213 1284 False 1901.00 1901 93.3590 1382 2670 1 chrUn.!!$F1 1288
14 TraesCS4B01G195700 chrUn 286676002 286677286 1284 True 1890.00 1890 93.2050 1382 2670 1 chrUn.!!$R1 1288
15 TraesCS4B01G195700 chrUn 316389957 316390939 982 False 1439.00 1439 93.0510 1382 2371 1 chrUn.!!$F2 989
16 TraesCS4B01G195700 chr6B 328338677 328340608 1931 False 1460.00 1507 93.6565 1 2136 2 chr6B.!!$F2 2135
17 TraesCS4B01G195700 chr7A 629777867 629780456 2589 True 991.25 1221 95.7685 1 2636 4 chr7A.!!$R1 2635

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
985 1085 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.0 12.44 8.34 40.80 4.35 F
987 1087 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.0 12.44 0.00 40.80 3.16 F
988 1088 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.0 12.44 0.00 40.80 3.33 F
1055 1155 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.0 0.00 0.00 37.28 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2253 0.984995 AGTTTGTCCTACCTGGGAGC 59.015 55.000 0.0 0.0 35.87 4.70 R
2291 2457 2.646175 GCTCTGCGGGTCAGTGGTA 61.646 63.158 0.0 0.0 43.32 3.25 R
2341 2507 3.687698 ACCAAGACGAATACCGAAAATGG 59.312 43.478 0.0 0.0 41.76 3.16 R
3039 3371 3.880608 TGTCCCCATATCCATCACCATA 58.119 45.455 0.0 0.0 0.00 2.74 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
98 99 5.830457 TCGATCTACTCTGTCATTTCCTGAT 59.170 40.000 0.00 0.00 35.97 2.90
251 253 3.278668 TTTTCAGTTTCACGGGGTACA 57.721 42.857 0.00 0.00 0.00 2.90
299 301 2.169144 CACATACCAGGTGAGATCAGCA 59.831 50.000 13.95 0.00 46.03 4.41
482 579 6.263842 TCATTTGAACTCTTTGACAGATGCTT 59.736 34.615 0.00 0.00 0.00 3.91
563 662 4.401925 ACAGATTCAAGTGCTAGGCTTTT 58.598 39.130 0.00 0.00 0.00 2.27
948 1048 9.849166 TTTTCTTGTTTTACAGTTTTAGGTCAG 57.151 29.630 0.00 0.00 0.00 3.51
949 1049 8.795842 TTCTTGTTTTACAGTTTTAGGTCAGA 57.204 30.769 0.00 0.00 0.00 3.27
950 1050 8.795842 TCTTGTTTTACAGTTTTAGGTCAGAA 57.204 30.769 0.00 0.00 0.00 3.02
951 1051 8.889717 TCTTGTTTTACAGTTTTAGGTCAGAAG 58.110 33.333 0.00 0.00 0.00 2.85
952 1052 7.562454 TGTTTTACAGTTTTAGGTCAGAAGG 57.438 36.000 0.00 0.00 0.00 3.46
953 1053 6.544564 TGTTTTACAGTTTTAGGTCAGAAGGG 59.455 38.462 0.00 0.00 0.00 3.95
954 1054 3.790089 ACAGTTTTAGGTCAGAAGGGG 57.210 47.619 0.00 0.00 0.00 4.79
955 1055 3.323775 ACAGTTTTAGGTCAGAAGGGGA 58.676 45.455 0.00 0.00 0.00 4.81
956 1056 3.328050 ACAGTTTTAGGTCAGAAGGGGAG 59.672 47.826 0.00 0.00 0.00 4.30
957 1057 2.306219 AGTTTTAGGTCAGAAGGGGAGC 59.694 50.000 0.00 0.00 0.00 4.70
958 1058 1.286248 TTTAGGTCAGAAGGGGAGCC 58.714 55.000 0.00 0.00 33.37 4.70
959 1059 0.417841 TTAGGTCAGAAGGGGAGCCT 59.582 55.000 0.00 0.00 33.37 4.58
960 1060 0.417841 TAGGTCAGAAGGGGAGCCTT 59.582 55.000 0.00 0.00 33.37 4.35
961 1061 1.204113 AGGTCAGAAGGGGAGCCTTG 61.204 60.000 0.00 0.00 33.37 3.61
962 1062 1.301293 GTCAGAAGGGGAGCCTTGG 59.699 63.158 0.00 0.00 0.00 3.61
963 1063 2.044551 CAGAAGGGGAGCCTTGGC 60.045 66.667 2.97 2.97 0.00 4.52
964 1064 3.721706 AGAAGGGGAGCCTTGGCG 61.722 66.667 5.95 0.00 0.00 5.69
972 1072 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
973 1073 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
974 1074 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
975 1075 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
976 1076 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
977 1077 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
978 1078 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
983 1083 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
984 1084 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
985 1085 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
986 1086 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
987 1087 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
988 1088 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
989 1089 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
990 1090 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
991 1091 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
992 1092 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
993 1093 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
994 1094 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
995 1095 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
996 1096 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
997 1097 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
1012 1112 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
1013 1113 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
1014 1114 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
1015 1115 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
1016 1116 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
1017 1117 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
1018 1118 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
1019 1119 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
1020 1120 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
1021 1121 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
1035 1135 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
1036 1136 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
1037 1137 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
1038 1138 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
1039 1139 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
1040 1140 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
1041 1141 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
1042 1142 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
1043 1143 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
1044 1144 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
1045 1145 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
1046 1146 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
1047 1147 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
1048 1148 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
1049 1149 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
1050 1150 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
1051 1151 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
1052 1152 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
1053 1153 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
1054 1154 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
1055 1155 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
1056 1156 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
1057 1157 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
1058 1158 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
1059 1159 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
1060 1160 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
1061 1161 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
1062 1162 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
1063 1163 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
1064 1164 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
1065 1165 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
1066 1166 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
1067 1167 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
1068 1168 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
1069 1169 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
1070 1170 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
1071 1171 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
1072 1172 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
1077 1177 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
1078 1178 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
1079 1179 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
1080 1180 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
1081 1181 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
1082 1182 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
1083 1183 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
1084 1184 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
1085 1185 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
1086 1186 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
1087 1187 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
1088 1188 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
1089 1189 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
1090 1190 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
1091 1191 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
1092 1192 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
1093 1193 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
1094 1194 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
1095 1195 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
1096 1196 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
1121 1221 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
1122 1222 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
1123 1223 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
1124 1224 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
1125 1225 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
1126 1226 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
1127 1227 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
1212 1312 6.102897 AGGTTCTGATCATACCGATTTAGG 57.897 41.667 17.01 0.00 37.04 2.69
1292 1394 9.408648 CTTCCACTGTACTATTGGGATAAATTT 57.591 33.333 0.00 0.00 30.37 1.82
1353 1455 6.127810 AGATTGTTTGAATCCATCATGACG 57.872 37.500 0.00 0.00 38.03 4.35
1370 1472 1.061131 GACGCAATGTTCTGACCATCG 59.939 52.381 0.00 0.00 0.00 3.84
1489 1593 1.129251 CAGAGCAACATGGCAGTTACG 59.871 52.381 0.00 0.00 35.83 3.18
1627 1731 8.570488 CCTCTGCTGCATTTGTTTTATATATCA 58.430 33.333 1.31 0.00 0.00 2.15
1700 1805 5.832595 TCTGTTGATTTTCCAGATTTGGTCA 59.167 36.000 1.59 0.00 45.26 4.02
1857 1963 2.803670 CAACGTCGACGCGATGGT 60.804 61.111 35.92 14.38 43.99 3.55
2087 2253 0.957395 ACCAGCTTCAGCAACATCGG 60.957 55.000 0.75 0.00 45.16 4.18
2214 2380 0.323908 AGTTAGCCCTCTCGAGCTGT 60.324 55.000 7.81 0.00 40.28 4.40
2341 2507 4.001652 GAGGGTTAGTTAGTTTCCTGCAC 58.998 47.826 0.00 0.00 0.00 4.57
2412 2580 9.855021 TTTTCTTGCTTATGCTATTTAGGAAAC 57.145 29.630 1.96 0.00 40.48 2.78
2554 2724 5.243730 TGGAGATGAAATTTTCACCAGGAAC 59.756 40.000 13.80 2.91 43.48 3.62
2596 2767 7.278646 TCGCTAAAGTACTAATCTGACGACTAA 59.721 37.037 0.00 0.00 0.00 2.24
2718 2890 6.990939 CACTGTGTCATCATATCTCCTTTCAT 59.009 38.462 0.00 0.00 0.00 2.57
2792 2964 3.638160 TGGCAAATGATAAATGAGCCCTC 59.362 43.478 0.00 0.00 39.85 4.30
2872 3203 0.251787 AAGGAGTTGGTGGGCCATTC 60.252 55.000 10.70 6.16 45.56 2.67
3039 3371 5.671493 CGGAGGAACCTTCACTTTGTATAT 58.329 41.667 0.00 0.00 36.31 0.86
3259 3591 2.418628 TGCTGCTGCCGACTAAAATTAC 59.581 45.455 13.47 0.00 38.71 1.89
3309 3641 9.669353 GTTGACATATTACTAGCAAATTGGATG 57.331 33.333 0.00 0.00 0.00 3.51
3368 3700 5.933617 AGGCTTTCATCTGCATATACAAGA 58.066 37.500 6.61 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
297 299 5.163713 GGAACTCAACTATCATTGTCCTTGC 60.164 44.000 0.00 0.00 0.00 4.01
299 301 6.380079 AGGAACTCAACTATCATTGTCCTT 57.620 37.500 0.00 0.00 31.72 3.36
563 662 5.769835 AGATTGGGATTTGCTTCATCCTTA 58.230 37.500 8.67 0.33 40.32 2.69
926 1026 8.129211 CCTTCTGACCTAAAACTGTAAAACAAG 58.871 37.037 0.00 0.00 0.00 3.16
929 1029 6.016527 CCCCTTCTGACCTAAAACTGTAAAAC 60.017 42.308 0.00 0.00 0.00 2.43
930 1030 6.066032 CCCCTTCTGACCTAAAACTGTAAAA 58.934 40.000 0.00 0.00 0.00 1.52
933 1033 4.495565 TCCCCTTCTGACCTAAAACTGTA 58.504 43.478 0.00 0.00 0.00 2.74
934 1034 3.323775 TCCCCTTCTGACCTAAAACTGT 58.676 45.455 0.00 0.00 0.00 3.55
935 1035 3.870299 GCTCCCCTTCTGACCTAAAACTG 60.870 52.174 0.00 0.00 0.00 3.16
936 1036 2.306219 GCTCCCCTTCTGACCTAAAACT 59.694 50.000 0.00 0.00 0.00 2.66
937 1037 2.618302 GGCTCCCCTTCTGACCTAAAAC 60.618 54.545 0.00 0.00 0.00 2.43
938 1038 1.633945 GGCTCCCCTTCTGACCTAAAA 59.366 52.381 0.00 0.00 0.00 1.52
939 1039 1.203440 AGGCTCCCCTTCTGACCTAAA 60.203 52.381 0.00 0.00 38.74 1.85
940 1040 0.417841 AGGCTCCCCTTCTGACCTAA 59.582 55.000 0.00 0.00 38.74 2.69
941 1041 2.106125 AGGCTCCCCTTCTGACCTA 58.894 57.895 0.00 0.00 38.74 3.08
942 1042 2.873427 AGGCTCCCCTTCTGACCT 59.127 61.111 0.00 0.00 38.74 3.85
954 1054 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
955 1055 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
956 1056 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
957 1057 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
958 1058 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
959 1059 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
960 1060 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
961 1061 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
965 1065 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
966 1066 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
967 1067 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
968 1068 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
969 1069 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
970 1070 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
971 1071 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
972 1072 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
973 1073 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
974 1074 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
975 1075 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
976 1076 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
977 1077 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
978 1078 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
979 1079 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
980 1080 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
992 1092 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
993 1093 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
994 1094 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
995 1095 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
996 1096 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
997 1097 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
998 1098 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
999 1099 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
1000 1100 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
1001 1101 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
1002 1102 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
1003 1103 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
1004 1104 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
1005 1105 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
1006 1106 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
1007 1107 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
1008 1108 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
1009 1109 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
1010 1110 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
1011 1111 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
1012 1112 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
1013 1113 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
1025 1125 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
1026 1126 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
1027 1127 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
1028 1128 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
1029 1129 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
1030 1130 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
1031 1131 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
1032 1132 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
1033 1133 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
1034 1134 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
1035 1135 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
1036 1136 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
1037 1137 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
1038 1138 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
1039 1139 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
1040 1140 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
1041 1141 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
1042 1142 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
1043 1143 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
1044 1144 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
1045 1145 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
1046 1146 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
1047 1147 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
1048 1148 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
1049 1149 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
1050 1150 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
1051 1151 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
1061 1161 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
1062 1162 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
1063 1163 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
1064 1164 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
1065 1165 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
1066 1166 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
1067 1167 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
1068 1168 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
1069 1169 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
1070 1170 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
1071 1171 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
1072 1172 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
1073 1173 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
1074 1174 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
1075 1175 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
1076 1176 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
1077 1177 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
1078 1178 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
1079 1179 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
1091 1191 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
1094 1194 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
1095 1195 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
1096 1196 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
1097 1197 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
1103 1203 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
1104 1204 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
1105 1205 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
1106 1206 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
1107 1207 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
1212 1312 5.001232 TGGCAATCAAACTGTAGTAAGTCC 58.999 41.667 0.00 0.00 0.00 3.85
1353 1455 2.350522 AGTCGATGGTCAGAACATTGC 58.649 47.619 10.62 6.44 31.22 3.56
1370 1472 0.375106 GCGCATTGAGCACCTTAGTC 59.625 55.000 0.30 0.00 46.13 2.59
1468 1572 2.154462 GTAACTGCCATGTTGCTCTGT 58.846 47.619 0.00 0.00 31.44 3.41
1489 1593 9.574516 AATAACTAATTAGGACATGGAACCATC 57.425 33.333 16.73 0.00 33.90 3.51
1528 1632 2.037772 CCTCCAAGATAATACGCCTGCT 59.962 50.000 0.00 0.00 0.00 4.24
1727 1833 2.004733 CAGAGCACATCGATCAAAGCA 58.995 47.619 0.00 0.00 0.00 3.91
1857 1963 1.553690 GCCCAACCTCCTCTGCTGTA 61.554 60.000 0.00 0.00 0.00 2.74
1939 2105 2.963371 GAGGTCACTCGAGCGGTT 59.037 61.111 13.61 0.00 44.60 4.44
2025 2191 1.898154 GAGCACCTCGGCCTTCTTA 59.102 57.895 0.00 0.00 0.00 2.10
2051 2217 1.447838 GTGACCATGCCGACATCGT 60.448 57.895 0.00 0.00 37.74 3.73
2087 2253 0.984995 AGTTTGTCCTACCTGGGAGC 59.015 55.000 0.00 0.00 35.87 4.70
2291 2457 2.646175 GCTCTGCGGGTCAGTGGTA 61.646 63.158 0.00 0.00 43.32 3.25
2341 2507 3.687698 ACCAAGACGAATACCGAAAATGG 59.312 43.478 0.00 0.00 41.76 3.16
2412 2580 5.884792 AGCCTCTTATTGATCCTTGTTCTTG 59.115 40.000 0.00 0.00 0.00 3.02
2554 2724 8.240883 ACTTTAGCGAGTACAATTTTCTGTAG 57.759 34.615 0.00 0.00 32.49 2.74
2596 2767 7.041167 TCAGTTTATCGCTAAATATGCAGCATT 60.041 33.333 14.58 0.00 37.66 3.56
2872 3203 4.451900 ACAAGACCAAGTTGTGACTAAGG 58.548 43.478 1.45 0.00 36.76 2.69
3039 3371 3.880608 TGTCCCCATATCCATCACCATA 58.119 45.455 0.00 0.00 0.00 2.74
3339 3671 2.097036 TGCAGATGAAAGCCTCCAATG 58.903 47.619 0.00 0.00 0.00 2.82
3368 3700 2.836981 ACTCACCTGCTTCTTCTGCTAT 59.163 45.455 0.00 0.00 0.00 2.97
3522 3855 8.397575 TCCTCTCTAATACTGTATGTGATGTC 57.602 38.462 0.22 0.00 0.00 3.06
3639 3972 9.922477 TTAACTAAAAACCCAATTTCCCAAATT 57.078 25.926 0.00 0.00 41.57 1.82


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

AutoCloner maintained by Alex Coulton.