Multiple sequence alignment - TraesCS7A01G453500

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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 TraesCS7A01G453500 chr7A 100.000 1331 0 0 1505 2835 647934158 647932828 0.000000e+00 2459.0
1 TraesCS7A01G453500 chr7A 100.000 1291 0 0 1 1291 647935662 647934372 0.000000e+00 2385.0
2 TraesCS7A01G453500 chr7A 86.811 508 50 14 1505 2001 647315476 647314975 4.130000e-153 551.0
3 TraesCS7A01G453500 chr7A 90.501 379 34 2 913 1291 647862940 647862564 1.520000e-137 499.0
4 TraesCS7A01G453500 chr7A 90.400 375 35 1 918 1291 647307697 647307323 2.540000e-135 492.0
5 TraesCS7A01G453500 chr7A 90.463 367 34 1 926 1291 648042883 648042517 1.530000e-132 483.0
6 TraesCS7A01G453500 chr7B 88.381 1007 72 20 1505 2491 611741718 611740737 0.000000e+00 1170.0
7 TraesCS7A01G453500 chr7B 89.297 626 39 11 1505 2117 611962028 611961418 0.000000e+00 760.0
8 TraesCS7A01G453500 chr7B 94.398 482 23 2 813 1291 611962937 611962457 0.000000e+00 737.0
9 TraesCS7A01G453500 chr7B 88.552 594 41 11 1563 2150 612006469 612005897 0.000000e+00 695.0
10 TraesCS7A01G453500 chr7B 92.541 429 20 5 873 1291 612256597 612256171 3.120000e-169 604.0
11 TraesCS7A01G453500 chr7B 95.751 353 12 2 1536 1885 612255601 612255249 1.470000e-157 566.0
12 TraesCS7A01G453500 chr7B 91.768 413 20 8 889 1291 612007317 612006909 1.910000e-156 562.0
13 TraesCS7A01G453500 chr7B 88.692 451 38 9 306 745 612007817 612007369 3.210000e-149 538.0
14 TraesCS7A01G453500 chr7B 90.349 373 33 3 921 1291 611731057 611730686 1.180000e-133 486.0
15 TraesCS7A01G453500 chr7B 87.597 258 10 8 1 254 611963666 611963427 2.150000e-71 279.0
16 TraesCS7A01G453500 chr7B 91.860 172 10 2 2508 2675 611740615 611740444 1.310000e-58 237.0
17 TraesCS7A01G453500 chr7B 82.743 226 18 7 1931 2150 612255253 612255043 6.240000e-42 182.0
18 TraesCS7A01G453500 chr7B 83.908 174 9 2 270 424 611963442 611963269 6.330000e-32 148.0
19 TraesCS7A01G453500 chr7B 77.352 287 29 21 1 256 612257411 612257130 1.370000e-28 137.0
20 TraesCS7A01G453500 chr7B 77.273 264 30 15 1 244 611743396 611743143 8.240000e-26 128.0
21 TraesCS7A01G453500 chr7D 88.030 802 45 22 1575 2347 562425698 562426477 0.000000e+00 902.0
22 TraesCS7A01G453500 chr7D 96.250 480 17 1 813 1291 562424685 562425164 0.000000e+00 785.0
23 TraesCS7A01G453500 chr7D 89.194 620 53 8 1506 2118 562389807 562390419 0.000000e+00 761.0
24 TraesCS7A01G453500 chr7D 87.759 531 45 9 1524 2046 562403042 562403560 1.120000e-168 603.0
25 TraesCS7A01G453500 chr7D 89.241 474 39 9 1505 1973 562257118 562256652 1.460000e-162 582.0
26 TraesCS7A01G453500 chr7D 89.574 470 31 9 270 724 562424154 562424620 5.260000e-162 580.0
27 TraesCS7A01G453500 chr7D 86.213 544 53 15 1505 2038 562148599 562148068 1.140000e-158 569.0
28 TraesCS7A01G453500 chr7D 92.464 345 25 1 948 1291 562149240 562148896 2.540000e-135 492.0
29 TraesCS7A01G453500 chr7D 87.815 238 18 8 26 256 562423938 562424171 4.660000e-68 268.0
30 TraesCS7A01G453500 chr7D 81.742 356 17 17 2484 2835 562426511 562426822 1.300000e-63 254.0
31 TraesCS7A01G453500 chr7D 79.643 280 31 11 384 652 562388571 562388835 8.070000e-41 178.0
32 TraesCS7A01G453500 chr7D 85.161 155 16 5 2688 2835 562404622 562404776 4.890000e-33 152.0
33 TraesCS7A01G453500 chr7D 93.407 91 6 0 2745 2835 562390763 562390853 4.930000e-28 135.0
34 TraesCS7A01G453500 chr7D 92.958 71 4 1 744 814 161480234 161480303 5.000000e-18 102.0
35 TraesCS7A01G453500 chr7D 77.711 166 19 14 2490 2649 562404469 562404622 5.030000e-13 86.1
36 TraesCS7A01G453500 chr7D 97.826 46 1 0 26 71 562150103 562150058 2.340000e-11 80.5
37 TraesCS7A01G453500 chr7D 88.525 61 6 1 15 75 562258370 562258311 3.920000e-09 73.1
38 TraesCS7A01G453500 chr6B 85.714 112 12 2 2042 2149 663531313 663531202 6.420000e-22 115.0
39 TraesCS7A01G453500 chr6D 93.056 72 5 0 743 814 36692867 36692796 3.860000e-19 106.0
40 TraesCS7A01G453500 chr2B 92.647 68 5 0 747 814 246575872 246575805 6.460000e-17 99.0
41 TraesCS7A01G453500 chr5B 90.541 74 5 2 740 813 615610292 615610221 2.320000e-16 97.1
42 TraesCS7A01G453500 chr5B 90.278 72 7 0 743 814 487609753 487609824 8.360000e-16 95.3
43 TraesCS7A01G453500 chr5B 100.000 31 0 0 2641 2671 532585773 532585743 1.100000e-04 58.4
44 TraesCS7A01G453500 chr3A 90.411 73 7 0 743 815 18825596 18825524 2.320000e-16 97.1
45 TraesCS7A01G453500 chr2D 90.278 72 7 0 743 814 624557143 624557072 8.360000e-16 95.3
46 TraesCS7A01G453500 chr1B 88.158 76 8 1 740 814 584904454 584904379 3.890000e-14 89.8
47 TraesCS7A01G453500 chr2A 88.000 75 8 1 741 815 420224582 420224655 1.400000e-13 87.9


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 TraesCS7A01G453500 chr7A 647932828 647935662 2834 True 2422.000000 2459 100.000000 1 2835 2 chr7A.!!$R5 2834
1 TraesCS7A01G453500 chr7A 647314975 647315476 501 True 551.000000 551 86.811000 1505 2001 1 chr7A.!!$R2 496
2 TraesCS7A01G453500 chr7B 612005897 612007817 1920 True 598.333333 695 89.670667 306 2150 3 chr7B.!!$R4 1844
3 TraesCS7A01G453500 chr7B 611740444 611743396 2952 True 511.666667 1170 85.838000 1 2675 3 chr7B.!!$R2 2674
4 TraesCS7A01G453500 chr7B 611961418 611963666 2248 True 481.000000 760 88.800000 1 2117 4 chr7B.!!$R3 2116
5 TraesCS7A01G453500 chr7B 612255043 612257411 2368 True 372.250000 604 87.096750 1 2150 4 chr7B.!!$R5 2149
6 TraesCS7A01G453500 chr7D 562423938 562426822 2884 False 557.800000 902 88.682200 26 2835 5 chr7D.!!$F4 2809
7 TraesCS7A01G453500 chr7D 562148068 562150103 2035 True 380.500000 569 92.167667 26 2038 3 chr7D.!!$R1 2012
8 TraesCS7A01G453500 chr7D 562388571 562390853 2282 False 358.000000 761 87.414667 384 2835 3 chr7D.!!$F2 2451
9 TraesCS7A01G453500 chr7D 562256652 562258370 1718 True 327.550000 582 88.883000 15 1973 2 chr7D.!!$R2 1958
10 TraesCS7A01G453500 chr7D 562403042 562404776 1734 False 280.366667 603 83.543667 1524 2835 3 chr7D.!!$F3 1311

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
128 144 0.179073 CCCTTGGATCGATCGTTGCT 60.179 55.0 18.81 0.0 0.0 3.91 F
758 1135 0.399949 ATGCTATTCCCTCCGTCCCA 60.400 55.0 0.00 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 2168 0.254178 CCTCCAGGGTGATGGTCTTG 59.746 60.0 0.0 0.0 41.43 3.02 R
2679 5768 0.677731 CGGCTGGCTGATCTTTGGAA 60.678 55.0 0.0 0.0 0.00 3.53 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
75 84 0.597637 CAAGGTATGCGAGGCTACGG 60.598 60.000 8.11 0.00 0.00 4.02
84 94 1.672145 GCGAGGCTACGGTTTCTTCTT 60.672 52.381 8.11 0.00 0.00 2.52
120 136 3.700970 TGCGTGCCCTTGGATCGA 61.701 61.111 0.00 0.00 0.00 3.59
122 138 2.247437 GCGTGCCCTTGGATCGATC 61.247 63.158 17.36 17.36 0.00 3.69
123 139 1.951130 CGTGCCCTTGGATCGATCG 60.951 63.158 18.81 9.36 0.00 3.69
125 141 0.462047 GTGCCCTTGGATCGATCGTT 60.462 55.000 18.81 6.71 0.00 3.85
127 143 1.776034 GCCCTTGGATCGATCGTTGC 61.776 60.000 18.81 12.90 0.00 4.17
128 144 0.179073 CCCTTGGATCGATCGTTGCT 60.179 55.000 18.81 0.00 0.00 3.91
131 147 1.789464 CTTGGATCGATCGTTGCTAGC 59.211 52.381 18.81 8.10 0.00 3.42
292 328 3.596214 AGGCCTGATTGTAGTTAACACG 58.404 45.455 3.11 0.00 38.00 4.49
310 349 2.791560 CACGTCTCTCTTGATTATGCCG 59.208 50.000 0.00 0.00 0.00 5.69
322 361 3.002246 TGATTATGCCGTGATTTTCGAGC 59.998 43.478 0.00 0.00 0.00 5.03
495 588 4.755411 TGTTGGTTCGGTTCATCTATCTC 58.245 43.478 0.00 0.00 0.00 2.75
500 605 5.301045 TGGTTCGGTTCATCTATCTCGTTAT 59.699 40.000 0.00 0.00 0.00 1.89
501 606 6.487668 TGGTTCGGTTCATCTATCTCGTTATA 59.512 38.462 0.00 0.00 0.00 0.98
503 608 7.094890 GGTTCGGTTCATCTATCTCGTTATAGA 60.095 40.741 10.47 10.47 41.50 1.98
607 766 0.989890 GTAGTTGCTTGTAGCGTCCG 59.010 55.000 0.00 0.00 46.26 4.79
619 779 1.743995 GCGTCCGTAGTTGGGCATT 60.744 57.895 0.00 0.00 31.24 3.56
677 1044 7.254455 CGATATTACTGTTGGTTTCTAGGCTTG 60.254 40.741 0.00 0.00 0.00 4.01
700 1069 3.728845 TGACAAGCTTCTCAGTACAACC 58.271 45.455 0.00 0.00 0.00 3.77
717 1086 3.521126 ACAACCAGATTACATCAGCTCCT 59.479 43.478 0.00 0.00 0.00 3.69
719 1089 5.367937 ACAACCAGATTACATCAGCTCCTAT 59.632 40.000 0.00 0.00 0.00 2.57
723 1100 6.100279 ACCAGATTACATCAGCTCCTATTGAA 59.900 38.462 0.00 0.00 0.00 2.69
725 1102 7.041508 CCAGATTACATCAGCTCCTATTGAAAC 60.042 40.741 0.00 0.00 0.00 2.78
745 1122 2.828520 ACTGCGCTGGTAGATATGCTAT 59.171 45.455 18.98 0.00 0.00 2.97
747 1124 3.849911 TGCGCTGGTAGATATGCTATTC 58.150 45.455 9.73 0.00 0.00 1.75
748 1125 3.190874 GCGCTGGTAGATATGCTATTCC 58.809 50.000 0.00 0.00 0.00 3.01
749 1126 3.786635 CGCTGGTAGATATGCTATTCCC 58.213 50.000 0.00 0.00 0.00 3.97
751 1128 4.440802 CGCTGGTAGATATGCTATTCCCTC 60.441 50.000 0.00 0.00 0.00 4.30
752 1129 4.141824 GCTGGTAGATATGCTATTCCCTCC 60.142 50.000 0.00 0.00 0.00 4.30
753 1130 4.023980 TGGTAGATATGCTATTCCCTCCG 58.976 47.826 0.00 0.00 0.00 4.63
755 1132 4.098196 GGTAGATATGCTATTCCCTCCGTC 59.902 50.000 0.00 0.00 0.00 4.79
756 1133 3.100671 AGATATGCTATTCCCTCCGTCC 58.899 50.000 0.00 0.00 0.00 4.79
757 1134 1.640917 TATGCTATTCCCTCCGTCCC 58.359 55.000 0.00 0.00 0.00 4.46
758 1135 0.399949 ATGCTATTCCCTCCGTCCCA 60.400 55.000 0.00 0.00 0.00 4.37
760 1137 1.132977 TGCTATTCCCTCCGTCCCATA 60.133 52.381 0.00 0.00 0.00 2.74
761 1138 1.975680 GCTATTCCCTCCGTCCCATAA 59.024 52.381 0.00 0.00 0.00 1.90
763 1140 3.773119 GCTATTCCCTCCGTCCCATAATA 59.227 47.826 0.00 0.00 0.00 0.98
764 1141 4.409247 GCTATTCCCTCCGTCCCATAATAT 59.591 45.833 0.00 0.00 0.00 1.28
765 1142 5.601313 GCTATTCCCTCCGTCCCATAATATA 59.399 44.000 0.00 0.00 0.00 0.86
767 1144 5.750352 TTCCCTCCGTCCCATAATATAAC 57.250 43.478 0.00 0.00 0.00 1.89
768 1145 4.754311 TCCCTCCGTCCCATAATATAACA 58.246 43.478 0.00 0.00 0.00 2.41
770 1147 4.504858 CCTCCGTCCCATAATATAACAGC 58.495 47.826 0.00 0.00 0.00 4.40
773 1150 4.039488 TCCGTCCCATAATATAACAGCGTT 59.961 41.667 0.02 0.02 0.00 4.84
776 1153 6.238538 CCGTCCCATAATATAACAGCGTTTTT 60.239 38.462 0.00 0.00 0.00 1.94
777 1154 6.631238 CGTCCCATAATATAACAGCGTTTTTG 59.369 38.462 0.00 0.00 0.00 2.44
779 1156 8.349983 GTCCCATAATATAACAGCGTTTTTGAT 58.650 33.333 0.00 0.00 0.00 2.57
781 1158 9.607285 CCCATAATATAACAGCGTTTTTGATAC 57.393 33.333 0.00 0.00 0.00 2.24
962 1859 3.821600 CGTACTGCAGATATCCCTGTACT 59.178 47.826 23.35 0.00 36.57 2.73
971 1877 7.343574 TGCAGATATCCCTGTACTGTAACTTAA 59.656 37.037 0.00 0.00 36.57 1.85
1068 1979 1.546476 GTCGAGTCCTCTGACACCATT 59.454 52.381 11.65 0.00 44.33 3.16
1164 2075 4.899239 CTCGAGGATGGCCGCACC 62.899 72.222 3.91 0.73 39.96 5.01
1167 2078 4.115199 GAGGATGGCCGCACCCTT 62.115 66.667 0.00 0.00 39.96 3.95
1227 2138 3.314331 CTCAGGCTCCGTGGTGGT 61.314 66.667 0.00 0.00 39.52 4.16
1238 2149 1.134401 CCGTGGTGGTATGCAGATCTT 60.134 52.381 0.00 0.00 0.00 2.40
1239 2150 2.632377 CGTGGTGGTATGCAGATCTTT 58.368 47.619 0.00 0.00 0.00 2.52
1240 2151 2.352651 CGTGGTGGTATGCAGATCTTTG 59.647 50.000 0.00 0.00 0.00 2.77
1241 2152 3.347216 GTGGTGGTATGCAGATCTTTGT 58.653 45.455 0.00 0.00 0.00 2.83
1242 2153 3.375299 GTGGTGGTATGCAGATCTTTGTC 59.625 47.826 0.00 0.00 0.00 3.18
1243 2154 3.008923 TGGTGGTATGCAGATCTTTGTCA 59.991 43.478 0.00 0.00 0.00 3.58
1244 2155 4.009675 GGTGGTATGCAGATCTTTGTCAA 58.990 43.478 0.00 0.00 0.00 3.18
1245 2156 4.095483 GGTGGTATGCAGATCTTTGTCAAG 59.905 45.833 0.00 0.00 0.00 3.02
1246 2157 4.937620 GTGGTATGCAGATCTTTGTCAAGA 59.062 41.667 0.00 0.00 43.45 3.02
1247 2158 4.937620 TGGTATGCAGATCTTTGTCAAGAC 59.062 41.667 0.00 0.00 42.05 3.01
1248 2159 4.333926 GGTATGCAGATCTTTGTCAAGACC 59.666 45.833 0.00 0.00 42.05 3.85
1249 2160 2.783135 TGCAGATCTTTGTCAAGACCC 58.217 47.619 0.00 0.00 42.05 4.46
1250 2161 2.373169 TGCAGATCTTTGTCAAGACCCT 59.627 45.455 0.00 0.00 42.05 4.34
1251 2162 3.006247 GCAGATCTTTGTCAAGACCCTC 58.994 50.000 0.00 0.00 42.05 4.30
1252 2163 3.557898 GCAGATCTTTGTCAAGACCCTCA 60.558 47.826 0.00 0.00 42.05 3.86
1253 2164 3.999663 CAGATCTTTGTCAAGACCCTCAC 59.000 47.826 0.00 0.00 42.05 3.51
1254 2165 2.930826 TCTTTGTCAAGACCCTCACC 57.069 50.000 0.00 0.00 33.80 4.02
1255 2166 1.070134 TCTTTGTCAAGACCCTCACCG 59.930 52.381 0.00 0.00 33.80 4.94
1256 2167 0.107831 TTTGTCAAGACCCTCACCGG 59.892 55.000 0.00 0.00 0.00 5.28
1257 2168 2.047179 GTCAAGACCCTCACCGGC 60.047 66.667 0.00 0.00 0.00 6.13
1258 2169 2.525629 TCAAGACCCTCACCGGCA 60.526 61.111 0.00 0.00 0.00 5.69
1259 2170 2.144078 TCAAGACCCTCACCGGCAA 61.144 57.895 0.00 0.00 0.00 4.52
1260 2171 1.672356 CAAGACCCTCACCGGCAAG 60.672 63.158 0.00 0.00 0.00 4.01
1261 2172 1.841556 AAGACCCTCACCGGCAAGA 60.842 57.895 0.00 0.00 0.00 3.02
1262 2173 2.047179 GACCCTCACCGGCAAGAC 60.047 66.667 0.00 0.00 0.00 3.01
1263 2174 3.607370 GACCCTCACCGGCAAGACC 62.607 68.421 0.00 0.00 0.00 3.85
1264 2175 3.636231 CCCTCACCGGCAAGACCA 61.636 66.667 0.00 0.00 39.03 4.02
1265 2176 2.671070 CCTCACCGGCAAGACCAT 59.329 61.111 0.00 0.00 39.03 3.55
1266 2177 1.450312 CCTCACCGGCAAGACCATC 60.450 63.158 0.00 0.00 39.03 3.51
1267 2178 1.296392 CTCACCGGCAAGACCATCA 59.704 57.895 0.00 0.00 39.03 3.07
1268 2179 1.003839 TCACCGGCAAGACCATCAC 60.004 57.895 0.00 0.00 39.03 3.06
1269 2180 2.040544 CACCGGCAAGACCATCACC 61.041 63.158 0.00 0.00 39.03 4.02
1270 2181 2.438434 CCGGCAAGACCATCACCC 60.438 66.667 0.00 0.00 39.03 4.61
1271 2182 2.671070 CGGCAAGACCATCACCCT 59.329 61.111 0.00 0.00 39.03 4.34
1272 2183 1.746615 CGGCAAGACCATCACCCTG 60.747 63.158 0.00 0.00 39.03 4.45
1273 2184 1.379044 GGCAAGACCATCACCCTGG 60.379 63.158 0.00 0.00 42.35 4.45
1274 2185 1.685224 GCAAGACCATCACCCTGGA 59.315 57.895 0.00 0.00 39.73 3.86
1275 2186 0.393537 GCAAGACCATCACCCTGGAG 60.394 60.000 0.00 0.00 39.73 3.86
1276 2187 0.254178 CAAGACCATCACCCTGGAGG 59.746 60.000 0.00 0.00 39.73 4.30
1285 2196 4.569214 CCCTGGAGGTTGAGTCCT 57.431 61.111 0.00 0.00 40.97 3.85
1522 2433 3.621892 CTTTGCCGGCAAGCAGCTC 62.622 63.158 37.88 2.10 45.13 4.09
1895 4269 1.808945 GTCTCGTCTTCGGTGTCCTTA 59.191 52.381 0.00 0.00 37.69 2.69
1909 4288 4.342359 GTGTCCTTAAGGAGTCTGGTCTA 58.658 47.826 24.91 0.00 46.49 2.59
1952 4350 8.340618 ACTGTCTTTGTTTCTATACCGTACTA 57.659 34.615 0.00 0.00 0.00 1.82
2018 4420 4.219070 TGCAGCAGCTTTGATGAACTTAAT 59.781 37.500 1.76 0.00 42.74 1.40
2020 4422 6.095860 TGCAGCAGCTTTGATGAACTTAATAT 59.904 34.615 1.76 0.00 42.74 1.28
2039 4441 9.342308 CTTAATATTAAGTGAGCCCTGAATTCA 57.658 33.333 22.14 8.12 36.31 2.57
2049 4451 6.716628 GTGAGCCCTGAATTCAATCCATAATA 59.283 38.462 9.88 0.00 0.00 0.98
2096 4584 5.163561 CCTGTTGTGTTATGTGGTTTCTTGT 60.164 40.000 0.00 0.00 0.00 3.16
2183 4685 1.872952 CCTCTGAAATGCGTGTGTTCA 59.127 47.619 0.00 0.00 0.00 3.18
2187 4689 3.127721 TCTGAAATGCGTGTGTTCAAACA 59.872 39.130 0.00 0.00 36.38 2.83
2235 4748 2.562296 TCTGGCCTGTAGAATCCCTTT 58.438 47.619 3.32 0.00 0.00 3.11
2236 4749 2.239654 TCTGGCCTGTAGAATCCCTTTG 59.760 50.000 3.32 0.00 0.00 2.77
2284 4810 4.012895 CCGTGTGCTGGTCGTTGC 62.013 66.667 0.00 0.00 0.00 4.17
2306 4832 7.192852 TGCCCCATTTTATTCAAACATATGT 57.807 32.000 1.41 1.41 0.00 2.29
2408 5359 0.951040 GACCTCCAGCCAAAGACGTG 60.951 60.000 0.00 0.00 0.00 4.49
2410 5361 1.672356 CTCCAGCCAAAGACGTGGG 60.672 63.158 0.00 0.00 39.26 4.61
2411 5362 2.672996 CCAGCCAAAGACGTGGGG 60.673 66.667 0.00 0.00 39.26 4.96
2412 5363 3.365265 CAGCCAAAGACGTGGGGC 61.365 66.667 0.00 0.00 46.77 5.80
2414 5365 3.670377 GCCAAAGACGTGGGGCAC 61.670 66.667 10.47 0.00 45.70 5.01
2551 5622 1.340017 GGGTCTAGCTTGCCACAATGA 60.340 52.381 0.00 0.00 0.00 2.57
2556 5627 4.635765 GTCTAGCTTGCCACAATGACAATA 59.364 41.667 0.00 0.00 0.00 1.90
2675 5764 1.524621 CAAAGATCAGCCGGCCGAT 60.525 57.895 30.73 25.07 0.00 4.18
2676 5765 1.227674 AAAGATCAGCCGGCCGATC 60.228 57.895 35.52 35.52 38.66 3.69
2677 5766 2.522923 AGATCAGCCGGCCGATCT 60.523 61.111 38.21 38.21 42.77 2.75
2678 5767 2.136878 AGATCAGCCGGCCGATCTT 61.137 57.895 38.21 26.12 44.70 2.40
2679 5768 1.227674 GATCAGCCGGCCGATCTTT 60.228 57.895 35.25 13.80 36.04 2.52
2680 5769 0.815615 GATCAGCCGGCCGATCTTTT 60.816 55.000 35.25 13.42 36.04 2.27
2681 5770 0.815615 ATCAGCCGGCCGATCTTTTC 60.816 55.000 30.73 6.15 0.00 2.29
2682 5771 2.124695 AGCCGGCCGATCTTTTCC 60.125 61.111 30.73 3.84 0.00 3.13
2683 5772 2.437716 GCCGGCCGATCTTTTCCA 60.438 61.111 30.73 0.00 0.00 3.53
2684 5773 2.043980 GCCGGCCGATCTTTTCCAA 61.044 57.895 30.73 0.00 0.00 3.53
2685 5774 1.591504 GCCGGCCGATCTTTTCCAAA 61.592 55.000 30.73 0.00 0.00 3.28
2686 5775 0.451783 CCGGCCGATCTTTTCCAAAG 59.548 55.000 30.73 0.00 0.00 2.77
2700 5789 1.372087 CCAAAGATCAGCCAGCCGAC 61.372 60.000 0.00 0.00 0.00 4.79
2702 5791 1.888436 AAAGATCAGCCAGCCGACGA 61.888 55.000 0.00 0.00 0.00 4.20
2709 5798 2.571757 CCAGCCGACGAGTAGCAA 59.428 61.111 0.00 0.00 0.00 3.91
2711 5800 2.161486 CAGCCGACGAGTAGCAAGC 61.161 63.158 0.00 0.00 0.00 4.01
2716 5805 0.454600 CGACGAGTAGCAAGCCCTAA 59.545 55.000 0.00 0.00 0.00 2.69
2717 5806 1.534175 CGACGAGTAGCAAGCCCTAAG 60.534 57.143 0.00 0.00 0.00 2.18
2727 5818 2.995939 GCAAGCCCTAAGAAAACAATGC 59.004 45.455 0.00 0.00 0.00 3.56
2735 5826 5.404946 CCTAAGAAAACAATGCTCACATGG 58.595 41.667 0.00 0.00 36.36 3.66
2744 5835 4.571580 ACAATGCTCACATGGTTTTGTTTG 59.428 37.500 0.00 0.00 37.10 2.93
2745 5836 3.883830 TGCTCACATGGTTTTGTTTGT 57.116 38.095 0.00 0.00 0.00 2.83
2746 5837 3.779759 TGCTCACATGGTTTTGTTTGTC 58.220 40.909 0.00 0.00 0.00 3.18
2747 5838 3.123050 GCTCACATGGTTTTGTTTGTCC 58.877 45.455 0.00 0.00 0.00 4.02
2766 5864 9.495572 GTTTGTCCCAATTTTCAATTATTGGTA 57.504 29.630 14.00 0.00 46.05 3.25
2788 5886 9.806448 TGGTATGTAGCATTTTGGATAATGTAT 57.194 29.630 0.00 0.00 37.72 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.364780 GGATCGGAGGTTTCCCGGT 61.365 63.158 0.00 0.00 46.47 5.28
75 84 2.659279 CACGAGAGAGCGAAGAAGAAAC 59.341 50.000 0.00 0.00 34.83 2.78
113 129 0.744281 TGCTAGCAACGATCGATCCA 59.256 50.000 24.34 6.25 0.00 3.41
123 139 2.820037 GAGGGCGGTGCTAGCAAC 60.820 66.667 23.31 23.31 36.08 4.17
127 143 2.336809 GATCGAGGGCGGTGCTAG 59.663 66.667 0.00 0.00 38.28 3.42
128 144 3.224324 GGATCGAGGGCGGTGCTA 61.224 66.667 0.00 0.00 35.94 3.49
131 147 4.899239 GCAGGATCGAGGGCGGTG 62.899 72.222 0.00 0.00 38.28 4.94
267 303 6.148150 CGTGTTAACTACAATCAGGCCTAAAA 59.852 38.462 3.98 0.00 38.80 1.52
269 305 5.172934 CGTGTTAACTACAATCAGGCCTAA 58.827 41.667 3.98 0.00 38.80 2.69
270 306 4.221262 ACGTGTTAACTACAATCAGGCCTA 59.779 41.667 3.98 0.00 38.80 3.93
272 308 3.332034 ACGTGTTAACTACAATCAGGCC 58.668 45.455 7.22 0.00 38.80 5.19
273 309 4.243270 AGACGTGTTAACTACAATCAGGC 58.757 43.478 7.22 0.00 38.80 4.85
274 310 5.710984 AGAGACGTGTTAACTACAATCAGG 58.289 41.667 7.22 0.00 38.80 3.86
275 311 6.613233 AGAGAGACGTGTTAACTACAATCAG 58.387 40.000 7.22 0.00 38.80 2.90
277 313 7.082602 TCAAGAGAGACGTGTTAACTACAATC 58.917 38.462 7.22 4.74 38.80 2.67
278 314 6.978338 TCAAGAGAGACGTGTTAACTACAAT 58.022 36.000 7.22 0.00 38.80 2.71
279 315 6.381481 TCAAGAGAGACGTGTTAACTACAA 57.619 37.500 7.22 0.00 38.80 2.41
280 316 6.570672 ATCAAGAGAGACGTGTTAACTACA 57.429 37.500 7.22 0.00 0.00 2.74
282 318 7.701078 GCATAATCAAGAGAGACGTGTTAACTA 59.299 37.037 7.22 0.00 0.00 2.24
283 319 6.531948 GCATAATCAAGAGAGACGTGTTAACT 59.468 38.462 7.22 0.00 0.00 2.24
284 320 6.237861 GGCATAATCAAGAGAGACGTGTTAAC 60.238 42.308 0.00 0.00 0.00 2.01
285 321 5.810587 GGCATAATCAAGAGAGACGTGTTAA 59.189 40.000 0.00 0.00 0.00 2.01
287 323 4.184629 GGCATAATCAAGAGAGACGTGTT 58.815 43.478 0.00 0.00 0.00 3.32
288 324 3.735208 CGGCATAATCAAGAGAGACGTGT 60.735 47.826 0.00 0.00 0.00 4.49
289 325 2.791560 CGGCATAATCAAGAGAGACGTG 59.208 50.000 0.00 0.00 0.00 4.49
290 326 2.427453 ACGGCATAATCAAGAGAGACGT 59.573 45.455 0.00 0.00 0.00 4.34
292 328 4.046938 TCACGGCATAATCAAGAGAGAC 57.953 45.455 0.00 0.00 0.00 3.36
322 361 3.055602 TCCCATCATAATCGGCAGATCTG 60.056 47.826 18.84 18.84 35.74 2.90
453 546 1.572941 CAATCGCATCGCATCCCAG 59.427 57.895 0.00 0.00 0.00 4.45
503 608 9.780186 ACAAAATCAGAAACTAGCTAACTAAGT 57.220 29.630 0.00 0.00 0.00 2.24
559 717 9.790344 AGCTGAACTATTAATCTAGCAAATCAT 57.210 29.630 0.00 0.00 32.42 2.45
607 766 5.183904 AGAGTTGAATTCAATGCCCAACTAC 59.816 40.000 23.05 7.70 44.93 2.73
677 1044 4.024809 GGTTGTACTGAGAAGCTTGTCAAC 60.025 45.833 24.69 20.69 29.49 3.18
700 1069 7.714377 AGTTTCAATAGGAGCTGATGTAATCTG 59.286 37.037 0.00 0.00 45.81 2.90
717 1086 3.603158 TCTACCAGCGCAGTTTCAATA 57.397 42.857 11.47 0.00 0.00 1.90
719 1089 2.472695 ATCTACCAGCGCAGTTTCAA 57.527 45.000 11.47 0.00 0.00 2.69
723 1100 1.414181 AGCATATCTACCAGCGCAGTT 59.586 47.619 11.47 0.00 0.00 3.16
725 1102 3.516981 ATAGCATATCTACCAGCGCAG 57.483 47.619 11.47 0.00 0.00 5.18
745 1122 5.156649 TGTTATATTATGGGACGGAGGGAA 58.843 41.667 0.00 0.00 0.00 3.97
747 1124 4.623171 GCTGTTATATTATGGGACGGAGGG 60.623 50.000 0.00 0.00 0.00 4.30
748 1125 4.504858 GCTGTTATATTATGGGACGGAGG 58.495 47.826 0.00 0.00 0.00 4.30
749 1126 4.174009 CGCTGTTATATTATGGGACGGAG 58.826 47.826 0.00 0.00 0.00 4.63
751 1128 3.921677 ACGCTGTTATATTATGGGACGG 58.078 45.455 0.00 0.00 0.00 4.79
752 1129 5.917541 AAACGCTGTTATATTATGGGACG 57.082 39.130 0.00 0.00 0.00 4.79
753 1130 7.699566 TCAAAAACGCTGTTATATTATGGGAC 58.300 34.615 0.00 0.00 0.00 4.46
755 1132 9.607285 GTATCAAAAACGCTGTTATATTATGGG 57.393 33.333 0.00 0.00 0.00 4.00
765 1142 9.084164 CACTATACTAGTATCAAAAACGCTGTT 57.916 33.333 18.68 0.00 37.23 3.16
767 1144 8.630278 ACACTATACTAGTATCAAAAACGCTG 57.370 34.615 18.68 5.28 37.23 5.18
768 1145 8.464404 TGACACTATACTAGTATCAAAAACGCT 58.536 33.333 18.68 0.00 39.11 5.07
800 1177 9.236006 GCCAATGGATTGACATAATATAAGAGT 57.764 33.333 2.05 0.00 40.14 3.24
801 1178 9.458727 AGCCAATGGATTGACATAATATAAGAG 57.541 33.333 2.05 0.00 40.14 2.85
802 1179 9.812347 AAGCCAATGGATTGACATAATATAAGA 57.188 29.630 0.33 0.00 40.14 2.10
962 1859 5.639506 GCAGACAGAAGCAGATTAAGTTACA 59.360 40.000 0.00 0.00 0.00 2.41
971 1877 3.137446 ACAAAGCAGACAGAAGCAGAT 57.863 42.857 0.00 0.00 0.00 2.90
1068 1979 3.507233 GGATCTTTGCCTTGACATTGTCA 59.493 43.478 15.41 15.41 41.09 3.58
1167 2078 1.262417 TCTGGATGTTGTAGTCCGCA 58.738 50.000 0.00 0.00 37.32 5.69
1170 2081 3.515901 ACTCCTTCTGGATGTTGTAGTCC 59.484 47.826 0.00 0.00 42.29 3.85
1197 2108 2.061220 CCTGAGCACCAAGTGGAGA 58.939 57.895 3.83 0.00 38.94 3.71
1206 2117 4.767255 CCACGGAGCCTGAGCACC 62.767 72.222 0.00 0.00 45.50 5.01
1227 2138 4.225942 AGGGTCTTGACAAAGATCTGCATA 59.774 41.667 0.00 0.00 44.18 3.14
1238 2149 1.752198 CCGGTGAGGGTCTTGACAA 59.248 57.895 0.00 0.00 35.97 3.18
1239 2150 2.879233 GCCGGTGAGGGTCTTGACA 61.879 63.158 1.90 0.00 41.48 3.58
1240 2151 2.047179 GCCGGTGAGGGTCTTGAC 60.047 66.667 1.90 0.00 41.48 3.18
1241 2152 2.111999 CTTGCCGGTGAGGGTCTTGA 62.112 60.000 1.90 0.00 41.48 3.02
1242 2153 1.672356 CTTGCCGGTGAGGGTCTTG 60.672 63.158 1.90 0.00 41.48 3.02
1243 2154 1.841556 TCTTGCCGGTGAGGGTCTT 60.842 57.895 1.90 0.00 41.48 3.01
1244 2155 2.203788 TCTTGCCGGTGAGGGTCT 60.204 61.111 1.90 0.00 41.48 3.85
1245 2156 2.047179 GTCTTGCCGGTGAGGGTC 60.047 66.667 1.90 0.00 41.48 4.46
1246 2157 3.637273 GGTCTTGCCGGTGAGGGT 61.637 66.667 1.90 0.00 41.48 4.34
1247 2158 2.876368 GATGGTCTTGCCGGTGAGGG 62.876 65.000 1.90 0.00 41.48 4.30
1248 2159 1.450312 GATGGTCTTGCCGGTGAGG 60.450 63.158 1.90 0.00 44.97 3.86
1249 2160 1.021390 GTGATGGTCTTGCCGGTGAG 61.021 60.000 1.90 0.94 41.21 3.51
1250 2161 1.003839 GTGATGGTCTTGCCGGTGA 60.004 57.895 1.90 0.00 41.21 4.02
1251 2162 2.040544 GGTGATGGTCTTGCCGGTG 61.041 63.158 1.90 0.00 41.21 4.94
1252 2163 2.351276 GGTGATGGTCTTGCCGGT 59.649 61.111 1.90 0.00 41.21 5.28
1253 2164 2.438434 GGGTGATGGTCTTGCCGG 60.438 66.667 0.00 0.00 41.21 6.13
1254 2165 1.746615 CAGGGTGATGGTCTTGCCG 60.747 63.158 0.00 0.00 41.21 5.69
1255 2166 1.379044 CCAGGGTGATGGTCTTGCC 60.379 63.158 0.00 0.00 35.47 4.52
1256 2167 0.393537 CTCCAGGGTGATGGTCTTGC 60.394 60.000 0.00 0.00 41.43 4.01
1257 2168 0.254178 CCTCCAGGGTGATGGTCTTG 59.746 60.000 0.00 0.00 41.43 3.02
1258 2169 2.702093 CCTCCAGGGTGATGGTCTT 58.298 57.895 0.00 0.00 41.43 3.01
1259 2170 4.488303 CCTCCAGGGTGATGGTCT 57.512 61.111 0.00 0.00 41.43 3.85
1268 2179 4.569214 AGGACTCAACCTCCAGGG 57.431 61.111 0.00 0.00 40.27 4.45
1510 2421 3.729965 ATCCTCGAGCTGCTTGCCG 62.730 63.158 12.16 7.44 44.23 5.69
1895 4269 4.020543 GACAGACATAGACCAGACTCCTT 58.979 47.826 0.00 0.00 0.00 3.36
1909 4288 1.070758 AGTTCAGGCAACGACAGACAT 59.929 47.619 0.00 0.00 46.39 3.06
1952 4350 6.763135 AGATACAAACGATAACACTGCATCAT 59.237 34.615 0.00 0.00 0.00 2.45
2018 4420 6.772716 GGATTGAATTCAGGGCTCACTTAATA 59.227 38.462 8.41 0.00 0.00 0.98
2020 4422 4.949856 GGATTGAATTCAGGGCTCACTTAA 59.050 41.667 8.41 0.00 0.00 1.85
2039 4441 8.199449 CAGGCAAGACAAACAATATTATGGATT 58.801 33.333 0.00 0.00 0.00 3.01
2049 4451 4.942761 AACATCAGGCAAGACAAACAAT 57.057 36.364 0.00 0.00 0.00 2.71
2096 4584 7.230712 AGCAGATCAAATGCATCAGAAATATCA 59.769 33.333 0.00 0.00 46.31 2.15
2208 4714 2.859165 TCTACAGGCCAGAAAGTTGG 57.141 50.000 5.01 0.00 41.35 3.77
2236 4749 8.552034 CCACGTATCTTAGAAAATTTGAGGATC 58.448 37.037 0.00 0.00 0.00 3.36
2284 4810 8.040132 ACACACATATGTTTGAATAAAATGGGG 58.960 33.333 25.02 5.49 36.72 4.96
2306 4832 2.291465 GCACAAGATCAGCAAGAACACA 59.709 45.455 0.00 0.00 0.00 3.72
2376 5318 3.736482 GAGGTCGCCGCGTCTACAG 62.736 68.421 13.39 0.00 0.00 2.74
2412 5363 4.041917 AACATTGCAGCGCCGGTG 62.042 61.111 12.67 12.67 0.00 4.94
2413 5364 4.041917 CAACATTGCAGCGCCGGT 62.042 61.111 2.29 0.00 0.00 5.28
2414 5365 4.781959 CCAACATTGCAGCGCCGG 62.782 66.667 2.29 0.00 0.00 6.13
2418 5369 3.682885 TGCCCCAACATTGCAGCG 61.683 61.111 0.00 0.00 0.00 5.18
2440 5403 4.781959 CGCCCCAACATTGCAGCG 62.782 66.667 10.69 10.69 40.13 5.18
2551 5622 4.258702 ACTTCAGCTCGTGTCTTATTGT 57.741 40.909 0.00 0.00 0.00 2.71
2556 5627 1.221414 GCAACTTCAGCTCGTGTCTT 58.779 50.000 0.00 0.00 0.00 3.01
2648 5737 3.445096 CCGGCTGATCTTTGGAAAAGATT 59.555 43.478 14.62 1.85 37.14 2.40
2675 5764 2.821969 GCTGGCTGATCTTTGGAAAAGA 59.178 45.455 4.99 4.99 0.00 2.52
2676 5765 2.094338 GGCTGGCTGATCTTTGGAAAAG 60.094 50.000 0.00 0.00 0.00 2.27
2677 5766 1.895131 GGCTGGCTGATCTTTGGAAAA 59.105 47.619 0.00 0.00 0.00 2.29
2678 5767 1.549203 GGCTGGCTGATCTTTGGAAA 58.451 50.000 0.00 0.00 0.00 3.13
2679 5768 0.677731 CGGCTGGCTGATCTTTGGAA 60.678 55.000 0.00 0.00 0.00 3.53
2680 5769 1.078214 CGGCTGGCTGATCTTTGGA 60.078 57.895 0.00 0.00 0.00 3.53
2681 5770 1.078214 TCGGCTGGCTGATCTTTGG 60.078 57.895 0.00 0.00 0.00 3.28
2682 5771 1.699656 CGTCGGCTGGCTGATCTTTG 61.700 60.000 7.39 0.00 33.49 2.77
2683 5772 1.448540 CGTCGGCTGGCTGATCTTT 60.449 57.895 7.39 0.00 33.49 2.52
2684 5773 2.185350 CGTCGGCTGGCTGATCTT 59.815 61.111 7.39 0.00 33.49 2.40
2685 5774 2.755876 TCGTCGGCTGGCTGATCT 60.756 61.111 7.39 0.00 33.49 2.75
2686 5775 1.725557 TACTCGTCGGCTGGCTGATC 61.726 60.000 7.39 1.56 33.49 2.92
2694 5783 2.182030 GCTTGCTACTCGTCGGCT 59.818 61.111 0.00 0.00 0.00 5.52
2700 5789 2.961526 TTCTTAGGGCTTGCTACTCG 57.038 50.000 0.00 0.00 0.00 4.18
2702 5791 4.367039 TGTTTTCTTAGGGCTTGCTACT 57.633 40.909 0.00 0.00 0.00 2.57
2709 5798 3.507622 GTGAGCATTGTTTTCTTAGGGCT 59.492 43.478 0.00 0.00 0.00 5.19
2711 5800 5.404946 CATGTGAGCATTGTTTTCTTAGGG 58.595 41.667 0.00 0.00 31.99 3.53
2716 5805 4.942761 AACCATGTGAGCATTGTTTTCT 57.057 36.364 0.00 0.00 37.60 2.52
2727 5818 3.131933 TGGGACAAACAAAACCATGTGAG 59.868 43.478 0.00 0.00 31.92 3.51


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

AutoCloner maintained by Alex Coulton.