Multiple sequence alignment - TraesCS2B01G356900

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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 TraesCS2B01G356900 chr2B 100.000 3426 0 0 1 3426 509998554 509995129 0.000000e+00 6327
1 TraesCS2B01G356900 chr2B 95.347 1053 26 5 2367 3413 509574070 509573035 0.000000e+00 1652
2 TraesCS2B01G356900 chr2B 92.344 1071 52 9 1140 2205 509575114 509574069 0.000000e+00 1496
3 TraesCS2B01G356900 chr2B 89.640 1168 69 11 1 1119 716768426 716769590 0.000000e+00 1439
4 TraesCS2B01G356900 chr2B 89.280 1166 73 16 1 1119 77914117 77912957 0.000000e+00 1413
5 TraesCS2B01G356900 chr2B 87.993 1166 75 18 1 1119 790428056 790426909 0.000000e+00 1317
6 TraesCS2B01G356900 chr2B 84.291 1114 112 28 1121 2205 510350488 510349409 0.000000e+00 1029
7 TraesCS2B01G356900 chr2B 84.316 1052 88 33 1159 2169 510062262 510061247 0.000000e+00 957
8 TraesCS2B01G356900 chr2B 86.816 713 71 14 2367 3064 510061224 510060520 0.000000e+00 774
9 TraesCS2B01G356900 chr2B 85.714 721 60 18 2367 3064 509706824 509706124 0.000000e+00 721
10 TraesCS2B01G356900 chr2B 87.662 462 24 12 1121 1574 509713307 509712871 1.100000e-139 507
11 TraesCS2B01G356900 chr2B 87.062 371 36 5 2367 2728 510349410 510349043 3.180000e-110 409
12 TraesCS2B01G356900 chr2B 78.720 672 60 46 1567 2205 509707444 509706823 4.180000e-99 372
13 TraesCS2B01G356900 chr2B 86.478 318 33 8 2732 3043 510348954 510348641 1.180000e-89 340
14 TraesCS2B01G356900 chr2B 95.783 166 7 0 2204 2369 775735582 775735417 5.640000e-68 268
15 TraesCS2B01G356900 chr2B 94.253 174 8 2 2203 2374 751258460 751258287 7.290000e-67 265
16 TraesCS2B01G356900 chr2B 88.152 211 18 4 3223 3426 510348635 510348425 9.500000e-61 244
17 TraesCS2B01G356900 chr2B 91.129 124 5 4 3220 3337 510060525 510060402 2.740000e-36 163
18 TraesCS2B01G356900 chr2B 90.323 124 6 4 3220 3337 509706129 509706006 1.270000e-34 158
19 TraesCS2B01G356900 chr2D 97.419 1085 28 0 1121 2205 431005876 431004792 0.000000e+00 1849
20 TraesCS2B01G356900 chr2D 97.238 1086 27 2 1121 2205 431385843 431384760 0.000000e+00 1836
21 TraesCS2B01G356900 chr2D 97.015 1005 24 3 2422 3426 431004771 431003773 0.000000e+00 1685
22 TraesCS2B01G356900 chr2D 89.658 1170 70 14 1 1120 624844388 624845556 0.000000e+00 1443
23 TraesCS2B01G356900 chr2D 89.546 1167 72 14 1 1118 600414423 600413258 0.000000e+00 1434
24 TraesCS2B01G356900 chr2D 85.534 1030 84 30 1121 2114 431429163 431428163 0.000000e+00 1016
25 TraesCS2B01G356900 chr2D 95.697 581 19 3 2367 2946 431384761 431384186 0.000000e+00 929
26 TraesCS2B01G356900 chr2D 98.163 490 9 0 2937 3426 431382202 431381713 0.000000e+00 856
27 TraesCS2B01G356900 chr2D 87.083 720 63 15 2367 3064 431425872 431425161 0.000000e+00 787
28 TraesCS2B01G356900 chr2D 94.767 172 7 2 2197 2368 32474299 32474468 2.030000e-67 267
29 TraesCS2B01G356900 chr2D 89.344 122 7 4 3220 3335 431425166 431425045 7.660000e-32 148
30 TraesCS2B01G356900 chr3D 90.223 1166 66 11 1 1119 569475957 569474793 0.000000e+00 1478
31 TraesCS2B01G356900 chr3D 89.922 1032 57 14 6 993 26196557 26197585 0.000000e+00 1286
32 TraesCS2B01G356900 chr3D 90.034 291 10 1 1 272 290023020 290023310 3.250000e-95 359
33 TraesCS2B01G356900 chr4D 90.198 1163 68 15 1 1119 340295448 340294288 0.000000e+00 1474
34 TraesCS2B01G356900 chr4D 87.892 1181 85 19 1 1123 485688738 485687558 0.000000e+00 1336
35 TraesCS2B01G356900 chr4D 87.404 1175 88 22 1 1119 301727804 301728974 0.000000e+00 1295
36 TraesCS2B01G356900 chr4A 90.146 1167 65 15 1 1119 674599196 674598032 0.000000e+00 1472
37 TraesCS2B01G356900 chr1B 90.311 1156 58 13 1 1109 622694284 622695432 0.000000e+00 1465
38 TraesCS2B01G356900 chr6D 89.966 1166 69 11 1 1119 121190011 121191175 0.000000e+00 1461
39 TraesCS2B01G356900 chr6D 94.798 173 8 1 2204 2376 392278577 392278748 5.640000e-68 268
40 TraesCS2B01G356900 chr6D 93.333 165 11 0 3063 3227 48458134 48457970 9.500000e-61 244
41 TraesCS2B01G356900 chr1D 89.726 1168 69 15 1 1119 241262885 241264050 0.000000e+00 1445
42 TraesCS2B01G356900 chr1D 89.708 1166 71 11 1 1119 454206896 454205733 0.000000e+00 1443
43 TraesCS2B01G356900 chr5B 89.155 1171 76 13 1 1123 145025369 145024202 0.000000e+00 1411
44 TraesCS2B01G356900 chr5B 88.955 1168 79 24 1 1120 33631648 33630483 0.000000e+00 1397
45 TraesCS2B01G356900 chr5B 90.925 573 29 5 1 551 182462410 182461839 0.000000e+00 749
46 TraesCS2B01G356900 chr5B 85.975 713 70 16 2371 3064 100837780 100838481 0.000000e+00 736
47 TraesCS2B01G356900 chr5B 90.278 216 12 5 3220 3426 100838476 100838691 1.210000e-69 274
48 TraesCS2B01G356900 chr5B 94.675 169 9 0 2203 2371 528369362 528369530 2.620000e-66 263
49 TraesCS2B01G356900 chr3B 88.697 1159 83 8 4 1116 539602158 539601002 0.000000e+00 1371
50 TraesCS2B01G356900 chr4B 88.879 1160 57 12 1 1112 3939468 3938333 0.000000e+00 1362
51 TraesCS2B01G356900 chr4B 90.960 177 15 1 3048 3224 532434987 532435162 1.590000e-58 237
52 TraesCS2B01G356900 chr7B 88.412 1165 72 13 1 1119 93272205 93271058 0.000000e+00 1345
53 TraesCS2B01G356900 chr7B 90.444 1036 54 8 1 992 137372876 137371842 0.000000e+00 1323
54 TraesCS2B01G356900 chr7B 95.349 172 7 1 2204 2374 678205440 678205611 4.360000e-69 272
55 TraesCS2B01G356900 chr7B 92.432 185 12 2 2189 2372 744022555 744022372 2.620000e-66 263
56 TraesCS2B01G356900 chr2A 86.345 725 64 19 2367 3064 554954350 554955066 0.000000e+00 758
57 TraesCS2B01G356900 chr2A 90.863 197 16 1 1121 1317 554953016 554953210 2.620000e-66 263
58 TraesCS2B01G356900 chr2A 89.252 214 16 4 3220 3426 554955061 554955274 9.430000e-66 261
59 TraesCS2B01G356900 chr2A 91.477 176 13 1 3063 3238 184561315 184561142 1.230000e-59 241
60 TraesCS2B01G356900 chr6B 85.503 338 24 3 807 1119 563332585 563332248 2.550000e-86 329
61 TraesCS2B01G356900 chr6A 95.266 169 7 1 2200 2368 604587853 604588020 2.030000e-67 267
62 TraesCS2B01G356900 chr5D 95.238 168 8 0 2204 2371 311349852 311349685 2.030000e-67 267
63 TraesCS2B01G356900 chr5D 94.479 163 9 0 3062 3224 150835567 150835729 5.680000e-63 252
64 TraesCS2B01G356900 chr7A 93.103 174 11 1 3063 3236 494786990 494786818 1.580000e-63 254
65 TraesCS2B01G356900 chr5A 93.491 169 11 0 3063 3231 320214244 320214412 5.680000e-63 252


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 TraesCS2B01G356900 chr2B 509995129 509998554 3425 True 6327.000000 6327 100.000000 1 3426 1 chr2B.!!$R3 3425
1 TraesCS2B01G356900 chr2B 509573035 509575114 2079 True 1574.000000 1652 93.845500 1140 3413 2 chr2B.!!$R7 2273
2 TraesCS2B01G356900 chr2B 716768426 716769590 1164 False 1439.000000 1439 89.640000 1 1119 1 chr2B.!!$F1 1118
3 TraesCS2B01G356900 chr2B 77912957 77914117 1160 True 1413.000000 1413 89.280000 1 1119 1 chr2B.!!$R1 1118
4 TraesCS2B01G356900 chr2B 790426909 790428056 1147 True 1317.000000 1317 87.993000 1 1119 1 chr2B.!!$R6 1118
5 TraesCS2B01G356900 chr2B 510060402 510062262 1860 True 631.333333 957 87.420333 1159 3337 3 chr2B.!!$R9 2178
6 TraesCS2B01G356900 chr2B 510348425 510350488 2063 True 505.500000 1029 86.495750 1121 3426 4 chr2B.!!$R10 2305
7 TraesCS2B01G356900 chr2B 509706006 509707444 1438 True 417.000000 721 84.919000 1567 3337 3 chr2B.!!$R8 1770
8 TraesCS2B01G356900 chr2D 431003773 431005876 2103 True 1767.000000 1849 97.217000 1121 3426 2 chr2D.!!$R2 2305
9 TraesCS2B01G356900 chr2D 624844388 624845556 1168 False 1443.000000 1443 89.658000 1 1120 1 chr2D.!!$F2 1119
10 TraesCS2B01G356900 chr2D 600413258 600414423 1165 True 1434.000000 1434 89.546000 1 1118 1 chr2D.!!$R1 1117
11 TraesCS2B01G356900 chr2D 431381713 431385843 4130 True 1207.000000 1836 97.032667 1121 3426 3 chr2D.!!$R3 2305
12 TraesCS2B01G356900 chr2D 431425045 431429163 4118 True 650.333333 1016 87.320333 1121 3335 3 chr2D.!!$R4 2214
13 TraesCS2B01G356900 chr3D 569474793 569475957 1164 True 1478.000000 1478 90.223000 1 1119 1 chr3D.!!$R1 1118
14 TraesCS2B01G356900 chr3D 26196557 26197585 1028 False 1286.000000 1286 89.922000 6 993 1 chr3D.!!$F1 987
15 TraesCS2B01G356900 chr4D 340294288 340295448 1160 True 1474.000000 1474 90.198000 1 1119 1 chr4D.!!$R1 1118
16 TraesCS2B01G356900 chr4D 485687558 485688738 1180 True 1336.000000 1336 87.892000 1 1123 1 chr4D.!!$R2 1122
17 TraesCS2B01G356900 chr4D 301727804 301728974 1170 False 1295.000000 1295 87.404000 1 1119 1 chr4D.!!$F1 1118
18 TraesCS2B01G356900 chr4A 674598032 674599196 1164 True 1472.000000 1472 90.146000 1 1119 1 chr4A.!!$R1 1118
19 TraesCS2B01G356900 chr1B 622694284 622695432 1148 False 1465.000000 1465 90.311000 1 1109 1 chr1B.!!$F1 1108
20 TraesCS2B01G356900 chr6D 121190011 121191175 1164 False 1461.000000 1461 89.966000 1 1119 1 chr6D.!!$F1 1118
21 TraesCS2B01G356900 chr1D 241262885 241264050 1165 False 1445.000000 1445 89.726000 1 1119 1 chr1D.!!$F1 1118
22 TraesCS2B01G356900 chr1D 454205733 454206896 1163 True 1443.000000 1443 89.708000 1 1119 1 chr1D.!!$R1 1118
23 TraesCS2B01G356900 chr5B 145024202 145025369 1167 True 1411.000000 1411 89.155000 1 1123 1 chr5B.!!$R2 1122
24 TraesCS2B01G356900 chr5B 33630483 33631648 1165 True 1397.000000 1397 88.955000 1 1120 1 chr5B.!!$R1 1119
25 TraesCS2B01G356900 chr5B 182461839 182462410 571 True 749.000000 749 90.925000 1 551 1 chr5B.!!$R3 550
26 TraesCS2B01G356900 chr5B 100837780 100838691 911 False 505.000000 736 88.126500 2371 3426 2 chr5B.!!$F2 1055
27 TraesCS2B01G356900 chr3B 539601002 539602158 1156 True 1371.000000 1371 88.697000 4 1116 1 chr3B.!!$R1 1112
28 TraesCS2B01G356900 chr4B 3938333 3939468 1135 True 1362.000000 1362 88.879000 1 1112 1 chr4B.!!$R1 1111
29 TraesCS2B01G356900 chr7B 93271058 93272205 1147 True 1345.000000 1345 88.412000 1 1119 1 chr7B.!!$R1 1118
30 TraesCS2B01G356900 chr7B 137371842 137372876 1034 True 1323.000000 1323 90.444000 1 992 1 chr7B.!!$R2 991
31 TraesCS2B01G356900 chr2A 554953016 554955274 2258 False 427.333333 758 88.820000 1121 3426 3 chr2A.!!$F1 2305

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
180 200 0.179240 GCAAGTCTCGTGATGCAACG 60.179 55.000 4.54 4.54 44.92 4.10 F
688 720 1.065418 AGACCCAAACCGCATTAGAGG 60.065 52.381 0.00 0.00 41.02 3.69 F
1138 1215 1.984570 CGCCTCTGGTCTCCCTCAA 60.985 63.158 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1148 0.179150 TCGCGCAAAACAGCTTTTGT 60.179 45.0 8.75 0.0 45.60 2.83 R
1629 2324 0.749454 GGGCGAGCTGTTCATCCAAT 60.749 55.0 0.00 0.0 0.00 3.16 R
2855 5915 0.035439 CGGTGCCTCCACAGGTAATT 60.035 55.0 0.00 0.0 43.88 1.40 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
180 200 0.179240 GCAAGTCTCGTGATGCAACG 60.179 55.000 4.54 4.54 44.92 4.10
276 297 5.816449 ATGATATCAATGTGTTGCAACGA 57.184 34.783 23.79 14.84 35.26 3.85
278 299 6.917217 TGATATCAATGTGTTGCAACGATA 57.083 33.333 23.79 21.37 35.26 2.92
304 325 7.279615 TCATTTATTTGCTAGGCTTGCTAGTA 58.720 34.615 20.97 12.13 0.00 1.82
342 363 3.694072 GCAACTACACTATCAATGGGCAA 59.306 43.478 0.00 0.00 0.00 4.52
416 438 5.856986 CACATTTGTCAAGAGCATCAAAGAG 59.143 40.000 0.00 0.00 37.82 2.85
574 605 5.448768 CCTTGAAGAACATCATGACATGCTC 60.449 44.000 10.76 4.86 0.00 4.26
688 720 1.065418 AGACCCAAACCGCATTAGAGG 60.065 52.381 0.00 0.00 41.02 3.69
697 729 3.344515 ACCGCATTAGAGGTTTTCTTCC 58.655 45.455 0.00 0.00 46.59 3.46
744 777 4.392940 AGACATCCACTTTCAACTTCAGG 58.607 43.478 0.00 0.00 0.00 3.86
836 880 7.812191 TGTATTCATGACAAGTTTTGTATTGCC 59.188 33.333 0.00 0.00 45.52 4.52
1032 1105 6.035843 TCCGCGAGTATACTTTTTACGAATT 58.964 36.000 8.23 0.00 0.00 2.17
1052 1129 6.510799 CGAATTCATTTGAGGTCTACATCTGC 60.511 42.308 6.22 0.00 0.00 4.26
1137 1214 2.363018 CGCCTCTGGTCTCCCTCA 60.363 66.667 0.00 0.00 0.00 3.86
1138 1215 1.984570 CGCCTCTGGTCTCCCTCAA 60.985 63.158 0.00 0.00 0.00 3.02
1227 1308 2.221169 TGTTGTTCAGACATGACTGCC 58.779 47.619 18.71 12.43 37.75 4.85
1278 1359 2.359107 ACGTACGAGGCCGACAGA 60.359 61.111 24.41 0.00 39.50 3.41
1317 1400 5.049198 TCTGAATCTTGTTTCTGTGATGCAC 60.049 40.000 0.00 0.00 34.56 4.57
1524 2219 2.423538 CCATGACCTTTTCGATGTTCCC 59.576 50.000 0.00 0.00 0.00 3.97
1629 2324 1.865788 GCATTGCAACGGAGAAGCCA 61.866 55.000 0.00 0.00 35.94 4.75
2066 2805 1.462731 ATGTGGCCATTGCACGTGTT 61.463 50.000 18.38 0.00 40.13 3.32
2159 5102 5.734720 TCTTTAGATGACTTTACCCTGCTG 58.265 41.667 0.00 0.00 0.00 4.41
2208 5151 7.976135 ATAATGCTCTTTCATCACATACTCC 57.024 36.000 0.00 0.00 0.00 3.85
2209 5152 4.142609 TGCTCTTTCATCACATACTCCC 57.857 45.455 0.00 0.00 0.00 4.30
2210 5153 3.776969 TGCTCTTTCATCACATACTCCCT 59.223 43.478 0.00 0.00 0.00 4.20
2211 5154 4.141846 TGCTCTTTCATCACATACTCCCTC 60.142 45.833 0.00 0.00 0.00 4.30
2212 5155 4.742138 GCTCTTTCATCACATACTCCCTCC 60.742 50.000 0.00 0.00 0.00 4.30
2213 5156 3.384789 TCTTTCATCACATACTCCCTCCG 59.615 47.826 0.00 0.00 0.00 4.63
2214 5157 2.454336 TCATCACATACTCCCTCCGT 57.546 50.000 0.00 0.00 0.00 4.69
2215 5158 2.747177 TCATCACATACTCCCTCCGTT 58.253 47.619 0.00 0.00 0.00 4.44
2216 5159 2.693591 TCATCACATACTCCCTCCGTTC 59.306 50.000 0.00 0.00 0.00 3.95
2217 5160 1.481871 TCACATACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
2218 5161 1.191535 CACATACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2219 5162 1.553248 CACATACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
2220 5163 2.027561 CACATACTCCCTCCGTTCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
2221 5164 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
2222 5165 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
2223 5166 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
2224 5167 5.132144 ACATACTCCCTCCGTTCCAAAATAT 59.868 40.000 0.00 0.00 0.00 1.28
2225 5168 4.586306 ACTCCCTCCGTTCCAAAATATT 57.414 40.909 0.00 0.00 0.00 1.28
2226 5169 4.930696 ACTCCCTCCGTTCCAAAATATTT 58.069 39.130 0.00 0.00 0.00 1.40
2227 5170 4.705023 ACTCCCTCCGTTCCAAAATATTTG 59.295 41.667 0.39 0.00 0.00 2.32
2228 5171 4.668636 TCCCTCCGTTCCAAAATATTTGT 58.331 39.130 0.39 0.00 0.00 2.83
2229 5172 4.703093 TCCCTCCGTTCCAAAATATTTGTC 59.297 41.667 0.39 0.00 0.00 3.18
2230 5173 4.705023 CCCTCCGTTCCAAAATATTTGTCT 59.295 41.667 0.39 0.00 0.00 3.41
2231 5174 5.185056 CCCTCCGTTCCAAAATATTTGTCTT 59.815 40.000 0.39 0.00 0.00 3.01
2232 5175 6.295067 CCCTCCGTTCCAAAATATTTGTCTTT 60.295 38.462 0.39 0.00 0.00 2.52
2233 5176 7.094118 CCCTCCGTTCCAAAATATTTGTCTTTA 60.094 37.037 0.39 0.00 0.00 1.85
2234 5177 8.466798 CCTCCGTTCCAAAATATTTGTCTTTAT 58.533 33.333 0.39 0.00 0.00 1.40
2261 5204 9.737427 AGAGATTTCAATAAGTGACTACATACG 57.263 33.333 0.00 0.00 35.39 3.06
2262 5205 9.731819 GAGATTTCAATAAGTGACTACATACGA 57.268 33.333 0.00 0.00 35.39 3.43
2265 5208 7.751047 TTCAATAAGTGACTACATACGAAGC 57.249 36.000 0.00 0.00 35.39 3.86
2266 5209 6.859017 TCAATAAGTGACTACATACGAAGCA 58.141 36.000 0.00 0.00 0.00 3.91
2267 5210 7.317390 TCAATAAGTGACTACATACGAAGCAA 58.683 34.615 0.00 0.00 0.00 3.91
2268 5211 7.815549 TCAATAAGTGACTACATACGAAGCAAA 59.184 33.333 0.00 0.00 0.00 3.68
2269 5212 8.440059 CAATAAGTGACTACATACGAAGCAAAA 58.560 33.333 0.00 0.00 0.00 2.44
2270 5213 8.718102 ATAAGTGACTACATACGAAGCAAAAT 57.282 30.769 0.00 0.00 0.00 1.82
2271 5214 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
2272 5215 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2273 5216 6.649141 AGTGACTACATACGAAGCAAAATGAA 59.351 34.615 0.00 0.00 0.00 2.57
2274 5217 7.334421 AGTGACTACATACGAAGCAAAATGAAT 59.666 33.333 0.00 0.00 0.00 2.57
2275 5218 7.426456 GTGACTACATACGAAGCAAAATGAATG 59.574 37.037 0.00 0.00 0.00 2.67
2276 5219 7.333174 TGACTACATACGAAGCAAAATGAATGA 59.667 33.333 0.00 0.00 0.00 2.57
2277 5220 8.039603 ACTACATACGAAGCAAAATGAATGAA 57.960 30.769 0.00 0.00 0.00 2.57
2278 5221 8.677300 ACTACATACGAAGCAAAATGAATGAAT 58.323 29.630 0.00 0.00 0.00 2.57
2279 5222 7.975866 ACATACGAAGCAAAATGAATGAATC 57.024 32.000 0.00 0.00 0.00 2.52
2280 5223 7.765307 ACATACGAAGCAAAATGAATGAATCT 58.235 30.769 0.00 0.00 0.00 2.40
2281 5224 8.892723 ACATACGAAGCAAAATGAATGAATCTA 58.107 29.630 0.00 0.00 0.00 1.98
2282 5225 9.162793 CATACGAAGCAAAATGAATGAATCTAC 57.837 33.333 0.00 0.00 0.00 2.59
2283 5226 7.144722 ACGAAGCAAAATGAATGAATCTACA 57.855 32.000 0.00 0.00 0.00 2.74
2284 5227 7.023575 ACGAAGCAAAATGAATGAATCTACAC 58.976 34.615 0.00 0.00 0.00 2.90
2285 5228 6.470235 CGAAGCAAAATGAATGAATCTACACC 59.530 38.462 0.00 0.00 0.00 4.16
2286 5229 6.212888 AGCAAAATGAATGAATCTACACCC 57.787 37.500 0.00 0.00 0.00 4.61
2287 5230 5.954150 AGCAAAATGAATGAATCTACACCCT 59.046 36.000 0.00 0.00 0.00 4.34
2288 5231 7.118723 AGCAAAATGAATGAATCTACACCCTA 58.881 34.615 0.00 0.00 0.00 3.53
2289 5232 7.615365 AGCAAAATGAATGAATCTACACCCTAA 59.385 33.333 0.00 0.00 0.00 2.69
2290 5233 8.250332 GCAAAATGAATGAATCTACACCCTAAA 58.750 33.333 0.00 0.00 0.00 1.85
2307 5250 9.998106 ACACCCTAAAATATGTCTACATACATC 57.002 33.333 4.98 0.00 41.15 3.06
2308 5251 9.436957 CACCCTAAAATATGTCTACATACATCC 57.563 37.037 4.98 0.00 41.15 3.51
2309 5252 8.311836 ACCCTAAAATATGTCTACATACATCCG 58.688 37.037 4.98 0.00 41.15 4.18
2310 5253 8.311836 CCCTAAAATATGTCTACATACATCCGT 58.688 37.037 4.98 0.00 41.15 4.69
2323 5266 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
2324 5267 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
2325 5268 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
2326 5269 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
2327 5270 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
2328 5271 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
2329 5272 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
2330 5273 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
2331 5274 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
2332 5275 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
2333 5276 7.361713 CCGTATGTTGTAGTCCATTTGAAATGT 60.362 37.037 15.93 1.43 0.00 2.71
2334 5277 7.692291 CGTATGTTGTAGTCCATTTGAAATGTC 59.308 37.037 15.93 9.10 0.00 3.06
2335 5278 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
2336 5279 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
2337 5280 8.322906 TGTTGTAGTCCATTTGAAATGTCTAG 57.677 34.615 15.93 1.90 0.00 2.43
2338 5281 8.154203 TGTTGTAGTCCATTTGAAATGTCTAGA 58.846 33.333 15.93 12.79 0.00 2.43
2339 5282 8.999431 GTTGTAGTCCATTTGAAATGTCTAGAA 58.001 33.333 15.93 16.70 0.00 2.10
2340 5283 9.567776 TTGTAGTCCATTTGAAATGTCTAGAAA 57.432 29.630 15.93 11.59 0.00 2.52
2341 5284 9.219603 TGTAGTCCATTTGAAATGTCTAGAAAG 57.780 33.333 15.93 0.00 0.00 2.62
2342 5285 9.436957 GTAGTCCATTTGAAATGTCTAGAAAGA 57.563 33.333 15.93 1.84 0.00 2.52
2359 5302 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2360 5303 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2361 5304 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2362 5305 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2363 5306 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2364 5307 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2365 5308 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2366 5309 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2367 5310 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2522 5473 2.604046 AGACACTGAAGTTGACGCTT 57.396 45.000 0.00 0.00 0.00 4.68
2534 5485 2.507102 ACGCTTGCGATGACGGAG 60.507 61.111 22.03 0.00 41.35 4.63
2615 5576 7.172019 AGGTAATCTGCATTTTTCTTTTTGCTG 59.828 33.333 0.00 0.00 36.10 4.41
2656 5617 7.885922 TGATTGGTTACTCAATTAGCAGGTAAA 59.114 33.333 0.00 0.00 37.47 2.01
2657 5618 8.644374 ATTGGTTACTCAATTAGCAGGTAAAA 57.356 30.769 0.00 0.00 34.01 1.52
2660 5621 6.972901 GGTTACTCAATTAGCAGGTAAAATGC 59.027 38.462 0.00 0.00 44.18 3.56
2661 5622 7.362574 GGTTACTCAATTAGCAGGTAAAATGCA 60.363 37.037 0.00 0.00 46.31 3.96
2662 5623 5.954335 ACTCAATTAGCAGGTAAAATGCAC 58.046 37.500 0.00 0.00 46.31 4.57
2663 5624 4.980590 TCAATTAGCAGGTAAAATGCACG 58.019 39.130 0.00 0.00 46.31 5.34
2664 5625 4.457603 TCAATTAGCAGGTAAAATGCACGT 59.542 37.500 0.00 0.00 46.31 4.49
2891 5968 3.367932 GCACCGATGGTATCATATGTTCG 59.632 47.826 1.90 3.88 32.11 3.95
2897 5974 7.444183 ACCGATGGTATCATATGTTCGAAAAAT 59.556 33.333 0.00 0.00 32.11 1.82
2940 8010 5.236047 GCAATAGAAGTAGAATGAGTGCTGG 59.764 44.000 0.00 0.00 0.00 4.85
3279 8353 7.550906 AGCCTAATTCTCACTTGACTTGAATAC 59.449 37.037 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 200 1.870167 GCTACGGCCTCTAGCACAATC 60.870 57.143 19.57 0.00 46.50 2.67
236 257 4.502105 TCATTTAGAGTGCCCAGCATAA 57.498 40.909 0.00 0.00 41.91 1.90
242 263 6.487668 CACATTGATATCATTTAGAGTGCCCA 59.512 38.462 6.17 0.00 0.00 5.36
276 297 7.771927 AGCAAGCCTAGCAAATAAATGATAT 57.228 32.000 0.00 0.00 0.00 1.63
278 299 6.774656 ACTAGCAAGCCTAGCAAATAAATGAT 59.225 34.615 0.00 0.00 46.17 2.45
304 325 0.251033 TTGCAAGCAGGAGCATCACT 60.251 50.000 0.00 0.00 45.49 3.41
342 363 7.653713 CGCAAGATAGTATCCTTTGTGTATTCT 59.346 37.037 13.62 0.00 43.02 2.40
574 605 7.741027 AGAATCATATTGTGCAGGATAACAG 57.259 36.000 0.00 0.00 0.00 3.16
688 720 5.235516 TCTCCTTGTATGTCGGAAGAAAAC 58.764 41.667 0.00 0.00 45.01 2.43
727 759 4.771114 TCTTCCTGAAGTTGAAAGTGGA 57.229 40.909 6.78 0.00 39.38 4.02
744 777 5.678107 GCCAATGGTGTTCAATGAGATCTTC 60.678 44.000 0.00 0.00 0.00 2.87
836 880 9.498307 CAAATAACCGTAGCAAACTTAAATAGG 57.502 33.333 0.00 0.00 0.00 2.57
921 991 3.249799 TCAGCCCGCAAATATCAAATACG 59.750 43.478 0.00 0.00 0.00 3.06
1026 1098 6.536582 CAGATGTAGACCTCAAATGAATTCGT 59.463 38.462 0.04 0.00 0.00 3.85
1032 1105 3.785486 CGCAGATGTAGACCTCAAATGA 58.215 45.455 0.00 0.00 0.00 2.57
1071 1148 0.179150 TCGCGCAAAACAGCTTTTGT 60.179 45.000 8.75 0.00 45.60 2.83
1227 1308 2.403987 GATGCGCTCTGCTTGCAG 59.596 61.111 15.74 15.74 46.63 4.41
1317 1400 3.262420 CACCAAAACTAGGGATGTCTCG 58.738 50.000 0.00 0.00 0.00 4.04
1629 2324 0.749454 GGGCGAGCTGTTCATCCAAT 60.749 55.000 0.00 0.00 0.00 3.16
1921 2650 5.048713 CGCTAAAGGATTTCCAGTTTTCAGT 60.049 40.000 0.00 0.00 40.09 3.41
2066 2805 4.095782 GCCTCGGCAATGAGTATTTTGTAA 59.904 41.667 2.41 0.00 41.49 2.41
2205 5148 4.705023 ACAAATATTTTGGAACGGAGGGAG 59.295 41.667 0.00 0.00 0.00 4.30
2206 5149 4.668636 ACAAATATTTTGGAACGGAGGGA 58.331 39.130 0.00 0.00 0.00 4.20
2207 5150 4.705023 AGACAAATATTTTGGAACGGAGGG 59.295 41.667 0.00 0.00 0.00 4.30
2208 5151 5.897377 AGACAAATATTTTGGAACGGAGG 57.103 39.130 0.00 0.00 0.00 4.30
2235 5178 9.737427 CGTATGTAGTCACTTATTGAAATCTCT 57.263 33.333 0.00 0.00 35.39 3.10
2236 5179 9.731819 TCGTATGTAGTCACTTATTGAAATCTC 57.268 33.333 0.00 0.00 35.39 2.75
2239 5182 8.818057 GCTTCGTATGTAGTCACTTATTGAAAT 58.182 33.333 0.00 0.00 35.39 2.17
2240 5183 7.815549 TGCTTCGTATGTAGTCACTTATTGAAA 59.184 33.333 0.00 0.00 35.39 2.69
2241 5184 7.317390 TGCTTCGTATGTAGTCACTTATTGAA 58.683 34.615 0.00 0.00 35.39 2.69
2242 5185 6.859017 TGCTTCGTATGTAGTCACTTATTGA 58.141 36.000 0.00 0.00 0.00 2.57
2243 5186 7.520119 TTGCTTCGTATGTAGTCACTTATTG 57.480 36.000 0.00 0.00 0.00 1.90
2244 5187 8.542497 TTTTGCTTCGTATGTAGTCACTTATT 57.458 30.769 0.00 0.00 0.00 1.40
2245 5188 8.604035 CATTTTGCTTCGTATGTAGTCACTTAT 58.396 33.333 0.00 0.00 0.00 1.73
2246 5189 7.815549 TCATTTTGCTTCGTATGTAGTCACTTA 59.184 33.333 0.00 0.00 0.00 2.24
2247 5190 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2248 5191 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
2249 5192 6.403333 TCATTTTGCTTCGTATGTAGTCAC 57.597 37.500 0.00 0.00 0.00 3.67
2250 5193 7.333174 TCATTCATTTTGCTTCGTATGTAGTCA 59.667 33.333 0.00 0.00 0.00 3.41
2251 5194 7.684670 TCATTCATTTTGCTTCGTATGTAGTC 58.315 34.615 0.00 0.00 0.00 2.59
2252 5195 7.609760 TCATTCATTTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
2253 5196 9.162793 GATTCATTCATTTTGCTTCGTATGTAG 57.837 33.333 0.00 0.00 0.00 2.74
2254 5197 8.892723 AGATTCATTCATTTTGCTTCGTATGTA 58.107 29.630 0.00 0.00 0.00 2.29
2255 5198 7.765307 AGATTCATTCATTTTGCTTCGTATGT 58.235 30.769 0.00 0.00 0.00 2.29
2256 5199 9.162793 GTAGATTCATTCATTTTGCTTCGTATG 57.837 33.333 0.00 0.00 0.00 2.39
2257 5200 8.892723 TGTAGATTCATTCATTTTGCTTCGTAT 58.107 29.630 0.00 0.00 0.00 3.06
2258 5201 8.175069 GTGTAGATTCATTCATTTTGCTTCGTA 58.825 33.333 0.00 0.00 0.00 3.43
2259 5202 7.023575 GTGTAGATTCATTCATTTTGCTTCGT 58.976 34.615 0.00 0.00 0.00 3.85
2260 5203 6.470235 GGTGTAGATTCATTCATTTTGCTTCG 59.530 38.462 0.00 0.00 0.00 3.79
2261 5204 6.753744 GGGTGTAGATTCATTCATTTTGCTTC 59.246 38.462 0.00 0.00 0.00 3.86
2262 5205 6.438425 AGGGTGTAGATTCATTCATTTTGCTT 59.562 34.615 0.00 0.00 0.00 3.91
2263 5206 5.954150 AGGGTGTAGATTCATTCATTTTGCT 59.046 36.000 0.00 0.00 0.00 3.91
2264 5207 6.212888 AGGGTGTAGATTCATTCATTTTGC 57.787 37.500 0.00 0.00 0.00 3.68
2281 5224 9.998106 GATGTATGTAGACATATTTTAGGGTGT 57.002 33.333 5.69 0.00 40.18 4.16
2282 5225 9.436957 GGATGTATGTAGACATATTTTAGGGTG 57.563 37.037 5.69 0.00 40.18 4.61
2283 5226 8.311836 CGGATGTATGTAGACATATTTTAGGGT 58.688 37.037 5.69 0.00 40.18 4.34
2284 5227 8.311836 ACGGATGTATGTAGACATATTTTAGGG 58.688 37.037 5.69 0.00 40.18 3.53
2301 5244 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
2302 5245 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
2304 5247 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
2305 5248 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
2306 5249 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
2307 5250 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
2308 5251 7.526608 ACATTTCAAATGGACTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
2309 5252 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
2310 5253 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
2311 5254 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
2312 5255 8.154203 TCTAGACATTTCAAATGGACTACAACA 58.846 33.333 14.70 0.00 0.00 3.33
2313 5256 8.547967 TCTAGACATTTCAAATGGACTACAAC 57.452 34.615 14.70 0.00 0.00 3.32
2314 5257 9.567776 TTTCTAGACATTTCAAATGGACTACAA 57.432 29.630 14.70 8.52 0.00 2.41
2315 5258 9.219603 CTTTCTAGACATTTCAAATGGACTACA 57.780 33.333 14.70 3.48 0.00 2.74
2316 5259 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
2333 5276 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2334 5277 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2335 5278 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2336 5279 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2337 5280 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2338 5281 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2339 5282 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2340 5283 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2341 5284 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2342 5285 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2343 5286 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2344 5287 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2345 5288 8.912614 ATATACTCCCTCCGTTCCTAAATATT 57.087 34.615 0.00 0.00 0.00 1.28
2346 5289 8.912614 AATATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
2348 5291 8.912614 ATAATATACTCCCTCCGTTCCTAAAT 57.087 34.615 0.00 0.00 0.00 1.40
2349 5292 8.731591 AATAATATACTCCCTCCGTTCCTAAA 57.268 34.615 0.00 0.00 0.00 1.85
2350 5293 8.731591 AAATAATATACTCCCTCCGTTCCTAA 57.268 34.615 0.00 0.00 0.00 2.69
2351 5294 7.398332 GGAAATAATATACTCCCTCCGTTCCTA 59.602 40.741 0.00 0.00 0.00 2.94
2352 5295 6.212993 GGAAATAATATACTCCCTCCGTTCCT 59.787 42.308 0.00 0.00 0.00 3.36
2353 5296 6.013984 TGGAAATAATATACTCCCTCCGTTCC 60.014 42.308 0.00 0.00 0.00 3.62
2354 5297 7.001099 TGGAAATAATATACTCCCTCCGTTC 57.999 40.000 0.48 0.00 0.00 3.95
2355 5298 7.147444 TGTTGGAAATAATATACTCCCTCCGTT 60.147 37.037 0.48 0.00 0.00 4.44
2356 5299 6.328148 TGTTGGAAATAATATACTCCCTCCGT 59.672 38.462 0.48 0.00 0.00 4.69
2357 5300 6.765403 TGTTGGAAATAATATACTCCCTCCG 58.235 40.000 0.48 0.00 0.00 4.63
2358 5301 7.996644 TGTTGTTGGAAATAATATACTCCCTCC 59.003 37.037 0.48 0.00 0.00 4.30
2359 5302 8.974060 TGTTGTTGGAAATAATATACTCCCTC 57.026 34.615 0.48 0.00 0.00 4.30
2360 5303 9.936329 ATTGTTGTTGGAAATAATATACTCCCT 57.064 29.630 0.48 0.00 0.00 4.20
2522 5473 1.102978 TCATCTTCTCCGTCATCGCA 58.897 50.000 0.00 0.00 35.54 5.10
2534 5485 9.286946 GTTCACATTTTCAGATTCATCATCTTC 57.713 33.333 0.00 0.00 40.67 2.87
2593 5552 6.764560 AGACAGCAAAAAGAAAAATGCAGATT 59.235 30.769 0.00 0.00 41.18 2.40
2596 5555 5.292589 ACAGACAGCAAAAAGAAAAATGCAG 59.707 36.000 0.00 0.00 41.18 4.41
2615 5576 8.784043 AGTAACCAATCAAAAAGATACACAGAC 58.216 33.333 0.00 0.00 35.39 3.51
2656 5617 4.370364 ACAAAACAAGAGAACGTGCATT 57.630 36.364 0.00 0.00 0.00 3.56
2657 5618 4.370364 AACAAAACAAGAGAACGTGCAT 57.630 36.364 0.00 0.00 0.00 3.96
2660 5621 9.710979 TTATAGAAAACAAAACAAGAGAACGTG 57.289 29.630 0.00 0.00 0.00 4.49
2661 5622 9.931210 CTTATAGAAAACAAAACAAGAGAACGT 57.069 29.630 0.00 0.00 0.00 3.99
2662 5623 9.382244 CCTTATAGAAAACAAAACAAGAGAACG 57.618 33.333 0.00 0.00 0.00 3.95
2855 5915 0.035439 CGGTGCCTCCACAGGTAATT 60.035 55.000 0.00 0.00 43.88 1.40
2891 5968 7.699812 GCTGACAATCATGTTCTCCTATTTTTC 59.300 37.037 0.00 0.00 40.74 2.29
2897 5974 4.824479 TGCTGACAATCATGTTCTCCTA 57.176 40.909 0.00 0.00 40.74 2.94
3279 8353 4.713792 ATAATCCCAGGCTTCAGGTTAG 57.286 45.455 0.00 0.00 0.00 2.34
3379 8456 7.624360 ACAAAAACAATAGAGACACTGAACA 57.376 32.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.