Multiple sequence alignment - TraesCS1B01G008600

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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 TraesCS1B01G008600 chr1B 100.000 4845 0 0 1 4845 4521058 4516214 0.000000e+00 8948.0
1 TraesCS1B01G008600 chr1B 90.655 3039 215 35 1310 4301 4109421 4112437 0.000000e+00 3975.0
2 TraesCS1B01G008600 chr1B 90.080 2762 200 33 1183 3916 4143872 4146587 0.000000e+00 3515.0
3 TraesCS1B01G008600 chr1B 87.140 2294 223 41 2080 4315 4597570 4595291 0.000000e+00 2536.0
4 TraesCS1B01G008600 chr1B 89.264 1127 101 9 3193 4301 4798955 4797831 0.000000e+00 1393.0
5 TraesCS1B01G008600 chr1B 93.881 572 34 1 3918 4488 3938097 3938668 0.000000e+00 861.0
6 TraesCS1B01G008600 chr1B 86.962 790 48 28 1250 2014 538505114 538505873 0.000000e+00 837.0
7 TraesCS1B01G008600 chr1B 78.082 1095 113 66 445 1481 46690477 46691502 4.210000e-160 575.0
8 TraesCS1B01G008600 chr1B 95.339 236 11 0 4610 4845 3938666 3938901 4.580000e-100 375.0
9 TraesCS1B01G008600 chr1B 93.532 201 11 1 244 442 46675032 46675232 1.020000e-76 298.0
10 TraesCS1B01G008600 chr1B 81.616 359 46 12 4472 4818 46694290 46694640 3.690000e-71 279.0
11 TraesCS1B01G008600 chr1B 78.906 384 53 18 1183 1554 4542982 4542615 8.110000e-58 235.0
12 TraesCS1B01G008600 chr1B 78.205 390 28 30 969 1315 4955505 4955130 3.830000e-46 196.0
13 TraesCS1B01G008600 chr1B 90.132 152 8 3 1310 1461 4597745 4597601 1.780000e-44 191.0
14 TraesCS1B01G008600 chr1B 84.974 193 11 9 1296 1484 4955100 4954922 3.850000e-41 180.0
15 TraesCS1B01G008600 chr1B 84.653 202 8 4 4465 4644 46827972 46827772 3.850000e-41 180.0
16 TraesCS1B01G008600 chr1B 92.453 106 8 0 4304 4409 4209349 4209454 8.400000e-33 152.0
17 TraesCS1B01G008600 chr1B 89.256 121 10 2 4291 4409 4803100 4802981 1.090000e-31 148.0
18 TraesCS1B01G008600 chr1B 81.218 197 24 9 4465 4648 4595211 4595015 3.910000e-31 147.0
19 TraesCS1B01G008600 chr1B 83.916 143 12 4 1284 1426 4598192 4598061 5.090000e-25 126.0
20 TraesCS1B01G008600 chr1B 88.889 90 4 6 1071 1154 4109262 4109351 6.630000e-19 106.0
21 TraesCS1B01G008600 chr1B 93.220 59 4 0 4465 4523 4147024 4147082 2.400000e-13 87.9
22 TraesCS1B01G008600 chr1B 92.063 63 3 2 1182 1243 4519389 4519328 2.400000e-13 87.9
23 TraesCS1B01G008600 chr1B 92.063 63 3 2 1670 1731 4519877 4519816 2.400000e-13 87.9
24 TraesCS1B01G008600 chr1B 93.220 59 4 0 4465 4523 4539354 4539296 2.400000e-13 87.9
25 TraesCS1B01G008600 chr1B 86.747 83 5 3 834 911 4955632 4955551 2.400000e-13 87.9
26 TraesCS1B01G008600 chr1B 91.379 58 1 1 1679 1732 46691709 46691766 5.200000e-10 76.8
27 TraesCS1B01G008600 chr1B 92.308 52 4 0 990 1041 4109213 4109264 1.870000e-09 75.0
28 TraesCS1B01G008600 chr1B 100.000 32 0 0 4814 4845 4594672 4594641 5.240000e-05 60.2
29 TraesCS1B01G008600 chr1B 100.000 32 0 0 4814 4845 46694991 46695022 5.240000e-05 60.2
30 TraesCS1B01G008600 chr3D 92.216 2672 148 32 1671 4301 560025277 560022625 0.000000e+00 3727.0
31 TraesCS1B01G008600 chr3D 88.475 1692 79 38 1 1654 560026941 560025328 0.000000e+00 1938.0
32 TraesCS1B01G008600 chr3D 83.401 247 36 5 1 244 577147642 577147886 1.750000e-54 224.0
33 TraesCS1B01G008600 chr3D 97.778 45 1 0 4469 4513 560022526 560022482 1.450000e-10 78.7
34 TraesCS1B01G008600 chr1A 90.046 2411 177 39 2116 4473 2943275 2945675 0.000000e+00 3064.0
35 TraesCS1B01G008600 chr1A 88.948 2452 187 24 1981 4398 32545493 32547894 0.000000e+00 2950.0
36 TraesCS1B01G008600 chr1A 79.287 729 81 35 961 1654 32545004 32545697 3.440000e-121 446.0
37 TraesCS1B01G008600 chr1A 88.182 220 23 2 4441 4660 32547894 32548110 4.810000e-65 259.0
38 TraesCS1B01G008600 chr1A 83.600 250 37 4 1 248 33868961 33868714 1.050000e-56 231.0
39 TraesCS1B01G008600 chr1A 80.769 312 33 15 4313 4624 3010991 3011275 8.160000e-53 219.0
40 TraesCS1B01G008600 chr1A 78.797 316 27 25 1296 1597 3533374 3533085 4.980000e-40 176.0
41 TraesCS1B01G008600 chr1A 79.921 254 27 12 4465 4705 3015434 3015676 1.080000e-36 165.0
42 TraesCS1B01G008600 chr1A 89.535 86 7 1 4387 4470 397738724 397738809 1.840000e-19 108.0
43 TraesCS1B01G008600 chr1A 93.846 65 3 1 1670 1734 32545240 32545303 3.990000e-16 97.1
44 TraesCS1B01G008600 chr5B 88.991 2398 195 34 1955 4301 60826101 60823722 0.000000e+00 2902.0
45 TraesCS1B01G008600 chr5B 84.364 275 37 4 483 753 60827176 60826904 1.030000e-66 265.0
46 TraesCS1B01G008600 chr5B 83.628 226 26 9 17 239 114912076 114912293 8.220000e-48 202.0
47 TraesCS1B01G008600 chr5B 85.057 174 18 5 1792 1959 60826299 60826128 2.320000e-38 171.0
48 TraesCS1B01G008600 chr5B 74.224 419 38 39 1061 1426 60826562 60826161 1.430000e-20 111.0
49 TraesCS1B01G008600 chr5D 88.988 2343 194 35 1955 4250 57819423 57821748 0.000000e+00 2839.0
50 TraesCS1B01G008600 chr5D 83.471 363 36 14 1306 1654 535497279 535496927 2.810000e-82 316.0
51 TraesCS1B01G008600 chr5D 85.019 267 33 5 483 744 57818291 57818555 1.030000e-66 265.0
52 TraesCS1B01G008600 chr5D 85.333 225 21 3 36 248 37208952 37209176 6.310000e-54 222.0
53 TraesCS1B01G008600 chr5D 81.938 227 25 13 1749 1959 57819172 57819398 1.390000e-40 178.0
54 TraesCS1B01G008600 chr5D 95.455 88 4 0 4469 4556 497870076 497870163 1.820000e-29 141.0
55 TraesCS1B01G008600 chr6A 88.096 2369 215 28 1977 4301 613493536 613495881 0.000000e+00 2750.0
56 TraesCS1B01G008600 chr6A 86.329 2465 236 48 1713 4148 64168188 64165796 0.000000e+00 2591.0
57 TraesCS1B01G008600 chr6A 84.621 1398 130 28 3047 4387 64065216 64063847 0.000000e+00 1312.0
58 TraesCS1B01G008600 chr6A 86.817 311 31 8 483 788 613492098 613492403 6.010000e-89 339.0
59 TraesCS1B01G008600 chr6A 74.431 571 62 40 1023 1554 613492566 613493091 8.340000e-38 169.0
60 TraesCS1B01G008600 chr6A 77.778 162 19 12 4465 4612 613495984 613496142 3.110000e-12 84.2
61 TraesCS1B01G008600 chr6B 87.369 2391 233 37 1963 4315 120132997 120130638 0.000000e+00 2678.0
62 TraesCS1B01G008600 chr6B 87.287 2352 224 34 1680 4003 120595801 120593497 0.000000e+00 2617.0
63 TraesCS1B01G008600 chr6B 87.688 2266 218 31 1743 3994 120355401 120353183 0.000000e+00 2582.0
64 TraesCS1B01G008600 chr6B 93.103 87 6 0 4468 4554 120130548 120130462 1.420000e-25 128.0
65 TraesCS1B01G008600 chr6D 87.126 2338 227 33 1670 3994 50955986 50958262 0.000000e+00 2582.0
66 TraesCS1B01G008600 chr6D 86.109 2426 248 46 1943 4315 53144951 53142562 0.000000e+00 2531.0
67 TraesCS1B01G008600 chr6D 94.253 87 5 0 4468 4554 53142471 53142385 3.040000e-27 134.0
68 TraesCS1B01G008600 chr6D 90.141 71 5 1 4317 4387 53142538 53142470 1.860000e-14 91.6
69 TraesCS1B01G008600 chr6D 96.154 52 2 0 4505 4556 51070693 51070744 8.640000e-13 86.1
70 TraesCS1B01G008600 chr6D 96.154 52 2 0 4505 4556 51345417 51345468 8.640000e-13 86.1
71 TraesCS1B01G008600 chr6D 97.727 44 1 0 4512 4555 51351115 51351158 5.200000e-10 76.8
72 TraesCS1B01G008600 chr2B 87.277 786 41 28 1250 2014 741895653 741896400 0.000000e+00 843.0
73 TraesCS1B01G008600 chr2B 88.750 80 7 1 4388 4465 113263421 113263500 3.990000e-16 97.1
74 TraesCS1B01G008600 chr1D 91.476 481 31 7 4181 4660 33987790 33988261 0.000000e+00 652.0
75 TraesCS1B01G008600 chr1D 82.056 535 48 18 3892 4383 387236 387765 3.490000e-111 412.0
76 TraesCS1B01G008600 chr1D 81.865 193 17 13 4466 4640 387769 387961 3.910000e-31 147.0
77 TraesCS1B01G008600 chr1D 92.424 66 2 3 1670 1734 33984027 33984090 1.860000e-14 91.6
78 TraesCS1B01G008600 chr3B 88.417 259 18 5 1679 1929 318290231 318290485 7.880000e-78 302.0
79 TraesCS1B01G008600 chr3B 81.423 253 44 3 1 251 766827132 766827383 2.290000e-48 204.0
80 TraesCS1B01G008600 chr4D 84.615 234 32 4 17 248 483207948 483208179 3.770000e-56 230.0
81 TraesCS1B01G008600 chr7B 83.636 220 32 4 32 248 714839665 714839447 2.290000e-48 204.0
82 TraesCS1B01G008600 chr5A 81.356 236 36 6 18 250 665890844 665891074 8.280000e-43 185.0
83 TraesCS1B01G008600 chr7A 88.136 118 14 0 1518 1635 725598521 725598404 1.820000e-29 141.0
84 TraesCS1B01G008600 chr4A 88.235 119 13 1 1518 1635 578290567 578290685 1.820000e-29 141.0
85 TraesCS1B01G008600 chr2A 88.235 119 13 1 1518 1635 31069537 31069419 1.820000e-29 141.0
86 TraesCS1B01G008600 chr2A 91.765 85 6 1 4386 4469 177658325 177658409 3.060000e-22 117.0
87 TraesCS1B01G008600 chr2D 91.765 85 6 1 4386 4469 172409750 172409666 3.060000e-22 117.0
88 TraesCS1B01G008600 chr2D 85.714 77 6 5 4388 4459 74129564 74129640 5.200000e-10 76.8
89 TraesCS1B01G008600 chr2D 81.707 82 9 3 4391 4469 567484211 567484133 4.050000e-06 63.9
90 TraesCS1B01G008600 chrUn 100.000 32 0 0 4814 4845 318172031 318172062 5.240000e-05 60.2


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 TraesCS1B01G008600 chr1B 4516214 4521058 4844 True 3041.266667 8948 94.708667 1 4845 3 chr1B.!!$R4 4844
1 TraesCS1B01G008600 chr1B 4143872 4147082 3210 False 1801.450000 3515 91.650000 1183 4523 2 chr1B.!!$F6 3340
2 TraesCS1B01G008600 chr1B 4797831 4798955 1124 True 1393.000000 1393 89.264000 3193 4301 1 chr1B.!!$R1 1108
3 TraesCS1B01G008600 chr1B 4109213 4112437 3224 False 1385.333333 3975 90.617333 990 4301 3 chr1B.!!$F5 3311
4 TraesCS1B01G008600 chr1B 538505114 538505873 759 False 837.000000 837 86.962000 1250 2014 1 chr1B.!!$F3 764
5 TraesCS1B01G008600 chr1B 3938097 3938901 804 False 618.000000 861 94.610000 3918 4845 2 chr1B.!!$F4 927
6 TraesCS1B01G008600 chr1B 4594641 4598192 3551 True 612.040000 2536 88.481200 1284 4845 5 chr1B.!!$R6 3561
7 TraesCS1B01G008600 chr1B 46690477 46695022 4545 False 247.750000 575 87.769250 445 4845 4 chr1B.!!$F7 4400
8 TraesCS1B01G008600 chr3D 560022482 560026941 4459 True 1914.566667 3727 92.823000 1 4513 3 chr3D.!!$R1 4512
9 TraesCS1B01G008600 chr1A 2943275 2945675 2400 False 3064.000000 3064 90.046000 2116 4473 1 chr1A.!!$F1 2357
10 TraesCS1B01G008600 chr1A 32545004 32548110 3106 False 938.025000 2950 87.565750 961 4660 4 chr1A.!!$F5 3699
11 TraesCS1B01G008600 chr5B 60823722 60827176 3454 True 862.250000 2902 83.159000 483 4301 4 chr5B.!!$R1 3818
12 TraesCS1B01G008600 chr5D 57818291 57821748 3457 False 1094.000000 2839 85.315000 483 4250 3 chr5D.!!$F3 3767
13 TraesCS1B01G008600 chr6A 64165796 64168188 2392 True 2591.000000 2591 86.329000 1713 4148 1 chr6A.!!$R2 2435
14 TraesCS1B01G008600 chr6A 64063847 64065216 1369 True 1312.000000 1312 84.621000 3047 4387 1 chr6A.!!$R1 1340
15 TraesCS1B01G008600 chr6A 613492098 613496142 4044 False 835.550000 2750 81.780500 483 4612 4 chr6A.!!$F1 4129
16 TraesCS1B01G008600 chr6B 120593497 120595801 2304 True 2617.000000 2617 87.287000 1680 4003 1 chr6B.!!$R2 2323
17 TraesCS1B01G008600 chr6B 120353183 120355401 2218 True 2582.000000 2582 87.688000 1743 3994 1 chr6B.!!$R1 2251
18 TraesCS1B01G008600 chr6B 120130462 120132997 2535 True 1403.000000 2678 90.236000 1963 4554 2 chr6B.!!$R3 2591
19 TraesCS1B01G008600 chr6D 50955986 50958262 2276 False 2582.000000 2582 87.126000 1670 3994 1 chr6D.!!$F1 2324
20 TraesCS1B01G008600 chr6D 53142385 53144951 2566 True 918.866667 2531 90.167667 1943 4554 3 chr6D.!!$R1 2611
21 TraesCS1B01G008600 chr2B 741895653 741896400 747 False 843.000000 843 87.277000 1250 2014 1 chr2B.!!$F2 764
22 TraesCS1B01G008600 chr1D 33984027 33988261 4234 False 371.800000 652 91.950000 1670 4660 2 chr1D.!!$F2 2990
23 TraesCS1B01G008600 chr1D 387236 387961 725 False 279.500000 412 81.960500 3892 4640 2 chr1D.!!$F1 748

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
975 1187 1.067250 GCACTCTCATCCGCCTCTC 59.933 63.158 0.00 0.00 0.00 3.20 F
1674 2073 0.251165 TGCCTGGTTGGACCTAAAGC 60.251 55.000 0.00 0.00 39.58 3.51 F
3179 4875 0.606604 TCGTGTTGTCCTAGGGAAGC 59.393 55.000 9.46 0.06 31.38 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2292 2.227626 GGGCAAGAAAGAAAGCAGAGAC 59.772 50.000 0.00 0.0 0.00 3.36 R
3475 5172 0.604578 CACAAATTGGGCAGGACTGG 59.395 55.000 0.00 0.0 0.00 4.00 R
4800 8023 1.001048 GCAAGCAGAACTGATGCAACA 60.001 47.619 19.96 0.0 46.31 3.33 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
49 50 7.992033 TCATTTCAAACCAAAATGTGAAGGATT 59.008 29.630 8.06 0.00 42.23 3.01
93 94 6.775629 TGTGGTAGCATGACATACATAGACTA 59.224 38.462 0.00 0.00 37.46 2.59
132 133 1.725641 TGCAAGACTCGCTTATGTGG 58.274 50.000 0.00 0.00 34.31 4.17
162 163 2.158696 GCATGGCTTAGTGGGAGAGAAT 60.159 50.000 0.00 0.00 0.00 2.40
185 186 3.194116 ACTTCAATGCATTGCTTAGTGGG 59.806 43.478 30.57 16.37 37.68 4.61
187 188 3.634504 TCAATGCATTGCTTAGTGGGAT 58.365 40.909 30.57 0.00 37.68 3.85
225 226 7.554118 CACCTTACATGTTGAGAGAATTGGTAT 59.446 37.037 2.30 0.00 0.00 2.73
236 237 9.658799 TTGAGAGAATTGGTATCAACTTCTTAG 57.341 33.333 11.99 0.00 34.29 2.18
237 238 9.035890 TGAGAGAATTGGTATCAACTTCTTAGA 57.964 33.333 11.99 0.00 34.29 2.10
315 316 5.545658 ACTGTCAACATTTACTAATGGCG 57.454 39.130 0.00 0.00 44.42 5.69
343 344 6.807230 GTCGAAAAGTGTCATGTCAGTAGTAT 59.193 38.462 0.54 0.00 0.00 2.12
536 540 9.994432 GAGAATACATGTCCAGTTTTTCATAAG 57.006 33.333 0.00 0.00 0.00 1.73
541 545 6.015180 ACATGTCCAGTTTTTCATAAGCACAT 60.015 34.615 0.00 0.00 0.00 3.21
843 927 3.003173 TGTAGAAGGCCCGCAGCT 61.003 61.111 0.00 0.00 43.05 4.24
948 1144 4.528596 TCTCTTCCTCCGAATCAAAGAAGT 59.471 41.667 0.00 0.00 33.94 3.01
965 1177 3.378602 TTAGCGGCGGCACTCTCA 61.379 61.111 19.21 0.00 43.41 3.27
972 1184 3.842923 CGGCACTCTCATCCGCCT 61.843 66.667 0.00 0.00 42.59 5.52
974 1186 2.430610 GGCACTCTCATCCGCCTCT 61.431 63.158 0.00 0.00 41.50 3.69
975 1187 1.067250 GCACTCTCATCCGCCTCTC 59.933 63.158 0.00 0.00 0.00 3.20
977 1189 1.826054 ACTCTCATCCGCCTCTCCG 60.826 63.158 0.00 0.00 0.00 4.63
1121 1351 2.093711 CCCCGACTTGACATGTACATGA 60.094 50.000 36.36 16.84 41.20 3.07
1318 1646 1.191489 TGGCCCTGTGAACTCATCGA 61.191 55.000 0.00 0.00 0.00 3.59
1361 1699 7.761038 TTGATTTCCCTACTTTCTTTCTTCC 57.239 36.000 0.00 0.00 0.00 3.46
1379 1717 1.530013 CCTTGCCCAACCAAGAGCTG 61.530 60.000 0.00 0.00 43.79 4.24
1576 1924 8.292444 AGCTAGTTTAATTTTATGATGTGGCA 57.708 30.769 0.00 0.00 0.00 4.92
1631 1979 6.942163 ATCCAGACACATATAAGGTGCTAT 57.058 37.500 7.58 0.00 39.87 2.97
1637 1989 8.580720 CAGACACATATAAGGTGCTATCTACTT 58.419 37.037 7.58 0.00 39.87 2.24
1650 2002 9.438228 GGTGCTATCTACTTTAATAAATCTCCC 57.562 37.037 0.00 0.00 0.00 4.30
1666 2018 4.641645 CCTGCGTGCCTGGTTGGA 62.642 66.667 0.00 0.00 38.35 3.53
1667 2019 3.357079 CTGCGTGCCTGGTTGGAC 61.357 66.667 0.00 0.00 38.35 4.02
1674 2073 0.251165 TGCCTGGTTGGACCTAAAGC 60.251 55.000 0.00 0.00 39.58 3.51
1676 2075 1.547901 GCCTGGTTGGACCTAAAGCTT 60.548 52.381 0.00 0.00 39.58 3.74
1757 2161 3.215151 CTGATCGAGTACTTGCCTAGGA 58.785 50.000 14.75 0.00 0.00 2.94
1764 2168 3.107601 AGTACTTGCCTAGGATTGCAGA 58.892 45.455 14.75 0.00 38.95 4.26
1770 2174 6.131961 ACTTGCCTAGGATTGCAGAAAATAT 58.868 36.000 14.75 0.00 38.95 1.28
1771 2175 6.264067 ACTTGCCTAGGATTGCAGAAAATATC 59.736 38.462 14.75 0.00 38.95 1.63
1838 2270 1.450312 CCCTGTGAACTCATCGGCC 60.450 63.158 0.00 0.00 0.00 6.13
1842 2274 1.080093 GTGAACTCATCGGCCGTGA 60.080 57.895 27.15 24.59 0.00 4.35
1852 2292 0.801872 TCGGCCGTGACAAAATGATG 59.198 50.000 27.15 0.00 0.00 3.07
2136 3306 7.175641 CACCATTTCTTTCTAACAATCTGGACT 59.824 37.037 0.00 0.00 0.00 3.85
2296 3958 7.609146 TCCATCTATCTTCACATGCATTATTCC 59.391 37.037 0.00 0.00 0.00 3.01
2353 4024 6.578545 CGTTGTTTTCTGAACCTTGATATGTG 59.421 38.462 0.00 0.00 0.00 3.21
2354 4025 7.425606 GTTGTTTTCTGAACCTTGATATGTGT 58.574 34.615 0.00 0.00 0.00 3.72
2497 4177 4.038642 CAGCTCTACAAGATAGAGGGGAAC 59.961 50.000 11.84 0.00 40.92 3.62
2536 4218 1.440938 TTGGTTCCGGTCTTTGCACG 61.441 55.000 0.00 0.00 0.00 5.34
2597 4279 2.559698 TCTGCGGAAAGTGGAAATCA 57.440 45.000 0.00 0.00 0.00 2.57
2882 4565 5.400066 TGAAATCGACAATGTAGAGTGGA 57.600 39.130 2.26 0.00 0.00 4.02
2991 4674 3.302375 CAGGATGGATGAAGCTCCG 57.698 57.895 0.00 0.00 38.21 4.63
3179 4875 0.606604 TCGTGTTGTCCTAGGGAAGC 59.393 55.000 9.46 0.06 31.38 3.86
3404 5101 3.998099 TGCTTCAGATGATAGACCTCG 57.002 47.619 0.00 0.00 0.00 4.63
3475 5172 2.087646 GAGGGTTTTCTGGTGCTCATC 58.912 52.381 0.00 0.00 0.00 2.92
3502 5199 3.320541 CCTGCCCAATTTGTGTTCTTGTA 59.679 43.478 0.00 0.00 0.00 2.41
3608 5305 0.251634 TCATGCGGTAACTGATGCCA 59.748 50.000 0.00 0.00 32.37 4.92
3981 5695 6.075315 ACTTTTTGTTGCCCTCTACCTTTAT 58.925 36.000 0.00 0.00 0.00 1.40
4150 5911 2.489722 GCCACAAGATTCCCTGTTTCTC 59.510 50.000 0.00 0.00 0.00 2.87
4419 7593 9.925268 CTGTAAACTAATGTAAGACGTTTTTGT 57.075 29.630 0.00 0.00 0.00 2.83
4502 7677 6.747280 GTGGATGTTTAGATTCCAAAATGACG 59.253 38.462 0.00 0.00 41.05 4.35
4667 7869 7.812191 CCTGTCAAGAGTATATATGAAGAGTGC 59.188 40.741 0.00 0.00 0.00 4.40
4708 7923 3.690460 AGACACCATTTGAGGGATTCAC 58.310 45.455 0.00 0.00 34.94 3.18
4746 7969 9.959749 GTACAAAGATCCTGAAATTGTAAAACA 57.040 29.630 0.00 0.00 37.97 2.83
4768 7991 4.279169 CAGCTCAAAGGGTTCTGATTTTCA 59.721 41.667 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.472007 TGTTAGTAATCCTTCACATTTTGGTT 57.528 30.769 0.00 0.00 0.00 3.67
117 118 1.186200 TCTGCCACATAAGCGAGTCT 58.814 50.000 0.00 0.00 0.00 3.24
162 163 4.398988 CCCACTAAGCAATGCATTGAAGTA 59.601 41.667 37.36 23.85 40.14 2.24
202 203 8.722480 TGATACCAATTCTCTCAACATGTAAG 57.278 34.615 0.00 0.00 0.00 2.34
209 210 7.913674 AGAAGTTGATACCAATTCTCTCAAC 57.086 36.000 5.77 5.77 43.70 3.18
249 250 7.463431 TGGCAACTTTTTCCCTAATTACTCTA 58.537 34.615 0.00 0.00 37.61 2.43
253 254 6.156519 CACTGGCAACTTTTTCCCTAATTAC 58.843 40.000 0.00 0.00 37.61 1.89
313 314 0.865769 ATGACACTTTTCGACCACGC 59.134 50.000 0.00 0.00 39.58 5.34
315 316 2.869801 TGACATGACACTTTTCGACCAC 59.130 45.455 0.00 0.00 0.00 4.16
343 344 7.809331 CACCATACTCGCGGTTAGTAAATAATA 59.191 37.037 6.13 0.00 33.36 0.98
358 359 2.461110 CGTTGCCCACCATACTCGC 61.461 63.158 0.00 0.00 0.00 5.03
384 385 3.520290 ATGCAAGAGATACGTTCCGAA 57.480 42.857 0.00 0.00 0.00 4.30
387 388 6.663944 AACTAAATGCAAGAGATACGTTCC 57.336 37.500 0.00 0.00 0.00 3.62
663 672 4.644234 TGTAAAATATGCCCATGTCCACTG 59.356 41.667 0.00 0.00 0.00 3.66
664 673 4.865905 TGTAAAATATGCCCATGTCCACT 58.134 39.130 0.00 0.00 0.00 4.00
820 904 1.244816 GCGGGCCTTCTACACTTTTT 58.755 50.000 0.84 0.00 0.00 1.94
821 905 0.109723 TGCGGGCCTTCTACACTTTT 59.890 50.000 0.84 0.00 0.00 2.27
822 906 0.321653 CTGCGGGCCTTCTACACTTT 60.322 55.000 0.84 0.00 0.00 2.66
823 907 1.296715 CTGCGGGCCTTCTACACTT 59.703 57.895 0.84 0.00 0.00 3.16
824 908 2.982130 CTGCGGGCCTTCTACACT 59.018 61.111 0.84 0.00 0.00 3.55
825 909 2.820037 GCTGCGGGCCTTCTACAC 60.820 66.667 0.84 0.00 34.27 2.90
826 910 3.003173 AGCTGCGGGCCTTCTACA 61.003 61.111 0.84 0.00 43.05 2.74
827 911 2.202946 GAGCTGCGGGCCTTCTAC 60.203 66.667 0.84 0.00 43.05 2.59
828 912 1.626356 AATGAGCTGCGGGCCTTCTA 61.626 55.000 0.84 0.00 43.05 2.10
829 913 2.883267 GAATGAGCTGCGGGCCTTCT 62.883 60.000 0.84 0.00 43.05 2.85
830 914 2.439156 AATGAGCTGCGGGCCTTC 60.439 61.111 0.84 0.00 43.05 3.46
831 915 2.439156 GAATGAGCTGCGGGCCTT 60.439 61.111 0.84 0.00 43.05 4.35
832 916 4.496336 GGAATGAGCTGCGGGCCT 62.496 66.667 0.84 0.00 43.05 5.19
843 927 0.608035 GCTTTCCACACCCGGAATGA 60.608 55.000 0.73 0.00 44.49 2.57
948 1144 2.629050 GATGAGAGTGCCGCCGCTAA 62.629 60.000 0.00 0.00 35.36 3.09
1121 1351 1.494189 CGAATCGAAAAACGGCGGT 59.506 52.632 13.24 0.00 42.82 5.68
1318 1646 1.636148 ATCATTTTGCCAGCCACAGT 58.364 45.000 0.00 0.00 0.00 3.55
1361 1699 1.962144 CAGCTCTTGGTTGGGCAAG 59.038 57.895 0.00 0.00 0.00 4.01
1379 1717 7.052565 TGCAAATTAGTTAGTACGTACTTGC 57.947 36.000 31.58 28.49 37.73 4.01
1421 1760 7.602517 ACTACTAATTGCTGAATCTGAACAC 57.397 36.000 0.00 0.00 0.00 3.32
1468 1807 2.154462 ACGTTCTGGAATTGAGGCAAG 58.846 47.619 0.00 0.00 0.00 4.01
1473 1812 5.821204 ACAAAGAAACGTTCTGGAATTGAG 58.179 37.500 0.00 0.00 40.59 3.02
1517 1862 0.520847 GAAGCAAGCAGAGCCTGAAC 59.479 55.000 6.40 0.00 32.44 3.18
1611 1959 8.116651 AGTAGATAGCACCTTATATGTGTCTG 57.883 38.462 5.20 0.00 36.11 3.51
1631 1979 6.984474 CACGCAGGGAGATTTATTAAAGTAGA 59.016 38.462 0.00 0.00 0.00 2.59
1637 1989 3.118038 AGGCACGCAGGGAGATTTATTAA 60.118 43.478 0.00 0.00 0.00 1.40
1650 2002 3.357079 GTCCAACCAGGCACGCAG 61.357 66.667 0.00 0.00 37.29 5.18
1666 2018 7.865889 GCTTTACAACATTAACAAGCTTTAGGT 59.134 33.333 0.00 0.00 34.94 3.08
1667 2019 7.328493 GGCTTTACAACATTAACAAGCTTTAGG 59.672 37.037 0.00 0.00 37.41 2.69
1674 2073 7.542130 GGAGAATGGCTTTACAACATTAACAAG 59.458 37.037 0.00 0.00 35.17 3.16
1676 2075 6.719370 AGGAGAATGGCTTTACAACATTAACA 59.281 34.615 0.00 0.00 35.17 2.41
1740 2139 2.100916 GCAATCCTAGGCAAGTACTCGA 59.899 50.000 2.96 0.00 0.00 4.04
1770 2174 9.638239 GCCAATTGTTCAAAATAGAAATACTGA 57.362 29.630 4.43 0.00 0.00 3.41
1771 2175 8.586273 CGCCAATTGTTCAAAATAGAAATACTG 58.414 33.333 4.43 0.00 0.00 2.74
1795 2212 9.968743 GGTGCAGTTATTATTAATAGATAACGC 57.031 33.333 23.72 23.72 39.83 4.84
1838 2270 3.434641 AGCAGAGACATCATTTTGTCACG 59.565 43.478 7.28 0.00 46.81 4.35
1842 2274 6.645790 AAGAAAGCAGAGACATCATTTTGT 57.354 33.333 0.00 0.00 0.00 2.83
1852 2292 2.227626 GGGCAAGAAAGAAAGCAGAGAC 59.772 50.000 0.00 0.00 0.00 3.36
1855 2295 2.233271 CTGGGCAAGAAAGAAAGCAGA 58.767 47.619 0.00 0.00 0.00 4.26
2114 3280 8.378565 TCTGAGTCCAGATTGTTAGAAAGAAAT 58.621 33.333 0.00 0.00 44.01 2.17
2296 3958 5.401550 TGGACTAAAACTTACGGTACATCG 58.598 41.667 0.00 0.00 0.00 3.84
2882 4565 3.657727 CCATCCCTACCAAGGTATTCCAT 59.342 47.826 0.00 0.00 41.89 3.41
2991 4674 6.318900 TCTTTTCCTCTCAAACTCAAACTTCC 59.681 38.462 0.00 0.00 0.00 3.46
3404 5101 4.453819 GTCAGCATCACATCCTATAAAGCC 59.546 45.833 0.00 0.00 0.00 4.35
3475 5172 0.604578 CACAAATTGGGCAGGACTGG 59.395 55.000 0.00 0.00 0.00 4.00
3502 5199 2.038387 AGAAGTTGGCGTTGTTGAGT 57.962 45.000 0.00 0.00 0.00 3.41
4206 7334 8.410141 CACTTACACAATAAAAAGAGGGTTCAA 58.590 33.333 0.00 0.00 0.00 2.69
4315 7488 7.807433 CGATGGAGTCAATATCAACAAAACAAA 59.193 33.333 0.00 0.00 0.00 2.83
4419 7593 8.455682 AGACGTTTTTGAAGTTCAATTCAACTA 58.544 29.630 18.69 0.00 46.12 2.24
4523 7698 2.869897 CCTTCAGTAGTCGCTCAAGTC 58.130 52.381 0.00 0.00 0.00 3.01
4589 7791 7.064229 AGGTAAGAAGAAAATGTTGTTGGGTA 58.936 34.615 0.00 0.00 0.00 3.69
4592 7794 8.716646 AAAAGGTAAGAAGAAAATGTTGTTGG 57.283 30.769 0.00 0.00 0.00 3.77
4667 7869 7.917505 GGTGTCTTAATTCCTGCTATTTTCATG 59.082 37.037 0.00 0.00 0.00 3.07
4708 7923 3.684103 TCTTTGTACCAAGCAAACACG 57.316 42.857 1.80 0.00 33.04 4.49
4746 7969 4.473444 TGAAAATCAGAACCCTTTGAGCT 58.527 39.130 0.00 0.00 0.00 4.09
4790 8013 3.743521 ACTGATGCAACAAGCTGTCTTA 58.256 40.909 0.00 0.00 45.94 2.10
4800 8023 1.001048 GCAAGCAGAACTGATGCAACA 60.001 47.619 19.96 0.00 46.31 3.33


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

AutoCloner maintained by Alex Coulton.