Multiple sequence alignment - TraesCS3B01G501300

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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 TraesCS3B01G501300 chr3B 100.000 3146 0 0 1 3146 745439959 745443104 0.000000e+00 5810.0
1 TraesCS3B01G501300 chr3B 80.153 2096 290 78 282 2279 744728626 744730693 0.000000e+00 1450.0
2 TraesCS3B01G501300 chr3B 84.068 1293 135 35 288 1554 745540183 745541430 0.000000e+00 1181.0
3 TraesCS3B01G501300 chr3B 82.552 1301 172 26 296 1551 747493104 747494394 0.000000e+00 1094.0
4 TraesCS3B01G501300 chr3B 82.448 1299 165 28 314 1564 744419778 744418495 0.000000e+00 1077.0
5 TraesCS3B01G501300 chr3B 82.299 1305 174 30 288 1555 745474806 745473522 0.000000e+00 1077.0
6 TraesCS3B01G501300 chr3B 81.665 1309 178 31 288 1564 745203341 745202063 0.000000e+00 1031.0
7 TraesCS3B01G501300 chr3B 83.178 1076 132 28 288 1320 744512857 744511788 0.000000e+00 939.0
8 TraesCS3B01G501300 chr3B 82.927 1066 136 26 296 1320 747384445 747385505 0.000000e+00 918.0
9 TraesCS3B01G501300 chr3B 78.766 989 138 42 1189 2127 746286040 746287006 5.810000e-167 597.0
10 TraesCS3B01G501300 chr3B 83.072 573 84 11 1651 2216 744545200 744544634 2.800000e-140 508.0
11 TraesCS3B01G501300 chr3B 81.435 641 94 19 1664 2289 744848657 744849287 4.680000e-138 501.0
12 TraesCS3B01G501300 chr3B 85.996 457 61 1 1649 2102 745473299 745472843 1.310000e-133 486.0
13 TraesCS3B01G501300 chr3B 76.844 678 98 24 870 1524 746357136 746356495 8.410000e-86 327.0
14 TraesCS3B01G501300 chr3B 84.577 201 30 1 1356 1556 744591698 744591897 6.880000e-47 198.0
15 TraesCS3B01G501300 chr3D 93.014 2190 90 21 93 2232 560752437 560754613 0.000000e+00 3138.0
16 TraesCS3B01G501300 chr3D 81.772 1964 268 50 329 2228 560640211 560642148 0.000000e+00 1561.0
17 TraesCS3B01G501300 chr3D 81.404 1909 226 74 288 2130 560826934 560828779 0.000000e+00 1439.0
18 TraesCS3B01G501300 chr3D 82.864 1278 153 35 288 1520 560551630 560552886 0.000000e+00 1086.0
19 TraesCS3B01G501300 chr3D 82.093 1290 178 24 314 1564 560235030 560233755 0.000000e+00 1053.0
20 TraesCS3B01G501300 chr3D 83.111 1048 135 18 289 1301 560785814 560784774 0.000000e+00 917.0
21 TraesCS3B01G501300 chr3D 84.034 952 135 13 296 1236 560331202 560332147 0.000000e+00 900.0
22 TraesCS3B01G501300 chr3D 83.074 1028 126 19 282 1267 560866764 560867785 0.000000e+00 891.0
23 TraesCS3B01G501300 chr3D 85.318 865 96 19 282 1123 560269545 560268689 0.000000e+00 865.0
24 TraesCS3B01G501300 chr3D 80.496 846 129 24 1284 2102 560784696 560783860 1.600000e-172 616.0
25 TraesCS3B01G501300 chr3D 79.530 894 135 33 1284 2161 560197908 560197047 7.510000e-166 593.0
26 TraesCS3B01G501300 chr3D 86.007 536 41 13 2229 2738 560754716 560755243 7.670000e-151 544.0
27 TraesCS3B01G501300 chr3D 92.663 368 22 3 2780 3145 560755246 560755610 2.780000e-145 525.0
28 TraesCS3B01G501300 chr3D 82.957 575 82 14 1651 2216 560285200 560284633 3.620000e-139 505.0
29 TraesCS3B01G501300 chr3D 84.615 507 73 3 1659 2161 560553126 560553631 1.680000e-137 499.0
30 TraesCS3B01G501300 chr3A 80.251 1676 232 57 351 1981 696477904 696476283 0.000000e+00 1170.0
31 TraesCS3B01G501300 chr3A 86.157 968 98 20 303 1241 696637292 696638252 0.000000e+00 1013.0
32 TraesCS3B01G501300 chr3A 80.336 834 121 32 1284 2104 696289167 696288364 2.700000e-165 592.0
33 TraesCS3B01G501300 chr1D 89.855 69 7 0 3 71 265522287 265522219 4.320000e-14 89.8
34 TraesCS3B01G501300 chr1D 93.333 60 4 0 3 62 387798836 387798777 4.320000e-14 89.8
35 TraesCS3B01G501300 chr2A 88.525 61 5 2 2 62 44024354 44024412 4.350000e-09 73.1


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 TraesCS3B01G501300 chr3B 745439959 745443104 3145 False 5810.000000 5810 100.000000 1 3146 1 chr3B.!!$F4 3145
1 TraesCS3B01G501300 chr3B 744728626 744730693 2067 False 1450.000000 1450 80.153000 282 2279 1 chr3B.!!$F2 1997
2 TraesCS3B01G501300 chr3B 745540183 745541430 1247 False 1181.000000 1181 84.068000 288 1554 1 chr3B.!!$F5 1266
3 TraesCS3B01G501300 chr3B 747493104 747494394 1290 False 1094.000000 1094 82.552000 296 1551 1 chr3B.!!$F8 1255
4 TraesCS3B01G501300 chr3B 744418495 744419778 1283 True 1077.000000 1077 82.448000 314 1564 1 chr3B.!!$R1 1250
5 TraesCS3B01G501300 chr3B 745202063 745203341 1278 True 1031.000000 1031 81.665000 288 1564 1 chr3B.!!$R4 1276
6 TraesCS3B01G501300 chr3B 744511788 744512857 1069 True 939.000000 939 83.178000 288 1320 1 chr3B.!!$R2 1032
7 TraesCS3B01G501300 chr3B 747384445 747385505 1060 False 918.000000 918 82.927000 296 1320 1 chr3B.!!$F7 1024
8 TraesCS3B01G501300 chr3B 745472843 745474806 1963 True 781.500000 1077 84.147500 288 2102 2 chr3B.!!$R6 1814
9 TraesCS3B01G501300 chr3B 746286040 746287006 966 False 597.000000 597 78.766000 1189 2127 1 chr3B.!!$F6 938
10 TraesCS3B01G501300 chr3B 744544634 744545200 566 True 508.000000 508 83.072000 1651 2216 1 chr3B.!!$R3 565
11 TraesCS3B01G501300 chr3B 744848657 744849287 630 False 501.000000 501 81.435000 1664 2289 1 chr3B.!!$F3 625
12 TraesCS3B01G501300 chr3B 746356495 746357136 641 True 327.000000 327 76.844000 870 1524 1 chr3B.!!$R5 654
13 TraesCS3B01G501300 chr3D 560640211 560642148 1937 False 1561.000000 1561 81.772000 329 2228 1 chr3D.!!$F2 1899
14 TraesCS3B01G501300 chr3D 560826934 560828779 1845 False 1439.000000 1439 81.404000 288 2130 1 chr3D.!!$F3 1842
15 TraesCS3B01G501300 chr3D 560752437 560755610 3173 False 1402.333333 3138 90.561333 93 3145 3 chr3D.!!$F6 3052
16 TraesCS3B01G501300 chr3D 560233755 560235030 1275 True 1053.000000 1053 82.093000 314 1564 1 chr3D.!!$R2 1250
17 TraesCS3B01G501300 chr3D 560331202 560332147 945 False 900.000000 900 84.034000 296 1236 1 chr3D.!!$F1 940
18 TraesCS3B01G501300 chr3D 560866764 560867785 1021 False 891.000000 891 83.074000 282 1267 1 chr3D.!!$F4 985
19 TraesCS3B01G501300 chr3D 560268689 560269545 856 True 865.000000 865 85.318000 282 1123 1 chr3D.!!$R3 841
20 TraesCS3B01G501300 chr3D 560551630 560553631 2001 False 792.500000 1086 83.739500 288 2161 2 chr3D.!!$F5 1873
21 TraesCS3B01G501300 chr3D 560783860 560785814 1954 True 766.500000 917 81.803500 289 2102 2 chr3D.!!$R5 1813
22 TraesCS3B01G501300 chr3D 560197047 560197908 861 True 593.000000 593 79.530000 1284 2161 1 chr3D.!!$R1 877
23 TraesCS3B01G501300 chr3D 560284633 560285200 567 True 505.000000 505 82.957000 1651 2216 1 chr3D.!!$R4 565
24 TraesCS3B01G501300 chr3A 696476283 696477904 1621 True 1170.000000 1170 80.251000 351 1981 1 chr3A.!!$R2 1630
25 TraesCS3B01G501300 chr3A 696637292 696638252 960 False 1013.000000 1013 86.157000 303 1241 1 chr3A.!!$F1 938
26 TraesCS3B01G501300 chr3A 696288364 696289167 803 True 592.000000 592 80.336000 1284 2104 1 chr3A.!!$R1 820

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 1004 0.249657 GAGGACCGTGATCTGGCATC 60.25 60.0 4.67 2.47 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2973 3616 0.040425 GAAATTGCGCAACAGGACGT 60.04 50.0 27.64 4.31 0.0 4.34 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
28 29 3.652057 TCCAATGAACTGGAATCCTCC 57.348 47.619 0.00 0.00 42.69 4.30
58 59 9.640952 ATTCCTATAAAAATCCTTCGATCCAAA 57.359 29.630 0.00 0.00 0.00 3.28
59 60 8.677148 TCCTATAAAAATCCTTCGATCCAAAG 57.323 34.615 0.00 0.00 0.00 2.77
60 61 8.491134 TCCTATAAAAATCCTTCGATCCAAAGA 58.509 33.333 4.46 0.00 0.00 2.52
61 62 8.778358 CCTATAAAAATCCTTCGATCCAAAGAG 58.222 37.037 4.46 0.00 0.00 2.85
62 63 4.972514 AAAATCCTTCGATCCAAAGAGC 57.027 40.909 4.46 0.00 0.00 4.09
63 64 2.629336 ATCCTTCGATCCAAAGAGCC 57.371 50.000 4.46 0.00 0.00 4.70
64 65 1.275666 TCCTTCGATCCAAAGAGCCA 58.724 50.000 4.46 0.00 0.00 4.75
65 66 1.208052 TCCTTCGATCCAAAGAGCCAG 59.792 52.381 4.46 0.00 0.00 4.85
66 67 1.065854 CCTTCGATCCAAAGAGCCAGT 60.066 52.381 4.46 0.00 0.00 4.00
67 68 2.616510 CCTTCGATCCAAAGAGCCAGTT 60.617 50.000 4.46 0.00 0.00 3.16
68 69 3.369471 CCTTCGATCCAAAGAGCCAGTTA 60.369 47.826 4.46 0.00 0.00 2.24
69 70 3.526931 TCGATCCAAAGAGCCAGTTAG 57.473 47.619 0.00 0.00 0.00 2.34
70 71 3.096852 TCGATCCAAAGAGCCAGTTAGA 58.903 45.455 0.00 0.00 0.00 2.10
71 72 3.131223 TCGATCCAAAGAGCCAGTTAGAG 59.869 47.826 0.00 0.00 0.00 2.43
72 73 3.131223 CGATCCAAAGAGCCAGTTAGAGA 59.869 47.826 0.00 0.00 0.00 3.10
73 74 4.202202 CGATCCAAAGAGCCAGTTAGAGAT 60.202 45.833 0.00 0.00 0.00 2.75
74 75 5.679601 GATCCAAAGAGCCAGTTAGAGATT 58.320 41.667 0.00 0.00 0.00 2.40
75 76 4.836825 TCCAAAGAGCCAGTTAGAGATTG 58.163 43.478 0.00 0.00 0.00 2.67
76 77 3.944015 CCAAAGAGCCAGTTAGAGATTGG 59.056 47.826 0.00 0.00 38.14 3.16
77 78 4.323792 CCAAAGAGCCAGTTAGAGATTGGA 60.324 45.833 0.00 0.00 37.32 3.53
78 79 5.435291 CAAAGAGCCAGTTAGAGATTGGAT 58.565 41.667 0.00 0.00 37.32 3.41
80 81 4.679373 GAGCCAGTTAGAGATTGGATCA 57.321 45.455 3.36 0.00 46.45 2.92
81 82 5.226194 GAGCCAGTTAGAGATTGGATCAT 57.774 43.478 3.36 0.00 46.45 2.45
82 83 5.226194 AGCCAGTTAGAGATTGGATCATC 57.774 43.478 0.00 0.00 37.32 2.92
83 84 4.657504 AGCCAGTTAGAGATTGGATCATCA 59.342 41.667 0.00 0.00 37.32 3.07
84 85 5.310068 AGCCAGTTAGAGATTGGATCATCAT 59.690 40.000 0.00 0.00 37.32 2.45
85 86 6.002704 GCCAGTTAGAGATTGGATCATCATT 58.997 40.000 0.00 0.00 37.32 2.57
86 87 6.489361 GCCAGTTAGAGATTGGATCATCATTT 59.511 38.462 0.00 0.00 37.32 2.32
87 88 7.014038 GCCAGTTAGAGATTGGATCATCATTTT 59.986 37.037 0.00 0.00 37.32 1.82
88 89 9.565090 CCAGTTAGAGATTGGATCATCATTTTA 57.435 33.333 0.00 0.00 37.32 1.52
105 106 9.708222 CATCATTTTATTTGTAGGAGAAAGTCG 57.292 33.333 0.00 0.00 0.00 4.18
192 194 1.749063 GTTCCCCAATCATTCGGTTCC 59.251 52.381 0.00 0.00 0.00 3.62
230 232 0.250553 AATCAAAACCCTCGCCGTCA 60.251 50.000 0.00 0.00 0.00 4.35
277 279 3.607370 GACCCGCAAGTGACCCTCC 62.607 68.421 0.00 0.00 0.00 4.30
281 283 1.961277 CGCAAGTGACCCTCCACAC 60.961 63.158 0.00 0.00 39.42 3.82
342 355 0.733729 GGCTCAAATCTGCTGCTCTG 59.266 55.000 0.00 0.00 0.00 3.35
364 377 0.613853 CCCTGTACGACTTCCTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
485 510 2.186903 GCGAAATCCTCTCCCGCA 59.813 61.111 0.00 0.00 44.55 5.69
760 785 2.755876 TGGCTCGACATCCTCGCT 60.756 61.111 0.00 0.00 42.62 4.93
975 1004 0.249657 GAGGACCGTGATCTGGCATC 60.250 60.000 4.67 2.47 0.00 3.91
1236 1308 1.209990 CTTCTGCCAGGAGAGCAAGAT 59.790 52.381 0.00 0.00 40.35 2.40
1272 1344 2.938451 CACCGTCATCGTGGTAGTACTA 59.062 50.000 0.00 0.00 36.50 1.82
1274 1346 3.201290 CCGTCATCGTGGTAGTACTACT 58.799 50.000 27.71 9.13 34.50 2.57
1275 1347 4.141937 ACCGTCATCGTGGTAGTACTACTA 60.142 45.833 27.71 21.66 36.50 1.82
1440 1636 1.101049 AGTTGCACTTTGGTGTCCGG 61.101 55.000 0.00 0.00 44.65 5.14
1491 1687 0.542333 GAGGCTTCCCTAACCTGGAC 59.458 60.000 0.00 0.00 43.12 4.02
1506 1702 4.693532 GACACGCTCCATGTCCAA 57.306 55.556 0.00 0.00 40.56 3.53
1614 1967 8.834004 ATGATATAAGTTATAACCGCCTCCTA 57.166 34.615 12.05 0.00 0.00 2.94
1636 2082 5.301835 ACTGCTGCATGATAAGATACCTT 57.698 39.130 1.31 0.00 36.43 3.50
1638 2084 4.392047 TGCTGCATGATAAGATACCTTGG 58.608 43.478 0.00 0.00 33.94 3.61
1846 2318 0.463295 TTATCGCGGAGAGAGGTCGT 60.463 55.000 6.13 0.00 41.36 4.34
2130 2616 1.024271 TGAGCCTCTTGTGTTGCAAC 58.976 50.000 22.83 22.83 32.90 4.17
2136 2622 2.942376 CCTCTTGTGTTGCAACAGTACA 59.058 45.455 31.81 22.73 40.05 2.90
2163 2651 4.256920 CCTAGCTAGACTTTGTGTTGCAT 58.743 43.478 22.70 0.00 0.00 3.96
2234 2740 4.379813 GCATGATGAGGTTGTTTGTACCAG 60.380 45.833 0.00 0.00 38.16 4.00
2258 2869 6.461110 AATTCTGGAATTCTTATGTGGCTG 57.539 37.500 5.23 0.00 36.34 4.85
2352 2969 8.902806 TGAAGGTATGTTTTATATTCAGCTTGG 58.097 33.333 0.00 0.00 0.00 3.61
2360 2977 6.827586 TTTATATTCAGCTTGGTTTTCGGT 57.172 33.333 0.00 0.00 0.00 4.69
2363 2980 6.827586 ATATTCAGCTTGGTTTTCGGTTTA 57.172 33.333 0.00 0.00 0.00 2.01
2368 2985 5.048991 TCAGCTTGGTTTTCGGTTTATCTTC 60.049 40.000 0.00 0.00 0.00 2.87
2371 2988 5.508320 GCTTGGTTTTCGGTTTATCTTCCAA 60.508 40.000 0.00 0.00 0.00 3.53
2383 3000 7.308435 GGTTTATCTTCCAAGTCAATTGTGAG 58.692 38.462 5.13 0.00 37.17 3.51
2413 3030 4.035612 TCTAGCAGTACTCCAGTCAGTT 57.964 45.455 0.00 0.00 0.00 3.16
2415 3032 5.567430 TCTAGCAGTACTCCAGTCAGTTAA 58.433 41.667 0.00 0.00 0.00 2.01
2436 3071 7.281100 AGTTAATAGCTAGTCCAACTGCAATTC 59.719 37.037 8.22 0.00 0.00 2.17
2439 3074 3.019564 GCTAGTCCAACTGCAATTCCAT 58.980 45.455 0.00 0.00 0.00 3.41
2443 3078 5.587388 AGTCCAACTGCAATTCCATTATG 57.413 39.130 0.00 0.00 0.00 1.90
2446 3081 5.577945 GTCCAACTGCAATTCCATTATGTTG 59.422 40.000 0.00 0.00 34.96 3.33
2465 3100 4.142293 TGTTGTGCAGTTGTTAGCATGAAA 60.142 37.500 0.00 0.00 43.44 2.69
2473 3108 7.331440 TGCAGTTGTTAGCATGAAATAATTTGG 59.669 33.333 0.00 0.00 35.51 3.28
2483 3118 9.701098 AGCATGAAATAATTTGGTATGCATTAG 57.299 29.630 3.54 0.00 41.22 1.73
2484 3119 9.695526 GCATGAAATAATTTGGTATGCATTAGA 57.304 29.630 3.54 0.00 39.25 2.10
2490 3125 8.725606 ATAATTTGGTATGCATTAGATTGGGT 57.274 30.769 3.54 0.00 0.00 4.51
2494 3129 5.132502 TGGTATGCATTAGATTGGGTTCAG 58.867 41.667 3.54 0.00 0.00 3.02
2497 3132 3.282021 TGCATTAGATTGGGTTCAGCTC 58.718 45.455 0.00 0.00 0.00 4.09
2507 3142 7.349598 AGATTGGGTTCAGCTCAAAATAGTAT 58.650 34.615 0.00 0.00 41.53 2.12
2603 3240 2.851263 TACTGGTTACTGCAACTGGG 57.149 50.000 0.00 0.00 37.30 4.45
2654 3297 6.655003 ACAACATCGAAGAAACATACTCCAAT 59.345 34.615 0.00 0.00 43.58 3.16
2664 3307 3.878778 ACATACTCCAATCCTGCTTCAC 58.121 45.455 0.00 0.00 0.00 3.18
2720 3363 4.094887 CACTCATAAAATTACACAGCGGCT 59.905 41.667 0.00 0.00 0.00 5.52
2721 3364 4.094887 ACTCATAAAATTACACAGCGGCTG 59.905 41.667 27.43 27.43 37.52 4.85
2747 3390 2.436115 GCCTGTTCCGTGGCCTAC 60.436 66.667 3.32 0.00 43.11 3.18
2748 3391 2.955881 GCCTGTTCCGTGGCCTACT 61.956 63.158 3.32 0.00 43.11 2.57
2749 3392 1.079127 CCTGTTCCGTGGCCTACTG 60.079 63.158 3.32 0.00 0.00 2.74
2750 3393 1.741770 CTGTTCCGTGGCCTACTGC 60.742 63.158 3.32 0.00 40.16 4.40
2759 3402 3.527641 GCCTACTGCCGCTCTACT 58.472 61.111 0.00 0.00 0.00 2.57
2760 3403 2.716814 GCCTACTGCCGCTCTACTA 58.283 57.895 0.00 0.00 0.00 1.82
2761 3404 0.311477 GCCTACTGCCGCTCTACTAC 59.689 60.000 0.00 0.00 0.00 2.73
2762 3405 0.953003 CCTACTGCCGCTCTACTACC 59.047 60.000 0.00 0.00 0.00 3.18
2763 3406 0.953003 CTACTGCCGCTCTACTACCC 59.047 60.000 0.00 0.00 0.00 3.69
2764 3407 0.256752 TACTGCCGCTCTACTACCCA 59.743 55.000 0.00 0.00 0.00 4.51
2765 3408 1.321074 ACTGCCGCTCTACTACCCAC 61.321 60.000 0.00 0.00 0.00 4.61
2766 3409 2.337749 CTGCCGCTCTACTACCCACG 62.338 65.000 0.00 0.00 0.00 4.94
2767 3410 3.117372 CCGCTCTACTACCCACGG 58.883 66.667 0.00 0.00 0.00 4.94
2768 3411 1.751927 CCGCTCTACTACCCACGGT 60.752 63.158 0.00 0.00 40.16 4.83
2769 3412 1.432251 CGCTCTACTACCCACGGTG 59.568 63.158 0.00 0.00 36.19 4.94
2770 3413 1.028330 CGCTCTACTACCCACGGTGA 61.028 60.000 10.28 0.00 36.19 4.02
2771 3414 0.739561 GCTCTACTACCCACGGTGAG 59.260 60.000 10.28 0.00 36.19 3.51
2772 3415 1.390565 CTCTACTACCCACGGTGAGG 58.609 60.000 10.28 11.54 36.19 3.86
2773 3416 0.682209 TCTACTACCCACGGTGAGGC 60.682 60.000 10.28 0.00 36.19 4.70
2774 3417 1.673808 CTACTACCCACGGTGAGGCC 61.674 65.000 10.28 0.00 36.19 5.19
2775 3418 2.444004 TACTACCCACGGTGAGGCCA 62.444 60.000 10.28 0.81 36.19 5.36
2776 3419 3.310860 CTACCCACGGTGAGGCCAC 62.311 68.421 10.28 0.00 42.46 5.01
2797 3440 3.270877 CCCGCTAAACAGTCTTGCTATT 58.729 45.455 0.00 0.00 0.00 1.73
2814 3457 1.617947 ATTCCGCAGTCCCCTGAGAC 61.618 60.000 0.00 0.00 40.57 3.36
2817 3460 1.668101 CCGCAGTCCCCTGAGACTAC 61.668 65.000 0.00 0.00 45.38 2.73
2819 3462 1.562783 GCAGTCCCCTGAGACTACTT 58.437 55.000 0.00 0.00 45.38 2.24
2826 3469 4.283722 GTCCCCTGAGACTACTTCTTGAAA 59.716 45.833 0.00 0.00 33.22 2.69
2832 3475 6.986817 CCTGAGACTACTTCTTGAAAGTTTCA 59.013 38.462 14.35 14.35 38.04 2.69
2884 3527 2.163010 CAGTGGGATTGCTGTTGTGATC 59.837 50.000 0.00 0.00 0.00 2.92
2888 3531 2.821969 GGGATTGCTGTTGTGATCTGTT 59.178 45.455 0.00 0.00 0.00 3.16
2896 3539 4.274459 GCTGTTGTGATCTGTTCTCTGTTT 59.726 41.667 0.00 0.00 0.00 2.83
2916 3559 0.035056 GGGCCTGCTGTTGTGAGTAT 60.035 55.000 0.84 0.00 0.00 2.12
2954 3597 0.319986 TATTCCGCTGCGTGTTGTGA 60.320 50.000 21.59 6.81 0.00 3.58
2956 3599 2.916502 TTCCGCTGCGTGTTGTGACT 62.917 55.000 21.59 0.00 0.00 3.41
2957 3600 2.246397 CGCTGCGTGTTGTGACTG 59.754 61.111 14.93 0.00 0.00 3.51
2973 3616 6.951062 TGTGACTGTATTGGTTTGAAATCA 57.049 33.333 0.00 0.00 0.00 2.57
3002 3645 2.468831 TGCGCAATTTCCAACAAGTTC 58.531 42.857 8.16 0.00 0.00 3.01
3011 3654 7.632721 CAATTTCCAACAAGTTCAATTTCAGG 58.367 34.615 0.00 0.00 0.00 3.86
3066 3709 0.101219 TGAGATCGATCGGTGTGCTG 59.899 55.000 19.33 0.00 0.00 4.41
3067 3710 0.101399 GAGATCGATCGGTGTGCTGT 59.899 55.000 19.33 0.00 0.00 4.40
3075 3718 3.309682 CGATCGGTGTGCTGTTATTGATT 59.690 43.478 7.38 0.00 0.00 2.57
3082 3725 6.348132 CGGTGTGCTGTTATTGATTTAACTGA 60.348 38.462 5.70 0.00 34.66 3.41
3083 3726 7.023575 GGTGTGCTGTTATTGATTTAACTGAG 58.976 38.462 5.70 0.00 34.66 3.35
3116 3761 4.136796 TGATGAATATTGTGTAGCCTGCC 58.863 43.478 0.00 0.00 0.00 4.85
3120 3765 0.107214 TATTGTGTAGCCTGCCTGCC 60.107 55.000 0.00 0.00 0.00 4.85
3145 3790 0.755686 GCCTCCACTCCACTCCATAG 59.244 60.000 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.038048 GGATTCCAGTTCATTGGATTTTTCTC 58.962 38.462 0.00 0.00 46.22 2.87
1 2 6.727697 AGGATTCCAGTTCATTGGATTTTTCT 59.272 34.615 5.29 0.00 46.22 2.52
2 3 6.939622 AGGATTCCAGTTCATTGGATTTTTC 58.060 36.000 5.29 0.00 46.22 2.29
4 5 5.423290 GGAGGATTCCAGTTCATTGGATTTT 59.577 40.000 5.29 0.00 46.22 1.82
6 7 4.540715 GGAGGATTCCAGTTCATTGGATT 58.459 43.478 5.29 0.00 46.22 3.01
7 8 4.176120 GGAGGATTCCAGTTCATTGGAT 57.824 45.455 5.29 0.00 46.22 3.41
8 9 3.652057 GGAGGATTCCAGTTCATTGGA 57.348 47.619 5.29 0.00 45.34 3.53
32 33 9.640952 TTTGGATCGAAGGATTTTTATAGGAAT 57.359 29.630 0.00 0.00 31.51 3.01
33 34 9.120538 CTTTGGATCGAAGGATTTTTATAGGAA 57.879 33.333 0.00 0.00 31.51 3.36
34 35 8.491134 TCTTTGGATCGAAGGATTTTTATAGGA 58.509 33.333 0.00 0.00 31.51 2.94
35 36 8.677148 TCTTTGGATCGAAGGATTTTTATAGG 57.323 34.615 0.00 0.00 31.51 2.57
36 37 8.286097 GCTCTTTGGATCGAAGGATTTTTATAG 58.714 37.037 2.79 0.00 31.51 1.31
37 38 7.228706 GGCTCTTTGGATCGAAGGATTTTTATA 59.771 37.037 2.79 0.00 31.51 0.98
38 39 6.039829 GGCTCTTTGGATCGAAGGATTTTTAT 59.960 38.462 2.79 0.00 31.51 1.40
39 40 5.357032 GGCTCTTTGGATCGAAGGATTTTTA 59.643 40.000 2.79 0.00 31.51 1.52
40 41 4.158579 GGCTCTTTGGATCGAAGGATTTTT 59.841 41.667 2.79 0.00 31.51 1.94
41 42 3.696548 GGCTCTTTGGATCGAAGGATTTT 59.303 43.478 2.79 0.00 31.51 1.82
42 43 3.282885 GGCTCTTTGGATCGAAGGATTT 58.717 45.455 2.79 0.00 31.51 2.17
43 44 2.239654 TGGCTCTTTGGATCGAAGGATT 59.760 45.455 2.79 0.00 31.51 3.01
44 45 1.839994 TGGCTCTTTGGATCGAAGGAT 59.160 47.619 2.79 0.00 34.96 3.24
45 46 1.208052 CTGGCTCTTTGGATCGAAGGA 59.792 52.381 2.40 2.40 0.00 3.36
46 47 1.065854 ACTGGCTCTTTGGATCGAAGG 60.066 52.381 0.00 1.01 0.00 3.46
47 48 2.393271 ACTGGCTCTTTGGATCGAAG 57.607 50.000 0.00 2.02 0.00 3.79
48 49 2.859165 AACTGGCTCTTTGGATCGAA 57.141 45.000 0.00 0.00 0.00 3.71
49 50 3.096852 TCTAACTGGCTCTTTGGATCGA 58.903 45.455 0.00 0.00 0.00 3.59
50 51 3.131223 TCTCTAACTGGCTCTTTGGATCG 59.869 47.826 0.00 0.00 0.00 3.69
51 52 4.744795 TCTCTAACTGGCTCTTTGGATC 57.255 45.455 0.00 0.00 0.00 3.36
52 53 5.435291 CAATCTCTAACTGGCTCTTTGGAT 58.565 41.667 0.00 0.00 0.00 3.41
53 54 4.323792 CCAATCTCTAACTGGCTCTTTGGA 60.324 45.833 0.00 0.00 34.40 3.53
54 55 3.944015 CCAATCTCTAACTGGCTCTTTGG 59.056 47.826 0.00 0.00 0.00 3.28
55 56 4.836825 TCCAATCTCTAACTGGCTCTTTG 58.163 43.478 0.00 0.00 0.00 2.77
56 57 5.190528 TGATCCAATCTCTAACTGGCTCTTT 59.809 40.000 0.00 0.00 0.00 2.52
57 58 4.718774 TGATCCAATCTCTAACTGGCTCTT 59.281 41.667 0.00 0.00 0.00 2.85
58 59 4.293494 TGATCCAATCTCTAACTGGCTCT 58.707 43.478 0.00 0.00 0.00 4.09
59 60 4.679373 TGATCCAATCTCTAACTGGCTC 57.321 45.455 0.00 0.00 0.00 4.70
60 61 4.657504 TGATGATCCAATCTCTAACTGGCT 59.342 41.667 0.00 0.00 0.00 4.75
61 62 4.965814 TGATGATCCAATCTCTAACTGGC 58.034 43.478 0.00 0.00 0.00 4.85
62 63 8.461249 AAAATGATGATCCAATCTCTAACTGG 57.539 34.615 0.00 0.00 0.00 4.00
73 74 9.919416 TCTCCTACAAATAAAATGATGATCCAA 57.081 29.630 0.00 0.00 0.00 3.53
74 75 9.919416 TTCTCCTACAAATAAAATGATGATCCA 57.081 29.630 0.00 0.00 0.00 3.41
79 80 9.708222 CGACTTTCTCCTACAAATAAAATGATG 57.292 33.333 0.00 0.00 0.00 3.07
80 81 9.449719 ACGACTTTCTCCTACAAATAAAATGAT 57.550 29.630 0.00 0.00 0.00 2.45
81 82 8.842358 ACGACTTTCTCCTACAAATAAAATGA 57.158 30.769 0.00 0.00 0.00 2.57
82 83 9.893305 AAACGACTTTCTCCTACAAATAAAATG 57.107 29.630 0.00 0.00 0.00 2.32
88 89 9.893305 CAATTTAAACGACTTTCTCCTACAAAT 57.107 29.630 0.00 0.00 0.00 2.32
89 90 9.111613 TCAATTTAAACGACTTTCTCCTACAAA 57.888 29.630 0.00 0.00 0.00 2.83
90 91 8.665643 TCAATTTAAACGACTTTCTCCTACAA 57.334 30.769 0.00 0.00 0.00 2.41
91 92 8.665643 TTCAATTTAAACGACTTTCTCCTACA 57.334 30.769 0.00 0.00 0.00 2.74
112 113 3.814283 GCCCATGAAACAGCATTTTTCAA 59.186 39.130 10.34 0.00 44.14 2.69
162 164 2.198304 ATTGGGGAACGGAGAGGTGC 62.198 60.000 0.00 0.00 0.00 5.01
172 174 1.749063 GGAACCGAATGATTGGGGAAC 59.251 52.381 10.99 1.90 33.93 3.62
192 194 0.041833 TTGGGGAGGAGAGGAGTGAG 59.958 60.000 0.00 0.00 0.00 3.51
267 269 1.843376 CCTGGTGTGGAGGGTCACT 60.843 63.158 0.00 0.00 38.40 3.41
277 279 4.767255 GCCGCTCCTCCTGGTGTG 62.767 72.222 0.00 0.00 37.16 3.82
342 355 0.108756 GAGGAAGTCGTACAGGGTGC 60.109 60.000 0.00 0.00 0.00 5.01
760 785 2.451493 TCTTGGACCCCCTTGGCA 60.451 61.111 0.00 0.00 37.83 4.92
781 806 1.228154 GGGGCGGTTGACAAAGACT 60.228 57.895 0.00 0.00 0.00 3.24
975 1004 2.611292 GACGAGGATCTTTCAAGCATGG 59.389 50.000 0.00 0.00 0.00 3.66
1236 1308 1.145325 ACGGTGTTGGTAATCCCCAAA 59.855 47.619 0.00 0.00 45.72 3.28
1272 1344 8.525290 AGCAAATTAAATTAGCAGGATGTAGT 57.475 30.769 0.00 0.00 39.31 2.73
1274 1346 8.748412 ACAAGCAAATTAAATTAGCAGGATGTA 58.252 29.630 0.00 0.00 39.31 2.29
1275 1347 7.546667 CACAAGCAAATTAAATTAGCAGGATGT 59.453 33.333 0.00 0.00 39.31 3.06
1440 1636 3.686726 CAGATACTTTCTTGACAGCACCC 59.313 47.826 0.00 0.00 29.93 4.61
1491 1687 2.093306 TTACTTGGACATGGAGCGTG 57.907 50.000 0.00 0.00 0.00 5.34
1506 1702 9.788889 AGTGTACTTAAGCTAACCAATTTTACT 57.211 29.630 1.29 0.00 0.00 2.24
1614 1967 4.970860 AGGTATCTTATCATGCAGCAGT 57.029 40.909 0.00 0.00 0.00 4.40
1636 2082 4.445052 GCGCGTACATAACATACATAACCA 59.555 41.667 8.43 0.00 0.00 3.67
1638 2084 5.400188 TCAGCGCGTACATAACATACATAAC 59.600 40.000 8.43 0.00 0.00 1.89
2130 2616 5.038651 AGTCTAGCTAGGTACCTGTACTG 57.961 47.826 25.33 11.57 36.36 2.74
2136 2622 4.675038 ACACAAAGTCTAGCTAGGTACCT 58.325 43.478 20.57 20.57 0.00 3.08
2163 2651 5.394224 GGAGAAATTCATGTCCGAGTAGTCA 60.394 44.000 0.00 0.00 0.00 3.41
2258 2869 0.618458 TGTTACTCCCACCAGCATCC 59.382 55.000 0.00 0.00 0.00 3.51
2323 2937 8.903820 AGCTGAATATAAAACATACCTTCAACC 58.096 33.333 0.00 0.00 0.00 3.77
2329 2943 8.823220 AACCAAGCTGAATATAAAACATACCT 57.177 30.769 0.00 0.00 0.00 3.08
2352 2969 6.308371 TGACTTGGAAGATAAACCGAAAAC 57.692 37.500 0.00 0.00 0.00 2.43
2360 2977 6.489700 TGCTCACAATTGACTTGGAAGATAAA 59.510 34.615 13.59 0.00 39.30 1.40
2363 2980 4.401022 TGCTCACAATTGACTTGGAAGAT 58.599 39.130 13.59 0.00 39.30 2.40
2368 2985 1.542915 CCCTGCTCACAATTGACTTGG 59.457 52.381 13.59 6.26 39.30 3.61
2371 2988 0.403271 AGCCCTGCTCACAATTGACT 59.597 50.000 13.59 0.00 30.62 3.41
2397 3014 6.458232 AGCTATTAACTGACTGGAGTACTG 57.542 41.667 0.00 0.00 0.00 2.74
2399 3016 7.255208 GGACTAGCTATTAACTGACTGGAGTAC 60.255 44.444 0.00 0.00 0.00 2.73
2400 3017 6.771749 GGACTAGCTATTAACTGACTGGAGTA 59.228 42.308 0.00 0.00 0.00 2.59
2401 3018 5.595133 GGACTAGCTATTAACTGACTGGAGT 59.405 44.000 0.00 0.00 0.00 3.85
2402 3019 5.594725 TGGACTAGCTATTAACTGACTGGAG 59.405 44.000 0.00 0.00 0.00 3.86
2406 3023 6.628398 GCAGTTGGACTAGCTATTAACTGACT 60.628 42.308 26.57 12.04 44.59 3.41
2407 3024 5.520649 GCAGTTGGACTAGCTATTAACTGAC 59.479 44.000 26.57 19.14 44.59 3.51
2413 3030 6.055588 GGAATTGCAGTTGGACTAGCTATTA 58.944 40.000 0.00 0.00 32.78 0.98
2415 3032 4.080356 TGGAATTGCAGTTGGACTAGCTAT 60.080 41.667 0.00 0.00 0.00 2.97
2436 3071 4.858692 GCTAACAACTGCACAACATAATGG 59.141 41.667 0.00 0.00 0.00 3.16
2439 3074 5.240403 TCATGCTAACAACTGCACAACATAA 59.760 36.000 0.00 0.00 42.26 1.90
2443 3078 3.624326 TCATGCTAACAACTGCACAAC 57.376 42.857 0.00 0.00 42.26 3.32
2446 3081 7.816945 AATTATTTCATGCTAACAACTGCAC 57.183 32.000 0.00 0.00 42.26 4.57
2465 3100 8.725606 ACCCAATCTAATGCATACCAAATTAT 57.274 30.769 0.00 0.00 0.00 1.28
2473 3108 4.823989 AGCTGAACCCAATCTAATGCATAC 59.176 41.667 0.00 0.00 0.00 2.39
2483 3118 5.904362 ACTATTTTGAGCTGAACCCAATC 57.096 39.130 0.00 0.00 0.00 2.67
2484 3119 7.961326 AATACTATTTTGAGCTGAACCCAAT 57.039 32.000 0.00 0.00 0.00 3.16
2575 3212 7.817962 CAGTTGCAGTAACCAGTAATACTACTT 59.182 37.037 0.00 0.00 40.24 2.24
2587 3224 1.534203 TGCCCAGTTGCAGTAACCA 59.466 52.632 0.00 0.00 40.24 3.67
2654 3297 2.655090 TGGTTGAATGTGAAGCAGGA 57.345 45.000 0.00 0.00 0.00 3.86
2664 3307 9.311916 TGTTCAGTAAGAAAATTTGGTTGAATG 57.688 29.630 0.00 0.00 38.13 2.67
2742 3385 0.311477 GTAGTAGAGCGGCAGTAGGC 59.689 60.000 1.45 0.00 43.74 3.93
2743 3386 0.953003 GGTAGTAGAGCGGCAGTAGG 59.047 60.000 1.45 0.00 0.00 3.18
2744 3387 0.953003 GGGTAGTAGAGCGGCAGTAG 59.047 60.000 1.45 0.00 0.00 2.57
2745 3388 0.256752 TGGGTAGTAGAGCGGCAGTA 59.743 55.000 1.45 0.00 0.00 2.74
2746 3389 1.000019 TGGGTAGTAGAGCGGCAGT 60.000 57.895 1.45 0.00 0.00 4.40
2747 3390 1.437986 GTGGGTAGTAGAGCGGCAG 59.562 63.158 1.45 0.00 0.00 4.85
2748 3391 2.412323 CGTGGGTAGTAGAGCGGCA 61.412 63.158 1.45 0.00 0.00 5.69
2749 3392 2.412112 CGTGGGTAGTAGAGCGGC 59.588 66.667 0.00 0.00 0.00 6.53
2750 3393 1.751927 ACCGTGGGTAGTAGAGCGG 60.752 63.158 0.00 0.00 44.10 5.52
2751 3394 1.028330 TCACCGTGGGTAGTAGAGCG 61.028 60.000 0.00 0.00 32.11 5.03
2752 3395 0.739561 CTCACCGTGGGTAGTAGAGC 59.260 60.000 0.00 0.00 32.11 4.09
2753 3396 1.390565 CCTCACCGTGGGTAGTAGAG 58.609 60.000 0.00 0.00 32.11 2.43
2754 3397 0.682209 GCCTCACCGTGGGTAGTAGA 60.682 60.000 0.00 0.00 32.11 2.59
2755 3398 1.673808 GGCCTCACCGTGGGTAGTAG 61.674 65.000 0.00 0.00 32.11 2.57
2756 3399 1.683365 GGCCTCACCGTGGGTAGTA 60.683 63.158 0.00 0.00 32.11 1.82
2757 3400 3.001406 GGCCTCACCGTGGGTAGT 61.001 66.667 0.00 0.00 32.11 2.73
2758 3401 3.000819 TGGCCTCACCGTGGGTAG 61.001 66.667 3.32 0.00 43.94 3.18
2759 3402 3.315949 GTGGCCTCACCGTGGGTA 61.316 66.667 3.32 0.00 43.94 3.69
2767 3410 2.038837 GTTTAGCGGGTGGCCTCAC 61.039 63.158 3.32 0.00 45.17 3.51
2768 3411 2.349755 GTTTAGCGGGTGGCCTCA 59.650 61.111 3.32 0.00 45.17 3.86
2769 3412 1.745489 CTGTTTAGCGGGTGGCCTC 60.745 63.158 3.32 0.00 45.17 4.70
2770 3413 2.351276 CTGTTTAGCGGGTGGCCT 59.649 61.111 3.32 0.00 45.17 5.19
2771 3414 2.033602 ACTGTTTAGCGGGTGGCC 59.966 61.111 0.00 0.00 45.17 5.36
2772 3415 0.605589 AAGACTGTTTAGCGGGTGGC 60.606 55.000 0.00 0.00 44.05 5.01
2773 3416 1.156736 CAAGACTGTTTAGCGGGTGG 58.843 55.000 0.00 0.00 0.00 4.61
2774 3417 0.517316 GCAAGACTGTTTAGCGGGTG 59.483 55.000 0.00 0.00 0.00 4.61
2775 3418 0.396811 AGCAAGACTGTTTAGCGGGT 59.603 50.000 0.00 0.00 0.00 5.28
2776 3419 2.380084 TAGCAAGACTGTTTAGCGGG 57.620 50.000 0.00 0.00 0.00 6.13
2777 3420 3.309954 GGAATAGCAAGACTGTTTAGCGG 59.690 47.826 0.00 0.00 28.46 5.52
2778 3421 3.000322 CGGAATAGCAAGACTGTTTAGCG 60.000 47.826 0.00 0.00 28.46 4.26
2884 3527 1.242076 CAGGCCCAAACAGAGAACAG 58.758 55.000 0.00 0.00 0.00 3.16
2888 3531 1.073722 CAGCAGGCCCAAACAGAGA 59.926 57.895 0.00 0.00 0.00 3.10
2896 3539 1.414866 TACTCACAACAGCAGGCCCA 61.415 55.000 0.00 0.00 0.00 5.36
2916 3559 1.067295 ACAGCAGAGGACCCATCAAA 58.933 50.000 0.00 0.00 0.00 2.69
2954 3597 5.048991 GGACGTGATTTCAAACCAATACAGT 60.049 40.000 0.00 0.00 0.00 3.55
2956 3599 5.049060 CAGGACGTGATTTCAAACCAATACA 60.049 40.000 0.00 0.00 0.00 2.29
2957 3600 5.048991 ACAGGACGTGATTTCAAACCAATAC 60.049 40.000 0.00 0.00 0.00 1.89
2973 3616 0.040425 GAAATTGCGCAACAGGACGT 60.040 50.000 27.64 4.31 0.00 4.34
3002 3645 2.169144 GGGATGCCCTTTCCTGAAATTG 59.831 50.000 0.00 0.00 41.34 2.32
3011 3654 2.193248 CGAGGGGGATGCCCTTTC 59.807 66.667 23.18 18.07 44.66 2.62
3028 3671 7.275341 CGATCTCACTAATTTCAGATAGATGCC 59.725 40.741 0.00 0.00 0.00 4.40
3066 3709 4.095782 TGCGGCCTCAGTTAAATCAATAAC 59.904 41.667 0.00 0.00 36.28 1.89
3067 3710 4.265893 TGCGGCCTCAGTTAAATCAATAA 58.734 39.130 0.00 0.00 0.00 1.40
3075 3718 0.618458 AATCCTGCGGCCTCAGTTAA 59.382 50.000 21.00 7.04 32.32 2.01
3082 3725 0.184451 ATTCATCAATCCTGCGGCCT 59.816 50.000 0.00 0.00 0.00 5.19
3083 3726 1.896220 TATTCATCAATCCTGCGGCC 58.104 50.000 0.00 0.00 0.00 6.13
3102 3745 1.379044 GGCAGGCAGGCTACACAAT 60.379 57.895 0.00 0.00 40.24 2.71
3120 3765 1.748122 GTGGAGTGGAGGCATGCAG 60.748 63.158 21.36 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.