Multiple sequence alignment - TraesCS3B01G325500

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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 TraesCS3B01G325500 chr3B 100.000 3341 0 0 1 3341 526647900 526651240 0.000000e+00 6170
1 TraesCS3B01G325500 chr3B 96.009 927 29 1 1 919 651709504 651708578 0.000000e+00 1500
2 TraesCS3B01G325500 chr3B 89.641 753 78 0 920 1672 358579863 358580615 0.000000e+00 959
3 TraesCS3B01G325500 chr4B 91.923 2080 154 6 919 2994 250849502 250847433 0.000000e+00 2898
4 TraesCS3B01G325500 chr4B 91.390 2079 164 7 919 2994 250793388 250791322 0.000000e+00 2833
5 TraesCS3B01G325500 chr4B 86.222 1604 184 20 923 2519 242355854 242357427 0.000000e+00 1703
6 TraesCS3B01G325500 chr4B 95.577 927 32 2 1 919 538031714 538030789 0.000000e+00 1476
7 TraesCS3B01G325500 chr6B 88.410 2088 184 21 919 2994 287346129 287344088 0.000000e+00 2462
8 TraesCS3B01G325500 chr6B 95.793 927 30 5 1 919 20139080 20140005 0.000000e+00 1487
9 TraesCS3B01G325500 chr6B 95.361 927 33 6 1 919 454106611 454105687 0.000000e+00 1465
10 TraesCS3B01G325500 chr6B 91.284 218 16 3 3124 3340 287326661 287326446 9.060000e-76 294
11 TraesCS3B01G325500 chr5B 89.726 1606 155 8 919 2516 140672337 140673940 0.000000e+00 2043
12 TraesCS3B01G325500 chr5B 95.469 927 34 1 1 919 483238352 483239278 0.000000e+00 1472
13 TraesCS3B01G325500 chr5B 95.361 927 34 2 1 919 580821935 580822860 0.000000e+00 1465
14 TraesCS3B01G325500 chr2B 88.612 1607 166 16 919 2516 346395768 346394170 0.000000e+00 1938
15 TraesCS3B01G325500 chr2B 95.469 927 34 1 1 919 569336421 569335495 0.000000e+00 1472
16 TraesCS3B01G325500 chr7B 87.508 1601 164 19 919 2512 266107869 266109440 0.000000e+00 1816
17 TraesCS3B01G325500 chr7B 95.793 927 29 3 1 919 706622362 706621438 0.000000e+00 1487
18 TraesCS3B01G325500 chr7B 90.728 755 69 1 919 1672 152828023 152828777 0.000000e+00 1005
19 TraesCS3B01G325500 chr7B 89.920 754 76 0 919 1672 173624034 173624787 0.000000e+00 972
20 TraesCS3B01G325500 chr7B 90.741 216 14 6 3130 3341 560818171 560817958 1.960000e-72 283
21 TraesCS3B01G325500 chr7B 86.087 115 14 2 3013 3125 358820869 358820983 4.530000e-24 122
22 TraesCS3B01G325500 chrUn 95.601 932 33 5 1 925 216078065 216078995 0.000000e+00 1487
23 TraesCS3B01G325500 chrUn 88.350 103 10 2 3028 3128 269108215 269108113 4.530000e-24 122
24 TraesCS3B01G325500 chr7D 88.779 1007 89 20 1529 2517 368269779 368270779 0.000000e+00 1212
25 TraesCS3B01G325500 chr7D 92.430 568 35 5 2429 2992 287512020 287512583 0.000000e+00 804
26 TraesCS3B01G325500 chr7D 91.244 217 17 2 3124 3340 287532181 287532395 9.060000e-76 294
27 TraesCS3B01G325500 chr7D 90.367 218 20 1 3124 3341 307642837 307643053 5.460000e-73 285
28 TraesCS3B01G325500 chr3D 88.648 1013 90 21 1523 2517 230428571 230429576 0.000000e+00 1210
29 TraesCS3B01G325500 chr3D 91.259 572 39 9 2431 2992 230429524 230430094 0.000000e+00 769
30 TraesCS3B01G325500 chr3D 91.364 220 17 2 3124 3341 230461452 230461671 1.950000e-77 300
31 TraesCS3B01G325500 chr4D 88.340 1012 96 18 1523 2517 163979638 163980644 0.000000e+00 1195
32 TraesCS3B01G325500 chr4D 90.419 908 76 10 1529 2431 423136309 423137210 0.000000e+00 1184
33 TraesCS3B01G325500 chr4D 92.430 568 37 5 2429 2992 143388652 143389217 0.000000e+00 806
34 TraesCS3B01G325500 chr4D 91.740 569 41 6 2429 2992 365592696 365592129 0.000000e+00 785
35 TraesCS3B01G325500 chr4D 91.404 570 41 8 2429 2992 163980590 163981157 0.000000e+00 774
36 TraesCS3B01G325500 chr4D 92.925 212 15 0 3130 3341 143804138 143803927 3.240000e-80 309
37 TraesCS3B01G325500 chr4D 92.857 210 11 4 3136 3341 130099068 130098859 5.420000e-78 302
38 TraesCS3B01G325500 chr4D 90.213 235 18 5 3112 3341 215374888 215374654 5.420000e-78 302
39 TraesCS3B01G325500 chr4D 90.090 222 15 6 3127 3341 215376134 215375913 7.060000e-72 281
40 TraesCS3B01G325500 chr4D 86.087 115 14 2 3013 3125 166483409 166483523 4.530000e-24 122
41 TraesCS3B01G325500 chr6A 92.443 569 36 6 2431 2994 266387212 266387778 0.000000e+00 806
42 TraesCS3B01G325500 chr6A 92.105 570 38 7 2429 2992 152423674 152424242 0.000000e+00 797
43 TraesCS3B01G325500 chr6A 88.350 103 10 2 3028 3128 589707432 589707330 4.530000e-24 122
44 TraesCS3B01G325500 chr6A 88.350 103 10 2 3028 3128 589709433 589709331 4.530000e-24 122


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 TraesCS3B01G325500 chr3B 526647900 526651240 3340 False 6170.0 6170 100.0000 1 3341 1 chr3B.!!$F2 3340
1 TraesCS3B01G325500 chr3B 651708578 651709504 926 True 1500.0 1500 96.0090 1 919 1 chr3B.!!$R1 918
2 TraesCS3B01G325500 chr3B 358579863 358580615 752 False 959.0 959 89.6410 920 1672 1 chr3B.!!$F1 752
3 TraesCS3B01G325500 chr4B 250847433 250849502 2069 True 2898.0 2898 91.9230 919 2994 1 chr4B.!!$R2 2075
4 TraesCS3B01G325500 chr4B 250791322 250793388 2066 True 2833.0 2833 91.3900 919 2994 1 chr4B.!!$R1 2075
5 TraesCS3B01G325500 chr4B 242355854 242357427 1573 False 1703.0 1703 86.2220 923 2519 1 chr4B.!!$F1 1596
6 TraesCS3B01G325500 chr4B 538030789 538031714 925 True 1476.0 1476 95.5770 1 919 1 chr4B.!!$R3 918
7 TraesCS3B01G325500 chr6B 287344088 287346129 2041 True 2462.0 2462 88.4100 919 2994 1 chr6B.!!$R2 2075
8 TraesCS3B01G325500 chr6B 20139080 20140005 925 False 1487.0 1487 95.7930 1 919 1 chr6B.!!$F1 918
9 TraesCS3B01G325500 chr6B 454105687 454106611 924 True 1465.0 1465 95.3610 1 919 1 chr6B.!!$R3 918
10 TraesCS3B01G325500 chr5B 140672337 140673940 1603 False 2043.0 2043 89.7260 919 2516 1 chr5B.!!$F1 1597
11 TraesCS3B01G325500 chr5B 483238352 483239278 926 False 1472.0 1472 95.4690 1 919 1 chr5B.!!$F2 918
12 TraesCS3B01G325500 chr5B 580821935 580822860 925 False 1465.0 1465 95.3610 1 919 1 chr5B.!!$F3 918
13 TraesCS3B01G325500 chr2B 346394170 346395768 1598 True 1938.0 1938 88.6120 919 2516 1 chr2B.!!$R1 1597
14 TraesCS3B01G325500 chr2B 569335495 569336421 926 True 1472.0 1472 95.4690 1 919 1 chr2B.!!$R2 918
15 TraesCS3B01G325500 chr7B 266107869 266109440 1571 False 1816.0 1816 87.5080 919 2512 1 chr7B.!!$F3 1593
16 TraesCS3B01G325500 chr7B 706621438 706622362 924 True 1487.0 1487 95.7930 1 919 1 chr7B.!!$R2 918
17 TraesCS3B01G325500 chr7B 152828023 152828777 754 False 1005.0 1005 90.7280 919 1672 1 chr7B.!!$F1 753
18 TraesCS3B01G325500 chr7B 173624034 173624787 753 False 972.0 972 89.9200 919 1672 1 chr7B.!!$F2 753
19 TraesCS3B01G325500 chrUn 216078065 216078995 930 False 1487.0 1487 95.6010 1 925 1 chrUn.!!$F1 924
20 TraesCS3B01G325500 chr7D 368269779 368270779 1000 False 1212.0 1212 88.7790 1529 2517 1 chr7D.!!$F4 988
21 TraesCS3B01G325500 chr7D 287512020 287512583 563 False 804.0 804 92.4300 2429 2992 1 chr7D.!!$F1 563
22 TraesCS3B01G325500 chr3D 230428571 230430094 1523 False 989.5 1210 89.9535 1523 2992 2 chr3D.!!$F2 1469
23 TraesCS3B01G325500 chr4D 423136309 423137210 901 False 1184.0 1184 90.4190 1529 2431 1 chr4D.!!$F3 902
24 TraesCS3B01G325500 chr4D 163979638 163981157 1519 False 984.5 1195 89.8720 1523 2992 2 chr4D.!!$F4 1469
25 TraesCS3B01G325500 chr4D 143388652 143389217 565 False 806.0 806 92.4300 2429 2992 1 chr4D.!!$F1 563
26 TraesCS3B01G325500 chr4D 365592129 365592696 567 True 785.0 785 91.7400 2429 2992 1 chr4D.!!$R3 563
27 TraesCS3B01G325500 chr4D 215374654 215376134 1480 True 291.5 302 90.1515 3112 3341 2 chr4D.!!$R4 229
28 TraesCS3B01G325500 chr6A 266387212 266387778 566 False 806.0 806 92.4430 2431 2994 1 chr6A.!!$F2 563
29 TraesCS3B01G325500 chr6A 152423674 152424242 568 False 797.0 797 92.1050 2429 2992 1 chr6A.!!$F1 563

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
301 302 0.727970 CGAGAGGTCATCGTCGAAGT 59.272 55.0 0.0 0.0 35.48 3.01 F
1279 1290 0.681564 AGACGAACCTCCGCAGAGAT 60.682 55.0 0.0 0.0 43.39 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1338 1.007849 ATTTTGTGGCCGTTGCGAC 60.008 52.632 0.00 0.0 45.43 5.19 R
3042 3129 0.025513 CTATCAAACGAGCGCACTGC 59.974 55.000 11.47 0.0 46.98 4.40 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
28 29 1.530183 GGGAATCTGGCATGGAGGC 60.530 63.158 0.00 0.00 44.50 4.70
301 302 0.727970 CGAGAGGTCATCGTCGAAGT 59.272 55.000 0.00 0.00 35.48 3.01
338 339 4.828829 CGGTCATAAGAAAACCACCTAGT 58.171 43.478 0.00 0.00 32.35 2.57
788 798 3.073062 ACATATCCCTATCGCCAAGCTTT 59.927 43.478 0.00 0.00 0.00 3.51
848 858 7.226325 GGGATGAAGTCTTCAATCTTGTATCTG 59.774 40.741 18.93 0.00 43.95 2.90
903 913 1.186267 GCTATCCGGACACCCCCTAG 61.186 65.000 6.12 3.64 0.00 3.02
990 1000 1.079819 CGAAGCCCACAGTCATCGT 60.080 57.895 0.00 0.00 0.00 3.73
1074 1084 1.007336 GCAACCTCGACGACGTTCAT 61.007 55.000 0.13 0.00 40.69 2.57
1103 1113 2.879462 GAAGCGCGAGTACACCCG 60.879 66.667 12.10 0.00 0.00 5.28
1179 1189 1.452145 GCAAACCAGACAAGGCCGAA 61.452 55.000 0.00 0.00 0.00 4.30
1279 1290 0.681564 AGACGAACCTCCGCAGAGAT 60.682 55.000 0.00 0.00 43.39 2.75
1326 1337 1.279271 GAACTCTGCCTGGTGTACCAT 59.721 52.381 3.88 0.00 46.46 3.55
1327 1338 0.615331 ACTCTGCCTGGTGTACCATG 59.385 55.000 3.88 3.05 46.46 3.66
1333 1344 0.321210 CCTGGTGTACCATGTCGCAA 60.321 55.000 3.88 0.00 46.46 4.85
1502 1513 5.925509 TCCCCAAAGTAGATGCACTATAAC 58.074 41.667 0.00 0.00 33.39 1.89
1602 1615 9.982291 GCACTCGATGTATTAAAAGATGTTTTA 57.018 29.630 3.78 3.78 37.12 1.52
1887 1908 9.440773 GCATATACTTCATGGATTCATCACTTA 57.559 33.333 0.00 0.00 0.00 2.24
1966 1990 1.204146 CTACCCTTGCAGGCCTAAGA 58.796 55.000 15.70 0.00 32.73 2.10
2058 2082 6.881602 AGGAGAAGTTGAAGATGTATGGTTTC 59.118 38.462 0.00 0.00 0.00 2.78
2139 2169 3.636153 AAAGAGTATGACTCCTTGGCC 57.364 47.619 0.00 0.00 46.18 5.36
2169 2199 0.680921 CCAGCGTCATCCACCCATTT 60.681 55.000 0.00 0.00 0.00 2.32
2195 2226 5.641209 ACAAAGACATGAAGAAGAAGATCGG 59.359 40.000 0.00 0.00 0.00 4.18
2205 2236 4.211920 AGAAGAAGATCGGTAGGAAGGAG 58.788 47.826 0.00 0.00 0.00 3.69
2214 2245 3.116862 TCGGTAGGAAGGAGGACCATAAT 60.117 47.826 0.00 0.00 38.94 1.28
2384 2415 1.137086 CCACTACACGGGATGAAGAGG 59.863 57.143 0.00 0.00 0.00 3.69
2457 2528 5.450412 CCAGTTTGCTTATGTCTTGTGTGTT 60.450 40.000 0.00 0.00 0.00 3.32
2558 2632 9.256477 TGCTTATCTCGTTATATAAGTTTGGTG 57.744 33.333 0.00 0.00 37.78 4.17
2640 2717 6.039493 GTGGCTGCTCTTCAGTACTAGTTATA 59.961 42.308 0.00 0.00 44.66 0.98
2847 2927 8.947055 AGTACTACAACCGAAAAGTTAAGAAA 57.053 30.769 0.00 0.00 0.00 2.52
2868 2948 7.978982 AGAAACATCAGCACACACTTATATTC 58.021 34.615 0.00 0.00 0.00 1.75
2891 2971 4.679106 CGTCACTGGCAGACTAAGAATGAT 60.679 45.833 23.66 0.00 33.89 2.45
2994 3081 6.551385 AAAAATGTCAGACTAAGCACAGAG 57.449 37.500 1.31 0.00 0.00 3.35
2995 3082 3.883830 ATGTCAGACTAAGCACAGAGG 57.116 47.619 1.31 0.00 0.00 3.69
2996 3083 1.273606 TGTCAGACTAAGCACAGAGGC 59.726 52.381 1.31 0.00 0.00 4.70
2997 3084 1.273606 GTCAGACTAAGCACAGAGGCA 59.726 52.381 0.00 0.00 35.83 4.75
2998 3085 2.093764 GTCAGACTAAGCACAGAGGCAT 60.094 50.000 0.00 0.00 35.83 4.40
2999 3086 2.167281 TCAGACTAAGCACAGAGGCATC 59.833 50.000 0.00 0.00 35.83 3.91
3000 3087 2.093816 CAGACTAAGCACAGAGGCATCA 60.094 50.000 0.00 0.00 35.83 3.07
3001 3088 2.168106 AGACTAAGCACAGAGGCATCAG 59.832 50.000 0.00 0.00 35.83 2.90
3002 3089 1.905215 ACTAAGCACAGAGGCATCAGT 59.095 47.619 0.00 0.00 35.83 3.41
3003 3090 2.093764 ACTAAGCACAGAGGCATCAGTC 60.094 50.000 0.00 0.00 35.83 3.51
3004 3091 0.035630 AAGCACAGAGGCATCAGTCC 60.036 55.000 0.00 0.00 35.83 3.85
3005 3092 1.451028 GCACAGAGGCATCAGTCCC 60.451 63.158 0.00 0.00 0.00 4.46
3006 3093 1.153489 CACAGAGGCATCAGTCCCG 60.153 63.158 0.00 0.00 0.00 5.14
3007 3094 1.305297 ACAGAGGCATCAGTCCCGA 60.305 57.895 0.00 0.00 0.00 5.14
3008 3095 1.142748 CAGAGGCATCAGTCCCGAC 59.857 63.158 0.00 0.00 0.00 4.79
3009 3096 2.060980 AGAGGCATCAGTCCCGACC 61.061 63.158 0.00 0.00 0.00 4.79
3010 3097 3.083997 AGGCATCAGTCCCGACCC 61.084 66.667 0.00 0.00 0.00 4.46
3011 3098 4.176752 GGCATCAGTCCCGACCCC 62.177 72.222 0.00 0.00 0.00 4.95
3012 3099 4.176752 GCATCAGTCCCGACCCCC 62.177 72.222 0.00 0.00 0.00 5.40
3013 3100 2.365635 CATCAGTCCCGACCCCCT 60.366 66.667 0.00 0.00 0.00 4.79
3014 3101 2.041819 ATCAGTCCCGACCCCCTC 60.042 66.667 0.00 0.00 0.00 4.30
3015 3102 3.698263 ATCAGTCCCGACCCCCTCC 62.698 68.421 0.00 0.00 0.00 4.30
3037 3124 2.978824 GGCTCCGCCTCACACTAA 59.021 61.111 0.00 0.00 46.69 2.24
3038 3125 1.522569 GGCTCCGCCTCACACTAAT 59.477 57.895 0.00 0.00 46.69 1.73
3039 3126 0.811616 GGCTCCGCCTCACACTAATG 60.812 60.000 0.00 0.00 46.69 1.90
3040 3127 1.432270 GCTCCGCCTCACACTAATGC 61.432 60.000 0.00 0.00 0.00 3.56
3041 3128 1.148157 CTCCGCCTCACACTAATGCG 61.148 60.000 0.00 0.00 44.47 4.73
3042 3129 3.398920 CGCCTCACACTAATGCGG 58.601 61.111 0.00 0.00 41.42 5.69
3043 3130 2.813179 CGCCTCACACTAATGCGGC 61.813 63.158 0.00 0.00 41.42 6.53
3044 3131 1.745115 GCCTCACACTAATGCGGCA 60.745 57.895 4.58 4.58 37.09 5.69
3045 3132 1.709147 GCCTCACACTAATGCGGCAG 61.709 60.000 9.25 0.00 37.09 4.85
3046 3133 0.391661 CCTCACACTAATGCGGCAGT 60.392 55.000 9.25 8.81 0.00 4.40
3047 3134 0.723414 CTCACACTAATGCGGCAGTG 59.277 55.000 13.87 15.38 46.15 3.66
3048 3135 1.135315 CACACTAATGCGGCAGTGC 59.865 57.895 13.87 6.55 44.89 4.40
3049 3136 2.390599 ACACTAATGCGGCAGTGCG 61.391 57.895 13.87 6.60 44.89 5.34
3050 3137 3.499737 ACTAATGCGGCAGTGCGC 61.500 61.111 20.27 20.27 37.81 6.09
3051 3138 3.197790 CTAATGCGGCAGTGCGCT 61.198 61.111 24.87 13.38 41.91 5.92
3052 3139 3.160557 CTAATGCGGCAGTGCGCTC 62.161 63.158 24.87 4.74 41.91 5.03
3057 3144 4.724697 CGGCAGTGCGCTCGTTTG 62.725 66.667 9.73 0.32 41.91 2.93
3058 3145 3.345808 GGCAGTGCGCTCGTTTGA 61.346 61.111 9.73 0.00 41.91 2.69
3059 3146 2.680913 GGCAGTGCGCTCGTTTGAT 61.681 57.895 9.73 0.00 41.91 2.57
3060 3147 1.358725 GGCAGTGCGCTCGTTTGATA 61.359 55.000 9.73 0.00 41.91 2.15
3061 3148 0.025513 GCAGTGCGCTCGTTTGATAG 59.974 55.000 9.73 0.00 37.77 2.08
3062 3149 0.647410 CAGTGCGCTCGTTTGATAGG 59.353 55.000 9.73 0.00 0.00 2.57
3063 3150 1.084370 AGTGCGCTCGTTTGATAGGC 61.084 55.000 9.73 0.00 0.00 3.93
3065 3152 2.621000 CGCTCGTTTGATAGGCGC 59.379 61.111 0.00 0.00 39.42 6.53
3066 3153 2.621000 GCTCGTTTGATAGGCGCG 59.379 61.111 0.00 0.00 0.00 6.86
3067 3154 2.871427 GCTCGTTTGATAGGCGCGG 61.871 63.158 8.83 0.00 0.00 6.46
3068 3155 1.518572 CTCGTTTGATAGGCGCGGT 60.519 57.895 8.83 0.00 0.00 5.68
3069 3156 1.752501 CTCGTTTGATAGGCGCGGTG 61.753 60.000 8.83 0.00 0.00 4.94
3070 3157 2.403586 GTTTGATAGGCGCGGTGC 59.596 61.111 8.83 4.64 45.38 5.01
3081 3168 3.884900 GCGGTGCGGTTATTCTGT 58.115 55.556 0.00 0.00 0.00 3.41
3082 3169 2.168054 GCGGTGCGGTTATTCTGTT 58.832 52.632 0.00 0.00 0.00 3.16
3083 3170 0.519961 GCGGTGCGGTTATTCTGTTT 59.480 50.000 0.00 0.00 0.00 2.83
3084 3171 1.465187 GCGGTGCGGTTATTCTGTTTC 60.465 52.381 0.00 0.00 0.00 2.78
3085 3172 1.129811 CGGTGCGGTTATTCTGTTTCC 59.870 52.381 0.00 0.00 0.00 3.13
3086 3173 1.471287 GGTGCGGTTATTCTGTTTCCC 59.529 52.381 0.00 0.00 0.00 3.97
3087 3174 2.156098 GTGCGGTTATTCTGTTTCCCA 58.844 47.619 0.00 0.00 0.00 4.37
3088 3175 2.095415 GTGCGGTTATTCTGTTTCCCAC 60.095 50.000 0.00 0.00 0.00 4.61
3089 3176 1.471287 GCGGTTATTCTGTTTCCCACC 59.529 52.381 0.00 0.00 0.00 4.61
3090 3177 2.089201 CGGTTATTCTGTTTCCCACCC 58.911 52.381 0.00 0.00 0.00 4.61
3091 3178 2.453521 GGTTATTCTGTTTCCCACCCC 58.546 52.381 0.00 0.00 0.00 4.95
3092 3179 2.453521 GTTATTCTGTTTCCCACCCCC 58.546 52.381 0.00 0.00 0.00 5.40
3111 3198 4.966274 ACGCACCCACACCCCCTA 62.966 66.667 0.00 0.00 0.00 3.53
3112 3199 3.642503 CGCACCCACACCCCCTAA 61.643 66.667 0.00 0.00 0.00 2.69
3113 3200 2.355115 GCACCCACACCCCCTAAG 59.645 66.667 0.00 0.00 0.00 2.18
3114 3201 2.228480 GCACCCACACCCCCTAAGA 61.228 63.158 0.00 0.00 0.00 2.10
3115 3202 1.571773 GCACCCACACCCCCTAAGAT 61.572 60.000 0.00 0.00 0.00 2.40
3116 3203 1.887797 CACCCACACCCCCTAAGATA 58.112 55.000 0.00 0.00 0.00 1.98
3117 3204 1.768870 CACCCACACCCCCTAAGATAG 59.231 57.143 0.00 0.00 0.00 2.08
3118 3205 1.654997 ACCCACACCCCCTAAGATAGA 59.345 52.381 0.00 0.00 0.00 1.98
3119 3206 2.252945 ACCCACACCCCCTAAGATAGAT 59.747 50.000 0.00 0.00 0.00 1.98
3120 3207 3.473621 ACCCACACCCCCTAAGATAGATA 59.526 47.826 0.00 0.00 0.00 1.98
3121 3208 4.077626 ACCCACACCCCCTAAGATAGATAA 60.078 45.833 0.00 0.00 0.00 1.75
3122 3209 5.101529 CCCACACCCCCTAAGATAGATAAT 58.898 45.833 0.00 0.00 0.00 1.28
3127 3214 5.548056 CACCCCCTAAGATAGATAATGGTGT 59.452 44.000 0.00 0.00 35.85 4.16
3128 3215 5.785940 ACCCCCTAAGATAGATAATGGTGTC 59.214 44.000 0.00 0.00 0.00 3.67
3143 3230 1.534163 GGTGTCGTGCTAGTTTTTCCC 59.466 52.381 0.00 0.00 0.00 3.97
3144 3231 2.490991 GTGTCGTGCTAGTTTTTCCCT 58.509 47.619 0.00 0.00 0.00 4.20
3145 3232 3.555586 GGTGTCGTGCTAGTTTTTCCCTA 60.556 47.826 0.00 0.00 0.00 3.53
3189 3915 3.878778 AGACCATACAAGGAAGATGTGC 58.121 45.455 0.00 0.00 32.27 4.57
3205 3931 1.006832 GTGCCAGTACAACTATGCCG 58.993 55.000 0.00 0.00 0.00 5.69
3210 3936 1.100510 AGTACAACTATGCCGCTCGA 58.899 50.000 0.00 0.00 0.00 4.04
3230 3956 2.044555 GCGGTGCTAGTTTTCCCCC 61.045 63.158 0.00 0.00 0.00 5.40
3237 3963 4.775780 GGTGCTAGTTTTCCCCCTAAAAAT 59.224 41.667 0.00 0.00 32.10 1.82
3238 3964 5.953548 GGTGCTAGTTTTCCCCCTAAAAATA 59.046 40.000 0.00 0.00 30.19 1.40
3239 3965 6.610020 GGTGCTAGTTTTCCCCCTAAAAATAT 59.390 38.462 0.00 0.00 31.00 1.28
3267 4084 0.035820 GGGGCAAGTCATGTTACGGA 60.036 55.000 0.00 0.00 0.00 4.69
3282 4099 4.148825 GGACTCGCCTCCGCATGT 62.149 66.667 0.00 0.00 34.03 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
338 339 2.016393 CTGCCGGTCAAGCTATCCGA 62.016 60.000 20.53 5.82 46.05 4.55
703 713 5.078256 CCCTCTCCGGTGTCTATATAAACT 58.922 45.833 0.00 0.00 0.00 2.66
774 784 1.943340 GGAAGGAAAGCTTGGCGATAG 59.057 52.381 0.00 0.00 0.00 2.08
788 798 0.250727 CTTTCCTTGGCGTGGAAGGA 60.251 55.000 12.77 7.18 45.99 3.36
826 836 6.466812 TGCAGATACAAGATTGAAGACTTCA 58.533 36.000 13.99 13.99 38.04 3.02
848 858 0.530870 GCCGGACTCCAAGACTATGC 60.531 60.000 5.05 0.00 0.00 3.14
903 913 0.836400 TGGTTGAGGGAGTCCTGGAC 60.836 60.000 19.20 19.20 45.05 4.02
990 1000 2.366301 TCCGCCATTGCCCTCCTA 60.366 61.111 0.00 0.00 0.00 2.94
1123 1133 1.153086 GCATCTCCTTGCCGTGGAT 60.153 57.895 0.00 0.00 36.60 3.41
1179 1189 1.689813 CAGAGCCTGCTGATCATCTCT 59.310 52.381 0.00 1.19 38.14 3.10
1327 1338 1.007849 ATTTTGTGGCCGTTGCGAC 60.008 52.632 0.00 0.00 45.43 5.19
1502 1513 5.125900 TCCAGTGCATCAGGTTCAAAATATG 59.874 40.000 0.00 0.00 0.00 1.78
1602 1615 8.643324 AGAAACTACTTCACTACATCAAGTTCT 58.357 33.333 0.00 0.00 36.40 3.01
1672 1685 2.226437 CACATACCAGTGCTTCACCAAC 59.774 50.000 0.00 0.00 34.49 3.77
1724 1737 3.526931 TCTATGTGCTGCTTCAGTACC 57.473 47.619 11.45 0.00 44.36 3.34
1966 1990 2.831333 CTTCAGCATATCGTTGAGGCT 58.169 47.619 0.00 0.00 36.10 4.58
2058 2082 2.185004 ACTTGTTGGGGTTGATCTCG 57.815 50.000 0.00 0.00 0.00 4.04
2139 2169 3.372676 GACGCTGGCTGCAACATCG 62.373 63.158 16.76 11.32 43.06 3.84
2169 2199 7.331934 CCGATCTTCTTCTTCATGTCTTTGTAA 59.668 37.037 0.00 0.00 0.00 2.41
2195 2226 4.902448 ACAGATTATGGTCCTCCTTCCTAC 59.098 45.833 0.00 0.00 34.23 3.18
2205 2236 1.518367 TCCCCCACAGATTATGGTCC 58.482 55.000 0.00 0.00 35.23 4.46
2235 2266 5.046878 TGTGTACTCGATGAGGTAATTTGGT 60.047 40.000 0.00 0.00 33.35 3.67
2270 2301 1.330234 TGACTTGTAGGTGGCGTACA 58.670 50.000 0.00 0.00 33.75 2.90
2384 2415 1.135859 CACGAAGGCAGACTTTGATGC 60.136 52.381 10.63 0.00 42.27 3.91
2457 2528 7.064229 ACATAAGGAAACTGTTTTCAACCCTA 58.936 34.615 13.73 2.63 42.72 3.53
2475 2546 3.751175 ACCATGACAAACACGACATAAGG 59.249 43.478 0.00 0.00 0.00 2.69
2640 2717 5.536161 ACATCCTTGTGTGATTAGTTGCTTT 59.464 36.000 0.00 0.00 33.85 3.51
2847 2927 5.419542 ACGAATATAAGTGTGTGCTGATGT 58.580 37.500 0.00 0.00 0.00 3.06
2868 2948 2.724977 TTCTTAGTCTGCCAGTGACG 57.275 50.000 0.00 0.00 39.24 4.35
2891 2971 2.162208 CCGTTCAAGCGTACTGGTACTA 59.838 50.000 8.89 0.00 34.04 1.82
2994 3081 4.176752 GGGGTCGGGACTGATGCC 62.177 72.222 0.00 0.00 0.00 4.40
2995 3082 4.176752 GGGGGTCGGGACTGATGC 62.177 72.222 0.00 0.00 0.00 3.91
2996 3083 2.365635 AGGGGGTCGGGACTGATG 60.366 66.667 0.00 0.00 0.00 3.07
2997 3084 2.041819 GAGGGGGTCGGGACTGAT 60.042 66.667 0.00 0.00 0.00 2.90
2998 3085 4.393778 GGAGGGGGTCGGGACTGA 62.394 72.222 0.00 0.00 0.00 3.41
3022 3109 1.148157 CGCATTAGTGTGAGGCGGAG 61.148 60.000 0.00 0.00 43.63 4.63
3023 3110 1.153647 CGCATTAGTGTGAGGCGGA 60.154 57.895 0.00 0.00 43.63 5.54
3024 3111 3.398920 CGCATTAGTGTGAGGCGG 58.601 61.111 0.00 0.00 43.63 6.13
3025 3112 3.398920 CCGCATTAGTGTGAGGCG 58.601 61.111 0.00 0.00 46.61 5.52
3027 3114 0.391661 ACTGCCGCATTAGTGTGAGG 60.392 55.000 0.00 0.00 41.40 3.86
3028 3115 0.723414 CACTGCCGCATTAGTGTGAG 59.277 55.000 4.14 0.00 39.48 3.51
3029 3116 1.298157 GCACTGCCGCATTAGTGTGA 61.298 55.000 12.50 0.00 44.66 3.58
3030 3117 1.135315 GCACTGCCGCATTAGTGTG 59.865 57.895 11.58 8.69 44.66 3.82
3031 3118 2.390599 CGCACTGCCGCATTAGTGT 61.391 57.895 11.58 0.00 44.66 3.55
3032 3119 2.400798 CGCACTGCCGCATTAGTG 59.599 61.111 6.83 6.83 45.40 2.74
3042 3129 0.025513 CTATCAAACGAGCGCACTGC 59.974 55.000 11.47 0.00 46.98 4.40
3043 3130 0.647410 CCTATCAAACGAGCGCACTG 59.353 55.000 11.47 0.02 0.00 3.66
3044 3131 1.084370 GCCTATCAAACGAGCGCACT 61.084 55.000 11.47 0.00 0.00 4.40
3045 3132 1.348594 GCCTATCAAACGAGCGCAC 59.651 57.895 11.47 0.96 0.00 5.34
3046 3133 2.164663 CGCCTATCAAACGAGCGCA 61.165 57.895 11.47 0.00 40.35 6.09
3047 3134 2.621000 CGCCTATCAAACGAGCGC 59.379 61.111 0.00 0.00 40.35 5.92
3049 3136 2.621000 CGCGCCTATCAAACGAGC 59.379 61.111 0.00 0.00 0.00 5.03
3050 3137 1.518572 ACCGCGCCTATCAAACGAG 60.519 57.895 0.00 0.00 0.00 4.18
3051 3138 1.807981 CACCGCGCCTATCAAACGA 60.808 57.895 0.00 0.00 0.00 3.85
3052 3139 2.701006 CACCGCGCCTATCAAACG 59.299 61.111 0.00 0.00 0.00 3.60
3053 3140 2.403586 GCACCGCGCCTATCAAAC 59.596 61.111 0.00 0.00 32.94 2.93
3064 3151 0.519961 AAACAGAATAACCGCACCGC 59.480 50.000 0.00 0.00 0.00 5.68
3065 3152 1.129811 GGAAACAGAATAACCGCACCG 59.870 52.381 0.00 0.00 0.00 4.94
3066 3153 1.471287 GGGAAACAGAATAACCGCACC 59.529 52.381 0.00 0.00 0.00 5.01
3067 3154 2.095415 GTGGGAAACAGAATAACCGCAC 60.095 50.000 0.00 0.00 0.00 5.34
3068 3155 2.156098 GTGGGAAACAGAATAACCGCA 58.844 47.619 0.00 0.00 0.00 5.69
3069 3156 1.471287 GGTGGGAAACAGAATAACCGC 59.529 52.381 0.00 0.00 0.00 5.68
3070 3157 2.089201 GGGTGGGAAACAGAATAACCG 58.911 52.381 0.00 0.00 0.00 4.44
3071 3158 2.453521 GGGGTGGGAAACAGAATAACC 58.546 52.381 0.00 0.00 0.00 2.85
3072 3159 2.453521 GGGGGTGGGAAACAGAATAAC 58.546 52.381 0.00 0.00 0.00 1.89
3073 3160 2.911552 GGGGGTGGGAAACAGAATAA 57.088 50.000 0.00 0.00 0.00 1.40
3094 3181 4.966274 TAGGGGGTGTGGGTGCGT 62.966 66.667 0.00 0.00 0.00 5.24
3095 3182 3.622060 CTTAGGGGGTGTGGGTGCG 62.622 68.421 0.00 0.00 0.00 5.34
3096 3183 1.571773 ATCTTAGGGGGTGTGGGTGC 61.572 60.000 0.00 0.00 0.00 5.01
3097 3184 1.768870 CTATCTTAGGGGGTGTGGGTG 59.231 57.143 0.00 0.00 0.00 4.61
3098 3185 1.654997 TCTATCTTAGGGGGTGTGGGT 59.345 52.381 0.00 0.00 0.00 4.51
3099 3186 2.489528 TCTATCTTAGGGGGTGTGGG 57.510 55.000 0.00 0.00 0.00 4.61
3100 3187 5.045578 CCATTATCTATCTTAGGGGGTGTGG 60.046 48.000 0.00 0.00 0.00 4.17
3101 3188 5.548056 ACCATTATCTATCTTAGGGGGTGTG 59.452 44.000 0.00 0.00 0.00 3.82
3102 3189 5.548056 CACCATTATCTATCTTAGGGGGTGT 59.452 44.000 0.00 0.00 37.78 4.16
3103 3190 5.548056 ACACCATTATCTATCTTAGGGGGTG 59.452 44.000 0.00 0.00 45.62 4.61
3104 3191 5.738401 ACACCATTATCTATCTTAGGGGGT 58.262 41.667 0.00 0.00 0.00 4.95
3105 3192 5.105310 CGACACCATTATCTATCTTAGGGGG 60.105 48.000 0.00 0.00 0.00 5.40
3106 3193 5.480772 ACGACACCATTATCTATCTTAGGGG 59.519 44.000 0.00 0.00 0.00 4.79
3107 3194 6.390721 CACGACACCATTATCTATCTTAGGG 58.609 44.000 0.00 0.00 0.00 3.53
3108 3195 5.864474 GCACGACACCATTATCTATCTTAGG 59.136 44.000 0.00 0.00 0.00 2.69
3109 3196 6.682746 AGCACGACACCATTATCTATCTTAG 58.317 40.000 0.00 0.00 0.00 2.18
3110 3197 6.650427 AGCACGACACCATTATCTATCTTA 57.350 37.500 0.00 0.00 0.00 2.10
3111 3198 5.537300 AGCACGACACCATTATCTATCTT 57.463 39.130 0.00 0.00 0.00 2.40
3112 3199 5.770663 ACTAGCACGACACCATTATCTATCT 59.229 40.000 0.00 0.00 0.00 1.98
3113 3200 6.015027 ACTAGCACGACACCATTATCTATC 57.985 41.667 0.00 0.00 0.00 2.08
3114 3201 6.406692 AACTAGCACGACACCATTATCTAT 57.593 37.500 0.00 0.00 0.00 1.98
3115 3202 5.847111 AACTAGCACGACACCATTATCTA 57.153 39.130 0.00 0.00 0.00 1.98
3116 3203 4.737855 AACTAGCACGACACCATTATCT 57.262 40.909 0.00 0.00 0.00 1.98
3117 3204 5.796350 AAAACTAGCACGACACCATTATC 57.204 39.130 0.00 0.00 0.00 1.75
3118 3205 5.123344 GGAAAAACTAGCACGACACCATTAT 59.877 40.000 0.00 0.00 0.00 1.28
3119 3206 4.453136 GGAAAAACTAGCACGACACCATTA 59.547 41.667 0.00 0.00 0.00 1.90
3120 3207 3.252458 GGAAAAACTAGCACGACACCATT 59.748 43.478 0.00 0.00 0.00 3.16
3121 3208 2.812011 GGAAAAACTAGCACGACACCAT 59.188 45.455 0.00 0.00 0.00 3.55
3122 3209 2.215196 GGAAAAACTAGCACGACACCA 58.785 47.619 0.00 0.00 0.00 4.17
3161 3887 0.331278 CCTTGTATGGTCTTGCCCCA 59.669 55.000 0.00 0.00 36.04 4.96
3170 3896 2.308570 TGGCACATCTTCCTTGTATGGT 59.691 45.455 0.00 0.00 0.00 3.55
3189 3915 1.571919 GAGCGGCATAGTTGTACTGG 58.428 55.000 1.45 0.00 0.00 4.00
3205 3931 1.084370 AAACTAGCACCGCATCGAGC 61.084 55.000 0.00 0.00 40.87 5.03
3210 3936 0.679960 GGGGAAAACTAGCACCGCAT 60.680 55.000 0.00 0.00 35.81 4.73
3230 3956 9.533831 ACTTGCCCCCATTATCTATATTTTTAG 57.466 33.333 0.00 0.00 0.00 1.85
3237 3963 5.551583 ACATGACTTGCCCCCATTATCTATA 59.448 40.000 0.00 0.00 0.00 1.31
3238 3964 4.354987 ACATGACTTGCCCCCATTATCTAT 59.645 41.667 0.00 0.00 0.00 1.98
3239 3965 3.721575 ACATGACTTGCCCCCATTATCTA 59.278 43.478 0.00 0.00 0.00 1.98
3267 4084 3.381983 TCACATGCGGAGGCGAGT 61.382 61.111 0.00 0.00 44.10 4.18


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

AutoCloner maintained by Alex Coulton.