Multiple sequence alignment - TraesCS7D01G135200

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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 TraesCS7D01G135200 chr7D 100.000 4266 0 0 1 4266 86769027 86764762 0.000000e+00 7878
1 TraesCS7D01G135200 chr7D 92.958 4104 228 21 1 4067 87212974 87208895 0.000000e+00 5921
2 TraesCS7D01G135200 chr7D 96.667 3540 102 9 537 4067 86924515 86920983 0.000000e+00 5869
3 TraesCS7D01G135200 chr7D 95.903 2514 88 7 1 2511 86927798 86925297 0.000000e+00 4058
4 TraesCS7D01G135200 chr7A 94.060 4091 201 15 1 4067 88014894 88010822 0.000000e+00 6170
5 TraesCS7D01G135200 chr7A 93.986 4074 214 16 1 4067 88128151 88124102 0.000000e+00 6137
6 TraesCS7D01G135200 chr7A 93.214 4067 225 23 1 4059 88178902 88174879 0.000000e+00 5934
7 TraesCS7D01G135200 chr7A 92.060 4106 256 31 1 4067 88442405 88438331 0.000000e+00 5712
8 TraesCS7D01G135200 chr7A 92.354 2655 164 14 1 2637 88324203 88321570 0.000000e+00 3742
9 TraesCS7D01G135200 chr7A 91.742 1429 100 9 2646 4067 88320596 88319179 0.000000e+00 1969
10 TraesCS7D01G135200 chr7A 95.495 222 9 1 4045 4266 72497636 72497416 1.890000e-93 353
11 TraesCS7D01G135200 chr7B 90.334 3807 287 35 310 4067 35313792 35310018 0.000000e+00 4916
12 TraesCS7D01G135200 chr7B 91.189 3405 211 37 1 3366 35513788 35510434 0.000000e+00 4543
13 TraesCS7D01G135200 chr7B 95.946 222 8 1 4045 4266 656170274 656170054 4.060000e-95 359
14 TraesCS7D01G135200 chr6D 95.946 222 8 1 4045 4266 330151249 330151469 4.060000e-95 359
15 TraesCS7D01G135200 chr6D 95.928 221 8 1 4045 4265 225967825 225968044 1.460000e-94 357
16 TraesCS7D01G135200 chr2D 95.946 222 8 1 4045 4266 348274713 348274493 4.060000e-95 359
17 TraesCS7D01G135200 chr2B 95.946 222 8 1 4045 4266 143915480 143915260 4.060000e-95 359
18 TraesCS7D01G135200 chr2B 95.946 222 8 1 4045 4266 316570950 316571170 4.060000e-95 359
19 TraesCS7D01G135200 chr1B 95.946 222 8 1 4045 4266 524535086 524535306 4.060000e-95 359
20 TraesCS7D01G135200 chr5A 95.133 226 9 2 4042 4266 397694784 397694560 5.250000e-94 355


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 TraesCS7D01G135200 chr7D 86764762 86769027 4265 True 7878.0 7878 100.000 1 4266 1 chr7D.!!$R1 4265
1 TraesCS7D01G135200 chr7D 87208895 87212974 4079 True 5921.0 5921 92.958 1 4067 1 chr7D.!!$R2 4066
2 TraesCS7D01G135200 chr7D 86920983 86927798 6815 True 4963.5 5869 96.285 1 4067 2 chr7D.!!$R3 4066
3 TraesCS7D01G135200 chr7A 88010822 88014894 4072 True 6170.0 6170 94.060 1 4067 1 chr7A.!!$R2 4066
4 TraesCS7D01G135200 chr7A 88124102 88128151 4049 True 6137.0 6137 93.986 1 4067 1 chr7A.!!$R3 4066
5 TraesCS7D01G135200 chr7A 88174879 88178902 4023 True 5934.0 5934 93.214 1 4059 1 chr7A.!!$R4 4058
6 TraesCS7D01G135200 chr7A 88438331 88442405 4074 True 5712.0 5712 92.060 1 4067 1 chr7A.!!$R5 4066
7 TraesCS7D01G135200 chr7A 88319179 88324203 5024 True 2855.5 3742 92.048 1 4067 2 chr7A.!!$R6 4066
8 TraesCS7D01G135200 chr7B 35310018 35313792 3774 True 4916.0 4916 90.334 310 4067 1 chr7B.!!$R1 3757
9 TraesCS7D01G135200 chr7B 35510434 35513788 3354 True 4543.0 4543 91.189 1 3366 1 chr7B.!!$R2 3365

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
444 473 0.605319 TGCGTTGGATGTGGGAAGAC 60.605 55.0 0.0 0.0 0.00 3.01 F
1157 3966 0.178987 TCCGAGGTAGAGGAGGCATC 60.179 60.0 0.0 0.0 31.95 3.91 F
1700 4519 0.438830 GAACACAGGTTCGTCGATGC 59.561 55.0 0.0 0.0 43.54 3.91 F
2976 6828 0.322008 CCTTTCTTTCGCCAGCCTCT 60.322 55.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 4479 2.609759 CGTCGGTCCAAAAACCCCG 61.610 63.158 0.0 0.0 41.75 5.73 R
2967 6819 0.464554 GGGTCATTGTAGAGGCTGGC 60.465 60.000 0.0 0.0 0.00 4.85 R
3261 7119 2.322161 ACGACAGTCCGTTTATTCACG 58.678 47.619 0.0 0.0 40.17 4.35 R
4183 8057 0.034477 CGAGGCCCCTGGTTTGTATT 60.034 55.000 0.0 0.0 0.00 1.89 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
128 130 1.153429 GAGTATGCACGTGGTCCCC 60.153 63.158 18.88 0.00 0.00 4.81
359 388 2.036958 TGATTGGCCCGTGTATTGAG 57.963 50.000 0.00 0.00 0.00 3.02
444 473 0.605319 TGCGTTGGATGTGGGAAGAC 60.605 55.000 0.00 0.00 0.00 3.01
632 679 3.510753 TCCTGTGTGCATTGCATATTTGT 59.489 39.130 15.49 0.00 41.91 2.83
650 697 0.955428 GTGAGCGGCAGAAACCATGA 60.955 55.000 1.45 0.00 0.00 3.07
787 838 5.796279 GCAATCTTCTTGCGTATATTTGC 57.204 39.130 0.00 0.00 35.58 3.68
887 941 4.701956 AAATAGTTTGGCATGTTCCTCG 57.298 40.909 0.00 0.00 0.00 4.63
946 1000 9.871238 GTTCAATCTACTTTAGTATGGACTGAA 57.129 33.333 1.36 1.36 36.28 3.02
1157 3966 0.178987 TCCGAGGTAGAGGAGGCATC 60.179 60.000 0.00 0.00 31.95 3.91
1292 4101 5.181245 AGACCATGAAACAGGTAACAAATCG 59.819 40.000 0.00 0.00 38.50 3.34
1489 4301 3.126171 CCATGCGAATGAAAACTTCGGTA 59.874 43.478 4.44 0.00 44.25 4.02
1614 4433 7.094805 GCAGACAATAACAAGATGAAGGTGTTA 60.095 37.037 0.00 0.00 40.83 2.41
1660 4479 3.586430 GTTGTTGCCCCACATCAAC 57.414 52.632 4.43 4.43 46.29 3.18
1700 4519 0.438830 GAACACAGGTTCGTCGATGC 59.561 55.000 0.00 0.00 43.54 3.91
1958 4796 3.610786 TTTTCATTTCGTTGCGCACTA 57.389 38.095 11.12 0.00 0.00 2.74
1991 4847 2.364448 AGGAAGACGGAGGAGGCC 60.364 66.667 0.00 0.00 0.00 5.19
2004 4860 1.415672 GGAGGCCCCGATGATGGTAA 61.416 60.000 0.00 0.00 0.00 2.85
2131 4987 7.022384 GTCGATACCTATATTCTTCCTTGTCG 58.978 42.308 0.00 0.00 0.00 4.35
2455 5331 7.747888 TCAATAACCTGTAATGATTGTCGTTG 58.252 34.615 0.00 0.00 0.00 4.10
2866 6718 7.192852 TCAAGAGAATAGAGAGAAAGGCATT 57.807 36.000 0.00 0.00 0.00 3.56
2967 6819 0.948678 TCGGCAAACCCTTTCTTTCG 59.051 50.000 0.00 0.00 0.00 3.46
2976 6828 0.322008 CCTTTCTTTCGCCAGCCTCT 60.322 55.000 0.00 0.00 0.00 3.69
3135 6987 0.617935 TACTGCAGCTGTAATGGGCA 59.382 50.000 15.27 3.85 0.00 5.36
3261 7119 1.123928 ACTAGCTAGGCATGTGTCCC 58.876 55.000 24.35 0.00 0.00 4.46
3262 7120 0.032678 CTAGCTAGGCATGTGTCCCG 59.967 60.000 13.32 0.00 0.00 5.14
3433 7291 7.481798 GCTAAAAATAAGTGTTTGTCATCTCCG 59.518 37.037 0.00 0.00 0.00 4.63
3639 7501 7.441890 TCAGTTGCCGAATTACTTGAAAATA 57.558 32.000 0.00 0.00 0.00 1.40
3867 7741 9.905713 ATATTTCACCATTACTGTAGTTCACAT 57.094 29.630 0.00 0.00 36.29 3.21
3896 7770 4.278419 CACTAGGGGGTCAAACAAAGAAAG 59.722 45.833 0.00 0.00 0.00 2.62
4061 7935 3.892284 TCTTGCTCTAGAGACCTAGGTG 58.108 50.000 22.10 4.22 42.06 4.00
4062 7936 3.267291 TCTTGCTCTAGAGACCTAGGTGT 59.733 47.826 22.10 17.08 42.06 4.16
4064 7938 2.576648 TGCTCTAGAGACCTAGGTGTGA 59.423 50.000 22.10 8.30 42.06 3.58
4065 7939 2.946990 GCTCTAGAGACCTAGGTGTGAC 59.053 54.545 22.10 4.42 42.06 3.67
4066 7940 3.199677 CTCTAGAGACCTAGGTGTGACG 58.800 54.545 22.10 5.45 42.06 4.35
4067 7941 1.671845 CTAGAGACCTAGGTGTGACGC 59.328 57.143 22.10 6.55 38.93 5.19
4068 7942 0.966370 AGAGACCTAGGTGTGACGCC 60.966 60.000 22.10 7.17 0.00 5.68
4069 7943 1.946475 GAGACCTAGGTGTGACGCCC 61.946 65.000 22.10 1.42 33.99 6.13
4070 7944 3.001406 ACCTAGGTGTGACGCCCC 61.001 66.667 15.42 0.00 33.99 5.80
4071 7945 3.782443 CCTAGGTGTGACGCCCCC 61.782 72.222 12.26 0.00 33.99 5.40
4072 7946 4.143333 CTAGGTGTGACGCCCCCG 62.143 72.222 12.26 0.00 41.14 5.73
4073 7947 4.682334 TAGGTGTGACGCCCCCGA 62.682 66.667 12.26 0.00 38.29 5.14
4074 7948 3.968837 TAGGTGTGACGCCCCCGAT 62.969 63.158 12.26 0.00 38.29 4.18
4075 7949 4.404098 GGTGTGACGCCCCCGATT 62.404 66.667 3.20 0.00 38.29 3.34
4076 7950 2.818274 GTGTGACGCCCCCGATTC 60.818 66.667 0.00 0.00 38.29 2.52
4077 7951 3.315140 TGTGACGCCCCCGATTCA 61.315 61.111 0.00 0.00 38.29 2.57
4078 7952 2.046700 GTGACGCCCCCGATTCAA 60.047 61.111 0.00 0.00 38.29 2.69
4079 7953 1.451387 GTGACGCCCCCGATTCAAT 60.451 57.895 0.00 0.00 38.29 2.57
4080 7954 1.153249 TGACGCCCCCGATTCAATC 60.153 57.895 0.00 0.00 38.29 2.67
4096 7970 7.177498 GATTCAATCGTACACTAATCATGCA 57.823 36.000 0.00 0.00 0.00 3.96
4097 7971 5.966636 TCAATCGTACACTAATCATGCAC 57.033 39.130 0.00 0.00 0.00 4.57
4098 7972 4.502645 TCAATCGTACACTAATCATGCACG 59.497 41.667 0.00 0.00 38.02 5.34
4099 7973 2.190161 TCGTACACTAATCATGCACGC 58.810 47.619 0.00 0.00 36.88 5.34
4100 7974 1.923864 CGTACACTAATCATGCACGCA 59.076 47.619 0.00 0.00 30.70 5.24
4101 7975 2.347150 CGTACACTAATCATGCACGCAA 59.653 45.455 0.00 0.00 30.70 4.85
4102 7976 3.181525 CGTACACTAATCATGCACGCAAA 60.182 43.478 0.00 0.00 30.70 3.68
4103 7977 3.201726 ACACTAATCATGCACGCAAAC 57.798 42.857 0.00 0.00 0.00 2.93
4116 7990 2.125168 CGCAAACGTGTACGATCAAG 57.875 50.000 11.79 0.00 43.02 3.02
4117 7991 1.717113 CGCAAACGTGTACGATCAAGA 59.283 47.619 11.79 0.00 43.02 3.02
4118 7992 2.344441 CGCAAACGTGTACGATCAAGAT 59.656 45.455 11.79 0.00 43.02 2.40
4119 7993 3.539592 CGCAAACGTGTACGATCAAGATC 60.540 47.826 11.79 0.00 43.02 2.75
4120 7994 3.366724 GCAAACGTGTACGATCAAGATCA 59.633 43.478 11.79 0.00 43.02 2.92
4121 7995 4.490959 GCAAACGTGTACGATCAAGATCAG 60.491 45.833 11.79 5.82 43.02 2.90
4122 7996 3.422417 ACGTGTACGATCAAGATCAGG 57.578 47.619 11.79 0.51 43.02 3.86
4123 7997 2.099263 ACGTGTACGATCAAGATCAGGG 59.901 50.000 11.79 0.00 43.02 4.45
4124 7998 2.357952 CGTGTACGATCAAGATCAGGGA 59.642 50.000 10.39 0.00 43.02 4.20
4125 7999 3.707793 GTGTACGATCAAGATCAGGGAC 58.292 50.000 10.39 2.84 37.69 4.46
4126 8000 3.381908 GTGTACGATCAAGATCAGGGACT 59.618 47.826 10.39 0.00 43.88 3.85
4127 8001 4.579340 GTGTACGATCAAGATCAGGGACTA 59.421 45.833 10.39 0.00 34.60 2.59
4128 8002 5.067413 GTGTACGATCAAGATCAGGGACTAA 59.933 44.000 10.39 0.00 34.60 2.24
4129 8003 4.657436 ACGATCAAGATCAGGGACTAAC 57.343 45.455 10.39 0.00 34.60 2.34
4130 8004 3.066900 ACGATCAAGATCAGGGACTAACG 59.933 47.826 10.39 0.00 34.60 3.18
4131 8005 3.551046 CGATCAAGATCAGGGACTAACGG 60.551 52.174 10.39 0.00 34.60 4.44
4132 8006 2.108168 TCAAGATCAGGGACTAACGGG 58.892 52.381 0.00 0.00 36.02 5.28
4133 8007 2.108168 CAAGATCAGGGACTAACGGGA 58.892 52.381 0.00 0.00 36.02 5.14
4134 8008 2.500098 CAAGATCAGGGACTAACGGGAA 59.500 50.000 0.00 0.00 36.02 3.97
4135 8009 2.389715 AGATCAGGGACTAACGGGAAG 58.610 52.381 0.00 0.00 36.02 3.46
4136 8010 2.024273 AGATCAGGGACTAACGGGAAGA 60.024 50.000 0.00 0.00 36.02 2.87
4137 8011 2.544844 TCAGGGACTAACGGGAAGAT 57.455 50.000 0.00 0.00 36.02 2.40
4138 8012 3.675348 TCAGGGACTAACGGGAAGATA 57.325 47.619 0.00 0.00 36.02 1.98
4139 8013 4.194678 TCAGGGACTAACGGGAAGATAT 57.805 45.455 0.00 0.00 36.02 1.63
4140 8014 4.150359 TCAGGGACTAACGGGAAGATATC 58.850 47.826 0.00 0.00 36.02 1.63
4141 8015 3.895656 CAGGGACTAACGGGAAGATATCA 59.104 47.826 5.32 0.00 36.02 2.15
4142 8016 3.896272 AGGGACTAACGGGAAGATATCAC 59.104 47.826 5.32 0.00 36.02 3.06
4143 8017 3.640029 GGGACTAACGGGAAGATATCACA 59.360 47.826 5.32 0.00 0.00 3.58
4144 8018 4.100498 GGGACTAACGGGAAGATATCACAA 59.900 45.833 5.32 0.00 0.00 3.33
4145 8019 5.048507 GGACTAACGGGAAGATATCACAAC 58.951 45.833 5.32 0.00 0.00 3.32
4146 8020 5.394883 GGACTAACGGGAAGATATCACAACA 60.395 44.000 5.32 0.00 0.00 3.33
4147 8021 5.416947 ACTAACGGGAAGATATCACAACAC 58.583 41.667 5.32 0.00 0.00 3.32
4148 8022 3.973206 ACGGGAAGATATCACAACACA 57.027 42.857 5.32 0.00 0.00 3.72
4149 8023 4.280436 ACGGGAAGATATCACAACACAA 57.720 40.909 5.32 0.00 0.00 3.33
4150 8024 4.000988 ACGGGAAGATATCACAACACAAC 58.999 43.478 5.32 0.00 0.00 3.32
4151 8025 4.253685 CGGGAAGATATCACAACACAACT 58.746 43.478 5.32 0.00 0.00 3.16
4152 8026 4.330074 CGGGAAGATATCACAACACAACTC 59.670 45.833 5.32 0.00 0.00 3.01
4153 8027 5.491982 GGGAAGATATCACAACACAACTCT 58.508 41.667 5.32 0.00 0.00 3.24
4154 8028 6.627287 CGGGAAGATATCACAACACAACTCTA 60.627 42.308 5.32 0.00 0.00 2.43
4155 8029 7.103641 GGGAAGATATCACAACACAACTCTAA 58.896 38.462 5.32 0.00 0.00 2.10
4156 8030 7.606456 GGGAAGATATCACAACACAACTCTAAA 59.394 37.037 5.32 0.00 0.00 1.85
4157 8031 9.167311 GGAAGATATCACAACACAACTCTAAAT 57.833 33.333 5.32 0.00 0.00 1.40
4159 8033 9.725019 AAGATATCACAACACAACTCTAAATCA 57.275 29.630 5.32 0.00 0.00 2.57
4160 8034 9.896645 AGATATCACAACACAACTCTAAATCAT 57.103 29.630 5.32 0.00 0.00 2.45
4192 8066 8.840321 AGTCATACAAGCATCATAATACAAACC 58.160 33.333 0.00 0.00 0.00 3.27
4193 8067 8.620416 GTCATACAAGCATCATAATACAAACCA 58.380 33.333 0.00 0.00 0.00 3.67
4194 8068 8.839343 TCATACAAGCATCATAATACAAACCAG 58.161 33.333 0.00 0.00 0.00 4.00
4195 8069 6.455360 ACAAGCATCATAATACAAACCAGG 57.545 37.500 0.00 0.00 0.00 4.45
4196 8070 5.360714 ACAAGCATCATAATACAAACCAGGG 59.639 40.000 0.00 0.00 0.00 4.45
4197 8071 4.473444 AGCATCATAATACAAACCAGGGG 58.527 43.478 0.00 0.00 0.00 4.79
4198 8072 3.005791 GCATCATAATACAAACCAGGGGC 59.994 47.826 0.00 0.00 0.00 5.80
4199 8073 3.306472 TCATAATACAAACCAGGGGCC 57.694 47.619 0.00 0.00 0.00 5.80
4200 8074 2.856231 TCATAATACAAACCAGGGGCCT 59.144 45.455 0.84 0.00 0.00 5.19
4201 8075 3.117663 TCATAATACAAACCAGGGGCCTC 60.118 47.826 0.84 0.00 0.00 4.70
4202 8076 0.034477 AATACAAACCAGGGGCCTCG 60.034 55.000 0.84 0.00 0.00 4.63
4203 8077 0.912487 ATACAAACCAGGGGCCTCGA 60.912 55.000 0.84 0.00 0.00 4.04
4204 8078 1.550130 TACAAACCAGGGGCCTCGAG 61.550 60.000 5.13 5.13 0.00 4.04
4205 8079 3.330720 AAACCAGGGGCCTCGAGG 61.331 66.667 27.83 27.83 38.53 4.63
4221 8095 1.291132 GAGGGCTCGAATACAAGTGC 58.709 55.000 0.00 0.00 0.00 4.40
4222 8096 0.905357 AGGGCTCGAATACAAGTGCT 59.095 50.000 0.00 0.00 0.00 4.40
4223 8097 1.134670 AGGGCTCGAATACAAGTGCTC 60.135 52.381 0.00 0.00 0.00 4.26
4224 8098 1.405526 GGGCTCGAATACAAGTGCTCA 60.406 52.381 0.00 0.00 0.00 4.26
4225 8099 2.346803 GGCTCGAATACAAGTGCTCAA 58.653 47.619 0.00 0.00 0.00 3.02
4226 8100 2.939103 GGCTCGAATACAAGTGCTCAAT 59.061 45.455 0.00 0.00 0.00 2.57
4227 8101 3.001736 GGCTCGAATACAAGTGCTCAATC 59.998 47.826 0.00 0.00 0.00 2.67
4228 8102 3.618594 GCTCGAATACAAGTGCTCAATCA 59.381 43.478 0.00 0.00 0.00 2.57
4229 8103 4.272018 GCTCGAATACAAGTGCTCAATCAT 59.728 41.667 0.00 0.00 0.00 2.45
4230 8104 5.463392 GCTCGAATACAAGTGCTCAATCATA 59.537 40.000 0.00 0.00 0.00 2.15
4231 8105 6.346439 GCTCGAATACAAGTGCTCAATCATAG 60.346 42.308 0.00 0.00 0.00 2.23
4232 8106 6.805713 TCGAATACAAGTGCTCAATCATAGA 58.194 36.000 0.00 0.00 0.00 1.98
4233 8107 6.697455 TCGAATACAAGTGCTCAATCATAGAC 59.303 38.462 0.00 0.00 0.00 2.59
4234 8108 6.345329 CGAATACAAGTGCTCAATCATAGACG 60.345 42.308 0.00 0.00 0.00 4.18
4235 8109 4.456280 ACAAGTGCTCAATCATAGACGA 57.544 40.909 0.00 0.00 0.00 4.20
4236 8110 4.428209 ACAAGTGCTCAATCATAGACGAG 58.572 43.478 0.00 0.00 0.00 4.18
4237 8111 4.081972 ACAAGTGCTCAATCATAGACGAGT 60.082 41.667 0.00 0.00 0.00 4.18
4238 8112 4.300189 AGTGCTCAATCATAGACGAGTC 57.700 45.455 0.00 0.00 0.00 3.36
4239 8113 3.696548 AGTGCTCAATCATAGACGAGTCA 59.303 43.478 5.99 0.00 0.00 3.41
4240 8114 4.158579 AGTGCTCAATCATAGACGAGTCAA 59.841 41.667 5.99 0.00 0.00 3.18
4241 8115 4.266502 GTGCTCAATCATAGACGAGTCAAC 59.733 45.833 5.99 0.00 0.00 3.18
4242 8116 3.483922 GCTCAATCATAGACGAGTCAACG 59.516 47.826 5.99 0.00 39.31 4.10
4243 8117 4.028852 TCAATCATAGACGAGTCAACGG 57.971 45.455 5.99 0.00 37.61 4.44
4244 8118 3.692593 TCAATCATAGACGAGTCAACGGA 59.307 43.478 5.99 0.00 37.61 4.69
4245 8119 4.157105 TCAATCATAGACGAGTCAACGGAA 59.843 41.667 5.99 0.00 37.61 4.30
4246 8120 3.759527 TCATAGACGAGTCAACGGAAG 57.240 47.619 5.99 0.00 37.61 3.46
4247 8121 2.159421 TCATAGACGAGTCAACGGAAGC 60.159 50.000 5.99 0.00 37.61 3.86
4248 8122 1.241165 TAGACGAGTCAACGGAAGCA 58.759 50.000 5.99 0.00 37.61 3.91
4249 8123 0.387929 AGACGAGTCAACGGAAGCAA 59.612 50.000 5.99 0.00 37.61 3.91
4250 8124 0.507358 GACGAGTCAACGGAAGCAAC 59.493 55.000 0.00 0.00 37.61 4.17
4251 8125 0.179094 ACGAGTCAACGGAAGCAACA 60.179 50.000 0.00 0.00 37.61 3.33
4252 8126 0.934496 CGAGTCAACGGAAGCAACAA 59.066 50.000 0.00 0.00 0.00 2.83
4253 8127 1.531149 CGAGTCAACGGAAGCAACAAT 59.469 47.619 0.00 0.00 0.00 2.71
4254 8128 2.734606 CGAGTCAACGGAAGCAACAATA 59.265 45.455 0.00 0.00 0.00 1.90
4255 8129 3.370978 CGAGTCAACGGAAGCAACAATAT 59.629 43.478 0.00 0.00 0.00 1.28
4256 8130 4.492570 CGAGTCAACGGAAGCAACAATATC 60.493 45.833 0.00 0.00 0.00 1.63
4257 8131 4.579869 AGTCAACGGAAGCAACAATATCT 58.420 39.130 0.00 0.00 0.00 1.98
4258 8132 4.393062 AGTCAACGGAAGCAACAATATCTG 59.607 41.667 0.00 0.00 0.00 2.90
4259 8133 4.391830 GTCAACGGAAGCAACAATATCTGA 59.608 41.667 0.00 0.00 0.00 3.27
4260 8134 4.631377 TCAACGGAAGCAACAATATCTGAG 59.369 41.667 0.00 0.00 0.00 3.35
4261 8135 4.207891 ACGGAAGCAACAATATCTGAGT 57.792 40.909 0.00 0.00 0.00 3.41
4262 8136 5.339008 ACGGAAGCAACAATATCTGAGTA 57.661 39.130 0.00 0.00 0.00 2.59
4263 8137 5.109903 ACGGAAGCAACAATATCTGAGTAC 58.890 41.667 0.00 0.00 0.00 2.73
4264 8138 5.109210 CGGAAGCAACAATATCTGAGTACA 58.891 41.667 0.00 0.00 0.00 2.90
4265 8139 5.233050 CGGAAGCAACAATATCTGAGTACAG 59.767 44.000 0.00 0.00 44.66 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 5.636837 TCATAAATGGCTTTTGCTTCGTAC 58.363 37.500 8.48 0.00 46.54 3.67
128 130 6.129053 TGATGCATCGTCTAGCTATCATAG 57.871 41.667 21.34 0.00 0.00 2.23
359 388 4.846779 TGGCACTTCATGGTAAAAAGAC 57.153 40.909 0.00 0.00 0.00 3.01
444 473 7.940850 TCTTTTCTCTTAATTTTGGTGACCAG 58.059 34.615 3.77 0.00 33.81 4.00
632 679 0.035152 ATCATGGTTTCTGCCGCTCA 60.035 50.000 0.00 0.00 0.00 4.26
650 697 4.640771 TCTTAGAGTGCAAGACCCAAAT 57.359 40.909 0.00 0.00 0.00 2.32
1157 3966 1.483827 TGAGCCTAGCAATGAGTGAGG 59.516 52.381 0.00 0.00 0.00 3.86
1292 4101 3.909430 TCCACGGCGAGATCAATATAAC 58.091 45.455 16.62 0.00 0.00 1.89
1489 4301 2.766263 TGATTGTTGCCTCCTCTCGTAT 59.234 45.455 0.00 0.00 0.00 3.06
1584 4403 6.127535 CCTTCATCTTGTTATTGTCTGCCATT 60.128 38.462 0.00 0.00 0.00 3.16
1614 4433 7.775561 GGTTGGTCTATGGAAATATTGTTCTCT 59.224 37.037 0.00 0.00 0.00 3.10
1660 4479 2.609759 CGTCGGTCCAAAAACCCCG 61.610 63.158 0.00 0.00 41.75 5.73
1696 4515 6.341316 TGACAAAGGAGAGTATACAAGCATC 58.659 40.000 5.50 0.00 0.00 3.91
1700 4519 8.470805 ACTACATGACAAAGGAGAGTATACAAG 58.529 37.037 5.50 0.00 0.00 3.16
1958 4796 5.068460 CGTCTTCCTGATTCTTGTATCCTCT 59.932 44.000 0.00 0.00 0.00 3.69
1991 4847 4.006989 TGTTCTTGTTTACCATCATCGGG 58.993 43.478 0.00 0.00 0.00 5.14
2004 4860 4.170468 AGACCACCATCTTGTTCTTGTT 57.830 40.909 0.00 0.00 0.00 2.83
2032 4888 3.876914 TGGTCGATCAATGGAAGTATTGC 59.123 43.478 0.00 0.00 37.83 3.56
2455 5331 6.327934 TCGTACCTCTATTTTTCTGTAGTGC 58.672 40.000 0.00 0.00 0.00 4.40
2572 5459 6.470877 ACAACACGTGCTTACTTTTGTTTATG 59.529 34.615 17.22 0.00 0.00 1.90
2726 6578 4.476846 TCCAGCCCATAAAGAAATGACCTA 59.523 41.667 0.00 0.00 0.00 3.08
2857 6709 1.909700 TGTCCCTGACAATGCCTTTC 58.090 50.000 0.00 0.00 39.78 2.62
2866 6718 1.139256 TGTAACGCTTTGTCCCTGACA 59.861 47.619 0.00 0.00 41.09 3.58
2967 6819 0.464554 GGGTCATTGTAGAGGCTGGC 60.465 60.000 0.00 0.00 0.00 4.85
2976 6828 4.650972 ACCTAAAGCTTGGGTCATTGTA 57.349 40.909 15.93 0.00 41.03 2.41
3135 6987 2.505819 CAGGCACATAGTTTCCTACCCT 59.494 50.000 0.00 0.00 0.00 4.34
3167 7022 5.127031 GCCAAGATAAAAATAAGCTGACCCA 59.873 40.000 0.00 0.00 0.00 4.51
3261 7119 2.322161 ACGACAGTCCGTTTATTCACG 58.678 47.619 0.00 0.00 40.17 4.35
3262 7120 3.967080 GACGACAGTCCGTTTATTCAC 57.033 47.619 0.00 0.00 43.49 3.18
3280 7138 4.072131 TGTCTTGTTGCCATCTTTAGGAC 58.928 43.478 0.00 0.00 0.00 3.85
3613 7475 5.759506 TTCAAGTAATTCGGCAACTGAAA 57.240 34.783 0.00 0.00 33.94 2.69
3639 7501 7.201750 GGATCTGACTATCAAGTAGAACGTCTT 60.202 40.741 0.00 0.00 35.56 3.01
3867 7741 3.053544 TGTTTGACCCCCTAGTGACAAAA 60.054 43.478 0.00 0.00 0.00 2.44
3896 7770 9.952188 GAGGGTAAGATTTTTATAACTGATTGC 57.048 33.333 0.00 0.00 0.00 3.56
3976 7850 3.243704 CCCTGATCTCTTCATTCTCCGTC 60.244 52.174 0.00 0.00 32.72 4.79
3978 7852 2.036992 CCCCTGATCTCTTCATTCTCCG 59.963 54.545 0.00 0.00 32.72 4.63
4061 7935 1.436983 GATTGAATCGGGGGCGTCAC 61.437 60.000 0.00 0.00 0.00 3.67
4062 7936 1.153249 GATTGAATCGGGGGCGTCA 60.153 57.895 0.00 0.00 0.00 4.35
4072 7946 7.065894 GTGCATGATTAGTGTACGATTGAATC 58.934 38.462 0.00 0.00 0.00 2.52
4073 7947 6.948353 GTGCATGATTAGTGTACGATTGAAT 58.052 36.000 0.00 0.00 0.00 2.57
4074 7948 6.344572 GTGCATGATTAGTGTACGATTGAA 57.655 37.500 0.00 0.00 0.00 2.69
4075 7949 5.966636 GTGCATGATTAGTGTACGATTGA 57.033 39.130 0.00 0.00 0.00 2.57
4081 7955 4.088648 GTTTGCGTGCATGATTAGTGTAC 58.911 43.478 10.93 0.00 0.00 2.90
4082 7956 3.181525 CGTTTGCGTGCATGATTAGTGTA 60.182 43.478 10.93 0.00 0.00 2.90
4083 7957 2.412716 CGTTTGCGTGCATGATTAGTGT 60.413 45.455 10.93 0.00 0.00 3.55
4084 7958 2.168384 CGTTTGCGTGCATGATTAGTG 58.832 47.619 10.93 0.00 0.00 2.74
4085 7959 2.525750 CGTTTGCGTGCATGATTAGT 57.474 45.000 10.93 0.00 0.00 2.24
4097 7971 1.717113 TCTTGATCGTACACGTTTGCG 59.283 47.619 5.81 5.81 44.93 4.85
4098 7972 3.366724 TGATCTTGATCGTACACGTTTGC 59.633 43.478 1.19 0.00 40.80 3.68
4099 7973 4.031765 CCTGATCTTGATCGTACACGTTTG 59.968 45.833 1.19 0.00 40.80 2.93
4100 7974 4.174009 CCTGATCTTGATCGTACACGTTT 58.826 43.478 1.19 0.00 40.80 3.60
4101 7975 3.428999 CCCTGATCTTGATCGTACACGTT 60.429 47.826 1.19 0.00 40.80 3.99
4102 7976 2.099263 CCCTGATCTTGATCGTACACGT 59.901 50.000 1.19 0.00 40.80 4.49
4103 7977 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
4104 7978 3.381908 AGTCCCTGATCTTGATCGTACAC 59.618 47.826 6.19 1.73 0.00 2.90
4105 7979 3.632333 AGTCCCTGATCTTGATCGTACA 58.368 45.455 6.19 0.00 0.00 2.90
4106 7980 5.521544 GTTAGTCCCTGATCTTGATCGTAC 58.478 45.833 6.19 2.53 0.00 3.67
4107 7981 4.275196 CGTTAGTCCCTGATCTTGATCGTA 59.725 45.833 6.19 0.00 0.00 3.43
4108 7982 3.066900 CGTTAGTCCCTGATCTTGATCGT 59.933 47.826 6.19 0.00 0.00 3.73
4109 7983 3.551046 CCGTTAGTCCCTGATCTTGATCG 60.551 52.174 6.19 2.03 0.00 3.69
4110 7984 3.243907 CCCGTTAGTCCCTGATCTTGATC 60.244 52.174 3.82 3.82 0.00 2.92
4111 7985 2.700897 CCCGTTAGTCCCTGATCTTGAT 59.299 50.000 0.00 0.00 0.00 2.57
4112 7986 2.108168 CCCGTTAGTCCCTGATCTTGA 58.892 52.381 0.00 0.00 0.00 3.02
4113 7987 2.108168 TCCCGTTAGTCCCTGATCTTG 58.892 52.381 0.00 0.00 0.00 3.02
4114 7988 2.544844 TCCCGTTAGTCCCTGATCTT 57.455 50.000 0.00 0.00 0.00 2.40
4115 7989 2.024273 TCTTCCCGTTAGTCCCTGATCT 60.024 50.000 0.00 0.00 0.00 2.75
4116 7990 2.385803 TCTTCCCGTTAGTCCCTGATC 58.614 52.381 0.00 0.00 0.00 2.92
4117 7991 2.544844 TCTTCCCGTTAGTCCCTGAT 57.455 50.000 0.00 0.00 0.00 2.90
4118 7992 2.544844 ATCTTCCCGTTAGTCCCTGA 57.455 50.000 0.00 0.00 0.00 3.86
4119 7993 3.895656 TGATATCTTCCCGTTAGTCCCTG 59.104 47.826 3.98 0.00 0.00 4.45
4120 7994 3.896272 GTGATATCTTCCCGTTAGTCCCT 59.104 47.826 3.98 0.00 0.00 4.20
4121 7995 3.640029 TGTGATATCTTCCCGTTAGTCCC 59.360 47.826 3.98 0.00 0.00 4.46
4122 7996 4.931661 TGTGATATCTTCCCGTTAGTCC 57.068 45.455 3.98 0.00 0.00 3.85
4123 7997 5.519206 GTGTTGTGATATCTTCCCGTTAGTC 59.481 44.000 3.98 0.00 0.00 2.59
4124 7998 5.046878 TGTGTTGTGATATCTTCCCGTTAGT 60.047 40.000 3.98 0.00 0.00 2.24
4125 7999 5.416083 TGTGTTGTGATATCTTCCCGTTAG 58.584 41.667 3.98 0.00 0.00 2.34
4126 8000 5.408880 TGTGTTGTGATATCTTCCCGTTA 57.591 39.130 3.98 0.00 0.00 3.18
4127 8001 4.280436 TGTGTTGTGATATCTTCCCGTT 57.720 40.909 3.98 0.00 0.00 4.44
4128 8002 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
4129 8003 4.253685 AGTTGTGTTGTGATATCTTCCCG 58.746 43.478 3.98 0.00 0.00 5.14
4130 8004 5.491982 AGAGTTGTGTTGTGATATCTTCCC 58.508 41.667 3.98 0.00 0.00 3.97
4131 8005 8.547967 TTTAGAGTTGTGTTGTGATATCTTCC 57.452 34.615 3.98 0.00 0.00 3.46
4133 8007 9.725019 TGATTTAGAGTTGTGTTGTGATATCTT 57.275 29.630 3.98 0.00 0.00 2.40
4134 8008 9.896645 ATGATTTAGAGTTGTGTTGTGATATCT 57.103 29.630 3.98 0.00 0.00 1.98
4166 8040 8.840321 GGTTTGTATTATGATGCTTGTATGACT 58.160 33.333 0.00 0.00 0.00 3.41
4167 8041 8.620416 TGGTTTGTATTATGATGCTTGTATGAC 58.380 33.333 0.00 0.00 0.00 3.06
4168 8042 8.744568 TGGTTTGTATTATGATGCTTGTATGA 57.255 30.769 0.00 0.00 0.00 2.15
4169 8043 8.077991 CCTGGTTTGTATTATGATGCTTGTATG 58.922 37.037 0.00 0.00 0.00 2.39
4170 8044 7.231317 CCCTGGTTTGTATTATGATGCTTGTAT 59.769 37.037 0.00 0.00 0.00 2.29
4171 8045 6.545666 CCCTGGTTTGTATTATGATGCTTGTA 59.454 38.462 0.00 0.00 0.00 2.41
4172 8046 5.360714 CCCTGGTTTGTATTATGATGCTTGT 59.639 40.000 0.00 0.00 0.00 3.16
4173 8047 5.221303 CCCCTGGTTTGTATTATGATGCTTG 60.221 44.000 0.00 0.00 0.00 4.01
4174 8048 4.895297 CCCCTGGTTTGTATTATGATGCTT 59.105 41.667 0.00 0.00 0.00 3.91
4175 8049 4.473444 CCCCTGGTTTGTATTATGATGCT 58.527 43.478 0.00 0.00 0.00 3.79
4176 8050 3.005791 GCCCCTGGTTTGTATTATGATGC 59.994 47.826 0.00 0.00 0.00 3.91
4177 8051 3.573967 GGCCCCTGGTTTGTATTATGATG 59.426 47.826 0.00 0.00 0.00 3.07
4178 8052 3.467103 AGGCCCCTGGTTTGTATTATGAT 59.533 43.478 0.00 0.00 0.00 2.45
4179 8053 2.856231 AGGCCCCTGGTTTGTATTATGA 59.144 45.455 0.00 0.00 0.00 2.15
4180 8054 3.222603 GAGGCCCCTGGTTTGTATTATG 58.777 50.000 0.00 0.00 0.00 1.90
4181 8055 2.158667 CGAGGCCCCTGGTTTGTATTAT 60.159 50.000 0.00 0.00 0.00 1.28
4182 8056 1.210967 CGAGGCCCCTGGTTTGTATTA 59.789 52.381 0.00 0.00 0.00 0.98
4183 8057 0.034477 CGAGGCCCCTGGTTTGTATT 60.034 55.000 0.00 0.00 0.00 1.89
4184 8058 0.912487 TCGAGGCCCCTGGTTTGTAT 60.912 55.000 0.00 0.00 0.00 2.29
4185 8059 1.536907 TCGAGGCCCCTGGTTTGTA 60.537 57.895 0.00 0.00 0.00 2.41
4186 8060 2.852075 TCGAGGCCCCTGGTTTGT 60.852 61.111 0.00 0.00 0.00 2.83
4187 8061 2.045926 CTCGAGGCCCCTGGTTTG 60.046 66.667 3.91 0.00 0.00 2.93
4188 8062 3.330720 CCTCGAGGCCCCTGGTTT 61.331 66.667 20.67 0.00 0.00 3.27
4202 8076 1.134670 AGCACTTGTATTCGAGCCCTC 60.135 52.381 0.00 0.00 0.00 4.30
4203 8077 0.905357 AGCACTTGTATTCGAGCCCT 59.095 50.000 0.00 0.00 0.00 5.19
4204 8078 1.291132 GAGCACTTGTATTCGAGCCC 58.709 55.000 0.00 0.00 0.00 5.19
4205 8079 2.010145 TGAGCACTTGTATTCGAGCC 57.990 50.000 0.00 0.00 0.00 4.70
4206 8080 3.618594 TGATTGAGCACTTGTATTCGAGC 59.381 43.478 0.00 0.00 0.00 5.03
4207 8081 5.980698 ATGATTGAGCACTTGTATTCGAG 57.019 39.130 0.00 0.00 0.00 4.04
4208 8082 6.697455 GTCTATGATTGAGCACTTGTATTCGA 59.303 38.462 0.00 0.00 0.00 3.71
4209 8083 6.345329 CGTCTATGATTGAGCACTTGTATTCG 60.345 42.308 0.00 0.00 0.00 3.34
4210 8084 6.697455 TCGTCTATGATTGAGCACTTGTATTC 59.303 38.462 0.00 0.00 0.00 1.75
4211 8085 6.573434 TCGTCTATGATTGAGCACTTGTATT 58.427 36.000 0.00 0.00 0.00 1.89
4212 8086 6.149129 TCGTCTATGATTGAGCACTTGTAT 57.851 37.500 0.00 0.00 0.00 2.29
4213 8087 5.125578 ACTCGTCTATGATTGAGCACTTGTA 59.874 40.000 0.00 0.00 31.64 2.41
4214 8088 4.081972 ACTCGTCTATGATTGAGCACTTGT 60.082 41.667 0.00 0.00 31.64 3.16
4215 8089 4.428209 ACTCGTCTATGATTGAGCACTTG 58.572 43.478 0.00 0.00 31.64 3.16
4216 8090 4.158579 TGACTCGTCTATGATTGAGCACTT 59.841 41.667 0.00 0.00 31.64 3.16
4217 8091 3.696548 TGACTCGTCTATGATTGAGCACT 59.303 43.478 0.00 0.00 31.64 4.40
4218 8092 4.033990 TGACTCGTCTATGATTGAGCAC 57.966 45.455 0.00 0.00 31.64 4.40
4219 8093 4.424626 GTTGACTCGTCTATGATTGAGCA 58.575 43.478 0.00 0.00 31.64 4.26
4220 8094 3.483922 CGTTGACTCGTCTATGATTGAGC 59.516 47.826 0.00 0.00 31.64 4.26
4221 8095 4.038361 CCGTTGACTCGTCTATGATTGAG 58.962 47.826 2.93 0.00 34.65 3.02
4222 8096 3.692593 TCCGTTGACTCGTCTATGATTGA 59.307 43.478 2.93 0.00 0.00 2.57
4223 8097 4.028852 TCCGTTGACTCGTCTATGATTG 57.971 45.455 2.93 0.00 0.00 2.67
4224 8098 4.673441 CTTCCGTTGACTCGTCTATGATT 58.327 43.478 2.93 0.00 0.00 2.57
4225 8099 3.489398 GCTTCCGTTGACTCGTCTATGAT 60.489 47.826 2.93 0.00 0.00 2.45
4226 8100 2.159421 GCTTCCGTTGACTCGTCTATGA 60.159 50.000 2.93 0.00 0.00 2.15
4227 8101 2.186076 GCTTCCGTTGACTCGTCTATG 58.814 52.381 0.00 0.00 0.00 2.23
4228 8102 1.816835 TGCTTCCGTTGACTCGTCTAT 59.183 47.619 0.00 0.00 0.00 1.98
4229 8103 1.241165 TGCTTCCGTTGACTCGTCTA 58.759 50.000 0.00 0.00 0.00 2.59
4230 8104 0.387929 TTGCTTCCGTTGACTCGTCT 59.612 50.000 0.00 0.00 0.00 4.18
4231 8105 0.507358 GTTGCTTCCGTTGACTCGTC 59.493 55.000 0.00 0.00 0.00 4.20
4232 8106 0.179094 TGTTGCTTCCGTTGACTCGT 60.179 50.000 0.00 0.00 0.00 4.18
4233 8107 0.934496 TTGTTGCTTCCGTTGACTCG 59.066 50.000 0.00 0.00 0.00 4.18
4234 8108 4.631813 AGATATTGTTGCTTCCGTTGACTC 59.368 41.667 0.00 0.00 0.00 3.36
4235 8109 4.393062 CAGATATTGTTGCTTCCGTTGACT 59.607 41.667 0.00 0.00 0.00 3.41
4236 8110 4.391830 TCAGATATTGTTGCTTCCGTTGAC 59.608 41.667 0.00 0.00 0.00 3.18
4237 8111 4.574892 TCAGATATTGTTGCTTCCGTTGA 58.425 39.130 0.00 0.00 0.00 3.18
4238 8112 4.393062 ACTCAGATATTGTTGCTTCCGTTG 59.607 41.667 0.00 0.00 0.00 4.10
4239 8113 4.579869 ACTCAGATATTGTTGCTTCCGTT 58.420 39.130 0.00 0.00 0.00 4.44
4240 8114 4.207891 ACTCAGATATTGTTGCTTCCGT 57.792 40.909 0.00 0.00 0.00 4.69
4241 8115 5.109210 TGTACTCAGATATTGTTGCTTCCG 58.891 41.667 0.00 0.00 0.00 4.30
4242 8116 6.595772 CTGTACTCAGATATTGTTGCTTCC 57.404 41.667 0.00 0.00 43.76 3.46


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

AutoCloner maintained by Alex Coulton.