Multiple sequence alignment - TraesCS1A01G195400

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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 TraesCS1A01G195400 chr1A 100.000 4745 0 0 1 4745 353252624 353257368 0.000000e+00 8763.0
1 TraesCS1A01G195400 chr1A 93.333 75 3 1 99 173 503380393 503380465 5.020000e-20 110.0
2 TraesCS1A01G195400 chr1D 96.339 3906 97 23 170 4048 281406326 281402440 0.000000e+00 6379.0
3 TraesCS1A01G195400 chr1D 90.355 197 7 5 4249 4434 281402321 281402126 1.020000e-61 248.0
4 TraesCS1A01G195400 chr1D 100.000 112 0 0 4632 4743 281402013 281401902 1.730000e-49 207.0
5 TraesCS1A01G195400 chr1D 96.078 102 4 0 1 102 281406426 281406325 2.940000e-37 167.0
6 TraesCS1A01G195400 chr1D 95.775 71 1 2 99 168 8284233 8284302 3.880000e-21 113.0
7 TraesCS1A01G195400 chr1D 95.714 70 3 0 99 168 8284305 8284236 3.880000e-21 113.0
8 TraesCS1A01G195400 chr1D 95.652 69 2 1 100 168 6327182 6327249 5.020000e-20 110.0
9 TraesCS1A01G195400 chr1B 95.072 3896 124 36 172 4033 382214764 382218625 0.000000e+00 6069.0
10 TraesCS1A01G195400 chr1B 88.016 509 36 12 4253 4745 382218716 382219215 3.180000e-161 579.0
11 TraesCS1A01G195400 chr7A 87.500 136 14 3 4481 4615 6627355 6627222 2.290000e-33 154.0
12 TraesCS1A01G195400 chr7A 97.143 70 1 1 100 168 28155549 28155618 3.000000e-22 117.0
13 TraesCS1A01G195400 chr5D 87.023 131 17 0 4481 4611 433340772 433340902 1.060000e-31 148.0
14 TraesCS1A01G195400 chr4B 85.246 122 18 0 4482 4603 612030451 612030330 4.980000e-25 126.0
15 TraesCS1A01G195400 chrUn 84.127 126 20 0 4481 4606 80232304 80232429 6.450000e-24 122.0
16 TraesCS1A01G195400 chr3D 85.246 122 15 2 4484 4605 325979840 325979958 6.450000e-24 122.0
17 TraesCS1A01G195400 chr3D 85.714 112 14 2 4494 4605 320919795 320919904 3.000000e-22 117.0
18 TraesCS1A01G195400 chr3A 95.775 71 2 1 98 168 478807292 478807223 3.880000e-21 113.0
19 TraesCS1A01G195400 chr5B 94.595 74 1 3 98 168 315165276 315165349 1.400000e-20 111.0
20 TraesCS1A01G195400 chr4D 82.400 125 22 0 4481 4605 198602537 198602413 5.020000e-20 110.0
21 TraesCS1A01G195400 chr4A 94.444 72 3 1 100 171 562402192 562402122 5.020000e-20 110.0
22 TraesCS1A01G195400 chr2D 91.250 80 4 2 98 174 619666416 619666337 6.490000e-19 106.0
23 TraesCS1A01G195400 chr7B 80.469 128 25 0 4481 4608 45269706 45269833 1.090000e-16 99.0
24 TraesCS1A01G195400 chr5A 100.000 33 0 0 2804 2836 646897111 646897143 1.430000e-05 62.1


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 TraesCS1A01G195400 chr1A 353252624 353257368 4744 False 8763.00 8763 100.000 1 4745 1 chr1A.!!$F1 4744
1 TraesCS1A01G195400 chr1D 281401902 281406426 4524 True 1750.25 6379 95.693 1 4743 4 chr1D.!!$R2 4742
2 TraesCS1A01G195400 chr1B 382214764 382219215 4451 False 3324.00 6069 91.544 172 4745 2 chr1B.!!$F1 4573

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
107 108 0.530870 GCGCAGGTGAATACTCCCTC 60.531 60.000 0.30 0.0 0.0 4.30 F
593 604 0.674895 GCGGTTTCTGCATGAGGACT 60.675 55.000 0.00 0.0 0.0 3.85 F
594 605 1.405526 GCGGTTTCTGCATGAGGACTA 60.406 52.381 0.00 0.0 0.0 2.59 F
1839 1873 2.681064 TTGCTGCAGGGAATGGGC 60.681 61.111 17.12 0.0 0.0 5.36 F
3259 3298 1.463674 CAAGTACACCTTGGATGCCC 58.536 55.000 0.00 0.0 45.7 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1873 3.071874 TCCTTGGAACCAATAGCAGTG 57.928 47.619 6.74 0.0 35.20 3.66 R
2169 2203 2.260639 AGATGGAGGTGAGTGGATGT 57.739 50.000 0.00 0.0 0.00 3.06 R
2174 2208 3.969287 TCTCAAAGATGGAGGTGAGTG 57.031 47.619 0.00 0.0 38.87 3.51 R
3398 3437 0.767375 TCAGGCTCCAACAAGAAGCT 59.233 50.000 0.00 0.0 0.00 3.74 R
4489 4624 0.108424 GAGTTGTGGAGCAGAGCGAT 60.108 55.000 0.00 0.0 0.00 4.58 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 1.972872 ATTTCCTGATTAGGCCAGCG 58.027 50.000 5.01 0.00 44.22 5.18
50 51 0.748005 TTTCCTGATTAGGCCAGCGC 60.748 55.000 5.01 0.00 44.22 5.92
73 74 7.221838 GCGCTTTCAAATAATATTTGGCTTACA 59.778 33.333 21.40 2.91 0.00 2.41
102 103 2.829043 TTCGCGCGCAGGTGAATACT 62.829 55.000 32.61 0.00 31.90 2.12
103 104 2.860628 CGCGCGCAGGTGAATACTC 61.861 63.158 32.61 0.00 0.00 2.59
104 105 2.526120 GCGCGCAGGTGAATACTCC 61.526 63.158 29.10 0.00 0.00 3.85
105 106 1.883084 CGCGCAGGTGAATACTCCC 60.883 63.158 8.75 0.00 0.00 4.30
106 107 1.522569 GCGCAGGTGAATACTCCCT 59.477 57.895 0.30 0.00 0.00 4.20
107 108 0.530870 GCGCAGGTGAATACTCCCTC 60.531 60.000 0.30 0.00 0.00 4.30
108 109 1.115467 CGCAGGTGAATACTCCCTCT 58.885 55.000 0.00 0.00 0.00 3.69
109 110 1.202463 CGCAGGTGAATACTCCCTCTG 60.202 57.143 0.00 0.00 0.00 3.35
110 111 1.834263 GCAGGTGAATACTCCCTCTGT 59.166 52.381 0.00 0.00 0.00 3.41
111 112 3.031736 GCAGGTGAATACTCCCTCTGTA 58.968 50.000 0.00 0.00 0.00 2.74
112 113 3.451178 GCAGGTGAATACTCCCTCTGTAA 59.549 47.826 0.00 0.00 0.00 2.41
113 114 4.081087 GCAGGTGAATACTCCCTCTGTAAA 60.081 45.833 0.00 0.00 0.00 2.01
114 115 5.420409 CAGGTGAATACTCCCTCTGTAAAC 58.580 45.833 0.00 0.00 0.00 2.01
115 116 5.187967 CAGGTGAATACTCCCTCTGTAAACT 59.812 44.000 0.00 0.00 0.00 2.66
116 117 6.380274 CAGGTGAATACTCCCTCTGTAAACTA 59.620 42.308 0.00 0.00 0.00 2.24
117 118 6.958192 AGGTGAATACTCCCTCTGTAAACTAA 59.042 38.462 0.00 0.00 0.00 2.24
118 119 7.624077 AGGTGAATACTCCCTCTGTAAACTAAT 59.376 37.037 0.00 0.00 0.00 1.73
119 120 8.921205 GGTGAATACTCCCTCTGTAAACTAATA 58.079 37.037 0.00 0.00 0.00 0.98
126 127 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
127 128 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
128 129 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
129 130 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
130 131 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
145 146 9.733219 ATAAGAGCGTTTAGATACTAAACACTC 57.267 33.333 26.97 26.97 42.39 3.51
146 147 7.393841 AGAGCGTTTAGATACTAAACACTCT 57.606 36.000 29.07 29.07 44.93 3.24
147 148 7.828712 AGAGCGTTTAGATACTAAACACTCTT 58.171 34.615 29.07 20.60 46.28 2.85
148 149 8.954350 AGAGCGTTTAGATACTAAACACTCTTA 58.046 33.333 29.07 2.03 46.28 2.10
149 150 9.733219 GAGCGTTTAGATACTAAACACTCTTAT 57.267 33.333 26.97 10.51 40.56 1.73
166 167 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
168 169 8.862085 ACTCTTATATTAGTTTACAGAGGGAGC 58.138 37.037 0.00 0.00 32.21 4.70
169 170 8.777578 TCTTATATTAGTTTACAGAGGGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
170 171 8.639761 TCTTATATTAGTTTACAGAGGGAGCAC 58.360 37.037 0.00 0.00 0.00 4.40
180 181 3.118482 ACAGAGGGAGCACATGATAGTTG 60.118 47.826 0.00 0.00 0.00 3.16
208 209 5.992217 GTCATAATCGTAATTTCTGAGCCCT 59.008 40.000 0.00 0.00 0.00 5.19
281 282 3.940209 TTAGGCCAGCTGTTTCAAATG 57.060 42.857 13.81 0.00 0.00 2.32
472 483 3.599514 GCGCGCAAATGAATACATGATAC 59.400 43.478 29.10 0.00 36.79 2.24
476 487 6.564686 CGCGCAAATGAATACATGATACTTCT 60.565 38.462 8.75 0.00 36.79 2.85
518 529 3.321682 TGAGCCCAATTAATGCAATAGCC 59.678 43.478 0.00 0.00 41.13 3.93
587 598 1.337074 ACAAATGGCGGTTTCTGCATG 60.337 47.619 3.03 0.00 0.00 4.06
588 599 1.067706 CAAATGGCGGTTTCTGCATGA 60.068 47.619 0.00 0.00 0.00 3.07
590 601 1.033746 ATGGCGGTTTCTGCATGAGG 61.034 55.000 0.00 0.00 0.00 3.86
591 602 1.377202 GGCGGTTTCTGCATGAGGA 60.377 57.895 0.00 0.00 0.00 3.71
592 603 1.648467 GGCGGTTTCTGCATGAGGAC 61.648 60.000 0.00 0.00 0.00 3.85
593 604 0.674895 GCGGTTTCTGCATGAGGACT 60.675 55.000 0.00 0.00 0.00 3.85
594 605 1.405526 GCGGTTTCTGCATGAGGACTA 60.406 52.381 0.00 0.00 0.00 2.59
596 607 2.868583 CGGTTTCTGCATGAGGACTATG 59.131 50.000 0.00 0.00 0.00 2.23
874 908 5.116882 CCGACCGATATTCTTTTTCTCCTT 58.883 41.667 0.00 0.00 0.00 3.36
1538 1572 6.883217 GGCAATGGAGATCATGTCTATGTTAT 59.117 38.462 0.00 0.00 37.29 1.89
1659 1693 3.699038 CCAGTGCTAAGAGAGTTAGAGCT 59.301 47.826 0.00 0.00 34.19 4.09
1666 1700 5.588648 GCTAAGAGAGTTAGAGCTGAGAAGA 59.411 44.000 0.00 0.00 0.00 2.87
1839 1873 2.681064 TTGCTGCAGGGAATGGGC 60.681 61.111 17.12 0.00 0.00 5.36
1934 1968 3.795688 TGATCTCTTCCAAAAGCAGGT 57.204 42.857 0.00 0.00 32.18 4.00
2188 2222 2.260639 ACATCCACTCACCTCCATCT 57.739 50.000 0.00 0.00 0.00 2.90
2191 2225 3.276857 CATCCACTCACCTCCATCTTTG 58.723 50.000 0.00 0.00 0.00 2.77
2192 2226 2.619931 TCCACTCACCTCCATCTTTGA 58.380 47.619 0.00 0.00 0.00 2.69
2193 2227 2.568956 TCCACTCACCTCCATCTTTGAG 59.431 50.000 0.00 0.00 41.14 3.02
2194 2228 2.568956 CCACTCACCTCCATCTTTGAGA 59.431 50.000 4.51 0.00 38.19 3.27
2195 2229 3.008375 CCACTCACCTCCATCTTTGAGAA 59.992 47.826 4.51 0.00 38.19 2.87
2283 2322 6.948886 TGGCACCATTTATTTACTTCCACTTA 59.051 34.615 0.00 0.00 0.00 2.24
2594 2633 9.690913 ATTACATTGTATGGGATATGAATCTGG 57.309 33.333 0.00 0.00 32.29 3.86
2736 2775 9.282247 GCAGTTCATAACAAATGTCAATCTAAG 57.718 33.333 0.00 0.00 0.00 2.18
2800 2839 5.991328 TCTTCACACAAGAAGATTGTCAC 57.009 39.130 2.50 0.00 46.62 3.67
3259 3298 1.463674 CAAGTACACCTTGGATGCCC 58.536 55.000 0.00 0.00 45.70 5.36
3380 3419 4.155826 CAGTTCTTGGTTGTTGTGTTCTCA 59.844 41.667 0.00 0.00 0.00 3.27
3398 3437 4.214310 TCTCAATTGAAAACTGGCCTTCA 58.786 39.130 9.88 2.04 0.00 3.02
3513 3552 1.537202 GTTGGTGACAGAATGCTGGTC 59.463 52.381 5.47 1.14 46.60 4.02
3544 3583 0.178068 TCGGCTCCAAGATAAGGTGC 59.822 55.000 0.00 0.00 43.13 5.01
3547 3586 0.815615 GCTCCAAGATAAGGTGCGGG 60.816 60.000 0.00 0.00 36.13 6.13
3559 3598 1.003233 GTGCGGGCCTTCTCTCTTT 60.003 57.895 0.84 0.00 0.00 2.52
3596 3635 1.679944 CCTGATTCATTGTCTGCCCGT 60.680 52.381 0.00 0.00 0.00 5.28
3775 3814 1.192146 TGGAGGAAGGAACTGGTCGG 61.192 60.000 0.00 0.00 40.86 4.79
3844 3884 0.390866 CTGTCTGTGAATCTGCCGCT 60.391 55.000 0.00 0.00 0.00 5.52
3845 3885 0.390340 TGTCTGTGAATCTGCCGCTC 60.390 55.000 0.00 0.00 0.00 5.03
3846 3886 0.108424 GTCTGTGAATCTGCCGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
3847 3887 0.108472 TCTGTGAATCTGCCGCTCTG 60.108 55.000 0.00 0.00 0.00 3.35
3869 3909 5.529791 TGTCTGTCTGTCTGTTTTAGTAGC 58.470 41.667 0.00 0.00 0.00 3.58
3928 3968 3.728385 AGATGGTTTCAAGGGAGAAGG 57.272 47.619 0.00 0.00 0.00 3.46
3929 3969 2.095461 GATGGTTTCAAGGGAGAAGGC 58.905 52.381 0.00 0.00 0.00 4.35
3982 4022 7.202016 TGTCCAATCAACATTGAGTTTAGTC 57.798 36.000 0.23 0.00 41.97 2.59
4033 4076 7.298507 TCTAACTTATGTGTTTATTCACGCC 57.701 36.000 0.00 0.00 40.74 5.68
4035 4078 6.569179 AACTTATGTGTTTATTCACGCCTT 57.431 33.333 0.00 0.00 40.74 4.35
4037 4080 6.608610 ACTTATGTGTTTATTCACGCCTTTC 58.391 36.000 0.00 0.00 40.74 2.62
4043 4086 1.355971 TATTCACGCCTTTCTGTCGC 58.644 50.000 0.00 0.00 0.00 5.19
4048 4091 1.667830 CGCCTTTCTGTCGCCTTCA 60.668 57.895 0.00 0.00 0.00 3.02
4049 4092 1.021390 CGCCTTTCTGTCGCCTTCAT 61.021 55.000 0.00 0.00 0.00 2.57
4050 4093 0.729690 GCCTTTCTGTCGCCTTCATC 59.270 55.000 0.00 0.00 0.00 2.92
4051 4094 1.677217 GCCTTTCTGTCGCCTTCATCT 60.677 52.381 0.00 0.00 0.00 2.90
4052 4095 2.275318 CCTTTCTGTCGCCTTCATCTC 58.725 52.381 0.00 0.00 0.00 2.75
4053 4096 2.275318 CTTTCTGTCGCCTTCATCTCC 58.725 52.381 0.00 0.00 0.00 3.71
4054 4097 0.173481 TTCTGTCGCCTTCATCTCCG 59.827 55.000 0.00 0.00 0.00 4.63
4055 4098 1.227089 CTGTCGCCTTCATCTCCGG 60.227 63.158 0.00 0.00 0.00 5.14
4056 4099 1.949847 CTGTCGCCTTCATCTCCGGT 61.950 60.000 0.00 0.00 0.00 5.28
4057 4100 0.681887 TGTCGCCTTCATCTCCGGTA 60.682 55.000 0.00 0.00 0.00 4.02
4058 4101 0.674534 GTCGCCTTCATCTCCGGTAT 59.325 55.000 0.00 0.00 0.00 2.73
4059 4102 0.673985 TCGCCTTCATCTCCGGTATG 59.326 55.000 0.00 7.30 0.00 2.39
4060 4103 0.673985 CGCCTTCATCTCCGGTATGA 59.326 55.000 15.38 15.38 0.00 2.15
4061 4104 1.603172 CGCCTTCATCTCCGGTATGAC 60.603 57.143 17.99 9.11 33.18 3.06
4062 4105 1.603172 GCCTTCATCTCCGGTATGACG 60.603 57.143 17.99 16.23 33.18 4.35
4063 4106 1.603172 CCTTCATCTCCGGTATGACGC 60.603 57.143 17.99 0.00 33.18 5.19
4064 4107 1.067060 CTTCATCTCCGGTATGACGCA 59.933 52.381 17.99 6.89 33.18 5.24
4065 4108 1.107945 TCATCTCCGGTATGACGCAA 58.892 50.000 15.38 0.00 0.00 4.85
4066 4109 1.478916 TCATCTCCGGTATGACGCAAA 59.521 47.619 15.38 0.00 0.00 3.68
4067 4110 1.860950 CATCTCCGGTATGACGCAAAG 59.139 52.381 12.46 0.00 0.00 2.77
4068 4111 0.174845 TCTCCGGTATGACGCAAAGG 59.825 55.000 0.00 0.00 0.00 3.11
4069 4112 0.810031 CTCCGGTATGACGCAAAGGG 60.810 60.000 0.00 0.00 0.00 3.95
4070 4113 1.219664 CCGGTATGACGCAAAGGGA 59.780 57.895 0.00 0.00 0.00 4.20
4071 4114 0.179056 CCGGTATGACGCAAAGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
4072 4115 0.937304 CGGTATGACGCAAAGGGATG 59.063 55.000 0.00 0.00 0.00 3.51
4073 4116 0.663153 GGTATGACGCAAAGGGATGC 59.337 55.000 0.00 0.00 42.94 3.91
4074 4117 0.663153 GTATGACGCAAAGGGATGCC 59.337 55.000 0.00 0.00 43.47 4.40
4075 4118 0.546122 TATGACGCAAAGGGATGCCT 59.454 50.000 0.00 0.00 43.47 4.75
4076 4119 1.033746 ATGACGCAAAGGGATGCCTG 61.034 55.000 6.51 0.00 43.47 4.85
4077 4120 3.056313 GACGCAAAGGGATGCCTGC 62.056 63.158 6.51 7.01 43.47 4.85
4078 4121 2.753043 CGCAAAGGGATGCCTGCT 60.753 61.111 6.51 0.00 43.47 4.24
4079 4122 2.768492 CGCAAAGGGATGCCTGCTC 61.768 63.158 6.51 0.00 43.47 4.26
4080 4123 2.768492 GCAAAGGGATGCCTGCTCG 61.768 63.158 6.51 0.00 40.49 5.03
4081 4124 1.078214 CAAAGGGATGCCTGCTCGA 60.078 57.895 6.51 0.00 0.00 4.04
4082 4125 1.078143 AAAGGGATGCCTGCTCGAC 60.078 57.895 6.51 0.00 0.00 4.20
4083 4126 2.859273 AAAGGGATGCCTGCTCGACG 62.859 60.000 6.51 0.00 0.00 5.12
4084 4127 4.899239 GGGATGCCTGCTCGACGG 62.899 72.222 0.00 0.00 0.00 4.79
4089 4132 3.917760 GCCTGCTCGACGGCCTAT 61.918 66.667 0.00 0.00 40.43 2.57
4090 4133 2.815308 CCTGCTCGACGGCCTATT 59.185 61.111 0.00 0.00 0.00 1.73
4091 4134 2.038690 CCTGCTCGACGGCCTATTA 58.961 57.895 0.00 0.00 0.00 0.98
4092 4135 0.387929 CCTGCTCGACGGCCTATTAA 59.612 55.000 0.00 0.00 0.00 1.40
4093 4136 1.603172 CCTGCTCGACGGCCTATTAAG 60.603 57.143 0.00 0.00 0.00 1.85
4094 4137 0.387929 TGCTCGACGGCCTATTAAGG 59.612 55.000 0.00 0.00 46.76 2.69
4105 4148 1.813513 CTATTAAGGAGGCCCGCATG 58.186 55.000 0.00 0.00 37.58 4.06
4106 4149 1.347707 CTATTAAGGAGGCCCGCATGA 59.652 52.381 0.00 0.00 37.58 3.07
4107 4150 0.773644 ATTAAGGAGGCCCGCATGAT 59.226 50.000 0.00 0.00 37.58 2.45
4108 4151 0.179020 TTAAGGAGGCCCGCATGATG 60.179 55.000 0.00 0.00 37.58 3.07
4109 4152 2.055689 TAAGGAGGCCCGCATGATGG 62.056 60.000 0.00 0.00 37.58 3.51
4136 4179 2.516227 TCTCAGTGGTAGAGAGGGTG 57.484 55.000 0.00 0.00 37.22 4.61
4138 4181 0.409876 TCAGTGGTAGAGAGGGTGCT 59.590 55.000 0.00 0.00 0.00 4.40
4139 4182 0.820871 CAGTGGTAGAGAGGGTGCTC 59.179 60.000 0.00 0.00 35.11 4.26
4140 4183 0.324830 AGTGGTAGAGAGGGTGCTCC 60.325 60.000 0.00 0.00 35.49 4.70
4150 4193 0.475906 AGGGTGCTCCTGATTATGGC 59.524 55.000 4.53 0.00 46.07 4.40
4151 4194 0.886490 GGGTGCTCCTGATTATGGCG 60.886 60.000 4.53 0.00 0.00 5.69
4152 4195 0.179045 GGTGCTCCTGATTATGGCGT 60.179 55.000 0.00 0.00 0.00 5.68
4153 4196 1.221414 GTGCTCCTGATTATGGCGTC 58.779 55.000 0.00 0.00 0.00 5.19
4156 4199 1.202580 GCTCCTGATTATGGCGTCTGT 60.203 52.381 0.00 0.00 0.00 3.41
4157 4200 2.743183 GCTCCTGATTATGGCGTCTGTT 60.743 50.000 0.00 0.00 0.00 3.16
4158 4201 2.868583 CTCCTGATTATGGCGTCTGTTG 59.131 50.000 0.00 0.00 0.00 3.33
4159 4202 1.942657 CCTGATTATGGCGTCTGTTGG 59.057 52.381 0.00 0.00 0.00 3.77
4160 4203 1.331756 CTGATTATGGCGTCTGTTGGC 59.668 52.381 0.00 0.00 0.00 4.52
4161 4204 1.339535 TGATTATGGCGTCTGTTGGCA 60.340 47.619 0.00 0.00 46.52 4.92
4168 4211 1.444119 GCGTCTGTTGGCAGGTGAAA 61.444 55.000 0.00 0.00 42.78 2.69
4175 4218 4.041567 TCTGTTGGCAGGTGAAATAGAGAA 59.958 41.667 0.00 0.00 42.78 2.87
4177 4220 4.701651 TGTTGGCAGGTGAAATAGAGAATG 59.298 41.667 0.00 0.00 0.00 2.67
4189 4232 7.487189 GTGAAATAGAGAATGTTGGCATTTCAG 59.513 37.037 6.99 0.00 44.61 3.02
4190 4233 3.863142 AGAGAATGTTGGCATTTCAGC 57.137 42.857 0.00 0.00 44.61 4.26
4206 4249 8.626093 GCATTTCAGCCTTTCTTCTATAAAAG 57.374 34.615 0.00 0.00 33.26 2.27
4207 4250 8.462016 GCATTTCAGCCTTTCTTCTATAAAAGA 58.538 33.333 0.00 0.00 35.02 2.52
4209 4252 9.965902 ATTTCAGCCTTTCTTCTATAAAAGAGA 57.034 29.630 0.00 0.00 36.66 3.10
4210 4253 9.793259 TTTCAGCCTTTCTTCTATAAAAGAGAA 57.207 29.630 0.00 0.00 36.66 2.87
4211 4254 9.965902 TTCAGCCTTTCTTCTATAAAAGAGAAT 57.034 29.630 0.00 0.00 36.66 2.40
4212 4255 9.606631 TCAGCCTTTCTTCTATAAAAGAGAATC 57.393 33.333 0.00 0.00 36.66 2.52
4213 4256 8.835439 CAGCCTTTCTTCTATAAAAGAGAATCC 58.165 37.037 0.00 0.00 36.66 3.01
4214 4257 8.552296 AGCCTTTCTTCTATAAAAGAGAATCCA 58.448 33.333 0.00 0.00 36.66 3.41
4215 4258 8.835439 GCCTTTCTTCTATAAAAGAGAATCCAG 58.165 37.037 0.00 0.00 36.66 3.86
4216 4259 9.898152 CCTTTCTTCTATAAAAGAGAATCCAGT 57.102 33.333 0.00 0.00 36.66 4.00
4231 4274 6.972722 AGAATCCAGTAGCGAATAAGAGTAC 58.027 40.000 0.00 0.00 0.00 2.73
4238 4281 2.947652 AGCGAATAAGAGTACGGCTGTA 59.052 45.455 0.00 0.00 0.00 2.74
4247 4290 2.820787 GAGTACGGCTGTATGAGGCTAT 59.179 50.000 9.01 0.00 45.32 2.97
4249 4292 0.034059 ACGGCTGTATGAGGCTATGC 59.966 55.000 0.00 0.00 45.32 3.14
4263 4319 2.548920 GGCTATGCTCTGTGTACATCCC 60.549 54.545 0.00 0.00 0.00 3.85
4271 4327 4.684485 GCTCTGTGTACATCCCTAAGCAAT 60.684 45.833 0.00 0.00 0.00 3.56
4276 4333 5.589855 TGTGTACATCCCTAAGCAATGAATG 59.410 40.000 0.00 0.00 0.00 2.67
4277 4334 5.009010 GTGTACATCCCTAAGCAATGAATGG 59.991 44.000 0.00 0.00 0.00 3.16
4291 4348 6.266103 AGCAATGAATGGAGTCTTGAAAAAGA 59.734 34.615 0.00 0.00 0.00 2.52
4294 4351 9.316730 CAATGAATGGAGTCTTGAAAAAGAAAA 57.683 29.630 0.00 0.00 0.00 2.29
4295 4352 9.538508 AATGAATGGAGTCTTGAAAAAGAAAAG 57.461 29.630 0.00 0.00 0.00 2.27
4296 4353 8.292444 TGAATGGAGTCTTGAAAAAGAAAAGA 57.708 30.769 0.00 0.00 0.00 2.52
4301 4358 9.942850 TGGAGTCTTGAAAAAGAAAAGAAAAAT 57.057 25.926 0.00 0.00 32.03 1.82
4345 4421 2.908940 GGCGGGGCATCTGATTGG 60.909 66.667 0.00 0.00 0.00 3.16
4453 4578 5.904941 ACACTGATGTCAATTTTCTTGCAA 58.095 33.333 0.00 0.00 31.55 4.08
4467 4602 9.685828 AATTTTCTTGCAAATTGAAATGGAATG 57.314 25.926 11.72 0.00 35.45 2.67
4481 4616 1.003118 TGGAATGTAAGGCGCTGTTCT 59.997 47.619 7.64 0.00 0.00 3.01
4482 4617 1.398390 GGAATGTAAGGCGCTGTTCTG 59.602 52.381 7.64 0.00 0.00 3.02
4484 4619 2.185004 ATGTAAGGCGCTGTTCTGTT 57.815 45.000 7.64 0.00 0.00 3.16
4485 4620 1.961793 TGTAAGGCGCTGTTCTGTTT 58.038 45.000 7.64 0.00 0.00 2.83
4487 4622 1.069227 GTAAGGCGCTGTTCTGTTTGG 60.069 52.381 7.64 0.00 0.00 3.28
4488 4623 0.751643 AAGGCGCTGTTCTGTTTGGT 60.752 50.000 7.64 0.00 0.00 3.67
4489 4624 0.107831 AGGCGCTGTTCTGTTTGGTA 59.892 50.000 7.64 0.00 0.00 3.25
4490 4625 1.165270 GGCGCTGTTCTGTTTGGTAT 58.835 50.000 7.64 0.00 0.00 2.73
4491 4626 1.130561 GGCGCTGTTCTGTTTGGTATC 59.869 52.381 7.64 0.00 0.00 2.24
4492 4627 1.201921 GCGCTGTTCTGTTTGGTATCG 60.202 52.381 0.00 0.00 0.00 2.92
4493 4628 1.201921 CGCTGTTCTGTTTGGTATCGC 60.202 52.381 0.00 0.00 0.00 4.58
4494 4629 2.076863 GCTGTTCTGTTTGGTATCGCT 58.923 47.619 0.00 0.00 0.00 4.93
4495 4630 2.094417 GCTGTTCTGTTTGGTATCGCTC 59.906 50.000 0.00 0.00 0.00 5.03
4496 4631 3.589988 CTGTTCTGTTTGGTATCGCTCT 58.410 45.455 0.00 0.00 0.00 4.09
4511 4646 1.079543 CTCTGCTCCACAACTCCGG 60.080 63.158 0.00 0.00 0.00 5.14
4512 4647 2.046892 CTGCTCCACAACTCCGGG 60.047 66.667 0.00 0.00 0.00 5.73
4529 4664 2.048127 GAGCGGAGTTGGCGAAGT 60.048 61.111 0.00 0.00 35.00 3.01
4542 4677 2.100584 TGGCGAAGTTGCAGTTCAAAAT 59.899 40.909 10.51 0.00 36.26 1.82
4544 4679 3.371168 GCGAAGTTGCAGTTCAAAATGA 58.629 40.909 10.51 0.00 36.26 2.57
4562 4697 1.425066 TGATGGAGTTGCAGTTTCCCT 59.575 47.619 9.80 1.85 0.00 4.20
4604 4740 0.252197 GTGATTACCGAACAGGGCCT 59.748 55.000 0.00 0.00 46.96 5.19
4615 4751 2.420058 ACAGGGCCTAAATGTAGCAC 57.580 50.000 5.28 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.179176 TGCGCGCGAAAATATGCTTT 60.179 45.000 37.18 0.00 0.00 3.51
87 88 1.883084 GGGAGTATTCACCTGCGCG 60.883 63.158 0.00 0.00 0.00 6.86
102 103 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
103 104 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
104 105 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
140 141 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
142 143 8.862085 GCTCCCTCTGTAAACTAATATAAGAGT 58.138 37.037 0.00 0.00 0.00 3.24
143 144 8.861086 TGCTCCCTCTGTAAACTAATATAAGAG 58.139 37.037 0.00 0.00 0.00 2.85
144 145 8.639761 GTGCTCCCTCTGTAAACTAATATAAGA 58.360 37.037 0.00 0.00 0.00 2.10
145 146 8.421784 TGTGCTCCCTCTGTAAACTAATATAAG 58.578 37.037 0.00 0.00 0.00 1.73
146 147 8.313944 TGTGCTCCCTCTGTAAACTAATATAA 57.686 34.615 0.00 0.00 0.00 0.98
147 148 7.907841 TGTGCTCCCTCTGTAAACTAATATA 57.092 36.000 0.00 0.00 0.00 0.86
148 149 6.808321 TGTGCTCCCTCTGTAAACTAATAT 57.192 37.500 0.00 0.00 0.00 1.28
149 150 6.382859 TCATGTGCTCCCTCTGTAAACTAATA 59.617 38.462 0.00 0.00 0.00 0.98
150 151 5.189736 TCATGTGCTCCCTCTGTAAACTAAT 59.810 40.000 0.00 0.00 0.00 1.73
151 152 4.530553 TCATGTGCTCCCTCTGTAAACTAA 59.469 41.667 0.00 0.00 0.00 2.24
152 153 4.093743 TCATGTGCTCCCTCTGTAAACTA 58.906 43.478 0.00 0.00 0.00 2.24
153 154 2.906389 TCATGTGCTCCCTCTGTAAACT 59.094 45.455 0.00 0.00 0.00 2.66
154 155 3.334583 TCATGTGCTCCCTCTGTAAAC 57.665 47.619 0.00 0.00 0.00 2.01
155 156 4.716784 ACTATCATGTGCTCCCTCTGTAAA 59.283 41.667 0.00 0.00 0.00 2.01
156 157 4.290093 ACTATCATGTGCTCCCTCTGTAA 58.710 43.478 0.00 0.00 0.00 2.41
157 158 3.916035 ACTATCATGTGCTCCCTCTGTA 58.084 45.455 0.00 0.00 0.00 2.74
158 159 2.756907 ACTATCATGTGCTCCCTCTGT 58.243 47.619 0.00 0.00 0.00 3.41
159 160 3.118482 ACAACTATCATGTGCTCCCTCTG 60.118 47.826 0.00 0.00 0.00 3.35
160 161 3.110705 ACAACTATCATGTGCTCCCTCT 58.889 45.455 0.00 0.00 0.00 3.69
161 162 3.201290 CACAACTATCATGTGCTCCCTC 58.799 50.000 0.00 0.00 41.42 4.30
162 163 3.272574 CACAACTATCATGTGCTCCCT 57.727 47.619 0.00 0.00 41.42 4.20
169 170 5.175673 CGATTATGACGCACAACTATCATGT 59.824 40.000 0.00 0.00 33.84 3.21
170 171 5.175673 ACGATTATGACGCACAACTATCATG 59.824 40.000 0.00 0.00 33.84 3.07
180 181 6.268797 TCAGAAATTACGATTATGACGCAC 57.731 37.500 0.00 0.00 0.00 5.34
385 386 4.801330 AATCAGGAGAACACGTGATACA 57.199 40.909 25.01 0.00 42.10 2.29
386 387 5.282510 CCTAATCAGGAGAACACGTGATAC 58.717 45.833 25.01 12.49 45.91 2.24
387 388 4.202121 GCCTAATCAGGAGAACACGTGATA 60.202 45.833 25.01 0.00 45.91 2.15
388 389 3.430929 GCCTAATCAGGAGAACACGTGAT 60.431 47.826 25.01 11.26 45.91 3.06
389 390 2.094182 GCCTAATCAGGAGAACACGTGA 60.094 50.000 25.01 0.00 45.91 4.35
390 391 2.271800 GCCTAATCAGGAGAACACGTG 58.728 52.381 15.48 15.48 45.91 4.49
391 392 1.899814 TGCCTAATCAGGAGAACACGT 59.100 47.619 0.00 0.00 45.91 4.49
392 393 2.672961 TGCCTAATCAGGAGAACACG 57.327 50.000 0.00 0.00 45.91 4.49
393 394 2.680339 GCTTGCCTAATCAGGAGAACAC 59.320 50.000 0.00 0.00 45.91 3.32
472 483 9.177608 TCAGAAATTACAATTATCACCCAGAAG 57.822 33.333 0.00 0.00 0.00 2.85
476 487 6.321181 GGCTCAGAAATTACAATTATCACCCA 59.679 38.462 0.00 0.00 0.00 4.51
518 529 2.242769 TATATAGCGCGCTTGAGACG 57.757 50.000 41.04 0.00 0.00 4.18
587 598 9.678260 ATTATCTATTGATTTGCCATAGTCCTC 57.322 33.333 0.00 0.00 34.32 3.71
591 602 9.812347 TGGAATTATCTATTGATTTGCCATAGT 57.188 29.630 0.00 0.00 34.32 2.12
798 819 5.347124 TGAAAAGGGAAGATAGGTCCTGTA 58.653 41.667 0.00 0.00 35.33 2.74
799 820 4.175962 TGAAAAGGGAAGATAGGTCCTGT 58.824 43.478 0.00 0.00 35.33 4.00
800 821 4.384647 CCTGAAAAGGGAAGATAGGTCCTG 60.385 50.000 0.00 0.00 35.33 3.86
801 822 3.783082 CCTGAAAAGGGAAGATAGGTCCT 59.217 47.826 0.00 0.00 35.33 3.85
803 824 4.846168 ACCTGAAAAGGGAAGATAGGTC 57.154 45.455 0.00 0.00 31.83 3.85
804 825 5.516768 GGAAACCTGAAAAGGGAAGATAGGT 60.517 44.000 0.00 0.00 38.62 3.08
805 826 4.950475 GGAAACCTGAAAAGGGAAGATAGG 59.050 45.833 0.00 0.00 0.00 2.57
874 908 7.228706 TGAGCATAGACTACTTCAATATCGACA 59.771 37.037 0.00 0.00 0.00 4.35
1510 1544 3.972133 AGACATGATCTCCATTGCCAAA 58.028 40.909 0.00 0.00 28.16 3.28
1512 1546 4.103627 ACATAGACATGATCTCCATTGCCA 59.896 41.667 0.00 0.00 39.04 4.92
1561 1595 6.698008 TGCTCCATACTGGTCATTTATTTG 57.302 37.500 0.00 0.00 39.03 2.32
1694 1728 5.186021 TCATTCTCTCCCACAGTTTCTCTAC 59.814 44.000 0.00 0.00 0.00 2.59
1839 1873 3.071874 TCCTTGGAACCAATAGCAGTG 57.928 47.619 6.74 0.00 35.20 3.66
2169 2203 2.260639 AGATGGAGGTGAGTGGATGT 57.739 50.000 0.00 0.00 0.00 3.06
2174 2208 3.969287 TCTCAAAGATGGAGGTGAGTG 57.031 47.619 0.00 0.00 38.87 3.51
2179 2213 8.207545 GTGAATATACTTCTCAAAGATGGAGGT 58.792 37.037 0.00 0.00 36.30 3.85
2301 2340 8.568732 AAAAATACAATGGTAAGTTGACAACG 57.431 30.769 12.54 0.00 36.23 4.10
2736 2775 5.527582 TGAGAAGGCTGACTTGTAAGAAAAC 59.472 40.000 0.00 0.00 40.21 2.43
2800 2839 3.247886 CCAGTGAAGCATCAGATGAATCG 59.752 47.826 15.12 0.00 35.88 3.34
3259 3298 8.483307 AAATAGCTGCAAATAACATGGAAAAG 57.517 30.769 1.02 0.00 0.00 2.27
3354 3393 5.418840 AGAACACAACAACCAAGAACTGATT 59.581 36.000 0.00 0.00 0.00 2.57
3380 3419 2.967887 AGCTGAAGGCCAGTTTTCAATT 59.032 40.909 5.01 0.00 44.71 2.32
3398 3437 0.767375 TCAGGCTCCAACAAGAAGCT 59.233 50.000 0.00 0.00 0.00 3.74
3399 3438 1.163554 CTCAGGCTCCAACAAGAAGC 58.836 55.000 0.00 0.00 0.00 3.86
3513 3552 2.917933 TGGAGCCGAATTATTGTGGAG 58.082 47.619 0.00 0.00 0.00 3.86
3544 3583 1.677217 CCTCAAAAGAGAGAAGGCCCG 60.677 57.143 0.00 0.00 37.87 6.13
3547 3586 1.082690 CGCCTCAAAAGAGAGAAGGC 58.917 55.000 1.59 1.59 37.87 4.35
3775 3814 4.943705 TCCTTCCAACTCATGATAACAAGC 59.056 41.667 0.00 0.00 0.00 4.01
3844 3884 5.854010 ACTAAAACAGACAGACAGACAGA 57.146 39.130 0.00 0.00 0.00 3.41
3845 3885 5.631512 GCTACTAAAACAGACAGACAGACAG 59.368 44.000 0.00 0.00 0.00 3.51
3846 3886 5.302059 AGCTACTAAAACAGACAGACAGACA 59.698 40.000 0.00 0.00 0.00 3.41
3847 3887 5.631512 CAGCTACTAAAACAGACAGACAGAC 59.368 44.000 0.00 0.00 0.00 3.51
3869 3909 1.532868 CGGACAGTTTCCTCTTTGCAG 59.467 52.381 0.00 0.00 43.25 4.41
3889 3929 7.783042 ACCATCTTAGGTTCACAAGTATACTC 58.217 38.462 5.70 0.00 39.34 2.59
3928 3968 2.838813 ACTAGGAGGGTAAACAAGGAGC 59.161 50.000 0.00 0.00 0.00 4.70
3929 3969 5.246307 CAAACTAGGAGGGTAAACAAGGAG 58.754 45.833 0.00 0.00 0.00 3.69
4012 4055 6.569179 AAGGCGTGAATAAACACATAAGTT 57.431 33.333 0.00 0.00 40.34 2.66
4014 4057 6.742718 CAGAAAGGCGTGAATAAACACATAAG 59.257 38.462 0.00 0.00 40.34 1.73
4017 4060 4.518970 ACAGAAAGGCGTGAATAAACACAT 59.481 37.500 0.00 0.00 40.34 3.21
4033 4076 2.275318 GGAGATGAAGGCGACAGAAAG 58.725 52.381 0.00 0.00 0.00 2.62
4035 4078 0.173481 CGGAGATGAAGGCGACAGAA 59.827 55.000 0.00 0.00 0.00 3.02
4037 4080 1.227089 CCGGAGATGAAGGCGACAG 60.227 63.158 0.00 0.00 0.00 3.51
4043 4086 1.603172 GCGTCATACCGGAGATGAAGG 60.603 57.143 25.52 19.73 0.00 3.46
4048 4091 1.202533 CCTTTGCGTCATACCGGAGAT 60.203 52.381 9.46 0.00 0.00 2.75
4049 4092 0.174845 CCTTTGCGTCATACCGGAGA 59.825 55.000 9.46 0.00 0.00 3.71
4050 4093 0.810031 CCCTTTGCGTCATACCGGAG 60.810 60.000 9.46 0.00 0.00 4.63
4051 4094 1.219664 CCCTTTGCGTCATACCGGA 59.780 57.895 9.46 0.00 0.00 5.14
4052 4095 0.179056 ATCCCTTTGCGTCATACCGG 60.179 55.000 0.00 0.00 0.00 5.28
4053 4096 0.937304 CATCCCTTTGCGTCATACCG 59.063 55.000 0.00 0.00 0.00 4.02
4054 4097 0.663153 GCATCCCTTTGCGTCATACC 59.337 55.000 0.00 0.00 32.06 2.73
4055 4098 0.663153 GGCATCCCTTTGCGTCATAC 59.337 55.000 0.00 0.00 43.71 2.39
4056 4099 0.546122 AGGCATCCCTTTGCGTCATA 59.454 50.000 0.00 0.00 43.71 2.15
4057 4100 1.033746 CAGGCATCCCTTTGCGTCAT 61.034 55.000 0.00 0.00 43.71 3.06
4058 4101 1.675310 CAGGCATCCCTTTGCGTCA 60.675 57.895 0.00 0.00 43.71 4.35
4059 4102 3.056313 GCAGGCATCCCTTTGCGTC 62.056 63.158 0.00 0.00 43.71 5.19
4060 4103 3.064324 GCAGGCATCCCTTTGCGT 61.064 61.111 0.00 0.00 43.71 5.24
4061 4104 2.753043 AGCAGGCATCCCTTTGCG 60.753 61.111 0.00 0.00 43.71 4.85
4062 4105 2.768492 CGAGCAGGCATCCCTTTGC 61.768 63.158 0.00 0.00 40.33 3.68
4063 4106 1.078214 TCGAGCAGGCATCCCTTTG 60.078 57.895 0.00 0.00 40.33 2.77
4064 4107 1.078143 GTCGAGCAGGCATCCCTTT 60.078 57.895 0.00 0.00 40.33 3.11
4065 4108 2.586792 GTCGAGCAGGCATCCCTT 59.413 61.111 0.00 0.00 40.33 3.95
4066 4109 3.842923 CGTCGAGCAGGCATCCCT 61.843 66.667 0.00 0.00 44.25 4.20
4067 4110 4.899239 CCGTCGAGCAGGCATCCC 62.899 72.222 0.00 0.00 0.00 3.85
4073 4116 0.387929 TTAATAGGCCGTCGAGCAGG 59.612 55.000 0.00 0.00 0.00 4.85
4074 4117 1.603172 CCTTAATAGGCCGTCGAGCAG 60.603 57.143 0.00 0.00 33.99 4.24
4075 4118 0.387929 CCTTAATAGGCCGTCGAGCA 59.612 55.000 0.00 0.00 33.99 4.26
4076 4119 0.672342 TCCTTAATAGGCCGTCGAGC 59.328 55.000 0.00 0.00 41.69 5.03
4077 4120 1.269998 CCTCCTTAATAGGCCGTCGAG 59.730 57.143 0.00 0.00 41.69 4.04
4078 4121 1.325355 CCTCCTTAATAGGCCGTCGA 58.675 55.000 0.00 0.00 41.69 4.20
4079 4122 3.888093 CCTCCTTAATAGGCCGTCG 57.112 57.895 0.00 0.00 41.69 5.12
4085 4128 0.693049 ATGCGGGCCTCCTTAATAGG 59.307 55.000 0.84 0.54 43.46 2.57
4086 4129 1.347707 TCATGCGGGCCTCCTTAATAG 59.652 52.381 0.84 0.00 0.00 1.73
4087 4130 1.429930 TCATGCGGGCCTCCTTAATA 58.570 50.000 0.84 0.00 0.00 0.98
4088 4131 0.773644 ATCATGCGGGCCTCCTTAAT 59.226 50.000 0.84 0.00 0.00 1.40
4089 4132 0.179020 CATCATGCGGGCCTCCTTAA 60.179 55.000 0.84 0.00 0.00 1.85
4090 4133 1.451504 CATCATGCGGGCCTCCTTA 59.548 57.895 0.84 0.00 0.00 2.69
4091 4134 2.194056 CATCATGCGGGCCTCCTT 59.806 61.111 0.84 0.00 0.00 3.36
4092 4135 3.882326 CCATCATGCGGGCCTCCT 61.882 66.667 0.84 0.00 0.00 3.69
4093 4136 4.962836 CCCATCATGCGGGCCTCC 62.963 72.222 0.84 0.00 36.72 4.30
4094 4137 4.962836 CCCCATCATGCGGGCCTC 62.963 72.222 13.27 0.00 42.99 4.70
4101 4144 2.976903 GAGAGCGCCCCATCATGC 60.977 66.667 2.29 0.00 0.00 4.06
4102 4145 1.301558 GAGAGAGCGCCCCATCATG 60.302 63.158 2.29 0.00 0.00 3.07
4103 4146 1.756408 CTGAGAGAGCGCCCCATCAT 61.756 60.000 2.29 0.00 0.00 2.45
4104 4147 2.364186 TGAGAGAGCGCCCCATCA 60.364 61.111 2.29 0.52 0.00 3.07
4105 4148 2.420890 CTGAGAGAGCGCCCCATC 59.579 66.667 2.29 0.00 0.00 3.51
4106 4149 2.364842 ACTGAGAGAGCGCCCCAT 60.365 61.111 2.29 0.00 0.00 4.00
4107 4150 3.385384 CACTGAGAGAGCGCCCCA 61.385 66.667 2.29 0.00 0.00 4.96
4108 4151 4.154347 CCACTGAGAGAGCGCCCC 62.154 72.222 2.29 0.00 0.00 5.80
4109 4152 2.010582 CTACCACTGAGAGAGCGCCC 62.011 65.000 2.29 0.00 0.00 6.13
4110 4153 1.032657 TCTACCACTGAGAGAGCGCC 61.033 60.000 2.29 0.00 0.00 6.53
4111 4154 0.380378 CTCTACCACTGAGAGAGCGC 59.620 60.000 0.00 0.00 42.69 5.92
4112 4155 2.031258 TCTCTACCACTGAGAGAGCG 57.969 55.000 0.00 0.00 43.57 5.03
4117 4160 1.617263 GCACCCTCTCTACCACTGAGA 60.617 57.143 0.00 0.00 38.13 3.27
4133 4176 0.179045 ACGCCATAATCAGGAGCACC 60.179 55.000 0.00 0.00 0.00 5.01
4135 4178 1.123077 AGACGCCATAATCAGGAGCA 58.877 50.000 0.00 0.00 0.00 4.26
4136 4179 1.202580 ACAGACGCCATAATCAGGAGC 60.203 52.381 0.00 0.00 0.00 4.70
4138 4181 2.419990 CCAACAGACGCCATAATCAGGA 60.420 50.000 0.00 0.00 0.00 3.86
4139 4182 1.942657 CCAACAGACGCCATAATCAGG 59.057 52.381 0.00 0.00 0.00 3.86
4140 4183 1.331756 GCCAACAGACGCCATAATCAG 59.668 52.381 0.00 0.00 0.00 2.90
4141 4184 1.339535 TGCCAACAGACGCCATAATCA 60.340 47.619 0.00 0.00 0.00 2.57
4142 4185 1.378531 TGCCAACAGACGCCATAATC 58.621 50.000 0.00 0.00 0.00 1.75
4153 4196 3.942829 TCTCTATTTCACCTGCCAACAG 58.057 45.455 0.00 0.00 44.05 3.16
4156 4199 4.922206 ACATTCTCTATTTCACCTGCCAA 58.078 39.130 0.00 0.00 0.00 4.52
4157 4200 4.574674 ACATTCTCTATTTCACCTGCCA 57.425 40.909 0.00 0.00 0.00 4.92
4158 4201 4.096984 CCAACATTCTCTATTTCACCTGCC 59.903 45.833 0.00 0.00 0.00 4.85
4159 4202 4.439289 GCCAACATTCTCTATTTCACCTGC 60.439 45.833 0.00 0.00 0.00 4.85
4160 4203 4.701651 TGCCAACATTCTCTATTTCACCTG 59.298 41.667 0.00 0.00 0.00 4.00
4161 4204 4.922206 TGCCAACATTCTCTATTTCACCT 58.078 39.130 0.00 0.00 0.00 4.00
4168 4211 5.511234 GCTGAAATGCCAACATTCTCTAT 57.489 39.130 0.00 0.00 45.90 1.98
4189 4232 8.738645 TGGATTCTCTTTTATAGAAGAAAGGC 57.261 34.615 7.11 0.00 36.46 4.35
4190 4233 9.898152 ACTGGATTCTCTTTTATAGAAGAAAGG 57.102 33.333 7.11 0.00 36.46 3.11
4195 4238 8.353684 TCGCTACTGGATTCTCTTTTATAGAAG 58.646 37.037 0.00 0.00 36.46 2.85
4196 4239 8.234136 TCGCTACTGGATTCTCTTTTATAGAA 57.766 34.615 0.00 0.00 37.38 2.10
4197 4240 7.818997 TCGCTACTGGATTCTCTTTTATAGA 57.181 36.000 0.00 0.00 0.00 1.98
4200 4243 9.482627 CTTATTCGCTACTGGATTCTCTTTTAT 57.517 33.333 0.00 0.00 0.00 1.40
4202 4245 7.556844 TCTTATTCGCTACTGGATTCTCTTTT 58.443 34.615 0.00 0.00 0.00 2.27
4203 4246 7.113658 TCTTATTCGCTACTGGATTCTCTTT 57.886 36.000 0.00 0.00 0.00 2.52
4204 4247 6.322712 ACTCTTATTCGCTACTGGATTCTCTT 59.677 38.462 0.00 0.00 0.00 2.85
4205 4248 5.830991 ACTCTTATTCGCTACTGGATTCTCT 59.169 40.000 0.00 0.00 0.00 3.10
4206 4249 6.079424 ACTCTTATTCGCTACTGGATTCTC 57.921 41.667 0.00 0.00 0.00 2.87
4207 4250 6.293516 CGTACTCTTATTCGCTACTGGATTCT 60.294 42.308 0.00 0.00 0.00 2.40
4208 4251 5.852229 CGTACTCTTATTCGCTACTGGATTC 59.148 44.000 0.00 0.00 0.00 2.52
4209 4252 5.278364 CCGTACTCTTATTCGCTACTGGATT 60.278 44.000 0.00 0.00 0.00 3.01
4210 4253 4.215827 CCGTACTCTTATTCGCTACTGGAT 59.784 45.833 0.00 0.00 0.00 3.41
4211 4254 3.562973 CCGTACTCTTATTCGCTACTGGA 59.437 47.826 0.00 0.00 0.00 3.86
4212 4255 3.852572 GCCGTACTCTTATTCGCTACTGG 60.853 52.174 0.00 0.00 0.00 4.00
4213 4256 3.003482 AGCCGTACTCTTATTCGCTACTG 59.997 47.826 0.00 0.00 0.00 2.74
4214 4257 3.003482 CAGCCGTACTCTTATTCGCTACT 59.997 47.826 0.00 0.00 0.00 2.57
4215 4258 3.243002 ACAGCCGTACTCTTATTCGCTAC 60.243 47.826 0.00 0.00 0.00 3.58
4216 4259 2.947652 ACAGCCGTACTCTTATTCGCTA 59.052 45.455 0.00 0.00 0.00 4.26
4217 4260 1.749634 ACAGCCGTACTCTTATTCGCT 59.250 47.619 0.00 0.00 0.00 4.93
4218 4261 2.205307 ACAGCCGTACTCTTATTCGC 57.795 50.000 0.00 0.00 0.00 4.70
4219 4262 5.104562 TCATACAGCCGTACTCTTATTCG 57.895 43.478 0.00 0.00 0.00 3.34
4231 4274 0.319728 AGCATAGCCTCATACAGCCG 59.680 55.000 0.00 0.00 0.00 5.52
4238 4281 3.033909 TGTACACAGAGCATAGCCTCAT 58.966 45.455 0.00 0.00 34.26 2.90
4247 4290 2.168521 GCTTAGGGATGTACACAGAGCA 59.831 50.000 0.00 0.00 34.06 4.26
4249 4292 4.471904 TTGCTTAGGGATGTACACAGAG 57.528 45.455 0.00 0.00 0.00 3.35
4263 4319 6.748333 TTCAAGACTCCATTCATTGCTTAG 57.252 37.500 0.00 0.00 0.00 2.18
4271 4327 8.292444 TCTTTTCTTTTTCAAGACTCCATTCA 57.708 30.769 0.00 0.00 38.86 2.57
4291 4348 8.011844 AGTCCAGCTTCAAGTATTTTTCTTTT 57.988 30.769 0.00 0.00 0.00 2.27
4294 4351 7.680730 TCTAGTCCAGCTTCAAGTATTTTTCT 58.319 34.615 0.00 0.00 0.00 2.52
4295 4352 7.907214 TCTAGTCCAGCTTCAAGTATTTTTC 57.093 36.000 0.00 0.00 0.00 2.29
4296 4353 7.885399 ACATCTAGTCCAGCTTCAAGTATTTTT 59.115 33.333 0.00 0.00 0.00 1.94
4301 4358 5.337571 CCAACATCTAGTCCAGCTTCAAGTA 60.338 44.000 0.00 0.00 0.00 2.24
4453 4578 4.160252 AGCGCCTTACATTCCATTTCAATT 59.840 37.500 2.29 0.00 0.00 2.32
4461 4596 1.003118 AGAACAGCGCCTTACATTCCA 59.997 47.619 2.29 0.00 0.00 3.53
4467 4602 1.069227 CCAAACAGAACAGCGCCTTAC 60.069 52.381 2.29 0.00 0.00 2.34
4481 4616 1.405526 GGAGCAGAGCGATACCAAACA 60.406 52.381 0.00 0.00 0.00 2.83
4482 4617 1.291132 GGAGCAGAGCGATACCAAAC 58.709 55.000 0.00 0.00 0.00 2.93
4484 4619 0.175760 GTGGAGCAGAGCGATACCAA 59.824 55.000 0.00 0.00 0.00 3.67
4485 4620 0.970427 TGTGGAGCAGAGCGATACCA 60.970 55.000 0.00 0.00 0.00 3.25
4487 4622 1.134965 AGTTGTGGAGCAGAGCGATAC 60.135 52.381 0.00 0.00 0.00 2.24
4488 4623 1.135139 GAGTTGTGGAGCAGAGCGATA 59.865 52.381 0.00 0.00 0.00 2.92
4489 4624 0.108424 GAGTTGTGGAGCAGAGCGAT 60.108 55.000 0.00 0.00 0.00 4.58
4490 4625 1.290324 GAGTTGTGGAGCAGAGCGA 59.710 57.895 0.00 0.00 0.00 4.93
4491 4626 1.739562 GGAGTTGTGGAGCAGAGCG 60.740 63.158 0.00 0.00 0.00 5.03
4492 4627 1.739562 CGGAGTTGTGGAGCAGAGC 60.740 63.158 0.00 0.00 0.00 4.09
4493 4628 1.079543 CCGGAGTTGTGGAGCAGAG 60.080 63.158 0.00 0.00 0.00 3.35
4494 4629 2.583441 CCCGGAGTTGTGGAGCAGA 61.583 63.158 0.73 0.00 0.00 4.26
4495 4630 2.046892 CCCGGAGTTGTGGAGCAG 60.047 66.667 0.73 0.00 0.00 4.24
4496 4631 2.525629 TCCCGGAGTTGTGGAGCA 60.526 61.111 0.73 0.00 0.00 4.26
4511 4646 2.815647 CTTCGCCAACTCCGCTCC 60.816 66.667 0.00 0.00 0.00 4.70
4512 4647 1.668151 AACTTCGCCAACTCCGCTC 60.668 57.895 0.00 0.00 0.00 5.03
4526 4661 5.069516 ACTCCATCATTTTGAACTGCAACTT 59.930 36.000 0.00 0.00 35.91 2.66
4529 4664 5.291178 CAACTCCATCATTTTGAACTGCAA 58.709 37.500 0.00 0.00 33.88 4.08
4542 4677 1.425066 AGGGAAACTGCAACTCCATCA 59.575 47.619 9.84 0.00 0.00 3.07
4544 4679 1.915141 CAGGGAAACTGCAACTCCAT 58.085 50.000 9.84 1.05 40.97 3.41
4562 4697 0.394488 CTCCCGGAGTCTACAGAGCA 60.394 60.000 0.73 0.00 0.00 4.26
4567 4702 1.000019 CCCACTCCCGGAGTCTACA 60.000 63.158 17.77 0.00 41.37 2.74
4569 4704 1.000019 CACCCACTCCCGGAGTCTA 60.000 63.158 17.77 0.00 41.37 2.59
4594 4730 2.683362 GTGCTACATTTAGGCCCTGTTC 59.317 50.000 0.00 0.00 0.00 3.18
4604 4740 0.808453 GCCGCCTCGTGCTACATTTA 60.808 55.000 0.00 0.00 38.05 1.40
4615 4751 2.047655 TAAACACCAGCCGCCTCG 60.048 61.111 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.