Multiple sequence alignment - TraesCS5D01G139900

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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 TraesCS5D01G139900 chr5D 100.000 4737 0 0 1 4737 223520614 223515878 0.000000e+00 8748
1 TraesCS5D01G139900 chr5D 94.389 499 27 1 139 636 486532318 486531820 0.000000e+00 765
2 TraesCS5D01G139900 chr5D 95.349 129 3 2 3 128 559051337 559051465 8.040000e-48 202
3 TraesCS5D01G139900 chr5D 94.615 130 3 3 3 128 421982448 421982577 1.040000e-46 198
4 TraesCS5D01G139900 chr5A 96.039 2272 58 10 816 3068 296198827 296196569 0.000000e+00 3668
5 TraesCS5D01G139900 chr5A 93.920 1431 29 10 3054 4434 296196556 296195134 0.000000e+00 2108
6 TraesCS5D01G139900 chr5A 92.759 290 18 3 4449 4736 296181279 296180991 2.640000e-112 416
7 TraesCS5D01G139900 chr5A 94.886 176 8 1 649 824 296199152 296198978 1.680000e-69 274
8 TraesCS5D01G139900 chr5B 92.666 1759 68 30 929 2654 249366376 249368106 0.000000e+00 2477
9 TraesCS5D01G139900 chr5B 93.516 987 41 11 3357 4328 249369046 249370024 0.000000e+00 1447
10 TraesCS5D01G139900 chr5B 97.480 635 11 4 2731 3361 249368292 249368925 0.000000e+00 1079
11 TraesCS5D01G139900 chrUn 95.510 490 20 2 148 636 96353215 96352727 0.000000e+00 782
12 TraesCS5D01G139900 chr3D 95.267 486 20 3 150 633 42515209 42515693 0.000000e+00 767
13 TraesCS5D01G139900 chr3D 93.964 497 29 1 141 636 51687456 51687952 0.000000e+00 750
14 TraesCS5D01G139900 chr3D 94.615 130 3 3 3 128 108290924 108291053 1.040000e-46 198
15 TraesCS5D01G139900 chr1D 94.567 497 25 2 141 636 92207199 92206704 0.000000e+00 767
16 TraesCS5D01G139900 chr1D 94.366 497 27 1 141 636 61445312 61444816 0.000000e+00 761
17 TraesCS5D01G139900 chr1D 95.349 129 3 2 3 128 46330899 46331027 8.040000e-48 202
18 TraesCS5D01G139900 chr2D 94.012 501 26 2 140 636 477632981 477632481 0.000000e+00 756
19 TraesCS5D01G139900 chr2D 94.118 493 24 2 145 636 600441550 600441062 0.000000e+00 745
20 TraesCS5D01G139900 chr2D 94.615 130 3 3 3 128 284560038 284560167 1.040000e-46 198
21 TraesCS5D01G139900 chr6D 93.939 495 24 4 148 636 115651605 115651111 0.000000e+00 743
22 TraesCS5D01G139900 chr6A 78.775 457 69 23 1786 2230 117196071 117196511 1.000000e-71 281
23 TraesCS5D01G139900 chr6A 78.509 456 72 22 1786 2230 117215635 117216075 4.670000e-70 276
24 TraesCS5D01G139900 chr7D 93.478 138 3 5 3 136 538520669 538520534 2.890000e-47 200
25 TraesCS5D01G139900 chr2B 94.615 130 3 3 3 128 782101506 782101377 1.040000e-46 198
26 TraesCS5D01G139900 chr4D 94.574 129 4 3 3 128 367049376 367049248 3.740000e-46 196
27 TraesCS5D01G139900 chr1B 94.574 129 4 3 3 128 640451376 640451248 3.740000e-46 196


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 TraesCS5D01G139900 chr5D 223515878 223520614 4736 True 8748.000000 8748 100.000000 1 4737 1 chr5D.!!$R1 4736
1 TraesCS5D01G139900 chr5A 296195134 296199152 4018 True 2016.666667 3668 94.948333 649 4434 3 chr5A.!!$R2 3785
2 TraesCS5D01G139900 chr5B 249366376 249370024 3648 False 1667.666667 2477 94.554000 929 4328 3 chr5B.!!$F1 3399
3 TraesCS5D01G139900 chr2D 477632481 477632981 500 True 756.000000 756 94.012000 140 636 1 chr2D.!!$R1 496

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
273 275 0.034756 TACACTGTGCAACGCCTCAT 59.965 50.000 7.90 0.00 42.39 2.90 F
540 545 0.534877 ATCTGTGAGGCGTTGCACAA 60.535 50.000 0.00 0.00 43.65 3.33 F
773 778 0.828762 AACATGGCCACAGTGCACAT 60.829 50.000 21.04 3.29 0.00 3.21 F
1900 2101 0.687757 TGAAGGAGGAGATGGACGGG 60.688 60.000 0.00 0.00 0.00 5.28 F
2053 2254 1.070786 GGCCGTCAAGTTCCTCACA 59.929 57.895 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1883 0.251341 GAAGGGCTGAGGCAAAAGGA 60.251 55.000 8.68 0.0 40.87 3.36 R
1900 2101 3.118445 CCATGTCCTTCTTCTCCCTCTTC 60.118 52.174 0.00 0.0 0.00 2.87 R
2474 2699 4.571984 GCAAACATGCTTTTGGAAGAAGTT 59.428 37.500 9.95 0.0 37.02 2.66 R
3722 4259 0.666577 GGTCGTCAAACAGACTCCGG 60.667 60.000 0.00 0.0 45.32 5.14 R
3747 4284 1.271840 TAAGGGCAGCCGAAGACCAT 61.272 55.000 5.00 0.0 0.00 3.55 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
37 38 8.697507 ACCTTTGAAAATAGAACATCTGAAGT 57.302 30.769 0.00 0.00 0.00 3.01
38 39 9.136323 ACCTTTGAAAATAGAACATCTGAAGTT 57.864 29.630 0.00 0.00 0.00 2.66
39 40 9.971922 CCTTTGAAAATAGAACATCTGAAGTTT 57.028 29.630 0.00 0.00 0.00 2.66
82 83 8.732746 AATGTATGACTTGTATTAGGTTGGTC 57.267 34.615 0.00 0.00 0.00 4.02
83 84 7.247456 TGTATGACTTGTATTAGGTTGGTCA 57.753 36.000 0.00 0.00 36.80 4.02
84 85 7.681679 TGTATGACTTGTATTAGGTTGGTCAA 58.318 34.615 0.00 0.00 36.16 3.18
85 86 8.158132 TGTATGACTTGTATTAGGTTGGTCAAA 58.842 33.333 0.00 0.00 36.16 2.69
86 87 9.174166 GTATGACTTGTATTAGGTTGGTCAAAT 57.826 33.333 0.00 0.00 36.16 2.32
87 88 8.650143 ATGACTTGTATTAGGTTGGTCAAATT 57.350 30.769 0.00 0.00 36.16 1.82
88 89 7.881142 TGACTTGTATTAGGTTGGTCAAATTG 58.119 34.615 0.00 0.00 30.81 2.32
89 90 7.721842 TGACTTGTATTAGGTTGGTCAAATTGA 59.278 33.333 0.00 0.00 30.81 2.57
90 91 7.882179 ACTTGTATTAGGTTGGTCAAATTGAC 58.118 34.615 17.16 17.16 46.23 3.18
100 101 3.329929 GTCAAATTGACGACCTAGGGT 57.670 47.619 14.81 1.35 37.67 4.34
101 102 4.460948 GTCAAATTGACGACCTAGGGTA 57.539 45.455 14.81 0.00 37.67 3.69
102 103 4.179298 GTCAAATTGACGACCTAGGGTAC 58.821 47.826 14.81 3.28 37.67 3.34
103 104 3.833650 TCAAATTGACGACCTAGGGTACA 59.166 43.478 14.81 4.97 35.25 2.90
104 105 3.881937 AATTGACGACCTAGGGTACAC 57.118 47.619 14.81 0.00 35.25 2.90
105 106 1.167851 TTGACGACCTAGGGTACACG 58.832 55.000 14.81 12.44 35.25 4.49
106 107 1.308069 TGACGACCTAGGGTACACGC 61.308 60.000 14.81 7.59 35.25 5.34
107 108 1.303561 ACGACCTAGGGTACACGCA 60.304 57.895 14.81 0.00 35.25 5.24
108 109 1.138247 CGACCTAGGGTACACGCAC 59.862 63.158 14.81 0.00 35.25 5.34
109 110 1.138247 GACCTAGGGTACACGCACG 59.862 63.158 14.81 0.00 35.25 5.34
110 111 1.589716 GACCTAGGGTACACGCACGT 61.590 60.000 14.81 0.00 35.25 4.49
111 112 1.138247 CCTAGGGTACACGCACGTC 59.862 63.158 0.00 0.00 0.00 4.34
112 113 1.138247 CTAGGGTACACGCACGTCC 59.862 63.158 0.00 0.00 0.00 4.79
113 114 1.303561 TAGGGTACACGCACGTCCT 60.304 57.895 6.43 6.43 0.00 3.85
114 115 1.588824 TAGGGTACACGCACGTCCTG 61.589 60.000 10.44 0.00 0.00 3.86
115 116 2.337532 GGTACACGCACGTCCTGT 59.662 61.111 0.00 0.00 0.00 4.00
116 117 1.580942 GGTACACGCACGTCCTGTA 59.419 57.895 0.00 0.00 0.00 2.74
117 118 0.039256 GGTACACGCACGTCCTGTAA 60.039 55.000 0.00 0.00 0.00 2.41
118 119 1.602668 GGTACACGCACGTCCTGTAAA 60.603 52.381 0.00 0.00 0.00 2.01
119 120 1.453148 GTACACGCACGTCCTGTAAAC 59.547 52.381 0.00 0.00 0.00 2.01
120 121 0.103572 ACACGCACGTCCTGTAAACT 59.896 50.000 0.00 0.00 0.00 2.66
121 122 0.506932 CACGCACGTCCTGTAAACTG 59.493 55.000 0.00 0.00 0.00 3.16
122 123 0.386476 ACGCACGTCCTGTAAACTGA 59.614 50.000 0.00 0.00 0.00 3.41
123 124 1.060713 CGCACGTCCTGTAAACTGAG 58.939 55.000 0.00 0.00 0.00 3.35
124 125 1.335597 CGCACGTCCTGTAAACTGAGA 60.336 52.381 0.00 0.00 0.00 3.27
125 126 2.329379 GCACGTCCTGTAAACTGAGAG 58.671 52.381 0.00 0.00 0.00 3.20
126 127 2.030185 GCACGTCCTGTAAACTGAGAGA 60.030 50.000 0.00 0.00 0.00 3.10
127 128 3.827625 CACGTCCTGTAAACTGAGAGAG 58.172 50.000 0.00 0.00 0.00 3.20
128 129 3.253677 CACGTCCTGTAAACTGAGAGAGT 59.746 47.826 0.00 0.00 35.94 3.24
129 130 4.454847 CACGTCCTGTAAACTGAGAGAGTA 59.545 45.833 0.00 0.00 33.09 2.59
130 131 4.696402 ACGTCCTGTAAACTGAGAGAGTAG 59.304 45.833 0.00 0.00 33.09 2.57
131 132 4.437659 CGTCCTGTAAACTGAGAGAGTAGC 60.438 50.000 0.00 0.00 33.09 3.58
132 133 4.703093 GTCCTGTAAACTGAGAGAGTAGCT 59.297 45.833 0.00 0.00 33.09 3.32
133 134 4.702612 TCCTGTAAACTGAGAGAGTAGCTG 59.297 45.833 0.00 0.00 33.09 4.24
134 135 4.702612 CCTGTAAACTGAGAGAGTAGCTGA 59.297 45.833 0.00 0.00 33.09 4.26
135 136 5.163663 CCTGTAAACTGAGAGAGTAGCTGAG 60.164 48.000 0.00 0.00 33.09 3.35
136 137 5.561679 TGTAAACTGAGAGAGTAGCTGAGA 58.438 41.667 0.00 0.00 33.09 3.27
137 138 6.184068 TGTAAACTGAGAGAGTAGCTGAGAT 58.816 40.000 0.00 0.00 33.09 2.75
138 139 6.661377 TGTAAACTGAGAGAGTAGCTGAGATT 59.339 38.462 0.00 0.00 33.09 2.40
167 169 6.747280 CGAATTTGACAATTTGACCTATGGAC 59.253 38.462 2.79 0.00 36.24 4.02
273 275 0.034756 TACACTGTGCAACGCCTCAT 59.965 50.000 7.90 0.00 42.39 2.90
299 301 2.897350 GATACACGCCTGGCCAGC 60.897 66.667 28.39 20.70 0.00 4.85
334 336 7.330946 TGTGTGATCCGAAAATTACTAAGTCAG 59.669 37.037 0.00 0.00 0.00 3.51
486 491 7.039784 ACAATGACTTAGCAATTTTTAGGCAGA 60.040 33.333 0.00 0.00 0.00 4.26
492 497 2.094026 GCAATTTTTAGGCAGACTGGGG 60.094 50.000 4.26 0.00 0.00 4.96
498 503 2.124507 TAGGCAGACTGGGGTGCAAC 62.125 60.000 4.26 0.00 41.75 4.17
530 535 1.032794 TGTAGCGCCTATCTGTGAGG 58.967 55.000 2.29 0.00 37.12 3.86
540 545 0.534877 ATCTGTGAGGCGTTGCACAA 60.535 50.000 0.00 0.00 43.65 3.33
557 562 3.671008 ACAATGTAGTGTGACGCCTTA 57.329 42.857 0.00 0.00 0.00 2.69
558 563 3.997762 ACAATGTAGTGTGACGCCTTAA 58.002 40.909 0.00 0.00 0.00 1.85
572 577 1.087771 CCTTAATGTCGGGCGTCACC 61.088 60.000 0.00 0.00 37.93 4.02
618 623 5.209818 AGTTTCACGGACAGTTCATTCTA 57.790 39.130 0.00 0.00 0.00 2.10
633 638 9.778993 CAGTTCATTCTATGATTTGATTTCGTT 57.221 29.630 0.00 0.00 39.39 3.85
636 641 9.992910 TTCATTCTATGATTTGATTTCGTTCAG 57.007 29.630 0.00 0.00 39.39 3.02
637 642 8.124823 TCATTCTATGATTTGATTTCGTTCAGC 58.875 33.333 0.00 0.00 33.59 4.26
638 643 6.363577 TCTATGATTTGATTTCGTTCAGCC 57.636 37.500 0.00 0.00 0.00 4.85
639 644 3.848272 TGATTTGATTTCGTTCAGCCC 57.152 42.857 0.00 0.00 0.00 5.19
640 645 3.420893 TGATTTGATTTCGTTCAGCCCT 58.579 40.909 0.00 0.00 0.00 5.19
641 646 3.191162 TGATTTGATTTCGTTCAGCCCTG 59.809 43.478 0.00 0.00 0.00 4.45
642 647 2.559698 TTGATTTCGTTCAGCCCTGA 57.440 45.000 0.00 0.00 37.91 3.86
643 648 2.099141 TGATTTCGTTCAGCCCTGAG 57.901 50.000 0.00 0.00 41.13 3.35
644 649 1.623311 TGATTTCGTTCAGCCCTGAGA 59.377 47.619 0.00 0.00 41.13 3.27
645 650 2.237143 TGATTTCGTTCAGCCCTGAGAT 59.763 45.455 0.00 0.00 41.13 2.75
646 651 2.859165 TTTCGTTCAGCCCTGAGATT 57.141 45.000 0.00 0.00 41.13 2.40
647 652 2.386661 TTCGTTCAGCCCTGAGATTC 57.613 50.000 0.00 0.00 41.13 2.52
655 660 2.943690 CAGCCCTGAGATTCATTCACAG 59.056 50.000 0.00 0.00 41.26 3.66
663 668 6.070951 TGAGATTCATTCACAGGAAGGATT 57.929 37.500 0.00 0.00 42.72 3.01
742 747 5.904362 ACAAAATCTTTCTAGCACATCCC 57.096 39.130 0.00 0.00 0.00 3.85
773 778 0.828762 AACATGGCCACAGTGCACAT 60.829 50.000 21.04 3.29 0.00 3.21
782 787 1.745087 CACAGTGCACATACATTCCCC 59.255 52.381 21.04 0.00 0.00 4.81
802 807 1.605710 CTTTTGGACCAGAGCACACAG 59.394 52.381 0.00 0.00 0.00 3.66
831 995 9.878667 TTTCTATCCATTAATTAACACTCGACA 57.121 29.630 0.00 0.00 0.00 4.35
849 1013 3.733337 GACACCTTTTCTCAAGCTCTCA 58.267 45.455 0.00 0.00 0.00 3.27
857 1021 3.883830 TCTCAAGCTCTCATCTCCAAC 57.116 47.619 0.00 0.00 0.00 3.77
1173 1341 4.521062 ACGCTGCGGCTGATCTCC 62.521 66.667 26.95 0.00 36.09 3.71
1386 1554 4.504916 CGCTCCCTGCTCCTCACG 62.505 72.222 0.00 0.00 40.11 4.35
1715 1883 1.005924 CCAGGCCCTCAAGGTGTTTAT 59.994 52.381 0.00 0.00 38.26 1.40
1900 2101 0.687757 TGAAGGAGGAGATGGACGGG 60.688 60.000 0.00 0.00 0.00 5.28
2053 2254 1.070786 GGCCGTCAAGTTCCTCACA 59.929 57.895 0.00 0.00 0.00 3.58
2417 2639 2.057922 AGACAGGGGTGATGTTGACTT 58.942 47.619 0.00 0.00 0.00 3.01
2474 2699 5.045942 TCTGCTATGAACACAAATCCTACCA 60.046 40.000 0.00 0.00 0.00 3.25
2525 2751 5.455392 TCTCCTCTTTTGTTTACTCGTACG 58.545 41.667 9.53 9.53 0.00 3.67
2626 2854 1.466167 CCTCTTCAGCCGATGTTGTTG 59.534 52.381 0.00 0.00 0.00 3.33
2685 3048 8.833493 TGCTTCTATTGATATTCTGTGTCAATG 58.167 33.333 9.40 1.98 45.00 2.82
2725 3088 7.533426 ACAGATGTCTTGCTGATTTGTTAATC 58.467 34.615 0.00 0.00 40.50 1.75
2727 3090 8.886719 CAGATGTCTTGCTGATTTGTTAATCTA 58.113 33.333 0.00 0.00 40.68 1.98
2939 3302 2.154462 AGCTCACTGGGATTTTTCACG 58.846 47.619 0.00 0.00 0.00 4.35
2961 3326 5.527582 ACGTCATAATAAGGAATGCCACTTC 59.472 40.000 0.00 0.00 36.29 3.01
3275 3668 2.264005 TTACGGTGCTGTTGGTCAAT 57.736 45.000 0.00 0.00 0.00 2.57
3603 4140 6.662865 TTGAAATTCCAAACTAAGATGCCA 57.337 33.333 0.00 0.00 0.00 4.92
3722 4259 1.218230 GATCAATCTCAGGCGGCGAC 61.218 60.000 12.98 8.50 0.00 5.19
3747 4284 2.546778 GTCTGTTTGACGACCTCACAA 58.453 47.619 0.00 0.00 35.81 3.33
3762 4299 1.675641 ACAATGGTCTTCGGCTGCC 60.676 57.895 9.11 9.11 0.00 4.85
3973 4518 4.751060 TGTCGCGTATTTGGATATATCCC 58.249 43.478 25.86 11.23 46.59 3.85
4187 4758 4.889519 TTTATTACACACGTACGCACAG 57.110 40.909 16.72 5.61 0.00 3.66
4289 4867 2.928801 TGCACCACACTCACTAACAT 57.071 45.000 0.00 0.00 0.00 2.71
4347 4925 1.813513 ACATCACCTTCCGCTGAAAG 58.186 50.000 0.00 0.00 0.00 2.62
4352 4930 4.487714 TCACCTTCCGCTGAAAGAATAT 57.512 40.909 0.00 0.00 34.07 1.28
4409 4993 1.486310 GTATGATCACCTGTGGGCTGA 59.514 52.381 0.00 0.00 35.63 4.26
4415 4999 1.003118 TCACCTGTGGGCTGAACATAC 59.997 52.381 0.00 0.00 35.63 2.39
4421 5005 2.094390 TGTGGGCTGAACATACGAGTAC 60.094 50.000 0.00 0.00 0.00 2.73
4422 5006 2.094390 GTGGGCTGAACATACGAGTACA 60.094 50.000 0.00 0.00 0.00 2.90
4428 5012 6.040878 GGCTGAACATACGAGTACAACTAAT 58.959 40.000 0.00 0.00 0.00 1.73
4440 5024 7.805071 ACGAGTACAACTAATAATGTATACGGC 59.195 37.037 0.00 0.00 37.53 5.68
4441 5025 8.019669 CGAGTACAACTAATAATGTATACGGCT 58.980 37.037 0.00 0.00 34.77 5.52
4533 5117 9.705290 AGGTTTACTATAAAACTGGCATTTTTG 57.295 29.630 21.48 10.40 38.98 2.44
4534 5118 9.483916 GGTTTACTATAAAACTGGCATTTTTGT 57.516 29.630 21.48 18.02 38.98 2.83
4538 5122 8.587952 ACTATAAAACTGGCATTTTTGTTCAC 57.412 30.769 21.48 0.00 33.80 3.18
4539 5123 6.859420 ATAAAACTGGCATTTTTGTTCACC 57.141 33.333 21.48 0.00 33.80 4.02
4540 5124 4.486125 AAACTGGCATTTTTGTTCACCT 57.514 36.364 0.00 0.00 0.00 4.00
4541 5125 4.486125 AACTGGCATTTTTGTTCACCTT 57.514 36.364 0.00 0.00 0.00 3.50
4542 5126 4.486125 ACTGGCATTTTTGTTCACCTTT 57.514 36.364 0.00 0.00 0.00 3.11
4543 5127 4.842574 ACTGGCATTTTTGTTCACCTTTT 58.157 34.783 0.00 0.00 0.00 2.27
4544 5128 4.875536 ACTGGCATTTTTGTTCACCTTTTC 59.124 37.500 0.00 0.00 0.00 2.29
4545 5129 5.096443 TGGCATTTTTGTTCACCTTTTCT 57.904 34.783 0.00 0.00 0.00 2.52
4546 5130 5.115480 TGGCATTTTTGTTCACCTTTTCTC 58.885 37.500 0.00 0.00 0.00 2.87
4547 5131 5.104982 TGGCATTTTTGTTCACCTTTTCTCT 60.105 36.000 0.00 0.00 0.00 3.10
4548 5132 6.097554 TGGCATTTTTGTTCACCTTTTCTCTA 59.902 34.615 0.00 0.00 0.00 2.43
4549 5133 6.420903 GGCATTTTTGTTCACCTTTTCTCTAC 59.579 38.462 0.00 0.00 0.00 2.59
4550 5134 6.978080 GCATTTTTGTTCACCTTTTCTCTACA 59.022 34.615 0.00 0.00 0.00 2.74
4551 5135 7.653311 GCATTTTTGTTCACCTTTTCTCTACAT 59.347 33.333 0.00 0.00 0.00 2.29
4552 5136 9.185192 CATTTTTGTTCACCTTTTCTCTACATC 57.815 33.333 0.00 0.00 0.00 3.06
4553 5137 6.877611 TTTGTTCACCTTTTCTCTACATCC 57.122 37.500 0.00 0.00 0.00 3.51
4554 5138 5.825593 TGTTCACCTTTTCTCTACATCCT 57.174 39.130 0.00 0.00 0.00 3.24
4555 5139 6.187727 TGTTCACCTTTTCTCTACATCCTT 57.812 37.500 0.00 0.00 0.00 3.36
4556 5140 6.231211 TGTTCACCTTTTCTCTACATCCTTC 58.769 40.000 0.00 0.00 0.00 3.46
4557 5141 6.043243 TGTTCACCTTTTCTCTACATCCTTCT 59.957 38.462 0.00 0.00 0.00 2.85
4558 5142 6.688073 TCACCTTTTCTCTACATCCTTCTT 57.312 37.500 0.00 0.00 0.00 2.52
4559 5143 6.702329 TCACCTTTTCTCTACATCCTTCTTC 58.298 40.000 0.00 0.00 0.00 2.87
4560 5144 6.270000 TCACCTTTTCTCTACATCCTTCTTCA 59.730 38.462 0.00 0.00 0.00 3.02
4561 5145 7.038017 TCACCTTTTCTCTACATCCTTCTTCAT 60.038 37.037 0.00 0.00 0.00 2.57
4562 5146 8.260818 CACCTTTTCTCTACATCCTTCTTCATA 58.739 37.037 0.00 0.00 0.00 2.15
4563 5147 8.997734 ACCTTTTCTCTACATCCTTCTTCATAT 58.002 33.333 0.00 0.00 0.00 1.78
4564 5148 9.487790 CCTTTTCTCTACATCCTTCTTCATATC 57.512 37.037 0.00 0.00 0.00 1.63
4595 5179 7.744087 ATTTGTTTAGAAGCATGTGTAGTGA 57.256 32.000 0.00 0.00 0.00 3.41
4596 5180 7.744087 TTTGTTTAGAAGCATGTGTAGTGAT 57.256 32.000 0.00 0.00 0.00 3.06
4597 5181 8.840833 TTTGTTTAGAAGCATGTGTAGTGATA 57.159 30.769 0.00 0.00 0.00 2.15
4598 5182 8.479313 TTGTTTAGAAGCATGTGTAGTGATAG 57.521 34.615 0.00 0.00 0.00 2.08
4599 5183 7.836842 TGTTTAGAAGCATGTGTAGTGATAGA 58.163 34.615 0.00 0.00 0.00 1.98
4600 5184 7.759886 TGTTTAGAAGCATGTGTAGTGATAGAC 59.240 37.037 0.00 0.00 0.00 2.59
4601 5185 7.646548 TTAGAAGCATGTGTAGTGATAGACT 57.353 36.000 0.00 0.00 38.88 3.24
4602 5186 6.537453 AGAAGCATGTGTAGTGATAGACTT 57.463 37.500 0.00 0.00 35.96 3.01
4603 5187 6.940739 AGAAGCATGTGTAGTGATAGACTTT 58.059 36.000 0.00 0.00 35.96 2.66
4604 5188 7.390027 AGAAGCATGTGTAGTGATAGACTTTT 58.610 34.615 0.00 0.00 35.96 2.27
4605 5189 6.974932 AGCATGTGTAGTGATAGACTTTTG 57.025 37.500 0.00 0.00 35.96 2.44
4606 5190 6.467677 AGCATGTGTAGTGATAGACTTTTGT 58.532 36.000 0.00 0.00 35.96 2.83
4607 5191 7.611770 AGCATGTGTAGTGATAGACTTTTGTA 58.388 34.615 0.00 0.00 35.96 2.41
4608 5192 7.545965 AGCATGTGTAGTGATAGACTTTTGTAC 59.454 37.037 0.00 0.00 35.96 2.90
4609 5193 7.545965 GCATGTGTAGTGATAGACTTTTGTACT 59.454 37.037 0.00 0.00 35.96 2.73
4612 5196 9.511272 TGTGTAGTGATAGACTTTTGTACTAGA 57.489 33.333 0.00 0.00 35.96 2.43
4613 5197 9.771915 GTGTAGTGATAGACTTTTGTACTAGAC 57.228 37.037 0.00 0.00 35.96 2.59
4614 5198 9.736414 TGTAGTGATAGACTTTTGTACTAGACT 57.264 33.333 0.00 0.00 35.96 3.24
4619 5203 9.204570 TGATAGACTTTTGTACTAGACTTTTGC 57.795 33.333 0.00 0.00 0.00 3.68
4620 5204 9.425577 GATAGACTTTTGTACTAGACTTTTGCT 57.574 33.333 0.00 0.00 0.00 3.91
4621 5205 9.780186 ATAGACTTTTGTACTAGACTTTTGCTT 57.220 29.630 0.00 0.00 0.00 3.91
4622 5206 7.920738 AGACTTTTGTACTAGACTTTTGCTTG 58.079 34.615 0.00 0.00 0.00 4.01
4623 5207 7.769044 AGACTTTTGTACTAGACTTTTGCTTGA 59.231 33.333 0.00 0.00 0.00 3.02
4624 5208 7.920738 ACTTTTGTACTAGACTTTTGCTTGAG 58.079 34.615 0.00 0.00 0.00 3.02
4625 5209 7.769044 ACTTTTGTACTAGACTTTTGCTTGAGA 59.231 33.333 0.00 0.00 0.00 3.27
4626 5210 7.715265 TTTGTACTAGACTTTTGCTTGAGAG 57.285 36.000 0.00 0.00 0.00 3.20
4636 5220 3.523806 GCTTGAGAGCTCGTTCCTT 57.476 52.632 8.37 0.00 45.65 3.36
4637 5221 1.802069 GCTTGAGAGCTCGTTCCTTT 58.198 50.000 8.37 0.00 45.65 3.11
4638 5222 2.147150 GCTTGAGAGCTCGTTCCTTTT 58.853 47.619 8.37 0.00 45.65 2.27
4639 5223 3.326747 GCTTGAGAGCTCGTTCCTTTTA 58.673 45.455 8.37 0.00 45.65 1.52
4640 5224 3.935828 GCTTGAGAGCTCGTTCCTTTTAT 59.064 43.478 8.37 0.00 45.65 1.40
4641 5225 4.393371 GCTTGAGAGCTCGTTCCTTTTATT 59.607 41.667 8.37 0.00 45.65 1.40
4642 5226 5.106515 GCTTGAGAGCTCGTTCCTTTTATTT 60.107 40.000 8.37 0.00 45.65 1.40
4643 5227 6.568653 GCTTGAGAGCTCGTTCCTTTTATTTT 60.569 38.462 8.37 0.00 45.65 1.82
4644 5228 6.877611 TGAGAGCTCGTTCCTTTTATTTTT 57.122 33.333 8.37 0.00 0.00 1.94
4645 5229 6.899114 TGAGAGCTCGTTCCTTTTATTTTTC 58.101 36.000 8.37 0.00 0.00 2.29
4646 5230 6.485313 TGAGAGCTCGTTCCTTTTATTTTTCA 59.515 34.615 8.37 0.00 0.00 2.69
4647 5231 6.669278 AGAGCTCGTTCCTTTTATTTTTCAC 58.331 36.000 8.37 0.00 0.00 3.18
4648 5232 6.262273 AGAGCTCGTTCCTTTTATTTTTCACA 59.738 34.615 8.37 0.00 0.00 3.58
4649 5233 6.981722 AGCTCGTTCCTTTTATTTTTCACAT 58.018 32.000 0.00 0.00 0.00 3.21
4650 5234 7.084486 AGCTCGTTCCTTTTATTTTTCACATC 58.916 34.615 0.00 0.00 0.00 3.06
4651 5235 6.308041 GCTCGTTCCTTTTATTTTTCACATCC 59.692 38.462 0.00 0.00 0.00 3.51
4652 5236 7.519032 TCGTTCCTTTTATTTTTCACATCCT 57.481 32.000 0.00 0.00 0.00 3.24
4653 5237 7.947282 TCGTTCCTTTTATTTTTCACATCCTT 58.053 30.769 0.00 0.00 0.00 3.36
4654 5238 8.079809 TCGTTCCTTTTATTTTTCACATCCTTC 58.920 33.333 0.00 0.00 0.00 3.46
4655 5239 8.082242 CGTTCCTTTTATTTTTCACATCCTTCT 58.918 33.333 0.00 0.00 0.00 2.85
4656 5240 9.764363 GTTCCTTTTATTTTTCACATCCTTCTT 57.236 29.630 0.00 0.00 0.00 2.52
4668 5252 8.657074 TTCACATCCTTCTTATTAACATACGG 57.343 34.615 0.00 0.00 0.00 4.02
4669 5253 8.014070 TCACATCCTTCTTATTAACATACGGA 57.986 34.615 0.00 0.00 0.00 4.69
4670 5254 8.479689 TCACATCCTTCTTATTAACATACGGAA 58.520 33.333 0.00 0.00 0.00 4.30
4671 5255 9.104965 CACATCCTTCTTATTAACATACGGAAA 57.895 33.333 0.00 0.00 0.00 3.13
4672 5256 9.675464 ACATCCTTCTTATTAACATACGGAAAA 57.325 29.630 0.00 0.00 0.00 2.29
4686 5270 8.883789 ACATACGGAAAAATGTAATGTAAACG 57.116 30.769 0.00 0.00 34.61 3.60
4687 5271 7.964011 ACATACGGAAAAATGTAATGTAAACGG 59.036 33.333 0.00 0.00 34.61 4.44
4688 5272 6.557291 ACGGAAAAATGTAATGTAAACGGA 57.443 33.333 0.00 0.00 0.00 4.69
4689 5273 6.372981 ACGGAAAAATGTAATGTAAACGGAC 58.627 36.000 0.00 0.00 0.00 4.79
4690 5274 6.205270 ACGGAAAAATGTAATGTAAACGGACT 59.795 34.615 0.00 0.00 0.00 3.85
4691 5275 7.387397 ACGGAAAAATGTAATGTAAACGGACTA 59.613 33.333 0.00 0.00 0.00 2.59
4692 5276 8.392612 CGGAAAAATGTAATGTAAACGGACTAT 58.607 33.333 0.00 0.00 0.00 2.12
4701 5285 9.481800 GTAATGTAAACGGACTATTAAGTTTGC 57.518 33.333 3.09 2.54 38.84 3.68
4702 5286 7.916914 ATGTAAACGGACTATTAAGTTTGCT 57.083 32.000 8.80 0.00 39.03 3.91
4703 5287 9.439500 AATGTAAACGGACTATTAAGTTTGCTA 57.561 29.630 8.80 0.00 39.03 3.49
4704 5288 9.609346 ATGTAAACGGACTATTAAGTTTGCTAT 57.391 29.630 8.80 0.84 39.03 2.97
4705 5289 9.090692 TGTAAACGGACTATTAAGTTTGCTATC 57.909 33.333 8.80 0.00 39.03 2.08
4706 5290 9.090692 GTAAACGGACTATTAAGTTTGCTATCA 57.909 33.333 3.09 0.00 37.38 2.15
4707 5291 8.732746 AAACGGACTATTAAGTTTGCTATCAT 57.267 30.769 0.00 0.00 35.56 2.45
4708 5292 9.826574 AAACGGACTATTAAGTTTGCTATCATA 57.173 29.630 0.00 0.00 35.56 2.15
4709 5293 8.813643 ACGGACTATTAAGTTTGCTATCATAC 57.186 34.615 0.00 0.00 35.56 2.39
4710 5294 8.639761 ACGGACTATTAAGTTTGCTATCATACT 58.360 33.333 0.00 0.00 35.56 2.12
4711 5295 9.477484 CGGACTATTAAGTTTGCTATCATACTT 57.523 33.333 7.42 7.42 43.55 2.24
4721 5305 8.903820 AGTTTGCTATCATACTTGATTTAACCC 58.096 33.333 0.00 0.00 42.61 4.11
4722 5306 7.817418 TTGCTATCATACTTGATTTAACCCC 57.183 36.000 0.00 0.00 42.61 4.95
4723 5307 6.905736 TGCTATCATACTTGATTTAACCCCA 58.094 36.000 0.00 0.00 42.61 4.96
4724 5308 6.770785 TGCTATCATACTTGATTTAACCCCAC 59.229 38.462 0.00 0.00 42.61 4.61
4725 5309 6.206829 GCTATCATACTTGATTTAACCCCACC 59.793 42.308 0.00 0.00 42.61 4.61
4726 5310 4.862371 TCATACTTGATTTAACCCCACCC 58.138 43.478 0.00 0.00 0.00 4.61
4727 5311 4.542525 TCATACTTGATTTAACCCCACCCT 59.457 41.667 0.00 0.00 0.00 4.34
4728 5312 3.915346 ACTTGATTTAACCCCACCCTT 57.085 42.857 0.00 0.00 0.00 3.95
4729 5313 3.774734 ACTTGATTTAACCCCACCCTTC 58.225 45.455 0.00 0.00 0.00 3.46
4730 5314 3.141272 ACTTGATTTAACCCCACCCTTCA 59.859 43.478 0.00 0.00 0.00 3.02
4731 5315 3.905493 TGATTTAACCCCACCCTTCAA 57.095 42.857 0.00 0.00 0.00 2.69
4732 5316 4.412060 TGATTTAACCCCACCCTTCAAT 57.588 40.909 0.00 0.00 0.00 2.57
4733 5317 4.349365 TGATTTAACCCCACCCTTCAATC 58.651 43.478 0.00 0.00 0.00 2.67
4734 5318 3.905493 TTTAACCCCACCCTTCAATCA 57.095 42.857 0.00 0.00 0.00 2.57
4735 5319 2.891191 TAACCCCACCCTTCAATCAC 57.109 50.000 0.00 0.00 0.00 3.06
4736 5320 0.114364 AACCCCACCCTTCAATCACC 59.886 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.793259 ACTTCAGATGTTCTATTTTCAAAGGTA 57.207 29.630 0.00 0.00 0.00 3.08
12 13 8.697507 ACTTCAGATGTTCTATTTTCAAAGGT 57.302 30.769 0.00 0.00 0.00 3.50
13 14 9.971922 AAACTTCAGATGTTCTATTTTCAAAGG 57.028 29.630 2.28 0.00 0.00 3.11
56 57 9.826574 GACCAACCTAATACAAGTCATACATTA 57.173 33.333 0.00 0.00 0.00 1.90
57 58 8.325787 TGACCAACCTAATACAAGTCATACATT 58.674 33.333 0.00 0.00 0.00 2.71
58 59 7.857456 TGACCAACCTAATACAAGTCATACAT 58.143 34.615 0.00 0.00 0.00 2.29
59 60 7.247456 TGACCAACCTAATACAAGTCATACA 57.753 36.000 0.00 0.00 0.00 2.29
60 61 8.556213 TTTGACCAACCTAATACAAGTCATAC 57.444 34.615 0.00 0.00 33.21 2.39
61 62 9.747898 AATTTGACCAACCTAATACAAGTCATA 57.252 29.630 0.00 0.00 33.21 2.15
62 63 8.522830 CAATTTGACCAACCTAATACAAGTCAT 58.477 33.333 0.00 0.00 33.21 3.06
63 64 7.721842 TCAATTTGACCAACCTAATACAAGTCA 59.278 33.333 0.00 0.00 0.00 3.41
64 65 8.021396 GTCAATTTGACCAACCTAATACAAGTC 58.979 37.037 17.07 0.00 41.37 3.01
65 66 7.308348 CGTCAATTTGACCAACCTAATACAAGT 60.308 37.037 20.87 0.00 44.20 3.16
66 67 7.021196 CGTCAATTTGACCAACCTAATACAAG 58.979 38.462 20.87 1.46 44.20 3.16
67 68 6.711194 TCGTCAATTTGACCAACCTAATACAA 59.289 34.615 20.87 0.00 44.20 2.41
68 69 6.148150 GTCGTCAATTTGACCAACCTAATACA 59.852 38.462 20.87 0.00 44.20 2.29
69 70 6.540205 GTCGTCAATTTGACCAACCTAATAC 58.460 40.000 20.87 5.03 44.20 1.89
70 71 6.730960 GTCGTCAATTTGACCAACCTAATA 57.269 37.500 20.87 0.00 44.20 0.98
71 72 5.622770 GTCGTCAATTTGACCAACCTAAT 57.377 39.130 20.87 0.00 44.20 1.73
80 81 3.329929 ACCCTAGGTCGTCAATTTGAC 57.670 47.619 17.76 17.76 43.65 3.18
81 82 3.833650 TGTACCCTAGGTCGTCAATTTGA 59.166 43.478 8.29 0.00 37.09 2.69
82 83 3.930848 GTGTACCCTAGGTCGTCAATTTG 59.069 47.826 8.29 0.00 37.09 2.32
83 84 3.367703 CGTGTACCCTAGGTCGTCAATTT 60.368 47.826 8.29 0.00 37.09 1.82
84 85 2.165030 CGTGTACCCTAGGTCGTCAATT 59.835 50.000 8.29 0.00 37.09 2.32
85 86 1.747355 CGTGTACCCTAGGTCGTCAAT 59.253 52.381 8.29 0.00 37.09 2.57
86 87 1.167851 CGTGTACCCTAGGTCGTCAA 58.832 55.000 8.29 0.00 37.09 3.18
87 88 1.308069 GCGTGTACCCTAGGTCGTCA 61.308 60.000 8.29 0.00 37.09 4.35
88 89 1.308069 TGCGTGTACCCTAGGTCGTC 61.308 60.000 8.29 0.00 37.09 4.20
89 90 1.303561 TGCGTGTACCCTAGGTCGT 60.304 57.895 8.29 1.64 37.09 4.34
90 91 1.138247 GTGCGTGTACCCTAGGTCG 59.862 63.158 8.29 5.71 37.09 4.79
91 92 1.138247 CGTGCGTGTACCCTAGGTC 59.862 63.158 8.29 0.00 37.09 3.85
92 93 1.589716 GACGTGCGTGTACCCTAGGT 61.590 60.000 8.29 0.00 40.16 3.08
93 94 1.138247 GACGTGCGTGTACCCTAGG 59.862 63.158 0.06 0.06 0.00 3.02
94 95 1.138247 GGACGTGCGTGTACCCTAG 59.862 63.158 0.67 0.00 0.00 3.02
95 96 1.303561 AGGACGTGCGTGTACCCTA 60.304 57.895 0.67 0.00 0.00 3.53
96 97 2.599578 AGGACGTGCGTGTACCCT 60.600 61.111 0.67 0.00 0.00 4.34
97 98 1.865788 TACAGGACGTGCGTGTACCC 61.866 60.000 13.01 0.00 43.29 3.69
98 99 0.039256 TTACAGGACGTGCGTGTACC 60.039 55.000 15.20 0.00 44.78 3.34
99 100 1.453148 GTTTACAGGACGTGCGTGTAC 59.547 52.381 15.20 7.46 44.78 2.90
100 101 1.337703 AGTTTACAGGACGTGCGTGTA 59.662 47.619 13.01 12.87 43.29 2.90
101 102 0.103572 AGTTTACAGGACGTGCGTGT 59.896 50.000 14.33 14.33 46.45 4.49
102 103 0.506932 CAGTTTACAGGACGTGCGTG 59.493 55.000 13.01 9.22 38.32 5.34
103 104 0.386476 TCAGTTTACAGGACGTGCGT 59.614 50.000 0.00 5.61 0.00 5.24
104 105 1.060713 CTCAGTTTACAGGACGTGCG 58.939 55.000 0.00 0.00 0.00 5.34
105 106 2.030185 TCTCTCAGTTTACAGGACGTGC 60.030 50.000 0.00 0.00 0.00 5.34
106 107 3.253677 ACTCTCTCAGTTTACAGGACGTG 59.746 47.826 0.00 0.00 26.56 4.49
107 108 3.488363 ACTCTCTCAGTTTACAGGACGT 58.512 45.455 0.00 0.00 26.56 4.34
108 109 4.437659 GCTACTCTCTCAGTTTACAGGACG 60.438 50.000 0.00 0.00 36.43 4.79
109 110 4.703093 AGCTACTCTCTCAGTTTACAGGAC 59.297 45.833 0.00 0.00 36.43 3.85
110 111 4.702612 CAGCTACTCTCTCAGTTTACAGGA 59.297 45.833 0.00 0.00 36.43 3.86
111 112 4.702612 TCAGCTACTCTCTCAGTTTACAGG 59.297 45.833 0.00 0.00 36.43 4.00
112 113 5.645929 TCTCAGCTACTCTCTCAGTTTACAG 59.354 44.000 0.00 0.00 36.43 2.74
113 114 5.561679 TCTCAGCTACTCTCTCAGTTTACA 58.438 41.667 0.00 0.00 36.43 2.41
114 115 6.693315 ATCTCAGCTACTCTCTCAGTTTAC 57.307 41.667 0.00 0.00 36.43 2.01
115 116 6.037720 CGAATCTCAGCTACTCTCTCAGTTTA 59.962 42.308 0.00 0.00 36.43 2.01
116 117 5.163663 CGAATCTCAGCTACTCTCTCAGTTT 60.164 44.000 0.00 0.00 36.43 2.66
117 118 4.335315 CGAATCTCAGCTACTCTCTCAGTT 59.665 45.833 0.00 0.00 36.43 3.16
118 119 3.876914 CGAATCTCAGCTACTCTCTCAGT 59.123 47.826 0.00 0.00 39.41 3.41
119 120 3.250762 CCGAATCTCAGCTACTCTCTCAG 59.749 52.174 0.00 0.00 0.00 3.35
120 121 3.210227 CCGAATCTCAGCTACTCTCTCA 58.790 50.000 0.00 0.00 0.00 3.27
121 122 2.031157 GCCGAATCTCAGCTACTCTCTC 60.031 54.545 0.00 0.00 0.00 3.20
122 123 1.953686 GCCGAATCTCAGCTACTCTCT 59.046 52.381 0.00 0.00 0.00 3.10
123 124 1.334599 CGCCGAATCTCAGCTACTCTC 60.335 57.143 0.00 0.00 0.00 3.20
124 125 0.665835 CGCCGAATCTCAGCTACTCT 59.334 55.000 0.00 0.00 0.00 3.24
125 126 0.663688 TCGCCGAATCTCAGCTACTC 59.336 55.000 0.00 0.00 0.00 2.59
126 127 1.103803 TTCGCCGAATCTCAGCTACT 58.896 50.000 0.00 0.00 0.00 2.57
127 128 2.141535 ATTCGCCGAATCTCAGCTAC 57.858 50.000 6.50 0.00 0.00 3.58
128 129 2.866156 CAAATTCGCCGAATCTCAGCTA 59.134 45.455 13.43 0.00 30.29 3.32
129 130 1.667724 CAAATTCGCCGAATCTCAGCT 59.332 47.619 13.43 0.00 30.29 4.24
130 131 1.665679 TCAAATTCGCCGAATCTCAGC 59.334 47.619 13.43 0.00 30.29 4.26
131 132 2.672874 TGTCAAATTCGCCGAATCTCAG 59.327 45.455 13.43 3.89 30.29 3.35
132 133 2.694213 TGTCAAATTCGCCGAATCTCA 58.306 42.857 13.43 7.33 30.29 3.27
133 134 3.740044 TTGTCAAATTCGCCGAATCTC 57.260 42.857 13.43 4.94 30.29 2.75
134 135 4.701956 AATTGTCAAATTCGCCGAATCT 57.298 36.364 13.43 0.00 29.70 2.40
135 136 4.856487 TCAAATTGTCAAATTCGCCGAATC 59.144 37.500 13.43 0.95 34.84 2.52
136 137 4.621034 GTCAAATTGTCAAATTCGCCGAAT 59.379 37.500 6.50 6.50 34.84 3.34
137 138 3.978217 GTCAAATTGTCAAATTCGCCGAA 59.022 39.130 0.33 0.33 34.84 4.30
138 139 3.560503 GTCAAATTGTCAAATTCGCCGA 58.439 40.909 0.00 0.00 34.84 5.54
143 144 6.747280 CGTCCATAGGTCAAATTGTCAAATTC 59.253 38.462 0.00 0.00 34.84 2.17
146 147 5.309638 TCGTCCATAGGTCAAATTGTCAAA 58.690 37.500 0.00 0.00 0.00 2.69
167 169 7.080099 ACAGTTCATTCTGTGATTTGATTTCG 58.920 34.615 0.00 0.00 45.40 3.46
214 216 1.268539 GGCGTCACACAAAAAGGTCAG 60.269 52.381 0.00 0.00 0.00 3.51
283 285 4.838152 CGCTGGCCAGGCGTGTAT 62.838 66.667 33.46 0.00 46.37 2.29
299 301 2.094659 GGATCACACAGGTGCGACG 61.095 63.158 0.00 0.00 44.87 5.12
308 310 7.156000 TGACTTAGTAATTTTCGGATCACACA 58.844 34.615 0.00 0.00 0.00 3.72
351 356 0.530744 CCACTAGTGCAACGCCTAGA 59.469 55.000 17.86 0.00 45.86 2.43
455 460 5.710513 AAATTGCTAAGTCATTGTGCAGA 57.289 34.783 0.00 0.00 33.13 4.26
486 491 4.954970 CCAGCGTTGCACCCCAGT 62.955 66.667 0.00 0.00 0.00 4.00
530 535 1.262950 TCACACTACATTGTGCAACGC 59.737 47.619 0.00 0.00 45.58 4.84
540 545 4.181578 GACATTAAGGCGTCACACTACAT 58.818 43.478 0.00 0.00 32.24 2.29
553 558 1.087771 GGTGACGCCCGACATTAAGG 61.088 60.000 0.00 0.00 0.00 2.69
572 577 2.255252 CGCGGCTGACCTTTTTGG 59.745 61.111 0.00 0.00 42.93 3.28
606 611 8.950210 ACGAAATCAAATCATAGAATGAACTGT 58.050 29.630 0.00 0.00 43.50 3.55
618 623 4.019174 AGGGCTGAACGAAATCAAATCAT 58.981 39.130 0.00 0.00 0.00 2.45
633 638 2.573009 TGTGAATGAATCTCAGGGCTGA 59.427 45.455 0.00 0.00 38.06 4.26
639 644 5.095145 TCCTTCCTGTGAATGAATCTCAG 57.905 43.478 1.58 1.58 45.19 3.35
640 645 5.705397 ATCCTTCCTGTGAATGAATCTCA 57.295 39.130 0.00 0.00 30.42 3.27
641 646 5.530543 GGAATCCTTCCTGTGAATGAATCTC 59.469 44.000 0.00 0.00 46.57 2.75
642 647 5.444176 GGAATCCTTCCTGTGAATGAATCT 58.556 41.667 0.00 0.00 46.57 2.40
643 648 5.764487 GGAATCCTTCCTGTGAATGAATC 57.236 43.478 0.00 0.00 46.57 2.52
742 747 1.880819 GCCATGTTGCTGGGGACAAG 61.881 60.000 0.00 0.00 42.06 3.16
773 778 2.990284 TCTGGTCCAAAAGGGGAATGTA 59.010 45.455 0.00 0.00 39.05 2.29
782 787 1.605710 CTGTGTGCTCTGGTCCAAAAG 59.394 52.381 0.00 0.00 0.00 2.27
831 995 4.323409 GGAGATGAGAGCTTGAGAAAAGGT 60.323 45.833 0.00 0.00 0.00 3.50
849 1013 8.372459 GTGGGTTTAAATAAAAAGGTTGGAGAT 58.628 33.333 0.00 0.00 0.00 2.75
1176 1344 2.125793 GGGTCGGGCGTCTTGTAC 60.126 66.667 0.00 0.00 0.00 2.90
1715 1883 0.251341 GAAGGGCTGAGGCAAAAGGA 60.251 55.000 8.68 0.00 40.87 3.36
1900 2101 3.118445 CCATGTCCTTCTTCTCCCTCTTC 60.118 52.174 0.00 0.00 0.00 2.87
2474 2699 4.571984 GCAAACATGCTTTTGGAAGAAGTT 59.428 37.500 9.95 0.00 37.02 2.66
2503 2729 5.455392 TCGTACGAGTAAACAAAAGAGGAG 58.545 41.667 15.28 0.00 0.00 3.69
2506 2732 6.141462 AGTCTCGTACGAGTAAACAAAAGAG 58.859 40.000 36.67 14.27 42.49 2.85
2657 2885 8.969260 TGACACAGAATATCAATAGAAGCAAT 57.031 30.769 0.00 0.00 0.00 3.56
2685 3048 8.338259 CAAGACATCTGTATTAATTGCACCTAC 58.662 37.037 0.00 0.00 0.00 3.18
2725 3088 8.514594 TCCTGTAAAATCAGCAAGACATTTTAG 58.485 33.333 0.00 0.00 34.28 1.85
2727 3090 7.288810 TCCTGTAAAATCAGCAAGACATTTT 57.711 32.000 0.00 0.00 34.75 1.82
2793 3156 3.657398 TGTAATCGACCCACTCTAGGA 57.343 47.619 0.00 0.00 0.00 2.94
2939 3302 5.049405 CGGAAGTGGCATTCCTTATTATGAC 60.049 44.000 19.52 0.00 45.60 3.06
2961 3326 2.609459 GTGTCTCATTTATCACCTGCGG 59.391 50.000 0.00 0.00 0.00 5.69
3275 3668 9.639601 CATAAGCCAAGATATAACAGAATACGA 57.360 33.333 0.00 0.00 0.00 3.43
3603 4140 9.768662 ATTTATGCACAAAGAAGAAATCAAAGT 57.231 25.926 0.00 0.00 0.00 2.66
3722 4259 0.666577 GGTCGTCAAACAGACTCCGG 60.667 60.000 0.00 0.00 45.32 5.14
3747 4284 1.271840 TAAGGGCAGCCGAAGACCAT 61.272 55.000 5.00 0.00 0.00 3.55
3762 4299 8.964420 TGTTTAATTTCGCTTTCAAGATAAGG 57.036 30.769 0.00 0.00 0.00 2.69
3973 4518 4.798907 AGTACGACGCATCTCATAAGTTTG 59.201 41.667 0.00 0.00 0.00 2.93
4015 4586 3.289911 CGTATCCTCTCGTTTCTTAGCG 58.710 50.000 0.00 0.00 0.00 4.26
4187 4758 1.164411 TGATGTTGTTCGGATGTGCC 58.836 50.000 0.00 0.00 0.00 5.01
4232 4803 3.558418 GGTGTTTCTAAAAGCGACTGTCA 59.442 43.478 8.73 0.00 0.00 3.58
4289 4867 8.202811 TGAAAGGTGATTGTCAATTTTGAATCA 58.797 29.630 0.00 4.36 39.21 2.57
4376 4960 5.674525 GGTGATCATACCTCAGATTTGACA 58.325 41.667 0.00 0.00 37.74 3.58
4415 4999 8.019669 AGCCGTATACATTATTAGTTGTACTCG 58.980 37.037 3.32 0.00 31.55 4.18
4507 5091 9.705290 CAAAAATGCCAGTTTTATAGTAAACCT 57.295 29.630 2.19 0.00 38.49 3.50
4508 5092 9.483916 ACAAAAATGCCAGTTTTATAGTAAACC 57.516 29.630 2.19 0.00 38.49 3.27
4512 5096 9.685828 GTGAACAAAAATGCCAGTTTTATAGTA 57.314 29.630 2.19 0.00 31.43 1.82
4513 5097 7.655732 GGTGAACAAAAATGCCAGTTTTATAGT 59.344 33.333 2.19 0.00 31.43 2.12
4514 5098 7.872483 AGGTGAACAAAAATGCCAGTTTTATAG 59.128 33.333 2.19 0.00 31.43 1.31
4515 5099 7.731054 AGGTGAACAAAAATGCCAGTTTTATA 58.269 30.769 2.19 0.00 31.43 0.98
4516 5100 6.591001 AGGTGAACAAAAATGCCAGTTTTAT 58.409 32.000 2.19 0.00 31.43 1.40
4517 5101 5.983540 AGGTGAACAAAAATGCCAGTTTTA 58.016 33.333 2.19 0.00 31.43 1.52
4518 5102 4.842574 AGGTGAACAAAAATGCCAGTTTT 58.157 34.783 0.00 0.00 32.94 2.43
4519 5103 4.486125 AGGTGAACAAAAATGCCAGTTT 57.514 36.364 0.00 0.00 0.00 2.66
4520 5104 4.486125 AAGGTGAACAAAAATGCCAGTT 57.514 36.364 0.00 0.00 0.00 3.16
4521 5105 4.486125 AAAGGTGAACAAAAATGCCAGT 57.514 36.364 0.00 0.00 0.00 4.00
4522 5106 5.118286 AGAAAAGGTGAACAAAAATGCCAG 58.882 37.500 0.00 0.00 0.00 4.85
4523 5107 5.096443 AGAAAAGGTGAACAAAAATGCCA 57.904 34.783 0.00 0.00 0.00 4.92
4524 5108 5.359756 AGAGAAAAGGTGAACAAAAATGCC 58.640 37.500 0.00 0.00 0.00 4.40
4525 5109 6.978080 TGTAGAGAAAAGGTGAACAAAAATGC 59.022 34.615 0.00 0.00 0.00 3.56
4526 5110 9.185192 GATGTAGAGAAAAGGTGAACAAAAATG 57.815 33.333 0.00 0.00 0.00 2.32
4527 5111 8.360390 GGATGTAGAGAAAAGGTGAACAAAAAT 58.640 33.333 0.00 0.00 0.00 1.82
4528 5112 7.559897 AGGATGTAGAGAAAAGGTGAACAAAAA 59.440 33.333 0.00 0.00 0.00 1.94
4529 5113 7.060421 AGGATGTAGAGAAAAGGTGAACAAAA 58.940 34.615 0.00 0.00 0.00 2.44
4530 5114 6.601332 AGGATGTAGAGAAAAGGTGAACAAA 58.399 36.000 0.00 0.00 0.00 2.83
4531 5115 6.187727 AGGATGTAGAGAAAAGGTGAACAA 57.812 37.500 0.00 0.00 0.00 2.83
4532 5116 5.825593 AGGATGTAGAGAAAAGGTGAACA 57.174 39.130 0.00 0.00 0.00 3.18
4533 5117 6.468543 AGAAGGATGTAGAGAAAAGGTGAAC 58.531 40.000 0.00 0.00 0.00 3.18
4534 5118 6.688073 AGAAGGATGTAGAGAAAAGGTGAA 57.312 37.500 0.00 0.00 0.00 3.18
4535 5119 6.270000 TGAAGAAGGATGTAGAGAAAAGGTGA 59.730 38.462 0.00 0.00 0.00 4.02
4536 5120 6.467677 TGAAGAAGGATGTAGAGAAAAGGTG 58.532 40.000 0.00 0.00 0.00 4.00
4537 5121 6.688073 TGAAGAAGGATGTAGAGAAAAGGT 57.312 37.500 0.00 0.00 0.00 3.50
4538 5122 9.487790 GATATGAAGAAGGATGTAGAGAAAAGG 57.512 37.037 0.00 0.00 0.00 3.11
4569 5153 9.448438 TCACTACACATGCTTCTAAACAAATAT 57.552 29.630 0.00 0.00 0.00 1.28
4570 5154 8.840833 TCACTACACATGCTTCTAAACAAATA 57.159 30.769 0.00 0.00 0.00 1.40
4571 5155 7.744087 TCACTACACATGCTTCTAAACAAAT 57.256 32.000 0.00 0.00 0.00 2.32
4572 5156 7.744087 ATCACTACACATGCTTCTAAACAAA 57.256 32.000 0.00 0.00 0.00 2.83
4573 5157 8.311109 TCTATCACTACACATGCTTCTAAACAA 58.689 33.333 0.00 0.00 0.00 2.83
4574 5158 7.759886 GTCTATCACTACACATGCTTCTAAACA 59.240 37.037 0.00 0.00 0.00 2.83
4575 5159 7.976734 AGTCTATCACTACACATGCTTCTAAAC 59.023 37.037 0.00 0.00 31.37 2.01
4576 5160 8.067751 AGTCTATCACTACACATGCTTCTAAA 57.932 34.615 0.00 0.00 31.37 1.85
4577 5161 7.646548 AGTCTATCACTACACATGCTTCTAA 57.353 36.000 0.00 0.00 31.37 2.10
4578 5162 7.646548 AAGTCTATCACTACACATGCTTCTA 57.353 36.000 0.00 0.00 32.30 2.10
4579 5163 6.537453 AAGTCTATCACTACACATGCTTCT 57.463 37.500 0.00 0.00 32.30 2.85
4580 5164 7.118390 ACAAAAGTCTATCACTACACATGCTTC 59.882 37.037 0.00 0.00 32.30 3.86
4581 5165 6.936900 ACAAAAGTCTATCACTACACATGCTT 59.063 34.615 0.00 0.00 32.30 3.91
4582 5166 6.467677 ACAAAAGTCTATCACTACACATGCT 58.532 36.000 0.00 0.00 32.30 3.79
4583 5167 6.727824 ACAAAAGTCTATCACTACACATGC 57.272 37.500 0.00 0.00 32.30 4.06
4584 5168 8.988064 AGTACAAAAGTCTATCACTACACATG 57.012 34.615 0.00 0.00 32.30 3.21
4586 5170 9.511272 TCTAGTACAAAAGTCTATCACTACACA 57.489 33.333 0.00 0.00 32.30 3.72
4587 5171 9.771915 GTCTAGTACAAAAGTCTATCACTACAC 57.228 37.037 0.00 0.00 32.30 2.90
4588 5172 9.736414 AGTCTAGTACAAAAGTCTATCACTACA 57.264 33.333 0.00 0.00 32.30 2.74
4593 5177 9.204570 GCAAAAGTCTAGTACAAAAGTCTATCA 57.795 33.333 0.00 0.00 0.00 2.15
4594 5178 9.425577 AGCAAAAGTCTAGTACAAAAGTCTATC 57.574 33.333 0.00 0.00 0.00 2.08
4595 5179 9.780186 AAGCAAAAGTCTAGTACAAAAGTCTAT 57.220 29.630 0.00 0.00 0.00 1.98
4596 5180 9.042008 CAAGCAAAAGTCTAGTACAAAAGTCTA 57.958 33.333 0.00 0.00 0.00 2.59
4597 5181 7.769044 TCAAGCAAAAGTCTAGTACAAAAGTCT 59.231 33.333 0.00 0.00 0.00 3.24
4598 5182 7.916552 TCAAGCAAAAGTCTAGTACAAAAGTC 58.083 34.615 0.00 0.00 0.00 3.01
4599 5183 7.769044 TCTCAAGCAAAAGTCTAGTACAAAAGT 59.231 33.333 0.00 0.00 0.00 2.66
4600 5184 8.142994 TCTCAAGCAAAAGTCTAGTACAAAAG 57.857 34.615 0.00 0.00 0.00 2.27
4601 5185 8.142994 CTCTCAAGCAAAAGTCTAGTACAAAA 57.857 34.615 0.00 0.00 0.00 2.44
4602 5186 7.715265 CTCTCAAGCAAAAGTCTAGTACAAA 57.285 36.000 0.00 0.00 0.00 2.83
4619 5203 6.487689 AAATAAAAGGAACGAGCTCTCAAG 57.512 37.500 12.85 0.00 0.00 3.02
4620 5204 6.877611 AAAATAAAAGGAACGAGCTCTCAA 57.122 33.333 12.85 0.00 0.00 3.02
4621 5205 6.485313 TGAAAAATAAAAGGAACGAGCTCTCA 59.515 34.615 12.85 0.00 0.00 3.27
4622 5206 6.797513 GTGAAAAATAAAAGGAACGAGCTCTC 59.202 38.462 12.85 3.05 0.00 3.20
4623 5207 6.262273 TGTGAAAAATAAAAGGAACGAGCTCT 59.738 34.615 12.85 0.00 0.00 4.09
4624 5208 6.435428 TGTGAAAAATAAAAGGAACGAGCTC 58.565 36.000 2.73 2.73 0.00 4.09
4625 5209 6.385649 TGTGAAAAATAAAAGGAACGAGCT 57.614 33.333 0.00 0.00 0.00 4.09
4626 5210 6.308041 GGATGTGAAAAATAAAAGGAACGAGC 59.692 38.462 0.00 0.00 0.00 5.03
4627 5211 7.593825 AGGATGTGAAAAATAAAAGGAACGAG 58.406 34.615 0.00 0.00 0.00 4.18
4628 5212 7.519032 AGGATGTGAAAAATAAAAGGAACGA 57.481 32.000 0.00 0.00 0.00 3.85
4629 5213 8.082242 AGAAGGATGTGAAAAATAAAAGGAACG 58.918 33.333 0.00 0.00 0.00 3.95
4630 5214 9.764363 AAGAAGGATGTGAAAAATAAAAGGAAC 57.236 29.630 0.00 0.00 0.00 3.62
4642 5226 9.104965 CCGTATGTTAATAAGAAGGATGTGAAA 57.895 33.333 0.00 0.00 0.00 2.69
4643 5227 8.479689 TCCGTATGTTAATAAGAAGGATGTGAA 58.520 33.333 0.00 0.00 0.00 3.18
4644 5228 8.014070 TCCGTATGTTAATAAGAAGGATGTGA 57.986 34.615 0.00 0.00 0.00 3.58
4645 5229 8.657074 TTCCGTATGTTAATAAGAAGGATGTG 57.343 34.615 0.00 0.00 0.00 3.21
4646 5230 9.675464 TTTTCCGTATGTTAATAAGAAGGATGT 57.325 29.630 0.00 0.00 0.00 3.06
4660 5244 9.332301 CGTTTACATTACATTTTTCCGTATGTT 57.668 29.630 0.00 0.00 36.46 2.71
4661 5245 7.964011 CCGTTTACATTACATTTTTCCGTATGT 59.036 33.333 0.00 0.00 38.46 2.29
4662 5246 8.176365 TCCGTTTACATTACATTTTTCCGTATG 58.824 33.333 0.00 0.00 0.00 2.39
4663 5247 8.177013 GTCCGTTTACATTACATTTTTCCGTAT 58.823 33.333 0.00 0.00 0.00 3.06
4664 5248 7.387397 AGTCCGTTTACATTACATTTTTCCGTA 59.613 33.333 0.00 0.00 0.00 4.02
4665 5249 6.205270 AGTCCGTTTACATTACATTTTTCCGT 59.795 34.615 0.00 0.00 0.00 4.69
4666 5250 6.604930 AGTCCGTTTACATTACATTTTTCCG 58.395 36.000 0.00 0.00 0.00 4.30
4675 5259 9.481800 GCAAACTTAATAGTCCGTTTACATTAC 57.518 33.333 0.00 0.00 31.99 1.89
4676 5260 9.439500 AGCAAACTTAATAGTCCGTTTACATTA 57.561 29.630 0.00 0.00 31.99 1.90
4677 5261 8.331730 AGCAAACTTAATAGTCCGTTTACATT 57.668 30.769 0.00 0.00 31.99 2.71
4678 5262 7.916914 AGCAAACTTAATAGTCCGTTTACAT 57.083 32.000 0.00 0.00 31.99 2.29
4679 5263 9.090692 GATAGCAAACTTAATAGTCCGTTTACA 57.909 33.333 0.00 0.00 31.99 2.41
4680 5264 9.090692 TGATAGCAAACTTAATAGTCCGTTTAC 57.909 33.333 0.00 0.00 31.99 2.01
4681 5265 9.826574 ATGATAGCAAACTTAATAGTCCGTTTA 57.173 29.630 0.00 0.00 31.99 2.01
4682 5266 8.732746 ATGATAGCAAACTTAATAGTCCGTTT 57.267 30.769 0.00 0.00 31.99 3.60
4683 5267 9.257651 GTATGATAGCAAACTTAATAGTCCGTT 57.742 33.333 0.00 0.00 31.99 4.44
4684 5268 8.639761 AGTATGATAGCAAACTTAATAGTCCGT 58.360 33.333 0.00 0.00 31.99 4.69
4685 5269 9.477484 AAGTATGATAGCAAACTTAATAGTCCG 57.523 33.333 0.00 0.00 31.99 4.79
4695 5279 8.903820 GGGTTAAATCAAGTATGATAGCAAACT 58.096 33.333 0.00 0.00 45.60 2.66
4696 5280 8.135529 GGGGTTAAATCAAGTATGATAGCAAAC 58.864 37.037 0.00 0.00 45.60 2.93
4697 5281 7.836685 TGGGGTTAAATCAAGTATGATAGCAAA 59.163 33.333 0.00 0.00 45.60 3.68
4698 5282 7.284489 GTGGGGTTAAATCAAGTATGATAGCAA 59.716 37.037 0.00 0.00 45.60 3.91
4699 5283 6.770785 GTGGGGTTAAATCAAGTATGATAGCA 59.229 38.462 0.00 0.00 45.60 3.49
4700 5284 6.206829 GGTGGGGTTAAATCAAGTATGATAGC 59.793 42.308 0.00 0.00 45.60 2.97
4701 5285 6.715264 GGGTGGGGTTAAATCAAGTATGATAG 59.285 42.308 0.00 0.00 45.60 2.08
4702 5286 6.391649 AGGGTGGGGTTAAATCAAGTATGATA 59.608 38.462 0.00 0.00 45.60 2.15
4704 5288 4.542525 AGGGTGGGGTTAAATCAAGTATGA 59.457 41.667 0.00 0.00 40.57 2.15
4705 5289 4.867086 AGGGTGGGGTTAAATCAAGTATG 58.133 43.478 0.00 0.00 0.00 2.39
4706 5290 5.015817 TGAAGGGTGGGGTTAAATCAAGTAT 59.984 40.000 0.00 0.00 0.00 2.12
4707 5291 4.354387 TGAAGGGTGGGGTTAAATCAAGTA 59.646 41.667 0.00 0.00 0.00 2.24
4708 5292 3.141272 TGAAGGGTGGGGTTAAATCAAGT 59.859 43.478 0.00 0.00 0.00 3.16
4709 5293 3.773560 TGAAGGGTGGGGTTAAATCAAG 58.226 45.455 0.00 0.00 0.00 3.02
4710 5294 3.905493 TGAAGGGTGGGGTTAAATCAA 57.095 42.857 0.00 0.00 0.00 2.57
4711 5295 3.905493 TTGAAGGGTGGGGTTAAATCA 57.095 42.857 0.00 0.00 0.00 2.57
4712 5296 4.159693 GTGATTGAAGGGTGGGGTTAAATC 59.840 45.833 0.00 0.00 0.00 2.17
4713 5297 4.093743 GTGATTGAAGGGTGGGGTTAAAT 58.906 43.478 0.00 0.00 0.00 1.40
4714 5298 3.502356 GTGATTGAAGGGTGGGGTTAAA 58.498 45.455 0.00 0.00 0.00 1.52
4715 5299 2.225167 GGTGATTGAAGGGTGGGGTTAA 60.225 50.000 0.00 0.00 0.00 2.01
4716 5300 1.356398 GGTGATTGAAGGGTGGGGTTA 59.644 52.381 0.00 0.00 0.00 2.85
4717 5301 0.114364 GGTGATTGAAGGGTGGGGTT 59.886 55.000 0.00 0.00 0.00 4.11
4718 5302 1.774300 GGTGATTGAAGGGTGGGGT 59.226 57.895 0.00 0.00 0.00 4.95
4719 5303 4.764143 GGTGATTGAAGGGTGGGG 57.236 61.111 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.