Multiple sequence alignment - TraesCS7B01G192100

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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 TraesCS7B01G192100 chr7B 100.000 4974 0 0 1 4974 329847501 329852474 0.000000e+00 9186
1 TraesCS7B01G192100 chr7A 95.259 4050 136 30 1 4017 198006946 198002920 0.000000e+00 6364
2 TraesCS7B01G192100 chr7A 94.746 571 28 2 4141 4710 198002921 198002352 0.000000e+00 887
3 TraesCS7B01G192100 chr7A 94.262 122 4 3 4855 4974 198002325 198002205 3.060000e-42 183
4 TraesCS7B01G192100 chr7D 94.514 4047 149 40 1 4017 187100018 187104021 0.000000e+00 6176
5 TraesCS7B01G192100 chr7D 95.622 571 23 2 4141 4710 187104020 187104589 0.000000e+00 915
6 TraesCS7B01G192100 chr7D 94.262 122 4 3 4855 4974 187104616 187104736 3.060000e-42 183
7 TraesCS7B01G192100 chr5B 96.350 137 4 1 4011 4147 581144517 581144382 1.800000e-54 224
8 TraesCS7B01G192100 chr5B 95.556 135 5 1 4009 4143 105764629 105764762 1.080000e-51 215
9 TraesCS7B01G192100 chr5B 93.617 141 7 2 4006 4146 640272875 640272737 5.050000e-50 209
10 TraesCS7B01G192100 chr4B 94.444 144 5 3 4015 4155 16092236 16092379 8.380000e-53 219
11 TraesCS7B01G192100 chr3B 96.899 129 4 0 4015 4143 595367142 595367270 3.020000e-52 217
12 TraesCS7B01G192100 chrUn 96.875 128 4 0 4016 4143 11031660 11031787 1.080000e-51 215
13 TraesCS7B01G192100 chr6A 94.286 140 8 0 4711 4850 123454923 123454784 1.080000e-51 215
14 TraesCS7B01G192100 chr4D 96.875 128 4 0 4015 4142 117644076 117643949 1.080000e-51 215
15 TraesCS7B01G192100 chr6B 94.891 137 6 1 4012 4148 715773222 715773357 3.900000e-51 213
16 TraesCS7B01G192100 chr6B 92.254 142 9 1 4711 4850 684417878 684417737 3.040000e-47 200
17 TraesCS7B01G192100 chr2B 93.617 141 7 2 4014 4154 598960848 598960986 5.050000e-50 209
18 TraesCS7B01G192100 chr3D 92.199 141 11 0 4711 4851 395039260 395039120 3.040000e-47 200
19 TraesCS7B01G192100 chr3D 86.897 145 19 0 4708 4852 288551583 288551727 3.980000e-36 163
20 TraesCS7B01G192100 chr1B 89.933 149 15 0 4703 4851 252035248 252035100 5.080000e-45 193
21 TraesCS7B01G192100 chr1D 89.262 149 16 0 4703 4851 176924498 176924350 2.360000e-43 187
22 TraesCS7B01G192100 chr4A 89.362 141 10 4 4713 4850 669209270 669209408 6.620000e-39 172
23 TraesCS7B01G192100 chr3A 86.667 150 19 1 4703 4851 600313105 600312956 1.110000e-36 165
24 TraesCS7B01G192100 chr3A 87.857 140 17 0 4711 4850 641335640 641335779 1.110000e-36 165


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 TraesCS7B01G192100 chr7B 329847501 329852474 4973 False 9186.000000 9186 100.000000 1 4974 1 chr7B.!!$F1 4973
1 TraesCS7B01G192100 chr7A 198002205 198006946 4741 True 2478.000000 6364 94.755667 1 4974 3 chr7A.!!$R1 4973
2 TraesCS7B01G192100 chr7D 187100018 187104736 4718 False 2424.666667 6176 94.799333 1 4974 3 chr7D.!!$F1 4973

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
815 831 1.009829 GCATAAGCAGAACAGACCCG 58.990 55.000 0.0 0.0 41.58 5.28 F
2533 2566 1.143684 AGAGTTGGCAGGCTCTGAAAA 59.856 47.619 18.6 0.0 40.24 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 2570 1.827789 GGCTGAAGCACCAACACCA 60.828 57.895 4.43 0.0 44.36 4.17 R
4122 4170 0.043637 TACTCCCTCCGTCCCCAAAT 59.956 55.000 0.00 0.0 0.00 2.32 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
51 56 1.656652 GCCGTCAGCACATGATAACT 58.343 50.000 0.00 0.00 40.92 2.24
52 57 2.821546 GCCGTCAGCACATGATAACTA 58.178 47.619 0.00 0.00 40.92 2.24
70 75 1.667724 CTAACTCAATTGAGCAGGGCG 59.332 52.381 30.95 10.75 45.79 6.13
258 263 2.978010 CACCACGTCCTTGCCCAC 60.978 66.667 0.00 0.00 0.00 4.61
360 369 3.074412 CCAGCAGGAGTCGTGTTTAATT 58.926 45.455 13.97 0.00 36.89 1.40
361 370 3.502211 CCAGCAGGAGTCGTGTTTAATTT 59.498 43.478 13.97 0.00 36.89 1.82
362 371 4.466828 CAGCAGGAGTCGTGTTTAATTTG 58.533 43.478 13.97 0.00 0.00 2.32
363 372 4.213270 CAGCAGGAGTCGTGTTTAATTTGA 59.787 41.667 13.97 0.00 0.00 2.69
365 374 6.092122 CAGCAGGAGTCGTGTTTAATTTGATA 59.908 38.462 13.97 0.00 0.00 2.15
366 375 6.092259 AGCAGGAGTCGTGTTTAATTTGATAC 59.908 38.462 13.97 0.00 0.00 2.24
367 376 6.092259 GCAGGAGTCGTGTTTAATTTGATACT 59.908 38.462 13.97 0.00 0.00 2.12
368 377 7.277098 GCAGGAGTCGTGTTTAATTTGATACTA 59.723 37.037 13.97 0.00 0.00 1.82
369 378 8.808529 CAGGAGTCGTGTTTAATTTGATACTAG 58.191 37.037 4.63 0.00 0.00 2.57
370 379 8.529476 AGGAGTCGTGTTTAATTTGATACTAGT 58.471 33.333 0.00 0.00 0.00 2.57
389 398 7.918579 ACTAGTATACTTAGGGAAGGGGATA 57.081 40.000 11.40 0.00 36.95 2.59
425 435 1.687493 CCAGGTGAGGGAGGAGGAC 60.687 68.421 0.00 0.00 0.00 3.85
431 441 4.467107 AGGGAGGAGGACGGCTCC 62.467 72.222 0.00 0.00 41.15 4.70
491 501 4.373116 TCGCCGGCGAAGAGCTTT 62.373 61.111 46.56 0.00 46.01 3.51
576 586 1.208052 CAGGCGAGAAGGAAGATTGGA 59.792 52.381 0.00 0.00 0.00 3.53
604 617 1.529244 GGGGAAGATGGGGATTGCG 60.529 63.158 0.00 0.00 0.00 4.85
696 711 9.508642 AATATTTATTTCTTCGGATTCTCCTCC 57.491 33.333 0.00 0.00 33.30 4.30
726 742 1.535444 ACTGACGGATGGACCCACA 60.535 57.895 0.00 0.00 34.64 4.17
732 748 2.125106 GATGGACCCACACCTCGC 60.125 66.667 0.00 0.00 0.00 5.03
764 780 1.658717 CTACGCGAGCCGGAATCTG 60.659 63.158 15.93 0.00 42.52 2.90
808 824 1.336125 GCCCATCAGCATAAGCAGAAC 59.664 52.381 0.00 0.00 45.49 3.01
815 831 1.009829 GCATAAGCAGAACAGACCCG 58.990 55.000 0.00 0.00 41.58 5.28
855 871 3.435671 CACTAGCTTCCCGTAAACCAAAG 59.564 47.826 0.00 0.00 0.00 2.77
926 943 2.170607 CAGTCCATACTTTCGTCCCCAT 59.829 50.000 0.00 0.00 31.97 4.00
927 944 2.434702 AGTCCATACTTTCGTCCCCATC 59.565 50.000 0.00 0.00 29.00 3.51
928 945 2.434702 GTCCATACTTTCGTCCCCATCT 59.565 50.000 0.00 0.00 0.00 2.90
1307 1324 3.181450 ACTTGCTTCTACAACAAGCCTCT 60.181 43.478 2.11 0.00 44.90 3.69
1312 1329 4.393371 GCTTCTACAACAAGCCTCTTTAGG 59.607 45.833 0.00 0.00 46.76 2.69
1326 1343 1.822990 CTTTAGGTCCGCAGTCCACTA 59.177 52.381 0.00 0.00 0.00 2.74
1442 1459 3.370953 GCATACTCCTGGAATCCAACACT 60.371 47.826 2.61 0.00 30.80 3.55
1525 1544 9.031360 GTTGTTTAGATAAATGTATCTGCGAGA 57.969 33.333 14.76 0.00 45.08 4.04
1529 1548 6.398234 AGATAAATGTATCTGCGAGAGTGT 57.602 37.500 4.50 0.00 44.03 3.55
1530 1549 6.442952 AGATAAATGTATCTGCGAGAGTGTC 58.557 40.000 4.50 0.00 44.03 3.67
1582 1609 1.146263 GGGCGAATGGGAGTCGATT 59.854 57.895 0.00 0.00 41.02 3.34
1603 1630 7.987458 TCGATTGTTAAAGCTTATGAGAAGGAT 59.013 33.333 0.00 0.00 0.00 3.24
1704 1734 8.018677 TCTCTCGTTTTTATTCTTGTGCTTAG 57.981 34.615 0.00 0.00 0.00 2.18
1725 1756 8.447053 GCTTAGCCTAGCATCTTCATATTTAAC 58.553 37.037 0.00 0.00 40.89 2.01
1988 2021 1.890489 TCATGTGCTGCTTGCTTTGAT 59.110 42.857 0.00 0.00 43.37 2.57
2213 2246 7.432148 TCTGGAAATTGCTATACAACTCCTA 57.568 36.000 8.86 0.00 42.27 2.94
2533 2566 1.143684 AGAGTTGGCAGGCTCTGAAAA 59.856 47.619 18.60 0.00 40.24 2.29
2537 2570 4.347607 AGTTGGCAGGCTCTGAAAATTAT 58.652 39.130 6.40 0.00 32.44 1.28
2597 2630 1.269621 GGCCTTACGTGCGATACATCT 60.270 52.381 0.00 0.00 0.00 2.90
2875 2908 8.823220 AGGCCTTATGTTTTGTATATCAAAGT 57.177 30.769 0.00 0.00 45.14 2.66
3255 3288 8.915057 ACTCTAAAAGGTAAGAAGGTTTAACC 57.085 34.615 5.91 5.91 38.99 2.85
3274 3307 4.222124 ACCTGAAAGTTCACACTCTTGT 57.778 40.909 0.00 0.00 35.84 3.16
3313 3346 5.499139 AACAAATGGTACTGACTTGTGTG 57.501 39.130 0.00 0.00 30.90 3.82
3314 3347 4.523083 ACAAATGGTACTGACTTGTGTGT 58.477 39.130 0.00 0.00 0.00 3.72
3320 3353 2.622064 ACTGACTTGTGTGTCTTCCC 57.378 50.000 0.00 0.00 37.79 3.97
3324 3357 1.604278 GACTTGTGTGTCTTCCCTTGC 59.396 52.381 0.00 0.00 34.39 4.01
3332 3371 1.630369 TGTCTTCCCTTGCTGCTATGT 59.370 47.619 0.00 0.00 0.00 2.29
3369 3408 1.160137 GCGTTGTCTTGAAGGCTCAT 58.840 50.000 0.00 0.00 34.58 2.90
3585 3624 0.107654 ATCCTGGCCGAAGCAAGTAC 60.108 55.000 0.00 0.00 38.53 2.73
3590 3629 1.623973 GGCCGAAGCAAGTACGTGAC 61.624 60.000 13.30 4.24 42.56 3.67
3625 3664 6.368791 TCCTATCATAGCGTTTGATTACATGC 59.631 38.462 0.00 0.00 35.50 4.06
3644 3683 6.732154 ACATGCATATTATTGTTCTCAGTGC 58.268 36.000 0.00 0.00 0.00 4.40
3721 3760 8.721478 TGAACAACTGCATTCTTACTTCTAATC 58.279 33.333 0.00 0.00 0.00 1.75
3759 3798 4.278310 ACTAGTTTTTGGTCCATATGGGC 58.722 43.478 21.78 20.24 39.63 5.36
3785 3831 9.226606 CATCCAAACACTATTACTTTCCTTGTA 57.773 33.333 0.00 0.00 0.00 2.41
3818 3864 9.821662 GTACTCAACCTGTATGTTAACAATTTC 57.178 33.333 13.23 4.33 0.00 2.17
3819 3865 7.882179 ACTCAACCTGTATGTTAACAATTTCC 58.118 34.615 13.23 0.00 0.00 3.13
3845 3893 4.883585 TCTAATGTTAGGAGGCAGCAATTG 59.116 41.667 0.00 0.00 0.00 2.32
3873 3921 4.646572 ACAAGGGAACTAAAGAAGCTCTG 58.353 43.478 0.00 0.00 42.68 3.35
3989 4037 5.126061 GCTGGGTGATTTGATTGATTGTACT 59.874 40.000 0.00 0.00 0.00 2.73
4017 4065 7.066525 TCGTCCCTGAACCAAAATAAATGATAC 59.933 37.037 0.00 0.00 0.00 2.24
4018 4066 7.067008 CGTCCCTGAACCAAAATAAATGATACT 59.933 37.037 0.00 0.00 0.00 2.12
4019 4067 8.406297 GTCCCTGAACCAAAATAAATGATACTC 58.594 37.037 0.00 0.00 0.00 2.59
4020 4068 7.559897 TCCCTGAACCAAAATAAATGATACTCC 59.440 37.037 0.00 0.00 0.00 3.85
4021 4069 7.201911 CCCTGAACCAAAATAAATGATACTCCC 60.202 40.741 0.00 0.00 0.00 4.30
4022 4070 7.561356 CCTGAACCAAAATAAATGATACTCCCT 59.439 37.037 0.00 0.00 0.00 4.20
4023 4071 8.519799 TGAACCAAAATAAATGATACTCCCTC 57.480 34.615 0.00 0.00 0.00 4.30
4024 4072 7.559897 TGAACCAAAATAAATGATACTCCCTCC 59.440 37.037 0.00 0.00 0.00 4.30
4025 4073 6.062095 ACCAAAATAAATGATACTCCCTCCG 58.938 40.000 0.00 0.00 0.00 4.63
4026 4074 6.062095 CCAAAATAAATGATACTCCCTCCGT 58.938 40.000 0.00 0.00 0.00 4.69
4027 4075 6.204882 CCAAAATAAATGATACTCCCTCCGTC 59.795 42.308 0.00 0.00 0.00 4.79
4028 4076 5.485209 AATAAATGATACTCCCTCCGTCC 57.515 43.478 0.00 0.00 0.00 4.79
4029 4077 1.718280 AATGATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
4030 4078 0.561184 ATGATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
4031 4079 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
4032 4080 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
4033 4081 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
4034 4082 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4035 4083 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4036 4084 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4037 4085 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4038 4086 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4039 4087 2.914278 TCCCTCCGTCCCAAAATTCTTA 59.086 45.455 0.00 0.00 0.00 2.10
4040 4088 3.526019 TCCCTCCGTCCCAAAATTCTTAT 59.474 43.478 0.00 0.00 0.00 1.73
4041 4089 3.883489 CCCTCCGTCCCAAAATTCTTATC 59.117 47.826 0.00 0.00 0.00 1.75
4042 4090 4.385310 CCCTCCGTCCCAAAATTCTTATCT 60.385 45.833 0.00 0.00 0.00 1.98
4043 4091 5.193679 CCTCCGTCCCAAAATTCTTATCTT 58.806 41.667 0.00 0.00 0.00 2.40
4044 4092 6.354130 CCTCCGTCCCAAAATTCTTATCTTA 58.646 40.000 0.00 0.00 0.00 2.10
4045 4093 6.483640 CCTCCGTCCCAAAATTCTTATCTTAG 59.516 42.308 0.00 0.00 0.00 2.18
4046 4094 7.190335 TCCGTCCCAAAATTCTTATCTTAGA 57.810 36.000 0.00 0.00 0.00 2.10
4047 4095 7.802117 TCCGTCCCAAAATTCTTATCTTAGAT 58.198 34.615 0.00 0.00 0.00 1.98
4048 4096 8.272173 TCCGTCCCAAAATTCTTATCTTAGATT 58.728 33.333 0.00 0.00 0.00 2.40
4049 4097 8.560374 CCGTCCCAAAATTCTTATCTTAGATTC 58.440 37.037 0.00 0.00 0.00 2.52
4050 4098 8.276325 CGTCCCAAAATTCTTATCTTAGATTCG 58.724 37.037 0.00 0.00 0.00 3.34
4051 4099 9.110502 GTCCCAAAATTCTTATCTTAGATTCGT 57.889 33.333 0.00 0.00 0.00 3.85
4052 4100 9.326413 TCCCAAAATTCTTATCTTAGATTCGTC 57.674 33.333 0.00 0.00 0.00 4.20
4053 4101 9.331282 CCCAAAATTCTTATCTTAGATTCGTCT 57.669 33.333 0.00 0.00 0.00 4.18
4061 4109 9.368674 TCTTATCTTAGATTCGTCTAGATACGG 57.631 37.037 0.00 0.00 43.05 4.02
4062 4110 9.368674 CTTATCTTAGATTCGTCTAGATACGGA 57.631 37.037 0.00 0.00 43.05 4.69
4063 4111 9.887629 TTATCTTAGATTCGTCTAGATACGGAT 57.112 33.333 0.00 0.00 43.73 4.18
4064 4112 7.598189 TCTTAGATTCGTCTAGATACGGATG 57.402 40.000 2.64 0.00 41.14 3.51
4065 4113 7.160049 TCTTAGATTCGTCTAGATACGGATGT 58.840 38.462 2.64 1.92 41.14 3.06
4066 4114 5.614923 AGATTCGTCTAGATACGGATGTG 57.385 43.478 2.64 0.00 41.14 3.21
4067 4115 5.064558 AGATTCGTCTAGATACGGATGTGT 58.935 41.667 2.64 0.00 41.14 3.72
4068 4116 4.808077 TTCGTCTAGATACGGATGTGTC 57.192 45.455 0.00 0.00 43.05 3.67
4069 4117 4.069300 TCGTCTAGATACGGATGTGTCT 57.931 45.455 0.00 0.50 46.74 3.41
4070 4118 5.205759 TCGTCTAGATACGGATGTGTCTA 57.794 43.478 0.00 2.61 43.80 2.59
4071 4119 5.604565 TCGTCTAGATACGGATGTGTCTAA 58.395 41.667 0.00 0.00 44.85 2.10
4072 4120 6.228995 TCGTCTAGATACGGATGTGTCTAAT 58.771 40.000 0.00 0.00 44.85 1.73
4073 4121 7.381323 TCGTCTAGATACGGATGTGTCTAATA 58.619 38.462 0.00 0.00 44.85 0.98
4074 4122 7.330454 TCGTCTAGATACGGATGTGTCTAATAC 59.670 40.741 0.00 4.67 44.85 1.89
4075 4123 7.331440 CGTCTAGATACGGATGTGTCTAATACT 59.669 40.741 0.00 0.00 44.85 2.12
4076 4124 9.650539 GTCTAGATACGGATGTGTCTAATACTA 57.349 37.037 0.00 0.00 44.85 1.82
4080 4128 9.962783 AGATACGGATGTGTCTAATACTAAAAC 57.037 33.333 0.00 0.00 43.80 2.43
4081 4129 9.740239 GATACGGATGTGTCTAATACTAAAACA 57.260 33.333 0.00 0.00 33.78 2.83
4083 4131 8.420374 ACGGATGTGTCTAATACTAAAACATG 57.580 34.615 0.00 0.00 0.00 3.21
4084 4132 8.255206 ACGGATGTGTCTAATACTAAAACATGA 58.745 33.333 0.00 0.00 0.00 3.07
4085 4133 8.540492 CGGATGTGTCTAATACTAAAACATGAC 58.460 37.037 0.00 0.00 0.00 3.06
4086 4134 9.601217 GGATGTGTCTAATACTAAAACATGACT 57.399 33.333 0.00 0.00 0.00 3.41
4089 4137 9.990360 TGTGTCTAATACTAAAACATGACTTGA 57.010 29.630 0.00 0.00 0.00 3.02
4097 4145 7.539712 ACTAAAACATGACTTGATACATCCG 57.460 36.000 0.00 0.00 0.00 4.18
4098 4146 7.103641 ACTAAAACATGACTTGATACATCCGT 58.896 34.615 0.00 0.00 0.00 4.69
4099 4147 8.255206 ACTAAAACATGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 0.00 4.02
4100 4148 9.261180 CTAAAACATGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
4101 4149 8.506168 AAAACATGACTTGATACATCCGTATT 57.494 30.769 0.00 0.00 38.48 1.89
4102 4150 8.506168 AAACATGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
4103 4151 9.607988 AAACATGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
4104 4152 8.818141 ACATGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
4105 4153 8.638873 ACATGACTTGATACATCCGTATTTAGA 58.361 33.333 0.00 0.00 38.48 2.10
4106 4154 8.916654 CATGACTTGATACATCCGTATTTAGAC 58.083 37.037 0.00 0.00 38.48 2.59
4107 4155 8.002984 TGACTTGATACATCCGTATTTAGACA 57.997 34.615 0.00 0.00 38.48 3.41
4108 4156 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
4109 4157 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
4110 4158 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
4117 4165 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
4118 4166 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
4120 4168 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
4121 4169 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
4128 4176 8.115490 AGACAAATCTAAGACAAGAATTTGGG 57.885 34.615 9.98 0.00 34.16 4.12
4129 4177 7.177392 AGACAAATCTAAGACAAGAATTTGGGG 59.823 37.037 9.98 0.00 34.16 4.96
4130 4178 7.010160 ACAAATCTAAGACAAGAATTTGGGGA 58.990 34.615 9.98 0.00 38.66 4.81
4131 4179 7.039714 ACAAATCTAAGACAAGAATTTGGGGAC 60.040 37.037 9.98 0.00 38.66 4.46
4132 4180 4.575885 TCTAAGACAAGAATTTGGGGACG 58.424 43.478 0.00 0.00 38.66 4.79
4133 4181 2.200373 AGACAAGAATTTGGGGACGG 57.800 50.000 0.00 0.00 38.66 4.79
4134 4182 1.702957 AGACAAGAATTTGGGGACGGA 59.297 47.619 0.00 0.00 38.66 4.69
4135 4183 2.084546 GACAAGAATTTGGGGACGGAG 58.915 52.381 0.00 0.00 38.66 4.63
4136 4184 1.271926 ACAAGAATTTGGGGACGGAGG 60.272 52.381 0.00 0.00 38.66 4.30
4137 4185 0.331616 AAGAATTTGGGGACGGAGGG 59.668 55.000 0.00 0.00 0.00 4.30
4138 4186 0.549169 AGAATTTGGGGACGGAGGGA 60.549 55.000 0.00 0.00 0.00 4.20
4139 4187 0.107165 GAATTTGGGGACGGAGGGAG 60.107 60.000 0.00 0.00 0.00 4.30
4140 4188 0.845102 AATTTGGGGACGGAGGGAGT 60.845 55.000 0.00 0.00 0.00 3.85
4141 4189 0.043637 ATTTGGGGACGGAGGGAGTA 59.956 55.000 0.00 0.00 0.00 2.59
4212 4260 4.618489 GTCCTTGTTCTTGCGATGATTTTG 59.382 41.667 0.00 0.00 0.00 2.44
4218 4266 0.456482 TTGCGATGATTTTGCTGCCG 60.456 50.000 0.00 0.00 35.56 5.69
4269 4317 8.641499 TTTAATTGCATTTTGAATATCGGACC 57.359 30.769 0.00 0.00 0.00 4.46
4273 4321 3.632145 GCATTTTGAATATCGGACCCAGT 59.368 43.478 0.00 0.00 0.00 4.00
4289 4337 5.221722 GGACCCAGTCTTATGAATATGCTCA 60.222 44.000 0.00 0.00 32.47 4.26
4290 4338 6.445451 ACCCAGTCTTATGAATATGCTCAT 57.555 37.500 0.00 0.00 39.41 2.90
4318 4366 7.563924 AGTCTACATAATAGGGCACTAGAAACA 59.436 37.037 0.40 0.00 31.54 2.83
4352 4400 7.921786 TGCAGTATAGAATGCAGTTAACTTT 57.078 32.000 8.62 0.00 46.97 2.66
4569 4617 6.615088 ACATCTATTGCTTGTTTAGTGCTTG 58.385 36.000 0.00 0.00 0.00 4.01
4681 4730 3.788227 TGGAAACAGTAGCATGTTCCT 57.212 42.857 9.60 0.00 42.49 3.36
4698 4747 7.274250 GCATGTTCCTGAAATTACAATGAAGTC 59.726 37.037 0.00 0.00 0.00 3.01
4710 4759 8.908786 ATTACAATGAAGTCACCCATACTATG 57.091 34.615 0.00 0.00 0.00 2.23
4720 4769 2.169832 CCATACTATGGCCCTGTTCG 57.830 55.000 0.00 0.00 44.70 3.95
4721 4770 1.691976 CCATACTATGGCCCTGTTCGA 59.308 52.381 0.00 0.00 44.70 3.71
4722 4771 2.104111 CCATACTATGGCCCTGTTCGAA 59.896 50.000 0.00 0.00 44.70 3.71
4723 4772 3.244561 CCATACTATGGCCCTGTTCGAAT 60.245 47.826 0.00 0.00 44.70 3.34
4724 4773 2.622064 ACTATGGCCCTGTTCGAATC 57.378 50.000 0.00 0.00 0.00 2.52
4725 4774 1.141053 ACTATGGCCCTGTTCGAATCC 59.859 52.381 0.00 0.00 0.00 3.01
4726 4775 1.417890 CTATGGCCCTGTTCGAATCCT 59.582 52.381 0.00 0.00 0.00 3.24
4727 4776 0.181350 ATGGCCCTGTTCGAATCCTC 59.819 55.000 0.00 0.00 0.00 3.71
4728 4777 0.909610 TGGCCCTGTTCGAATCCTCT 60.910 55.000 0.00 0.00 0.00 3.69
4730 4779 0.179070 GCCCTGTTCGAATCCTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
4731 4780 0.103208 CCCTGTTCGAATCCTCTCCG 59.897 60.000 0.00 0.00 0.00 4.63
4732 4781 0.528684 CCTGTTCGAATCCTCTCCGC 60.529 60.000 0.00 0.00 0.00 5.54
4733 4782 0.457851 CTGTTCGAATCCTCTCCGCT 59.542 55.000 0.00 0.00 0.00 5.52
4734 4783 0.456221 TGTTCGAATCCTCTCCGCTC 59.544 55.000 0.00 0.00 0.00 5.03
4735 4784 0.249114 GTTCGAATCCTCTCCGCTCC 60.249 60.000 0.00 0.00 0.00 4.70
4736 4785 0.683179 TTCGAATCCTCTCCGCTCCA 60.683 55.000 0.00 0.00 0.00 3.86
4737 4786 1.066587 CGAATCCTCTCCGCTCCAC 59.933 63.158 0.00 0.00 0.00 4.02
4738 4787 1.667154 CGAATCCTCTCCGCTCCACA 61.667 60.000 0.00 0.00 0.00 4.17
4739 4788 0.537188 GAATCCTCTCCGCTCCACAA 59.463 55.000 0.00 0.00 0.00 3.33
4740 4789 0.250513 AATCCTCTCCGCTCCACAAC 59.749 55.000 0.00 0.00 0.00 3.32
4741 4790 0.616111 ATCCTCTCCGCTCCACAACT 60.616 55.000 0.00 0.00 0.00 3.16
4742 4791 1.079543 CCTCTCCGCTCCACAACTG 60.080 63.158 0.00 0.00 0.00 3.16
4743 4792 1.739562 CTCTCCGCTCCACAACTGC 60.740 63.158 0.00 0.00 0.00 4.40
4744 4793 2.031012 CTCCGCTCCACAACTGCA 59.969 61.111 0.00 0.00 0.00 4.41
4745 4794 2.031012 TCCGCTCCACAACTGCAG 59.969 61.111 13.48 13.48 0.00 4.41
4746 4795 3.730761 CCGCTCCACAACTGCAGC 61.731 66.667 15.27 0.00 0.00 5.25
4747 4796 2.667536 CGCTCCACAACTGCAGCT 60.668 61.111 15.27 0.00 0.00 4.24
4748 4797 2.675056 CGCTCCACAACTGCAGCTC 61.675 63.158 15.27 0.00 0.00 4.09
4749 4798 2.331132 GCTCCACAACTGCAGCTCC 61.331 63.158 15.27 0.00 0.00 4.70
4750 4799 1.673665 CTCCACAACTGCAGCTCCC 60.674 63.158 15.27 0.00 0.00 4.30
4751 4800 3.052082 CCACAACTGCAGCTCCCG 61.052 66.667 15.27 0.00 0.00 5.14
4752 4801 3.052082 CACAACTGCAGCTCCCGG 61.052 66.667 15.27 0.00 0.00 5.73
4753 4802 3.241530 ACAACTGCAGCTCCCGGA 61.242 61.111 15.27 0.00 0.00 5.14
4754 4803 2.435586 CAACTGCAGCTCCCGGAG 60.436 66.667 15.27 10.41 0.00 4.63
4788 4837 1.588082 CACAATTGCAGGGAGTGGC 59.412 57.895 5.05 0.00 0.00 5.01
4789 4838 0.896940 CACAATTGCAGGGAGTGGCT 60.897 55.000 5.05 0.00 0.00 4.75
4790 4839 0.610232 ACAATTGCAGGGAGTGGCTC 60.610 55.000 5.05 0.00 0.00 4.70
4791 4840 0.609957 CAATTGCAGGGAGTGGCTCA 60.610 55.000 0.00 0.00 31.08 4.26
4792 4841 0.112995 AATTGCAGGGAGTGGCTCAA 59.887 50.000 0.00 0.00 31.08 3.02
4793 4842 0.112995 ATTGCAGGGAGTGGCTCAAA 59.887 50.000 0.00 0.00 31.08 2.69
4794 4843 0.823356 TTGCAGGGAGTGGCTCAAAC 60.823 55.000 0.00 0.00 31.08 2.93
4795 4844 1.973812 GCAGGGAGTGGCTCAAACC 60.974 63.158 0.00 0.00 31.08 3.27
4796 4845 1.672356 CAGGGAGTGGCTCAAACCG 60.672 63.158 0.00 0.00 31.08 4.44
4797 4846 1.841556 AGGGAGTGGCTCAAACCGA 60.842 57.895 0.00 0.00 31.08 4.69
4798 4847 1.376037 GGGAGTGGCTCAAACCGAG 60.376 63.158 0.00 0.00 45.37 4.63
4827 4876 2.458592 CGGAGCGAAATTTCATGACC 57.541 50.000 17.99 12.94 0.00 4.02
4828 4877 1.267532 CGGAGCGAAATTTCATGACCG 60.268 52.381 17.99 19.25 0.00 4.79
4829 4878 1.064060 GGAGCGAAATTTCATGACCGG 59.936 52.381 17.99 0.00 0.00 5.28
4830 4879 2.006888 GAGCGAAATTTCATGACCGGA 58.993 47.619 17.99 0.00 0.00 5.14
4831 4880 2.009774 AGCGAAATTTCATGACCGGAG 58.990 47.619 17.99 0.00 0.00 4.63
4832 4881 2.006888 GCGAAATTTCATGACCGGAGA 58.993 47.619 17.99 0.00 0.00 3.71
4833 4882 2.030946 GCGAAATTTCATGACCGGAGAG 59.969 50.000 17.99 0.00 0.00 3.20
4846 4895 1.079057 GGAGAGGTTCCGAACAGGC 60.079 63.158 13.23 1.98 40.77 4.85
4847 4896 1.671742 GAGAGGTTCCGAACAGGCA 59.328 57.895 13.23 0.00 40.77 4.75
4848 4897 0.670854 GAGAGGTTCCGAACAGGCAC 60.671 60.000 13.23 0.00 40.77 5.01
4849 4898 1.122019 AGAGGTTCCGAACAGGCACT 61.122 55.000 13.23 0.50 40.77 4.40
4850 4899 0.606604 GAGGTTCCGAACAGGCACTA 59.393 55.000 13.23 0.00 40.77 2.74
4851 4900 0.608640 AGGTTCCGAACAGGCACTAG 59.391 55.000 13.23 0.00 40.77 2.57
4852 4901 0.320697 GGTTCCGAACAGGCACTAGT 59.679 55.000 13.23 0.00 40.77 2.57
4853 4902 1.547372 GGTTCCGAACAGGCACTAGTA 59.453 52.381 13.23 0.00 40.77 1.82
4886 4935 8.152898 ACTGATGAATGCTAGCTATCACAATAA 58.847 33.333 20.41 7.95 0.00 1.40
4911 4961 5.357742 TGTATCCATATGCTGACACTGTT 57.642 39.130 0.00 0.00 0.00 3.16
4912 4962 6.478512 TGTATCCATATGCTGACACTGTTA 57.521 37.500 0.00 0.00 0.00 2.41
4913 4963 6.280643 TGTATCCATATGCTGACACTGTTAC 58.719 40.000 0.00 0.00 0.00 2.50
4914 4964 5.620738 ATCCATATGCTGACACTGTTACT 57.379 39.130 0.00 0.00 0.00 2.24
4915 4965 6.731292 ATCCATATGCTGACACTGTTACTA 57.269 37.500 0.00 0.00 0.00 1.82
4916 4966 5.902681 TCCATATGCTGACACTGTTACTAC 58.097 41.667 0.00 0.00 0.00 2.73
4917 4967 5.420739 TCCATATGCTGACACTGTTACTACA 59.579 40.000 0.00 0.00 0.00 2.74
4918 4968 6.098266 TCCATATGCTGACACTGTTACTACAT 59.902 38.462 0.00 0.00 32.86 2.29
4922 4972 9.884636 ATATGCTGACACTGTTACTACATAAAA 57.115 29.630 0.00 0.00 32.86 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.238441 GCTATCTCGTCTGCTTAATCCG 58.762 50.000 0.00 0.00 0.00 4.18
30 31 2.430694 AGTTATCATGTGCTGACGGCTA 59.569 45.455 7.96 0.00 42.39 3.93
31 32 1.208052 AGTTATCATGTGCTGACGGCT 59.792 47.619 7.96 0.00 42.39 5.52
41 42 7.281774 CCTGCTCAATTGAGTTAGTTATCATGT 59.718 37.037 30.88 0.00 43.85 3.21
45 50 5.008118 GCCCTGCTCAATTGAGTTAGTTATC 59.992 44.000 30.88 15.54 43.85 1.75
48 53 3.084786 GCCCTGCTCAATTGAGTTAGTT 58.915 45.455 30.88 0.00 43.85 2.24
50 55 1.667724 CGCCCTGCTCAATTGAGTTAG 59.332 52.381 30.88 26.83 43.85 2.34
51 56 1.003118 ACGCCCTGCTCAATTGAGTTA 59.997 47.619 30.88 20.97 43.85 2.24
52 57 0.250901 ACGCCCTGCTCAATTGAGTT 60.251 50.000 30.88 9.05 43.85 3.01
70 75 1.226603 CGTCGGGGACAAGATCGAC 60.227 63.158 0.00 0.00 45.61 4.20
258 263 0.378962 CTACGAGAAGCTGGAGTCGG 59.621 60.000 10.78 0.00 36.74 4.79
360 369 8.175431 CCCCTTCCCTAAGTATACTAGTATCAA 58.825 40.741 18.68 0.00 0.00 2.57
361 370 7.522175 TCCCCTTCCCTAAGTATACTAGTATCA 59.478 40.741 18.68 3.68 0.00 2.15
362 371 7.937591 TCCCCTTCCCTAAGTATACTAGTATC 58.062 42.308 18.68 10.64 0.00 2.24
363 372 7.918579 TCCCCTTCCCTAAGTATACTAGTAT 57.081 40.000 19.07 19.07 0.00 2.12
365 374 6.817119 ATCCCCTTCCCTAAGTATACTAGT 57.183 41.667 5.65 0.00 0.00 2.57
366 375 7.035985 ACCTATCCCCTTCCCTAAGTATACTAG 60.036 44.444 5.65 4.37 0.00 2.57
367 376 6.806795 ACCTATCCCCTTCCCTAAGTATACTA 59.193 42.308 5.65 0.00 0.00 1.82
368 377 5.624838 ACCTATCCCCTTCCCTAAGTATACT 59.375 44.000 0.00 0.00 0.00 2.12
369 378 5.913277 ACCTATCCCCTTCCCTAAGTATAC 58.087 45.833 0.00 0.00 0.00 1.47
370 379 6.221240 CCTACCTATCCCCTTCCCTAAGTATA 59.779 46.154 0.00 0.00 0.00 1.47
389 398 1.991722 GTGCCCCGGTAACCTACCT 60.992 63.158 0.00 0.00 46.81 3.08
431 441 4.194720 CTCTTCCTCGCCGACCGG 62.195 72.222 0.00 0.00 37.59 5.28
489 499 1.067749 TCGACGGCCACTTCGAAAA 59.932 52.632 16.49 0.00 43.21 2.29
576 586 1.006400 CCATCTTCCCCTCCAAGCTTT 59.994 52.381 0.00 0.00 0.00 3.51
604 617 0.908180 TTCTTTCCTCGGACTCCCCC 60.908 60.000 0.00 0.00 0.00 5.40
716 731 3.717294 GGCGAGGTGTGGGTCCAT 61.717 66.667 0.00 0.00 0.00 3.41
754 770 2.506472 GGAGGACCAGATTCCGGC 59.494 66.667 0.00 0.00 41.04 6.13
784 800 1.803366 GCTTATGCTGATGGGCTGCC 61.803 60.000 11.05 11.05 40.39 4.85
808 824 2.099921 CAGATTAGTGGTCTCGGGTCTG 59.900 54.545 0.00 0.00 0.00 3.51
815 831 1.134371 GTGGGCCAGATTAGTGGTCTC 60.134 57.143 6.40 0.00 42.36 3.36
926 943 1.337823 CGGAGCTTTTCGGGAAGAAGA 60.338 52.381 0.00 0.00 40.40 2.87
927 944 1.079503 CGGAGCTTTTCGGGAAGAAG 58.920 55.000 0.00 0.00 40.40 2.85
928 945 0.321298 CCGGAGCTTTTCGGGAAGAA 60.321 55.000 13.93 0.00 46.44 2.52
1165 1182 0.549413 AGGGTTTGGAGGTAGGGGTC 60.549 60.000 0.00 0.00 0.00 4.46
1241 1258 5.508320 GGGATTTCGCCAAACTTAAACAGAA 60.508 40.000 0.00 0.00 0.00 3.02
1307 1324 1.822990 CTAGTGGACTGCGGACCTAAA 59.177 52.381 15.20 0.00 0.00 1.85
1312 1329 4.644103 TTATTACTAGTGGACTGCGGAC 57.356 45.455 5.39 0.00 0.00 4.79
1326 1343 7.715249 AGATTCCACGCACACATAATTATTACT 59.285 33.333 0.00 0.00 0.00 2.24
1442 1459 3.195396 GGCCAAAAATGTTCCTGCTATCA 59.805 43.478 0.00 0.00 0.00 2.15
1529 1548 4.545208 TCAAAACATATGTCAGTCCCGA 57.455 40.909 9.23 0.00 0.00 5.14
1530 1549 4.496341 GCATCAAAACATATGTCAGTCCCG 60.496 45.833 9.23 0.00 0.00 5.14
1582 1609 8.049117 ACATGATCCTTCTCATAAGCTTTAACA 58.951 33.333 3.20 0.00 34.11 2.41
1603 1630 3.822735 CTGCCTCTCCAAGAAAAACATGA 59.177 43.478 0.00 0.00 0.00 3.07
1725 1756 4.941873 AGGTAGCCAAAGAACGGATTAAAG 59.058 41.667 0.00 0.00 0.00 1.85
1988 2021 7.224297 GCACATCTATCCCCTACAGATAAAAA 58.776 38.462 0.00 0.00 0.00 1.94
2533 2566 2.493278 GCTGAAGCACCAACACCATAAT 59.507 45.455 0.00 0.00 41.59 1.28
2537 2570 1.827789 GGCTGAAGCACCAACACCA 60.828 57.895 4.43 0.00 44.36 4.17
2597 2630 3.009363 TGTCCCAGCAAATCTGATTCTCA 59.991 43.478 2.92 0.00 45.72 3.27
2714 2747 7.741554 ATTATTTCTGTACTCCTTCTCCAGT 57.258 36.000 0.00 0.00 0.00 4.00
2987 3020 3.399330 TGAGCTAACCTCGGACAAAAAG 58.601 45.455 0.00 0.00 43.82 2.27
3253 3286 4.222124 ACAAGAGTGTGAACTTTCAGGT 57.778 40.909 0.00 0.00 37.98 4.00
3255 3288 7.227512 AGGATAAACAAGAGTGTGAACTTTCAG 59.772 37.037 0.00 0.00 38.27 3.02
3299 3332 3.069729 AGGGAAGACACACAAGTCAGTAC 59.930 47.826 0.00 0.00 40.98 2.73
3313 3346 2.409948 ACATAGCAGCAAGGGAAGAC 57.590 50.000 0.00 0.00 0.00 3.01
3314 3347 3.107601 AGTACATAGCAGCAAGGGAAGA 58.892 45.455 0.00 0.00 0.00 2.87
3320 3353 8.839310 AGGAATAATAAGTACATAGCAGCAAG 57.161 34.615 0.00 0.00 0.00 4.01
3324 3357 9.776158 CTACGAGGAATAATAAGTACATAGCAG 57.224 37.037 0.00 0.00 0.00 4.24
3332 3371 7.012704 AGACAACGCTACGAGGAATAATAAGTA 59.987 37.037 0.00 0.00 0.00 2.24
3602 3641 7.120789 TGCATGTAATCAAACGCTATGATAG 57.879 36.000 0.00 0.00 36.53 2.08
3625 3664 6.220579 CGGAGCACTGAGAACAATAATATG 57.779 41.667 0.00 0.00 0.00 1.78
3721 3760 9.185192 CAAAAACTAGTCCTTCAGCAAATTTAG 57.815 33.333 0.00 0.00 0.00 1.85
3754 3793 5.129368 AGTAATAGTGTTTGGATGCCCAT 57.871 39.130 0.00 0.00 43.12 4.00
3755 3794 4.584638 AGTAATAGTGTTTGGATGCCCA 57.415 40.909 0.00 0.00 41.64 5.36
3756 3795 5.163550 GGAAAGTAATAGTGTTTGGATGCCC 60.164 44.000 0.00 0.00 0.00 5.36
3759 3798 8.110860 ACAAGGAAAGTAATAGTGTTTGGATG 57.889 34.615 0.00 0.00 0.00 3.51
3785 3831 6.420913 ACATACAGGTTGAGTACAGAAAGT 57.579 37.500 0.00 0.00 0.00 2.66
3818 3864 3.879892 GCTGCCTCCTAACATTAGAAAGG 59.120 47.826 12.36 12.36 36.96 3.11
3819 3865 4.517285 TGCTGCCTCCTAACATTAGAAAG 58.483 43.478 0.00 0.00 32.47 2.62
3845 3893 5.234329 GCTTCTTTAGTTCCCTTGTTTTTGC 59.766 40.000 0.00 0.00 0.00 3.68
3873 3921 1.160137 AGATGAAAGCGTTGCCTCAC 58.840 50.000 0.00 0.00 0.00 3.51
3989 4037 6.265649 TCATTTATTTTGGTTCAGGGACGAAA 59.734 34.615 0.00 0.00 0.00 3.46
4017 4065 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4018 4066 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4019 4067 2.215942 AAGAATTTTGGGACGGAGGG 57.784 50.000 0.00 0.00 0.00 4.30
4020 4068 4.781934 AGATAAGAATTTTGGGACGGAGG 58.218 43.478 0.00 0.00 0.00 4.30
4021 4069 7.272978 TCTAAGATAAGAATTTTGGGACGGAG 58.727 38.462 0.00 0.00 0.00 4.63
4022 4070 7.190335 TCTAAGATAAGAATTTTGGGACGGA 57.810 36.000 0.00 0.00 0.00 4.69
4023 4071 8.451908 AATCTAAGATAAGAATTTTGGGACGG 57.548 34.615 0.00 0.00 0.00 4.79
4024 4072 8.276325 CGAATCTAAGATAAGAATTTTGGGACG 58.724 37.037 0.00 0.00 0.00 4.79
4025 4073 9.110502 ACGAATCTAAGATAAGAATTTTGGGAC 57.889 33.333 0.00 0.00 0.00 4.46
4026 4074 9.326413 GACGAATCTAAGATAAGAATTTTGGGA 57.674 33.333 0.00 0.00 0.00 4.37
4027 4075 9.331282 AGACGAATCTAAGATAAGAATTTTGGG 57.669 33.333 0.00 0.00 31.46 4.12
4035 4083 9.368674 CCGTATCTAGACGAATCTAAGATAAGA 57.631 37.037 5.60 0.00 45.82 2.10
4036 4084 9.368674 TCCGTATCTAGACGAATCTAAGATAAG 57.631 37.037 5.60 0.00 45.82 1.73
4037 4085 9.887629 ATCCGTATCTAGACGAATCTAAGATAA 57.112 33.333 5.60 0.00 45.82 1.75
4038 4086 9.315525 CATCCGTATCTAGACGAATCTAAGATA 57.684 37.037 5.60 0.00 45.82 1.98
4039 4087 7.825270 ACATCCGTATCTAGACGAATCTAAGAT 59.175 37.037 5.60 0.00 45.82 2.40
4040 4088 7.117956 CACATCCGTATCTAGACGAATCTAAGA 59.882 40.741 5.60 0.00 45.82 2.10
4041 4089 7.095144 ACACATCCGTATCTAGACGAATCTAAG 60.095 40.741 5.60 0.00 45.82 2.18
4042 4090 6.709397 ACACATCCGTATCTAGACGAATCTAA 59.291 38.462 5.60 0.00 45.82 2.10
4043 4091 6.228995 ACACATCCGTATCTAGACGAATCTA 58.771 40.000 5.60 0.00 45.82 1.98
4044 4092 5.064558 ACACATCCGTATCTAGACGAATCT 58.935 41.667 5.60 0.00 45.82 2.40
4045 4093 5.179742 AGACACATCCGTATCTAGACGAATC 59.820 44.000 5.60 0.00 45.82 2.52
4046 4094 5.064558 AGACACATCCGTATCTAGACGAAT 58.935 41.667 5.60 0.00 45.82 3.34
4047 4095 4.449131 AGACACATCCGTATCTAGACGAA 58.551 43.478 5.60 0.00 45.82 3.85
4048 4096 4.069300 AGACACATCCGTATCTAGACGA 57.931 45.455 5.60 0.00 45.82 4.20
4049 4097 5.919272 TTAGACACATCCGTATCTAGACG 57.081 43.478 0.00 0.00 42.55 4.18
4050 4098 8.550710 AGTATTAGACACATCCGTATCTAGAC 57.449 38.462 0.00 0.00 0.00 2.59
4054 4102 9.962783 GTTTTAGTATTAGACACATCCGTATCT 57.037 33.333 0.00 0.00 0.00 1.98
4055 4103 9.740239 TGTTTTAGTATTAGACACATCCGTATC 57.260 33.333 0.00 0.00 0.00 2.24
4057 4105 9.524106 CATGTTTTAGTATTAGACACATCCGTA 57.476 33.333 0.00 0.00 0.00 4.02
4058 4106 8.255206 TCATGTTTTAGTATTAGACACATCCGT 58.745 33.333 0.00 0.00 0.00 4.69
4059 4107 8.540492 GTCATGTTTTAGTATTAGACACATCCG 58.460 37.037 0.00 0.00 0.00 4.18
4060 4108 9.601217 AGTCATGTTTTAGTATTAGACACATCC 57.399 33.333 0.00 0.00 0.00 3.51
4063 4111 9.990360 TCAAGTCATGTTTTAGTATTAGACACA 57.010 29.630 0.00 0.00 0.00 3.72
4071 4119 9.261180 CGGATGTATCAAGTCATGTTTTAGTAT 57.739 33.333 0.00 0.00 0.00 2.12
4072 4120 8.255206 ACGGATGTATCAAGTCATGTTTTAGTA 58.745 33.333 0.00 0.00 0.00 1.82
4073 4121 7.103641 ACGGATGTATCAAGTCATGTTTTAGT 58.896 34.615 0.00 0.00 0.00 2.24
4074 4122 7.539712 ACGGATGTATCAAGTCATGTTTTAG 57.460 36.000 0.00 0.00 0.00 1.85
4075 4123 9.607988 AATACGGATGTATCAAGTCATGTTTTA 57.392 29.630 0.00 0.00 40.42 1.52
4076 4124 8.506168 AATACGGATGTATCAAGTCATGTTTT 57.494 30.769 0.00 0.00 40.42 2.43
4077 4125 8.506168 AAATACGGATGTATCAAGTCATGTTT 57.494 30.769 0.00 0.00 40.42 2.83
4078 4126 9.261180 CTAAATACGGATGTATCAAGTCATGTT 57.739 33.333 0.00 0.00 40.42 2.71
4079 4127 8.638873 TCTAAATACGGATGTATCAAGTCATGT 58.361 33.333 0.00 0.00 40.42 3.21
4080 4128 8.916654 GTCTAAATACGGATGTATCAAGTCATG 58.083 37.037 0.00 0.00 40.42 3.07
4081 4129 8.638873 TGTCTAAATACGGATGTATCAAGTCAT 58.361 33.333 0.00 0.00 40.42 3.06
4082 4130 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
4083 4131 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
4084 4132 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
4091 4139 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
4092 4140 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
4094 4142 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
4095 4143 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
4102 4150 9.231297 CCCAAATTCTTGTCTTAGATTTGTCTA 57.769 33.333 0.00 0.00 0.00 2.59
4103 4151 7.177392 CCCCAAATTCTTGTCTTAGATTTGTCT 59.823 37.037 0.00 0.00 0.00 3.41
4104 4152 7.176690 TCCCCAAATTCTTGTCTTAGATTTGTC 59.823 37.037 0.00 0.00 0.00 3.18
4105 4153 7.010160 TCCCCAAATTCTTGTCTTAGATTTGT 58.990 34.615 0.00 0.00 0.00 2.83
4106 4154 7.315890 GTCCCCAAATTCTTGTCTTAGATTTG 58.684 38.462 0.00 0.00 0.00 2.32
4107 4155 6.151144 CGTCCCCAAATTCTTGTCTTAGATTT 59.849 38.462 0.00 0.00 0.00 2.17
4108 4156 5.648092 CGTCCCCAAATTCTTGTCTTAGATT 59.352 40.000 0.00 0.00 0.00 2.40
4109 4157 5.186198 CGTCCCCAAATTCTTGTCTTAGAT 58.814 41.667 0.00 0.00 0.00 1.98
4110 4158 4.564821 CCGTCCCCAAATTCTTGTCTTAGA 60.565 45.833 0.00 0.00 0.00 2.10
4111 4159 3.689649 CCGTCCCCAAATTCTTGTCTTAG 59.310 47.826 0.00 0.00 0.00 2.18
4112 4160 3.328343 TCCGTCCCCAAATTCTTGTCTTA 59.672 43.478 0.00 0.00 0.00 2.10
4113 4161 2.107552 TCCGTCCCCAAATTCTTGTCTT 59.892 45.455 0.00 0.00 0.00 3.01
4114 4162 1.702957 TCCGTCCCCAAATTCTTGTCT 59.297 47.619 0.00 0.00 0.00 3.41
4115 4163 2.084546 CTCCGTCCCCAAATTCTTGTC 58.915 52.381 0.00 0.00 0.00 3.18
4116 4164 1.271926 CCTCCGTCCCCAAATTCTTGT 60.272 52.381 0.00 0.00 0.00 3.16
4117 4165 1.463674 CCTCCGTCCCCAAATTCTTG 58.536 55.000 0.00 0.00 0.00 3.02
4118 4166 0.331616 CCCTCCGTCCCCAAATTCTT 59.668 55.000 0.00 0.00 0.00 2.52
4119 4167 0.549169 TCCCTCCGTCCCCAAATTCT 60.549 55.000 0.00 0.00 0.00 2.40
4120 4168 0.107165 CTCCCTCCGTCCCCAAATTC 60.107 60.000 0.00 0.00 0.00 2.17
4121 4169 0.845102 ACTCCCTCCGTCCCCAAATT 60.845 55.000 0.00 0.00 0.00 1.82
4122 4170 0.043637 TACTCCCTCCGTCCCCAAAT 59.956 55.000 0.00 0.00 0.00 2.32
4123 4171 0.043637 ATACTCCCTCCGTCCCCAAA 59.956 55.000 0.00 0.00 0.00 3.28
4124 4172 0.689745 CATACTCCCTCCGTCCCCAA 60.690 60.000 0.00 0.00 0.00 4.12
4125 4173 1.075525 CATACTCCCTCCGTCCCCA 60.076 63.158 0.00 0.00 0.00 4.96
4126 4174 0.186873 TACATACTCCCTCCGTCCCC 59.813 60.000 0.00 0.00 0.00 4.81
4127 4175 2.077687 TTACATACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
4128 4176 2.223994 GCTTTACATACTCCCTCCGTCC 60.224 54.545 0.00 0.00 0.00 4.79
4129 4177 2.429610 TGCTTTACATACTCCCTCCGTC 59.570 50.000 0.00 0.00 0.00 4.79
4130 4178 2.431057 CTGCTTTACATACTCCCTCCGT 59.569 50.000 0.00 0.00 0.00 4.69
4131 4179 2.224066 CCTGCTTTACATACTCCCTCCG 60.224 54.545 0.00 0.00 0.00 4.63
4132 4180 2.772515 ACCTGCTTTACATACTCCCTCC 59.227 50.000 0.00 0.00 0.00 4.30
4133 4181 4.081087 TCAACCTGCTTTACATACTCCCTC 60.081 45.833 0.00 0.00 0.00 4.30
4134 4182 3.844211 TCAACCTGCTTTACATACTCCCT 59.156 43.478 0.00 0.00 0.00 4.20
4135 4183 4.216411 TCAACCTGCTTTACATACTCCC 57.784 45.455 0.00 0.00 0.00 4.30
4136 4184 7.934120 AGATATTCAACCTGCTTTACATACTCC 59.066 37.037 0.00 0.00 0.00 3.85
4137 4185 8.894768 AGATATTCAACCTGCTTTACATACTC 57.105 34.615 0.00 0.00 0.00 2.59
4141 4189 9.071276 CCATAAGATATTCAACCTGCTTTACAT 57.929 33.333 0.00 0.00 0.00 2.29
4212 4260 5.547181 AGTTTAAGAAGATTTACGGCAGC 57.453 39.130 0.00 0.00 0.00 5.25
4269 4317 7.160049 ACTGATGAGCATATTCATAAGACTGG 58.840 38.462 8.28 0.00 38.01 4.00
4273 4321 9.082313 TGTAGACTGATGAGCATATTCATAAGA 57.918 33.333 8.28 0.00 38.01 2.10
4289 4337 7.471041 TCTAGTGCCCTATTATGTAGACTGAT 58.529 38.462 0.00 0.00 0.00 2.90
4290 4338 6.849151 TCTAGTGCCCTATTATGTAGACTGA 58.151 40.000 0.00 0.00 0.00 3.41
4318 4366 5.295292 GCATTCTATACTGCACTCATGTTGT 59.705 40.000 0.00 0.00 38.28 3.32
4349 4397 3.727673 CGTGACATTATTCACCGGCAAAG 60.728 47.826 0.00 0.00 42.63 2.77
4352 4400 1.338294 ACGTGACATTATTCACCGGCA 60.338 47.619 0.00 0.00 42.63 5.69
4442 4490 9.283768 CATATAAATACTTATGTTGGGTGAGCA 57.716 33.333 0.00 0.00 0.00 4.26
4569 4617 3.752222 TGGAATGAAAACATGGCATTTGC 59.248 39.130 0.00 0.00 41.14 3.68
4681 4730 7.888021 AGTATGGGTGACTTCATTGTAATTTCA 59.112 33.333 0.00 0.00 0.00 2.69
4710 4759 0.179070 GAGAGGATTCGAACAGGGCC 60.179 60.000 0.00 0.00 0.00 5.80
4711 4760 0.179070 GGAGAGGATTCGAACAGGGC 60.179 60.000 0.00 0.00 0.00 5.19
4712 4761 0.103208 CGGAGAGGATTCGAACAGGG 59.897 60.000 0.00 0.00 0.00 4.45
4713 4762 0.528684 GCGGAGAGGATTCGAACAGG 60.529 60.000 0.00 0.00 0.00 4.00
4714 4763 0.457851 AGCGGAGAGGATTCGAACAG 59.542 55.000 0.00 0.00 0.00 3.16
4715 4764 0.456221 GAGCGGAGAGGATTCGAACA 59.544 55.000 0.00 0.00 0.00 3.18
4716 4765 0.249114 GGAGCGGAGAGGATTCGAAC 60.249 60.000 0.00 0.00 0.00 3.95
4717 4766 0.683179 TGGAGCGGAGAGGATTCGAA 60.683 55.000 0.00 0.00 0.00 3.71
4718 4767 1.076995 TGGAGCGGAGAGGATTCGA 60.077 57.895 0.00 0.00 0.00 3.71
4719 4768 1.066587 GTGGAGCGGAGAGGATTCG 59.933 63.158 0.00 0.00 0.00 3.34
4720 4769 0.537188 TTGTGGAGCGGAGAGGATTC 59.463 55.000 0.00 0.00 0.00 2.52
4721 4770 0.250513 GTTGTGGAGCGGAGAGGATT 59.749 55.000 0.00 0.00 0.00 3.01
4722 4771 0.616111 AGTTGTGGAGCGGAGAGGAT 60.616 55.000 0.00 0.00 0.00 3.24
4723 4772 1.228894 AGTTGTGGAGCGGAGAGGA 60.229 57.895 0.00 0.00 0.00 3.71
4724 4773 1.079543 CAGTTGTGGAGCGGAGAGG 60.080 63.158 0.00 0.00 0.00 3.69
4725 4774 1.739562 GCAGTTGTGGAGCGGAGAG 60.740 63.158 0.00 0.00 0.00 3.20
4726 4775 2.343758 GCAGTTGTGGAGCGGAGA 59.656 61.111 0.00 0.00 0.00 3.71
4727 4776 2.031012 TGCAGTTGTGGAGCGGAG 59.969 61.111 0.00 0.00 0.00 4.63
4728 4777 2.031012 CTGCAGTTGTGGAGCGGA 59.969 61.111 5.25 0.00 35.07 5.54
4732 4781 1.673665 GGGAGCTGCAGTTGTGGAG 60.674 63.158 16.64 0.00 44.77 3.86
4733 4782 2.431683 GGGAGCTGCAGTTGTGGA 59.568 61.111 16.64 0.00 0.00 4.02
4734 4783 3.052082 CGGGAGCTGCAGTTGTGG 61.052 66.667 16.64 0.00 0.00 4.17
4735 4784 3.052082 CCGGGAGCTGCAGTTGTG 61.052 66.667 16.64 0.92 0.00 3.33
4736 4785 3.241530 TCCGGGAGCTGCAGTTGT 61.242 61.111 16.64 0.00 0.00 3.32
4737 4786 2.435586 CTCCGGGAGCTGCAGTTG 60.436 66.667 16.64 0.00 0.00 3.16
4757 4806 3.984193 ATTGTGCTGCCGCTCCCTC 62.984 63.158 0.70 0.00 36.97 4.30
4758 4807 3.574074 AATTGTGCTGCCGCTCCCT 62.574 57.895 0.70 0.00 36.97 4.20
4759 4808 3.064324 AATTGTGCTGCCGCTCCC 61.064 61.111 0.70 0.00 36.97 4.30
4760 4809 2.180017 CAATTGTGCTGCCGCTCC 59.820 61.111 0.70 0.00 36.97 4.70
4770 4819 0.896940 AGCCACTCCCTGCAATTGTG 60.897 55.000 7.40 0.56 0.00 3.33
4771 4820 0.610232 GAGCCACTCCCTGCAATTGT 60.610 55.000 7.40 0.00 0.00 2.71
4772 4821 0.609957 TGAGCCACTCCCTGCAATTG 60.610 55.000 0.00 0.00 0.00 2.32
4773 4822 0.112995 TTGAGCCACTCCCTGCAATT 59.887 50.000 0.00 0.00 0.00 2.32
4774 4823 0.112995 TTTGAGCCACTCCCTGCAAT 59.887 50.000 0.00 0.00 0.00 3.56
4775 4824 0.823356 GTTTGAGCCACTCCCTGCAA 60.823 55.000 0.00 0.00 0.00 4.08
4776 4825 1.228245 GTTTGAGCCACTCCCTGCA 60.228 57.895 0.00 0.00 0.00 4.41
4777 4826 1.973812 GGTTTGAGCCACTCCCTGC 60.974 63.158 0.00 0.00 0.00 4.85
4778 4827 1.672356 CGGTTTGAGCCACTCCCTG 60.672 63.158 0.00 0.00 0.00 4.45
4779 4828 1.831652 CTCGGTTTGAGCCACTCCCT 61.832 60.000 0.00 0.00 38.03 4.20
4780 4829 1.376037 CTCGGTTTGAGCCACTCCC 60.376 63.158 0.00 0.00 38.03 4.30
4781 4830 4.285851 CTCGGTTTGAGCCACTCC 57.714 61.111 0.00 0.00 38.03 3.85
4807 4856 1.531883 GGTCATGAAATTTCGCTCCGC 60.532 52.381 13.34 2.04 0.00 5.54
4808 4857 1.267532 CGGTCATGAAATTTCGCTCCG 60.268 52.381 20.46 20.46 0.00 4.63
4809 4858 1.064060 CCGGTCATGAAATTTCGCTCC 59.936 52.381 13.34 11.25 0.00 4.70
4810 4859 2.006888 TCCGGTCATGAAATTTCGCTC 58.993 47.619 13.34 4.27 0.00 5.03
4811 4860 2.009774 CTCCGGTCATGAAATTTCGCT 58.990 47.619 13.34 0.69 0.00 4.93
4812 4861 2.006888 TCTCCGGTCATGAAATTTCGC 58.993 47.619 13.34 3.97 0.00 4.70
4813 4862 2.609459 CCTCTCCGGTCATGAAATTTCG 59.391 50.000 13.34 0.98 0.00 3.46
4814 4863 3.610911 ACCTCTCCGGTCATGAAATTTC 58.389 45.455 11.41 11.41 44.93 2.17
4815 4864 3.721087 ACCTCTCCGGTCATGAAATTT 57.279 42.857 0.00 0.00 44.93 1.82
4828 4877 1.079057 GCCTGTTCGGAACCTCTCC 60.079 63.158 17.62 0.00 41.40 3.71
4829 4878 0.670854 GTGCCTGTTCGGAACCTCTC 60.671 60.000 17.62 5.68 34.95 3.20
4830 4879 1.122019 AGTGCCTGTTCGGAACCTCT 61.122 55.000 17.62 6.43 43.11 3.69
4831 4880 0.606604 TAGTGCCTGTTCGGAACCTC 59.393 55.000 17.62 7.60 43.11 3.85
4832 4881 0.608640 CTAGTGCCTGTTCGGAACCT 59.391 55.000 17.62 9.59 43.11 3.50
4833 4882 0.320697 ACTAGTGCCTGTTCGGAACC 59.679 55.000 17.62 3.79 43.11 3.62
4834 4883 3.521947 ATACTAGTGCCTGTTCGGAAC 57.478 47.619 13.86 13.86 42.31 3.62
4835 4884 5.864418 AATATACTAGTGCCTGTTCGGAA 57.136 39.130 5.39 0.00 33.16 4.30
4836 4885 7.886970 AGTATAATATACTAGTGCCTGTTCGGA 59.113 37.037 10.96 0.00 33.16 4.55
4837 4886 7.968956 CAGTATAATATACTAGTGCCTGTTCGG 59.031 40.741 12.14 0.00 0.00 4.30
4838 4887 8.727910 TCAGTATAATATACTAGTGCCTGTTCG 58.272 37.037 12.14 0.00 0.00 3.95
4841 4890 9.755122 TCATCAGTATAATATACTAGTGCCTGT 57.245 33.333 12.14 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.