Multiple sequence alignment - TraesCS4A01G086600

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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 TraesCS4A01G086600 chr4A 100.000 4717 0 0 1 4717 90785305 90790021 0.000000e+00 8711
1 TraesCS4A01G086600 chr4D 92.382 3111 154 31 710 3768 373812691 373809612 0.000000e+00 4355
2 TraesCS4A01G086600 chr4D 88.826 886 51 23 3762 4645 373809586 373808747 0.000000e+00 1044
3 TraesCS4A01G086600 chr4B 90.572 3235 192 45 602 3761 459925497 459922301 0.000000e+00 4180
4 TraesCS4A01G086600 chr4B 99.834 601 1 0 1 601 25738344 25738944 0.000000e+00 1105
5 TraesCS4A01G086600 chr4B 85.939 889 44 36 3762 4645 459922262 459921450 0.000000e+00 874
6 TraesCS4A01G086600 chr5A 99.834 604 1 0 1 604 149389135 149388532 0.000000e+00 1110
7 TraesCS4A01G086600 chr5A 98.706 618 5 3 1 617 118391708 118391093 0.000000e+00 1094
8 TraesCS4A01G086600 chr6A 99.834 602 1 0 1 602 180192343 180192944 0.000000e+00 1107
9 TraesCS4A01G086600 chr5B 99.834 602 1 0 1 602 336100842 336100241 0.000000e+00 1107
10 TraesCS4A01G086600 chr5B 99.344 610 3 1 1 609 653234053 653233444 0.000000e+00 1103
11 TraesCS4A01G086600 chr3A 99.834 602 1 0 1 602 265381411 265380810 0.000000e+00 1107
12 TraesCS4A01G086600 chr2A 99.669 604 2 0 1 604 762877623 762878226 0.000000e+00 1105
13 TraesCS4A01G086600 chr6B 99.343 609 4 0 1 609 82548973 82549581 0.000000e+00 1103
14 TraesCS4A01G086600 chr2D 79.518 166 27 6 1286 1445 93589073 93589237 1.390000e-20 111


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 TraesCS4A01G086600 chr4A 90785305 90790021 4716 False 8711.0 8711 100.0000 1 4717 1 chr4A.!!$F1 4716
1 TraesCS4A01G086600 chr4D 373808747 373812691 3944 True 2699.5 4355 90.6040 710 4645 2 chr4D.!!$R1 3935
2 TraesCS4A01G086600 chr4B 459921450 459925497 4047 True 2527.0 4180 88.2555 602 4645 2 chr4B.!!$R1 4043
3 TraesCS4A01G086600 chr4B 25738344 25738944 600 False 1105.0 1105 99.8340 1 601 1 chr4B.!!$F1 600
4 TraesCS4A01G086600 chr5A 149388532 149389135 603 True 1110.0 1110 99.8340 1 604 1 chr5A.!!$R2 603
5 TraesCS4A01G086600 chr5A 118391093 118391708 615 True 1094.0 1094 98.7060 1 617 1 chr5A.!!$R1 616
6 TraesCS4A01G086600 chr6A 180192343 180192944 601 False 1107.0 1107 99.8340 1 602 1 chr6A.!!$F1 601
7 TraesCS4A01G086600 chr5B 336100241 336100842 601 True 1107.0 1107 99.8340 1 602 1 chr5B.!!$R1 601
8 TraesCS4A01G086600 chr5B 653233444 653234053 609 True 1103.0 1103 99.3440 1 609 1 chr5B.!!$R2 608
9 TraesCS4A01G086600 chr3A 265380810 265381411 601 True 1107.0 1107 99.8340 1 602 1 chr3A.!!$R1 601
10 TraesCS4A01G086600 chr2A 762877623 762878226 603 False 1105.0 1105 99.6690 1 604 1 chr2A.!!$F1 603
11 TraesCS4A01G086600 chr6B 82548973 82549581 608 False 1103.0 1103 99.3430 1 609 1 chr6B.!!$F1 608

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
985 1029 0.528684 CGCAGTAGCCAGGAGTAAGC 60.529 60.0 0.00 0.0 37.52 3.09 F
1674 1753 0.458543 GCGAAGAGATCACGCCTGAA 60.459 55.0 12.88 0.0 45.35 3.02 F
2600 2680 0.038166 TGTCCTTGTCCTTGGATGGC 59.962 55.0 0.00 0.0 34.58 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2077 0.250989 AAATTGAACGGGCCGAGGAA 60.251 50.0 35.78 20.67 0.00 3.36 R
3497 3595 0.389166 CGATTATCGCCAGCCTCTCC 60.389 60.0 0.46 0.00 31.14 3.71 R
4342 4484 0.031857 CCACACGTACGTACCAACCA 59.968 55.0 22.34 0.00 0.00 3.67 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
262 263 5.125417 GCTACATACCTTTCTGCAAATCCAA 59.875 40.000 0.00 0.00 0.00 3.53
611 612 3.293311 TTGTCTTACACTCGGCACTAC 57.707 47.619 0.00 0.00 0.00 2.73
612 613 1.542915 TGTCTTACACTCGGCACTACC 59.457 52.381 0.00 0.00 0.00 3.18
617 618 1.375523 CACTCGGCACTACCCAACC 60.376 63.158 0.00 0.00 33.26 3.77
618 619 2.125673 CTCGGCACTACCCAACCG 60.126 66.667 0.00 0.00 46.97 4.44
619 620 4.382320 TCGGCACTACCCAACCGC 62.382 66.667 0.00 0.00 45.23 5.68
648 649 4.557895 CGTCCATTTTCCAAGTAACCCAAC 60.558 45.833 0.00 0.00 0.00 3.77
669 670 1.388768 CACGTACGTACACATTGGCTG 59.611 52.381 22.34 8.04 0.00 4.85
671 672 0.725117 GTACGTACACATTGGCTGGC 59.275 55.000 20.67 0.00 0.00 4.85
672 673 0.611200 TACGTACACATTGGCTGGCT 59.389 50.000 2.00 0.00 0.00 4.75
673 674 0.955428 ACGTACACATTGGCTGGCTG 60.955 55.000 2.00 0.00 0.00 4.85
675 676 1.678635 TACACATTGGCTGGCTGGC 60.679 57.895 11.09 11.09 42.18 4.85
676 677 2.141011 TACACATTGGCTGGCTGGCT 62.141 55.000 18.27 0.30 42.34 4.75
677 678 1.378911 CACATTGGCTGGCTGGCTA 60.379 57.895 18.27 11.70 42.34 3.93
716 731 4.352887 GAAGAATTCTAACCTCGTCCTCG 58.647 47.826 8.75 0.00 43.23 4.63
854 878 1.583054 AAGCTTCAACACACGACTCC 58.417 50.000 0.00 0.00 0.00 3.85
880 923 0.679960 CACCCCCAACCCGATTCTTC 60.680 60.000 0.00 0.00 0.00 2.87
893 936 2.541556 GATTCTTCCTTTCCTCGGTCG 58.458 52.381 0.00 0.00 0.00 4.79
966 1010 4.794439 GGTTTTCATGCCGCGGCC 62.794 66.667 44.42 27.69 41.09 6.13
981 1025 3.775654 GCCGCAGTAGCCAGGAGT 61.776 66.667 0.00 0.00 37.52 3.85
982 1026 2.423898 GCCGCAGTAGCCAGGAGTA 61.424 63.158 0.00 0.00 37.52 2.59
983 1027 1.956629 GCCGCAGTAGCCAGGAGTAA 61.957 60.000 0.00 0.00 37.52 2.24
985 1029 0.528684 CGCAGTAGCCAGGAGTAAGC 60.529 60.000 0.00 0.00 37.52 3.09
987 1031 1.202475 GCAGTAGCCAGGAGTAAGCTC 60.202 57.143 0.00 0.00 38.06 4.09
988 1032 2.103373 CAGTAGCCAGGAGTAAGCTCA 58.897 52.381 0.00 0.00 43.37 4.26
989 1033 2.100584 CAGTAGCCAGGAGTAAGCTCAG 59.899 54.545 0.00 0.00 43.37 3.35
991 1035 0.980231 AGCCAGGAGTAAGCTCAGGG 60.980 60.000 0.00 0.00 43.37 4.45
992 1036 1.524482 CCAGGAGTAAGCTCAGGGC 59.476 63.158 0.00 0.00 43.37 5.19
1122 1171 3.123620 CTGCTGCTCCTCAACGGC 61.124 66.667 0.00 0.00 38.70 5.68
1162 1211 2.890961 GCTTCGCCGCCTACTTCC 60.891 66.667 0.00 0.00 0.00 3.46
1374 1429 2.907236 GAGGGCTGCCTCTCTTCC 59.093 66.667 19.68 0.00 34.30 3.46
1393 1448 1.072015 CCTGGAAGAGGGAGATGATGC 59.928 57.143 0.00 0.00 38.36 3.91
1440 1495 1.080705 CTGCTCTTGCTGCAAAGCC 60.081 57.895 29.14 17.24 40.13 4.35
1446 1501 2.467946 CTTGCTGCAAAGCCCTCGTG 62.468 60.000 16.74 0.00 0.00 4.35
1491 1567 0.905357 AGGATCCTGCTGTACACCAC 59.095 55.000 15.29 0.00 0.00 4.16
1533 1609 3.589988 ACAAGATCAAGGCTACGTTCTG 58.410 45.455 0.00 0.00 0.00 3.02
1587 1666 1.873591 GAGCAAAACGAAGAGGAAGCA 59.126 47.619 0.00 0.00 0.00 3.91
1590 1669 2.223479 GCAAAACGAAGAGGAAGCACAA 60.223 45.455 0.00 0.00 0.00 3.33
1593 1672 2.910688 ACGAAGAGGAAGCACAAGAA 57.089 45.000 0.00 0.00 0.00 2.52
1602 1681 2.687935 GGAAGCACAAGAACAACAAGGA 59.312 45.455 0.00 0.00 0.00 3.36
1674 1753 0.458543 GCGAAGAGATCACGCCTGAA 60.459 55.000 12.88 0.00 45.35 3.02
1686 1765 2.224885 GCCTGAAGACGACGATCGC 61.225 63.158 16.60 7.26 45.12 4.58
1785 1864 1.631072 GGACGACATGAATCGCACG 59.369 57.895 0.00 0.00 46.22 5.34
1895 1974 0.810031 ACGGCCGAGAATTCCATTCG 60.810 55.000 35.90 5.24 43.92 3.34
1896 1975 1.649267 GGCCGAGAATTCCATTCGC 59.351 57.895 9.43 6.00 43.92 4.70
2023 2102 1.807742 CGGCCCGTTCAATTTTACTCA 59.192 47.619 0.00 0.00 0.00 3.41
2066 2145 7.954835 TCATCTCATGATTTTTGTTTGGTTCT 58.045 30.769 0.00 0.00 33.59 3.01
2067 2146 9.076781 TCATCTCATGATTTTTGTTTGGTTCTA 57.923 29.630 0.00 0.00 33.59 2.10
2068 2147 9.132521 CATCTCATGATTTTTGTTTGGTTCTAC 57.867 33.333 0.00 0.00 0.00 2.59
2069 2148 8.463930 TCTCATGATTTTTGTTTGGTTCTACT 57.536 30.769 0.00 0.00 0.00 2.57
2070 2149 8.912988 TCTCATGATTTTTGTTTGGTTCTACTT 58.087 29.630 0.00 0.00 0.00 2.24
2071 2150 9.185192 CTCATGATTTTTGTTTGGTTCTACTTC 57.815 33.333 0.00 0.00 0.00 3.01
2072 2151 8.912988 TCATGATTTTTGTTTGGTTCTACTTCT 58.087 29.630 0.00 0.00 0.00 2.85
2187 2266 3.285215 GATGGCCATGCTGCTCCG 61.285 66.667 26.56 0.00 0.00 4.63
2258 2337 0.462047 GATGACCGGACATCACCACC 60.462 60.000 32.82 12.45 44.00 4.61
2289 2368 2.747855 GAAACAGCCCCAGCCGAG 60.748 66.667 0.00 0.00 41.25 4.63
2298 2377 2.512515 CCAGCCGAGCAAGGTAGC 60.513 66.667 0.00 0.00 0.00 3.58
2316 2395 2.009774 AGCGGTACAATCATTGCAGAC 58.990 47.619 0.00 0.00 0.00 3.51
2343 2423 4.280677 TCTCACTTTTACTTTTGCCCCATG 59.719 41.667 0.00 0.00 0.00 3.66
2357 2437 1.064166 CCCCATGGAGATGCTTTCACT 60.064 52.381 15.22 0.00 0.00 3.41
2395 2475 7.230510 TGTCTGTCCACAACTTTAATTTGCTAT 59.769 33.333 0.00 0.00 0.00 2.97
2443 2523 0.392729 AGTGAAGCAGAGCATGAGGC 60.393 55.000 0.00 0.00 45.30 4.70
2600 2680 0.038166 TGTCCTTGTCCTTGGATGGC 59.962 55.000 0.00 0.00 34.58 4.40
2630 2710 2.179517 GAGGTCGAGTGTGCCGAG 59.820 66.667 0.00 0.00 36.66 4.63
2975 3055 2.206536 GGAGAGGAGGAGGATGCCG 61.207 68.421 0.00 0.00 0.00 5.69
2982 3062 4.918201 GGAGGATGCCGGCCTTCG 62.918 72.222 26.77 0.00 35.44 3.79
3022 3102 3.818787 CGGCAATGGCACCTCTGC 61.819 66.667 7.75 0.00 43.71 4.26
3173 3253 0.745845 ATCTTGTGGCGCTGGATGAC 60.746 55.000 7.64 0.00 0.00 3.06
3230 3310 1.220477 GGAGGAGCTCAAGGCACTC 59.780 63.158 17.19 11.18 44.79 3.51
3237 3317 1.153667 CTCAAGGCACTCGAGGAGC 60.154 63.158 18.41 19.34 38.49 4.70
3299 3382 2.034687 GCTGCTGGCCTTTCCTCA 59.965 61.111 3.32 0.00 35.26 3.86
3306 3389 0.537188 TGGCCTTTCCTCAGACGATC 59.463 55.000 3.32 0.00 35.26 3.69
3410 3508 0.809385 TCCTACCTCTCTTTGACGCG 59.191 55.000 3.53 3.53 0.00 6.01
3443 3541 4.595538 GTCGACCGTGCACCACCA 62.596 66.667 12.15 0.00 0.00 4.17
3444 3542 4.293648 TCGACCGTGCACCACCAG 62.294 66.667 12.15 0.00 0.00 4.00
3497 3595 1.205064 CGTGTTCGCCAAAGAGCAG 59.795 57.895 0.00 0.00 32.15 4.24
3512 3610 2.502492 GCAGGAGAGGCTGGCGATA 61.502 63.158 0.00 0.00 0.00 2.92
3515 3613 0.972883 AGGAGAGGCTGGCGATAATC 59.027 55.000 0.00 0.00 0.00 1.75
3524 3622 0.673985 TGGCGATAATCGAGGAGGTG 59.326 55.000 0.00 0.00 43.74 4.00
3707 3805 1.361793 GCGATGCCATTGTTGCAAAT 58.638 45.000 0.00 0.00 42.92 2.32
3828 3964 4.321230 GCTGTTTAATTACCTGCAGCAACT 60.321 41.667 8.66 0.00 45.83 3.16
3833 3969 4.970662 AATTACCTGCAGCAACTATGTG 57.029 40.909 8.66 0.00 0.00 3.21
3844 3980 4.488126 GCAACTATGTGCTGAAACAAGA 57.512 40.909 0.00 0.00 41.51 3.02
3895 4031 1.335142 GGCTATGGTGAGTCGATCGAC 60.335 57.143 35.26 35.26 44.86 4.20
3966 4102 2.295909 TGCAAGGTAATGGCTTGTGTTC 59.704 45.455 0.00 0.00 0.00 3.18
4029 4165 3.846180 CAGCATGGCCGGCTTTAT 58.154 55.556 28.56 15.65 40.23 1.40
4030 4166 1.361271 CAGCATGGCCGGCTTTATG 59.639 57.895 28.56 26.10 40.23 1.90
4031 4167 1.102809 CAGCATGGCCGGCTTTATGA 61.103 55.000 29.71 10.85 40.23 2.15
4098 4234 1.466856 TCACCAAGCTGAATCATGGC 58.533 50.000 1.53 0.00 36.37 4.40
4118 4254 3.570638 CAGCTTCGGAGGCATGCG 61.571 66.667 14.82 5.73 42.35 4.73
4130 4272 1.730547 GCATGCGCACCACTTCAAC 60.731 57.895 14.90 0.00 38.36 3.18
4131 4273 1.951510 CATGCGCACCACTTCAACT 59.048 52.632 14.90 0.00 0.00 3.16
4132 4274 0.311790 CATGCGCACCACTTCAACTT 59.688 50.000 14.90 0.00 0.00 2.66
4133 4275 0.593128 ATGCGCACCACTTCAACTTC 59.407 50.000 14.90 0.00 0.00 3.01
4134 4276 0.746204 TGCGCACCACTTCAACTTCA 60.746 50.000 5.66 0.00 0.00 3.02
4135 4277 0.380378 GCGCACCACTTCAACTTCAA 59.620 50.000 0.30 0.00 0.00 2.69
4148 4290 3.390967 TCAACTTCAACAGGACAGATGGA 59.609 43.478 0.00 0.00 0.00 3.41
4149 4291 4.042062 TCAACTTCAACAGGACAGATGGAT 59.958 41.667 0.00 0.00 0.00 3.41
4150 4292 5.248248 TCAACTTCAACAGGACAGATGGATA 59.752 40.000 0.00 0.00 0.00 2.59
4151 4293 5.965033 ACTTCAACAGGACAGATGGATAT 57.035 39.130 0.00 0.00 0.00 1.63
4152 4294 7.125659 TCAACTTCAACAGGACAGATGGATATA 59.874 37.037 0.00 0.00 0.00 0.86
4153 4295 7.623999 ACTTCAACAGGACAGATGGATATAT 57.376 36.000 0.00 0.00 0.00 0.86
4154 4296 8.727100 ACTTCAACAGGACAGATGGATATATA 57.273 34.615 0.00 0.00 0.00 0.86
4155 4297 9.331466 ACTTCAACAGGACAGATGGATATATAT 57.669 33.333 0.00 0.00 0.00 0.86
4219 4361 2.360165 GGATGCAGATGTGGTGGATTTC 59.640 50.000 0.00 0.00 0.00 2.17
4227 4369 5.068198 CAGATGTGGTGGATTTCCTATTTGG 59.932 44.000 0.00 0.00 36.82 3.28
4257 4399 7.254117 CGCTTCTTTTTCCCTTTTCTTTCTTTC 60.254 37.037 0.00 0.00 0.00 2.62
4258 4400 7.766278 GCTTCTTTTTCCCTTTTCTTTCTTTCT 59.234 33.333 0.00 0.00 0.00 2.52
4259 4401 9.658799 CTTCTTTTTCCCTTTTCTTTCTTTCTT 57.341 29.630 0.00 0.00 0.00 2.52
4268 4410 9.098355 CCCTTTTCTTTCTTTCTTTTGGTTAAG 57.902 33.333 0.00 0.00 0.00 1.85
4294 4436 3.316029 TCAGATTTGTTTGTGCAGAGGTG 59.684 43.478 0.00 0.00 0.00 4.00
4298 4440 0.836606 TGTTTGTGCAGAGGTGGAGA 59.163 50.000 0.00 0.00 0.00 3.71
4299 4441 1.202687 TGTTTGTGCAGAGGTGGAGAG 60.203 52.381 0.00 0.00 0.00 3.20
4305 4447 1.153939 CAGAGGTGGAGAGCGTTCG 60.154 63.158 0.00 0.00 0.00 3.95
4308 4450 1.587933 GAGGTGGAGAGCGTTCGAGT 61.588 60.000 0.00 0.00 0.00 4.18
4340 4482 6.094881 TGTTTTATATGAGGTTGTAGGCTTGC 59.905 38.462 0.00 0.00 0.00 4.01
4342 4484 2.814805 ATGAGGTTGTAGGCTTGCAT 57.185 45.000 0.00 0.00 0.00 3.96
4343 4485 1.825090 TGAGGTTGTAGGCTTGCATG 58.175 50.000 0.00 0.00 0.00 4.06
4344 4486 1.098050 GAGGTTGTAGGCTTGCATGG 58.902 55.000 0.00 0.00 0.00 3.66
4346 4488 1.203050 AGGTTGTAGGCTTGCATGGTT 60.203 47.619 0.00 0.00 0.00 3.67
4347 4489 1.067635 GGTTGTAGGCTTGCATGGTTG 60.068 52.381 0.00 0.00 0.00 3.77
4348 4490 1.067635 GTTGTAGGCTTGCATGGTTGG 60.068 52.381 0.00 0.00 0.00 3.77
4349 4491 0.112218 TGTAGGCTTGCATGGTTGGT 59.888 50.000 0.00 0.00 0.00 3.67
4350 4492 1.352687 TGTAGGCTTGCATGGTTGGTA 59.647 47.619 0.00 0.00 0.00 3.25
4351 4493 1.743394 GTAGGCTTGCATGGTTGGTAC 59.257 52.381 0.00 0.00 0.00 3.34
4405 4547 5.947228 TGTAGCCAGTTTTGATGAAGAAG 57.053 39.130 0.00 0.00 0.00 2.85
4409 4552 4.522022 AGCCAGTTTTGATGAAGAAGGAAG 59.478 41.667 0.00 0.00 0.00 3.46
4413 4556 4.764308 AGTTTTGATGAAGAAGGAAGGCTC 59.236 41.667 0.00 0.00 0.00 4.70
4417 4560 2.169832 TGAAGAAGGAAGGCTCGTTG 57.830 50.000 0.00 0.00 29.89 4.10
4425 4568 1.464997 GGAAGGCTCGTTGTGATGAAC 59.535 52.381 0.00 0.00 0.00 3.18
4446 4589 3.321682 ACCCTGTTTCATTTGACATGGTG 59.678 43.478 0.00 0.00 41.33 4.17
4447 4590 3.319755 CCTGTTTCATTTGACATGGTGC 58.680 45.455 0.00 0.00 0.00 5.01
4448 4591 3.006110 CCTGTTTCATTTGACATGGTGCT 59.994 43.478 0.00 0.00 0.00 4.40
4449 4592 4.232221 CTGTTTCATTTGACATGGTGCTC 58.768 43.478 0.00 0.00 0.00 4.26
4450 4593 3.890756 TGTTTCATTTGACATGGTGCTCT 59.109 39.130 0.00 0.00 0.00 4.09
4453 4596 4.025040 TCATTTGACATGGTGCTCTTCT 57.975 40.909 0.00 0.00 0.00 2.85
4479 4622 2.746362 GGTCCTTGATGCTTCTTCTGTG 59.254 50.000 0.88 0.00 0.00 3.66
4480 4623 2.161211 GTCCTTGATGCTTCTTCTGTGC 59.839 50.000 0.88 0.00 0.00 4.57
4481 4624 2.156917 CCTTGATGCTTCTTCTGTGCA 58.843 47.619 0.88 0.00 41.13 4.57
4487 4630 4.634184 ATGCTTCTTCTGTGCATCATTC 57.366 40.909 0.00 0.00 42.92 2.67
4488 4631 2.417586 TGCTTCTTCTGTGCATCATTCG 59.582 45.455 0.00 0.00 0.00 3.34
4489 4632 2.674852 GCTTCTTCTGTGCATCATTCGA 59.325 45.455 0.00 0.00 0.00 3.71
4524 4669 1.131218 CGTGTGCAAGCTGTCGATG 59.869 57.895 0.00 0.00 0.00 3.84
4563 4708 1.766494 TCTTTATGGTGGCATGGCAG 58.234 50.000 24.03 9.18 0.00 4.85
4564 4709 1.284491 TCTTTATGGTGGCATGGCAGA 59.716 47.619 24.03 12.85 0.00 4.26
4565 4710 2.091720 TCTTTATGGTGGCATGGCAGAT 60.092 45.455 24.03 18.95 0.00 2.90
4566 4711 1.694844 TTATGGTGGCATGGCAGATG 58.305 50.000 24.03 0.00 0.00 2.90
4567 4712 0.178984 TATGGTGGCATGGCAGATGG 60.179 55.000 24.03 0.00 0.00 3.51
4568 4713 3.534056 GGTGGCATGGCAGATGGC 61.534 66.667 24.03 10.31 43.83 4.40
4619 4764 1.555075 GATGGGTGTCCTTGAGCTGTA 59.445 52.381 0.00 0.00 0.00 2.74
4630 4775 7.010552 GTGTCCTTGAGCTGTACATTACTATTG 59.989 40.741 0.00 0.00 0.00 1.90
4645 4790 3.126453 ACTATTGAGCCCTGGGAAGATT 58.874 45.455 19.27 0.00 0.00 2.40
4646 4791 2.744352 ATTGAGCCCTGGGAAGATTC 57.256 50.000 19.27 5.84 0.00 2.52
4647 4792 1.673767 TTGAGCCCTGGGAAGATTCT 58.326 50.000 19.27 1.77 0.00 2.40
4648 4793 1.673767 TGAGCCCTGGGAAGATTCTT 58.326 50.000 19.27 0.00 0.00 2.52
4649 4794 1.283029 TGAGCCCTGGGAAGATTCTTG 59.717 52.381 19.27 0.00 0.00 3.02
4650 4795 0.033699 AGCCCTGGGAAGATTCTTGC 60.034 55.000 19.27 9.26 0.00 4.01
4651 4796 0.323725 GCCCTGGGAAGATTCTTGCA 60.324 55.000 19.27 5.37 0.00 4.08
4652 4797 1.687368 GCCCTGGGAAGATTCTTGCAT 60.687 52.381 19.27 0.00 0.00 3.96
4653 4798 2.743553 CCCTGGGAAGATTCTTGCATT 58.256 47.619 18.13 0.00 0.00 3.56
4654 4799 3.902218 CCCTGGGAAGATTCTTGCATTA 58.098 45.455 18.13 4.84 0.00 1.90
4655 4800 3.633986 CCCTGGGAAGATTCTTGCATTAC 59.366 47.826 18.13 3.19 0.00 1.89
4656 4801 4.530875 CCTGGGAAGATTCTTGCATTACT 58.469 43.478 18.13 0.00 0.00 2.24
4657 4802 4.578105 CCTGGGAAGATTCTTGCATTACTC 59.422 45.833 18.13 2.23 0.00 2.59
4658 4803 5.178096 TGGGAAGATTCTTGCATTACTCA 57.822 39.130 18.13 4.60 0.00 3.41
4659 4804 5.569355 TGGGAAGATTCTTGCATTACTCAA 58.431 37.500 18.13 0.00 0.00 3.02
4660 4805 6.009589 TGGGAAGATTCTTGCATTACTCAAA 58.990 36.000 18.13 0.00 0.00 2.69
4661 4806 6.493115 TGGGAAGATTCTTGCATTACTCAAAA 59.507 34.615 18.13 0.00 0.00 2.44
4662 4807 7.015098 TGGGAAGATTCTTGCATTACTCAAAAA 59.985 33.333 18.13 0.00 0.00 1.94
4663 4808 7.543520 GGGAAGATTCTTGCATTACTCAAAAAG 59.456 37.037 18.13 0.00 0.00 2.27
4664 4809 8.084684 GGAAGATTCTTGCATTACTCAAAAAGT 58.915 33.333 12.51 0.00 42.33 2.66
4665 4810 9.468532 GAAGATTCTTGCATTACTCAAAAAGTT 57.531 29.630 3.03 0.00 39.55 2.66
4666 4811 9.822185 AAGATTCTTGCATTACTCAAAAAGTTT 57.178 25.926 0.00 0.00 39.55 2.66
4669 4814 9.696917 ATTCTTGCATTACTCAAAAAGTTTAGG 57.303 29.630 0.00 0.00 39.55 2.69
4670 4815 8.458573 TCTTGCATTACTCAAAAAGTTTAGGA 57.541 30.769 0.00 0.00 39.55 2.94
4671 4816 8.908903 TCTTGCATTACTCAAAAAGTTTAGGAA 58.091 29.630 0.00 0.00 39.55 3.36
4672 4817 9.696917 CTTGCATTACTCAAAAAGTTTAGGAAT 57.303 29.630 0.00 0.00 39.55 3.01
4682 4827 9.672086 TCAAAAAGTTTAGGAATTACAATCACG 57.328 29.630 0.00 0.00 0.00 4.35
4683 4828 9.458374 CAAAAAGTTTAGGAATTACAATCACGT 57.542 29.630 0.00 0.00 0.00 4.49
4684 4829 9.673454 AAAAAGTTTAGGAATTACAATCACGTC 57.327 29.630 0.00 0.00 0.00 4.34
4685 4830 6.980051 AGTTTAGGAATTACAATCACGTCC 57.020 37.500 0.00 0.00 0.00 4.79
4686 4831 6.469410 AGTTTAGGAATTACAATCACGTCCA 58.531 36.000 0.00 0.00 0.00 4.02
4687 4832 6.938030 AGTTTAGGAATTACAATCACGTCCAA 59.062 34.615 0.00 0.00 0.00 3.53
4688 4833 6.730960 TTAGGAATTACAATCACGTCCAAC 57.269 37.500 0.00 0.00 0.00 3.77
4689 4834 4.647611 AGGAATTACAATCACGTCCAACA 58.352 39.130 0.00 0.00 0.00 3.33
4690 4835 5.067273 AGGAATTACAATCACGTCCAACAA 58.933 37.500 0.00 0.00 0.00 2.83
4691 4836 5.710099 AGGAATTACAATCACGTCCAACAAT 59.290 36.000 0.00 0.00 0.00 2.71
4692 4837 6.208599 AGGAATTACAATCACGTCCAACAATT 59.791 34.615 0.00 0.00 0.00 2.32
4693 4838 7.392113 AGGAATTACAATCACGTCCAACAATTA 59.608 33.333 0.00 0.00 0.00 1.40
4694 4839 7.483691 GGAATTACAATCACGTCCAACAATTAC 59.516 37.037 0.00 0.00 0.00 1.89
4695 4840 4.759516 ACAATCACGTCCAACAATTACC 57.240 40.909 0.00 0.00 0.00 2.85
4696 4841 4.138290 ACAATCACGTCCAACAATTACCA 58.862 39.130 0.00 0.00 0.00 3.25
4697 4842 4.215399 ACAATCACGTCCAACAATTACCAG 59.785 41.667 0.00 0.00 0.00 4.00
4698 4843 2.773487 TCACGTCCAACAATTACCAGG 58.227 47.619 0.00 0.00 0.00 4.45
4699 4844 2.369203 TCACGTCCAACAATTACCAGGA 59.631 45.455 0.00 0.00 0.00 3.86
4700 4845 2.482721 CACGTCCAACAATTACCAGGAC 59.517 50.000 0.00 0.00 44.05 3.85
4703 4848 4.965119 GTCCAACAATTACCAGGACATC 57.035 45.455 11.49 0.00 46.15 3.06
4704 4849 4.589908 GTCCAACAATTACCAGGACATCT 58.410 43.478 11.49 0.00 46.15 2.90
4705 4850 5.010282 GTCCAACAATTACCAGGACATCTT 58.990 41.667 11.49 0.00 46.15 2.40
4706 4851 5.123979 GTCCAACAATTACCAGGACATCTTC 59.876 44.000 11.49 0.00 46.15 2.87
4707 4852 5.014123 TCCAACAATTACCAGGACATCTTCT 59.986 40.000 0.00 0.00 0.00 2.85
4708 4853 5.124457 CCAACAATTACCAGGACATCTTCTG 59.876 44.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
617 618 1.693083 GGAAAATGGACGAGACCGCG 61.693 60.000 0.00 0.00 39.95 6.46
618 619 0.672401 TGGAAAATGGACGAGACCGC 60.672 55.000 0.00 0.00 39.95 5.68
619 620 1.732259 CTTGGAAAATGGACGAGACCG 59.268 52.381 0.00 0.00 42.50 4.79
620 621 2.779506 ACTTGGAAAATGGACGAGACC 58.220 47.619 0.00 0.00 0.00 3.85
648 649 0.717224 GCCAATGTGTACGTACGTGG 59.283 55.000 30.25 20.82 33.67 4.94
671 672 1.376543 CTCATGGTTGTGCTAGCCAG 58.623 55.000 13.29 0.00 43.38 4.85
672 673 0.677731 GCTCATGGTTGTGCTAGCCA 60.678 55.000 13.29 7.05 44.33 4.75
673 674 1.379642 GGCTCATGGTTGTGCTAGCC 61.380 60.000 13.29 4.15 42.40 3.93
675 676 1.091771 CCGGCTCATGGTTGTGCTAG 61.092 60.000 0.00 0.00 41.12 3.42
676 677 1.078497 CCGGCTCATGGTTGTGCTA 60.078 57.895 0.00 0.00 41.12 3.49
677 678 2.360350 CCGGCTCATGGTTGTGCT 60.360 61.111 0.00 0.00 41.12 4.40
687 690 2.838202 AGGTTAGAATTCTTCCGGCTCA 59.162 45.455 14.36 0.00 0.00 4.26
716 731 2.270297 ATCCGCGTTTGAATGCAGGC 62.270 55.000 4.92 0.00 40.94 4.85
802 826 1.743321 TTTCAGCTTTTGTGCGGGGG 61.743 55.000 0.00 0.00 38.13 5.40
826 850 4.437390 CGTGTGTTGAAGCTTTCTTCTTGT 60.437 41.667 0.00 0.00 46.81 3.16
827 851 4.031028 CGTGTGTTGAAGCTTTCTTCTTG 58.969 43.478 0.00 0.00 46.81 3.02
828 852 3.938963 TCGTGTGTTGAAGCTTTCTTCTT 59.061 39.130 0.00 0.00 46.81 2.52
854 878 4.366684 GGTTGGGGGTGGCTGGAG 62.367 72.222 0.00 0.00 0.00 3.86
880 923 3.934391 AAGCGCGACCGAGGAAAGG 62.934 63.158 12.10 0.00 36.29 3.11
906 949 4.587189 GGGAATCGGAGTCGGGCG 62.587 72.222 0.00 0.00 36.95 6.13
909 952 2.104331 CGTGGGAATCGGAGTCGG 59.896 66.667 0.00 0.00 36.95 4.79
940 983 1.538276 GCATGAAAACCGCGATCTTG 58.462 50.000 8.23 9.80 0.00 3.02
966 1010 0.528684 GCTTACTCCTGGCTACTGCG 60.529 60.000 0.00 0.00 40.82 5.18
974 1018 1.524482 GCCCTGAGCTTACTCCTGG 59.476 63.158 0.00 0.00 42.74 4.45
975 1019 1.142748 CGCCCTGAGCTTACTCCTG 59.857 63.158 0.00 0.00 42.74 3.86
977 1021 2.501610 CCGCCCTGAGCTTACTCC 59.498 66.667 0.00 0.00 42.74 3.85
978 1022 2.022240 CTCCCGCCCTGAGCTTACTC 62.022 65.000 0.00 0.00 43.76 2.59
1219 1268 2.415010 CTGATCGGCGTCCTCCTG 59.585 66.667 6.85 0.00 0.00 3.86
1374 1429 1.270199 CGCATCATCTCCCTCTTCCAG 60.270 57.143 0.00 0.00 0.00 3.86
1422 1477 4.554163 GCTTTGCAGCAAGAGCAG 57.446 55.556 25.19 15.46 46.49 4.24
1440 1495 3.849911 TGAAGAAGTAATCTGCACGAGG 58.150 45.455 0.00 0.00 38.91 4.63
1446 1501 1.267087 GCGCGTGAAGAAGTAATCTGC 60.267 52.381 8.43 0.00 38.79 4.26
1489 1565 0.603707 TCTTCTTCGGCTGCCTTGTG 60.604 55.000 17.92 0.47 0.00 3.33
1491 1567 0.801251 CTTCTTCTTCGGCTGCCTTG 59.199 55.000 17.92 6.61 0.00 3.61
1533 1609 1.066858 TCGTGGTCTTCTTGATCCAGC 60.067 52.381 0.00 0.00 30.45 4.85
1587 1666 5.296151 TGATCTCTCCTTGTTGTTCTTGT 57.704 39.130 0.00 0.00 0.00 3.16
1590 1669 4.349342 ACCTTGATCTCTCCTTGTTGTTCT 59.651 41.667 0.00 0.00 0.00 3.01
1593 1672 3.244700 CCACCTTGATCTCTCCTTGTTGT 60.245 47.826 0.00 0.00 0.00 3.32
1602 1681 1.606531 GGCAGCCACCTTGATCTCT 59.393 57.895 6.55 0.00 0.00 3.10
1671 1750 0.456142 CCAAGCGATCGTCGTCTTCA 60.456 55.000 17.81 0.00 42.81 3.02
1674 1753 1.154016 CACCAAGCGATCGTCGTCT 60.154 57.895 17.81 1.67 42.81 4.18
1707 1786 2.033407 GTCGGCAATTGTCATCTCATCG 60.033 50.000 11.22 0.00 0.00 3.84
1762 1841 1.482621 CGATTCATGTCGTCCCGCTG 61.483 60.000 0.00 0.00 36.88 5.18
1765 1844 1.518352 TGCGATTCATGTCGTCCCG 60.518 57.895 7.46 0.00 43.27 5.14
1801 1880 1.960689 TGCGGTATCAAGATCATCCGA 59.039 47.619 18.32 7.07 40.29 4.55
1895 1974 3.350833 AGAACCAGTTCATCATCTTGGC 58.649 45.455 12.76 0.00 41.84 4.52
1896 1975 5.005740 TCAAGAACCAGTTCATCATCTTGG 58.994 41.667 12.76 0.00 42.36 3.61
1998 2077 0.250989 AAATTGAACGGGCCGAGGAA 60.251 50.000 35.78 20.67 0.00 3.36
2000 2079 1.131693 GTAAAATTGAACGGGCCGAGG 59.868 52.381 35.78 3.58 0.00 4.63
2066 2145 4.826274 ATTGCTTCAGTGGCTAGAAGTA 57.174 40.909 13.00 7.92 42.42 2.24
2067 2146 3.710209 ATTGCTTCAGTGGCTAGAAGT 57.290 42.857 13.00 0.00 42.42 3.01
2068 2147 3.376546 GGAATTGCTTCAGTGGCTAGAAG 59.623 47.826 0.00 8.95 43.12 2.85
2069 2148 3.009473 AGGAATTGCTTCAGTGGCTAGAA 59.991 43.478 0.00 0.00 32.70 2.10
2070 2149 2.573462 AGGAATTGCTTCAGTGGCTAGA 59.427 45.455 0.00 0.00 32.70 2.43
2071 2150 2.681848 CAGGAATTGCTTCAGTGGCTAG 59.318 50.000 0.00 0.00 32.70 3.42
2072 2151 2.305635 TCAGGAATTGCTTCAGTGGCTA 59.694 45.455 0.00 0.00 32.70 3.93
2187 2266 0.317854 GCGCCACCAGTTCTTGAAAC 60.318 55.000 0.00 0.00 0.00 2.78
2289 2368 2.018542 TGATTGTACCGCTACCTTGC 57.981 50.000 0.00 0.00 0.00 4.01
2298 2377 2.223112 GCAGTCTGCAATGATTGTACCG 60.223 50.000 20.16 0.00 44.26 4.02
2316 2395 4.540824 GGCAAAAGTAAAAGTGAGAGCAG 58.459 43.478 0.00 0.00 0.00 4.24
2343 2423 2.999355 GAGTCACAGTGAAAGCATCTCC 59.001 50.000 4.32 0.00 0.00 3.71
2357 2437 1.957177 GGACAGACAGACAGAGTCACA 59.043 52.381 0.00 0.00 38.46 3.58
2400 2480 7.597743 ACTTGCTTCTGATCAAATCATCAAAAC 59.402 33.333 0.00 0.00 38.85 2.43
2402 2482 7.040271 TCACTTGCTTCTGATCAAATCATCAAA 60.040 33.333 0.00 0.00 38.85 2.69
2404 2484 5.941647 TCACTTGCTTCTGATCAAATCATCA 59.058 36.000 0.00 0.00 38.85 3.07
2405 2485 6.432607 TCACTTGCTTCTGATCAAATCATC 57.567 37.500 0.00 0.00 38.85 2.92
2406 2486 6.625300 GCTTCACTTGCTTCTGATCAAATCAT 60.625 38.462 0.00 0.00 38.85 2.45
2407 2487 5.335426 GCTTCACTTGCTTCTGATCAAATCA 60.335 40.000 0.00 0.00 37.76 2.57
2408 2488 5.094134 GCTTCACTTGCTTCTGATCAAATC 58.906 41.667 0.00 0.00 0.00 2.17
2409 2489 4.521639 TGCTTCACTTGCTTCTGATCAAAT 59.478 37.500 0.00 0.00 0.00 2.32
2450 2530 1.480954 TGGTACTCAAATCTCCGGCTC 59.519 52.381 0.00 0.00 0.00 4.70
2540 2620 1.605753 AGAACCTTTTGCCGGAGTTC 58.394 50.000 5.05 7.68 37.65 3.01
2600 2680 4.406173 ACCTCGCTCGACACGCTG 62.406 66.667 0.00 0.00 0.00 5.18
2630 2710 1.519455 CTGATCGACGGTGGAAGGC 60.519 63.158 0.00 0.00 0.00 4.35
2690 2770 1.589993 CTCCAGCTCGGCGTACATG 60.590 63.158 6.85 1.93 33.14 3.21
2933 3013 0.671781 CCTCGTACTGCAGCAGCTTT 60.672 55.000 23.05 5.74 42.74 3.51
2937 3017 0.457509 CTGTCCTCGTACTGCAGCAG 60.458 60.000 21.54 21.54 37.52 4.24
2975 3055 2.464459 CGCATTGTCCTCGAAGGCC 61.464 63.158 0.00 0.00 34.61 5.19
2982 3062 2.526120 GGCTACGCGCATTGTCCTC 61.526 63.158 5.73 0.00 41.67 3.71
3003 3083 2.045926 AGAGGTGCCATTGCCGTC 60.046 61.111 0.00 0.00 36.33 4.79
3047 3127 2.736978 CAGGAGTCATCGGAATTCTCG 58.263 52.381 5.23 7.63 0.00 4.04
3230 3310 2.202676 GTGAAGAGCCGCTCCTCG 60.203 66.667 16.99 0.00 36.95 4.63
3237 3317 2.048222 TTCCAGCGTGAAGAGCCG 60.048 61.111 0.00 0.00 34.64 5.52
3292 3375 1.201647 GACCGTGATCGTCTGAGGAAA 59.798 52.381 3.97 0.00 35.01 3.13
3426 3524 4.595538 TGGTGGTGCACGGTCGAC 62.596 66.667 11.45 7.13 34.83 4.20
3427 3525 4.293648 CTGGTGGTGCACGGTCGA 62.294 66.667 11.45 0.16 34.83 4.20
3438 3536 4.415150 ATCGGTGGCTGCTGGTGG 62.415 66.667 0.00 0.00 0.00 4.61
3457 3555 3.770424 CGGCCGGTTTCGTCGAAC 61.770 66.667 20.10 3.27 34.72 3.95
3485 3583 1.449246 CCTCTCCTGCTCTTTGGCG 60.449 63.158 0.00 0.00 34.52 5.69
3488 3586 0.392729 CCAGCCTCTCCTGCTCTTTG 60.393 60.000 0.00 0.00 36.81 2.77
3497 3595 0.389166 CGATTATCGCCAGCCTCTCC 60.389 60.000 0.46 0.00 31.14 3.71
3512 3610 2.103771 CACATGATCCACCTCCTCGATT 59.896 50.000 0.00 0.00 0.00 3.34
3515 3613 0.826715 ACACATGATCCACCTCCTCG 59.173 55.000 0.00 0.00 0.00 4.63
3524 3622 1.683917 AGCCTCTCGTACACATGATCC 59.316 52.381 0.00 0.00 0.00 3.36
3636 3734 3.004283 CTCGCGAAGATGCTGCAG 58.996 61.111 11.33 10.11 0.00 4.41
3660 3758 3.512516 GGCATGAAGCTCCACGCC 61.513 66.667 0.00 0.00 44.79 5.68
3689 3787 2.994578 TGAATTTGCAACAATGGCATCG 59.005 40.909 0.00 0.00 41.58 3.84
3700 3798 4.496840 CGATCTGCTATGCTGAATTTGCAA 60.497 41.667 10.36 0.00 44.01 4.08
3701 3799 3.002965 CGATCTGCTATGCTGAATTTGCA 59.997 43.478 9.04 9.04 44.95 4.08
3702 3800 3.249320 TCGATCTGCTATGCTGAATTTGC 59.751 43.478 3.47 0.00 39.70 3.68
3707 3805 5.006386 TCTAGATCGATCTGCTATGCTGAA 58.994 41.667 33.22 11.85 39.70 3.02
3746 3844 6.985117 AGACAAGATACAAACTTACCACGTA 58.015 36.000 0.00 0.00 0.00 3.57
3748 3846 6.128634 GGAAGACAAGATACAAACTTACCACG 60.129 42.308 0.00 0.00 0.00 4.94
3828 3964 8.453320 CACAATAATCTCTTGTTTCAGCACATA 58.547 33.333 0.00 0.00 34.69 2.29
3833 3969 5.947443 AGCACAATAATCTCTTGTTTCAGC 58.053 37.500 0.00 0.00 34.69 4.26
3843 3979 6.558009 TGAATCTGCAAAGCACAATAATCTC 58.442 36.000 0.00 0.00 33.79 2.75
3844 3980 6.152323 ACTGAATCTGCAAAGCACAATAATCT 59.848 34.615 0.00 0.00 33.79 2.40
3895 4031 1.137086 CCACTACTCGGACCATTCCAG 59.863 57.143 0.00 0.00 43.00 3.86
3907 4043 6.665680 ACCATATCATAGATCCACCACTACTC 59.334 42.308 0.00 0.00 0.00 2.59
3914 4050 4.366267 AGGGACCATATCATAGATCCACC 58.634 47.826 0.00 0.00 0.00 4.61
3951 4087 3.153919 TCCCTTGAACACAAGCCATTAC 58.846 45.455 0.00 0.00 39.47 1.89
3966 4102 1.207593 CGAGCAAAGCGTTCCCTTG 59.792 57.895 0.00 0.00 0.00 3.61
4018 4154 1.956477 ACATCATTCATAAAGCCGGCC 59.044 47.619 26.15 5.07 0.00 6.13
4021 4157 4.353737 CAACCACATCATTCATAAAGCCG 58.646 43.478 0.00 0.00 0.00 5.52
4028 4164 2.827322 CACCACCAACCACATCATTCAT 59.173 45.455 0.00 0.00 0.00 2.57
4029 4165 2.237643 CACCACCAACCACATCATTCA 58.762 47.619 0.00 0.00 0.00 2.57
4030 4166 1.545582 CCACCACCAACCACATCATTC 59.454 52.381 0.00 0.00 0.00 2.67
4031 4167 1.631405 CCACCACCAACCACATCATT 58.369 50.000 0.00 0.00 0.00 2.57
4098 4234 4.845580 ATGCCTCCGAAGCTGGCG 62.846 66.667 7.45 5.02 44.80 5.69
4118 4254 2.223572 CCTGTTGAAGTTGAAGTGGTGC 60.224 50.000 0.00 0.00 0.00 5.01
4152 4294 8.097038 GCCGATCATCTCTCTCTCTCTATATAT 58.903 40.741 0.00 0.00 0.00 0.86
4153 4295 7.070571 TGCCGATCATCTCTCTCTCTCTATATA 59.929 40.741 0.00 0.00 0.00 0.86
4154 4296 6.126796 TGCCGATCATCTCTCTCTCTCTATAT 60.127 42.308 0.00 0.00 0.00 0.86
4155 4297 5.188751 TGCCGATCATCTCTCTCTCTCTATA 59.811 44.000 0.00 0.00 0.00 1.31
4156 4298 4.019411 TGCCGATCATCTCTCTCTCTCTAT 60.019 45.833 0.00 0.00 0.00 1.98
4157 4299 3.326297 TGCCGATCATCTCTCTCTCTCTA 59.674 47.826 0.00 0.00 0.00 2.43
4171 4313 2.224917 ACCTTTACCCTTTTGCCGATCA 60.225 45.455 0.00 0.00 0.00 2.92
4172 4314 2.163613 CACCTTTACCCTTTTGCCGATC 59.836 50.000 0.00 0.00 0.00 3.69
4219 4361 5.633601 GGAAAAAGAAGCGAAACCAAATAGG 59.366 40.000 0.00 0.00 45.67 2.57
4227 4369 5.348986 AGAAAAGGGAAAAAGAAGCGAAAC 58.651 37.500 0.00 0.00 0.00 2.78
4259 4401 9.495572 ACAAACAAATCTGAAAACTTAACCAAA 57.504 25.926 0.00 0.00 0.00 3.28
4260 4402 8.930760 CACAAACAAATCTGAAAACTTAACCAA 58.069 29.630 0.00 0.00 0.00 3.67
4268 4410 5.232838 CCTCTGCACAAACAAATCTGAAAAC 59.767 40.000 0.00 0.00 0.00 2.43
4324 4466 1.614051 CCATGCAAGCCTACAACCTCA 60.614 52.381 0.00 0.00 0.00 3.86
4340 4482 1.722464 CACACGTACGTACCAACCATG 59.278 52.381 22.34 7.89 0.00 3.66
4342 4484 0.031857 CCACACGTACGTACCAACCA 59.968 55.000 22.34 0.00 0.00 3.67
4343 4485 0.031994 ACCACACGTACGTACCAACC 59.968 55.000 22.34 0.00 0.00 3.77
4344 4486 1.851658 AACCACACGTACGTACCAAC 58.148 50.000 22.34 0.00 0.00 3.77
4346 4488 1.537776 CCAAACCACACGTACGTACCA 60.538 52.381 22.34 0.00 0.00 3.25
4347 4489 1.139163 CCAAACCACACGTACGTACC 58.861 55.000 22.34 2.84 0.00 3.34
4348 4490 1.786579 GACCAAACCACACGTACGTAC 59.213 52.381 22.34 15.90 0.00 3.67
4349 4491 1.680735 AGACCAAACCACACGTACGTA 59.319 47.619 22.34 0.00 0.00 3.57
4350 4492 0.461135 AGACCAAACCACACGTACGT 59.539 50.000 16.72 16.72 0.00 3.57
4351 4493 1.574134 AAGACCAAACCACACGTACG 58.426 50.000 15.01 15.01 0.00 3.67
4405 4547 1.464997 GTTCATCACAACGAGCCTTCC 59.535 52.381 0.00 0.00 0.00 3.46
4409 4552 0.321653 AGGGTTCATCACAACGAGCC 60.322 55.000 0.00 0.00 0.00 4.70
4413 4556 2.616376 TGAAACAGGGTTCATCACAACG 59.384 45.455 0.00 0.00 32.56 4.10
4417 4560 5.221224 TGTCAAATGAAACAGGGTTCATCAC 60.221 40.000 12.58 10.23 45.42 3.06
4446 4589 2.175202 TCAAGGACCAGAGAGAAGAGC 58.825 52.381 0.00 0.00 0.00 4.09
4447 4590 3.430651 GCATCAAGGACCAGAGAGAAGAG 60.431 52.174 0.00 0.00 0.00 2.85
4448 4591 2.499289 GCATCAAGGACCAGAGAGAAGA 59.501 50.000 0.00 0.00 0.00 2.87
4449 4592 2.500910 AGCATCAAGGACCAGAGAGAAG 59.499 50.000 0.00 0.00 0.00 2.85
4450 4593 2.544721 AGCATCAAGGACCAGAGAGAA 58.455 47.619 0.00 0.00 0.00 2.87
4453 4596 2.544721 AGAAGCATCAAGGACCAGAGA 58.455 47.619 0.00 0.00 0.00 3.10
4479 4622 1.227973 GGGAGGGGTCGAATGATGC 60.228 63.158 0.00 0.00 0.00 3.91
4480 4623 1.069765 CGGGAGGGGTCGAATGATG 59.930 63.158 0.00 0.00 0.00 3.07
4481 4624 1.382695 ACGGGAGGGGTCGAATGAT 60.383 57.895 0.00 0.00 0.00 2.45
4482 4625 2.038329 ACGGGAGGGGTCGAATGA 59.962 61.111 0.00 0.00 0.00 2.57
4506 4651 1.131218 CATCGACAGCTTGCACACG 59.869 57.895 0.00 0.00 0.00 4.49
4537 4682 6.828273 TGCCATGCCACCATAAAGATATATAC 59.172 38.462 0.00 0.00 0.00 1.47
4538 4683 6.967897 TGCCATGCCACCATAAAGATATATA 58.032 36.000 0.00 0.00 0.00 0.86
4539 4684 5.829986 TGCCATGCCACCATAAAGATATAT 58.170 37.500 0.00 0.00 0.00 0.86
4552 4697 2.756691 TGCCATCTGCCATGCCAC 60.757 61.111 0.00 0.00 40.16 5.01
4554 4699 3.534056 GGTGCCATCTGCCATGCC 61.534 66.667 0.00 0.00 40.16 4.40
4563 4708 2.048603 GCAACCTCAGGGTGCCATC 61.049 63.158 24.83 0.00 46.67 3.51
4564 4709 2.036256 GCAACCTCAGGGTGCCAT 59.964 61.111 24.83 0.00 46.67 4.40
4565 4710 3.177884 AGCAACCTCAGGGTGCCA 61.178 61.111 31.22 0.00 46.67 4.92
4566 4711 2.360475 GAGCAACCTCAGGGTGCC 60.360 66.667 31.22 18.02 46.67 5.01
4567 4712 2.431683 TGAGCAACCTCAGGGTGC 59.568 61.111 27.92 27.92 46.67 5.01
4619 4764 3.393687 TCCCAGGGCTCAATAGTAATGT 58.606 45.455 0.00 0.00 0.00 2.71
4630 4775 2.021208 GCAAGAATCTTCCCAGGGCTC 61.021 57.143 0.00 0.00 0.00 4.70
4645 4790 8.458573 TCCTAAACTTTTTGAGTAATGCAAGA 57.541 30.769 0.00 0.00 37.72 3.02
4646 4791 9.696917 ATTCCTAAACTTTTTGAGTAATGCAAG 57.303 29.630 0.00 0.00 37.72 4.01
4656 4801 9.672086 CGTGATTGTAATTCCTAAACTTTTTGA 57.328 29.630 0.00 0.00 0.00 2.69
4657 4802 9.458374 ACGTGATTGTAATTCCTAAACTTTTTG 57.542 29.630 0.00 0.00 0.00 2.44
4658 4803 9.673454 GACGTGATTGTAATTCCTAAACTTTTT 57.327 29.630 0.00 0.00 0.00 1.94
4659 4804 8.294577 GGACGTGATTGTAATTCCTAAACTTTT 58.705 33.333 0.00 0.00 0.00 2.27
4660 4805 7.446013 TGGACGTGATTGTAATTCCTAAACTTT 59.554 33.333 0.00 0.00 0.00 2.66
4661 4806 6.938030 TGGACGTGATTGTAATTCCTAAACTT 59.062 34.615 0.00 0.00 0.00 2.66
4662 4807 6.469410 TGGACGTGATTGTAATTCCTAAACT 58.531 36.000 0.00 0.00 0.00 2.66
4663 4808 6.730960 TGGACGTGATTGTAATTCCTAAAC 57.269 37.500 0.00 0.00 0.00 2.01
4664 4809 6.711194 TGTTGGACGTGATTGTAATTCCTAAA 59.289 34.615 0.00 0.00 0.00 1.85
4665 4810 6.231951 TGTTGGACGTGATTGTAATTCCTAA 58.768 36.000 0.00 0.00 0.00 2.69
4666 4811 5.795972 TGTTGGACGTGATTGTAATTCCTA 58.204 37.500 0.00 0.00 0.00 2.94
4667 4812 4.647611 TGTTGGACGTGATTGTAATTCCT 58.352 39.130 0.00 0.00 0.00 3.36
4668 4813 5.365403 TTGTTGGACGTGATTGTAATTCC 57.635 39.130 0.00 0.00 0.00 3.01
4669 4814 7.483691 GGTAATTGTTGGACGTGATTGTAATTC 59.516 37.037 0.00 0.00 0.00 2.17
4670 4815 7.040340 TGGTAATTGTTGGACGTGATTGTAATT 60.040 33.333 0.00 0.00 0.00 1.40
4671 4816 6.431543 TGGTAATTGTTGGACGTGATTGTAAT 59.568 34.615 0.00 0.00 0.00 1.89
4672 4817 5.763698 TGGTAATTGTTGGACGTGATTGTAA 59.236 36.000 0.00 0.00 0.00 2.41
4673 4818 5.306394 TGGTAATTGTTGGACGTGATTGTA 58.694 37.500 0.00 0.00 0.00 2.41
4674 4819 4.138290 TGGTAATTGTTGGACGTGATTGT 58.862 39.130 0.00 0.00 0.00 2.71
4675 4820 4.379394 CCTGGTAATTGTTGGACGTGATTG 60.379 45.833 0.00 0.00 0.00 2.67
4676 4821 3.756434 CCTGGTAATTGTTGGACGTGATT 59.244 43.478 0.00 0.00 0.00 2.57
4677 4822 3.008594 TCCTGGTAATTGTTGGACGTGAT 59.991 43.478 0.00 0.00 0.00 3.06
4678 4823 2.369203 TCCTGGTAATTGTTGGACGTGA 59.631 45.455 0.00 0.00 0.00 4.35
4679 4824 2.482721 GTCCTGGTAATTGTTGGACGTG 59.517 50.000 0.00 0.00 37.93 4.49
4680 4825 2.774687 GTCCTGGTAATTGTTGGACGT 58.225 47.619 0.00 0.00 37.93 4.34
4682 4827 4.589908 AGATGTCCTGGTAATTGTTGGAC 58.410 43.478 12.02 12.02 45.22 4.02
4683 4828 4.927267 AGATGTCCTGGTAATTGTTGGA 57.073 40.909 0.00 0.00 0.00 3.53
4684 4829 5.124457 CAGAAGATGTCCTGGTAATTGTTGG 59.876 44.000 0.00 0.00 0.00 3.77
4685 4830 5.124457 CCAGAAGATGTCCTGGTAATTGTTG 59.876 44.000 0.00 0.00 43.71 3.33
4686 4831 5.256474 CCAGAAGATGTCCTGGTAATTGTT 58.744 41.667 0.00 0.00 43.71 2.83
4687 4832 4.848357 CCAGAAGATGTCCTGGTAATTGT 58.152 43.478 0.00 0.00 43.71 2.71
4695 4840 2.746362 GCTGTTTCCAGAAGATGTCCTG 59.254 50.000 0.00 0.00 41.50 3.86
4696 4841 3.064900 GCTGTTTCCAGAAGATGTCCT 57.935 47.619 0.00 0.00 41.50 3.85


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

AutoCloner maintained by Alex Coulton.