Multiple sequence alignment - TraesCS2D01G422200

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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 TraesCS2D01G422200 chr2D 100.000 4331 0 0 1 4331 535572228 535576558 0.000000e+00 7998.0
1 TraesCS2D01G422200 chr2D 96.218 238 6 1 4089 4323 535576193 535576430 1.890000e-103 387.0
2 TraesCS2D01G422200 chr2D 96.218 238 6 1 3966 4203 535576316 535576550 1.890000e-103 387.0
3 TraesCS2D01G422200 chr2D 92.373 118 6 1 4209 4323 535576193 535576310 9.640000e-37 165.0
4 TraesCS2D01G422200 chr2D 92.373 118 6 1 3966 4083 535576436 535576550 9.640000e-37 165.0
5 TraesCS2D01G422200 chr2A 94.248 4138 138 36 1 4083 678671855 678675947 0.000000e+00 6231.0
6 TraesCS2D01G422200 chr2A 89.683 126 10 1 4209 4331 678675830 678675955 1.610000e-34 158.0
7 TraesCS2D01G422200 chr2B 93.008 4133 190 50 3 4083 636776301 636780386 0.000000e+00 5939.0
8 TraesCS2D01G422200 chr2B 94.444 126 4 1 4209 4331 636780269 636780394 1.590000e-44 191.0
9 TraesCS2D01G422200 chr2B 92.373 118 6 1 4089 4203 636780269 636780386 9.640000e-37 165.0
10 TraesCS2D01G422200 chr4A 82.667 375 55 8 3559 3926 635366190 635365819 1.500000e-84 324.0
11 TraesCS2D01G422200 chr5A 81.081 370 47 17 3559 3921 597485222 597484869 1.530000e-69 274.0
12 TraesCS2D01G422200 chr5A 76.923 169 22 11 3575 3738 378524226 378524070 3.590000e-11 80.5
13 TraesCS2D01G422200 chr3B 81.329 316 38 11 3563 3870 465697398 465697096 2.010000e-58 237.0
14 TraesCS2D01G422200 chr6A 79.701 335 52 12 3597 3925 549054640 549054964 1.210000e-55 228.0
15 TraesCS2D01G422200 chr6D 79.916 239 31 13 3607 3835 111950217 111950448 4.480000e-35 159.0
16 TraesCS2D01G422200 chr5D 75.658 304 53 18 3629 3922 467260927 467261219 9.770000e-27 132.0
17 TraesCS2D01G422200 chr3A 84.375 128 18 2 3790 3917 497097747 497097872 1.640000e-24 124.0
18 TraesCS2D01G422200 chr1B 91.667 48 4 0 3562 3609 298252983 298253030 2.800000e-07 67.6
19 TraesCS2D01G422200 chr4B 72.857 210 38 15 3649 3853 324922618 324922423 2.000000e-03 54.7


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 TraesCS2D01G422200 chr2D 535572228 535576558 4330 False 1820.400000 7998 95.4364 1 4331 5 chr2D.!!$F1 4330
1 TraesCS2D01G422200 chr2A 678671855 678675955 4100 False 3194.500000 6231 91.9655 1 4331 2 chr2A.!!$F1 4330
2 TraesCS2D01G422200 chr2B 636776301 636780394 4093 False 2098.333333 5939 93.2750 3 4331 3 chr2B.!!$F1 4328

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
839 886 0.259356 AGACGAAGGGAGGTAGGAGG 59.741 60.000 0.00 0.0 0.00 4.30 F
1654 1724 0.036010 CTTTCATGGCCTCCAGACGT 60.036 55.000 3.32 0.0 36.75 4.34 F
2403 2473 1.421485 CATTGAAGTGACCGCGAGC 59.579 57.895 8.23 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2793 2863 0.820226 CCGCACTCTCCTCATTCTCA 59.180 55.0 0.0 0.0 0.0 3.27 R
3129 3199 0.108585 GGACAACCTTGCTCACCTCA 59.891 55.0 0.0 0.0 0.0 3.86 R
3846 3923 0.033504 GGGAAAGACGACTGAGTGCA 59.966 55.0 0.0 0.0 0.0 4.57 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
41 42 4.161001 GGAGCATCAATCAAACCTGGAAAT 59.839 41.667 0.00 0.00 36.25 2.17
149 150 2.496899 TTGCTTCTCCTGATGGGAAC 57.503 50.000 0.00 0.00 44.58 3.62
150 151 1.361204 TGCTTCTCCTGATGGGAACA 58.639 50.000 0.00 0.00 44.58 3.18
247 248 5.911378 TGGTTGCAGATATTAAATGTGCA 57.089 34.783 14.18 14.18 42.24 4.57
287 288 3.678289 AGCAAACACAGCTCATATGACA 58.322 40.909 0.00 0.00 38.01 3.58
290 291 2.322355 ACACAGCTCATATGACAGCC 57.678 50.000 12.09 0.00 36.17 4.85
357 363 2.544486 CCCAAACTTTTCAGAGTGCTGC 60.544 50.000 0.00 0.00 42.01 5.25
367 379 0.536260 AGAGTGCTGCATCTGAGACC 59.464 55.000 5.27 0.00 0.00 3.85
380 392 5.568423 GCATCTGAGACCCCATACTTATCTG 60.568 48.000 0.00 0.00 0.00 2.90
469 483 2.034179 CGTACTGATTCATAGGCACGGA 59.966 50.000 0.00 0.00 0.00 4.69
531 545 4.953579 TGGTTAAACCACAGAAAAGCTCTT 59.046 37.500 0.00 0.00 44.79 2.85
568 582 7.384932 CCAAAGGTTGAAGCTACCAAAATTTAG 59.615 37.037 6.91 0.91 38.16 1.85
576 590 4.640647 AGCTACCAAAATTTAGCAGCCTAC 59.359 41.667 12.08 0.00 42.78 3.18
598 627 4.128643 CGGAGGACTACTACTACTTCCAG 58.871 52.174 0.00 0.00 0.00 3.86
637 666 7.365840 ACTCGAATCAATCAACCTAGAAAAC 57.634 36.000 0.00 0.00 0.00 2.43
638 667 6.934645 ACTCGAATCAATCAACCTAGAAAACA 59.065 34.615 0.00 0.00 0.00 2.83
640 669 8.335532 TCGAATCAATCAACCTAGAAAACAAT 57.664 30.769 0.00 0.00 0.00 2.71
641 670 8.792633 TCGAATCAATCAACCTAGAAAACAATT 58.207 29.630 0.00 0.00 0.00 2.32
716 746 2.228822 CCAAATTACACACAGACAGGGC 59.771 50.000 0.00 0.00 0.00 5.19
740 770 2.355108 GGAGCTTACTTGATCTGGTGCA 60.355 50.000 0.00 0.00 0.00 4.57
765 795 2.034221 AAACAGGGCGCTCCTTCC 59.966 61.111 13.96 3.05 45.47 3.46
808 854 3.090532 AGGGGGCGATCTGGTTCC 61.091 66.667 0.00 0.00 0.00 3.62
839 886 0.259356 AGACGAAGGGAGGTAGGAGG 59.741 60.000 0.00 0.00 0.00 4.30
842 889 0.259356 CGAAGGGAGGTAGGAGGAGT 59.741 60.000 0.00 0.00 0.00 3.85
846 893 0.556747 GGGAGGTAGGAGGAGTAGCA 59.443 60.000 0.00 0.00 0.00 3.49
847 894 1.479757 GGGAGGTAGGAGGAGTAGCAG 60.480 61.905 0.00 0.00 0.00 4.24
848 895 1.324383 GAGGTAGGAGGAGTAGCAGC 58.676 60.000 0.00 0.00 0.00 5.25
852 899 1.957877 GTAGGAGGAGTAGCAGCGAAT 59.042 52.381 0.00 0.00 0.00 3.34
853 900 2.366640 AGGAGGAGTAGCAGCGAATA 57.633 50.000 0.00 0.00 0.00 1.75
854 901 2.667470 AGGAGGAGTAGCAGCGAATAA 58.333 47.619 0.00 0.00 0.00 1.40
855 902 2.625790 AGGAGGAGTAGCAGCGAATAAG 59.374 50.000 0.00 0.00 0.00 1.73
857 904 1.069358 AGGAGTAGCAGCGAATAAGCC 59.931 52.381 0.00 0.00 38.01 4.35
858 905 1.202533 GGAGTAGCAGCGAATAAGCCA 60.203 52.381 0.00 0.00 38.01 4.75
859 906 1.861575 GAGTAGCAGCGAATAAGCCAC 59.138 52.381 0.00 0.00 38.01 5.01
860 907 0.577269 GTAGCAGCGAATAAGCCACG 59.423 55.000 0.00 0.00 38.01 4.94
899 947 2.362077 CCTTTTGGGCTCGATATTTGGG 59.638 50.000 0.00 0.00 35.46 4.12
900 948 1.398692 TTTGGGCTCGATATTTGGGC 58.601 50.000 0.00 0.00 0.00 5.36
901 949 0.467290 TTGGGCTCGATATTTGGGCC 60.467 55.000 10.56 10.56 43.45 5.80
903 951 1.227853 GGCTCGATATTTGGGCCGT 60.228 57.895 4.24 0.00 33.30 5.68
904 952 1.507141 GGCTCGATATTTGGGCCGTG 61.507 60.000 4.24 0.00 33.30 4.94
905 953 0.814010 GCTCGATATTTGGGCCGTGT 60.814 55.000 0.00 0.00 0.00 4.49
906 954 1.539496 GCTCGATATTTGGGCCGTGTA 60.539 52.381 0.00 0.00 0.00 2.90
907 955 2.870435 GCTCGATATTTGGGCCGTGTAT 60.870 50.000 0.00 0.00 0.00 2.29
908 956 2.993899 CTCGATATTTGGGCCGTGTATC 59.006 50.000 0.00 5.49 0.00 2.24
910 958 2.433436 GATATTTGGGCCGTGTATCCC 58.567 52.381 0.00 0.00 42.93 3.85
911 959 0.475044 TATTTGGGCCGTGTATCCCC 59.525 55.000 0.00 0.00 41.92 4.81
917 978 1.752198 GCCGTGTATCCCCATGCTA 59.248 57.895 0.00 0.00 0.00 3.49
963 1024 3.898123 TCACAGGCTCTTCAACTACTTCT 59.102 43.478 0.00 0.00 0.00 2.85
968 1029 4.345257 AGGCTCTTCAACTACTTCTGAACA 59.655 41.667 0.00 0.00 0.00 3.18
978 1039 1.964223 ACTTCTGAACAGCCGAGAAGA 59.036 47.619 13.51 0.00 43.65 2.87
987 1048 0.323360 AGCCGAGAAGAGCTGAGAGT 60.323 55.000 0.00 0.00 38.11 3.24
1015 1085 3.226429 GATATGCTCCTCCGCGCCA 62.226 63.158 0.00 0.00 0.00 5.69
1203 1273 3.728373 GCCGACCCCACCATCCTT 61.728 66.667 0.00 0.00 0.00 3.36
1448 1518 1.448922 CCCTCCGACGATCTGTCCTC 61.449 65.000 0.00 0.00 45.23 3.71
1626 1696 3.939837 CTGCTTCAAGCGCCTCCGA 62.940 63.158 2.29 0.00 46.26 4.55
1654 1724 0.036010 CTTTCATGGCCTCCAGACGT 60.036 55.000 3.32 0.00 36.75 4.34
1851 1921 2.092753 TGAAATGAGACAGAGGGATGGC 60.093 50.000 0.00 0.00 0.00 4.40
1900 1970 2.299993 CACTATGGTCGATGTGCTGT 57.700 50.000 0.00 0.00 0.00 4.40
2403 2473 1.421485 CATTGAAGTGACCGCGAGC 59.579 57.895 8.23 0.00 0.00 5.03
2793 2863 5.184892 AGTTCTTCCAAGGCATTGACTAT 57.815 39.130 13.66 0.00 38.83 2.12
3225 3295 1.847328 TCCTGCTCAACGAGATACCA 58.153 50.000 0.00 0.00 0.00 3.25
3511 3581 3.848301 ATGCACGGCTCCTGTTGCA 62.848 57.895 8.50 8.50 36.69 4.08
3515 3587 1.148273 ACGGCTCCTGTTGCAAAGA 59.852 52.632 0.00 0.00 0.00 2.52
3582 3654 2.516227 TATCCAATTTTGTGCCCGGA 57.484 45.000 0.73 0.00 0.00 5.14
3686 3759 0.107897 TTGAGTGTGTGAGGTGCGTT 60.108 50.000 0.00 0.00 0.00 4.84
3787 3864 9.298774 CTTTTTCATAGATCTCAAATTTGCCTC 57.701 33.333 13.54 9.31 0.00 4.70
3792 3869 9.028284 TCATAGATCTCAAATTTGCCTCTTTTT 57.972 29.630 13.54 2.33 0.00 1.94
3824 3901 6.208204 AGAGCTACTCAAACATTCAAATGCTT 59.792 34.615 2.66 0.00 34.89 3.91
3846 3923 5.423704 TTGAAATTTGGCATGGACATCAT 57.576 34.783 0.00 0.00 36.31 2.45
4052 4138 9.489084 TCCAGTGTACTTCAATAACATATATGC 57.511 33.333 12.79 0.00 0.00 3.14
4053 4139 9.271828 CCAGTGTACTTCAATAACATATATGCA 57.728 33.333 12.79 1.41 0.00 3.96
4055 4141 9.494271 AGTGTACTTCAATAACATATATGCAGG 57.506 33.333 12.79 0.00 0.00 4.85
4056 4142 8.721478 GTGTACTTCAATAACATATATGCAGGG 58.279 37.037 12.79 0.00 0.00 4.45
4057 4143 8.436778 TGTACTTCAATAACATATATGCAGGGT 58.563 33.333 12.79 4.38 0.00 4.34
4058 4144 9.938280 GTACTTCAATAACATATATGCAGGGTA 57.062 33.333 12.79 3.56 0.00 3.69
4059 4145 8.848474 ACTTCAATAACATATATGCAGGGTAC 57.152 34.615 12.79 0.00 0.00 3.34
4060 4146 8.436778 ACTTCAATAACATATATGCAGGGTACA 58.563 33.333 12.79 0.00 0.00 2.90
4061 4147 9.283768 CTTCAATAACATATATGCAGGGTACAA 57.716 33.333 12.79 0.00 0.00 2.41
4062 4148 8.615878 TCAATAACATATATGCAGGGTACAAC 57.384 34.615 12.79 0.00 0.00 3.32
4063 4149 8.214364 TCAATAACATATATGCAGGGTACAACA 58.786 33.333 12.79 0.00 0.00 3.33
4064 4150 8.845227 CAATAACATATATGCAGGGTACAACAA 58.155 33.333 12.79 0.00 0.00 2.83
4065 4151 9.586732 AATAACATATATGCAGGGTACAACAAT 57.413 29.630 12.79 0.00 0.00 2.71
4067 4153 7.979444 ACATATATGCAGGGTACAACAATAC 57.021 36.000 12.79 0.00 0.00 1.89
4068 4154 7.513856 ACATATATGCAGGGTACAACAATACA 58.486 34.615 12.79 0.00 0.00 2.29
4069 4155 8.163408 ACATATATGCAGGGTACAACAATACAT 58.837 33.333 12.79 0.00 0.00 2.29
4070 4156 9.013229 CATATATGCAGGGTACAACAATACATT 57.987 33.333 0.00 0.00 0.00 2.71
4071 4157 5.581126 ATGCAGGGTACAACAATACATTG 57.419 39.130 0.00 0.37 43.26 2.82
4072 4158 3.761218 TGCAGGGTACAACAATACATTGG 59.239 43.478 6.87 0.00 41.96 3.16
4073 4159 3.130340 GCAGGGTACAACAATACATTGGG 59.870 47.826 6.87 1.54 41.96 4.12
4074 4160 3.130340 CAGGGTACAACAATACATTGGGC 59.870 47.826 6.87 0.00 41.96 5.36
4075 4161 2.429250 GGGTACAACAATACATTGGGCC 59.571 50.000 0.00 0.00 41.96 5.80
4076 4162 3.093057 GGTACAACAATACATTGGGCCA 58.907 45.455 0.00 0.00 41.96 5.36
4077 4163 3.511934 GGTACAACAATACATTGGGCCAA 59.488 43.478 23.33 23.33 41.96 4.52
4078 4164 4.021016 GGTACAACAATACATTGGGCCAAA 60.021 41.667 24.97 7.42 41.96 3.28
4079 4165 4.906747 ACAACAATACATTGGGCCAAAT 57.093 36.364 24.97 16.90 41.96 2.32
4080 4166 5.240013 ACAACAATACATTGGGCCAAATT 57.760 34.783 24.97 15.66 41.96 1.82
4081 4167 6.365970 ACAACAATACATTGGGCCAAATTA 57.634 33.333 24.97 17.06 41.96 1.40
4082 4168 6.773638 ACAACAATACATTGGGCCAAATTAA 58.226 32.000 24.97 9.68 41.96 1.40
4083 4169 7.401246 ACAACAATACATTGGGCCAAATTAAT 58.599 30.769 24.97 11.61 41.96 1.40
4084 4170 8.543774 ACAACAATACATTGGGCCAAATTAATA 58.456 29.630 24.97 11.38 41.96 0.98
4085 4171 9.388506 CAACAATACATTGGGCCAAATTAATAA 57.611 29.630 24.97 5.21 41.96 1.40
4086 4172 9.612066 AACAATACATTGGGCCAAATTAATAAG 57.388 29.630 24.97 11.61 41.96 1.73
4087 4173 7.714813 ACAATACATTGGGCCAAATTAATAAGC 59.285 33.333 24.97 0.00 41.96 3.09
4088 4174 5.690464 ACATTGGGCCAAATTAATAAGCA 57.310 34.783 24.97 0.00 0.00 3.91
4089 4175 6.251255 ACATTGGGCCAAATTAATAAGCAT 57.749 33.333 24.97 0.00 0.00 3.79
4090 4176 6.290605 ACATTGGGCCAAATTAATAAGCATC 58.709 36.000 24.97 0.00 0.00 3.91
4091 4177 4.953940 TGGGCCAAATTAATAAGCATCC 57.046 40.909 2.13 1.56 0.00 3.51
4092 4178 4.555689 TGGGCCAAATTAATAAGCATCCT 58.444 39.130 2.13 0.00 0.00 3.24
4093 4179 5.710646 TGGGCCAAATTAATAAGCATCCTA 58.289 37.500 2.13 0.00 0.00 2.94
4094 4180 6.322126 TGGGCCAAATTAATAAGCATCCTAT 58.678 36.000 2.13 0.00 0.00 2.57
4095 4181 6.786959 TGGGCCAAATTAATAAGCATCCTATT 59.213 34.615 2.13 0.00 0.00 1.73
4096 4182 7.292120 TGGGCCAAATTAATAAGCATCCTATTT 59.708 33.333 2.13 0.00 0.00 1.40
4097 4183 8.811994 GGGCCAAATTAATAAGCATCCTATTTA 58.188 33.333 4.39 0.00 0.00 1.40
4123 4209 7.870509 ATGAACAGATGTTACATACTGCATT 57.129 32.000 17.96 10.29 38.56 3.56
4124 4210 7.075674 TGAACAGATGTTACATACTGCATTG 57.924 36.000 17.96 0.00 38.56 2.82
4125 4211 6.654582 TGAACAGATGTTACATACTGCATTGT 59.345 34.615 17.96 0.00 38.56 2.71
4126 4212 7.174772 TGAACAGATGTTACATACTGCATTGTT 59.825 33.333 17.96 11.36 38.56 2.83
4127 4213 8.560355 AACAGATGTTACATACTGCATTGTTA 57.440 30.769 17.96 0.00 36.32 2.41
4128 4214 7.974675 ACAGATGTTACATACTGCATTGTTAC 58.025 34.615 17.96 5.04 34.25 2.50
4129 4215 7.824289 ACAGATGTTACATACTGCATTGTTACT 59.176 33.333 17.96 0.00 34.25 2.24
4130 4216 8.118607 CAGATGTTACATACTGCATTGTTACTG 58.881 37.037 0.00 0.00 0.00 2.74
4131 4217 7.824289 AGATGTTACATACTGCATTGTTACTGT 59.176 33.333 0.00 5.27 0.00 3.55
4132 4218 7.359262 TGTTACATACTGCATTGTTACTGTC 57.641 36.000 12.11 0.00 0.00 3.51
4133 4219 7.158697 TGTTACATACTGCATTGTTACTGTCT 58.841 34.615 12.11 0.00 0.00 3.41
4134 4220 7.330946 TGTTACATACTGCATTGTTACTGTCTC 59.669 37.037 12.11 0.00 0.00 3.36
4135 4221 5.793817 ACATACTGCATTGTTACTGTCTCA 58.206 37.500 0.00 0.00 0.00 3.27
4136 4222 5.871524 ACATACTGCATTGTTACTGTCTCAG 59.128 40.000 0.00 0.00 37.52 3.35
4137 4223 4.607293 ACTGCATTGTTACTGTCTCAGA 57.393 40.909 3.70 0.00 35.18 3.27
4138 4224 4.960938 ACTGCATTGTTACTGTCTCAGAA 58.039 39.130 3.70 0.00 35.18 3.02
4139 4225 5.368145 ACTGCATTGTTACTGTCTCAGAAA 58.632 37.500 3.70 0.00 35.18 2.52
4140 4226 5.822519 ACTGCATTGTTACTGTCTCAGAAAA 59.177 36.000 3.70 0.00 35.18 2.29
4141 4227 6.488006 ACTGCATTGTTACTGTCTCAGAAAAT 59.512 34.615 3.70 0.00 35.18 1.82
4142 4228 6.902341 TGCATTGTTACTGTCTCAGAAAATC 58.098 36.000 3.70 0.00 35.18 2.17
4143 4229 6.072508 TGCATTGTTACTGTCTCAGAAAATCC 60.073 38.462 3.70 0.00 35.18 3.01
4144 4230 6.072508 GCATTGTTACTGTCTCAGAAAATCCA 60.073 38.462 3.70 0.00 35.18 3.41
4145 4231 7.362401 GCATTGTTACTGTCTCAGAAAATCCAT 60.362 37.037 3.70 0.00 35.18 3.41
4146 4232 8.517878 CATTGTTACTGTCTCAGAAAATCCATT 58.482 33.333 3.70 0.00 35.18 3.16
4147 4233 7.672983 TGTTACTGTCTCAGAAAATCCATTC 57.327 36.000 3.70 0.00 35.18 2.67
4148 4234 6.655003 TGTTACTGTCTCAGAAAATCCATTCC 59.345 38.462 3.70 0.00 35.18 3.01
4149 4235 5.246981 ACTGTCTCAGAAAATCCATTCCA 57.753 39.130 3.70 0.00 35.18 3.53
4150 4236 5.251764 ACTGTCTCAGAAAATCCATTCCAG 58.748 41.667 3.70 0.00 35.18 3.86
4151 4237 5.222007 ACTGTCTCAGAAAATCCATTCCAGT 60.222 40.000 3.70 0.00 35.18 4.00
4152 4238 5.005740 TGTCTCAGAAAATCCATTCCAGTG 58.994 41.667 0.00 0.00 0.00 3.66
4153 4239 5.006386 GTCTCAGAAAATCCATTCCAGTGT 58.994 41.667 0.00 0.00 0.00 3.55
4154 4240 6.173339 GTCTCAGAAAATCCATTCCAGTGTA 58.827 40.000 0.00 0.00 0.00 2.90
4155 4241 6.092807 GTCTCAGAAAATCCATTCCAGTGTAC 59.907 42.308 0.00 0.00 0.00 2.90
4156 4242 6.013379 TCTCAGAAAATCCATTCCAGTGTACT 60.013 38.462 0.00 0.00 0.00 2.73
4157 4243 6.542821 TCAGAAAATCCATTCCAGTGTACTT 58.457 36.000 0.00 0.00 0.00 2.24
4158 4244 6.655003 TCAGAAAATCCATTCCAGTGTACTTC 59.345 38.462 0.00 0.00 0.00 3.01
4159 4245 6.430925 CAGAAAATCCATTCCAGTGTACTTCA 59.569 38.462 0.00 0.00 0.00 3.02
4160 4246 7.004086 AGAAAATCCATTCCAGTGTACTTCAA 58.996 34.615 0.00 0.00 0.00 2.69
4161 4247 7.671398 AGAAAATCCATTCCAGTGTACTTCAAT 59.329 33.333 0.00 0.00 0.00 2.57
4162 4248 8.877864 AAAATCCATTCCAGTGTACTTCAATA 57.122 30.769 0.00 0.00 0.00 1.90
4163 4249 8.877864 AAATCCATTCCAGTGTACTTCAATAA 57.122 30.769 0.00 0.00 0.00 1.40
4164 4250 7.865706 ATCCATTCCAGTGTACTTCAATAAC 57.134 36.000 0.00 0.00 0.00 1.89
4165 4251 6.774673 TCCATTCCAGTGTACTTCAATAACA 58.225 36.000 0.00 0.00 0.00 2.41
4166 4252 7.402054 TCCATTCCAGTGTACTTCAATAACAT 58.598 34.615 0.00 0.00 0.00 2.71
4167 4253 8.544622 TCCATTCCAGTGTACTTCAATAACATA 58.455 33.333 0.00 0.00 0.00 2.29
4168 4254 9.342308 CCATTCCAGTGTACTTCAATAACATAT 57.658 33.333 0.00 0.00 0.00 1.78
4172 4258 9.489084 TCCAGTGTACTTCAATAACATATATGC 57.511 33.333 12.79 0.00 0.00 3.14
4173 4259 9.271828 CCAGTGTACTTCAATAACATATATGCA 57.728 33.333 12.79 1.41 0.00 3.96
4175 4261 9.494271 AGTGTACTTCAATAACATATATGCAGG 57.506 33.333 12.79 0.00 0.00 4.85
4176 4262 8.721478 GTGTACTTCAATAACATATATGCAGGG 58.279 37.037 12.79 0.00 0.00 4.45
4177 4263 8.436778 TGTACTTCAATAACATATATGCAGGGT 58.563 33.333 12.79 4.38 0.00 4.34
4178 4264 9.938280 GTACTTCAATAACATATATGCAGGGTA 57.062 33.333 12.79 3.56 0.00 3.69
4179 4265 8.848474 ACTTCAATAACATATATGCAGGGTAC 57.152 34.615 12.79 0.00 0.00 3.34
4180 4266 8.436778 ACTTCAATAACATATATGCAGGGTACA 58.563 33.333 12.79 0.00 0.00 2.90
4181 4267 9.283768 CTTCAATAACATATATGCAGGGTACAA 57.716 33.333 12.79 0.00 0.00 2.41
4182 4268 8.615878 TCAATAACATATATGCAGGGTACAAC 57.384 34.615 12.79 0.00 0.00 3.32
4183 4269 8.214364 TCAATAACATATATGCAGGGTACAACA 58.786 33.333 12.79 0.00 0.00 3.33
4184 4270 8.845227 CAATAACATATATGCAGGGTACAACAA 58.155 33.333 12.79 0.00 0.00 2.83
4185 4271 9.586732 AATAACATATATGCAGGGTACAACAAT 57.413 29.630 12.79 0.00 0.00 2.71
4187 4273 7.979444 ACATATATGCAGGGTACAACAATAC 57.021 36.000 12.79 0.00 0.00 1.89
4188 4274 7.513856 ACATATATGCAGGGTACAACAATACA 58.486 34.615 12.79 0.00 0.00 2.29
4189 4275 8.163408 ACATATATGCAGGGTACAACAATACAT 58.837 33.333 12.79 0.00 0.00 2.29
4190 4276 9.013229 CATATATGCAGGGTACAACAATACATT 57.987 33.333 0.00 0.00 0.00 2.71
4192 4278 6.942532 ATGCAGGGTACAACAATACATTAG 57.057 37.500 0.00 0.00 0.00 1.73
4193 4279 5.189928 TGCAGGGTACAACAATACATTAGG 58.810 41.667 0.00 0.00 0.00 2.69
4194 4280 4.036380 GCAGGGTACAACAATACATTAGGC 59.964 45.833 0.00 0.00 0.00 3.93
4195 4281 4.578928 CAGGGTACAACAATACATTAGGCC 59.421 45.833 0.00 0.00 0.00 5.19
4196 4282 4.228666 AGGGTACAACAATACATTAGGCCA 59.771 41.667 5.01 0.00 0.00 5.36
4197 4283 4.951094 GGGTACAACAATACATTAGGCCAA 59.049 41.667 5.01 0.00 0.00 4.52
4198 4284 5.419471 GGGTACAACAATACATTAGGCCAAA 59.581 40.000 5.01 0.00 0.00 3.28
4199 4285 6.097696 GGGTACAACAATACATTAGGCCAAAT 59.902 38.462 5.01 0.00 0.00 2.32
4200 4286 7.364320 GGGTACAACAATACATTAGGCCAAATT 60.364 37.037 5.01 0.00 0.00 1.82
4201 4287 8.688151 GGTACAACAATACATTAGGCCAAATTA 58.312 33.333 5.01 0.00 0.00 1.40
4207 4293 9.981114 ACAATACATTAGGCCAAATTAATAAGC 57.019 29.630 5.01 0.00 0.00 3.09
4208 4294 9.979578 CAATACATTAGGCCAAATTAATAAGCA 57.020 29.630 5.01 0.00 0.00 3.91
4211 4297 7.670364 ACATTAGGCCAAATTAATAAGCATCC 58.330 34.615 5.01 0.00 0.00 3.51
4212 4298 7.510343 ACATTAGGCCAAATTAATAAGCATCCT 59.490 33.333 5.01 3.89 0.00 3.24
4213 4299 9.023962 CATTAGGCCAAATTAATAAGCATCCTA 57.976 33.333 5.01 3.14 0.00 2.94
4214 4300 9.774071 ATTAGGCCAAATTAATAAGCATCCTAT 57.226 29.630 5.01 0.00 0.00 2.57
4215 4301 9.600432 TTAGGCCAAATTAATAAGCATCCTATT 57.400 29.630 5.01 0.00 0.00 1.73
4216 4302 8.496534 AGGCCAAATTAATAAGCATCCTATTT 57.503 30.769 5.01 0.00 0.00 1.40
4217 4303 9.600432 AGGCCAAATTAATAAGCATCCTATTTA 57.400 29.630 5.01 0.00 0.00 1.40
4243 4329 7.870509 ATGAACAGATGTTACATACTGCATT 57.129 32.000 17.96 10.29 38.56 3.56
4244 4330 7.075674 TGAACAGATGTTACATACTGCATTG 57.924 36.000 17.96 0.00 38.56 2.82
4245 4331 6.654582 TGAACAGATGTTACATACTGCATTGT 59.345 34.615 17.96 0.00 38.56 2.71
4246 4332 7.174772 TGAACAGATGTTACATACTGCATTGTT 59.825 33.333 17.96 11.36 38.56 2.83
4247 4333 8.560355 AACAGATGTTACATACTGCATTGTTA 57.440 30.769 17.96 0.00 36.32 2.41
4248 4334 7.974675 ACAGATGTTACATACTGCATTGTTAC 58.025 34.615 17.96 5.04 34.25 2.50
4249 4335 7.824289 ACAGATGTTACATACTGCATTGTTACT 59.176 33.333 17.96 0.00 34.25 2.24
4250 4336 8.118607 CAGATGTTACATACTGCATTGTTACTG 58.881 37.037 0.00 0.00 0.00 2.74
4251 4337 7.824289 AGATGTTACATACTGCATTGTTACTGT 59.176 33.333 0.00 5.27 0.00 3.55
4252 4338 7.359262 TGTTACATACTGCATTGTTACTGTC 57.641 36.000 12.11 0.00 0.00 3.51
4253 4339 7.158697 TGTTACATACTGCATTGTTACTGTCT 58.841 34.615 12.11 0.00 0.00 3.41
4254 4340 7.330946 TGTTACATACTGCATTGTTACTGTCTC 59.669 37.037 12.11 0.00 0.00 3.36
4255 4341 5.793817 ACATACTGCATTGTTACTGTCTCA 58.206 37.500 0.00 0.00 0.00 3.27
4256 4342 5.871524 ACATACTGCATTGTTACTGTCTCAG 59.128 40.000 0.00 0.00 37.52 3.35
4257 4343 4.607293 ACTGCATTGTTACTGTCTCAGA 57.393 40.909 3.70 0.00 35.18 3.27
4258 4344 4.960938 ACTGCATTGTTACTGTCTCAGAA 58.039 39.130 3.70 0.00 35.18 3.02
4259 4345 5.368145 ACTGCATTGTTACTGTCTCAGAAA 58.632 37.500 3.70 0.00 35.18 2.52
4260 4346 5.822519 ACTGCATTGTTACTGTCTCAGAAAA 59.177 36.000 3.70 0.00 35.18 2.29
4261 4347 6.488006 ACTGCATTGTTACTGTCTCAGAAAAT 59.512 34.615 3.70 0.00 35.18 1.82
4262 4348 6.902341 TGCATTGTTACTGTCTCAGAAAATC 58.098 36.000 3.70 0.00 35.18 2.17
4263 4349 6.072508 TGCATTGTTACTGTCTCAGAAAATCC 60.073 38.462 3.70 0.00 35.18 3.01
4264 4350 6.072508 GCATTGTTACTGTCTCAGAAAATCCA 60.073 38.462 3.70 0.00 35.18 3.41
4265 4351 7.362401 GCATTGTTACTGTCTCAGAAAATCCAT 60.362 37.037 3.70 0.00 35.18 3.41
4266 4352 8.517878 CATTGTTACTGTCTCAGAAAATCCATT 58.482 33.333 3.70 0.00 35.18 3.16
4267 4353 7.672983 TGTTACTGTCTCAGAAAATCCATTC 57.327 36.000 3.70 0.00 35.18 2.67
4268 4354 6.655003 TGTTACTGTCTCAGAAAATCCATTCC 59.345 38.462 3.70 0.00 35.18 3.01
4269 4355 5.246981 ACTGTCTCAGAAAATCCATTCCA 57.753 39.130 3.70 0.00 35.18 3.53
4270 4356 5.251764 ACTGTCTCAGAAAATCCATTCCAG 58.748 41.667 3.70 0.00 35.18 3.86
4271 4357 5.222007 ACTGTCTCAGAAAATCCATTCCAGT 60.222 40.000 3.70 0.00 35.18 4.00
4272 4358 5.005740 TGTCTCAGAAAATCCATTCCAGTG 58.994 41.667 0.00 0.00 0.00 3.66
4273 4359 5.006386 GTCTCAGAAAATCCATTCCAGTGT 58.994 41.667 0.00 0.00 0.00 3.55
4274 4360 6.173339 GTCTCAGAAAATCCATTCCAGTGTA 58.827 40.000 0.00 0.00 0.00 2.90
4275 4361 6.092807 GTCTCAGAAAATCCATTCCAGTGTAC 59.907 42.308 0.00 0.00 0.00 2.90
4276 4362 4.935205 TCAGAAAATCCATTCCAGTGTACG 59.065 41.667 0.00 0.00 0.00 3.67
4277 4363 4.695455 CAGAAAATCCATTCCAGTGTACGT 59.305 41.667 0.00 0.00 0.00 3.57
4278 4364 4.935808 AGAAAATCCATTCCAGTGTACGTC 59.064 41.667 0.00 0.00 0.00 4.34
4279 4365 3.973206 AATCCATTCCAGTGTACGTCA 57.027 42.857 0.00 0.00 0.00 4.35
4280 4366 2.736144 TCCATTCCAGTGTACGTCAC 57.264 50.000 0.00 0.00 46.46 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.119245 CCAGGTTTGATTGATGCTCCTTG 60.119 47.826 0.00 0.00 0.00 3.61
24 25 6.493166 ACCAGATATTTCCAGGTTTGATTGA 58.507 36.000 0.00 0.00 29.09 2.57
41 42 8.966155 TCATGTATGGGTTTATCTACCAGATA 57.034 34.615 0.00 0.00 40.09 1.98
149 150 5.757886 TCTTGCCTTTTTATCAACGTTCTG 58.242 37.500 0.00 0.00 0.00 3.02
150 151 6.575162 ATCTTGCCTTTTTATCAACGTTCT 57.425 33.333 0.00 0.00 0.00 3.01
151 152 7.008357 GCTTATCTTGCCTTTTTATCAACGTTC 59.992 37.037 0.00 0.00 0.00 3.95
152 153 6.806739 GCTTATCTTGCCTTTTTATCAACGTT 59.193 34.615 0.00 0.00 0.00 3.99
153 154 6.072175 TGCTTATCTTGCCTTTTTATCAACGT 60.072 34.615 0.00 0.00 0.00 3.99
154 155 6.321717 TGCTTATCTTGCCTTTTTATCAACG 58.678 36.000 0.00 0.00 0.00 4.10
155 156 7.254218 GCATGCTTATCTTGCCTTTTTATCAAC 60.254 37.037 11.37 0.00 39.24 3.18
156 157 6.757947 GCATGCTTATCTTGCCTTTTTATCAA 59.242 34.615 11.37 0.00 39.24 2.57
247 248 7.282224 TGTTTGCTTGTCTAAGATGTTTACTGT 59.718 33.333 0.00 0.00 35.92 3.55
287 288 0.593128 GCGAAATCACAGTTGTGGCT 59.407 50.000 11.98 0.00 45.65 4.75
290 291 2.159627 GGGTAGCGAAATCACAGTTGTG 59.840 50.000 5.91 5.91 46.91 3.33
301 302 1.906574 AGGTCAGATTGGGTAGCGAAA 59.093 47.619 0.00 0.00 0.00 3.46
357 363 5.568423 GCAGATAAGTATGGGGTCTCAGATG 60.568 48.000 0.00 0.00 0.00 2.90
367 379 6.412362 ACTGTAGAAGCAGATAAGTATGGG 57.588 41.667 0.00 0.00 39.62 4.00
380 392 1.478916 GGAGGAGTGGACTGTAGAAGC 59.521 57.143 0.00 0.00 0.00 3.86
469 483 4.436242 TTTCGTTCAGTAATCGCTCTCT 57.564 40.909 0.00 0.00 0.00 3.10
576 590 4.128643 CTGGAAGTAGTAGTAGTCCTCCG 58.871 52.174 8.18 0.00 0.00 4.63
594 608 4.339530 CGAGTCCTTGATTAGATGACTGGA 59.660 45.833 0.00 0.00 36.48 3.86
598 627 6.507900 TGATTCGAGTCCTTGATTAGATGAC 58.492 40.000 5.38 0.00 0.00 3.06
637 666 4.516698 CCACCGAGATGGAATTAGGAATTG 59.483 45.833 0.00 0.00 43.02 2.32
638 667 4.412199 TCCACCGAGATGGAATTAGGAATT 59.588 41.667 1.01 0.00 46.08 2.17
640 669 3.380393 TCCACCGAGATGGAATTAGGAA 58.620 45.455 1.01 0.00 46.08 3.36
641 670 3.040655 TCCACCGAGATGGAATTAGGA 57.959 47.619 1.01 0.00 46.08 2.94
690 720 6.208599 CCCTGTCTGTGTGTAATTTGGTATTT 59.791 38.462 0.00 0.00 0.00 1.40
693 723 4.647611 CCCTGTCTGTGTGTAATTTGGTA 58.352 43.478 0.00 0.00 0.00 3.25
708 738 0.543749 GTAAGCTCCATGCCCTGTCT 59.456 55.000 0.00 0.00 44.23 3.41
710 740 0.995024 AAGTAAGCTCCATGCCCTGT 59.005 50.000 0.00 0.00 44.23 4.00
716 746 3.875727 CACCAGATCAAGTAAGCTCCATG 59.124 47.826 0.00 0.00 0.00 3.66
740 770 3.357079 CGCCCTGTTTGCTTCGCT 61.357 61.111 0.00 0.00 0.00 4.93
765 795 3.164269 CCCCCTCCAGATCGGTGG 61.164 72.222 14.16 14.16 46.52 4.61
808 854 0.179150 CTTCGTCTTCCTCTGCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
839 886 1.861575 GTGGCTTATTCGCTGCTACTC 59.138 52.381 0.00 0.00 35.72 2.59
842 889 0.529773 CCGTGGCTTATTCGCTGCTA 60.530 55.000 0.00 0.00 0.00 3.49
846 893 1.144057 CTCCCGTGGCTTATTCGCT 59.856 57.895 0.00 0.00 0.00 4.93
847 894 1.887707 CCTCCCGTGGCTTATTCGC 60.888 63.158 0.00 0.00 0.00 4.70
848 895 0.249489 CTCCTCCCGTGGCTTATTCG 60.249 60.000 0.00 0.00 0.00 3.34
852 899 2.365105 CCCTCCTCCCGTGGCTTA 60.365 66.667 0.00 0.00 0.00 3.09
857 904 2.972589 ATCATCCCCCTCCTCCCGTG 62.973 65.000 0.00 0.00 0.00 4.94
858 905 2.727071 ATCATCCCCCTCCTCCCGT 61.727 63.158 0.00 0.00 0.00 5.28
859 906 2.205462 ATCATCCCCCTCCTCCCG 59.795 66.667 0.00 0.00 0.00 5.14
860 907 2.533463 GCATCATCCCCCTCCTCCC 61.533 68.421 0.00 0.00 0.00 4.30
892 940 0.475044 GGGGATACACGGCCCAAATA 59.525 55.000 0.00 0.00 46.57 1.40
903 951 2.102420 CGTCAACTAGCATGGGGATACA 59.898 50.000 0.00 0.00 39.74 2.29
904 952 2.102588 ACGTCAACTAGCATGGGGATAC 59.897 50.000 0.00 0.00 0.00 2.24
905 953 2.394632 ACGTCAACTAGCATGGGGATA 58.605 47.619 0.00 0.00 0.00 2.59
906 954 1.204146 ACGTCAACTAGCATGGGGAT 58.796 50.000 0.00 0.00 0.00 3.85
907 955 0.981183 AACGTCAACTAGCATGGGGA 59.019 50.000 0.00 0.00 0.00 4.81
908 956 1.468520 CAAACGTCAACTAGCATGGGG 59.531 52.381 0.00 0.00 0.00 4.96
910 958 1.468520 CCCAAACGTCAACTAGCATGG 59.531 52.381 0.00 0.00 0.00 3.66
911 959 1.135689 GCCCAAACGTCAACTAGCATG 60.136 52.381 0.00 0.00 0.00 4.06
917 978 2.184167 CACGGCCCAAACGTCAACT 61.184 57.895 0.00 0.00 43.58 3.16
950 1011 3.430218 CGGCTGTTCAGAAGTAGTTGAAG 59.570 47.826 3.84 0.00 34.25 3.02
963 1024 2.355946 AGCTCTTCTCGGCTGTTCA 58.644 52.632 0.00 0.00 37.41 3.18
968 1029 0.323360 ACTCTCAGCTCTTCTCGGCT 60.323 55.000 0.00 0.00 39.60 5.52
978 1039 2.152297 CTGCGTGGTCACTCTCAGCT 62.152 60.000 0.00 0.00 0.00 4.24
1533 1603 1.000771 GGTCTTGGGGAAAGAGGCC 60.001 63.158 0.00 0.00 45.69 5.19
1602 1672 0.444260 GGCGCTTGAAGCAGTAGAAC 59.556 55.000 18.22 0.00 42.58 3.01
1626 1696 2.436646 CCATGAAAGCCGGCGTCT 60.437 61.111 26.84 14.89 0.00 4.18
1638 1708 2.359169 GGACGTCTGGAGGCCATGA 61.359 63.158 16.46 0.00 30.82 3.07
1654 1724 2.356278 GAGGGCATTGCAGGTGGA 59.644 61.111 11.39 0.00 0.00 4.02
1689 1759 3.689002 CTTGAAGGCGAGCCCCCTC 62.689 68.421 10.95 6.05 36.58 4.30
1900 1970 1.004745 GTCAAGCCTCCCTGATTTGGA 59.995 52.381 0.00 0.00 0.00 3.53
1987 2057 2.535317 AAGCCCCTCCACCATGGT 60.535 61.111 13.00 13.00 39.03 3.55
2388 2458 3.666253 TCGCTCGCGGTCACTTCA 61.666 61.111 6.13 0.00 40.25 3.02
2583 2653 1.973281 CATGTCCACCTTTGCCGCT 60.973 57.895 0.00 0.00 0.00 5.52
2664 2734 2.543012 CACGCTCAGGATGTTCATGATC 59.457 50.000 0.00 0.00 36.54 2.92
2793 2863 0.820226 CCGCACTCTCCTCATTCTCA 59.180 55.000 0.00 0.00 0.00 3.27
3129 3199 0.108585 GGACAACCTTGCTCACCTCA 59.891 55.000 0.00 0.00 0.00 3.86
3237 3307 0.397564 TCAGCTTGTGCATCAGGACA 59.602 50.000 0.00 0.00 44.86 4.02
3511 3581 2.024176 AGTGCAACACGTCACTCTTT 57.976 45.000 2.01 0.00 39.11 2.52
3515 3587 3.548014 GCAAATAAGTGCAACACGTCACT 60.548 43.478 2.01 2.01 44.64 3.41
3582 3654 4.774726 ACTGTTCACTGGATGTAGATGAGT 59.225 41.667 0.00 0.00 0.00 3.41
3649 3722 6.209192 ACACTCAATCATCTTACATGCCAAAA 59.791 34.615 0.00 0.00 0.00 2.44
3796 3873 8.096556 GCATTTGAATGTTTGAGTAGCTCTCAG 61.097 40.741 13.29 2.87 44.16 3.35
3824 3901 4.886496 TGATGTCCATGCCAAATTTCAA 57.114 36.364 0.00 0.00 0.00 2.69
3837 3914 1.404583 CGACTGAGTGCATGATGTCCA 60.405 52.381 0.00 0.00 0.00 4.02
3846 3923 0.033504 GGGAAAGACGACTGAGTGCA 59.966 55.000 0.00 0.00 0.00 4.57
4050 4136 3.761218 CCAATGTATTGTTGTACCCTGCA 59.239 43.478 4.12 0.00 36.06 4.41
4051 4137 3.130340 CCCAATGTATTGTTGTACCCTGC 59.870 47.826 4.12 0.00 36.06 4.85
4052 4138 3.130340 GCCCAATGTATTGTTGTACCCTG 59.870 47.826 4.12 0.00 36.06 4.45
4053 4139 3.361786 GCCCAATGTATTGTTGTACCCT 58.638 45.455 4.12 0.00 36.06 4.34
4054 4140 2.429250 GGCCCAATGTATTGTTGTACCC 59.571 50.000 0.00 0.00 36.06 3.69
4055 4141 3.093057 TGGCCCAATGTATTGTTGTACC 58.907 45.455 0.00 0.00 36.06 3.34
4056 4142 4.792521 TTGGCCCAATGTATTGTTGTAC 57.207 40.909 0.00 0.00 36.06 2.90
4057 4143 6.365970 AATTTGGCCCAATGTATTGTTGTA 57.634 33.333 2.20 0.00 36.06 2.41
4058 4144 4.906747 ATTTGGCCCAATGTATTGTTGT 57.093 36.364 0.24 0.00 36.06 3.32
4059 4145 7.862512 ATTAATTTGGCCCAATGTATTGTTG 57.137 32.000 2.20 0.00 36.06 3.33
4060 4146 9.612066 CTTATTAATTTGGCCCAATGTATTGTT 57.388 29.630 2.20 0.00 36.06 2.83
4061 4147 7.714813 GCTTATTAATTTGGCCCAATGTATTGT 59.285 33.333 2.20 0.00 36.06 2.71
4062 4148 7.714377 TGCTTATTAATTTGGCCCAATGTATTG 59.286 33.333 2.20 0.00 37.52 1.90
4063 4149 7.800092 TGCTTATTAATTTGGCCCAATGTATT 58.200 30.769 2.20 0.00 0.00 1.89
4064 4150 7.372260 TGCTTATTAATTTGGCCCAATGTAT 57.628 32.000 2.20 2.82 0.00 2.29
4065 4151 6.798427 TGCTTATTAATTTGGCCCAATGTA 57.202 33.333 2.20 0.00 0.00 2.29
4066 4152 5.690464 TGCTTATTAATTTGGCCCAATGT 57.310 34.783 2.20 0.00 0.00 2.71
4067 4153 5.702209 GGATGCTTATTAATTTGGCCCAATG 59.298 40.000 2.20 0.00 0.00 2.82
4068 4154 5.608015 AGGATGCTTATTAATTTGGCCCAAT 59.392 36.000 0.00 0.00 0.00 3.16
4069 4155 4.968080 AGGATGCTTATTAATTTGGCCCAA 59.032 37.500 0.00 0.00 0.00 4.12
4070 4156 4.555689 AGGATGCTTATTAATTTGGCCCA 58.444 39.130 0.00 0.00 0.00 5.36
4071 4157 6.857437 ATAGGATGCTTATTAATTTGGCCC 57.143 37.500 0.00 0.00 0.00 5.80
4097 4183 9.565090 AATGCAGTATGTAACATCTGTTCATAT 57.435 29.630 0.00 0.00 39.31 1.78
4098 4184 8.829612 CAATGCAGTATGTAACATCTGTTCATA 58.170 33.333 0.00 5.32 39.31 2.15
4099 4185 7.337689 ACAATGCAGTATGTAACATCTGTTCAT 59.662 33.333 0.00 6.15 39.31 2.57
4100 4186 6.654582 ACAATGCAGTATGTAACATCTGTTCA 59.345 34.615 0.00 0.00 39.31 3.18
4101 4187 7.076842 ACAATGCAGTATGTAACATCTGTTC 57.923 36.000 0.00 0.00 39.31 3.18
4102 4188 7.452880 AACAATGCAGTATGTAACATCTGTT 57.547 32.000 3.35 0.69 39.31 3.16
4103 4189 7.824289 AGTAACAATGCAGTATGTAACATCTGT 59.176 33.333 3.35 0.00 39.31 3.41
4104 4190 8.118607 CAGTAACAATGCAGTATGTAACATCTG 58.881 37.037 3.35 0.00 39.31 2.90
4105 4191 7.824289 ACAGTAACAATGCAGTATGTAACATCT 59.176 33.333 3.35 0.00 39.31 2.90
4106 4192 7.974675 ACAGTAACAATGCAGTATGTAACATC 58.025 34.615 3.35 0.00 39.31 3.06
4107 4193 7.824289 AGACAGTAACAATGCAGTATGTAACAT 59.176 33.333 3.35 0.00 39.31 2.71
4108 4194 7.158697 AGACAGTAACAATGCAGTATGTAACA 58.841 34.615 3.35 0.00 39.31 2.41
4109 4195 7.330946 TGAGACAGTAACAATGCAGTATGTAAC 59.669 37.037 3.35 0.00 39.31 2.50
4110 4196 7.382898 TGAGACAGTAACAATGCAGTATGTAA 58.617 34.615 3.35 0.00 39.31 2.41
4111 4197 6.930731 TGAGACAGTAACAATGCAGTATGTA 58.069 36.000 3.35 0.00 39.31 2.29
4112 4198 5.793817 TGAGACAGTAACAATGCAGTATGT 58.206 37.500 0.00 0.00 39.31 2.29
4113 4199 6.101997 TCTGAGACAGTAACAATGCAGTATG 58.898 40.000 0.00 0.00 33.75 2.39
4114 4200 6.286240 TCTGAGACAGTAACAATGCAGTAT 57.714 37.500 0.00 0.00 32.61 2.12
4115 4201 5.722021 TCTGAGACAGTAACAATGCAGTA 57.278 39.130 0.00 0.00 32.61 2.74
4116 4202 4.607293 TCTGAGACAGTAACAATGCAGT 57.393 40.909 0.00 0.00 32.61 4.40
4117 4203 5.929697 TTTCTGAGACAGTAACAATGCAG 57.070 39.130 0.00 0.00 32.61 4.41
4118 4204 6.072508 GGATTTTCTGAGACAGTAACAATGCA 60.073 38.462 0.00 0.00 32.61 3.96
4119 4205 6.072508 TGGATTTTCTGAGACAGTAACAATGC 60.073 38.462 0.00 0.00 32.61 3.56
4120 4206 7.439157 TGGATTTTCTGAGACAGTAACAATG 57.561 36.000 0.00 0.00 32.61 2.82
4121 4207 8.641498 AATGGATTTTCTGAGACAGTAACAAT 57.359 30.769 0.00 0.00 32.61 2.71
4122 4208 7.174946 GGAATGGATTTTCTGAGACAGTAACAA 59.825 37.037 0.00 0.00 32.61 2.83
4123 4209 6.655003 GGAATGGATTTTCTGAGACAGTAACA 59.345 38.462 0.00 0.00 32.61 2.41
4124 4210 6.655003 TGGAATGGATTTTCTGAGACAGTAAC 59.345 38.462 0.00 0.00 32.61 2.50
4125 4211 6.778821 TGGAATGGATTTTCTGAGACAGTAA 58.221 36.000 0.00 0.00 32.61 2.24
4126 4212 6.013379 ACTGGAATGGATTTTCTGAGACAGTA 60.013 38.462 0.00 0.00 33.10 2.74
4127 4213 5.222007 ACTGGAATGGATTTTCTGAGACAGT 60.222 40.000 0.00 0.00 32.61 3.55
4128 4214 5.123502 CACTGGAATGGATTTTCTGAGACAG 59.876 44.000 0.00 0.00 0.00 3.51
4129 4215 5.005740 CACTGGAATGGATTTTCTGAGACA 58.994 41.667 0.00 0.00 0.00 3.41
4130 4216 5.006386 ACACTGGAATGGATTTTCTGAGAC 58.994 41.667 0.00 0.00 0.00 3.36
4131 4217 5.246981 ACACTGGAATGGATTTTCTGAGA 57.753 39.130 0.00 0.00 0.00 3.27
4132 4218 6.176183 AGTACACTGGAATGGATTTTCTGAG 58.824 40.000 0.00 0.00 0.00 3.35
4133 4219 6.126863 AGTACACTGGAATGGATTTTCTGA 57.873 37.500 0.00 0.00 0.00 3.27
4134 4220 6.430925 TGAAGTACACTGGAATGGATTTTCTG 59.569 38.462 0.00 0.00 0.00 3.02
4135 4221 6.542821 TGAAGTACACTGGAATGGATTTTCT 58.457 36.000 0.00 0.00 0.00 2.52
4136 4222 6.817765 TGAAGTACACTGGAATGGATTTTC 57.182 37.500 0.00 0.00 0.00 2.29
4137 4223 7.781324 ATTGAAGTACACTGGAATGGATTTT 57.219 32.000 0.00 0.00 0.00 1.82
4138 4224 8.739972 GTTATTGAAGTACACTGGAATGGATTT 58.260 33.333 0.00 0.00 0.00 2.17
4139 4225 7.888021 TGTTATTGAAGTACACTGGAATGGATT 59.112 33.333 0.00 0.00 0.00 3.01
4140 4226 7.402054 TGTTATTGAAGTACACTGGAATGGAT 58.598 34.615 0.00 0.00 0.00 3.41
4141 4227 6.774673 TGTTATTGAAGTACACTGGAATGGA 58.225 36.000 0.00 0.00 0.00 3.41
4142 4228 7.630242 ATGTTATTGAAGTACACTGGAATGG 57.370 36.000 0.00 0.00 0.00 3.16
4146 4232 9.489084 GCATATATGTTATTGAAGTACACTGGA 57.511 33.333 14.14 0.00 0.00 3.86
4147 4233 9.271828 TGCATATATGTTATTGAAGTACACTGG 57.728 33.333 14.14 0.00 0.00 4.00
4149 4235 9.494271 CCTGCATATATGTTATTGAAGTACACT 57.506 33.333 14.14 0.00 0.00 3.55
4150 4236 8.721478 CCCTGCATATATGTTATTGAAGTACAC 58.279 37.037 14.14 0.00 0.00 2.90
4151 4237 8.436778 ACCCTGCATATATGTTATTGAAGTACA 58.563 33.333 14.14 0.00 0.00 2.90
4152 4238 8.848474 ACCCTGCATATATGTTATTGAAGTAC 57.152 34.615 14.14 0.00 0.00 2.73
4153 4239 9.938280 GTACCCTGCATATATGTTATTGAAGTA 57.062 33.333 14.14 3.84 0.00 2.24
4154 4240 8.436778 TGTACCCTGCATATATGTTATTGAAGT 58.563 33.333 14.14 4.64 0.00 3.01
4155 4241 8.846943 TGTACCCTGCATATATGTTATTGAAG 57.153 34.615 14.14 0.00 0.00 3.02
4156 4242 9.062524 GTTGTACCCTGCATATATGTTATTGAA 57.937 33.333 14.14 0.00 0.00 2.69
4157 4243 8.214364 TGTTGTACCCTGCATATATGTTATTGA 58.786 33.333 14.14 0.00 0.00 2.57
4158 4244 8.389779 TGTTGTACCCTGCATATATGTTATTG 57.610 34.615 14.14 2.93 0.00 1.90
4159 4245 8.988546 TTGTTGTACCCTGCATATATGTTATT 57.011 30.769 14.14 0.00 0.00 1.40
4161 4247 9.496873 GTATTGTTGTACCCTGCATATATGTTA 57.503 33.333 14.14 3.52 0.00 2.41
4162 4248 7.996066 TGTATTGTTGTACCCTGCATATATGTT 59.004 33.333 14.14 0.00 0.00 2.71
4163 4249 7.513856 TGTATTGTTGTACCCTGCATATATGT 58.486 34.615 14.14 0.00 0.00 2.29
4164 4250 7.977789 TGTATTGTTGTACCCTGCATATATG 57.022 36.000 8.45 8.45 0.00 1.78
4166 4252 9.719355 CTAATGTATTGTTGTACCCTGCATATA 57.281 33.333 0.00 0.00 0.00 0.86
4167 4253 7.665559 CCTAATGTATTGTTGTACCCTGCATAT 59.334 37.037 0.00 0.00 0.00 1.78
4168 4254 6.995686 CCTAATGTATTGTTGTACCCTGCATA 59.004 38.462 0.00 0.00 0.00 3.14
4169 4255 5.827797 CCTAATGTATTGTTGTACCCTGCAT 59.172 40.000 0.00 0.00 0.00 3.96
4170 4256 5.189928 CCTAATGTATTGTTGTACCCTGCA 58.810 41.667 0.00 0.00 0.00 4.41
4171 4257 4.036380 GCCTAATGTATTGTTGTACCCTGC 59.964 45.833 0.00 0.00 0.00 4.85
4172 4258 4.578928 GGCCTAATGTATTGTTGTACCCTG 59.421 45.833 0.00 0.00 0.00 4.45
4173 4259 4.228666 TGGCCTAATGTATTGTTGTACCCT 59.771 41.667 3.32 0.00 0.00 4.34
4174 4260 4.528920 TGGCCTAATGTATTGTTGTACCC 58.471 43.478 3.32 0.00 0.00 3.69
4175 4261 6.518208 TTTGGCCTAATGTATTGTTGTACC 57.482 37.500 3.32 0.00 0.00 3.34
4181 4267 9.981114 GCTTATTAATTTGGCCTAATGTATTGT 57.019 29.630 13.37 0.00 0.00 2.71
4182 4268 9.979578 TGCTTATTAATTTGGCCTAATGTATTG 57.020 29.630 13.37 4.41 0.00 1.90
4185 4271 8.802267 GGATGCTTATTAATTTGGCCTAATGTA 58.198 33.333 13.37 5.08 0.00 2.29
4186 4272 7.510343 AGGATGCTTATTAATTTGGCCTAATGT 59.490 33.333 13.37 6.53 0.00 2.71
4187 4273 7.899973 AGGATGCTTATTAATTTGGCCTAATG 58.100 34.615 13.37 1.07 0.00 1.90
4188 4274 9.774071 ATAGGATGCTTATTAATTTGGCCTAAT 57.226 29.630 6.60 6.60 0.00 1.73
4189 4275 9.600432 AATAGGATGCTTATTAATTTGGCCTAA 57.400 29.630 3.32 2.09 0.00 2.69
4190 4276 9.600432 AAATAGGATGCTTATTAATTTGGCCTA 57.400 29.630 3.32 0.00 0.00 3.93
4191 4277 8.496534 AAATAGGATGCTTATTAATTTGGCCT 57.503 30.769 3.32 0.00 0.00 5.19
4217 4303 9.565090 AATGCAGTATGTAACATCTGTTCATAT 57.435 29.630 0.00 0.00 39.31 1.78
4218 4304 8.829612 CAATGCAGTATGTAACATCTGTTCATA 58.170 33.333 0.00 5.32 39.31 2.15
4219 4305 7.337689 ACAATGCAGTATGTAACATCTGTTCAT 59.662 33.333 0.00 6.15 39.31 2.57
4220 4306 6.654582 ACAATGCAGTATGTAACATCTGTTCA 59.345 34.615 0.00 0.00 39.31 3.18
4221 4307 7.076842 ACAATGCAGTATGTAACATCTGTTC 57.923 36.000 0.00 0.00 39.31 3.18
4222 4308 7.452880 AACAATGCAGTATGTAACATCTGTT 57.547 32.000 3.35 0.69 39.31 3.16
4223 4309 7.824289 AGTAACAATGCAGTATGTAACATCTGT 59.176 33.333 3.35 0.00 39.31 3.41
4224 4310 8.118607 CAGTAACAATGCAGTATGTAACATCTG 58.881 37.037 3.35 0.00 39.31 2.90
4225 4311 7.824289 ACAGTAACAATGCAGTATGTAACATCT 59.176 33.333 3.35 0.00 39.31 2.90
4226 4312 7.974675 ACAGTAACAATGCAGTATGTAACATC 58.025 34.615 3.35 0.00 39.31 3.06
4227 4313 7.824289 AGACAGTAACAATGCAGTATGTAACAT 59.176 33.333 3.35 0.00 39.31 2.71
4228 4314 7.158697 AGACAGTAACAATGCAGTATGTAACA 58.841 34.615 3.35 0.00 39.31 2.41
4229 4315 7.330946 TGAGACAGTAACAATGCAGTATGTAAC 59.669 37.037 3.35 0.00 39.31 2.50
4230 4316 7.382898 TGAGACAGTAACAATGCAGTATGTAA 58.617 34.615 3.35 0.00 39.31 2.41
4231 4317 6.930731 TGAGACAGTAACAATGCAGTATGTA 58.069 36.000 3.35 0.00 39.31 2.29
4232 4318 5.793817 TGAGACAGTAACAATGCAGTATGT 58.206 37.500 0.00 0.00 39.31 2.29
4233 4319 6.101997 TCTGAGACAGTAACAATGCAGTATG 58.898 40.000 0.00 0.00 33.75 2.39
4234 4320 6.286240 TCTGAGACAGTAACAATGCAGTAT 57.714 37.500 0.00 0.00 32.61 2.12
4235 4321 5.722021 TCTGAGACAGTAACAATGCAGTA 57.278 39.130 0.00 0.00 32.61 2.74
4236 4322 4.607293 TCTGAGACAGTAACAATGCAGT 57.393 40.909 0.00 0.00 32.61 4.40
4237 4323 5.929697 TTTCTGAGACAGTAACAATGCAG 57.070 39.130 0.00 0.00 32.61 4.41
4238 4324 6.072508 GGATTTTCTGAGACAGTAACAATGCA 60.073 38.462 0.00 0.00 32.61 3.96
4239 4325 6.072508 TGGATTTTCTGAGACAGTAACAATGC 60.073 38.462 0.00 0.00 32.61 3.56
4240 4326 7.439157 TGGATTTTCTGAGACAGTAACAATG 57.561 36.000 0.00 0.00 32.61 2.82
4241 4327 8.641498 AATGGATTTTCTGAGACAGTAACAAT 57.359 30.769 0.00 0.00 32.61 2.71
4242 4328 7.174946 GGAATGGATTTTCTGAGACAGTAACAA 59.825 37.037 0.00 0.00 32.61 2.83
4243 4329 6.655003 GGAATGGATTTTCTGAGACAGTAACA 59.345 38.462 0.00 0.00 32.61 2.41
4244 4330 6.655003 TGGAATGGATTTTCTGAGACAGTAAC 59.345 38.462 0.00 0.00 32.61 2.50
4245 4331 6.778821 TGGAATGGATTTTCTGAGACAGTAA 58.221 36.000 0.00 0.00 32.61 2.24
4246 4332 6.013379 ACTGGAATGGATTTTCTGAGACAGTA 60.013 38.462 0.00 0.00 33.10 2.74
4247 4333 5.222007 ACTGGAATGGATTTTCTGAGACAGT 60.222 40.000 0.00 0.00 32.61 3.55
4248 4334 5.123502 CACTGGAATGGATTTTCTGAGACAG 59.876 44.000 0.00 0.00 0.00 3.51
4249 4335 5.005740 CACTGGAATGGATTTTCTGAGACA 58.994 41.667 0.00 0.00 0.00 3.41
4250 4336 5.006386 ACACTGGAATGGATTTTCTGAGAC 58.994 41.667 0.00 0.00 0.00 3.36
4251 4337 5.246981 ACACTGGAATGGATTTTCTGAGA 57.753 39.130 0.00 0.00 0.00 3.27
4252 4338 5.063944 CGTACACTGGAATGGATTTTCTGAG 59.936 44.000 0.00 0.00 0.00 3.35
4253 4339 4.935205 CGTACACTGGAATGGATTTTCTGA 59.065 41.667 0.00 0.00 0.00 3.27
4254 4340 4.695455 ACGTACACTGGAATGGATTTTCTG 59.305 41.667 0.00 0.00 0.00 3.02
4255 4341 4.906618 ACGTACACTGGAATGGATTTTCT 58.093 39.130 0.00 0.00 0.00 2.52
4256 4342 4.693566 TGACGTACACTGGAATGGATTTTC 59.306 41.667 0.00 0.00 0.00 2.29
4257 4343 4.454504 GTGACGTACACTGGAATGGATTTT 59.545 41.667 9.86 0.00 45.13 1.82
4258 4344 4.000988 GTGACGTACACTGGAATGGATTT 58.999 43.478 9.86 0.00 45.13 2.17
4259 4345 3.596214 GTGACGTACACTGGAATGGATT 58.404 45.455 9.86 0.00 45.13 3.01
4260 4346 3.247006 GTGACGTACACTGGAATGGAT 57.753 47.619 9.86 0.00 45.13 3.41
4261 4347 2.736144 GTGACGTACACTGGAATGGA 57.264 50.000 9.86 0.00 45.13 3.41
4271 4357 5.522097 CCTGCATATATGTTTGTGACGTACA 59.478 40.000 14.14 0.00 37.56 2.90
4272 4358 5.050363 CCCTGCATATATGTTTGTGACGTAC 60.050 44.000 14.14 0.00 32.74 3.67
4273 4359 5.053811 CCCTGCATATATGTTTGTGACGTA 58.946 41.667 14.14 0.00 34.38 3.57
4274 4360 3.876914 CCCTGCATATATGTTTGTGACGT 59.123 43.478 14.14 0.00 0.00 4.34
4275 4361 3.876914 ACCCTGCATATATGTTTGTGACG 59.123 43.478 14.14 0.00 0.00 4.35
4276 4362 5.820423 TGTACCCTGCATATATGTTTGTGAC 59.180 40.000 14.14 7.13 0.00 3.67
4277 4363 5.995446 TGTACCCTGCATATATGTTTGTGA 58.005 37.500 14.14 0.00 0.00 3.58
4278 4364 5.277974 GCTGTACCCTGCATATATGTTTGTG 60.278 44.000 14.14 2.93 35.75 3.33
4279 4365 4.821805 GCTGTACCCTGCATATATGTTTGT 59.178 41.667 14.14 8.94 35.75 2.83
4280 4366 4.821260 TGCTGTACCCTGCATATATGTTTG 59.179 41.667 14.14 5.00 40.17 2.93
4281 4367 5.047566 TGCTGTACCCTGCATATATGTTT 57.952 39.130 14.14 0.00 40.17 2.83
4282 4368 4.705110 TGCTGTACCCTGCATATATGTT 57.295 40.909 14.14 0.00 40.17 2.71
4283 4369 4.705110 TTGCTGTACCCTGCATATATGT 57.295 40.909 14.14 0.00 43.82 2.29
4284 4370 6.172630 TGTATTGCTGTACCCTGCATATATG 58.827 40.000 8.45 8.45 43.82 1.78
4285 4371 6.373005 TGTATTGCTGTACCCTGCATATAT 57.627 37.500 6.21 1.53 43.82 0.86
4286 4372 5.816955 TGTATTGCTGTACCCTGCATATA 57.183 39.130 6.21 5.38 43.82 0.86
4287 4373 4.705110 TGTATTGCTGTACCCTGCATAT 57.295 40.909 6.21 6.08 43.82 1.78
4288 4374 4.705110 ATGTATTGCTGTACCCTGCATA 57.295 40.909 6.21 0.30 43.82 3.14
4289 4375 3.582998 ATGTATTGCTGTACCCTGCAT 57.417 42.857 6.21 1.51 43.82 3.96


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

AutoCloner maintained by Alex Coulton.