Multiple sequence alignment - TraesCS4B01G274400

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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 TraesCS4B01G274400 chr4B 100.000 1716 0 0 1 1716 552029452 552027737 0.000000e+00 3169.0
1 TraesCS4B01G274400 chr4B 100.000 638 0 0 2059 2696 552027394 552026757 0.000000e+00 1179.0
2 TraesCS4B01G274400 chr4D 89.448 815 47 15 1 799 442904068 442903277 0.000000e+00 992.0
3 TraesCS4B01G274400 chr4D 82.710 428 60 7 2086 2504 442902893 442902471 4.240000e-98 368.0
4 TraesCS4B01G274400 chr4D 97.283 184 5 0 1422 1605 442903189 442903006 2.020000e-81 313.0
5 TraesCS4B01G274400 chr4D 91.146 192 15 2 2506 2696 442902206 442902016 2.660000e-65 259.0
6 TraesCS4B01G274400 chr4A 93.031 287 20 0 1430 1716 24758849 24759135 1.150000e-113 420.0
7 TraesCS4B01G274400 chr4A 85.185 405 27 15 144 528 24757958 24758349 4.210000e-103 385.0
8 TraesCS4B01G274400 chr4A 95.763 236 10 0 1040 1275 24758555 24758790 5.450000e-102 381.0
9 TraesCS4B01G274400 chr4A 92.810 153 4 7 1 152 24757645 24757791 5.850000e-52 215.0
10 TraesCS4B01G274400 chr1B 78.815 557 88 19 2152 2694 600608813 600608273 5.520000e-92 348.0
11 TraesCS4B01G274400 chr3B 83.944 355 49 5 1339 1686 779307436 779307083 1.550000e-87 333.0
12 TraesCS4B01G274400 chr3B 87.649 251 25 5 1339 1583 779525403 779525653 1.220000e-73 287.0
13 TraesCS4B01G274400 chr3B 74.775 222 41 12 1052 1270 778370918 778371127 4.780000e-13 86.1
14 TraesCS4B01G274400 chr3D 76.211 681 125 30 1028 1684 559916596 559915929 2.590000e-85 326.0
15 TraesCS4B01G274400 chr3D 83.152 368 51 8 1339 1696 582056430 582056064 2.590000e-85 326.0
16 TraesCS4B01G274400 chr3D 82.486 354 54 5 1339 1685 582157259 582157611 1.210000e-78 303.0
17 TraesCS4B01G274400 chr3D 82.545 275 35 8 1052 1324 580318516 580318253 2.090000e-56 230.0
18 TraesCS4B01G274400 chr3D 83.085 201 31 1 1040 1240 582116213 582116016 2.130000e-41 180.0
19 TraesCS4B01G274400 chr7A 79.204 226 41 3 1019 1244 48442705 48442924 4.650000e-33 152.0


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 TraesCS4B01G274400 chr4B 552026757 552029452 2695 True 2174.00 3169 100.00000 1 2696 2 chr4B.!!$R1 2695
1 TraesCS4B01G274400 chr4D 442902016 442904068 2052 True 483.00 992 90.14675 1 2696 4 chr4D.!!$R1 2695
2 TraesCS4B01G274400 chr4A 24757645 24759135 1490 False 350.25 420 91.69725 1 1716 4 chr4A.!!$F1 1715
3 TraesCS4B01G274400 chr1B 600608273 600608813 540 True 348.00 348 78.81500 2152 2694 1 chr1B.!!$R1 542
4 TraesCS4B01G274400 chr3D 559915929 559916596 667 True 326.00 326 76.21100 1028 1684 1 chr3D.!!$R1 656

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
804 1011 0.108424 CAGTGGCGGGAGAAGAGAAG 60.108 60.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2660 0.032117 ACGGAGATGATCCCCAGTCA 60.032 55.0 0.0 0.0 46.5 3.41 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
103 109 3.610040 TGGTTTCGTATCTGCTGATGT 57.390 42.857 15.71 0.00 34.32 3.06
238 429 1.455959 TTGTGGTTCCGTTTGGGGG 60.456 57.895 0.00 0.00 36.01 5.40
271 462 1.593196 GTGTGCTTGGTTGAGTGCTA 58.407 50.000 0.00 0.00 0.00 3.49
298 489 2.551721 CCTCACTGCTTGTCCACTTGAT 60.552 50.000 0.00 0.00 0.00 2.57
313 508 7.177216 TGTCCACTTGATATGCTTCAGAATTTT 59.823 33.333 0.00 0.00 0.00 1.82
345 540 0.465460 TGGTTGCTTGGTGAGTGGTC 60.465 55.000 0.00 0.00 0.00 4.02
400 595 4.202030 GGTTTGTATCCTAGAGAGGTGTCG 60.202 50.000 0.00 0.00 44.19 4.35
417 612 3.067106 TGTCGAGCTCAGCTTAAAAAGG 58.933 45.455 15.40 0.00 39.88 3.11
441 640 2.375146 TGGAACGATCACTAGCTGCTA 58.625 47.619 9.34 9.34 0.00 3.49
462 661 1.229428 GTGTCATGGTGGTGTCACTG 58.771 55.000 2.35 0.00 43.17 3.66
467 666 1.174712 ATGGTGGTGTCACTGCTTGC 61.175 55.000 2.35 0.00 43.17 4.01
468 667 1.823470 GGTGGTGTCACTGCTTGCA 60.823 57.895 2.35 0.00 43.17 4.08
469 668 1.356624 GTGGTGTCACTGCTTGCAC 59.643 57.895 2.35 0.00 40.58 4.57
470 669 1.097547 GTGGTGTCACTGCTTGCACT 61.098 55.000 2.35 0.00 40.58 4.40
471 670 1.096967 TGGTGTCACTGCTTGCACTG 61.097 55.000 2.35 0.00 34.50 3.66
472 671 0.815213 GGTGTCACTGCTTGCACTGA 60.815 55.000 2.35 1.79 34.50 3.41
473 672 1.016627 GTGTCACTGCTTGCACTGAA 58.983 50.000 6.54 0.00 32.57 3.02
474 673 1.003116 GTGTCACTGCTTGCACTGAAG 60.003 52.381 6.54 0.00 32.57 3.02
475 674 0.590195 GTCACTGCTTGCACTGAAGG 59.410 55.000 6.54 0.00 0.00 3.46
476 675 0.469494 TCACTGCTTGCACTGAAGGA 59.531 50.000 3.18 0.00 0.00 3.36
477 676 1.072806 TCACTGCTTGCACTGAAGGAT 59.927 47.619 3.18 0.00 0.00 3.24
478 677 1.199327 CACTGCTTGCACTGAAGGATG 59.801 52.381 0.00 0.00 0.00 3.51
479 678 0.170561 CTGCTTGCACTGAAGGATGC 59.829 55.000 0.00 0.00 42.40 3.91
536 738 4.322953 CCAGGGAAATTGGGATCTTTGTTG 60.323 45.833 0.00 0.00 31.87 3.33
537 739 4.527816 CAGGGAAATTGGGATCTTTGTTGA 59.472 41.667 0.00 0.00 0.00 3.18
547 749 5.419788 TGGGATCTTTGTTGATCAATTCCTG 59.580 40.000 12.12 2.17 43.27 3.86
554 756 7.723616 TCTTTGTTGATCAATTCCTGGACTAAA 59.276 33.333 12.12 0.75 35.84 1.85
566 768 3.191371 CCTGGACTAAAATGCACCTTGTC 59.809 47.826 0.00 0.00 0.00 3.18
568 770 4.072131 TGGACTAAAATGCACCTTGTCTC 58.928 43.478 0.00 0.00 0.00 3.36
582 784 3.186409 CCTTGTCTCACATGGTTGTAACG 59.814 47.826 0.00 0.00 38.28 3.18
601 804 6.936900 TGTAACGAGTGTAGGGTATATACCTC 59.063 42.308 27.24 18.52 45.72 3.85
630 833 4.212214 CCTCTTGTTTTGACCTCTTCGAAG 59.788 45.833 19.35 19.35 0.00 3.79
635 838 6.340962 TGTTTTGACCTCTTCGAAGATCTA 57.659 37.500 27.19 16.70 35.04 1.98
664 868 1.222113 GGAGAGGCTACCCTTGCAC 59.778 63.158 0.00 0.00 43.12 4.57
673 877 2.035632 CTACCCTTGCACCCAAAACAA 58.964 47.619 0.00 0.00 0.00 2.83
680 884 4.359706 CTTGCACCCAAAACAAGAAGTAC 58.640 43.478 0.00 0.00 42.71 2.73
709 913 9.569122 AAAATTGTACCTCACTAAACACATACT 57.431 29.630 0.00 0.00 0.00 2.12
711 915 9.649167 AATTGTACCTCACTAAACACATACTAC 57.351 33.333 0.00 0.00 0.00 2.73
717 921 9.171877 ACCTCACTAAACACATACTACTACTAC 57.828 37.037 0.00 0.00 0.00 2.73
725 929 9.558396 AAACACATACTACTACTACTAGCTAGG 57.442 37.037 24.35 10.32 0.00 3.02
733 937 9.777297 ACTACTACTACTAGCTAGGTAACAATC 57.223 37.037 24.35 0.00 41.41 2.67
735 939 5.435820 ACTACTAGCTAGGTAACAATCGC 57.564 43.478 24.35 0.00 41.41 4.58
756 960 7.603963 TCGCTTGTTATTTGTTTATAGCTGA 57.396 32.000 0.00 0.00 0.00 4.26
757 961 8.035165 TCGCTTGTTATTTGTTTATAGCTGAA 57.965 30.769 0.00 0.00 0.00 3.02
758 962 8.508062 TCGCTTGTTATTTGTTTATAGCTGAAA 58.492 29.630 0.00 0.00 0.00 2.69
779 986 5.595257 AAGATTAAGACTTCCGGTAGGTC 57.405 43.478 13.15 13.28 39.05 3.85
788 995 0.896940 TCCGGTAGGTCGCTTTCAGT 60.897 55.000 0.00 0.00 39.05 3.41
799 1006 1.301677 GCTTTCAGTGGCGGGAGAAG 61.302 60.000 0.00 0.00 0.00 2.85
801 1008 0.321671 TTTCAGTGGCGGGAGAAGAG 59.678 55.000 0.00 0.00 0.00 2.85
803 1010 0.541998 TCAGTGGCGGGAGAAGAGAA 60.542 55.000 0.00 0.00 0.00 2.87
804 1011 0.108424 CAGTGGCGGGAGAAGAGAAG 60.108 60.000 0.00 0.00 0.00 2.85
806 1013 0.827368 GTGGCGGGAGAAGAGAAGAT 59.173 55.000 0.00 0.00 0.00 2.40
807 1014 2.032620 GTGGCGGGAGAAGAGAAGATA 58.967 52.381 0.00 0.00 0.00 1.98
809 1016 2.894126 TGGCGGGAGAAGAGAAGATATC 59.106 50.000 0.00 0.00 0.00 1.63
810 1017 2.894126 GGCGGGAGAAGAGAAGATATCA 59.106 50.000 5.32 0.00 0.00 2.15
811 1018 3.513515 GGCGGGAGAAGAGAAGATATCAT 59.486 47.826 5.32 0.00 0.00 2.45
812 1019 4.707448 GGCGGGAGAAGAGAAGATATCATA 59.293 45.833 5.32 0.00 0.00 2.15
813 1020 5.186021 GGCGGGAGAAGAGAAGATATCATAA 59.814 44.000 5.32 0.00 0.00 1.90
815 1022 6.588373 GCGGGAGAAGAGAAGATATCATAAAC 59.412 42.308 5.32 0.00 0.00 2.01
816 1023 7.524698 GCGGGAGAAGAGAAGATATCATAAACT 60.525 40.741 5.32 0.00 0.00 2.66
817 1024 9.015367 CGGGAGAAGAGAAGATATCATAAACTA 57.985 37.037 5.32 0.00 0.00 2.24
823 1030 9.995003 AAGAGAAGATATCATAAACTAAGCAGG 57.005 33.333 5.32 0.00 0.00 4.85
824 1031 8.093927 AGAGAAGATATCATAAACTAAGCAGGC 58.906 37.037 5.32 0.00 0.00 4.85
825 1032 7.739825 AGAAGATATCATAAACTAAGCAGGCA 58.260 34.615 5.32 0.00 0.00 4.75
826 1033 8.213679 AGAAGATATCATAAACTAAGCAGGCAA 58.786 33.333 5.32 0.00 0.00 4.52
827 1034 8.930846 AAGATATCATAAACTAAGCAGGCAAT 57.069 30.769 5.32 0.00 0.00 3.56
828 1035 8.930846 AGATATCATAAACTAAGCAGGCAATT 57.069 30.769 5.32 0.00 0.00 2.32
829 1036 9.007901 AGATATCATAAACTAAGCAGGCAATTC 57.992 33.333 5.32 0.00 0.00 2.17
830 1037 8.930846 ATATCATAAACTAAGCAGGCAATTCT 57.069 30.769 0.00 0.00 0.00 2.40
831 1038 6.683974 TCATAAACTAAGCAGGCAATTCTC 57.316 37.500 0.00 0.00 0.00 2.87
832 1039 6.418101 TCATAAACTAAGCAGGCAATTCTCT 58.582 36.000 0.00 0.00 0.00 3.10
833 1040 7.564793 TCATAAACTAAGCAGGCAATTCTCTA 58.435 34.615 0.00 0.00 0.00 2.43
834 1041 7.495934 TCATAAACTAAGCAGGCAATTCTCTAC 59.504 37.037 0.00 0.00 0.00 2.59
835 1042 5.428184 AACTAAGCAGGCAATTCTCTACT 57.572 39.130 0.00 0.00 0.00 2.57
836 1043 4.764172 ACTAAGCAGGCAATTCTCTACTG 58.236 43.478 0.00 0.00 0.00 2.74
843 1050 6.690194 CAGGCAATTCTCTACTGCTTAATT 57.310 37.500 0.00 0.00 36.32 1.40
844 1051 7.792374 CAGGCAATTCTCTACTGCTTAATTA 57.208 36.000 0.00 0.00 36.32 1.40
845 1052 8.213518 CAGGCAATTCTCTACTGCTTAATTAA 57.786 34.615 0.00 0.00 36.32 1.40
846 1053 8.844244 CAGGCAATTCTCTACTGCTTAATTAAT 58.156 33.333 0.00 0.00 36.32 1.40
847 1054 9.061435 AGGCAATTCTCTACTGCTTAATTAATC 57.939 33.333 0.00 0.00 36.32 1.75
848 1055 8.012241 GGCAATTCTCTACTGCTTAATTAATCG 58.988 37.037 0.00 0.00 36.32 3.34
849 1056 8.765219 GCAATTCTCTACTGCTTAATTAATCGA 58.235 33.333 0.00 0.00 33.20 3.59
853 1060 9.684448 TTCTCTACTGCTTAATTAATCGATGAG 57.316 33.333 0.00 0.00 0.00 2.90
854 1061 8.300286 TCTCTACTGCTTAATTAATCGATGAGG 58.700 37.037 0.00 0.00 0.00 3.86
855 1062 7.952671 TCTACTGCTTAATTAATCGATGAGGT 58.047 34.615 0.00 0.00 0.00 3.85
856 1063 8.421784 TCTACTGCTTAATTAATCGATGAGGTT 58.578 33.333 0.00 0.00 0.00 3.50
857 1064 9.692749 CTACTGCTTAATTAATCGATGAGGTTA 57.307 33.333 0.00 0.00 0.00 2.85
858 1065 8.958119 ACTGCTTAATTAATCGATGAGGTTAA 57.042 30.769 0.00 0.88 39.50 2.01
859 1066 9.391006 ACTGCTTAATTAATCGATGAGGTTAAA 57.609 29.630 0.00 0.00 38.74 1.52
861 1068 9.997482 TGCTTAATTAATCGATGAGGTTAAAAC 57.003 29.630 0.00 0.00 38.74 2.43
875 1082 4.751600 AGGTTAAAACTTACCTCCGTTTCG 59.248 41.667 0.00 0.00 40.78 3.46
876 1083 4.749598 GGTTAAAACTTACCTCCGTTTCGA 59.250 41.667 0.00 0.00 32.60 3.71
877 1084 5.333339 GGTTAAAACTTACCTCCGTTTCGAC 60.333 44.000 0.00 0.00 32.60 4.20
878 1085 3.457610 AAACTTACCTCCGTTTCGACA 57.542 42.857 0.00 0.00 0.00 4.35
879 1086 3.457610 AACTTACCTCCGTTTCGACAA 57.542 42.857 0.00 0.00 0.00 3.18
880 1087 3.457610 ACTTACCTCCGTTTCGACAAA 57.542 42.857 0.00 0.00 0.00 2.83
881 1088 3.126073 ACTTACCTCCGTTTCGACAAAC 58.874 45.455 0.00 0.00 38.91 2.93
882 1089 3.181472 ACTTACCTCCGTTTCGACAAACT 60.181 43.478 0.00 0.00 39.97 2.66
883 1090 4.037923 ACTTACCTCCGTTTCGACAAACTA 59.962 41.667 0.00 0.00 39.97 2.24
887 1094 3.556775 CCTCCGTTTCGACAAACTAAACA 59.443 43.478 0.00 0.00 39.97 2.83
893 1100 5.949787 CGTTTCGACAAACTAAACATATCGG 59.050 40.000 0.00 0.00 39.97 4.18
899 1106 7.042992 TCGACAAACTAAACATATCGGCAATAG 60.043 37.037 0.00 0.00 0.00 1.73
908 1115 8.539770 AAACATATCGGCAATAGTTATCTCTG 57.460 34.615 0.00 0.00 0.00 3.35
911 1118 5.808366 ATCGGCAATAGTTATCTCTGGAA 57.192 39.130 0.00 0.00 0.00 3.53
912 1119 5.201713 TCGGCAATAGTTATCTCTGGAAG 57.798 43.478 0.00 0.00 0.00 3.46
913 1120 3.743396 CGGCAATAGTTATCTCTGGAAGC 59.257 47.826 0.00 0.00 0.00 3.86
934 1141 2.662156 CACGAAGCTACGAGGAAGTTTC 59.338 50.000 0.00 0.00 37.03 2.78
936 1143 3.172824 CGAAGCTACGAGGAAGTTTCTC 58.827 50.000 0.46 0.46 33.49 2.87
947 1154 6.986904 GAGGAAGTTTCTCGGAAACAATAT 57.013 37.500 22.86 11.69 32.81 1.28
949 1156 8.664211 GAGGAAGTTTCTCGGAAACAATATAT 57.336 34.615 22.86 9.98 32.81 0.86
950 1157 9.110502 GAGGAAGTTTCTCGGAAACAATATATT 57.889 33.333 22.86 12.43 32.81 1.28
951 1158 9.110502 AGGAAGTTTCTCGGAAACAATATATTC 57.889 33.333 22.86 17.44 32.81 1.75
952 1159 8.889717 GGAAGTTTCTCGGAAACAATATATTCA 58.110 33.333 22.86 0.00 32.81 2.57
953 1160 9.922305 GAAGTTTCTCGGAAACAATATATTCAG 57.078 33.333 22.86 0.00 32.81 3.02
954 1161 8.438676 AGTTTCTCGGAAACAATATATTCAGG 57.561 34.615 22.86 0.00 32.81 3.86
955 1162 7.499232 AGTTTCTCGGAAACAATATATTCAGGG 59.501 37.037 22.86 0.00 32.81 4.45
956 1163 5.865085 TCTCGGAAACAATATATTCAGGGG 58.135 41.667 0.00 0.00 0.00 4.79
983 1190 0.815734 TCGACCGGAGAAATCAGGAC 59.184 55.000 9.46 0.00 0.00 3.85
984 1191 0.525668 CGACCGGAGAAATCAGGACG 60.526 60.000 9.46 3.46 35.91 4.79
997 1204 1.558294 TCAGGACGGAGCAGTAGACTA 59.442 52.381 0.00 0.00 0.00 2.59
1002 1212 3.003897 GGACGGAGCAGTAGACTAAGATG 59.996 52.174 0.00 0.00 0.00 2.90
1011 1221 6.661377 AGCAGTAGACTAAGATGTCTGAAGAA 59.339 38.462 7.34 0.00 45.70 2.52
1012 1222 6.972328 GCAGTAGACTAAGATGTCTGAAGAAG 59.028 42.308 7.34 0.00 45.70 2.85
1013 1223 7.148154 GCAGTAGACTAAGATGTCTGAAGAAGA 60.148 40.741 7.34 0.00 45.70 2.87
1014 1224 8.397906 CAGTAGACTAAGATGTCTGAAGAAGAG 58.602 40.741 7.34 0.00 45.70 2.85
1015 1225 6.773976 AGACTAAGATGTCTGAAGAAGAGG 57.226 41.667 0.00 0.00 44.64 3.69
1016 1226 5.127031 AGACTAAGATGTCTGAAGAAGAGGC 59.873 44.000 0.00 0.00 44.64 4.70
1017 1227 5.022787 ACTAAGATGTCTGAAGAAGAGGCT 58.977 41.667 0.00 0.00 34.84 4.58
1018 1228 6.191315 ACTAAGATGTCTGAAGAAGAGGCTA 58.809 40.000 0.00 0.00 34.84 3.93
1019 1229 6.665680 ACTAAGATGTCTGAAGAAGAGGCTAA 59.334 38.462 0.00 0.00 34.84 3.09
1020 1230 5.596836 AGATGTCTGAAGAAGAGGCTAAG 57.403 43.478 0.00 0.00 34.84 2.18
1021 1231 3.601443 TGTCTGAAGAAGAGGCTAAGC 57.399 47.619 0.00 0.00 34.84 3.09
1022 1232 3.169099 TGTCTGAAGAAGAGGCTAAGCT 58.831 45.455 0.00 0.00 34.84 3.74
1023 1233 3.194542 TGTCTGAAGAAGAGGCTAAGCTC 59.805 47.826 0.00 0.00 34.84 4.09
1024 1234 3.194542 GTCTGAAGAAGAGGCTAAGCTCA 59.805 47.826 0.00 0.00 34.84 4.26
1025 1235 4.029520 TCTGAAGAAGAGGCTAAGCTCAT 58.970 43.478 0.00 0.00 0.00 2.90
1026 1236 4.099266 TCTGAAGAAGAGGCTAAGCTCATC 59.901 45.833 0.00 0.00 0.00 2.92
1027 1237 3.181482 TGAAGAAGAGGCTAAGCTCATCG 60.181 47.826 0.00 0.00 0.00 3.84
1028 1238 1.686052 AGAAGAGGCTAAGCTCATCGG 59.314 52.381 0.00 0.00 0.00 4.18
1029 1239 0.755686 AAGAGGCTAAGCTCATCGGG 59.244 55.000 0.00 0.00 0.00 5.14
1030 1240 0.397816 AGAGGCTAAGCTCATCGGGT 60.398 55.000 0.00 0.00 0.00 5.28
1031 1241 0.032815 GAGGCTAAGCTCATCGGGTC 59.967 60.000 0.00 0.00 0.00 4.46
1038 1248 2.107141 CTCATCGGGTCCTTCGGC 59.893 66.667 0.00 0.00 0.00 5.54
1331 1548 4.657824 CGACGACAAGTGCGGGGT 62.658 66.667 0.00 0.00 0.00 4.95
1397 1617 4.856607 GGCGAGGGAGACGAAGCG 62.857 72.222 0.00 0.00 0.00 4.68
1405 1625 1.585006 GAGACGAAGCGGAACCTGA 59.415 57.895 0.00 0.00 0.00 3.86
1697 1924 1.349627 CAATGGCGCGCAAGTAGAG 59.650 57.895 34.42 5.20 41.68 2.43
2080 2307 1.592131 GCTCTGCTCTGCTGATCCG 60.592 63.158 0.00 0.00 36.06 4.18
2084 2311 1.144565 CTGCTCTGCTGATCCGTTCG 61.145 60.000 0.00 0.00 0.00 3.95
2119 2376 2.094286 CGGATTGTTGGCAGGCAAATAA 60.094 45.455 11.69 10.24 0.00 1.40
2120 2377 3.616076 CGGATTGTTGGCAGGCAAATAAA 60.616 43.478 11.69 7.05 0.00 1.40
2127 2384 4.840716 TGGCAGGCAAATAAATGGATTT 57.159 36.364 0.00 0.00 0.00 2.17
2139 2396 3.866883 AATGGATTTGTTAAGGTGGCG 57.133 42.857 0.00 0.00 0.00 5.69
2146 2403 0.319211 TGTTAAGGTGGCGTCTCGTG 60.319 55.000 0.00 0.00 0.00 4.35
2181 2438 4.677378 TGAAATTTCGCACACCATTAAACG 59.323 37.500 13.34 0.00 0.00 3.60
2206 2463 5.024768 TGTCAAATTACAACACGGAATCG 57.975 39.130 0.00 0.00 43.02 3.34
2207 2464 3.844099 GTCAAATTACAACACGGAATCGC 59.156 43.478 0.00 0.00 40.63 4.58
2208 2465 3.498777 TCAAATTACAACACGGAATCGCA 59.501 39.130 0.00 0.00 40.63 5.10
2215 2472 0.312729 ACACGGAATCGCAAAAACCC 59.687 50.000 0.00 0.00 40.63 4.11
2216 2473 0.312416 CACGGAATCGCAAAAACCCA 59.688 50.000 0.00 0.00 40.63 4.51
2225 2482 2.072298 CGCAAAAACCCAGAGAGAGAG 58.928 52.381 0.00 0.00 0.00 3.20
2256 2513 1.135315 CGCATGTCCAGGAACATTTGG 60.135 52.381 0.00 0.00 37.78 3.28
2261 2518 4.286297 TGTCCAGGAACATTTGGTAGAG 57.714 45.455 0.00 0.00 35.89 2.43
2277 2534 6.121776 TGGTAGAGAACTCCATTAAAGCAA 57.878 37.500 0.00 0.00 0.00 3.91
2375 2632 0.603707 CAAAGAAGAGGACTGCCGCA 60.604 55.000 0.00 0.00 39.96 5.69
2391 2648 1.243342 CGCAGGAAAGGCCATTGTCA 61.243 55.000 5.01 0.00 40.02 3.58
2403 2660 1.541147 CCATTGTCATTGTGGCTCGTT 59.459 47.619 0.00 0.00 0.00 3.85
2418 2675 1.759445 CTCGTTGACTGGGGATCATCT 59.241 52.381 0.00 0.00 0.00 2.90
2426 2683 1.369321 GGGGATCATCTCCGTGCTC 59.631 63.158 0.00 0.00 46.01 4.26
2429 2686 0.755686 GGATCATCTCCGTGCTCCTT 59.244 55.000 0.00 0.00 32.86 3.36
2441 2698 0.555769 TGCTCCTTGAAACCCAGGTT 59.444 50.000 0.00 0.00 40.45 3.50
2442 2699 1.777878 TGCTCCTTGAAACCCAGGTTA 59.222 47.619 1.71 0.00 37.35 2.85
2444 2701 2.437413 CTCCTTGAAACCCAGGTTAGC 58.563 52.381 1.71 0.00 37.35 3.09
2445 2702 1.074889 TCCTTGAAACCCAGGTTAGCC 59.925 52.381 1.71 0.00 37.35 3.93
2451 2708 2.137177 AACCCAGGTTAGCCGCATGT 62.137 55.000 0.00 0.00 40.50 3.21
2465 2731 1.268589 CGCATGTCGTCGAGGTAGAAT 60.269 52.381 4.85 0.00 0.00 2.40
2466 2732 2.120232 GCATGTCGTCGAGGTAGAATG 58.880 52.381 4.85 6.41 0.00 2.67
2468 2734 1.460504 TGTCGTCGAGGTAGAATGCT 58.539 50.000 4.85 0.00 0.00 3.79
2472 2738 3.059461 GTCGTCGAGGTAGAATGCTAGAG 60.059 52.174 4.85 0.00 0.00 2.43
2531 3060 2.082140 ACCTTCCCCCAAACAAAGAC 57.918 50.000 0.00 0.00 0.00 3.01
2553 3082 3.726607 GACACCACATGAGATGAGATCC 58.273 50.000 0.00 0.00 0.00 3.36
2615 3144 5.174037 AGGAAACGATGGAATAAGGTTCA 57.826 39.130 0.00 0.00 33.90 3.18
2620 3149 4.843728 ACGATGGAATAAGGTTCACACAT 58.156 39.130 0.00 0.00 0.00 3.21
2622 3151 5.815740 ACGATGGAATAAGGTTCACACATAC 59.184 40.000 0.00 0.00 0.00 2.39
2639 3168 1.946984 TACCCCTCGATTTCACCACT 58.053 50.000 0.00 0.00 0.00 4.00
2642 3171 1.003118 CCCCTCGATTTCACCACTGAA 59.997 52.381 0.00 0.00 34.39 3.02
2667 3197 0.460987 CGTGAGATGGGGTTGAGCTC 60.461 60.000 6.82 6.82 0.00 4.09
2669 3199 0.614697 TGAGATGGGGTTGAGCTCGA 60.615 55.000 9.64 3.88 0.00 4.04
2678 3208 3.119814 GGGGTTGAGCTCGAGAAATTTTC 60.120 47.826 18.75 0.66 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 2.483877 CAGCAGATACGAAACCAAAGCA 59.516 45.455 0.00 0.00 0.00 3.91
166 347 1.382420 ACACCTTTGCCTTTGCCCA 60.382 52.632 0.00 0.00 36.33 5.36
238 429 1.678101 AGCACACCACTGCTTTTCTTC 59.322 47.619 0.00 0.00 45.64 2.87
271 462 1.242076 GACAAGCAGTGAGGCAACAT 58.758 50.000 0.00 0.00 41.41 2.71
298 489 5.419788 ACAGGCATCAAAATTCTGAAGCATA 59.580 36.000 10.82 0.00 40.86 3.14
313 508 1.761784 AGCAACCAAAAACAGGCATCA 59.238 42.857 0.00 0.00 0.00 3.07
345 540 6.348786 CCACTGACAAGGACATTTATTCACAG 60.349 42.308 0.00 0.00 0.00 3.66
400 595 5.183904 TCCAAATCCTTTTTAAGCTGAGCTC 59.816 40.000 7.72 6.82 38.25 4.09
417 612 3.001736 GCAGCTAGTGATCGTTCCAAATC 59.998 47.826 0.00 0.00 0.00 2.17
441 640 1.421268 AGTGACACCACCATGACACAT 59.579 47.619 0.84 0.00 44.42 3.21
467 666 1.267806 GGTGTTGTGCATCCTTCAGTG 59.732 52.381 0.00 0.00 0.00 3.66
468 667 1.133823 TGGTGTTGTGCATCCTTCAGT 60.134 47.619 0.00 0.00 0.00 3.41
469 668 1.267806 GTGGTGTTGTGCATCCTTCAG 59.732 52.381 0.00 0.00 0.00 3.02
470 669 1.133823 AGTGGTGTTGTGCATCCTTCA 60.134 47.619 0.00 0.00 0.00 3.02
471 670 1.537202 GAGTGGTGTTGTGCATCCTTC 59.463 52.381 0.00 0.00 0.00 3.46
472 671 1.609208 GAGTGGTGTTGTGCATCCTT 58.391 50.000 0.00 0.00 0.00 3.36
473 672 0.250901 GGAGTGGTGTTGTGCATCCT 60.251 55.000 0.00 0.00 0.00 3.24
474 673 0.537143 TGGAGTGGTGTTGTGCATCC 60.537 55.000 0.00 0.00 0.00 3.51
475 674 1.200716 CATGGAGTGGTGTTGTGCATC 59.799 52.381 0.00 0.00 0.00 3.91
476 675 1.250328 CATGGAGTGGTGTTGTGCAT 58.750 50.000 0.00 0.00 0.00 3.96
477 676 0.822944 CCATGGAGTGGTGTTGTGCA 60.823 55.000 5.56 0.00 43.44 4.57
478 677 1.959085 CCATGGAGTGGTGTTGTGC 59.041 57.895 5.56 0.00 43.44 4.57
508 709 3.273084 AGATCCCAATTTCCCTGGACAAT 59.727 43.478 0.00 0.00 35.85 2.71
511 713 3.388552 AAGATCCCAATTTCCCTGGAC 57.611 47.619 0.00 0.00 35.85 4.02
536 738 6.268566 GTGCATTTTAGTCCAGGAATTGATC 58.731 40.000 0.00 0.00 0.00 2.92
537 739 5.127682 GGTGCATTTTAGTCCAGGAATTGAT 59.872 40.000 0.00 0.00 0.00 2.57
547 749 4.072131 TGAGACAAGGTGCATTTTAGTCC 58.928 43.478 0.00 0.00 0.00 3.85
554 756 2.165167 CCATGTGAGACAAGGTGCATT 58.835 47.619 0.00 0.00 32.64 3.56
566 768 3.390135 ACACTCGTTACAACCATGTGAG 58.610 45.455 11.24 4.13 40.84 3.51
568 770 3.678072 CCTACACTCGTTACAACCATGTG 59.322 47.826 0.00 0.00 40.84 3.21
601 804 1.547901 GGTCAAAACAAGAGGGGAGGG 60.548 57.143 0.00 0.00 0.00 4.30
605 808 2.959465 AGAGGTCAAAACAAGAGGGG 57.041 50.000 0.00 0.00 0.00 4.79
630 833 4.195416 CCTCTCCAACCAAGCTTTAGATC 58.805 47.826 0.00 0.00 0.00 2.75
635 838 0.480252 AGCCTCTCCAACCAAGCTTT 59.520 50.000 0.00 0.00 0.00 3.51
664 868 7.335673 ACAATTTTTGGTACTTCTTGTTTTGGG 59.664 33.333 0.00 0.00 34.12 4.12
673 877 7.287810 AGTGAGGTACAATTTTTGGTACTTCT 58.712 34.615 13.51 1.92 43.20 2.85
680 884 7.484975 TGTGTTTAGTGAGGTACAATTTTTGG 58.515 34.615 0.00 0.00 34.12 3.28
709 913 7.386299 GCGATTGTTACCTAGCTAGTAGTAGTA 59.614 40.741 19.31 10.72 0.00 1.82
710 914 6.204495 GCGATTGTTACCTAGCTAGTAGTAGT 59.796 42.308 19.31 11.67 0.00 2.73
711 915 6.427547 AGCGATTGTTACCTAGCTAGTAGTAG 59.572 42.308 19.31 6.23 32.73 2.57
717 921 4.683832 ACAAGCGATTGTTACCTAGCTAG 58.316 43.478 14.32 14.20 34.24 3.42
733 937 8.667987 TTTCAGCTATAAACAAATAACAAGCG 57.332 30.769 0.00 0.00 34.01 4.68
750 954 5.187186 ACCGGAAGTCTTAATCTTTCAGCTA 59.813 40.000 9.46 0.00 0.00 3.32
756 960 5.393896 CGACCTACCGGAAGTCTTAATCTTT 60.394 44.000 9.46 0.00 0.00 2.52
757 961 4.097589 CGACCTACCGGAAGTCTTAATCTT 59.902 45.833 9.46 0.00 0.00 2.40
758 962 3.631227 CGACCTACCGGAAGTCTTAATCT 59.369 47.826 9.46 0.00 0.00 2.40
769 976 0.896940 ACTGAAAGCGACCTACCGGA 60.897 55.000 9.46 0.00 37.60 5.14
788 995 2.454336 TATCTTCTCTTCTCCCGCCA 57.546 50.000 0.00 0.00 0.00 5.69
799 1006 7.875041 TGCCTGCTTAGTTTATGATATCTTCTC 59.125 37.037 3.98 0.00 0.00 2.87
801 1008 7.969536 TGCCTGCTTAGTTTATGATATCTTC 57.030 36.000 3.98 0.00 0.00 2.87
803 1010 8.930846 AATTGCCTGCTTAGTTTATGATATCT 57.069 30.769 3.98 0.00 0.00 1.98
804 1011 9.007901 AGAATTGCCTGCTTAGTTTATGATATC 57.992 33.333 0.00 0.00 0.00 1.63
806 1013 8.213679 AGAGAATTGCCTGCTTAGTTTATGATA 58.786 33.333 0.00 0.00 0.00 2.15
807 1014 7.059156 AGAGAATTGCCTGCTTAGTTTATGAT 58.941 34.615 0.00 0.00 0.00 2.45
809 1016 6.690194 AGAGAATTGCCTGCTTAGTTTATG 57.310 37.500 0.00 0.00 0.00 1.90
810 1017 7.497249 CAGTAGAGAATTGCCTGCTTAGTTTAT 59.503 37.037 0.00 0.00 0.00 1.40
811 1018 6.818644 CAGTAGAGAATTGCCTGCTTAGTTTA 59.181 38.462 0.00 0.00 0.00 2.01
812 1019 5.645497 CAGTAGAGAATTGCCTGCTTAGTTT 59.355 40.000 0.00 0.00 0.00 2.66
813 1020 5.181748 CAGTAGAGAATTGCCTGCTTAGTT 58.818 41.667 0.00 0.00 0.00 2.24
815 1022 3.559242 GCAGTAGAGAATTGCCTGCTTAG 59.441 47.826 0.00 0.00 43.89 2.18
816 1023 3.535561 GCAGTAGAGAATTGCCTGCTTA 58.464 45.455 0.00 0.00 43.89 3.09
817 1024 2.363683 GCAGTAGAGAATTGCCTGCTT 58.636 47.619 0.00 0.00 43.89 3.91
818 1025 2.035530 GCAGTAGAGAATTGCCTGCT 57.964 50.000 0.00 0.00 43.89 4.24
819 1026 2.035530 AGCAGTAGAGAATTGCCTGC 57.964 50.000 0.00 0.00 46.78 4.85
820 1027 6.690194 AATTAAGCAGTAGAGAATTGCCTG 57.310 37.500 0.00 0.00 38.58 4.85
821 1028 8.986929 ATTAATTAAGCAGTAGAGAATTGCCT 57.013 30.769 3.94 0.00 38.58 4.75
822 1029 8.012241 CGATTAATTAAGCAGTAGAGAATTGCC 58.988 37.037 13.48 0.00 38.58 4.52
823 1030 8.765219 TCGATTAATTAAGCAGTAGAGAATTGC 58.235 33.333 13.48 0.00 38.09 3.56
827 1034 9.684448 CTCATCGATTAATTAAGCAGTAGAGAA 57.316 33.333 13.48 0.00 0.00 2.87
828 1035 8.300286 CCTCATCGATTAATTAAGCAGTAGAGA 58.700 37.037 13.48 2.24 0.00 3.10
829 1036 8.085296 ACCTCATCGATTAATTAAGCAGTAGAG 58.915 37.037 13.48 12.52 0.00 2.43
830 1037 7.952671 ACCTCATCGATTAATTAAGCAGTAGA 58.047 34.615 13.48 3.23 0.00 2.59
831 1038 8.594881 AACCTCATCGATTAATTAAGCAGTAG 57.405 34.615 13.48 5.09 0.00 2.57
833 1040 8.958119 TTAACCTCATCGATTAATTAAGCAGT 57.042 30.769 13.48 0.00 0.00 4.40
835 1042 9.997482 GTTTTAACCTCATCGATTAATTAAGCA 57.003 29.630 13.48 1.88 0.00 3.91
841 1048 9.901172 AGGTAAGTTTTAACCTCATCGATTAAT 57.099 29.630 0.00 0.00 42.60 1.40
853 1060 4.749598 TCGAAACGGAGGTAAGTTTTAACC 59.250 41.667 0.00 0.00 40.24 2.85
854 1061 5.234116 TGTCGAAACGGAGGTAAGTTTTAAC 59.766 40.000 0.00 0.00 40.24 2.01
855 1062 5.355596 TGTCGAAACGGAGGTAAGTTTTAA 58.644 37.500 0.00 0.00 40.24 1.52
856 1063 4.942852 TGTCGAAACGGAGGTAAGTTTTA 58.057 39.130 0.00 0.00 40.24 1.52
857 1064 3.795877 TGTCGAAACGGAGGTAAGTTTT 58.204 40.909 0.00 0.00 40.24 2.43
858 1065 3.457610 TGTCGAAACGGAGGTAAGTTT 57.542 42.857 0.00 0.00 42.50 2.66
859 1066 3.457610 TTGTCGAAACGGAGGTAAGTT 57.542 42.857 0.00 0.00 0.00 2.66
860 1067 3.126073 GTTTGTCGAAACGGAGGTAAGT 58.874 45.455 0.00 0.00 32.49 2.24
861 1068 3.387397 AGTTTGTCGAAACGGAGGTAAG 58.613 45.455 0.00 0.00 45.34 2.34
862 1069 3.457610 AGTTTGTCGAAACGGAGGTAA 57.542 42.857 0.00 0.00 45.34 2.85
863 1070 4.582701 TTAGTTTGTCGAAACGGAGGTA 57.417 40.909 0.00 0.00 45.34 3.08
864 1071 3.457610 TTAGTTTGTCGAAACGGAGGT 57.542 42.857 0.00 0.00 45.34 3.85
865 1072 3.556775 TGTTTAGTTTGTCGAAACGGAGG 59.443 43.478 0.00 0.00 45.34 4.30
866 1073 4.782252 TGTTTAGTTTGTCGAAACGGAG 57.218 40.909 0.00 0.00 45.34 4.63
867 1074 6.183360 CGATATGTTTAGTTTGTCGAAACGGA 60.183 38.462 0.00 0.00 45.34 4.69
868 1075 5.949787 CGATATGTTTAGTTTGTCGAAACGG 59.050 40.000 0.00 0.00 45.34 4.44
869 1076 5.949787 CCGATATGTTTAGTTTGTCGAAACG 59.050 40.000 0.00 0.00 45.34 3.60
870 1077 5.731263 GCCGATATGTTTAGTTTGTCGAAAC 59.269 40.000 0.00 0.00 41.69 2.78
871 1078 5.408909 TGCCGATATGTTTAGTTTGTCGAAA 59.591 36.000 0.00 0.00 0.00 3.46
872 1079 4.930405 TGCCGATATGTTTAGTTTGTCGAA 59.070 37.500 0.00 0.00 0.00 3.71
873 1080 4.496360 TGCCGATATGTTTAGTTTGTCGA 58.504 39.130 0.00 0.00 0.00 4.20
874 1081 4.850859 TGCCGATATGTTTAGTTTGTCG 57.149 40.909 0.00 0.00 0.00 4.35
875 1082 7.916552 ACTATTGCCGATATGTTTAGTTTGTC 58.083 34.615 0.00 0.00 0.00 3.18
876 1083 7.859325 ACTATTGCCGATATGTTTAGTTTGT 57.141 32.000 0.00 0.00 0.00 2.83
879 1086 9.998106 AGATAACTATTGCCGATATGTTTAGTT 57.002 29.630 0.00 0.00 34.06 2.24
880 1087 9.640963 GAGATAACTATTGCCGATATGTTTAGT 57.359 33.333 0.00 0.00 0.00 2.24
881 1088 9.862371 AGAGATAACTATTGCCGATATGTTTAG 57.138 33.333 0.00 0.00 0.00 1.85
882 1089 9.639601 CAGAGATAACTATTGCCGATATGTTTA 57.360 33.333 0.00 0.00 0.00 2.01
883 1090 7.604164 CCAGAGATAACTATTGCCGATATGTTT 59.396 37.037 0.00 0.00 0.00 2.83
887 1094 7.482169 TTCCAGAGATAACTATTGCCGATAT 57.518 36.000 0.00 0.00 0.00 1.63
893 1100 4.210120 CGTGCTTCCAGAGATAACTATTGC 59.790 45.833 0.00 0.00 0.00 3.56
899 1106 2.605366 GCTTCGTGCTTCCAGAGATAAC 59.395 50.000 0.00 0.00 38.95 1.89
912 1119 0.109226 ACTTCCTCGTAGCTTCGTGC 60.109 55.000 12.66 0.00 43.29 5.34
913 1120 2.349297 AACTTCCTCGTAGCTTCGTG 57.651 50.000 12.66 10.05 0.00 4.35
934 1141 5.003804 CCCCCTGAATATATTGTTTCCGAG 58.996 45.833 1.78 0.00 0.00 4.63
936 1143 4.725490 ACCCCCTGAATATATTGTTTCCG 58.275 43.478 1.78 0.00 0.00 4.30
938 1145 5.701224 TGGACCCCCTGAATATATTGTTTC 58.299 41.667 1.78 0.00 0.00 2.78
942 1149 5.316987 GAGTTGGACCCCCTGAATATATTG 58.683 45.833 1.78 0.00 0.00 1.90
944 1151 3.583086 CGAGTTGGACCCCCTGAATATAT 59.417 47.826 0.00 0.00 0.00 0.86
945 1152 2.969950 CGAGTTGGACCCCCTGAATATA 59.030 50.000 0.00 0.00 0.00 0.86
946 1153 1.768870 CGAGTTGGACCCCCTGAATAT 59.231 52.381 0.00 0.00 0.00 1.28
947 1154 1.200519 CGAGTTGGACCCCCTGAATA 58.799 55.000 0.00 0.00 0.00 1.75
948 1155 0.546747 TCGAGTTGGACCCCCTGAAT 60.547 55.000 0.00 0.00 0.00 2.57
949 1156 1.152204 TCGAGTTGGACCCCCTGAA 60.152 57.895 0.00 0.00 0.00 3.02
950 1157 1.911766 GTCGAGTTGGACCCCCTGA 60.912 63.158 0.00 0.00 0.00 3.86
951 1158 2.663196 GTCGAGTTGGACCCCCTG 59.337 66.667 0.00 0.00 0.00 4.45
983 1190 3.880490 AGACATCTTAGTCTACTGCTCCG 59.120 47.826 0.00 0.00 46.52 4.63
984 1191 4.884744 TCAGACATCTTAGTCTACTGCTCC 59.115 45.833 0.00 0.00 46.65 4.70
997 1204 5.626578 GCTTAGCCTCTTCTTCAGACATCTT 60.627 44.000 0.00 0.00 0.00 2.40
1002 1212 3.194542 TGAGCTTAGCCTCTTCTTCAGAC 59.805 47.826 0.00 0.00 33.02 3.51
1011 1221 0.397816 ACCCGATGAGCTTAGCCTCT 60.398 55.000 0.00 0.00 33.02 3.69
1012 1222 0.032815 GACCCGATGAGCTTAGCCTC 59.967 60.000 0.00 0.00 0.00 4.70
1013 1223 1.403687 GGACCCGATGAGCTTAGCCT 61.404 60.000 0.00 0.00 0.00 4.58
1014 1224 1.069935 GGACCCGATGAGCTTAGCC 59.930 63.158 0.00 0.00 0.00 3.93
1015 1225 0.466124 AAGGACCCGATGAGCTTAGC 59.534 55.000 0.00 0.00 0.00 3.09
1016 1226 1.269309 CGAAGGACCCGATGAGCTTAG 60.269 57.143 0.00 0.00 0.00 2.18
1017 1227 0.744874 CGAAGGACCCGATGAGCTTA 59.255 55.000 0.00 0.00 0.00 3.09
1018 1228 1.517832 CGAAGGACCCGATGAGCTT 59.482 57.895 0.00 0.00 0.00 3.74
1019 1229 3.211288 CGAAGGACCCGATGAGCT 58.789 61.111 0.00 0.00 0.00 4.09
1136 1347 3.637273 GGACGGGGTTGTGCTCCT 61.637 66.667 0.00 0.00 34.84 3.69
1378 1598 4.856607 CTTCGTCTCCCTCGCCGC 62.857 72.222 0.00 0.00 0.00 6.53
1379 1599 4.856607 GCTTCGTCTCCCTCGCCG 62.857 72.222 0.00 0.00 0.00 6.46
1380 1600 4.856607 CGCTTCGTCTCCCTCGCC 62.857 72.222 0.00 0.00 0.00 5.54
1382 1602 2.697761 TTCCGCTTCGTCTCCCTCG 61.698 63.158 0.00 0.00 0.00 4.63
1384 1604 2.647158 GGTTCCGCTTCGTCTCCCT 61.647 63.158 0.00 0.00 0.00 4.20
1385 1605 2.125633 GGTTCCGCTTCGTCTCCC 60.126 66.667 0.00 0.00 0.00 4.30
1390 1610 2.049433 CGTCAGGTTCCGCTTCGT 60.049 61.111 0.00 0.00 0.00 3.85
1397 1617 2.232298 CTCCAGGAGCGTCAGGTTCC 62.232 65.000 2.60 0.00 45.78 3.62
1530 1750 2.363018 TCCTCCTCGGTGAGCAGG 60.363 66.667 0.00 0.00 38.89 4.85
1644 1870 1.541310 CGTACCTGTCCTTCCTGGCA 61.541 60.000 0.00 0.00 35.26 4.92
1688 1915 2.793790 CAGCATGATCGTCTCTACTTGC 59.206 50.000 0.00 0.00 39.69 4.01
2058 2285 1.900545 ATCAGCAGAGCAGAGCAGCA 61.901 55.000 0.00 0.00 36.85 4.41
2059 2286 1.153329 ATCAGCAGAGCAGAGCAGC 60.153 57.895 0.00 0.00 0.00 5.25
2060 2287 0.531090 GGATCAGCAGAGCAGAGCAG 60.531 60.000 0.00 0.00 32.31 4.24
2061 2288 1.521141 GGATCAGCAGAGCAGAGCA 59.479 57.895 0.00 0.00 32.31 4.26
2062 2289 1.592131 CGGATCAGCAGAGCAGAGC 60.592 63.158 0.00 0.00 29.96 4.09
2063 2290 0.175302 AACGGATCAGCAGAGCAGAG 59.825 55.000 0.96 0.00 0.00 3.35
2064 2291 0.174389 GAACGGATCAGCAGAGCAGA 59.826 55.000 0.96 0.00 0.00 4.26
2065 2292 1.144565 CGAACGGATCAGCAGAGCAG 61.145 60.000 0.00 0.00 0.00 4.24
2066 2293 1.153765 CGAACGGATCAGCAGAGCA 60.154 57.895 0.00 0.00 0.00 4.26
2067 2294 0.737715 AACGAACGGATCAGCAGAGC 60.738 55.000 0.00 0.00 0.00 4.09
2068 2295 1.391485 CAAACGAACGGATCAGCAGAG 59.609 52.381 0.00 0.00 0.00 3.35
2073 2300 1.359848 CCTCCAAACGAACGGATCAG 58.640 55.000 0.00 0.00 0.00 2.90
2080 2307 3.733960 GCCGGCCTCCAAACGAAC 61.734 66.667 18.11 0.00 0.00 3.95
2103 2360 2.902486 TCCATTTATTTGCCTGCCAACA 59.098 40.909 0.00 0.00 31.97 3.33
2119 2376 3.161866 ACGCCACCTTAACAAATCCATT 58.838 40.909 0.00 0.00 0.00 3.16
2120 2377 2.752903 GACGCCACCTTAACAAATCCAT 59.247 45.455 0.00 0.00 0.00 3.41
2127 2384 0.319211 CACGAGACGCCACCTTAACA 60.319 55.000 0.00 0.00 0.00 2.41
2156 2413 6.291849 CGTTTAATGGTGTGCGAAATTTCAAA 60.292 34.615 17.99 2.52 0.00 2.69
2157 2414 5.174035 CGTTTAATGGTGTGCGAAATTTCAA 59.826 36.000 17.99 2.88 0.00 2.69
2158 2415 4.677378 CGTTTAATGGTGTGCGAAATTTCA 59.323 37.500 17.99 0.00 0.00 2.69
2181 2438 6.681178 CGATTCCGTGTTGTAATTTGACATAC 59.319 38.462 0.00 0.00 0.00 2.39
2206 2463 3.007398 TCTCTCTCTCTCTGGGTTTTTGC 59.993 47.826 0.00 0.00 0.00 3.68
2207 2464 4.526262 TCTCTCTCTCTCTCTGGGTTTTTG 59.474 45.833 0.00 0.00 0.00 2.44
2208 2465 4.746466 TCTCTCTCTCTCTCTGGGTTTTT 58.254 43.478 0.00 0.00 0.00 1.94
2215 2472 3.491619 CGTCCTCTCTCTCTCTCTCTCTG 60.492 56.522 0.00 0.00 0.00 3.35
2216 2473 2.695666 CGTCCTCTCTCTCTCTCTCTCT 59.304 54.545 0.00 0.00 0.00 3.10
2225 2482 3.936585 GACATGCGTCCTCTCTCTC 57.063 57.895 0.00 0.00 36.02 3.20
2256 2513 9.561270 GAAATTTGCTTTAATGGAGTTCTCTAC 57.439 33.333 0.00 0.00 0.00 2.59
2261 2518 6.646240 TGCAGAAATTTGCTTTAATGGAGTTC 59.354 34.615 0.00 0.00 44.38 3.01
2277 2534 1.895131 AGGATGGCGTTTGCAGAAATT 59.105 42.857 0.00 0.00 45.35 1.82
2357 2614 0.321122 CTGCGGCAGTCCTCTTCTTT 60.321 55.000 21.60 0.00 0.00 2.52
2375 2632 2.564062 CACAATGACAATGGCCTTTCCT 59.436 45.455 3.32 0.00 35.26 3.36
2388 2645 1.195448 CAGTCAACGAGCCACAATGAC 59.805 52.381 0.00 0.00 40.45 3.06
2391 2648 0.606401 CCCAGTCAACGAGCCACAAT 60.606 55.000 0.00 0.00 0.00 2.71
2399 2656 1.757118 GAGATGATCCCCAGTCAACGA 59.243 52.381 0.00 0.00 0.00 3.85
2403 2660 0.032117 ACGGAGATGATCCCCAGTCA 60.032 55.000 0.00 0.00 46.50 3.41
2418 2675 1.072505 GGGTTTCAAGGAGCACGGA 59.927 57.895 0.00 0.00 0.00 4.69
2426 2683 1.545841 GGCTAACCTGGGTTTCAAGG 58.454 55.000 10.42 0.00 39.31 3.61
2429 2686 1.302993 GCGGCTAACCTGGGTTTCA 60.303 57.895 10.42 0.00 39.31 2.69
2444 2701 1.298413 CTACCTCGACGACATGCGG 60.298 63.158 12.85 0.00 46.49 5.69
2451 2708 3.132160 CTCTAGCATTCTACCTCGACGA 58.868 50.000 0.00 0.00 0.00 4.20
2466 2732 4.840005 GTGGGTGGCGGCTCTAGC 62.840 72.222 11.43 0.00 41.14 3.42
2531 3060 2.947448 TCTCATCTCATGTGGTGTCG 57.053 50.000 7.84 1.77 0.00 4.35
2553 3082 0.527169 TGTTTGTTGTGTGCATGGCG 60.527 50.000 0.00 0.00 0.00 5.69
2615 3144 2.093128 GGTGAAATCGAGGGGTATGTGT 60.093 50.000 0.00 0.00 0.00 3.72
2620 3149 1.553248 CAGTGGTGAAATCGAGGGGTA 59.447 52.381 0.00 0.00 0.00 3.69
2622 3151 0.613260 TCAGTGGTGAAATCGAGGGG 59.387 55.000 0.00 0.00 0.00 4.79
2639 3168 1.482182 CCCCATCTCACGACATCTTCA 59.518 52.381 0.00 0.00 0.00 3.02
2642 3171 1.208052 CAACCCCATCTCACGACATCT 59.792 52.381 0.00 0.00 0.00 2.90
2667 3197 4.089923 GGCGTTTGGAATGAAAATTTCTCG 59.910 41.667 7.29 1.57 0.00 4.04
2669 3199 3.987220 CGGCGTTTGGAATGAAAATTTCT 59.013 39.130 7.29 0.00 0.00 2.52
2678 3208 2.884367 ATGCCGGCGTTTGGAATG 59.116 55.556 23.90 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.