Multiple sequence alignment - TraesCS4A01G151700

Loading Multiple Alignment...

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 TraesCS4A01G151700 chr4A 100.000 2282 0 0 1 2282 308057611 308059892 0.000000e+00 4215
1 TraesCS4A01G151700 chr6D 93.216 1076 65 3 1208 2282 366440304 366441372 0.000000e+00 1576
2 TraesCS4A01G151700 chr6D 92.653 980 65 4 3 976 83626450 83627428 0.000000e+00 1404
3 TraesCS4A01G151700 chr6D 92.143 980 70 4 3 976 270501960 270500982 0.000000e+00 1376
4 TraesCS4A01G151700 chr6D 92.041 980 70 5 3 976 366439313 366440290 0.000000e+00 1371
5 TraesCS4A01G151700 chr6D 97.071 239 5 1 972 1208 172744052 172743814 3.530000e-108 401
6 TraesCS4A01G151700 chr3D 93.209 1075 67 3 1208 2282 377097205 377098273 0.000000e+00 1576
7 TraesCS4A01G151700 chr3D 92.253 981 67 6 3 976 284863339 284864317 0.000000e+00 1382
8 TraesCS4A01G151700 chr3D 97.083 240 4 1 972 1208 589264006 589263767 3.530000e-108 401
9 TraesCS4A01G151700 chr5D 93.116 1075 69 2 1208 2282 134351779 134352848 0.000000e+00 1570
10 TraesCS4A01G151700 chr5D 92.943 1077 66 7 1208 2282 383706856 383707924 0.000000e+00 1559
11 TraesCS4A01G151700 chr5D 92.316 976 68 4 7 976 211578080 211579054 0.000000e+00 1380
12 TraesCS4A01G151700 chr5D 92.143 980 70 4 3 976 105240018 105240996 0.000000e+00 1376
13 TraesCS4A01G151700 chr5D 92.041 980 70 5 3 976 307521445 307522422 0.000000e+00 1371
14 TraesCS4A01G151700 chr5D 97.083 240 4 1 972 1208 503265785 503265546 3.530000e-108 401
15 TraesCS4A01G151700 chr5D 96.694 242 3 1 972 1208 503244790 503245031 4.570000e-107 398
16 TraesCS4A01G151700 chr2D 93.116 1075 69 2 1208 2282 293592529 293591460 0.000000e+00 1570
17 TraesCS4A01G151700 chr2D 92.347 980 68 4 3 976 357506411 357507389 0.000000e+00 1387
18 TraesCS4A01G151700 chr2D 96.694 242 3 1 972 1208 591984127 591984368 4.570000e-107 398
19 TraesCS4A01G151700 chr1D 93.116 1075 67 4 1208 2282 29847524 29848591 0.000000e+00 1568
20 TraesCS4A01G151700 chr1D 92.930 1075 71 2 1208 2282 182285565 182286634 0.000000e+00 1559
21 TraesCS4A01G151700 chr1D 92.930 1075 70 3 1208 2282 318601253 318602321 0.000000e+00 1559
22 TraesCS4A01G151700 chr1D 91.717 990 73 5 3 985 61871389 61872376 0.000000e+00 1365
23 TraesCS4A01G151700 chr1D 96.680 241 4 1 972 1208 254382503 254382263 4.570000e-107 398
24 TraesCS4A01G151700 chr4D 93.030 1076 69 3 1208 2282 80999017 81000087 0.000000e+00 1567
25 TraesCS4A01G151700 chr7D 97.500 240 3 1 972 1208 77248781 77248542 7.590000e-110 407
26 TraesCS4A01G151700 chr7D 96.680 241 4 1 972 1208 231554907 231554667 4.570000e-107 398
27 TraesCS4A01G151700 chr3A 97.095 241 3 1 972 1208 66005614 66005374 9.820000e-109 403


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 TraesCS4A01G151700 chr4A 308057611 308059892 2281 False 4215.0 4215 100.0000 1 2282 1 chr4A.!!$F1 2281
1 TraesCS4A01G151700 chr6D 366439313 366441372 2059 False 1473.5 1576 92.6285 3 2282 2 chr6D.!!$F2 2279
2 TraesCS4A01G151700 chr6D 83626450 83627428 978 False 1404.0 1404 92.6530 3 976 1 chr6D.!!$F1 973
3 TraesCS4A01G151700 chr6D 270500982 270501960 978 True 1376.0 1376 92.1430 3 976 1 chr6D.!!$R2 973
4 TraesCS4A01G151700 chr3D 377097205 377098273 1068 False 1576.0 1576 93.2090 1208 2282 1 chr3D.!!$F2 1074
5 TraesCS4A01G151700 chr3D 284863339 284864317 978 False 1382.0 1382 92.2530 3 976 1 chr3D.!!$F1 973
6 TraesCS4A01G151700 chr5D 134351779 134352848 1069 False 1570.0 1570 93.1160 1208 2282 1 chr5D.!!$F2 1074
7 TraesCS4A01G151700 chr5D 383706856 383707924 1068 False 1559.0 1559 92.9430 1208 2282 1 chr5D.!!$F5 1074
8 TraesCS4A01G151700 chr5D 211578080 211579054 974 False 1380.0 1380 92.3160 7 976 1 chr5D.!!$F3 969
9 TraesCS4A01G151700 chr5D 105240018 105240996 978 False 1376.0 1376 92.1430 3 976 1 chr5D.!!$F1 973
10 TraesCS4A01G151700 chr5D 307521445 307522422 977 False 1371.0 1371 92.0410 3 976 1 chr5D.!!$F4 973
11 TraesCS4A01G151700 chr2D 293591460 293592529 1069 True 1570.0 1570 93.1160 1208 2282 1 chr2D.!!$R1 1074
12 TraesCS4A01G151700 chr2D 357506411 357507389 978 False 1387.0 1387 92.3470 3 976 1 chr2D.!!$F1 973
13 TraesCS4A01G151700 chr1D 29847524 29848591 1067 False 1568.0 1568 93.1160 1208 2282 1 chr1D.!!$F1 1074
14 TraesCS4A01G151700 chr1D 182285565 182286634 1069 False 1559.0 1559 92.9300 1208 2282 1 chr1D.!!$F3 1074
15 TraesCS4A01G151700 chr1D 318601253 318602321 1068 False 1559.0 1559 92.9300 1208 2282 1 chr1D.!!$F4 1074
16 TraesCS4A01G151700 chr1D 61871389 61872376 987 False 1365.0 1365 91.7170 3 985 1 chr1D.!!$F2 982
17 TraesCS4A01G151700 chr4D 80999017 81000087 1070 False 1567.0 1567 93.0300 1208 2282 1 chr4D.!!$F1 1074

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
478 480 0.402121 GGATGAAGATACCCAGGGCC 59.598 60.0 4.91 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 1870 0.179124 GTCTTCTGCTAGCCGTCCTG 60.179 60.0 13.29 0.0 0.0 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 9.751542 GTACTAGTACTCTGCATGTAAATTGAT 57.248 33.333 23.17 0.00 33.45 2.57
105 106 0.767375 ACAATATGGAGCGCCCTCAT 59.233 50.000 2.29 8.41 39.96 2.90
114 115 3.072330 TGGAGCGCCCTCATTAATTATGA 59.928 43.478 2.29 0.00 40.96 2.15
186 188 8.736751 ATCCGTGTATTAATGTTGTTGTTTTC 57.263 30.769 0.00 0.00 0.00 2.29
238 240 3.812053 GGAACAATCTCGATGGATGAAGG 59.188 47.826 0.00 0.00 0.00 3.46
257 259 2.169769 AGGATCGGAAAACCGCAGATTA 59.830 45.455 3.67 0.00 0.00 1.75
263 265 5.361427 TCGGAAAACCGCAGATTATATCAA 58.639 37.500 3.67 0.00 0.00 2.57
289 291 4.083855 GCGTGACAGAGTTCATGAATTTGA 60.084 41.667 12.12 0.00 34.86 2.69
346 348 7.441836 GGATTACATCATGTGTCCATGTACTA 58.558 38.462 15.64 0.00 46.99 1.82
370 372 7.502120 AATTGTGCCAATATAGAGTCACATC 57.498 36.000 0.00 0.00 34.88 3.06
389 391 2.497138 TCAAGTTGCAGATGTCCAGTG 58.503 47.619 0.00 0.00 0.00 3.66
391 393 1.059098 AGTTGCAGATGTCCAGTGGA 58.941 50.000 8.12 8.12 0.00 4.02
478 480 0.402121 GGATGAAGATACCCAGGGCC 59.598 60.000 4.91 0.00 0.00 5.80
535 537 4.661222 TGTTGAATCTAACATCAGGGCAA 58.339 39.130 0.00 0.00 35.75 4.52
559 561 1.393539 CGTCAAGCTACCAATGGAACG 59.606 52.381 6.16 0.45 0.00 3.95
560 562 1.737793 GTCAAGCTACCAATGGAACGG 59.262 52.381 6.16 0.00 0.00 4.44
566 568 0.674269 TACCAATGGAACGGCGGAAC 60.674 55.000 13.24 0.22 0.00 3.62
594 596 1.632589 GCCCACTGGAAAACCAAGAT 58.367 50.000 0.00 0.00 0.00 2.40
691 693 6.786843 AGGATATGATTGGGTACAAGGATT 57.213 37.500 0.00 0.00 40.49 3.01
707 709 7.301868 ACAAGGATTTACCAACAATTGATGT 57.698 32.000 13.59 8.32 42.04 3.06
731 733 6.881602 GTGGACTCCAAGAAAGAATTGTATCT 59.118 38.462 0.00 0.00 34.18 1.98
804 806 3.347958 TTTAAAGCAGCAAACGGTCTG 57.652 42.857 0.00 0.00 0.00 3.51
811 813 1.670811 CAGCAAACGGTCTGTCAAACT 59.329 47.619 0.00 0.00 0.00 2.66
825 827 3.067833 GTCAAACTAGGGCTTCACAGAC 58.932 50.000 0.00 0.00 0.00 3.51
894 897 2.350522 AGAAGCACGAATGAAGCGAAT 58.649 42.857 0.00 0.00 0.00 3.34
899 908 5.235305 AGCACGAATGAAGCGAATAATTT 57.765 34.783 0.00 0.00 0.00 1.82
921 930 4.394729 TCCCATTGGAACTTGAAGTACAC 58.605 43.478 3.62 0.00 37.86 2.90
933 942 3.581755 TGAAGTACACAAGATACACGCC 58.418 45.455 0.00 0.00 0.00 5.68
976 985 3.040147 ACCGTGGTGAGTACAAAGATG 57.960 47.619 0.00 0.00 0.00 2.90
979 988 2.736721 CGTGGTGAGTACAAAGATGTGG 59.263 50.000 0.00 0.00 40.84 4.17
982 991 4.631813 GTGGTGAGTACAAAGATGTGGATC 59.368 45.833 0.00 0.00 40.84 3.36
983 992 4.285775 TGGTGAGTACAAAGATGTGGATCA 59.714 41.667 0.00 0.00 40.84 2.92
984 993 5.045651 TGGTGAGTACAAAGATGTGGATCAT 60.046 40.000 0.00 0.00 40.84 2.45
996 1005 2.832643 TGGATCATCCAAGGCACATT 57.167 45.000 2.95 0.00 45.00 2.71
997 1006 3.949586 TGGATCATCCAAGGCACATTA 57.050 42.857 2.95 0.00 45.00 1.90
998 1007 3.824133 TGGATCATCCAAGGCACATTAG 58.176 45.455 2.95 0.00 45.00 1.73
999 1008 2.555757 GGATCATCCAAGGCACATTAGC 59.444 50.000 0.00 0.00 36.28 3.09
1000 1009 2.804986 TCATCCAAGGCACATTAGCA 57.195 45.000 0.00 0.00 35.83 3.49
1001 1010 3.301794 TCATCCAAGGCACATTAGCAT 57.698 42.857 0.00 0.00 35.83 3.79
1002 1011 2.953648 TCATCCAAGGCACATTAGCATG 59.046 45.455 0.00 0.00 35.83 4.06
1003 1012 1.766494 TCCAAGGCACATTAGCATGG 58.234 50.000 0.00 0.00 41.61 3.66
1004 1013 0.103572 CCAAGGCACATTAGCATGGC 59.896 55.000 0.00 0.00 41.52 4.40
1005 1014 0.248743 CAAGGCACATTAGCATGGCG 60.249 55.000 0.00 0.00 45.57 5.69
1006 1015 0.680921 AAGGCACATTAGCATGGCGT 60.681 50.000 0.00 0.00 45.57 5.68
1007 1016 0.180171 AGGCACATTAGCATGGCGTA 59.820 50.000 0.00 0.00 45.57 4.42
1008 1017 0.307760 GGCACATTAGCATGGCGTAC 59.692 55.000 0.00 0.00 34.27 3.67
1009 1018 1.299541 GCACATTAGCATGGCGTACT 58.700 50.000 0.00 0.00 34.27 2.73
1010 1019 1.261619 GCACATTAGCATGGCGTACTC 59.738 52.381 0.00 0.00 34.27 2.59
1011 1020 1.867233 CACATTAGCATGGCGTACTCC 59.133 52.381 0.00 0.00 34.27 3.85
1012 1021 1.762957 ACATTAGCATGGCGTACTCCT 59.237 47.619 3.08 0.00 34.27 3.69
1013 1022 2.224066 ACATTAGCATGGCGTACTCCTC 60.224 50.000 3.08 0.00 34.27 3.71
1014 1023 0.750850 TTAGCATGGCGTACTCCTCC 59.249 55.000 3.08 0.00 0.00 4.30
1015 1024 0.106167 TAGCATGGCGTACTCCTCCT 60.106 55.000 3.08 0.00 0.00 3.69
1016 1025 1.227380 GCATGGCGTACTCCTCCTG 60.227 63.158 3.08 0.00 0.00 3.86
1017 1026 1.961180 GCATGGCGTACTCCTCCTGT 61.961 60.000 3.08 0.00 0.00 4.00
1018 1027 0.537188 CATGGCGTACTCCTCCTGTT 59.463 55.000 3.08 0.00 0.00 3.16
1019 1028 1.066143 CATGGCGTACTCCTCCTGTTT 60.066 52.381 3.08 0.00 0.00 2.83
1020 1029 0.320374 TGGCGTACTCCTCCTGTTTG 59.680 55.000 3.08 0.00 0.00 2.93
1021 1030 0.606604 GGCGTACTCCTCCTGTTTGA 59.393 55.000 0.00 0.00 0.00 2.69
1022 1031 1.001633 GGCGTACTCCTCCTGTTTGAA 59.998 52.381 0.00 0.00 0.00 2.69
1023 1032 2.354805 GGCGTACTCCTCCTGTTTGAAT 60.355 50.000 0.00 0.00 0.00 2.57
1024 1033 2.930682 GCGTACTCCTCCTGTTTGAATC 59.069 50.000 0.00 0.00 0.00 2.52
1025 1034 3.179830 CGTACTCCTCCTGTTTGAATCG 58.820 50.000 0.00 0.00 0.00 3.34
1026 1035 2.770164 ACTCCTCCTGTTTGAATCGG 57.230 50.000 0.00 0.00 0.00 4.18
1027 1036 1.978580 ACTCCTCCTGTTTGAATCGGT 59.021 47.619 0.00 0.00 0.00 4.69
1028 1037 2.289694 ACTCCTCCTGTTTGAATCGGTG 60.290 50.000 0.00 0.00 0.00 4.94
1029 1038 1.697432 TCCTCCTGTTTGAATCGGTGT 59.303 47.619 0.00 0.00 0.00 4.16
1030 1039 2.105821 TCCTCCTGTTTGAATCGGTGTT 59.894 45.455 0.00 0.00 0.00 3.32
1031 1040 2.884639 CCTCCTGTTTGAATCGGTGTTT 59.115 45.455 0.00 0.00 0.00 2.83
1032 1041 3.304659 CCTCCTGTTTGAATCGGTGTTTG 60.305 47.826 0.00 0.00 0.00 2.93
1033 1042 3.546724 TCCTGTTTGAATCGGTGTTTGA 58.453 40.909 0.00 0.00 0.00 2.69
1034 1043 3.948473 TCCTGTTTGAATCGGTGTTTGAA 59.052 39.130 0.00 0.00 0.00 2.69
1035 1044 4.399618 TCCTGTTTGAATCGGTGTTTGAAA 59.600 37.500 0.00 0.00 0.00 2.69
1036 1045 4.502645 CCTGTTTGAATCGGTGTTTGAAAC 59.497 41.667 0.14 0.14 0.00 2.78
1037 1046 4.425520 TGTTTGAATCGGTGTTTGAAACC 58.574 39.130 5.50 0.00 0.00 3.27
1038 1047 4.082190 TGTTTGAATCGGTGTTTGAAACCA 60.082 37.500 5.50 0.00 37.57 3.67
1039 1048 4.720649 TTGAATCGGTGTTTGAAACCAA 57.279 36.364 5.50 0.00 37.57 3.67
1040 1049 4.720649 TGAATCGGTGTTTGAAACCAAA 57.279 36.364 5.50 0.00 37.57 3.28
1052 1061 5.993748 TTGAAACCAAACAAACTTCTCCT 57.006 34.783 0.00 0.00 0.00 3.69
1053 1062 5.576447 TGAAACCAAACAAACTTCTCCTC 57.424 39.130 0.00 0.00 0.00 3.71
1054 1063 5.013547 TGAAACCAAACAAACTTCTCCTCA 58.986 37.500 0.00 0.00 0.00 3.86
1055 1064 5.125417 TGAAACCAAACAAACTTCTCCTCAG 59.875 40.000 0.00 0.00 0.00 3.35
1056 1065 3.555966 ACCAAACAAACTTCTCCTCAGG 58.444 45.455 0.00 0.00 0.00 3.86
1057 1066 3.202151 ACCAAACAAACTTCTCCTCAGGA 59.798 43.478 0.00 0.00 0.00 3.86
1070 1079 1.274712 CTCAGGAGGATAGATGGGGC 58.725 60.000 0.00 0.00 0.00 5.80
1071 1080 0.542938 TCAGGAGGATAGATGGGGCG 60.543 60.000 0.00 0.00 0.00 6.13
1072 1081 0.542938 CAGGAGGATAGATGGGGCGA 60.543 60.000 0.00 0.00 0.00 5.54
1073 1082 0.415429 AGGAGGATAGATGGGGCGAT 59.585 55.000 0.00 0.00 0.00 4.58
1074 1083 1.203364 AGGAGGATAGATGGGGCGATT 60.203 52.381 0.00 0.00 0.00 3.34
1075 1084 1.208293 GGAGGATAGATGGGGCGATTC 59.792 57.143 0.00 0.00 0.00 2.52
1076 1085 1.902508 GAGGATAGATGGGGCGATTCA 59.097 52.381 0.00 0.00 0.00 2.57
1077 1086 1.905215 AGGATAGATGGGGCGATTCAG 59.095 52.381 0.00 0.00 0.00 3.02
1078 1087 1.065854 GGATAGATGGGGCGATTCAGG 60.066 57.143 0.00 0.00 0.00 3.86
1079 1088 1.625818 GATAGATGGGGCGATTCAGGT 59.374 52.381 0.00 0.00 0.00 4.00
1080 1089 0.758734 TAGATGGGGCGATTCAGGTG 59.241 55.000 0.00 0.00 0.00 4.00
1081 1090 0.982852 AGATGGGGCGATTCAGGTGA 60.983 55.000 0.00 0.00 0.00 4.02
1082 1091 0.533755 GATGGGGCGATTCAGGTGAG 60.534 60.000 0.00 0.00 0.00 3.51
1083 1092 0.982852 ATGGGGCGATTCAGGTGAGA 60.983 55.000 0.00 0.00 0.00 3.27
1084 1093 0.982852 TGGGGCGATTCAGGTGAGAT 60.983 55.000 0.00 0.00 0.00 2.75
1085 1094 0.250081 GGGGCGATTCAGGTGAGATC 60.250 60.000 0.00 0.00 0.00 2.75
1086 1095 0.250081 GGGCGATTCAGGTGAGATCC 60.250 60.000 0.00 0.00 0.00 3.36
1087 1096 0.250081 GGCGATTCAGGTGAGATCCC 60.250 60.000 0.00 0.00 0.00 3.85
1088 1097 0.465705 GCGATTCAGGTGAGATCCCA 59.534 55.000 0.00 0.00 0.00 4.37
1089 1098 1.071385 GCGATTCAGGTGAGATCCCAT 59.929 52.381 0.00 0.00 0.00 4.00
1090 1099 2.763933 CGATTCAGGTGAGATCCCATG 58.236 52.381 0.00 0.00 0.00 3.66
1091 1100 2.103771 CGATTCAGGTGAGATCCCATGT 59.896 50.000 0.00 0.00 0.00 3.21
1092 1101 3.321968 CGATTCAGGTGAGATCCCATGTA 59.678 47.826 0.00 0.00 0.00 2.29
1093 1102 4.560311 CGATTCAGGTGAGATCCCATGTAG 60.560 50.000 0.00 0.00 0.00 2.74
1094 1103 3.688049 TCAGGTGAGATCCCATGTAGA 57.312 47.619 0.00 0.00 0.00 2.59
1095 1104 4.204792 TCAGGTGAGATCCCATGTAGAT 57.795 45.455 0.00 0.00 0.00 1.98
1096 1105 4.155709 TCAGGTGAGATCCCATGTAGATC 58.844 47.826 12.80 12.80 40.42 2.75
1107 1116 9.836179 AGATCCCATGTAGATCTAACTTTCTAT 57.164 33.333 18.99 0.00 46.76 1.98
1110 1119 9.434275 TCCCATGTAGATCTAACTTTCTATTCA 57.566 33.333 3.40 0.00 0.00 2.57
1111 1120 9.482627 CCCATGTAGATCTAACTTTCTATTCAC 57.517 37.037 3.40 0.00 0.00 3.18
1115 1124 9.175312 TGTAGATCTAACTTTCTATTCACTCGT 57.825 33.333 3.40 0.00 0.00 4.18
1116 1125 9.440784 GTAGATCTAACTTTCTATTCACTCGTG 57.559 37.037 3.40 0.00 0.00 4.35
1117 1126 7.484975 AGATCTAACTTTCTATTCACTCGTGG 58.515 38.462 0.00 0.00 0.00 4.94
1118 1127 5.962433 TCTAACTTTCTATTCACTCGTGGG 58.038 41.667 0.00 0.00 0.00 4.61
1119 1128 4.884668 AACTTTCTATTCACTCGTGGGA 57.115 40.909 0.00 0.00 0.00 4.37
1120 1129 5.422214 AACTTTCTATTCACTCGTGGGAT 57.578 39.130 0.00 0.00 0.00 3.85
1121 1130 5.012328 ACTTTCTATTCACTCGTGGGATC 57.988 43.478 0.00 0.00 0.00 3.36
1122 1131 4.141914 ACTTTCTATTCACTCGTGGGATCC 60.142 45.833 1.92 1.92 0.00 3.36
1123 1132 3.026707 TCTATTCACTCGTGGGATCCA 57.973 47.619 15.23 0.00 0.00 3.41
1124 1133 2.959030 TCTATTCACTCGTGGGATCCAG 59.041 50.000 15.23 4.54 32.34 3.86
1125 1134 0.833287 ATTCACTCGTGGGATCCAGG 59.167 55.000 15.23 5.86 40.34 4.45
1126 1135 1.899437 TTCACTCGTGGGATCCAGGC 61.899 60.000 15.23 1.58 39.03 4.85
1127 1136 3.461773 ACTCGTGGGATCCAGGCG 61.462 66.667 15.23 14.15 39.03 5.52
1128 1137 4.227134 CTCGTGGGATCCAGGCGG 62.227 72.222 15.23 5.25 39.03 6.13
1130 1139 4.530857 CGTGGGATCCAGGCGGTC 62.531 72.222 15.23 0.00 32.34 4.79
1131 1140 4.176752 GTGGGATCCAGGCGGTCC 62.177 72.222 15.23 0.00 32.34 4.46
1152 1161 4.459089 GGCACCACGGCTCCTCTC 62.459 72.222 0.00 0.00 37.17 3.20
1153 1162 3.386237 GCACCACGGCTCCTCTCT 61.386 66.667 0.00 0.00 0.00 3.10
1154 1163 2.948720 GCACCACGGCTCCTCTCTT 61.949 63.158 0.00 0.00 0.00 2.85
1155 1164 1.216710 CACCACGGCTCCTCTCTTC 59.783 63.158 0.00 0.00 0.00 2.87
1156 1165 1.077625 ACCACGGCTCCTCTCTTCT 59.922 57.895 0.00 0.00 0.00 2.85
1157 1166 0.968393 ACCACGGCTCCTCTCTTCTC 60.968 60.000 0.00 0.00 0.00 2.87
1158 1167 1.431440 CACGGCTCCTCTCTTCTCG 59.569 63.158 0.00 0.00 0.00 4.04
1159 1168 1.027255 CACGGCTCCTCTCTTCTCGA 61.027 60.000 0.00 0.00 0.00 4.04
1160 1169 0.746563 ACGGCTCCTCTCTTCTCGAG 60.747 60.000 5.93 5.93 41.30 4.04
1161 1170 0.462937 CGGCTCCTCTCTTCTCGAGA 60.463 60.000 12.08 12.08 46.32 4.04
1172 1181 6.567687 TCTCTTCTCGAGAATCCATACATC 57.432 41.667 27.19 0.00 45.55 3.06
1173 1182 5.475220 TCTCTTCTCGAGAATCCATACATCC 59.525 44.000 27.19 0.00 45.55 3.51
1174 1183 4.524714 TCTTCTCGAGAATCCATACATCCC 59.475 45.833 27.19 0.00 33.01 3.85
1175 1184 4.119556 TCTCGAGAATCCATACATCCCT 57.880 45.455 14.01 0.00 0.00 4.20
1176 1185 4.483950 TCTCGAGAATCCATACATCCCTT 58.516 43.478 14.01 0.00 0.00 3.95
1177 1186 5.641155 TCTCGAGAATCCATACATCCCTTA 58.359 41.667 14.01 0.00 0.00 2.69
1178 1187 6.256819 TCTCGAGAATCCATACATCCCTTAT 58.743 40.000 14.01 0.00 0.00 1.73
1179 1188 6.378564 TCTCGAGAATCCATACATCCCTTATC 59.621 42.308 14.01 0.00 0.00 1.75
1180 1189 6.016555 TCGAGAATCCATACATCCCTTATCA 58.983 40.000 0.00 0.00 0.00 2.15
1181 1190 6.153510 TCGAGAATCCATACATCCCTTATCAG 59.846 42.308 0.00 0.00 0.00 2.90
1182 1191 6.071108 CGAGAATCCATACATCCCTTATCAGT 60.071 42.308 0.00 0.00 0.00 3.41
1183 1192 7.122799 CGAGAATCCATACATCCCTTATCAGTA 59.877 40.741 0.00 0.00 0.00 2.74
1184 1193 8.923838 AGAATCCATACATCCCTTATCAGTAT 57.076 34.615 0.00 0.00 0.00 2.12
1188 1197 8.553085 TCCATACATCCCTTATCAGTATATGG 57.447 38.462 0.00 0.00 38.48 2.74
1189 1198 8.351414 TCCATACATCCCTTATCAGTATATGGA 58.649 37.037 5.28 5.28 41.91 3.41
1190 1199 8.646004 CCATACATCCCTTATCAGTATATGGAG 58.354 40.741 0.00 0.00 39.15 3.86
1191 1200 9.426534 CATACATCCCTTATCAGTATATGGAGA 57.573 37.037 0.00 0.00 35.73 3.71
1192 1201 7.969690 ACATCCCTTATCAGTATATGGAGAG 57.030 40.000 0.00 0.00 35.73 3.20
1193 1202 6.382570 ACATCCCTTATCAGTATATGGAGAGC 59.617 42.308 0.00 0.00 35.73 4.09
1194 1203 6.159172 TCCCTTATCAGTATATGGAGAGCT 57.841 41.667 0.00 0.00 35.73 4.09
1195 1204 7.285340 TCCCTTATCAGTATATGGAGAGCTA 57.715 40.000 0.00 0.00 35.73 3.32
1196 1205 7.888105 TCCCTTATCAGTATATGGAGAGCTAT 58.112 38.462 0.00 0.00 35.73 2.97
1197 1206 8.001875 TCCCTTATCAGTATATGGAGAGCTATC 58.998 40.741 0.00 0.00 35.73 2.08
1198 1207 8.004215 CCCTTATCAGTATATGGAGAGCTATCT 58.996 40.741 8.50 0.00 35.73 1.98
1249 1258 0.251077 AAGCACAGGAGAGCAAAGGG 60.251 55.000 0.00 0.00 33.43 3.95
1266 1275 3.237268 AGGGCAAGTACAAATTGGACA 57.763 42.857 11.35 0.00 32.29 4.02
1414 1423 3.195825 GCGGATAAGTATATGAGGCACCT 59.804 47.826 0.00 0.00 0.00 4.00
1416 1425 4.382040 CGGATAAGTATATGAGGCACCTGG 60.382 50.000 0.00 0.00 0.00 4.45
1501 1510 2.400467 ATAAGGCTCGGGGAGTGTAT 57.600 50.000 0.00 0.00 31.39 2.29
1516 1525 4.442893 GGAGTGTATTGACGGGATGAATCA 60.443 45.833 0.00 0.00 0.00 2.57
1547 1556 2.896801 GAGCACCAACCACAGCACG 61.897 63.158 0.00 0.00 0.00 5.34
1569 1578 0.721718 GTCGGTGCTTCTGTGCATAC 59.278 55.000 0.00 0.00 45.23 2.39
1579 1588 5.128663 TGCTTCTGTGCATACATAACCTAGA 59.871 40.000 0.00 0.00 38.12 2.43
1594 1603 4.820894 ACCTAGATCCTTGGTTGTGTAC 57.179 45.455 0.00 0.00 36.26 2.90
1691 1701 6.042208 ACTTTCAGCTACTGGTAGAAGAACTT 59.958 38.462 11.44 0.00 35.21 2.66
1765 1775 8.454106 CAAAAAGGAGATTTTCGATCTACATGT 58.546 33.333 2.69 2.69 40.27 3.21
1859 1870 0.523072 GGTGTGTCACATGCATGGAC 59.477 55.000 29.41 28.39 35.86 4.02
1865 1876 0.391528 TCACATGCATGGACAGGACG 60.392 55.000 29.41 8.16 0.00 4.79
1977 1989 2.163412 GCTGAATTTGATGGTACGGCAA 59.837 45.455 0.00 0.00 0.00 4.52
2150 2163 7.989947 AATTACCTTACTGGGAGATTCTACA 57.010 36.000 0.00 0.00 41.11 2.74
2186 2199 3.969899 TCGATGTCATGCATGTAGAGAC 58.030 45.455 25.43 16.25 38.06 3.36
2191 2204 4.640364 TGTCATGCATGTAGAGACAAACA 58.360 39.130 25.43 15.83 39.59 2.83
2192 2205 5.247862 TGTCATGCATGTAGAGACAAACAT 58.752 37.500 25.43 0.00 39.59 2.71
2193 2206 6.405538 TGTCATGCATGTAGAGACAAACATA 58.594 36.000 25.43 0.00 39.59 2.29
2194 2207 7.049754 TGTCATGCATGTAGAGACAAACATAT 58.950 34.615 25.43 0.00 39.59 1.78
2195 2208 8.203485 TGTCATGCATGTAGAGACAAACATATA 58.797 33.333 25.43 0.00 39.59 0.86
2211 2224 8.796475 ACAAACATATATATGTGAAAGCATCCC 58.204 33.333 25.42 0.00 45.55 3.85
2246 2259 9.349713 TGCTCAAGATTAAAGGTAAAAGAAAGA 57.650 29.630 0.00 0.00 0.00 2.52
2261 2274 6.923199 AAAGAAAGAATGGTGATGGTTCAT 57.077 33.333 0.00 0.00 33.56 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.598517 GAGTACTAGTACAACACTACAGATAGT 57.401 37.037 29.87 7.72 39.09 2.12
51 52 5.766670 TGCAATGACAAAAATTAATGGCCAA 59.233 32.000 10.96 0.00 0.00 4.52
257 259 3.827008 ACTCTGTCACGCCATTGATAT 57.173 42.857 0.00 0.00 0.00 1.63
263 265 1.276138 TCATGAACTCTGTCACGCCAT 59.724 47.619 0.00 0.00 0.00 4.40
289 291 7.724061 ACCAATTATCCACTTTGTACTTTCAGT 59.276 33.333 0.00 0.00 0.00 3.41
304 306 3.507162 ATCCGCATCACCAATTATCCA 57.493 42.857 0.00 0.00 0.00 3.41
308 310 5.372373 TGATGTAATCCGCATCACCAATTA 58.628 37.500 4.13 0.00 45.18 1.40
370 372 1.538512 CCACTGGACATCTGCAACTTG 59.461 52.381 0.00 0.00 0.00 3.16
389 391 2.140839 TCCCCGAGAGACTAAGTTCC 57.859 55.000 0.00 0.00 0.00 3.62
391 393 3.709587 TGAATCCCCGAGAGACTAAGTT 58.290 45.455 0.00 0.00 0.00 2.66
403 405 3.939740 ATATCCATCCATGAATCCCCG 57.060 47.619 0.00 0.00 0.00 5.73
478 480 3.508840 GGGGTTTGCCATCTCGCG 61.509 66.667 0.00 0.00 36.17 5.87
487 489 1.000274 GTGACACTGATTGGGGTTTGC 60.000 52.381 0.00 0.00 0.00 3.68
535 537 1.453155 CATTGGTAGCTTGACGCCTT 58.547 50.000 0.00 0.00 40.39 4.35
566 568 4.341502 CCAGTGGGCGTTTTGGCG 62.342 66.667 0.00 0.00 46.04 5.69
691 693 4.764823 GGAGTCCACATCAATTGTTGGTAA 59.235 41.667 18.35 3.07 36.00 2.85
707 709 7.020827 AGATACAATTCTTTCTTGGAGTCCA 57.979 36.000 8.12 8.12 0.00 4.02
731 733 7.953493 ACCTGGAATATTTCTTTTTCCAACCTA 59.047 33.333 0.00 0.00 46.07 3.08
804 806 3.067833 GTCTGTGAAGCCCTAGTTTGAC 58.932 50.000 0.00 0.00 0.00 3.18
811 813 3.197766 CCTAACATGTCTGTGAAGCCCTA 59.802 47.826 0.00 0.00 35.22 3.53
825 827 9.971922 AGAATTTCTTTGAAAAGACCTAACATG 57.028 29.630 4.99 0.00 44.18 3.21
870 873 2.735444 CGCTTCATTCGTGCTTCTAGGA 60.735 50.000 0.00 0.00 0.00 2.94
899 908 4.141367 TGTGTACTTCAAGTTCCAATGGGA 60.141 41.667 0.00 0.00 43.03 4.37
933 942 7.043391 CGGTACAATATACAGTCATTCACACAG 60.043 40.741 0.00 0.00 0.00 3.66
945 954 5.258456 ACTCACCACGGTACAATATACAG 57.742 43.478 0.00 0.00 0.00 2.74
979 988 3.216800 TGCTAATGTGCCTTGGATGATC 58.783 45.455 0.00 0.00 0.00 2.92
982 991 2.035449 CCATGCTAATGTGCCTTGGATG 59.965 50.000 0.00 0.00 37.39 3.51
983 992 2.313317 CCATGCTAATGTGCCTTGGAT 58.687 47.619 0.00 0.00 37.39 3.41
984 993 1.766494 CCATGCTAATGTGCCTTGGA 58.234 50.000 0.00 0.00 37.39 3.53
985 994 0.103572 GCCATGCTAATGTGCCTTGG 59.896 55.000 0.00 0.00 37.90 3.61
986 995 0.248743 CGCCATGCTAATGTGCCTTG 60.249 55.000 0.00 0.00 31.27 3.61
987 996 0.680921 ACGCCATGCTAATGTGCCTT 60.681 50.000 0.00 0.00 31.27 4.35
988 997 0.180171 TACGCCATGCTAATGTGCCT 59.820 50.000 0.00 0.00 31.27 4.75
989 998 0.307760 GTACGCCATGCTAATGTGCC 59.692 55.000 0.00 0.00 31.27 5.01
990 999 1.261619 GAGTACGCCATGCTAATGTGC 59.738 52.381 0.00 0.00 31.27 4.57
991 1000 1.867233 GGAGTACGCCATGCTAATGTG 59.133 52.381 11.20 0.00 31.27 3.21
992 1001 1.762957 AGGAGTACGCCATGCTAATGT 59.237 47.619 18.53 0.00 31.27 2.71
993 1002 2.408050 GAGGAGTACGCCATGCTAATG 58.592 52.381 18.53 0.00 0.00 1.90
994 1003 1.344763 GGAGGAGTACGCCATGCTAAT 59.655 52.381 18.53 0.00 39.13 1.73
995 1004 0.750850 GGAGGAGTACGCCATGCTAA 59.249 55.000 18.53 0.00 39.13 3.09
996 1005 0.106167 AGGAGGAGTACGCCATGCTA 60.106 55.000 18.53 0.00 42.23 3.49
997 1006 1.381872 AGGAGGAGTACGCCATGCT 60.382 57.895 18.53 10.33 42.23 3.79
998 1007 1.227380 CAGGAGGAGTACGCCATGC 60.227 63.158 18.53 8.25 42.23 4.06
999 1008 0.537188 AACAGGAGGAGTACGCCATG 59.463 55.000 18.53 14.73 42.23 3.66
1000 1009 1.066143 CAAACAGGAGGAGTACGCCAT 60.066 52.381 18.53 2.87 42.23 4.40
1001 1010 0.320374 CAAACAGGAGGAGTACGCCA 59.680 55.000 18.53 0.00 42.23 5.69
1002 1011 0.606604 TCAAACAGGAGGAGTACGCC 59.393 55.000 7.70 7.70 39.70 5.68
1003 1012 2.450609 TTCAAACAGGAGGAGTACGC 57.549 50.000 0.00 0.00 0.00 4.42
1004 1013 3.179830 CGATTCAAACAGGAGGAGTACG 58.820 50.000 0.00 0.00 0.00 3.67
1005 1014 3.056035 ACCGATTCAAACAGGAGGAGTAC 60.056 47.826 0.00 0.00 0.00 2.73
1006 1015 3.056107 CACCGATTCAAACAGGAGGAGTA 60.056 47.826 0.00 0.00 0.00 2.59
1007 1016 1.978580 ACCGATTCAAACAGGAGGAGT 59.021 47.619 0.00 0.00 0.00 3.85
1008 1017 2.289694 ACACCGATTCAAACAGGAGGAG 60.290 50.000 0.00 0.00 0.00 3.69
1009 1018 1.697432 ACACCGATTCAAACAGGAGGA 59.303 47.619 0.00 0.00 0.00 3.71
1010 1019 2.185004 ACACCGATTCAAACAGGAGG 57.815 50.000 0.00 0.00 0.00 4.30
1011 1020 3.563808 TCAAACACCGATTCAAACAGGAG 59.436 43.478 0.00 0.00 0.00 3.69
1012 1021 3.546724 TCAAACACCGATTCAAACAGGA 58.453 40.909 0.00 0.00 0.00 3.86
1013 1022 3.980646 TCAAACACCGATTCAAACAGG 57.019 42.857 0.00 0.00 0.00 4.00
1014 1023 4.502645 GGTTTCAAACACCGATTCAAACAG 59.497 41.667 1.93 0.00 0.00 3.16
1015 1024 4.082190 TGGTTTCAAACACCGATTCAAACA 60.082 37.500 1.93 0.00 37.07 2.83
1016 1025 4.425520 TGGTTTCAAACACCGATTCAAAC 58.574 39.130 1.93 0.00 37.07 2.93
1017 1026 4.720649 TGGTTTCAAACACCGATTCAAA 57.279 36.364 1.93 0.00 37.07 2.69
1018 1027 4.720649 TTGGTTTCAAACACCGATTCAA 57.279 36.364 1.93 0.00 37.07 2.69
1019 1028 4.720649 TTTGGTTTCAAACACCGATTCA 57.279 36.364 1.93 0.00 37.89 2.57
1029 1038 6.015010 TGAGGAGAAGTTTGTTTGGTTTCAAA 60.015 34.615 0.00 0.00 40.23 2.69
1030 1039 5.478679 TGAGGAGAAGTTTGTTTGGTTTCAA 59.521 36.000 0.00 0.00 0.00 2.69
1031 1040 5.013547 TGAGGAGAAGTTTGTTTGGTTTCA 58.986 37.500 0.00 0.00 0.00 2.69
1032 1041 5.450550 CCTGAGGAGAAGTTTGTTTGGTTTC 60.451 44.000 0.00 0.00 0.00 2.78
1033 1042 4.402474 CCTGAGGAGAAGTTTGTTTGGTTT 59.598 41.667 0.00 0.00 0.00 3.27
1034 1043 3.954258 CCTGAGGAGAAGTTTGTTTGGTT 59.046 43.478 0.00 0.00 0.00 3.67
1035 1044 3.202151 TCCTGAGGAGAAGTTTGTTTGGT 59.798 43.478 0.00 0.00 0.00 3.67
1036 1045 3.820557 TCCTGAGGAGAAGTTTGTTTGG 58.179 45.455 0.00 0.00 0.00 3.28
1051 1060 1.274712 GCCCCATCTATCCTCCTGAG 58.725 60.000 0.00 0.00 0.00 3.35
1052 1061 0.542938 CGCCCCATCTATCCTCCTGA 60.543 60.000 0.00 0.00 0.00 3.86
1053 1062 0.542938 TCGCCCCATCTATCCTCCTG 60.543 60.000 0.00 0.00 0.00 3.86
1054 1063 0.415429 ATCGCCCCATCTATCCTCCT 59.585 55.000 0.00 0.00 0.00 3.69
1055 1064 1.208293 GAATCGCCCCATCTATCCTCC 59.792 57.143 0.00 0.00 0.00 4.30
1056 1065 1.902508 TGAATCGCCCCATCTATCCTC 59.097 52.381 0.00 0.00 0.00 3.71
1057 1066 1.905215 CTGAATCGCCCCATCTATCCT 59.095 52.381 0.00 0.00 0.00 3.24
1058 1067 1.065854 CCTGAATCGCCCCATCTATCC 60.066 57.143 0.00 0.00 0.00 2.59
1059 1068 1.625818 ACCTGAATCGCCCCATCTATC 59.374 52.381 0.00 0.00 0.00 2.08
1060 1069 1.349026 CACCTGAATCGCCCCATCTAT 59.651 52.381 0.00 0.00 0.00 1.98
1061 1070 0.758734 CACCTGAATCGCCCCATCTA 59.241 55.000 0.00 0.00 0.00 1.98
1062 1071 0.982852 TCACCTGAATCGCCCCATCT 60.983 55.000 0.00 0.00 0.00 2.90
1063 1072 0.533755 CTCACCTGAATCGCCCCATC 60.534 60.000 0.00 0.00 0.00 3.51
1064 1073 0.982852 TCTCACCTGAATCGCCCCAT 60.983 55.000 0.00 0.00 0.00 4.00
1065 1074 0.982852 ATCTCACCTGAATCGCCCCA 60.983 55.000 0.00 0.00 0.00 4.96
1066 1075 0.250081 GATCTCACCTGAATCGCCCC 60.250 60.000 0.00 0.00 0.00 5.80
1067 1076 0.250081 GGATCTCACCTGAATCGCCC 60.250 60.000 0.00 0.00 0.00 6.13
1068 1077 0.250081 GGGATCTCACCTGAATCGCC 60.250 60.000 0.00 0.00 0.00 5.54
1069 1078 0.465705 TGGGATCTCACCTGAATCGC 59.534 55.000 0.00 0.00 0.00 4.58
1070 1079 2.103771 ACATGGGATCTCACCTGAATCG 59.896 50.000 0.00 0.00 0.00 3.34
1071 1080 3.853355 ACATGGGATCTCACCTGAATC 57.147 47.619 0.00 0.00 0.00 2.52
1072 1081 4.560739 TCTACATGGGATCTCACCTGAAT 58.439 43.478 0.00 0.00 0.00 2.57
1073 1082 3.994317 TCTACATGGGATCTCACCTGAA 58.006 45.455 0.00 0.00 0.00 3.02
1074 1083 3.688049 TCTACATGGGATCTCACCTGA 57.312 47.619 0.00 0.00 0.00 3.86
1075 1084 4.158786 AGATCTACATGGGATCTCACCTG 58.841 47.826 20.51 0.00 44.33 4.00
1076 1085 4.484026 AGATCTACATGGGATCTCACCT 57.516 45.455 20.51 5.99 44.33 4.00
1077 1086 5.777732 AGTTAGATCTACATGGGATCTCACC 59.222 44.000 25.98 18.14 44.33 4.02
1078 1087 6.909550 AGTTAGATCTACATGGGATCTCAC 57.090 41.667 25.98 24.46 44.33 3.51
1079 1088 7.786943 AGAAAGTTAGATCTACATGGGATCTCA 59.213 37.037 25.98 17.80 44.33 3.27
1080 1089 8.189119 AGAAAGTTAGATCTACATGGGATCTC 57.811 38.462 25.98 17.44 44.33 2.75
1084 1093 9.434275 TGAATAGAAAGTTAGATCTACATGGGA 57.566 33.333 0.67 0.00 31.35 4.37
1085 1094 9.482627 GTGAATAGAAAGTTAGATCTACATGGG 57.517 37.037 0.67 0.00 31.35 4.00
1089 1098 9.175312 ACGAGTGAATAGAAAGTTAGATCTACA 57.825 33.333 0.67 0.00 31.35 2.74
1090 1099 9.440784 CACGAGTGAATAGAAAGTTAGATCTAC 57.559 37.037 0.67 0.00 31.35 2.59
1091 1100 8.622157 CCACGAGTGAATAGAAAGTTAGATCTA 58.378 37.037 4.59 0.00 33.00 1.98
1092 1101 7.416890 CCCACGAGTGAATAGAAAGTTAGATCT 60.417 40.741 4.59 0.00 0.00 2.75
1093 1102 6.697892 CCCACGAGTGAATAGAAAGTTAGATC 59.302 42.308 4.59 0.00 0.00 2.75
1094 1103 6.380274 TCCCACGAGTGAATAGAAAGTTAGAT 59.620 38.462 4.59 0.00 0.00 1.98
1095 1104 5.713389 TCCCACGAGTGAATAGAAAGTTAGA 59.287 40.000 4.59 0.00 0.00 2.10
1096 1105 5.962433 TCCCACGAGTGAATAGAAAGTTAG 58.038 41.667 4.59 0.00 0.00 2.34
1097 1106 5.988310 TCCCACGAGTGAATAGAAAGTTA 57.012 39.130 4.59 0.00 0.00 2.24
1098 1107 4.884668 TCCCACGAGTGAATAGAAAGTT 57.115 40.909 4.59 0.00 0.00 2.66
1099 1108 4.141914 GGATCCCACGAGTGAATAGAAAGT 60.142 45.833 0.00 0.00 0.00 2.66
1100 1109 4.141937 TGGATCCCACGAGTGAATAGAAAG 60.142 45.833 9.90 0.00 0.00 2.62
1101 1110 3.772572 TGGATCCCACGAGTGAATAGAAA 59.227 43.478 9.90 0.00 0.00 2.52
1102 1111 3.371034 TGGATCCCACGAGTGAATAGAA 58.629 45.455 9.90 0.00 0.00 2.10
1103 1112 2.959030 CTGGATCCCACGAGTGAATAGA 59.041 50.000 9.90 0.00 0.00 1.98
1104 1113 2.036475 CCTGGATCCCACGAGTGAATAG 59.964 54.545 9.90 0.00 0.00 1.73
1105 1114 2.039418 CCTGGATCCCACGAGTGAATA 58.961 52.381 9.90 0.00 0.00 1.75
1106 1115 0.833287 CCTGGATCCCACGAGTGAAT 59.167 55.000 9.90 0.00 0.00 2.57
1107 1116 1.899437 GCCTGGATCCCACGAGTGAA 61.899 60.000 9.90 0.00 0.00 3.18
1108 1117 2.359169 GCCTGGATCCCACGAGTGA 61.359 63.158 9.90 0.00 0.00 3.41
1109 1118 2.187946 GCCTGGATCCCACGAGTG 59.812 66.667 9.90 0.00 0.00 3.51
1110 1119 3.461773 CGCCTGGATCCCACGAGT 61.462 66.667 9.90 0.00 0.00 4.18
1111 1120 4.227134 CCGCCTGGATCCCACGAG 62.227 72.222 17.01 4.97 37.49 4.18
1113 1122 4.530857 GACCGCCTGGATCCCACG 62.531 72.222 9.90 10.16 39.21 4.94
1114 1123 4.176752 GGACCGCCTGGATCCCAC 62.177 72.222 9.90 0.00 39.21 4.61
1135 1144 4.459089 GAGAGGAGCCGTGGTGCC 62.459 72.222 0.00 0.00 0.00 5.01
1136 1145 2.844072 GAAGAGAGGAGCCGTGGTGC 62.844 65.000 0.00 0.00 0.00 5.01
1137 1146 1.216710 GAAGAGAGGAGCCGTGGTG 59.783 63.158 0.00 0.00 0.00 4.17
1138 1147 0.968393 GAGAAGAGAGGAGCCGTGGT 60.968 60.000 0.00 0.00 0.00 4.16
1139 1148 1.813192 GAGAAGAGAGGAGCCGTGG 59.187 63.158 0.00 0.00 0.00 4.94
1140 1149 1.027255 TCGAGAAGAGAGGAGCCGTG 61.027 60.000 0.00 0.00 0.00 4.94
1141 1150 1.300305 TCGAGAAGAGAGGAGCCGT 59.700 57.895 0.00 0.00 0.00 5.68
1142 1151 4.227197 TCGAGAAGAGAGGAGCCG 57.773 61.111 0.00 0.00 0.00 5.52
1151 1160 4.524714 GGGATGTATGGATTCTCGAGAAGA 59.475 45.833 29.89 17.93 37.48 2.87
1152 1161 4.526262 AGGGATGTATGGATTCTCGAGAAG 59.474 45.833 29.89 0.00 37.48 2.85
1153 1162 4.483950 AGGGATGTATGGATTCTCGAGAA 58.516 43.478 28.85 28.85 38.56 2.87
1154 1163 4.119556 AGGGATGTATGGATTCTCGAGA 57.880 45.455 12.08 12.08 0.00 4.04
1155 1164 4.881019 AAGGGATGTATGGATTCTCGAG 57.119 45.455 5.93 5.93 0.00 4.04
1156 1165 6.016555 TGATAAGGGATGTATGGATTCTCGA 58.983 40.000 0.00 0.00 0.00 4.04
1157 1166 6.071108 ACTGATAAGGGATGTATGGATTCTCG 60.071 42.308 0.00 0.00 0.00 4.04
1158 1167 7.251321 ACTGATAAGGGATGTATGGATTCTC 57.749 40.000 0.00 0.00 0.00 2.87
1159 1168 8.923838 ATACTGATAAGGGATGTATGGATTCT 57.076 34.615 0.00 0.00 0.00 2.40
1162 1171 9.163894 CCATATACTGATAAGGGATGTATGGAT 57.836 37.037 0.00 0.00 38.73 3.41
1163 1172 8.351414 TCCATATACTGATAAGGGATGTATGGA 58.649 37.037 6.26 6.26 41.41 3.41
1164 1173 8.553085 TCCATATACTGATAAGGGATGTATGG 57.447 38.462 0.00 0.00 38.12 2.74
1165 1174 9.426534 TCTCCATATACTGATAAGGGATGTATG 57.573 37.037 0.00 0.00 29.47 2.39
1166 1175 9.653516 CTCTCCATATACTGATAAGGGATGTAT 57.346 37.037 0.00 0.00 29.47 2.29
1167 1176 7.561722 GCTCTCCATATACTGATAAGGGATGTA 59.438 40.741 0.00 0.00 29.47 2.29
1168 1177 6.382570 GCTCTCCATATACTGATAAGGGATGT 59.617 42.308 0.00 0.00 29.47 3.06
1169 1178 6.610830 AGCTCTCCATATACTGATAAGGGATG 59.389 42.308 0.00 0.00 29.47 3.51
1170 1179 6.751050 AGCTCTCCATATACTGATAAGGGAT 58.249 40.000 0.00 0.00 29.47 3.85
1171 1180 6.159172 AGCTCTCCATATACTGATAAGGGA 57.841 41.667 0.00 0.00 28.95 4.20
1172 1181 8.004215 AGATAGCTCTCCATATACTGATAAGGG 58.996 40.741 0.00 0.00 28.95 3.95
1173 1182 8.995027 AGATAGCTCTCCATATACTGATAAGG 57.005 38.462 0.00 0.00 0.00 2.69
1190 1199 1.001815 GTGGTGCTCGAGAGATAGCTC 60.002 57.143 18.75 0.00 40.84 4.09
1191 1200 1.028905 GTGGTGCTCGAGAGATAGCT 58.971 55.000 18.75 0.00 40.84 3.32
1192 1201 0.741326 TGTGGTGCTCGAGAGATAGC 59.259 55.000 18.75 8.96 40.84 2.97
1193 1202 3.010624 CATGTGGTGCTCGAGAGATAG 57.989 52.381 18.75 0.00 40.84 2.08
1249 1258 4.024387 TCTCGTTGTCCAATTTGTACTTGC 60.024 41.667 0.00 0.00 0.00 4.01
1266 1275 7.060383 ACATGATTCCTATCTTGATCTCGTT 57.940 36.000 0.00 0.00 38.59 3.85
1414 1423 0.918983 CCACTAAGCCCCATCTTCCA 59.081 55.000 0.00 0.00 0.00 3.53
1416 1425 1.213296 TCCCACTAAGCCCCATCTTC 58.787 55.000 0.00 0.00 0.00 2.87
1501 1510 4.082300 CACCAAAATGATTCATCCCGTCAA 60.082 41.667 0.00 0.00 0.00 3.18
1547 1556 2.607892 GCACAGAAGCACCGACCAC 61.608 63.158 0.00 0.00 0.00 4.16
1569 1578 5.745227 ACACAACCAAGGATCTAGGTTATG 58.255 41.667 16.02 16.02 43.56 1.90
1579 1588 4.345859 TTCTTCGTACACAACCAAGGAT 57.654 40.909 0.00 0.00 28.26 3.24
1616 1626 2.816087 CGGGCCTTGGATAATCATTGAG 59.184 50.000 0.84 0.00 0.00 3.02
1691 1701 3.490933 GCGCATCTATCCACACTGTTAGA 60.491 47.826 0.30 0.00 0.00 2.10
1859 1870 0.179124 GTCTTCTGCTAGCCGTCCTG 60.179 60.000 13.29 0.00 0.00 3.86
1865 1876 0.905357 TGGGAAGTCTTCTGCTAGCC 59.095 55.000 13.29 4.70 0.00 3.93
1977 1989 1.776710 TTGGGCCCACACCTACCTT 60.777 57.895 28.70 0.00 0.00 3.50
2049 2061 2.558359 CAAAGGGTGGTTCTTGCTAAGG 59.442 50.000 0.00 0.00 0.00 2.69
2053 2065 1.692411 GTCAAAGGGTGGTTCTTGCT 58.308 50.000 0.00 0.00 0.00 3.91
2150 2163 2.159240 ACATCGATGCAGTGACGTACAT 60.159 45.455 25.11 0.00 0.00 2.29
2186 2199 9.017509 AGGGATGCTTTCACATATATATGTTTG 57.982 33.333 23.03 14.41 43.99 2.93
2191 2204 7.276088 ACCAGGGATGCTTTCACATATATAT 57.724 36.000 0.00 0.00 0.00 0.86
2192 2205 6.702449 ACCAGGGATGCTTTCACATATATA 57.298 37.500 0.00 0.00 0.00 0.86
2193 2206 5.589367 ACCAGGGATGCTTTCACATATAT 57.411 39.130 0.00 0.00 0.00 0.86
2194 2207 5.606749 AGTACCAGGGATGCTTTCACATATA 59.393 40.000 0.00 0.00 0.00 0.86
2195 2208 3.959495 ACCAGGGATGCTTTCACATAT 57.041 42.857 0.00 0.00 0.00 1.78
2211 2224 5.814705 CCTTTAATCTTGAGCAGAGTACCAG 59.185 44.000 0.00 0.00 31.69 4.00
2246 2259 2.498481 CAAGCCATGAACCATCACCATT 59.502 45.455 0.00 0.00 38.69 3.16


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

AutoCloner maintained by Alex Coulton.