Multiple sequence alignment - TraesCS7A01G449200

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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 TraesCS7A01G449200 chr7A 100.000 2289 0 0 1 2289 643241752 643244040 0.000000e+00 4228
1 TraesCS7A01G449200 chr7A 94.099 949 53 2 1 946 52432299 52433247 0.000000e+00 1439
2 TraesCS7A01G449200 chr7A 87.164 335 27 6 968 1291 643298263 643298592 1.290000e-97 366
3 TraesCS7A01G449200 chr7A 84.900 351 32 9 941 1291 642903270 642902941 3.640000e-88 335
4 TraesCS7A01G449200 chr6A 95.949 938 35 3 1 936 104524143 104525079 0.000000e+00 1519
5 TraesCS7A01G449200 chr6A 95.304 937 43 1 1 936 602926826 602927762 0.000000e+00 1485
6 TraesCS7A01G449200 chr2A 95.754 942 37 2 1 939 729209724 729208783 0.000000e+00 1515
7 TraesCS7A01G449200 chr2A 94.953 951 46 2 1 949 93982825 93981875 0.000000e+00 1489
8 TraesCS7A01G449200 chr2A 94.989 938 45 2 1 936 716465746 716466683 0.000000e+00 1471
9 TraesCS7A01G449200 chr2A 94.715 946 45 4 1 944 591263550 591264492 0.000000e+00 1465
10 TraesCS7A01G449200 chr2D 95.445 944 41 2 1347 2289 423301041 423300099 0.000000e+00 1504
11 TraesCS7A01G449200 chr2D 95.334 943 42 1 1347 2289 369687358 369688298 0.000000e+00 1496
12 TraesCS7A01G449200 chr2D 95.228 943 40 2 1347 2289 11590309 11589372 0.000000e+00 1487
13 TraesCS7A01G449200 chr2D 88.372 86 6 4 1027 1110 618132586 618132669 1.450000e-17 100
14 TraesCS7A01G449200 chr7D 95.334 943 39 2 1347 2289 295300163 295299226 0.000000e+00 1493
15 TraesCS7A01G449200 chr7D 95.228 943 40 2 1347 2289 136931299 136930362 0.000000e+00 1487
16 TraesCS7A01G449200 chr7D 84.659 352 32 13 938 1289 557348301 557347972 4.710000e-87 331
17 TraesCS7A01G449200 chr7D 83.082 331 37 10 975 1303 557779063 557779376 1.340000e-72 283
18 TraesCS7A01G449200 chr3D 95.334 943 39 2 1347 2289 209459087 209460024 0.000000e+00 1493
19 TraesCS7A01G449200 chr5D 95.228 943 40 2 1347 2289 306174159 306175096 0.000000e+00 1487
20 TraesCS7A01G449200 chr5D 95.016 943 40 3 1347 2289 43400083 43401018 0.000000e+00 1474
21 TraesCS7A01G449200 chr1D 95.228 943 40 2 1347 2289 79156817 79157754 0.000000e+00 1487
22 TraesCS7A01G449200 chr4A 95.309 938 40 4 1 936 636057386 636058321 0.000000e+00 1485
23 TraesCS7A01G449200 chr1A 94.557 937 49 2 1 936 443662954 443663889 0.000000e+00 1447
24 TraesCS7A01G449200 chr7B 87.826 345 28 6 966 1301 605872237 605872576 2.130000e-105 392
25 TraesCS7A01G449200 chr7B 83.911 404 34 20 956 1349 605770677 605771059 7.780000e-95 357
26 TraesCS7A01G449200 chr7B 84.322 236 24 9 975 1210 605112254 605112032 3.830000e-53 219
27 TraesCS7A01G449200 chr7B 92.222 90 7 0 1202 1291 605111130 605111041 6.640000e-26 128
28 TraesCS7A01G449200 chrUn 81.513 238 27 9 1058 1295 86733754 86733534 1.810000e-41 180


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 TraesCS7A01G449200 chr7A 643241752 643244040 2288 False 4228 4228 100.000 1 2289 1 chr7A.!!$F2 2288
1 TraesCS7A01G449200 chr7A 52432299 52433247 948 False 1439 1439 94.099 1 946 1 chr7A.!!$F1 945
2 TraesCS7A01G449200 chr6A 104524143 104525079 936 False 1519 1519 95.949 1 936 1 chr6A.!!$F1 935
3 TraesCS7A01G449200 chr6A 602926826 602927762 936 False 1485 1485 95.304 1 936 1 chr6A.!!$F2 935
4 TraesCS7A01G449200 chr2A 729208783 729209724 941 True 1515 1515 95.754 1 939 1 chr2A.!!$R2 938
5 TraesCS7A01G449200 chr2A 93981875 93982825 950 True 1489 1489 94.953 1 949 1 chr2A.!!$R1 948
6 TraesCS7A01G449200 chr2A 716465746 716466683 937 False 1471 1471 94.989 1 936 1 chr2A.!!$F2 935
7 TraesCS7A01G449200 chr2A 591263550 591264492 942 False 1465 1465 94.715 1 944 1 chr2A.!!$F1 943
8 TraesCS7A01G449200 chr2D 423300099 423301041 942 True 1504 1504 95.445 1347 2289 1 chr2D.!!$R2 942
9 TraesCS7A01G449200 chr2D 369687358 369688298 940 False 1496 1496 95.334 1347 2289 1 chr2D.!!$F1 942
10 TraesCS7A01G449200 chr2D 11589372 11590309 937 True 1487 1487 95.228 1347 2289 1 chr2D.!!$R1 942
11 TraesCS7A01G449200 chr7D 295299226 295300163 937 True 1493 1493 95.334 1347 2289 1 chr7D.!!$R2 942
12 TraesCS7A01G449200 chr7D 136930362 136931299 937 True 1487 1487 95.228 1347 2289 1 chr7D.!!$R1 942
13 TraesCS7A01G449200 chr3D 209459087 209460024 937 False 1493 1493 95.334 1347 2289 1 chr3D.!!$F1 942
14 TraesCS7A01G449200 chr5D 306174159 306175096 937 False 1487 1487 95.228 1347 2289 1 chr5D.!!$F2 942
15 TraesCS7A01G449200 chr5D 43400083 43401018 935 False 1474 1474 95.016 1347 2289 1 chr5D.!!$F1 942
16 TraesCS7A01G449200 chr1D 79156817 79157754 937 False 1487 1487 95.228 1347 2289 1 chr1D.!!$F1 942
17 TraesCS7A01G449200 chr4A 636057386 636058321 935 False 1485 1485 95.309 1 936 1 chr4A.!!$F1 935
18 TraesCS7A01G449200 chr1A 443662954 443663889 935 False 1447 1447 94.557 1 936 1 chr1A.!!$F1 935

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
982 993 0.106669 AGATCGACCTGTCCATCGGA 60.107 55.0 0.0 0.0 38.86 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 1950 1.173444 ACACTCGACGCTCCACTTCT 61.173 55.0 0.0 0.0 0.0 2.85 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
75 76 3.512516 GCATTGAGCCTGCCGGAC 61.513 66.667 5.05 0.00 37.23 4.79
104 105 2.978824 GTTGGTGGCCTCGAGCTA 59.021 61.111 6.99 0.00 43.05 3.32
134 135 2.119029 GGCGGCGGAAATAAGGCTT 61.119 57.895 9.78 4.58 0.00 4.35
949 960 1.529244 GCCCTCACAAGCACAACCT 60.529 57.895 0.00 0.00 0.00 3.50
950 961 1.518903 GCCCTCACAAGCACAACCTC 61.519 60.000 0.00 0.00 0.00 3.85
951 962 1.230635 CCCTCACAAGCACAACCTCG 61.231 60.000 0.00 0.00 0.00 4.63
952 963 1.230635 CCTCACAAGCACAACCTCGG 61.231 60.000 0.00 0.00 0.00 4.63
953 964 1.845809 CTCACAAGCACAACCTCGGC 61.846 60.000 0.00 0.00 0.00 5.54
954 965 1.893808 CACAAGCACAACCTCGGCT 60.894 57.895 0.00 0.00 40.14 5.52
955 966 1.598130 ACAAGCACAACCTCGGCTC 60.598 57.895 0.00 0.00 36.76 4.70
956 967 2.357517 AAGCACAACCTCGGCTCG 60.358 61.111 0.00 0.00 36.76 5.03
959 970 4.717629 CACAACCTCGGCTCGCGA 62.718 66.667 9.26 9.26 0.00 5.87
960 971 4.421479 ACAACCTCGGCTCGCGAG 62.421 66.667 31.37 31.37 0.00 5.03
961 972 4.116328 CAACCTCGGCTCGCGAGA 62.116 66.667 38.74 18.11 35.69 4.04
971 982 3.720531 TCGCGAGAGAGATCGACC 58.279 61.111 3.71 0.00 45.56 4.79
972 983 1.144276 TCGCGAGAGAGATCGACCT 59.856 57.895 3.71 0.00 45.56 3.85
973 984 1.154814 TCGCGAGAGAGATCGACCTG 61.155 60.000 3.71 0.00 45.56 4.00
974 985 1.433053 CGCGAGAGAGATCGACCTGT 61.433 60.000 0.00 0.00 45.56 4.00
975 986 0.306533 GCGAGAGAGATCGACCTGTC 59.693 60.000 0.00 0.00 45.56 3.51
976 987 0.941542 CGAGAGAGATCGACCTGTCC 59.058 60.000 0.00 0.00 45.56 4.02
977 988 1.744114 CGAGAGAGATCGACCTGTCCA 60.744 57.143 0.00 0.00 45.56 4.02
978 989 2.582052 GAGAGAGATCGACCTGTCCAT 58.418 52.381 0.00 0.00 0.00 3.41
979 990 2.552315 GAGAGAGATCGACCTGTCCATC 59.448 54.545 0.00 0.00 0.00 3.51
980 991 1.265635 GAGAGATCGACCTGTCCATCG 59.734 57.143 0.00 0.00 39.72 3.84
981 992 0.312416 GAGATCGACCTGTCCATCGG 59.688 60.000 0.00 0.00 38.86 4.18
982 993 0.106669 AGATCGACCTGTCCATCGGA 60.107 55.000 0.00 0.00 38.86 4.55
983 994 0.744874 GATCGACCTGTCCATCGGAA 59.255 55.000 0.00 0.00 38.86 4.30
984 995 0.747255 ATCGACCTGTCCATCGGAAG 59.253 55.000 0.00 0.00 38.86 3.46
985 996 1.519455 CGACCTGTCCATCGGAAGC 60.519 63.158 0.00 0.00 34.67 3.86
986 997 1.596934 GACCTGTCCATCGGAAGCA 59.403 57.895 0.00 0.00 31.38 3.91
987 998 0.741221 GACCTGTCCATCGGAAGCAC 60.741 60.000 0.00 0.00 31.38 4.40
988 999 1.296392 CCTGTCCATCGGAAGCACA 59.704 57.895 0.00 0.00 31.38 4.57
989 1000 0.742281 CCTGTCCATCGGAAGCACAG 60.742 60.000 0.00 0.00 31.38 3.66
990 1001 0.742281 CTGTCCATCGGAAGCACAGG 60.742 60.000 0.00 0.00 31.38 4.00
991 1002 1.191489 TGTCCATCGGAAGCACAGGA 61.191 55.000 0.00 0.00 31.38 3.86
992 1003 0.741221 GTCCATCGGAAGCACAGGAC 60.741 60.000 0.00 0.00 38.77 3.85
993 1004 1.450312 CCATCGGAAGCACAGGACC 60.450 63.158 0.00 0.00 0.00 4.46
994 1005 1.811266 CATCGGAAGCACAGGACCG 60.811 63.158 0.00 0.00 45.61 4.79
996 1007 2.342279 CGGAAGCACAGGACCGAA 59.658 61.111 0.00 0.00 46.94 4.30
997 1008 1.301401 CGGAAGCACAGGACCGAAA 60.301 57.895 0.00 0.00 46.94 3.46
998 1009 0.882927 CGGAAGCACAGGACCGAAAA 60.883 55.000 0.00 0.00 46.94 2.29
999 1010 0.875059 GGAAGCACAGGACCGAAAAG 59.125 55.000 0.00 0.00 0.00 2.27
1000 1011 1.542547 GGAAGCACAGGACCGAAAAGA 60.543 52.381 0.00 0.00 0.00 2.52
1001 1012 2.427506 GAAGCACAGGACCGAAAAGAT 58.572 47.619 0.00 0.00 0.00 2.40
1002 1013 1.813513 AGCACAGGACCGAAAAGATG 58.186 50.000 0.00 0.00 0.00 2.90
1003 1014 1.347707 AGCACAGGACCGAAAAGATGA 59.652 47.619 0.00 0.00 0.00 2.92
1004 1015 1.734465 GCACAGGACCGAAAAGATGAG 59.266 52.381 0.00 0.00 0.00 2.90
1005 1016 1.734465 CACAGGACCGAAAAGATGAGC 59.266 52.381 0.00 0.00 0.00 4.26
1006 1017 1.625818 ACAGGACCGAAAAGATGAGCT 59.374 47.619 0.00 0.00 0.00 4.09
1007 1018 2.275318 CAGGACCGAAAAGATGAGCTC 58.725 52.381 6.82 6.82 0.00 4.09
1008 1019 1.134965 AGGACCGAAAAGATGAGCTCG 60.135 52.381 9.64 0.00 0.00 5.03
1009 1020 1.404315 GGACCGAAAAGATGAGCTCGT 60.404 52.381 8.55 8.55 0.00 4.18
1010 1021 1.921230 GACCGAAAAGATGAGCTCGTC 59.079 52.381 25.65 25.65 0.00 4.20
1011 1022 0.917259 CCGAAAAGATGAGCTCGTCG 59.083 55.000 26.30 16.56 36.99 5.12
1012 1023 0.917259 CGAAAAGATGAGCTCGTCGG 59.083 55.000 26.30 13.01 36.99 4.79
1013 1024 0.647925 GAAAAGATGAGCTCGTCGGC 59.352 55.000 26.30 14.95 36.99 5.54
1014 1025 1.078759 AAAAGATGAGCTCGTCGGCG 61.079 55.000 26.30 1.15 36.99 6.46
1015 1026 1.934220 AAAGATGAGCTCGTCGGCGA 61.934 55.000 26.30 13.29 45.79 5.54
1016 1027 2.600122 AAGATGAGCTCGTCGGCGAC 62.600 60.000 29.06 29.06 42.81 5.19
1017 1028 4.194720 ATGAGCTCGTCGGCGACC 62.195 66.667 31.86 19.19 42.81 4.79
1019 1030 4.415332 GAGCTCGTCGGCGACCAA 62.415 66.667 31.86 20.03 42.81 3.67
1020 1031 4.421479 AGCTCGTCGGCGACCAAG 62.421 66.667 31.86 27.78 42.81 3.61
1021 1032 4.415332 GCTCGTCGGCGACCAAGA 62.415 66.667 31.86 22.24 42.81 3.02
1022 1033 2.257371 CTCGTCGGCGACCAAGAA 59.743 61.111 31.86 12.89 42.81 2.52
1023 1034 1.801913 CTCGTCGGCGACCAAGAAG 60.802 63.158 31.86 17.91 42.81 2.85
1024 1035 2.809601 CGTCGGCGACCAAGAAGG 60.810 66.667 31.86 13.91 45.67 3.46
1025 1036 2.434359 GTCGGCGACCAAGAAGGG 60.434 66.667 28.72 0.00 43.89 3.95
1026 1037 3.702048 TCGGCGACCAAGAAGGGG 61.702 66.667 4.99 0.00 43.89 4.79
1027 1038 4.778143 CGGCGACCAAGAAGGGGG 62.778 72.222 0.00 0.00 43.89 5.40
1031 1042 2.046217 GACCAAGAAGGGGGCGTC 60.046 66.667 0.00 0.00 43.89 5.19
1032 1043 3.952628 GACCAAGAAGGGGGCGTCG 62.953 68.421 0.00 0.00 43.89 5.12
1034 1045 4.394712 CAAGAAGGGGGCGTCGCT 62.395 66.667 18.11 0.00 40.66 4.93
1035 1046 4.394712 AAGAAGGGGGCGTCGCTG 62.395 66.667 18.11 0.00 38.75 5.18
1075 1086 2.515523 CCATGGAGGCGCTCAAGG 60.516 66.667 5.56 6.59 31.08 3.61
1076 1087 2.586245 CATGGAGGCGCTCAAGGA 59.414 61.111 7.64 0.00 31.08 3.36
1077 1088 1.817099 CATGGAGGCGCTCAAGGAC 60.817 63.158 7.64 0.00 31.08 3.85
1078 1089 3.036429 ATGGAGGCGCTCAAGGACC 62.036 63.158 7.64 1.36 31.08 4.46
1079 1090 3.706373 GGAGGCGCTCAAGGACCA 61.706 66.667 7.64 0.00 31.08 4.02
1080 1091 2.125350 GAGGCGCTCAAGGACCAG 60.125 66.667 7.64 0.00 0.00 4.00
1081 1092 3.672295 GAGGCGCTCAAGGACCAGG 62.672 68.421 7.64 0.00 0.00 4.45
1085 1096 4.785453 GCTCAAGGACCAGGCGGG 62.785 72.222 0.79 0.79 44.81 6.13
1086 1097 4.101448 CTCAAGGACCAGGCGGGG 62.101 72.222 8.94 2.25 42.91 5.73
1103 1114 4.082523 GCTGTGCCGCTGGGACTA 62.083 66.667 17.10 6.17 44.53 2.59
1104 1115 2.903357 CTGTGCCGCTGGGACTAT 59.097 61.111 17.10 0.00 44.53 2.12
1105 1116 1.522355 CTGTGCCGCTGGGACTATG 60.522 63.158 17.10 6.83 44.53 2.23
1106 1117 2.897350 GTGCCGCTGGGACTATGC 60.897 66.667 10.96 0.00 40.95 3.14
1110 1121 2.963854 CGCTGGGACTATGCGCTG 60.964 66.667 9.73 0.99 43.08 5.18
1111 1122 3.275338 GCTGGGACTATGCGCTGC 61.275 66.667 9.73 0.00 38.18 5.25
1112 1123 2.963854 CTGGGACTATGCGCTGCG 60.964 66.667 19.17 19.17 0.00 5.18
1113 1124 3.723235 CTGGGACTATGCGCTGCGT 62.723 63.158 24.04 7.18 0.00 5.24
1114 1125 2.511600 GGGACTATGCGCTGCGTT 60.512 61.111 24.04 13.82 0.00 4.84
1115 1126 2.526120 GGGACTATGCGCTGCGTTC 61.526 63.158 24.04 8.35 0.00 3.95
1116 1127 2.615618 GACTATGCGCTGCGTTCG 59.384 61.111 24.04 11.87 0.00 3.95
1123 1134 3.248171 CGCTGCGTTCGCTCTACC 61.248 66.667 14.93 1.95 0.00 3.18
1124 1135 2.126071 GCTGCGTTCGCTCTACCA 60.126 61.111 17.63 0.00 0.00 3.25
1125 1136 2.161486 GCTGCGTTCGCTCTACCAG 61.161 63.158 17.63 7.10 0.00 4.00
1126 1137 2.126071 TGCGTTCGCTCTACCAGC 60.126 61.111 17.63 0.00 45.85 4.85
1164 1175 4.856607 CGCGCCGTCCTTCTCCTC 62.857 72.222 0.00 0.00 0.00 3.71
1165 1176 4.516195 GCGCCGTCCTTCTCCTCC 62.516 72.222 0.00 0.00 0.00 4.30
1166 1177 3.068691 CGCCGTCCTTCTCCTCCA 61.069 66.667 0.00 0.00 0.00 3.86
1167 1178 2.579738 GCCGTCCTTCTCCTCCAC 59.420 66.667 0.00 0.00 0.00 4.02
1168 1179 3.020237 GCCGTCCTTCTCCTCCACC 62.020 68.421 0.00 0.00 0.00 4.61
1169 1180 1.305381 CCGTCCTTCTCCTCCACCT 60.305 63.158 0.00 0.00 0.00 4.00
1170 1181 1.324005 CCGTCCTTCTCCTCCACCTC 61.324 65.000 0.00 0.00 0.00 3.85
1171 1182 1.324005 CGTCCTTCTCCTCCACCTCC 61.324 65.000 0.00 0.00 0.00 4.30
1172 1183 1.000486 TCCTTCTCCTCCACCTCCG 60.000 63.158 0.00 0.00 0.00 4.63
1173 1184 2.726351 CCTTCTCCTCCACCTCCGC 61.726 68.421 0.00 0.00 0.00 5.54
1174 1185 3.068691 TTCTCCTCCACCTCCGCG 61.069 66.667 0.00 0.00 0.00 6.46
1175 1186 3.881019 TTCTCCTCCACCTCCGCGT 62.881 63.158 4.92 0.00 0.00 6.01
1176 1187 3.827898 CTCCTCCACCTCCGCGTC 61.828 72.222 4.92 0.00 0.00 5.19
1241 1252 3.610669 CTGGGCGATCCGAGGAGG 61.611 72.222 0.00 0.00 42.97 4.30
1249 1260 4.346049 TCCGAGGAGGAGAAGCTG 57.654 61.111 0.00 0.00 45.98 4.24
1250 1261 2.055042 TCCGAGGAGGAGAAGCTGC 61.055 63.158 0.00 0.00 45.98 5.25
1251 1262 2.354401 CCGAGGAGGAGAAGCTGCA 61.354 63.158 1.02 0.00 45.00 4.41
1252 1263 1.153667 CGAGGAGGAGAAGCTGCAC 60.154 63.158 1.02 0.00 0.00 4.57
1253 1264 1.881903 CGAGGAGGAGAAGCTGCACA 61.882 60.000 1.02 0.00 0.00 4.57
1254 1265 0.322975 GAGGAGGAGAAGCTGCACAA 59.677 55.000 1.02 0.00 0.00 3.33
1255 1266 0.324285 AGGAGGAGAAGCTGCACAAG 59.676 55.000 1.02 0.00 0.00 3.16
1256 1267 0.676151 GGAGGAGAAGCTGCACAAGG 60.676 60.000 1.02 0.00 0.00 3.61
1257 1268 1.303155 AGGAGAAGCTGCACAAGGC 60.303 57.895 1.02 0.00 45.13 4.35
1266 1277 3.870606 GCACAAGGCGTATCACGT 58.129 55.556 0.26 0.00 44.73 4.49
1272 1283 3.978373 GGCGTATCACGTCGTCTG 58.022 61.111 0.00 0.00 44.73 3.51
1273 1284 2.222217 GGCGTATCACGTCGTCTGC 61.222 63.158 0.00 0.00 44.73 4.26
1274 1285 1.226323 GCGTATCACGTCGTCTGCT 60.226 57.895 0.00 0.00 44.73 4.24
1275 1286 1.464429 GCGTATCACGTCGTCTGCTG 61.464 60.000 0.00 0.00 44.73 4.41
1276 1287 0.861866 CGTATCACGTCGTCTGCTGG 60.862 60.000 0.00 0.00 36.74 4.85
1277 1288 0.525668 GTATCACGTCGTCTGCTGGG 60.526 60.000 0.00 0.00 0.00 4.45
1278 1289 1.663379 TATCACGTCGTCTGCTGGGG 61.663 60.000 0.00 0.00 0.00 4.96
1279 1290 3.680786 CACGTCGTCTGCTGGGGA 61.681 66.667 0.00 0.00 0.00 4.81
1280 1291 3.681835 ACGTCGTCTGCTGGGGAC 61.682 66.667 0.00 5.34 0.00 4.46
1295 1306 0.521735 GGGACCAAACTGATTCGTGC 59.478 55.000 0.00 0.00 0.00 5.34
1296 1307 1.523758 GGACCAAACTGATTCGTGCT 58.476 50.000 0.00 0.00 0.00 4.40
1297 1308 2.614481 GGGACCAAACTGATTCGTGCTA 60.614 50.000 0.00 0.00 0.00 3.49
1298 1309 2.673368 GGACCAAACTGATTCGTGCTAG 59.327 50.000 0.00 0.00 0.00 3.42
1299 1310 2.076863 ACCAAACTGATTCGTGCTAGC 58.923 47.619 8.10 8.10 0.00 3.42
1300 1311 2.076100 CCAAACTGATTCGTGCTAGCA 58.924 47.619 14.93 14.93 0.00 3.49
1301 1312 2.094894 CCAAACTGATTCGTGCTAGCAG 59.905 50.000 20.03 12.53 0.00 4.24
1302 1313 1.363744 AACTGATTCGTGCTAGCAGC 58.636 50.000 20.03 12.19 42.82 5.25
1303 1314 0.534412 ACTGATTCGTGCTAGCAGCT 59.466 50.000 20.03 0.00 42.97 4.24
1304 1315 1.066573 ACTGATTCGTGCTAGCAGCTT 60.067 47.619 20.03 3.13 42.97 3.74
1305 1316 2.166459 ACTGATTCGTGCTAGCAGCTTA 59.834 45.455 20.03 4.35 42.97 3.09
1306 1317 2.793790 CTGATTCGTGCTAGCAGCTTAG 59.206 50.000 20.03 8.34 42.97 2.18
1307 1318 2.131183 GATTCGTGCTAGCAGCTTAGG 58.869 52.381 20.03 1.05 42.97 2.69
1308 1319 1.182667 TTCGTGCTAGCAGCTTAGGA 58.817 50.000 20.03 3.81 42.97 2.94
1309 1320 0.456221 TCGTGCTAGCAGCTTAGGAC 59.544 55.000 20.03 6.83 42.97 3.85
1310 1321 0.457851 CGTGCTAGCAGCTTAGGACT 59.542 55.000 20.03 0.00 42.97 3.85
1311 1322 1.676529 CGTGCTAGCAGCTTAGGACTA 59.323 52.381 20.03 0.00 42.97 2.59
1312 1323 2.287308 CGTGCTAGCAGCTTAGGACTAG 60.287 54.545 20.03 7.51 42.97 2.57
1315 1326 3.363341 CTAGCAGCTTAGGACTAGCAC 57.637 52.381 0.00 0.00 0.00 4.40
1316 1327 1.859302 AGCAGCTTAGGACTAGCACT 58.141 50.000 0.00 0.00 0.00 4.40
1317 1328 3.019799 AGCAGCTTAGGACTAGCACTA 57.980 47.619 0.00 0.00 0.00 2.74
1318 1329 2.955660 AGCAGCTTAGGACTAGCACTAG 59.044 50.000 3.10 3.10 39.04 2.57
1319 1330 2.952978 GCAGCTTAGGACTAGCACTAGA 59.047 50.000 11.59 0.00 36.97 2.43
1320 1331 3.004315 GCAGCTTAGGACTAGCACTAGAG 59.996 52.174 11.59 0.00 36.97 2.43
1321 1332 3.568007 CAGCTTAGGACTAGCACTAGAGG 59.432 52.174 11.59 0.00 36.97 3.69
1322 1333 3.460340 AGCTTAGGACTAGCACTAGAGGA 59.540 47.826 11.59 0.00 36.97 3.71
1323 1334 3.566742 GCTTAGGACTAGCACTAGAGGAC 59.433 52.174 11.59 0.00 36.97 3.85
1324 1335 2.740506 AGGACTAGCACTAGAGGACC 57.259 55.000 11.59 8.63 36.97 4.46
1325 1336 1.215924 AGGACTAGCACTAGAGGACCC 59.784 57.143 11.59 4.75 36.97 4.46
1326 1337 1.310904 GACTAGCACTAGAGGACCCG 58.689 60.000 11.59 0.00 36.97 5.28
1327 1338 0.752376 ACTAGCACTAGAGGACCCGC 60.752 60.000 11.59 0.00 36.97 6.13
1328 1339 1.455217 TAGCACTAGAGGACCCGCC 60.455 63.158 0.00 0.00 0.00 6.13
1329 1340 2.923634 TAGCACTAGAGGACCCGCCC 62.924 65.000 0.00 0.00 37.37 6.13
1330 1341 2.042843 CACTAGAGGACCCGCCCT 60.043 66.667 0.00 0.00 39.77 5.19
1331 1342 1.686110 CACTAGAGGACCCGCCCTT 60.686 63.158 0.00 0.00 36.49 3.95
1332 1343 1.080538 ACTAGAGGACCCGCCCTTT 59.919 57.895 0.00 0.00 36.49 3.11
1333 1344 0.546988 ACTAGAGGACCCGCCCTTTT 60.547 55.000 0.00 0.00 36.49 2.27
1334 1345 0.618981 CTAGAGGACCCGCCCTTTTT 59.381 55.000 0.00 0.00 36.49 1.94
1335 1346 0.326927 TAGAGGACCCGCCCTTTTTG 59.673 55.000 0.00 0.00 36.49 2.44
1336 1347 1.228459 GAGGACCCGCCCTTTTTGT 60.228 57.895 0.00 0.00 36.49 2.83
1337 1348 0.826256 GAGGACCCGCCCTTTTTGTT 60.826 55.000 0.00 0.00 36.49 2.83
1338 1349 1.112916 AGGACCCGCCCTTTTTGTTG 61.113 55.000 0.00 0.00 37.37 3.33
1339 1350 1.396607 GGACCCGCCCTTTTTGTTGT 61.397 55.000 0.00 0.00 0.00 3.32
1340 1351 0.249280 GACCCGCCCTTTTTGTTGTG 60.249 55.000 0.00 0.00 0.00 3.33
1341 1352 0.684805 ACCCGCCCTTTTTGTTGTGA 60.685 50.000 0.00 0.00 0.00 3.58
1342 1353 0.031994 CCCGCCCTTTTTGTTGTGAG 59.968 55.000 0.00 0.00 0.00 3.51
1343 1354 0.744281 CCGCCCTTTTTGTTGTGAGT 59.256 50.000 0.00 0.00 0.00 3.41
1344 1355 1.269051 CCGCCCTTTTTGTTGTGAGTC 60.269 52.381 0.00 0.00 0.00 3.36
1345 1356 1.269051 CGCCCTTTTTGTTGTGAGTCC 60.269 52.381 0.00 0.00 0.00 3.85
1441 1452 6.201615 TGTCTCCTAAGATACACGTACATACG 59.798 42.308 9.82 9.82 43.56 3.06
1457 1468 3.117625 ACATACGGAGGGAGACAGATACA 60.118 47.826 0.00 0.00 0.00 2.29
1637 1649 0.908910 TCGGTGGGCACATGTAGAAT 59.091 50.000 0.00 0.00 0.00 2.40
1652 1664 4.229096 TGTAGAATACGAACACGACCAAC 58.771 43.478 0.00 0.00 46.99 3.77
1656 1668 0.102663 TACGAACACGACCAACTGCA 59.897 50.000 0.00 0.00 0.00 4.41
1703 1715 0.817654 AGCTCGATGTGATTCGTCCA 59.182 50.000 0.00 0.00 40.03 4.02
1728 1740 2.490270 GATGGACAGGGTTGGCAGCT 62.490 60.000 0.24 0.00 32.23 4.24
1732 1744 2.439156 CAGGGTTGGCAGCTAGGC 60.439 66.667 0.24 0.00 44.50 3.93
1741 1753 4.435436 CAGCTAGGCACACCGCGA 62.435 66.667 8.23 0.00 43.84 5.87
1752 1764 0.795735 ACACCGCGAAGACGTTATCG 60.796 55.000 8.23 16.64 41.98 2.92
1794 1806 3.601443 GTGACCTCACATAGCAACTCT 57.399 47.619 0.31 0.00 45.75 3.24
1797 1809 3.578282 TGACCTCACATAGCAACTCTTGA 59.422 43.478 0.00 0.00 0.00 3.02
1805 1817 6.152831 TCACATAGCAACTCTTGAAGTAGCTA 59.847 38.462 10.86 10.86 37.17 3.32
1815 1827 8.820892 AACTCTTGAAGTAGCTATCGTAGCCAT 61.821 40.741 11.71 0.64 44.94 4.40
1926 1938 1.152440 CAGAGAGGGCCCGAGGTAT 60.152 63.158 18.44 0.00 0.00 2.73
1938 1950 2.304092 CCGAGGTATACACAGTAGCCA 58.696 52.381 5.01 0.00 0.00 4.75
2007 2019 1.523938 GGCGACAAGGCTGGTATCC 60.524 63.158 0.00 0.00 42.90 2.59
2193 2205 0.099968 CGACGATGGAGCGGTAGAAA 59.900 55.000 0.00 0.00 35.12 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
555 556 3.391382 CGTCCCTCGCCCTTCCTT 61.391 66.667 0.00 0.00 0.00 3.36
743 744 1.435515 GGCGAACTGTTTTGGTGCA 59.564 52.632 0.00 0.00 0.00 4.57
746 747 2.190841 CGGGGCGAACTGTTTTGGT 61.191 57.895 0.00 0.00 0.00 3.67
936 947 1.845809 GAGCCGAGGTTGTGCTTGTG 61.846 60.000 0.00 0.00 34.99 3.33
949 960 2.203084 ATCTCTCTCGCGAGCCGA 60.203 61.111 30.97 25.23 45.15 5.54
950 961 2.251075 GATCTCTCTCGCGAGCCG 59.749 66.667 30.97 22.63 37.19 5.52
951 962 2.248135 TCGATCTCTCTCGCGAGCC 61.248 63.158 30.97 13.41 38.52 4.70
952 963 1.083015 GTCGATCTCTCTCGCGAGC 60.083 63.158 30.97 14.72 38.52 5.03
953 964 0.878523 AGGTCGATCTCTCTCGCGAG 60.879 60.000 30.03 30.03 38.52 5.03
954 965 1.144276 AGGTCGATCTCTCTCGCGA 59.856 57.895 9.26 9.26 38.52 5.87
955 966 1.278337 CAGGTCGATCTCTCTCGCG 59.722 63.158 0.00 0.00 38.52 5.87
956 967 0.306533 GACAGGTCGATCTCTCTCGC 59.693 60.000 0.00 0.00 38.52 5.03
957 968 0.941542 GGACAGGTCGATCTCTCTCG 59.058 60.000 0.00 0.00 39.99 4.04
958 969 2.045561 TGGACAGGTCGATCTCTCTC 57.954 55.000 0.00 0.00 0.00 3.20
959 970 2.582052 GATGGACAGGTCGATCTCTCT 58.418 52.381 14.71 0.00 40.32 3.10
960 971 1.265635 CGATGGACAGGTCGATCTCTC 59.734 57.143 18.18 0.00 41.00 3.20
961 972 1.313772 CGATGGACAGGTCGATCTCT 58.686 55.000 18.18 0.00 41.00 3.10
962 973 0.312416 CCGATGGACAGGTCGATCTC 59.688 60.000 18.18 0.00 41.00 2.75
963 974 0.106669 TCCGATGGACAGGTCGATCT 60.107 55.000 18.18 0.00 41.00 2.75
964 975 0.744874 TTCCGATGGACAGGTCGATC 59.255 55.000 12.67 12.67 40.15 3.69
965 976 0.747255 CTTCCGATGGACAGGTCGAT 59.253 55.000 0.00 0.00 40.11 3.59
966 977 1.945354 GCTTCCGATGGACAGGTCGA 61.945 60.000 0.00 0.00 40.11 4.20
967 978 1.519455 GCTTCCGATGGACAGGTCG 60.519 63.158 0.00 0.00 37.58 4.79
968 979 0.741221 GTGCTTCCGATGGACAGGTC 60.741 60.000 1.60 0.00 0.00 3.85
969 980 1.296715 GTGCTTCCGATGGACAGGT 59.703 57.895 1.60 0.00 0.00 4.00
970 981 0.742281 CTGTGCTTCCGATGGACAGG 60.742 60.000 21.42 8.61 45.77 4.00
971 982 2.759783 CTGTGCTTCCGATGGACAG 58.240 57.895 17.65 17.65 44.72 3.51
972 983 1.191489 TCCTGTGCTTCCGATGGACA 61.191 55.000 8.12 8.12 34.72 4.02
973 984 0.741221 GTCCTGTGCTTCCGATGGAC 60.741 60.000 0.00 0.00 37.42 4.02
974 985 1.596934 GTCCTGTGCTTCCGATGGA 59.403 57.895 0.00 0.00 0.00 3.41
975 986 1.450312 GGTCCTGTGCTTCCGATGG 60.450 63.158 0.00 0.00 0.00 3.51
976 987 1.811266 CGGTCCTGTGCTTCCGATG 60.811 63.158 0.00 0.00 44.86 3.84
977 988 1.982395 TCGGTCCTGTGCTTCCGAT 60.982 57.895 0.97 0.00 45.49 4.18
979 990 0.882927 TTTTCGGTCCTGTGCTTCCG 60.883 55.000 0.00 0.00 43.65 4.30
980 991 0.875059 CTTTTCGGTCCTGTGCTTCC 59.125 55.000 0.00 0.00 0.00 3.46
981 992 1.878953 TCTTTTCGGTCCTGTGCTTC 58.121 50.000 0.00 0.00 0.00 3.86
982 993 2.154462 CATCTTTTCGGTCCTGTGCTT 58.846 47.619 0.00 0.00 0.00 3.91
983 994 1.347707 TCATCTTTTCGGTCCTGTGCT 59.652 47.619 0.00 0.00 0.00 4.40
984 995 1.734465 CTCATCTTTTCGGTCCTGTGC 59.266 52.381 0.00 0.00 0.00 4.57
985 996 1.734465 GCTCATCTTTTCGGTCCTGTG 59.266 52.381 0.00 0.00 0.00 3.66
986 997 1.625818 AGCTCATCTTTTCGGTCCTGT 59.374 47.619 0.00 0.00 0.00 4.00
987 998 2.275318 GAGCTCATCTTTTCGGTCCTG 58.725 52.381 9.40 0.00 0.00 3.86
988 999 1.134965 CGAGCTCATCTTTTCGGTCCT 60.135 52.381 15.40 0.00 0.00 3.85
989 1000 1.281899 CGAGCTCATCTTTTCGGTCC 58.718 55.000 15.40 0.00 0.00 4.46
990 1001 1.921230 GACGAGCTCATCTTTTCGGTC 59.079 52.381 15.40 5.72 37.38 4.79
991 1002 1.732732 CGACGAGCTCATCTTTTCGGT 60.733 52.381 15.40 0.00 37.38 4.69
992 1003 0.917259 CGACGAGCTCATCTTTTCGG 59.083 55.000 15.40 0.00 37.38 4.30
993 1004 0.917259 CCGACGAGCTCATCTTTTCG 59.083 55.000 15.40 10.54 38.88 3.46
994 1005 0.647925 GCCGACGAGCTCATCTTTTC 59.352 55.000 15.40 0.00 0.00 2.29
995 1006 1.078759 CGCCGACGAGCTCATCTTTT 61.079 55.000 15.40 0.00 43.93 2.27
996 1007 1.517257 CGCCGACGAGCTCATCTTT 60.517 57.895 15.40 0.00 43.93 2.52
997 1008 2.103143 CGCCGACGAGCTCATCTT 59.897 61.111 15.40 0.00 43.93 2.40
998 1009 2.824489 TCGCCGACGAGCTCATCT 60.824 61.111 15.40 0.00 45.12 2.90
1007 1018 2.809601 CCTTCTTGGTCGCCGACG 60.810 66.667 11.60 0.00 42.01 5.12
1008 1019 2.434359 CCCTTCTTGGTCGCCGAC 60.434 66.667 9.15 9.15 0.00 4.79
1009 1020 3.702048 CCCCTTCTTGGTCGCCGA 61.702 66.667 0.00 0.00 0.00 5.54
1010 1021 4.778143 CCCCCTTCTTGGTCGCCG 62.778 72.222 0.00 0.00 0.00 6.46
1013 1024 3.952628 GACGCCCCCTTCTTGGTCG 62.953 68.421 0.00 0.00 0.00 4.79
1014 1025 2.046217 GACGCCCCCTTCTTGGTC 60.046 66.667 0.00 0.00 0.00 4.02
1015 1026 4.016706 CGACGCCCCCTTCTTGGT 62.017 66.667 0.00 0.00 0.00 3.67
1017 1028 4.394712 AGCGACGCCCCCTTCTTG 62.395 66.667 17.79 0.00 0.00 3.02
1018 1029 4.394712 CAGCGACGCCCCCTTCTT 62.395 66.667 17.79 0.00 0.00 2.52
1035 1046 4.760047 ATGCTCGTCGCCACCACC 62.760 66.667 0.00 0.00 38.05 4.61
1036 1047 3.490759 CATGCTCGTCGCCACCAC 61.491 66.667 0.00 0.00 38.05 4.16
1037 1048 4.758251 CCATGCTCGTCGCCACCA 62.758 66.667 0.00 0.00 38.05 4.17
1058 1069 2.515523 CCTTGAGCGCCTCCATGG 60.516 66.667 4.97 4.97 39.35 3.66
1059 1070 1.817099 GTCCTTGAGCGCCTCCATG 60.817 63.158 2.29 2.34 0.00 3.66
1060 1071 2.586792 GTCCTTGAGCGCCTCCAT 59.413 61.111 2.29 0.00 0.00 3.41
1061 1072 3.706373 GGTCCTTGAGCGCCTCCA 61.706 66.667 2.29 0.00 0.00 3.86
1062 1073 3.672295 CTGGTCCTTGAGCGCCTCC 62.672 68.421 2.29 0.00 32.15 4.30
1063 1074 2.125350 CTGGTCCTTGAGCGCCTC 60.125 66.667 2.29 1.22 32.15 4.70
1064 1075 3.710722 CCTGGTCCTTGAGCGCCT 61.711 66.667 2.29 0.00 32.15 5.52
1068 1079 4.785453 CCCGCCTGGTCCTTGAGC 62.785 72.222 0.00 0.00 0.00 4.26
1069 1080 4.101448 CCCCGCCTGGTCCTTGAG 62.101 72.222 0.00 0.00 0.00 3.02
1086 1097 3.391665 ATAGTCCCAGCGGCACAGC 62.392 63.158 1.45 0.00 37.41 4.40
1087 1098 1.522355 CATAGTCCCAGCGGCACAG 60.522 63.158 1.45 0.00 0.00 3.66
1088 1099 2.584064 CATAGTCCCAGCGGCACA 59.416 61.111 1.45 0.00 0.00 4.57
1089 1100 2.897350 GCATAGTCCCAGCGGCAC 60.897 66.667 1.45 0.00 0.00 5.01
1094 1105 3.275338 GCAGCGCATAGTCCCAGC 61.275 66.667 11.47 0.00 0.00 4.85
1095 1106 2.963854 CGCAGCGCATAGTCCCAG 60.964 66.667 11.47 0.00 0.00 4.45
1096 1107 3.309436 AACGCAGCGCATAGTCCCA 62.309 57.895 16.61 0.00 0.00 4.37
1097 1108 2.511600 AACGCAGCGCATAGTCCC 60.512 61.111 16.61 0.00 0.00 4.46
1098 1109 2.860628 CGAACGCAGCGCATAGTCC 61.861 63.158 16.61 0.00 0.00 3.85
1099 1110 2.615618 CGAACGCAGCGCATAGTC 59.384 61.111 16.61 3.87 0.00 2.59
1106 1117 3.248171 GGTAGAGCGAACGCAGCG 61.248 66.667 20.66 14.82 44.88 5.18
1107 1118 2.126071 TGGTAGAGCGAACGCAGC 60.126 61.111 20.66 12.06 44.88 5.25
1108 1119 2.161486 GCTGGTAGAGCGAACGCAG 61.161 63.158 20.66 9.36 44.88 5.18
1109 1120 2.126071 GCTGGTAGAGCGAACGCA 60.126 61.111 20.66 0.00 44.88 5.24
1147 1158 4.856607 GAGGAGAAGGACGGCGCG 62.857 72.222 6.90 0.00 0.00 6.86
1148 1159 4.516195 GGAGGAGAAGGACGGCGC 62.516 72.222 6.90 0.00 0.00 6.53
1149 1160 3.068691 TGGAGGAGAAGGACGGCG 61.069 66.667 4.80 4.80 0.00 6.46
1150 1161 2.579738 GTGGAGGAGAAGGACGGC 59.420 66.667 0.00 0.00 0.00 5.68
1151 1162 1.305381 AGGTGGAGGAGAAGGACGG 60.305 63.158 0.00 0.00 0.00 4.79
1152 1163 1.324005 GGAGGTGGAGGAGAAGGACG 61.324 65.000 0.00 0.00 0.00 4.79
1153 1164 1.324005 CGGAGGTGGAGGAGAAGGAC 61.324 65.000 0.00 0.00 0.00 3.85
1154 1165 1.000486 CGGAGGTGGAGGAGAAGGA 60.000 63.158 0.00 0.00 0.00 3.36
1155 1166 2.726351 GCGGAGGTGGAGGAGAAGG 61.726 68.421 0.00 0.00 0.00 3.46
1156 1167 2.896443 GCGGAGGTGGAGGAGAAG 59.104 66.667 0.00 0.00 0.00 2.85
1157 1168 3.068691 CGCGGAGGTGGAGGAGAA 61.069 66.667 0.00 0.00 0.00 2.87
1158 1169 4.361971 ACGCGGAGGTGGAGGAGA 62.362 66.667 12.47 0.00 0.00 3.71
1159 1170 3.827898 GACGCGGAGGTGGAGGAG 61.828 72.222 12.47 0.00 0.00 3.69
1223 1234 3.610669 CTCCTCGGATCGCCCAGG 61.611 72.222 0.00 0.00 35.69 4.45
1224 1235 3.610669 CCTCCTCGGATCGCCCAG 61.611 72.222 0.00 0.00 33.16 4.45
1225 1236 4.137615 TCCTCCTCGGATCGCCCA 62.138 66.667 0.00 0.00 36.69 5.36
1226 1237 3.299190 CTCCTCCTCGGATCGCCC 61.299 72.222 0.00 0.00 42.12 6.13
1227 1238 1.801309 CTTCTCCTCCTCGGATCGCC 61.801 65.000 0.00 0.00 42.12 5.54
1228 1239 1.657556 CTTCTCCTCCTCGGATCGC 59.342 63.158 0.00 0.00 42.12 4.58
1229 1240 0.821711 AGCTTCTCCTCCTCGGATCG 60.822 60.000 0.00 0.00 42.12 3.69
1230 1241 0.673437 CAGCTTCTCCTCCTCGGATC 59.327 60.000 0.00 0.00 42.12 3.36
1231 1242 1.398958 GCAGCTTCTCCTCCTCGGAT 61.399 60.000 0.00 0.00 42.12 4.18
1232 1243 2.055042 GCAGCTTCTCCTCCTCGGA 61.055 63.158 0.00 0.00 40.30 4.55
1233 1244 2.354401 TGCAGCTTCTCCTCCTCGG 61.354 63.158 0.00 0.00 0.00 4.63
1234 1245 1.153667 GTGCAGCTTCTCCTCCTCG 60.154 63.158 0.00 0.00 0.00 4.63
1235 1246 0.322975 TTGTGCAGCTTCTCCTCCTC 59.677 55.000 0.00 0.00 0.00 3.71
1236 1247 0.324285 CTTGTGCAGCTTCTCCTCCT 59.676 55.000 0.00 0.00 0.00 3.69
1237 1248 0.676151 CCTTGTGCAGCTTCTCCTCC 60.676 60.000 0.00 0.00 0.00 4.30
1238 1249 1.304509 GCCTTGTGCAGCTTCTCCTC 61.305 60.000 0.00 0.00 40.77 3.71
1239 1250 1.303155 GCCTTGTGCAGCTTCTCCT 60.303 57.895 0.00 0.00 40.77 3.69
1240 1251 2.684843 CGCCTTGTGCAGCTTCTCC 61.685 63.158 0.00 0.00 41.33 3.71
1241 1252 0.670546 TACGCCTTGTGCAGCTTCTC 60.671 55.000 0.00 0.00 41.33 2.87
1242 1253 0.036010 ATACGCCTTGTGCAGCTTCT 60.036 50.000 0.00 0.00 41.33 2.85
1243 1254 0.375106 GATACGCCTTGTGCAGCTTC 59.625 55.000 0.00 0.00 41.33 3.86
1244 1255 0.321564 TGATACGCCTTGTGCAGCTT 60.322 50.000 0.00 0.00 41.33 3.74
1245 1256 1.021390 GTGATACGCCTTGTGCAGCT 61.021 55.000 0.00 0.00 41.33 4.24
1246 1257 1.425428 GTGATACGCCTTGTGCAGC 59.575 57.895 0.00 0.00 41.33 5.25
1247 1258 1.709760 CGTGATACGCCTTGTGCAG 59.290 57.895 0.00 0.00 41.33 4.41
1248 1259 3.869187 CGTGATACGCCTTGTGCA 58.131 55.556 0.00 0.00 41.33 4.57
1258 1269 0.525668 CCCAGCAGACGACGTGATAC 60.526 60.000 4.58 0.00 0.00 2.24
1259 1270 1.663379 CCCCAGCAGACGACGTGATA 61.663 60.000 4.58 0.00 0.00 2.15
1260 1271 2.573869 CCCAGCAGACGACGTGAT 59.426 61.111 4.58 0.00 0.00 3.06
1261 1272 3.680786 CCCCAGCAGACGACGTGA 61.681 66.667 4.58 0.00 0.00 4.35
1262 1273 3.680786 TCCCCAGCAGACGACGTG 61.681 66.667 4.58 0.00 0.00 4.49
1263 1274 3.681835 GTCCCCAGCAGACGACGT 61.682 66.667 0.00 0.00 0.00 4.34
1264 1275 4.436998 GGTCCCCAGCAGACGACG 62.437 72.222 0.00 0.00 34.97 5.12
1265 1276 2.391724 TTTGGTCCCCAGCAGACGAC 62.392 60.000 0.00 0.00 33.81 4.34
1266 1277 2.144078 TTTGGTCCCCAGCAGACGA 61.144 57.895 0.00 0.00 33.81 4.20
1267 1278 1.966451 GTTTGGTCCCCAGCAGACG 60.966 63.158 0.00 0.00 33.81 4.18
1268 1279 0.890996 CAGTTTGGTCCCCAGCAGAC 60.891 60.000 0.00 0.00 35.77 3.51
1269 1280 1.059584 TCAGTTTGGTCCCCAGCAGA 61.060 55.000 0.00 0.00 33.81 4.26
1270 1281 0.038744 ATCAGTTTGGTCCCCAGCAG 59.961 55.000 0.00 0.00 33.81 4.24
1271 1282 0.482446 AATCAGTTTGGTCCCCAGCA 59.518 50.000 0.00 0.00 33.81 4.41
1272 1283 1.177401 GAATCAGTTTGGTCCCCAGC 58.823 55.000 0.00 0.00 33.81 4.85
1273 1284 1.271379 ACGAATCAGTTTGGTCCCCAG 60.271 52.381 0.00 0.00 33.81 4.45
1274 1285 0.768622 ACGAATCAGTTTGGTCCCCA 59.231 50.000 0.00 0.00 0.00 4.96
1275 1286 1.165270 CACGAATCAGTTTGGTCCCC 58.835 55.000 0.00 0.00 0.00 4.81
1276 1287 0.521735 GCACGAATCAGTTTGGTCCC 59.478 55.000 0.00 0.00 0.00 4.46
1277 1288 1.523758 AGCACGAATCAGTTTGGTCC 58.476 50.000 0.00 0.00 0.00 4.46
1278 1289 2.094417 GCTAGCACGAATCAGTTTGGTC 59.906 50.000 10.63 0.00 0.00 4.02
1279 1290 2.076863 GCTAGCACGAATCAGTTTGGT 58.923 47.619 10.63 0.00 0.00 3.67
1280 1291 2.076100 TGCTAGCACGAATCAGTTTGG 58.924 47.619 14.93 0.00 0.00 3.28
1281 1292 2.475187 GCTGCTAGCACGAATCAGTTTG 60.475 50.000 14.93 0.11 41.89 2.93
1282 1293 1.734465 GCTGCTAGCACGAATCAGTTT 59.266 47.619 14.93 0.00 41.89 2.66
1283 1294 1.066573 AGCTGCTAGCACGAATCAGTT 60.067 47.619 14.93 0.00 45.56 3.16
1284 1295 0.534412 AGCTGCTAGCACGAATCAGT 59.466 50.000 14.93 0.00 45.56 3.41
1285 1296 1.649664 AAGCTGCTAGCACGAATCAG 58.350 50.000 14.93 3.13 45.56 2.90
1286 1297 2.481969 CCTAAGCTGCTAGCACGAATCA 60.482 50.000 14.93 0.00 45.56 2.57
1287 1298 2.131183 CCTAAGCTGCTAGCACGAATC 58.869 52.381 14.93 0.79 45.56 2.52
1288 1299 1.757118 TCCTAAGCTGCTAGCACGAAT 59.243 47.619 14.93 3.04 45.56 3.34
1289 1300 1.135083 GTCCTAAGCTGCTAGCACGAA 60.135 52.381 14.93 4.26 45.56 3.85
1290 1301 0.456221 GTCCTAAGCTGCTAGCACGA 59.544 55.000 14.93 4.38 45.56 4.35
1291 1302 0.457851 AGTCCTAAGCTGCTAGCACG 59.542 55.000 14.93 11.37 45.56 5.34
1292 1303 3.363341 CTAGTCCTAAGCTGCTAGCAC 57.637 52.381 14.93 11.12 45.56 4.40
1294 1305 2.432206 GCTAGTCCTAAGCTGCTAGC 57.568 55.000 8.10 8.10 46.02 3.42
1295 1306 2.955660 AGTGCTAGTCCTAAGCTGCTAG 59.044 50.000 0.90 0.87 35.35 3.42
1296 1307 3.019799 AGTGCTAGTCCTAAGCTGCTA 57.980 47.619 0.90 0.00 0.00 3.49
1297 1308 1.859302 AGTGCTAGTCCTAAGCTGCT 58.141 50.000 0.00 0.00 0.00 4.24
1298 1309 2.952978 TCTAGTGCTAGTCCTAAGCTGC 59.047 50.000 6.18 0.00 34.84 5.25
1299 1310 3.568007 CCTCTAGTGCTAGTCCTAAGCTG 59.432 52.174 6.18 0.00 34.84 4.24
1300 1311 3.460340 TCCTCTAGTGCTAGTCCTAAGCT 59.540 47.826 6.18 0.00 34.84 3.74
1301 1312 3.566742 GTCCTCTAGTGCTAGTCCTAAGC 59.433 52.174 6.18 0.00 34.84 3.09
1302 1313 4.139038 GGTCCTCTAGTGCTAGTCCTAAG 58.861 52.174 6.18 0.00 34.84 2.18
1303 1314 3.117587 GGGTCCTCTAGTGCTAGTCCTAA 60.118 52.174 6.18 0.00 34.84 2.69
1304 1315 2.442502 GGGTCCTCTAGTGCTAGTCCTA 59.557 54.545 6.18 0.00 34.84 2.94
1305 1316 1.215924 GGGTCCTCTAGTGCTAGTCCT 59.784 57.143 6.18 0.00 34.84 3.85
1306 1317 1.694844 GGGTCCTCTAGTGCTAGTCC 58.305 60.000 6.18 5.50 34.84 3.85
1307 1318 1.310904 CGGGTCCTCTAGTGCTAGTC 58.689 60.000 6.18 0.00 34.84 2.59
1308 1319 0.752376 GCGGGTCCTCTAGTGCTAGT 60.752 60.000 6.18 0.00 34.84 2.57
1309 1320 1.457009 GGCGGGTCCTCTAGTGCTAG 61.457 65.000 0.00 0.00 34.56 3.42
1310 1321 1.455217 GGCGGGTCCTCTAGTGCTA 60.455 63.158 0.00 0.00 0.00 3.49
1311 1322 2.760385 GGCGGGTCCTCTAGTGCT 60.760 66.667 0.00 0.00 0.00 4.40
1312 1323 3.851128 GGGCGGGTCCTCTAGTGC 61.851 72.222 0.00 0.00 34.39 4.40
1313 1324 1.265454 AAAGGGCGGGTCCTCTAGTG 61.265 60.000 0.00 0.00 35.80 2.74
1314 1325 0.546988 AAAAGGGCGGGTCCTCTAGT 60.547 55.000 0.00 0.00 35.80 2.57
1315 1326 0.618981 AAAAAGGGCGGGTCCTCTAG 59.381 55.000 0.00 0.00 35.80 2.43
1316 1327 0.326927 CAAAAAGGGCGGGTCCTCTA 59.673 55.000 0.00 0.00 35.80 2.43
1317 1328 1.074951 CAAAAAGGGCGGGTCCTCT 59.925 57.895 0.00 0.00 35.80 3.69
1318 1329 0.826256 AACAAAAAGGGCGGGTCCTC 60.826 55.000 0.00 0.00 35.80 3.71
1319 1330 1.112916 CAACAAAAAGGGCGGGTCCT 61.113 55.000 0.00 0.00 39.17 3.85
1320 1331 1.365999 CAACAAAAAGGGCGGGTCC 59.634 57.895 0.00 0.00 0.00 4.46
1321 1332 0.249280 CACAACAAAAAGGGCGGGTC 60.249 55.000 0.00 0.00 0.00 4.46
1322 1333 0.684805 TCACAACAAAAAGGGCGGGT 60.685 50.000 0.00 0.00 0.00 5.28
1323 1334 0.031994 CTCACAACAAAAAGGGCGGG 59.968 55.000 0.00 0.00 0.00 6.13
1324 1335 0.744281 ACTCACAACAAAAAGGGCGG 59.256 50.000 0.00 0.00 0.00 6.13
1325 1336 1.269051 GGACTCACAACAAAAAGGGCG 60.269 52.381 0.00 0.00 0.00 6.13
1326 1337 1.269051 CGGACTCACAACAAAAAGGGC 60.269 52.381 0.00 0.00 0.00 5.19
1327 1338 1.336755 CCGGACTCACAACAAAAAGGG 59.663 52.381 0.00 0.00 0.00 3.95
1328 1339 2.021457 ACCGGACTCACAACAAAAAGG 58.979 47.619 9.46 0.00 0.00 3.11
1329 1340 2.794631 GCACCGGACTCACAACAAAAAG 60.795 50.000 9.46 0.00 0.00 2.27
1330 1341 1.133407 GCACCGGACTCACAACAAAAA 59.867 47.619 9.46 0.00 0.00 1.94
1331 1342 0.736053 GCACCGGACTCACAACAAAA 59.264 50.000 9.46 0.00 0.00 2.44
1332 1343 0.393132 TGCACCGGACTCACAACAAA 60.393 50.000 9.46 0.00 0.00 2.83
1333 1344 0.179032 ATGCACCGGACTCACAACAA 60.179 50.000 9.46 0.00 0.00 2.83
1334 1345 0.602638 GATGCACCGGACTCACAACA 60.603 55.000 9.46 0.00 0.00 3.33
1335 1346 1.626654 CGATGCACCGGACTCACAAC 61.627 60.000 9.46 0.00 0.00 3.32
1336 1347 1.374125 CGATGCACCGGACTCACAA 60.374 57.895 9.46 0.00 0.00 3.33
1337 1348 1.604147 ATCGATGCACCGGACTCACA 61.604 55.000 9.46 0.00 0.00 3.58
1338 1349 0.384309 TATCGATGCACCGGACTCAC 59.616 55.000 9.46 0.00 0.00 3.51
1339 1350 1.107945 TTATCGATGCACCGGACTCA 58.892 50.000 9.46 2.46 0.00 3.41
1340 1351 2.440539 ATTATCGATGCACCGGACTC 57.559 50.000 9.46 0.00 0.00 3.36
1341 1352 2.102420 TCAATTATCGATGCACCGGACT 59.898 45.455 9.46 0.00 0.00 3.85
1342 1353 2.479837 TCAATTATCGATGCACCGGAC 58.520 47.619 9.46 0.00 0.00 4.79
1343 1354 2.900716 TCAATTATCGATGCACCGGA 57.099 45.000 9.46 0.00 0.00 5.14
1344 1355 3.498018 TCAATCAATTATCGATGCACCGG 59.502 43.478 8.54 0.00 0.00 5.28
1345 1356 4.730600 TCAATCAATTATCGATGCACCG 57.269 40.909 8.54 0.00 0.00 4.94
1441 1452 2.432510 CCTGTTGTATCTGTCTCCCTCC 59.567 54.545 0.00 0.00 0.00 4.30
1457 1468 2.236395 GGTCCTGTATGCAGTACCTGTT 59.764 50.000 16.74 0.00 45.13 3.16
1475 1486 2.097825 ACATGTACGTAGGTCTGGGTC 58.902 52.381 0.00 0.00 0.00 4.46
1582 1594 2.521126 TGTGATGACGAAGGGACTACA 58.479 47.619 0.00 0.00 38.49 2.74
1637 1649 0.102663 TGCAGTTGGTCGTGTTCGTA 59.897 50.000 0.00 0.00 38.33 3.43
1656 1668 1.597027 CTTTGTCCGGGAGCACGTT 60.597 57.895 0.00 0.00 0.00 3.99
1703 1715 0.253044 CAACCCTGTCCATCACCGAT 59.747 55.000 0.00 0.00 0.00 4.18
1728 1740 2.260434 GTCTTCGCGGTGTGCCTA 59.740 61.111 6.13 0.00 42.08 3.93
1732 1744 0.638746 GATAACGTCTTCGCGGTGTG 59.361 55.000 6.13 0.00 41.18 3.82
1741 1753 2.674852 TCGTCTACTGCGATAACGTCTT 59.325 45.455 0.00 0.00 41.98 3.01
1752 1764 2.945066 GCGACGCTCGTCTACTGC 60.945 66.667 13.73 11.42 42.81 4.40
1805 1817 1.202417 CGGAGTGTTCATGGCTACGAT 60.202 52.381 6.36 0.00 38.74 3.73
1926 1938 2.826128 CTCCACTTCTGGCTACTGTGTA 59.174 50.000 0.00 0.00 37.49 2.90
1938 1950 1.173444 ACACTCGACGCTCCACTTCT 61.173 55.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.