Multiple sequence alignment - TraesCS7D01G125600

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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 TraesCS7D01G125600 chr7D 100.000 2141 0 0 1 2141 78500193 78502333 0.000000e+00 3954.0
1 TraesCS7D01G125600 chr7D 87.554 233 22 4 694 920 511194007 511194238 1.630000e-66 263.0
2 TraesCS7D01G125600 chr7D 88.571 210 22 1 1154 1361 511194241 511194450 9.810000e-64 254.0
3 TraesCS7D01G125600 chr7D 89.394 132 10 2 1436 1565 407792699 407792828 1.700000e-36 163.0
4 TraesCS7D01G125600 chr4D 95.956 989 35 4 1154 2140 472519005 472519990 0.000000e+00 1600.0
5 TraesCS7D01G125600 chr4D 98.734 237 3 0 921 1157 30386837 30386601 2.540000e-114 422.0
6 TraesCS7D01G125600 chr4D 90.517 232 17 4 692 920 472518773 472519002 3.450000e-78 302.0
7 TraesCS7D01G125600 chr4D 91.579 95 7 1 582 675 472518694 472518788 1.720000e-26 130.0
8 TraesCS7D01G125600 chr4A 92.518 989 55 10 1160 2140 679273571 679274548 0.000000e+00 1399.0
9 TraesCS7D01G125600 chr4A 87.209 86 6 5 66 150 679272906 679272987 2.260000e-15 93.5
10 TraesCS7D01G125600 chr4B 91.820 599 29 13 1555 2141 594872428 594873018 0.000000e+00 817.0
11 TraesCS7D01G125600 chr4B 96.154 312 11 1 365 675 594871530 594871841 1.900000e-140 508.0
12 TraesCS7D01G125600 chr4B 90.859 361 28 3 1154 1512 594872065 594872422 1.490000e-131 479.0
13 TraesCS7D01G125600 chr4B 93.289 298 13 1 1 298 594871210 594871500 1.170000e-117 433.0
14 TraesCS7D01G125600 chr4B 90.795 239 12 7 691 920 594871825 594872062 5.740000e-81 311.0
15 TraesCS7D01G125600 chrUn 98.734 237 3 0 921 1157 93408471 93408235 2.540000e-114 422.0
16 TraesCS7D01G125600 chrUn 98.734 237 3 0 921 1157 389360296 389360532 2.540000e-114 422.0
17 TraesCS7D01G125600 chrUn 98.734 237 3 0 921 1157 444245271 444245035 2.540000e-114 422.0
18 TraesCS7D01G125600 chrUn 92.424 132 8 1 1434 1565 477284226 477284097 1.010000e-43 187.0
19 TraesCS7D01G125600 chr3B 98.734 237 3 0 921 1157 101912336 101912572 2.540000e-114 422.0
20 TraesCS7D01G125600 chr3B 98.734 237 3 0 921 1157 201528185 201528421 2.540000e-114 422.0
21 TraesCS7D01G125600 chr3A 98.734 237 3 0 921 1157 594898463 594898227 2.540000e-114 422.0
22 TraesCS7D01G125600 chr2D 98.734 237 3 0 921 1157 272792752 272792516 2.540000e-114 422.0
23 TraesCS7D01G125600 chr2D 92.424 132 8 1 1434 1565 538391016 538390887 1.010000e-43 187.0
24 TraesCS7D01G125600 chr1A 98.734 237 3 0 921 1157 554513409 554513645 2.540000e-114 422.0
25 TraesCS7D01G125600 chr3D 88.034 234 20 5 694 920 581944888 581945120 9.740000e-69 270.0
26 TraesCS7D01G125600 chr3D 89.048 210 21 1 1154 1361 581945123 581945332 2.110000e-65 259.0
27 TraesCS7D01G125600 chr3D 92.424 132 8 1 1434 1565 464061272 464061401 1.010000e-43 187.0
28 TraesCS7D01G125600 chr5D 92.424 132 8 1 1434 1565 367591879 367592008 1.010000e-43 187.0
29 TraesCS7D01G125600 chr5B 91.667 132 9 1 1434 1565 434923969 434924098 4.690000e-42 182.0


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 TraesCS7D01G125600 chr7D 78500193 78502333 2140 False 3954.000000 3954 100.0000 1 2141 1 chr7D.!!$F1 2140
1 TraesCS7D01G125600 chr4D 472518694 472519990 1296 False 677.333333 1600 92.6840 582 2140 3 chr4D.!!$F1 1558
2 TraesCS7D01G125600 chr4A 679272906 679274548 1642 False 746.250000 1399 89.8635 66 2140 2 chr4A.!!$F1 2074
3 TraesCS7D01G125600 chr4B 594871210 594873018 1808 False 509.600000 817 92.5834 1 2141 5 chr4B.!!$F1 2140

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
76 77 0.60762 GCATTTTTGGGCTACTGGCA 59.392 50.0 0.0 0.0 44.01 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1221 0.031585 TTGACCTCGACCGACTGTTG 59.968 55.0 0.0 0.0 0.0 3.33 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
76 77 0.607620 GCATTTTTGGGCTACTGGCA 59.392 50.000 0.00 0.00 44.01 4.92
152 153 8.567198 TTCCTGGAAATAGGAGAGATGAATAA 57.433 34.615 6.68 0.00 46.94 1.40
153 154 8.200024 TCCTGGAAATAGGAGAGATGAATAAG 57.800 38.462 0.00 0.00 41.85 1.73
157 165 8.443176 TGGAAATAGGAGAGATGAATAAGCAAT 58.557 33.333 0.00 0.00 0.00 3.56
179 187 7.201600 GCAATTAAAAACAGAGCAAAACAGGAA 60.202 33.333 0.00 0.00 0.00 3.36
180 188 8.663911 CAATTAAAAACAGAGCAAAACAGGAAA 58.336 29.630 0.00 0.00 0.00 3.13
181 189 8.785329 ATTAAAAACAGAGCAAAACAGGAAAA 57.215 26.923 0.00 0.00 0.00 2.29
182 190 6.480524 AAAAACAGAGCAAAACAGGAAAAC 57.519 33.333 0.00 0.00 0.00 2.43
183 191 3.801114 ACAGAGCAAAACAGGAAAACC 57.199 42.857 0.00 0.00 0.00 3.27
184 192 2.430694 ACAGAGCAAAACAGGAAAACCC 59.569 45.455 0.00 0.00 0.00 4.11
185 193 2.039418 AGAGCAAAACAGGAAAACCCC 58.961 47.619 0.00 0.00 34.66 4.95
245 253 8.441312 TTTAGTTTCCGTTTTCTGTACAGAAT 57.559 30.769 33.02 19.69 45.78 2.40
261 269 5.587388 ACAGAATGGCTCCATTAAACATG 57.413 39.130 13.64 10.11 45.50 3.21
271 279 5.586243 GCTCCATTAAACATGAAGCTACTCA 59.414 40.000 0.00 0.00 0.00 3.41
298 306 4.956085 TCAAGCTGAAACTTACTGTGCTA 58.044 39.130 0.00 0.00 0.00 3.49
312 320 3.835378 TGTGCTACAGAACAATGCATG 57.165 42.857 0.00 0.00 36.04 4.06
314 322 3.189080 TGTGCTACAGAACAATGCATGTC 59.811 43.478 0.00 0.00 42.99 3.06
315 323 2.749076 TGCTACAGAACAATGCATGTCC 59.251 45.455 0.00 0.00 42.99 4.02
316 324 3.012518 GCTACAGAACAATGCATGTCCT 58.987 45.455 0.00 0.00 42.99 3.85
327 335 2.710377 TGCATGTCCTATGAACACCAC 58.290 47.619 0.00 0.00 0.00 4.16
331 339 3.627395 TGTCCTATGAACACCACCATC 57.373 47.619 0.00 0.00 0.00 3.51
332 340 2.909662 TGTCCTATGAACACCACCATCA 59.090 45.455 0.00 0.00 0.00 3.07
333 341 3.523157 TGTCCTATGAACACCACCATCAT 59.477 43.478 0.00 0.00 37.54 2.45
334 342 3.879295 GTCCTATGAACACCACCATCATG 59.121 47.826 0.00 0.00 35.53 3.07
335 343 2.620115 CCTATGAACACCACCATCATGC 59.380 50.000 0.00 0.00 35.53 4.06
336 344 1.477553 ATGAACACCACCATCATGCC 58.522 50.000 0.00 0.00 32.77 4.40
337 345 0.611618 TGAACACCACCATCATGCCC 60.612 55.000 0.00 0.00 0.00 5.36
338 346 1.305213 AACACCACCATCATGCCCC 60.305 57.895 0.00 0.00 0.00 5.80
339 347 2.442643 CACCACCATCATGCCCCC 60.443 66.667 0.00 0.00 0.00 5.40
371 379 3.219281 TCCCTGGACAAAACAGCTTTAC 58.781 45.455 0.00 0.00 34.65 2.01
384 392 5.862678 ACAGCTTTACCTTTAGCCAAAAA 57.137 34.783 0.00 0.00 38.14 1.94
674 703 5.975939 GCATTATCAAAAGCCAGTGAATCTC 59.024 40.000 0.00 0.00 0.00 2.75
675 704 6.501781 CATTATCAAAAGCCAGTGAATCTCC 58.498 40.000 0.00 0.00 0.00 3.71
676 705 2.795329 TCAAAAGCCAGTGAATCTCCC 58.205 47.619 0.00 0.00 0.00 4.30
677 706 2.376518 TCAAAAGCCAGTGAATCTCCCT 59.623 45.455 0.00 0.00 0.00 4.20
678 707 3.160269 CAAAAGCCAGTGAATCTCCCTT 58.840 45.455 0.00 0.00 0.00 3.95
679 708 3.532641 AAAGCCAGTGAATCTCCCTTT 57.467 42.857 0.00 0.00 0.00 3.11
680 709 2.797177 AGCCAGTGAATCTCCCTTTC 57.203 50.000 0.00 0.00 0.00 2.62
681 710 1.988107 AGCCAGTGAATCTCCCTTTCA 59.012 47.619 0.00 0.00 0.00 2.69
682 711 2.376518 AGCCAGTGAATCTCCCTTTCAA 59.623 45.455 0.00 0.00 35.03 2.69
683 712 3.157087 GCCAGTGAATCTCCCTTTCAAA 58.843 45.455 0.00 0.00 35.03 2.69
684 713 3.573967 GCCAGTGAATCTCCCTTTCAAAA 59.426 43.478 0.00 0.00 35.03 2.44
685 714 4.039124 GCCAGTGAATCTCCCTTTCAAAAA 59.961 41.667 0.00 0.00 35.03 1.94
740 769 0.756294 TATGTGGCCGGACGATTCAT 59.244 50.000 5.05 9.03 0.00 2.57
777 806 3.019564 GCCAGTGCAAGGACAAATCTAT 58.980 45.455 10.49 0.00 37.47 1.98
779 808 4.640201 GCCAGTGCAAGGACAAATCTATAA 59.360 41.667 10.49 0.00 37.47 0.98
813 842 4.946157 CCATCAGCTAGAATGTTCTGGTTT 59.054 41.667 5.55 0.00 37.99 3.27
815 844 5.227569 TCAGCTAGAATGTTCTGGTTTCA 57.772 39.130 5.55 0.00 37.99 2.69
828 863 5.159273 TCTGGTTTCACAGTGCATGTATA 57.841 39.130 0.00 0.00 41.41 1.47
873 908 3.319122 ACTGTTTGATTCCAGTTTGAGCC 59.681 43.478 0.00 0.00 38.76 4.70
920 958 3.648067 CTGGGGAATATCTTGCCTGTAGA 59.352 47.826 1.41 0.00 42.26 2.59
921 959 4.242811 TGGGGAATATCTTGCCTGTAGAT 58.757 43.478 1.41 0.00 42.26 1.98
922 960 4.665009 TGGGGAATATCTTGCCTGTAGATT 59.335 41.667 1.41 0.00 42.26 2.40
923 961 5.221925 TGGGGAATATCTTGCCTGTAGATTC 60.222 44.000 1.41 0.00 42.26 2.52
924 962 5.221925 GGGGAATATCTTGCCTGTAGATTCA 60.222 44.000 1.41 0.00 42.26 2.57
925 963 5.936956 GGGAATATCTTGCCTGTAGATTCAG 59.063 44.000 0.00 0.00 39.64 3.02
926 964 5.411053 GGAATATCTTGCCTGTAGATTCAGC 59.589 44.000 0.00 0.00 34.35 4.26
927 965 2.698855 TCTTGCCTGTAGATTCAGCC 57.301 50.000 0.00 0.00 34.47 4.85
928 966 1.908619 TCTTGCCTGTAGATTCAGCCA 59.091 47.619 0.00 0.00 34.47 4.75
929 967 2.507058 TCTTGCCTGTAGATTCAGCCAT 59.493 45.455 0.00 0.00 34.47 4.40
930 968 2.336945 TGCCTGTAGATTCAGCCATG 57.663 50.000 0.00 0.00 34.47 3.66
931 969 1.134007 TGCCTGTAGATTCAGCCATGG 60.134 52.381 7.63 7.63 34.47 3.66
932 970 1.141657 GCCTGTAGATTCAGCCATGGA 59.858 52.381 18.40 0.00 34.47 3.41
933 971 2.224719 GCCTGTAGATTCAGCCATGGAT 60.225 50.000 18.40 6.18 34.47 3.41
934 972 3.409570 CCTGTAGATTCAGCCATGGATG 58.590 50.000 24.32 24.32 34.47 3.51
935 973 2.812591 CTGTAGATTCAGCCATGGATGC 59.187 50.000 25.40 11.48 0.00 3.91
936 974 2.440627 TGTAGATTCAGCCATGGATGCT 59.559 45.455 25.40 18.10 40.41 3.79
937 975 2.750141 AGATTCAGCCATGGATGCTT 57.250 45.000 25.40 14.34 36.81 3.91
938 976 3.870538 AGATTCAGCCATGGATGCTTA 57.129 42.857 25.40 12.90 36.81 3.09
939 977 4.174704 AGATTCAGCCATGGATGCTTAA 57.825 40.909 25.40 14.74 36.81 1.85
940 978 3.887716 AGATTCAGCCATGGATGCTTAAC 59.112 43.478 25.40 13.40 36.81 2.01
941 979 2.804986 TCAGCCATGGATGCTTAACA 57.195 45.000 25.40 3.68 36.81 2.41
942 980 2.646930 TCAGCCATGGATGCTTAACAG 58.353 47.619 25.40 0.00 36.81 3.16
943 981 1.679680 CAGCCATGGATGCTTAACAGG 59.320 52.381 18.60 0.00 36.81 4.00
944 982 1.035139 GCCATGGATGCTTAACAGGG 58.965 55.000 18.40 0.00 38.96 4.45
945 983 1.410083 GCCATGGATGCTTAACAGGGA 60.410 52.381 18.40 0.00 38.25 4.20
946 984 2.754186 GCCATGGATGCTTAACAGGGAT 60.754 50.000 18.40 0.00 38.25 3.85
947 985 3.152341 CCATGGATGCTTAACAGGGATC 58.848 50.000 5.56 0.00 38.25 3.36
948 986 3.435457 CCATGGATGCTTAACAGGGATCA 60.435 47.826 5.56 0.00 38.25 2.92
949 987 4.404640 CATGGATGCTTAACAGGGATCAT 58.595 43.478 0.00 0.00 34.04 2.45
950 988 4.090761 TGGATGCTTAACAGGGATCATC 57.909 45.455 0.00 0.00 34.04 2.92
951 989 3.070018 GGATGCTTAACAGGGATCATCG 58.930 50.000 0.00 0.00 34.04 3.84
952 990 3.495100 GGATGCTTAACAGGGATCATCGT 60.495 47.826 0.00 0.00 34.04 3.73
953 991 4.262463 GGATGCTTAACAGGGATCATCGTA 60.262 45.833 0.00 0.00 34.04 3.43
954 992 4.054780 TGCTTAACAGGGATCATCGTAC 57.945 45.455 0.00 0.00 0.00 3.67
955 993 3.449377 TGCTTAACAGGGATCATCGTACA 59.551 43.478 0.00 0.00 0.00 2.90
956 994 4.100963 TGCTTAACAGGGATCATCGTACAT 59.899 41.667 0.00 0.00 0.00 2.29
957 995 4.686554 GCTTAACAGGGATCATCGTACATC 59.313 45.833 0.00 0.00 0.00 3.06
958 996 3.371102 AACAGGGATCATCGTACATCG 57.629 47.619 0.00 0.00 41.41 3.84
959 997 2.307768 ACAGGGATCATCGTACATCGT 58.692 47.619 0.00 0.00 40.80 3.73
960 998 3.483421 ACAGGGATCATCGTACATCGTA 58.517 45.455 0.00 0.00 40.80 3.43
961 999 3.887110 ACAGGGATCATCGTACATCGTAA 59.113 43.478 0.00 0.00 40.80 3.18
962 1000 4.340097 ACAGGGATCATCGTACATCGTAAA 59.660 41.667 0.00 0.00 40.80 2.01
963 1001 5.010719 ACAGGGATCATCGTACATCGTAAAT 59.989 40.000 0.00 0.00 40.80 1.40
964 1002 6.208007 ACAGGGATCATCGTACATCGTAAATA 59.792 38.462 0.00 0.00 40.80 1.40
965 1003 7.088272 CAGGGATCATCGTACATCGTAAATAA 58.912 38.462 0.00 0.00 40.80 1.40
966 1004 7.759886 CAGGGATCATCGTACATCGTAAATAAT 59.240 37.037 0.00 0.00 40.80 1.28
967 1005 7.974501 AGGGATCATCGTACATCGTAAATAATC 59.025 37.037 0.00 0.00 40.80 1.75
968 1006 7.758076 GGGATCATCGTACATCGTAAATAATCA 59.242 37.037 0.00 0.00 40.80 2.57
969 1007 9.135843 GGATCATCGTACATCGTAAATAATCAA 57.864 33.333 0.00 0.00 40.80 2.57
1020 1058 9.109393 AGAAAAATGAGATCGAAAATATTCCGA 57.891 29.630 13.07 13.07 31.52 4.55
1021 1059 9.374960 GAAAAATGAGATCGAAAATATTCCGAG 57.625 33.333 15.09 0.00 31.52 4.63
1022 1060 8.662781 AAAATGAGATCGAAAATATTCCGAGA 57.337 30.769 15.09 3.26 31.52 4.04
1023 1061 8.839310 AAATGAGATCGAAAATATTCCGAGAT 57.161 30.769 15.09 7.04 31.52 2.75
1024 1062 7.824704 ATGAGATCGAAAATATTCCGAGATG 57.175 36.000 15.09 0.00 31.52 2.90
1025 1063 6.159293 TGAGATCGAAAATATTCCGAGATGG 58.841 40.000 15.09 0.00 40.09 3.51
1026 1064 4.932200 AGATCGAAAATATTCCGAGATGGC 59.068 41.667 15.09 5.84 37.80 4.40
1027 1065 4.066646 TCGAAAATATTCCGAGATGGCA 57.933 40.909 8.31 0.00 37.80 4.92
1028 1066 4.447290 TCGAAAATATTCCGAGATGGCAA 58.553 39.130 8.31 0.00 37.80 4.52
1029 1067 4.878971 TCGAAAATATTCCGAGATGGCAAA 59.121 37.500 8.31 0.00 37.80 3.68
1030 1068 5.530915 TCGAAAATATTCCGAGATGGCAAAT 59.469 36.000 8.31 0.00 37.80 2.32
1031 1069 6.708502 TCGAAAATATTCCGAGATGGCAAATA 59.291 34.615 8.31 0.00 37.80 1.40
1032 1070 7.390440 TCGAAAATATTCCGAGATGGCAAATAT 59.610 33.333 8.31 0.00 37.80 1.28
1033 1071 8.023128 CGAAAATATTCCGAGATGGCAAATATT 58.977 33.333 6.72 6.72 38.12 1.28
1034 1072 9.346725 GAAAATATTCCGAGATGGCAAATATTC 57.653 33.333 11.12 0.00 36.68 1.75
1035 1073 6.668541 ATATTCCGAGATGGCAAATATTCG 57.331 37.500 0.00 0.00 37.80 3.34
1036 1074 2.766313 TCCGAGATGGCAAATATTCGG 58.234 47.619 16.95 16.95 46.55 4.30
1039 1077 3.653344 CGAGATGGCAAATATTCGGAGA 58.347 45.455 0.00 0.00 0.00 3.71
1040 1078 4.248859 CGAGATGGCAAATATTCGGAGAT 58.751 43.478 0.00 0.00 35.04 2.75
1041 1079 4.092529 CGAGATGGCAAATATTCGGAGATG 59.907 45.833 0.00 0.00 35.04 2.90
1042 1080 5.233083 AGATGGCAAATATTCGGAGATGA 57.767 39.130 0.00 0.00 35.04 2.92
1043 1081 4.999950 AGATGGCAAATATTCGGAGATGAC 59.000 41.667 0.00 0.00 35.04 3.06
1044 1082 4.422073 TGGCAAATATTCGGAGATGACT 57.578 40.909 0.00 0.00 35.04 3.41
1045 1083 5.545063 TGGCAAATATTCGGAGATGACTA 57.455 39.130 0.00 0.00 35.04 2.59
1046 1084 6.114187 TGGCAAATATTCGGAGATGACTAT 57.886 37.500 0.00 0.00 35.04 2.12
1047 1085 5.934043 TGGCAAATATTCGGAGATGACTATG 59.066 40.000 0.00 0.00 35.04 2.23
1048 1086 6.166279 GGCAAATATTCGGAGATGACTATGA 58.834 40.000 0.00 0.00 35.04 2.15
1049 1087 6.650807 GGCAAATATTCGGAGATGACTATGAA 59.349 38.462 0.00 0.00 35.04 2.57
1050 1088 7.173218 GGCAAATATTCGGAGATGACTATGAAA 59.827 37.037 0.00 0.00 35.04 2.69
1051 1089 8.559536 GCAAATATTCGGAGATGACTATGAAAA 58.440 33.333 0.00 0.00 35.04 2.29
1052 1090 9.869844 CAAATATTCGGAGATGACTATGAAAAC 57.130 33.333 0.00 0.00 35.04 2.43
1053 1091 9.613428 AAATATTCGGAGATGACTATGAAAACA 57.387 29.630 0.00 0.00 35.04 2.83
1054 1092 6.910536 ATTCGGAGATGACTATGAAAACAC 57.089 37.500 0.00 0.00 35.04 3.32
1055 1093 4.755411 TCGGAGATGACTATGAAAACACC 58.245 43.478 0.00 0.00 0.00 4.16
1056 1094 4.466370 TCGGAGATGACTATGAAAACACCT 59.534 41.667 0.00 0.00 0.00 4.00
1057 1095 4.806247 CGGAGATGACTATGAAAACACCTC 59.194 45.833 0.00 0.00 0.00 3.85
1058 1096 5.394663 CGGAGATGACTATGAAAACACCTCT 60.395 44.000 0.00 0.00 0.00 3.69
1059 1097 6.045955 GGAGATGACTATGAAAACACCTCTC 58.954 44.000 0.00 0.00 0.00 3.20
1060 1098 6.127196 GGAGATGACTATGAAAACACCTCTCT 60.127 42.308 0.00 0.00 0.00 3.10
1061 1099 6.638610 AGATGACTATGAAAACACCTCTCTG 58.361 40.000 0.00 0.00 0.00 3.35
1062 1100 5.152623 TGACTATGAAAACACCTCTCTGG 57.847 43.478 0.00 0.00 42.93 3.86
1063 1101 4.838423 TGACTATGAAAACACCTCTCTGGA 59.162 41.667 0.00 0.00 39.71 3.86
1064 1102 5.485353 TGACTATGAAAACACCTCTCTGGAT 59.515 40.000 0.00 0.00 39.71 3.41
1065 1103 5.983540 ACTATGAAAACACCTCTCTGGATC 58.016 41.667 0.00 0.00 39.71 3.36
1066 1104 3.703001 TGAAAACACCTCTCTGGATCC 57.297 47.619 4.20 4.20 39.71 3.36
1067 1105 3.251484 TGAAAACACCTCTCTGGATCCT 58.749 45.455 14.23 0.00 39.71 3.24
1068 1106 3.261897 TGAAAACACCTCTCTGGATCCTC 59.738 47.826 14.23 0.00 39.71 3.71
1069 1107 1.479709 AACACCTCTCTGGATCCTCG 58.520 55.000 14.23 4.22 39.71 4.63
1070 1108 0.626382 ACACCTCTCTGGATCCTCGA 59.374 55.000 14.23 8.63 39.71 4.04
1071 1109 1.006043 ACACCTCTCTGGATCCTCGAA 59.994 52.381 14.23 0.00 39.71 3.71
1072 1110 2.315176 CACCTCTCTGGATCCTCGAAT 58.685 52.381 14.23 0.00 39.71 3.34
1073 1111 2.697751 CACCTCTCTGGATCCTCGAATT 59.302 50.000 14.23 0.00 39.71 2.17
1074 1112 2.697751 ACCTCTCTGGATCCTCGAATTG 59.302 50.000 14.23 3.49 39.71 2.32
1075 1113 2.961741 CCTCTCTGGATCCTCGAATTGA 59.038 50.000 14.23 3.15 38.35 2.57
1076 1114 3.386078 CCTCTCTGGATCCTCGAATTGAA 59.614 47.826 14.23 0.00 38.35 2.69
1077 1115 4.141846 CCTCTCTGGATCCTCGAATTGAAA 60.142 45.833 14.23 0.00 38.35 2.69
1078 1116 5.016051 TCTCTGGATCCTCGAATTGAAAG 57.984 43.478 14.23 0.00 0.00 2.62
1079 1117 4.711846 TCTCTGGATCCTCGAATTGAAAGA 59.288 41.667 14.23 2.13 0.00 2.52
1080 1118 5.016051 TCTGGATCCTCGAATTGAAAGAG 57.984 43.478 14.23 0.00 0.00 2.85
1081 1119 4.711846 TCTGGATCCTCGAATTGAAAGAGA 59.288 41.667 14.23 0.00 34.13 3.10
1082 1120 5.016051 TGGATCCTCGAATTGAAAGAGAG 57.984 43.478 14.23 0.00 34.13 3.20
1083 1121 4.711846 TGGATCCTCGAATTGAAAGAGAGA 59.288 41.667 14.23 0.00 34.13 3.10
1084 1122 5.365025 TGGATCCTCGAATTGAAAGAGAGAT 59.635 40.000 14.23 0.00 34.13 2.75
1085 1123 6.126940 TGGATCCTCGAATTGAAAGAGAGATT 60.127 38.462 14.23 0.00 34.13 2.40
1086 1124 6.202570 GGATCCTCGAATTGAAAGAGAGATTG 59.797 42.308 3.84 0.00 34.13 2.67
1087 1125 6.286240 TCCTCGAATTGAAAGAGAGATTGA 57.714 37.500 0.00 0.00 34.13 2.57
1088 1126 6.336566 TCCTCGAATTGAAAGAGAGATTGAG 58.663 40.000 0.00 0.00 34.13 3.02
1089 1127 6.153510 TCCTCGAATTGAAAGAGAGATTGAGA 59.846 38.462 0.00 0.00 34.13 3.27
1090 1128 6.476380 CCTCGAATTGAAAGAGAGATTGAGAG 59.524 42.308 0.00 0.00 34.13 3.20
1091 1129 6.336566 TCGAATTGAAAGAGAGATTGAGAGG 58.663 40.000 0.00 0.00 0.00 3.69
1092 1130 5.523188 CGAATTGAAAGAGAGATTGAGAGGG 59.477 44.000 0.00 0.00 0.00 4.30
1093 1131 6.629068 CGAATTGAAAGAGAGATTGAGAGGGA 60.629 42.308 0.00 0.00 0.00 4.20
1094 1132 6.828307 ATTGAAAGAGAGATTGAGAGGGAT 57.172 37.500 0.00 0.00 0.00 3.85
1095 1133 5.867903 TGAAAGAGAGATTGAGAGGGATC 57.132 43.478 0.00 0.00 0.00 3.36
1096 1134 5.275630 TGAAAGAGAGATTGAGAGGGATCA 58.724 41.667 0.00 0.00 0.00 2.92
1097 1135 5.723405 TGAAAGAGAGATTGAGAGGGATCAA 59.277 40.000 0.00 0.00 43.04 2.57
1098 1136 5.874897 AAGAGAGATTGAGAGGGATCAAG 57.125 43.478 0.00 0.00 42.20 3.02
1099 1137 5.141455 AGAGAGATTGAGAGGGATCAAGA 57.859 43.478 0.00 0.00 42.20 3.02
1100 1138 5.527385 AGAGAGATTGAGAGGGATCAAGAA 58.473 41.667 0.00 0.00 42.20 2.52
1101 1139 6.145336 AGAGAGATTGAGAGGGATCAAGAAT 58.855 40.000 0.00 0.00 42.20 2.40
1102 1140 6.268387 AGAGAGATTGAGAGGGATCAAGAATC 59.732 42.308 0.00 0.00 42.20 2.52
1122 1160 7.730364 GAATCCTAATTCTCGCTATTTGGAA 57.270 36.000 9.67 0.00 39.28 3.53
1123 1161 8.329203 GAATCCTAATTCTCGCTATTTGGAAT 57.671 34.615 9.67 4.15 39.28 3.01
1124 1162 7.678947 ATCCTAATTCTCGCTATTTGGAATG 57.321 36.000 9.67 0.00 39.28 2.67
1125 1163 5.997746 TCCTAATTCTCGCTATTTGGAATGG 59.002 40.000 0.00 0.00 35.13 3.16
1126 1164 5.997746 CCTAATTCTCGCTATTTGGAATGGA 59.002 40.000 0.00 0.00 31.99 3.41
1127 1165 6.656693 CCTAATTCTCGCTATTTGGAATGGAT 59.343 38.462 0.00 0.00 31.99 3.41
1128 1166 6.566197 AATTCTCGCTATTTGGAATGGATC 57.434 37.500 0.00 0.00 0.00 3.36
1145 1183 8.097078 GAATGGATCCAATTCTATTGAGTCTG 57.903 38.462 20.67 0.00 28.21 3.51
1146 1184 6.813293 TGGATCCAATTCTATTGAGTCTGA 57.187 37.500 13.46 0.00 0.00 3.27
1147 1185 6.586344 TGGATCCAATTCTATTGAGTCTGAC 58.414 40.000 13.46 0.00 0.00 3.51
1148 1186 6.385176 TGGATCCAATTCTATTGAGTCTGACT 59.615 38.462 13.46 10.66 0.00 3.41
1149 1187 6.928492 GGATCCAATTCTATTGAGTCTGACTC 59.072 42.308 26.86 26.86 45.26 3.36
1170 1208 7.067615 TGACTCATAGTGACTAGGATGAACTTC 59.932 40.741 7.48 1.42 0.00 3.01
1183 1221 0.670854 GAACTTCGTGGCTGGAGGAC 60.671 60.000 0.00 0.00 0.00 3.85
1198 1236 1.080705 GGACAACAGTCGGTCGAGG 60.081 63.158 0.00 0.00 34.87 4.63
1214 1252 4.681978 GGTCAACAGCGGCGTCCT 62.682 66.667 9.37 0.00 0.00 3.85
1233 1273 2.837532 TGCTGCACAGATAGACACAA 57.162 45.000 0.00 0.00 0.00 3.33
1264 1304 3.181473 TGCAGAATCAGCTTTGTTGCTTT 60.181 39.130 0.00 0.00 41.98 3.51
1306 1347 2.607771 CCTTGCCAAACAAATCTCACCG 60.608 50.000 0.00 0.00 37.96 4.94
1430 1474 2.094752 GCAATTTTCGGGAGCTTAGCAA 60.095 45.455 7.07 0.00 0.00 3.91
1432 1477 1.821216 TTTTCGGGAGCTTAGCAAGG 58.179 50.000 7.07 0.00 0.00 3.61
1434 1479 1.836999 TTCGGGAGCTTAGCAAGGCA 61.837 55.000 7.07 0.00 0.00 4.75
1495 1542 9.533253 CAAATACAAATGACAAAGAAAGGAAGT 57.467 29.630 0.00 0.00 0.00 3.01
1551 1598 7.488471 GCGGCTACATATAAGAAAGATATCGTT 59.512 37.037 3.37 3.37 0.00 3.85
1552 1599 9.355215 CGGCTACATATAAGAAAGATATCGTTT 57.645 33.333 5.34 3.09 0.00 3.60
1692 1742 4.566545 TTGATACAAACTTGTGCCACAG 57.433 40.909 5.34 0.00 42.31 3.66
1695 1745 1.029408 ACAAACTTGTGCCACAGCGA 61.029 50.000 0.00 0.00 44.31 4.93
1696 1752 0.317269 CAAACTTGTGCCACAGCGAG 60.317 55.000 0.00 0.00 44.31 5.03
1752 1808 0.036590 TAGTACCCACCCGCAAAACC 59.963 55.000 0.00 0.00 0.00 3.27
2056 2119 3.758554 TCATCTCAACAGTCTCATCGTCA 59.241 43.478 0.00 0.00 0.00 4.35
2128 2191 4.309950 GGCCCACTTCCGACGTGT 62.310 66.667 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.946377 CCCAGTAGCTCCTAGTCAAAATTTT 59.054 40.000 0.00 0.00 0.00 1.82
71 72 2.687700 AGCTAACTCTGTGATGCCAG 57.312 50.000 0.00 0.00 0.00 4.85
76 77 6.299805 TCCAACAATAGCTAACTCTGTGAT 57.700 37.500 0.00 0.00 0.00 3.06
152 153 6.258507 CCTGTTTTGCTCTGTTTTTAATTGCT 59.741 34.615 0.00 0.00 0.00 3.91
153 154 6.257630 TCCTGTTTTGCTCTGTTTTTAATTGC 59.742 34.615 0.00 0.00 0.00 3.56
157 165 7.118535 GGTTTTCCTGTTTTGCTCTGTTTTTAA 59.881 33.333 0.00 0.00 36.94 1.52
261 269 5.114780 TCAGCTTGATTCATGAGTAGCTTC 58.885 41.667 11.63 0.00 36.88 3.86
271 279 6.569226 GCACAGTAAGTTTCAGCTTGATTCAT 60.569 38.462 0.00 0.00 0.00 2.57
275 283 4.392940 AGCACAGTAAGTTTCAGCTTGAT 58.607 39.130 0.00 0.00 0.00 2.57
298 306 4.847198 TCATAGGACATGCATTGTTCTGT 58.153 39.130 16.07 9.52 44.38 3.41
301 309 5.335127 GTGTTCATAGGACATGCATTGTTC 58.665 41.667 0.00 0.00 39.18 3.18
302 310 4.158394 GGTGTTCATAGGACATGCATTGTT 59.842 41.667 0.00 0.00 39.18 2.83
303 311 3.696051 GGTGTTCATAGGACATGCATTGT 59.304 43.478 0.00 0.00 42.79 2.71
304 312 3.695556 TGGTGTTCATAGGACATGCATTG 59.304 43.478 0.00 0.00 0.00 2.82
305 313 3.696051 GTGGTGTTCATAGGACATGCATT 59.304 43.478 0.00 0.00 0.00 3.56
309 317 3.348647 TGGTGGTGTTCATAGGACATG 57.651 47.619 0.00 0.00 0.00 3.21
312 320 3.627395 TGATGGTGGTGTTCATAGGAC 57.373 47.619 0.00 0.00 0.00 3.85
314 322 2.620115 GCATGATGGTGGTGTTCATAGG 59.380 50.000 0.00 0.00 0.00 2.57
315 323 2.620115 GGCATGATGGTGGTGTTCATAG 59.380 50.000 0.00 0.00 0.00 2.23
316 324 2.653726 GGCATGATGGTGGTGTTCATA 58.346 47.619 0.00 0.00 0.00 2.15
345 353 3.711190 AGCTGTTTTGTCCAGGGATTTTT 59.289 39.130 0.00 0.00 0.00 1.94
346 354 3.308401 AGCTGTTTTGTCCAGGGATTTT 58.692 40.909 0.00 0.00 0.00 1.82
347 355 2.962859 AGCTGTTTTGTCCAGGGATTT 58.037 42.857 0.00 0.00 0.00 2.17
348 356 2.683211 AGCTGTTTTGTCCAGGGATT 57.317 45.000 0.00 0.00 0.00 3.01
349 357 2.683211 AAGCTGTTTTGTCCAGGGAT 57.317 45.000 0.00 0.00 0.00 3.85
350 358 2.452600 AAAGCTGTTTTGTCCAGGGA 57.547 45.000 0.00 0.00 0.00 4.20
351 359 2.296190 GGTAAAGCTGTTTTGTCCAGGG 59.704 50.000 0.00 0.00 0.00 4.45
352 360 3.222603 AGGTAAAGCTGTTTTGTCCAGG 58.777 45.455 12.46 0.00 31.18 4.45
353 361 4.918810 AAGGTAAAGCTGTTTTGTCCAG 57.081 40.909 12.46 0.00 31.18 3.86
354 362 5.221165 GCTAAAGGTAAAGCTGTTTTGTCCA 60.221 40.000 12.46 0.00 35.80 4.02
355 363 5.220381 GCTAAAGGTAAAGCTGTTTTGTCC 58.780 41.667 0.00 3.01 35.80 4.02
356 364 5.220381 GGCTAAAGGTAAAGCTGTTTTGTC 58.780 41.667 0.00 0.00 38.80 3.18
357 365 4.647399 TGGCTAAAGGTAAAGCTGTTTTGT 59.353 37.500 0.00 0.00 38.80 2.83
358 366 5.195001 TGGCTAAAGGTAAAGCTGTTTTG 57.805 39.130 0.00 0.00 38.80 2.44
359 367 5.862678 TTGGCTAAAGGTAAAGCTGTTTT 57.137 34.783 0.00 0.00 38.80 2.43
360 368 5.862678 TTTGGCTAAAGGTAAAGCTGTTT 57.137 34.783 0.00 0.00 38.80 2.83
361 369 5.862678 TTTTGGCTAAAGGTAAAGCTGTT 57.137 34.783 0.00 0.00 38.80 3.16
362 370 5.862678 TTTTTGGCTAAAGGTAAAGCTGT 57.137 34.783 0.00 0.00 38.80 4.40
363 371 7.728847 AAATTTTTGGCTAAAGGTAAAGCTG 57.271 32.000 0.00 0.00 38.80 4.24
438 446 7.607607 ACAAGAACTATGTTCATTGCATGACTA 59.392 33.333 12.16 0.00 39.39 2.59
460 468 6.427853 TGGAACAACTATCAGTTCATGACAAG 59.572 38.462 0.00 0.00 44.46 3.16
689 718 2.863809 ACCGAGATTCACTGGCTTTTT 58.136 42.857 0.00 0.00 0.00 1.94
690 719 2.568623 ACCGAGATTCACTGGCTTTT 57.431 45.000 0.00 0.00 0.00 2.27
691 720 2.427506 GAACCGAGATTCACTGGCTTT 58.572 47.619 0.00 0.00 0.00 3.51
692 721 1.339151 GGAACCGAGATTCACTGGCTT 60.339 52.381 0.00 0.00 0.00 4.35
693 722 0.250513 GGAACCGAGATTCACTGGCT 59.749 55.000 0.00 0.00 0.00 4.75
694 723 0.744771 GGGAACCGAGATTCACTGGC 60.745 60.000 0.00 0.00 40.86 4.85
695 724 3.460648 GGGAACCGAGATTCACTGG 57.539 57.895 0.00 0.00 40.86 4.00
740 769 2.179764 GGCGACTGGCATAGCAAAA 58.820 52.632 10.33 0.00 46.16 2.44
813 842 6.280855 ACAGTTACTATACATGCACTGTGA 57.719 37.500 12.86 0.00 42.49 3.58
815 844 6.464222 ACAACAGTTACTATACATGCACTGT 58.536 36.000 0.00 0.00 45.25 3.55
828 863 1.068127 ACCGAAGCGACAACAGTTACT 59.932 47.619 0.00 0.00 0.00 2.24
920 958 3.634504 TGTTAAGCATCCATGGCTGAAT 58.365 40.909 19.76 9.01 41.66 2.57
921 959 3.018856 CTGTTAAGCATCCATGGCTGAA 58.981 45.455 19.76 3.98 41.66 3.02
922 960 2.646930 CTGTTAAGCATCCATGGCTGA 58.353 47.619 19.76 0.00 41.66 4.26
923 961 1.679680 CCTGTTAAGCATCCATGGCTG 59.320 52.381 11.37 11.37 41.66 4.85
924 962 1.410648 CCCTGTTAAGCATCCATGGCT 60.411 52.381 6.96 0.00 45.15 4.75
925 963 1.035139 CCCTGTTAAGCATCCATGGC 58.965 55.000 6.96 0.00 0.00 4.40
926 964 2.734755 TCCCTGTTAAGCATCCATGG 57.265 50.000 4.97 4.97 0.00 3.66
927 965 3.824133 TGATCCCTGTTAAGCATCCATG 58.176 45.455 0.00 0.00 0.00 3.66
928 966 4.660168 GATGATCCCTGTTAAGCATCCAT 58.340 43.478 0.00 0.00 0.00 3.41
929 967 3.494924 CGATGATCCCTGTTAAGCATCCA 60.495 47.826 0.00 0.00 31.02 3.41
930 968 3.070018 CGATGATCCCTGTTAAGCATCC 58.930 50.000 0.00 0.00 31.02 3.51
931 969 3.733337 ACGATGATCCCTGTTAAGCATC 58.267 45.455 0.00 0.00 0.00 3.91
932 970 3.845781 ACGATGATCCCTGTTAAGCAT 57.154 42.857 0.00 0.00 0.00 3.79
933 971 3.449377 TGTACGATGATCCCTGTTAAGCA 59.551 43.478 0.00 0.00 0.00 3.91
934 972 4.054780 TGTACGATGATCCCTGTTAAGC 57.945 45.455 0.00 0.00 0.00 3.09
935 973 4.917998 CGATGTACGATGATCCCTGTTAAG 59.082 45.833 0.00 0.00 45.77 1.85
936 974 4.340097 ACGATGTACGATGATCCCTGTTAA 59.660 41.667 0.00 0.00 45.77 2.01
937 975 3.887110 ACGATGTACGATGATCCCTGTTA 59.113 43.478 0.00 0.00 45.77 2.41
938 976 2.693591 ACGATGTACGATGATCCCTGTT 59.306 45.455 0.00 0.00 45.77 3.16
939 977 2.307768 ACGATGTACGATGATCCCTGT 58.692 47.619 0.00 0.00 45.77 4.00
940 978 4.499037 TTACGATGTACGATGATCCCTG 57.501 45.455 0.00 0.00 45.77 4.45
941 979 5.723672 ATTTACGATGTACGATGATCCCT 57.276 39.130 0.00 0.00 45.77 4.20
942 980 7.758076 TGATTATTTACGATGTACGATGATCCC 59.242 37.037 0.00 0.00 45.77 3.85
943 981 8.683550 TGATTATTTACGATGTACGATGATCC 57.316 34.615 0.00 0.00 45.77 3.36
994 1032 9.109393 TCGGAATATTTTCGATCTCATTTTTCT 57.891 29.630 9.71 0.00 32.28 2.52
995 1033 9.374960 CTCGGAATATTTTCGATCTCATTTTTC 57.625 33.333 12.88 0.00 32.28 2.29
996 1034 9.109393 TCTCGGAATATTTTCGATCTCATTTTT 57.891 29.630 12.88 0.00 32.28 1.94
997 1035 8.662781 TCTCGGAATATTTTCGATCTCATTTT 57.337 30.769 12.88 0.00 32.28 1.82
998 1036 8.715998 CATCTCGGAATATTTTCGATCTCATTT 58.284 33.333 12.88 0.00 32.28 2.32
999 1037 7.332926 CCATCTCGGAATATTTTCGATCTCATT 59.667 37.037 12.88 0.00 36.56 2.57
1000 1038 6.815641 CCATCTCGGAATATTTTCGATCTCAT 59.184 38.462 12.88 4.13 36.56 2.90
1001 1039 6.159293 CCATCTCGGAATATTTTCGATCTCA 58.841 40.000 12.88 2.52 36.56 3.27
1002 1040 5.062809 GCCATCTCGGAATATTTTCGATCTC 59.937 44.000 12.88 2.21 36.56 2.75
1003 1041 4.932200 GCCATCTCGGAATATTTTCGATCT 59.068 41.667 12.88 4.17 36.56 2.75
1004 1042 4.690748 TGCCATCTCGGAATATTTTCGATC 59.309 41.667 12.88 0.00 36.56 3.69
1005 1043 4.641396 TGCCATCTCGGAATATTTTCGAT 58.359 39.130 12.88 1.61 36.56 3.59
1006 1044 4.066646 TGCCATCTCGGAATATTTTCGA 57.933 40.909 12.20 12.20 36.56 3.71
1007 1045 4.811555 TTGCCATCTCGGAATATTTTCG 57.188 40.909 5.99 5.99 36.56 3.46
1008 1046 9.346725 GAATATTTGCCATCTCGGAATATTTTC 57.653 33.333 0.00 0.00 36.56 2.29
1009 1047 8.023128 CGAATATTTGCCATCTCGGAATATTTT 58.977 33.333 0.00 0.00 36.56 1.82
1010 1048 7.362056 CCGAATATTTGCCATCTCGGAATATTT 60.362 37.037 2.19 0.00 46.83 1.40
1011 1049 6.094048 CCGAATATTTGCCATCTCGGAATATT 59.906 38.462 2.19 0.00 46.83 1.28
1012 1050 5.586243 CCGAATATTTGCCATCTCGGAATAT 59.414 40.000 2.19 0.00 46.83 1.28
1013 1051 4.935205 CCGAATATTTGCCATCTCGGAATA 59.065 41.667 2.19 0.00 46.83 1.75
1014 1052 3.753272 CCGAATATTTGCCATCTCGGAAT 59.247 43.478 2.19 0.00 46.83 3.01
1015 1053 3.138304 CCGAATATTTGCCATCTCGGAA 58.862 45.455 2.19 0.00 46.83 4.30
1016 1054 2.766313 CCGAATATTTGCCATCTCGGA 58.234 47.619 2.19 0.00 46.83 4.55
1017 1055 2.738846 CTCCGAATATTTGCCATCTCGG 59.261 50.000 1.95 1.95 45.59 4.63
1018 1056 3.653344 TCTCCGAATATTTGCCATCTCG 58.347 45.455 0.00 0.00 0.00 4.04
1019 1057 5.121454 GTCATCTCCGAATATTTGCCATCTC 59.879 44.000 0.00 0.00 0.00 2.75
1020 1058 4.999950 GTCATCTCCGAATATTTGCCATCT 59.000 41.667 0.00 0.00 0.00 2.90
1021 1059 4.999950 AGTCATCTCCGAATATTTGCCATC 59.000 41.667 0.00 0.00 0.00 3.51
1022 1060 4.978099 AGTCATCTCCGAATATTTGCCAT 58.022 39.130 0.00 0.00 0.00 4.40
1023 1061 4.422073 AGTCATCTCCGAATATTTGCCA 57.578 40.909 0.00 0.00 0.00 4.92
1024 1062 6.166279 TCATAGTCATCTCCGAATATTTGCC 58.834 40.000 0.00 0.00 0.00 4.52
1025 1063 7.658179 TTCATAGTCATCTCCGAATATTTGC 57.342 36.000 0.00 0.00 0.00 3.68
1026 1064 9.869844 GTTTTCATAGTCATCTCCGAATATTTG 57.130 33.333 0.00 0.00 0.00 2.32
1027 1065 9.613428 TGTTTTCATAGTCATCTCCGAATATTT 57.387 29.630 0.00 0.00 0.00 1.40
1028 1066 9.046296 GTGTTTTCATAGTCATCTCCGAATATT 57.954 33.333 0.00 0.00 0.00 1.28
1029 1067 7.657761 GGTGTTTTCATAGTCATCTCCGAATAT 59.342 37.037 0.00 0.00 0.00 1.28
1030 1068 6.984474 GGTGTTTTCATAGTCATCTCCGAATA 59.016 38.462 0.00 0.00 0.00 1.75
1031 1069 5.817816 GGTGTTTTCATAGTCATCTCCGAAT 59.182 40.000 0.00 0.00 0.00 3.34
1032 1070 5.046591 AGGTGTTTTCATAGTCATCTCCGAA 60.047 40.000 0.00 0.00 0.00 4.30
1033 1071 4.466370 AGGTGTTTTCATAGTCATCTCCGA 59.534 41.667 0.00 0.00 0.00 4.55
1034 1072 4.759782 AGGTGTTTTCATAGTCATCTCCG 58.240 43.478 0.00 0.00 0.00 4.63
1035 1073 5.983540 AGAGGTGTTTTCATAGTCATCTCC 58.016 41.667 0.00 0.00 38.39 3.71
1036 1074 6.756074 CAGAGAGGTGTTTTCATAGTCATCTC 59.244 42.308 0.00 0.00 38.05 2.75
1037 1075 6.351711 CCAGAGAGGTGTTTTCATAGTCATCT 60.352 42.308 0.00 0.00 0.00 2.90
1038 1076 5.814705 CCAGAGAGGTGTTTTCATAGTCATC 59.185 44.000 0.00 0.00 0.00 2.92
1039 1077 5.485353 TCCAGAGAGGTGTTTTCATAGTCAT 59.515 40.000 0.00 0.00 39.02 3.06
1040 1078 4.838423 TCCAGAGAGGTGTTTTCATAGTCA 59.162 41.667 0.00 0.00 39.02 3.41
1041 1079 5.407407 TCCAGAGAGGTGTTTTCATAGTC 57.593 43.478 0.00 0.00 39.02 2.59
1042 1080 5.104735 GGATCCAGAGAGGTGTTTTCATAGT 60.105 44.000 6.95 0.00 39.02 2.12
1043 1081 5.130145 AGGATCCAGAGAGGTGTTTTCATAG 59.870 44.000 15.82 0.00 39.02 2.23
1044 1082 5.032846 AGGATCCAGAGAGGTGTTTTCATA 58.967 41.667 15.82 0.00 39.02 2.15
1045 1083 3.848975 AGGATCCAGAGAGGTGTTTTCAT 59.151 43.478 15.82 0.00 39.02 2.57
1046 1084 3.251484 AGGATCCAGAGAGGTGTTTTCA 58.749 45.455 15.82 0.00 39.02 2.69
1047 1085 3.677424 CGAGGATCCAGAGAGGTGTTTTC 60.677 52.174 15.82 0.00 39.02 2.29
1048 1086 2.234908 CGAGGATCCAGAGAGGTGTTTT 59.765 50.000 15.82 0.00 39.02 2.43
1049 1087 1.827969 CGAGGATCCAGAGAGGTGTTT 59.172 52.381 15.82 0.00 39.02 2.83
1050 1088 1.006043 TCGAGGATCCAGAGAGGTGTT 59.994 52.381 15.82 0.00 39.02 3.32
1051 1089 0.626382 TCGAGGATCCAGAGAGGTGT 59.374 55.000 15.82 0.00 39.02 4.16
1052 1090 1.769026 TTCGAGGATCCAGAGAGGTG 58.231 55.000 15.82 0.00 39.02 4.00
1053 1091 2.697751 CAATTCGAGGATCCAGAGAGGT 59.302 50.000 15.82 0.00 39.02 3.85
1054 1092 2.961741 TCAATTCGAGGATCCAGAGAGG 59.038 50.000 15.82 6.22 39.47 3.69
1055 1093 4.662468 TTCAATTCGAGGATCCAGAGAG 57.338 45.455 15.82 6.87 0.00 3.20
1056 1094 4.711846 TCTTTCAATTCGAGGATCCAGAGA 59.288 41.667 15.82 7.13 0.00 3.10
1057 1095 5.016051 TCTTTCAATTCGAGGATCCAGAG 57.984 43.478 15.82 4.59 0.00 3.35
1058 1096 4.711846 TCTCTTTCAATTCGAGGATCCAGA 59.288 41.667 15.82 10.27 0.00 3.86
1059 1097 5.016051 TCTCTTTCAATTCGAGGATCCAG 57.984 43.478 15.82 7.77 0.00 3.86
1060 1098 4.711846 TCTCTCTTTCAATTCGAGGATCCA 59.288 41.667 15.82 0.00 0.00 3.41
1061 1099 5.269505 TCTCTCTTTCAATTCGAGGATCC 57.730 43.478 2.48 2.48 0.00 3.36
1062 1100 6.983307 TCAATCTCTCTTTCAATTCGAGGATC 59.017 38.462 0.00 0.00 0.00 3.36
1063 1101 6.882656 TCAATCTCTCTTTCAATTCGAGGAT 58.117 36.000 0.00 0.00 0.00 3.24
1064 1102 6.153510 TCTCAATCTCTCTTTCAATTCGAGGA 59.846 38.462 0.00 0.00 0.00 3.71
1065 1103 6.336566 TCTCAATCTCTCTTTCAATTCGAGG 58.663 40.000 0.00 0.00 0.00 4.63
1066 1104 6.476380 CCTCTCAATCTCTCTTTCAATTCGAG 59.524 42.308 0.00 0.00 0.00 4.04
1067 1105 6.336566 CCTCTCAATCTCTCTTTCAATTCGA 58.663 40.000 0.00 0.00 0.00 3.71
1068 1106 5.523188 CCCTCTCAATCTCTCTTTCAATTCG 59.477 44.000 0.00 0.00 0.00 3.34
1069 1107 6.648192 TCCCTCTCAATCTCTCTTTCAATTC 58.352 40.000 0.00 0.00 0.00 2.17
1070 1108 6.633325 TCCCTCTCAATCTCTCTTTCAATT 57.367 37.500 0.00 0.00 0.00 2.32
1071 1109 6.386342 TGATCCCTCTCAATCTCTCTTTCAAT 59.614 38.462 0.00 0.00 0.00 2.57
1072 1110 5.723405 TGATCCCTCTCAATCTCTCTTTCAA 59.277 40.000 0.00 0.00 0.00 2.69
1073 1111 5.275630 TGATCCCTCTCAATCTCTCTTTCA 58.724 41.667 0.00 0.00 0.00 2.69
1074 1112 5.867903 TGATCCCTCTCAATCTCTCTTTC 57.132 43.478 0.00 0.00 0.00 2.62
1075 1113 5.963253 TCTTGATCCCTCTCAATCTCTCTTT 59.037 40.000 0.00 0.00 34.76 2.52
1076 1114 5.527385 TCTTGATCCCTCTCAATCTCTCTT 58.473 41.667 0.00 0.00 34.76 2.85
1077 1115 5.141455 TCTTGATCCCTCTCAATCTCTCT 57.859 43.478 0.00 0.00 34.76 3.10
1078 1116 5.867903 TTCTTGATCCCTCTCAATCTCTC 57.132 43.478 0.00 0.00 34.76 3.20
1079 1117 6.423776 GATTCTTGATCCCTCTCAATCTCT 57.576 41.667 0.00 0.00 34.76 3.10
1098 1136 7.730364 TTCCAAATAGCGAGAATTAGGATTC 57.270 36.000 0.00 0.00 41.63 2.52
1099 1137 7.175641 CCATTCCAAATAGCGAGAATTAGGATT 59.824 37.037 0.00 0.00 0.00 3.01
1100 1138 6.656693 CCATTCCAAATAGCGAGAATTAGGAT 59.343 38.462 0.00 0.00 0.00 3.24
1101 1139 5.997746 CCATTCCAAATAGCGAGAATTAGGA 59.002 40.000 0.00 0.00 0.00 2.94
1102 1140 5.997746 TCCATTCCAAATAGCGAGAATTAGG 59.002 40.000 0.00 0.00 0.00 2.69
1103 1141 7.148340 GGATCCATTCCAAATAGCGAGAATTAG 60.148 40.741 6.95 0.00 44.74 1.73
1104 1142 6.655003 GGATCCATTCCAAATAGCGAGAATTA 59.345 38.462 6.95 0.00 44.74 1.40
1105 1143 5.474876 GGATCCATTCCAAATAGCGAGAATT 59.525 40.000 6.95 0.00 44.74 2.17
1106 1144 5.006386 GGATCCATTCCAAATAGCGAGAAT 58.994 41.667 6.95 0.00 44.74 2.40
1107 1145 4.389374 GGATCCATTCCAAATAGCGAGAA 58.611 43.478 6.95 0.00 44.74 2.87
1108 1146 4.008074 GGATCCATTCCAAATAGCGAGA 57.992 45.455 6.95 0.00 44.74 4.04
1119 1157 7.174599 CAGACTCAATAGAATTGGATCCATTCC 59.825 40.741 17.06 7.45 45.69 3.01
1120 1158 7.935755 TCAGACTCAATAGAATTGGATCCATTC 59.064 37.037 17.06 19.35 0.00 2.67
1121 1159 7.718753 GTCAGACTCAATAGAATTGGATCCATT 59.281 37.037 17.06 9.61 0.00 3.16
1122 1160 7.072202 AGTCAGACTCAATAGAATTGGATCCAT 59.928 37.037 17.06 0.06 0.00 3.41
1123 1161 6.385176 AGTCAGACTCAATAGAATTGGATCCA 59.615 38.462 11.44 11.44 0.00 3.41
1124 1162 6.825610 AGTCAGACTCAATAGAATTGGATCC 58.174 40.000 4.20 4.20 0.00 3.36
1125 1163 7.945033 GAGTCAGACTCAATAGAATTGGATC 57.055 40.000 23.62 0.00 44.45 3.36
1139 1177 5.676552 TCCTAGTCACTATGAGTCAGACTC 58.323 45.833 22.09 22.09 45.26 3.36
1140 1178 5.702065 TCCTAGTCACTATGAGTCAGACT 57.298 43.478 14.92 14.92 41.88 3.24
1141 1179 6.058833 TCATCCTAGTCACTATGAGTCAGAC 58.941 44.000 0.00 0.34 31.49 3.51
1142 1180 6.253946 TCATCCTAGTCACTATGAGTCAGA 57.746 41.667 0.00 0.00 31.49 3.27
1143 1181 6.545666 AGTTCATCCTAGTCACTATGAGTCAG 59.454 42.308 0.00 0.00 31.49 3.51
1144 1182 6.427441 AGTTCATCCTAGTCACTATGAGTCA 58.573 40.000 0.00 0.00 31.49 3.41
1145 1183 6.952773 AGTTCATCCTAGTCACTATGAGTC 57.047 41.667 0.00 0.00 31.49 3.36
1146 1184 6.038825 CGAAGTTCATCCTAGTCACTATGAGT 59.961 42.308 3.32 0.00 33.94 3.41
1147 1185 6.038825 ACGAAGTTCATCCTAGTCACTATGAG 59.961 42.308 3.32 0.00 37.78 2.90
1148 1186 5.886474 ACGAAGTTCATCCTAGTCACTATGA 59.114 40.000 3.32 0.00 37.78 2.15
1149 1187 5.974158 CACGAAGTTCATCCTAGTCACTATG 59.026 44.000 3.32 0.00 41.61 2.23
1150 1188 5.067936 CCACGAAGTTCATCCTAGTCACTAT 59.932 44.000 3.32 0.00 41.61 2.12
1151 1189 4.398358 CCACGAAGTTCATCCTAGTCACTA 59.602 45.833 3.32 0.00 41.61 2.74
1152 1190 3.193691 CCACGAAGTTCATCCTAGTCACT 59.806 47.826 3.32 0.00 41.61 3.41
1155 1193 2.166664 AGCCACGAAGTTCATCCTAGTC 59.833 50.000 3.32 0.00 41.61 2.59
1170 1208 1.669115 CTGTTGTCCTCCAGCCACG 60.669 63.158 0.00 0.00 0.00 4.94
1183 1221 0.031585 TTGACCTCGACCGACTGTTG 59.968 55.000 0.00 0.00 0.00 3.33
1198 1236 3.414700 CAGGACGCCGCTGTTGAC 61.415 66.667 0.00 0.00 0.00 3.18
1214 1252 2.416747 GTTGTGTCTATCTGTGCAGCA 58.583 47.619 0.00 0.00 0.00 4.41
1232 1272 2.095059 GCTGATTCTGCATTTCGTGGTT 60.095 45.455 10.32 0.00 0.00 3.67
1233 1273 1.470098 GCTGATTCTGCATTTCGTGGT 59.530 47.619 10.32 0.00 0.00 4.16
1264 1304 3.254629 GCATGAAGCCCAAGTGAGA 57.745 52.632 0.00 0.00 37.23 3.27
1306 1347 5.483685 TGGACCACATGGATACTATAAGC 57.516 43.478 4.53 0.00 38.94 3.09
1386 1430 5.505286 CGAGAAGCCAAATTCACATATGTC 58.495 41.667 5.07 0.00 0.00 3.06
1430 1474 0.185901 TTTGGGAGCTTGTTCTGCCT 59.814 50.000 3.14 0.00 43.97 4.75
1432 1477 1.888512 TGATTTGGGAGCTTGTTCTGC 59.111 47.619 0.00 0.00 0.00 4.26
1434 1479 3.073650 ACTCTGATTTGGGAGCTTGTTCT 59.926 43.478 0.00 0.00 33.29 3.01
1495 1542 5.005394 GCTAATTCGCGAACAAATCTACTGA 59.995 40.000 26.00 0.00 0.00 3.41
1551 1598 6.114187 TCCTGCTGATTCTGAAGTCTAAAA 57.886 37.500 0.00 0.00 0.00 1.52
1552 1599 5.728471 CTCCTGCTGATTCTGAAGTCTAAA 58.272 41.667 0.00 0.00 0.00 1.85
1672 1722 2.293122 GCTGTGGCACAAGTTTGTATCA 59.707 45.455 22.31 0.00 44.16 2.15
1692 1742 4.212214 AGTCTTCTTGATGTTGTTTCTCGC 59.788 41.667 0.00 0.00 0.00 5.03
1695 1745 4.883585 TGCAGTCTTCTTGATGTTGTTTCT 59.116 37.500 0.00 0.00 0.00 2.52
1696 1752 5.173774 TGCAGTCTTCTTGATGTTGTTTC 57.826 39.130 0.00 0.00 0.00 2.78
1752 1808 2.744202 AGCAATAAAGAAGCTGTGACGG 59.256 45.455 0.00 0.00 37.20 4.79
2089 2152 3.939740 AATCATGGCCACTACATCAGT 57.060 42.857 8.16 0.00 38.32 3.41


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

AutoCloner maintained by Alex Coulton.