Multiple sequence alignment - TraesCS5D01G291200

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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 TraesCS5D01G291200 chr5D 100.000 3864 0 0 1 3864 388874403 388870540 0.000000e+00 7136
1 TraesCS5D01G291200 chr5D 84.690 1032 137 16 1746 2769 428700457 428701475 0.000000e+00 1011
2 TraesCS5D01G291200 chr5D 88.128 438 40 4 1232 1657 428699956 428700393 9.580000e-141 510
3 TraesCS5D01G291200 chr5D 83.582 335 33 19 300 614 389005106 389004774 1.050000e-75 294
4 TraesCS5D01G291200 chr5B 95.154 1754 57 15 1694 3446 467371153 467369427 0.000000e+00 2743
5 TraesCS5D01G291200 chr5B 90.560 964 61 18 2 937 467374157 467373196 0.000000e+00 1249
6 TraesCS5D01G291200 chr5B 84.884 1032 136 16 1744 2769 517852967 517853984 0.000000e+00 1024
7 TraesCS5D01G291200 chr5B 93.013 687 35 7 1015 1696 467373196 467372518 0.000000e+00 990
8 TraesCS5D01G291200 chr5B 88.128 438 40 4 1232 1657 517852467 517852904 9.580000e-141 510
9 TraesCS5D01G291200 chr5B 91.623 191 16 0 3517 3707 467369420 467369230 8.230000e-67 265
10 TraesCS5D01G291200 chr5B 92.174 115 7 1 3751 3863 467369231 467369117 1.110000e-35 161
11 TraesCS5D01G291200 chr5B 91.579 95 8 0 3 97 544944798 544944704 8.710000e-27 132
12 TraesCS5D01G291200 chr5B 88.776 98 11 0 1 98 488187760 488187663 1.890000e-23 121
13 TraesCS5D01G291200 chr7B 81.847 1570 231 39 1199 2740 741226443 741227986 0.000000e+00 1271
14 TraesCS5D01G291200 chr7B 82.176 763 106 18 1980 2730 741261807 741261063 2.530000e-176 628
15 TraesCS5D01G291200 chr5A 84.541 1035 139 15 1746 2769 544534367 544535391 0.000000e+00 1005
16 TraesCS5D01G291200 chr5A 87.443 438 43 2 1232 1657 544533870 544534307 9.640000e-136 494
17 TraesCS5D01G291200 chr7D 83.799 1037 134 17 1744 2762 634919955 634918935 0.000000e+00 953
18 TraesCS5D01G291200 chr7D 91.579 95 8 0 2 96 58135831 58135737 8.710000e-27 132
19 TraesCS5D01G291200 chr7A 81.500 1027 141 26 1744 2757 730722658 730721668 0.000000e+00 798
20 TraesCS5D01G291200 chr2B 93.814 97 6 0 1 97 226520673 226520577 3.110000e-31 147
21 TraesCS5D01G291200 chr3B 90.526 95 9 0 3 97 821758644 821758738 4.050000e-25 126
22 TraesCS5D01G291200 chr1B 89.583 96 9 1 2 97 22398664 22398570 1.890000e-23 121
23 TraesCS5D01G291200 chr1B 89.583 96 9 1 2 97 22518609 22518515 1.890000e-23 121
24 TraesCS5D01G291200 chr4B 86.667 105 14 0 2 106 672942092 672941988 2.440000e-22 117


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 TraesCS5D01G291200 chr5D 388870540 388874403 3863 True 7136.0 7136 100.0000 1 3864 1 chr5D.!!$R1 3863
1 TraesCS5D01G291200 chr5D 428699956 428701475 1519 False 760.5 1011 86.4090 1232 2769 2 chr5D.!!$F1 1537
2 TraesCS5D01G291200 chr5B 467369117 467374157 5040 True 1081.6 2743 92.5048 2 3863 5 chr5B.!!$R3 3861
3 TraesCS5D01G291200 chr5B 517852467 517853984 1517 False 767.0 1024 86.5060 1232 2769 2 chr5B.!!$F1 1537
4 TraesCS5D01G291200 chr7B 741226443 741227986 1543 False 1271.0 1271 81.8470 1199 2740 1 chr7B.!!$F1 1541
5 TraesCS5D01G291200 chr7B 741261063 741261807 744 True 628.0 628 82.1760 1980 2730 1 chr7B.!!$R1 750
6 TraesCS5D01G291200 chr5A 544533870 544535391 1521 False 749.5 1005 85.9920 1232 2769 2 chr5A.!!$F1 1537
7 TraesCS5D01G291200 chr7D 634918935 634919955 1020 True 953.0 953 83.7990 1744 2762 1 chr7D.!!$R2 1018
8 TraesCS5D01G291200 chr7A 730721668 730722658 990 True 798.0 798 81.5000 1744 2757 1 chr7A.!!$R1 1013

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
992 1017 0.25363 TTATCCAAGGAGGGGCAGGT 60.254 55.0 0.0 0.0 38.24 4.00 F
1001 1026 0.17899 GAGGGGCAGGTGAACTTTGT 60.179 55.0 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 3970 1.148157 CGGCGAACAGAGGTAGCATG 61.148 60.000 0.0 0.0 33.91 4.06 R
2927 4402 1.202758 AGACTGGGAAAACATGCACGA 60.203 47.619 0.0 0.0 0.00 4.35 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
17 18 2.364973 TCGCACCTCCATGCCCTA 60.365 61.111 0.00 0.00 42.99 3.53
38 39 2.029666 GCCATCGGAGATGGGACG 59.970 66.667 25.10 5.65 45.12 4.79
65 66 4.367023 CGGTGCCGACGGAAGGAA 62.367 66.667 20.50 0.00 42.83 3.36
67 68 1.598685 GGTGCCGACGGAAGGAAAA 60.599 57.895 20.50 0.00 0.00 2.29
111 112 7.334858 AGGAAAGAGATGGAAGAATTGTAGTC 58.665 38.462 0.00 0.00 0.00 2.59
118 119 7.241628 AGATGGAAGAATTGTAGTCCCTTTTT 58.758 34.615 0.00 0.00 0.00 1.94
131 132 6.825944 AGTCCCTTTTTCTCTTTTCTATGC 57.174 37.500 0.00 0.00 0.00 3.14
174 175 8.028938 CCTGGTGTATCCTCATAAAAGTTTTTG 58.971 37.037 6.10 5.36 37.07 2.44
295 296 3.234386 GCTTACGAACAATGTTGAAGGC 58.766 45.455 2.20 0.00 0.00 4.35
296 297 3.304391 GCTTACGAACAATGTTGAAGGCA 60.304 43.478 2.20 0.00 0.00 4.75
301 302 3.440173 CGAACAATGTTGAAGGCAGGTAT 59.560 43.478 2.20 0.00 0.00 2.73
321 322 6.163476 GGTATTGCCTATATTGTGTCGATCA 58.837 40.000 0.00 0.00 0.00 2.92
338 339 1.410004 TCAGACCGGCCCATTAGTAG 58.590 55.000 0.00 0.00 0.00 2.57
346 347 1.335145 GCCCATTAGTAGCGGGAGTA 58.665 55.000 9.62 0.00 43.21 2.59
419 420 8.894731 GGGAAGGTTCTAGAAAATGTTTATCTC 58.105 37.037 6.78 0.00 0.00 2.75
420 421 8.894731 GGAAGGTTCTAGAAAATGTTTATCTCC 58.105 37.037 6.78 0.00 0.00 3.71
441 442 9.739276 ATCTCCCTTTCTTTTTCTTTTTGTTTT 57.261 25.926 0.00 0.00 0.00 2.43
616 635 9.825972 TTTCAAATTCGTGAACATTTATCTCTC 57.174 29.630 0.00 0.00 37.24 3.20
617 636 8.546597 TCAAATTCGTGAACATTTATCTCTCA 57.453 30.769 0.00 0.00 0.00 3.27
618 637 8.443160 TCAAATTCGTGAACATTTATCTCTCAC 58.557 33.333 0.00 0.00 34.40 3.51
619 638 7.905604 AATTCGTGAACATTTATCTCTCACA 57.094 32.000 0.00 0.00 36.95 3.58
620 639 6.951256 TTCGTGAACATTTATCTCTCACAG 57.049 37.500 0.00 0.00 36.95 3.66
621 640 5.410924 TCGTGAACATTTATCTCTCACAGG 58.589 41.667 0.00 0.00 36.95 4.00
622 641 4.033358 CGTGAACATTTATCTCTCACAGGC 59.967 45.833 0.00 0.00 36.95 4.85
623 642 4.937620 GTGAACATTTATCTCTCACAGGCA 59.062 41.667 0.00 0.00 37.07 4.75
624 643 5.587844 GTGAACATTTATCTCTCACAGGCAT 59.412 40.000 0.00 0.00 37.07 4.40
625 644 6.094603 GTGAACATTTATCTCTCACAGGCATT 59.905 38.462 0.00 0.00 37.07 3.56
626 645 6.660521 TGAACATTTATCTCTCACAGGCATTT 59.339 34.615 0.00 0.00 0.00 2.32
793 815 1.152756 AAAAAGGCGTGCTGGGAGT 60.153 52.632 0.00 0.00 0.00 3.85
794 816 0.755327 AAAAAGGCGTGCTGGGAGTT 60.755 50.000 0.00 0.00 0.00 3.01
827 849 4.056125 CGCGCTGGACCAGTCTCA 62.056 66.667 22.58 0.00 33.43 3.27
870 895 1.742880 TGAGCGATGCAGTGGCTTC 60.743 57.895 9.87 5.16 42.41 3.86
884 909 2.671177 GCTTCTTGCTCGCAGCGAA 61.671 57.895 20.04 1.17 46.26 4.70
933 958 6.399639 CAGAGGGTGCTACCTTTTTAAAAA 57.600 37.500 12.62 12.62 42.10 1.94
934 959 6.447162 CAGAGGGTGCTACCTTTTTAAAAAG 58.553 40.000 26.90 26.90 42.10 2.27
935 960 6.040504 CAGAGGGTGCTACCTTTTTAAAAAGT 59.959 38.462 29.65 22.05 42.92 2.66
937 962 7.230108 AGAGGGTGCTACCTTTTTAAAAAGTAC 59.770 37.037 29.65 19.42 42.92 2.73
938 963 7.064866 AGGGTGCTACCTTTTTAAAAAGTACT 58.935 34.615 29.65 18.27 42.92 2.73
939 964 7.230108 AGGGTGCTACCTTTTTAAAAAGTACTC 59.770 37.037 29.65 19.63 42.92 2.59
940 965 7.365741 GGTGCTACCTTTTTAAAAAGTACTCC 58.634 38.462 29.65 22.09 42.92 3.85
941 966 7.365741 GTGCTACCTTTTTAAAAAGTACTCCC 58.634 38.462 29.65 17.26 42.92 4.30
942 967 7.230108 GTGCTACCTTTTTAAAAAGTACTCCCT 59.770 37.037 29.65 11.99 42.92 4.20
943 968 7.781219 TGCTACCTTTTTAAAAAGTACTCCCTT 59.219 33.333 29.65 12.24 42.92 3.95
945 970 9.961265 CTACCTTTTTAAAAAGTACTCCCTTTG 57.039 33.333 29.65 17.28 42.92 2.77
946 971 8.370266 ACCTTTTTAAAAAGTACTCCCTTTGT 57.630 30.769 29.65 17.78 42.92 2.83
947 972 8.818860 ACCTTTTTAAAAAGTACTCCCTTTGTT 58.181 29.630 29.65 7.34 42.92 2.83
948 973 9.309516 CCTTTTTAAAAAGTACTCCCTTTGTTC 57.690 33.333 29.65 0.00 42.92 3.18
962 987 9.588096 ACTCCCTTTGTTCTAAAATAAATGTCT 57.412 29.630 0.00 0.00 0.00 3.41
981 1006 9.840427 AAATGTCTTAACGATGTTTTATCCAAG 57.160 29.630 0.00 0.00 0.00 3.61
982 1007 7.372451 TGTCTTAACGATGTTTTATCCAAGG 57.628 36.000 0.00 0.00 0.00 3.61
983 1008 7.162761 TGTCTTAACGATGTTTTATCCAAGGA 58.837 34.615 0.00 0.00 0.00 3.36
984 1009 7.333423 TGTCTTAACGATGTTTTATCCAAGGAG 59.667 37.037 0.00 0.00 0.00 3.69
985 1010 6.821665 TCTTAACGATGTTTTATCCAAGGAGG 59.178 38.462 0.00 0.00 39.47 4.30
986 1011 3.886123 ACGATGTTTTATCCAAGGAGGG 58.114 45.455 0.00 0.00 38.24 4.30
987 1012 3.214328 CGATGTTTTATCCAAGGAGGGG 58.786 50.000 0.00 0.00 38.24 4.79
988 1013 2.525105 TGTTTTATCCAAGGAGGGGC 57.475 50.000 0.00 0.00 38.24 5.80
989 1014 1.713647 TGTTTTATCCAAGGAGGGGCA 59.286 47.619 0.00 0.00 38.24 5.36
990 1015 2.291540 TGTTTTATCCAAGGAGGGGCAG 60.292 50.000 0.00 0.00 38.24 4.85
991 1016 0.926293 TTTATCCAAGGAGGGGCAGG 59.074 55.000 0.00 0.00 38.24 4.85
992 1017 0.253630 TTATCCAAGGAGGGGCAGGT 60.254 55.000 0.00 0.00 38.24 4.00
993 1018 0.988145 TATCCAAGGAGGGGCAGGTG 60.988 60.000 0.00 0.00 38.24 4.00
994 1019 2.788230 ATCCAAGGAGGGGCAGGTGA 62.788 60.000 0.00 0.00 38.24 4.02
995 1020 2.538141 CCAAGGAGGGGCAGGTGAA 61.538 63.158 0.00 0.00 0.00 3.18
996 1021 1.303643 CAAGGAGGGGCAGGTGAAC 60.304 63.158 0.00 0.00 0.00 3.18
997 1022 1.464198 AAGGAGGGGCAGGTGAACT 60.464 57.895 0.00 0.00 0.00 3.01
998 1023 1.068352 AAGGAGGGGCAGGTGAACTT 61.068 55.000 0.00 0.00 0.00 2.66
999 1024 1.068352 AGGAGGGGCAGGTGAACTTT 61.068 55.000 0.00 0.00 0.00 2.66
1000 1025 0.895559 GGAGGGGCAGGTGAACTTTG 60.896 60.000 0.00 0.00 0.00 2.77
1001 1026 0.178990 GAGGGGCAGGTGAACTTTGT 60.179 55.000 0.00 0.00 0.00 2.83
1002 1027 1.073284 GAGGGGCAGGTGAACTTTGTA 59.927 52.381 0.00 0.00 0.00 2.41
1003 1028 1.710809 AGGGGCAGGTGAACTTTGTAT 59.289 47.619 0.00 0.00 0.00 2.29
1004 1029 2.916934 AGGGGCAGGTGAACTTTGTATA 59.083 45.455 0.00 0.00 0.00 1.47
1005 1030 3.332485 AGGGGCAGGTGAACTTTGTATAA 59.668 43.478 0.00 0.00 0.00 0.98
1006 1031 3.694566 GGGGCAGGTGAACTTTGTATAAG 59.305 47.826 0.00 0.00 0.00 1.73
1007 1032 4.332828 GGGCAGGTGAACTTTGTATAAGT 58.667 43.478 0.00 0.00 0.00 2.24
1008 1033 4.765339 GGGCAGGTGAACTTTGTATAAGTT 59.235 41.667 2.78 2.78 42.62 2.66
1009 1034 5.335661 GGGCAGGTGAACTTTGTATAAGTTG 60.336 44.000 7.56 0.00 40.27 3.16
1010 1035 5.472137 GGCAGGTGAACTTTGTATAAGTTGA 59.528 40.000 7.56 0.00 40.27 3.18
1011 1036 6.016610 GGCAGGTGAACTTTGTATAAGTTGAA 60.017 38.462 7.56 0.00 40.27 2.69
1012 1037 6.856426 GCAGGTGAACTTTGTATAAGTTGAAC 59.144 38.462 7.56 2.59 40.27 3.18
1013 1038 7.069569 CAGGTGAACTTTGTATAAGTTGAACG 58.930 38.462 7.56 0.00 40.27 3.95
1014 1039 6.987992 AGGTGAACTTTGTATAAGTTGAACGA 59.012 34.615 7.56 0.00 40.27 3.85
1015 1040 7.496591 AGGTGAACTTTGTATAAGTTGAACGAA 59.503 33.333 7.56 0.00 40.27 3.85
1016 1041 7.585210 GGTGAACTTTGTATAAGTTGAACGAAC 59.415 37.037 7.56 0.00 40.27 3.95
1017 1042 7.585210 GTGAACTTTGTATAAGTTGAACGAACC 59.415 37.037 7.56 0.00 40.27 3.62
1018 1043 7.496591 TGAACTTTGTATAAGTTGAACGAACCT 59.503 33.333 7.56 0.00 40.27 3.50
1019 1044 8.891671 AACTTTGTATAAGTTGAACGAACCTA 57.108 30.769 2.36 0.00 38.88 3.08
1032 1057 9.807386 GTTGAACGAACCTATATTATACATTGC 57.193 33.333 0.00 0.00 0.00 3.56
1081 1106 3.733224 CGTCTGATCTGGATCGACATTTC 59.267 47.826 22.04 0.00 40.63 2.17
1082 1107 4.498850 CGTCTGATCTGGATCGACATTTCT 60.499 45.833 22.04 0.00 40.63 2.52
1085 1110 6.314896 GTCTGATCTGGATCGACATTTCTTTT 59.685 38.462 19.78 0.00 40.63 2.27
1086 1111 6.881065 TCTGATCTGGATCGACATTTCTTTTT 59.119 34.615 6.17 0.00 40.63 1.94
1087 1112 7.065085 TCTGATCTGGATCGACATTTCTTTTTC 59.935 37.037 6.17 0.00 40.63 2.29
1137 1162 2.037136 CAGGAGAAAGCGCCCACAG 61.037 63.158 2.29 0.00 34.01 3.66
1138 1163 3.435186 GGAGAAAGCGCCCACAGC 61.435 66.667 2.29 0.00 38.52 4.40
1156 1181 1.810030 CCGGCGACCTAGCTTGTTC 60.810 63.158 9.30 0.00 37.29 3.18
1159 1184 0.179108 GGCGACCTAGCTTGTTCGAT 60.179 55.000 18.24 0.00 37.29 3.59
1160 1185 1.201343 GCGACCTAGCTTGTTCGATC 58.799 55.000 18.24 0.00 0.00 3.69
1161 1186 1.467875 CGACCTAGCTTGTTCGATCG 58.532 55.000 9.35 9.36 0.00 3.69
1162 1187 1.202154 CGACCTAGCTTGTTCGATCGT 60.202 52.381 15.94 0.00 0.00 3.73
1163 1188 2.186076 GACCTAGCTTGTTCGATCGTG 58.814 52.381 15.94 3.08 0.00 4.35
1165 1190 2.230508 ACCTAGCTTGTTCGATCGTGAA 59.769 45.455 15.94 0.00 0.00 3.18
1166 1191 2.599082 CCTAGCTTGTTCGATCGTGAAC 59.401 50.000 15.94 13.43 46.63 3.18
1167 1192 1.429463 AGCTTGTTCGATCGTGAACC 58.571 50.000 15.94 1.17 46.04 3.62
1169 1194 1.126846 GCTTGTTCGATCGTGAACCTG 59.873 52.381 15.94 9.24 46.04 4.00
1170 1195 1.126846 CTTGTTCGATCGTGAACCTGC 59.873 52.381 15.94 0.00 46.04 4.85
1171 1196 0.317160 TGTTCGATCGTGAACCTGCT 59.683 50.000 15.94 0.00 46.04 4.24
1172 1197 0.992802 GTTCGATCGTGAACCTGCTC 59.007 55.000 15.94 0.00 41.88 4.26
1173 1198 0.456142 TTCGATCGTGAACCTGCTCG 60.456 55.000 15.94 0.00 0.00 5.03
1174 1199 1.874019 CGATCGTGAACCTGCTCGG 60.874 63.158 7.03 0.00 39.35 4.63
1178 1203 4.681978 GTGAACCTGCTCGGCCGT 62.682 66.667 27.15 2.66 35.61 5.68
1179 1204 4.373116 TGAACCTGCTCGGCCGTC 62.373 66.667 27.15 18.51 35.61 4.79
1181 1206 4.681978 AACCTGCTCGGCCGTCAC 62.682 66.667 27.15 16.11 35.61 3.67
1191 1216 2.809601 GCCGTCACGTTGCGAGAT 60.810 61.111 9.72 0.00 0.00 2.75
1192 1217 2.789203 GCCGTCACGTTGCGAGATC 61.789 63.158 9.72 0.00 0.00 2.75
1862 3279 2.190578 GGCGGAGGACTTCATGGG 59.809 66.667 0.00 0.00 0.00 4.00
2140 3572 1.373748 GAAGCTGTTGCCGACCGTA 60.374 57.895 0.00 0.00 40.80 4.02
2662 4133 1.686110 GAGGGCGAGGAAGGGAAGA 60.686 63.158 0.00 0.00 0.00 2.87
2664 4135 2.585153 GGCGAGGAAGGGAAGACC 59.415 66.667 0.00 0.00 40.67 3.85
2771 4246 3.903783 GCGACTGCAATAGGGCAA 58.096 55.556 0.00 0.00 44.40 4.52
2772 4247 1.723870 GCGACTGCAATAGGGCAAG 59.276 57.895 0.00 0.00 44.40 4.01
2773 4248 1.723870 CGACTGCAATAGGGCAAGC 59.276 57.895 0.00 0.00 44.40 4.01
2774 4249 0.745845 CGACTGCAATAGGGCAAGCT 60.746 55.000 0.00 0.00 44.40 3.74
2813 4288 6.037062 TGCCTGTCGAAATGTGTAATCAATAG 59.963 38.462 0.00 0.00 0.00 1.73
2825 4300 6.183360 TGTGTAATCAATAGTCGTGCATGTTC 60.183 38.462 5.68 0.96 0.00 3.18
2835 4310 1.399440 CGTGCATGTTCCCTCAATCTG 59.601 52.381 0.00 0.00 0.00 2.90
2847 4322 1.411977 CTCAATCTGCTCGATGTCCCT 59.588 52.381 0.00 0.00 31.20 4.20
2863 4338 8.425703 TCGATGTCCCTGAAATATGTAAATGTA 58.574 33.333 0.00 0.00 0.00 2.29
2885 4360 8.596271 TGTAATAATCGTGTCTGTTTTCTGAA 57.404 30.769 0.00 0.00 0.00 3.02
2920 4395 6.432783 TGTCCCCTGAAATGTGTAAATGTAAG 59.567 38.462 0.00 0.00 0.00 2.34
2921 4396 6.433093 GTCCCCTGAAATGTGTAAATGTAAGT 59.567 38.462 0.00 0.00 0.00 2.24
2924 4399 8.966868 CCCCTGAAATGTGTAAATGTAAGTAAT 58.033 33.333 0.00 0.00 0.00 1.89
3003 4479 3.421844 GTGCCTGTTTTCCCAATCTACT 58.578 45.455 0.00 0.00 0.00 2.57
3004 4480 4.585879 GTGCCTGTTTTCCCAATCTACTA 58.414 43.478 0.00 0.00 0.00 1.82
3005 4481 4.395231 GTGCCTGTTTTCCCAATCTACTAC 59.605 45.833 0.00 0.00 0.00 2.73
3012 4488 3.323774 TCCCAATCTACTACCCGATGT 57.676 47.619 0.00 0.00 0.00 3.06
3029 4505 4.153475 CCGATGTTCCTGAAACGTGTAAAT 59.847 41.667 0.00 0.00 41.02 1.40
3030 4506 5.079406 CGATGTTCCTGAAACGTGTAAATG 58.921 41.667 0.00 0.00 41.02 2.32
3039 4515 9.438228 TCCTGAAACGTGTAAATGTAATAATCA 57.562 29.630 0.00 0.00 0.00 2.57
3043 4519 9.716507 GAAACGTGTAAATGTAATAATCATGCT 57.283 29.630 0.00 0.00 0.00 3.79
3060 4536 8.773033 AATCATGCTTATTTTCCCAATCTACT 57.227 30.769 0.00 0.00 0.00 2.57
3061 4537 7.807977 TCATGCTTATTTTCCCAATCTACTC 57.192 36.000 0.00 0.00 0.00 2.59
3062 4538 6.483307 TCATGCTTATTTTCCCAATCTACTCG 59.517 38.462 0.00 0.00 0.00 4.18
3063 4539 5.984725 TGCTTATTTTCCCAATCTACTCGA 58.015 37.500 0.00 0.00 0.00 4.04
3064 4540 6.591935 TGCTTATTTTCCCAATCTACTCGAT 58.408 36.000 0.00 0.00 0.00 3.59
3065 4541 6.483307 TGCTTATTTTCCCAATCTACTCGATG 59.517 38.462 0.00 0.00 31.20 3.84
3066 4542 6.483640 GCTTATTTTCCCAATCTACTCGATGT 59.516 38.462 0.00 0.00 31.20 3.06
3067 4543 7.307455 GCTTATTTTCCCAATCTACTCGATGTC 60.307 40.741 0.00 0.00 31.20 3.06
3070 4546 1.603172 CCCAATCTACTCGATGTCCGC 60.603 57.143 0.00 0.00 38.37 5.54
3090 4566 4.104776 CGCATTAATTCTGCATTTTCCGT 58.895 39.130 12.01 0.00 39.64 4.69
3185 4661 9.948964 TTCATCTTCACTATTTCAATTCTCTCA 57.051 29.630 0.00 0.00 0.00 3.27
3221 4697 3.741388 GCTACCTCACCACATATGTCACC 60.741 52.174 5.07 0.00 0.00 4.02
3225 4701 3.525537 CTCACCACATATGTCACCTCAC 58.474 50.000 5.07 0.00 0.00 3.51
3229 4705 3.118261 ACCACATATGTCACCTCACCATC 60.118 47.826 5.07 0.00 0.00 3.51
3292 4768 0.609957 CACATGCCACCTCACCACAT 60.610 55.000 0.00 0.00 0.00 3.21
3372 4848 0.843309 ACATCCCAACTCACCACACA 59.157 50.000 0.00 0.00 0.00 3.72
3378 4854 1.202806 CCAACTCACCACACACCATCT 60.203 52.381 0.00 0.00 0.00 2.90
3381 4857 4.326826 CAACTCACCACACACCATCTAAT 58.673 43.478 0.00 0.00 0.00 1.73
3382 4858 4.207891 ACTCACCACACACCATCTAATC 57.792 45.455 0.00 0.00 0.00 1.75
3383 4859 3.582647 ACTCACCACACACCATCTAATCA 59.417 43.478 0.00 0.00 0.00 2.57
3384 4860 4.186926 CTCACCACACACCATCTAATCAG 58.813 47.826 0.00 0.00 0.00 2.90
3427 4903 2.868899 TGCACACACCCATGTATTTCA 58.131 42.857 0.00 0.00 36.72 2.69
3446 4922 0.764369 ACTCACCTGAGGCAGAACCA 60.764 55.000 0.00 0.00 46.13 3.67
3447 4923 0.036577 CTCACCTGAGGCAGAACCAG 60.037 60.000 0.00 0.00 43.14 4.00
3448 4924 1.673665 CACCTGAGGCAGAACCAGC 60.674 63.158 0.00 0.00 43.14 4.85
3456 4932 3.160872 GCAGAACCAGCCTAGAACC 57.839 57.895 0.00 0.00 0.00 3.62
3457 4933 0.393132 GCAGAACCAGCCTAGAACCC 60.393 60.000 0.00 0.00 0.00 4.11
3458 4934 0.253327 CAGAACCAGCCTAGAACCCC 59.747 60.000 0.00 0.00 0.00 4.95
3459 4935 0.914902 AGAACCAGCCTAGAACCCCC 60.915 60.000 0.00 0.00 0.00 5.40
3481 4957 4.539083 ACCCGCGCCGCATTGATA 62.539 61.111 10.75 0.00 0.00 2.15
3482 4958 3.716006 CCCGCGCCGCATTGATAG 61.716 66.667 10.75 0.00 0.00 2.08
3483 4959 3.716006 CCGCGCCGCATTGATAGG 61.716 66.667 10.75 0.00 0.00 2.57
3484 4960 3.716006 CGCGCCGCATTGATAGGG 61.716 66.667 10.75 0.00 0.00 3.53
3485 4961 4.030452 GCGCCGCATTGATAGGGC 62.030 66.667 3.15 0.00 42.14 5.19
3491 4967 1.934463 GCATTGATAGGGCGACACG 59.066 57.895 0.00 0.00 0.00 4.49
3492 4968 1.498865 GCATTGATAGGGCGACACGG 61.499 60.000 0.00 0.00 0.00 4.94
3493 4969 0.104120 CATTGATAGGGCGACACGGA 59.896 55.000 0.00 0.00 0.00 4.69
3494 4970 0.389391 ATTGATAGGGCGACACGGAG 59.611 55.000 0.00 0.00 0.00 4.63
3495 4971 1.672854 TTGATAGGGCGACACGGAGG 61.673 60.000 0.00 0.00 0.00 4.30
3496 4972 2.838225 ATAGGGCGACACGGAGGG 60.838 66.667 0.00 0.00 0.00 4.30
3543 5019 0.629596 TCTCCGCTTCCCTCTCCTTA 59.370 55.000 0.00 0.00 0.00 2.69
3600 5076 4.697756 CGCGGCCAAGGAAGGTGA 62.698 66.667 2.24 0.00 0.00 4.02
3627 5103 4.141883 GCATGTTGTTGCGCTCAG 57.858 55.556 9.73 0.00 32.06 3.35
3632 5108 1.279840 GTTGTTGCGCTCAGTGGTC 59.720 57.895 9.73 0.00 0.00 4.02
3649 5125 2.109799 CGGCGCCTGGATCAGATT 59.890 61.111 26.68 0.00 32.44 2.40
3650 5126 1.958205 CGGCGCCTGGATCAGATTC 60.958 63.158 26.68 0.00 32.44 2.52
3658 5134 3.409570 CCTGGATCAGATTCGCATGATT 58.590 45.455 0.00 0.00 36.30 2.57
3660 5136 3.062042 TGGATCAGATTCGCATGATTCG 58.938 45.455 0.00 0.00 36.30 3.34
3668 5144 3.640000 GCATGATTCGTCCGGCCG 61.640 66.667 21.04 21.04 0.00 6.13
3703 5179 1.847506 ACCTCCACATGGGTCAGCA 60.848 57.895 0.00 0.00 38.11 4.41
3705 5181 1.077930 CTCCACATGGGTCAGCAGG 60.078 63.158 0.00 0.00 38.11 4.85
3706 5182 2.753043 CCACATGGGTCAGCAGGC 60.753 66.667 0.00 0.00 0.00 4.85
3707 5183 3.129502 CACATGGGTCAGCAGGCG 61.130 66.667 0.00 0.00 0.00 5.52
3723 5199 4.812476 CGCGGCGATCCAAGGTGA 62.812 66.667 19.16 0.00 0.00 4.02
3724 5200 2.892425 GCGGCGATCCAAGGTGAG 60.892 66.667 12.98 0.00 0.00 3.51
3725 5201 2.892425 CGGCGATCCAAGGTGAGC 60.892 66.667 0.00 0.00 0.00 4.26
3726 5202 2.586792 GGCGATCCAAGGTGAGCT 59.413 61.111 0.00 0.00 0.00 4.09
3727 5203 1.823295 GGCGATCCAAGGTGAGCTA 59.177 57.895 0.00 0.00 0.00 3.32
3728 5204 0.394565 GGCGATCCAAGGTGAGCTAT 59.605 55.000 0.00 0.00 0.00 2.97
3729 5205 1.202698 GGCGATCCAAGGTGAGCTATT 60.203 52.381 0.00 0.00 0.00 1.73
3730 5206 1.869767 GCGATCCAAGGTGAGCTATTG 59.130 52.381 0.00 0.00 0.00 1.90
3731 5207 2.487934 CGATCCAAGGTGAGCTATTGG 58.512 52.381 11.43 11.43 44.00 3.16
3734 5210 3.845781 TCCAAGGTGAGCTATTGGATC 57.154 47.619 14.82 0.00 45.76 3.36
3735 5211 2.103094 TCCAAGGTGAGCTATTGGATCG 59.897 50.000 14.82 0.00 45.76 3.69
3736 5212 2.487934 CAAGGTGAGCTATTGGATCGG 58.512 52.381 0.00 0.00 32.20 4.18
3737 5213 2.088104 AGGTGAGCTATTGGATCGGA 57.912 50.000 0.00 0.00 32.20 4.55
3738 5214 2.614259 AGGTGAGCTATTGGATCGGAT 58.386 47.619 0.00 0.00 32.20 4.18
3739 5215 2.564947 AGGTGAGCTATTGGATCGGATC 59.435 50.000 9.54 9.54 32.20 3.36
3798 5274 4.436998 GGGTGCCCGACAGTCGAG 62.437 72.222 24.88 12.85 43.74 4.04
3825 5301 4.678256 CCCTGAGGTGCCTAATCTAGATA 58.322 47.826 5.46 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.364973 TAGGGCATGGAGGTGCGA 60.365 61.111 0.00 0.00 45.97 5.10
13 14 0.252012 ATCTCCGATGGCCTCTAGGG 60.252 60.000 3.32 0.00 35.18 3.53
14 15 0.894141 CATCTCCGATGGCCTCTAGG 59.106 60.000 3.32 2.19 38.53 3.02
15 16 0.894141 CCATCTCCGATGGCCTCTAG 59.106 60.000 3.32 0.23 31.75 2.43
17 18 1.840650 CCCATCTCCGATGGCCTCT 60.841 63.158 15.70 0.00 37.85 3.69
26 27 3.900892 CGGTCCGTCCCATCTCCG 61.901 72.222 2.08 0.00 0.00 4.63
28 29 4.222847 GCCGGTCCGTCCCATCTC 62.223 72.222 11.06 0.00 0.00 2.75
48 49 3.869473 TTTCCTTCCGTCGGCACCG 62.869 63.158 6.34 1.73 41.35 4.94
51 52 0.320421 CTCTTTTCCTTCCGTCGGCA 60.320 55.000 6.34 0.00 0.00 5.69
65 66 5.782845 TCCTCCTCTAGAAGAAAAGCTCTTT 59.217 40.000 0.00 0.00 44.82 2.52
67 68 4.941713 TCCTCCTCTAGAAGAAAAGCTCT 58.058 43.478 0.00 0.00 35.13 4.09
78 79 5.194740 TCTTCCATCTCTTTCCTCCTCTAGA 59.805 44.000 0.00 0.00 0.00 2.43
79 80 5.454062 TCTTCCATCTCTTTCCTCCTCTAG 58.546 45.833 0.00 0.00 0.00 2.43
111 112 5.478332 AGTGGCATAGAAAAGAGAAAAAGGG 59.522 40.000 0.00 0.00 0.00 3.95
118 119 6.341316 GTGTATGAGTGGCATAGAAAAGAGA 58.659 40.000 0.00 0.00 40.04 3.10
131 132 1.759445 CAGGGAGAGGTGTATGAGTGG 59.241 57.143 0.00 0.00 0.00 4.00
187 188 7.814587 GTGCAACTTTTTCAATCTAGGCTTTAT 59.185 33.333 0.00 0.00 0.00 1.40
199 200 8.394121 GGAATTAATTGTGTGCAACTTTTTCAA 58.606 29.630 5.17 0.00 37.44 2.69
200 201 7.768120 AGGAATTAATTGTGTGCAACTTTTTCA 59.232 29.630 5.17 0.00 37.44 2.69
245 246 1.463056 TCTTTTGCGCTACATCAACCG 59.537 47.619 9.73 0.00 0.00 4.44
301 302 5.289595 GTCTGATCGACACAATATAGGCAA 58.710 41.667 11.26 0.00 42.37 4.52
321 322 1.745320 CGCTACTAATGGGCCGGTCT 61.745 60.000 5.77 0.00 0.00 3.85
324 325 2.030562 CCGCTACTAATGGGCCGG 59.969 66.667 0.00 0.00 0.00 6.13
327 328 1.272769 CTACTCCCGCTACTAATGGGC 59.727 57.143 0.00 0.00 42.98 5.36
338 339 3.942439 GGCATCCCCTACTCCCGC 61.942 72.222 0.00 0.00 0.00 6.13
346 347 2.037208 CCAAAACCGGCATCCCCT 59.963 61.111 0.00 0.00 0.00 4.79
599 618 4.033358 GCCTGTGAGAGATAAATGTTCACG 59.967 45.833 0.00 0.00 40.67 4.35
625 644 6.917217 AGAAAATGTTTGCGGATTCAAAAA 57.083 29.167 0.00 0.00 37.65 1.94
626 645 8.425577 TTTAGAAAATGTTTGCGGATTCAAAA 57.574 26.923 0.00 0.00 37.65 2.44
793 815 2.649349 GCAACAACACGCGCGAAA 60.649 55.556 39.36 0.00 0.00 3.46
823 845 3.962718 TCCTACATGAGACATGCATGAGA 59.037 43.478 32.75 13.10 44.49 3.27
827 849 3.474600 GCTTCCTACATGAGACATGCAT 58.525 45.455 0.00 0.00 0.00 3.96
870 895 3.105782 TCGTTCGCTGCGAGCAAG 61.106 61.111 32.08 20.00 42.58 4.01
884 909 1.006102 GGGCGCTGCTATATGTCGT 60.006 57.895 7.64 0.00 0.00 4.34
955 980 9.840427 CTTGGATAAAACATCGTTAAGACATTT 57.160 29.630 0.00 0.00 0.00 2.32
956 981 8.458843 CCTTGGATAAAACATCGTTAAGACATT 58.541 33.333 0.00 0.00 0.00 2.71
957 982 7.827236 TCCTTGGATAAAACATCGTTAAGACAT 59.173 33.333 0.00 0.00 0.00 3.06
958 983 7.162761 TCCTTGGATAAAACATCGTTAAGACA 58.837 34.615 0.00 0.00 0.00 3.41
959 984 7.201617 CCTCCTTGGATAAAACATCGTTAAGAC 60.202 40.741 0.00 0.00 38.35 3.01
960 985 6.821665 CCTCCTTGGATAAAACATCGTTAAGA 59.178 38.462 0.00 0.00 38.35 2.10
961 986 6.038271 CCCTCCTTGGATAAAACATCGTTAAG 59.962 42.308 0.00 0.00 38.35 1.85
962 987 5.883673 CCCTCCTTGGATAAAACATCGTTAA 59.116 40.000 0.00 0.00 38.35 2.01
963 988 5.433526 CCCTCCTTGGATAAAACATCGTTA 58.566 41.667 0.00 0.00 38.35 3.18
964 989 4.270008 CCCTCCTTGGATAAAACATCGTT 58.730 43.478 0.00 0.00 38.35 3.85
965 990 3.371595 CCCCTCCTTGGATAAAACATCGT 60.372 47.826 0.00 0.00 38.35 3.73
966 991 3.214328 CCCCTCCTTGGATAAAACATCG 58.786 50.000 0.00 0.00 38.35 3.84
967 992 2.959030 GCCCCTCCTTGGATAAAACATC 59.041 50.000 0.00 0.00 38.35 3.06
968 993 2.314549 TGCCCCTCCTTGGATAAAACAT 59.685 45.455 0.00 0.00 38.35 2.71
969 994 1.713647 TGCCCCTCCTTGGATAAAACA 59.286 47.619 0.00 0.00 38.35 2.83
970 995 2.379005 CTGCCCCTCCTTGGATAAAAC 58.621 52.381 0.00 0.00 38.35 2.43
971 996 1.287739 CCTGCCCCTCCTTGGATAAAA 59.712 52.381 0.00 0.00 38.35 1.52
972 997 0.926293 CCTGCCCCTCCTTGGATAAA 59.074 55.000 0.00 0.00 38.35 1.40
973 998 0.253630 ACCTGCCCCTCCTTGGATAA 60.254 55.000 0.00 0.00 38.35 1.75
974 999 0.988145 CACCTGCCCCTCCTTGGATA 60.988 60.000 0.00 0.00 38.35 2.59
975 1000 2.128226 ACCTGCCCCTCCTTGGAT 59.872 61.111 0.00 0.00 38.35 3.41
976 1001 2.935481 CACCTGCCCCTCCTTGGA 60.935 66.667 0.00 0.00 38.35 3.53
977 1002 2.538141 TTCACCTGCCCCTCCTTGG 61.538 63.158 0.00 0.00 0.00 3.61
978 1003 1.303643 GTTCACCTGCCCCTCCTTG 60.304 63.158 0.00 0.00 0.00 3.61
979 1004 1.068352 AAGTTCACCTGCCCCTCCTT 61.068 55.000 0.00 0.00 0.00 3.36
980 1005 1.068352 AAAGTTCACCTGCCCCTCCT 61.068 55.000 0.00 0.00 0.00 3.69
981 1006 0.895559 CAAAGTTCACCTGCCCCTCC 60.896 60.000 0.00 0.00 0.00 4.30
982 1007 0.178990 ACAAAGTTCACCTGCCCCTC 60.179 55.000 0.00 0.00 0.00 4.30
983 1008 1.145571 TACAAAGTTCACCTGCCCCT 58.854 50.000 0.00 0.00 0.00 4.79
984 1009 2.215942 ATACAAAGTTCACCTGCCCC 57.784 50.000 0.00 0.00 0.00 5.80
985 1010 4.332828 ACTTATACAAAGTTCACCTGCCC 58.667 43.478 0.00 0.00 0.00 5.36
986 1011 5.472137 TCAACTTATACAAAGTTCACCTGCC 59.528 40.000 0.28 0.00 38.32 4.85
987 1012 6.554334 TCAACTTATACAAAGTTCACCTGC 57.446 37.500 0.28 0.00 38.32 4.85
988 1013 7.042321 TCGTTCAACTTATACAAAGTTCACCTG 60.042 37.037 0.28 0.00 38.32 4.00
989 1014 6.987992 TCGTTCAACTTATACAAAGTTCACCT 59.012 34.615 0.28 0.00 38.32 4.00
990 1015 7.181143 TCGTTCAACTTATACAAAGTTCACC 57.819 36.000 0.28 0.00 38.32 4.02
991 1016 7.585210 GGTTCGTTCAACTTATACAAAGTTCAC 59.415 37.037 0.28 1.16 38.32 3.18
992 1017 7.496591 AGGTTCGTTCAACTTATACAAAGTTCA 59.503 33.333 0.28 0.00 38.32 3.18
993 1018 7.858583 AGGTTCGTTCAACTTATACAAAGTTC 58.141 34.615 0.28 0.00 38.32 3.01
994 1019 7.797038 AGGTTCGTTCAACTTATACAAAGTT 57.203 32.000 0.00 0.00 40.80 2.66
1006 1031 9.807386 GCAATGTATAATATAGGTTCGTTCAAC 57.193 33.333 0.00 0.00 0.00 3.18
1007 1032 8.995220 GGCAATGTATAATATAGGTTCGTTCAA 58.005 33.333 0.00 0.00 0.00 2.69
1008 1033 8.151596 TGGCAATGTATAATATAGGTTCGTTCA 58.848 33.333 0.00 0.00 0.00 3.18
1009 1034 8.542497 TGGCAATGTATAATATAGGTTCGTTC 57.458 34.615 0.00 0.00 0.00 3.95
1010 1035 8.911918 TTGGCAATGTATAATATAGGTTCGTT 57.088 30.769 0.00 0.00 0.00 3.85
1011 1036 8.911918 TTTGGCAATGTATAATATAGGTTCGT 57.088 30.769 0.00 0.00 0.00 3.85
1012 1037 8.999431 ACTTTGGCAATGTATAATATAGGTTCG 58.001 33.333 16.20 0.00 0.00 3.95
1014 1039 8.999431 CGACTTTGGCAATGTATAATATAGGTT 58.001 33.333 17.51 0.00 0.00 3.50
1015 1040 8.154856 ACGACTTTGGCAATGTATAATATAGGT 58.845 33.333 17.51 4.06 0.00 3.08
1016 1041 8.547967 ACGACTTTGGCAATGTATAATATAGG 57.452 34.615 17.51 3.56 0.00 2.57
1017 1042 9.811655 CAACGACTTTGGCAATGTATAATATAG 57.188 33.333 17.51 3.00 0.00 1.31
1018 1043 8.286800 GCAACGACTTTGGCAATGTATAATATA 58.713 33.333 17.51 0.00 35.51 0.86
1019 1044 7.138736 GCAACGACTTTGGCAATGTATAATAT 58.861 34.615 17.51 0.98 35.51 1.28
1022 1047 4.216472 TGCAACGACTTTGGCAATGTATAA 59.784 37.500 17.51 0.00 35.51 0.98
1027 1052 1.987770 GATGCAACGACTTTGGCAATG 59.012 47.619 11.20 11.20 35.51 2.82
1031 1056 1.212751 GGGATGCAACGACTTTGGC 59.787 57.895 0.00 0.00 35.51 4.52
1032 1057 0.609131 AGGGGATGCAACGACTTTGG 60.609 55.000 0.00 0.00 35.51 3.28
1081 1106 6.029607 CGAGAGAGATGAGACAGAGAAAAAG 58.970 44.000 0.00 0.00 0.00 2.27
1082 1107 5.621104 GCGAGAGAGATGAGACAGAGAAAAA 60.621 44.000 0.00 0.00 0.00 1.94
1085 1110 2.942376 GCGAGAGAGATGAGACAGAGAA 59.058 50.000 0.00 0.00 0.00 2.87
1086 1111 2.560504 GCGAGAGAGATGAGACAGAGA 58.439 52.381 0.00 0.00 0.00 3.10
1087 1112 1.603802 GGCGAGAGAGATGAGACAGAG 59.396 57.143 0.00 0.00 0.00 3.35
1137 1162 3.952628 AACAAGCTAGGTCGCCGGC 62.953 63.158 19.07 19.07 0.00 6.13
1138 1163 1.810030 GAACAAGCTAGGTCGCCGG 60.810 63.158 0.00 0.00 0.00 6.13
1156 1181 1.874019 CCGAGCAGGTTCACGATCG 60.874 63.158 14.88 14.88 34.51 3.69
1159 1184 4.373116 GGCCGAGCAGGTTCACGA 62.373 66.667 0.00 0.00 43.70 4.35
1161 1186 4.681978 ACGGCCGAGCAGGTTCAC 62.682 66.667 35.90 0.00 43.70 3.18
1162 1187 4.373116 GACGGCCGAGCAGGTTCA 62.373 66.667 35.90 0.00 43.70 3.18
1163 1188 4.373116 TGACGGCCGAGCAGGTTC 62.373 66.667 35.90 17.86 43.70 3.62
1174 1199 2.789203 GATCTCGCAACGTGACGGC 61.789 63.158 10.66 2.65 32.42 5.68
1177 1202 0.734253 AGCTGATCTCGCAACGTGAC 60.734 55.000 9.64 0.00 32.42 3.67
1178 1203 0.733909 CAGCTGATCTCGCAACGTGA 60.734 55.000 8.42 0.00 34.06 4.35
1179 1204 1.690283 CCAGCTGATCTCGCAACGTG 61.690 60.000 17.39 0.00 0.00 4.49
1181 1206 2.806856 GCCAGCTGATCTCGCAACG 61.807 63.158 17.39 0.00 0.00 4.10
1184 1209 0.033090 CATAGCCAGCTGATCTCGCA 59.967 55.000 17.39 1.14 30.81 5.10
1185 1210 0.669932 CCATAGCCAGCTGATCTCGC 60.670 60.000 17.39 9.76 0.00 5.03
1186 1211 0.669932 GCCATAGCCAGCTGATCTCG 60.670 60.000 17.39 6.78 0.00 4.04
1187 1212 0.395686 TGCCATAGCCAGCTGATCTC 59.604 55.000 17.39 1.00 38.69 2.75
1188 1213 0.841961 TTGCCATAGCCAGCTGATCT 59.158 50.000 17.39 14.12 38.69 2.75
1189 1214 1.683943 TTTGCCATAGCCAGCTGATC 58.316 50.000 17.39 6.56 38.69 2.92
1190 1215 2.029623 CTTTTGCCATAGCCAGCTGAT 58.970 47.619 17.39 5.91 38.69 2.90
1191 1216 1.466856 CTTTTGCCATAGCCAGCTGA 58.533 50.000 17.39 0.00 38.69 4.26
1192 1217 0.179119 GCTTTTGCCATAGCCAGCTG 60.179 55.000 6.78 6.78 40.15 4.24
1215 1240 2.032681 GACCTTGCGGTGGCTTCT 59.967 61.111 0.00 0.00 45.73 2.85
1519 1550 3.912745 GAAAGCCGGCGAAAGGGGA 62.913 63.158 23.20 0.00 0.00 4.81
2004 3424 2.504899 CTGCGCACGATGACGAGT 60.505 61.111 5.66 0.00 42.66 4.18
2176 3629 3.561213 CAGCCAGCGCATGAGACG 61.561 66.667 11.47 0.00 37.52 4.18
2502 3970 1.148157 CGGCGAACAGAGGTAGCATG 61.148 60.000 0.00 0.00 33.91 4.06
2771 4246 2.995574 AACACGGCGTCCCTAGCT 60.996 61.111 10.85 0.00 34.52 3.32
2772 4247 2.813908 CAACACGGCGTCCCTAGC 60.814 66.667 10.85 0.00 0.00 3.42
2773 4248 2.813908 GCAACACGGCGTCCCTAG 60.814 66.667 10.85 0.00 0.00 3.02
2774 4249 4.382320 GGCAACACGGCGTCCCTA 62.382 66.667 10.85 0.00 33.57 3.53
2813 4288 1.398390 GATTGAGGGAACATGCACGAC 59.602 52.381 0.00 0.00 0.00 4.34
2825 4300 1.539929 GGACATCGAGCAGATTGAGGG 60.540 57.143 0.00 0.00 37.52 4.30
2835 4310 3.733337 ACATATTTCAGGGACATCGAGC 58.267 45.455 0.00 0.00 0.00 5.03
2863 4338 8.553459 AGATTCAGAAAACAGACACGATTATT 57.447 30.769 0.00 0.00 0.00 1.40
2882 4357 2.959030 CAGGGGACATCGAGTAGATTCA 59.041 50.000 0.00 0.00 37.52 2.57
2885 4360 3.314307 TTCAGGGGACATCGAGTAGAT 57.686 47.619 0.00 0.00 41.01 1.98
2920 4395 5.885881 TGGGAAAACATGCACGATTATTAC 58.114 37.500 0.00 0.00 0.00 1.89
2921 4396 5.650266 ACTGGGAAAACATGCACGATTATTA 59.350 36.000 0.00 0.00 0.00 0.98
2924 4399 3.417101 ACTGGGAAAACATGCACGATTA 58.583 40.909 0.00 0.00 0.00 1.75
2925 4400 2.228822 GACTGGGAAAACATGCACGATT 59.771 45.455 0.00 0.00 0.00 3.34
2926 4401 1.812571 GACTGGGAAAACATGCACGAT 59.187 47.619 0.00 0.00 0.00 3.73
2927 4402 1.202758 AGACTGGGAAAACATGCACGA 60.203 47.619 0.00 0.00 0.00 4.35
3003 4479 1.619827 ACGTTTCAGGAACATCGGGTA 59.380 47.619 0.00 0.00 38.18 3.69
3004 4480 0.395312 ACGTTTCAGGAACATCGGGT 59.605 50.000 0.00 0.00 38.18 5.28
3005 4481 0.796312 CACGTTTCAGGAACATCGGG 59.204 55.000 0.00 0.00 38.18 5.14
3037 4513 6.483307 CGAGTAGATTGGGAAAATAAGCATGA 59.517 38.462 0.00 0.00 0.00 3.07
3038 4514 6.483307 TCGAGTAGATTGGGAAAATAAGCATG 59.517 38.462 0.00 0.00 0.00 4.06
3039 4515 6.591935 TCGAGTAGATTGGGAAAATAAGCAT 58.408 36.000 0.00 0.00 0.00 3.79
3040 4516 5.984725 TCGAGTAGATTGGGAAAATAAGCA 58.015 37.500 0.00 0.00 0.00 3.91
3041 4517 6.483640 ACATCGAGTAGATTGGGAAAATAAGC 59.516 38.462 0.00 0.00 37.52 3.09
3043 4519 6.990349 GGACATCGAGTAGATTGGGAAAATAA 59.010 38.462 0.00 0.00 37.52 1.40
3044 4520 6.522054 GGACATCGAGTAGATTGGGAAAATA 58.478 40.000 0.00 0.00 37.52 1.40
3045 4521 5.368989 GGACATCGAGTAGATTGGGAAAAT 58.631 41.667 0.00 0.00 37.52 1.82
3046 4522 4.679639 CGGACATCGAGTAGATTGGGAAAA 60.680 45.833 0.00 0.00 42.43 2.29
3047 4523 3.181479 CGGACATCGAGTAGATTGGGAAA 60.181 47.826 0.00 0.00 42.43 3.13
3048 4524 2.361119 CGGACATCGAGTAGATTGGGAA 59.639 50.000 0.00 0.00 42.43 3.97
3049 4525 1.954382 CGGACATCGAGTAGATTGGGA 59.046 52.381 0.00 0.00 42.43 4.37
3051 4527 1.067060 TGCGGACATCGAGTAGATTGG 59.933 52.381 0.00 0.00 42.43 3.16
3052 4528 2.492019 TGCGGACATCGAGTAGATTG 57.508 50.000 0.00 0.00 42.43 2.67
3053 4529 3.735237 AATGCGGACATCGAGTAGATT 57.265 42.857 0.00 0.00 42.43 2.40
3054 4530 4.848562 TTAATGCGGACATCGAGTAGAT 57.151 40.909 0.00 0.00 42.43 1.98
3055 4531 4.848562 ATTAATGCGGACATCGAGTAGA 57.151 40.909 0.00 0.00 42.43 2.59
3056 4532 5.117745 CAGAATTAATGCGGACATCGAGTAG 59.882 44.000 0.00 0.00 42.43 2.57
3057 4533 4.982295 CAGAATTAATGCGGACATCGAGTA 59.018 41.667 0.00 0.00 42.43 2.59
3058 4534 3.804325 CAGAATTAATGCGGACATCGAGT 59.196 43.478 0.00 0.00 42.43 4.18
3059 4535 3.363378 GCAGAATTAATGCGGACATCGAG 60.363 47.826 0.00 0.00 42.43 4.04
3060 4536 2.543848 GCAGAATTAATGCGGACATCGA 59.456 45.455 0.00 0.00 42.43 3.59
3061 4537 2.287644 TGCAGAATTAATGCGGACATCG 59.712 45.455 9.79 0.00 46.87 3.84
3062 4538 3.969117 TGCAGAATTAATGCGGACATC 57.031 42.857 9.79 0.00 46.87 3.06
3063 4539 4.924305 AATGCAGAATTAATGCGGACAT 57.076 36.364 9.79 0.00 46.87 3.06
3064 4540 4.717233 AAATGCAGAATTAATGCGGACA 57.283 36.364 9.79 0.00 46.87 4.02
3065 4541 4.504097 GGAAAATGCAGAATTAATGCGGAC 59.496 41.667 9.79 0.00 46.87 4.79
3066 4542 4.681744 GGAAAATGCAGAATTAATGCGGA 58.318 39.130 9.79 0.00 46.87 5.54
3067 4543 3.486841 CGGAAAATGCAGAATTAATGCGG 59.513 43.478 9.79 0.00 46.87 5.69
3070 4546 7.967854 TCTTGTACGGAAAATGCAGAATTAATG 59.032 33.333 0.00 0.00 0.00 1.90
3090 4566 4.304110 GAAATCACGTGGACAGTCTTGTA 58.696 43.478 17.00 0.00 37.76 2.41
3208 4684 3.470709 GATGGTGAGGTGACATATGTGG 58.529 50.000 14.43 0.00 0.00 4.17
3221 4697 8.970859 AAGAGAAATAATTAGTGGATGGTGAG 57.029 34.615 0.00 0.00 0.00 3.51
3270 4746 1.228245 GGTGAGGTGGCATGTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
3292 4768 7.379059 AATTAGTGGATGATGAGGTGACATA 57.621 36.000 0.00 0.00 0.00 2.29
3333 4809 8.603181 GGGATGTGTGCATATTAAAATTTTCAC 58.397 33.333 6.72 8.72 35.07 3.18
3372 4848 6.540189 GCAATTAGTGTGACTGATTAGATGGT 59.460 38.462 0.00 0.00 32.90 3.55
3378 4854 6.878389 TGTGATGCAATTAGTGTGACTGATTA 59.122 34.615 0.00 0.00 32.90 1.75
3381 4857 4.640364 TGTGATGCAATTAGTGTGACTGA 58.360 39.130 0.00 0.00 0.00 3.41
3382 4858 5.179929 TCTTGTGATGCAATTAGTGTGACTG 59.820 40.000 0.00 0.00 36.36 3.51
3383 4859 5.308014 TCTTGTGATGCAATTAGTGTGACT 58.692 37.500 0.00 0.00 36.36 3.41
3384 4860 5.611796 TCTTGTGATGCAATTAGTGTGAC 57.388 39.130 0.00 0.00 36.36 3.67
3415 4891 4.194640 CTCAGGTGAGTGAAATACATGGG 58.805 47.826 0.00 0.00 37.40 4.00
3427 4903 0.764369 TGGTTCTGCCTCAGGTGAGT 60.764 55.000 6.25 0.00 40.48 3.41
3464 4940 4.539083 TATCAATGCGGCGCGGGT 62.539 61.111 28.09 17.61 0.00 5.28
3465 4941 3.716006 CTATCAATGCGGCGCGGG 61.716 66.667 28.09 18.53 0.00 6.13
3466 4942 3.716006 CCTATCAATGCGGCGCGG 61.716 66.667 28.09 18.91 0.00 6.46
3467 4943 3.716006 CCCTATCAATGCGGCGCG 61.716 66.667 28.09 13.46 0.00 6.86
3468 4944 4.030452 GCCCTATCAATGCGGCGC 62.030 66.667 27.44 27.44 0.00 6.53
3473 4949 1.498865 CCGTGTCGCCCTATCAATGC 61.499 60.000 0.00 0.00 0.00 3.56
3474 4950 0.104120 TCCGTGTCGCCCTATCAATG 59.896 55.000 0.00 0.00 0.00 2.82
3475 4951 0.389391 CTCCGTGTCGCCCTATCAAT 59.611 55.000 0.00 0.00 0.00 2.57
3476 4952 1.672854 CCTCCGTGTCGCCCTATCAA 61.673 60.000 0.00 0.00 0.00 2.57
3477 4953 2.125326 CCTCCGTGTCGCCCTATCA 61.125 63.158 0.00 0.00 0.00 2.15
3478 4954 2.728817 CCTCCGTGTCGCCCTATC 59.271 66.667 0.00 0.00 0.00 2.08
3479 4955 2.838225 CCCTCCGTGTCGCCCTAT 60.838 66.667 0.00 0.00 0.00 2.57
3500 4976 4.222847 GGTGACGCGAGATCCCCC 62.223 72.222 15.93 0.00 0.00 5.40
3501 4977 1.797211 CTAGGTGACGCGAGATCCCC 61.797 65.000 15.93 0.00 0.00 4.81
3502 4978 1.655329 CTAGGTGACGCGAGATCCC 59.345 63.158 15.93 4.93 0.00 3.85
3503 4979 1.655329 CCTAGGTGACGCGAGATCC 59.345 63.158 15.93 9.71 0.00 3.36
3504 4980 1.008309 GCCTAGGTGACGCGAGATC 60.008 63.158 15.93 0.00 0.00 2.75
3505 4981 1.038130 AAGCCTAGGTGACGCGAGAT 61.038 55.000 15.93 0.00 0.00 2.75
3506 4982 1.654954 GAAGCCTAGGTGACGCGAGA 61.655 60.000 15.93 0.00 0.00 4.04
3507 4983 1.226717 GAAGCCTAGGTGACGCGAG 60.227 63.158 15.93 0.00 0.00 5.03
3508 4984 1.654954 GAGAAGCCTAGGTGACGCGA 61.655 60.000 15.93 0.00 0.00 5.87
3509 4985 1.226717 GAGAAGCCTAGGTGACGCG 60.227 63.158 11.31 3.53 0.00 6.01
3510 4986 1.142097 GGAGAAGCCTAGGTGACGC 59.858 63.158 11.31 3.75 0.00 5.19
3511 4987 1.433879 CGGAGAAGCCTAGGTGACG 59.566 63.158 11.31 3.52 0.00 4.35
3512 4988 1.142097 GCGGAGAAGCCTAGGTGAC 59.858 63.158 11.31 1.93 0.00 3.67
3513 4989 0.614979 AAGCGGAGAAGCCTAGGTGA 60.615 55.000 11.31 0.00 38.01 4.02
3514 4990 0.179097 GAAGCGGAGAAGCCTAGGTG 60.179 60.000 11.31 0.00 38.01 4.00
3515 4991 1.331399 GGAAGCGGAGAAGCCTAGGT 61.331 60.000 11.31 0.00 38.01 3.08
3543 5019 4.286320 CCTCTAGCGGCGGCGATT 62.286 66.667 36.87 23.61 46.35 3.34
3588 5064 3.173965 TCCTAGTCTTCACCTTCCTTGG 58.826 50.000 0.00 0.00 0.00 3.61
3600 5076 3.077359 GCAACAACATGCTCCTAGTCTT 58.923 45.455 0.00 0.00 43.06 3.01
3632 5108 1.958205 GAATCTGATCCAGGCGCCG 60.958 63.158 23.20 16.10 31.51 6.46
3649 5125 2.584970 GCCGGACGAATCATGCGA 60.585 61.111 5.05 0.00 0.00 5.10
3650 5126 3.640000 GGCCGGACGAATCATGCG 61.640 66.667 5.05 0.00 0.00 4.73
3685 5161 1.845627 CTGCTGACCCATGTGGAGGT 61.846 60.000 0.00 0.00 39.75 3.85
3688 5164 3.080641 CCTGCTGACCCATGTGGA 58.919 61.111 0.00 0.00 37.39 4.02
3706 5182 4.812476 TCACCTTGGATCGCCGCG 62.812 66.667 6.39 6.39 36.79 6.46
3707 5183 2.892425 CTCACCTTGGATCGCCGC 60.892 66.667 0.00 0.00 36.79 6.53
3708 5184 2.016393 TAGCTCACCTTGGATCGCCG 62.016 60.000 0.00 0.00 36.79 6.46
3709 5185 0.394565 ATAGCTCACCTTGGATCGCC 59.605 55.000 0.00 0.00 0.00 5.54
3710 5186 1.869767 CAATAGCTCACCTTGGATCGC 59.130 52.381 0.00 0.00 0.00 4.58
3711 5187 2.103094 TCCAATAGCTCACCTTGGATCG 59.897 50.000 13.16 0.00 42.60 3.69
3712 5188 3.845781 TCCAATAGCTCACCTTGGATC 57.154 47.619 13.16 0.00 42.60 3.36
3715 5191 2.487934 CGATCCAATAGCTCACCTTGG 58.512 52.381 9.77 9.77 40.66 3.61
3716 5192 2.103094 TCCGATCCAATAGCTCACCTTG 59.897 50.000 0.00 0.00 0.00 3.61
3717 5193 2.398588 TCCGATCCAATAGCTCACCTT 58.601 47.619 0.00 0.00 0.00 3.50
3718 5194 2.088104 TCCGATCCAATAGCTCACCT 57.912 50.000 0.00 0.00 0.00 4.00
3719 5195 2.966050 GATCCGATCCAATAGCTCACC 58.034 52.381 0.00 0.00 0.00 4.02
3743 5219 0.460311 AGAAGTATCTGGCGGAACGG 59.540 55.000 0.00 0.00 44.05 4.44
3757 5233 1.002087 GTGTCCCGAATGTCCAGAAGT 59.998 52.381 0.00 0.00 0.00 3.01
3765 5241 1.374947 CCCACAGTGTCCCGAATGT 59.625 57.895 0.00 0.00 0.00 2.71
3767 5243 1.374947 CACCCACAGTGTCCCGAAT 59.625 57.895 0.00 0.00 41.93 3.34
3790 5266 1.303074 TCAGGGCGTACTCGACTGT 60.303 57.895 6.21 0.00 45.51 3.55
3797 5273 2.509931 TAGGCACCTCAGGGCGTACT 62.510 60.000 0.00 0.00 35.63 2.73
3798 5274 1.610554 TTAGGCACCTCAGGGCGTAC 61.611 60.000 0.00 0.00 35.63 3.67
3825 5301 0.548510 GAAGGCTTGTAGGCATCCCT 59.451 55.000 3.46 0.00 44.19 4.20


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

AutoCloner maintained by Alex Coulton.