Multiple sequence alignment - TraesCS5B01G438100

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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 TraesCS5B01G438100 chr5B 100.000 3059 0 0 1 3059 611044399 611047457 0.000000e+00 5650
1 TraesCS5B01G438100 chr5B 85.205 1095 156 6 987 2078 610965573 610966664 0.000000e+00 1120
2 TraesCS5B01G438100 chr5B 81.079 1316 216 24 758 2055 610922722 610924022 0.000000e+00 1020
3 TraesCS5B01G438100 chr5B 84.357 863 133 2 1206 2067 610876840 610877701 0.000000e+00 845
4 TraesCS5B01G438100 chr5B 86.441 118 13 1 2631 2745 610967038 610967155 3.200000e-25 126
5 TraesCS5B01G438100 chr5A 95.859 1280 32 9 1324 2595 618460962 618462228 0.000000e+00 2050
6 TraesCS5B01G438100 chr5A 83.758 1059 158 8 998 2055 618273234 618274279 0.000000e+00 990
7 TraesCS5B01G438100 chr5A 83.257 1087 167 11 990 2067 618270571 618271651 0.000000e+00 985
8 TraesCS5B01G438100 chr5A 88.727 754 55 13 1 727 618441194 618441944 0.000000e+00 894
9 TraesCS5B01G438100 chr5A 83.763 930 145 6 1152 2078 618430316 618431242 0.000000e+00 876
10 TraesCS5B01G438100 chr5A 80.092 1090 190 15 1010 2081 618463736 618464816 0.000000e+00 785
11 TraesCS5B01G438100 chr5A 95.333 450 14 5 799 1247 618447925 618448368 0.000000e+00 708
12 TraesCS5B01G438100 chr5A 92.265 181 14 0 2879 3059 618371346 618371526 1.090000e-64 257
13 TraesCS5B01G438100 chr5A 82.807 285 43 5 996 1277 618644187 618644468 1.820000e-62 250
14 TraesCS5B01G438100 chr5A 90.625 160 15 0 987 1146 618404791 618404950 2.390000e-51 213
15 TraesCS5B01G438100 chr5A 96.809 94 3 0 2784 2877 618370785 618370878 1.140000e-34 158
16 TraesCS5B01G438100 chr5A 86.441 118 13 1 2631 2745 618431484 618431601 3.200000e-25 126
17 TraesCS5B01G438100 chr5D 81.056 1383 215 32 713 2067 494684497 494685860 0.000000e+00 1059
18 TraesCS5B01G438100 chr5D 82.450 1094 172 14 987 2067 494654382 494655468 0.000000e+00 939
19 TraesCS5B01G438100 chr5D 80.823 1142 197 15 881 2010 494761671 494762802 0.000000e+00 876
20 TraesCS5B01G438100 chr5D 86.154 130 17 1 2617 2745 494472985 494473114 4.110000e-29 139
21 TraesCS5B01G438100 chr2D 78.235 170 29 7 253 421 158683817 158683655 5.400000e-18 102


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 TraesCS5B01G438100 chr5B 611044399 611047457 3058 False 5650.0 5650 100.0000 1 3059 1 chr5B.!!$F3 3058
1 TraesCS5B01G438100 chr5B 610922722 610924022 1300 False 1020.0 1020 81.0790 758 2055 1 chr5B.!!$F2 1297
2 TraesCS5B01G438100 chr5B 610876840 610877701 861 False 845.0 845 84.3570 1206 2067 1 chr5B.!!$F1 861
3 TraesCS5B01G438100 chr5B 610965573 610967155 1582 False 623.0 1120 85.8230 987 2745 2 chr5B.!!$F4 1758
4 TraesCS5B01G438100 chr5A 618460962 618464816 3854 False 1417.5 2050 87.9755 1010 2595 2 chr5A.!!$F8 1585
5 TraesCS5B01G438100 chr5A 618270571 618274279 3708 False 987.5 990 83.5075 990 2067 2 chr5A.!!$F5 1077
6 TraesCS5B01G438100 chr5A 618441194 618441944 750 False 894.0 894 88.7270 1 727 1 chr5A.!!$F2 726
7 TraesCS5B01G438100 chr5A 618430316 618431601 1285 False 501.0 876 85.1020 1152 2745 2 chr5A.!!$F7 1593
8 TraesCS5B01G438100 chr5A 618370785 618371526 741 False 207.5 257 94.5370 2784 3059 2 chr5A.!!$F6 275
9 TraesCS5B01G438100 chr5D 494684497 494685860 1363 False 1059.0 1059 81.0560 713 2067 1 chr5D.!!$F3 1354
10 TraesCS5B01G438100 chr5D 494654382 494655468 1086 False 939.0 939 82.4500 987 2067 1 chr5D.!!$F2 1080
11 TraesCS5B01G438100 chr5D 494761671 494762802 1131 False 876.0 876 80.8230 881 2010 1 chr5D.!!$F4 1129

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
114 115 0.038892 CAACAGACATTGCTGCCCAC 60.039 55.0 0.00 0.0 39.51 4.61 F
609 636 0.106419 TGACCGGGGCTTTCACTTTT 60.106 50.0 6.32 0.0 0.00 2.27 F
1200 2996 0.252197 ACCCTAAGGATTGCACCGAC 59.748 55.0 0.00 0.0 36.73 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1044 2828 0.032130 GCACACACGACTTCTCCTGA 59.968 55.0 0.00 0.0 0.00 3.86 R
1615 3429 0.034767 CTCTCCTGCATGGCTCCAAA 60.035 55.0 0.00 0.0 35.26 3.28 R
2941 6796 0.034896 GTTTGAGGCGAACTCTCCCA 59.965 55.0 8.68 0.0 46.72 4.37 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
20 21 1.153168 ACCGGATTCAAGGGATGCG 60.153 57.895 9.46 0.00 0.00 4.73
33 34 2.358247 ATGCGGTTGTGGTCGTCC 60.358 61.111 0.00 0.00 0.00 4.79
94 95 2.432628 GGCTCGACACCTTCACGG 60.433 66.667 0.00 0.00 39.35 4.94
96 97 2.338620 CTCGACACCTTCACGGCA 59.661 61.111 0.00 0.00 35.61 5.69
97 98 1.300620 CTCGACACCTTCACGGCAA 60.301 57.895 0.00 0.00 35.61 4.52
98 99 1.557443 CTCGACACCTTCACGGCAAC 61.557 60.000 0.00 0.00 35.61 4.17
103 104 0.813610 CACCTTCACGGCAACAGACA 60.814 55.000 0.00 0.00 35.61 3.41
114 115 0.038892 CAACAGACATTGCTGCCCAC 60.039 55.000 0.00 0.00 39.51 4.61
116 117 3.058160 AGACATTGCTGCCCACGC 61.058 61.111 0.00 0.00 0.00 5.34
160 161 1.979693 GTCCTGCCGTCTGAGAGGT 60.980 63.158 1.20 0.00 0.00 3.85
175 176 0.398318 GAGGTGCAACTTCCCAGAGT 59.602 55.000 5.31 0.00 36.88 3.24
270 271 0.250252 TGCATTGTTGTCGAGGAGCA 60.250 50.000 0.00 0.00 0.00 4.26
316 317 2.700773 GGCGATGGTGAGGTTTGCC 61.701 63.158 0.00 0.00 32.96 4.52
329 330 0.389025 GTTTGCCAAGGAACACCCAG 59.611 55.000 0.00 0.00 37.41 4.45
333 334 0.690762 GCCAAGGAACACCCAGAGTA 59.309 55.000 0.00 0.00 37.41 2.59
335 336 1.978580 CCAAGGAACACCCAGAGTACT 59.021 52.381 0.00 0.00 37.41 2.73
393 394 3.328931 AGGGATCTCAAGAAGTCAAAGCA 59.671 43.478 0.00 0.00 0.00 3.91
401 402 3.951979 AGAAGTCAAAGCACAAGAACG 57.048 42.857 0.00 0.00 0.00 3.95
411 412 0.924090 CACAAGAACGATAGCGAGGC 59.076 55.000 7.69 0.00 41.64 4.70
545 572 3.484407 ACAGCCATTATTGGAGATGCTC 58.516 45.455 7.86 0.00 46.92 4.26
546 573 3.137913 ACAGCCATTATTGGAGATGCTCT 59.862 43.478 7.86 0.00 46.92 4.09
573 600 3.311871 GTGCTCATCTTGCAACATCTAGG 59.688 47.826 0.00 0.00 42.41 3.02
587 614 3.056035 ACATCTAGGTCGAGGTGTTTTCC 60.056 47.826 0.00 0.00 37.52 3.13
600 627 0.826256 GTTTTCCTTTGACCGGGGCT 60.826 55.000 6.32 0.00 0.00 5.19
609 636 0.106419 TGACCGGGGCTTTCACTTTT 60.106 50.000 6.32 0.00 0.00 2.27
686 713 1.135972 CGATTTTCTCACAACCGGCAG 60.136 52.381 0.00 0.00 0.00 4.85
690 717 1.593196 TTCTCACAACCGGCAGAAAG 58.407 50.000 0.00 0.00 0.00 2.62
737 765 1.541368 CCACCCCTCTTCTTCCCCA 60.541 63.158 0.00 0.00 0.00 4.96
753 781 4.135153 CACGCGTCTCTCCCCCTG 62.135 72.222 9.86 0.00 0.00 4.45
754 782 4.361971 ACGCGTCTCTCCCCCTGA 62.362 66.667 5.58 0.00 0.00 3.86
755 783 3.827898 CGCGTCTCTCCCCCTGAC 61.828 72.222 0.00 0.00 0.00 3.51
766 795 3.775654 CCCTGACACCCTCCGCTC 61.776 72.222 0.00 0.00 0.00 5.03
859 889 3.842923 CGCGCTCTGACTCCCCAT 61.843 66.667 5.56 0.00 0.00 4.00
863 893 1.383803 GCTCTGACTCCCCATCCCT 60.384 63.158 0.00 0.00 0.00 4.20
864 894 0.985490 GCTCTGACTCCCCATCCCTT 60.985 60.000 0.00 0.00 0.00 3.95
865 895 1.692762 GCTCTGACTCCCCATCCCTTA 60.693 57.143 0.00 0.00 0.00 2.69
866 896 2.324541 CTCTGACTCCCCATCCCTTAG 58.675 57.143 0.00 0.00 0.00 2.18
868 898 1.048724 TGACTCCCCATCCCTTAGCG 61.049 60.000 0.00 0.00 0.00 4.26
869 899 2.384653 GACTCCCCATCCCTTAGCGC 62.385 65.000 0.00 0.00 0.00 5.92
871 901 3.488569 CCCCATCCCTTAGCGCCA 61.489 66.667 2.29 0.00 0.00 5.69
872 902 2.111878 CCCATCCCTTAGCGCCAG 59.888 66.667 2.29 0.00 0.00 4.85
901 947 2.892425 GGCCGTGCTTCCGATGAG 60.892 66.667 0.00 0.00 0.00 2.90
912 958 2.355126 CGATGAGATCACCGGGCG 60.355 66.667 6.32 0.00 0.00 6.13
941 987 7.024768 GCGAGAAGGAACATACATAGATAGAC 58.975 42.308 0.00 0.00 0.00 2.59
943 989 6.915349 AGAAGGAACATACATAGATAGACGC 58.085 40.000 0.00 0.00 0.00 5.19
945 991 6.260870 AGGAACATACATAGATAGACGCAG 57.739 41.667 0.00 0.00 0.00 5.18
949 995 5.465051 ACATACATAGATAGACGCAGCAAG 58.535 41.667 0.00 0.00 0.00 4.01
950 996 3.377346 ACATAGATAGACGCAGCAAGG 57.623 47.619 0.00 0.00 0.00 3.61
956 1002 3.639094 AGATAGACGCAGCAAGGTAATCT 59.361 43.478 0.00 0.00 0.00 2.40
969 1015 2.025887 AGGTAATCTTTGCACCCTCCAG 60.026 50.000 0.00 0.00 32.43 3.86
970 1016 2.369394 GTAATCTTTGCACCCTCCAGG 58.631 52.381 0.00 0.00 43.78 4.45
972 1018 1.792757 ATCTTTGCACCCTCCAGGCA 61.793 55.000 0.00 0.00 40.58 4.75
975 1021 3.626996 TTGCACCCTCCAGGCATCG 62.627 63.158 0.00 0.00 40.58 3.84
984 1030 2.288702 CCTCCAGGCATCGATCTTACTG 60.289 54.545 0.00 1.63 0.00 2.74
987 1033 2.133553 CAGGCATCGATCTTACTGCAG 58.866 52.381 13.48 13.48 36.34 4.41
988 1034 2.034878 AGGCATCGATCTTACTGCAGA 58.965 47.619 23.35 0.48 36.34 4.26
992 1038 2.941453 TCGATCTTACTGCAGACCAC 57.059 50.000 23.35 5.59 0.00 4.16
993 1039 1.132453 TCGATCTTACTGCAGACCACG 59.868 52.381 23.35 16.70 0.00 4.94
1036 2820 3.472283 AGATCTCTGCTGCCATTGTAG 57.528 47.619 0.00 0.00 0.00 2.74
1041 2825 4.643795 GCTGCCATTGTAGCTGGA 57.356 55.556 0.00 0.00 45.63 3.86
1042 2826 3.106738 GCTGCCATTGTAGCTGGAT 57.893 52.632 0.00 0.00 45.63 3.41
1043 2827 0.950116 GCTGCCATTGTAGCTGGATC 59.050 55.000 0.00 0.00 45.63 3.36
1044 2828 1.476471 GCTGCCATTGTAGCTGGATCT 60.476 52.381 0.00 0.00 45.63 2.75
1045 2829 2.492012 CTGCCATTGTAGCTGGATCTC 58.508 52.381 0.00 0.00 35.70 2.75
1069 2865 1.409064 AGAAGTCGTGTGTGCTCAAGA 59.591 47.619 0.00 0.00 0.00 3.02
1075 2871 4.640647 AGTCGTGTGTGCTCAAGATAGATA 59.359 41.667 0.00 0.00 0.00 1.98
1161 2957 3.305314 GGCCACGACTGGACCATA 58.695 61.111 0.00 0.00 40.28 2.74
1163 2959 1.327690 GGCCACGACTGGACCATAGA 61.328 60.000 0.00 0.00 40.28 1.98
1184 2980 3.912496 ATACTACCCAAACGGTTACCC 57.088 47.619 0.00 0.00 45.36 3.69
1200 2996 0.252197 ACCCTAAGGATTGCACCGAC 59.748 55.000 0.00 0.00 36.73 4.79
1218 3014 6.364706 GCACCGACTTCATATCTCTTTATCTG 59.635 42.308 0.00 0.00 0.00 2.90
1220 3016 5.866633 CCGACTTCATATCTCTTTATCTGGC 59.133 44.000 0.00 0.00 0.00 4.85
1235 3031 3.819188 GGCTCTTCAATCTGCCGG 58.181 61.111 0.00 0.00 35.79 6.13
1239 3038 1.699656 CTCTTCAATCTGCCGGTGCG 61.700 60.000 1.90 0.00 41.78 5.34
1251 3050 1.787847 CGGTGCGGAAGATGTGAAC 59.212 57.895 0.00 0.00 0.00 3.18
1292 3091 3.515602 ACTTGGCAAGAATGGAGAACT 57.484 42.857 32.50 4.00 0.00 3.01
1294 3093 1.538047 TGGCAAGAATGGAGAACTGC 58.462 50.000 0.00 0.00 0.00 4.40
1319 3118 2.402182 TCATATAGCCGTACCCCCAA 57.598 50.000 0.00 0.00 0.00 4.12
1343 3143 2.332063 ATACGCACATTCTCAAGGGG 57.668 50.000 0.00 0.00 0.00 4.79
1397 3197 0.924823 AAGGCTGATCTGGAGGCATT 59.075 50.000 7.68 0.14 38.46 3.56
1454 3266 1.995484 CGATATCACCGTCATCCATGC 59.005 52.381 3.12 0.00 0.00 4.06
1456 3268 0.396435 TATCACCGTCATCCATGCCC 59.604 55.000 0.00 0.00 0.00 5.36
1479 3291 4.236527 AGAAACAAGTGTTCCTCCAAGT 57.763 40.909 0.00 0.00 37.25 3.16
1488 3300 2.306805 TGTTCCTCCAAGTGATCTGCAT 59.693 45.455 0.00 0.00 0.00 3.96
1531 3343 0.445436 GAACAAGGATGCAGCAGACG 59.555 55.000 3.51 0.00 0.00 4.18
1689 3503 3.141398 GGAAGCAGATGTGTTCAAGTCA 58.859 45.455 0.00 0.00 0.00 3.41
1716 3530 4.866921 TCCATTTCATATACACCGACTCG 58.133 43.478 0.00 0.00 0.00 4.18
1727 3541 1.677966 CCGACTCGGTTCCTCCTGA 60.678 63.158 9.51 0.00 42.73 3.86
1729 3543 0.961358 CGACTCGGTTCCTCCTGAGT 60.961 60.000 2.44 2.44 45.34 3.41
1789 3603 2.963782 GACAGGTACAATATCGGGAGGT 59.036 50.000 0.00 0.00 0.00 3.85
1893 3707 2.036733 TGGTTTCCGTCGTCTCAAAGAT 59.963 45.455 0.00 0.00 0.00 2.40
1902 3716 4.458708 GTCGTCTCAAAGATGCTTGTTTC 58.541 43.478 0.00 0.00 31.39 2.78
1912 3726 4.985538 AGATGCTTGTTTCCAGTTCCTTA 58.014 39.130 0.00 0.00 0.00 2.69
1929 3743 5.237236 TCCTTACTTCTCCGTCCAATTTT 57.763 39.130 0.00 0.00 0.00 1.82
1940 3754 2.476185 CGTCCAATTTTGAGGCGATGAC 60.476 50.000 0.00 0.00 31.34 3.06
1941 3755 2.487762 GTCCAATTTTGAGGCGATGACA 59.512 45.455 0.00 0.00 0.00 3.58
1944 3761 1.825090 ATTTTGAGGCGATGACAGCA 58.175 45.000 0.00 0.00 36.08 4.41
1989 3806 1.409064 TCTAGCTGCCCGTATGTTCTG 59.591 52.381 0.00 0.00 0.00 3.02
1991 3808 0.176680 AGCTGCCCGTATGTTCTGAG 59.823 55.000 0.00 0.00 0.00 3.35
2017 3834 5.584253 GCTGATAGCTAGAATAATCCCGA 57.416 43.478 0.00 0.00 38.45 5.14
2019 3836 5.105716 GCTGATAGCTAGAATAATCCCGACA 60.106 44.000 0.00 0.00 38.45 4.35
2025 3842 6.831976 AGCTAGAATAATCCCGACAGAATTT 58.168 36.000 0.00 0.00 0.00 1.82
2074 3891 8.293867 TGACAATTTAGTAGTAATGTGTTTGGC 58.706 33.333 2.04 0.94 0.00 4.52
2105 3998 6.017440 TGTCTGAACAAAAATGCTACCAGTAC 60.017 38.462 0.00 0.00 30.70 2.73
2116 4009 9.461312 AAAATGCTACCAGTACTAATCATTCAA 57.539 29.630 0.00 0.00 0.00 2.69
2143 4036 9.244292 TCTAAATATATGTTCAGGCGAGTAGAT 57.756 33.333 0.00 0.00 0.00 1.98
2146 4039 5.791336 ATATGTTCAGGCGAGTAGATTGA 57.209 39.130 0.00 0.00 0.00 2.57
2149 4042 5.592104 TGTTCAGGCGAGTAGATTGATTA 57.408 39.130 0.00 0.00 0.00 1.75
2151 4044 5.985530 TGTTCAGGCGAGTAGATTGATTATG 59.014 40.000 0.00 0.00 0.00 1.90
2152 4045 4.560128 TCAGGCGAGTAGATTGATTATGC 58.440 43.478 0.00 0.00 0.00 3.14
2153 4046 4.281941 TCAGGCGAGTAGATTGATTATGCT 59.718 41.667 0.00 0.00 0.00 3.79
2154 4047 5.476945 TCAGGCGAGTAGATTGATTATGCTA 59.523 40.000 0.00 0.00 0.00 3.49
2155 4048 5.574830 CAGGCGAGTAGATTGATTATGCTAC 59.425 44.000 0.00 0.00 34.81 3.58
2156 4049 5.478679 AGGCGAGTAGATTGATTATGCTACT 59.521 40.000 0.00 0.00 44.41 2.57
2157 4050 5.574830 GGCGAGTAGATTGATTATGCTACTG 59.425 44.000 0.00 0.00 42.47 2.74
2201 4094 2.502213 TGTGACTGACTACAACGGTG 57.498 50.000 0.00 0.00 0.00 4.94
2215 4108 1.591594 CGGTGAGTTGTGTGCGTCT 60.592 57.895 0.00 0.00 0.00 4.18
2218 4111 1.400494 GGTGAGTTGTGTGCGTCTTTT 59.600 47.619 0.00 0.00 0.00 2.27
2219 4112 2.159435 GGTGAGTTGTGTGCGTCTTTTT 60.159 45.455 0.00 0.00 0.00 1.94
2220 4113 2.845967 GTGAGTTGTGTGCGTCTTTTTG 59.154 45.455 0.00 0.00 0.00 2.44
2224 4117 4.844267 AGTTGTGTGCGTCTTTTTGATAC 58.156 39.130 0.00 0.00 0.00 2.24
2226 4119 5.008613 AGTTGTGTGCGTCTTTTTGATACAT 59.991 36.000 0.00 0.00 0.00 2.29
2230 4123 4.083537 TGTGCGTCTTTTTGATACATCACC 60.084 41.667 0.00 0.00 36.36 4.02
2232 4125 4.083537 TGCGTCTTTTTGATACATCACCAC 60.084 41.667 0.00 0.00 36.36 4.16
2233 4126 4.671766 GCGTCTTTTTGATACATCACCACC 60.672 45.833 0.00 0.00 36.36 4.61
2247 4140 2.105649 TCACCACCAGATGCTTGTGTTA 59.894 45.455 0.00 0.00 0.00 2.41
2251 4144 3.189287 CCACCAGATGCTTGTGTTACTTC 59.811 47.826 0.00 0.00 0.00 3.01
2252 4145 3.814842 CACCAGATGCTTGTGTTACTTCA 59.185 43.478 0.00 0.00 0.00 3.02
2255 4148 5.048504 ACCAGATGCTTGTGTTACTTCATTG 60.049 40.000 0.00 0.00 0.00 2.82
2256 4149 5.048504 CCAGATGCTTGTGTTACTTCATTGT 60.049 40.000 0.00 0.00 0.00 2.71
2257 4150 5.854866 CAGATGCTTGTGTTACTTCATTGTG 59.145 40.000 0.00 0.00 0.00 3.33
2259 4152 5.574891 TGCTTGTGTTACTTCATTGTGTT 57.425 34.783 0.00 0.00 0.00 3.32
2260 4153 5.577835 TGCTTGTGTTACTTCATTGTGTTC 58.422 37.500 0.00 0.00 0.00 3.18
2262 4155 4.804608 TGTGTTACTTCATTGTGTTCGG 57.195 40.909 0.00 0.00 0.00 4.30
2264 4157 4.636648 TGTGTTACTTCATTGTGTTCGGTT 59.363 37.500 0.00 0.00 0.00 4.44
2268 4161 7.858879 GTGTTACTTCATTGTGTTCGGTTTTAT 59.141 33.333 0.00 0.00 0.00 1.40
2269 4162 8.407064 TGTTACTTCATTGTGTTCGGTTTTATT 58.593 29.630 0.00 0.00 0.00 1.40
2272 4165 8.791355 ACTTCATTGTGTTCGGTTTTATTAAC 57.209 30.769 0.00 0.00 0.00 2.01
2273 4166 8.407064 ACTTCATTGTGTTCGGTTTTATTAACA 58.593 29.630 0.00 0.00 0.00 2.41
2285 4178 6.523201 CGGTTTTATTAACACTCAACTCATGC 59.477 38.462 0.00 0.00 0.00 4.06
2299 4192 2.496070 ACTCATGCCTACTTTCGCACTA 59.504 45.455 0.00 0.00 37.93 2.74
2326 4219 7.944729 AAACTGACTGTAAATTATGGATGCT 57.055 32.000 0.00 0.00 0.00 3.79
2327 4220 6.932356 ACTGACTGTAAATTATGGATGCTG 57.068 37.500 0.00 0.00 0.00 4.41
2331 4224 7.334858 TGACTGTAAATTATGGATGCTGTGTA 58.665 34.615 0.00 0.00 0.00 2.90
2342 4259 7.886629 ATGGATGCTGTGTATAATTCAGTTT 57.113 32.000 0.00 0.00 0.00 2.66
2345 4262 8.892723 TGGATGCTGTGTATAATTCAGTTTAAG 58.107 33.333 0.00 0.00 0.00 1.85
2346 4263 7.857885 GGATGCTGTGTATAATTCAGTTTAAGC 59.142 37.037 0.00 0.00 0.00 3.09
2347 4264 7.680442 TGCTGTGTATAATTCAGTTTAAGCA 57.320 32.000 0.00 0.00 33.69 3.91
2348 4265 7.526608 TGCTGTGTATAATTCAGTTTAAGCAC 58.473 34.615 0.00 0.00 31.33 4.40
2349 4266 7.390440 TGCTGTGTATAATTCAGTTTAAGCACT 59.610 33.333 0.00 0.00 31.33 4.40
2350 4267 8.879759 GCTGTGTATAATTCAGTTTAAGCACTA 58.120 33.333 0.00 0.00 0.00 2.74
2355 4272 7.938140 ATAATTCAGTTTAAGCACTAAGGCA 57.062 32.000 0.00 0.00 35.83 4.75
2356 4273 6.648879 AATTCAGTTTAAGCACTAAGGCAA 57.351 33.333 0.00 0.00 35.83 4.52
2359 4276 6.458232 TCAGTTTAAGCACTAAGGCAAAAA 57.542 33.333 0.00 0.00 35.83 1.94
2386 4346 5.001237 TGCATGTAATCCTCAAGCATTTG 57.999 39.130 0.00 0.00 35.21 2.32
2388 4348 5.039333 GCATGTAATCCTCAAGCATTTGAC 58.961 41.667 0.00 0.00 38.37 3.18
2394 4354 7.828717 TGTAATCCTCAAGCATTTGACTATTGA 59.171 33.333 0.00 0.00 38.37 2.57
2404 4364 6.654161 AGCATTTGACTATTGATATCCTCTGC 59.346 38.462 0.00 0.00 0.00 4.26
2405 4365 6.128063 GCATTTGACTATTGATATCCTCTGCC 60.128 42.308 0.00 0.00 0.00 4.85
2411 4371 4.550076 ATTGATATCCTCTGCCAGCTAC 57.450 45.455 0.00 0.00 0.00 3.58
2414 4374 4.740902 TGATATCCTCTGCCAGCTACTAA 58.259 43.478 0.00 0.00 0.00 2.24
2415 4375 5.336945 TGATATCCTCTGCCAGCTACTAAT 58.663 41.667 0.00 0.00 0.00 1.73
2416 4376 6.494059 TGATATCCTCTGCCAGCTACTAATA 58.506 40.000 0.00 0.00 0.00 0.98
2417 4377 6.605194 TGATATCCTCTGCCAGCTACTAATAG 59.395 42.308 0.00 0.00 0.00 1.73
2418 4378 4.186077 TCCTCTGCCAGCTACTAATAGT 57.814 45.455 0.00 0.00 0.00 2.12
2419 4379 4.547671 TCCTCTGCCAGCTACTAATAGTT 58.452 43.478 0.00 0.00 0.00 2.24
2420 4380 4.342378 TCCTCTGCCAGCTACTAATAGTTG 59.658 45.833 0.00 0.00 38.89 3.16
2422 4382 5.011090 TCTGCCAGCTACTAATAGTTGTG 57.989 43.478 0.00 0.00 37.81 3.33
2423 4383 4.709886 TCTGCCAGCTACTAATAGTTGTGA 59.290 41.667 0.00 0.00 37.81 3.58
2424 4384 4.755411 TGCCAGCTACTAATAGTTGTGAC 58.245 43.478 0.00 0.00 37.81 3.67
2425 4385 3.797256 GCCAGCTACTAATAGTTGTGACG 59.203 47.826 0.00 0.00 37.81 4.35
2429 4390 3.382546 GCTACTAATAGTTGTGACGGGGA 59.617 47.826 0.00 0.00 0.00 4.81
2440 4401 3.768878 TGTGACGGGGAATTGGTTATTT 58.231 40.909 0.00 0.00 0.00 1.40
2441 4402 3.759618 TGTGACGGGGAATTGGTTATTTC 59.240 43.478 0.00 0.00 0.00 2.17
2452 4413 6.319911 GGAATTGGTTATTTCTTCCCTCTGAG 59.680 42.308 0.00 0.00 31.19 3.35
2455 4416 4.228210 TGGTTATTTCTTCCCTCTGAGCAT 59.772 41.667 0.00 0.00 0.00 3.79
2467 4428 0.731417 CTGAGCATTGCTGGTAGTGC 59.269 55.000 17.51 0.00 39.88 4.40
2488 4449 1.267533 TGCTGTGCACTTGTTATGCTG 59.732 47.619 19.41 0.00 43.77 4.41
2489 4450 1.536766 GCTGTGCACTTGTTATGCTGA 59.463 47.619 19.41 0.00 43.77 4.26
2501 4466 2.427095 GTTATGCTGATGGGGGTTGTTC 59.573 50.000 0.00 0.00 0.00 3.18
2502 4467 0.409092 ATGCTGATGGGGGTTGTTCA 59.591 50.000 0.00 0.00 0.00 3.18
2504 4469 0.038166 GCTGATGGGGGTTGTTCAGA 59.962 55.000 3.11 0.00 38.25 3.27
2514 4479 4.262036 GGGGGTTGTTCAGATTCAGTTTTC 60.262 45.833 0.00 0.00 0.00 2.29
2534 4499 7.457868 GTTTTCGAAAACTTGGTTTTAAAGGG 58.542 34.615 35.26 0.00 44.33 3.95
2569 4539 9.646427 ATTTTGTAGTTTTCTGTTAAGCACAAA 57.354 25.926 0.00 0.00 33.87 2.83
2571 4541 8.627487 TTGTAGTTTTCTGTTAAGCACAAATG 57.373 30.769 0.00 0.00 33.87 2.32
2572 4542 7.767261 TGTAGTTTTCTGTTAAGCACAAATGT 58.233 30.769 0.00 0.00 33.87 2.71
2575 4545 7.096551 AGTTTTCTGTTAAGCACAAATGTTGT 58.903 30.769 0.00 0.00 46.75 3.32
2587 4557 5.804979 GCACAAATGTTGTAGTTCTGTTGTT 59.195 36.000 0.00 0.00 43.23 2.83
2595 4565 7.024768 TGTTGTAGTTCTGTTGTTTGCTAAAC 58.975 34.615 5.22 5.22 41.73 2.01
2606 4576 5.565592 TGTTTGCTAAACATAGCCATGAG 57.434 39.130 0.00 0.00 45.79 2.90
2608 4578 4.502105 TTGCTAAACATAGCCATGAGGA 57.498 40.909 0.00 0.00 42.17 3.71
2613 4583 5.513094 GCTAAACATAGCCATGAGGATACCA 60.513 44.000 0.00 0.00 38.89 3.25
2614 4584 5.387113 AAACATAGCCATGAGGATACCAA 57.613 39.130 0.00 0.00 38.89 3.67
2620 4590 3.979347 AGCCATGAGGATACCAAGAGAAT 59.021 43.478 0.00 0.00 36.89 2.40
2622 4592 4.202398 GCCATGAGGATACCAAGAGAATCA 60.202 45.833 0.00 0.00 34.88 2.57
2625 4595 6.409005 CCATGAGGATACCAAGAGAATCAGTT 60.409 42.308 0.00 0.00 34.88 3.16
2627 4597 5.721480 TGAGGATACCAAGAGAATCAGTTGA 59.279 40.000 0.00 0.00 34.47 3.18
2628 4598 6.213397 TGAGGATACCAAGAGAATCAGTTGAA 59.787 38.462 0.00 0.00 34.47 2.69
2646 4647 4.241590 TGAACATGACCAAATGACAAGC 57.758 40.909 0.00 0.00 0.00 4.01
2665 4666 2.434884 CTGATGACCGCACGGCTT 60.435 61.111 9.43 0.46 39.32 4.35
2670 4671 3.712881 GACCGCACGGCTTGTCAC 61.713 66.667 9.43 0.00 39.32 3.67
2696 4697 1.191647 CACTGTTTTGTAGCGACCGAC 59.808 52.381 0.00 0.00 0.00 4.79
2697 4698 1.068127 ACTGTTTTGTAGCGACCGACT 59.932 47.619 0.00 0.00 0.00 4.18
2745 4749 9.416794 CCTTAATACATCACTACTAGATGCTTG 57.583 37.037 0.00 0.00 45.19 4.01
2746 4750 8.818141 TTAATACATCACTACTAGATGCTTGC 57.182 34.615 0.00 0.00 45.19 4.01
2747 4751 3.711086 ACATCACTACTAGATGCTTGCG 58.289 45.455 0.00 0.00 45.19 4.85
2748 4752 2.871182 TCACTACTAGATGCTTGCGG 57.129 50.000 0.00 0.00 0.00 5.69
2749 4753 1.409064 TCACTACTAGATGCTTGCGGG 59.591 52.381 0.00 0.00 0.00 6.13
2750 4754 1.409064 CACTACTAGATGCTTGCGGGA 59.591 52.381 0.00 0.00 0.00 5.14
2751 4755 1.409427 ACTACTAGATGCTTGCGGGAC 59.591 52.381 0.00 0.00 0.00 4.46
2764 4768 3.872027 GGGACGCGGAGTTTCTTC 58.128 61.111 12.47 0.00 0.00 2.87
2765 4769 1.292541 GGGACGCGGAGTTTCTTCT 59.707 57.895 12.47 0.00 0.00 2.85
2766 4770 0.736672 GGGACGCGGAGTTTCTTCTC 60.737 60.000 12.47 0.00 0.00 2.87
2767 4771 0.244178 GGACGCGGAGTTTCTTCTCT 59.756 55.000 12.47 0.00 35.11 3.10
2768 4772 1.619983 GACGCGGAGTTTCTTCTCTC 58.380 55.000 12.47 0.00 35.11 3.20
2769 4773 0.109689 ACGCGGAGTTTCTTCTCTCG 60.110 55.000 12.47 0.00 36.91 4.04
2770 4774 0.168348 CGCGGAGTTTCTTCTCTCGA 59.832 55.000 0.00 0.00 34.88 4.04
2771 4775 1.792273 CGCGGAGTTTCTTCTCTCGAG 60.792 57.143 5.93 5.93 34.88 4.04
2772 4776 1.902840 CGGAGTTTCTTCTCTCGAGC 58.097 55.000 7.81 0.00 35.11 5.03
2773 4777 1.200252 CGGAGTTTCTTCTCTCGAGCA 59.800 52.381 7.81 0.00 35.11 4.26
2774 4778 2.601804 GGAGTTTCTTCTCTCGAGCAC 58.398 52.381 7.81 0.00 35.11 4.40
2775 4779 2.029828 GGAGTTTCTTCTCTCGAGCACA 60.030 50.000 7.81 0.00 35.11 4.57
2776 4780 3.241701 GAGTTTCTTCTCTCGAGCACAG 58.758 50.000 7.81 0.00 0.00 3.66
2777 4781 2.887783 AGTTTCTTCTCTCGAGCACAGA 59.112 45.455 7.81 2.50 0.00 3.41
2778 4782 3.509575 AGTTTCTTCTCTCGAGCACAGAT 59.490 43.478 7.81 0.00 0.00 2.90
2779 4783 3.500558 TTCTTCTCTCGAGCACAGATG 57.499 47.619 7.81 8.21 0.00 2.90
2796 4800 3.005155 CAGATGCTCGTGATATCCTGTGA 59.995 47.826 0.00 0.00 0.00 3.58
2810 4814 2.230508 TCCTGTGAGTAAGTTAGTGCGG 59.769 50.000 0.00 0.00 0.00 5.69
2869 4873 3.003897 GGAGCGTTGTAAATGTTTGTGGA 59.996 43.478 0.00 0.00 34.61 4.02
2877 4881 7.305474 GTTGTAAATGTTTGTGGACCATCTAG 58.695 38.462 0.00 0.00 0.00 2.43
2885 6559 0.755698 TGGACCATCTAGCCTCCGTC 60.756 60.000 0.00 0.00 0.00 4.79
2886 6560 1.655329 GACCATCTAGCCTCCGTCG 59.345 63.158 0.00 0.00 0.00 5.12
2895 6569 3.062466 CCTCCGTCGGCAGTGAGA 61.062 66.667 6.34 0.00 0.00 3.27
2924 6779 1.897615 GCATCCTGGAGGCAGATGC 60.898 63.158 26.87 14.59 39.28 3.91
2941 6796 4.320456 CGGCAGTGGCTGTGAGGT 62.320 66.667 15.48 0.00 41.67 3.85
2942 6797 2.670934 GGCAGTGGCTGTGAGGTG 60.671 66.667 9.90 0.00 40.87 4.00
2959 6814 0.034896 GTGGGAGAGTTCGCCTCAAA 59.965 55.000 1.94 0.00 43.12 2.69
2963 6818 1.673329 GGAGAGTTCGCCTCAAACCTC 60.673 57.143 4.99 0.00 43.12 3.85
3038 6893 3.077359 AGGTGAGCATCTTTCGGAAAAG 58.923 45.455 4.53 0.00 42.77 2.27
3041 6896 4.467735 GTGAGCATCTTTCGGAAAAGTTC 58.532 43.478 4.53 6.03 42.17 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.109593 AACCGGACGACCACAACC 59.890 61.111 9.46 0.00 35.59 3.77
77 78 2.432628 CCGTGAAGGTGTCGAGCC 60.433 66.667 0.00 0.00 34.51 4.70
96 97 1.518056 CGTGGGCAGCAATGTCTGTT 61.518 55.000 0.00 0.00 36.49 3.16
97 98 1.968017 CGTGGGCAGCAATGTCTGT 60.968 57.895 0.00 0.00 36.49 3.41
98 99 2.872557 CGTGGGCAGCAATGTCTG 59.127 61.111 0.00 1.30 37.15 3.51
103 104 2.438434 GTAGGCGTGGGCAGCAAT 60.438 61.111 0.00 0.00 42.47 3.56
140 141 2.033602 TCTCAGACGGCAGGACGA 59.966 61.111 0.00 0.00 37.61 4.20
143 144 1.979155 CACCTCTCAGACGGCAGGA 60.979 63.158 0.00 0.00 0.00 3.86
145 146 2.125753 GCACCTCTCAGACGGCAG 60.126 66.667 0.00 0.00 0.00 4.85
150 151 1.609320 GGGAAGTTGCACCTCTCAGAC 60.609 57.143 0.00 0.00 0.00 3.51
160 161 0.756294 TCGAACTCTGGGAAGTTGCA 59.244 50.000 0.00 0.00 39.55 4.08
235 236 0.694771 TGCAGGTCTCCAGCTTCATT 59.305 50.000 4.94 0.00 36.95 2.57
281 282 1.202394 CGCCTCCTCATCACTCTCTTG 60.202 57.143 0.00 0.00 0.00 3.02
283 284 0.257328 TCGCCTCCTCATCACTCTCT 59.743 55.000 0.00 0.00 0.00 3.10
316 317 3.181454 ACAAGTACTCTGGGTGTTCCTTG 60.181 47.826 0.00 0.50 36.20 3.61
329 330 5.641209 TCTCGTACTAGACCAACAAGTACTC 59.359 44.000 0.00 0.00 42.13 2.59
333 334 4.158025 CCATCTCGTACTAGACCAACAAGT 59.842 45.833 0.00 0.00 0.00 3.16
335 336 4.338012 TCCATCTCGTACTAGACCAACAA 58.662 43.478 0.00 0.00 0.00 2.83
366 367 3.772025 TGACTTCTTGAGATCCCTCTTCC 59.228 47.826 0.00 0.00 40.10 3.46
393 394 0.530744 TGCCTCGCTATCGTTCTTGT 59.469 50.000 0.00 0.00 36.96 3.16
411 412 1.303236 TTGACCCGTGAAGGCCATG 60.303 57.895 5.01 0.00 39.21 3.66
489 516 8.550376 GCATCAAAATGTGTGTGAATTAAAAGT 58.450 29.630 0.00 0.00 35.18 2.66
545 572 2.408271 TGCAAGATGAGCACCCTAAG 57.592 50.000 0.00 0.00 37.02 2.18
546 573 2.224744 TGTTGCAAGATGAGCACCCTAA 60.225 45.455 0.00 0.00 42.54 2.69
573 600 2.289820 GGTCAAAGGAAAACACCTCGAC 59.710 50.000 0.00 0.00 39.62 4.20
587 614 0.537371 AGTGAAAGCCCCGGTCAAAG 60.537 55.000 0.00 0.00 0.00 2.77
600 627 2.494073 ACAACGCCCTGAAAAAGTGAAA 59.506 40.909 0.00 0.00 0.00 2.69
609 636 1.272490 CTGAGACTACAACGCCCTGAA 59.728 52.381 0.00 0.00 0.00 3.02
663 690 1.732259 CCGGTTGTGAGAAAATCGGAG 59.268 52.381 1.66 0.00 38.42 4.63
665 692 0.168128 GCCGGTTGTGAGAAAATCGG 59.832 55.000 1.90 3.53 39.07 4.18
686 713 1.134694 GGGATTGTCGCGTGCTTTC 59.865 57.895 5.77 0.00 0.00 2.62
690 717 2.125512 AGAGGGATTGTCGCGTGC 60.126 61.111 5.77 0.57 34.19 5.34
728 756 1.874345 GAGAGACGCGTGGGGAAGAA 61.874 60.000 20.70 0.00 0.00 2.52
729 757 2.282958 AGAGACGCGTGGGGAAGA 60.283 61.111 20.70 0.00 0.00 2.87
730 758 2.182030 GAGAGACGCGTGGGGAAG 59.818 66.667 20.70 0.00 0.00 3.46
731 759 3.379445 GGAGAGACGCGTGGGGAA 61.379 66.667 20.70 0.00 0.00 3.97
737 765 4.361971 TCAGGGGGAGAGACGCGT 62.362 66.667 13.85 13.85 0.00 6.01
749 777 3.775654 GAGCGGAGGGTGTCAGGG 61.776 72.222 0.00 0.00 0.00 4.45
750 778 3.775654 GGAGCGGAGGGTGTCAGG 61.776 72.222 0.00 0.00 0.00 3.86
851 881 2.444256 GCGCTAAGGGATGGGGAGT 61.444 63.158 0.00 0.00 0.00 3.85
852 882 2.427753 GCGCTAAGGGATGGGGAG 59.572 66.667 0.00 0.00 0.00 4.30
858 888 4.241555 CCGCTGGCGCTAAGGGAT 62.242 66.667 22.69 0.00 38.24 3.85
912 958 1.143183 TATGTTCCTTCTCGCCGCC 59.857 57.895 0.00 0.00 0.00 6.13
923 969 4.859798 GCTGCGTCTATCTATGTATGTTCC 59.140 45.833 0.00 0.00 0.00 3.62
927 973 4.861462 CCTTGCTGCGTCTATCTATGTATG 59.139 45.833 0.00 0.00 0.00 2.39
941 987 1.199789 TGCAAAGATTACCTTGCTGCG 59.800 47.619 8.13 0.00 40.02 5.18
943 989 2.094545 GGGTGCAAAGATTACCTTGCTG 60.095 50.000 8.13 0.00 34.79 4.41
945 991 2.164422 GAGGGTGCAAAGATTACCTTGC 59.836 50.000 0.00 0.00 34.79 4.01
949 995 2.369394 CTGGAGGGTGCAAAGATTACC 58.631 52.381 0.00 0.00 0.00 2.85
950 996 2.369394 CCTGGAGGGTGCAAAGATTAC 58.631 52.381 0.00 0.00 0.00 1.89
956 1002 1.304381 GATGCCTGGAGGGTGCAAA 60.304 57.895 0.00 0.00 38.69 3.68
961 1007 0.692419 AAGATCGATGCCTGGAGGGT 60.692 55.000 0.54 0.00 37.43 4.34
963 1009 1.967066 AGTAAGATCGATGCCTGGAGG 59.033 52.381 0.54 0.00 38.53 4.30
964 1010 2.865670 GCAGTAAGATCGATGCCTGGAG 60.866 54.545 0.54 0.00 32.49 3.86
969 1015 2.131183 GTCTGCAGTAAGATCGATGCC 58.869 52.381 14.67 0.00 37.89 4.40
970 1016 2.131183 GGTCTGCAGTAAGATCGATGC 58.869 52.381 14.67 0.00 39.14 3.91
972 1018 2.223595 CGTGGTCTGCAGTAAGATCGAT 60.224 50.000 14.67 0.00 29.17 3.59
975 1021 2.531206 GTCGTGGTCTGCAGTAAGATC 58.469 52.381 14.67 0.00 0.00 2.75
984 1030 1.021390 CCATTCTGGTCGTGGTCTGC 61.021 60.000 0.00 0.00 31.35 4.26
987 1033 1.003839 TGCCATTCTGGTCGTGGTC 60.004 57.895 0.00 0.00 40.46 4.02
988 1034 1.003355 CTGCCATTCTGGTCGTGGT 60.003 57.895 0.00 0.00 40.46 4.16
992 1038 0.463295 ATGCTCTGCCATTCTGGTCG 60.463 55.000 0.00 0.00 40.46 4.79
993 1039 1.404391 CAATGCTCTGCCATTCTGGTC 59.596 52.381 0.00 0.00 40.46 4.02
1036 2820 1.066908 CGACTTCTCCTGAGATCCAGC 59.933 57.143 0.00 0.00 41.57 4.85
1040 2824 2.490115 ACACACGACTTCTCCTGAGATC 59.510 50.000 0.00 0.00 37.29 2.75
1041 2825 2.230025 CACACACGACTTCTCCTGAGAT 59.770 50.000 0.00 0.00 37.29 2.75
1042 2826 1.609072 CACACACGACTTCTCCTGAGA 59.391 52.381 0.00 0.00 35.27 3.27
1043 2827 1.932604 GCACACACGACTTCTCCTGAG 60.933 57.143 0.00 0.00 0.00 3.35
1044 2828 0.032130 GCACACACGACTTCTCCTGA 59.968 55.000 0.00 0.00 0.00 3.86
1045 2829 0.032678 AGCACACACGACTTCTCCTG 59.967 55.000 0.00 0.00 0.00 3.86
1069 2865 6.154363 GCCTTGGCTCTTGAGTATCTATCTAT 59.846 42.308 4.11 0.00 34.92 1.98
1075 2871 1.137872 CGCCTTGGCTCTTGAGTATCT 59.862 52.381 10.12 0.00 34.92 1.98
1184 2980 2.972625 TGAAGTCGGTGCAATCCTTAG 58.027 47.619 0.00 0.00 0.00 2.18
1200 2996 8.366401 TGAAGAGCCAGATAAAGAGATATGAAG 58.634 37.037 0.00 0.00 0.00 3.02
1218 3014 1.078143 ACCGGCAGATTGAAGAGCC 60.078 57.895 0.00 0.00 43.61 4.70
1220 3016 1.699656 CGCACCGGCAGATTGAAGAG 61.700 60.000 0.00 0.00 41.24 2.85
1235 3031 1.132640 GCGTTCACATCTTCCGCAC 59.867 57.895 0.00 0.00 43.53 5.34
1239 3038 3.369756 TGTATTTCGCGTTCACATCTTCC 59.630 43.478 5.77 0.00 0.00 3.46
1277 3076 1.135460 GCAGCAGTTCTCCATTCTTGC 60.135 52.381 0.00 0.00 0.00 4.01
1292 3091 0.758734 ACGGCTATATGAAGGCAGCA 59.241 50.000 0.00 0.00 41.95 4.41
1294 3093 2.353803 GGGTACGGCTATATGAAGGCAG 60.354 54.545 0.56 0.00 41.95 4.85
1332 3132 4.952335 CAGCTTGTAATTCCCCTTGAGAAT 59.048 41.667 0.00 0.00 35.46 2.40
1397 3197 0.100682 GTCGTCTCTTAGATGCGCCA 59.899 55.000 4.18 0.00 31.39 5.69
1438 3238 1.149174 GGGCATGGATGACGGTGAT 59.851 57.895 0.00 0.00 36.40 3.06
1454 3266 2.623416 GGAGGAACACTTGTTTCTTGGG 59.377 50.000 4.36 0.00 43.59 4.12
1456 3268 4.399303 ACTTGGAGGAACACTTGTTTCTTG 59.601 41.667 4.36 0.00 43.59 3.02
1488 3300 2.362503 AGGTCACCGAGATGCCGA 60.363 61.111 0.00 0.00 0.00 5.54
1531 3343 0.794473 CCGCCGACTTGAAAGGTTAC 59.206 55.000 0.00 0.00 0.00 2.50
1555 3367 1.162698 CACCTGTGAGCAGACAATGG 58.837 55.000 0.00 0.00 45.28 3.16
1614 3428 0.405198 TCTCCTGCATGGCTCCAAAA 59.595 50.000 0.00 0.00 35.26 2.44
1615 3429 0.034767 CTCTCCTGCATGGCTCCAAA 60.035 55.000 0.00 0.00 35.26 3.28
1620 3434 0.252479 CAGAACTCTCCTGCATGGCT 59.748 55.000 0.00 0.00 35.26 4.75
1689 3503 5.470098 GTCGGTGTATATGAAATGGAGCAAT 59.530 40.000 0.00 0.00 0.00 3.56
1716 3530 3.077359 CACATCAAACTCAGGAGGAACC 58.923 50.000 0.83 0.00 39.35 3.62
1727 3541 2.165167 CAGCCATCACCACATCAAACT 58.835 47.619 0.00 0.00 0.00 2.66
1729 3543 1.548081 CCAGCCATCACCACATCAAA 58.452 50.000 0.00 0.00 0.00 2.69
1755 3569 4.056125 CTGTCAGCCGCCACGAGA 62.056 66.667 0.00 0.00 0.00 4.04
1789 3603 2.695147 TCTCCTCGCATATCAGCTTCAA 59.305 45.455 0.00 0.00 0.00 2.69
1880 3694 4.458708 GAAACAAGCATCTTTGAGACGAC 58.541 43.478 0.00 0.00 0.00 4.34
1893 3707 4.164843 AGTAAGGAACTGGAAACAAGCA 57.835 40.909 0.00 0.00 40.86 3.91
1902 3716 2.094130 GGACGGAGAAGTAAGGAACTGG 60.094 54.545 0.00 0.00 40.86 4.00
1912 3726 3.412386 CCTCAAAATTGGACGGAGAAGT 58.588 45.455 0.00 0.00 0.00 3.01
1929 3743 0.671472 CACTTGCTGTCATCGCCTCA 60.671 55.000 0.00 0.00 0.00 3.86
1940 3754 1.945394 GCTCATACCCATCACTTGCTG 59.055 52.381 0.00 0.00 0.00 4.41
1941 3755 1.561076 TGCTCATACCCATCACTTGCT 59.439 47.619 0.00 0.00 0.00 3.91
1944 3761 3.713248 TGAGATGCTCATACCCATCACTT 59.287 43.478 0.00 0.00 40.15 3.16
2010 3827 5.751243 CCGATTTAAATTCTGTCGGGATT 57.249 39.130 16.10 0.00 45.92 3.01
2017 3834 5.975693 TCCTTTGCCGATTTAAATTCTGT 57.024 34.783 1.43 0.00 0.00 3.41
2025 3842 8.946085 GTCATGATAATATCCTTTGCCGATTTA 58.054 33.333 0.00 0.00 0.00 1.40
2029 3846 5.863965 TGTCATGATAATATCCTTTGCCGA 58.136 37.500 0.00 0.00 0.00 5.54
2067 3884 4.203226 TGTTCAGACAATAGTGCCAAACA 58.797 39.130 0.00 0.00 31.49 2.83
2068 3885 4.829064 TGTTCAGACAATAGTGCCAAAC 57.171 40.909 0.00 0.00 31.49 2.93
2074 3891 7.538678 GGTAGCATTTTTGTTCAGACAATAGTG 59.461 37.037 0.00 0.00 44.71 2.74
2081 3898 5.438761 ACTGGTAGCATTTTTGTTCAGAC 57.561 39.130 0.00 0.00 0.00 3.51
2116 4009 9.244292 TCTACTCGCCTGAACATATATTTAGAT 57.756 33.333 0.00 0.00 0.00 1.98
2122 4015 7.468141 TCAATCTACTCGCCTGAACATATAT 57.532 36.000 0.00 0.00 0.00 0.86
2123 4016 6.894339 TCAATCTACTCGCCTGAACATATA 57.106 37.500 0.00 0.00 0.00 0.86
2135 4028 6.385843 AGCAGTAGCATAATCAATCTACTCG 58.614 40.000 0.00 0.00 45.49 4.18
2143 4036 4.112634 GTGACGAGCAGTAGCATAATCAA 58.887 43.478 0.00 0.00 45.49 2.57
2146 4039 3.099267 GGTGACGAGCAGTAGCATAAT 57.901 47.619 0.00 0.00 45.49 1.28
2201 4094 3.398954 TCAAAAAGACGCACACAACTC 57.601 42.857 0.00 0.00 0.00 3.01
2215 4108 5.105797 GCATCTGGTGGTGATGTATCAAAAA 60.106 40.000 0.00 0.00 42.21 1.94
2218 4111 3.200605 AGCATCTGGTGGTGATGTATCAA 59.799 43.478 0.00 0.00 42.21 2.57
2219 4112 2.773661 AGCATCTGGTGGTGATGTATCA 59.226 45.455 0.00 0.00 42.21 2.15
2220 4113 3.482156 AGCATCTGGTGGTGATGTATC 57.518 47.619 0.00 0.00 42.21 2.24
2224 4117 1.830279 ACAAGCATCTGGTGGTGATG 58.170 50.000 0.00 0.00 42.86 3.07
2230 4123 3.814842 TGAAGTAACACAAGCATCTGGTG 59.185 43.478 0.06 0.06 40.93 4.17
2232 4125 5.048504 ACAATGAAGTAACACAAGCATCTGG 60.049 40.000 0.00 0.00 0.00 3.86
2233 4126 5.854866 CACAATGAAGTAACACAAGCATCTG 59.145 40.000 0.00 0.00 0.00 2.90
2247 4140 8.407064 TGTTAATAAAACCGAACACAATGAAGT 58.593 29.630 0.00 0.00 0.00 3.01
2256 4149 7.280428 TGAGTTGAGTGTTAATAAAACCGAACA 59.720 33.333 7.42 0.00 0.00 3.18
2257 4150 7.632721 TGAGTTGAGTGTTAATAAAACCGAAC 58.367 34.615 0.00 0.00 0.00 3.95
2259 4152 7.572353 GCATGAGTTGAGTGTTAATAAAACCGA 60.572 37.037 0.00 0.00 0.00 4.69
2260 4153 6.523201 GCATGAGTTGAGTGTTAATAAAACCG 59.477 38.462 0.00 0.00 0.00 4.44
2262 4155 7.593825 AGGCATGAGTTGAGTGTTAATAAAAC 58.406 34.615 0.00 0.00 0.00 2.43
2264 4157 8.100791 AGTAGGCATGAGTTGAGTGTTAATAAA 58.899 33.333 0.00 0.00 0.00 1.40
2268 4161 5.483685 AGTAGGCATGAGTTGAGTGTTAA 57.516 39.130 0.00 0.00 0.00 2.01
2269 4162 5.483685 AAGTAGGCATGAGTTGAGTGTTA 57.516 39.130 0.00 0.00 0.00 2.41
2271 4164 4.319177 GAAAGTAGGCATGAGTTGAGTGT 58.681 43.478 0.00 0.00 0.00 3.55
2272 4165 3.369147 CGAAAGTAGGCATGAGTTGAGTG 59.631 47.826 0.00 0.00 0.00 3.51
2273 4166 3.589988 CGAAAGTAGGCATGAGTTGAGT 58.410 45.455 0.00 0.00 0.00 3.41
2274 4167 2.349886 GCGAAAGTAGGCATGAGTTGAG 59.650 50.000 0.00 0.00 0.00 3.02
2275 4168 2.289382 TGCGAAAGTAGGCATGAGTTGA 60.289 45.455 0.00 0.00 33.52 3.18
2276 4169 2.076100 TGCGAAAGTAGGCATGAGTTG 58.924 47.619 0.00 0.00 33.52 3.16
2277 4170 2.076863 GTGCGAAAGTAGGCATGAGTT 58.923 47.619 0.00 0.00 41.83 3.01
2316 4209 8.978874 AACTGAATTATACACAGCATCCATAA 57.021 30.769 0.00 0.00 35.38 1.90
2331 4224 7.938140 TGCCTTAGTGCTTAAACTGAATTAT 57.062 32.000 0.00 0.00 0.00 1.28
2359 4276 4.523943 TGCTTGAGGATTACATGCAGTTTT 59.476 37.500 0.00 0.00 41.20 2.43
2360 4277 4.081406 TGCTTGAGGATTACATGCAGTTT 58.919 39.130 0.00 0.00 41.20 2.66
2361 4278 3.689347 TGCTTGAGGATTACATGCAGTT 58.311 40.909 0.00 0.00 41.20 3.16
2362 4279 3.354948 TGCTTGAGGATTACATGCAGT 57.645 42.857 0.00 0.00 41.20 4.40
2363 4280 4.913335 AATGCTTGAGGATTACATGCAG 57.087 40.909 0.00 0.00 46.01 4.41
2364 4281 4.705991 TCAAATGCTTGAGGATTACATGCA 59.294 37.500 0.00 0.00 46.53 3.96
2365 4282 5.039333 GTCAAATGCTTGAGGATTACATGC 58.961 41.667 0.00 0.00 42.27 4.06
2368 4285 7.828717 TCAATAGTCAAATGCTTGAGGATTACA 59.171 33.333 0.00 0.00 42.27 2.41
2386 4346 4.222588 AGCTGGCAGAGGATATCAATAGTC 59.777 45.833 20.86 0.00 0.00 2.59
2388 4348 4.822685 AGCTGGCAGAGGATATCAATAG 57.177 45.455 20.86 0.00 0.00 1.73
2394 4354 6.498538 ACTATTAGTAGCTGGCAGAGGATAT 58.501 40.000 20.86 6.21 0.00 1.63
2404 4364 4.360563 CCGTCACAACTATTAGTAGCTGG 58.639 47.826 0.00 0.00 30.06 4.85
2405 4365 4.360563 CCCGTCACAACTATTAGTAGCTG 58.639 47.826 0.00 0.00 31.73 4.24
2411 4371 4.574828 CCAATTCCCCGTCACAACTATTAG 59.425 45.833 0.00 0.00 0.00 1.73
2414 4374 2.307686 ACCAATTCCCCGTCACAACTAT 59.692 45.455 0.00 0.00 0.00 2.12
2415 4375 1.700739 ACCAATTCCCCGTCACAACTA 59.299 47.619 0.00 0.00 0.00 2.24
2416 4376 0.476771 ACCAATTCCCCGTCACAACT 59.523 50.000 0.00 0.00 0.00 3.16
2417 4377 1.324383 AACCAATTCCCCGTCACAAC 58.676 50.000 0.00 0.00 0.00 3.32
2418 4378 2.953284 TAACCAATTCCCCGTCACAA 57.047 45.000 0.00 0.00 0.00 3.33
2419 4379 3.443145 AATAACCAATTCCCCGTCACA 57.557 42.857 0.00 0.00 0.00 3.58
2420 4380 4.014406 AGAAATAACCAATTCCCCGTCAC 58.986 43.478 0.00 0.00 0.00 3.67
2422 4382 4.097437 GGAAGAAATAACCAATTCCCCGTC 59.903 45.833 0.00 0.00 34.58 4.79
2423 4383 4.021229 GGAAGAAATAACCAATTCCCCGT 58.979 43.478 0.00 0.00 34.58 5.28
2424 4384 4.649088 GGAAGAAATAACCAATTCCCCG 57.351 45.455 0.00 0.00 34.58 5.73
2429 4390 5.654209 GCTCAGAGGGAAGAAATAACCAATT 59.346 40.000 0.00 0.00 0.00 2.32
2440 4401 1.065636 CAGCAATGCTCAGAGGGAAGA 60.066 52.381 4.03 0.00 36.40 2.87
2441 4402 1.380524 CAGCAATGCTCAGAGGGAAG 58.619 55.000 4.03 0.00 36.40 3.46
2452 4413 1.138247 GCAGCACTACCAGCAATGC 59.862 57.895 0.00 0.00 38.39 3.56
2455 4416 0.886043 CACAGCAGCACTACCAGCAA 60.886 55.000 0.00 0.00 0.00 3.91
2467 4428 1.538512 AGCATAACAAGTGCACAGCAG 59.461 47.619 21.04 7.93 44.87 4.24
2488 4449 3.019564 CTGAATCTGAACAACCCCCATC 58.980 50.000 0.00 0.00 0.00 3.51
2489 4450 2.379907 ACTGAATCTGAACAACCCCCAT 59.620 45.455 0.00 0.00 0.00 4.00
2514 4479 5.265350 TCCCCTTTAAAACCAAGTTTTCG 57.735 39.130 8.62 0.72 43.43 3.46
2542 4512 8.627487 TGTGCTTAACAGAAAACTACAAAATG 57.373 30.769 0.00 0.00 33.78 2.32
2545 4515 9.081997 CATTTGTGCTTAACAGAAAACTACAAA 57.918 29.630 0.00 0.00 43.91 2.83
2561 4531 5.835113 ACAGAACTACAACATTTGTGCTT 57.165 34.783 1.73 0.00 45.03 3.91
2569 4539 5.835113 AGCAAACAACAGAACTACAACAT 57.165 34.783 0.00 0.00 0.00 2.71
2571 4541 7.432543 GTTTAGCAAACAACAGAACTACAAC 57.567 36.000 6.82 0.00 41.04 3.32
2595 4565 4.529769 TCTCTTGGTATCCTCATGGCTATG 59.470 45.833 3.17 3.17 35.57 2.23
2597 4567 4.199002 TCTCTTGGTATCCTCATGGCTA 57.801 45.455 0.00 0.00 0.00 3.93
2600 4570 5.071519 ACTGATTCTCTTGGTATCCTCATGG 59.928 44.000 0.00 0.00 0.00 3.66
2601 4571 6.172136 ACTGATTCTCTTGGTATCCTCATG 57.828 41.667 0.00 0.00 0.00 3.07
2602 4572 6.385176 TCAACTGATTCTCTTGGTATCCTCAT 59.615 38.462 0.00 0.00 0.00 2.90
2603 4573 5.721480 TCAACTGATTCTCTTGGTATCCTCA 59.279 40.000 0.00 0.00 0.00 3.86
2606 4576 6.173339 TGTTCAACTGATTCTCTTGGTATCC 58.827 40.000 0.00 0.00 0.00 2.59
2608 4578 7.335422 GTCATGTTCAACTGATTCTCTTGGTAT 59.665 37.037 0.00 0.00 0.00 2.73
2613 4583 5.624159 TGGTCATGTTCAACTGATTCTCTT 58.376 37.500 0.00 0.00 0.00 2.85
2614 4584 5.233083 TGGTCATGTTCAACTGATTCTCT 57.767 39.130 0.00 0.00 0.00 3.10
2620 4590 4.886489 TGTCATTTGGTCATGTTCAACTGA 59.114 37.500 14.49 14.49 32.65 3.41
2622 4592 5.737063 GCTTGTCATTTGGTCATGTTCAACT 60.737 40.000 0.00 0.00 0.00 3.16
2625 4595 3.304592 CGCTTGTCATTTGGTCATGTTCA 60.305 43.478 0.00 0.00 0.00 3.18
2627 4597 2.607771 GCGCTTGTCATTTGGTCATGTT 60.608 45.455 0.00 0.00 0.00 2.71
2628 4598 1.068333 GCGCTTGTCATTTGGTCATGT 60.068 47.619 0.00 0.00 0.00 3.21
2661 4662 4.030452 GTGCAGCGGTGACAAGCC 62.030 66.667 20.69 0.00 0.00 4.35
2665 4666 1.029408 AAAACAGTGCAGCGGTGACA 61.029 50.000 20.69 13.08 0.00 3.58
2670 4671 0.385974 GCTACAAAACAGTGCAGCGG 60.386 55.000 0.00 0.00 28.57 5.52
2671 4672 3.077339 GCTACAAAACAGTGCAGCG 57.923 52.632 0.00 0.00 28.57 5.18
2677 4678 1.068127 AGTCGGTCGCTACAAAACAGT 59.932 47.619 0.00 0.00 0.00 3.55
2697 4698 4.457603 GGACACATGCAAACTACCATTGTA 59.542 41.667 0.00 0.00 0.00 2.41
2746 4750 2.048503 AAGAAACTCCGCGTCCCG 60.049 61.111 4.92 0.00 0.00 5.14
2747 4751 0.736672 GAGAAGAAACTCCGCGTCCC 60.737 60.000 4.92 0.00 0.00 4.46
2748 4752 0.244178 AGAGAAGAAACTCCGCGTCC 59.756 55.000 4.92 0.00 37.60 4.79
2749 4753 1.619983 GAGAGAAGAAACTCCGCGTC 58.380 55.000 4.92 0.00 37.60 5.19
2750 4754 0.109689 CGAGAGAAGAAACTCCGCGT 60.110 55.000 4.92 0.00 37.60 6.01
2751 4755 0.168348 TCGAGAGAAGAAACTCCGCG 59.832 55.000 0.00 0.00 37.60 6.46
2752 4756 1.902840 CTCGAGAGAAGAAACTCCGC 58.097 55.000 6.58 0.00 41.32 5.54
2753 4757 1.200252 TGCTCGAGAGAAGAAACTCCG 59.800 52.381 18.75 0.00 41.32 4.63
2754 4758 2.029828 TGTGCTCGAGAGAAGAAACTCC 60.030 50.000 18.75 0.00 41.32 3.85
2755 4759 3.057876 TCTGTGCTCGAGAGAAGAAACTC 60.058 47.826 18.75 0.00 41.32 3.01
2756 4760 2.887783 TCTGTGCTCGAGAGAAGAAACT 59.112 45.455 18.75 0.00 41.32 2.66
2757 4761 3.290308 TCTGTGCTCGAGAGAAGAAAC 57.710 47.619 18.75 2.61 41.32 2.78
2758 4762 3.842820 CATCTGTGCTCGAGAGAAGAAA 58.157 45.455 18.75 0.00 41.32 2.52
2759 4763 3.500558 CATCTGTGCTCGAGAGAAGAA 57.499 47.619 18.75 0.00 41.32 2.52
2772 4776 3.243670 ACAGGATATCACGAGCATCTGTG 60.244 47.826 4.83 0.00 39.68 3.66
2773 4777 2.961741 ACAGGATATCACGAGCATCTGT 59.038 45.455 4.83 3.35 0.00 3.41
2774 4778 3.005155 TCACAGGATATCACGAGCATCTG 59.995 47.826 4.83 2.73 0.00 2.90
2775 4779 3.225940 TCACAGGATATCACGAGCATCT 58.774 45.455 4.83 0.00 0.00 2.90
2776 4780 3.005261 ACTCACAGGATATCACGAGCATC 59.995 47.826 4.83 0.00 0.00 3.91
2777 4781 2.961741 ACTCACAGGATATCACGAGCAT 59.038 45.455 4.83 0.00 0.00 3.79
2778 4782 2.379005 ACTCACAGGATATCACGAGCA 58.621 47.619 4.83 0.00 0.00 4.26
2779 4783 4.036971 ACTTACTCACAGGATATCACGAGC 59.963 45.833 4.83 0.00 0.00 5.03
2780 4784 5.759506 ACTTACTCACAGGATATCACGAG 57.240 43.478 4.83 6.70 0.00 4.18
2781 4785 6.827251 ACTAACTTACTCACAGGATATCACGA 59.173 38.462 4.83 0.00 0.00 4.35
2782 4786 6.913132 CACTAACTTACTCACAGGATATCACG 59.087 42.308 4.83 0.00 0.00 4.35
2796 4800 2.226962 TCCTCCCGCACTAACTTACT 57.773 50.000 0.00 0.00 0.00 2.24
2810 4814 3.004752 AGTAATTGGCACACATCCTCC 57.995 47.619 0.00 0.00 39.29 4.30
2869 4873 1.828660 CCGACGGAGGCTAGATGGT 60.829 63.158 8.64 0.00 0.00 3.55
2885 6559 2.507992 CTTCCGCTCTCACTGCCG 60.508 66.667 0.00 0.00 0.00 5.69
2886 6560 2.817396 GCTTCCGCTCTCACTGCC 60.817 66.667 0.00 0.00 0.00 4.85
2905 6760 1.597302 CATCTGCCTCCAGGATGCG 60.597 63.158 11.73 7.12 39.61 4.73
2924 6779 4.320456 ACCTCACAGCCACTGCCG 62.320 66.667 0.00 0.00 38.69 5.69
2941 6796 0.034896 GTTTGAGGCGAACTCTCCCA 59.965 55.000 8.68 0.00 46.72 4.37
2942 6797 0.673956 GGTTTGAGGCGAACTCTCCC 60.674 60.000 8.68 3.20 46.72 4.30
2959 6814 0.610687 CCTCTTGAAAGCTCGGAGGT 59.389 55.000 3.41 3.41 38.42 3.85
2963 6818 1.276421 TCTTCCCTCTTGAAAGCTCGG 59.724 52.381 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.