Multiple sequence alignment - TraesCS6A01G228600

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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 TraesCS6A01G228600 chr6A 100.000 6278 0 0 1 6278 431048635 431054912 0.000000e+00 11594
1 TraesCS6A01G228600 chr6D 94.180 5395 229 44 824 6179 292035411 292030063 0.000000e+00 8144
2 TraesCS6A01G228600 chr6B 94.238 3280 148 18 3030 6274 454076962 454073689 0.000000e+00 4972
3 TraesCS6A01G228600 chr6B 92.962 2046 113 14 946 2974 454078988 454076957 0.000000e+00 2952
4 TraesCS6A01G228600 chr6B 92.829 767 31 10 1 767 675205642 675206384 0.000000e+00 1090
5 TraesCS6A01G228600 chr2A 95.306 767 36 0 1 767 122054278 122053512 0.000000e+00 1218
6 TraesCS6A01G228600 chr2A 95.046 767 38 0 1 767 4701325 4700559 0.000000e+00 1206
7 TraesCS6A01G228600 chr4A 94.915 767 37 1 1 767 674441636 674442400 0.000000e+00 1199
8 TraesCS6A01G228600 chr4A 96.552 203 7 0 1 203 719937694 719937492 2.800000e-88 337
9 TraesCS6A01G228600 chr3B 94.654 767 35 3 1 767 546910617 546911377 0.000000e+00 1184
10 TraesCS6A01G228600 chr7B 94.489 744 40 1 24 767 526390396 526389654 0.000000e+00 1146
11 TraesCS6A01G228600 chr2D 89.831 767 75 3 2 767 585467188 585467952 0.000000e+00 981
12 TraesCS6A01G228600 chr5A 89.700 767 79 0 1 767 24361388 24362154 0.000000e+00 979
13 TraesCS6A01G228600 chr5D 87.135 754 95 2 15 767 133317447 133316695 0.000000e+00 854


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 TraesCS6A01G228600 chr6A 431048635 431054912 6277 False 11594 11594 100.000 1 6278 1 chr6A.!!$F1 6277
1 TraesCS6A01G228600 chr6D 292030063 292035411 5348 True 8144 8144 94.180 824 6179 1 chr6D.!!$R1 5355
2 TraesCS6A01G228600 chr6B 454073689 454078988 5299 True 3962 4972 93.600 946 6274 2 chr6B.!!$R1 5328
3 TraesCS6A01G228600 chr6B 675205642 675206384 742 False 1090 1090 92.829 1 767 1 chr6B.!!$F1 766
4 TraesCS6A01G228600 chr2A 122053512 122054278 766 True 1218 1218 95.306 1 767 1 chr2A.!!$R2 766
5 TraesCS6A01G228600 chr2A 4700559 4701325 766 True 1206 1206 95.046 1 767 1 chr2A.!!$R1 766
6 TraesCS6A01G228600 chr4A 674441636 674442400 764 False 1199 1199 94.915 1 767 1 chr4A.!!$F1 766
7 TraesCS6A01G228600 chr3B 546910617 546911377 760 False 1184 1184 94.654 1 767 1 chr3B.!!$F1 766
8 TraesCS6A01G228600 chr7B 526389654 526390396 742 True 1146 1146 94.489 24 767 1 chr7B.!!$R1 743
9 TraesCS6A01G228600 chr2D 585467188 585467952 764 False 981 981 89.831 2 767 1 chr2D.!!$F1 765
10 TraesCS6A01G228600 chr5A 24361388 24362154 766 False 979 979 89.700 1 767 1 chr5A.!!$F1 766
11 TraesCS6A01G228600 chr5D 133316695 133317447 752 True 854 854 87.135 15 767 1 chr5D.!!$R1 752

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
821 822 0.038618 TGGATCACACGGTTCAGACG 60.039 55.000 0.00 0.0 37.36 4.18 F
926 928 0.304705 CTTGTCAGTTGACCACACGC 59.695 55.000 9.60 0.0 44.15 5.34 F
1455 1457 0.958091 TTTCCATGCGTTCCTTGTGG 59.042 50.000 0.00 0.0 0.00 4.17 F
1803 1816 1.076350 AGGTGCCTCTAGTCTCACTGT 59.924 52.381 9.54 0.0 0.00 3.55 F
2568 2588 1.576421 GCACAAGAAGTTCCCTGCG 59.424 57.895 0.00 0.0 0.00 5.18 F
3911 3942 0.392706 ATGGTTCACAGACGTGCTCA 59.607 50.000 0.00 0.0 43.28 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2787 2807 2.957402 TGACCCATTGGCAGGATATC 57.043 50.000 0.00 0.00 33.59 1.63 R
2843 2863 3.242739 CGGTATTTCTTGAAATCCCTGCG 60.243 47.826 11.31 0.00 0.00 5.18 R
3069 3096 1.203038 TCACTCCCATTGCAACCATGT 60.203 47.619 0.00 0.00 0.00 3.21 R
3479 3509 1.063912 TGCGTCTATTACCGGTACACG 59.936 52.381 15.53 19.59 43.80 4.49 R
4103 4134 1.629861 TCTCATGTGCTCCATTGTCCA 59.370 47.619 0.00 0.00 0.00 4.02 R
5616 5654 0.179045 AATGTATCTGGTCCAGCGGC 60.179 55.000 14.64 6.72 0.00 6.53 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
35 36 2.542907 CCGATGAATTTCCCGCGGG 61.543 63.158 39.13 39.13 35.42 6.13
81 82 4.503123 CCCGCCTGTATGATCTTCAACATA 60.503 45.833 0.00 0.00 0.00 2.29
171 172 2.348998 CTTCGGCTTCCCTGCTGT 59.651 61.111 0.00 0.00 40.06 4.40
258 259 3.006430 TCTCCGTGCACAAATTGTCTCTA 59.994 43.478 18.64 0.00 0.00 2.43
261 262 4.021807 TCCGTGCACAAATTGTCTCTACTA 60.022 41.667 18.64 0.00 0.00 1.82
265 266 5.643777 GTGCACAAATTGTCTCTACTACCAT 59.356 40.000 13.17 0.00 0.00 3.55
333 334 3.068307 GGGTCTGAGTACATACGCTGATT 59.932 47.826 0.00 0.00 36.66 2.57
351 352 7.488187 GCTGATTAGCTTCATCACATAAGAA 57.512 36.000 1.49 0.00 46.57 2.52
468 469 2.358957 GCATGAGAACAGTACATGGCA 58.641 47.619 0.00 0.00 40.83 4.92
523 524 5.643777 GCATTGAGAGTTAGTACCAACATGT 59.356 40.000 6.94 0.00 0.00 3.21
539 540 5.575606 CCAACATGTCGATTAGTTAGAACGT 59.424 40.000 0.00 0.00 0.00 3.99
615 616 2.318908 TGGCAGTTTGAGCTTCCAAAT 58.681 42.857 4.11 0.00 38.18 2.32
767 768 8.744652 AGTGACATGCTATATAATCCTCTGTAC 58.255 37.037 0.00 0.00 0.00 2.90
768 769 8.523658 GTGACATGCTATATAATCCTCTGTACA 58.476 37.037 0.00 0.00 0.00 2.90
769 770 9.259832 TGACATGCTATATAATCCTCTGTACAT 57.740 33.333 0.00 0.00 0.00 2.29
771 772 9.881649 ACATGCTATATAATCCTCTGTACATTG 57.118 33.333 0.00 0.00 0.00 2.82
772 773 9.322773 CATGCTATATAATCCTCTGTACATTGG 57.677 37.037 0.00 1.71 0.00 3.16
773 774 8.664669 TGCTATATAATCCTCTGTACATTGGA 57.335 34.615 16.20 16.20 0.00 3.53
774 775 9.271921 TGCTATATAATCCTCTGTACATTGGAT 57.728 33.333 18.55 18.55 40.65 3.41
775 776 9.539825 GCTATATAATCCTCTGTACATTGGATG 57.460 37.037 22.55 13.85 39.06 3.51
776 777 9.539825 CTATATAATCCTCTGTACATTGGATGC 57.460 37.037 22.55 0.00 39.06 3.91
777 778 4.508551 AATCCTCTGTACATTGGATGCA 57.491 40.909 22.55 0.00 39.06 3.96
778 779 3.266510 TCCTCTGTACATTGGATGCAC 57.733 47.619 11.53 0.00 0.00 4.57
779 780 2.840038 TCCTCTGTACATTGGATGCACT 59.160 45.455 11.53 0.00 0.00 4.40
780 781 4.030216 TCCTCTGTACATTGGATGCACTA 58.970 43.478 11.53 0.00 0.00 2.74
781 782 4.655649 TCCTCTGTACATTGGATGCACTAT 59.344 41.667 11.53 0.00 0.00 2.12
782 783 4.753610 CCTCTGTACATTGGATGCACTATG 59.246 45.833 8.17 0.00 0.00 2.23
783 784 5.357742 TCTGTACATTGGATGCACTATGT 57.642 39.130 9.19 9.19 0.00 2.29
784 785 5.744171 TCTGTACATTGGATGCACTATGTT 58.256 37.500 9.46 0.00 0.00 2.71
785 786 5.585844 TCTGTACATTGGATGCACTATGTTG 59.414 40.000 9.46 2.75 0.00 3.33
786 787 5.495640 TGTACATTGGATGCACTATGTTGA 58.504 37.500 9.46 0.00 0.00 3.18
787 788 5.942826 TGTACATTGGATGCACTATGTTGAA 59.057 36.000 9.46 0.00 0.00 2.69
788 789 5.571784 ACATTGGATGCACTATGTTGAAG 57.428 39.130 0.00 0.00 0.00 3.02
789 790 4.400251 ACATTGGATGCACTATGTTGAAGG 59.600 41.667 0.00 0.00 0.00 3.46
790 791 3.003394 TGGATGCACTATGTTGAAGGG 57.997 47.619 0.00 0.00 0.00 3.95
791 792 2.308570 TGGATGCACTATGTTGAAGGGT 59.691 45.455 0.00 0.00 0.00 4.34
792 793 3.521531 TGGATGCACTATGTTGAAGGGTA 59.478 43.478 0.00 0.00 0.00 3.69
793 794 4.018870 TGGATGCACTATGTTGAAGGGTAA 60.019 41.667 0.00 0.00 0.00 2.85
794 795 4.947388 GGATGCACTATGTTGAAGGGTAAA 59.053 41.667 0.00 0.00 0.00 2.01
795 796 5.417580 GGATGCACTATGTTGAAGGGTAAAA 59.582 40.000 0.00 0.00 0.00 1.52
796 797 6.071616 GGATGCACTATGTTGAAGGGTAAAAA 60.072 38.462 0.00 0.00 0.00 1.94
797 798 6.325919 TGCACTATGTTGAAGGGTAAAAAG 57.674 37.500 0.00 0.00 0.00 2.27
798 799 5.830991 TGCACTATGTTGAAGGGTAAAAAGT 59.169 36.000 0.00 0.00 0.00 2.66
799 800 6.149633 GCACTATGTTGAAGGGTAAAAAGTG 58.850 40.000 0.00 0.00 35.02 3.16
800 801 6.238925 GCACTATGTTGAAGGGTAAAAAGTGT 60.239 38.462 0.00 0.00 34.54 3.55
801 802 7.683463 GCACTATGTTGAAGGGTAAAAAGTGTT 60.683 37.037 0.00 0.00 34.54 3.32
802 803 8.194769 CACTATGTTGAAGGGTAAAAAGTGTTT 58.805 33.333 0.00 0.00 0.00 2.83
803 804 8.194769 ACTATGTTGAAGGGTAAAAAGTGTTTG 58.805 33.333 0.00 0.00 0.00 2.93
804 805 5.725362 TGTTGAAGGGTAAAAAGTGTTTGG 58.275 37.500 0.00 0.00 0.00 3.28
805 806 5.480772 TGTTGAAGGGTAAAAAGTGTTTGGA 59.519 36.000 0.00 0.00 0.00 3.53
806 807 6.155393 TGTTGAAGGGTAAAAAGTGTTTGGAT 59.845 34.615 0.00 0.00 0.00 3.41
807 808 6.399639 TGAAGGGTAAAAAGTGTTTGGATC 57.600 37.500 0.00 0.00 0.00 3.36
808 809 5.894393 TGAAGGGTAAAAAGTGTTTGGATCA 59.106 36.000 0.00 0.00 0.00 2.92
809 810 5.784578 AGGGTAAAAAGTGTTTGGATCAC 57.215 39.130 0.00 0.00 36.22 3.06
810 811 5.205056 AGGGTAAAAAGTGTTTGGATCACA 58.795 37.500 0.00 0.00 38.16 3.58
811 812 5.068591 AGGGTAAAAAGTGTTTGGATCACAC 59.931 40.000 6.68 6.68 44.25 3.82
816 817 2.681152 GTGTTTGGATCACACGGTTC 57.319 50.000 0.00 0.00 35.50 3.62
817 818 1.944024 GTGTTTGGATCACACGGTTCA 59.056 47.619 0.00 0.00 35.50 3.18
818 819 2.032030 GTGTTTGGATCACACGGTTCAG 60.032 50.000 0.00 0.00 35.50 3.02
819 820 2.158885 TGTTTGGATCACACGGTTCAGA 60.159 45.455 0.00 0.00 0.00 3.27
820 821 2.163818 TTGGATCACACGGTTCAGAC 57.836 50.000 0.00 0.00 0.00 3.51
821 822 0.038618 TGGATCACACGGTTCAGACG 60.039 55.000 0.00 0.00 37.36 4.18
822 823 1.352156 GGATCACACGGTTCAGACGC 61.352 60.000 0.00 0.00 34.00 5.19
885 886 3.304592 GGGCATTCGCAAAAAGCAAAAAT 60.305 39.130 0.00 0.00 46.13 1.82
889 890 6.129483 GGCATTCGCAAAAAGCAAAAATAAAC 60.129 34.615 0.00 0.00 46.13 2.01
890 891 6.632434 GCATTCGCAAAAAGCAAAAATAAACT 59.368 30.769 0.00 0.00 46.13 2.66
926 928 0.304705 CTTGTCAGTTGACCACACGC 59.695 55.000 9.60 0.00 44.15 5.34
1049 1051 4.162690 CCGCCCTCTTAAGCCGCT 62.163 66.667 0.00 0.00 0.00 5.52
1167 1169 6.047231 GCTGTTACGATTCTTGTATTACCCT 58.953 40.000 0.00 0.00 0.00 4.34
1179 1181 5.988310 TGTATTACCCTTCGAGTTCTTGA 57.012 39.130 0.00 0.00 0.00 3.02
1203 1205 4.401022 ACCAAGATTGATGCAGAAGTTCA 58.599 39.130 5.50 0.00 0.00 3.18
1204 1206 4.828939 ACCAAGATTGATGCAGAAGTTCAA 59.171 37.500 5.50 2.36 34.18 2.69
1221 1223 3.644966 TCAAGTCTTGTGGGTTGAGTT 57.355 42.857 12.30 0.00 0.00 3.01
1229 1231 3.039252 TGTGGGTTGAGTTGGGATTTT 57.961 42.857 0.00 0.00 0.00 1.82
1230 1232 3.379452 TGTGGGTTGAGTTGGGATTTTT 58.621 40.909 0.00 0.00 0.00 1.94
1231 1233 3.133721 TGTGGGTTGAGTTGGGATTTTTG 59.866 43.478 0.00 0.00 0.00 2.44
1250 1252 2.593956 GGGGTTCAGGAAGACGCCT 61.594 63.158 2.74 0.00 39.37 5.52
1251 1253 1.079057 GGGTTCAGGAAGACGCCTC 60.079 63.158 0.00 0.00 35.66 4.70
1266 1268 1.300481 GCCTCGGAGTTAAATCTGCC 58.700 55.000 6.87 0.00 0.00 4.85
1282 1284 4.118093 TCTGCCGTTCGATTCTAATTGA 57.882 40.909 0.00 0.00 0.00 2.57
1294 1296 6.547141 TCGATTCTAATTGAATTGGAATGCCT 59.453 34.615 26.99 10.07 46.26 4.75
1311 1313 1.227556 CTATCCTGCGTTTCCCCCG 60.228 63.158 0.00 0.00 0.00 5.73
1333 1335 4.434588 CGCAAAGAAAAACAGAAGAGTTCG 59.565 41.667 0.00 0.00 34.02 3.95
1388 1390 6.711194 CACTCTCGATTTAGTAGGATCTGGTA 59.289 42.308 0.00 0.00 0.00 3.25
1391 1393 7.691213 TCTCGATTTAGTAGGATCTGGTATCT 58.309 38.462 0.00 0.00 0.00 1.98
1421 1423 4.697756 TGCGCTTCCGTTCCCCAG 62.698 66.667 9.73 0.00 36.67 4.45
1429 1431 1.819632 CCGTTCCCCAGCTACATGC 60.820 63.158 0.00 0.00 43.29 4.06
1443 1445 2.995466 ACATGCTGACGTTTTCCATG 57.005 45.000 14.01 14.01 39.23 3.66
1444 1446 1.068333 ACATGCTGACGTTTTCCATGC 60.068 47.619 14.96 5.07 37.41 4.06
1455 1457 0.958091 TTTCCATGCGTTCCTTGTGG 59.042 50.000 0.00 0.00 0.00 4.17
1544 1547 3.838244 TTTTGTCTGTACAGCTCTGGT 57.162 42.857 18.45 0.00 36.83 4.00
1545 1548 4.948341 TTTTGTCTGTACAGCTCTGGTA 57.052 40.909 18.45 0.00 36.83 3.25
1546 1549 5.483685 TTTTGTCTGTACAGCTCTGGTAT 57.516 39.130 18.45 0.00 36.83 2.73
1548 1551 4.456280 TGTCTGTACAGCTCTGGTATTG 57.544 45.455 18.45 0.00 34.19 1.90
1549 1552 3.190874 GTCTGTACAGCTCTGGTATTGC 58.809 50.000 18.45 0.00 34.19 3.56
1550 1553 2.159240 TCTGTACAGCTCTGGTATTGCG 60.159 50.000 18.45 0.00 34.19 4.85
1551 1554 1.822371 TGTACAGCTCTGGTATTGCGA 59.178 47.619 0.00 0.00 34.19 5.10
1563 1568 5.294306 TCTGGTATTGCGAAATCTTGCTAAG 59.706 40.000 0.00 0.00 0.00 2.18
1653 1658 4.970662 TTCTGTATTTCTGGCTTCATGC 57.029 40.909 0.00 0.00 41.94 4.06
1803 1816 1.076350 AGGTGCCTCTAGTCTCACTGT 59.924 52.381 9.54 0.00 0.00 3.55
1933 1949 7.960319 TTGTGCCACAACTATAATCTGGTAACA 60.960 37.037 6.08 0.00 37.45 2.41
2021 2039 5.290400 GCTCTAAATTCAAAAGGATGCTTGC 59.710 40.000 0.00 0.00 0.00 4.01
2051 2069 2.677836 TGTTAGATTGTTCGAGCCATGC 59.322 45.455 0.00 0.00 0.00 4.06
2083 2101 6.923199 ATTTTCTGTTGGAAGGATCAATGT 57.077 33.333 0.00 0.00 35.16 2.71
2085 2103 6.729690 TTTCTGTTGGAAGGATCAATGTTT 57.270 33.333 0.00 0.00 35.16 2.83
2158 2176 7.175467 TGCAAAATACACAGAATCAGACAATCT 59.825 33.333 0.00 0.00 0.00 2.40
2173 2191 6.463995 AGACAATCTAGTCTGCCTAAGAAG 57.536 41.667 0.00 0.00 46.58 2.85
2174 2192 6.191315 AGACAATCTAGTCTGCCTAAGAAGA 58.809 40.000 0.00 0.00 46.58 2.87
2415 2433 7.763985 GGGTGATAGAATGGGTTTGTAATTTTG 59.236 37.037 0.00 0.00 0.00 2.44
2488 2506 7.408756 TTCATACATTAAAAGGAGCTGCAAT 57.591 32.000 8.35 0.00 0.00 3.56
2490 2508 3.853475 ACATTAAAAGGAGCTGCAATGC 58.147 40.909 8.35 0.00 0.00 3.56
2504 2522 3.881089 CTGCAATGCATCAGTCCTATGAA 59.119 43.478 8.91 0.00 38.13 2.57
2568 2588 1.576421 GCACAAGAAGTTCCCTGCG 59.424 57.895 0.00 0.00 0.00 5.18
2612 2632 4.035102 GACCCCAGCCACACCCTC 62.035 72.222 0.00 0.00 0.00 4.30
2682 2702 2.436542 TGGTCCGGTTTTCTTTCTCTGA 59.563 45.455 0.00 0.00 0.00 3.27
2787 2807 6.429692 TGATACACCTCAGTTAAAACCATGTG 59.570 38.462 0.00 0.00 0.00 3.21
2843 2863 5.796935 CACGATTCAGACACCATTTGAAATC 59.203 40.000 0.00 0.00 34.80 2.17
3025 3052 9.177304 GTTATACTAAAGGCTTTGTTGTTGTTC 57.823 33.333 22.32 2.42 0.00 3.18
3052 3079 8.776376 TGTACAGTTATATGACATATGGCATG 57.224 34.615 30.66 18.35 44.95 4.06
3205 3234 4.256920 TGCTCTTTTTCCTTGCTAGCTAG 58.743 43.478 16.84 16.84 0.00 3.42
3245 3274 9.770097 TTGAAATGTACATAATTTTTCCTTGCA 57.230 25.926 9.21 0.00 0.00 4.08
3388 3418 3.019799 TCTTTTGTAAGGTTGTGCCCA 57.980 42.857 0.00 0.00 38.26 5.36
3479 3509 7.255277 GCTAATCCCATTATGTTTCCACTTCTC 60.255 40.741 0.00 0.00 0.00 2.87
3517 3547 2.047179 GAACCTGGGAGTGGACGC 60.047 66.667 0.00 0.00 0.00 5.19
3582 3612 6.455513 GCAAAAACTGTGTCAATGGAAAGTTC 60.456 38.462 0.00 0.00 0.00 3.01
3693 3724 6.093219 CGGTGATTGAACTTTTCAGATCAGAT 59.907 38.462 0.00 0.00 41.38 2.90
3742 3773 3.505449 GCGCCAACGACATAATAAGAG 57.495 47.619 0.00 0.00 43.93 2.85
3911 3942 0.392706 ATGGTTCACAGACGTGCTCA 59.607 50.000 0.00 0.00 43.28 4.26
3923 3954 1.278985 ACGTGCTCATTCTGATCCCAA 59.721 47.619 0.00 0.00 0.00 4.12
3951 3982 8.938906 GGTCATTTTGAAAACATGCTTGATTAT 58.061 29.630 6.60 0.00 0.00 1.28
3960 3991 3.117016 ACATGCTTGATTATGGGGGTGAT 60.117 43.478 6.60 0.00 0.00 3.06
4103 4134 7.390440 TGATTGGAAAGACGATTTATCTTGTGT 59.610 33.333 0.00 0.00 36.52 3.72
4123 4154 1.629861 TGGACAATGGAGCACATGAGA 59.370 47.619 0.00 0.00 40.44 3.27
4147 4178 6.008331 AGCATGTCATTACCATCAGCATATT 58.992 36.000 0.00 0.00 0.00 1.28
4234 4265 3.055819 GCTAGAGGATGTTCAACACCTCA 60.056 47.826 27.28 17.82 43.03 3.86
4342 4373 1.625315 TGCTAGCAGTCACTGAACCAT 59.375 47.619 14.93 0.00 32.44 3.55
4353 4384 4.215399 GTCACTGAACCATTTCCAAATCGA 59.785 41.667 0.00 0.00 0.00 3.59
4460 4491 7.014711 CAGATCCCTAGAGCATTGTACTTCTAA 59.985 40.741 0.00 0.00 0.00 2.10
4566 4597 4.214758 CAGTCACATGAGAAATGCACTTCA 59.785 41.667 10.94 2.34 0.00 3.02
4567 4598 4.454847 AGTCACATGAGAAATGCACTTCAG 59.545 41.667 10.94 0.00 0.00 3.02
4568 4599 3.754850 TCACATGAGAAATGCACTTCAGG 59.245 43.478 10.94 6.23 0.00 3.86
4639 4673 6.758886 CAGTATCTCCAACTTCCATGTTAGTC 59.241 42.308 0.00 0.00 0.00 2.59
4657 4691 2.149578 GTCAGAGCAAGAGCATTGTGT 58.850 47.619 3.93 0.00 45.49 3.72
4658 4692 2.551459 GTCAGAGCAAGAGCATTGTGTT 59.449 45.455 3.93 0.00 45.49 3.32
4669 4703 2.821969 AGCATTGTGTTGAATCCAGACC 59.178 45.455 0.00 0.00 0.00 3.85
4751 4785 1.876156 CTTTTGTGACTCTGCTGTCCC 59.124 52.381 0.00 0.00 36.21 4.46
4753 4787 0.394192 TTGTGACTCTGCTGTCCCTG 59.606 55.000 0.00 0.00 36.21 4.45
4758 4792 1.410882 GACTCTGCTGTCCCTGTATCC 59.589 57.143 0.00 0.00 0.00 2.59
4779 4813 3.497405 CCTGTATGGATGGAATGGTGGAG 60.497 52.174 0.00 0.00 38.35 3.86
4781 4815 3.392285 TGTATGGATGGAATGGTGGAGAG 59.608 47.826 0.00 0.00 0.00 3.20
4876 4910 7.524294 TTGAAATTCACTGCTTCAAGTTTTC 57.476 32.000 0.00 0.00 34.88 2.29
4924 4958 3.524789 TCATCATCATGACCCAAAGGACT 59.475 43.478 0.00 0.00 33.80 3.85
5062 5096 3.460103 CGGTCATCATCACATCATGTCA 58.540 45.455 0.00 0.00 0.00 3.58
5078 5112 3.755112 TGTCAAATCTCGTGGTGGTAA 57.245 42.857 0.00 0.00 0.00 2.85
5087 5121 2.747446 CTCGTGGTGGTAATTTGGAAGG 59.253 50.000 0.00 0.00 0.00 3.46
5143 5177 6.514063 TGCAATGATTTTGAAGATGACAACA 58.486 32.000 0.00 0.00 0.00 3.33
5148 5182 9.850628 AATGATTTTGAAGATGACAACAGTATG 57.149 29.630 0.00 0.00 46.00 2.39
5176 5210 0.886490 CGAAGGCAACACCAAGAGCT 60.886 55.000 0.00 0.00 43.14 4.09
5253 5287 1.847328 TCAGCGAGACTCCCATGTTA 58.153 50.000 0.00 0.00 0.00 2.41
5309 5343 4.943705 TCCATTGTTCCTTGAAGTGCTATC 59.056 41.667 0.00 0.00 0.00 2.08
5358 5395 3.869065 TGGACGATAAATTCCACTGGAC 58.131 45.455 0.00 0.00 36.96 4.02
5373 5410 1.286880 GGACGCAACTGCATGCTTT 59.713 52.632 20.33 9.28 44.21 3.51
5374 5411 0.521291 GGACGCAACTGCATGCTTTA 59.479 50.000 20.33 0.00 44.21 1.85
5387 5424 1.076777 GCTTTATGGCCCTGGCTGA 60.077 57.895 8.29 0.00 41.60 4.26
5389 5426 0.257039 CTTTATGGCCCTGGCTGAGT 59.743 55.000 8.29 0.00 41.60 3.41
5447 5484 4.766891 CCAATCAAGGTGAATAAGTGTGGT 59.233 41.667 0.00 0.00 0.00 4.16
5454 5491 1.073763 TGAATAAGTGTGGTGCTGGCT 59.926 47.619 0.00 0.00 0.00 4.75
5498 5536 3.499737 GGTGATGGAACGCCTGCG 61.500 66.667 10.40 10.40 46.03 5.18
5558 5596 1.421646 AGCTGGCACCTACAGTTCTTT 59.578 47.619 0.00 0.00 38.22 2.52
5616 5654 2.704464 TCTGATGCCATCCTCAACAG 57.296 50.000 1.49 0.00 36.19 3.16
5630 5668 2.596851 AACAGCCGCTGGACCAGAT 61.597 57.895 26.25 4.42 35.51 2.90
5699 5737 0.396435 TGTGGAAATCAGCGACACCT 59.604 50.000 0.00 0.00 0.00 4.00
5772 5810 7.987458 TGACTAAGGTTCCTATTCAGCTAAATG 59.013 37.037 0.00 0.00 0.00 2.32
5839 5878 2.482326 GGATGGGCTCCGTTGAAAG 58.518 57.895 0.00 0.00 33.29 2.62
5841 5880 0.322546 GATGGGCTCCGTTGAAAGGT 60.323 55.000 0.00 0.00 0.00 3.50
5842 5881 0.322546 ATGGGCTCCGTTGAAAGGTC 60.323 55.000 0.00 0.00 0.00 3.85
5843 5882 1.375326 GGGCTCCGTTGAAAGGTCT 59.625 57.895 0.00 0.00 0.00 3.85
5844 5883 0.250770 GGGCTCCGTTGAAAGGTCTT 60.251 55.000 0.00 0.00 0.00 3.01
5845 5884 1.002773 GGGCTCCGTTGAAAGGTCTTA 59.997 52.381 0.00 0.00 0.00 2.10
5898 5945 0.302890 GCAGATCATCTCAAACGCCG 59.697 55.000 0.00 0.00 0.00 6.46
5932 5979 1.218047 CCCCTTCGCGATCAGACAA 59.782 57.895 10.88 0.00 0.00 3.18
5995 6046 0.546267 ACAGGTCTGGCATGAGGTCT 60.546 55.000 0.00 0.00 32.48 3.85
6086 6137 2.361610 AACATGCGCAGGGGAAGG 60.362 61.111 27.21 6.79 0.00 3.46
6087 6138 2.905996 AACATGCGCAGGGGAAGGA 61.906 57.895 27.21 0.00 0.00 3.36
6089 6140 1.678635 CATGCGCAGGGGAAGGAAA 60.679 57.895 18.32 0.00 0.00 3.13
6090 6141 1.076549 ATGCGCAGGGGAAGGAAAA 59.923 52.632 18.32 0.00 0.00 2.29
6118 6169 1.394917 GTGCACGATCACTCAACATCC 59.605 52.381 0.00 0.00 34.29 3.51
6119 6170 1.276138 TGCACGATCACTCAACATCCT 59.724 47.619 0.00 0.00 0.00 3.24
6120 6171 1.929836 GCACGATCACTCAACATCCTC 59.070 52.381 0.00 0.00 0.00 3.71
6162 6214 2.684001 AACGACTGTGGTCTTGAACA 57.316 45.000 0.00 0.00 40.10 3.18
6165 6217 2.276201 CGACTGTGGTCTTGAACAACA 58.724 47.619 0.00 0.00 39.61 3.33
6166 6218 2.872245 CGACTGTGGTCTTGAACAACAT 59.128 45.455 0.00 0.00 41.09 2.71
6172 6224 3.066621 GTGGTCTTGAACAACATCTTGCA 59.933 43.478 0.00 0.00 31.45 4.08
6262 6332 8.341892 AGTTCTTTTCTCTTCTTTGTTTGTCT 57.658 30.769 0.00 0.00 0.00 3.41
6274 6344 3.577649 TGTTTGTCTTTGGTTTTGCGA 57.422 38.095 0.00 0.00 0.00 5.10
6275 6345 3.246619 TGTTTGTCTTTGGTTTTGCGAC 58.753 40.909 0.00 0.00 0.00 5.19
6276 6346 3.057174 TGTTTGTCTTTGGTTTTGCGACT 60.057 39.130 0.00 0.00 0.00 4.18
6277 6347 3.859411 TTGTCTTTGGTTTTGCGACTT 57.141 38.095 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.024271 AATTCATCGGGGCATCAACG 58.976 50.000 0.00 0.00 0.00 4.10
35 36 3.506455 TGTGGAGCAGTAGTAAGAGACAC 59.494 47.826 0.00 0.00 0.00 3.67
171 172 5.123344 GCTCTAAGCCTAAATTTTGTTCGGA 59.877 40.000 0.00 0.00 34.48 4.55
203 204 1.400494 GCCGGAACAAACTGCGATATT 59.600 47.619 5.05 0.00 30.81 1.28
205 206 2.462503 GCCGGAACAAACTGCGATA 58.537 52.632 5.05 0.00 30.81 2.92
258 259 3.647636 AGCTGGTACATCTGATGGTAGT 58.352 45.455 20.83 3.41 38.20 2.73
351 352 6.291377 TCTGGAGCAGCGATAATAGATTTTT 58.709 36.000 0.00 0.00 0.00 1.94
428 429 1.067142 CCCACGTGCTCTAGCTGTTTA 60.067 52.381 10.91 0.00 42.66 2.01
468 469 4.748892 CAAGATGGACGCGGAAGATATAT 58.251 43.478 12.47 0.00 0.00 0.86
523 524 5.463286 TGCTTCAACGTTCTAACTAATCGA 58.537 37.500 0.00 0.00 0.00 3.59
539 540 3.057386 CACAATGTGCTACCATGCTTCAA 60.057 43.478 0.00 0.00 0.00 2.69
594 595 3.511362 TGGAAGCTCAAACTGCCAA 57.489 47.368 0.00 0.00 42.84 4.52
767 768 4.202080 CCCTTCAACATAGTGCATCCAATG 60.202 45.833 0.00 0.00 0.00 2.82
768 769 3.956199 CCCTTCAACATAGTGCATCCAAT 59.044 43.478 0.00 0.00 0.00 3.16
769 770 3.245229 ACCCTTCAACATAGTGCATCCAA 60.245 43.478 0.00 0.00 0.00 3.53
770 771 2.308570 ACCCTTCAACATAGTGCATCCA 59.691 45.455 0.00 0.00 0.00 3.41
771 772 3.004752 ACCCTTCAACATAGTGCATCC 57.995 47.619 0.00 0.00 0.00 3.51
772 773 6.509418 TTTTACCCTTCAACATAGTGCATC 57.491 37.500 0.00 0.00 0.00 3.91
773 774 6.493458 ACTTTTTACCCTTCAACATAGTGCAT 59.507 34.615 0.00 0.00 0.00 3.96
774 775 5.830991 ACTTTTTACCCTTCAACATAGTGCA 59.169 36.000 0.00 0.00 0.00 4.57
775 776 6.149633 CACTTTTTACCCTTCAACATAGTGC 58.850 40.000 0.00 0.00 0.00 4.40
776 777 7.272037 ACACTTTTTACCCTTCAACATAGTG 57.728 36.000 0.00 0.00 36.32 2.74
777 778 7.891498 AACACTTTTTACCCTTCAACATAGT 57.109 32.000 0.00 0.00 0.00 2.12
778 779 7.651704 CCAAACACTTTTTACCCTTCAACATAG 59.348 37.037 0.00 0.00 0.00 2.23
779 780 7.342284 TCCAAACACTTTTTACCCTTCAACATA 59.658 33.333 0.00 0.00 0.00 2.29
780 781 6.155393 TCCAAACACTTTTTACCCTTCAACAT 59.845 34.615 0.00 0.00 0.00 2.71
781 782 5.480772 TCCAAACACTTTTTACCCTTCAACA 59.519 36.000 0.00 0.00 0.00 3.33
782 783 5.968254 TCCAAACACTTTTTACCCTTCAAC 58.032 37.500 0.00 0.00 0.00 3.18
783 784 6.381420 TGATCCAAACACTTTTTACCCTTCAA 59.619 34.615 0.00 0.00 0.00 2.69
784 785 5.894393 TGATCCAAACACTTTTTACCCTTCA 59.106 36.000 0.00 0.00 0.00 3.02
785 786 6.183360 TGTGATCCAAACACTTTTTACCCTTC 60.183 38.462 0.00 0.00 38.81 3.46
786 787 5.659079 TGTGATCCAAACACTTTTTACCCTT 59.341 36.000 0.00 0.00 38.81 3.95
787 788 5.068591 GTGTGATCCAAACACTTTTTACCCT 59.931 40.000 7.39 0.00 43.69 4.34
788 789 5.286438 GTGTGATCCAAACACTTTTTACCC 58.714 41.667 7.39 0.00 43.69 3.69
789 790 4.973663 CGTGTGATCCAAACACTTTTTACC 59.026 41.667 11.67 0.00 44.64 2.85
790 791 4.973663 CCGTGTGATCCAAACACTTTTTAC 59.026 41.667 11.67 0.00 44.64 2.01
791 792 4.641094 ACCGTGTGATCCAAACACTTTTTA 59.359 37.500 11.67 0.00 44.64 1.52
792 793 3.445805 ACCGTGTGATCCAAACACTTTTT 59.554 39.130 11.67 0.00 44.64 1.94
793 794 3.020984 ACCGTGTGATCCAAACACTTTT 58.979 40.909 11.67 0.00 44.64 2.27
794 795 2.650322 ACCGTGTGATCCAAACACTTT 58.350 42.857 11.67 0.00 44.64 2.66
795 796 2.341846 ACCGTGTGATCCAAACACTT 57.658 45.000 11.67 0.00 44.64 3.16
796 797 2.218603 GAACCGTGTGATCCAAACACT 58.781 47.619 11.67 0.00 44.64 3.55
797 798 1.944024 TGAACCGTGTGATCCAAACAC 59.056 47.619 5.02 5.02 43.62 3.32
798 799 2.158885 TCTGAACCGTGTGATCCAAACA 60.159 45.455 0.00 0.00 0.00 2.83
799 800 2.223377 GTCTGAACCGTGTGATCCAAAC 59.777 50.000 0.00 0.00 0.00 2.93
800 801 2.489971 GTCTGAACCGTGTGATCCAAA 58.510 47.619 0.00 0.00 0.00 3.28
801 802 1.604438 CGTCTGAACCGTGTGATCCAA 60.604 52.381 0.00 0.00 0.00 3.53
802 803 0.038618 CGTCTGAACCGTGTGATCCA 60.039 55.000 0.00 0.00 0.00 3.41
803 804 1.352156 GCGTCTGAACCGTGTGATCC 61.352 60.000 0.00 0.00 0.00 3.36
804 805 0.388649 AGCGTCTGAACCGTGTGATC 60.389 55.000 0.00 0.00 0.00 2.92
805 806 0.667487 CAGCGTCTGAACCGTGTGAT 60.667 55.000 1.18 0.00 32.44 3.06
806 807 1.299850 CAGCGTCTGAACCGTGTGA 60.300 57.895 1.18 0.00 32.44 3.58
807 808 2.943345 GCAGCGTCTGAACCGTGTG 61.943 63.158 10.46 0.00 32.44 3.82
808 809 2.661866 GCAGCGTCTGAACCGTGT 60.662 61.111 10.46 0.00 32.44 4.49
809 810 1.568612 AATGCAGCGTCTGAACCGTG 61.569 55.000 10.46 0.00 32.44 4.94
810 811 0.884704 AAATGCAGCGTCTGAACCGT 60.885 50.000 10.46 0.00 32.44 4.83
811 812 0.238289 AAAATGCAGCGTCTGAACCG 59.762 50.000 10.46 0.00 32.44 4.44
812 813 1.266718 TCAAAATGCAGCGTCTGAACC 59.733 47.619 10.46 0.00 32.44 3.62
813 814 2.686558 TCAAAATGCAGCGTCTGAAC 57.313 45.000 10.46 0.00 32.44 3.18
814 815 3.206034 CATCAAAATGCAGCGTCTGAA 57.794 42.857 10.46 0.82 32.44 3.02
815 816 2.905959 CATCAAAATGCAGCGTCTGA 57.094 45.000 10.46 2.60 32.44 3.27
885 886 2.092538 TGGAACCCACGTGGAAAGTTTA 60.093 45.455 36.07 19.09 37.39 2.01
889 890 2.327228 GTGGAACCCACGTGGAAAG 58.673 57.895 36.07 21.23 44.95 2.62
890 891 4.563404 GTGGAACCCACGTGGAAA 57.437 55.556 36.07 12.94 44.95 3.13
926 928 2.934324 TTTGCGCGTTCGGTTCTCG 61.934 57.895 8.43 0.00 40.90 4.04
1105 1107 2.690510 GCCTGGAGAGGAGGGCTT 60.691 66.667 0.00 0.00 42.93 4.35
1146 1148 6.974622 TCGAAGGGTAATACAAGAATCGTAAC 59.025 38.462 0.00 0.00 0.00 2.50
1179 1181 5.302568 TGAACTTCTGCATCAATCTTGGTTT 59.697 36.000 0.00 0.00 0.00 3.27
1203 1205 2.654863 CCAACTCAACCCACAAGACTT 58.345 47.619 0.00 0.00 0.00 3.01
1204 1206 1.133792 CCCAACTCAACCCACAAGACT 60.134 52.381 0.00 0.00 0.00 3.24
1221 1223 1.484065 CCTGAACCCCCAAAAATCCCA 60.484 52.381 0.00 0.00 0.00 4.37
1229 1231 1.758592 CGTCTTCCTGAACCCCCAA 59.241 57.895 0.00 0.00 0.00 4.12
1230 1232 2.890766 GCGTCTTCCTGAACCCCCA 61.891 63.158 0.00 0.00 0.00 4.96
1231 1233 2.046217 GCGTCTTCCTGAACCCCC 60.046 66.667 0.00 0.00 0.00 5.40
1250 1252 2.613691 GAACGGCAGATTTAACTCCGA 58.386 47.619 5.96 0.00 42.43 4.55
1251 1253 1.323534 CGAACGGCAGATTTAACTCCG 59.676 52.381 0.00 0.00 45.04 4.63
1266 1268 7.096885 GCATTCCAATTCAATTAGAATCGAACG 60.097 37.037 1.18 0.00 46.09 3.95
1282 1284 2.233271 CGCAGGATAGGCATTCCAATT 58.767 47.619 8.25 0.00 35.59 2.32
1284 1286 0.546122 ACGCAGGATAGGCATTCCAA 59.454 50.000 8.25 0.00 35.59 3.53
1294 1296 2.904905 CGGGGGAAACGCAGGATA 59.095 61.111 0.00 0.00 46.93 2.59
1311 1313 5.228012 CACGAACTCTTCTGTTTTTCTTTGC 59.772 40.000 0.00 0.00 0.00 3.68
1333 1335 1.273327 CAACTCTCCCCAAAATGCCAC 59.727 52.381 0.00 0.00 0.00 5.01
1388 1390 0.802494 CGCACGGCCTTTAAACAGAT 59.198 50.000 0.00 0.00 0.00 2.90
1391 1393 1.448922 AAGCGCACGGCCTTTAAACA 61.449 50.000 11.47 0.00 45.17 2.83
1421 1423 1.804151 TGGAAAACGTCAGCATGTAGC 59.196 47.619 0.00 0.00 46.19 3.58
1429 1431 1.399727 GGAACGCATGGAAAACGTCAG 60.400 52.381 0.00 0.00 39.49 3.51
1433 1435 1.001815 ACAAGGAACGCATGGAAAACG 60.002 47.619 0.00 0.00 0.00 3.60
1443 1445 1.264288 CTCAAGAACCACAAGGAACGC 59.736 52.381 0.00 0.00 38.69 4.84
1444 1446 2.287915 CACTCAAGAACCACAAGGAACG 59.712 50.000 0.00 0.00 38.69 3.95
1455 1457 1.197721 CCGAACATGCCACTCAAGAAC 59.802 52.381 0.00 0.00 0.00 3.01
1530 1533 2.159240 TCGCAATACCAGAGCTGTACAG 60.159 50.000 18.93 18.93 0.00 2.74
1544 1547 5.064707 GGTCACTTAGCAAGATTTCGCAATA 59.935 40.000 3.37 0.00 0.00 1.90
1545 1548 4.142600 GGTCACTTAGCAAGATTTCGCAAT 60.143 41.667 3.37 0.00 0.00 3.56
1546 1549 3.188460 GGTCACTTAGCAAGATTTCGCAA 59.812 43.478 3.37 0.00 0.00 4.85
1548 1551 2.096013 GGGTCACTTAGCAAGATTTCGC 59.904 50.000 3.37 0.00 0.00 4.70
1549 1552 3.600388 AGGGTCACTTAGCAAGATTTCG 58.400 45.455 3.37 0.00 0.00 3.46
1550 1553 6.655425 ACTTAAGGGTCACTTAGCAAGATTTC 59.345 38.462 7.53 0.00 42.34 2.17
1551 1554 6.543735 ACTTAAGGGTCACTTAGCAAGATTT 58.456 36.000 7.53 0.00 42.34 2.17
1563 1568 4.648651 ACATGTTGGTACTTAAGGGTCAC 58.351 43.478 7.53 0.00 0.00 3.67
1653 1658 7.974482 TCTGCCATTAGATAGTGAATCATTG 57.026 36.000 0.00 0.00 37.03 2.82
1803 1816 8.358148 CAGTACTGTTAAGAAAGACAGGAGTTA 58.642 37.037 15.06 0.00 45.78 2.24
2021 2039 6.455646 GCTCGAACAATCTAACAGGTACATTG 60.456 42.308 0.00 0.00 0.00 2.82
2158 2176 5.273208 ACTCCAATCTTCTTAGGCAGACTA 58.727 41.667 0.00 0.00 0.00 2.59
2415 2433 4.946478 ATAGGACAGCAAGAGTGGATAC 57.054 45.455 0.00 0.00 0.00 2.24
2488 2506 5.423015 GAAGAAGTTCATAGGACTGATGCA 58.577 41.667 5.50 0.00 32.36 3.96
2490 2508 5.655488 ACGAAGAAGTTCATAGGACTGATG 58.345 41.667 5.50 0.00 32.36 3.07
2504 2522 3.798202 AGTGCAGAAAGAACGAAGAAGT 58.202 40.909 0.00 0.00 0.00 3.01
2568 2588 3.681897 CAGGACACAGAGTAACATTCTGC 59.318 47.826 2.37 0.00 44.63 4.26
2612 2632 6.617879 TGCTCATCAGAGATTTCATTGTTTG 58.382 36.000 0.00 0.00 44.98 2.93
2709 2729 8.862325 ATCAATAGTGAGAAGAGTCTATCGAT 57.138 34.615 2.16 2.16 37.14 3.59
2713 2733 8.448008 AGAGGATCAATAGTGAGAAGAGTCTAT 58.552 37.037 0.00 0.00 37.14 1.98
2787 2807 2.957402 TGACCCATTGGCAGGATATC 57.043 50.000 0.00 0.00 33.59 1.63
2843 2863 3.242739 CGGTATTTCTTGAAATCCCTGCG 60.243 47.826 11.31 0.00 0.00 5.18
3007 3031 4.893608 ACAAGAACAACAACAAAGCCTTT 58.106 34.783 0.00 0.00 0.00 3.11
3025 3052 8.831715 TGCCATATGTCATATAACTGTACAAG 57.168 34.615 4.99 0.00 0.00 3.16
3048 3075 8.442384 CCATGTTAAATAAAGTTTCAACCATGC 58.558 33.333 0.00 0.00 0.00 4.06
3052 3079 8.279800 GCAACCATGTTAAATAAAGTTTCAACC 58.720 33.333 0.00 0.00 0.00 3.77
3069 3096 1.203038 TCACTCCCATTGCAACCATGT 60.203 47.619 0.00 0.00 0.00 3.21
3180 3209 3.181492 GCTAGCAAGGAAAAAGAGCATCC 60.181 47.826 10.63 0.00 33.66 3.51
3205 3234 7.247728 TGTACATTTCAAAAACAGATATCCGC 58.752 34.615 0.00 0.00 0.00 5.54
3245 3274 3.181448 TGCAGGACACATATCAGCATCAT 60.181 43.478 0.00 0.00 0.00 2.45
3298 3328 8.708378 TCATCTCAACAAGGTGATGTATCTAAT 58.292 33.333 0.00 0.00 40.31 1.73
3388 3418 7.278135 ACACTGCTAACAACATATGATCTCAT 58.722 34.615 10.38 0.00 40.22 2.90
3430 3460 6.546403 AGCATCTCATCTGAATGTAGCAATTT 59.454 34.615 0.00 0.00 34.32 1.82
3479 3509 1.063912 TGCGTCTATTACCGGTACACG 59.936 52.381 15.53 19.59 43.80 4.49
3582 3612 3.420839 ACCTTTTTCGCAACAACTCAG 57.579 42.857 0.00 0.00 0.00 3.35
3742 3773 2.293170 GGGCTCAGCAAAGAATACCTC 58.707 52.381 0.00 0.00 0.00 3.85
3811 3842 8.203681 AGGTAAACCAACTAGATAACAGAACT 57.796 34.615 0.00 0.00 38.89 3.01
3911 3942 6.018469 TCAAAATGACCTTTGGGATCAGAAT 58.982 36.000 0.00 0.00 37.00 2.40
3923 3954 6.347696 TCAAGCATGTTTTCAAAATGACCTT 58.652 32.000 0.00 0.00 0.00 3.50
3951 3982 4.058417 TGATGATTTGAAATCACCCCCA 57.942 40.909 21.54 14.08 0.00 4.96
4103 4134 1.629861 TCTCATGTGCTCCATTGTCCA 59.370 47.619 0.00 0.00 0.00 4.02
4123 4154 3.286329 TGCTGATGGTAATGACATGCT 57.714 42.857 0.00 0.00 0.00 3.79
4234 4265 2.231235 CCGAAGCTAATTTGCCTTTGGT 59.769 45.455 8.30 0.00 0.00 3.67
4342 4373 3.761752 GGGAAGGACAATCGATTTGGAAA 59.238 43.478 8.21 0.00 39.80 3.13
4353 4384 2.044793 TCTGACAGGGGAAGGACAAT 57.955 50.000 1.81 0.00 0.00 2.71
4566 4597 4.948004 CCGTTTCTAAGGCCTAAAAATCCT 59.052 41.667 5.16 0.00 0.00 3.24
4567 4598 4.945543 TCCGTTTCTAAGGCCTAAAAATCC 59.054 41.667 5.16 0.00 0.00 3.01
4568 4599 6.505044 TTCCGTTTCTAAGGCCTAAAAATC 57.495 37.500 5.16 0.00 0.00 2.17
4639 4673 2.551032 TCAACACAATGCTCTTGCTCTG 59.449 45.455 0.26 0.00 40.48 3.35
4657 4691 2.151202 GCAACTTCGGTCTGGATTCAA 58.849 47.619 0.00 0.00 0.00 2.69
4658 4692 1.610624 GGCAACTTCGGTCTGGATTCA 60.611 52.381 0.00 0.00 0.00 2.57
4758 4792 3.392285 TCTCCACCATTCCATCCATACAG 59.608 47.826 0.00 0.00 0.00 2.74
4779 4813 3.260740 CTCTGCCTCTGTCAAATGTCTC 58.739 50.000 0.00 0.00 0.00 3.36
4781 4815 3.051081 ACTCTGCCTCTGTCAAATGTC 57.949 47.619 0.00 0.00 0.00 3.06
4876 4910 2.762535 ATTCCAGACGTGTACTTGGG 57.237 50.000 0.00 0.00 0.00 4.12
5062 5096 4.658063 TCCAAATTACCACCACGAGATTT 58.342 39.130 0.00 0.00 0.00 2.17
5078 5112 6.294508 CGAGAAACCAAACATACCTTCCAAAT 60.295 38.462 0.00 0.00 0.00 2.32
5087 5121 4.977741 TTCGACGAGAAACCAAACATAC 57.022 40.909 0.00 0.00 35.61 2.39
5143 5177 1.334243 GCCTTCGACTAGCGTCATACT 59.666 52.381 6.49 0.00 40.23 2.12
5148 5182 0.388134 TGTTGCCTTCGACTAGCGTC 60.388 55.000 6.49 0.00 41.80 5.19
5176 5210 2.552599 TCCGATGTACCAAACAAGCA 57.447 45.000 0.00 0.00 42.70 3.91
5253 5287 4.998051 ACCACCTTACACCATCAAAAGAT 58.002 39.130 0.00 0.00 0.00 2.40
5309 5343 3.322254 AGGGTCAGTCTACACAGAAACAG 59.678 47.826 0.00 0.00 30.85 3.16
5373 5410 0.913934 TTGACTCAGCCAGGGCCATA 60.914 55.000 6.18 0.00 43.17 2.74
5374 5411 2.207501 CTTGACTCAGCCAGGGCCAT 62.208 60.000 6.18 0.00 43.17 4.40
5389 5426 0.395312 GTTTGGAGGGGTCGACTTGA 59.605 55.000 16.46 0.00 0.00 3.02
5447 5484 2.340809 GCATGCACAAAGCCAGCA 59.659 55.556 14.21 0.00 44.83 4.41
5454 5491 4.948576 CGAAGCTGCATGCACAAA 57.051 50.000 18.46 0.00 45.94 2.83
5498 5536 3.365220 GCGATCTATCTGTTCATAACCGC 59.635 47.826 0.00 0.00 0.00 5.68
5558 5596 3.299977 CACGACCCTGACCACGGA 61.300 66.667 0.00 0.00 0.00 4.69
5616 5654 0.179045 AATGTATCTGGTCCAGCGGC 60.179 55.000 14.64 6.72 0.00 6.53
5630 5668 4.696877 CACATTCAGAGTTCCAGCAATGTA 59.303 41.667 0.00 0.00 33.69 2.29
5682 5720 0.321564 CCAGGTGTCGCTGATTTCCA 60.322 55.000 0.00 0.00 0.00 3.53
5699 5737 0.327480 ATGCCAGGGTAGATGGACCA 60.327 55.000 0.00 0.00 41.73 4.02
5794 5832 4.499188 CCGAAGTGTTGACTCAGAAGTACA 60.499 45.833 0.00 0.00 35.28 2.90
5801 5840 1.784525 GTCCCGAAGTGTTGACTCAG 58.215 55.000 0.00 0.00 0.00 3.35
5839 5878 3.153919 TGCACCAACCAAGAATAAGACC 58.846 45.455 0.00 0.00 0.00 3.85
5841 5880 2.819608 GCTGCACCAACCAAGAATAAGA 59.180 45.455 0.00 0.00 0.00 2.10
5842 5881 2.557924 TGCTGCACCAACCAAGAATAAG 59.442 45.455 0.00 0.00 0.00 1.73
5843 5882 2.591923 TGCTGCACCAACCAAGAATAA 58.408 42.857 0.00 0.00 0.00 1.40
5844 5883 2.284754 TGCTGCACCAACCAAGAATA 57.715 45.000 0.00 0.00 0.00 1.75
5845 5884 1.412079 TTGCTGCACCAACCAAGAAT 58.588 45.000 0.00 0.00 0.00 2.40
5932 5979 2.874701 GCATGTCTGACAGTGTTTCAGT 59.125 45.455 16.46 0.00 41.22 3.41
5964 6011 3.559171 GCCAGACCTGTCTTACAAATGGA 60.559 47.826 0.00 0.00 37.98 3.41
5995 6046 2.048222 CAGCGACAAGGGCGAGAA 60.048 61.111 0.00 0.00 35.00 2.87
6026 6077 1.019805 GCAAGTCTTACCCGACTGCC 61.020 60.000 0.00 0.00 43.14 4.85
6033 6084 2.427506 CAGGAGTTGCAAGTCTTACCC 58.572 52.381 28.62 15.74 0.00 3.69
6036 6087 3.857157 AACCAGGAGTTGCAAGTCTTA 57.143 42.857 28.62 0.00 37.29 2.10
6073 6124 0.541764 AATTTTCCTTCCCCTGCGCA 60.542 50.000 10.98 10.98 0.00 6.09
6078 6129 2.996742 ACCTCTCAATTTTCCTTCCCCT 59.003 45.455 0.00 0.00 0.00 4.79
6086 6137 3.436704 TGATCGTGCACCTCTCAATTTTC 59.563 43.478 12.15 0.00 0.00 2.29
6087 6138 3.189287 GTGATCGTGCACCTCTCAATTTT 59.811 43.478 12.15 0.00 32.68 1.82
6089 6140 2.027745 AGTGATCGTGCACCTCTCAATT 60.028 45.455 12.15 1.55 39.59 2.32
6090 6141 1.552337 AGTGATCGTGCACCTCTCAAT 59.448 47.619 12.15 8.09 39.59 2.57
6118 6169 0.249238 GCTCGCCACATAGTCAGGAG 60.249 60.000 0.00 0.00 0.00 3.69
6119 6170 0.684479 AGCTCGCCACATAGTCAGGA 60.684 55.000 0.00 0.00 0.00 3.86
6120 6171 0.529337 CAGCTCGCCACATAGTCAGG 60.529 60.000 0.00 0.00 0.00 3.86
6162 6214 0.729116 CGATTCGGCTGCAAGATGTT 59.271 50.000 0.50 0.00 34.07 2.71
6165 6217 1.202568 TGATCGATTCGGCTGCAAGAT 60.203 47.619 6.18 0.00 34.07 2.40
6166 6218 0.175531 TGATCGATTCGGCTGCAAGA 59.824 50.000 6.18 0.00 34.07 3.02
6172 6224 0.250038 CCACCATGATCGATTCGGCT 60.250 55.000 6.18 0.00 0.00 5.52
6225 6295 9.092876 GAAGAGAAAAGAACTATACACATGGAG 57.907 37.037 0.00 0.00 0.00 3.86
6254 6324 3.057174 AGTCGCAAAACCAAAGACAAACA 60.057 39.130 0.00 0.00 34.56 2.83


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

AutoCloner maintained by Alex Coulton.