Multiple sequence alignment - TraesCS6D01G016800

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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 TraesCS6D01G016800 chr6D 100.000 4691 0 0 1 4691 7031273 7035963 0.000000e+00 8663.0
1 TraesCS6D01G016800 chr6D 81.346 1560 280 9 2121 3676 6371597 6373149 0.000000e+00 1258.0
2 TraesCS6D01G016800 chr6D 81.098 1566 280 16 2121 3678 6353193 6354750 0.000000e+00 1238.0
3 TraesCS6D01G016800 chr6D 80.863 1552 282 13 2121 3669 6426528 6428067 0.000000e+00 1206.0
4 TraesCS6D01G016800 chr6D 80.591 1556 288 13 2121 3669 6497721 6499269 0.000000e+00 1188.0
5 TraesCS6D01G016800 chr6D 80.920 1174 183 15 993 2138 6496290 6497450 0.000000e+00 889.0
6 TraesCS6D01G016800 chr6D 82.098 1039 178 7 2635 3669 6465693 6466727 0.000000e+00 881.0
7 TraesCS6D01G016800 chr6D 78.337 1371 242 31 991 2335 6425185 6426526 0.000000e+00 835.0
8 TraesCS6D01G016800 chr6D 77.039 1324 244 34 991 2286 6441814 6443105 0.000000e+00 706.0
9 TraesCS6D01G016800 chr6D 81.746 504 79 7 993 1494 6351618 6352110 4.370000e-110 409.0
10 TraesCS6D01G016800 chr6A 95.747 3809 109 20 708 4493 6698419 6702197 0.000000e+00 6087.0
11 TraesCS6D01G016800 chr6A 81.302 1551 277 10 2121 3669 5940895 5942434 0.000000e+00 1245.0
12 TraesCS6D01G016800 chr6A 80.813 1574 292 7 2121 3689 5901941 5903509 0.000000e+00 1225.0
13 TraesCS6D01G016800 chr6A 80.824 1554 288 10 2121 3669 5917921 5919469 0.000000e+00 1210.0
14 TraesCS6D01G016800 chr6A 89.546 727 41 12 1 717 6697691 6698392 0.000000e+00 889.0
15 TraesCS6D01G016800 chr6A 78.045 1371 246 32 991 2335 5939552 5940893 0.000000e+00 813.0
16 TraesCS6D01G016800 chr6A 79.969 639 108 16 1504 2138 5901264 5901886 1.990000e-123 453.0
17 TraesCS6D01G016800 chr6A 81.174 494 76 10 993 1482 5900723 5901203 9.530000e-102 381.0
18 TraesCS6D01G016800 chr6B 82.632 1117 186 8 2557 3669 11599607 11600719 0.000000e+00 981.0
19 TraesCS6D01G016800 chr6B 79.812 743 114 20 993 1714 11592851 11593578 4.190000e-140 508.0
20 TraesCS6D01G016800 chr6B 82.273 440 60 11 993 1426 11792353 11792780 9.590000e-97 364.0
21 TraesCS6D01G016800 chr6B 85.714 70 9 1 112 180 713492675 713492606 6.510000e-09 73.1
22 TraesCS6D01G016800 chr6B 97.297 37 1 0 1118 1154 134807264 134807300 3.920000e-06 63.9
23 TraesCS6D01G016800 chr7D 75.584 385 83 7 1115 1492 1091466 1091086 3.730000e-41 180.0
24 TraesCS6D01G016800 chrUn 75.000 304 65 7 1192 1488 51405312 51405611 3.810000e-26 130.0
25 TraesCS6D01G016800 chr7B 80.833 120 13 9 36 148 487819766 487819882 8.360000e-13 86.1
26 TraesCS6D01G016800 chr4D 89.091 55 6 0 106 160 43672562 43672616 8.420000e-08 69.4
27 TraesCS6D01G016800 chr1D 93.478 46 3 0 113 158 483960740 483960695 8.420000e-08 69.4
28 TraesCS6D01G016800 chr5B 78.151 119 16 8 24 140 661532474 661532584 3.030000e-07 67.6
29 TraesCS6D01G016800 chr1B 81.176 85 15 1 108 192 427226090 427226007 3.030000e-07 67.6
30 TraesCS6D01G016800 chr1A 91.489 47 3 1 113 158 63855032 63855078 3.920000e-06 63.9
31 TraesCS6D01G016800 chr3B 100.000 32 0 0 113 144 818290269 818290300 5.070000e-05 60.2


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 TraesCS6D01G016800 chr6D 7031273 7035963 4690 False 8663.000000 8663 100.0000 1 4691 1 chr6D.!!$F4 4690
1 TraesCS6D01G016800 chr6D 6371597 6373149 1552 False 1258.000000 1258 81.3460 2121 3676 1 chr6D.!!$F1 1555
2 TraesCS6D01G016800 chr6D 6496290 6499269 2979 False 1038.500000 1188 80.7555 993 3669 2 chr6D.!!$F7 2676
3 TraesCS6D01G016800 chr6D 6425185 6428067 2882 False 1020.500000 1206 79.6000 991 3669 2 chr6D.!!$F6 2678
4 TraesCS6D01G016800 chr6D 6465693 6466727 1034 False 881.000000 881 82.0980 2635 3669 1 chr6D.!!$F3 1034
5 TraesCS6D01G016800 chr6D 6351618 6354750 3132 False 823.500000 1238 81.4220 993 3678 2 chr6D.!!$F5 2685
6 TraesCS6D01G016800 chr6D 6441814 6443105 1291 False 706.000000 706 77.0390 991 2286 1 chr6D.!!$F2 1295
7 TraesCS6D01G016800 chr6A 6697691 6702197 4506 False 3488.000000 6087 92.6465 1 4493 2 chr6A.!!$F4 4492
8 TraesCS6D01G016800 chr6A 5917921 5919469 1548 False 1210.000000 1210 80.8240 2121 3669 1 chr6A.!!$F1 1548
9 TraesCS6D01G016800 chr6A 5939552 5942434 2882 False 1029.000000 1245 79.6735 991 3669 2 chr6A.!!$F3 2678
10 TraesCS6D01G016800 chr6A 5900723 5903509 2786 False 686.333333 1225 80.6520 993 3689 3 chr6A.!!$F2 2696
11 TraesCS6D01G016800 chr6B 11599607 11600719 1112 False 981.000000 981 82.6320 2557 3669 1 chr6B.!!$F2 1112
12 TraesCS6D01G016800 chr6B 11592851 11593578 727 False 508.000000 508 79.8120 993 1714 1 chr6B.!!$F1 721

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
815 864 0.253044 ACACGTTAGCTGCCATGGAT 59.747 50.0 18.4 0.0 0.00 3.41 F
1449 1517 0.179045 ATTGCTCCGATACAGTGCCC 60.179 55.0 0.0 0.0 0.00 5.36 F
2514 3215 1.120530 TCCGGATAGAAACTGGAGCC 58.879 55.0 0.0 0.0 37.81 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 3197 0.106894 GGGCTCCAGTTTCTATCCGG 59.893 60.0 0.00 0.0 0.00 5.14 R
3204 3905 0.108585 TCATAGCCCCAATCTTCGCC 59.891 55.0 0.00 0.0 0.00 5.54 R
4476 5197 0.179062 GCTGTCTGGGCAGATCGAAT 60.179 55.0 6.37 0.0 39.97 3.34 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
30 31 4.574599 ATGAAAAGCACAGTTGTCCTTC 57.425 40.909 0.00 0.00 0.00 3.46
40 41 3.053619 ACAGTTGTCCTTCCAGTTTTCCT 60.054 43.478 0.00 0.00 0.00 3.36
87 88 5.165676 GTTTCAGTTTTCTTTGTTTCCGGT 58.834 37.500 0.00 0.00 0.00 5.28
88 89 5.394224 TTCAGTTTTCTTTGTTTCCGGTT 57.606 34.783 0.00 0.00 0.00 4.44
89 90 5.394224 TCAGTTTTCTTTGTTTCCGGTTT 57.606 34.783 0.00 0.00 0.00 3.27
90 91 5.785243 TCAGTTTTCTTTGTTTCCGGTTTT 58.215 33.333 0.00 0.00 0.00 2.43
91 92 5.865013 TCAGTTTTCTTTGTTTCCGGTTTTC 59.135 36.000 0.00 0.00 0.00 2.29
92 93 5.867174 CAGTTTTCTTTGTTTCCGGTTTTCT 59.133 36.000 0.00 0.00 0.00 2.52
93 94 6.367695 CAGTTTTCTTTGTTTCCGGTTTTCTT 59.632 34.615 0.00 0.00 0.00 2.52
95 96 7.442969 AGTTTTCTTTGTTTCCGGTTTTCTTTT 59.557 29.630 0.00 0.00 0.00 2.27
96 97 7.731882 TTTCTTTGTTTCCGGTTTTCTTTTT 57.268 28.000 0.00 0.00 0.00 1.94
97 98 6.713792 TCTTTGTTTCCGGTTTTCTTTTTG 57.286 33.333 0.00 0.00 0.00 2.44
98 99 5.639931 TCTTTGTTTCCGGTTTTCTTTTTGG 59.360 36.000 0.00 0.00 0.00 3.28
99 100 4.803098 TGTTTCCGGTTTTCTTTTTGGA 57.197 36.364 0.00 0.00 0.00 3.53
100 101 5.148651 TGTTTCCGGTTTTCTTTTTGGAA 57.851 34.783 0.00 0.00 33.90 3.53
101 102 5.735766 TGTTTCCGGTTTTCTTTTTGGAAT 58.264 33.333 0.00 0.00 35.58 3.01
102 103 6.174049 TGTTTCCGGTTTTCTTTTTGGAATT 58.826 32.000 0.00 0.00 35.58 2.17
103 104 6.655425 TGTTTCCGGTTTTCTTTTTGGAATTT 59.345 30.769 0.00 0.00 35.58 1.82
104 105 7.175119 TGTTTCCGGTTTTCTTTTTGGAATTTT 59.825 29.630 0.00 0.00 35.58 1.82
105 106 7.689446 TTCCGGTTTTCTTTTTGGAATTTTT 57.311 28.000 0.00 0.00 30.93 1.94
161 162 7.962964 TCAAAGATATCAACTCAAGAAACGT 57.037 32.000 5.32 0.00 0.00 3.99
164 165 7.527084 AAGATATCAACTCAAGAAACGTAGC 57.473 36.000 5.32 0.00 0.00 3.58
170 171 1.986378 CTCAAGAAACGTAGCGGTGAG 59.014 52.381 0.00 0.00 0.00 3.51
234 235 0.321346 GGGCCCAACAGGTCAAAATG 59.679 55.000 19.95 0.00 44.85 2.32
241 242 4.971939 CCAACAGGTCAAAATGGGAAAAT 58.028 39.130 0.00 0.00 0.00 1.82
419 424 4.347000 TGAGCAGAAACTTACCCTTGTAGT 59.653 41.667 0.00 0.00 0.00 2.73
420 425 5.163237 TGAGCAGAAACTTACCCTTGTAGTT 60.163 40.000 0.00 0.00 0.00 2.24
424 429 6.916387 GCAGAAACTTACCCTTGTAGTTTTTC 59.084 38.462 0.00 0.00 32.95 2.29
479 484 7.293018 GTGAAAATCACAAAATGGATTTCTGC 58.707 34.615 5.65 0.00 46.22 4.26
486 491 1.386533 AATGGATTTCTGCGGCAGAG 58.613 50.000 29.29 7.84 41.75 3.35
563 568 6.196910 TCGCAAATGATCATAATTTTTCTGCG 59.803 34.615 9.04 16.80 37.19 5.18
566 571 7.170320 GCAAATGATCATAATTTTTCTGCGGAT 59.830 33.333 9.04 0.00 0.00 4.18
567 572 9.037737 CAAATGATCATAATTTTTCTGCGGATT 57.962 29.630 9.04 0.00 0.00 3.01
569 574 7.990541 TGATCATAATTTTTCTGCGGATTTG 57.009 32.000 0.00 0.00 0.00 2.32
587 598 6.073548 CGGATTTGCTAATTCTCATCTACACC 60.074 42.308 0.00 0.00 0.00 4.16
588 599 6.767902 GGATTTGCTAATTCTCATCTACACCA 59.232 38.462 0.00 0.00 0.00 4.17
600 611 8.196802 TCTCATCTACACCATTTGATTTTACG 57.803 34.615 0.00 0.00 0.00 3.18
622 633 4.549680 CGCAGAGATTCGTGCAAATCTTAG 60.550 45.833 13.54 10.61 44.16 2.18
661 672 9.376075 GGAAAAGTTCCTACCAAATACTAGTAC 57.624 37.037 4.31 0.00 46.57 2.73
662 673 9.933723 GAAAAGTTCCTACCAAATACTAGTACA 57.066 33.333 4.31 0.00 0.00 2.90
664 675 9.716531 AAAGTTCCTACCAAATACTAGTACAAC 57.283 33.333 4.31 0.00 0.00 3.32
665 676 7.542025 AGTTCCTACCAAATACTAGTACAACG 58.458 38.462 4.31 0.00 0.00 4.10
666 677 7.177392 AGTTCCTACCAAATACTAGTACAACGT 59.823 37.037 4.31 2.58 0.00 3.99
667 678 8.458843 GTTCCTACCAAATACTAGTACAACGTA 58.541 37.037 4.31 3.59 0.00 3.57
668 679 7.985476 TCCTACCAAATACTAGTACAACGTAC 58.015 38.462 4.31 0.00 0.00 3.67
669 680 6.907212 CCTACCAAATACTAGTACAACGTACG 59.093 42.308 15.01 15.01 0.00 3.67
670 681 6.254281 ACCAAATACTAGTACAACGTACGT 57.746 37.500 16.72 16.72 0.00 3.57
671 682 7.372451 ACCAAATACTAGTACAACGTACGTA 57.628 36.000 23.12 2.73 0.00 3.57
767 814 0.535102 CTTGACCGGCCCATATGACC 60.535 60.000 0.00 4.46 0.00 4.02
771 818 4.329545 CGGCCCATATGACCGGGG 62.330 72.222 22.43 9.43 43.31 5.73
775 822 2.030562 CCATATGACCGGGGCGAC 59.969 66.667 6.32 0.00 0.00 5.19
815 864 0.253044 ACACGTTAGCTGCCATGGAT 59.747 50.000 18.40 0.00 0.00 3.41
939 988 7.035004 ACCGTTCGTAGCACAAACTAATAATA 58.965 34.615 0.00 0.00 0.00 0.98
970 1019 3.679980 CCAGTCTTTGTAACATCTCACCG 59.320 47.826 0.00 0.00 0.00 4.94
1078 1127 2.639347 TGGATCAGCTTCTTCCTTGTCA 59.361 45.455 7.63 0.00 0.00 3.58
1088 1137 3.103911 CCTTGTCACCGACGCGTC 61.104 66.667 28.96 28.96 34.95 5.19
1343 1398 3.366396 TCCAGTACCTCAATCTCCAGTC 58.634 50.000 0.00 0.00 0.00 3.51
1344 1399 3.011821 TCCAGTACCTCAATCTCCAGTCT 59.988 47.826 0.00 0.00 0.00 3.24
1347 1402 4.950475 CAGTACCTCAATCTCCAGTCTACA 59.050 45.833 0.00 0.00 0.00 2.74
1348 1403 5.596361 CAGTACCTCAATCTCCAGTCTACAT 59.404 44.000 0.00 0.00 0.00 2.29
1349 1404 5.830991 AGTACCTCAATCTCCAGTCTACATC 59.169 44.000 0.00 0.00 0.00 3.06
1350 1405 3.964031 ACCTCAATCTCCAGTCTACATCC 59.036 47.826 0.00 0.00 0.00 3.51
1449 1517 0.179045 ATTGCTCCGATACAGTGCCC 60.179 55.000 0.00 0.00 0.00 5.36
1872 2051 4.083003 CGCCAGCTAAACTTTTATCACCAA 60.083 41.667 0.00 0.00 0.00 3.67
1977 2174 6.294286 GGAGTCTCTCCTCTGGAAATATAACG 60.294 46.154 8.38 0.00 46.41 3.18
2166 2651 4.854399 TGGAAAATTGCACTAGTTTGTCG 58.146 39.130 0.00 0.00 0.00 4.35
2496 3197 6.760770 CACATAATTCTTTCTCAGGACCTCTC 59.239 42.308 0.00 0.00 0.00 3.20
2498 3199 1.840737 TCTTTCTCAGGACCTCTCCG 58.159 55.000 0.00 0.00 42.22 4.63
2514 3215 1.120530 TCCGGATAGAAACTGGAGCC 58.879 55.000 0.00 0.00 37.81 4.70
2864 3565 5.317733 GGAGATATTCCGGTGACTATCAG 57.682 47.826 0.00 0.00 36.24 2.90
2936 3637 6.497259 TCTGGAGTTATACCTGAGTCTTTGTT 59.503 38.462 0.00 0.00 32.95 2.83
3036 3737 6.311735 AGGTAAATTTAGAGGAGTTTGGCAA 58.688 36.000 0.00 0.00 0.00 4.52
3297 3998 2.352127 GGCAAGCTTGTCTGAATTGACC 60.352 50.000 26.55 11.85 36.21 4.02
3619 4320 0.951558 TTTCCGCCTCTTTGACAAGC 59.048 50.000 0.00 0.00 0.00 4.01
3697 4398 3.062234 GGCAAGTACAAGTTGAGCGATAC 59.938 47.826 10.54 1.14 30.18 2.24
3723 4424 4.002982 TGACAATTAGATGGTGCTGTCAC 58.997 43.478 0.00 0.00 38.52 3.67
3737 4438 4.809426 GTGCTGTCACCCTATTGTACATAC 59.191 45.833 0.00 0.00 37.24 2.39
3748 4449 2.097110 TGTACATACTGGGCCCTAGG 57.903 55.000 25.70 12.52 0.00 3.02
3765 4466 7.039714 GGGCCCTAGGAATAAATGAATGTAAAG 60.040 40.741 17.04 0.00 0.00 1.85
3848 4549 9.869844 GTCTGATGCATGTAATTAAGTGTTATC 57.130 33.333 2.46 0.35 0.00 1.75
4099 4811 8.275040 AGTAATTCATATGCCAACTACCTTTCT 58.725 33.333 0.00 0.00 0.00 2.52
4113 4825 6.522946 ACTACCTTTCTAACTCTTCAACACC 58.477 40.000 0.00 0.00 0.00 4.16
4128 4840 4.507710 TCAACACCTCAACAGATATGAGC 58.492 43.478 0.00 0.00 42.36 4.26
4160 4872 8.778358 ACAAAGAGATTAAAGTGCTTCTACTTG 58.222 33.333 0.00 0.00 40.58 3.16
4166 4878 7.885399 AGATTAAAGTGCTTCTACTTGGTCATT 59.115 33.333 0.00 0.00 40.58 2.57
4167 4879 9.162764 GATTAAAGTGCTTCTACTTGGTCATTA 57.837 33.333 0.00 0.00 40.58 1.90
4174 4886 7.982354 GTGCTTCTACTTGGTCATTACTCTAAT 59.018 37.037 0.00 0.00 0.00 1.73
4239 4958 2.035576 GCCATGCAATTCTCTCCCAATC 59.964 50.000 0.00 0.00 0.00 2.67
4247 4966 5.393896 GCAATTCTCTCCCAATCTCAAAAGG 60.394 44.000 0.00 0.00 0.00 3.11
4249 4968 4.559862 TCTCTCCCAATCTCAAAAGGTC 57.440 45.455 0.00 0.00 0.00 3.85
4318 5037 6.040247 TGCTCCAAGAACTACACATATTACG 58.960 40.000 0.00 0.00 0.00 3.18
4320 5039 6.216801 TCCAAGAACTACACATATTACGCT 57.783 37.500 0.00 0.00 0.00 5.07
4362 5081 6.550108 GGTCCAACAGAGACATTACTCCTATA 59.450 42.308 0.00 0.00 37.60 1.31
4363 5082 7.069578 GGTCCAACAGAGACATTACTCCTATAA 59.930 40.741 0.00 0.00 37.60 0.98
4364 5083 8.475639 GTCCAACAGAGACATTACTCCTATAAA 58.524 37.037 0.00 0.00 37.60 1.40
4365 5084 8.696374 TCCAACAGAGACATTACTCCTATAAAG 58.304 37.037 0.00 0.00 37.60 1.85
4366 5085 8.696374 CCAACAGAGACATTACTCCTATAAAGA 58.304 37.037 0.00 0.00 37.60 2.52
4383 5102 8.160106 CCTATAAAGAAAAGGATGCTGGAGTAT 58.840 37.037 0.00 0.00 31.64 2.12
4489 5210 2.203056 CGCCATTCGATCTGCCCA 60.203 61.111 0.00 0.00 41.67 5.36
4493 5214 0.178767 CCATTCGATCTGCCCAGACA 59.821 55.000 0.00 0.00 40.75 3.41
4494 5215 1.579698 CATTCGATCTGCCCAGACAG 58.420 55.000 0.00 0.00 40.75 3.51
4495 5216 0.179062 ATTCGATCTGCCCAGACAGC 60.179 55.000 0.00 0.00 40.75 4.40
4496 5217 2.202987 CGATCTGCCCAGACAGCC 60.203 66.667 0.00 0.00 40.75 4.85
4497 5218 2.202987 GATCTGCCCAGACAGCCG 60.203 66.667 0.00 0.00 40.75 5.52
4498 5219 3.005539 ATCTGCCCAGACAGCCGT 61.006 61.111 0.00 0.00 40.75 5.68
4499 5220 3.320879 ATCTGCCCAGACAGCCGTG 62.321 63.158 0.00 0.00 40.75 4.94
4500 5221 4.320456 CTGCCCAGACAGCCGTGT 62.320 66.667 0.00 0.00 40.71 4.49
4509 5230 4.135153 CAGCCGTGTCTCCTCGGG 62.135 72.222 5.78 0.00 45.53 5.14
4510 5231 4.361971 AGCCGTGTCTCCTCGGGA 62.362 66.667 5.78 0.00 45.53 5.14
4511 5232 3.148279 GCCGTGTCTCCTCGGGAT 61.148 66.667 5.78 0.00 45.53 3.85
4512 5233 2.722201 GCCGTGTCTCCTCGGGATT 61.722 63.158 5.78 0.00 45.53 3.01
4513 5234 1.437986 CCGTGTCTCCTCGGGATTC 59.562 63.158 0.00 0.00 42.56 2.52
4514 5235 1.320344 CCGTGTCTCCTCGGGATTCA 61.320 60.000 0.00 0.00 42.56 2.57
4515 5236 0.747255 CGTGTCTCCTCGGGATTCAT 59.253 55.000 0.00 0.00 0.00 2.57
4516 5237 1.536922 CGTGTCTCCTCGGGATTCATG 60.537 57.143 0.00 0.00 0.00 3.07
4517 5238 1.757118 GTGTCTCCTCGGGATTCATGA 59.243 52.381 0.00 0.00 0.00 3.07
4518 5239 1.757118 TGTCTCCTCGGGATTCATGAC 59.243 52.381 0.00 0.00 0.00 3.06
4519 5240 1.757118 GTCTCCTCGGGATTCATGACA 59.243 52.381 0.00 0.00 0.00 3.58
4520 5241 2.034878 TCTCCTCGGGATTCATGACAG 58.965 52.381 0.00 0.00 0.00 3.51
4521 5242 1.069823 CTCCTCGGGATTCATGACAGG 59.930 57.143 0.00 0.00 0.00 4.00
4522 5243 0.833287 CCTCGGGATTCATGACAGGT 59.167 55.000 0.00 0.00 0.00 4.00
4523 5244 1.473965 CCTCGGGATTCATGACAGGTG 60.474 57.143 0.00 0.00 0.00 4.00
4524 5245 0.541392 TCGGGATTCATGACAGGTGG 59.459 55.000 0.00 0.00 0.00 4.61
4525 5246 0.541392 CGGGATTCATGACAGGTGGA 59.459 55.000 0.00 0.00 0.00 4.02
4526 5247 1.743772 CGGGATTCATGACAGGTGGAC 60.744 57.143 0.00 0.00 0.00 4.02
4527 5248 1.408822 GGGATTCATGACAGGTGGACC 60.409 57.143 0.00 0.00 0.00 4.46
4528 5249 1.656652 GATTCATGACAGGTGGACCG 58.343 55.000 0.00 0.00 42.08 4.79
4529 5250 0.392998 ATTCATGACAGGTGGACCGC 60.393 55.000 0.00 0.00 42.08 5.68
4530 5251 2.779951 TTCATGACAGGTGGACCGCG 62.780 60.000 0.00 0.00 42.08 6.46
4531 5252 4.082523 ATGACAGGTGGACCGCGG 62.083 66.667 26.86 26.86 42.08 6.46
4553 5274 4.759205 GCCCGGGGCCACAATCTT 62.759 66.667 28.23 0.00 44.06 2.40
4554 5275 2.755469 CCCGGGGCCACAATCTTG 60.755 66.667 14.71 0.00 0.00 3.02
4555 5276 2.035626 CCGGGGCCACAATCTTGT 59.964 61.111 5.46 0.00 43.36 3.16
4567 5288 4.135747 ACAATCTTGTGGTGTTTTTGGG 57.864 40.909 0.00 0.00 40.49 4.12
4568 5289 2.871633 CAATCTTGTGGTGTTTTTGGGC 59.128 45.455 0.00 0.00 0.00 5.36
4569 5290 0.457851 TCTTGTGGTGTTTTTGGGCG 59.542 50.000 0.00 0.00 0.00 6.13
4570 5291 1.151172 CTTGTGGTGTTTTTGGGCGC 61.151 55.000 0.00 0.00 0.00 6.53
4571 5292 2.656973 GTGGTGTTTTTGGGCGCG 60.657 61.111 0.00 0.00 0.00 6.86
4572 5293 4.577246 TGGTGTTTTTGGGCGCGC 62.577 61.111 25.94 25.94 0.00 6.86
4574 5295 4.279043 GTGTTTTTGGGCGCGCCT 62.279 61.111 45.23 0.00 36.10 5.52
4575 5296 4.277593 TGTTTTTGGGCGCGCCTG 62.278 61.111 45.23 0.00 36.10 4.85
4587 5308 4.969196 CGCCTGCGTGTGGAGTGT 62.969 66.667 2.83 0.00 34.35 3.55
4588 5309 3.044305 GCCTGCGTGTGGAGTGTC 61.044 66.667 0.00 0.00 0.00 3.67
4589 5310 2.734723 CCTGCGTGTGGAGTGTCG 60.735 66.667 0.00 0.00 0.00 4.35
4592 5313 3.406361 GCGTGTGGAGTGTCGCAG 61.406 66.667 0.00 0.00 46.40 5.18
4593 5314 3.406361 CGTGTGGAGTGTCGCAGC 61.406 66.667 0.00 0.00 0.00 5.25
4594 5315 2.029666 GTGTGGAGTGTCGCAGCT 59.970 61.111 0.00 0.00 0.00 4.24
4595 5316 2.029518 TGTGGAGTGTCGCAGCTG 59.970 61.111 10.11 10.11 0.00 4.24
4596 5317 2.029666 GTGGAGTGTCGCAGCTGT 59.970 61.111 16.64 0.00 0.00 4.40
4597 5318 2.024319 GTGGAGTGTCGCAGCTGTC 61.024 63.158 16.64 6.83 0.00 3.51
4598 5319 2.807045 GGAGTGTCGCAGCTGTCG 60.807 66.667 16.64 18.63 0.00 4.35
4599 5320 3.474034 GAGTGTCGCAGCTGTCGC 61.474 66.667 20.86 16.77 0.00 5.19
4600 5321 4.284860 AGTGTCGCAGCTGTCGCA 62.285 61.111 20.86 18.53 39.10 5.10
4601 5322 4.064491 GTGTCGCAGCTGTCGCAC 62.064 66.667 25.05 25.05 39.10 5.34
4622 5343 4.530857 CGACGGGCCATCCAGACC 62.531 72.222 4.39 0.00 34.36 3.85
4623 5344 3.083997 GACGGGCCATCCAGACCT 61.084 66.667 4.39 0.00 34.36 3.85
4624 5345 1.760875 GACGGGCCATCCAGACCTA 60.761 63.158 4.39 0.00 34.36 3.08
4625 5346 2.029307 GACGGGCCATCCAGACCTAC 62.029 65.000 4.39 0.00 34.36 3.18
4626 5347 2.808206 CGGGCCATCCAGACCTACC 61.808 68.421 4.39 0.00 34.36 3.18
4627 5348 1.384643 GGGCCATCCAGACCTACCT 60.385 63.158 4.39 0.00 35.00 3.08
4628 5349 1.700042 GGGCCATCCAGACCTACCTG 61.700 65.000 4.39 0.00 35.00 4.00
4629 5350 0.983378 GGCCATCCAGACCTACCTGT 60.983 60.000 0.00 0.00 32.43 4.00
4630 5351 0.466124 GCCATCCAGACCTACCTGTC 59.534 60.000 0.00 0.00 35.43 3.51
4631 5352 1.123928 CCATCCAGACCTACCTGTCC 58.876 60.000 0.00 0.00 35.83 4.02
4632 5353 0.747255 CATCCAGACCTACCTGTCCG 59.253 60.000 0.00 0.00 35.83 4.79
4633 5354 0.335361 ATCCAGACCTACCTGTCCGT 59.665 55.000 0.00 0.00 35.83 4.69
4634 5355 0.323178 TCCAGACCTACCTGTCCGTC 60.323 60.000 0.00 0.00 35.83 4.79
4635 5356 1.654954 CCAGACCTACCTGTCCGTCG 61.655 65.000 0.00 0.00 35.83 5.12
4636 5357 1.378250 AGACCTACCTGTCCGTCGG 60.378 63.158 4.39 4.39 35.83 4.79
4637 5358 3.061260 GACCTACCTGTCCGTCGGC 62.061 68.421 6.34 2.31 0.00 5.54
4638 5359 4.189188 CCTACCTGTCCGTCGGCG 62.189 72.222 6.34 0.29 37.95 6.46
4639 5360 3.437795 CTACCTGTCCGTCGGCGT 61.438 66.667 9.28 2.47 36.15 5.68
4640 5361 3.392595 CTACCTGTCCGTCGGCGTC 62.393 68.421 9.28 0.00 36.15 5.19
4641 5362 3.907260 TACCTGTCCGTCGGCGTCT 62.907 63.158 9.28 0.00 36.15 4.18
4642 5363 4.052229 CCTGTCCGTCGGCGTCTT 62.052 66.667 9.28 0.00 36.15 3.01
4643 5364 2.504244 CTGTCCGTCGGCGTCTTC 60.504 66.667 9.28 0.00 36.15 2.87
4644 5365 3.263503 CTGTCCGTCGGCGTCTTCA 62.264 63.158 9.28 0.67 36.15 3.02
4645 5366 2.504244 GTCCGTCGGCGTCTTCAG 60.504 66.667 9.28 0.00 36.15 3.02
4646 5367 2.670592 TCCGTCGGCGTCTTCAGA 60.671 61.111 9.28 0.00 36.15 3.27
4647 5368 2.504244 CCGTCGGCGTCTTCAGAC 60.504 66.667 9.28 0.00 41.47 3.51
4648 5369 2.504244 CGTCGGCGTCTTCAGACC 60.504 66.667 6.85 0.00 41.86 3.85
4649 5370 2.126031 GTCGGCGTCTTCAGACCC 60.126 66.667 6.85 3.44 41.86 4.46
4650 5371 3.379445 TCGGCGTCTTCAGACCCC 61.379 66.667 6.85 1.13 41.86 4.95
4654 5375 4.796231 CGTCTTCAGACCCCGCCG 62.796 72.222 1.25 0.00 41.86 6.46
4655 5376 4.452733 GTCTTCAGACCCCGCCGG 62.453 72.222 0.00 0.00 39.07 6.13
4671 5392 4.309950 GGGCTGGTTCGGTCGTGT 62.310 66.667 0.00 0.00 0.00 4.49
4672 5393 2.737376 GGCTGGTTCGGTCGTGTC 60.737 66.667 0.00 0.00 0.00 3.67
4673 5394 2.737376 GCTGGTTCGGTCGTGTCC 60.737 66.667 0.00 0.00 0.00 4.02
4684 5405 4.619227 CGTGTCCGCCTGTGGGTT 62.619 66.667 0.00 0.00 34.45 4.11
4685 5406 2.978010 GTGTCCGCCTGTGGGTTG 60.978 66.667 0.00 0.00 34.45 3.77
4686 5407 3.484806 TGTCCGCCTGTGGGTTGT 61.485 61.111 0.00 0.00 34.45 3.32
4687 5408 2.978010 GTCCGCCTGTGGGTTGTG 60.978 66.667 0.00 0.00 34.45 3.33
4688 5409 3.484806 TCCGCCTGTGGGTTGTGT 61.485 61.111 0.00 0.00 34.45 3.72
4689 5410 2.518349 CCGCCTGTGGGTTGTGTT 60.518 61.111 0.00 0.00 34.45 3.32
4690 5411 1.228003 CCGCCTGTGGGTTGTGTTA 60.228 57.895 0.00 0.00 34.45 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.555966 AGGAAAACTGGAAGGACAACTG 58.444 45.455 0.00 0.00 39.30 3.16
68 69 5.867174 AGAAAACCGGAAACAAAGAAAACTG 59.133 36.000 9.46 0.00 0.00 3.16
79 80 6.671614 AATTCCAAAAAGAAAACCGGAAAC 57.328 33.333 9.46 0.00 36.21 2.78
102 103 5.786264 TGTTAATAGGTTTGGGCGAAAAA 57.214 34.783 0.00 0.00 0.00 1.94
103 104 5.477291 TCATGTTAATAGGTTTGGGCGAAAA 59.523 36.000 0.00 0.00 0.00 2.29
104 105 5.010933 TCATGTTAATAGGTTTGGGCGAAA 58.989 37.500 0.00 0.00 0.00 3.46
105 106 4.590918 TCATGTTAATAGGTTTGGGCGAA 58.409 39.130 0.00 0.00 0.00 4.70
106 107 4.080807 TCTCATGTTAATAGGTTTGGGCGA 60.081 41.667 0.00 0.00 0.00 5.54
107 108 4.196193 TCTCATGTTAATAGGTTTGGGCG 58.804 43.478 0.00 0.00 0.00 6.13
108 109 6.064717 AGATCTCATGTTAATAGGTTTGGGC 58.935 40.000 0.00 0.00 0.00 5.36
109 110 8.432805 ACTAGATCTCATGTTAATAGGTTTGGG 58.567 37.037 0.00 0.00 0.00 4.12
110 111 9.838339 AACTAGATCTCATGTTAATAGGTTTGG 57.162 33.333 0.00 0.00 0.00 3.28
161 162 0.390124 ACAAACCGTTCTCACCGCTA 59.610 50.000 0.00 0.00 0.00 4.26
164 165 1.508632 ATGACAAACCGTTCTCACCG 58.491 50.000 0.00 0.00 0.00 4.94
170 171 4.151867 GGTGTCTAGAATGACAAACCGTTC 59.848 45.833 0.00 0.00 46.77 3.95
193 194 3.376234 CACTTGTTAGGCTGACATGGATG 59.624 47.826 23.18 13.15 0.00 3.51
195 196 2.290260 CCACTTGTTAGGCTGACATGGA 60.290 50.000 21.35 4.49 31.72 3.41
203 204 1.725169 TTGGGCCCACTTGTTAGGCT 61.725 55.000 28.70 0.00 46.31 4.58
259 263 4.022068 CCCAAGTTGTTGCATTGTGTCTAT 60.022 41.667 1.45 0.00 31.64 1.98
399 404 6.387041 AAAACTACAAGGGTAAGTTTCTGC 57.613 37.500 0.63 0.00 33.60 4.26
400 405 7.130269 CGAAAAACTACAAGGGTAAGTTTCTG 58.870 38.462 0.63 0.00 33.60 3.02
500 505 8.542497 AATTTACGACACTAAAAGCTATGACA 57.458 30.769 0.00 0.00 0.00 3.58
541 546 7.990541 TCCGCAGAAAAATTATGATCATTTG 57.009 32.000 14.65 0.00 0.00 2.32
551 556 8.250332 AGAATTAGCAAATCCGCAGAAAAATTA 58.750 29.630 0.00 0.00 0.00 1.40
559 564 4.514441 AGATGAGAATTAGCAAATCCGCAG 59.486 41.667 0.00 0.00 0.00 5.18
560 565 4.454678 AGATGAGAATTAGCAAATCCGCA 58.545 39.130 0.00 0.00 0.00 5.69
563 568 6.767902 TGGTGTAGATGAGAATTAGCAAATCC 59.232 38.462 0.00 0.00 0.00 3.01
566 571 8.461222 CAAATGGTGTAGATGAGAATTAGCAAA 58.539 33.333 0.00 0.00 0.00 3.68
567 572 7.828717 TCAAATGGTGTAGATGAGAATTAGCAA 59.171 33.333 0.00 0.00 0.00 3.91
569 574 7.792374 TCAAATGGTGTAGATGAGAATTAGC 57.208 36.000 0.00 0.00 0.00 3.09
587 598 6.193410 CACGAATCTCTGCGTAAAATCAAATG 59.807 38.462 0.00 0.00 38.92 2.32
588 599 6.250819 CACGAATCTCTGCGTAAAATCAAAT 58.749 36.000 0.00 0.00 38.92 2.32
600 611 3.754188 AAGATTTGCACGAATCTCTGC 57.246 42.857 12.85 0.00 43.66 4.26
622 633 3.643159 ACTTTTCCTTGTGAATTCGCC 57.357 42.857 16.14 2.39 31.67 5.54
661 672 1.670971 CGTGGCTGCTACGTACGTTG 61.671 60.000 27.92 25.04 36.83 4.10
662 673 1.443194 CGTGGCTGCTACGTACGTT 60.443 57.895 27.92 10.83 36.83 3.99
663 674 2.177531 CGTGGCTGCTACGTACGT 59.822 61.111 27.16 25.98 36.83 3.57
664 675 2.578713 CCGTGGCTGCTACGTACG 60.579 66.667 31.29 15.01 39.76 3.67
665 676 1.804326 CACCGTGGCTGCTACGTAC 60.804 63.158 31.29 9.03 39.76 3.67
666 677 2.569657 CACCGTGGCTGCTACGTA 59.430 61.111 31.29 0.00 39.76 3.57
667 678 4.373116 CCACCGTGGCTGCTACGT 62.373 66.667 31.29 19.28 39.76 3.57
669 680 4.778143 CCCCACCGTGGCTGCTAC 62.778 72.222 12.54 6.02 35.79 3.58
767 814 4.868900 CGTACGTACGTCGCCCCG 62.869 72.222 33.95 15.73 44.13 5.73
815 864 2.011222 GTTGGGATTTATGCCGTTCGA 58.989 47.619 0.00 0.00 41.80 3.71
960 1009 0.176680 GACAGATGGCGGTGAGATGT 59.823 55.000 0.00 0.00 0.00 3.06
970 1019 0.249615 TGCTAGCGATGACAGATGGC 60.250 55.000 10.77 0.00 32.10 4.40
1187 1242 2.753043 AGCAATCTTGGCGCCCTG 60.753 61.111 26.77 16.96 36.08 4.45
1324 1379 4.950475 TGTAGACTGGAGATTGAGGTACTG 59.050 45.833 0.00 0.00 41.55 2.74
1350 1405 2.420568 GCCATCATGCCCACACAGG 61.421 63.158 0.00 0.00 37.03 4.00
1449 1517 0.829182 AAAGGTTGCCAAGCTGAGGG 60.829 55.000 10.32 1.55 39.57 4.30
1872 2051 4.278419 GCTGTGTTACCAGTTCCAAAAGAT 59.722 41.667 3.57 0.00 34.84 2.40
1977 2174 3.057245 GTGGCAATTTCTCCAGAAACTCC 60.057 47.826 3.84 6.53 45.55 3.85
2075 2272 7.488471 CGAGACTAGATAAGTTTGTTAAGTGGG 59.512 40.741 0.00 0.00 39.07 4.61
2166 2651 7.984617 AGACTATTGCTGGAAAGAGAAAGATAC 59.015 37.037 2.04 0.00 0.00 2.24
2496 3197 0.106894 GGGCTCCAGTTTCTATCCGG 59.893 60.000 0.00 0.00 0.00 5.14
2498 3199 3.584733 ATTGGGCTCCAGTTTCTATCC 57.415 47.619 0.00 0.00 33.81 2.59
2657 3358 7.580007 ACTTAAGAGGAGGAAAACCAAGTTAA 58.420 34.615 10.09 0.00 0.00 2.01
2864 3565 7.758076 TCAATTGATGAAGATGTTGAAGATTGC 59.242 33.333 3.38 0.00 34.30 3.56
2936 3637 8.924511 TTTTTGGGCCATTGATGTTAAATTTA 57.075 26.923 7.26 0.00 0.00 1.40
3036 3737 0.877071 CTTGGCGCTTCATCACAACT 59.123 50.000 7.64 0.00 0.00 3.16
3204 3905 0.108585 TCATAGCCCCAATCTTCGCC 59.891 55.000 0.00 0.00 0.00 5.54
3297 3998 5.299279 TGACAAGTCCAAGGAGCTTAAAAAG 59.701 40.000 0.00 0.00 0.00 2.27
3619 4320 6.127925 ACAAACACATATGCCTTGTCATACAG 60.128 38.462 1.58 0.00 32.40 2.74
3697 4398 4.880120 ACAGCACCATCTAATTGTCATCTG 59.120 41.667 0.00 0.00 0.00 2.90
3723 4424 2.039879 GGGCCCAGTATGTACAATAGGG 59.960 54.545 19.95 17.16 37.87 3.53
3729 4430 1.576757 TCCTAGGGCCCAGTATGTACA 59.423 52.381 27.56 0.00 0.00 2.90
3737 4438 4.453480 TTCATTTATTCCTAGGGCCCAG 57.547 45.455 27.56 18.88 0.00 4.45
3848 4549 9.239002 TGTTGAATTTTGATTTAGTACAAACCG 57.761 29.630 0.00 0.00 36.06 4.44
3897 4609 1.204704 TGATAGGTTGCTCCACTCACG 59.795 52.381 1.79 0.00 39.02 4.35
3924 4636 8.537049 TGGCAATTGATTTTAGACAATTTGAG 57.463 30.769 10.34 0.00 42.35 3.02
4074 4786 8.451908 AGAAAGGTAGTTGGCATATGAATTAC 57.548 34.615 6.97 4.32 0.00 1.89
4099 4811 5.607939 TCTGTTGAGGTGTTGAAGAGTTA 57.392 39.130 0.00 0.00 0.00 2.24
4113 4825 5.105063 TGTTCTTCGCTCATATCTGTTGAG 58.895 41.667 0.00 0.00 42.83 3.02
4128 4840 6.892691 AGCACTTTAATCTCTTTGTTCTTCG 58.107 36.000 0.00 0.00 0.00 3.79
4211 4923 4.400567 GGAGAGAATTGCATGGCTAAAAGT 59.599 41.667 0.00 0.00 0.00 2.66
4215 4927 2.241941 TGGGAGAGAATTGCATGGCTAA 59.758 45.455 0.00 0.00 0.00 3.09
4216 4928 1.845791 TGGGAGAGAATTGCATGGCTA 59.154 47.619 0.00 0.00 0.00 3.93
4218 4930 1.477553 TTGGGAGAGAATTGCATGGC 58.522 50.000 0.00 0.00 0.00 4.40
4283 5002 6.661304 AGTTCTTGGAGCATCATTTCTTTT 57.339 33.333 0.00 0.00 36.25 2.27
4286 5005 5.645497 GTGTAGTTCTTGGAGCATCATTTCT 59.355 40.000 0.00 0.00 36.25 2.52
4362 5081 5.196695 GGATACTCCAGCATCCTTTTCTTT 58.803 41.667 0.00 0.00 38.16 2.52
4363 5082 4.684485 CGGATACTCCAGCATCCTTTTCTT 60.684 45.833 4.60 0.00 38.90 2.52
4364 5083 3.181461 CGGATACTCCAGCATCCTTTTCT 60.181 47.826 4.60 0.00 38.90 2.52
4365 5084 3.134458 CGGATACTCCAGCATCCTTTTC 58.866 50.000 4.60 0.00 38.90 2.29
4366 5085 2.746472 GCGGATACTCCAGCATCCTTTT 60.746 50.000 4.60 0.00 38.90 2.27
4469 5190 4.005472 GCAGATCGAATGGCGCGG 62.005 66.667 8.83 0.00 40.61 6.46
4471 5192 3.654020 GGGCAGATCGAATGGCGC 61.654 66.667 17.55 0.00 43.74 6.53
4473 5194 1.146930 TCTGGGCAGATCGAATGGC 59.853 57.895 16.37 16.37 42.19 4.40
4476 5197 0.179062 GCTGTCTGGGCAGATCGAAT 60.179 55.000 6.37 0.00 39.97 3.34
4496 5217 0.747255 ATGAATCCCGAGGAGACACG 59.253 55.000 0.00 0.00 44.43 4.49
4497 5218 1.757118 TCATGAATCCCGAGGAGACAC 59.243 52.381 0.00 0.00 34.05 3.67
4498 5219 1.757118 GTCATGAATCCCGAGGAGACA 59.243 52.381 0.00 2.65 34.05 3.41
4499 5220 1.757118 TGTCATGAATCCCGAGGAGAC 59.243 52.381 0.00 0.00 34.05 3.36
4500 5221 2.034878 CTGTCATGAATCCCGAGGAGA 58.965 52.381 0.00 0.00 34.05 3.71
4501 5222 1.069823 CCTGTCATGAATCCCGAGGAG 59.930 57.143 0.00 0.00 34.05 3.69
4502 5223 1.123077 CCTGTCATGAATCCCGAGGA 58.877 55.000 0.00 0.00 35.55 3.71
4503 5224 0.833287 ACCTGTCATGAATCCCGAGG 59.167 55.000 0.00 0.00 0.00 4.63
4504 5225 1.473965 CCACCTGTCATGAATCCCGAG 60.474 57.143 0.00 0.00 0.00 4.63
4505 5226 0.541392 CCACCTGTCATGAATCCCGA 59.459 55.000 0.00 0.00 0.00 5.14
4506 5227 0.541392 TCCACCTGTCATGAATCCCG 59.459 55.000 0.00 0.00 0.00 5.14
4507 5228 1.408822 GGTCCACCTGTCATGAATCCC 60.409 57.143 0.00 0.00 0.00 3.85
4508 5229 1.743772 CGGTCCACCTGTCATGAATCC 60.744 57.143 0.00 0.00 0.00 3.01
4509 5230 1.656652 CGGTCCACCTGTCATGAATC 58.343 55.000 0.00 0.00 0.00 2.52
4510 5231 0.392998 GCGGTCCACCTGTCATGAAT 60.393 55.000 0.00 0.00 0.00 2.57
4511 5232 1.003839 GCGGTCCACCTGTCATGAA 60.004 57.895 0.00 0.00 0.00 2.57
4512 5233 2.662596 GCGGTCCACCTGTCATGA 59.337 61.111 0.00 0.00 0.00 3.07
4513 5234 2.815211 CGCGGTCCACCTGTCATG 60.815 66.667 0.00 0.00 0.00 3.07
4514 5235 4.082523 CCGCGGTCCACCTGTCAT 62.083 66.667 19.50 0.00 0.00 3.06
4537 5258 2.755469 CAAGATTGTGGCCCCGGG 60.755 66.667 15.80 15.80 0.00 5.73
4538 5259 2.035626 ACAAGATTGTGGCCCCGG 59.964 61.111 0.00 0.00 40.49 5.73
4546 5267 3.681313 GCCCAAAAACACCACAAGATTGT 60.681 43.478 0.00 0.00 43.36 2.71
4547 5268 2.871633 GCCCAAAAACACCACAAGATTG 59.128 45.455 0.00 0.00 0.00 2.67
4548 5269 2.482839 CGCCCAAAAACACCACAAGATT 60.483 45.455 0.00 0.00 0.00 2.40
4549 5270 1.068434 CGCCCAAAAACACCACAAGAT 59.932 47.619 0.00 0.00 0.00 2.40
4550 5271 0.457851 CGCCCAAAAACACCACAAGA 59.542 50.000 0.00 0.00 0.00 3.02
4551 5272 1.151172 GCGCCCAAAAACACCACAAG 61.151 55.000 0.00 0.00 0.00 3.16
4552 5273 1.153549 GCGCCCAAAAACACCACAA 60.154 52.632 0.00 0.00 0.00 3.33
4553 5274 2.496817 GCGCCCAAAAACACCACA 59.503 55.556 0.00 0.00 0.00 4.17
4554 5275 2.656973 CGCGCCCAAAAACACCAC 60.657 61.111 0.00 0.00 0.00 4.16
4555 5276 4.577246 GCGCGCCCAAAAACACCA 62.577 61.111 23.24 0.00 0.00 4.17
4557 5278 4.279043 AGGCGCGCCCAAAAACAC 62.279 61.111 44.47 18.37 36.58 3.32
4558 5279 4.277593 CAGGCGCGCCCAAAAACA 62.278 61.111 44.47 0.00 36.58 2.83
4570 5291 4.969196 ACACTCCACACGCAGGCG 62.969 66.667 12.71 12.71 46.03 5.52
4571 5292 3.044305 GACACTCCACACGCAGGC 61.044 66.667 0.00 0.00 0.00 4.85
4572 5293 2.734723 CGACACTCCACACGCAGG 60.735 66.667 0.00 0.00 0.00 4.85
4576 5297 3.406361 GCTGCGACACTCCACACG 61.406 66.667 0.00 0.00 0.00 4.49
4577 5298 2.029666 AGCTGCGACACTCCACAC 59.970 61.111 0.00 0.00 0.00 3.82
4578 5299 2.029518 CAGCTGCGACACTCCACA 59.970 61.111 0.00 0.00 0.00 4.17
4579 5300 2.024319 GACAGCTGCGACACTCCAC 61.024 63.158 15.27 0.00 0.00 4.02
4580 5301 2.340078 GACAGCTGCGACACTCCA 59.660 61.111 15.27 0.00 0.00 3.86
4581 5302 2.807045 CGACAGCTGCGACACTCC 60.807 66.667 21.01 0.00 0.00 3.85
4582 5303 3.474034 GCGACAGCTGCGACACTC 61.474 66.667 27.07 11.32 41.01 3.51
4583 5304 4.284860 TGCGACAGCTGCGACACT 62.285 61.111 27.07 3.41 45.42 3.55
4584 5305 4.064491 GTGCGACAGCTGCGACAC 62.064 66.667 27.07 25.89 45.42 3.67
4605 5326 4.530857 GGTCTGGATGGCCCGTCG 62.531 72.222 0.00 0.00 37.93 5.12
4606 5327 1.760875 TAGGTCTGGATGGCCCGTC 60.761 63.158 0.00 0.00 42.71 4.79
4607 5328 2.064581 GTAGGTCTGGATGGCCCGT 61.065 63.158 0.00 0.00 42.71 5.28
4608 5329 2.808206 GGTAGGTCTGGATGGCCCG 61.808 68.421 0.00 0.00 42.71 6.13
4609 5330 1.384643 AGGTAGGTCTGGATGGCCC 60.385 63.158 0.00 0.00 42.71 5.80
4610 5331 0.983378 ACAGGTAGGTCTGGATGGCC 60.983 60.000 0.00 0.00 41.82 5.36
4611 5332 0.466124 GACAGGTAGGTCTGGATGGC 59.534 60.000 0.00 0.00 38.98 4.40
4612 5333 1.123928 GGACAGGTAGGTCTGGATGG 58.876 60.000 0.00 0.00 38.98 3.51
4613 5334 0.747255 CGGACAGGTAGGTCTGGATG 59.253 60.000 0.00 0.00 39.89 3.51
4614 5335 0.335361 ACGGACAGGTAGGTCTGGAT 59.665 55.000 7.03 0.00 46.25 3.41
4615 5336 0.323178 GACGGACAGGTAGGTCTGGA 60.323 60.000 7.03 0.00 46.25 3.86
4616 5337 1.654954 CGACGGACAGGTAGGTCTGG 61.655 65.000 7.03 0.00 46.25 3.86
4618 5339 1.378250 CCGACGGACAGGTAGGTCT 60.378 63.158 8.64 0.00 37.91 3.85
4619 5340 3.061260 GCCGACGGACAGGTAGGTC 62.061 68.421 20.50 0.00 35.39 3.85
4620 5341 3.066814 GCCGACGGACAGGTAGGT 61.067 66.667 20.50 0.00 35.39 3.08
4621 5342 4.189188 CGCCGACGGACAGGTAGG 62.189 72.222 20.50 0.00 35.97 3.18
4622 5343 3.392595 GACGCCGACGGACAGGTAG 62.393 68.421 20.50 1.46 46.04 3.18
4623 5344 3.434319 GACGCCGACGGACAGGTA 61.434 66.667 20.50 0.00 46.04 3.08
4625 5346 3.966026 GAAGACGCCGACGGACAGG 62.966 68.421 20.50 5.58 46.04 4.00
4626 5347 2.504244 GAAGACGCCGACGGACAG 60.504 66.667 20.50 10.51 46.04 3.51
4627 5348 3.263503 CTGAAGACGCCGACGGACA 62.264 63.158 20.50 6.16 46.04 4.02
4628 5349 2.504244 CTGAAGACGCCGACGGAC 60.504 66.667 20.50 8.22 46.04 4.79
4629 5350 2.670592 TCTGAAGACGCCGACGGA 60.671 61.111 20.50 0.00 46.04 4.69
4630 5351 2.504244 GTCTGAAGACGCCGACGG 60.504 66.667 10.29 10.29 46.04 4.79
4631 5352 2.504244 GGTCTGAAGACGCCGACG 60.504 66.667 4.44 0.00 45.65 5.12
4637 5358 4.796231 CGGCGGGGTCTGAAGACG 62.796 72.222 0.00 0.00 45.65 4.18
4638 5359 4.452733 CCGGCGGGGTCTGAAGAC 62.453 72.222 20.56 1.63 44.04 3.01
4654 5375 4.309950 ACACGACCGAACCAGCCC 62.310 66.667 0.00 0.00 0.00 5.19
4655 5376 2.737376 GACACGACCGAACCAGCC 60.737 66.667 0.00 0.00 0.00 4.85
4656 5377 2.737376 GGACACGACCGAACCAGC 60.737 66.667 0.00 0.00 0.00 4.85
4667 5388 4.619227 AACCCACAGGCGGACACG 62.619 66.667 0.00 0.00 44.63 4.49
4668 5389 2.978010 CAACCCACAGGCGGACAC 60.978 66.667 0.00 0.00 36.11 3.67
4669 5390 3.484806 ACAACCCACAGGCGGACA 61.485 61.111 0.00 0.00 36.11 4.02
4670 5391 2.978010 CACAACCCACAGGCGGAC 60.978 66.667 0.00 0.00 36.11 4.79
4671 5392 1.697082 TAACACAACCCACAGGCGGA 61.697 55.000 0.00 0.00 36.11 5.54
4672 5393 1.228003 TAACACAACCCACAGGCGG 60.228 57.895 0.00 0.00 36.11 6.13
4673 5394 4.466133 TAACACAACCCACAGGCG 57.534 55.556 0.00 0.00 36.11 5.52


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

AutoCloner maintained by Alex Coulton.