Multiple sequence alignment - TraesCS6D01G243000

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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 TraesCS6D01G243000 chr6D 100.000 3575 0 0 1 3575 345048527 345044953 0.000000e+00 6602
1 TraesCS6D01G243000 chr6A 89.434 2915 91 66 690 3549 485379043 485376291 0.000000e+00 3476
2 TraesCS6D01G243000 chr6A 88.489 278 15 7 414 674 485379306 485379029 1.600000e-83 320
3 TraesCS6D01G243000 chr6A 94.167 120 5 1 94 213 485379908 485379791 7.880000e-42 182
4 TraesCS6D01G243000 chr6A 91.346 104 9 0 208 311 485379407 485379304 3.720000e-30 143
5 TraesCS6D01G243000 chr6B 90.504 2401 79 47 690 3028 520848921 520846608 0.000000e+00 3033
6 TraesCS6D01G243000 chr6B 90.058 513 19 9 3052 3549 520846614 520846119 1.400000e-178 636
7 TraesCS6D01G243000 chr6B 86.022 186 3 5 513 675 520849091 520848906 1.020000e-40 178
8 TraesCS6D01G243000 chr6B 92.035 113 8 1 4 116 682544394 682544283 1.330000e-34 158
9 TraesCS6D01G243000 chr1D 98.214 112 2 0 307 418 279934340 279934451 2.820000e-46 196
10 TraesCS6D01G243000 chr1D 95.690 116 4 1 305 419 314706650 314706765 6.090000e-43 185
11 TraesCS6D01G243000 chrUn 97.297 111 3 0 306 416 218382244 218382134 4.710000e-44 189
12 TraesCS6D01G243000 chrUn 97.297 111 3 0 306 416 218399792 218399682 4.710000e-44 189
13 TraesCS6D01G243000 chrUn 96.040 101 2 2 1 101 200950299 200950201 2.860000e-36 163
14 TraesCS6D01G243000 chr3B 97.297 111 3 0 305 415 178397166 178397276 4.710000e-44 189
15 TraesCS6D01G243000 chr3B 92.800 125 7 2 295 418 425080897 425081020 2.840000e-41 180
16 TraesCS6D01G243000 chr7D 96.460 113 4 0 309 421 42694853 42694741 1.690000e-43 187
17 TraesCS6D01G243000 chr7D 98.913 92 1 0 1 92 211868386 211868477 7.940000e-37 165
18 TraesCS6D01G243000 chr1B 96.491 114 3 1 309 422 359907346 359907234 1.690000e-43 187
19 TraesCS6D01G243000 chr1B 100.000 91 0 0 1 91 592409222 592409312 6.140000e-38 169
20 TraesCS6D01G243000 chr4B 92.562 121 7 1 297 415 623124003 623124123 4.750000e-39 172
21 TraesCS6D01G243000 chr3D 100.000 93 0 0 1 93 12368870 12368778 4.750000e-39 172
22 TraesCS6D01G243000 chr5D 100.000 91 0 0 1 91 415748903 415748993 6.140000e-38 169
23 TraesCS6D01G243000 chr5A 95.146 103 5 0 1 103 683947063 683946961 2.860000e-36 163
24 TraesCS6D01G243000 chr7A 93.578 109 3 3 4 110 47492857 47492751 3.690000e-35 159
25 TraesCS6D01G243000 chr2A 91.892 111 8 1 1 111 726417603 726417712 1.720000e-33 154


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 TraesCS6D01G243000 chr6D 345044953 345048527 3574 True 6602.000000 6602 100.000000 1 3575 1 chr6D.!!$R1 3574
1 TraesCS6D01G243000 chr6A 485376291 485379908 3617 True 1030.250000 3476 90.859000 94 3549 4 chr6A.!!$R1 3455
2 TraesCS6D01G243000 chr6B 520846119 520849091 2972 True 1282.333333 3033 88.861333 513 3549 3 chr6B.!!$R2 3036

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
667 1079 0.030603 AACCAAAACCACCACCCCAT 60.031 50.0 0.0 0.0 0.0 4.00 F
790 1214 0.179020 CCCGCAATCCAGCCAATCTA 60.179 55.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2240 0.811616 GCTTCATCTGTCCGGCGAAT 60.812 55.0 9.3 0.0 0.00 3.34 R
2724 3231 0.319040 AGTATAGCACTGCATCGCCG 60.319 55.0 3.3 0.0 35.62 6.46 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
19 20 2.936919 ATCCAGGAATAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
20 21 1.953559 TCCAGGAATAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
21 22 0.947244 CCAGGAATAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
22 23 1.667236 CAGGAATAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
23 24 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
24 25 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
25 26 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
26 27 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
27 28 2.645838 ATAATGCGAGCACCAGGATT 57.354 45.000 0.00 0.00 33.17 3.01
28 29 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
29 30 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
30 31 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.000 0.00 0.00 0.00 2.69
31 32 0.250684 TGCGAGCACCAGGATTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
32 33 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
33 34 0.804989 CGAGCACCAGGATTTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
34 35 1.177401 GAGCACCAGGATTTGAACCC 58.823 55.000 0.00 0.00 0.00 4.11
35 36 0.779997 AGCACCAGGATTTGAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
40 41 1.549203 CAGGATTTGAACCCTGGTGG 58.451 55.000 0.00 0.00 44.68 4.61
50 51 4.179896 CCTGGTGGGTTGGGGATA 57.820 61.111 0.00 0.00 0.00 2.59
51 52 1.613061 CCTGGTGGGTTGGGGATAC 59.387 63.158 0.00 0.00 0.00 2.24
66 67 3.538634 GGATACCACTGTCCACCTAAC 57.461 52.381 0.00 0.00 34.57 2.34
67 68 2.169978 GGATACCACTGTCCACCTAACC 59.830 54.545 0.00 0.00 34.57 2.85
68 69 2.402182 TACCACTGTCCACCTAACCA 57.598 50.000 0.00 0.00 0.00 3.67
69 70 1.742308 ACCACTGTCCACCTAACCAT 58.258 50.000 0.00 0.00 0.00 3.55
70 71 1.628846 ACCACTGTCCACCTAACCATC 59.371 52.381 0.00 0.00 0.00 3.51
71 72 1.909302 CCACTGTCCACCTAACCATCT 59.091 52.381 0.00 0.00 0.00 2.90
72 73 2.093447 CCACTGTCCACCTAACCATCTC 60.093 54.545 0.00 0.00 0.00 2.75
73 74 2.567169 CACTGTCCACCTAACCATCTCA 59.433 50.000 0.00 0.00 0.00 3.27
74 75 3.007940 CACTGTCCACCTAACCATCTCAA 59.992 47.826 0.00 0.00 0.00 3.02
75 76 3.008049 ACTGTCCACCTAACCATCTCAAC 59.992 47.826 0.00 0.00 0.00 3.18
76 77 2.304761 TGTCCACCTAACCATCTCAACC 59.695 50.000 0.00 0.00 0.00 3.77
77 78 2.304761 GTCCACCTAACCATCTCAACCA 59.695 50.000 0.00 0.00 0.00 3.67
78 79 2.304761 TCCACCTAACCATCTCAACCAC 59.695 50.000 0.00 0.00 0.00 4.16
79 80 2.039746 CCACCTAACCATCTCAACCACA 59.960 50.000 0.00 0.00 0.00 4.17
80 81 3.338249 CACCTAACCATCTCAACCACAG 58.662 50.000 0.00 0.00 0.00 3.66
81 82 2.305927 ACCTAACCATCTCAACCACAGG 59.694 50.000 0.00 0.00 0.00 4.00
82 83 2.305927 CCTAACCATCTCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
91 92 2.244000 AACCACAGGTTGATTCGCG 58.756 52.632 0.00 0.00 45.07 5.87
92 93 0.250124 AACCACAGGTTGATTCGCGA 60.250 50.000 3.71 3.71 45.07 5.87
115 116 7.602644 GCGAAGGATCTAAACCATTGATATGTA 59.397 37.037 0.00 0.00 0.00 2.29
123 124 9.613428 TCTAAACCATTGATATGTAGACAAAGG 57.387 33.333 0.00 0.00 38.04 3.11
147 148 5.557576 TGTGATCCCTCCATCTAGAAATG 57.442 43.478 0.00 0.00 0.00 2.32
241 629 9.768662 ATCACTTCATAATATATGATATGCGCA 57.231 29.630 14.96 14.96 31.11 6.09
260 648 4.505191 GCGCATTAAAGAGGTATACGAACA 59.495 41.667 0.30 0.00 0.00 3.18
317 705 5.367945 TTTCCATAACACATACTCCCTCC 57.632 43.478 0.00 0.00 0.00 4.30
318 706 2.963101 TCCATAACACATACTCCCTCCG 59.037 50.000 0.00 0.00 0.00 4.63
319 707 2.698797 CCATAACACATACTCCCTCCGT 59.301 50.000 0.00 0.00 0.00 4.69
320 708 3.243771 CCATAACACATACTCCCTCCGTC 60.244 52.174 0.00 0.00 0.00 4.79
321 709 1.192428 AACACATACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
322 710 0.686769 ACACATACTCCCTCCGTCCC 60.687 60.000 0.00 0.00 0.00 4.46
323 711 0.686441 CACATACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
324 712 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
325 713 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
326 714 1.768870 CATACTCCCTCCGTCCCAAAT 59.231 52.381 0.00 0.00 0.00 2.32
327 715 1.961133 TACTCCCTCCGTCCCAAATT 58.039 50.000 0.00 0.00 0.00 1.82
328 716 1.961133 ACTCCCTCCGTCCCAAATTA 58.039 50.000 0.00 0.00 0.00 1.40
329 717 1.558294 ACTCCCTCCGTCCCAAATTAC 59.442 52.381 0.00 0.00 0.00 1.89
330 718 1.838077 CTCCCTCCGTCCCAAATTACT 59.162 52.381 0.00 0.00 0.00 2.24
331 719 1.835531 TCCCTCCGTCCCAAATTACTC 59.164 52.381 0.00 0.00 0.00 2.59
332 720 1.472728 CCCTCCGTCCCAAATTACTCG 60.473 57.143 0.00 0.00 0.00 4.18
333 721 1.206371 CCTCCGTCCCAAATTACTCGT 59.794 52.381 0.00 0.00 0.00 4.18
334 722 2.537401 CTCCGTCCCAAATTACTCGTC 58.463 52.381 0.00 0.00 0.00 4.20
335 723 1.135315 TCCGTCCCAAATTACTCGTCG 60.135 52.381 0.00 0.00 0.00 5.12
336 724 0.643820 CGTCCCAAATTACTCGTCGC 59.356 55.000 0.00 0.00 0.00 5.19
337 725 1.734707 CGTCCCAAATTACTCGTCGCT 60.735 52.381 0.00 0.00 0.00 4.93
338 726 1.659098 GTCCCAAATTACTCGTCGCTG 59.341 52.381 0.00 0.00 0.00 5.18
339 727 1.546923 TCCCAAATTACTCGTCGCTGA 59.453 47.619 0.00 0.00 0.00 4.26
340 728 2.028839 TCCCAAATTACTCGTCGCTGAA 60.029 45.455 0.00 0.00 0.00 3.02
341 729 2.739913 CCCAAATTACTCGTCGCTGAAA 59.260 45.455 0.00 0.00 0.00 2.69
342 730 3.374058 CCCAAATTACTCGTCGCTGAAAT 59.626 43.478 0.00 0.00 0.00 2.17
343 731 4.334443 CCAAATTACTCGTCGCTGAAATG 58.666 43.478 0.00 0.00 0.00 2.32
344 732 4.334443 CAAATTACTCGTCGCTGAAATGG 58.666 43.478 0.00 0.00 0.00 3.16
345 733 3.520290 ATTACTCGTCGCTGAAATGGA 57.480 42.857 0.00 0.00 0.00 3.41
346 734 3.520290 TTACTCGTCGCTGAAATGGAT 57.480 42.857 0.00 0.00 0.00 3.41
347 735 4.642445 TTACTCGTCGCTGAAATGGATA 57.358 40.909 0.00 0.00 0.00 2.59
348 736 3.735237 ACTCGTCGCTGAAATGGATAT 57.265 42.857 0.00 0.00 0.00 1.63
349 737 4.848562 ACTCGTCGCTGAAATGGATATA 57.151 40.909 0.00 0.00 0.00 0.86
350 738 5.392767 ACTCGTCGCTGAAATGGATATAT 57.607 39.130 0.00 0.00 0.00 0.86
351 739 5.403246 ACTCGTCGCTGAAATGGATATATC 58.597 41.667 3.96 3.96 0.00 1.63
352 740 5.184096 ACTCGTCGCTGAAATGGATATATCT 59.816 40.000 12.42 0.00 0.00 1.98
353 741 6.374613 ACTCGTCGCTGAAATGGATATATCTA 59.625 38.462 12.42 6.97 0.00 1.98
354 742 6.786207 TCGTCGCTGAAATGGATATATCTAG 58.214 40.000 12.42 3.81 0.00 2.43
355 743 6.598064 TCGTCGCTGAAATGGATATATCTAGA 59.402 38.462 12.42 0.00 0.00 2.43
356 744 7.120726 TCGTCGCTGAAATGGATATATCTAGAA 59.879 37.037 12.42 0.00 0.00 2.10
357 745 7.219154 CGTCGCTGAAATGGATATATCTAGAAC 59.781 40.741 12.42 3.21 0.00 3.01
358 746 8.247562 GTCGCTGAAATGGATATATCTAGAACT 58.752 37.037 12.42 0.00 0.00 3.01
359 747 9.462606 TCGCTGAAATGGATATATCTAGAACTA 57.537 33.333 12.42 0.00 0.00 2.24
388 776 6.960468 ACATCTAGATATATCCATACGTGCG 58.040 40.000 4.54 0.00 0.00 5.34
389 777 6.766467 ACATCTAGATATATCCATACGTGCGA 59.234 38.462 4.54 0.00 0.00 5.10
390 778 6.600246 TCTAGATATATCCATACGTGCGAC 57.400 41.667 9.18 0.00 0.00 5.19
391 779 6.110707 TCTAGATATATCCATACGTGCGACA 58.889 40.000 9.18 0.00 0.00 4.35
392 780 5.638596 AGATATATCCATACGTGCGACAA 57.361 39.130 9.18 0.00 0.00 3.18
393 781 5.641709 AGATATATCCATACGTGCGACAAG 58.358 41.667 9.18 0.00 0.00 3.16
394 782 3.728076 ATATCCATACGTGCGACAAGT 57.272 42.857 0.00 0.00 0.00 3.16
395 783 4.841443 ATATCCATACGTGCGACAAGTA 57.159 40.909 0.00 7.72 33.49 2.24
396 784 3.513680 ATCCATACGTGCGACAAGTAA 57.486 42.857 0.00 0.00 32.82 2.24
397 785 3.513680 TCCATACGTGCGACAAGTAAT 57.486 42.857 0.00 0.00 32.82 1.89
398 786 3.852286 TCCATACGTGCGACAAGTAATT 58.148 40.909 0.00 0.00 32.82 1.40
399 787 3.861113 TCCATACGTGCGACAAGTAATTC 59.139 43.478 0.00 0.00 32.82 2.17
400 788 3.301579 CCATACGTGCGACAAGTAATTCG 60.302 47.826 0.00 0.00 32.82 3.34
401 789 1.065358 ACGTGCGACAAGTAATTCGG 58.935 50.000 0.00 0.00 35.73 4.30
402 790 1.336148 ACGTGCGACAAGTAATTCGGA 60.336 47.619 0.00 0.00 35.73 4.55
403 791 1.722464 CGTGCGACAAGTAATTCGGAA 59.278 47.619 0.00 0.00 37.32 4.30
404 792 2.471749 CGTGCGACAAGTAATTCGGAAC 60.472 50.000 0.00 0.00 37.32 3.62
448 836 6.612306 TCTTATCGATGGTCAACATAGATCG 58.388 40.000 8.54 0.00 45.22 3.69
482 870 7.171508 CGCATTAGACACTACATTTATGGACAT 59.828 37.037 0.00 0.00 0.00 3.06
564 958 7.172703 ACGAGTAATCCAAACTTCGAAAGATTT 59.827 33.333 0.00 0.00 41.60 2.17
660 1072 0.594602 GCTCCGTAACCAAAACCACC 59.405 55.000 0.00 0.00 0.00 4.61
661 1073 1.970092 CTCCGTAACCAAAACCACCA 58.030 50.000 0.00 0.00 0.00 4.17
662 1074 1.605232 CTCCGTAACCAAAACCACCAC 59.395 52.381 0.00 0.00 0.00 4.16
663 1075 0.669619 CCGTAACCAAAACCACCACC 59.330 55.000 0.00 0.00 0.00 4.61
664 1076 0.669619 CGTAACCAAAACCACCACCC 59.330 55.000 0.00 0.00 0.00 4.61
665 1077 1.042229 GTAACCAAAACCACCACCCC 58.958 55.000 0.00 0.00 0.00 4.95
666 1078 0.635009 TAACCAAAACCACCACCCCA 59.365 50.000 0.00 0.00 0.00 4.96
667 1079 0.030603 AACCAAAACCACCACCCCAT 60.031 50.000 0.00 0.00 0.00 4.00
668 1080 0.030603 ACCAAAACCACCACCCCATT 60.031 50.000 0.00 0.00 0.00 3.16
669 1081 1.135960 CCAAAACCACCACCCCATTT 58.864 50.000 0.00 0.00 0.00 2.32
670 1082 2.330216 CCAAAACCACCACCCCATTTA 58.670 47.619 0.00 0.00 0.00 1.40
671 1083 2.706190 CCAAAACCACCACCCCATTTAA 59.294 45.455 0.00 0.00 0.00 1.52
672 1084 3.329225 CCAAAACCACCACCCCATTTAAT 59.671 43.478 0.00 0.00 0.00 1.40
673 1085 4.564613 CCAAAACCACCACCCCATTTAATC 60.565 45.833 0.00 0.00 0.00 1.75
674 1086 3.845109 AACCACCACCCCATTTAATCT 57.155 42.857 0.00 0.00 0.00 2.40
675 1087 3.100207 ACCACCACCCCATTTAATCTG 57.900 47.619 0.00 0.00 0.00 2.90
676 1088 2.381961 ACCACCACCCCATTTAATCTGT 59.618 45.455 0.00 0.00 0.00 3.41
677 1089 3.181412 ACCACCACCCCATTTAATCTGTT 60.181 43.478 0.00 0.00 0.00 3.16
678 1090 3.837731 CCACCACCCCATTTAATCTGTTT 59.162 43.478 0.00 0.00 0.00 2.83
679 1091 5.020132 CCACCACCCCATTTAATCTGTTTA 58.980 41.667 0.00 0.00 0.00 2.01
680 1092 5.660864 CCACCACCCCATTTAATCTGTTTAT 59.339 40.000 0.00 0.00 0.00 1.40
681 1093 6.836527 CCACCACCCCATTTAATCTGTTTATA 59.163 38.462 0.00 0.00 0.00 0.98
682 1094 7.014230 CCACCACCCCATTTAATCTGTTTATAG 59.986 40.741 0.00 0.00 0.00 1.31
683 1095 7.777910 CACCACCCCATTTAATCTGTTTATAGA 59.222 37.037 0.00 0.00 0.00 1.98
684 1096 8.340757 ACCACCCCATTTAATCTGTTTATAGAA 58.659 33.333 0.00 0.00 0.00 2.10
685 1097 9.196139 CCACCCCATTTAATCTGTTTATAGAAA 57.804 33.333 0.00 0.00 0.00 2.52
789 1213 1.454479 CCCGCAATCCAGCCAATCT 60.454 57.895 0.00 0.00 0.00 2.40
790 1214 0.179020 CCCGCAATCCAGCCAATCTA 60.179 55.000 0.00 0.00 0.00 1.98
791 1215 1.233019 CCGCAATCCAGCCAATCTAG 58.767 55.000 0.00 0.00 0.00 2.43
792 1216 1.475751 CCGCAATCCAGCCAATCTAGT 60.476 52.381 0.00 0.00 0.00 2.57
793 1217 2.224281 CCGCAATCCAGCCAATCTAGTA 60.224 50.000 0.00 0.00 0.00 1.82
794 1218 2.802816 CGCAATCCAGCCAATCTAGTAC 59.197 50.000 0.00 0.00 0.00 2.73
795 1219 3.493350 CGCAATCCAGCCAATCTAGTACT 60.493 47.826 0.00 0.00 0.00 2.73
796 1220 4.262036 CGCAATCCAGCCAATCTAGTACTA 60.262 45.833 1.89 1.89 0.00 1.82
797 1221 5.567623 CGCAATCCAGCCAATCTAGTACTAT 60.568 44.000 2.33 0.00 0.00 2.12
798 1222 5.872070 GCAATCCAGCCAATCTAGTACTATC 59.128 44.000 2.33 0.00 0.00 2.08
799 1223 6.295575 GCAATCCAGCCAATCTAGTACTATCT 60.296 42.308 2.33 0.00 0.00 1.98
800 1224 7.093727 GCAATCCAGCCAATCTAGTACTATCTA 60.094 40.741 2.33 0.00 0.00 1.98
801 1225 8.976353 CAATCCAGCCAATCTAGTACTATCTAT 58.024 37.037 2.33 0.00 0.00 1.98
802 1226 7.946381 TCCAGCCAATCTAGTACTATCTATG 57.054 40.000 2.33 1.22 0.00 2.23
1076 1537 0.537653 CCGTTTCTTCTCCTCTCCCC 59.462 60.000 0.00 0.00 0.00 4.81
1077 1538 1.267121 CGTTTCTTCTCCTCTCCCCA 58.733 55.000 0.00 0.00 0.00 4.96
1078 1539 1.066787 CGTTTCTTCTCCTCTCCCCAC 60.067 57.143 0.00 0.00 0.00 4.61
1079 1540 1.279558 GTTTCTTCTCCTCTCCCCACC 59.720 57.143 0.00 0.00 0.00 4.61
1080 1541 0.793617 TTCTTCTCCTCTCCCCACCT 59.206 55.000 0.00 0.00 0.00 4.00
1081 1542 0.336737 TCTTCTCCTCTCCCCACCTC 59.663 60.000 0.00 0.00 0.00 3.85
1082 1543 0.689412 CTTCTCCTCTCCCCACCTCC 60.689 65.000 0.00 0.00 0.00 4.30
1083 1544 1.156322 TTCTCCTCTCCCCACCTCCT 61.156 60.000 0.00 0.00 0.00 3.69
1184 1654 3.452786 CCGCCCTCTCTCGCTCAA 61.453 66.667 0.00 0.00 0.00 3.02
1185 1655 2.790791 CCGCCCTCTCTCGCTCAAT 61.791 63.158 0.00 0.00 0.00 2.57
1186 1656 1.299773 CGCCCTCTCTCGCTCAATC 60.300 63.158 0.00 0.00 0.00 2.67
1187 1657 1.068921 GCCCTCTCTCGCTCAATCC 59.931 63.158 0.00 0.00 0.00 3.01
1188 1658 1.398958 GCCCTCTCTCGCTCAATCCT 61.399 60.000 0.00 0.00 0.00 3.24
1189 1659 0.673437 CCCTCTCTCGCTCAATCCTC 59.327 60.000 0.00 0.00 0.00 3.71
1190 1660 0.673437 CCTCTCTCGCTCAATCCTCC 59.327 60.000 0.00 0.00 0.00 4.30
1229 1699 3.349022 TGTTCGTCTGGTTTGGTTTTCT 58.651 40.909 0.00 0.00 0.00 2.52
1247 1717 1.487976 TCTGGTGATCTCATGGCTTCC 59.512 52.381 0.00 0.00 0.00 3.46
1252 1722 2.433604 GTGATCTCATGGCTTCCTCTCA 59.566 50.000 0.00 0.00 0.00 3.27
1308 1790 3.068691 CCCAAGCAGCAGCAGCAT 61.069 61.111 12.92 0.00 45.49 3.79
1316 1798 1.077716 AGCAGCAGCATCAGCATCA 60.078 52.632 3.17 0.00 45.49 3.07
1477 1964 1.082104 GGTTCGGTTTCTTGCAGCG 60.082 57.895 0.00 0.00 36.47 5.18
1483 1970 1.081840 GTTTCTTGCAGCGAGTGGC 60.082 57.895 9.65 0.00 44.05 5.01
1687 2180 2.508887 GACGAGCAGCAGCAGAGG 60.509 66.667 3.17 0.00 45.49 3.69
1747 2240 1.476891 CTCGTTCCCTTCTCCGATGAA 59.523 52.381 0.00 0.00 0.00 2.57
1810 2303 1.039233 TCGTCCGGGACCAGGTAATC 61.039 60.000 21.06 0.17 0.00 1.75
1846 2339 4.868195 GCCACGGCAATTCAGTTC 57.132 55.556 2.36 0.00 41.49 3.01
1847 2340 1.956043 GCCACGGCAATTCAGTTCA 59.044 52.632 2.36 0.00 41.49 3.18
1848 2341 0.109597 GCCACGGCAATTCAGTTCAG 60.110 55.000 2.36 0.00 41.49 3.02
2217 2710 3.255379 GCCGAATCGTGCTCGTCC 61.255 66.667 8.17 0.00 38.33 4.79
2429 2922 2.280797 GTGTTGACAGAGCCGGCA 60.281 61.111 31.54 2.66 0.00 5.69
2496 3002 1.537202 GGCGCCATAGCTTATTCCAAG 59.463 52.381 24.80 0.00 36.60 3.61
2669 3176 1.321474 TAATACTACCCAGCCCGTCG 58.679 55.000 0.00 0.00 0.00 5.12
2679 3186 3.423154 GCCCGTCGAGTGCAAAGG 61.423 66.667 0.00 0.00 0.00 3.11
2680 3187 2.030562 CCCGTCGAGTGCAAAGGT 59.969 61.111 0.00 0.00 0.00 3.50
2681 3188 2.317609 CCCGTCGAGTGCAAAGGTG 61.318 63.158 0.00 0.00 0.00 4.00
2682 3189 1.594293 CCGTCGAGTGCAAAGGTGT 60.594 57.895 0.00 0.00 0.00 4.16
2724 3231 4.060038 TCTTTCTCCGATCATTACTGCC 57.940 45.455 0.00 0.00 0.00 4.85
2727 3234 0.946221 CTCCGATCATTACTGCCGGC 60.946 60.000 22.73 22.73 37.85 6.13
2728 3235 2.310233 CCGATCATTACTGCCGGCG 61.310 63.158 23.90 18.98 33.72 6.46
2733 3240 2.179547 CATTACTGCCGGCGATGCA 61.180 57.895 23.90 9.91 37.17 3.96
2820 3338 7.175293 GGAGTGGTATCAGACTAGATAATCGTT 59.825 40.741 0.00 0.00 32.64 3.85
3004 3522 2.048597 CGTCCTGTGCCGTGCTTA 60.049 61.111 0.00 0.00 0.00 3.09
3146 3664 4.175489 GAGGCACGCGCGAGAGTA 62.175 66.667 39.36 0.00 44.22 2.59
3341 3868 4.910585 GTGATAGCCGCGGGTGGG 62.911 72.222 38.34 7.63 0.00 4.61
3470 4016 1.092348 GCTTACCGCCCCTTTTACTG 58.908 55.000 0.00 0.00 0.00 2.74
3471 4017 1.092348 CTTACCGCCCCTTTTACTGC 58.908 55.000 0.00 0.00 0.00 4.40
3472 4018 0.694196 TTACCGCCCCTTTTACTGCT 59.306 50.000 0.00 0.00 0.00 4.24
3534 4080 1.663445 GGCGATCTTCACGTATCTCCG 60.663 57.143 0.00 0.00 0.00 4.63
3558 4104 4.153256 CGTTGTTTTACGGCTTTATGTCC 58.847 43.478 0.00 0.00 37.86 4.02
3559 4105 4.478699 GTTGTTTTACGGCTTTATGTCCC 58.521 43.478 0.00 0.00 0.00 4.46
3560 4106 3.752665 TGTTTTACGGCTTTATGTCCCA 58.247 40.909 0.00 0.00 0.00 4.37
3561 4107 3.502979 TGTTTTACGGCTTTATGTCCCAC 59.497 43.478 0.00 0.00 0.00 4.61
3562 4108 2.012937 TTACGGCTTTATGTCCCACG 57.987 50.000 0.00 0.00 0.00 4.94
3563 4109 1.184431 TACGGCTTTATGTCCCACGA 58.816 50.000 0.00 0.00 0.00 4.35
3564 4110 0.539986 ACGGCTTTATGTCCCACGAT 59.460 50.000 0.00 0.00 0.00 3.73
3565 4111 1.065709 ACGGCTTTATGTCCCACGATT 60.066 47.619 0.00 0.00 0.00 3.34
3566 4112 1.330521 CGGCTTTATGTCCCACGATTG 59.669 52.381 0.00 0.00 0.00 2.67
3567 4113 1.676006 GGCTTTATGTCCCACGATTGG 59.324 52.381 0.00 0.00 43.50 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.498167 GTGCTCGCATTATTCCTGGAT 58.502 47.619 0.00 0.00 0.00 3.41
1 2 1.475034 GGTGCTCGCATTATTCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
2 3 0.947244 GGTGCTCGCATTATTCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
3 4 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
4 5 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
5 6 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
6 7 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
7 8 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
8 9 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
9 10 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
10 11 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
11 12 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
12 13 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
13 14 0.169009 GTTCAAATCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
14 15 0.804989 GGTTCAAATCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
15 16 1.177401 GGGTTCAAATCCTGGTGCTC 58.823 55.000 0.00 0.00 0.00 4.26
16 17 0.779997 AGGGTTCAAATCCTGGTGCT 59.220 50.000 0.00 0.00 38.36 4.40
17 18 3.363787 AGGGTTCAAATCCTGGTGC 57.636 52.632 0.00 0.00 38.36 5.01
33 34 1.613061 GTATCCCCAACCCACCAGG 59.387 63.158 0.00 0.00 43.78 4.45
34 35 1.211567 TGGTATCCCCAACCCACCAG 61.212 60.000 0.00 0.00 41.50 4.00
35 36 1.151565 TGGTATCCCCAACCCACCA 60.152 57.895 0.00 0.00 41.50 4.17
36 37 3.844063 TGGTATCCCCAACCCACC 58.156 61.111 0.00 0.00 41.50 4.61
43 44 0.912487 GGTGGACAGTGGTATCCCCA 60.912 60.000 0.00 0.00 42.51 4.96
44 45 0.620700 AGGTGGACAGTGGTATCCCC 60.621 60.000 0.00 0.00 33.69 4.81
45 46 2.169978 GTTAGGTGGACAGTGGTATCCC 59.830 54.545 0.00 0.00 33.69 3.85
46 47 2.169978 GGTTAGGTGGACAGTGGTATCC 59.830 54.545 0.00 0.00 35.37 2.59
47 48 2.835764 TGGTTAGGTGGACAGTGGTATC 59.164 50.000 0.00 0.00 0.00 2.24
48 49 2.910544 TGGTTAGGTGGACAGTGGTAT 58.089 47.619 0.00 0.00 0.00 2.73
49 50 2.402182 TGGTTAGGTGGACAGTGGTA 57.598 50.000 0.00 0.00 0.00 3.25
50 51 1.628846 GATGGTTAGGTGGACAGTGGT 59.371 52.381 0.00 0.00 0.00 4.16
51 52 1.909302 AGATGGTTAGGTGGACAGTGG 59.091 52.381 0.00 0.00 0.00 4.00
52 53 2.567169 TGAGATGGTTAGGTGGACAGTG 59.433 50.000 0.00 0.00 0.00 3.66
53 54 2.902608 TGAGATGGTTAGGTGGACAGT 58.097 47.619 0.00 0.00 0.00 3.55
54 55 3.600388 GTTGAGATGGTTAGGTGGACAG 58.400 50.000 0.00 0.00 0.00 3.51
55 56 2.304761 GGTTGAGATGGTTAGGTGGACA 59.695 50.000 0.00 0.00 0.00 4.02
56 57 2.304761 TGGTTGAGATGGTTAGGTGGAC 59.695 50.000 0.00 0.00 0.00 4.02
57 58 2.304761 GTGGTTGAGATGGTTAGGTGGA 59.695 50.000 0.00 0.00 0.00 4.02
58 59 2.039746 TGTGGTTGAGATGGTTAGGTGG 59.960 50.000 0.00 0.00 0.00 4.61
59 60 3.338249 CTGTGGTTGAGATGGTTAGGTG 58.662 50.000 0.00 0.00 0.00 4.00
60 61 2.305927 CCTGTGGTTGAGATGGTTAGGT 59.694 50.000 0.00 0.00 0.00 3.08
61 62 2.305927 ACCTGTGGTTGAGATGGTTAGG 59.694 50.000 0.00 0.00 27.29 2.69
62 63 3.703001 ACCTGTGGTTGAGATGGTTAG 57.297 47.619 0.00 0.00 27.29 2.34
74 75 0.250124 TTCGCGAATCAACCTGTGGT 60.250 50.000 19.38 0.00 37.65 4.16
75 76 0.443869 CTTCGCGAATCAACCTGTGG 59.556 55.000 23.67 2.23 0.00 4.17
76 77 0.443869 CCTTCGCGAATCAACCTGTG 59.556 55.000 23.67 6.99 0.00 3.66
77 78 0.320374 TCCTTCGCGAATCAACCTGT 59.680 50.000 23.67 0.00 0.00 4.00
78 79 1.594862 GATCCTTCGCGAATCAACCTG 59.405 52.381 23.67 8.55 0.00 4.00
79 80 1.482593 AGATCCTTCGCGAATCAACCT 59.517 47.619 23.67 12.77 0.00 3.50
80 81 1.941325 AGATCCTTCGCGAATCAACC 58.059 50.000 23.67 10.71 0.00 3.77
81 82 4.260253 GGTTTAGATCCTTCGCGAATCAAC 60.260 45.833 23.67 16.42 0.00 3.18
82 83 3.869246 GGTTTAGATCCTTCGCGAATCAA 59.131 43.478 23.67 11.10 0.00 2.57
83 84 3.118920 TGGTTTAGATCCTTCGCGAATCA 60.119 43.478 23.67 12.21 0.00 2.57
84 85 3.454375 TGGTTTAGATCCTTCGCGAATC 58.546 45.455 23.67 17.09 0.00 2.52
85 86 3.536956 TGGTTTAGATCCTTCGCGAAT 57.463 42.857 23.67 7.72 0.00 3.34
86 87 3.536956 ATGGTTTAGATCCTTCGCGAA 57.463 42.857 22.01 22.01 0.00 4.70
87 88 3.118920 TCAATGGTTTAGATCCTTCGCGA 60.119 43.478 3.71 3.71 0.00 5.87
88 89 3.194861 TCAATGGTTTAGATCCTTCGCG 58.805 45.455 0.00 0.00 0.00 5.87
89 90 6.428159 ACATATCAATGGTTTAGATCCTTCGC 59.572 38.462 0.00 0.00 37.43 4.70
90 91 7.969536 ACATATCAATGGTTTAGATCCTTCG 57.030 36.000 0.00 0.00 37.43 3.79
115 116 2.040412 GGAGGGATCACAACCTTTGTCT 59.960 50.000 0.00 0.00 43.23 3.41
123 124 5.359194 TTTCTAGATGGAGGGATCACAAC 57.641 43.478 0.00 0.00 0.00 3.32
196 197 8.885494 AAGTGATGCTTAAAGTAAATTTGCAA 57.115 26.923 9.04 0.00 34.56 4.08
197 198 8.140628 TGAAGTGATGCTTAAAGTAAATTTGCA 58.859 29.630 9.04 4.44 37.59 4.08
234 622 6.016213 TCGTATACCTCTTTAATGCGCATA 57.984 37.500 25.61 5.93 0.00 3.14
239 627 9.434559 GAATTTGTTCGTATACCTCTTTAATGC 57.565 33.333 0.00 0.00 0.00 3.56
311 699 1.835531 GAGTAATTTGGGACGGAGGGA 59.164 52.381 0.00 0.00 0.00 4.20
312 700 1.472728 CGAGTAATTTGGGACGGAGGG 60.473 57.143 0.00 0.00 0.00 4.30
313 701 1.206371 ACGAGTAATTTGGGACGGAGG 59.794 52.381 0.00 0.00 0.00 4.30
314 702 2.537401 GACGAGTAATTTGGGACGGAG 58.463 52.381 0.00 0.00 0.00 4.63
315 703 1.135315 CGACGAGTAATTTGGGACGGA 60.135 52.381 0.00 0.00 0.00 4.69
316 704 1.274596 CGACGAGTAATTTGGGACGG 58.725 55.000 0.00 0.00 0.00 4.79
317 705 0.643820 GCGACGAGTAATTTGGGACG 59.356 55.000 0.00 0.00 0.00 4.79
318 706 1.659098 CAGCGACGAGTAATTTGGGAC 59.341 52.381 0.00 0.00 0.00 4.46
319 707 1.546923 TCAGCGACGAGTAATTTGGGA 59.453 47.619 0.00 0.00 0.00 4.37
320 708 2.004583 TCAGCGACGAGTAATTTGGG 57.995 50.000 0.00 0.00 0.00 4.12
321 709 4.334443 CATTTCAGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
322 710 4.092821 TCCATTTCAGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
323 711 4.250464 TCCATTTCAGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
324 712 3.857052 TCCATTTCAGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
325 713 3.520290 TCCATTTCAGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
326 714 3.520290 ATCCATTTCAGCGACGAGTAA 57.480 42.857 0.00 0.00 0.00 2.24
327 715 4.848562 ATATCCATTTCAGCGACGAGTA 57.151 40.909 0.00 0.00 0.00 2.59
328 716 3.735237 ATATCCATTTCAGCGACGAGT 57.265 42.857 0.00 0.00 0.00 4.18
329 717 5.645624 AGATATATCCATTTCAGCGACGAG 58.354 41.667 9.18 0.00 0.00 4.18
330 718 5.644977 AGATATATCCATTTCAGCGACGA 57.355 39.130 9.18 0.00 0.00 4.20
331 719 6.786207 TCTAGATATATCCATTTCAGCGACG 58.214 40.000 9.18 0.00 0.00 5.12
332 720 8.247562 AGTTCTAGATATATCCATTTCAGCGAC 58.752 37.037 9.18 1.73 0.00 5.19
333 721 8.354711 AGTTCTAGATATATCCATTTCAGCGA 57.645 34.615 9.18 0.00 0.00 4.93
362 750 8.722394 CGCACGTATGGATATATCTAGATGTAT 58.278 37.037 18.82 18.82 29.44 2.29
363 751 7.929785 TCGCACGTATGGATATATCTAGATGTA 59.070 37.037 15.79 13.32 29.44 2.29
364 752 6.766467 TCGCACGTATGGATATATCTAGATGT 59.234 38.462 15.79 11.55 30.36 3.06
365 753 7.072647 GTCGCACGTATGGATATATCTAGATG 58.927 42.308 15.79 11.33 0.00 2.90
366 754 6.766467 TGTCGCACGTATGGATATATCTAGAT 59.234 38.462 10.73 10.73 0.00 1.98
367 755 6.110707 TGTCGCACGTATGGATATATCTAGA 58.889 40.000 12.42 0.76 0.00 2.43
368 756 6.359480 TGTCGCACGTATGGATATATCTAG 57.641 41.667 12.42 0.00 0.00 2.43
369 757 6.373495 ACTTGTCGCACGTATGGATATATCTA 59.627 38.462 12.42 6.97 0.00 1.98
370 758 5.183331 ACTTGTCGCACGTATGGATATATCT 59.817 40.000 12.42 0.00 0.00 1.98
371 759 5.399858 ACTTGTCGCACGTATGGATATATC 58.600 41.667 3.96 3.96 0.00 1.63
372 760 5.386958 ACTTGTCGCACGTATGGATATAT 57.613 39.130 0.00 0.00 0.00 0.86
373 761 4.841443 ACTTGTCGCACGTATGGATATA 57.159 40.909 0.00 0.00 0.00 0.86
374 762 3.728076 ACTTGTCGCACGTATGGATAT 57.272 42.857 0.00 0.00 0.00 1.63
375 763 4.635833 TTACTTGTCGCACGTATGGATA 57.364 40.909 0.00 0.00 0.00 2.59
376 764 3.513680 TTACTTGTCGCACGTATGGAT 57.486 42.857 0.00 0.00 0.00 3.41
377 765 3.513680 ATTACTTGTCGCACGTATGGA 57.486 42.857 0.00 0.00 0.00 3.41
378 766 3.301579 CGAATTACTTGTCGCACGTATGG 60.302 47.826 0.00 0.00 0.00 2.74
379 767 3.301579 CCGAATTACTTGTCGCACGTATG 60.302 47.826 0.00 0.00 35.93 2.39
380 768 2.855963 CCGAATTACTTGTCGCACGTAT 59.144 45.455 0.00 0.00 35.93 3.06
381 769 2.095314 TCCGAATTACTTGTCGCACGTA 60.095 45.455 0.00 0.00 35.93 3.57
382 770 1.065358 CCGAATTACTTGTCGCACGT 58.935 50.000 0.00 0.00 35.93 4.49
383 771 1.342555 TCCGAATTACTTGTCGCACG 58.657 50.000 0.00 0.00 35.93 5.34
384 772 2.471749 CGTTCCGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 35.93 5.34
385 773 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
386 774 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
387 775 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
388 776 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
389 777 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
390 778 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
391 779 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
392 780 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
393 781 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
394 782 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
395 783 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
396 784 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
397 785 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
398 786 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
399 787 0.822164 AATGTACTCCCTCCGTTCCG 59.178 55.000 0.00 0.00 0.00 4.30
400 788 4.100498 TCAATAATGTACTCCCTCCGTTCC 59.900 45.833 0.00 0.00 0.00 3.62
401 789 5.272283 TCAATAATGTACTCCCTCCGTTC 57.728 43.478 0.00 0.00 0.00 3.95
402 790 5.602978 AGATCAATAATGTACTCCCTCCGTT 59.397 40.000 0.00 0.00 0.00 4.44
403 791 5.148502 AGATCAATAATGTACTCCCTCCGT 58.851 41.667 0.00 0.00 0.00 4.69
404 792 5.730296 AGATCAATAATGTACTCCCTCCG 57.270 43.478 0.00 0.00 0.00 4.63
405 793 7.976734 CGATAAGATCAATAATGTACTCCCTCC 59.023 40.741 0.00 0.00 0.00 4.30
406 794 8.740906 TCGATAAGATCAATAATGTACTCCCTC 58.259 37.037 0.00 0.00 0.00 4.30
407 795 8.651589 TCGATAAGATCAATAATGTACTCCCT 57.348 34.615 0.00 0.00 0.00 4.20
408 796 9.307121 CATCGATAAGATCAATAATGTACTCCC 57.693 37.037 0.00 0.00 37.52 4.30
409 797 9.307121 CCATCGATAAGATCAATAATGTACTCC 57.693 37.037 0.00 0.00 37.52 3.85
410 798 9.862371 ACCATCGATAAGATCAATAATGTACTC 57.138 33.333 0.00 0.00 37.52 2.59
411 799 9.862371 GACCATCGATAAGATCAATAATGTACT 57.138 33.333 0.00 0.00 37.52 2.73
412 800 9.639601 TGACCATCGATAAGATCAATAATGTAC 57.360 33.333 0.00 0.00 37.52 2.90
414 802 8.993121 GTTGACCATCGATAAGATCAATAATGT 58.007 33.333 0.00 0.00 37.52 2.71
415 803 8.992073 TGTTGACCATCGATAAGATCAATAATG 58.008 33.333 0.00 0.00 37.52 1.90
420 808 7.951591 TCTATGTTGACCATCGATAAGATCAA 58.048 34.615 0.00 3.28 37.52 2.57
471 859 5.314306 AGATTGCCCCTCTATGTCCATAAAT 59.686 40.000 0.00 0.00 0.00 1.40
482 870 6.377146 GTGTTTATCAAAAGATTGCCCCTCTA 59.623 38.462 0.00 0.00 36.45 2.43
564 958 0.311165 GAGGCTCGTAGCTTCGCATA 59.689 55.000 8.00 0.00 41.99 3.14
684 1096 4.917040 AGGGGATTAAAATGGGGTGTTTTT 59.083 37.500 0.00 0.00 31.71 1.94
685 1097 4.288366 CAGGGGATTAAAATGGGGTGTTTT 59.712 41.667 0.00 0.00 33.67 2.43
686 1098 3.843619 CAGGGGATTAAAATGGGGTGTTT 59.156 43.478 0.00 0.00 0.00 2.83
687 1099 3.449918 CAGGGGATTAAAATGGGGTGTT 58.550 45.455 0.00 0.00 0.00 3.32
688 1100 2.892301 GCAGGGGATTAAAATGGGGTGT 60.892 50.000 0.00 0.00 0.00 4.16
789 1213 7.522073 CGCGGGGTTAAAACATAGATAGTACTA 60.522 40.741 4.77 4.77 0.00 1.82
790 1214 6.519382 GCGGGGTTAAAACATAGATAGTACT 58.481 40.000 0.00 0.00 0.00 2.73
791 1215 5.403466 CGCGGGGTTAAAACATAGATAGTAC 59.597 44.000 0.00 0.00 0.00 2.73
792 1216 5.301551 TCGCGGGGTTAAAACATAGATAGTA 59.698 40.000 6.13 0.00 0.00 1.82
793 1217 4.099881 TCGCGGGGTTAAAACATAGATAGT 59.900 41.667 6.13 0.00 0.00 2.12
794 1218 4.624015 TCGCGGGGTTAAAACATAGATAG 58.376 43.478 6.13 0.00 0.00 2.08
795 1219 4.099881 ACTCGCGGGGTTAAAACATAGATA 59.900 41.667 12.42 0.00 0.00 1.98
796 1220 3.118519 ACTCGCGGGGTTAAAACATAGAT 60.119 43.478 12.42 0.00 0.00 1.98
797 1221 2.234414 ACTCGCGGGGTTAAAACATAGA 59.766 45.455 12.42 0.00 0.00 1.98
798 1222 2.624636 ACTCGCGGGGTTAAAACATAG 58.375 47.619 12.42 0.00 0.00 2.23
799 1223 2.766345 ACTCGCGGGGTTAAAACATA 57.234 45.000 12.42 0.00 0.00 2.29
800 1224 2.766345 TACTCGCGGGGTTAAAACAT 57.234 45.000 12.42 0.00 0.00 2.71
801 1225 2.540265 TTACTCGCGGGGTTAAAACA 57.460 45.000 12.42 0.00 0.00 2.83
802 1226 4.424061 AAATTACTCGCGGGGTTAAAAC 57.576 40.909 12.42 0.00 0.00 2.43
1076 1537 2.112190 GTTAAGGAGGAGGAGGAGGTG 58.888 57.143 0.00 0.00 0.00 4.00
1077 1538 1.722851 TGTTAAGGAGGAGGAGGAGGT 59.277 52.381 0.00 0.00 0.00 3.85
1078 1539 2.552093 TGTTAAGGAGGAGGAGGAGG 57.448 55.000 0.00 0.00 0.00 4.30
1079 1540 4.962995 TGTTATGTTAAGGAGGAGGAGGAG 59.037 45.833 0.00 0.00 0.00 3.69
1080 1541 4.955335 TGTTATGTTAAGGAGGAGGAGGA 58.045 43.478 0.00 0.00 0.00 3.71
1081 1542 5.693769 TTGTTATGTTAAGGAGGAGGAGG 57.306 43.478 0.00 0.00 0.00 4.30
1082 1543 6.058183 CCATTGTTATGTTAAGGAGGAGGAG 58.942 44.000 0.00 0.00 0.00 3.69
1083 1544 5.631481 GCCATTGTTATGTTAAGGAGGAGGA 60.631 44.000 0.00 0.00 0.00 3.71
1181 1651 1.909302 GTGGTGGAAGAGGAGGATTGA 59.091 52.381 0.00 0.00 0.00 2.57
1182 1652 1.912043 AGTGGTGGAAGAGGAGGATTG 59.088 52.381 0.00 0.00 0.00 2.67
1183 1653 1.912043 CAGTGGTGGAAGAGGAGGATT 59.088 52.381 0.00 0.00 0.00 3.01
1184 1654 1.577736 CAGTGGTGGAAGAGGAGGAT 58.422 55.000 0.00 0.00 0.00 3.24
1185 1655 1.194781 GCAGTGGTGGAAGAGGAGGA 61.195 60.000 0.00 0.00 0.00 3.71
1186 1656 1.298014 GCAGTGGTGGAAGAGGAGG 59.702 63.158 0.00 0.00 0.00 4.30
1187 1657 0.036577 CTGCAGTGGTGGAAGAGGAG 60.037 60.000 5.25 0.00 0.00 3.69
1188 1658 2.061220 CTGCAGTGGTGGAAGAGGA 58.939 57.895 5.25 0.00 0.00 3.71
1189 1659 1.673665 GCTGCAGTGGTGGAAGAGG 60.674 63.158 16.64 0.00 0.00 3.69
1190 1660 0.954449 CAGCTGCAGTGGTGGAAGAG 60.954 60.000 16.64 0.00 0.00 2.85
1229 1699 1.487976 GAGGAAGCCATGAGATCACCA 59.512 52.381 0.00 0.00 0.00 4.17
1247 1717 3.429547 CGGGTCACCTCTGTAAATGAGAG 60.430 52.174 0.00 0.00 37.33 3.20
1252 1722 1.831736 CTCCGGGTCACCTCTGTAAAT 59.168 52.381 0.00 0.00 33.28 1.40
1430 1912 3.111536 ACAATCCGTGAACCGTACG 57.888 52.632 8.69 8.69 40.98 3.67
1477 1964 1.092345 GCTTCCTCCGATTGCCACTC 61.092 60.000 0.00 0.00 0.00 3.51
1483 1970 3.929948 GCGCGCTTCCTCCGATTG 61.930 66.667 26.67 0.00 0.00 2.67
1672 2165 4.754667 TGCCTCTGCTGCTGCTCG 62.755 66.667 17.00 7.98 40.48 5.03
1687 2180 5.448632 CGGGTAACACAAGGAATTAATCTGC 60.449 44.000 0.00 0.00 39.74 4.26
1747 2240 0.811616 GCTTCATCTGTCCGGCGAAT 60.812 55.000 9.30 0.00 0.00 3.34
1835 2328 1.668047 GCACAGCCTGAACTGAATTGC 60.668 52.381 0.00 0.00 40.25 3.56
1838 2331 1.580845 GCGCACAGCCTGAACTGAAT 61.581 55.000 0.30 0.00 40.25 2.57
1840 2333 2.666190 GCGCACAGCCTGAACTGA 60.666 61.111 0.30 0.00 40.25 3.41
1989 2482 3.665675 CTCCAACGCCTTCTCCCGG 62.666 68.421 0.00 0.00 0.00 5.73
2217 2710 2.322422 CGAGGGTCTACGTACGCG 59.678 66.667 16.72 3.53 44.93 6.01
2298 2791 1.812922 GCTCAGATGTCTGCACGGG 60.813 63.158 5.14 0.00 43.46 5.28
2373 2866 2.690778 GGTCCTCACGCAATGGCAC 61.691 63.158 0.00 0.00 41.24 5.01
2496 3002 8.977412 TCCATTTTAGGACTATTTTTCCATTCC 58.023 33.333 0.00 0.00 35.33 3.01
2669 3176 2.859806 GCATTCACACACCTTTGCACTC 60.860 50.000 0.00 0.00 0.00 3.51
2679 3186 3.668191 CGTTTAACCATGCATTCACACAC 59.332 43.478 0.00 0.00 0.00 3.82
2680 3187 3.316588 ACGTTTAACCATGCATTCACACA 59.683 39.130 0.00 0.00 0.00 3.72
2681 3188 3.896122 ACGTTTAACCATGCATTCACAC 58.104 40.909 0.00 0.00 0.00 3.82
2682 3189 4.277174 AGAACGTTTAACCATGCATTCACA 59.723 37.500 0.46 0.00 0.00 3.58
2724 3231 0.319040 AGTATAGCACTGCATCGCCG 60.319 55.000 3.30 0.00 35.62 6.46
2733 3240 3.961408 CAACCCTCCTACAGTATAGCACT 59.039 47.826 0.00 0.00 38.32 4.40
2739 3256 3.055094 CACAAGCAACCCTCCTACAGTAT 60.055 47.826 0.00 0.00 0.00 2.12
2820 3338 0.874390 GCGATCACTTGCAGTTTGGA 59.126 50.000 0.00 0.00 0.00 3.53
2962 3480 4.832608 CTCCTAACCCGGCGGTGC 62.833 72.222 26.32 0.00 43.71 5.01
2963 3481 4.157120 CCTCCTAACCCGGCGGTG 62.157 72.222 26.32 18.46 43.71 4.94
2965 3483 3.537874 CTCCTCCTAACCCGGCGG 61.538 72.222 21.46 21.46 0.00 6.13
2966 3484 2.758737 ACTCCTCCTAACCCGGCG 60.759 66.667 0.00 0.00 0.00 6.46
2967 3485 2.901042 CACTCCTCCTAACCCGGC 59.099 66.667 0.00 0.00 0.00 6.13
2968 3486 2.901042 GCACTCCTCCTAACCCGG 59.099 66.667 0.00 0.00 0.00 5.73
2969 3487 2.494918 CGCACTCCTCCTAACCCG 59.505 66.667 0.00 0.00 0.00 5.28
3004 3522 2.094904 CCGAAACGGCCGAATCATT 58.905 52.632 35.90 17.66 41.17 2.57
3115 3633 0.891373 TGCCTCTCCACTCTTCTTCG 59.109 55.000 0.00 0.00 0.00 3.79
3452 3998 1.092348 GCAGTAAAAGGGGCGGTAAG 58.908 55.000 0.00 0.00 0.00 2.34
3489 4035 2.404789 CAACGACGATGGCATGGC 59.595 61.111 13.29 13.29 0.00 4.40
3490 4036 0.809636 TAGCAACGACGATGGCATGG 60.810 55.000 3.81 6.26 0.00 3.66
3491 4037 1.193203 GATAGCAACGACGATGGCATG 59.807 52.381 3.81 0.00 0.00 4.06
3492 4038 1.502231 GATAGCAACGACGATGGCAT 58.498 50.000 0.00 0.00 0.00 4.40
3493 4039 0.529773 GGATAGCAACGACGATGGCA 60.530 55.000 0.00 0.00 0.00 4.92
3550 4096 2.092646 CCCTCCAATCGTGGGACATAAA 60.093 50.000 0.00 0.00 46.81 1.40
3551 4097 1.488812 CCCTCCAATCGTGGGACATAA 59.511 52.381 0.00 0.00 46.81 1.90
3552 4098 1.128200 CCCTCCAATCGTGGGACATA 58.872 55.000 0.00 0.00 46.81 2.29
3553 4099 1.635817 CCCCTCCAATCGTGGGACAT 61.636 60.000 0.00 0.00 46.81 3.06
3554 4100 2.297895 CCCCTCCAATCGTGGGACA 61.298 63.158 0.00 0.00 46.81 4.02
3555 4101 1.993391 TCCCCTCCAATCGTGGGAC 60.993 63.158 0.00 0.00 46.81 4.46
3556 4102 1.993391 GTCCCCTCCAATCGTGGGA 60.993 63.158 0.00 0.00 46.81 4.37
3557 4103 2.590092 GTCCCCTCCAATCGTGGG 59.410 66.667 0.00 0.00 46.01 4.61


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

AutoCloner maintained by Alex Coulton.