Multiple sequence alignment - TraesCS6A01G322500

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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 TraesCS6A01G322500 chr6A 100.000 3787 0 0 1 3787 556554194 556550408 0.000000e+00 6994.0
1 TraesCS6A01G322500 chr6D 92.052 3221 181 42 1 3189 411669375 411666198 0.000000e+00 4460.0
2 TraesCS6A01G322500 chr6D 79.083 349 37 12 3319 3642 411665979 411665642 1.380000e-49 207.0
3 TraesCS6A01G322500 chr6D 88.660 97 11 0 3689 3785 411663872 411663776 6.650000e-23 119.0
4 TraesCS6A01G322500 chr6D 87.629 97 11 1 3689 3785 411635698 411635603 1.110000e-20 111.0
5 TraesCS6A01G322500 chr6D 86.813 91 8 1 3193 3283 411666133 411666047 8.660000e-17 99.0
6 TraesCS6A01G322500 chr6B 91.220 2722 126 44 527 3194 619026172 619023510 0.000000e+00 3598.0
7 TraesCS6A01G322500 chr5D 93.617 47 3 0 3143 3189 467346038 467345992 1.890000e-08 71.3


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 TraesCS6A01G322500 chr6A 556550408 556554194 3786 True 6994.00 6994 100.000 1 3787 1 chr6A.!!$R1 3786
1 TraesCS6A01G322500 chr6D 411663776 411669375 5599 True 1221.25 4460 86.652 1 3785 4 chr6D.!!$R2 3784
2 TraesCS6A01G322500 chr6B 619023510 619026172 2662 True 3598.00 3598 91.220 527 3194 1 chr6B.!!$R1 2667

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
805 824 0.397675 ATCTGAGCCGTCCATCAGGA 60.398 55.0 2.63 0.00 42.62 3.86 F
953 972 0.478507 CCAAAACCTGACCTCCCACT 59.521 55.0 0.00 0.00 0.00 4.00 F
1532 1559 0.767108 CGAAATCGATCGCTCTGACG 59.233 55.0 11.09 7.46 43.02 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1813 1.051812 AGAACTGTGAGTCTGTGGGG 58.948 55.000 0.00 0.00 0.00 4.96 R
2320 2357 1.134128 TGAACCAGAGCAGCAACTGAA 60.134 47.619 17.56 2.33 36.38 3.02 R
3465 3635 0.034337 GTTGGAGGTTGGTGCGACTA 59.966 55.000 0.00 0.00 0.00 2.59 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.228245 GGTGGCAGCTTGAAGTGGA 60.228 57.895 9.90 0.00 0.00 4.02
22 23 0.595095 GTGGCAGCTTGAAGTGGAAG 59.405 55.000 0.00 0.00 0.00 3.46
24 25 1.074405 TGGCAGCTTGAAGTGGAAGAT 59.926 47.619 0.00 0.00 0.00 2.40
41 42 3.444703 AGATGTTGCGTCCATCTACTC 57.555 47.619 9.95 0.00 45.46 2.59
42 43 2.760650 AGATGTTGCGTCCATCTACTCA 59.239 45.455 9.95 0.00 45.46 3.41
43 44 3.386078 AGATGTTGCGTCCATCTACTCAT 59.614 43.478 9.95 0.00 45.46 2.90
44 45 3.165058 TGTTGCGTCCATCTACTCATC 57.835 47.619 0.00 0.00 0.00 2.92
45 46 2.159099 TGTTGCGTCCATCTACTCATCC 60.159 50.000 0.00 0.00 0.00 3.51
50 51 3.218453 CGTCCATCTACTCATCCTCACT 58.782 50.000 0.00 0.00 0.00 3.41
52 53 4.454161 CGTCCATCTACTCATCCTCACTAG 59.546 50.000 0.00 0.00 0.00 2.57
73 74 0.999712 ACCCCCTTTTCGACCATCAT 59.000 50.000 0.00 0.00 0.00 2.45
82 83 5.163713 CCTTTTCGACCATCATTTCTCCTTC 60.164 44.000 0.00 0.00 0.00 3.46
83 84 4.551702 TTCGACCATCATTTCTCCTTCA 57.448 40.909 0.00 0.00 0.00 3.02
87 89 4.684214 CGACCATCATTTCTCCTTCATCCA 60.684 45.833 0.00 0.00 0.00 3.41
91 93 6.010850 CCATCATTTCTCCTTCATCCATCAT 58.989 40.000 0.00 0.00 0.00 2.45
100 102 5.944135 TCCTTCATCCATCATGCTTTATCA 58.056 37.500 0.00 0.00 31.70 2.15
106 108 8.473358 TCATCCATCATGCTTTATCAATCTTT 57.527 30.769 0.00 0.00 31.70 2.52
110 113 7.977293 TCCATCATGCTTTATCAATCTTTGTTG 59.023 33.333 0.00 0.00 0.00 3.33
119 122 8.883954 TTTATCAATCTTTGTTGCAAATCACA 57.116 26.923 0.00 0.00 0.00 3.58
120 123 8.883954 TTATCAATCTTTGTTGCAAATCACAA 57.116 26.923 0.00 0.00 0.00 3.33
131 134 2.801679 GCAAATCACAACCAACACCATG 59.198 45.455 0.00 0.00 0.00 3.66
135 138 2.028130 TCACAACCAACACCATGTTCC 58.972 47.619 0.00 0.00 38.77 3.62
138 141 0.471022 AACCAACACCATGTTCCCCC 60.471 55.000 0.00 0.00 38.77 5.40
140 143 0.611896 CCAACACCATGTTCCCCCTC 60.612 60.000 0.00 0.00 38.77 4.30
154 157 4.724279 TCCCCCTCCTCATATAAAAAGC 57.276 45.455 0.00 0.00 0.00 3.51
161 164 7.119846 CCCCTCCTCATATAAAAAGCTATTTCG 59.880 40.741 0.00 0.00 0.00 3.46
162 165 7.361286 CCCTCCTCATATAAAAAGCTATTTCGC 60.361 40.741 0.00 0.00 0.00 4.70
174 177 9.508567 AAAAAGCTATTTCGCATTCTTTATCTC 57.491 29.630 0.00 0.00 0.00 2.75
176 179 7.792374 AGCTATTTCGCATTCTTTATCTCAA 57.208 32.000 0.00 0.00 0.00 3.02
215 219 9.666626 CGTTCTACAATAAACCAAATGTTAACA 57.333 29.630 11.41 11.41 35.67 2.41
230 234 5.804692 TGTTAACACACGAAAAGACACAT 57.195 34.783 3.59 0.00 0.00 3.21
234 238 8.399425 TGTTAACACACGAAAAGACACATAATT 58.601 29.630 3.59 0.00 0.00 1.40
237 241 7.022055 ACACACGAAAAGACACATAATTTCA 57.978 32.000 0.00 0.00 32.64 2.69
250 256 6.540189 ACACATAATTTCAGTGAGGCTACATC 59.460 38.462 10.39 0.00 37.05 3.06
310 316 2.720915 AGTCTCGTGGTTAGTAGGGAC 58.279 52.381 0.00 0.00 0.00 4.46
317 323 6.100279 TCTCGTGGTTAGTAGGGACTAGAATA 59.900 42.308 0.00 0.00 44.14 1.75
343 349 8.483758 AGAGGTTGGACTATAATTTGTACGAAT 58.516 33.333 2.21 2.21 0.00 3.34
356 362 8.556213 AATTTGTACGAATGAAGCCTACTAAA 57.444 30.769 9.16 0.00 0.00 1.85
358 364 9.826574 ATTTGTACGAATGAAGCCTACTAAATA 57.173 29.630 7.58 0.00 0.00 1.40
417 425 9.996554 TGAATGAGTAGACTTTATTGAACTTCA 57.003 29.630 0.00 0.00 0.00 3.02
441 449 2.792674 TGCGTCTTAACTCGTCACTTTG 59.207 45.455 0.00 0.00 0.00 2.77
444 452 4.039703 CGTCTTAACTCGTCACTTTGTCA 58.960 43.478 0.00 0.00 0.00 3.58
446 454 5.041940 GTCTTAACTCGTCACTTTGTCAGT 58.958 41.667 0.00 0.00 35.35 3.41
447 455 5.173492 GTCTTAACTCGTCACTTTGTCAGTC 59.827 44.000 0.00 0.00 30.92 3.51
457 465 3.245284 CACTTTGTCAGTCGTGTGGTTAG 59.755 47.826 0.00 0.00 30.92 2.34
469 477 3.243101 CGTGTGGTTAGCTATGATCGAGT 60.243 47.826 0.00 0.00 0.00 4.18
472 480 4.036852 TGTGGTTAGCTATGATCGAGTGAG 59.963 45.833 0.00 0.00 0.00 3.51
492 500 9.447040 GAGTGAGGTCTGTTTTAAACATTTAAC 57.553 33.333 11.12 7.42 41.26 2.01
493 501 9.185680 AGTGAGGTCTGTTTTAAACATTTAACT 57.814 29.630 11.12 7.91 41.26 2.24
497 505 8.126700 AGGTCTGTTTTAAACATTTAACTCACG 58.873 33.333 11.12 0.00 41.26 4.35
498 506 7.911727 GGTCTGTTTTAAACATTTAACTCACGT 59.088 33.333 11.12 0.00 41.26 4.49
500 508 7.911205 TCTGTTTTAAACATTTAACTCACGTGG 59.089 33.333 17.00 9.11 41.26 4.94
502 510 6.380095 TTTAAACATTTAACTCACGTGGCT 57.620 33.333 17.00 2.89 32.77 4.75
542 550 7.946776 CCCTAACATCTCAATCCCTAAAATCAT 59.053 37.037 0.00 0.00 0.00 2.45
562 570 8.410673 AATCATTATGTAGTACTCACGGATCT 57.589 34.615 0.00 0.00 0.00 2.75
574 582 2.099263 TCACGGATCTCGGTCATTCTTC 59.901 50.000 8.20 0.00 44.45 2.87
585 593 2.017049 GTCATTCTTCAACCCCGGATG 58.983 52.381 0.73 0.00 0.00 3.51
606 621 8.433421 GGATGTTCTTCCGTATGAATTAAAGA 57.567 34.615 0.00 0.00 31.06 2.52
648 663 4.434989 CGCTATCGTCTCTAGAGGAATTCG 60.435 50.000 19.67 15.12 41.50 3.34
659 674 7.227711 TCTCTAGAGGAATTCGTGATAGTTGAG 59.772 40.741 19.67 4.13 0.00 3.02
708 727 2.125961 GGGAGTAGGACGGCGACAT 61.126 63.158 16.62 8.13 0.00 3.06
710 729 1.027357 GGAGTAGGACGGCGACATTA 58.973 55.000 16.62 0.84 0.00 1.90
742 761 1.270839 TGAAGAAGGGCAGAGGAAACG 60.271 52.381 0.00 0.00 0.00 3.60
805 824 0.397675 ATCTGAGCCGTCCATCAGGA 60.398 55.000 2.63 0.00 42.62 3.86
930 949 1.449246 CTGCTGAGAAGGGCGAAGG 60.449 63.158 0.00 0.00 0.00 3.46
952 971 1.179174 GCCAAAACCTGACCTCCCAC 61.179 60.000 0.00 0.00 0.00 4.61
953 972 0.478507 CCAAAACCTGACCTCCCACT 59.521 55.000 0.00 0.00 0.00 4.00
954 973 1.545651 CCAAAACCTGACCTCCCACTC 60.546 57.143 0.00 0.00 0.00 3.51
957 976 2.122729 CCTGACCTCCCACTCCCA 59.877 66.667 0.00 0.00 0.00 4.37
1257 1284 2.738480 CGACAAGTTCGTCCCCCA 59.262 61.111 0.00 0.00 43.24 4.96
1258 1285 1.070105 CGACAAGTTCGTCCCCCAA 59.930 57.895 0.00 0.00 43.24 4.12
1507 1534 4.520846 GCTCAATTGCGCGACGGG 62.521 66.667 12.10 7.67 0.00 5.28
1532 1559 0.767108 CGAAATCGATCGCTCTGACG 59.233 55.000 11.09 7.46 43.02 4.35
1545 1576 2.796304 CTCTGACGCTCTGATTCTGAC 58.204 52.381 0.00 0.00 0.00 3.51
1782 1813 1.373570 CGAAGTGAGCCCCAAATCTC 58.626 55.000 0.00 0.00 0.00 2.75
1783 1814 1.756430 GAAGTGAGCCCCAAATCTCC 58.244 55.000 0.00 0.00 0.00 3.71
1937 1974 2.183046 GACCTCGGAGCAGCTGAC 59.817 66.667 20.43 10.42 0.00 3.51
2054 2091 4.555511 CGCCAAGGTGAAAGAAAGAAAGAG 60.556 45.833 0.00 0.00 0.00 2.85
2283 2320 3.691342 TCCGGGACCGTGCTTGAG 61.691 66.667 10.17 0.00 37.81 3.02
2317 2354 4.080582 TGCTCCCCGAATCTTCTGAATTTA 60.081 41.667 0.00 0.00 0.00 1.40
2320 2357 6.500589 TCCCCGAATCTTCTGAATTTATCT 57.499 37.500 0.00 0.00 0.00 1.98
2373 2418 4.205065 ACTGGAGCTCTGAATTCTTCTG 57.795 45.455 14.64 0.17 0.00 3.02
2711 2765 2.668550 GAAGTGGAGCGGGCGTTT 60.669 61.111 0.00 0.00 0.00 3.60
2852 2906 4.201589 CGAAAATACACACCTGAAGCTACG 60.202 45.833 0.00 0.00 0.00 3.51
2893 2947 2.554272 CGCTGACCCCGAAAAACG 59.446 61.111 0.00 0.00 42.18 3.60
2901 2955 2.008697 CCCGAAAAACGCAGCAACG 61.009 57.895 0.00 0.00 41.07 4.10
2968 3022 2.223572 GCCATTTTTATGGGAGCTGACG 60.224 50.000 0.00 0.00 41.94 4.35
2971 3025 5.938004 CCATTTTTATGGGAGCTGACGCTT 61.938 45.833 0.00 0.00 39.73 4.68
2972 3026 7.888964 CCATTTTTATGGGAGCTGACGCTTG 62.889 48.000 0.00 0.00 39.73 4.01
2999 3053 3.562182 TCTTTCTGTCACTTTTTCCCCC 58.438 45.455 0.00 0.00 0.00 5.40
3001 3055 3.680777 TTCTGTCACTTTTTCCCCCTT 57.319 42.857 0.00 0.00 0.00 3.95
3002 3056 3.223674 TCTGTCACTTTTTCCCCCTTC 57.776 47.619 0.00 0.00 0.00 3.46
3003 3057 2.783510 TCTGTCACTTTTTCCCCCTTCT 59.216 45.455 0.00 0.00 0.00 2.85
3004 3058 2.887152 CTGTCACTTTTTCCCCCTTCTG 59.113 50.000 0.00 0.00 0.00 3.02
3005 3059 2.512056 TGTCACTTTTTCCCCCTTCTGA 59.488 45.455 0.00 0.00 0.00 3.27
3006 3060 3.053245 TGTCACTTTTTCCCCCTTCTGAA 60.053 43.478 0.00 0.00 0.00 3.02
3007 3061 4.152647 GTCACTTTTTCCCCCTTCTGAAT 58.847 43.478 0.00 0.00 0.00 2.57
3008 3062 4.021981 GTCACTTTTTCCCCCTTCTGAATG 60.022 45.833 0.00 0.00 0.00 2.67
3039 3093 4.035558 TGTTTTCTTGCTCTGCAACACTAG 59.964 41.667 0.45 0.00 43.99 2.57
3079 3133 2.724977 TTTGACGCCAACAACAACAA 57.275 40.000 0.00 0.00 30.88 2.83
3080 3134 1.983972 TTGACGCCAACAACAACAAC 58.016 45.000 0.00 0.00 0.00 3.32
3082 3136 1.269723 TGACGCCAACAACAACAACAA 59.730 42.857 0.00 0.00 0.00 2.83
3083 3137 1.651631 GACGCCAACAACAACAACAAC 59.348 47.619 0.00 0.00 0.00 3.32
3084 3138 1.000163 ACGCCAACAACAACAACAACA 60.000 42.857 0.00 0.00 0.00 3.33
3085 3139 2.061773 CGCCAACAACAACAACAACAA 58.938 42.857 0.00 0.00 0.00 2.83
3086 3140 2.091899 CGCCAACAACAACAACAACAAG 59.908 45.455 0.00 0.00 0.00 3.16
3095 3149 6.481644 ACAACAACAACAACAAGAACAACAAT 59.518 30.769 0.00 0.00 0.00 2.71
3097 3151 8.655092 CAACAACAACAACAAGAACAACAATAT 58.345 29.630 0.00 0.00 0.00 1.28
3098 3152 9.862371 AACAACAACAACAAGAACAACAATATA 57.138 25.926 0.00 0.00 0.00 0.86
3123 3177 8.914213 AGTCATATGGAAGATGGATATCTCTT 57.086 34.615 6.88 6.88 42.80 2.85
3124 3178 8.760735 AGTCATATGGAAGATGGATATCTCTTG 58.239 37.037 10.97 0.00 42.80 3.02
3125 3179 8.538701 GTCATATGGAAGATGGATATCTCTTGT 58.461 37.037 10.97 2.26 42.80 3.16
3126 3180 9.109246 TCATATGGAAGATGGATATCTCTTGTT 57.891 33.333 10.97 1.94 42.80 2.83
3127 3181 9.381033 CATATGGAAGATGGATATCTCTTGTTC 57.619 37.037 10.97 9.06 42.80 3.18
3128 3182 6.179906 TGGAAGATGGATATCTCTTGTTCC 57.820 41.667 18.48 18.48 42.80 3.62
3189 3259 5.585047 CCTATAATAGGGCATAACCGCTTTC 59.415 44.000 0.00 0.00 42.42 2.62
3198 3328 3.189702 GCATAACCGCTTTCTACACCAAA 59.810 43.478 0.00 0.00 0.00 3.28
3227 3357 0.031449 TTTGCAACACTTAAGCGGCC 59.969 50.000 0.00 0.00 0.00 6.13
3230 3360 1.946267 CAACACTTAAGCGGCCGTT 59.054 52.632 28.70 20.13 0.00 4.44
3231 3361 1.149987 CAACACTTAAGCGGCCGTTA 58.850 50.000 28.70 19.93 0.00 3.18
3238 3368 1.590932 TAAGCGGCCGTTACAAAACA 58.409 45.000 28.70 0.03 35.16 2.83
3239 3369 0.739561 AAGCGGCCGTTACAAAACAA 59.260 45.000 28.70 0.00 35.16 2.83
3240 3370 0.739561 AGCGGCCGTTACAAAACAAA 59.260 45.000 28.70 0.00 35.16 2.83
3241 3371 1.134560 AGCGGCCGTTACAAAACAAAA 59.865 42.857 28.70 0.00 35.16 2.44
3250 3380 4.545519 CGTTACAAAACAAAAAGCAGTCGC 60.546 41.667 0.00 0.00 35.16 5.19
3268 3398 4.072088 GCGAACGTCCAACCGCTG 62.072 66.667 0.00 0.00 43.75 5.18
3273 3403 3.803082 CGTCCAACCGCTGCATGG 61.803 66.667 9.19 9.19 35.49 3.66
3285 3415 3.203086 TGCATGGAACCTTCCCGCA 62.203 57.895 12.15 12.15 46.30 5.69
3291 3453 3.175710 AACCTTCCCGCACCACCT 61.176 61.111 0.00 0.00 0.00 4.00
3293 3455 3.322466 CCTTCCCGCACCACCTCT 61.322 66.667 0.00 0.00 0.00 3.69
3295 3457 2.847234 TTCCCGCACCACCTCTGT 60.847 61.111 0.00 0.00 0.00 3.41
3296 3458 2.397413 CTTCCCGCACCACCTCTGTT 62.397 60.000 0.00 0.00 0.00 3.16
3299 3461 3.357079 CGCACCACCTCTGTTGCC 61.357 66.667 0.00 0.00 0.00 4.52
3300 3462 2.203337 GCACCACCTCTGTTGCCA 60.203 61.111 0.00 0.00 0.00 4.92
3301 3463 1.827789 GCACCACCTCTGTTGCCAA 60.828 57.895 0.00 0.00 0.00 4.52
3304 3466 1.688197 CACCACCTCTGTTGCCAAATT 59.312 47.619 0.00 0.00 0.00 1.82
3310 3472 2.233676 CCTCTGTTGCCAAATTTACCCC 59.766 50.000 0.00 0.00 0.00 4.95
3311 3473 3.165071 CTCTGTTGCCAAATTTACCCCT 58.835 45.455 0.00 0.00 0.00 4.79
3313 3475 1.889829 TGTTGCCAAATTTACCCCTCG 59.110 47.619 0.00 0.00 0.00 4.63
3314 3476 1.890489 GTTGCCAAATTTACCCCTCGT 59.110 47.619 0.00 0.00 0.00 4.18
3317 3479 1.403647 GCCAAATTTACCCCTCGTTGC 60.404 52.381 0.00 0.00 0.00 4.17
3368 3530 2.359354 CGTGCAACCCCATTCCGA 60.359 61.111 0.00 0.00 0.00 4.55
3372 3534 2.359354 CAACCCCATTCCGACGCA 60.359 61.111 0.00 0.00 0.00 5.24
3379 3541 1.671054 CATTCCGACGCACCACCTT 60.671 57.895 0.00 0.00 0.00 3.50
3425 3587 1.853319 GATATTCGGCCGTCGCAAG 59.147 57.895 27.15 0.00 39.05 4.01
3436 3606 2.609299 TCGCAAGTCCCCATCCCA 60.609 61.111 0.00 0.00 39.48 4.37
3480 3650 4.164252 CGTAGTCGCACCAACCTC 57.836 61.111 0.00 0.00 0.00 3.85
3481 3651 1.445582 CGTAGTCGCACCAACCTCC 60.446 63.158 0.00 0.00 0.00 4.30
3482 3652 1.669440 GTAGTCGCACCAACCTCCA 59.331 57.895 0.00 0.00 0.00 3.86
3483 3653 0.034337 GTAGTCGCACCAACCTCCAA 59.966 55.000 0.00 0.00 0.00 3.53
3485 3655 2.280524 TCGCACCAACCTCCAACG 60.281 61.111 0.00 0.00 0.00 4.10
3486 3656 4.025401 CGCACCAACCTCCAACGC 62.025 66.667 0.00 0.00 0.00 4.84
3487 3657 3.670377 GCACCAACCTCCAACGCC 61.670 66.667 0.00 0.00 0.00 5.68
3488 3658 3.353836 CACCAACCTCCAACGCCG 61.354 66.667 0.00 0.00 0.00 6.46
3514 3684 1.871080 CAGCACTCCGTTGTCTCTTT 58.129 50.000 0.00 0.00 0.00 2.52
3530 3700 1.135527 TCTTTCTTGTCACCGTGTCGT 59.864 47.619 0.00 0.00 0.00 4.34
3533 3703 1.009335 CTTGTCACCGTGTCGTCGA 60.009 57.895 0.00 0.00 0.00 4.20
3535 3705 1.991099 TTGTCACCGTGTCGTCGACA 61.991 55.000 23.70 23.70 40.50 4.35
3536 3706 1.081641 GTCACCGTGTCGTCGACAT 60.082 57.895 29.19 12.50 44.63 3.06
3537 3707 1.081708 TCACCGTGTCGTCGACATG 60.082 57.895 31.67 31.67 44.63 3.21
3540 3710 3.532792 CGTGTCGTCGACATGCCG 61.533 66.667 29.03 23.54 44.63 5.69
3541 3711 3.838795 GTGTCGTCGACATGCCGC 61.839 66.667 29.19 13.54 44.63 6.53
3568 3755 2.872245 CTCAAGTCCAAAAGCAAGTCGA 59.128 45.455 0.00 0.00 0.00 4.20
3581 3768 1.128188 AAGTCGAGCTTCAAGGGGGT 61.128 55.000 0.00 0.00 30.06 4.95
3582 3769 1.376037 GTCGAGCTTCAAGGGGGTG 60.376 63.158 0.00 0.00 0.00 4.61
3583 3770 2.747855 CGAGCTTCAAGGGGGTGC 60.748 66.667 0.00 0.00 0.00 5.01
3584 3771 2.747855 GAGCTTCAAGGGGGTGCG 60.748 66.667 0.00 0.00 0.00 5.34
3585 3772 3.553095 GAGCTTCAAGGGGGTGCGT 62.553 63.158 0.00 0.00 0.00 5.24
3586 3773 2.180159 GAGCTTCAAGGGGGTGCGTA 62.180 60.000 0.00 0.00 0.00 4.42
3587 3774 2.038837 GCTTCAAGGGGGTGCGTAC 61.039 63.158 0.00 0.00 0.00 3.67
3588 3775 1.740296 CTTCAAGGGGGTGCGTACG 60.740 63.158 11.84 11.84 0.00 3.67
3589 3776 2.444700 CTTCAAGGGGGTGCGTACGT 62.445 60.000 17.90 0.00 0.00 3.57
3590 3777 2.718747 TTCAAGGGGGTGCGTACGTG 62.719 60.000 17.90 4.49 0.00 4.49
3635 3822 2.254546 TTCAAGTGCGACAACCATCT 57.745 45.000 0.00 0.00 0.00 2.90
3637 3824 1.344438 TCAAGTGCGACAACCATCTCT 59.656 47.619 0.00 0.00 0.00 3.10
3639 3826 2.656560 AGTGCGACAACCATCTCTAC 57.343 50.000 0.00 0.00 0.00 2.59
3640 3827 2.171840 AGTGCGACAACCATCTCTACT 58.828 47.619 0.00 0.00 0.00 2.57
3641 3828 2.094494 AGTGCGACAACCATCTCTACTG 60.094 50.000 0.00 0.00 0.00 2.74
3642 3829 1.893137 TGCGACAACCATCTCTACTGT 59.107 47.619 0.00 0.00 0.00 3.55
3643 3830 2.094700 TGCGACAACCATCTCTACTGTC 60.095 50.000 0.00 0.00 34.40 3.51
3644 3831 2.164624 GCGACAACCATCTCTACTGTCT 59.835 50.000 0.00 0.00 35.36 3.41
3645 3832 3.732471 GCGACAACCATCTCTACTGTCTC 60.732 52.174 0.00 0.00 35.36 3.36
3646 3833 3.486043 CGACAACCATCTCTACTGTCTCG 60.486 52.174 0.00 0.00 35.36 4.04
3647 3834 2.755655 ACAACCATCTCTACTGTCTCGG 59.244 50.000 0.00 0.00 0.00 4.63
3648 3835 1.394618 ACCATCTCTACTGTCTCGGC 58.605 55.000 0.00 0.00 0.00 5.54
3649 3836 1.341089 ACCATCTCTACTGTCTCGGCA 60.341 52.381 0.00 0.00 0.00 5.69
3650 3837 1.066303 CCATCTCTACTGTCTCGGCAC 59.934 57.143 0.00 0.00 0.00 5.01
3651 3838 2.020720 CATCTCTACTGTCTCGGCACT 58.979 52.381 0.00 0.00 0.00 4.40
3652 3839 2.201921 TCTCTACTGTCTCGGCACTT 57.798 50.000 0.00 0.00 0.00 3.16
3653 3840 2.515854 TCTCTACTGTCTCGGCACTTT 58.484 47.619 0.00 0.00 0.00 2.66
3654 3841 2.488545 TCTCTACTGTCTCGGCACTTTC 59.511 50.000 0.00 0.00 0.00 2.62
3655 3842 2.229062 CTCTACTGTCTCGGCACTTTCA 59.771 50.000 0.00 0.00 0.00 2.69
3656 3843 2.626266 TCTACTGTCTCGGCACTTTCAA 59.374 45.455 0.00 0.00 0.00 2.69
3657 3844 1.871080 ACTGTCTCGGCACTTTCAAG 58.129 50.000 0.00 0.00 0.00 3.02
3658 3845 1.412710 ACTGTCTCGGCACTTTCAAGA 59.587 47.619 0.00 0.00 0.00 3.02
3659 3846 1.795286 CTGTCTCGGCACTTTCAAGAC 59.205 52.381 0.00 0.00 37.47 3.01
3660 3847 0.784778 GTCTCGGCACTTTCAAGACG 59.215 55.000 0.00 0.00 0.00 4.18
3661 3848 0.319555 TCTCGGCACTTTCAAGACGG 60.320 55.000 0.00 0.00 0.00 4.79
3662 3849 1.291877 CTCGGCACTTTCAAGACGGG 61.292 60.000 0.00 0.00 0.00 5.28
3663 3850 2.954611 GGCACTTTCAAGACGGGC 59.045 61.111 0.00 0.00 0.00 6.13
3664 3851 1.896660 GGCACTTTCAAGACGGGCA 60.897 57.895 0.00 0.00 0.00 5.36
3665 3852 1.452145 GGCACTTTCAAGACGGGCAA 61.452 55.000 0.00 0.00 0.00 4.52
3666 3853 0.040067 GCACTTTCAAGACGGGCAAG 60.040 55.000 0.00 0.00 0.00 4.01
3669 3856 0.519077 CTTTCAAGACGGGCAAGCTC 59.481 55.000 0.00 0.00 0.00 4.09
3691 3878 2.260434 GGCGAGCCTACAACGTCA 59.740 61.111 6.90 0.00 0.00 4.35
3694 5632 1.800315 CGAGCCTACAACGTCACCG 60.800 63.158 0.00 0.00 40.83 4.94
3748 5686 1.078708 TTCCGGAAGATCGCAACCC 60.079 57.895 14.35 0.00 0.00 4.11
3778 5716 1.359117 GAGTTCATCGATCCGCCGA 59.641 57.895 0.00 0.00 43.16 5.54
3785 5723 1.536073 ATCGATCCGCCGATGACCAT 61.536 55.000 0.00 0.00 46.22 3.55
3786 5724 1.300931 CGATCCGCCGATGACCATT 60.301 57.895 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.549754 ACGCAACATCTTCCACTTCAAG 59.450 45.455 0.00 0.00 0.00 3.02
15 16 0.396435 TGGACGCAACATCTTCCACT 59.604 50.000 0.00 0.00 33.02 4.00
22 23 3.165058 TGAGTAGATGGACGCAACATC 57.835 47.619 6.50 6.50 43.87 3.06
24 25 2.159099 GGATGAGTAGATGGACGCAACA 60.159 50.000 0.00 0.00 32.66 3.33
41 42 2.777459 AGGGGGTACTAGTGAGGATG 57.223 55.000 5.39 0.00 0.00 3.51
42 43 3.797671 AAAGGGGGTACTAGTGAGGAT 57.202 47.619 5.39 0.00 0.00 3.24
43 44 3.447950 GAAAAGGGGGTACTAGTGAGGA 58.552 50.000 5.39 0.00 0.00 3.71
44 45 2.167900 CGAAAAGGGGGTACTAGTGAGG 59.832 54.545 5.39 0.00 0.00 3.86
45 46 3.094572 TCGAAAAGGGGGTACTAGTGAG 58.905 50.000 5.39 0.00 0.00 3.51
50 51 2.323999 TGGTCGAAAAGGGGGTACTA 57.676 50.000 0.00 0.00 0.00 1.82
52 53 1.279846 TGATGGTCGAAAAGGGGGTAC 59.720 52.381 0.00 0.00 0.00 3.34
73 74 4.515028 AGCATGATGGATGAAGGAGAAA 57.485 40.909 0.00 0.00 33.31 2.52
82 83 8.141909 ACAAAGATTGATAAAGCATGATGGATG 58.858 33.333 0.00 0.00 34.84 3.51
83 84 8.246430 ACAAAGATTGATAAAGCATGATGGAT 57.754 30.769 0.00 0.00 0.00 3.41
87 89 7.324935 TGCAACAAAGATTGATAAAGCATGAT 58.675 30.769 0.00 0.00 0.00 2.45
91 93 7.656542 TGATTTGCAACAAAGATTGATAAAGCA 59.343 29.630 0.00 0.00 34.33 3.91
100 102 5.426504 TGGTTGTGATTTGCAACAAAGATT 58.573 33.333 0.00 0.00 45.64 2.40
106 108 3.257393 GTGTTGGTTGTGATTTGCAACA 58.743 40.909 0.00 0.00 45.64 3.33
110 113 2.593346 TGGTGTTGGTTGTGATTTGC 57.407 45.000 0.00 0.00 0.00 3.68
119 122 0.471022 GGGGGAACATGGTGTTGGTT 60.471 55.000 0.00 0.00 41.28 3.67
120 123 1.155155 GGGGGAACATGGTGTTGGT 59.845 57.895 0.00 0.00 41.28 3.67
131 134 4.827835 GCTTTTTATATGAGGAGGGGGAAC 59.172 45.833 0.00 0.00 0.00 3.62
135 138 7.119846 CGAAATAGCTTTTTATATGAGGAGGGG 59.880 40.741 1.87 0.00 0.00 4.79
138 141 8.087982 TGCGAAATAGCTTTTTATATGAGGAG 57.912 34.615 1.87 0.00 38.13 3.69
140 143 9.334693 GAATGCGAAATAGCTTTTTATATGAGG 57.665 33.333 1.87 0.00 35.13 3.86
189 192 9.666626 TGTTAACATTTGGTTTATTGTAGAACG 57.333 29.630 3.59 0.00 40.96 3.95
193 196 8.897809 CGTGTGTTAACATTTGGTTTATTGTAG 58.102 33.333 12.26 0.00 40.96 2.74
204 208 6.524933 TGTGTCTTTTCGTGTGTTAACATTTG 59.475 34.615 12.26 4.69 38.92 2.32
215 219 7.011950 TCACTGAAATTATGTGTCTTTTCGTGT 59.988 33.333 0.00 0.00 35.96 4.49
230 234 7.994425 TTTTGATGTAGCCTCACTGAAATTA 57.006 32.000 0.00 0.00 0.00 1.40
234 238 6.899393 AAATTTTGATGTAGCCTCACTGAA 57.101 33.333 0.00 0.00 0.00 3.02
237 241 9.851686 TCATATAAATTTTGATGTAGCCTCACT 57.148 29.630 0.00 0.00 0.00 3.41
271 277 8.399425 ACGAGACTTTGTATATCTACTTGTGAG 58.601 37.037 0.00 0.00 0.00 3.51
278 284 8.619546 ACTAACCACGAGACTTTGTATATCTAC 58.380 37.037 0.00 0.00 0.00 2.59
283 289 6.319658 CCCTACTAACCACGAGACTTTGTATA 59.680 42.308 0.00 0.00 0.00 1.47
285 291 4.460382 CCCTACTAACCACGAGACTTTGTA 59.540 45.833 0.00 0.00 0.00 2.41
287 293 3.508793 TCCCTACTAACCACGAGACTTTG 59.491 47.826 0.00 0.00 0.00 2.77
317 323 7.414222 TCGTACAAATTATAGTCCAACCTCT 57.586 36.000 0.00 0.00 0.00 3.69
409 417 5.333035 CGAGTTAAGACGCAAATGAAGTTCA 60.333 40.000 8.27 8.27 0.00 3.18
417 425 3.650139 AGTGACGAGTTAAGACGCAAAT 58.350 40.909 0.00 0.00 0.00 2.32
441 449 3.119602 TCATAGCTAACCACACGACTGAC 60.120 47.826 0.00 0.00 0.00 3.51
444 452 3.243101 CGATCATAGCTAACCACACGACT 60.243 47.826 0.00 0.00 0.00 4.18
446 454 2.946990 TCGATCATAGCTAACCACACGA 59.053 45.455 0.00 2.49 0.00 4.35
447 455 3.243101 ACTCGATCATAGCTAACCACACG 60.243 47.826 0.00 0.01 0.00 4.49
457 465 2.621055 ACAGACCTCACTCGATCATAGC 59.379 50.000 0.00 0.00 0.00 2.97
469 477 9.179909 TGAGTTAAATGTTTAAAACAGACCTCA 57.820 29.630 0.00 4.63 45.95 3.86
472 480 7.911727 ACGTGAGTTAAATGTTTAAAACAGACC 59.088 33.333 0.00 0.00 46.40 3.85
502 510 3.355378 TGTTAGGGGTCGATTTCTACGA 58.645 45.455 0.00 0.00 37.43 3.43
508 516 4.837093 TTGAGATGTTAGGGGTCGATTT 57.163 40.909 0.00 0.00 0.00 2.17
542 550 4.753610 CCGAGATCCGTGAGTACTACATAA 59.246 45.833 0.00 0.00 36.31 1.90
548 556 1.065636 TGACCGAGATCCGTGAGTACT 60.066 52.381 0.00 0.00 36.31 2.73
562 570 0.036765 CGGGGTTGAAGAATGACCGA 60.037 55.000 0.00 0.00 42.19 4.69
574 582 2.868253 GGAAGAACATCCGGGGTTG 58.132 57.895 15.68 7.64 0.00 3.77
606 621 7.744715 CGATAGCGAGTGAAGTTTGTTTTAAAT 59.255 33.333 0.00 0.00 40.82 1.40
618 633 4.052608 TCTAGAGACGATAGCGAGTGAAG 58.947 47.826 7.69 0.00 41.64 3.02
659 674 6.481954 GCAGGTAGCCATGTATACAATTAC 57.518 41.667 10.14 9.58 37.23 1.89
701 720 5.297547 TCATACTCCAAATCTAATGTCGCC 58.702 41.667 0.00 0.00 0.00 5.54
702 721 6.701841 TCTTCATACTCCAAATCTAATGTCGC 59.298 38.462 0.00 0.00 0.00 5.19
708 727 6.069673 TGCCCTTCTTCATACTCCAAATCTAA 60.070 38.462 0.00 0.00 0.00 2.10
710 729 4.228210 TGCCCTTCTTCATACTCCAAATCT 59.772 41.667 0.00 0.00 0.00 2.40
742 761 1.987770 CACGTTTTGATTGATGGCTGC 59.012 47.619 0.00 0.00 0.00 5.25
824 843 6.162777 TCTTTGGAGGTCAACAAACAAAAAG 58.837 36.000 0.00 0.00 34.67 2.27
825 844 6.102897 TCTTTGGAGGTCAACAAACAAAAA 57.897 33.333 0.00 0.00 34.67 1.94
826 845 5.719173 CTCTTTGGAGGTCAACAAACAAAA 58.281 37.500 0.00 0.00 36.03 2.44
827 846 5.323371 CTCTTTGGAGGTCAACAAACAAA 57.677 39.130 0.00 0.00 36.03 2.83
828 847 4.981806 CTCTTTGGAGGTCAACAAACAA 57.018 40.909 0.00 0.00 36.03 2.83
930 949 1.527433 GGAGGTCAGGTTTTGGCTGC 61.527 60.000 0.00 0.00 0.00 5.25
1486 1513 1.137404 GTCGCGCAATTGAGCCAAT 59.863 52.632 25.55 0.00 37.57 3.16
1487 1514 2.560861 GTCGCGCAATTGAGCCAA 59.439 55.556 25.55 13.20 37.57 4.52
1488 1515 3.787676 CGTCGCGCAATTGAGCCA 61.788 61.111 25.55 12.90 37.57 4.75
1489 1516 4.520846 CCGTCGCGCAATTGAGCC 62.521 66.667 25.55 13.32 37.57 4.70
1532 1559 2.181205 CGAACGAGTCAGAATCAGAGC 58.819 52.381 0.00 0.00 0.00 4.09
1545 1576 4.379243 ACCTGCAGCCCGAACGAG 62.379 66.667 8.66 0.00 0.00 4.18
1782 1813 1.051812 AGAACTGTGAGTCTGTGGGG 58.948 55.000 0.00 0.00 0.00 4.96
1783 1814 2.487934 CAAGAACTGTGAGTCTGTGGG 58.512 52.381 0.00 0.00 0.00 4.61
1937 1974 2.038689 AGCATGATGGAGTAGAGCCATG 59.961 50.000 0.00 0.00 45.81 3.66
2082 2119 7.474398 TTTCTCAAGAATCTATTCTGCATCG 57.526 36.000 5.99 0.00 45.83 3.84
2244 2281 1.136363 CAGTTCGCAATGGTGTACACG 60.136 52.381 19.41 7.41 0.00 4.49
2317 2354 1.350351 ACCAGAGCAGCAACTGAAGAT 59.650 47.619 17.56 2.18 36.38 2.40
2320 2357 1.134128 TGAACCAGAGCAGCAACTGAA 60.134 47.619 17.56 2.33 36.38 3.02
2325 2362 1.970640 TCTACTGAACCAGAGCAGCAA 59.029 47.619 0.00 0.00 35.57 3.91
2373 2418 1.746220 ACCAGCGAGACTACACAGATC 59.254 52.381 0.00 0.00 0.00 2.75
2852 2906 5.062183 GCAAGAGAAAAACAACAAGAACACC 59.938 40.000 0.00 0.00 0.00 4.16
2893 2947 2.437359 AGATGGCTCCGTTGCTGC 60.437 61.111 0.00 0.00 0.00 5.25
2968 3022 3.879892 AGTGACAGAAAGAAGGAACAAGC 59.120 43.478 0.00 0.00 0.00 4.01
2971 3025 6.127730 GGAAAAAGTGACAGAAAGAAGGAACA 60.128 38.462 0.00 0.00 0.00 3.18
2972 3026 6.266323 GGAAAAAGTGACAGAAAGAAGGAAC 58.734 40.000 0.00 0.00 0.00 3.62
2999 3053 9.343103 CAAGAAAACAGAATCATCATTCAGAAG 57.657 33.333 0.00 0.00 41.03 2.85
3001 3055 7.176165 AGCAAGAAAACAGAATCATCATTCAGA 59.824 33.333 0.00 0.00 41.03 3.27
3002 3056 7.313646 AGCAAGAAAACAGAATCATCATTCAG 58.686 34.615 0.00 0.00 41.03 3.02
3003 3057 7.176165 AGAGCAAGAAAACAGAATCATCATTCA 59.824 33.333 0.00 0.00 41.03 2.57
3004 3058 7.485277 CAGAGCAAGAAAACAGAATCATCATTC 59.515 37.037 0.00 0.00 39.10 2.67
3005 3059 7.313646 CAGAGCAAGAAAACAGAATCATCATT 58.686 34.615 0.00 0.00 0.00 2.57
3006 3060 6.625300 GCAGAGCAAGAAAACAGAATCATCAT 60.625 38.462 0.00 0.00 0.00 2.45
3007 3061 5.335426 GCAGAGCAAGAAAACAGAATCATCA 60.335 40.000 0.00 0.00 0.00 3.07
3008 3062 5.094134 GCAGAGCAAGAAAACAGAATCATC 58.906 41.667 0.00 0.00 0.00 2.92
3071 3125 5.896922 TGTTGTTCTTGTTGTTGTTGTTG 57.103 34.783 0.00 0.00 0.00 3.33
3076 3130 8.898761 TGACTATATTGTTGTTCTTGTTGTTGT 58.101 29.630 0.00 0.00 0.00 3.32
3077 3131 9.897744 ATGACTATATTGTTGTTCTTGTTGTTG 57.102 29.630 0.00 0.00 0.00 3.33
3098 3152 8.760735 CAAGAGATATCCATCTTCCATATGACT 58.239 37.037 3.65 0.00 41.78 3.41
3122 3176 7.867921 TCTTAGCTCCCATAAAATAGGAACAA 58.132 34.615 0.00 0.00 0.00 2.83
3123 3177 7.446106 TCTTAGCTCCCATAAAATAGGAACA 57.554 36.000 0.00 0.00 0.00 3.18
3124 3178 6.428465 GCTCTTAGCTCCCATAAAATAGGAAC 59.572 42.308 0.00 0.00 38.45 3.62
3125 3179 6.101150 TGCTCTTAGCTCCCATAAAATAGGAA 59.899 38.462 0.00 0.00 42.97 3.36
3126 3180 5.606749 TGCTCTTAGCTCCCATAAAATAGGA 59.393 40.000 0.00 0.00 42.97 2.94
3127 3181 5.869579 TGCTCTTAGCTCCCATAAAATAGG 58.130 41.667 0.00 0.00 42.97 2.57
3128 3182 7.393216 AGATGCTCTTAGCTCCCATAAAATAG 58.607 38.462 0.00 0.00 42.97 1.73
3136 3206 2.468301 AGAGATGCTCTTAGCTCCCA 57.532 50.000 0.00 0.00 42.97 4.37
3169 3239 4.699925 AGAAAGCGGTTATGCCCTATTA 57.300 40.909 0.00 0.00 34.65 0.98
3184 3254 2.030007 TGCAGCATTTGGTGTAGAAAGC 60.030 45.455 11.04 0.00 44.70 3.51
3189 3259 5.272167 CAAATTTGCAGCATTTGGTGTAG 57.728 39.130 19.02 0.94 44.70 2.74
3227 3357 4.545519 GCGACTGCTTTTTGTTTTGTAACG 60.546 41.667 0.00 0.00 36.13 3.18
3230 3360 3.102276 CGCGACTGCTTTTTGTTTTGTA 58.898 40.909 0.00 0.00 39.65 2.41
3231 3361 1.917303 CGCGACTGCTTTTTGTTTTGT 59.083 42.857 0.00 0.00 39.65 2.83
3238 3368 1.368850 GTTCGCGCGACTGCTTTTT 60.369 52.632 35.02 0.00 39.65 1.94
3239 3369 2.248431 GTTCGCGCGACTGCTTTT 59.752 55.556 35.02 0.00 39.65 2.27
3240 3370 4.059459 CGTTCGCGCGACTGCTTT 62.059 61.111 35.02 0.00 39.65 3.51
3273 3403 2.671963 GGTGGTGCGGGAAGGTTC 60.672 66.667 0.00 0.00 0.00 3.62
3295 3457 2.296073 ACGAGGGGTAAATTTGGCAA 57.704 45.000 0.00 0.00 0.00 4.52
3296 3458 1.889829 CAACGAGGGGTAAATTTGGCA 59.110 47.619 0.00 0.00 0.00 4.92
3299 3461 2.647529 GGCAACGAGGGGTAAATTTG 57.352 50.000 0.00 0.00 0.00 2.32
3327 3489 1.132640 GATTGAGTCGTTGCGGTGC 59.867 57.895 0.00 0.00 0.00 5.01
3329 3491 3.856508 CGATTGAGTCGTTGCGGT 58.143 55.556 0.00 0.00 45.19 5.68
3372 3534 4.619227 CGGTGGCGTGAAGGTGGT 62.619 66.667 0.00 0.00 0.00 4.16
3397 3559 4.245054 CGAATATCGGCCGGTGAG 57.755 61.111 27.83 7.62 36.00 3.51
3406 3568 1.876453 CTTGCGACGGCCGAATATCG 61.876 60.000 35.90 30.09 41.76 2.92
3408 3570 0.874607 GACTTGCGACGGCCGAATAT 60.875 55.000 35.90 9.58 41.76 1.28
3409 3571 1.517694 GACTTGCGACGGCCGAATA 60.518 57.895 35.90 12.31 41.76 1.75
3421 3583 2.046285 CGTTGGGATGGGGACTTGC 61.046 63.158 0.00 0.00 0.00 4.01
3465 3635 0.034337 GTTGGAGGTTGGTGCGACTA 59.966 55.000 0.00 0.00 0.00 2.59
3468 3638 2.280524 CGTTGGAGGTTGGTGCGA 60.281 61.111 0.00 0.00 0.00 5.10
3470 3640 3.670377 GGCGTTGGAGGTTGGTGC 61.670 66.667 0.00 0.00 0.00 5.01
3471 3641 3.353836 CGGCGTTGGAGGTTGGTG 61.354 66.667 0.00 0.00 0.00 4.17
3489 3659 2.356313 AACGGAGTGCTGCAGTCG 60.356 61.111 26.19 22.79 45.00 4.18
3490 3660 1.560860 GACAACGGAGTGCTGCAGTC 61.561 60.000 25.57 25.57 45.00 3.51
3491 3661 1.595382 GACAACGGAGTGCTGCAGT 60.595 57.895 16.64 10.24 45.00 4.40
3492 3662 1.287730 GAGACAACGGAGTGCTGCAG 61.288 60.000 10.11 10.11 45.00 4.41
3493 3663 1.300931 GAGACAACGGAGTGCTGCA 60.301 57.895 0.00 0.00 45.00 4.41
3494 3664 0.601311 AAGAGACAACGGAGTGCTGC 60.601 55.000 0.00 0.00 45.00 5.25
3495 3665 1.795286 GAAAGAGACAACGGAGTGCTG 59.205 52.381 0.00 0.00 45.00 4.41
3503 3673 2.218759 CGGTGACAAGAAAGAGACAACG 59.781 50.000 0.00 0.00 32.64 4.10
3514 3684 1.009335 CGACGACACGGTGACAAGA 60.009 57.895 16.29 0.00 0.00 3.02
3533 3703 3.899981 TTGAGCTTCCGCGGCATGT 62.900 57.895 23.51 4.67 42.32 3.21
3535 3705 2.821366 CTTGAGCTTCCGCGGCAT 60.821 61.111 23.51 5.47 42.32 4.40
3536 3706 4.314440 ACTTGAGCTTCCGCGGCA 62.314 61.111 23.51 9.50 42.32 5.69
3537 3707 3.491652 GACTTGAGCTTCCGCGGC 61.492 66.667 23.51 9.39 42.32 6.53
3540 3710 0.951558 TTTTGGACTTGAGCTTCCGC 59.048 50.000 0.00 0.00 34.24 5.54
3541 3711 1.068954 GCTTTTGGACTTGAGCTTCCG 60.069 52.381 0.00 0.00 34.24 4.30
3542 3712 1.956477 TGCTTTTGGACTTGAGCTTCC 59.044 47.619 0.00 0.00 36.16 3.46
3544 3714 3.026694 ACTTGCTTTTGGACTTGAGCTT 58.973 40.909 0.00 0.00 36.16 3.74
3568 3755 2.221299 TACGCACCCCCTTGAAGCT 61.221 57.895 0.00 0.00 0.00 3.74
3583 3770 4.487412 GTCGGAGCCCCACGTACG 62.487 72.222 15.01 15.01 0.00 3.67
3584 3771 4.139234 GGTCGGAGCCCCACGTAC 62.139 72.222 0.00 0.00 0.00 3.67
3585 3772 4.682334 TGGTCGGAGCCCCACGTA 62.682 66.667 4.54 0.00 0.00 3.57
3588 3775 3.192103 AAAGTGGTCGGAGCCCCAC 62.192 63.158 7.91 7.91 45.42 4.61
3589 3776 2.852075 AAAGTGGTCGGAGCCCCA 60.852 61.111 4.54 0.00 0.00 4.96
3590 3777 2.359975 CAAAGTGGTCGGAGCCCC 60.360 66.667 4.54 0.00 0.00 5.80
3612 3799 2.571212 TGGTTGTCGCACTTGAAATCT 58.429 42.857 0.00 0.00 0.00 2.40
3615 3802 2.548057 GAGATGGTTGTCGCACTTGAAA 59.452 45.455 0.00 0.00 0.00 2.69
3619 3806 2.563179 AGTAGAGATGGTTGTCGCACTT 59.437 45.455 0.00 0.00 0.00 3.16
3635 3822 2.235891 TGAAAGTGCCGAGACAGTAGA 58.764 47.619 0.00 0.00 0.00 2.59
3637 3824 2.626266 TCTTGAAAGTGCCGAGACAGTA 59.374 45.455 0.00 0.00 0.00 2.74
3639 3826 1.795286 GTCTTGAAAGTGCCGAGACAG 59.205 52.381 0.00 0.00 42.10 3.51
3640 3827 1.865865 GTCTTGAAAGTGCCGAGACA 58.134 50.000 0.00 0.00 42.10 3.41
3641 3828 0.784778 CGTCTTGAAAGTGCCGAGAC 59.215 55.000 0.00 0.00 40.17 3.36
3642 3829 0.319555 CCGTCTTGAAAGTGCCGAGA 60.320 55.000 0.00 0.00 0.00 4.04
3643 3830 1.291877 CCCGTCTTGAAAGTGCCGAG 61.292 60.000 0.00 0.00 0.00 4.63
3644 3831 1.301401 CCCGTCTTGAAAGTGCCGA 60.301 57.895 0.00 0.00 0.00 5.54
3645 3832 2.966309 GCCCGTCTTGAAAGTGCCG 61.966 63.158 0.00 0.00 0.00 5.69
3646 3833 1.452145 TTGCCCGTCTTGAAAGTGCC 61.452 55.000 0.00 0.00 0.00 5.01
3647 3834 0.040067 CTTGCCCGTCTTGAAAGTGC 60.040 55.000 0.00 0.00 0.00 4.40
3648 3835 0.040067 GCTTGCCCGTCTTGAAAGTG 60.040 55.000 0.00 0.00 0.00 3.16
3649 3836 0.179018 AGCTTGCCCGTCTTGAAAGT 60.179 50.000 0.00 0.00 0.00 2.66
3650 3837 0.519077 GAGCTTGCCCGTCTTGAAAG 59.481 55.000 0.00 0.00 0.00 2.62
3651 3838 1.227999 CGAGCTTGCCCGTCTTGAAA 61.228 55.000 0.00 0.00 0.00 2.69
3652 3839 1.667830 CGAGCTTGCCCGTCTTGAA 60.668 57.895 0.00 0.00 0.00 2.69
3653 3840 2.048222 CGAGCTTGCCCGTCTTGA 60.048 61.111 0.00 0.00 0.00 3.02
3654 3841 3.793144 GCGAGCTTGCCCGTCTTG 61.793 66.667 15.66 0.00 0.00 3.02
3673 3860 2.508663 GACGTTGTAGGCTCGCCC 60.509 66.667 3.92 0.00 36.58 6.13
3674 3861 2.092882 GTGACGTTGTAGGCTCGCC 61.093 63.158 0.00 0.00 0.00 5.54
3702 5640 4.373116 TCCTGCGACTGGCCGAAC 62.373 66.667 0.00 0.00 42.61 3.95
3707 5645 1.078143 ATTTCCTCCTGCGACTGGC 60.078 57.895 0.00 0.00 43.96 4.85
3710 5648 1.625818 AGTTCATTTCCTCCTGCGACT 59.374 47.619 0.00 0.00 0.00 4.18
3711 5649 2.100605 AGTTCATTTCCTCCTGCGAC 57.899 50.000 0.00 0.00 0.00 5.19
3712 5650 2.615493 GGAAGTTCATTTCCTCCTGCGA 60.615 50.000 5.01 0.00 42.73 5.10
3716 5654 2.266279 TCCGGAAGTTCATTTCCTCCT 58.734 47.619 0.00 0.00 43.64 3.69
3738 5676 0.533755 CATCCTCCTGGGTTGCGATC 60.534 60.000 0.00 0.00 36.25 3.69
3748 5686 0.467384 ATGAACTCCGCATCCTCCTG 59.533 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.