Multiple sequence alignment - TraesCS6A01G387100

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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 TraesCS6A01G387100 chr6A 100.000 4070 0 0 1 4070 603692495 603688426 0.000000e+00 7516.0
1 TraesCS6A01G387100 chr6A 86.695 466 58 4 3608 4070 591940418 591940882 7.800000e-142 514.0
2 TraesCS6A01G387100 chr6A 93.220 59 4 0 3539 3597 581803387 581803329 2.020000e-13 87.9
3 TraesCS6A01G387100 chr6B 91.453 4095 280 43 1 4070 695443228 695439179 0.000000e+00 5559.0
4 TraesCS6A01G387100 chr6B 86.586 2162 231 29 954 3081 695783266 695785402 0.000000e+00 2331.0
5 TraesCS6A01G387100 chr6B 86.266 466 60 4 3608 4070 61212076 61211612 1.690000e-138 503.0
6 TraesCS6A01G387100 chr5A 82.046 2033 304 34 1018 3020 480788419 480786418 0.000000e+00 1676.0
7 TraesCS6A01G387100 chr5A 89.855 69 6 1 3538 3605 569527238 569527306 2.020000e-13 87.9
8 TraesCS6A01G387100 chr3D 81.499 2081 325 25 996 3046 2881651 2879601 0.000000e+00 1655.0
9 TraesCS6A01G387100 chr3D 83.707 669 104 5 996 1663 2785062 2785726 9.600000e-176 627.0
10 TraesCS6A01G387100 chr3B 81.448 2086 305 46 996 3040 2901063 2903107 0.000000e+00 1633.0
11 TraesCS6A01G387100 chr3B 86.481 466 59 4 3608 4070 463484056 463483592 3.630000e-140 508.0
12 TraesCS6A01G387100 chr3B 86.481 466 59 4 3608 4070 534159550 534159086 3.630000e-140 508.0
13 TraesCS6A01G387100 chr3B 91.525 59 5 0 3547 3605 252360125 252360067 9.380000e-12 82.4
14 TraesCS6A01G387100 chr5B 80.168 2027 334 51 1018 3010 456460932 456462924 0.000000e+00 1454.0
15 TraesCS6A01G387100 chr5B 85.622 466 63 4 3608 4070 710235738 710236202 1.700000e-133 486.0
16 TraesCS6A01G387100 chrUn 78.970 1845 341 33 1188 3004 105377303 105375478 0.000000e+00 1214.0
17 TraesCS6A01G387100 chrUn 76.930 1114 219 24 1912 3004 77052764 77053860 2.090000e-167 599.0
18 TraesCS6A01G387100 chrUn 86.266 466 60 4 3608 4070 136395226 136394762 1.690000e-138 503.0
19 TraesCS6A01G387100 chrUn 82.034 590 92 9 1018 1598 76986377 76986961 1.310000e-134 490.0
20 TraesCS6A01G387100 chrUn 82.034 590 92 9 1018 1598 341414472 341415056 1.310000e-134 490.0
21 TraesCS6A01G387100 chrUn 82.267 547 86 6 1018 1555 440995510 440996054 2.870000e-126 462.0
22 TraesCS6A01G387100 chr7B 86.481 466 59 4 3608 4070 380073200 380072736 3.630000e-140 508.0
23 TraesCS6A01G387100 chr7B 86.052 466 61 4 3608 4070 648273620 648274084 7.860000e-137 497.0
24 TraesCS6A01G387100 chr2A 86.266 466 60 4 3608 4070 669746862 669747326 1.690000e-138 503.0
25 TraesCS6A01G387100 chr2B 70.701 884 219 33 1706 2571 25487635 25486774 1.170000e-35 161.0
26 TraesCS6A01G387100 chr2B 90.769 65 6 0 3541 3605 476455154 476455090 2.020000e-13 87.9
27 TraesCS6A01G387100 chr1D 93.443 61 3 1 3541 3600 483106275 483106335 5.600000e-14 89.8
28 TraesCS6A01G387100 chr3A 93.220 59 4 0 3541 3599 49327378 49327320 2.020000e-13 87.9
29 TraesCS6A01G387100 chr4D 92.063 63 2 2 3539 3600 49876795 49876855 7.250000e-13 86.1
30 TraesCS6A01G387100 chr1A 88.571 70 5 2 3539 3607 20167451 20167384 9.380000e-12 82.4


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 TraesCS6A01G387100 chr6A 603688426 603692495 4069 True 7516 7516 100.000 1 4070 1 chr6A.!!$R2 4069
1 TraesCS6A01G387100 chr6B 695439179 695443228 4049 True 5559 5559 91.453 1 4070 1 chr6B.!!$R2 4069
2 TraesCS6A01G387100 chr6B 695783266 695785402 2136 False 2331 2331 86.586 954 3081 1 chr6B.!!$F1 2127
3 TraesCS6A01G387100 chr5A 480786418 480788419 2001 True 1676 1676 82.046 1018 3020 1 chr5A.!!$R1 2002
4 TraesCS6A01G387100 chr3D 2879601 2881651 2050 True 1655 1655 81.499 996 3046 1 chr3D.!!$R1 2050
5 TraesCS6A01G387100 chr3D 2785062 2785726 664 False 627 627 83.707 996 1663 1 chr3D.!!$F1 667
6 TraesCS6A01G387100 chr3B 2901063 2903107 2044 False 1633 1633 81.448 996 3040 1 chr3B.!!$F1 2044
7 TraesCS6A01G387100 chr5B 456460932 456462924 1992 False 1454 1454 80.168 1018 3010 1 chr5B.!!$F1 1992
8 TraesCS6A01G387100 chrUn 105375478 105377303 1825 True 1214 1214 78.970 1188 3004 1 chrUn.!!$R1 1816
9 TraesCS6A01G387100 chrUn 77052764 77053860 1096 False 599 599 76.930 1912 3004 1 chrUn.!!$F2 1092
10 TraesCS6A01G387100 chrUn 76986377 76986961 584 False 490 490 82.034 1018 1598 1 chrUn.!!$F1 580
11 TraesCS6A01G387100 chrUn 341414472 341415056 584 False 490 490 82.034 1018 1598 1 chrUn.!!$F3 580
12 TraesCS6A01G387100 chrUn 440995510 440996054 544 False 462 462 82.267 1018 1555 1 chrUn.!!$F4 537

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
107 108 0.033011 TGGCCAGACCCTCTAGAGTC 60.033 60.0 18.42 11.07 37.83 3.36 F
1140 1159 0.242825 CATTGCTGTGGTTCCTGCTG 59.757 55.0 0.00 0.00 0.00 4.41 F
2322 2375 0.476771 ACAACGAAGGGGGTGTGAAT 59.523 50.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1588 0.170561 CTCGTCTAAGTGTCCACCCG 59.829 60.0 0.00 0.0 0.00 5.28 R
2633 2693 0.312416 GCGCCTAGATGTCATCGACT 59.688 55.0 7.18 0.0 33.15 4.18 R
3731 3817 0.040514 TTCATTCGTGGCGCTTGTTG 60.041 50.0 7.64 0.0 0.00 3.33 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
21 22 4.797800 CAGGTCAATCAGAGTCTTGAGA 57.202 45.455 0.00 0.00 32.33 3.27
34 35 2.935201 GTCTTGAGAGCTACTGCATTGG 59.065 50.000 0.00 0.00 42.74 3.16
45 46 1.137872 ACTGCATTGGCGTTTTGGAAA 59.862 42.857 0.00 0.00 45.35 3.13
107 108 0.033011 TGGCCAGACCCTCTAGAGTC 60.033 60.000 18.42 11.07 37.83 3.36
111 112 1.210967 CCAGACCCTCTAGAGTCTCGT 59.789 57.143 18.42 8.59 41.38 4.18
112 113 2.356330 CCAGACCCTCTAGAGTCTCGTT 60.356 54.545 18.42 0.00 41.38 3.85
135 136 1.065701 CTACTATGTCCGCGCAAGACT 59.934 52.381 23.37 13.87 43.02 3.24
136 137 0.458543 ACTATGTCCGCGCAAGACTG 60.459 55.000 23.37 16.68 43.02 3.51
162 163 6.751888 CACAATCCGGAAATTTAAAGATGACC 59.248 38.462 9.01 0.00 0.00 4.02
172 173 0.539051 AAAGATGACCCTCGAGCCAG 59.461 55.000 6.99 0.00 0.00 4.85
183 184 2.817396 GAGCCAGCCTTGCTCGTC 60.817 66.667 1.62 0.00 45.05 4.20
186 187 1.520342 GCCAGCCTTGCTCGTCTAG 60.520 63.158 0.00 0.00 36.40 2.43
213 214 2.611292 GGCTCGAGCGTTACTAGACTTA 59.389 50.000 29.81 0.00 43.26 2.24
263 264 5.543507 AAGAGAACGCCAGATAGATTCAT 57.456 39.130 0.00 0.00 0.00 2.57
285 286 2.202837 CCAACCCGTAGTAGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
286 287 2.581409 CAACCCGTAGTAGCCGCG 60.581 66.667 0.00 0.00 0.00 6.46
511 512 8.934023 AAAGGTCTTATTACCATGAGTTCAAA 57.066 30.769 0.00 0.00 42.40 2.69
512 513 9.533831 AAAGGTCTTATTACCATGAGTTCAAAT 57.466 29.630 0.00 0.00 42.40 2.32
522 523 9.967451 TTACCATGAGTTCAAATATACAAAGGA 57.033 29.630 0.00 0.00 0.00 3.36
523 524 8.877864 ACCATGAGTTCAAATATACAAAGGAA 57.122 30.769 0.00 0.00 0.00 3.36
524 525 8.960591 ACCATGAGTTCAAATATACAAAGGAAG 58.039 33.333 0.00 0.00 0.00 3.46
527 528 8.635765 TGAGTTCAAATATACAAAGGAAGCTT 57.364 30.769 0.00 0.00 0.00 3.74
528 529 9.077885 TGAGTTCAAATATACAAAGGAAGCTTT 57.922 29.630 0.00 0.00 0.00 3.51
542 543 7.864108 AAGGAAGCTTTAAAATGCAAGTTTT 57.136 28.000 0.00 3.97 34.98 2.43
543 544 7.250445 AGGAAGCTTTAAAATGCAAGTTTTG 57.750 32.000 0.00 0.00 34.98 2.44
544 545 6.823182 AGGAAGCTTTAAAATGCAAGTTTTGT 59.177 30.769 0.00 0.00 34.98 2.83
546 547 7.967854 GGAAGCTTTAAAATGCAAGTTTTGTTT 59.032 29.630 0.00 0.00 34.98 2.83
598 599 7.748691 ACAAGAAATAAAAGGCATGCATTTT 57.251 28.000 36.10 36.10 41.71 1.82
600 601 8.077386 ACAAGAAATAAAAGGCATGCATTTTTG 58.923 29.630 38.12 30.73 39.93 2.44
627 629 4.081198 TGAGAGAGGAGAAAGAATGGAAGC 60.081 45.833 0.00 0.00 0.00 3.86
679 684 5.186256 ACTATGTTGAGTGGAGAGAGAGA 57.814 43.478 0.00 0.00 0.00 3.10
685 690 3.449918 TGAGTGGAGAGAGAGAGAGAGA 58.550 50.000 0.00 0.00 0.00 3.10
686 691 3.197766 TGAGTGGAGAGAGAGAGAGAGAC 59.802 52.174 0.00 0.00 0.00 3.36
687 692 3.181329 AGTGGAGAGAGAGAGAGAGACA 58.819 50.000 0.00 0.00 0.00 3.41
688 693 3.198635 AGTGGAGAGAGAGAGAGAGACAG 59.801 52.174 0.00 0.00 0.00 3.51
689 694 3.197766 GTGGAGAGAGAGAGAGAGACAGA 59.802 52.174 0.00 0.00 0.00 3.41
690 695 3.452264 TGGAGAGAGAGAGAGAGACAGAG 59.548 52.174 0.00 0.00 0.00 3.35
794 802 3.717452 ACCGTAAGTCTGGAGTACTCT 57.283 47.619 21.88 4.14 0.00 3.24
813 821 0.323087 TGCTAGGTACTGACGGCAGA 60.323 55.000 28.78 5.68 45.17 4.26
864 874 4.821589 GGCGCCGCTAGAAGTGCT 62.822 66.667 12.58 0.00 39.45 4.40
913 923 4.530710 TGCCGGTATGTATACTCCATTC 57.469 45.455 1.90 0.00 33.81 2.67
914 924 4.157246 TGCCGGTATGTATACTCCATTCT 58.843 43.478 1.90 0.00 33.81 2.40
920 931 7.331934 CCGGTATGTATACTCCATTCTCAATTG 59.668 40.741 4.17 0.00 33.81 2.32
922 933 9.561069 GGTATGTATACTCCATTCTCAATTGTT 57.439 33.333 5.13 0.00 33.81 2.83
929 940 4.728772 TCCATTCTCAATTGTTGTGGAGT 58.271 39.130 15.50 1.35 31.21 3.85
934 945 3.118075 TCTCAATTGTTGTGGAGTGGACA 60.118 43.478 5.13 0.00 0.00 4.02
938 949 3.417069 TTGTTGTGGAGTGGACATAGG 57.583 47.619 0.00 0.00 0.00 2.57
944 955 2.116238 TGGAGTGGACATAGGTTAGCC 58.884 52.381 0.00 0.00 0.00 3.93
994 1010 0.608640 GCCGGAACAGAAGAGGAGAA 59.391 55.000 5.05 0.00 0.00 2.87
1140 1159 0.242825 CATTGCTGTGGTTCCTGCTG 59.757 55.000 0.00 0.00 0.00 4.41
1562 1588 1.078848 AGGATCACGTGCTCAAGGC 60.079 57.895 20.02 3.78 42.22 4.35
1563 1589 2.456119 GGATCACGTGCTCAAGGCG 61.456 63.158 20.02 0.00 45.43 5.52
1564 1590 2.434884 ATCACGTGCTCAAGGCGG 60.435 61.111 11.67 0.00 45.43 6.13
1565 1591 3.958147 ATCACGTGCTCAAGGCGGG 62.958 63.158 11.67 0.00 45.43 6.13
1570 1596 4.329545 TGCTCAAGGCGGGTGGAC 62.330 66.667 0.00 0.00 45.43 4.02
1851 1892 4.088634 TGTTTAAGCTCATTGGCAAGGAT 58.911 39.130 15.59 3.33 34.17 3.24
2043 2084 2.867472 CGGCTTAGGCGTTTGGTG 59.133 61.111 20.07 0.00 46.33 4.17
2293 2343 6.090483 AGGATCGTATCTCTAAACACATGG 57.910 41.667 0.00 0.00 0.00 3.66
2322 2375 0.476771 ACAACGAAGGGGGTGTGAAT 59.523 50.000 0.00 0.00 0.00 2.57
2331 2384 1.633945 GGGGGTGTGAATTCACTAGGT 59.366 52.381 32.57 0.00 46.55 3.08
2379 2432 3.053619 AACCACTGGTTCTCAGGAAACTT 60.054 43.478 7.72 0.00 43.05 2.66
2381 2434 5.339695 AACCACTGGTTCTCAGGAAACTTTA 60.340 40.000 7.72 0.00 43.05 1.85
2418 2477 2.431057 AGACTCACTCGGTGTTGAGTTT 59.569 45.455 5.75 0.00 46.85 2.66
2481 2540 4.742201 GTCAAGAGCGAGCGGGCA 62.742 66.667 4.87 0.00 34.64 5.36
2497 2556 0.960364 GGCAAAGGACGAGGATGCAA 60.960 55.000 0.00 0.00 38.73 4.08
2503 2562 1.446099 GACGAGGATGCAACGCTCA 60.446 57.895 11.18 0.00 0.00 4.26
2620 2680 4.250464 TCAACGAACCTGCGAAAATCTAT 58.750 39.130 0.00 0.00 34.83 1.98
2629 2689 5.352569 ACCTGCGAAAATCTATTGAAGACTG 59.647 40.000 0.00 0.00 36.93 3.51
2633 2693 5.351465 GCGAAAATCTATTGAAGACTGGACA 59.649 40.000 0.00 0.00 36.93 4.02
2665 2725 2.646117 TAGGCGCCAACACACGAACA 62.646 55.000 31.54 0.00 0.00 3.18
2666 2726 2.405594 GCGCCAACACACGAACAA 59.594 55.556 0.00 0.00 0.00 2.83
2673 2733 2.375110 CAACACACGAACAACATCTGC 58.625 47.619 0.00 0.00 0.00 4.26
2676 2736 1.507713 CACGAACAACATCTGCGCG 60.508 57.895 0.00 0.00 0.00 6.86
2698 2758 1.830477 AGCTCAAGAATCTCTTCCGCT 59.170 47.619 4.11 4.11 33.78 5.52
3054 3136 9.877178 AAAGAGAAGGATAAGTTACATGTAGTG 57.123 33.333 5.56 0.00 0.00 2.74
3061 3143 4.910458 AAGTTACATGTAGTGGAAGGCT 57.090 40.909 5.56 0.00 29.06 4.58
3081 3163 1.215173 TCCAATTAGGCAGGGACATGG 59.785 52.381 0.00 0.00 37.29 3.66
3082 3164 1.063717 CCAATTAGGCAGGGACATGGT 60.064 52.381 0.00 0.00 0.00 3.55
3083 3165 2.624029 CCAATTAGGCAGGGACATGGTT 60.624 50.000 0.00 0.00 0.00 3.67
3091 3173 3.088532 GCAGGGACATGGTTATGACAAA 58.911 45.455 0.00 0.00 37.73 2.83
3093 3175 4.202050 GCAGGGACATGGTTATGACAAATC 60.202 45.833 0.00 0.00 37.73 2.17
3100 3182 7.072177 ACATGGTTATGACAAATCTAACGTG 57.928 36.000 0.00 0.00 37.73 4.49
3102 3184 6.474819 TGGTTATGACAAATCTAACGTGTG 57.525 37.500 0.00 0.00 0.00 3.82
3104 3186 7.153315 TGGTTATGACAAATCTAACGTGTGTA 58.847 34.615 0.00 0.00 0.00 2.90
3105 3187 7.820386 TGGTTATGACAAATCTAACGTGTGTAT 59.180 33.333 0.00 0.00 0.00 2.29
3107 3189 8.865978 GTTATGACAAATCTAACGTGTGTATCA 58.134 33.333 0.00 0.00 0.00 2.15
3108 3190 6.699895 TGACAAATCTAACGTGTGTATCAC 57.300 37.500 0.00 0.00 43.03 3.06
3109 3191 5.636121 TGACAAATCTAACGTGTGTATCACC 59.364 40.000 0.00 0.00 43.51 4.02
3110 3192 5.543714 ACAAATCTAACGTGTGTATCACCA 58.456 37.500 0.00 0.00 43.51 4.17
3112 3194 6.653320 ACAAATCTAACGTGTGTATCACCATT 59.347 34.615 0.00 0.00 43.51 3.16
3115 3197 6.715344 TCTAACGTGTGTATCACCATTTTC 57.285 37.500 0.00 0.00 43.51 2.29
3117 3199 6.932400 TCTAACGTGTGTATCACCATTTTCTT 59.068 34.615 0.00 0.00 43.51 2.52
3118 3200 6.385649 AACGTGTGTATCACCATTTTCTTT 57.614 33.333 0.00 0.00 43.51 2.52
3119 3201 5.997385 ACGTGTGTATCACCATTTTCTTTC 58.003 37.500 0.00 0.00 43.51 2.62
3143 3227 8.347004 TCTTGATTGAAGCCATGTAAATTGTA 57.653 30.769 0.00 0.00 0.00 2.41
3144 3228 8.970020 TCTTGATTGAAGCCATGTAAATTGTAT 58.030 29.630 0.00 0.00 0.00 2.29
3148 3232 9.241317 GATTGAAGCCATGTAAATTGTATCTTG 57.759 33.333 0.00 0.00 0.00 3.02
3221 3305 5.087323 TCAAAGACTATGAGGGTGAACTCT 58.913 41.667 0.00 0.00 38.32 3.24
3229 3313 3.576861 TGAGGGTGAACTCTTCTTCTCA 58.423 45.455 0.00 0.00 38.32 3.27
3256 3340 6.932356 ATGTTGGTCTAATCTATTGTGCAG 57.068 37.500 0.00 0.00 0.00 4.41
3292 3376 5.065235 TCGGTACCGTATATCATCTGACAA 58.935 41.667 32.16 5.63 40.74 3.18
3293 3377 5.532032 TCGGTACCGTATATCATCTGACAAA 59.468 40.000 32.16 5.23 40.74 2.83
3402 3487 2.904915 CTCGGCGAAGAAGTTTTGTTC 58.095 47.619 12.13 0.00 0.00 3.18
3427 3513 1.270625 CCAGTTGGCTCGTTCCTGTTA 60.271 52.381 0.00 0.00 0.00 2.41
3430 3516 3.502211 CAGTTGGCTCGTTCCTGTTAAAT 59.498 43.478 0.00 0.00 0.00 1.40
3439 3525 2.755103 GTTCCTGTTAAATCCAGCCTGG 59.245 50.000 3.69 3.69 39.43 4.45
3481 3567 2.414824 GCCTCGAGTTACAGTGAGTCAG 60.415 54.545 12.31 0.00 0.00 3.51
3488 3574 5.334957 CGAGTTACAGTGAGTCAGTGTGTAT 60.335 44.000 34.12 22.44 45.99 2.29
3496 3582 3.138304 GAGTCAGTGTGTATGGTGCAAA 58.862 45.455 0.00 0.00 0.00 3.68
3527 3613 3.933332 GGAACAAGTGAGTAGGTGCATAC 59.067 47.826 0.00 0.00 0.00 2.39
3528 3614 4.562757 GGAACAAGTGAGTAGGTGCATACA 60.563 45.833 0.00 0.00 0.00 2.29
3568 3654 8.615878 TTCCGAGAAAACTTTCAATCTATTCA 57.384 30.769 5.07 0.00 39.61 2.57
3618 3704 0.305313 GTAGTAGACTGGAGCGAGCG 59.695 60.000 0.00 0.00 0.00 5.03
3648 3734 4.458829 TCGCCATCGTCCCTCCCT 62.459 66.667 0.00 0.00 36.96 4.20
3652 3738 2.491022 CCATCGTCCCTCCCTCGTC 61.491 68.421 0.00 0.00 0.00 4.20
3653 3739 2.516460 ATCGTCCCTCCCTCGTCG 60.516 66.667 0.00 0.00 0.00 5.12
3654 3740 3.040206 ATCGTCCCTCCCTCGTCGA 62.040 63.158 0.00 0.00 0.00 4.20
3659 3745 3.068691 CCTCCCTCGTCGAAGCCA 61.069 66.667 0.00 0.00 0.00 4.75
3662 3748 1.595993 CTCCCTCGTCGAAGCCAGAA 61.596 60.000 0.00 0.00 0.00 3.02
3674 3760 3.060339 CGAAGCCAGAAAAACATTGTTGC 60.060 43.478 2.13 1.12 0.00 4.17
3683 3769 6.415867 CAGAAAAACATTGTTGCAGTAGACAG 59.584 38.462 2.13 0.00 0.00 3.51
3684 3770 6.318648 AGAAAAACATTGTTGCAGTAGACAGA 59.681 34.615 2.13 0.00 0.00 3.41
3702 3788 3.955145 ACGGGAAGTCAATCATGCA 57.045 47.368 0.00 0.00 0.00 3.96
3707 3793 3.091545 GGGAAGTCAATCATGCAAAGGA 58.908 45.455 0.00 0.00 0.00 3.36
3710 3796 3.446442 AGTCAATCATGCAAAGGACCT 57.554 42.857 0.00 0.00 0.00 3.85
3714 3800 6.294473 AGTCAATCATGCAAAGGACCTATAG 58.706 40.000 0.00 0.00 0.00 1.31
3725 3811 0.032267 GACCTATAGGACCAGCGCAC 59.968 60.000 26.01 0.00 38.94 5.34
3731 3817 2.167398 TAGGACCAGCGCACCAGAAC 62.167 60.000 11.47 0.00 0.00 3.01
3732 3818 2.280797 GACCAGCGCACCAGAACA 60.281 61.111 11.47 0.00 0.00 3.18
3733 3819 1.891919 GACCAGCGCACCAGAACAA 60.892 57.895 11.47 0.00 0.00 2.83
3734 3820 2.117941 GACCAGCGCACCAGAACAAC 62.118 60.000 11.47 0.00 0.00 3.32
3735 3821 2.186160 CCAGCGCACCAGAACAACA 61.186 57.895 11.47 0.00 0.00 3.33
3736 3822 1.723608 CCAGCGCACCAGAACAACAA 61.724 55.000 11.47 0.00 0.00 2.83
3737 3823 0.317269 CAGCGCACCAGAACAACAAG 60.317 55.000 11.47 0.00 0.00 3.16
3738 3824 1.658409 GCGCACCAGAACAACAAGC 60.658 57.895 0.30 0.00 0.00 4.01
3739 3825 1.369209 CGCACCAGAACAACAAGCG 60.369 57.895 0.00 0.00 37.68 4.68
3740 3826 1.658409 GCACCAGAACAACAAGCGC 60.658 57.895 0.00 0.00 0.00 5.92
3741 3827 1.008538 CACCAGAACAACAAGCGCC 60.009 57.895 2.29 0.00 0.00 6.53
3742 3828 1.453015 ACCAGAACAACAAGCGCCA 60.453 52.632 2.29 0.00 0.00 5.69
3743 3829 1.008538 CCAGAACAACAAGCGCCAC 60.009 57.895 2.29 0.00 0.00 5.01
3744 3830 1.369209 CAGAACAACAAGCGCCACG 60.369 57.895 2.29 0.00 0.00 4.94
3751 3837 0.665835 AACAAGCGCCACGAATGAAA 59.334 45.000 2.29 0.00 0.00 2.69
3759 3845 1.069227 GCCACGAATGAAAAGAAGCGT 60.069 47.619 0.00 0.00 0.00 5.07
3760 3846 2.158841 GCCACGAATGAAAAGAAGCGTA 59.841 45.455 0.00 0.00 0.00 4.42
3766 3854 4.499399 CGAATGAAAAGAAGCGTAGATCGA 59.501 41.667 0.00 0.00 42.86 3.59
3772 3860 3.423996 AGAAGCGTAGATCGAAAGGAC 57.576 47.619 0.00 0.00 42.86 3.85
3791 3879 1.331214 CCCAACCTGCAGACAAACAT 58.669 50.000 17.39 0.00 0.00 2.71
3799 3887 4.528596 ACCTGCAGACAAACATAGTAGACT 59.471 41.667 17.39 0.00 0.00 3.24
3805 3893 7.976175 TGCAGACAAACATAGTAGACTAATGAG 59.024 37.037 1.89 0.00 31.39 2.90
3806 3894 8.191446 GCAGACAAACATAGTAGACTAATGAGA 58.809 37.037 1.89 0.00 31.39 3.27
3807 3895 9.509855 CAGACAAACATAGTAGACTAATGAGAC 57.490 37.037 1.89 0.00 31.39 3.36
3809 3897 8.362464 ACAAACATAGTAGACTAATGAGACCA 57.638 34.615 1.89 0.00 31.39 4.02
3814 3903 7.668052 ACATAGTAGACTAATGAGACCAGATCC 59.332 40.741 1.89 0.00 31.39 3.36
3837 3926 2.225727 GTCGGATCCACCAAAGACAAAC 59.774 50.000 13.41 0.00 38.90 2.93
3846 3935 1.227321 AAAGACAAACGCCGACCGA 60.227 52.632 0.00 0.00 41.02 4.69
3847 3936 1.219522 AAAGACAAACGCCGACCGAG 61.220 55.000 0.00 0.00 41.02 4.63
3851 3940 3.300765 AAACGCCGACCGAGTCCT 61.301 61.111 0.00 0.00 41.02 3.85
3854 3943 3.129502 CGCCGACCGAGTCCTACA 61.130 66.667 0.00 0.00 40.02 2.74
3889 3978 1.164041 AAACCTTCACACGCCTTCCG 61.164 55.000 0.00 0.00 44.21 4.30
3909 3998 1.792949 GACGACGCTTGAAACATCACT 59.207 47.619 0.00 0.00 0.00 3.41
3910 3999 1.526887 ACGACGCTTGAAACATCACTG 59.473 47.619 0.00 0.00 0.00 3.66
3914 4003 1.197721 CGCTTGAAACATCACTGGGAC 59.802 52.381 0.00 0.00 0.00 4.46
3915 4004 1.197721 GCTTGAAACATCACTGGGACG 59.802 52.381 0.00 0.00 0.00 4.79
3955 4045 5.397334 GGACCTATTCCATCTTGAAGAAGCT 60.397 44.000 0.00 0.00 45.10 3.74
3972 4062 4.680237 TGCCACCGCCTCGTCTTG 62.680 66.667 0.00 0.00 0.00 3.02
3974 4064 2.967397 CCACCGCCTCGTCTTGTA 59.033 61.111 0.00 0.00 0.00 2.41
3979 4069 1.506718 CGCCTCGTCTTGTAGAGCA 59.493 57.895 0.00 0.00 33.39 4.26
3985 4075 1.002366 CGTCTTGTAGAGCATGGCAC 58.998 55.000 0.00 0.00 0.00 5.01
4004 4094 4.359706 GCACAAACCCTAACAAAACTCTG 58.640 43.478 0.00 0.00 0.00 3.35
4012 4102 5.598417 ACCCTAACAAAACTCTGAAAAGCAT 59.402 36.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.460811 CGCCAATGCAGTAGCTCTCA 60.461 55.000 2.64 0.00 42.74 3.27
21 22 1.068333 CAAAACGCCAATGCAGTAGCT 60.068 47.619 2.64 0.00 42.74 3.32
34 35 7.626446 AGTTGTCATTTTAATTTCCAAAACGC 58.374 30.769 0.00 0.00 0.00 4.84
65 66 4.895889 AGACTGGACCGATGATCTTTATCA 59.104 41.667 0.00 0.00 46.01 2.15
107 108 1.864435 GCGGACATAGTAGGCAACGAG 60.864 57.143 0.00 0.00 46.39 4.18
111 112 1.227147 GCGCGGACATAGTAGGCAA 60.227 57.895 8.83 0.00 0.00 4.52
112 113 1.950973 TTGCGCGGACATAGTAGGCA 61.951 55.000 8.83 0.00 0.00 4.75
135 136 5.713792 TCTTTAAATTTCCGGATTGTGCA 57.286 34.783 4.15 0.00 0.00 4.57
136 137 6.253512 GTCATCTTTAAATTTCCGGATTGTGC 59.746 38.462 4.15 0.00 0.00 4.57
162 163 4.093291 AGCAAGGCTGGCTCGAGG 62.093 66.667 11.57 0.00 36.81 4.63
186 187 0.317186 GTAACGCTCGAGCCTCTAGC 60.317 60.000 30.66 8.12 44.25 3.42
213 214 8.583296 AGAAATAGCTTTGCTCTTGAAATCTTT 58.417 29.630 0.00 0.00 40.44 2.52
263 264 1.002315 GGCTACTACGGGTTGGTTCAA 59.998 52.381 0.00 0.00 0.00 2.69
285 286 1.165270 GAACCAACCCACAATCTCCG 58.835 55.000 0.00 0.00 0.00 4.63
286 287 2.286365 TGAACCAACCCACAATCTCC 57.714 50.000 0.00 0.00 0.00 3.71
338 339 1.364626 GAGTGACCTGCGCAATGGAG 61.365 60.000 21.44 4.58 35.45 3.86
470 471 7.553504 AAGACCTTTAAAACAAGGCCAATAT 57.446 32.000 5.01 0.00 46.71 1.28
498 499 8.877864 TTCCTTTGTATATTTGAACTCATGGT 57.122 30.769 0.00 0.00 0.00 3.55
499 500 7.917505 GCTTCCTTTGTATATTTGAACTCATGG 59.082 37.037 0.00 0.00 0.00 3.66
512 513 9.638239 CTTGCATTTTAAAGCTTCCTTTGTATA 57.362 29.630 0.00 0.00 41.24 1.47
514 515 7.496747 ACTTGCATTTTAAAGCTTCCTTTGTA 58.503 30.769 0.00 0.00 41.24 2.41
515 516 6.348498 ACTTGCATTTTAAAGCTTCCTTTGT 58.652 32.000 0.00 0.00 41.24 2.83
516 517 6.849588 ACTTGCATTTTAAAGCTTCCTTTG 57.150 33.333 0.00 0.00 41.24 2.77
517 518 7.864108 AAACTTGCATTTTAAAGCTTCCTTT 57.136 28.000 0.00 0.00 43.43 3.11
519 520 6.823182 ACAAAACTTGCATTTTAAAGCTTCCT 59.177 30.769 0.00 0.00 30.57 3.36
520 521 7.015226 ACAAAACTTGCATTTTAAAGCTTCC 57.985 32.000 0.00 0.00 30.57 3.46
521 522 8.894409 AAACAAAACTTGCATTTTAAAGCTTC 57.106 26.923 0.00 0.00 30.57 3.86
575 576 8.077386 ACAAAAATGCATGCCTTTTATTTCTTG 58.923 29.630 26.99 22.33 0.00 3.02
582 583 4.447054 CACGACAAAAATGCATGCCTTTTA 59.553 37.500 26.99 5.65 0.00 1.52
598 599 3.487372 TCTTTCTCCTCTCTCACGACAA 58.513 45.455 0.00 0.00 0.00 3.18
600 601 4.420168 CATTCTTTCTCCTCTCTCACGAC 58.580 47.826 0.00 0.00 0.00 4.34
627 629 2.425578 TGATAATTGCATGCATGGCG 57.574 45.000 27.34 3.29 0.00 5.69
679 684 2.630617 TTGCGCGCTCTGTCTCTCT 61.631 57.895 33.29 0.00 0.00 3.10
687 692 4.704833 ATGTGGGTTGCGCGCTCT 62.705 61.111 33.29 6.21 0.00 4.09
688 693 4.465512 CATGTGGGTTGCGCGCTC 62.466 66.667 33.29 23.57 0.00 5.03
794 802 0.323087 TCTGCCGTCAGTACCTAGCA 60.323 55.000 0.00 0.00 41.10 3.49
813 821 1.296068 GCTCCAGACAGCTTGCTCT 59.704 57.895 0.00 0.00 36.38 4.09
821 829 4.594367 GCAGAGTGCTCCAGACAG 57.406 61.111 0.00 0.00 40.96 3.51
864 874 1.841556 AGTCTGGTCTCCGGCCAAA 60.842 57.895 2.24 0.00 35.32 3.28
899 909 8.896744 CACAACAATTGAGAATGGAGTATACAT 58.103 33.333 13.59 0.00 0.00 2.29
913 923 3.213506 TGTCCACTCCACAACAATTGAG 58.786 45.455 13.59 6.78 0.00 3.02
914 924 3.289407 TGTCCACTCCACAACAATTGA 57.711 42.857 13.59 0.00 0.00 2.57
920 931 3.418684 AACCTATGTCCACTCCACAAC 57.581 47.619 0.00 0.00 0.00 3.32
922 933 2.500098 GCTAACCTATGTCCACTCCACA 59.500 50.000 0.00 0.00 0.00 4.17
929 940 2.236146 CAGTGTGGCTAACCTATGTCCA 59.764 50.000 0.00 0.00 36.63 4.02
934 945 3.451178 CCTGTACAGTGTGGCTAACCTAT 59.549 47.826 21.18 0.00 36.63 2.57
938 949 1.439679 GCCTGTACAGTGTGGCTAAC 58.560 55.000 21.18 1.39 41.92 2.34
944 955 1.698165 CTACACGCCTGTACAGTGTG 58.302 55.000 29.53 29.53 46.94 3.82
994 1010 1.524621 CCCGAGCTGCCATTTCGAT 60.525 57.895 10.13 0.00 36.49 3.59
1110 1129 4.431131 AGCAATGGGTGGGCTCCG 62.431 66.667 0.00 0.00 30.74 4.63
1245 1264 1.078567 GAGGTGCAGCAGGAGGAAG 60.079 63.158 19.63 0.00 0.00 3.46
1562 1588 0.170561 CTCGTCTAAGTGTCCACCCG 59.829 60.000 0.00 0.00 0.00 5.28
1563 1589 0.531200 CCTCGTCTAAGTGTCCACCC 59.469 60.000 0.00 0.00 0.00 4.61
1564 1590 1.473278 CTCCTCGTCTAAGTGTCCACC 59.527 57.143 0.00 0.00 0.00 4.61
1565 1591 2.161030 ACTCCTCGTCTAAGTGTCCAC 58.839 52.381 0.00 0.00 0.00 4.02
1570 1596 2.131776 AGGGACTCCTCGTCTAAGTG 57.868 55.000 0.00 0.00 39.80 3.16
1744 1785 2.588034 GACGGGCGCCTTGGTATC 60.588 66.667 28.56 11.08 0.00 2.24
1746 1787 3.379865 GATGACGGGCGCCTTGGTA 62.380 63.158 28.56 12.62 0.00 3.25
2043 2084 4.454678 TCACAAGATGGTGAAGATATGCC 58.545 43.478 0.00 0.00 44.34 4.40
2161 2211 2.183046 GAGCAGAGGCCTCGTGAC 59.817 66.667 26.95 16.84 42.56 3.67
2307 2357 1.165270 GTGAATTCACACCCCCTTCG 58.835 55.000 29.43 0.00 45.75 3.79
2322 2375 4.093743 TGTTCCTGAGCATACCTAGTGAA 58.906 43.478 0.00 0.00 0.00 3.18
2331 2384 0.911769 CCCACCTGTTCCTGAGCATA 59.088 55.000 0.00 0.00 0.00 3.14
2379 2432 5.045942 TGAGTCTTTGAGTATGCCATGGTAA 60.046 40.000 14.67 2.23 0.00 2.85
2381 2434 3.264193 TGAGTCTTTGAGTATGCCATGGT 59.736 43.478 14.67 0.00 0.00 3.55
2418 2477 2.104281 CCAGATGATGATGCACTCCTGA 59.896 50.000 0.00 0.00 0.00 3.86
2481 2540 1.298859 GCGTTGCATCCTCGTCCTTT 61.299 55.000 0.00 0.00 0.00 3.11
2497 2556 2.284798 ATCGCCTCGACATTGAGCGT 62.285 55.000 2.45 0.00 39.18 5.07
2503 2562 0.537188 ACCTTGATCGCCTCGACATT 59.463 50.000 0.00 0.00 39.18 2.71
2569 2629 3.333219 CTGGGAGAGGCCTGGCAA 61.333 66.667 22.05 0.00 36.66 4.52
2629 2689 2.287909 GCCTAGATGTCATCGACTGTCC 60.288 54.545 7.18 0.00 33.15 4.02
2633 2693 0.312416 GCGCCTAGATGTCATCGACT 59.688 55.000 7.18 0.00 33.15 4.18
2639 2699 0.391130 GTGTTGGCGCCTAGATGTCA 60.391 55.000 29.70 11.16 0.00 3.58
2643 2703 1.447838 CGTGTGTTGGCGCCTAGAT 60.448 57.895 29.70 0.00 0.00 1.98
2665 2725 0.950555 TTGAGCTTCGCGCAGATGTT 60.951 50.000 10.74 6.22 39.77 2.71
2666 2726 1.357258 CTTGAGCTTCGCGCAGATGT 61.357 55.000 10.74 0.00 39.77 3.06
2673 2733 1.919918 AGAGATTCTTGAGCTTCGCG 58.080 50.000 0.00 0.00 0.00 5.87
2676 2736 2.607180 GCGGAAGAGATTCTTGAGCTTC 59.393 50.000 0.00 0.00 36.73 3.86
2698 2758 3.185299 AACCGGGGTCATCGTGCAA 62.185 57.895 6.32 0.00 0.00 4.08
2836 2905 2.675348 CAGCCGTTCCATCTTTCTCTTC 59.325 50.000 0.00 0.00 0.00 2.87
3054 3136 1.685148 CTGCCTAATTGGAGCCTTCC 58.315 55.000 0.00 0.00 44.31 3.46
3061 3143 1.215173 CCATGTCCCTGCCTAATTGGA 59.785 52.381 0.00 0.00 38.35 3.53
3081 3163 8.865978 TGATACACACGTTAGATTTGTCATAAC 58.134 33.333 0.00 0.00 0.00 1.89
3082 3164 8.865978 GTGATACACACGTTAGATTTGTCATAA 58.134 33.333 0.00 0.00 39.78 1.90
3083 3165 8.402326 GTGATACACACGTTAGATTTGTCATA 57.598 34.615 0.00 0.00 39.78 2.15
3100 3182 9.132521 CAATCAAGAAAGAAAATGGTGATACAC 57.867 33.333 0.00 0.00 0.00 2.90
3102 3184 9.912634 TTCAATCAAGAAAGAAAATGGTGATAC 57.087 29.630 0.00 0.00 0.00 2.24
3104 3186 7.601508 GCTTCAATCAAGAAAGAAAATGGTGAT 59.398 33.333 0.00 0.00 33.29 3.06
3105 3187 6.925165 GCTTCAATCAAGAAAGAAAATGGTGA 59.075 34.615 0.00 0.00 33.29 4.02
3107 3189 6.183360 TGGCTTCAATCAAGAAAGAAAATGGT 60.183 34.615 0.00 0.00 33.29 3.55
3108 3190 6.225318 TGGCTTCAATCAAGAAAGAAAATGG 58.775 36.000 0.00 0.00 33.29 3.16
3109 3191 7.386848 ACATGGCTTCAATCAAGAAAGAAAATG 59.613 33.333 0.00 0.00 33.29 2.32
3110 3192 7.447594 ACATGGCTTCAATCAAGAAAGAAAAT 58.552 30.769 0.00 0.00 33.29 1.82
3112 3194 6.409524 ACATGGCTTCAATCAAGAAAGAAA 57.590 33.333 0.00 0.00 33.29 2.52
3115 3197 8.653338 CAATTTACATGGCTTCAATCAAGAAAG 58.347 33.333 0.00 0.00 33.29 2.62
3117 3199 7.669427 ACAATTTACATGGCTTCAATCAAGAA 58.331 30.769 0.00 0.00 33.29 2.52
3118 3200 7.230849 ACAATTTACATGGCTTCAATCAAGA 57.769 32.000 0.00 0.00 33.29 3.02
3119 3201 9.241317 GATACAATTTACATGGCTTCAATCAAG 57.759 33.333 0.00 0.00 34.85 3.02
3143 3227 3.594134 CTTCAAGAACCGAGAGCAAGAT 58.406 45.455 0.00 0.00 0.00 2.40
3144 3228 2.289072 CCTTCAAGAACCGAGAGCAAGA 60.289 50.000 0.00 0.00 0.00 3.02
3148 3232 1.021920 GGCCTTCAAGAACCGAGAGC 61.022 60.000 0.00 0.00 0.00 4.09
3196 3280 6.043243 AGAGTTCACCCTCATAGTCTTTGAAA 59.957 38.462 0.00 0.00 33.75 2.69
3201 3285 5.337788 AGAAGAGTTCACCCTCATAGTCTT 58.662 41.667 0.00 0.00 34.02 3.01
3203 3287 5.420739 AGAAGAAGAGTTCACCCTCATAGTC 59.579 44.000 0.00 0.00 33.75 2.59
3221 3305 7.939039 AGATTAGACCAACATTGTTGAGAAGAA 59.061 33.333 27.08 15.38 0.00 2.52
3229 3313 7.176515 TGCACAATAGATTAGACCAACATTGTT 59.823 33.333 0.00 0.00 33.98 2.83
3292 3376 7.936847 TGCCGTTCAATTAGTCCTCATATATTT 59.063 33.333 0.00 0.00 0.00 1.40
3293 3377 7.387948 GTGCCGTTCAATTAGTCCTCATATATT 59.612 37.037 0.00 0.00 0.00 1.28
3321 3405 1.945394 CCATGATCTACTTGCACCTGC 59.055 52.381 0.00 0.00 42.50 4.85
3481 3567 5.119931 TGAATCTTTTGCACCATACACAC 57.880 39.130 0.00 0.00 0.00 3.82
3488 3574 3.640498 TGTTCCATGAATCTTTTGCACCA 59.360 39.130 0.00 0.00 0.00 4.17
3496 3582 6.176183 CCTACTCACTTGTTCCATGAATCTT 58.824 40.000 0.00 0.00 0.00 2.40
3544 3630 8.792830 ATGAATAGATTGAAAGTTTTCTCGGA 57.207 30.769 6.21 0.00 38.02 4.55
3545 3631 8.668353 TGATGAATAGATTGAAAGTTTTCTCGG 58.332 33.333 6.21 0.00 38.02 4.63
3591 3677 4.395542 CGCTCCAGTCTACTACTAGTGTTT 59.604 45.833 5.39 0.00 35.76 2.83
3600 3686 0.814410 CCGCTCGCTCCAGTCTACTA 60.814 60.000 0.00 0.00 0.00 1.82
3605 3691 2.202676 CTTCCGCTCGCTCCAGTC 60.203 66.667 0.00 0.00 0.00 3.51
3629 3715 4.570663 GGAGGGACGATGGCGACG 62.571 72.222 0.00 0.00 41.64 5.12
3632 3718 3.917760 GAGGGAGGGACGATGGCG 61.918 72.222 0.00 0.00 44.79 5.69
3636 3722 2.516460 CGACGAGGGAGGGACGAT 60.516 66.667 0.00 0.00 0.00 3.73
3640 3726 2.754658 GCTTCGACGAGGGAGGGA 60.755 66.667 9.18 0.00 0.00 4.20
3648 3734 1.942677 TGTTTTTCTGGCTTCGACGA 58.057 45.000 0.00 0.00 0.00 4.20
3652 3738 3.060339 GCAACAATGTTTTTCTGGCTTCG 60.060 43.478 0.00 0.00 0.00 3.79
3653 3739 3.870419 TGCAACAATGTTTTTCTGGCTTC 59.130 39.130 0.00 0.00 0.00 3.86
3654 3740 3.871485 TGCAACAATGTTTTTCTGGCTT 58.129 36.364 0.00 0.00 0.00 4.35
3659 3745 6.318648 TCTGTCTACTGCAACAATGTTTTTCT 59.681 34.615 0.00 0.00 0.00 2.52
3662 3748 5.504010 CGTCTGTCTACTGCAACAATGTTTT 60.504 40.000 0.00 0.00 0.00 2.43
3674 3760 2.160205 TGACTTCCCGTCTGTCTACTG 58.840 52.381 0.00 0.00 43.25 2.74
3683 3769 1.737838 TGCATGATTGACTTCCCGTC 58.262 50.000 0.00 0.00 43.14 4.79
3684 3770 2.198827 TTGCATGATTGACTTCCCGT 57.801 45.000 0.00 0.00 0.00 5.28
3695 3781 4.042187 GGTCCTATAGGTCCTTTGCATGAT 59.958 45.833 23.44 0.00 39.79 2.45
3698 3784 3.392616 CTGGTCCTATAGGTCCTTTGCAT 59.607 47.826 28.40 0.00 42.76 3.96
3702 3788 2.040178 CGCTGGTCCTATAGGTCCTTT 58.960 52.381 28.40 0.00 42.76 3.11
3707 3793 1.400530 GGTGCGCTGGTCCTATAGGT 61.401 60.000 18.51 0.00 36.34 3.08
3710 3796 0.396556 TCTGGTGCGCTGGTCCTATA 60.397 55.000 9.73 0.00 0.00 1.31
3714 3800 3.050275 GTTCTGGTGCGCTGGTCC 61.050 66.667 9.73 6.75 0.00 4.46
3722 3808 1.658409 GCGCTTGTTGTTCTGGTGC 60.658 57.895 0.00 0.00 0.00 5.01
3725 3811 1.008538 GTGGCGCTTGTTGTTCTGG 60.009 57.895 7.64 0.00 0.00 3.86
3731 3817 0.040514 TTCATTCGTGGCGCTTGTTG 60.041 50.000 7.64 0.00 0.00 3.33
3732 3818 0.665835 TTTCATTCGTGGCGCTTGTT 59.334 45.000 7.64 0.00 0.00 2.83
3733 3819 0.665835 TTTTCATTCGTGGCGCTTGT 59.334 45.000 7.64 0.00 0.00 3.16
3734 3820 1.069296 TCTTTTCATTCGTGGCGCTTG 60.069 47.619 7.64 0.00 0.00 4.01
3735 3821 1.234821 TCTTTTCATTCGTGGCGCTT 58.765 45.000 7.64 0.00 0.00 4.68
3736 3822 1.197721 CTTCTTTTCATTCGTGGCGCT 59.802 47.619 7.64 0.00 0.00 5.92
3737 3823 1.606606 CTTCTTTTCATTCGTGGCGC 58.393 50.000 0.00 0.00 0.00 6.53
3738 3824 1.606606 GCTTCTTTTCATTCGTGGCG 58.393 50.000 0.00 0.00 0.00 5.69
3739 3825 1.069227 ACGCTTCTTTTCATTCGTGGC 60.069 47.619 0.00 0.00 0.00 5.01
3740 3826 2.969443 ACGCTTCTTTTCATTCGTGG 57.031 45.000 0.00 0.00 0.00 4.94
3741 3827 4.903638 TCTACGCTTCTTTTCATTCGTG 57.096 40.909 0.00 0.00 0.00 4.35
3742 3828 4.265556 CGATCTACGCTTCTTTTCATTCGT 59.734 41.667 0.00 0.00 34.51 3.85
3743 3829 4.499399 TCGATCTACGCTTCTTTTCATTCG 59.501 41.667 0.00 0.00 42.26 3.34
3744 3830 5.950965 TCGATCTACGCTTCTTTTCATTC 57.049 39.130 0.00 0.00 42.26 2.67
3751 3837 3.429135 GGTCCTTTCGATCTACGCTTCTT 60.429 47.826 0.00 0.00 42.26 2.52
3759 3845 2.500098 CAGGTTGGGTCCTTTCGATCTA 59.500 50.000 0.00 0.00 35.37 1.98
3760 3846 1.279271 CAGGTTGGGTCCTTTCGATCT 59.721 52.381 0.00 0.00 35.37 2.75
3766 3854 0.178990 GTCTGCAGGTTGGGTCCTTT 60.179 55.000 15.13 0.00 35.37 3.11
3772 3860 1.331214 ATGTTTGTCTGCAGGTTGGG 58.669 50.000 15.13 0.00 0.00 4.12
3791 3879 7.147284 ACTGGATCTGGTCTCATTAGTCTACTA 60.147 40.741 0.00 0.00 0.00 1.82
3799 3887 2.959030 CCGACTGGATCTGGTCTCATTA 59.041 50.000 13.57 0.00 37.49 1.90
3814 3903 1.001974 TGTCTTTGGTGGATCCGACTG 59.998 52.381 7.39 0.00 39.52 3.51
3828 3917 1.219522 CTCGGTCGGCGTTTGTCTTT 61.220 55.000 6.85 0.00 0.00 2.52
3837 3926 2.594119 CTTGTAGGACTCGGTCGGCG 62.594 65.000 0.00 0.00 32.65 6.46
3846 3935 1.064906 TCCGACGGATCTTGTAGGACT 60.065 52.381 13.88 0.00 36.39 3.85
3847 3936 1.334243 CTCCGACGGATCTTGTAGGAC 59.666 57.143 18.71 0.00 36.39 3.85
3851 3940 2.118313 TGTCTCCGACGGATCTTGTA 57.882 50.000 18.71 0.00 34.95 2.41
3854 3943 1.067071 GGTTTGTCTCCGACGGATCTT 60.067 52.381 18.71 0.00 34.95 2.40
3872 3961 2.030562 CGGAAGGCGTGTGAAGGT 59.969 61.111 0.00 0.00 0.00 3.50
3889 3978 1.792949 AGTGATGTTTCAAGCGTCGTC 59.207 47.619 0.00 0.00 32.48 4.20
3935 4024 4.275443 GGCAGCTTCTTCAAGATGGAATAG 59.725 45.833 2.65 0.00 44.80 1.73
3955 4045 4.680237 CAAGACGAGGCGGTGGCA 62.680 66.667 0.00 0.00 42.47 4.92
3972 4062 0.811281 GGGTTTGTGCCATGCTCTAC 59.189 55.000 0.00 0.00 0.00 2.59
3974 4064 0.698238 TAGGGTTTGTGCCATGCTCT 59.302 50.000 0.00 0.00 0.00 4.09
3979 4069 3.709141 AGTTTTGTTAGGGTTTGTGCCAT 59.291 39.130 0.00 0.00 0.00 4.40
3985 4075 6.255670 GCTTTTCAGAGTTTTGTTAGGGTTTG 59.744 38.462 0.00 0.00 0.00 2.93
4004 4094 6.213677 AGGACTCCGTTTTAAAATGCTTTTC 58.786 36.000 13.68 7.41 34.19 2.29


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

AutoCloner maintained by Alex Coulton.