Multiple sequence alignment - TraesCS3D01G266700

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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 TraesCS3D01G266700 chr3D 100.000 5895 0 0 1 5895 370113631 370107737 0.000000e+00 10887.0
1 TraesCS3D01G266700 chr3D 96.875 96 2 1 4432 4527 370109151 370109057 6.110000e-35 159.0
2 TraesCS3D01G266700 chr3D 96.875 96 2 1 4481 4575 370109200 370109105 6.110000e-35 159.0
3 TraesCS3D01G266700 chr3D 97.500 80 2 0 2616 2695 370110938 370110859 2.870000e-28 137.0
4 TraesCS3D01G266700 chr3D 97.500 80 2 0 2694 2773 370111016 370110937 2.870000e-28 137.0
5 TraesCS3D01G266700 chr3D 80.952 126 20 4 5209 5332 368836103 368835980 4.860000e-16 97.1
6 TraesCS3D01G266700 chr3A 95.086 2971 104 21 1 2947 491187317 491184365 0.000000e+00 4639.0
7 TraesCS3D01G266700 chr3A 93.127 1484 55 12 3050 4527 491184204 491182762 0.000000e+00 2132.0
8 TraesCS3D01G266700 chr3A 89.693 815 45 10 4481 5287 491182857 491182074 0.000000e+00 1003.0
9 TraesCS3D01G266700 chr3A 90.545 624 48 7 5274 5895 491180798 491180184 0.000000e+00 815.0
10 TraesCS3D01G266700 chr3A 98.750 80 1 0 2694 2773 491184696 491184617 6.160000e-30 143.0
11 TraesCS3D01G266700 chr3A 88.764 89 1 3 2963 3051 491184370 491184291 3.760000e-17 100.0
12 TraesCS3D01G266700 chr3B 92.336 3040 139 40 1 3011 481623589 481620615 0.000000e+00 4237.0
13 TraesCS3D01G266700 chr3B 92.222 900 43 15 3050 3946 481620500 481619625 0.000000e+00 1249.0
14 TraesCS3D01G266700 chr3B 93.033 732 45 6 4481 5209 481619080 481618352 0.000000e+00 1064.0
15 TraesCS3D01G266700 chr3B 90.080 625 30 17 5282 5895 481618219 481617616 0.000000e+00 782.0
16 TraesCS3D01G266700 chr3B 89.385 537 38 11 3953 4480 481619509 481618983 0.000000e+00 658.0
17 TraesCS3D01G266700 chr3B 96.154 104 4 0 4424 4527 481619088 481618985 2.820000e-38 171.0
18 TraesCS3D01G266700 chr3B 97.500 80 2 0 2694 2773 481621010 481620931 2.870000e-28 137.0
19 TraesCS3D01G266700 chr3B 84.848 99 14 1 5797 5895 468713972 468713875 1.350000e-16 99.0
20 TraesCS3D01G266700 chr3B 80.412 97 15 2 5220 5316 611699905 611699813 2.950000e-08 71.3
21 TraesCS3D01G266700 chr5B 80.620 258 38 10 4098 4352 328373999 328373751 7.800000e-44 189.0
22 TraesCS3D01G266700 chr2A 80.000 230 33 9 4123 4348 504339077 504339297 2.200000e-34 158.0
23 TraesCS3D01G266700 chr2D 79.654 231 34 9 4123 4349 372929901 372929680 2.840000e-33 154.0
24 TraesCS3D01G266700 chr2D 89.773 88 7 2 3526 3611 313635462 313635375 1.740000e-20 111.0
25 TraesCS3D01G266700 chr7A 79.204 226 31 11 4126 4341 177333450 177333669 6.160000e-30 143.0
26 TraesCS3D01G266700 chr7A 92.135 89 4 1 3525 3610 190473066 190472978 8.020000e-24 122.0
27 TraesCS3D01G266700 chr5D 77.528 267 38 12 4088 4352 289080797 289080551 2.210000e-29 141.0
28 TraesCS3D01G266700 chr5D 86.567 67 7 2 5249 5314 464928438 464928503 8.190000e-09 73.1
29 TraesCS3D01G266700 chr7D 78.667 225 33 9 4126 4341 175652399 175652617 1.030000e-27 135.0
30 TraesCS3D01G266700 chr7D 82.759 116 15 4 3521 3632 151326534 151326420 1.350000e-16 99.0
31 TraesCS3D01G266700 chr2B 78.112 233 30 13 4123 4352 442520368 442520154 1.720000e-25 128.0
32 TraesCS3D01G266700 chr2B 89.655 87 6 2 3526 3609 680200176 680200090 2.250000e-19 108.0
33 TraesCS3D01G266700 chr7B 90.698 86 6 1 3525 3610 149610258 149610341 4.830000e-21 113.0
34 TraesCS3D01G266700 chr7B 92.500 40 3 0 5274 5313 651492549 651492588 2.290000e-04 58.4
35 TraesCS3D01G266700 chr1B 86.869 99 8 3 3515 3608 606319328 606319230 8.080000e-19 106.0
36 TraesCS3D01G266700 chr4D 87.500 88 9 2 3526 3613 48537943 48537858 3.760000e-17 100.0
37 TraesCS3D01G266700 chr4A 81.633 98 9 6 5216 5313 73135235 73135147 8.190000e-09 73.1
38 TraesCS3D01G266700 chr6A 82.857 70 11 1 5270 5338 146547186 146547255 1.770000e-05 62.1


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 TraesCS3D01G266700 chr3D 370107737 370113631 5894 True 10887.000000 10887 100.000000 1 5895 1 chr3D.!!$R2 5894
1 TraesCS3D01G266700 chr3A 491180184 491187317 7133 True 1472.000000 4639 92.660833 1 5895 6 chr3A.!!$R1 5894
2 TraesCS3D01G266700 chr3B 481617616 481623589 5973 True 1185.428571 4237 92.958571 1 5895 7 chr3B.!!$R3 5894

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
105 106 0.453390 AGCAGCGCCAGATTAAAAGC 59.547 50.000 2.29 0.0 0.00 3.51 F
969 999 0.976073 TCAAAGGTCTAGCCCCCTCG 60.976 60.000 0.00 0.0 38.26 4.63 F
1104 1142 2.270205 CAGATCCTGGTGCGGCTT 59.730 61.111 0.00 0.0 0.00 4.35 F
2635 2679 1.270518 TGCTCCTGAGAACACTTCTGC 60.271 52.381 0.00 0.0 40.87 4.26 F
3492 3648 0.251653 TCCCTCTTGTCTACGCCAGT 60.252 55.000 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1272 2.490685 GACGGAGGAAGGCGAGAC 59.509 66.667 0.0 0.0 0.00 3.36 R
2576 2620 1.003233 CCCTCACACTCCAAACTACCC 59.997 57.143 0.0 0.0 0.00 3.69 R
2871 2915 1.627834 AGGCTCCTCTGAAAGAAGTGG 59.372 52.381 0.0 0.0 46.34 4.00 R
3954 4252 1.138859 CCCACAGCATGAAGGATACGA 59.861 52.381 0.0 0.0 39.69 3.43 R
5446 7134 1.359833 CAGCGACTGCCAAGCAAAA 59.640 52.632 0.0 0.0 44.31 2.44 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
69 70 1.524002 GCATAGAGCCAGCACTCCA 59.476 57.895 0.00 0.00 37.39 3.86
104 105 2.919229 CAAAGCAGCGCCAGATTAAAAG 59.081 45.455 2.29 0.00 0.00 2.27
105 106 0.453390 AGCAGCGCCAGATTAAAAGC 59.547 50.000 2.29 0.00 0.00 3.51
130 131 2.872245 GCAATCGCTACAGGCTCATAAA 59.128 45.455 0.00 0.00 39.13 1.40
131 132 3.312421 GCAATCGCTACAGGCTCATAAAA 59.688 43.478 0.00 0.00 39.13 1.52
132 133 4.553547 GCAATCGCTACAGGCTCATAAAAG 60.554 45.833 0.00 0.00 39.13 2.27
133 134 3.179443 TCGCTACAGGCTCATAAAAGG 57.821 47.619 0.00 0.00 39.13 3.11
138 139 4.336713 GCTACAGGCTCATAAAAGGAAAGG 59.663 45.833 0.00 0.00 38.06 3.11
392 393 1.541233 GGGATTCCGGAGCTATGTGTG 60.541 57.143 3.34 0.00 0.00 3.82
398 399 1.086067 CGGAGCTATGTGTGTGCAGG 61.086 60.000 0.00 0.00 0.00 4.85
431 432 2.717639 TCCAAGCTTAGGATTCCTGC 57.282 50.000 15.80 10.96 34.61 4.85
646 653 1.512310 GTCTTCTCTCGACGCCGTG 60.512 63.158 0.00 0.00 37.05 4.94
648 655 2.979197 CTTCTCTCGACGCCGTGGT 61.979 63.158 0.00 0.00 37.05 4.16
668 681 1.823169 TTGTGCTGGTCTACGGGGAC 61.823 60.000 2.10 2.10 35.66 4.46
758 771 1.830408 CGGAGAAGGGAGAGGCGAT 60.830 63.158 0.00 0.00 0.00 4.58
878 891 1.138266 ACGTGTGGAATAATCGGGGAG 59.862 52.381 0.00 0.00 0.00 4.30
923 936 3.873883 GACGCGAGATCGGACGGT 61.874 66.667 15.93 6.56 40.23 4.83
926 939 2.816360 CGCGAGATCGGACGGTGTA 61.816 63.158 0.00 0.00 40.23 2.90
927 940 1.009900 GCGAGATCGGACGGTGTAG 60.010 63.158 4.18 0.00 40.23 2.74
929 942 1.359475 GAGATCGGACGGTGTAGGC 59.641 63.158 0.00 0.00 0.00 3.93
931 944 1.065928 GATCGGACGGTGTAGGCTG 59.934 63.158 0.00 0.00 0.00 4.85
948 969 1.273606 GCTGATCCTAGGCGCTTCATA 59.726 52.381 7.64 0.00 0.00 2.15
949 970 2.673610 GCTGATCCTAGGCGCTTCATAG 60.674 54.545 7.64 4.98 0.00 2.23
955 985 3.126831 CCTAGGCGCTTCATAGTCAAAG 58.873 50.000 7.64 0.00 0.00 2.77
969 999 0.976073 TCAAAGGTCTAGCCCCCTCG 60.976 60.000 0.00 0.00 38.26 4.63
1104 1142 2.270205 CAGATCCTGGTGCGGCTT 59.730 61.111 0.00 0.00 0.00 4.35
1135 1173 4.410400 CCCACTGCCTCCGGTTCC 62.410 72.222 0.00 0.00 0.00 3.62
1602 1640 2.510238 GCCGAGAGCTGCGTCAAT 60.510 61.111 0.00 0.00 38.99 2.57
1620 1658 4.131088 GCCGTGGAGGAGTCGGTC 62.131 72.222 0.00 0.00 45.11 4.79
1715 1753 7.655732 AGTGCTAAAACAACAACTTTTCTGTTT 59.344 29.630 0.00 0.00 42.30 2.83
1735 1773 5.221601 TGTTTTGGTGTATACCCGACTGTAA 60.222 40.000 6.15 0.00 46.96 2.41
1857 1895 8.194769 TGTTTTCCTCTGGAATTTTAGTGTTTC 58.805 33.333 0.00 0.00 41.71 2.78
1874 1912 9.921637 TTAGTGTTTCATTTTGTTGAGAAGTTT 57.078 25.926 0.00 0.00 0.00 2.66
1916 1956 7.039993 TCAGTAGCTTGTCTGTACAATTGAGTA 60.040 37.037 13.59 0.00 44.43 2.59
1978 2018 7.187824 TGCTTGAGATCCTGTCTAATAGTTT 57.812 36.000 0.00 0.00 37.29 2.66
2010 2050 7.201513 GCTTAAATCGTAACCACAAATACGGTA 60.202 37.037 5.62 0.00 43.72 4.02
2011 2051 8.715191 TTAAATCGTAACCACAAATACGGTAT 57.285 30.769 5.62 0.00 43.72 2.73
2018 2058 3.938963 ACCACAAATACGGTATTGCTCTG 59.061 43.478 13.77 10.58 32.31 3.35
2020 2060 5.113383 CCACAAATACGGTATTGCTCTGTA 58.887 41.667 13.77 0.00 0.00 2.74
2133 2173 5.062308 CGTAAGTGGCTAATTTCAGTCAGTC 59.938 44.000 0.00 0.00 32.63 3.51
2233 2275 5.949952 TGTTATACTGAAGAGCTGGACTGTA 59.050 40.000 0.00 0.00 0.00 2.74
2321 2365 4.916983 AGTAGCAGATGATGAGAGTGAC 57.083 45.455 0.00 0.00 0.00 3.67
2408 2452 9.075678 GATCATGGGAATTACTCAAATGAATCT 57.924 33.333 0.00 0.00 33.52 2.40
2426 2470 4.550076 ATCTGACAAAAGTGAGGAGGAG 57.450 45.455 0.00 0.00 0.00 3.69
2576 2620 2.017049 GGATGTGATTTTGAGTCGGGG 58.983 52.381 0.00 0.00 0.00 5.73
2635 2679 1.270518 TGCTCCTGAGAACACTTCTGC 60.271 52.381 0.00 0.00 40.87 4.26
2871 2915 7.701445 AGAATCTGCTGATGTAAATAACAAGC 58.299 34.615 6.88 0.00 42.70 4.01
2873 2917 5.252547 TCTGCTGATGTAAATAACAAGCCA 58.747 37.500 0.00 0.00 40.01 4.75
2942 3007 4.218417 GCAGAATTGGAGGTATGTTGTGTT 59.782 41.667 0.00 0.00 0.00 3.32
2947 3012 8.919145 AGAATTGGAGGTATGTTGTGTTTTTAA 58.081 29.630 0.00 0.00 0.00 1.52
2948 3013 8.880878 AATTGGAGGTATGTTGTGTTTTTAAC 57.119 30.769 0.00 0.00 0.00 2.01
2949 3014 6.394025 TGGAGGTATGTTGTGTTTTTAACC 57.606 37.500 0.00 0.00 0.00 2.85
2950 3015 5.302313 TGGAGGTATGTTGTGTTTTTAACCC 59.698 40.000 0.00 0.00 0.00 4.11
2951 3016 5.279106 GGAGGTATGTTGTGTTTTTAACCCC 60.279 44.000 0.00 0.00 0.00 4.95
2952 3017 5.460416 AGGTATGTTGTGTTTTTAACCCCT 58.540 37.500 0.00 0.00 0.00 4.79
2953 3018 5.537295 AGGTATGTTGTGTTTTTAACCCCTC 59.463 40.000 0.00 0.00 0.00 4.30
2954 3019 4.948341 ATGTTGTGTTTTTAACCCCTCC 57.052 40.909 0.00 0.00 0.00 4.30
2955 3020 2.688958 TGTTGTGTTTTTAACCCCTCCG 59.311 45.455 0.00 0.00 0.00 4.63
2956 3021 1.984066 TGTGTTTTTAACCCCTCCGG 58.016 50.000 0.00 0.00 37.81 5.14
3011 3079 3.008375 ACTGTGCCAGACATGTTGATAGT 59.992 43.478 0.00 0.00 35.18 2.12
3012 3080 3.337358 TGTGCCAGACATGTTGATAGTG 58.663 45.455 0.00 0.00 0.00 2.74
3013 3081 3.007831 TGTGCCAGACATGTTGATAGTGA 59.992 43.478 0.00 0.00 0.00 3.41
3014 3082 4.194640 GTGCCAGACATGTTGATAGTGAT 58.805 43.478 0.00 0.00 0.00 3.06
3015 3083 5.104982 TGTGCCAGACATGTTGATAGTGATA 60.105 40.000 0.00 0.00 0.00 2.15
3016 3084 5.464722 GTGCCAGACATGTTGATAGTGATAG 59.535 44.000 0.00 0.00 0.00 2.08
3017 3085 4.993584 GCCAGACATGTTGATAGTGATAGG 59.006 45.833 0.00 0.00 0.00 2.57
3018 3086 5.453903 GCCAGACATGTTGATAGTGATAGGT 60.454 44.000 0.00 0.00 0.00 3.08
3019 3087 6.239317 GCCAGACATGTTGATAGTGATAGGTA 60.239 42.308 0.00 0.00 0.00 3.08
3020 3088 7.374272 CCAGACATGTTGATAGTGATAGGTAG 58.626 42.308 0.00 0.00 0.00 3.18
3021 3089 7.374272 CAGACATGTTGATAGTGATAGGTAGG 58.626 42.308 0.00 0.00 0.00 3.18
3022 3090 7.231519 CAGACATGTTGATAGTGATAGGTAGGA 59.768 40.741 0.00 0.00 0.00 2.94
3141 3297 6.430007 AGATCAAATTACTTTCAGCCCATCT 58.570 36.000 0.00 0.00 0.00 2.90
3174 3330 9.599866 CATTCATGGTTCTAGTCACAATAGTTA 57.400 33.333 0.00 0.00 0.00 2.24
3278 3434 2.562298 GGTGCTGATGGGAATTGTGAAA 59.438 45.455 0.00 0.00 0.00 2.69
3283 3439 5.701750 TGCTGATGGGAATTGTGAAATTTTG 59.298 36.000 0.00 0.00 0.00 2.44
3286 3442 7.550196 GCTGATGGGAATTGTGAAATTTTGTAT 59.450 33.333 0.00 0.00 0.00 2.29
3287 3443 8.774890 TGATGGGAATTGTGAAATTTTGTATG 57.225 30.769 0.00 0.00 0.00 2.39
3288 3444 7.333921 TGATGGGAATTGTGAAATTTTGTATGC 59.666 33.333 0.00 0.00 0.00 3.14
3289 3445 6.528321 TGGGAATTGTGAAATTTTGTATGCA 58.472 32.000 0.00 0.00 0.00 3.96
3290 3446 7.166851 TGGGAATTGTGAAATTTTGTATGCAT 58.833 30.769 3.79 3.79 0.00 3.96
3291 3447 8.316946 TGGGAATTGTGAAATTTTGTATGCATA 58.683 29.630 1.16 1.16 0.00 3.14
3292 3448 8.819974 GGGAATTGTGAAATTTTGTATGCATAG 58.180 33.333 6.67 0.00 0.00 2.23
3370 3526 3.571571 TCGTGTAGAACTTCCATTGTCG 58.428 45.455 0.00 0.00 0.00 4.35
3383 3539 2.754472 CATTGTCGTTCAGTGGACTCA 58.246 47.619 0.00 0.00 34.31 3.41
3398 3554 3.003480 GGACTCAACCTGTGATAACAGC 58.997 50.000 4.45 0.00 35.07 4.40
3437 3593 3.117738 AGGTACTATAGCCGGTGTACTGT 60.118 47.826 1.90 0.00 36.02 3.55
3479 3635 3.394836 GAGTTGCCGCCTCCCTCT 61.395 66.667 0.00 0.00 0.00 3.69
3480 3636 2.930562 AGTTGCCGCCTCCCTCTT 60.931 61.111 0.00 0.00 0.00 2.85
3481 3637 2.747855 GTTGCCGCCTCCCTCTTG 60.748 66.667 0.00 0.00 0.00 3.02
3482 3638 3.249189 TTGCCGCCTCCCTCTTGT 61.249 61.111 0.00 0.00 0.00 3.16
3483 3639 3.254024 TTGCCGCCTCCCTCTTGTC 62.254 63.158 0.00 0.00 0.00 3.18
3484 3640 3.394836 GCCGCCTCCCTCTTGTCT 61.395 66.667 0.00 0.00 0.00 3.41
3485 3641 2.058595 GCCGCCTCCCTCTTGTCTA 61.059 63.158 0.00 0.00 0.00 2.59
3486 3642 1.817209 CCGCCTCCCTCTTGTCTAC 59.183 63.158 0.00 0.00 0.00 2.59
3487 3643 1.433879 CGCCTCCCTCTTGTCTACG 59.566 63.158 0.00 0.00 0.00 3.51
3488 3644 1.142097 GCCTCCCTCTTGTCTACGC 59.858 63.158 0.00 0.00 0.00 4.42
3489 3645 1.817209 CCTCCCTCTTGTCTACGCC 59.183 63.158 0.00 0.00 0.00 5.68
3490 3646 0.970937 CCTCCCTCTTGTCTACGCCA 60.971 60.000 0.00 0.00 0.00 5.69
3491 3647 0.457851 CTCCCTCTTGTCTACGCCAG 59.542 60.000 0.00 0.00 0.00 4.85
3492 3648 0.251653 TCCCTCTTGTCTACGCCAGT 60.252 55.000 0.00 0.00 0.00 4.00
3493 3649 1.005097 TCCCTCTTGTCTACGCCAGTA 59.995 52.381 0.00 0.00 0.00 2.74
3494 3650 2.032620 CCCTCTTGTCTACGCCAGTAT 58.967 52.381 0.00 0.00 31.58 2.12
3495 3651 2.431057 CCCTCTTGTCTACGCCAGTATT 59.569 50.000 0.00 0.00 31.58 1.89
3496 3652 3.448686 CCTCTTGTCTACGCCAGTATTG 58.551 50.000 0.00 0.00 31.58 1.90
3497 3653 3.130516 CCTCTTGTCTACGCCAGTATTGA 59.869 47.826 0.00 0.00 31.58 2.57
3498 3654 4.202161 CCTCTTGTCTACGCCAGTATTGAT 60.202 45.833 0.00 0.00 31.58 2.57
3499 3655 4.682787 TCTTGTCTACGCCAGTATTGATG 58.317 43.478 0.00 0.00 31.58 3.07
3500 3656 4.159693 TCTTGTCTACGCCAGTATTGATGT 59.840 41.667 0.00 0.00 31.58 3.06
3501 3657 5.358725 TCTTGTCTACGCCAGTATTGATGTA 59.641 40.000 0.00 0.00 31.58 2.29
3502 3658 5.784578 TGTCTACGCCAGTATTGATGTAT 57.215 39.130 0.00 0.00 31.58 2.29
3511 3691 6.468956 CGCCAGTATTGATGTATTTGTTTGAC 59.531 38.462 0.00 0.00 0.00 3.18
3547 3727 6.436532 TCTTACTCCCTCCGATCCATATTAAC 59.563 42.308 0.00 0.00 0.00 2.01
3551 3731 4.905456 TCCCTCCGATCCATATTAACTGTT 59.095 41.667 0.00 0.00 0.00 3.16
3636 3816 6.418057 AATTTTGACCTGGCAATTCTAACA 57.582 33.333 0.00 0.00 0.00 2.41
3785 3968 8.454894 GTCTTTCTACCATCAAAATTCTTCTCC 58.545 37.037 0.00 0.00 0.00 3.71
3787 3970 5.755849 TCTACCATCAAAATTCTTCTCCCC 58.244 41.667 0.00 0.00 0.00 4.81
3835 4018 8.200792 GGTGACAAGTTGAATCATCTCTATAGT 58.799 37.037 10.54 0.00 0.00 2.12
3870 4053 5.876651 TTGCATAGCTTAGGAGATGAAGA 57.123 39.130 0.00 0.00 0.00 2.87
3954 4252 9.716556 TTTCTCCCTATTCTAGTATCTTGTTCT 57.283 33.333 0.00 0.00 0.00 3.01
3973 4271 2.101415 TCTCGTATCCTTCATGCTGTGG 59.899 50.000 0.00 0.00 0.00 4.17
4039 4340 1.277273 TGACAAGACATCCAGCTCCAG 59.723 52.381 0.00 0.00 0.00 3.86
4071 4372 5.241506 TGGTCTGAGCTTTTTGTTCTAATGG 59.758 40.000 8.47 0.00 0.00 3.16
4090 4391 2.167693 TGGCCTCCTTATGTTCAGTACG 59.832 50.000 3.32 0.00 0.00 3.67
4095 4396 2.835764 TCCTTATGTTCAGTACGCCCTT 59.164 45.455 0.00 0.00 0.00 3.95
4111 4412 3.494223 CGCCCTTTGTTCCAAATTTCCTT 60.494 43.478 0.00 0.00 0.00 3.36
4379 4685 9.508567 GTAAAATCTATTTGCCATCTTCTGTTC 57.491 33.333 0.00 0.00 0.00 3.18
4387 4693 4.851843 TGCCATCTTCTGTTCAATCTCAT 58.148 39.130 0.00 0.00 0.00 2.90
4388 4694 5.258841 TGCCATCTTCTGTTCAATCTCATT 58.741 37.500 0.00 0.00 0.00 2.57
4515 4821 8.731275 TGTTTTGAAGTTTGAAGTATCTCTGA 57.269 30.769 0.00 0.00 0.00 3.27
4516 4822 8.612619 TGTTTTGAAGTTTGAAGTATCTCTGAC 58.387 33.333 0.00 0.00 0.00 3.51
4517 4823 8.612619 GTTTTGAAGTTTGAAGTATCTCTGACA 58.387 33.333 0.00 0.00 0.00 3.58
4518 4824 8.908786 TTTGAAGTTTGAAGTATCTCTGACAT 57.091 30.769 0.00 0.00 0.00 3.06
4519 4825 9.996554 TTTGAAGTTTGAAGTATCTCTGACATA 57.003 29.630 0.00 0.00 0.00 2.29
4521 4827 9.809096 TGAAGTTTGAAGTATCTCTGACATATC 57.191 33.333 0.00 0.00 0.00 1.63
4522 4828 9.809096 GAAGTTTGAAGTATCTCTGACATATCA 57.191 33.333 0.00 0.00 0.00 2.15
4524 4830 9.761504 AGTTTGAAGTATCTCTGACATATCATG 57.238 33.333 0.00 0.00 33.22 3.07
4530 4836 9.973450 AAGTATCTCTGACATATCATGTTACAC 57.027 33.333 0.00 0.00 45.03 2.90
4531 4837 9.360901 AGTATCTCTGACATATCATGTTACACT 57.639 33.333 0.00 0.00 45.03 3.55
4532 4838 9.619316 GTATCTCTGACATATCATGTTACACTC 57.381 37.037 0.00 0.00 45.03 3.51
4533 4839 7.645058 TCTCTGACATATCATGTTACACTCA 57.355 36.000 0.00 0.00 45.03 3.41
4534 4840 8.242729 TCTCTGACATATCATGTTACACTCAT 57.757 34.615 0.00 0.00 45.03 2.90
4535 4841 8.699130 TCTCTGACATATCATGTTACACTCATT 58.301 33.333 0.00 0.00 45.03 2.57
4536 4842 9.971922 CTCTGACATATCATGTTACACTCATTA 57.028 33.333 0.00 0.00 45.03 1.90
4553 4859 9.725019 ACACTCATTATATGTTCTGAAGTTTGA 57.275 29.630 0.00 0.00 0.00 2.69
4555 4861 9.950496 ACTCATTATATGTTCTGAAGTTTGAGT 57.050 29.630 0.00 0.00 35.40 3.41
4653 4959 5.738909 CTCCAGACTCATGGACTAAAATGT 58.261 41.667 0.00 0.00 44.56 2.71
4765 5071 4.026744 CAACTCTGGAGGGAAGTGAGATA 58.973 47.826 2.58 0.00 0.00 1.98
4802 5108 8.575649 AACGATTACTATCCCAAGAAAACAAT 57.424 30.769 0.00 0.00 0.00 2.71
4804 5110 9.675464 ACGATTACTATCCCAAGAAAACAATTA 57.325 29.630 0.00 0.00 0.00 1.40
4805 5111 9.931210 CGATTACTATCCCAAGAAAACAATTAC 57.069 33.333 0.00 0.00 0.00 1.89
4806 5112 9.931210 GATTACTATCCCAAGAAAACAATTACG 57.069 33.333 0.00 0.00 0.00 3.18
4807 5113 9.675464 ATTACTATCCCAAGAAAACAATTACGA 57.325 29.630 0.00 0.00 0.00 3.43
4824 5130 6.668541 ATTACGAATGTCAAGTTCATCTGG 57.331 37.500 0.00 0.00 0.00 3.86
4870 5177 5.357878 TGATAAGAAATCTTTCGCTTGGCAT 59.642 36.000 0.29 0.00 41.92 4.40
4898 5205 9.400638 GGAAATTAACGAGATCTCTGTATGTAG 57.599 37.037 20.26 4.94 0.00 2.74
4929 5236 2.735134 CCTTGCTGCTGCTTGATTTTTC 59.265 45.455 17.00 0.00 40.48 2.29
4964 5271 4.021925 GGTGCCTCGGCCTCAAGT 62.022 66.667 0.00 0.00 41.09 3.16
4981 5289 6.148811 GCCTCAAGTGCTAAGTTTGTACATTA 59.851 38.462 8.09 0.00 0.00 1.90
4997 5305 8.574251 TTGTACATTAACATATTGTGAGGCTT 57.426 30.769 0.00 0.00 0.00 4.35
4999 5307 9.845740 TGTACATTAACATATTGTGAGGCTTAT 57.154 29.630 0.00 0.00 0.00 1.73
5024 5332 4.046938 TCTTGTAATCTCTGACGCCATC 57.953 45.455 0.00 0.00 0.00 3.51
5091 5399 1.377725 CTGCCGCTTCCATGGAGTT 60.378 57.895 15.53 0.00 0.00 3.01
5138 5446 3.438087 CACTGTTCTAATGTTGGCTCCTG 59.562 47.826 0.00 0.00 0.00 3.86
5194 5502 6.034898 GCTGTGTGATTTTGGTTGCAATATAC 59.965 38.462 0.59 0.00 0.00 1.47
5200 5508 9.023967 GTGATTTTGGTTGCAATATACTTCATC 57.976 33.333 0.59 0.00 0.00 2.92
5358 7046 2.614983 ACGAAAACGGCTGAGCTTTTTA 59.385 40.909 14.34 0.00 0.00 1.52
5360 7048 3.547214 CGAAAACGGCTGAGCTTTTTACA 60.547 43.478 14.34 0.00 0.00 2.41
5361 7049 4.546570 GAAAACGGCTGAGCTTTTTACAT 58.453 39.130 14.34 0.00 0.00 2.29
5362 7050 3.559238 AACGGCTGAGCTTTTTACATG 57.441 42.857 3.72 0.00 0.00 3.21
5363 7051 2.504367 ACGGCTGAGCTTTTTACATGT 58.496 42.857 3.72 2.69 0.00 3.21
5366 7054 5.424757 ACGGCTGAGCTTTTTACATGTATA 58.575 37.500 6.36 0.00 0.00 1.47
5400 7088 5.102313 GGCATTGCAACAACCTCTATTTAC 58.898 41.667 11.39 0.00 0.00 2.01
5466 7154 1.383456 TTTGCTTGGCAGTCGCTGTT 61.383 50.000 8.32 0.00 40.61 3.16
5479 7167 4.932200 CAGTCGCTGTTCTAAATTTCTCCT 59.068 41.667 0.00 0.00 0.00 3.69
5484 7172 5.230306 CGCTGTTCTAAATTTCTCCTAGACG 59.770 44.000 0.00 0.00 0.00 4.18
5499 7187 5.470368 TCCTAGACGAAATCAAGTGAACTG 58.530 41.667 0.00 0.00 0.00 3.16
5518 7206 2.896044 CTGCTCCTATGGCTACTCATCA 59.104 50.000 0.00 0.00 0.00 3.07
5521 7209 3.576118 GCTCCTATGGCTACTCATCAAGA 59.424 47.826 0.00 0.00 0.00 3.02
5532 7220 2.434884 ATCAAGACGTGGGCAGCG 60.435 61.111 0.00 0.00 0.00 5.18
5571 7259 1.269257 GGTTGCGCTTTTGCTTTCTCT 60.269 47.619 9.73 0.00 44.80 3.10
5584 7272 6.560253 TTGCTTTCTCTCTTTACCATGTTC 57.440 37.500 0.00 0.00 0.00 3.18
5717 7411 4.502962 CAAGAATCTCTTCACTCAGGTCC 58.497 47.826 0.00 0.00 33.78 4.46
5727 7421 2.123208 TCAGGTCCGGTGGTGACA 60.123 61.111 0.00 0.00 34.36 3.58
5729 7423 2.200370 AGGTCCGGTGGTGACAGA 59.800 61.111 0.00 0.00 44.46 3.41
5761 7456 2.854076 CCAAAGGCCCCTCAACCT 59.146 61.111 0.00 0.00 38.14 3.50
5836 7531 3.380479 TTCTACGTGACCAAGTTCAGG 57.620 47.619 0.00 0.00 37.40 3.86
5847 7542 1.978455 AAGTTCAGGCGTGTGGTGGA 61.978 55.000 6.26 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.811555 TTATGTGTGACAAGTGCAGTTC 57.188 40.909 3.08 0.00 0.00 3.01
51 52 0.108207 ATGGAGTGCTGGCTCTATGC 59.892 55.000 0.00 0.00 35.75 3.14
61 62 2.738643 CGGTAACAATCGATGGAGTGCT 60.739 50.000 6.84 0.00 41.80 4.40
69 70 2.080693 TGCTTTGCGGTAACAATCGAT 58.919 42.857 0.00 0.00 0.00 3.59
94 95 5.755813 AGCGATTGCATAGCTTTTAATCTG 58.244 37.500 7.90 0.00 46.23 2.90
104 105 0.514691 GCCTGTAGCGATTGCATAGC 59.485 55.000 7.90 0.00 46.23 2.97
130 131 1.708551 TGGATTCGTTCCCCTTTCCTT 59.291 47.619 4.99 0.00 44.77 3.36
131 132 1.368374 TGGATTCGTTCCCCTTTCCT 58.632 50.000 4.99 0.00 44.77 3.36
132 133 1.816835 GTTGGATTCGTTCCCCTTTCC 59.183 52.381 4.99 0.00 44.77 3.13
133 134 1.467342 CGTTGGATTCGTTCCCCTTTC 59.533 52.381 4.99 0.00 44.77 2.62
138 139 0.743345 CTCCCGTTGGATTCGTTCCC 60.743 60.000 4.99 0.00 44.77 3.97
163 164 3.698820 ACGCCAACTCCGGTACCC 61.699 66.667 6.25 0.00 0.00 3.69
305 306 4.912395 AAGCCCAAGGTTGCCGCA 62.912 61.111 0.00 0.00 30.94 5.69
381 382 2.322355 ATCCTGCACACACATAGCTC 57.678 50.000 0.00 0.00 0.00 4.09
392 393 2.514824 GGCGGAGGAATCCTGCAC 60.515 66.667 20.67 10.96 42.30 4.57
398 399 0.464554 CTTGGAAGGGCGGAGGAATC 60.465 60.000 0.00 0.00 0.00 2.52
620 627 1.137825 CGAGAGAAGACACCGCTCC 59.862 63.158 0.00 0.00 0.00 4.70
621 628 0.179184 GTCGAGAGAAGACACCGCTC 60.179 60.000 0.00 0.00 45.01 5.03
646 653 0.953960 CCCGTAGACCAGCACAAACC 60.954 60.000 0.00 0.00 0.00 3.27
648 655 1.122632 TCCCCGTAGACCAGCACAAA 61.123 55.000 0.00 0.00 0.00 2.83
668 681 4.176752 GCCTACTTCCCCGGCCTG 62.177 72.222 0.00 0.00 37.86 4.85
797 810 0.045623 TCCAAGCCCAGATCCCCTTA 59.954 55.000 0.00 0.00 0.00 2.69
906 919 3.873883 ACCGTCCGATCTCGCGTC 61.874 66.667 5.77 0.00 38.18 5.19
927 940 1.301322 GAAGCGCCTAGGATCAGCC 60.301 63.158 14.75 0.00 0.00 4.85
929 942 2.560542 ACTATGAAGCGCCTAGGATCAG 59.439 50.000 14.75 0.98 0.00 2.90
931 944 2.558795 TGACTATGAAGCGCCTAGGATC 59.441 50.000 14.75 5.17 0.00 3.36
948 969 0.119358 AGGGGGCTAGACCTTTGACT 59.881 55.000 16.16 2.52 39.10 3.41
949 970 0.542333 GAGGGGGCTAGACCTTTGAC 59.458 60.000 16.16 0.00 37.18 3.18
955 985 1.381463 AGAACGAGGGGGCTAGACC 60.381 63.158 5.86 5.86 37.93 3.85
969 999 4.323180 GGAAGGGGAAAAGAGAGAGAGAAC 60.323 50.000 0.00 0.00 0.00 3.01
1234 1272 2.490685 GACGGAGGAAGGCGAGAC 59.509 66.667 0.00 0.00 0.00 3.36
1242 1280 3.437795 GACGCGAGGACGGAGGAA 61.438 66.667 15.93 0.00 40.15 3.36
1620 1658 3.628646 CTTCCCAAGGGAGGCACGG 62.629 68.421 8.06 0.00 46.06 4.94
1760 1798 8.821894 GTTGAAACAATATGCACCAGTTTTTAA 58.178 29.630 9.00 6.30 33.04 1.52
1765 1803 4.343526 TGGTTGAAACAATATGCACCAGTT 59.656 37.500 0.00 0.00 0.00 3.16
1766 1804 3.894427 TGGTTGAAACAATATGCACCAGT 59.106 39.130 0.00 0.00 0.00 4.00
1767 1805 4.517952 TGGTTGAAACAATATGCACCAG 57.482 40.909 0.00 0.00 0.00 4.00
1768 1806 5.714333 ACTATGGTTGAAACAATATGCACCA 59.286 36.000 0.00 0.00 0.00 4.17
1769 1807 6.207691 ACTATGGTTGAAACAATATGCACC 57.792 37.500 0.00 0.00 0.00 5.01
1770 1808 7.312154 TGAACTATGGTTGAAACAATATGCAC 58.688 34.615 0.00 0.00 35.58 4.57
1857 1895 5.581874 ACTTGGCAAACTTCTCAACAAAATG 59.418 36.000 0.00 0.00 0.00 2.32
1874 1912 9.056005 CAAGCTACTGATTATATTAACTTGGCA 57.944 33.333 0.00 0.00 0.00 4.92
1916 1956 3.181436 CCAGACTTATCCTTGGCATCCAT 60.181 47.826 0.00 0.00 31.53 3.41
1978 2018 9.968870 ATTTGTGGTTACGATTTAAGCTAAAAA 57.031 25.926 0.00 0.00 0.00 1.94
2010 2050 8.338259 GTCACATAAAATCGAATACAGAGCAAT 58.662 33.333 0.00 0.00 0.00 3.56
2011 2051 7.333174 TGTCACATAAAATCGAATACAGAGCAA 59.667 33.333 0.00 0.00 0.00 3.91
2018 2058 9.767684 TCATGTTTGTCACATAAAATCGAATAC 57.232 29.630 0.00 0.00 45.06 1.89
2020 2060 9.859427 AATCATGTTTGTCACATAAAATCGAAT 57.141 25.926 0.00 0.00 45.06 3.34
2133 2173 3.194542 CCTTTATAGCCTCTCATCCCTCG 59.805 52.174 0.00 0.00 0.00 4.63
2233 2275 8.202137 AGTTAGCACCGTAATAGAATAACACAT 58.798 33.333 0.00 0.00 0.00 3.21
2321 2365 2.798847 CACATCACTGTCACTGTCACTG 59.201 50.000 0.00 0.00 31.62 3.66
2408 2452 3.071602 CCTTCTCCTCCTCACTTTTGTCA 59.928 47.826 0.00 0.00 0.00 3.58
2426 2470 3.064900 ACTGAAGCCAGATCAACCTTC 57.935 47.619 10.53 10.53 43.02 3.46
2576 2620 1.003233 CCCTCACACTCCAAACTACCC 59.997 57.143 0.00 0.00 0.00 3.69
2635 2679 5.972107 ACCATTCTCAGAAGTTCCATTTG 57.028 39.130 0.00 0.00 0.00 2.32
2871 2915 1.627834 AGGCTCCTCTGAAAGAAGTGG 59.372 52.381 0.00 0.00 46.34 4.00
2873 2917 2.038295 CACAGGCTCCTCTGAAAGAAGT 59.962 50.000 0.00 0.00 46.34 3.01
2951 3016 5.221561 TGTGGTGATAAATATGTACCCGGAG 60.222 44.000 0.73 0.00 0.00 4.63
2952 3017 4.654724 TGTGGTGATAAATATGTACCCGGA 59.345 41.667 0.73 0.00 0.00 5.14
2953 3018 4.963373 TGTGGTGATAAATATGTACCCGG 58.037 43.478 0.00 0.00 0.00 5.73
2954 3019 5.607477 ACTGTGGTGATAAATATGTACCCG 58.393 41.667 0.00 0.00 0.00 5.28
2955 3020 7.988599 TGTAACTGTGGTGATAAATATGTACCC 59.011 37.037 0.00 0.00 0.00 3.69
2956 3021 8.951787 TGTAACTGTGGTGATAAATATGTACC 57.048 34.615 0.00 0.00 0.00 3.34
2966 3031 9.594478 CAGTGTTATTATGTAACTGTGGTGATA 57.406 33.333 0.00 0.00 34.81 2.15
2967 3032 8.492673 CAGTGTTATTATGTAACTGTGGTGAT 57.507 34.615 0.00 0.00 34.81 3.06
3011 3079 9.132923 CAAAATCACTACTACTCCTACCTATCA 57.867 37.037 0.00 0.00 0.00 2.15
3012 3080 9.134055 ACAAAATCACTACTACTCCTACCTATC 57.866 37.037 0.00 0.00 0.00 2.08
3013 3081 9.134055 GACAAAATCACTACTACTCCTACCTAT 57.866 37.037 0.00 0.00 0.00 2.57
3014 3082 8.111545 TGACAAAATCACTACTACTCCTACCTA 58.888 37.037 0.00 0.00 29.99 3.08
3015 3083 6.952358 TGACAAAATCACTACTACTCCTACCT 59.048 38.462 0.00 0.00 29.99 3.08
3016 3084 7.166691 TGACAAAATCACTACTACTCCTACC 57.833 40.000 0.00 0.00 29.99 3.18
3062 3218 7.624661 GTCATTGTGATAGTATGACATGTGTG 58.375 38.462 1.15 2.05 44.67 3.82
3141 3297 8.264347 TGTGACTAGAACCATGAATGCTATTTA 58.736 33.333 0.00 0.00 0.00 1.40
3188 3344 6.767456 TCGGAGGGTAACATTAAACTTGTTA 58.233 36.000 0.00 0.00 38.26 2.41
3278 3434 6.548622 ACCAGCTGATTCTATGCATACAAAAT 59.451 34.615 17.39 3.36 0.00 1.82
3283 3439 3.188048 GCACCAGCTGATTCTATGCATAC 59.812 47.826 17.39 0.00 37.91 2.39
3286 3442 1.065272 TGCACCAGCTGATTCTATGCA 60.065 47.619 17.39 16.73 42.74 3.96
3287 3443 1.602851 CTGCACCAGCTGATTCTATGC 59.397 52.381 17.39 14.44 41.71 3.14
3288 3444 3.189618 TCTGCACCAGCTGATTCTATG 57.810 47.619 17.39 4.60 42.77 2.23
3289 3445 3.806380 CTTCTGCACCAGCTGATTCTAT 58.194 45.455 17.39 0.00 46.18 1.98
3290 3446 2.679059 GCTTCTGCACCAGCTGATTCTA 60.679 50.000 17.39 0.00 46.18 2.10
3291 3447 1.949547 GCTTCTGCACCAGCTGATTCT 60.950 52.381 17.39 0.00 46.18 2.40
3292 3448 0.450983 GCTTCTGCACCAGCTGATTC 59.549 55.000 17.39 3.62 46.18 2.52
3333 3489 3.198068 ACACGAGCTAATTATGCAGGTG 58.802 45.455 17.91 17.91 39.77 4.00
3370 3526 2.158957 TCACAGGTTGAGTCCACTGAAC 60.159 50.000 11.39 0.77 38.98 3.18
3437 3593 3.314693 CTGTCCTAAGGGCCCATAACTA 58.685 50.000 27.56 5.97 0.00 2.24
3481 3637 6.479001 ACAAATACATCAATACTGGCGTAGAC 59.521 38.462 0.00 0.00 0.00 2.59
3482 3638 6.578944 ACAAATACATCAATACTGGCGTAGA 58.421 36.000 0.00 0.00 0.00 2.59
3483 3639 6.844696 ACAAATACATCAATACTGGCGTAG 57.155 37.500 0.00 0.00 0.00 3.51
3484 3640 7.334671 TCAAACAAATACATCAATACTGGCGTA 59.665 33.333 0.00 0.00 0.00 4.42
3485 3641 6.150307 TCAAACAAATACATCAATACTGGCGT 59.850 34.615 0.00 0.00 0.00 5.68
3486 3642 6.468956 GTCAAACAAATACATCAATACTGGCG 59.531 38.462 0.00 0.00 0.00 5.69
3487 3643 7.538575 AGTCAAACAAATACATCAATACTGGC 58.461 34.615 0.00 0.00 0.00 4.85
3511 3691 7.328737 TCGGAGGGAGTAAGAAAATTTTCTAG 58.671 38.462 28.95 12.80 46.22 2.43
3547 3727 4.743493 ACAACTTTGTAAACCAGCAACAG 58.257 39.130 0.00 0.00 40.16 3.16
3551 3731 7.415429 GGTTTAGTACAACTTTGTAAACCAGCA 60.415 37.037 22.20 0.00 46.52 4.41
3785 3968 7.071321 ACCTAAGACTTCCAAACATAGATAGGG 59.929 40.741 0.00 0.00 0.00 3.53
3787 3970 8.696374 TCACCTAAGACTTCCAAACATAGATAG 58.304 37.037 0.00 0.00 0.00 2.08
3949 4247 3.195610 ACAGCATGAAGGATACGAGAACA 59.804 43.478 0.00 0.00 39.69 3.18
3950 4248 3.553511 CACAGCATGAAGGATACGAGAAC 59.446 47.826 0.00 0.00 39.69 3.01
3951 4249 3.430790 CCACAGCATGAAGGATACGAGAA 60.431 47.826 0.00 0.00 39.69 2.87
3952 4250 2.101415 CCACAGCATGAAGGATACGAGA 59.899 50.000 0.00 0.00 39.69 4.04
3953 4251 2.477825 CCACAGCATGAAGGATACGAG 58.522 52.381 0.00 0.00 39.69 4.18
3954 4252 1.138859 CCCACAGCATGAAGGATACGA 59.861 52.381 0.00 0.00 39.69 3.43
4039 4340 5.297029 ACAAAAAGCTCAGACCAAAGTAGTC 59.703 40.000 0.00 0.00 34.31 2.59
4058 4359 6.252995 ACATAAGGAGGCCATTAGAACAAAA 58.747 36.000 5.01 0.00 0.00 2.44
4071 4372 2.202566 GCGTACTGAACATAAGGAGGC 58.797 52.381 0.00 0.00 32.66 4.70
4111 4412 7.534723 TTGACTTAGGACAAGCTAGAACTTA 57.465 36.000 0.00 0.00 0.00 2.24
4509 4815 7.645058 TGAGTGTAACATGATATGTCAGAGA 57.355 36.000 0.00 0.00 44.07 3.10
4510 4816 8.883954 AATGAGTGTAACATGATATGTCAGAG 57.116 34.615 0.00 0.00 44.07 3.35
4527 4833 9.725019 TCAAACTTCAGAACATATAATGAGTGT 57.275 29.630 0.00 0.00 0.00 3.55
4529 4835 9.950496 ACTCAAACTTCAGAACATATAATGAGT 57.050 29.630 0.00 0.00 38.15 3.41
4536 4842 9.814899 CAGAGATACTCAAACTTCAGAACATAT 57.185 33.333 0.00 0.00 32.06 1.78
4537 4843 9.025041 TCAGAGATACTCAAACTTCAGAACATA 57.975 33.333 0.00 0.00 32.06 2.29
4538 4844 7.816995 GTCAGAGATACTCAAACTTCAGAACAT 59.183 37.037 0.00 0.00 32.06 2.71
4539 4845 7.148641 GTCAGAGATACTCAAACTTCAGAACA 58.851 38.462 0.00 0.00 32.06 3.18
4540 4846 7.148641 TGTCAGAGATACTCAAACTTCAGAAC 58.851 38.462 0.00 0.00 32.06 3.01
4541 4847 7.290110 TGTCAGAGATACTCAAACTTCAGAA 57.710 36.000 0.00 0.00 32.06 3.02
4542 4848 6.901081 TGTCAGAGATACTCAAACTTCAGA 57.099 37.500 0.00 0.00 32.06 3.27
4543 4849 9.462174 GATATGTCAGAGATACTCAAACTTCAG 57.538 37.037 0.00 0.00 32.06 3.02
4544 4850 8.971073 TGATATGTCAGAGATACTCAAACTTCA 58.029 33.333 0.00 0.00 32.06 3.02
4545 4851 9.979578 ATGATATGTCAGAGATACTCAAACTTC 57.020 33.333 0.00 0.00 37.87 3.01
4546 4852 9.761504 CATGATATGTCAGAGATACTCAAACTT 57.238 33.333 0.00 0.00 37.87 2.66
4547 4853 8.922237 ACATGATATGTCAGAGATACTCAAACT 58.078 33.333 0.00 0.00 39.92 2.66
4548 4854 9.539825 AACATGATATGTCAGAGATACTCAAAC 57.460 33.333 0.00 0.00 44.07 2.93
4549 4855 9.538508 CAACATGATATGTCAGAGATACTCAAA 57.461 33.333 0.00 0.00 44.07 2.69
4550 4856 7.654923 GCAACATGATATGTCAGAGATACTCAA 59.345 37.037 0.00 0.00 44.07 3.02
4551 4857 7.015001 AGCAACATGATATGTCAGAGATACTCA 59.985 37.037 0.00 0.00 44.07 3.41
4552 4858 7.377398 AGCAACATGATATGTCAGAGATACTC 58.623 38.462 0.00 0.00 44.07 2.59
4553 4859 7.015001 TGAGCAACATGATATGTCAGAGATACT 59.985 37.037 0.00 0.00 44.07 2.12
4554 4860 7.150640 TGAGCAACATGATATGTCAGAGATAC 58.849 38.462 0.00 0.00 44.07 2.24
4555 4861 7.294017 TGAGCAACATGATATGTCAGAGATA 57.706 36.000 0.00 0.00 44.07 1.98
4556 4862 6.170846 TGAGCAACATGATATGTCAGAGAT 57.829 37.500 0.00 0.00 44.07 2.75
4653 4959 1.606668 CGCTCTTTTAAAGTGCCACCA 59.393 47.619 21.09 0.00 43.20 4.17
4802 5108 5.789521 TCCAGATGAACTTGACATTCGTAA 58.210 37.500 0.00 0.00 0.00 3.18
4804 5110 4.271696 TCCAGATGAACTTGACATTCGT 57.728 40.909 0.00 0.00 0.00 3.85
4805 5111 5.808042 ATTCCAGATGAACTTGACATTCG 57.192 39.130 0.00 0.00 35.31 3.34
4806 5112 7.335422 ACAGTATTCCAGATGAACTTGACATTC 59.665 37.037 0.00 0.00 35.31 2.67
4807 5113 7.170965 ACAGTATTCCAGATGAACTTGACATT 58.829 34.615 0.00 0.00 35.31 2.71
4850 5156 4.240096 CAATGCCAAGCGAAAGATTTCTT 58.760 39.130 3.98 0.00 37.83 2.52
4861 5168 2.598192 CGTTAATTTCCAATGCCAAGCG 59.402 45.455 0.00 0.00 0.00 4.68
4862 5169 3.843999 TCGTTAATTTCCAATGCCAAGC 58.156 40.909 0.00 0.00 0.00 4.01
4870 5177 8.258007 ACATACAGAGATCTCGTTAATTTCCAA 58.742 33.333 20.11 5.10 34.09 3.53
4898 5205 1.394917 CAGCAGCAAGGAACGACATAC 59.605 52.381 0.00 0.00 0.00 2.39
4929 5236 4.320494 GGCACCTCCAGCGATAATAAAATG 60.320 45.833 0.00 0.00 34.01 2.32
4981 5289 9.643693 CAAGAAAAATAAGCCTCACAATATGTT 57.356 29.630 0.00 0.00 0.00 2.71
4988 5296 8.635765 AGATTACAAGAAAAATAAGCCTCACA 57.364 30.769 0.00 0.00 0.00 3.58
4989 5297 8.951243 AGAGATTACAAGAAAAATAAGCCTCAC 58.049 33.333 0.00 0.00 0.00 3.51
4997 5305 6.876789 TGGCGTCAGAGATTACAAGAAAAATA 59.123 34.615 0.00 0.00 0.00 1.40
4999 5307 5.060506 TGGCGTCAGAGATTACAAGAAAAA 58.939 37.500 0.00 0.00 0.00 1.94
5049 5357 6.825213 AGCTCATCTTGTATTATGTCTTTGCA 59.175 34.615 0.00 0.00 0.00 4.08
5091 5399 9.513906 TGAAAATCACAACAATAGATAGGTTCA 57.486 29.630 0.00 0.00 0.00 3.18
5138 5446 4.681942 GGTGTATCATCTCATTGCGTCTAC 59.318 45.833 0.00 0.00 0.00 2.59
5358 7046 8.469200 GCAATGCCCATTAACATATATACATGT 58.531 33.333 2.69 2.69 40.90 3.21
5360 7048 8.592529 TGCAATGCCCATTAACATATATACAT 57.407 30.769 1.53 0.00 0.00 2.29
5361 7049 8.303156 GTTGCAATGCCCATTAACATATATACA 58.697 33.333 0.59 0.00 0.00 2.29
5362 7050 8.303156 TGTTGCAATGCCCATTAACATATATAC 58.697 33.333 0.59 0.00 29.33 1.47
5363 7051 8.414629 TGTTGCAATGCCCATTAACATATATA 57.585 30.769 0.59 0.00 29.33 0.86
5366 7054 5.611128 TGTTGCAATGCCCATTAACATAT 57.389 34.783 0.59 0.00 29.33 1.78
5418 7106 3.129813 TGCCAAGTCTACGACGTATTCAT 59.870 43.478 8.39 0.00 37.67 2.57
5446 7134 1.359833 CAGCGACTGCCAAGCAAAA 59.640 52.632 0.00 0.00 44.31 2.44
5447 7135 1.383456 AACAGCGACTGCCAAGCAAA 61.383 50.000 6.74 0.00 44.31 3.68
5466 7154 9.587772 CTTGATTTCGTCTAGGAGAAATTTAGA 57.412 33.333 19.78 10.49 44.29 2.10
5479 7167 4.883083 AGCAGTTCACTTGATTTCGTCTA 58.117 39.130 0.00 0.00 0.00 2.59
5484 7172 5.065731 CCATAGGAGCAGTTCACTTGATTTC 59.934 44.000 0.00 0.00 0.00 2.17
5499 7187 3.576118 TCTTGATGAGTAGCCATAGGAGC 59.424 47.826 0.00 0.00 0.00 4.70
5518 7206 4.681978 GACCGCTGCCCACGTCTT 62.682 66.667 0.00 0.00 0.00 3.01
5538 7226 2.690778 GCAACCGAGACATGGGCAC 61.691 63.158 0.00 0.00 0.00 5.01
5539 7227 2.359850 GCAACCGAGACATGGGCA 60.360 61.111 0.00 0.00 0.00 5.36
5571 7259 5.164031 CGTTTCGAATCGAACATGGTAAAGA 60.164 40.000 18.30 0.00 45.64 2.52
5584 7272 0.179181 TCCGAGACCGTTTCGAATCG 60.179 55.000 19.20 19.20 40.36 3.34
5600 7292 1.883084 GCAACGTGAGGCCTATCCG 60.883 63.158 4.42 11.24 40.77 4.18
5717 7411 5.181245 ACTTGATAAAATTCTGTCACCACCG 59.819 40.000 0.00 0.00 0.00 4.94
5727 7421 5.569428 GCCTTTGGCCACTTGATAAAATTCT 60.569 40.000 3.88 0.00 44.06 2.40
5729 7423 4.578871 GCCTTTGGCCACTTGATAAAATT 58.421 39.130 3.88 0.00 44.06 1.82
5758 7453 0.620556 ATTCCGTGAATGCCAGAGGT 59.379 50.000 0.00 0.00 30.42 3.85
5761 7456 3.476740 GGATTCCGTGAATGCCAGA 57.523 52.632 4.18 0.00 34.96 3.86
5836 7531 1.606668 TCTGAAATTTCCACCACACGC 59.393 47.619 15.48 0.00 0.00 5.34
5847 7542 6.438763 CAAGCGACTTTTACCTCTGAAATTT 58.561 36.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.