Multiple sequence alignment - TraesCS5D01G081700

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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 TraesCS5D01G081700 chr5D 100.000 4090 0 0 1 4090 82186115 82190204 0.000000e+00 7553.0
1 TraesCS5D01G081700 chr5D 96.774 62 2 0 3354 3415 277724055 277724116 2.010000e-18 104.0
2 TraesCS5D01G081700 chr5A 94.124 1736 63 20 1649 3357 78158323 78160046 0.000000e+00 2604.0
3 TraesCS5D01G081700 chr5A 92.179 716 32 10 537 1245 78157209 78157907 0.000000e+00 990.0
4 TraesCS5D01G081700 chr5A 90.807 533 25 10 12 529 78156592 78157115 0.000000e+00 691.0
5 TraesCS5D01G081700 chr5A 87.857 560 42 11 3417 3963 78160065 78160611 5.770000e-178 634.0
6 TraesCS5D01G081700 chr5A 84.197 386 33 17 1244 1604 78157938 78158320 2.340000e-92 350.0
7 TraesCS5D01G081700 chr5A 96.212 132 5 0 3959 4090 78169515 78169646 2.480000e-52 217.0
8 TraesCS5D01G081700 chr5A 91.429 70 6 0 3354 3423 703193834 703193903 3.370000e-16 97.1
9 TraesCS5D01G081700 chr5A 94.000 50 3 0 3647 3696 698196039 698195990 4.380000e-10 76.8
10 TraesCS5D01G081700 chr5B 91.700 1735 76 27 1649 3357 90508054 90509746 0.000000e+00 2344.0
11 TraesCS5D01G081700 chr5B 91.060 906 31 23 748 1623 90507181 90508066 0.000000e+00 1179.0
12 TraesCS5D01G081700 chr5B 93.725 255 10 4 544 798 90506948 90507196 1.070000e-100 377.0
13 TraesCS5D01G081700 chr5B 93.162 117 6 2 3417 3532 90509765 90509880 1.950000e-38 171.0
14 TraesCS5D01G081700 chr4D 89.623 106 11 0 1461 1566 52472640 52472535 7.130000e-28 135.0
15 TraesCS5D01G081700 chr4B 89.623 106 11 0 1461 1566 76818827 76818722 7.130000e-28 135.0
16 TraesCS5D01G081700 chr4B 88.679 53 5 1 3647 3698 657476909 657476961 3.410000e-06 63.9
17 TraesCS5D01G081700 chr4A 89.623 106 11 0 1461 1566 544198873 544198978 7.130000e-28 135.0
18 TraesCS5D01G081700 chr4A 89.831 59 4 1 3642 3698 620504172 620504114 1.580000e-09 75.0
19 TraesCS5D01G081700 chr3A 86.792 106 4 5 1095 1191 127349239 127349343 4.320000e-20 110.0
20 TraesCS5D01G081700 chr3A 75.352 284 32 18 1674 1944 127351362 127351620 7.230000e-18 102.0
21 TraesCS5D01G081700 chr3A 88.889 54 4 1 3642 3693 10152066 10152013 9.490000e-07 65.8
22 TraesCS5D01G081700 chr3B 74.128 344 51 18 1674 2004 172728096 172727778 1.550000e-19 108.0
23 TraesCS5D01G081700 chr2D 96.721 61 2 0 3354 3414 179133282 179133222 7.230000e-18 102.0
24 TraesCS5D01G081700 chr2D 95.161 62 3 0 3355 3416 7890175 7890114 9.360000e-17 99.0
25 TraesCS5D01G081700 chr2D 95.000 60 2 1 3354 3413 38531793 38531851 4.350000e-15 93.5
26 TraesCS5D01G081700 chr6D 93.939 66 3 1 3354 3419 17237050 17236986 9.360000e-17 99.0
27 TraesCS5D01G081700 chr1A 96.610 59 2 0 3356 3414 554949748 554949806 9.360000e-17 99.0
28 TraesCS5D01G081700 chr1A 88.333 60 5 1 3642 3699 461031721 461031780 2.040000e-08 71.3
29 TraesCS5D01G081700 chr7B 95.161 62 2 1 3354 3415 512330460 512330520 3.370000e-16 97.1
30 TraesCS5D01G081700 chr3D 93.750 64 3 1 3354 3416 2339267 2339204 1.210000e-15 95.3
31 TraesCS5D01G081700 chr3D 75.758 198 25 15 1697 1892 120740653 120740477 1.220000e-10 78.7
32 TraesCS5D01G081700 chr2B 90.196 51 4 1 23 72 6206231 6206181 9.490000e-07 65.8


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 TraesCS5D01G081700 chr5D 82186115 82190204 4089 False 7553.00 7553 100.00000 1 4090 1 chr5D.!!$F1 4089
1 TraesCS5D01G081700 chr5A 78156592 78160611 4019 False 1053.80 2604 89.83280 12 3963 5 chr5A.!!$F3 3951
2 TraesCS5D01G081700 chr5B 90506948 90509880 2932 False 1017.75 2344 92.41175 544 3532 4 chr5B.!!$F1 2988

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
499 514 0.317160 AAACCTGATGCGTGAGACGA 59.683 50.0 0.0 0.0 46.05 4.20 F
1393 1572 0.582005 GTGATACAATCGCCTTCGCC 59.418 55.0 0.0 0.0 33.78 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2203 0.036010 ATAAGCAAGCACTCAGGCGT 60.036 50.0 0.00 0.00 39.27 5.68 R
3357 3604 0.786581 CATCAGTCGATGCATACGGC 59.213 55.0 13.06 13.06 42.54 5.68 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
66 67 4.228237 ACATTATGGGATGGAGGGAGTA 57.772 45.455 0.00 0.00 0.00 2.59
94 95 4.508461 TGTTGCTCGTACTGTAAAGCTA 57.492 40.909 18.61 11.85 35.76 3.32
112 115 3.000727 GCTACAGGTTGCGATGTTTACT 58.999 45.455 0.00 0.00 0.00 2.24
122 125 1.530720 CGATGTTTACTGTGCAGTGCA 59.469 47.619 15.37 15.37 42.52 4.57
123 126 2.411935 CGATGTTTACTGTGCAGTGCAG 60.412 50.000 20.42 10.70 42.52 4.41
232 235 1.406898 CTGCAATCTCGCTCTACCAGA 59.593 52.381 0.00 0.00 0.00 3.86
245 248 2.950309 TCTACCAGAGAAGTACGATGCC 59.050 50.000 0.00 0.00 0.00 4.40
297 309 2.224042 CGGAGGCAAAAGCTTTTCCTTT 60.224 45.455 28.39 16.80 36.65 3.11
298 310 3.393800 GGAGGCAAAAGCTTTTCCTTTC 58.606 45.455 28.39 22.59 34.12 2.62
299 311 3.181466 GGAGGCAAAAGCTTTTCCTTTCA 60.181 43.478 28.39 0.00 34.12 2.69
329 341 5.897050 ACTAAGAAGAAGATAGTTGCTCGG 58.103 41.667 0.00 0.00 0.00 4.63
394 406 7.202016 TGATCTTTTAGTCATTTTTGCGTCT 57.798 32.000 0.00 0.00 0.00 4.18
395 407 7.077605 TGATCTTTTAGTCATTTTTGCGTCTG 58.922 34.615 0.00 0.00 0.00 3.51
499 514 0.317160 AAACCTGATGCGTGAGACGA 59.683 50.000 0.00 0.00 46.05 4.20
504 519 1.132453 CTGATGCGTGAGACGAAGGTA 59.868 52.381 0.00 0.00 46.05 3.08
511 526 1.812571 GTGAGACGAAGGTACCGGTAA 59.187 52.381 17.78 0.00 0.00 2.85
686 787 1.270094 CGCACTCCAGTTACCTTGACA 60.270 52.381 0.00 0.00 0.00 3.58
688 789 2.548480 GCACTCCAGTTACCTTGACAAC 59.452 50.000 0.00 0.00 0.00 3.32
760 861 1.698506 CTAGTCAGGTGAGCCTAGGG 58.301 60.000 11.72 0.00 44.97 3.53
776 907 5.104735 AGCCTAGGGTAGAATGTCAAAGAAG 60.105 44.000 12.99 0.00 0.00 2.85
782 913 8.712228 AGGGTAGAATGTCAAAGAAGAAAAAT 57.288 30.769 0.00 0.00 0.00 1.82
785 916 7.329471 GGTAGAATGTCAAAGAAGAAAAATGGC 59.671 37.037 0.00 0.00 0.00 4.40
1110 1246 4.324991 GGGTCCGGCAACTTCGGT 62.325 66.667 0.00 0.00 46.82 4.69
1191 1327 2.183555 GGCGAGAAGGTACCACCG 59.816 66.667 15.94 12.20 44.90 4.94
1225 1364 8.620416 CACACTTCGATTATTTATTCATTCCCA 58.380 33.333 0.00 0.00 0.00 4.37
1304 1475 1.165270 TCGATGAGAACGTGCAGAGA 58.835 50.000 0.00 0.00 0.00 3.10
1375 1554 2.106166 AGGAGGTGAGTATACGATCGGT 59.894 50.000 20.98 10.25 0.00 4.69
1393 1572 0.582005 GTGATACAATCGCCTTCGCC 59.418 55.000 0.00 0.00 33.78 5.54
1539 1743 1.808799 CTTCGAGCGCATCTGCACT 60.809 57.895 11.47 0.00 42.21 4.40
1566 1770 1.134530 GATTCAGCGTCGACGAGGTG 61.135 60.000 39.74 29.66 43.02 4.00
1600 1804 4.004314 TCATAGCTCTGCCGTATAGTCTC 58.996 47.826 0.00 0.00 0.00 3.36
1694 1905 6.636850 CAGTTTGGTTAACTCAGTTTGTATGC 59.363 38.462 5.42 0.00 45.29 3.14
1786 2007 4.207165 TCTGCTTCCCAAATTATACTGCC 58.793 43.478 0.00 0.00 0.00 4.85
1826 2047 6.322201 CCTTTCCATGTAGTTTCCTATGCAAT 59.678 38.462 0.00 0.00 0.00 3.56
1862 2083 4.990543 TGTTCTATTCGTCAAGCAAGTG 57.009 40.909 0.00 0.00 0.00 3.16
1964 2188 8.591072 GGTTATTCCAAGGTATACTGTGCTATA 58.409 37.037 2.25 0.48 35.97 1.31
1976 2200 5.435686 ACTGTGCTATAAATCTGGTGGAA 57.564 39.130 0.00 0.00 0.00 3.53
1979 2203 4.081365 TGTGCTATAAATCTGGTGGAACGA 60.081 41.667 0.00 0.00 38.12 3.85
2218 2455 4.318974 GCGCTTTCAAGTTTAAACCGTCTA 60.319 41.667 14.72 0.00 0.00 2.59
2219 2456 5.135330 CGCTTTCAAGTTTAAACCGTCTAC 58.865 41.667 14.72 0.00 0.00 2.59
2249 2486 1.379642 GCCACCATCTGCTGCCTAAC 61.380 60.000 0.00 0.00 0.00 2.34
2263 2500 6.991938 TGCTGCCTAACTTGAATAATTTTGT 58.008 32.000 0.00 0.00 0.00 2.83
2268 2505 7.088272 GCCTAACTTGAATAATTTTGTTCGGT 58.912 34.615 0.00 0.00 31.81 4.69
2324 2561 2.422597 CACCTTTCGTTGGCATGAGTA 58.577 47.619 0.00 0.00 0.00 2.59
2359 2596 5.007682 TGAGGAGCAACCATTTAAAGTACC 58.992 41.667 0.00 0.00 42.04 3.34
2404 2641 6.371809 AGTACTTCATGTTTTTCGCTCAAA 57.628 33.333 0.00 0.00 0.00 2.69
2448 2685 0.392998 AGATTGCCGATGTGTGGTCC 60.393 55.000 0.00 0.00 0.00 4.46
2502 2739 1.789523 CCTACCCTTTCGAGGATCCA 58.210 55.000 15.82 0.00 31.45 3.41
2524 2761 7.444299 TCCAGAAAATCCCAAGAATTTCAAAG 58.556 34.615 6.43 0.00 42.17 2.77
2601 2838 9.057089 GCAGTTATAGCCAAACATCTAAATACT 57.943 33.333 0.00 0.00 0.00 2.12
3026 3263 1.226323 CCTCGACGACGACATGGAC 60.226 63.158 5.75 0.00 43.81 4.02
3159 3400 4.441913 CCACCTTGTTTGCTTCTTGAACAT 60.442 41.667 0.00 0.00 33.73 2.71
3237 3478 6.373759 TGAGAGGATTGTATTCAGGCTACTA 58.626 40.000 0.00 0.00 0.00 1.82
3265 3506 2.294233 TCTGAAATTGGTGTTGCTGCTC 59.706 45.455 0.00 0.00 0.00 4.26
3270 3511 1.689984 TTGGTGTTGCTGCTCATTGA 58.310 45.000 0.00 0.00 0.00 2.57
3313 3560 6.808008 CAGTATGTTGGAGTTTTCTGTGAT 57.192 37.500 0.00 0.00 0.00 3.06
3314 3561 6.835914 CAGTATGTTGGAGTTTTCTGTGATC 58.164 40.000 0.00 0.00 0.00 2.92
3315 3562 6.652481 CAGTATGTTGGAGTTTTCTGTGATCT 59.348 38.462 0.00 0.00 0.00 2.75
3318 3565 8.999431 GTATGTTGGAGTTTTCTGTGATCTTTA 58.001 33.333 0.00 0.00 0.00 1.85
3319 3566 7.496529 TGTTGGAGTTTTCTGTGATCTTTAG 57.503 36.000 0.00 0.00 0.00 1.85
3321 3568 7.556275 TGTTGGAGTTTTCTGTGATCTTTAGTT 59.444 33.333 0.00 0.00 0.00 2.24
3322 3569 7.496529 TGGAGTTTTCTGTGATCTTTAGTTG 57.503 36.000 0.00 0.00 0.00 3.16
3323 3570 7.279615 TGGAGTTTTCTGTGATCTTTAGTTGA 58.720 34.615 0.00 0.00 0.00 3.18
3324 3571 7.939039 TGGAGTTTTCTGTGATCTTTAGTTGAT 59.061 33.333 0.00 0.00 0.00 2.57
3325 3572 9.436957 GGAGTTTTCTGTGATCTTTAGTTGATA 57.563 33.333 0.00 0.00 0.00 2.15
3357 3604 0.105964 TACCCGAAATCGCTGGATGG 59.894 55.000 5.32 0.00 38.18 3.51
3358 3605 2.546494 CCCGAAATCGCTGGATGGC 61.546 63.158 0.00 0.00 38.18 4.40
3360 3607 2.885676 CGAAATCGCTGGATGGCCG 61.886 63.158 0.00 0.00 36.79 6.13
3361 3608 1.819632 GAAATCGCTGGATGGCCGT 60.820 57.895 0.00 0.00 36.79 5.68
3362 3609 0.531974 GAAATCGCTGGATGGCCGTA 60.532 55.000 0.00 0.00 36.79 4.02
3363 3610 0.108585 AAATCGCTGGATGGCCGTAT 59.891 50.000 0.00 0.00 36.79 3.06
3364 3611 0.603707 AATCGCTGGATGGCCGTATG 60.604 55.000 0.00 0.00 36.79 2.39
3365 3612 3.349006 CGCTGGATGGCCGTATGC 61.349 66.667 0.00 1.50 36.79 3.14
3366 3613 2.203195 GCTGGATGGCCGTATGCA 60.203 61.111 0.00 0.00 43.89 3.96
3368 3615 1.580845 GCTGGATGGCCGTATGCATC 61.581 60.000 0.19 0.00 43.89 3.91
3369 3616 1.293963 CTGGATGGCCGTATGCATCG 61.294 60.000 0.19 7.03 43.89 3.84
3370 3617 1.005037 GGATGGCCGTATGCATCGA 60.005 57.895 16.69 0.00 43.89 3.59
3371 3618 1.291877 GGATGGCCGTATGCATCGAC 61.292 60.000 16.69 5.03 43.89 4.20
3374 3621 1.067416 GGCCGTATGCATCGACTGA 59.933 57.895 16.69 0.00 43.89 3.41
3375 3622 0.319900 GGCCGTATGCATCGACTGAT 60.320 55.000 16.69 0.00 43.89 2.90
3383 3630 2.602738 CATCGACTGATGCAGAGGC 58.397 57.895 0.82 0.00 45.06 4.70
3384 3631 0.879400 CATCGACTGATGCAGAGGCC 60.879 60.000 0.00 0.00 45.06 5.19
3385 3632 2.360949 ATCGACTGATGCAGAGGCCG 62.361 60.000 0.00 0.00 40.13 6.13
3386 3633 2.202987 GACTGATGCAGAGGCCGG 60.203 66.667 0.00 0.00 40.13 6.13
3387 3634 3.746949 GACTGATGCAGAGGCCGGG 62.747 68.421 2.18 0.00 40.13 5.73
3388 3635 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
3393 3640 4.678743 GCAGAGGCCGGGGGTTTT 62.679 66.667 2.18 0.00 0.00 2.43
3394 3641 3.083386 CAGAGGCCGGGGGTTTTA 58.917 61.111 2.18 0.00 0.00 1.52
3395 3642 1.381076 CAGAGGCCGGGGGTTTTAA 59.619 57.895 2.18 0.00 0.00 1.52
3396 3643 0.963856 CAGAGGCCGGGGGTTTTAAC 60.964 60.000 2.18 0.00 0.00 2.01
3444 3691 4.094294 TCATGTATACGCAAAGCTGGTTTC 59.906 41.667 1.18 0.00 0.00 2.78
3447 3694 0.591170 TACGCAAAGCTGGTTTCTGC 59.409 50.000 1.18 4.13 38.00 4.26
3448 3695 1.372128 CGCAAAGCTGGTTTCTGCC 60.372 57.895 9.81 0.00 38.41 4.85
3466 3713 3.797546 GCAACGCCAGCTCTGCTC 61.798 66.667 3.46 0.00 36.40 4.26
3558 3805 5.912396 TCGTTTGTTGATCAATTGCTAACAC 59.088 36.000 12.12 0.00 35.84 3.32
3559 3806 5.914635 CGTTTGTTGATCAATTGCTAACACT 59.085 36.000 12.12 0.00 35.84 3.55
3606 3861 3.990469 GAGGTGATGTGTATGCGATTAGG 59.010 47.826 0.00 0.00 0.00 2.69
3730 3986 2.415893 CCAATTGCGAACAATCCCTGAC 60.416 50.000 0.00 0.00 45.90 3.51
3756 4012 1.293179 CACGACATGCTGTGGAGGA 59.707 57.895 9.47 0.00 32.47 3.71
3757 4013 0.107993 CACGACATGCTGTGGAGGAT 60.108 55.000 9.47 0.00 32.47 3.24
3762 4018 0.107993 CATGCTGTGGAGGATGTCGT 60.108 55.000 0.00 0.00 41.82 4.34
3770 4026 0.317103 GGAGGATGTCGTCGATGTCG 60.317 60.000 4.21 0.00 41.45 4.35
3782 4038 1.392710 CGATGTCGGGGAAGTAGCCT 61.393 60.000 0.00 0.00 35.37 4.58
3792 4048 3.142174 GGGAAGTAGCCTTGTCATATGC 58.858 50.000 0.00 0.00 0.00 3.14
3793 4049 3.142174 GGAAGTAGCCTTGTCATATGCC 58.858 50.000 0.00 0.00 0.00 4.40
3827 4083 2.660552 CGCTCACGAAACACGGGT 60.661 61.111 0.00 0.00 46.47 5.28
3828 4084 2.935955 GCTCACGAAACACGGGTG 59.064 61.111 0.00 0.00 46.47 4.61
3838 4094 0.836400 AACACGGGTGATGGAGGAGT 60.836 55.000 5.71 0.00 0.00 3.85
3848 4104 1.070758 GATGGAGGAGTGTGTGTGTGT 59.929 52.381 0.00 0.00 0.00 3.72
3850 4106 0.178068 GGAGGAGTGTGTGTGTGTGT 59.822 55.000 0.00 0.00 0.00 3.72
3851 4107 1.290203 GAGGAGTGTGTGTGTGTGTG 58.710 55.000 0.00 0.00 0.00 3.82
3852 4108 0.613260 AGGAGTGTGTGTGTGTGTGT 59.387 50.000 0.00 0.00 0.00 3.72
3853 4109 1.828595 AGGAGTGTGTGTGTGTGTGTA 59.171 47.619 0.00 0.00 0.00 2.90
3854 4110 2.434336 AGGAGTGTGTGTGTGTGTGTAT 59.566 45.455 0.00 0.00 0.00 2.29
3855 4111 2.543848 GGAGTGTGTGTGTGTGTGTATG 59.456 50.000 0.00 0.00 0.00 2.39
3856 4112 3.194861 GAGTGTGTGTGTGTGTGTATGT 58.805 45.455 0.00 0.00 0.00 2.29
3857 4113 2.935849 AGTGTGTGTGTGTGTGTATGTG 59.064 45.455 0.00 0.00 0.00 3.21
3858 4114 1.668237 TGTGTGTGTGTGTGTATGTGC 59.332 47.619 0.00 0.00 0.00 4.57
3859 4115 1.002900 GTGTGTGTGTGTGTATGTGCC 60.003 52.381 0.00 0.00 0.00 5.01
3860 4116 0.591170 GTGTGTGTGTGTATGTGCCC 59.409 55.000 0.00 0.00 0.00 5.36
3861 4117 0.472044 TGTGTGTGTGTATGTGCCCT 59.528 50.000 0.00 0.00 0.00 5.19
3862 4118 1.156736 GTGTGTGTGTATGTGCCCTC 58.843 55.000 0.00 0.00 0.00 4.30
3863 4119 1.055849 TGTGTGTGTATGTGCCCTCT 58.944 50.000 0.00 0.00 0.00 3.69
3864 4120 1.419762 TGTGTGTGTATGTGCCCTCTT 59.580 47.619 0.00 0.00 0.00 2.85
3879 4135 6.760770 TGTGCCCTCTTTTCAAAATTTTAGTG 59.239 34.615 2.44 0.00 0.00 2.74
3887 4143 8.307483 TCTTTTCAAAATTTTAGTGGTGTGTGA 58.693 29.630 2.44 0.00 0.00 3.58
3898 4154 1.064758 TGGTGTGTGAAAGAGCCAACT 60.065 47.619 0.00 0.00 0.00 3.16
3936 4196 0.537371 CTTCACAACCAGGGTGGGAC 60.537 60.000 9.79 0.00 43.37 4.46
3950 4210 3.245122 GGGTGGGACTAAACTTTCCATGA 60.245 47.826 0.00 0.00 33.01 3.07
3951 4211 4.569865 GGGTGGGACTAAACTTTCCATGAT 60.570 45.833 0.00 0.00 33.01 2.45
3968 4228 3.301794 TGATCCCCTTGTCATGAATGG 57.698 47.619 0.00 0.00 0.00 3.16
3969 4229 2.851821 TGATCCCCTTGTCATGAATGGA 59.148 45.455 0.00 0.00 0.00 3.41
3970 4230 3.117776 TGATCCCCTTGTCATGAATGGAG 60.118 47.826 0.00 0.00 0.00 3.86
3971 4231 1.064463 TCCCCTTGTCATGAATGGAGC 60.064 52.381 0.00 0.00 0.00 4.70
3972 4232 1.341285 CCCCTTGTCATGAATGGAGCA 60.341 52.381 0.00 0.00 0.00 4.26
3973 4233 2.662866 CCCTTGTCATGAATGGAGCAT 58.337 47.619 0.00 0.00 0.00 3.79
3974 4234 3.435457 CCCCTTGTCATGAATGGAGCATA 60.435 47.826 0.00 0.00 0.00 3.14
3975 4235 4.404640 CCCTTGTCATGAATGGAGCATAT 58.595 43.478 0.00 0.00 0.00 1.78
3976 4236 4.217767 CCCTTGTCATGAATGGAGCATATG 59.782 45.833 0.00 0.00 0.00 1.78
3977 4237 5.067954 CCTTGTCATGAATGGAGCATATGA 58.932 41.667 6.97 0.00 0.00 2.15
3978 4238 5.181433 CCTTGTCATGAATGGAGCATATGAG 59.819 44.000 6.97 0.00 0.00 2.90
3979 4239 4.070009 TGTCATGAATGGAGCATATGAGC 58.930 43.478 6.97 0.00 0.00 4.26
3980 4240 3.439476 GTCATGAATGGAGCATATGAGCC 59.561 47.826 6.97 7.11 34.23 4.70
3981 4241 3.329814 TCATGAATGGAGCATATGAGCCT 59.670 43.478 6.97 0.00 34.23 4.58
3982 4242 3.413846 TGAATGGAGCATATGAGCCTC 57.586 47.619 6.97 3.60 34.23 4.70
3983 4243 2.977580 TGAATGGAGCATATGAGCCTCT 59.022 45.455 6.97 0.00 34.23 3.69
3984 4244 4.162651 TGAATGGAGCATATGAGCCTCTA 58.837 43.478 6.97 2.14 34.23 2.43
3985 4245 4.222366 TGAATGGAGCATATGAGCCTCTAG 59.778 45.833 6.97 0.00 34.23 2.43
3986 4246 2.533916 TGGAGCATATGAGCCTCTAGG 58.466 52.381 6.97 0.00 38.53 3.02
3987 4247 2.110721 TGGAGCATATGAGCCTCTAGGA 59.889 50.000 6.97 0.00 37.39 2.94
3988 4248 3.245911 TGGAGCATATGAGCCTCTAGGAT 60.246 47.826 6.97 0.00 37.39 3.24
3989 4249 3.774216 GGAGCATATGAGCCTCTAGGATT 59.226 47.826 6.97 0.00 37.39 3.01
3990 4250 4.141959 GGAGCATATGAGCCTCTAGGATTC 60.142 50.000 6.97 0.00 37.39 2.52
3991 4251 4.423913 AGCATATGAGCCTCTAGGATTCA 58.576 43.478 6.97 3.32 37.39 2.57
3992 4252 4.842948 AGCATATGAGCCTCTAGGATTCAA 59.157 41.667 6.97 0.00 35.16 2.69
3993 4253 5.046448 AGCATATGAGCCTCTAGGATTCAAG 60.046 44.000 6.97 0.20 35.16 3.02
3994 4254 5.046735 GCATATGAGCCTCTAGGATTCAAGA 60.047 44.000 6.97 0.00 35.16 3.02
3995 4255 6.519721 GCATATGAGCCTCTAGGATTCAAGAA 60.520 42.308 6.97 0.00 35.16 2.52
3996 4256 7.622713 CATATGAGCCTCTAGGATTCAAGAAT 58.377 38.462 0.00 0.00 35.16 2.40
3997 4257 5.965033 TGAGCCTCTAGGATTCAAGAATT 57.035 39.130 0.00 0.00 37.39 2.17
3998 4258 5.678583 TGAGCCTCTAGGATTCAAGAATTG 58.321 41.667 0.00 0.00 42.67 2.32
3999 4259 5.190528 TGAGCCTCTAGGATTCAAGAATTGT 59.809 40.000 0.00 0.00 42.16 2.71
4000 4260 6.072199 AGCCTCTAGGATTCAAGAATTGTT 57.928 37.500 0.00 0.00 42.16 2.83
4001 4261 5.884792 AGCCTCTAGGATTCAAGAATTGTTG 59.115 40.000 8.99 8.99 42.16 3.33
4002 4262 5.067023 GCCTCTAGGATTCAAGAATTGTTGG 59.933 44.000 14.72 0.00 42.16 3.77
4003 4263 6.418101 CCTCTAGGATTCAAGAATTGTTGGA 58.582 40.000 14.72 7.14 42.16 3.53
4004 4264 6.886459 CCTCTAGGATTCAAGAATTGTTGGAA 59.114 38.462 14.72 8.58 42.16 3.53
4005 4265 7.394359 CCTCTAGGATTCAAGAATTGTTGGAAA 59.606 37.037 14.72 4.00 42.16 3.13
4017 4277 8.962884 AGAATTGTTGGAAATAATAAATGGGC 57.037 30.769 0.00 0.00 36.59 5.36
4018 4278 8.771286 AGAATTGTTGGAAATAATAAATGGGCT 58.229 29.630 0.00 0.00 36.59 5.19
4023 4283 9.883142 TGTTGGAAATAATAAATGGGCTAAAAG 57.117 29.630 0.00 0.00 0.00 2.27
4024 4284 8.826710 GTTGGAAATAATAAATGGGCTAAAAGC 58.173 33.333 0.00 0.00 41.46 3.51
4042 4302 9.249457 GCTAAAAGCCTAATAATTCCAACAATC 57.751 33.333 0.00 0.00 34.48 2.67
4043 4303 9.750125 CTAAAAGCCTAATAATTCCAACAATCC 57.250 33.333 0.00 0.00 0.00 3.01
4044 4304 6.731292 AAGCCTAATAATTCCAACAATCCC 57.269 37.500 0.00 0.00 0.00 3.85
4045 4305 5.147767 AGCCTAATAATTCCAACAATCCCC 58.852 41.667 0.00 0.00 0.00 4.81
4046 4306 5.103086 AGCCTAATAATTCCAACAATCCCCT 60.103 40.000 0.00 0.00 0.00 4.79
4047 4307 6.104094 AGCCTAATAATTCCAACAATCCCCTA 59.896 38.462 0.00 0.00 0.00 3.53
4048 4308 6.954102 GCCTAATAATTCCAACAATCCCCTAT 59.046 38.462 0.00 0.00 0.00 2.57
4049 4309 7.122799 GCCTAATAATTCCAACAATCCCCTATC 59.877 40.741 0.00 0.00 0.00 2.08
4050 4310 8.170061 CCTAATAATTCCAACAATCCCCTATCA 58.830 37.037 0.00 0.00 0.00 2.15
4051 4311 9.236006 CTAATAATTCCAACAATCCCCTATCAG 57.764 37.037 0.00 0.00 0.00 2.90
4052 4312 5.732331 AATTCCAACAATCCCCTATCAGA 57.268 39.130 0.00 0.00 0.00 3.27
4053 4313 5.937492 ATTCCAACAATCCCCTATCAGAT 57.063 39.130 0.00 0.00 0.00 2.90
4054 4314 4.982241 TCCAACAATCCCCTATCAGATC 57.018 45.455 0.00 0.00 0.00 2.75
4055 4315 3.652869 TCCAACAATCCCCTATCAGATCC 59.347 47.826 0.00 0.00 0.00 3.36
4056 4316 3.245052 CCAACAATCCCCTATCAGATCCC 60.245 52.174 0.00 0.00 0.00 3.85
4057 4317 3.367280 ACAATCCCCTATCAGATCCCA 57.633 47.619 0.00 0.00 0.00 4.37
4058 4318 3.680169 ACAATCCCCTATCAGATCCCAA 58.320 45.455 0.00 0.00 0.00 4.12
4059 4319 4.054369 ACAATCCCCTATCAGATCCCAAA 58.946 43.478 0.00 0.00 0.00 3.28
4060 4320 4.105377 ACAATCCCCTATCAGATCCCAAAG 59.895 45.833 0.00 0.00 0.00 2.77
4061 4321 2.706350 TCCCCTATCAGATCCCAAAGG 58.294 52.381 0.00 0.00 0.00 3.11
4062 4322 1.074566 CCCCTATCAGATCCCAAAGGC 59.925 57.143 0.00 0.00 0.00 4.35
4063 4323 2.061061 CCCTATCAGATCCCAAAGGCT 58.939 52.381 0.00 0.00 0.00 4.58
4064 4324 2.224719 CCCTATCAGATCCCAAAGGCTG 60.225 54.545 0.00 0.00 0.00 4.85
4065 4325 2.707791 CCTATCAGATCCCAAAGGCTGA 59.292 50.000 0.00 0.00 41.14 4.26
4066 4326 3.330110 CCTATCAGATCCCAAAGGCTGAT 59.670 47.826 0.00 0.00 46.50 2.90
4067 4327 4.533707 CCTATCAGATCCCAAAGGCTGATA 59.466 45.833 0.00 0.00 43.97 2.15
4068 4328 5.013495 CCTATCAGATCCCAAAGGCTGATAA 59.987 44.000 0.00 0.00 44.86 1.75
4069 4329 4.860802 TCAGATCCCAAAGGCTGATAAA 57.139 40.909 0.00 0.00 32.85 1.40
4070 4330 4.785301 TCAGATCCCAAAGGCTGATAAAG 58.215 43.478 0.00 0.00 32.85 1.85
4071 4331 4.228210 TCAGATCCCAAAGGCTGATAAAGT 59.772 41.667 0.00 0.00 32.85 2.66
4072 4332 4.952335 CAGATCCCAAAGGCTGATAAAGTT 59.048 41.667 0.00 0.00 0.00 2.66
4073 4333 5.420104 CAGATCCCAAAGGCTGATAAAGTTT 59.580 40.000 0.00 0.00 0.00 2.66
4074 4334 5.420104 AGATCCCAAAGGCTGATAAAGTTTG 59.580 40.000 0.00 0.00 0.00 2.93
4075 4335 3.258123 TCCCAAAGGCTGATAAAGTTTGC 59.742 43.478 0.00 0.00 0.00 3.68
4076 4336 3.259123 CCCAAAGGCTGATAAAGTTTGCT 59.741 43.478 0.00 0.00 0.00 3.91
4077 4337 4.262592 CCCAAAGGCTGATAAAGTTTGCTT 60.263 41.667 0.00 0.00 36.30 3.91
4078 4338 5.047377 CCCAAAGGCTGATAAAGTTTGCTTA 60.047 40.000 0.00 0.00 33.95 3.09
4079 4339 6.351286 CCCAAAGGCTGATAAAGTTTGCTTAT 60.351 38.462 0.00 0.00 33.95 1.73
4080 4340 6.532657 CCAAAGGCTGATAAAGTTTGCTTATG 59.467 38.462 0.00 0.00 33.95 1.90
4081 4341 5.841957 AGGCTGATAAAGTTTGCTTATGG 57.158 39.130 0.00 0.00 33.95 2.74
4082 4342 5.264395 AGGCTGATAAAGTTTGCTTATGGT 58.736 37.500 0.00 0.00 33.95 3.55
4083 4343 5.716703 AGGCTGATAAAGTTTGCTTATGGTT 59.283 36.000 0.00 0.00 33.95 3.67
4084 4344 6.036470 GGCTGATAAAGTTTGCTTATGGTTC 58.964 40.000 0.00 0.00 33.95 3.62
4085 4345 6.036470 GCTGATAAAGTTTGCTTATGGTTCC 58.964 40.000 0.00 0.00 33.95 3.62
4086 4346 6.350110 GCTGATAAAGTTTGCTTATGGTTCCA 60.350 38.462 0.00 0.00 33.95 3.53
4087 4347 7.631377 GCTGATAAAGTTTGCTTATGGTTCCAT 60.631 37.037 9.37 9.37 33.95 3.41
4088 4348 8.815565 TGATAAAGTTTGCTTATGGTTCCATA 57.184 30.769 7.38 7.38 33.95 2.74
4089 4349 9.249053 TGATAAAGTTTGCTTATGGTTCCATAA 57.751 29.630 19.19 19.19 36.80 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.537688 CCCTCCATCCCATAATGTAGATGT 59.462 45.833 0.00 0.00 35.42 3.06
40 41 4.784838 TCCCTCCATCCCATAATGTAGATG 59.215 45.833 0.00 0.00 36.66 2.90
41 42 5.035556 CTCCCTCCATCCCATAATGTAGAT 58.964 45.833 0.00 0.00 0.00 1.98
42 43 4.140447 ACTCCCTCCATCCCATAATGTAGA 60.140 45.833 0.00 0.00 0.00 2.59
56 57 1.656587 ACATGCAACTACTCCCTCCA 58.343 50.000 0.00 0.00 0.00 3.86
94 95 2.548057 CACAGTAAACATCGCAACCTGT 59.452 45.455 0.00 0.00 0.00 4.00
112 115 0.180171 AACACTACCTGCACTGCACA 59.820 50.000 0.00 0.00 33.79 4.57
164 167 4.863131 CGAGGGTTGACTGTTAACATCTAC 59.137 45.833 15.95 14.06 0.00 2.59
232 235 3.535561 CATTTCCTGGCATCGTACTTCT 58.464 45.455 0.00 0.00 0.00 2.85
245 248 5.982890 AAGTTGGTTACATCCATTTCCTG 57.017 39.130 0.00 0.00 37.33 3.86
371 383 7.078228 ACAGACGCAAAAATGACTAAAAGATC 58.922 34.615 0.00 0.00 0.00 2.75
373 385 6.037720 TGACAGACGCAAAAATGACTAAAAGA 59.962 34.615 0.00 0.00 0.00 2.52
465 479 1.442017 GTTTTCGTGGTGCATCGCC 60.442 57.895 4.63 0.00 34.12 5.54
470 484 0.950836 CATCAGGTTTTCGTGGTGCA 59.049 50.000 0.00 0.00 39.40 4.57
499 514 5.184711 TGCGAAATAAATTACCGGTACCTT 58.815 37.500 15.53 12.85 0.00 3.50
529 544 6.542735 GGGATCAAATTACTGGTACCTTCTTC 59.457 42.308 14.36 0.00 0.00 2.87
530 545 6.424032 GGGATCAAATTACTGGTACCTTCTT 58.576 40.000 14.36 0.00 0.00 2.52
532 547 5.131067 GGGGATCAAATTACTGGTACCTTC 58.869 45.833 14.36 0.00 0.00 3.46
533 548 4.384868 CGGGGATCAAATTACTGGTACCTT 60.385 45.833 14.36 2.42 0.00 3.50
535 550 3.473625 CGGGGATCAAATTACTGGTACC 58.526 50.000 4.43 4.43 0.00 3.34
686 787 1.961277 CCACTCGCGGCTTTGAGTT 60.961 57.895 6.13 0.00 42.61 3.01
688 789 1.021390 AATCCACTCGCGGCTTTGAG 61.021 55.000 6.13 0.00 38.21 3.02
760 861 7.061094 CGCCATTTTTCTTCTTTGACATTCTAC 59.939 37.037 0.00 0.00 0.00 2.59
776 907 1.024579 TCCGAGGCTCGCCATTTTTC 61.025 55.000 30.55 0.00 38.82 2.29
782 913 3.129300 CTTATCCGAGGCTCGCCA 58.871 61.111 30.55 19.24 38.82 5.69
785 916 1.658717 CGTGCTTATCCGAGGCTCG 60.659 63.158 29.16 29.16 40.07 5.03
913 1048 3.572539 CTCTCTCGCTCGCTCGCT 61.573 66.667 0.00 0.00 0.00 4.93
914 1049 1.561717 TATCTCTCTCGCTCGCTCGC 61.562 60.000 0.00 0.00 0.00 5.03
915 1050 0.862490 TTATCTCTCTCGCTCGCTCG 59.138 55.000 0.00 0.00 0.00 5.03
916 1051 1.196808 CCTTATCTCTCTCGCTCGCTC 59.803 57.143 0.00 0.00 0.00 5.03
965 1100 2.280823 GACTCTACCGCCGACCAAGG 62.281 65.000 0.00 0.00 0.00 3.61
1155 1291 0.455464 CGCGGTCGATGTACTTGACA 60.455 55.000 0.00 0.00 43.97 3.58
1191 1327 4.980805 TCGAAGTGTGGTGGCGCC 62.981 66.667 22.73 22.73 37.90 6.53
1225 1364 3.276846 GTGTGCGCGTGGGAAACT 61.277 61.111 8.43 0.00 0.00 2.66
1304 1475 2.167281 CGACCTGTGGTTGATGATCTCT 59.833 50.000 0.00 0.00 39.36 3.10
1334 1505 0.617935 TGAAGCGGATGATGTTGGGA 59.382 50.000 0.00 0.00 0.00 4.37
1393 1572 4.483711 TCGAAGACGATGCTGCAG 57.516 55.556 10.11 10.11 43.81 4.41
1545 1749 1.934956 CTCGTCGACGCTGAATCGG 60.935 63.158 32.19 10.52 40.05 4.18
1566 1770 5.460646 GCAGAGCTATGAGTCAAGAGATAC 58.539 45.833 13.69 0.00 0.00 2.24
1635 1839 7.181569 ACAACTCTTGATCCCTTTTCAAAAA 57.818 32.000 0.00 0.00 32.98 1.94
1636 1840 6.790232 ACAACTCTTGATCCCTTTTCAAAA 57.210 33.333 0.00 0.00 32.98 2.44
1637 1841 7.723616 TCATACAACTCTTGATCCCTTTTCAAA 59.276 33.333 0.00 0.00 32.98 2.69
1638 1842 7.230747 TCATACAACTCTTGATCCCTTTTCAA 58.769 34.615 0.00 0.00 0.00 2.69
1639 1843 6.778821 TCATACAACTCTTGATCCCTTTTCA 58.221 36.000 0.00 0.00 0.00 2.69
1640 1844 7.201767 CCATCATACAACTCTTGATCCCTTTTC 60.202 40.741 0.00 0.00 0.00 2.29
1641 1845 6.604795 CCATCATACAACTCTTGATCCCTTTT 59.395 38.462 0.00 0.00 0.00 2.27
1642 1846 6.125029 CCATCATACAACTCTTGATCCCTTT 58.875 40.000 0.00 0.00 0.00 3.11
1643 1847 5.192522 ACCATCATACAACTCTTGATCCCTT 59.807 40.000 0.00 0.00 0.00 3.95
1644 1848 4.723789 ACCATCATACAACTCTTGATCCCT 59.276 41.667 0.00 0.00 0.00 4.20
1645 1849 5.041191 ACCATCATACAACTCTTGATCCC 57.959 43.478 0.00 0.00 0.00 3.85
1646 1850 6.582636 TGTACCATCATACAACTCTTGATCC 58.417 40.000 0.00 0.00 32.07 3.36
1647 1851 7.268586 ACTGTACCATCATACAACTCTTGATC 58.731 38.462 0.00 0.00 34.68 2.92
1671 1875 5.623673 CGCATACAAACTGAGTTAACCAAAC 59.376 40.000 0.00 0.00 38.46 2.93
1694 1905 0.600255 AAGAACCGAGCCTGAACACG 60.600 55.000 0.00 0.00 0.00 4.49
1786 2007 5.782893 TGGAAAGGTAAAATCAAGTGGTG 57.217 39.130 0.00 0.00 0.00 4.17
1826 2047 8.349245 ACGAATAGAACAAATTCATGTTGTCAA 58.651 29.630 0.25 0.00 43.31 3.18
1862 2083 2.076863 AGCTTTAAGTCACGATGGCAC 58.923 47.619 0.00 0.00 0.00 5.01
1954 2175 5.186198 GTTCCACCAGATTTATAGCACAGT 58.814 41.667 0.00 0.00 0.00 3.55
1964 2188 0.953960 GGCGTCGTTCCACCAGATTT 60.954 55.000 0.00 0.00 0.00 2.17
1976 2200 2.356313 CAAGCACTCAGGCGTCGT 60.356 61.111 0.00 0.00 39.27 4.34
1979 2203 0.036010 ATAAGCAAGCACTCAGGCGT 60.036 50.000 0.00 0.00 39.27 5.68
2070 2307 6.237861 GCACCGATGACTGTAAATTAGAGAAC 60.238 42.308 4.07 0.00 0.00 3.01
2187 2424 0.751643 ACTTGAAAGCGCCAAGGTGT 60.752 50.000 23.04 7.21 43.81 4.16
2249 2486 8.741101 TTCATGACCGAACAAAATTATTCAAG 57.259 30.769 0.00 0.00 0.00 3.02
2263 2500 4.320202 GCAAGTAAAGCTTTCATGACCGAA 60.320 41.667 16.57 0.00 34.69 4.30
2324 2561 1.561076 TGCTCCTCAATACCATGCACT 59.439 47.619 0.00 0.00 0.00 4.40
2385 2622 5.036737 AGTGTTTGAGCGAAAAACATGAAG 58.963 37.500 14.74 0.00 46.14 3.02
2397 2634 7.689812 CAGAGACAAATTATTAGTGTTTGAGCG 59.310 37.037 4.31 0.00 36.58 5.03
2404 2641 9.388506 CTCCATTCAGAGACAAATTATTAGTGT 57.611 33.333 0.00 0.00 35.82 3.55
2502 2739 7.928167 GTCACTTTGAAATTCTTGGGATTTTCT 59.072 33.333 11.77 0.00 40.03 2.52
2524 2761 1.064060 GCGGCATACCTGAATTGTCAC 59.936 52.381 0.00 0.00 0.00 3.67
3026 3263 2.361357 AGGTCCGAGTCCAGGTCG 60.361 66.667 0.00 0.00 37.17 4.79
3159 3400 3.719268 AATGGCACTCAATCTGGTGTA 57.281 42.857 0.00 0.00 36.03 2.90
3213 3454 5.211973 AGTAGCCTGAATACAATCCTCTCA 58.788 41.667 0.00 0.00 0.00 3.27
3237 3478 4.202050 GCAACACCAATTTCAGACTCAAGT 60.202 41.667 0.00 0.00 0.00 3.16
3265 3506 9.676195 TGTATTTTGTTAGACAACACATCAATG 57.324 29.630 0.00 0.00 44.28 2.82
3318 3565 7.052248 CGGGTAAATACTCCCTTTTATCAACT 58.948 38.462 0.00 0.00 41.40 3.16
3319 3566 7.049754 TCGGGTAAATACTCCCTTTTATCAAC 58.950 38.462 0.00 0.00 41.40 3.18
3321 3568 6.811634 TCGGGTAAATACTCCCTTTTATCA 57.188 37.500 0.00 0.00 41.40 2.15
3322 3569 8.687292 ATTTCGGGTAAATACTCCCTTTTATC 57.313 34.615 0.00 0.00 41.40 1.75
3323 3570 7.443272 CGATTTCGGGTAAATACTCCCTTTTAT 59.557 37.037 0.00 0.00 41.40 1.40
3324 3571 6.762661 CGATTTCGGGTAAATACTCCCTTTTA 59.237 38.462 0.00 0.00 41.40 1.52
3325 3572 5.587443 CGATTTCGGGTAAATACTCCCTTTT 59.413 40.000 0.00 0.00 41.40 2.27
3329 3576 2.804527 GCGATTTCGGGTAAATACTCCC 59.195 50.000 1.75 0.00 37.93 4.30
3357 3604 0.786581 CATCAGTCGATGCATACGGC 59.213 55.000 13.06 13.06 42.54 5.68
3366 3613 1.445095 GGCCTCTGCATCAGTCGAT 59.555 57.895 0.00 0.00 40.13 3.59
3368 3615 2.584418 CGGCCTCTGCATCAGTCG 60.584 66.667 0.00 0.00 40.13 4.18
3369 3616 2.202987 CCGGCCTCTGCATCAGTC 60.203 66.667 0.00 0.00 40.13 3.51
3370 3617 3.790437 CCCGGCCTCTGCATCAGT 61.790 66.667 0.00 0.00 40.13 3.41
3371 3618 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
3376 3623 2.774687 TTAAAACCCCCGGCCTCTGC 62.775 60.000 0.00 0.00 0.00 4.26
3377 3624 0.963856 GTTAAAACCCCCGGCCTCTG 60.964 60.000 0.00 0.00 0.00 3.35
3378 3625 1.381463 GTTAAAACCCCCGGCCTCT 59.619 57.895 0.00 0.00 0.00 3.69
3379 3626 1.679977 GGTTAAAACCCCCGGCCTC 60.680 63.158 0.00 0.00 43.43 4.70
3380 3627 2.441959 GGTTAAAACCCCCGGCCT 59.558 61.111 0.00 0.00 43.43 5.19
3411 3658 7.696453 GCTTTGCGTATACATGATACACTTTTT 59.304 33.333 0.00 0.00 40.58 1.94
3412 3659 7.065803 AGCTTTGCGTATACATGATACACTTTT 59.934 33.333 0.00 0.00 40.58 2.27
3413 3660 6.538742 AGCTTTGCGTATACATGATACACTTT 59.461 34.615 0.00 0.00 40.58 2.66
3414 3661 6.018751 CAGCTTTGCGTATACATGATACACTT 60.019 38.462 0.00 0.00 40.58 3.16
3415 3662 5.463392 CAGCTTTGCGTATACATGATACACT 59.537 40.000 0.00 0.00 40.58 3.55
3428 3675 0.591170 GCAGAAACCAGCTTTGCGTA 59.409 50.000 0.00 0.00 0.00 4.42
3477 3724 0.250234 GCATAGGTGGAGTGCAGTCA 59.750 55.000 22.68 6.72 38.68 3.41
3536 3783 6.086765 CGAGTGTTAGCAATTGATCAACAAAC 59.913 38.462 11.07 10.87 42.03 2.93
3558 3805 1.595003 GCGGTCGATACTCTGTTCGAG 60.595 57.143 0.00 0.00 44.27 4.04
3559 3806 0.376152 GCGGTCGATACTCTGTTCGA 59.624 55.000 0.00 0.00 41.70 3.71
3568 3815 0.591741 CCTCGAACAGCGGTCGATAC 60.592 60.000 16.68 0.00 41.33 2.24
3606 3861 3.160478 AACCTTTCCAGCCACCCCC 62.160 63.158 0.00 0.00 0.00 5.40
3705 3961 3.829601 AGGGATTGTTCGCAATTGGTTTA 59.170 39.130 7.72 0.00 46.84 2.01
3706 3962 2.632512 AGGGATTGTTCGCAATTGGTTT 59.367 40.909 7.72 0.00 46.84 3.27
3707 3963 2.029110 CAGGGATTGTTCGCAATTGGTT 60.029 45.455 7.72 0.00 46.84 3.67
3708 3964 1.545582 CAGGGATTGTTCGCAATTGGT 59.454 47.619 7.72 0.00 46.84 3.67
3709 3965 1.818060 TCAGGGATTGTTCGCAATTGG 59.182 47.619 7.72 0.00 46.84 3.16
3747 4003 0.741326 ATCGACGACATCCTCCACAG 59.259 55.000 0.00 0.00 0.00 3.66
3756 4012 1.317431 TTCCCCGACATCGACGACAT 61.317 55.000 0.00 0.00 43.02 3.06
3757 4013 1.929806 CTTCCCCGACATCGACGACA 61.930 60.000 0.00 0.00 43.02 4.35
3762 4018 1.389609 GGCTACTTCCCCGACATCGA 61.390 60.000 2.09 0.00 43.02 3.59
3770 4026 3.744660 CATATGACAAGGCTACTTCCCC 58.255 50.000 0.00 0.00 33.81 4.81
3782 4038 1.760029 TCAGGCTACGGCATATGACAA 59.240 47.619 9.77 0.00 40.87 3.18
3827 4083 1.070601 CACACACACACTCCTCCATCA 59.929 52.381 0.00 0.00 0.00 3.07
3828 4084 1.070758 ACACACACACACTCCTCCATC 59.929 52.381 0.00 0.00 0.00 3.51
3838 4094 1.668237 GCACATACACACACACACACA 59.332 47.619 0.00 0.00 0.00 3.72
3848 4104 3.500448 TGAAAAGAGGGCACATACACA 57.500 42.857 0.00 0.00 0.00 3.72
3850 4106 6.418057 AATTTTGAAAAGAGGGCACATACA 57.582 33.333 0.00 0.00 0.00 2.29
3851 4107 7.728847 AAAATTTTGAAAAGAGGGCACATAC 57.271 32.000 1.75 0.00 0.00 2.39
3852 4108 8.646900 ACTAAAATTTTGAAAAGAGGGCACATA 58.353 29.630 13.76 0.00 0.00 2.29
3853 4109 7.442062 CACTAAAATTTTGAAAAGAGGGCACAT 59.558 33.333 13.76 0.00 0.00 3.21
3854 4110 6.760770 CACTAAAATTTTGAAAAGAGGGCACA 59.239 34.615 13.76 0.00 0.00 4.57
3855 4111 6.202762 CCACTAAAATTTTGAAAAGAGGGCAC 59.797 38.462 13.76 0.00 0.00 5.01
3856 4112 6.126911 ACCACTAAAATTTTGAAAAGAGGGCA 60.127 34.615 13.76 0.00 0.00 5.36
3857 4113 6.202762 CACCACTAAAATTTTGAAAAGAGGGC 59.797 38.462 13.76 0.00 0.00 5.19
3858 4114 7.224557 CACACCACTAAAATTTTGAAAAGAGGG 59.775 37.037 13.76 11.37 0.00 4.30
3859 4115 7.763985 ACACACCACTAAAATTTTGAAAAGAGG 59.236 33.333 13.76 12.27 0.00 3.69
3860 4116 8.594687 CACACACCACTAAAATTTTGAAAAGAG 58.405 33.333 13.76 4.31 0.00 2.85
3861 4117 8.307483 TCACACACCACTAAAATTTTGAAAAGA 58.693 29.630 13.76 0.00 0.00 2.52
3862 4118 8.472683 TCACACACCACTAAAATTTTGAAAAG 57.527 30.769 13.76 5.37 0.00 2.27
3863 4119 8.833231 TTCACACACCACTAAAATTTTGAAAA 57.167 26.923 13.76 0.00 0.00 2.29
3864 4120 8.833231 TTTCACACACCACTAAAATTTTGAAA 57.167 26.923 13.76 8.18 0.00 2.69
3879 4135 1.680338 AGTTGGCTCTTTCACACACC 58.320 50.000 0.00 0.00 0.00 4.16
3923 4183 1.829138 AGTTTAGTCCCACCCTGGTT 58.171 50.000 0.00 0.00 35.17 3.67
3936 4196 5.264395 ACAAGGGGATCATGGAAAGTTTAG 58.736 41.667 0.00 0.00 0.00 1.85
3950 4210 2.423947 GCTCCATTCATGACAAGGGGAT 60.424 50.000 10.54 0.00 0.00 3.85
3951 4211 1.064463 GCTCCATTCATGACAAGGGGA 60.064 52.381 10.54 5.79 0.00 4.81
3963 4223 3.699411 AGAGGCTCATATGCTCCATTC 57.301 47.619 18.26 5.50 0.00 2.67
3964 4224 3.518705 CCTAGAGGCTCATATGCTCCATT 59.481 47.826 18.26 0.00 0.00 3.16
3965 4225 3.106054 CCTAGAGGCTCATATGCTCCAT 58.894 50.000 18.26 0.00 0.00 3.41
3966 4226 2.110721 TCCTAGAGGCTCATATGCTCCA 59.889 50.000 18.26 0.00 34.44 3.86
3967 4227 2.813907 TCCTAGAGGCTCATATGCTCC 58.186 52.381 18.26 1.40 34.44 4.70
3968 4228 4.465660 TGAATCCTAGAGGCTCATATGCTC 59.534 45.833 18.26 6.95 34.44 4.26
3969 4229 4.423913 TGAATCCTAGAGGCTCATATGCT 58.576 43.478 18.26 0.00 34.44 3.79
3970 4230 4.815533 TGAATCCTAGAGGCTCATATGC 57.184 45.455 18.26 3.57 34.44 3.14
3971 4231 6.602410 TCTTGAATCCTAGAGGCTCATATG 57.398 41.667 18.26 0.00 34.44 1.78
3972 4232 7.811482 ATTCTTGAATCCTAGAGGCTCATAT 57.189 36.000 18.26 0.00 34.44 1.78
3973 4233 7.071698 ACAATTCTTGAATCCTAGAGGCTCATA 59.928 37.037 18.26 5.47 34.44 2.15
3974 4234 6.126536 ACAATTCTTGAATCCTAGAGGCTCAT 60.127 38.462 18.26 4.50 34.44 2.90
3975 4235 5.190528 ACAATTCTTGAATCCTAGAGGCTCA 59.809 40.000 18.26 1.80 34.44 4.26
3976 4236 5.679601 ACAATTCTTGAATCCTAGAGGCTC 58.320 41.667 6.34 6.34 34.44 4.70
3977 4237 5.707066 ACAATTCTTGAATCCTAGAGGCT 57.293 39.130 0.00 0.00 34.44 4.58
3978 4238 5.067023 CCAACAATTCTTGAATCCTAGAGGC 59.933 44.000 0.00 0.00 34.44 4.70
3979 4239 6.418101 TCCAACAATTCTTGAATCCTAGAGG 58.582 40.000 0.00 0.00 0.00 3.69
3980 4240 7.928307 TTCCAACAATTCTTGAATCCTAGAG 57.072 36.000 0.00 0.00 0.00 2.43
3981 4241 8.884124 ATTTCCAACAATTCTTGAATCCTAGA 57.116 30.769 0.00 0.00 0.00 2.43
3991 4251 9.394767 GCCCATTTATTATTTCCAACAATTCTT 57.605 29.630 0.00 0.00 0.00 2.52
3992 4252 8.771286 AGCCCATTTATTATTTCCAACAATTCT 58.229 29.630 0.00 0.00 0.00 2.40
3993 4253 8.962884 AGCCCATTTATTATTTCCAACAATTC 57.037 30.769 0.00 0.00 0.00 2.17
3997 4257 9.883142 CTTTTAGCCCATTTATTATTTCCAACA 57.117 29.630 0.00 0.00 0.00 3.33
3998 4258 8.826710 GCTTTTAGCCCATTTATTATTTCCAAC 58.173 33.333 0.00 0.00 34.48 3.77
3999 4259 8.956533 GCTTTTAGCCCATTTATTATTTCCAA 57.043 30.769 0.00 0.00 34.48 3.53
4016 4276 9.249457 GATTGTTGGAATTATTAGGCTTTTAGC 57.751 33.333 0.00 0.00 41.46 3.09
4017 4277 9.750125 GGATTGTTGGAATTATTAGGCTTTTAG 57.250 33.333 0.00 0.00 0.00 1.85
4018 4278 8.700973 GGGATTGTTGGAATTATTAGGCTTTTA 58.299 33.333 0.00 0.00 0.00 1.52
4019 4279 7.365563 GGGGATTGTTGGAATTATTAGGCTTTT 60.366 37.037 0.00 0.00 0.00 2.27
4020 4280 6.099701 GGGGATTGTTGGAATTATTAGGCTTT 59.900 38.462 0.00 0.00 0.00 3.51
4021 4281 5.602561 GGGGATTGTTGGAATTATTAGGCTT 59.397 40.000 0.00 0.00 0.00 4.35
4022 4282 5.103086 AGGGGATTGTTGGAATTATTAGGCT 60.103 40.000 0.00 0.00 0.00 4.58
4023 4283 5.147767 AGGGGATTGTTGGAATTATTAGGC 58.852 41.667 0.00 0.00 0.00 3.93
4024 4284 8.170061 TGATAGGGGATTGTTGGAATTATTAGG 58.830 37.037 0.00 0.00 0.00 2.69
4025 4285 9.236006 CTGATAGGGGATTGTTGGAATTATTAG 57.764 37.037 0.00 0.00 0.00 1.73
4026 4286 8.954729 TCTGATAGGGGATTGTTGGAATTATTA 58.045 33.333 0.00 0.00 0.00 0.98
4027 4287 7.825709 TCTGATAGGGGATTGTTGGAATTATT 58.174 34.615 0.00 0.00 0.00 1.40
4028 4288 7.406620 TCTGATAGGGGATTGTTGGAATTAT 57.593 36.000 0.00 0.00 0.00 1.28
4029 4289 6.840090 TCTGATAGGGGATTGTTGGAATTA 57.160 37.500 0.00 0.00 0.00 1.40
4030 4290 5.732331 TCTGATAGGGGATTGTTGGAATT 57.268 39.130 0.00 0.00 0.00 2.17
4031 4291 5.222213 GGATCTGATAGGGGATTGTTGGAAT 60.222 44.000 0.00 0.00 0.00 3.01
4032 4292 4.104738 GGATCTGATAGGGGATTGTTGGAA 59.895 45.833 0.00 0.00 0.00 3.53
4033 4293 3.652869 GGATCTGATAGGGGATTGTTGGA 59.347 47.826 0.00 0.00 0.00 3.53
4034 4294 3.245052 GGGATCTGATAGGGGATTGTTGG 60.245 52.174 0.00 0.00 0.00 3.77
4035 4295 3.395607 TGGGATCTGATAGGGGATTGTTG 59.604 47.826 0.00 0.00 0.00 3.33
4036 4296 3.680169 TGGGATCTGATAGGGGATTGTT 58.320 45.455 0.00 0.00 0.00 2.83
4037 4297 3.367280 TGGGATCTGATAGGGGATTGT 57.633 47.619 0.00 0.00 0.00 2.71
4038 4298 4.508047 CCTTTGGGATCTGATAGGGGATTG 60.508 50.000 0.00 0.00 33.58 2.67
4039 4299 3.659686 CCTTTGGGATCTGATAGGGGATT 59.340 47.826 0.00 0.00 33.58 3.01
4040 4300 3.263724 CCTTTGGGATCTGATAGGGGAT 58.736 50.000 0.00 0.00 33.58 3.85
4041 4301 2.706350 CCTTTGGGATCTGATAGGGGA 58.294 52.381 0.00 0.00 33.58 4.81
4042 4302 1.074566 GCCTTTGGGATCTGATAGGGG 59.925 57.143 5.75 0.00 33.58 4.79
4043 4303 2.061061 AGCCTTTGGGATCTGATAGGG 58.939 52.381 5.75 0.00 33.58 3.53
4044 4304 2.707791 TCAGCCTTTGGGATCTGATAGG 59.292 50.000 0.00 0.00 30.41 2.57
4045 4305 4.637387 ATCAGCCTTTGGGATCTGATAG 57.363 45.455 2.14 0.00 39.21 2.08
4046 4306 6.101734 ACTTTATCAGCCTTTGGGATCTGATA 59.898 38.462 6.68 6.68 40.46 2.15
4047 4307 5.103771 ACTTTATCAGCCTTTGGGATCTGAT 60.104 40.000 8.39 8.39 41.75 2.90
4048 4308 4.228210 ACTTTATCAGCCTTTGGGATCTGA 59.772 41.667 0.00 0.00 36.60 3.27
4049 4309 4.530875 ACTTTATCAGCCTTTGGGATCTG 58.469 43.478 0.00 0.00 33.58 2.90
4050 4310 4.870021 ACTTTATCAGCCTTTGGGATCT 57.130 40.909 0.00 0.00 33.58 2.75
4051 4311 5.654497 CAAACTTTATCAGCCTTTGGGATC 58.346 41.667 0.00 0.00 33.58 3.36
4052 4312 4.081476 GCAAACTTTATCAGCCTTTGGGAT 60.081 41.667 0.00 0.00 33.58 3.85
4053 4313 3.258123 GCAAACTTTATCAGCCTTTGGGA 59.742 43.478 0.00 0.00 33.58 4.37
4054 4314 3.259123 AGCAAACTTTATCAGCCTTTGGG 59.741 43.478 0.00 0.00 0.00 4.12
4055 4315 4.525912 AGCAAACTTTATCAGCCTTTGG 57.474 40.909 0.00 0.00 0.00 3.28
4056 4316 6.532657 CCATAAGCAAACTTTATCAGCCTTTG 59.467 38.462 0.00 0.00 37.33 2.77
4057 4317 6.211384 ACCATAAGCAAACTTTATCAGCCTTT 59.789 34.615 0.00 0.00 37.33 3.11
4058 4318 5.716703 ACCATAAGCAAACTTTATCAGCCTT 59.283 36.000 0.00 0.00 37.33 4.35
4059 4319 5.264395 ACCATAAGCAAACTTTATCAGCCT 58.736 37.500 0.00 0.00 37.33 4.58
4060 4320 5.582689 ACCATAAGCAAACTTTATCAGCC 57.417 39.130 0.00 0.00 37.33 4.85
4061 4321 6.036470 GGAACCATAAGCAAACTTTATCAGC 58.964 40.000 0.00 0.00 37.33 4.26
4062 4322 7.156876 TGGAACCATAAGCAAACTTTATCAG 57.843 36.000 0.00 0.00 37.33 2.90
4063 4323 7.716799 ATGGAACCATAAGCAAACTTTATCA 57.283 32.000 4.37 0.00 37.33 2.15


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

AutoCloner maintained by Alex Coulton.