Multiple sequence alignment - TraesCS5D01G232400

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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 TraesCS5D01G232400 chr5D 100.000 5746 0 0 1 5746 339351408 339357153 0.000000e+00 10611.0
1 TraesCS5D01G232400 chr5D 87.407 135 13 3 5478 5609 215302118 215301985 9.970000e-33 152.0
2 TraesCS5D01G232400 chr5D 86.567 134 17 1 5478 5610 221149431 221149564 4.640000e-31 147.0
3 TraesCS5D01G232400 chr5D 93.878 49 3 0 4449 4497 461211550 461211502 2.220000e-09 75.0
4 TraesCS5D01G232400 chr5D 96.970 33 1 0 4654 4686 264017285 264017253 8.040000e-04 56.5
5 TraesCS5D01G232400 chr5A 91.843 3114 152 45 2106 5174 440263045 440266101 0.000000e+00 4250.0
6 TraesCS5D01G232400 chr5A 92.688 1354 57 16 717 2056 440261734 440263059 0.000000e+00 1914.0
7 TraesCS5D01G232400 chr5A 88.082 730 29 28 6 699 440261042 440261749 0.000000e+00 813.0
8 TraesCS5D01G232400 chr5A 91.250 480 33 3 3695 4165 186134161 186134640 0.000000e+00 645.0
9 TraesCS5D01G232400 chr5A 87.879 363 38 5 5386 5746 440280493 440280851 6.880000e-114 422.0
10 TraesCS5D01G232400 chr5A 95.783 166 7 0 5222 5387 440266114 440266279 9.490000e-68 268.0
11 TraesCS5D01G232400 chr5A 94.000 100 6 0 3698 3797 515748008 515747909 9.970000e-33 152.0
12 TraesCS5D01G232400 chr5A 88.542 96 11 0 1055 1150 478993120 478993025 3.640000e-22 117.0
13 TraesCS5D01G232400 chr5A 85.149 101 14 1 1050 1149 479046974 479047074 1.020000e-17 102.0
14 TraesCS5D01G232400 chr5A 94.118 51 1 2 4444 4493 126268531 126268482 6.170000e-10 76.8
15 TraesCS5D01G232400 chr5A 96.970 33 1 0 4654 4686 350236269 350236237 8.040000e-04 56.5
16 TraesCS5D01G232400 chr5B 92.524 1351 53 12 717 2053 398345858 398347174 0.000000e+00 1892.0
17 TraesCS5D01G232400 chr5B 93.081 1243 65 6 4507 5746 398349802 398351026 0.000000e+00 1799.0
18 TraesCS5D01G232400 chr5B 91.013 1046 62 12 2106 3143 398347188 398348209 0.000000e+00 1382.0
19 TraesCS5D01G232400 chr5B 93.890 851 32 6 3617 4455 398348936 398349778 0.000000e+00 1266.0
20 TraesCS5D01G232400 chr5B 89.456 607 35 16 100 699 398345289 398345873 0.000000e+00 739.0
21 TraesCS5D01G232400 chr5B 90.343 466 26 9 3159 3619 398348414 398348865 1.380000e-165 593.0
22 TraesCS5D01G232400 chr5B 90.722 97 6 2 13 109 398344974 398345067 6.040000e-25 126.0
23 TraesCS5D01G232400 chr5B 96.970 33 1 0 4654 4686 296377150 296377118 8.040000e-04 56.5
24 TraesCS5D01G232400 chr7D 86.598 194 26 0 1510 1703 99873536 99873343 1.250000e-51 215.0
25 TraesCS5D01G232400 chr7D 86.614 127 16 1 5478 5603 101394305 101394431 7.760000e-29 139.0
26 TraesCS5D01G232400 chr7B 86.667 195 24 2 1510 1703 55066337 55066144 1.250000e-51 215.0
27 TraesCS5D01G232400 chr7B 85.567 194 28 0 1510 1703 55035182 55034989 2.710000e-48 204.0
28 TraesCS5D01G232400 chr7A 85.567 194 28 0 1510 1703 102289786 102289593 2.710000e-48 204.0
29 TraesCS5D01G232400 chr1A 97.087 103 3 0 3695 3797 578255850 578255952 2.130000e-39 174.0
30 TraesCS5D01G232400 chr1A 87.143 140 13 5 5474 5610 298614264 298614401 2.770000e-33 154.0
31 TraesCS5D01G232400 chr1A 85.821 134 16 2 5478 5610 98236318 98236449 7.760000e-29 139.0
32 TraesCS5D01G232400 chr6A 89.286 140 6 4 3695 3827 437966559 437966696 3.560000e-37 167.0
33 TraesCS5D01G232400 chr6B 84.810 158 18 3 5455 5611 711626338 711626490 2.770000e-33 154.0
34 TraesCS5D01G232400 chr6B 91.071 56 5 0 4436 4491 495438456 495438511 6.170000e-10 76.8
35 TraesCS5D01G232400 chr2D 85.075 134 18 2 5478 5610 28412907 28412775 1.000000e-27 135.0
36 TraesCS5D01G232400 chr2D 94.118 51 2 1 4443 4493 117843035 117843084 6.170000e-10 76.8
37 TraesCS5D01G232400 chr1B 85.393 89 8 2 2941 3024 626236679 626236767 2.850000e-13 87.9
38 TraesCS5D01G232400 chr1D 94.444 54 2 1 4441 4494 45495782 45495834 1.330000e-11 82.4
39 TraesCS5D01G232400 chr3D 92.727 55 3 1 4440 4493 436676994 436676940 1.720000e-10 78.7
40 TraesCS5D01G232400 chr6D 92.593 54 2 2 4444 4496 7865911 7865963 6.170000e-10 76.8
41 TraesCS5D01G232400 chr3A 90.909 55 5 0 4439 4493 427762644 427762698 2.220000e-09 75.0


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 TraesCS5D01G232400 chr5D 339351408 339357153 5745 False 10611.000000 10611 100.000000 1 5746 1 chr5D.!!$F2 5745
1 TraesCS5D01G232400 chr5A 440261042 440266279 5237 False 1811.250000 4250 92.099000 6 5387 4 chr5A.!!$F4 5381
2 TraesCS5D01G232400 chr5B 398344974 398351026 6052 False 1113.857143 1892 91.575571 13 5746 7 chr5B.!!$F1 5733

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
707 978 0.108329 TTCGTTCGAGCATTCCCCTC 60.108 55.0 0.00 0.00 0.00 4.30 F
1458 1741 0.041312 GTTCGTTGCGTGCTGATGTT 60.041 50.0 0.00 0.00 0.00 2.71 F
2095 2390 0.035725 ACTTACGGGTTAAGCAGCCC 60.036 55.0 7.03 0.00 41.03 5.19 F
2472 2777 0.037326 ATGCATGTCCTTGTCGACGT 60.037 50.0 11.62 0.00 35.40 4.34 F
3820 4415 0.027194 CGTCTGCTCAATGATTGGCG 59.973 55.0 5.20 5.14 32.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2371 0.035725 GGGCTGCTTAACCCGTAAGT 60.036 55.000 0.00 0.0 41.28 2.24 R
2451 2752 0.647410 GTCGACAAGGACATGCATCG 59.353 55.000 11.55 0.0 36.91 3.84 R
3801 4396 0.027194 CGCCAATCATTGAGCAGACG 59.973 55.000 0.00 0.0 0.00 4.18 R
4162 4760 0.107066 TGGCCCATATGTCTGCACTG 60.107 55.000 0.00 0.0 0.00 3.66 R
5198 5818 1.064017 GCATGTGATTACCCTTCCCCA 60.064 52.381 0.00 0.0 0.00 4.96 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
27 34 2.738013 AAGTTGGTAGTCGTAGTGGC 57.262 50.000 0.00 0.00 0.00 5.01
28 35 1.920610 AGTTGGTAGTCGTAGTGGCT 58.079 50.000 0.00 0.00 0.00 4.75
57 64 1.600076 ATGGATCGCATCAGCCAGC 60.600 57.895 0.00 0.00 37.52 4.85
58 65 2.053259 ATGGATCGCATCAGCCAGCT 62.053 55.000 0.00 0.00 37.52 4.24
59 66 2.252346 GGATCGCATCAGCCAGCTG 61.252 63.158 13.54 13.54 44.86 4.24
155 393 1.202710 TGCTCTTTTGCCGTCCAACTA 60.203 47.619 0.00 0.00 31.97 2.24
165 403 2.042261 TCCAACTAGCCCTCCCCC 59.958 66.667 0.00 0.00 0.00 5.40
196 439 1.478137 CGCGCCTACAGTACAATCTC 58.522 55.000 0.00 0.00 0.00 2.75
206 449 3.255888 ACAGTACAATCTCAGAGCGTCAA 59.744 43.478 0.00 0.00 0.00 3.18
220 463 2.139336 CGTCAATTCCGCTGTTAACG 57.861 50.000 0.26 0.00 0.00 3.18
351 603 0.961857 TGTCCCACATGCATGCAGAC 60.962 55.000 26.69 26.12 0.00 3.51
378 630 7.482169 TCCAATATCCAAATACTATCTCGCT 57.518 36.000 0.00 0.00 0.00 4.93
408 672 4.481870 CGCGAGGCAAATGCAAAT 57.518 50.000 0.00 0.00 44.36 2.32
409 673 1.992947 CGCGAGGCAAATGCAAATG 59.007 52.632 0.00 0.00 44.36 2.32
410 674 1.711500 GCGAGGCAAATGCAAATGC 59.289 52.632 16.38 16.38 44.36 3.56
432 697 1.737793 CGCCTCGTGCCTAATTCTTTT 59.262 47.619 0.00 0.00 36.24 2.27
445 710 6.127980 GCCTAATTCTTTTCCTAACACTCACC 60.128 42.308 0.00 0.00 0.00 4.02
622 889 1.073284 GTTGGTGGTGGTGGTACAGAT 59.927 52.381 0.00 0.00 41.80 2.90
623 890 2.303600 GTTGGTGGTGGTGGTACAGATA 59.696 50.000 0.00 0.00 41.80 1.98
691 962 2.936498 AGTTTCACCCGCTAATGATTCG 59.064 45.455 0.00 0.00 0.00 3.34
699 970 1.852280 CGCTAATGATTCGTTCGAGCA 59.148 47.619 11.88 0.00 31.11 4.26
700 971 2.472861 CGCTAATGATTCGTTCGAGCAT 59.527 45.455 11.88 6.76 31.11 3.79
702 973 4.449779 GCTAATGATTCGTTCGAGCATTC 58.550 43.478 19.87 9.95 32.13 2.67
703 974 3.951979 AATGATTCGTTCGAGCATTCC 57.048 42.857 14.60 0.00 0.00 3.01
704 975 1.651987 TGATTCGTTCGAGCATTCCC 58.348 50.000 0.00 0.00 0.00 3.97
705 976 0.938008 GATTCGTTCGAGCATTCCCC 59.062 55.000 0.00 0.00 0.00 4.81
706 977 0.541863 ATTCGTTCGAGCATTCCCCT 59.458 50.000 0.00 0.00 0.00 4.79
707 978 0.108329 TTCGTTCGAGCATTCCCCTC 60.108 55.000 0.00 0.00 0.00 4.30
708 979 1.218047 CGTTCGAGCATTCCCCTCA 59.782 57.895 0.00 0.00 0.00 3.86
709 980 0.391130 CGTTCGAGCATTCCCCTCAA 60.391 55.000 0.00 0.00 0.00 3.02
710 981 1.821216 GTTCGAGCATTCCCCTCAAA 58.179 50.000 0.00 0.00 0.00 2.69
711 982 2.159382 GTTCGAGCATTCCCCTCAAAA 58.841 47.619 0.00 0.00 0.00 2.44
712 983 2.556622 GTTCGAGCATTCCCCTCAAAAA 59.443 45.455 0.00 0.00 0.00 1.94
734 1005 4.701956 AAAAATGATTCGTTCGAGCCAT 57.298 36.364 0.00 1.23 0.00 4.40
735 1006 3.680642 AAATGATTCGTTCGAGCCATG 57.319 42.857 10.32 0.00 0.00 3.66
887 1161 1.472728 CCCTATAAAGTTGGCGACGCT 60.473 52.381 20.77 0.39 0.00 5.07
1240 1523 0.806884 TCGGGGCTAATTAACGTGCG 60.807 55.000 0.00 0.00 0.00 5.34
1241 1524 1.085501 CGGGGCTAATTAACGTGCGT 61.086 55.000 0.00 0.00 0.00 5.24
1242 1525 0.375803 GGGGCTAATTAACGTGCGTG 59.624 55.000 0.00 0.00 0.00 5.34
1243 1526 1.361793 GGGCTAATTAACGTGCGTGA 58.638 50.000 0.00 0.00 0.00 4.35
1244 1527 1.937899 GGGCTAATTAACGTGCGTGAT 59.062 47.619 0.00 0.00 0.00 3.06
1458 1741 0.041312 GTTCGTTGCGTGCTGATGTT 60.041 50.000 0.00 0.00 0.00 2.71
1469 1752 1.262950 TGCTGATGTTTGTTCGGTTCG 59.737 47.619 0.00 0.00 0.00 3.95
1470 1753 1.950472 CTGATGTTTGTTCGGTTCGC 58.050 50.000 0.00 0.00 0.00 4.70
1637 1920 2.856988 ACCATGGACCCCAACCGT 60.857 61.111 21.47 0.00 36.95 4.83
1708 1991 2.159114 GCAAGAAAACCAAGGTCAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
1709 1992 3.447742 CAAGAAAACCAAGGTCAGCAAC 58.552 45.455 0.00 0.00 0.00 4.17
1718 2001 2.741092 GTCAGCAACCCGACCAGA 59.259 61.111 0.00 0.00 0.00 3.86
1719 2002 1.668151 GTCAGCAACCCGACCAGAC 60.668 63.158 0.00 0.00 0.00 3.51
1720 2003 1.837051 TCAGCAACCCGACCAGACT 60.837 57.895 0.00 0.00 0.00 3.24
1721 2004 1.374758 CAGCAACCCGACCAGACTC 60.375 63.158 0.00 0.00 0.00 3.36
1722 2005 1.534235 AGCAACCCGACCAGACTCT 60.534 57.895 0.00 0.00 0.00 3.24
1730 2013 2.289694 CCCGACCAGACTCTGTTCAATT 60.290 50.000 5.32 0.00 0.00 2.32
1764 2047 3.717707 TGTTCCACTTCAGAAGTCTTCG 58.282 45.455 13.27 2.24 40.46 3.79
1774 2057 9.193133 CACTTCAGAAGTCTTCGTTTATCTTTA 57.807 33.333 13.27 0.00 40.46 1.85
1829 2112 3.845781 TCCATCCAGAATAGGCAGAAC 57.154 47.619 0.00 0.00 0.00 3.01
1837 2120 3.881688 CAGAATAGGCAGAACATCCCTTG 59.118 47.826 0.00 0.00 0.00 3.61
1852 2139 5.960202 ACATCCCTTGAAAAAGAATAGGCAT 59.040 36.000 0.00 0.00 0.00 4.40
1881 2169 5.357742 AATGGTTTAATTTCATGCCCTCC 57.642 39.130 0.00 0.00 0.00 4.30
1903 2191 2.069273 GTGATCGAGACACAAACAGGG 58.931 52.381 16.91 0.00 38.05 4.45
1942 2233 0.318022 TGTTGCATGCACAAGCGAAG 60.318 50.000 22.58 0.00 46.23 3.79
1981 2272 8.442605 TTTTAGAAGTTTTCTCAACAACAACG 57.557 30.769 0.00 0.00 41.14 4.10
1989 2280 6.921332 TTTCTCAACAACAACGAAAAAGAC 57.079 33.333 0.00 0.00 0.00 3.01
1992 2283 5.410132 TCTCAACAACAACGAAAAAGACAGA 59.590 36.000 0.00 0.00 0.00 3.41
1993 2284 5.627172 TCAACAACAACGAAAAAGACAGAG 58.373 37.500 0.00 0.00 0.00 3.35
1995 2286 6.369340 TCAACAACAACGAAAAAGACAGAGTA 59.631 34.615 0.00 0.00 0.00 2.59
1996 2287 6.920569 ACAACAACGAAAAAGACAGAGTAT 57.079 33.333 0.00 0.00 0.00 2.12
1997 2288 6.715464 ACAACAACGAAAAAGACAGAGTATG 58.285 36.000 0.00 0.00 0.00 2.39
1999 2290 6.287107 ACAACGAAAAAGACAGAGTATGTG 57.713 37.500 0.00 0.00 44.17 3.21
2043 2338 5.639506 CCTAAGTGTGTCGATGAGAAATTGT 59.360 40.000 0.00 0.00 0.00 2.71
2048 2343 6.912591 AGTGTGTCGATGAGAAATTGTTTTTC 59.087 34.615 0.00 0.00 0.00 2.29
2052 2347 8.807581 GTGTCGATGAGAAATTGTTTTTCTTTT 58.192 29.630 2.43 0.00 38.73 2.27
2053 2348 9.364989 TGTCGATGAGAAATTGTTTTTCTTTTT 57.635 25.926 2.43 0.00 38.73 1.94
2085 2380 8.946797 ACTCCTATTATATTGTACTTACGGGT 57.053 34.615 0.00 0.00 0.00 5.28
2086 2381 9.372189 ACTCCTATTATATTGTACTTACGGGTT 57.628 33.333 0.00 0.00 0.00 4.11
2092 2387 8.876275 TTATATTGTACTTACGGGTTAAGCAG 57.124 34.615 7.03 5.03 41.03 4.24
2093 2388 2.963432 TGTACTTACGGGTTAAGCAGC 58.037 47.619 7.03 0.00 41.03 5.25
2094 2389 2.274437 GTACTTACGGGTTAAGCAGCC 58.726 52.381 7.03 0.00 41.03 4.85
2095 2390 0.035725 ACTTACGGGTTAAGCAGCCC 60.036 55.000 7.03 0.00 41.03 5.19
2145 2440 5.068987 ACCCGTACTTATACCGATTAAGCAA 59.931 40.000 0.00 0.00 0.00 3.91
2149 2444 4.374399 ACTTATACCGATTAAGCAACCCG 58.626 43.478 0.00 0.00 0.00 5.28
2401 2701 6.481954 AAGACGATTAACCAACAGATCAAC 57.518 37.500 0.00 0.00 0.00 3.18
2402 2702 5.794894 AGACGATTAACCAACAGATCAACT 58.205 37.500 0.00 0.00 0.00 3.16
2451 2752 5.356882 TCGAAGTCAATTTGTTCATGGTC 57.643 39.130 0.00 0.00 0.00 4.02
2465 2770 1.332686 CATGGTCGATGCATGTCCTTG 59.667 52.381 2.46 8.22 0.00 3.61
2472 2777 0.037326 ATGCATGTCCTTGTCGACGT 60.037 50.000 11.62 0.00 35.40 4.34
2490 2797 4.378910 CGACGTGTATCATTACATTCCTCG 59.621 45.833 0.00 0.00 40.35 4.63
2577 2888 7.861176 GACATAGATGTCGACTAGAAAATCC 57.139 40.000 17.92 0.00 46.46 3.01
2597 2909 2.419667 CGGAAAAGTATTCACCACGGT 58.580 47.619 0.00 0.00 0.00 4.83
2634 2946 3.121328 GCTGTCGCGTAACTATTGCATAG 60.121 47.826 5.77 0.00 38.81 2.23
2638 2950 2.729882 CGCGTAACTATTGCATAGGGAC 59.270 50.000 0.00 0.00 37.18 4.46
2658 2970 4.717629 CGTCAGCGCCGAACCTGA 62.718 66.667 2.29 0.00 35.84 3.86
2661 2973 3.114616 CAGCGCCGAACCTGACAG 61.115 66.667 2.29 0.00 0.00 3.51
2663 2975 2.811317 GCGCCGAACCTGACAGAG 60.811 66.667 3.32 0.00 0.00 3.35
2664 2976 2.651361 CGCCGAACCTGACAGAGT 59.349 61.111 3.32 0.00 0.00 3.24
2665 2977 1.444553 CGCCGAACCTGACAGAGTC 60.445 63.158 3.32 0.00 0.00 3.36
2668 2980 0.962489 CCGAACCTGACAGAGTCACT 59.038 55.000 3.32 0.00 37.67 3.41
2684 2996 3.123804 GTCACTGACGATCTTGTGTTGT 58.876 45.455 0.00 0.00 0.00 3.32
2685 2997 3.060272 GTCACTGACGATCTTGTGTTGTG 60.060 47.826 0.00 0.00 0.00 3.33
2686 2998 2.866156 CACTGACGATCTTGTGTTGTGT 59.134 45.455 0.00 0.00 0.00 3.72
2687 2999 3.309682 CACTGACGATCTTGTGTTGTGTT 59.690 43.478 0.00 0.00 0.00 3.32
2688 3000 3.938963 ACTGACGATCTTGTGTTGTGTTT 59.061 39.130 0.00 0.00 0.00 2.83
2689 3001 4.201812 ACTGACGATCTTGTGTTGTGTTTG 60.202 41.667 0.00 0.00 0.00 2.93
3036 3348 0.326264 ACATCCTCGGCAAGCTCTTT 59.674 50.000 0.00 0.00 0.00 2.52
3070 3382 1.152777 CCAACAAGGTGAGTGCCCA 60.153 57.895 0.00 0.00 0.00 5.36
3083 3395 1.228800 TGCCCACATGCAACATCCA 60.229 52.632 0.00 0.00 38.56 3.41
3091 3403 4.759096 GCAACATCCACCGTGCGC 62.759 66.667 0.00 0.00 0.00 6.09
3120 3432 5.276536 GCAACAACATTTCTTGCTCTGTTTC 60.277 40.000 0.00 0.00 37.82 2.78
3122 3434 5.585390 ACAACATTTCTTGCTCTGTTTCAG 58.415 37.500 0.00 0.00 29.74 3.02
3124 3436 3.887716 ACATTTCTTGCTCTGTTTCAGCT 59.112 39.130 0.00 0.00 37.79 4.24
3129 3441 1.813513 TGCTCTGTTTCAGCTTAGCC 58.186 50.000 0.00 0.00 37.79 3.93
3150 3462 3.615937 CCGTCTCATGTTCTGATCTTGTG 59.384 47.826 0.00 1.32 32.10 3.33
3173 3674 4.985538 TCTCACTTCGGAGGATTTACTC 57.014 45.455 0.00 0.00 35.58 2.59
3191 3692 4.810191 ACTCGCTCTACTTGAGGATTTT 57.190 40.909 0.00 0.00 42.87 1.82
3192 3693 5.153950 ACTCGCTCTACTTGAGGATTTTT 57.846 39.130 0.00 0.00 42.87 1.94
3193 3694 6.282199 ACTCGCTCTACTTGAGGATTTTTA 57.718 37.500 0.00 0.00 42.87 1.52
3194 3695 6.698380 ACTCGCTCTACTTGAGGATTTTTAA 58.302 36.000 0.00 0.00 42.87 1.52
3195 3696 7.159372 ACTCGCTCTACTTGAGGATTTTTAAA 58.841 34.615 0.00 0.00 42.87 1.52
3314 3819 3.597255 GTTGGTAAGTAGGGACAAGAGC 58.403 50.000 0.00 0.00 0.00 4.09
3510 4019 3.070446 ACTTGTCCTGACGTGTAAATGGA 59.930 43.478 0.00 0.00 0.00 3.41
3535 4044 4.007457 TTGCTGGCAGGCAAGATC 57.993 55.556 17.64 0.00 45.64 2.75
3546 4055 3.575630 CAGGCAAGATCAATATGCATGC 58.424 45.455 11.82 11.82 43.55 4.06
3801 4396 9.881649 TGGCATCAAGATATCTTAGACATATTC 57.118 33.333 17.53 3.34 34.28 1.75
3820 4415 0.027194 CGTCTGCTCAATGATTGGCG 59.973 55.000 5.20 5.14 32.00 5.69
3877 4472 9.077885 AGTGACCAAATTAATTACACTTCATGT 57.922 29.630 16.86 0.00 46.06 3.21
3909 4504 1.005924 ACAAGTGGAGCAATTAGGGGG 59.994 52.381 0.00 0.00 0.00 5.40
3941 4536 2.632996 TGGTCAGGAAGTAGTGAAGTGG 59.367 50.000 0.00 0.00 0.00 4.00
3980 4576 7.656707 AAAATTGTGCACTTTGGCTAAATAG 57.343 32.000 19.41 0.00 34.04 1.73
3999 4595 9.893305 CTAAATAGCATATCCCGGTTTTAAAAG 57.107 33.333 0.00 0.00 0.00 2.27
4093 4691 1.189752 TCTGCTCCTGATGACCTGAC 58.810 55.000 0.00 0.00 0.00 3.51
4106 4704 2.875933 TGACCTGACGCCTTGTTTAAAG 59.124 45.455 0.00 0.00 0.00 1.85
4136 4734 4.476628 TGTGCTGTGTGATCATCATACT 57.523 40.909 14.91 0.00 38.97 2.12
4224 4822 4.027572 TCAAAACTAACTGTTGTGCTGC 57.972 40.909 2.69 0.00 42.23 5.25
4226 4824 0.307760 AACTAACTGTTGTGCTGCGC 59.692 50.000 6.19 6.19 37.52 6.09
4236 4834 2.586914 TGCTGCGCGATCATCCAG 60.587 61.111 12.10 7.65 0.00 3.86
4256 4859 5.826208 TCCAGAAACACTTTTCCTACCTTTC 59.174 40.000 0.00 0.00 42.00 2.62
4268 4871 3.632604 TCCTACCTTTCATCTAGTGAGCG 59.367 47.826 0.00 0.00 38.29 5.03
4352 4966 4.238514 AGAATGACAAGTTCGTCTGTAGC 58.761 43.478 6.89 0.00 36.82 3.58
4353 4967 3.944055 ATGACAAGTTCGTCTGTAGCT 57.056 42.857 0.00 0.00 36.82 3.32
4354 4968 5.183331 AGAATGACAAGTTCGTCTGTAGCTA 59.817 40.000 0.00 0.00 36.82 3.32
4355 4969 4.421033 TGACAAGTTCGTCTGTAGCTAG 57.579 45.455 0.00 0.00 36.82 3.42
4356 4970 3.172824 GACAAGTTCGTCTGTAGCTAGC 58.827 50.000 6.62 6.62 32.92 3.42
4357 4971 2.557056 ACAAGTTCGTCTGTAGCTAGCA 59.443 45.455 18.83 0.00 0.00 3.49
4358 4972 3.193691 ACAAGTTCGTCTGTAGCTAGCAT 59.806 43.478 18.83 4.67 0.00 3.79
4360 4974 2.755655 AGTTCGTCTGTAGCTAGCATGT 59.244 45.455 18.83 0.00 0.00 3.21
4361 4975 3.945921 AGTTCGTCTGTAGCTAGCATGTA 59.054 43.478 18.83 0.00 0.00 2.29
4362 4976 4.035792 AGTTCGTCTGTAGCTAGCATGTAG 59.964 45.833 18.83 9.51 0.00 2.74
4363 4977 3.542648 TCGTCTGTAGCTAGCATGTAGT 58.457 45.455 18.83 0.00 0.00 2.73
4364 4978 3.312697 TCGTCTGTAGCTAGCATGTAGTG 59.687 47.826 18.83 1.73 0.00 2.74
4456 5070 5.945784 TGCTGCAGTTTCATAATACTTCCTT 59.054 36.000 16.64 0.00 0.00 3.36
4497 5111 7.702772 AGAGCATTTAGATCACTAAAGTGTACG 59.297 37.037 9.81 0.00 46.97 3.67
4537 5151 2.923605 GCATCTTTGGTGACATGTGTGC 60.924 50.000 1.15 0.00 42.32 4.57
4549 5163 4.409218 GTGTGCCATGGCTGTGCG 62.409 66.667 35.53 0.00 42.51 5.34
4634 5248 1.280421 GATCTTGGCCTCCAGTTCACT 59.720 52.381 3.32 0.00 33.81 3.41
4721 5338 2.464157 GGAAAGATATCCTCCCAGCG 57.536 55.000 9.45 0.00 36.50 5.18
4824 5441 7.064134 CGTATGTGGTCTGTTTGTGTATACATT 59.936 37.037 9.18 0.00 36.53 2.71
5159 5779 2.049888 AGAAATAGCCTTCTGCCAGC 57.950 50.000 0.00 0.00 42.71 4.85
5160 5780 0.659957 GAAATAGCCTTCTGCCAGCG 59.340 55.000 0.00 0.00 42.71 5.18
5175 5795 1.476833 CCAGCGCAATAATGGTAGGGT 60.477 52.381 11.47 0.00 0.00 4.34
5177 5797 2.806244 CAGCGCAATAATGGTAGGGTAC 59.194 50.000 11.47 0.00 0.00 3.34
5193 5813 1.406887 GGTACGATGATGGCAACCTGT 60.407 52.381 0.00 0.00 0.00 4.00
5194 5814 2.159014 GGTACGATGATGGCAACCTGTA 60.159 50.000 0.00 0.00 0.00 2.74
5195 5815 2.024176 ACGATGATGGCAACCTGTAC 57.976 50.000 0.00 0.00 0.00 2.90
5196 5816 1.299541 CGATGATGGCAACCTGTACC 58.700 55.000 0.00 0.00 0.00 3.34
5197 5817 1.406751 CGATGATGGCAACCTGTACCA 60.407 52.381 0.00 0.00 37.99 3.25
5198 5818 2.746142 CGATGATGGCAACCTGTACCAT 60.746 50.000 0.00 4.84 46.82 3.55
5199 5819 2.127271 TGATGGCAACCTGTACCATG 57.873 50.000 8.93 0.00 44.20 3.66
5223 5843 2.442236 AGGGTAATCACATGCCAAGG 57.558 50.000 0.00 0.00 0.00 3.61
5286 5906 8.998558 ACTTATACGAGTAACAAAACAAAAGC 57.001 30.769 0.00 0.00 0.00 3.51
5391 6012 6.967199 GGTGTAACTTTCAAGTTTCAGTTGAG 59.033 38.462 10.15 0.00 46.52 3.02
5393 6014 4.639135 ACTTTCAAGTTTCAGTTGAGCC 57.361 40.909 0.00 0.00 38.62 4.70
5399 6020 7.994425 TTCAAGTTTCAGTTGAGCCATAATA 57.006 32.000 0.00 0.00 38.62 0.98
5409 6030 6.597672 CAGTTGAGCCATAATACTGGTTACAA 59.402 38.462 0.00 0.00 38.63 2.41
5452 6074 9.443283 GCATGTTTCTTATAGCATTTCAAGTAG 57.557 33.333 0.00 0.00 0.00 2.57
5467 6089 9.388506 CATTTCAAGTAGATATCACCTCTGTTT 57.611 33.333 5.32 0.00 0.00 2.83
5473 6095 9.965902 AAGTAGATATCACCTCTGTTTTGAATT 57.034 29.630 5.32 0.00 0.00 2.17
5528 6150 5.339008 ACTAATACGGACTGAAATGAGCA 57.661 39.130 0.00 0.00 0.00 4.26
5546 6168 7.840342 ATGAGCAAACAAACACATTAAAACA 57.160 28.000 0.00 0.00 0.00 2.83
5547 6169 7.054855 TGAGCAAACAAACACATTAAAACAC 57.945 32.000 0.00 0.00 0.00 3.32
5548 6170 6.088719 AGCAAACAAACACATTAAAACACG 57.911 33.333 0.00 0.00 0.00 4.49
5549 6171 5.635700 AGCAAACAAACACATTAAAACACGT 59.364 32.000 0.00 0.00 0.00 4.49
5550 6172 5.949219 GCAAACAAACACATTAAAACACGTC 59.051 36.000 0.00 0.00 0.00 4.34
5551 6173 6.183360 GCAAACAAACACATTAAAACACGTCT 60.183 34.615 0.00 0.00 0.00 4.18
5552 6174 7.008447 GCAAACAAACACATTAAAACACGTCTA 59.992 33.333 0.00 0.00 0.00 2.59
5612 6234 2.544844 TCGGAATGGAGGGAGTAACT 57.455 50.000 0.00 0.00 0.00 2.24
5641 6263 5.878669 AGGGTCTATTTAGTTAAGGTTTGCG 59.121 40.000 0.00 0.00 0.00 4.85
5700 6323 9.415544 AGTGAATCTAAGATGATTTTTGTTTGC 57.584 29.630 0.00 0.00 36.86 3.68
5711 6334 3.889196 TTTTGTTTGCGCTATTCTCGT 57.111 38.095 9.73 0.00 0.00 4.18
5714 6337 1.337354 TGTTTGCGCTATTCTCGTGGA 60.337 47.619 9.73 0.00 0.00 4.02
5734 6357 5.406780 GTGGACTTATGTATACTGCTCATGC 59.593 44.000 4.17 0.00 40.20 4.06
5737 6360 6.367422 GGACTTATGTATACTGCTCATGCTTC 59.633 42.308 4.17 0.00 40.48 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.303600 ACGACTACCAACTTTATGGGCA 59.696 45.455 0.00 0.00 45.18 5.36
1 2 2.981898 ACGACTACCAACTTTATGGGC 58.018 47.619 0.00 0.00 45.18 5.36
2 3 5.107133 CACTACGACTACCAACTTTATGGG 58.893 45.833 0.00 0.00 45.18 4.00
3 4 5.107133 CCACTACGACTACCAACTTTATGG 58.893 45.833 0.00 0.00 46.38 2.74
4 5 4.565564 GCCACTACGACTACCAACTTTATG 59.434 45.833 0.00 0.00 0.00 1.90
19 20 1.751351 TGGAAGATCTGAGCCACTACG 59.249 52.381 0.00 0.00 0.00 3.51
27 34 2.036862 TGCGATCCATGGAAGATCTGAG 59.963 50.000 20.67 5.27 38.39 3.35
28 35 2.041701 TGCGATCCATGGAAGATCTGA 58.958 47.619 20.67 0.00 38.39 3.27
57 64 0.519077 GCTGGAAAGAAGGCGTTCAG 59.481 55.000 20.38 10.50 34.70 3.02
58 65 1.227999 CGCTGGAAAGAAGGCGTTCA 61.228 55.000 20.38 0.00 42.23 3.18
59 66 1.497722 CGCTGGAAAGAAGGCGTTC 59.502 57.895 11.17 11.17 42.23 3.95
60 67 1.966451 CCGCTGGAAAGAAGGCGTT 60.966 57.895 0.00 0.00 45.11 4.84
107 345 1.070786 ACTGCACAACCACTACGGG 59.929 57.895 0.00 0.00 40.22 5.28
111 349 1.165907 GCTGCACTGCACAACCACTA 61.166 55.000 0.00 0.00 33.79 2.74
117 355 3.813606 ATGGGGCTGCACTGCACAA 62.814 57.895 0.21 0.00 38.27 3.33
338 590 0.606130 TGGAACGTCTGCATGCATGT 60.606 50.000 26.79 17.01 0.00 3.21
351 603 7.201444 GCGAGATAGTATTTGGATATTGGAACG 60.201 40.741 0.00 0.00 0.00 3.95
378 630 2.281139 TCGCGGCAACCACATCAA 60.281 55.556 6.13 0.00 0.00 2.57
411 675 0.249398 AAGAATTAGGCACGAGGCGT 59.751 50.000 0.00 2.66 46.16 5.68
432 697 0.472925 TGGCAGGGTGAGTGTTAGGA 60.473 55.000 0.00 0.00 0.00 2.94
445 710 3.331889 AGGGTAGGAATAATGATGGCAGG 59.668 47.826 0.00 0.00 0.00 4.85
539 805 6.844097 TTTAGGCCCAAATTAAACTTCGAT 57.156 33.333 0.00 0.00 0.00 3.59
622 889 1.082300 GCGCGATCGACGGAAGATA 60.082 57.895 21.57 0.00 42.83 1.98
623 890 2.353607 GCGCGATCGACGGAAGAT 60.354 61.111 21.57 0.00 42.83 2.40
691 962 1.821216 TTTGAGGGGAATGCTCGAAC 58.179 50.000 0.00 0.00 0.00 3.95
713 984 4.155826 TCATGGCTCGAACGAATCATTTTT 59.844 37.500 0.00 0.00 0.00 1.94
714 985 3.689161 TCATGGCTCGAACGAATCATTTT 59.311 39.130 0.00 0.00 0.00 1.82
715 986 3.270027 TCATGGCTCGAACGAATCATTT 58.730 40.909 0.00 0.00 0.00 2.32
716 987 2.905075 TCATGGCTCGAACGAATCATT 58.095 42.857 0.00 0.00 0.00 2.57
717 988 2.602257 TCATGGCTCGAACGAATCAT 57.398 45.000 0.00 2.90 0.00 2.45
718 989 2.378445 TTCATGGCTCGAACGAATCA 57.622 45.000 0.00 0.69 0.00 2.57
719 990 2.223044 GGTTTCATGGCTCGAACGAATC 60.223 50.000 0.00 0.00 0.00 2.52
720 991 1.737793 GGTTTCATGGCTCGAACGAAT 59.262 47.619 0.00 0.00 0.00 3.34
721 992 1.153353 GGTTTCATGGCTCGAACGAA 58.847 50.000 0.00 0.00 0.00 3.85
722 993 0.034198 TGGTTTCATGGCTCGAACGA 59.966 50.000 0.00 0.00 0.00 3.85
723 994 0.443869 CTGGTTTCATGGCTCGAACG 59.556 55.000 0.00 0.00 0.00 3.95
724 995 0.804989 CCTGGTTTCATGGCTCGAAC 59.195 55.000 0.00 0.00 0.00 3.95
725 996 0.690192 TCCTGGTTTCATGGCTCGAA 59.310 50.000 0.00 0.00 0.00 3.71
726 997 0.690192 TTCCTGGTTTCATGGCTCGA 59.310 50.000 0.00 0.00 0.00 4.04
727 998 1.089920 CTTCCTGGTTTCATGGCTCG 58.910 55.000 0.00 0.00 0.00 5.03
728 999 0.813821 GCTTCCTGGTTTCATGGCTC 59.186 55.000 0.00 0.00 0.00 4.70
729 1000 0.407139 AGCTTCCTGGTTTCATGGCT 59.593 50.000 0.00 0.00 0.00 4.75
730 1001 1.260544 AAGCTTCCTGGTTTCATGGC 58.739 50.000 0.00 0.00 31.57 4.40
731 1002 5.220854 CGTAATAAGCTTCCTGGTTTCATGG 60.221 44.000 0.00 0.00 37.56 3.66
732 1003 5.354234 ACGTAATAAGCTTCCTGGTTTCATG 59.646 40.000 0.00 0.00 37.56 3.07
733 1004 5.497474 ACGTAATAAGCTTCCTGGTTTCAT 58.503 37.500 0.00 0.00 37.56 2.57
734 1005 4.901868 ACGTAATAAGCTTCCTGGTTTCA 58.098 39.130 0.00 0.00 37.56 2.69
735 1006 6.074463 CGATACGTAATAAGCTTCCTGGTTTC 60.074 42.308 0.00 0.66 37.56 2.78
887 1161 3.626930 ACTGCTGTTGGTTAAGTTTGGA 58.373 40.909 0.00 0.00 0.00 3.53
1214 1496 5.122082 CACGTTAATTAGCCCCGAAGTTAAA 59.878 40.000 0.00 0.00 0.00 1.52
1240 1523 2.285977 TCATCTGCAGCATCACATCAC 58.714 47.619 9.47 0.00 0.00 3.06
1241 1524 2.702592 TCATCTGCAGCATCACATCA 57.297 45.000 9.47 0.00 0.00 3.07
1242 1525 2.484651 GGATCATCTGCAGCATCACATC 59.515 50.000 9.47 4.33 0.00 3.06
1243 1526 2.505405 GGATCATCTGCAGCATCACAT 58.495 47.619 9.47 0.00 0.00 3.21
1244 1527 1.808891 CGGATCATCTGCAGCATCACA 60.809 52.381 9.47 0.00 0.00 3.58
1458 1741 0.812014 TGAGCAAGCGAACCGAACAA 60.812 50.000 0.00 0.00 0.00 2.83
1708 1991 2.352817 GAACAGAGTCTGGTCGGGT 58.647 57.895 22.01 0.00 38.47 5.28
1713 1996 2.982488 AGGGAATTGAACAGAGTCTGGT 59.018 45.455 23.79 18.55 35.51 4.00
1714 1997 3.710209 AGGGAATTGAACAGAGTCTGG 57.290 47.619 23.79 6.57 35.51 3.86
1715 1998 3.681897 CGAAGGGAATTGAACAGAGTCTG 59.318 47.826 18.83 18.83 37.52 3.51
1716 1999 3.931578 CGAAGGGAATTGAACAGAGTCT 58.068 45.455 0.00 0.00 0.00 3.24
1730 2013 0.183971 TGGAACAAAAGCCGAAGGGA 59.816 50.000 0.00 0.00 44.01 4.20
1798 2081 3.998913 TCTGGATGGATGCAACTAACA 57.001 42.857 0.00 0.00 0.00 2.41
1829 2112 5.920193 TGCCTATTCTTTTTCAAGGGATG 57.080 39.130 0.00 0.00 0.00 3.51
1871 2159 0.687427 TCGATCACAGGAGGGCATGA 60.687 55.000 0.00 0.00 0.00 3.07
1881 2169 2.733552 CCTGTTTGTGTCTCGATCACAG 59.266 50.000 18.21 10.35 44.71 3.66
1903 2191 6.143438 GCAACAGCTCATACAATTAATCATGC 59.857 38.462 0.00 0.00 0.00 4.06
1993 2284 9.612620 GCCATAGCATTTTTAATCTACACATAC 57.387 33.333 0.00 0.00 39.53 2.39
1995 2286 7.506938 AGGCCATAGCATTTTTAATCTACACAT 59.493 33.333 5.01 0.00 42.56 3.21
1996 2287 6.833416 AGGCCATAGCATTTTTAATCTACACA 59.167 34.615 5.01 0.00 42.56 3.72
1997 2288 7.277174 AGGCCATAGCATTTTTAATCTACAC 57.723 36.000 5.01 0.00 42.56 2.90
1999 2290 9.067986 ACTTAGGCCATAGCATTTTTAATCTAC 57.932 33.333 5.01 0.00 42.56 2.59
2018 2313 2.941453 TCTCATCGACACACTTAGGC 57.059 50.000 0.00 0.00 0.00 3.93
2066 2361 9.485206 CTGCTTAACCCGTAAGTACAATATAAT 57.515 33.333 0.00 0.00 41.28 1.28
2067 2362 7.439056 GCTGCTTAACCCGTAAGTACAATATAA 59.561 37.037 0.00 0.00 41.28 0.98
2068 2363 6.925165 GCTGCTTAACCCGTAAGTACAATATA 59.075 38.462 0.00 0.00 41.28 0.86
2069 2364 5.756833 GCTGCTTAACCCGTAAGTACAATAT 59.243 40.000 0.00 0.00 41.28 1.28
2070 2365 5.111293 GCTGCTTAACCCGTAAGTACAATA 58.889 41.667 0.00 0.00 41.28 1.90
2071 2366 3.937079 GCTGCTTAACCCGTAAGTACAAT 59.063 43.478 0.00 0.00 41.28 2.71
2072 2367 3.328505 GCTGCTTAACCCGTAAGTACAA 58.671 45.455 0.00 0.00 41.28 2.41
2073 2368 2.354003 GGCTGCTTAACCCGTAAGTACA 60.354 50.000 0.00 0.00 41.28 2.90
2074 2369 2.274437 GGCTGCTTAACCCGTAAGTAC 58.726 52.381 0.00 0.00 41.28 2.73
2075 2370 1.207811 GGGCTGCTTAACCCGTAAGTA 59.792 52.381 0.00 0.00 41.28 2.24
2076 2371 0.035725 GGGCTGCTTAACCCGTAAGT 60.036 55.000 0.00 0.00 41.28 2.24
2077 2372 2.776659 GGGCTGCTTAACCCGTAAG 58.223 57.895 0.00 0.00 42.01 2.34
2096 2391 3.303881 AAAAAGAAGAATGCCGGAAGC 57.696 42.857 5.05 0.00 44.14 3.86
2118 2413 6.293955 GCTTAATCGGTATAAGTACGGGTACA 60.294 42.308 11.23 0.00 38.48 2.90
2124 2419 5.403466 GGGTTGCTTAATCGGTATAAGTACG 59.597 44.000 0.00 0.00 33.77 3.67
2130 2425 2.758009 GCGGGTTGCTTAATCGGTATA 58.242 47.619 0.00 0.00 41.73 1.47
2149 2444 3.004734 ACATAATTTAGCATGCCGGAAGC 59.995 43.478 15.66 5.14 44.14 3.86
2154 2449 4.466567 TTCGACATAATTTAGCATGCCG 57.533 40.909 15.66 6.70 30.45 5.69
2401 2701 3.364023 GTGGTTTCGTGATACGTCTTCAG 59.636 47.826 0.00 0.00 43.14 3.02
2402 2702 3.243468 TGTGGTTTCGTGATACGTCTTCA 60.243 43.478 0.00 0.00 43.14 3.02
2451 2752 0.647410 GTCGACAAGGACATGCATCG 59.353 55.000 11.55 0.00 36.91 3.84
2465 2770 5.279384 AGGAATGTAATGATACACGTCGAC 58.721 41.667 5.18 5.18 44.47 4.20
2472 2777 9.586435 CTATTATGCGAGGAATGTAATGATACA 57.414 33.333 0.00 0.00 45.67 2.29
2490 2797 4.130118 AGGCTTGTGCTACACTATTATGC 58.870 43.478 0.00 0.00 39.59 3.14
2558 2869 3.952323 TCCGGATTTTCTAGTCGACATCT 59.048 43.478 19.50 0.00 0.00 2.90
2577 2888 2.414138 GACCGTGGTGAATACTTTTCCG 59.586 50.000 0.00 0.00 0.00 4.30
2597 2909 4.393155 AGCGCGCATCTTGTGGGA 62.393 61.111 35.10 0.00 42.48 4.37
2657 2969 3.057876 ACAAGATCGTCAGTGACTCTGTC 60.058 47.826 20.64 12.35 43.97 3.51
2658 2970 2.887783 ACAAGATCGTCAGTGACTCTGT 59.112 45.455 20.64 13.93 43.97 3.41
2659 2971 3.240884 CACAAGATCGTCAGTGACTCTG 58.759 50.000 20.64 13.41 44.85 3.35
2661 2973 3.290308 ACACAAGATCGTCAGTGACTC 57.710 47.619 20.64 12.40 35.97 3.36
2663 2975 3.060272 CACAACACAAGATCGTCAGTGAC 60.060 47.826 13.56 13.56 35.97 3.67
2664 2976 3.123050 CACAACACAAGATCGTCAGTGA 58.877 45.455 13.97 0.00 35.97 3.41
2665 2977 2.866156 ACACAACACAAGATCGTCAGTG 59.134 45.455 7.87 7.87 37.95 3.66
2668 2980 3.687212 ACAAACACAACACAAGATCGTCA 59.313 39.130 0.00 0.00 0.00 4.35
2684 2996 2.806929 GCACCAGCAGCACAAACA 59.193 55.556 0.00 0.00 41.58 2.83
3036 3348 4.447342 GGGACGGGGTACTCGGGA 62.447 72.222 5.19 0.00 0.00 5.14
3070 3382 1.865788 GCACGGTGGATGTTGCATGT 61.866 55.000 10.60 0.00 0.00 3.21
3091 3403 2.664916 CAAGAAATGTTGTTGCGAGGG 58.335 47.619 0.00 0.00 0.00 4.30
3098 3410 5.964758 TGAAACAGAGCAAGAAATGTTGTT 58.035 33.333 0.00 0.00 36.09 2.83
3120 3432 1.929836 GAACATGAGACGGCTAAGCTG 59.070 52.381 0.00 0.00 41.29 4.24
3122 3434 1.929836 CAGAACATGAGACGGCTAAGC 59.070 52.381 0.00 0.00 0.00 3.09
3124 3436 3.701542 AGATCAGAACATGAGACGGCTAA 59.298 43.478 0.00 0.00 42.53 3.09
3129 3441 4.488879 TCACAAGATCAGAACATGAGACG 58.511 43.478 0.00 0.00 42.53 4.18
3150 3462 5.523438 AGTAAATCCTCCGAAGTGAGATC 57.477 43.478 0.00 0.00 34.11 2.75
3173 3674 7.365840 ACTTTAAAAATCCTCAAGTAGAGCG 57.634 36.000 0.00 0.00 43.31 5.03
3210 3711 8.251026 CACTCATCAAGTTACCAGTACTCATAA 58.749 37.037 0.00 0.00 35.45 1.90
3213 3714 5.566826 GCACTCATCAAGTTACCAGTACTCA 60.567 44.000 0.00 0.00 35.45 3.41
3215 3716 4.528596 AGCACTCATCAAGTTACCAGTACT 59.471 41.667 0.00 0.00 35.45 2.73
3218 3719 3.324846 TCAGCACTCATCAAGTTACCAGT 59.675 43.478 0.00 0.00 35.45 4.00
3221 3722 5.392380 CCAAATCAGCACTCATCAAGTTACC 60.392 44.000 0.00 0.00 35.45 2.85
3510 4019 1.304713 CCTGCCAGCAAGGGAATGT 60.305 57.895 0.00 0.00 37.23 2.71
3535 4044 4.380841 AGGTTTGTCAGCATGCATATTG 57.619 40.909 21.98 9.53 34.76 1.90
3546 4055 6.135290 TGATCAAACTGAAAGGTTTGTCAG 57.865 37.500 16.20 0.00 45.56 3.51
3801 4396 0.027194 CGCCAATCATTGAGCAGACG 59.973 55.000 0.00 0.00 0.00 4.18
3877 4472 4.019411 TGCTCCACTTGTCAATTCATAGGA 60.019 41.667 0.00 0.00 0.00 2.94
3909 4504 0.620556 TCCTGACCATGAAGCTTCCC 59.379 55.000 23.42 8.20 0.00 3.97
3910 4505 2.290577 ACTTCCTGACCATGAAGCTTCC 60.291 50.000 23.42 8.27 41.31 3.46
3911 4506 3.064900 ACTTCCTGACCATGAAGCTTC 57.935 47.619 19.89 19.89 41.31 3.86
3941 4536 8.323140 GTGCACAATTTTAATATGATCACTTGC 58.677 33.333 13.17 0.00 0.00 4.01
3980 4576 3.955551 TCCCTTTTAAAACCGGGATATGC 59.044 43.478 19.28 0.00 40.69 3.14
4093 4691 3.305110 ATTGTTCGCTTTAAACAAGGCG 58.695 40.909 11.97 11.97 46.45 5.52
4106 4704 1.122849 CACACAGCACAATTGTTCGC 58.877 50.000 8.77 10.61 0.00 4.70
4159 4757 1.019673 CCCATATGTCTGCACTGCAC 58.980 55.000 0.00 0.00 33.79 4.57
4160 4758 0.749091 GCCCATATGTCTGCACTGCA 60.749 55.000 3.11 3.11 36.92 4.41
4161 4759 1.450531 GGCCCATATGTCTGCACTGC 61.451 60.000 1.24 0.00 0.00 4.40
4162 4760 0.107066 TGGCCCATATGTCTGCACTG 60.107 55.000 0.00 0.00 0.00 3.66
4163 4761 0.848735 ATGGCCCATATGTCTGCACT 59.151 50.000 0.00 0.00 0.00 4.40
4224 4822 1.645034 AGTGTTTCTGGATGATCGCG 58.355 50.000 0.00 0.00 0.00 5.87
4226 4824 4.697352 AGGAAAAGTGTTTCTGGATGATCG 59.303 41.667 0.00 0.00 42.45 3.69
4236 4834 7.511959 AGATGAAAGGTAGGAAAAGTGTTTC 57.488 36.000 0.00 0.00 42.16 2.78
4256 4859 1.107114 AGGTCACCGCTCACTAGATG 58.893 55.000 0.00 0.00 0.00 2.90
4268 4871 1.679153 TCCGCAAAAAGAAAGGTCACC 59.321 47.619 0.00 0.00 0.00 4.02
4356 4970 0.680921 CCCTTGGGTGGCACTACATG 60.681 60.000 18.45 16.96 0.00 3.21
4357 4971 0.844661 TCCCTTGGGTGGCACTACAT 60.845 55.000 18.45 0.00 0.00 2.29
4358 4972 1.462432 TCCCTTGGGTGGCACTACA 60.462 57.895 18.45 14.04 0.00 2.74
4360 4974 2.602676 GCTCCCTTGGGTGGCACTA 61.603 63.158 18.45 4.22 0.00 2.74
4361 4975 3.971702 GCTCCCTTGGGTGGCACT 61.972 66.667 18.45 0.00 0.00 4.40
4362 4976 3.690624 TATTGCTCCCTTGGGTGGCAC 62.691 57.143 21.02 9.70 32.47 5.01
4363 4977 1.505151 TATTGCTCCCTTGGGTGGCA 61.505 55.000 18.78 18.78 0.00 4.92
4364 4978 1.037579 GTATTGCTCCCTTGGGTGGC 61.038 60.000 15.24 15.24 0.00 5.01
4365 4979 0.625849 AGTATTGCTCCCTTGGGTGG 59.374 55.000 5.51 1.81 0.00 4.61
4366 4980 2.514458 AAGTATTGCTCCCTTGGGTG 57.486 50.000 5.51 4.47 0.00 4.61
4367 4981 3.181423 TGAAAAGTATTGCTCCCTTGGGT 60.181 43.478 5.51 0.00 0.00 4.51
4368 4982 3.430453 TGAAAAGTATTGCTCCCTTGGG 58.570 45.455 0.00 0.00 0.00 4.12
4369 4983 5.665916 AATGAAAAGTATTGCTCCCTTGG 57.334 39.130 0.00 0.00 0.00 3.61
4370 4984 6.128472 GCAAAATGAAAAGTATTGCTCCCTTG 60.128 38.462 0.00 0.00 42.24 3.61
4497 5111 0.381801 CCGCATACACCAAAGATGCC 59.618 55.000 0.00 0.00 42.43 4.40
4549 5163 2.125753 CCTCGTCAGAGCACCTGC 60.126 66.667 1.69 0.00 43.05 4.85
4634 5248 1.982660 ACAGAGAGTCGTTGACAGGA 58.017 50.000 0.00 0.00 34.60 3.86
4721 5338 1.507141 CTGTTGCACCGTCCAGTTCC 61.507 60.000 0.00 0.00 0.00 3.62
4973 5591 3.244665 TGTGAGAGAATGTTCAGGCACAT 60.245 43.478 0.00 0.00 39.17 3.21
5159 5779 3.374220 TCGTACCCTACCATTATTGCG 57.626 47.619 0.00 0.00 0.00 4.85
5160 5780 4.890088 TCATCGTACCCTACCATTATTGC 58.110 43.478 0.00 0.00 0.00 3.56
5175 5795 2.159014 GGTACAGGTTGCCATCATCGTA 60.159 50.000 0.00 0.00 0.00 3.43
5177 5797 1.299541 GGTACAGGTTGCCATCATCG 58.700 55.000 0.00 0.00 0.00 3.84
5193 5813 2.781174 GTGATTACCCTTCCCCATGGTA 59.219 50.000 11.73 0.00 33.55 3.25
5194 5814 1.569072 GTGATTACCCTTCCCCATGGT 59.431 52.381 11.73 0.00 36.15 3.55
5195 5815 1.568597 TGTGATTACCCTTCCCCATGG 59.431 52.381 4.14 4.14 0.00 3.66
5196 5816 3.225104 CATGTGATTACCCTTCCCCATG 58.775 50.000 0.00 0.00 0.00 3.66
5197 5817 2.424812 GCATGTGATTACCCTTCCCCAT 60.425 50.000 0.00 0.00 0.00 4.00
5198 5818 1.064017 GCATGTGATTACCCTTCCCCA 60.064 52.381 0.00 0.00 0.00 4.96
5199 5819 1.692411 GCATGTGATTACCCTTCCCC 58.308 55.000 0.00 0.00 0.00 4.81
5223 5843 1.492764 TGTTCTCCGGTATCCCCTTC 58.507 55.000 0.00 0.00 0.00 3.46
5245 5865 8.355272 TCGTATAAGTTAATATTGCTTTCGCA 57.645 30.769 10.85 0.00 46.24 5.10
5437 6058 9.099071 AGAGGTGATATCTACTTGAAATGCTAT 57.901 33.333 3.98 0.00 0.00 2.97
5438 6059 8.363390 CAGAGGTGATATCTACTTGAAATGCTA 58.637 37.037 3.98 0.00 0.00 3.49
5439 6060 7.147585 ACAGAGGTGATATCTACTTGAAATGCT 60.148 37.037 3.98 0.00 0.00 3.79
5440 6061 6.989169 ACAGAGGTGATATCTACTTGAAATGC 59.011 38.462 3.98 0.00 0.00 3.56
5475 6097 9.985730 ACCGAAATATCCAAAACGTCTTATATA 57.014 29.630 0.00 0.00 0.00 0.86
5476 6098 8.897872 ACCGAAATATCCAAAACGTCTTATAT 57.102 30.769 0.00 0.00 0.00 0.86
5499 6121 5.779529 TTCAGTCCGTATTAGTCCATACC 57.220 43.478 0.00 0.00 0.00 2.73
5500 6122 7.431249 TCATTTCAGTCCGTATTAGTCCATAC 58.569 38.462 0.00 0.00 0.00 2.39
5599 6221 3.013648 ACCCTTATGAGTTACTCCCTCCA 59.986 47.826 10.10 0.00 0.00 3.86
5641 6263 4.627611 TTAGCTTGATCATCTGCAAAGC 57.372 40.909 8.63 8.63 0.00 3.51
5675 6298 8.368126 CGCAAACAAAAATCATCTTAGATTCAC 58.632 33.333 0.00 0.00 37.24 3.18
5700 6323 3.966154 ACATAAGTCCACGAGAATAGCG 58.034 45.455 0.00 0.00 0.00 4.26
5711 6334 5.305386 AGCATGAGCAGTATACATAAGTCCA 59.695 40.000 5.50 0.00 45.49 4.02
5714 6337 6.042552 AGGAAGCATGAGCAGTATACATAAGT 59.957 38.462 5.50 0.00 45.49 2.24


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

AutoCloner maintained by Alex Coulton.