Multiple sequence alignment - TraesCS1D01G294500

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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 TraesCS1D01G294500 chr1D 100.000 5352 0 0 977 6328 393732812 393738163 0.000000e+00 9884.0
1 TraesCS1D01G294500 chr1D 100.000 605 0 0 1 605 393731836 393732440 0.000000e+00 1118.0
2 TraesCS1D01G294500 chr1A 89.924 3285 226 64 2507 5732 492126879 492123641 0.000000e+00 4135.0
3 TraesCS1D01G294500 chr1A 92.613 731 49 3 1187 1915 492128191 492127464 0.000000e+00 1046.0
4 TraesCS1D01G294500 chr1A 94.231 416 22 1 2035 2448 492127381 492126966 8.950000e-178 634.0
5 TraesCS1D01G294500 chr1A 86.590 522 53 7 1938 2448 94122551 94122036 1.540000e-155 560.0
6 TraesCS1D01G294500 chr1A 91.813 342 23 2 1 342 492131139 492130803 7.430000e-129 472.0
7 TraesCS1D01G294500 chr1A 86.192 449 42 11 5676 6121 492123645 492123214 9.610000e-128 468.0
8 TraesCS1D01G294500 chr1A 91.667 252 18 3 357 605 492128928 492128677 4.700000e-91 346.0
9 TraesCS1D01G294500 chr1A 98.230 113 2 0 977 1089 492128686 492128574 1.390000e-46 198.0
10 TraesCS1D01G294500 chr1B 90.575 2122 127 43 2507 4598 529395224 529393146 0.000000e+00 2743.0
11 TraesCS1D01G294500 chr1B 88.586 1174 61 30 4596 5738 529393063 529391932 0.000000e+00 1358.0
12 TraesCS1D01G294500 chr1B 95.345 580 27 0 1133 1712 529396619 529396040 0.000000e+00 922.0
13 TraesCS1D01G294500 chr1B 91.806 598 36 7 5740 6326 529391803 529391208 0.000000e+00 821.0
14 TraesCS1D01G294500 chr1B 83.511 655 64 24 1805 2448 529395932 529395311 7.120000e-159 571.0
15 TraesCS1D01G294500 chr1B 86.717 527 53 8 1938 2448 646898148 646897623 2.560000e-158 569.0
16 TraesCS1D01G294500 chr1B 86.641 524 54 9 1938 2448 9369585 9370105 3.310000e-157 566.0
17 TraesCS1D01G294500 chr1B 91.026 234 20 1 14 247 529428507 529428275 1.320000e-81 315.0
18 TraesCS1D01G294500 chr1B 90.517 232 13 5 349 580 529397299 529397077 1.330000e-76 298.0
19 TraesCS1D01G294500 chr1B 98.824 85 1 0 977 1061 529397053 529396969 1.100000e-32 152.0
20 TraesCS1D01G294500 chr1B 91.176 102 8 1 2510 2610 646897535 646897434 3.080000e-28 137.0
21 TraesCS1D01G294500 chr1B 85.393 89 11 2 263 351 529426566 529426480 2.430000e-14 91.6
22 TraesCS1D01G294500 chrUn 87.452 526 50 8 1938 2448 10181536 10182060 5.460000e-165 592.0
23 TraesCS1D01G294500 chrUn 92.308 104 7 1 2508 2610 10182146 10182249 5.110000e-31 147.0
24 TraesCS1D01G294500 chr5A 87.356 522 54 5 1938 2448 461509380 461509900 7.070000e-164 588.0
25 TraesCS1D01G294500 chr5A 92.308 104 7 1 2508 2610 461509986 461510089 5.110000e-31 147.0
26 TraesCS1D01G294500 chr3B 87.356 522 54 5 1938 2448 463210085 463209565 7.070000e-164 588.0
27 TraesCS1D01G294500 chr3B 86.879 282 33 4 2831 3110 598190529 598190808 4.760000e-81 313.0
28 TraesCS1D01G294500 chr3B 81.308 214 34 3 1497 1707 598189336 598189546 1.090000e-37 169.0
29 TraesCS1D01G294500 chr3B 91.346 104 8 1 2508 2610 463209479 463209376 2.380000e-29 141.0
30 TraesCS1D01G294500 chr3B 79.528 127 23 3 121 246 755238356 755238480 3.140000e-13 87.9
31 TraesCS1D01G294500 chr2B 86.782 522 56 6 1938 2448 462938675 462939194 2.560000e-158 569.0
32 TraesCS1D01G294500 chr2B 91.549 71 5 1 2538 2607 462939301 462939371 5.220000e-16 97.1
33 TraesCS1D01G294500 chr3A 87.589 282 31 4 2831 3110 597331449 597331728 2.200000e-84 324.0
34 TraesCS1D01G294500 chr3A 80.930 215 33 6 1497 1707 597330106 597330316 5.080000e-36 163.0
35 TraesCS1D01G294500 chr3D 86.879 282 33 4 2831 3110 455053221 455053500 4.760000e-81 313.0
36 TraesCS1D01G294500 chr3D 80.841 214 35 3 1497 1707 455052017 455052227 5.080000e-36 163.0
37 TraesCS1D01G294500 chr6B 95.122 41 0 2 2444 2484 18127933 18127971 5.300000e-06 63.9
38 TraesCS1D01G294500 chr6D 85.484 62 5 3 95 153 50740212 50740272 1.900000e-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 TraesCS1D01G294500 chr1D 393731836 393738163 6327 False 5501.000000 9884 100.000000 1 6328 2 chr1D.!!$F1 6327
1 TraesCS1D01G294500 chr1A 492123214 492131139 7925 True 1042.714286 4135 92.095714 1 6121 7 chr1A.!!$R2 6120
2 TraesCS1D01G294500 chr1A 94122036 94122551 515 True 560.000000 560 86.590000 1938 2448 1 chr1A.!!$R1 510
3 TraesCS1D01G294500 chr1B 529391208 529397299 6091 True 980.714286 2743 91.309143 349 6326 7 chr1B.!!$R1 5977
4 TraesCS1D01G294500 chr1B 9369585 9370105 520 False 566.000000 566 86.641000 1938 2448 1 chr1B.!!$F1 510
5 TraesCS1D01G294500 chr1B 646897434 646898148 714 True 353.000000 569 88.946500 1938 2610 2 chr1B.!!$R3 672
6 TraesCS1D01G294500 chr1B 529426480 529428507 2027 True 203.300000 315 88.209500 14 351 2 chr1B.!!$R2 337
7 TraesCS1D01G294500 chrUn 10181536 10182249 713 False 369.500000 592 89.880000 1938 2610 2 chrUn.!!$F1 672
8 TraesCS1D01G294500 chr5A 461509380 461510089 709 False 367.500000 588 89.832000 1938 2610 2 chr5A.!!$F1 672
9 TraesCS1D01G294500 chr3B 463209376 463210085 709 True 364.500000 588 89.351000 1938 2610 2 chr3B.!!$R1 672
10 TraesCS1D01G294500 chr3B 598189336 598190808 1472 False 241.000000 313 84.093500 1497 3110 2 chr3B.!!$F2 1613
11 TraesCS1D01G294500 chr2B 462938675 462939371 696 False 333.050000 569 89.165500 1938 2607 2 chr2B.!!$F1 669
12 TraesCS1D01G294500 chr3A 597330106 597331728 1622 False 243.500000 324 84.259500 1497 3110 2 chr3A.!!$F1 1613
13 TraesCS1D01G294500 chr3D 455052017 455053500 1483 False 238.000000 313 83.860000 1497 3110 2 chr3D.!!$F1 1613

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
439 2302 0.605589 CACCACCGGAAAAGGACCTC 60.606 60.000 9.46 0.00 34.73 3.85 F
1100 2972 0.033894 GTCCTCCTCGTCCTCTTCCT 60.034 60.000 0.00 0.00 0.00 3.36 F
1103 2975 0.107606 CTCCTCGTCCTCTTCCTCGA 60.108 60.000 0.00 0.00 0.00 4.04 F
1110 2982 0.256464 TCCTCTTCCTCGACTCCTCC 59.744 60.000 0.00 0.00 0.00 4.30 F
2765 6422 0.322816 AATGCTGCCATCGGTTGTCT 60.323 50.000 0.00 0.00 0.00 3.41 F
3527 7185 1.408702 CTAGAGAGAAGTGAGGCAGCC 59.591 57.143 1.84 1.84 0.00 4.85 F
3787 7454 1.545136 CATGTGGCAGCAATGGTTACA 59.455 47.619 0.00 0.00 0.00 2.41 F
4039 7706 2.169352 GCATCTAGTGGCCTCTTTCTGA 59.831 50.000 13.50 7.22 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 3925 1.017387 GTTGACCTCCCAATCGCATC 58.983 55.000 0.00 0.0 0.00 3.91 R
2009 4503 1.486726 ACCCATAGCTACAGAAGGCAC 59.513 52.381 0.00 0.0 0.00 5.01 R
2874 6531 1.704628 ACACCACATCCAACATCCAGA 59.295 47.619 0.00 0.0 0.00 3.86 R
3209 6866 4.651778 TGCACATCCCAATAGTAATAGGC 58.348 43.478 0.00 0.0 0.00 3.93 R
4567 8252 0.178924 ATGGCAAAAACTCAGGCCCT 60.179 50.000 0.00 0.0 45.83 5.19 R
4684 8454 2.037641 CAGACATCTGACTTGGTGGTCA 59.962 50.000 2.51 0.0 46.59 4.02 R
5166 8979 2.231478 CAGGCCTCAATATACGGTCGAT 59.769 50.000 0.00 0.0 0.00 3.59 R
6066 10074 0.654683 CTGCGCAGTGCCTATTTCTC 59.345 55.000 29.24 0.0 45.60 2.87 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
71 72 4.201910 ACGGCCATTTTTCATAGAATCACG 60.202 41.667 2.24 0.00 0.00 4.35
81 82 3.889538 TCATAGAATCACGGTCGAATCCT 59.110 43.478 0.00 0.00 0.00 3.24
95 96 3.834813 TCGAATCCTAGCTGCCAATAGAT 59.165 43.478 0.00 0.00 0.00 1.98
284 285 6.432581 TGTATGAACTGAGGGAGTACATAGT 58.567 40.000 0.00 0.00 33.09 2.12
290 291 6.783517 ACTGAGGGAGTACATAGTACCTAT 57.216 41.667 0.00 0.00 40.13 2.57
309 310 7.374975 ACCTATAGTATTATGTGGTGCACTT 57.625 36.000 17.98 2.17 35.11 3.16
314 315 1.240641 TTATGTGGTGCACTTGGCCG 61.241 55.000 17.98 0.00 43.89 6.13
323 324 2.038975 ACTTGGCCGCTAGGAGGA 59.961 61.111 0.00 0.00 41.02 3.71
342 343 4.385825 AGGAACACTTGCGAGTTTCATAA 58.614 39.130 20.87 0.00 32.54 1.90
343 344 4.452455 AGGAACACTTGCGAGTTTCATAAG 59.548 41.667 20.87 7.31 32.54 1.73
344 345 4.451096 GGAACACTTGCGAGTTTCATAAGA 59.549 41.667 20.87 0.00 32.54 2.10
345 346 5.122396 GGAACACTTGCGAGTTTCATAAGAT 59.878 40.000 20.87 1.26 32.54 2.40
346 347 5.786401 ACACTTGCGAGTTTCATAAGATC 57.214 39.130 3.02 0.00 32.54 2.75
347 348 4.327357 ACACTTGCGAGTTTCATAAGATCG 59.673 41.667 3.02 0.00 32.54 3.69
354 355 5.399892 GCGAGTTTCATAAGATCGAAGTAGG 59.600 44.000 0.00 0.00 35.47 3.18
358 2220 7.848128 AGTTTCATAAGATCGAAGTAGGGAAA 58.152 34.615 0.00 0.00 0.00 3.13
362 2224 3.528597 AGATCGAAGTAGGGAAACAGC 57.471 47.619 0.00 0.00 0.00 4.40
385 2247 5.255710 TGCAGAAAATTGAAACGAAAGGA 57.744 34.783 0.00 0.00 0.00 3.36
439 2302 0.605589 CACCACCGGAAAAGGACCTC 60.606 60.000 9.46 0.00 34.73 3.85
500 2363 2.507102 CGCGACGCTCCACTTCAT 60.507 61.111 19.02 0.00 0.00 2.57
507 2370 1.002366 CGCTCCACTTCATTCCTTCG 58.998 55.000 0.00 0.00 0.00 3.79
535 2399 2.203625 CACCCACCCCACCCAAAG 60.204 66.667 0.00 0.00 0.00 2.77
540 2404 3.110031 ACCCCACCCAAAGCCAGT 61.110 61.111 0.00 0.00 0.00 4.00
1074 2946 2.042843 TTCCTCCTCCTCTCCGCC 60.043 66.667 0.00 0.00 0.00 6.13
1089 2961 3.844090 GCCCTGCTCGTCCTCCTC 61.844 72.222 0.00 0.00 0.00 3.71
1090 2962 3.522731 CCCTGCTCGTCCTCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
1091 2963 2.752238 CCTGCTCGTCCTCCTCGT 60.752 66.667 0.00 0.00 0.00 4.18
1092 2964 2.766400 CCTGCTCGTCCTCCTCGTC 61.766 68.421 0.00 0.00 0.00 4.20
1093 2965 2.750637 TGCTCGTCCTCCTCGTCC 60.751 66.667 0.00 0.00 0.00 4.79
1094 2966 2.438795 GCTCGTCCTCCTCGTCCT 60.439 66.667 0.00 0.00 0.00 3.85
1095 2967 2.474612 GCTCGTCCTCCTCGTCCTC 61.475 68.421 0.00 0.00 0.00 3.71
1096 2968 1.222387 CTCGTCCTCCTCGTCCTCT 59.778 63.158 0.00 0.00 0.00 3.69
1097 2969 0.393267 CTCGTCCTCCTCGTCCTCTT 60.393 60.000 0.00 0.00 0.00 2.85
1098 2970 0.392729 TCGTCCTCCTCGTCCTCTTC 60.393 60.000 0.00 0.00 0.00 2.87
1099 2971 1.378124 CGTCCTCCTCGTCCTCTTCC 61.378 65.000 0.00 0.00 0.00 3.46
1100 2972 0.033894 GTCCTCCTCGTCCTCTTCCT 60.034 60.000 0.00 0.00 0.00 3.36
1101 2973 0.256464 TCCTCCTCGTCCTCTTCCTC 59.744 60.000 0.00 0.00 0.00 3.71
1102 2974 1.098712 CCTCCTCGTCCTCTTCCTCG 61.099 65.000 0.00 0.00 0.00 4.63
1103 2975 0.107606 CTCCTCGTCCTCTTCCTCGA 60.108 60.000 0.00 0.00 0.00 4.04
1104 2976 0.392729 TCCTCGTCCTCTTCCTCGAC 60.393 60.000 0.00 0.00 0.00 4.20
1105 2977 0.393267 CCTCGTCCTCTTCCTCGACT 60.393 60.000 0.00 0.00 0.00 4.18
1106 2978 1.011333 CTCGTCCTCTTCCTCGACTC 58.989 60.000 0.00 0.00 0.00 3.36
1107 2979 0.392729 TCGTCCTCTTCCTCGACTCC 60.393 60.000 0.00 0.00 0.00 3.85
1108 2980 0.393267 CGTCCTCTTCCTCGACTCCT 60.393 60.000 0.00 0.00 0.00 3.69
1109 2981 1.385528 GTCCTCTTCCTCGACTCCTC 58.614 60.000 0.00 0.00 0.00 3.71
1110 2982 0.256464 TCCTCTTCCTCGACTCCTCC 59.744 60.000 0.00 0.00 0.00 4.30
1111 2983 1.098712 CCTCTTCCTCGACTCCTCCG 61.099 65.000 0.00 0.00 0.00 4.63
1112 2984 1.720694 CTCTTCCTCGACTCCTCCGC 61.721 65.000 0.00 0.00 0.00 5.54
1113 2985 2.754658 TTCCTCGACTCCTCCGCC 60.755 66.667 0.00 0.00 0.00 6.13
1114 2986 4.816984 TCCTCGACTCCTCCGCCC 62.817 72.222 0.00 0.00 0.00 6.13
1116 2988 3.522731 CTCGACTCCTCCGCCCAG 61.523 72.222 0.00 0.00 0.00 4.45
1117 2989 4.361971 TCGACTCCTCCGCCCAGT 62.362 66.667 0.00 0.00 0.00 4.00
1118 2990 3.827898 CGACTCCTCCGCCCAGTC 61.828 72.222 0.00 0.00 34.36 3.51
1119 2991 3.462678 GACTCCTCCGCCCAGTCC 61.463 72.222 0.00 0.00 31.93 3.85
1121 2993 4.787280 CTCCTCCGCCCAGTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
1122 2994 4.779733 TCCTCCGCCCAGTCCCTC 62.780 72.222 0.00 0.00 0.00 4.30
1128 3000 3.412408 GCCCAGTCCCTCCCCTTC 61.412 72.222 0.00 0.00 0.00 3.46
1129 3001 2.692741 CCCAGTCCCTCCCCTTCC 60.693 72.222 0.00 0.00 0.00 3.46
1130 3002 2.456840 CCAGTCCCTCCCCTTCCT 59.543 66.667 0.00 0.00 0.00 3.36
1131 3003 1.690985 CCAGTCCCTCCCCTTCCTC 60.691 68.421 0.00 0.00 0.00 3.71
1530 3687 1.599047 CCTCGACAACATCAGGGCT 59.401 57.895 0.00 0.00 0.00 5.19
1757 3917 0.657840 GTCTGTGTTATCCATGCCGC 59.342 55.000 0.00 0.00 0.00 6.53
1765 3925 4.739716 GTGTTATCCATGCCGCTTTTATTG 59.260 41.667 0.00 0.00 0.00 1.90
1769 3929 2.129607 CCATGCCGCTTTTATTGATGC 58.870 47.619 0.00 0.00 0.00 3.91
1777 3937 4.305989 GCTTTTATTGATGCGATTGGGA 57.694 40.909 0.00 0.00 0.00 4.37
1779 3939 4.794003 GCTTTTATTGATGCGATTGGGAGG 60.794 45.833 0.00 0.00 0.00 4.30
1832 4022 9.439500 TGGTACTAGAACATAACCAATAAACAC 57.561 33.333 0.00 0.00 37.29 3.32
1865 4056 3.956848 AGCATTCTCCTTTTATGGAAGCC 59.043 43.478 0.00 0.00 35.43 4.35
1928 4259 8.973835 GTGTAACTATCTGATAGCATTAGGAC 57.026 38.462 21.58 10.86 36.30 3.85
1930 4261 6.613153 AACTATCTGATAGCATTAGGACCC 57.387 41.667 21.58 0.00 36.30 4.46
1931 4262 5.909760 ACTATCTGATAGCATTAGGACCCT 58.090 41.667 21.58 0.00 36.30 4.34
1932 4263 6.326970 ACTATCTGATAGCATTAGGACCCTT 58.673 40.000 21.58 0.00 36.30 3.95
1933 4264 4.963318 TCTGATAGCATTAGGACCCTTG 57.037 45.455 0.00 0.00 0.00 3.61
1934 4265 4.556697 TCTGATAGCATTAGGACCCTTGA 58.443 43.478 0.00 0.00 0.00 3.02
1935 4266 4.968719 TCTGATAGCATTAGGACCCTTGAA 59.031 41.667 0.00 0.00 0.00 2.69
1936 4267 5.608437 TCTGATAGCATTAGGACCCTTGAAT 59.392 40.000 0.00 0.00 0.00 2.57
1948 4295 4.203226 GACCCTTGAATCTTGATCCTTCC 58.797 47.826 0.00 0.00 0.00 3.46
1958 4305 4.464008 TCTTGATCCTTCCACCATTATGC 58.536 43.478 0.00 0.00 0.00 3.14
1961 4308 3.202818 TGATCCTTCCACCATTATGCAGT 59.797 43.478 0.00 0.00 0.00 4.40
1984 4331 3.272574 TCAAGGCAGATGGTGAATCTC 57.727 47.619 0.00 0.00 44.24 2.75
2002 4496 7.009357 GTGAATCTCGTACAGTTTACCTTGATC 59.991 40.741 0.00 0.00 0.00 2.92
2009 4503 7.330946 TCGTACAGTTTACCTTGATCAAATCAG 59.669 37.037 9.88 0.00 40.94 2.90
2024 4518 4.222810 TCAAATCAGTGCCTTCTGTAGCTA 59.777 41.667 0.00 0.00 36.85 3.32
2025 4519 5.104776 TCAAATCAGTGCCTTCTGTAGCTAT 60.105 40.000 0.00 0.00 36.85 2.97
2257 5575 9.853555 GATATTACTCTGTCACCTTGATCTATG 57.146 37.037 0.00 0.00 0.00 2.23
2345 5918 5.164620 TGAATGGAGATGCTTCTTGTGTA 57.835 39.130 3.29 0.00 30.30 2.90
2356 5929 4.157656 TGCTTCTTGTGTATATGTTTGCCC 59.842 41.667 0.00 0.00 0.00 5.36
2381 5954 4.214545 TGTTCAGTATTGCCTTTGGTAACG 59.785 41.667 0.00 0.00 42.51 3.18
2430 6004 3.790744 TGCAATCGCATCCAACAAC 57.209 47.368 0.00 0.00 45.36 3.32
2441 6015 3.987220 GCATCCAACAACAATAACACCAC 59.013 43.478 0.00 0.00 0.00 4.16
2449 6023 6.254281 ACAACAATAACACCACTAGCAATC 57.746 37.500 0.00 0.00 0.00 2.67
2450 6024 6.003950 ACAACAATAACACCACTAGCAATCT 58.996 36.000 0.00 0.00 0.00 2.40
2451 6025 6.490040 ACAACAATAACACCACTAGCAATCTT 59.510 34.615 0.00 0.00 0.00 2.40
2452 6026 6.500684 ACAATAACACCACTAGCAATCTTG 57.499 37.500 0.00 0.00 0.00 3.02
2490 6064 7.971183 AAAACAAACAAACAATAACACCACT 57.029 28.000 0.00 0.00 0.00 4.00
2492 6066 8.696410 AAACAAACAAACAATAACACCACTAG 57.304 30.769 0.00 0.00 0.00 2.57
2494 6068 6.127591 ACAAACAAACAATAACACCACTAGCA 60.128 34.615 0.00 0.00 0.00 3.49
2495 6069 6.458232 AACAAACAATAACACCACTAGCAA 57.542 33.333 0.00 0.00 0.00 3.91
2612 6265 9.806203 GTTGTTTTACCCTGTTTTAACAAGTAT 57.194 29.630 0.00 0.00 38.66 2.12
2633 6286 9.547753 AAGTATAACAGGTAATTATGTGCTCTG 57.452 33.333 0.00 0.00 0.00 3.35
2652 6305 8.417884 GTGCTCTGAGAGGTAGAGTAAAATATT 58.582 37.037 12.01 0.00 42.83 1.28
2703 6357 8.786826 ACTACTGTGCTTGTATTGCTTAAATA 57.213 30.769 0.00 0.00 0.00 1.40
2736 6393 9.400208 TCCTATTGGGGTATAGTCATTTAATGA 57.600 33.333 3.20 3.20 34.48 2.57
2757 6414 1.477553 TTCCCAAGAATGCTGCCATC 58.522 50.000 0.00 0.00 0.00 3.51
2761 6418 0.813184 CAAGAATGCTGCCATCGGTT 59.187 50.000 0.00 0.00 0.00 4.44
2762 6419 0.813184 AAGAATGCTGCCATCGGTTG 59.187 50.000 0.00 0.00 0.00 3.77
2765 6422 0.322816 AATGCTGCCATCGGTTGTCT 60.323 50.000 0.00 0.00 0.00 3.41
2772 6429 1.608025 GCCATCGGTTGTCTTCACAGA 60.608 52.381 0.00 0.00 32.71 3.41
2778 6435 3.071023 TCGGTTGTCTTCACAGATCCTTT 59.929 43.478 0.00 0.00 32.71 3.11
2780 6437 4.083802 CGGTTGTCTTCACAGATCCTTTTC 60.084 45.833 0.00 0.00 32.71 2.29
2785 6442 7.264373 TGTCTTCACAGATCCTTTTCTTTTC 57.736 36.000 0.00 0.00 0.00 2.29
2874 6531 3.556423 GGGGAACACATACGAGAACTGTT 60.556 47.826 0.00 0.00 0.00 3.16
3126 6783 5.538053 TGGCAAGTGTTTTATTTCTCCATGA 59.462 36.000 0.00 0.00 0.00 3.07
3142 6799 6.480763 TCTCCATGACATTTTTAAGCTACCA 58.519 36.000 0.00 0.00 0.00 3.25
3210 6867 8.532977 TCTCCTGCTAATTTGTTTTTAAATGC 57.467 30.769 0.00 0.00 31.05 3.56
3297 6954 3.222603 AGGATTTTTCGTTTGGTCTGCT 58.777 40.909 0.00 0.00 0.00 4.24
3370 7027 9.623687 GTTCGTGACCGTATTGTATAAAATTAC 57.376 33.333 0.00 0.00 35.01 1.89
3396 7053 3.921104 TCAGCCTCAGTTCTCATCCTAT 58.079 45.455 0.00 0.00 0.00 2.57
3454 7112 8.546083 AGGAAGTGAACTGATAGTCATATCTT 57.454 34.615 0.00 0.00 38.92 2.40
3512 7170 4.318332 TGATGCAAAGTTGGACACTAGAG 58.682 43.478 0.00 0.00 32.94 2.43
3520 7178 4.730966 AGTTGGACACTAGAGAGAAGTGA 58.269 43.478 10.02 0.00 45.89 3.41
3523 7181 2.425668 GGACACTAGAGAGAAGTGAGGC 59.574 54.545 10.02 0.05 45.89 4.70
3527 7185 1.408702 CTAGAGAGAAGTGAGGCAGCC 59.591 57.143 1.84 1.84 0.00 4.85
3535 7193 2.887151 AGTGAGGCAGCCACTTTTAT 57.113 45.000 15.80 0.00 41.68 1.40
3539 7197 3.084039 TGAGGCAGCCACTTTTATCTTG 58.916 45.455 15.80 0.00 0.00 3.02
3591 7257 4.631131 TCCTCCTATATGAAACATGCGTG 58.369 43.478 3.82 3.82 0.00 5.34
3615 7281 4.941873 GGAGGTAGAACAAGTAAATGGTGG 59.058 45.833 0.00 0.00 0.00 4.61
3680 7346 6.034044 CGAGTTTCTAAAGATGTCTACAGCAC 59.966 42.308 0.75 0.00 34.14 4.40
3681 7347 6.759272 AGTTTCTAAAGATGTCTACAGCACA 58.241 36.000 0.75 0.00 34.14 4.57
3684 7350 3.407424 AAAGATGTCTACAGCACAGCA 57.593 42.857 0.75 0.00 32.37 4.41
3685 7351 2.669300 AGATGTCTACAGCACAGCAG 57.331 50.000 0.75 0.00 32.37 4.24
3686 7352 1.898472 AGATGTCTACAGCACAGCAGT 59.102 47.619 0.75 0.00 32.37 4.40
3687 7353 3.092301 AGATGTCTACAGCACAGCAGTA 58.908 45.455 0.75 0.00 32.37 2.74
3688 7354 3.703556 AGATGTCTACAGCACAGCAGTAT 59.296 43.478 0.75 0.00 32.37 2.12
3692 7358 3.129462 GTCTACAGCACAGCAGTATCTCA 59.871 47.826 0.00 0.00 30.71 3.27
3699 7365 6.927936 ACAGCACAGCAGTATCTCATTAATAG 59.072 38.462 0.00 0.00 0.00 1.73
3734 7400 9.724839 GTTTGCAAGTAACTAGTGTCATTTTTA 57.275 29.630 0.00 0.00 0.00 1.52
3787 7454 1.545136 CATGTGGCAGCAATGGTTACA 59.455 47.619 0.00 0.00 0.00 2.41
3922 7589 2.312323 TGAACCCCACCTGTGTTCA 58.688 52.632 0.00 0.00 44.32 3.18
3976 7643 7.593825 ACGTTATAGCTTGCTTCATTTTTCTT 58.406 30.769 0.00 0.00 0.00 2.52
3980 7647 9.762933 TTATAGCTTGCTTCATTTTTCTTGTTT 57.237 25.926 0.00 0.00 0.00 2.83
4000 7667 6.284459 TGTTTTTGTTTCACCAAAGTTCAGT 58.716 32.000 0.00 0.00 35.85 3.41
4001 7668 6.763610 TGTTTTTGTTTCACCAAAGTTCAGTT 59.236 30.769 0.00 0.00 35.85 3.16
4010 7677 4.335315 CACCAAAGTTCAGTTTGCTAGTGA 59.665 41.667 8.29 0.00 36.29 3.41
4015 7682 7.420800 CAAAGTTCAGTTTGCTAGTGATCTTT 58.579 34.615 17.93 17.93 46.93 2.52
4034 7701 4.471386 TCTTTTAGCATCTAGTGGCCTCTT 59.529 41.667 13.50 0.00 0.00 2.85
4036 7703 2.998316 AGCATCTAGTGGCCTCTTTC 57.002 50.000 13.50 0.00 0.00 2.62
4039 7706 2.169352 GCATCTAGTGGCCTCTTTCTGA 59.831 50.000 13.50 7.22 0.00 3.27
4049 7716 7.406104 AGTGGCCTCTTTCTGATTATAACTTT 58.594 34.615 3.32 0.00 0.00 2.66
4053 7721 7.122799 GGCCTCTTTCTGATTATAACTTTTGGT 59.877 37.037 0.00 0.00 0.00 3.67
4108 7778 5.770162 ACCATTTGCAGCCTATCCTTATTAC 59.230 40.000 0.00 0.00 0.00 1.89
4113 7783 5.798132 TGCAGCCTATCCTTATTACAGATG 58.202 41.667 0.00 0.00 0.00 2.90
4161 7845 8.924303 TGTAACCAATACTGCTTCATCTATACT 58.076 33.333 0.00 0.00 35.42 2.12
4165 7849 8.368668 ACCAATACTGCTTCATCTATACTAACC 58.631 37.037 0.00 0.00 0.00 2.85
4458 8142 5.534654 TGGAGGGTAAGAGAACACAAATTTG 59.465 40.000 16.67 16.67 0.00 2.32
4504 8189 7.894753 TCATTTTCTTATGCCACCAATATCA 57.105 32.000 0.00 0.00 0.00 2.15
4510 8195 6.240894 TCTTATGCCACCAATATCAATCCTC 58.759 40.000 0.00 0.00 0.00 3.71
4567 8252 6.377712 TGGTGATGTTGCTTCATTGATGATTA 59.622 34.615 3.86 0.00 36.56 1.75
4581 8266 4.934356 TGATGATTAGGGCCTGAGTTTTT 58.066 39.130 18.53 0.00 0.00 1.94
4715 8485 7.173907 ACCAAGTCAGATGTCTGTTTTCTTATG 59.826 37.037 9.65 7.81 44.12 1.90
4754 8524 6.872547 CCAGAAACTTCCTTTAGTGGTACTAC 59.127 42.308 0.19 0.19 28.93 2.73
4759 8529 7.793948 ACTTCCTTTAGTGGTACTACAGATT 57.206 36.000 12.29 0.00 31.80 2.40
4789 8559 6.796426 TCTGTAGTTAGATGTAGATGTGCAC 58.204 40.000 10.75 10.75 0.00 4.57
4848 8650 9.084533 TGATATTAACCAGGCTTAGTTTTGTTT 57.915 29.630 5.10 0.00 0.00 2.83
4975 8788 5.661503 TTGGGGTATATCATGATTGGTGT 57.338 39.130 14.65 0.00 0.00 4.16
4978 8791 5.221904 TGGGGTATATCATGATTGGTGTGAG 60.222 44.000 14.65 0.00 0.00 3.51
5058 8871 7.830201 TGGAAGTCTTACAAAGAGGTAAACAAA 59.170 33.333 0.00 0.00 38.41 2.83
5079 8892 4.142609 ACAGTCACGCCTCATGAATTAT 57.857 40.909 0.00 0.00 0.00 1.28
5080 8893 5.276461 ACAGTCACGCCTCATGAATTATA 57.724 39.130 0.00 0.00 0.00 0.98
5166 8979 1.346395 TCCTTGAAGTAGCAGCCGAAA 59.654 47.619 0.00 0.00 0.00 3.46
5174 8987 1.940883 TAGCAGCCGAAATCGACCGT 61.941 55.000 4.04 0.00 43.02 4.83
5365 9178 4.625607 ACTTCTAAGGGAGTCAACCAAG 57.374 45.455 0.00 0.00 0.00 3.61
5400 9213 9.730705 ATTCTGTTGATTCTTTGAGTTCTGATA 57.269 29.630 0.00 0.00 0.00 2.15
5401 9214 9.730705 TTCTGTTGATTCTTTGAGTTCTGATAT 57.269 29.630 0.00 0.00 0.00 1.63
5438 9252 5.824904 ATACAACAGAGATGTGATTTGGC 57.175 39.130 0.00 0.00 32.27 4.52
5451 9267 1.502527 ATTTGGCCGGGTCCAGGTAA 61.503 55.000 10.03 3.14 37.44 2.85
5480 9298 9.226606 CTGAAGTTTTTGGTGGTATAGATACAA 57.773 33.333 2.28 0.00 34.98 2.41
5481 9299 9.005777 TGAAGTTTTTGGTGGTATAGATACAAC 57.994 33.333 2.28 0.74 36.64 3.32
5482 9300 7.605410 AGTTTTTGGTGGTATAGATACAACG 57.395 36.000 2.28 0.00 37.94 4.10
5539 9357 4.775664 GCCAAAGCAAAGCAAAACAATAG 58.224 39.130 0.00 0.00 39.53 1.73
5664 9482 8.075593 TGAACAATAAAGATTTTGAAGCTTGC 57.924 30.769 2.10 0.00 37.18 4.01
5670 9488 4.924305 AGATTTTGAAGCTTGCTCAACA 57.076 36.364 2.10 0.00 32.61 3.33
5748 9745 4.314961 TGTATGCCAGGTTTATATCTGCG 58.685 43.478 0.00 0.00 0.00 5.18
5783 9781 1.538419 GCGGGCTACCAGAATGTAGAC 60.538 57.143 2.54 0.00 44.65 2.59
5814 9812 3.188460 ACGGTGCACAGATGTACATTTTC 59.812 43.478 24.13 0.00 42.79 2.29
5815 9813 3.188254 CGGTGCACAGATGTACATTTTCA 59.812 43.478 20.43 1.93 42.79 2.69
5873 9873 3.501349 TCTGATGAGGCAGATACCTACC 58.499 50.000 0.00 0.00 41.32 3.18
5920 9920 5.178252 CGAACTTGTCAAGGATAGCCATATG 59.822 44.000 16.85 0.00 36.29 1.78
5944 9944 5.504665 GCATTCTCCGTTCAAGATTGTATGG 60.505 44.000 4.53 4.53 36.35 2.74
5946 9946 5.614324 TCTCCGTTCAAGATTGTATGGAT 57.386 39.130 11.99 0.00 41.07 3.41
6008 10008 3.325135 AGAACTTCGGCCTCCCAATATAG 59.675 47.826 0.00 0.00 0.00 1.31
6017 10017 4.141482 GGCCTCCCAATATAGTGTTCTTCA 60.141 45.833 0.00 0.00 0.00 3.02
6035 10043 2.880443 TCATTGGAAGCTTTTGAGGCT 58.120 42.857 0.00 0.00 42.31 4.58
6066 10074 3.521531 AGCTTCCTCCTTTTTAGAGAGGG 59.478 47.826 5.50 0.00 46.07 4.30
6141 10149 9.685828 CAGTTACTGGACTAGCTAGAATAATTC 57.314 37.037 27.45 12.47 0.00 2.17
6165 10173 1.591248 CGCTTGGATTGTCGTTTTCG 58.409 50.000 0.00 0.00 45.64 3.46
6198 10206 6.073765 CGAAAATAAAGCATACGCCTGTAGAT 60.074 38.462 0.00 0.00 39.83 1.98
6212 10220 5.452776 CGCCTGTAGATTAAATCTGGGTGTA 60.453 44.000 0.00 0.00 40.51 2.90
6249 10257 0.106519 AATCCAATCGGGGCCTCAAG 60.107 55.000 1.96 0.00 37.22 3.02
6326 10334 3.775654 GCAGCTGTACGAGGCCCT 61.776 66.667 16.64 0.00 0.00 5.19
6327 10335 2.185350 CAGCTGTACGAGGCCCTG 59.815 66.667 5.25 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.619316 TCAAATTTAAACGATGTACCAAATGAG 57.381 29.630 0.00 0.00 0.00 2.90
7 8 9.974980 ACTTCAAATTTAAACGATGTACCAAAT 57.025 25.926 0.00 0.00 0.00 2.32
18 19 6.196724 TGGCGTTTGTACTTCAAATTTAAACG 59.803 34.615 20.46 20.46 45.88 3.60
71 72 0.178068 TTGGCAGCTAGGATTCGACC 59.822 55.000 0.00 0.00 0.00 4.79
95 96 9.075678 GAGCAGTGGGAGTAAATAATAGTAGTA 57.924 37.037 0.00 0.00 0.00 1.82
247 248 7.116948 CCTCAGTTCATACAAAAGTACAGTGAG 59.883 40.741 0.00 0.00 0.00 3.51
248 249 6.929049 CCTCAGTTCATACAAAAGTACAGTGA 59.071 38.462 0.00 0.00 0.00 3.41
261 262 6.963083 ACTATGTACTCCCTCAGTTCATAC 57.037 41.667 0.00 0.00 40.39 2.39
284 285 8.364894 CAAGTGCACCACATAATACTATAGGTA 58.635 37.037 14.63 0.00 36.74 3.08
290 291 4.196193 GCCAAGTGCACCACATAATACTA 58.804 43.478 14.63 0.00 40.77 1.82
309 310 2.284331 TGTTCCTCCTAGCGGCCA 60.284 61.111 2.24 0.00 0.00 5.36
314 315 0.246635 TCGCAAGTGTTCCTCCTAGC 59.753 55.000 0.00 0.00 39.48 3.42
316 317 1.629043 ACTCGCAAGTGTTCCTCCTA 58.371 50.000 0.00 0.00 42.12 2.94
342 343 3.100671 AGCTGTTTCCCTACTTCGATCT 58.899 45.455 0.00 0.00 0.00 2.75
343 344 3.190874 CAGCTGTTTCCCTACTTCGATC 58.809 50.000 5.25 0.00 0.00 3.69
344 345 2.678190 GCAGCTGTTTCCCTACTTCGAT 60.678 50.000 16.64 0.00 0.00 3.59
345 346 1.337823 GCAGCTGTTTCCCTACTTCGA 60.338 52.381 16.64 0.00 0.00 3.71
346 347 1.079503 GCAGCTGTTTCCCTACTTCG 58.920 55.000 16.64 0.00 0.00 3.79
347 348 2.079925 CTGCAGCTGTTTCCCTACTTC 58.920 52.381 16.64 0.00 0.00 3.01
354 355 3.981211 TCAATTTTCTGCAGCTGTTTCC 58.019 40.909 16.64 0.00 0.00 3.13
358 2220 3.066621 TCGTTTCAATTTTCTGCAGCTGT 59.933 39.130 16.64 0.00 0.00 4.40
362 2224 5.280945 TCCTTTCGTTTCAATTTTCTGCAG 58.719 37.500 7.63 7.63 0.00 4.41
391 2253 8.327941 TCGAGATTTGAGATCTGTTTGATTTT 57.672 30.769 0.00 0.00 35.14 1.82
433 2296 4.097361 GGCGGAAGGTGGAGGTCC 62.097 72.222 0.00 0.00 0.00 4.46
500 2363 3.961414 GGTGGGTGGGCGAAGGAA 61.961 66.667 0.00 0.00 0.00 3.36
532 2396 2.750350 CGAGGTGGGACTGGCTTT 59.250 61.111 0.00 0.00 0.00 3.51
1074 2946 2.752238 ACGAGGAGGACGAGCAGG 60.752 66.667 0.00 0.00 34.70 4.85
1089 2961 0.393267 AGGAGTCGAGGAAGAGGACG 60.393 60.000 0.00 0.00 35.87 4.79
1090 2962 1.385528 GAGGAGTCGAGGAAGAGGAC 58.614 60.000 0.00 0.00 0.00 3.85
1091 2963 0.256464 GGAGGAGTCGAGGAAGAGGA 59.744 60.000 0.00 0.00 0.00 3.71
1092 2964 1.098712 CGGAGGAGTCGAGGAAGAGG 61.099 65.000 0.00 0.00 0.00 3.69
1093 2965 1.720694 GCGGAGGAGTCGAGGAAGAG 61.721 65.000 0.00 0.00 0.00 2.85
1094 2966 1.749638 GCGGAGGAGTCGAGGAAGA 60.750 63.158 0.00 0.00 0.00 2.87
1095 2967 2.776913 GGCGGAGGAGTCGAGGAAG 61.777 68.421 0.00 0.00 0.00 3.46
1096 2968 2.754658 GGCGGAGGAGTCGAGGAA 60.755 66.667 0.00 0.00 0.00 3.36
1097 2969 4.816984 GGGCGGAGGAGTCGAGGA 62.817 72.222 0.00 0.00 0.00 3.71
1099 2971 3.522731 CTGGGCGGAGGAGTCGAG 61.523 72.222 0.00 0.00 0.00 4.04
1100 2972 4.361971 ACTGGGCGGAGGAGTCGA 62.362 66.667 0.00 0.00 0.00 4.20
1101 2973 3.827898 GACTGGGCGGAGGAGTCG 61.828 72.222 0.00 0.00 0.00 4.18
1102 2974 3.462678 GGACTGGGCGGAGGAGTC 61.463 72.222 0.00 0.00 36.22 3.36
1104 2976 4.787280 AGGGACTGGGCGGAGGAG 62.787 72.222 0.00 0.00 37.18 3.69
1105 2977 4.779733 GAGGGACTGGGCGGAGGA 62.780 72.222 0.00 0.00 41.55 3.71
1111 2983 3.412408 GAAGGGGAGGGACTGGGC 61.412 72.222 0.00 0.00 41.55 5.36
1112 2984 2.692741 GGAAGGGGAGGGACTGGG 60.693 72.222 0.00 0.00 41.55 4.45
1113 2985 1.690985 GAGGAAGGGGAGGGACTGG 60.691 68.421 0.00 0.00 41.55 4.00
1114 2986 1.690985 GGAGGAAGGGGAGGGACTG 60.691 68.421 0.00 0.00 41.55 3.51
1116 2988 2.367107 GGGAGGAAGGGGAGGGAC 60.367 72.222 0.00 0.00 0.00 4.46
1117 2989 3.707189 GGGGAGGAAGGGGAGGGA 61.707 72.222 0.00 0.00 0.00 4.20
1118 2990 3.711782 AGGGGAGGAAGGGGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
1119 2991 2.040359 GAGGGGAGGAAGGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
1120 2992 2.040359 GGAGGGGAGGAAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
1121 2993 3.707189 GGGAGGGGAGGAAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
1222 3379 2.943653 GTTTGGTTGCGAGTCGGG 59.056 61.111 15.52 0.00 0.00 5.14
1396 3553 4.592192 CACTCCCGCCGCATCGAT 62.592 66.667 0.00 0.00 0.00 3.59
1757 3917 4.339247 ACCTCCCAATCGCATCAATAAAAG 59.661 41.667 0.00 0.00 0.00 2.27
1765 3925 1.017387 GTTGACCTCCCAATCGCATC 58.983 55.000 0.00 0.00 0.00 3.91
1769 3929 1.026718 GGCAGTTGACCTCCCAATCG 61.027 60.000 0.00 0.00 0.00 3.34
1777 3937 6.662755 TGAATAAGATATTGGCAGTTGACCT 58.337 36.000 0.00 0.00 0.00 3.85
1779 3939 9.807649 AAATTGAATAAGATATTGGCAGTTGAC 57.192 29.630 0.00 0.00 0.00 3.18
1865 4056 6.183360 CCAAATTAGACATCCTAAGCACAGTG 60.183 42.308 0.00 0.00 40.40 3.66
1928 4259 3.950395 GTGGAAGGATCAAGATTCAAGGG 59.050 47.826 0.00 0.00 0.00 3.95
1930 4261 4.592942 TGGTGGAAGGATCAAGATTCAAG 58.407 43.478 0.00 0.00 0.00 3.02
1931 4262 4.656100 TGGTGGAAGGATCAAGATTCAA 57.344 40.909 0.00 0.00 0.00 2.69
1932 4263 4.868172 ATGGTGGAAGGATCAAGATTCA 57.132 40.909 0.00 0.00 0.00 2.57
1933 4264 6.294397 GCATAATGGTGGAAGGATCAAGATTC 60.294 42.308 0.00 0.00 0.00 2.52
1934 4265 5.537674 GCATAATGGTGGAAGGATCAAGATT 59.462 40.000 0.00 0.00 0.00 2.40
1935 4266 5.075493 GCATAATGGTGGAAGGATCAAGAT 58.925 41.667 0.00 0.00 0.00 2.40
1936 4267 4.079844 TGCATAATGGTGGAAGGATCAAGA 60.080 41.667 0.00 0.00 0.00 3.02
1948 4295 3.928375 GCCTTGAAAACTGCATAATGGTG 59.072 43.478 0.00 0.00 0.00 4.17
1958 4305 2.886523 TCACCATCTGCCTTGAAAACTG 59.113 45.455 0.00 0.00 0.00 3.16
1961 4308 4.410099 AGATTCACCATCTGCCTTGAAAA 58.590 39.130 0.00 0.00 41.13 2.29
1984 4331 7.117812 ACTGATTTGATCAAGGTAAACTGTACG 59.882 37.037 8.41 0.00 39.11 3.67
2002 4496 3.341823 AGCTACAGAAGGCACTGATTTG 58.658 45.455 16.25 6.32 40.86 2.32
2009 4503 1.486726 ACCCATAGCTACAGAAGGCAC 59.513 52.381 0.00 0.00 0.00 5.01
2024 4518 4.949856 CAGTGGTCTGCTAATTAAACCCAT 59.050 41.667 0.00 0.00 34.79 4.00
2025 4519 4.042311 TCAGTGGTCTGCTAATTAAACCCA 59.958 41.667 0.00 0.00 41.10 4.51
2122 4957 4.993705 TGTAACCCAGTTCTGATCCTTT 57.006 40.909 1.00 0.00 0.00 3.11
2345 5918 6.683610 GCAATACTGAACATGGGCAAACATAT 60.684 38.462 0.00 0.00 0.00 1.78
2356 5929 4.789012 ACCAAAGGCAATACTGAACATG 57.211 40.909 0.00 0.00 0.00 3.21
2465 6039 8.384607 AGTGGTGTTATTGTTTGTTTGTTTTT 57.615 26.923 0.00 0.00 0.00 1.94
2467 6041 7.276878 GCTAGTGGTGTTATTGTTTGTTTGTTT 59.723 33.333 0.00 0.00 0.00 2.83
2468 6042 6.754675 GCTAGTGGTGTTATTGTTTGTTTGTT 59.245 34.615 0.00 0.00 0.00 2.83
2469 6043 6.127591 TGCTAGTGGTGTTATTGTTTGTTTGT 60.128 34.615 0.00 0.00 0.00 2.83
2470 6044 6.269315 TGCTAGTGGTGTTATTGTTTGTTTG 58.731 36.000 0.00 0.00 0.00 2.93
2471 6045 6.458232 TGCTAGTGGTGTTATTGTTTGTTT 57.542 33.333 0.00 0.00 0.00 2.83
2474 6048 7.945033 ATTTTGCTAGTGGTGTTATTGTTTG 57.055 32.000 0.00 0.00 0.00 2.93
2475 6049 9.471084 GTTATTTTGCTAGTGGTGTTATTGTTT 57.529 29.630 0.00 0.00 0.00 2.83
2476 6050 8.634444 TGTTATTTTGCTAGTGGTGTTATTGTT 58.366 29.630 0.00 0.00 0.00 2.83
2477 6051 8.079809 GTGTTATTTTGCTAGTGGTGTTATTGT 58.920 33.333 0.00 0.00 0.00 2.71
2478 6052 8.296713 AGTGTTATTTTGCTAGTGGTGTTATTG 58.703 33.333 0.00 0.00 0.00 1.90
2480 6054 7.996098 AGTGTTATTTTGCTAGTGGTGTTAT 57.004 32.000 0.00 0.00 0.00 1.89
2482 6056 7.996098 ATAGTGTTATTTTGCTAGTGGTGTT 57.004 32.000 0.00 0.00 0.00 3.32
2483 6057 7.996098 AATAGTGTTATTTTGCTAGTGGTGT 57.004 32.000 0.00 0.00 0.00 4.16
2484 6058 9.691362 AAAAATAGTGTTATTTTGCTAGTGGTG 57.309 29.630 6.15 0.00 44.64 4.17
2612 6265 7.417911 CCTCTCAGAGCACATAATTACCTGTTA 60.418 40.741 0.00 0.00 0.00 2.41
2652 6305 7.197017 ACGTGCAAATCAAACAATAACAGTAA 58.803 30.769 0.00 0.00 0.00 2.24
2718 6372 8.934023 TGGGAAATCATTAAATGACTATACCC 57.066 34.615 0.00 0.00 43.01 3.69
2727 6382 7.254658 GCAGCATTCTTGGGAAATCATTAAATG 60.255 37.037 0.00 0.00 34.90 2.32
2736 6393 1.941377 TGGCAGCATTCTTGGGAAAT 58.059 45.000 0.00 0.00 34.90 2.17
2757 6414 2.751166 AGGATCTGTGAAGACAACCG 57.249 50.000 0.00 0.00 0.00 4.44
2761 6418 7.056635 AGAAAAGAAAAGGATCTGTGAAGACA 58.943 34.615 0.00 0.00 0.00 3.41
2762 6419 7.503521 AGAAAAGAAAAGGATCTGTGAAGAC 57.496 36.000 0.00 0.00 0.00 3.01
2765 6422 8.971073 AGAAAAGAAAAGAAAAGGATCTGTGAA 58.029 29.630 0.00 0.00 0.00 3.18
2772 6429 7.782168 ACCTCAGAGAAAAGAAAAGAAAAGGAT 59.218 33.333 0.00 0.00 0.00 3.24
2778 6435 9.442047 GATATGACCTCAGAGAAAAGAAAAGAA 57.558 33.333 0.00 0.00 0.00 2.52
2780 6437 8.783833 TGATATGACCTCAGAGAAAAGAAAAG 57.216 34.615 0.00 0.00 0.00 2.27
2785 6442 8.905660 AATCATGATATGACCTCAGAGAAAAG 57.094 34.615 9.04 0.00 43.01 2.27
2874 6531 1.704628 ACACCACATCCAACATCCAGA 59.295 47.619 0.00 0.00 0.00 3.86
3209 6866 4.651778 TGCACATCCCAATAGTAATAGGC 58.348 43.478 0.00 0.00 0.00 3.93
3210 6867 5.221925 ACCTGCACATCCCAATAGTAATAGG 60.222 44.000 0.00 0.00 0.00 2.57
3297 6954 6.822667 TGTTCTTTACGATAGACAGGTGTA 57.177 37.500 0.00 0.00 41.38 2.90
3358 7015 8.800370 TGAGGCTGAACATGTAATTTTATACA 57.200 30.769 0.00 0.00 39.91 2.29
3359 7016 8.893727 ACTGAGGCTGAACATGTAATTTTATAC 58.106 33.333 0.00 0.00 0.00 1.47
3370 7027 3.049708 TGAGAACTGAGGCTGAACATG 57.950 47.619 0.00 0.00 0.00 3.21
3396 7053 8.840833 TGCGGCAATCTTAATGATAGTATTAA 57.159 30.769 0.00 0.00 34.45 1.40
3407 7064 5.393027 CCTTAACACTTGCGGCAATCTTAAT 60.393 40.000 16.80 3.78 0.00 1.40
3410 7067 2.228822 CCTTAACACTTGCGGCAATCTT 59.771 45.455 16.80 9.88 0.00 2.40
3454 7112 3.243035 CGTGTTTTGTCAGCAATCCTCAA 60.243 43.478 0.00 0.00 34.18 3.02
3512 7170 1.676384 AGTGGCTGCCTCACTTCTC 59.324 57.895 21.03 0.66 42.17 2.87
3520 7178 2.041620 TCCAAGATAAAAGTGGCTGCCT 59.958 45.455 21.03 0.83 32.10 4.75
3523 7181 5.902613 TTGATCCAAGATAAAAGTGGCTG 57.097 39.130 0.00 0.00 32.10 4.85
3535 7193 7.689299 TCCTTTTCTACAGAATTGATCCAAGA 58.311 34.615 0.00 0.00 33.54 3.02
3539 7197 9.225436 GGATATCCTTTTCTACAGAATTGATCC 57.775 37.037 14.97 0.00 33.54 3.36
3577 7242 1.280710 ACCTCCCACGCATGTTTCATA 59.719 47.619 0.00 0.00 0.00 2.15
3591 7257 4.941873 CACCATTTACTTGTTCTACCTCCC 59.058 45.833 0.00 0.00 0.00 4.30
3615 7281 4.253685 TGATGTCCTTTGCTTAGTAGTGC 58.746 43.478 0.00 0.00 0.00 4.40
3656 7322 6.868864 TGTGCTGTAGACATCTTTAGAAACTC 59.131 38.462 0.00 0.00 0.00 3.01
3734 7400 0.601057 GTTAGCACAAAACCGCCCAT 59.399 50.000 0.00 0.00 0.00 4.00
3787 7454 2.559668 CCAGCACATTGATTTGGTCAGT 59.440 45.455 0.00 0.00 38.29 3.41
3922 7589 5.770162 AGGAAAACGTGATCCATCTTTCTTT 59.230 36.000 18.93 0.00 38.23 2.52
3976 7643 6.284459 ACTGAACTTTGGTGAAACAAAAACA 58.716 32.000 0.00 0.00 39.72 2.83
3980 7647 5.178438 GCAAACTGAACTTTGGTGAAACAAA 59.822 36.000 0.00 0.00 39.98 2.83
4000 7667 8.260818 ACTAGATGCTAAAAGATCACTAGCAAA 58.739 33.333 20.51 12.06 45.30 3.68
4001 7668 7.708322 CACTAGATGCTAAAAGATCACTAGCAA 59.292 37.037 20.51 9.16 45.30 3.91
4010 7677 4.657969 AGAGGCCACTAGATGCTAAAAGAT 59.342 41.667 5.01 0.00 0.00 2.40
4015 7682 4.033709 AGAAAGAGGCCACTAGATGCTAA 58.966 43.478 5.01 0.00 0.00 3.09
4034 7701 7.094549 CCCGTGAACCAAAAGTTATAATCAGAA 60.095 37.037 0.00 0.00 39.40 3.02
4036 7703 6.551736 CCCGTGAACCAAAAGTTATAATCAG 58.448 40.000 0.00 0.00 39.40 2.90
4039 7706 4.767928 TGCCCGTGAACCAAAAGTTATAAT 59.232 37.500 0.00 0.00 39.40 1.28
4049 7716 0.605319 GATGTCTGCCCGTGAACCAA 60.605 55.000 0.00 0.00 0.00 3.67
4053 7721 0.396435 AACTGATGTCTGCCCGTGAA 59.604 50.000 0.00 0.00 0.00 3.18
4057 7725 0.603707 ACACAACTGATGTCTGCCCG 60.604 55.000 0.00 0.00 41.46 6.13
4141 7811 9.416794 CAGGTTAGTATAGATGAAGCAGTATTG 57.583 37.037 0.00 0.00 0.00 1.90
4161 7845 7.268586 TGCAAAAGCAAAGATAAAACAGGTTA 58.731 30.769 0.00 0.00 0.00 2.85
4162 7846 6.112058 TGCAAAAGCAAAGATAAAACAGGTT 58.888 32.000 0.00 0.00 0.00 3.50
4165 7849 5.754890 ACCTGCAAAAGCAAAGATAAAACAG 59.245 36.000 0.00 0.00 0.00 3.16
4504 8189 4.473477 AGCACTAAAAGCTACGAGGATT 57.527 40.909 0.00 0.00 41.32 3.01
4510 8195 6.707599 AAAGTAGAAGCACTAAAAGCTACG 57.292 37.500 0.00 0.00 42.53 3.51
4567 8252 0.178924 ATGGCAAAAACTCAGGCCCT 60.179 50.000 0.00 0.00 45.83 5.19
4581 8266 5.284861 ACGGACTACATATTTGTATGGCA 57.715 39.130 0.00 0.00 37.68 4.92
4684 8454 2.037641 CAGACATCTGACTTGGTGGTCA 59.962 50.000 2.51 0.00 46.59 4.02
4689 8459 5.041191 AGAAAACAGACATCTGACTTGGT 57.959 39.130 15.76 0.00 46.59 3.67
4715 8485 2.430694 GTTTCTGGGTTGCATAATCCCC 59.569 50.000 12.18 6.63 40.41 4.81
4771 8541 6.668541 AACATGTGCACATCTACATCTAAC 57.331 37.500 29.23 0.00 35.46 2.34
4815 8588 8.220559 ACTAAGCCTGGTTAATATCAATCACAT 58.779 33.333 0.00 0.00 0.00 3.21
4819 8592 9.736023 CAAAACTAAGCCTGGTTAATATCAATC 57.264 33.333 0.00 0.00 0.00 2.67
4822 8595 8.644374 AACAAAACTAAGCCTGGTTAATATCA 57.356 30.769 0.00 0.00 0.00 2.15
4831 8633 5.508994 CCTGGTTAAACAAAACTAAGCCTGG 60.509 44.000 0.00 0.00 0.00 4.45
4848 8650 2.340427 GCTGCTGCAAACCTGGTTA 58.660 52.632 13.37 0.00 39.41 2.85
4975 8788 4.698201 TGGGTATGTGTTGAAAGACTCA 57.302 40.909 0.00 0.00 0.00 3.41
4978 8791 4.215613 GTCCTTGGGTATGTGTTGAAAGAC 59.784 45.833 0.00 0.00 0.00 3.01
5058 8871 2.479566 AATTCATGAGGCGTGACTGT 57.520 45.000 0.00 0.00 0.00 3.55
5079 8892 6.245408 ACAAAAAGGAGCACATGTCCTATTA 58.755 36.000 5.07 0.00 44.17 0.98
5080 8893 5.079643 ACAAAAAGGAGCACATGTCCTATT 58.920 37.500 5.07 2.12 44.17 1.73
5166 8979 2.231478 CAGGCCTCAATATACGGTCGAT 59.769 50.000 0.00 0.00 0.00 3.59
5174 8987 2.306805 CCATCTGCCAGGCCTCAATATA 59.693 50.000 9.64 0.00 0.00 0.86
5333 9146 2.755103 CCCTTAGAAGTTTGGTCCATGC 59.245 50.000 0.00 0.00 0.00 4.06
5365 9178 6.749923 AAGAATCAACAGAATCTTAGTGCC 57.250 37.500 0.00 0.00 31.47 5.01
5412 9226 7.912250 GCCAAATCACATCTCTGTTGTATAAAG 59.088 37.037 0.00 0.00 31.62 1.85
5451 9267 2.543037 ACCACCAAAAACTTCAGGGT 57.457 45.000 0.00 0.00 0.00 4.34
5464 9280 4.160814 ACAAGCGTTGTATCTATACCACCA 59.839 41.667 2.19 0.00 43.27 4.17
5480 9298 3.142393 AGGAGACTGCACAAGCGT 58.858 55.556 0.00 0.00 46.23 5.07
5561 9379 5.917462 TGTGTATGCATCTGTTAGCACTAT 58.083 37.500 0.19 0.00 44.49 2.12
5682 9500 5.507637 AGACAGATAGAAGAACGTAAGGGA 58.492 41.667 0.00 0.00 46.39 4.20
5727 9597 3.684788 CCGCAGATATAAACCTGGCATAC 59.315 47.826 0.00 0.00 0.00 2.39
5738 9608 4.219944 GGTACTGGACATCCGCAGATATAA 59.780 45.833 0.00 0.00 39.43 0.98
5873 9873 2.610219 TGTGTTCAATTCAATCGCCG 57.390 45.000 0.00 0.00 0.00 6.46
5920 9920 5.504665 CCATACAATCTTGAACGGAGAATGC 60.505 44.000 0.00 0.00 29.14 3.56
5946 9946 9.868277 AGTAAATTCAGTCACATTTCAAAAACA 57.132 25.926 0.00 0.00 0.00 2.83
5971 9971 4.147653 CGAAGTTCTGCAAGCATTTGAAAG 59.852 41.667 0.56 0.00 36.36 2.62
6066 10074 0.654683 CTGCGCAGTGCCTATTTCTC 59.345 55.000 29.24 0.00 45.60 2.87
6141 10149 0.108329 ACGACAATCCAAGCGGGTAG 60.108 55.000 0.00 0.00 38.11 3.18
6165 10173 6.355638 CGTATGCTTTATTTTCGTCTGGATC 58.644 40.000 0.00 0.00 0.00 3.36
6237 10245 2.351924 AAAACAGCTTGAGGCCCCGA 62.352 55.000 0.00 0.00 43.05 5.14
6249 10257 2.095059 AGCAATGATCGTGGAAAACAGC 60.095 45.455 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.