Multiple sequence alignment - TraesCS3D01G223600

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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 TraesCS3D01G223600 chr3D 100.000 3156 0 0 1 3156 305319152 305315997 0.000000e+00 5829.0
1 TraesCS3D01G223600 chr3D 87.143 70 6 3 3089 3156 282958059 282958127 3.380000e-10 76.8
2 TraesCS3D01G223600 chr3B 86.827 2042 154 48 4 1979 416564558 416566550 0.000000e+00 2174.0
3 TraesCS3D01G223600 chr3B 86.571 767 71 21 2008 2750 10168585 10169343 0.000000e+00 817.0
4 TraesCS3D01G223600 chr3B 87.065 201 24 1 2756 2956 85796204 85796402 3.170000e-55 226.0
5 TraesCS3D01G223600 chr3A 93.017 1074 44 18 920 1979 429490634 429491690 0.000000e+00 1539.0
6 TraesCS3D01G223600 chr3A 86.032 809 73 18 102 881 429485381 429486178 0.000000e+00 832.0
7 TraesCS3D01G223600 chr3A 85.940 761 84 15 2007 2750 164566112 164565358 0.000000e+00 791.0
8 TraesCS3D01G223600 chr3A 88.679 212 20 3 2756 2966 164565182 164564974 4.040000e-64 255.0
9 TraesCS3D01G223600 chr3A 89.231 65 5 2 3089 3151 158495858 158495794 2.610000e-11 80.5
10 TraesCS3D01G223600 chr1A 87.220 759 72 14 2007 2748 506643021 506642271 0.000000e+00 841.0
11 TraesCS3D01G223600 chr1A 85.844 770 78 19 2007 2752 258181662 258182424 0.000000e+00 789.0
12 TraesCS3D01G223600 chr1A 86.239 218 26 3 2750 2966 258182594 258182808 1.890000e-57 233.0
13 TraesCS3D01G223600 chr1A 84.058 69 9 2 3089 3156 42450025 42449958 7.310000e-07 65.8
14 TraesCS3D01G223600 chr2B 86.917 772 69 19 2006 2752 597874686 597873922 0.000000e+00 837.0
15 TraesCS3D01G223600 chr5A 86.991 761 71 16 2007 2750 493170217 493169468 0.000000e+00 832.0
16 TraesCS3D01G223600 chr5A 87.736 212 22 3 2756 2966 493169296 493169088 8.740000e-61 244.0
17 TraesCS3D01G223600 chr4A 86.701 767 77 13 2003 2752 244689894 244689136 0.000000e+00 828.0
18 TraesCS3D01G223600 chr4A 97.059 34 0 1 3122 3154 478478043 478478076 4.400000e-04 56.5
19 TraesCS3D01G223600 chr6B 86.641 771 72 19 2007 2752 147954193 147954957 0.000000e+00 824.0
20 TraesCS3D01G223600 chr2A 86.693 759 78 15 2007 2748 91006079 91005327 0.000000e+00 821.0
21 TraesCS3D01G223600 chrUn 86.571 767 72 19 2007 2749 5570615 5571374 0.000000e+00 817.0
22 TraesCS3D01G223600 chr1D 84.058 69 9 2 3089 3156 42824809 42824742 7.310000e-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 TraesCS3D01G223600 chr3D 305315997 305319152 3155 True 5829 5829 100.0000 1 3156 1 chr3D.!!$R1 3155
1 TraesCS3D01G223600 chr3B 416564558 416566550 1992 False 2174 2174 86.8270 4 1979 1 chr3B.!!$F3 1975
2 TraesCS3D01G223600 chr3B 10168585 10169343 758 False 817 817 86.5710 2008 2750 1 chr3B.!!$F1 742
3 TraesCS3D01G223600 chr3A 429490634 429491690 1056 False 1539 1539 93.0170 920 1979 1 chr3A.!!$F2 1059
4 TraesCS3D01G223600 chr3A 429485381 429486178 797 False 832 832 86.0320 102 881 1 chr3A.!!$F1 779
5 TraesCS3D01G223600 chr3A 164564974 164566112 1138 True 523 791 87.3095 2007 2966 2 chr3A.!!$R2 959
6 TraesCS3D01G223600 chr1A 506642271 506643021 750 True 841 841 87.2200 2007 2748 1 chr1A.!!$R2 741
7 TraesCS3D01G223600 chr1A 258181662 258182808 1146 False 511 789 86.0415 2007 2966 2 chr1A.!!$F1 959
8 TraesCS3D01G223600 chr2B 597873922 597874686 764 True 837 837 86.9170 2006 2752 1 chr2B.!!$R1 746
9 TraesCS3D01G223600 chr5A 493169088 493170217 1129 True 538 832 87.3635 2007 2966 2 chr5A.!!$R1 959
10 TraesCS3D01G223600 chr4A 244689136 244689894 758 True 828 828 86.7010 2003 2752 1 chr4A.!!$R1 749
11 TraesCS3D01G223600 chr6B 147954193 147954957 764 False 824 824 86.6410 2007 2752 1 chr6B.!!$F1 745
12 TraesCS3D01G223600 chr2A 91005327 91006079 752 True 821 821 86.6930 2007 2748 1 chr2A.!!$R1 741
13 TraesCS3D01G223600 chrUn 5570615 5571374 759 False 817 817 86.5710 2007 2749 1 chrUn.!!$F1 742

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
460 497 0.039165 CGCATAGATAGCCGCTGTCA 60.039 55.0 18.21 5.94 0.0 3.58 F
1095 1175 0.098728 GCTGGCGCGACATTGTAATT 59.901 50.0 18.76 0.00 0.0 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2173 0.615544 CCATTGGGTGGCACCATTCT 60.616 55.0 35.69 15.76 42.12 2.40 R
2786 3082 0.323999 TAGGCTAGGTTCTCCGTGCA 60.324 55.0 0.00 0.00 38.08 4.57 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
96 98 6.425210 AGATAAGGCTGCTATGACATAACA 57.575 37.500 0.00 0.00 0.00 2.41
140 143 2.462456 TTGTGTTTGCCAACAAAGCA 57.538 40.000 4.72 0.00 46.17 3.91
141 144 2.462456 TGTGTTTGCCAACAAAGCAA 57.538 40.000 4.72 0.00 46.17 3.91
288 303 4.141251 TCCAGACTGCTTAAAACCCTTCTT 60.141 41.667 0.00 0.00 0.00 2.52
289 304 4.216472 CCAGACTGCTTAAAACCCTTCTTC 59.784 45.833 0.00 0.00 0.00 2.87
290 305 4.216472 CAGACTGCTTAAAACCCTTCTTCC 59.784 45.833 0.00 0.00 0.00 3.46
310 325 0.591236 CCGTTTGCAGTTTCCACACG 60.591 55.000 0.00 0.00 36.46 4.49
311 326 1.199852 CGTTTGCAGTTTCCACACGC 61.200 55.000 0.00 0.00 31.01 5.34
314 329 0.463654 TTGCAGTTTCCACACGCTCT 60.464 50.000 0.00 0.00 0.00 4.09
315 330 0.391228 TGCAGTTTCCACACGCTCTA 59.609 50.000 0.00 0.00 0.00 2.43
316 331 0.790814 GCAGTTTCCACACGCTCTAC 59.209 55.000 0.00 0.00 0.00 2.59
317 332 1.429463 CAGTTTCCACACGCTCTACC 58.571 55.000 0.00 0.00 0.00 3.18
318 333 0.320697 AGTTTCCACACGCTCTACCC 59.679 55.000 0.00 0.00 0.00 3.69
319 334 0.320697 GTTTCCACACGCTCTACCCT 59.679 55.000 0.00 0.00 0.00 4.34
320 335 0.320374 TTTCCACACGCTCTACCCTG 59.680 55.000 0.00 0.00 0.00 4.45
321 336 2.125512 CCACACGCTCTACCCTGC 60.126 66.667 0.00 0.00 0.00 4.85
361 376 1.558756 CCCTTGCAAGACATCTCTCCT 59.441 52.381 28.05 0.00 0.00 3.69
364 379 3.055240 CCTTGCAAGACATCTCTCCTTCT 60.055 47.826 28.05 0.00 0.00 2.85
390 405 6.660949 CACCTTCTTTCCTCTCCATTTGTATT 59.339 38.462 0.00 0.00 0.00 1.89
437 469 1.280142 CGATAGCGGTCGTCCTCAG 59.720 63.158 0.00 0.00 36.88 3.35
460 497 0.039165 CGCATAGATAGCCGCTGTCA 60.039 55.000 18.21 5.94 0.00 3.58
475 512 2.746362 GCTGTCAAGATCCTCAGGTTTG 59.254 50.000 0.00 0.00 0.00 2.93
483 520 1.661463 TCCTCAGGTTTGCATCTCCT 58.339 50.000 0.00 0.00 0.00 3.69
491 528 2.291217 GGTTTGCATCTCCTTCCCTTCT 60.291 50.000 0.00 0.00 0.00 2.85
514 551 4.099573 TCAGGTGAGTCCGAATTATTCCTC 59.900 45.833 0.00 1.71 41.99 3.71
518 555 5.068723 GGTGAGTCCGAATTATTCCTCTGTA 59.931 44.000 9.77 0.00 0.00 2.74
519 556 6.239345 GGTGAGTCCGAATTATTCCTCTGTAT 60.239 42.308 9.77 0.00 0.00 2.29
530 567 7.572523 TTATTCCTCTGTATGCTGAATTTGG 57.427 36.000 0.00 0.00 0.00 3.28
566 603 7.036220 CGTGGTTAGTGATTTCTCTTATCAGT 58.964 38.462 0.00 0.00 38.74 3.41
619 656 2.159198 CCAATTGCCTGGTAATGCTGTC 60.159 50.000 10.89 0.00 0.00 3.51
624 661 2.224744 TGCCTGGTAATGCTGTCAGAAA 60.225 45.455 3.32 0.00 0.00 2.52
655 692 4.789629 CGTTTCGTTTTCCTTCGTTTCTTT 59.210 37.500 0.00 0.00 0.00 2.52
679 716 7.418840 TGCATTTGTTGAACATGTTATTTCC 57.581 32.000 11.95 0.00 0.00 3.13
713 753 1.014352 TCGCTGATTCGAGTCGATCA 58.986 50.000 17.34 18.76 35.23 2.92
720 764 2.631418 TTCGAGTCGATCAACCTGTC 57.369 50.000 17.34 0.00 35.23 3.51
729 773 1.028330 ATCAACCTGTCGCATGCCTG 61.028 55.000 13.15 2.95 0.00 4.85
740 784 1.379642 GCATGCCTGTGCCTAAGTCC 61.380 60.000 6.36 0.00 39.18 3.85
748 792 0.321653 GTGCCTAAGTCCCCAGTGTG 60.322 60.000 0.00 0.00 0.00 3.82
802 846 0.879839 TCGTAGTGGTCGTCGTCACA 60.880 55.000 18.21 3.94 36.43 3.58
857 901 1.308069 ACGTGCTTGCCACATCATCC 61.308 55.000 0.00 0.00 44.91 3.51
858 902 1.811860 GTGCTTGCCACATCATCCC 59.188 57.895 0.00 0.00 44.06 3.85
866 931 1.963515 GCCACATCATCCCCCAAATAC 59.036 52.381 0.00 0.00 0.00 1.89
882 947 5.823045 CCCAAATACTTTCCATCAGACCTAC 59.177 44.000 0.00 0.00 0.00 3.18
901 969 5.127031 ACCTACTGATCTTCTCTTCTTCTGC 59.873 44.000 0.00 0.00 0.00 4.26
902 970 5.360714 CCTACTGATCTTCTCTTCTTCTGCT 59.639 44.000 0.00 0.00 0.00 4.24
957 1030 9.643693 GTACCTAGCTGTTTTGTAACAACTATA 57.356 33.333 0.00 0.00 43.33 1.31
958 1031 8.543862 ACCTAGCTGTTTTGTAACAACTATAC 57.456 34.615 0.00 0.00 43.33 1.47
959 1032 8.373220 ACCTAGCTGTTTTGTAACAACTATACT 58.627 33.333 0.00 0.00 43.33 2.12
960 1033 9.865321 CCTAGCTGTTTTGTAACAACTATACTA 57.135 33.333 0.00 0.00 43.33 1.82
983 1058 4.839668 ACATTTTAAAAGGCAGTACGCA 57.160 36.364 12.27 0.00 45.17 5.24
1083 1163 5.295292 ACAGATTATAATATCATGCTGGCGC 59.705 40.000 0.00 0.00 0.00 6.53
1093 1173 1.024046 ATGCTGGCGCGACATTGTAA 61.024 50.000 18.76 0.00 39.65 2.41
1095 1175 0.098728 GCTGGCGCGACATTGTAATT 59.901 50.000 18.76 0.00 0.00 1.40
1096 1176 1.813896 CTGGCGCGACATTGTAATTG 58.186 50.000 18.76 0.00 0.00 2.32
1097 1177 1.130373 CTGGCGCGACATTGTAATTGT 59.870 47.619 18.76 0.00 0.00 2.71
1098 1178 2.347731 TGGCGCGACATTGTAATTGTA 58.652 42.857 12.71 0.00 0.00 2.41
1099 1179 2.094575 TGGCGCGACATTGTAATTGTAC 59.905 45.455 12.71 0.00 0.00 2.90
1100 1180 2.350498 GGCGCGACATTGTAATTGTACT 59.650 45.455 12.10 0.00 0.00 2.73
1101 1181 3.552699 GGCGCGACATTGTAATTGTACTA 59.447 43.478 12.10 0.00 0.00 1.82
1102 1182 4.502558 GCGCGACATTGTAATTGTACTAC 58.497 43.478 12.10 0.00 0.00 2.73
1103 1183 4.266976 GCGCGACATTGTAATTGTACTACT 59.733 41.667 12.10 0.00 0.00 2.57
1104 1184 5.714272 CGCGACATTGTAATTGTACTACTG 58.286 41.667 0.00 0.00 0.00 2.74
1105 1185 5.513849 CGCGACATTGTAATTGTACTACTGA 59.486 40.000 0.00 0.00 0.00 3.41
1106 1186 6.034150 CGCGACATTGTAATTGTACTACTGAA 59.966 38.462 0.00 0.00 0.00 3.02
1542 1622 2.125512 CGACCAGCTGTACCAGGC 60.126 66.667 13.81 0.00 31.21 4.85
1591 1671 4.821589 CGGGCGAGCAAGGAGGAC 62.822 72.222 0.00 0.00 0.00 3.85
1813 1899 2.592993 CGACCCAGAGCCCCAAGAA 61.593 63.158 0.00 0.00 0.00 2.52
1909 1995 1.654137 CTTTGTTGCACGCGGTGAC 60.654 57.895 12.47 4.03 35.23 3.67
1951 2037 3.350219 AATACGGAATGGACAGCTTGT 57.650 42.857 0.00 0.00 0.00 3.16
1952 2038 2.851263 TACGGAATGGACAGCTTGTT 57.149 45.000 0.00 0.00 0.00 2.83
1961 2047 3.030291 TGGACAGCTTGTTTTGGTGATT 58.970 40.909 0.00 0.00 36.81 2.57
1965 2051 3.044986 CAGCTTGTTTTGGTGATTGACG 58.955 45.455 0.00 0.00 35.20 4.35
1979 2065 1.495584 TTGACGAGCACCGCTGTTTC 61.496 55.000 0.00 0.00 39.88 2.78
1980 2066 1.954146 GACGAGCACCGCTGTTTCA 60.954 57.895 0.00 0.00 39.88 2.69
1981 2067 1.495584 GACGAGCACCGCTGTTTCAA 61.496 55.000 0.00 0.00 39.88 2.69
1982 2068 1.082756 CGAGCACCGCTGTTTCAAC 60.083 57.895 0.00 0.00 39.88 3.18
1983 2069 1.498865 CGAGCACCGCTGTTTCAACT 61.499 55.000 0.00 0.00 39.88 3.16
1984 2070 1.508632 GAGCACCGCTGTTTCAACTA 58.491 50.000 0.00 0.00 39.88 2.24
1985 2071 1.194772 GAGCACCGCTGTTTCAACTAC 59.805 52.381 0.00 0.00 39.88 2.73
1986 2072 0.110823 GCACCGCTGTTTCAACTACG 60.111 55.000 0.00 0.00 0.00 3.51
1987 2073 1.214367 CACCGCTGTTTCAACTACGT 58.786 50.000 0.00 0.00 0.00 3.57
1988 2074 2.396601 CACCGCTGTTTCAACTACGTA 58.603 47.619 0.00 0.00 0.00 3.57
1989 2075 2.154389 CACCGCTGTTTCAACTACGTAC 59.846 50.000 0.00 0.00 0.00 3.67
1990 2076 2.035066 ACCGCTGTTTCAACTACGTACT 59.965 45.455 0.00 0.00 0.00 2.73
1991 2077 2.660236 CCGCTGTTTCAACTACGTACTC 59.340 50.000 0.00 0.00 0.00 2.59
1992 2078 2.660236 CGCTGTTTCAACTACGTACTCC 59.340 50.000 0.00 0.00 0.00 3.85
1993 2079 2.991866 GCTGTTTCAACTACGTACTCCC 59.008 50.000 0.00 0.00 0.00 4.30
1994 2080 3.305881 GCTGTTTCAACTACGTACTCCCT 60.306 47.826 0.00 0.00 0.00 4.20
1995 2081 4.483311 CTGTTTCAACTACGTACTCCCTC 58.517 47.826 0.00 0.00 0.00 4.30
1996 2082 4.147321 TGTTTCAACTACGTACTCCCTCT 58.853 43.478 0.00 0.00 0.00 3.69
1997 2083 4.022589 TGTTTCAACTACGTACTCCCTCTG 60.023 45.833 0.00 0.00 0.00 3.35
1998 2084 3.430042 TCAACTACGTACTCCCTCTGT 57.570 47.619 0.00 0.00 0.00 3.41
1999 2085 3.759581 TCAACTACGTACTCCCTCTGTT 58.240 45.455 0.00 0.00 0.00 3.16
2000 2086 4.147321 TCAACTACGTACTCCCTCTGTTT 58.853 43.478 0.00 0.00 0.00 2.83
2001 2087 4.217118 TCAACTACGTACTCCCTCTGTTTC 59.783 45.833 0.00 0.00 0.00 2.78
2002 2088 3.759581 ACTACGTACTCCCTCTGTTTCA 58.240 45.455 0.00 0.00 0.00 2.69
2003 2089 4.147321 ACTACGTACTCCCTCTGTTTCAA 58.853 43.478 0.00 0.00 0.00 2.69
2004 2090 4.586001 ACTACGTACTCCCTCTGTTTCAAA 59.414 41.667 0.00 0.00 0.00 2.69
2037 2123 0.250510 TGCCCGTGCATTACAACAGA 60.251 50.000 0.00 0.00 44.23 3.41
2055 2141 8.018677 ACAACAGAAGAGATAATTAACGTGTG 57.981 34.615 0.00 0.00 0.00 3.82
2068 2154 1.582424 CGTGTGCACCACAACAACG 60.582 57.895 15.69 11.77 46.28 4.10
2069 2155 1.797441 GTGTGCACCACAACAACGA 59.203 52.632 15.69 0.00 46.28 3.85
2070 2156 0.522495 GTGTGCACCACAACAACGAC 60.522 55.000 15.69 0.00 46.28 4.34
2071 2157 1.297304 GTGCACCACAACAACGACG 60.297 57.895 5.22 0.00 34.08 5.12
2087 2173 3.697982 ACGACGCGACATAACAATATCA 58.302 40.909 15.93 0.00 0.00 2.15
2143 2229 5.031066 ACGCTACCAGAAATGCCTATAAA 57.969 39.130 0.00 0.00 0.00 1.40
2144 2230 5.621193 ACGCTACCAGAAATGCCTATAAAT 58.379 37.500 0.00 0.00 0.00 1.40
2179 2265 7.684062 AAATCAGCACGTATGATATTTTTGC 57.316 32.000 13.97 0.00 36.38 3.68
2198 2284 7.672351 TTTTGCTACGATTTTTGTACAACTG 57.328 32.000 8.07 0.00 0.00 3.16
2238 2324 5.527214 TGCCTCATTTCAAATCCTACATACG 59.473 40.000 0.00 0.00 0.00 3.06
2276 2362 6.986231 AGAAGTTGGAGCAATTTTTCGAAATT 59.014 30.769 12.12 0.74 32.97 1.82
2288 2374 1.336877 TCGAAATTCGCACAGAGTCG 58.663 50.000 10.93 0.00 40.21 4.18
2337 2423 1.133668 CCCATCTCACCTCCCAAATCC 60.134 57.143 0.00 0.00 0.00 3.01
2344 2430 0.905357 ACCTCCCAAATCCACTCTCG 59.095 55.000 0.00 0.00 0.00 4.04
2396 2482 5.356751 TCCATTGTGTTATTAGTCCACATGC 59.643 40.000 0.00 0.00 38.75 4.06
2400 2486 4.155826 TGTGTTATTAGTCCACATGCTTGC 59.844 41.667 0.00 0.00 34.37 4.01
2402 2488 0.734889 ATTAGTCCACATGCTTGCGC 59.265 50.000 0.00 0.00 0.00 6.09
2421 2524 0.173029 CCATTGCTATTTGCCGTGCA 59.827 50.000 0.00 0.00 42.00 4.57
2432 2535 3.314331 CCGTGCACCCTCACCTCT 61.314 66.667 12.15 0.00 33.57 3.69
2447 2550 8.122481 ACCCTCACCTCTTTGGATATTTAATTT 58.878 33.333 0.00 0.00 39.71 1.82
2448 2551 9.640952 CCCTCACCTCTTTGGATATTTAATTTA 57.359 33.333 0.00 0.00 39.71 1.40
2516 2619 6.036577 ACACACACTTCATCCTTTTTGTTT 57.963 33.333 0.00 0.00 0.00 2.83
2560 2675 4.401525 GTCTTCAAGACAACTCATGCAG 57.598 45.455 13.01 0.00 44.45 4.41
2576 2691 9.935241 AACTCATGCAGGTATATAAATCTGTAG 57.065 33.333 0.00 0.00 0.00 2.74
2594 2709 7.548196 TCTGTAGAATTTGGTATAAAAGGCG 57.452 36.000 0.00 0.00 0.00 5.52
2613 2728 3.985925 GGCGAGGTGGTACTATTTAATCG 59.014 47.826 0.00 0.00 0.00 3.34
2667 2786 0.109132 CGAAGCAGGCCCAATTTGAC 60.109 55.000 0.00 0.00 0.00 3.18
2668 2787 0.968405 GAAGCAGGCCCAATTTGACA 59.032 50.000 0.00 0.00 0.00 3.58
2673 2792 4.939399 GCCCAATTTGACATGGCC 57.061 55.556 0.00 0.00 36.07 5.36
2721 2847 6.737622 GCCATCAATTAGTACGGTGTATCAGA 60.738 42.308 0.00 0.00 0.00 3.27
2729 2855 6.636562 AGTACGGTGTATCAGATAAGAAGG 57.363 41.667 0.00 0.00 0.00 3.46
2737 2863 7.987458 GGTGTATCAGATAAGAAGGTCATCAAA 59.013 37.037 0.00 0.00 0.00 2.69
2743 2869 2.770164 AGAAGGTCATCAAACCCTCG 57.230 50.000 0.00 0.00 40.42 4.63
2777 3073 3.119990 CCTACACGTAGGCATTGTTTTGG 60.120 47.826 10.25 0.00 45.36 3.28
2785 3081 1.202510 GGCATTGTTTTGGCTCACACA 60.203 47.619 0.00 0.00 39.00 3.72
2786 3082 2.548493 GGCATTGTTTTGGCTCACACAT 60.548 45.455 0.00 0.00 39.00 3.21
2791 3087 0.030504 TTTTGGCTCACACATGCACG 59.969 50.000 0.00 0.00 0.00 5.34
2814 3110 5.507650 CGGAGAACCTAGCCTACATAACTTC 60.508 48.000 0.00 0.00 0.00 3.01
2825 3121 7.328737 AGCCTACATAACTTCGTCAAAAGTAT 58.671 34.615 0.00 0.00 38.52 2.12
2826 3122 8.472413 AGCCTACATAACTTCGTCAAAAGTATA 58.528 33.333 0.00 0.00 38.52 1.47
2827 3123 9.090692 GCCTACATAACTTCGTCAAAAGTATAA 57.909 33.333 0.00 0.00 38.52 0.98
2858 3154 9.185192 CAAATAGAAAAGAACCTGTGACAATTC 57.815 33.333 1.98 1.98 0.00 2.17
2870 3166 3.074390 TGTGACAATTCAGGGGAGACAAT 59.926 43.478 0.00 0.00 30.10 2.71
2897 3193 6.127897 GGATAAGTTGGTGGAGAAGATTTGTG 60.128 42.308 0.00 0.00 0.00 3.33
2908 3204 4.997565 AGAAGATTTGTGTGTTTGTGTGG 58.002 39.130 0.00 0.00 0.00 4.17
2915 3211 1.226831 GTGTTTGTGTGGGGTTGCG 60.227 57.895 0.00 0.00 0.00 4.85
2924 3220 3.110178 GGGGTTGCGAGTTCGACG 61.110 66.667 5.60 0.00 43.02 5.12
2958 3254 3.731089 CCAATTCTTTTTGGCTTGCAGA 58.269 40.909 0.00 0.00 39.76 4.26
2959 3255 3.495753 CCAATTCTTTTTGGCTTGCAGAC 59.504 43.478 0.00 0.00 39.76 3.51
2960 3256 2.888834 TTCTTTTTGGCTTGCAGACC 57.111 45.000 0.20 0.20 0.00 3.85
2966 3262 0.749818 TTGGCTTGCAGACCGTTGAA 60.750 50.000 2.95 0.00 0.00 2.69
2967 3263 0.537143 TGGCTTGCAGACCGTTGAAT 60.537 50.000 2.95 0.00 0.00 2.57
2968 3264 0.109597 GGCTTGCAGACCGTTGAATG 60.110 55.000 0.00 0.00 0.00 2.67
2969 3265 0.593128 GCTTGCAGACCGTTGAATGT 59.407 50.000 0.00 0.00 0.00 2.71
2970 3266 1.001378 GCTTGCAGACCGTTGAATGTT 60.001 47.619 0.00 0.00 0.00 2.71
2971 3267 2.918131 GCTTGCAGACCGTTGAATGTTC 60.918 50.000 0.00 0.00 0.00 3.18
2972 3268 1.960417 TGCAGACCGTTGAATGTTCA 58.040 45.000 0.00 0.00 34.92 3.18
2973 3269 2.293170 TGCAGACCGTTGAATGTTCAA 58.707 42.857 4.16 4.16 44.31 2.69
3022 3318 8.842358 AATAGGAATTAGAAAAGACGTTCACA 57.158 30.769 0.00 0.00 0.00 3.58
3023 3319 8.842358 ATAGGAATTAGAAAAGACGTTCACAA 57.158 30.769 0.00 0.00 0.00 3.33
3024 3320 7.562454 AGGAATTAGAAAAGACGTTCACAAA 57.438 32.000 0.00 0.00 0.00 2.83
3025 3321 7.992008 AGGAATTAGAAAAGACGTTCACAAAA 58.008 30.769 0.00 0.00 0.00 2.44
3026 3322 8.463607 AGGAATTAGAAAAGACGTTCACAAAAA 58.536 29.630 0.00 0.00 0.00 1.94
3027 3323 9.244799 GGAATTAGAAAAGACGTTCACAAAAAT 57.755 29.630 0.00 0.00 0.00 1.82
3038 3334 9.360093 AGACGTTCACAAAAATAAAAACATTCA 57.640 25.926 0.00 0.00 0.00 2.57
3039 3335 9.403869 GACGTTCACAAAAATAAAAACATTCAC 57.596 29.630 0.00 0.00 0.00 3.18
3040 3336 8.105135 ACGTTCACAAAAATAAAAACATTCACG 58.895 29.630 0.00 0.00 0.00 4.35
3041 3337 7.577312 CGTTCACAAAAATAAAAACATTCACGG 59.423 33.333 0.00 0.00 0.00 4.94
3042 3338 7.470289 TCACAAAAATAAAAACATTCACGGG 57.530 32.000 0.00 0.00 0.00 5.28
3043 3339 7.042335 TCACAAAAATAAAAACATTCACGGGT 58.958 30.769 0.00 0.00 0.00 5.28
3044 3340 7.549488 TCACAAAAATAAAAACATTCACGGGTT 59.451 29.630 0.00 0.00 0.00 4.11
3045 3341 8.818057 CACAAAAATAAAAACATTCACGGGTTA 58.182 29.630 0.00 0.00 0.00 2.85
3046 3342 9.379791 ACAAAAATAAAAACATTCACGGGTTAA 57.620 25.926 0.00 0.00 0.00 2.01
3076 3372 9.647797 AAGGTTGACGAATTTAAAAGAAAAAGT 57.352 25.926 0.00 0.00 0.00 2.66
3077 3373 9.297586 AGGTTGACGAATTTAAAAGAAAAAGTC 57.702 29.630 0.00 0.00 0.00 3.01
3078 3374 9.078753 GGTTGACGAATTTAAAAGAAAAAGTCA 57.921 29.630 0.00 0.00 32.06 3.41
3079 3375 9.881414 GTTGACGAATTTAAAAGAAAAAGTCAC 57.119 29.630 0.00 0.00 34.32 3.67
3080 3376 8.318000 TGACGAATTTAAAAGAAAAAGTCACG 57.682 30.769 0.00 0.00 32.06 4.35
3081 3377 8.176365 TGACGAATTTAAAAGAAAAAGTCACGA 58.824 29.630 0.00 0.00 32.06 4.35
3082 3378 8.898983 ACGAATTTAAAAGAAAAAGTCACGAA 57.101 26.923 0.00 0.00 32.06 3.85
3083 3379 9.344309 ACGAATTTAAAAGAAAAAGTCACGAAA 57.656 25.926 0.00 0.00 32.06 3.46
3088 3384 9.640963 TTTAAAAGAAAAAGTCACGAAAATGGA 57.359 25.926 0.00 0.00 0.00 3.41
3089 3385 9.640963 TTAAAAGAAAAAGTCACGAAAATGGAA 57.359 25.926 0.00 0.00 0.00 3.53
3090 3386 8.541133 AAAAGAAAAAGTCACGAAAATGGAAA 57.459 26.923 0.00 0.00 0.00 3.13
3091 3387 8.541133 AAAGAAAAAGTCACGAAAATGGAAAA 57.459 26.923 0.00 0.00 0.00 2.29
3092 3388 7.755582 AGAAAAAGTCACGAAAATGGAAAAG 57.244 32.000 0.00 0.00 0.00 2.27
3093 3389 7.320399 AGAAAAAGTCACGAAAATGGAAAAGT 58.680 30.769 0.00 0.00 0.00 2.66
3094 3390 7.817478 AGAAAAAGTCACGAAAATGGAAAAGTT 59.183 29.630 0.00 0.00 0.00 2.66
3095 3391 7.520119 AAAAGTCACGAAAATGGAAAAGTTC 57.480 32.000 0.00 0.00 0.00 3.01
3096 3392 5.828299 AGTCACGAAAATGGAAAAGTTCA 57.172 34.783 0.00 0.00 0.00 3.18
3097 3393 6.391227 AGTCACGAAAATGGAAAAGTTCAT 57.609 33.333 0.00 0.00 0.00 2.57
3098 3394 6.438763 AGTCACGAAAATGGAAAAGTTCATC 58.561 36.000 0.00 0.00 0.00 2.92
3099 3395 5.339611 GTCACGAAAATGGAAAAGTTCATCG 59.660 40.000 0.00 0.00 0.00 3.84
3100 3396 5.237561 TCACGAAAATGGAAAAGTTCATCGA 59.762 36.000 0.00 0.00 0.00 3.59
3101 3397 6.072728 TCACGAAAATGGAAAAGTTCATCGAT 60.073 34.615 0.00 0.00 0.00 3.59
3102 3398 6.249260 CACGAAAATGGAAAAGTTCATCGATC 59.751 38.462 0.00 0.00 0.00 3.69
3103 3399 6.149474 ACGAAAATGGAAAAGTTCATCGATCT 59.851 34.615 0.00 0.00 0.00 2.75
3104 3400 7.023575 CGAAAATGGAAAAGTTCATCGATCTT 58.976 34.615 0.00 0.00 0.00 2.40
3105 3401 7.217070 CGAAAATGGAAAAGTTCATCGATCTTC 59.783 37.037 0.00 0.00 0.00 2.87
3106 3402 7.452880 AAATGGAAAAGTTCATCGATCTTCA 57.547 32.000 0.00 0.00 0.00 3.02
3107 3403 7.452880 AATGGAAAAGTTCATCGATCTTCAA 57.547 32.000 0.00 0.00 0.00 2.69
3108 3404 6.875948 TGGAAAAGTTCATCGATCTTCAAA 57.124 33.333 0.00 0.00 0.00 2.69
3109 3405 7.270757 TGGAAAAGTTCATCGATCTTCAAAA 57.729 32.000 0.00 0.00 0.00 2.44
3110 3406 7.885297 TGGAAAAGTTCATCGATCTTCAAAAT 58.115 30.769 0.00 0.00 0.00 1.82
3111 3407 9.008965 TGGAAAAGTTCATCGATCTTCAAAATA 57.991 29.630 0.00 0.00 0.00 1.40
3112 3408 9.495754 GGAAAAGTTCATCGATCTTCAAAATAG 57.504 33.333 0.00 0.00 0.00 1.73
3116 3412 8.777865 AGTTCATCGATCTTCAAAATAGTTCA 57.222 30.769 0.00 0.00 0.00 3.18
3117 3413 9.388506 AGTTCATCGATCTTCAAAATAGTTCAT 57.611 29.630 0.00 0.00 0.00 2.57
3118 3414 9.643652 GTTCATCGATCTTCAAAATAGTTCATC 57.356 33.333 0.00 0.00 0.00 2.92
3119 3415 8.065557 TCATCGATCTTCAAAATAGTTCATCG 57.934 34.615 0.00 0.00 34.55 3.84
3120 3416 6.828502 TCGATCTTCAAAATAGTTCATCGG 57.171 37.500 0.00 0.00 34.14 4.18
3121 3417 6.338146 TCGATCTTCAAAATAGTTCATCGGT 58.662 36.000 0.00 0.00 34.14 4.69
3122 3418 6.816640 TCGATCTTCAAAATAGTTCATCGGTT 59.183 34.615 0.00 0.00 34.14 4.44
3123 3419 7.333423 TCGATCTTCAAAATAGTTCATCGGTTT 59.667 33.333 0.00 0.00 34.14 3.27
3124 3420 7.962918 CGATCTTCAAAATAGTTCATCGGTTTT 59.037 33.333 0.00 0.00 0.00 2.43
3125 3421 8.970691 ATCTTCAAAATAGTTCATCGGTTTTG 57.029 30.769 0.00 0.00 39.73 2.44
3126 3422 7.367285 TCTTCAAAATAGTTCATCGGTTTTGG 58.633 34.615 8.46 0.00 39.18 3.28
3127 3423 6.885952 TCAAAATAGTTCATCGGTTTTGGA 57.114 33.333 8.46 0.00 39.18 3.53
3128 3424 7.278461 TCAAAATAGTTCATCGGTTTTGGAA 57.722 32.000 8.46 0.00 39.18 3.53
3129 3425 7.717568 TCAAAATAGTTCATCGGTTTTGGAAA 58.282 30.769 8.46 0.00 39.18 3.13
3130 3426 8.198109 TCAAAATAGTTCATCGGTTTTGGAAAA 58.802 29.630 8.46 0.00 39.18 2.29
3131 3427 8.821894 CAAAATAGTTCATCGGTTTTGGAAAAA 58.178 29.630 0.00 0.00 36.58 1.94
3132 3428 8.587952 AAATAGTTCATCGGTTTTGGAAAAAG 57.412 30.769 0.00 0.00 0.00 2.27
3133 3429 5.592104 AGTTCATCGGTTTTGGAAAAAGT 57.408 34.783 0.00 0.00 0.00 2.66
3134 3430 5.972935 AGTTCATCGGTTTTGGAAAAAGTT 58.027 33.333 0.00 0.00 0.00 2.66
3135 3431 6.040247 AGTTCATCGGTTTTGGAAAAAGTTC 58.960 36.000 0.00 0.00 0.00 3.01
3136 3432 5.584253 TCATCGGTTTTGGAAAAAGTTCA 57.416 34.783 0.00 0.00 35.25 3.18
3137 3433 6.155475 TCATCGGTTTTGGAAAAAGTTCAT 57.845 33.333 0.00 0.00 35.25 2.57
3138 3434 6.578023 TCATCGGTTTTGGAAAAAGTTCATT 58.422 32.000 0.00 0.00 35.25 2.57
3139 3435 6.699642 TCATCGGTTTTGGAAAAAGTTCATTC 59.300 34.615 0.00 0.00 35.25 2.67
3140 3436 5.967088 TCGGTTTTGGAAAAAGTTCATTCA 58.033 33.333 4.37 0.00 35.25 2.57
3141 3437 6.578023 TCGGTTTTGGAAAAAGTTCATTCAT 58.422 32.000 4.37 0.00 35.25 2.57
3142 3438 7.044798 TCGGTTTTGGAAAAAGTTCATTCATT 58.955 30.769 4.37 0.00 35.25 2.57
3143 3439 7.550906 TCGGTTTTGGAAAAAGTTCATTCATTT 59.449 29.630 4.37 0.00 35.25 2.32
3144 3440 7.639461 CGGTTTTGGAAAAAGTTCATTCATTTG 59.361 33.333 4.37 0.00 35.25 2.32
3145 3441 8.672815 GGTTTTGGAAAAAGTTCATTCATTTGA 58.327 29.630 4.37 0.00 35.25 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 8.422577 ACAGCAAGAAAAATACCTCCTTATTT 57.577 30.769 0.00 0.00 33.84 1.40
41 43 7.833285 TTTACAGCAAGAAAAATACCTCCTT 57.167 32.000 0.00 0.00 0.00 3.36
76 78 6.657117 TGTTTTGTTATGTCATAGCAGCCTTA 59.343 34.615 9.07 0.00 0.00 2.69
226 235 8.598916 TGGGATAAACTAGTATTGAACTGTTGA 58.401 33.333 0.00 0.00 39.39 3.18
288 303 1.104577 GTGGAAACTGCAAACGGGGA 61.105 55.000 0.00 0.00 0.00 4.81
289 304 1.362355 GTGGAAACTGCAAACGGGG 59.638 57.895 0.00 0.00 0.00 5.73
290 305 0.248866 GTGTGGAAACTGCAAACGGG 60.249 55.000 0.00 0.00 0.00 5.28
310 325 0.761802 ATAAGCTGGCAGGGTAGAGC 59.238 55.000 17.64 0.00 0.00 4.09
311 326 2.224402 GGAATAAGCTGGCAGGGTAGAG 60.224 54.545 17.64 0.00 0.00 2.43
314 329 1.590591 TGGAATAAGCTGGCAGGGTA 58.409 50.000 17.64 0.00 0.00 3.69
315 330 0.929244 ATGGAATAAGCTGGCAGGGT 59.071 50.000 17.64 0.00 0.00 4.34
316 331 1.613836 GATGGAATAAGCTGGCAGGG 58.386 55.000 17.64 0.00 0.00 4.45
317 332 1.613836 GGATGGAATAAGCTGGCAGG 58.386 55.000 17.64 0.00 0.00 4.85
318 333 1.613836 GGGATGGAATAAGCTGGCAG 58.386 55.000 10.94 10.94 0.00 4.85
319 334 0.179020 CGGGATGGAATAAGCTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
320 335 1.518903 GCGGGATGGAATAAGCTGGC 61.519 60.000 0.00 0.00 0.00 4.85
321 336 0.890996 GGCGGGATGGAATAAGCTGG 60.891 60.000 0.00 0.00 0.00 4.85
361 376 3.587498 TGGAGAGGAAAGAAGGTGAGAA 58.413 45.455 0.00 0.00 0.00 2.87
364 379 4.104738 ACAAATGGAGAGGAAAGAAGGTGA 59.895 41.667 0.00 0.00 0.00 4.02
460 497 3.371380 GGAGATGCAAACCTGAGGATCTT 60.371 47.826 4.99 0.00 34.92 2.40
475 512 1.140652 CCTGAGAAGGGAAGGAGATGC 59.859 57.143 0.00 0.00 32.43 3.91
483 520 1.645710 GGACTCACCTGAGAAGGGAA 58.354 55.000 9.35 0.00 44.74 3.97
491 528 4.030913 AGGAATAATTCGGACTCACCTGA 58.969 43.478 0.00 0.00 36.31 3.86
519 556 1.192803 TGGGCATGCCAAATTCAGCA 61.193 50.000 36.56 20.23 44.45 4.41
566 603 2.428171 AGCTAAACGCGGGACTAATGTA 59.572 45.455 12.47 0.00 45.59 2.29
646 683 5.164233 TGTTCAACAAATGCAAAGAAACGA 58.836 33.333 0.00 0.00 0.00 3.85
655 692 6.145209 CGGAAATAACATGTTCAACAAATGCA 59.855 34.615 15.85 0.00 0.00 3.96
706 746 0.647410 CATGCGACAGGTTGATCGAC 59.353 55.000 4.31 4.31 40.86 4.20
713 753 1.968017 CACAGGCATGCGACAGGTT 60.968 57.895 12.44 0.00 0.00 3.50
729 773 0.321653 CACACTGGGGACTTAGGCAC 60.322 60.000 0.00 0.00 0.00 5.01
740 784 2.030007 CCTTGCACAAATACACACTGGG 60.030 50.000 0.00 0.00 0.00 4.45
748 792 6.372659 TCTTCATCTCTTCCTTGCACAAATAC 59.627 38.462 0.00 0.00 0.00 1.89
857 901 3.954258 GGTCTGATGGAAAGTATTTGGGG 59.046 47.826 0.00 0.00 39.27 4.96
858 902 4.860022 AGGTCTGATGGAAAGTATTTGGG 58.140 43.478 0.00 0.00 39.27 4.12
882 947 5.327616 TCAGCAGAAGAAGAGAAGATCAG 57.672 43.478 0.00 0.00 0.00 2.90
885 953 6.709281 TCATTTCAGCAGAAGAAGAGAAGAT 58.291 36.000 0.00 0.00 34.71 2.40
957 1030 7.334921 TGCGTACTGCCTTTTAAAATGTATAGT 59.665 33.333 0.09 7.76 45.60 2.12
958 1031 7.638683 GTGCGTACTGCCTTTTAAAATGTATAG 59.361 37.037 0.09 2.80 45.60 1.31
959 1032 7.465989 GTGCGTACTGCCTTTTAAAATGTATA 58.534 34.615 0.09 0.00 45.60 1.47
960 1033 6.319399 GTGCGTACTGCCTTTTAAAATGTAT 58.681 36.000 0.09 0.00 45.60 2.29
961 1034 5.615106 CGTGCGTACTGCCTTTTAAAATGTA 60.615 40.000 0.09 0.00 45.60 2.29
1083 1163 9.083080 TCATTCAGTAGTACAATTACAATGTCG 57.917 33.333 2.52 0.00 32.27 4.35
1106 1186 9.717942 GGAGACAGTAATTAAGCTATGATTCAT 57.282 33.333 4.28 4.28 0.00 2.57
1520 1600 1.116536 TGGTACAGCTGGTCGTCCAA 61.117 55.000 19.93 1.82 43.81 3.53
1793 1879 3.612247 CTTGGGGCTCTGGGTCGTG 62.612 68.421 0.00 0.00 0.00 4.35
1878 1964 4.753233 TGCAACAAAGTTTGTAGCACAAT 58.247 34.783 21.14 1.37 44.59 2.71
1909 1995 2.614520 TCCGTACAAACCACACACAATG 59.385 45.455 0.00 0.00 0.00 2.82
1961 2047 1.954146 GAAACAGCGGTGCTCGTCA 60.954 57.895 15.82 0.00 36.40 4.35
1965 2051 1.194772 GTAGTTGAAACAGCGGTGCTC 59.805 52.381 15.82 12.22 36.40 4.26
1979 2065 4.022589 TGAAACAGAGGGAGTACGTAGTTG 60.023 45.833 4.03 1.02 37.78 3.16
1980 2066 4.147321 TGAAACAGAGGGAGTACGTAGTT 58.853 43.478 4.03 0.00 37.78 2.24
1982 2068 4.778534 TTGAAACAGAGGGAGTACGTAG 57.221 45.455 0.00 0.00 0.00 3.51
1983 2069 5.534207 TTTTGAAACAGAGGGAGTACGTA 57.466 39.130 0.00 0.00 0.00 3.57
1984 2070 4.411256 TTTTGAAACAGAGGGAGTACGT 57.589 40.909 0.00 0.00 0.00 3.57
1985 2071 6.164176 AGTATTTTGAAACAGAGGGAGTACG 58.836 40.000 0.00 0.00 0.00 3.67
1986 2072 7.278203 GCTAGTATTTTGAAACAGAGGGAGTAC 59.722 40.741 0.00 0.00 0.00 2.73
1987 2073 7.038587 TGCTAGTATTTTGAAACAGAGGGAGTA 60.039 37.037 0.00 0.00 0.00 2.59
1988 2074 6.174049 GCTAGTATTTTGAAACAGAGGGAGT 58.826 40.000 0.00 0.00 0.00 3.85
1989 2075 6.092807 GTGCTAGTATTTTGAAACAGAGGGAG 59.907 42.308 0.00 0.00 0.00 4.30
1990 2076 5.938125 GTGCTAGTATTTTGAAACAGAGGGA 59.062 40.000 0.00 0.00 0.00 4.20
1991 2077 5.705441 TGTGCTAGTATTTTGAAACAGAGGG 59.295 40.000 0.00 0.00 0.00 4.30
1992 2078 6.801539 TGTGCTAGTATTTTGAAACAGAGG 57.198 37.500 0.00 0.00 0.00 3.69
1993 2079 9.926751 CATATGTGCTAGTATTTTGAAACAGAG 57.073 33.333 0.00 0.00 0.00 3.35
2037 2123 5.121768 GTGGTGCACACGTTAATTATCTCTT 59.878 40.000 20.43 0.00 40.85 2.85
2055 2141 2.351888 GCGTCGTTGTTGTGGTGC 60.352 61.111 0.00 0.00 0.00 5.01
2068 2154 5.883328 TTCTGATATTGTTATGTCGCGTC 57.117 39.130 5.77 0.00 0.00 5.19
2069 2155 5.177511 CCATTCTGATATTGTTATGTCGCGT 59.822 40.000 5.77 0.00 0.00 6.01
2070 2156 5.177511 ACCATTCTGATATTGTTATGTCGCG 59.822 40.000 0.00 0.00 0.00 5.87
2071 2157 6.365839 CACCATTCTGATATTGTTATGTCGC 58.634 40.000 0.00 0.00 0.00 5.19
2087 2173 0.615544 CCATTGGGTGGCACCATTCT 60.616 55.000 35.69 15.76 42.12 2.40
2119 2205 1.739067 AGGCATTTCTGGTAGCGTTC 58.261 50.000 0.00 0.00 0.00 3.95
2143 2229 6.417191 ACGTGCTGATTTTTAATGTACGAT 57.583 33.333 8.63 0.00 39.33 3.73
2144 2230 5.849357 ACGTGCTGATTTTTAATGTACGA 57.151 34.783 8.63 0.00 39.33 3.43
2158 2244 6.292114 CGTAGCAAAAATATCATACGTGCTGA 60.292 38.462 0.00 1.06 40.81 4.26
2161 2247 5.969741 TCGTAGCAAAAATATCATACGTGC 58.030 37.500 0.00 0.00 37.74 5.34
2179 2265 6.073765 ACAGAGCAGTTGTACAAAAATCGTAG 60.074 38.462 10.51 0.41 0.00 3.51
2198 2284 8.707938 AAATGAGGCATTTTAAATAACAGAGC 57.292 30.769 0.00 0.00 40.60 4.09
2214 2300 5.527214 CGTATGTAGGATTTGAAATGAGGCA 59.473 40.000 0.00 0.00 0.00 4.75
2238 2324 5.449725 GCTCCAACTTCTGAATAATGCCTTC 60.450 44.000 0.00 0.00 0.00 3.46
2276 2362 0.666374 TTCTTCACGACTCTGTGCGA 59.334 50.000 0.00 0.00 39.73 5.10
2288 2374 8.579682 AAACACATTTAGCAAGATTTCTTCAC 57.420 30.769 0.00 0.00 33.11 3.18
2344 2430 1.946475 GAGGTAGGAGGGCACGACAC 61.946 65.000 0.00 0.00 0.00 3.67
2421 2524 6.652205 TTAAATATCCAAAGAGGTGAGGGT 57.348 37.500 0.00 0.00 39.02 4.34
2454 2557 7.657354 GTGGGCACAAAAAGAAAGAGAAATTAT 59.343 33.333 0.00 0.00 0.00 1.28
2468 2571 0.468214 TCATCCGGTGGGCACAAAAA 60.468 50.000 0.00 0.00 0.00 1.94
2473 2576 1.077787 TCATTCATCCGGTGGGCAC 60.078 57.895 0.00 0.00 0.00 5.01
2516 2619 2.790433 ACAAGGCGCCTCAAGAATAAA 58.210 42.857 32.93 0.00 0.00 1.40
2576 2691 5.449999 CCACCTCGCCTTTTATACCAAATTC 60.450 44.000 0.00 0.00 0.00 2.17
2592 2707 3.985925 CCGATTAAATAGTACCACCTCGC 59.014 47.826 0.00 0.00 0.00 5.03
2594 2709 5.541953 ACCCGATTAAATAGTACCACCTC 57.458 43.478 0.00 0.00 0.00 3.85
2613 2728 3.179443 TGATCAATCAGTTCGCTACCC 57.821 47.619 0.00 0.00 32.11 3.69
2661 2780 1.337118 AAACGTGGGCCATGTCAAAT 58.663 45.000 30.47 13.30 31.86 2.32
2691 2811 2.802816 CCGTACTAATTGATGGCAGAGC 59.197 50.000 0.00 0.00 0.00 4.09
2721 2847 4.469945 TCGAGGGTTTGATGACCTTCTTAT 59.530 41.667 4.93 0.00 42.04 1.73
2725 2851 2.762535 TCGAGGGTTTGATGACCTTC 57.237 50.000 0.00 0.00 41.12 3.46
2766 3062 2.222007 TGTGTGAGCCAAAACAATGC 57.778 45.000 0.00 0.00 0.00 3.56
2777 3073 0.950555 TTCTCCGTGCATGTGTGAGC 60.951 55.000 4.96 0.00 0.00 4.26
2785 3081 0.978146 AGGCTAGGTTCTCCGTGCAT 60.978 55.000 0.00 0.00 38.08 3.96
2786 3082 0.323999 TAGGCTAGGTTCTCCGTGCA 60.324 55.000 0.00 0.00 38.08 4.57
2791 3087 5.507650 CGAAGTTATGTAGGCTAGGTTCTCC 60.508 48.000 0.00 0.00 0.00 3.71
2826 3122 9.349713 TCACAGGTTCTTTTCTATTTGTACATT 57.650 29.630 0.00 0.00 0.00 2.71
2827 3123 8.784043 GTCACAGGTTCTTTTCTATTTGTACAT 58.216 33.333 0.00 0.00 0.00 2.29
2832 3128 9.185192 GAATTGTCACAGGTTCTTTTCTATTTG 57.815 33.333 0.00 0.00 0.00 2.32
2849 3145 2.859165 TGTCTCCCCTGAATTGTCAC 57.141 50.000 0.00 0.00 0.00 3.67
2858 3154 4.510167 ACTTATCCAATTGTCTCCCCTG 57.490 45.455 4.43 0.00 0.00 4.45
2861 3157 4.399303 CACCAACTTATCCAATTGTCTCCC 59.601 45.833 4.43 0.00 0.00 4.30
2863 3159 5.253330 TCCACCAACTTATCCAATTGTCTC 58.747 41.667 4.43 0.00 0.00 3.36
2870 3166 5.779241 ATCTTCTCCACCAACTTATCCAA 57.221 39.130 0.00 0.00 0.00 3.53
2897 3193 1.226831 CGCAACCCCACACAAACAC 60.227 57.895 0.00 0.00 0.00 3.32
2953 3249 1.960417 TGAACATTCAACGGTCTGCA 58.040 45.000 0.00 0.00 33.55 4.41
2996 3292 9.280174 TGTGAACGTCTTTTCTAATTCCTATTT 57.720 29.630 0.00 0.00 0.00 1.40
2997 3293 8.842358 TGTGAACGTCTTTTCTAATTCCTATT 57.158 30.769 0.00 0.00 0.00 1.73
2998 3294 8.842358 TTGTGAACGTCTTTTCTAATTCCTAT 57.158 30.769 0.00 0.00 0.00 2.57
2999 3295 8.665643 TTTGTGAACGTCTTTTCTAATTCCTA 57.334 30.769 0.00 0.00 0.00 2.94
3000 3296 7.562454 TTTGTGAACGTCTTTTCTAATTCCT 57.438 32.000 0.00 0.00 0.00 3.36
3001 3297 8.623310 TTTTTGTGAACGTCTTTTCTAATTCC 57.377 30.769 0.00 0.00 0.00 3.01
3012 3308 9.360093 TGAATGTTTTTATTTTTGTGAACGTCT 57.640 25.926 0.00 0.00 0.00 4.18
3013 3309 9.403869 GTGAATGTTTTTATTTTTGTGAACGTC 57.596 29.630 0.00 0.00 0.00 4.34
3014 3310 8.105135 CGTGAATGTTTTTATTTTTGTGAACGT 58.895 29.630 0.00 0.00 0.00 3.99
3015 3311 7.577312 CCGTGAATGTTTTTATTTTTGTGAACG 59.423 33.333 0.00 0.00 0.00 3.95
3016 3312 7.848539 CCCGTGAATGTTTTTATTTTTGTGAAC 59.151 33.333 0.00 0.00 0.00 3.18
3017 3313 7.549488 ACCCGTGAATGTTTTTATTTTTGTGAA 59.451 29.630 0.00 0.00 0.00 3.18
3018 3314 7.042335 ACCCGTGAATGTTTTTATTTTTGTGA 58.958 30.769 0.00 0.00 0.00 3.58
3019 3315 7.240414 ACCCGTGAATGTTTTTATTTTTGTG 57.760 32.000 0.00 0.00 0.00 3.33
3020 3316 7.851387 AACCCGTGAATGTTTTTATTTTTGT 57.149 28.000 0.00 0.00 0.00 2.83
3050 3346 9.647797 ACTTTTTCTTTTAAATTCGTCAACCTT 57.352 25.926 0.00 0.00 0.00 3.50
3051 3347 9.297586 GACTTTTTCTTTTAAATTCGTCAACCT 57.702 29.630 0.00 0.00 0.00 3.50
3052 3348 9.078753 TGACTTTTTCTTTTAAATTCGTCAACC 57.921 29.630 0.00 0.00 0.00 3.77
3053 3349 9.881414 GTGACTTTTTCTTTTAAATTCGTCAAC 57.119 29.630 0.00 0.00 30.63 3.18
3054 3350 8.790674 CGTGACTTTTTCTTTTAAATTCGTCAA 58.209 29.630 0.00 0.00 30.63 3.18
3055 3351 8.176365 TCGTGACTTTTTCTTTTAAATTCGTCA 58.824 29.630 0.00 0.00 0.00 4.35
3056 3352 8.537729 TCGTGACTTTTTCTTTTAAATTCGTC 57.462 30.769 0.00 0.00 0.00 4.20
3057 3353 8.898983 TTCGTGACTTTTTCTTTTAAATTCGT 57.101 26.923 0.00 0.00 0.00 3.85
3062 3358 9.640963 TCCATTTTCGTGACTTTTTCTTTTAAA 57.359 25.926 0.00 0.00 0.00 1.52
3063 3359 9.640963 TTCCATTTTCGTGACTTTTTCTTTTAA 57.359 25.926 0.00 0.00 0.00 1.52
3064 3360 9.640963 TTTCCATTTTCGTGACTTTTTCTTTTA 57.359 25.926 0.00 0.00 0.00 1.52
3065 3361 8.541133 TTTCCATTTTCGTGACTTTTTCTTTT 57.459 26.923 0.00 0.00 0.00 2.27
3066 3362 8.541133 TTTTCCATTTTCGTGACTTTTTCTTT 57.459 26.923 0.00 0.00 0.00 2.52
3067 3363 7.817478 ACTTTTCCATTTTCGTGACTTTTTCTT 59.183 29.630 0.00 0.00 0.00 2.52
3068 3364 7.320399 ACTTTTCCATTTTCGTGACTTTTTCT 58.680 30.769 0.00 0.00 0.00 2.52
3069 3365 7.520119 ACTTTTCCATTTTCGTGACTTTTTC 57.480 32.000 0.00 0.00 0.00 2.29
3070 3366 7.600752 TGAACTTTTCCATTTTCGTGACTTTTT 59.399 29.630 0.00 0.00 0.00 1.94
3071 3367 7.093992 TGAACTTTTCCATTTTCGTGACTTTT 58.906 30.769 0.00 0.00 0.00 2.27
3072 3368 6.626302 TGAACTTTTCCATTTTCGTGACTTT 58.374 32.000 0.00 0.00 0.00 2.66
3073 3369 6.202516 TGAACTTTTCCATTTTCGTGACTT 57.797 33.333 0.00 0.00 0.00 3.01
3074 3370 5.828299 TGAACTTTTCCATTTTCGTGACT 57.172 34.783 0.00 0.00 0.00 3.41
3075 3371 5.339611 CGATGAACTTTTCCATTTTCGTGAC 59.660 40.000 0.00 0.00 0.00 3.67
3076 3372 5.237561 TCGATGAACTTTTCCATTTTCGTGA 59.762 36.000 0.00 0.00 0.00 4.35
3077 3373 5.448438 TCGATGAACTTTTCCATTTTCGTG 58.552 37.500 0.00 0.00 0.00 4.35
3078 3374 5.682943 TCGATGAACTTTTCCATTTTCGT 57.317 34.783 0.00 0.00 0.00 3.85
3079 3375 6.546395 AGATCGATGAACTTTTCCATTTTCG 58.454 36.000 0.54 0.00 0.00 3.46
3080 3376 8.023128 TGAAGATCGATGAACTTTTCCATTTTC 58.977 33.333 0.54 0.00 0.00 2.29
3081 3377 7.885297 TGAAGATCGATGAACTTTTCCATTTT 58.115 30.769 0.54 0.00 0.00 1.82
3082 3378 7.452880 TGAAGATCGATGAACTTTTCCATTT 57.547 32.000 0.54 0.00 0.00 2.32
3083 3379 7.452880 TTGAAGATCGATGAACTTTTCCATT 57.547 32.000 0.54 0.00 0.00 3.16
3084 3380 7.452880 TTTGAAGATCGATGAACTTTTCCAT 57.547 32.000 0.54 0.00 0.00 3.41
3085 3381 6.875948 TTTGAAGATCGATGAACTTTTCCA 57.124 33.333 0.54 0.00 0.00 3.53
3086 3382 9.495754 CTATTTTGAAGATCGATGAACTTTTCC 57.504 33.333 0.54 0.00 0.00 3.13
3090 3386 9.219603 TGAACTATTTTGAAGATCGATGAACTT 57.780 29.630 0.54 0.00 0.00 2.66
3091 3387 8.777865 TGAACTATTTTGAAGATCGATGAACT 57.222 30.769 0.54 0.00 0.00 3.01
3092 3388 9.643652 GATGAACTATTTTGAAGATCGATGAAC 57.356 33.333 0.54 0.00 0.00 3.18
3093 3389 8.542953 CGATGAACTATTTTGAAGATCGATGAA 58.457 33.333 0.54 0.00 34.75 2.57
3094 3390 7.169813 CCGATGAACTATTTTGAAGATCGATGA 59.830 37.037 0.54 0.00 34.75 2.92
3095 3391 7.042456 ACCGATGAACTATTTTGAAGATCGATG 60.042 37.037 0.54 0.00 34.75 3.84
3096 3392 6.986817 ACCGATGAACTATTTTGAAGATCGAT 59.013 34.615 0.00 0.00 34.75 3.59
3097 3393 6.338146 ACCGATGAACTATTTTGAAGATCGA 58.662 36.000 0.00 0.00 34.75 3.59
3098 3394 6.589830 ACCGATGAACTATTTTGAAGATCG 57.410 37.500 0.00 0.00 33.06 3.69
3099 3395 9.065871 CAAAACCGATGAACTATTTTGAAGATC 57.934 33.333 2.36 0.00 40.89 2.75
3100 3396 8.028938 CCAAAACCGATGAACTATTTTGAAGAT 58.971 33.333 8.84 0.00 40.89 2.40
3101 3397 7.229707 TCCAAAACCGATGAACTATTTTGAAGA 59.770 33.333 8.84 0.00 40.89 2.87
3102 3398 7.367285 TCCAAAACCGATGAACTATTTTGAAG 58.633 34.615 8.84 0.00 40.89 3.02
3103 3399 7.278461 TCCAAAACCGATGAACTATTTTGAA 57.722 32.000 8.84 0.00 40.89 2.69
3104 3400 6.885952 TCCAAAACCGATGAACTATTTTGA 57.114 33.333 8.84 0.00 40.89 2.69
3105 3401 7.938563 TTTCCAAAACCGATGAACTATTTTG 57.061 32.000 0.00 0.00 39.08 2.44
3106 3402 8.950208 TTTTTCCAAAACCGATGAACTATTTT 57.050 26.923 0.00 0.00 0.00 1.82
3107 3403 8.201464 ACTTTTTCCAAAACCGATGAACTATTT 58.799 29.630 0.00 0.00 0.00 1.40
3108 3404 7.722363 ACTTTTTCCAAAACCGATGAACTATT 58.278 30.769 0.00 0.00 0.00 1.73
3109 3405 7.284919 ACTTTTTCCAAAACCGATGAACTAT 57.715 32.000 0.00 0.00 0.00 2.12
3110 3406 6.702716 ACTTTTTCCAAAACCGATGAACTA 57.297 33.333 0.00 0.00 0.00 2.24
3111 3407 5.592104 ACTTTTTCCAAAACCGATGAACT 57.408 34.783 0.00 0.00 0.00 3.01
3112 3408 5.808030 TGAACTTTTTCCAAAACCGATGAAC 59.192 36.000 0.00 0.00 0.00 3.18
3113 3409 5.967088 TGAACTTTTTCCAAAACCGATGAA 58.033 33.333 0.00 0.00 0.00 2.57
3114 3410 5.584253 TGAACTTTTTCCAAAACCGATGA 57.416 34.783 0.00 0.00 0.00 2.92
3115 3411 6.478344 TGAATGAACTTTTTCCAAAACCGATG 59.522 34.615 0.00 0.00 0.00 3.84
3116 3412 6.578023 TGAATGAACTTTTTCCAAAACCGAT 58.422 32.000 0.00 0.00 0.00 4.18
3117 3413 5.967088 TGAATGAACTTTTTCCAAAACCGA 58.033 33.333 0.00 0.00 0.00 4.69
3118 3414 6.843069 ATGAATGAACTTTTTCCAAAACCG 57.157 33.333 0.00 0.00 0.00 4.44
3119 3415 8.672815 TCAAATGAATGAACTTTTTCCAAAACC 58.327 29.630 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.