Multiple sequence alignment - TraesCS4D01G069800

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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 TraesCS4D01G069800 chr4D 100.000 7116 0 0 1 7116 44977234 44984349 0.000000e+00 13141.0
1 TraesCS4D01G069800 chr4B 94.779 6033 196 60 169 6158 64799567 64805523 0.000000e+00 9286.0
2 TraesCS4D01G069800 chr4B 88.783 838 60 12 6298 7116 64824791 64825613 0.000000e+00 996.0
3 TraesCS4D01G069800 chr4B 88.305 838 64 12 6298 7116 65162332 65163154 0.000000e+00 974.0
4 TraesCS4D01G069800 chr4B 87.470 846 64 16 6298 7116 65113039 65113869 0.000000e+00 937.0
5 TraesCS4D01G069800 chr4B 87.470 846 64 16 6298 7116 65540311 65541141 0.000000e+00 937.0
6 TraesCS4D01G069800 chr4B 85.977 870 64 25 6255 7116 65618129 65618948 0.000000e+00 878.0
7 TraesCS4D01G069800 chr4B 85.174 688 57 23 6446 7116 64806057 64806716 0.000000e+00 664.0
8 TraesCS4D01G069800 chr4B 94.000 250 10 4 6156 6403 64805678 64805924 2.420000e-99 374.0
9 TraesCS4D01G069800 chr4B 97.674 86 2 0 6160 6245 64808899 64808984 1.600000e-31 148.0
10 TraesCS4D01G069800 chr4B 97.674 86 2 0 6160 6245 65115964 65116049 1.600000e-31 148.0
11 TraesCS4D01G069800 chr4B 80.537 149 28 1 4 151 481582151 481582003 5.830000e-21 113.0
12 TraesCS4D01G069800 chr4B 100.000 43 0 0 6160 6202 65094943 65094985 5.920000e-11 80.5
13 TraesCS4D01G069800 chr4B 100.000 43 0 0 6160 6202 65523551 65523593 5.920000e-11 80.5
14 TraesCS4D01G069800 chr4A 90.082 2813 221 38 149 2929 554638643 554635857 0.000000e+00 3596.0
15 TraesCS4D01G069800 chr4A 93.036 2312 108 24 4838 7116 554634029 554631738 0.000000e+00 3328.0
16 TraesCS4D01G069800 chr4A 87.263 1688 122 41 3159 4778 554635859 554634197 0.000000e+00 1840.0
17 TraesCS4D01G069800 chr4A 87.667 300 23 5 6684 6969 554558122 554557823 3.180000e-88 337.0
18 TraesCS4D01G069800 chr1D 84.499 1058 162 2 5071 6127 458828678 458829734 0.000000e+00 1044.0
19 TraesCS4D01G069800 chr1D 81.423 253 33 10 2493 2733 458825883 458826133 2.030000e-45 195.0
20 TraesCS4D01G069800 chr1B 84.117 1064 161 4 5071 6127 630709506 630710568 0.000000e+00 1022.0
21 TraesCS4D01G069800 chr1B 95.541 157 7 0 1 157 613243684 613243840 1.180000e-62 252.0
22 TraesCS4D01G069800 chr1B 94.805 154 8 0 4 157 282284325 282284172 2.570000e-59 241.0
23 TraesCS4D01G069800 chr1B 82.979 235 28 8 2493 2716 630706675 630706908 1.210000e-47 202.0
24 TraesCS4D01G069800 chrUn 87.470 846 64 16 6298 7116 309937694 309938524 0.000000e+00 937.0
25 TraesCS4D01G069800 chrUn 97.674 86 2 0 6160 6245 416652427 416652512 1.600000e-31 148.0
26 TraesCS4D01G069800 chr1A 85.216 602 65 12 5071 5671 551299574 551300152 1.320000e-166 597.0
27 TraesCS4D01G069800 chr1A 83.200 250 32 8 2476 2716 551284128 551284376 3.340000e-53 220.0


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 TraesCS4D01G069800 chr4D 44977234 44984349 7115 False 13141.000000 13141 100.00000 1 7116 1 chr4D.!!$F1 7115
1 TraesCS4D01G069800 chr4B 64799567 64808984 9417 False 2618.000000 9286 92.90675 169 7116 4 chr4B.!!$F7 6947
2 TraesCS4D01G069800 chr4B 64824791 64825613 822 False 996.000000 996 88.78300 6298 7116 1 chr4B.!!$F1 818
3 TraesCS4D01G069800 chr4B 65162332 65163154 822 False 974.000000 974 88.30500 6298 7116 1 chr4B.!!$F3 818
4 TraesCS4D01G069800 chr4B 65540311 65541141 830 False 937.000000 937 87.47000 6298 7116 1 chr4B.!!$F5 818
5 TraesCS4D01G069800 chr4B 65618129 65618948 819 False 878.000000 878 85.97700 6255 7116 1 chr4B.!!$F6 861
6 TraesCS4D01G069800 chr4B 65113039 65116049 3010 False 542.500000 937 92.57200 6160 7116 2 chr4B.!!$F8 956
7 TraesCS4D01G069800 chr4A 554631738 554638643 6905 True 2921.333333 3596 90.12700 149 7116 3 chr4A.!!$R2 6967
8 TraesCS4D01G069800 chr1D 458825883 458829734 3851 False 619.500000 1044 82.96100 2493 6127 2 chr1D.!!$F1 3634
9 TraesCS4D01G069800 chr1B 630706675 630710568 3893 False 612.000000 1022 83.54800 2493 6127 2 chr1B.!!$F2 3634
10 TraesCS4D01G069800 chrUn 309937694 309938524 830 False 937.000000 937 87.47000 6298 7116 1 chrUn.!!$F1 818
11 TraesCS4D01G069800 chr1A 551299574 551300152 578 False 597.000000 597 85.21600 5071 5671 1 chr1A.!!$F2 600

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
143 144 0.108756 GTCGCGAGGCTCCTAAGTTT 60.109 55.000 10.24 0.0 0.00 2.66 F
144 145 0.172803 TCGCGAGGCTCCTAAGTTTC 59.827 55.000 3.71 0.0 0.00 2.78 F
147 148 0.179108 CGAGGCTCCTAAGTTTCCGG 60.179 60.000 9.32 0.0 0.00 5.14 F
2038 2074 0.109458 TTACGCAGCGAGTGGTAGTG 60.109 55.000 24.65 0.0 0.00 2.74 F
3198 3522 0.322456 TTGCCTTCCTGTCGGGATTG 60.322 55.000 0.00 0.0 44.66 2.67 F
3469 3820 0.923729 TGTAGGGGGAGTACGGGGTA 60.924 60.000 0.00 0.0 0.00 3.69 F
3831 4201 1.083489 GCAGCGCCTAATTGTGTGTA 58.917 50.000 2.29 0.0 0.00 2.90 F
4754 5570 4.032445 GCGATGTGCTGATTCGTACTTAAA 59.968 41.667 0.00 0.0 41.73 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1009 1031 0.115745 TTGGGGTCTTCCTCGGTAGT 59.884 55.000 0.00 0.0 36.91 2.73 R
2037 2073 1.669760 GAAATGTCGACACCGCCCA 60.670 57.895 22.71 0.0 35.37 5.36 R
2128 2166 2.974794 CTGGATCATGTAGGGATGGTGA 59.025 50.000 0.00 0.0 0.00 4.02 R
3286 3614 0.608640 CCGGTTGACTACTTCCTGCT 59.391 55.000 0.00 0.0 0.00 4.24 R
4723 5539 0.179127 TCAGCACATCGCAGTAGCTC 60.179 55.000 0.00 0.0 46.13 4.09 R
5254 6282 0.878416 GGCCAATGACAGCGTTGTAA 59.122 50.000 4.38 0.0 38.97 2.41 R
5356 6384 1.210155 GAATGCAACAGCCGTCACC 59.790 57.895 0.00 0.0 0.00 4.02 R
6658 7963 0.034756 CACCCACCACAGATCGTTGA 59.965 55.000 0.00 0.0 0.00 3.18 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
17 18 2.435059 GGTGAGAGTGCGCCTTCC 60.435 66.667 4.18 0.00 35.56 3.46
18 19 2.659610 GTGAGAGTGCGCCTTCCT 59.340 61.111 4.18 0.00 0.00 3.36
19 20 1.004440 GTGAGAGTGCGCCTTCCTT 60.004 57.895 4.18 0.00 0.00 3.36
20 21 1.004560 TGAGAGTGCGCCTTCCTTG 60.005 57.895 4.18 0.00 0.00 3.61
21 22 2.359230 AGAGTGCGCCTTCCTTGC 60.359 61.111 4.18 0.00 0.00 4.01
22 23 3.435186 GAGTGCGCCTTCCTTGCC 61.435 66.667 4.18 0.00 0.00 4.52
23 24 4.269523 AGTGCGCCTTCCTTGCCA 62.270 61.111 4.18 0.00 0.00 4.92
24 25 3.064324 GTGCGCCTTCCTTGCCAT 61.064 61.111 4.18 0.00 0.00 4.40
25 26 2.283101 TGCGCCTTCCTTGCCATT 60.283 55.556 4.18 0.00 0.00 3.16
26 27 2.182537 GCGCCTTCCTTGCCATTG 59.817 61.111 0.00 0.00 0.00 2.82
27 28 2.182537 CGCCTTCCTTGCCATTGC 59.817 61.111 0.00 0.00 38.26 3.56
28 29 2.580815 GCCTTCCTTGCCATTGCC 59.419 61.111 0.00 0.00 36.33 4.52
29 30 2.285024 GCCTTCCTTGCCATTGCCA 61.285 57.895 0.00 0.00 36.33 4.92
30 31 1.895238 CCTTCCTTGCCATTGCCAG 59.105 57.895 0.00 0.00 36.33 4.85
31 32 1.217244 CTTCCTTGCCATTGCCAGC 59.783 57.895 0.00 0.00 36.33 4.85
32 33 2.552585 CTTCCTTGCCATTGCCAGCG 62.553 60.000 0.00 0.00 36.33 5.18
33 34 4.807039 CCTTGCCATTGCCAGCGC 62.807 66.667 0.00 0.00 36.33 5.92
34 35 4.807039 CTTGCCATTGCCAGCGCC 62.807 66.667 2.29 0.00 36.33 6.53
38 39 2.831742 CCATTGCCAGCGCCAGAT 60.832 61.111 2.29 0.00 0.00 2.90
39 40 2.411701 CATTGCCAGCGCCAGATG 59.588 61.111 2.29 0.00 0.00 2.90
40 41 3.524606 ATTGCCAGCGCCAGATGC 61.525 61.111 2.29 0.00 31.28 3.91
42 43 4.807631 TGCCAGCGCCAGATGCAT 62.808 61.111 2.29 0.00 41.33 3.96
43 44 3.962421 GCCAGCGCCAGATGCATC 61.962 66.667 19.37 19.37 41.33 3.91
44 45 3.285215 CCAGCGCCAGATGCATCC 61.285 66.667 23.06 7.42 41.33 3.51
45 46 2.515290 CAGCGCCAGATGCATCCA 60.515 61.111 23.06 0.00 41.33 3.41
46 47 1.897137 CAGCGCCAGATGCATCCAT 60.897 57.895 23.06 2.49 41.33 3.41
47 48 1.600076 AGCGCCAGATGCATCCATC 60.600 57.895 23.06 10.82 46.61 3.51
53 54 4.937781 GATGCATCCATCTTGCGC 57.062 55.556 16.23 0.00 43.62 6.09
54 55 1.285023 GATGCATCCATCTTGCGCC 59.715 57.895 16.23 0.00 43.62 6.53
55 56 2.453773 GATGCATCCATCTTGCGCCG 62.454 60.000 16.23 0.00 43.62 6.46
56 57 4.619140 GCATCCATCTTGCGCCGC 62.619 66.667 4.18 0.00 0.00 6.53
57 58 3.957535 CATCCATCTTGCGCCGCC 61.958 66.667 6.63 0.00 0.00 6.13
77 78 3.564027 CAAAGCGCCCCGTCGATC 61.564 66.667 2.29 0.00 0.00 3.69
78 79 4.077184 AAAGCGCCCCGTCGATCA 62.077 61.111 2.29 0.00 0.00 2.92
79 80 3.599285 AAAGCGCCCCGTCGATCAA 62.599 57.895 2.29 0.00 0.00 2.57
80 81 4.514577 AGCGCCCCGTCGATCAAG 62.515 66.667 2.29 0.00 0.00 3.02
81 82 4.508128 GCGCCCCGTCGATCAAGA 62.508 66.667 0.00 0.00 0.00 3.02
82 83 2.417516 CGCCCCGTCGATCAAGAT 59.582 61.111 0.00 0.00 0.00 2.40
83 84 1.661821 CGCCCCGTCGATCAAGATC 60.662 63.158 0.00 0.00 34.56 2.75
92 93 2.208074 GATCAAGATCGGACGTGCG 58.792 57.895 24.40 24.40 0.00 5.34
93 94 1.812214 GATCAAGATCGGACGTGCGC 61.812 60.000 25.53 11.90 0.00 6.09
94 95 3.554692 CAAGATCGGACGTGCGCC 61.555 66.667 25.53 17.93 0.00 6.53
116 117 2.037687 TCGCCCCTCGAAACCCTA 59.962 61.111 0.00 0.00 45.36 3.53
117 118 2.056223 TCGCCCCTCGAAACCCTAG 61.056 63.158 0.00 0.00 45.36 3.02
118 119 2.356780 CGCCCCTCGAAACCCTAGT 61.357 63.158 0.00 0.00 41.67 2.57
119 120 1.521141 GCCCCTCGAAACCCTAGTC 59.479 63.158 0.00 0.00 0.00 2.59
120 121 1.814527 CCCCTCGAAACCCTAGTCG 59.185 63.158 0.00 0.00 38.62 4.18
121 122 1.141234 CCCTCGAAACCCTAGTCGC 59.859 63.158 0.00 0.00 37.19 5.19
122 123 1.141234 CCTCGAAACCCTAGTCGCC 59.859 63.158 0.00 0.00 37.19 5.54
123 124 1.321074 CCTCGAAACCCTAGTCGCCT 61.321 60.000 0.00 0.00 37.19 5.52
124 125 0.179134 CTCGAAACCCTAGTCGCCTG 60.179 60.000 0.00 0.00 37.19 4.85
125 126 0.896940 TCGAAACCCTAGTCGCCTGT 60.897 55.000 0.00 0.00 37.19 4.00
126 127 0.458025 CGAAACCCTAGTCGCCTGTC 60.458 60.000 0.00 0.00 0.00 3.51
127 128 0.458025 GAAACCCTAGTCGCCTGTCG 60.458 60.000 0.00 0.00 40.15 4.35
128 129 2.502692 AAACCCTAGTCGCCTGTCGC 62.503 60.000 0.00 0.00 38.27 5.19
138 139 2.829003 CCTGTCGCGAGGCTCCTA 60.829 66.667 10.24 0.00 36.07 2.94
139 140 2.415608 CCTGTCGCGAGGCTCCTAA 61.416 63.158 10.24 0.00 36.07 2.69
140 141 1.064946 CTGTCGCGAGGCTCCTAAG 59.935 63.158 10.24 0.00 36.07 2.18
141 142 1.658686 CTGTCGCGAGGCTCCTAAGT 61.659 60.000 10.24 0.00 36.07 2.24
142 143 1.248785 TGTCGCGAGGCTCCTAAGTT 61.249 55.000 10.24 0.00 36.07 2.66
143 144 0.108756 GTCGCGAGGCTCCTAAGTTT 60.109 55.000 10.24 0.00 0.00 2.66
144 145 0.172803 TCGCGAGGCTCCTAAGTTTC 59.827 55.000 3.71 0.00 0.00 2.78
145 146 0.806492 CGCGAGGCTCCTAAGTTTCC 60.806 60.000 9.32 0.00 0.00 3.13
146 147 0.806492 GCGAGGCTCCTAAGTTTCCG 60.806 60.000 9.32 0.00 0.00 4.30
147 148 0.179108 CGAGGCTCCTAAGTTTCCGG 60.179 60.000 9.32 0.00 0.00 5.14
257 259 3.766591 CACCACAATGTTTAGGCCCATTA 59.233 43.478 0.00 0.00 30.41 1.90
258 260 4.405358 CACCACAATGTTTAGGCCCATTAT 59.595 41.667 0.00 0.00 30.41 1.28
265 267 7.038373 ACAATGTTTAGGCCCATTATGTTTCTT 60.038 33.333 0.00 0.00 30.41 2.52
464 473 2.210013 CCATAGGCCCTCGCTAGCA 61.210 63.158 16.45 0.92 34.44 3.49
486 495 2.669569 CGCCACCACACTCCCTTG 60.670 66.667 0.00 0.00 0.00 3.61
645 663 0.397564 TGTCTGCATGCCTCTTGTGA 59.602 50.000 16.68 0.00 0.00 3.58
649 667 1.134367 CTGCATGCCTCTTGTGATTGG 59.866 52.381 16.68 0.00 0.00 3.16
657 675 1.394917 CTCTTGTGATTGGCGCTACAC 59.605 52.381 7.64 7.52 0.00 2.90
677 695 6.579666 ACACATTCAAGATGTTATGCTGTT 57.420 33.333 0.00 0.00 0.00 3.16
701 719 6.463995 AAAAACTGAAACACAATCCTGCTA 57.536 33.333 0.00 0.00 0.00 3.49
735 755 5.396654 GTCTGAAACTGAAAATCTGCGTTTC 59.603 40.000 0.00 0.00 42.11 2.78
750 770 4.130857 TGCGTTTCCATGTTCTGTAGAAA 58.869 39.130 0.00 0.00 35.58 2.52
772 792 9.292195 AGAAATTTCGGTTTTACTATTTCAGGA 57.708 29.630 12.42 0.00 35.51 3.86
867 887 4.142609 CTTCCAGTAGAAGCCATGCTAA 57.857 45.455 0.00 0.00 45.38 3.09
882 902 3.302365 TGCTAAAAGAATGTTGCTGCC 57.698 42.857 0.00 0.00 0.00 4.85
926 946 3.194005 TGATATCCCCTCGAGTTTTGC 57.806 47.619 12.31 0.00 0.00 3.68
927 947 2.158813 TGATATCCCCTCGAGTTTTGCC 60.159 50.000 12.31 0.00 0.00 4.52
985 1006 2.937149 GTCTCGCCATTTCTACTTTCCC 59.063 50.000 0.00 0.00 0.00 3.97
986 1007 2.569853 TCTCGCCATTTCTACTTTCCCA 59.430 45.455 0.00 0.00 0.00 4.37
988 1009 2.304761 TCGCCATTTCTACTTTCCCACT 59.695 45.455 0.00 0.00 0.00 4.00
1009 1031 1.348008 GGTGAGCAGGATGGGGATCA 61.348 60.000 0.00 0.00 35.86 2.92
1023 1045 1.682323 GGGATCACTACCGAGGAAGAC 59.318 57.143 0.00 0.00 0.00 3.01
1123 1145 3.129109 GCTAACTTGGCGGTAGGATAAC 58.871 50.000 0.00 0.00 0.00 1.89
1161 1183 4.806225 CGTTGAAGTTCAGCGCTG 57.194 55.556 31.53 31.53 43.48 5.18
1187 1218 4.921470 CTTTGCTGATTGAAAAGCATGG 57.079 40.909 6.74 0.92 43.65 3.66
1188 1219 4.312443 CTTTGCTGATTGAAAAGCATGGT 58.688 39.130 6.74 0.00 43.65 3.55
1408 1444 8.935614 ATAACAGTGATCATGATTTGATGGAT 57.064 30.769 10.14 3.21 45.29 3.41
1421 1457 6.263842 TGATTTGATGGATTCTGGTATTCTGC 59.736 38.462 0.00 0.00 0.00 4.26
1791 1827 5.565592 TTGCATGAACTTATGGTGCTTAG 57.434 39.130 0.00 0.00 36.78 2.18
2028 2064 5.859114 AGAAGACATATAGATTTACGCAGCG 59.141 40.000 14.82 14.82 0.00 5.18
2030 2066 5.394802 AGACATATAGATTTACGCAGCGAG 58.605 41.667 24.65 0.00 0.00 5.03
2031 2067 5.048643 AGACATATAGATTTACGCAGCGAGT 60.049 40.000 24.65 1.58 0.00 4.18
2033 2069 2.203800 TAGATTTACGCAGCGAGTGG 57.796 50.000 24.65 0.00 0.00 4.00
2037 2073 0.599558 TTTACGCAGCGAGTGGTAGT 59.400 50.000 24.65 0.00 0.00 2.73
2038 2074 0.109458 TTACGCAGCGAGTGGTAGTG 60.109 55.000 24.65 0.00 0.00 2.74
2043 2079 4.814294 GCGAGTGGTAGTGGGCGG 62.814 72.222 0.00 0.00 0.00 6.13
2128 2166 2.988010 TGTGTTCTCTGAAGCTGTGT 57.012 45.000 0.00 0.00 0.00 3.72
2136 2174 1.002430 TCTGAAGCTGTGTCACCATCC 59.998 52.381 0.00 0.00 0.00 3.51
2461 2500 4.456280 TTCTGTGCTCGTATGTTCTGAT 57.544 40.909 0.00 0.00 0.00 2.90
2757 2834 5.968175 TTGGAACACATTCACCATTTGAAGC 60.968 40.000 0.00 0.00 43.45 3.86
2811 2889 7.675062 CAAGCCTGGTCTAGTATGATCTTAAT 58.325 38.462 0.00 0.00 0.00 1.40
2814 2893 8.371699 AGCCTGGTCTAGTATGATCTTAATTTC 58.628 37.037 0.00 0.00 0.00 2.17
2842 2922 9.116067 AGTCAAAATGCAGTTGTAGTAAAAGTA 57.884 29.630 0.00 0.00 0.00 2.24
2891 2980 4.983671 ACAGAAGGTTTGAGTTTGGTTC 57.016 40.909 0.00 0.00 0.00 3.62
3054 3158 1.225704 GGATGTTGAGGGCAGGGAG 59.774 63.158 0.00 0.00 0.00 4.30
3068 3173 2.962421 GCAGGGAGCTAGATCTAGTTGT 59.038 50.000 26.73 14.46 41.15 3.32
3074 3179 5.065346 GGGAGCTAGATCTAGTTGTTTTTGC 59.935 44.000 26.73 12.83 35.65 3.68
3123 3429 6.672147 CGGCTAAAATTCAGATCAAATAGGG 58.328 40.000 0.00 0.00 0.00 3.53
3142 3448 3.813724 AGGGCGAGTTCAGTTTAGTTTTC 59.186 43.478 0.00 0.00 0.00 2.29
3198 3522 0.322456 TTGCCTTCCTGTCGGGATTG 60.322 55.000 0.00 0.00 44.66 2.67
3286 3614 2.270850 GCGGCCACCTGGAACATA 59.729 61.111 2.24 0.00 38.20 2.29
3298 3634 3.452627 CCTGGAACATAGCAGGAAGTAGT 59.547 47.826 0.00 0.00 38.20 2.73
3348 3684 3.812053 GCATGTGAGGGCTAGAATTACAG 59.188 47.826 0.00 0.00 0.00 2.74
3463 3814 1.673808 CGTGGCTGTAGGGGGAGTAC 61.674 65.000 0.00 0.00 0.00 2.73
3469 3820 0.923729 TGTAGGGGGAGTACGGGGTA 60.924 60.000 0.00 0.00 0.00 3.69
3504 3855 5.379187 TGTTCTCATGTCATGAATATGGGG 58.621 41.667 16.20 3.66 39.11 4.96
3516 3867 4.882559 TGAATATGGGGGATTTCTTGCTT 58.117 39.130 0.00 0.00 0.00 3.91
3537 3888 2.263545 GTGTGGGACCCTACCTTTACT 58.736 52.381 13.00 0.00 0.00 2.24
3597 3948 4.503123 CCCAATCGTCCACATATCTGCTAA 60.503 45.833 0.00 0.00 0.00 3.09
3671 4030 1.179152 TCGTAATTCTCCTCGTGCCA 58.821 50.000 0.00 0.00 0.00 4.92
3831 4201 1.083489 GCAGCGCCTAATTGTGTGTA 58.917 50.000 2.29 0.00 0.00 2.90
3930 4417 5.422331 CCTGGTCAAATCCTACTCTTGTCTA 59.578 44.000 0.00 0.00 0.00 2.59
4183 4718 7.441836 TCAACATGTTTCTTCTGCTAGTCTTA 58.558 34.615 8.77 0.00 0.00 2.10
4184 4719 7.600375 TCAACATGTTTCTTCTGCTAGTCTTAG 59.400 37.037 8.77 0.00 0.00 2.18
4197 4732 5.646577 CTAGTCTTAGCTGTTACCACACT 57.353 43.478 0.00 0.00 0.00 3.55
4198 4733 6.754702 CTAGTCTTAGCTGTTACCACACTA 57.245 41.667 0.00 0.00 0.00 2.74
4199 4734 7.336161 CTAGTCTTAGCTGTTACCACACTAT 57.664 40.000 0.00 0.00 0.00 2.12
4754 5570 4.032445 GCGATGTGCTGATTCGTACTTAAA 59.968 41.667 0.00 0.00 41.73 1.52
5254 6282 4.141482 ACAGATGTTATGCGGGTAAATCCT 60.141 41.667 0.00 0.00 36.25 3.24
5383 6411 1.372087 CTGTTGCATTCGAGAGGGGC 61.372 60.000 0.00 0.00 0.00 5.80
6046 7080 4.225497 GGGCATCCCGACAAGAAG 57.775 61.111 0.00 0.00 32.13 2.85
6129 7163 9.661187 CAAGCAATCATGATCTTGTTTATCTAC 57.339 33.333 21.04 1.79 33.27 2.59
6133 7167 7.976135 ATCATGATCTTGTTTATCTACCAGC 57.024 36.000 1.18 0.00 0.00 4.85
6139 7173 5.865085 TCTTGTTTATCTACCAGCTTGTGT 58.135 37.500 0.00 0.00 0.00 3.72
6143 7177 5.238432 TGTTTATCTACCAGCTTGTGTTGTG 59.762 40.000 0.00 0.00 0.00 3.33
6144 7178 3.492102 ATCTACCAGCTTGTGTTGTGT 57.508 42.857 0.00 0.00 0.00 3.72
6145 7179 4.617253 ATCTACCAGCTTGTGTTGTGTA 57.383 40.909 0.00 0.00 0.00 2.90
6146 7180 3.990092 TCTACCAGCTTGTGTTGTGTAG 58.010 45.455 0.00 0.00 33.75 2.74
6149 7183 2.170607 ACCAGCTTGTGTTGTGTAGTCT 59.829 45.455 0.00 0.00 0.00 3.24
6150 7184 3.386726 ACCAGCTTGTGTTGTGTAGTCTA 59.613 43.478 0.00 0.00 0.00 2.59
6151 7185 4.040461 ACCAGCTTGTGTTGTGTAGTCTAT 59.960 41.667 0.00 0.00 0.00 1.98
6152 7186 4.627467 CCAGCTTGTGTTGTGTAGTCTATC 59.373 45.833 0.00 0.00 0.00 2.08
6207 7401 1.270785 ACATGCCACATGAGACAACGA 60.271 47.619 14.17 0.00 0.00 3.85
6218 7412 2.289444 TGAGACAACGATGGGAAAGGAC 60.289 50.000 0.00 0.00 0.00 3.85
6361 7559 0.536460 TGGTGGAGCCTTTTCGGTTC 60.536 55.000 0.00 0.00 41.90 3.62
6372 7570 1.956297 TTTCGGTTCGGTGTCAACAT 58.044 45.000 0.00 0.00 0.00 2.71
6380 7578 5.050227 CGGTTCGGTGTCAACATAACTTTAA 60.050 40.000 3.79 0.00 0.00 1.52
6405 7603 4.558178 TGCAAGTTCCATGTGCATTTTAG 58.442 39.130 3.97 0.00 43.09 1.85
6408 7606 5.771469 CAAGTTCCATGTGCATTTTAGTGA 58.229 37.500 0.00 0.00 0.00 3.41
6410 7608 6.594788 AGTTCCATGTGCATTTTAGTGATT 57.405 33.333 0.00 0.00 0.00 2.57
6412 7610 5.233957 TCCATGTGCATTTTAGTGATTCG 57.766 39.130 0.00 0.00 0.00 3.34
6413 7611 4.940654 TCCATGTGCATTTTAGTGATTCGA 59.059 37.500 0.00 0.00 0.00 3.71
6414 7612 5.414144 TCCATGTGCATTTTAGTGATTCGAA 59.586 36.000 0.00 0.00 0.00 3.71
6451 7739 2.553028 CCACACTGGGAATGCTACAACT 60.553 50.000 0.00 0.00 32.67 3.16
6480 7775 6.783708 TGTGTTTGGTTCAGAAAAGGTTAT 57.216 33.333 0.00 0.00 0.00 1.89
6535 7830 7.497249 GCTCTCTTCCATTTGTAAGTATGATGT 59.503 37.037 0.00 0.00 0.00 3.06
6545 7840 7.987750 TTGTAAGTATGATGTAACAAGCCAA 57.012 32.000 0.00 0.00 0.00 4.52
6552 7847 3.951037 TGATGTAACAAGCCAACAACTGT 59.049 39.130 0.00 0.00 0.00 3.55
6658 7963 0.235665 CACACGCGTGCAGAAAGAAT 59.764 50.000 37.35 13.37 36.06 2.40
6761 8068 5.756195 TCAGATCCAAGTGTGTCAAAAAG 57.244 39.130 0.00 0.00 0.00 2.27
6796 8108 5.534278 TGTATGGATGTTCACAACACATGTT 59.466 36.000 0.00 0.00 45.50 2.71
6801 8113 5.685511 GGATGTTCACAACACATGTTTACAC 59.314 40.000 0.00 0.00 45.50 2.90
6812 8125 9.050601 CAACACATGTTTACACCCAATAAAAAT 57.949 29.630 0.00 0.00 35.83 1.82
6906 8224 8.895737 AGGACAAAAATAAAAACTCGACACTAA 58.104 29.630 0.00 0.00 0.00 2.24
6926 8244 2.247358 ACCATGCCGGATTTGTCTTTT 58.753 42.857 5.05 0.00 38.63 2.27
6940 8261 7.596621 GGATTTGTCTTTTCATTTCTCTTGGAC 59.403 37.037 0.00 0.00 0.00 4.02
6953 8274 6.935741 TTCTCTTGGACTTCGAATTTTGAA 57.064 33.333 0.00 0.00 0.00 2.69
6960 8281 8.885494 TTGGACTTCGAATTTTGAATTGAATT 57.115 26.923 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.435059 GGAAGGCGCACTCTCACC 60.435 66.667 10.83 1.28 0.00 4.02
3 4 2.394563 GCAAGGAAGGCGCACTCTC 61.395 63.158 10.83 0.00 0.00 3.20
4 5 2.359230 GCAAGGAAGGCGCACTCT 60.359 61.111 10.83 0.00 0.00 3.24
5 6 3.435186 GGCAAGGAAGGCGCACTC 61.435 66.667 10.83 4.29 0.00 3.51
6 7 3.574074 ATGGCAAGGAAGGCGCACT 62.574 57.895 10.83 0.02 36.77 4.40
7 8 2.639327 AATGGCAAGGAAGGCGCAC 61.639 57.895 10.83 0.00 36.77 5.34
8 9 2.283101 AATGGCAAGGAAGGCGCA 60.283 55.556 10.83 0.00 36.77 6.09
9 10 2.182537 CAATGGCAAGGAAGGCGC 59.817 61.111 0.00 0.00 36.77 6.53
10 11 2.182537 GCAATGGCAAGGAAGGCG 59.817 61.111 0.00 0.00 40.72 5.52
11 12 2.234913 CTGGCAATGGCAAGGAAGGC 62.235 60.000 11.45 0.00 43.71 4.35
12 13 1.895238 CTGGCAATGGCAAGGAAGG 59.105 57.895 11.45 0.00 43.71 3.46
13 14 1.217244 GCTGGCAATGGCAAGGAAG 59.783 57.895 11.45 0.00 41.71 3.46
14 15 2.638354 CGCTGGCAATGGCAAGGAA 61.638 57.895 11.45 0.00 41.71 3.36
15 16 3.063704 CGCTGGCAATGGCAAGGA 61.064 61.111 11.45 0.00 41.71 3.36
16 17 4.807039 GCGCTGGCAATGGCAAGG 62.807 66.667 11.45 6.67 41.71 3.61
17 18 4.807039 GGCGCTGGCAATGGCAAG 62.807 66.667 11.45 9.12 44.45 4.01
21 22 2.831742 ATCTGGCGCTGGCAATGG 60.832 61.111 7.64 0.00 42.47 3.16
22 23 2.411701 CATCTGGCGCTGGCAATG 59.588 61.111 7.64 0.83 42.47 2.82
23 24 3.524606 GCATCTGGCGCTGGCAAT 61.525 61.111 7.64 0.00 42.47 3.56
31 32 3.332242 GCAAGATGGATGCATCTGGCG 62.332 57.143 32.85 22.77 45.38 5.69
33 34 0.591659 CGCAAGATGGATGCATCTGG 59.408 55.000 27.93 25.70 44.01 3.86
34 35 0.040336 GCGCAAGATGGATGCATCTG 60.040 55.000 27.93 21.40 44.01 2.90
35 36 1.170919 GGCGCAAGATGGATGCATCT 61.171 55.000 22.75 22.75 44.01 2.90
36 37 1.285023 GGCGCAAGATGGATGCATC 59.715 57.895 18.73 18.73 44.01 3.91
37 38 2.549198 CGGCGCAAGATGGATGCAT 61.549 57.895 10.83 0.00 44.01 3.96
38 39 3.204119 CGGCGCAAGATGGATGCA 61.204 61.111 10.83 0.00 44.01 3.96
39 40 4.619140 GCGGCGCAAGATGGATGC 62.619 66.667 29.21 0.00 43.02 3.91
40 41 3.957535 GGCGGCGCAAGATGGATG 61.958 66.667 34.36 0.00 43.02 3.51
60 61 3.564027 GATCGACGGGGCGCTTTG 61.564 66.667 7.64 0.00 0.00 2.77
61 62 3.599285 TTGATCGACGGGGCGCTTT 62.599 57.895 7.64 0.00 0.00 3.51
62 63 4.077184 TTGATCGACGGGGCGCTT 62.077 61.111 7.64 0.00 0.00 4.68
63 64 4.514577 CTTGATCGACGGGGCGCT 62.515 66.667 7.64 0.00 0.00 5.92
64 65 3.792053 ATCTTGATCGACGGGGCGC 62.792 63.158 0.00 0.00 0.00 6.53
65 66 1.661821 GATCTTGATCGACGGGGCG 60.662 63.158 0.00 0.00 0.00 6.13
66 67 1.661821 CGATCTTGATCGACGGGGC 60.662 63.158 23.64 0.00 46.12 5.80
67 68 1.007271 CCGATCTTGATCGACGGGG 60.007 63.158 27.89 11.71 46.12 5.73
68 69 0.317938 GTCCGATCTTGATCGACGGG 60.318 60.000 27.89 14.85 46.12 5.28
69 70 0.657659 CGTCCGATCTTGATCGACGG 60.658 60.000 27.89 15.96 46.12 4.79
70 71 0.027716 ACGTCCGATCTTGATCGACG 59.972 55.000 30.88 30.88 46.12 5.12
71 72 1.467875 CACGTCCGATCTTGATCGAC 58.532 55.000 27.89 21.80 46.12 4.20
72 73 0.248498 GCACGTCCGATCTTGATCGA 60.248 55.000 27.89 14.81 46.12 3.59
73 74 1.532343 CGCACGTCCGATCTTGATCG 61.532 60.000 21.77 21.77 43.15 3.69
74 75 1.812214 GCGCACGTCCGATCTTGATC 61.812 60.000 1.32 0.78 0.00 2.92
75 76 1.878522 GCGCACGTCCGATCTTGAT 60.879 57.895 1.32 0.00 0.00 2.57
76 77 2.506217 GCGCACGTCCGATCTTGA 60.506 61.111 1.32 0.00 0.00 3.02
77 78 3.554692 GGCGCACGTCCGATCTTG 61.555 66.667 10.83 0.00 0.00 3.02
100 101 2.294132 GACTAGGGTTTCGAGGGGCG 62.294 65.000 0.00 0.00 42.69 6.13
101 102 1.521141 GACTAGGGTTTCGAGGGGC 59.479 63.158 0.00 0.00 0.00 5.80
102 103 1.814527 CGACTAGGGTTTCGAGGGG 59.185 63.158 0.00 0.00 37.43 4.79
103 104 1.141234 GCGACTAGGGTTTCGAGGG 59.859 63.158 4.79 0.00 37.43 4.30
104 105 1.141234 GGCGACTAGGGTTTCGAGG 59.859 63.158 4.79 0.00 37.43 4.63
105 106 0.179134 CAGGCGACTAGGGTTTCGAG 60.179 60.000 0.00 0.00 40.21 4.04
106 107 0.896940 ACAGGCGACTAGGGTTTCGA 60.897 55.000 0.00 0.00 40.21 3.71
107 108 0.458025 GACAGGCGACTAGGGTTTCG 60.458 60.000 0.00 0.00 40.21 3.46
108 109 0.458025 CGACAGGCGACTAGGGTTTC 60.458 60.000 0.00 0.00 44.57 2.78
109 110 1.590147 CGACAGGCGACTAGGGTTT 59.410 57.895 0.00 0.00 44.57 3.27
110 111 3.003113 GCGACAGGCGACTAGGGTT 62.003 63.158 0.00 0.00 44.57 4.11
111 112 3.450115 GCGACAGGCGACTAGGGT 61.450 66.667 0.00 0.00 44.57 4.34
121 122 2.343163 CTTAGGAGCCTCGCGACAGG 62.343 65.000 3.71 7.51 36.50 4.00
122 123 1.064946 CTTAGGAGCCTCGCGACAG 59.935 63.158 3.71 0.00 0.00 3.51
123 124 1.248785 AACTTAGGAGCCTCGCGACA 61.249 55.000 3.71 0.00 0.00 4.35
124 125 0.108756 AAACTTAGGAGCCTCGCGAC 60.109 55.000 3.71 0.00 0.00 5.19
125 126 0.172803 GAAACTTAGGAGCCTCGCGA 59.827 55.000 9.26 9.26 0.00 5.87
126 127 0.806492 GGAAACTTAGGAGCCTCGCG 60.806 60.000 0.00 0.00 0.00 5.87
127 128 0.806492 CGGAAACTTAGGAGCCTCGC 60.806 60.000 0.00 0.00 0.00 5.03
128 129 0.179108 CCGGAAACTTAGGAGCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
129 130 0.178301 CCCGGAAACTTAGGAGCCTC 59.822 60.000 0.73 0.00 0.00 4.70
130 131 1.272554 CCCCGGAAACTTAGGAGCCT 61.273 60.000 0.73 0.00 0.00 4.58
131 132 1.223763 CCCCGGAAACTTAGGAGCC 59.776 63.158 0.73 0.00 0.00 4.70
132 133 0.107800 GTCCCCGGAAACTTAGGAGC 60.108 60.000 0.73 0.00 0.00 4.70
133 134 1.272807 TGTCCCCGGAAACTTAGGAG 58.727 55.000 0.73 0.00 0.00 3.69
134 135 1.732117 TTGTCCCCGGAAACTTAGGA 58.268 50.000 0.73 0.00 0.00 2.94
135 136 2.555325 GTTTTGTCCCCGGAAACTTAGG 59.445 50.000 0.73 0.00 32.13 2.69
136 137 2.555325 GGTTTTGTCCCCGGAAACTTAG 59.445 50.000 0.73 0.00 34.55 2.18
137 138 2.585330 GGTTTTGTCCCCGGAAACTTA 58.415 47.619 0.73 0.00 34.55 2.24
138 139 1.405872 GGTTTTGTCCCCGGAAACTT 58.594 50.000 0.73 0.00 34.55 2.66
139 140 0.820482 CGGTTTTGTCCCCGGAAACT 60.820 55.000 0.73 0.00 40.54 2.66
140 141 0.818852 TCGGTTTTGTCCCCGGAAAC 60.819 55.000 0.73 4.91 44.32 2.78
141 142 0.110869 ATCGGTTTTGTCCCCGGAAA 59.889 50.000 0.73 0.00 44.32 3.13
142 143 0.982704 TATCGGTTTTGTCCCCGGAA 59.017 50.000 0.73 0.00 44.32 4.30
143 144 0.982704 TTATCGGTTTTGTCCCCGGA 59.017 50.000 0.73 0.00 44.32 5.14
144 145 2.047002 ATTATCGGTTTTGTCCCCGG 57.953 50.000 0.00 0.00 44.32 5.73
145 146 4.193865 AGTAATTATCGGTTTTGTCCCCG 58.806 43.478 0.00 0.00 45.55 5.73
146 147 6.038603 GGTTAGTAATTATCGGTTTTGTCCCC 59.961 42.308 0.00 0.00 0.00 4.81
147 148 6.238184 CGGTTAGTAATTATCGGTTTTGTCCC 60.238 42.308 0.00 0.00 0.00 4.46
186 187 4.513406 TCAGGGGCTATAAAACCGAAAT 57.487 40.909 0.00 0.00 0.00 2.17
221 222 4.339872 TTGTGGTGGTAATACACTTCGT 57.660 40.909 0.00 0.00 41.09 3.85
222 223 4.693566 ACATTGTGGTGGTAATACACTTCG 59.306 41.667 0.00 0.00 41.09 3.79
257 259 1.818674 CGGGCCTTTAGCAAGAAACAT 59.181 47.619 0.84 0.00 46.50 2.71
258 260 1.202830 TCGGGCCTTTAGCAAGAAACA 60.203 47.619 0.84 0.00 46.50 2.83
446 455 2.210013 TGCTAGCGAGGGCCTATGG 61.210 63.158 5.73 0.00 41.24 2.74
447 456 1.005630 GTGCTAGCGAGGGCCTATG 60.006 63.158 5.73 2.82 41.24 2.23
448 457 2.210711 GGTGCTAGCGAGGGCCTAT 61.211 63.158 5.73 0.00 41.24 2.57
449 458 2.838225 GGTGCTAGCGAGGGCCTA 60.838 66.667 5.73 0.00 41.24 3.93
464 473 3.626924 GAGTGTGGTGGCGGAGGT 61.627 66.667 0.00 0.00 0.00 3.85
622 640 1.738350 CAAGAGGCATGCAGACAAGAG 59.262 52.381 21.36 0.00 0.00 2.85
645 663 2.710377 TCTTGAATGTGTAGCGCCAAT 58.290 42.857 2.29 0.00 0.00 3.16
649 667 3.747099 AACATCTTGAATGTGTAGCGC 57.253 42.857 0.00 0.00 31.80 5.92
677 695 6.463995 AGCAGGATTGTGTTTCAGTTTTTA 57.536 33.333 0.00 0.00 0.00 1.52
683 701 5.916883 CACTTTTAGCAGGATTGTGTTTCAG 59.083 40.000 0.00 0.00 0.00 3.02
725 745 2.783135 ACAGAACATGGAAACGCAGAT 58.217 42.857 0.00 0.00 0.00 2.90
735 755 5.880054 ACCGAAATTTCTACAGAACATGG 57.120 39.130 15.92 8.00 33.13 3.66
750 770 6.657541 TGCTCCTGAAATAGTAAAACCGAAAT 59.342 34.615 0.00 0.00 0.00 2.17
772 792 5.200368 AGATGTGAAAACCGAAATTTGCT 57.800 34.783 0.00 0.00 0.00 3.91
867 887 4.972591 GCGGCAGCAACATTCTTT 57.027 50.000 3.18 0.00 44.35 2.52
882 902 9.340695 TCATGAAATTGACAAGTTAAATTAGCG 57.659 29.630 0.04 0.00 0.00 4.26
926 946 3.115554 CAAACGAAGCCACTTTTCAAGG 58.884 45.455 0.00 0.00 0.00 3.61
927 947 3.769536 ACAAACGAAGCCACTTTTCAAG 58.230 40.909 0.00 0.00 0.00 3.02
985 1006 1.077930 CCATCCTGCTCACCCAGTG 60.078 63.158 0.00 0.00 34.45 3.66
986 1007 2.304056 CCCATCCTGCTCACCCAGT 61.304 63.158 0.00 0.00 0.00 4.00
988 1009 2.863383 ATCCCCATCCTGCTCACCCA 62.863 60.000 0.00 0.00 0.00 4.51
1009 1031 0.115745 TTGGGGTCTTCCTCGGTAGT 59.884 55.000 0.00 0.00 36.91 2.73
1023 1045 3.084786 GTGGTTCTTCATCTCTTTGGGG 58.915 50.000 0.00 0.00 0.00 4.96
1161 1183 4.720530 CTTTTCAATCAGCAAAGCAACC 57.279 40.909 0.00 0.00 0.00 3.77
1187 1218 6.549952 TCACAATGAAACAAAAATGCCAAAC 58.450 32.000 0.00 0.00 0.00 2.93
1188 1219 6.748333 TCACAATGAAACAAAAATGCCAAA 57.252 29.167 0.00 0.00 0.00 3.28
1393 1429 8.222637 AGAATACCAGAATCCATCAAATCATGA 58.777 33.333 0.00 0.00 43.67 3.07
1408 1444 4.350368 TCAACAGTGCAGAATACCAGAA 57.650 40.909 0.00 0.00 0.00 3.02
1727 1763 7.685712 GCACAAAAATGATAGATATGTCGATCG 59.314 37.037 9.36 9.36 38.77 3.69
1809 1845 1.750778 CAGGGAATTTCAATGGGTCCG 59.249 52.381 0.00 0.00 0.00 4.79
1856 1892 6.868622 AGTACGAAGATCAAGAAGCATAAGT 58.131 36.000 0.00 0.00 0.00 2.24
2028 2064 2.264794 CACCGCCCACTACCACTC 59.735 66.667 0.00 0.00 0.00 3.51
2030 2066 2.047560 GACACCGCCCACTACCAC 60.048 66.667 0.00 0.00 0.00 4.16
2031 2067 3.687102 CGACACCGCCCACTACCA 61.687 66.667 0.00 0.00 0.00 3.25
2033 2069 2.126189 GTCGACACCGCCCACTAC 60.126 66.667 11.55 0.00 35.37 2.73
2037 2073 1.669760 GAAATGTCGACACCGCCCA 60.670 57.895 22.71 0.00 35.37 5.36
2038 2074 3.174788 GAAATGTCGACACCGCCC 58.825 61.111 22.71 4.98 35.37 6.13
2102 2138 7.148086 ACACAGCTTCAGAGAACACAAAATAAA 60.148 33.333 0.00 0.00 0.00 1.40
2104 2140 5.822519 ACACAGCTTCAGAGAACACAAAATA 59.177 36.000 0.00 0.00 0.00 1.40
2128 2166 2.974794 CTGGATCATGTAGGGATGGTGA 59.025 50.000 0.00 0.00 0.00 4.02
2136 2174 6.826668 TGTTATTGGTACTGGATCATGTAGG 58.173 40.000 0.00 0.00 0.00 3.18
2426 2465 2.097347 GCACAGAAAAACTCTCGTCGAC 60.097 50.000 5.18 5.18 29.07 4.20
2428 2467 2.128035 AGCACAGAAAAACTCTCGTCG 58.872 47.619 0.00 0.00 29.07 5.12
2487 2526 6.840527 TGATAGTCAGCATTTATCAATGGGA 58.159 36.000 1.95 0.00 40.36 4.37
2497 2536 5.184892 AGGGAAGTTGATAGTCAGCATTT 57.815 39.130 0.00 0.00 29.40 2.32
2757 2834 7.327032 AGCTTAATTTTTGAGAAAAGCGCTAAG 59.673 33.333 12.05 6.38 38.09 2.18
2811 2889 7.801716 ACTACAACTGCATTTTGACTAGAAA 57.198 32.000 13.65 0.00 0.00 2.52
2814 2893 9.599322 CTTTTACTACAACTGCATTTTGACTAG 57.401 33.333 13.65 8.85 0.00 2.57
3054 3158 9.709600 GAAATAGCAAAAACAACTAGATCTAGC 57.290 33.333 26.50 12.23 36.66 3.42
3074 3179 7.480855 CGCTAGCAATCAAAGCATATGAAATAG 59.519 37.037 16.45 0.00 35.98 1.73
3123 3429 4.750598 AGGAGAAAACTAAACTGAACTCGC 59.249 41.667 0.00 0.00 0.00 5.03
3142 3448 6.425417 GTGAGGACTTTTCAGTTTCTTAGGAG 59.575 42.308 0.00 0.00 31.22 3.69
3245 3573 2.743718 CCATCGCCCGCCTAGAAT 59.256 61.111 0.00 0.00 0.00 2.40
3286 3614 0.608640 CCGGTTGACTACTTCCTGCT 59.391 55.000 0.00 0.00 0.00 4.24
3298 3634 4.329545 GCTCAGGTGCCCGGTTGA 62.330 66.667 0.00 0.00 0.00 3.18
3330 3666 4.500716 GCTCTCTGTAATTCTAGCCCTCAC 60.501 50.000 0.00 0.00 0.00 3.51
3348 3684 1.750778 CTTCTCCCTCACTCTGCTCTC 59.249 57.143 0.00 0.00 0.00 3.20
3463 3814 1.699634 ACATCATCTTCCCATACCCCG 59.300 52.381 0.00 0.00 0.00 5.73
3469 3820 5.104235 TGACATGAGAACATCATCTTCCCAT 60.104 40.000 0.00 0.00 46.01 4.00
3504 3855 2.029918 GTCCCACACAAGCAAGAAATCC 60.030 50.000 0.00 0.00 0.00 3.01
3516 3867 1.980036 GTAAAGGTAGGGTCCCACACA 59.020 52.381 11.55 0.00 0.00 3.72
3671 4030 1.882989 GCGAGAAGAGGAGTGGCTGT 61.883 60.000 0.00 0.00 0.00 4.40
3831 4201 6.435164 ACAATAAAGACAATCAAGGGCCTAT 58.565 36.000 6.41 0.00 0.00 2.57
3836 4206 6.573664 TGTGACAATAAAGACAATCAAGGG 57.426 37.500 0.00 0.00 0.00 3.95
3930 4417 4.846940 AGGATAGTTCTGGAGAAAAGTGGT 59.153 41.667 0.00 0.00 35.58 4.16
4187 4722 8.173130 CCGAAAATCAAACTATAGTGTGGTAAC 58.827 37.037 20.69 9.36 34.08 2.50
4188 4723 7.148373 GCCGAAAATCAAACTATAGTGTGGTAA 60.148 37.037 20.69 4.52 34.08 2.85
4189 4724 6.314400 GCCGAAAATCAAACTATAGTGTGGTA 59.686 38.462 20.69 5.20 34.08 3.25
4190 4725 5.123344 GCCGAAAATCAAACTATAGTGTGGT 59.877 40.000 20.69 12.79 34.08 4.16
4191 4726 5.448632 GGCCGAAAATCAAACTATAGTGTGG 60.449 44.000 20.69 6.16 34.08 4.17
4192 4727 5.123186 TGGCCGAAAATCAAACTATAGTGTG 59.877 40.000 15.93 15.93 34.60 3.82
4193 4728 5.123344 GTGGCCGAAAATCAAACTATAGTGT 59.877 40.000 6.06 0.00 0.00 3.55
4194 4729 5.448632 GGTGGCCGAAAATCAAACTATAGTG 60.449 44.000 6.06 0.00 0.00 2.74
4195 4730 4.638865 GGTGGCCGAAAATCAAACTATAGT 59.361 41.667 0.00 0.00 0.00 2.12
4196 4731 4.881850 AGGTGGCCGAAAATCAAACTATAG 59.118 41.667 0.00 0.00 0.00 1.31
4197 4732 4.850680 AGGTGGCCGAAAATCAAACTATA 58.149 39.130 0.00 0.00 0.00 1.31
4198 4733 3.697166 AGGTGGCCGAAAATCAAACTAT 58.303 40.909 0.00 0.00 0.00 2.12
4199 4734 3.149005 AGGTGGCCGAAAATCAAACTA 57.851 42.857 0.00 0.00 0.00 2.24
4701 5517 8.682710 AGCTCAACTGTTTAGTACAAAAATGAA 58.317 29.630 3.89 0.00 35.69 2.57
4723 5539 0.179127 TCAGCACATCGCAGTAGCTC 60.179 55.000 0.00 0.00 46.13 4.09
4754 5570 7.125811 TGGATGCTACTTTACTAGTTCTCCAAT 59.874 37.037 0.00 0.00 38.33 3.16
4802 5618 2.798689 TCGGCTCATCGAGGTTCG 59.201 61.111 0.00 0.17 42.10 3.95
5128 6156 2.095567 CGATGCCAAGAGGAAGTGTTTG 60.096 50.000 0.00 0.00 36.89 2.93
5254 6282 0.878416 GGCCAATGACAGCGTTGTAA 59.122 50.000 4.38 0.00 38.97 2.41
5356 6384 1.210155 GAATGCAACAGCCGTCACC 59.790 57.895 0.00 0.00 0.00 4.02
5362 6390 1.372087 CCCTCTCGAATGCAACAGCC 61.372 60.000 0.00 0.00 0.00 4.85
5383 6411 1.331756 GCAGTTGCCATAAGATGACCG 59.668 52.381 0.00 0.00 34.31 4.79
6129 7163 2.838736 AGACTACACAACACAAGCTGG 58.161 47.619 0.00 0.00 0.00 4.85
6133 7167 7.009631 GCTACATGATAGACTACACAACACAAG 59.990 40.741 0.00 0.00 0.00 3.16
6139 7173 5.451937 GCCAGCTACATGATAGACTACACAA 60.452 44.000 0.00 0.00 0.00 3.33
6143 7177 4.855715 TGCCAGCTACATGATAGACTAC 57.144 45.455 0.00 0.00 0.00 2.73
6144 7178 4.895889 ACTTGCCAGCTACATGATAGACTA 59.104 41.667 0.00 0.00 0.00 2.59
6145 7179 3.708631 ACTTGCCAGCTACATGATAGACT 59.291 43.478 0.00 0.00 0.00 3.24
6146 7180 4.065321 ACTTGCCAGCTACATGATAGAC 57.935 45.455 0.00 0.00 0.00 2.59
6149 7183 6.918067 ATACTACTTGCCAGCTACATGATA 57.082 37.500 0.00 0.00 0.00 2.15
6150 7184 5.815233 ATACTACTTGCCAGCTACATGAT 57.185 39.130 0.00 0.00 0.00 2.45
6151 7185 5.614324 AATACTACTTGCCAGCTACATGA 57.386 39.130 0.00 0.00 0.00 3.07
6152 7186 5.817296 TCAAATACTACTTGCCAGCTACATG 59.183 40.000 0.00 0.00 0.00 3.21
6207 7401 0.539438 TTTGCTGCGTCCTTTCCCAT 60.539 50.000 0.00 0.00 0.00 4.00
6218 7412 0.783579 CGGGACAAAAATTTGCTGCG 59.216 50.000 5.82 0.00 41.79 5.18
6361 7559 5.567534 GCACATTAAAGTTATGTTGACACCG 59.432 40.000 0.00 0.00 0.00 4.94
6372 7570 7.144661 CACATGGAACTTGCACATTAAAGTTA 58.855 34.615 0.00 0.00 44.53 2.24
6380 7578 1.330234 TGCACATGGAACTTGCACAT 58.670 45.000 3.97 0.00 41.29 3.21
6405 7603 4.268884 GCTCACCATAAGAGTTCGAATCAC 59.731 45.833 0.00 0.00 35.55 3.06
6408 7606 4.184629 GTGCTCACCATAAGAGTTCGAAT 58.815 43.478 0.00 0.00 35.55 3.34
6410 7608 3.232213 GTGCTCACCATAAGAGTTCGA 57.768 47.619 0.00 0.00 35.55 3.71
6451 7739 7.123547 ACCTTTTCTGAACCAAACACATTCTAA 59.876 33.333 0.00 0.00 0.00 2.10
6480 7775 9.371136 GAAGTGTGTGATTTGATTACATCTAGA 57.629 33.333 0.00 0.00 31.17 2.43
6535 7830 5.899120 TGTTTACAGTTGTTGGCTTGTTA 57.101 34.783 0.00 0.00 0.00 2.41
6545 7840 4.839796 CGATTTCGGTTGTTTACAGTTGT 58.160 39.130 0.00 0.00 35.37 3.32
6643 7948 1.595609 GTTGATTCTTTCTGCACGCG 58.404 50.000 3.53 3.53 0.00 6.01
6658 7963 0.034756 CACCCACCACAGATCGTTGA 59.965 55.000 0.00 0.00 0.00 3.18
6733 8040 7.815840 TTGACACACTTGGATCTGATTTTTA 57.184 32.000 0.00 0.00 0.00 1.52
6742 8049 5.241506 TGGATCTTTTTGACACACTTGGATC 59.758 40.000 0.00 0.00 0.00 3.36
6746 8053 7.775397 AAAATGGATCTTTTTGACACACTTG 57.225 32.000 6.24 0.00 0.00 3.16
6796 8108 8.123639 TGATCCGAAATTTTTATTGGGTGTAA 57.876 30.769 0.00 0.00 0.00 2.41
6801 8113 9.986833 GAATTTTGATCCGAAATTTTTATTGGG 57.013 29.630 14.45 0.00 37.51 4.12
6863 8180 9.883142 TTTTTGTCCTTTCTGTATTTCAAATGT 57.117 25.926 0.00 0.00 0.00 2.71
6906 8224 1.923356 AAAGACAAATCCGGCATGGT 58.077 45.000 0.00 0.00 39.52 3.55
6926 8244 7.228507 TCAAAATTCGAAGTCCAAGAGAAATGA 59.771 33.333 3.35 0.00 0.00 2.57
6960 8281 7.620880 AGACATGTATGTACAGCTCCTAAAAA 58.379 34.615 0.00 0.00 41.95 1.94


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

AutoCloner maintained by Alex Coulton.