Multiple sequence alignment - TraesCS7B01G008400

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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 TraesCS7B01G008400 chr7B 100.000 4163 0 0 1 4163 5058012 5062174 0.000000e+00 7688
1 TraesCS7B01G008400 chr7B 84.971 173 24 2 3910 4082 5052670 5052500 1.540000e-39 174
2 TraesCS7B01G008400 chr7B 75.815 368 62 19 3790 4148 5145922 5146271 1.200000e-35 161
3 TraesCS7B01G008400 chr7B 94.444 90 4 1 1 89 726369798 726369709 2.020000e-28 137
4 TraesCS7B01G008400 chr7D 93.346 3126 134 28 1060 4150 64011878 64014964 0.000000e+00 4553
5 TraesCS7B01G008400 chr7D 86.927 872 47 36 297 1141 64011059 64011890 0.000000e+00 917
6 TraesCS7B01G008400 chr7D 88.718 195 15 4 3910 4098 64005871 64005678 9.000000e-57 231
7 TraesCS7B01G008400 chr7A 91.899 3123 153 44 97 3174 67674379 67671312 0.000000e+00 4274
8 TraesCS7B01G008400 chr7A 88.933 1012 69 25 3173 4163 67671348 67670359 0.000000e+00 1208
9 TraesCS7B01G008400 chr7A 82.400 375 35 19 3794 4163 67678891 67679239 8.750000e-77 298
10 TraesCS7B01G008400 chr7A 76.840 557 82 27 1106 1654 629879594 629879077 1.910000e-68 270
11 TraesCS7B01G008400 chr2B 80.132 604 87 17 1153 1750 708391507 708392083 1.790000e-113 420
12 TraesCS7B01G008400 chr2B 80.168 595 85 17 1159 1750 66034137 66033573 8.330000e-112 414
13 TraesCS7B01G008400 chr2B 90.816 98 9 0 1659 1756 128531570 128531473 9.390000e-27 132
14 TraesCS7B01G008400 chr2B 89.796 98 10 0 1659 1756 775419168 775419265 4.370000e-25 126
15 TraesCS7B01G008400 chr2A 78.229 542 83 20 1183 1721 764661263 764660754 8.690000e-82 315
16 TraesCS7B01G008400 chr4A 81.690 284 45 5 1469 1750 714217647 714217925 3.240000e-56 230
17 TraesCS7B01G008400 chr4A 95.181 83 4 0 1 83 705606426 705606344 9.390000e-27 132
18 TraesCS7B01G008400 chr4B 97.500 80 2 0 1 80 462241200 462241279 2.020000e-28 137
19 TraesCS7B01G008400 chr3B 98.701 77 1 0 1 77 45782657 45782733 2.020000e-28 137
20 TraesCS7B01G008400 chr3B 98.701 77 1 0 1 77 45851047 45851123 2.020000e-28 137
21 TraesCS7B01G008400 chr3B 98.701 77 1 0 1 77 45946140 45946216 2.020000e-28 137
22 TraesCS7B01G008400 chr3B 98.701 77 1 0 1 77 45996103 45996179 2.020000e-28 137
23 TraesCS7B01G008400 chrUn 92.308 91 7 0 1 91 258961 258871 3.380000e-26 130
24 TraesCS7B01G008400 chrUn 92.308 91 7 0 1 91 289867 289777 3.380000e-26 130
25 TraesCS7B01G008400 chr1B 89.796 98 10 0 1659 1756 189691025 189690928 4.370000e-25 126
26 TraesCS7B01G008400 chr6B 88.889 99 11 0 1393 1491 172276947 172277045 5.650000e-24 122


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 TraesCS7B01G008400 chr7B 5058012 5062174 4162 False 7688 7688 100.0000 1 4163 1 chr7B.!!$F1 4162
1 TraesCS7B01G008400 chr7D 64011059 64014964 3905 False 2735 4553 90.1365 297 4150 2 chr7D.!!$F1 3853
2 TraesCS7B01G008400 chr7A 67670359 67674379 4020 True 2741 4274 90.4160 97 4163 2 chr7A.!!$R2 4066
3 TraesCS7B01G008400 chr7A 629879077 629879594 517 True 270 270 76.8400 1106 1654 1 chr7A.!!$R1 548
4 TraesCS7B01G008400 chr2B 708391507 708392083 576 False 420 420 80.1320 1153 1750 1 chr2B.!!$F1 597
5 TraesCS7B01G008400 chr2B 66033573 66034137 564 True 414 414 80.1680 1159 1750 1 chr2B.!!$R1 591
6 TraesCS7B01G008400 chr2A 764660754 764661263 509 True 315 315 78.2290 1183 1721 1 chr2A.!!$R1 538

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
130 131 0.036765 TTCCGGACGAAATGGGTGAG 60.037 55.000 1.83 0.0 0.00 3.51 F
349 355 0.042013 GGTACGAGACGAGATCGCTG 60.042 60.000 1.39 0.0 43.91 5.18 F
927 972 1.081092 CTCCTCTTCCCCTCACCCA 59.919 63.158 0.00 0.0 0.00 4.51 F
2409 2573 0.610687 GTGACTGGGAGGAGGTTGAG 59.389 60.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2171 3.011517 AGCTCCTCCATTGCCGGT 61.012 61.111 1.90 0.0 0.00 5.28 R
2247 2411 1.557371 GCTAGCCTCCTAATCCCATCC 59.443 57.143 2.29 0.0 0.00 3.51 R
2736 2900 0.323178 CCAGCTTCATCTTGGCCAGT 60.323 55.000 5.11 0.0 0.00 4.00 R
3299 3498 0.099436 GATCATCGCAAGCAACCCAC 59.901 55.000 0.00 0.0 37.18 4.61 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.628500 TCTAGACTCATTTAAGTGCTAGATACA 57.372 33.333 8.67 0.00 34.60 2.29
30 31 8.364142 AGACTCATTTAAGTGCTAGATACATCC 58.636 37.037 0.00 0.00 0.00 3.51
31 32 7.148641 ACTCATTTAAGTGCTAGATACATCCG 58.851 38.462 0.00 0.00 0.00 4.18
32 33 7.050970 TCATTTAAGTGCTAGATACATCCGT 57.949 36.000 0.00 0.00 0.00 4.69
33 34 8.173542 TCATTTAAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
34 35 8.803235 TCATTTAAGTGCTAGATACATCCGTAT 58.197 33.333 0.00 0.00 41.16 3.06
50 51 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
51 52 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
52 53 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
53 54 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
54 55 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
55 56 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
63 64 9.793259 AGACAAATCTAAGACAAGTAATTTGGA 57.207 29.630 9.60 0.00 38.04 3.53
66 67 9.329913 CAAATCTAAGACAAGTAATTTGGAACG 57.670 33.333 0.00 0.00 41.25 3.95
67 68 7.611213 ATCTAAGACAAGTAATTTGGAACGG 57.389 36.000 0.00 0.00 41.25 4.44
68 69 6.761312 TCTAAGACAAGTAATTTGGAACGGA 58.239 36.000 0.00 0.00 41.25 4.69
69 70 5.941948 AAGACAAGTAATTTGGAACGGAG 57.058 39.130 0.00 0.00 41.25 4.63
70 71 4.324267 AGACAAGTAATTTGGAACGGAGG 58.676 43.478 0.00 0.00 41.25 4.30
71 72 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
72 73 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
73 74 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
74 75 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
75 76 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
76 77 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
77 78 0.611714 TTTGGAACGGAGGGAGTAGC 59.388 55.000 0.00 0.00 0.00 3.58
78 79 0.252103 TTGGAACGGAGGGAGTAGCT 60.252 55.000 0.00 0.00 0.00 3.32
79 80 0.970937 TGGAACGGAGGGAGTAGCTG 60.971 60.000 0.00 0.00 0.00 4.24
80 81 0.683504 GGAACGGAGGGAGTAGCTGA 60.684 60.000 0.00 0.00 0.00 4.26
81 82 1.404843 GAACGGAGGGAGTAGCTGAT 58.595 55.000 0.00 0.00 0.00 2.90
82 83 1.757699 GAACGGAGGGAGTAGCTGATT 59.242 52.381 0.00 0.00 0.00 2.57
83 84 1.404843 ACGGAGGGAGTAGCTGATTC 58.595 55.000 0.00 0.00 0.00 2.52
84 85 0.676736 CGGAGGGAGTAGCTGATTCC 59.323 60.000 0.00 0.00 33.06 3.01
85 86 1.755977 CGGAGGGAGTAGCTGATTCCT 60.756 57.143 0.00 0.00 34.32 3.36
86 87 1.967779 GGAGGGAGTAGCTGATTCCTC 59.032 57.143 15.86 15.86 39.84 3.71
87 88 1.967779 GAGGGAGTAGCTGATTCCTCC 59.032 57.143 13.96 11.23 42.28 4.30
88 89 1.292242 AGGGAGTAGCTGATTCCTCCA 59.708 52.381 15.52 0.00 44.34 3.86
89 90 2.090267 AGGGAGTAGCTGATTCCTCCAT 60.090 50.000 15.52 9.00 44.34 3.41
90 91 2.301583 GGGAGTAGCTGATTCCTCCATC 59.698 54.545 15.52 1.93 44.34 3.51
91 92 2.029470 GGAGTAGCTGATTCCTCCATCG 60.029 54.545 0.00 0.00 42.51 3.84
92 93 1.967066 AGTAGCTGATTCCTCCATCGG 59.033 52.381 0.00 0.00 33.21 4.18
93 94 4.055654 GCTGATTCCTCCATCGGC 57.944 61.111 0.00 0.00 45.96 5.54
94 95 1.958205 GCTGATTCCTCCATCGGCG 60.958 63.158 0.00 0.00 43.90 6.46
95 96 1.443407 CTGATTCCTCCATCGGCGT 59.557 57.895 6.85 0.00 0.00 5.68
106 107 1.867233 CCATCGGCGTTATTTCTGGAG 59.133 52.381 6.85 0.00 0.00 3.86
110 111 1.396996 CGGCGTTATTTCTGGAGTTGG 59.603 52.381 0.00 0.00 0.00 3.77
112 113 2.817844 GGCGTTATTTCTGGAGTTGGTT 59.182 45.455 0.00 0.00 0.00 3.67
115 116 3.124636 CGTTATTTCTGGAGTTGGTTCCG 59.875 47.826 0.00 0.00 40.27 4.30
127 128 1.002990 GGTTCCGGACGAAATGGGT 60.003 57.895 1.83 0.00 30.39 4.51
130 131 0.036765 TTCCGGACGAAATGGGTGAG 60.037 55.000 1.83 0.00 0.00 3.51
151 152 1.485066 GATTCTCCCCTAACCTGCGAA 59.515 52.381 0.00 0.00 0.00 4.70
156 157 2.125269 CCTAACCTGCGAACCCCG 60.125 66.667 0.00 0.00 42.21 5.73
168 169 1.542915 CGAACCCCGTCTGAGAAACTA 59.457 52.381 0.00 0.00 0.00 2.24
169 170 2.165845 CGAACCCCGTCTGAGAAACTAT 59.834 50.000 0.00 0.00 0.00 2.12
174 175 3.430929 CCCCGTCTGAGAAACTATCCAAG 60.431 52.174 0.00 0.00 0.00 3.61
178 179 4.269603 CGTCTGAGAAACTATCCAAGCATG 59.730 45.833 0.00 0.00 0.00 4.06
181 182 6.018098 GTCTGAGAAACTATCCAAGCATGATG 60.018 42.308 0.00 0.00 0.00 3.07
194 195 1.068127 GCATGATGCAATCCTTCCACC 59.932 52.381 13.36 0.00 44.73 4.61
195 196 1.684983 CATGATGCAATCCTTCCACCC 59.315 52.381 0.00 0.00 44.73 4.61
196 197 0.703488 TGATGCAATCCTTCCACCCA 59.297 50.000 0.00 0.00 44.73 4.51
197 198 1.288633 TGATGCAATCCTTCCACCCAT 59.711 47.619 0.00 0.00 44.73 4.00
198 199 2.292389 TGATGCAATCCTTCCACCCATT 60.292 45.455 0.00 0.00 44.73 3.16
199 200 2.323999 TGCAATCCTTCCACCCATTT 57.676 45.000 0.00 0.00 0.00 2.32
200 201 2.178580 TGCAATCCTTCCACCCATTTC 58.821 47.619 0.00 0.00 0.00 2.17
203 204 0.258774 ATCCTTCCACCCATTTCCCG 59.741 55.000 0.00 0.00 0.00 5.14
216 222 1.540267 TTTCCCGGCTACCAAACATG 58.460 50.000 0.00 0.00 0.00 3.21
225 231 3.278574 GCTACCAAACATGCATAGGTCA 58.721 45.455 13.53 3.60 33.91 4.02
227 233 4.261322 GCTACCAAACATGCATAGGTCATG 60.261 45.833 13.53 9.29 44.99 3.07
242 248 1.004277 GTCATGGCCTCCAACCAACTA 59.996 52.381 3.32 0.00 41.49 2.24
271 277 4.565028 GGAAAATTCCCCAACTACTCGTCT 60.565 45.833 0.43 0.00 41.62 4.18
279 285 1.935327 AACTACTCGTCTGCCCGCTC 61.935 60.000 0.00 0.00 0.00 5.03
301 307 2.508439 CGATCCGTCCAACCCACG 60.508 66.667 0.00 0.00 36.99 4.94
344 350 1.094073 CACCGGGTACGAGACGAGAT 61.094 60.000 6.32 0.00 44.60 2.75
345 351 0.813210 ACCGGGTACGAGACGAGATC 60.813 60.000 6.32 0.00 44.60 2.75
346 352 1.563655 CGGGTACGAGACGAGATCG 59.436 63.158 0.00 0.00 44.60 3.69
347 353 1.279238 GGGTACGAGACGAGATCGC 59.721 63.158 1.39 0.00 43.91 4.58
348 354 1.159098 GGGTACGAGACGAGATCGCT 61.159 60.000 1.39 0.59 43.91 4.93
349 355 0.042013 GGTACGAGACGAGATCGCTG 60.042 60.000 1.39 0.00 43.91 5.18
419 440 2.946650 CTCCCCCACCCACCCAAT 60.947 66.667 0.00 0.00 0.00 3.16
449 470 1.411977 CAGCAACCAACCAACCAATCA 59.588 47.619 0.00 0.00 0.00 2.57
450 471 2.114616 AGCAACCAACCAACCAATCAA 58.885 42.857 0.00 0.00 0.00 2.57
451 472 2.705127 AGCAACCAACCAACCAATCAAT 59.295 40.909 0.00 0.00 0.00 2.57
701 740 4.706233 CGCGAGCGAGAAAACTTG 57.294 55.556 12.58 0.00 42.83 3.16
721 760 3.526029 GCTTTGCGGCGACAAAAG 58.474 55.556 22.64 21.01 38.96 2.27
722 761 2.648318 GCTTTGCGGCGACAAAAGC 61.648 57.895 27.13 27.13 46.14 3.51
723 762 2.352915 TTTGCGGCGACAAAAGCG 60.353 55.556 21.11 0.00 36.62 4.68
731 770 1.268845 GGCGACAAAAGCGGAGAAAAA 60.269 47.619 0.00 0.00 35.00 1.94
740 779 8.126871 ACAAAAGCGGAGAAAAAGATAAAAAC 57.873 30.769 0.00 0.00 0.00 2.43
741 780 7.762159 ACAAAAGCGGAGAAAAAGATAAAAACA 59.238 29.630 0.00 0.00 0.00 2.83
743 782 8.887036 AAAGCGGAGAAAAAGATAAAAACAAT 57.113 26.923 0.00 0.00 0.00 2.71
744 783 7.873739 AGCGGAGAAAAAGATAAAAACAATG 57.126 32.000 0.00 0.00 0.00 2.82
746 785 6.401047 GCGGAGAAAAAGATAAAAACAATGGC 60.401 38.462 0.00 0.00 0.00 4.40
747 786 6.183359 CGGAGAAAAAGATAAAAACAATGGCG 60.183 38.462 0.00 0.00 0.00 5.69
748 787 6.090763 GGAGAAAAAGATAAAAACAATGGCGG 59.909 38.462 0.00 0.00 0.00 6.13
749 788 5.408299 AGAAAAAGATAAAAACAATGGCGGC 59.592 36.000 0.00 0.00 0.00 6.53
750 789 3.951775 AAGATAAAAACAATGGCGGCA 57.048 38.095 16.34 16.34 0.00 5.69
751 790 3.508744 AGATAAAAACAATGGCGGCAG 57.491 42.857 19.29 7.31 0.00 4.85
752 791 1.926510 GATAAAAACAATGGCGGCAGC 59.073 47.619 19.29 0.00 44.18 5.25
915 960 2.272797 CTCCGTCCCGTCTCCTCT 59.727 66.667 0.00 0.00 0.00 3.69
916 961 1.378778 CTCCGTCCCGTCTCCTCTT 60.379 63.158 0.00 0.00 0.00 2.85
917 962 1.378124 CTCCGTCCCGTCTCCTCTTC 61.378 65.000 0.00 0.00 0.00 2.87
918 963 2.416432 CCGTCCCGTCTCCTCTTCC 61.416 68.421 0.00 0.00 0.00 3.46
927 972 1.081092 CTCCTCTTCCCCTCACCCA 59.919 63.158 0.00 0.00 0.00 4.51
929 974 2.660064 CCTCTTCCCCTCACCCACG 61.660 68.421 0.00 0.00 0.00 4.94
1082 1159 3.270839 GCTGCTGCTCATCCTCGC 61.271 66.667 8.53 0.00 36.03 5.03
2028 2192 3.267860 GCAATGGAGGAGCTCGCG 61.268 66.667 7.83 0.00 0.00 5.87
2079 2243 4.432741 GGGTGCTTCCAGGGGCTC 62.433 72.222 6.83 3.66 38.11 4.70
2247 2411 1.990563 GGATGTAACCTTGTCACGTCG 59.009 52.381 0.00 0.00 0.00 5.12
2256 2420 0.611200 TTGTCACGTCGGATGGGATT 59.389 50.000 5.30 0.00 0.00 3.01
2270 2434 2.890814 TGGGATTAGGAGGCTAGCTAC 58.109 52.381 15.72 8.81 0.00 3.58
2305 2469 2.439507 ACATTGAAGGAGGTCAGTGTGT 59.560 45.455 2.95 0.00 44.15 3.72
2388 2552 3.006752 GGATCGAGAGCCTTGAGATCAAT 59.993 47.826 0.00 0.00 39.39 2.57
2409 2573 0.610687 GTGACTGGGAGGAGGTTGAG 59.389 60.000 0.00 0.00 0.00 3.02
2475 2639 0.965439 ATGAGGATGACGAGCCTAGC 59.035 55.000 0.00 0.00 38.46 3.42
2532 2696 4.019231 AGGTTCTCCTACTTGGAAATGGAC 60.019 45.833 0.00 0.00 45.63 4.02
2589 2753 2.580155 TTTGGTGCCCTGCTGGTCAA 62.580 55.000 9.00 5.13 36.04 3.18
2592 2756 1.374947 GTGCCCTGCTGGTCAACTA 59.625 57.895 9.00 0.00 36.04 2.24
2781 2945 2.590092 GAGGCGGTGGGTTATGCT 59.410 61.111 0.00 0.00 0.00 3.79
2833 2997 2.159382 CACAGTGGGAGCGGTTTTATT 58.841 47.619 0.00 0.00 0.00 1.40
2838 3002 2.817844 GTGGGAGCGGTTTTATTTGAGT 59.182 45.455 0.00 0.00 0.00 3.41
2841 3005 2.415491 GGAGCGGTTTTATTTGAGTGGC 60.415 50.000 0.00 0.00 0.00 5.01
2844 3008 3.258123 AGCGGTTTTATTTGAGTGGCATT 59.742 39.130 0.00 0.00 0.00 3.56
2847 3011 5.226396 CGGTTTTATTTGAGTGGCATTGAA 58.774 37.500 0.00 0.00 0.00 2.69
2892 3056 2.690881 TACTGGCCGCCCCAAGAT 60.691 61.111 7.03 0.00 44.81 2.40
3021 3185 1.815003 AGCTTCTTCCAGAAAATGCCG 59.185 47.619 0.00 0.00 33.19 5.69
3027 3191 4.647611 TCTTCCAGAAAATGCCGAACTTA 58.352 39.130 0.00 0.00 0.00 2.24
3102 3266 1.521010 CACAGAGATGCGGGCTGAG 60.521 63.158 0.00 0.00 33.94 3.35
3158 3357 2.353605 GGCAATTTCGGCAAATTCCTGA 60.354 45.455 5.15 0.00 39.75 3.86
3159 3358 3.524541 GCAATTTCGGCAAATTCCTGAT 58.475 40.909 5.15 0.00 39.75 2.90
3160 3359 3.934579 GCAATTTCGGCAAATTCCTGATT 59.065 39.130 5.15 0.00 39.75 2.57
3161 3360 4.201744 GCAATTTCGGCAAATTCCTGATTG 60.202 41.667 5.15 0.00 39.75 2.67
3162 3361 5.170021 CAATTTCGGCAAATTCCTGATTGA 58.830 37.500 5.15 0.00 39.75 2.57
3163 3362 5.603170 ATTTCGGCAAATTCCTGATTGAT 57.397 34.783 0.00 0.00 0.00 2.57
3164 3363 4.374843 TTCGGCAAATTCCTGATTGATG 57.625 40.909 0.00 0.00 0.00 3.07
3165 3364 2.099592 TCGGCAAATTCCTGATTGATGC 59.900 45.455 0.00 0.00 32.92 3.91
3166 3365 2.100252 CGGCAAATTCCTGATTGATGCT 59.900 45.455 0.00 0.00 33.78 3.79
3167 3366 3.454375 GGCAAATTCCTGATTGATGCTG 58.546 45.455 0.00 0.00 33.78 4.41
3168 3367 3.131577 GGCAAATTCCTGATTGATGCTGA 59.868 43.478 0.00 0.00 33.78 4.26
3169 3368 4.382254 GGCAAATTCCTGATTGATGCTGAA 60.382 41.667 0.00 0.00 33.78 3.02
3170 3369 5.357257 GCAAATTCCTGATTGATGCTGAAT 58.643 37.500 0.00 0.00 31.64 2.57
3171 3370 5.815740 GCAAATTCCTGATTGATGCTGAATT 59.184 36.000 0.00 0.00 31.64 2.17
3172 3371 6.238103 GCAAATTCCTGATTGATGCTGAATTG 60.238 38.462 0.00 0.00 31.64 2.32
3173 3372 4.994907 TTCCTGATTGATGCTGAATTGG 57.005 40.909 0.00 0.00 0.00 3.16
3174 3373 2.691526 TCCTGATTGATGCTGAATTGGC 59.308 45.455 0.00 0.00 0.00 4.52
3175 3374 2.429250 CCTGATTGATGCTGAATTGGCA 59.571 45.455 5.35 5.35 44.05 4.92
3176 3375 3.118920 CCTGATTGATGCTGAATTGGCAA 60.119 43.478 0.68 0.68 43.14 4.52
3177 3376 4.442893 CCTGATTGATGCTGAATTGGCAAT 60.443 41.667 6.96 6.96 43.14 3.56
3178 3377 5.092554 TGATTGATGCTGAATTGGCAATT 57.907 34.783 24.57 24.57 43.14 2.32
3179 3378 5.492895 TGATTGATGCTGAATTGGCAATTT 58.507 33.333 25.02 10.15 43.14 1.82
3180 3379 5.583061 TGATTGATGCTGAATTGGCAATTTC 59.417 36.000 25.02 18.08 43.14 2.17
3181 3380 3.513662 TGATGCTGAATTGGCAATTTCG 58.486 40.909 25.02 18.94 43.14 3.46
3182 3381 2.367030 TGCTGAATTGGCAATTTCGG 57.633 45.000 25.02 21.22 36.71 4.30
3183 3382 1.001624 GCTGAATTGGCAATTTCGGC 58.998 50.000 25.02 25.49 0.00 5.54
3184 3383 1.672441 GCTGAATTGGCAATTTCGGCA 60.672 47.619 30.08 21.91 40.11 5.69
3190 3389 2.091852 TGGCAATTTCGGCAAATTCC 57.908 45.000 5.15 9.06 39.75 3.01
3191 3390 1.622811 TGGCAATTTCGGCAAATTCCT 59.377 42.857 15.44 0.00 39.75 3.36
3192 3391 2.001872 GGCAATTTCGGCAAATTCCTG 58.998 47.619 5.15 0.00 39.75 3.86
3229 3428 3.081061 GGTGCACCATTACAGTGATTCA 58.919 45.455 31.23 0.00 37.42 2.57
3260 3459 2.173569 ACTTCAACACAGAGAGCCCTTT 59.826 45.455 0.00 0.00 0.00 3.11
3318 3517 0.099436 GTGGGTTGCTTGCGATGATC 59.901 55.000 0.00 0.00 0.00 2.92
3370 3569 9.039870 CCATTGATGATAAGAGTAGAAGACAAC 57.960 37.037 0.00 0.00 0.00 3.32
3657 3857 4.218200 TGTTTGTCATATGCCCTTGTTCTG 59.782 41.667 0.00 0.00 0.00 3.02
3695 3895 3.776969 ACTCTCATTGTGAAGATGGCCTA 59.223 43.478 3.32 0.00 0.00 3.93
3696 3896 4.225942 ACTCTCATTGTGAAGATGGCCTAA 59.774 41.667 3.32 0.00 0.00 2.69
3730 3930 6.935741 TTGCTGCTTAATTATACGAATGGT 57.064 33.333 0.00 0.00 0.00 3.55
3731 3931 6.539649 TGCTGCTTAATTATACGAATGGTC 57.460 37.500 0.00 0.00 0.00 4.02
3736 3936 8.270080 TGCTTAATTATACGAATGGTCAAACA 57.730 30.769 0.00 0.00 0.00 2.83
3737 3937 8.178964 TGCTTAATTATACGAATGGTCAAACAC 58.821 33.333 0.00 0.00 0.00 3.32
3738 3938 8.178964 GCTTAATTATACGAATGGTCAAACACA 58.821 33.333 0.00 0.00 0.00 3.72
3741 3941 7.624360 ATTATACGAATGGTCAAACACATGT 57.376 32.000 0.00 0.00 0.00 3.21
3761 3961 3.244976 GTGTACATGATTGGTTTGCTGC 58.755 45.455 0.00 0.00 0.00 5.25
3762 3962 2.230992 TGTACATGATTGGTTTGCTGCC 59.769 45.455 0.00 0.00 0.00 4.85
3763 3963 0.609662 ACATGATTGGTTTGCTGCCC 59.390 50.000 0.00 0.00 0.00 5.36
3764 3964 0.899720 CATGATTGGTTTGCTGCCCT 59.100 50.000 0.00 0.00 0.00 5.19
3765 3965 1.276989 CATGATTGGTTTGCTGCCCTT 59.723 47.619 0.00 0.00 0.00 3.95
3766 3966 0.680618 TGATTGGTTTGCTGCCCTTG 59.319 50.000 0.00 0.00 0.00 3.61
3768 3968 0.393820 ATTGGTTTGCTGCCCTTGTG 59.606 50.000 0.00 0.00 0.00 3.33
3770 3970 0.975040 TGGTTTGCTGCCCTTGTGTT 60.975 50.000 0.00 0.00 0.00 3.32
3771 3971 0.177836 GGTTTGCTGCCCTTGTGTTT 59.822 50.000 0.00 0.00 0.00 2.83
3772 3972 1.410882 GGTTTGCTGCCCTTGTGTTTA 59.589 47.619 0.00 0.00 0.00 2.01
3773 3973 2.469826 GTTTGCTGCCCTTGTGTTTAC 58.530 47.619 0.00 0.00 0.00 2.01
3774 3974 2.065899 TTGCTGCCCTTGTGTTTACT 57.934 45.000 0.00 0.00 0.00 2.24
3775 3975 2.940994 TGCTGCCCTTGTGTTTACTA 57.059 45.000 0.00 0.00 0.00 1.82
3776 3976 2.500229 TGCTGCCCTTGTGTTTACTAC 58.500 47.619 0.00 0.00 0.00 2.73
3781 3981 3.134985 TGCCCTTGTGTTTACTACTGTCA 59.865 43.478 0.00 0.00 0.00 3.58
3787 3987 4.116961 TGTGTTTACTACTGTCACTGTGC 58.883 43.478 2.12 0.00 0.00 4.57
3795 3995 0.464373 CTGTCACTGTGCCCTTGTGT 60.464 55.000 2.12 0.00 33.82 3.72
3807 4007 3.134985 TGCCCTTGTGTTTACTACTGTCA 59.865 43.478 0.00 0.00 0.00 3.58
3808 4008 4.131596 GCCCTTGTGTTTACTACTGTCAA 58.868 43.478 0.00 0.00 0.00 3.18
3809 4009 4.760204 GCCCTTGTGTTTACTACTGTCAAT 59.240 41.667 0.00 0.00 0.00 2.57
3810 4010 5.240844 GCCCTTGTGTTTACTACTGTCAATT 59.759 40.000 0.00 0.00 0.00 2.32
3822 4022 5.598417 ACTACTGTCAATTTCCTTTGCCTTT 59.402 36.000 0.00 0.00 0.00 3.11
3824 4024 4.651045 ACTGTCAATTTCCTTTGCCTTTCT 59.349 37.500 0.00 0.00 0.00 2.52
3825 4025 4.947645 TGTCAATTTCCTTTGCCTTTCTG 58.052 39.130 0.00 0.00 0.00 3.02
3827 4027 3.387374 TCAATTTCCTTTGCCTTTCTGCA 59.613 39.130 0.00 0.00 40.07 4.41
3828 4028 4.040706 TCAATTTCCTTTGCCTTTCTGCAT 59.959 37.500 0.00 0.00 41.70 3.96
3829 4029 3.665745 TTTCCTTTGCCTTTCTGCATC 57.334 42.857 0.00 0.00 41.70 3.91
3830 4030 2.291209 TCCTTTGCCTTTCTGCATCA 57.709 45.000 0.00 0.00 41.70 3.07
3873 4073 2.706339 TTGCATGGCAAACAGGTTTT 57.294 40.000 0.41 0.00 45.96 2.43
3874 4074 1.950828 TGCATGGCAAACAGGTTTTG 58.049 45.000 0.00 0.00 34.76 2.44
3884 4084 2.806608 ACAGGTTTTGCAATCTGCTG 57.193 45.000 18.68 12.52 44.13 4.41
3914 4121 8.535335 AGTACTGACATGAGATGAACTTGTAAT 58.465 33.333 0.00 0.00 0.00 1.89
3935 4144 6.619801 AATACCTGACACAAGAAAGTTCAC 57.380 37.500 0.00 0.00 0.00 3.18
3938 4147 2.285083 TGACACAAGAAAGTTCACCCG 58.715 47.619 0.00 0.00 0.00 5.28
3949 4158 1.564348 AGTTCACCCGGCCATTAAGAT 59.436 47.619 2.24 0.00 0.00 2.40
3961 4170 5.991606 CGGCCATTAAGATTTCAGTCTGATA 59.008 40.000 2.24 0.00 0.00 2.15
3966 4189 8.997323 CCATTAAGATTTCAGTCTGATATGACC 58.003 37.037 10.16 0.00 37.66 4.02
3976 4199 3.812053 GTCTGATATGACCACAGAATGCC 59.188 47.826 0.00 0.00 42.53 4.40
3977 4200 3.713248 TCTGATATGACCACAGAATGCCT 59.287 43.478 0.00 0.00 42.53 4.75
4038 4261 2.883386 CAAAGAAGCTTCTGCAAGGTCT 59.117 45.455 29.09 8.47 39.53 3.85
4043 4266 1.349026 AGCTTCTGCAAGGTCTAAGCA 59.651 47.619 7.96 0.00 43.87 3.91
4048 4271 2.157738 CTGCAAGGTCTAAGCAAAGCT 58.842 47.619 0.00 0.00 42.56 3.74
4059 4282 1.440476 GCAAAGCTGCCCATCATCC 59.560 57.895 0.00 0.00 43.26 3.51
4069 4292 1.301558 CCATCATCCGAGCAGGCTC 60.302 63.158 11.21 11.21 40.77 4.70
4077 4300 2.110967 CGAGCAGGCTCCCACAATG 61.111 63.158 15.16 0.00 39.77 2.82
4087 4322 2.095059 GCTCCCACAATGTGCTTGTTAG 60.095 50.000 8.05 0.00 45.98 2.34
4130 4368 1.302112 TGGTTCCGCAAATCGCAGA 60.302 52.632 0.00 0.00 42.60 4.26
4152 4390 1.889530 GACAAGGAGGACAGGACGGG 61.890 65.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.628500 TGTATCTAGCACTTAAATGAGTCTAGA 57.372 33.333 12.39 12.39 38.80 2.43
4 5 8.364142 GGATGTATCTAGCACTTAAATGAGTCT 58.636 37.037 0.00 0.00 0.00 3.24
5 6 7.327275 CGGATGTATCTAGCACTTAAATGAGTC 59.673 40.741 0.00 0.00 0.00 3.36
6 7 7.148641 CGGATGTATCTAGCACTTAAATGAGT 58.851 38.462 0.00 0.00 0.00 3.41
8 9 7.050970 ACGGATGTATCTAGCACTTAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
9 10 8.988064 ATACGGATGTATCTAGCACTTAAATG 57.012 34.615 0.00 0.00 36.56 2.32
24 25 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
25 26 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
26 27 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
27 28 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
28 29 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
29 30 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
37 38 9.793259 TCCAAATTACTTGTCTTAGATTTGTCT 57.207 29.630 0.00 0.00 34.40 3.41
40 41 9.329913 CGTTCCAAATTACTTGTCTTAGATTTG 57.670 33.333 0.00 0.00 35.40 2.32
41 42 8.512138 CCGTTCCAAATTACTTGTCTTAGATTT 58.488 33.333 0.00 0.00 32.65 2.17
42 43 7.881232 TCCGTTCCAAATTACTTGTCTTAGATT 59.119 33.333 0.00 0.00 32.65 2.40
43 44 7.391620 TCCGTTCCAAATTACTTGTCTTAGAT 58.608 34.615 0.00 0.00 32.65 1.98
44 45 6.761312 TCCGTTCCAAATTACTTGTCTTAGA 58.239 36.000 0.00 0.00 32.65 2.10
45 46 6.092259 CCTCCGTTCCAAATTACTTGTCTTAG 59.908 42.308 0.00 0.00 32.65 2.18
46 47 5.935789 CCTCCGTTCCAAATTACTTGTCTTA 59.064 40.000 0.00 0.00 32.65 2.10
47 48 4.760204 CCTCCGTTCCAAATTACTTGTCTT 59.240 41.667 0.00 0.00 32.65 3.01
48 49 4.324267 CCTCCGTTCCAAATTACTTGTCT 58.676 43.478 0.00 0.00 32.65 3.41
49 50 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
50 51 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
51 52 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
52 53 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
53 54 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
54 55 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
55 56 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
56 57 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
57 58 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
58 59 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
59 60 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
60 61 0.970937 CAGCTACTCCCTCCGTTCCA 60.971 60.000 0.00 0.00 0.00 3.53
61 62 0.683504 TCAGCTACTCCCTCCGTTCC 60.684 60.000 0.00 0.00 0.00 3.62
62 63 1.404843 ATCAGCTACTCCCTCCGTTC 58.595 55.000 0.00 0.00 0.00 3.95
63 64 1.757699 GAATCAGCTACTCCCTCCGTT 59.242 52.381 0.00 0.00 0.00 4.44
64 65 1.404843 GAATCAGCTACTCCCTCCGT 58.595 55.000 0.00 0.00 0.00 4.69
65 66 0.676736 GGAATCAGCTACTCCCTCCG 59.323 60.000 0.00 0.00 0.00 4.63
66 67 1.967779 GAGGAATCAGCTACTCCCTCC 59.032 57.143 11.32 2.01 35.39 4.30
67 68 1.967779 GGAGGAATCAGCTACTCCCTC 59.032 57.143 13.14 13.14 42.87 4.30
68 69 2.095604 GGAGGAATCAGCTACTCCCT 57.904 55.000 0.00 3.66 42.87 4.20
71 72 2.029470 CCGATGGAGGAATCAGCTACTC 60.029 54.545 0.00 0.00 0.00 2.59
72 73 1.967066 CCGATGGAGGAATCAGCTACT 59.033 52.381 0.00 0.00 0.00 2.57
73 74 1.606737 GCCGATGGAGGAATCAGCTAC 60.607 57.143 0.00 0.00 29.09 3.58
74 75 0.681733 GCCGATGGAGGAATCAGCTA 59.318 55.000 0.00 0.00 29.09 3.32
75 76 1.449353 GCCGATGGAGGAATCAGCT 59.551 57.895 0.00 0.00 29.09 4.24
76 77 1.958205 CGCCGATGGAGGAATCAGC 60.958 63.158 0.00 0.00 0.00 4.26
77 78 0.179073 AACGCCGATGGAGGAATCAG 60.179 55.000 0.00 0.00 0.00 2.90
78 79 1.116308 TAACGCCGATGGAGGAATCA 58.884 50.000 0.00 0.00 0.00 2.57
79 80 2.457366 ATAACGCCGATGGAGGAATC 57.543 50.000 0.00 0.00 0.00 2.52
80 81 2.930826 AATAACGCCGATGGAGGAAT 57.069 45.000 0.00 0.00 0.00 3.01
81 82 2.169769 AGAAATAACGCCGATGGAGGAA 59.830 45.455 0.00 0.00 0.00 3.36
82 83 1.760613 AGAAATAACGCCGATGGAGGA 59.239 47.619 0.00 0.00 0.00 3.71
83 84 1.867233 CAGAAATAACGCCGATGGAGG 59.133 52.381 0.00 0.00 0.00 4.30
84 85 1.867233 CCAGAAATAACGCCGATGGAG 59.133 52.381 0.00 0.00 0.00 3.86
85 86 1.483004 TCCAGAAATAACGCCGATGGA 59.517 47.619 0.00 0.00 33.11 3.41
86 87 1.867233 CTCCAGAAATAACGCCGATGG 59.133 52.381 0.00 0.00 0.00 3.51
87 88 2.550978 ACTCCAGAAATAACGCCGATG 58.449 47.619 0.00 0.00 0.00 3.84
88 89 2.936498 CAACTCCAGAAATAACGCCGAT 59.064 45.455 0.00 0.00 0.00 4.18
89 90 2.343101 CAACTCCAGAAATAACGCCGA 58.657 47.619 0.00 0.00 0.00 5.54
90 91 1.396996 CCAACTCCAGAAATAACGCCG 59.603 52.381 0.00 0.00 0.00 6.46
91 92 2.433436 ACCAACTCCAGAAATAACGCC 58.567 47.619 0.00 0.00 0.00 5.68
92 93 3.119955 GGAACCAACTCCAGAAATAACGC 60.120 47.826 0.00 0.00 35.36 4.84
93 94 3.124636 CGGAACCAACTCCAGAAATAACG 59.875 47.826 0.00 0.00 34.91 3.18
94 95 3.439129 CCGGAACCAACTCCAGAAATAAC 59.561 47.826 0.00 0.00 34.91 1.89
95 96 3.328343 TCCGGAACCAACTCCAGAAATAA 59.672 43.478 0.00 0.00 34.91 1.40
106 107 0.519961 CCATTTCGTCCGGAACCAAC 59.480 55.000 5.23 0.00 33.42 3.77
110 111 0.320946 TCACCCATTTCGTCCGGAAC 60.321 55.000 5.23 0.00 33.42 3.62
112 113 1.594833 CTCACCCATTTCGTCCGGA 59.405 57.895 0.00 0.00 0.00 5.14
115 116 2.092914 AGAATCCTCACCCATTTCGTCC 60.093 50.000 0.00 0.00 0.00 4.79
151 152 2.108970 GGATAGTTTCTCAGACGGGGT 58.891 52.381 0.00 0.00 0.00 4.95
156 157 5.423015 TCATGCTTGGATAGTTTCTCAGAC 58.577 41.667 0.00 0.00 0.00 3.51
168 169 2.958818 AGGATTGCATCATGCTTGGAT 58.041 42.857 11.84 0.00 45.31 3.41
169 170 2.447408 AGGATTGCATCATGCTTGGA 57.553 45.000 11.84 0.00 45.31 3.53
181 182 1.482182 GGAAATGGGTGGAAGGATTGC 59.518 52.381 0.00 0.00 36.73 3.56
186 187 1.379843 CCGGGAAATGGGTGGAAGG 60.380 63.158 0.00 0.00 0.00 3.46
187 188 2.052104 GCCGGGAAATGGGTGGAAG 61.052 63.158 2.18 0.00 0.00 3.46
189 190 1.616930 TAGCCGGGAAATGGGTGGA 60.617 57.895 2.18 0.00 37.84 4.02
190 191 1.453197 GTAGCCGGGAAATGGGTGG 60.453 63.158 2.18 0.00 37.84 4.61
194 195 0.815095 GTTTGGTAGCCGGGAAATGG 59.185 55.000 2.18 0.00 0.00 3.16
195 196 1.540267 TGTTTGGTAGCCGGGAAATG 58.460 50.000 2.18 0.00 0.00 2.32
196 197 2.099405 CATGTTTGGTAGCCGGGAAAT 58.901 47.619 2.18 0.00 0.00 2.17
197 198 1.540267 CATGTTTGGTAGCCGGGAAA 58.460 50.000 2.18 0.00 0.00 3.13
198 199 0.963355 GCATGTTTGGTAGCCGGGAA 60.963 55.000 2.18 0.00 0.00 3.97
199 200 1.377987 GCATGTTTGGTAGCCGGGA 60.378 57.895 2.18 0.00 0.00 5.14
200 201 1.037030 ATGCATGTTTGGTAGCCGGG 61.037 55.000 2.18 0.00 0.00 5.73
203 204 2.618709 GACCTATGCATGTTTGGTAGCC 59.381 50.000 10.16 0.00 0.00 3.93
216 222 0.183492 TTGGAGGCCATGACCTATGC 59.817 55.000 5.01 0.00 41.32 3.14
225 231 0.034089 GCTAGTTGGTTGGAGGCCAT 60.034 55.000 5.01 0.00 35.71 4.40
227 233 1.378646 GGCTAGTTGGTTGGAGGCC 60.379 63.158 0.00 0.00 0.00 5.19
295 301 4.394712 GGCTAGCTGTGCGTGGGT 62.395 66.667 15.72 0.00 0.00 4.51
329 335 1.159098 AGCGATCTCGTCTCGTACCC 61.159 60.000 1.14 0.00 42.22 3.69
344 350 2.750637 GTCGAGGTCCTCCAGCGA 60.751 66.667 13.54 4.79 39.27 4.93
345 351 4.180946 CGTCGAGGTCCTCCAGCG 62.181 72.222 13.54 10.98 35.93 5.18
346 352 2.750637 TCGTCGAGGTCCTCCAGC 60.751 66.667 13.54 2.93 35.89 4.85
347 353 2.115911 CCTCGTCGAGGTCCTCCAG 61.116 68.421 29.66 4.91 44.25 3.86
348 354 2.045242 CCTCGTCGAGGTCCTCCA 60.045 66.667 29.66 0.00 44.25 3.86
434 455 2.899256 CTGGATTGATTGGTTGGTTGGT 59.101 45.455 0.00 0.00 0.00 3.67
449 470 0.313672 GCTCGCTCGATCTCTGGATT 59.686 55.000 0.00 0.00 31.46 3.01
450 471 0.537143 AGCTCGCTCGATCTCTGGAT 60.537 55.000 0.00 0.00 34.45 3.41
451 472 1.153066 AGCTCGCTCGATCTCTGGA 60.153 57.895 0.00 0.00 0.00 3.86
721 760 6.401047 GCCATTGTTTTTATCTTTTTCTCCGC 60.401 38.462 0.00 0.00 0.00 5.54
722 761 6.183359 CGCCATTGTTTTTATCTTTTTCTCCG 60.183 38.462 0.00 0.00 0.00 4.63
723 762 6.090763 CCGCCATTGTTTTTATCTTTTTCTCC 59.909 38.462 0.00 0.00 0.00 3.71
725 764 5.408299 GCCGCCATTGTTTTTATCTTTTTCT 59.592 36.000 0.00 0.00 0.00 2.52
731 770 2.417243 GCTGCCGCCATTGTTTTTATCT 60.417 45.455 0.00 0.00 0.00 1.98
740 779 4.492160 CTGCTGCTGCCGCCATTG 62.492 66.667 13.49 0.00 38.71 2.82
746 785 4.834453 CTCCTCCTGCTGCTGCCG 62.834 72.222 13.47 6.57 38.71 5.69
747 786 4.486503 CCTCCTCCTGCTGCTGCC 62.487 72.222 13.47 0.00 38.71 4.85
748 787 3.388703 CTCCTCCTCCTGCTGCTGC 62.389 68.421 8.89 8.89 40.20 5.25
749 788 0.685785 TACTCCTCCTCCTGCTGCTG 60.686 60.000 0.00 0.00 0.00 4.41
750 789 0.686112 GTACTCCTCCTCCTGCTGCT 60.686 60.000 0.00 0.00 0.00 4.24
751 790 0.972983 TGTACTCCTCCTCCTGCTGC 60.973 60.000 0.00 0.00 0.00 5.25
752 791 1.561643 TTGTACTCCTCCTCCTGCTG 58.438 55.000 0.00 0.00 0.00 4.41
753 792 2.559381 ATTGTACTCCTCCTCCTGCT 57.441 50.000 0.00 0.00 0.00 4.24
832 871 5.451937 CGCTTTCCTTTTCTTTCCCTCTTTT 60.452 40.000 0.00 0.00 0.00 2.27
837 876 2.239400 CCGCTTTCCTTTTCTTTCCCT 58.761 47.619 0.00 0.00 0.00 4.20
841 880 1.338107 CCCCCGCTTTCCTTTTCTTT 58.662 50.000 0.00 0.00 0.00 2.52
903 948 2.226149 GAGGGGAAGAGGAGACGGGA 62.226 65.000 0.00 0.00 0.00 5.14
910 955 1.229529 GTGGGTGAGGGGAAGAGGA 60.230 63.158 0.00 0.00 0.00 3.71
1401 1555 4.171103 GCCACGGCGGGGAAGTAT 62.171 66.667 36.08 0.00 34.06 2.12
1785 1949 4.720902 TGGTCGACGTAGCGGGGA 62.721 66.667 9.92 0.00 0.00 4.81
1936 2100 3.804193 GAGCGCGGCAAAGAAGGG 61.804 66.667 8.83 0.00 0.00 3.95
2007 2171 3.011517 AGCTCCTCCATTGCCGGT 61.012 61.111 1.90 0.00 0.00 5.28
2247 2411 1.557371 GCTAGCCTCCTAATCCCATCC 59.443 57.143 2.29 0.00 0.00 3.51
2256 2420 1.600076 CGCCGTAGCTAGCCTCCTA 60.600 63.158 12.13 0.00 36.60 2.94
2305 2469 2.844451 GCAGAAACCGGCAGTGCAA 61.844 57.895 18.61 0.00 34.18 4.08
2370 2534 3.309138 CACAATTGATCTCAAGGCTCTCG 59.691 47.826 13.59 0.00 39.47 4.04
2388 2552 0.764890 CAACCTCCTCCCAGTCACAA 59.235 55.000 0.00 0.00 0.00 3.33
2475 2639 1.334960 GCGGATTGGTATGCCATTTCG 60.335 52.381 17.99 17.99 45.24 3.46
2484 2648 1.525995 CTTGGGCGCGGATTGGTAT 60.526 57.895 8.83 0.00 0.00 2.73
2490 2654 2.774799 GCATTTCTTGGGCGCGGAT 61.775 57.895 8.83 0.00 0.00 4.18
2532 2696 4.583489 AGCATCTCCCAGCTTTCATAATTG 59.417 41.667 0.00 0.00 38.01 2.32
2559 2723 0.606673 GGCACCAAAGGGAGAGTGAC 60.607 60.000 0.00 0.00 38.05 3.67
2589 2753 1.757699 GAAATGAGCGGGGAGAGTAGT 59.242 52.381 0.00 0.00 0.00 2.73
2592 2756 0.539051 CAGAAATGAGCGGGGAGAGT 59.461 55.000 0.00 0.00 0.00 3.24
2736 2900 0.323178 CCAGCTTCATCTTGGCCAGT 60.323 55.000 5.11 0.00 0.00 4.00
2833 2997 3.512329 AGCAATGATTCAATGCCACTCAA 59.488 39.130 20.36 0.00 40.72 3.02
2838 3002 3.093814 ACTCAGCAATGATTCAATGCCA 58.906 40.909 20.36 8.90 40.72 4.92
2841 3005 7.971722 TCATACAAACTCAGCAATGATTCAATG 59.028 33.333 0.00 0.00 0.00 2.82
2844 3008 6.403964 GCTCATACAAACTCAGCAATGATTCA 60.404 38.462 0.00 0.00 0.00 2.57
2847 3011 5.066117 CAGCTCATACAAACTCAGCAATGAT 59.934 40.000 0.00 0.00 32.17 2.45
2892 3056 1.553248 CTCCGGTGGTTCACATCCTTA 59.447 52.381 0.00 0.00 35.86 2.69
3021 3185 0.796927 GCTGCACGTCCCTTAAGTTC 59.203 55.000 0.97 0.00 0.00 3.01
3027 3191 1.296715 CCTTAGCTGCACGTCCCTT 59.703 57.895 1.02 0.00 0.00 3.95
3075 3239 3.056322 CCCGCATCTCTGTGATCATCATA 60.056 47.826 0.00 0.00 34.71 2.15
3102 3266 0.733223 GCTCGAACCGGAGACAAGAC 60.733 60.000 9.46 0.00 36.08 3.01
3158 3357 4.569162 CGAAATTGCCAATTCAGCATCAAT 59.431 37.500 2.61 0.00 40.59 2.57
3159 3358 3.927758 CGAAATTGCCAATTCAGCATCAA 59.072 39.130 2.61 0.00 40.59 2.57
3160 3359 3.513662 CGAAATTGCCAATTCAGCATCA 58.486 40.909 2.61 0.00 40.59 3.07
3161 3360 2.861935 CCGAAATTGCCAATTCAGCATC 59.138 45.455 2.61 0.00 40.59 3.91
3162 3361 2.896168 CCGAAATTGCCAATTCAGCAT 58.104 42.857 2.61 0.00 40.59 3.79
3163 3362 1.672441 GCCGAAATTGCCAATTCAGCA 60.672 47.619 2.61 0.00 38.81 4.41
3164 3363 1.001624 GCCGAAATTGCCAATTCAGC 58.998 50.000 2.61 3.48 0.00 4.26
3165 3364 2.367030 TGCCGAAATTGCCAATTCAG 57.633 45.000 2.61 0.89 0.00 3.02
3166 3365 2.827800 TTGCCGAAATTGCCAATTCA 57.172 40.000 2.61 0.00 0.00 2.57
3167 3366 4.437255 GGAATTTGCCGAAATTGCCAATTC 60.437 41.667 2.61 13.28 44.14 2.17
3168 3367 3.439825 GGAATTTGCCGAAATTGCCAATT 59.560 39.130 0.00 0.00 41.60 2.32
3169 3368 3.009026 GGAATTTGCCGAAATTGCCAAT 58.991 40.909 0.00 0.00 41.60 3.16
3170 3369 2.038295 AGGAATTTGCCGAAATTGCCAA 59.962 40.909 9.26 0.00 46.01 4.52
3171 3370 1.622811 AGGAATTTGCCGAAATTGCCA 59.377 42.857 9.26 0.00 46.01 4.92
3172 3371 2.001872 CAGGAATTTGCCGAAATTGCC 58.998 47.619 9.26 6.45 46.01 4.52
3173 3372 2.958213 TCAGGAATTTGCCGAAATTGC 58.042 42.857 5.84 5.84 45.50 3.56
3174 3373 6.254157 CACTAATCAGGAATTTGCCGAAATTG 59.746 38.462 0.00 0.00 41.06 2.32
3175 3374 6.332630 CACTAATCAGGAATTTGCCGAAATT 58.667 36.000 0.00 0.00 43.20 1.82
3176 3375 5.679638 GCACTAATCAGGAATTTGCCGAAAT 60.680 40.000 0.00 0.00 32.87 2.17
3177 3376 4.380444 GCACTAATCAGGAATTTGCCGAAA 60.380 41.667 0.00 0.00 28.74 3.46
3178 3377 3.128589 GCACTAATCAGGAATTTGCCGAA 59.871 43.478 0.00 0.00 28.74 4.30
3179 3378 2.682856 GCACTAATCAGGAATTTGCCGA 59.317 45.455 0.00 0.00 28.74 5.54
3180 3379 2.684881 AGCACTAATCAGGAATTTGCCG 59.315 45.455 0.00 0.00 33.40 5.69
3181 3380 3.696051 TCAGCACTAATCAGGAATTTGCC 59.304 43.478 0.00 0.00 33.40 4.52
3182 3381 4.970662 TCAGCACTAATCAGGAATTTGC 57.029 40.909 0.00 0.00 33.20 3.68
3183 3382 6.755141 CCAATTCAGCACTAATCAGGAATTTG 59.245 38.462 0.00 0.00 33.93 2.32
3184 3383 6.127253 CCCAATTCAGCACTAATCAGGAATTT 60.127 38.462 0.00 0.00 33.93 1.82
3185 3384 5.361857 CCCAATTCAGCACTAATCAGGAATT 59.638 40.000 0.00 0.00 35.89 2.17
3186 3385 4.891756 CCCAATTCAGCACTAATCAGGAAT 59.108 41.667 0.00 0.00 0.00 3.01
3187 3386 4.263905 ACCCAATTCAGCACTAATCAGGAA 60.264 41.667 0.00 0.00 0.00 3.36
3188 3387 3.266772 ACCCAATTCAGCACTAATCAGGA 59.733 43.478 0.00 0.00 0.00 3.86
3189 3388 3.379372 CACCCAATTCAGCACTAATCAGG 59.621 47.826 0.00 0.00 0.00 3.86
3190 3389 3.181493 GCACCCAATTCAGCACTAATCAG 60.181 47.826 0.00 0.00 0.00 2.90
3191 3390 2.754552 GCACCCAATTCAGCACTAATCA 59.245 45.455 0.00 0.00 0.00 2.57
3192 3391 2.754552 TGCACCCAATTCAGCACTAATC 59.245 45.455 0.00 0.00 31.05 1.75
3241 3440 2.575532 CAAAGGGCTCTCTGTGTTGAA 58.424 47.619 0.00 0.00 0.00 2.69
3260 3459 2.703536 TCTGGGTGACTAAACAAGAGCA 59.296 45.455 0.00 0.00 0.00 4.26
3299 3498 0.099436 GATCATCGCAAGCAACCCAC 59.901 55.000 0.00 0.00 37.18 4.61
3318 3517 3.596214 AGCAATTCCAGTTACTACACCG 58.404 45.455 0.00 0.00 0.00 4.94
3370 3569 1.073964 CACTGTCACTTGATCAGGCG 58.926 55.000 4.46 0.00 34.02 5.52
3657 3857 1.610522 AGAGTGAAATGTGGCACTTGC 59.389 47.619 19.83 9.69 44.77 4.01
3661 3861 3.254166 ACAATGAGAGTGAAATGTGGCAC 59.746 43.478 11.55 11.55 35.30 5.01
3738 3938 4.618927 GCAGCAAACCAATCATGTACACAT 60.619 41.667 0.00 0.00 36.96 3.21
3741 3941 2.230992 GGCAGCAAACCAATCATGTACA 59.769 45.455 0.00 0.00 0.00 2.90
3748 3948 0.681175 ACAAGGGCAGCAAACCAATC 59.319 50.000 0.00 0.00 0.00 2.67
3749 3949 0.393820 CACAAGGGCAGCAAACCAAT 59.606 50.000 0.00 0.00 0.00 3.16
3751 3951 0.975040 AACACAAGGGCAGCAAACCA 60.975 50.000 0.00 0.00 0.00 3.67
3753 3953 2.100749 AGTAAACACAAGGGCAGCAAAC 59.899 45.455 0.00 0.00 0.00 2.93
3754 3954 2.383855 AGTAAACACAAGGGCAGCAAA 58.616 42.857 0.00 0.00 0.00 3.68
3755 3955 2.065899 AGTAAACACAAGGGCAGCAA 57.934 45.000 0.00 0.00 0.00 3.91
3756 3956 2.105821 AGTAGTAAACACAAGGGCAGCA 59.894 45.455 0.00 0.00 0.00 4.41
3757 3957 2.484264 CAGTAGTAAACACAAGGGCAGC 59.516 50.000 0.00 0.00 0.00 5.25
3761 3961 4.750098 CAGTGACAGTAGTAAACACAAGGG 59.250 45.833 0.00 0.00 34.47 3.95
3762 3962 5.234329 CACAGTGACAGTAGTAAACACAAGG 59.766 44.000 0.00 0.00 34.47 3.61
3763 3963 5.276868 GCACAGTGACAGTAGTAAACACAAG 60.277 44.000 4.15 0.00 34.47 3.16
3764 3964 4.569162 GCACAGTGACAGTAGTAAACACAA 59.431 41.667 4.15 0.00 34.47 3.33
3765 3965 4.116961 GCACAGTGACAGTAGTAAACACA 58.883 43.478 4.15 0.00 34.47 3.72
3766 3966 3.493503 GGCACAGTGACAGTAGTAAACAC 59.506 47.826 4.15 0.00 0.00 3.32
3768 3968 3.064931 GGGCACAGTGACAGTAGTAAAC 58.935 50.000 9.17 0.00 0.00 2.01
3770 3970 2.605257 AGGGCACAGTGACAGTAGTAA 58.395 47.619 9.17 0.00 0.00 2.24
3771 3971 2.299013 CAAGGGCACAGTGACAGTAGTA 59.701 50.000 9.17 0.00 0.00 1.82
3772 3972 1.070758 CAAGGGCACAGTGACAGTAGT 59.929 52.381 9.17 0.00 0.00 2.73
3773 3973 1.070758 ACAAGGGCACAGTGACAGTAG 59.929 52.381 9.17 0.00 0.00 2.57
3774 3974 1.128200 ACAAGGGCACAGTGACAGTA 58.872 50.000 9.17 0.00 0.00 2.74
3775 3975 0.464373 CACAAGGGCACAGTGACAGT 60.464 55.000 9.17 0.17 35.33 3.55
3776 3976 0.464373 ACACAAGGGCACAGTGACAG 60.464 55.000 17.14 0.00 37.05 3.51
3781 3981 2.729028 AGTAAACACAAGGGCACAGT 57.271 45.000 0.00 0.00 0.00 3.55
3787 3987 6.877611 AATTGACAGTAGTAAACACAAGGG 57.122 37.500 0.00 0.00 0.00 3.95
3795 3995 6.775629 AGGCAAAGGAAATTGACAGTAGTAAA 59.224 34.615 0.00 0.00 40.96 2.01
3822 4022 1.545428 GGTCAACCCTGTTGATGCAGA 60.545 52.381 12.31 0.00 38.70 4.26
3824 4024 0.184692 TGGTCAACCCTGTTGATGCA 59.815 50.000 12.31 0.00 34.29 3.96
3825 4025 1.549203 ATGGTCAACCCTGTTGATGC 58.451 50.000 12.31 1.76 34.29 3.91
3827 4027 4.657814 ACTTATGGTCAACCCTGTTGAT 57.342 40.909 12.31 0.70 34.29 2.57
3828 4028 4.141367 TGAACTTATGGTCAACCCTGTTGA 60.141 41.667 5.59 5.59 34.29 3.18
3829 4029 4.141287 TGAACTTATGGTCAACCCTGTTG 58.859 43.478 0.55 0.55 34.29 3.33
3830 4030 4.447138 TGAACTTATGGTCAACCCTGTT 57.553 40.909 0.00 0.00 34.29 3.16
3874 4074 1.664659 CAGTACTCAGCAGCAGATTGC 59.335 52.381 0.00 0.00 45.46 3.56
3884 4084 4.645762 TCATCTCATGTCAGTACTCAGC 57.354 45.455 0.00 0.00 0.00 4.26
3914 4121 4.448210 GGTGAACTTTCTTGTGTCAGGTA 58.552 43.478 0.00 0.00 0.00 3.08
3935 4144 2.618709 GACTGAAATCTTAATGGCCGGG 59.381 50.000 2.18 0.00 0.00 5.73
3938 4147 7.663081 TCATATCAGACTGAAATCTTAATGGCC 59.337 37.037 9.70 0.00 0.00 5.36
3949 4158 6.358974 TTCTGTGGTCATATCAGACTGAAA 57.641 37.500 9.70 0.00 37.84 2.69
3961 4170 6.891908 AGTTAATTTAGGCATTCTGTGGTCAT 59.108 34.615 0.00 0.00 0.00 3.06
3966 4189 9.346725 GAAGAAAGTTAATTTAGGCATTCTGTG 57.653 33.333 0.00 0.00 0.00 3.66
3977 4200 9.691362 GCATCAACAAGGAAGAAAGTTAATTTA 57.309 29.630 0.00 0.00 0.00 1.40
4038 4261 2.026641 GATGATGGGCAGCTTTGCTTA 58.973 47.619 0.00 0.00 36.40 3.09
4043 4266 0.465097 CTCGGATGATGGGCAGCTTT 60.465 55.000 0.00 0.00 32.29 3.51
4048 4271 2.507452 CTGCTCGGATGATGGGCA 59.493 61.111 0.00 0.00 0.00 5.36
4059 4282 2.110967 CATTGTGGGAGCCTGCTCG 61.111 63.158 12.65 0.00 43.59 5.03
4130 4368 1.276421 CGTCCTGTCCTCCTTGTCATT 59.724 52.381 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.