Multiple sequence alignment - TraesCS5B01G291700

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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 TraesCS5B01G291700 chr5B 100.000 3570 0 0 1 3570 477083648 477080079 0.000000e+00 6593.0
1 TraesCS5B01G291700 chr5B 97.917 48 1 0 708 755 477082901 477082854 2.280000e-12 84.2
2 TraesCS5B01G291700 chr5B 97.917 48 1 0 748 795 477082941 477082894 2.280000e-12 84.2
3 TraesCS5B01G291700 chr5B 84.058 69 7 2 2907 2975 9224628 9224692 2.980000e-06 63.9
4 TraesCS5B01G291700 chr5B 97.059 34 0 1 28 60 91200768 91200735 4.980000e-04 56.5
5 TraesCS5B01G291700 chr5D 88.819 2057 134 43 816 2825 397016711 397014704 0.000000e+00 2436.0
6 TraesCS5B01G291700 chr5D 88.315 368 23 11 368 731 397017097 397016746 1.180000e-114 424.0
7 TraesCS5B01G291700 chr5D 87.619 105 12 1 126 230 397017597 397017494 1.740000e-23 121.0
8 TraesCS5B01G291700 chr5D 86.441 59 7 1 2945 3002 298760244 298760302 2.980000e-06 63.9
9 TraesCS5B01G291700 chr5A 88.828 1101 62 25 753 1824 502548374 502547306 0.000000e+00 1295.0
10 TraesCS5B01G291700 chr5A 88.621 747 66 9 2828 3570 502545801 502545070 0.000000e+00 891.0
11 TraesCS5B01G291700 chr5A 88.519 601 61 6 2196 2788 502546923 502546323 0.000000e+00 721.0
12 TraesCS5B01G291700 chr5A 83.206 393 37 16 365 755 502548697 502548332 2.050000e-87 333.0
13 TraesCS5B01G291700 chr5A 84.475 219 17 8 1963 2177 502547188 502546983 2.170000e-47 200.0
14 TraesCS5B01G291700 chr6D 90.909 55 5 0 25 79 94283307 94283361 1.370000e-09 75.0
15 TraesCS5B01G291700 chr6B 87.097 62 8 0 1 62 54877298 54877237 1.780000e-08 71.3
16 TraesCS5B01G291700 chr6B 85.075 67 6 2 2907 2973 19032762 19032700 8.270000e-07 65.8
17 TraesCS5B01G291700 chr3B 84.000 75 6 6 2907 2975 782462089 782462015 2.300000e-07 67.6
18 TraesCS5B01G291700 chr3B 93.023 43 3 0 20 62 654338508 654338466 2.980000e-06 63.9
19 TraesCS5B01G291700 chr3B 97.143 35 1 0 28 62 775072507 775072473 3.850000e-05 60.2
20 TraesCS5B01G291700 chr3B 100.000 31 0 0 2906 2936 73689445 73689475 1.380000e-04 58.4
21 TraesCS5B01G291700 chr7D 87.273 55 6 1 2945 2998 131709574 131709628 1.070000e-05 62.1
22 TraesCS5B01G291700 chr7B 82.667 75 7 3 2907 2975 501519435 501519509 1.070000e-05 62.1
23 TraesCS5B01G291700 chr4D 87.273 55 6 1 2945 2998 465609738 465609684 1.070000e-05 62.1
24 TraesCS5B01G291700 chr4B 78.095 105 14 4 2906 3002 655776240 655776137 1.380000e-04 58.4
25 TraesCS5B01G291700 chr1A 86.538 52 7 0 11 62 561595046 561595097 1.380000e-04 58.4


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 TraesCS5B01G291700 chr5B 477080079 477083648 3569 True 2253.800000 6593 98.611333 1 3570 3 chr5B.!!$R2 3569
1 TraesCS5B01G291700 chr5D 397014704 397017597 2893 True 993.666667 2436 88.251000 126 2825 3 chr5D.!!$R1 2699
2 TraesCS5B01G291700 chr5A 502545070 502548697 3627 True 688.000000 1295 86.729800 365 3570 5 chr5A.!!$R1 3205

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
116 117 0.332972 GAGGGGGAGGAAACAAGCAT 59.667 55.0 0.00 0.0 0.0 3.79 F
245 246 0.913924 TTAACCCCCTTTAGCGGAGG 59.086 55.0 0.00 0.0 0.0 4.30 F
1429 1783 0.236187 CATTCGTTTTGGTTCGCGGA 59.764 50.0 6.13 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1769 0.658897 TTCACTCCGCGAACCAAAAC 59.341 50.0 8.23 0.0 0.0 2.43 R
2180 2651 0.037447 GGGTGAAGCCTGAAGAAGCT 59.963 55.0 0.00 0.0 42.4 3.74 R
2835 3807 0.038892 CTTGCAGCCACACAATCACC 60.039 55.0 0.00 0.0 0.0 4.02 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
66 67 7.317842 ACTAATATATGATACTCCCACGACG 57.682 40.000 0.00 0.00 0.00 5.12
67 68 7.108194 ACTAATATATGATACTCCCACGACGA 58.892 38.462 0.00 0.00 0.00 4.20
68 69 6.438259 AATATATGATACTCCCACGACGAG 57.562 41.667 0.00 0.00 0.00 4.18
69 70 2.054232 ATGATACTCCCACGACGAGT 57.946 50.000 0.00 0.00 43.05 4.18
70 71 2.696989 TGATACTCCCACGACGAGTA 57.303 50.000 0.00 11.45 44.67 2.59
71 72 2.558378 TGATACTCCCACGACGAGTAG 58.442 52.381 0.00 0.00 44.01 2.57
72 73 1.263752 GATACTCCCACGACGAGTAGC 59.736 57.143 0.00 11.58 44.01 3.58
73 74 0.745845 TACTCCCACGACGAGTAGCC 60.746 60.000 0.00 0.00 40.93 3.93
74 75 1.749638 CTCCCACGACGAGTAGCCT 60.750 63.158 0.00 0.00 0.00 4.58
75 76 1.994507 CTCCCACGACGAGTAGCCTG 61.995 65.000 0.00 0.00 0.00 4.85
76 77 2.044555 CCCACGACGAGTAGCCTGA 61.045 63.158 0.00 0.00 0.00 3.86
77 78 1.384989 CCCACGACGAGTAGCCTGAT 61.385 60.000 0.00 0.00 0.00 2.90
78 79 1.306148 CCACGACGAGTAGCCTGATA 58.694 55.000 0.00 0.00 0.00 2.15
79 80 1.880675 CCACGACGAGTAGCCTGATAT 59.119 52.381 0.00 0.00 0.00 1.63
80 81 2.350868 CCACGACGAGTAGCCTGATATG 60.351 54.545 0.00 0.00 0.00 1.78
81 82 2.290916 CACGACGAGTAGCCTGATATGT 59.709 50.000 0.00 0.00 0.00 2.29
82 83 2.950309 ACGACGAGTAGCCTGATATGTT 59.050 45.455 0.00 0.00 0.00 2.71
83 84 3.380637 ACGACGAGTAGCCTGATATGTTT 59.619 43.478 0.00 0.00 0.00 2.83
84 85 3.731216 CGACGAGTAGCCTGATATGTTTG 59.269 47.826 0.00 0.00 0.00 2.93
85 86 4.497507 CGACGAGTAGCCTGATATGTTTGA 60.498 45.833 0.00 0.00 0.00 2.69
86 87 4.938080 ACGAGTAGCCTGATATGTTTGAG 58.062 43.478 0.00 0.00 0.00 3.02
87 88 4.202161 ACGAGTAGCCTGATATGTTTGAGG 60.202 45.833 0.00 0.00 0.00 3.86
88 89 4.636249 GAGTAGCCTGATATGTTTGAGGG 58.364 47.826 0.00 0.00 0.00 4.30
89 90 3.392616 AGTAGCCTGATATGTTTGAGGGG 59.607 47.826 0.00 0.00 0.00 4.79
90 91 1.496429 AGCCTGATATGTTTGAGGGGG 59.504 52.381 0.00 0.00 0.00 5.40
108 109 3.707189 GAGGGGGAGGGGGAGGAA 61.707 72.222 0.00 0.00 0.00 3.36
109 110 3.224269 AGGGGGAGGGGGAGGAAA 61.224 66.667 0.00 0.00 0.00 3.13
110 111 3.021880 GGGGGAGGGGGAGGAAAC 61.022 72.222 0.00 0.00 0.00 2.78
111 112 2.204244 GGGGAGGGGGAGGAAACA 60.204 66.667 0.00 0.00 0.00 2.83
112 113 1.855451 GGGGAGGGGGAGGAAACAA 60.855 63.158 0.00 0.00 0.00 2.83
113 114 1.691823 GGGAGGGGGAGGAAACAAG 59.308 63.158 0.00 0.00 0.00 3.16
114 115 1.000771 GGAGGGGGAGGAAACAAGC 60.001 63.158 0.00 0.00 0.00 4.01
115 116 1.767692 GAGGGGGAGGAAACAAGCA 59.232 57.895 0.00 0.00 0.00 3.91
116 117 0.332972 GAGGGGGAGGAAACAAGCAT 59.667 55.000 0.00 0.00 0.00 3.79
117 118 1.564348 GAGGGGGAGGAAACAAGCATA 59.436 52.381 0.00 0.00 0.00 3.14
118 119 2.000048 AGGGGGAGGAAACAAGCATAA 59.000 47.619 0.00 0.00 0.00 1.90
119 120 2.587307 AGGGGGAGGAAACAAGCATAAT 59.413 45.455 0.00 0.00 0.00 1.28
120 121 3.791545 AGGGGGAGGAAACAAGCATAATA 59.208 43.478 0.00 0.00 0.00 0.98
121 122 4.420214 AGGGGGAGGAAACAAGCATAATAT 59.580 41.667 0.00 0.00 0.00 1.28
122 123 4.524328 GGGGGAGGAAACAAGCATAATATG 59.476 45.833 0.00 0.00 0.00 1.78
149 150 5.593968 TGCCATCATGAAGATTATTTGTGC 58.406 37.500 0.00 0.00 33.72 4.57
200 201 6.862608 TGCAATTAGTGAAATTAGTGTTGCTG 59.137 34.615 0.00 0.00 39.88 4.41
202 203 6.824305 ATTAGTGAAATTAGTGTTGCTGCT 57.176 33.333 0.00 0.00 0.00 4.24
209 210 8.450964 GTGAAATTAGTGTTGCTGCTAGAATAA 58.549 33.333 0.00 2.26 0.00 1.40
211 212 9.840427 GAAATTAGTGTTGCTGCTAGAATAAAA 57.160 29.630 5.43 0.00 0.00 1.52
216 217 7.978982 AGTGTTGCTGCTAGAATAAAATACAG 58.021 34.615 0.00 0.00 0.00 2.74
241 242 7.571080 TTAATGTAATTAACCCCCTTTAGCG 57.429 36.000 0.00 0.00 43.40 4.26
242 243 3.888583 TGTAATTAACCCCCTTTAGCGG 58.111 45.455 0.00 0.00 0.00 5.52
243 244 3.522750 TGTAATTAACCCCCTTTAGCGGA 59.477 43.478 0.00 0.00 0.00 5.54
244 245 3.292492 AATTAACCCCCTTTAGCGGAG 57.708 47.619 0.00 0.00 0.00 4.63
245 246 0.913924 TTAACCCCCTTTAGCGGAGG 59.086 55.000 0.00 0.00 0.00 4.30
255 256 5.485209 CCTTTAGCGGAGGGAGTATATTT 57.515 43.478 0.00 0.00 0.00 1.40
256 257 5.480205 CCTTTAGCGGAGGGAGTATATTTC 58.520 45.833 0.00 0.00 0.00 2.17
257 258 5.011738 CCTTTAGCGGAGGGAGTATATTTCA 59.988 44.000 0.00 0.00 0.00 2.69
258 259 6.463897 CCTTTAGCGGAGGGAGTATATTTCAA 60.464 42.308 0.00 0.00 0.00 2.69
259 260 6.488769 TTAGCGGAGGGAGTATATTTCAAA 57.511 37.500 0.00 0.00 0.00 2.69
260 261 5.367945 AGCGGAGGGAGTATATTTCAAAA 57.632 39.130 0.00 0.00 0.00 2.44
261 262 5.751586 AGCGGAGGGAGTATATTTCAAAAA 58.248 37.500 0.00 0.00 0.00 1.94
322 323 6.408858 AATTTATCGCGATGTCATGGATAC 57.591 37.500 31.05 0.00 0.00 2.24
346 446 6.205464 ACATCATTAGAATAAGAATGGCGTGG 59.795 38.462 0.00 0.00 34.45 4.94
348 448 5.991606 TCATTAGAATAAGAATGGCGTGGAG 59.008 40.000 0.00 0.00 34.45 3.86
349 449 3.914426 AGAATAAGAATGGCGTGGAGT 57.086 42.857 0.00 0.00 0.00 3.85
350 450 3.535561 AGAATAAGAATGGCGTGGAGTG 58.464 45.455 0.00 0.00 0.00 3.51
351 451 3.055094 AGAATAAGAATGGCGTGGAGTGT 60.055 43.478 0.00 0.00 0.00 3.55
354 454 2.851263 AGAATGGCGTGGAGTGTTTA 57.149 45.000 0.00 0.00 0.00 2.01
357 457 4.079253 AGAATGGCGTGGAGTGTTTAATT 58.921 39.130 0.00 0.00 0.00 1.40
358 458 4.522789 AGAATGGCGTGGAGTGTTTAATTT 59.477 37.500 0.00 0.00 0.00 1.82
359 459 4.864704 ATGGCGTGGAGTGTTTAATTTT 57.135 36.364 0.00 0.00 0.00 1.82
360 460 4.657436 TGGCGTGGAGTGTTTAATTTTT 57.343 36.364 0.00 0.00 0.00 1.94
395 679 2.632996 AGAGGATCGGTTGACTTTGACA 59.367 45.455 0.00 0.00 42.67 3.58
483 768 3.578688 ACGAAAACGACCCACACTATAC 58.421 45.455 0.00 0.00 0.00 1.47
527 820 1.466167 CCACAAGCAACGAATCCTGAG 59.534 52.381 0.00 0.00 0.00 3.35
528 821 2.146342 CACAAGCAACGAATCCTGAGT 58.854 47.619 0.00 0.00 0.00 3.41
529 822 2.549754 CACAAGCAACGAATCCTGAGTT 59.450 45.455 0.00 0.00 0.00 3.01
531 824 2.100605 AGCAACGAATCCTGAGTTCC 57.899 50.000 0.00 0.00 0.00 3.62
533 826 1.734465 GCAACGAATCCTGAGTTCCTG 59.266 52.381 0.00 0.00 0.00 3.86
534 827 2.612972 GCAACGAATCCTGAGTTCCTGA 60.613 50.000 0.00 0.00 0.00 3.86
535 828 2.996621 CAACGAATCCTGAGTTCCTGAC 59.003 50.000 0.00 0.00 0.00 3.51
536 829 2.530701 ACGAATCCTGAGTTCCTGACT 58.469 47.619 0.00 0.00 42.70 3.41
537 830 2.232452 ACGAATCCTGAGTTCCTGACTG 59.768 50.000 0.00 0.00 39.19 3.51
538 831 2.493675 CGAATCCTGAGTTCCTGACTGA 59.506 50.000 0.00 0.00 39.19 3.41
539 832 3.056536 CGAATCCTGAGTTCCTGACTGAA 60.057 47.826 0.00 0.00 39.19 3.02
540 833 3.971245 ATCCTGAGTTCCTGACTGAAC 57.029 47.619 0.00 0.00 43.95 3.18
575 868 1.806461 GACCCTGCACTGTCTCGTGA 61.806 60.000 4.05 0.00 37.06 4.35
576 869 1.080230 CCCTGCACTGTCTCGTGAG 60.080 63.158 0.00 0.00 37.06 3.51
736 1034 2.738480 GTGCACCGGGTCTACACA 59.262 61.111 5.22 0.77 0.00 3.72
737 1035 1.374252 GTGCACCGGGTCTACACAG 60.374 63.158 5.22 0.00 0.00 3.66
738 1036 2.264794 GCACCGGGTCTACACAGG 59.735 66.667 6.32 0.00 0.00 4.00
739 1037 2.978824 CACCGGGTCTACACAGGG 59.021 66.667 6.32 0.00 0.00 4.45
740 1038 2.284405 ACCGGGTCTACACAGGGG 60.284 66.667 6.32 0.00 0.00 4.79
741 1039 3.782443 CCGGGTCTACACAGGGGC 61.782 72.222 0.00 0.00 0.00 5.80
742 1040 4.143333 CGGGTCTACACAGGGGCG 62.143 72.222 0.00 0.00 0.00 6.13
743 1041 3.782443 GGGTCTACACAGGGGCGG 61.782 72.222 0.00 0.00 0.00 6.13
744 1042 4.468689 GGTCTACACAGGGGCGGC 62.469 72.222 0.00 0.00 0.00 6.53
745 1043 3.702048 GTCTACACAGGGGCGGCA 61.702 66.667 12.47 0.00 0.00 5.69
746 1044 3.702048 TCTACACAGGGGCGGCAC 61.702 66.667 12.47 7.44 0.00 5.01
747 1045 4.778143 CTACACAGGGGCGGCACC 62.778 72.222 15.02 15.02 37.93 5.01
775 1073 2.431942 CGTGCACCGGGTCTACAC 60.432 66.667 12.15 12.34 0.00 2.90
776 1074 2.738480 GTGCACCGGGTCTACACA 59.262 61.111 5.22 0.77 0.00 3.72
777 1075 1.374252 GTGCACCGGGTCTACACAG 60.374 63.158 5.22 0.00 0.00 3.66
782 1080 4.143333 CGGGTCTACACAGGGGCG 62.143 72.222 0.00 0.00 0.00 6.13
812 1115 2.507339 CGAAGCTTCCTCCTCTCATC 57.493 55.000 20.62 0.00 0.00 2.92
813 1116 1.753649 CGAAGCTTCCTCCTCTCATCA 59.246 52.381 20.62 0.00 0.00 3.07
814 1117 2.167281 CGAAGCTTCCTCCTCTCATCAA 59.833 50.000 20.62 0.00 0.00 2.57
815 1118 3.530535 GAAGCTTCCTCCTCTCATCAAC 58.469 50.000 15.97 0.00 0.00 3.18
816 1119 2.831565 AGCTTCCTCCTCTCATCAACT 58.168 47.619 0.00 0.00 0.00 3.16
817 1120 2.765699 AGCTTCCTCCTCTCATCAACTC 59.234 50.000 0.00 0.00 0.00 3.01
818 1121 2.765699 GCTTCCTCCTCTCATCAACTCT 59.234 50.000 0.00 0.00 0.00 3.24
819 1122 3.181476 GCTTCCTCCTCTCATCAACTCTC 60.181 52.174 0.00 0.00 0.00 3.20
834 1137 1.099689 CTCTCCTCTCCCGAGTTGTC 58.900 60.000 0.00 0.00 35.43 3.18
896 1206 4.595538 GCCACCCGACGACACACA 62.596 66.667 0.00 0.00 0.00 3.72
897 1207 2.660552 CCACCCGACGACACACAC 60.661 66.667 0.00 0.00 0.00 3.82
898 1208 2.660552 CACCCGACGACACACACC 60.661 66.667 0.00 0.00 0.00 4.16
899 1209 3.148963 ACCCGACGACACACACCA 61.149 61.111 0.00 0.00 0.00 4.17
900 1210 2.660552 CCCGACGACACACACCAC 60.661 66.667 0.00 0.00 0.00 4.16
933 1243 2.393764 CAACGCAACAATCTCCAAACC 58.606 47.619 0.00 0.00 0.00 3.27
996 1330 2.179517 CTCGTCGACCAGCCAGAC 59.820 66.667 10.58 0.00 0.00 3.51
1403 1755 2.811317 GTGAACTGAGGAGCGCGG 60.811 66.667 8.83 0.00 0.00 6.46
1420 1774 4.163902 GCGCGCGCATTCGTTTTG 62.164 61.111 46.11 12.36 41.49 2.44
1429 1783 0.236187 CATTCGTTTTGGTTCGCGGA 59.764 50.000 6.13 0.00 0.00 5.54
1674 2029 4.202295 CCAGAGTAAGCTAGCCATTCATCA 60.202 45.833 12.13 0.00 0.00 3.07
1735 2091 2.862541 TGCCGATCAAATGGGGATTAG 58.137 47.619 0.00 0.00 0.00 1.73
1738 2094 3.412386 CCGATCAAATGGGGATTAGTCC 58.588 50.000 0.00 0.00 44.29 3.85
1786 2156 6.034898 GGTTGTTTGATTCTGTTGTTTGTGAG 59.965 38.462 0.00 0.00 0.00 3.51
1804 2174 6.279513 TGTGAGACAAACCATTTTCAAGTT 57.720 33.333 0.00 0.00 0.00 2.66
1805 2175 6.098679 TGTGAGACAAACCATTTTCAAGTTG 58.901 36.000 0.00 0.00 0.00 3.16
1843 2264 3.225104 AGTTCTGCACCATTCATGTGTT 58.775 40.909 0.00 0.00 0.00 3.32
1844 2265 4.397420 AGTTCTGCACCATTCATGTGTTA 58.603 39.130 0.00 0.00 0.00 2.41
1880 2306 9.208022 TGAATCATCCGTAATTCAGAATATGTC 57.792 33.333 0.00 0.00 37.06 3.06
1948 2374 3.821421 AGTCTCTGACAAACCGTCTTT 57.179 42.857 0.46 0.00 45.60 2.52
1949 2375 3.458189 AGTCTCTGACAAACCGTCTTTG 58.542 45.455 0.46 2.14 45.60 2.77
1958 2384 3.692101 ACAAACCGTCTTTGTTCATGTGA 59.308 39.130 3.26 0.00 39.36 3.58
1994 2420 5.596845 TGGTTTACTCATTTTTGTCTTGCC 58.403 37.500 0.00 0.00 0.00 4.52
2003 2429 7.011669 ACTCATTTTTGTCTTGCCTGAAATTTG 59.988 33.333 0.00 0.00 0.00 2.32
2005 2431 7.336427 TCATTTTTGTCTTGCCTGAAATTTGTT 59.664 29.630 0.00 0.00 0.00 2.83
2020 2446 3.374042 TTTGTTTCTCCCACCACTTCA 57.626 42.857 0.00 0.00 0.00 3.02
2054 2480 8.439971 AGGATTCAGCAATGTAATATAGACCAA 58.560 33.333 0.00 0.00 0.00 3.67
2059 2485 7.931407 TCAGCAATGTAATATAGACCAATCGTT 59.069 33.333 0.00 0.00 0.00 3.85
2061 2487 9.204570 AGCAATGTAATATAGACCAATCGTTAC 57.795 33.333 0.00 0.00 0.00 2.50
2178 2649 8.758633 TTACTACTCTGAAAAGTGTATGAAGC 57.241 34.615 2.69 0.00 0.00 3.86
2179 2650 5.864474 ACTACTCTGAAAAGTGTATGAAGCG 59.136 40.000 0.00 0.00 0.00 4.68
2180 2651 4.883083 ACTCTGAAAAGTGTATGAAGCGA 58.117 39.130 0.00 0.00 0.00 4.93
2181 2652 4.926238 ACTCTGAAAAGTGTATGAAGCGAG 59.074 41.667 0.00 0.00 0.00 5.03
2182 2653 3.679980 TCTGAAAAGTGTATGAAGCGAGC 59.320 43.478 0.00 0.00 0.00 5.03
2184 2655 4.065088 TGAAAAGTGTATGAAGCGAGCTT 58.935 39.130 10.40 10.40 39.23 3.74
2207 2680 3.749665 TCAGGCTTCACCCAAAATTTG 57.250 42.857 0.00 0.00 40.58 2.32
2232 2706 2.716217 CTCAGCCCAAGGGACTAAAAG 58.284 52.381 9.92 1.42 38.49 2.27
2265 2739 9.474920 AATCAGCATTTCAAAATTTTACTTCGA 57.525 25.926 2.44 0.00 0.00 3.71
2274 2748 5.796350 AAATTTTACTTCGATCGAGTGGG 57.204 39.130 18.54 11.97 0.00 4.61
2278 2752 0.537188 ACTTCGATCGAGTGGGCAAT 59.463 50.000 18.54 0.00 0.00 3.56
2296 2770 6.928492 TGGGCAATTAACATCTTGAGTTTTTC 59.072 34.615 0.00 0.00 0.00 2.29
2298 2772 7.329471 GGGCAATTAACATCTTGAGTTTTTCTC 59.671 37.037 0.00 0.00 43.03 2.87
2367 2842 6.998258 CAGAAATTTCTACCTGCACAAAAG 57.002 37.500 20.07 0.06 35.34 2.27
2376 2851 2.729491 GCACAAAAGCGGCGGAAC 60.729 61.111 9.78 0.00 0.00 3.62
2425 2903 1.870055 CTGGTGTGCATTCAGGTGGC 61.870 60.000 0.00 0.00 0.00 5.01
2428 2906 4.120331 GTGCATTCAGGTGGCGGC 62.120 66.667 0.00 0.00 0.00 6.53
2431 2909 3.197790 CATTCAGGTGGCGGCGAG 61.198 66.667 12.98 0.00 0.00 5.03
2605 3085 0.464036 TGATGGTAGCCTAACAGCCG 59.536 55.000 2.04 0.00 28.83 5.52
2672 3160 1.808390 GTTAGAATCGGTGCGCGGT 60.808 57.895 8.83 0.00 0.00 5.68
2686 3174 2.822255 CGGTGCCGGTGGTATTGG 60.822 66.667 1.90 0.00 35.56 3.16
2745 3233 3.119101 ACGAAAGTTATCCTCGTGCTGAT 60.119 43.478 0.00 0.00 46.40 2.90
2759 3247 4.805719 TCGTGCTGATGTGTTGATAGATTC 59.194 41.667 0.00 0.00 0.00 2.52
2776 3264 3.134804 AGATTCGGTTGATCAGGTTAGGG 59.865 47.826 0.00 0.00 0.00 3.53
2825 3766 0.870393 GCAGTCCACACACATCACTG 59.130 55.000 0.00 0.00 38.01 3.66
2826 3767 1.541015 GCAGTCCACACACATCACTGA 60.541 52.381 1.57 0.00 37.28 3.41
2835 3807 3.999001 ACACACATCACTGATAAGCACTG 59.001 43.478 0.00 0.00 0.00 3.66
2885 3857 9.153721 AGGTAGACTCTCGACTAATATAAATCG 57.846 37.037 0.00 0.00 35.91 3.34
2907 3881 5.872617 TCGATACAAATATATTTCCTGCCCG 59.127 40.000 7.76 7.53 0.00 6.13
2919 3893 1.353022 TCCTGCCCGGAATTACTTGTT 59.647 47.619 0.73 0.00 39.40 2.83
2926 3900 3.304794 CCCGGAATTACTTGTTGCGAAAA 60.305 43.478 0.73 0.00 41.99 2.29
2939 3913 9.039870 ACTTGTTGCGAAAATGAATAAAAATGA 57.960 25.926 0.00 0.00 0.00 2.57
2940 3914 9.861138 CTTGTTGCGAAAATGAATAAAAATGAA 57.139 25.926 0.00 0.00 0.00 2.57
2941 3915 9.643652 TTGTTGCGAAAATGAATAAAAATGAAC 57.356 25.926 0.00 0.00 0.00 3.18
2998 3972 3.262405 TGCTAAGTATTTTGGACGGAGGT 59.738 43.478 0.00 0.00 0.00 3.85
3002 3976 4.467198 AGTATTTTGGACGGAGGTAGTG 57.533 45.455 0.00 0.00 0.00 2.74
3015 3989 6.803642 ACGGAGGTAGTGTTAGATTATTCAC 58.196 40.000 0.00 0.00 0.00 3.18
3035 4009 2.104111 ACGACTCAAGGGTCAATGACAA 59.896 45.455 15.86 0.00 36.12 3.18
3038 4012 1.197721 CTCAAGGGTCAATGACAACGC 59.802 52.381 15.86 0.00 33.68 4.84
3056 4030 0.802494 GCAGGTTACGGGTCATGTTG 59.198 55.000 0.00 0.00 0.00 3.33
3057 4031 1.609580 GCAGGTTACGGGTCATGTTGA 60.610 52.381 0.00 0.00 0.00 3.18
3058 4032 2.346803 CAGGTTACGGGTCATGTTGAG 58.653 52.381 0.00 0.00 0.00 3.02
3123 4097 5.057149 AGCTAAACTGTAGGCAATAATCGG 58.943 41.667 0.00 0.00 0.00 4.18
3128 4102 3.243434 ACTGTAGGCAATAATCGGTCGAG 60.243 47.826 0.00 0.00 0.00 4.04
3132 4106 1.865340 GGCAATAATCGGTCGAGGTTC 59.135 52.381 0.00 0.00 0.00 3.62
3135 4109 1.396653 ATAATCGGTCGAGGTTCGGT 58.603 50.000 0.00 0.00 40.88 4.69
3136 4110 0.734889 TAATCGGTCGAGGTTCGGTC 59.265 55.000 0.00 0.00 40.88 4.79
3137 4111 2.262471 AATCGGTCGAGGTTCGGTCG 62.262 60.000 0.00 3.85 40.88 4.79
3138 4112 3.425713 CGGTCGAGGTTCGGTCGA 61.426 66.667 0.00 0.00 43.97 4.20
3139 4113 2.484203 GGTCGAGGTTCGGTCGAG 59.516 66.667 0.00 0.00 46.62 4.04
3140 4114 2.484203 GTCGAGGTTCGGTCGAGG 59.516 66.667 0.00 0.00 46.62 4.63
3141 4115 2.033141 TCGAGGTTCGGTCGAGGT 59.967 61.111 0.00 0.00 41.41 3.85
3142 4116 1.601759 TCGAGGTTCGGTCGAGGTT 60.602 57.895 0.00 0.00 41.41 3.50
3143 4117 1.154073 CGAGGTTCGGTCGAGGTTC 60.154 63.158 0.00 0.00 39.92 3.62
3144 4118 1.154073 GAGGTTCGGTCGAGGTTCG 60.154 63.158 0.00 0.00 42.10 3.95
3215 4189 7.227512 AGGACTGCATATAATAAGAGTTGTTGC 59.772 37.037 0.00 0.00 0.00 4.17
3219 4193 6.136071 GCATATAATAAGAGTTGTTGCACCG 58.864 40.000 0.00 0.00 0.00 4.94
3226 4200 2.230266 AGAGTTGTTGCACCGTTGTTTT 59.770 40.909 0.00 0.00 0.00 2.43
3237 4211 2.288640 ACCGTTGTTTTAGGACCTCTCG 60.289 50.000 0.00 0.00 0.00 4.04
3240 4214 0.245539 TGTTTTAGGACCTCTCGCGG 59.754 55.000 6.13 0.00 0.00 6.46
3288 4262 3.904571 TCTTGCTTGATTGTTGTCATGC 58.095 40.909 7.55 7.55 44.79 4.06
3293 4267 4.701171 TGCTTGATTGTTGTCATGCTGATA 59.299 37.500 13.50 0.00 44.81 2.15
3320 4294 1.889573 GCTTATGCTGCCTCCGTCC 60.890 63.158 0.00 0.00 36.03 4.79
3327 4301 1.004918 CTGCCTCCGTCCGAAAAGT 60.005 57.895 0.00 0.00 0.00 2.66
3347 4321 0.109319 ATGTCGCCGTGGCAATTTTC 60.109 50.000 12.06 0.00 42.06 2.29
3348 4322 1.169661 TGTCGCCGTGGCAATTTTCT 61.170 50.000 12.06 0.00 42.06 2.52
3349 4323 0.729140 GTCGCCGTGGCAATTTTCTG 60.729 55.000 12.06 0.00 42.06 3.02
3350 4324 1.444212 CGCCGTGGCAATTTTCTGG 60.444 57.895 12.06 0.00 42.06 3.86
3354 4328 2.403259 CCGTGGCAATTTTCTGGAAAC 58.597 47.619 0.00 0.00 0.00 2.78
3355 4329 2.403259 CGTGGCAATTTTCTGGAAACC 58.597 47.619 0.00 0.00 0.00 3.27
3362 4336 1.541275 TTTTCTGGAAACCCCCTCCT 58.459 50.000 0.00 0.00 33.77 3.69
3378 4352 0.960364 TCCTCAAATTGTGCGCCTCC 60.960 55.000 4.18 0.00 0.00 4.30
3399 4373 2.282180 GCGTTGCTTCCCCTTCCA 60.282 61.111 0.00 0.00 0.00 3.53
3404 4378 2.361737 GCTTCCCCTTCCACTGCC 60.362 66.667 0.00 0.00 0.00 4.85
3435 4409 1.984570 CGGGTGAGGAGAAGGCTCA 60.985 63.158 0.00 0.00 43.14 4.26
3436 4410 1.544825 CGGGTGAGGAGAAGGCTCAA 61.545 60.000 0.00 0.00 43.14 3.02
3465 4441 3.616956 TTGATTTGCTCTCCGACTGAT 57.383 42.857 0.00 0.00 0.00 2.90
3467 4443 2.234661 TGATTTGCTCTCCGACTGATGT 59.765 45.455 0.00 0.00 0.00 3.06
3479 4455 1.272490 GACTGATGTGTCCTTCCACGA 59.728 52.381 0.00 0.00 38.20 4.35
3520 4496 3.220999 CTGCCCGTCGTCAACCTCA 62.221 63.158 0.00 0.00 0.00 3.86
3522 4498 1.810030 GCCCGTCGTCAACCTCATC 60.810 63.158 0.00 0.00 0.00 2.92
3527 4503 1.743958 CGTCGTCAACCTCATCTACCT 59.256 52.381 0.00 0.00 0.00 3.08
3543 4519 1.079127 CCTCGCCATCAACCTCGTT 60.079 57.895 0.00 0.00 0.00 3.85
3562 4538 0.827925 TCACCTCGCTGTCAACCTCT 60.828 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.053840 CGTCGTGGGAGTATCATATATTAGTAT 57.946 37.037 0.00 0.00 36.25 2.12
41 42 8.260114 TCGTCGTGGGAGTATCATATATTAGTA 58.740 37.037 0.00 0.00 36.25 1.82
42 43 7.108194 TCGTCGTGGGAGTATCATATATTAGT 58.892 38.462 0.00 0.00 36.25 2.24
43 44 7.280428 ACTCGTCGTGGGAGTATCATATATTAG 59.720 40.741 4.42 0.00 42.69 1.73
44 45 7.108194 ACTCGTCGTGGGAGTATCATATATTA 58.892 38.462 4.42 0.00 42.69 0.98
45 46 5.944599 ACTCGTCGTGGGAGTATCATATATT 59.055 40.000 4.42 0.00 42.69 1.28
46 47 5.498393 ACTCGTCGTGGGAGTATCATATAT 58.502 41.667 4.42 0.00 42.69 0.86
47 48 4.903054 ACTCGTCGTGGGAGTATCATATA 58.097 43.478 4.42 0.00 42.69 0.86
48 49 3.752665 ACTCGTCGTGGGAGTATCATAT 58.247 45.455 4.42 0.00 42.69 1.78
49 50 3.204306 ACTCGTCGTGGGAGTATCATA 57.796 47.619 4.42 0.00 42.69 2.15
50 51 2.054232 ACTCGTCGTGGGAGTATCAT 57.946 50.000 4.42 0.00 42.69 2.45
51 52 2.558378 CTACTCGTCGTGGGAGTATCA 58.442 52.381 11.38 0.00 43.81 2.15
52 53 1.263752 GCTACTCGTCGTGGGAGTATC 59.736 57.143 11.38 6.13 43.81 2.24
53 54 1.307097 GCTACTCGTCGTGGGAGTAT 58.693 55.000 11.38 0.00 43.81 2.12
54 55 0.745845 GGCTACTCGTCGTGGGAGTA 60.746 60.000 10.78 10.78 42.69 2.59
55 56 2.045131 GGCTACTCGTCGTGGGAGT 61.045 63.158 9.84 9.84 46.05 3.85
56 57 1.749638 AGGCTACTCGTCGTGGGAG 60.750 63.158 0.00 0.00 37.54 4.30
57 58 2.044555 CAGGCTACTCGTCGTGGGA 61.045 63.158 0.00 0.00 0.00 4.37
58 59 1.384989 ATCAGGCTACTCGTCGTGGG 61.385 60.000 0.00 0.00 0.00 4.61
59 60 1.306148 TATCAGGCTACTCGTCGTGG 58.694 55.000 0.00 0.00 0.00 4.94
60 61 2.290916 ACATATCAGGCTACTCGTCGTG 59.709 50.000 0.00 0.00 0.00 4.35
61 62 2.573369 ACATATCAGGCTACTCGTCGT 58.427 47.619 0.00 0.00 0.00 4.34
62 63 3.627732 AACATATCAGGCTACTCGTCG 57.372 47.619 0.00 0.00 0.00 5.12
63 64 4.933330 TCAAACATATCAGGCTACTCGTC 58.067 43.478 0.00 0.00 0.00 4.20
64 65 4.202161 CCTCAAACATATCAGGCTACTCGT 60.202 45.833 0.00 0.00 0.00 4.18
65 66 4.302455 CCTCAAACATATCAGGCTACTCG 58.698 47.826 0.00 0.00 0.00 4.18
66 67 4.503991 CCCCTCAAACATATCAGGCTACTC 60.504 50.000 0.00 0.00 0.00 2.59
67 68 3.392616 CCCCTCAAACATATCAGGCTACT 59.607 47.826 0.00 0.00 0.00 2.57
68 69 3.496870 CCCCCTCAAACATATCAGGCTAC 60.497 52.174 0.00 0.00 0.00 3.58
69 70 2.711009 CCCCCTCAAACATATCAGGCTA 59.289 50.000 0.00 0.00 0.00 3.93
70 71 1.496429 CCCCCTCAAACATATCAGGCT 59.504 52.381 0.00 0.00 0.00 4.58
71 72 1.986882 CCCCCTCAAACATATCAGGC 58.013 55.000 0.00 0.00 0.00 4.85
91 92 3.283467 TTTCCTCCCCCTCCCCCTC 62.283 68.421 0.00 0.00 0.00 4.30
92 93 3.224269 TTTCCTCCCCCTCCCCCT 61.224 66.667 0.00 0.00 0.00 4.79
93 94 3.021880 GTTTCCTCCCCCTCCCCC 61.022 72.222 0.00 0.00 0.00 5.40
94 95 1.855451 TTGTTTCCTCCCCCTCCCC 60.855 63.158 0.00 0.00 0.00 4.81
95 96 1.691823 CTTGTTTCCTCCCCCTCCC 59.308 63.158 0.00 0.00 0.00 4.30
96 97 1.000771 GCTTGTTTCCTCCCCCTCC 60.001 63.158 0.00 0.00 0.00 4.30
97 98 0.332972 ATGCTTGTTTCCTCCCCCTC 59.667 55.000 0.00 0.00 0.00 4.30
98 99 1.681229 TATGCTTGTTTCCTCCCCCT 58.319 50.000 0.00 0.00 0.00 4.79
99 100 2.525105 TTATGCTTGTTTCCTCCCCC 57.475 50.000 0.00 0.00 0.00 5.40
100 101 5.712152 CATATTATGCTTGTTTCCTCCCC 57.288 43.478 0.00 0.00 0.00 4.81
109 110 9.667866 CATGATGGCATGGCATATTATGCTTGT 62.668 40.741 32.28 9.02 46.15 3.16
110 111 7.394280 CATGATGGCATGGCATATTATGCTTG 61.394 42.308 32.28 21.29 46.15 4.01
111 112 5.395214 CATGATGGCATGGCATATTATGCTT 60.395 40.000 32.28 15.05 46.15 3.91
112 113 4.099419 CATGATGGCATGGCATATTATGCT 59.901 41.667 32.28 11.13 46.15 3.79
113 114 4.368315 CATGATGGCATGGCATATTATGC 58.632 43.478 32.28 19.67 46.45 3.14
132 133 9.961265 ACATTCATAGCACAAATAATCTTCATG 57.039 29.630 0.00 0.00 0.00 3.07
145 146 3.669536 TGGAACGAACATTCATAGCACA 58.330 40.909 0.00 0.00 0.00 4.57
146 147 4.391830 TCTTGGAACGAACATTCATAGCAC 59.608 41.667 0.00 0.00 0.00 4.40
147 148 4.574892 TCTTGGAACGAACATTCATAGCA 58.425 39.130 0.00 0.00 0.00 3.49
148 149 5.741388 ATCTTGGAACGAACATTCATAGC 57.259 39.130 0.00 0.00 0.00 2.97
156 157 5.697473 TGCATTTTATCTTGGAACGAACA 57.303 34.783 0.00 0.00 0.00 3.18
160 161 7.967854 TCACTAATTGCATTTTATCTTGGAACG 59.032 33.333 0.00 0.00 0.00 3.95
192 193 7.752695 ACTGTATTTTATTCTAGCAGCAACAC 58.247 34.615 0.00 0.00 0.00 3.32
233 234 5.011738 TGAAATATACTCCCTCCGCTAAAGG 59.988 44.000 0.00 0.00 0.00 3.11
234 235 6.097915 TGAAATATACTCCCTCCGCTAAAG 57.902 41.667 0.00 0.00 0.00 1.85
238 239 5.367945 TTTTGAAATATACTCCCTCCGCT 57.632 39.130 0.00 0.00 0.00 5.52
289 290 8.793472 TGACATCGCGATAAATTAAAAACAATG 58.207 29.630 23.22 7.49 0.00 2.82
298 299 7.093992 TGTATCCATGACATCGCGATAAATTA 58.906 34.615 23.22 7.67 0.00 1.40
322 323 6.427853 TCCACGCCATTCTTATTCTAATGATG 59.572 38.462 0.00 0.00 35.53 3.07
323 324 6.533730 TCCACGCCATTCTTATTCTAATGAT 58.466 36.000 0.00 0.00 35.53 2.45
325 326 5.760253 ACTCCACGCCATTCTTATTCTAATG 59.240 40.000 0.00 0.00 33.72 1.90
326 327 5.760253 CACTCCACGCCATTCTTATTCTAAT 59.240 40.000 0.00 0.00 0.00 1.73
327 328 5.116180 CACTCCACGCCATTCTTATTCTAA 58.884 41.667 0.00 0.00 0.00 2.10
330 331 3.270877 ACACTCCACGCCATTCTTATTC 58.729 45.455 0.00 0.00 0.00 1.75
332 333 3.350219 AACACTCCACGCCATTCTTAT 57.650 42.857 0.00 0.00 0.00 1.73
335 336 2.851263 TAAACACTCCACGCCATTCT 57.149 45.000 0.00 0.00 0.00 2.40
371 655 4.515567 GTCAAAGTCAACCGATCCTCTTTT 59.484 41.667 0.00 0.00 0.00 2.27
375 659 2.737252 GTGTCAAAGTCAACCGATCCTC 59.263 50.000 0.00 0.00 0.00 3.71
376 660 2.104111 TGTGTCAAAGTCAACCGATCCT 59.896 45.455 0.00 0.00 0.00 3.24
381 665 1.063469 GGTGTGTGTCAAAGTCAACCG 59.937 52.381 0.00 0.00 0.00 4.44
395 679 4.936823 GGTCGTGCGTCGGTGTGT 62.937 66.667 0.00 0.00 40.32 3.72
418 702 1.040893 CCGGGACAAATTAAGGGCCC 61.041 60.000 16.46 16.46 0.00 5.80
527 820 1.700186 AGGAAGGGTTCAGTCAGGAAC 59.300 52.381 0.00 0.00 45.01 3.62
528 821 2.118403 AGGAAGGGTTCAGTCAGGAA 57.882 50.000 0.00 0.00 0.00 3.36
529 822 1.978580 GAAGGAAGGGTTCAGTCAGGA 59.021 52.381 0.00 0.00 0.00 3.86
531 824 1.981495 AGGAAGGAAGGGTTCAGTCAG 59.019 52.381 0.00 0.00 0.00 3.51
533 826 1.611936 GCAGGAAGGAAGGGTTCAGTC 60.612 57.143 0.00 0.00 0.00 3.51
534 827 0.402121 GCAGGAAGGAAGGGTTCAGT 59.598 55.000 0.00 0.00 0.00 3.41
535 828 0.401738 TGCAGGAAGGAAGGGTTCAG 59.598 55.000 0.00 0.00 0.00 3.02
536 829 0.110486 GTGCAGGAAGGAAGGGTTCA 59.890 55.000 0.00 0.00 0.00 3.18
537 830 0.955919 CGTGCAGGAAGGAAGGGTTC 60.956 60.000 0.00 0.00 0.00 3.62
538 831 1.073199 CGTGCAGGAAGGAAGGGTT 59.927 57.895 0.00 0.00 0.00 4.11
539 832 1.841556 TCGTGCAGGAAGGAAGGGT 60.842 57.895 6.64 0.00 0.00 4.34
540 833 1.376037 GTCGTGCAGGAAGGAAGGG 60.376 63.158 11.28 0.00 0.00 3.95
615 912 2.459202 GAAACCGGGCGAAGGAAGGA 62.459 60.000 6.32 0.00 0.00 3.36
643 940 4.452733 CGGGAGAAGGGACGGCAC 62.453 72.222 0.00 0.00 0.00 5.01
648 945 2.683933 TGAGCCGGGAGAAGGGAC 60.684 66.667 2.18 0.00 0.00 4.46
758 1056 2.431942 GTGTAGACCCGGTGCACG 60.432 66.667 11.45 6.23 43.80 5.34
759 1057 1.374252 CTGTGTAGACCCGGTGCAC 60.374 63.158 8.80 8.80 0.00 4.57
760 1058 2.579657 CCTGTGTAGACCCGGTGCA 61.580 63.158 0.00 0.00 0.00 4.57
761 1059 2.264794 CCTGTGTAGACCCGGTGC 59.735 66.667 0.00 0.00 0.00 5.01
762 1060 2.656069 CCCCTGTGTAGACCCGGTG 61.656 68.421 0.00 0.00 0.00 4.94
763 1061 2.284405 CCCCTGTGTAGACCCGGT 60.284 66.667 0.00 0.00 0.00 5.28
764 1062 3.782443 GCCCCTGTGTAGACCCGG 61.782 72.222 0.00 0.00 0.00 5.73
765 1063 4.143333 CGCCCCTGTGTAGACCCG 62.143 72.222 0.00 0.00 0.00 5.28
766 1064 3.782443 CCGCCCCTGTGTAGACCC 61.782 72.222 0.00 0.00 0.00 4.46
767 1065 4.468689 GCCGCCCCTGTGTAGACC 62.469 72.222 0.00 0.00 0.00 3.85
768 1066 3.702048 TGCCGCCCCTGTGTAGAC 61.702 66.667 0.00 0.00 0.00 2.59
769 1067 3.702048 GTGCCGCCCCTGTGTAGA 61.702 66.667 0.00 0.00 0.00 2.59
770 1068 4.778143 GGTGCCGCCCCTGTGTAG 62.778 72.222 0.00 0.00 0.00 2.74
834 1137 2.478539 GGCGAGCTTCTTTATGCTTTGG 60.479 50.000 0.00 0.00 39.91 3.28
894 1204 2.191109 GTTGGTCGGTGGTGGTGT 59.809 61.111 0.00 0.00 0.00 4.16
895 1205 2.970324 CGTTGGTCGGTGGTGGTG 60.970 66.667 0.00 0.00 35.71 4.17
896 1206 4.922026 GCGTTGGTCGGTGGTGGT 62.922 66.667 0.00 0.00 40.26 4.16
897 1207 4.920112 TGCGTTGGTCGGTGGTGG 62.920 66.667 0.00 0.00 40.26 4.61
898 1208 2.897846 TTGCGTTGGTCGGTGGTG 60.898 61.111 0.00 0.00 40.26 4.17
899 1209 2.898343 GTTGCGTTGGTCGGTGGT 60.898 61.111 0.00 0.00 40.26 4.16
900 1210 4.007940 CGTTGCGTTGGTCGGTGG 62.008 66.667 0.00 0.00 40.26 4.61
933 1243 0.890996 GGAGTGGAGTGCAGTTTGGG 60.891 60.000 0.00 0.00 0.00 4.12
996 1330 1.453379 CCTCCCCTGCTGCATCTTG 60.453 63.158 1.31 0.00 0.00 3.02
1231 1574 2.286121 ATGGGTCACGGGGTGGAT 60.286 61.111 0.00 0.00 33.87 3.41
1403 1755 4.163902 CAAAACGAATGCGCGCGC 62.164 61.111 45.02 45.02 42.48 6.86
1415 1769 0.658897 TTCACTCCGCGAACCAAAAC 59.341 50.000 8.23 0.00 0.00 2.43
1420 1774 2.027625 CCAGTTCACTCCGCGAACC 61.028 63.158 8.23 0.00 43.07 3.62
1429 1783 3.395941 AGAGAAAACCCATCCAGTTCACT 59.604 43.478 0.00 0.00 0.00 3.41
1568 1923 4.410033 CCCCTCCCGGTGGTACCT 62.410 72.222 14.36 0.00 35.66 3.08
1693 2049 1.774110 TTGGCATGGCATATTCCGTT 58.226 45.000 23.96 0.00 0.00 4.44
1694 2050 1.999648 ATTGGCATGGCATATTCCGT 58.000 45.000 23.96 0.85 0.00 4.69
1695 2051 3.061322 CAAATTGGCATGGCATATTCCG 58.939 45.455 23.96 14.50 0.00 4.30
1696 2052 2.809696 GCAAATTGGCATGGCATATTCC 59.190 45.455 23.96 7.71 0.00 3.01
1697 2053 2.809696 GGCAAATTGGCATGGCATATTC 59.190 45.455 23.96 12.95 43.14 1.75
1698 2054 2.807472 CGGCAAATTGGCATGGCATATT 60.807 45.455 23.96 20.06 43.94 1.28
1735 2091 5.751243 TCTTTAGCAACAGAAAACTGGAC 57.249 39.130 0.00 0.00 0.00 4.02
1738 2094 5.916883 CCACATCTTTAGCAACAGAAAACTG 59.083 40.000 0.00 0.00 0.00 3.16
1748 2118 5.843673 TCAAACAACCACATCTTTAGCAA 57.156 34.783 0.00 0.00 0.00 3.91
1786 2156 5.866633 TGACACAACTTGAAAATGGTTTGTC 59.133 36.000 0.00 0.00 34.98 3.18
1804 2174 1.066215 ACTTGCTGTGACAGTGACACA 60.066 47.619 23.61 23.61 44.34 3.72
1805 2175 1.656652 ACTTGCTGTGACAGTGACAC 58.343 50.000 17.28 17.28 38.55 3.67
1918 2344 5.176592 GTTTGTCAGAGACTTACCCCATAC 58.823 45.833 0.00 0.00 33.15 2.39
1919 2345 4.224370 GGTTTGTCAGAGACTTACCCCATA 59.776 45.833 8.90 0.00 33.74 2.74
1920 2346 3.009143 GGTTTGTCAGAGACTTACCCCAT 59.991 47.826 8.90 0.00 33.74 4.00
1921 2347 2.370849 GGTTTGTCAGAGACTTACCCCA 59.629 50.000 8.90 0.00 33.74 4.96
1924 2350 3.382048 ACGGTTTGTCAGAGACTTACC 57.618 47.619 9.63 9.63 35.22 2.85
1948 2374 2.865119 AGCCAGATGTCACATGAACA 57.135 45.000 0.00 3.72 0.00 3.18
1949 2375 5.449588 CCAAATAGCCAGATGTCACATGAAC 60.450 44.000 0.00 0.00 0.00 3.18
1958 2384 5.815581 TGAGTAAACCAAATAGCCAGATGT 58.184 37.500 0.00 0.00 0.00 3.06
1994 2420 4.342092 AGTGGTGGGAGAAACAAATTTCAG 59.658 41.667 2.86 0.00 45.78 3.02
2003 2429 3.756117 AGAATGAAGTGGTGGGAGAAAC 58.244 45.455 0.00 0.00 0.00 2.78
2005 2431 4.453480 AAAGAATGAAGTGGTGGGAGAA 57.547 40.909 0.00 0.00 0.00 2.87
2050 2476 4.100498 ACATCCTAATCCGTAACGATTGGT 59.900 41.667 0.00 0.00 34.35 3.67
2054 2480 5.766670 TGTCTACATCCTAATCCGTAACGAT 59.233 40.000 0.00 0.00 0.00 3.73
2059 2485 7.414222 AAGTTTGTCTACATCCTAATCCGTA 57.586 36.000 0.00 0.00 0.00 4.02
2061 2487 8.888579 AATAAGTTTGTCTACATCCTAATCCG 57.111 34.615 0.00 0.00 0.00 4.18
2126 2555 7.944729 ATTTTAGAAGTCCTTGCATACATGT 57.055 32.000 2.69 2.69 0.00 3.21
2158 2587 4.883083 TCGCTTCATACACTTTTCAGAGT 58.117 39.130 0.00 0.00 0.00 3.24
2159 2588 4.201666 GCTCGCTTCATACACTTTTCAGAG 60.202 45.833 0.00 0.00 0.00 3.35
2160 2589 3.679980 GCTCGCTTCATACACTTTTCAGA 59.320 43.478 0.00 0.00 0.00 3.27
2177 2648 0.671781 TGAAGCCTGAAGAAGCTCGC 60.672 55.000 0.00 0.00 38.74 5.03
2178 2649 1.074752 GTGAAGCCTGAAGAAGCTCG 58.925 55.000 0.00 0.00 38.74 5.03
2179 2650 1.447945 GGTGAAGCCTGAAGAAGCTC 58.552 55.000 0.00 0.00 38.74 4.09
2180 2651 0.037447 GGGTGAAGCCTGAAGAAGCT 59.963 55.000 0.00 0.00 42.40 3.74
2181 2652 0.250901 TGGGTGAAGCCTGAAGAAGC 60.251 55.000 0.00 0.00 37.43 3.86
2182 2653 2.276732 TTGGGTGAAGCCTGAAGAAG 57.723 50.000 0.00 0.00 37.43 2.85
2184 2655 2.746279 TTTTGGGTGAAGCCTGAAGA 57.254 45.000 0.00 0.00 37.43 2.87
2185 2656 4.060205 CAAATTTTGGGTGAAGCCTGAAG 58.940 43.478 0.97 0.00 37.43 3.02
2186 2657 4.070630 CAAATTTTGGGTGAAGCCTGAA 57.929 40.909 0.97 0.00 37.43 3.02
2187 2658 3.749665 CAAATTTTGGGTGAAGCCTGA 57.250 42.857 0.97 0.00 37.43 3.86
2207 2680 2.677875 CCCTTGGGCTGAGCAACC 60.678 66.667 6.82 0.00 0.00 3.77
2258 2732 1.179152 TTGCCCACTCGATCGAAGTA 58.821 50.000 19.92 5.13 0.00 2.24
2265 2739 4.156455 AGATGTTAATTGCCCACTCGAT 57.844 40.909 0.00 0.00 0.00 3.59
2296 2770 6.292381 CGTTCTTGTTTAAACCTGTCAGAGAG 60.292 42.308 15.59 0.00 0.00 3.20
2298 2772 5.522460 TCGTTCTTGTTTAAACCTGTCAGAG 59.478 40.000 15.59 3.19 0.00 3.35
2425 2903 1.226435 GCTCTGTGTAGTCTCGCCG 60.226 63.158 0.00 0.00 0.00 6.46
2428 2906 1.202348 CCATGGCTCTGTGTAGTCTCG 60.202 57.143 0.00 0.00 0.00 4.04
2431 2909 1.137872 CCTCCATGGCTCTGTGTAGTC 59.862 57.143 6.96 0.00 0.00 2.59
2479 2957 1.191489 TGACAATGGCGAGGAGGTGA 61.191 55.000 0.00 0.00 0.00 4.02
2482 2960 0.178767 TCATGACAATGGCGAGGAGG 59.821 55.000 0.00 0.00 34.30 4.30
2530 3008 0.393673 GGAGCCTCCAAAGCCTCTTC 60.394 60.000 5.69 0.00 36.28 2.87
2605 3085 3.439476 ACCAGACAGTCACAGTATACGAC 59.561 47.826 2.66 0.00 0.00 4.34
2643 3130 4.330074 CACCGATTCTAACCTAACTTGCTG 59.670 45.833 0.00 0.00 0.00 4.41
2672 3160 1.560146 TCAATACCAATACCACCGGCA 59.440 47.619 0.00 0.00 0.00 5.69
2675 3163 4.025229 CGTCAATCAATACCAATACCACCG 60.025 45.833 0.00 0.00 0.00 4.94
2683 3171 7.201696 GCCTTCTTTATCGTCAATCAATACCAA 60.202 37.037 0.00 0.00 0.00 3.67
2686 3174 7.126398 GTGCCTTCTTTATCGTCAATCAATAC 58.874 38.462 0.00 0.00 0.00 1.89
2725 3213 4.033358 CACATCAGCACGAGGATAACTTTC 59.967 45.833 0.00 0.00 0.00 2.62
2741 3229 5.812127 TCAACCGAATCTATCAACACATCAG 59.188 40.000 0.00 0.00 0.00 2.90
2745 3233 5.729510 TGATCAACCGAATCTATCAACACA 58.270 37.500 0.00 0.00 0.00 3.72
2759 3247 1.831736 ACTCCCTAACCTGATCAACCG 59.168 52.381 0.00 0.00 0.00 4.44
2776 3264 4.458295 TGCACTCCGCTATATACCTTACTC 59.542 45.833 0.00 0.00 43.06 2.59
2825 3766 3.127548 CCACACAATCACCAGTGCTTATC 59.872 47.826 0.00 0.00 39.30 1.75
2826 3767 3.084039 CCACACAATCACCAGTGCTTAT 58.916 45.455 0.00 0.00 39.30 1.73
2835 3807 0.038892 CTTGCAGCCACACAATCACC 60.039 55.000 0.00 0.00 0.00 4.02
2885 3857 6.436843 CCGGGCAGGAAATATATTTGTATC 57.563 41.667 15.39 1.13 45.00 2.24
2902 3874 0.885196 GCAACAAGTAATTCCGGGCA 59.115 50.000 0.00 0.00 0.00 5.36
2903 3875 0.179174 CGCAACAAGTAATTCCGGGC 60.179 55.000 0.00 0.00 0.00 6.13
2907 3881 7.581011 ATTCATTTTCGCAACAAGTAATTCC 57.419 32.000 0.00 0.00 0.00 3.01
2919 3893 7.630470 ACGTTCATTTTTATTCATTTTCGCA 57.370 28.000 0.00 0.00 0.00 5.10
2957 3931 7.714377 ACTTAGCAGAGAAATGAATGTATCTGG 59.286 37.037 7.12 0.00 35.75 3.86
2989 3963 6.040166 TGAATAATCTAACACTACCTCCGTCC 59.960 42.308 0.00 0.00 0.00 4.79
2998 3972 8.188799 CCTTGAGTCGTGAATAATCTAACACTA 58.811 37.037 0.00 0.00 0.00 2.74
3002 3976 6.338937 ACCCTTGAGTCGTGAATAATCTAAC 58.661 40.000 0.00 0.00 0.00 2.34
3015 3989 2.455674 TGTCATTGACCCTTGAGTCG 57.544 50.000 14.05 0.00 39.77 4.18
3035 4009 1.079405 CATGACCCGTAACCTGCGT 60.079 57.895 0.00 0.00 0.00 5.24
3038 4012 2.346803 CTCAACATGACCCGTAACCTG 58.653 52.381 0.00 0.00 0.00 4.00
3123 4097 1.860484 AACCTCGACCGAACCTCGAC 61.860 60.000 0.00 0.00 43.74 4.20
3128 4102 1.154073 CTCGAACCTCGACCGAACC 60.154 63.158 0.00 0.00 44.82 3.62
3132 4106 1.153823 ATTGCTCGAACCTCGACCG 60.154 57.895 0.00 0.00 44.82 4.79
3136 4110 0.443869 CAACCATTGCTCGAACCTCG 59.556 55.000 0.00 0.00 42.10 4.63
3137 4111 1.197721 CACAACCATTGCTCGAACCTC 59.802 52.381 0.00 0.00 0.00 3.85
3138 4112 1.238439 CACAACCATTGCTCGAACCT 58.762 50.000 0.00 0.00 0.00 3.50
3139 4113 0.951558 ACACAACCATTGCTCGAACC 59.048 50.000 0.00 0.00 0.00 3.62
3140 4114 2.384382 CAACACAACCATTGCTCGAAC 58.616 47.619 0.00 0.00 0.00 3.95
3141 4115 1.336440 CCAACACAACCATTGCTCGAA 59.664 47.619 0.00 0.00 0.00 3.71
3142 4116 0.950836 CCAACACAACCATTGCTCGA 59.049 50.000 0.00 0.00 0.00 4.04
3143 4117 0.950836 TCCAACACAACCATTGCTCG 59.049 50.000 0.00 0.00 0.00 5.03
3144 4118 1.956477 AGTCCAACACAACCATTGCTC 59.044 47.619 0.00 0.00 0.00 4.26
3145 4119 1.682854 CAGTCCAACACAACCATTGCT 59.317 47.619 0.00 0.00 0.00 3.91
3146 4120 1.680735 TCAGTCCAACACAACCATTGC 59.319 47.619 0.00 0.00 0.00 3.56
3198 4172 6.651643 ACAACGGTGCAACAACTCTTATTATA 59.348 34.615 0.00 0.00 39.98 0.98
3215 4189 3.064931 GAGAGGTCCTAAAACAACGGTG 58.935 50.000 0.00 0.00 0.00 4.94
3219 4193 1.725164 CGCGAGAGGTCCTAAAACAAC 59.275 52.381 0.00 0.00 0.00 3.32
3226 4200 3.138798 GCACCGCGAGAGGTCCTA 61.139 66.667 8.23 0.00 43.89 2.94
3237 4211 6.368791 TCTTATCATGATACTTATTGCACCGC 59.631 38.462 15.10 0.00 0.00 5.68
3308 4282 2.358247 TTTTCGGACGGAGGCAGC 60.358 61.111 0.00 0.00 0.00 5.25
3311 4285 1.287425 CATACTTTTCGGACGGAGGC 58.713 55.000 0.00 0.00 0.00 4.70
3316 4290 0.643820 GGCGACATACTTTTCGGACG 59.356 55.000 0.00 0.00 35.73 4.79
3320 4294 0.368907 CCACGGCGACATACTTTTCG 59.631 55.000 16.62 0.00 38.31 3.46
3327 4301 1.131504 GAAAATTGCCACGGCGACATA 59.868 47.619 16.62 0.00 45.51 2.29
3347 4321 0.777446 TTTGAGGAGGGGGTTTCCAG 59.223 55.000 0.00 0.00 37.18 3.86
3348 4322 1.466858 ATTTGAGGAGGGGGTTTCCA 58.533 50.000 0.00 0.00 37.18 3.53
3349 4323 2.179427 CAATTTGAGGAGGGGGTTTCC 58.821 52.381 0.00 0.00 34.83 3.13
3350 4324 2.562738 CACAATTTGAGGAGGGGGTTTC 59.437 50.000 2.79 0.00 0.00 2.78
3354 4328 1.315257 CGCACAATTTGAGGAGGGGG 61.315 60.000 2.79 0.00 0.00 5.40
3355 4329 1.937546 GCGCACAATTTGAGGAGGGG 61.938 60.000 0.30 0.00 0.00 4.79
3362 4336 2.976840 GCGGAGGCGCACAATTTGA 61.977 57.895 10.83 0.00 34.62 2.69
3399 4373 2.985847 GGGAAGCAAAGCGGCAGT 60.986 61.111 1.45 0.00 35.83 4.40
3407 4381 2.434331 CTCACCCGGGGAAGCAAA 59.566 61.111 27.92 0.20 0.00 3.68
3448 4422 2.027745 ACACATCAGTCGGAGAGCAAAT 60.028 45.455 0.00 0.00 36.95 2.32
3449 4423 1.344438 ACACATCAGTCGGAGAGCAAA 59.656 47.619 0.00 0.00 36.95 3.68
3450 4424 0.969149 ACACATCAGTCGGAGAGCAA 59.031 50.000 0.00 0.00 36.95 3.91
3465 4441 0.034756 CACCATCGTGGAAGGACACA 59.965 55.000 10.46 0.00 40.96 3.72
3505 4481 1.100510 TAGATGAGGTTGACGACGGG 58.899 55.000 0.00 0.00 0.00 5.28
3508 4484 2.223294 CGAGGTAGATGAGGTTGACGAC 60.223 54.545 0.00 0.00 0.00 4.34
3520 4496 1.689273 GAGGTTGATGGCGAGGTAGAT 59.311 52.381 0.00 0.00 0.00 1.98
3522 4498 0.249073 CGAGGTTGATGGCGAGGTAG 60.249 60.000 0.00 0.00 0.00 3.18
3527 4503 0.669318 GTGAACGAGGTTGATGGCGA 60.669 55.000 0.00 0.00 0.00 5.54
3543 4519 0.827925 AGAGGTTGACAGCGAGGTGA 60.828 55.000 9.41 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.