Multiple sequence alignment - TraesCS2D01G407700

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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 TraesCS2D01G407700 chr2D 100.000 3502 0 0 1 3502 522988769 522985268 0.000000e+00 6468.0
1 TraesCS2D01G407700 chr2B 91.965 2875 141 40 655 3455 616476002 616473144 0.000000e+00 3947.0
2 TraesCS2D01G407700 chr2B 80.537 149 25 4 1906 2053 182551478 182551333 1.030000e-20 111.0
3 TraesCS2D01G407700 chr2B 87.778 90 6 3 568 653 616480100 616480012 2.220000e-17 100.0
4 TraesCS2D01G407700 chr2B 89.796 49 4 1 37 85 363763577 363763530 1.050000e-05 62.1
5 TraesCS2D01G407700 chr2A 91.801 2537 149 21 1006 3502 668051606 668049089 0.000000e+00 3478.0
6 TraesCS2D01G407700 chr2A 87.912 364 14 8 558 899 668052381 668052026 5.440000e-108 401.0
7 TraesCS2D01G407700 chr2A 85.797 345 32 6 177 514 668052717 668052383 2.000000e-92 350.0
8 TraesCS2D01G407700 chr2A 100.000 28 0 0 55 82 371725160 371725187 6.000000e-03 52.8
9 TraesCS2D01G407700 chr6A 85.393 178 26 0 2201 2378 457402901 457402724 5.970000e-43 185.0
10 TraesCS2D01G407700 chr6B 83.505 194 29 1 2199 2389 503522923 503523116 9.990000e-41 178.0
11 TraesCS2D01G407700 chr6B 81.879 149 25 2 1906 2053 241058013 241058160 1.320000e-24 124.0
12 TraesCS2D01G407700 chr6B 92.857 56 3 1 1004 1059 503521507 503521561 2.900000e-11 80.5
13 TraesCS2D01G407700 chr4B 82.000 150 24 3 1906 2053 180695453 180695305 1.320000e-24 124.0
14 TraesCS2D01G407700 chr1A 80.851 141 26 1 1907 2047 505524664 505524525 3.700000e-20 110.0
15 TraesCS2D01G407700 chr7D 87.805 82 8 2 20 100 209796013 209795933 1.030000e-15 95.3
16 TraesCS2D01G407700 chr6D 95.745 47 2 0 1004 1050 319709558 319709512 3.750000e-10 76.8
17 TraesCS2D01G407700 chr1B 80.682 88 17 0 256 343 566820567 566820654 6.270000e-08 69.4
18 TraesCS2D01G407700 chr3D 90.698 43 3 1 38 80 588409834 588409793 4.880000e-04 56.5


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 TraesCS2D01G407700 chr2D 522985268 522988769 3501 True 6468.000000 6468 100.000000 1 3502 1 chr2D.!!$R1 3501
1 TraesCS2D01G407700 chr2B 616473144 616476002 2858 True 3947.000000 3947 91.965000 655 3455 1 chr2B.!!$R3 2800
2 TraesCS2D01G407700 chr2A 668049089 668052717 3628 True 1409.666667 3478 88.503333 177 3502 3 chr2A.!!$R1 3325

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
26 27 0.110373 GTTGAAACTTAGCGGTGCGG 60.110 55.0 0.0 0.0 0.00 5.69 F
584 592 0.239082 ACACGAGAATACGACACGCA 59.761 50.0 0.0 0.0 37.03 5.24 F
929 960 0.323957 AAACTCCCAACTACCCGCTC 59.676 55.0 0.0 0.0 0.00 5.03 F
2327 2716 0.107831 TTGGTTGACAAGGAGGGTCG 59.892 55.0 0.0 0.0 38.10 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1752 0.110238 GTCGTACGTACCACTGCGAA 60.110 55.0 19.67 0.00 0.00 4.70 R
1410 1755 0.455633 CAGGTCGTACGTACCACTGC 60.456 60.0 27.28 7.38 39.64 4.40 R
2385 2774 0.676466 GGGATGTGAATCACGGTGCA 60.676 55.0 9.00 0.00 37.14 4.57 R
3468 3867 0.532640 TGCGCAGAAGCTCACAAAGA 60.533 50.0 5.66 0.00 39.10 2.52 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
21 22 3.873529 GACACTTGTTGAAACTTAGCGG 58.126 45.455 0.00 0.00 0.00 5.52
22 23 3.275999 ACACTTGTTGAAACTTAGCGGT 58.724 40.909 0.00 0.00 0.00 5.68
23 24 3.064820 ACACTTGTTGAAACTTAGCGGTG 59.935 43.478 0.00 0.00 0.00 4.94
24 25 2.032924 ACTTGTTGAAACTTAGCGGTGC 59.967 45.455 0.00 0.00 0.00 5.01
25 26 0.584396 TGTTGAAACTTAGCGGTGCG 59.416 50.000 0.00 0.00 0.00 5.34
26 27 0.110373 GTTGAAACTTAGCGGTGCGG 60.110 55.000 0.00 0.00 0.00 5.69
27 28 0.533308 TTGAAACTTAGCGGTGCGGT 60.533 50.000 0.00 0.00 41.50 5.68
28 29 1.225376 TGAAACTTAGCGGTGCGGTG 61.225 55.000 0.00 0.00 38.30 4.94
29 30 0.947180 GAAACTTAGCGGTGCGGTGA 60.947 55.000 0.00 0.00 38.30 4.02
30 31 0.949105 AAACTTAGCGGTGCGGTGAG 60.949 55.000 0.00 0.00 44.32 3.51
31 32 1.812686 AACTTAGCGGTGCGGTGAGA 61.813 55.000 0.00 0.00 42.07 3.27
32 33 1.080093 CTTAGCGGTGCGGTGAGAA 60.080 57.895 0.00 0.00 42.07 2.87
33 34 1.352156 CTTAGCGGTGCGGTGAGAAC 61.352 60.000 0.00 0.00 42.07 3.01
34 35 3.620300 TAGCGGTGCGGTGAGAACG 62.620 63.158 0.00 0.00 38.30 3.95
69 70 4.875713 CCCGAGGGGCCAAATCCG 62.876 72.222 4.39 0.00 35.35 4.18
70 71 4.875713 CCGAGGGGCCAAATCCGG 62.876 72.222 4.39 5.96 0.00 5.14
97 98 4.410400 CCAGAGGCGACCCCCAAC 62.410 72.222 0.00 0.00 0.00 3.77
98 99 4.410400 CAGAGGCGACCCCCAACC 62.410 72.222 0.00 0.00 0.00 3.77
101 102 4.342086 AGGCGACCCCCAACCCTA 62.342 66.667 0.00 0.00 0.00 3.53
102 103 3.332385 GGCGACCCCCAACCCTAA 61.332 66.667 0.00 0.00 0.00 2.69
103 104 2.045634 GCGACCCCCAACCCTAAC 60.046 66.667 0.00 0.00 0.00 2.34
104 105 2.599757 GCGACCCCCAACCCTAACT 61.600 63.158 0.00 0.00 0.00 2.24
105 106 1.298667 CGACCCCCAACCCTAACTG 59.701 63.158 0.00 0.00 0.00 3.16
106 107 1.001269 GACCCCCAACCCTAACTGC 60.001 63.158 0.00 0.00 0.00 4.40
107 108 1.776710 ACCCCCAACCCTAACTGCA 60.777 57.895 0.00 0.00 0.00 4.41
108 109 1.304134 CCCCCAACCCTAACTGCAC 60.304 63.158 0.00 0.00 0.00 4.57
109 110 1.767692 CCCCAACCCTAACTGCACT 59.232 57.895 0.00 0.00 0.00 4.40
110 111 0.322546 CCCCAACCCTAACTGCACTC 60.323 60.000 0.00 0.00 0.00 3.51
111 112 0.400213 CCCAACCCTAACTGCACTCA 59.600 55.000 0.00 0.00 0.00 3.41
112 113 1.523758 CCAACCCTAACTGCACTCAC 58.476 55.000 0.00 0.00 0.00 3.51
113 114 1.202758 CCAACCCTAACTGCACTCACA 60.203 52.381 0.00 0.00 0.00 3.58
114 115 2.553028 CCAACCCTAACTGCACTCACAT 60.553 50.000 0.00 0.00 0.00 3.21
115 116 3.149196 CAACCCTAACTGCACTCACATT 58.851 45.455 0.00 0.00 0.00 2.71
116 117 3.508845 ACCCTAACTGCACTCACATTT 57.491 42.857 0.00 0.00 0.00 2.32
117 118 3.412386 ACCCTAACTGCACTCACATTTC 58.588 45.455 0.00 0.00 0.00 2.17
118 119 3.073062 ACCCTAACTGCACTCACATTTCT 59.927 43.478 0.00 0.00 0.00 2.52
119 120 3.686726 CCCTAACTGCACTCACATTTCTC 59.313 47.826 0.00 0.00 0.00 2.87
120 121 4.564406 CCCTAACTGCACTCACATTTCTCT 60.564 45.833 0.00 0.00 0.00 3.10
121 122 4.999950 CCTAACTGCACTCACATTTCTCTT 59.000 41.667 0.00 0.00 0.00 2.85
122 123 5.121454 CCTAACTGCACTCACATTTCTCTTC 59.879 44.000 0.00 0.00 0.00 2.87
123 124 4.077300 ACTGCACTCACATTTCTCTTCA 57.923 40.909 0.00 0.00 0.00 3.02
124 125 3.812053 ACTGCACTCACATTTCTCTTCAC 59.188 43.478 0.00 0.00 0.00 3.18
125 126 3.807553 TGCACTCACATTTCTCTTCACA 58.192 40.909 0.00 0.00 0.00 3.58
126 127 4.392047 TGCACTCACATTTCTCTTCACAT 58.608 39.130 0.00 0.00 0.00 3.21
127 128 4.453478 TGCACTCACATTTCTCTTCACATC 59.547 41.667 0.00 0.00 0.00 3.06
128 129 4.694509 GCACTCACATTTCTCTTCACATCT 59.305 41.667 0.00 0.00 0.00 2.90
129 130 5.390673 GCACTCACATTTCTCTTCACATCTG 60.391 44.000 0.00 0.00 0.00 2.90
130 131 4.694509 ACTCACATTTCTCTTCACATCTGC 59.305 41.667 0.00 0.00 0.00 4.26
131 132 4.903054 TCACATTTCTCTTCACATCTGCT 58.097 39.130 0.00 0.00 0.00 4.24
132 133 5.311265 TCACATTTCTCTTCACATCTGCTT 58.689 37.500 0.00 0.00 0.00 3.91
133 134 5.180680 TCACATTTCTCTTCACATCTGCTTG 59.819 40.000 0.00 0.00 0.00 4.01
134 135 4.082895 ACATTTCTCTTCACATCTGCTTGC 60.083 41.667 0.00 0.00 0.00 4.01
135 136 2.845363 TCTCTTCACATCTGCTTGCA 57.155 45.000 0.00 0.00 0.00 4.08
136 137 2.696506 TCTCTTCACATCTGCTTGCAG 58.303 47.619 15.74 15.74 0.00 4.41
137 138 1.738350 CTCTTCACATCTGCTTGCAGG 59.262 52.381 20.62 9.54 0.00 4.85
138 139 1.072806 TCTTCACATCTGCTTGCAGGT 59.927 47.619 20.62 12.52 0.00 4.00
139 140 1.467734 CTTCACATCTGCTTGCAGGTC 59.532 52.381 20.62 0.00 0.00 3.85
140 141 0.671472 TCACATCTGCTTGCAGGTCG 60.671 55.000 20.62 11.81 0.00 4.79
141 142 0.952497 CACATCTGCTTGCAGGTCGT 60.952 55.000 20.62 12.37 0.00 4.34
142 143 0.671781 ACATCTGCTTGCAGGTCGTC 60.672 55.000 20.62 0.00 0.00 4.20
143 144 0.390866 CATCTGCTTGCAGGTCGTCT 60.391 55.000 20.62 0.00 0.00 4.18
144 145 0.390866 ATCTGCTTGCAGGTCGTCTG 60.391 55.000 20.62 4.59 46.03 3.51
151 152 3.051210 CAGGTCGTCTGCCTGTGA 58.949 61.111 3.37 0.00 46.22 3.58
152 153 1.373497 CAGGTCGTCTGCCTGTGAC 60.373 63.158 3.37 0.00 46.22 3.67
153 154 2.048127 GGTCGTCTGCCTGTGACC 60.048 66.667 0.00 0.00 43.60 4.02
154 155 2.734591 GTCGTCTGCCTGTGACCA 59.265 61.111 0.00 0.00 0.00 4.02
155 156 1.293498 GTCGTCTGCCTGTGACCAT 59.707 57.895 0.00 0.00 0.00 3.55
156 157 1.016130 GTCGTCTGCCTGTGACCATG 61.016 60.000 0.00 0.00 0.00 3.66
157 158 1.742880 CGTCTGCCTGTGACCATGG 60.743 63.158 11.19 11.19 0.00 3.66
158 159 2.042831 GTCTGCCTGTGACCATGGC 61.043 63.158 13.04 5.35 46.26 4.40
159 160 2.753043 CTGCCTGTGACCATGGCC 60.753 66.667 13.04 0.00 45.56 5.36
160 161 4.365111 TGCCTGTGACCATGGCCC 62.365 66.667 13.04 4.53 45.56 5.80
162 163 4.802051 CCTGTGACCATGGCCCGG 62.802 72.222 13.04 2.83 0.00 5.73
163 164 4.802051 CTGTGACCATGGCCCGGG 62.802 72.222 19.09 19.09 0.00 5.73
165 166 4.489771 GTGACCATGGCCCGGGAG 62.490 72.222 29.31 10.43 0.00 4.30
173 174 3.868985 GGCCCGGGAGCGGAATAA 61.869 66.667 29.31 0.00 0.00 1.40
174 175 2.430367 GCCCGGGAGCGGAATAAT 59.570 61.111 29.31 0.00 0.00 1.28
175 176 1.675219 GCCCGGGAGCGGAATAATA 59.325 57.895 29.31 0.00 0.00 0.98
179 180 2.564062 CCCGGGAGCGGAATAATACTTA 59.436 50.000 18.48 0.00 0.00 2.24
186 187 4.868067 AGCGGAATAATACTTACACTCGG 58.132 43.478 0.00 0.00 0.00 4.63
187 188 3.985925 GCGGAATAATACTTACACTCGGG 59.014 47.826 0.00 0.00 0.00 5.14
212 213 1.120530 AGATGGAGATAAACCGCCGT 58.879 50.000 0.00 0.00 0.00 5.68
219 220 2.362077 GAGATAAACCGCCGTTACCCTA 59.638 50.000 0.00 0.00 0.00 3.53
235 236 3.456431 CTACGAGAGGCACGAGCGG 62.456 68.421 0.00 0.00 43.41 5.52
244 245 3.680786 CACGAGCGGAGGTGGACA 61.681 66.667 0.00 0.00 39.88 4.02
252 253 1.442769 CGGAGGTGGACACAATCTTG 58.557 55.000 4.69 0.00 0.00 3.02
253 254 1.001974 CGGAGGTGGACACAATCTTGA 59.998 52.381 4.69 0.00 0.00 3.02
254 255 2.704572 GGAGGTGGACACAATCTTGAG 58.295 52.381 4.69 0.00 0.00 3.02
261 265 3.012518 GGACACAATCTTGAGGGACATG 58.987 50.000 0.00 0.00 0.00 3.21
264 268 3.276857 CACAATCTTGAGGGACATGGAG 58.723 50.000 0.00 0.00 0.00 3.86
362 366 2.162681 CAGACTTCCCGCTCCAAAATT 58.837 47.619 0.00 0.00 0.00 1.82
426 434 1.244019 GCTCTTTTCCGGCATGGTGT 61.244 55.000 0.00 0.00 39.52 4.16
479 487 4.612712 GCATTTTCATTCCGACGACAAGAA 60.613 41.667 0.00 0.00 0.00 2.52
481 489 4.921470 TTTCATTCCGACGACAAGAATC 57.079 40.909 0.00 0.00 0.00 2.52
514 522 6.928979 TTTTCTTTTCCAACGAGATGTGTA 57.071 33.333 0.00 0.00 0.00 2.90
515 523 6.928979 TTTCTTTTCCAACGAGATGTGTAA 57.071 33.333 0.00 0.00 0.00 2.41
516 524 7.504924 TTTCTTTTCCAACGAGATGTGTAAT 57.495 32.000 0.00 0.00 0.00 1.89
517 525 6.480524 TCTTTTCCAACGAGATGTGTAATG 57.519 37.500 0.00 0.00 0.00 1.90
518 526 5.995282 TCTTTTCCAACGAGATGTGTAATGT 59.005 36.000 0.00 0.00 0.00 2.71
519 527 5.605564 TTTCCAACGAGATGTGTAATGTG 57.394 39.130 0.00 0.00 0.00 3.21
520 528 4.265904 TCCAACGAGATGTGTAATGTGT 57.734 40.909 0.00 0.00 0.00 3.72
521 529 4.637276 TCCAACGAGATGTGTAATGTGTT 58.363 39.130 0.00 0.00 0.00 3.32
522 530 4.688879 TCCAACGAGATGTGTAATGTGTTC 59.311 41.667 0.00 0.00 0.00 3.18
523 531 4.450757 CCAACGAGATGTGTAATGTGTTCA 59.549 41.667 0.00 0.00 0.00 3.18
524 532 5.122239 CCAACGAGATGTGTAATGTGTTCAT 59.878 40.000 0.00 0.00 35.59 2.57
525 533 6.312672 CCAACGAGATGTGTAATGTGTTCATA 59.687 38.462 0.00 0.00 33.49 2.15
526 534 6.887376 ACGAGATGTGTAATGTGTTCATAC 57.113 37.500 0.00 0.00 33.49 2.39
527 535 5.810587 ACGAGATGTGTAATGTGTTCATACC 59.189 40.000 0.00 0.00 33.49 2.73
528 536 5.234329 CGAGATGTGTAATGTGTTCATACCC 59.766 44.000 0.00 0.00 33.49 3.69
529 537 5.437060 AGATGTGTAATGTGTTCATACCCC 58.563 41.667 0.00 0.00 33.49 4.95
530 538 3.601435 TGTGTAATGTGTTCATACCCCG 58.399 45.455 0.00 0.00 33.49 5.73
531 539 2.353579 GTGTAATGTGTTCATACCCCGC 59.646 50.000 0.00 0.00 33.49 6.13
532 540 2.027100 TGTAATGTGTTCATACCCCGCA 60.027 45.455 0.00 0.00 33.49 5.69
533 541 2.208132 AATGTGTTCATACCCCGCAA 57.792 45.000 0.00 0.00 33.49 4.85
534 542 2.208132 ATGTGTTCATACCCCGCAAA 57.792 45.000 0.00 0.00 31.89 3.68
535 543 1.982660 TGTGTTCATACCCCGCAAAA 58.017 45.000 0.00 0.00 0.00 2.44
536 544 2.307768 TGTGTTCATACCCCGCAAAAA 58.692 42.857 0.00 0.00 0.00 1.94
584 592 0.239082 ACACGAGAATACGACACGCA 59.761 50.000 0.00 0.00 37.03 5.24
592 600 0.739813 ATACGACACGCAGGAAAGCC 60.740 55.000 0.00 0.00 0.00 4.35
602 610 1.012486 CAGGAAAGCCGACCACGTAC 61.012 60.000 0.00 0.00 39.96 3.67
645 653 3.745332 CGTACACGTACAGTACATGGA 57.255 47.619 19.60 0.00 41.40 3.41
646 654 4.282950 CGTACACGTACAGTACATGGAT 57.717 45.455 19.60 0.00 41.40 3.41
647 655 4.665212 CGTACACGTACAGTACATGGATT 58.335 43.478 19.60 0.00 41.40 3.01
648 656 4.731961 CGTACACGTACAGTACATGGATTC 59.268 45.833 19.60 0.00 41.40 2.52
649 657 5.448225 CGTACACGTACAGTACATGGATTCT 60.448 44.000 19.60 0.00 41.40 2.40
661 669 0.384309 TGGATTCTTCCGTCCGATCG 59.616 55.000 8.51 8.51 45.89 3.69
707 716 3.133365 AAGTTGACCCCAGCGCCTT 62.133 57.895 2.29 0.00 0.00 4.35
763 794 2.286595 CGCGCATTCATTATTCACTGCT 60.287 45.455 8.75 0.00 0.00 4.24
804 835 3.381590 GTCCATAACAAGATTCCAAGCCC 59.618 47.826 0.00 0.00 0.00 5.19
805 836 2.695147 CCATAACAAGATTCCAAGCCCC 59.305 50.000 0.00 0.00 0.00 5.80
903 934 4.208686 CCACGCTACCGCCTCCTC 62.209 72.222 0.00 0.00 38.22 3.71
929 960 0.323957 AAACTCCCAACTACCCGCTC 59.676 55.000 0.00 0.00 0.00 5.03
930 961 0.544595 AACTCCCAACTACCCGCTCT 60.545 55.000 0.00 0.00 0.00 4.09
931 962 1.258445 ACTCCCAACTACCCGCTCTG 61.258 60.000 0.00 0.00 0.00 3.35
943 974 1.153667 CGCTCTGCTCCTGAGTTCC 60.154 63.158 0.00 0.00 33.06 3.62
951 982 4.821589 CCTGAGTTCCGAGCCCGC 62.822 72.222 0.00 0.00 0.00 6.13
993 1034 1.375523 GTCAACTCGCACGGGGAAT 60.376 57.895 0.00 0.00 0.00 3.01
1151 1496 4.577246 CGGGCTAGCTCGAGGTGC 62.577 72.222 33.26 24.20 43.62 5.01
1169 1514 4.030452 GCCTGCTTCGCGCTTTGT 62.030 61.111 5.56 0.00 40.11 2.83
1190 1535 1.548081 TGTTCGGGTGGATCTTCGTA 58.452 50.000 0.00 0.00 0.00 3.43
1238 1583 1.040646 AGACTGCTGAACCGTCTGAA 58.959 50.000 0.00 0.00 36.70 3.02
1319 1664 4.437930 GCGGTAGTACGACTGTATTGAACT 60.438 45.833 15.29 0.00 35.47 3.01
1324 1669 5.467705 AGTACGACTGTATTGAACTGGTTC 58.532 41.667 6.53 6.53 35.14 3.62
1365 1710 2.432628 GGCAAGGACGTCGACCTG 60.433 66.667 16.95 11.77 37.85 4.00
1407 1752 3.909430 TCTTCTCATTGTTAACGTCGCT 58.091 40.909 0.26 0.00 0.00 4.93
1410 1755 2.659757 TCTCATTGTTAACGTCGCTTCG 59.340 45.455 0.26 0.00 0.00 3.79
1443 1788 1.888436 GACCTGTGACCTCGCATCCA 61.888 60.000 0.00 0.00 35.63 3.41
1444 1789 1.267574 ACCTGTGACCTCGCATCCAT 61.268 55.000 0.00 0.00 35.63 3.41
1445 1790 0.531532 CCTGTGACCTCGCATCCATC 60.532 60.000 0.00 0.00 35.63 3.51
1452 1798 3.209410 GACCTCGCATCCATCATTCTTT 58.791 45.455 0.00 0.00 0.00 2.52
1467 1813 2.094762 TCTTTACTTTCAGCTCGGCC 57.905 50.000 0.00 0.00 0.00 6.13
1474 1820 0.324614 TTTCAGCTCGGCCATGAGAA 59.675 50.000 11.49 1.56 38.28 2.87
1488 1834 3.684788 CCATGAGAAACCTCCAACTTACG 59.315 47.826 0.00 0.00 0.00 3.18
1495 1841 1.692519 ACCTCCAACTTACGAGCAGTT 59.307 47.619 0.00 0.00 34.67 3.16
1517 1863 9.782028 CAGTTCGTTGAATCAAATTATTTTGTG 57.218 29.630 0.00 0.00 42.37 3.33
1525 1871 9.258826 TGAATCAAATTATTTTGTGTTGTCCAG 57.741 29.630 9.31 0.00 42.37 3.86
1565 1937 2.380084 TGCCGTGTCCTACTTGATTC 57.620 50.000 0.00 0.00 0.00 2.52
1588 1960 8.786826 TTCTCCAAAATAATGATTGTCTACGT 57.213 30.769 0.00 0.00 0.00 3.57
1602 1974 6.864560 TTGTCTACGTCATTAAACATCGAG 57.135 37.500 0.00 0.00 0.00 4.04
1605 1977 5.454877 GTCTACGTCATTAAACATCGAGTCC 59.545 44.000 0.00 0.00 0.00 3.85
1614 1986 8.810427 TCATTAAACATCGAGTCCGTATTAAAC 58.190 33.333 0.00 0.00 37.05 2.01
1811 2197 9.881773 ATGTCATATGGATTACTGGGTTTAATT 57.118 29.630 2.13 0.00 0.00 1.40
1835 2223 6.422776 TTCTAATTGCTTAACACTGCTAGC 57.577 37.500 8.10 8.10 0.00 3.42
1847 2235 5.578005 ACACTGCTAGCTAGTCGATTTAA 57.422 39.130 21.62 0.00 0.00 1.52
1851 2239 6.020281 CACTGCTAGCTAGTCGATTTAAACAG 60.020 42.308 21.62 16.61 0.00 3.16
1861 2249 3.810941 TCGATTTAAACAGCAAACTCCGT 59.189 39.130 0.00 0.00 0.00 4.69
1896 2284 3.412386 ACCTCTGTGTTCTATTGCCAAC 58.588 45.455 0.00 0.00 0.00 3.77
2037 2426 5.279256 CCCCATTTTCGACAAGGTACATTTT 60.279 40.000 0.00 0.00 0.00 1.82
2047 2436 6.160576 ACAAGGTACATTTTTGCTGTGATT 57.839 33.333 0.00 0.00 0.00 2.57
2057 2446 2.128771 TGCTGTGATTTTCCTAGGCC 57.871 50.000 2.96 0.00 0.00 5.19
2107 2496 2.857152 GACAGCGTTGCAAATGTTTCAA 59.143 40.909 0.00 0.00 34.61 2.69
2217 2606 4.356405 TGTCTGTCAGGTTGATGTCAAT 57.644 40.909 0.00 0.00 38.24 2.57
2327 2716 0.107831 TTGGTTGACAAGGAGGGTCG 59.892 55.000 0.00 0.00 38.10 4.79
2334 2723 1.290955 CAAGGAGGGTCGCGTTGTA 59.709 57.895 5.77 0.00 0.00 2.41
2410 2800 0.734889 GTGATTCACATCCCCTTGCG 59.265 55.000 11.93 0.00 34.08 4.85
2415 2805 3.142838 ACATCCCCTTGCGCATGC 61.143 61.111 12.75 7.91 43.20 4.06
2417 2807 2.043652 ATCCCCTTGCGCATGCTT 60.044 55.556 12.75 0.00 43.34 3.91
2436 2827 3.738281 GCTTAATCCTGAAGCACTAGCGA 60.738 47.826 2.59 0.00 46.97 4.93
2448 2839 4.443850 GCACTAGCGATCAACATAACAG 57.556 45.455 0.00 0.00 0.00 3.16
2630 3021 6.623114 GCATCTGCTATATTTTCAGCATCCTG 60.623 42.308 0.00 0.00 46.15 3.86
2652 3043 6.477033 CCTGCTCTGTACTTGTTGTATATGTC 59.523 42.308 0.00 0.00 33.23 3.06
2864 3255 3.899052 ATTTTGTGCCAAGATCATGGG 57.101 42.857 18.26 6.07 41.01 4.00
2884 3275 3.393278 GGGTAGCATAGGTAAATCCCACA 59.607 47.826 0.00 0.00 36.75 4.17
2908 3299 0.598065 ACAAATGTTCAGAAGGCGCC 59.402 50.000 21.89 21.89 0.00 6.53
2958 3354 7.687941 AATCCTTCGACATAAAATGACTTGT 57.312 32.000 0.00 0.00 0.00 3.16
2982 3378 8.013947 TGTTATTACTAGTTTATAGCTCTCGCG 58.986 37.037 0.00 0.00 42.32 5.87
2992 3388 7.551974 AGTTTATAGCTCTCGCGGATATAAGTA 59.448 37.037 6.13 0.00 42.32 2.24
3187 3586 9.745880 CTTACAACTGTTACGTTATATCTCCAT 57.254 33.333 0.00 0.00 0.00 3.41
3188 3587 9.740239 TTACAACTGTTACGTTATATCTCCATC 57.260 33.333 0.00 0.00 0.00 3.51
3189 3588 7.778083 ACAACTGTTACGTTATATCTCCATCA 58.222 34.615 0.00 0.00 0.00 3.07
3395 3794 0.687354 TCACTGGTCTTTGGCTCCTC 59.313 55.000 0.00 0.00 0.00 3.71
3411 3810 2.903135 CTCCTCCTTTTCCTCTGTCACT 59.097 50.000 0.00 0.00 0.00 3.41
3468 3867 9.240159 GGTAACAAAACACGATACAAAAATTCT 57.760 29.630 0.00 0.00 0.00 2.40
3471 3870 9.581099 AACAAAACACGATACAAAAATTCTCTT 57.419 25.926 0.00 0.00 0.00 2.85
3483 3882 6.976925 ACAAAAATTCTCTTTGTGAGCTTCTG 59.023 34.615 6.04 0.00 43.57 3.02
3485 3884 1.788258 TCTCTTTGTGAGCTTCTGCG 58.212 50.000 0.00 0.00 45.42 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.311596 ACCGCTAAGTTTCAACAAGTGTC 59.688 43.478 0.00 0.00 0.00 3.67
1 2 3.064820 CACCGCTAAGTTTCAACAAGTGT 59.935 43.478 0.00 0.00 0.00 3.55
2 3 3.617669 CACCGCTAAGTTTCAACAAGTG 58.382 45.455 0.00 0.00 0.00 3.16
3 4 2.032924 GCACCGCTAAGTTTCAACAAGT 59.967 45.455 0.00 0.00 0.00 3.16
4 5 2.650608 GCACCGCTAAGTTTCAACAAG 58.349 47.619 0.00 0.00 0.00 3.16
5 6 1.003331 CGCACCGCTAAGTTTCAACAA 60.003 47.619 0.00 0.00 0.00 2.83
6 7 0.584396 CGCACCGCTAAGTTTCAACA 59.416 50.000 0.00 0.00 0.00 3.33
7 8 0.110373 CCGCACCGCTAAGTTTCAAC 60.110 55.000 0.00 0.00 0.00 3.18
8 9 0.533308 ACCGCACCGCTAAGTTTCAA 60.533 50.000 0.00 0.00 0.00 2.69
9 10 1.070105 ACCGCACCGCTAAGTTTCA 59.930 52.632 0.00 0.00 0.00 2.69
10 11 0.947180 TCACCGCACCGCTAAGTTTC 60.947 55.000 0.00 0.00 0.00 2.78
11 12 0.949105 CTCACCGCACCGCTAAGTTT 60.949 55.000 0.00 0.00 0.00 2.66
12 13 1.374252 CTCACCGCACCGCTAAGTT 60.374 57.895 0.00 0.00 0.00 2.66
13 14 1.812686 TTCTCACCGCACCGCTAAGT 61.813 55.000 0.00 0.00 0.00 2.24
14 15 1.080093 TTCTCACCGCACCGCTAAG 60.080 57.895 0.00 0.00 0.00 2.18
15 16 1.373748 GTTCTCACCGCACCGCTAA 60.374 57.895 0.00 0.00 0.00 3.09
16 17 2.260434 GTTCTCACCGCACCGCTA 59.740 61.111 0.00 0.00 0.00 4.26
53 54 4.875713 CCGGATTTGGCCCCTCGG 62.876 72.222 0.00 2.73 0.00 4.63
80 81 4.410400 GTTGGGGGTCGCCTCTGG 62.410 72.222 5.82 0.00 0.00 3.86
81 82 4.410400 GGTTGGGGGTCGCCTCTG 62.410 72.222 5.82 0.00 0.00 3.35
84 85 3.876255 TTAGGGTTGGGGGTCGCCT 62.876 63.158 5.82 0.00 0.00 5.52
85 86 3.332385 TTAGGGTTGGGGGTCGCC 61.332 66.667 0.00 0.00 0.00 5.54
86 87 2.045634 GTTAGGGTTGGGGGTCGC 60.046 66.667 0.00 0.00 0.00 5.19
87 88 1.298667 CAGTTAGGGTTGGGGGTCG 59.701 63.158 0.00 0.00 0.00 4.79
88 89 1.001269 GCAGTTAGGGTTGGGGGTC 60.001 63.158 0.00 0.00 0.00 4.46
89 90 1.776710 TGCAGTTAGGGTTGGGGGT 60.777 57.895 0.00 0.00 0.00 4.95
90 91 1.304134 GTGCAGTTAGGGTTGGGGG 60.304 63.158 0.00 0.00 0.00 5.40
91 92 0.322546 GAGTGCAGTTAGGGTTGGGG 60.323 60.000 0.00 0.00 0.00 4.96
92 93 0.400213 TGAGTGCAGTTAGGGTTGGG 59.600 55.000 0.00 0.00 0.00 4.12
93 94 1.202758 TGTGAGTGCAGTTAGGGTTGG 60.203 52.381 0.00 0.00 0.00 3.77
94 95 2.254546 TGTGAGTGCAGTTAGGGTTG 57.745 50.000 0.00 0.00 0.00 3.77
95 96 3.508845 AATGTGAGTGCAGTTAGGGTT 57.491 42.857 0.00 0.00 0.00 4.11
96 97 3.073062 AGAAATGTGAGTGCAGTTAGGGT 59.927 43.478 0.00 0.00 0.00 4.34
97 98 3.679389 AGAAATGTGAGTGCAGTTAGGG 58.321 45.455 0.00 0.00 0.00 3.53
98 99 4.573900 AGAGAAATGTGAGTGCAGTTAGG 58.426 43.478 0.00 0.00 0.00 2.69
99 100 5.698089 TGAAGAGAAATGTGAGTGCAGTTAG 59.302 40.000 0.00 0.00 0.00 2.34
100 101 5.466728 GTGAAGAGAAATGTGAGTGCAGTTA 59.533 40.000 0.00 0.00 0.00 2.24
101 102 4.274459 GTGAAGAGAAATGTGAGTGCAGTT 59.726 41.667 0.00 0.00 0.00 3.16
102 103 3.812053 GTGAAGAGAAATGTGAGTGCAGT 59.188 43.478 0.00 0.00 0.00 4.40
103 104 3.811497 TGTGAAGAGAAATGTGAGTGCAG 59.189 43.478 0.00 0.00 0.00 4.41
104 105 3.807553 TGTGAAGAGAAATGTGAGTGCA 58.192 40.909 0.00 0.00 0.00 4.57
105 106 4.694509 AGATGTGAAGAGAAATGTGAGTGC 59.305 41.667 0.00 0.00 0.00 4.40
106 107 5.390673 GCAGATGTGAAGAGAAATGTGAGTG 60.391 44.000 0.00 0.00 0.00 3.51
107 108 4.694509 GCAGATGTGAAGAGAAATGTGAGT 59.305 41.667 0.00 0.00 0.00 3.41
108 109 4.936411 AGCAGATGTGAAGAGAAATGTGAG 59.064 41.667 0.00 0.00 0.00 3.51
109 110 4.903054 AGCAGATGTGAAGAGAAATGTGA 58.097 39.130 0.00 0.00 0.00 3.58
110 111 5.391449 CAAGCAGATGTGAAGAGAAATGTG 58.609 41.667 0.00 0.00 0.00 3.21
111 112 4.082895 GCAAGCAGATGTGAAGAGAAATGT 60.083 41.667 0.00 0.00 0.00 2.71
112 113 4.082949 TGCAAGCAGATGTGAAGAGAAATG 60.083 41.667 0.00 0.00 0.00 2.32
113 114 4.077108 TGCAAGCAGATGTGAAGAGAAAT 58.923 39.130 0.00 0.00 0.00 2.17
114 115 3.479489 TGCAAGCAGATGTGAAGAGAAA 58.521 40.909 0.00 0.00 0.00 2.52
115 116 3.072211 CTGCAAGCAGATGTGAAGAGAA 58.928 45.455 16.75 0.00 46.30 2.87
116 117 2.614734 CCTGCAAGCAGATGTGAAGAGA 60.615 50.000 22.76 0.00 46.30 3.10
117 118 1.738350 CCTGCAAGCAGATGTGAAGAG 59.262 52.381 22.76 0.00 46.30 2.85
118 119 1.072806 ACCTGCAAGCAGATGTGAAGA 59.927 47.619 22.76 0.00 46.30 2.87
119 120 1.467734 GACCTGCAAGCAGATGTGAAG 59.532 52.381 22.76 7.10 46.30 3.02
120 121 1.527034 GACCTGCAAGCAGATGTGAA 58.473 50.000 22.76 0.00 46.30 3.18
121 122 0.671472 CGACCTGCAAGCAGATGTGA 60.671 55.000 22.76 0.00 46.30 3.58
122 123 0.952497 ACGACCTGCAAGCAGATGTG 60.952 55.000 22.76 11.69 46.30 3.21
123 124 0.671781 GACGACCTGCAAGCAGATGT 60.672 55.000 22.76 16.43 46.30 3.06
124 125 0.390866 AGACGACCTGCAAGCAGATG 60.391 55.000 22.76 13.62 46.30 2.90
125 126 0.390866 CAGACGACCTGCAAGCAGAT 60.391 55.000 22.76 6.04 46.30 2.90
126 127 1.005748 CAGACGACCTGCAAGCAGA 60.006 57.895 22.76 0.00 46.30 4.26
127 128 3.559024 CAGACGACCTGCAAGCAG 58.441 61.111 14.91 14.91 43.26 4.24
135 136 2.574955 GGTCACAGGCAGACGACCT 61.575 63.158 13.21 0.00 43.79 3.85
136 137 2.048127 GGTCACAGGCAGACGACC 60.048 66.667 7.30 7.30 41.08 4.79
137 138 1.016130 CATGGTCACAGGCAGACGAC 61.016 60.000 0.00 0.00 36.87 4.34
138 139 1.293179 CATGGTCACAGGCAGACGA 59.707 57.895 0.00 0.00 36.87 4.20
139 140 1.742880 CCATGGTCACAGGCAGACG 60.743 63.158 2.57 0.00 36.87 4.18
140 141 4.308526 CCATGGTCACAGGCAGAC 57.691 61.111 2.57 0.00 35.29 3.51
145 146 4.802051 CCGGGCCATGGTCACAGG 62.802 72.222 20.13 14.28 0.00 4.00
146 147 4.802051 CCCGGGCCATGGTCACAG 62.802 72.222 20.13 8.71 0.00 3.66
148 149 4.489771 CTCCCGGGCCATGGTCAC 62.490 72.222 20.13 8.56 0.00 3.67
158 159 3.615834 GTAAGTATTATTCCGCTCCCGGG 60.616 52.174 16.85 16.85 43.62 5.73
159 160 3.006110 TGTAAGTATTATTCCGCTCCCGG 59.994 47.826 0.00 0.00 44.33 5.73
160 161 3.985925 GTGTAAGTATTATTCCGCTCCCG 59.014 47.826 0.00 0.00 30.46 5.14
161 162 5.211174 AGTGTAAGTATTATTCCGCTCCC 57.789 43.478 0.00 0.00 30.46 4.30
162 163 4.916249 CGAGTGTAAGTATTATTCCGCTCC 59.084 45.833 0.00 0.00 31.73 4.70
163 164 4.916249 CCGAGTGTAAGTATTATTCCGCTC 59.084 45.833 0.00 0.00 31.95 5.03
164 165 4.261909 CCCGAGTGTAAGTATTATTCCGCT 60.262 45.833 0.00 0.00 30.46 5.52
165 166 3.985925 CCCGAGTGTAAGTATTATTCCGC 59.014 47.826 0.00 0.00 30.46 5.54
166 167 4.279169 TCCCCGAGTGTAAGTATTATTCCG 59.721 45.833 0.00 0.00 30.46 4.30
167 168 5.536260 GTCCCCGAGTGTAAGTATTATTCC 58.464 45.833 0.00 0.00 30.46 3.01
168 169 5.009010 TCGTCCCCGAGTGTAAGTATTATTC 59.991 44.000 0.00 0.00 38.40 1.75
169 170 4.889409 TCGTCCCCGAGTGTAAGTATTATT 59.111 41.667 0.00 0.00 38.40 1.40
170 171 4.464008 TCGTCCCCGAGTGTAAGTATTAT 58.536 43.478 0.00 0.00 38.40 1.28
171 172 3.884895 TCGTCCCCGAGTGTAAGTATTA 58.115 45.455 0.00 0.00 38.40 0.98
172 173 2.726821 TCGTCCCCGAGTGTAAGTATT 58.273 47.619 0.00 0.00 38.40 1.89
173 174 2.425143 TCGTCCCCGAGTGTAAGTAT 57.575 50.000 0.00 0.00 38.40 2.12
174 175 2.086869 CTTCGTCCCCGAGTGTAAGTA 58.913 52.381 0.00 0.00 45.24 2.24
175 176 0.886563 CTTCGTCCCCGAGTGTAAGT 59.113 55.000 0.00 0.00 45.24 2.24
179 180 1.605058 CCATCTTCGTCCCCGAGTGT 61.605 60.000 0.00 0.00 45.24 3.55
186 187 3.729966 GGTTTATCTCCATCTTCGTCCC 58.270 50.000 0.00 0.00 0.00 4.46
187 188 3.381949 CGGTTTATCTCCATCTTCGTCC 58.618 50.000 0.00 0.00 0.00 4.79
195 196 2.484241 GGTAACGGCGGTTTATCTCCAT 60.484 50.000 15.31 0.00 37.58 3.41
201 202 1.202405 CGTAGGGTAACGGCGGTTTAT 60.202 52.381 15.31 2.25 39.19 1.40
202 203 0.172352 CGTAGGGTAACGGCGGTTTA 59.828 55.000 15.31 0.00 39.19 2.01
212 213 0.035152 TCGTGCCTCTCGTAGGGTAA 60.035 55.000 8.36 0.00 46.65 2.85
235 236 2.616510 CCCTCAAGATTGTGTCCACCTC 60.617 54.545 0.00 0.00 0.00 3.85
243 244 3.276857 CTCCATGTCCCTCAAGATTGTG 58.723 50.000 0.00 0.00 0.00 3.33
244 245 2.915604 ACTCCATGTCCCTCAAGATTGT 59.084 45.455 0.00 0.00 0.00 2.71
261 265 2.851071 CGGCTCCTCATCGGACTCC 61.851 68.421 0.00 0.00 36.69 3.85
264 268 2.833582 TCCGGCTCCTCATCGGAC 60.834 66.667 0.00 0.00 46.48 4.79
287 291 1.383109 TGATGGATGACCGCCTCCT 60.383 57.895 0.00 0.00 39.42 3.69
338 342 1.985116 GGAGCGGGAAGTCTGACCT 60.985 63.158 3.76 0.00 0.00 3.85
339 343 1.827399 TTGGAGCGGGAAGTCTGACC 61.827 60.000 3.76 0.00 0.00 4.02
340 344 0.034896 TTTGGAGCGGGAAGTCTGAC 59.965 55.000 0.00 0.00 0.00 3.51
341 345 0.762418 TTTTGGAGCGGGAAGTCTGA 59.238 50.000 0.00 0.00 0.00 3.27
342 346 1.826385 ATTTTGGAGCGGGAAGTCTG 58.174 50.000 0.00 0.00 0.00 3.51
343 347 2.586648 AATTTTGGAGCGGGAAGTCT 57.413 45.000 0.00 0.00 0.00 3.24
344 348 2.414161 CGAAATTTTGGAGCGGGAAGTC 60.414 50.000 0.00 0.00 0.00 3.01
345 349 1.539827 CGAAATTTTGGAGCGGGAAGT 59.460 47.619 0.00 0.00 0.00 3.01
399 403 2.954611 GGAAAAGAGCACGTGGCC 59.045 61.111 18.88 0.00 46.50 5.36
405 409 1.244019 ACCATGCCGGAAAAGAGCAC 61.244 55.000 5.05 0.00 39.77 4.40
406 410 1.074775 ACCATGCCGGAAAAGAGCA 59.925 52.632 5.05 0.00 41.50 4.26
407 411 1.244019 ACACCATGCCGGAAAAGAGC 61.244 55.000 5.05 0.00 38.63 4.09
426 434 0.319469 TCGCAATGCTTGAGACACGA 60.319 50.000 2.94 0.00 34.50 4.35
450 458 3.851403 CGTCGGAATGAAAATGCGAAAAT 59.149 39.130 0.00 0.00 42.24 1.82
463 471 2.979006 CGATTCTTGTCGTCGGAATG 57.021 50.000 5.71 0.00 36.88 2.67
495 503 6.079763 CACATTACACATCTCGTTGGAAAAG 58.920 40.000 0.00 0.00 0.00 2.27
500 508 4.450757 TGAACACATTACACATCTCGTTGG 59.549 41.667 0.00 0.00 0.00 3.77
510 518 2.353579 GCGGGGTATGAACACATTACAC 59.646 50.000 0.00 0.00 0.00 2.90
514 522 2.208132 TTGCGGGGTATGAACACATT 57.792 45.000 0.00 0.00 0.00 2.71
515 523 2.208132 TTTGCGGGGTATGAACACAT 57.792 45.000 0.00 0.00 0.00 3.21
516 524 1.982660 TTTTGCGGGGTATGAACACA 58.017 45.000 0.00 0.00 0.00 3.72
536 544 5.749596 TGTCATGAACACATCTCGTTTTT 57.250 34.783 0.00 0.00 31.20 1.94
537 545 4.319766 GCTGTCATGAACACATCTCGTTTT 60.320 41.667 0.00 0.00 33.24 2.43
538 546 3.187227 GCTGTCATGAACACATCTCGTTT 59.813 43.478 0.00 0.00 33.24 3.60
539 547 2.738846 GCTGTCATGAACACATCTCGTT 59.261 45.455 0.00 0.00 33.24 3.85
540 548 2.341257 GCTGTCATGAACACATCTCGT 58.659 47.619 0.00 0.00 33.24 4.18
541 549 1.322637 CGCTGTCATGAACACATCTCG 59.677 52.381 0.00 0.00 33.24 4.04
542 550 2.602211 CTCGCTGTCATGAACACATCTC 59.398 50.000 0.00 0.00 33.24 2.75
543 551 2.232208 TCTCGCTGTCATGAACACATCT 59.768 45.455 0.00 0.00 33.24 2.90
544 552 2.610433 TCTCGCTGTCATGAACACATC 58.390 47.619 0.00 0.00 33.24 3.06
545 553 2.738846 GTTCTCGCTGTCATGAACACAT 59.261 45.455 0.00 0.00 38.74 3.21
546 554 2.135139 GTTCTCGCTGTCATGAACACA 58.865 47.619 0.00 0.00 38.74 3.72
547 555 2.135139 TGTTCTCGCTGTCATGAACAC 58.865 47.619 0.00 0.00 42.25 3.32
548 556 2.135139 GTGTTCTCGCTGTCATGAACA 58.865 47.619 0.00 0.00 44.06 3.18
549 557 1.125021 CGTGTTCTCGCTGTCATGAAC 59.875 52.381 0.00 0.00 39.18 3.18
550 558 1.000717 TCGTGTTCTCGCTGTCATGAA 60.001 47.619 0.00 0.00 0.00 2.57
551 559 0.596082 TCGTGTTCTCGCTGTCATGA 59.404 50.000 0.00 0.00 0.00 3.07
552 560 0.987715 CTCGTGTTCTCGCTGTCATG 59.012 55.000 0.00 0.00 0.00 3.07
553 561 0.881796 TCTCGTGTTCTCGCTGTCAT 59.118 50.000 0.00 0.00 0.00 3.06
554 562 0.666374 TTCTCGTGTTCTCGCTGTCA 59.334 50.000 0.00 0.00 0.00 3.58
555 563 1.983972 ATTCTCGTGTTCTCGCTGTC 58.016 50.000 0.00 0.00 0.00 3.51
556 564 2.728225 CGTATTCTCGTGTTCTCGCTGT 60.728 50.000 0.00 0.00 0.00 4.40
584 592 1.291272 GTACGTGGTCGGCTTTCCT 59.709 57.895 0.00 0.00 41.85 3.36
638 646 2.380941 TCGGACGGAAGAATCCATGTA 58.619 47.619 0.00 0.00 46.97 2.29
639 647 1.191535 TCGGACGGAAGAATCCATGT 58.808 50.000 0.00 0.00 46.97 3.21
640 648 2.408050 GATCGGACGGAAGAATCCATG 58.592 52.381 0.00 0.00 46.97 3.66
641 649 1.000163 CGATCGGACGGAAGAATCCAT 60.000 52.381 7.38 0.00 46.97 3.41
642 650 0.384309 CGATCGGACGGAAGAATCCA 59.616 55.000 7.38 0.00 46.97 3.41
643 651 3.180984 CGATCGGACGGAAGAATCC 57.819 57.895 7.38 0.00 42.80 3.01
965 996 4.719369 GAGTTGACGGAGCGGCGT 62.719 66.667 9.37 0.00 37.93 5.68
970 1001 3.470567 CGTGCGAGTTGACGGAGC 61.471 66.667 0.00 0.00 33.91 4.70
1056 1400 1.522917 AAGGGGAGGAGAGGAGAGCA 61.523 60.000 0.00 0.00 0.00 4.26
1129 1474 2.044252 TCGAGCTAGCCCGGAGTT 60.044 61.111 19.04 0.00 0.00 3.01
1157 1502 0.764226 CGAACAAACAAAGCGCGAAG 59.236 50.000 12.10 0.00 0.00 3.79
1160 1505 2.008697 CCCGAACAAACAAAGCGCG 61.009 57.895 0.00 0.00 0.00 6.86
1169 1514 1.071071 ACGAAGATCCACCCGAACAAA 59.929 47.619 0.00 0.00 0.00 2.83
1190 1535 2.158900 ACGGATCGGCAGAGAAATTCAT 60.159 45.455 0.00 0.00 0.00 2.57
1238 1583 1.734707 CGAACTACCGGTCAGCGAATT 60.735 52.381 12.40 0.00 0.00 2.17
1319 1664 0.179020 CTGCACACCAAGGAGAACCA 60.179 55.000 0.00 0.00 38.94 3.67
1324 1669 1.310933 GCATCCTGCACACCAAGGAG 61.311 60.000 0.00 0.00 44.26 3.69
1365 1710 0.175989 CCTTCCCCTTGTAGACGCTC 59.824 60.000 0.00 0.00 0.00 5.03
1407 1752 0.110238 GTCGTACGTACCACTGCGAA 60.110 55.000 19.67 0.00 0.00 4.70
1410 1755 0.455633 CAGGTCGTACGTACCACTGC 60.456 60.000 27.28 7.38 39.64 4.40
1443 1788 4.333926 GCCGAGCTGAAAGTAAAGAATGAT 59.666 41.667 0.00 0.00 35.30 2.45
1444 1789 3.684788 GCCGAGCTGAAAGTAAAGAATGA 59.315 43.478 0.00 0.00 35.30 2.57
1445 1790 3.181506 GGCCGAGCTGAAAGTAAAGAATG 60.182 47.826 0.00 0.00 35.30 2.67
1452 1798 0.901827 TCATGGCCGAGCTGAAAGTA 59.098 50.000 0.00 0.00 35.30 2.24
1467 1813 4.566004 TCGTAAGTTGGAGGTTTCTCATG 58.434 43.478 0.00 0.00 39.26 3.07
1474 1820 1.692519 ACTGCTCGTAAGTTGGAGGTT 59.307 47.619 7.59 0.00 35.60 3.50
1488 1834 8.452989 AAATAATTTGATTCAACGAACTGCTC 57.547 30.769 0.00 0.00 0.00 4.26
1517 1863 8.538409 AATAATTTTCATTTGCTCTGGACAAC 57.462 30.769 0.00 0.00 0.00 3.32
1525 1871 9.410556 ACGGCATATAATAATTTTCATTTGCTC 57.589 29.630 0.00 0.00 0.00 4.26
1565 1937 8.196802 TGACGTAGACAATCATTATTTTGGAG 57.803 34.615 0.00 0.00 0.00 3.86
1580 1952 5.946298 ACTCGATGTTTAATGACGTAGACA 58.054 37.500 0.00 0.00 36.25 3.41
1588 1960 8.810427 GTTTAATACGGACTCGATGTTTAATGA 58.190 33.333 0.00 0.00 40.11 2.57
1602 1974 8.885722 TCTGTATGGAATTTGTTTAATACGGAC 58.114 33.333 0.00 0.00 32.53 4.79
1605 1977 9.498307 GGTTCTGTATGGAATTTGTTTAATACG 57.502 33.333 0.00 0.00 0.00 3.06
1614 1986 8.567285 AGAAGTAAGGTTCTGTATGGAATTTG 57.433 34.615 0.00 0.00 35.37 2.32
1811 2197 6.655003 AGCTAGCAGTGTTAAGCAATTAGAAA 59.345 34.615 18.83 0.00 37.44 2.52
1813 2199 5.734720 AGCTAGCAGTGTTAAGCAATTAGA 58.265 37.500 18.83 0.00 37.44 2.10
1816 2202 5.491982 ACTAGCTAGCAGTGTTAAGCAATT 58.508 37.500 20.91 0.00 37.44 2.32
1824 2210 4.457834 AAATCGACTAGCTAGCAGTGTT 57.542 40.909 20.91 7.16 0.00 3.32
1826 2212 5.805486 TGTTTAAATCGACTAGCTAGCAGTG 59.195 40.000 20.91 8.73 0.00 3.66
1827 2213 5.962433 TGTTTAAATCGACTAGCTAGCAGT 58.038 37.500 20.91 17.43 0.00 4.40
1828 2214 5.051374 GCTGTTTAAATCGACTAGCTAGCAG 60.051 44.000 20.91 14.39 0.00 4.24
1835 2223 6.534934 GGAGTTTGCTGTTTAAATCGACTAG 58.465 40.000 0.00 0.00 0.00 2.57
1861 2249 5.815581 ACACAGAGGTTAGCATCCAATAAA 58.184 37.500 0.00 0.00 0.00 1.40
1896 2284 3.882888 TCTCAAAGCCTGTAAACCACAAG 59.117 43.478 0.00 0.00 36.48 3.16
2037 2426 2.224992 TGGCCTAGGAAAATCACAGCAA 60.225 45.455 14.75 0.00 0.00 3.91
2047 2436 4.040936 TGCATTACTTTGGCCTAGGAAA 57.959 40.909 14.75 4.05 0.00 3.13
2057 2446 9.630098 ACTGAAACAGATAAATGCATTACTTTG 57.370 29.630 13.39 11.60 35.18 2.77
2217 2606 1.133199 AGGGGAGAAACATTGTTGCCA 60.133 47.619 2.13 0.00 0.00 4.92
2334 2723 3.537874 GTCGGGGCATAGCGGTCT 61.538 66.667 0.00 0.00 0.00 3.85
2385 2774 0.676466 GGGATGTGAATCACGGTGCA 60.676 55.000 9.00 0.00 37.14 4.57
2386 2775 1.376609 GGGGATGTGAATCACGGTGC 61.377 60.000 9.00 5.33 37.14 5.01
2415 2805 4.046938 TCGCTAGTGCTTCAGGATTAAG 57.953 45.455 0.00 0.00 36.97 1.85
2417 2807 3.636764 TGATCGCTAGTGCTTCAGGATTA 59.363 43.478 0.00 0.00 36.97 1.75
2429 2819 7.291516 AAGCAACTGTTATGTTGATCGCTAGT 61.292 38.462 10.98 0.00 44.37 2.57
2448 2839 6.094048 TCCTTCTGCAGATTATACAAAGCAAC 59.906 38.462 19.04 0.00 0.00 4.17
2525 2916 2.961526 TACAGAGTGCCGATTTCTCC 57.038 50.000 0.00 0.00 0.00 3.71
2630 3021 6.020599 CACGACATATACAACAAGTACAGAGC 60.021 42.308 0.00 0.00 35.05 4.09
2864 3255 7.549488 GTGATATGTGGGATTTACCTATGCTAC 59.451 40.741 0.00 0.00 38.98 3.58
2884 3275 4.201950 GCGCCTTCTGAACATTTGTGATAT 60.202 41.667 0.00 0.00 0.00 1.63
2908 3299 5.123344 TGAAATGCACATTCAGATGACAGAG 59.877 40.000 11.62 0.00 36.73 3.35
2980 3376 5.808540 TGTAATTCCGCATACTTATATCCGC 59.191 40.000 0.00 0.00 0.00 5.54
2982 3378 6.255020 CGGTGTAATTCCGCATACTTATATCC 59.745 42.308 0.00 0.00 41.48 2.59
3187 3586 9.090692 CGACATATGCATGAAGATAATACATGA 57.909 33.333 10.16 0.00 42.41 3.07
3188 3587 7.849515 GCGACATATGCATGAAGATAATACATG 59.150 37.037 10.16 2.78 42.60 3.21
3189 3588 7.550196 TGCGACATATGCATGAAGATAATACAT 59.450 33.333 10.16 0.00 37.44 2.29
3395 3794 3.199880 ACACAGTGACAGAGGAAAAGG 57.800 47.619 7.81 0.00 0.00 3.11
3468 3867 0.532640 TGCGCAGAAGCTCACAAAGA 60.533 50.000 5.66 0.00 39.10 2.52
3471 3870 0.532640 TCTTGCGCAGAAGCTCACAA 60.533 50.000 11.31 0.00 34.76 3.33


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

AutoCloner maintained by Alex Coulton.