Multiple sequence alignment - TraesCS7B01G193400

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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 TraesCS7B01G193400 chr7B 100.000 2877 0 0 1 2877 332257030 332254154 0.000000e+00 5313.0
1 TraesCS7B01G193400 chr7B 83.905 379 42 6 751 1124 332243255 332242891 7.630000e-91 344.0
2 TraesCS7B01G193400 chr7B 83.554 377 43 6 751 1122 332172972 332172610 4.590000e-88 335.0
3 TraesCS7B01G193400 chr7B 76.772 254 32 13 1467 1708 328802807 328802569 1.810000e-22 117.0
4 TraesCS7B01G193400 chr7B 87.368 95 8 2 1167 1260 539323390 539323481 3.920000e-19 106.0
5 TraesCS7B01G193400 chr7A 91.022 1125 89 8 1761 2877 195550774 195551894 0.000000e+00 1507.0
6 TraesCS7B01G193400 chr7A 92.992 528 28 3 643 1169 195549845 195550364 0.000000e+00 761.0
7 TraesCS7B01G193400 chr7A 82.303 469 52 12 659 1122 195567677 195568119 7.520000e-101 377.0
8 TraesCS7B01G193400 chr7A 93.852 244 12 1 1258 1498 195550382 195550625 5.860000e-97 364.0
9 TraesCS7B01G193400 chr7A 85.319 361 34 7 751 1106 195733700 195734046 3.530000e-94 355.0
10 TraesCS7B01G193400 chr7A 91.139 237 21 0 1577 1813 195550626 195550862 3.580000e-84 322.0
11 TraesCS7B01G193400 chr7A 77.778 378 50 16 1466 1820 195568341 195568707 4.860000e-48 202.0
12 TraesCS7B01G193400 chr7A 95.000 120 6 0 477 596 195549727 195549846 3.780000e-44 189.0
13 TraesCS7B01G193400 chr7A 77.604 192 34 5 1467 1649 194009925 194009734 1.090000e-19 108.0
14 TraesCS7B01G193400 chr7A 76.720 189 33 6 1431 1609 194009982 194009795 8.490000e-16 95.3
15 TraesCS7B01G193400 chr7A 97.619 42 1 0 609 650 15699304 15699345 3.980000e-09 73.1
16 TraesCS7B01G193400 chr7D 92.479 944 58 9 1761 2695 188360402 188359463 0.000000e+00 1338.0
17 TraesCS7B01G193400 chr7D 95.345 537 22 2 1279 1812 188360851 188360315 0.000000e+00 850.0
18 TraesCS7B01G193400 chr7D 94.369 515 12 3 646 1157 188361738 188361238 0.000000e+00 774.0
19 TraesCS7B01G193400 chr7D 91.391 302 19 3 296 596 188362035 188361740 9.600000e-110 407.0
20 TraesCS7B01G193400 chr7D 88.341 223 26 0 900 1122 188319255 188319033 4.730000e-68 268.0
21 TraesCS7B01G193400 chr7D 92.614 176 11 1 108 281 188363894 188363719 4.760000e-63 252.0
22 TraesCS7B01G193400 chr7D 92.614 176 10 2 2702 2877 188359420 188359248 1.710000e-62 250.0
23 TraesCS7B01G193400 chr7D 79.134 254 29 10 1467 1708 185927356 185927115 1.380000e-33 154.0
24 TraesCS7B01G193400 chrUn 88.172 93 7 3 1171 1260 76050920 76051011 1.090000e-19 108.0
25 TraesCS7B01G193400 chrUn 92.157 51 3 1 2616 2666 423256976 423257025 1.430000e-08 71.3
26 TraesCS7B01G193400 chrUn 92.157 51 3 1 2616 2666 441344345 441344296 1.430000e-08 71.3
27 TraesCS7B01G193400 chr1B 91.358 81 2 5 1150 1227 572202586 572202508 3.920000e-19 106.0
28 TraesCS7B01G193400 chr1B 85.556 90 9 3 1175 1260 595420491 595420402 1.100000e-14 91.6
29 TraesCS7B01G193400 chr6B 89.412 85 4 5 1145 1227 350784891 350784972 5.070000e-18 102.0
30 TraesCS7B01G193400 chr6A 90.667 75 5 2 1155 1227 594857753 594857679 6.560000e-17 99.0
31 TraesCS7B01G193400 chr3A 91.667 72 4 2 1157 1227 110030043 110030113 6.560000e-17 99.0
32 TraesCS7B01G193400 chr3A 95.455 44 2 0 603 646 21358961 21358918 1.430000e-08 71.3
33 TraesCS7B01G193400 chr2D 87.805 82 10 0 1171 1252 125452640 125452559 2.360000e-16 97.1
34 TraesCS7B01G193400 chr2D 90.667 75 4 3 1171 1244 481971397 481971469 2.360000e-16 97.1
35 TraesCS7B01G193400 chr2D 95.455 44 2 0 609 652 382442457 382442414 1.430000e-08 71.3
36 TraesCS7B01G193400 chr2A 93.878 49 3 0 609 657 705503476 705503524 1.110000e-09 75.0
37 TraesCS7B01G193400 chr6D 92.157 51 3 1 2616 2666 277318595 277318644 1.430000e-08 71.3
38 TraesCS7B01G193400 chr5D 92.157 51 3 1 2616 2666 80075626 80075577 1.430000e-08 71.3
39 TraesCS7B01G193400 chr5D 97.297 37 1 0 609 645 273556613 273556649 2.390000e-06 63.9
40 TraesCS7B01G193400 chr5A 97.561 41 1 0 609 649 577942922 577942962 1.430000e-08 71.3
41 TraesCS7B01G193400 chr5A 95.455 44 1 1 609 652 10900629 10900587 5.140000e-08 69.4
42 TraesCS7B01G193400 chr4D 92.157 51 3 1 2616 2666 123308809 123308858 1.430000e-08 71.3
43 TraesCS7B01G193400 chr4D 92.157 51 3 1 2616 2666 123459620 123459571 1.430000e-08 71.3
44 TraesCS7B01G193400 chr1D 92.157 51 3 1 2616 2666 351067807 351067856 1.430000e-08 71.3
45 TraesCS7B01G193400 chr1D 95.455 44 1 1 601 644 10724296 10724254 5.140000e-08 69.4
46 TraesCS7B01G193400 chr1D 88.889 54 4 2 609 661 394862548 394862496 6.650000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G193400 chr7B 332254154 332257030 2876 True 5313.000000 5313 100.000000 1 2877 1 chr7B.!!$R4 2876
1 TraesCS7B01G193400 chr7A 195549727 195551894 2167 False 628.600000 1507 92.801000 477 2877 5 chr7A.!!$F3 2400
2 TraesCS7B01G193400 chr7A 195567677 195568707 1030 False 289.500000 377 80.040500 659 1820 2 chr7A.!!$F4 1161
3 TraesCS7B01G193400 chr7D 188359248 188363894 4646 True 645.166667 1338 93.135333 108 2877 6 chr7D.!!$R3 2769

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
907 2584 0.034756 AGGTGTAGACGTGCATGCAA 59.965 50.0 24.58 2.76 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2830 4910 0.108585 ACAAAGCGGGTCACATGTCT 59.891 50.0 0.0 0.0 0.0 3.41 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
20 21 2.809446 GGGACAAAACACTCAGCAAAC 58.191 47.619 0.00 0.00 0.00 2.93
21 22 2.165437 GGGACAAAACACTCAGCAAACA 59.835 45.455 0.00 0.00 0.00 2.83
22 23 3.438360 GGACAAAACACTCAGCAAACAG 58.562 45.455 0.00 0.00 0.00 3.16
23 24 3.438360 GACAAAACACTCAGCAAACAGG 58.562 45.455 0.00 0.00 0.00 4.00
24 25 3.088532 ACAAAACACTCAGCAAACAGGA 58.911 40.909 0.00 0.00 0.00 3.86
25 26 3.129287 ACAAAACACTCAGCAAACAGGAG 59.871 43.478 0.00 0.00 34.85 3.69
26 27 1.312815 AACACTCAGCAAACAGGAGC 58.687 50.000 0.00 0.00 31.88 4.70
27 28 0.536006 ACACTCAGCAAACAGGAGCC 60.536 55.000 0.00 0.00 31.88 4.70
28 29 0.535780 CACTCAGCAAACAGGAGCCA 60.536 55.000 0.00 0.00 31.88 4.75
29 30 0.536006 ACTCAGCAAACAGGAGCCAC 60.536 55.000 0.00 0.00 31.88 5.01
30 31 1.572085 CTCAGCAAACAGGAGCCACG 61.572 60.000 0.00 0.00 0.00 4.94
31 32 1.893808 CAGCAAACAGGAGCCACGT 60.894 57.895 0.00 0.00 0.00 4.49
32 33 1.893808 AGCAAACAGGAGCCACGTG 60.894 57.895 9.08 9.08 39.84 4.49
33 34 2.908073 GCAAACAGGAGCCACGTGG 61.908 63.158 30.66 30.66 38.51 4.94
43 44 3.041940 CCACGTGGCACGACCTTC 61.042 66.667 42.65 2.55 46.05 3.46
44 45 3.041940 CACGTGGCACGACCTTCC 61.042 66.667 42.65 1.70 46.05 3.46
45 46 4.657824 ACGTGGCACGACCTTCCG 62.658 66.667 42.65 17.31 46.05 4.30
46 47 4.657824 CGTGGCACGACCTTCCGT 62.658 66.667 34.85 0.00 46.05 4.69
52 53 3.541072 ACGACCTTCCGTGGTTGA 58.459 55.556 11.99 0.00 42.68 3.18
53 54 1.068585 ACGACCTTCCGTGGTTGAC 59.931 57.895 11.99 0.00 42.68 3.18
61 62 2.029073 CGTGGTTGACGGCTCTGT 59.971 61.111 0.00 0.00 44.85 3.41
62 63 1.287815 CGTGGTTGACGGCTCTGTA 59.712 57.895 0.00 0.00 44.85 2.74
63 64 0.108804 CGTGGTTGACGGCTCTGTAT 60.109 55.000 0.00 0.00 44.85 2.29
64 65 1.133598 CGTGGTTGACGGCTCTGTATA 59.866 52.381 0.00 0.00 44.85 1.47
65 66 2.223735 CGTGGTTGACGGCTCTGTATAT 60.224 50.000 0.00 0.00 44.85 0.86
66 67 3.004002 CGTGGTTGACGGCTCTGTATATA 59.996 47.826 0.00 0.00 44.85 0.86
67 68 4.296690 GTGGTTGACGGCTCTGTATATAC 58.703 47.826 5.89 5.89 0.00 1.47
68 69 4.037684 GTGGTTGACGGCTCTGTATATACT 59.962 45.833 13.89 0.00 0.00 2.12
69 70 4.277672 TGGTTGACGGCTCTGTATATACTC 59.722 45.833 13.89 2.33 0.00 2.59
70 71 4.321082 GGTTGACGGCTCTGTATATACTCC 60.321 50.000 13.89 8.62 0.00 3.85
71 72 3.418995 TGACGGCTCTGTATATACTCCC 58.581 50.000 13.89 7.72 0.00 4.30
72 73 2.754002 GACGGCTCTGTATATACTCCCC 59.246 54.545 13.89 8.01 0.00 4.81
73 74 1.743958 CGGCTCTGTATATACTCCCCG 59.256 57.143 13.89 14.67 0.00 5.73
74 75 2.805194 GGCTCTGTATATACTCCCCGT 58.195 52.381 13.89 0.00 0.00 5.28
75 76 3.163467 GGCTCTGTATATACTCCCCGTT 58.837 50.000 13.89 0.00 0.00 4.44
76 77 3.577415 GGCTCTGTATATACTCCCCGTTT 59.423 47.826 13.89 0.00 0.00 3.60
77 78 4.321824 GGCTCTGTATATACTCCCCGTTTC 60.322 50.000 13.89 0.00 0.00 2.78
78 79 4.280174 GCTCTGTATATACTCCCCGTTTCA 59.720 45.833 13.89 0.00 0.00 2.69
79 80 5.221382 GCTCTGTATATACTCCCCGTTTCAA 60.221 44.000 13.89 0.00 0.00 2.69
80 81 6.684613 GCTCTGTATATACTCCCCGTTTCAAA 60.685 42.308 13.89 0.00 0.00 2.69
81 82 7.185318 TCTGTATATACTCCCCGTTTCAAAA 57.815 36.000 13.89 0.00 0.00 2.44
82 83 7.798071 TCTGTATATACTCCCCGTTTCAAAAT 58.202 34.615 13.89 0.00 0.00 1.82
83 84 8.926374 TCTGTATATACTCCCCGTTTCAAAATA 58.074 33.333 13.89 0.00 0.00 1.40
84 85 9.550406 CTGTATATACTCCCCGTTTCAAAATAA 57.450 33.333 13.89 0.00 0.00 1.40
85 86 9.550406 TGTATATACTCCCCGTTTCAAAATAAG 57.450 33.333 13.89 0.00 0.00 1.73
86 87 9.551734 GTATATACTCCCCGTTTCAAAATAAGT 57.448 33.333 5.58 0.00 0.00 2.24
88 89 5.700722 ACTCCCCGTTTCAAAATAAGTTC 57.299 39.130 0.00 0.00 0.00 3.01
89 90 4.521639 ACTCCCCGTTTCAAAATAAGTTCC 59.478 41.667 0.00 0.00 0.00 3.62
90 91 4.471548 TCCCCGTTTCAAAATAAGTTCCA 58.528 39.130 0.00 0.00 0.00 3.53
91 92 5.081032 TCCCCGTTTCAAAATAAGTTCCAT 58.919 37.500 0.00 0.00 0.00 3.41
92 93 5.047660 TCCCCGTTTCAAAATAAGTTCCATG 60.048 40.000 0.00 0.00 0.00 3.66
93 94 5.167845 CCCGTTTCAAAATAAGTTCCATGG 58.832 41.667 4.97 4.97 0.00 3.66
94 95 5.047660 CCCGTTTCAAAATAAGTTCCATGGA 60.048 40.000 11.44 11.44 0.00 3.41
95 96 6.092748 CCGTTTCAAAATAAGTTCCATGGAG 58.907 40.000 15.53 0.00 0.00 3.86
96 97 6.092748 CGTTTCAAAATAAGTTCCATGGAGG 58.907 40.000 15.53 0.00 39.47 4.30
97 98 6.398095 GTTTCAAAATAAGTTCCATGGAGGG 58.602 40.000 15.53 0.00 38.24 4.30
98 99 5.528600 TCAAAATAAGTTCCATGGAGGGA 57.471 39.130 15.53 0.00 38.24 4.20
99 100 5.509498 TCAAAATAAGTTCCATGGAGGGAG 58.491 41.667 15.53 0.10 38.42 4.30
100 101 5.015178 TCAAAATAAGTTCCATGGAGGGAGT 59.985 40.000 15.53 0.00 38.42 3.85
101 102 6.216662 TCAAAATAAGTTCCATGGAGGGAGTA 59.783 38.462 15.53 5.00 38.42 2.59
102 103 6.848562 AAATAAGTTCCATGGAGGGAGTAT 57.151 37.500 15.53 7.05 38.42 2.12
103 104 7.947782 AAATAAGTTCCATGGAGGGAGTATA 57.052 36.000 15.53 3.58 38.42 1.47
104 105 8.525729 AAATAAGTTCCATGGAGGGAGTATAT 57.474 34.615 15.53 5.66 38.42 0.86
105 106 9.629649 AAATAAGTTCCATGGAGGGAGTATATA 57.370 33.333 15.53 0.00 38.42 0.86
106 107 9.805204 AATAAGTTCCATGGAGGGAGTATATAT 57.195 33.333 15.53 2.75 38.42 0.86
114 115 9.434275 CCATGGAGGGAGTATATATATACACAA 57.566 37.037 27.07 11.91 40.70 3.33
131 132 1.949525 ACAAACATATCGGCAGGCATC 59.050 47.619 0.00 0.00 0.00 3.91
139 142 1.347062 TCGGCAGGCATCACCATATA 58.653 50.000 0.00 0.00 43.14 0.86
150 153 5.049886 GGCATCACCATATACATCGCATATG 60.050 44.000 0.00 0.00 38.86 1.78
176 179 7.912250 GTCCATACAAGCTATCAATTTGTCAAG 59.088 37.037 0.00 0.00 36.52 3.02
195 198 4.817464 TCAAGTACCGCAACAATTACTTGT 59.183 37.500 16.10 0.00 46.12 3.16
209 212 8.415950 ACAATTACTTGTCCATATCCAACAAA 57.584 30.769 0.00 0.00 41.86 2.83
221 224 8.306038 TCCATATCCAACAAATCACAGAAAAAG 58.694 33.333 0.00 0.00 0.00 2.27
282 1367 1.452025 CGTATGTCTCATTAAGGCGCG 59.548 52.381 0.00 0.00 29.57 6.86
288 1373 5.128992 TGTCTCATTAAGGCGCGATATTA 57.871 39.130 12.10 1.59 29.57 0.98
301 1386 3.433274 CGCGATATTATGTGCAAGGTGAT 59.567 43.478 0.00 0.00 0.00 3.06
311 1396 2.095919 GTGCAAGGTGATGTTTCCGTAC 60.096 50.000 0.00 0.00 0.00 3.67
315 1987 0.719465 GGTGATGTTTCCGTACAGCG 59.281 55.000 0.00 0.00 37.24 5.18
347 2019 5.741510 TGTTGTGACTTGTAAATTTTGCTCG 59.258 36.000 0.00 0.00 0.00 5.03
380 2052 2.103898 TCAATAATCATTGTGCGCGC 57.896 45.000 27.26 27.26 41.96 6.86
384 2056 1.631144 TAATCATTGTGCGCGCGTGT 61.631 50.000 32.35 9.58 0.00 4.49
385 2057 3.649896 ATCATTGTGCGCGCGTGTG 62.650 57.895 32.35 21.08 0.00 3.82
386 2058 4.664864 CATTGTGCGCGCGTGTGT 62.665 61.111 32.35 11.29 0.00 3.72
448 2120 5.764487 TTCACAACAAATCTACATGTGCA 57.236 34.783 9.11 0.00 40.80 4.57
449 2121 5.361135 TCACAACAAATCTACATGTGCAG 57.639 39.130 9.11 0.00 40.80 4.41
453 2125 4.691860 ACAAATCTACATGTGCAGCTTC 57.308 40.909 9.11 0.00 0.00 3.86
456 2128 1.730501 TCTACATGTGCAGCTTCAGC 58.269 50.000 9.11 0.00 42.49 4.26
471 2143 1.054574 TCAGCGCGTACGTTTGTAAG 58.945 50.000 17.90 1.30 42.83 2.34
472 2144 0.780002 CAGCGCGTACGTTTGTAAGT 59.220 50.000 17.90 0.00 42.83 2.24
553 2226 4.804139 ACAGGACGTAATCGATCAATGAAC 59.196 41.667 0.00 0.00 40.62 3.18
554 2227 4.803613 CAGGACGTAATCGATCAATGAACA 59.196 41.667 0.00 0.00 40.62 3.18
578 2251 6.574832 CACGATAATTAATTCAAGGATGCACG 59.425 38.462 3.39 0.00 0.00 5.34
616 2289 9.871238 TCTCTAATACTCAGTTCATAAAACCAC 57.129 33.333 0.00 0.00 0.00 4.16
617 2290 8.697846 TCTAATACTCAGTTCATAAAACCACG 57.302 34.615 0.00 0.00 0.00 4.94
618 2291 8.525316 TCTAATACTCAGTTCATAAAACCACGA 58.475 33.333 0.00 0.00 0.00 4.35
619 2292 6.963049 ATACTCAGTTCATAAAACCACGAC 57.037 37.500 0.00 0.00 0.00 4.34
620 2293 3.739300 ACTCAGTTCATAAAACCACGACG 59.261 43.478 0.00 0.00 0.00 5.12
621 2294 3.979948 TCAGTTCATAAAACCACGACGA 58.020 40.909 0.00 0.00 0.00 4.20
622 2295 3.985279 TCAGTTCATAAAACCACGACGAG 59.015 43.478 0.00 0.00 0.00 4.18
623 2296 3.739300 CAGTTCATAAAACCACGACGAGT 59.261 43.478 0.00 0.00 0.00 4.18
624 2297 4.919168 CAGTTCATAAAACCACGACGAGTA 59.081 41.667 0.00 0.00 0.00 2.59
625 2298 5.403166 CAGTTCATAAAACCACGACGAGTAA 59.597 40.000 0.00 0.00 0.00 2.24
626 2299 6.090358 CAGTTCATAAAACCACGACGAGTAAT 59.910 38.462 0.00 0.00 0.00 1.89
627 2300 6.647895 AGTTCATAAAACCACGACGAGTAATT 59.352 34.615 0.00 1.08 0.00 1.40
628 2301 7.172019 AGTTCATAAAACCACGACGAGTAATTT 59.828 33.333 0.00 0.34 0.00 1.82
629 2302 6.823531 TCATAAAACCACGACGAGTAATTTG 58.176 36.000 0.00 0.00 0.00 2.32
630 2303 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
631 2304 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
632 2305 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
633 2306 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
634 2307 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
635 2308 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
636 2309 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
637 2310 2.988493 CGACGAGTAATTTGGAACGGAA 59.012 45.455 0.00 0.00 0.00 4.30
638 2311 3.060363 CGACGAGTAATTTGGAACGGAAG 59.940 47.826 0.00 0.00 0.00 3.46
639 2312 3.332034 ACGAGTAATTTGGAACGGAAGG 58.668 45.455 0.00 0.00 0.00 3.46
640 2313 3.007182 ACGAGTAATTTGGAACGGAAGGA 59.993 43.478 0.00 0.00 0.00 3.36
641 2314 3.617263 CGAGTAATTTGGAACGGAAGGAG 59.383 47.826 0.00 0.00 0.00 3.69
642 2315 4.576879 GAGTAATTTGGAACGGAAGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
643 2316 5.622914 CGAGTAATTTGGAACGGAAGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
644 2317 6.309389 AGTAATTTGGAACGGAAGGAGTAT 57.691 37.500 0.00 0.00 0.00 2.12
683 2356 0.106268 TGCCAAGTGGTTCCACACAT 60.106 50.000 21.71 6.88 43.72 3.21
741 2414 4.035102 GCCCCGTTCTGGCCTTCT 62.035 66.667 3.32 0.00 43.33 2.85
744 2417 2.045926 CCGTTCTGGCCTTCTGGG 60.046 66.667 3.32 0.00 38.36 4.45
745 2418 2.750350 CGTTCTGGCCTTCTGGGT 59.250 61.111 3.32 0.00 37.43 4.51
746 2419 1.672356 CGTTCTGGCCTTCTGGGTG 60.672 63.158 3.32 0.00 37.43 4.61
747 2420 1.303643 GTTCTGGCCTTCTGGGTGG 60.304 63.158 3.32 0.00 37.43 4.61
834 2511 0.389426 ACAGCCAACCGTAGCGTTAG 60.389 55.000 0.00 0.00 0.00 2.34
891 2568 6.783892 GTCTATTAACTCGACGAGATAGGT 57.216 41.667 30.56 16.78 33.32 3.08
892 2569 6.592166 GTCTATTAACTCGACGAGATAGGTG 58.408 44.000 30.56 15.24 33.32 4.00
907 2584 0.034756 AGGTGTAGACGTGCATGCAA 59.965 50.000 24.58 2.76 0.00 4.08
913 2594 1.174712 AGACGTGCATGCAAGCCTTT 61.175 50.000 29.87 13.32 0.00 3.11
1155 2867 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1156 2868 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1158 2870 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1159 2871 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1160 2872 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1161 2873 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1162 2874 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1163 2875 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1167 2879 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1168 2880 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1170 2882 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
1171 2883 6.614657 TCTCTCTCTCTCTCTCTCTCTCATA 58.385 44.000 0.00 0.00 0.00 2.15
1172 2884 6.491745 TCTCTCTCTCTCTCTCTCTCTCATAC 59.508 46.154 0.00 0.00 0.00 2.39
1174 2886 4.593206 TCTCTCTCTCTCTCTCTCATACCC 59.407 50.000 0.00 0.00 0.00 3.69
1175 2887 3.650942 TCTCTCTCTCTCTCTCATACCCC 59.349 52.174 0.00 0.00 0.00 4.95
1176 2888 3.652869 CTCTCTCTCTCTCTCATACCCCT 59.347 52.174 0.00 0.00 0.00 4.79
1177 2889 3.650942 TCTCTCTCTCTCTCATACCCCTC 59.349 52.174 0.00 0.00 0.00 4.30
1178 2890 2.714250 TCTCTCTCTCTCATACCCCTCC 59.286 54.545 0.00 0.00 0.00 4.30
1179 2891 1.422024 TCTCTCTCTCATACCCCTCCG 59.578 57.143 0.00 0.00 0.00 4.63
1180 2892 1.144093 CTCTCTCTCATACCCCTCCGT 59.856 57.143 0.00 0.00 0.00 4.69
1181 2893 1.143277 TCTCTCTCATACCCCTCCGTC 59.857 57.143 0.00 0.00 0.00 4.79
1182 2894 0.185416 TCTCTCATACCCCTCCGTCC 59.815 60.000 0.00 0.00 0.00 4.79
1184 2896 2.123597 TCATACCCCTCCGTCCGG 60.124 66.667 0.00 0.00 0.00 5.14
1189 2901 0.261402 TACCCCTCCGTCCGGAAATA 59.739 55.000 5.23 0.00 44.66 1.40
1191 2903 1.047034 CCCCTCCGTCCGGAAATACT 61.047 60.000 5.23 0.00 44.66 2.12
1193 2905 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1195 2907 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1196 2908 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1198 2910 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1200 2912 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1202 2914 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1204 2916 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1207 2919 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
1215 2927 9.918630 ACTTGTCATCAAAATGAATAAAAGGAG 57.081 29.630 0.00 0.00 43.42 3.69
1237 3200 9.295825 AGGAGATGTATCTAGAACTATGACAAG 57.704 37.037 0.00 0.00 37.25 3.16
1249 3212 7.950236 AGAACTATGACAAGTATTTTCGAACG 58.050 34.615 0.00 0.00 0.00 3.95
1250 3213 6.642683 ACTATGACAAGTATTTTCGAACGG 57.357 37.500 0.00 0.00 0.00 4.44
1251 3214 6.392354 ACTATGACAAGTATTTTCGAACGGA 58.608 36.000 0.00 0.00 0.00 4.69
1255 3218 4.320870 ACAAGTATTTTCGAACGGATGGT 58.679 39.130 0.00 0.00 0.00 3.55
1275 3238 8.621286 GGATGGTGTATTTCATAACAAAGTAGG 58.379 37.037 0.00 0.00 0.00 3.18
1328 3328 4.067896 ACAGTACCTCAAGCAATGTTCAG 58.932 43.478 0.00 0.00 0.00 3.02
1333 3333 4.718961 ACCTCAAGCAATGTTCAGTAAGT 58.281 39.130 0.00 0.00 0.00 2.24
1522 3540 1.149101 GGGGAGGCTATGGAAATGGA 58.851 55.000 0.00 0.00 0.00 3.41
1618 3636 2.089638 TGGTGGGTATGGTGGAGGATAT 60.090 50.000 0.00 0.00 0.00 1.63
1675 3705 1.339727 GGTTATGGACCCGGATATGGC 60.340 57.143 0.73 0.00 43.06 4.40
1688 3718 0.109723 ATATGGCGGCGGTTATGGTT 59.890 50.000 9.78 0.00 0.00 3.67
1717 3747 3.068064 GGTGGTGGATTTGGCGGG 61.068 66.667 0.00 0.00 0.00 6.13
1722 3752 4.440829 TGGATTTGGCGGGGGCTC 62.441 66.667 0.00 0.00 0.00 4.70
1724 3757 2.752807 GGATTTGGCGGGGGCTCTA 61.753 63.158 0.00 0.00 0.00 2.43
1765 3798 0.974010 GTGGATACGGTGGAGGTGGA 60.974 60.000 0.00 0.00 42.51 4.02
1766 3799 0.686441 TGGATACGGTGGAGGTGGAG 60.686 60.000 0.00 0.00 42.51 3.86
1767 3800 1.400530 GGATACGGTGGAGGTGGAGG 61.401 65.000 0.00 0.00 0.00 4.30
1768 3801 0.396695 GATACGGTGGAGGTGGAGGA 60.397 60.000 0.00 0.00 0.00 3.71
1769 3802 0.264955 ATACGGTGGAGGTGGAGGAT 59.735 55.000 0.00 0.00 0.00 3.24
1770 3803 0.928505 TACGGTGGAGGTGGAGGATA 59.071 55.000 0.00 0.00 0.00 2.59
1771 3804 0.686769 ACGGTGGAGGTGGAGGATAC 60.687 60.000 0.00 0.00 0.00 2.24
1772 3805 1.735376 CGGTGGAGGTGGAGGATACG 61.735 65.000 0.00 0.00 46.39 3.06
1773 3806 1.400530 GGTGGAGGTGGAGGATACGG 61.401 65.000 0.00 0.00 46.39 4.02
1774 3807 0.686769 GTGGAGGTGGAGGATACGGT 60.687 60.000 0.00 0.00 46.39 4.83
1775 3808 0.686441 TGGAGGTGGAGGATACGGTG 60.686 60.000 0.00 0.00 46.39 4.94
1776 3809 1.400530 GGAGGTGGAGGATACGGTGG 61.401 65.000 0.00 0.00 46.39 4.61
1777 3810 0.686769 GAGGTGGAGGATACGGTGGT 60.687 60.000 0.00 0.00 46.39 4.16
1778 3811 0.976073 AGGTGGAGGATACGGTGGTG 60.976 60.000 0.00 0.00 46.39 4.17
1779 3812 1.520666 GTGGAGGATACGGTGGTGG 59.479 63.158 0.00 0.00 46.39 4.61
1780 3813 2.363975 TGGAGGATACGGTGGTGGC 61.364 63.158 0.00 0.00 46.39 5.01
1781 3814 2.106332 GAGGATACGGTGGTGGCG 59.894 66.667 0.00 0.00 46.39 5.69
1782 3815 3.441011 GAGGATACGGTGGTGGCGG 62.441 68.421 0.00 0.00 46.39 6.13
1813 3846 0.398318 GAGGTGGAGGATATGGTGGC 59.602 60.000 0.00 0.00 0.00 5.01
1855 3888 1.745890 CGGTTATGGCGGAGGATCA 59.254 57.895 0.00 0.00 36.25 2.92
1911 3944 3.376546 GGAAGAGGTCACAATGAATGAGC 59.623 47.826 0.00 0.00 43.42 4.26
2026 4063 0.807496 AGAAATCGAGCAAGCAAGCC 59.193 50.000 0.00 0.00 34.23 4.35
2144 4184 8.147058 AGATTAAGAGACTAATATGTGCACCAG 58.853 37.037 15.69 6.20 0.00 4.00
2145 4185 5.683876 AAGAGACTAATATGTGCACCAGT 57.316 39.130 15.69 9.42 0.00 4.00
2275 4315 4.104086 TGTGGTCCCAGAGTCAATATTCT 58.896 43.478 0.00 0.00 0.00 2.40
2369 4412 0.889638 AACTGTCTCGGTCTCTGCGA 60.890 55.000 0.00 0.00 0.00 5.10
2382 4425 3.799420 GTCTCTGCGAAGTTCCATATCAC 59.201 47.826 0.00 0.00 0.00 3.06
2407 4451 4.386711 CTCTCGGTAAACCAAACCTTTCT 58.613 43.478 0.00 0.00 34.66 2.52
2463 4507 6.460261 CGATAGAGGCTTCAGTTCACTGATAA 60.460 42.308 10.46 0.00 46.13 1.75
2500 4544 2.034939 TCAGCAATGGCAAAACACTCAG 59.965 45.455 0.00 0.00 44.61 3.35
2587 4632 3.521524 GTCTGTGGTTGACGACATTTC 57.478 47.619 0.00 0.00 34.18 2.17
2622 4667 9.740239 CATGTACCATTATTTTGATCCAAAGAG 57.260 33.333 0.00 0.00 34.72 2.85
2624 4669 9.967451 TGTACCATTATTTTGATCCAAAGAGTA 57.033 29.630 0.00 0.00 34.72 2.59
2656 4701 4.401022 ACACATTGAAATGGAAGCTCTCA 58.599 39.130 7.87 0.00 40.70 3.27
2679 4724 2.301870 ACCTATTCGTTTCTGCACTCCA 59.698 45.455 0.00 0.00 0.00 3.86
2680 4725 3.055094 ACCTATTCGTTTCTGCACTCCAT 60.055 43.478 0.00 0.00 0.00 3.41
2755 4835 9.218440 ACTCGGCAAATATTTTCAAAATTCATT 57.782 25.926 0.00 0.00 0.00 2.57
2830 4910 3.955524 TTAAAGGTGTTCCCAGGTTCA 57.044 42.857 0.00 0.00 34.66 3.18
2835 4915 1.073923 GGTGTTCCCAGGTTCAGACAT 59.926 52.381 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.165437 TGTTTGCTGAGTGTTTTGTCCC 59.835 45.455 0.00 0.00 0.00 4.46
1 2 3.438360 CTGTTTGCTGAGTGTTTTGTCC 58.562 45.455 0.00 0.00 0.00 4.02
2 3 3.128589 TCCTGTTTGCTGAGTGTTTTGTC 59.871 43.478 0.00 0.00 0.00 3.18
3 4 3.088532 TCCTGTTTGCTGAGTGTTTTGT 58.911 40.909 0.00 0.00 0.00 2.83
4 5 3.699067 CTCCTGTTTGCTGAGTGTTTTG 58.301 45.455 0.00 0.00 0.00 2.44
5 6 2.099756 GCTCCTGTTTGCTGAGTGTTTT 59.900 45.455 0.00 0.00 0.00 2.43
6 7 1.678101 GCTCCTGTTTGCTGAGTGTTT 59.322 47.619 0.00 0.00 0.00 2.83
7 8 1.312815 GCTCCTGTTTGCTGAGTGTT 58.687 50.000 0.00 0.00 0.00 3.32
8 9 0.536006 GGCTCCTGTTTGCTGAGTGT 60.536 55.000 0.00 0.00 0.00 3.55
9 10 0.535780 TGGCTCCTGTTTGCTGAGTG 60.536 55.000 0.00 0.00 0.00 3.51
10 11 0.536006 GTGGCTCCTGTTTGCTGAGT 60.536 55.000 0.00 0.00 0.00 3.41
11 12 1.572085 CGTGGCTCCTGTTTGCTGAG 61.572 60.000 0.00 0.00 0.00 3.35
12 13 1.597854 CGTGGCTCCTGTTTGCTGA 60.598 57.895 0.00 0.00 0.00 4.26
13 14 1.893808 ACGTGGCTCCTGTTTGCTG 60.894 57.895 0.00 0.00 0.00 4.41
14 15 1.893808 CACGTGGCTCCTGTTTGCT 60.894 57.895 7.95 0.00 0.00 3.91
15 16 2.639286 CACGTGGCTCCTGTTTGC 59.361 61.111 7.95 0.00 0.00 3.68
16 17 3.343972 CCACGTGGCTCCTGTTTG 58.656 61.111 24.02 0.00 0.00 2.93
26 27 3.041940 GAAGGTCGTGCCACGTGG 61.042 66.667 30.66 30.66 43.14 4.94
27 28 3.041940 GGAAGGTCGTGCCACGTG 61.042 66.667 17.83 9.08 43.14 4.49
28 29 4.657824 CGGAAGGTCGTGCCACGT 62.658 66.667 17.83 0.00 43.14 4.49
29 30 4.657824 ACGGAAGGTCGTGCCACG 62.658 66.667 11.80 11.80 42.21 4.94
35 36 1.068585 GTCAACCACGGAAGGTCGT 59.931 57.895 0.00 0.00 42.25 4.34
36 37 2.019951 CGTCAACCACGGAAGGTCG 61.020 63.158 0.00 0.00 45.46 4.79
37 38 3.946907 CGTCAACCACGGAAGGTC 58.053 61.111 0.00 0.00 45.46 3.85
45 46 2.953466 TATACAGAGCCGTCAACCAC 57.047 50.000 0.00 0.00 0.00 4.16
46 47 4.212716 AGTATATACAGAGCCGTCAACCA 58.787 43.478 15.18 0.00 0.00 3.67
47 48 4.321082 GGAGTATATACAGAGCCGTCAACC 60.321 50.000 15.18 0.00 0.00 3.77
48 49 4.321082 GGGAGTATATACAGAGCCGTCAAC 60.321 50.000 15.18 0.00 0.00 3.18
49 50 3.825014 GGGAGTATATACAGAGCCGTCAA 59.175 47.826 15.18 0.00 0.00 3.18
50 51 3.418995 GGGAGTATATACAGAGCCGTCA 58.581 50.000 15.18 0.00 0.00 4.35
51 52 2.754002 GGGGAGTATATACAGAGCCGTC 59.246 54.545 15.18 2.07 0.00 4.79
52 53 2.805194 GGGGAGTATATACAGAGCCGT 58.195 52.381 15.18 0.00 0.00 5.68
53 54 1.743958 CGGGGAGTATATACAGAGCCG 59.256 57.143 15.18 0.00 0.00 5.52
54 55 2.805194 ACGGGGAGTATATACAGAGCC 58.195 52.381 15.18 9.83 0.00 4.70
55 56 4.280174 TGAAACGGGGAGTATATACAGAGC 59.720 45.833 15.18 1.81 0.00 4.09
56 57 6.401047 TTGAAACGGGGAGTATATACAGAG 57.599 41.667 15.18 4.42 0.00 3.35
57 58 6.795144 TTTGAAACGGGGAGTATATACAGA 57.205 37.500 15.18 0.00 0.00 3.41
58 59 9.550406 TTATTTTGAAACGGGGAGTATATACAG 57.450 33.333 15.18 3.79 0.00 2.74
59 60 9.550406 CTTATTTTGAAACGGGGAGTATATACA 57.450 33.333 15.18 0.00 0.00 2.29
60 61 9.551734 ACTTATTTTGAAACGGGGAGTATATAC 57.448 33.333 4.60 4.60 0.00 1.47
62 63 9.117183 GAACTTATTTTGAAACGGGGAGTATAT 57.883 33.333 0.00 0.00 0.00 0.86
63 64 7.553760 GGAACTTATTTTGAAACGGGGAGTATA 59.446 37.037 0.00 0.00 0.00 1.47
64 65 6.376299 GGAACTTATTTTGAAACGGGGAGTAT 59.624 38.462 0.00 0.00 0.00 2.12
65 66 5.706833 GGAACTTATTTTGAAACGGGGAGTA 59.293 40.000 0.00 0.00 0.00 2.59
66 67 4.521639 GGAACTTATTTTGAAACGGGGAGT 59.478 41.667 0.00 0.00 0.00 3.85
67 68 4.521256 TGGAACTTATTTTGAAACGGGGAG 59.479 41.667 0.00 0.00 0.00 4.30
68 69 4.471548 TGGAACTTATTTTGAAACGGGGA 58.528 39.130 0.00 0.00 0.00 4.81
69 70 4.857509 TGGAACTTATTTTGAAACGGGG 57.142 40.909 0.00 0.00 0.00 5.73
70 71 5.047660 TCCATGGAACTTATTTTGAAACGGG 60.048 40.000 13.46 0.00 0.00 5.28
71 72 6.019779 TCCATGGAACTTATTTTGAAACGG 57.980 37.500 13.46 0.00 0.00 4.44
72 73 6.092748 CCTCCATGGAACTTATTTTGAAACG 58.907 40.000 17.00 0.00 38.35 3.60
73 74 6.210584 TCCCTCCATGGAACTTATTTTGAAAC 59.789 38.462 17.00 0.00 38.35 2.78
74 75 6.318913 TCCCTCCATGGAACTTATTTTGAAA 58.681 36.000 17.00 0.00 38.35 2.69
75 76 5.898120 TCCCTCCATGGAACTTATTTTGAA 58.102 37.500 17.00 0.00 38.35 2.69
76 77 5.015178 ACTCCCTCCATGGAACTTATTTTGA 59.985 40.000 17.00 1.46 38.35 2.69
77 78 5.264395 ACTCCCTCCATGGAACTTATTTTG 58.736 41.667 17.00 0.03 38.35 2.44
78 79 5.536497 ACTCCCTCCATGGAACTTATTTT 57.464 39.130 17.00 0.00 38.35 1.82
79 80 6.848562 ATACTCCCTCCATGGAACTTATTT 57.151 37.500 17.00 0.00 38.35 1.40
80 81 9.805204 ATATATACTCCCTCCATGGAACTTATT 57.195 33.333 17.00 1.38 38.35 1.40
84 85 9.884814 GTATATATATACTCCCTCCATGGAACT 57.115 37.037 21.00 0.00 36.49 3.01
85 86 9.656323 TGTATATATATACTCCCTCCATGGAAC 57.344 37.037 25.95 5.54 39.36 3.62
86 87 9.656323 GTGTATATATATACTCCCTCCATGGAA 57.344 37.037 25.95 0.00 39.36 3.53
87 88 8.797674 TGTGTATATATATACTCCCTCCATGGA 58.202 37.037 25.95 15.27 39.36 3.41
88 89 9.434275 TTGTGTATATATATACTCCCTCCATGG 57.566 37.037 25.95 4.97 39.36 3.66
91 92 9.831682 TGTTTGTGTATATATATACTCCCTCCA 57.168 33.333 25.95 15.81 39.36 3.86
101 102 9.764363 CCTGCCGATATGTTTGTGTATATATAT 57.236 33.333 0.00 0.00 0.00 0.86
102 103 7.709182 GCCTGCCGATATGTTTGTGTATATATA 59.291 37.037 0.00 0.00 0.00 0.86
103 104 6.538742 GCCTGCCGATATGTTTGTGTATATAT 59.461 38.462 0.00 0.00 0.00 0.86
104 105 5.872617 GCCTGCCGATATGTTTGTGTATATA 59.127 40.000 0.00 0.00 0.00 0.86
105 106 4.695455 GCCTGCCGATATGTTTGTGTATAT 59.305 41.667 0.00 0.00 0.00 0.86
106 107 4.062293 GCCTGCCGATATGTTTGTGTATA 58.938 43.478 0.00 0.00 0.00 1.47
114 115 1.597742 GTGATGCCTGCCGATATGTT 58.402 50.000 0.00 0.00 0.00 2.71
115 116 0.250467 GGTGATGCCTGCCGATATGT 60.250 55.000 0.00 0.00 0.00 2.29
131 132 5.418676 TGGACATATGCGATGTATATGGTG 58.581 41.667 15.92 0.00 40.93 4.17
139 142 3.748048 GCTTGTATGGACATATGCGATGT 59.252 43.478 1.58 3.84 34.86 3.06
150 153 7.320443 TGACAAATTGATAGCTTGTATGGAC 57.680 36.000 0.00 0.00 33.53 4.02
176 179 3.499157 TGGACAAGTAATTGTTGCGGTAC 59.501 43.478 10.27 0.00 34.90 3.34
195 198 7.773489 TTTTCTGTGATTTGTTGGATATGGA 57.227 32.000 0.00 0.00 0.00 3.41
209 212 7.818930 TGCTTTTTGAACTTCTTTTTCTGTGAT 59.181 29.630 0.00 0.00 0.00 3.06
221 224 7.706607 AGGAACTTTGTATGCTTTTTGAACTTC 59.293 33.333 0.00 0.00 27.25 3.01
262 265 1.452025 CGCGCCTTAATGAGACATACG 59.548 52.381 0.00 0.00 0.00 3.06
282 1367 7.141363 GGAAACATCACCTTGCACATAATATC 58.859 38.462 0.00 0.00 0.00 1.63
288 1373 1.541147 CGGAAACATCACCTTGCACAT 59.459 47.619 0.00 0.00 0.00 3.21
301 1386 1.246649 TACCTCGCTGTACGGAAACA 58.753 50.000 5.68 0.00 43.89 2.83
311 1396 4.046938 AGTCACAACATATACCTCGCTG 57.953 45.455 0.00 0.00 0.00 5.18
347 2019 6.455360 TGATTATTGAAGACCAGAATTGCC 57.545 37.500 0.00 0.00 0.00 4.52
352 2024 6.403527 CGCACAATGATTATTGAAGACCAGAA 60.404 38.462 16.43 0.00 45.21 3.02
384 2056 6.915843 CAGAGTATAACATGTATACGTGCACA 59.084 38.462 22.36 9.95 35.99 4.57
385 2057 6.916387 ACAGAGTATAACATGTATACGTGCAC 59.084 38.462 22.36 6.82 35.99 4.57
386 2058 7.034685 ACAGAGTATAACATGTATACGTGCA 57.965 36.000 22.36 12.52 35.99 4.57
395 2067 9.809096 CTTCAACATCTACAGAGTATAACATGT 57.191 33.333 0.00 0.00 0.00 3.21
396 2068 9.809096 ACTTCAACATCTACAGAGTATAACATG 57.191 33.333 0.00 0.00 0.00 3.21
437 2109 1.730501 GCTGAAGCTGCACATGTAGA 58.269 50.000 0.00 0.00 38.21 2.59
442 2114 3.796443 CGCGCTGAAGCTGCACAT 61.796 61.111 5.56 0.00 39.33 3.21
448 2120 1.663702 AAACGTACGCGCTGAAGCT 60.664 52.632 16.72 0.00 42.83 3.74
449 2121 1.507096 CAAACGTACGCGCTGAAGC 60.507 57.895 16.72 0.00 42.83 3.86
453 2125 0.780002 ACTTACAAACGTACGCGCTG 59.220 50.000 16.72 12.42 42.83 5.18
456 2128 6.722972 AATATCTACTTACAAACGTACGCG 57.277 37.500 16.72 3.53 44.93 6.01
553 2226 6.574832 CGTGCATCCTTGAATTAATTATCGTG 59.425 38.462 0.00 0.00 0.00 4.35
554 2227 6.293407 CCGTGCATCCTTGAATTAATTATCGT 60.293 38.462 0.00 0.00 0.00 3.73
596 2269 5.575606 CGTCGTGGTTTTATGAACTGAGTAT 59.424 40.000 0.00 0.00 0.00 2.12
597 2270 4.919168 CGTCGTGGTTTTATGAACTGAGTA 59.081 41.667 0.00 0.00 0.00 2.59
598 2271 3.739300 CGTCGTGGTTTTATGAACTGAGT 59.261 43.478 0.00 0.00 0.00 3.41
599 2272 3.985279 TCGTCGTGGTTTTATGAACTGAG 59.015 43.478 0.00 0.00 0.00 3.35
600 2273 3.979948 TCGTCGTGGTTTTATGAACTGA 58.020 40.909 0.00 0.00 0.00 3.41
601 2274 3.739300 ACTCGTCGTGGTTTTATGAACTG 59.261 43.478 0.00 0.00 0.00 3.16
602 2275 3.986277 ACTCGTCGTGGTTTTATGAACT 58.014 40.909 0.00 0.00 0.00 3.01
603 2276 5.827568 TTACTCGTCGTGGTTTTATGAAC 57.172 39.130 0.00 0.00 0.00 3.18
604 2277 7.292292 CAAATTACTCGTCGTGGTTTTATGAA 58.708 34.615 0.00 0.00 0.00 2.57
605 2278 6.128499 CCAAATTACTCGTCGTGGTTTTATGA 60.128 38.462 0.00 0.00 0.00 2.15
606 2279 6.019152 CCAAATTACTCGTCGTGGTTTTATG 58.981 40.000 0.00 0.00 0.00 1.90
607 2280 5.933463 TCCAAATTACTCGTCGTGGTTTTAT 59.067 36.000 0.00 0.00 0.00 1.40
608 2281 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
609 2282 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
610 2283 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
611 2284 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
612 2285 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
613 2286 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
614 2287 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
615 2288 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
616 2289 2.598589 TCCGTTCCAAATTACTCGTCG 58.401 47.619 0.00 0.00 0.00 5.12
617 2290 3.370061 CCTTCCGTTCCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
618 2291 3.007182 TCCTTCCGTTCCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
619 2292 3.592059 TCCTTCCGTTCCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
620 2293 4.576879 ACTCCTTCCGTTCCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
621 2294 4.635699 ACTCCTTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
622 2295 6.997239 AATACTCCTTCCGTTCCAAATTAC 57.003 37.500 0.00 0.00 0.00 1.89
623 2296 7.449086 ACAAAATACTCCTTCCGTTCCAAATTA 59.551 33.333 0.00 0.00 0.00 1.40
624 2297 6.266786 ACAAAATACTCCTTCCGTTCCAAATT 59.733 34.615 0.00 0.00 0.00 1.82
625 2298 5.773176 ACAAAATACTCCTTCCGTTCCAAAT 59.227 36.000 0.00 0.00 0.00 2.32
626 2299 5.134661 ACAAAATACTCCTTCCGTTCCAAA 58.865 37.500 0.00 0.00 0.00 3.28
627 2300 4.721132 ACAAAATACTCCTTCCGTTCCAA 58.279 39.130 0.00 0.00 0.00 3.53
628 2301 4.360951 ACAAAATACTCCTTCCGTTCCA 57.639 40.909 0.00 0.00 0.00 3.53
629 2302 5.163784 GCTAACAAAATACTCCTTCCGTTCC 60.164 44.000 0.00 0.00 0.00 3.62
630 2303 5.642491 AGCTAACAAAATACTCCTTCCGTTC 59.358 40.000 0.00 0.00 0.00 3.95
631 2304 5.411669 CAGCTAACAAAATACTCCTTCCGTT 59.588 40.000 0.00 0.00 0.00 4.44
632 2305 4.935808 CAGCTAACAAAATACTCCTTCCGT 59.064 41.667 0.00 0.00 0.00 4.69
633 2306 5.175859 TCAGCTAACAAAATACTCCTTCCG 58.824 41.667 0.00 0.00 0.00 4.30
634 2307 7.051000 AGATCAGCTAACAAAATACTCCTTCC 58.949 38.462 0.00 0.00 0.00 3.46
635 2308 8.394121 CAAGATCAGCTAACAAAATACTCCTTC 58.606 37.037 0.00 0.00 0.00 3.46
636 2309 7.337942 CCAAGATCAGCTAACAAAATACTCCTT 59.662 37.037 0.00 0.00 0.00 3.36
637 2310 6.825721 CCAAGATCAGCTAACAAAATACTCCT 59.174 38.462 0.00 0.00 0.00 3.69
638 2311 6.599638 ACCAAGATCAGCTAACAAAATACTCC 59.400 38.462 0.00 0.00 0.00 3.85
639 2312 7.617041 ACCAAGATCAGCTAACAAAATACTC 57.383 36.000 0.00 0.00 0.00 2.59
640 2313 7.575720 GCAACCAAGATCAGCTAACAAAATACT 60.576 37.037 0.00 0.00 0.00 2.12
641 2314 6.528072 GCAACCAAGATCAGCTAACAAAATAC 59.472 38.462 0.00 0.00 0.00 1.89
642 2315 6.350110 GGCAACCAAGATCAGCTAACAAAATA 60.350 38.462 0.00 0.00 0.00 1.40
643 2316 5.473039 GCAACCAAGATCAGCTAACAAAAT 58.527 37.500 0.00 0.00 0.00 1.82
644 2317 4.261994 GGCAACCAAGATCAGCTAACAAAA 60.262 41.667 0.00 0.00 0.00 2.44
683 2356 4.261072 GCCTTGAGTACGTATGATCGAGAA 60.261 45.833 17.66 2.43 34.70 2.87
736 2409 1.078143 GCTACTGCCACCCAGAAGG 60.078 63.158 0.00 0.00 44.64 3.46
737 2410 1.195115 TAGCTACTGCCACCCAGAAG 58.805 55.000 0.00 0.00 44.64 2.85
738 2411 1.651737 TTAGCTACTGCCACCCAGAA 58.348 50.000 0.00 0.00 44.64 3.02
741 2414 1.578897 TGATTAGCTACTGCCACCCA 58.421 50.000 0.00 0.00 40.80 4.51
744 2417 3.868077 CAGACTTGATTAGCTACTGCCAC 59.132 47.826 0.00 0.00 40.80 5.01
745 2418 3.769300 TCAGACTTGATTAGCTACTGCCA 59.231 43.478 0.00 0.00 40.80 4.92
746 2419 4.116238 GTCAGACTTGATTAGCTACTGCC 58.884 47.826 0.00 0.00 36.28 4.85
747 2420 4.748892 TGTCAGACTTGATTAGCTACTGC 58.251 43.478 1.31 0.00 35.39 4.40
748 2421 5.287274 CGTTGTCAGACTTGATTAGCTACTG 59.713 44.000 1.31 0.00 35.39 2.74
749 2422 5.183331 TCGTTGTCAGACTTGATTAGCTACT 59.817 40.000 1.31 0.00 35.39 2.57
834 2511 7.454260 AGTTTCAACCTTCAATAACTCCATC 57.546 36.000 0.00 0.00 0.00 3.51
891 2568 1.298157 GGCTTGCATGCACGTCTACA 61.298 55.000 22.58 2.30 34.04 2.74
892 2569 1.021390 AGGCTTGCATGCACGTCTAC 61.021 55.000 27.73 14.09 28.21 2.59
907 2584 5.278858 CCGTATTTATAGACGAGGAAAGGCT 60.279 44.000 1.78 0.00 41.30 4.58
913 2594 5.717078 ATTGCCGTATTTATAGACGAGGA 57.283 39.130 1.78 0.00 41.30 3.71
1155 2867 3.650942 GAGGGGTATGAGAGAGAGAGAGA 59.349 52.174 0.00 0.00 0.00 3.10
1156 2868 3.244911 GGAGGGGTATGAGAGAGAGAGAG 60.245 56.522 0.00 0.00 0.00 3.20
1158 2870 2.552155 CGGAGGGGTATGAGAGAGAGAG 60.552 59.091 0.00 0.00 0.00 3.20
1159 2871 1.422024 CGGAGGGGTATGAGAGAGAGA 59.578 57.143 0.00 0.00 0.00 3.10
1160 2872 1.144093 ACGGAGGGGTATGAGAGAGAG 59.856 57.143 0.00 0.00 0.00 3.20
1161 2873 1.143277 GACGGAGGGGTATGAGAGAGA 59.857 57.143 0.00 0.00 0.00 3.10
1162 2874 1.611519 GACGGAGGGGTATGAGAGAG 58.388 60.000 0.00 0.00 0.00 3.20
1163 2875 0.185416 GGACGGAGGGGTATGAGAGA 59.815 60.000 0.00 0.00 0.00 3.10
1167 2879 2.123597 CCGGACGGAGGGGTATGA 60.124 66.667 4.40 0.00 37.50 2.15
1168 2880 1.332144 TTTCCGGACGGAGGGGTATG 61.332 60.000 13.64 0.00 46.06 2.39
1170 2882 0.261402 TATTTCCGGACGGAGGGGTA 59.739 55.000 13.64 3.49 46.06 3.69
1171 2883 1.002017 TATTTCCGGACGGAGGGGT 59.998 57.895 13.64 4.38 46.06 4.95
1172 2884 1.047034 AGTATTTCCGGACGGAGGGG 61.047 60.000 13.64 0.00 46.06 4.79
1174 2886 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1175 2887 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1176 2888 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1177 2889 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1178 2890 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1179 2891 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1180 2892 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
1181 2893 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
1182 2894 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
1189 2901 9.918630 CTCCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
1211 2923 9.295825 CTTGTCATAGTTCTAGATACATCTCCT 57.704 37.037 0.00 0.00 38.32 3.69
1212 2924 9.073475 ACTTGTCATAGTTCTAGATACATCTCC 57.927 37.037 0.00 0.00 38.32 3.71
1224 3187 7.063074 CCGTTCGAAAATACTTGTCATAGTTCT 59.937 37.037 0.00 0.00 0.00 3.01
1228 3191 6.880822 TCCGTTCGAAAATACTTGTCATAG 57.119 37.500 0.00 0.00 0.00 2.23
1230 3193 5.064707 CCATCCGTTCGAAAATACTTGTCAT 59.935 40.000 0.00 0.00 0.00 3.06
1234 3197 4.153475 ACACCATCCGTTCGAAAATACTTG 59.847 41.667 0.00 0.00 0.00 3.16
1237 3200 5.978934 ATACACCATCCGTTCGAAAATAC 57.021 39.130 0.00 0.00 0.00 1.89
1239 3202 5.413213 TGAAATACACCATCCGTTCGAAAAT 59.587 36.000 0.00 0.00 0.00 1.82
1245 3208 6.671614 TGTTATGAAATACACCATCCGTTC 57.328 37.500 0.00 0.00 0.00 3.95
1248 3211 7.083875 ACTTTGTTATGAAATACACCATCCG 57.916 36.000 0.00 0.00 0.00 4.18
1249 3212 8.621286 CCTACTTTGTTATGAAATACACCATCC 58.379 37.037 0.00 0.00 0.00 3.51
1250 3213 8.129211 GCCTACTTTGTTATGAAATACACCATC 58.871 37.037 0.00 0.00 0.00 3.51
1251 3214 7.613801 TGCCTACTTTGTTATGAAATACACCAT 59.386 33.333 0.00 0.00 0.00 3.55
1255 3218 7.987750 TGTGCCTACTTTGTTATGAAATACA 57.012 32.000 0.00 0.00 0.00 2.29
1275 3238 5.048083 TCCATGGAAGTGACTTAATTTGTGC 60.048 40.000 13.46 0.00 0.00 4.57
1328 3328 7.169982 GGACTCTGCATACATACAATCACTTAC 59.830 40.741 0.00 0.00 0.00 2.34
1333 3333 5.612725 TGGACTCTGCATACATACAATCA 57.387 39.130 0.00 0.00 0.00 2.57
1391 3391 1.982226 TCCCCATTTCTCGTCCTTCAA 59.018 47.619 0.00 0.00 0.00 2.69
1522 3540 1.271707 CCACCATTGTTTCCGTACCCT 60.272 52.381 0.00 0.00 0.00 4.34
1618 3636 2.949963 GCCACCATGCCTAGAATTTCCA 60.950 50.000 0.00 0.00 0.00 3.53
1675 3705 1.508632 CTGGATAACCATAACCGCCG 58.491 55.000 0.00 0.00 45.87 6.46
1688 3718 1.298340 CACCACCGTTGCCTGGATA 59.702 57.895 0.00 0.00 0.00 2.59
1717 3747 1.249407 CGTATCCTCCACTAGAGCCC 58.751 60.000 0.00 0.00 41.74 5.19
1722 3752 1.681793 CACCACCGTATCCTCCACTAG 59.318 57.143 0.00 0.00 0.00 2.57
1724 3757 0.976073 CCACCACCGTATCCTCCACT 60.976 60.000 0.00 0.00 0.00 4.00
1765 3798 3.467226 CCGCCACCACCGTATCCT 61.467 66.667 0.00 0.00 0.00 3.24
1779 3812 4.944372 CTCCACCGTATCCGCCGC 62.944 72.222 0.00 0.00 0.00 6.53
1780 3813 4.280494 CCTCCACCGTATCCGCCG 62.280 72.222 0.00 0.00 0.00 6.46
1781 3814 3.152400 ACCTCCACCGTATCCGCC 61.152 66.667 0.00 0.00 0.00 6.13
1782 3815 2.106332 CACCTCCACCGTATCCGC 59.894 66.667 0.00 0.00 0.00 5.54
1783 3816 1.735376 CTCCACCTCCACCGTATCCG 61.735 65.000 0.00 0.00 0.00 4.18
1784 3817 1.400530 CCTCCACCTCCACCGTATCC 61.401 65.000 0.00 0.00 0.00 2.59
1785 3818 0.396695 TCCTCCACCTCCACCGTATC 60.397 60.000 0.00 0.00 0.00 2.24
1786 3819 0.264955 ATCCTCCACCTCCACCGTAT 59.735 55.000 0.00 0.00 0.00 3.06
1787 3820 0.928505 TATCCTCCACCTCCACCGTA 59.071 55.000 0.00 0.00 0.00 4.02
1788 3821 0.264955 ATATCCTCCACCTCCACCGT 59.735 55.000 0.00 0.00 0.00 4.83
1789 3822 0.681733 CATATCCTCCACCTCCACCG 59.318 60.000 0.00 0.00 0.00 4.94
1790 3823 1.059913 CCATATCCTCCACCTCCACC 58.940 60.000 0.00 0.00 0.00 4.61
1791 3824 1.417890 CACCATATCCTCCACCTCCAC 59.582 57.143 0.00 0.00 0.00 4.02
1792 3825 1.695664 CCACCATATCCTCCACCTCCA 60.696 57.143 0.00 0.00 0.00 3.86
1793 3826 1.059913 CCACCATATCCTCCACCTCC 58.940 60.000 0.00 0.00 0.00 4.30
1794 3827 0.398318 GCCACCATATCCTCCACCTC 59.602 60.000 0.00 0.00 0.00 3.85
1795 3828 1.410850 CGCCACCATATCCTCCACCT 61.411 60.000 0.00 0.00 0.00 4.00
1796 3829 1.071471 CGCCACCATATCCTCCACC 59.929 63.158 0.00 0.00 0.00 4.61
1797 3830 1.071471 CCGCCACCATATCCTCCAC 59.929 63.158 0.00 0.00 0.00 4.02
1798 3831 1.383943 ACCGCCACCATATCCTCCA 60.384 57.895 0.00 0.00 0.00 3.86
1799 3832 1.071471 CACCGCCACCATATCCTCC 59.929 63.158 0.00 0.00 0.00 4.30
1800 3833 1.071471 CCACCGCCACCATATCCTC 59.929 63.158 0.00 0.00 0.00 3.71
1813 3846 4.849310 CCACCATACCCGCCACCG 62.849 72.222 0.00 0.00 0.00 4.94
1855 3888 3.480133 GGATAGCCGGCACCACCT 61.480 66.667 31.54 9.39 35.61 4.00
1950 3984 9.146984 CAAATCTTTTATTCAAGCACATCACAT 57.853 29.630 0.00 0.00 0.00 3.21
2034 4071 7.353414 TCTCTTTCATACATAGGAGACAAGG 57.647 40.000 0.00 0.00 0.00 3.61
2064 4101 7.054491 AGCCAAACACTATCAATTCAAAAGT 57.946 32.000 0.00 0.00 0.00 2.66
2144 4184 8.554528 GTTTTAGGACTAAACCAAGACTACAAC 58.445 37.037 4.11 0.00 35.05 3.32
2145 4185 8.488668 AGTTTTAGGACTAAACCAAGACTACAA 58.511 33.333 4.11 0.00 35.05 2.41
2239 4279 4.016444 GGGACCACATCATGTAAACACAT 58.984 43.478 0.00 0.00 0.00 3.21
2275 4315 6.007076 TGTGCCTAAAATATGGTCAGACAAA 58.993 36.000 2.17 0.00 0.00 2.83
2343 4384 1.072331 AGACCGAGACAGTTGGCAAAT 59.928 47.619 0.00 0.00 31.65 2.32
2369 4412 2.223829 CGAGAGCCGTGATATGGAACTT 60.224 50.000 0.00 0.00 0.00 2.66
2382 4425 0.794473 GTTTGGTTTACCGAGAGCCG 59.206 55.000 0.00 0.00 39.43 5.52
2429 4473 0.470833 AGCCTCTATCGAGTGCCCAT 60.471 55.000 0.00 0.00 35.41 4.00
2463 4507 7.215789 CCATTGCTGAGTATTTCTCTGATAGT 58.784 38.462 6.05 0.00 42.30 2.12
2466 4510 4.820716 GCCATTGCTGAGTATTTCTCTGAT 59.179 41.667 6.05 0.00 42.30 2.90
2472 4516 5.119125 GTGTTTTGCCATTGCTGAGTATTTC 59.881 40.000 0.00 0.00 38.71 2.17
2488 4532 4.036262 TGTGTATTGGTCTGAGTGTTTTGC 59.964 41.667 0.00 0.00 0.00 3.68
2500 4544 2.147958 TCGGCAAAGTGTGTATTGGTC 58.852 47.619 0.00 0.00 0.00 4.02
2622 4667 6.747280 CCATTTCAATGTGTCTTTCCGAATAC 59.253 38.462 0.00 0.00 34.60 1.89
2624 4669 5.476599 TCCATTTCAATGTGTCTTTCCGAAT 59.523 36.000 0.00 0.00 34.60 3.34
2656 4701 3.751698 GGAGTGCAGAAACGAATAGGTTT 59.248 43.478 0.00 0.00 42.50 3.27
2679 4724 5.162637 TGCCCCTAAACACTCCATCTATAT 58.837 41.667 0.00 0.00 0.00 0.86
2680 4725 4.562767 TGCCCCTAAACACTCCATCTATA 58.437 43.478 0.00 0.00 0.00 1.31
2696 4741 0.899720 CATTCTGCAAACATGCCCCT 59.100 50.000 0.00 0.00 0.00 4.79
2764 4844 4.457949 AGAACTGGTCAAACGTTTTCTGTT 59.542 37.500 11.66 17.54 0.00 3.16
2781 4861 3.750130 CCATGTTCCTTGTGAGAGAACTG 59.250 47.826 0.00 0.00 40.42 3.16
2830 4910 0.108585 ACAAAGCGGGTCACATGTCT 59.891 50.000 0.00 0.00 0.00 3.41
2835 4915 0.250124 ATTCGACAAAGCGGGTCACA 60.250 50.000 6.33 0.00 34.97 3.58


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

AutoCloner maintained by Alex Coulton.