Multiple sequence alignment - TraesCS5D01G086300

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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 TraesCS5D01G086300 chr5D 100.000 2735 0 0 1 2735 91616084 91618818 0.000000e+00 5051.0
1 TraesCS5D01G086300 chr5D 89.354 1146 95 11 587 1712 91865993 91867131 0.000000e+00 1415.0
2 TraesCS5D01G086300 chr5D 87.636 461 43 4 893 1339 91637287 91637747 8.680000e-145 523.0
3 TraesCS5D01G086300 chr5D 89.607 356 27 7 516 865 91634117 91634468 6.950000e-121 444.0
4 TraesCS5D01G086300 chr5D 85.379 383 45 4 1334 1712 91652017 91652392 1.190000e-103 387.0
5 TraesCS5D01G086300 chr5D 97.222 144 4 0 1789 1932 37872640 37872783 7.570000e-61 244.0
6 TraesCS5D01G086300 chr5D 90.909 99 8 1 77 174 91863581 91863679 6.150000e-27 132.0
7 TraesCS5D01G086300 chr5A 91.542 1407 78 15 330 1712 85266573 85267962 0.000000e+00 1901.0
8 TraesCS5D01G086300 chr5A 89.369 602 51 6 614 1205 85352734 85353332 0.000000e+00 745.0
9 TraesCS5D01G086300 chr5A 98.667 75 1 0 1712 1786 85267992 85268066 1.710000e-27 134.0
10 TraesCS5D01G086300 chr5B 89.722 1187 104 8 539 1712 96906082 96907263 0.000000e+00 1500.0
11 TraesCS5D01G086300 chr5B 89.088 559 43 9 447 1004 96903821 96904362 0.000000e+00 678.0
12 TraesCS5D01G086300 chr5B 91.912 136 10 1 330 464 535331571 535331436 3.600000e-44 189.0
13 TraesCS5D01G086300 chr4D 93.112 842 58 0 1894 2735 493737410 493738251 0.000000e+00 1234.0
14 TraesCS5D01G086300 chr2D 82.785 1185 154 19 558 1715 559229417 559228256 0.000000e+00 1013.0
15 TraesCS5D01G086300 chr2D 91.176 136 12 0 330 465 91799062 91799197 4.650000e-43 185.0
16 TraesCS5D01G086300 chr2A 82.492 971 140 15 763 1715 699818426 699817468 0.000000e+00 824.0
17 TraesCS5D01G086300 chr6D 81.829 842 148 3 1894 2732 456324778 456325617 0.000000e+00 702.0
18 TraesCS5D01G086300 chr1D 98.758 161 2 0 1789 1949 296631587 296631427 1.240000e-73 287.0
19 TraesCS5D01G086300 chr4A 78.674 347 63 6 678 1017 625658057 625657715 1.270000e-53 220.0
20 TraesCS5D01G086300 chr4A 94.958 119 6 0 330 448 166994088 166994206 1.290000e-43 187.0
21 TraesCS5D01G086300 chr4A 94.118 119 7 0 330 448 166997278 166997396 6.020000e-42 182.0
22 TraesCS5D01G086300 chr6A 97.458 118 3 0 330 447 63310587 63310470 4.620000e-48 202.0
23 TraesCS5D01G086300 chr7A 95.935 123 5 0 330 452 8660354 8660476 1.660000e-47 200.0
24 TraesCS5D01G086300 chr4B 97.436 117 3 0 330 446 586244259 586244375 1.660000e-47 200.0
25 TraesCS5D01G086300 chr3A 96.667 120 4 0 330 449 700723426 700723307 1.660000e-47 200.0
26 TraesCS5D01G086300 chr3A 95.902 122 5 0 330 451 515736894 515736773 5.970000e-47 198.0
27 TraesCS5D01G086300 chr2B 100.000 28 0 0 935 962 37742227 37742200 5.000000e-03 52.8


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 TraesCS5D01G086300 chr5D 91616084 91618818 2734 False 5051.0 5051 100.0000 1 2735 1 chr5D.!!$F2 2734
1 TraesCS5D01G086300 chr5D 91863581 91867131 3550 False 773.5 1415 90.1315 77 1712 2 chr5D.!!$F5 1635
2 TraesCS5D01G086300 chr5D 91634117 91637747 3630 False 483.5 523 88.6215 516 1339 2 chr5D.!!$F4 823
3 TraesCS5D01G086300 chr5A 85266573 85268066 1493 False 1017.5 1901 95.1045 330 1786 2 chr5A.!!$F2 1456
4 TraesCS5D01G086300 chr5A 85352734 85353332 598 False 745.0 745 89.3690 614 1205 1 chr5A.!!$F1 591
5 TraesCS5D01G086300 chr5B 96903821 96907263 3442 False 1089.0 1500 89.4050 447 1712 2 chr5B.!!$F1 1265
6 TraesCS5D01G086300 chr4D 493737410 493738251 841 False 1234.0 1234 93.1120 1894 2735 1 chr4D.!!$F1 841
7 TraesCS5D01G086300 chr2D 559228256 559229417 1161 True 1013.0 1013 82.7850 558 1715 1 chr2D.!!$R1 1157
8 TraesCS5D01G086300 chr2A 699817468 699818426 958 True 824.0 824 82.4920 763 1715 1 chr2A.!!$R1 952
9 TraesCS5D01G086300 chr6D 456324778 456325617 839 False 702.0 702 81.8290 1894 2732 1 chr6D.!!$F1 838

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
138 139 0.171455 CACGACTGACCTAGTGCTCC 59.829 60.0 0.0 0.0 40.53 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 8916 0.034089 GCTTAGCCCCAATGACCAGT 60.034 55.0 0.0 0.0 0.0 4.0 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
18 19 4.979657 CTGCATGTGGAGGATGCT 57.020 55.556 0.00 0.00 45.45 3.79
19 20 2.704108 CTGCATGTGGAGGATGCTC 58.296 57.895 5.52 5.52 45.45 4.26
20 21 0.818445 CTGCATGTGGAGGATGCTCC 60.818 60.000 25.49 25.49 45.45 4.70
29 30 4.891037 GGATGCTCCTGCTGCCCC 62.891 72.222 0.00 0.00 40.48 5.80
30 31 4.891037 GATGCTCCTGCTGCCCCC 62.891 72.222 0.00 0.00 40.48 5.40
43 44 4.388499 CCCCCACCGTCGGTCAAG 62.388 72.222 15.67 6.29 31.02 3.02
44 45 3.622826 CCCCACCGTCGGTCAAGT 61.623 66.667 15.67 0.00 31.02 3.16
45 46 2.357034 CCCACCGTCGGTCAAGTG 60.357 66.667 15.67 2.52 31.02 3.16
46 47 2.732016 CCACCGTCGGTCAAGTGA 59.268 61.111 15.67 0.00 31.02 3.41
47 48 1.663702 CCACCGTCGGTCAAGTGAC 60.664 63.158 15.67 2.69 44.04 3.67
48 49 1.066752 CACCGTCGGTCAAGTGACA 59.933 57.895 15.67 0.00 46.47 3.58
49 50 0.528901 CACCGTCGGTCAAGTGACAA 60.529 55.000 15.67 0.00 46.47 3.18
50 51 0.249322 ACCGTCGGTCAAGTGACAAG 60.249 55.000 12.23 6.77 46.47 3.16
51 52 1.557443 CCGTCGGTCAAGTGACAAGC 61.557 60.000 13.21 1.94 46.47 4.01
52 53 1.557443 CGTCGGTCAAGTGACAAGCC 61.557 60.000 13.21 0.00 46.47 4.35
53 54 1.070786 TCGGTCAAGTGACAAGCCC 59.929 57.895 13.21 0.00 46.47 5.19
54 55 1.966451 CGGTCAAGTGACAAGCCCC 60.966 63.158 13.21 0.00 46.47 5.80
55 56 1.150536 GGTCAAGTGACAAGCCCCA 59.849 57.895 13.21 0.00 46.47 4.96
56 57 0.467290 GGTCAAGTGACAAGCCCCAA 60.467 55.000 13.21 0.00 46.47 4.12
57 58 0.668535 GTCAAGTGACAAGCCCCAAC 59.331 55.000 6.57 0.00 44.18 3.77
58 59 0.467290 TCAAGTGACAAGCCCCAACC 60.467 55.000 0.00 0.00 0.00 3.77
59 60 1.528309 AAGTGACAAGCCCCAACCG 60.528 57.895 0.00 0.00 0.00 4.44
60 61 2.976494 AAGTGACAAGCCCCAACCGG 62.976 60.000 0.00 0.00 0.00 5.28
61 62 3.172106 TGACAAGCCCCAACCGGA 61.172 61.111 9.46 0.00 0.00 5.14
62 63 2.355115 GACAAGCCCCAACCGGAT 59.645 61.111 9.46 0.00 0.00 4.18
63 64 2.035626 ACAAGCCCCAACCGGATG 59.964 61.111 9.46 6.59 0.00 3.51
64 65 3.451894 CAAGCCCCAACCGGATGC 61.452 66.667 9.46 2.54 0.00 3.91
65 66 3.978193 AAGCCCCAACCGGATGCA 61.978 61.111 9.46 0.00 33.60 3.96
66 67 4.740822 AGCCCCAACCGGATGCAC 62.741 66.667 9.46 0.00 33.60 4.57
67 68 4.740822 GCCCCAACCGGATGCACT 62.741 66.667 9.46 0.00 32.01 4.40
68 69 2.994699 CCCCAACCGGATGCACTA 59.005 61.111 9.46 0.00 0.00 2.74
69 70 1.153168 CCCCAACCGGATGCACTAG 60.153 63.158 9.46 0.00 0.00 2.57
70 71 1.819632 CCCAACCGGATGCACTAGC 60.820 63.158 9.46 0.00 42.57 3.42
114 115 0.823356 TTGCCTGCTCTGGAACAACC 60.823 55.000 0.00 0.00 38.70 3.77
122 123 0.462937 TCTGGAACAACCACACCACG 60.463 55.000 0.00 0.00 44.64 4.94
123 124 0.462937 CTGGAACAACCACACCACGA 60.463 55.000 0.00 0.00 44.64 4.35
128 129 0.461339 ACAACCACACCACGACTGAC 60.461 55.000 0.00 0.00 0.00 3.51
130 131 1.335132 AACCACACCACGACTGACCT 61.335 55.000 0.00 0.00 0.00 3.85
138 139 0.171455 CACGACTGACCTAGTGCTCC 59.829 60.000 0.00 0.00 40.53 4.70
143 144 0.387202 CTGACCTAGTGCTCCCATCG 59.613 60.000 0.00 0.00 0.00 3.84
161 163 1.134367 TCGCAAGATTAGACTCCACGG 59.866 52.381 0.00 0.00 45.01 4.94
174 176 1.203052 CTCCACGGCAATGCTTTCAAT 59.797 47.619 4.82 0.00 0.00 2.57
175 177 1.067706 TCCACGGCAATGCTTTCAATG 60.068 47.619 4.82 0.00 0.00 2.82
177 179 2.609984 CCACGGCAATGCTTTCAATGAA 60.610 45.455 4.82 0.00 0.00 2.57
178 180 2.664568 CACGGCAATGCTTTCAATGAAG 59.335 45.455 4.82 0.00 0.00 3.02
179 181 2.297033 ACGGCAATGCTTTCAATGAAGT 59.703 40.909 4.82 0.00 0.00 3.01
180 182 3.505680 ACGGCAATGCTTTCAATGAAGTA 59.494 39.130 4.82 0.00 0.00 2.24
181 183 4.022416 ACGGCAATGCTTTCAATGAAGTAA 60.022 37.500 4.82 0.00 0.00 2.24
182 184 5.104374 CGGCAATGCTTTCAATGAAGTAAT 58.896 37.500 4.82 0.00 0.00 1.89
183 185 5.005012 CGGCAATGCTTTCAATGAAGTAATG 59.995 40.000 4.82 0.00 0.00 1.90
184 186 6.101332 GGCAATGCTTTCAATGAAGTAATGA 58.899 36.000 4.82 0.00 27.55 2.57
189 584 5.769662 TGCTTTCAATGAAGTAATGACACCT 59.230 36.000 0.00 0.00 0.00 4.00
191 586 6.480524 TTTCAATGAAGTAATGACACCTCG 57.519 37.500 0.00 0.00 0.00 4.63
192 587 4.503910 TCAATGAAGTAATGACACCTCGG 58.496 43.478 0.00 0.00 0.00 4.63
196 591 2.233305 AGTAATGACACCTCGGGAGT 57.767 50.000 0.00 0.00 0.00 3.85
201 596 1.153549 GACACCTCGGGAGTCATGC 60.154 63.158 13.03 0.00 41.69 4.06
204 599 2.765807 CCTCGGGAGTCATGCCCT 60.766 66.667 5.47 0.00 43.72 5.19
205 600 1.457643 CCTCGGGAGTCATGCCCTA 60.458 63.158 5.47 0.00 43.72 3.53
208 603 0.830648 TCGGGAGTCATGCCCTAAAG 59.169 55.000 5.47 0.00 43.72 1.85
228 623 1.229359 CTGACTAGCTACCCCGGGA 59.771 63.158 26.32 0.34 0.00 5.14
243 650 4.179579 GGAAAGCATCCCACGCGC 62.180 66.667 5.73 0.00 43.00 6.86
254 661 4.170062 CACGCGCTGGGATGCAAG 62.170 66.667 5.73 0.00 0.00 4.01
272 679 4.697756 CCCGCCGAAAGCCTCACA 62.698 66.667 0.00 0.00 38.78 3.58
273 680 3.423154 CCGCCGAAAGCCTCACAC 61.423 66.667 0.00 0.00 38.78 3.82
274 681 2.664851 CGCCGAAAGCCTCACACA 60.665 61.111 0.00 0.00 38.78 3.72
275 682 2.034879 CGCCGAAAGCCTCACACAT 61.035 57.895 0.00 0.00 38.78 3.21
276 683 0.739462 CGCCGAAAGCCTCACACATA 60.739 55.000 0.00 0.00 38.78 2.29
277 684 1.668419 GCCGAAAGCCTCACACATAT 58.332 50.000 0.00 0.00 34.35 1.78
278 685 2.017049 GCCGAAAGCCTCACACATATT 58.983 47.619 0.00 0.00 34.35 1.28
279 686 2.223340 GCCGAAAGCCTCACACATATTG 60.223 50.000 0.00 0.00 34.35 1.90
280 687 3.009723 CCGAAAGCCTCACACATATTGT 58.990 45.455 0.00 0.00 39.97 2.71
284 732 3.855689 AGCCTCACACATATTGTTTGC 57.144 42.857 0.00 0.00 35.67 3.68
287 735 2.518949 CTCACACATATTGTTTGCGCC 58.481 47.619 4.18 0.00 35.67 6.53
293 741 3.929334 TATTGTTTGCGCCCCGGCT 62.929 57.895 4.18 0.00 39.32 5.52
312 760 2.235016 CTGATAGAGCCTAACGCCTCT 58.765 52.381 0.00 0.00 38.78 3.69
314 762 3.821600 CTGATAGAGCCTAACGCCTCTAA 59.178 47.826 1.97 0.00 38.78 2.10
316 764 0.739561 AGAGCCTAACGCCTCTAACG 59.260 55.000 0.00 0.00 38.78 3.18
318 766 1.141234 GCCTAACGCCTCTAACGCT 59.859 57.895 0.00 0.00 0.00 5.07
320 768 0.527817 CCTAACGCCTCTAACGCTGG 60.528 60.000 0.00 0.00 0.00 4.85
321 769 0.527817 CTAACGCCTCTAACGCTGGG 60.528 60.000 0.00 0.00 0.00 4.45
322 770 0.966875 TAACGCCTCTAACGCTGGGA 60.967 55.000 0.00 0.00 0.00 4.37
324 772 1.144057 CGCCTCTAACGCTGGGATT 59.856 57.895 0.00 0.00 0.00 3.01
325 773 0.462047 CGCCTCTAACGCTGGGATTT 60.462 55.000 0.00 0.00 0.00 2.17
326 774 1.202486 CGCCTCTAACGCTGGGATTTA 60.202 52.381 0.00 0.00 0.00 1.40
358 806 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
362 810 5.827797 CCGGAAATCCTGAAATAAATCCAGA 59.172 40.000 0.00 0.00 0.00 3.86
373 821 9.390795 CTGAAATAAATCCAGAAATAATGCGAG 57.609 33.333 0.00 0.00 0.00 5.03
391 839 2.681976 CGAGCATCAGGATTTGAACCCT 60.682 50.000 0.00 0.00 39.77 4.34
427 875 1.909302 CCACTGTCCACCTAACCATCT 59.091 52.381 0.00 0.00 0.00 2.90
429 877 2.567169 CACTGTCCACCTAACCATCTCA 59.433 50.000 0.00 0.00 0.00 3.27
430 878 3.007940 CACTGTCCACCTAACCATCTCAA 59.992 47.826 0.00 0.00 0.00 3.02
432 880 4.080863 ACTGTCCACCTAACCATCTCAATC 60.081 45.833 0.00 0.00 0.00 2.67
433 881 3.843619 TGTCCACCTAACCATCTCAATCA 59.156 43.478 0.00 0.00 0.00 2.57
434 882 4.192317 GTCCACCTAACCATCTCAATCAC 58.808 47.826 0.00 0.00 0.00 3.06
436 884 4.080919 TCCACCTAACCATCTCAATCACAG 60.081 45.833 0.00 0.00 0.00 3.66
437 885 4.194640 CACCTAACCATCTCAATCACAGG 58.805 47.826 0.00 0.00 0.00 4.00
451 979 1.601903 TCACAGGTTGTTTCGCATCAC 59.398 47.619 0.00 0.00 0.00 3.06
475 1003 6.500049 ACCCCTTCATTTGTTTCCATTGAATA 59.500 34.615 0.00 0.00 0.00 1.75
563 3458 6.455360 AAAACCCGACTACTCGTATAATCA 57.545 37.500 0.00 0.00 38.32 2.57
734 4857 1.698506 CGAGCCAATCTACCTCCTCT 58.301 55.000 0.00 0.00 0.00 3.69
760 4883 1.668294 CCTCGTCTCCAAGCACTGT 59.332 57.895 0.00 0.00 0.00 3.55
791 4915 3.691342 CGACGCCAGGTTCCTCCA 61.691 66.667 0.00 0.00 39.02 3.86
799 4923 1.536662 AGGTTCCTCCACCGCTTCT 60.537 57.895 0.00 0.00 42.33 2.85
907 7825 2.283966 CAGTCCCCTCCTCCACGT 60.284 66.667 0.00 0.00 0.00 4.49
1188 8120 2.045242 TCCGCCTGCGTCTACTCT 60.045 61.111 10.94 0.00 37.81 3.24
1452 8387 4.952071 TGATCTCATTCTCCATCTCCAC 57.048 45.455 0.00 0.00 0.00 4.02
1453 8388 4.292643 TGATCTCATTCTCCATCTCCACA 58.707 43.478 0.00 0.00 0.00 4.17
1526 8461 5.426689 AGAGCCATTGATCTGAACAAGTA 57.573 39.130 6.51 0.00 35.49 2.24
1617 8552 6.757237 TGCTGATGTGGTTTTCATTTATGTT 58.243 32.000 0.00 0.00 0.00 2.71
1619 8554 7.714377 TGCTGATGTGGTTTTCATTTATGTTTT 59.286 29.630 0.00 0.00 0.00 2.43
1627 8562 8.896744 TGGTTTTCATTTATGTTTTTGATTGCA 58.103 25.926 0.00 0.00 0.00 4.08
1661 8596 4.334759 CCATCTCAAGTCTATGCAGTTTGG 59.665 45.833 0.00 0.00 0.00 3.28
1670 8605 2.071778 ATGCAGTTTGGTGAGGTGTT 57.928 45.000 0.00 0.00 0.00 3.32
1712 8650 3.252458 AGCATTTTTCCGTACACCAGTTC 59.748 43.478 0.00 0.00 0.00 3.01
1787 8755 8.786826 ACTCGTTATCCAAAGATGAACATTAA 57.213 30.769 0.00 0.00 33.67 1.40
1788 8756 9.396022 ACTCGTTATCCAAAGATGAACATTAAT 57.604 29.630 0.00 0.00 33.67 1.40
1813 8781 3.338818 TTTTTGACGAAAGAGCAGCAG 57.661 42.857 0.00 0.00 0.00 4.24
1814 8782 1.229428 TTTGACGAAAGAGCAGCAGG 58.771 50.000 0.00 0.00 0.00 4.85
1815 8783 0.392706 TTGACGAAAGAGCAGCAGGA 59.607 50.000 0.00 0.00 0.00 3.86
1816 8784 0.610174 TGACGAAAGAGCAGCAGGAT 59.390 50.000 0.00 0.00 0.00 3.24
1817 8785 1.005340 GACGAAAGAGCAGCAGGATG 58.995 55.000 0.00 0.00 40.87 3.51
1834 8802 5.902681 CAGGATGCTGATTTTCATTGATGT 58.097 37.500 8.85 0.00 0.00 3.06
1835 8803 7.034685 CAGGATGCTGATTTTCATTGATGTA 57.965 36.000 8.85 0.00 0.00 2.29
1836 8804 7.139392 CAGGATGCTGATTTTCATTGATGTAG 58.861 38.462 8.85 0.00 0.00 2.74
1837 8805 6.832384 AGGATGCTGATTTTCATTGATGTAGT 59.168 34.615 0.00 0.00 0.00 2.73
1838 8806 6.916387 GGATGCTGATTTTCATTGATGTAGTG 59.084 38.462 0.00 0.00 0.00 2.74
1839 8807 6.198650 TGCTGATTTTCATTGATGTAGTGG 57.801 37.500 0.00 0.00 0.00 4.00
1840 8808 5.945191 TGCTGATTTTCATTGATGTAGTGGA 59.055 36.000 0.00 0.00 0.00 4.02
1841 8809 6.433716 TGCTGATTTTCATTGATGTAGTGGAA 59.566 34.615 0.00 0.00 0.00 3.53
1842 8810 7.039853 TGCTGATTTTCATTGATGTAGTGGAAA 60.040 33.333 0.00 0.00 29.29 3.13
1843 8811 7.487189 GCTGATTTTCATTGATGTAGTGGAAAG 59.513 37.037 0.00 0.00 28.35 2.62
1844 8812 7.829725 TGATTTTCATTGATGTAGTGGAAAGG 58.170 34.615 0.00 0.00 28.35 3.11
1845 8813 7.669304 TGATTTTCATTGATGTAGTGGAAAGGA 59.331 33.333 0.00 0.00 28.35 3.36
1846 8814 6.817765 TTTCATTGATGTAGTGGAAAGGAC 57.182 37.500 0.00 0.00 0.00 3.85
1847 8815 4.503910 TCATTGATGTAGTGGAAAGGACG 58.496 43.478 0.00 0.00 0.00 4.79
1848 8816 3.328382 TTGATGTAGTGGAAAGGACGG 57.672 47.619 0.00 0.00 0.00 4.79
1849 8817 2.253610 TGATGTAGTGGAAAGGACGGT 58.746 47.619 0.00 0.00 0.00 4.83
1850 8818 3.433343 TGATGTAGTGGAAAGGACGGTA 58.567 45.455 0.00 0.00 0.00 4.02
1851 8819 3.194116 TGATGTAGTGGAAAGGACGGTAC 59.806 47.826 0.00 0.00 0.00 3.34
1852 8820 2.596346 TGTAGTGGAAAGGACGGTACA 58.404 47.619 0.00 0.00 0.00 2.90
1853 8821 2.559668 TGTAGTGGAAAGGACGGTACAG 59.440 50.000 0.00 0.00 0.00 2.74
1854 8822 1.713297 AGTGGAAAGGACGGTACAGT 58.287 50.000 0.00 0.00 0.00 3.55
1855 8823 2.044758 AGTGGAAAGGACGGTACAGTT 58.955 47.619 0.00 0.00 0.00 3.16
1856 8824 2.140717 GTGGAAAGGACGGTACAGTTG 58.859 52.381 0.00 0.00 0.00 3.16
1857 8825 1.154197 GGAAAGGACGGTACAGTTGC 58.846 55.000 0.00 0.00 0.00 4.17
1858 8826 1.541670 GGAAAGGACGGTACAGTTGCA 60.542 52.381 0.00 0.00 0.00 4.08
1859 8827 2.215196 GAAAGGACGGTACAGTTGCAA 58.785 47.619 0.00 0.00 0.00 4.08
1860 8828 1.878953 AAGGACGGTACAGTTGCAAG 58.121 50.000 0.00 0.00 0.00 4.01
1861 8829 1.045407 AGGACGGTACAGTTGCAAGA 58.955 50.000 0.00 0.00 0.00 3.02
1862 8830 1.414919 AGGACGGTACAGTTGCAAGAA 59.585 47.619 0.00 0.00 0.00 2.52
1863 8831 2.158871 AGGACGGTACAGTTGCAAGAAA 60.159 45.455 0.00 0.00 0.00 2.52
1864 8832 2.223377 GGACGGTACAGTTGCAAGAAAG 59.777 50.000 0.00 0.00 0.00 2.62
1865 8833 2.218603 ACGGTACAGTTGCAAGAAAGG 58.781 47.619 0.00 0.00 0.00 3.11
1866 8834 1.535462 CGGTACAGTTGCAAGAAAGGG 59.465 52.381 0.00 0.00 0.00 3.95
1867 8835 2.583143 GGTACAGTTGCAAGAAAGGGT 58.417 47.619 0.00 0.00 0.00 4.34
1868 8836 2.552743 GGTACAGTTGCAAGAAAGGGTC 59.447 50.000 0.00 0.00 0.00 4.46
1869 8837 2.435372 ACAGTTGCAAGAAAGGGTCA 57.565 45.000 0.00 0.00 0.00 4.02
1870 8838 2.301346 ACAGTTGCAAGAAAGGGTCAG 58.699 47.619 0.00 0.00 0.00 3.51
1871 8839 1.610522 CAGTTGCAAGAAAGGGTCAGG 59.389 52.381 0.00 0.00 0.00 3.86
1872 8840 0.961753 GTTGCAAGAAAGGGTCAGGG 59.038 55.000 0.00 0.00 0.00 4.45
1873 8841 0.850100 TTGCAAGAAAGGGTCAGGGA 59.150 50.000 0.00 0.00 0.00 4.20
1874 8842 0.850100 TGCAAGAAAGGGTCAGGGAA 59.150 50.000 0.00 0.00 0.00 3.97
1875 8843 1.248486 GCAAGAAAGGGTCAGGGAAC 58.752 55.000 0.00 0.00 0.00 3.62
1891 8859 2.644676 GGAACCCTAGCAAATCAGGAC 58.355 52.381 0.00 0.00 33.42 3.85
1892 8860 2.239907 GGAACCCTAGCAAATCAGGACT 59.760 50.000 0.00 0.00 33.42 3.85
1900 8868 1.673168 CAAATCAGGACTAGCAGCCC 58.327 55.000 0.00 0.00 0.00 5.19
1908 8876 2.365095 GACTAGCAGCCCCGCGTAAT 62.365 60.000 4.92 0.00 36.85 1.89
1910 8878 0.814010 CTAGCAGCCCCGCGTAATTT 60.814 55.000 4.92 0.00 36.85 1.82
1912 8880 3.107447 CAGCCCCGCGTAATTTCC 58.893 61.111 4.92 0.00 0.00 3.13
1913 8881 1.451387 CAGCCCCGCGTAATTTCCT 60.451 57.895 4.92 0.00 0.00 3.36
1941 8909 0.323360 ACCCGGAATCATGGTGGTTG 60.323 55.000 0.73 0.00 0.00 3.77
1948 8916 3.831911 GGAATCATGGTGGTTGGAAGAAA 59.168 43.478 0.00 0.00 0.00 2.52
1983 8951 4.752879 GCCCGCTTGTAGCCACGA 62.753 66.667 0.00 0.00 38.18 4.35
1998 8966 0.309302 CACGATCTGGCCTCGTCTAG 59.691 60.000 14.99 1.99 45.63 2.43
2011 8979 2.621055 CTCGTCTAGGATTCTGGAGTGG 59.379 54.545 0.00 0.00 30.95 4.00
2018 8986 1.630878 GGATTCTGGAGTGGACTTGGT 59.369 52.381 0.00 0.00 0.00 3.67
2037 9005 4.680237 CGTCGTGCTGGCCTTGGA 62.680 66.667 3.32 0.00 0.00 3.53
2062 9030 3.254892 GAAAATCCGCTCGTTTCTCTCT 58.745 45.455 0.00 0.00 0.00 3.10
2083 9051 2.435372 TCCAAATGCACCAGGATACC 57.565 50.000 0.00 0.00 37.17 2.73
2140 9108 1.138883 TGGTAGCGATCGTGTCTGC 59.861 57.895 17.81 8.75 0.00 4.26
2145 9113 1.446099 GCGATCGTGTCTGCTTCCA 60.446 57.895 17.81 0.00 0.00 3.53
2154 9122 2.048222 CTGCTTCCAGAACCGCGA 60.048 61.111 8.23 0.00 41.77 5.87
2184 9152 2.821366 GCCAGTGTCCATCGGCAG 60.821 66.667 0.00 0.00 44.25 4.85
2192 9160 1.918293 TCCATCGGCAGGTTGGAGT 60.918 57.895 5.57 0.00 34.65 3.85
2222 9190 1.005037 AGTGATTGCGCCGTCTTGA 60.005 52.632 4.18 0.00 0.00 3.02
2265 9233 4.773117 GGTCGCGACGAGGTGGAC 62.773 72.222 30.99 12.33 36.23 4.02
2311 9279 3.361977 GCGCAAACCGGGTCATGT 61.362 61.111 6.32 0.00 37.44 3.21
2371 9339 2.507944 CCCCGCAGAAGGATCCAG 59.492 66.667 15.82 1.67 0.00 3.86
2374 9342 2.587194 CGCAGAAGGATCCAGGCG 60.587 66.667 15.82 18.25 35.69 5.52
2377 9345 0.392998 GCAGAAGGATCCAGGCGAAA 60.393 55.000 15.82 0.00 0.00 3.46
2380 9348 1.087501 GAAGGATCCAGGCGAAACAC 58.912 55.000 15.82 0.00 0.00 3.32
2386 9354 2.192861 CCAGGCGAAACACTTGGCA 61.193 57.895 0.00 0.00 37.97 4.92
2392 9360 2.826738 AAACACTTGGCACGCGGT 60.827 55.556 12.47 0.00 0.00 5.68
2517 9486 1.332997 CTTCCATCGCAAGGAATCTGC 59.667 52.381 2.40 0.00 43.74 4.26
2519 9488 0.942962 CCATCGCAAGGAATCTGCTC 59.057 55.000 0.00 0.00 38.47 4.26
2522 9491 0.610174 TCGCAAGGAATCTGCTCTGT 59.390 50.000 0.00 0.00 38.47 3.41
2533 9502 0.035881 CTGCTCTGTCCTCCTGCAAA 59.964 55.000 0.00 0.00 33.07 3.68
2608 9577 5.622007 CGTGCTTGGATTTGGTTTGACATAT 60.622 40.000 0.00 0.00 0.00 1.78
2677 9646 2.028925 TTGCAGTGCGCGAAGAGA 59.971 55.556 12.10 0.00 46.97 3.10
2689 9658 0.319383 CGAAGAGATCAGGCCATCGG 60.319 60.000 5.01 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.837578 GCATCCTCCACATGCAGG 58.162 61.111 0.00 0.00 45.19 4.85
13 14 4.891037 GGGGGCAGCAGGAGCATC 62.891 72.222 0.00 0.00 45.49 3.91
26 27 4.388499 CTTGACCGACGGTGGGGG 62.388 72.222 27.26 7.85 35.25 5.40
27 28 3.622826 ACTTGACCGACGGTGGGG 61.623 66.667 27.26 15.44 35.25 4.96
28 29 2.357034 CACTTGACCGACGGTGGG 60.357 66.667 27.26 15.80 35.25 4.61
29 30 1.663702 GTCACTTGACCGACGGTGG 60.664 63.158 27.26 16.17 39.07 4.61
30 31 0.528901 TTGTCACTTGACCGACGGTG 60.529 55.000 27.26 13.10 44.15 4.94
31 32 0.249322 CTTGTCACTTGACCGACGGT 60.249 55.000 21.93 21.93 44.15 4.83
32 33 1.557443 GCTTGTCACTTGACCGACGG 61.557 60.000 13.61 13.61 44.15 4.79
33 34 1.557443 GGCTTGTCACTTGACCGACG 61.557 60.000 6.91 0.00 44.15 5.12
34 35 1.228657 GGGCTTGTCACTTGACCGAC 61.229 60.000 6.91 0.53 44.15 4.79
35 36 1.070786 GGGCTTGTCACTTGACCGA 59.929 57.895 6.91 0.00 44.15 4.69
36 37 1.966451 GGGGCTTGTCACTTGACCG 60.966 63.158 6.91 0.00 44.15 4.79
37 38 0.467290 TTGGGGCTTGTCACTTGACC 60.467 55.000 6.91 0.00 44.15 4.02
38 39 0.668535 GTTGGGGCTTGTCACTTGAC 59.331 55.000 2.19 2.19 44.97 3.18
39 40 0.467290 GGTTGGGGCTTGTCACTTGA 60.467 55.000 0.00 0.00 0.00 3.02
40 41 1.795170 CGGTTGGGGCTTGTCACTTG 61.795 60.000 0.00 0.00 0.00 3.16
41 42 1.528309 CGGTTGGGGCTTGTCACTT 60.528 57.895 0.00 0.00 0.00 3.16
42 43 2.113139 CGGTTGGGGCTTGTCACT 59.887 61.111 0.00 0.00 0.00 3.41
43 44 2.764637 ATCCGGTTGGGGCTTGTCAC 62.765 60.000 0.00 0.00 36.01 3.67
44 45 2.534396 ATCCGGTTGGGGCTTGTCA 61.534 57.895 0.00 0.00 36.01 3.58
45 46 2.046285 CATCCGGTTGGGGCTTGTC 61.046 63.158 0.00 0.00 36.01 3.18
46 47 2.035626 CATCCGGTTGGGGCTTGT 59.964 61.111 0.00 0.00 36.01 3.16
47 48 3.451894 GCATCCGGTTGGGGCTTG 61.452 66.667 14.27 0.00 36.01 4.01
48 49 3.978193 TGCATCCGGTTGGGGCTT 61.978 61.111 14.27 0.00 37.03 4.35
49 50 4.740822 GTGCATCCGGTTGGGGCT 62.741 66.667 14.27 0.00 37.03 5.19
50 51 3.338275 TAGTGCATCCGGTTGGGGC 62.338 63.158 14.27 6.63 36.75 5.80
51 52 1.153168 CTAGTGCATCCGGTTGGGG 60.153 63.158 14.27 0.00 36.01 4.96
52 53 1.819632 GCTAGTGCATCCGGTTGGG 60.820 63.158 14.27 0.00 39.41 4.12
53 54 1.078497 TGCTAGTGCATCCGGTTGG 60.078 57.895 14.27 0.10 45.31 3.77
54 55 4.615901 TGCTAGTGCATCCGGTTG 57.384 55.556 8.23 8.23 45.31 3.77
62 63 5.941455 AGCATGGAGTTGTTGCTAGTGCA 62.941 47.826 0.00 0.00 44.51 4.57
63 64 1.135575 GCATGGAGTTGTTGCTAGTGC 60.136 52.381 0.00 0.00 40.20 4.40
64 65 2.417933 GAGCATGGAGTTGTTGCTAGTG 59.582 50.000 0.00 0.00 46.21 2.74
65 66 2.038952 TGAGCATGGAGTTGTTGCTAGT 59.961 45.455 0.00 0.00 46.21 2.57
66 67 2.417933 GTGAGCATGGAGTTGTTGCTAG 59.582 50.000 0.00 0.00 46.21 3.42
67 68 2.426522 GTGAGCATGGAGTTGTTGCTA 58.573 47.619 0.00 0.00 46.21 3.49
69 70 0.242017 GGTGAGCATGGAGTTGTTGC 59.758 55.000 0.00 0.00 36.63 4.17
70 71 1.267806 GTGGTGAGCATGGAGTTGTTG 59.732 52.381 0.00 0.00 0.00 3.33
71 72 1.133823 TGTGGTGAGCATGGAGTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
72 73 0.473755 TGTGGTGAGCATGGAGTTGT 59.526 50.000 0.00 0.00 0.00 3.32
73 74 1.741706 GATGTGGTGAGCATGGAGTTG 59.258 52.381 0.00 0.00 0.00 3.16
74 75 1.352017 TGATGTGGTGAGCATGGAGTT 59.648 47.619 0.00 0.00 0.00 3.01
75 76 0.986527 TGATGTGGTGAGCATGGAGT 59.013 50.000 0.00 0.00 0.00 3.85
114 115 0.959553 ACTAGGTCAGTCGTGGTGTG 59.040 55.000 0.00 0.00 28.33 3.82
122 123 1.410882 GATGGGAGCACTAGGTCAGTC 59.589 57.143 0.00 0.00 43.97 3.51
123 124 1.490574 GATGGGAGCACTAGGTCAGT 58.509 55.000 0.00 0.00 43.97 3.41
128 129 0.531532 CTTGCGATGGGAGCACTAGG 60.532 60.000 0.00 0.00 45.10 3.02
130 131 1.123077 ATCTTGCGATGGGAGCACTA 58.877 50.000 0.00 0.00 45.10 2.74
138 139 3.126831 GTGGAGTCTAATCTTGCGATGG 58.873 50.000 0.00 0.00 0.00 3.51
143 144 1.291132 GCCGTGGAGTCTAATCTTGC 58.709 55.000 0.00 0.00 0.00 4.01
161 163 6.587226 TGTCATTACTTCATTGAAAGCATTGC 59.413 34.615 0.00 0.00 0.00 3.56
174 176 2.496070 CTCCCGAGGTGTCATTACTTCA 59.504 50.000 0.00 0.00 0.00 3.02
175 177 2.496470 ACTCCCGAGGTGTCATTACTTC 59.504 50.000 0.00 0.00 0.00 3.01
177 179 2.100989 GACTCCCGAGGTGTCATTACT 58.899 52.381 15.76 0.00 43.28 2.24
178 180 1.822990 TGACTCCCGAGGTGTCATTAC 59.177 52.381 18.08 1.03 46.73 1.89
179 181 2.225382 TGACTCCCGAGGTGTCATTA 57.775 50.000 18.08 3.09 46.73 1.90
180 182 3.067011 TGACTCCCGAGGTGTCATT 57.933 52.632 18.08 0.00 46.73 2.57
181 183 4.865629 TGACTCCCGAGGTGTCAT 57.134 55.556 18.08 0.00 46.73 3.06
183 185 1.153549 GCATGACTCCCGAGGTGTC 60.154 63.158 14.49 14.49 43.84 3.67
184 186 2.660064 GGCATGACTCCCGAGGTGT 61.660 63.158 0.00 0.00 31.68 4.16
191 586 3.808984 CCTTTAGGGCATGACTCCC 57.191 57.895 0.00 0.00 44.25 4.30
211 606 0.041535 TTTCCCGGGGTAGCTAGTCA 59.958 55.000 23.50 0.00 0.00 3.41
213 608 1.335882 GCTTTCCCGGGGTAGCTAGT 61.336 60.000 29.50 0.00 32.11 2.57
219 614 3.326900 GGATGCTTTCCCGGGGTA 58.673 61.111 23.50 6.35 38.75 3.69
228 623 3.434319 CAGCGCGTGGGATGCTTT 61.434 61.111 8.43 0.00 36.69 3.51
247 654 3.401243 CTTTCGGCGGGCTTGCATC 62.401 63.158 7.21 0.00 36.28 3.91
248 655 3.443045 CTTTCGGCGGGCTTGCAT 61.443 61.111 7.21 0.00 36.28 3.96
261 668 4.622740 GCAAACAATATGTGTGAGGCTTTC 59.377 41.667 4.87 0.00 37.81 2.62
268 675 1.201181 GGGCGCAAACAATATGTGTGA 59.799 47.619 10.83 0.00 37.81 3.58
269 676 1.627879 GGGCGCAAACAATATGTGTG 58.372 50.000 10.83 0.00 40.60 3.82
271 678 0.525242 CGGGGCGCAAACAATATGTG 60.525 55.000 10.83 0.00 0.00 3.21
272 679 1.662438 CCGGGGCGCAAACAATATGT 61.662 55.000 10.83 0.00 0.00 2.29
273 680 1.065600 CCGGGGCGCAAACAATATG 59.934 57.895 10.83 0.00 0.00 1.78
274 681 2.781158 GCCGGGGCGCAAACAATAT 61.781 57.895 10.83 0.00 0.00 1.28
275 682 3.444805 GCCGGGGCGCAAACAATA 61.445 61.111 10.83 0.00 0.00 1.90
312 760 1.930567 GCTCGTAAATCCCAGCGTTA 58.069 50.000 0.00 0.00 0.00 3.18
314 762 4.515404 GCTCGTAAATCCCAGCGT 57.485 55.556 0.00 0.00 0.00 5.07
316 764 1.160329 ATGCGCTCGTAAATCCCAGC 61.160 55.000 9.73 0.00 0.00 4.85
318 766 0.874175 CGATGCGCTCGTAAATCCCA 60.874 55.000 9.73 0.00 42.56 4.37
358 806 3.058432 CCTGATGCTCGCATTATTTCTGG 60.058 47.826 5.79 3.80 36.70 3.86
362 810 5.300034 TCAAATCCTGATGCTCGCATTATTT 59.700 36.000 5.79 7.47 36.70 1.40
391 839 3.444955 TGGTATCCCCAACCCATCA 57.555 52.632 0.00 0.00 41.50 3.07
400 848 0.620700 AGGTGGACAGTGGTATCCCC 60.621 60.000 0.00 0.00 33.69 4.81
401 849 2.169978 GTTAGGTGGACAGTGGTATCCC 59.830 54.545 0.00 0.00 33.69 3.85
407 855 1.909302 AGATGGTTAGGTGGACAGTGG 59.091 52.381 0.00 0.00 0.00 4.00
416 864 3.846588 ACCTGTGATTGAGATGGTTAGGT 59.153 43.478 0.00 0.00 0.00 3.08
421 869 3.795688 ACAACCTGTGATTGAGATGGT 57.204 42.857 0.00 0.00 0.00 3.55
427 875 2.293170 TGCGAAACAACCTGTGATTGA 58.707 42.857 0.00 0.00 0.00 2.57
429 877 2.884012 TGATGCGAAACAACCTGTGATT 59.116 40.909 0.00 0.00 0.00 2.57
430 878 2.226437 GTGATGCGAAACAACCTGTGAT 59.774 45.455 0.00 0.00 0.00 3.06
432 880 1.334960 GGTGATGCGAAACAACCTGTG 60.335 52.381 0.00 0.00 0.00 3.66
433 881 0.951558 GGTGATGCGAAACAACCTGT 59.048 50.000 0.00 0.00 0.00 4.00
434 882 0.240945 GGGTGATGCGAAACAACCTG 59.759 55.000 0.00 0.00 40.35 4.00
436 884 0.893727 AGGGGTGATGCGAAACAACC 60.894 55.000 0.00 0.00 42.49 3.77
437 885 0.958822 AAGGGGTGATGCGAAACAAC 59.041 50.000 0.00 0.00 0.00 3.32
451 979 5.807909 ATTCAATGGAAACAAATGAAGGGG 58.192 37.500 0.00 0.00 46.57 4.79
475 1003 4.516365 AATGTACGGTCTTCGACTCTTT 57.484 40.909 0.00 0.00 42.43 2.52
555 3450 4.018960 AGAGGGCATCCATGGTGATTATAC 60.019 45.833 12.58 0.00 34.83 1.47
563 3458 2.446848 CGGAGAGGGCATCCATGGT 61.447 63.158 12.58 0.00 36.57 3.55
907 7825 1.458777 ACCAGGAGTCGTGGGACAA 60.459 57.895 30.17 0.00 45.92 3.18
1039 7962 1.860399 GCAATCGTACTCATCGAGCGT 60.860 52.381 0.00 0.00 40.57 5.07
1188 8120 1.617018 CCCAGATGCCGGTCTCAGAA 61.617 60.000 1.90 0.00 0.00 3.02
1452 8387 2.154462 GTGGTCACCCTTGAGAACATG 58.846 52.381 0.00 0.00 33.46 3.21
1453 8388 1.073923 GGTGGTCACCCTTGAGAACAT 59.926 52.381 8.89 0.00 45.68 2.71
1627 8562 4.900652 AGACTTGAGATGGAGCATGTAGAT 59.099 41.667 0.00 0.00 0.00 1.98
1661 8596 2.814280 TCCTTTCTCGAACACCTCAC 57.186 50.000 0.00 0.00 0.00 3.51
1670 8605 3.493350 GCTGCCATAGATTCCTTTCTCGA 60.493 47.826 0.00 0.00 0.00 4.04
1712 8650 7.989741 ACAACTACATTTCATCATTCCTAGAGG 59.010 37.037 0.00 0.00 0.00 3.69
1793 8761 2.033299 CCTGCTGCTCTTTCGTCAAAAA 59.967 45.455 0.00 0.00 0.00 1.94
1794 8762 1.603802 CCTGCTGCTCTTTCGTCAAAA 59.396 47.619 0.00 0.00 0.00 2.44
1795 8763 1.202639 TCCTGCTGCTCTTTCGTCAAA 60.203 47.619 0.00 0.00 0.00 2.69
1796 8764 0.392706 TCCTGCTGCTCTTTCGTCAA 59.607 50.000 0.00 0.00 0.00 3.18
1797 8765 0.610174 ATCCTGCTGCTCTTTCGTCA 59.390 50.000 0.00 0.00 0.00 4.35
1798 8766 1.005340 CATCCTGCTGCTCTTTCGTC 58.995 55.000 0.00 0.00 0.00 4.20
1799 8767 1.023513 GCATCCTGCTGCTCTTTCGT 61.024 55.000 0.00 0.00 40.96 3.85
1800 8768 1.720301 GCATCCTGCTGCTCTTTCG 59.280 57.895 0.00 0.00 40.96 3.46
1810 8778 4.380841 TCAATGAAAATCAGCATCCTGC 57.619 40.909 0.00 0.00 45.46 4.85
1811 8779 5.902681 ACATCAATGAAAATCAGCATCCTG 58.097 37.500 0.00 0.00 40.54 3.86
1812 8780 6.832384 ACTACATCAATGAAAATCAGCATCCT 59.168 34.615 0.00 0.00 0.00 3.24
1813 8781 6.916387 CACTACATCAATGAAAATCAGCATCC 59.084 38.462 0.00 0.00 0.00 3.51
1814 8782 6.916387 CCACTACATCAATGAAAATCAGCATC 59.084 38.462 0.00 0.00 0.00 3.91
1815 8783 6.604396 TCCACTACATCAATGAAAATCAGCAT 59.396 34.615 0.00 0.00 0.00 3.79
1816 8784 5.945191 TCCACTACATCAATGAAAATCAGCA 59.055 36.000 0.00 0.00 0.00 4.41
1817 8785 6.441093 TCCACTACATCAATGAAAATCAGC 57.559 37.500 0.00 0.00 0.00 4.26
1818 8786 7.972277 CCTTTCCACTACATCAATGAAAATCAG 59.028 37.037 0.00 0.00 0.00 2.90
1819 8787 7.669304 TCCTTTCCACTACATCAATGAAAATCA 59.331 33.333 0.00 0.00 0.00 2.57
1820 8788 7.970614 GTCCTTTCCACTACATCAATGAAAATC 59.029 37.037 0.00 0.00 0.00 2.17
1821 8789 7.362056 CGTCCTTTCCACTACATCAATGAAAAT 60.362 37.037 0.00 0.00 0.00 1.82
1822 8790 6.072728 CGTCCTTTCCACTACATCAATGAAAA 60.073 38.462 0.00 0.00 0.00 2.29
1823 8791 5.411361 CGTCCTTTCCACTACATCAATGAAA 59.589 40.000 0.00 0.00 0.00 2.69
1824 8792 4.935205 CGTCCTTTCCACTACATCAATGAA 59.065 41.667 0.00 0.00 0.00 2.57
1825 8793 4.503910 CGTCCTTTCCACTACATCAATGA 58.496 43.478 0.00 0.00 0.00 2.57
1826 8794 3.623060 CCGTCCTTTCCACTACATCAATG 59.377 47.826 0.00 0.00 0.00 2.82
1827 8795 3.263425 ACCGTCCTTTCCACTACATCAAT 59.737 43.478 0.00 0.00 0.00 2.57
1828 8796 2.635915 ACCGTCCTTTCCACTACATCAA 59.364 45.455 0.00 0.00 0.00 2.57
1829 8797 2.253610 ACCGTCCTTTCCACTACATCA 58.746 47.619 0.00 0.00 0.00 3.07
1830 8798 3.194116 TGTACCGTCCTTTCCACTACATC 59.806 47.826 0.00 0.00 0.00 3.06
1831 8799 3.167485 TGTACCGTCCTTTCCACTACAT 58.833 45.455 0.00 0.00 0.00 2.29
1832 8800 2.559668 CTGTACCGTCCTTTCCACTACA 59.440 50.000 0.00 0.00 0.00 2.74
1833 8801 2.560105 ACTGTACCGTCCTTTCCACTAC 59.440 50.000 0.00 0.00 0.00 2.73
1834 8802 2.880443 ACTGTACCGTCCTTTCCACTA 58.120 47.619 0.00 0.00 0.00 2.74
1835 8803 1.713297 ACTGTACCGTCCTTTCCACT 58.287 50.000 0.00 0.00 0.00 4.00
1836 8804 2.140717 CAACTGTACCGTCCTTTCCAC 58.859 52.381 0.00 0.00 0.00 4.02
1837 8805 1.541670 GCAACTGTACCGTCCTTTCCA 60.542 52.381 0.00 0.00 0.00 3.53
1838 8806 1.154197 GCAACTGTACCGTCCTTTCC 58.846 55.000 0.00 0.00 0.00 3.13
1839 8807 1.873698 TGCAACTGTACCGTCCTTTC 58.126 50.000 0.00 0.00 0.00 2.62
1840 8808 2.158871 TCTTGCAACTGTACCGTCCTTT 60.159 45.455 0.00 0.00 0.00 3.11
1841 8809 1.414919 TCTTGCAACTGTACCGTCCTT 59.585 47.619 0.00 0.00 0.00 3.36
1842 8810 1.045407 TCTTGCAACTGTACCGTCCT 58.955 50.000 0.00 0.00 0.00 3.85
1843 8811 1.873698 TTCTTGCAACTGTACCGTCC 58.126 50.000 0.00 0.00 0.00 4.79
1844 8812 2.223377 CCTTTCTTGCAACTGTACCGTC 59.777 50.000 0.00 0.00 0.00 4.79
1845 8813 2.218603 CCTTTCTTGCAACTGTACCGT 58.781 47.619 0.00 0.00 0.00 4.83
1846 8814 1.535462 CCCTTTCTTGCAACTGTACCG 59.465 52.381 0.00 0.00 0.00 4.02
1847 8815 2.552743 GACCCTTTCTTGCAACTGTACC 59.447 50.000 0.00 0.00 0.00 3.34
1848 8816 3.211045 TGACCCTTTCTTGCAACTGTAC 58.789 45.455 0.00 0.00 0.00 2.90
1849 8817 3.476552 CTGACCCTTTCTTGCAACTGTA 58.523 45.455 0.00 0.00 0.00 2.74
1850 8818 2.301346 CTGACCCTTTCTTGCAACTGT 58.699 47.619 0.00 0.00 0.00 3.55
1851 8819 1.610522 CCTGACCCTTTCTTGCAACTG 59.389 52.381 0.00 0.00 0.00 3.16
1852 8820 1.479389 CCCTGACCCTTTCTTGCAACT 60.479 52.381 0.00 0.00 0.00 3.16
1853 8821 0.961753 CCCTGACCCTTTCTTGCAAC 59.038 55.000 0.00 0.00 0.00 4.17
1854 8822 0.850100 TCCCTGACCCTTTCTTGCAA 59.150 50.000 0.00 0.00 0.00 4.08
1855 8823 0.850100 TTCCCTGACCCTTTCTTGCA 59.150 50.000 0.00 0.00 0.00 4.08
1856 8824 1.248486 GTTCCCTGACCCTTTCTTGC 58.752 55.000 0.00 0.00 0.00 4.01
1857 8825 1.911057 GGTTCCCTGACCCTTTCTTG 58.089 55.000 0.00 0.00 33.41 3.02
1865 8833 0.696501 TTTGCTAGGGTTCCCTGACC 59.303 55.000 19.58 8.56 37.64 4.02
1866 8834 2.026262 TGATTTGCTAGGGTTCCCTGAC 60.026 50.000 19.58 11.82 37.64 3.51
1867 8835 2.239654 CTGATTTGCTAGGGTTCCCTGA 59.760 50.000 19.58 1.80 37.64 3.86
1868 8836 2.648059 CTGATTTGCTAGGGTTCCCTG 58.352 52.381 19.58 10.86 37.64 4.45
1869 8837 1.566231 CCTGATTTGCTAGGGTTCCCT 59.434 52.381 15.19 15.19 40.06 4.20
1870 8838 1.564348 TCCTGATTTGCTAGGGTTCCC 59.436 52.381 0.00 0.00 34.76 3.97
1871 8839 2.239907 AGTCCTGATTTGCTAGGGTTCC 59.760 50.000 0.00 0.00 34.76 3.62
1872 8840 3.636153 AGTCCTGATTTGCTAGGGTTC 57.364 47.619 0.00 0.00 34.76 3.62
1873 8841 3.118223 GCTAGTCCTGATTTGCTAGGGTT 60.118 47.826 0.00 0.00 34.76 4.11
1874 8842 2.436173 GCTAGTCCTGATTTGCTAGGGT 59.564 50.000 0.00 0.00 34.76 4.34
1875 8843 2.435805 TGCTAGTCCTGATTTGCTAGGG 59.564 50.000 0.00 0.00 34.76 3.53
1876 8844 3.726607 CTGCTAGTCCTGATTTGCTAGG 58.273 50.000 0.00 0.00 33.49 3.02
1877 8845 3.129871 GCTGCTAGTCCTGATTTGCTAG 58.870 50.000 0.00 0.00 35.35 3.42
1878 8846 2.158900 GGCTGCTAGTCCTGATTTGCTA 60.159 50.000 0.00 0.00 0.00 3.49
1879 8847 1.407989 GGCTGCTAGTCCTGATTTGCT 60.408 52.381 0.00 0.00 0.00 3.91
1880 8848 1.020437 GGCTGCTAGTCCTGATTTGC 58.980 55.000 0.00 0.00 0.00 3.68
1881 8849 1.673168 GGGCTGCTAGTCCTGATTTG 58.327 55.000 0.00 0.00 36.93 2.32
1882 8850 0.548510 GGGGCTGCTAGTCCTGATTT 59.451 55.000 0.00 0.00 40.65 2.17
1883 8851 2.225792 GGGGCTGCTAGTCCTGATT 58.774 57.895 0.00 0.00 40.65 2.57
1884 8852 3.978164 GGGGCTGCTAGTCCTGAT 58.022 61.111 0.00 0.00 40.65 2.90
1889 8857 2.365095 ATTACGCGGGGCTGCTAGTC 62.365 60.000 12.47 0.00 0.00 2.59
1890 8858 1.968050 AATTACGCGGGGCTGCTAGT 61.968 55.000 12.47 0.00 0.00 2.57
1891 8859 0.814010 AAATTACGCGGGGCTGCTAG 60.814 55.000 12.47 0.00 0.00 3.42
1892 8860 0.812412 GAAATTACGCGGGGCTGCTA 60.812 55.000 12.47 0.00 0.00 3.49
1900 8868 1.029947 AGGCCAAGGAAATTACGCGG 61.030 55.000 12.47 0.00 0.00 6.46
1908 8876 1.559065 CCGGGTAGAGGCCAAGGAAA 61.559 60.000 5.01 0.00 32.08 3.13
1910 8878 2.365105 CCGGGTAGAGGCCAAGGA 60.365 66.667 5.01 0.00 32.08 3.36
1912 8880 0.106894 GATTCCGGGTAGAGGCCAAG 59.893 60.000 5.01 0.00 0.00 3.61
1913 8881 0.619255 TGATTCCGGGTAGAGGCCAA 60.619 55.000 5.01 0.00 0.00 4.52
1941 8909 2.171003 CCCCAATGACCAGTTTCTTCC 58.829 52.381 0.00 0.00 0.00 3.46
1948 8916 0.034089 GCTTAGCCCCAATGACCAGT 60.034 55.000 0.00 0.00 0.00 4.00
1983 8951 2.158385 AGAATCCTAGACGAGGCCAGAT 60.158 50.000 5.01 0.00 46.25 2.90
1998 8966 1.630878 ACCAAGTCCACTCCAGAATCC 59.369 52.381 0.00 0.00 0.00 3.01
2011 8979 2.022129 CAGCACGACGGACCAAGTC 61.022 63.158 0.00 0.00 35.41 3.01
2018 8986 4.680237 CAAGGCCAGCACGACGGA 62.680 66.667 5.01 0.00 0.00 4.69
2037 9005 3.139077 AGAAACGAGCGGATTTTCAACT 58.861 40.909 0.00 0.00 32.62 3.16
2062 9030 3.096092 GGTATCCTGGTGCATTTGGAAA 58.904 45.455 8.26 0.00 31.87 3.13
2083 9051 3.429141 CGAGCCACTTGCCTGCTG 61.429 66.667 0.00 0.00 42.71 4.41
2140 9108 3.693245 CGATCGCGGTTCTGGAAG 58.307 61.111 6.13 0.00 0.00 3.46
2170 9138 1.003355 CAACCTGCCGATGGACACT 60.003 57.895 0.00 0.00 0.00 3.55
2174 9142 0.616395 TACTCCAACCTGCCGATGGA 60.616 55.000 0.80 0.80 40.84 3.41
2184 9152 1.608154 GGAAGCCCCTACTCCAACC 59.392 63.158 0.00 0.00 0.00 3.77
2222 9190 1.123861 TTCTCTGCACAGGTCTGGCT 61.124 55.000 2.87 0.00 34.19 4.75
2311 9279 0.889638 TTCAACGCCGGCAAATACCA 60.890 50.000 28.98 0.00 0.00 3.25
2362 9330 0.693049 AGTGTTTCGCCTGGATCCTT 59.307 50.000 14.23 0.00 0.00 3.36
2371 9339 2.051345 CGTGCCAAGTGTTTCGCC 60.051 61.111 0.00 0.00 0.00 5.54
2374 9342 2.051345 CCGCGTGCCAAGTGTTTC 60.051 61.111 4.92 0.00 0.00 2.78
2488 9456 2.511600 CGATGGAAGTGGACGGCC 60.512 66.667 0.00 0.00 0.00 6.13
2517 9486 1.345741 TCACTTTGCAGGAGGACAGAG 59.654 52.381 4.47 0.00 0.00 3.35
2519 9488 2.082231 CATCACTTTGCAGGAGGACAG 58.918 52.381 4.47 0.00 0.00 3.51
2522 9491 0.322816 GGCATCACTTTGCAGGAGGA 60.323 55.000 4.47 0.27 44.59 3.71
2677 9646 2.507944 GCAGACCGATGGCCTGAT 59.492 61.111 3.32 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.