Multiple sequence alignment - TraesCS1B01G331500

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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 TraesCS1B01G331500 chr1B 100.000 2834 0 0 1 2834 557412788 557409955 0.000000e+00 5234.0
1 TraesCS1B01G331500 chr1B 86.809 1410 165 13 376 1778 557464402 557463007 0.000000e+00 1554.0
2 TraesCS1B01G331500 chr1B 95.192 104 5 0 1 104 484295643 484295540 6.280000e-37 165.0
3 TraesCS1B01G331500 chr1B 100.000 29 0 0 1956 1984 49985455 49985483 1.000000e-03 54.7
4 TraesCS1B01G331500 chr1B 100.000 28 0 0 1958 1985 543741447 543741420 5.000000e-03 52.8
5 TraesCS1B01G331500 chr1D 92.018 1779 105 12 109 1876 413234724 413232972 0.000000e+00 2464.0
6 TraesCS1B01G331500 chr1D 87.997 1383 149 12 376 1753 413224960 413226330 0.000000e+00 1618.0
7 TraesCS1B01G331500 chr1D 87.250 800 87 6 868 1665 413359768 413358982 0.000000e+00 898.0
8 TraesCS1B01G331500 chr1D 87.192 609 56 11 1178 1778 413297941 413297347 0.000000e+00 673.0
9 TraesCS1B01G331500 chr1D 82.229 664 84 17 753 1408 413319370 413318733 2.480000e-150 542.0
10 TraesCS1B01G331500 chr1D 81.308 535 88 9 2310 2834 32758964 32759496 9.390000e-115 424.0
11 TraesCS1B01G331500 chr1D 82.262 451 68 9 376 820 413373712 413373268 2.060000e-101 379.0
12 TraesCS1B01G331500 chr1D 90.244 205 11 3 1988 2191 413232947 413232751 2.800000e-65 259.0
13 TraesCS1B01G331500 chr1D 82.895 228 27 3 375 601 413319632 413319416 8.010000e-46 195.0
14 TraesCS1B01G331500 chr1A 91.380 1659 125 7 255 1895 510343322 510341664 0.000000e+00 2255.0
15 TraesCS1B01G331500 chr1A 87.881 1411 151 13 376 1778 510354283 510352885 0.000000e+00 1640.0
16 TraesCS1B01G331500 chr1A 83.721 688 95 12 376 1059 510292967 510293641 3.980000e-178 634.0
17 TraesCS1B01G331500 chr1A 88.158 152 16 2 102 253 510345230 510345081 2.240000e-41 180.0
18 TraesCS1B01G331500 chr1A 80.729 192 24 6 2030 2214 510320362 510320177 1.370000e-28 137.0
19 TraesCS1B01G331500 chr1A 100.000 29 0 0 1958 1986 487569978 487569950 1.000000e-03 54.7
20 TraesCS1B01G331500 chr7A 84.582 1401 185 20 375 1771 62279350 62277977 0.000000e+00 1362.0
21 TraesCS1B01G331500 chr7A 75.271 461 96 14 2218 2665 646843592 646843137 1.330000e-48 204.0
22 TraesCS1B01G331500 chr2A 88.927 578 52 4 1330 1895 754464720 754464143 0.000000e+00 702.0
23 TraesCS1B01G331500 chr2B 82.264 530 85 6 2310 2834 399839093 399839618 1.550000e-122 449.0
24 TraesCS1B01G331500 chr2B 77.802 455 92 5 2377 2824 707976529 707976981 3.600000e-69 272.0
25 TraesCS1B01G331500 chr2B 76.324 321 72 2 2377 2693 382936334 382936654 4.860000e-38 169.0
26 TraesCS1B01G331500 chr2D 82.136 515 87 3 2316 2825 603132672 603132158 1.210000e-118 436.0
27 TraesCS1B01G331500 chr2D 78.390 472 70 15 2226 2667 600438983 600439452 7.730000e-71 278.0
28 TraesCS1B01G331500 chr6D 81.698 530 85 10 2310 2832 264689745 264690269 5.610000e-117 431.0
29 TraesCS1B01G331500 chr5D 81.157 536 85 10 2310 2834 118004990 118005520 1.570000e-112 416.0
30 TraesCS1B01G331500 chr5A 72.798 1408 302 54 383 1752 584716390 584717754 1.220000e-108 403.0
31 TraesCS1B01G331500 chr5A 93.519 108 5 2 1 107 35513011 35513117 2.920000e-35 159.0
32 TraesCS1B01G331500 chr3A 80.340 529 96 5 2310 2832 681330717 681331243 7.360000e-106 394.0
33 TraesCS1B01G331500 chr3A 76.136 352 78 4 2381 2727 544165076 544165426 2.240000e-41 180.0
34 TraesCS1B01G331500 chr3A 93.458 107 6 1 1 107 371626610 371626715 1.050000e-34 158.0
35 TraesCS1B01G331500 chr3A 100.000 28 0 0 1958 1985 697785761 697785788 5.000000e-03 52.8
36 TraesCS1B01G331500 chr7D 80.074 537 90 14 2310 2834 227296934 227296403 1.590000e-102 383.0
37 TraesCS1B01G331500 chr7D 97.143 35 1 0 1924 1958 52708862 52708828 3.050000e-05 60.2
38 TraesCS1B01G331500 chr3B 80.114 528 94 7 2314 2834 778307156 778306633 1.590000e-102 383.0
39 TraesCS1B01G331500 chr3B 95.146 103 5 0 1 103 421050619 421050721 2.260000e-36 163.0
40 TraesCS1B01G331500 chr6B 77.974 622 128 7 2219 2834 394300820 394301438 5.730000e-102 381.0
41 TraesCS1B01G331500 chr6B 94.393 107 5 1 1 107 224288724 224288829 2.260000e-36 163.0
42 TraesCS1B01G331500 chr4B 95.146 103 5 0 1 103 625997568 625997466 2.260000e-36 163.0
43 TraesCS1B01G331500 chr4B 93.458 107 7 0 1 107 515148792 515148686 2.920000e-35 159.0
44 TraesCS1B01G331500 chr5B 93.458 107 6 1 1 107 538274815 538274710 1.050000e-34 158.0
45 TraesCS1B01G331500 chrUn 89.256 121 11 2 1 120 23715037 23715156 1.760000e-32 150.0
46 TraesCS1B01G331500 chr3D 84.337 83 13 0 2259 2341 50422825 50422743 6.510000e-12 82.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G331500 chr1B 557409955 557412788 2833 True 5234.0 5234 100.000 1 2834 1 chr1B.!!$R3 2833
1 TraesCS1B01G331500 chr1B 557463007 557464402 1395 True 1554.0 1554 86.809 376 1778 1 chr1B.!!$R4 1402
2 TraesCS1B01G331500 chr1D 413224960 413226330 1370 False 1618.0 1618 87.997 376 1753 1 chr1D.!!$F2 1377
3 TraesCS1B01G331500 chr1D 413232751 413234724 1973 True 1361.5 2464 91.131 109 2191 2 chr1D.!!$R4 2082
4 TraesCS1B01G331500 chr1D 413358982 413359768 786 True 898.0 898 87.250 868 1665 1 chr1D.!!$R2 797
5 TraesCS1B01G331500 chr1D 413297347 413297941 594 True 673.0 673 87.192 1178 1778 1 chr1D.!!$R1 600
6 TraesCS1B01G331500 chr1D 32758964 32759496 532 False 424.0 424 81.308 2310 2834 1 chr1D.!!$F1 524
7 TraesCS1B01G331500 chr1D 413318733 413319632 899 True 368.5 542 82.562 375 1408 2 chr1D.!!$R5 1033
8 TraesCS1B01G331500 chr1A 510352885 510354283 1398 True 1640.0 1640 87.881 376 1778 1 chr1A.!!$R3 1402
9 TraesCS1B01G331500 chr1A 510341664 510345230 3566 True 1217.5 2255 89.769 102 1895 2 chr1A.!!$R4 1793
10 TraesCS1B01G331500 chr1A 510292967 510293641 674 False 634.0 634 83.721 376 1059 1 chr1A.!!$F1 683
11 TraesCS1B01G331500 chr7A 62277977 62279350 1373 True 1362.0 1362 84.582 375 1771 1 chr7A.!!$R1 1396
12 TraesCS1B01G331500 chr2A 754464143 754464720 577 True 702.0 702 88.927 1330 1895 1 chr2A.!!$R1 565
13 TraesCS1B01G331500 chr2B 399839093 399839618 525 False 449.0 449 82.264 2310 2834 1 chr2B.!!$F2 524
14 TraesCS1B01G331500 chr2D 603132158 603132672 514 True 436.0 436 82.136 2316 2825 1 chr2D.!!$R1 509
15 TraesCS1B01G331500 chr6D 264689745 264690269 524 False 431.0 431 81.698 2310 2832 1 chr6D.!!$F1 522
16 TraesCS1B01G331500 chr5D 118004990 118005520 530 False 416.0 416 81.157 2310 2834 1 chr5D.!!$F1 524
17 TraesCS1B01G331500 chr5A 584716390 584717754 1364 False 403.0 403 72.798 383 1752 1 chr5A.!!$F2 1369
18 TraesCS1B01G331500 chr3A 681330717 681331243 526 False 394.0 394 80.340 2310 2832 1 chr3A.!!$F3 522
19 TraesCS1B01G331500 chr7D 227296403 227296934 531 True 383.0 383 80.074 2310 2834 1 chr7D.!!$R2 524
20 TraesCS1B01G331500 chr3B 778306633 778307156 523 True 383.0 383 80.114 2314 2834 1 chr3B.!!$R1 520
21 TraesCS1B01G331500 chr6B 394300820 394301438 618 False 381.0 381 77.974 2219 2834 1 chr6B.!!$F2 615

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
291 2050 0.181587 TCCCAACCACGAGCTTCAAA 59.818 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 3748 0.036199 ATAAGCGGCCGGTGTTACAA 60.036 50.0 33.14 12.62 0.0 2.41 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
44 45 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
78 79 9.271828 ACATTCCTTTTTGTCCATTTTAATGAC 57.728 29.630 4.07 2.18 38.70 3.06
79 80 9.270640 CATTCCTTTTTGTCCATTTTAATGACA 57.729 29.630 4.07 4.41 38.70 3.58
80 81 9.844257 ATTCCTTTTTGTCCATTTTAATGACAA 57.156 25.926 4.07 9.25 38.70 3.18
81 82 8.885494 TCCTTTTTGTCCATTTTAATGACAAG 57.115 30.769 4.07 2.77 37.53 3.16
82 83 8.482128 TCCTTTTTGTCCATTTTAATGACAAGT 58.518 29.630 4.07 0.00 37.53 3.16
83 84 9.757227 CCTTTTTGTCCATTTTAATGACAAGTA 57.243 29.630 4.07 3.71 37.53 2.24
97 98 7.678947 AATGACAAGTATTTTCAGACAGAGG 57.321 36.000 0.00 0.00 0.00 3.69
98 99 5.551233 TGACAAGTATTTTCAGACAGAGGG 58.449 41.667 0.00 0.00 0.00 4.30
99 100 5.306937 TGACAAGTATTTTCAGACAGAGGGA 59.693 40.000 0.00 0.00 0.00 4.20
100 101 5.799213 ACAAGTATTTTCAGACAGAGGGAG 58.201 41.667 0.00 0.00 0.00 4.30
101 102 5.308237 ACAAGTATTTTCAGACAGAGGGAGT 59.692 40.000 0.00 0.00 0.00 3.85
102 103 6.497259 ACAAGTATTTTCAGACAGAGGGAGTA 59.503 38.462 0.00 0.00 0.00 2.59
103 104 7.181125 ACAAGTATTTTCAGACAGAGGGAGTAT 59.819 37.037 0.00 0.00 0.00 2.12
104 105 7.354751 AGTATTTTCAGACAGAGGGAGTATC 57.645 40.000 0.00 0.00 0.00 2.24
105 106 7.129425 AGTATTTTCAGACAGAGGGAGTATCT 58.871 38.462 0.00 0.00 33.73 1.98
106 107 8.282982 AGTATTTTCAGACAGAGGGAGTATCTA 58.717 37.037 0.00 0.00 33.73 1.98
107 108 9.084533 GTATTTTCAGACAGAGGGAGTATCTAT 57.915 37.037 0.00 0.00 33.73 1.98
198 199 2.158971 TGTGCTTCAGTTCAGTGCTACA 60.159 45.455 0.00 0.00 0.00 2.74
199 200 2.872245 GTGCTTCAGTTCAGTGCTACAA 59.128 45.455 0.00 0.00 0.00 2.41
208 209 3.678056 TCAGTGCTACAACTACCCAAG 57.322 47.619 0.00 0.00 0.00 3.61
209 210 2.969950 TCAGTGCTACAACTACCCAAGT 59.030 45.455 0.00 0.00 41.49 3.16
213 214 3.252458 GTGCTACAACTACCCAAGTTTGG 59.748 47.826 3.85 3.85 46.61 3.28
229 230 7.158021 CCAAGTTTGGCTCCATTATTTTACAA 58.842 34.615 0.00 0.00 42.21 2.41
234 235 8.520351 GTTTGGCTCCATTATTTTACAAGTACT 58.480 33.333 0.00 0.00 0.00 2.73
236 237 7.172342 TGGCTCCATTATTTTACAAGTACTGT 58.828 34.615 0.00 0.00 42.47 3.55
248 249 5.883503 ACAAGTACTGTAGTAGCTGAGAC 57.116 43.478 0.00 0.00 36.10 3.36
274 2032 0.721718 CTTCTTTGGCATCGACGTCC 59.278 55.000 10.58 0.00 0.00 4.79
290 2049 0.534203 GTCCCAACCACGAGCTTCAA 60.534 55.000 0.00 0.00 0.00 2.69
291 2050 0.181587 TCCCAACCACGAGCTTCAAA 59.818 50.000 0.00 0.00 0.00 2.69
349 2114 1.285023 CAGCACTCCAAAGCAGCAC 59.715 57.895 0.00 0.00 31.25 4.40
365 2130 1.203100 AGCACCAAGAAAATGGCCTCT 60.203 47.619 3.32 0.00 44.75 3.69
590 2376 1.105167 CGTCCGGATAGCCACCTACA 61.105 60.000 7.81 0.00 0.00 2.74
591 2377 1.339097 GTCCGGATAGCCACCTACAT 58.661 55.000 7.81 0.00 0.00 2.29
594 2380 1.000955 CCGGATAGCCACCTACATGTC 59.999 57.143 0.00 0.00 0.00 3.06
775 2564 4.223032 GTCCACTTCTTCTGGAACTCCATA 59.777 45.833 0.00 0.00 46.46 2.74
776 2565 4.223032 TCCACTTCTTCTGGAACTCCATAC 59.777 45.833 0.00 0.00 46.46 2.39
930 2741 1.568504 TTTCAGGCCCTGAGATACGT 58.431 50.000 14.22 0.00 41.75 3.57
1014 2831 4.445710 ATCATGGCGGGGCAAGCA 62.446 61.111 0.00 0.00 36.08 3.91
1071 2888 1.062845 GGAGAGCGAGTACTGCGAC 59.937 63.158 15.79 11.62 37.44 5.19
1213 3041 0.532573 CAGATGCTCGGTGGTGTACT 59.467 55.000 0.00 0.00 0.00 2.73
1254 3082 3.891805 TCCATCTCTGGAGATCAGCTA 57.108 47.619 9.84 0.00 46.95 3.32
1524 3366 1.541379 TCGACCAGTTCATCGAGGAA 58.459 50.000 8.70 8.70 42.18 3.36
1778 3629 4.508124 GCTTATCGACGACCTGATGAAAAT 59.492 41.667 0.00 0.00 0.00 1.82
1876 3748 3.886505 TGCTTCAATCCGTTTGTAAACCT 59.113 39.130 2.19 0.00 36.65 3.50
1895 3767 0.036199 TTGTAACACCGGCCGCTTAT 60.036 50.000 22.85 8.39 0.00 1.73
1896 3768 0.741574 TGTAACACCGGCCGCTTATG 60.742 55.000 22.85 16.99 0.00 1.90
1897 3769 0.741927 GTAACACCGGCCGCTTATGT 60.742 55.000 22.85 17.68 0.00 2.29
1898 3770 0.460635 TAACACCGGCCGCTTATGTC 60.461 55.000 22.85 0.00 0.00 3.06
1899 3771 2.180159 AACACCGGCCGCTTATGTCT 62.180 55.000 22.85 8.84 0.00 3.41
1901 3773 0.179094 CACCGGCCGCTTATGTCTTA 60.179 55.000 22.85 0.00 0.00 2.10
1902 3774 0.179092 ACCGGCCGCTTATGTCTTAC 60.179 55.000 22.85 0.00 0.00 2.34
1904 3776 1.488527 CGGCCGCTTATGTCTTACTC 58.511 55.000 14.67 0.00 0.00 2.59
1905 3777 1.867166 GGCCGCTTATGTCTTACTCC 58.133 55.000 0.00 0.00 0.00 3.85
1906 3778 1.540580 GGCCGCTTATGTCTTACTCCC 60.541 57.143 0.00 0.00 0.00 4.30
1907 3779 1.413077 GCCGCTTATGTCTTACTCCCT 59.587 52.381 0.00 0.00 0.00 4.20
1908 3780 2.546162 GCCGCTTATGTCTTACTCCCTC 60.546 54.545 0.00 0.00 0.00 4.30
1909 3781 2.036089 CCGCTTATGTCTTACTCCCTCC 59.964 54.545 0.00 0.00 0.00 4.30
1910 3782 2.287668 CGCTTATGTCTTACTCCCTCCG 60.288 54.545 0.00 0.00 0.00 4.63
1911 3783 2.957006 GCTTATGTCTTACTCCCTCCGA 59.043 50.000 0.00 0.00 0.00 4.55
1912 3784 3.243468 GCTTATGTCTTACTCCCTCCGAC 60.243 52.174 0.00 0.00 0.00 4.79
1913 3785 1.777941 ATGTCTTACTCCCTCCGACC 58.222 55.000 0.00 0.00 0.00 4.79
1914 3786 0.324091 TGTCTTACTCCCTCCGACCC 60.324 60.000 0.00 0.00 0.00 4.46
1915 3787 0.324091 GTCTTACTCCCTCCGACCCA 60.324 60.000 0.00 0.00 0.00 4.51
1916 3788 0.635009 TCTTACTCCCTCCGACCCAT 59.365 55.000 0.00 0.00 0.00 4.00
1917 3789 1.854939 TCTTACTCCCTCCGACCCATA 59.145 52.381 0.00 0.00 0.00 2.74
1918 3790 2.245546 TCTTACTCCCTCCGACCCATAA 59.754 50.000 0.00 0.00 0.00 1.90
1919 3791 3.116862 TCTTACTCCCTCCGACCCATAAT 60.117 47.826 0.00 0.00 0.00 1.28
1920 3792 1.424638 ACTCCCTCCGACCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1921 3793 1.344087 ACTCCCTCCGACCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
1922 3794 1.070758 CTCCCTCCGACCCATAATGTG 59.929 57.143 0.00 0.00 0.00 3.21
1923 3795 1.128200 CCCTCCGACCCATAATGTGA 58.872 55.000 0.00 0.00 0.00 3.58
1924 3796 1.202651 CCCTCCGACCCATAATGTGAC 60.203 57.143 0.00 0.00 0.00 3.67
1925 3797 1.484653 CCTCCGACCCATAATGTGACA 59.515 52.381 0.00 0.00 0.00 3.58
1926 3798 2.104792 CCTCCGACCCATAATGTGACAT 59.895 50.000 0.00 0.00 0.00 3.06
1927 3799 3.433598 CCTCCGACCCATAATGTGACATT 60.434 47.826 15.80 15.80 0.00 2.71
1928 3800 4.202315 CCTCCGACCCATAATGTGACATTA 60.202 45.833 19.14 19.14 0.00 1.90
1929 3801 4.699637 TCCGACCCATAATGTGACATTAC 58.300 43.478 19.22 6.51 0.00 1.89
1930 3802 4.162509 TCCGACCCATAATGTGACATTACA 59.837 41.667 19.22 1.62 34.63 2.41
1931 3803 5.063204 CCGACCCATAATGTGACATTACAT 58.937 41.667 19.22 4.06 42.82 2.29
1971 3843 9.908152 TGTCTTACATTATACATTATGAGACGG 57.092 33.333 0.00 0.00 32.49 4.79
1974 3846 9.574458 CTTACATTATACATTATGAGACGGAGG 57.426 37.037 0.00 0.00 0.00 4.30
1975 3847 6.936279 ACATTATACATTATGAGACGGAGGG 58.064 40.000 0.00 0.00 0.00 4.30
1976 3848 6.724441 ACATTATACATTATGAGACGGAGGGA 59.276 38.462 0.00 0.00 0.00 4.20
1977 3849 6.835819 TTATACATTATGAGACGGAGGGAG 57.164 41.667 0.00 0.00 0.00 4.30
1978 3850 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
1979 3851 4.180377 ACATTATGAGACGGAGGGAGTA 57.820 45.455 0.00 0.00 0.00 2.59
1980 3852 3.890147 ACATTATGAGACGGAGGGAGTAC 59.110 47.826 0.00 0.00 0.00 2.73
1981 3853 3.947612 TTATGAGACGGAGGGAGTACT 57.052 47.619 0.00 0.00 0.00 2.73
1982 3854 5.163120 ACATTATGAGACGGAGGGAGTACTA 60.163 44.000 0.00 0.00 0.00 1.82
1983 3855 5.579753 TTATGAGACGGAGGGAGTACTAT 57.420 43.478 0.00 0.00 0.00 2.12
1986 3858 3.053842 TGAGACGGAGGGAGTACTATGTT 60.054 47.826 0.00 0.00 0.00 2.71
2012 3885 5.656213 TCCTTTGCCTACTAACTAGTGTC 57.344 43.478 0.00 0.00 37.10 3.67
2067 3940 3.460103 GCATCTGCATTTACATTTGGGG 58.540 45.455 0.00 0.00 41.59 4.96
2069 3942 1.476085 TCTGCATTTACATTTGGGGCG 59.524 47.619 0.00 0.00 0.00 6.13
2071 3944 0.534873 GCATTTACATTTGGGGCGGT 59.465 50.000 0.00 0.00 0.00 5.68
2072 3945 1.470805 GCATTTACATTTGGGGCGGTC 60.471 52.381 0.00 0.00 0.00 4.79
2073 3946 2.099405 CATTTACATTTGGGGCGGTCT 58.901 47.619 0.00 0.00 0.00 3.85
2074 3947 3.283751 CATTTACATTTGGGGCGGTCTA 58.716 45.455 0.00 0.00 0.00 2.59
2075 3948 3.655615 TTTACATTTGGGGCGGTCTAT 57.344 42.857 0.00 0.00 0.00 1.98
2076 3949 2.631160 TACATTTGGGGCGGTCTATG 57.369 50.000 0.00 0.00 0.00 2.23
2077 3950 0.751643 ACATTTGGGGCGGTCTATGC 60.752 55.000 0.00 0.00 0.00 3.14
2078 3951 1.525995 ATTTGGGGCGGTCTATGCG 60.526 57.895 0.00 0.00 0.00 4.73
2079 3952 4.849310 TTGGGGCGGTCTATGCGC 62.849 66.667 0.00 0.00 43.79 6.09
2120 3993 1.079543 GCTCTGTCTGCACCGATGT 60.080 57.895 0.00 0.00 0.00 3.06
2124 3997 1.202348 TCTGTCTGCACCGATGTACAG 59.798 52.381 0.33 3.46 37.23 2.74
2131 4004 0.532573 CACCGATGTACAGCTGGTCT 59.467 55.000 19.93 0.00 0.00 3.85
2132 4005 1.066858 CACCGATGTACAGCTGGTCTT 60.067 52.381 19.93 8.46 0.00 3.01
2151 4024 3.588842 TCTTGAAACATCACCATCTCCCT 59.411 43.478 0.00 0.00 0.00 4.20
2184 4057 8.026026 TCGAAATGCAAAAGCAGAATTTGTATA 58.974 29.630 0.00 0.00 40.61 1.47
2191 4064 9.443283 GCAAAAGCAGAATTTGTATATCTGTAG 57.557 33.333 4.19 0.00 42.00 2.74
2192 4065 9.941664 CAAAAGCAGAATTTGTATATCTGTAGG 57.058 33.333 4.19 0.00 42.00 3.18
2193 4066 9.905713 AAAAGCAGAATTTGTATATCTGTAGGA 57.094 29.630 4.19 0.00 42.00 2.94
2194 4067 9.905713 AAAGCAGAATTTGTATATCTGTAGGAA 57.094 29.630 4.19 0.00 42.00 3.36
2195 4068 9.905713 AAGCAGAATTTGTATATCTGTAGGAAA 57.094 29.630 4.19 0.00 42.00 3.13
2196 4069 9.331282 AGCAGAATTTGTATATCTGTAGGAAAC 57.669 33.333 4.19 0.00 42.00 2.78
2197 4070 9.109393 GCAGAATTTGTATATCTGTAGGAAACA 57.891 33.333 4.19 0.00 42.00 2.83
2204 4077 9.542462 TTGTATATCTGTAGGAAACATAGTTGC 57.458 33.333 0.00 0.00 37.50 4.17
2205 4078 8.700973 TGTATATCTGTAGGAAACATAGTTGCA 58.299 33.333 0.00 0.00 37.50 4.08
2206 4079 9.197694 GTATATCTGTAGGAAACATAGTTGCAG 57.802 37.037 0.00 0.00 37.50 4.41
2207 4080 4.832248 TCTGTAGGAAACATAGTTGCAGG 58.168 43.478 0.00 0.00 37.50 4.85
2208 4081 4.286032 TCTGTAGGAAACATAGTTGCAGGT 59.714 41.667 0.00 0.00 37.50 4.00
2209 4082 4.980573 TGTAGGAAACATAGTTGCAGGTT 58.019 39.130 0.00 0.00 31.43 3.50
2210 4083 4.759693 TGTAGGAAACATAGTTGCAGGTTG 59.240 41.667 0.00 0.00 31.43 3.77
2211 4084 3.832527 AGGAAACATAGTTGCAGGTTGT 58.167 40.909 0.00 0.00 0.00 3.32
2212 4085 4.215109 AGGAAACATAGTTGCAGGTTGTT 58.785 39.130 0.00 0.00 32.19 2.83
2213 4086 5.381757 AGGAAACATAGTTGCAGGTTGTTA 58.618 37.500 6.77 0.00 30.76 2.41
2214 4087 5.830991 AGGAAACATAGTTGCAGGTTGTTAA 59.169 36.000 6.77 0.00 30.76 2.01
2215 4088 6.322712 AGGAAACATAGTTGCAGGTTGTTAAA 59.677 34.615 6.77 0.00 30.76 1.52
2216 4089 6.640907 GGAAACATAGTTGCAGGTTGTTAAAG 59.359 38.462 6.77 0.00 30.76 1.85
2217 4090 5.121221 ACATAGTTGCAGGTTGTTAAAGC 57.879 39.130 0.00 0.00 0.00 3.51
2229 4102 1.003118 TGTTAAAGCAGCCTCGATGGT 59.997 47.619 0.00 0.00 38.35 3.55
2236 4109 1.303309 CAGCCTCGATGGTCAAATCC 58.697 55.000 0.00 0.00 38.35 3.01
2238 4111 1.160329 GCCTCGATGGTCAAATCCGG 61.160 60.000 0.00 0.00 38.35 5.14
2239 4112 0.464036 CCTCGATGGTCAAATCCGGA 59.536 55.000 6.61 6.61 0.00 5.14
2248 4121 2.167662 GTCAAATCCGGACCCACAAAT 58.832 47.619 6.12 0.00 0.00 2.32
2252 4125 3.439540 CCGGACCCACAAATGCCG 61.440 66.667 0.00 0.00 41.53 5.69
2277 4150 2.341543 CGTCTGCTGGCACTGACT 59.658 61.111 17.69 0.00 36.63 3.41
2284 4157 0.819259 GCTGGCACTGACTGGTCAAA 60.819 55.000 4.94 0.00 39.39 2.69
2290 4163 2.917933 CACTGACTGGTCAAACCTCAA 58.082 47.619 4.94 0.00 39.58 3.02
2298 4171 4.832266 ACTGGTCAAACCTCAAATAATGCA 59.168 37.500 0.00 0.00 39.58 3.96
2301 4174 6.397272 TGGTCAAACCTCAAATAATGCAATC 58.603 36.000 0.00 0.00 39.58 2.67
2302 4175 6.211184 TGGTCAAACCTCAAATAATGCAATCT 59.789 34.615 0.00 0.00 39.58 2.40
2310 4183 7.994911 ACCTCAAATAATGCAATCTACATCTGA 59.005 33.333 0.00 0.00 0.00 3.27
2357 4232 2.603560 GCAACGTAGCGATCTTTAAGCT 59.396 45.455 0.00 0.00 44.24 3.74
2361 4236 3.128938 ACGTAGCGATCTTTAAGCTGAGT 59.871 43.478 2.68 0.62 41.80 3.41
2368 4243 4.932200 CGATCTTTAAGCTGAGTTTGTCCT 59.068 41.667 0.00 0.00 0.00 3.85
2374 4253 0.601311 GCTGAGTTTGTCCTGTCGCT 60.601 55.000 0.00 0.00 0.00 4.93
2413 4299 0.320596 AGCTGTGCTTCTCAGAGTGC 60.321 55.000 10.04 10.04 38.27 4.40
2422 4309 1.979155 CTCAGAGTGCTGGTCCGGA 60.979 63.158 0.00 0.00 42.53 5.14
2444 4331 2.720915 GTCGACAAGGTAGAGTAGGGT 58.279 52.381 11.55 0.00 0.00 4.34
2463 4350 2.915659 TGGGACACGAGTCGGCTT 60.916 61.111 18.30 0.00 45.92 4.35
2486 4373 2.203153 ACTCAAGGCGCCGTTGTT 60.203 55.556 26.93 14.10 0.00 2.83
2500 4387 1.884497 CGTTGTTTCCCATGCCCTACA 60.884 52.381 0.00 0.00 0.00 2.74
2563 4450 1.533994 AGGGCGATGATGGATCCGA 60.534 57.895 7.39 0.00 0.00 4.55
2564 4451 1.121407 AGGGCGATGATGGATCCGAA 61.121 55.000 7.39 0.00 0.00 4.30
2607 4494 4.884257 ACGACACAGTTGCGGCGT 62.884 61.111 9.37 0.00 0.00 5.68
2628 4519 2.737881 GGGTGCACTATACGGGGCA 61.738 63.158 17.98 0.00 0.00 5.36
2735 4626 0.456653 GTCGCACCATGTTTGCATCC 60.457 55.000 14.89 1.01 40.20 3.51
2739 4630 0.171007 CACCATGTTTGCATCCGACC 59.829 55.000 0.00 0.00 31.99 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
52 53 9.271828 GTCATTAAAATGGACAAAAAGGAATGT 57.728 29.630 3.00 0.00 37.03 2.71
53 54 9.270640 TGTCATTAAAATGGACAAAAAGGAATG 57.729 29.630 3.00 0.00 37.03 2.67
54 55 9.844257 TTGTCATTAAAATGGACAAAAAGGAAT 57.156 25.926 13.47 0.00 35.52 3.01
55 56 9.323985 CTTGTCATTAAAATGGACAAAAAGGAA 57.676 29.630 15.23 0.00 36.72 3.36
56 57 8.482128 ACTTGTCATTAAAATGGACAAAAAGGA 58.518 29.630 15.23 0.00 36.72 3.36
57 58 8.661352 ACTTGTCATTAAAATGGACAAAAAGG 57.339 30.769 15.23 9.93 36.72 3.11
71 72 9.219603 CCTCTGTCTGAAAATACTTGTCATTAA 57.780 33.333 0.00 0.00 0.00 1.40
72 73 7.824289 CCCTCTGTCTGAAAATACTTGTCATTA 59.176 37.037 0.00 0.00 0.00 1.90
73 74 6.656693 CCCTCTGTCTGAAAATACTTGTCATT 59.343 38.462 0.00 0.00 0.00 2.57
74 75 6.013379 TCCCTCTGTCTGAAAATACTTGTCAT 60.013 38.462 0.00 0.00 0.00 3.06
75 76 5.306937 TCCCTCTGTCTGAAAATACTTGTCA 59.693 40.000 0.00 0.00 0.00 3.58
76 77 5.794894 TCCCTCTGTCTGAAAATACTTGTC 58.205 41.667 0.00 0.00 0.00 3.18
77 78 5.308237 ACTCCCTCTGTCTGAAAATACTTGT 59.692 40.000 0.00 0.00 0.00 3.16
78 79 5.799213 ACTCCCTCTGTCTGAAAATACTTG 58.201 41.667 0.00 0.00 0.00 3.16
79 80 7.621683 AGATACTCCCTCTGTCTGAAAATACTT 59.378 37.037 0.00 0.00 0.00 2.24
80 81 7.129425 AGATACTCCCTCTGTCTGAAAATACT 58.871 38.462 0.00 0.00 0.00 2.12
81 82 7.354751 AGATACTCCCTCTGTCTGAAAATAC 57.645 40.000 0.00 0.00 0.00 1.89
82 83 9.083422 CATAGATACTCCCTCTGTCTGAAAATA 57.917 37.037 0.00 0.00 0.00 1.40
83 84 7.786943 TCATAGATACTCCCTCTGTCTGAAAAT 59.213 37.037 0.00 0.00 0.00 1.82
84 85 7.126061 TCATAGATACTCCCTCTGTCTGAAAA 58.874 38.462 0.00 0.00 0.00 2.29
85 86 6.673583 TCATAGATACTCCCTCTGTCTGAAA 58.326 40.000 0.00 0.00 0.00 2.69
86 87 6.267492 TCATAGATACTCCCTCTGTCTGAA 57.733 41.667 0.00 0.00 0.00 3.02
87 88 5.747545 GCTCATAGATACTCCCTCTGTCTGA 60.748 48.000 0.00 0.00 0.00 3.27
88 89 4.458989 GCTCATAGATACTCCCTCTGTCTG 59.541 50.000 0.00 0.00 0.00 3.51
89 90 4.353788 AGCTCATAGATACTCCCTCTGTCT 59.646 45.833 0.00 0.00 0.00 3.41
90 91 4.662278 AGCTCATAGATACTCCCTCTGTC 58.338 47.826 0.00 0.00 0.00 3.51
91 92 4.740154 AGCTCATAGATACTCCCTCTGT 57.260 45.455 0.00 0.00 0.00 3.41
92 93 5.324409 AGAAGCTCATAGATACTCCCTCTG 58.676 45.833 0.00 0.00 0.00 3.35
93 94 5.599048 AGAAGCTCATAGATACTCCCTCT 57.401 43.478 0.00 0.00 0.00 3.69
94 95 5.566627 GCAAGAAGCTCATAGATACTCCCTC 60.567 48.000 0.00 0.00 41.15 4.30
95 96 4.283212 GCAAGAAGCTCATAGATACTCCCT 59.717 45.833 0.00 0.00 41.15 4.20
96 97 4.565022 GCAAGAAGCTCATAGATACTCCC 58.435 47.826 0.00 0.00 41.15 4.30
208 209 8.520351 AGTACTTGTAAAATAATGGAGCCAAAC 58.480 33.333 0.00 0.00 0.00 2.93
209 210 8.519526 CAGTACTTGTAAAATAATGGAGCCAAA 58.480 33.333 0.00 0.00 0.00 3.28
213 214 9.379791 ACTACAGTACTTGTAAAATAATGGAGC 57.620 33.333 0.00 0.00 41.57 4.70
229 230 4.396790 GCAAGTCTCAGCTACTACAGTACT 59.603 45.833 0.00 0.00 0.00 2.73
234 235 4.082845 AGAAGCAAGTCTCAGCTACTACA 58.917 43.478 0.64 0.00 40.90 2.74
236 237 5.013547 AGAAGAAGCAAGTCTCAGCTACTA 58.986 41.667 0.64 0.00 40.90 1.82
242 243 3.058363 GCCAAAGAAGAAGCAAGTCTCAG 60.058 47.826 0.00 0.00 0.00 3.35
245 246 2.936202 TGCCAAAGAAGAAGCAAGTCT 58.064 42.857 0.00 0.00 30.97 3.24
248 249 2.485426 TCGATGCCAAAGAAGAAGCAAG 59.515 45.455 0.00 0.00 38.99 4.01
274 2032 1.200020 GGATTTGAAGCTCGTGGTTGG 59.800 52.381 6.65 0.00 33.64 3.77
290 2049 5.235305 CTTTTGTAGCATTAGCACGGATT 57.765 39.130 0.00 0.00 45.49 3.01
291 2050 4.882671 CTTTTGTAGCATTAGCACGGAT 57.117 40.909 0.00 0.00 45.49 4.18
349 2114 3.944015 CTCTGTAGAGGCCATTTTCTTGG 59.056 47.826 5.01 0.00 38.48 3.61
365 2130 1.079819 GCCGTGCTCTTGCTCTGTA 60.080 57.895 0.00 0.00 40.48 2.74
393 2158 0.692419 AAGGGCACGATCAGGATCCT 60.692 55.000 9.02 9.02 34.40 3.24
859 2660 1.334992 CGCCGTCGACTGTAACTGTG 61.335 60.000 14.70 0.00 38.10 3.66
860 2661 1.081641 CGCCGTCGACTGTAACTGT 60.082 57.895 14.70 0.00 38.10 3.55
861 2662 1.208358 TCGCCGTCGACTGTAACTG 59.792 57.895 14.70 0.00 40.21 3.16
862 2663 3.659334 TCGCCGTCGACTGTAACT 58.341 55.556 14.70 0.00 40.21 2.24
930 2741 1.834378 CAGCTCAGCCCTCGGGATA 60.834 63.158 6.08 0.00 37.50 2.59
955 2766 4.468153 GTCTTTCTCCTGGTACCTCAAGAT 59.532 45.833 14.36 0.00 0.00 2.40
1014 2831 3.621892 GACTACGCCGAAGCACCGT 62.622 63.158 0.00 0.00 39.83 4.83
1015 2832 2.879462 GACTACGCCGAAGCACCG 60.879 66.667 0.00 0.00 39.83 4.94
1157 2982 2.887568 GGATGCACGGCGACTCAG 60.888 66.667 16.62 0.00 0.00 3.35
1254 3082 1.617536 TCCAAGAGCCAGCTCCCAT 60.618 57.895 15.87 0.41 43.70 4.00
1524 3366 0.249911 GAACGTCTGTGACCAGCCTT 60.250 55.000 0.00 0.00 38.66 4.35
1876 3748 0.036199 ATAAGCGGCCGGTGTTACAA 60.036 50.000 33.14 12.62 0.00 2.41
1895 3767 0.324091 GGGTCGGAGGGAGTAAGACA 60.324 60.000 0.00 0.00 33.84 3.41
1896 3768 0.324091 TGGGTCGGAGGGAGTAAGAC 60.324 60.000 0.00 0.00 0.00 3.01
1897 3769 0.635009 ATGGGTCGGAGGGAGTAAGA 59.365 55.000 0.00 0.00 0.00 2.10
1898 3770 2.376695 TATGGGTCGGAGGGAGTAAG 57.623 55.000 0.00 0.00 0.00 2.34
1899 3771 2.852714 TTATGGGTCGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
1901 3773 1.344087 ACATTATGGGTCGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
1902 3774 1.070758 CACATTATGGGTCGGAGGGAG 59.929 57.143 0.00 0.00 0.00 4.30
1904 3776 1.128200 TCACATTATGGGTCGGAGGG 58.872 55.000 0.00 0.00 0.00 4.30
1905 3777 1.484653 TGTCACATTATGGGTCGGAGG 59.515 52.381 0.00 0.00 0.00 4.30
1906 3778 2.979814 TGTCACATTATGGGTCGGAG 57.020 50.000 0.00 0.00 0.00 4.63
1907 3779 3.924114 AATGTCACATTATGGGTCGGA 57.076 42.857 0.00 0.00 0.00 4.55
1908 3780 4.447290 TGTAATGTCACATTATGGGTCGG 58.553 43.478 13.42 0.00 0.00 4.79
1909 3781 6.618287 AATGTAATGTCACATTATGGGTCG 57.382 37.500 13.42 0.00 45.13 4.79
1910 3782 9.897744 CATTAATGTAATGTCACATTATGGGTC 57.102 33.333 13.42 1.26 45.86 4.46
1945 3817 9.908152 CCGTCTCATAATGTATAATGTAAGACA 57.092 33.333 0.00 0.00 0.00 3.41
1948 3820 9.574458 CCTCCGTCTCATAATGTATAATGTAAG 57.426 37.037 0.00 0.00 0.00 2.34
1949 3821 8.528643 CCCTCCGTCTCATAATGTATAATGTAA 58.471 37.037 0.00 0.00 0.00 2.41
1950 3822 7.891712 TCCCTCCGTCTCATAATGTATAATGTA 59.108 37.037 0.00 0.00 0.00 2.29
1951 3823 6.724441 TCCCTCCGTCTCATAATGTATAATGT 59.276 38.462 0.00 0.00 0.00 2.71
1952 3824 7.093727 ACTCCCTCCGTCTCATAATGTATAATG 60.094 40.741 0.00 0.00 0.00 1.90
1953 3825 6.954684 ACTCCCTCCGTCTCATAATGTATAAT 59.045 38.462 0.00 0.00 0.00 1.28
1954 3826 6.312529 ACTCCCTCCGTCTCATAATGTATAA 58.687 40.000 0.00 0.00 0.00 0.98
1955 3827 5.888901 ACTCCCTCCGTCTCATAATGTATA 58.111 41.667 0.00 0.00 0.00 1.47
1956 3828 4.742012 ACTCCCTCCGTCTCATAATGTAT 58.258 43.478 0.00 0.00 0.00 2.29
1957 3829 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
1958 3830 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
1959 3831 4.145807 AGTACTCCCTCCGTCTCATAATG 58.854 47.826 0.00 0.00 0.00 1.90
1960 3832 4.456662 AGTACTCCCTCCGTCTCATAAT 57.543 45.455 0.00 0.00 0.00 1.28
1961 3833 3.947612 AGTACTCCCTCCGTCTCATAA 57.052 47.619 0.00 0.00 0.00 1.90
1962 3834 4.350225 ACATAGTACTCCCTCCGTCTCATA 59.650 45.833 0.00 0.00 0.00 2.15
1963 3835 3.138653 ACATAGTACTCCCTCCGTCTCAT 59.861 47.826 0.00 0.00 0.00 2.90
1964 3836 2.508716 ACATAGTACTCCCTCCGTCTCA 59.491 50.000 0.00 0.00 0.00 3.27
1965 3837 3.211718 ACATAGTACTCCCTCCGTCTC 57.788 52.381 0.00 0.00 0.00 3.36
1966 3838 3.666345 AACATAGTACTCCCTCCGTCT 57.334 47.619 0.00 0.00 0.00 4.18
1967 3839 4.732672 AAAACATAGTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
1986 3858 7.284820 ACACTAGTTAGTAGGCAAAGGAAAAA 58.715 34.615 0.00 0.00 34.13 1.94
1990 3862 5.185249 CAGACACTAGTTAGTAGGCAAAGGA 59.815 44.000 0.00 0.00 34.13 3.36
2012 3885 1.202639 TGCAGTACCAACAGGTGACAG 60.203 52.381 0.00 0.00 36.84 3.51
2069 3942 1.336332 ACGAGATGATGCGCATAGACC 60.336 52.381 25.40 11.61 37.34 3.85
2071 3944 2.800881 AACGAGATGATGCGCATAGA 57.199 45.000 25.40 13.74 37.34 1.98
2072 3945 3.867055 AAAACGAGATGATGCGCATAG 57.133 42.857 25.40 12.67 37.34 2.23
2073 3946 3.181575 CGTAAAACGAGATGATGCGCATA 59.818 43.478 25.40 12.30 46.05 3.14
2074 3947 2.033747 CGTAAAACGAGATGATGCGCAT 60.034 45.455 25.66 25.66 46.05 4.73
2075 3948 1.323235 CGTAAAACGAGATGATGCGCA 59.677 47.619 14.96 14.96 46.05 6.09
2076 3949 1.911709 GCGTAAAACGAGATGATGCGC 60.912 52.381 0.00 0.00 46.05 6.09
2077 3950 1.332028 GGCGTAAAACGAGATGATGCG 60.332 52.381 3.22 0.00 46.05 4.73
2078 3951 1.933853 AGGCGTAAAACGAGATGATGC 59.066 47.619 3.22 0.00 46.05 3.91
2079 3952 2.285220 CCAGGCGTAAAACGAGATGATG 59.715 50.000 3.22 0.00 46.05 3.07
2080 3953 2.550978 CCAGGCGTAAAACGAGATGAT 58.449 47.619 3.22 0.00 46.05 2.45
2120 3993 4.065088 GTGATGTTTCAAGACCAGCTGTA 58.935 43.478 13.81 0.00 32.48 2.74
2124 3997 2.229792 TGGTGATGTTTCAAGACCAGC 58.770 47.619 0.00 0.00 32.48 4.85
2131 4004 4.081406 CAAGGGAGATGGTGATGTTTCAA 58.919 43.478 0.00 0.00 32.48 2.69
2132 4005 3.689347 CAAGGGAGATGGTGATGTTTCA 58.311 45.455 0.00 0.00 0.00 2.69
2151 4024 2.408032 GCTTTTGCATTTCGAATCGCAA 59.592 40.909 23.33 23.33 46.58 4.85
2184 4057 5.045578 ACCTGCAACTATGTTTCCTACAGAT 60.046 40.000 0.00 0.00 40.83 2.90
2191 4064 4.584327 AACAACCTGCAACTATGTTTCC 57.416 40.909 0.00 0.00 30.50 3.13
2192 4065 6.143919 GCTTTAACAACCTGCAACTATGTTTC 59.856 38.462 10.76 0.00 35.89 2.78
2193 4066 5.983118 GCTTTAACAACCTGCAACTATGTTT 59.017 36.000 10.76 0.00 35.89 2.83
2194 4067 5.068460 TGCTTTAACAACCTGCAACTATGTT 59.932 36.000 10.45 10.45 37.86 2.71
2195 4068 4.582656 TGCTTTAACAACCTGCAACTATGT 59.417 37.500 0.00 0.00 0.00 2.29
2196 4069 5.119931 TGCTTTAACAACCTGCAACTATG 57.880 39.130 0.00 0.00 0.00 2.23
2197 4070 4.321230 GCTGCTTTAACAACCTGCAACTAT 60.321 41.667 0.00 0.00 33.07 2.12
2198 4071 3.004315 GCTGCTTTAACAACCTGCAACTA 59.996 43.478 0.00 0.00 33.07 2.24
2199 4072 2.223805 GCTGCTTTAACAACCTGCAACT 60.224 45.455 0.00 0.00 33.07 3.16
2200 4073 2.127251 GCTGCTTTAACAACCTGCAAC 58.873 47.619 0.00 0.00 33.07 4.17
2201 4074 1.068434 GGCTGCTTTAACAACCTGCAA 59.932 47.619 0.00 0.00 33.07 4.08
2202 4075 0.673437 GGCTGCTTTAACAACCTGCA 59.327 50.000 0.00 0.00 0.00 4.41
2203 4076 0.961753 AGGCTGCTTTAACAACCTGC 59.038 50.000 0.00 0.00 34.81 4.85
2204 4077 1.197721 CGAGGCTGCTTTAACAACCTG 59.802 52.381 0.00 0.00 36.26 4.00
2205 4078 1.071699 TCGAGGCTGCTTTAACAACCT 59.928 47.619 0.00 0.00 38.85 3.50
2206 4079 1.519408 TCGAGGCTGCTTTAACAACC 58.481 50.000 0.00 0.00 0.00 3.77
2207 4080 2.159517 CCATCGAGGCTGCTTTAACAAC 60.160 50.000 0.00 0.00 0.00 3.32
2208 4081 2.083774 CCATCGAGGCTGCTTTAACAA 58.916 47.619 0.00 0.00 0.00 2.83
2209 4082 1.003118 ACCATCGAGGCTGCTTTAACA 59.997 47.619 0.00 0.00 43.14 2.41
2210 4083 1.666189 GACCATCGAGGCTGCTTTAAC 59.334 52.381 0.00 0.00 43.14 2.01
2211 4084 1.277842 TGACCATCGAGGCTGCTTTAA 59.722 47.619 0.00 0.00 43.14 1.52
2212 4085 0.901827 TGACCATCGAGGCTGCTTTA 59.098 50.000 0.00 0.00 43.14 1.85
2213 4086 0.036732 TTGACCATCGAGGCTGCTTT 59.963 50.000 0.00 0.00 43.14 3.51
2214 4087 0.036732 TTTGACCATCGAGGCTGCTT 59.963 50.000 0.00 0.00 43.14 3.91
2215 4088 0.254178 ATTTGACCATCGAGGCTGCT 59.746 50.000 0.00 0.00 43.14 4.24
2216 4089 0.659957 GATTTGACCATCGAGGCTGC 59.340 55.000 0.00 0.00 43.14 5.25
2217 4090 1.303309 GGATTTGACCATCGAGGCTG 58.697 55.000 0.00 0.00 43.14 4.85
2222 4095 3.752796 GTCCGGATTTGACCATCGA 57.247 52.632 7.81 0.00 0.00 3.59
2229 4102 2.166829 CATTTGTGGGTCCGGATTTGA 58.833 47.619 7.81 0.00 0.00 2.69
2236 4109 3.439540 CCGGCATTTGTGGGTCCG 61.440 66.667 0.00 0.00 39.79 4.79
2238 4111 4.114997 CGCCGGCATTTGTGGGTC 62.115 66.667 28.98 0.00 0.00 4.46
2239 4112 4.652131 TCGCCGGCATTTGTGGGT 62.652 61.111 28.98 0.00 0.00 4.51
2241 4114 2.126502 GTTCGCCGGCATTTGTGG 60.127 61.111 28.98 8.23 0.00 4.17
2242 4115 2.501650 CGTTCGCCGGCATTTGTG 60.502 61.111 28.98 9.08 0.00 3.33
2243 4116 4.398598 GCGTTCGCCGGCATTTGT 62.399 61.111 28.98 0.00 36.94 2.83
2264 4137 1.981951 TTGACCAGTCAGTGCCAGCA 61.982 55.000 0.09 0.00 41.13 4.41
2267 4140 0.465460 GGTTTGACCAGTCAGTGCCA 60.465 55.000 0.09 0.00 41.13 4.92
2269 4142 1.230324 GAGGTTTGACCAGTCAGTGC 58.770 55.000 0.09 0.00 41.95 4.40
2277 4150 5.798125 TTGCATTATTTGAGGTTTGACCA 57.202 34.783 0.00 0.00 41.95 4.02
2284 4157 7.994911 TCAGATGTAGATTGCATTATTTGAGGT 59.005 33.333 0.00 0.00 0.00 3.85
2298 4171 8.717717 TGGATTTGAGGTATTCAGATGTAGATT 58.282 33.333 0.00 0.00 37.07 2.40
2357 4232 0.464036 ACAGCGACAGGACAAACTCA 59.536 50.000 0.00 0.00 0.00 3.41
2361 4236 1.891919 GCCACAGCGACAGGACAAA 60.892 57.895 0.00 0.00 0.00 2.83
2368 4243 2.358615 GACATGGCCACAGCGACA 60.359 61.111 8.16 0.00 41.24 4.35
2405 4291 2.117423 TCCGGACCAGCACTCTGA 59.883 61.111 0.00 0.00 42.95 3.27
2413 4299 2.797866 CTTGTCGACGTCCGGACCAG 62.798 65.000 28.52 17.85 39.14 4.00
2422 4309 2.354259 CCTACTCTACCTTGTCGACGT 58.646 52.381 11.62 5.43 0.00 4.34
2444 4331 0.968901 AAGCCGACTCGTGTCCCATA 60.969 55.000 11.74 0.00 39.94 2.74
2457 4344 0.830648 CCTTGAGTCCCATAAGCCGA 59.169 55.000 0.00 0.00 0.00 5.54
2463 4350 2.908015 GGCGCCTTGAGTCCCATA 59.092 61.111 22.15 0.00 0.00 2.74
2482 4369 1.427368 AGTGTAGGGCATGGGAAACAA 59.573 47.619 0.00 0.00 0.00 2.83
2486 4373 0.623723 GGAAGTGTAGGGCATGGGAA 59.376 55.000 0.00 0.00 0.00 3.97
2500 4387 4.070552 GGGCTGCGACGAGGAAGT 62.071 66.667 0.00 0.00 0.00 3.01
2547 4434 0.034059 AGTTCGGATCCATCATCGCC 59.966 55.000 13.41 0.00 31.26 5.54
2548 4435 2.600731 CTAGTTCGGATCCATCATCGC 58.399 52.381 13.41 0.00 31.26 4.58
2563 4450 3.823330 CGCCGGCTCGTCCTAGTT 61.823 66.667 26.68 0.00 0.00 2.24
2581 4468 0.944386 AACTGTGTCGTTGTGGATGC 59.056 50.000 0.00 0.00 0.00 3.91
2589 4476 3.636043 CGCCGCAACTGTGTCGTT 61.636 61.111 0.00 0.00 0.00 3.85
2607 4494 2.129146 CCCGTATAGTGCACCCGGA 61.129 63.158 26.71 8.28 41.08 5.14
2796 4688 1.511305 GTCTGGCATCCGAACGAGA 59.489 57.895 0.00 0.00 0.00 4.04
2798 4690 2.180769 CGTCTGGCATCCGAACGA 59.819 61.111 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.