Multiple sequence alignment - TraesCS7A01G055200

Loading Multiple Alignment...

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 TraesCS7A01G055200 chr7A 100.000 2647 0 0 1 2647 26666194 26663548 0.000000e+00 4889.0
1 TraesCS7A01G055200 chr7A 86.620 142 17 2 2507 2647 589466548 589466408 3.530000e-34 156.0
2 TraesCS7A01G055200 chr7A 75.771 227 46 7 4 227 121554422 121554202 3.600000e-19 106.0
3 TraesCS7A01G055200 chr4A 92.498 1493 87 17 1014 2499 710174873 710173399 0.000000e+00 2113.0
4 TraesCS7A01G055200 chr4A 84.793 605 50 20 1 575 710176048 710175456 1.060000e-158 569.0
5 TraesCS7A01G055200 chr4A 85.832 487 30 26 583 1033 710175364 710174881 5.120000e-132 481.0
6 TraesCS7A01G055200 chr4A 90.299 134 12 1 2512 2644 478168588 478168721 9.740000e-40 174.0
7 TraesCS7A01G055200 chr4A 78.750 160 31 2 1088 1244 625634244 625634403 1.300000e-18 104.0
8 TraesCS7A01G055200 chr4A 78.616 159 31 2 1089 1244 593204592 593204750 4.660000e-18 102.0
9 TraesCS7A01G055200 chr4A 96.774 31 1 0 735 765 710175251 710175221 5.000000e-03 52.8
10 TraesCS7A01G055200 chr3A 82.692 312 51 3 1804 2114 171541199 171541508 9.330000e-70 274.0
11 TraesCS7A01G055200 chr3A 90.845 142 12 1 2507 2647 34833880 34834021 3.480000e-44 189.0
12 TraesCS7A01G055200 chr3A 89.510 143 13 2 2507 2647 81667505 81667647 2.090000e-41 180.0
13 TraesCS7A01G055200 chr3A 90.071 141 10 2 2507 2647 676202530 676202666 2.090000e-41 180.0
14 TraesCS7A01G055200 chr3A 78.756 193 34 4 1058 1247 63476991 63476803 3.580000e-24 122.0
15 TraesCS7A01G055200 chr3B 77.710 489 80 18 1807 2273 650808937 650808456 3.360000e-69 272.0
16 TraesCS7A01G055200 chr3B 78.698 169 33 1 1082 1247 79956112 79955944 2.790000e-20 110.0
17 TraesCS7A01G055200 chr5D 81.194 335 62 1 1803 2137 519437189 519436856 4.340000e-68 268.0
18 TraesCS7A01G055200 chr5B 81.138 334 59 3 1807 2139 512940404 512940734 5.620000e-67 265.0
19 TraesCS7A01G055200 chr5B 76.660 467 86 15 1806 2251 565538554 565538090 1.220000e-58 237.0
20 TraesCS7A01G055200 chr5B 79.412 136 25 2 1088 1220 685219158 685219023 2.810000e-15 93.5
21 TraesCS7A01G055200 chr1D 80.838 334 64 0 1803 2136 311755291 311755624 2.020000e-66 263.0
22 TraesCS7A01G055200 chr1D 87.640 89 10 1 2172 2260 28613303 28613216 4.660000e-18 102.0
23 TraesCS7A01G055200 chr2D 77.106 463 90 12 1806 2256 616534243 616533785 1.220000e-63 254.0
24 TraesCS7A01G055200 chr2D 90.845 142 12 1 2507 2647 437917113 437917254 3.480000e-44 189.0
25 TraesCS7A01G055200 chr2D 90.323 124 11 1 2507 2629 35257423 35257300 7.580000e-36 161.0
26 TraesCS7A01G055200 chr6A 80.180 333 61 4 1807 2139 28668826 28668499 7.320000e-61 244.0
27 TraesCS7A01G055200 chr6A 86.047 86 10 2 2189 2273 530114630 530114546 1.010000e-14 91.6
28 TraesCS7A01G055200 chr3D 79.822 337 65 3 1804 2139 156729845 156729511 2.630000e-60 243.0
29 TraesCS7A01G055200 chr3D 78.238 193 35 4 1058 1247 50401159 50400971 1.660000e-22 117.0
30 TraesCS7A01G055200 chrUn 76.509 464 88 17 1803 2253 79653312 79653767 1.580000e-57 233.0
31 TraesCS7A01G055200 chrUn 93.151 73 5 0 2575 2647 460715519 460715447 1.000000e-19 108.0
32 TraesCS7A01G055200 chr5A 78.747 367 63 9 4 366 631913176 631913531 5.700000e-57 231.0
33 TraesCS7A01G055200 chr1B 87.755 147 11 6 2507 2647 154631743 154631598 5.860000e-37 165.0
34 TraesCS7A01G055200 chr1B 88.158 76 7 2 2187 2260 25120127 25120202 3.630000e-14 89.8
35 TraesCS7A01G055200 chr4B 79.012 243 35 9 127 366 44942620 44942391 4.560000e-33 152.0
36 TraesCS7A01G055200 chr4D 81.132 159 27 2 1089 1244 10744017 10744175 9.950000e-25 124.0
37 TraesCS7A01G055200 chr2B 87.912 91 10 1 2171 2260 441104462 441104552 3.600000e-19 106.0
38 TraesCS7A01G055200 chr2A 86.517 89 12 0 2172 2260 284606141 284606229 6.030000e-17 99.0


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 TraesCS7A01G055200 chr7A 26663548 26666194 2646 True 4889.00 4889 100.00000 1 2647 1 chr7A.!!$R1 2646
1 TraesCS7A01G055200 chr4A 710173399 710176048 2649 True 803.95 2113 89.97425 1 2499 4 chr4A.!!$R1 2498

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
682 795 0.027063 GGTTGGACGTTGTTGTGACG 59.973 55.0 0.0 0.0 45.46 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2804 0.101579 GTAGCTGGAAGAGTCGCCTC 59.898 60.0 0.0 0.0 34.07 4.7 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 3.755112 GTATCTTTCCCTCTGGTAGGC 57.245 52.381 0.00 0.00 45.03 3.93
38 41 1.339644 GCCACCGTTATCCCTACCCA 61.340 60.000 0.00 0.00 0.00 4.51
55 58 4.140575 ACCCAAAAACCAACCCTGATAT 57.859 40.909 0.00 0.00 0.00 1.63
58 61 4.285775 CCCAAAAACCAACCCTGATATGTT 59.714 41.667 0.00 0.00 0.00 2.71
63 66 2.308570 ACCAACCCTGATATGTTGAGCA 59.691 45.455 4.08 0.00 43.50 4.26
88 91 3.415087 CCCTTCCCCTCAGGCTGG 61.415 72.222 15.73 5.31 34.51 4.85
163 166 2.094700 GCGATGAAGCATATACCTCCGA 60.095 50.000 0.00 0.00 37.05 4.55
170 173 1.827969 GCATATACCTCCGAGGCTCAT 59.172 52.381 14.86 8.01 39.63 2.90
202 205 2.102588 CACGGGGAAGATAACGGAGATT 59.897 50.000 0.00 0.00 0.00 2.40
204 207 2.364324 CGGGGAAGATAACGGAGATTCA 59.636 50.000 0.00 0.00 0.00 2.57
227 232 2.421399 GGCCGGCCGTAGACTAGTT 61.421 63.158 33.60 0.00 0.00 2.24
251 256 4.395625 AGAGTATCCATGTCGTCGGAATA 58.604 43.478 0.00 0.00 34.22 1.75
284 289 4.973055 CGGCCGTTGACCCGTTGA 62.973 66.667 19.50 0.00 39.67 3.18
285 290 3.351416 GGCCGTTGACCCGTTGAC 61.351 66.667 0.00 0.00 0.00 3.18
286 291 2.280592 GCCGTTGACCCGTTGACT 60.281 61.111 0.00 0.00 0.00 3.41
287 292 1.005867 GCCGTTGACCCGTTGACTA 60.006 57.895 0.00 0.00 0.00 2.59
288 293 1.012486 GCCGTTGACCCGTTGACTAG 61.012 60.000 0.00 0.00 0.00 2.57
289 294 0.316204 CCGTTGACCCGTTGACTAGT 59.684 55.000 0.00 0.00 0.00 2.57
290 295 1.269936 CCGTTGACCCGTTGACTAGTT 60.270 52.381 0.00 0.00 0.00 2.24
291 296 2.476821 CGTTGACCCGTTGACTAGTTT 58.523 47.619 0.00 0.00 0.00 2.66
292 297 2.473984 CGTTGACCCGTTGACTAGTTTC 59.526 50.000 0.00 0.00 0.00 2.78
371 376 9.569122 TTTCTTCTGGTTAGTATAAAACTTGCT 57.431 29.630 0.00 0.00 39.80 3.91
379 384 8.132995 GGTTAGTATAAAACTTGCTGTGTTTGT 58.867 33.333 0.00 0.00 39.80 2.83
394 399 5.228665 TGTGTTTGTATGTATTTCGTCCGA 58.771 37.500 0.00 0.00 0.00 4.55
401 406 8.706492 TTGTATGTATTTCGTCCGATTAGTTT 57.294 30.769 0.00 0.00 0.00 2.66
410 415 6.258230 TCGTCCGATTAGTTTAAAGAGTGA 57.742 37.500 0.00 0.00 0.00 3.41
435 440 3.425577 AATGTATGCGAGCAATGTTGG 57.574 42.857 0.57 0.00 0.00 3.77
443 459 1.402613 CGAGCAATGTTGGATGCATCA 59.597 47.619 27.25 11.43 44.95 3.07
445 461 2.426024 GAGCAATGTTGGATGCATCAGT 59.574 45.455 27.25 4.60 44.95 3.41
455 471 3.188786 GCATCAGTGTCCGCGGAC 61.189 66.667 43.88 43.88 44.77 4.79
483 499 3.460648 GTCCAGGGACGAATTCAGG 57.539 57.895 6.22 0.00 35.30 3.86
485 501 1.486726 GTCCAGGGACGAATTCAGGAT 59.513 52.381 6.22 0.00 35.30 3.24
488 504 3.973973 TCCAGGGACGAATTCAGGATAAT 59.026 43.478 6.22 0.00 0.00 1.28
493 509 8.100791 CCAGGGACGAATTCAGGATAATATTTA 58.899 37.037 6.22 0.00 0.00 1.40
499 515 7.601508 ACGAATTCAGGATAATATTTACGGGTC 59.398 37.037 6.22 0.00 0.00 4.46
502 518 6.653526 TCAGGATAATATTTACGGGTCGAA 57.346 37.500 0.00 0.00 0.00 3.71
504 520 5.347907 CAGGATAATATTTACGGGTCGAAGC 59.652 44.000 0.00 0.00 0.00 3.86
511 540 0.529773 TACGGGTCGAAGCATGCATC 60.530 55.000 21.98 17.19 0.00 3.91
522 551 4.624024 CGAAGCATGCATCAAATCTTGTTT 59.376 37.500 21.98 0.00 0.00 2.83
527 556 2.295629 TGCATCAAATCTTGTTTCCGCA 59.704 40.909 0.00 0.00 0.00 5.69
547 576 3.733960 TCCGCGGACACGTCTGAG 61.734 66.667 27.28 6.49 43.45 3.35
572 601 1.003355 CACCAAGATCCCTGCGTGT 60.003 57.895 0.00 0.00 0.00 4.49
575 604 0.249120 CCAAGATCCCTGCGTGTGTA 59.751 55.000 0.00 0.00 0.00 2.90
576 605 1.645034 CAAGATCCCTGCGTGTGTAG 58.355 55.000 0.00 0.00 0.00 2.74
577 606 1.066858 CAAGATCCCTGCGTGTGTAGT 60.067 52.381 0.00 0.00 0.00 2.73
578 607 2.139323 AGATCCCTGCGTGTGTAGTA 57.861 50.000 0.00 0.00 0.00 1.82
579 608 2.667470 AGATCCCTGCGTGTGTAGTAT 58.333 47.619 0.00 0.00 0.00 2.12
580 609 3.031736 AGATCCCTGCGTGTGTAGTATT 58.968 45.455 0.00 0.00 0.00 1.89
620 733 1.202486 TCTTTGTCTCGTCCACCACAC 60.202 52.381 0.00 0.00 0.00 3.82
627 740 2.819550 GTCCACCACACCACTCGT 59.180 61.111 0.00 0.00 0.00 4.18
647 760 2.105993 GTGTGGGTTGGTCTAGTCCTTT 59.894 50.000 7.56 0.00 0.00 3.11
648 761 2.781174 TGTGGGTTGGTCTAGTCCTTTT 59.219 45.455 7.56 0.00 0.00 2.27
682 795 0.027063 GGTTGGACGTTGTTGTGACG 59.973 55.000 0.00 0.00 45.46 4.35
700 813 2.671276 TACGTACGGTGCCGGTCA 60.671 61.111 21.06 0.00 44.69 4.02
725 882 4.827087 CAGCCGTCCATGCGAGCT 62.827 66.667 0.00 0.00 38.32 4.09
762 919 1.140161 GTACGTAGCCGTCCATGCA 59.860 57.895 0.00 0.00 46.28 3.96
770 927 2.434884 CGTCCATGCAAGAGCGGT 60.435 61.111 0.00 0.00 46.23 5.68
791 948 0.161024 GTTCAAACGAGTCGCTTCGG 59.839 55.000 13.59 0.00 44.57 4.30
792 949 0.249155 TTCAAACGAGTCGCTTCGGT 60.249 50.000 13.59 3.56 43.46 4.69
793 950 0.592637 TCAAACGAGTCGCTTCGGTA 59.407 50.000 13.59 0.00 40.11 4.02
794 951 1.001487 TCAAACGAGTCGCTTCGGTAA 60.001 47.619 13.59 0.00 40.11 2.85
795 952 1.788308 CAAACGAGTCGCTTCGGTAAA 59.212 47.619 13.59 0.00 40.11 2.01
796 953 1.412387 AACGAGTCGCTTCGGTAAAC 58.588 50.000 13.59 0.00 44.57 2.01
797 954 0.311790 ACGAGTCGCTTCGGTAAACA 59.688 50.000 13.59 0.00 44.57 2.83
798 955 0.706729 CGAGTCGCTTCGGTAAACAC 59.293 55.000 0.00 0.00 36.95 3.32
799 956 1.066136 GAGTCGCTTCGGTAAACACC 58.934 55.000 0.00 0.00 0.00 4.16
809 966 1.366679 GGTAAACACCGGCTAGAAGC 58.633 55.000 0.00 0.00 41.46 3.86
810 967 1.338389 GGTAAACACCGGCTAGAAGCA 60.338 52.381 0.00 0.00 44.75 3.91
811 968 2.419667 GTAAACACCGGCTAGAAGCAA 58.580 47.619 0.00 0.00 44.75 3.91
812 969 1.523758 AAACACCGGCTAGAAGCAAG 58.476 50.000 0.00 0.00 44.75 4.01
813 970 0.955919 AACACCGGCTAGAAGCAAGC 60.956 55.000 0.00 0.00 44.75 4.01
814 971 1.375908 CACCGGCTAGAAGCAAGCA 60.376 57.895 0.00 0.00 44.75 3.91
849 1006 0.179234 TGGTGGAGAAGCAAACGACA 59.821 50.000 0.00 0.00 32.00 4.35
949 1109 0.806492 GCACGAAGCTAGCCAGTACC 60.806 60.000 12.13 0.66 41.15 3.34
950 1110 0.818296 CACGAAGCTAGCCAGTACCT 59.182 55.000 12.13 0.00 0.00 3.08
951 1111 0.818296 ACGAAGCTAGCCAGTACCTG 59.182 55.000 12.13 0.00 0.00 4.00
961 1129 9.543231 AAGCTAGCCAGTACCTGTATAAATATA 57.457 33.333 12.13 0.00 0.00 0.86
962 1130 8.968969 AGCTAGCCAGTACCTGTATAAATATAC 58.031 37.037 12.13 4.05 39.14 1.47
963 1131 8.746530 GCTAGCCAGTACCTGTATAAATATACA 58.253 37.037 2.29 11.64 44.42 2.29
986 1154 2.895372 GCCCGGTAGTGCATTCCG 60.895 66.667 16.45 16.45 43.30 4.30
992 1160 2.125310 TAGTGCATTCCGGTGCCG 60.125 61.111 13.95 3.25 44.43 5.69
1029 1197 1.286553 GTCTCTGGAGGAAGGAGGAGA 59.713 57.143 0.00 0.00 0.00 3.71
1033 1201 0.618968 TGGAGGAAGGAGGAGAAGCC 60.619 60.000 0.00 0.00 0.00 4.35
1034 1202 1.681486 GGAGGAAGGAGGAGAAGCCG 61.681 65.000 0.00 0.00 43.43 5.52
1148 1343 1.380515 CTCTTCTCCCTCCTCGCCA 60.381 63.158 0.00 0.00 0.00 5.69
1192 1387 4.609018 CTCGCCGCGGATCCCATT 62.609 66.667 33.48 0.00 0.00 3.16
1252 1447 1.585521 CGGCACCTACATCGTCGAC 60.586 63.158 5.18 5.18 0.00 4.20
1411 1606 1.406065 CCCCCATGTCTCGCATCTCT 61.406 60.000 0.00 0.00 35.19 3.10
1432 1627 4.907457 ATCCCCATGATCAACGCC 57.093 55.556 0.00 0.00 0.00 5.68
1500 1695 1.883084 GCCGCACCGAGGTATGAAG 60.883 63.158 0.00 0.00 0.00 3.02
1505 1700 1.870167 GCACCGAGGTATGAAGCTAGC 60.870 57.143 6.62 6.62 32.30 3.42
1517 1713 7.945664 AGGTATGAAGCTAGCACTATACTACTT 59.054 37.037 18.83 0.00 0.00 2.24
1558 1754 7.393234 TCTCGGTTGAATTAATTTTGATGGAGT 59.607 33.333 1.43 0.00 0.00 3.85
1559 1755 7.535139 TCGGTTGAATTAATTTTGATGGAGTC 58.465 34.615 1.43 0.00 0.00 3.36
1589 1785 9.462174 GATGTTTATCAGAGTCTGAAGATACTG 57.538 37.037 26.06 0.00 44.04 2.74
1643 1839 0.976590 ACGTCTTCCTTAGGAGGCCC 60.977 60.000 5.43 0.00 43.21 5.80
1662 1858 2.618045 CCCTAAACCGCAACCTCAAGAT 60.618 50.000 0.00 0.00 0.00 2.40
1699 1895 1.279496 TGATCCCCACCAGAGTTCAG 58.721 55.000 0.00 0.00 0.00 3.02
1703 1899 0.322975 CCCCACCAGAGTTCAGAGTG 59.677 60.000 0.00 0.00 0.00 3.51
1755 1951 3.807622 GTGTGCTTGTGTGTCTAGCTTTA 59.192 43.478 0.00 0.00 43.33 1.85
1804 2000 7.222999 CCGTGAAGAATATCAAGTAAAGAGTCC 59.777 40.741 0.00 0.00 0.00 3.85
1826 2022 3.261643 CGGTTAGTGGTTTAGGTTAGGGT 59.738 47.826 0.00 0.00 0.00 4.34
1829 2025 5.707298 GGTTAGTGGTTTAGGTTAGGGTTTC 59.293 44.000 0.00 0.00 0.00 2.78
1833 2029 5.831525 AGTGGTTTAGGTTAGGGTTTCTTTG 59.168 40.000 0.00 0.00 0.00 2.77
1841 2037 0.250770 AGGGTTTCTTTGGTCCTCGC 60.251 55.000 0.00 0.00 0.00 5.03
1868 2064 1.524621 CACTCGGATGGATGGTGGC 60.525 63.158 0.00 0.00 0.00 5.01
1870 2066 3.080765 TCGGATGGATGGTGGCGT 61.081 61.111 0.00 0.00 0.00 5.68
1895 2091 2.443416 TCTTCGAGATTGTCTTCCGGA 58.557 47.619 0.00 0.00 0.00 5.14
1900 2096 2.531206 GAGATTGTCTTCCGGACTTCG 58.469 52.381 1.83 0.00 44.74 3.79
1909 2105 0.465824 TCCGGACTTCGATCCTCCTC 60.466 60.000 0.00 0.00 42.43 3.71
1922 2118 2.955614 TCCTCCTCGAATTTGTTCGTC 58.044 47.619 9.95 0.00 44.18 4.20
1958 2154 1.067821 GAGCTCCGGTGTAGATTCCTG 59.932 57.143 0.87 0.00 0.00 3.86
1961 2157 1.146263 CCGGTGTAGATTCCTGCCC 59.854 63.158 0.00 0.00 0.00 5.36
1982 2178 1.460689 TCCTTGGGACGGTGAGGTT 60.461 57.895 0.00 0.00 0.00 3.50
2017 2213 3.057969 TGTGGCGAGATTTGATGTCTT 57.942 42.857 0.00 0.00 0.00 3.01
2021 2217 2.476854 GGCGAGATTTGATGTCTTGTGC 60.477 50.000 0.00 0.00 31.09 4.57
2034 2230 4.960938 TGTCTTGTGCTTCAGTTCTATGT 58.039 39.130 0.00 0.00 0.00 2.29
2042 2238 5.705905 GTGCTTCAGTTCTATGTAAGGGTTT 59.294 40.000 0.00 0.00 0.00 3.27
2083 2279 4.176752 GGCGCTGGTCCTTAGGGG 62.177 72.222 7.64 0.00 0.00 4.79
2090 2286 2.267961 GTCCTTAGGGGCACGTGG 59.732 66.667 18.88 0.00 37.14 4.94
2096 2292 0.035820 TTAGGGGCACGTGGATGAAC 60.036 55.000 18.88 0.00 0.00 3.18
2114 2310 6.263842 GGATGAACATTTTCCAGCTATCATCA 59.736 38.462 12.73 0.00 42.17 3.07
2124 2320 4.962362 TCCAGCTATCATCAACTAGGTCAA 59.038 41.667 0.00 0.00 0.00 3.18
2125 2321 5.425217 TCCAGCTATCATCAACTAGGTCAAA 59.575 40.000 0.00 0.00 0.00 2.69
2132 2328 1.418637 TCAACTAGGTCAAACCGGCTT 59.581 47.619 0.00 0.00 44.90 4.35
2154 2350 2.807472 CGGTAGTCTAGCGGTGATCTCT 60.807 54.545 21.08 0.00 45.08 3.10
2156 2352 1.686355 AGTCTAGCGGTGATCTCTGG 58.314 55.000 0.00 0.00 0.00 3.86
2157 2353 1.213182 AGTCTAGCGGTGATCTCTGGA 59.787 52.381 0.00 0.00 0.00 3.86
2158 2354 1.335496 GTCTAGCGGTGATCTCTGGAC 59.665 57.143 0.00 5.88 32.65 4.02
2160 2356 1.101635 TAGCGGTGATCTCTGGACGG 61.102 60.000 0.00 0.00 0.00 4.79
2162 2358 2.501610 GGTGATCTCTGGACGGCC 59.498 66.667 0.00 0.00 0.00 6.13
2163 2359 2.501610 GTGATCTCTGGACGGCCC 59.498 66.667 3.83 0.00 0.00 5.80
2164 2360 2.038813 TGATCTCTGGACGGCCCA 59.961 61.111 3.83 0.78 44.25 5.36
2165 2361 1.383109 TGATCTCTGGACGGCCCAT 60.383 57.895 3.83 0.00 45.57 4.00
2166 2362 1.369321 GATCTCTGGACGGCCCATC 59.631 63.158 3.83 0.00 45.57 3.51
2170 2366 2.765807 CTGGACGGCCCATCCTCT 60.766 66.667 19.16 0.00 45.57 3.69
2171 2367 3.083349 TGGACGGCCCATCCTCTG 61.083 66.667 19.16 0.00 40.82 3.35
2172 2368 3.083997 GGACGGCCCATCCTCTGT 61.084 66.667 12.66 0.00 33.03 3.41
2173 2369 2.670148 GGACGGCCCATCCTCTGTT 61.670 63.158 12.66 0.00 33.03 3.16
2174 2370 1.153349 GACGGCCCATCCTCTGTTC 60.153 63.158 0.00 0.00 0.00 3.18
2264 2465 8.754230 TTCATAATAGATCTGATCTTTCTGCG 57.246 34.615 23.98 10.02 40.76 5.18
2303 2504 8.526978 GTTATCATCTGGTATCTATTCAGCTGA 58.473 37.037 13.74 13.74 37.82 4.26
2346 2547 0.321671 ACTGGTCCCATCGTGTTCAG 59.678 55.000 0.00 0.00 0.00 3.02
2355 2556 2.069273 CATCGTGTTCAGTTGGTCCTC 58.931 52.381 0.00 0.00 0.00 3.71
2359 2560 2.557317 GTGTTCAGTTGGTCCTCGAAA 58.443 47.619 0.00 0.00 0.00 3.46
2368 2569 4.062991 GTTGGTCCTCGAAACAACTATGT 58.937 43.478 10.17 0.00 43.14 2.29
2396 2597 2.588877 GTGACGGTGCACTGTGCT 60.589 61.111 35.17 11.86 45.31 4.40
2414 2615 3.821033 GTGCTATCTTGGTTGGACTTTGT 59.179 43.478 0.00 0.00 0.00 2.83
2418 2619 2.993937 TCTTGGTTGGACTTTGTCGTT 58.006 42.857 0.00 0.00 32.65 3.85
2426 2627 4.609691 TGGACTTTGTCGTTCTTTTGAC 57.390 40.909 0.00 0.00 32.65 3.18
2485 2686 8.598916 TCACACCTATACAGAAAATTTCCTACA 58.401 33.333 1.57 0.00 0.00 2.74
2499 2700 4.901785 TTCCTACAGGTAATCTCCTCCT 57.098 45.455 0.00 0.00 35.37 3.69
2504 2705 3.922171 CAGGTAATCTCCTCCTGCTTT 57.078 47.619 0.00 0.00 41.46 3.51
2505 2706 4.227864 CAGGTAATCTCCTCCTGCTTTT 57.772 45.455 0.00 0.00 41.46 2.27
2506 2707 3.944015 CAGGTAATCTCCTCCTGCTTTTG 59.056 47.826 0.00 0.00 41.46 2.44
2507 2708 3.054065 AGGTAATCTCCTCCTGCTTTTGG 60.054 47.826 0.00 0.00 31.32 3.28
2508 2709 2.521547 AATCTCCTCCTGCTTTTGGG 57.478 50.000 0.00 0.00 0.00 4.12
2509 2710 0.033699 ATCTCCTCCTGCTTTTGGGC 60.034 55.000 0.00 0.00 0.00 5.36
2510 2711 1.136329 TCTCCTCCTGCTTTTGGGCT 61.136 55.000 0.00 0.00 0.00 5.19
2511 2712 0.679321 CTCCTCCTGCTTTTGGGCTC 60.679 60.000 0.00 0.00 0.00 4.70
2512 2713 2.042831 CCTCCTGCTTTTGGGCTCG 61.043 63.158 0.00 0.00 0.00 5.03
2513 2714 2.672996 TCCTGCTTTTGGGCTCGC 60.673 61.111 0.00 0.00 0.00 5.03
2514 2715 2.674380 CCTGCTTTTGGGCTCGCT 60.674 61.111 0.00 0.00 0.00 4.93
2515 2716 2.564975 CTGCTTTTGGGCTCGCTG 59.435 61.111 0.00 0.00 0.00 5.18
2516 2717 2.985282 TGCTTTTGGGCTCGCTGG 60.985 61.111 0.00 0.00 0.00 4.85
2517 2718 2.985847 GCTTTTGGGCTCGCTGGT 60.986 61.111 0.00 0.00 0.00 4.00
2518 2719 2.982744 GCTTTTGGGCTCGCTGGTC 61.983 63.158 0.00 0.00 0.00 4.02
2519 2720 1.302832 CTTTTGGGCTCGCTGGTCT 60.303 57.895 0.00 0.00 0.00 3.85
2520 2721 1.580845 CTTTTGGGCTCGCTGGTCTG 61.581 60.000 0.00 0.00 0.00 3.51
2521 2722 2.337879 TTTTGGGCTCGCTGGTCTGT 62.338 55.000 0.00 0.00 0.00 3.41
2522 2723 3.535629 TTGGGCTCGCTGGTCTGTG 62.536 63.158 0.00 0.00 0.00 3.66
2523 2724 4.767255 GGGCTCGCTGGTCTGTGG 62.767 72.222 0.00 0.00 0.00 4.17
2525 2726 4.687215 GCTCGCTGGTCTGTGGCA 62.687 66.667 0.00 0.00 0.00 4.92
2526 2727 2.267006 CTCGCTGGTCTGTGGCAT 59.733 61.111 0.00 0.00 0.00 4.40
2527 2728 1.517361 CTCGCTGGTCTGTGGCATA 59.483 57.895 0.00 0.00 0.00 3.14
2528 2729 0.105593 CTCGCTGGTCTGTGGCATAT 59.894 55.000 0.00 0.00 0.00 1.78
2529 2730 0.541392 TCGCTGGTCTGTGGCATATT 59.459 50.000 0.00 0.00 0.00 1.28
2530 2731 0.659427 CGCTGGTCTGTGGCATATTG 59.341 55.000 0.00 0.00 0.00 1.90
2531 2732 1.027357 GCTGGTCTGTGGCATATTGG 58.973 55.000 0.00 0.00 0.00 3.16
2532 2733 1.027357 CTGGTCTGTGGCATATTGGC 58.973 55.000 0.00 0.00 44.03 4.52
2543 2744 1.688735 GCATATTGGCCTTCTTTCCCC 59.311 52.381 3.32 0.00 0.00 4.81
2544 2745 2.319844 CATATTGGCCTTCTTTCCCCC 58.680 52.381 3.32 0.00 0.00 5.40
2545 2746 0.257616 TATTGGCCTTCTTTCCCCCG 59.742 55.000 3.32 0.00 0.00 5.73
2546 2747 2.514516 ATTGGCCTTCTTTCCCCCGG 62.515 60.000 3.32 0.00 0.00 5.73
2549 2750 3.657350 CCTTCTTTCCCCCGGCCA 61.657 66.667 2.24 0.00 0.00 5.36
2550 2751 2.438795 CTTCTTTCCCCCGGCCAA 59.561 61.111 2.24 0.00 0.00 4.52
2551 2752 1.977009 CTTCTTTCCCCCGGCCAAC 60.977 63.158 2.24 0.00 0.00 3.77
2552 2753 2.706952 CTTCTTTCCCCCGGCCAACA 62.707 60.000 2.24 0.00 0.00 3.33
2553 2754 2.203567 CTTTCCCCCGGCCAACAA 60.204 61.111 2.24 0.00 0.00 2.83
2554 2755 2.203567 TTTCCCCCGGCCAACAAG 60.204 61.111 2.24 0.00 0.00 3.16
2555 2756 4.986708 TTCCCCCGGCCAACAAGC 62.987 66.667 2.24 0.00 0.00 4.01
2558 2759 3.989787 CCCCGGCCAACAAGCAAC 61.990 66.667 2.24 0.00 0.00 4.17
2559 2760 3.989787 CCCGGCCAACAAGCAACC 61.990 66.667 2.24 0.00 0.00 3.77
2560 2761 3.989787 CCGGCCAACAAGCAACCC 61.990 66.667 2.24 0.00 0.00 4.11
2561 2762 2.912025 CGGCCAACAAGCAACCCT 60.912 61.111 2.24 0.00 0.00 4.34
2562 2763 2.919494 CGGCCAACAAGCAACCCTC 61.919 63.158 2.24 0.00 0.00 4.30
2563 2764 2.644992 GCCAACAAGCAACCCTCG 59.355 61.111 0.00 0.00 0.00 4.63
2564 2765 2.644992 CCAACAAGCAACCCTCGC 59.355 61.111 0.00 0.00 0.00 5.03
2565 2766 1.898574 CCAACAAGCAACCCTCGCT 60.899 57.895 0.00 0.00 42.98 4.93
2566 2767 1.576421 CAACAAGCAACCCTCGCTC 59.424 57.895 0.00 0.00 39.29 5.03
2567 2768 1.600916 AACAAGCAACCCTCGCTCC 60.601 57.895 0.00 0.00 39.29 4.70
2568 2769 2.747855 CAAGCAACCCTCGCTCCC 60.748 66.667 0.00 0.00 39.29 4.30
2569 2770 4.394712 AAGCAACCCTCGCTCCCG 62.395 66.667 0.00 0.00 39.29 5.14
2586 2787 4.131088 GCCTCCTCCGTCACCGAC 62.131 72.222 0.00 0.00 35.63 4.79
2601 2802 3.747976 GACGCTGCCGCCCATTTT 61.748 61.111 0.00 0.00 38.22 1.82
2602 2803 3.281359 GACGCTGCCGCCCATTTTT 62.281 57.895 0.00 0.00 38.22 1.94
2603 2804 2.810458 CGCTGCCGCCCATTTTTG 60.810 61.111 0.00 0.00 0.00 2.44
2604 2805 2.656055 GCTGCCGCCCATTTTTGA 59.344 55.556 0.00 0.00 0.00 2.69
2605 2806 1.446618 GCTGCCGCCCATTTTTGAG 60.447 57.895 0.00 0.00 0.00 3.02
2606 2807 1.216178 CTGCCGCCCATTTTTGAGG 59.784 57.895 0.00 0.00 0.00 3.86
2607 2808 2.125552 GCCGCCCATTTTTGAGGC 60.126 61.111 0.00 0.00 43.53 4.70
2610 2811 4.889427 GCCCATTTTTGAGGCGAC 57.111 55.556 0.00 0.00 36.84 5.19
2621 2822 4.766272 AGGCGACTCTTCCAGCTA 57.234 55.556 0.00 0.00 32.90 3.32
2622 2823 2.194460 AGGCGACTCTTCCAGCTAC 58.806 57.895 0.00 0.00 32.90 3.58
2623 2824 1.142097 GGCGACTCTTCCAGCTACC 59.858 63.158 0.00 0.00 0.00 3.18
2624 2825 1.226717 GCGACTCTTCCAGCTACCG 60.227 63.158 0.00 0.00 0.00 4.02
2625 2826 1.226717 CGACTCTTCCAGCTACCGC 60.227 63.158 0.00 0.00 0.00 5.68
2626 2827 1.142097 GACTCTTCCAGCTACCGCC 59.858 63.158 0.00 0.00 36.60 6.13
2627 2828 2.105128 CTCTTCCAGCTACCGCCG 59.895 66.667 0.00 0.00 36.60 6.46
2628 2829 4.143333 TCTTCCAGCTACCGCCGC 62.143 66.667 0.00 0.00 36.60 6.53
2629 2830 4.148825 CTTCCAGCTACCGCCGCT 62.149 66.667 0.00 0.00 38.49 5.52
2630 2831 3.665675 CTTCCAGCTACCGCCGCTT 62.666 63.158 0.00 0.00 35.07 4.68
2631 2832 3.659089 TTCCAGCTACCGCCGCTTC 62.659 63.158 0.00 0.00 35.07 3.86
2633 2834 4.451150 CAGCTACCGCCGCTTCCA 62.451 66.667 0.00 0.00 35.07 3.53
2634 2835 3.470888 AGCTACCGCCGCTTCCAT 61.471 61.111 0.00 0.00 32.98 3.41
2635 2836 2.131709 AGCTACCGCCGCTTCCATA 61.132 57.895 0.00 0.00 32.98 2.74
2636 2837 1.004918 GCTACCGCCGCTTCCATAT 60.005 57.895 0.00 0.00 0.00 1.78
2637 2838 1.014564 GCTACCGCCGCTTCCATATC 61.015 60.000 0.00 0.00 0.00 1.63
2638 2839 0.389948 CTACCGCCGCTTCCATATCC 60.390 60.000 0.00 0.00 0.00 2.59
2639 2840 2.149803 TACCGCCGCTTCCATATCCG 62.150 60.000 0.00 0.00 0.00 4.18
2640 2841 3.414700 CGCCGCTTCCATATCCGC 61.415 66.667 0.00 0.00 0.00 5.54
2641 2842 3.050275 GCCGCTTCCATATCCGCC 61.050 66.667 0.00 0.00 0.00 6.13
2642 2843 2.358737 CCGCTTCCATATCCGCCC 60.359 66.667 0.00 0.00 0.00 6.13
2643 2844 2.425592 CGCTTCCATATCCGCCCA 59.574 61.111 0.00 0.00 0.00 5.36
2644 2845 1.669115 CGCTTCCATATCCGCCCAG 60.669 63.158 0.00 0.00 0.00 4.45
2645 2846 1.968540 GCTTCCATATCCGCCCAGC 60.969 63.158 0.00 0.00 0.00 4.85
2646 2847 1.451504 CTTCCATATCCGCCCAGCA 59.548 57.895 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.205966 TTGGGTAGGGATAACGGTGG 58.794 55.000 0.00 0.00 0.00 4.61
28 29 2.493875 GGGTTGGTTTTTGGGTAGGGAT 60.494 50.000 0.00 0.00 0.00 3.85
38 41 5.279456 GCTCAACATATCAGGGTTGGTTTTT 60.279 40.000 0.00 0.00 43.44 1.94
55 58 1.207488 AGGGTGCCCTATGCTCAACA 61.207 55.000 8.24 0.00 46.14 3.33
145 148 2.234908 GCCTCGGAGGTATATGCTTCAT 59.765 50.000 24.30 0.00 37.80 2.57
163 166 3.866582 GCCGGTAGCCATGAGCCT 61.867 66.667 1.90 0.00 45.47 4.58
183 186 2.364324 TGAATCTCCGTTATCTTCCCCG 59.636 50.000 0.00 0.00 0.00 5.73
185 188 3.729966 GGTGAATCTCCGTTATCTTCCC 58.270 50.000 0.00 0.00 0.00 3.97
216 219 8.380743 ACATGGATACTCTTAACTAGTCTACG 57.619 38.462 0.00 0.00 37.61 3.51
227 232 3.812262 TCCGACGACATGGATACTCTTA 58.188 45.455 0.00 0.00 37.61 2.10
278 283 4.567159 GGCTAAGATGAAACTAGTCAACGG 59.433 45.833 0.00 0.00 0.00 4.44
279 284 5.289675 CAGGCTAAGATGAAACTAGTCAACG 59.710 44.000 0.00 0.00 0.00 4.10
283 288 5.346181 ACCAGGCTAAGATGAAACTAGTC 57.654 43.478 0.00 0.00 0.00 2.59
284 289 6.611642 TGATACCAGGCTAAGATGAAACTAGT 59.388 38.462 0.00 0.00 0.00 2.57
285 290 7.055667 TGATACCAGGCTAAGATGAAACTAG 57.944 40.000 0.00 0.00 0.00 2.57
286 291 7.618019 ATGATACCAGGCTAAGATGAAACTA 57.382 36.000 0.00 0.00 0.00 2.24
287 292 5.957771 TGATACCAGGCTAAGATGAAACT 57.042 39.130 0.00 0.00 0.00 2.66
288 293 7.573968 AAATGATACCAGGCTAAGATGAAAC 57.426 36.000 0.00 0.00 0.00 2.78
289 294 8.593945 AAAAATGATACCAGGCTAAGATGAAA 57.406 30.769 0.00 0.00 0.00 2.69
290 295 9.342308 CTAAAAATGATACCAGGCTAAGATGAA 57.658 33.333 0.00 0.00 0.00 2.57
291 296 7.939039 CCTAAAAATGATACCAGGCTAAGATGA 59.061 37.037 0.00 0.00 0.00 2.92
292 297 7.721399 ACCTAAAAATGATACCAGGCTAAGATG 59.279 37.037 0.00 0.00 0.00 2.90
357 362 8.846211 ACATACAAACACAGCAAGTTTTATACT 58.154 29.630 0.00 0.00 37.10 2.12
366 371 6.370593 ACGAAATACATACAAACACAGCAAG 58.629 36.000 0.00 0.00 0.00 4.01
367 372 6.307031 ACGAAATACATACAAACACAGCAA 57.693 33.333 0.00 0.00 0.00 3.91
368 373 5.106869 GGACGAAATACATACAAACACAGCA 60.107 40.000 0.00 0.00 0.00 4.41
371 376 5.228665 TCGGACGAAATACATACAAACACA 58.771 37.500 0.00 0.00 0.00 3.72
401 406 8.335356 GCTCGCATACATTTTAATCACTCTTTA 58.665 33.333 0.00 0.00 0.00 1.85
404 409 5.817296 TGCTCGCATACATTTTAATCACTCT 59.183 36.000 0.00 0.00 0.00 3.24
405 410 6.048073 TGCTCGCATACATTTTAATCACTC 57.952 37.500 0.00 0.00 0.00 3.51
410 415 6.476380 CCAACATTGCTCGCATACATTTTAAT 59.524 34.615 0.00 0.00 0.00 1.40
435 440 2.528743 CCGCGGACACTGATGCATC 61.529 63.158 24.07 20.14 0.00 3.91
462 478 0.613260 TGAATTCGTCCCTGGACTGG 59.387 55.000 14.10 0.22 42.54 4.00
464 480 0.905357 CCTGAATTCGTCCCTGGACT 59.095 55.000 14.10 0.00 42.54 3.85
469 485 7.817962 CGTAAATATTATCCTGAATTCGTCCCT 59.182 37.037 0.04 0.00 0.00 4.20
476 492 7.673180 TCGACCCGTAAATATTATCCTGAATT 58.327 34.615 0.00 0.00 0.00 2.17
481 497 5.011329 TGCTTCGACCCGTAAATATTATCCT 59.989 40.000 0.00 0.00 0.00 3.24
482 498 5.232463 TGCTTCGACCCGTAAATATTATCC 58.768 41.667 0.00 0.00 0.00 2.59
483 499 6.672357 GCATGCTTCGACCCGTAAATATTATC 60.672 42.308 11.37 0.00 0.00 1.75
485 501 4.449743 GCATGCTTCGACCCGTAAATATTA 59.550 41.667 11.37 0.00 0.00 0.98
488 504 2.206750 GCATGCTTCGACCCGTAAATA 58.793 47.619 11.37 0.00 0.00 1.40
493 509 1.815421 GATGCATGCTTCGACCCGT 60.815 57.895 20.33 0.00 0.00 5.28
499 515 3.766151 ACAAGATTTGATGCATGCTTCG 58.234 40.909 23.82 12.89 0.00 3.79
502 518 4.501071 GGAAACAAGATTTGATGCATGCT 58.499 39.130 20.33 4.11 0.00 3.79
504 520 3.305094 GCGGAAACAAGATTTGATGCATG 59.695 43.478 2.46 0.00 0.00 4.06
511 540 3.244976 GGACATGCGGAAACAAGATTTG 58.755 45.455 0.00 0.00 0.00 2.32
547 576 2.109126 GGGATCTTGGTGCTCGTGC 61.109 63.158 1.71 1.71 40.20 5.34
598 711 2.069273 GTGGTGGACGAGACAAAGATG 58.931 52.381 0.00 0.00 0.00 2.90
627 740 2.112279 AAGGACTAGACCAACCCACA 57.888 50.000 13.84 0.00 0.00 4.17
647 760 2.034053 CCAACCTTGTTAGCTTTCGCAA 59.966 45.455 0.00 0.00 39.10 4.85
648 761 1.606668 CCAACCTTGTTAGCTTTCGCA 59.393 47.619 0.00 0.00 39.10 5.10
682 795 2.202479 GACCGGCACCGTACGTAC 60.202 66.667 15.90 15.90 37.81 3.67
708 821 2.906182 TAAGCTCGCATGGACGGCTG 62.906 60.000 0.00 0.00 38.80 4.85
725 882 2.259204 CCGACGACCAACCGCTAA 59.741 61.111 0.00 0.00 0.00 3.09
762 919 0.179067 TCGTTTGAACCACCGCTCTT 60.179 50.000 0.00 0.00 0.00 2.85
770 927 1.214367 GAAGCGACTCGTTTGAACCA 58.786 50.000 5.16 0.00 29.28 3.67
791 948 2.088950 TGCTTCTAGCCGGTGTTTAC 57.911 50.000 1.90 0.00 41.51 2.01
792 949 2.695359 CTTGCTTCTAGCCGGTGTTTA 58.305 47.619 1.90 0.00 41.51 2.01
793 950 1.523758 CTTGCTTCTAGCCGGTGTTT 58.476 50.000 1.90 0.00 41.51 2.83
794 951 0.955919 GCTTGCTTCTAGCCGGTGTT 60.956 55.000 1.90 0.00 41.51 3.32
795 952 1.376037 GCTTGCTTCTAGCCGGTGT 60.376 57.895 1.90 0.00 41.51 4.16
796 953 0.955428 TTGCTTGCTTCTAGCCGGTG 60.955 55.000 1.90 0.00 41.51 4.94
797 954 0.674895 CTTGCTTGCTTCTAGCCGGT 60.675 55.000 1.90 0.00 41.51 5.28
798 955 1.986575 GCTTGCTTGCTTCTAGCCGG 61.987 60.000 0.00 0.00 41.51 6.13
799 956 1.427020 GCTTGCTTGCTTCTAGCCG 59.573 57.895 0.00 0.00 41.51 5.52
800 957 1.021390 TCGCTTGCTTGCTTCTAGCC 61.021 55.000 0.00 0.00 41.51 3.93
801 958 0.096108 GTCGCTTGCTTGCTTCTAGC 59.904 55.000 0.00 0.00 42.82 3.42
802 959 0.368227 CGTCGCTTGCTTGCTTCTAG 59.632 55.000 0.00 0.00 0.00 2.43
803 960 0.038618 TCGTCGCTTGCTTGCTTCTA 60.039 50.000 0.00 0.00 0.00 2.10
804 961 0.880278 TTCGTCGCTTGCTTGCTTCT 60.880 50.000 0.00 0.00 0.00 2.85
805 962 0.166814 ATTCGTCGCTTGCTTGCTTC 59.833 50.000 0.00 0.00 0.00 3.86
806 963 0.110056 CATTCGTCGCTTGCTTGCTT 60.110 50.000 0.00 0.00 0.00 3.91
807 964 1.230635 ACATTCGTCGCTTGCTTGCT 61.231 50.000 0.00 0.00 0.00 3.91
808 965 1.061799 CACATTCGTCGCTTGCTTGC 61.062 55.000 0.00 0.00 0.00 4.01
809 966 0.512518 TCACATTCGTCGCTTGCTTG 59.487 50.000 0.00 0.00 0.00 4.01
810 967 0.512952 GTCACATTCGTCGCTTGCTT 59.487 50.000 0.00 0.00 0.00 3.91
811 968 0.319900 AGTCACATTCGTCGCTTGCT 60.320 50.000 0.00 0.00 0.00 3.91
812 969 0.179240 CAGTCACATTCGTCGCTTGC 60.179 55.000 0.00 0.00 0.00 4.01
813 970 0.439985 CCAGTCACATTCGTCGCTTG 59.560 55.000 0.00 0.00 0.00 4.01
814 971 0.033504 ACCAGTCACATTCGTCGCTT 59.966 50.000 0.00 0.00 0.00 4.68
900 1057 4.337304 TGAGGGGCTGAGGGCAGA 62.337 66.667 0.00 0.00 45.17 4.26
951 1111 9.472361 CTACCGGGCATGTATGTATATTTATAC 57.528 37.037 6.32 1.54 39.14 1.47
961 1129 0.179056 GCACTACCGGGCATGTATGT 60.179 55.000 6.32 0.00 0.00 2.29
962 1130 0.179059 TGCACTACCGGGCATGTATG 60.179 55.000 6.32 0.00 34.58 2.39
963 1131 2.217106 TGCACTACCGGGCATGTAT 58.783 52.632 6.32 0.00 34.58 2.29
986 1154 2.972505 CCATATCGCACCGGCACC 60.973 66.667 0.00 0.00 41.24 5.01
992 1160 1.620819 AGACCATCTCCATATCGCACC 59.379 52.381 0.00 0.00 0.00 5.01
999 1167 2.791774 TCCTCCAGAGACCATCTCCATA 59.208 50.000 2.18 0.00 44.42 2.74
1046 1241 1.064060 CCAGTAGCTTTATTGTGCGCC 59.936 52.381 4.18 0.00 0.00 6.53
1108 1303 1.078426 GTCCACCACATCCTTCCCG 60.078 63.158 0.00 0.00 0.00 5.14
1111 1306 2.115343 GGAAGTCCACCACATCCTTC 57.885 55.000 0.00 0.00 39.47 3.46
1148 1343 3.861797 GACGGTGCCGATGGGGAT 61.862 66.667 18.16 0.00 42.83 3.85
1192 1387 4.927782 AAGTTGCCGACGCTGCCA 62.928 61.111 0.00 0.00 35.36 4.92
1252 1447 2.480555 GCGTCCCTTGCATGTTCG 59.519 61.111 0.00 0.00 0.00 3.95
1369 1564 0.179134 CCTTGAGGTCGTCCGTGATC 60.179 60.000 0.00 0.00 39.05 2.92
1432 1627 2.440817 GGGGTCCCTGATACGGTGG 61.441 68.421 8.15 0.00 0.00 4.61
1438 1633 4.146156 TCGCGGGGGTCCCTGATA 62.146 66.667 18.61 2.50 45.10 2.15
1532 1728 7.393234 ACTCCATCAAAATTAATTCAACCGAGA 59.607 33.333 0.10 0.00 0.00 4.04
1533 1729 7.538575 ACTCCATCAAAATTAATTCAACCGAG 58.461 34.615 0.10 5.60 0.00 4.63
1558 1754 9.413734 TCTTCAGACTCTGATAAACATCATAGA 57.586 33.333 9.63 3.13 40.39 1.98
1570 1766 5.068987 GCCTTCAGTATCTTCAGACTCTGAT 59.931 44.000 9.63 0.00 40.39 2.90
1589 1785 2.029844 GGACTGCAGTGACGCCTTC 61.030 63.158 27.27 6.74 0.00 3.46
1643 1839 3.751175 TGAATCTTGAGGTTGCGGTTTAG 59.249 43.478 0.00 0.00 0.00 1.85
1699 1895 0.666577 CCGACACGGGAAGAACACTC 60.667 60.000 0.00 0.00 44.15 3.51
1739 1935 4.948341 TCACCTAAAGCTAGACACACAA 57.052 40.909 0.00 0.00 0.00 3.33
1755 1951 9.381038 ACGGCCATATATAGATATAAATCACCT 57.619 33.333 2.24 0.00 34.28 4.00
1778 1974 7.222999 GGACTCTTTACTTGATATTCTTCACGG 59.777 40.741 0.00 0.00 0.00 4.94
1788 1984 6.127535 CCACTAACCGGACTCTTTACTTGATA 60.128 42.308 9.46 0.00 0.00 2.15
1791 1987 4.243270 CCACTAACCGGACTCTTTACTTG 58.757 47.826 9.46 0.00 0.00 3.16
1804 2000 3.261643 ACCCTAACCTAAACCACTAACCG 59.738 47.826 0.00 0.00 0.00 4.44
1868 2064 5.164041 GGAAGACAATCTCGAAGAAGAAACG 60.164 44.000 0.00 0.00 34.09 3.60
1870 2066 4.923871 CGGAAGACAATCTCGAAGAAGAAA 59.076 41.667 0.00 0.00 34.09 2.52
1922 2118 3.126831 GAGCTCCATTGATTACGTCCAG 58.873 50.000 0.87 0.00 0.00 3.86
1928 2124 2.213499 CACCGGAGCTCCATTGATTAC 58.787 52.381 31.67 2.06 35.14 1.89
1934 2130 1.794714 ATCTACACCGGAGCTCCATT 58.205 50.000 31.67 15.33 35.14 3.16
1935 2131 1.689273 GAATCTACACCGGAGCTCCAT 59.311 52.381 31.67 16.95 35.14 3.41
1958 2154 3.787001 CCGTCCCAAGGAGAGGGC 61.787 72.222 0.00 0.00 46.36 5.19
1961 2157 1.608717 CCTCACCGTCCCAAGGAGAG 61.609 65.000 3.27 3.27 43.24 3.20
1982 2178 1.066430 GCCACATGACGAGAAACCCTA 60.066 52.381 0.00 0.00 0.00 3.53
2011 2207 5.555017 ACATAGAACTGAAGCACAAGACAT 58.445 37.500 0.00 0.00 0.00 3.06
2017 2213 4.286032 ACCCTTACATAGAACTGAAGCACA 59.714 41.667 0.00 0.00 0.00 4.57
2021 2217 8.893727 CCATTAAACCCTTACATAGAACTGAAG 58.106 37.037 0.00 0.00 0.00 3.02
2034 2230 2.620242 GTCGTCGCCATTAAACCCTTA 58.380 47.619 0.00 0.00 0.00 2.69
2065 2261 3.399181 CCCTAAGGACCAGCGCCA 61.399 66.667 2.29 0.00 33.47 5.69
2067 2263 4.858680 GCCCCTAAGGACCAGCGC 62.859 72.222 0.00 0.00 38.24 5.92
2069 2265 2.272471 GTGCCCCTAAGGACCAGC 59.728 66.667 0.00 0.00 38.24 4.85
2070 2266 2.291043 ACGTGCCCCTAAGGACCAG 61.291 63.158 0.00 0.00 38.24 4.00
2071 2267 2.203877 ACGTGCCCCTAAGGACCA 60.204 61.111 0.00 0.00 38.24 4.02
2083 2279 2.030363 TGGAAAATGTTCATCCACGTGC 60.030 45.455 10.91 0.00 38.30 5.34
2090 2286 7.268199 TGATGATAGCTGGAAAATGTTCATC 57.732 36.000 0.00 0.00 38.96 2.92
2096 2292 6.769822 ACCTAGTTGATGATAGCTGGAAAATG 59.230 38.462 0.00 0.00 0.00 2.32
2114 2310 1.607251 CGAAGCCGGTTTGACCTAGTT 60.607 52.381 8.82 0.00 35.66 2.24
2132 2328 1.140452 AGATCACCGCTAGACTACCGA 59.860 52.381 0.00 0.00 0.00 4.69
2141 2337 1.101635 CCGTCCAGAGATCACCGCTA 61.102 60.000 0.00 0.00 0.00 4.26
2156 2352 1.153349 GAACAGAGGATGGGCCGTC 60.153 63.158 17.76 17.76 43.43 4.79
2157 2353 2.990479 GAACAGAGGATGGGCCGT 59.010 61.111 0.00 0.00 43.43 5.68
2158 2354 2.032860 ATCGAACAGAGGATGGGCCG 62.033 60.000 0.00 0.00 43.43 6.13
2160 2356 2.997899 CATCGAACAGAGGATGGGC 58.002 57.895 0.00 0.00 37.09 5.36
2163 2359 2.428530 TGAGACCATCGAACAGAGGATG 59.571 50.000 0.00 0.00 39.74 3.51
2164 2360 2.739943 TGAGACCATCGAACAGAGGAT 58.260 47.619 0.00 0.00 31.12 3.24
2165 2361 2.215942 TGAGACCATCGAACAGAGGA 57.784 50.000 0.00 0.00 31.12 3.71
2166 2362 3.319137 TTTGAGACCATCGAACAGAGG 57.681 47.619 0.00 0.00 0.00 3.69
2170 2366 4.893608 TGAGATTTTGAGACCATCGAACA 58.106 39.130 0.00 0.00 30.58 3.18
2171 2367 5.862924 TTGAGATTTTGAGACCATCGAAC 57.137 39.130 0.00 0.00 30.58 3.95
2172 2368 5.939883 ACATTGAGATTTTGAGACCATCGAA 59.060 36.000 0.00 0.00 0.00 3.71
2173 2369 5.491070 ACATTGAGATTTTGAGACCATCGA 58.509 37.500 0.00 0.00 0.00 3.59
2174 2370 5.808042 ACATTGAGATTTTGAGACCATCG 57.192 39.130 0.00 0.00 0.00 3.84
2303 2504 5.487433 TGATCGGTGATTTACAGTCACATT 58.513 37.500 8.33 0.00 45.99 2.71
2346 2547 4.062991 ACATAGTTGTTTCGAGGACCAAC 58.937 43.478 0.00 9.28 37.93 3.77
2378 2579 2.894879 GCACAGTGCACCGTCACA 60.895 61.111 21.22 0.00 44.26 3.58
2396 2597 4.345859 ACGACAAAGTCCAACCAAGATA 57.654 40.909 0.00 0.00 0.00 1.98
2414 2615 4.698304 AGAAGGTTGTTGTCAAAAGAACGA 59.302 37.500 0.00 0.00 35.20 3.85
2418 2619 4.640201 CAGGAGAAGGTTGTTGTCAAAAGA 59.360 41.667 0.00 0.00 35.20 2.52
2426 2627 4.797275 GCAAAATCCAGGAGAAGGTTGTTG 60.797 45.833 0.00 0.00 0.00 3.33
2432 2633 2.113860 TCGCAAAATCCAGGAGAAGG 57.886 50.000 0.00 0.00 0.00 3.46
2485 2686 3.054065 CCAAAAGCAGGAGGAGATTACCT 60.054 47.826 0.00 0.00 43.64 3.08
2499 2700 2.985282 CCAGCGAGCCCAAAAGCA 60.985 61.111 0.00 0.00 34.23 3.91
2500 2701 2.982744 GACCAGCGAGCCCAAAAGC 61.983 63.158 0.00 0.00 0.00 3.51
2501 2702 1.302832 AGACCAGCGAGCCCAAAAG 60.303 57.895 0.00 0.00 0.00 2.27
2502 2703 1.600636 CAGACCAGCGAGCCCAAAA 60.601 57.895 0.00 0.00 0.00 2.44
2503 2704 2.032528 CAGACCAGCGAGCCCAAA 59.967 61.111 0.00 0.00 0.00 3.28
2504 2705 3.241530 ACAGACCAGCGAGCCCAA 61.242 61.111 0.00 0.00 0.00 4.12
2505 2706 4.007644 CACAGACCAGCGAGCCCA 62.008 66.667 0.00 0.00 0.00 5.36
2506 2707 4.767255 CCACAGACCAGCGAGCCC 62.767 72.222 0.00 0.00 0.00 5.19
2508 2709 2.578163 TATGCCACAGACCAGCGAGC 62.578 60.000 0.00 0.00 0.00 5.03
2509 2710 0.105593 ATATGCCACAGACCAGCGAG 59.894 55.000 0.00 0.00 0.00 5.03
2510 2711 0.541392 AATATGCCACAGACCAGCGA 59.459 50.000 0.00 0.00 0.00 4.93
2511 2712 0.659427 CAATATGCCACAGACCAGCG 59.341 55.000 0.00 0.00 0.00 5.18
2512 2713 1.027357 CCAATATGCCACAGACCAGC 58.973 55.000 0.00 0.00 0.00 4.85
2513 2714 1.027357 GCCAATATGCCACAGACCAG 58.973 55.000 0.00 0.00 0.00 4.00
2514 2715 3.189568 GCCAATATGCCACAGACCA 57.810 52.632 0.00 0.00 0.00 4.02
2523 2724 1.688735 GGGGAAAGAAGGCCAATATGC 59.311 52.381 5.01 0.00 0.00 3.14
2524 2725 2.319844 GGGGGAAAGAAGGCCAATATG 58.680 52.381 5.01 0.00 0.00 1.78
2525 2726 1.133482 CGGGGGAAAGAAGGCCAATAT 60.133 52.381 5.01 0.00 0.00 1.28
2526 2727 0.257616 CGGGGGAAAGAAGGCCAATA 59.742 55.000 5.01 0.00 0.00 1.90
2527 2728 1.000359 CGGGGGAAAGAAGGCCAAT 60.000 57.895 5.01 0.00 0.00 3.16
2528 2729 2.438795 CGGGGGAAAGAAGGCCAA 59.561 61.111 5.01 0.00 0.00 4.52
2529 2730 3.657350 CCGGGGGAAAGAAGGCCA 61.657 66.667 5.01 0.00 0.00 5.36
2532 2733 3.218386 TTGGCCGGGGGAAAGAAGG 62.218 63.158 2.18 0.00 0.00 3.46
2533 2734 1.977009 GTTGGCCGGGGGAAAGAAG 60.977 63.158 2.18 0.00 0.00 2.85
2534 2735 2.116556 GTTGGCCGGGGGAAAGAA 59.883 61.111 2.18 0.00 0.00 2.52
2535 2736 2.706952 CTTGTTGGCCGGGGGAAAGA 62.707 60.000 2.18 0.00 0.00 2.52
2536 2737 2.203567 TTGTTGGCCGGGGGAAAG 60.204 61.111 2.18 0.00 0.00 2.62
2537 2738 2.203567 CTTGTTGGCCGGGGGAAA 60.204 61.111 2.18 0.00 0.00 3.13
2538 2739 4.986708 GCTTGTTGGCCGGGGGAA 62.987 66.667 2.18 0.00 0.00 3.97
2541 2742 3.989787 GTTGCTTGTTGGCCGGGG 61.990 66.667 2.18 0.00 0.00 5.73
2542 2743 3.989787 GGTTGCTTGTTGGCCGGG 61.990 66.667 2.18 0.00 0.00 5.73
2543 2744 3.989787 GGGTTGCTTGTTGGCCGG 61.990 66.667 0.00 0.00 0.00 6.13
2544 2745 2.912025 AGGGTTGCTTGTTGGCCG 60.912 61.111 0.00 0.00 0.00 6.13
2545 2746 2.919494 CGAGGGTTGCTTGTTGGCC 61.919 63.158 0.00 0.00 0.00 5.36
2546 2747 2.644992 CGAGGGTTGCTTGTTGGC 59.355 61.111 0.00 0.00 0.00 4.52
2547 2748 1.856265 GAGCGAGGGTTGCTTGTTGG 61.856 60.000 0.00 0.00 44.18 3.77
2548 2749 1.576421 GAGCGAGGGTTGCTTGTTG 59.424 57.895 0.00 0.00 44.18 3.33
2549 2750 1.600916 GGAGCGAGGGTTGCTTGTT 60.601 57.895 0.00 0.00 44.18 2.83
2550 2751 2.032681 GGAGCGAGGGTTGCTTGT 59.967 61.111 0.00 0.00 44.18 3.16
2551 2752 2.747855 GGGAGCGAGGGTTGCTTG 60.748 66.667 0.00 0.00 44.18 4.01
2552 2753 4.394712 CGGGAGCGAGGGTTGCTT 62.395 66.667 0.00 0.00 44.18 3.91
2584 2785 3.281359 AAAAATGGGCGGCAGCGTC 62.281 57.895 12.47 0.00 46.35 5.19
2585 2786 3.302344 AAAAATGGGCGGCAGCGT 61.302 55.556 12.47 0.00 46.35 5.07
2586 2787 2.810458 CAAAAATGGGCGGCAGCG 60.810 61.111 12.47 0.00 46.35 5.18
2587 2788 1.446618 CTCAAAAATGGGCGGCAGC 60.447 57.895 12.47 0.00 44.18 5.25
2588 2789 1.216178 CCTCAAAAATGGGCGGCAG 59.784 57.895 12.47 0.00 0.00 4.85
2589 2790 2.941616 GCCTCAAAAATGGGCGGCA 61.942 57.895 12.47 0.00 37.48 5.69
2590 2791 2.125552 GCCTCAAAAATGGGCGGC 60.126 61.111 0.00 0.00 36.37 6.53
2593 2794 0.171231 GAGTCGCCTCAAAAATGGGC 59.829 55.000 0.00 0.00 42.18 5.36
2594 2795 1.826385 AGAGTCGCCTCAAAAATGGG 58.174 50.000 0.00 0.00 40.40 4.00
2595 2796 2.162408 GGAAGAGTCGCCTCAAAAATGG 59.838 50.000 0.00 0.00 40.40 3.16
2596 2797 2.813754 TGGAAGAGTCGCCTCAAAAATG 59.186 45.455 0.00 0.00 40.40 2.32
2597 2798 3.077359 CTGGAAGAGTCGCCTCAAAAAT 58.923 45.455 0.00 0.00 40.40 1.82
2598 2799 2.494059 CTGGAAGAGTCGCCTCAAAAA 58.506 47.619 0.00 0.00 40.40 1.94
2599 2800 1.878102 GCTGGAAGAGTCGCCTCAAAA 60.878 52.381 0.00 0.00 40.40 2.44
2600 2801 0.320771 GCTGGAAGAGTCGCCTCAAA 60.321 55.000 0.00 0.00 40.40 2.69
2601 2802 1.188219 AGCTGGAAGAGTCGCCTCAA 61.188 55.000 0.00 0.00 40.40 3.02
2602 2803 0.323451 TAGCTGGAAGAGTCGCCTCA 60.323 55.000 0.00 0.00 40.40 3.86
2603 2804 0.101579 GTAGCTGGAAGAGTCGCCTC 59.898 60.000 0.00 0.00 34.07 4.70
2604 2805 1.324005 GGTAGCTGGAAGAGTCGCCT 61.324 60.000 0.00 0.00 34.07 5.52
2605 2806 1.142097 GGTAGCTGGAAGAGTCGCC 59.858 63.158 0.00 0.00 34.07 5.54
2606 2807 1.226717 CGGTAGCTGGAAGAGTCGC 60.227 63.158 0.00 0.00 34.07 5.19
2607 2808 1.226717 GCGGTAGCTGGAAGAGTCG 60.227 63.158 0.00 0.00 41.01 4.18
2608 2809 1.142097 GGCGGTAGCTGGAAGAGTC 59.858 63.158 0.00 0.00 44.37 3.36
2609 2810 2.711922 CGGCGGTAGCTGGAAGAGT 61.712 63.158 0.00 0.00 45.75 3.24
2610 2811 2.105128 CGGCGGTAGCTGGAAGAG 59.895 66.667 0.00 0.00 45.75 2.85
2618 2819 1.004918 ATATGGAAGCGGCGGTAGC 60.005 57.895 13.69 7.75 44.18 3.58
2619 2820 0.389948 GGATATGGAAGCGGCGGTAG 60.390 60.000 13.69 0.00 0.00 3.18
2620 2821 1.669440 GGATATGGAAGCGGCGGTA 59.331 57.895 13.69 0.00 0.00 4.02
2621 2822 2.426023 GGATATGGAAGCGGCGGT 59.574 61.111 5.44 5.44 0.00 5.68
2622 2823 2.738521 CGGATATGGAAGCGGCGG 60.739 66.667 9.78 0.00 0.00 6.13
2623 2824 3.414700 GCGGATATGGAAGCGGCG 61.415 66.667 0.51 0.51 0.00 6.46
2624 2825 3.050275 GGCGGATATGGAAGCGGC 61.050 66.667 0.00 0.00 0.00 6.53
2625 2826 2.358737 GGGCGGATATGGAAGCGG 60.359 66.667 0.00 0.00 0.00 5.52
2626 2827 1.669115 CTGGGCGGATATGGAAGCG 60.669 63.158 0.00 0.00 0.00 4.68
2627 2828 1.968540 GCTGGGCGGATATGGAAGC 60.969 63.158 0.00 0.00 0.00 3.86
2628 2829 1.451504 TGCTGGGCGGATATGGAAG 59.548 57.895 0.00 0.00 0.00 3.46
2629 2830 3.654021 TGCTGGGCGGATATGGAA 58.346 55.556 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.