Multiple sequence alignment - TraesCS4A01G085100

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 TraesCS4A01G085100 chr4A 100.000 3708 0 0 1 3708 89895177 89898884 0.000000e+00 6848
1 TraesCS4A01G085100 chr4A 88.439 173 19 1 870 1042 89680934 89681105 1.350000e-49 207
2 TraesCS4A01G085100 chr4B 90.658 1702 129 18 757 2441 461196678 461194990 0.000000e+00 2235
3 TraesCS4A01G085100 chr4B 95.380 606 26 2 1 606 610119839 610120442 0.000000e+00 963
4 TraesCS4A01G085100 chr4B 83.974 624 53 26 2497 3100 461194973 461194377 4.180000e-154 555
5 TraesCS4A01G085100 chr4B 85.989 364 40 7 3125 3487 461194387 461194034 2.700000e-101 379
6 TraesCS4A01G085100 chr4D 88.279 1331 96 20 1807 3100 374613791 374612484 0.000000e+00 1539
7 TraesCS4A01G085100 chr4D 90.538 1152 60 11 640 1754 374614929 374613790 0.000000e+00 1478
8 TraesCS4A01G085100 chr4D 80.345 290 26 12 3124 3411 374612496 374612236 1.360000e-44 191
9 TraesCS4A01G085100 chr4D 84.021 194 24 3 732 924 374773052 374772865 2.940000e-41 180
10 TraesCS4A01G085100 chr4D 91.736 121 10 0 922 1042 374783786 374783666 6.370000e-38 169
11 TraesCS4A01G085100 chr4D 90.984 122 10 1 922 1042 374772373 374772252 2.960000e-36 163
12 TraesCS4A01G085100 chr5D 95.888 608 21 2 1 605 413676084 413676690 0.000000e+00 981
13 TraesCS4A01G085100 chr1D 95.447 615 24 2 1 612 58117873 58118486 0.000000e+00 977
14 TraesCS4A01G085100 chr3D 95.574 610 23 2 1 607 603318552 603319160 0.000000e+00 974
15 TraesCS4A01G085100 chr3D 95.559 608 23 2 1 605 522951223 522951829 0.000000e+00 970
16 TraesCS4A01G085100 chr2D 95.395 608 24 2 1 605 102291824 102292430 0.000000e+00 965
17 TraesCS4A01G085100 chr1B 95.380 606 26 2 1 606 625080919 625080316 0.000000e+00 963
18 TraesCS4A01G085100 chr3B 95.222 607 23 4 1 604 168700936 168701539 0.000000e+00 955
19 TraesCS4A01G085100 chr2B 94.926 611 27 2 1 608 790304622 790304013 0.000000e+00 953


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 TraesCS4A01G085100 chr4A 89895177 89898884 3707 False 6848.000000 6848 100.000000 1 3708 1 chr4A.!!$F2 3707
1 TraesCS4A01G085100 chr4B 461194034 461196678 2644 True 1056.333333 2235 86.873667 757 3487 3 chr4B.!!$R1 2730
2 TraesCS4A01G085100 chr4B 610119839 610120442 603 False 963.000000 963 95.380000 1 606 1 chr4B.!!$F1 605
3 TraesCS4A01G085100 chr4D 374612236 374614929 2693 True 1069.333333 1539 86.387333 640 3411 3 chr4D.!!$R2 2771
4 TraesCS4A01G085100 chr5D 413676084 413676690 606 False 981.000000 981 95.888000 1 605 1 chr5D.!!$F1 604
5 TraesCS4A01G085100 chr1D 58117873 58118486 613 False 977.000000 977 95.447000 1 612 1 chr1D.!!$F1 611
6 TraesCS4A01G085100 chr3D 603318552 603319160 608 False 974.000000 974 95.574000 1 607 1 chr3D.!!$F2 606
7 TraesCS4A01G085100 chr3D 522951223 522951829 606 False 970.000000 970 95.559000 1 605 1 chr3D.!!$F1 604
8 TraesCS4A01G085100 chr2D 102291824 102292430 606 False 965.000000 965 95.395000 1 605 1 chr2D.!!$F1 604
9 TraesCS4A01G085100 chr1B 625080316 625080919 603 True 963.000000 963 95.380000 1 606 1 chr1B.!!$R1 605
10 TraesCS4A01G085100 chr3B 168700936 168701539 603 False 955.000000 955 95.222000 1 604 1 chr3B.!!$F1 603
11 TraesCS4A01G085100 chr2B 790304013 790304622 609 True 953.000000 953 94.926000 1 608 1 chr2B.!!$R1 607

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
686 690 0.108329 GTGCATGCCTGTACGTACCT 60.108 55.0 22.43 0.11 0.00 3.08 F
1077 1112 0.178961 AGTCAAACCCCCAAGCTTCC 60.179 55.0 0.00 0.00 0.00 3.46 F
2598 2681 0.172578 TGGCGTAGACACCTCATTCG 59.827 55.0 0.00 0.00 34.89 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 2681 0.519961 AAGCGCGTGGGAATTACAAC 59.480 50.000 8.43 0.0 0.00 3.32 R
2679 2763 1.277557 TCTTCTCCTTGCTCTCTTGCC 59.722 52.381 0.00 0.0 0.00 4.52 R
3521 3617 0.392336 TTGCTTTGCACCACCCATTC 59.608 50.000 0.00 0.0 38.71 2.67 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
79 80 2.631062 TCGCAGAAGGAAACCAGAACTA 59.369 45.455 0.00 0.00 0.00 2.24
89 90 0.834687 ACCAGAACTACCCGCCTTCA 60.835 55.000 0.00 0.00 0.00 3.02
119 120 3.054361 ACCCAACACAAGATACTCCATCC 60.054 47.826 0.00 0.00 33.75 3.51
326 327 2.158798 AGGGATCGACAGAGACACGATA 60.159 50.000 0.00 0.00 44.73 2.92
347 348 2.341101 ATCAACTCCGAGACGCCGT 61.341 57.895 1.33 0.00 0.00 5.68
362 363 1.292223 CCGTCATGAAGGACACCGT 59.708 57.895 21.80 0.00 37.66 4.83
399 400 4.192317 GGTTGAGGCAGATTTATTCGTCT 58.808 43.478 0.00 0.00 0.00 4.18
401 402 4.736126 TGAGGCAGATTTATTCGTCTGA 57.264 40.909 6.56 0.00 43.50 3.27
404 405 3.118629 AGGCAGATTTATTCGTCTGAGCA 60.119 43.478 6.56 0.00 43.50 4.26
577 578 3.138798 GTCGCCTCGCCCTAGTCA 61.139 66.667 0.00 0.00 0.00 3.41
612 616 2.892215 GCTAGGGTAGGAAACGATAGCT 59.108 50.000 0.00 0.00 38.67 3.32
613 617 3.057386 GCTAGGGTAGGAAACGATAGCTC 60.057 52.174 0.00 0.00 38.67 4.09
614 618 2.317973 AGGGTAGGAAACGATAGCTCC 58.682 52.381 0.00 0.00 40.73 4.70
615 619 1.000496 GGGTAGGAAACGATAGCTCCG 60.000 57.143 6.86 6.86 44.08 4.63
616 620 1.680207 GGTAGGAAACGATAGCTCCGT 59.320 52.381 8.09 8.09 44.08 4.69
623 627 3.978718 AACGATAGCTCCGTTACCTAC 57.021 47.619 20.65 0.00 46.73 3.18
624 628 1.869767 ACGATAGCTCCGTTACCTACG 59.130 52.381 8.09 0.00 45.79 3.51
625 629 2.743183 ACGATAGCTCCGTTACCTACGT 60.743 50.000 8.09 0.00 45.06 3.57
626 630 4.836215 ACGATAGCTCCGTTACCTACGTG 61.836 52.174 8.09 0.00 45.06 4.49
636 640 4.789075 CCTACGTGGTCGCGGTGG 62.789 72.222 6.13 0.00 41.18 4.61
637 641 3.740397 CTACGTGGTCGCGGTGGA 61.740 66.667 6.13 0.00 41.18 4.02
638 642 3.060020 CTACGTGGTCGCGGTGGAT 62.060 63.158 6.13 0.00 41.18 3.41
669 673 2.744202 GACAGCCTTATCAACCACTGTG 59.256 50.000 0.00 0.00 38.42 3.66
673 677 2.159338 GCCTTATCAACCACTGTGCATG 60.159 50.000 1.29 3.60 0.00 4.06
676 680 0.251474 ATCAACCACTGTGCATGCCT 60.251 50.000 16.68 0.00 0.00 4.75
677 681 1.174078 TCAACCACTGTGCATGCCTG 61.174 55.000 16.68 12.66 0.00 4.85
686 690 0.108329 GTGCATGCCTGTACGTACCT 60.108 55.000 22.43 0.11 0.00 3.08
697 701 4.374399 CTGTACGTACCTTGAAAACCAGT 58.626 43.478 22.43 0.00 0.00 4.00
700 704 5.984926 TGTACGTACCTTGAAAACCAGTAAG 59.015 40.000 22.43 0.00 0.00 2.34
716 720 4.389374 CAGTAAGTTGCCCTCAAGAGAAA 58.611 43.478 0.00 0.00 31.93 2.52
717 721 4.821805 CAGTAAGTTGCCCTCAAGAGAAAA 59.178 41.667 0.00 0.00 31.93 2.29
771 802 0.529378 AACAGTAAGTAGACGGGCCG 59.471 55.000 27.06 27.06 0.00 6.13
777 808 0.686769 AAGTAGACGGGCCGGATCTT 60.687 55.000 31.78 23.02 0.00 2.40
787 818 0.815615 GCCGGATCTTAGTTGGGCTG 60.816 60.000 5.05 0.00 37.57 4.85
797 828 1.454847 GTTGGGCTGTGTGGAACCA 60.455 57.895 0.00 0.00 34.36 3.67
822 857 2.043604 AACAGCCCAAAAGCCCTTGC 62.044 55.000 0.00 0.00 37.95 4.01
843 878 1.359848 CCCGAATCTCTTCCACGTTG 58.640 55.000 0.00 0.00 0.00 4.10
854 889 3.047877 CACGTTGTCCCTTCGGCC 61.048 66.667 0.00 0.00 0.00 6.13
872 907 1.070134 GCCACCAAAGAAAGGGGAAAC 59.930 52.381 0.00 0.00 0.00 2.78
952 987 4.542697 ACTCCAACTTCTCCTAGATCTCC 58.457 47.826 0.00 0.00 0.00 3.71
1066 1101 1.343465 TCGAGGAAGGTGAGTCAAACC 59.657 52.381 0.00 0.00 38.03 3.27
1071 1106 0.930726 AAGGTGAGTCAAACCCCCAA 59.069 50.000 0.00 0.00 38.57 4.12
1077 1112 0.178961 AGTCAAACCCCCAAGCTTCC 60.179 55.000 0.00 0.00 0.00 3.46
1079 1114 0.263172 TCAAACCCCCAAGCTTCCAA 59.737 50.000 0.00 0.00 0.00 3.53
1085 1120 1.551883 CCCCCAAGCTTCCAATTCTTG 59.448 52.381 0.00 0.00 37.52 3.02
1122 1157 1.277557 AGAAATGCAGAGCTCGTCCTT 59.722 47.619 8.37 0.74 0.00 3.36
1138 1173 1.093159 CCTTGTTCTCCAGCAGATGC 58.907 55.000 0.00 0.00 42.49 3.91
1148 1183 2.329339 GCAGATGCGAAATCGGGC 59.671 61.111 4.84 0.00 40.23 6.13
1185 1220 2.159382 GGGCGTTTCCTCTTGAAATCA 58.841 47.619 0.00 0.00 44.44 2.57
1187 1222 2.552315 GGCGTTTCCTCTTGAAATCACA 59.448 45.455 0.00 0.00 44.44 3.58
1201 1236 1.812235 ATCACAACGCAATCTGAGCA 58.188 45.000 0.00 0.00 0.00 4.26
1296 1337 4.698304 TCTTATTTAAGGGAGGCGTTGTTG 59.302 41.667 0.00 0.00 34.14 3.33
1365 1406 5.046529 AGCTGAATTGATGTTACTAGCTCG 58.953 41.667 0.00 0.00 35.54 5.03
1373 1414 9.811995 AATTGATGTTACTAGCTCGTGTTATTA 57.188 29.630 0.22 0.00 0.00 0.98
1374 1415 8.624701 TTGATGTTACTAGCTCGTGTTATTAC 57.375 34.615 0.22 0.00 0.00 1.89
1375 1416 6.908820 TGATGTTACTAGCTCGTGTTATTACG 59.091 38.462 0.22 0.00 44.98 3.18
1376 1417 6.182039 TGTTACTAGCTCGTGTTATTACGT 57.818 37.500 0.22 0.00 44.06 3.57
1377 1418 6.023435 TGTTACTAGCTCGTGTTATTACGTG 58.977 40.000 0.00 0.00 44.06 4.49
1378 1419 4.691860 ACTAGCTCGTGTTATTACGTGT 57.308 40.909 0.00 0.00 44.06 4.49
1396 1441 6.399639 ACGTGTTTATGAAATTTGGGAACT 57.600 33.333 0.00 0.00 0.00 3.01
1441 1486 3.505680 TGGTTCACCGGAATGAGAAATTG 59.494 43.478 9.46 0.00 39.43 2.32
1460 1505 8.374743 AGAAATTGTGGGCATGTTTTAAAGTAT 58.625 29.630 0.00 0.00 0.00 2.12
1461 1506 7.903995 AATTGTGGGCATGTTTTAAAGTATG 57.096 32.000 0.00 8.57 0.00 2.39
1465 1510 6.092748 GTGGGCATGTTTTAAAGTATGTCAG 58.907 40.000 15.67 0.00 0.00 3.51
1480 1525 6.756221 AGTATGTCAGTTAAAGGTTCTCGTT 58.244 36.000 0.00 0.00 0.00 3.85
1481 1526 6.867293 AGTATGTCAGTTAAAGGTTCTCGTTC 59.133 38.462 0.00 0.00 0.00 3.95
1482 1527 5.272283 TGTCAGTTAAAGGTTCTCGTTCT 57.728 39.130 0.00 0.00 0.00 3.01
1483 1528 5.667466 TGTCAGTTAAAGGTTCTCGTTCTT 58.333 37.500 0.00 0.00 0.00 2.52
1484 1529 5.522460 TGTCAGTTAAAGGTTCTCGTTCTTG 59.478 40.000 0.00 0.00 0.00 3.02
1485 1530 5.522824 GTCAGTTAAAGGTTCTCGTTCTTGT 59.477 40.000 0.00 0.00 0.00 3.16
1486 1531 6.036844 GTCAGTTAAAGGTTCTCGTTCTTGTT 59.963 38.462 0.00 0.00 0.00 2.83
1487 1532 6.596497 TCAGTTAAAGGTTCTCGTTCTTGTTT 59.404 34.615 0.00 0.00 0.00 2.83
1488 1533 7.765360 TCAGTTAAAGGTTCTCGTTCTTGTTTA 59.235 33.333 0.00 0.00 0.00 2.01
1514 1559 4.022068 TGAAAGAGCTAGTTTTGCCCATTG 60.022 41.667 0.00 0.00 0.00 2.82
1521 1566 4.501400 GCTAGTTTTGCCCATTGTGTTTCT 60.501 41.667 0.00 0.00 0.00 2.52
1800 1845 6.428159 AGTCTCACTCGTGCAAATAGAAAATT 59.572 34.615 0.00 0.00 0.00 1.82
1801 1846 7.602644 AGTCTCACTCGTGCAAATAGAAAATTA 59.397 33.333 0.00 0.00 0.00 1.40
1802 1847 8.227791 GTCTCACTCGTGCAAATAGAAAATTAA 58.772 33.333 0.00 0.00 0.00 1.40
1818 1863 4.783764 AATTAAAGCTTTGAAGACCCCG 57.216 40.909 22.02 0.00 0.00 5.73
1834 1879 3.046374 ACCCCGATATTGCTCCTTAAGT 58.954 45.455 0.97 0.00 0.00 2.24
1869 1914 4.782019 TTGTGCTTGTGGATTAATCACC 57.218 40.909 17.07 7.15 34.46 4.02
1887 1932 2.354821 CACCGAAACTAATAAGCTGGCC 59.645 50.000 0.00 0.00 0.00 5.36
1909 1954 5.220931 GCCTTTATTCGTCATTCAGCAGAAT 60.221 40.000 0.00 0.00 45.16 2.40
1910 1955 6.678900 GCCTTTATTCGTCATTCAGCAGAATT 60.679 38.462 0.91 0.00 42.46 2.17
1958 2003 2.165167 ACAGACAATGAGGCAATGTGG 58.835 47.619 0.00 0.00 26.67 4.17
1962 2007 4.036027 CAGACAATGAGGCAATGTGGATAC 59.964 45.833 0.00 0.00 26.67 2.24
2009 2054 7.148507 CCTGTGAGTTTCTCATGATTCTAACAC 60.149 40.741 0.00 4.75 42.73 3.32
2028 2073 6.536731 AACACCTCATATACTACGTAGACG 57.463 41.667 28.74 11.43 46.33 4.18
2045 2091 7.256286 ACGTAGACGCTAGATTTTTCATTACT 58.744 34.615 1.14 0.00 44.43 2.24
2050 2096 7.276658 AGACGCTAGATTTTTCATTACTGACAG 59.723 37.037 0.00 0.00 0.00 3.51
2053 2099 7.900352 CGCTAGATTTTTCATTACTGACAGAAC 59.100 37.037 10.08 0.00 0.00 3.01
2088 2134 8.995027 TTTTATATGCAAGTCCTTCATATGGT 57.005 30.769 2.13 2.40 35.65 3.55
2092 2138 4.513442 TGCAAGTCCTTCATATGGTGTAC 58.487 43.478 2.13 0.00 0.00 2.90
2100 2146 6.097839 GTCCTTCATATGGTGTACTTCTGGTA 59.902 42.308 2.13 0.00 0.00 3.25
2207 2254 9.657419 CATTTGGAATTTTATAGAGCCAAGTTT 57.343 29.630 0.00 0.00 36.82 2.66
2208 2255 9.657419 ATTTGGAATTTTATAGAGCCAAGTTTG 57.343 29.630 0.00 0.00 36.82 2.93
2216 2263 0.523519 GAGCCAAGTTTGCTGTAGGC 59.476 55.000 6.12 0.00 39.69 3.93
2225 2272 4.874970 AGTTTGCTGTAGGCTTTGATTTG 58.125 39.130 0.00 0.00 42.39 2.32
2244 2291 1.538512 TGTAGTCCGAAGTTCTGACCG 59.461 52.381 20.05 0.00 32.02 4.79
2250 2297 0.670546 CGAAGTTCTGACCGTGCCAT 60.671 55.000 0.56 0.00 0.00 4.40
2258 2305 1.210155 GACCGTGCCATGAACTTGC 59.790 57.895 0.00 0.00 0.00 4.01
2262 2309 2.596923 TGCCATGAACTTGCGCCA 60.597 55.556 4.18 0.00 0.00 5.69
2275 2322 1.669115 GCGCCAGTTCTTGAGAGCA 60.669 57.895 0.00 0.00 0.00 4.26
2283 2330 2.793160 TTCTTGAGAGCAGCGCCTGG 62.793 60.000 2.29 0.00 31.21 4.45
2338 2385 9.911788 AAAGAATATGATCTACTTGTCACCAAT 57.088 29.630 0.00 0.00 0.00 3.16
2339 2386 8.899427 AGAATATGATCTACTTGTCACCAATG 57.101 34.615 0.00 0.00 0.00 2.82
2341 2388 4.908601 TGATCTACTTGTCACCAATGGT 57.091 40.909 0.00 0.00 35.62 3.55
2342 2389 6.560003 ATGATCTACTTGTCACCAATGGTA 57.440 37.500 3.85 0.00 32.11 3.25
2347 2397 6.597562 TCTACTTGTCACCAATGGTAGTTTT 58.402 36.000 3.85 0.00 33.90 2.43
2363 2413 6.713450 TGGTAGTTTTCATTTGAGGAACCTAC 59.287 38.462 0.00 0.00 0.00 3.18
2450 2500 0.738762 CTGACCACATGGCGTCTCTG 60.739 60.000 13.60 0.00 39.32 3.35
2453 2520 1.807165 CCACATGGCGTCTCTGTCG 60.807 63.158 0.00 0.00 0.00 4.35
2489 2556 7.944729 ATAACCAAAATCTGTTATGAGCTGT 57.055 32.000 0.00 0.00 36.55 4.40
2583 2663 1.670295 TGTTGCATACTAGCATTGGCG 59.330 47.619 0.00 0.00 45.19 5.69
2598 2681 0.172578 TGGCGTAGACACCTCATTCG 59.827 55.000 0.00 0.00 34.89 3.34
2679 2763 3.889815 TGAAGAAGGCTTACATGGATGG 58.110 45.455 0.00 0.00 33.61 3.51
2733 2817 3.715628 ATGCACGGATAAATGGAAAGC 57.284 42.857 0.00 0.00 0.00 3.51
2893 2986 9.832445 TCAAGGAATCCATGTAGTACTTTTATC 57.168 33.333 0.00 0.00 0.00 1.75
2953 3046 1.963515 CTGGTTTAGCTGGCCAAAGTT 59.036 47.619 7.01 0.00 0.00 2.66
3023 3116 7.728847 AAAATACATTTTCAAGCTTTGGTCC 57.271 32.000 0.00 0.00 35.18 4.46
3088 3181 8.200792 TGTAAAAACATAATGCCAGAAAGTTGT 58.799 29.630 0.00 0.00 0.00 3.32
3094 3187 7.147976 ACATAATGCCAGAAAGTTGTCTTTTC 58.852 34.615 0.00 0.00 42.99 2.29
3139 3232 2.559998 AACGCCTTGTGTTTCTGTTG 57.440 45.000 0.00 0.00 31.91 3.33
3194 3287 3.127895 TCGGTTGTTCAGTGTTTTCCTTG 59.872 43.478 0.00 0.00 0.00 3.61
3209 3302 8.338986 GTGTTTTCCTTGTTCTTTTTGACAAAA 58.661 29.630 9.30 9.30 0.00 2.44
3210 3303 8.338986 TGTTTTCCTTGTTCTTTTTGACAAAAC 58.661 29.630 12.86 3.41 0.00 2.43
3214 3307 6.015010 TCCTTGTTCTTTTTGACAAAACCTGA 60.015 34.615 12.86 8.94 0.00 3.86
3233 3326 6.133356 ACCTGACCCTCTTTTGAATGTTTAA 58.867 36.000 0.00 0.00 0.00 1.52
3236 3329 5.009210 TGACCCTCTTTTGAATGTTTAACCG 59.991 40.000 0.00 0.00 0.00 4.44
3248 3342 6.041069 TGAATGTTTAACCGAAAATGACCCTT 59.959 34.615 0.00 0.00 0.00 3.95
3256 3350 3.189287 CCGAAAATGACCCTTGTCTGAAG 59.811 47.826 0.00 0.00 42.28 3.02
3263 3357 4.134563 TGACCCTTGTCTGAAGCTTTAAC 58.865 43.478 0.00 0.00 42.28 2.01
3276 3370 8.267894 TCTGAAGCTTTAACCAAATATAGCTCT 58.732 33.333 0.00 0.00 38.65 4.09
3277 3371 9.547753 CTGAAGCTTTAACCAAATATAGCTCTA 57.452 33.333 0.00 0.00 38.65 2.43
3281 3377 9.289782 AGCTTTAACCAAATATAGCTCTATTGG 57.710 33.333 15.19 15.19 35.99 3.16
3357 3453 3.550275 GGTTTTGAGAAAAACTTGGCGAC 59.450 43.478 12.36 0.00 41.20 5.19
3397 3493 2.621526 ACGATTTGGGTTCAACTCCAAC 59.378 45.455 9.34 0.97 42.10 3.77
3413 3509 0.951040 CAACGACCTTGGAGCTGACC 60.951 60.000 0.00 0.00 0.00 4.02
3427 3523 4.578105 GGAGCTGACCTATTTTCCATTCTG 59.422 45.833 0.00 0.00 0.00 3.02
3440 3536 2.019984 CCATTCTGGGCAGTAGCTTTC 58.980 52.381 0.00 0.00 41.70 2.62
3452 3548 0.891373 TAGCTTTCGTGCTGAGCTCT 59.109 50.000 16.19 0.00 44.99 4.09
3454 3550 0.668706 GCTTTCGTGCTGAGCTCTCA 60.669 55.000 16.19 10.10 38.06 3.27
3457 3553 1.788258 TTCGTGCTGAGCTCTCAAAG 58.212 50.000 16.19 4.76 39.39 2.77
3480 3576 2.678836 TGAGCGTCAGAGTAAGTAGCTC 59.321 50.000 7.50 7.50 46.73 4.09
3487 3583 2.645802 AGAGTAAGTAGCTCTGACCCG 58.354 52.381 0.00 0.00 41.32 5.28
3488 3584 2.026075 AGAGTAAGTAGCTCTGACCCGT 60.026 50.000 0.00 0.00 41.32 5.28
3489 3585 2.093106 AGTAAGTAGCTCTGACCCGTG 58.907 52.381 0.00 0.00 0.00 4.94
3490 3586 0.815734 TAAGTAGCTCTGACCCGTGC 59.184 55.000 0.00 0.00 0.00 5.34
3491 3587 2.202623 GTAGCTCTGACCCGTGCG 60.203 66.667 0.00 0.00 0.00 5.34
3492 3588 3.449227 TAGCTCTGACCCGTGCGG 61.449 66.667 3.25 3.25 37.81 5.69
3502 3598 3.897936 CCGTGCGGGAAATTGCTA 58.102 55.556 2.15 0.00 38.47 3.49
3503 3599 2.176140 CCGTGCGGGAAATTGCTAA 58.824 52.632 2.15 0.00 38.47 3.09
3504 3600 0.098728 CCGTGCGGGAAATTGCTAAG 59.901 55.000 2.15 0.00 38.47 2.18
3505 3601 0.802494 CGTGCGGGAAATTGCTAAGT 59.198 50.000 0.00 0.00 0.00 2.24
3506 3602 1.199097 CGTGCGGGAAATTGCTAAGTT 59.801 47.619 0.00 0.00 0.00 2.66
3507 3603 2.351350 CGTGCGGGAAATTGCTAAGTTT 60.351 45.455 0.00 0.00 0.00 2.66
3508 3604 3.649073 GTGCGGGAAATTGCTAAGTTTT 58.351 40.909 0.00 0.00 0.00 2.43
3509 3605 4.055360 GTGCGGGAAATTGCTAAGTTTTT 58.945 39.130 0.00 0.00 0.00 1.94
3510 3606 4.149922 GTGCGGGAAATTGCTAAGTTTTTC 59.850 41.667 0.00 0.00 0.00 2.29
3511 3607 4.038642 TGCGGGAAATTGCTAAGTTTTTCT 59.961 37.500 0.00 0.00 0.00 2.52
3512 3608 4.621460 GCGGGAAATTGCTAAGTTTTTCTC 59.379 41.667 0.00 0.00 0.00 2.87
3513 3609 5.161358 CGGGAAATTGCTAAGTTTTTCTCC 58.839 41.667 0.00 0.00 0.00 3.71
3514 3610 5.479306 GGGAAATTGCTAAGTTTTTCTCCC 58.521 41.667 0.00 0.00 0.00 4.30
3515 3611 5.479306 GGAAATTGCTAAGTTTTTCTCCCC 58.521 41.667 0.00 0.00 0.00 4.81
3516 3612 5.011635 GGAAATTGCTAAGTTTTTCTCCCCA 59.988 40.000 0.00 0.00 0.00 4.96
3517 3613 5.468540 AATTGCTAAGTTTTTCTCCCCAC 57.531 39.130 0.00 0.00 0.00 4.61
3518 3614 2.871453 TGCTAAGTTTTTCTCCCCACC 58.129 47.619 0.00 0.00 0.00 4.61
3519 3615 2.175931 TGCTAAGTTTTTCTCCCCACCA 59.824 45.455 0.00 0.00 0.00 4.17
3520 3616 3.227614 GCTAAGTTTTTCTCCCCACCAA 58.772 45.455 0.00 0.00 0.00 3.67
3521 3617 3.255888 GCTAAGTTTTTCTCCCCACCAAG 59.744 47.826 0.00 0.00 0.00 3.61
3522 3618 3.680777 AAGTTTTTCTCCCCACCAAGA 57.319 42.857 0.00 0.00 0.00 3.02
3523 3619 3.680777 AGTTTTTCTCCCCACCAAGAA 57.319 42.857 0.00 0.00 0.00 2.52
3524 3620 4.199002 AGTTTTTCTCCCCACCAAGAAT 57.801 40.909 0.00 0.00 31.89 2.40
3525 3621 3.897505 AGTTTTTCTCCCCACCAAGAATG 59.102 43.478 0.00 0.00 31.89 2.67
3534 3630 4.517663 CCAAGAATGGGTGGTGCA 57.482 55.556 0.00 0.00 43.51 4.57
3535 3631 2.744062 CCAAGAATGGGTGGTGCAA 58.256 52.632 0.00 0.00 43.51 4.08
3536 3632 1.047002 CCAAGAATGGGTGGTGCAAA 58.953 50.000 0.00 0.00 43.51 3.68
3537 3633 1.001181 CCAAGAATGGGTGGTGCAAAG 59.999 52.381 0.00 0.00 43.51 2.77
3538 3634 0.681175 AAGAATGGGTGGTGCAAAGC 59.319 50.000 0.00 0.00 0.00 3.51
3539 3635 0.469705 AGAATGGGTGGTGCAAAGCA 60.470 50.000 0.00 0.00 35.60 3.91
3540 3636 0.392336 GAATGGGTGGTGCAAAGCAA 59.608 50.000 0.00 0.00 41.47 3.91
3541 3637 0.393820 AATGGGTGGTGCAAAGCAAG 59.606 50.000 0.00 0.00 41.47 4.01
3542 3638 0.469705 ATGGGTGGTGCAAAGCAAGA 60.470 50.000 0.00 0.00 41.47 3.02
3543 3639 1.108727 TGGGTGGTGCAAAGCAAGAG 61.109 55.000 0.00 0.00 41.47 2.85
3544 3640 1.109323 GGGTGGTGCAAAGCAAGAGT 61.109 55.000 0.00 0.00 41.47 3.24
3545 3641 1.604604 GGTGGTGCAAAGCAAGAGTA 58.395 50.000 0.00 0.00 41.47 2.59
3546 3642 1.953686 GGTGGTGCAAAGCAAGAGTAA 59.046 47.619 0.00 0.00 41.47 2.24
3547 3643 2.360801 GGTGGTGCAAAGCAAGAGTAAA 59.639 45.455 0.00 0.00 41.47 2.01
3548 3644 3.181480 GGTGGTGCAAAGCAAGAGTAAAA 60.181 43.478 0.00 0.00 41.47 1.52
3549 3645 4.501400 GGTGGTGCAAAGCAAGAGTAAAAT 60.501 41.667 0.00 0.00 41.47 1.82
3550 3646 5.049828 GTGGTGCAAAGCAAGAGTAAAATT 58.950 37.500 0.00 0.00 41.47 1.82
3551 3647 5.523552 GTGGTGCAAAGCAAGAGTAAAATTT 59.476 36.000 0.00 0.00 41.47 1.82
3552 3648 6.037062 GTGGTGCAAAGCAAGAGTAAAATTTT 59.963 34.615 8.75 8.75 41.47 1.82
3553 3649 6.036953 TGGTGCAAAGCAAGAGTAAAATTTTG 59.963 34.615 13.76 0.00 41.47 2.44
3554 3650 6.037062 GGTGCAAAGCAAGAGTAAAATTTTGT 59.963 34.615 13.76 0.50 41.47 2.83
3555 3651 7.413988 GGTGCAAAGCAAGAGTAAAATTTTGTT 60.414 33.333 13.76 1.35 41.47 2.83
3556 3652 8.599774 GTGCAAAGCAAGAGTAAAATTTTGTTA 58.400 29.630 13.76 0.00 41.47 2.41
3557 3653 9.155975 TGCAAAGCAAGAGTAAAATTTTGTTAA 57.844 25.926 13.76 0.00 34.76 2.01
3558 3654 9.980780 GCAAAGCAAGAGTAAAATTTTGTTAAA 57.019 25.926 13.76 0.00 0.00 1.52
3585 3681 9.495754 CTTTTGCAGTATCATCTTTAACTAAGC 57.504 33.333 0.00 0.00 33.66 3.09
3586 3682 8.792830 TTTGCAGTATCATCTTTAACTAAGCT 57.207 30.769 0.00 0.00 33.66 3.74
3587 3683 8.792830 TTGCAGTATCATCTTTAACTAAGCTT 57.207 30.769 3.48 3.48 33.66 3.74
3588 3684 8.792830 TGCAGTATCATCTTTAACTAAGCTTT 57.207 30.769 3.20 0.00 33.66 3.51
3589 3685 9.231297 TGCAGTATCATCTTTAACTAAGCTTTT 57.769 29.630 3.20 0.00 33.66 2.27
3599 3695 9.636789 TCTTTAACTAAGCTTTTAGAAAAGGGT 57.363 29.630 3.20 1.85 44.24 4.34
3630 3726 7.214467 TGTCTATTTTCACTCATTTTCACCC 57.786 36.000 0.00 0.00 0.00 4.61
3631 3727 6.775142 TGTCTATTTTCACTCATTTTCACCCA 59.225 34.615 0.00 0.00 0.00 4.51
3632 3728 7.286546 TGTCTATTTTCACTCATTTTCACCCAA 59.713 33.333 0.00 0.00 0.00 4.12
3633 3729 8.141268 GTCTATTTTCACTCATTTTCACCCAAA 58.859 33.333 0.00 0.00 0.00 3.28
3634 3730 8.869109 TCTATTTTCACTCATTTTCACCCAAAT 58.131 29.630 0.00 0.00 0.00 2.32
3637 3733 9.844257 ATTTTCACTCATTTTCACCCAAATAAA 57.156 25.926 0.00 0.00 0.00 1.40
3638 3734 9.844257 TTTTCACTCATTTTCACCCAAATAAAT 57.156 25.926 0.00 0.00 0.00 1.40
3639 3735 9.844257 TTTCACTCATTTTCACCCAAATAAATT 57.156 25.926 0.00 0.00 0.00 1.82
3640 3736 9.844257 TTCACTCATTTTCACCCAAATAAATTT 57.156 25.926 0.00 0.00 0.00 1.82
3641 3737 9.487790 TCACTCATTTTCACCCAAATAAATTTC 57.512 29.630 0.00 0.00 0.00 2.17
3642 3738 9.270640 CACTCATTTTCACCCAAATAAATTTCA 57.729 29.630 0.00 0.00 0.00 2.69
3671 3767 8.674263 AGATTTAGAGAATGTGATCATGTTCC 57.326 34.615 15.40 9.67 34.19 3.62
3672 3768 8.492782 AGATTTAGAGAATGTGATCATGTTCCT 58.507 33.333 15.40 14.23 34.19 3.36
3673 3769 8.674263 ATTTAGAGAATGTGATCATGTTCCTC 57.326 34.615 15.40 11.12 34.19 3.71
3674 3770 5.688814 AGAGAATGTGATCATGTTCCTCA 57.311 39.130 15.40 1.79 34.19 3.86
3675 3771 6.058553 AGAGAATGTGATCATGTTCCTCAA 57.941 37.500 15.40 0.00 34.19 3.02
3676 3772 6.479006 AGAGAATGTGATCATGTTCCTCAAA 58.521 36.000 15.40 0.00 34.19 2.69
3677 3773 6.598457 AGAGAATGTGATCATGTTCCTCAAAG 59.402 38.462 15.40 0.00 34.19 2.77
3678 3774 6.479006 AGAATGTGATCATGTTCCTCAAAGA 58.521 36.000 15.40 0.00 34.19 2.52
3679 3775 7.117397 AGAATGTGATCATGTTCCTCAAAGAT 58.883 34.615 15.40 0.00 34.19 2.40
3680 3776 6.939132 ATGTGATCATGTTCCTCAAAGATC 57.061 37.500 0.00 0.00 39.69 2.75
3681 3777 4.872124 TGTGATCATGTTCCTCAAAGATCG 59.128 41.667 0.00 0.00 40.89 3.69
3682 3778 5.111989 GTGATCATGTTCCTCAAAGATCGA 58.888 41.667 0.00 0.00 40.89 3.59
3683 3779 5.757320 GTGATCATGTTCCTCAAAGATCGAT 59.243 40.000 0.00 0.00 40.89 3.59
3684 3780 5.756833 TGATCATGTTCCTCAAAGATCGATG 59.243 40.000 0.54 0.00 40.89 3.84
3685 3781 5.089970 TCATGTTCCTCAAAGATCGATGT 57.910 39.130 0.54 0.00 0.00 3.06
3686 3782 6.220726 TCATGTTCCTCAAAGATCGATGTA 57.779 37.500 0.54 0.00 0.00 2.29
3687 3783 6.820335 TCATGTTCCTCAAAGATCGATGTAT 58.180 36.000 0.54 0.00 0.00 2.29
3688 3784 7.951591 TCATGTTCCTCAAAGATCGATGTATA 58.048 34.615 0.54 0.00 0.00 1.47
3689 3785 8.588472 TCATGTTCCTCAAAGATCGATGTATAT 58.412 33.333 0.54 0.00 0.00 0.86
3690 3786 9.212641 CATGTTCCTCAAAGATCGATGTATATT 57.787 33.333 0.54 0.00 0.00 1.28
3691 3787 8.818141 TGTTCCTCAAAGATCGATGTATATTC 57.182 34.615 0.54 0.00 0.00 1.75
3692 3788 8.642432 TGTTCCTCAAAGATCGATGTATATTCT 58.358 33.333 0.54 0.00 0.00 2.40
3696 3792 9.526713 CCTCAAAGATCGATGTATATTCTATGG 57.473 37.037 0.54 0.00 0.00 2.74
3702 3798 9.645059 AGATCGATGTATATTCTATGGTTGTTG 57.355 33.333 0.54 0.00 0.00 3.33
3703 3799 9.424319 GATCGATGTATATTCTATGGTTGTTGT 57.576 33.333 0.54 0.00 0.00 3.32
3704 3800 9.778741 ATCGATGTATATTCTATGGTTGTTGTT 57.221 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.676093 GGGTAGTTCTGGTTTCCTTCTG 58.324 50.000 0.00 0.00 0.00 3.02
79 80 2.113139 CTGTGGTTGAAGGCGGGT 59.887 61.111 0.00 0.00 0.00 5.28
89 90 1.283613 TCTTGTGTTGGGTCTGTGGTT 59.716 47.619 0.00 0.00 0.00 3.67
119 120 3.559024 CGCAAGTGACAGCTGGAG 58.441 61.111 19.93 1.92 0.00 3.86
265 266 2.811431 GTTCATGGATGGTGTTGACGAA 59.189 45.455 0.00 0.00 0.00 3.85
326 327 1.215647 GCGTCTCGGAGTTGATGGT 59.784 57.895 4.69 0.00 0.00 3.55
347 348 1.183030 ACCGACGGTGTCCTTCATGA 61.183 55.000 21.02 0.00 32.98 3.07
362 363 4.567597 ACCCCACTCCCACACCGA 62.568 66.667 0.00 0.00 0.00 4.69
619 623 4.789075 CCACCGCGACCACGTAGG 62.789 72.222 8.23 0.00 45.67 3.18
620 624 1.717791 TATCCACCGCGACCACGTAG 61.718 60.000 8.23 0.00 41.98 3.51
621 625 1.102809 ATATCCACCGCGACCACGTA 61.103 55.000 8.23 0.00 41.98 3.57
622 626 1.102809 TATATCCACCGCGACCACGT 61.103 55.000 8.23 0.00 41.98 4.49
623 627 0.031043 TTATATCCACCGCGACCACG 59.969 55.000 8.23 0.00 42.93 4.94
624 628 1.338973 TCTTATATCCACCGCGACCAC 59.661 52.381 8.23 0.00 0.00 4.16
625 629 1.694844 TCTTATATCCACCGCGACCA 58.305 50.000 8.23 0.00 0.00 4.02
626 630 4.157289 TCTTATCTTATATCCACCGCGACC 59.843 45.833 8.23 0.00 0.00 4.79
627 631 5.094134 GTCTTATCTTATATCCACCGCGAC 58.906 45.833 8.23 0.00 0.00 5.19
628 632 4.763279 TGTCTTATCTTATATCCACCGCGA 59.237 41.667 8.23 0.00 0.00 5.87
629 633 5.055642 TGTCTTATCTTATATCCACCGCG 57.944 43.478 0.00 0.00 0.00 6.46
630 634 4.865365 GCTGTCTTATCTTATATCCACCGC 59.135 45.833 0.00 0.00 0.00 5.68
631 635 5.186021 AGGCTGTCTTATCTTATATCCACCG 59.814 44.000 0.00 0.00 0.00 4.94
632 636 6.613153 AGGCTGTCTTATCTTATATCCACC 57.387 41.667 0.00 0.00 0.00 4.61
665 669 0.999406 GTACGTACAGGCATGCACAG 59.001 55.000 21.36 10.82 0.00 3.66
669 673 1.006832 CAAGGTACGTACAGGCATGC 58.993 55.000 26.02 9.90 0.00 4.06
673 677 2.481568 GGTTTTCAAGGTACGTACAGGC 59.518 50.000 26.02 9.95 0.00 4.85
676 680 4.405116 ACTGGTTTTCAAGGTACGTACA 57.595 40.909 26.02 3.64 0.00 2.90
677 681 5.985530 ACTTACTGGTTTTCAAGGTACGTAC 59.014 40.000 17.56 17.56 0.00 3.67
686 690 3.634910 GAGGGCAACTTACTGGTTTTCAA 59.365 43.478 0.00 0.00 0.00 2.69
762 793 0.686769 AACTAAGATCCGGCCCGTCT 60.687 55.000 0.85 0.00 0.00 4.18
771 802 2.359900 CACACAGCCCAACTAAGATCC 58.640 52.381 0.00 0.00 0.00 3.36
777 808 0.109723 GGTTCCACACAGCCCAACTA 59.890 55.000 0.00 0.00 0.00 2.24
787 818 0.684805 TGTTGGGGTTGGTTCCACAC 60.685 55.000 0.00 0.00 40.96 3.82
797 828 1.695114 GCTTTTGGGCTGTTGGGGTT 61.695 55.000 0.00 0.00 0.00 4.11
822 857 1.144057 CGTGGAAGAGATTCGGGGG 59.856 63.158 0.00 0.00 0.00 5.40
872 907 0.759346 CAGGGAGGTTTCCTATCGGG 59.241 60.000 0.00 0.00 43.49 5.14
887 922 4.431131 AGGCGGCCATTGACAGGG 62.431 66.667 23.09 0.00 0.00 4.45
919 954 6.274908 AGGAGAAGTTGGAGTTAAACCCTAAT 59.725 38.462 0.00 0.00 0.00 1.73
1035 1070 2.563620 ACCTTCCTCGACCTTCTTCTTC 59.436 50.000 0.00 0.00 0.00 2.87
1079 1114 5.063204 TCAATATTCCGAATCGCCAAGAAT 58.937 37.500 0.00 3.71 0.00 2.40
1085 1120 5.385617 CATTTCTCAATATTCCGAATCGCC 58.614 41.667 0.00 0.00 0.00 5.54
1122 1157 0.321346 TTCGCATCTGCTGGAGAACA 59.679 50.000 2.14 0.00 39.32 3.18
1138 1173 3.118454 ACGCACTGCCCGATTTCG 61.118 61.111 0.00 0.00 39.44 3.46
1185 1220 1.882912 TTCTGCTCAGATTGCGTTGT 58.117 45.000 0.00 0.00 37.29 3.32
1187 1222 4.497006 GCATTATTCTGCTCAGATTGCGTT 60.497 41.667 0.00 0.00 39.12 4.84
1201 1236 2.673833 GCTACCGCTACGCATTATTCT 58.326 47.619 0.00 0.00 0.00 2.40
1296 1337 1.815003 ACTACCACTACCACTACGCAC 59.185 52.381 0.00 0.00 0.00 5.34
1373 1414 6.264518 AGAGTTCCCAAATTTCATAAACACGT 59.735 34.615 0.00 0.00 0.00 4.49
1374 1415 6.582295 CAGAGTTCCCAAATTTCATAAACACG 59.418 38.462 0.00 0.00 0.00 4.49
1375 1416 7.433680 ACAGAGTTCCCAAATTTCATAAACAC 58.566 34.615 0.00 0.00 0.00 3.32
1376 1417 7.595819 ACAGAGTTCCCAAATTTCATAAACA 57.404 32.000 0.00 0.00 0.00 2.83
1377 1418 8.360390 AGAACAGAGTTCCCAAATTTCATAAAC 58.640 33.333 6.29 0.00 0.00 2.01
1378 1419 8.359642 CAGAACAGAGTTCCCAAATTTCATAAA 58.640 33.333 6.29 0.00 0.00 1.40
1396 1441 5.126222 CACTAGCAGATTCTACCAGAACAGA 59.874 44.000 0.00 0.00 37.00 3.41
1441 1486 6.019779 TGACATACTTTAAAACATGCCCAC 57.980 37.500 0.00 1.51 0.00 4.61
1460 1505 5.272283 AGAACGAGAACCTTTAACTGACA 57.728 39.130 0.00 0.00 0.00 3.58
1461 1506 5.522824 ACAAGAACGAGAACCTTTAACTGAC 59.477 40.000 0.00 0.00 0.00 3.51
1465 1510 8.771766 AGATAAACAAGAACGAGAACCTTTAAC 58.228 33.333 0.00 0.00 0.00 2.01
1480 1525 9.561069 AAAACTAGCTCTTTCAGATAAACAAGA 57.439 29.630 0.00 0.00 0.00 3.02
1481 1526 9.604626 CAAAACTAGCTCTTTCAGATAAACAAG 57.395 33.333 0.00 0.00 0.00 3.16
1482 1527 8.076178 GCAAAACTAGCTCTTTCAGATAAACAA 58.924 33.333 0.00 0.00 0.00 2.83
1483 1528 7.308589 GGCAAAACTAGCTCTTTCAGATAAACA 60.309 37.037 0.00 0.00 0.00 2.83
1484 1529 7.024171 GGCAAAACTAGCTCTTTCAGATAAAC 58.976 38.462 0.00 0.00 0.00 2.01
1485 1530 6.151144 GGGCAAAACTAGCTCTTTCAGATAAA 59.849 38.462 0.00 0.00 0.00 1.40
1486 1531 5.648092 GGGCAAAACTAGCTCTTTCAGATAA 59.352 40.000 0.00 0.00 0.00 1.75
1487 1532 5.186198 GGGCAAAACTAGCTCTTTCAGATA 58.814 41.667 0.00 0.00 0.00 1.98
1488 1533 4.013050 GGGCAAAACTAGCTCTTTCAGAT 58.987 43.478 0.00 0.00 0.00 2.90
1497 1542 2.597455 ACACAATGGGCAAAACTAGCT 58.403 42.857 0.00 0.00 0.00 3.32
1502 1547 4.058721 AGAGAAACACAATGGGCAAAAC 57.941 40.909 0.00 0.00 0.00 2.43
1514 1559 3.483558 CGCAAAGCTGAAAAGAGAAACAC 59.516 43.478 0.00 0.00 0.00 3.32
1521 1566 4.406688 TTGCTGCGCAAAGCTGAAAAGA 62.407 45.455 20.56 0.00 45.96 2.52
1769 1814 1.271434 TGCACGAGTGAGACTCTACCT 60.271 52.381 7.50 0.00 42.92 3.08
1800 1845 3.713826 ATCGGGGTCTTCAAAGCTTTA 57.286 42.857 12.25 0.00 0.00 1.85
1801 1846 2.586648 ATCGGGGTCTTCAAAGCTTT 57.413 45.000 5.69 5.69 0.00 3.51
1802 1847 3.933861 ATATCGGGGTCTTCAAAGCTT 57.066 42.857 0.00 0.00 0.00 3.74
1834 1879 9.237187 TCCACAAGCACAATGTTTCTATTTATA 57.763 29.630 0.00 0.00 0.00 0.98
1858 1903 8.283291 CAGCTTATTAGTTTCGGTGATTAATCC 58.717 37.037 12.90 4.44 0.00 3.01
1869 1914 4.965119 AAAGGCCAGCTTATTAGTTTCG 57.035 40.909 5.01 0.00 0.00 3.46
1950 1995 5.984233 TTTATCAGACGTATCCACATTGC 57.016 39.130 0.00 0.00 0.00 3.56
1958 2003 8.436200 GGCATGAACTAATTTATCAGACGTATC 58.564 37.037 0.00 0.00 0.00 2.24
1962 2007 6.258727 ACAGGCATGAACTAATTTATCAGACG 59.741 38.462 4.84 0.00 0.00 4.18
2009 2054 6.328714 TCTAGCGTCTACGTAGTATATGAGG 58.671 44.000 21.53 8.71 44.56 3.86
2028 2073 8.940952 AGTTCTGTCAGTAATGAAAAATCTAGC 58.059 33.333 0.00 0.00 0.00 3.42
2050 2096 9.331282 ACTTGCATATAAAAGGAGACATAGTTC 57.669 33.333 0.00 0.00 0.00 3.01
2053 2099 8.153550 AGGACTTGCATATAAAAGGAGACATAG 58.846 37.037 0.00 0.00 0.00 2.23
2071 2117 4.770795 AGTACACCATATGAAGGACTTGC 58.229 43.478 3.65 0.00 0.00 4.01
2088 2134 5.046159 ACCCAAATCGATTACCAGAAGTACA 60.046 40.000 11.83 0.00 0.00 2.90
2092 2138 5.897377 AAACCCAAATCGATTACCAGAAG 57.103 39.130 11.83 0.00 0.00 2.85
2100 2146 5.010282 ACAGCTTCTAAACCCAAATCGATT 58.990 37.500 4.39 4.39 0.00 3.34
2208 2255 4.095036 GGACTACAAATCAAAGCCTACAGC 59.905 45.833 0.00 0.00 44.25 4.40
2216 2263 6.423905 TCAGAACTTCGGACTACAAATCAAAG 59.576 38.462 0.00 0.00 0.00 2.77
2225 2272 1.538950 ACGGTCAGAACTTCGGACTAC 59.461 52.381 18.02 5.50 40.62 2.73
2244 2291 2.126346 GGCGCAAGTTCATGGCAC 60.126 61.111 10.83 0.00 41.68 5.01
2258 2305 1.633852 GCTGCTCTCAAGAACTGGCG 61.634 60.000 0.00 0.00 0.00 5.69
2262 2309 1.375268 GGCGCTGCTCTCAAGAACT 60.375 57.895 7.64 0.00 0.00 3.01
2275 2322 1.185618 TTACACTCTGTCCAGGCGCT 61.186 55.000 7.64 0.00 0.00 5.92
2283 2330 4.819630 TGTCCAATGGTTTTACACTCTGTC 59.180 41.667 0.00 0.00 0.00 3.51
2338 2385 5.701224 AGGTTCCTCAAATGAAAACTACCA 58.299 37.500 0.00 0.00 0.00 3.25
2339 2386 6.940867 AGTAGGTTCCTCAAATGAAAACTACC 59.059 38.462 14.83 5.92 36.31 3.18
2341 2388 6.430000 GCAGTAGGTTCCTCAAATGAAAACTA 59.570 38.462 0.00 0.41 0.00 2.24
2342 2389 5.241728 GCAGTAGGTTCCTCAAATGAAAACT 59.758 40.000 0.00 1.18 0.00 2.66
2347 2397 3.582647 TCAGCAGTAGGTTCCTCAAATGA 59.417 43.478 0.00 0.00 0.00 2.57
2363 2413 5.705902 TGATCATCAAACATGTTTCAGCAG 58.294 37.500 20.85 9.77 0.00 4.24
2441 2491 0.729816 GTCACTTCGACAGAGACGCC 60.730 60.000 8.50 0.00 44.69 5.68
2450 2500 5.856126 TTGGTTATGATTGTCACTTCGAC 57.144 39.130 0.00 0.00 45.61 4.20
2453 2520 8.299570 ACAGATTTTGGTTATGATTGTCACTTC 58.700 33.333 0.00 0.00 0.00 3.01
2467 2534 5.565439 GCACAGCTCATAACAGATTTTGGTT 60.565 40.000 0.00 0.00 0.00 3.67
2471 2538 4.081406 TGGCACAGCTCATAACAGATTTT 58.919 39.130 0.00 0.00 0.00 1.82
2512 2579 5.020795 GGTAATGGTAACCACCTTCCAATT 58.979 41.667 0.00 0.00 45.98 2.32
2583 2663 6.035758 GGAATTACAACGAATGAGGTGTCTAC 59.964 42.308 0.00 0.00 0.00 2.59
2598 2681 0.519961 AAGCGCGTGGGAATTACAAC 59.480 50.000 8.43 0.00 0.00 3.32
2679 2763 1.277557 TCTTCTCCTTGCTCTCTTGCC 59.722 52.381 0.00 0.00 0.00 4.52
2727 2811 3.670105 TGGAGAACCATGGCTTTCC 57.330 52.632 16.18 16.18 41.77 3.13
3034 3127 3.105937 GTTGAACAAAACTGGCGACTTC 58.894 45.455 0.00 0.00 0.00 3.01
3119 3212 2.490115 TCAACAGAAACACAAGGCGTTT 59.510 40.909 0.00 0.00 39.23 3.60
3120 3213 2.088423 TCAACAGAAACACAAGGCGTT 58.912 42.857 0.00 0.00 0.00 4.84
3121 3214 1.745232 TCAACAGAAACACAAGGCGT 58.255 45.000 0.00 0.00 0.00 5.68
3122 3215 2.842208 TTCAACAGAAACACAAGGCG 57.158 45.000 0.00 0.00 0.00 5.52
3123 3216 4.622740 GCATATTCAACAGAAACACAAGGC 59.377 41.667 0.00 0.00 0.00 4.35
3124 3217 5.771469 TGCATATTCAACAGAAACACAAGG 58.229 37.500 0.00 0.00 0.00 3.61
3125 3218 7.878477 ATTGCATATTCAACAGAAACACAAG 57.122 32.000 0.00 0.00 0.00 3.16
3133 3226 9.489084 GGTACAGTATATTGCATATTCAACAGA 57.511 33.333 0.00 0.00 0.00 3.41
3134 3227 9.494271 AGGTACAGTATATTGCATATTCAACAG 57.506 33.333 0.00 0.00 0.00 3.16
3135 3228 9.845740 AAGGTACAGTATATTGCATATTCAACA 57.154 29.630 0.00 0.00 0.00 3.33
3138 3231 9.710900 CAGAAGGTACAGTATATTGCATATTCA 57.289 33.333 0.00 0.00 0.00 2.57
3139 3232 9.155975 CCAGAAGGTACAGTATATTGCATATTC 57.844 37.037 0.00 0.00 0.00 1.75
3155 3248 1.471676 CCGAGTGCATCCAGAAGGTAC 60.472 57.143 0.00 0.00 35.89 3.34
3194 3287 4.868171 GGGTCAGGTTTTGTCAAAAAGAAC 59.132 41.667 12.26 12.44 35.96 3.01
3209 3302 3.884037 ACATTCAAAAGAGGGTCAGGT 57.116 42.857 0.00 0.00 0.00 4.00
3210 3303 6.447162 GTTAAACATTCAAAAGAGGGTCAGG 58.553 40.000 0.00 0.00 0.00 3.86
3214 3307 5.134661 TCGGTTAAACATTCAAAAGAGGGT 58.865 37.500 0.00 0.00 0.00 4.34
3233 3326 2.105821 TCAGACAAGGGTCATTTTCGGT 59.894 45.455 0.00 0.00 46.80 4.69
3236 3329 3.823304 AGCTTCAGACAAGGGTCATTTTC 59.177 43.478 0.00 0.00 46.80 2.29
3248 3342 7.829211 AGCTATATTTGGTTAAAGCTTCAGACA 59.171 33.333 0.00 0.00 0.00 3.41
3256 3350 9.067986 ACCAATAGAGCTATATTTGGTTAAAGC 57.932 33.333 20.31 0.00 29.69 3.51
3276 3370 7.387673 CGCTGGAATGAGTTATATTGACCAATA 59.612 37.037 5.08 5.08 37.64 1.90
3277 3371 6.205464 CGCTGGAATGAGTTATATTGACCAAT 59.795 38.462 0.64 0.64 34.93 3.16
3281 3377 4.752101 AGCGCTGGAATGAGTTATATTGAC 59.248 41.667 10.39 0.00 0.00 3.18
3287 3383 4.770795 AGTTTAGCGCTGGAATGAGTTAT 58.229 39.130 22.90 0.00 0.00 1.89
3289 3385 3.059352 AGTTTAGCGCTGGAATGAGTT 57.941 42.857 22.90 0.00 0.00 3.01
3292 3388 2.083774 CCAAGTTTAGCGCTGGAATGA 58.916 47.619 22.90 0.00 0.00 2.57
3369 3465 5.912892 AGTTGAACCCAAATCGTCATTTTT 58.087 33.333 0.00 0.00 33.49 1.94
3397 3493 1.115467 ATAGGTCAGCTCCAAGGTCG 58.885 55.000 0.00 0.00 0.00 4.79
3427 3523 1.376037 AGCACGAAAGCTACTGCCC 60.376 57.895 0.00 0.00 44.50 5.36
3452 3548 0.676184 ACTCTGACGCTCAGCTTTGA 59.324 50.000 0.00 0.00 43.95 2.69
3454 3550 2.297597 ACTTACTCTGACGCTCAGCTTT 59.702 45.455 0.00 0.00 43.95 3.51
3457 3553 2.793237 GCTACTTACTCTGACGCTCAGC 60.793 54.545 9.34 0.00 43.95 4.26
3468 3564 2.097791 CACGGGTCAGAGCTACTTACTC 59.902 54.545 0.00 0.00 0.00 2.59
3472 3568 1.592223 GCACGGGTCAGAGCTACTT 59.408 57.895 0.00 0.00 0.00 2.24
3475 3571 3.449227 CCGCACGGGTCAGAGCTA 61.449 66.667 0.00 0.00 0.00 3.32
3487 3583 3.297830 AAACTTAGCAATTTCCCGCAC 57.702 42.857 0.00 0.00 0.00 5.34
3488 3584 4.038642 AGAAAAACTTAGCAATTTCCCGCA 59.961 37.500 0.00 0.00 33.35 5.69
3489 3585 4.556233 AGAAAAACTTAGCAATTTCCCGC 58.444 39.130 0.00 0.00 33.35 6.13
3490 3586 5.161358 GGAGAAAAACTTAGCAATTTCCCG 58.839 41.667 0.00 0.00 33.35 5.14
3491 3587 5.479306 GGGAGAAAAACTTAGCAATTTCCC 58.521 41.667 0.00 0.00 33.35 3.97
3492 3588 5.011635 TGGGGAGAAAAACTTAGCAATTTCC 59.988 40.000 0.00 0.00 33.35 3.13
3493 3589 5.926542 GTGGGGAGAAAAACTTAGCAATTTC 59.073 40.000 0.00 0.00 33.13 2.17
3494 3590 5.221641 GGTGGGGAGAAAAACTTAGCAATTT 60.222 40.000 0.00 0.00 0.00 1.82
3495 3591 4.283467 GGTGGGGAGAAAAACTTAGCAATT 59.717 41.667 0.00 0.00 0.00 2.32
3496 3592 3.832490 GGTGGGGAGAAAAACTTAGCAAT 59.168 43.478 0.00 0.00 0.00 3.56
3497 3593 3.227614 GGTGGGGAGAAAAACTTAGCAA 58.772 45.455 0.00 0.00 0.00 3.91
3498 3594 2.175931 TGGTGGGGAGAAAAACTTAGCA 59.824 45.455 0.00 0.00 0.00 3.49
3499 3595 2.871453 TGGTGGGGAGAAAAACTTAGC 58.129 47.619 0.00 0.00 0.00 3.09
3500 3596 4.725490 TCTTGGTGGGGAGAAAAACTTAG 58.275 43.478 0.00 0.00 0.00 2.18
3501 3597 4.799715 TCTTGGTGGGGAGAAAAACTTA 57.200 40.909 0.00 0.00 0.00 2.24
3502 3598 3.680777 TCTTGGTGGGGAGAAAAACTT 57.319 42.857 0.00 0.00 0.00 2.66
3503 3599 3.680777 TTCTTGGTGGGGAGAAAAACT 57.319 42.857 0.00 0.00 0.00 2.66
3504 3600 3.006859 CCATTCTTGGTGGGGAGAAAAAC 59.993 47.826 0.00 0.00 38.30 2.43
3505 3601 3.238597 CCATTCTTGGTGGGGAGAAAAA 58.761 45.455 0.00 0.00 38.30 1.94
3506 3602 2.888212 CCATTCTTGGTGGGGAGAAAA 58.112 47.619 0.00 0.00 38.30 2.29
3507 3603 2.603075 CCATTCTTGGTGGGGAGAAA 57.397 50.000 0.00 0.00 38.30 2.52
3517 3613 1.001181 CTTTGCACCACCCATTCTTGG 59.999 52.381 0.00 0.00 43.23 3.61
3518 3614 1.606224 GCTTTGCACCACCCATTCTTG 60.606 52.381 0.00 0.00 0.00 3.02
3519 3615 0.681175 GCTTTGCACCACCCATTCTT 59.319 50.000 0.00 0.00 0.00 2.52
3520 3616 0.469705 TGCTTTGCACCACCCATTCT 60.470 50.000 0.00 0.00 31.71 2.40
3521 3617 0.392336 TTGCTTTGCACCACCCATTC 59.608 50.000 0.00 0.00 38.71 2.67
3522 3618 0.393820 CTTGCTTTGCACCACCCATT 59.606 50.000 0.00 0.00 38.71 3.16
3523 3619 0.469705 TCTTGCTTTGCACCACCCAT 60.470 50.000 0.00 0.00 38.71 4.00
3524 3620 1.076412 TCTTGCTTTGCACCACCCA 60.076 52.632 0.00 0.00 38.71 4.51
3525 3621 1.109323 ACTCTTGCTTTGCACCACCC 61.109 55.000 0.00 0.00 38.71 4.61
3526 3622 1.604604 TACTCTTGCTTTGCACCACC 58.395 50.000 0.00 0.00 38.71 4.61
3527 3623 3.708563 TTTACTCTTGCTTTGCACCAC 57.291 42.857 0.00 0.00 38.71 4.16
3528 3624 4.935352 ATTTTACTCTTGCTTTGCACCA 57.065 36.364 0.00 0.00 38.71 4.17
3529 3625 6.037062 ACAAAATTTTACTCTTGCTTTGCACC 59.963 34.615 2.44 0.00 38.71 5.01
3530 3626 7.003939 ACAAAATTTTACTCTTGCTTTGCAC 57.996 32.000 2.44 0.00 38.71 4.57
3531 3627 7.608308 AACAAAATTTTACTCTTGCTTTGCA 57.392 28.000 2.44 0.00 36.47 4.08
3532 3628 9.980780 TTTAACAAAATTTTACTCTTGCTTTGC 57.019 25.926 2.44 0.00 0.00 3.68
3559 3655 9.495754 GCTTAGTTAAAGATGATACTGCAAAAG 57.504 33.333 0.00 0.00 37.38 2.27
3560 3656 9.231297 AGCTTAGTTAAAGATGATACTGCAAAA 57.769 29.630 0.00 0.00 37.38 2.44
3561 3657 8.792830 AGCTTAGTTAAAGATGATACTGCAAA 57.207 30.769 0.00 0.00 37.38 3.68
3562 3658 8.792830 AAGCTTAGTTAAAGATGATACTGCAA 57.207 30.769 0.00 0.00 37.38 4.08
3563 3659 8.792830 AAAGCTTAGTTAAAGATGATACTGCA 57.207 30.769 0.00 0.00 37.38 4.41
3573 3669 9.636789 ACCCTTTTCTAAAAGCTTAGTTAAAGA 57.363 29.630 18.08 7.62 43.07 2.52
3604 3700 8.306761 GGGTGAAAATGAGTGAAAATAGACAAT 58.693 33.333 0.00 0.00 0.00 2.71
3605 3701 7.286546 TGGGTGAAAATGAGTGAAAATAGACAA 59.713 33.333 0.00 0.00 0.00 3.18
3606 3702 6.775142 TGGGTGAAAATGAGTGAAAATAGACA 59.225 34.615 0.00 0.00 0.00 3.41
3607 3703 7.214467 TGGGTGAAAATGAGTGAAAATAGAC 57.786 36.000 0.00 0.00 0.00 2.59
3608 3704 7.831691 TTGGGTGAAAATGAGTGAAAATAGA 57.168 32.000 0.00 0.00 0.00 1.98
3611 3707 9.844257 TTTATTTGGGTGAAAATGAGTGAAAAT 57.156 25.926 0.00 0.00 32.16 1.82
3612 3708 9.844257 ATTTATTTGGGTGAAAATGAGTGAAAA 57.156 25.926 0.00 0.00 32.16 2.29
3613 3709 9.844257 AATTTATTTGGGTGAAAATGAGTGAAA 57.156 25.926 0.00 0.00 32.16 2.69
3614 3710 9.844257 AAATTTATTTGGGTGAAAATGAGTGAA 57.156 25.926 0.00 0.00 32.16 3.18
3615 3711 9.487790 GAAATTTATTTGGGTGAAAATGAGTGA 57.512 29.630 0.00 0.00 32.16 3.41
3616 3712 9.270640 TGAAATTTATTTGGGTGAAAATGAGTG 57.729 29.630 0.00 0.00 32.16 3.51
3645 3741 9.118300 GGAACATGATCACATTCTCTAAATCTT 57.882 33.333 16.46 0.00 34.15 2.40
3646 3742 8.492782 AGGAACATGATCACATTCTCTAAATCT 58.507 33.333 16.46 4.93 34.15 2.40
3647 3743 8.674263 AGGAACATGATCACATTCTCTAAATC 57.326 34.615 16.46 3.21 34.15 2.17
3648 3744 8.270030 TGAGGAACATGATCACATTCTCTAAAT 58.730 33.333 16.46 2.04 34.15 1.40
3649 3745 7.623630 TGAGGAACATGATCACATTCTCTAAA 58.376 34.615 16.46 5.85 34.15 1.85
3650 3746 7.186570 TGAGGAACATGATCACATTCTCTAA 57.813 36.000 16.46 6.52 34.15 2.10
3651 3747 6.796785 TGAGGAACATGATCACATTCTCTA 57.203 37.500 16.46 4.86 34.15 2.43
3652 3748 5.688814 TGAGGAACATGATCACATTCTCT 57.311 39.130 16.46 12.80 34.15 3.10
3653 3749 6.596888 TCTTTGAGGAACATGATCACATTCTC 59.403 38.462 16.46 11.33 34.15 2.87
3654 3750 6.479006 TCTTTGAGGAACATGATCACATTCT 58.521 36.000 16.46 3.40 34.15 2.40
3655 3751 6.748333 TCTTTGAGGAACATGATCACATTC 57.252 37.500 0.00 4.84 34.15 2.67
3656 3752 6.037940 CGATCTTTGAGGAACATGATCACATT 59.962 38.462 0.00 0.00 38.01 2.71
3657 3753 5.526479 CGATCTTTGAGGAACATGATCACAT 59.474 40.000 0.00 0.00 38.01 3.21
3658 3754 4.872124 CGATCTTTGAGGAACATGATCACA 59.128 41.667 0.00 0.00 38.01 3.58
3659 3755 5.111989 TCGATCTTTGAGGAACATGATCAC 58.888 41.667 0.00 0.00 38.01 3.06
3660 3756 5.343307 TCGATCTTTGAGGAACATGATCA 57.657 39.130 0.00 0.00 38.01 2.92
3661 3757 5.757320 ACATCGATCTTTGAGGAACATGATC 59.243 40.000 0.00 0.00 36.48 2.92
3662 3758 5.678583 ACATCGATCTTTGAGGAACATGAT 58.321 37.500 0.00 0.00 0.00 2.45
3663 3759 5.089970 ACATCGATCTTTGAGGAACATGA 57.910 39.130 0.00 0.00 0.00 3.07
3664 3760 8.768957 ATATACATCGATCTTTGAGGAACATG 57.231 34.615 0.00 0.00 0.00 3.21
3665 3761 9.429359 GAATATACATCGATCTTTGAGGAACAT 57.571 33.333 0.00 0.00 0.00 2.71
3666 3762 8.642432 AGAATATACATCGATCTTTGAGGAACA 58.358 33.333 0.00 0.00 0.00 3.18
3670 3766 9.526713 CCATAGAATATACATCGATCTTTGAGG 57.473 37.037 0.00 0.00 0.00 3.86
3676 3772 9.645059 CAACAACCATAGAATATACATCGATCT 57.355 33.333 0.00 0.00 0.00 2.75
3677 3773 9.424319 ACAACAACCATAGAATATACATCGATC 57.576 33.333 0.00 0.00 0.00 3.69
3678 3774 9.778741 AACAACAACCATAGAATATACATCGAT 57.221 29.630 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.