Multiple sequence alignment - TraesCS7A01G490500

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 TraesCS7A01G490500 chr7A 100.000 4786 0 0 846 5631 679927610 679922825 0.000000e+00 8839.0
1 TraesCS7A01G490500 chr7A 100.000 627 0 0 1 627 679928455 679927829 0.000000e+00 1158.0
2 TraesCS7A01G490500 chr7B 94.363 2111 94 14 849 2950 660362677 660360583 0.000000e+00 3216.0
3 TraesCS7A01G490500 chr7B 93.929 1186 47 10 2948 4118 660360502 660359327 0.000000e+00 1768.0
4 TraesCS7A01G490500 chr7B 92.605 1190 63 14 4133 5307 660359348 660358169 0.000000e+00 1687.0
5 TraesCS7A01G490500 chr7B 88.848 538 47 9 899 1430 699156350 699155820 0.000000e+00 649.0
6 TraesCS7A01G490500 chr7B 84.848 264 15 7 5372 5631 660358063 660357821 5.640000e-60 243.0
7 TraesCS7A01G490500 chr7D 93.474 2176 87 32 849 3004 588068298 588066158 0.000000e+00 3181.0
8 TraesCS7A01G490500 chr7D 94.799 1692 61 6 3003 4668 588065996 588064306 0.000000e+00 2612.0
9 TraesCS7A01G490500 chr7D 93.813 695 35 4 4620 5307 588064308 588063615 0.000000e+00 1038.0
10 TraesCS7A01G490500 chr7D 89.785 372 27 5 35 401 588069069 588068704 3.070000e-127 466.0
11 TraesCS7A01G490500 chr7D 83.891 329 26 9 5306 5631 588063561 588063257 7.140000e-74 289.0
12 TraesCS7A01G490500 chr7D 89.032 155 9 7 477 626 588068668 588068517 9.630000e-43 185.0
13 TraesCS7A01G490500 chr2B 89.052 612 49 12 899 1502 369808859 369808258 0.000000e+00 743.0
14 TraesCS7A01G490500 chr6D 91.026 78 7 0 1025 1102 114228937 114229014 7.720000e-19 106.0
15 TraesCS7A01G490500 chr6A 91.026 78 7 0 1025 1102 142780236 142780313 7.720000e-19 106.0
16 TraesCS7A01G490500 chr6A 96.078 51 2 0 5306 5356 608892036 608892086 3.620000e-12 84.2
17 TraesCS7A01G490500 chr6B 90.909 77 7 0 1025 1101 203919922 203919998 2.780000e-18 104.0


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 TraesCS7A01G490500 chr7A 679922825 679928455 5630 True 4998.500000 8839 100.00000 1 5631 2 chr7A.!!$R1 5630
1 TraesCS7A01G490500 chr7B 660357821 660362677 4856 True 1728.500000 3216 91.43625 849 5631 4 chr7B.!!$R2 4782
2 TraesCS7A01G490500 chr7B 699155820 699156350 530 True 649.000000 649 88.84800 899 1430 1 chr7B.!!$R1 531
3 TraesCS7A01G490500 chr7D 588063257 588069069 5812 True 1295.166667 3181 90.79900 35 5631 6 chr7D.!!$R1 5596
4 TraesCS7A01G490500 chr2B 369808258 369808859 601 True 743.000000 743 89.05200 899 1502 1 chr2B.!!$R1 603

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
24 25 0.038159 ACGTTCTCCACTGTGCTAGC 60.038 55.0 8.10 8.1 0.0 3.42 F
25 26 0.244994 CGTTCTCCACTGTGCTAGCT 59.755 55.0 17.23 0.0 0.0 3.32 F
1102 1149 0.244994 CAGCGAGTACAAGGTCAGCT 59.755 55.0 0.00 0.0 0.0 4.24 F
1655 1730 0.316841 TTTGGTGCATCGAAAAGGGC 59.683 50.0 0.00 0.0 0.0 5.19 F
3209 3537 0.106708 AGTGTGGTGAGTGCGTTCAT 59.893 50.0 0.00 0.0 0.0 2.57 F
4192 4545 0.398696 AGGTACCACAATGCCGAACA 59.601 50.0 15.94 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1102 1149 0.181114 CATTGCAAGGGATCGGAGGA 59.819 55.000 4.94 0.00 0.00 3.71 R
1806 1881 0.460311 AACCTAATGGGCTCGAGTCG 59.540 55.000 15.13 6.09 39.10 4.18 R
2270 2345 1.299541 ATGGTATCAAAGAAGCGCGG 58.700 50.000 8.83 0.00 0.00 6.46 R
3529 3860 1.144936 GAGCGGCATAGGAGCAAGT 59.855 57.895 1.45 0.00 35.83 3.16 R
4291 4644 0.674581 CGATTTGCTGCCTCCTCACA 60.675 55.000 0.00 0.00 0.00 3.58 R
5376 5868 0.460311 CCGGGCTTAGTGATCGAAGT 59.540 55.000 0.00 0.00 0.00 3.01 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
19 20 2.522060 GAGCACGTTCTCCACTGTG 58.478 57.895 3.60 0.00 34.77 3.66
20 21 1.560860 GAGCACGTTCTCCACTGTGC 61.561 60.000 3.60 8.04 46.99 4.57
21 22 1.595382 GCACGTTCTCCACTGTGCT 60.595 57.895 8.78 0.00 45.06 4.40
22 23 0.319555 GCACGTTCTCCACTGTGCTA 60.320 55.000 8.78 0.00 45.06 3.49
23 24 1.702886 CACGTTCTCCACTGTGCTAG 58.297 55.000 1.29 2.26 0.00 3.42
24 25 0.038159 ACGTTCTCCACTGTGCTAGC 60.038 55.000 8.10 8.10 0.00 3.42
25 26 0.244994 CGTTCTCCACTGTGCTAGCT 59.755 55.000 17.23 0.00 0.00 3.32
26 27 1.734047 CGTTCTCCACTGTGCTAGCTC 60.734 57.143 17.23 13.38 0.00 4.09
27 28 1.548269 GTTCTCCACTGTGCTAGCTCT 59.452 52.381 17.23 0.00 0.00 4.09
28 29 1.930251 TCTCCACTGTGCTAGCTCTT 58.070 50.000 17.23 0.93 0.00 2.85
29 30 1.821753 TCTCCACTGTGCTAGCTCTTC 59.178 52.381 17.23 4.71 0.00 2.87
30 31 1.547820 CTCCACTGTGCTAGCTCTTCA 59.452 52.381 17.23 8.95 0.00 3.02
31 32 1.547820 TCCACTGTGCTAGCTCTTCAG 59.452 52.381 17.23 18.81 0.00 3.02
49 50 0.917533 AGCCAGAGATGAGCCACATT 59.082 50.000 0.00 0.00 39.56 2.71
62 63 4.018506 TGAGCCACATTGAAGGAAATAGGA 60.019 41.667 4.47 0.00 0.00 2.94
69 70 6.600822 CACATTGAAGGAAATAGGATGTCAGT 59.399 38.462 0.00 0.00 0.00 3.41
75 76 4.100808 AGGAAATAGGATGTCAGTCTGAGC 59.899 45.833 1.75 0.00 0.00 4.26
76 77 3.724508 AATAGGATGTCAGTCTGAGCG 57.275 47.619 1.75 0.00 0.00 5.03
78 79 1.520342 GGATGTCAGTCTGAGCGGC 60.520 63.158 1.75 0.00 0.00 6.53
79 80 1.875813 GATGTCAGTCTGAGCGGCG 60.876 63.158 1.75 0.51 0.00 6.46
90 91 1.139734 GAGCGGCGATTGAGTGAGA 59.860 57.895 12.98 0.00 0.00 3.27
102 103 0.387565 GAGTGAGAATCTCTCCCGCC 59.612 60.000 11.92 0.00 46.91 6.13
103 104 1.066587 GTGAGAATCTCTCCCGCCG 59.933 63.158 11.92 0.00 42.73 6.46
108 109 0.601311 GAATCTCTCCCGCCGAATGG 60.601 60.000 0.00 0.00 38.77 3.16
138 139 9.191479 TCAACTCCAGTCTTTTATGGTTAAAAA 57.809 29.630 0.00 0.00 36.97 1.94
174 175 1.069227 GGACTGGATTGTCAAACACGC 60.069 52.381 0.00 0.00 38.61 5.34
194 195 3.132925 GCCCTAAACGTACACTTCAACA 58.867 45.455 0.00 0.00 0.00 3.33
292 296 9.098355 TCGATCAAGTTTACAATAGATCAAAGG 57.902 33.333 0.00 0.00 33.33 3.11
299 303 4.422073 ACAATAGATCAAAGGCGGATGA 57.578 40.909 0.00 0.00 0.00 2.92
300 304 4.130118 ACAATAGATCAAAGGCGGATGAC 58.870 43.478 0.00 0.00 0.00 3.06
308 312 0.698818 AAGGCGGATGACTTTCCCTT 59.301 50.000 0.00 0.00 42.23 3.95
362 368 9.650371 CATACAATATACCAGACAAACGAAATG 57.350 33.333 0.00 0.00 0.00 2.32
401 407 5.249622 TGGTGGATCTGACAGTAATTTGGTA 59.750 40.000 1.59 0.00 0.00 3.25
411 442 9.701098 CTGACAGTAATTTGGTAAGTACTAACA 57.299 33.333 0.00 0.00 41.71 2.41
421 452 6.103997 TGGTAAGTACTAACAATACAGCAGC 58.896 40.000 0.00 0.00 0.00 5.25
423 454 4.819105 AGTACTAACAATACAGCAGCCA 57.181 40.909 0.00 0.00 0.00 4.75
424 455 5.359194 AGTACTAACAATACAGCAGCCAT 57.641 39.130 0.00 0.00 0.00 4.40
425 456 5.745227 AGTACTAACAATACAGCAGCCATT 58.255 37.500 0.00 0.00 0.00 3.16
426 457 6.180472 AGTACTAACAATACAGCAGCCATTT 58.820 36.000 0.00 0.00 0.00 2.32
427 458 5.982890 ACTAACAATACAGCAGCCATTTT 57.017 34.783 0.00 0.00 0.00 1.82
428 459 6.345096 ACTAACAATACAGCAGCCATTTTT 57.655 33.333 0.00 0.00 0.00 1.94
448 479 3.691049 TTTTTGCTGTGCTGTGAGTAC 57.309 42.857 0.00 0.00 0.00 2.73
449 480 2.620251 TTTGCTGTGCTGTGAGTACT 57.380 45.000 0.00 0.00 31.77 2.73
450 481 2.154854 TTGCTGTGCTGTGAGTACTC 57.845 50.000 16.32 16.32 31.77 2.59
451 482 1.332195 TGCTGTGCTGTGAGTACTCT 58.668 50.000 23.01 0.00 31.77 3.24
452 483 1.688735 TGCTGTGCTGTGAGTACTCTT 59.311 47.619 23.01 0.00 31.77 2.85
453 484 2.103094 TGCTGTGCTGTGAGTACTCTTT 59.897 45.455 23.01 0.00 31.77 2.52
454 485 2.734079 GCTGTGCTGTGAGTACTCTTTC 59.266 50.000 23.01 13.66 31.77 2.62
455 486 3.553922 GCTGTGCTGTGAGTACTCTTTCT 60.554 47.826 23.01 0.00 31.77 2.52
456 487 4.626042 CTGTGCTGTGAGTACTCTTTCTT 58.374 43.478 23.01 0.00 31.77 2.52
457 488 5.023533 TGTGCTGTGAGTACTCTTTCTTT 57.976 39.130 23.01 0.00 31.77 2.52
458 489 5.428253 TGTGCTGTGAGTACTCTTTCTTTT 58.572 37.500 23.01 0.00 31.77 2.27
459 490 5.880332 TGTGCTGTGAGTACTCTTTCTTTTT 59.120 36.000 23.01 0.00 31.77 1.94
480 511 4.503741 TTTTGCTCTGTTGATTAGGCAC 57.496 40.909 0.00 0.00 0.00 5.01
481 512 2.857186 TGCTCTGTTGATTAGGCACA 57.143 45.000 0.00 0.00 0.00 4.57
482 513 2.703416 TGCTCTGTTGATTAGGCACAG 58.297 47.619 0.00 0.00 0.00 3.66
483 514 1.399791 GCTCTGTTGATTAGGCACAGC 59.600 52.381 0.00 0.00 0.00 4.40
484 515 2.703416 CTCTGTTGATTAGGCACAGCA 58.297 47.619 0.00 0.00 0.00 4.41
485 516 2.676839 CTCTGTTGATTAGGCACAGCAG 59.323 50.000 0.00 0.00 43.24 4.24
486 517 1.131883 CTGTTGATTAGGCACAGCAGC 59.868 52.381 0.00 0.00 38.17 5.25
626 662 2.813908 GGTGTTAGCGCCGAGGTG 60.814 66.667 2.29 0.00 35.34 4.00
923 959 2.334181 TACCATCGTCCGTCGTGCA 61.334 57.895 0.00 0.00 40.80 4.57
1102 1149 0.244994 CAGCGAGTACAAGGTCAGCT 59.755 55.000 0.00 0.00 0.00 4.24
1114 1161 1.456705 GTCAGCTCCTCCGATCCCT 60.457 63.158 0.00 0.00 0.00 4.20
1140 1204 2.493035 TGGTTGCCGCATACTCATATG 58.507 47.619 0.00 0.00 41.16 1.78
1250 1320 7.098074 AGAAATTTCTGATCTTTGCAGGATC 57.902 36.000 19.86 18.76 39.76 3.36
1283 1353 1.593209 GTGAAGGCGACGAACCACA 60.593 57.895 0.00 0.00 0.00 4.17
1383 1458 3.751175 GGCCTTGGTAAAATCTTTTTGCC 59.249 43.478 11.47 11.47 0.00 4.52
1460 1535 3.508845 ACTCCATATGTACATTGGCCC 57.491 47.619 22.28 0.00 0.00 5.80
1506 1581 2.838202 GGATAGTGGGTCTTGTTCCTCA 59.162 50.000 0.00 0.00 0.00 3.86
1508 1583 1.807814 AGTGGGTCTTGTTCCTCACT 58.192 50.000 0.00 0.00 34.30 3.41
1509 1584 2.127708 AGTGGGTCTTGTTCCTCACTT 58.872 47.619 0.00 0.00 34.96 3.16
1510 1585 2.158755 AGTGGGTCTTGTTCCTCACTTG 60.159 50.000 0.00 0.00 34.96 3.16
1515 1590 3.694566 GGTCTTGTTCCTCACTTGTTTGT 59.305 43.478 0.00 0.00 0.00 2.83
1525 1600 7.377766 TCCTCACTTGTTTGTTTATCTATGC 57.622 36.000 0.00 0.00 0.00 3.14
1526 1601 6.374333 TCCTCACTTGTTTGTTTATCTATGCC 59.626 38.462 0.00 0.00 0.00 4.40
1534 1609 7.416817 TGTTTGTTTATCTATGCCGATTGATG 58.583 34.615 0.00 0.00 0.00 3.07
1535 1610 6.558771 TTGTTTATCTATGCCGATTGATGG 57.441 37.500 0.00 0.00 0.00 3.51
1555 1630 3.198635 TGGTCCTTGATTCAGTCATCTCC 59.801 47.826 0.00 0.00 36.54 3.71
1558 1633 5.055812 GTCCTTGATTCAGTCATCTCCATC 58.944 45.833 0.00 0.00 36.54 3.51
1561 1636 3.662078 TGATTCAGTCATCTCCATCCCT 58.338 45.455 0.00 0.00 0.00 4.20
1563 1638 4.102210 TGATTCAGTCATCTCCATCCCTTC 59.898 45.833 0.00 0.00 0.00 3.46
1565 1640 3.303938 TCAGTCATCTCCATCCCTTCTC 58.696 50.000 0.00 0.00 0.00 2.87
1611 1686 3.054948 TCTGTCCATTGTGAGATGCATGA 60.055 43.478 2.46 0.00 0.00 3.07
1612 1687 3.688235 TGTCCATTGTGAGATGCATGAA 58.312 40.909 2.46 0.00 0.00 2.57
1613 1688 3.441222 TGTCCATTGTGAGATGCATGAAC 59.559 43.478 2.46 0.00 0.00 3.18
1655 1730 0.316841 TTTGGTGCATCGAAAAGGGC 59.683 50.000 0.00 0.00 0.00 5.19
1668 1743 1.453155 AAAGGGCGTGCATTGACTAG 58.547 50.000 0.00 0.00 0.00 2.57
1699 1774 3.365969 GCTACAGGTTGCGCTTAAAACAT 60.366 43.478 9.73 0.00 0.00 2.71
1806 1881 2.353109 GCAGCTTCCAAATTTCAGGGAC 60.353 50.000 0.00 0.00 0.00 4.46
1839 1914 1.552226 TAGGTTTGTTCTATCGCGCG 58.448 50.000 26.76 26.76 0.00 6.86
1849 1924 1.048494 CTATCGCGCGTCATTCTGAG 58.952 55.000 30.98 11.91 0.00 3.35
1865 1940 2.203195 AGCTGCAGCAACCAACGA 60.203 55.556 38.24 0.00 45.16 3.85
1992 2067 2.661504 TGAACGTGTCGAATGCTTTG 57.338 45.000 0.00 0.00 0.00 2.77
2060 2135 1.541588 CAGGCTTCTGGCAAGGTAAAC 59.458 52.381 0.00 0.00 44.01 2.01
2080 2155 7.064728 GGTAAACACTGATTTCTCATACAGTCC 59.935 40.741 0.00 0.00 40.84 3.85
2103 2178 3.806949 ACAGTCAACACCCATTATGGT 57.193 42.857 10.65 0.00 39.96 3.55
2270 2345 5.437060 TGCCAGGTTTGATTATAGGAAGAC 58.563 41.667 0.00 0.00 0.00 3.01
2274 2349 3.493503 GGTTTGATTATAGGAAGACCGCG 59.506 47.826 0.00 0.00 41.83 6.46
2344 2420 0.674895 CTGAAGGTACAGCCTGCACC 60.675 60.000 5.94 5.94 45.92 5.01
2563 2639 6.754702 ACAATTCTTCTGAATGTCATCCTG 57.245 37.500 0.00 0.00 41.62 3.86
2572 2648 0.392998 ATGTCATCCTGCGTGTTCCC 60.393 55.000 0.00 0.00 0.00 3.97
2712 2788 2.037772 CCAGCAGGTACAGAAAGTCAGT 59.962 50.000 0.00 0.00 0.00 3.41
2713 2789 3.495100 CCAGCAGGTACAGAAAGTCAGTT 60.495 47.826 0.00 0.00 0.00 3.16
2714 2790 4.130118 CAGCAGGTACAGAAAGTCAGTTT 58.870 43.478 0.00 0.00 0.00 2.66
2715 2791 4.576463 CAGCAGGTACAGAAAGTCAGTTTT 59.424 41.667 0.00 0.00 0.00 2.43
2741 2823 7.751768 TTTTTCATCTTCTTCTTCTCCTTCC 57.248 36.000 0.00 0.00 0.00 3.46
2990 3155 4.074970 CCAATTGGCCATGACCTATAGTC 58.925 47.826 12.53 0.00 46.51 2.59
3209 3537 0.106708 AGTGTGGTGAGTGCGTTCAT 59.893 50.000 0.00 0.00 0.00 2.57
3224 3552 4.679197 TGCGTTCATTGTCAGTAAAATTGC 59.321 37.500 0.00 0.00 0.00 3.56
3227 3555 6.614162 GCGTTCATTGTCAGTAAAATTGCAAG 60.614 38.462 4.94 0.00 0.00 4.01
3245 3573 4.810491 TGCAAGCAAAAAGGAAATCAAGAC 59.190 37.500 0.00 0.00 0.00 3.01
3260 3588 7.970614 GGAAATCAAGACACTCAACATAAATCC 59.029 37.037 0.00 0.00 0.00 3.01
3272 3600 8.950210 ACTCAACATAAATCCACTATTGTTCTG 58.050 33.333 0.00 0.00 0.00 3.02
3441 3769 1.306056 ATGAACCCCCACCATTGCC 60.306 57.895 0.00 0.00 0.00 4.52
3529 3860 4.216257 GCCTGCTTCTTTGAATCTTACACA 59.784 41.667 0.00 0.00 0.00 3.72
3669 4000 3.020274 TCAGCAAAACCACAAGTAGCAA 58.980 40.909 0.00 0.00 0.00 3.91
3765 4101 5.104527 AGGTTGTATCTGCTGCTAAATACCA 60.105 40.000 0.00 0.00 0.00 3.25
3832 4168 1.676014 CCCCTCTAGACTTGTTTGCCG 60.676 57.143 0.00 0.00 0.00 5.69
3865 4201 1.303236 TGGGAATTGGCACTGGTCG 60.303 57.895 0.00 0.00 0.00 4.79
3920 4256 5.610398 TGTCAGCCAAGTGGTATGTATATG 58.390 41.667 0.00 0.00 37.57 1.78
3987 4330 2.158827 TCACTAGTTGGCTCAGTTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
4046 4389 9.616156 TCTAGTTAATTACGGGCAATTTTATCA 57.384 29.630 0.00 0.00 30.84 2.15
4153 4506 7.840931 AGTATTCAATCCCCAAAATCAGAAAC 58.159 34.615 0.00 0.00 0.00 2.78
4192 4545 0.398696 AGGTACCACAATGCCGAACA 59.601 50.000 15.94 0.00 0.00 3.18
4206 4559 2.286418 GCCGAACACAGCATATAACTGC 60.286 50.000 6.14 0.00 42.62 4.40
4291 4644 3.478509 AGACAGCCTATACGAAGACGAT 58.521 45.455 0.00 0.00 42.66 3.73
4293 4646 2.950309 ACAGCCTATACGAAGACGATGT 59.050 45.455 0.00 0.00 42.66 3.06
4326 4679 0.973632 ATCGCCAGTGTGACCTACAA 59.026 50.000 0.00 0.00 41.89 2.41
4369 4722 0.186386 TTGACCCCAATGACCCGTTT 59.814 50.000 0.00 0.00 0.00 3.60
4466 4825 1.099879 GCAGCATGGCTACTTCCAGG 61.100 60.000 0.00 0.00 39.89 4.45
4489 4848 0.596577 AGCAGCAGCAACAACATCAG 59.403 50.000 3.17 0.00 45.49 2.90
4678 5086 8.746530 TGTATCTTACTCTAATTTCGGTCAGTT 58.253 33.333 0.00 0.00 0.00 3.16
4686 5094 7.093640 ACTCTAATTTCGGTCAGTTGTATACCA 60.094 37.037 0.00 0.00 32.55 3.25
4730 5142 9.116067 AGCAACTTGTATAGTTTGAACTTTGTA 57.884 29.630 1.20 0.00 44.73 2.41
4784 5196 6.425735 ACATGTTTGGGAGATGATACAATCA 58.574 36.000 0.00 0.00 44.55 2.57
4808 5220 4.191033 TGAATGCCATGACACAATTTCC 57.809 40.909 0.00 0.00 0.00 3.13
4811 5223 2.596346 TGCCATGACACAATTTCCACT 58.404 42.857 0.00 0.00 0.00 4.00
4817 5229 5.353956 CCATGACACAATTTCCACTATCGAA 59.646 40.000 0.00 0.00 0.00 3.71
4826 5238 4.386867 TTCCACTATCGAACACATCTCC 57.613 45.455 0.00 0.00 0.00 3.71
4938 5350 3.257393 CAGTAGCACAAGAGATGGTGAC 58.743 50.000 0.00 0.00 37.18 3.67
5140 5559 2.669569 CCCACTTCACCCAGTGCG 60.670 66.667 0.00 0.00 42.63 5.34
5151 5570 1.009829 CCCAGTGCGATGAAACTAGC 58.990 55.000 0.00 0.00 0.00 3.42
5194 5617 3.193267 CAGCTAGATCTGCATCCTCTACC 59.807 52.174 5.18 0.00 0.00 3.18
5204 5627 2.694397 CATCCTCTACCAATCCCTCCA 58.306 52.381 0.00 0.00 0.00 3.86
5218 5641 2.041922 TCCACCTCCTCATCCGGG 60.042 66.667 0.00 0.00 0.00 5.73
5263 5686 4.843728 TCCAGGTTTTAGTAAGGATGCAG 58.156 43.478 0.00 0.00 0.00 4.41
5279 5702 0.029834 GCAGGTGCAAGAACACAGTG 59.970 55.000 0.00 0.00 42.55 3.66
5339 5817 7.122138 AGATGAGAACTAGAGATGAAATGCA 57.878 36.000 0.00 0.00 0.00 3.96
5341 5819 6.291648 TGAGAACTAGAGATGAAATGCACT 57.708 37.500 0.00 0.00 0.00 4.40
5345 5823 6.593382 AGAACTAGAGATGAAATGCACTTGAC 59.407 38.462 0.00 0.00 0.00 3.18
5350 5828 7.317842 AGAGATGAAATGCACTTGACTTATG 57.682 36.000 0.00 0.00 0.00 1.90
5357 5835 4.916983 TGCACTTGACTTATGCTTTGTT 57.083 36.364 0.00 0.00 40.13 2.83
5358 5836 6.573664 ATGCACTTGACTTATGCTTTGTTA 57.426 33.333 0.00 0.00 40.13 2.41
5359 5837 6.384258 TGCACTTGACTTATGCTTTGTTAA 57.616 33.333 0.00 0.00 40.13 2.01
5360 5838 6.980593 TGCACTTGACTTATGCTTTGTTAAT 58.019 32.000 0.00 0.00 40.13 1.40
5361 5839 7.432869 TGCACTTGACTTATGCTTTGTTAATT 58.567 30.769 0.00 0.00 40.13 1.40
5362 5840 7.925483 TGCACTTGACTTATGCTTTGTTAATTT 59.075 29.630 0.00 0.00 40.13 1.82
5363 5841 8.764287 GCACTTGACTTATGCTTTGTTAATTTT 58.236 29.630 0.00 0.00 36.40 1.82
5368 5846 9.284594 TGACTTATGCTTTGTTAATTTTATCGC 57.715 29.630 0.00 0.00 0.00 4.58
5369 5847 9.284594 GACTTATGCTTTGTTAATTTTATCGCA 57.715 29.630 0.00 0.00 0.00 5.10
5370 5848 9.072294 ACTTATGCTTTGTTAATTTTATCGCAC 57.928 29.630 0.00 0.00 0.00 5.34
5376 5868 9.284594 GCTTTGTTAATTTTATCGCACTAATCA 57.715 29.630 0.00 0.00 0.00 2.57
5386 5878 3.435566 TCGCACTAATCACTTCGATCAC 58.564 45.455 0.00 0.00 31.11 3.06
5402 5894 2.981859 TCACTAAGCCCGGAAGAATC 57.018 50.000 0.73 0.00 0.00 2.52
5444 5940 1.303888 CAGGGCCACATGAGCTTGT 60.304 57.895 6.18 0.00 0.00 3.16
5447 5943 1.133976 AGGGCCACATGAGCTTGTATC 60.134 52.381 6.18 0.00 0.00 2.24
5462 5958 3.699779 TGTATCGCAGAGCAAGACTAG 57.300 47.619 0.00 0.00 43.63 2.57
5464 5960 3.444034 TGTATCGCAGAGCAAGACTAGTT 59.556 43.478 0.00 0.00 43.63 2.24
5466 5962 2.947852 TCGCAGAGCAAGACTAGTTTC 58.052 47.619 0.00 0.00 0.00 2.78
5467 5963 2.558795 TCGCAGAGCAAGACTAGTTTCT 59.441 45.455 0.00 0.00 0.00 2.52
5468 5964 3.756963 TCGCAGAGCAAGACTAGTTTCTA 59.243 43.478 0.00 0.00 0.00 2.10
5469 5965 4.217767 TCGCAGAGCAAGACTAGTTTCTAA 59.782 41.667 0.00 0.00 0.00 2.10
5470 5966 4.923871 CGCAGAGCAAGACTAGTTTCTAAA 59.076 41.667 0.00 0.00 0.00 1.85
5471 5967 5.578727 CGCAGAGCAAGACTAGTTTCTAAAT 59.421 40.000 0.00 0.00 0.00 1.40
5472 5968 6.237701 CGCAGAGCAAGACTAGTTTCTAAATC 60.238 42.308 0.00 0.00 0.00 2.17
5473 5969 6.237701 GCAGAGCAAGACTAGTTTCTAAATCG 60.238 42.308 0.00 0.00 0.00 3.34
5474 5970 6.809196 CAGAGCAAGACTAGTTTCTAAATCGT 59.191 38.462 0.00 0.00 0.00 3.73
5475 5971 7.968956 CAGAGCAAGACTAGTTTCTAAATCGTA 59.031 37.037 0.00 0.00 0.00 3.43
5476 5972 8.185505 AGAGCAAGACTAGTTTCTAAATCGTAG 58.814 37.037 0.00 0.00 0.00 3.51
5477 5973 7.828712 AGCAAGACTAGTTTCTAAATCGTAGT 58.171 34.615 0.00 0.00 0.00 2.73
5478 5974 7.755822 AGCAAGACTAGTTTCTAAATCGTAGTG 59.244 37.037 0.00 0.00 0.00 2.74
5479 5975 7.009357 GCAAGACTAGTTTCTAAATCGTAGTGG 59.991 40.741 0.00 0.00 0.00 4.00
5480 5976 7.934855 AGACTAGTTTCTAAATCGTAGTGGA 57.065 36.000 0.00 0.00 0.00 4.02
5481 5977 8.522542 AGACTAGTTTCTAAATCGTAGTGGAT 57.477 34.615 0.00 0.00 0.00 3.41
5482 5978 8.968969 AGACTAGTTTCTAAATCGTAGTGGATT 58.031 33.333 0.00 0.00 38.24 3.01
5483 5979 9.235537 GACTAGTTTCTAAATCGTAGTGGATTC 57.764 37.037 0.00 0.00 35.65 2.52
5484 5980 8.196103 ACTAGTTTCTAAATCGTAGTGGATTCC 58.804 37.037 0.00 0.00 35.65 3.01
5485 5981 6.942976 AGTTTCTAAATCGTAGTGGATTCCA 58.057 36.000 0.00 0.00 35.65 3.53
5539 6035 0.393267 CTGGGGCGTTTCGGGAATTA 60.393 55.000 0.00 0.00 0.00 1.40
5546 6042 4.979815 GGGCGTTTCGGGAATTATTTATTG 59.020 41.667 0.00 0.00 0.00 1.90
5548 6044 6.443792 GGCGTTTCGGGAATTATTTATTGAT 58.556 36.000 0.00 0.00 0.00 2.57
5549 6045 6.921307 GGCGTTTCGGGAATTATTTATTGATT 59.079 34.615 0.00 0.00 0.00 2.57
5550 6046 7.436970 GGCGTTTCGGGAATTATTTATTGATTT 59.563 33.333 0.00 0.00 0.00 2.17
5551 6047 9.453325 GCGTTTCGGGAATTATTTATTGATTTA 57.547 29.630 0.00 0.00 0.00 1.40
5602 6101 0.862554 ATGAAATGGGGGATCTGGGG 59.137 55.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.560860 GCACAGTGGAGAACGTGCTC 61.561 60.000 15.81 15.81 46.47 4.26
2 3 1.595382 GCACAGTGGAGAACGTGCT 60.595 57.895 0.00 0.00 46.47 4.40
3 4 2.939022 GCACAGTGGAGAACGTGC 59.061 61.111 1.84 0.00 45.20 5.34
4 5 1.702886 CTAGCACAGTGGAGAACGTG 58.297 55.000 1.84 0.00 36.79 4.49
5 6 0.038159 GCTAGCACAGTGGAGAACGT 60.038 55.000 10.63 0.00 0.00 3.99
6 7 0.244994 AGCTAGCACAGTGGAGAACG 59.755 55.000 18.83 0.00 0.00 3.95
7 8 1.548269 AGAGCTAGCACAGTGGAGAAC 59.452 52.381 18.83 0.00 0.00 3.01
8 9 1.930251 AGAGCTAGCACAGTGGAGAA 58.070 50.000 18.83 0.00 0.00 2.87
9 10 1.821753 GAAGAGCTAGCACAGTGGAGA 59.178 52.381 18.83 0.00 0.00 3.71
10 11 1.547820 TGAAGAGCTAGCACAGTGGAG 59.452 52.381 18.83 0.00 0.00 3.86
11 12 1.547820 CTGAAGAGCTAGCACAGTGGA 59.452 52.381 18.83 0.00 0.00 4.02
12 13 2.006056 GCTGAAGAGCTAGCACAGTGG 61.006 57.143 18.83 4.02 42.52 4.00
13 14 1.357907 GCTGAAGAGCTAGCACAGTG 58.642 55.000 18.83 0.00 42.52 3.66
14 15 0.248843 GGCTGAAGAGCTAGCACAGT 59.751 55.000 18.83 2.51 45.44 3.55
15 16 0.248565 TGGCTGAAGAGCTAGCACAG 59.751 55.000 18.83 19.18 45.44 3.66
16 17 0.248565 CTGGCTGAAGAGCTAGCACA 59.751 55.000 18.83 10.21 45.67 4.57
17 18 3.062585 CTGGCTGAAGAGCTAGCAC 57.937 57.895 18.83 11.32 45.67 4.40
21 22 2.957680 CTCATCTCTGGCTGAAGAGCTA 59.042 50.000 6.71 0.00 45.44 3.32
22 23 1.758280 CTCATCTCTGGCTGAAGAGCT 59.242 52.381 0.00 0.00 45.44 4.09
23 24 1.807377 GCTCATCTCTGGCTGAAGAGC 60.807 57.143 19.47 19.47 42.95 4.09
24 25 1.202557 GGCTCATCTCTGGCTGAAGAG 60.203 57.143 11.33 11.33 44.34 2.85
25 26 0.829333 GGCTCATCTCTGGCTGAAGA 59.171 55.000 0.00 0.00 0.00 2.87
26 27 0.540454 TGGCTCATCTCTGGCTGAAG 59.460 55.000 0.00 0.00 0.00 3.02
27 28 0.251354 GTGGCTCATCTCTGGCTGAA 59.749 55.000 0.00 0.00 0.00 3.02
28 29 0.906282 TGTGGCTCATCTCTGGCTGA 60.906 55.000 0.00 0.00 0.00 4.26
29 30 0.180642 ATGTGGCTCATCTCTGGCTG 59.819 55.000 0.00 0.00 29.76 4.85
30 31 0.917533 AATGTGGCTCATCTCTGGCT 59.082 50.000 2.07 0.00 35.48 4.75
31 32 1.022735 CAATGTGGCTCATCTCTGGC 58.977 55.000 2.07 0.00 35.48 4.85
32 33 2.704464 TCAATGTGGCTCATCTCTGG 57.296 50.000 2.07 0.00 35.48 3.86
33 34 2.943690 CCTTCAATGTGGCTCATCTCTG 59.056 50.000 2.07 0.00 35.48 3.35
39 40 4.018506 TCCTATTTCCTTCAATGTGGCTCA 60.019 41.667 0.00 0.00 0.00 4.26
49 50 5.721480 TCAGACTGACATCCTATTTCCTTCA 59.279 40.000 0.00 0.00 0.00 3.02
62 63 1.670949 ATCGCCGCTCAGACTGACAT 61.671 55.000 0.00 0.00 0.00 3.06
69 70 1.153765 CACTCAATCGCCGCTCAGA 60.154 57.895 0.00 0.00 0.00 3.27
75 76 2.123342 GAGATTCTCACTCAATCGCCG 58.877 52.381 8.84 0.00 35.69 6.46
76 77 3.380142 GAGAGATTCTCACTCAATCGCC 58.620 50.000 15.83 0.00 42.90 5.54
78 79 3.549827 CGGGAGAGATTCTCACTCAATCG 60.550 52.174 15.83 7.13 44.59 3.34
79 80 3.798548 GCGGGAGAGATTCTCACTCAATC 60.799 52.174 15.83 3.50 44.59 2.67
90 91 1.338136 ACCATTCGGCGGGAGAGATT 61.338 55.000 7.21 0.00 34.57 2.40
98 99 3.101019 GTTGAAAACCATTCGGCGG 57.899 52.632 7.21 0.00 42.21 6.13
108 109 7.039313 ACCATAAAAGACTGGAGTTGAAAAC 57.961 36.000 0.00 0.00 40.63 2.43
156 157 0.951558 GGCGTGTTTGACAATCCAGT 59.048 50.000 0.00 0.00 0.00 4.00
157 158 0.240945 GGGCGTGTTTGACAATCCAG 59.759 55.000 0.00 0.00 0.00 3.86
163 164 0.938713 CGTTTAGGGCGTGTTTGACA 59.061 50.000 0.00 0.00 0.00 3.58
174 175 4.992319 TCATGTTGAAGTGTACGTTTAGGG 59.008 41.667 0.00 0.00 0.00 3.53
194 195 5.934402 ACGGATGGAGTACTAAAAGTCAT 57.066 39.130 0.00 0.00 0.00 3.06
282 286 4.442706 GAAAGTCATCCGCCTTTGATCTA 58.557 43.478 0.00 0.00 31.30 1.98
292 296 2.044123 ATCAAGGGAAAGTCATCCGC 57.956 50.000 0.00 0.00 40.62 5.54
336 342 9.650371 CATTTCGTTTGTCTGGTATATTGTATG 57.350 33.333 0.00 0.00 0.00 2.39
338 344 8.780846 ACATTTCGTTTGTCTGGTATATTGTA 57.219 30.769 0.00 0.00 0.00 2.41
343 349 9.881529 GTTTTTACATTTCGTTTGTCTGGTATA 57.118 29.630 0.00 0.00 0.00 1.47
344 350 8.407064 TGTTTTTACATTTCGTTTGTCTGGTAT 58.593 29.630 0.00 0.00 0.00 2.73
345 351 7.697291 GTGTTTTTACATTTCGTTTGTCTGGTA 59.303 33.333 0.00 0.00 0.00 3.25
362 368 7.708752 TCAGATCCACCAAAAATGTGTTTTTAC 59.291 33.333 0.00 0.00 43.69 2.01
401 407 5.160607 TGGCTGCTGTATTGTTAGTACTT 57.839 39.130 0.00 0.00 0.00 2.24
428 459 3.278574 AGTACTCACAGCACAGCAAAAA 58.721 40.909 0.00 0.00 0.00 1.94
429 460 2.872245 GAGTACTCACAGCACAGCAAAA 59.128 45.455 18.20 0.00 0.00 2.44
430 461 2.103094 AGAGTACTCACAGCACAGCAAA 59.897 45.455 24.44 0.00 0.00 3.68
431 462 1.688735 AGAGTACTCACAGCACAGCAA 59.311 47.619 24.44 0.00 0.00 3.91
432 463 1.332195 AGAGTACTCACAGCACAGCA 58.668 50.000 24.44 0.00 0.00 4.41
433 464 2.447244 AAGAGTACTCACAGCACAGC 57.553 50.000 24.44 0.00 0.00 4.40
434 465 4.250116 AGAAAGAGTACTCACAGCACAG 57.750 45.455 24.44 0.00 0.00 3.66
435 466 4.672587 AAGAAAGAGTACTCACAGCACA 57.327 40.909 24.44 0.00 0.00 4.57
436 467 5.993106 AAAAGAAAGAGTACTCACAGCAC 57.007 39.130 24.44 9.41 0.00 4.40
458 489 4.340666 TGTGCCTAATCAACAGAGCAAAAA 59.659 37.500 0.00 0.00 31.03 1.94
459 490 3.888323 TGTGCCTAATCAACAGAGCAAAA 59.112 39.130 0.00 0.00 31.03 2.44
460 491 3.485394 TGTGCCTAATCAACAGAGCAAA 58.515 40.909 0.00 0.00 31.03 3.68
461 492 3.076621 CTGTGCCTAATCAACAGAGCAA 58.923 45.455 0.00 0.00 31.03 3.91
462 493 2.703416 CTGTGCCTAATCAACAGAGCA 58.297 47.619 0.00 0.00 0.00 4.26
463 494 1.399791 GCTGTGCCTAATCAACAGAGC 59.600 52.381 6.24 0.00 42.43 4.09
464 495 2.676839 CTGCTGTGCCTAATCAACAGAG 59.323 50.000 6.24 0.00 31.82 3.35
465 496 2.703416 CTGCTGTGCCTAATCAACAGA 58.297 47.619 6.24 0.00 31.82 3.41
466 497 1.131883 GCTGCTGTGCCTAATCAACAG 59.868 52.381 0.00 0.00 32.88 3.16
467 498 1.167851 GCTGCTGTGCCTAATCAACA 58.832 50.000 0.00 0.00 0.00 3.33
492 523 3.071459 GATGACGAACAGCCGCGTG 62.071 63.158 4.92 0.00 41.34 5.34
493 524 2.809601 GATGACGAACAGCCGCGT 60.810 61.111 4.92 0.00 44.33 6.01
494 525 3.902063 CGATGACGAACAGCCGCG 61.902 66.667 0.00 0.00 42.66 6.46
495 526 3.554692 CCGATGACGAACAGCCGC 61.555 66.667 0.00 0.00 42.66 6.53
496 527 3.554692 GCCGATGACGAACAGCCG 61.555 66.667 0.00 0.00 42.66 5.52
497 528 3.554692 CGCCGATGACGAACAGCC 61.555 66.667 0.00 0.00 42.66 4.85
498 529 2.789203 GACGCCGATGACGAACAGC 61.789 63.158 0.00 0.00 42.66 4.40
846 882 1.529713 GAGGGAGAGGAGGTAGGCG 60.530 68.421 0.00 0.00 0.00 5.52
847 883 1.152419 GGAGGGAGAGGAGGTAGGC 60.152 68.421 0.00 0.00 0.00 3.93
849 885 2.324541 CAATGGAGGGAGAGGAGGTAG 58.675 57.143 0.00 0.00 0.00 3.18
850 886 1.062121 CCAATGGAGGGAGAGGAGGTA 60.062 57.143 0.00 0.00 0.00 3.08
851 887 0.327000 CCAATGGAGGGAGAGGAGGT 60.327 60.000 0.00 0.00 0.00 3.85
852 888 1.704007 GCCAATGGAGGGAGAGGAGG 61.704 65.000 2.05 0.00 0.00 4.30
853 889 1.835693 GCCAATGGAGGGAGAGGAG 59.164 63.158 2.05 0.00 0.00 3.69
1102 1149 0.181114 CATTGCAAGGGATCGGAGGA 59.819 55.000 4.94 0.00 0.00 3.71
1140 1204 3.521560 TGCAGGATAATCAGACGAACAC 58.478 45.455 0.00 0.00 0.00 3.32
1250 1320 2.332104 CTTCACGATGGCGATATCCAG 58.668 52.381 0.00 0.00 39.89 3.86
1283 1353 4.431131 CTTGGGCGGGCACTCCAT 62.431 66.667 0.00 0.00 34.36 3.41
1383 1458 2.287788 GCAAACATTATCCCTGCATCCG 60.288 50.000 0.00 0.00 33.19 4.18
1460 1535 2.028112 TCTTGGTCTTGGACAATCTCCG 60.028 50.000 0.14 0.00 43.03 4.63
1506 1581 7.120579 TCAATCGGCATAGATAAACAAACAAGT 59.879 33.333 0.00 0.00 0.00 3.16
1508 1583 7.384439 TCAATCGGCATAGATAAACAAACAA 57.616 32.000 0.00 0.00 0.00 2.83
1509 1584 6.993786 TCAATCGGCATAGATAAACAAACA 57.006 33.333 0.00 0.00 0.00 2.83
1510 1585 6.857964 CCATCAATCGGCATAGATAAACAAAC 59.142 38.462 0.00 0.00 0.00 2.93
1515 1590 5.013079 AGGACCATCAATCGGCATAGATAAA 59.987 40.000 0.00 0.00 0.00 1.40
1525 1600 3.544684 TGAATCAAGGACCATCAATCGG 58.455 45.455 0.00 0.00 0.00 4.18
1526 1601 4.194640 ACTGAATCAAGGACCATCAATCG 58.805 43.478 0.00 0.00 0.00 3.34
1534 1609 3.198635 TGGAGATGACTGAATCAAGGACC 59.801 47.826 0.00 0.00 41.93 4.46
1535 1610 4.478206 TGGAGATGACTGAATCAAGGAC 57.522 45.455 0.00 0.00 41.93 3.85
1555 1630 3.118445 GGAGAACCAAGAGAGAAGGGATG 60.118 52.174 0.00 0.00 35.97 3.51
1558 1633 2.545810 AGGAGAACCAAGAGAGAAGGG 58.454 52.381 0.00 0.00 38.94 3.95
1561 1636 7.017651 AGGAAAATTAGGAGAACCAAGAGAGAA 59.982 37.037 0.00 0.00 38.94 2.87
1563 1638 6.716284 AGGAAAATTAGGAGAACCAAGAGAG 58.284 40.000 0.00 0.00 38.94 3.20
1565 1640 7.667635 AGAAAGGAAAATTAGGAGAACCAAGAG 59.332 37.037 0.00 0.00 38.94 2.85
1611 1686 6.296026 TGAATACTCCTTGCTAGTTGTTGTT 58.704 36.000 0.00 0.00 0.00 2.83
1612 1687 5.865085 TGAATACTCCTTGCTAGTTGTTGT 58.135 37.500 0.00 0.00 0.00 3.32
1613 1688 6.992063 ATGAATACTCCTTGCTAGTTGTTG 57.008 37.500 0.00 0.00 0.00 3.33
1655 1730 4.788100 GCAAACATTACTAGTCAATGCACG 59.212 41.667 17.67 11.03 36.96 5.34
1668 1743 3.488489 CGCAACCTGTAGCAAACATTAC 58.512 45.455 0.00 0.00 37.50 1.89
1699 1774 9.862149 TCTCAGTAACCTATGTATCACTATCAA 57.138 33.333 0.00 0.00 0.00 2.57
1806 1881 0.460311 AACCTAATGGGCTCGAGTCG 59.540 55.000 15.13 6.09 39.10 4.18
1839 1914 1.135746 GTTGCTGCAGCTCAGAATGAC 60.136 52.381 36.61 18.19 45.72 3.06
1849 1924 0.936297 CTTTCGTTGGTTGCTGCAGC 60.936 55.000 31.89 31.89 42.50 5.25
1882 1957 2.394708 CGTCGCATCAGATACCGAAAT 58.605 47.619 6.85 0.00 0.00 2.17
1992 2067 2.854185 CGACGTCGTATTTTAGAACCCC 59.146 50.000 29.08 0.00 34.11 4.95
2060 2135 5.089970 TGGGACTGTATGAGAAATCAGTG 57.910 43.478 1.41 0.00 40.53 3.66
2080 2155 3.193267 CCATAATGGGTGTTGACTGTTGG 59.807 47.826 0.00 0.00 32.67 3.77
2103 2178 5.049167 GTCATGACAACCAAATCAGCAAAA 58.951 37.500 21.07 0.00 0.00 2.44
2225 2300 5.350640 GCAAGAAATAAGCCGTTGTAGTAGT 59.649 40.000 0.00 0.00 0.00 2.73
2270 2345 1.299541 ATGGTATCAAAGAAGCGCGG 58.700 50.000 8.83 0.00 0.00 6.46
2274 2349 6.601217 AGAGGAAAGAATGGTATCAAAGAAGC 59.399 38.462 0.00 0.00 0.00 3.86
2344 2420 7.592533 GCTAATGCATATTGTACAAGGTGATTG 59.407 37.037 20.89 10.70 40.99 2.67
2448 2524 2.990740 AACCTGAGGCCCATAAAACA 57.009 45.000 0.00 0.00 0.00 2.83
2552 2628 1.453155 GGAACACGCAGGATGACATT 58.547 50.000 0.00 0.00 39.69 2.71
2563 2639 2.112815 GGGCATACAGGGAACACGC 61.113 63.158 0.00 0.00 0.00 5.34
2572 2648 7.041635 TCACAAATTGATTATGGGCATACAG 57.958 36.000 0.00 0.00 0.00 2.74
2723 2799 8.100135 ACAATATGGAAGGAGAAGAAGAAGAT 57.900 34.615 0.00 0.00 0.00 2.40
2990 3155 8.332464 TCCAAGAAAATAATAGTTGCGAATACG 58.668 33.333 0.00 0.00 42.93 3.06
3209 3537 6.974932 TTTTGCTTGCAATTTTACTGACAA 57.025 29.167 8.93 0.00 0.00 3.18
3224 3552 6.044682 AGTGTCTTGATTTCCTTTTTGCTTG 58.955 36.000 0.00 0.00 0.00 4.01
3227 3555 5.591099 TGAGTGTCTTGATTTCCTTTTTGC 58.409 37.500 0.00 0.00 0.00 3.68
3245 3573 8.950210 AGAACAATAGTGGATTTATGTTGAGTG 58.050 33.333 0.00 0.00 0.00 3.51
3260 3588 8.292448 ACAGCAAGAATTAACAGAACAATAGTG 58.708 33.333 0.00 0.00 0.00 2.74
3441 3769 1.622607 TAGATCCCCAGTGGTTGGCG 61.623 60.000 8.74 0.00 46.32 5.69
3529 3860 1.144936 GAGCGGCATAGGAGCAAGT 59.855 57.895 1.45 0.00 35.83 3.16
3736 4067 6.737254 TTAGCAGCAGATACAACCTTAAAC 57.263 37.500 0.00 0.00 0.00 2.01
3765 4101 3.842732 TTACTCACGACGTCATGATGT 57.157 42.857 20.50 20.50 0.00 3.06
3832 4168 0.467290 TCCCACCCAGCTTTGTCAAC 60.467 55.000 0.00 0.00 0.00 3.18
3865 4201 0.955919 GTGTGGTTACTCTGGGCAGC 60.956 60.000 0.00 0.00 0.00 5.25
3945 4281 6.093219 AGTGAGCTGTGTAAAATCTTATGCAG 59.907 38.462 0.00 0.00 0.00 4.41
3947 4283 6.428385 AGTGAGCTGTGTAAAATCTTATGC 57.572 37.500 0.00 0.00 0.00 3.14
3987 4330 6.624423 GCTCAGCATATCACAACTCAACAAAT 60.624 38.462 0.00 0.00 0.00 2.32
4028 4371 7.138736 CGAGAATTGATAAAATTGCCCGTAAT 58.861 34.615 0.00 0.00 0.00 1.89
4046 4389 9.823647 ATGTAACAGAAGAATATCACGAGAATT 57.176 29.630 0.00 0.00 0.00 2.17
4119 4462 9.540538 TTTTGGGGATTGAATACTAATTTGAGA 57.459 29.630 0.00 0.00 0.00 3.27
4206 4559 6.754675 TGCAGATGAATCAGTAAAATTGCATG 59.245 34.615 0.00 0.00 33.43 4.06
4291 4644 0.674581 CGATTTGCTGCCTCCTCACA 60.675 55.000 0.00 0.00 0.00 3.58
4293 4646 1.746615 GCGATTTGCTGCCTCCTCA 60.747 57.895 0.00 0.00 41.73 3.86
4369 4722 1.236616 CGAAGCTGTTGGACATGGCA 61.237 55.000 0.00 0.00 0.00 4.92
4466 4825 1.947642 GTTGTTGCTGCTGCTGCAC 60.948 57.895 29.84 23.63 45.31 4.57
4477 4836 1.403249 GCCACCATCTGATGTTGTTGC 60.403 52.381 15.95 10.99 0.00 4.17
4600 4962 2.611225 TGTTTTGCTTTGGCGGATTT 57.389 40.000 0.00 0.00 42.25 2.17
4678 5086 8.059461 TCCTCAGAATTAGAAGAGTGGTATACA 58.941 37.037 5.01 0.00 0.00 2.29
4686 5094 5.483583 AGTTGCTCCTCAGAATTAGAAGAGT 59.516 40.000 7.46 0.00 0.00 3.24
4730 5142 9.975218 ACAATTTCCATAAGGTTTACAGTATCT 57.025 29.630 0.00 0.00 35.89 1.98
4784 5196 5.644636 GGAAATTGTGTCATGGCATTCAAAT 59.355 36.000 1.89 0.00 0.00 2.32
4808 5220 2.120232 GCGGAGATGTGTTCGATAGTG 58.880 52.381 0.00 0.00 37.40 2.74
4811 5223 2.927477 GTTTGCGGAGATGTGTTCGATA 59.073 45.455 0.00 0.00 0.00 2.92
4817 5229 1.536766 CATGTGTTTGCGGAGATGTGT 59.463 47.619 0.00 0.00 0.00 3.72
4848 5260 5.682234 TCTAGGTTGTGTGATGATGATGT 57.318 39.130 0.00 0.00 0.00 3.06
4938 5350 8.633561 TCAATATTGAGATCAGTAGTACTGTGG 58.366 37.037 25.83 5.12 38.71 4.17
5140 5559 2.973945 ACTGGAACCGCTAGTTTCATC 58.026 47.619 0.00 0.00 43.28 2.92
5151 5570 0.969894 AGAGGACTGAACTGGAACCG 59.030 55.000 0.00 0.00 0.00 4.44
5194 5617 1.419387 GATGAGGAGGTGGAGGGATTG 59.581 57.143 0.00 0.00 0.00 2.67
5204 5627 2.066999 GCTTCCCGGATGAGGAGGT 61.067 63.158 0.73 0.00 34.08 3.85
5263 5686 1.094785 ACACACTGTGTTCTTGCACC 58.905 50.000 11.40 0.00 45.08 5.01
5312 5790 7.495279 GCATTTCATCTCTAGTTCTCATCTTGT 59.505 37.037 0.00 0.00 0.00 3.16
5315 5793 6.985645 GTGCATTTCATCTCTAGTTCTCATCT 59.014 38.462 0.00 0.00 0.00 2.90
5345 5823 9.289303 AGTGCGATAAAATTAACAAAGCATAAG 57.711 29.630 0.00 0.00 34.54 1.73
5350 5828 9.284594 TGATTAGTGCGATAAAATTAACAAAGC 57.715 29.630 0.00 0.00 0.00 3.51
5357 5835 8.637281 TCGAAGTGATTAGTGCGATAAAATTA 57.363 30.769 0.00 0.00 32.35 1.40
5358 5836 7.534085 TCGAAGTGATTAGTGCGATAAAATT 57.466 32.000 0.00 0.00 32.35 1.82
5359 5837 7.438160 TGATCGAAGTGATTAGTGCGATAAAAT 59.562 33.333 8.12 0.00 45.81 1.82
5360 5838 6.754675 TGATCGAAGTGATTAGTGCGATAAAA 59.245 34.615 8.12 0.00 45.81 1.52
5361 5839 6.198403 GTGATCGAAGTGATTAGTGCGATAAA 59.802 38.462 8.12 0.00 45.81 1.40
5362 5840 5.685954 GTGATCGAAGTGATTAGTGCGATAA 59.314 40.000 8.12 0.00 45.81 1.75
5363 5841 5.008712 AGTGATCGAAGTGATTAGTGCGATA 59.991 40.000 8.12 0.00 45.81 2.92
5365 5843 3.128764 AGTGATCGAAGTGATTAGTGCGA 59.871 43.478 0.00 0.00 41.38 5.10
5366 5844 3.439293 AGTGATCGAAGTGATTAGTGCG 58.561 45.455 0.00 0.00 37.47 5.34
5367 5845 5.051374 GCTTAGTGATCGAAGTGATTAGTGC 60.051 44.000 0.00 0.00 37.47 4.40
5368 5846 5.460419 GGCTTAGTGATCGAAGTGATTAGTG 59.540 44.000 0.00 0.00 37.47 2.74
5369 5847 5.452077 GGGCTTAGTGATCGAAGTGATTAGT 60.452 44.000 0.00 0.00 37.47 2.24
5370 5848 4.985409 GGGCTTAGTGATCGAAGTGATTAG 59.015 45.833 0.00 0.00 37.47 1.73
5376 5868 0.460311 CCGGGCTTAGTGATCGAAGT 59.540 55.000 0.00 0.00 0.00 3.01
5386 5878 2.596904 TTCGATTCTTCCGGGCTTAG 57.403 50.000 0.00 0.00 0.00 2.18
5402 5894 8.437443 TGTTTAGCAATTTACCGTAAAATTCG 57.563 30.769 7.78 0.00 37.03 3.34
5444 5940 4.399618 AGAAACTAGTCTTGCTCTGCGATA 59.600 41.667 0.00 0.00 0.00 2.92
5447 5943 2.953020 AGAAACTAGTCTTGCTCTGCG 58.047 47.619 0.00 0.00 0.00 5.18
5477 5973 2.668632 GACAGCCGGTGGAATCCA 59.331 61.111 1.90 0.00 0.00 3.41
5478 5974 2.124695 GGACAGCCGGTGGAATCC 60.125 66.667 1.90 0.00 0.00 3.01
5479 5975 1.026718 CAAGGACAGCCGGTGGAATC 61.027 60.000 1.90 0.00 39.96 2.52
5480 5976 1.002134 CAAGGACAGCCGGTGGAAT 60.002 57.895 1.90 0.00 39.96 3.01
5481 5977 2.429930 CAAGGACAGCCGGTGGAA 59.570 61.111 1.90 0.00 39.96 3.53
5482 5978 4.329545 GCAAGGACAGCCGGTGGA 62.330 66.667 1.90 0.00 39.96 4.02
5561 6060 3.265489 TCCCCCTCTCCAAGTAACAATT 58.735 45.455 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.