Multiple sequence alignment - TraesCS4A01G139600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G139600 chr4A 100.000 2796 0 0 1 2796 210999054 211001849 0.000000e+00 5164.0
1 TraesCS4A01G139600 chr4D 84.705 1713 88 53 1 1606 291738080 291736435 0.000000e+00 1552.0
2 TraesCS4A01G139600 chr4D 87.942 622 45 18 1629 2248 291736278 291735685 0.000000e+00 706.0
3 TraesCS4A01G139600 chr4D 79.846 521 46 28 2304 2796 291735688 291735199 2.690000e-85 326.0
4 TraesCS4A01G139600 chr4B 83.579 1699 107 63 1 1606 273687344 273688963 0.000000e+00 1434.0
5 TraesCS4A01G139600 chr4B 83.889 720 53 21 678 1362 565111688 565112379 1.830000e-176 628.0
6 TraesCS4A01G139600 chr4B 89.047 493 30 10 1566 2035 273688958 273689449 8.630000e-165 590.0
7 TraesCS4A01G139600 chr4B 83.028 601 42 22 678 1244 10622227 10621653 9.000000e-135 490.0
8 TraesCS4A01G139600 chr7B 83.056 720 59 23 678 1362 709128678 709129369 1.850000e-166 595.0
9 TraesCS4A01G139600 chr7B 83.728 676 59 21 711 1362 613375597 613374949 2.400000e-165 592.0
10 TraesCS4A01G139600 chr7B 83.871 558 40 23 711 1244 718399844 718400375 1.160000e-133 486.0
11 TraesCS4A01G139600 chr3B 83.079 721 57 25 678 1362 16180715 16180024 1.850000e-166 595.0
12 TraesCS4A01G139600 chr3B 100.000 41 0 0 2463 2503 437594242 437594282 2.990000e-10 76.8
13 TraesCS4A01G139600 chr3B 100.000 41 0 0 2463 2503 796324348 796324388 2.990000e-10 76.8
14 TraesCS4A01G139600 chr2B 82.917 720 60 20 678 1362 29006114 29005423 8.630000e-165 590.0
15 TraesCS4A01G139600 chr6B 83.038 678 61 24 711 1362 387720062 387719413 1.450000e-157 566.0
16 TraesCS4A01G139600 chr7D 86.500 200 19 5 1718 1914 548774971 548774777 2.180000e-51 213.0
17 TraesCS4A01G139600 chr7D 100.000 41 0 0 2463 2503 635512691 635512731 2.990000e-10 76.8
18 TraesCS4A01G139600 chr7A 83.636 220 21 7 1756 1967 632549685 632549473 2.840000e-45 193.0
19 TraesCS4A01G139600 chr7A 100.000 41 0 0 2463 2503 439811061 439811101 2.990000e-10 76.8
20 TraesCS4A01G139600 chr7A 100.000 41 0 0 2463 2503 537202883 537202843 2.990000e-10 76.8
21 TraesCS4A01G139600 chr7A 100.000 41 0 0 2463 2503 634341627 634341667 2.990000e-10 76.8
22 TraesCS4A01G139600 chr3D 100.000 43 0 0 2461 2503 220649218 220649260 2.310000e-11 80.5
23 TraesCS4A01G139600 chr3D 100.000 43 0 0 2461 2503 220652597 220652639 2.310000e-11 80.5
24 TraesCS4A01G139600 chr1D 100.000 41 0 0 2463 2503 51866734 51866694 2.990000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G139600 chr4A 210999054 211001849 2795 False 5164.000000 5164 100.000000 1 2796 1 chr4A.!!$F1 2795
1 TraesCS4A01G139600 chr4D 291735199 291738080 2881 True 861.333333 1552 84.164333 1 2796 3 chr4D.!!$R1 2795
2 TraesCS4A01G139600 chr4B 273687344 273689449 2105 False 1012.000000 1434 86.313000 1 2035 2 chr4B.!!$F2 2034
3 TraesCS4A01G139600 chr4B 565111688 565112379 691 False 628.000000 628 83.889000 678 1362 1 chr4B.!!$F1 684
4 TraesCS4A01G139600 chr4B 10621653 10622227 574 True 490.000000 490 83.028000 678 1244 1 chr4B.!!$R1 566
5 TraesCS4A01G139600 chr7B 709128678 709129369 691 False 595.000000 595 83.056000 678 1362 1 chr7B.!!$F1 684
6 TraesCS4A01G139600 chr7B 613374949 613375597 648 True 592.000000 592 83.728000 711 1362 1 chr7B.!!$R1 651
7 TraesCS4A01G139600 chr7B 718399844 718400375 531 False 486.000000 486 83.871000 711 1244 1 chr7B.!!$F2 533
8 TraesCS4A01G139600 chr3B 16180024 16180715 691 True 595.000000 595 83.079000 678 1362 1 chr3B.!!$R1 684
9 TraesCS4A01G139600 chr2B 29005423 29006114 691 True 590.000000 590 82.917000 678 1362 1 chr2B.!!$R1 684
10 TraesCS4A01G139600 chr6B 387719413 387720062 649 True 566.000000 566 83.038000 711 1362 1 chr6B.!!$R1 651

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
914 1030 0.178861 ACCCACTTCCCATGTCCTCT 60.179 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 2906 0.037326 GATCACCGTGGCAGAGTTCA 60.037 55.0 0.0 0.0 0.0 3.18 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
91 120 2.825836 GCCGGTGAGGAATGGCAG 60.826 66.667 1.90 0.00 46.76 4.85
100 129 2.036256 GAATGGCAGGTGTGGGCT 59.964 61.111 0.00 0.00 0.00 5.19
229 260 2.827642 GACAGCTCCATGGCCTGC 60.828 66.667 23.97 19.19 0.00 4.85
256 287 2.602267 GGGGGTTTCGGGGGTTTG 60.602 66.667 0.00 0.00 0.00 2.93
261 292 1.904865 GTTTCGGGGGTTTGGGGAC 60.905 63.158 0.00 0.00 0.00 4.46
288 319 1.078356 GAGGAGCGGGAGGGAAAAC 60.078 63.158 0.00 0.00 0.00 2.43
289 320 2.436115 GGAGCGGGAGGGAAAACG 60.436 66.667 0.00 0.00 0.00 3.60
290 321 2.436115 GAGCGGGAGGGAAAACGG 60.436 66.667 0.00 0.00 0.00 4.44
300 336 0.402887 GGGAAAACGGAAAGGAGGGA 59.597 55.000 0.00 0.00 0.00 4.20
330 366 1.616994 GCTTTGGAGTATTGGGCTGGT 60.617 52.381 0.00 0.00 0.00 4.00
353 405 4.659172 CCACGGCCCAAGGAGCAA 62.659 66.667 0.00 0.00 0.00 3.91
432 502 0.544223 TGGCCGCTCCTGCTATAAAA 59.456 50.000 0.00 0.00 36.97 1.52
435 505 2.494059 GCCGCTCCTGCTATAAAATCA 58.506 47.619 0.00 0.00 36.97 2.57
436 506 2.878406 GCCGCTCCTGCTATAAAATCAA 59.122 45.455 0.00 0.00 36.97 2.57
536 610 3.386237 GTGCGTCCCTCTCTGCCT 61.386 66.667 0.00 0.00 0.00 4.75
537 611 3.071206 TGCGTCCCTCTCTGCCTC 61.071 66.667 0.00 0.00 0.00 4.70
538 612 3.844090 GCGTCCCTCTCTGCCTCC 61.844 72.222 0.00 0.00 0.00 4.30
539 613 3.151022 CGTCCCTCTCTGCCTCCC 61.151 72.222 0.00 0.00 0.00 4.30
540 614 2.766229 GTCCCTCTCTGCCTCCCC 60.766 72.222 0.00 0.00 0.00 4.81
541 615 2.955246 TCCCTCTCTGCCTCCCCT 60.955 66.667 0.00 0.00 0.00 4.79
542 616 2.445654 CCCTCTCTGCCTCCCCTC 60.446 72.222 0.00 0.00 0.00 4.30
543 617 2.445654 CCTCTCTGCCTCCCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
544 618 2.445654 CTCTCTGCCTCCCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
545 619 4.095400 TCTCTGCCTCCCCTCCCC 62.095 72.222 0.00 0.00 0.00 4.81
546 620 4.421554 CTCTGCCTCCCCTCCCCA 62.422 72.222 0.00 0.00 0.00 4.96
547 621 4.421554 TCTGCCTCCCCTCCCCAG 62.422 72.222 0.00 0.00 0.00 4.45
561 635 2.234296 CCCAGCCACCCTCCTTTCT 61.234 63.158 0.00 0.00 0.00 2.52
590 664 2.492019 TGCTCGATCTTGTATGTCCG 57.508 50.000 0.00 0.00 0.00 4.79
595 669 1.860950 CGATCTTGTATGTCCGCCTTG 59.139 52.381 0.00 0.00 0.00 3.61
600 674 1.450312 GTATGTCCGCCTTGCTGCT 60.450 57.895 0.00 0.00 0.00 4.24
606 680 2.554636 CCGCCTTGCTGCTTGTTCA 61.555 57.895 0.00 0.00 0.00 3.18
629 703 0.744414 ATTCGTTCCCATCCTGCGTG 60.744 55.000 0.00 0.00 0.00 5.34
656 730 3.246226 CGTCTTCTTCTTGTCACCAAGTG 59.754 47.826 2.69 0.00 46.70 3.16
657 731 3.002759 GTCTTCTTCTTGTCACCAAGTGC 59.997 47.826 2.69 0.00 46.70 4.40
701 780 2.809665 GCTTGGTCAGGATCTATGGCTG 60.810 54.545 0.00 0.00 0.00 4.85
805 895 8.948631 TGTGTCTCAGATCCTGTTATTATTTC 57.051 34.615 0.00 0.00 32.61 2.17
806 896 7.706607 TGTGTCTCAGATCCTGTTATTATTTCG 59.293 37.037 0.00 0.00 32.61 3.46
807 897 7.707035 GTGTCTCAGATCCTGTTATTATTTCGT 59.293 37.037 0.00 0.00 32.61 3.85
808 898 8.909923 TGTCTCAGATCCTGTTATTATTTCGTA 58.090 33.333 0.00 0.00 32.61 3.43
809 899 9.915629 GTCTCAGATCCTGTTATTATTTCGTAT 57.084 33.333 0.00 0.00 32.61 3.06
840 932 1.602311 AGCAATCGATTCCTGCCATC 58.398 50.000 15.23 0.00 36.73 3.51
841 933 1.142465 AGCAATCGATTCCTGCCATCT 59.858 47.619 15.23 0.00 36.73 2.90
842 934 1.266175 GCAATCGATTCCTGCCATCTG 59.734 52.381 7.92 0.00 0.00 2.90
843 935 2.569059 CAATCGATTCCTGCCATCTGT 58.431 47.619 7.92 0.00 0.00 3.41
854 946 2.749621 CTGCCATCTGTTTGTTAGGGTC 59.250 50.000 0.00 0.00 0.00 4.46
876 974 7.148239 GGGTCGATAAGAATTTCTGTTGATGTT 60.148 37.037 0.00 0.00 0.00 2.71
886 984 6.500684 TTTCTGTTGATGTTGCTAGATTCC 57.499 37.500 0.00 0.00 0.00 3.01
898 1014 1.409427 CTAGATTCCTGGACACGACCC 59.591 57.143 0.00 0.00 0.00 4.46
909 1025 1.374947 CACGACCCACTTCCCATGT 59.625 57.895 0.00 0.00 0.00 3.21
914 1030 0.178861 ACCCACTTCCCATGTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
915 1031 1.080498 ACCCACTTCCCATGTCCTCTA 59.920 52.381 0.00 0.00 0.00 2.43
916 1032 1.765314 CCCACTTCCCATGTCCTCTAG 59.235 57.143 0.00 0.00 0.00 2.43
917 1033 1.139853 CCACTTCCCATGTCCTCTAGC 59.860 57.143 0.00 0.00 0.00 3.42
951 1067 4.415881 TCCTCTTGTGCTTAGTTTGTGA 57.584 40.909 0.00 0.00 0.00 3.58
1052 1187 0.472352 TACGTCCCCAGGAAGTGGTT 60.472 55.000 11.78 0.00 46.37 3.67
1081 1216 4.244425 TGCACACTCTCTTTAGTCTGAC 57.756 45.455 0.00 0.00 0.00 3.51
1082 1217 3.891977 TGCACACTCTCTTTAGTCTGACT 59.108 43.478 15.57 15.57 0.00 3.41
1083 1218 5.070685 TGCACACTCTCTTTAGTCTGACTA 58.929 41.667 13.34 13.34 0.00 2.59
1097 1232 4.881273 AGTCTGACTATGTGTGTTTTGCAA 59.119 37.500 8.91 0.00 0.00 4.08
1098 1233 4.970003 GTCTGACTATGTGTGTTTTGCAAC 59.030 41.667 0.00 0.00 0.00 4.17
1112 1247 3.049674 CAACGGTGGATGCGTGCT 61.050 61.111 0.00 0.00 0.00 4.40
1282 1418 3.318275 GTCCGTGCTCAGGTAATCATCTA 59.682 47.826 0.00 0.00 0.00 1.98
1350 1488 8.579850 TGCTCATCAAATTACTATTTCCAGTT 57.420 30.769 0.00 0.00 31.63 3.16
1370 1508 7.765819 TCCAGTTATCATGTTACTGTTGATGAG 59.234 37.037 17.15 6.33 38.04 2.90
1388 1526 7.503521 TGATGAGATAGTACTAAGCTCAGTG 57.496 40.000 28.06 0.00 35.51 3.66
1389 1527 7.057264 TGATGAGATAGTACTAAGCTCAGTGT 58.943 38.462 28.06 19.06 35.51 3.55
1390 1528 8.211629 TGATGAGATAGTACTAAGCTCAGTGTA 58.788 37.037 28.06 18.03 35.51 2.90
1391 1529 7.789273 TGAGATAGTACTAAGCTCAGTGTAC 57.211 40.000 24.04 5.25 36.48 2.90
1392 1530 6.766944 TGAGATAGTACTAAGCTCAGTGTACC 59.233 42.308 24.04 7.19 36.79 3.34
1393 1531 6.660800 AGATAGTACTAAGCTCAGTGTACCA 58.339 40.000 6.70 0.00 36.79 3.25
1394 1532 7.291566 AGATAGTACTAAGCTCAGTGTACCAT 58.708 38.462 6.70 0.17 36.79 3.55
1440 1579 5.827797 TCAGATATTTTCTATTGGTGGTGCC 59.172 40.000 0.00 0.00 31.77 5.01
1454 1595 2.678336 GTGGTGCCTACTTGCTTATGTC 59.322 50.000 0.00 0.00 0.00 3.06
1495 1643 7.764331 TGACCATGAACATGTATTTTCATCTG 58.236 34.615 7.62 5.61 39.86 2.90
1554 1703 5.820947 TGAAGACTTGTCACCTTTTAGTTCC 59.179 40.000 3.49 0.00 0.00 3.62
1562 1711 5.163426 TGTCACCTTTTAGTTCCGAGTGTTA 60.163 40.000 0.00 0.00 0.00 2.41
1633 1930 9.313118 ACTTTGGTTTTGATACTTTGAATTCAC 57.687 29.630 7.89 0.00 0.00 3.18
1634 1931 8.655651 TTTGGTTTTGATACTTTGAATTCACC 57.344 30.769 7.89 2.05 0.00 4.02
1718 2036 8.989980 ACATTACTTTACTCTTACAGCTTGTTC 58.010 33.333 0.00 0.00 0.00 3.18
1750 2068 0.534652 GTGATGCTGATGGCTCCCTC 60.535 60.000 0.00 0.00 42.39 4.30
1860 2178 4.277423 GTCTACCTAGCTCTTGGATGTCTC 59.723 50.000 4.44 0.00 0.00 3.36
1932 2250 4.680440 GCCTGGTTTCTTGTGAACATGTTT 60.680 41.667 13.36 0.00 31.02 2.83
1973 2291 7.013559 TGTTGAATGCTTGATATATGTCCCTTG 59.986 37.037 0.00 0.00 0.00 3.61
1977 2295 6.252599 TGCTTGATATATGTCCCTTGTCTT 57.747 37.500 0.00 0.00 0.00 3.01
1993 2311 6.808212 CCCTTGTCTTGTTGCTTAATGTTATG 59.192 38.462 0.00 0.00 0.00 1.90
2023 2341 6.321181 TGATTTGGCCCTTATTTTACTAGCAG 59.679 38.462 0.00 0.00 0.00 4.24
2029 2347 6.464465 GGCCCTTATTTTACTAGCAGATCTGA 60.464 42.308 27.04 5.37 0.00 3.27
2030 2348 6.425417 GCCCTTATTTTACTAGCAGATCTGAC 59.575 42.308 27.04 16.75 0.00 3.51
2032 2350 7.419057 CCCTTATTTTACTAGCAGATCTGACCA 60.419 40.741 27.04 8.86 0.00 4.02
2033 2351 8.153550 CCTTATTTTACTAGCAGATCTGACCAT 58.846 37.037 27.04 10.64 0.00 3.55
2037 2355 6.596309 TTACTAGCAGATCTGACCATATGG 57.404 41.667 27.04 20.68 42.17 2.74
2038 2356 2.855209 AGCAGATCTGACCATATGGC 57.145 50.000 27.04 14.55 39.32 4.40
2039 2357 2.336891 AGCAGATCTGACCATATGGCT 58.663 47.619 27.04 9.69 39.32 4.75
2040 2358 2.302445 AGCAGATCTGACCATATGGCTC 59.698 50.000 27.04 17.36 39.32 4.70
2041 2359 2.302445 GCAGATCTGACCATATGGCTCT 59.698 50.000 27.04 12.50 39.32 4.09
2042 2360 3.865302 GCAGATCTGACCATATGGCTCTG 60.865 52.174 27.04 22.20 39.32 3.35
2043 2361 3.324268 CAGATCTGACCATATGGCTCTGT 59.676 47.826 22.18 5.47 39.32 3.41
2044 2362 3.324268 AGATCTGACCATATGGCTCTGTG 59.676 47.826 22.18 11.87 39.32 3.66
2045 2363 2.470990 TCTGACCATATGGCTCTGTGT 58.529 47.619 22.18 0.00 39.32 3.72
2046 2364 2.840038 TCTGACCATATGGCTCTGTGTT 59.160 45.455 22.18 0.00 39.32 3.32
2047 2365 2.941064 CTGACCATATGGCTCTGTGTTG 59.059 50.000 22.18 0.00 39.32 3.33
2048 2366 2.571202 TGACCATATGGCTCTGTGTTGA 59.429 45.455 22.18 0.00 39.32 3.18
2069 2387 6.633500 TGAGTTTGTCCCTTGTTATTCTTG 57.367 37.500 0.00 0.00 0.00 3.02
2087 2406 5.710513 TCTTGCTTCAAAATGCATGTACT 57.289 34.783 0.00 0.00 39.07 2.73
2088 2407 5.702865 TCTTGCTTCAAAATGCATGTACTC 58.297 37.500 0.00 0.00 39.07 2.59
2099 2418 4.245845 TGCATGTACTCGAGTAACAACA 57.754 40.909 26.21 21.98 31.52 3.33
2101 2420 3.060895 GCATGTACTCGAGTAACAACAGC 59.939 47.826 26.21 22.36 31.52 4.40
2106 2425 1.457303 CTCGAGTAACAACAGCAGCAC 59.543 52.381 3.62 0.00 0.00 4.40
2108 2427 1.597195 CGAGTAACAACAGCAGCACAA 59.403 47.619 0.00 0.00 0.00 3.33
2109 2428 2.348872 CGAGTAACAACAGCAGCACAAG 60.349 50.000 0.00 0.00 0.00 3.16
2110 2429 2.614057 GAGTAACAACAGCAGCACAAGT 59.386 45.455 0.00 0.00 0.00 3.16
2111 2430 3.804036 AGTAACAACAGCAGCACAAGTA 58.196 40.909 0.00 0.00 0.00 2.24
2112 2431 4.196193 AGTAACAACAGCAGCACAAGTAA 58.804 39.130 0.00 0.00 0.00 2.24
2114 2433 1.334869 ACAACAGCAGCACAAGTAAGC 59.665 47.619 0.00 0.00 0.00 3.09
2117 2436 0.110509 CAGCAGCACAAGTAAGCACG 60.111 55.000 0.00 0.00 0.00 5.34
2118 2437 1.441016 GCAGCACAAGTAAGCACGC 60.441 57.895 0.00 0.00 0.00 5.34
2119 2438 1.941072 CAGCACAAGTAAGCACGCA 59.059 52.632 0.00 0.00 0.00 5.24
2120 2439 0.518636 CAGCACAAGTAAGCACGCAT 59.481 50.000 0.00 0.00 0.00 4.73
2121 2440 1.069022 CAGCACAAGTAAGCACGCATT 60.069 47.619 0.00 0.00 0.00 3.56
2122 2441 1.608590 AGCACAAGTAAGCACGCATTT 59.391 42.857 0.00 0.00 0.00 2.32
2123 2442 2.034558 AGCACAAGTAAGCACGCATTTT 59.965 40.909 0.00 0.00 0.00 1.82
2124 2443 2.153627 GCACAAGTAAGCACGCATTTTG 59.846 45.455 0.00 0.00 0.00 2.44
2125 2444 2.153627 CACAAGTAAGCACGCATTTTGC 59.846 45.455 0.00 0.00 40.69 3.68
2126 2445 1.720852 CAAGTAAGCACGCATTTTGCC 59.279 47.619 0.00 0.00 41.12 4.52
2127 2446 0.958091 AGTAAGCACGCATTTTGCCA 59.042 45.000 0.00 0.00 41.12 4.92
2128 2447 1.545582 AGTAAGCACGCATTTTGCCAT 59.454 42.857 0.00 0.00 41.12 4.40
2129 2448 1.655099 GTAAGCACGCATTTTGCCATG 59.345 47.619 0.00 0.00 41.12 3.66
2130 2449 1.293267 AAGCACGCATTTTGCCATGC 61.293 50.000 12.90 12.90 46.44 4.06
2138 2457 3.520290 CATTTTGCCATGCAGACATCT 57.480 42.857 0.00 0.00 40.61 2.90
2164 2483 5.233988 CGTTTTGGCCAATTGAAATCCTTA 58.766 37.500 21.26 0.00 0.00 2.69
2248 2568 1.354506 GGCTGACGATTGATGCTGC 59.645 57.895 0.00 0.00 0.00 5.25
2250 2570 0.027716 GCTGACGATTGATGCTGCAG 59.972 55.000 10.11 10.11 0.00 4.41
2251 2571 1.366679 CTGACGATTGATGCTGCAGT 58.633 50.000 16.64 0.00 0.00 4.40
2253 2573 1.338011 TGACGATTGATGCTGCAGTCA 60.338 47.619 16.64 14.12 35.18 3.41
2254 2574 1.938577 GACGATTGATGCTGCAGTCAT 59.061 47.619 19.30 19.30 0.00 3.06
2255 2575 2.353889 GACGATTGATGCTGCAGTCATT 59.646 45.455 16.64 8.40 0.00 2.57
2256 2576 2.353889 ACGATTGATGCTGCAGTCATTC 59.646 45.455 16.64 15.35 0.00 2.67
2257 2577 2.353579 CGATTGATGCTGCAGTCATTCA 59.646 45.455 16.64 14.58 0.00 2.57
2258 2578 3.003378 CGATTGATGCTGCAGTCATTCAT 59.997 43.478 16.64 9.55 0.00 2.57
2259 2579 4.212636 CGATTGATGCTGCAGTCATTCATA 59.787 41.667 16.64 6.70 0.00 2.15
2260 2580 4.888038 TTGATGCTGCAGTCATTCATAC 57.112 40.909 16.64 7.51 0.00 2.39
2261 2581 3.876341 TGATGCTGCAGTCATTCATACA 58.124 40.909 16.64 9.78 0.00 2.29
2262 2582 3.875134 TGATGCTGCAGTCATTCATACAG 59.125 43.478 16.64 0.00 0.00 2.74
2263 2583 3.615224 TGCTGCAGTCATTCATACAGA 57.385 42.857 16.64 0.00 0.00 3.41
2264 2584 4.146745 TGCTGCAGTCATTCATACAGAT 57.853 40.909 16.64 0.00 0.00 2.90
2265 2585 5.280654 TGCTGCAGTCATTCATACAGATA 57.719 39.130 16.64 0.00 0.00 1.98
2266 2586 5.052481 TGCTGCAGTCATTCATACAGATAC 58.948 41.667 16.64 0.00 0.00 2.24
2267 2587 4.149571 GCTGCAGTCATTCATACAGATACG 59.850 45.833 16.64 0.00 0.00 3.06
2268 2588 4.620982 TGCAGTCATTCATACAGATACGG 58.379 43.478 0.00 0.00 0.00 4.02
2269 2589 3.990469 GCAGTCATTCATACAGATACGGG 59.010 47.826 0.00 0.00 0.00 5.28
2270 2590 3.990469 CAGTCATTCATACAGATACGGGC 59.010 47.826 0.00 0.00 0.00 6.13
2271 2591 3.898123 AGTCATTCATACAGATACGGGCT 59.102 43.478 0.00 0.00 0.00 5.19
2272 2592 4.345257 AGTCATTCATACAGATACGGGCTT 59.655 41.667 0.00 0.00 0.00 4.35
2273 2593 5.538813 AGTCATTCATACAGATACGGGCTTA 59.461 40.000 0.00 0.00 0.00 3.09
2274 2594 5.864474 GTCATTCATACAGATACGGGCTTAG 59.136 44.000 0.00 0.00 0.00 2.18
2275 2595 5.538813 TCATTCATACAGATACGGGCTTAGT 59.461 40.000 0.00 0.00 0.00 2.24
2276 2596 5.864418 TTCATACAGATACGGGCTTAGTT 57.136 39.130 0.00 0.00 0.00 2.24
2277 2597 6.964807 TTCATACAGATACGGGCTTAGTTA 57.035 37.500 0.00 0.00 0.00 2.24
2278 2598 6.964807 TCATACAGATACGGGCTTAGTTAA 57.035 37.500 0.00 0.00 0.00 2.01
2279 2599 7.534723 TCATACAGATACGGGCTTAGTTAAT 57.465 36.000 0.00 0.00 0.00 1.40
2280 2600 7.959175 TCATACAGATACGGGCTTAGTTAATT 58.041 34.615 0.00 0.00 0.00 1.40
2281 2601 8.426489 TCATACAGATACGGGCTTAGTTAATTT 58.574 33.333 0.00 0.00 0.00 1.82
2282 2602 6.920569 ACAGATACGGGCTTAGTTAATTTG 57.079 37.500 0.00 0.00 0.00 2.32
2283 2603 5.296035 ACAGATACGGGCTTAGTTAATTTGC 59.704 40.000 0.00 0.00 0.00 3.68
2284 2604 5.527582 CAGATACGGGCTTAGTTAATTTGCT 59.472 40.000 0.00 0.00 0.00 3.91
2285 2605 5.527582 AGATACGGGCTTAGTTAATTTGCTG 59.472 40.000 0.00 0.00 0.00 4.41
2286 2606 3.418047 ACGGGCTTAGTTAATTTGCTGT 58.582 40.909 0.00 0.00 0.00 4.40
2287 2607 3.439129 ACGGGCTTAGTTAATTTGCTGTC 59.561 43.478 0.00 0.00 0.00 3.51
2288 2608 3.438781 CGGGCTTAGTTAATTTGCTGTCA 59.561 43.478 0.00 0.00 0.00 3.58
2289 2609 4.671766 CGGGCTTAGTTAATTTGCTGTCAC 60.672 45.833 0.00 0.00 0.00 3.67
2290 2610 4.217550 GGGCTTAGTTAATTTGCTGTCACA 59.782 41.667 0.00 0.00 0.00 3.58
2291 2611 5.105756 GGGCTTAGTTAATTTGCTGTCACAT 60.106 40.000 0.00 0.00 0.00 3.21
2292 2612 6.389906 GGCTTAGTTAATTTGCTGTCACATT 58.610 36.000 0.00 0.00 0.00 2.71
2293 2613 6.308766 GGCTTAGTTAATTTGCTGTCACATTG 59.691 38.462 0.00 0.00 0.00 2.82
2294 2614 6.863126 GCTTAGTTAATTTGCTGTCACATTGT 59.137 34.615 0.00 0.00 0.00 2.71
2295 2615 7.382218 GCTTAGTTAATTTGCTGTCACATTGTT 59.618 33.333 0.00 0.00 0.00 2.83
2296 2616 9.891828 CTTAGTTAATTTGCTGTCACATTGTTA 57.108 29.630 0.00 0.00 0.00 2.41
2298 2618 8.970691 AGTTAATTTGCTGTCACATTGTTATC 57.029 30.769 0.00 0.00 0.00 1.75
2299 2619 8.575589 AGTTAATTTGCTGTCACATTGTTATCA 58.424 29.630 0.00 0.00 0.00 2.15
2300 2620 8.638565 GTTAATTTGCTGTCACATTGTTATCAC 58.361 33.333 0.00 0.00 0.00 3.06
2301 2621 5.764487 TTTGCTGTCACATTGTTATCACA 57.236 34.783 0.00 0.00 0.00 3.58
2303 2623 5.361135 TGCTGTCACATTGTTATCACAAG 57.639 39.130 0.00 0.00 46.25 3.16
2304 2624 4.161333 GCTGTCACATTGTTATCACAAGC 58.839 43.478 0.00 0.00 46.25 4.01
2305 2625 4.083110 GCTGTCACATTGTTATCACAAGCT 60.083 41.667 0.00 0.00 46.25 3.74
2306 2626 5.361135 TGTCACATTGTTATCACAAGCTG 57.639 39.130 0.00 0.00 46.25 4.24
2307 2627 4.821260 TGTCACATTGTTATCACAAGCTGT 59.179 37.500 0.00 0.00 46.25 4.40
2308 2628 5.994668 TGTCACATTGTTATCACAAGCTGTA 59.005 36.000 0.00 0.00 46.25 2.74
2309 2629 6.484977 TGTCACATTGTTATCACAAGCTGTAA 59.515 34.615 0.00 0.00 46.25 2.41
2310 2630 7.012799 TGTCACATTGTTATCACAAGCTGTAAA 59.987 33.333 0.00 0.00 46.25 2.01
2311 2631 7.323656 GTCACATTGTTATCACAAGCTGTAAAC 59.676 37.037 0.00 0.00 46.25 2.01
2312 2632 6.303022 CACATTGTTATCACAAGCTGTAAACG 59.697 38.462 0.00 0.00 46.25 3.60
2323 2643 0.165944 CTGTAAACGGCTTGCGAAGG 59.834 55.000 0.00 0.00 0.00 3.46
2330 2650 1.355066 CGGCTTGCGAAGGAACTCTC 61.355 60.000 0.00 0.00 38.49 3.20
2341 2661 4.035324 CGAAGGAACTCTCGTGCTATCTTA 59.965 45.833 0.00 0.00 38.49 2.10
2359 2679 2.791501 TACCGTTTGCTCCTTCCGGC 62.792 60.000 0.00 0.00 42.29 6.13
2508 2837 1.745232 TTATTTTGCATCTCGGGCGT 58.255 45.000 0.00 0.00 0.00 5.68
2512 2841 4.794439 TGCATCTCGGGCGTCACG 62.794 66.667 0.00 0.00 0.00 4.35
2523 2852 4.436998 CGTCACGGTGAGCCCCTC 62.437 72.222 11.83 0.00 0.00 4.30
2530 2859 2.579738 GTGAGCCCCTCGTCCTTC 59.420 66.667 0.00 0.00 32.35 3.46
2538 2872 1.192146 CCCTCGTCCTTCACCCTTCA 61.192 60.000 0.00 0.00 0.00 3.02
2557 2891 1.071471 CCAGCTGGTTTCTCGTGGT 59.929 57.895 25.53 0.00 0.00 4.16
2563 2897 0.391597 TGGTTTCTCGTGGTGGAGAC 59.608 55.000 0.00 0.00 42.50 3.36
2564 2898 0.666577 GGTTTCTCGTGGTGGAGACG 60.667 60.000 0.00 0.00 42.50 4.18
2565 2899 1.006571 TTTCTCGTGGTGGAGACGC 60.007 57.895 0.00 0.00 42.50 5.19
2566 2900 2.742710 TTTCTCGTGGTGGAGACGCG 62.743 60.000 3.53 3.53 42.50 6.01
2567 2901 3.733960 CTCGTGGTGGAGACGCGA 61.734 66.667 15.93 0.00 46.99 5.87
2568 2902 3.060000 TCGTGGTGGAGACGCGAT 61.060 61.111 15.93 0.00 44.71 4.58
2569 2903 2.579787 CGTGGTGGAGACGCGATC 60.580 66.667 15.93 10.64 43.92 3.69
2570 2904 2.579787 GTGGTGGAGACGCGATCG 60.580 66.667 15.93 11.69 43.50 3.69
2571 2905 3.822192 TGGTGGAGACGCGATCGG 61.822 66.667 15.93 9.59 43.50 4.18
2572 2906 3.823330 GGTGGAGACGCGATCGGT 61.823 66.667 15.93 12.97 43.50 4.69
2573 2907 2.579787 GTGGAGACGCGATCGGTG 60.580 66.667 15.93 6.90 40.69 4.94
2574 2908 2.748647 TGGAGACGCGATCGGTGA 60.749 61.111 15.93 0.00 40.69 4.02
2624 2958 4.280494 ACCGTCTCGTGCTTGCGT 62.280 61.111 0.00 0.00 0.00 5.24
2640 2974 3.106407 GTTCGAAGAGCAGCGCGT 61.106 61.111 8.43 0.00 37.80 6.01
2657 2991 2.915659 TGGAAGACGGCGTCCTGT 60.916 61.111 34.04 20.94 42.39 4.00
2661 2995 4.988716 AGACGGCGTCCTGTCCCA 62.989 66.667 34.04 0.00 35.71 4.37
2706 3040 7.873739 GCAAGAAACTGCAACAAATAATAGT 57.126 32.000 0.00 0.00 42.17 2.12
2707 3041 8.964420 GCAAGAAACTGCAACAAATAATAGTA 57.036 30.769 0.00 0.00 42.17 1.82
2709 3043 9.891828 CAAGAAACTGCAACAAATAATAGTACA 57.108 29.630 0.00 0.00 0.00 2.90
2713 3047 9.638239 AAACTGCAACAAATAATAGTACAATGG 57.362 29.630 0.00 0.00 0.00 3.16
2715 3049 8.802267 ACTGCAACAAATAATAGTACAATGGTT 58.198 29.630 0.00 0.00 0.00 3.67
2729 3069 5.972107 ACAATGGTTACTACGAGTAGTGT 57.028 39.130 22.10 9.55 45.25 3.55
2744 3084 1.660167 AGTGTCGATGTGCATGGATG 58.340 50.000 0.00 0.00 0.00 3.51
2759 3099 0.887933 GGATGCGTTGTTGGATGGTT 59.112 50.000 0.00 0.00 0.00 3.67
2766 3106 3.316283 CGTTGTTGGATGGTTGATTTGG 58.684 45.455 0.00 0.00 0.00 3.28
2771 3117 4.022762 TGTTGGATGGTTGATTTGGTTACG 60.023 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.673368 GCGGTTCTCACGATTTCAATCT 59.327 45.455 0.00 0.00 33.24 2.40
58 76 1.011968 CGGCGGTTCTCACGATTTCA 61.012 55.000 0.00 0.00 0.00 2.69
91 120 4.767255 CTCCTCGCAGCCCACACC 62.767 72.222 0.00 0.00 0.00 4.16
229 260 3.202216 GAAACCCCCAAACGCACGG 62.202 63.158 0.00 0.00 0.00 4.94
231 262 2.333581 CGAAACCCCCAAACGCAC 59.666 61.111 0.00 0.00 0.00 5.34
232 263 2.907917 CCGAAACCCCCAAACGCA 60.908 61.111 0.00 0.00 0.00 5.24
256 287 0.689412 CTCCTCCTCCTCTTGTCCCC 60.689 65.000 0.00 0.00 0.00 4.81
261 292 2.430610 CCCGCTCCTCCTCCTCTTG 61.431 68.421 0.00 0.00 0.00 3.02
264 295 2.520741 CTCCCGCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
265 296 4.150454 CCTCCCGCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
288 319 2.184579 GTCGCTCCCTCCTTTCCG 59.815 66.667 0.00 0.00 0.00 4.30
289 320 2.184579 CGTCGCTCCCTCCTTTCC 59.815 66.667 0.00 0.00 0.00 3.13
290 321 1.446272 CACGTCGCTCCCTCCTTTC 60.446 63.158 0.00 0.00 0.00 2.62
300 336 3.883744 CTCCAAAGCCCACGTCGCT 62.884 63.158 0.74 0.74 38.53 4.93
432 502 1.136329 AGGGTGTGTGAGGCCTTGAT 61.136 55.000 6.77 0.00 0.00 2.57
435 505 1.151450 CAAGGGTGTGTGAGGCCTT 59.849 57.895 6.77 0.00 0.00 4.35
436 506 2.839098 CAAGGGTGTGTGAGGCCT 59.161 61.111 3.86 3.86 0.00 5.19
499 572 4.701765 CACCTTGATCTCTTGGATTCGAT 58.298 43.478 0.00 0.00 34.33 3.59
540 614 4.748798 AGGAGGGTGGCTGGGGAG 62.749 72.222 0.00 0.00 0.00 4.30
541 615 3.829311 AAAGGAGGGTGGCTGGGGA 62.829 63.158 0.00 0.00 0.00 4.81
542 616 3.268032 AAAGGAGGGTGGCTGGGG 61.268 66.667 0.00 0.00 0.00 4.96
543 617 2.234296 AGAAAGGAGGGTGGCTGGG 61.234 63.158 0.00 0.00 0.00 4.45
544 618 1.001641 CAGAAAGGAGGGTGGCTGG 60.002 63.158 0.00 0.00 0.00 4.85
545 619 0.984230 TACAGAAAGGAGGGTGGCTG 59.016 55.000 0.00 0.00 0.00 4.85
546 620 1.742308 TTACAGAAAGGAGGGTGGCT 58.258 50.000 0.00 0.00 0.00 4.75
547 621 2.239907 AGATTACAGAAAGGAGGGTGGC 59.760 50.000 0.00 0.00 0.00 5.01
548 622 3.264450 ACAGATTACAGAAAGGAGGGTGG 59.736 47.826 0.00 0.00 0.00 4.61
549 623 4.559862 ACAGATTACAGAAAGGAGGGTG 57.440 45.455 0.00 0.00 0.00 4.61
550 624 4.807643 GCAACAGATTACAGAAAGGAGGGT 60.808 45.833 0.00 0.00 0.00 4.34
551 625 3.691609 GCAACAGATTACAGAAAGGAGGG 59.308 47.826 0.00 0.00 0.00 4.30
561 635 4.820897 ACAAGATCGAGCAACAGATTACA 58.179 39.130 2.38 0.00 0.00 2.41
590 664 0.455633 CGATGAACAAGCAGCAAGGC 60.456 55.000 0.00 0.00 0.00 4.35
595 669 1.394917 ACGAATCGATGAACAAGCAGC 59.605 47.619 10.55 0.00 0.00 5.25
600 674 3.046968 TGGGAACGAATCGATGAACAA 57.953 42.857 10.55 0.00 0.00 2.83
606 680 1.541233 GCAGGATGGGAACGAATCGAT 60.541 52.381 10.55 0.00 35.86 3.59
629 703 3.245519 GGTGACAAGAAGAAGACGTGAAC 59.754 47.826 0.00 0.00 0.00 3.18
656 730 3.806316 ACGGCGCTAACAATAATATGC 57.194 42.857 6.90 0.00 0.00 3.14
657 731 5.667888 GCACTACGGCGCTAACAATAATATG 60.668 44.000 6.90 0.00 0.00 1.78
701 780 3.988517 GACGAAACTATGCATACTAGGCC 59.011 47.826 1.16 0.00 0.00 5.19
754 844 1.722011 CGCTTAACCACGAATCCAGT 58.278 50.000 0.00 0.00 0.00 4.00
810 900 8.507249 GCAGGAATCGATTGCTACTTAATTTAT 58.493 33.333 28.64 3.05 36.24 1.40
840 932 7.611213 AATTCTTATCGACCCTAACAAACAG 57.389 36.000 0.00 0.00 0.00 3.16
841 933 7.881232 AGAAATTCTTATCGACCCTAACAAACA 59.119 33.333 0.00 0.00 0.00 2.83
842 934 8.175716 CAGAAATTCTTATCGACCCTAACAAAC 58.824 37.037 0.00 0.00 0.00 2.93
843 935 7.881232 ACAGAAATTCTTATCGACCCTAACAAA 59.119 33.333 0.00 0.00 0.00 2.83
854 946 7.246311 AGCAACATCAACAGAAATTCTTATCG 58.754 34.615 0.00 0.00 0.00 2.92
876 974 1.476891 GTCGTGTCCAGGAATCTAGCA 59.523 52.381 0.00 0.00 0.00 3.49
886 984 1.004918 GGAAGTGGGTCGTGTCCAG 60.005 63.158 0.00 0.00 34.56 3.86
898 1014 1.833630 TGCTAGAGGACATGGGAAGTG 59.166 52.381 0.00 0.00 0.00 3.16
951 1067 3.281727 TGGCAGAAGAAACAGTTGAGT 57.718 42.857 0.00 0.00 0.00 3.41
1052 1187 3.758755 AAGAGAGTGTGCATGAGACAA 57.241 42.857 0.00 0.00 0.00 3.18
1081 1216 3.042189 CACCGTTGCAAAACACACATAG 58.958 45.455 0.00 0.00 0.00 2.23
1082 1217 2.223595 CCACCGTTGCAAAACACACATA 60.224 45.455 0.00 0.00 0.00 2.29
1083 1218 1.470632 CCACCGTTGCAAAACACACAT 60.471 47.619 0.00 0.00 0.00 3.21
1097 1232 0.392461 ATTAAGCACGCATCCACCGT 60.392 50.000 0.00 0.00 39.91 4.83
1098 1233 0.304705 GATTAAGCACGCATCCACCG 59.695 55.000 0.00 0.00 0.00 4.94
1325 1462 8.579850 AACTGGAAATAGTAATTTGATGAGCA 57.420 30.769 0.00 0.00 35.41 4.26
1345 1483 7.765819 TCTCATCAACAGTAACATGATAACTGG 59.234 37.037 21.89 11.36 43.91 4.00
1370 1508 6.939132 TGGTACACTGAGCTTAGTACTATC 57.061 41.667 11.29 5.04 37.55 2.08
1393 1531 6.553100 TGACACCTGTTCCATTTCCTTAAAAT 59.447 34.615 0.00 0.00 38.11 1.82
1394 1532 5.894393 TGACACCTGTTCCATTTCCTTAAAA 59.106 36.000 0.00 0.00 0.00 1.52
1412 1551 6.828785 ACCACCAATAGAAAATATCTGACACC 59.171 38.462 0.00 0.00 39.30 4.16
1417 1556 5.829924 AGGCACCACCAATAGAAAATATCTG 59.170 40.000 0.00 0.00 43.14 2.90
1418 1557 6.018433 AGGCACCACCAATAGAAAATATCT 57.982 37.500 0.00 0.00 43.14 1.98
1440 1579 6.801539 TCAGGTTTTGACATAAGCAAGTAG 57.198 37.500 9.91 0.00 0.00 2.57
1454 1595 7.395190 TCATGGTCAAGATTATCAGGTTTTG 57.605 36.000 0.00 0.00 0.00 2.44
1495 1643 3.877508 AGTGCAAGGACAAGACAAAGTAC 59.122 43.478 0.00 0.00 0.00 2.73
1562 1711 9.228949 GAGCATCCATTTGAATCAGATAACTAT 57.771 33.333 0.00 0.00 0.00 2.12
1710 2028 1.410153 CCTGCCAAAACAGAACAAGCT 59.590 47.619 0.00 0.00 40.25 3.74
1718 2036 0.037975 GCATCACCCTGCCAAAACAG 60.038 55.000 0.00 0.00 36.10 3.16
1750 2068 2.031012 TTCTGCCACAGCCTGTCG 59.969 61.111 0.00 0.00 38.69 4.35
1860 2178 3.214328 AGTAGCAACTGAAACCAACCAG 58.786 45.455 0.00 0.00 33.57 4.00
1932 2250 7.715657 AGCATTCAACACAGATTAAACTCAAA 58.284 30.769 0.00 0.00 0.00 2.69
1973 2291 6.611381 TCAGCATAACATTAAGCAACAAGAC 58.389 36.000 2.10 0.00 30.32 3.01
1977 2295 6.756299 TCATCAGCATAACATTAAGCAACA 57.244 33.333 2.10 0.00 30.32 3.33
1993 2311 4.677673 AAATAAGGGCCAAATCATCAGC 57.322 40.909 6.18 0.00 0.00 4.26
2023 2341 3.070734 ACACAGAGCCATATGGTCAGATC 59.929 47.826 22.79 12.76 44.10 2.75
2029 2347 2.573462 ACTCAACACAGAGCCATATGGT 59.427 45.455 22.79 9.86 39.26 3.55
2030 2348 3.272574 ACTCAACACAGAGCCATATGG 57.727 47.619 18.07 18.07 39.26 2.74
2032 2350 4.655963 ACAAACTCAACACAGAGCCATAT 58.344 39.130 0.00 0.00 39.26 1.78
2033 2351 4.065088 GACAAACTCAACACAGAGCCATA 58.935 43.478 0.00 0.00 39.26 2.74
2035 2353 2.288666 GACAAACTCAACACAGAGCCA 58.711 47.619 0.00 0.00 39.26 4.75
2036 2354 1.604278 GGACAAACTCAACACAGAGCC 59.396 52.381 0.00 0.00 39.26 4.70
2037 2355 1.604278 GGGACAAACTCAACACAGAGC 59.396 52.381 0.00 0.00 39.26 4.09
2038 2356 3.199880 AGGGACAAACTCAACACAGAG 57.800 47.619 0.00 0.00 41.44 3.35
2039 2357 3.278574 CAAGGGACAAACTCAACACAGA 58.721 45.455 0.00 0.00 0.00 3.41
2040 2358 3.016736 ACAAGGGACAAACTCAACACAG 58.983 45.455 0.00 0.00 0.00 3.66
2041 2359 3.080300 ACAAGGGACAAACTCAACACA 57.920 42.857 0.00 0.00 0.00 3.72
2042 2360 5.767816 ATAACAAGGGACAAACTCAACAC 57.232 39.130 0.00 0.00 0.00 3.32
2043 2361 6.126409 AGAATAACAAGGGACAAACTCAACA 58.874 36.000 0.00 0.00 0.00 3.33
2044 2362 6.635030 AGAATAACAAGGGACAAACTCAAC 57.365 37.500 0.00 0.00 0.00 3.18
2045 2363 6.460953 GCAAGAATAACAAGGGACAAACTCAA 60.461 38.462 0.00 0.00 0.00 3.02
2046 2364 5.009610 GCAAGAATAACAAGGGACAAACTCA 59.990 40.000 0.00 0.00 0.00 3.41
2047 2365 5.241728 AGCAAGAATAACAAGGGACAAACTC 59.758 40.000 0.00 0.00 0.00 3.01
2048 2366 5.140454 AGCAAGAATAACAAGGGACAAACT 58.860 37.500 0.00 0.00 0.00 2.66
2069 2387 4.142816 ACTCGAGTACATGCATTTTGAAGC 60.143 41.667 18.46 0.00 0.00 3.86
2087 2406 1.202475 TGTGCTGCTGTTGTTACTCGA 60.202 47.619 0.00 0.00 0.00 4.04
2088 2407 1.217001 TGTGCTGCTGTTGTTACTCG 58.783 50.000 0.00 0.00 0.00 4.18
2099 2418 1.845809 GCGTGCTTACTTGTGCTGCT 61.846 55.000 0.00 0.00 0.00 4.24
2101 2420 0.518636 ATGCGTGCTTACTTGTGCTG 59.481 50.000 0.00 0.00 0.00 4.41
2106 2425 1.720852 GGCAAAATGCGTGCTTACTTG 59.279 47.619 0.00 0.00 46.21 3.16
2108 2427 0.958091 TGGCAAAATGCGTGCTTACT 59.042 45.000 0.00 0.00 46.21 2.24
2109 2428 1.655099 CATGGCAAAATGCGTGCTTAC 59.345 47.619 0.00 0.00 46.21 2.34
2110 2429 1.993542 CATGGCAAAATGCGTGCTTA 58.006 45.000 0.00 0.00 46.21 3.09
2111 2430 1.293267 GCATGGCAAAATGCGTGCTT 61.293 50.000 18.14 0.00 46.21 3.91
2112 2431 1.738830 GCATGGCAAAATGCGTGCT 60.739 52.632 18.14 0.00 46.21 4.40
2118 2437 3.520290 AGATGTCTGCATGGCAAAATG 57.480 42.857 0.00 0.00 38.41 2.32
2119 2438 3.857052 CAAGATGTCTGCATGGCAAAAT 58.143 40.909 0.00 0.00 38.41 1.82
2120 2439 2.610976 GCAAGATGTCTGCATGGCAAAA 60.611 45.455 0.00 0.00 38.41 2.44
2121 2440 1.067425 GCAAGATGTCTGCATGGCAAA 60.067 47.619 0.00 0.00 38.41 3.68
2122 2441 0.528924 GCAAGATGTCTGCATGGCAA 59.471 50.000 0.00 0.00 38.41 4.52
2123 2442 1.650314 CGCAAGATGTCTGCATGGCA 61.650 55.000 0.00 0.00 43.02 4.92
2124 2443 1.063649 CGCAAGATGTCTGCATGGC 59.936 57.895 0.00 0.00 43.02 4.40
2125 2444 0.806868 AACGCAAGATGTCTGCATGG 59.193 50.000 0.00 0.00 43.62 3.66
2126 2445 2.624316 AAACGCAAGATGTCTGCATG 57.376 45.000 0.00 0.00 43.62 4.06
2127 2446 2.352030 CCAAAACGCAAGATGTCTGCAT 60.352 45.455 0.00 0.00 43.62 3.96
2128 2447 1.001487 CCAAAACGCAAGATGTCTGCA 60.001 47.619 0.00 0.00 43.62 4.41
2129 2448 1.689959 CCAAAACGCAAGATGTCTGC 58.310 50.000 0.00 0.00 43.62 4.26
2130 2449 1.666888 GGCCAAAACGCAAGATGTCTG 60.667 52.381 0.00 0.00 43.62 3.51
2131 2450 0.598065 GGCCAAAACGCAAGATGTCT 59.402 50.000 0.00 0.00 43.62 3.41
2132 2451 0.313672 TGGCCAAAACGCAAGATGTC 59.686 50.000 0.61 0.00 43.62 3.06
2133 2452 0.749649 TTGGCCAAAACGCAAGATGT 59.250 45.000 17.98 0.00 43.62 3.06
2134 2453 2.083167 ATTGGCCAAAACGCAAGATG 57.917 45.000 24.71 0.00 43.62 2.90
2135 2454 2.036992 TCAATTGGCCAAAACGCAAGAT 59.963 40.909 24.71 0.00 43.62 2.40
2136 2455 1.410517 TCAATTGGCCAAAACGCAAGA 59.589 42.857 24.71 9.71 43.62 3.02
2138 2457 2.315925 TTCAATTGGCCAAAACGCAA 57.684 40.000 24.71 8.36 0.00 4.85
2164 2483 2.927014 GCGTCTGACGTCTTGGAAATCT 60.927 50.000 28.38 0.00 44.73 2.40
2171 2490 1.069159 AGTACAGCGTCTGACGTCTTG 60.069 52.381 28.38 24.15 44.73 3.02
2179 2498 2.656560 AGGCTTAAGTACAGCGTCTG 57.343 50.000 4.02 5.47 38.24 3.51
2188 2507 9.154632 TGTGATGGAATAAGATAGGCTTAAGTA 57.845 33.333 4.02 0.00 42.10 2.24
2194 2513 7.805083 ATAGTGTGATGGAATAAGATAGGCT 57.195 36.000 0.00 0.00 0.00 4.58
2223 2542 3.181493 GCATCAATCGTCAGCCAGAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
2248 2568 3.990469 GCCCGTATCTGTATGAATGACTG 59.010 47.826 0.00 0.00 0.00 3.51
2250 2570 4.258702 AGCCCGTATCTGTATGAATGAC 57.741 45.455 0.00 0.00 0.00 3.06
2251 2571 4.955811 AAGCCCGTATCTGTATGAATGA 57.044 40.909 0.00 0.00 0.00 2.57
2253 2573 6.420913 AACTAAGCCCGTATCTGTATGAAT 57.579 37.500 0.00 0.00 0.00 2.57
2254 2574 5.864418 AACTAAGCCCGTATCTGTATGAA 57.136 39.130 0.00 0.00 0.00 2.57
2255 2575 6.964807 TTAACTAAGCCCGTATCTGTATGA 57.035 37.500 0.00 0.00 0.00 2.15
2256 2576 8.495949 CAAATTAACTAAGCCCGTATCTGTATG 58.504 37.037 0.00 0.00 0.00 2.39
2257 2577 7.172703 GCAAATTAACTAAGCCCGTATCTGTAT 59.827 37.037 0.00 0.00 0.00 2.29
2258 2578 6.480981 GCAAATTAACTAAGCCCGTATCTGTA 59.519 38.462 0.00 0.00 0.00 2.74
2259 2579 5.296035 GCAAATTAACTAAGCCCGTATCTGT 59.704 40.000 0.00 0.00 0.00 3.41
2260 2580 5.527582 AGCAAATTAACTAAGCCCGTATCTG 59.472 40.000 0.00 0.00 0.00 2.90
2261 2581 5.527582 CAGCAAATTAACTAAGCCCGTATCT 59.472 40.000 0.00 0.00 0.00 1.98
2262 2582 5.296035 ACAGCAAATTAACTAAGCCCGTATC 59.704 40.000 0.00 0.00 0.00 2.24
2263 2583 5.190677 ACAGCAAATTAACTAAGCCCGTAT 58.809 37.500 0.00 0.00 0.00 3.06
2264 2584 4.581868 ACAGCAAATTAACTAAGCCCGTA 58.418 39.130 0.00 0.00 0.00 4.02
2265 2585 3.418047 ACAGCAAATTAACTAAGCCCGT 58.582 40.909 0.00 0.00 0.00 5.28
2266 2586 3.438781 TGACAGCAAATTAACTAAGCCCG 59.561 43.478 0.00 0.00 0.00 6.13
2267 2587 4.217550 TGTGACAGCAAATTAACTAAGCCC 59.782 41.667 0.00 0.00 0.00 5.19
2268 2588 5.371115 TGTGACAGCAAATTAACTAAGCC 57.629 39.130 0.00 0.00 0.00 4.35
2269 2589 6.863126 ACAATGTGACAGCAAATTAACTAAGC 59.137 34.615 0.00 0.00 30.10 3.09
2270 2590 8.801715 AACAATGTGACAGCAAATTAACTAAG 57.198 30.769 0.00 0.00 30.10 2.18
2273 2593 8.575589 TGATAACAATGTGACAGCAAATTAACT 58.424 29.630 0.00 0.00 30.10 2.24
2274 2594 8.638565 GTGATAACAATGTGACAGCAAATTAAC 58.361 33.333 0.00 0.00 30.10 2.01
2275 2595 8.355913 TGTGATAACAATGTGACAGCAAATTAA 58.644 29.630 0.00 0.00 30.10 1.40
2276 2596 7.880105 TGTGATAACAATGTGACAGCAAATTA 58.120 30.769 0.00 0.00 30.10 1.40
2277 2597 6.747125 TGTGATAACAATGTGACAGCAAATT 58.253 32.000 0.00 0.00 32.05 1.82
2278 2598 6.330004 TGTGATAACAATGTGACAGCAAAT 57.670 33.333 0.00 0.00 0.00 2.32
2279 2599 5.764487 TGTGATAACAATGTGACAGCAAA 57.236 34.783 0.00 0.00 0.00 3.68
2280 2600 5.761003 CTTGTGATAACAATGTGACAGCAA 58.239 37.500 0.00 0.00 0.00 3.91
2281 2601 4.320421 GCTTGTGATAACAATGTGACAGCA 60.320 41.667 0.00 0.00 0.00 4.41
2282 2602 4.083110 AGCTTGTGATAACAATGTGACAGC 60.083 41.667 0.00 0.00 0.00 4.40
2283 2603 5.049198 ACAGCTTGTGATAACAATGTGACAG 60.049 40.000 10.39 0.00 0.00 3.51
2284 2604 4.821260 ACAGCTTGTGATAACAATGTGACA 59.179 37.500 10.39 0.00 0.00 3.58
2285 2605 5.362556 ACAGCTTGTGATAACAATGTGAC 57.637 39.130 10.39 0.00 0.00 3.67
2286 2606 7.359595 GTTTACAGCTTGTGATAACAATGTGA 58.640 34.615 11.12 2.24 29.21 3.58
2287 2607 6.303022 CGTTTACAGCTTGTGATAACAATGTG 59.697 38.462 11.12 7.51 29.21 3.21
2288 2608 6.370593 CGTTTACAGCTTGTGATAACAATGT 58.629 36.000 7.25 7.25 30.76 2.71
2289 2609 5.794945 CCGTTTACAGCTTGTGATAACAATG 59.205 40.000 0.00 0.00 0.00 2.82
2290 2610 5.619086 GCCGTTTACAGCTTGTGATAACAAT 60.619 40.000 0.00 0.00 0.00 2.71
2291 2611 4.319911 GCCGTTTACAGCTTGTGATAACAA 60.320 41.667 0.00 0.00 0.00 2.83
2292 2612 3.187637 GCCGTTTACAGCTTGTGATAACA 59.812 43.478 0.00 0.00 0.00 2.41
2293 2613 3.435671 AGCCGTTTACAGCTTGTGATAAC 59.564 43.478 0.00 0.00 35.22 1.89
2294 2614 3.670625 AGCCGTTTACAGCTTGTGATAA 58.329 40.909 0.00 0.00 35.22 1.75
2295 2615 3.328382 AGCCGTTTACAGCTTGTGATA 57.672 42.857 0.00 0.00 35.22 2.15
2296 2616 2.185004 AGCCGTTTACAGCTTGTGAT 57.815 45.000 0.00 0.00 35.22 3.06
2297 2617 3.698250 AGCCGTTTACAGCTTGTGA 57.302 47.368 0.00 0.00 35.22 3.58
2302 2622 0.882927 TTCGCAAGCCGTTTACAGCT 60.883 50.000 0.00 0.00 42.40 4.24
2303 2623 0.452784 CTTCGCAAGCCGTTTACAGC 60.453 55.000 0.00 0.00 38.35 4.40
2304 2624 0.165944 CCTTCGCAAGCCGTTTACAG 59.834 55.000 0.00 0.00 38.35 2.74
2305 2625 0.249953 TCCTTCGCAAGCCGTTTACA 60.250 50.000 0.00 0.00 38.35 2.41
2306 2626 0.869730 TTCCTTCGCAAGCCGTTTAC 59.130 50.000 0.00 0.00 38.35 2.01
2307 2627 0.869730 GTTCCTTCGCAAGCCGTTTA 59.130 50.000 0.00 0.00 38.35 2.01
2308 2628 0.818040 AGTTCCTTCGCAAGCCGTTT 60.818 50.000 0.00 0.00 38.35 3.60
2309 2629 1.227853 AGTTCCTTCGCAAGCCGTT 60.228 52.632 0.00 0.00 38.35 4.44
2310 2630 1.668151 GAGTTCCTTCGCAAGCCGT 60.668 57.895 0.00 0.00 38.35 5.68
2311 2631 1.355066 GAGAGTTCCTTCGCAAGCCG 61.355 60.000 0.00 0.00 38.61 5.52
2312 2632 1.355066 CGAGAGTTCCTTCGCAAGCC 61.355 60.000 0.00 0.00 37.18 4.35
2319 2639 4.379339 AAGATAGCACGAGAGTTCCTTC 57.621 45.455 0.00 0.00 46.40 3.46
2323 2643 3.065095 ACGGTAAGATAGCACGAGAGTTC 59.935 47.826 0.00 0.00 46.40 3.01
2330 2650 2.268298 AGCAAACGGTAAGATAGCACG 58.732 47.619 0.00 0.00 0.00 5.34
2359 2679 2.289945 GCATATCCCTGGTGGCTTCTAG 60.290 54.545 0.00 0.00 0.00 2.43
2420 2749 1.529713 GGACTCCCTCTCCTAGCCG 60.530 68.421 0.00 0.00 0.00 5.52
2421 2750 1.152419 GGGACTCCCTCTCCTAGCC 60.152 68.421 6.90 0.00 41.34 3.93
2468 2797 2.287977 AAAGTGAAGTAAGGGTGCCC 57.712 50.000 0.00 0.00 0.00 5.36
2486 2815 3.057174 ACGCCCGAGATGCAAAATAAAAA 60.057 39.130 0.00 0.00 0.00 1.94
2487 2816 2.490115 ACGCCCGAGATGCAAAATAAAA 59.510 40.909 0.00 0.00 0.00 1.52
2488 2817 2.088423 ACGCCCGAGATGCAAAATAAA 58.912 42.857 0.00 0.00 0.00 1.40
2489 2818 1.668751 GACGCCCGAGATGCAAAATAA 59.331 47.619 0.00 0.00 0.00 1.40
2490 2819 1.295792 GACGCCCGAGATGCAAAATA 58.704 50.000 0.00 0.00 0.00 1.40
2491 2820 0.676466 TGACGCCCGAGATGCAAAAT 60.676 50.000 0.00 0.00 0.00 1.82
2492 2821 1.302112 TGACGCCCGAGATGCAAAA 60.302 52.632 0.00 0.00 0.00 2.44
2493 2822 2.032634 GTGACGCCCGAGATGCAAA 61.033 57.895 0.00 0.00 0.00 3.68
2494 2823 2.434185 GTGACGCCCGAGATGCAA 60.434 61.111 0.00 0.00 0.00 4.08
2495 2824 4.794439 CGTGACGCCCGAGATGCA 62.794 66.667 0.00 0.00 0.00 3.96
2497 2826 4.129737 ACCGTGACGCCCGAGATG 62.130 66.667 0.00 0.00 0.00 2.90
2498 2827 4.129737 CACCGTGACGCCCGAGAT 62.130 66.667 0.00 0.00 0.00 2.75
2508 2837 4.988716 ACGAGGGGCTCACCGTGA 62.989 66.667 4.06 0.29 41.60 4.35
2512 2841 3.003763 AAGGACGAGGGGCTCACC 61.004 66.667 0.00 0.00 39.11 4.02
2523 2852 0.320771 CTGGTGAAGGGTGAAGGACG 60.321 60.000 0.00 0.00 0.00 4.79
2557 2891 2.337246 TTCACCGATCGCGTCTCCA 61.337 57.895 10.32 0.00 35.23 3.86
2563 2897 2.508891 GCAGAGTTCACCGATCGCG 61.509 63.158 10.32 0.00 37.24 5.87
2564 2898 2.167861 GGCAGAGTTCACCGATCGC 61.168 63.158 10.32 0.00 0.00 4.58
2565 2899 1.078759 GTGGCAGAGTTCACCGATCG 61.079 60.000 8.51 8.51 0.00 3.69
2566 2900 1.078759 CGTGGCAGAGTTCACCGATC 61.079 60.000 0.00 0.00 0.00 3.69
2567 2901 1.079819 CGTGGCAGAGTTCACCGAT 60.080 57.895 0.00 0.00 0.00 4.18
2568 2902 2.338620 CGTGGCAGAGTTCACCGA 59.661 61.111 0.00 0.00 0.00 4.69
2569 2903 2.738521 CCGTGGCAGAGTTCACCG 60.739 66.667 0.00 0.00 0.00 4.94
2570 2904 1.961277 CACCGTGGCAGAGTTCACC 60.961 63.158 0.00 0.00 0.00 4.02
2571 2905 0.320771 ATCACCGTGGCAGAGTTCAC 60.321 55.000 0.00 0.00 0.00 3.18
2572 2906 0.037326 GATCACCGTGGCAGAGTTCA 60.037 55.000 0.00 0.00 0.00 3.18
2573 2907 0.741221 GGATCACCGTGGCAGAGTTC 60.741 60.000 0.00 0.00 0.00 3.01
2574 2908 1.296715 GGATCACCGTGGCAGAGTT 59.703 57.895 0.00 0.00 0.00 3.01
2621 2955 4.491328 GCGCTGCTCTTCGAACGC 62.491 66.667 11.90 11.90 39.49 4.84
2624 2958 3.105782 CACGCGCTGCTCTTCGAA 61.106 61.111 5.73 0.00 0.00 3.71
2640 2974 2.915659 ACAGGACGCCGTCTTCCA 60.916 61.111 17.76 0.00 33.37 3.53
2657 2991 2.363795 CTAGGCGTGGAGGTGGGA 60.364 66.667 0.00 0.00 0.00 4.37
2661 2995 2.663196 GTTGCTAGGCGTGGAGGT 59.337 61.111 0.00 0.00 0.00 3.85
2687 3021 9.638239 CCATTGTACTATTATTTGTTGCAGTTT 57.362 29.630 0.00 0.00 0.00 2.66
2689 3023 8.348285 ACCATTGTACTATTATTTGTTGCAGT 57.652 30.769 0.00 0.00 0.00 4.40
2702 3036 8.834465 CACTACTCGTAGTAACCATTGTACTAT 58.166 37.037 9.23 0.00 43.98 2.12
2703 3037 7.824289 ACACTACTCGTAGTAACCATTGTACTA 59.176 37.037 9.23 0.00 43.98 1.82
2705 3039 6.846350 ACACTACTCGTAGTAACCATTGTAC 58.154 40.000 9.23 0.00 43.98 2.90
2706 3040 6.183360 CGACACTACTCGTAGTAACCATTGTA 60.183 42.308 9.23 0.00 43.98 2.41
2707 3041 5.391310 CGACACTACTCGTAGTAACCATTGT 60.391 44.000 9.23 2.42 43.98 2.71
2709 3043 4.937620 TCGACACTACTCGTAGTAACCATT 59.062 41.667 9.23 0.00 43.98 3.16
2710 3044 4.507710 TCGACACTACTCGTAGTAACCAT 58.492 43.478 9.23 0.00 43.98 3.55
2711 3045 3.925379 TCGACACTACTCGTAGTAACCA 58.075 45.455 9.23 0.00 43.98 3.67
2712 3046 4.331168 ACATCGACACTACTCGTAGTAACC 59.669 45.833 9.23 2.21 43.98 2.85
2713 3047 5.254088 CACATCGACACTACTCGTAGTAAC 58.746 45.833 9.23 6.21 43.98 2.50
2715 3049 3.308053 GCACATCGACACTACTCGTAGTA 59.692 47.826 9.23 0.00 43.98 1.82
2716 3050 2.095532 GCACATCGACACTACTCGTAGT 59.904 50.000 3.97 3.97 46.52 2.73
2717 3051 2.095372 TGCACATCGACACTACTCGTAG 59.905 50.000 2.66 2.66 39.04 3.51
2718 3052 2.078392 TGCACATCGACACTACTCGTA 58.922 47.619 0.00 0.00 35.10 3.43
2719 3053 0.879090 TGCACATCGACACTACTCGT 59.121 50.000 0.00 0.00 35.10 4.18
2721 3055 2.159240 TCCATGCACATCGACACTACTC 60.159 50.000 0.00 0.00 0.00 2.59
2723 3057 2.293677 TCCATGCACATCGACACTAC 57.706 50.000 0.00 0.00 0.00 2.73
2744 3084 2.723124 AATCAACCATCCAACAACGC 57.277 45.000 0.00 0.00 0.00 4.84
2747 3087 5.508153 CGTAACCAAATCAACCATCCAACAA 60.508 40.000 0.00 0.00 0.00 2.83
2759 3099 5.467399 CCAGACTAAACACGTAACCAAATCA 59.533 40.000 0.00 0.00 0.00 2.57
2766 3106 3.922850 GGCTACCAGACTAAACACGTAAC 59.077 47.826 0.00 0.00 0.00 2.50
2771 3117 2.603953 GACGGCTACCAGACTAAACAC 58.396 52.381 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.