Multiple sequence alignment - TraesCS6A01G102500

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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 TraesCS6A01G102500 chr6A 100.000 7713 0 0 1 7713 71535110 71542822 0.000000e+00 14244
1 TraesCS6A01G102500 chr6D 91.861 3219 163 46 3973 7146 56911386 56914550 0.000000e+00 4401
2 TraesCS6A01G102500 chr6D 90.820 1743 96 20 1348 3064 56908532 56910236 0.000000e+00 2274
3 TraesCS6A01G102500 chr6D 88.889 756 65 10 3224 3964 56910359 56911110 0.000000e+00 913
4 TraesCS6A01G102500 chr6D 83.368 487 37 27 897 1351 56907949 56908423 2.000000e-110 411
5 TraesCS6A01G102500 chr6D 83.510 473 41 16 7268 7713 56914794 56915256 2.590000e-109 407
6 TraesCS6A01G102500 chr6B 93.535 2676 93 21 3257 5898 127605976 127608605 0.000000e+00 3910
7 TraesCS6A01G102500 chr6B 93.314 2408 88 25 886 3259 127603445 127605813 0.000000e+00 3487
8 TraesCS6A01G102500 chr6B 90.225 1422 84 22 5883 7271 127608755 127610154 0.000000e+00 1805
9 TraesCS6A01G102500 chr6B 95.692 325 13 1 547 870 485308300 485308624 8.870000e-144 521
10 TraesCS6A01G102500 chr6B 93.787 338 18 2 532 869 485307550 485307216 8.930000e-139 505
11 TraesCS6A01G102500 chr1B 96.114 875 27 4 1 875 111678941 111678074 0.000000e+00 1421
12 TraesCS6A01G102500 chr1B 99.035 518 5 0 1 518 365459631 365459114 0.000000e+00 929
13 TraesCS6A01G102500 chr1B 92.966 526 23 4 349 870 365459002 365458487 0.000000e+00 754
14 TraesCS6A01G102500 chr5A 93.660 899 19 11 1 868 535679821 535678930 0.000000e+00 1310
15 TraesCS6A01G102500 chr5A 96.625 563 14 3 1 562 510266173 510266731 0.000000e+00 929
16 TraesCS6A01G102500 chr5A 99.010 505 5 0 1 505 535680653 535680149 0.000000e+00 905
17 TraesCS6A01G102500 chr5A 95.253 316 14 1 553 867 618281686 618282001 4.160000e-137 499
18 TraesCS6A01G102500 chr2B 94.002 867 24 11 1 867 54341481 54342319 0.000000e+00 1288
19 TraesCS6A01G102500 chr2B 87.630 768 83 8 1830 2587 385568378 385567613 0.000000e+00 881
20 TraesCS6A01G102500 chr2B 86.604 530 60 8 4168 4689 385565516 385564990 6.710000e-160 575
21 TraesCS6A01G102500 chr2B 78.409 616 89 23 3239 3836 385566793 385566204 2.050000e-95 361
22 TraesCS6A01G102500 chr2B 90.751 173 13 2 6119 6289 385564000 385563829 2.170000e-55 228
23 TraesCS6A01G102500 chr2B 75.879 398 59 24 5492 5873 385564522 385564146 1.330000e-37 169
24 TraesCS6A01G102500 chr2D 85.769 1047 113 26 1839 2867 317947877 317946849 0.000000e+00 1075
25 TraesCS6A01G102500 chr2D 86.389 529 63 6 4168 4689 317945651 317945125 3.120000e-158 569
26 TraesCS6A01G102500 chr2D 77.693 789 114 38 3080 3836 317946697 317945939 7.150000e-115 425
27 TraesCS6A01G102500 chr2D 90.173 173 14 2 6119 6289 317944015 317943844 1.010000e-53 222
28 TraesCS6A01G102500 chr2A 86.059 954 103 21 1925 2867 414989680 414990614 0.000000e+00 998
29 TraesCS6A01G102500 chr2A 85.688 552 67 9 4168 4712 414992374 414992920 8.680000e-159 571
30 TraesCS6A01G102500 chr2A 80.282 568 86 19 3080 3627 414990764 414991325 9.320000e-109 405
31 TraesCS6A01G102500 chr2A 90.058 171 14 3 6119 6287 414993902 414994071 1.300000e-52 219
32 TraesCS6A01G102500 chr2A 77.078 397 58 22 5492 5873 414993368 414993746 1.700000e-46 198
33 TraesCS6A01G102500 chr1A 96.435 561 15 3 1 560 286250497 286251053 0.000000e+00 920
34 TraesCS6A01G102500 chr1A 96.270 563 16 3 1 562 287791168 287791726 0.000000e+00 918
35 TraesCS6A01G102500 chr3A 96.422 559 12 6 1 551 84659167 84658609 0.000000e+00 915
36 TraesCS6A01G102500 chr3A 96.085 562 17 3 2 562 673463367 673463924 0.000000e+00 911
37 TraesCS6A01G102500 chr7B 95.055 364 18 0 504 867 669208654 669208291 2.410000e-159 573
38 TraesCS6A01G102500 chr7B 95.224 335 16 0 537 871 750078259 750078593 1.470000e-146 531
39 TraesCS6A01G102500 chr3B 82.648 438 47 15 1525 1946 795255483 795255059 2.050000e-95 361


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 TraesCS6A01G102500 chr6A 71535110 71542822 7712 False 14244.000000 14244 100.0000 1 7713 1 chr6A.!!$F1 7712
1 TraesCS6A01G102500 chr6D 56907949 56915256 7307 False 1681.200000 4401 87.6896 897 7713 5 chr6D.!!$F1 6816
2 TraesCS6A01G102500 chr6B 127603445 127610154 6709 False 3067.333333 3910 92.3580 886 7271 3 chr6B.!!$F2 6385
3 TraesCS6A01G102500 chr1B 111678074 111678941 867 True 1421.000000 1421 96.1140 1 875 1 chr1B.!!$R1 874
4 TraesCS6A01G102500 chr1B 365458487 365459631 1144 True 841.500000 929 96.0005 1 870 2 chr1B.!!$R2 869
5 TraesCS6A01G102500 chr5A 535678930 535680653 1723 True 1107.500000 1310 96.3350 1 868 2 chr5A.!!$R1 867
6 TraesCS6A01G102500 chr5A 510266173 510266731 558 False 929.000000 929 96.6250 1 562 1 chr5A.!!$F1 561
7 TraesCS6A01G102500 chr2B 54341481 54342319 838 False 1288.000000 1288 94.0020 1 867 1 chr2B.!!$F1 866
8 TraesCS6A01G102500 chr2B 385563829 385568378 4549 True 442.800000 881 83.8546 1830 6289 5 chr2B.!!$R1 4459
9 TraesCS6A01G102500 chr2D 317943844 317947877 4033 True 572.750000 1075 85.0060 1839 6289 4 chr2D.!!$R1 4450
10 TraesCS6A01G102500 chr2A 414989680 414994071 4391 False 478.200000 998 83.8330 1925 6287 5 chr2A.!!$F1 4362
11 TraesCS6A01G102500 chr1A 286250497 286251053 556 False 920.000000 920 96.4350 1 560 1 chr1A.!!$F1 559
12 TraesCS6A01G102500 chr1A 287791168 287791726 558 False 918.000000 918 96.2700 1 562 1 chr1A.!!$F2 561
13 TraesCS6A01G102500 chr3A 84658609 84659167 558 True 915.000000 915 96.4220 1 551 1 chr3A.!!$R1 550
14 TraesCS6A01G102500 chr3A 673463367 673463924 557 False 911.000000 911 96.0850 2 562 1 chr3A.!!$F1 560

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
895 2066 0.100861 TCCCCGCAAACGAAAAACAC 59.899 50.000 0.00 0.0 43.93 3.32 F
1939 3298 0.108186 ATTCACGAGAGGCGCATTGA 60.108 50.000 10.83 0.0 46.04 2.57 F
2229 3588 0.451783 GCCCAAACAACTATGGCTCG 59.548 55.000 0.00 0.0 39.05 5.03 F
2328 3687 0.681175 GTGCAGTGAAAATGGGCCTT 59.319 50.000 4.53 0.0 28.90 4.35 F
3017 4554 1.064758 AGGTGAAGTGGTGAACTGCAA 60.065 47.619 0.00 0.0 46.63 4.08 F
4571 7306 0.257039 ATTTGATGCCCGAGCTTCCT 59.743 50.000 2.36 0.0 41.35 3.36 F
5199 7963 0.100146 GCTGCTGCACTAATTCTGGC 59.900 55.000 11.11 0.0 39.41 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 3630 0.250684 TCAGAAGCGGCAATGTTCCA 60.251 50.000 1.45 0.0 0.00 3.53 R
2995 4480 1.747206 GCAGTTCACCACTTCACCTGT 60.747 52.381 0.00 0.0 30.92 4.00 R
4137 6858 2.290641 ACAGCGAACAAACAATGAGGAC 59.709 45.455 0.00 0.0 0.00 3.85 R
4571 7306 2.434185 CGCCTACGCTTTGCCTCA 60.434 61.111 0.00 0.0 0.00 3.86 R
4821 7560 1.420138 TGGGTTGTCAGGAAAGGAGAC 59.580 52.381 0.00 0.0 0.00 3.36 R
5616 8391 0.110056 CAGAACACGAGGCATGCAAC 60.110 55.000 21.36 11.5 0.00 4.17 R
6910 9943 0.040781 CCGGACGTGCGTTTGAAAAT 60.041 50.000 27.59 0.0 0.00 1.82 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
273 1099 1.088306 ACAACAAACAGAAACGGCGA 58.912 45.000 16.62 0.00 0.00 5.54
422 1529 1.766059 TGGCTCCCGATATGGCACT 60.766 57.895 0.00 0.00 35.87 4.40
695 1866 0.323087 TGCATCTGCCAAGTCAGCAT 60.323 50.000 0.00 0.00 40.04 3.79
815 1986 4.627284 TGATCCGGTTTTAGACTTTGGA 57.373 40.909 0.00 0.00 0.00 3.53
818 1989 2.974099 TCCGGTTTTAGACTTTGGAGGA 59.026 45.455 0.00 0.00 0.00 3.71
824 1995 6.016610 CGGTTTTAGACTTTGGAGGAAAATCA 60.017 38.462 0.00 0.00 0.00 2.57
870 2041 5.802173 GGGGAAAACGATACTTTCCTCTTCA 60.802 44.000 12.70 0.00 46.10 3.02
875 2046 7.562454 AAACGATACTTTCCTCTTCACAAAA 57.438 32.000 0.00 0.00 0.00 2.44
876 2047 7.745620 AACGATACTTTCCTCTTCACAAAAT 57.254 32.000 0.00 0.00 0.00 1.82
877 2048 7.365840 ACGATACTTTCCTCTTCACAAAATC 57.634 36.000 0.00 0.00 0.00 2.17
878 2049 6.371825 ACGATACTTTCCTCTTCACAAAATCC 59.628 38.462 0.00 0.00 0.00 3.01
879 2050 6.183360 CGATACTTTCCTCTTCACAAAATCCC 60.183 42.308 0.00 0.00 0.00 3.85
880 2051 4.152647 ACTTTCCTCTTCACAAAATCCCC 58.847 43.478 0.00 0.00 0.00 4.81
881 2052 2.489938 TCCTCTTCACAAAATCCCCG 57.510 50.000 0.00 0.00 0.00 5.73
882 2053 0.811281 CCTCTTCACAAAATCCCCGC 59.189 55.000 0.00 0.00 0.00 6.13
883 2054 1.533625 CTCTTCACAAAATCCCCGCA 58.466 50.000 0.00 0.00 0.00 5.69
884 2055 1.885887 CTCTTCACAAAATCCCCGCAA 59.114 47.619 0.00 0.00 0.00 4.85
885 2056 2.295909 CTCTTCACAAAATCCCCGCAAA 59.704 45.455 0.00 0.00 0.00 3.68
886 2057 2.035321 TCTTCACAAAATCCCCGCAAAC 59.965 45.455 0.00 0.00 0.00 2.93
887 2058 0.312416 TCACAAAATCCCCGCAAACG 59.688 50.000 0.00 0.00 39.67 3.60
888 2059 0.312416 CACAAAATCCCCGCAAACGA 59.688 50.000 0.00 0.00 43.93 3.85
889 2060 1.033574 ACAAAATCCCCGCAAACGAA 58.966 45.000 0.00 0.00 43.93 3.85
890 2061 1.409427 ACAAAATCCCCGCAAACGAAA 59.591 42.857 0.00 0.00 43.93 3.46
891 2062 2.159085 ACAAAATCCCCGCAAACGAAAA 60.159 40.909 0.00 0.00 43.93 2.29
892 2063 2.866762 CAAAATCCCCGCAAACGAAAAA 59.133 40.909 0.00 0.00 43.93 1.94
893 2064 2.143008 AATCCCCGCAAACGAAAAAC 57.857 45.000 0.00 0.00 43.93 2.43
894 2065 1.033574 ATCCCCGCAAACGAAAAACA 58.966 45.000 0.00 0.00 43.93 2.83
895 2066 0.100861 TCCCCGCAAACGAAAAACAC 59.899 50.000 0.00 0.00 43.93 3.32
925 2096 0.316204 CAAAAGAGCTGGCCCAACAG 59.684 55.000 0.00 0.00 41.41 3.16
933 2104 3.706373 GGCCCAACAGGAGCGAGA 61.706 66.667 0.00 0.00 38.24 4.04
957 2128 2.125952 GCAAGGCCCATTTGCGTC 60.126 61.111 11.94 0.00 41.16 5.19
1086 2257 2.699321 CTGAATCATCTCTGCTCCCAGA 59.301 50.000 0.00 0.00 45.54 3.86
1104 2275 5.540337 TCCCAGAGGTAAGCAGAGTAATATG 59.460 44.000 0.00 0.00 0.00 1.78
1312 2520 2.876368 GATTGGGAGTGGGACTGGCG 62.876 65.000 0.00 0.00 0.00 5.69
1337 2547 7.643764 CGCCGATCACACATCTTAAAATTATTT 59.356 33.333 0.00 0.00 0.00 1.40
1457 2799 4.851639 ATATCCGTATCTACTACCCGGT 57.148 45.455 0.00 0.00 39.62 5.28
1529 2871 7.337938 ACCCAATTTTCAAACAGTGATTTTCT 58.662 30.769 0.00 0.00 35.70 2.52
1692 3034 7.839680 AAATCACCTCTGAAAATTAGGTTGT 57.160 32.000 0.00 0.00 41.75 3.32
1693 3035 8.934023 AAATCACCTCTGAAAATTAGGTTGTA 57.066 30.769 0.00 0.00 41.75 2.41
1694 3036 8.567285 AATCACCTCTGAAAATTAGGTTGTAG 57.433 34.615 0.00 0.00 41.75 2.74
1695 3037 5.938125 TCACCTCTGAAAATTAGGTTGTAGC 59.062 40.000 0.00 0.00 41.75 3.58
1696 3038 5.123979 CACCTCTGAAAATTAGGTTGTAGCC 59.876 44.000 0.00 0.00 41.75 3.93
1697 3039 5.222048 ACCTCTGAAAATTAGGTTGTAGCCA 60.222 40.000 0.00 0.00 40.82 4.75
1698 3040 5.710099 CCTCTGAAAATTAGGTTGTAGCCAA 59.290 40.000 0.00 0.00 0.00 4.52
1765 3115 5.070001 ACCTTGCTAATGTCTTGCAGTTTA 58.930 37.500 0.00 0.00 38.01 2.01
1795 3145 3.075148 ACTTCGAGTCTCGTTCTCATCA 58.925 45.455 21.15 0.00 41.35 3.07
1849 3199 5.799213 ACAGGTTTCTTCTGTTATCCTGAG 58.201 41.667 13.98 0.00 42.17 3.35
1870 3220 7.974482 TGAGATCAGGCTGTATTCAATATTG 57.026 36.000 15.27 9.29 0.00 1.90
1876 3229 7.771183 TCAGGCTGTATTCAATATTGTTTTCC 58.229 34.615 15.27 8.46 0.00 3.13
1919 3278 3.009723 ACCCAGTAGATTGTGAATTGCG 58.990 45.455 0.00 0.00 0.00 4.85
1939 3298 0.108186 ATTCACGAGAGGCGCATTGA 60.108 50.000 10.83 0.00 46.04 2.57
2024 3383 2.484770 GCCTGTTCTGTACCACTCAACA 60.485 50.000 0.00 0.00 0.00 3.33
2027 3386 2.132762 GTTCTGTACCACTCAACACCG 58.867 52.381 0.00 0.00 0.00 4.94
2094 3453 3.053828 CCCAAAGCAGTGCCCAAG 58.946 61.111 12.58 0.00 0.00 3.61
2112 3471 4.074970 CCAAGTCAATTCAACAGGCTACT 58.925 43.478 0.00 0.00 0.00 2.57
2151 3510 5.523369 CAGAAGACACAAGGTTTTGAATCC 58.477 41.667 0.00 0.00 37.73 3.01
2229 3588 0.451783 GCCCAAACAACTATGGCTCG 59.548 55.000 0.00 0.00 39.05 5.03
2284 3643 2.676471 ACCCTGGAACATTGCCGC 60.676 61.111 0.00 0.00 38.20 6.53
2307 3666 4.572985 TCTGAATGCAAAGGTTGTTGAG 57.427 40.909 0.00 0.00 0.00 3.02
2328 3687 0.681175 GTGCAGTGAAAATGGGCCTT 59.319 50.000 4.53 0.00 28.90 4.35
2756 4232 9.102757 TCATAAATGCTAAAGATGAAGAGTCAC 57.897 33.333 0.00 0.00 36.31 3.67
2923 4408 2.025699 GTCATTGGTTTACCCCTGCCTA 60.026 50.000 0.00 0.00 34.29 3.93
2935 4420 4.763355 ACCCCTGCCTATCATACAGAATA 58.237 43.478 0.00 0.00 33.10 1.75
2995 4480 1.962807 CACAACTTCATGGGGCAAGAA 59.037 47.619 0.00 0.00 0.00 2.52
3017 4554 1.064758 AGGTGAAGTGGTGAACTGCAA 60.065 47.619 0.00 0.00 46.63 4.08
3133 4676 3.430236 GGGGGCAACTTGTAATAATGTGC 60.430 47.826 0.00 0.00 0.00 4.57
3142 4685 9.236691 CAACTTGTAATAATGTGCCAATACATC 57.763 33.333 0.00 0.00 40.24 3.06
3209 4753 3.331889 ACACCCTCCAATCTGAACAGAAT 59.668 43.478 8.59 0.00 41.36 2.40
3210 4754 3.944015 CACCCTCCAATCTGAACAGAATC 59.056 47.826 8.59 0.00 41.36 2.52
3211 4755 3.588842 ACCCTCCAATCTGAACAGAATCA 59.411 43.478 8.59 0.00 41.36 2.57
3212 4756 4.043310 ACCCTCCAATCTGAACAGAATCAA 59.957 41.667 8.59 0.00 41.36 2.57
3214 4758 5.125097 CCCTCCAATCTGAACAGAATCAAAG 59.875 44.000 8.59 3.89 41.36 2.77
3216 4760 6.602406 CCTCCAATCTGAACAGAATCAAAGAT 59.398 38.462 8.59 0.00 41.36 2.40
3217 4761 7.387119 TCCAATCTGAACAGAATCAAAGATG 57.613 36.000 8.59 0.03 41.36 2.90
3285 5120 6.761242 TGGCTAATTGCACTAGTAACTACATG 59.239 38.462 0.00 0.00 45.15 3.21
3294 5129 7.170828 TGCACTAGTAACTACATGTTTCAAGTG 59.829 37.037 2.30 10.22 39.91 3.16
3308 5143 8.950210 CATGTTTCAAGTGGTTAATCTGTATCT 58.050 33.333 0.00 0.00 0.00 1.98
3421 5256 2.159000 TGCTGAGTATGGTGCTGAGATG 60.159 50.000 0.00 0.00 0.00 2.90
3496 5331 2.485426 CCTTCGCTGTGATGTGAATGTT 59.515 45.455 0.00 0.00 36.13 2.71
3610 5452 1.405933 CCAGAACATCTGCATCACGGA 60.406 52.381 1.79 0.00 42.98 4.69
3788 5643 7.650504 AGCATACAATATTGACATTGCATGTTC 59.349 33.333 22.16 1.23 45.03 3.18
3898 5920 5.875224 TGGACAAAAGTCCTTCATGTATGA 58.125 37.500 15.01 0.00 43.68 2.15
3905 5927 7.621428 AAAGTCCTTCATGTATGATTGTCAG 57.379 36.000 0.00 0.00 36.56 3.51
4154 6875 8.574196 AAATTAAAGTCCTCATTGTTTGTTCG 57.426 30.769 0.00 0.00 0.00 3.95
4571 7306 0.257039 ATTTGATGCCCGAGCTTCCT 59.743 50.000 2.36 0.00 41.35 3.36
4631 7366 6.602803 TCAGCATGCAAGATGTTATTTTCCTA 59.397 34.615 21.98 0.00 34.76 2.94
4662 7400 7.203218 TGACGATAAGGTAATCATCTTCAGTG 58.797 38.462 0.00 0.00 0.00 3.66
4694 7432 1.202371 CCTTGTCATGGATGTGCATGC 60.202 52.381 11.82 11.82 0.00 4.06
4821 7560 8.197439 ACATTTAAAAGTTCCTCCAGTTTCTTG 58.803 33.333 0.00 0.00 0.00 3.02
4998 7737 8.862325 TTACTGCTTATCTGAAGGATGAAAAA 57.138 30.769 0.00 0.00 35.98 1.94
5148 7910 3.605634 ACGCTGGTCAAAGCATGTTATA 58.394 40.909 0.00 0.00 43.73 0.98
5149 7911 4.199310 ACGCTGGTCAAAGCATGTTATAT 58.801 39.130 0.00 0.00 43.73 0.86
5191 7955 1.153765 CTACGCTGCTGCTGCACTA 60.154 57.895 27.13 15.95 45.31 2.74
5199 7963 0.100146 GCTGCTGCACTAATTCTGGC 59.900 55.000 11.11 0.00 39.41 4.85
5200 7964 1.456296 CTGCTGCACTAATTCTGGCA 58.544 50.000 0.00 0.00 34.66 4.92
5201 7965 2.022195 CTGCTGCACTAATTCTGGCAT 58.978 47.619 0.00 0.00 35.45 4.40
5217 7981 4.142609 TGGCATCCAGAACTTGATACTC 57.857 45.455 0.00 0.00 0.00 2.59
5220 7984 4.433615 GCATCCAGAACTTGATACTCGAA 58.566 43.478 0.00 0.00 0.00 3.71
5271 8035 8.802267 TCTTTTTGTAGGGTCTATTTTGATTGG 58.198 33.333 0.00 0.00 0.00 3.16
5274 8038 9.589461 TTTTGTAGGGTCTATTTTGATTGGTTA 57.411 29.630 0.00 0.00 0.00 2.85
5275 8039 9.589461 TTTGTAGGGTCTATTTTGATTGGTTAA 57.411 29.630 0.00 0.00 0.00 2.01
5276 8040 8.801882 TGTAGGGTCTATTTTGATTGGTTAAG 57.198 34.615 0.00 0.00 0.00 1.85
5277 8041 8.607713 TGTAGGGTCTATTTTGATTGGTTAAGA 58.392 33.333 0.00 0.00 0.00 2.10
5278 8042 7.939784 AGGGTCTATTTTGATTGGTTAAGAC 57.060 36.000 0.00 0.00 33.10 3.01
5279 8043 7.466804 AGGGTCTATTTTGATTGGTTAAGACA 58.533 34.615 0.00 0.00 35.04 3.41
5280 8044 7.947890 AGGGTCTATTTTGATTGGTTAAGACAA 59.052 33.333 0.00 0.00 35.04 3.18
5281 8045 8.244113 GGGTCTATTTTGATTGGTTAAGACAAG 58.756 37.037 0.00 0.00 35.04 3.16
5282 8046 8.244113 GGTCTATTTTGATTGGTTAAGACAAGG 58.756 37.037 0.00 0.00 35.04 3.61
5283 8047 7.755373 GTCTATTTTGATTGGTTAAGACAAGGC 59.245 37.037 0.00 0.00 33.86 4.35
5284 8048 6.670695 ATTTTGATTGGTTAAGACAAGGCT 57.329 33.333 0.00 0.00 0.00 4.58
5285 8049 6.478512 TTTTGATTGGTTAAGACAAGGCTT 57.521 33.333 0.00 0.00 0.00 4.35
5286 8050 7.589958 TTTTGATTGGTTAAGACAAGGCTTA 57.410 32.000 0.00 0.00 0.00 3.09
5287 8051 6.817765 TTGATTGGTTAAGACAAGGCTTAG 57.182 37.500 0.00 0.00 32.42 2.18
5288 8052 4.700213 TGATTGGTTAAGACAAGGCTTAGC 59.300 41.667 0.00 0.00 32.42 3.09
5289 8053 2.695359 TGGTTAAGACAAGGCTTAGCG 58.305 47.619 0.00 0.00 33.85 4.26
5290 8054 1.397343 GGTTAAGACAAGGCTTAGCGC 59.603 52.381 0.00 0.00 33.85 5.92
5424 8195 1.398692 TGTTGGTCAAAGCCTTGTCC 58.601 50.000 4.56 4.56 40.13 4.02
5466 8237 5.243730 CCCTACAAAAAGAAATGGCTGAAGA 59.756 40.000 0.00 0.00 0.00 2.87
5481 8252 4.361420 GCTGAAGATTTCCGTAGTAGGAC 58.639 47.826 0.00 0.00 40.56 3.85
5550 8325 2.134630 CTGGTCTTTCCCCTGCTGCT 62.135 60.000 0.00 0.00 34.77 4.24
5560 8335 1.407437 CCCCTGCTGCTTAGTACCAAG 60.407 57.143 0.00 0.00 0.00 3.61
5690 8476 7.420800 CCATTAGTCATGGCATTCTAAACTTC 58.579 38.462 19.03 0.00 46.59 3.01
5714 8500 2.393271 ACCTTCTTCCTGATTCTGCG 57.607 50.000 0.00 0.00 0.00 5.18
5783 8569 5.385198 AGTCTGTGATAGAGGAGAAGGATC 58.615 45.833 0.00 0.00 35.70 3.36
5916 8867 2.944129 ACTTTTGGCTTGTAGCTTCCA 58.056 42.857 0.00 0.00 41.99 3.53
5946 8897 3.057734 CAACCAGACAACGAGTACCTTC 58.942 50.000 0.00 0.00 0.00 3.46
5948 8899 3.759581 ACCAGACAACGAGTACCTTCTA 58.240 45.455 0.00 0.00 0.00 2.10
6058 9011 8.905850 TGTGATGAGATAATTAATGTTGTGCAT 58.094 29.630 0.00 0.00 40.03 3.96
6238 9255 0.249868 GGAAAACCAAGTTGCAGGGC 60.250 55.000 0.00 0.00 0.00 5.19
6269 9288 5.622233 GCTGGCCAGGTTAGTTATTTTTGAG 60.622 44.000 33.46 3.07 0.00 3.02
6300 9319 3.462579 TGTGTTCCCCTTGGTTAACCTTA 59.537 43.478 24.78 12.23 36.82 2.69
6496 9522 2.338809 AGTGGTCCTTGATGACTGGAA 58.661 47.619 0.00 0.00 35.54 3.53
6534 9560 1.003839 CCTGCAGCGGGAACTACAA 60.004 57.895 16.28 0.00 29.82 2.41
6579 9607 4.075963 TCTGGTTTTTGTAGGCGTAGTT 57.924 40.909 0.00 0.00 0.00 2.24
6694 9726 9.547753 GTTTGAGCTGATAATAAGAATGGAGTA 57.452 33.333 0.00 0.00 0.00 2.59
6700 9732 7.095439 GCTGATAATAAGAATGGAGTAGTGTGC 60.095 40.741 0.00 0.00 0.00 4.57
6743 9775 9.544314 CTGCGTAGAGTTACATGTTACTATATC 57.456 37.037 18.96 14.76 0.00 1.63
6793 9825 5.877012 TCCTAGAACTTCAAATGTGAGCATC 59.123 40.000 0.00 0.00 34.49 3.91
6795 9827 7.044181 CCTAGAACTTCAAATGTGAGCATCTA 58.956 38.462 0.00 0.00 34.49 1.98
6809 9841 6.658816 TGTGAGCATCTACATTTTGGTTGTAT 59.341 34.615 0.00 0.00 34.92 2.29
6887 9920 7.750229 ATTTCTTCACTGAAATAAGCTGACA 57.250 32.000 0.00 0.00 42.68 3.58
6910 9943 3.306902 TGGCAACACCCTTCCAAAA 57.693 47.368 0.00 0.00 46.17 2.44
6914 9947 3.054065 TGGCAACACCCTTCCAAAATTTT 60.054 39.130 0.00 0.00 46.17 1.82
6925 9958 3.512680 TCCAAAATTTTCAAACGCACGT 58.487 36.364 0.00 0.00 0.00 4.49
7006 10059 1.896660 GAAGAAGCAACCGTGGGCA 60.897 57.895 0.00 0.00 0.00 5.36
7074 10127 3.851105 GCTGATCACTTGCTTGTCAACAC 60.851 47.826 0.00 0.00 0.00 3.32
7075 10128 3.544684 TGATCACTTGCTTGTCAACACT 58.455 40.909 0.00 0.00 0.00 3.55
7106 10159 3.629398 GTGAATTCTTGGTATGGAGGCAG 59.371 47.826 7.05 0.00 0.00 4.85
7154 10374 3.269486 GTTGCGAAAGAAACCTCCTTC 57.731 47.619 0.00 0.00 44.15 3.46
7155 10375 1.892209 TGCGAAAGAAACCTCCTTCC 58.108 50.000 0.00 0.00 0.00 3.46
7158 10378 1.166129 GAAAGAAACCTCCTTCCGGC 58.834 55.000 0.00 0.00 0.00 6.13
7238 10458 5.365314 ACCACCACAACATTGATAACCTTTT 59.635 36.000 0.00 0.00 0.00 2.27
7245 10465 7.710475 CACAACATTGATAACCTTTTTCCAACT 59.290 33.333 0.00 0.00 0.00 3.16
7298 10518 8.962679 GTTGGTTAAACTATTGGGACATTCATA 58.037 33.333 0.00 0.00 35.00 2.15
7310 10530 5.762711 TGGGACATTCATATACAATGGAACG 59.237 40.000 9.86 0.00 35.82 3.95
7312 10532 5.342806 ACATTCATATACAATGGAACGCG 57.657 39.130 3.53 3.53 35.82 6.01
7318 10538 5.813157 TCATATACAATGGAACGCGAAAGAA 59.187 36.000 15.93 0.00 0.00 2.52
7321 10541 1.069296 CAATGGAACGCGAAAGAAGCA 60.069 47.619 15.93 0.00 34.19 3.91
7327 10547 1.865865 ACGCGAAAGAAGCAGAGAAA 58.134 45.000 15.93 0.00 34.19 2.52
7339 10559 4.595762 AGCAGAGAAAACAACAATGCAT 57.404 36.364 0.00 0.00 34.71 3.96
7340 10560 5.710513 AGCAGAGAAAACAACAATGCATA 57.289 34.783 0.00 0.00 34.71 3.14
7341 10561 6.276832 AGCAGAGAAAACAACAATGCATAT 57.723 33.333 0.00 0.00 34.71 1.78
7366 10586 9.935682 ATGCATTATCAAGAGTTAAACATTACG 57.064 29.630 0.00 0.00 0.00 3.18
7380 10600 9.061610 GTTAAACATTACGTTCATTCCTTGATG 57.938 33.333 0.00 0.00 36.59 3.07
7412 10632 8.026026 CACTGCATACCTCTATGTATAACTGAG 58.974 40.741 0.00 0.00 33.39 3.35
7413 10633 6.925211 TGCATACCTCTATGTATAACTGAGC 58.075 40.000 0.00 0.00 33.39 4.26
7438 10658 4.885907 AGTCAAATCTTATGGCACTGATGG 59.114 41.667 0.00 0.00 0.00 3.51
7483 10704 5.461032 AAATCTCTATTAGTGCCTCCTCG 57.539 43.478 0.00 0.00 0.00 4.63
7485 10706 1.957177 CTCTATTAGTGCCTCCTCGCA 59.043 52.381 0.00 0.00 36.08 5.10
7501 10722 6.293626 CCTCCTCGCATCCAAATTATACTTTG 60.294 42.308 8.25 8.25 36.17 2.77
7509 10730 9.585099 GCATCCAAATTATACTTTGAAACATGA 57.415 29.630 15.13 5.20 38.17 3.07
7519 10740 8.853077 ATACTTTGAAACATGACATTCTCAGA 57.147 30.769 0.00 0.00 30.20 3.27
7520 10741 6.963796 ACTTTGAAACATGACATTCTCAGAC 58.036 36.000 0.00 0.00 30.20 3.51
7521 10742 6.543465 ACTTTGAAACATGACATTCTCAGACA 59.457 34.615 0.00 0.00 30.20 3.41
7522 10743 5.929697 TGAAACATGACATTCTCAGACAC 57.070 39.130 0.00 0.00 30.20 3.67
7532 10778 7.475015 TGACATTCTCAGACACAAAAAGAAAG 58.525 34.615 0.00 0.00 30.43 2.62
7536 10782 5.496556 TCTCAGACACAAAAAGAAAGTGGA 58.503 37.500 0.00 0.00 37.58 4.02
7537 10783 6.122277 TCTCAGACACAAAAAGAAAGTGGAT 58.878 36.000 0.00 0.00 37.58 3.41
7551 10797 6.821388 AGAAAGTGGATATAGCCAGTAACAG 58.179 40.000 17.57 0.00 40.68 3.16
7552 10798 6.611642 AGAAAGTGGATATAGCCAGTAACAGA 59.388 38.462 17.57 0.00 40.68 3.41
7553 10799 7.291182 AGAAAGTGGATATAGCCAGTAACAGAT 59.709 37.037 17.57 0.00 40.68 2.90
7559 10805 7.728532 TGGATATAGCCAGTAACAGATCACTTA 59.271 37.037 5.37 0.00 33.10 2.24
7561 10807 4.744795 AGCCAGTAACAGATCACTTAGG 57.255 45.455 0.00 0.00 0.00 2.69
7564 10810 4.684485 GCCAGTAACAGATCACTTAGGCAT 60.684 45.833 0.00 0.00 35.16 4.40
7587 10833 7.228108 GCATGATCTCATCACTTCCTTTCATAA 59.772 37.037 0.00 0.00 43.01 1.90
7590 10836 9.690913 TGATCTCATCACTTCCTTTCATAAATT 57.309 29.630 0.00 0.00 33.59 1.82
7598 10844 7.867403 TCACTTCCTTTCATAAATTTGAACTGC 59.133 33.333 0.00 0.00 35.42 4.40
7599 10845 6.863126 ACTTCCTTTCATAAATTTGAACTGCG 59.137 34.615 0.00 0.00 35.42 5.18
7611 10857 1.534235 AACTGCGGGAGGTCACTCT 60.534 57.895 0.51 0.00 43.46 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.892755 AAGTGCAGCATTGGTGATGG 59.107 50.000 19.53 0.00 41.92 3.51
273 1099 4.861196 TCTCTGGTAACTAGATCTGTGCT 58.139 43.478 5.18 0.00 37.61 4.40
695 1866 1.070758 GTCTCCTTGCTGACTGGACAA 59.929 52.381 0.00 0.00 0.00 3.18
815 1986 4.324099 CCTGTCTGATGGACTGATTTTCCT 60.324 45.833 0.00 0.00 43.62 3.36
818 1989 4.916041 TCCTGTCTGATGGACTGATTTT 57.084 40.909 0.00 0.00 43.62 1.82
824 1995 3.199508 CCTCAAATCCTGTCTGATGGACT 59.800 47.826 4.82 0.00 44.74 3.85
870 2041 1.033574 TTCGTTTGCGGGGATTTTGT 58.966 45.000 0.00 0.00 38.89 2.83
875 2046 1.033574 TGTTTTTCGTTTGCGGGGAT 58.966 45.000 0.00 0.00 38.89 3.85
876 2047 0.100861 GTGTTTTTCGTTTGCGGGGA 59.899 50.000 0.00 0.00 38.89 4.81
877 2048 0.101579 AGTGTTTTTCGTTTGCGGGG 59.898 50.000 0.00 0.00 38.89 5.73
878 2049 2.223294 TGTAGTGTTTTTCGTTTGCGGG 60.223 45.455 0.00 0.00 38.89 6.13
879 2050 3.054276 TGTAGTGTTTTTCGTTTGCGG 57.946 42.857 0.00 0.00 38.89 5.69
880 2051 5.423097 TTTTGTAGTGTTTTTCGTTTGCG 57.577 34.783 0.00 0.00 39.92 4.85
881 2052 5.061684 AGCTTTTGTAGTGTTTTTCGTTTGC 59.938 36.000 0.00 0.00 0.00 3.68
882 2053 6.306837 TGAGCTTTTGTAGTGTTTTTCGTTTG 59.693 34.615 0.00 0.00 0.00 2.93
883 2054 6.383415 TGAGCTTTTGTAGTGTTTTTCGTTT 58.617 32.000 0.00 0.00 0.00 3.60
884 2055 5.945155 TGAGCTTTTGTAGTGTTTTTCGTT 58.055 33.333 0.00 0.00 0.00 3.85
885 2056 5.554822 TGAGCTTTTGTAGTGTTTTTCGT 57.445 34.783 0.00 0.00 0.00 3.85
886 2057 6.862944 TTTGAGCTTTTGTAGTGTTTTTCG 57.137 33.333 0.00 0.00 0.00 3.46
887 2058 8.460831 TCTTTTGAGCTTTTGTAGTGTTTTTC 57.539 30.769 0.00 0.00 0.00 2.29
888 2059 8.466086 CTCTTTTGAGCTTTTGTAGTGTTTTT 57.534 30.769 0.00 0.00 39.99 1.94
925 2096 3.612247 TTGCTGGGCTTCTCGCTCC 62.612 63.158 0.00 0.00 38.81 4.70
941 2112 2.179018 CGACGCAAATGGGCCTTG 59.821 61.111 4.53 2.64 0.00 3.61
957 2128 1.519455 GATGTCCAGGGTTCGCTCG 60.519 63.158 0.00 0.00 0.00 5.03
1086 2257 4.262079 GCCGTCATATTACTCTGCTTACCT 60.262 45.833 0.00 0.00 0.00 3.08
1312 2520 8.856490 AAATAATTTTAAGATGTGTGATCGGC 57.144 30.769 0.00 0.00 0.00 5.54
1457 2799 8.902806 CAGCCACCTAAAATTCATGAAAGTATA 58.097 33.333 13.09 3.22 0.00 1.47
1529 2871 6.839124 AGTATGGTTTGATGCATCTTTTCA 57.161 33.333 26.32 18.62 0.00 2.69
1692 3034 3.178865 AGTTTAGGTGGCTAGTTGGCTA 58.821 45.455 0.00 0.00 42.34 3.93
1693 3035 1.985895 AGTTTAGGTGGCTAGTTGGCT 59.014 47.619 0.00 0.00 42.34 4.75
1694 3036 2.491675 AGTTTAGGTGGCTAGTTGGC 57.508 50.000 0.00 0.00 42.18 4.52
1695 3037 4.015872 TGAAGTTTAGGTGGCTAGTTGG 57.984 45.455 0.00 0.00 0.00 3.77
1696 3038 5.245531 TGATGAAGTTTAGGTGGCTAGTTG 58.754 41.667 0.00 0.00 0.00 3.16
1697 3039 5.499004 TGATGAAGTTTAGGTGGCTAGTT 57.501 39.130 0.00 0.00 0.00 2.24
1698 3040 5.499004 TTGATGAAGTTTAGGTGGCTAGT 57.501 39.130 0.00 0.00 0.00 2.57
1699 3041 5.940470 ACTTTGATGAAGTTTAGGTGGCTAG 59.060 40.000 0.00 0.00 46.34 3.42
1765 3115 7.987649 AGAACGAGACTCGAAGTAATTTAGAT 58.012 34.615 30.56 0.74 43.74 1.98
1849 3199 9.455847 GAAAACAATATTGAATACAGCCTGATC 57.544 33.333 22.16 0.00 0.00 2.92
1870 3220 3.431725 CTGCGAGCGGGGGAAAAC 61.432 66.667 0.00 0.00 0.00 2.43
1919 3278 0.302890 CAATGCGCCTCTCGTGAATC 59.697 55.000 4.18 0.00 41.07 2.52
1939 3298 0.324943 AGCGTTAGAGCCATTGTGGT 59.675 50.000 0.00 0.00 40.46 4.16
2024 3383 0.889306 GAAGTGAGCTAGTGGACGGT 59.111 55.000 0.00 0.00 0.00 4.83
2027 3386 3.060602 GTTGTGAAGTGAGCTAGTGGAC 58.939 50.000 0.00 0.00 0.00 4.02
2094 3453 5.488341 TCCTTAGTAGCCTGTTGAATTGAC 58.512 41.667 0.00 0.00 0.00 3.18
2151 3510 1.217882 GGGTCTCAATGCCGATAACG 58.782 55.000 0.00 0.00 39.43 3.18
2229 3588 4.386413 ACAGTGCTGTTAGGCTGC 57.614 55.556 0.00 0.00 41.83 5.25
2271 3630 0.250684 TCAGAAGCGGCAATGTTCCA 60.251 50.000 1.45 0.00 0.00 3.53
2274 3633 1.403249 GCATTCAGAAGCGGCAATGTT 60.403 47.619 1.45 0.00 0.00 2.71
2284 3643 4.935702 TCAACAACCTTTGCATTCAGAAG 58.064 39.130 0.00 0.00 0.00 2.85
2307 3666 0.319813 GGCCCATTTTCACTGCACAC 60.320 55.000 0.00 0.00 0.00 3.82
2328 3687 2.354503 GGAGATCTTGCAGTTGAGAGCA 60.355 50.000 0.00 0.00 39.32 4.26
2630 4105 6.566187 GCAGCATAACAGAATAGCATGAGAAG 60.566 42.308 0.00 0.00 0.00 2.85
2914 4399 5.965033 ATATTCTGTATGATAGGCAGGGG 57.035 43.478 0.00 0.00 0.00 4.79
2935 4420 7.016563 TCAGTTGGATATGATGCTGGTACTTAT 59.983 37.037 0.00 0.00 0.00 1.73
2947 4432 7.308408 CGCATTTGAATCTCAGTTGGATATGAT 60.308 37.037 0.00 0.00 0.00 2.45
2995 4480 1.747206 GCAGTTCACCACTTCACCTGT 60.747 52.381 0.00 0.00 30.92 4.00
3082 4625 7.497249 CCTCATCTTCTTGTATTAGGTTTGAGG 59.503 40.741 0.00 0.00 39.36 3.86
3133 4676 6.348498 TCTCACATAACCACAGATGTATTGG 58.652 40.000 0.00 0.00 34.52 3.16
3142 4685 7.323420 TCAGAAATACTCTCACATAACCACAG 58.677 38.462 0.00 0.00 29.07 3.66
3209 4753 6.122277 ACTTTGTTCTTGTCTCCATCTTTGA 58.878 36.000 0.00 0.00 0.00 2.69
3210 4754 6.382869 ACTTTGTTCTTGTCTCCATCTTTG 57.617 37.500 0.00 0.00 0.00 2.77
3211 4755 8.406297 GTTAACTTTGTTCTTGTCTCCATCTTT 58.594 33.333 0.00 0.00 0.00 2.52
3212 4756 7.775561 AGTTAACTTTGTTCTTGTCTCCATCTT 59.224 33.333 1.12 0.00 0.00 2.40
3214 4758 7.226720 TGAGTTAACTTTGTTCTTGTCTCCATC 59.773 37.037 10.02 0.00 0.00 3.51
3216 4760 6.411376 TGAGTTAACTTTGTTCTTGTCTCCA 58.589 36.000 10.02 0.00 0.00 3.86
3217 4761 6.761714 TCTGAGTTAACTTTGTTCTTGTCTCC 59.238 38.462 10.02 0.00 0.00 3.71
3237 4907 9.241317 GCCAATACATAATTGTTTGATTCTGAG 57.759 33.333 0.00 0.00 43.03 3.35
3285 5120 8.779354 AGAGATACAGATTAACCACTTGAAAC 57.221 34.615 0.00 0.00 0.00 2.78
3294 5129 8.024285 CGACCAGAATAGAGATACAGATTAACC 58.976 40.741 0.00 0.00 0.00 2.85
3308 5143 2.693591 CAACCTAGCCGACCAGAATAGA 59.306 50.000 0.00 0.00 0.00 1.98
3421 5256 2.488153 CAGGTACCTAACAAGCCTTTGC 59.512 50.000 15.80 0.00 37.85 3.68
3496 5331 3.201353 TGTCCAATTGGTCGAACAGAA 57.799 42.857 23.76 0.00 36.34 3.02
3788 5643 6.483640 GGCTAACCAGATAACTTCCTTATGTG 59.516 42.308 0.00 0.00 36.35 3.21
3898 5920 4.717233 TTTCACAAGCACAACTGACAAT 57.283 36.364 0.00 0.00 0.00 2.71
3905 5927 6.697019 ACATCTACAATTTTCACAAGCACAAC 59.303 34.615 0.00 0.00 0.00 3.32
4137 6858 2.290641 ACAGCGAACAAACAATGAGGAC 59.709 45.455 0.00 0.00 0.00 3.85
4571 7306 2.434185 CGCCTACGCTTTGCCTCA 60.434 61.111 0.00 0.00 0.00 3.86
4631 7366 8.128322 AGATGATTACCTTATCGTCATTAGCT 57.872 34.615 0.00 0.00 41.14 3.32
4662 7400 3.368739 CCATGACAAGGGAAAATGGAAGC 60.369 47.826 0.00 0.00 40.23 3.86
4694 7432 4.827284 ACTTCCAAATACACCTCCACAAAG 59.173 41.667 0.00 0.00 0.00 2.77
4821 7560 1.420138 TGGGTTGTCAGGAAAGGAGAC 59.580 52.381 0.00 0.00 0.00 3.36
5120 7860 3.932822 TGCTTTGACCAGCGTAGATAAA 58.067 40.909 0.00 0.00 43.37 1.40
5122 7862 3.118775 ACATGCTTTGACCAGCGTAGATA 60.119 43.478 0.00 0.00 43.37 1.98
5132 7872 5.297776 AGACTGCATATAACATGCTTTGACC 59.702 40.000 10.30 0.00 44.79 4.02
5135 7875 6.615264 AGAGACTGCATATAACATGCTTTG 57.385 37.500 10.30 4.07 44.79 2.77
5148 7910 6.810182 GCACAATTAAAATGAAGAGACTGCAT 59.190 34.615 0.00 0.00 29.55 3.96
5149 7911 6.016024 AGCACAATTAAAATGAAGAGACTGCA 60.016 34.615 0.00 0.00 0.00 4.41
5199 7963 6.102663 ACTTTCGAGTATCAAGTTCTGGATG 58.897 40.000 0.38 0.00 28.12 3.51
5200 7964 6.287589 ACTTTCGAGTATCAAGTTCTGGAT 57.712 37.500 0.00 0.00 28.12 3.41
5201 7965 5.723672 ACTTTCGAGTATCAAGTTCTGGA 57.276 39.130 0.00 0.00 28.12 3.86
5217 7981 5.758784 AGAGGGAGTACAAAAGAAACTTTCG 59.241 40.000 0.00 0.00 34.02 3.46
5220 7984 6.002653 ACAGAGGGAGTACAAAAGAAACTT 57.997 37.500 0.00 0.00 0.00 2.66
5271 8035 2.808157 GCGCTAAGCCTTGTCTTAAC 57.192 50.000 0.00 0.00 40.81 2.01
5424 8195 5.593909 TGTAGGGCATATTTTGATTGGTCAG 59.406 40.000 0.00 0.00 35.39 3.51
5466 8237 3.705051 TCCTGTGTCCTACTACGGAAAT 58.295 45.455 0.00 0.00 34.20 2.17
5514 8286 5.880901 AGACCAGAAATTGCTCTTTTCCTA 58.119 37.500 0.00 0.00 34.34 2.94
5515 8287 4.734266 AGACCAGAAATTGCTCTTTTCCT 58.266 39.130 0.00 0.00 34.34 3.36
5516 8288 5.459536 AAGACCAGAAATTGCTCTTTTCC 57.540 39.130 0.00 0.00 29.32 3.13
5518 8290 5.221521 GGGAAAGACCAGAAATTGCTCTTTT 60.222 40.000 1.74 0.00 40.25 2.27
5550 8325 4.141574 ACCTGCAAACACTCTTGGTACTAA 60.142 41.667 0.00 0.00 0.00 2.24
5560 8335 1.658409 GCGCAACCTGCAAACACTC 60.658 57.895 0.30 0.00 45.36 3.51
5577 8352 8.089115 ACTGAAGTACTAAAGTTCATTCTTGC 57.911 34.615 0.00 0.00 44.63 4.01
5611 8386 1.672363 ACACGAGGCATGCAACATATG 59.328 47.619 21.36 11.69 0.00 1.78
5616 8391 0.110056 CAGAACACGAGGCATGCAAC 60.110 55.000 21.36 11.50 0.00 4.17
5676 8462 8.966069 AGAAGGTATTAGAAGTTTAGAATGCC 57.034 34.615 0.00 0.00 35.11 4.40
5687 8473 7.440856 GCAGAATCAGGAAGAAGGTATTAGAAG 59.559 40.741 0.00 0.00 0.00 2.85
5690 8476 5.694006 CGCAGAATCAGGAAGAAGGTATTAG 59.306 44.000 0.00 0.00 0.00 1.73
5714 8500 2.030805 GGTCAACCACAATCTGCAAGAC 60.031 50.000 0.00 0.00 40.58 3.01
5783 8569 3.502211 GTGACCACATTTACCTGAACCAG 59.498 47.826 0.00 0.00 0.00 4.00
5916 8867 2.767505 GTTGTCTGGTTGTTCCTCGAT 58.232 47.619 0.00 0.00 37.07 3.59
5948 8899 9.681692 GCCAATTTTCAGCTTTAAATTTCATTT 57.318 25.926 11.13 0.00 33.04 2.32
5958 8909 8.449251 AATCTTTTTGCCAATTTTCAGCTTTA 57.551 26.923 0.00 0.00 0.00 1.85
6050 9002 3.791122 GCATCAGCTACATCATGCACAAC 60.791 47.826 0.00 0.00 41.16 3.32
6083 9096 5.394773 GGAAAACCCAAGCACAGACTAAAAA 60.395 40.000 0.00 0.00 34.14 1.94
6238 9255 3.356290 ACTAACCTGGCCAGCAAAATAG 58.644 45.455 28.39 22.29 0.00 1.73
6269 9288 0.396811 AGGGGAACACAGCTACACAC 59.603 55.000 0.00 0.00 0.00 3.82
6464 9490 1.503542 GACCACTTGATGCGCCAAG 59.496 57.895 20.51 20.51 46.61 3.61
6496 9522 2.287368 GGGTTTTGCTTTCGTTCGATGT 60.287 45.455 0.00 0.00 0.00 3.06
6534 9560 2.094752 CGGAGATGTTTTCGCCCAAAAT 60.095 45.455 0.00 0.00 40.99 1.82
6579 9607 4.158786 TCCATCCCAAATTCAAAGCAAGA 58.841 39.130 0.00 0.00 0.00 3.02
6694 9726 6.882656 AGATAATTCATCTGTACAGCACACT 58.117 36.000 18.45 3.55 42.69 3.55
6793 9825 5.097529 CAGCTGCATACAACCAAAATGTAG 58.902 41.667 0.00 0.00 36.75 2.74
6795 9827 3.321682 ACAGCTGCATACAACCAAAATGT 59.678 39.130 15.27 0.00 34.81 2.71
6887 9920 1.047801 GGAAGGGTGTTGCCACAAAT 58.952 50.000 0.00 0.00 43.71 2.32
6900 9933 3.873952 TGCGTTTGAAAATTTTGGAAGGG 59.126 39.130 8.47 0.13 0.00 3.95
6910 9943 0.040781 CCGGACGTGCGTTTGAAAAT 60.041 50.000 27.59 0.00 0.00 1.82
6914 9947 1.372004 CTACCGGACGTGCGTTTGA 60.372 57.895 27.59 8.97 0.00 2.69
6956 9989 9.535878 AATTGAAACACCAATTTAAACGTACAT 57.464 25.926 0.00 0.00 42.26 2.29
6985 10038 1.679032 GCCCACGGTTGCTTCTTCTAT 60.679 52.381 0.00 0.00 0.00 1.98
7006 10059 7.201600 GCAAAATGTACAATTTTTCCACTGTGT 60.202 33.333 6.16 0.00 0.00 3.72
7012 10065 7.768120 ACTGAAGCAAAATGTACAATTTTTCCA 59.232 29.630 6.16 2.77 0.00 3.53
7074 10127 3.057315 ACCAAGAATTCACGCCATTCAAG 60.057 43.478 8.44 0.00 33.67 3.02
7075 10128 2.890311 ACCAAGAATTCACGCCATTCAA 59.110 40.909 8.44 0.00 33.67 2.69
7106 10159 3.181516 GCAGTTGACTAGCATGCTGTAAC 60.182 47.826 30.42 24.43 34.42 2.50
7154 10374 1.525995 ATGAAACATAGGGCGCCGG 60.526 57.895 22.54 12.45 0.00 6.13
7155 10375 1.648720 CATGAAACATAGGGCGCCG 59.351 57.895 22.54 9.21 0.00 6.46
7158 10378 1.093972 TGTGCATGAAACATAGGGCG 58.906 50.000 0.00 0.00 0.00 6.13
7197 10417 1.421410 GGTACATCGACAAGCCGCAG 61.421 60.000 0.00 0.00 0.00 5.18
7206 10426 2.157834 TGTTGTGGTGGTACATCGAC 57.842 50.000 0.00 0.00 46.67 4.20
7212 10432 5.007682 AGGTTATCAATGTTGTGGTGGTAC 58.992 41.667 0.00 0.00 0.00 3.34
7271 10491 6.778069 TGAATGTCCCAATAGTTTAACCAACA 59.222 34.615 0.00 0.00 37.93 3.33
7272 10492 7.222000 TGAATGTCCCAATAGTTTAACCAAC 57.778 36.000 0.00 0.00 35.32 3.77
7273 10493 9.707957 ATATGAATGTCCCAATAGTTTAACCAA 57.292 29.630 0.00 0.00 0.00 3.67
7298 10518 3.181510 GCTTCTTTCGCGTTCCATTGTAT 60.182 43.478 5.77 0.00 0.00 2.29
7303 10523 0.798776 CTGCTTCTTTCGCGTTCCAT 59.201 50.000 5.77 0.00 0.00 3.41
7310 10530 3.609103 TGTTTTCTCTGCTTCTTTCGC 57.391 42.857 0.00 0.00 0.00 4.70
7312 10532 6.292008 GCATTGTTGTTTTCTCTGCTTCTTTC 60.292 38.462 0.00 0.00 0.00 2.62
7318 10538 4.595762 ATGCATTGTTGTTTTCTCTGCT 57.404 36.364 0.00 0.00 0.00 4.24
7340 10560 9.935682 CGTAATGTTTAACTCTTGATAATGCAT 57.064 29.630 0.00 0.00 0.00 3.96
7341 10561 8.941977 ACGTAATGTTTAACTCTTGATAATGCA 58.058 29.630 0.00 0.00 0.00 3.96
7363 10583 4.814234 GCCATACATCAAGGAATGAACGTA 59.186 41.667 0.00 0.00 42.54 3.57
7364 10584 3.627577 GCCATACATCAAGGAATGAACGT 59.372 43.478 0.00 0.00 42.54 3.99
7365 10585 3.627123 TGCCATACATCAAGGAATGAACG 59.373 43.478 0.00 0.00 42.54 3.95
7366 10586 4.641989 AGTGCCATACATCAAGGAATGAAC 59.358 41.667 0.00 0.00 42.54 3.18
7380 10600 2.918712 AGAGGTATGCAGTGCCATAC 57.081 50.000 13.72 18.13 44.25 2.39
7412 10632 5.118990 TCAGTGCCATAAGATTTGACTAGC 58.881 41.667 0.00 0.00 0.00 3.42
7413 10633 6.204301 CCATCAGTGCCATAAGATTTGACTAG 59.796 42.308 0.00 0.00 0.00 2.57
7438 10658 1.003438 GTAATTAGCTCCTGCGCTTGC 60.003 52.381 9.73 7.68 45.42 4.01
7443 10663 6.870965 AGAGATTTATGTAATTAGCTCCTGCG 59.129 38.462 0.00 0.00 45.42 5.18
7475 10696 1.967319 TAATTTGGATGCGAGGAGGC 58.033 50.000 0.00 0.00 0.00 4.70
7483 10704 9.585099 TCATGTTTCAAAGTATAATTTGGATGC 57.415 29.630 21.73 11.99 39.99 3.91
7501 10722 5.929697 TGTGTCTGAGAATGTCATGTTTC 57.070 39.130 0.00 0.00 33.51 2.78
7509 10730 7.253422 CACTTTCTTTTTGTGTCTGAGAATGT 58.747 34.615 0.00 0.00 36.05 2.71
7514 10735 5.818136 TCCACTTTCTTTTTGTGTCTGAG 57.182 39.130 0.00 0.00 0.00 3.35
7516 10737 7.965107 GCTATATCCACTTTCTTTTTGTGTCTG 59.035 37.037 0.00 0.00 0.00 3.51
7517 10738 7.121315 GGCTATATCCACTTTCTTTTTGTGTCT 59.879 37.037 0.00 0.00 0.00 3.41
7518 10739 7.094377 TGGCTATATCCACTTTCTTTTTGTGTC 60.094 37.037 0.00 0.00 0.00 3.67
7519 10740 6.719370 TGGCTATATCCACTTTCTTTTTGTGT 59.281 34.615 0.00 0.00 0.00 3.72
7520 10741 7.094205 ACTGGCTATATCCACTTTCTTTTTGTG 60.094 37.037 0.00 0.00 31.74 3.33
7521 10742 6.948309 ACTGGCTATATCCACTTTCTTTTTGT 59.052 34.615 0.00 0.00 31.74 2.83
7522 10743 7.396540 ACTGGCTATATCCACTTTCTTTTTG 57.603 36.000 0.00 0.00 31.74 2.44
7532 10778 6.015010 AGTGATCTGTTACTGGCTATATCCAC 60.015 42.308 0.00 0.00 31.74 4.02
7536 10782 7.310113 GCCTAAGTGATCTGTTACTGGCTATAT 60.310 40.741 0.00 0.00 34.74 0.86
7537 10783 6.015350 GCCTAAGTGATCTGTTACTGGCTATA 60.015 42.308 0.00 0.00 34.74 1.31
7551 10797 5.638657 GTGATGAGATCATGCCTAAGTGATC 59.361 44.000 0.00 7.15 46.99 2.92
7552 10798 5.307456 AGTGATGAGATCATGCCTAAGTGAT 59.693 40.000 0.00 0.00 42.04 3.06
7553 10799 4.652881 AGTGATGAGATCATGCCTAAGTGA 59.347 41.667 0.00 0.00 42.04 3.41
7559 10805 3.047115 AGGAAGTGATGAGATCATGCCT 58.953 45.455 0.00 0.00 42.04 4.75
7561 10807 4.880120 TGAAAGGAAGTGATGAGATCATGC 59.120 41.667 0.00 0.00 42.04 4.06
7564 10810 9.690913 AATTTATGAAAGGAAGTGATGAGATCA 57.309 29.630 0.00 0.00 36.84 2.92
7587 10833 1.202879 TGACCTCCCGCAGTTCAAATT 60.203 47.619 0.00 0.00 0.00 1.82
7590 10836 1.070786 GTGACCTCCCGCAGTTCAA 59.929 57.895 0.00 0.00 0.00 2.69
7598 10844 1.192146 TTCCCAAGAGTGACCTCCCG 61.192 60.000 0.00 0.00 38.58 5.14
7599 10845 1.003696 CTTTCCCAAGAGTGACCTCCC 59.996 57.143 0.00 0.00 38.58 4.30
7611 10857 6.620877 TTCTCATAAGTAGCTCTTTCCCAA 57.379 37.500 0.00 0.00 37.56 4.12
7627 10873 8.567948 GTGGAACAAGAGTTTCAATTTCTCATA 58.432 33.333 0.00 0.00 44.60 2.15
7642 10888 0.326264 CCTCCCCAGTGGAACAAGAG 59.674 60.000 11.95 8.26 44.57 2.85


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

AutoCloner maintained by Alex Coulton.