Multiple sequence alignment - TraesCS5A01G008900

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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 TraesCS5A01G008900 chr5A 100.000 3880 0 0 1 3880 6421168 6425047 0.000000e+00 7166.0
1 TraesCS5A01G008900 chr5A 78.901 564 98 15 977 1528 6411083 6411637 2.850000e-96 363.0
2 TraesCS5A01G008900 chr5A 99.346 153 1 0 3727 3879 341672868 341673020 1.060000e-70 278.0
3 TraesCS5A01G008900 chr5A 99.342 152 1 0 3728 3879 255608907 255609058 3.820000e-70 276.0
4 TraesCS5A01G008900 chr5A 76.036 338 63 14 1157 1485 649365206 649365534 4.010000e-35 159.0
5 TraesCS5A01G008900 chr5B 91.085 3051 150 47 1 2975 8350864 8353868 0.000000e+00 4015.0
6 TraesCS5A01G008900 chr5B 94.379 676 30 4 2305 2976 652936582 652935911 0.000000e+00 1031.0
7 TraesCS5A01G008900 chr5B 88.904 712 48 22 1618 2307 652947069 652946367 0.000000e+00 848.0
8 TraesCS5A01G008900 chr5B 86.084 618 54 12 3086 3675 8354201 8354814 1.520000e-178 636.0
9 TraesCS5A01G008900 chr5B 74.569 1101 212 46 984 2053 8342596 8343659 1.670000e-113 420.0
10 TraesCS5A01G008900 chr5B 75.148 338 66 14 1157 1485 656468456 656468784 4.040000e-30 143.0
11 TraesCS5A01G008900 chr5B 96.226 53 2 0 1072 1124 652947123 652947071 1.920000e-13 87.9
12 TraesCS5A01G008900 chr5B 95.918 49 2 0 2979 3027 382074721 382074673 3.210000e-11 80.5
13 TraesCS5A01G008900 chr5D 93.874 2514 108 23 485 2981 8032855 8035339 0.000000e+00 3747.0
14 TraesCS5A01G008900 chr5D 88.014 559 52 9 3174 3728 8035528 8036075 0.000000e+00 647.0
15 TraesCS5A01G008900 chr5D 78.886 682 116 15 858 1528 7966852 7966188 1.660000e-118 436.0
16 TraesCS5A01G008900 chr5D 79.070 559 106 9 977 1528 8020015 8020569 1.320000e-99 374.0
17 TraesCS5A01G008900 chr5D 97.468 158 3 1 3723 3879 10072893 10072736 6.390000e-68 268.0
18 TraesCS5A01G008900 chr5D 76.106 339 61 16 1157 1485 520805317 520805645 4.010000e-35 159.0
19 TraesCS5A01G008900 chr5D 76.036 338 63 16 1157 1485 520839477 520839805 4.010000e-35 159.0
20 TraesCS5A01G008900 chr5D 90.000 120 12 0 518 637 8027108 8027227 5.190000e-34 156.0
21 TraesCS5A01G008900 chr5D 90.698 86 5 2 383 468 8032848 8032930 1.140000e-20 111.0
22 TraesCS5A01G008900 chr5D 92.157 51 2 2 2972 3021 26273678 26273727 1.930000e-08 71.3
23 TraesCS5A01G008900 chr7A 99.338 151 1 0 3729 3879 184120413 184120563 1.370000e-69 274.0
24 TraesCS5A01G008900 chr6A 99.338 151 1 0 3729 3879 543790158 543790308 1.370000e-69 274.0
25 TraesCS5A01G008900 chr3A 99.338 151 1 0 3729 3879 55238556 55238706 1.370000e-69 274.0
26 TraesCS5A01G008900 chr2D 99.338 151 1 0 3729 3879 296370064 296369914 1.370000e-69 274.0
27 TraesCS5A01G008900 chr2A 99.338 151 1 0 3729 3879 759551410 759551260 1.370000e-69 274.0
28 TraesCS5A01G008900 chr3D 97.468 158 3 1 3723 3879 583162702 583162545 6.390000e-68 268.0
29 TraesCS5A01G008900 chr4D 80.328 183 28 6 1284 1462 357527156 357526978 8.750000e-27 132.0
30 TraesCS5A01G008900 chr4A 80.220 182 28 6 1284 1461 108374182 108374359 3.150000e-26 130.0
31 TraesCS5A01G008900 chr6B 95.918 49 2 0 2979 3027 717148935 717148983 3.210000e-11 80.5
32 TraesCS5A01G008900 chr6B 92.453 53 4 0 2972 3024 680086196 680086248 4.160000e-10 76.8
33 TraesCS5A01G008900 chr2B 95.833 48 2 0 2980 3027 444233593 444233546 1.160000e-10 78.7
34 TraesCS5A01G008900 chr2B 86.957 69 5 3 2962 3027 410266545 410266478 1.500000e-09 75.0
35 TraesCS5A01G008900 chr1B 95.833 48 2 0 2980 3027 27581561 27581608 1.160000e-10 78.7
36 TraesCS5A01G008900 chr1B 94.118 51 3 0 2977 3027 160439602 160439652 1.160000e-10 78.7
37 TraesCS5A01G008900 chr3B 90.741 54 5 0 2974 3027 661726035 661726088 5.380000e-09 73.1


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 TraesCS5A01G008900 chr5A 6421168 6425047 3879 False 7166.000000 7166 100.0000 1 3880 1 chr5A.!!$F2 3879
1 TraesCS5A01G008900 chr5A 6411083 6411637 554 False 363.000000 363 78.9010 977 1528 1 chr5A.!!$F1 551
2 TraesCS5A01G008900 chr5B 8350864 8354814 3950 False 2325.500000 4015 88.5845 1 3675 2 chr5B.!!$F3 3674
3 TraesCS5A01G008900 chr5B 652935911 652936582 671 True 1031.000000 1031 94.3790 2305 2976 1 chr5B.!!$R2 671
4 TraesCS5A01G008900 chr5B 652946367 652947123 756 True 467.950000 848 92.5650 1072 2307 2 chr5B.!!$R3 1235
5 TraesCS5A01G008900 chr5B 8342596 8343659 1063 False 420.000000 420 74.5690 984 2053 1 chr5B.!!$F1 1069
6 TraesCS5A01G008900 chr5D 8032848 8036075 3227 False 1501.666667 3747 90.8620 383 3728 3 chr5D.!!$F6 3345
7 TraesCS5A01G008900 chr5D 7966188 7966852 664 True 436.000000 436 78.8860 858 1528 1 chr5D.!!$R1 670
8 TraesCS5A01G008900 chr5D 8020015 8020569 554 False 374.000000 374 79.0700 977 1528 1 chr5D.!!$F1 551

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
862 906 0.179048 CAGTGGTGGAGAAGTGCACA 60.179 55.0 21.04 0.00 46.50 4.57 F
1407 1472 0.473755 ACATCATTCGCTATGGGCCA 59.526 50.0 9.61 9.61 37.74 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 2891 0.179040 CGCCGGTACCCACCATATTT 60.179 55.0 6.25 0.0 46.14 1.40 R
3166 3562 0.445436 CGCTTTGCTCACCACATCTC 59.555 55.0 0.00 0.0 0.00 2.75 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
83 84 6.875972 ATACTCCAGAGTTAACTTGGTGAT 57.124 37.500 27.21 18.88 42.54 3.06
84 85 5.568620 ACTCCAGAGTTAACTTGGTGATT 57.431 39.130 27.21 14.62 38.83 2.57
142 143 9.525409 CTCATTTATTTGTGATGAAAATCCTCC 57.475 33.333 0.00 0.00 30.13 4.30
220 221 2.218603 AGGTCAAACCGTGTAAGCAAG 58.781 47.619 0.00 0.00 44.90 4.01
221 222 1.334689 GGTCAAACCGTGTAAGCAAGC 60.335 52.381 0.00 0.00 0.00 4.01
244 245 5.048434 GCAAGTCAAGAGGAAAAGCATTACT 60.048 40.000 0.00 0.00 0.00 2.24
275 276 3.744559 GCTTCACGCAACCCTCAA 58.255 55.556 0.00 0.00 38.92 3.02
379 385 7.055667 TGATGTGTTTATAGGGAGAGATGAC 57.944 40.000 0.00 0.00 0.00 3.06
422 428 8.642908 AACATGGTAAAAAGCAAAGAAGTAAC 57.357 30.769 0.00 0.00 0.00 2.50
435 441 6.699642 GCAAAGAAGTAACCAATTAAACAGCA 59.300 34.615 0.00 0.00 0.00 4.41
436 442 7.223777 GCAAAGAAGTAACCAATTAAACAGCAA 59.776 33.333 0.00 0.00 0.00 3.91
454 460 9.660180 AAACAGCAAAAAGAAGTAACCAATTAA 57.340 25.926 0.00 0.00 0.00 1.40
731 766 9.457436 AATATTATACGGTTTATTGGATGGTCC 57.543 33.333 0.00 0.00 36.96 4.46
754 789 5.121142 CCATAACTTCTTTGGCTTTGCAATG 59.879 40.000 0.00 3.50 0.00 2.82
759 794 1.497223 TTTGGCTTTGCAATGCACGC 61.497 50.000 31.07 13.73 38.71 5.34
804 846 9.778741 AAGTATTTTTCTAGAGATGTTGTGTGA 57.221 29.630 0.00 0.00 0.00 3.58
833 877 2.728690 ATACACGTTACAGCCGTTGA 57.271 45.000 0.00 0.00 36.17 3.18
862 906 0.179048 CAGTGGTGGAGAAGTGCACA 60.179 55.000 21.04 0.00 46.50 4.57
882 927 6.045698 CACAAGCAGTGCTATTCTGATTAG 57.954 41.667 20.09 2.91 42.15 1.73
883 928 5.583854 CACAAGCAGTGCTATTCTGATTAGT 59.416 40.000 20.09 0.00 42.15 2.24
884 929 6.758416 CACAAGCAGTGCTATTCTGATTAGTA 59.242 38.462 20.09 1.88 42.15 1.82
1120 1185 1.330655 ACTAGCATGGGTGAGGACCG 61.331 60.000 0.00 0.00 44.23 4.79
1401 1466 1.229428 CCGCCAACATCATTCGCTAT 58.771 50.000 0.00 0.00 0.00 2.97
1404 1469 1.267806 GCCAACATCATTCGCTATGGG 59.732 52.381 0.00 0.00 34.85 4.00
1407 1472 0.473755 ACATCATTCGCTATGGGCCA 59.526 50.000 9.61 9.61 37.74 5.36
1485 1550 1.274770 CACACATATGCTCAGCGCG 59.725 57.895 0.00 0.00 43.27 6.86
1544 1609 4.004314 GAGGTAAGAACTTTTCCTCCTGC 58.996 47.826 18.27 0.00 36.95 4.85
1560 1631 1.071239 CCTGCGCAGAAACGAATATCG 60.071 52.381 38.06 13.09 46.93 2.92
1597 1668 4.585581 CCATCACTCATCATCTGACTCTCT 59.414 45.833 0.00 0.00 0.00 3.10
1641 1712 4.024556 CCTCATTATCAACAAGATCCGTGC 60.025 45.833 0.00 0.00 38.19 5.34
1699 1776 0.907704 TCCTGTCCGGCTACACCAAT 60.908 55.000 0.00 0.00 39.03 3.16
1723 1800 2.809706 GTATGCCGTGCGGTCCTA 59.190 61.111 12.46 0.00 37.65 2.94
1783 1860 1.755959 AGCGAGCTCACAGAGATCAAT 59.244 47.619 15.40 0.00 44.21 2.57
1798 1875 3.848975 AGATCAATGTCTCCCTTCTTGGT 59.151 43.478 0.00 0.00 0.00 3.67
1848 1925 3.367292 CCAAATATGGTAATGGCGGATGC 60.367 47.826 0.00 0.00 42.18 3.91
2041 2118 3.297134 ACGGATAACATCAAGGCCATT 57.703 42.857 5.01 0.00 0.00 3.16
2063 2141 9.243637 CCATTTTGGTGGTAATAATTACATTCG 57.756 33.333 0.00 0.00 33.56 3.34
2072 2154 8.952278 TGGTAATAATTACATTCGCAGTTTTCT 58.048 29.630 0.00 0.00 37.88 2.52
2102 2190 9.502091 GCAAATAATTGTCCATGTCCTATACTA 57.498 33.333 0.00 0.00 38.85 1.82
2109 2197 7.669089 TGTCCATGTCCTATACTATTGTCAA 57.331 36.000 0.00 0.00 0.00 3.18
2111 2199 8.713971 TGTCCATGTCCTATACTATTGTCAATT 58.286 33.333 2.79 0.00 0.00 2.32
2112 2200 9.561069 GTCCATGTCCTATACTATTGTCAATTT 57.439 33.333 2.79 0.00 0.00 1.82
2113 2201 9.559732 TCCATGTCCTATACTATTGTCAATTTG 57.440 33.333 2.79 0.45 0.00 2.32
2114 2202 9.342308 CCATGTCCTATACTATTGTCAATTTGT 57.658 33.333 2.79 6.30 0.00 2.83
2165 2253 8.056400 AGCTGGAGGGAGTATATAAGTAGTATG 58.944 40.741 0.00 0.00 0.00 2.39
2190 2289 5.505173 AAGAGTTGCCATGTTGCATATAC 57.495 39.130 0.00 0.00 41.70 1.47
2239 2347 6.854496 TGATAAACACACACTAAGTTGGAC 57.146 37.500 0.00 0.00 0.00 4.02
2241 2349 3.637911 AACACACACTAAGTTGGACCA 57.362 42.857 0.00 0.00 0.00 4.02
2300 2408 6.464222 AGAAACATCTTATCTGACGTTGGAA 58.536 36.000 0.00 0.00 0.00 3.53
2717 2828 5.344566 AGGATTTGTCCAGGGATGAATTTT 58.655 37.500 0.00 0.00 0.00 1.82
2780 2891 4.166539 ACCATTTTGATTGGGATGTTCCA 58.833 39.130 0.00 0.00 38.64 3.53
2891 3002 7.361457 TCAGATTCCCTAAACCTACTATGTG 57.639 40.000 0.00 0.00 0.00 3.21
2997 3393 9.892444 TTACTATATACTCCCTCCATCTCAAAA 57.108 33.333 0.00 0.00 0.00 2.44
2998 3394 8.980832 ACTATATACTCCCTCCATCTCAAAAT 57.019 34.615 0.00 0.00 0.00 1.82
3002 3398 7.698163 ATACTCCCTCCATCTCAAAATAAGT 57.302 36.000 0.00 0.00 0.00 2.24
3003 3399 5.749462 ACTCCCTCCATCTCAAAATAAGTG 58.251 41.667 0.00 0.00 0.00 3.16
3004 3400 5.251700 ACTCCCTCCATCTCAAAATAAGTGT 59.748 40.000 0.00 0.00 0.00 3.55
3005 3401 5.745227 TCCCTCCATCTCAAAATAAGTGTC 58.255 41.667 0.00 0.00 0.00 3.67
3006 3402 5.488919 TCCCTCCATCTCAAAATAAGTGTCT 59.511 40.000 0.00 0.00 0.00 3.41
3007 3403 6.672218 TCCCTCCATCTCAAAATAAGTGTCTA 59.328 38.462 0.00 0.00 0.00 2.59
3008 3404 7.182026 TCCCTCCATCTCAAAATAAGTGTCTAA 59.818 37.037 0.00 0.00 0.00 2.10
3009 3405 7.829211 CCCTCCATCTCAAAATAAGTGTCTAAA 59.171 37.037 0.00 0.00 0.00 1.85
3010 3406 8.669243 CCTCCATCTCAAAATAAGTGTCTAAAC 58.331 37.037 0.00 0.00 0.00 2.01
3011 3407 9.442047 CTCCATCTCAAAATAAGTGTCTAAACT 57.558 33.333 0.00 0.00 0.00 2.66
3012 3408 9.793259 TCCATCTCAAAATAAGTGTCTAAACTT 57.207 29.630 0.00 0.00 42.89 2.66
3022 3418 9.780186 AATAAGTGTCTAAACTTTGTTCTAGCT 57.220 29.630 0.00 0.00 40.77 3.32
3023 3419 7.716768 AAGTGTCTAAACTTTGTTCTAGCTC 57.283 36.000 0.00 0.00 37.05 4.09
3024 3420 7.056844 AGTGTCTAAACTTTGTTCTAGCTCT 57.943 36.000 0.00 0.00 0.00 4.09
3077 3473 7.455953 ACAGATCATATATGATGTACCACAGGT 59.544 37.037 28.79 15.60 46.84 4.00
3120 3516 5.172934 CAATTTGCATACATTTGAGTGGCT 58.827 37.500 0.00 0.00 0.00 4.75
3132 3528 6.554982 ACATTTGAGTGGCTATAGACCTATCA 59.445 38.462 2.28 9.24 0.00 2.15
3139 3535 4.448537 GCTATAGACCTATCAGCCACAG 57.551 50.000 3.21 0.00 0.00 3.66
3365 3821 4.690748 GCTGCTGTGTGTCTAAGACAATTA 59.309 41.667 0.00 0.00 44.49 1.40
3370 3826 7.384115 TGCTGTGTGTCTAAGACAATTAGTAAC 59.616 37.037 0.00 0.00 44.49 2.50
3402 3859 1.866015 AGGGGAATCAGTGACGATCA 58.134 50.000 0.00 0.00 0.00 2.92
3446 3903 0.603707 AACCATGTGTCCTGCTGTCG 60.604 55.000 0.00 0.00 0.00 4.35
3447 3904 1.004560 CCATGTGTCCTGCTGTCGT 60.005 57.895 0.00 0.00 0.00 4.34
3450 3907 2.196749 CATGTGTCCTGCTGTCGTATC 58.803 52.381 0.00 0.00 0.00 2.24
3478 3935 3.330267 CACTGGTTGAGGAACTTCTAGC 58.670 50.000 0.00 0.00 41.55 3.42
3493 3950 1.118838 CTAGCTGAGTAGGGCTTGCT 58.881 55.000 0.00 0.00 39.65 3.91
3500 3957 2.093288 TGAGTAGGGCTTGCTTCATCAG 60.093 50.000 0.00 0.00 0.00 2.90
3510 3967 1.820519 TGCTTCATCAGGTCATTTGGC 59.179 47.619 0.00 0.00 0.00 4.52
3548 4005 5.233083 TGTTTTCATCATCAGACTGGTCT 57.767 39.130 1.81 0.00 41.37 3.85
3562 4019 0.889186 TGGTCTTTCTCTTTGGCCGC 60.889 55.000 0.00 0.00 0.00 6.53
3577 4034 1.905843 CCGCGATCAGAGAGGGGAT 60.906 63.158 8.23 0.00 39.96 3.85
3584 4041 3.085942 GATCAGAGAGGGGATCTGGTCC 61.086 59.091 0.00 0.00 45.35 4.46
3622 4079 3.227276 ATAGAGCACCGAGGCCCG 61.227 66.667 0.00 2.20 38.18 6.13
3737 4194 6.655078 TTTTTAGGTACGACTGTTAGACCT 57.345 37.500 11.59 11.59 43.06 3.85
3738 4195 6.655078 TTTTAGGTACGACTGTTAGACCTT 57.345 37.500 11.98 0.92 40.92 3.50
3739 4196 6.655078 TTTAGGTACGACTGTTAGACCTTT 57.345 37.500 11.98 0.00 40.92 3.11
3740 4197 4.516365 AGGTACGACTGTTAGACCTTTG 57.484 45.455 0.00 0.00 37.20 2.77
3741 4198 4.147321 AGGTACGACTGTTAGACCTTTGA 58.853 43.478 0.00 0.00 37.20 2.69
3742 4199 4.586001 AGGTACGACTGTTAGACCTTTGAA 59.414 41.667 0.00 0.00 37.20 2.69
3743 4200 4.683320 GGTACGACTGTTAGACCTTTGAAC 59.317 45.833 0.00 0.00 0.00 3.18
3744 4201 3.725490 ACGACTGTTAGACCTTTGAACC 58.275 45.455 0.00 0.00 0.00 3.62
3745 4202 3.387050 ACGACTGTTAGACCTTTGAACCT 59.613 43.478 0.00 0.00 0.00 3.50
3746 4203 3.741344 CGACTGTTAGACCTTTGAACCTG 59.259 47.826 0.00 0.00 0.00 4.00
3747 4204 4.500887 CGACTGTTAGACCTTTGAACCTGA 60.501 45.833 0.00 0.00 0.00 3.86
3748 4205 4.962155 ACTGTTAGACCTTTGAACCTGAG 58.038 43.478 0.00 0.00 0.00 3.35
3749 4206 3.740115 TGTTAGACCTTTGAACCTGAGC 58.260 45.455 0.00 0.00 0.00 4.26
3750 4207 3.135712 TGTTAGACCTTTGAACCTGAGCA 59.864 43.478 0.00 0.00 0.00 4.26
3751 4208 4.202461 TGTTAGACCTTTGAACCTGAGCAT 60.202 41.667 0.00 0.00 0.00 3.79
3752 4209 3.515602 AGACCTTTGAACCTGAGCATT 57.484 42.857 0.00 0.00 0.00 3.56
3753 4210 3.152341 AGACCTTTGAACCTGAGCATTG 58.848 45.455 0.00 0.00 0.00 2.82
3754 4211 3.149196 GACCTTTGAACCTGAGCATTGA 58.851 45.455 0.00 0.00 0.00 2.57
3755 4212 3.760684 GACCTTTGAACCTGAGCATTGAT 59.239 43.478 0.00 0.00 0.00 2.57
3756 4213 4.922206 ACCTTTGAACCTGAGCATTGATA 58.078 39.130 0.00 0.00 0.00 2.15
3757 4214 4.946157 ACCTTTGAACCTGAGCATTGATAG 59.054 41.667 0.00 0.00 0.00 2.08
3758 4215 4.946157 CCTTTGAACCTGAGCATTGATAGT 59.054 41.667 0.00 0.00 0.00 2.12
3759 4216 5.416952 CCTTTGAACCTGAGCATTGATAGTT 59.583 40.000 0.00 0.00 0.00 2.24
3760 4217 5.885230 TTGAACCTGAGCATTGATAGTTG 57.115 39.130 0.00 0.00 0.00 3.16
3761 4218 4.910195 TGAACCTGAGCATTGATAGTTGT 58.090 39.130 0.00 0.00 0.00 3.32
3762 4219 4.696877 TGAACCTGAGCATTGATAGTTGTG 59.303 41.667 0.00 0.00 0.00 3.33
3763 4220 3.614092 ACCTGAGCATTGATAGTTGTGG 58.386 45.455 0.00 0.00 0.00 4.17
3764 4221 3.264193 ACCTGAGCATTGATAGTTGTGGA 59.736 43.478 0.00 0.00 0.00 4.02
3765 4222 4.080129 ACCTGAGCATTGATAGTTGTGGAT 60.080 41.667 0.00 0.00 0.00 3.41
3766 4223 4.275196 CCTGAGCATTGATAGTTGTGGATG 59.725 45.833 0.00 0.00 0.00 3.51
3767 4224 5.101648 TGAGCATTGATAGTTGTGGATGA 57.898 39.130 0.00 0.00 0.00 2.92
3768 4225 4.877823 TGAGCATTGATAGTTGTGGATGAC 59.122 41.667 0.00 0.00 0.00 3.06
3769 4226 3.873361 AGCATTGATAGTTGTGGATGACG 59.127 43.478 0.00 0.00 0.00 4.35
3770 4227 3.546815 GCATTGATAGTTGTGGATGACGC 60.547 47.826 0.00 0.00 0.00 5.19
3771 4228 3.610040 TTGATAGTTGTGGATGACGCT 57.390 42.857 0.00 0.00 0.00 5.07
3772 4229 4.729227 TTGATAGTTGTGGATGACGCTA 57.271 40.909 0.00 0.00 0.00 4.26
3773 4230 4.307443 TGATAGTTGTGGATGACGCTAG 57.693 45.455 0.00 0.00 0.00 3.42
3774 4231 3.068165 TGATAGTTGTGGATGACGCTAGG 59.932 47.826 0.00 0.00 0.00 3.02
3775 4232 1.557099 AGTTGTGGATGACGCTAGGA 58.443 50.000 0.00 0.00 0.00 2.94
3776 4233 1.478510 AGTTGTGGATGACGCTAGGAG 59.521 52.381 0.00 0.00 0.00 3.69
3777 4234 1.476891 GTTGTGGATGACGCTAGGAGA 59.523 52.381 0.00 0.00 0.00 3.71
3778 4235 1.393603 TGTGGATGACGCTAGGAGAG 58.606 55.000 0.00 0.00 0.00 3.20
3779 4236 1.341089 TGTGGATGACGCTAGGAGAGT 60.341 52.381 0.00 0.00 0.00 3.24
3780 4237 1.751924 GTGGATGACGCTAGGAGAGTT 59.248 52.381 0.00 0.00 0.00 3.01
3781 4238 1.751351 TGGATGACGCTAGGAGAGTTG 59.249 52.381 0.00 0.00 0.00 3.16
3782 4239 1.067821 GGATGACGCTAGGAGAGTTGG 59.932 57.143 0.00 0.00 0.00 3.77
3783 4240 1.067821 GATGACGCTAGGAGAGTTGGG 59.932 57.143 0.00 0.00 0.00 4.12
3784 4241 0.039180 TGACGCTAGGAGAGTTGGGA 59.961 55.000 0.00 0.00 0.00 4.37
3785 4242 0.456628 GACGCTAGGAGAGTTGGGAC 59.543 60.000 0.00 0.00 0.00 4.46
3786 4243 0.251653 ACGCTAGGAGAGTTGGGACA 60.252 55.000 0.00 0.00 0.00 4.02
3802 4259 5.793030 TGGGACAATTTTCGTTGGTTTAT 57.207 34.783 0.00 0.00 31.92 1.40
3803 4260 6.163135 TGGGACAATTTTCGTTGGTTTATT 57.837 33.333 0.00 0.00 31.92 1.40
3804 4261 6.583562 TGGGACAATTTTCGTTGGTTTATTT 58.416 32.000 0.00 0.00 31.92 1.40
3805 4262 6.702282 TGGGACAATTTTCGTTGGTTTATTTC 59.298 34.615 0.00 0.00 31.92 2.17
3806 4263 6.926826 GGGACAATTTTCGTTGGTTTATTTCT 59.073 34.615 0.00 0.00 33.40 2.52
3807 4264 7.115805 GGGACAATTTTCGTTGGTTTATTTCTC 59.884 37.037 0.00 0.00 33.40 2.87
3808 4265 7.650104 GGACAATTTTCGTTGGTTTATTTCTCA 59.350 33.333 0.00 0.00 33.40 3.27
3809 4266 8.347729 ACAATTTTCGTTGGTTTATTTCTCAC 57.652 30.769 0.00 0.00 33.40 3.51
3810 4267 7.976734 ACAATTTTCGTTGGTTTATTTCTCACA 59.023 29.630 0.00 0.00 33.40 3.58
3811 4268 7.924103 ATTTTCGTTGGTTTATTTCTCACAC 57.076 32.000 0.00 0.00 0.00 3.82
3812 4269 6.438259 TTTCGTTGGTTTATTTCTCACACA 57.562 33.333 0.00 0.00 0.00 3.72
3813 4270 6.438259 TTCGTTGGTTTATTTCTCACACAA 57.562 33.333 0.00 0.00 0.00 3.33
3814 4271 6.627395 TCGTTGGTTTATTTCTCACACAAT 57.373 33.333 0.00 0.00 0.00 2.71
3815 4272 6.434596 TCGTTGGTTTATTTCTCACACAATG 58.565 36.000 0.00 0.00 0.00 2.82
3816 4273 5.116983 CGTTGGTTTATTTCTCACACAATGC 59.883 40.000 0.00 0.00 0.00 3.56
3817 4274 5.132897 TGGTTTATTTCTCACACAATGCC 57.867 39.130 0.00 0.00 0.00 4.40
3818 4275 4.586421 TGGTTTATTTCTCACACAATGCCA 59.414 37.500 0.00 0.00 0.00 4.92
3819 4276 5.245751 TGGTTTATTTCTCACACAATGCCAT 59.754 36.000 0.00 0.00 0.00 4.40
3820 4277 5.577945 GGTTTATTTCTCACACAATGCCATG 59.422 40.000 0.00 0.00 0.00 3.66
3821 4278 2.728690 TTTCTCACACAATGCCATGC 57.271 45.000 0.00 0.00 0.00 4.06
3822 4279 0.889994 TTCTCACACAATGCCATGCC 59.110 50.000 0.00 0.00 0.00 4.40
3823 4280 0.251253 TCTCACACAATGCCATGCCA 60.251 50.000 0.00 0.00 0.00 4.92
3824 4281 0.604073 CTCACACAATGCCATGCCAA 59.396 50.000 0.00 0.00 0.00 4.52
3825 4282 0.317799 TCACACAATGCCATGCCAAC 59.682 50.000 0.00 0.00 0.00 3.77
3826 4283 0.671163 CACACAATGCCATGCCAACC 60.671 55.000 0.00 0.00 0.00 3.77
3827 4284 0.832983 ACACAATGCCATGCCAACCT 60.833 50.000 0.00 0.00 0.00 3.50
3828 4285 0.390603 CACAATGCCATGCCAACCTG 60.391 55.000 0.00 0.00 0.00 4.00
3829 4286 0.542467 ACAATGCCATGCCAACCTGA 60.542 50.000 0.00 0.00 0.00 3.86
3830 4287 0.174845 CAATGCCATGCCAACCTGAG 59.825 55.000 0.00 0.00 0.00 3.35
3831 4288 0.974010 AATGCCATGCCAACCTGAGG 60.974 55.000 0.00 0.00 0.00 3.86
3832 4289 2.757099 GCCATGCCAACCTGAGGG 60.757 66.667 2.38 0.00 38.88 4.30
3833 4290 2.043652 CCATGCCAACCTGAGGGG 60.044 66.667 2.38 0.00 41.89 4.79
3842 4299 4.851784 CCTGAGGGGTTGGGGATA 57.148 61.111 0.00 0.00 0.00 2.59
3843 4300 2.231642 CCTGAGGGGTTGGGGATAC 58.768 63.158 0.00 0.00 0.00 2.24
3844 4301 0.623324 CCTGAGGGGTTGGGGATACA 60.623 60.000 0.00 0.00 39.74 2.29
3845 4302 1.522900 CTGAGGGGTTGGGGATACAT 58.477 55.000 0.00 0.00 39.74 2.29
3846 4303 2.698967 CCTGAGGGGTTGGGGATACATA 60.699 54.545 0.00 0.00 39.74 2.29
3847 4304 2.372172 CTGAGGGGTTGGGGATACATAC 59.628 54.545 0.00 0.00 39.74 2.39
3848 4305 2.021441 TGAGGGGTTGGGGATACATACT 60.021 50.000 0.00 0.00 39.74 2.12
3849 4306 3.053826 GAGGGGTTGGGGATACATACTT 58.946 50.000 0.00 0.00 39.74 2.24
3850 4307 4.237018 GAGGGGTTGGGGATACATACTTA 58.763 47.826 0.00 0.00 39.74 2.24
3851 4308 4.850386 GAGGGGTTGGGGATACATACTTAT 59.150 45.833 0.00 0.00 39.74 1.73
3852 4309 5.997094 AGGGGTTGGGGATACATACTTATA 58.003 41.667 0.00 0.00 39.74 0.98
3853 4310 6.030082 AGGGGTTGGGGATACATACTTATAG 58.970 44.000 0.00 0.00 39.74 1.31
3854 4311 5.191124 GGGGTTGGGGATACATACTTATAGG 59.809 48.000 0.00 0.00 39.74 2.57
3855 4312 5.338953 GGGTTGGGGATACATACTTATAGGC 60.339 48.000 0.00 0.00 39.74 3.93
3856 4313 5.487845 GGTTGGGGATACATACTTATAGGCT 59.512 44.000 0.00 0.00 39.74 4.58
3857 4314 6.407202 GTTGGGGATACATACTTATAGGCTG 58.593 44.000 0.00 0.00 39.74 4.85
3858 4315 4.469945 TGGGGATACATACTTATAGGCTGC 59.530 45.833 0.00 0.00 39.74 5.25
3859 4316 4.717280 GGGGATACATACTTATAGGCTGCT 59.283 45.833 0.00 0.00 39.74 4.24
3860 4317 5.897824 GGGGATACATACTTATAGGCTGCTA 59.102 44.000 0.00 0.00 39.74 3.49
3861 4318 6.041069 GGGGATACATACTTATAGGCTGCTAG 59.959 46.154 0.00 0.00 39.74 3.42
3862 4319 6.461788 GGGATACATACTTATAGGCTGCTAGC 60.462 46.154 8.10 8.10 38.65 3.42
3874 4331 4.885426 GCTAGCCAGCCAAGCATA 57.115 55.556 2.29 0.00 42.37 3.14
3875 4332 3.336122 GCTAGCCAGCCAAGCATAT 57.664 52.632 2.29 0.00 42.37 1.78
3876 4333 0.879765 GCTAGCCAGCCAAGCATATG 59.120 55.000 2.29 0.00 42.37 1.78
3877 4334 0.879765 CTAGCCAGCCAAGCATATGC 59.120 55.000 20.36 20.36 42.49 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 7.673504 TGGAGGAGGATTTTCATCACAAATAAA 59.326 33.333 0.00 0.00 29.82 1.40
142 143 7.550551 TCAGTCTTTTGATATTACTTGCTGGAG 59.449 37.037 0.00 0.00 0.00 3.86
199 200 3.395639 CTTGCTTACACGGTTTGACCTA 58.604 45.455 0.00 0.00 35.66 3.08
205 206 2.021457 ACTTGCTTGCTTACACGGTTT 58.979 42.857 0.00 0.00 0.00 3.27
220 221 3.930634 ATGCTTTTCCTCTTGACTTGC 57.069 42.857 0.00 0.00 0.00 4.01
221 222 6.566197 AGTAATGCTTTTCCTCTTGACTTG 57.434 37.500 0.00 0.00 0.00 3.16
275 276 4.406456 TGCATTTGTATGTGGAACTCCTT 58.594 39.130 0.00 0.00 38.04 3.36
357 363 7.453126 CCTAGTCATCTCTCCCTATAAACACAT 59.547 40.741 0.00 0.00 0.00 3.21
358 364 6.778069 CCTAGTCATCTCTCCCTATAAACACA 59.222 42.308 0.00 0.00 0.00 3.72
369 375 3.033659 TGGGTTCCTAGTCATCTCTCC 57.966 52.381 0.00 0.00 0.00 3.71
379 385 8.533569 ACCATGTTAATTAATTGGGTTCCTAG 57.466 34.615 23.48 6.63 0.00 3.02
422 428 8.547894 GGTTACTTCTTTTTGCTGTTTAATTGG 58.452 33.333 0.00 0.00 0.00 3.16
731 766 5.390145 GCATTGCAAAGCCAAAGAAGTTATG 60.390 40.000 15.60 0.00 0.00 1.90
754 789 2.010817 CTTGCTTTTCCGTGCGTGC 61.011 57.895 0.00 0.00 0.00 5.34
759 794 5.121221 ACTTATTTCCTTGCTTTTCCGTG 57.879 39.130 0.00 0.00 0.00 4.94
804 846 4.806330 CTGTAACGTGTATTCACTCCAGT 58.194 43.478 0.77 0.00 41.89 4.00
833 877 1.228367 CCACCACTGGCTGAGCTTT 60.228 57.895 3.72 0.00 0.00 3.51
862 906 8.206867 TCAATACTAATCAGAATAGCACTGCTT 58.793 33.333 9.30 0.00 40.44 3.91
882 927 7.976135 AGCTCTCCATCAATTATGTCAATAC 57.024 36.000 0.00 0.00 33.34 1.89
883 928 8.212995 TCAAGCTCTCCATCAATTATGTCAATA 58.787 33.333 0.00 0.00 33.34 1.90
884 929 7.058525 TCAAGCTCTCCATCAATTATGTCAAT 58.941 34.615 0.00 0.00 33.34 2.57
915 960 9.990360 TCCTACTCATCTCTATCTATATAAGCG 57.010 37.037 0.00 0.00 0.00 4.68
1018 1071 1.293498 CGAGCTGCAGGTAGTGGTT 59.707 57.895 20.22 0.00 0.00 3.67
1120 1185 0.040425 AATCTTGTTGACGCGGTTGC 60.040 50.000 12.47 0.00 37.91 4.17
1387 1452 1.133823 TGGCCCATAGCGAATGATGTT 60.134 47.619 0.00 0.00 45.17 2.71
1401 1466 2.359850 GCGATGTCTGTTGGCCCA 60.360 61.111 0.00 0.00 0.00 5.36
1404 1469 0.725784 CAAACGCGATGTCTGTTGGC 60.726 55.000 15.93 0.00 0.00 4.52
1407 1472 0.041312 GTGCAAACGCGATGTCTGTT 60.041 50.000 15.93 0.00 0.00 3.16
1544 1609 1.187271 CGGTCGATATTCGTTTCTGCG 59.813 52.381 0.00 0.00 41.35 5.18
1560 1631 4.157289 TGAGTGATGGACTAACTAACGGTC 59.843 45.833 0.00 0.00 33.83 4.79
1597 1668 1.371337 GCACCTGCAGCAATCGATCA 61.371 55.000 8.66 0.00 41.59 2.92
1622 1693 2.872245 CCGCACGGATCTTGTTGATAAT 59.128 45.455 2.01 0.00 35.14 1.28
1723 1800 1.604378 CTTGCGGTGGGATTCTCCT 59.396 57.895 0.00 0.00 36.57 3.69
1798 1875 0.984230 AATTCTCGAGGCTGAACCCA 59.016 50.000 13.56 0.00 40.58 4.51
1831 1908 3.225272 CGCATCCGCCATTACCATA 57.775 52.632 0.00 0.00 33.11 2.74
1848 1925 1.301677 GGAAACCAGCCTCAAGAGCG 61.302 60.000 0.00 0.00 34.64 5.03
2041 2118 7.121463 ACTGCGAATGTAATTATTACCACCAAA 59.879 33.333 11.97 0.00 36.07 3.28
2063 2141 8.382875 GGACAATTATTTGCAATAGAAAACTGC 58.617 33.333 0.00 0.00 36.22 4.40
2072 2154 7.658525 AGGACATGGACAATTATTTGCAATA 57.341 32.000 0.00 0.00 36.22 1.90
2116 2204 9.315363 AGCTCCAAATGTTATAGTAGCTAGTAT 57.685 33.333 21.83 21.83 37.30 2.12
2117 2205 8.577296 CAGCTCCAAATGTTATAGTAGCTAGTA 58.423 37.037 10.71 10.71 36.97 1.82
2118 2206 7.437748 CAGCTCCAAATGTTATAGTAGCTAGT 58.562 38.462 6.29 6.29 36.97 2.57
2119 2207 6.870965 CCAGCTCCAAATGTTATAGTAGCTAG 59.129 42.308 0.00 0.00 36.97 3.42
2120 2208 6.553476 TCCAGCTCCAAATGTTATAGTAGCTA 59.447 38.462 0.00 0.00 36.97 3.32
2121 2209 5.366768 TCCAGCTCCAAATGTTATAGTAGCT 59.633 40.000 0.00 0.00 39.54 3.32
2122 2210 5.611374 TCCAGCTCCAAATGTTATAGTAGC 58.389 41.667 0.00 0.00 0.00 3.58
2124 2212 5.071788 CCCTCCAGCTCCAAATGTTATAGTA 59.928 44.000 0.00 0.00 0.00 1.82
2126 2214 4.103153 TCCCTCCAGCTCCAAATGTTATAG 59.897 45.833 0.00 0.00 0.00 1.31
2127 2215 4.044308 TCCCTCCAGCTCCAAATGTTATA 58.956 43.478 0.00 0.00 0.00 0.98
2128 2216 2.852449 TCCCTCCAGCTCCAAATGTTAT 59.148 45.455 0.00 0.00 0.00 1.89
2129 2217 2.239654 CTCCCTCCAGCTCCAAATGTTA 59.760 50.000 0.00 0.00 0.00 2.41
2130 2218 1.005215 CTCCCTCCAGCTCCAAATGTT 59.995 52.381 0.00 0.00 0.00 2.71
2131 2219 0.622665 CTCCCTCCAGCTCCAAATGT 59.377 55.000 0.00 0.00 0.00 2.71
2132 2220 0.622665 ACTCCCTCCAGCTCCAAATG 59.377 55.000 0.00 0.00 0.00 2.32
2165 2253 3.641437 TGCAACATGGCAACTCTTAAC 57.359 42.857 0.00 0.00 41.65 2.01
2190 2289 8.999431 ACATCACCACATAAAAAGTACTAACTG 58.001 33.333 0.00 0.00 35.62 3.16
2220 2322 3.958018 TGGTCCAACTTAGTGTGTGTTT 58.042 40.909 0.00 0.00 0.00 2.83
2239 2347 6.764308 ACATGTCCTGTTAAGATCAAATGG 57.236 37.500 0.00 0.00 32.90 3.16
2300 2408 1.070445 GAGCTCAGCCATGCCGTAT 59.930 57.895 9.40 0.00 0.00 3.06
2341 2449 6.768381 GGATCTTACCTCCTCCTGTAATTTTG 59.232 42.308 0.00 0.00 0.00 2.44
2465 2573 1.539124 GTGTGGGAGGAGGAAGGGT 60.539 63.158 0.00 0.00 0.00 4.34
2780 2891 0.179040 CGCCGGTACCCACCATATTT 60.179 55.000 6.25 0.00 46.14 1.40
2891 3002 8.227791 TCTTGTGCTCATTCGAAATAAACTTAC 58.772 33.333 0.00 0.00 0.00 2.34
2981 3377 5.749462 ACACTTATTTTGAGATGGAGGGAG 58.251 41.667 0.00 0.00 0.00 4.30
2982 3378 5.488919 AGACACTTATTTTGAGATGGAGGGA 59.511 40.000 0.00 0.00 0.00 4.20
2983 3379 5.749462 AGACACTTATTTTGAGATGGAGGG 58.251 41.667 0.00 0.00 0.00 4.30
2984 3380 8.669243 GTTTAGACACTTATTTTGAGATGGAGG 58.331 37.037 0.00 0.00 0.00 4.30
2985 3381 9.442047 AGTTTAGACACTTATTTTGAGATGGAG 57.558 33.333 0.00 0.00 0.00 3.86
2986 3382 9.793259 AAGTTTAGACACTTATTTTGAGATGGA 57.207 29.630 0.00 0.00 35.10 3.41
2996 3392 9.780186 AGCTAGAACAAAGTTTAGACACTTATT 57.220 29.630 0.00 0.00 35.87 1.40
2997 3393 9.425577 GAGCTAGAACAAAGTTTAGACACTTAT 57.574 33.333 0.00 0.00 35.87 1.73
2998 3394 8.639761 AGAGCTAGAACAAAGTTTAGACACTTA 58.360 33.333 0.00 0.00 35.87 2.24
2999 3395 7.501844 AGAGCTAGAACAAAGTTTAGACACTT 58.498 34.615 0.00 0.00 38.74 3.16
3000 3396 7.056844 AGAGCTAGAACAAAGTTTAGACACT 57.943 36.000 0.00 0.00 0.00 3.55
3001 3397 8.298140 TCTAGAGCTAGAACAAAGTTTAGACAC 58.702 37.037 4.80 0.00 39.08 3.67
3002 3398 8.405418 TCTAGAGCTAGAACAAAGTTTAGACA 57.595 34.615 4.80 0.00 39.08 3.41
3003 3399 9.296400 CATCTAGAGCTAGAACAAAGTTTAGAC 57.704 37.037 10.94 0.00 44.44 2.59
3004 3400 8.470805 CCATCTAGAGCTAGAACAAAGTTTAGA 58.529 37.037 10.94 0.00 44.44 2.10
3005 3401 8.470805 TCCATCTAGAGCTAGAACAAAGTTTAG 58.529 37.037 10.94 0.00 44.44 1.85
3006 3402 8.362464 TCCATCTAGAGCTAGAACAAAGTTTA 57.638 34.615 10.94 0.00 44.44 2.01
3007 3403 7.246171 TCCATCTAGAGCTAGAACAAAGTTT 57.754 36.000 10.94 0.00 44.44 2.66
3008 3404 6.859112 TCCATCTAGAGCTAGAACAAAGTT 57.141 37.500 10.94 0.00 44.44 2.66
3009 3405 6.609212 TCATCCATCTAGAGCTAGAACAAAGT 59.391 38.462 10.94 0.00 44.44 2.66
3010 3406 7.014134 TCTCATCCATCTAGAGCTAGAACAAAG 59.986 40.741 10.94 5.42 44.44 2.77
3011 3407 6.836007 TCTCATCCATCTAGAGCTAGAACAAA 59.164 38.462 10.94 0.00 44.44 2.83
3012 3408 6.368805 TCTCATCCATCTAGAGCTAGAACAA 58.631 40.000 10.94 1.08 44.44 2.83
3013 3409 5.946486 TCTCATCCATCTAGAGCTAGAACA 58.054 41.667 10.94 0.00 44.44 3.18
3014 3410 6.490040 ACTTCTCATCCATCTAGAGCTAGAAC 59.510 42.308 10.94 0.00 44.44 3.01
3015 3411 6.609876 ACTTCTCATCCATCTAGAGCTAGAA 58.390 40.000 10.94 1.37 44.44 2.10
3016 3412 6.199557 ACTTCTCATCCATCTAGAGCTAGA 57.800 41.667 9.47 9.47 45.24 2.43
3017 3413 6.899393 AACTTCTCATCCATCTAGAGCTAG 57.101 41.667 0.00 0.00 34.56 3.42
3018 3414 8.948401 ATTAACTTCTCATCCATCTAGAGCTA 57.052 34.615 0.00 0.00 0.00 3.32
3019 3415 7.854166 ATTAACTTCTCATCCATCTAGAGCT 57.146 36.000 0.00 0.00 0.00 4.09
3020 3416 8.900983 AAATTAACTTCTCATCCATCTAGAGC 57.099 34.615 0.00 0.00 0.00 4.09
3049 3445 8.193953 TGTGGTACATCATATATGATCTGTGT 57.806 34.615 22.76 20.51 45.23 3.72
3072 3468 7.339212 TGCTTTATTCTTTATGTATGCACCTGT 59.661 33.333 0.00 0.00 0.00 4.00
3120 3516 3.574396 GTGCTGTGGCTGATAGGTCTATA 59.426 47.826 0.00 0.00 39.59 1.31
3166 3562 0.445436 CGCTTTGCTCACCACATCTC 59.555 55.000 0.00 0.00 0.00 2.75
3322 3768 2.286833 GCTTAACTTGTGAGTTGCGACA 59.713 45.455 6.90 0.00 45.46 4.35
3333 3779 2.614057 GACACACAGCAGCTTAACTTGT 59.386 45.455 0.00 0.00 0.00 3.16
3365 3821 5.476983 TCCCCTTGGAGATATGATGTTACT 58.523 41.667 0.00 0.00 35.03 2.24
3370 3826 5.013913 ACTGATTCCCCTTGGAGATATGATG 59.986 44.000 0.00 0.00 43.07 3.07
3376 3832 2.507471 GTCACTGATTCCCCTTGGAGAT 59.493 50.000 0.00 0.00 43.07 2.75
3384 3841 1.941325 GTGATCGTCACTGATTCCCC 58.059 55.000 9.86 0.00 43.73 4.81
3402 3859 6.552445 ATCTAGAGGTAAGCTCAAACATGT 57.448 37.500 0.00 0.00 0.00 3.21
3411 3868 6.384305 ACACATGGTTTATCTAGAGGTAAGCT 59.616 38.462 0.00 0.00 0.00 3.74
3478 3935 2.093288 TGATGAAGCAAGCCCTACTCAG 60.093 50.000 0.00 0.00 0.00 3.35
3493 3950 2.905415 AGGCCAAATGACCTGATGAA 57.095 45.000 5.01 0.00 34.07 2.57
3500 3957 3.608432 GCCTCAGGCCAAATGACC 58.392 61.111 3.37 0.00 44.06 4.02
3510 3967 4.821805 TGAAAACAACTTTCTAGCCTCAGG 59.178 41.667 0.00 0.00 43.42 3.86
3548 4005 0.321210 TGATCGCGGCCAAAGAGAAA 60.321 50.000 6.13 0.00 0.00 2.52
3562 4019 1.255882 CCAGATCCCCTCTCTGATCG 58.744 60.000 1.99 0.00 42.22 3.69
3584 4041 7.262772 TCTATGACCGTGTAAAATCCTTACAG 58.737 38.462 0.00 0.00 35.77 2.74
3622 4079 0.813821 GCTCCAAGCAGAACAATCCC 59.186 55.000 0.00 0.00 41.89 3.85
3624 4081 3.505293 AGAAAGCTCCAAGCAGAACAATC 59.495 43.478 1.29 0.00 45.56 2.67
3629 4086 2.551721 CCAGAGAAAGCTCCAAGCAGAA 60.552 50.000 1.29 0.00 45.56 3.02
3724 4181 3.741344 CAGGTTCAAAGGTCTAACAGTCG 59.259 47.826 0.00 0.00 0.00 4.18
3728 4185 3.135712 TGCTCAGGTTCAAAGGTCTAACA 59.864 43.478 0.00 0.00 0.00 2.41
3729 4186 3.740115 TGCTCAGGTTCAAAGGTCTAAC 58.260 45.455 0.00 0.00 0.00 2.34
3730 4187 4.640771 ATGCTCAGGTTCAAAGGTCTAA 57.359 40.909 0.00 0.00 0.00 2.10
3731 4188 4.041567 TCAATGCTCAGGTTCAAAGGTCTA 59.958 41.667 0.00 0.00 0.00 2.59
3732 4189 3.152341 CAATGCTCAGGTTCAAAGGTCT 58.848 45.455 0.00 0.00 0.00 3.85
3733 4190 3.149196 TCAATGCTCAGGTTCAAAGGTC 58.851 45.455 0.00 0.00 0.00 3.85
3734 4191 3.228188 TCAATGCTCAGGTTCAAAGGT 57.772 42.857 0.00 0.00 0.00 3.50
3735 4192 4.946157 ACTATCAATGCTCAGGTTCAAAGG 59.054 41.667 0.00 0.00 0.00 3.11
3736 4193 6.072286 ACAACTATCAATGCTCAGGTTCAAAG 60.072 38.462 0.00 0.00 0.00 2.77
3737 4194 5.769662 ACAACTATCAATGCTCAGGTTCAAA 59.230 36.000 0.00 0.00 0.00 2.69
3738 4195 5.181811 CACAACTATCAATGCTCAGGTTCAA 59.818 40.000 0.00 0.00 0.00 2.69
3739 4196 4.696877 CACAACTATCAATGCTCAGGTTCA 59.303 41.667 0.00 0.00 0.00 3.18
3740 4197 4.095483 CCACAACTATCAATGCTCAGGTTC 59.905 45.833 0.00 0.00 0.00 3.62
3741 4198 4.012374 CCACAACTATCAATGCTCAGGTT 58.988 43.478 0.00 0.00 0.00 3.50
3742 4199 3.264193 TCCACAACTATCAATGCTCAGGT 59.736 43.478 0.00 0.00 0.00 4.00
3743 4200 3.877559 TCCACAACTATCAATGCTCAGG 58.122 45.455 0.00 0.00 0.00 3.86
3744 4201 5.007430 GTCATCCACAACTATCAATGCTCAG 59.993 44.000 0.00 0.00 0.00 3.35
3745 4202 4.877823 GTCATCCACAACTATCAATGCTCA 59.122 41.667 0.00 0.00 0.00 4.26
3746 4203 4.025396 CGTCATCCACAACTATCAATGCTC 60.025 45.833 0.00 0.00 0.00 4.26
3747 4204 3.873361 CGTCATCCACAACTATCAATGCT 59.127 43.478 0.00 0.00 0.00 3.79
3748 4205 3.546815 GCGTCATCCACAACTATCAATGC 60.547 47.826 0.00 0.00 0.00 3.56
3749 4206 3.873361 AGCGTCATCCACAACTATCAATG 59.127 43.478 0.00 0.00 0.00 2.82
3750 4207 4.142609 AGCGTCATCCACAACTATCAAT 57.857 40.909 0.00 0.00 0.00 2.57
3751 4208 3.610040 AGCGTCATCCACAACTATCAA 57.390 42.857 0.00 0.00 0.00 2.57
3752 4209 3.068165 CCTAGCGTCATCCACAACTATCA 59.932 47.826 0.00 0.00 0.00 2.15
3753 4210 3.318275 TCCTAGCGTCATCCACAACTATC 59.682 47.826 0.00 0.00 0.00 2.08
3754 4211 3.296854 TCCTAGCGTCATCCACAACTAT 58.703 45.455 0.00 0.00 0.00 2.12
3755 4212 2.688446 CTCCTAGCGTCATCCACAACTA 59.312 50.000 0.00 0.00 0.00 2.24
3756 4213 1.478510 CTCCTAGCGTCATCCACAACT 59.521 52.381 0.00 0.00 0.00 3.16
3757 4214 1.476891 TCTCCTAGCGTCATCCACAAC 59.523 52.381 0.00 0.00 0.00 3.32
3758 4215 1.751351 CTCTCCTAGCGTCATCCACAA 59.249 52.381 0.00 0.00 0.00 3.33
3759 4216 1.341089 ACTCTCCTAGCGTCATCCACA 60.341 52.381 0.00 0.00 0.00 4.17
3760 4217 1.394618 ACTCTCCTAGCGTCATCCAC 58.605 55.000 0.00 0.00 0.00 4.02
3761 4218 1.751351 CAACTCTCCTAGCGTCATCCA 59.249 52.381 0.00 0.00 0.00 3.41
3762 4219 1.067821 CCAACTCTCCTAGCGTCATCC 59.932 57.143 0.00 0.00 0.00 3.51
3763 4220 1.067821 CCCAACTCTCCTAGCGTCATC 59.932 57.143 0.00 0.00 0.00 2.92
3764 4221 1.115467 CCCAACTCTCCTAGCGTCAT 58.885 55.000 0.00 0.00 0.00 3.06
3765 4222 0.039180 TCCCAACTCTCCTAGCGTCA 59.961 55.000 0.00 0.00 0.00 4.35
3766 4223 0.456628 GTCCCAACTCTCCTAGCGTC 59.543 60.000 0.00 0.00 0.00 5.19
3767 4224 0.251653 TGTCCCAACTCTCCTAGCGT 60.252 55.000 0.00 0.00 0.00 5.07
3768 4225 0.895530 TTGTCCCAACTCTCCTAGCG 59.104 55.000 0.00 0.00 0.00 4.26
3769 4226 3.636153 AATTGTCCCAACTCTCCTAGC 57.364 47.619 0.00 0.00 0.00 3.42
3770 4227 4.631813 CGAAAATTGTCCCAACTCTCCTAG 59.368 45.833 0.00 0.00 0.00 3.02
3771 4228 4.041198 ACGAAAATTGTCCCAACTCTCCTA 59.959 41.667 0.00 0.00 0.00 2.94
3772 4229 3.181443 ACGAAAATTGTCCCAACTCTCCT 60.181 43.478 0.00 0.00 0.00 3.69
3773 4230 3.146847 ACGAAAATTGTCCCAACTCTCC 58.853 45.455 0.00 0.00 0.00 3.71
3774 4231 4.537015 CAACGAAAATTGTCCCAACTCTC 58.463 43.478 0.00 0.00 0.00 3.20
3775 4232 3.317993 CCAACGAAAATTGTCCCAACTCT 59.682 43.478 0.00 0.00 0.00 3.24
3776 4233 3.067601 ACCAACGAAAATTGTCCCAACTC 59.932 43.478 0.00 0.00 0.00 3.01
3777 4234 3.028130 ACCAACGAAAATTGTCCCAACT 58.972 40.909 0.00 0.00 0.00 3.16
3778 4235 3.446310 ACCAACGAAAATTGTCCCAAC 57.554 42.857 0.00 0.00 0.00 3.77
3779 4236 4.473477 AAACCAACGAAAATTGTCCCAA 57.527 36.364 0.00 0.00 0.00 4.12
3780 4237 5.793030 ATAAACCAACGAAAATTGTCCCA 57.207 34.783 0.00 0.00 0.00 4.37
3781 4238 6.926826 AGAAATAAACCAACGAAAATTGTCCC 59.073 34.615 0.00 0.00 0.00 4.46
3782 4239 7.650104 TGAGAAATAAACCAACGAAAATTGTCC 59.350 33.333 0.00 0.00 0.00 4.02
3783 4240 8.476925 GTGAGAAATAAACCAACGAAAATTGTC 58.523 33.333 0.00 0.00 0.00 3.18
3784 4241 7.976734 TGTGAGAAATAAACCAACGAAAATTGT 59.023 29.630 0.00 0.00 0.00 2.71
3785 4242 8.265998 GTGTGAGAAATAAACCAACGAAAATTG 58.734 33.333 0.00 0.00 0.00 2.32
3786 4243 7.976734 TGTGTGAGAAATAAACCAACGAAAATT 59.023 29.630 0.00 0.00 0.00 1.82
3787 4244 7.484975 TGTGTGAGAAATAAACCAACGAAAAT 58.515 30.769 0.00 0.00 0.00 1.82
3788 4245 6.853720 TGTGTGAGAAATAAACCAACGAAAA 58.146 32.000 0.00 0.00 0.00 2.29
3789 4246 6.438259 TGTGTGAGAAATAAACCAACGAAA 57.562 33.333 0.00 0.00 0.00 3.46
3790 4247 6.438259 TTGTGTGAGAAATAAACCAACGAA 57.562 33.333 0.00 0.00 0.00 3.85
3791 4248 6.434596 CATTGTGTGAGAAATAAACCAACGA 58.565 36.000 0.00 0.00 0.00 3.85
3792 4249 5.116983 GCATTGTGTGAGAAATAAACCAACG 59.883 40.000 0.00 0.00 0.00 4.10
3793 4250 5.405269 GGCATTGTGTGAGAAATAAACCAAC 59.595 40.000 0.00 0.00 0.00 3.77
3794 4251 5.069648 TGGCATTGTGTGAGAAATAAACCAA 59.930 36.000 0.00 0.00 0.00 3.67
3795 4252 4.586421 TGGCATTGTGTGAGAAATAAACCA 59.414 37.500 0.00 0.00 0.00 3.67
3796 4253 5.132897 TGGCATTGTGTGAGAAATAAACC 57.867 39.130 0.00 0.00 0.00 3.27
3797 4254 5.062558 GCATGGCATTGTGTGAGAAATAAAC 59.937 40.000 0.00 0.00 0.00 2.01
3798 4255 5.170021 GCATGGCATTGTGTGAGAAATAAA 58.830 37.500 0.00 0.00 0.00 1.40
3799 4256 4.381825 GGCATGGCATTGTGTGAGAAATAA 60.382 41.667 15.47 0.00 0.00 1.40
3800 4257 3.130869 GGCATGGCATTGTGTGAGAAATA 59.869 43.478 15.47 0.00 0.00 1.40
3801 4258 2.093869 GGCATGGCATTGTGTGAGAAAT 60.094 45.455 15.47 0.00 0.00 2.17
3802 4259 1.273048 GGCATGGCATTGTGTGAGAAA 59.727 47.619 15.47 0.00 0.00 2.52
3803 4260 0.889994 GGCATGGCATTGTGTGAGAA 59.110 50.000 15.47 0.00 0.00 2.87
3804 4261 0.251253 TGGCATGGCATTGTGTGAGA 60.251 50.000 19.43 0.00 0.00 3.27
3805 4262 0.604073 TTGGCATGGCATTGTGTGAG 59.396 50.000 23.96 0.00 0.00 3.51
3806 4263 0.317799 GTTGGCATGGCATTGTGTGA 59.682 50.000 23.96 2.73 0.00 3.58
3807 4264 0.671163 GGTTGGCATGGCATTGTGTG 60.671 55.000 23.96 0.00 0.00 3.82
3808 4265 0.832983 AGGTTGGCATGGCATTGTGT 60.833 50.000 23.96 3.60 0.00 3.72
3809 4266 0.390603 CAGGTTGGCATGGCATTGTG 60.391 55.000 23.96 15.63 0.00 3.33
3810 4267 0.542467 TCAGGTTGGCATGGCATTGT 60.542 50.000 23.96 7.36 0.00 2.71
3811 4268 0.174845 CTCAGGTTGGCATGGCATTG 59.825 55.000 23.96 19.97 0.00 2.82
3812 4269 0.974010 CCTCAGGTTGGCATGGCATT 60.974 55.000 23.96 9.13 0.00 3.56
3813 4270 1.380785 CCTCAGGTTGGCATGGCAT 60.381 57.895 23.96 5.26 0.00 4.40
3814 4271 2.036098 CCTCAGGTTGGCATGGCA 59.964 61.111 19.43 19.43 0.00 4.92
3815 4272 2.757099 CCCTCAGGTTGGCATGGC 60.757 66.667 13.29 13.29 0.00 4.40
3816 4273 2.043652 CCCCTCAGGTTGGCATGG 60.044 66.667 0.00 0.00 0.00 3.66
3825 4282 0.623324 TGTATCCCCAACCCCTCAGG 60.623 60.000 0.00 0.00 43.78 3.86
3826 4283 1.522900 ATGTATCCCCAACCCCTCAG 58.477 55.000 0.00 0.00 0.00 3.35
3827 4284 2.021441 AGTATGTATCCCCAACCCCTCA 60.021 50.000 0.00 0.00 0.00 3.86
3828 4285 2.702748 AGTATGTATCCCCAACCCCTC 58.297 52.381 0.00 0.00 0.00 4.30
3829 4286 2.910360 AGTATGTATCCCCAACCCCT 57.090 50.000 0.00 0.00 0.00 4.79
3830 4287 5.191124 CCTATAAGTATGTATCCCCAACCCC 59.809 48.000 0.00 0.00 0.00 4.95
3831 4288 5.338953 GCCTATAAGTATGTATCCCCAACCC 60.339 48.000 0.00 0.00 0.00 4.11
3832 4289 5.487845 AGCCTATAAGTATGTATCCCCAACC 59.512 44.000 0.00 0.00 0.00 3.77
3833 4290 6.407202 CAGCCTATAAGTATGTATCCCCAAC 58.593 44.000 0.00 0.00 0.00 3.77
3834 4291 5.045869 GCAGCCTATAAGTATGTATCCCCAA 60.046 44.000 0.00 0.00 0.00 4.12
3835 4292 4.469945 GCAGCCTATAAGTATGTATCCCCA 59.530 45.833 0.00 0.00 0.00 4.96
3836 4293 4.717280 AGCAGCCTATAAGTATGTATCCCC 59.283 45.833 0.00 0.00 0.00 4.81
3837 4294 5.941555 AGCAGCCTATAAGTATGTATCCC 57.058 43.478 0.00 0.00 0.00 3.85
3838 4295 6.508777 GCTAGCAGCCTATAAGTATGTATCC 58.491 44.000 10.63 0.00 34.48 2.59
3857 4314 3.079237 GCATATGCTTGGCTGGCTAGC 62.079 57.143 25.85 25.85 42.80 3.42
3858 4315 0.879765 GCATATGCTTGGCTGGCTAG 59.120 55.000 20.64 8.24 38.21 3.42
3859 4316 3.025924 GCATATGCTTGGCTGGCTA 57.974 52.632 20.64 0.00 38.21 3.93
3860 4317 3.851955 GCATATGCTTGGCTGGCT 58.148 55.556 20.64 0.00 38.21 4.75


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

AutoCloner maintained by Alex Coulton.