Multiple sequence alignment - TraesCS2A01G383600

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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 TraesCS2A01G383600 chr2A 100.000 4148 0 0 1 4148 628581526 628585673 0.000000e+00 7661.0
1 TraesCS2A01G383600 chr2A 87.965 457 44 3 1001 1453 115430361 115430810 2.840000e-146 529.0
2 TraesCS2A01G383600 chr2A 84.717 530 60 13 1448 1976 115430834 115431343 1.030000e-140 510.0
3 TraesCS2A01G383600 chr2A 91.775 231 14 3 3853 4078 735757244 735757014 2.410000e-82 316.0
4 TraesCS2A01G383600 chr2A 86.869 99 6 4 2113 2211 80987387 80987296 2.040000e-18 104.0
5 TraesCS2A01G383600 chr2D 93.889 1440 63 10 1968 3390 484328341 484329772 0.000000e+00 2148.0
6 TraesCS2A01G383600 chr2D 91.910 754 39 10 692 1444 484326585 484327317 0.000000e+00 1035.0
7 TraesCS2A01G383600 chr2D 92.243 477 31 3 1501 1975 484327318 484327790 0.000000e+00 671.0
8 TraesCS2A01G383600 chr2D 83.221 596 67 13 1001 1572 640333819 640334405 2.210000e-142 516.0
9 TraesCS2A01G383600 chr2D 95.062 243 8 3 3615 3854 484329860 484330101 3.030000e-101 379.0
10 TraesCS2A01G383600 chr2D 90.811 185 13 4 3438 3620 56541177 56540995 1.150000e-60 244.0
11 TraesCS2A01G383600 chr2D 87.097 93 4 5 2115 2207 590342335 590342251 9.490000e-17 99.0
12 TraesCS2A01G383600 chr2D 85.393 89 9 2 2127 2215 8781490 8781406 5.710000e-14 89.8
13 TraesCS2A01G383600 chr2B 91.655 1462 74 18 692 2142 569016834 569018258 0.000000e+00 1980.0
14 TraesCS2A01G383600 chr2B 94.874 1190 39 6 2223 3390 569018256 569019445 0.000000e+00 1840.0
15 TraesCS2A01G383600 chr2B 90.625 128 10 2 3600 3726 569020064 569020190 7.130000e-38 169.0
16 TraesCS2A01G383600 chr2B 88.298 94 5 4 2115 2208 715343132 715343045 1.580000e-19 108.0
17 TraesCS2A01G383600 chr2B 96.721 61 2 0 3385 3445 569019464 569019524 7.340000e-18 102.0
18 TraesCS2A01G383600 chr7A 98.310 710 12 0 1 710 670031927 670032636 0.000000e+00 1245.0
19 TraesCS2A01G383600 chr7A 83.960 1010 101 26 1001 1976 611767719 611768701 0.000000e+00 911.0
20 TraesCS2A01G383600 chr7A 91.416 233 16 2 3850 4078 671404601 671404833 2.410000e-82 316.0
21 TraesCS2A01G383600 chr7A 90.960 177 12 4 3460 3633 213836234 213836059 6.930000e-58 235.0
22 TraesCS2A01G383600 chr7A 93.333 90 6 0 4059 4148 133934013 133934102 2.600000e-27 134.0
23 TraesCS2A01G383600 chr6A 98.135 697 11 2 1 697 49140444 49141138 0.000000e+00 1214.0
24 TraesCS2A01G383600 chr6A 97.550 694 15 2 1 694 49137698 49138389 0.000000e+00 1186.0
25 TraesCS2A01G383600 chr6A 97.550 694 15 2 1 694 49139071 49139762 0.000000e+00 1186.0
26 TraesCS2A01G383600 chr6A 92.576 229 13 2 3854 4078 359051623 359051395 4.000000e-85 326.0
27 TraesCS2A01G383600 chr6A 91.176 136 12 0 2682 2817 421754023 421753888 7.080000e-43 185.0
28 TraesCS2A01G383600 chr6A 98.718 78 0 1 4072 4148 571036433 571036510 2.010000e-28 137.0
29 TraesCS2A01G383600 chr6A 97.468 79 2 0 4070 4148 410575445 410575523 7.230000e-28 135.0
30 TraesCS2A01G383600 chr6A 96.296 81 2 1 4069 4148 104306954 104307034 9.360000e-27 132.0
31 TraesCS2A01G383600 chr6A 94.048 84 5 0 4065 4148 570032740 570032823 1.210000e-25 128.0
32 TraesCS2A01G383600 chr6A 86.869 99 6 4 2113 2211 551840521 551840430 2.040000e-18 104.0
33 TraesCS2A01G383600 chr5B 97.977 692 11 3 3 693 480747107 480746418 0.000000e+00 1197.0
34 TraesCS2A01G383600 chr5B 92.174 230 14 2 3853 4078 90506562 90506791 5.170000e-84 322.0
35 TraesCS2A01G383600 chr5B 94.048 168 9 1 3456 3622 595395321 595395488 1.910000e-63 254.0
36 TraesCS2A01G383600 chr3B 97.403 693 18 0 1 693 807806638 807807330 0.000000e+00 1181.0
37 TraesCS2A01G383600 chr3B 91.819 709 44 2 2 697 77702747 77703454 0.000000e+00 976.0
38 TraesCS2A01G383600 chr3B 85.094 530 57 14 1448 1976 71455426 71454918 4.750000e-144 521.0
39 TraesCS2A01G383600 chr3B 94.545 165 7 2 3459 3622 243784206 243784043 1.910000e-63 254.0
40 TraesCS2A01G383600 chr3B 91.813 171 12 2 3460 3629 524326293 524326124 1.930000e-58 237.0
41 TraesCS2A01G383600 chr3B 90.449 178 14 3 3460 3635 505013354 505013530 8.970000e-57 231.0
42 TraesCS2A01G383600 chr7B 91.445 713 40 9 1 696 290954338 290953630 0.000000e+00 959.0
43 TraesCS2A01G383600 chr7B 91.739 230 15 2 3853 4078 51911020 51911249 2.410000e-82 316.0
44 TraesCS2A01G383600 chr7B 91.429 175 13 2 3460 3633 647129019 647128846 5.360000e-59 239.0
45 TraesCS2A01G383600 chr7B 86.420 81 7 1 2132 2212 634299298 634299374 7.390000e-13 86.1
46 TraesCS2A01G383600 chr1B 91.210 694 53 6 1 692 97369853 97370540 0.000000e+00 937.0
47 TraesCS2A01G383600 chr1B 90.544 698 57 7 1 696 636492543 636491853 0.000000e+00 915.0
48 TraesCS2A01G383600 chr1B 83.661 1016 98 32 1001 1976 93950281 93951268 0.000000e+00 894.0
49 TraesCS2A01G383600 chr1B 86.133 512 46 7 988 1496 76951302 76951791 2.840000e-146 529.0
50 TraesCS2A01G383600 chr1B 95.152 165 7 1 3458 3621 183877363 183877199 4.110000e-65 259.0
51 TraesCS2A01G383600 chr1B 86.905 84 7 2 2127 2210 30728218 30728297 1.590000e-14 91.6
52 TraesCS2A01G383600 chr4B 92.101 671 38 7 34 692 142427041 142426374 0.000000e+00 931.0
53 TraesCS2A01G383600 chr4B 92.268 582 32 2 126 694 604143942 604144523 0.000000e+00 813.0
54 TraesCS2A01G383600 chr4B 89.888 178 17 1 3457 3633 83144084 83144261 1.160000e-55 228.0
55 TraesCS2A01G383600 chr7D 88.121 463 46 9 1448 1908 511057367 511057822 3.650000e-150 542.0
56 TraesCS2A01G383600 chr7D 87.555 458 45 4 1001 1453 511056893 511057343 1.710000e-143 520.0
57 TraesCS2A01G383600 chr7D 84.906 530 59 13 1448 1976 580167087 580166578 2.210000e-142 516.0
58 TraesCS2A01G383600 chr7D 85.567 291 32 2 1167 1453 580167395 580167111 3.140000e-76 296.0
59 TraesCS2A01G383600 chr7D 94.012 167 9 1 3460 3625 414094772 414094938 6.880000e-63 252.0
60 TraesCS2A01G383600 chr7D 91.111 180 11 4 3457 3633 171308154 171307977 5.360000e-59 239.0
61 TraesCS2A01G383600 chr6B 85.283 530 56 14 1448 1976 182642323 182641815 1.020000e-145 527.0
62 TraesCS2A01G383600 chr6B 87.309 457 48 2 1001 1453 182642797 182642347 7.950000e-142 514.0
63 TraesCS2A01G383600 chr6B 91.176 136 12 0 2682 2817 461334125 461334260 7.080000e-43 185.0
64 TraesCS2A01G383600 chr6B 88.095 84 6 2 2127 2210 162181185 162181264 3.410000e-16 97.1
65 TraesCS2A01G383600 chr4A 91.213 239 15 4 3846 4078 683915603 683915841 1.860000e-83 320.0
66 TraesCS2A01G383600 chr4A 91.739 230 15 2 3853 4078 605057870 605057641 2.410000e-82 316.0
67 TraesCS2A01G383600 chr5A 91.739 230 15 2 3853 4078 121639462 121639691 2.410000e-82 316.0
68 TraesCS2A01G383600 chr5A 86.869 99 6 4 2113 2211 5695995 5695904 2.040000e-18 104.0
69 TraesCS2A01G383600 chr5A 86.869 99 6 4 2113 2211 493820312 493820221 2.040000e-18 104.0
70 TraesCS2A01G383600 chr3A 91.739 230 15 2 3853 4078 197848038 197847809 2.410000e-82 316.0
71 TraesCS2A01G383600 chr3A 97.468 79 0 2 4072 4148 24049228 24049306 2.600000e-27 134.0
72 TraesCS2A01G383600 chr3A 93.333 90 6 0 4059 4148 739283178 739283267 2.600000e-27 134.0
73 TraesCS2A01G383600 chr3D 94.186 172 8 2 3456 3626 410670059 410670229 1.140000e-65 261.0
74 TraesCS2A01G383600 chr3D 92.982 171 10 2 3458 3627 397162708 397162539 8.900000e-62 248.0
75 TraesCS2A01G383600 chr3D 91.379 174 11 3 3459 3629 486424950 486424778 6.930000e-58 235.0
76 TraesCS2A01G383600 chr6D 91.209 182 14 2 3458 3637 422936402 422936583 3.200000e-61 246.0
77 TraesCS2A01G383600 chr6D 76.749 486 75 29 2682 3142 296194582 296194110 1.930000e-58 237.0
78 TraesCS2A01G383600 chr6D 84.906 106 11 4 2106 2210 105820674 105820775 7.340000e-18 102.0
79 TraesCS2A01G383600 chr6D 82.692 104 9 6 2111 2212 206553861 206553957 2.660000e-12 84.2
80 TraesCS2A01G383600 chr6D 85.366 82 8 2 2132 2213 53672123 53672046 9.560000e-12 82.4
81 TraesCS2A01G383600 chr6D 90.385 52 4 1 2168 2218 158568998 158568947 2.680000e-07 67.6
82 TraesCS2A01G383600 chr6D 89.583 48 2 2 2116 2163 8565635 8565591 1.610000e-04 58.4
83 TraesCS2A01G383600 chr5D 92.090 177 11 3 3457 3631 539916016 539915841 3.200000e-61 246.0
84 TraesCS2A01G383600 chr5D 85.714 84 8 2 2132 2215 37920320 37920399 7.390000e-13 86.1
85 TraesCS2A01G383600 chr1A 98.667 75 1 0 4074 4148 382255919 382255993 2.600000e-27 134.0
86 TraesCS2A01G383600 chr1A 96.250 80 2 1 4069 4148 363450746 363450824 3.370000e-26 130.0
87 TraesCS2A01G383600 chr1A 86.869 99 6 4 2110 2208 478362854 478362945 2.040000e-18 104.0
88 TraesCS2A01G383600 chr1A 85.859 99 7 4 2110 2208 146184618 146184709 9.490000e-17 99.0
89 TraesCS2A01G383600 chr4D 90.789 76 3 1 2132 2207 489181780 489181709 9.490000e-17 99.0
90 TraesCS2A01G383600 chr4D 81.308 107 13 4 2115 2221 9996470 9996371 3.440000e-11 80.5
91 TraesCS2A01G383600 chr4D 82.143 84 11 2 2127 2210 18771322 18771243 7.440000e-08 69.4
92 TraesCS2A01G383600 chr4D 79.245 106 14 5 2105 2210 30415632 30415729 2.680000e-07 67.6
93 TraesCS2A01G383600 chr1D 85.714 84 8 2 2132 2215 477587744 477587665 7.390000e-13 86.1
94 TraesCS2A01G383600 chr1D 86.076 79 7 3 2132 2210 466362994 466363068 9.560000e-12 82.4
95 TraesCS2A01G383600 chr1D 96.875 32 0 1 2180 2210 200211806 200211775 7.000000e-03 52.8
96 TraesCS2A01G383600 chrUn 84.270 89 3 6 2127 2212 134238934 134239014 4.450000e-10 76.8
97 TraesCS2A01G383600 chrUn 100.000 29 0 0 2132 2160 85641962 85641934 2.000000e-03 54.7


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 TraesCS2A01G383600 chr2A 628581526 628585673 4147 False 7661.000000 7661 100.00000 1 4148 1 chr2A.!!$F1 4147
1 TraesCS2A01G383600 chr2A 115430361 115431343 982 False 519.500000 529 86.34100 1001 1976 2 chr2A.!!$F2 975
2 TraesCS2A01G383600 chr2D 484326585 484330101 3516 False 1058.250000 2148 93.27600 692 3854 4 chr2D.!!$F2 3162
3 TraesCS2A01G383600 chr2D 640333819 640334405 586 False 516.000000 516 83.22100 1001 1572 1 chr2D.!!$F1 571
4 TraesCS2A01G383600 chr2B 569016834 569020190 3356 False 1022.750000 1980 93.46875 692 3726 4 chr2B.!!$F1 3034
5 TraesCS2A01G383600 chr7A 670031927 670032636 709 False 1245.000000 1245 98.31000 1 710 1 chr7A.!!$F3 709
6 TraesCS2A01G383600 chr7A 611767719 611768701 982 False 911.000000 911 83.96000 1001 1976 1 chr7A.!!$F2 975
7 TraesCS2A01G383600 chr6A 49137698 49141138 3440 False 1195.333333 1214 97.74500 1 697 3 chr6A.!!$F5 696
8 TraesCS2A01G383600 chr5B 480746418 480747107 689 True 1197.000000 1197 97.97700 3 693 1 chr5B.!!$R1 690
9 TraesCS2A01G383600 chr3B 807806638 807807330 692 False 1181.000000 1181 97.40300 1 693 1 chr3B.!!$F3 692
10 TraesCS2A01G383600 chr3B 77702747 77703454 707 False 976.000000 976 91.81900 2 697 1 chr3B.!!$F1 695
11 TraesCS2A01G383600 chr3B 71454918 71455426 508 True 521.000000 521 85.09400 1448 1976 1 chr3B.!!$R1 528
12 TraesCS2A01G383600 chr7B 290953630 290954338 708 True 959.000000 959 91.44500 1 696 1 chr7B.!!$R1 695
13 TraesCS2A01G383600 chr1B 97369853 97370540 687 False 937.000000 937 91.21000 1 692 1 chr1B.!!$F4 691
14 TraesCS2A01G383600 chr1B 636491853 636492543 690 True 915.000000 915 90.54400 1 696 1 chr1B.!!$R2 695
15 TraesCS2A01G383600 chr1B 93950281 93951268 987 False 894.000000 894 83.66100 1001 1976 1 chr1B.!!$F3 975
16 TraesCS2A01G383600 chr4B 142426374 142427041 667 True 931.000000 931 92.10100 34 692 1 chr4B.!!$R1 658
17 TraesCS2A01G383600 chr4B 604143942 604144523 581 False 813.000000 813 92.26800 126 694 1 chr4B.!!$F2 568
18 TraesCS2A01G383600 chr7D 511056893 511057822 929 False 531.000000 542 87.83800 1001 1908 2 chr7D.!!$F2 907
19 TraesCS2A01G383600 chr7D 580166578 580167395 817 True 406.000000 516 85.23650 1167 1976 2 chr7D.!!$R2 809
20 TraesCS2A01G383600 chr6B 182641815 182642797 982 True 520.500000 527 86.29600 1001 1976 2 chr6B.!!$R1 975

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
869 3638 1.343789 GTCGGCTCTTATAGAACCCCC 59.656 57.143 0.0 0.0 26.41 5.40 F
1694 4511 0.250338 CGGCCCTTTATCTACCCTGC 60.250 60.000 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 5865 1.044231 TTGCAGCATAATGGGCAGGG 61.044 55.0 0.0 0.0 37.59 4.45 R
3158 6557 0.183492 AAAGCTCAACAGTCTGCCCA 59.817 50.0 0.0 0.0 0.00 5.36 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
44 46 2.112815 GGCAATGACGGCACCTACC 61.113 63.158 0.00 0.00 0.00 3.18
866 3635 4.521256 AGATCTGTCGGCTCTTATAGAACC 59.479 45.833 0.00 0.00 0.00 3.62
869 3638 1.343789 GTCGGCTCTTATAGAACCCCC 59.656 57.143 0.00 0.00 26.41 5.40
909 3678 2.423446 GCTACATCCAGCCCCTCG 59.577 66.667 0.00 0.00 35.40 4.63
910 3679 2.134287 GCTACATCCAGCCCCTCGA 61.134 63.158 0.00 0.00 35.40 4.04
1156 3928 1.571773 GGGTGGCCCTGGTGAACTAT 61.572 60.000 0.00 0.00 41.34 2.12
1218 3990 1.416401 TGACCAGAACAGGGTGAGTTC 59.584 52.381 0.00 0.00 44.32 3.01
1232 4004 1.289830 TGAGTTCGATCCCCTTCCCTA 59.710 52.381 0.00 0.00 0.00 3.53
1233 4005 1.964933 GAGTTCGATCCCCTTCCCTAG 59.035 57.143 0.00 0.00 0.00 3.02
1324 4101 6.423905 GCTCAGTTTCATGTTTAGTGTAGACA 59.576 38.462 0.00 0.00 0.00 3.41
1391 4173 4.532126 AGGTGTGGACTTCTGTATGATTCA 59.468 41.667 0.00 0.00 0.00 2.57
1444 4226 6.198687 CAGTGTTTCTGCGATTTCTTGTTAA 58.801 36.000 0.00 0.00 37.36 2.01
1587 4404 7.954788 TTTTACATGCCATTTGAAGTTTACC 57.045 32.000 0.00 0.00 0.00 2.85
1599 4416 4.394729 TGAAGTTTACCCTTGGCAAGTAG 58.605 43.478 24.57 17.73 0.00 2.57
1635 4452 2.093783 GTCAGCGCAGTTATGTTACCAC 59.906 50.000 11.47 0.00 0.00 4.16
1663 4480 9.445786 ACTTGTTTATGTTTTGTATTTGACTCG 57.554 29.630 0.00 0.00 0.00 4.18
1667 4484 9.659830 GTTTATGTTTTGTATTTGACTCGTCTT 57.340 29.630 0.00 0.00 0.00 3.01
1694 4511 0.250338 CGGCCCTTTATCTACCCTGC 60.250 60.000 0.00 0.00 0.00 4.85
1741 4558 1.065401 GCTCACCTGATCAGTCTCGAG 59.935 57.143 21.11 18.78 0.00 4.04
1743 4560 3.536570 CTCACCTGATCAGTCTCGAGTA 58.463 50.000 21.11 0.00 0.00 2.59
1768 4585 2.032680 TGCGGCCTTACCTAAATGTC 57.967 50.000 0.00 0.00 35.61 3.06
1774 4591 4.200092 GGCCTTACCTAAATGTCTTGAGG 58.800 47.826 0.00 0.00 38.81 3.86
1822 4639 7.501559 AGACATGCTATTGCTCAAATATCTGTT 59.498 33.333 0.00 0.00 40.48 3.16
1955 4774 9.458727 TTCTTTTTCTTCTTCTCATGATAGCAT 57.541 29.630 0.00 0.00 34.29 3.79
1991 5368 9.448294 GTTCTACTACTGTTTCTTGGTATATCG 57.552 37.037 0.00 0.00 0.00 2.92
2102 5479 8.682128 TCTGTTGGCGAATCATATTTTTAAAC 57.318 30.769 0.00 0.00 0.00 2.01
2123 5500 6.509418 AACGCAACATAAATTGTACTCCAT 57.491 33.333 0.00 0.00 37.68 3.41
2124 5501 6.119144 ACGCAACATAAATTGTACTCCATC 57.881 37.500 0.00 0.00 37.68 3.51
2125 5502 5.880332 ACGCAACATAAATTGTACTCCATCT 59.120 36.000 0.00 0.00 37.68 2.90
2130 5507 7.559590 ACATAAATTGTACTCCATCTTCTGC 57.440 36.000 0.00 0.00 36.57 4.26
2145 5522 9.547753 TCCATCTTCTGCAAACTAATATAAGAC 57.452 33.333 0.00 0.00 0.00 3.01
2221 5598 6.377712 ACAGAGGGAGTATTAGTTACAGTGTC 59.622 42.308 0.00 0.00 32.87 3.67
2324 5704 8.154649 TCTTCTCTGAGTTGGTGTTTAAAATC 57.845 34.615 4.32 0.00 0.00 2.17
2339 5720 7.490079 GTGTTTAAAATCGTTCTTTGACCCTTT 59.510 33.333 0.00 0.00 0.00 3.11
2347 5728 4.686554 CGTTCTTTGACCCTTTAGTCTCAG 59.313 45.833 0.00 0.00 37.66 3.35
2479 5865 4.567959 GCCCATTATGCTTGATGTCAAAAC 59.432 41.667 4.05 0.00 35.15 2.43
2505 5894 3.052036 CCCATTATGCTGCAAATAACGC 58.948 45.455 6.36 0.00 0.00 4.84
2570 5959 8.668353 TCTGCTTTTGATATGTGTTGATACTTC 58.332 33.333 0.00 0.00 0.00 3.01
2587 5976 6.808212 TGATACTTCTTTAACCGTTACCTTCG 59.192 38.462 0.00 0.00 0.00 3.79
2595 5984 1.742268 ACCGTTACCTTCGCTAGAGTC 59.258 52.381 0.00 0.00 0.00 3.36
3158 6557 3.341823 CTGCTGCTTAGATCACTTTGGT 58.658 45.455 0.00 0.00 0.00 3.67
3344 6743 9.625747 TCTGTTATTTGTGATGCCATCTAAATA 57.374 29.630 16.59 16.59 32.84 1.40
3354 6753 3.655291 TGCCATCTAAATACATGGGCCTA 59.345 43.478 4.53 0.00 40.16 3.93
3377 6778 1.656095 GCTTACTGTTAGTCTGCTGCG 59.344 52.381 0.00 0.00 0.00 5.18
3395 6822 0.322322 CGTGTTTACCCCAGTGGCTA 59.678 55.000 2.61 0.00 37.83 3.93
3413 6840 2.038033 GCTACACCGGGCATTATTCCTA 59.962 50.000 6.32 0.00 0.00 2.94
3447 6874 8.499403 TTGTTCCAATCGATCATGTTTATGTA 57.501 30.769 0.00 0.00 35.73 2.29
3448 6875 8.675705 TGTTCCAATCGATCATGTTTATGTAT 57.324 30.769 0.00 0.00 35.73 2.29
3480 6907 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3507 6934 7.777095 AGTCTTTGTAGAGATTCCACTATGAC 58.223 38.462 0.00 0.00 0.00 3.06
3508 6935 6.981559 GTCTTTGTAGAGATTCCACTATGACC 59.018 42.308 0.00 0.00 0.00 4.02
3509 6936 6.667848 TCTTTGTAGAGATTCCACTATGACCA 59.332 38.462 0.00 0.00 0.00 4.02
3510 6937 5.854010 TGTAGAGATTCCACTATGACCAC 57.146 43.478 0.00 0.00 0.00 4.16
3511 6938 5.269189 TGTAGAGATTCCACTATGACCACA 58.731 41.667 0.00 0.00 0.00 4.17
3513 6940 7.066781 TGTAGAGATTCCACTATGACCACATA 58.933 38.462 0.00 0.00 37.87 2.29
3515 6942 5.010112 AGAGATTCCACTATGACCACATACG 59.990 44.000 0.00 0.00 37.87 3.06
3516 6943 3.812156 TTCCACTATGACCACATACGG 57.188 47.619 0.00 0.00 37.87 4.02
3517 6944 3.021177 TCCACTATGACCACATACGGA 57.979 47.619 0.00 0.00 37.87 4.69
3518 6945 3.572642 TCCACTATGACCACATACGGAT 58.427 45.455 0.00 0.00 37.87 4.18
3519 6946 3.572682 TCCACTATGACCACATACGGATC 59.427 47.826 0.00 0.00 37.87 3.36
3541 7072 9.107177 GGATCTATATAGATGCATTTTGGAGTG 57.893 37.037 29.37 0.00 46.50 3.51
3542 7073 9.664332 GATCTATATAGATGCATTTTGGAGTGT 57.336 33.333 26.47 0.98 42.79 3.55
3550 7249 5.627499 TGCATTTTGGAGTGTAGATTCAC 57.373 39.130 0.00 0.00 38.46 3.18
3562 7261 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
3569 7268 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
3570 7269 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
3571 7270 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
3572 7271 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
3573 7272 5.581085 ACTCATTTTGCTTCGTATGTAGTCC 59.419 40.000 0.00 0.00 0.00 3.85
3574 7273 5.483811 TCATTTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
3575 7274 6.112734 TCATTTTGCTTCGTATGTAGTCCAT 58.887 36.000 0.00 0.00 37.58 3.41
3576 7275 7.269316 TCATTTTGCTTCGTATGTAGTCCATA 58.731 34.615 0.00 0.00 34.86 2.74
3577 7276 7.438160 TCATTTTGCTTCGTATGTAGTCCATAG 59.562 37.037 0.00 0.00 36.71 2.23
3578 7277 5.847111 TTGCTTCGTATGTAGTCCATAGT 57.153 39.130 0.00 0.00 36.71 2.12
3584 7283 7.438459 GCTTCGTATGTAGTCCATAGTGAAATT 59.562 37.037 0.00 0.00 36.71 1.82
3629 7462 0.107643 GGAGGGAGTAGATGGCAAGC 59.892 60.000 0.00 0.00 0.00 4.01
3753 7588 4.196193 TGCGTGCTTTAGCTTTATATGGT 58.804 39.130 0.00 0.00 42.66 3.55
3758 7593 6.183360 CGTGCTTTAGCTTTATATGGTTGGAA 60.183 38.462 0.00 0.00 42.66 3.53
3786 7621 7.455058 TGGTAAAGTAAGATAGAACTTGCCAA 58.545 34.615 8.41 0.00 38.00 4.52
3856 7691 6.824305 ACTCAACTTTGTCCATCAATAAGG 57.176 37.500 0.00 0.00 35.84 2.69
3857 7692 5.183904 ACTCAACTTTGTCCATCAATAAGGC 59.816 40.000 0.00 0.00 35.84 4.35
3858 7693 4.462483 TCAACTTTGTCCATCAATAAGGCC 59.538 41.667 0.00 0.00 35.84 5.19
3859 7694 4.322057 ACTTTGTCCATCAATAAGGCCT 57.678 40.909 0.00 0.00 35.84 5.19
3860 7695 4.273318 ACTTTGTCCATCAATAAGGCCTC 58.727 43.478 5.23 0.00 35.84 4.70
3861 7696 3.297134 TTGTCCATCAATAAGGCCTCC 57.703 47.619 5.23 0.00 0.00 4.30
3862 7697 2.492025 TGTCCATCAATAAGGCCTCCT 58.508 47.619 5.23 0.00 33.87 3.69
3863 7698 2.852449 TGTCCATCAATAAGGCCTCCTT 59.148 45.455 5.23 0.00 46.63 3.36
3864 7699 3.269381 TGTCCATCAATAAGGCCTCCTTT 59.731 43.478 5.23 0.00 41.69 3.11
3865 7700 3.633986 GTCCATCAATAAGGCCTCCTTTG 59.366 47.826 5.23 10.82 41.69 2.77
3866 7701 2.961062 CCATCAATAAGGCCTCCTTTGG 59.039 50.000 5.23 5.32 41.69 3.28
3867 7702 3.628257 CCATCAATAAGGCCTCCTTTGGT 60.628 47.826 5.23 3.75 41.69 3.67
3868 7703 3.825908 TCAATAAGGCCTCCTTTGGTT 57.174 42.857 5.23 0.00 41.69 3.67
3869 7704 3.697166 TCAATAAGGCCTCCTTTGGTTC 58.303 45.455 5.23 0.00 41.69 3.62
3870 7705 3.075283 TCAATAAGGCCTCCTTTGGTTCA 59.925 43.478 5.23 0.00 41.69 3.18
3871 7706 4.026052 CAATAAGGCCTCCTTTGGTTCAT 58.974 43.478 5.23 0.00 41.69 2.57
3872 7707 5.044476 TCAATAAGGCCTCCTTTGGTTCATA 60.044 40.000 5.23 0.00 41.69 2.15
3873 7708 3.372440 AAGGCCTCCTTTGGTTCATAG 57.628 47.619 5.23 0.00 41.69 2.23
3874 7709 1.566231 AGGCCTCCTTTGGTTCATAGG 59.434 52.381 0.00 0.00 34.61 2.57
3875 7710 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
3876 7711 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.00 39.94 3.24
3877 7712 3.373110 GGCCTCCTTTGGTTCATAGGATT 60.373 47.826 0.00 0.00 39.94 3.01
3878 7713 4.141251 GGCCTCCTTTGGTTCATAGGATTA 60.141 45.833 0.00 0.00 39.94 1.75
3879 7714 5.445964 GCCTCCTTTGGTTCATAGGATTAA 58.554 41.667 7.38 0.00 39.94 1.40
3880 7715 5.891551 GCCTCCTTTGGTTCATAGGATTAAA 59.108 40.000 7.38 0.00 39.94 1.52
3881 7716 6.379988 GCCTCCTTTGGTTCATAGGATTAAAA 59.620 38.462 7.38 0.00 39.94 1.52
3882 7717 7.093509 GCCTCCTTTGGTTCATAGGATTAAAAA 60.094 37.037 7.38 0.00 39.94 1.94
3883 7718 8.981659 CCTCCTTTGGTTCATAGGATTAAAAAT 58.018 33.333 7.38 0.00 39.94 1.82
3885 7720 9.540538 TCCTTTGGTTCATAGGATTAAAAATCA 57.459 29.630 3.54 0.00 36.84 2.57
3903 7738 8.451908 AAAAATCATAGGAATAGGAAAGTCGG 57.548 34.615 0.00 0.00 0.00 4.79
3904 7739 6.996180 AATCATAGGAATAGGAAAGTCGGA 57.004 37.500 0.00 0.00 0.00 4.55
3905 7740 6.996180 ATCATAGGAATAGGAAAGTCGGAA 57.004 37.500 0.00 0.00 0.00 4.30
3906 7741 6.801718 TCATAGGAATAGGAAAGTCGGAAA 57.198 37.500 0.00 0.00 0.00 3.13
3907 7742 7.374975 TCATAGGAATAGGAAAGTCGGAAAT 57.625 36.000 0.00 0.00 0.00 2.17
3908 7743 7.217200 TCATAGGAATAGGAAAGTCGGAAATG 58.783 38.462 0.00 0.00 0.00 2.32
3909 7744 5.693769 AGGAATAGGAAAGTCGGAAATGA 57.306 39.130 0.00 0.00 0.00 2.57
3910 7745 5.675538 AGGAATAGGAAAGTCGGAAATGAG 58.324 41.667 0.00 0.00 0.00 2.90
3911 7746 5.425539 AGGAATAGGAAAGTCGGAAATGAGA 59.574 40.000 0.00 0.00 0.00 3.27
3912 7747 6.100424 AGGAATAGGAAAGTCGGAAATGAGAT 59.900 38.462 0.00 0.00 0.00 2.75
3913 7748 7.290248 AGGAATAGGAAAGTCGGAAATGAGATA 59.710 37.037 0.00 0.00 0.00 1.98
3914 7749 7.931948 GGAATAGGAAAGTCGGAAATGAGATAA 59.068 37.037 0.00 0.00 0.00 1.75
3915 7750 8.664211 AATAGGAAAGTCGGAAATGAGATAAC 57.336 34.615 0.00 0.00 0.00 1.89
3916 7751 6.049955 AGGAAAGTCGGAAATGAGATAACA 57.950 37.500 0.00 0.00 0.00 2.41
3917 7752 6.653989 AGGAAAGTCGGAAATGAGATAACAT 58.346 36.000 0.00 0.00 0.00 2.71
3918 7753 6.540189 AGGAAAGTCGGAAATGAGATAACATG 59.460 38.462 0.00 0.00 0.00 3.21
3919 7754 5.741388 AAGTCGGAAATGAGATAACATGC 57.259 39.130 0.00 0.00 0.00 4.06
3920 7755 4.769688 AGTCGGAAATGAGATAACATGCA 58.230 39.130 0.00 0.00 0.00 3.96
3921 7756 5.371526 AGTCGGAAATGAGATAACATGCAT 58.628 37.500 0.00 0.00 0.00 3.96
3922 7757 5.468072 AGTCGGAAATGAGATAACATGCATC 59.532 40.000 0.00 0.00 0.00 3.91
3923 7758 5.468072 GTCGGAAATGAGATAACATGCATCT 59.532 40.000 9.57 9.57 35.43 2.90
3924 7759 5.698089 TCGGAAATGAGATAACATGCATCTC 59.302 40.000 22.40 22.40 45.76 2.75
3933 7768 8.789825 GAGATAACATGCATCTCAAATCCTAT 57.210 34.615 23.49 0.00 45.17 2.57
3934 7769 8.563123 AGATAACATGCATCTCAAATCCTATG 57.437 34.615 0.00 0.00 0.00 2.23
3935 7770 5.449107 AACATGCATCTCAAATCCTATGC 57.551 39.130 0.00 0.00 43.92 3.14
3970 7805 4.591321 AGGAGATGCCCTTTAATTCACA 57.409 40.909 0.00 0.00 37.37 3.58
3971 7806 4.273318 AGGAGATGCCCTTTAATTCACAC 58.727 43.478 0.00 0.00 37.37 3.82
3972 7807 3.381590 GGAGATGCCCTTTAATTCACACC 59.618 47.826 0.00 0.00 0.00 4.16
3973 7808 4.016444 GAGATGCCCTTTAATTCACACCA 58.984 43.478 0.00 0.00 0.00 4.17
3974 7809 4.613437 AGATGCCCTTTAATTCACACCAT 58.387 39.130 0.00 0.00 0.00 3.55
3975 7810 5.765510 AGATGCCCTTTAATTCACACCATA 58.234 37.500 0.00 0.00 0.00 2.74
3976 7811 6.194235 AGATGCCCTTTAATTCACACCATAA 58.806 36.000 0.00 0.00 0.00 1.90
3977 7812 5.913137 TGCCCTTTAATTCACACCATAAG 57.087 39.130 0.00 0.00 0.00 1.73
3978 7813 5.575157 TGCCCTTTAATTCACACCATAAGA 58.425 37.500 0.00 0.00 0.00 2.10
3979 7814 6.194235 TGCCCTTTAATTCACACCATAAGAT 58.806 36.000 0.00 0.00 0.00 2.40
3980 7815 6.667414 TGCCCTTTAATTCACACCATAAGATT 59.333 34.615 0.00 0.00 0.00 2.40
3981 7816 7.180051 TGCCCTTTAATTCACACCATAAGATTT 59.820 33.333 0.00 0.00 0.00 2.17
3982 7817 8.040727 GCCCTTTAATTCACACCATAAGATTTT 58.959 33.333 0.00 0.00 0.00 1.82
3983 7818 9.942850 CCCTTTAATTCACACCATAAGATTTTT 57.057 29.630 0.00 0.00 0.00 1.94
4035 7870 9.973661 TTTTTCTATCAAATGTGAAGGATAGGA 57.026 29.630 0.00 0.00 39.61 2.94
4036 7871 9.973661 TTTTCTATCAAATGTGAAGGATAGGAA 57.026 29.630 0.00 0.00 39.61 3.36
4037 7872 9.973661 TTTCTATCAAATGTGAAGGATAGGAAA 57.026 29.630 0.00 0.00 39.61 3.13
4038 7873 9.973661 TTCTATCAAATGTGAAGGATAGGAAAA 57.026 29.630 0.00 0.00 39.61 2.29
4039 7874 9.973661 TCTATCAAATGTGAAGGATAGGAAAAA 57.026 29.630 0.00 0.00 39.61 1.94
4078 7913 6.840780 AGGATTTCATTCCTACAAACCAAG 57.159 37.500 0.00 0.00 44.50 3.61
4079 7914 5.716703 AGGATTTCATTCCTACAAACCAAGG 59.283 40.000 0.00 0.00 44.50 3.61
4080 7915 4.864704 TTTCATTCCTACAAACCAAGGC 57.135 40.909 0.00 0.00 32.55 4.35
4081 7916 2.802719 TCATTCCTACAAACCAAGGCC 58.197 47.619 0.00 0.00 32.55 5.19
4082 7917 2.378547 TCATTCCTACAAACCAAGGCCT 59.621 45.455 0.00 0.00 32.55 5.19
4083 7918 2.579410 TTCCTACAAACCAAGGCCTC 57.421 50.000 5.23 0.00 32.55 4.70
4084 7919 1.742308 TCCTACAAACCAAGGCCTCT 58.258 50.000 5.23 0.00 32.55 3.69
4085 7920 2.062636 TCCTACAAACCAAGGCCTCTT 58.937 47.619 5.23 0.00 32.55 2.85
4086 7921 2.445525 TCCTACAAACCAAGGCCTCTTT 59.554 45.455 5.23 0.88 32.55 2.52
4087 7922 3.117284 TCCTACAAACCAAGGCCTCTTTT 60.117 43.478 5.23 2.67 32.55 2.27
4088 7923 3.005791 CCTACAAACCAAGGCCTCTTTTG 59.994 47.826 22.88 22.88 0.00 2.44
4093 7928 1.703411 CCAAGGCCTCTTTTGGTTCA 58.297 50.000 5.23 0.00 39.18 3.18
4094 7929 2.250924 CCAAGGCCTCTTTTGGTTCAT 58.749 47.619 5.23 0.00 39.18 2.57
4095 7930 3.430453 CCAAGGCCTCTTTTGGTTCATA 58.570 45.455 5.23 0.00 39.18 2.15
4096 7931 3.445096 CCAAGGCCTCTTTTGGTTCATAG 59.555 47.826 5.23 0.00 39.18 2.23
4097 7932 3.372440 AGGCCTCTTTTGGTTCATAGG 57.628 47.619 0.00 0.00 0.00 2.57
4098 7933 2.919602 AGGCCTCTTTTGGTTCATAGGA 59.080 45.455 0.00 0.00 0.00 2.94
4099 7934 3.529319 AGGCCTCTTTTGGTTCATAGGAT 59.471 43.478 0.00 0.00 0.00 3.24
4100 7935 4.726825 AGGCCTCTTTTGGTTCATAGGATA 59.273 41.667 0.00 0.00 0.00 2.59
4101 7936 5.066593 GGCCTCTTTTGGTTCATAGGATAG 58.933 45.833 0.00 0.00 0.00 2.08
4102 7937 5.066593 GCCTCTTTTGGTTCATAGGATAGG 58.933 45.833 0.00 0.00 0.00 2.57
4103 7938 5.163195 GCCTCTTTTGGTTCATAGGATAGGA 60.163 44.000 0.00 0.00 0.00 2.94
4104 7939 6.466470 GCCTCTTTTGGTTCATAGGATAGGAT 60.466 42.308 0.00 0.00 28.27 3.24
4105 7940 7.521669 CCTCTTTTGGTTCATAGGATAGGATT 58.478 38.462 0.00 0.00 28.27 3.01
4106 7941 8.660435 CCTCTTTTGGTTCATAGGATAGGATTA 58.340 37.037 0.00 0.00 28.27 1.75
4113 7948 9.439461 TGGTTCATAGGATAGGATTATCATAGG 57.561 37.037 0.00 0.00 36.37 2.57
4114 7949 9.661954 GGTTCATAGGATAGGATTATCATAGGA 57.338 37.037 0.00 1.09 39.88 2.94
4132 7967 9.621239 ATCATAGGAATAGGAATCTTGTAGGAA 57.379 33.333 0.00 0.00 0.00 3.36
4133 7968 9.447279 TCATAGGAATAGGAATCTTGTAGGAAA 57.553 33.333 0.00 0.00 0.00 3.13
4136 7971 8.337118 AGGAATAGGAATCTTGTAGGAAATGA 57.663 34.615 0.00 0.00 0.00 2.57
4137 7972 8.435982 AGGAATAGGAATCTTGTAGGAAATGAG 58.564 37.037 0.00 0.00 0.00 2.90
4138 7973 8.432805 GGAATAGGAATCTTGTAGGAAATGAGA 58.567 37.037 0.00 0.00 0.00 3.27
4140 7975 9.790344 AATAGGAATCTTGTAGGAAATGAGATG 57.210 33.333 0.00 0.00 0.00 2.90
4141 7976 7.443302 AGGAATCTTGTAGGAAATGAGATGA 57.557 36.000 0.00 0.00 0.00 2.92
4142 7977 7.278875 AGGAATCTTGTAGGAAATGAGATGAC 58.721 38.462 0.00 0.00 0.00 3.06
4143 7978 7.050377 GGAATCTTGTAGGAAATGAGATGACA 58.950 38.462 0.00 0.00 0.00 3.58
4144 7979 7.718753 GGAATCTTGTAGGAAATGAGATGACAT 59.281 37.037 0.00 0.00 0.00 3.06
4145 7980 8.447924 AATCTTGTAGGAAATGAGATGACATG 57.552 34.615 0.00 0.00 0.00 3.21
4146 7981 6.950842 TCTTGTAGGAAATGAGATGACATGT 58.049 36.000 0.00 0.00 0.00 3.21
4147 7982 8.078060 TCTTGTAGGAAATGAGATGACATGTA 57.922 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 2845 0.962489 CACTGACGTCCTCCAAGTCT 59.038 55.000 14.12 0.00 36.01 3.24
611 3377 1.490490 ACAGATCCAATACCACCGCAT 59.510 47.619 0.00 0.00 0.00 4.73
909 3678 2.737830 GCGGCTAGACAGGGGATC 59.262 66.667 0.00 0.00 0.00 3.36
910 3679 2.844839 GGCGGCTAGACAGGGGAT 60.845 66.667 0.00 0.00 0.00 3.85
1083 3855 1.199624 GAGCACAAAAACAAGGCACG 58.800 50.000 0.00 0.00 0.00 5.34
1156 3928 4.077184 CGGCCGTAGTCCTTGCCA 62.077 66.667 19.50 0.00 44.22 4.92
1218 3990 1.049402 GGAACTAGGGAAGGGGATCG 58.951 60.000 0.00 0.00 0.00 3.69
1233 4005 3.383185 AGATCGAGAATGACAGGAGGAAC 59.617 47.826 0.00 0.00 0.00 3.62
1324 4101 0.318762 GGGACACGCAGAGAAGAAGT 59.681 55.000 0.00 0.00 0.00 3.01
1391 4173 3.064820 CCGTGCAGTCACACTTTTACTTT 59.935 43.478 0.00 0.00 43.28 2.66
1404 4186 2.196749 CACTGTGATATCCGTGCAGTC 58.803 52.381 0.32 0.00 38.21 3.51
1540 4355 6.875926 ATCAACTAGCATTTTCAAATTCGC 57.124 33.333 0.00 0.00 0.00 4.70
1663 4480 5.705905 AGATAAAGGGCCGCATATTAAAGAC 59.294 40.000 0.00 0.00 0.00 3.01
1667 4484 5.493809 GGTAGATAAAGGGCCGCATATTAA 58.506 41.667 0.00 0.00 0.00 1.40
1671 4488 1.626825 GGGTAGATAAAGGGCCGCATA 59.373 52.381 0.00 0.00 0.00 3.14
1768 4585 8.443937 GCTGTTTATTTTCAGTAGTACCTCAAG 58.556 37.037 0.00 0.00 34.57 3.02
1774 4591 7.386848 TGTCTGGCTGTTTATTTTCAGTAGTAC 59.613 37.037 0.00 0.00 34.57 2.73
1955 4774 5.984695 ACAGTAGTAGAACAGAGCAATGA 57.015 39.130 0.00 0.00 0.00 2.57
1991 5368 1.444119 TTGCAAACCACGACCTGCTC 61.444 55.000 0.00 0.00 35.78 4.26
2078 5455 7.600039 CGTTTAAAAATATGATTCGCCAACAG 58.400 34.615 0.00 0.00 0.00 3.16
2080 5457 6.034044 TGCGTTTAAAAATATGATTCGCCAAC 59.966 34.615 10.31 0.00 40.29 3.77
2102 5479 6.363577 AGATGGAGTACAATTTATGTTGCG 57.636 37.500 0.00 0.00 43.63 4.85
2203 5580 8.622157 TGAGCTATGACACTGTAACTAATACTC 58.378 37.037 0.00 0.00 35.42 2.59
2245 5622 8.986477 ACAAACATTAGAAAATCATTACCAGC 57.014 30.769 0.00 0.00 0.00 4.85
2282 5659 6.370994 CAGAGAAGATGTTGCAGTAAGTGATT 59.629 38.462 0.00 0.00 0.00 2.57
2302 5679 6.053005 ACGATTTTAAACACCAACTCAGAGA 58.947 36.000 3.79 0.00 0.00 3.10
2324 5704 4.628074 TGAGACTAAAGGGTCAAAGAACG 58.372 43.478 0.00 0.00 38.57 3.95
2347 5728 6.372659 ACATGACATTCCAGATAAACAGTCAC 59.627 38.462 0.00 0.00 37.55 3.67
2479 5865 1.044231 TTGCAGCATAATGGGCAGGG 61.044 55.000 0.00 0.00 37.59 4.45
2505 5894 8.750416 CATTGAGAATGTAGACAATAGAAGTCG 58.250 37.037 0.00 0.00 36.36 4.18
2570 5959 4.737054 TCTAGCGAAGGTAACGGTTAAAG 58.263 43.478 1.47 0.00 41.17 1.85
2800 6189 6.079712 AGTTTAATACCAGCTTCCTCCATT 57.920 37.500 0.00 0.00 0.00 3.16
2856 6252 6.211184 TCAGGATGCCATTTTAAACAGTTGAT 59.789 34.615 0.00 0.00 34.76 2.57
2857 6253 5.538053 TCAGGATGCCATTTTAAACAGTTGA 59.462 36.000 0.00 0.00 34.76 3.18
3158 6557 0.183492 AAAGCTCAACAGTCTGCCCA 59.817 50.000 0.00 0.00 0.00 5.36
3344 6743 1.210478 CAGTAAGCACTAGGCCCATGT 59.790 52.381 0.00 0.00 46.50 3.21
3354 6753 3.862642 GCAGCAGACTAACAGTAAGCACT 60.863 47.826 0.00 0.00 32.51 4.40
3395 6822 2.404559 TCTAGGAATAATGCCCGGTGT 58.595 47.619 0.00 0.00 0.00 4.16
3461 6888 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3462 6889 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3463 6890 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3464 6891 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
3465 6892 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
3480 6907 9.475620 TCATAGTGGAATCTCTACAAAGACTTA 57.524 33.333 0.00 0.00 29.47 2.24
3492 6919 5.223382 CGTATGTGGTCATAGTGGAATCTC 58.777 45.833 0.00 0.00 37.23 2.75
3498 6925 3.574396 AGATCCGTATGTGGTCATAGTGG 59.426 47.826 0.00 0.00 37.23 4.00
3507 6934 7.277174 TGCATCTATATAGATCCGTATGTGG 57.723 40.000 20.31 8.84 40.91 4.17
3508 6935 9.755804 AAATGCATCTATATAGATCCGTATGTG 57.244 33.333 20.31 10.83 40.91 3.21
3511 6938 9.770097 CCAAAATGCATCTATATAGATCCGTAT 57.230 33.333 20.31 13.09 40.91 3.06
3513 6940 7.851228 TCCAAAATGCATCTATATAGATCCGT 58.149 34.615 20.31 11.79 40.91 4.69
3515 6942 9.107177 CACTCCAAAATGCATCTATATAGATCC 57.893 37.037 20.31 13.64 40.91 3.36
3516 6943 9.664332 ACACTCCAAAATGCATCTATATAGATC 57.336 33.333 20.31 15.43 40.91 2.75
3540 7071 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
3541 7072 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
3542 7073 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
3543 7074 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
3544 7075 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
3545 7076 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
3546 7077 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
3550 7249 5.580691 TGGACTACATACGAAGCAAAATGAG 59.419 40.000 0.00 0.00 0.00 2.90
3559 7258 8.873215 AATTTCACTATGGACTACATACGAAG 57.127 34.615 0.00 0.00 41.03 3.79
3562 7261 8.873215 AGAAATTTCACTATGGACTACATACG 57.127 34.615 19.99 0.00 41.03 3.06
3589 7288 7.325694 CCTCCGTTCCTAAATACAAGTCTTTA 58.674 38.462 0.00 0.00 0.00 1.85
3629 7462 1.864711 TGACCGTTTCGAGCTCTTTTG 59.135 47.619 12.85 0.00 0.00 2.44
3753 7588 9.886132 GTTCTATCTTACTTTACCATCTTCCAA 57.114 33.333 0.00 0.00 0.00 3.53
3758 7593 7.988028 GGCAAGTTCTATCTTACTTTACCATCT 59.012 37.037 0.00 0.00 32.50 2.90
3786 7621 4.595538 TGCGTTCGTGCCGGAGTT 62.596 61.111 5.05 0.00 0.00 3.01
3815 7650 8.972262 AGTTGAGTATATACATATGCGTTGAG 57.028 34.615 15.18 0.00 31.71 3.02
3854 7689 1.566231 CCTATGAACCAAAGGAGGCCT 59.434 52.381 3.86 3.86 33.87 5.19
3855 7690 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
3856 7691 3.584733 ATCCTATGAACCAAAGGAGGC 57.415 47.619 0.00 0.00 42.53 4.70
3857 7692 7.954666 TTTTAATCCTATGAACCAAAGGAGG 57.045 36.000 0.00 0.00 42.53 4.30
3859 7694 9.540538 TGATTTTTAATCCTATGAACCAAAGGA 57.459 29.630 0.00 0.00 43.38 3.36
3877 7712 9.555727 CCGACTTTCCTATTCCTATGATTTTTA 57.444 33.333 0.00 0.00 0.00 1.52
3878 7713 8.272173 TCCGACTTTCCTATTCCTATGATTTTT 58.728 33.333 0.00 0.00 0.00 1.94
3879 7714 7.802117 TCCGACTTTCCTATTCCTATGATTTT 58.198 34.615 0.00 0.00 0.00 1.82
3880 7715 7.374975 TCCGACTTTCCTATTCCTATGATTT 57.625 36.000 0.00 0.00 0.00 2.17
3881 7716 6.996180 TCCGACTTTCCTATTCCTATGATT 57.004 37.500 0.00 0.00 0.00 2.57
3882 7717 6.996180 TTCCGACTTTCCTATTCCTATGAT 57.004 37.500 0.00 0.00 0.00 2.45
3883 7718 6.801718 TTTCCGACTTTCCTATTCCTATGA 57.198 37.500 0.00 0.00 0.00 2.15
3884 7719 7.217200 TCATTTCCGACTTTCCTATTCCTATG 58.783 38.462 0.00 0.00 0.00 2.23
3885 7720 7.290248 TCTCATTTCCGACTTTCCTATTCCTAT 59.710 37.037 0.00 0.00 0.00 2.57
3886 7721 6.610020 TCTCATTTCCGACTTTCCTATTCCTA 59.390 38.462 0.00 0.00 0.00 2.94
3887 7722 5.425539 TCTCATTTCCGACTTTCCTATTCCT 59.574 40.000 0.00 0.00 0.00 3.36
3888 7723 5.671493 TCTCATTTCCGACTTTCCTATTCC 58.329 41.667 0.00 0.00 0.00 3.01
3889 7724 8.766151 GTTATCTCATTTCCGACTTTCCTATTC 58.234 37.037 0.00 0.00 0.00 1.75
3890 7725 8.265055 TGTTATCTCATTTCCGACTTTCCTATT 58.735 33.333 0.00 0.00 0.00 1.73
3891 7726 7.792032 TGTTATCTCATTTCCGACTTTCCTAT 58.208 34.615 0.00 0.00 0.00 2.57
3892 7727 7.177832 TGTTATCTCATTTCCGACTTTCCTA 57.822 36.000 0.00 0.00 0.00 2.94
3893 7728 6.049955 TGTTATCTCATTTCCGACTTTCCT 57.950 37.500 0.00 0.00 0.00 3.36
3894 7729 6.719365 CATGTTATCTCATTTCCGACTTTCC 58.281 40.000 0.00 0.00 0.00 3.13
3895 7730 6.183360 TGCATGTTATCTCATTTCCGACTTTC 60.183 38.462 0.00 0.00 0.00 2.62
3896 7731 5.647658 TGCATGTTATCTCATTTCCGACTTT 59.352 36.000 0.00 0.00 0.00 2.66
3897 7732 5.185454 TGCATGTTATCTCATTTCCGACTT 58.815 37.500 0.00 0.00 0.00 3.01
3898 7733 4.769688 TGCATGTTATCTCATTTCCGACT 58.230 39.130 0.00 0.00 0.00 4.18
3899 7734 5.468072 AGATGCATGTTATCTCATTTCCGAC 59.532 40.000 2.46 0.00 29.05 4.79
3900 7735 5.614308 AGATGCATGTTATCTCATTTCCGA 58.386 37.500 2.46 0.00 29.05 4.55
3901 7736 5.924786 GAGATGCATGTTATCTCATTTCCG 58.075 41.667 24.83 0.00 46.22 4.30
3908 7743 8.666573 CATAGGATTTGAGATGCATGTTATCTC 58.333 37.037 23.83 23.83 46.82 2.75
3909 7744 7.120873 GCATAGGATTTGAGATGCATGTTATCT 59.879 37.037 2.46 12.53 43.36 1.98
3910 7745 7.249147 GCATAGGATTTGAGATGCATGTTATC 58.751 38.462 2.46 5.04 43.36 1.75
3911 7746 7.154435 GCATAGGATTTGAGATGCATGTTAT 57.846 36.000 2.46 0.00 43.36 1.89
3912 7747 6.564709 GCATAGGATTTGAGATGCATGTTA 57.435 37.500 2.46 0.00 43.36 2.41
3913 7748 5.449107 GCATAGGATTTGAGATGCATGTT 57.551 39.130 2.46 0.00 43.36 2.71
3949 7784 4.273318 GTGTGAATTAAAGGGCATCTCCT 58.727 43.478 0.00 0.00 39.17 3.69
3950 7785 3.381590 GGTGTGAATTAAAGGGCATCTCC 59.618 47.826 0.00 0.00 0.00 3.71
3951 7786 4.016444 TGGTGTGAATTAAAGGGCATCTC 58.984 43.478 0.00 0.00 0.00 2.75
3952 7787 4.046286 TGGTGTGAATTAAAGGGCATCT 57.954 40.909 0.00 0.00 0.00 2.90
3953 7788 6.321181 TCTTATGGTGTGAATTAAAGGGCATC 59.679 38.462 0.00 0.00 0.00 3.91
3954 7789 6.194235 TCTTATGGTGTGAATTAAAGGGCAT 58.806 36.000 0.00 0.00 0.00 4.40
3955 7790 5.575157 TCTTATGGTGTGAATTAAAGGGCA 58.425 37.500 0.00 0.00 0.00 5.36
3956 7791 6.715347 ATCTTATGGTGTGAATTAAAGGGC 57.285 37.500 0.00 0.00 0.00 5.19
3957 7792 9.942850 AAAAATCTTATGGTGTGAATTAAAGGG 57.057 29.630 0.00 0.00 0.00 3.95
4009 7844 9.973661 TCCTATCCTTCACATTTGATAGAAAAA 57.026 29.630 6.89 0.00 39.21 1.94
4010 7845 9.973661 TTCCTATCCTTCACATTTGATAGAAAA 57.026 29.630 6.89 0.22 39.21 2.29
4011 7846 9.973661 TTTCCTATCCTTCACATTTGATAGAAA 57.026 29.630 6.89 4.08 39.21 2.52
4012 7847 9.973661 TTTTCCTATCCTTCACATTTGATAGAA 57.026 29.630 6.89 0.00 39.21 2.10
4013 7848 9.973661 TTTTTCCTATCCTTCACATTTGATAGA 57.026 29.630 6.89 0.00 39.21 1.98
4017 7852 8.531146 GGAATTTTTCCTATCCTTCACATTTGA 58.469 33.333 0.00 0.00 46.57 2.69
4018 7853 8.707938 GGAATTTTTCCTATCCTTCACATTTG 57.292 34.615 0.00 0.00 46.57 2.32
4056 7891 5.624509 GCCTTGGTTTGTAGGAATGAAATCC 60.625 44.000 0.00 0.00 39.96 3.01
4057 7892 5.410924 GCCTTGGTTTGTAGGAATGAAATC 58.589 41.667 0.00 0.00 33.13 2.17
4058 7893 4.222810 GGCCTTGGTTTGTAGGAATGAAAT 59.777 41.667 0.00 0.00 33.13 2.17
4059 7894 3.576550 GGCCTTGGTTTGTAGGAATGAAA 59.423 43.478 0.00 0.00 33.13 2.69
4060 7895 3.161866 GGCCTTGGTTTGTAGGAATGAA 58.838 45.455 0.00 0.00 33.13 2.57
4061 7896 2.378547 AGGCCTTGGTTTGTAGGAATGA 59.621 45.455 0.00 0.00 33.13 2.57
4062 7897 2.755103 GAGGCCTTGGTTTGTAGGAATG 59.245 50.000 6.77 0.00 33.13 2.67
4063 7898 2.649816 AGAGGCCTTGGTTTGTAGGAAT 59.350 45.455 6.77 0.00 33.13 3.01
4064 7899 2.062636 AGAGGCCTTGGTTTGTAGGAA 58.937 47.619 6.77 0.00 33.13 3.36
4065 7900 1.742308 AGAGGCCTTGGTTTGTAGGA 58.258 50.000 6.77 0.00 33.13 2.94
4066 7901 2.586648 AAGAGGCCTTGGTTTGTAGG 57.413 50.000 6.77 0.00 34.54 3.18
4067 7902 3.005791 CCAAAAGAGGCCTTGGTTTGTAG 59.994 47.826 24.02 13.20 37.83 2.74
4068 7903 2.962421 CCAAAAGAGGCCTTGGTTTGTA 59.038 45.455 24.02 0.00 37.83 2.41
4069 7904 1.762370 CCAAAAGAGGCCTTGGTTTGT 59.238 47.619 24.02 6.56 37.83 2.83
4070 7905 2.531522 CCAAAAGAGGCCTTGGTTTG 57.468 50.000 21.29 21.29 37.83 2.93
4074 7909 1.703411 TGAACCAAAAGAGGCCTTGG 58.297 50.000 18.11 18.11 46.36 3.61
4075 7910 3.445096 CCTATGAACCAAAAGAGGCCTTG 59.555 47.826 6.77 0.00 31.91 3.61
4076 7911 3.333680 TCCTATGAACCAAAAGAGGCCTT 59.666 43.478 6.77 0.00 0.00 4.35
4077 7912 2.919602 TCCTATGAACCAAAAGAGGCCT 59.080 45.455 3.86 3.86 0.00 5.19
4078 7913 3.366052 TCCTATGAACCAAAAGAGGCC 57.634 47.619 0.00 0.00 0.00 5.19
4079 7914 5.066593 CCTATCCTATGAACCAAAAGAGGC 58.933 45.833 0.00 0.00 0.00 4.70
4080 7915 6.500589 TCCTATCCTATGAACCAAAAGAGG 57.499 41.667 0.00 0.00 0.00 3.69
4087 7922 9.439461 CCTATGATAATCCTATCCTATGAACCA 57.561 37.037 0.00 0.00 34.10 3.67
4088 7923 9.661954 TCCTATGATAATCCTATCCTATGAACC 57.338 37.037 0.00 0.00 34.10 3.62
4106 7941 9.621239 TTCCTACAAGATTCCTATTCCTATGAT 57.379 33.333 0.00 0.00 0.00 2.45
4107 7942 9.447279 TTTCCTACAAGATTCCTATTCCTATGA 57.553 33.333 0.00 0.00 0.00 2.15
4110 7945 9.447279 TCATTTCCTACAAGATTCCTATTCCTA 57.553 33.333 0.00 0.00 0.00 2.94
4111 7946 8.337118 TCATTTCCTACAAGATTCCTATTCCT 57.663 34.615 0.00 0.00 0.00 3.36
4112 7947 8.432805 TCTCATTTCCTACAAGATTCCTATTCC 58.567 37.037 0.00 0.00 0.00 3.01
4114 7949 9.790344 CATCTCATTTCCTACAAGATTCCTATT 57.210 33.333 0.00 0.00 0.00 1.73
4115 7950 9.163894 TCATCTCATTTCCTACAAGATTCCTAT 57.836 33.333 0.00 0.00 0.00 2.57
4116 7951 8.424918 GTCATCTCATTTCCTACAAGATTCCTA 58.575 37.037 0.00 0.00 0.00 2.94
4117 7952 7.092712 TGTCATCTCATTTCCTACAAGATTCCT 60.093 37.037 0.00 0.00 0.00 3.36
4118 7953 7.050377 TGTCATCTCATTTCCTACAAGATTCC 58.950 38.462 0.00 0.00 0.00 3.01
4119 7954 8.557864 CATGTCATCTCATTTCCTACAAGATTC 58.442 37.037 0.00 0.00 0.00 2.52
4120 7955 8.051535 ACATGTCATCTCATTTCCTACAAGATT 58.948 33.333 0.00 0.00 0.00 2.40
4121 7956 7.571919 ACATGTCATCTCATTTCCTACAAGAT 58.428 34.615 0.00 0.00 0.00 2.40
4122 7957 6.950842 ACATGTCATCTCATTTCCTACAAGA 58.049 36.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.