Multiple sequence alignment - TraesCS2D01G573300

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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 TraesCS2D01G573300 chr2D 100.000 3944 0 0 1 3944 638437074 638441017 0.000000e+00 7284.0
1 TraesCS2D01G573300 chr2D 86.093 1057 111 20 1959 2994 638506098 638505057 0.000000e+00 1105.0
2 TraesCS2D01G573300 chr2D 87.564 981 37 13 971 1912 638507130 638506196 0.000000e+00 1057.0
3 TraesCS2D01G573300 chr2D 90.391 281 27 0 3214 3494 43670006 43669726 1.730000e-98 370.0
4 TraesCS2D01G573300 chr2D 90.106 283 28 0 3212 3494 7467079 7467361 6.230000e-98 368.0
5 TraesCS2D01G573300 chr2D 90.438 251 23 1 3209 3459 602769870 602769621 2.940000e-86 329.0
6 TraesCS2D01G573300 chr2D 84.516 310 39 3 1329 1637 350623221 350622920 8.290000e-77 298.0
7 TraesCS2D01G573300 chr2D 86.264 182 24 1 520 701 638507665 638507485 3.110000e-46 196.0
8 TraesCS2D01G573300 chr2D 97.297 37 1 0 1914 1950 638506160 638506124 3.290000e-06 63.9
9 TraesCS2D01G573300 chr2B 87.583 2110 164 54 943 2994 797464173 797466242 0.000000e+00 2355.0
10 TraesCS2D01G573300 chr2B 87.575 2012 155 46 1001 2994 785942991 785944925 0.000000e+00 2242.0
11 TraesCS2D01G573300 chr2B 91.746 739 52 4 3209 3944 263808029 263807297 0.000000e+00 1018.0
12 TraesCS2D01G573300 chr2B 90.499 621 39 13 311 924 797463582 797464189 0.000000e+00 802.0
13 TraesCS2D01G573300 chr2B 84.247 730 81 18 2237 2934 797708750 797709477 0.000000e+00 680.0
14 TraesCS2D01G573300 chr2B 91.852 270 21 1 1294 1562 797707714 797707983 3.720000e-100 375.0
15 TraesCS2D01G573300 chr2B 89.701 301 15 5 1 297 797463134 797463422 1.730000e-98 370.0
16 TraesCS2D01G573300 chr2B 88.302 265 25 3 1649 1913 797708063 797708321 2.960000e-81 313.0
17 TraesCS2D01G573300 chr2B 91.124 169 15 0 2024 2192 797708479 797708647 3.070000e-56 230.0
18 TraesCS2D01G573300 chr2B 81.404 285 30 13 1003 1286 797706232 797706494 1.110000e-50 211.0
19 TraesCS2D01G573300 chr2B 91.129 124 9 2 1 122 797704925 797705048 2.440000e-37 167.0
20 TraesCS2D01G573300 chr2B 100.000 34 0 0 756 789 547092644 547092677 3.290000e-06 63.9
21 TraesCS2D01G573300 chr2A 92.487 1584 85 14 1003 2558 763454969 763453392 0.000000e+00 2235.0
22 TraesCS2D01G573300 chr2A 92.381 315 24 0 3630 3944 696278713 696278399 2.160000e-122 449.0
23 TraesCS2D01G573300 chr2A 87.728 383 47 0 2623 3005 763453378 763452996 7.770000e-122 448.0
24 TraesCS2D01G573300 chr2A 86.349 315 30 3 3630 3944 593357245 593356944 8.170000e-87 331.0
25 TraesCS2D01G573300 chr2A 91.667 204 17 0 1212 1415 763396984 763396781 2.320000e-72 283.0
26 TraesCS2D01G573300 chr2A 85.315 143 17 4 1003 1142 763397125 763396984 1.140000e-30 145.0
27 TraesCS2D01G573300 chr2A 97.436 39 1 0 756 794 71439039 71439001 2.540000e-07 67.6
28 TraesCS2D01G573300 chr5D 95.213 376 17 1 3569 3944 361668836 361668462 9.440000e-166 593.0
29 TraesCS2D01G573300 chr5D 86.415 530 52 10 1051 1575 87429786 87429272 2.660000e-156 562.0
30 TraesCS2D01G573300 chr5D 80.000 780 121 23 2246 3005 87428480 87427716 9.640000e-151 544.0
31 TraesCS2D01G573300 chr5D 92.177 294 23 0 3540 3833 478955345 478955638 2.190000e-112 416.0
32 TraesCS2D01G573300 chr5D 90.175 285 28 0 3210 3494 478955065 478955349 4.810000e-99 372.0
33 TraesCS2D01G573300 chr5D 80.861 418 50 18 1793 2187 87428995 87428585 6.400000e-78 302.0
34 TraesCS2D01G573300 chr5D 86.486 74 5 4 714 786 543708356 543708425 4.230000e-10 76.8
35 TraesCS2D01G573300 chr6D 94.054 370 21 1 3569 3938 425994955 425994587 9.570000e-156 560.0
36 TraesCS2D01G573300 chr6D 91.459 281 19 2 3213 3493 425995221 425994946 8.000000e-102 381.0
37 TraesCS2D01G573300 chr6D 93.038 158 11 0 3003 3160 8317193 8317350 8.520000e-57 231.0
38 TraesCS2D01G573300 chr6D 92.473 93 7 0 3470 3562 456323386 456323294 2.470000e-27 134.0
39 TraesCS2D01G573300 chr6D 94.186 86 5 0 3477 3562 456323474 456323389 8.890000e-27 132.0
40 TraesCS2D01G573300 chr6D 81.132 159 28 2 543 700 426042561 426042404 4.140000e-25 126.0
41 TraesCS2D01G573300 chr6D 92.308 52 3 1 3512 3562 456324143 456324092 5.470000e-09 73.1
42 TraesCS2D01G573300 chr5A 93.404 379 22 1 3569 3944 9500194 9499816 3.440000e-155 558.0
43 TraesCS2D01G573300 chr5A 94.677 263 13 1 3213 3475 9501712 9501451 1.320000e-109 407.0
44 TraesCS2D01G573300 chr5A 90.798 163 12 3 3004 3163 623217711 623217873 8.580000e-52 215.0
45 TraesCS2D01G573300 chr5A 100.000 30 0 0 760 789 267000357 267000328 5.510000e-04 56.5
46 TraesCS2D01G573300 chr1D 81.132 742 92 25 1817 2534 189820343 189819626 5.760000e-153 551.0
47 TraesCS2D01G573300 chr1D 81.283 561 79 15 2457 3005 468988464 468987918 7.830000e-117 431.0
48 TraesCS2D01G573300 chr1D 77.954 567 84 19 1647 2191 468989755 468989208 2.290000e-82 316.0
49 TraesCS2D01G573300 chr1D 94.545 110 5 1 2348 2456 468988841 468988732 6.780000e-38 169.0
50 TraesCS2D01G573300 chr1D 84.000 150 17 4 3004 3153 132848742 132848600 1.910000e-28 137.0
51 TraesCS2D01G573300 chr7A 95.152 330 16 0 3615 3944 690833931 690833602 4.520000e-144 521.0
52 TraesCS2D01G573300 chr7A 95.318 299 13 1 3215 3513 690834228 690833931 1.280000e-129 473.0
53 TraesCS2D01G573300 chr7A 93.007 286 20 0 3209 3494 30719245 30718960 6.100000e-113 418.0
54 TraesCS2D01G573300 chr7A 90.066 151 11 4 3011 3157 725192049 725192199 4.020000e-45 193.0
55 TraesCS2D01G573300 chr5B 80.614 619 68 22 3354 3944 28809598 28810192 7.830000e-117 431.0
56 TraesCS2D01G573300 chr5B 79.720 286 46 5 1346 1620 128355921 128356205 3.110000e-46 196.0
57 TraesCS2D01G573300 chr5B 100.000 34 0 0 756 789 289771129 289771096 3.290000e-06 63.9
58 TraesCS2D01G573300 chr7D 92.177 294 23 0 3540 3833 409614028 409614321 2.190000e-112 416.0
59 TraesCS2D01G573300 chr7D 91.497 294 25 0 3540 3833 510412583 510412290 4.750000e-109 405.0
60 TraesCS2D01G573300 chr7D 89.825 285 29 0 3210 3494 409613748 409614032 2.240000e-97 366.0
61 TraesCS2D01G573300 chr7D 89.937 159 12 4 3003 3157 164852073 164851915 6.680000e-48 202.0
62 TraesCS2D01G573300 chr3B 76.781 758 108 27 1488 2191 505027860 505027117 2.900000e-96 363.0
63 TraesCS2D01G573300 chr3B 87.975 316 23 3 3630 3944 771765908 771766209 3.750000e-95 359.0
64 TraesCS2D01G573300 chr3B 88.119 202 24 0 2666 2867 505023998 505023797 1.420000e-59 241.0
65 TraesCS2D01G573300 chr3B 95.556 90 3 1 2415 2504 505025483 505025395 4.110000e-30 143.0
66 TraesCS2D01G573300 chr1B 91.463 164 11 1 3003 3163 390700644 390700481 5.130000e-54 222.0
67 TraesCS2D01G573300 chr1B 82.028 217 37 2 1405 1620 629830663 629830878 2.420000e-42 183.0
68 TraesCS2D01G573300 chr1B 78.947 171 36 0 530 700 83626803 83626973 2.490000e-22 117.0
69 TraesCS2D01G573300 chr1B 79.042 167 32 3 531 697 657422366 657422529 1.160000e-20 111.0
70 TraesCS2D01G573300 chr3A 78.859 298 50 8 1335 1620 700425653 700425949 5.200000e-44 189.0
71 TraesCS2D01G573300 chr3A 100.000 34 0 0 757 790 560132200 560132167 3.290000e-06 63.9
72 TraesCS2D01G573300 chrUn 89.655 145 15 0 3471 3615 87834834 87834978 6.730000e-43 185.0
73 TraesCS2D01G573300 chrUn 83.636 220 12 4 1 197 286974436 286974218 6.730000e-43 185.0
74 TraesCS2D01G573300 chr1A 86.184 152 14 4 3003 3153 568132962 568133107 1.470000e-34 158.0
75 TraesCS2D01G573300 chr1A 86.184 152 14 4 3003 3153 568135013 568135158 1.470000e-34 158.0
76 TraesCS2D01G573300 chr1A 86.184 152 14 4 3003 3153 568138413 568138558 1.470000e-34 158.0
77 TraesCS2D01G573300 chr6A 79.006 181 35 3 525 704 260483235 260483413 1.920000e-23 121.0
78 TraesCS2D01G573300 chr4B 76.087 184 37 5 521 700 663907172 663906992 5.430000e-14 89.8
79 TraesCS2D01G573300 chr3D 97.368 38 0 1 754 790 547620031 547619994 3.290000e-06 63.9
80 TraesCS2D01G573300 chr6B 100.000 32 0 0 758 789 671389915 671389884 4.260000e-05 60.2


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 TraesCS2D01G573300 chr2D 638437074 638441017 3943 False 7284.000000 7284 100.000000 1 3944 1 chr2D.!!$F2 3943
1 TraesCS2D01G573300 chr2D 638505057 638507665 2608 True 605.475000 1105 89.304500 520 2994 4 chr2D.!!$R4 2474
2 TraesCS2D01G573300 chr2B 785942991 785944925 1934 False 2242.000000 2242 87.575000 1001 2994 1 chr2B.!!$F2 1993
3 TraesCS2D01G573300 chr2B 797463134 797466242 3108 False 1175.666667 2355 89.261000 1 2994 3 chr2B.!!$F3 2993
4 TraesCS2D01G573300 chr2B 263807297 263808029 732 True 1018.000000 1018 91.746000 3209 3944 1 chr2B.!!$R1 735
5 TraesCS2D01G573300 chr2B 797704925 797709477 4552 False 329.333333 680 88.009667 1 2934 6 chr2B.!!$F4 2933
6 TraesCS2D01G573300 chr2A 763452996 763454969 1973 True 1341.500000 2235 90.107500 1003 3005 2 chr2A.!!$R5 2002
7 TraesCS2D01G573300 chr5D 87427716 87429786 2070 True 469.333333 562 82.425333 1051 3005 3 chr5D.!!$R2 1954
8 TraesCS2D01G573300 chr5D 478955065 478955638 573 False 394.000000 416 91.176000 3210 3833 2 chr5D.!!$F2 623
9 TraesCS2D01G573300 chr6D 425994587 425995221 634 True 470.500000 560 92.756500 3213 3938 2 chr6D.!!$R2 725
10 TraesCS2D01G573300 chr5A 9499816 9501712 1896 True 482.500000 558 94.040500 3213 3944 2 chr5A.!!$R2 731
11 TraesCS2D01G573300 chr1D 189819626 189820343 717 True 551.000000 551 81.132000 1817 2534 1 chr1D.!!$R2 717
12 TraesCS2D01G573300 chr1D 468987918 468989755 1837 True 305.333333 431 84.594000 1647 3005 3 chr1D.!!$R3 1358
13 TraesCS2D01G573300 chr7A 690833602 690834228 626 True 497.000000 521 95.235000 3215 3944 2 chr7A.!!$R2 729
14 TraesCS2D01G573300 chr5B 28809598 28810192 594 False 431.000000 431 80.614000 3354 3944 1 chr5B.!!$F1 590
15 TraesCS2D01G573300 chr7D 409613748 409614321 573 False 391.000000 416 91.001000 3210 3833 2 chr7D.!!$F1 623
16 TraesCS2D01G573300 chr3B 505023797 505027860 4063 True 249.000000 363 86.818667 1488 2867 3 chr3B.!!$R1 1379

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
220 250 0.028374 ACACGTTTAACAAGCACGGC 59.972 50.0 2.1 0.0 38.26 5.68 F
1147 1885 0.179012 CTACGACCTCTCTCCCTCCC 60.179 65.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1149 1887 0.041238 TGTGATCGAGGGAGGAAGGT 59.959 55.0 0.0 0.0 0.0 3.50 R
3025 8191 0.116143 TGTTAGGCCCCCATTTTGCT 59.884 50.0 0.0 0.0 0.0 3.91 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
63 64 7.122204 AGGGGTTTCGGTTAGAAGAAAAATATG 59.878 37.037 0.00 0.00 40.40 1.78
143 169 6.885952 TTAATTTGAATCTTTGGTGACGGA 57.114 33.333 0.00 0.00 0.00 4.69
178 204 5.841957 AGTGATAGATGCAATGGGTTTTC 57.158 39.130 0.00 0.00 0.00 2.29
189 215 1.285950 GGGTTTTCGCTTGTGGCTC 59.714 57.895 0.00 0.00 39.13 4.70
207 233 2.543653 GCTCAAATTTGCAGGACACGTT 60.544 45.455 13.54 0.00 0.00 3.99
220 250 0.028374 ACACGTTTAACAAGCACGGC 59.972 50.000 2.10 0.00 38.26 5.68
266 296 2.381589 GCGTAACTTTGGCTGTTGTTC 58.618 47.619 0.00 0.00 0.00 3.18
297 327 0.397941 CTTCCAAGAGTCAGCACCCA 59.602 55.000 0.00 0.00 0.00 4.51
300 330 1.669115 CAAGAGTCAGCACCCACCG 60.669 63.158 0.00 0.00 0.00 4.94
301 331 3.537206 AAGAGTCAGCACCCACCGC 62.537 63.158 0.00 0.00 0.00 5.68
328 504 3.485463 CCCCCTTCTATTACAATGCGA 57.515 47.619 0.00 0.00 0.00 5.10
333 509 4.634004 CCCTTCTATTACAATGCGAACACA 59.366 41.667 0.00 0.00 0.00 3.72
334 510 5.447279 CCCTTCTATTACAATGCGAACACAC 60.447 44.000 0.00 0.00 0.00 3.82
341 520 4.514781 ACAATGCGAACACACTACTAGA 57.485 40.909 0.00 0.00 0.00 2.43
358 537 5.653255 ACTAGAGTTTGGGGCATGAATAT 57.347 39.130 0.00 0.00 0.00 1.28
363 542 5.537674 AGAGTTTGGGGCATGAATATTGATC 59.462 40.000 0.00 0.00 0.00 2.92
428 611 0.556380 TCCTCCTCCTCCTCCCTTCT 60.556 60.000 0.00 0.00 0.00 2.85
431 614 1.571457 CTCCTCCTCCTCCCTTCTACA 59.429 57.143 0.00 0.00 0.00 2.74
444 627 7.626084 TCCTCCCTTCTACACTTCCATTTTATA 59.374 37.037 0.00 0.00 0.00 0.98
523 706 0.741915 AAAAATGTTGGCGACGTGGT 59.258 45.000 0.00 0.00 0.00 4.16
671 1141 2.644299 TGATGACTCCATGAGGGTTGTT 59.356 45.455 0.00 0.00 38.11 2.83
709 1313 1.207089 TCGGGATGTTGACATGTCCTC 59.793 52.381 22.85 15.35 36.57 3.71
712 1316 3.118775 CGGGATGTTGACATGTCCTCTAA 60.119 47.826 22.85 7.78 36.57 2.10
717 1321 6.431234 GGATGTTGACATGTCCTCTAAGTTTT 59.569 38.462 22.85 0.00 36.57 2.43
739 1343 7.441903 TTTACCCGGTCTTCCTCTAATTAAT 57.558 36.000 0.00 0.00 0.00 1.40
743 1347 4.557205 CGGTCTTCCTCTAATTAATCGGG 58.443 47.826 0.00 0.00 0.00 5.14
752 1356 5.120830 CCTCTAATTAATCGGGCAAATCTCG 59.879 44.000 0.00 0.00 0.00 4.04
755 1437 2.234300 TAATCGGGCAAATCTCGTCC 57.766 50.000 0.00 0.00 0.00 4.79
791 1475 9.729281 ATAAAAATGACAAATCTTTTGCCTCAT 57.271 25.926 0.06 1.26 33.65 2.90
793 1477 6.600882 AATGACAAATCTTTTGCCTCATCT 57.399 33.333 0.06 0.00 0.00 2.90
854 1538 2.428071 GCAGCAAGCACTTGACGC 60.428 61.111 14.44 10.91 42.93 5.19
855 1539 3.024784 CAGCAAGCACTTGACGCA 58.975 55.556 14.44 0.00 42.93 5.24
856 1540 1.577922 CAGCAAGCACTTGACGCAT 59.422 52.632 14.44 0.00 42.93 4.73
857 1541 0.453950 CAGCAAGCACTTGACGCATC 60.454 55.000 14.44 0.00 42.93 3.91
895 1591 2.159184 GCTTATTTTCTTCAGGCAGGCC 60.159 50.000 0.97 0.97 0.00 5.19
897 1593 1.844687 ATTTTCTTCAGGCAGGCCTC 58.155 50.000 10.50 0.00 46.28 4.70
898 1594 0.478072 TTTTCTTCAGGCAGGCCTCA 59.522 50.000 10.50 0.00 46.28 3.86
924 1620 8.914328 TCGTTATTGACTGAATTATTGACGTA 57.086 30.769 0.00 0.00 0.00 3.57
961 1657 6.780706 AAAAGACTGAATTATTGACGTCGT 57.219 33.333 11.62 0.00 0.00 4.34
962 1658 6.390987 AAAGACTGAATTATTGACGTCGTC 57.609 37.500 18.51 18.51 0.00 4.20
963 1659 4.096311 AGACTGAATTATTGACGTCGTCG 58.904 43.478 19.81 0.00 43.34 5.12
964 1660 4.087510 ACTGAATTATTGACGTCGTCGA 57.912 40.909 17.43 17.43 40.62 4.20
965 1661 3.850273 ACTGAATTATTGACGTCGTCGAC 59.150 43.478 17.46 15.51 40.62 4.20
966 1662 3.824151 TGAATTATTGACGTCGTCGACA 58.176 40.909 24.13 3.10 39.51 4.35
967 1663 3.605056 TGAATTATTGACGTCGTCGACAC 59.395 43.478 24.13 17.04 40.69 3.67
968 1664 1.967762 TTATTGACGTCGTCGACACC 58.032 50.000 24.13 15.02 40.69 4.16
969 1665 0.873721 TATTGACGTCGTCGACACCA 59.126 50.000 24.13 17.24 40.69 4.17
1071 1796 2.840102 CCGCCTCCTTCCTCCGAT 60.840 66.667 0.00 0.00 0.00 4.18
1147 1885 0.179012 CTACGACCTCTCTCCCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
1149 1887 2.997584 CGACCTCTCTCCCTCCCCA 61.998 68.421 0.00 0.00 0.00 4.96
1630 3611 1.652124 CACCGTCGGTAATTTCAGTCG 59.348 52.381 18.38 0.00 32.11 4.18
1642 3623 1.520600 TTCAGTCGAGCCGTGCTACA 61.521 55.000 0.00 0.00 39.88 2.74
1686 3717 1.160137 GTGTCTGAACATCCCAGTGC 58.840 55.000 0.00 0.00 37.81 4.40
1954 4093 7.719633 TGCAGAGTATAGGTTTTCTGAAACTTT 59.280 33.333 1.58 0.00 43.68 2.66
1963 4103 4.637483 TTTCTGAAACTTTCTGCAGGTG 57.363 40.909 15.13 6.92 0.00 4.00
1995 4148 4.934001 CAGGGCATGTCAGCTTACATATAG 59.066 45.833 13.06 3.20 38.01 1.31
2177 4353 0.313987 TCTCACGTGTCATGCGAGTT 59.686 50.000 16.51 0.00 0.00 3.01
2209 4402 4.258935 GTGCAATCACAACATACCTACG 57.741 45.455 0.00 0.00 42.66 3.51
2240 4445 5.914635 CACGTGATATCATAAAATTGTGCCC 59.085 40.000 10.90 0.00 0.00 5.36
2462 6362 0.250038 CCATTGCGTCGGAGGATGAT 60.250 55.000 1.18 0.00 0.00 2.45
2621 7785 8.874816 GCAGTAGTAGGAGTTGATTTTTCTTAG 58.125 37.037 0.00 0.00 0.00 2.18
2936 8100 2.282462 CGCAGCCTGGGGTTCTTT 60.282 61.111 0.00 0.00 0.00 2.52
2937 8101 2.629656 CGCAGCCTGGGGTTCTTTG 61.630 63.158 0.00 0.00 0.00 2.77
2960 8124 5.233988 GGCTTAGCCTAACTCTGTCATATG 58.766 45.833 17.16 0.00 46.69 1.78
2962 8126 5.923684 GCTTAGCCTAACTCTGTCATATGTC 59.076 44.000 1.90 0.00 0.00 3.06
3012 8178 8.729805 TGTATGATTTTATTTGAATTTGGGGC 57.270 30.769 0.00 0.00 0.00 5.80
3013 8179 7.772757 TGTATGATTTTATTTGAATTTGGGGCC 59.227 33.333 0.00 0.00 0.00 5.80
3014 8180 5.504853 TGATTTTATTTGAATTTGGGGCCC 58.495 37.500 18.17 18.17 0.00 5.80
3015 8181 4.308526 TTTTATTTGAATTTGGGGCCCC 57.691 40.909 36.14 36.14 0.00 5.80
3016 8182 1.490574 TATTTGAATTTGGGGCCCCG 58.509 50.000 36.00 0.00 39.42 5.73
3017 8183 1.271127 ATTTGAATTTGGGGCCCCGG 61.271 55.000 36.00 0.00 39.42 5.73
3018 8184 2.681273 TTTGAATTTGGGGCCCCGGT 62.681 55.000 36.00 21.18 39.42 5.28
3019 8185 3.074369 GAATTTGGGGCCCCGGTG 61.074 66.667 36.00 0.00 39.42 4.94
3038 8204 2.839629 CGAAAAGCAAAATGGGGGC 58.160 52.632 0.00 0.00 0.00 5.80
3039 8205 0.673333 CGAAAAGCAAAATGGGGGCC 60.673 55.000 0.00 0.00 0.00 5.80
3040 8206 0.692476 GAAAAGCAAAATGGGGGCCT 59.308 50.000 0.84 0.00 0.00 5.19
3041 8207 1.905894 GAAAAGCAAAATGGGGGCCTA 59.094 47.619 0.84 0.00 0.00 3.93
3042 8208 2.037385 AAAGCAAAATGGGGGCCTAA 57.963 45.000 0.84 0.00 0.00 2.69
3043 8209 1.275666 AAGCAAAATGGGGGCCTAAC 58.724 50.000 0.84 0.00 0.00 2.34
3044 8210 0.116143 AGCAAAATGGGGGCCTAACA 59.884 50.000 0.84 0.33 0.00 2.41
3045 8211 1.203237 GCAAAATGGGGGCCTAACAT 58.797 50.000 0.84 3.09 0.00 2.71
3046 8212 1.559219 GCAAAATGGGGGCCTAACATT 59.441 47.619 0.84 9.54 36.46 2.71
3047 8213 2.026356 GCAAAATGGGGGCCTAACATTT 60.026 45.455 20.60 20.60 44.18 2.32
3048 8214 3.608796 CAAAATGGGGGCCTAACATTTG 58.391 45.455 24.24 16.56 42.21 2.32
3049 8215 2.938428 AATGGGGGCCTAACATTTGA 57.062 45.000 0.84 0.00 31.21 2.69
3050 8216 2.938428 ATGGGGGCCTAACATTTGAA 57.062 45.000 0.84 0.00 0.00 2.69
3051 8217 2.704190 TGGGGGCCTAACATTTGAAA 57.296 45.000 0.84 0.00 0.00 2.69
3052 8218 2.977808 TGGGGGCCTAACATTTGAAAA 58.022 42.857 0.84 0.00 0.00 2.29
3053 8219 3.318313 TGGGGGCCTAACATTTGAAAAA 58.682 40.909 0.84 0.00 0.00 1.94
3095 8261 9.613428 ACTCAAGCATAAGCACTTAATTATACA 57.387 29.630 0.00 0.00 45.49 2.29
3144 8310 9.914131 ATAGTTTTTGGAAAATTCTCAAGTAGC 57.086 29.630 0.00 0.00 0.00 3.58
3145 8311 7.781056 AGTTTTTGGAAAATTCTCAAGTAGCA 58.219 30.769 0.00 0.00 0.00 3.49
3146 8312 8.257306 AGTTTTTGGAAAATTCTCAAGTAGCAA 58.743 29.630 0.00 0.00 0.00 3.91
3147 8313 9.045223 GTTTTTGGAAAATTCTCAAGTAGCAAT 57.955 29.630 0.00 0.00 0.00 3.56
3148 8314 8.592105 TTTTGGAAAATTCTCAAGTAGCAATG 57.408 30.769 0.00 0.00 0.00 2.82
3149 8315 5.713025 TGGAAAATTCTCAAGTAGCAATGC 58.287 37.500 0.00 0.00 0.00 3.56
3150 8316 5.243507 TGGAAAATTCTCAAGTAGCAATGCA 59.756 36.000 8.35 0.00 0.00 3.96
3151 8317 6.158598 GGAAAATTCTCAAGTAGCAATGCAA 58.841 36.000 8.35 0.00 0.00 4.08
3152 8318 6.646240 GGAAAATTCTCAAGTAGCAATGCAAA 59.354 34.615 8.35 0.00 0.00 3.68
3153 8319 7.332678 GGAAAATTCTCAAGTAGCAATGCAAAT 59.667 33.333 8.35 0.00 0.00 2.32
3154 8320 8.611654 AAAATTCTCAAGTAGCAATGCAAATT 57.388 26.923 8.35 0.00 0.00 1.82
3155 8321 7.823149 AATTCTCAAGTAGCAATGCAAATTC 57.177 32.000 8.35 0.00 0.00 2.17
3156 8322 6.579666 TTCTCAAGTAGCAATGCAAATTCT 57.420 33.333 8.35 0.00 0.00 2.40
3157 8323 6.187125 TCTCAAGTAGCAATGCAAATTCTC 57.813 37.500 8.35 0.00 0.00 2.87
3158 8324 5.706833 TCTCAAGTAGCAATGCAAATTCTCA 59.293 36.000 8.35 0.00 0.00 3.27
3159 8325 5.702865 TCAAGTAGCAATGCAAATTCTCAC 58.297 37.500 8.35 0.00 0.00 3.51
3160 8326 5.241285 TCAAGTAGCAATGCAAATTCTCACA 59.759 36.000 8.35 0.00 0.00 3.58
3161 8327 5.710513 AGTAGCAATGCAAATTCTCACAA 57.289 34.783 8.35 0.00 0.00 3.33
3162 8328 5.464168 AGTAGCAATGCAAATTCTCACAAC 58.536 37.500 8.35 0.00 0.00 3.32
3163 8329 4.595762 AGCAATGCAAATTCTCACAACT 57.404 36.364 8.35 0.00 0.00 3.16
3164 8330 4.304110 AGCAATGCAAATTCTCACAACTG 58.696 39.130 8.35 0.00 0.00 3.16
3165 8331 4.053295 GCAATGCAAATTCTCACAACTGT 58.947 39.130 0.00 0.00 0.00 3.55
3166 8332 4.508861 GCAATGCAAATTCTCACAACTGTT 59.491 37.500 0.00 0.00 0.00 3.16
3167 8333 5.006941 GCAATGCAAATTCTCACAACTGTTT 59.993 36.000 0.00 0.00 0.00 2.83
3168 8334 6.642917 CAATGCAAATTCTCACAACTGTTTC 58.357 36.000 0.00 0.00 0.00 2.78
3169 8335 5.581126 TGCAAATTCTCACAACTGTTTCT 57.419 34.783 0.00 0.00 0.00 2.52
3170 8336 5.964758 TGCAAATTCTCACAACTGTTTCTT 58.035 33.333 0.00 0.00 0.00 2.52
3171 8337 6.035843 TGCAAATTCTCACAACTGTTTCTTC 58.964 36.000 0.00 0.00 0.00 2.87
3172 8338 6.127647 TGCAAATTCTCACAACTGTTTCTTCT 60.128 34.615 0.00 0.00 0.00 2.85
3173 8339 6.753744 GCAAATTCTCACAACTGTTTCTTCTT 59.246 34.615 0.00 0.00 0.00 2.52
3174 8340 7.915397 GCAAATTCTCACAACTGTTTCTTCTTA 59.085 33.333 0.00 0.00 0.00 2.10
3175 8341 9.226345 CAAATTCTCACAACTGTTTCTTCTTAC 57.774 33.333 0.00 0.00 0.00 2.34
3176 8342 8.506168 AATTCTCACAACTGTTTCTTCTTACA 57.494 30.769 0.00 0.00 0.00 2.41
3177 8343 6.903883 TCTCACAACTGTTTCTTCTTACAC 57.096 37.500 0.00 0.00 0.00 2.90
3178 8344 6.640518 TCTCACAACTGTTTCTTCTTACACT 58.359 36.000 0.00 0.00 0.00 3.55
3179 8345 7.103641 TCTCACAACTGTTTCTTCTTACACTT 58.896 34.615 0.00 0.00 0.00 3.16
3180 8346 7.064609 TCTCACAACTGTTTCTTCTTACACTTG 59.935 37.037 0.00 0.00 0.00 3.16
3181 8347 6.876789 TCACAACTGTTTCTTCTTACACTTGA 59.123 34.615 0.00 0.00 0.00 3.02
3182 8348 7.389330 TCACAACTGTTTCTTCTTACACTTGAA 59.611 33.333 0.00 0.00 0.00 2.69
3183 8349 7.693951 CACAACTGTTTCTTCTTACACTTGAAG 59.306 37.037 0.00 0.00 40.53 3.02
3184 8350 6.927294 ACTGTTTCTTCTTACACTTGAAGG 57.073 37.500 0.00 0.00 39.85 3.46
3185 8351 5.297029 ACTGTTTCTTCTTACACTTGAAGGC 59.703 40.000 0.00 0.00 39.85 4.35
3186 8352 5.189928 TGTTTCTTCTTACACTTGAAGGCA 58.810 37.500 0.00 0.00 39.85 4.75
3187 8353 5.065988 TGTTTCTTCTTACACTTGAAGGCAC 59.934 40.000 0.00 0.00 39.85 5.01
3188 8354 4.415881 TCTTCTTACACTTGAAGGCACA 57.584 40.909 0.00 0.00 39.85 4.57
3189 8355 4.776349 TCTTCTTACACTTGAAGGCACAA 58.224 39.130 0.00 0.00 39.85 3.33
3190 8356 5.189928 TCTTCTTACACTTGAAGGCACAAA 58.810 37.500 0.00 0.00 39.85 2.83
3191 8357 5.650266 TCTTCTTACACTTGAAGGCACAAAA 59.350 36.000 0.00 0.00 39.85 2.44
3192 8358 6.321181 TCTTCTTACACTTGAAGGCACAAAAT 59.679 34.615 0.00 0.00 39.85 1.82
3193 8359 6.072112 TCTTACACTTGAAGGCACAAAATC 57.928 37.500 0.00 0.00 0.00 2.17
3194 8360 5.592282 TCTTACACTTGAAGGCACAAAATCA 59.408 36.000 0.00 0.00 0.00 2.57
3195 8361 4.942761 ACACTTGAAGGCACAAAATCAT 57.057 36.364 0.00 0.00 0.00 2.45
3196 8362 7.446931 TCTTACACTTGAAGGCACAAAATCATA 59.553 33.333 0.00 0.00 0.00 2.15
3197 8363 5.772521 ACACTTGAAGGCACAAAATCATAC 58.227 37.500 0.00 0.00 0.00 2.39
3198 8364 5.536161 ACACTTGAAGGCACAAAATCATACT 59.464 36.000 0.00 0.00 0.00 2.12
3199 8365 6.040842 ACACTTGAAGGCACAAAATCATACTT 59.959 34.615 0.00 0.00 0.00 2.24
3200 8366 6.583806 CACTTGAAGGCACAAAATCATACTTC 59.416 38.462 0.00 0.00 34.88 3.01
3201 8367 5.643379 TGAAGGCACAAAATCATACTTCC 57.357 39.130 0.00 0.00 33.73 3.46
3202 8368 5.324409 TGAAGGCACAAAATCATACTTCCT 58.676 37.500 0.00 0.00 33.73 3.36
3203 8369 5.774690 TGAAGGCACAAAATCATACTTCCTT 59.225 36.000 0.00 0.00 33.73 3.36
3204 8370 5.904362 AGGCACAAAATCATACTTCCTTC 57.096 39.130 0.00 0.00 0.00 3.46
3205 8371 5.574188 AGGCACAAAATCATACTTCCTTCT 58.426 37.500 0.00 0.00 0.00 2.85
3206 8372 6.721318 AGGCACAAAATCATACTTCCTTCTA 58.279 36.000 0.00 0.00 0.00 2.10
3207 8373 6.825721 AGGCACAAAATCATACTTCCTTCTAG 59.174 38.462 0.00 0.00 0.00 2.43
3208 8374 6.823689 GGCACAAAATCATACTTCCTTCTAGA 59.176 38.462 0.00 0.00 0.00 2.43
3209 8375 7.011857 GGCACAAAATCATACTTCCTTCTAGAG 59.988 40.741 0.00 0.00 0.00 2.43
3210 8376 7.766278 GCACAAAATCATACTTCCTTCTAGAGA 59.234 37.037 0.00 0.00 0.00 3.10
3211 8377 9.829507 CACAAAATCATACTTCCTTCTAGAGAT 57.170 33.333 0.00 0.00 0.00 2.75
3250 8416 1.269448 CACATTTGCGGCTAGGTTTGT 59.731 47.619 0.00 0.00 0.00 2.83
3445 8611 6.943899 AAATAAAAAGCAATCAACCCCCTA 57.056 33.333 0.00 0.00 0.00 3.53
3562 9319 1.003839 CGTGCCTTGCTCCAACCTA 60.004 57.895 0.00 0.00 0.00 3.08
3565 9322 0.476338 TGCCTTGCTCCAACCTAACA 59.524 50.000 0.00 0.00 0.00 2.41
3577 9931 0.319083 ACCTAACAATGTCGCCGTCA 59.681 50.000 0.00 0.00 0.00 4.35
3657 10014 2.623418 TCCTCACTAGAGAAGGGCAA 57.377 50.000 0.00 0.00 44.98 4.52
3660 10017 2.503356 CCTCACTAGAGAAGGGCAACAT 59.497 50.000 0.00 0.00 44.98 2.71
3848 10219 2.962569 CGTGGCTCTCTTGGACGA 59.037 61.111 0.00 0.00 31.71 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 79 4.172807 AGGGACTAGTGGGTGTTAATGAA 58.827 43.478 0.00 0.00 36.02 2.57
143 169 8.565896 TGCATCTATCACTTTTTGACATAACT 57.434 30.769 0.00 0.00 36.92 2.24
189 215 4.800993 TGTTAAACGTGTCCTGCAAATTTG 59.199 37.500 14.03 14.03 0.00 2.32
224 254 0.952280 TAGGCTAGCGAAGATGGACG 59.048 55.000 9.00 0.00 37.64 4.79
247 277 2.616842 AGGAACAACAGCCAAAGTTACG 59.383 45.455 0.00 0.00 30.22 3.18
266 296 2.681848 CTCTTGGAAGTGCTTGCATAGG 59.318 50.000 6.95 2.25 40.52 2.57
308 338 3.485463 TCGCATTGTAATAGAAGGGGG 57.515 47.619 0.00 0.00 0.00 5.40
309 339 4.035208 GTGTTCGCATTGTAATAGAAGGGG 59.965 45.833 0.00 0.00 0.00 4.79
310 340 4.634004 TGTGTTCGCATTGTAATAGAAGGG 59.366 41.667 0.00 0.00 0.00 3.95
311 341 5.351465 AGTGTGTTCGCATTGTAATAGAAGG 59.649 40.000 0.00 0.00 0.00 3.46
312 342 6.408858 AGTGTGTTCGCATTGTAATAGAAG 57.591 37.500 0.00 0.00 0.00 2.85
315 491 6.887376 AGTAGTGTGTTCGCATTGTAATAG 57.113 37.500 0.00 0.00 0.00 1.73
328 504 3.244457 GCCCCAAACTCTAGTAGTGTGTT 60.244 47.826 5.67 3.55 41.32 3.32
333 509 3.450904 TCATGCCCCAAACTCTAGTAGT 58.549 45.455 0.00 0.00 41.49 2.73
334 510 4.487714 TTCATGCCCCAAACTCTAGTAG 57.512 45.455 0.00 0.00 0.00 2.57
341 520 4.279169 CGATCAATATTCATGCCCCAAACT 59.721 41.667 0.00 0.00 0.00 2.66
358 537 1.482182 CATGGAGACCAGACCGATCAA 59.518 52.381 0.00 0.00 36.75 2.57
363 542 0.826715 ACATCATGGAGACCAGACCG 59.173 55.000 0.00 0.00 36.75 4.79
444 627 9.600646 CTCCAACGTTTTTGTTTTTGTTTTTAT 57.399 25.926 0.00 0.00 0.00 1.40
449 632 4.752604 AGCTCCAACGTTTTTGTTTTTGTT 59.247 33.333 0.00 0.00 0.00 2.83
451 634 4.919677 AGCTCCAACGTTTTTGTTTTTG 57.080 36.364 0.00 0.00 0.00 2.44
509 692 1.736365 TACTCACCACGTCGCCAACA 61.736 55.000 0.00 0.00 0.00 3.33
587 1057 4.990543 TCACAACACGAAATCATCAGAC 57.009 40.909 0.00 0.00 0.00 3.51
630 1100 3.066814 GTCGTAGTGGACCCGCCT 61.067 66.667 0.00 0.00 37.63 5.52
709 1313 4.222366 AGAGGAAGACCGGGTAAAACTTAG 59.778 45.833 6.32 0.00 41.83 2.18
712 1316 2.617658 AGAGGAAGACCGGGTAAAACT 58.382 47.619 6.32 0.00 41.83 2.66
717 1321 5.242393 CGATTAATTAGAGGAAGACCGGGTA 59.758 44.000 6.32 0.00 41.83 3.69
739 1343 0.970937 AGAGGACGAGATTTGCCCGA 60.971 55.000 0.00 0.00 0.00 5.14
743 1347 6.610741 ATTGATTAAGAGGACGAGATTTGC 57.389 37.500 0.00 0.00 0.00 3.68
834 1518 0.950555 CGTCAAGTGCTTGCTGCCTA 60.951 55.000 7.03 0.00 42.00 3.93
854 1538 0.609957 TGCCTGGTTTGAGCCTGATG 60.610 55.000 0.00 0.00 0.00 3.07
855 1539 0.323178 CTGCCTGGTTTGAGCCTGAT 60.323 55.000 0.00 0.00 0.00 2.90
856 1540 1.073722 CTGCCTGGTTTGAGCCTGA 59.926 57.895 0.00 0.00 0.00 3.86
857 1541 2.633509 GCTGCCTGGTTTGAGCCTG 61.634 63.158 0.00 0.00 0.00 4.85
895 1591 9.855361 GTCAATAATTCAGTCAATAACGATGAG 57.145 33.333 0.00 0.00 0.00 2.90
896 1592 8.539674 CGTCAATAATTCAGTCAATAACGATGA 58.460 33.333 0.00 0.00 0.00 2.92
897 1593 8.328146 ACGTCAATAATTCAGTCAATAACGATG 58.672 33.333 0.00 0.00 0.00 3.84
898 1594 8.420374 ACGTCAATAATTCAGTCAATAACGAT 57.580 30.769 0.00 0.00 0.00 3.73
937 1633 7.186021 ACGACGTCAATAATTCAGTCTTTTT 57.814 32.000 17.16 0.00 0.00 1.94
938 1634 6.399669 CGACGACGTCAATAATTCAGTCTTTT 60.400 38.462 26.26 0.00 32.09 2.27
939 1635 5.060569 CGACGACGTCAATAATTCAGTCTTT 59.939 40.000 26.26 0.00 32.09 2.52
941 1637 4.096311 CGACGACGTCAATAATTCAGTCT 58.904 43.478 26.26 0.00 32.09 3.24
942 1638 4.028670 GTCGACGACGTCAATAATTCAGTC 60.029 45.833 26.26 10.00 40.69 3.51
944 1640 3.849708 TGTCGACGACGTCAATAATTCAG 59.150 43.478 26.26 7.95 40.69 3.02
945 1641 3.605056 GTGTCGACGACGTCAATAATTCA 59.395 43.478 26.26 11.36 38.92 2.57
946 1642 3.001365 GGTGTCGACGACGTCAATAATTC 60.001 47.826 26.26 10.01 38.92 2.17
947 1643 2.919229 GGTGTCGACGACGTCAATAATT 59.081 45.455 26.26 0.00 38.92 1.40
948 1644 2.095110 TGGTGTCGACGACGTCAATAAT 60.095 45.455 26.26 0.00 38.92 1.28
949 1645 1.266446 TGGTGTCGACGACGTCAATAA 59.734 47.619 26.26 7.13 38.92 1.40
950 1646 0.873721 TGGTGTCGACGACGTCAATA 59.126 50.000 26.26 4.92 38.92 1.90
951 1647 0.242825 ATGGTGTCGACGACGTCAAT 59.757 50.000 26.26 13.77 38.92 2.57
952 1648 0.873721 TATGGTGTCGACGACGTCAA 59.126 50.000 26.26 6.67 38.92 3.18
953 1649 1.063027 GATATGGTGTCGACGACGTCA 59.937 52.381 26.26 20.93 40.69 4.35
954 1650 1.596464 GGATATGGTGTCGACGACGTC 60.596 57.143 22.06 18.04 40.69 4.34
955 1651 0.379669 GGATATGGTGTCGACGACGT 59.620 55.000 22.06 0.00 40.69 4.34
956 1652 0.661552 AGGATATGGTGTCGACGACG 59.338 55.000 22.06 0.00 34.95 5.12
957 1653 1.864435 GCAGGATATGGTGTCGACGAC 60.864 57.143 20.97 20.97 0.00 4.34
958 1654 0.384309 GCAGGATATGGTGTCGACGA 59.616 55.000 11.62 0.00 0.00 4.20
959 1655 0.385751 AGCAGGATATGGTGTCGACG 59.614 55.000 11.62 0.00 38.49 5.12
960 1656 1.269831 GGAGCAGGATATGGTGTCGAC 60.270 57.143 9.11 9.11 40.53 4.20
961 1657 1.040646 GGAGCAGGATATGGTGTCGA 58.959 55.000 0.00 0.00 40.53 4.20
962 1658 1.043816 AGGAGCAGGATATGGTGTCG 58.956 55.000 0.00 0.00 40.53 4.35
963 1659 3.196685 GGATAGGAGCAGGATATGGTGTC 59.803 52.174 0.00 0.00 40.53 3.67
964 1660 3.177228 GGATAGGAGCAGGATATGGTGT 58.823 50.000 0.00 0.00 40.53 4.16
965 1661 3.176411 TGGATAGGAGCAGGATATGGTG 58.824 50.000 0.00 0.00 40.53 4.17
966 1662 3.567375 TGGATAGGAGCAGGATATGGT 57.433 47.619 0.00 0.00 44.02 3.55
967 1663 4.040217 GCTATGGATAGGAGCAGGATATGG 59.960 50.000 0.00 0.00 36.20 2.74
968 1664 4.261952 CGCTATGGATAGGAGCAGGATATG 60.262 50.000 0.00 0.00 35.91 1.78
969 1665 3.894427 CGCTATGGATAGGAGCAGGATAT 59.106 47.826 0.00 0.00 35.91 1.63
1147 1885 0.687757 TGATCGAGGGAGGAAGGTGG 60.688 60.000 0.00 0.00 0.00 4.61
1149 1887 0.041238 TGTGATCGAGGGAGGAAGGT 59.959 55.000 0.00 0.00 0.00 3.50
1576 3535 1.676635 ATGGGGACGACGTTCTCGA 60.677 57.895 6.18 0.00 46.14 4.04
1630 3611 0.734253 CACTGACTGTAGCACGGCTC 60.734 60.000 1.46 0.00 40.44 4.70
1642 3623 8.150945 ACTTATACAACTGAATGAACACTGACT 58.849 33.333 0.00 0.00 0.00 3.41
1686 3717 3.194005 ACCACCCTGTAAGCATAATCG 57.806 47.619 0.00 0.00 0.00 3.34
1963 4103 2.516460 CATGCCCTGCTCTGCTCC 60.516 66.667 0.00 0.00 0.00 4.70
1995 4148 4.192317 ACCTCACAAGTTTCAGACACTTC 58.808 43.478 0.00 0.00 31.83 3.01
2120 4296 1.067565 ACACACGACGATGATGCTTCT 60.068 47.619 0.00 0.00 0.00 2.85
2177 4353 3.988379 GTGATTGCACACCTTTGAAGA 57.012 42.857 0.00 0.00 44.51 2.87
2240 4445 3.118775 TCTGACGGTGGAATCATGGTAAG 60.119 47.826 0.00 0.00 0.00 2.34
2462 6362 3.937778 TGAAGATCATCCATGGCAGAA 57.062 42.857 6.96 0.00 0.00 3.02
2516 7654 2.567615 TGAGTTTACCTTGAGGAGAGCC 59.432 50.000 3.59 0.00 38.94 4.70
2621 7785 6.360329 CAAATTCATTCAAGCAGAGCAAAAC 58.640 36.000 0.00 0.00 0.00 2.43
2719 7883 1.254284 CGGAAGTCCTCCAGCAGAGT 61.254 60.000 3.41 0.00 45.74 3.24
2721 7885 1.984570 CCGGAAGTCCTCCAGCAGA 60.985 63.158 0.00 0.00 45.74 4.26
2742 7906 3.325753 AGCAGCGAGAAGGCCCTT 61.326 61.111 0.00 0.00 0.00 3.95
3019 8185 1.298157 GCCCCCATTTTGCTTTTCGC 61.298 55.000 0.00 0.00 39.77 4.70
3020 8186 0.673333 GGCCCCCATTTTGCTTTTCG 60.673 55.000 0.00 0.00 0.00 3.46
3021 8187 0.692476 AGGCCCCCATTTTGCTTTTC 59.308 50.000 0.00 0.00 0.00 2.29
3022 8188 2.037385 TAGGCCCCCATTTTGCTTTT 57.963 45.000 0.00 0.00 0.00 2.27
3023 8189 1.628340 GTTAGGCCCCCATTTTGCTTT 59.372 47.619 0.00 0.00 0.00 3.51
3024 8190 1.275666 GTTAGGCCCCCATTTTGCTT 58.724 50.000 0.00 0.00 0.00 3.91
3025 8191 0.116143 TGTTAGGCCCCCATTTTGCT 59.884 50.000 0.00 0.00 0.00 3.91
3026 8192 1.203237 ATGTTAGGCCCCCATTTTGC 58.797 50.000 0.00 0.00 0.00 3.68
3027 8193 3.262915 TCAAATGTTAGGCCCCCATTTTG 59.737 43.478 17.59 14.00 36.84 2.44
3028 8194 3.525862 TCAAATGTTAGGCCCCCATTTT 58.474 40.909 17.59 4.02 36.84 1.82
3029 8195 3.197927 TCAAATGTTAGGCCCCCATTT 57.802 42.857 15.47 15.47 38.87 2.32
3030 8196 2.938428 TCAAATGTTAGGCCCCCATT 57.062 45.000 0.00 2.32 0.00 3.16
3031 8197 2.938428 TTCAAATGTTAGGCCCCCAT 57.062 45.000 0.00 0.00 0.00 4.00
3032 8198 2.704190 TTTCAAATGTTAGGCCCCCA 57.296 45.000 0.00 0.00 0.00 4.96
3069 8235 9.613428 TGTATAATTAAGTGCTTATGCTTGAGT 57.387 29.630 1.96 0.00 40.48 3.41
3118 8284 9.914131 GCTACTTGAGAATTTTCCAAAAACTAT 57.086 29.630 0.00 0.00 0.00 2.12
3119 8285 8.908903 TGCTACTTGAGAATTTTCCAAAAACTA 58.091 29.630 0.00 0.00 0.00 2.24
3120 8286 7.781056 TGCTACTTGAGAATTTTCCAAAAACT 58.219 30.769 0.00 0.00 0.00 2.66
3121 8287 8.419076 TTGCTACTTGAGAATTTTCCAAAAAC 57.581 30.769 0.00 0.00 0.00 2.43
3122 8288 9.044150 CATTGCTACTTGAGAATTTTCCAAAAA 57.956 29.630 0.00 0.00 0.00 1.94
3123 8289 7.171337 GCATTGCTACTTGAGAATTTTCCAAAA 59.829 33.333 0.16 0.00 0.00 2.44
3124 8290 6.646240 GCATTGCTACTTGAGAATTTTCCAAA 59.354 34.615 0.16 0.00 0.00 3.28
3125 8291 6.158598 GCATTGCTACTTGAGAATTTTCCAA 58.841 36.000 0.16 0.00 0.00 3.53
3126 8292 5.243507 TGCATTGCTACTTGAGAATTTTCCA 59.756 36.000 10.49 0.00 0.00 3.53
3127 8293 5.713025 TGCATTGCTACTTGAGAATTTTCC 58.287 37.500 10.49 0.00 0.00 3.13
3128 8294 7.642071 TTTGCATTGCTACTTGAGAATTTTC 57.358 32.000 10.49 0.00 0.00 2.29
3129 8295 8.611654 AATTTGCATTGCTACTTGAGAATTTT 57.388 26.923 10.49 0.00 0.00 1.82
3130 8296 8.092687 AGAATTTGCATTGCTACTTGAGAATTT 58.907 29.630 10.49 0.00 0.00 1.82
3131 8297 7.609056 AGAATTTGCATTGCTACTTGAGAATT 58.391 30.769 10.49 0.00 0.00 2.17
3132 8298 7.094075 TGAGAATTTGCATTGCTACTTGAGAAT 60.094 33.333 10.49 0.00 0.00 2.40
3133 8299 6.207221 TGAGAATTTGCATTGCTACTTGAGAA 59.793 34.615 10.49 0.00 0.00 2.87
3134 8300 5.706833 TGAGAATTTGCATTGCTACTTGAGA 59.293 36.000 10.49 0.00 0.00 3.27
3135 8301 5.798934 GTGAGAATTTGCATTGCTACTTGAG 59.201 40.000 10.49 0.00 0.00 3.02
3136 8302 5.241285 TGTGAGAATTTGCATTGCTACTTGA 59.759 36.000 10.49 0.00 0.00 3.02
3137 8303 5.463286 TGTGAGAATTTGCATTGCTACTTG 58.537 37.500 10.49 0.00 0.00 3.16
3138 8304 5.710513 TGTGAGAATTTGCATTGCTACTT 57.289 34.783 10.49 2.73 0.00 2.24
3139 8305 5.242393 AGTTGTGAGAATTTGCATTGCTACT 59.758 36.000 10.49 2.28 0.00 2.57
3140 8306 5.344128 CAGTTGTGAGAATTTGCATTGCTAC 59.656 40.000 10.49 0.00 0.00 3.58
3141 8307 5.009911 ACAGTTGTGAGAATTTGCATTGCTA 59.990 36.000 10.49 0.00 0.00 3.49
3142 8308 4.202182 ACAGTTGTGAGAATTTGCATTGCT 60.202 37.500 10.49 0.00 0.00 3.91
3143 8309 4.053295 ACAGTTGTGAGAATTTGCATTGC 58.947 39.130 0.46 0.46 0.00 3.56
3144 8310 6.477688 AGAAACAGTTGTGAGAATTTGCATTG 59.522 34.615 0.00 0.00 0.00 2.82
3145 8311 6.576185 AGAAACAGTTGTGAGAATTTGCATT 58.424 32.000 0.00 0.00 0.00 3.56
3146 8312 6.152932 AGAAACAGTTGTGAGAATTTGCAT 57.847 33.333 0.00 0.00 0.00 3.96
3147 8313 5.581126 AGAAACAGTTGTGAGAATTTGCA 57.419 34.783 0.00 0.00 0.00 4.08
3148 8314 6.268566 AGAAGAAACAGTTGTGAGAATTTGC 58.731 36.000 0.00 0.00 0.00 3.68
3149 8315 9.226345 GTAAGAAGAAACAGTTGTGAGAATTTG 57.774 33.333 0.00 0.00 0.00 2.32
3150 8316 8.956426 TGTAAGAAGAAACAGTTGTGAGAATTT 58.044 29.630 0.00 0.00 0.00 1.82
3151 8317 8.398665 GTGTAAGAAGAAACAGTTGTGAGAATT 58.601 33.333 0.00 0.00 0.00 2.17
3152 8318 7.770897 AGTGTAAGAAGAAACAGTTGTGAGAAT 59.229 33.333 0.00 0.00 0.00 2.40
3153 8319 7.103641 AGTGTAAGAAGAAACAGTTGTGAGAA 58.896 34.615 0.00 0.00 0.00 2.87
3154 8320 6.640518 AGTGTAAGAAGAAACAGTTGTGAGA 58.359 36.000 0.00 0.00 0.00 3.27
3155 8321 6.910536 AGTGTAAGAAGAAACAGTTGTGAG 57.089 37.500 0.00 0.00 0.00 3.51
3156 8322 7.072177 CAAGTGTAAGAAGAAACAGTTGTGA 57.928 36.000 12.62 0.00 45.56 3.58
3160 8326 6.183360 GCCTTCAAGTGTAAGAAGAAACAGTT 60.183 38.462 0.00 0.00 42.95 3.16
3161 8327 5.297029 GCCTTCAAGTGTAAGAAGAAACAGT 59.703 40.000 0.00 0.00 42.95 3.55
3162 8328 5.296780 TGCCTTCAAGTGTAAGAAGAAACAG 59.703 40.000 0.00 0.00 42.95 3.16
3163 8329 5.065988 GTGCCTTCAAGTGTAAGAAGAAACA 59.934 40.000 0.00 0.00 42.95 2.83
3164 8330 5.065988 TGTGCCTTCAAGTGTAAGAAGAAAC 59.934 40.000 0.00 0.00 42.95 2.78
3165 8331 5.189928 TGTGCCTTCAAGTGTAAGAAGAAA 58.810 37.500 0.00 0.00 42.95 2.52
3166 8332 4.776349 TGTGCCTTCAAGTGTAAGAAGAA 58.224 39.130 0.00 0.00 42.95 2.52
3167 8333 4.415881 TGTGCCTTCAAGTGTAAGAAGA 57.584 40.909 0.00 0.00 42.95 2.87
3168 8334 5.499139 TTTGTGCCTTCAAGTGTAAGAAG 57.501 39.130 0.00 0.00 40.64 2.85
3169 8335 5.906113 TTTTGTGCCTTCAAGTGTAAGAA 57.094 34.783 0.00 0.00 0.00 2.52
3170 8336 5.592282 TGATTTTGTGCCTTCAAGTGTAAGA 59.408 36.000 0.00 0.00 0.00 2.10
3171 8337 5.830912 TGATTTTGTGCCTTCAAGTGTAAG 58.169 37.500 0.00 0.00 0.00 2.34
3172 8338 5.843673 TGATTTTGTGCCTTCAAGTGTAA 57.156 34.783 0.00 0.00 0.00 2.41
3173 8339 6.714810 AGTATGATTTTGTGCCTTCAAGTGTA 59.285 34.615 0.00 0.00 0.00 2.90
3174 8340 4.942761 ATGATTTTGTGCCTTCAAGTGT 57.057 36.364 0.00 0.00 0.00 3.55
3175 8341 6.017400 AGTATGATTTTGTGCCTTCAAGTG 57.983 37.500 0.00 0.00 0.00 3.16
3176 8342 6.294731 GGAAGTATGATTTTGTGCCTTCAAGT 60.295 38.462 0.00 0.00 30.91 3.16
3177 8343 6.071728 AGGAAGTATGATTTTGTGCCTTCAAG 60.072 38.462 0.00 0.00 30.91 3.02
3178 8344 5.774690 AGGAAGTATGATTTTGTGCCTTCAA 59.225 36.000 0.00 0.00 30.91 2.69
3179 8345 5.324409 AGGAAGTATGATTTTGTGCCTTCA 58.676 37.500 0.00 0.00 30.91 3.02
3180 8346 5.904362 AGGAAGTATGATTTTGTGCCTTC 57.096 39.130 0.00 0.00 0.00 3.46
3181 8347 6.012745 AGAAGGAAGTATGATTTTGTGCCTT 58.987 36.000 0.00 0.00 36.04 4.35
3182 8348 5.574188 AGAAGGAAGTATGATTTTGTGCCT 58.426 37.500 0.00 0.00 0.00 4.75
3183 8349 5.904362 AGAAGGAAGTATGATTTTGTGCC 57.096 39.130 0.00 0.00 0.00 5.01
3184 8350 7.766278 TCTCTAGAAGGAAGTATGATTTTGTGC 59.234 37.037 0.00 0.00 0.00 4.57
3185 8351 9.829507 ATCTCTAGAAGGAAGTATGATTTTGTG 57.170 33.333 0.00 0.00 0.00 3.33
3193 8359 8.772705 GCAATTGAATCTCTAGAAGGAAGTATG 58.227 37.037 10.34 0.00 0.00 2.39
3194 8360 8.489489 TGCAATTGAATCTCTAGAAGGAAGTAT 58.511 33.333 10.34 0.00 0.00 2.12
3195 8361 7.766278 GTGCAATTGAATCTCTAGAAGGAAGTA 59.234 37.037 10.34 0.00 0.00 2.24
3196 8362 6.597280 GTGCAATTGAATCTCTAGAAGGAAGT 59.403 38.462 10.34 0.00 0.00 3.01
3197 8363 6.596888 TGTGCAATTGAATCTCTAGAAGGAAG 59.403 38.462 10.34 0.00 0.00 3.46
3198 8364 6.475504 TGTGCAATTGAATCTCTAGAAGGAA 58.524 36.000 10.34 0.00 0.00 3.36
3199 8365 6.053632 TGTGCAATTGAATCTCTAGAAGGA 57.946 37.500 10.34 0.00 0.00 3.36
3200 8366 6.748333 TTGTGCAATTGAATCTCTAGAAGG 57.252 37.500 10.34 0.00 0.00 3.46
3201 8367 8.295288 AGTTTTGTGCAATTGAATCTCTAGAAG 58.705 33.333 10.34 0.00 0.00 2.85
3202 8368 8.169977 AGTTTTGTGCAATTGAATCTCTAGAA 57.830 30.769 10.34 0.00 0.00 2.10
3203 8369 7.750229 AGTTTTGTGCAATTGAATCTCTAGA 57.250 32.000 10.34 0.00 0.00 2.43
3204 8370 7.965107 GGTAGTTTTGTGCAATTGAATCTCTAG 59.035 37.037 10.34 0.00 0.00 2.43
3205 8371 7.446931 TGGTAGTTTTGTGCAATTGAATCTCTA 59.553 33.333 10.34 0.08 0.00 2.43
3206 8372 6.265196 TGGTAGTTTTGTGCAATTGAATCTCT 59.735 34.615 10.34 1.00 0.00 3.10
3207 8373 6.363357 GTGGTAGTTTTGTGCAATTGAATCTC 59.637 38.462 10.34 0.00 0.00 2.75
3208 8374 6.183360 TGTGGTAGTTTTGTGCAATTGAATCT 60.183 34.615 10.34 1.90 0.00 2.40
3209 8375 5.982516 TGTGGTAGTTTTGTGCAATTGAATC 59.017 36.000 10.34 0.00 0.00 2.52
3210 8376 5.911752 TGTGGTAGTTTTGTGCAATTGAAT 58.088 33.333 10.34 0.00 0.00 2.57
3211 8377 5.330455 TGTGGTAGTTTTGTGCAATTGAA 57.670 34.783 10.34 0.00 0.00 2.69
3250 8416 6.816640 CGGATTAGTGACTTGATGGTTTTCTA 59.183 38.462 0.00 0.00 0.00 2.10
3260 8426 3.394674 TGCAACGGATTAGTGACTTGA 57.605 42.857 0.00 0.00 0.00 3.02
3445 8611 1.307691 AGCAGGGGGATTGAGAGCT 60.308 57.895 0.00 0.00 0.00 4.09
3513 8704 3.531207 TCTGCGCCATCGAGGGAG 61.531 66.667 22.53 19.06 38.09 4.30
3514 8705 3.838271 GTCTGCGCCATCGAGGGA 61.838 66.667 22.53 0.00 38.09 4.20
3562 9319 1.196808 GACATTGACGGCGACATTGTT 59.803 47.619 29.36 18.63 33.85 2.83
3565 9322 0.036388 AGGACATTGACGGCGACATT 60.036 50.000 16.62 7.52 0.00 2.71
3577 9931 1.376424 CACGGCAGCTCAGGACATT 60.376 57.895 0.00 0.00 0.00 2.71
3657 10014 4.457496 CGCTGAGGGTGCCGATGT 62.457 66.667 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.