Multiple sequence alignment - TraesCS7B01G061900

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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 TraesCS7B01G061900 chr7B 100.000 3520 0 0 3236 6755 64320364 64323883 0.000000e+00 6501.0
1 TraesCS7B01G061900 chr7B 100.000 2858 0 0 1 2858 64317129 64319986 0.000000e+00 5278.0
2 TraesCS7B01G061900 chr7B 92.000 50 3 1 6705 6754 448633031 448632983 1.220000e-07 69.4
3 TraesCS7B01G061900 chr7B 100.000 30 0 0 199 228 524720358 524720329 1.000000e-03 56.5
4 TraesCS7B01G061900 chr3A 91.207 2536 184 25 3247 5756 26405018 26407540 0.000000e+00 3411.0
5 TraesCS7B01G061900 chr3A 90.621 1546 125 9 4403 5938 26261463 26262998 0.000000e+00 2034.0
6 TraesCS7B01G061900 chr3A 89.130 1564 153 13 4478 6033 26481456 26483010 0.000000e+00 1930.0
7 TraesCS7B01G061900 chr3A 80.155 1164 164 36 3236 4368 26480169 26481296 0.000000e+00 808.0
8 TraesCS7B01G061900 chr3A 90.244 574 47 8 2291 2858 26479549 26480119 0.000000e+00 741.0
9 TraesCS7B01G061900 chr3A 88.007 567 44 15 2291 2853 26404454 26405000 0.000000e+00 649.0
10 TraesCS7B01G061900 chr3A 85.060 502 46 13 6207 6699 26429482 26429963 1.020000e-132 484.0
11 TraesCS7B01G061900 chr3A 77.104 808 121 23 954 1748 26259940 26260696 6.310000e-110 409.0
12 TraesCS7B01G061900 chr3A 88.213 263 29 1 2032 2292 26404110 26404372 5.090000e-81 313.0
13 TraesCS7B01G061900 chr3A 87.554 233 19 6 6078 6304 26263139 26263367 1.870000e-65 261.0
14 TraesCS7B01G061900 chr7D 96.231 1592 53 1 4446 6037 105686151 105687735 0.000000e+00 2601.0
15 TraesCS7B01G061900 chr7D 92.344 1698 71 22 221 1876 105681928 105683608 0.000000e+00 2361.0
16 TraesCS7B01G061900 chr7D 93.023 774 50 4 3236 4008 105684885 105685655 0.000000e+00 1127.0
17 TraesCS7B01G061900 chr7D 96.491 570 17 3 2291 2858 105684268 105684836 0.000000e+00 939.0
18 TraesCS7B01G061900 chr7D 92.840 419 23 6 1876 2292 105683775 105684188 9.690000e-168 601.0
19 TraesCS7B01G061900 chr7D 95.960 198 8 0 4252 4449 105685654 105685851 8.450000e-84 322.0
20 TraesCS7B01G061900 chr7D 91.011 178 13 2 1 175 105681625 105681802 3.150000e-58 237.0
21 TraesCS7B01G061900 chr3B 88.805 2108 173 26 4403 6460 29781853 29783947 0.000000e+00 2527.0
22 TraesCS7B01G061900 chr3B 86.630 2341 209 40 4372 6699 29853849 29856098 0.000000e+00 2494.0
23 TraesCS7B01G061900 chr3B 88.312 2079 178 22 4403 6453 30517248 30519289 0.000000e+00 2433.0
24 TraesCS7B01G061900 chr3B 85.272 2356 255 43 4139 6460 30376476 30378773 0.000000e+00 2344.0
25 TraesCS7B01G061900 chr3B 89.141 1851 154 22 4405 6238 30504240 30506060 0.000000e+00 2261.0
26 TraesCS7B01G061900 chr3B 89.970 1655 138 13 4403 6041 30207241 30208883 0.000000e+00 2111.0
27 TraesCS7B01G061900 chr3B 85.874 1430 139 31 3286 4684 29527672 29526275 0.000000e+00 1463.0
28 TraesCS7B01G061900 chr3B 87.808 894 94 10 1008 1891 30529136 30530024 0.000000e+00 1033.0
29 TraesCS7B01G061900 chr3B 79.542 1178 166 47 3237 4368 30502963 30504111 0.000000e+00 771.0
30 TraesCS7B01G061900 chr3B 79.460 1149 162 44 3236 4368 30532002 30533092 0.000000e+00 747.0
31 TraesCS7B01G061900 chr3B 88.929 551 41 6 2299 2849 30236686 30237216 0.000000e+00 662.0
32 TraesCS7B01G061900 chr3B 91.068 459 39 2 2392 2849 30531486 30531943 2.680000e-173 619.0
33 TraesCS7B01G061900 chr3B 89.641 473 45 3 2390 2858 30514885 30515357 3.490000e-167 599.0
34 TraesCS7B01G061900 chr3B 83.163 588 74 10 2287 2854 29779954 29780536 1.300000e-141 514.0
35 TraesCS7B01G061900 chr3B 83.077 585 79 10 2287 2854 30204800 30205381 1.300000e-141 514.0
36 TraesCS7B01G061900 chr3B 82.842 577 72 10 2291 2852 30502342 30502906 6.090000e-135 492.0
37 TraesCS7B01G061900 chr3B 87.154 397 45 5 1896 2289 30530182 30530575 4.810000e-121 446.0
38 TraesCS7B01G061900 chr3B 87.571 354 25 9 6207 6551 29736343 29736686 6.350000e-105 392.0
39 TraesCS7B01G061900 chr3B 80.747 509 83 15 1795 2292 30501777 30502281 3.820000e-102 383.0
40 TraesCS7B01G061900 chr3B 88.110 328 30 6 1971 2292 30514299 30514623 1.370000e-101 381.0
41 TraesCS7B01G061900 chr3B 87.459 303 36 2 3236 3537 30515407 30515708 1.390000e-91 348.0
42 TraesCS7B01G061900 chr3B 88.593 263 26 3 3236 3497 30237275 30237534 3.930000e-82 316.0
43 TraesCS7B01G061900 chr3B 82.857 350 49 7 3678 4027 29564403 29564065 3.060000e-78 303.0
44 TraesCS7B01G061900 chr3B 83.434 332 40 7 3238 3558 30473173 30473500 1.840000e-75 294.0
45 TraesCS7B01G061900 chr3B 88.430 242 17 6 6226 6456 30209141 30209382 1.430000e-71 281.0
46 TraesCS7B01G061900 chr3B 75.676 629 116 23 1153 1761 29418820 29418209 5.160000e-71 279.0
47 TraesCS7B01G061900 chr3B 86.328 256 30 3 6096 6350 30535577 30535828 2.400000e-69 274.0
48 TraesCS7B01G061900 chr3B 77.149 477 76 16 3912 4366 30206645 30207110 5.230000e-61 246.0
49 TraesCS7B01G061900 chr3B 77.053 475 77 15 3914 4366 29781257 29781721 1.880000e-60 244.0
50 TraesCS7B01G061900 chr3B 89.189 185 14 2 254 432 29483705 29483521 6.820000e-55 226.0
51 TraesCS7B01G061900 chr3B 88.372 129 15 0 6498 6626 30209393 30209521 9.070000e-34 156.0
52 TraesCS7B01G061900 chr3B 87.500 128 11 2 4102 4224 29564048 29563921 7.060000e-30 143.0
53 TraesCS7B01G061900 chr3B 86.822 129 11 2 4102 4224 30067666 30067538 9.130000e-29 139.0
54 TraesCS7B01G061900 chr3B 91.579 95 8 0 6532 6626 29785812 29785906 1.530000e-26 132.0
55 TraesCS7B01G061900 chr3B 74.807 389 38 21 6311 6699 30247036 30247364 3.310000e-23 121.0
56 TraesCS7B01G061900 chr3B 92.857 70 2 2 1153 1219 75476702 75476633 1.550000e-16 99.0
57 TraesCS7B01G061900 chr3D 91.535 1524 109 12 4372 5888 18908559 18910069 0.000000e+00 2082.0
58 TraesCS7B01G061900 chr3D 86.290 496 46 11 6207 6699 18954454 18954930 2.790000e-143 520.0
59 TraesCS7B01G061900 chr3D 84.388 237 26 11 4141 4368 18800784 18801018 8.820000e-54 222.0
60 TraesCS7B01G061900 chr3D 89.247 93 9 1 4276 4368 19013746 19013837 1.540000e-21 115.0
61 TraesCS7B01G061900 chr3D 93.478 46 2 1 6706 6750 31760902 31760857 4.370000e-07 67.6
62 TraesCS7B01G061900 chr3D 91.837 49 1 3 6705 6753 560151537 560151492 1.570000e-06 65.8
63 TraesCS7B01G061900 chr4A 92.000 50 3 1 6706 6755 146050051 146050099 1.220000e-07 69.4
64 TraesCS7B01G061900 chr4A 97.500 40 1 0 6716 6755 668156729 668156768 1.220000e-07 69.4
65 TraesCS7B01G061900 chr5B 90.196 51 5 0 6703 6753 672249096 672249146 4.370000e-07 67.6
66 TraesCS7B01G061900 chr2A 91.667 48 2 2 6704 6750 653911067 653911113 1.570000e-06 65.8
67 TraesCS7B01G061900 chr2A 97.368 38 1 0 6717 6754 741096676 741096639 1.570000e-06 65.8
68 TraesCS7B01G061900 chr1D 91.489 47 2 2 6706 6750 308193241 308193287 5.660000e-06 63.9
69 TraesCS7B01G061900 chrUn 92.683 41 3 0 202 242 289050699 289050659 7.320000e-05 60.2
70 TraesCS7B01G061900 chrUn 92.500 40 3 0 206 245 42479276 42479237 2.630000e-04 58.4
71 TraesCS7B01G061900 chr5A 92.683 41 3 0 202 242 476958935 476958895 7.320000e-05 60.2
72 TraesCS7B01G061900 chr5A 100.000 28 0 0 200 227 536862517 536862544 1.200000e-02 52.8
73 TraesCS7B01G061900 chr6B 100.000 29 0 0 203 231 704026492 704026464 3.000000e-03 54.7
74 TraesCS7B01G061900 chr2D 100.000 28 0 0 200 227 624976487 624976460 1.200000e-02 52.8
75 TraesCS7B01G061900 chr1B 100.000 28 0 0 200 227 495804630 495804657 1.200000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G061900 chr7B 64317129 64323883 6754 False 5889.500000 6501 100.000000 1 6755 2 chr7B.!!$F1 6754
1 TraesCS7B01G061900 chr3A 26404110 26407540 3430 False 1457.666667 3411 89.142333 2032 5756 3 chr3A.!!$F3 3724
2 TraesCS7B01G061900 chr3A 26479549 26483010 3461 False 1159.666667 1930 86.509667 2291 6033 3 chr3A.!!$F4 3742
3 TraesCS7B01G061900 chr3A 26259940 26263367 3427 False 901.333333 2034 85.093000 954 6304 3 chr3A.!!$F2 5350
4 TraesCS7B01G061900 chr7D 105681625 105687735 6110 False 1169.714286 2601 93.985714 1 6037 7 chr7D.!!$F1 6036
5 TraesCS7B01G061900 chr3B 29853849 29856098 2249 False 2494.000000 2494 86.630000 4372 6699 1 chr3B.!!$F2 2327
6 TraesCS7B01G061900 chr3B 30376476 30378773 2297 False 2344.000000 2344 85.272000 4139 6460 1 chr3B.!!$F4 2321
7 TraesCS7B01G061900 chr3B 29526275 29527672 1397 True 1463.000000 1463 85.874000 3286 4684 1 chr3B.!!$R3 1398
8 TraesCS7B01G061900 chr3B 30501777 30506060 4283 False 976.750000 2261 83.068000 1795 6238 4 chr3B.!!$F9 4443
9 TraesCS7B01G061900 chr3B 30514299 30519289 4990 False 940.250000 2433 88.380500 1971 6453 4 chr3B.!!$F10 4482
10 TraesCS7B01G061900 chr3B 29779954 29785906 5952 False 854.250000 2527 85.150000 2287 6626 4 chr3B.!!$F6 4339
11 TraesCS7B01G061900 chr3B 30204800 30209521 4721 False 661.600000 2111 85.399600 2287 6626 5 chr3B.!!$F7 4339
12 TraesCS7B01G061900 chr3B 30529136 30535828 6692 False 623.800000 1033 86.363600 1008 6350 5 chr3B.!!$F11 5342
13 TraesCS7B01G061900 chr3B 30236686 30237534 848 False 489.000000 662 88.761000 2299 3497 2 chr3B.!!$F8 1198
14 TraesCS7B01G061900 chr3B 29418209 29418820 611 True 279.000000 279 75.676000 1153 1761 1 chr3B.!!$R1 608
15 TraesCS7B01G061900 chr3D 18908559 18910069 1510 False 2082.000000 2082 91.535000 4372 5888 1 chr3D.!!$F2 1516

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
852 970 0.107703 TGCATGAATGTCCCGTCTCC 60.108 55.000 0.00 0.00 0.00 3.71 F
1676 1851 0.317603 CTTGTCGAGTATACGGCCGG 60.318 60.000 31.76 11.88 37.06 6.13 F
2299 2665 0.966920 TTCCTTCTTCCTTCGACGCT 59.033 50.000 0.00 0.00 0.00 5.07 F
2301 2667 1.071605 CCTTCTTCCTTCGACGCTTG 58.928 55.000 0.00 0.00 0.00 4.01 F
3574 5264 1.831736 AGTTAGGGGGTTCTGATCGTG 59.168 52.381 0.00 0.00 0.00 4.35 F
3999 7041 2.608546 CCCATGCAATGCCATTTAAACG 59.391 45.455 1.53 0.00 44.97 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2669 4033 0.037447 AGAAGAGCTCTTGGTTGGCC 59.963 55.000 33.07 16.38 36.11 5.36 R
3553 5240 3.028850 CACGATCAGAACCCCCTAACTA 58.971 50.000 0.00 0.00 0.00 2.24 R
3871 6287 3.071479 GTGTGGCTAAACCGAAGATTGA 58.929 45.455 0.00 0.00 43.94 2.57 R
3980 7021 5.101628 AGTACGTTTAAATGGCATTGCATG 58.898 37.500 14.47 8.59 0.00 4.06 R
4720 8254 1.529226 TGAAAACCACACCATAGCCG 58.471 50.000 0.00 0.00 0.00 5.52 R
5801 9363 0.389948 GTACAGGCCACCTTCTCACG 60.390 60.000 5.01 0.00 0.00 4.35 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 45 8.265055 ACTAATTAAGATTTTGATGTCCTCGGA 58.735 33.333 0.00 0.00 0.00 4.55
48 49 6.840780 AAGATTTTGATGTCCTCGGAAAAT 57.159 33.333 0.00 0.00 0.00 1.82
83 84 5.995282 ACGAATAATGACTTTGACCAACTCA 59.005 36.000 0.00 0.00 0.00 3.41
100 101 6.282930 CCAACTCATCATTGGTTTGTTTCTT 58.717 36.000 0.00 0.00 41.55 2.52
122 123 3.053455 GTCTCTCATATAGTTGCACGCC 58.947 50.000 0.00 0.00 0.00 5.68
153 156 2.820197 GTGCGGAAGAAAAGGGATCTTT 59.180 45.455 0.00 0.00 44.40 2.52
171 174 5.277857 TCTTTTCATCTATTCCCTCCGTC 57.722 43.478 0.00 0.00 0.00 4.79
173 176 3.330126 TTCATCTATTCCCTCCGTCCT 57.670 47.619 0.00 0.00 0.00 3.85
174 177 4.464652 TTCATCTATTCCCTCCGTCCTA 57.535 45.455 0.00 0.00 0.00 2.94
175 178 4.676799 TCATCTATTCCCTCCGTCCTAT 57.323 45.455 0.00 0.00 0.00 2.57
177 180 5.756918 TCATCTATTCCCTCCGTCCTATAG 58.243 45.833 0.00 0.00 0.00 1.31
179 182 5.595814 TCTATTCCCTCCGTCCTATAGTT 57.404 43.478 0.00 0.00 0.00 2.24
181 184 4.957684 ATTCCCTCCGTCCTATAGTTTG 57.042 45.455 0.00 0.00 0.00 2.93
182 185 2.037144 TCCCTCCGTCCTATAGTTTGC 58.963 52.381 0.00 0.00 0.00 3.68
183 186 1.760613 CCCTCCGTCCTATAGTTTGCA 59.239 52.381 0.00 0.00 0.00 4.08
184 187 2.169769 CCCTCCGTCCTATAGTTTGCAA 59.830 50.000 0.00 0.00 0.00 4.08
185 188 3.370103 CCCTCCGTCCTATAGTTTGCAAA 60.370 47.826 8.05 8.05 0.00 3.68
186 189 4.258543 CCTCCGTCCTATAGTTTGCAAAA 58.741 43.478 14.67 0.00 0.00 2.44
187 190 4.698304 CCTCCGTCCTATAGTTTGCAAAAA 59.302 41.667 14.67 5.65 0.00 1.94
189 192 6.189677 TCCGTCCTATAGTTTGCAAAAATG 57.810 37.500 14.67 2.98 0.00 2.32
191 194 6.027749 CCGTCCTATAGTTTGCAAAAATGTC 58.972 40.000 14.67 0.55 0.00 3.06
192 195 6.128007 CCGTCCTATAGTTTGCAAAAATGTCT 60.128 38.462 14.67 8.91 0.00 3.41
193 196 7.305474 CGTCCTATAGTTTGCAAAAATGTCTT 58.695 34.615 14.67 1.04 0.00 3.01
194 197 8.447833 CGTCCTATAGTTTGCAAAAATGTCTTA 58.552 33.333 14.67 2.05 0.00 2.10
229 313 9.382244 GCTTGCAAAAACGTCTTATATTATAGG 57.618 33.333 0.00 0.00 0.00 2.57
249 333 2.737252 GGACGGAAGAAGTACTTTGCAG 59.263 50.000 10.02 5.85 39.13 4.41
268 352 3.239941 GCAGACTTGTAATACACGCTACG 59.760 47.826 0.00 0.00 0.00 3.51
318 402 2.483745 CTGCAGCTGCCATGTTCG 59.516 61.111 34.64 11.01 41.18 3.95
377 461 3.303990 CCACCAGTGATGTTTCTTTGTCG 60.304 47.826 0.00 0.00 0.00 4.35
378 462 3.312421 CACCAGTGATGTTTCTTTGTCGT 59.688 43.478 0.00 0.00 0.00 4.34
379 463 3.945285 ACCAGTGATGTTTCTTTGTCGTT 59.055 39.130 0.00 0.00 0.00 3.85
380 464 4.201910 ACCAGTGATGTTTCTTTGTCGTTG 60.202 41.667 0.00 0.00 0.00 4.10
381 465 4.201910 CCAGTGATGTTTCTTTGTCGTTGT 60.202 41.667 0.00 0.00 0.00 3.32
382 466 4.963953 CAGTGATGTTTCTTTGTCGTTGTC 59.036 41.667 0.00 0.00 0.00 3.18
384 468 3.619483 TGATGTTTCTTTGTCGTTGTCGT 59.381 39.130 0.00 0.00 38.33 4.34
386 470 3.993547 TGTTTCTTTGTCGTTGTCGTTC 58.006 40.909 0.00 0.00 38.33 3.95
387 471 3.181518 TGTTTCTTTGTCGTTGTCGTTCC 60.182 43.478 0.00 0.00 38.33 3.62
388 472 2.589798 TCTTTGTCGTTGTCGTTCCT 57.410 45.000 0.00 0.00 38.33 3.36
389 473 2.198406 TCTTTGTCGTTGTCGTTCCTG 58.802 47.619 0.00 0.00 38.33 3.86
390 474 0.653636 TTTGTCGTTGTCGTTCCTGC 59.346 50.000 0.00 0.00 38.33 4.85
391 475 1.484227 TTGTCGTTGTCGTTCCTGCG 61.484 55.000 0.00 0.00 38.33 5.18
444 528 4.477975 CGCCGTGTCCTCTCGTCC 62.478 72.222 0.00 0.00 0.00 4.79
460 544 3.006940 TCGTCCAGATAAAACCATGCAC 58.993 45.455 0.00 0.00 0.00 4.57
472 556 1.181786 CCATGCACCCACCGTATTTT 58.818 50.000 0.00 0.00 0.00 1.82
571 655 3.897141 TCACTGTATTATTCGCCCACA 57.103 42.857 0.00 0.00 0.00 4.17
591 675 1.135083 ACGGCTATGAACAGAACGAGG 60.135 52.381 0.00 0.00 0.00 4.63
626 710 4.035909 GTCGTCAGTAATGGTTTTGGTTGT 59.964 41.667 0.00 0.00 0.00 3.32
627 711 4.641094 TCGTCAGTAATGGTTTTGGTTGTT 59.359 37.500 0.00 0.00 0.00 2.83
628 712 5.125739 TCGTCAGTAATGGTTTTGGTTGTTT 59.874 36.000 0.00 0.00 0.00 2.83
629 713 5.808030 CGTCAGTAATGGTTTTGGTTGTTTT 59.192 36.000 0.00 0.00 0.00 2.43
630 714 6.020201 CGTCAGTAATGGTTTTGGTTGTTTTC 60.020 38.462 0.00 0.00 0.00 2.29
631 715 6.256975 GTCAGTAATGGTTTTGGTTGTTTTCC 59.743 38.462 0.00 0.00 0.00 3.13
636 746 3.133183 TGGTTTTGGTTGTTTTCCCTAGC 59.867 43.478 0.00 0.00 0.00 3.42
672 782 3.680458 GCGTTCAAAGTTCAAACCCAAAA 59.320 39.130 0.00 0.00 0.00 2.44
673 783 4.201676 GCGTTCAAAGTTCAAACCCAAAAG 60.202 41.667 0.00 0.00 0.00 2.27
686 796 2.356673 AAAAGCCGGACCGACGAC 60.357 61.111 17.49 1.48 35.47 4.34
687 797 3.871248 AAAAGCCGGACCGACGACC 62.871 63.158 17.49 0.00 35.47 4.79
690 800 4.790861 GCCGGACCGACGACCTTC 62.791 72.222 17.49 0.00 35.47 3.46
691 801 4.125695 CCGGACCGACGACCTTCC 62.126 72.222 17.49 0.00 35.47 3.46
692 802 3.367743 CGGACCGACGACCTTCCA 61.368 66.667 8.64 0.00 35.47 3.53
694 804 1.368579 GGACCGACGACCTTCCAAA 59.631 57.895 0.00 0.00 0.00 3.28
751 869 1.681327 GTGAGCTCCCCACTACCGA 60.681 63.158 12.15 0.00 0.00 4.69
852 970 0.107703 TGCATGAATGTCCCGTCTCC 60.108 55.000 0.00 0.00 0.00 3.71
862 980 3.991051 CCGTCTCCCGTGTGTGCT 61.991 66.667 0.00 0.00 33.66 4.40
864 982 2.022129 CGTCTCCCGTGTGTGCTTC 61.022 63.158 0.00 0.00 0.00 3.86
865 983 1.367840 GTCTCCCGTGTGTGCTTCT 59.632 57.895 0.00 0.00 0.00 2.85
867 985 1.000506 GTCTCCCGTGTGTGCTTCTTA 59.999 52.381 0.00 0.00 0.00 2.10
894 1014 5.413833 GCAATCTCCTTCTCAATTCTCAACA 59.586 40.000 0.00 0.00 0.00 3.33
912 1032 4.070716 CAACATCTTCAACTGCCTCTCTT 58.929 43.478 0.00 0.00 0.00 2.85
913 1033 3.936564 ACATCTTCAACTGCCTCTCTTC 58.063 45.455 0.00 0.00 0.00 2.87
914 1034 3.326006 ACATCTTCAACTGCCTCTCTTCA 59.674 43.478 0.00 0.00 0.00 3.02
945 1065 4.135153 CCCTCTCTGCGTCACCCG 62.135 72.222 0.00 0.00 40.40 5.28
972 1092 0.931005 GCCGTTAGCCTCTTCAATCG 59.069 55.000 0.00 0.00 34.35 3.34
985 1105 1.083489 TCAATCGTCCATTCCGTTGC 58.917 50.000 0.00 0.00 0.00 4.17
1088 1217 2.415426 CGCCCAAAACACCACCAC 59.585 61.111 0.00 0.00 0.00 4.16
1090 1219 2.415426 CCCAAAACACCACCACGC 59.585 61.111 0.00 0.00 0.00 5.34
1110 1239 2.803670 ACGTTGCCGTCATCGTCG 60.804 61.111 0.00 0.00 46.28 5.12
1125 1284 4.671590 TCGACCTCCTGCGACCCA 62.672 66.667 0.00 0.00 0.00 4.51
1133 1292 2.887568 CTGCGACCCAGCGATGTC 60.888 66.667 0.00 0.00 40.67 3.06
1136 1295 2.887568 CGACCCAGCGATGTCTGC 60.888 66.667 0.00 0.00 32.87 4.26
1145 1304 2.377004 CGATGTCTGCGCATCAAGT 58.623 52.632 12.24 0.00 43.92 3.16
1146 1305 1.559831 CGATGTCTGCGCATCAAGTA 58.440 50.000 12.24 0.00 43.92 2.24
1147 1306 1.520174 CGATGTCTGCGCATCAAGTAG 59.480 52.381 12.24 0.00 43.92 2.57
1148 1307 2.796032 CGATGTCTGCGCATCAAGTAGA 60.796 50.000 12.24 0.00 43.92 2.59
1219 1381 1.821061 CTTCCAGGTCAGGTGCGACT 61.821 60.000 0.00 0.00 36.12 4.18
1304 1473 3.047877 CGACAACGGCACCTTCCC 61.048 66.667 0.00 0.00 35.72 3.97
1430 1605 3.381272 CAGGAGCTCTTCTTCCTCTACAG 59.619 52.174 14.64 0.00 0.00 2.74
1528 1703 1.299926 AACTCGTTCGCGTTGCTCT 60.300 52.632 5.77 0.00 42.11 4.09
1581 1756 3.462199 GATACCGGGGAGCTGCACC 62.462 68.421 6.32 7.65 36.39 5.01
1668 1843 1.549170 AGCGGGTTTCTTGTCGAGTAT 59.451 47.619 0.00 0.00 0.00 2.12
1676 1851 0.317603 CTTGTCGAGTATACGGCCGG 60.318 60.000 31.76 11.88 37.06 6.13
1707 1882 3.071206 TGCGAGGAGAGTGGAGGC 61.071 66.667 0.00 0.00 0.00 4.70
1788 1963 4.033990 TGACTTCATCATCTGTCGTAGC 57.966 45.455 0.00 0.00 29.99 3.58
2004 2358 5.807520 ACTTCTGTAAGATTACATGTCTGCG 59.192 40.000 0.00 0.00 46.36 5.18
2010 2364 8.887036 TGTAAGATTACATGTCTGCGATTTAT 57.113 30.769 0.00 0.00 38.64 1.40
2023 2377 8.664798 TGTCTGCGATTTATATATAACATTGCC 58.335 33.333 21.75 14.39 0.00 4.52
2160 2517 9.248291 TCAATTAACTCTCATTTTTGTCTTTGC 57.752 29.630 0.00 0.00 0.00 3.68
2200 2557 6.292381 GGTTGACGAAATATCAATCTTCCTCG 60.292 42.308 0.00 0.00 38.31 4.63
2201 2558 5.289595 TGACGAAATATCAATCTTCCTCGG 58.710 41.667 0.00 0.00 0.00 4.63
2247 2608 4.523173 TCCTAGGTGATTATCTAGTTGGCG 59.477 45.833 9.08 0.00 36.13 5.69
2292 2658 6.950860 ATCTCTTCTTCTTCCTTCTTCCTT 57.049 37.500 0.00 0.00 0.00 3.36
2293 2659 6.353404 TCTCTTCTTCTTCCTTCTTCCTTC 57.647 41.667 0.00 0.00 0.00 3.46
2294 2660 5.047660 TCTCTTCTTCTTCCTTCTTCCTTCG 60.048 44.000 0.00 0.00 0.00 3.79
2295 2661 4.833380 TCTTCTTCTTCCTTCTTCCTTCGA 59.167 41.667 0.00 0.00 0.00 3.71
2296 2662 4.522722 TCTTCTTCCTTCTTCCTTCGAC 57.477 45.455 0.00 0.00 0.00 4.20
2297 2663 3.057456 TCTTCTTCCTTCTTCCTTCGACG 60.057 47.826 0.00 0.00 0.00 5.12
2299 2665 0.966920 TTCCTTCTTCCTTCGACGCT 59.033 50.000 0.00 0.00 0.00 5.07
2300 2666 0.966920 TCCTTCTTCCTTCGACGCTT 59.033 50.000 0.00 0.00 0.00 4.68
2301 2667 1.071605 CCTTCTTCCTTCGACGCTTG 58.928 55.000 0.00 0.00 0.00 4.01
2350 2799 2.017049 AGTTCAGTGTTCAACCACAGC 58.983 47.619 0.00 0.00 37.82 4.40
2382 2831 6.098838 GCTTATCATTTTTCTCCCCTCCAAAT 59.901 38.462 0.00 0.00 0.00 2.32
2536 3888 2.149383 AGCACAGACAAGGCCTCCA 61.149 57.895 5.23 0.00 0.00 3.86
2658 4022 3.390639 CACCTCTTCTGATATTGGCCTCT 59.609 47.826 3.32 0.00 0.00 3.69
3404 5074 9.268268 AGTGAGTTTGATCGTAAAATAAGACAA 57.732 29.630 0.00 0.00 0.00 3.18
3423 5098 5.638234 AGACAAACCGCTTCTGTAGATTAAC 59.362 40.000 0.00 0.00 0.00 2.01
3428 5103 7.636150 AACCGCTTCTGTAGATTAACTAGTA 57.364 36.000 0.00 0.00 0.00 1.82
3485 5160 6.108015 ACAAGAAAAATGAACACAACATGCT 58.892 32.000 0.00 0.00 0.00 3.79
3493 5168 2.080286 ACACAACATGCTCGTACCTC 57.920 50.000 0.00 0.00 0.00 3.85
3508 5183 4.280174 TCGTACCTCCTAGATGTAAATGGC 59.720 45.833 0.00 0.00 0.00 4.40
3515 5190 6.013379 CCTCCTAGATGTAAATGGCTTCCATA 60.013 42.308 0.00 0.00 44.40 2.74
3574 5264 1.831736 AGTTAGGGGGTTCTGATCGTG 59.168 52.381 0.00 0.00 0.00 4.35
3628 5492 4.728882 GCTCATATGTGTAAGTTGCAGCAC 60.729 45.833 2.55 2.27 0.00 4.40
3654 5521 6.959366 TGATTATGGGGTCTGGAAAAGATTTT 59.041 34.615 0.00 0.00 37.23 1.82
3663 5530 3.828451 CTGGAAAAGATTTTGGCTGAGGA 59.172 43.478 0.00 0.00 0.00 3.71
3692 5559 5.774498 ACTTGATTGAACCTTTTGAGTCC 57.226 39.130 0.00 0.00 0.00 3.85
3708 5575 7.581213 TTTGAGTCCATCACAAAACTATGTT 57.419 32.000 0.00 0.00 37.77 2.71
3711 5578 8.006298 TGAGTCCATCACAAAACTATGTTTTT 57.994 30.769 5.78 0.00 31.12 1.94
3792 5661 3.705579 TGCCCGTACCTGCTAATTACTAA 59.294 43.478 3.28 0.00 0.00 2.24
3804 5673 9.654663 CCTGCTAATTACTAAACTATGGATACC 57.345 37.037 0.00 0.00 0.00 2.73
3870 6286 5.363868 TGGTCTAGTTCTGTAGCATAAGCAT 59.636 40.000 0.00 0.00 45.49 3.79
3871 6287 6.127054 TGGTCTAGTTCTGTAGCATAAGCATT 60.127 38.462 0.00 0.00 45.49 3.56
3980 7021 3.953612 TGTAGATTGAAATGCACCATCCC 59.046 43.478 0.00 0.00 0.00 3.85
3999 7041 2.608546 CCCATGCAATGCCATTTAAACG 59.391 45.455 1.53 0.00 44.97 3.60
4144 7190 6.039941 AGTCAGATAGGTAGCACATGTTCTAC 59.960 42.308 22.74 22.74 35.60 2.59
4720 8254 4.260784 CGTAATGATCAGCTTGGTAAAGGC 60.261 45.833 0.09 0.00 33.68 4.35
5029 8563 1.739371 GCTCGTGGCCTCGAATACTTT 60.739 52.381 27.96 0.00 39.34 2.66
5169 8703 3.965694 AGGAGAGCAAGCTTTCAATGAT 58.034 40.909 13.63 0.00 0.00 2.45
5239 8773 1.871039 ACATTCGGAGTGGTTTCAACG 59.129 47.619 5.46 0.00 0.00 4.10
5415 8949 8.163408 TGAAGTCATAGGAGAAATTGAGGAAAA 58.837 33.333 0.00 0.00 0.00 2.29
5440 8974 5.106157 CGCAAGAAAGATGACCTTAATTGGT 60.106 40.000 0.00 0.00 41.62 3.67
5566 9100 6.959639 AACTTTTCTGGATTGCTGTAAGAA 57.040 33.333 0.00 0.00 34.07 2.52
5728 9288 6.350780 GGAGATCAGCCTTGTGAATTCAAAAT 60.351 38.462 11.50 0.00 0.00 1.82
5797 9359 5.649395 TCAAAGAGCCTACATTCATTTCCAG 59.351 40.000 0.00 0.00 0.00 3.86
5798 9360 5.441718 AAGAGCCTACATTCATTTCCAGA 57.558 39.130 0.00 0.00 0.00 3.86
5801 9363 4.273318 AGCCTACATTCATTTCCAGAACC 58.727 43.478 0.00 0.00 0.00 3.62
5825 9395 3.097614 GAGAAGGTGGCCTGTACTAGAA 58.902 50.000 3.32 0.00 32.13 2.10
5944 10400 4.040461 ACATGCCAGCGTCCTAAGTTATAT 59.960 41.667 0.00 0.00 0.00 0.86
5987 10472 4.997905 ATTCTGATGAGTGTTGTGTTCG 57.002 40.909 0.00 0.00 0.00 3.95
6139 10753 8.498358 CAATTCATAGCAAGCAGATTAATCGTA 58.502 33.333 9.78 0.00 0.00 3.43
6167 10781 0.535102 AGGCGCACAGTTACTTGCTT 60.535 50.000 10.83 0.00 36.54 3.91
6168 10782 0.385974 GGCGCACAGTTACTTGCTTG 60.386 55.000 10.83 4.88 36.54 4.01
6169 10783 0.385974 GCGCACAGTTACTTGCTTGG 60.386 55.000 0.30 4.38 36.54 3.61
6170 10784 0.944386 CGCACAGTTACTTGCTTGGT 59.056 50.000 14.11 0.00 36.54 3.67
6278 10895 1.661509 CGCGCGCATATTCCTCTCA 60.662 57.895 32.61 0.00 0.00 3.27
6487 11115 3.649986 GTGACGGCAGCCACACAC 61.650 66.667 25.07 19.84 33.24 3.82
6488 11116 3.860605 TGACGGCAGCCACACACT 61.861 61.111 13.30 0.00 0.00 3.55
6489 11117 3.349006 GACGGCAGCCACACACTG 61.349 66.667 13.30 0.00 38.22 3.66
6494 11122 4.021631 CAGCCACACACTGCAGCG 62.022 66.667 15.27 6.98 0.00 5.18
6495 11123 4.552365 AGCCACACACTGCAGCGT 62.552 61.111 15.27 7.82 0.00 5.07
6496 11124 4.318021 GCCACACACTGCAGCGTG 62.318 66.667 28.69 28.69 40.67 5.34
6497 11125 4.318021 CCACACACTGCAGCGTGC 62.318 66.667 29.88 3.44 45.29 5.34
6528 11168 3.592814 CGAGCGCGGTGGGAGATA 61.593 66.667 18.92 0.00 0.00 1.98
6589 13042 3.118454 CAACGCCGATCCACGCTT 61.118 61.111 0.00 0.00 41.07 4.68
6640 13093 0.459585 GCAACATTGATGGCAGGCTG 60.460 55.000 10.94 10.94 0.00 4.85
6641 13094 0.459585 CAACATTGATGGCAGGCTGC 60.460 55.000 30.93 30.93 44.08 5.25
6645 13098 0.816825 ATTGATGGCAGGCTGCGTAG 60.817 55.000 31.22 0.00 46.21 3.51
6659 13112 1.218316 CGTAGGACCCAGGAAGCAC 59.782 63.158 0.00 0.00 0.00 4.40
6666 13119 3.970410 CCAGGAAGCACCCAGGCA 61.970 66.667 0.00 0.00 40.05 4.75
6667 13120 2.115910 CAGGAAGCACCCAGGCAA 59.884 61.111 0.00 0.00 40.05 4.52
6680 13133 1.001378 CCAGGCAAAGTTTGTTCTCGG 60.001 52.381 16.70 13.18 0.00 4.63
6692 13145 2.184533 TGTTCTCGGAGCCCAATTCTA 58.815 47.619 0.00 0.00 0.00 2.10
6693 13146 2.093658 TGTTCTCGGAGCCCAATTCTAC 60.094 50.000 0.00 0.00 0.00 2.59
6699 13152 2.372172 CGGAGCCCAATTCTACCCTTAT 59.628 50.000 0.00 0.00 0.00 1.73
6700 13153 3.557264 CGGAGCCCAATTCTACCCTTATC 60.557 52.174 0.00 0.00 0.00 1.75
6701 13154 3.394606 GGAGCCCAATTCTACCCTTATCA 59.605 47.826 0.00 0.00 0.00 2.15
6702 13155 4.505742 GGAGCCCAATTCTACCCTTATCAG 60.506 50.000 0.00 0.00 0.00 2.90
6703 13156 3.149981 GCCCAATTCTACCCTTATCAGC 58.850 50.000 0.00 0.00 0.00 4.26
6704 13157 3.181439 GCCCAATTCTACCCTTATCAGCT 60.181 47.826 0.00 0.00 0.00 4.24
6705 13158 4.689983 GCCCAATTCTACCCTTATCAGCTT 60.690 45.833 0.00 0.00 0.00 3.74
6706 13159 5.449553 CCCAATTCTACCCTTATCAGCTTT 58.550 41.667 0.00 0.00 0.00 3.51
6707 13160 5.893824 CCCAATTCTACCCTTATCAGCTTTT 59.106 40.000 0.00 0.00 0.00 2.27
6708 13161 6.381133 CCCAATTCTACCCTTATCAGCTTTTT 59.619 38.462 0.00 0.00 0.00 1.94
6709 13162 7.260603 CCAATTCTACCCTTATCAGCTTTTTG 58.739 38.462 0.00 0.00 0.00 2.44
6710 13163 7.122650 CCAATTCTACCCTTATCAGCTTTTTGA 59.877 37.037 0.00 0.00 0.00 2.69
6711 13164 7.631717 ATTCTACCCTTATCAGCTTTTTGAC 57.368 36.000 0.00 0.00 0.00 3.18
6712 13165 6.374417 TCTACCCTTATCAGCTTTTTGACT 57.626 37.500 0.00 0.00 0.00 3.41
6713 13166 7.490657 TCTACCCTTATCAGCTTTTTGACTA 57.509 36.000 0.00 0.00 0.00 2.59
6714 13167 7.328737 TCTACCCTTATCAGCTTTTTGACTAC 58.671 38.462 0.00 0.00 0.00 2.73
6715 13168 6.128138 ACCCTTATCAGCTTTTTGACTACT 57.872 37.500 0.00 0.00 0.00 2.57
6716 13169 7.253905 ACCCTTATCAGCTTTTTGACTACTA 57.746 36.000 0.00 0.00 0.00 1.82
6717 13170 7.104290 ACCCTTATCAGCTTTTTGACTACTAC 58.896 38.462 0.00 0.00 0.00 2.73
6718 13171 7.038231 ACCCTTATCAGCTTTTTGACTACTACT 60.038 37.037 0.00 0.00 0.00 2.57
6719 13172 8.475639 CCCTTATCAGCTTTTTGACTACTACTA 58.524 37.037 0.00 0.00 0.00 1.82
6720 13173 9.522804 CCTTATCAGCTTTTTGACTACTACTAG 57.477 37.037 0.00 0.00 0.00 2.57
6721 13174 8.928270 TTATCAGCTTTTTGACTACTACTAGC 57.072 34.615 0.00 0.00 0.00 3.42
6722 13175 6.340962 TCAGCTTTTTGACTACTACTAGCA 57.659 37.500 0.00 0.00 0.00 3.49
6723 13176 6.157211 TCAGCTTTTTGACTACTACTAGCAC 58.843 40.000 0.00 0.00 0.00 4.40
6724 13177 5.926542 CAGCTTTTTGACTACTACTAGCACA 59.073 40.000 0.00 0.00 0.00 4.57
6725 13178 6.591834 CAGCTTTTTGACTACTACTAGCACAT 59.408 38.462 0.00 0.00 0.00 3.21
6726 13179 7.759886 CAGCTTTTTGACTACTACTAGCACATA 59.240 37.037 0.00 0.00 0.00 2.29
6727 13180 8.478877 AGCTTTTTGACTACTACTAGCACATAT 58.521 33.333 0.00 0.00 0.00 1.78
6728 13181 8.543774 GCTTTTTGACTACTACTAGCACATATG 58.456 37.037 0.00 0.00 0.00 1.78
6729 13182 9.587772 CTTTTTGACTACTACTAGCACATATGT 57.412 33.333 1.41 1.41 0.00 2.29
6730 13183 9.582431 TTTTTGACTACTACTAGCACATATGTC 57.418 33.333 5.07 1.35 0.00 3.06
6731 13184 6.879276 TGACTACTACTAGCACATATGTCC 57.121 41.667 5.07 0.00 0.00 4.02
6732 13185 5.469084 TGACTACTACTAGCACATATGTCCG 59.531 44.000 5.07 0.00 0.00 4.79
6733 13186 5.374921 ACTACTACTAGCACATATGTCCGT 58.625 41.667 5.07 3.52 0.00 4.69
6734 13187 4.569761 ACTACTAGCACATATGTCCGTG 57.430 45.455 5.07 0.00 36.18 4.94
6739 13192 3.875813 CACATATGTCCGTGCGTTG 57.124 52.632 5.07 0.00 0.00 4.10
6740 13193 0.247655 CACATATGTCCGTGCGTTGC 60.248 55.000 5.07 0.00 0.00 4.17
6741 13194 0.672091 ACATATGTCCGTGCGTTGCA 60.672 50.000 1.41 0.00 35.60 4.08
6742 13195 0.445829 CATATGTCCGTGCGTTGCAA 59.554 50.000 0.00 0.00 41.47 4.08
6743 13196 0.446222 ATATGTCCGTGCGTTGCAAC 59.554 50.000 19.89 19.89 41.47 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.938140 ATTTTCCGAGGACATCAAAATCTTA 57.062 32.000 0.00 0.00 0.00 2.10
44 45 3.915437 ATTCGTCGACTTGCCAATTTT 57.085 38.095 14.70 0.00 0.00 1.82
48 49 3.369756 GTCATTATTCGTCGACTTGCCAA 59.630 43.478 14.70 1.67 0.00 4.52
83 84 6.547141 TGAGAGACAAGAAACAAACCAATGAT 59.453 34.615 0.00 0.00 0.00 2.45
95 96 6.531594 CGTGCAACTATATGAGAGACAAGAAA 59.468 38.462 0.00 0.00 31.75 2.52
100 101 3.490933 GGCGTGCAACTATATGAGAGACA 60.491 47.826 0.00 0.00 31.75 3.41
153 156 3.330126 AGGACGGAGGGAATAGATGAA 57.670 47.619 0.00 0.00 0.00 2.57
154 157 4.676799 ATAGGACGGAGGGAATAGATGA 57.323 45.455 0.00 0.00 0.00 2.92
161 164 2.433239 GCAAACTATAGGACGGAGGGAA 59.567 50.000 4.43 0.00 0.00 3.97
163 166 1.760613 TGCAAACTATAGGACGGAGGG 59.239 52.381 4.43 0.00 0.00 4.30
203 206 9.382244 CCTATAATATAAGACGTTTTTGCAAGC 57.618 33.333 0.00 0.00 0.00 4.01
207 210 8.219105 CCGTCCTATAATATAAGACGTTTTTGC 58.781 37.037 22.33 0.00 46.62 3.68
208 211 9.467258 TCCGTCCTATAATATAAGACGTTTTTG 57.533 33.333 22.33 11.80 46.62 2.44
210 213 9.688592 CTTCCGTCCTATAATATAAGACGTTTT 57.311 33.333 22.33 0.00 46.62 2.43
212 215 8.627208 TCTTCCGTCCTATAATATAAGACGTT 57.373 34.615 22.33 0.00 46.62 3.99
225 309 4.222145 TGCAAAGTACTTCTTCCGTCCTAT 59.778 41.667 8.95 0.00 35.02 2.57
226 310 3.575256 TGCAAAGTACTTCTTCCGTCCTA 59.425 43.478 8.95 0.00 35.02 2.94
227 311 2.367567 TGCAAAGTACTTCTTCCGTCCT 59.632 45.455 8.95 0.00 35.02 3.85
229 313 3.429207 GTCTGCAAAGTACTTCTTCCGTC 59.571 47.826 8.95 0.00 35.02 4.79
235 319 8.148351 TGTATTACAAGTCTGCAAAGTACTTCT 58.852 33.333 8.95 0.00 31.21 2.85
237 321 7.095774 CGTGTATTACAAGTCTGCAAAGTACTT 60.096 37.037 1.12 1.12 33.82 2.24
242 326 4.152402 AGCGTGTATTACAAGTCTGCAAAG 59.848 41.667 10.72 0.00 30.18 2.77
249 333 3.476379 CGTCGTAGCGTGTATTACAAGTC 59.524 47.826 10.72 4.49 30.18 3.01
318 402 1.669779 GAGCACAAGCATGACTGATCC 59.330 52.381 0.00 0.00 45.49 3.36
371 455 0.653636 GCAGGAACGACAACGACAAA 59.346 50.000 0.00 0.00 42.66 2.83
373 457 1.947146 CGCAGGAACGACAACGACA 60.947 57.895 0.00 0.00 42.66 4.35
377 461 2.668280 GGCTCGCAGGAACGACAAC 61.668 63.158 0.00 0.00 37.09 3.32
378 462 2.357034 GGCTCGCAGGAACGACAA 60.357 61.111 0.00 0.00 37.09 3.18
379 463 3.573772 CTGGCTCGCAGGAACGACA 62.574 63.158 0.00 0.00 37.09 4.35
380 464 2.811317 CTGGCTCGCAGGAACGAC 60.811 66.667 0.00 0.00 37.09 4.34
381 465 4.742201 GCTGGCTCGCAGGAACGA 62.742 66.667 0.00 0.00 40.36 3.85
444 528 2.166254 GGTGGGTGCATGGTTTTATCTG 59.834 50.000 0.00 0.00 0.00 2.90
460 544 3.630312 CCTATCCAACAAAATACGGTGGG 59.370 47.826 0.00 0.00 0.00 4.61
472 556 1.264749 ACGAGGCAGCCTATCCAACA 61.265 55.000 16.16 0.00 31.76 3.33
571 655 1.135083 CCTCGTTCTGTTCATAGCCGT 60.135 52.381 0.00 0.00 0.00 5.68
591 675 4.500116 GACGACCTGAGAGGCGGC 62.500 72.222 0.00 0.00 39.63 6.53
626 710 4.691238 TCCTTACCTACTGCTAGGGAAAA 58.309 43.478 4.20 0.00 41.82 2.29
627 711 4.287552 CTCCTTACCTACTGCTAGGGAAA 58.712 47.826 4.20 0.00 41.82 3.13
628 712 3.373877 CCTCCTTACCTACTGCTAGGGAA 60.374 52.174 4.20 0.73 43.87 3.97
629 713 2.177233 CCTCCTTACCTACTGCTAGGGA 59.823 54.545 4.20 0.00 43.87 4.20
630 714 2.599677 CCTCCTTACCTACTGCTAGGG 58.400 57.143 4.20 0.00 43.87 3.53
631 715 1.964933 GCCTCCTTACCTACTGCTAGG 59.035 57.143 0.00 0.00 44.99 3.02
636 746 1.822990 TGAACGCCTCCTTACCTACTG 59.177 52.381 0.00 0.00 0.00 2.74
673 783 4.790861 GAAGGTCGTCGGTCCGGC 62.791 72.222 12.29 9.07 0.00 6.13
687 797 4.878397 CCTATAGCAAGTGACCTTTGGAAG 59.122 45.833 0.00 0.00 0.00 3.46
688 798 4.324254 CCCTATAGCAAGTGACCTTTGGAA 60.324 45.833 0.00 0.00 0.00 3.53
689 799 3.199946 CCCTATAGCAAGTGACCTTTGGA 59.800 47.826 0.00 0.00 0.00 3.53
690 800 3.545703 CCCTATAGCAAGTGACCTTTGG 58.454 50.000 0.00 0.00 0.00 3.28
691 801 2.945668 GCCCTATAGCAAGTGACCTTTG 59.054 50.000 0.00 0.00 0.00 2.77
692 802 2.092375 GGCCCTATAGCAAGTGACCTTT 60.092 50.000 0.00 0.00 0.00 3.11
694 804 1.132500 GGCCCTATAGCAAGTGACCT 58.868 55.000 0.00 0.00 0.00 3.85
702 820 0.471971 GTCCTCAGGGCCCTATAGCA 60.472 60.000 28.13 8.68 0.00 3.49
751 869 0.391661 GGCATCACCACGACACTCAT 60.392 55.000 0.00 0.00 38.86 2.90
816 934 1.661480 CATGCATATGGTTGCCGGG 59.339 57.895 2.18 0.00 42.06 5.73
852 970 0.512952 GCTGTAAGAAGCACACACGG 59.487 55.000 0.00 0.00 43.01 4.94
862 980 5.745312 TGAGAAGGAGATTGCTGTAAGAA 57.255 39.130 0.00 0.00 34.07 2.52
864 982 6.822676 AGAATTGAGAAGGAGATTGCTGTAAG 59.177 38.462 0.00 0.00 0.00 2.34
865 983 6.715280 AGAATTGAGAAGGAGATTGCTGTAA 58.285 36.000 0.00 0.00 0.00 2.41
867 985 5.176741 AGAATTGAGAAGGAGATTGCTGT 57.823 39.130 0.00 0.00 0.00 4.40
894 1014 4.224594 TGATGAAGAGAGGCAGTTGAAGAT 59.775 41.667 0.00 0.00 0.00 2.40
912 1032 2.265739 GGAGGCGTGCAGTGATGA 59.734 61.111 0.00 0.00 0.00 2.92
913 1033 2.821366 GGGAGGCGTGCAGTGATG 60.821 66.667 0.00 0.00 0.00 3.07
914 1034 3.005539 AGGGAGGCGTGCAGTGAT 61.006 61.111 0.00 0.00 0.00 3.06
972 1092 1.606668 TCTTGTTGCAACGGAATGGAC 59.393 47.619 23.79 0.00 0.00 4.02
985 1105 1.353103 GCATCGGGCGATCTTGTTG 59.647 57.895 0.00 0.00 31.62 3.33
1110 1239 4.459089 GCTGGGTCGCAGGAGGTC 62.459 72.222 17.75 0.00 0.00 3.85
1133 1292 2.341257 ACTTGTCTACTTGATGCGCAG 58.659 47.619 18.32 4.18 0.00 5.18
1136 1295 3.187700 GGGTACTTGTCTACTTGATGCG 58.812 50.000 0.00 0.00 0.00 4.73
1138 1297 4.451629 ACGGGTACTTGTCTACTTGATG 57.548 45.455 0.00 0.00 0.00 3.07
1139 1298 4.771054 AGAACGGGTACTTGTCTACTTGAT 59.229 41.667 0.00 0.00 0.00 2.57
1140 1299 4.022589 CAGAACGGGTACTTGTCTACTTGA 60.023 45.833 0.00 0.00 0.00 3.02
1142 1301 3.257624 CCAGAACGGGTACTTGTCTACTT 59.742 47.826 0.00 0.00 0.00 2.24
1143 1302 2.824341 CCAGAACGGGTACTTGTCTACT 59.176 50.000 0.00 0.00 0.00 2.57
1144 1303 2.673326 GCCAGAACGGGTACTTGTCTAC 60.673 54.545 0.00 0.00 34.06 2.59
1145 1304 1.547372 GCCAGAACGGGTACTTGTCTA 59.453 52.381 0.00 0.00 34.06 2.59
1146 1305 0.320697 GCCAGAACGGGTACTTGTCT 59.679 55.000 0.00 0.00 34.06 3.41
1147 1306 0.320697 AGCCAGAACGGGTACTTGTC 59.679 55.000 0.00 0.00 46.31 3.18
1148 1307 2.448749 AGCCAGAACGGGTACTTGT 58.551 52.632 0.00 0.00 46.31 3.16
1430 1605 2.743928 CCTGAAGGTCGGTGCAGC 60.744 66.667 5.64 5.64 0.00 5.25
1581 1756 2.202743 ACCGGCATCATCGACACG 60.203 61.111 0.00 0.00 0.00 4.49
1688 1863 1.979155 CCTCCACTCTCCTCGCACA 60.979 63.158 0.00 0.00 0.00 4.57
1707 1882 2.352323 GGTGGTGTTAATCCGGCAAAAG 60.352 50.000 0.00 0.00 0.00 2.27
1788 1963 1.066303 CTGCCGCTAGAGTTACCTGAG 59.934 57.143 0.00 0.00 0.00 3.35
1893 2069 8.889717 CACGGACTAAACTGGTTGAATAATAAT 58.110 33.333 0.00 0.00 0.00 1.28
1894 2070 8.095792 TCACGGACTAAACTGGTTGAATAATAA 58.904 33.333 0.00 0.00 0.00 1.40
1896 2072 6.469410 TCACGGACTAAACTGGTTGAATAAT 58.531 36.000 0.00 0.00 0.00 1.28
1897 2073 5.856156 TCACGGACTAAACTGGTTGAATAA 58.144 37.500 0.00 0.00 0.00 1.40
1973 2327 9.436957 ACATGTAATCTTACAGAAGTTTACCAG 57.563 33.333 0.00 9.22 45.80 4.00
2160 2517 9.801873 ATTTCGTCAACCTTATCAATATTTTGG 57.198 29.630 0.00 0.00 33.44 3.28
2292 2658 1.603678 GGACAGGTAAACAAGCGTCGA 60.604 52.381 0.00 0.00 33.12 4.20
2293 2659 0.788391 GGACAGGTAAACAAGCGTCG 59.212 55.000 0.00 0.00 33.12 5.12
2294 2660 1.529865 GTGGACAGGTAAACAAGCGTC 59.470 52.381 0.00 0.00 0.00 5.19
2295 2661 1.140252 AGTGGACAGGTAAACAAGCGT 59.860 47.619 0.00 0.00 0.00 5.07
2296 2662 1.878953 AGTGGACAGGTAAACAAGCG 58.121 50.000 0.00 0.00 0.00 4.68
2297 2663 3.335579 CCTAGTGGACAGGTAAACAAGC 58.664 50.000 0.00 0.00 34.57 4.01
2299 2665 3.589641 TCCCTAGTGGACAGGTAAACAA 58.410 45.455 0.00 0.00 38.61 2.83
2300 2666 3.263369 TCCCTAGTGGACAGGTAAACA 57.737 47.619 0.00 0.00 38.61 2.83
2301 2667 4.838904 ATTCCCTAGTGGACAGGTAAAC 57.161 45.455 0.00 0.00 45.11 2.01
2350 2799 5.010415 GGGAGAAAAATGATAAGCATCCCAG 59.990 44.000 0.00 0.00 35.78 4.45
2382 2831 3.256704 ACCCTGACCAGATACAAAGGAA 58.743 45.455 0.00 0.00 0.00 3.36
2669 4033 0.037447 AGAAGAGCTCTTGGTTGGCC 59.963 55.000 33.07 16.38 36.11 5.36
3404 5074 6.527057 ACTAGTTAATCTACAGAAGCGGTT 57.473 37.500 0.00 0.00 0.00 4.44
3423 5098 5.235305 AGTGCGCCAAAATTGAATACTAG 57.765 39.130 4.18 0.00 0.00 2.57
3428 5103 4.454728 ACATAGTGCGCCAAAATTGAAT 57.545 36.364 4.18 0.00 0.00 2.57
3485 5160 4.280174 GCCATTTACATCTAGGAGGTACGA 59.720 45.833 0.00 0.00 28.46 3.43
3493 5168 9.553064 GATATATGGAAGCCATTTACATCTAGG 57.447 37.037 4.03 0.00 42.23 3.02
3508 5183 9.073475 GCCATACTAGTAGGAGATATATGGAAG 57.927 40.741 15.94 0.00 39.90 3.46
3515 5190 6.410222 ACCAGCCATACTAGTAGGAGATAT 57.590 41.667 15.94 0.00 0.00 1.63
3553 5240 3.028850 CACGATCAGAACCCCCTAACTA 58.971 50.000 0.00 0.00 0.00 2.24
3628 5492 5.116084 TCTTTTCCAGACCCCATAATCAG 57.884 43.478 0.00 0.00 0.00 2.90
3654 5521 5.894298 ATCAAGTATTACATCCTCAGCCA 57.106 39.130 0.00 0.00 0.00 4.75
3743 5610 6.884836 GCTTTTCTTAGAATTAAGGAGGTCCA 59.115 38.462 8.07 0.00 37.47 4.02
3792 5661 5.594317 GTCAGGCATTTTGGTATCCATAGTT 59.406 40.000 0.00 0.00 31.53 2.24
3804 5673 5.335661 GGGTTTACACTAGTCAGGCATTTTG 60.336 44.000 0.00 0.00 0.00 2.44
3870 6286 3.500680 GTGTGGCTAAACCGAAGATTGAA 59.499 43.478 0.00 0.00 43.94 2.69
3871 6287 3.071479 GTGTGGCTAAACCGAAGATTGA 58.929 45.455 0.00 0.00 43.94 2.57
3980 7021 5.101628 AGTACGTTTAAATGGCATTGCATG 58.898 37.500 14.47 8.59 0.00 4.06
4041 7085 7.938140 AGTTATAGGCTTTGTGCAGATTTAA 57.062 32.000 0.00 0.00 45.15 1.52
4082 7126 6.283694 AGCAGCTATTTTGATCGAATACAGA 58.716 36.000 0.00 0.00 0.00 3.41
4090 7135 6.775939 TTGATAGAGCAGCTATTTTGATCG 57.224 37.500 0.00 0.00 39.90 3.69
4097 7142 6.657875 ACTTCCTTTTGATAGAGCAGCTATT 58.342 36.000 0.00 0.00 39.90 1.73
4144 7190 6.492007 ACATTGCAAGATAGTGAAGAACAG 57.508 37.500 4.94 0.00 0.00 3.16
4349 7414 8.368668 ACTAGTACTACATATGAAAAGATGGCC 58.631 37.037 10.38 0.00 0.00 5.36
4484 8016 3.006323 GCTGATGTAGTACCTGAGATGGG 59.994 52.174 0.00 0.00 0.00 4.00
4720 8254 1.529226 TGAAAACCACACCATAGCCG 58.471 50.000 0.00 0.00 0.00 5.52
5029 8563 3.131400 TGCGTGTATTACAGCTATGGTGA 59.869 43.478 14.86 0.00 34.87 4.02
5169 8703 3.420893 CCAATTGTTCCTCTAGCACCAA 58.579 45.455 4.43 0.00 0.00 3.67
5415 8949 5.106157 CCAATTAAGGTCATCTTTCTTGCGT 60.106 40.000 0.00 0.00 36.93 5.24
5440 8974 3.304123 GCAGTATTTGTACGCACCACAAA 60.304 43.478 9.20 9.20 46.64 2.83
5566 9100 5.330233 AGGGACAAAAATACGGGAGAAATT 58.670 37.500 0.00 0.00 0.00 1.82
5728 9288 3.880490 AGAGTTGGCGATTGTTGTACAAA 59.120 39.130 10.51 0.00 41.96 2.83
5797 9359 1.671379 GGCCACCTTCTCACGGTTC 60.671 63.158 0.00 0.00 30.82 3.62
5798 9360 2.147387 AGGCCACCTTCTCACGGTT 61.147 57.895 5.01 0.00 30.82 4.44
5801 9363 0.389948 GTACAGGCCACCTTCTCACG 60.390 60.000 5.01 0.00 0.00 4.35
5825 9395 5.801947 GCGCTTGTTCAATTTCTGAATGTAT 59.198 36.000 0.00 0.00 45.74 2.29
5964 10420 6.220201 TCGAACACAACACTCATCAGAATTA 58.780 36.000 0.00 0.00 0.00 1.40
5965 10421 5.056480 TCGAACACAACACTCATCAGAATT 58.944 37.500 0.00 0.00 0.00 2.17
6047 10657 8.659527 TGCATCCAGATTCTGATATTTTAGGTA 58.340 33.333 15.36 0.00 32.44 3.08
6155 10769 2.808543 GTGAGGACCAAGCAAGTAACTG 59.191 50.000 0.00 0.00 0.00 3.16
6157 10771 2.152016 GGTGAGGACCAAGCAAGTAAC 58.848 52.381 0.00 0.00 42.59 2.50
6167 10781 1.933021 ACAATCTACGGTGAGGACCA 58.067 50.000 0.00 0.00 43.33 4.02
6168 10782 3.005578 GGATACAATCTACGGTGAGGACC 59.994 52.174 0.00 0.00 39.14 4.46
6169 10783 4.240175 GGATACAATCTACGGTGAGGAC 57.760 50.000 0.00 0.00 0.00 3.85
6305 10922 1.982612 CGATGTTGTCTGAGAAGCGA 58.017 50.000 0.00 0.00 0.00 4.93
6405 11033 2.611964 ATCTCCTGGGGCGTGGATCT 62.612 60.000 0.00 0.00 0.00 2.75
6442 11070 4.441695 CCCGCGCAGAGAAGAGCA 62.442 66.667 8.75 0.00 33.67 4.26
6470 11098 3.649986 GTGTGTGGCTGCCGTCAC 61.650 66.667 27.82 27.82 45.85 3.67
6471 11099 3.860605 AGTGTGTGGCTGCCGTCA 61.861 61.111 14.98 12.91 0.00 4.35
6514 11154 2.279517 CACTATCTCCCACCGCGC 60.280 66.667 0.00 0.00 0.00 6.86
6520 11160 0.399949 ATTCCCCGCACTATCTCCCA 60.400 55.000 0.00 0.00 0.00 4.37
6522 11162 1.543429 CCAATTCCCCGCACTATCTCC 60.543 57.143 0.00 0.00 0.00 3.71
6528 11168 4.060667 CCCCCAATTCCCCGCACT 62.061 66.667 0.00 0.00 0.00 4.40
6587 13040 2.952310 GCCTATAGCCCAAAACCTCAAG 59.048 50.000 0.00 0.00 34.35 3.02
6588 13041 3.012934 GCCTATAGCCCAAAACCTCAA 57.987 47.619 0.00 0.00 34.35 3.02
6589 13042 2.729028 GCCTATAGCCCAAAACCTCA 57.271 50.000 0.00 0.00 34.35 3.86
6615 13068 3.250744 CTGCCATCAATGTTGCTTCTTG 58.749 45.455 0.00 0.00 0.00 3.02
6626 13079 0.816825 CTACGCAGCCTGCCATCAAT 60.817 55.000 11.83 0.00 41.12 2.57
6627 13080 1.450134 CTACGCAGCCTGCCATCAA 60.450 57.895 11.83 0.00 41.12 2.57
6628 13081 2.187685 CTACGCAGCCTGCCATCA 59.812 61.111 11.83 0.00 41.12 3.07
6629 13082 2.590007 CCTACGCAGCCTGCCATC 60.590 66.667 11.83 0.00 41.12 3.51
6630 13083 3.083349 TCCTACGCAGCCTGCCAT 61.083 61.111 11.83 1.87 41.12 4.40
6640 13093 2.187163 GCTTCCTGGGTCCTACGC 59.813 66.667 0.00 0.00 0.00 4.42
6641 13094 1.218316 GTGCTTCCTGGGTCCTACG 59.782 63.158 0.00 0.00 0.00 3.51
6645 13098 3.256960 TGGGTGCTTCCTGGGTCC 61.257 66.667 0.00 0.00 36.25 4.46
6659 13112 1.001378 CGAGAACAAACTTTGCCTGGG 60.001 52.381 1.14 0.00 0.00 4.45
6666 13119 1.133915 TGGGCTCCGAGAACAAACTTT 60.134 47.619 0.00 0.00 0.00 2.66
6667 13120 0.472471 TGGGCTCCGAGAACAAACTT 59.528 50.000 0.00 0.00 0.00 2.66
6680 13133 4.646572 CTGATAAGGGTAGAATTGGGCTC 58.353 47.826 0.00 0.00 0.00 4.70
6692 13145 6.128138 AGTAGTCAAAAAGCTGATAAGGGT 57.872 37.500 0.00 0.00 0.00 4.34
6693 13146 7.331791 AGTAGTAGTCAAAAAGCTGATAAGGG 58.668 38.462 0.00 0.00 0.00 3.95
6699 13152 6.157211 GTGCTAGTAGTAGTCAAAAAGCTGA 58.843 40.000 6.47 0.00 0.00 4.26
6700 13153 5.926542 TGTGCTAGTAGTAGTCAAAAAGCTG 59.073 40.000 6.47 0.00 0.00 4.24
6701 13154 6.097915 TGTGCTAGTAGTAGTCAAAAAGCT 57.902 37.500 6.47 0.00 0.00 3.74
6702 13155 6.969828 ATGTGCTAGTAGTAGTCAAAAAGC 57.030 37.500 6.47 0.00 0.00 3.51
6703 13156 9.587772 ACATATGTGCTAGTAGTAGTCAAAAAG 57.412 33.333 7.78 0.00 0.00 2.27
6704 13157 9.582431 GACATATGTGCTAGTAGTAGTCAAAAA 57.418 33.333 14.43 0.00 0.00 1.94
6705 13158 8.195436 GGACATATGTGCTAGTAGTAGTCAAAA 58.805 37.037 19.13 1.41 33.32 2.44
6706 13159 7.468220 CGGACATATGTGCTAGTAGTAGTCAAA 60.468 40.741 22.88 1.29 33.97 2.69
6707 13160 6.017357 CGGACATATGTGCTAGTAGTAGTCAA 60.017 42.308 22.88 0.00 33.97 3.18
6708 13161 5.469084 CGGACATATGTGCTAGTAGTAGTCA 59.531 44.000 22.88 6.74 33.97 3.41
6709 13162 5.469421 ACGGACATATGTGCTAGTAGTAGTC 59.531 44.000 22.88 0.37 33.97 2.59
6710 13163 5.238868 CACGGACATATGTGCTAGTAGTAGT 59.761 44.000 22.88 9.56 33.97 2.73
6711 13164 5.690816 CACGGACATATGTGCTAGTAGTAG 58.309 45.833 22.88 8.98 33.97 2.57
6712 13165 5.684550 CACGGACATATGTGCTAGTAGTA 57.315 43.478 22.88 0.00 33.97 1.82
6713 13166 4.569761 CACGGACATATGTGCTAGTAGT 57.430 45.455 22.88 11.51 33.97 2.73
6721 13174 0.247655 GCAACGCACGGACATATGTG 60.248 55.000 14.43 2.00 39.10 3.21
6722 13175 0.672091 TGCAACGCACGGACATATGT 60.672 50.000 8.43 8.43 31.71 2.29
6723 13176 0.445829 TTGCAACGCACGGACATATG 59.554 50.000 0.00 0.00 38.71 1.78
6724 13177 0.446222 GTTGCAACGCACGGACATAT 59.554 50.000 14.90 0.00 38.71 1.78
6725 13178 1.863491 GTTGCAACGCACGGACATA 59.137 52.632 14.90 0.00 38.71 2.29
6726 13179 2.637025 GTTGCAACGCACGGACAT 59.363 55.556 14.90 0.00 38.71 3.06
6727 13180 3.931130 CGTTGCAACGCACGGACA 61.931 61.111 35.89 0.00 46.06 4.02


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

AutoCloner maintained by Alex Coulton.