Multiple sequence alignment - TraesCS2B01G627000

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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 TraesCS2B01G627000 chr2B 100.000 3118 0 0 1 3118 798956711 798959828 0.000000e+00 5758.0
1 TraesCS2B01G627000 chr2B 81.590 1988 210 80 190 2106 799028424 799030326 0.000000e+00 1500.0
2 TraesCS2B01G627000 chr2B 84.186 860 94 21 1286 2106 799047289 799046433 0.000000e+00 797.0
3 TraesCS2B01G627000 chr2B 87.152 646 60 9 997 1624 799107610 799106970 0.000000e+00 712.0
4 TraesCS2B01G627000 chr2B 83.238 698 71 27 190 877 799108436 799107775 1.600000e-167 599.0
5 TraesCS2B01G627000 chr2B 86.085 424 46 7 1695 2106 799106644 799106222 7.930000e-121 444.0
6 TraesCS2B01G627000 chr2B 87.427 342 23 7 899 1234 799047708 799047381 2.940000e-100 375.0
7 TraesCS2B01G627000 chr2B 86.970 330 28 7 2093 2421 799046413 799046098 1.060000e-94 357.0
8 TraesCS2B01G627000 chr2B 84.036 332 44 5 2679 3008 799046094 799045770 8.400000e-81 311.0
9 TraesCS2B01G627000 chr2B 95.580 181 7 1 654 834 799047911 799047732 3.930000e-74 289.0
10 TraesCS2B01G627000 chr2B 78.405 514 53 23 138 617 799048395 799047906 6.580000e-72 281.0
11 TraesCS2B01G627000 chr2B 88.043 184 17 4 2239 2421 799030449 799030628 2.440000e-51 213.0
12 TraesCS2B01G627000 chr2B 87.845 181 17 5 2428 2605 366017519 366017697 1.130000e-49 207.0
13 TraesCS2B01G627000 chr2B 86.207 87 5 5 2093 2172 799106202 799106116 1.540000e-13 87.9
14 TraesCS2B01G627000 chr2D 86.192 1912 155 43 555 2421 639822282 639820435 0.000000e+00 1967.0
15 TraesCS2B01G627000 chr2D 87.229 1566 119 35 591 2106 639732799 639734333 0.000000e+00 1709.0
16 TraesCS2B01G627000 chr2D 83.929 840 83 25 1287 2094 639746464 639745645 0.000000e+00 756.0
17 TraesCS2B01G627000 chr2D 88.871 611 31 17 1 578 639732033 639732639 0.000000e+00 717.0
18 TraesCS2B01G627000 chr2D 83.880 732 49 26 507 1230 639747229 639746559 4.390000e-178 634.0
19 TraesCS2B01G627000 chr2D 86.262 313 23 12 2111 2421 639745595 639745301 3.880000e-84 322.0
20 TraesCS2B01G627000 chr2D 85.342 307 30 8 183 480 639891686 639891386 1.410000e-78 303.0
21 TraesCS2B01G627000 chr2D 82.698 341 39 10 859 1191 639872369 639872041 5.090000e-73 285.0
22 TraesCS2B01G627000 chr2D 83.730 252 20 12 170 402 639747540 639747291 5.240000e-53 219.0
23 TraesCS2B01G627000 chr2D 87.845 181 17 5 2428 2605 296364209 296364031 1.130000e-49 207.0
24 TraesCS2B01G627000 chr2D 83.178 107 7 6 38 133 639747742 639747636 1.540000e-13 87.9
25 TraesCS2B01G627000 chr2A 87.354 1542 117 36 926 2418 765442335 765440823 0.000000e+00 1696.0
26 TraesCS2B01G627000 chr2A 83.992 1468 129 40 772 2172 765373507 765374935 0.000000e+00 1312.0
27 TraesCS2B01G627000 chr2A 82.131 1192 120 48 1287 2415 765393317 765392156 0.000000e+00 935.0
28 TraesCS2B01G627000 chr2A 87.183 749 38 19 1 719 765372792 765373512 0.000000e+00 798.0
29 TraesCS2B01G627000 chr2A 84.044 727 64 19 138 833 765394458 765393753 0.000000e+00 652.0
30 TraesCS2B01G627000 chr2A 79.799 797 73 33 138 889 765443093 765442340 1.670000e-137 499.0
31 TraesCS2B01G627000 chr2A 93.114 334 16 4 907 1234 765393749 765393417 1.680000e-132 483.0
32 TraesCS2B01G627000 chr2A 83.743 529 46 21 1303 1802 765547546 765547029 6.090000e-127 464.0
33 TraesCS2B01G627000 chr2A 82.227 512 62 17 321 820 765548531 765548037 6.220000e-112 414.0
34 TraesCS2B01G627000 chr2A 84.524 336 45 5 2673 3008 765392060 765391732 3.000000e-85 326.0
35 TraesCS2B01G627000 chr2A 79.572 421 55 13 1706 2096 765278535 765278954 3.960000e-69 272.0
36 TraesCS2B01G627000 chr2A 87.912 182 17 5 2428 2606 367649321 367649142 3.150000e-50 209.0
37 TraesCS2B01G627000 chr2A 88.824 170 18 1 2424 2593 135473392 135473224 1.130000e-49 207.0
38 TraesCS2B01G627000 chr2A 85.149 101 2 6 38 126 765443253 765443154 1.190000e-14 91.6
39 TraesCS2B01G627000 chr6A 90.184 163 16 0 2428 2590 151466970 151467132 2.440000e-51 213.0
40 TraesCS2B01G627000 chr3D 89.820 167 15 2 2426 2591 31577240 31577075 2.440000e-51 213.0
41 TraesCS2B01G627000 chr1B 87.435 191 16 8 2408 2592 539577863 539577675 2.440000e-51 213.0
42 TraesCS2B01G627000 chr1D 87.845 181 17 4 2414 2591 155961850 155961672 1.130000e-49 207.0
43 TraesCS2B01G627000 chr4D 88.372 172 19 1 2428 2599 310479440 310479270 4.080000e-49 206.0


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 TraesCS2B01G627000 chr2B 798956711 798959828 3117 False 5758.000000 5758 100.000000 1 3118 1 chr2B.!!$F2 3117
1 TraesCS2B01G627000 chr2B 799028424 799030628 2204 False 856.500000 1500 84.816500 190 2421 2 chr2B.!!$F3 2231
2 TraesCS2B01G627000 chr2B 799106116 799108436 2320 True 460.725000 712 85.670500 190 2172 4 chr2B.!!$R2 1982
3 TraesCS2B01G627000 chr2B 799045770 799048395 2625 True 401.666667 797 86.100667 138 3008 6 chr2B.!!$R1 2870
4 TraesCS2B01G627000 chr2D 639820435 639822282 1847 True 1967.000000 1967 86.192000 555 2421 1 chr2D.!!$R2 1866
5 TraesCS2B01G627000 chr2D 639732033 639734333 2300 False 1213.000000 1709 88.050000 1 2106 2 chr2D.!!$F1 2105
6 TraesCS2B01G627000 chr2D 639745301 639747742 2441 True 403.780000 756 84.195800 38 2421 5 chr2D.!!$R5 2383
7 TraesCS2B01G627000 chr2A 765372792 765374935 2143 False 1055.000000 1312 85.587500 1 2172 2 chr2A.!!$F2 2171
8 TraesCS2B01G627000 chr2A 765440823 765443253 2430 True 762.200000 1696 84.100667 38 2418 3 chr2A.!!$R4 2380
9 TraesCS2B01G627000 chr2A 765391732 765394458 2726 True 599.000000 935 85.953250 138 3008 4 chr2A.!!$R3 2870
10 TraesCS2B01G627000 chr2A 765547029 765548531 1502 True 439.000000 464 82.985000 321 1802 2 chr2A.!!$R5 1481

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
500 643 1.04535 TAGCTGGCTAGAGCACCCAG 61.045 60.0 0.0 8.55 46.95 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 3277 0.254462 TGTGTCCAGGTGCAACAGAA 59.746 50.0 3.64 0.0 39.98 3.02 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
36 37 8.204160 TCTACCATGTAAAGTGACCTGATATTG 58.796 37.037 0.00 0.00 0.00 1.90
92 104 4.453136 GCACCTACCGTTGAGTTTGAATTA 59.547 41.667 0.00 0.00 0.00 1.40
202 297 1.267121 TGCCTGTAGTTCAGTCCTCC 58.733 55.000 0.00 0.00 42.19 4.30
205 300 1.205893 CCTGTAGTTCAGTCCTCCAGC 59.794 57.143 0.00 0.00 42.19 4.85
285 384 2.440796 CGGTACCAGTAGGCCGGA 60.441 66.667 13.54 0.00 37.03 5.14
394 527 2.170166 CATGCCCCTAAAAGCTTCACA 58.830 47.619 0.00 0.00 0.00 3.58
497 640 1.068921 GCTAGCTGGCTAGAGCACC 59.931 63.158 27.45 10.14 46.56 5.01
498 641 1.745264 CTAGCTGGCTAGAGCACCC 59.255 63.158 21.08 0.00 46.56 4.61
500 643 1.045350 TAGCTGGCTAGAGCACCCAG 61.045 60.000 0.00 8.55 46.95 4.45
501 644 2.188994 CTGGCTAGAGCACCCAGC 59.811 66.667 3.54 0.00 44.36 4.85
552 709 9.981114 AATTGTACTTTGTCCTTAGAAAATTGG 57.019 29.630 0.00 0.00 0.00 3.16
678 1003 1.844003 CGTGCGCATACATACGTCC 59.156 57.895 15.91 0.00 0.00 4.79
766 1091 1.734137 CAGCAGCCATGATCCTTGC 59.266 57.895 0.00 0.00 35.09 4.01
835 1225 7.977293 GGTCCACACGCATACAACATATATATA 59.023 37.037 0.00 0.00 0.00 0.86
836 1226 9.529325 GTCCACACGCATACAACATATATATAT 57.471 33.333 0.00 0.00 0.00 0.86
866 1256 2.753055 TCAATCGATCGGTGGACAAA 57.247 45.000 16.41 0.00 0.00 2.83
1158 1691 5.085275 TCATCCAGGAGGTTGATCTCTAT 57.915 43.478 0.00 0.00 38.42 1.98
1244 1807 3.703001 TTACTCCCTCTGCTCCAAAAG 57.297 47.619 0.00 0.00 0.00 2.27
1297 1926 7.767198 TGCTAGTGAGGTGGTATATTAACAAAC 59.233 37.037 0.00 0.00 0.00 2.93
1298 1927 7.042925 GCTAGTGAGGTGGTATATTAACAAACG 60.043 40.741 0.00 0.00 0.00 3.60
1301 1930 5.352016 TGAGGTGGTATATTAACAAACGTGC 59.648 40.000 0.00 0.00 0.00 5.34
1384 2019 2.099921 GCAGTCATCGTCAGAGTGGTAT 59.900 50.000 9.94 0.00 37.02 2.73
1462 2097 4.344865 GCCGGGTTCTGGAAGGCA 62.345 66.667 2.18 0.00 46.48 4.75
1468 2103 1.971695 GTTCTGGAAGGCAACCGGG 60.972 63.158 6.32 0.00 34.80 5.73
1531 2166 0.100682 GCATGAGGAAGACGCTCGTA 59.899 55.000 0.00 0.00 0.00 3.43
1676 2354 0.889306 ACACGCCTACACCTCTTCTC 59.111 55.000 0.00 0.00 0.00 2.87
1677 2355 0.888619 CACGCCTACACCTCTTCTCA 59.111 55.000 0.00 0.00 0.00 3.27
2099 3064 1.954362 GCCTGCTGTCCTCGTCTCAT 61.954 60.000 0.00 0.00 0.00 2.90
2106 3137 0.528017 GTCCTCGTCTCATCTGCACA 59.472 55.000 0.00 0.00 0.00 4.57
2152 3198 0.595053 CATACCGTAGCAGCACCGAG 60.595 60.000 5.38 0.00 0.00 4.63
2219 3275 5.828328 TCAGATAGTAGATGACGTCCATGTT 59.172 40.000 14.12 0.00 35.17 2.71
2221 3277 6.016693 CAGATAGTAGATGACGTCCATGTTCT 60.017 42.308 14.12 10.40 35.17 3.01
2232 3288 2.030805 GTCCATGTTCTTCTGTTGCACC 60.031 50.000 0.00 0.00 0.00 5.01
2233 3289 2.158623 TCCATGTTCTTCTGTTGCACCT 60.159 45.455 0.00 0.00 0.00 4.00
2234 3290 2.030540 CCATGTTCTTCTGTTGCACCTG 60.031 50.000 0.00 0.00 0.00 4.00
2235 3291 1.679139 TGTTCTTCTGTTGCACCTGG 58.321 50.000 0.00 0.00 0.00 4.45
2236 3292 1.211703 TGTTCTTCTGTTGCACCTGGA 59.788 47.619 0.00 0.00 0.00 3.86
2237 3293 1.604278 GTTCTTCTGTTGCACCTGGAC 59.396 52.381 0.00 0.00 0.00 4.02
2252 3308 2.575532 CTGGACACACTTGGTTGACAT 58.424 47.619 0.00 0.00 0.00 3.06
2255 3311 3.766591 TGGACACACTTGGTTGACATTTT 59.233 39.130 0.00 0.00 0.00 1.82
2307 3371 3.813166 CCGAGTCCATGTGTTTTACTGTT 59.187 43.478 0.00 0.00 0.00 3.16
2371 3436 8.997323 TGTAGACTACTCTGTTTCACTTAGTAC 58.003 37.037 13.67 0.00 0.00 2.73
2372 3437 9.218440 GTAGACTACTCTGTTTCACTTAGTACT 57.782 37.037 5.32 0.00 0.00 2.73
2374 3439 9.962809 AGACTACTCTGTTTCACTTAGTACTAT 57.037 33.333 2.79 0.00 0.00 2.12
2383 3448 9.595823 TGTTTCACTTAGTACTATATTTCAGGC 57.404 33.333 2.79 0.00 0.00 4.85
2401 3466 5.670485 TCAGGCACAGTTGATTTATCGTAT 58.330 37.500 0.00 0.00 0.00 3.06
2442 3507 7.941795 ATAATTAATTACTCCGTCTGTTCCG 57.058 36.000 10.07 0.00 0.00 4.30
2443 3508 5.587388 ATTAATTACTCCGTCTGTTCCGA 57.413 39.130 0.00 0.00 0.00 4.55
2444 3509 3.947910 AATTACTCCGTCTGTTCCGAA 57.052 42.857 0.00 0.00 0.00 4.30
2445 3510 3.947910 ATTACTCCGTCTGTTCCGAAA 57.052 42.857 0.00 0.00 0.00 3.46
2446 3511 3.947910 TTACTCCGTCTGTTCCGAAAT 57.052 42.857 0.00 0.00 0.00 2.17
2447 3512 5.587388 ATTACTCCGTCTGTTCCGAAATA 57.413 39.130 0.00 0.00 0.00 1.40
2448 3513 5.587388 TTACTCCGTCTGTTCCGAAATAT 57.413 39.130 0.00 0.00 0.00 1.28
2449 3514 6.698008 TTACTCCGTCTGTTCCGAAATATA 57.302 37.500 0.00 0.00 0.00 0.86
2450 3515 5.587388 ACTCCGTCTGTTCCGAAATATAA 57.413 39.130 0.00 0.00 0.00 0.98
2451 3516 5.969423 ACTCCGTCTGTTCCGAAATATAAA 58.031 37.500 0.00 0.00 0.00 1.40
2452 3517 6.579865 ACTCCGTCTGTTCCGAAATATAAAT 58.420 36.000 0.00 0.00 0.00 1.40
2453 3518 6.700520 ACTCCGTCTGTTCCGAAATATAAATC 59.299 38.462 0.00 0.00 0.00 2.17
2454 3519 6.812998 TCCGTCTGTTCCGAAATATAAATCT 58.187 36.000 0.00 0.00 0.00 2.40
2455 3520 7.270047 TCCGTCTGTTCCGAAATATAAATCTT 58.730 34.615 0.00 0.00 0.00 2.40
2456 3521 7.767198 TCCGTCTGTTCCGAAATATAAATCTTT 59.233 33.333 0.00 0.00 0.00 2.52
2457 3522 8.395633 CCGTCTGTTCCGAAATATAAATCTTTT 58.604 33.333 0.00 0.00 0.00 2.27
2458 3523 9.769093 CGTCTGTTCCGAAATATAAATCTTTTT 57.231 29.630 0.00 0.00 0.00 1.94
2485 3550 7.683437 ATATTTCGATGAGGACTACATACGA 57.317 36.000 0.00 0.00 0.00 3.43
2486 3551 5.823209 TTTCGATGAGGACTACATACGAA 57.177 39.130 0.00 0.00 36.55 3.85
2487 3552 5.419760 TTCGATGAGGACTACATACGAAG 57.580 43.478 0.00 0.00 35.17 3.79
2488 3553 3.250280 TCGATGAGGACTACATACGAAGC 59.750 47.826 0.00 0.00 30.90 3.86
2489 3554 3.251245 CGATGAGGACTACATACGAAGCT 59.749 47.826 0.00 0.00 0.00 3.74
2490 3555 4.451435 CGATGAGGACTACATACGAAGCTA 59.549 45.833 0.00 0.00 0.00 3.32
2491 3556 5.049612 CGATGAGGACTACATACGAAGCTAA 60.050 44.000 0.00 0.00 0.00 3.09
2492 3557 6.512903 CGATGAGGACTACATACGAAGCTAAA 60.513 42.308 0.00 0.00 0.00 1.85
2493 3558 6.710597 TGAGGACTACATACGAAGCTAAAT 57.289 37.500 0.00 0.00 0.00 1.40
2494 3559 6.504398 TGAGGACTACATACGAAGCTAAATG 58.496 40.000 0.00 0.00 0.00 2.32
2495 3560 6.320418 TGAGGACTACATACGAAGCTAAATGA 59.680 38.462 0.00 0.00 0.00 2.57
2496 3561 6.740110 AGGACTACATACGAAGCTAAATGAG 58.260 40.000 0.00 0.00 0.00 2.90
2497 3562 6.321690 AGGACTACATACGAAGCTAAATGAGT 59.678 38.462 0.00 0.00 0.00 3.41
2498 3563 6.418226 GGACTACATACGAAGCTAAATGAGTG 59.582 42.308 0.00 0.00 0.00 3.51
2499 3564 7.096884 ACTACATACGAAGCTAAATGAGTGA 57.903 36.000 0.00 0.00 0.00 3.41
2500 3565 7.544622 ACTACATACGAAGCTAAATGAGTGAA 58.455 34.615 0.00 0.00 0.00 3.18
2501 3566 8.198109 ACTACATACGAAGCTAAATGAGTGAAT 58.802 33.333 0.00 0.00 0.00 2.57
2502 3567 7.470289 ACATACGAAGCTAAATGAGTGAATC 57.530 36.000 0.00 0.00 0.00 2.52
2503 3568 7.268586 ACATACGAAGCTAAATGAGTGAATCT 58.731 34.615 0.00 0.00 0.00 2.40
2504 3569 8.414003 ACATACGAAGCTAAATGAGTGAATCTA 58.586 33.333 0.00 0.00 0.00 1.98
2505 3570 8.695284 CATACGAAGCTAAATGAGTGAATCTAC 58.305 37.037 0.00 0.00 0.00 2.59
2506 3571 6.631016 ACGAAGCTAAATGAGTGAATCTACA 58.369 36.000 0.00 0.00 0.00 2.74
2507 3572 7.268586 ACGAAGCTAAATGAGTGAATCTACAT 58.731 34.615 0.00 0.00 0.00 2.29
2508 3573 7.766278 ACGAAGCTAAATGAGTGAATCTACATT 59.234 33.333 0.00 0.00 34.99 2.71
2509 3574 8.272176 CGAAGCTAAATGAGTGAATCTACATTC 58.728 37.037 0.00 0.00 39.24 2.67
2510 3575 9.102757 GAAGCTAAATGAGTGAATCTACATTCA 57.897 33.333 0.00 0.00 45.20 2.57
2549 3614 6.971726 ACATCCGTATGTAGTCCTTATTGA 57.028 37.500 0.00 0.00 44.66 2.57
2550 3615 7.356089 ACATCCGTATGTAGTCCTTATTGAA 57.644 36.000 0.00 0.00 44.66 2.69
2551 3616 7.788026 ACATCCGTATGTAGTCCTTATTGAAA 58.212 34.615 0.00 0.00 44.66 2.69
2552 3617 8.429641 ACATCCGTATGTAGTCCTTATTGAAAT 58.570 33.333 0.00 0.00 44.66 2.17
2553 3618 8.926710 CATCCGTATGTAGTCCTTATTGAAATC 58.073 37.037 0.00 0.00 0.00 2.17
2554 3619 8.246430 TCCGTATGTAGTCCTTATTGAAATCT 57.754 34.615 0.00 0.00 0.00 2.40
2555 3620 8.358148 TCCGTATGTAGTCCTTATTGAAATCTC 58.642 37.037 0.00 0.00 0.00 2.75
2556 3621 8.361139 CCGTATGTAGTCCTTATTGAAATCTCT 58.639 37.037 0.00 0.00 0.00 3.10
2597 3662 4.611564 AATGGAGGGAGTAGTACAGAGT 57.388 45.455 2.52 0.00 0.00 3.24
2600 3665 4.110072 TGGAGGGAGTAGTACAGAGTACT 58.890 47.826 13.64 13.64 43.32 2.73
2621 3686 0.305922 GCAACATAGAGCCGACATGC 59.694 55.000 0.00 0.00 0.00 4.06
2622 3687 1.945387 CAACATAGAGCCGACATGCT 58.055 50.000 0.00 0.00 46.37 3.79
2623 3688 1.596260 CAACATAGAGCCGACATGCTG 59.404 52.381 0.00 0.00 42.95 4.41
2624 3689 0.826715 ACATAGAGCCGACATGCTGT 59.173 50.000 0.00 0.00 42.95 4.40
2625 3690 2.031870 ACATAGAGCCGACATGCTGTA 58.968 47.619 0.00 0.00 42.95 2.74
2626 3691 2.223829 ACATAGAGCCGACATGCTGTAC 60.224 50.000 0.00 0.00 42.95 2.90
2627 3692 0.744874 TAGAGCCGACATGCTGTACC 59.255 55.000 0.00 0.00 42.95 3.34
2629 3694 0.528684 GAGCCGACATGCTGTACCTC 60.529 60.000 0.00 0.00 42.95 3.85
2631 3696 1.897423 CCGACATGCTGTACCTCCA 59.103 57.895 0.00 0.00 0.00 3.86
2633 3698 1.575244 CGACATGCTGTACCTCCATG 58.425 55.000 12.98 12.98 41.49 3.66
2635 3700 2.698855 ACATGCTGTACCTCCATGTC 57.301 50.000 13.95 0.00 44.39 3.06
2638 3703 0.904649 TGCTGTACCTCCATGTCCAG 59.095 55.000 0.00 0.00 0.00 3.86
2639 3704 0.179000 GCTGTACCTCCATGTCCAGG 59.821 60.000 0.00 0.00 35.69 4.45
2640 3705 1.573108 CTGTACCTCCATGTCCAGGT 58.427 55.000 11.79 11.79 45.50 4.00
2641 3706 1.208052 CTGTACCTCCATGTCCAGGTG 59.792 57.143 15.37 0.00 43.30 4.00
2642 3707 1.276622 GTACCTCCATGTCCAGGTGT 58.723 55.000 15.37 0.00 43.30 4.16
2643 3708 1.628846 GTACCTCCATGTCCAGGTGTT 59.371 52.381 15.37 0.00 43.30 3.32
2648 3713 1.492599 TCCATGTCCAGGTGTTTGTGA 59.507 47.619 0.00 0.00 0.00 3.58
2649 3714 2.108075 TCCATGTCCAGGTGTTTGTGAT 59.892 45.455 0.00 0.00 0.00 3.06
2650 3715 2.229543 CCATGTCCAGGTGTTTGTGATG 59.770 50.000 0.00 0.00 0.00 3.07
2651 3716 1.317613 TGTCCAGGTGTTTGTGATGC 58.682 50.000 0.00 0.00 0.00 3.91
2652 3717 1.317613 GTCCAGGTGTTTGTGATGCA 58.682 50.000 0.00 0.00 0.00 3.96
2653 3718 1.001378 GTCCAGGTGTTTGTGATGCAC 60.001 52.381 0.00 0.00 34.56 4.57
2664 3729 5.767665 TGTTTGTGATGCACCTAGTTTACAT 59.232 36.000 0.00 0.00 32.73 2.29
2665 3730 6.937465 TGTTTGTGATGCACCTAGTTTACATA 59.063 34.615 0.00 0.00 32.73 2.29
2668 3733 5.584649 TGTGATGCACCTAGTTTACATAAGC 59.415 40.000 0.00 0.00 32.73 3.09
2669 3734 5.584649 GTGATGCACCTAGTTTACATAAGCA 59.415 40.000 0.00 0.00 0.00 3.91
2671 3736 6.316140 TGATGCACCTAGTTTACATAAGCAAG 59.684 38.462 0.00 0.00 32.83 4.01
2681 3746 3.692257 ACATAAGCAAGACAGAGCACT 57.308 42.857 0.00 0.00 0.00 4.40
2695 3760 4.348863 AGAGCACTCTGTTTCACTCATT 57.651 40.909 0.00 0.00 38.75 2.57
2706 3771 7.813645 TCTGTTTCACTCATTCTGATGAATTG 58.186 34.615 0.00 0.00 41.55 2.32
2715 3780 7.014518 ACTCATTCTGATGAATTGGTTGAACAA 59.985 33.333 0.00 0.00 41.55 2.83
2717 3782 6.713762 TTCTGATGAATTGGTTGAACAACT 57.286 33.333 15.60 0.00 40.94 3.16
2736 3801 5.642491 ACAACTTGATCATCATCACTCAGTG 59.358 40.000 0.00 0.00 38.86 3.66
2737 3802 5.417754 ACTTGATCATCATCACTCAGTGT 57.582 39.130 4.28 0.00 38.86 3.55
2738 3803 6.535963 ACTTGATCATCATCACTCAGTGTA 57.464 37.500 4.28 0.00 38.86 2.90
2739 3804 6.336566 ACTTGATCATCATCACTCAGTGTAC 58.663 40.000 4.28 0.00 38.86 2.90
2740 3805 5.268118 TGATCATCATCACTCAGTGTACC 57.732 43.478 4.28 0.00 33.80 3.34
2757 3823 8.033038 TCAGTGTACCTATATGTTTCACTCAAC 58.967 37.037 12.19 0.00 33.32 3.18
2758 3824 7.817478 CAGTGTACCTATATGTTTCACTCAACA 59.183 37.037 12.19 0.00 40.92 3.33
2772 3838 6.377327 TCACTCAACAAAGAACCTTTCATC 57.623 37.500 0.00 0.00 0.00 2.92
2774 3840 6.038603 TCACTCAACAAAGAACCTTTCATCTG 59.961 38.462 0.00 0.00 0.00 2.90
2776 3842 5.200483 TCAACAAAGAACCTTTCATCTGGT 58.800 37.500 0.00 0.00 38.35 4.00
2778 3844 3.815401 ACAAAGAACCTTTCATCTGGTCG 59.185 43.478 0.00 0.00 35.17 4.79
2788 3854 0.861866 CATCTGGTCGTACGCGTGAG 60.862 60.000 24.59 15.78 39.49 3.51
2796 3862 2.775149 GTCGTACGCGTGAGATAACTTC 59.225 50.000 24.59 4.20 39.49 3.01
2806 3872 5.732528 GCGTGAGATAACTTCGGTTGATCTA 60.733 44.000 0.00 0.00 38.76 1.98
2815 3881 0.758734 CGGTTGATCTATCTGGGCCA 59.241 55.000 5.85 5.85 0.00 5.36
2817 3883 2.567169 CGGTTGATCTATCTGGGCCATA 59.433 50.000 6.72 0.00 0.00 2.74
2831 3897 2.282407 GGCCATACACGAACGGTTAAT 58.718 47.619 0.00 0.00 0.00 1.40
2832 3898 2.286025 GGCCATACACGAACGGTTAATC 59.714 50.000 0.00 0.00 0.00 1.75
2851 3917 2.527497 TCAAATGTGTGATGTGCCCAT 58.473 42.857 0.00 0.00 0.00 4.00
2853 3919 1.187974 AATGTGTGATGTGCCCATGG 58.812 50.000 4.14 4.14 0.00 3.66
2889 3955 2.286477 CGATCGAGCGTGATAGTGAGTT 60.286 50.000 16.15 0.00 0.00 3.01
2911 3977 8.955061 AGTTGATTAATTGAGTTTTCATGTCG 57.045 30.769 0.00 0.00 32.27 4.35
2913 3979 9.393249 GTTGATTAATTGAGTTTTCATGTCGAA 57.607 29.630 0.00 0.00 32.27 3.71
2915 3981 8.783093 TGATTAATTGAGTTTTCATGTCGAACT 58.217 29.630 9.67 9.67 36.40 3.01
2923 3989 6.495706 AGTTTTCATGTCGAACTTCTTTTCC 58.504 36.000 0.00 0.00 31.73 3.13
2924 3990 6.318900 AGTTTTCATGTCGAACTTCTTTTCCT 59.681 34.615 0.00 0.00 31.73 3.36
2925 3991 5.924475 TTCATGTCGAACTTCTTTTCCTC 57.076 39.130 0.00 0.00 0.00 3.71
2966 4032 5.010282 GTCATGGGATTGTAGGTTTGAGTT 58.990 41.667 0.00 0.00 0.00 3.01
2967 4033 6.177610 GTCATGGGATTGTAGGTTTGAGTTA 58.822 40.000 0.00 0.00 0.00 2.24
2971 4037 8.621286 CATGGGATTGTAGGTTTGAGTTATAAC 58.379 37.037 7.57 7.57 0.00 1.89
2993 4059 1.539157 AGTCGAGATGCAGACAGACA 58.461 50.000 14.63 0.00 39.67 3.41
3005 4071 1.077828 AGACAGACAGATGGGTCTCCA 59.922 52.381 0.00 0.00 46.05 3.86
3008 4074 1.625315 CAGACAGATGGGTCTCCAACA 59.375 52.381 0.00 0.00 46.05 3.33
3009 4075 2.038952 CAGACAGATGGGTCTCCAACAA 59.961 50.000 0.00 0.00 46.05 2.83
3010 4076 2.039084 AGACAGATGGGTCTCCAACAAC 59.961 50.000 0.00 0.00 44.63 3.32
3011 4077 5.145574 AGACAGATGGGTCTCCAACAACC 62.146 52.174 0.00 0.00 44.63 3.77
3016 4082 3.266240 GGTCTCCAACAACCCCATC 57.734 57.895 0.00 0.00 0.00 3.51
3017 4083 0.676782 GGTCTCCAACAACCCCATCG 60.677 60.000 0.00 0.00 0.00 3.84
3018 4084 0.323629 GTCTCCAACAACCCCATCGA 59.676 55.000 0.00 0.00 0.00 3.59
3019 4085 0.613260 TCTCCAACAACCCCATCGAG 59.387 55.000 0.00 0.00 0.00 4.04
3020 4086 0.324943 CTCCAACAACCCCATCGAGT 59.675 55.000 0.00 0.00 0.00 4.18
3021 4087 1.553248 CTCCAACAACCCCATCGAGTA 59.447 52.381 0.00 0.00 0.00 2.59
3022 4088 1.276989 TCCAACAACCCCATCGAGTAC 59.723 52.381 0.00 0.00 0.00 2.73
3023 4089 1.002659 CCAACAACCCCATCGAGTACA 59.997 52.381 0.00 0.00 0.00 2.90
3024 4090 2.073816 CAACAACCCCATCGAGTACAC 58.926 52.381 0.00 0.00 0.00 2.90
3025 4091 1.344065 ACAACCCCATCGAGTACACA 58.656 50.000 0.00 0.00 0.00 3.72
3026 4092 1.906574 ACAACCCCATCGAGTACACAT 59.093 47.619 0.00 0.00 0.00 3.21
3027 4093 2.093658 ACAACCCCATCGAGTACACATC 60.094 50.000 0.00 0.00 0.00 3.06
3028 4094 0.744874 ACCCCATCGAGTACACATCG 59.255 55.000 0.00 0.00 41.50 3.84
3038 4104 6.947903 TCGAGTACACATCGAGTATCTATC 57.052 41.667 1.90 0.00 43.79 2.08
3039 4105 6.453092 TCGAGTACACATCGAGTATCTATCA 58.547 40.000 1.90 0.00 43.79 2.15
3040 4106 6.927381 TCGAGTACACATCGAGTATCTATCAA 59.073 38.462 1.90 0.00 43.79 2.57
3041 4107 7.603024 TCGAGTACACATCGAGTATCTATCAAT 59.397 37.037 1.90 0.00 43.79 2.57
3042 4108 8.870879 CGAGTACACATCGAGTATCTATCAATA 58.129 37.037 0.00 0.00 42.76 1.90
3062 4128 8.056407 TCAATATAGTCAATAGATGGGTCTCG 57.944 38.462 0.00 0.00 35.87 4.04
3063 4129 7.888546 TCAATATAGTCAATAGATGGGTCTCGA 59.111 37.037 0.00 0.00 35.87 4.04
3064 4130 8.523658 CAATATAGTCAATAGATGGGTCTCGAA 58.476 37.037 0.00 0.00 35.87 3.71
3065 4131 4.657436 AGTCAATAGATGGGTCTCGAAC 57.343 45.455 0.00 0.00 35.87 3.95
3066 4132 4.282496 AGTCAATAGATGGGTCTCGAACT 58.718 43.478 0.00 0.00 35.87 3.01
3067 4133 4.339814 AGTCAATAGATGGGTCTCGAACTC 59.660 45.833 0.00 0.00 35.87 3.01
3068 4134 3.637229 TCAATAGATGGGTCTCGAACTCC 59.363 47.826 0.00 0.00 35.87 3.85
3069 4135 2.068834 TAGATGGGTCTCGAACTCCC 57.931 55.000 11.00 11.00 41.41 4.30
3070 4136 0.336737 AGATGGGTCTCGAACTCCCT 59.663 55.000 16.60 6.07 41.58 4.20
3071 4137 1.569548 AGATGGGTCTCGAACTCCCTA 59.430 52.381 16.60 7.09 41.58 3.53
3072 4138 2.178106 AGATGGGTCTCGAACTCCCTAT 59.822 50.000 16.60 10.38 41.58 2.57
3073 4139 2.068834 TGGGTCTCGAACTCCCTATC 57.931 55.000 16.60 0.00 41.58 2.08
3074 4140 0.953003 GGGTCTCGAACTCCCTATCG 59.047 60.000 10.73 0.00 38.29 2.92
3075 4141 0.953003 GGTCTCGAACTCCCTATCGG 59.047 60.000 0.00 0.00 39.45 4.18
3076 4142 1.476471 GGTCTCGAACTCCCTATCGGA 60.476 57.143 0.00 0.00 39.45 4.55
3077 4143 2.506444 GTCTCGAACTCCCTATCGGAT 58.494 52.381 0.00 0.00 41.00 4.18
3078 4144 2.485038 GTCTCGAACTCCCTATCGGATC 59.515 54.545 0.00 0.00 41.00 3.36
3079 4145 1.813786 CTCGAACTCCCTATCGGATCC 59.186 57.143 0.00 0.00 41.00 3.36
3080 4146 1.424302 TCGAACTCCCTATCGGATCCT 59.576 52.381 10.75 0.00 41.00 3.24
3081 4147 1.542030 CGAACTCCCTATCGGATCCTG 59.458 57.143 10.75 3.62 41.00 3.86
3082 4148 2.599677 GAACTCCCTATCGGATCCTGT 58.400 52.381 10.75 0.20 41.00 4.00
3083 4149 2.002505 ACTCCCTATCGGATCCTGTG 57.997 55.000 10.75 0.00 41.00 3.66
3084 4150 0.605589 CTCCCTATCGGATCCTGTGC 59.394 60.000 10.75 0.00 41.00 4.57
3085 4151 0.105709 TCCCTATCGGATCCTGTGCA 60.106 55.000 10.75 0.00 34.86 4.57
3086 4152 0.758734 CCCTATCGGATCCTGTGCAA 59.241 55.000 10.75 0.00 0.00 4.08
3087 4153 1.140852 CCCTATCGGATCCTGTGCAAA 59.859 52.381 10.75 0.00 0.00 3.68
3088 4154 2.213499 CCTATCGGATCCTGTGCAAAC 58.787 52.381 10.75 0.00 0.00 2.93
3089 4155 2.419990 CCTATCGGATCCTGTGCAAACA 60.420 50.000 10.75 0.00 0.00 2.83
3090 4156 2.198827 ATCGGATCCTGTGCAAACAA 57.801 45.000 10.75 0.00 0.00 2.83
3091 4157 1.974265 TCGGATCCTGTGCAAACAAA 58.026 45.000 10.75 0.00 0.00 2.83
3092 4158 1.606668 TCGGATCCTGTGCAAACAAAC 59.393 47.619 10.75 0.00 0.00 2.93
3093 4159 1.608590 CGGATCCTGTGCAAACAAACT 59.391 47.619 10.75 0.00 0.00 2.66
3094 4160 2.034558 CGGATCCTGTGCAAACAAACTT 59.965 45.455 10.75 0.00 0.00 2.66
3095 4161 3.490761 CGGATCCTGTGCAAACAAACTTT 60.491 43.478 10.75 0.00 0.00 2.66
3096 4162 3.803778 GGATCCTGTGCAAACAAACTTTG 59.196 43.478 3.84 0.00 0.00 2.77
3098 4164 5.451242 GGATCCTGTGCAAACAAACTTTGTA 60.451 40.000 3.84 0.00 44.59 2.41
3099 4165 5.392767 TCCTGTGCAAACAAACTTTGTAA 57.607 34.783 7.59 0.00 44.59 2.41
3100 4166 5.971763 TCCTGTGCAAACAAACTTTGTAAT 58.028 33.333 7.59 0.00 44.59 1.89
3101 4167 6.039616 TCCTGTGCAAACAAACTTTGTAATC 58.960 36.000 7.59 1.35 44.59 1.75
3102 4168 6.042143 CCTGTGCAAACAAACTTTGTAATCT 58.958 36.000 7.59 0.00 44.59 2.40
3103 4169 6.534793 CCTGTGCAAACAAACTTTGTAATCTT 59.465 34.615 7.59 0.00 44.59 2.40
3104 4170 7.064490 CCTGTGCAAACAAACTTTGTAATCTTT 59.936 33.333 7.59 0.00 44.59 2.52
3105 4171 7.958674 TGTGCAAACAAACTTTGTAATCTTTC 58.041 30.769 7.59 0.00 44.59 2.62
3106 4172 7.064016 TGTGCAAACAAACTTTGTAATCTTTCC 59.936 33.333 7.59 0.00 44.59 3.13
3107 4173 7.064016 GTGCAAACAAACTTTGTAATCTTTCCA 59.936 33.333 7.59 0.00 44.59 3.53
3108 4174 7.604164 TGCAAACAAACTTTGTAATCTTTCCAA 59.396 29.630 7.59 0.00 44.59 3.53
3109 4175 8.447053 GCAAACAAACTTTGTAATCTTTCCAAA 58.553 29.630 7.59 0.00 44.59 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.158755 AGTACCAGCAGGAATATGGTGC 60.159 50.000 0.35 5.04 46.64 5.01
92 104 3.476552 TGCAGAGACGAATTTCAACCTT 58.523 40.909 0.00 0.00 0.00 3.50
202 297 1.270252 GGTCAATTTTGTGGTGGGCTG 60.270 52.381 0.00 0.00 0.00 4.85
205 300 2.297033 CTCTGGTCAATTTTGTGGTGGG 59.703 50.000 0.00 0.00 0.00 4.61
285 384 6.808212 CGTGTATTTTCCATCATTTTTCTGCT 59.192 34.615 0.00 0.00 0.00 4.24
394 527 1.121407 TGGGTGTAGCAGCTGTGAGT 61.121 55.000 16.64 0.31 31.98 3.41
487 630 2.510238 CACGCTGGGTGCTCTAGC 60.510 66.667 12.04 6.05 40.33 3.42
497 640 2.202388 CGATTGCAAGCACGCTGG 60.202 61.111 15.98 0.00 0.00 4.85
498 641 2.202388 CCGATTGCAAGCACGCTG 60.202 61.111 15.98 0.00 0.00 5.18
501 644 2.040213 CTAGGCCGATTGCAAGCACG 62.040 60.000 15.98 14.67 43.89 5.34
550 707 0.697658 TGCAATCATGTCCTGGACCA 59.302 50.000 23.42 12.21 0.00 4.02
552 709 1.741706 CACTGCAATCATGTCCTGGAC 59.258 52.381 19.96 19.96 0.00 4.02
678 1003 2.434534 AGCAAGCAGAGCAGAGCG 60.435 61.111 0.00 0.00 35.48 5.03
705 1030 1.003928 TGCAATGAGAGGTGAGCACAT 59.996 47.619 2.75 0.00 0.00 3.21
849 1239 2.762535 AGTTTGTCCACCGATCGATT 57.237 45.000 18.66 0.00 0.00 3.34
866 1256 1.710809 AGGGGAAACAATGGTGCTAGT 59.289 47.619 0.00 0.00 0.00 2.57
990 1448 3.406764 CATTGCTAGCATCTACCTTCCC 58.593 50.000 20.13 0.00 0.00 3.97
1158 1691 0.832135 GGTCCCATGGCTCGATCCTA 60.832 60.000 6.09 0.00 0.00 2.94
1244 1807 6.865205 ACTATGTACTAAAACCACGACAAGTC 59.135 38.462 0.00 0.00 0.00 3.01
1301 1930 1.002990 TGCACCTCTCTGCACCATG 60.003 57.895 0.00 0.00 42.36 3.66
1350 1985 3.781770 GACTGCTCATCCTCCGCCG 62.782 68.421 0.00 0.00 0.00 6.46
1360 1995 1.200948 CACTCTGACGATGACTGCTCA 59.799 52.381 0.00 0.00 0.00 4.26
1384 2019 2.494059 CGGTCCTTGAAGCTGAAGAAA 58.506 47.619 7.22 0.00 0.00 2.52
1462 2097 3.647771 GGCTTGTCCCTCCCGGTT 61.648 66.667 0.00 0.00 0.00 4.44
1468 2103 2.047179 GTCACCGGCTTGTCCCTC 60.047 66.667 0.00 0.00 0.00 4.30
1531 2166 2.297895 TGCACGGCCCCTGTAGAAT 61.298 57.895 0.00 0.00 0.00 2.40
1618 2253 5.373812 AGAGGAACTGAAGAAAAACCTGA 57.626 39.130 0.00 0.00 41.55 3.86
1676 2354 3.614176 TCAACGCGAGATTCTCAAGAATG 59.386 43.478 15.93 10.41 44.14 2.67
1677 2355 3.849911 TCAACGCGAGATTCTCAAGAAT 58.150 40.909 15.93 4.94 46.54 2.40
2091 3056 2.033927 GCTCTATGTGCAGATGAGACGA 59.966 50.000 20.06 5.10 0.00 4.20
2106 3137 5.888724 TGCTAACTCTACTTCACTGCTCTAT 59.111 40.000 0.00 0.00 0.00 1.98
2210 3266 1.872952 TGCAACAGAAGAACATGGACG 59.127 47.619 0.00 0.00 0.00 4.79
2219 3275 0.836606 TGTCCAGGTGCAACAGAAGA 59.163 50.000 3.64 0.00 39.98 2.87
2221 3277 0.254462 TGTGTCCAGGTGCAACAGAA 59.746 50.000 3.64 0.00 39.98 3.02
2232 3288 2.036958 TGTCAACCAAGTGTGTCCAG 57.963 50.000 0.00 0.00 0.00 3.86
2233 3289 2.727123 ATGTCAACCAAGTGTGTCCA 57.273 45.000 0.00 0.00 0.00 4.02
2234 3290 4.385358 AAAATGTCAACCAAGTGTGTCC 57.615 40.909 0.00 0.00 0.00 4.02
2235 3291 5.746721 GGTAAAAATGTCAACCAAGTGTGTC 59.253 40.000 0.00 0.00 32.04 3.67
2236 3292 5.420739 AGGTAAAAATGTCAACCAAGTGTGT 59.579 36.000 0.00 0.00 34.29 3.72
2237 3293 5.901552 AGGTAAAAATGTCAACCAAGTGTG 58.098 37.500 0.00 0.00 34.29 3.82
2255 3311 9.393512 GTGAAACAGAGTAGTCTATCTAGGTAA 57.606 37.037 0.00 0.00 36.32 2.85
2307 3371 3.069586 CAGTAAGTGGAACAGAGTGGTCA 59.930 47.826 0.00 0.00 41.80 4.02
2372 3437 8.773645 CGATAAATCAACTGTGCCTGAAATATA 58.226 33.333 0.00 0.00 0.00 0.86
2373 3438 7.283127 ACGATAAATCAACTGTGCCTGAAATAT 59.717 33.333 0.00 0.00 0.00 1.28
2374 3439 6.597672 ACGATAAATCAACTGTGCCTGAAATA 59.402 34.615 0.00 0.00 0.00 1.40
2383 3448 6.947258 TCATGCATACGATAAATCAACTGTG 58.053 36.000 0.00 0.00 0.00 3.66
2429 3494 6.924060 AGATTTATATTTCGGAACAGACGGAG 59.076 38.462 0.00 0.00 0.00 4.63
2430 3495 6.812998 AGATTTATATTTCGGAACAGACGGA 58.187 36.000 0.00 0.00 0.00 4.69
2431 3496 7.478520 AAGATTTATATTTCGGAACAGACGG 57.521 36.000 0.00 0.00 0.00 4.79
2432 3497 9.769093 AAAAAGATTTATATTTCGGAACAGACG 57.231 29.630 0.00 0.00 0.00 4.18
2459 3524 9.392259 TCGTATGTAGTCCTCATCGAAATATAT 57.608 33.333 0.00 0.00 0.00 0.86
2460 3525 8.782339 TCGTATGTAGTCCTCATCGAAATATA 57.218 34.615 0.00 0.00 0.00 0.86
2461 3526 7.683437 TCGTATGTAGTCCTCATCGAAATAT 57.317 36.000 0.00 0.00 0.00 1.28
2462 3527 7.500720 TTCGTATGTAGTCCTCATCGAAATA 57.499 36.000 0.00 0.00 34.97 1.40
2463 3528 6.387041 TTCGTATGTAGTCCTCATCGAAAT 57.613 37.500 0.00 0.00 34.97 2.17
2464 3529 5.732528 GCTTCGTATGTAGTCCTCATCGAAA 60.733 44.000 0.00 0.00 36.08 3.46
2465 3530 4.261072 GCTTCGTATGTAGTCCTCATCGAA 60.261 45.833 0.00 0.00 35.68 3.71
2466 3531 3.250280 GCTTCGTATGTAGTCCTCATCGA 59.750 47.826 0.00 0.00 0.00 3.59
2467 3532 3.251245 AGCTTCGTATGTAGTCCTCATCG 59.749 47.826 0.00 0.00 0.00 3.84
2468 3533 4.839668 AGCTTCGTATGTAGTCCTCATC 57.160 45.455 0.00 0.00 0.00 2.92
2469 3534 6.710597 TTTAGCTTCGTATGTAGTCCTCAT 57.289 37.500 0.00 0.00 0.00 2.90
2470 3535 6.320418 TCATTTAGCTTCGTATGTAGTCCTCA 59.680 38.462 0.00 0.00 0.00 3.86
2471 3536 6.736123 TCATTTAGCTTCGTATGTAGTCCTC 58.264 40.000 0.00 0.00 0.00 3.71
2472 3537 6.321690 ACTCATTTAGCTTCGTATGTAGTCCT 59.678 38.462 0.00 0.00 0.00 3.85
2473 3538 6.418226 CACTCATTTAGCTTCGTATGTAGTCC 59.582 42.308 0.00 0.00 0.00 3.85
2474 3539 7.194278 TCACTCATTTAGCTTCGTATGTAGTC 58.806 38.462 0.00 0.00 0.00 2.59
2475 3540 7.096884 TCACTCATTTAGCTTCGTATGTAGT 57.903 36.000 0.00 0.00 0.00 2.73
2476 3541 7.987268 TTCACTCATTTAGCTTCGTATGTAG 57.013 36.000 0.00 0.00 0.00 2.74
2477 3542 8.414003 AGATTCACTCATTTAGCTTCGTATGTA 58.586 33.333 0.00 0.00 0.00 2.29
2478 3543 7.268586 AGATTCACTCATTTAGCTTCGTATGT 58.731 34.615 0.00 0.00 0.00 2.29
2479 3544 7.706281 AGATTCACTCATTTAGCTTCGTATG 57.294 36.000 0.00 0.00 0.00 2.39
2480 3545 8.414003 TGTAGATTCACTCATTTAGCTTCGTAT 58.586 33.333 0.00 0.00 0.00 3.06
2481 3546 7.768240 TGTAGATTCACTCATTTAGCTTCGTA 58.232 34.615 0.00 0.00 0.00 3.43
2482 3547 6.631016 TGTAGATTCACTCATTTAGCTTCGT 58.369 36.000 0.00 0.00 0.00 3.85
2483 3548 7.706281 ATGTAGATTCACTCATTTAGCTTCG 57.294 36.000 0.00 0.00 0.00 3.79
2484 3549 9.102757 TGAATGTAGATTCACTCATTTAGCTTC 57.897 33.333 11.06 0.00 42.56 3.86
2485 3550 9.453572 TTGAATGTAGATTCACTCATTTAGCTT 57.546 29.630 14.43 0.00 46.23 3.74
2486 3551 9.453572 TTTGAATGTAGATTCACTCATTTAGCT 57.546 29.630 14.43 0.00 46.23 3.32
2516 3581 9.339850 GGACTACATACGGATGTATATAGACAT 57.660 37.037 20.64 12.70 45.42 3.06
2517 3582 8.546322 AGGACTACATACGGATGTATATAGACA 58.454 37.037 20.64 2.07 45.42 3.41
2518 3583 8.961294 AGGACTACATACGGATGTATATAGAC 57.039 38.462 20.64 10.95 45.42 2.59
2523 3588 9.743581 TCAATAAGGACTACATACGGATGTATA 57.256 33.333 20.64 10.32 45.42 1.47
2524 3589 8.645814 TCAATAAGGACTACATACGGATGTAT 57.354 34.615 20.64 11.04 45.42 2.29
2525 3590 8.467963 TTCAATAAGGACTACATACGGATGTA 57.532 34.615 19.32 19.32 44.77 2.29
2527 3592 8.833231 ATTTCAATAAGGACTACATACGGATG 57.167 34.615 5.94 5.94 39.16 3.51
2528 3593 8.871125 AGATTTCAATAAGGACTACATACGGAT 58.129 33.333 0.00 0.00 0.00 4.18
2529 3594 8.246430 AGATTTCAATAAGGACTACATACGGA 57.754 34.615 0.00 0.00 0.00 4.69
2530 3595 8.361139 AGAGATTTCAATAAGGACTACATACGG 58.639 37.037 0.00 0.00 0.00 4.02
2561 3626 9.453830 ACTCCCTCCATTTCTAAATATAAGTCT 57.546 33.333 0.00 0.00 0.00 3.24
2567 3632 9.670442 TGTACTACTCCCTCCATTTCTAAATAT 57.330 33.333 0.00 0.00 0.00 1.28
2568 3633 9.144298 CTGTACTACTCCCTCCATTTCTAAATA 57.856 37.037 0.00 0.00 0.00 1.40
2569 3634 7.844779 TCTGTACTACTCCCTCCATTTCTAAAT 59.155 37.037 0.00 0.00 0.00 1.40
2570 3635 7.186972 TCTGTACTACTCCCTCCATTTCTAAA 58.813 38.462 0.00 0.00 0.00 1.85
2571 3636 6.738635 TCTGTACTACTCCCTCCATTTCTAA 58.261 40.000 0.00 0.00 0.00 2.10
2572 3637 6.068971 ACTCTGTACTACTCCCTCCATTTCTA 60.069 42.308 0.00 0.00 0.00 2.10
2573 3638 5.205056 CTCTGTACTACTCCCTCCATTTCT 58.795 45.833 0.00 0.00 0.00 2.52
2574 3639 4.957327 ACTCTGTACTACTCCCTCCATTTC 59.043 45.833 0.00 0.00 0.00 2.17
2575 3640 4.949121 ACTCTGTACTACTCCCTCCATTT 58.051 43.478 0.00 0.00 0.00 2.32
2576 3641 4.611564 ACTCTGTACTACTCCCTCCATT 57.388 45.455 0.00 0.00 0.00 3.16
2577 3642 4.727841 AGTACTCTGTACTACTCCCTCCAT 59.272 45.833 8.43 0.00 0.00 3.41
2578 3643 4.080469 CAGTACTCTGTACTACTCCCTCCA 60.080 50.000 9.65 0.00 36.97 3.86
2579 3644 4.453751 CAGTACTCTGTACTACTCCCTCC 58.546 52.174 9.65 0.00 36.97 4.30
2580 3645 4.453751 CCAGTACTCTGTACTACTCCCTC 58.546 52.174 9.65 0.00 39.82 4.30
2581 3646 3.371810 GCCAGTACTCTGTACTACTCCCT 60.372 52.174 9.65 0.00 39.82 4.20
2582 3647 2.950975 GCCAGTACTCTGTACTACTCCC 59.049 54.545 9.65 0.00 39.82 4.30
2583 3648 3.618351 TGCCAGTACTCTGTACTACTCC 58.382 50.000 9.65 1.44 39.82 3.85
2584 3649 4.458295 TGTTGCCAGTACTCTGTACTACTC 59.542 45.833 9.65 4.03 39.82 2.59
2585 3650 4.404640 TGTTGCCAGTACTCTGTACTACT 58.595 43.478 9.65 0.00 39.82 2.57
2586 3651 4.778534 TGTTGCCAGTACTCTGTACTAC 57.221 45.455 9.65 5.99 39.82 2.73
2605 3670 3.675086 CAGCATGTCGGCTCTATGT 57.325 52.632 0.00 0.00 43.68 2.29
2617 3682 1.210234 TGGACATGGAGGTACAGCATG 59.790 52.381 0.00 0.00 46.00 4.06
2622 3687 1.275666 CACCTGGACATGGAGGTACA 58.724 55.000 11.74 0.00 40.85 2.90
2623 3688 1.276622 ACACCTGGACATGGAGGTAC 58.723 55.000 11.74 0.00 40.85 3.34
2624 3689 2.038863 AACACCTGGACATGGAGGTA 57.961 50.000 11.74 0.00 40.85 3.08
2625 3690 1.149101 AAACACCTGGACATGGAGGT 58.851 50.000 0.00 7.36 43.79 3.85
2626 3691 1.202927 ACAAACACCTGGACATGGAGG 60.203 52.381 0.00 1.68 35.26 4.30
2627 3692 1.881973 CACAAACACCTGGACATGGAG 59.118 52.381 0.00 0.00 0.00 3.86
2629 3694 1.979855 TCACAAACACCTGGACATGG 58.020 50.000 0.00 0.00 0.00 3.66
2631 3696 1.888512 GCATCACAAACACCTGGACAT 59.111 47.619 0.00 0.00 0.00 3.06
2633 3698 1.001378 GTGCATCACAAACACCTGGAC 60.001 52.381 0.00 0.00 34.08 4.02
2634 3699 1.317613 GTGCATCACAAACACCTGGA 58.682 50.000 0.00 0.00 34.08 3.86
2635 3700 3.871775 GTGCATCACAAACACCTGG 57.128 52.632 0.00 0.00 34.08 4.45
2639 3704 4.568152 AAACTAGGTGCATCACAAACAC 57.432 40.909 0.00 0.00 35.86 3.32
2640 3705 5.126779 TGTAAACTAGGTGCATCACAAACA 58.873 37.500 0.00 0.00 35.86 2.83
2641 3706 5.682943 TGTAAACTAGGTGCATCACAAAC 57.317 39.130 0.00 0.00 35.86 2.93
2642 3707 7.361713 GCTTATGTAAACTAGGTGCATCACAAA 60.362 37.037 0.00 0.00 35.86 2.83
2643 3708 6.093495 GCTTATGTAAACTAGGTGCATCACAA 59.907 38.462 0.00 0.00 35.86 3.33
2648 3713 6.316390 GTCTTGCTTATGTAAACTAGGTGCAT 59.684 38.462 0.00 0.00 0.00 3.96
2649 3714 5.642063 GTCTTGCTTATGTAAACTAGGTGCA 59.358 40.000 0.00 0.00 0.00 4.57
2650 3715 5.642063 TGTCTTGCTTATGTAAACTAGGTGC 59.358 40.000 0.00 0.00 0.00 5.01
2651 3716 7.097192 TCTGTCTTGCTTATGTAAACTAGGTG 58.903 38.462 0.00 0.00 0.00 4.00
2652 3717 7.241042 TCTGTCTTGCTTATGTAAACTAGGT 57.759 36.000 0.00 0.00 0.00 3.08
2653 3718 6.256757 GCTCTGTCTTGCTTATGTAAACTAGG 59.743 42.308 0.00 0.00 0.00 3.02
2657 3722 5.409826 AGTGCTCTGTCTTGCTTATGTAAAC 59.590 40.000 0.00 0.00 0.00 2.01
2694 3759 6.713762 AGTTGTTCAACCAATTCATCAGAA 57.286 33.333 11.38 0.00 38.31 3.02
2695 3760 6.320926 TCAAGTTGTTCAACCAATTCATCAGA 59.679 34.615 11.38 0.00 0.00 3.27
2706 3771 6.072286 AGTGATGATGATCAAGTTGTTCAACC 60.072 38.462 18.10 13.73 40.39 3.77
2715 3780 5.417754 ACACTGAGTGATGATGATCAAGT 57.582 39.130 20.97 0.00 40.39 3.16
2717 3782 5.423290 AGGTACACTGAGTGATGATGATCAA 59.577 40.000 20.97 0.00 40.39 2.57
2736 3801 9.431887 TCTTTGTTGAGTGAAACATATAGGTAC 57.568 33.333 0.00 0.00 41.43 3.34
2738 3803 8.784043 GTTCTTTGTTGAGTGAAACATATAGGT 58.216 33.333 0.00 0.00 41.43 3.08
2739 3804 8.237267 GGTTCTTTGTTGAGTGAAACATATAGG 58.763 37.037 0.00 0.00 41.43 2.57
2740 3805 9.003658 AGGTTCTTTGTTGAGTGAAACATATAG 57.996 33.333 0.00 0.00 41.43 1.31
2757 3823 3.815401 ACGACCAGATGAAAGGTTCTTTG 59.185 43.478 0.00 0.00 38.50 2.77
2758 3824 4.086706 ACGACCAGATGAAAGGTTCTTT 57.913 40.909 0.00 0.00 38.50 2.52
2772 3838 0.654160 TATCTCACGCGTACGACCAG 59.346 55.000 21.65 8.46 43.93 4.00
2774 3840 1.063174 AGTTATCTCACGCGTACGACC 59.937 52.381 21.65 0.32 43.93 4.79
2776 3842 2.535534 CGAAGTTATCTCACGCGTACGA 60.536 50.000 21.65 12.15 43.93 3.43
2778 3844 2.107178 CCGAAGTTATCTCACGCGTAC 58.893 52.381 13.44 5.24 0.00 3.67
2788 3854 6.159988 CCCAGATAGATCAACCGAAGTTATC 58.840 44.000 0.00 0.00 33.27 1.75
2796 3862 0.758734 TGGCCCAGATAGATCAACCG 59.241 55.000 0.00 0.00 0.00 4.44
2806 3872 0.179084 CGTTCGTGTATGGCCCAGAT 60.179 55.000 0.00 0.00 0.00 2.90
2815 3881 6.148150 ACACATTTGATTAACCGTTCGTGTAT 59.852 34.615 0.00 0.00 32.49 2.29
2817 3883 4.273969 ACACATTTGATTAACCGTTCGTGT 59.726 37.500 0.00 0.00 0.00 4.49
2831 3897 1.992538 TGGGCACATCACACATTTGA 58.007 45.000 0.00 0.00 0.00 2.69
2832 3898 2.612604 CATGGGCACATCACACATTTG 58.387 47.619 0.00 0.00 34.35 2.32
2851 3917 3.317149 CGATCGATGTTAACTAGTCCCCA 59.683 47.826 10.26 0.00 0.00 4.96
2853 3919 4.785417 CTCGATCGATGTTAACTAGTCCC 58.215 47.826 19.78 0.00 0.00 4.46
2889 3955 8.783093 AGTTCGACATGAAAACTCAATTAATCA 58.217 29.630 0.00 0.00 38.60 2.57
2904 3970 4.991056 CAGAGGAAAAGAAGTTCGACATGA 59.009 41.667 0.00 0.00 0.00 3.07
2906 3972 4.962155 ACAGAGGAAAAGAAGTTCGACAT 58.038 39.130 0.00 0.00 0.00 3.06
2923 3989 7.582679 CCATGACGCGTAAATTAAATTACAGAG 59.417 37.037 13.97 9.54 35.89 3.35
2924 3990 7.403421 CCATGACGCGTAAATTAAATTACAGA 58.597 34.615 13.97 0.00 35.89 3.41
2925 3991 6.631238 CCCATGACGCGTAAATTAAATTACAG 59.369 38.462 13.97 8.60 35.89 2.74
2966 4032 6.766467 TCTGTCTGCATCTCGACTTAGTTATA 59.234 38.462 5.54 0.00 0.00 0.98
2967 4033 5.590663 TCTGTCTGCATCTCGACTTAGTTAT 59.409 40.000 5.54 0.00 0.00 1.89
2971 4037 3.127721 TGTCTGTCTGCATCTCGACTTAG 59.872 47.826 5.54 0.00 0.00 2.18
2977 4043 2.461903 CATCTGTCTGTCTGCATCTCG 58.538 52.381 0.00 0.00 0.00 4.04
3005 4071 1.695242 TGTGTACTCGATGGGGTTGTT 59.305 47.619 0.00 0.00 0.00 2.83
3008 4074 1.136305 CGATGTGTACTCGATGGGGTT 59.864 52.381 0.00 0.00 38.38 4.11
3009 4075 0.744874 CGATGTGTACTCGATGGGGT 59.255 55.000 0.00 0.00 38.38 4.95
3010 4076 1.001268 CTCGATGTGTACTCGATGGGG 60.001 57.143 6.20 0.00 43.53 4.96
3011 4077 1.676529 ACTCGATGTGTACTCGATGGG 59.323 52.381 6.20 0.00 43.53 4.00
3012 4078 4.452795 AGATACTCGATGTGTACTCGATGG 59.547 45.833 6.20 0.00 43.53 3.51
3013 4079 5.599359 AGATACTCGATGTGTACTCGATG 57.401 43.478 6.20 4.31 43.53 3.84
3014 4080 7.097834 TGATAGATACTCGATGTGTACTCGAT 58.902 38.462 6.20 1.34 43.53 3.59
3015 4081 6.453092 TGATAGATACTCGATGTGTACTCGA 58.547 40.000 5.69 5.69 42.44 4.04
3016 4082 6.707599 TGATAGATACTCGATGTGTACTCG 57.292 41.667 0.00 0.00 37.47 4.18
3036 4102 8.690884 CGAGACCCATCTATTGACTATATTGAT 58.309 37.037 0.00 0.00 34.34 2.57
3037 4103 7.888546 TCGAGACCCATCTATTGACTATATTGA 59.111 37.037 0.00 0.00 34.34 2.57
3038 4104 8.056407 TCGAGACCCATCTATTGACTATATTG 57.944 38.462 0.00 0.00 34.34 1.90
3039 4105 8.524487 GTTCGAGACCCATCTATTGACTATATT 58.476 37.037 0.00 0.00 34.34 1.28
3040 4106 7.891183 AGTTCGAGACCCATCTATTGACTATAT 59.109 37.037 0.00 0.00 34.34 0.86
3041 4107 7.232188 AGTTCGAGACCCATCTATTGACTATA 58.768 38.462 0.00 0.00 34.34 1.31
3042 4108 6.071984 AGTTCGAGACCCATCTATTGACTAT 58.928 40.000 0.00 0.00 34.34 2.12
3043 4109 5.446860 AGTTCGAGACCCATCTATTGACTA 58.553 41.667 0.00 0.00 34.34 2.59
3044 4110 4.282496 AGTTCGAGACCCATCTATTGACT 58.718 43.478 0.00 0.00 34.34 3.41
3045 4111 4.500035 GGAGTTCGAGACCCATCTATTGAC 60.500 50.000 0.00 0.00 34.34 3.18
3046 4112 3.637229 GGAGTTCGAGACCCATCTATTGA 59.363 47.826 0.00 0.00 34.34 2.57
3047 4113 3.243907 GGGAGTTCGAGACCCATCTATTG 60.244 52.174 15.52 0.00 42.81 1.90
3048 4114 2.966516 GGGAGTTCGAGACCCATCTATT 59.033 50.000 15.52 0.00 42.81 1.73
3049 4115 2.178106 AGGGAGTTCGAGACCCATCTAT 59.822 50.000 20.27 2.74 45.43 1.98
3050 4116 1.569548 AGGGAGTTCGAGACCCATCTA 59.430 52.381 20.27 0.00 45.43 1.98
3051 4117 0.336737 AGGGAGTTCGAGACCCATCT 59.663 55.000 20.27 3.31 45.43 2.90
3052 4118 2.068834 TAGGGAGTTCGAGACCCATC 57.931 55.000 20.27 3.03 45.43 3.51
3053 4119 2.599677 GATAGGGAGTTCGAGACCCAT 58.400 52.381 20.27 13.51 45.43 4.00
3054 4120 1.749635 CGATAGGGAGTTCGAGACCCA 60.750 57.143 20.27 10.44 45.43 4.51
3055 4121 0.953003 CGATAGGGAGTTCGAGACCC 59.047 60.000 13.43 13.43 43.55 4.46
3067 4133 6.968604 TTGTTTGCACAGGATCCGATAGGG 62.969 50.000 5.98 0.00 46.21 3.53
3069 4135 2.905075 TGTTTGCACAGGATCCGATAG 58.095 47.619 5.98 0.39 0.00 2.08
3070 4136 3.342377 TTGTTTGCACAGGATCCGATA 57.658 42.857 5.98 0.00 33.22 2.92
3071 4137 2.198827 TTGTTTGCACAGGATCCGAT 57.801 45.000 5.98 0.00 33.22 4.18
3072 4138 1.606668 GTTTGTTTGCACAGGATCCGA 59.393 47.619 5.98 0.00 33.22 4.55
3073 4139 1.608590 AGTTTGTTTGCACAGGATCCG 59.391 47.619 5.98 3.99 33.22 4.18
3074 4140 3.733443 AAGTTTGTTTGCACAGGATCC 57.267 42.857 2.48 2.48 33.22 3.36
3075 4141 4.432712 ACAAAGTTTGTTTGCACAGGATC 58.567 39.130 15.58 0.00 42.22 3.36
3076 4142 4.470334 ACAAAGTTTGTTTGCACAGGAT 57.530 36.364 15.58 0.00 42.22 3.24
3077 4143 3.951775 ACAAAGTTTGTTTGCACAGGA 57.048 38.095 15.58 0.00 42.22 3.86
3078 4144 6.042143 AGATTACAAAGTTTGTTTGCACAGG 58.958 36.000 25.35 0.00 42.22 4.00
3079 4145 7.524294 AAGATTACAAAGTTTGTTTGCACAG 57.476 32.000 25.35 0.00 42.22 3.66
3080 4146 7.064016 GGAAAGATTACAAAGTTTGTTTGCACA 59.936 33.333 25.35 4.58 42.22 4.57
3081 4147 7.064016 TGGAAAGATTACAAAGTTTGTTTGCAC 59.936 33.333 25.35 12.87 42.22 4.57
3082 4148 7.099764 TGGAAAGATTACAAAGTTTGTTTGCA 58.900 30.769 25.35 19.89 42.22 4.08
3083 4149 7.532682 TGGAAAGATTACAAAGTTTGTTTGC 57.467 32.000 25.35 17.79 42.22 3.68


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

AutoCloner maintained by Alex Coulton.