Multiple sequence alignment - TraesCS3D01G406600

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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 TraesCS3D01G406600 chr3D 100.000 3678 0 0 1 3678 520425487 520429164 0.000000e+00 6793.0
1 TraesCS3D01G406600 chr3D 87.712 1180 107 21 1223 2373 520097641 520096471 0.000000e+00 1341.0
2 TraesCS3D01G406600 chr3D 87.260 887 103 7 1 887 181799816 181798940 0.000000e+00 1003.0
3 TraesCS3D01G406600 chr3D 89.173 665 55 13 3018 3678 520082568 520081917 0.000000e+00 813.0
4 TraesCS3D01G406600 chr3D 75.755 1159 210 41 1103 2227 569119555 569118434 5.440000e-143 518.0
5 TraesCS3D01G406600 chr3D 79.560 455 66 16 1038 1468 520080597 520080146 2.150000e-77 300.0
6 TraesCS3D01G406600 chr3D 99.342 152 1 0 2366 2517 520427780 520427931 3.620000e-70 276.0
7 TraesCS3D01G406600 chr3D 99.342 152 1 0 2294 2445 520427852 520428003 3.620000e-70 276.0
8 TraesCS3D01G406600 chr3D 88.732 213 21 3 1103 1312 568234916 568235128 1.310000e-64 257.0
9 TraesCS3D01G406600 chr3D 87.225 227 28 1 1100 1326 568819221 568818996 1.310000e-64 257.0
10 TraesCS3D01G406600 chr3D 92.623 122 7 2 899 1019 520151823 520151703 1.360000e-39 174.0
11 TraesCS3D01G406600 chr3D 98.750 80 1 0 2438 2517 520427780 520427859 3.830000e-30 143.0
12 TraesCS3D01G406600 chr3D 98.750 80 1 0 2294 2373 520427924 520428003 3.830000e-30 143.0
13 TraesCS3D01G406600 chr3D 76.025 317 50 18 3101 3401 568021001 568021307 1.380000e-29 141.0
14 TraesCS3D01G406600 chr3B 94.348 1557 63 9 903 2445 685393340 685394885 0.000000e+00 2364.0
15 TraesCS3D01G406600 chr3B 96.184 891 32 2 1485 2373 684638628 684637738 0.000000e+00 1456.0
16 TraesCS3D01G406600 chr3B 87.869 1253 98 27 2444 3678 684512806 684511590 0.000000e+00 1423.0
17 TraesCS3D01G406600 chr3B 88.534 1160 92 18 2366 3518 685394734 685395859 0.000000e+00 1367.0
18 TraesCS3D01G406600 chr3B 85.628 1329 132 24 1066 2366 684514036 684512739 0.000000e+00 1341.0
19 TraesCS3D01G406600 chr3B 88.050 887 104 1 1 887 260234182 260233298 0.000000e+00 1050.0
20 TraesCS3D01G406600 chr3B 87.064 889 109 4 1 887 260124116 260123232 0.000000e+00 1000.0
21 TraesCS3D01G406600 chr3B 83.794 1086 115 34 2444 3518 684637811 684636776 0.000000e+00 974.0
22 TraesCS3D01G406600 chr3B 85.905 525 59 7 3155 3678 684635544 684635034 2.500000e-151 545.0
23 TraesCS3D01G406600 chr3B 73.976 1172 224 48 1092 2220 685471561 685472694 2.060000e-107 399.0
24 TraesCS3D01G406600 chr3B 96.951 164 5 0 1313 1476 684638848 684638685 3.620000e-70 276.0
25 TraesCS3D01G406600 chr3B 88.182 220 24 2 1100 1318 752973257 752973039 1.010000e-65 261.0
26 TraesCS3D01G406600 chr3B 97.500 80 2 0 2438 2517 685394734 685394813 1.780000e-28 137.0
27 TraesCS3D01G406600 chr3B 97.500 80 2 0 2294 2373 685394806 685394885 1.780000e-28 137.0
28 TraesCS3D01G406600 chr3B 95.946 74 3 0 2372 2445 684637811 684637738 1.790000e-23 121.0
29 TraesCS3D01G406600 chr3B 93.478 46 3 0 2535 2580 752225665 752225620 6.590000e-08 69.4
30 TraesCS3D01G406600 chr3B 93.478 46 3 0 2535 2580 752262520 752262475 6.590000e-08 69.4
31 TraesCS3D01G406600 chr3A 87.352 1439 138 26 971 2373 655570771 655569341 0.000000e+00 1609.0
32 TraesCS3D01G406600 chr3A 89.912 1249 100 14 2444 3678 655569415 655568179 0.000000e+00 1585.0
33 TraesCS3D01G406600 chr3A 75.360 1181 212 50 1082 2227 66914242 66913106 2.550000e-136 496.0
34 TraesCS3D01G406600 chr3A 75.022 1149 214 44 1113 2227 701643433 701644542 7.190000e-127 464.0
35 TraesCS3D01G406600 chr3A 74.205 1163 241 35 1092 2228 655920278 655921407 7.300000e-117 431.0
36 TraesCS3D01G406600 chr3A 73.349 863 196 30 23 869 21279604 21280448 4.650000e-74 289.0
37 TraesCS3D01G406600 chr3A 88.073 218 20 6 1093 1306 699533367 699533582 1.700000e-63 254.0
38 TraesCS3D01G406600 chr3A 86.076 79 4 3 923 1000 655570918 655570846 1.100000e-10 78.7
39 TraesCS3D01G406600 chr3A 97.143 35 1 0 3097 3131 702420398 702420364 3.970000e-05 60.2
40 TraesCS3D01G406600 chr5D 98.649 888 9 2 1 887 494778990 494778105 0.000000e+00 1570.0
41 TraesCS3D01G406600 chr7D 98.198 888 13 2 1 887 134839773 134838888 0.000000e+00 1548.0
42 TraesCS3D01G406600 chr2D 98.733 868 10 1 1 867 545497144 545496277 0.000000e+00 1541.0
43 TraesCS3D01G406600 chr1D 98.066 879 8 2 1 878 382251299 382250429 0.000000e+00 1520.0
44 TraesCS3D01G406600 chr1D 75.547 503 86 24 2926 3412 26268672 26268191 2.880000e-51 213.0
45 TraesCS3D01G406600 chr1D 86.905 84 8 2 3214 3295 38282296 38282214 1.410000e-14 91.6
46 TraesCS3D01G406600 chrUn 90.766 888 78 3 1 887 1511271 1512155 0.000000e+00 1182.0
47 TraesCS3D01G406600 chr5A 90.755 887 80 1 1 887 707465085 707464201 0.000000e+00 1182.0
48 TraesCS3D01G406600 chr2A 74.581 775 158 24 1621 2370 45073218 45073978 1.660000e-78 303.0
49 TraesCS3D01G406600 chr2A 84.252 127 18 1 2438 2562 45073900 45074026 4.990000e-24 122.0
50 TraesCS3D01G406600 chr2A 83.544 79 11 1 2366 2442 45073900 45073978 5.090000e-09 73.1
51 TraesCS3D01G406600 chr1B 74.606 508 88 26 2926 3412 41842087 41842574 6.270000e-43 185.0


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 TraesCS3D01G406600 chr3D 520425487 520429164 3677 False 1526.20 6793 99.2368 1 3678 5 chr3D.!!$F3 3677
1 TraesCS3D01G406600 chr3D 520096471 520097641 1170 True 1341.00 1341 87.7120 1223 2373 1 chr3D.!!$R2 1150
2 TraesCS3D01G406600 chr3D 181798940 181799816 876 True 1003.00 1003 87.2600 1 887 1 chr3D.!!$R1 886
3 TraesCS3D01G406600 chr3D 520080146 520082568 2422 True 556.50 813 84.3665 1038 3678 2 chr3D.!!$R6 2640
4 TraesCS3D01G406600 chr3D 569118434 569119555 1121 True 518.00 518 75.7550 1103 2227 1 chr3D.!!$R5 1124
5 TraesCS3D01G406600 chr3B 684511590 684514036 2446 True 1382.00 1423 86.7485 1066 3678 2 chr3B.!!$R6 2612
6 TraesCS3D01G406600 chr3B 260233298 260234182 884 True 1050.00 1050 88.0500 1 887 1 chr3B.!!$R2 886
7 TraesCS3D01G406600 chr3B 685393340 685395859 2519 False 1001.25 2364 94.4705 903 3518 4 chr3B.!!$F2 2615
8 TraesCS3D01G406600 chr3B 260123232 260124116 884 True 1000.00 1000 87.0640 1 887 1 chr3B.!!$R1 886
9 TraesCS3D01G406600 chr3B 684635034 684638848 3814 True 674.40 1456 91.7560 1313 3678 5 chr3B.!!$R7 2365
10 TraesCS3D01G406600 chr3B 685471561 685472694 1133 False 399.00 399 73.9760 1092 2220 1 chr3B.!!$F1 1128
11 TraesCS3D01G406600 chr3A 655568179 655570918 2739 True 1090.90 1609 87.7800 923 3678 3 chr3A.!!$R3 2755
12 TraesCS3D01G406600 chr3A 66913106 66914242 1136 True 496.00 496 75.3600 1082 2227 1 chr3A.!!$R1 1145
13 TraesCS3D01G406600 chr3A 701643433 701644542 1109 False 464.00 464 75.0220 1113 2227 1 chr3A.!!$F4 1114
14 TraesCS3D01G406600 chr3A 655920278 655921407 1129 False 431.00 431 74.2050 1092 2228 1 chr3A.!!$F2 1136
15 TraesCS3D01G406600 chr3A 21279604 21280448 844 False 289.00 289 73.3490 23 869 1 chr3A.!!$F1 846
16 TraesCS3D01G406600 chr5D 494778105 494778990 885 True 1570.00 1570 98.6490 1 887 1 chr5D.!!$R1 886
17 TraesCS3D01G406600 chr7D 134838888 134839773 885 True 1548.00 1548 98.1980 1 887 1 chr7D.!!$R1 886
18 TraesCS3D01G406600 chr2D 545496277 545497144 867 True 1541.00 1541 98.7330 1 867 1 chr2D.!!$R1 866
19 TraesCS3D01G406600 chr1D 382250429 382251299 870 True 1520.00 1520 98.0660 1 878 1 chr1D.!!$R3 877
20 TraesCS3D01G406600 chrUn 1511271 1512155 884 False 1182.00 1182 90.7660 1 887 1 chrUn.!!$F1 886
21 TraesCS3D01G406600 chr5A 707464201 707465085 884 True 1182.00 1182 90.7550 1 887 1 chr5A.!!$R1 886

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
926 930 0.318784 GTCGAGATGGCCGTGGTATC 60.319 60.0 0.0 0.0 0.0 2.24 F
1076 2012 0.107752 CTCCTCTTTGCTCTGCTCCC 60.108 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 3540 0.981183 ACCGGCTCATAGTGAAACCA 59.019 50.0 0.00 0.0 37.8 3.67 R
2971 4163 0.622665 AATCTGGAACCTGAGCCTGG 59.377 55.0 6.58 0.0 0.0 4.45 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
879 882 7.596621 GCTTTTCTCCATTAAAAGAAACTGAGG 59.403 37.037 11.41 0.00 43.51 3.86
882 885 6.848069 TCTCCATTAAAAGAAACTGAGGGAA 58.152 36.000 0.00 0.00 0.00 3.97
885 888 7.294584 TCCATTAAAAGAAACTGAGGGAAAGA 58.705 34.615 0.00 0.00 0.00 2.52
886 889 7.782644 TCCATTAAAAGAAACTGAGGGAAAGAA 59.217 33.333 0.00 0.00 0.00 2.52
889 892 8.589701 TTAAAAGAAACTGAGGGAAAGAAGTT 57.410 30.769 0.00 0.00 34.40 2.66
890 893 6.701145 AAAGAAACTGAGGGAAAGAAGTTC 57.299 37.500 0.00 0.00 31.81 3.01
909 912 4.049869 GTTCCTAGCTATAGTTTGCCGTC 58.950 47.826 0.84 0.00 0.00 4.79
926 930 0.318784 GTCGAGATGGCCGTGGTATC 60.319 60.000 0.00 0.00 0.00 2.24
964 968 4.424711 CCAAGCCCAGCCCGCTTA 62.425 66.667 2.53 0.00 44.65 3.09
990 1094 3.454858 AGAATGAGAAGAGGTGGCCTAA 58.545 45.455 3.32 0.00 31.76 2.69
1032 1138 6.652062 TCTGTTATTTTCGGGAAAGACCTAAC 59.348 38.462 0.00 3.67 38.98 2.34
1076 2012 0.107752 CTCCTCTTTGCTCTGCTCCC 60.108 60.000 0.00 0.00 0.00 4.30
1519 2550 4.025401 GCAACCCGGCAACTCGTG 62.025 66.667 0.00 0.00 0.00 4.35
1863 2939 3.267812 ACCTGATTGAGATGGGTGACATT 59.732 43.478 0.00 0.00 40.72 2.71
1915 2991 2.287009 GCAAGCGTTAATATCTGGGTGC 60.287 50.000 0.00 0.00 0.00 5.01
1923 2999 3.589951 AATATCTGGGTGCTGCAAGAT 57.410 42.857 16.83 16.83 34.07 2.40
1936 3012 1.942657 TGCAAGATTATGAAGCCGAGC 59.057 47.619 0.00 0.00 0.00 5.03
2147 3229 3.308473 GGCCTTGGTCCTACAAATCTTCT 60.308 47.826 0.00 0.00 0.00 2.85
2184 3266 2.627699 TGTTCAACATGCCTTCTTTCCC 59.372 45.455 0.00 0.00 0.00 3.97
2231 3313 3.513912 TCTTCGCCTTTGGTCTGATAGAA 59.486 43.478 0.00 0.00 0.00 2.10
2278 3381 1.482182 TGTCAGTATCCTCATGCGCTT 59.518 47.619 9.73 0.00 0.00 4.68
2281 3384 2.366590 TCAGTATCCTCATGCGCTTCAT 59.633 45.455 9.73 0.00 35.31 2.57
2338 3513 9.979578 TTAGTTTCATTTTGATGTATGCAAACT 57.020 25.926 0.00 0.00 36.79 2.66
2344 3519 9.955208 TCATTTTGATGTATGCAAACTATGATC 57.045 29.630 0.00 0.00 35.20 2.92
2345 3520 9.738832 CATTTTGATGTATGCAAACTATGATCA 57.261 29.630 0.00 0.00 35.20 2.92
2347 3522 9.791820 TTTTGATGTATGCAAACTATGATCAAG 57.208 29.630 0.00 1.33 35.20 3.02
2348 3523 8.735692 TTGATGTATGCAAACTATGATCAAGA 57.264 30.769 0.00 0.00 0.00 3.02
2349 3524 8.735692 TGATGTATGCAAACTATGATCAAGAA 57.264 30.769 0.00 0.00 0.00 2.52
2350 3525 8.833493 TGATGTATGCAAACTATGATCAAGAAG 58.167 33.333 0.00 0.20 0.00 2.85
2351 3526 8.743085 ATGTATGCAAACTATGATCAAGAAGT 57.257 30.769 0.00 0.89 0.00 3.01
2352 3527 8.565896 TGTATGCAAACTATGATCAAGAAGTT 57.434 30.769 13.01 13.01 33.72 2.66
2353 3528 8.668353 TGTATGCAAACTATGATCAAGAAGTTC 58.332 33.333 17.02 0.00 31.15 3.01
2354 3529 6.500684 TGCAAACTATGATCAAGAAGTTCC 57.499 37.500 17.02 13.06 31.15 3.62
2355 3530 5.122239 TGCAAACTATGATCAAGAAGTTCCG 59.878 40.000 17.02 13.54 31.15 4.30
2356 3531 5.351465 GCAAACTATGATCAAGAAGTTCCGA 59.649 40.000 17.02 0.00 31.15 4.55
2357 3532 6.673316 GCAAACTATGATCAAGAAGTTCCGAC 60.673 42.308 17.02 7.68 31.15 4.79
2358 3533 5.012328 ACTATGATCAAGAAGTTCCGACC 57.988 43.478 0.00 0.00 0.00 4.79
2359 3534 2.762535 TGATCAAGAAGTTCCGACCC 57.237 50.000 0.00 0.00 0.00 4.46
2360 3535 2.257207 TGATCAAGAAGTTCCGACCCT 58.743 47.619 0.00 0.00 0.00 4.34
2361 3536 2.637872 TGATCAAGAAGTTCCGACCCTT 59.362 45.455 0.00 0.00 0.00 3.95
2362 3537 3.072476 TGATCAAGAAGTTCCGACCCTTT 59.928 43.478 0.00 0.00 0.00 3.11
2363 3538 3.121738 TCAAGAAGTTCCGACCCTTTC 57.878 47.619 0.00 0.00 0.00 2.62
2364 3539 2.436542 TCAAGAAGTTCCGACCCTTTCA 59.563 45.455 0.00 0.00 0.00 2.69
2365 3540 3.072476 TCAAGAAGTTCCGACCCTTTCAT 59.928 43.478 0.00 0.00 0.00 2.57
2366 3541 3.059352 AGAAGTTCCGACCCTTTCATG 57.941 47.619 0.00 0.00 0.00 3.07
2367 3542 2.084546 GAAGTTCCGACCCTTTCATGG 58.915 52.381 0.00 0.00 0.00 3.66
2368 3543 1.064825 AGTTCCGACCCTTTCATGGT 58.935 50.000 0.00 0.00 39.32 3.55
2369 3544 1.423921 AGTTCCGACCCTTTCATGGTT 59.576 47.619 0.00 0.00 35.85 3.67
2370 3545 2.158519 AGTTCCGACCCTTTCATGGTTT 60.159 45.455 0.00 0.00 35.85 3.27
2371 3546 2.194201 TCCGACCCTTTCATGGTTTC 57.806 50.000 0.00 0.00 35.85 2.78
2372 3547 1.422024 TCCGACCCTTTCATGGTTTCA 59.578 47.619 0.00 0.00 35.85 2.69
2373 3548 1.539827 CCGACCCTTTCATGGTTTCAC 59.460 52.381 0.00 0.00 35.85 3.18
2374 3549 2.504367 CGACCCTTTCATGGTTTCACT 58.496 47.619 0.00 0.00 35.85 3.41
2375 3550 3.558321 CCGACCCTTTCATGGTTTCACTA 60.558 47.826 0.00 0.00 35.85 2.74
2376 3551 4.261801 CGACCCTTTCATGGTTTCACTAT 58.738 43.478 0.00 0.00 35.85 2.12
2377 3552 4.094887 CGACCCTTTCATGGTTTCACTATG 59.905 45.833 0.00 0.00 38.28 2.23
2378 3553 5.253330 GACCCTTTCATGGTTTCACTATGA 58.747 41.667 0.00 0.00 43.04 2.15
2379 3554 5.256474 ACCCTTTCATGGTTTCACTATGAG 58.744 41.667 3.53 0.00 44.88 2.90
2380 3555 4.096984 CCCTTTCATGGTTTCACTATGAGC 59.903 45.833 3.53 0.00 44.88 4.26
2381 3556 4.096984 CCTTTCATGGTTTCACTATGAGCC 59.903 45.833 3.53 0.00 44.88 4.70
2382 3557 2.905075 TCATGGTTTCACTATGAGCCG 58.095 47.619 0.00 0.00 40.47 5.52
2383 3558 1.942657 CATGGTTTCACTATGAGCCGG 59.057 52.381 0.00 0.00 39.12 6.13
2384 3559 0.981183 TGGTTTCACTATGAGCCGGT 59.019 50.000 1.90 0.00 0.00 5.28
2385 3560 1.349688 TGGTTTCACTATGAGCCGGTT 59.650 47.619 1.90 0.00 0.00 4.44
2386 3561 2.568062 TGGTTTCACTATGAGCCGGTTA 59.432 45.455 1.90 0.00 0.00 2.85
2387 3562 3.195661 GGTTTCACTATGAGCCGGTTAG 58.804 50.000 1.90 2.35 0.00 2.34
2388 3563 3.369157 GGTTTCACTATGAGCCGGTTAGT 60.369 47.826 1.90 3.02 0.00 2.24
2389 3564 4.251268 GTTTCACTATGAGCCGGTTAGTT 58.749 43.478 1.90 0.00 0.00 2.24
2390 3565 4.546829 TTCACTATGAGCCGGTTAGTTT 57.453 40.909 1.90 0.00 0.00 2.66
2391 3566 4.119442 TCACTATGAGCCGGTTAGTTTC 57.881 45.455 1.90 0.00 0.00 2.78
2392 3567 3.512329 TCACTATGAGCCGGTTAGTTTCA 59.488 43.478 1.90 0.00 0.00 2.69
2393 3568 4.161565 TCACTATGAGCCGGTTAGTTTCAT 59.838 41.667 1.90 6.18 33.44 2.57
2394 3569 4.876107 CACTATGAGCCGGTTAGTTTCATT 59.124 41.667 1.90 0.00 31.49 2.57
2395 3570 5.354234 CACTATGAGCCGGTTAGTTTCATTT 59.646 40.000 1.90 0.00 31.49 2.32
2396 3571 5.944007 ACTATGAGCCGGTTAGTTTCATTTT 59.056 36.000 1.90 0.00 31.49 1.82
2397 3572 4.497473 TGAGCCGGTTAGTTTCATTTTG 57.503 40.909 1.90 0.00 0.00 2.44
2398 3573 4.138290 TGAGCCGGTTAGTTTCATTTTGA 58.862 39.130 1.90 0.00 0.00 2.69
2399 3574 4.764823 TGAGCCGGTTAGTTTCATTTTGAT 59.235 37.500 1.90 0.00 0.00 2.57
2400 3575 5.059404 AGCCGGTTAGTTTCATTTTGATG 57.941 39.130 1.90 0.00 0.00 3.07
2401 3576 4.522789 AGCCGGTTAGTTTCATTTTGATGT 59.477 37.500 1.90 0.00 0.00 3.06
2402 3577 5.708230 AGCCGGTTAGTTTCATTTTGATGTA 59.292 36.000 1.90 0.00 0.00 2.29
2403 3578 6.377146 AGCCGGTTAGTTTCATTTTGATGTAT 59.623 34.615 1.90 0.00 0.00 2.29
2404 3579 6.472163 GCCGGTTAGTTTCATTTTGATGTATG 59.528 38.462 1.90 0.00 0.00 2.39
2405 3580 6.472163 CCGGTTAGTTTCATTTTGATGTATGC 59.528 38.462 0.00 0.00 0.00 3.14
2406 3581 7.026562 CGGTTAGTTTCATTTTGATGTATGCA 58.973 34.615 0.00 0.00 0.00 3.96
2407 3582 7.540400 CGGTTAGTTTCATTTTGATGTATGCAA 59.460 33.333 0.00 0.00 0.00 4.08
2408 3583 9.202273 GGTTAGTTTCATTTTGATGTATGCAAA 57.798 29.630 0.00 0.00 33.76 3.68
2410 3585 9.979578 TTAGTTTCATTTTGATGTATGCAAACT 57.020 25.926 0.00 0.00 36.79 2.66
2416 3591 9.955208 TCATTTTGATGTATGCAAACTATGATC 57.045 29.630 0.00 0.00 35.20 2.92
2417 3592 9.738832 CATTTTGATGTATGCAAACTATGATCA 57.261 29.630 0.00 0.00 35.20 2.92
2419 3594 9.791820 TTTTGATGTATGCAAACTATGATCAAG 57.208 29.630 0.00 1.33 35.20 3.02
2420 3595 8.735692 TTGATGTATGCAAACTATGATCAAGA 57.264 30.769 0.00 0.00 0.00 3.02
2421 3596 8.735692 TGATGTATGCAAACTATGATCAAGAA 57.264 30.769 0.00 0.00 0.00 2.52
2422 3597 8.833493 TGATGTATGCAAACTATGATCAAGAAG 58.167 33.333 0.00 0.20 0.00 2.85
2423 3598 8.743085 ATGTATGCAAACTATGATCAAGAAGT 57.257 30.769 0.00 0.89 0.00 3.01
2424 3599 8.565896 TGTATGCAAACTATGATCAAGAAGTT 57.434 30.769 13.01 13.01 33.72 2.66
2425 3600 8.668353 TGTATGCAAACTATGATCAAGAAGTTC 58.332 33.333 17.02 0.00 31.15 3.01
2426 3601 6.500684 TGCAAACTATGATCAAGAAGTTCC 57.499 37.500 17.02 13.06 31.15 3.62
2427 3602 5.122239 TGCAAACTATGATCAAGAAGTTCCG 59.878 40.000 17.02 13.54 31.15 4.30
2428 3603 5.351465 GCAAACTATGATCAAGAAGTTCCGA 59.649 40.000 17.02 0.00 31.15 4.55
2429 3604 6.673316 GCAAACTATGATCAAGAAGTTCCGAC 60.673 42.308 17.02 7.68 31.15 4.79
2430 3605 5.012328 ACTATGATCAAGAAGTTCCGACC 57.988 43.478 0.00 0.00 0.00 4.79
2431 3606 2.762535 TGATCAAGAAGTTCCGACCC 57.237 50.000 0.00 0.00 0.00 4.46
2432 3607 2.257207 TGATCAAGAAGTTCCGACCCT 58.743 47.619 0.00 0.00 0.00 4.34
2433 3608 2.637872 TGATCAAGAAGTTCCGACCCTT 59.362 45.455 0.00 0.00 0.00 3.95
2434 3609 3.072476 TGATCAAGAAGTTCCGACCCTTT 59.928 43.478 0.00 0.00 0.00 3.11
2435 3610 3.121738 TCAAGAAGTTCCGACCCTTTC 57.878 47.619 0.00 0.00 0.00 2.62
2436 3611 2.436542 TCAAGAAGTTCCGACCCTTTCA 59.563 45.455 0.00 0.00 0.00 2.69
2437 3612 3.072476 TCAAGAAGTTCCGACCCTTTCAT 59.928 43.478 0.00 0.00 0.00 2.57
2438 3613 3.059352 AGAAGTTCCGACCCTTTCATG 57.941 47.619 0.00 0.00 0.00 3.07
2439 3614 2.084546 GAAGTTCCGACCCTTTCATGG 58.915 52.381 0.00 0.00 0.00 3.66
2440 3615 1.064825 AGTTCCGACCCTTTCATGGT 58.935 50.000 0.00 0.00 39.32 3.55
2441 3616 1.423921 AGTTCCGACCCTTTCATGGTT 59.576 47.619 0.00 0.00 35.85 3.67
2442 3617 2.158519 AGTTCCGACCCTTTCATGGTTT 60.159 45.455 0.00 0.00 35.85 3.27
2443 3618 2.194201 TCCGACCCTTTCATGGTTTC 57.806 50.000 0.00 0.00 35.85 2.78
2444 3619 1.422024 TCCGACCCTTTCATGGTTTCA 59.578 47.619 0.00 0.00 35.85 2.69
2445 3620 1.539827 CCGACCCTTTCATGGTTTCAC 59.460 52.381 0.00 0.00 35.85 3.18
2446 3621 2.504367 CGACCCTTTCATGGTTTCACT 58.496 47.619 0.00 0.00 35.85 3.41
2447 3622 3.558321 CCGACCCTTTCATGGTTTCACTA 60.558 47.826 0.00 0.00 35.85 2.74
2448 3623 4.261801 CGACCCTTTCATGGTTTCACTAT 58.738 43.478 0.00 0.00 35.85 2.12
2449 3624 4.094887 CGACCCTTTCATGGTTTCACTATG 59.905 45.833 0.00 0.00 38.28 2.23
2450 3625 5.253330 GACCCTTTCATGGTTTCACTATGA 58.747 41.667 0.00 0.00 43.04 2.15
2451 3626 5.256474 ACCCTTTCATGGTTTCACTATGAG 58.744 41.667 3.53 0.00 44.88 2.90
2452 3627 4.096984 CCCTTTCATGGTTTCACTATGAGC 59.903 45.833 3.53 0.00 44.88 4.26
2453 3628 4.096984 CCTTTCATGGTTTCACTATGAGCC 59.903 45.833 3.53 0.00 44.88 4.70
2454 3629 2.905075 TCATGGTTTCACTATGAGCCG 58.095 47.619 0.00 0.00 40.47 5.52
2455 3630 1.942657 CATGGTTTCACTATGAGCCGG 59.057 52.381 0.00 0.00 39.12 6.13
2456 3631 0.981183 TGGTTTCACTATGAGCCGGT 59.019 50.000 1.90 0.00 0.00 5.28
2457 3632 1.349688 TGGTTTCACTATGAGCCGGTT 59.650 47.619 1.90 0.00 0.00 4.44
2458 3633 2.568062 TGGTTTCACTATGAGCCGGTTA 59.432 45.455 1.90 0.00 0.00 2.85
2459 3634 3.195661 GGTTTCACTATGAGCCGGTTAG 58.804 50.000 1.90 2.35 0.00 2.34
2460 3635 3.369157 GGTTTCACTATGAGCCGGTTAGT 60.369 47.826 1.90 3.02 0.00 2.24
2461 3636 4.251268 GTTTCACTATGAGCCGGTTAGTT 58.749 43.478 1.90 0.00 0.00 2.24
2462 3637 4.546829 TTCACTATGAGCCGGTTAGTTT 57.453 40.909 1.90 0.00 0.00 2.66
2463 3638 4.119442 TCACTATGAGCCGGTTAGTTTC 57.881 45.455 1.90 0.00 0.00 2.78
2464 3639 3.512329 TCACTATGAGCCGGTTAGTTTCA 59.488 43.478 1.90 0.00 0.00 2.69
2465 3640 4.161565 TCACTATGAGCCGGTTAGTTTCAT 59.838 41.667 1.90 6.18 33.44 2.57
2466 3641 4.876107 CACTATGAGCCGGTTAGTTTCATT 59.124 41.667 1.90 0.00 31.49 2.57
2467 3642 5.354234 CACTATGAGCCGGTTAGTTTCATTT 59.646 40.000 1.90 0.00 31.49 2.32
2468 3643 5.944007 ACTATGAGCCGGTTAGTTTCATTTT 59.056 36.000 1.90 0.00 31.49 1.82
2469 3644 4.497473 TGAGCCGGTTAGTTTCATTTTG 57.503 40.909 1.90 0.00 0.00 2.44
2470 3645 4.138290 TGAGCCGGTTAGTTTCATTTTGA 58.862 39.130 1.90 0.00 0.00 2.69
2471 3646 4.764823 TGAGCCGGTTAGTTTCATTTTGAT 59.235 37.500 1.90 0.00 0.00 2.57
2472 3647 5.059404 AGCCGGTTAGTTTCATTTTGATG 57.941 39.130 1.90 0.00 0.00 3.07
2473 3648 4.522789 AGCCGGTTAGTTTCATTTTGATGT 59.477 37.500 1.90 0.00 0.00 3.06
2474 3649 5.708230 AGCCGGTTAGTTTCATTTTGATGTA 59.292 36.000 1.90 0.00 0.00 2.29
2475 3650 6.377146 AGCCGGTTAGTTTCATTTTGATGTAT 59.623 34.615 1.90 0.00 0.00 2.29
2476 3651 6.472163 GCCGGTTAGTTTCATTTTGATGTATG 59.528 38.462 1.90 0.00 0.00 2.39
2477 3652 6.472163 CCGGTTAGTTTCATTTTGATGTATGC 59.528 38.462 0.00 0.00 0.00 3.14
2478 3653 7.026562 CGGTTAGTTTCATTTTGATGTATGCA 58.973 34.615 0.00 0.00 0.00 3.96
2479 3654 7.540400 CGGTTAGTTTCATTTTGATGTATGCAA 59.460 33.333 0.00 0.00 0.00 4.08
2739 3927 6.552859 TGTTTTAGCTGACGATGAAATGAA 57.447 33.333 0.00 0.00 0.00 2.57
2750 3938 6.988580 TGACGATGAAATGAAGCAGATTATCT 59.011 34.615 0.00 0.00 0.00 1.98
2849 4037 4.530553 TCTGGTTAGGTGCTGAAAGATACA 59.469 41.667 0.00 0.00 34.07 2.29
2931 4120 2.903135 CCCAACATTTTAAGGGCTGGAA 59.097 45.455 0.00 0.00 33.91 3.53
2965 4157 9.892130 ACCTGTATTGATAAGAAGAAAGGTTAG 57.108 33.333 0.00 0.00 30.19 2.34
2971 4163 5.938125 TGATAAGAAGAAAGGTTAGTGTGGC 59.062 40.000 0.00 0.00 0.00 5.01
2983 4175 3.177884 TGTGGCCAGGCTCAGGTT 61.178 61.111 5.11 0.00 0.00 3.50
2996 4188 2.887152 GCTCAGGTTCCAGATTGTGTTT 59.113 45.455 0.00 0.00 0.00 2.83
3003 4195 4.262036 GGTTCCAGATTGTGTTTCCCTTTC 60.262 45.833 0.00 0.00 0.00 2.62
3015 4207 5.912955 GTGTTTCCCTTTCAATTCTGTAACG 59.087 40.000 0.00 0.00 0.00 3.18
3028 4220 2.038689 TCTGTAACGGCCAACCATGTTA 59.961 45.455 2.24 0.00 34.57 2.41
3032 4224 4.395542 TGTAACGGCCAACCATGTTATTAC 59.604 41.667 2.24 0.00 34.57 1.89
3035 4227 4.083565 ACGGCCAACCATGTTATTACTTT 58.916 39.130 2.24 0.00 34.57 2.66
3036 4228 4.525100 ACGGCCAACCATGTTATTACTTTT 59.475 37.500 2.24 0.00 34.57 2.27
3046 4240 7.504238 ACCATGTTATTACTTTTTCTGTGACCA 59.496 33.333 0.00 0.00 0.00 4.02
3048 4242 8.567948 CATGTTATTACTTTTTCTGTGACCAGT 58.432 33.333 0.00 0.00 39.82 4.00
3053 4247 3.119495 ACTTTTTCTGTGACCAGTGCAAC 60.119 43.478 0.00 0.00 39.82 4.17
3056 4250 2.124942 TGTGACCAGTGCAACGCA 60.125 55.556 0.00 0.00 45.86 5.24
3097 4291 1.737793 CGCCGGCTAGTTTCTTTGATT 59.262 47.619 26.68 0.00 0.00 2.57
3147 4344 4.685165 TCATGGTCGCATGAAATTTGTTTG 59.315 37.500 0.00 0.00 38.50 2.93
3177 4374 1.039856 TCCTTTTTGGGCTGAAGTGC 58.960 50.000 0.00 0.00 36.20 4.40
3199 4396 5.163622 TGCCTAGCATGCTGATTCTAAAAAC 60.164 40.000 30.42 6.60 31.71 2.43
3200 4397 5.163622 GCCTAGCATGCTGATTCTAAAAACA 60.164 40.000 30.42 4.03 0.00 2.83
3201 4398 6.493116 CCTAGCATGCTGATTCTAAAAACAG 58.507 40.000 30.42 13.79 38.09 3.16
3261 6043 4.935205 CCAATTGATCCGTCAGTGTCTTAA 59.065 41.667 7.12 0.00 35.39 1.85
3345 6129 4.878397 GGTCATCCAGTGGTTTCTTCATAG 59.122 45.833 9.54 0.00 0.00 2.23
3346 6130 5.491982 GTCATCCAGTGGTTTCTTCATAGT 58.508 41.667 9.54 0.00 0.00 2.12
3347 6131 6.351881 GGTCATCCAGTGGTTTCTTCATAGTA 60.352 42.308 9.54 0.00 0.00 1.82
3348 6132 7.275920 GTCATCCAGTGGTTTCTTCATAGTAT 58.724 38.462 9.54 0.00 0.00 2.12
3415 6199 3.610040 TGTAGCTGATGATGAAACGGT 57.390 42.857 0.00 0.00 0.00 4.83
3436 6220 7.371936 ACGGTCTAGCTTTTAGTATCATCATC 58.628 38.462 0.00 0.00 0.00 2.92
3449 6233 5.811100 AGTATCATCATCAGCTGCAATATCG 59.189 40.000 9.47 0.00 0.00 2.92
3499 6284 8.581578 TGCTGATGCATATAAATTTGTGATCAT 58.418 29.630 0.00 0.00 45.31 2.45
3521 6306 5.791336 TGAAGCTCTTGTAAGAAGTCTCA 57.209 39.130 0.00 0.00 34.03 3.27
3522 6307 5.777802 TGAAGCTCTTGTAAGAAGTCTCAG 58.222 41.667 0.00 0.00 34.03 3.35
3661 6446 1.526917 GGTGCTGGTGCTGTGAAGT 60.527 57.895 0.00 0.00 40.48 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
882 885 6.350103 GGCAAACTATAGCTAGGAACTTCTT 58.650 40.000 0.00 0.00 41.75 2.52
885 888 4.161754 ACGGCAAACTATAGCTAGGAACTT 59.838 41.667 0.00 0.00 41.75 2.66
886 889 3.705072 ACGGCAAACTATAGCTAGGAACT 59.295 43.478 0.00 0.00 46.37 3.01
889 892 2.292569 CGACGGCAAACTATAGCTAGGA 59.707 50.000 0.00 0.00 0.00 2.94
890 893 2.292569 TCGACGGCAAACTATAGCTAGG 59.707 50.000 0.00 0.00 0.00 3.02
891 894 3.250280 TCTCGACGGCAAACTATAGCTAG 59.750 47.826 0.00 0.00 0.00 3.42
892 895 3.208594 TCTCGACGGCAAACTATAGCTA 58.791 45.455 0.00 0.00 0.00 3.32
893 896 2.022195 TCTCGACGGCAAACTATAGCT 58.978 47.619 0.00 0.00 0.00 3.32
894 897 2.486951 TCTCGACGGCAAACTATAGC 57.513 50.000 0.00 0.00 0.00 2.97
897 900 2.225068 CCATCTCGACGGCAAACTAT 57.775 50.000 0.00 0.00 0.00 2.12
898 901 3.733236 CCATCTCGACGGCAAACTA 57.267 52.632 0.00 0.00 0.00 2.24
899 902 4.598257 CCATCTCGACGGCAAACT 57.402 55.556 0.00 0.00 0.00 2.66
909 912 1.006102 GGATACCACGGCCATCTCG 60.006 63.158 2.24 0.00 0.00 4.04
926 930 1.871039 CCCACACTCGTTTACAACTGG 59.129 52.381 0.00 0.00 0.00 4.00
964 968 4.323868 GGCCACCTCTTCTCATTCTTAACT 60.324 45.833 0.00 0.00 0.00 2.24
1000 1104 4.340617 TCCCGAAAATAACAGAGGCATTT 58.659 39.130 0.00 0.00 0.00 2.32
1076 2012 1.009449 GAGCTCTCGATCCGTTCCG 60.009 63.158 6.43 0.00 0.00 4.30
1519 2550 2.806237 CGGAAGGGGAGCGTACTC 59.194 66.667 0.00 0.00 42.66 2.59
1915 2991 2.032204 GCTCGGCTTCATAATCTTGCAG 60.032 50.000 0.00 0.00 0.00 4.41
1923 2999 1.137086 GTCCAGAGCTCGGCTTCATAA 59.863 52.381 16.74 0.00 39.88 1.90
1936 3012 2.420129 CCCGGTATTTGAAGGTCCAGAG 60.420 54.545 0.00 0.00 0.00 3.35
2184 3266 3.195610 TCACAACATAGCCCTCTAGTGTG 59.804 47.826 0.00 0.00 37.36 3.82
2231 3313 2.494059 CCGTTCAGAACCACAACTGAT 58.506 47.619 7.76 0.00 41.71 2.90
2278 3381 4.887071 GTGAACCCAAGGCATACATAATGA 59.113 41.667 0.00 0.00 37.86 2.57
2281 3384 4.584638 AGTGAACCCAAGGCATACATAA 57.415 40.909 0.00 0.00 0.00 1.90
2337 3512 4.100189 AGGGTCGGAACTTCTTGATCATAG 59.900 45.833 0.00 0.00 0.00 2.23
2338 3513 4.030913 AGGGTCGGAACTTCTTGATCATA 58.969 43.478 0.00 0.00 0.00 2.15
2339 3514 2.840651 AGGGTCGGAACTTCTTGATCAT 59.159 45.455 0.00 0.00 0.00 2.45
2340 3515 2.257207 AGGGTCGGAACTTCTTGATCA 58.743 47.619 0.00 0.00 0.00 2.92
2341 3516 3.336138 AAGGGTCGGAACTTCTTGATC 57.664 47.619 0.00 0.00 0.00 2.92
2342 3517 3.072476 TGAAAGGGTCGGAACTTCTTGAT 59.928 43.478 0.00 0.00 0.00 2.57
2343 3518 2.436542 TGAAAGGGTCGGAACTTCTTGA 59.563 45.455 0.00 0.00 0.00 3.02
2344 3519 2.846193 TGAAAGGGTCGGAACTTCTTG 58.154 47.619 0.00 0.00 0.00 3.02
2345 3520 3.412386 CATGAAAGGGTCGGAACTTCTT 58.588 45.455 0.00 0.00 0.00 2.52
2346 3521 2.290323 CCATGAAAGGGTCGGAACTTCT 60.290 50.000 0.00 0.00 29.31 2.85
2347 3522 2.084546 CCATGAAAGGGTCGGAACTTC 58.915 52.381 0.00 0.00 29.31 3.01
2348 3523 2.200373 CCATGAAAGGGTCGGAACTT 57.800 50.000 0.00 0.00 29.31 2.66
2349 3524 3.957288 CCATGAAAGGGTCGGAACT 57.043 52.632 0.00 0.00 29.31 3.01
2358 3533 4.096984 GGCTCATAGTGAAACCATGAAAGG 59.903 45.833 0.00 0.00 37.80 3.11
2359 3534 4.201851 CGGCTCATAGTGAAACCATGAAAG 60.202 45.833 0.00 0.00 37.80 2.62
2360 3535 3.689161 CGGCTCATAGTGAAACCATGAAA 59.311 43.478 0.00 0.00 37.80 2.69
2361 3536 3.270027 CGGCTCATAGTGAAACCATGAA 58.730 45.455 0.00 0.00 37.80 2.57
2362 3537 2.419990 CCGGCTCATAGTGAAACCATGA 60.420 50.000 0.00 0.00 37.80 3.07
2363 3538 1.942657 CCGGCTCATAGTGAAACCATG 59.057 52.381 0.00 0.00 37.80 3.66
2364 3539 1.559682 ACCGGCTCATAGTGAAACCAT 59.440 47.619 0.00 0.00 37.80 3.55
2365 3540 0.981183 ACCGGCTCATAGTGAAACCA 59.019 50.000 0.00 0.00 37.80 3.67
2366 3541 2.109425 AACCGGCTCATAGTGAAACC 57.891 50.000 0.00 0.00 37.80 3.27
2367 3542 3.858247 ACTAACCGGCTCATAGTGAAAC 58.142 45.455 0.00 0.00 0.00 2.78
2368 3543 4.546829 AACTAACCGGCTCATAGTGAAA 57.453 40.909 0.00 0.00 30.61 2.69
2369 3544 4.020928 TGAAACTAACCGGCTCATAGTGAA 60.021 41.667 0.00 0.00 30.61 3.18
2370 3545 3.512329 TGAAACTAACCGGCTCATAGTGA 59.488 43.478 0.00 0.00 30.61 3.41
2371 3546 3.857052 TGAAACTAACCGGCTCATAGTG 58.143 45.455 0.00 0.00 30.61 2.74
2372 3547 4.755266 ATGAAACTAACCGGCTCATAGT 57.245 40.909 0.00 2.38 0.00 2.12
2373 3548 6.093495 TCAAAATGAAACTAACCGGCTCATAG 59.907 38.462 0.00 1.67 0.00 2.23
2374 3549 5.941058 TCAAAATGAAACTAACCGGCTCATA 59.059 36.000 0.00 0.00 0.00 2.15
2375 3550 4.764823 TCAAAATGAAACTAACCGGCTCAT 59.235 37.500 0.00 0.00 0.00 2.90
2376 3551 4.138290 TCAAAATGAAACTAACCGGCTCA 58.862 39.130 0.00 0.00 0.00 4.26
2377 3552 4.759516 TCAAAATGAAACTAACCGGCTC 57.240 40.909 0.00 0.00 0.00 4.70
2378 3553 4.522789 ACATCAAAATGAAACTAACCGGCT 59.477 37.500 0.00 0.00 36.67 5.52
2379 3554 4.805219 ACATCAAAATGAAACTAACCGGC 58.195 39.130 0.00 0.00 36.67 6.13
2380 3555 6.472163 GCATACATCAAAATGAAACTAACCGG 59.528 38.462 0.00 0.00 36.67 5.28
2381 3556 7.026562 TGCATACATCAAAATGAAACTAACCG 58.973 34.615 0.00 0.00 36.67 4.44
2382 3557 8.755696 TTGCATACATCAAAATGAAACTAACC 57.244 30.769 0.00 0.00 36.67 2.85
2384 3559 9.979578 AGTTTGCATACATCAAAATGAAACTAA 57.020 25.926 10.02 0.00 34.90 2.24
2390 3565 9.955208 GATCATAGTTTGCATACATCAAAATGA 57.045 29.630 10.02 8.38 36.21 2.57
2391 3566 9.738832 TGATCATAGTTTGCATACATCAAAATG 57.261 29.630 10.02 4.00 35.49 2.32
2393 3568 9.791820 CTTGATCATAGTTTGCATACATCAAAA 57.208 29.630 16.09 2.87 35.49 2.44
2394 3569 9.176460 TCTTGATCATAGTTTGCATACATCAAA 57.824 29.630 16.09 8.87 30.65 2.69
2395 3570 8.735692 TCTTGATCATAGTTTGCATACATCAA 57.264 30.769 15.15 15.15 0.00 2.57
2396 3571 8.735692 TTCTTGATCATAGTTTGCATACATCA 57.264 30.769 10.02 6.94 0.00 3.07
2397 3572 8.834465 ACTTCTTGATCATAGTTTGCATACATC 58.166 33.333 10.02 4.56 0.00 3.06
2398 3573 8.743085 ACTTCTTGATCATAGTTTGCATACAT 57.257 30.769 10.02 0.00 0.00 2.29
2399 3574 8.565896 AACTTCTTGATCATAGTTTGCATACA 57.434 30.769 10.02 0.00 0.00 2.29
2400 3575 8.125448 GGAACTTCTTGATCATAGTTTGCATAC 58.875 37.037 15.39 0.00 31.41 2.39
2401 3576 7.011389 CGGAACTTCTTGATCATAGTTTGCATA 59.989 37.037 15.39 0.00 31.41 3.14
2402 3577 6.183360 CGGAACTTCTTGATCATAGTTTGCAT 60.183 38.462 15.39 0.00 31.41 3.96
2403 3578 5.122239 CGGAACTTCTTGATCATAGTTTGCA 59.878 40.000 15.39 0.00 31.41 4.08
2404 3579 5.351465 TCGGAACTTCTTGATCATAGTTTGC 59.649 40.000 15.39 7.46 31.41 3.68
2405 3580 6.183360 GGTCGGAACTTCTTGATCATAGTTTG 60.183 42.308 15.39 12.40 31.41 2.93
2406 3581 5.875359 GGTCGGAACTTCTTGATCATAGTTT 59.125 40.000 15.39 0.06 31.41 2.66
2407 3582 5.420409 GGTCGGAACTTCTTGATCATAGTT 58.580 41.667 14.60 14.60 33.78 2.24
2408 3583 4.141914 GGGTCGGAACTTCTTGATCATAGT 60.142 45.833 0.00 0.00 0.00 2.12
2409 3584 4.100189 AGGGTCGGAACTTCTTGATCATAG 59.900 45.833 0.00 0.00 0.00 2.23
2410 3585 4.030913 AGGGTCGGAACTTCTTGATCATA 58.969 43.478 0.00 0.00 0.00 2.15
2411 3586 2.840651 AGGGTCGGAACTTCTTGATCAT 59.159 45.455 0.00 0.00 0.00 2.45
2412 3587 2.257207 AGGGTCGGAACTTCTTGATCA 58.743 47.619 0.00 0.00 0.00 2.92
2413 3588 3.336138 AAGGGTCGGAACTTCTTGATC 57.664 47.619 0.00 0.00 0.00 2.92
2414 3589 3.072476 TGAAAGGGTCGGAACTTCTTGAT 59.928 43.478 0.00 0.00 0.00 2.57
2415 3590 2.436542 TGAAAGGGTCGGAACTTCTTGA 59.563 45.455 0.00 0.00 0.00 3.02
2416 3591 2.846193 TGAAAGGGTCGGAACTTCTTG 58.154 47.619 0.00 0.00 0.00 3.02
2417 3592 3.412386 CATGAAAGGGTCGGAACTTCTT 58.588 45.455 0.00 0.00 0.00 2.52
2418 3593 2.290323 CCATGAAAGGGTCGGAACTTCT 60.290 50.000 0.00 0.00 29.31 2.85
2419 3594 2.084546 CCATGAAAGGGTCGGAACTTC 58.915 52.381 0.00 0.00 29.31 3.01
2420 3595 2.200373 CCATGAAAGGGTCGGAACTT 57.800 50.000 0.00 0.00 29.31 2.66
2421 3596 3.957288 CCATGAAAGGGTCGGAACT 57.043 52.632 0.00 0.00 29.31 3.01
2430 3605 4.096984 GGCTCATAGTGAAACCATGAAAGG 59.903 45.833 0.00 0.00 37.80 3.11
2431 3606 4.201851 CGGCTCATAGTGAAACCATGAAAG 60.202 45.833 0.00 0.00 37.80 2.62
2432 3607 3.689161 CGGCTCATAGTGAAACCATGAAA 59.311 43.478 0.00 0.00 37.80 2.69
2433 3608 3.270027 CGGCTCATAGTGAAACCATGAA 58.730 45.455 0.00 0.00 37.80 2.57
2434 3609 2.419990 CCGGCTCATAGTGAAACCATGA 60.420 50.000 0.00 0.00 37.80 3.07
2435 3610 1.942657 CCGGCTCATAGTGAAACCATG 59.057 52.381 0.00 0.00 37.80 3.66
2436 3611 1.559682 ACCGGCTCATAGTGAAACCAT 59.440 47.619 0.00 0.00 37.80 3.55
2437 3612 0.981183 ACCGGCTCATAGTGAAACCA 59.019 50.000 0.00 0.00 37.80 3.67
2438 3613 2.109425 AACCGGCTCATAGTGAAACC 57.891 50.000 0.00 0.00 37.80 3.27
2439 3614 3.858247 ACTAACCGGCTCATAGTGAAAC 58.142 45.455 0.00 0.00 0.00 2.78
2440 3615 4.546829 AACTAACCGGCTCATAGTGAAA 57.453 40.909 0.00 0.00 30.61 2.69
2441 3616 4.020928 TGAAACTAACCGGCTCATAGTGAA 60.021 41.667 0.00 0.00 30.61 3.18
2442 3617 3.512329 TGAAACTAACCGGCTCATAGTGA 59.488 43.478 0.00 0.00 30.61 3.41
2443 3618 3.857052 TGAAACTAACCGGCTCATAGTG 58.143 45.455 0.00 0.00 30.61 2.74
2444 3619 4.755266 ATGAAACTAACCGGCTCATAGT 57.245 40.909 0.00 2.38 0.00 2.12
2445 3620 6.093495 TCAAAATGAAACTAACCGGCTCATAG 59.907 38.462 0.00 1.67 0.00 2.23
2446 3621 5.941058 TCAAAATGAAACTAACCGGCTCATA 59.059 36.000 0.00 0.00 0.00 2.15
2447 3622 4.764823 TCAAAATGAAACTAACCGGCTCAT 59.235 37.500 0.00 0.00 0.00 2.90
2448 3623 4.138290 TCAAAATGAAACTAACCGGCTCA 58.862 39.130 0.00 0.00 0.00 4.26
2449 3624 4.759516 TCAAAATGAAACTAACCGGCTC 57.240 40.909 0.00 0.00 0.00 4.70
2450 3625 4.522789 ACATCAAAATGAAACTAACCGGCT 59.477 37.500 0.00 0.00 36.67 5.52
2451 3626 4.805219 ACATCAAAATGAAACTAACCGGC 58.195 39.130 0.00 0.00 36.67 6.13
2452 3627 6.472163 GCATACATCAAAATGAAACTAACCGG 59.528 38.462 0.00 0.00 36.67 5.28
2453 3628 7.026562 TGCATACATCAAAATGAAACTAACCG 58.973 34.615 0.00 0.00 36.67 4.44
2454 3629 8.755696 TTGCATACATCAAAATGAAACTAACC 57.244 30.769 0.00 0.00 36.67 2.85
2456 3631 9.979578 AGTTTGCATACATCAAAATGAAACTAA 57.020 25.926 10.02 0.00 34.90 2.24
2462 3637 9.955208 GATCATAGTTTGCATACATCAAAATGA 57.045 29.630 10.02 8.38 36.21 2.57
2463 3638 9.738832 TGATCATAGTTTGCATACATCAAAATG 57.261 29.630 10.02 4.00 35.49 2.32
2465 3640 9.791820 CTTGATCATAGTTTGCATACATCAAAA 57.208 29.630 16.09 2.87 35.49 2.44
2466 3641 9.176460 TCTTGATCATAGTTTGCATACATCAAA 57.824 29.630 16.09 8.87 30.65 2.69
2467 3642 8.735692 TCTTGATCATAGTTTGCATACATCAA 57.264 30.769 15.15 15.15 0.00 2.57
2468 3643 8.735692 TTCTTGATCATAGTTTGCATACATCA 57.264 30.769 10.02 6.94 0.00 3.07
2469 3644 8.834465 ACTTCTTGATCATAGTTTGCATACATC 58.166 33.333 10.02 4.56 0.00 3.06
2470 3645 8.743085 ACTTCTTGATCATAGTTTGCATACAT 57.257 30.769 10.02 0.00 0.00 2.29
2471 3646 8.565896 AACTTCTTGATCATAGTTTGCATACA 57.434 30.769 10.02 0.00 0.00 2.29
2472 3647 8.125448 GGAACTTCTTGATCATAGTTTGCATAC 58.875 37.037 15.39 0.00 31.41 2.39
2473 3648 7.011389 CGGAACTTCTTGATCATAGTTTGCATA 59.989 37.037 15.39 0.00 31.41 3.14
2474 3649 6.183360 CGGAACTTCTTGATCATAGTTTGCAT 60.183 38.462 15.39 0.00 31.41 3.96
2475 3650 5.122239 CGGAACTTCTTGATCATAGTTTGCA 59.878 40.000 15.39 0.00 31.41 4.08
2476 3651 5.351465 TCGGAACTTCTTGATCATAGTTTGC 59.649 40.000 15.39 7.46 31.41 3.68
2477 3652 6.183360 GGTCGGAACTTCTTGATCATAGTTTG 60.183 42.308 15.39 12.40 31.41 2.93
2478 3653 5.875359 GGTCGGAACTTCTTGATCATAGTTT 59.125 40.000 15.39 0.06 31.41 2.66
2479 3654 5.420409 GGTCGGAACTTCTTGATCATAGTT 58.580 41.667 14.60 14.60 33.78 2.24
2761 3949 9.926158 CATCTCACTGAAAAGCTGACTATATAT 57.074 33.333 0.00 0.00 0.00 0.86
2762 3950 8.918116 ACATCTCACTGAAAAGCTGACTATATA 58.082 33.333 0.00 0.00 0.00 0.86
2763 3951 7.790027 ACATCTCACTGAAAAGCTGACTATAT 58.210 34.615 0.00 0.00 0.00 0.86
2772 3960 5.210715 CAACAGAACATCTCACTGAAAAGC 58.789 41.667 0.00 0.00 35.85 3.51
2838 4026 9.553064 AGGCAGAATTATAACTGTATCTTTCAG 57.447 33.333 5.32 0.00 36.62 3.02
2895 4084 8.528044 AAAATGTTGGGAGACAAAGTTAAGTA 57.472 30.769 0.00 0.00 41.58 2.24
2900 4089 6.183360 CCCTTAAAATGTTGGGAGACAAAGTT 60.183 38.462 0.00 0.00 41.58 2.66
2906 4095 3.193479 CAGCCCTTAAAATGTTGGGAGAC 59.807 47.826 0.00 0.00 42.11 3.36
2965 4157 3.497884 AACCTGAGCCTGGCCACAC 62.498 63.158 16.57 5.47 0.00 3.82
2971 4163 0.622665 AATCTGGAACCTGAGCCTGG 59.377 55.000 6.58 0.00 0.00 4.45
2983 4175 4.177537 TGAAAGGGAAACACAATCTGGA 57.822 40.909 0.00 0.00 0.00 3.86
2996 4188 3.078837 GCCGTTACAGAATTGAAAGGGA 58.921 45.455 0.00 0.00 0.00 4.20
3003 4195 1.883275 TGGTTGGCCGTTACAGAATTG 59.117 47.619 0.00 0.00 37.67 2.32
3015 4207 6.589907 CAGAAAAAGTAATAACATGGTTGGCC 59.410 38.462 0.00 0.00 0.00 5.36
3046 4240 2.099592 CCCAATTCATATGCGTTGCACT 59.900 45.455 11.99 0.00 43.04 4.40
3048 4242 2.098614 ACCCAATTCATATGCGTTGCA 58.901 42.857 11.99 0.00 44.86 4.08
3053 4247 1.267806 GCTGGACCCAATTCATATGCG 59.732 52.381 0.00 0.00 0.00 4.73
3056 4250 2.895404 GCATGCTGGACCCAATTCATAT 59.105 45.455 11.37 0.00 0.00 1.78
3097 4291 6.104665 CAGTCAGAGCTTCTTGATCATAACA 58.895 40.000 0.00 0.00 32.67 2.41
3110 4307 3.406764 GACCATGAAACAGTCAGAGCTT 58.593 45.455 0.00 0.00 40.43 3.74
3111 4308 2.611473 CGACCATGAAACAGTCAGAGCT 60.611 50.000 0.00 0.00 40.43 4.09
3112 4309 1.728971 CGACCATGAAACAGTCAGAGC 59.271 52.381 0.00 0.00 40.43 4.09
3147 4344 4.220602 AGCCCAAAAAGGATATTCACACAC 59.779 41.667 0.00 0.00 41.22 3.82
3177 4374 6.441093 TGTTTTTAGAATCAGCATGCTAGG 57.559 37.500 22.19 9.54 34.76 3.02
3199 4396 1.600413 GCCAAAACGACTCCAAAGCTG 60.600 52.381 0.00 0.00 0.00 4.24
3200 4397 0.668535 GCCAAAACGACTCCAAAGCT 59.331 50.000 0.00 0.00 0.00 3.74
3201 4398 0.318699 GGCCAAAACGACTCCAAAGC 60.319 55.000 0.00 0.00 0.00 3.51
3202 4399 1.001378 CTGGCCAAAACGACTCCAAAG 60.001 52.381 7.01 0.00 0.00 2.77
3203 4400 1.028905 CTGGCCAAAACGACTCCAAA 58.971 50.000 7.01 0.00 0.00 3.28
3204 4401 1.452145 GCTGGCCAAAACGACTCCAA 61.452 55.000 7.01 0.00 0.00 3.53
3261 6043 7.016563 AGCCAATTCTTCAGTTTAAAGGGAAAT 59.983 33.333 0.00 0.00 0.00 2.17
3316 6100 5.701224 AGAAACCACTGGATGACCTTTAAA 58.299 37.500 0.71 0.00 37.04 1.52
3347 6131 9.444600 CCAGTGTATACCCGCTAAATATTTAAT 57.555 33.333 9.15 2.07 0.00 1.40
3348 6132 8.431222 ACCAGTGTATACCCGCTAAATATTTAA 58.569 33.333 9.15 0.00 0.00 1.52
3363 6147 9.216117 ACTTAGAAACATGAAACCAGTGTATAC 57.784 33.333 0.00 0.00 0.00 1.47
3415 6199 8.087136 CAGCTGATGATGATACTAAAAGCTAGA 58.913 37.037 8.42 0.00 36.38 2.43
3436 6220 2.938451 TGGAACTTCGATATTGCAGCTG 59.062 45.455 10.11 10.11 0.00 4.24
3489 6274 6.936335 TCTTACAAGAGCTTCATGATCACAAA 59.064 34.615 0.00 0.00 32.67 2.83
3499 6284 5.303078 ACTGAGACTTCTTACAAGAGCTTCA 59.697 40.000 0.00 0.00 36.22 3.02
3521 6306 5.056480 GCAGCCAAATTTCCTGTTTAAACT 58.944 37.500 18.72 0.00 0.00 2.66
3522 6307 5.050159 CAGCAGCCAAATTTCCTGTTTAAAC 60.050 40.000 11.54 11.54 0.00 2.01
3644 6429 1.813513 ATACTTCACAGCACCAGCAC 58.186 50.000 0.00 0.00 45.49 4.40


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

AutoCloner maintained by Alex Coulton.