Multiple sequence alignment - TraesCS6A01G264300

Loading Multiple Alignment...

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 TraesCS6A01G264300 chr6A 100.000 4123 0 0 1 4123 487772851 487768729 0.000000e+00 7614.0
1 TraesCS6A01G264300 chr6A 97.998 849 15 2 1 849 566432003 566431157 0.000000e+00 1472.0
2 TraesCS6A01G264300 chr6A 96.729 214 7 0 629 842 487773812 487774025 1.410000e-94 357.0
3 TraesCS6A01G264300 chr6A 95.794 214 9 0 629 842 566432991 566433204 3.050000e-91 346.0
4 TraesCS6A01G264300 chr6A 78.030 132 25 3 2008 2137 552208769 552208640 3.420000e-11 80.5
5 TraesCS6A01G264300 chr6A 93.023 43 2 1 4003 4045 542340522 542340563 1.240000e-05 62.1
6 TraesCS6A01G264300 chr6B 90.768 2708 129 46 841 3490 523882200 523879556 0.000000e+00 3504.0
7 TraesCS6A01G264300 chr6B 86.944 337 36 5 3538 3869 523879326 523878993 5.030000e-99 372.0
8 TraesCS6A01G264300 chr6B 76.596 141 29 3 1995 2133 609854828 609854690 1.590000e-09 75.0
9 TraesCS6A01G264300 chr6D 89.644 2694 142 48 841 3464 354368373 354370999 0.000000e+00 3302.0
10 TraesCS6A01G264300 chr6D 85.893 319 39 5 3558 3872 354372185 354372501 6.600000e-88 335.0
11 TraesCS6A01G264300 chr6D 81.988 161 21 6 1995 2154 436716636 436716483 3.340000e-26 130.0
12 TraesCS6A01G264300 chr6D 88.636 88 4 4 3452 3539 354371992 354372073 7.290000e-18 102.0
13 TraesCS6A01G264300 chr6D 77.241 145 29 3 1995 2137 405650833 405650691 9.500000e-12 82.4
14 TraesCS6A01G264300 chr6D 90.476 42 4 0 4000 4041 405676652 405676693 5.760000e-04 56.5
15 TraesCS6A01G264300 chr2B 92.857 574 26 5 6 579 267901535 267900977 0.000000e+00 819.0
16 TraesCS6A01G264300 chr2B 83.792 654 88 9 1540 2184 665858218 665858862 4.560000e-169 604.0
17 TraesCS6A01G264300 chr2B 97.222 36 1 0 4087 4122 691996063 691996028 1.240000e-05 62.1
18 TraesCS6A01G264300 chr2B 97.222 36 1 0 4087 4122 692037425 692037390 1.240000e-05 62.1
19 TraesCS6A01G264300 chr5D 90.062 644 38 11 8 629 351404955 351405594 0.000000e+00 811.0
20 TraesCS6A01G264300 chr5A 86.470 643 33 15 7 633 451742263 451742867 0.000000e+00 656.0
21 TraesCS6A01G264300 chr5A 95.495 222 7 3 623 842 376844952 376844732 6.560000e-93 351.0
22 TraesCS6A01G264300 chr5A 98.780 164 2 0 230 393 376845106 376844943 4.030000e-75 292.0
23 TraesCS6A01G264300 chr5B 85.933 654 41 20 6 633 412462773 412463401 0.000000e+00 651.0
24 TraesCS6A01G264300 chr5B 93.607 219 10 4 625 842 625120712 625120927 1.430000e-84 324.0
25 TraesCS6A01G264300 chr2A 84.557 654 83 9 1540 2184 698092606 698093250 2.090000e-177 632.0
26 TraesCS6A01G264300 chr2D 84.178 651 88 8 1540 2184 557684086 557684727 5.860000e-173 617.0
27 TraesCS6A01G264300 chr2D 90.698 43 4 0 3999 4041 536154245 536154287 1.600000e-04 58.4
28 TraesCS6A01G264300 chr7B 95.327 214 10 0 629 842 656195711 656195498 1.420000e-89 340.0
29 TraesCS6A01G264300 chr1B 94.470 217 12 0 629 845 570298783 570298567 6.600000e-88 335.0
30 TraesCS6A01G264300 chr1B 87.037 54 5 2 3999 4052 625185924 625185873 4.450000e-05 60.2
31 TraesCS6A01G264300 chr7A 92.982 228 14 2 625 852 487477325 487477100 8.540000e-87 331.0
32 TraesCS6A01G264300 chr3A 93.013 229 10 6 623 849 435354508 435354284 3.070000e-86 329.0
33 TraesCS6A01G264300 chr3A 99.390 164 1 0 230 393 435354662 435354499 8.660000e-77 298.0
34 TraesCS6A01G264300 chrUn 97.222 36 1 0 4087 4122 22220165 22220130 1.240000e-05 62.1
35 TraesCS6A01G264300 chr1A 92.857 42 3 0 4000 4041 410438197 410438238 1.240000e-05 62.1
36 TraesCS6A01G264300 chr3B 84.127 63 6 4 4013 4074 506238511 506238570 1.600000e-04 58.4
37 TraesCS6A01G264300 chr4D 92.308 39 3 0 4003 4041 427028017 427028055 5.760000e-04 56.5
38 TraesCS6A01G264300 chr1D 92.500 40 1 2 4003 4041 419070126 419070088 5.760000e-04 56.5
39 TraesCS6A01G264300 chr7D 92.308 39 2 1 4003 4041 19405020 19404983 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G264300 chr6A 487768729 487772851 4122 True 7614.000000 7614 100.000000 1 4123 1 chr6A.!!$R1 4122
1 TraesCS6A01G264300 chr6A 566431157 566432003 846 True 1472.000000 1472 97.998000 1 849 1 chr6A.!!$R3 848
2 TraesCS6A01G264300 chr6B 523878993 523882200 3207 True 1938.000000 3504 88.856000 841 3869 2 chr6B.!!$R2 3028
3 TraesCS6A01G264300 chr6D 354368373 354372501 4128 False 1246.333333 3302 88.057667 841 3872 3 chr6D.!!$F2 3031
4 TraesCS6A01G264300 chr2B 267900977 267901535 558 True 819.000000 819 92.857000 6 579 1 chr2B.!!$R1 573
5 TraesCS6A01G264300 chr2B 665858218 665858862 644 False 604.000000 604 83.792000 1540 2184 1 chr2B.!!$F1 644
6 TraesCS6A01G264300 chr5D 351404955 351405594 639 False 811.000000 811 90.062000 8 629 1 chr5D.!!$F1 621
7 TraesCS6A01G264300 chr5A 451742263 451742867 604 False 656.000000 656 86.470000 7 633 1 chr5A.!!$F1 626
8 TraesCS6A01G264300 chr5B 412462773 412463401 628 False 651.000000 651 85.933000 6 633 1 chr5B.!!$F1 627
9 TraesCS6A01G264300 chr2A 698092606 698093250 644 False 632.000000 632 84.557000 1540 2184 1 chr2A.!!$F1 644
10 TraesCS6A01G264300 chr2D 557684086 557684727 641 False 617.000000 617 84.178000 1540 2184 1 chr2D.!!$F2 644

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
934 1008 0.035630 AGAGGAGCAGCATCAACCAC 60.036 55.0 0.0 0.0 0.0 4.16 F
1352 1428 0.031994 GCTTCTCTCATCTCCCTCGC 59.968 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2642 2775 0.990818 GGCCTGGATCCTTCCCTCTT 60.991 60.0 14.23 0.00 41.83 2.85 R
3302 3477 0.174845 TACAGATCAAAGGGGACGCG 59.825 55.0 3.53 3.53 0.00 6.01 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
190 206 1.075896 GTCATCGGGGAGGAGGAGT 60.076 63.158 0.00 0.00 0.00 3.85
570 622 1.762460 GCAGATCGGAGGGAAGGGA 60.762 63.158 0.00 0.00 0.00 4.20
703 777 1.326213 GGCTCTGCTGACTAGGCTCA 61.326 60.000 0.00 0.00 33.32 4.26
722 796 4.473199 CTCAACTTGTCGTCGTCTGATTA 58.527 43.478 0.00 0.00 0.00 1.75
746 820 5.126061 AGCTAGGACTAAATTTGCACATTGG 59.874 40.000 0.00 0.00 0.00 3.16
802 876 3.982576 AGTTTTGGACCAAATCGTCAC 57.017 42.857 20.22 14.38 33.19 3.67
809 883 3.118775 TGGACCAAATCGTCACATCTAGG 60.119 47.826 0.00 0.00 34.24 3.02
826 900 0.393077 AGGACAAGTTGTGGGACTCG 59.607 55.000 14.57 0.00 0.00 4.18
829 903 0.828022 ACAAGTTGTGGGACTCGTGA 59.172 50.000 7.96 0.00 0.00 4.35
861 935 6.071984 ACCTCCTACTTTATCATCTGACGAT 58.928 40.000 0.00 0.00 0.00 3.73
887 961 6.239572 CCAAACACCTCATTTCCCTTGTATTT 60.240 38.462 0.00 0.00 0.00 1.40
909 983 3.312421 TCAAAGGAGACAAAACGAAGCAG 59.688 43.478 0.00 0.00 0.00 4.24
934 1008 0.035630 AGAGGAGCAGCATCAACCAC 60.036 55.000 0.00 0.00 0.00 4.16
989 1063 0.179062 CAGAGCAGCCTATGTGACCC 60.179 60.000 0.00 0.00 0.00 4.46
1083 1157 2.591715 ACAAGCACGCACAGGTCC 60.592 61.111 0.00 0.00 0.00 4.46
1116 1190 3.911661 ATTTCAGACTTTGAGCAGCAC 57.088 42.857 0.00 0.00 37.07 4.40
1135 1209 0.828343 CCAGATCGAGTACCCCCTCC 60.828 65.000 0.00 0.00 0.00 4.30
1164 1238 0.882042 CAGCGGGCAAGGTAGCATAG 60.882 60.000 0.00 0.00 35.83 2.23
1165 1239 2.254464 GCGGGCAAGGTAGCATAGC 61.254 63.158 0.00 0.00 39.93 2.97
1166 1240 1.146041 CGGGCAAGGTAGCATAGCA 59.854 57.895 0.00 0.00 42.67 3.49
1167 1241 1.160329 CGGGCAAGGTAGCATAGCAC 61.160 60.000 0.00 0.00 42.67 4.40
1168 1242 0.107214 GGGCAAGGTAGCATAGCACA 60.107 55.000 0.00 0.00 42.67 4.57
1201 1277 5.172934 GGAAGCATCTCATCTCATCTCATC 58.827 45.833 0.00 0.00 0.00 2.92
1202 1278 5.279556 GGAAGCATCTCATCTCATCTCATCA 60.280 44.000 0.00 0.00 0.00 3.07
1203 1279 6.367374 AAGCATCTCATCTCATCTCATCAT 57.633 37.500 0.00 0.00 0.00 2.45
1204 1280 5.972935 AGCATCTCATCTCATCTCATCATC 58.027 41.667 0.00 0.00 0.00 2.92
1222 1298 0.539901 TCGATCGATCCCCTTCTCCC 60.540 60.000 19.51 0.00 0.00 4.30
1245 1321 1.376037 CCTCCCTCGCCTTTCACAC 60.376 63.158 0.00 0.00 0.00 3.82
1254 1330 1.515521 GCCTTTCACACTCCCCAACG 61.516 60.000 0.00 0.00 0.00 4.10
1320 1396 3.387374 CAGACAGGATAGCCACTCATCTT 59.613 47.826 0.00 0.00 36.29 2.40
1322 1398 2.703007 ACAGGATAGCCACTCATCTTCC 59.297 50.000 0.00 0.00 36.29 3.46
1323 1399 2.038295 CAGGATAGCCACTCATCTTCCC 59.962 54.545 0.00 0.00 36.29 3.97
1324 1400 2.090267 AGGATAGCCACTCATCTTCCCT 60.090 50.000 0.00 0.00 36.29 4.20
1325 1401 2.301583 GGATAGCCACTCATCTTCCCTC 59.698 54.545 0.00 0.00 0.00 4.30
1326 1402 2.856760 TAGCCACTCATCTTCCCTCT 57.143 50.000 0.00 0.00 0.00 3.69
1327 1403 1.963985 AGCCACTCATCTTCCCTCTT 58.036 50.000 0.00 0.00 0.00 2.85
1328 1404 1.558756 AGCCACTCATCTTCCCTCTTG 59.441 52.381 0.00 0.00 0.00 3.02
1332 1408 3.560882 CCACTCATCTTCCCTCTTGCTTT 60.561 47.826 0.00 0.00 0.00 3.51
1350 1426 3.795877 CTTTGCTTCTCTCATCTCCCTC 58.204 50.000 0.00 0.00 0.00 4.30
1351 1427 1.397672 TGCTTCTCTCATCTCCCTCG 58.602 55.000 0.00 0.00 0.00 4.63
1352 1428 0.031994 GCTTCTCTCATCTCCCTCGC 59.968 60.000 0.00 0.00 0.00 5.03
1353 1429 0.673437 CTTCTCTCATCTCCCTCGCC 59.327 60.000 0.00 0.00 0.00 5.54
1354 1430 0.033109 TTCTCTCATCTCCCTCGCCA 60.033 55.000 0.00 0.00 0.00 5.69
1355 1431 0.467106 TCTCTCATCTCCCTCGCCAG 60.467 60.000 0.00 0.00 0.00 4.85
1356 1432 0.754957 CTCTCATCTCCCTCGCCAGT 60.755 60.000 0.00 0.00 0.00 4.00
1373 1449 3.115892 TCGCCACAATTCGTCGGC 61.116 61.111 0.00 0.00 38.02 5.54
1426 1513 2.361992 TTGGCAGGCTCAGCATGG 60.362 61.111 14.25 0.00 40.87 3.66
1435 1522 3.002583 TCAGCATGGCCTGACGGA 61.003 61.111 3.32 0.00 36.96 4.69
1455 1547 1.569708 GCAGAGATTTGCTCCTCTCG 58.430 55.000 0.00 0.00 45.10 4.04
1481 1573 2.978978 TGTTCCCTGTGATTCTTCTCCA 59.021 45.455 0.00 0.00 0.00 3.86
1529 1647 2.840102 AATCCTCCTCCGGCTCCG 60.840 66.667 0.00 0.48 39.44 4.63
1730 1854 0.603065 CCCTCGTCATCGCCATCATA 59.397 55.000 0.00 0.00 36.96 2.15
1908 2038 2.055042 CAGGAGGAGTGGGAGGTCG 61.055 68.421 0.00 0.00 0.00 4.79
2069 2202 2.519302 AAGTGCAGCCACGCCTTT 60.519 55.556 0.00 0.00 46.62 3.11
2077 2210 2.281761 CCACGCCTTTCACCTGCT 60.282 61.111 0.00 0.00 0.00 4.24
2315 2448 2.586792 GGCGACAATCAGGAGGCT 59.413 61.111 0.00 0.00 0.00 4.58
2324 2457 0.972883 ATCAGGAGGCTAAGGATCGC 59.027 55.000 0.00 0.00 0.00 4.58
2494 2627 3.621892 AAGACGAGCGTACGGTGGC 62.622 63.158 26.54 18.44 37.61 5.01
2558 2691 2.360475 GGGGAGCACAGCAAGGAC 60.360 66.667 0.00 0.00 0.00 3.85
2710 2843 4.946157 TGATTTCTCAGGCATTCTTCTTCC 59.054 41.667 0.00 0.00 0.00 3.46
2714 2847 3.197333 TCTCAGGCATTCTTCTTCCTCTG 59.803 47.826 0.00 0.00 0.00 3.35
2715 2848 2.909006 TCAGGCATTCTTCTTCCTCTGT 59.091 45.455 0.00 0.00 0.00 3.41
2718 2851 5.013079 TCAGGCATTCTTCTTCCTCTGTTAA 59.987 40.000 0.00 0.00 0.00 2.01
2719 2852 5.123027 CAGGCATTCTTCTTCCTCTGTTAAC 59.877 44.000 0.00 0.00 0.00 2.01
2720 2853 4.396478 GGCATTCTTCTTCCTCTGTTAACC 59.604 45.833 2.48 0.00 0.00 2.85
2833 2975 8.640091 TTTCTTCTTCATCGTTATGATCTCTG 57.360 34.615 0.00 0.00 41.73 3.35
2907 3053 3.079480 ACCTGCTGACTGGTGAGAT 57.921 52.632 0.00 0.00 45.61 2.75
2908 3054 0.612229 ACCTGCTGACTGGTGAGATG 59.388 55.000 0.00 0.00 45.61 2.90
2912 3058 0.107945 GCTGACTGGTGAGATGTCCC 60.108 60.000 0.00 0.00 0.00 4.46
3032 3207 1.139654 CGATTGGATTCTGCTCCAGGA 59.860 52.381 0.00 0.00 45.80 3.86
3060 3235 7.397892 TCTCTCTGGATTAGTGAGTTAACTG 57.602 40.000 14.14 0.00 43.94 3.16
3099 3274 1.872952 GTTTTGTTTGCAATGGGGAGC 59.127 47.619 0.00 0.00 34.18 4.70
3144 3319 0.813610 CCTCACGTGTGTGCCTTTGA 60.814 55.000 16.51 0.00 46.01 2.69
3172 3347 6.064846 ACTACATTTCAAGCTGTCAAAGTG 57.935 37.500 0.00 0.00 0.00 3.16
3205 3380 1.139520 GGGATGTGCGTGGAAATGC 59.860 57.895 0.00 0.00 0.00 3.56
3241 3416 1.354040 ATCAAGCTGAGCTCGAAACG 58.646 50.000 7.72 0.00 38.25 3.60
3250 3425 0.935196 AGCTCGAAACGTGTTTGGTC 59.065 50.000 2.15 0.00 32.11 4.02
3266 3441 2.038837 GTCTTGTTAGGTGGCCGGC 61.039 63.158 21.18 21.18 0.00 6.13
3296 3471 4.930963 TGCTAATAATGTTTGCCATTCGG 58.069 39.130 0.00 0.00 42.81 4.30
3298 3473 5.215160 GCTAATAATGTTTGCCATTCGGAG 58.785 41.667 0.00 0.00 42.81 4.63
3299 3474 5.221048 GCTAATAATGTTTGCCATTCGGAGT 60.221 40.000 0.00 0.00 42.81 3.85
3301 3476 1.176527 ATGTTTGCCATTCGGAGTGG 58.823 50.000 14.67 14.67 39.80 4.00
3307 3482 3.554692 CATTCGGAGTGGCGCGTC 61.555 66.667 2.29 2.29 0.00 5.19
3308 3483 4.814294 ATTCGGAGTGGCGCGTCC 62.814 66.667 8.89 10.74 0.00 4.79
3313 3488 4.699522 GAGTGGCGCGTCCCCTTT 62.700 66.667 8.89 0.00 0.00 3.11
3316 3491 4.028490 TGGCGCGTCCCCTTTGAT 62.028 61.111 8.89 0.00 0.00 2.57
3317 3492 3.202706 GGCGCGTCCCCTTTGATC 61.203 66.667 8.43 0.00 0.00 2.92
3318 3493 2.125106 GCGCGTCCCCTTTGATCT 60.125 61.111 8.43 0.00 0.00 2.75
3319 3494 2.464459 GCGCGTCCCCTTTGATCTG 61.464 63.158 8.43 0.00 0.00 2.90
3320 3495 1.079127 CGCGTCCCCTTTGATCTGT 60.079 57.895 0.00 0.00 0.00 3.41
3321 3496 0.174845 CGCGTCCCCTTTGATCTGTA 59.825 55.000 0.00 0.00 0.00 2.74
3331 3506 4.201851 CCCTTTGATCTGTAATCTGTTGCG 60.202 45.833 0.00 0.00 0.00 4.85
3339 3514 3.845178 TGTAATCTGTTGCGTAGGACAG 58.155 45.455 0.00 0.00 43.54 3.51
3404 3579 3.489416 GCGAATAACATGTGCGTCTCATA 59.511 43.478 0.00 0.00 0.00 2.15
3405 3580 4.150627 GCGAATAACATGTGCGTCTCATAT 59.849 41.667 0.00 0.00 0.00 1.78
3414 3589 6.538381 ACATGTGCGTCTCATATATGTCAAAA 59.462 34.615 12.42 0.00 0.00 2.44
3445 3620 0.179153 GTTAGGTCGACGGTGTAGCC 60.179 60.000 9.92 0.00 0.00 3.93
3490 4670 8.705594 CCTGAGGGAGAACAGTTCTTTATTATA 58.294 37.037 17.19 1.35 40.87 0.98
3491 4671 9.535878 CTGAGGGAGAACAGTTCTTTATTATAC 57.464 37.037 17.19 1.86 40.87 1.47
3492 4672 8.195436 TGAGGGAGAACAGTTCTTTATTATACG 58.805 37.037 17.19 0.00 40.87 3.06
3493 4673 8.075761 AGGGAGAACAGTTCTTTATTATACGT 57.924 34.615 17.19 0.00 40.87 3.57
3494 4674 9.193806 AGGGAGAACAGTTCTTTATTATACGTA 57.806 33.333 17.19 0.00 40.87 3.57
3495 4675 9.978044 GGGAGAACAGTTCTTTATTATACGTAT 57.022 33.333 17.19 13.54 40.87 3.06
3514 4694 7.772332 ACGTATTTGTAAGACATCTGGATTC 57.228 36.000 0.00 0.00 0.00 2.52
3520 4700 4.943705 TGTAAGACATCTGGATTCCTTTGC 59.056 41.667 3.95 0.00 0.00 3.68
3553 4928 5.550232 TCGATCAATCATGTTTTGGACTG 57.450 39.130 10.01 0.00 0.00 3.51
3636 5011 0.240411 GTGCTTGCAGCTTCTTCTGG 59.760 55.000 9.12 0.00 42.97 3.86
3650 5025 9.941325 CAGCTTCTTCTGGATATAATCATAAGT 57.059 33.333 0.00 0.00 0.00 2.24
3692 5067 2.283298 CATTTGATCTGTCCCGTCTGG 58.717 52.381 0.00 0.00 0.00 3.86
3693 5068 0.036388 TTTGATCTGTCCCGTCTGGC 60.036 55.000 0.00 0.00 0.00 4.85
3753 5133 6.072508 TCAGTTTTCATCATTCAACCTGTAGC 60.073 38.462 0.00 0.00 0.00 3.58
3755 5135 5.885230 TTTCATCATTCAACCTGTAGCTG 57.115 39.130 0.00 0.00 0.00 4.24
3786 5166 0.460987 GCTAGTCGCCAACTCAGCAT 60.461 55.000 0.00 0.00 39.55 3.79
3789 5169 1.154150 GTCGCCAACTCAGCATTGC 60.154 57.895 0.00 0.00 0.00 3.56
3795 5175 2.546373 GCCAACTCAGCATTGCAGAAAA 60.546 45.455 11.91 0.00 0.00 2.29
3797 5177 3.924686 CCAACTCAGCATTGCAGAAAATC 59.075 43.478 11.91 0.00 0.00 2.17
3807 5187 5.062558 GCATTGCAGAAAATCGTTTAAGCAT 59.937 36.000 3.15 0.00 36.82 3.79
3833 5213 8.972262 TCTATATAGACACTGAATTTCGCATC 57.028 34.615 8.44 0.00 0.00 3.91
3854 5234 2.282180 GGAAGCCCGGAAGTGCAA 60.282 61.111 0.73 0.00 0.00 4.08
3857 5237 0.733150 GAAGCCCGGAAGTGCAATAC 59.267 55.000 0.73 0.00 0.00 1.89
3872 5252 2.830480 GCAATACTTTTACGCAACGTCG 59.170 45.455 0.00 0.00 41.54 5.12
3873 5253 3.400995 CAATACTTTTACGCAACGTCGG 58.599 45.455 0.00 0.00 41.54 4.79
3874 5254 2.414058 TACTTTTACGCAACGTCGGA 57.586 45.000 0.00 0.00 41.54 4.55
3875 5255 1.787012 ACTTTTACGCAACGTCGGAT 58.213 45.000 0.00 0.00 41.54 4.18
3876 5256 2.945278 ACTTTTACGCAACGTCGGATA 58.055 42.857 0.00 0.00 41.54 2.59
3877 5257 2.919229 ACTTTTACGCAACGTCGGATAG 59.081 45.455 0.00 0.00 41.54 2.08
3878 5258 2.917701 TTTACGCAACGTCGGATAGA 57.082 45.000 0.00 0.00 41.54 1.98
3879 5259 2.917701 TTACGCAACGTCGGATAGAA 57.082 45.000 0.00 0.00 41.54 2.10
3880 5260 2.463553 TACGCAACGTCGGATAGAAG 57.536 50.000 0.00 0.00 41.54 2.85
3881 5261 0.806868 ACGCAACGTCGGATAGAAGA 59.193 50.000 0.00 0.00 33.69 2.87
3882 5262 1.200716 ACGCAACGTCGGATAGAAGAA 59.799 47.619 0.00 0.00 33.69 2.52
3883 5263 1.582502 CGCAACGTCGGATAGAAGAAC 59.417 52.381 0.00 0.00 32.54 3.01
3884 5264 1.925185 GCAACGTCGGATAGAAGAACC 59.075 52.381 0.00 0.00 32.54 3.62
3885 5265 2.673043 GCAACGTCGGATAGAAGAACCA 60.673 50.000 0.00 0.00 32.54 3.67
3886 5266 3.581755 CAACGTCGGATAGAAGAACCAA 58.418 45.455 0.00 0.00 32.54 3.67
3887 5267 3.505464 ACGTCGGATAGAAGAACCAAG 57.495 47.619 0.00 0.00 32.54 3.61
3888 5268 2.194271 CGTCGGATAGAAGAACCAAGC 58.806 52.381 0.00 0.00 0.00 4.01
3889 5269 2.159226 CGTCGGATAGAAGAACCAAGCT 60.159 50.000 0.00 0.00 0.00 3.74
3890 5270 3.676324 CGTCGGATAGAAGAACCAAGCTT 60.676 47.826 0.00 0.00 0.00 3.74
3891 5271 4.254492 GTCGGATAGAAGAACCAAGCTTT 58.746 43.478 0.00 0.00 0.00 3.51
3892 5272 5.416947 GTCGGATAGAAGAACCAAGCTTTA 58.583 41.667 0.00 0.00 0.00 1.85
3893 5273 6.049790 GTCGGATAGAAGAACCAAGCTTTAT 58.950 40.000 0.00 0.00 0.00 1.40
3894 5274 6.539103 GTCGGATAGAAGAACCAAGCTTTATT 59.461 38.462 0.00 0.00 0.00 1.40
3895 5275 7.709613 GTCGGATAGAAGAACCAAGCTTTATTA 59.290 37.037 0.00 0.00 0.00 0.98
3896 5276 8.429641 TCGGATAGAAGAACCAAGCTTTATTAT 58.570 33.333 0.00 0.00 0.00 1.28
3897 5277 9.057089 CGGATAGAAGAACCAAGCTTTATTATT 57.943 33.333 0.00 0.00 0.00 1.40
3902 5282 9.466497 AGAAGAACCAAGCTTTATTATTGATCA 57.534 29.630 0.00 0.00 0.00 2.92
3906 5286 9.860898 GAACCAAGCTTTATTATTGATCAAAGT 57.139 29.630 13.09 0.00 31.95 2.66
3908 5288 9.860898 ACCAAGCTTTATTATTGATCAAAGTTC 57.139 29.630 13.09 0.00 31.95 3.01
3909 5289 9.859427 CCAAGCTTTATTATTGATCAAAGTTCA 57.141 29.630 13.09 0.00 31.95 3.18
3911 5291 9.860898 AAGCTTTATTATTGATCAAAGTTCACC 57.139 29.630 13.09 0.00 31.95 4.02
3912 5292 9.023962 AGCTTTATTATTGATCAAAGTTCACCA 57.976 29.630 13.09 0.00 31.95 4.17
3913 5293 9.076596 GCTTTATTATTGATCAAAGTTCACCAC 57.923 33.333 13.09 0.00 31.95 4.16
3917 5297 4.916983 TTGATCAAAGTTCACCACAAGG 57.083 40.909 5.45 0.00 42.21 3.61
3918 5298 3.221771 TGATCAAAGTTCACCACAAGGG 58.778 45.455 0.00 0.00 44.81 3.95
3919 5299 2.065899 TCAAAGTTCACCACAAGGGG 57.934 50.000 0.00 0.00 42.91 4.79
3926 5306 2.038863 TCACCACAAGGGGATACAGT 57.961 50.000 0.00 0.00 44.30 3.55
3927 5307 2.344592 TCACCACAAGGGGATACAGTT 58.655 47.619 0.00 0.00 44.30 3.16
3928 5308 2.714250 TCACCACAAGGGGATACAGTTT 59.286 45.455 0.00 0.00 44.30 2.66
3929 5309 3.911260 TCACCACAAGGGGATACAGTTTA 59.089 43.478 0.00 0.00 44.30 2.01
3930 5310 4.351407 TCACCACAAGGGGATACAGTTTAA 59.649 41.667 0.00 0.00 44.30 1.52
3931 5311 5.074115 CACCACAAGGGGATACAGTTTAAA 58.926 41.667 0.00 0.00 42.79 1.52
3932 5312 5.714806 CACCACAAGGGGATACAGTTTAAAT 59.285 40.000 0.00 0.00 42.79 1.40
3933 5313 5.714806 ACCACAAGGGGATACAGTTTAAATG 59.285 40.000 0.00 0.00 42.91 2.32
3934 5314 5.127031 CCACAAGGGGATACAGTTTAAATGG 59.873 44.000 0.00 0.00 39.74 3.16
3935 5315 5.714806 CACAAGGGGATACAGTTTAAATGGT 59.285 40.000 0.00 0.00 39.74 3.55
3936 5316 5.714806 ACAAGGGGATACAGTTTAAATGGTG 59.285 40.000 0.00 0.00 39.74 4.17
3937 5317 4.867086 AGGGGATACAGTTTAAATGGTGG 58.133 43.478 0.00 0.00 39.74 4.61
3938 5318 3.958147 GGGGATACAGTTTAAATGGTGGG 59.042 47.826 0.00 0.00 39.74 4.61
3939 5319 3.383505 GGGATACAGTTTAAATGGTGGGC 59.616 47.826 0.00 0.00 39.74 5.36
3940 5320 4.278310 GGATACAGTTTAAATGGTGGGCT 58.722 43.478 0.00 0.00 0.00 5.19
3941 5321 4.709886 GGATACAGTTTAAATGGTGGGCTT 59.290 41.667 0.00 0.00 0.00 4.35
3942 5322 5.394115 GGATACAGTTTAAATGGTGGGCTTG 60.394 44.000 0.00 0.00 0.00 4.01
3943 5323 2.632512 ACAGTTTAAATGGTGGGCTTGG 59.367 45.455 0.00 0.00 0.00 3.61
3944 5324 1.623311 AGTTTAAATGGTGGGCTTGGC 59.377 47.619 0.00 0.00 0.00 4.52
3967 5347 2.440946 CCATACATGGCTCTCCCGA 58.559 57.895 0.00 0.00 41.75 5.14
3968 5348 0.979665 CCATACATGGCTCTCCCGAT 59.020 55.000 0.00 0.00 41.75 4.18
3969 5349 1.349026 CCATACATGGCTCTCCCGATT 59.651 52.381 0.00 0.00 41.75 3.34
3970 5350 2.613977 CCATACATGGCTCTCCCGATTC 60.614 54.545 0.00 0.00 41.75 2.52
3971 5351 1.788229 TACATGGCTCTCCCGATTCA 58.212 50.000 0.00 0.00 35.87 2.57
3972 5352 0.911769 ACATGGCTCTCCCGATTCAA 59.088 50.000 0.00 0.00 35.87 2.69
3973 5353 1.303309 CATGGCTCTCCCGATTCAAC 58.697 55.000 0.00 0.00 35.87 3.18
3974 5354 0.911769 ATGGCTCTCCCGATTCAACA 59.088 50.000 0.00 0.00 35.87 3.33
3975 5355 0.690192 TGGCTCTCCCGATTCAACAA 59.310 50.000 0.00 0.00 35.87 2.83
3976 5356 1.087501 GGCTCTCCCGATTCAACAAC 58.912 55.000 0.00 0.00 0.00 3.32
3977 5357 1.610624 GGCTCTCCCGATTCAACAACA 60.611 52.381 0.00 0.00 0.00 3.33
3978 5358 2.359900 GCTCTCCCGATTCAACAACAT 58.640 47.619 0.00 0.00 0.00 2.71
3979 5359 3.531538 GCTCTCCCGATTCAACAACATA 58.468 45.455 0.00 0.00 0.00 2.29
3980 5360 3.557595 GCTCTCCCGATTCAACAACATAG 59.442 47.826 0.00 0.00 0.00 2.23
3981 5361 4.122776 CTCTCCCGATTCAACAACATAGG 58.877 47.826 0.00 0.00 0.00 2.57
3982 5362 3.772572 TCTCCCGATTCAACAACATAGGA 59.227 43.478 0.00 0.00 0.00 2.94
3983 5363 4.224147 TCTCCCGATTCAACAACATAGGAA 59.776 41.667 0.00 0.00 0.00 3.36
3984 5364 4.912586 TCCCGATTCAACAACATAGGAAA 58.087 39.130 0.00 0.00 0.00 3.13
3985 5365 4.698304 TCCCGATTCAACAACATAGGAAAC 59.302 41.667 0.00 0.00 0.00 2.78
3987 5367 5.183140 CCCGATTCAACAACATAGGAAACTT 59.817 40.000 0.00 0.00 43.67 2.66
3988 5368 6.086222 CCGATTCAACAACATAGGAAACTTG 58.914 40.000 0.00 0.00 43.67 3.16
3989 5369 6.086222 CGATTCAACAACATAGGAAACTTGG 58.914 40.000 0.00 0.00 43.67 3.61
3990 5370 4.846779 TCAACAACATAGGAAACTTGGC 57.153 40.909 0.00 0.00 43.67 4.52
3991 5371 4.469657 TCAACAACATAGGAAACTTGGCT 58.530 39.130 0.00 0.00 43.67 4.75
3992 5372 5.626142 TCAACAACATAGGAAACTTGGCTA 58.374 37.500 0.00 0.00 43.67 3.93
3993 5373 6.065374 TCAACAACATAGGAAACTTGGCTAA 58.935 36.000 0.00 0.00 43.67 3.09
3994 5374 5.959618 ACAACATAGGAAACTTGGCTAAC 57.040 39.130 0.00 0.00 43.67 2.34
3995 5375 5.381757 ACAACATAGGAAACTTGGCTAACA 58.618 37.500 0.00 0.00 43.67 2.41
3996 5376 5.473504 ACAACATAGGAAACTTGGCTAACAG 59.526 40.000 0.00 0.00 43.67 3.16
3997 5377 5.499004 ACATAGGAAACTTGGCTAACAGA 57.501 39.130 0.00 0.00 43.67 3.41
3998 5378 5.876357 ACATAGGAAACTTGGCTAACAGAA 58.124 37.500 0.00 0.00 43.67 3.02
3999 5379 5.940470 ACATAGGAAACTTGGCTAACAGAAG 59.060 40.000 0.00 0.00 43.67 2.85
4000 5380 4.439253 AGGAAACTTGGCTAACAGAAGT 57.561 40.909 0.00 0.00 37.44 3.01
4001 5381 4.137543 AGGAAACTTGGCTAACAGAAGTG 58.862 43.478 0.00 0.00 37.44 3.16
4002 5382 3.304726 GGAAACTTGGCTAACAGAAGTGC 60.305 47.826 0.00 0.00 30.33 4.40
4003 5383 2.938956 ACTTGGCTAACAGAAGTGCT 57.061 45.000 0.00 0.00 0.00 4.40
4004 5384 2.772287 ACTTGGCTAACAGAAGTGCTC 58.228 47.619 0.00 0.00 0.00 4.26
4005 5385 2.079925 CTTGGCTAACAGAAGTGCTCC 58.920 52.381 0.00 0.00 0.00 4.70
4006 5386 0.324943 TGGCTAACAGAAGTGCTCCC 59.675 55.000 0.00 0.00 0.00 4.30
4007 5387 0.615850 GGCTAACAGAAGTGCTCCCT 59.384 55.000 0.00 0.00 0.00 4.20
4008 5388 1.677217 GGCTAACAGAAGTGCTCCCTG 60.677 57.143 4.77 4.77 0.00 4.45
4009 5389 1.731720 CTAACAGAAGTGCTCCCTGC 58.268 55.000 5.90 0.00 43.25 4.85
4026 5406 8.396272 GCTCCCTGCATAAAGAAAATATAAGA 57.604 34.615 0.00 0.00 42.31 2.10
4027 5407 8.510505 GCTCCCTGCATAAAGAAAATATAAGAG 58.489 37.037 0.00 0.00 42.31 2.85
4028 5408 8.396272 TCCCTGCATAAAGAAAATATAAGAGC 57.604 34.615 0.00 0.00 0.00 4.09
4029 5409 7.173218 TCCCTGCATAAAGAAAATATAAGAGCG 59.827 37.037 0.00 0.00 0.00 5.03
4030 5410 7.041098 CCCTGCATAAAGAAAATATAAGAGCGT 60.041 37.037 0.00 0.00 0.00 5.07
4031 5411 8.345565 CCTGCATAAAGAAAATATAAGAGCGTT 58.654 33.333 0.00 0.00 0.00 4.84
4032 5412 9.722056 CTGCATAAAGAAAATATAAGAGCGTTT 57.278 29.630 0.00 0.00 0.00 3.60
4042 5422 9.601217 AAAATATAAGAGCGTTTAGATCACTGT 57.399 29.630 0.00 0.00 37.82 3.55
4043 5423 9.601217 AAATATAAGAGCGTTTAGATCACTGTT 57.399 29.630 0.00 0.00 37.82 3.16
4049 5429 9.601217 AAGAGCGTTTAGATCACTGTTATATTT 57.399 29.630 0.00 0.00 37.82 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.971702 GACAGCAAGGGCAGGGGT 61.972 66.667 0.00 0.00 44.61 4.95
157 173 4.021925 GACCGCCACCTGCTCCTT 62.022 66.667 0.00 0.00 38.05 3.36
190 206 2.765807 GCCCTGCTCCTCCTGCTA 60.766 66.667 0.00 0.00 0.00 3.49
570 622 0.977108 CTGCTCCCTCTCTGCTTCCT 60.977 60.000 0.00 0.00 0.00 3.36
703 777 3.057456 AGCTAATCAGACGACGACAAGTT 60.057 43.478 0.00 0.00 0.00 2.66
722 796 5.126061 CCAATGTGCAAATTTAGTCCTAGCT 59.874 40.000 0.00 0.00 0.00 3.32
746 820 2.543777 TGAGTCCTACAACTTGCACC 57.456 50.000 0.00 0.00 0.00 5.01
753 827 4.833390 AGCCAACTATTGAGTCCTACAAC 58.167 43.478 0.00 0.00 33.58 3.32
758 832 3.507622 GCAAAAGCCAACTATTGAGTCCT 59.492 43.478 0.00 0.00 33.58 3.85
789 863 4.113354 GTCCTAGATGTGACGATTTGGTC 58.887 47.826 0.00 0.00 37.45 4.02
802 876 3.261897 AGTCCCACAACTTGTCCTAGATG 59.738 47.826 0.00 0.00 0.00 2.90
809 883 1.202486 TCACGAGTCCCACAACTTGTC 60.202 52.381 0.00 0.00 41.08 3.18
826 900 8.585881 TGATAAAGTAGGAGGTAATAGCATCAC 58.414 37.037 0.00 0.00 0.00 3.06
829 903 9.554053 AGATGATAAAGTAGGAGGTAATAGCAT 57.446 33.333 0.00 0.00 0.00 3.79
858 932 2.423538 GGGAAATGAGGTGTTTGGATCG 59.576 50.000 0.00 0.00 0.00 3.69
861 935 3.230134 CAAGGGAAATGAGGTGTTTGGA 58.770 45.455 0.00 0.00 0.00 3.53
887 961 3.275143 TGCTTCGTTTTGTCTCCTTTGA 58.725 40.909 0.00 0.00 0.00 2.69
909 983 1.687660 TGATGCTGCTCCTCTCATCTC 59.312 52.381 0.00 0.00 37.00 2.75
965 1039 0.464870 ACATAGGCTGCTCTGCTCTG 59.535 55.000 0.00 0.00 0.00 3.35
966 1040 0.464870 CACATAGGCTGCTCTGCTCT 59.535 55.000 0.00 0.00 0.00 4.09
967 1041 0.463204 TCACATAGGCTGCTCTGCTC 59.537 55.000 0.00 0.00 0.00 4.26
968 1042 0.177604 GTCACATAGGCTGCTCTGCT 59.822 55.000 0.00 0.00 0.00 4.24
969 1043 0.813210 GGTCACATAGGCTGCTCTGC 60.813 60.000 0.00 0.00 0.00 4.26
970 1044 0.179062 GGGTCACATAGGCTGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
989 1063 2.202570 CTTCGGTGCCGTCCTACG 60.203 66.667 10.60 0.00 42.11 3.51
1116 1190 0.828343 GGAGGGGGTACTCGATCTGG 60.828 65.000 0.00 0.00 38.39 3.86
1164 1238 2.595463 TTCCACCAGCTGCTGTGC 60.595 61.111 26.41 0.00 0.00 4.57
1165 1239 2.623915 GCTTCCACCAGCTGCTGTG 61.624 63.158 26.41 22.10 36.79 3.66
1166 1240 2.282040 GCTTCCACCAGCTGCTGT 60.282 61.111 26.41 13.01 36.79 4.40
1167 1241 1.654954 GATGCTTCCACCAGCTGCTG 61.655 60.000 22.44 22.44 40.79 4.41
1168 1242 1.378250 GATGCTTCCACCAGCTGCT 60.378 57.895 8.66 0.00 40.79 4.24
1201 1277 1.203523 GGAGAAGGGGATCGATCGATG 59.796 57.143 33.86 0.00 34.60 3.84
1202 1278 1.551452 GGAGAAGGGGATCGATCGAT 58.449 55.000 29.76 29.76 37.59 3.59
1203 1279 0.539901 GGGAGAAGGGGATCGATCGA 60.540 60.000 21.86 21.86 0.00 3.59
1204 1280 1.536943 GGGGAGAAGGGGATCGATCG 61.537 65.000 18.81 9.36 0.00 3.69
1222 1298 4.806339 AAGGCGAGGGAGGGAGGG 62.806 72.222 0.00 0.00 0.00 4.30
1245 1321 1.305930 GCTTTACAGGCGTTGGGGAG 61.306 60.000 0.00 0.00 0.00 4.30
1320 1396 1.701847 AGAGAAGCAAAGCAAGAGGGA 59.298 47.619 0.00 0.00 0.00 4.20
1322 1398 2.775890 TGAGAGAAGCAAAGCAAGAGG 58.224 47.619 0.00 0.00 0.00 3.69
1323 1399 4.255301 AGATGAGAGAAGCAAAGCAAGAG 58.745 43.478 0.00 0.00 0.00 2.85
1324 1400 4.252073 GAGATGAGAGAAGCAAAGCAAGA 58.748 43.478 0.00 0.00 0.00 3.02
1325 1401 3.374678 GGAGATGAGAGAAGCAAAGCAAG 59.625 47.826 0.00 0.00 0.00 4.01
1326 1402 3.341823 GGAGATGAGAGAAGCAAAGCAA 58.658 45.455 0.00 0.00 0.00 3.91
1327 1403 2.355513 GGGAGATGAGAGAAGCAAAGCA 60.356 50.000 0.00 0.00 0.00 3.91
1328 1404 2.093021 AGGGAGATGAGAGAAGCAAAGC 60.093 50.000 0.00 0.00 0.00 3.51
1332 1408 1.397672 CGAGGGAGATGAGAGAAGCA 58.602 55.000 0.00 0.00 0.00 3.91
1350 1426 2.480555 GAATTGTGGCGACTGGCG 59.519 61.111 0.00 0.00 44.92 5.69
1351 1427 2.240612 GACGAATTGTGGCGACTGGC 62.241 60.000 0.00 0.00 42.51 4.85
1352 1428 1.787847 GACGAATTGTGGCGACTGG 59.212 57.895 0.00 0.00 0.00 4.00
1353 1429 1.416049 CGACGAATTGTGGCGACTG 59.584 57.895 0.00 0.00 0.00 3.51
1354 1430 1.736645 CCGACGAATTGTGGCGACT 60.737 57.895 4.16 0.00 0.00 4.18
1355 1431 2.776072 CCGACGAATTGTGGCGAC 59.224 61.111 4.16 0.00 0.00 5.19
1356 1432 3.115892 GCCGACGAATTGTGGCGA 61.116 61.111 4.16 0.00 35.86 5.54
1373 1449 2.092538 AGGATCTGCATGAGTTTCTGGG 60.093 50.000 0.00 0.00 0.00 4.45
1421 1508 4.783621 TGCTCCGTCAGGCCATGC 62.784 66.667 5.01 0.00 37.47 4.06
1422 1509 2.513204 CTGCTCCGTCAGGCCATG 60.513 66.667 5.01 0.00 37.47 3.66
1426 1513 0.107945 AAATCTCTGCTCCGTCAGGC 60.108 55.000 0.00 0.00 37.47 4.85
1450 1537 1.201181 CACAGGGAACAGAGACGAGAG 59.799 57.143 0.00 0.00 0.00 3.20
1455 1547 3.971245 AGAATCACAGGGAACAGAGAC 57.029 47.619 0.00 0.00 0.00 3.36
1887 2017 3.086600 CTCCCACTCCTCCTGGCC 61.087 72.222 0.00 0.00 0.00 5.36
2077 2210 2.358615 GCCAGGTGTCGATGCACA 60.359 61.111 8.27 0.00 40.89 4.57
2302 2435 2.366916 CGATCCTTAGCCTCCTGATTGT 59.633 50.000 0.00 0.00 0.00 2.71
2315 2448 2.382023 ATCTCCCCGGGCGATCCTTA 62.382 60.000 17.73 0.00 0.00 2.69
2642 2775 0.990818 GGCCTGGATCCTTCCCTCTT 60.991 60.000 14.23 0.00 41.83 2.85
2710 2843 7.216973 AGTGTTCTACTAGTGGTTAACAGAG 57.783 40.000 12.06 1.23 38.04 3.35
2714 2847 6.644181 GGTCAAGTGTTCTACTAGTGGTTAAC 59.356 42.308 5.39 4.81 39.18 2.01
2715 2848 6.515531 CGGTCAAGTGTTCTACTAGTGGTTAA 60.516 42.308 5.39 0.00 39.18 2.01
2718 2851 3.255149 CGGTCAAGTGTTCTACTAGTGGT 59.745 47.826 5.39 0.00 39.18 4.16
2719 2852 3.255149 ACGGTCAAGTGTTCTACTAGTGG 59.745 47.826 5.39 1.87 39.18 4.00
2720 2853 4.023450 TCACGGTCAAGTGTTCTACTAGTG 60.023 45.833 5.39 0.00 42.40 2.74
2818 2960 3.055591 CGCAAGCAGAGATCATAACGAT 58.944 45.455 0.00 0.00 36.91 3.73
2907 3053 4.263572 CCAACCAGGTGCGGGACA 62.264 66.667 1.14 0.00 0.00 4.02
3032 3207 6.865834 AACTCACTAATCCAGAGAGAATGT 57.134 37.500 5.84 0.00 42.74 2.71
3060 3235 7.472543 ACAAAACATTTCGCCTAATGAGATAC 58.527 34.615 11.26 0.00 38.56 2.24
3099 3274 2.551912 AAAAGGTGAAGCGGCCACG 61.552 57.895 2.24 0.00 44.63 4.94
3144 3319 9.683069 CTTTGACAGCTTGAAATGTAGTAATTT 57.317 29.630 0.00 0.00 32.43 1.82
3172 3347 2.236766 CATCCCCAAATGATCAGCTCC 58.763 52.381 0.09 0.00 0.00 4.70
3205 3380 4.348656 CTTGATTGGCGATGATCAGTTTG 58.651 43.478 0.09 0.00 34.10 2.93
3241 3416 2.034179 GCCACCTAACAAGACCAAACAC 59.966 50.000 0.00 0.00 0.00 3.32
3250 3425 3.124921 CGCCGGCCACCTAACAAG 61.125 66.667 23.46 0.00 0.00 3.16
3266 3441 4.031652 GCAAACATTATTAGCAACAAGGCG 59.968 41.667 0.00 0.00 39.27 5.52
3299 3474 3.969250 GATCAAAGGGGACGCGCCA 62.969 63.158 18.87 0.63 39.05 5.69
3301 3476 2.125106 AGATCAAAGGGGACGCGC 60.125 61.111 5.73 0.00 0.00 6.86
3302 3477 0.174845 TACAGATCAAAGGGGACGCG 59.825 55.000 3.53 3.53 0.00 6.01
3303 3478 2.396590 TTACAGATCAAAGGGGACGC 57.603 50.000 0.00 0.00 0.00 5.19
3304 3479 4.122776 CAGATTACAGATCAAAGGGGACG 58.877 47.826 0.00 0.00 0.00 4.79
3306 3481 5.500234 CAACAGATTACAGATCAAAGGGGA 58.500 41.667 0.00 0.00 0.00 4.81
3307 3482 4.096984 GCAACAGATTACAGATCAAAGGGG 59.903 45.833 0.00 0.00 0.00 4.79
3308 3483 4.201851 CGCAACAGATTACAGATCAAAGGG 60.202 45.833 0.00 0.00 0.00 3.95
3309 3484 4.393062 ACGCAACAGATTACAGATCAAAGG 59.607 41.667 0.00 0.00 0.00 3.11
3310 3485 5.536554 ACGCAACAGATTACAGATCAAAG 57.463 39.130 0.00 0.00 0.00 2.77
3312 3487 5.105513 TCCTACGCAACAGATTACAGATCAA 60.106 40.000 0.00 0.00 0.00 2.57
3313 3488 4.401202 TCCTACGCAACAGATTACAGATCA 59.599 41.667 0.00 0.00 0.00 2.92
3314 3489 4.740695 GTCCTACGCAACAGATTACAGATC 59.259 45.833 0.00 0.00 0.00 2.75
3315 3490 4.159693 TGTCCTACGCAACAGATTACAGAT 59.840 41.667 0.00 0.00 0.00 2.90
3316 3491 3.508402 TGTCCTACGCAACAGATTACAGA 59.492 43.478 0.00 0.00 0.00 3.41
3317 3492 3.845178 TGTCCTACGCAACAGATTACAG 58.155 45.455 0.00 0.00 0.00 2.74
3318 3493 3.257375 ACTGTCCTACGCAACAGATTACA 59.743 43.478 9.32 0.00 44.54 2.41
3319 3494 3.612860 CACTGTCCTACGCAACAGATTAC 59.387 47.826 9.32 0.00 44.54 1.89
3320 3495 3.257375 ACACTGTCCTACGCAACAGATTA 59.743 43.478 9.32 0.00 44.54 1.75
3321 3496 2.037251 ACACTGTCCTACGCAACAGATT 59.963 45.455 9.32 0.00 44.54 2.40
3331 3506 1.677552 CCCACCCACACTGTCCTAC 59.322 63.158 0.00 0.00 0.00 3.18
3363 3538 3.050275 GGCCGACACTCAACAGCC 61.050 66.667 0.00 0.00 0.00 4.85
3404 3579 4.527816 ACACCCAACTGCATTTTGACATAT 59.472 37.500 9.28 0.00 0.00 1.78
3405 3580 3.894427 ACACCCAACTGCATTTTGACATA 59.106 39.130 9.28 0.00 0.00 2.29
3414 3589 1.610624 CGACCTAACACCCAACTGCAT 60.611 52.381 0.00 0.00 0.00 3.96
3445 3620 7.443575 CCCTCAGGAATAATAACTGTTGATCTG 59.556 40.741 2.69 2.30 34.02 2.90
3490 4670 6.761714 GGAATCCAGATGTCTTACAAATACGT 59.238 38.462 0.00 0.00 0.00 3.57
3491 4671 6.986817 AGGAATCCAGATGTCTTACAAATACG 59.013 38.462 0.61 0.00 0.00 3.06
3492 4672 8.738645 AAGGAATCCAGATGTCTTACAAATAC 57.261 34.615 0.61 0.00 0.00 1.89
3493 4673 9.177608 CAAAGGAATCCAGATGTCTTACAAATA 57.822 33.333 0.61 0.00 0.00 1.40
3494 4674 7.363268 GCAAAGGAATCCAGATGTCTTACAAAT 60.363 37.037 0.61 0.00 0.00 2.32
3495 4675 6.071952 GCAAAGGAATCCAGATGTCTTACAAA 60.072 38.462 0.61 0.00 0.00 2.83
3496 4676 5.415701 GCAAAGGAATCCAGATGTCTTACAA 59.584 40.000 0.61 0.00 0.00 2.41
3497 4677 4.943705 GCAAAGGAATCCAGATGTCTTACA 59.056 41.667 0.61 0.00 0.00 2.41
3498 4678 4.034510 CGCAAAGGAATCCAGATGTCTTAC 59.965 45.833 0.61 0.00 0.00 2.34
3499 4679 4.191544 CGCAAAGGAATCCAGATGTCTTA 58.808 43.478 0.61 0.00 0.00 2.10
3514 4694 1.921887 TCGAAATACGCTACGCAAAGG 59.078 47.619 0.00 0.00 42.26 3.11
3520 4700 5.117135 ACATGATTGATCGAAATACGCTACG 59.883 40.000 0.00 0.00 42.26 3.51
3525 4705 7.164171 GTCCAAAACATGATTGATCGAAATACG 59.836 37.037 14.70 0.00 44.09 3.06
3553 4928 5.922544 TCTTGAAAAGTAAGTACAGCCGTAC 59.077 40.000 1.76 1.76 46.34 3.67
3650 5025 3.004315 GCAGCAAAAGTGGCACTAAGTAA 59.996 43.478 22.37 0.00 0.00 2.24
3661 5036 4.304110 ACAGATCAAATGCAGCAAAAGTG 58.696 39.130 0.00 0.00 0.00 3.16
3728 5108 6.072508 GCTACAGGTTGAATGATGAAAACTGA 60.073 38.462 11.13 0.00 40.36 3.41
3729 5109 6.072286 AGCTACAGGTTGAATGATGAAAACTG 60.072 38.462 4.41 4.41 42.95 3.16
3732 5112 5.769662 ACAGCTACAGGTTGAATGATGAAAA 59.230 36.000 0.00 0.00 0.00 2.29
3736 5116 4.256110 TCACAGCTACAGGTTGAATGATG 58.744 43.478 0.00 0.00 0.00 3.07
3739 5119 4.256110 TCATCACAGCTACAGGTTGAATG 58.744 43.478 0.00 0.00 0.00 2.67
3753 5133 3.855154 GCGACTAGCCAGTATCATCACAG 60.855 52.174 0.00 0.00 40.81 3.66
3755 5135 2.667137 GCGACTAGCCAGTATCATCAC 58.333 52.381 0.00 0.00 40.81 3.06
3786 5166 6.446318 AGAATGCTTAAACGATTTTCTGCAA 58.554 32.000 0.00 0.00 36.94 4.08
3797 5177 9.678941 TCAGTGTCTATATAGAATGCTTAAACG 57.321 33.333 14.09 2.10 33.47 3.60
3807 5187 9.411801 GATGCGAAATTCAGTGTCTATATAGAA 57.588 33.333 14.09 2.75 33.47 2.10
3815 5195 3.005554 CCAGATGCGAAATTCAGTGTCT 58.994 45.455 0.00 0.00 0.00 3.41
3816 5196 2.096496 CCCAGATGCGAAATTCAGTGTC 59.904 50.000 0.00 0.00 0.00 3.67
3854 5234 2.945278 TCCGACGTTGCGTAAAAGTAT 58.055 42.857 0.00 0.00 41.37 2.12
3857 5237 3.173599 TCTATCCGACGTTGCGTAAAAG 58.826 45.455 0.00 0.00 41.37 2.27
3876 5256 9.466497 TGATCAATAATAAAGCTTGGTTCTTCT 57.534 29.630 0.00 0.00 0.00 2.85
3880 5260 9.860898 ACTTTGATCAATAATAAAGCTTGGTTC 57.139 29.630 9.40 0.00 34.38 3.62
3882 5262 9.860898 GAACTTTGATCAATAATAAAGCTTGGT 57.139 29.630 9.40 0.00 34.38 3.67
3883 5263 9.859427 TGAACTTTGATCAATAATAAAGCTTGG 57.141 29.630 9.40 0.00 34.38 3.61
3885 5265 9.860898 GGTGAACTTTGATCAATAATAAAGCTT 57.139 29.630 9.40 0.00 34.38 3.74
3886 5266 9.023962 TGGTGAACTTTGATCAATAATAAAGCT 57.976 29.630 9.40 0.00 34.38 3.74
3887 5267 9.076596 GTGGTGAACTTTGATCAATAATAAAGC 57.923 33.333 9.40 4.67 34.38 3.51
3891 5271 8.739039 CCTTGTGGTGAACTTTGATCAATAATA 58.261 33.333 9.40 0.00 0.00 0.98
3892 5272 7.309990 CCCTTGTGGTGAACTTTGATCAATAAT 60.310 37.037 9.40 0.00 0.00 1.28
3893 5273 6.015519 CCCTTGTGGTGAACTTTGATCAATAA 60.016 38.462 9.40 0.00 0.00 1.40
3894 5274 5.476599 CCCTTGTGGTGAACTTTGATCAATA 59.523 40.000 9.40 0.00 0.00 1.90
3895 5275 4.281688 CCCTTGTGGTGAACTTTGATCAAT 59.718 41.667 9.40 0.00 0.00 2.57
3896 5276 3.636300 CCCTTGTGGTGAACTTTGATCAA 59.364 43.478 3.38 3.38 0.00 2.57
3897 5277 3.221771 CCCTTGTGGTGAACTTTGATCA 58.778 45.455 0.00 0.00 0.00 2.92
3898 5278 2.558359 CCCCTTGTGGTGAACTTTGATC 59.442 50.000 0.00 0.00 0.00 2.92
3899 5279 2.176798 TCCCCTTGTGGTGAACTTTGAT 59.823 45.455 0.00 0.00 0.00 2.57
3900 5280 1.566703 TCCCCTTGTGGTGAACTTTGA 59.433 47.619 0.00 0.00 0.00 2.69
3901 5281 2.065899 TCCCCTTGTGGTGAACTTTG 57.934 50.000 0.00 0.00 0.00 2.77
3902 5282 3.139397 TGTATCCCCTTGTGGTGAACTTT 59.861 43.478 0.00 0.00 0.00 2.66
3903 5283 2.714250 TGTATCCCCTTGTGGTGAACTT 59.286 45.455 0.00 0.00 0.00 2.66
3904 5284 2.305927 CTGTATCCCCTTGTGGTGAACT 59.694 50.000 0.00 0.00 0.00 3.01
3905 5285 2.039879 ACTGTATCCCCTTGTGGTGAAC 59.960 50.000 0.00 0.00 0.00 3.18
3906 5286 2.344592 ACTGTATCCCCTTGTGGTGAA 58.655 47.619 0.00 0.00 0.00 3.18
3907 5287 2.038863 ACTGTATCCCCTTGTGGTGA 57.961 50.000 0.00 0.00 0.00 4.02
3908 5288 2.879103 AACTGTATCCCCTTGTGGTG 57.121 50.000 0.00 0.00 0.00 4.17
3909 5289 5.327737 TTTAAACTGTATCCCCTTGTGGT 57.672 39.130 0.00 0.00 0.00 4.16
3910 5290 5.127031 CCATTTAAACTGTATCCCCTTGTGG 59.873 44.000 0.00 0.00 0.00 4.17
3911 5291 5.714806 ACCATTTAAACTGTATCCCCTTGTG 59.285 40.000 0.00 0.00 0.00 3.33
3912 5292 5.714806 CACCATTTAAACTGTATCCCCTTGT 59.285 40.000 0.00 0.00 0.00 3.16
3913 5293 5.127031 CCACCATTTAAACTGTATCCCCTTG 59.873 44.000 0.00 0.00 0.00 3.61
3914 5294 5.269189 CCACCATTTAAACTGTATCCCCTT 58.731 41.667 0.00 0.00 0.00 3.95
3915 5295 4.325816 CCCACCATTTAAACTGTATCCCCT 60.326 45.833 0.00 0.00 0.00 4.79
3916 5296 3.958147 CCCACCATTTAAACTGTATCCCC 59.042 47.826 0.00 0.00 0.00 4.81
3917 5297 3.383505 GCCCACCATTTAAACTGTATCCC 59.616 47.826 0.00 0.00 0.00 3.85
3918 5298 4.278310 AGCCCACCATTTAAACTGTATCC 58.722 43.478 0.00 0.00 0.00 2.59
3919 5299 5.394115 CCAAGCCCACCATTTAAACTGTATC 60.394 44.000 0.00 0.00 0.00 2.24
3920 5300 4.466015 CCAAGCCCACCATTTAAACTGTAT 59.534 41.667 0.00 0.00 0.00 2.29
3921 5301 3.829601 CCAAGCCCACCATTTAAACTGTA 59.170 43.478 0.00 0.00 0.00 2.74
3922 5302 2.632512 CCAAGCCCACCATTTAAACTGT 59.367 45.455 0.00 0.00 0.00 3.55
3923 5303 2.612721 GCCAAGCCCACCATTTAAACTG 60.613 50.000 0.00 0.00 0.00 3.16
3924 5304 1.623311 GCCAAGCCCACCATTTAAACT 59.377 47.619 0.00 0.00 0.00 2.66
3925 5305 1.338674 GGCCAAGCCCACCATTTAAAC 60.339 52.381 0.00 0.00 44.06 2.01
3926 5306 0.980423 GGCCAAGCCCACCATTTAAA 59.020 50.000 0.00 0.00 44.06 1.52
3927 5307 2.677508 GGCCAAGCCCACCATTTAA 58.322 52.632 0.00 0.00 44.06 1.52
3928 5308 4.451544 GGCCAAGCCCACCATTTA 57.548 55.556 0.00 0.00 44.06 1.40
3946 5326 5.384367 ATCGGGAGAGCCATGTATGGTTG 62.384 52.174 12.21 0.00 45.41 3.77
3947 5327 3.293257 ATCGGGAGAGCCATGTATGGTT 61.293 50.000 12.21 6.36 45.41 3.67
3948 5328 1.762827 ATCGGGAGAGCCATGTATGGT 60.763 52.381 12.21 0.00 45.41 3.55
3949 5329 0.979665 ATCGGGAGAGCCATGTATGG 59.020 55.000 6.53 6.53 46.02 2.74
3950 5330 2.037641 TGAATCGGGAGAGCCATGTATG 59.962 50.000 0.00 0.00 45.48 2.39
3951 5331 2.329267 TGAATCGGGAGAGCCATGTAT 58.671 47.619 0.00 0.00 45.48 2.29
3952 5332 1.788229 TGAATCGGGAGAGCCATGTA 58.212 50.000 0.00 0.00 45.48 2.29
3953 5333 0.911769 TTGAATCGGGAGAGCCATGT 59.088 50.000 0.00 0.00 45.48 3.21
3954 5334 1.303309 GTTGAATCGGGAGAGCCATG 58.697 55.000 0.00 0.00 45.48 3.66
3955 5335 0.911769 TGTTGAATCGGGAGAGCCAT 59.088 50.000 0.00 0.00 45.48 4.40
3956 5336 0.690192 TTGTTGAATCGGGAGAGCCA 59.310 50.000 0.00 0.00 45.48 4.75
3957 5337 1.087501 GTTGTTGAATCGGGAGAGCC 58.912 55.000 0.00 0.00 45.48 4.70
3958 5338 1.808411 TGTTGTTGAATCGGGAGAGC 58.192 50.000 0.00 0.00 45.48 4.09
3959 5339 4.122776 CCTATGTTGTTGAATCGGGAGAG 58.877 47.826 0.00 0.00 45.48 3.20
3960 5340 3.772572 TCCTATGTTGTTGAATCGGGAGA 59.227 43.478 0.00 0.00 46.90 3.71
3961 5341 4.137116 TCCTATGTTGTTGAATCGGGAG 57.863 45.455 0.00 0.00 0.00 4.30
3962 5342 4.561500 TTCCTATGTTGTTGAATCGGGA 57.438 40.909 0.00 0.00 0.00 5.14
3963 5343 4.700213 AGTTTCCTATGTTGTTGAATCGGG 59.300 41.667 0.00 0.00 0.00 5.14
3964 5344 5.880054 AGTTTCCTATGTTGTTGAATCGG 57.120 39.130 0.00 0.00 0.00 4.18
3965 5345 6.086222 CCAAGTTTCCTATGTTGTTGAATCG 58.914 40.000 0.00 0.00 0.00 3.34
3966 5346 5.863935 GCCAAGTTTCCTATGTTGTTGAATC 59.136 40.000 0.00 0.00 0.00 2.52
3967 5347 5.539955 AGCCAAGTTTCCTATGTTGTTGAAT 59.460 36.000 0.00 0.00 0.00 2.57
3968 5348 4.892934 AGCCAAGTTTCCTATGTTGTTGAA 59.107 37.500 0.00 0.00 0.00 2.69
3969 5349 4.469657 AGCCAAGTTTCCTATGTTGTTGA 58.530 39.130 0.00 0.00 0.00 3.18
3970 5350 4.853924 AGCCAAGTTTCCTATGTTGTTG 57.146 40.909 0.00 0.00 0.00 3.33
3971 5351 5.830991 TGTTAGCCAAGTTTCCTATGTTGTT 59.169 36.000 0.00 0.00 0.00 2.83
3972 5352 5.381757 TGTTAGCCAAGTTTCCTATGTTGT 58.618 37.500 0.00 0.00 0.00 3.32
3973 5353 5.705441 TCTGTTAGCCAAGTTTCCTATGTTG 59.295 40.000 0.00 0.00 0.00 3.33
3974 5354 5.876357 TCTGTTAGCCAAGTTTCCTATGTT 58.124 37.500 0.00 0.00 0.00 2.71
3975 5355 5.499004 TCTGTTAGCCAAGTTTCCTATGT 57.501 39.130 0.00 0.00 0.00 2.29
3976 5356 5.940470 ACTTCTGTTAGCCAAGTTTCCTATG 59.060 40.000 0.00 0.00 0.00 2.23
3977 5357 5.940470 CACTTCTGTTAGCCAAGTTTCCTAT 59.060 40.000 0.00 0.00 0.00 2.57
3978 5358 5.305585 CACTTCTGTTAGCCAAGTTTCCTA 58.694 41.667 0.00 0.00 0.00 2.94
3979 5359 4.137543 CACTTCTGTTAGCCAAGTTTCCT 58.862 43.478 0.00 0.00 0.00 3.36
3980 5360 3.304726 GCACTTCTGTTAGCCAAGTTTCC 60.305 47.826 0.00 0.00 0.00 3.13
3981 5361 3.565902 AGCACTTCTGTTAGCCAAGTTTC 59.434 43.478 0.00 0.00 0.00 2.78
3982 5362 3.555966 AGCACTTCTGTTAGCCAAGTTT 58.444 40.909 0.00 0.00 0.00 2.66
3983 5363 3.142174 GAGCACTTCTGTTAGCCAAGTT 58.858 45.455 0.00 0.00 0.00 2.66
3984 5364 2.551071 GGAGCACTTCTGTTAGCCAAGT 60.551 50.000 0.00 0.00 0.00 3.16
3985 5365 2.079925 GGAGCACTTCTGTTAGCCAAG 58.920 52.381 0.00 0.00 0.00 3.61
3986 5366 1.271379 GGGAGCACTTCTGTTAGCCAA 60.271 52.381 0.00 0.00 0.00 4.52
3987 5367 0.324943 GGGAGCACTTCTGTTAGCCA 59.675 55.000 0.00 0.00 0.00 4.75
3988 5368 0.615850 AGGGAGCACTTCTGTTAGCC 59.384 55.000 0.00 0.00 0.00 3.93
3989 5369 1.731720 CAGGGAGCACTTCTGTTAGC 58.268 55.000 0.00 0.00 0.00 3.09
3990 5370 1.731720 GCAGGGAGCACTTCTGTTAG 58.268 55.000 0.00 0.00 44.79 2.34
3991 5371 3.935993 GCAGGGAGCACTTCTGTTA 57.064 52.632 0.00 0.00 44.79 2.41
3992 5372 4.809070 GCAGGGAGCACTTCTGTT 57.191 55.556 0.00 0.00 44.79 3.16
4001 5381 8.396272 TCTTATATTTTCTTTATGCAGGGAGC 57.604 34.615 0.00 0.00 45.96 4.70
4002 5382 8.510505 GCTCTTATATTTTCTTTATGCAGGGAG 58.489 37.037 0.00 0.00 0.00 4.30
4003 5383 7.173218 CGCTCTTATATTTTCTTTATGCAGGGA 59.827 37.037 0.00 0.00 0.00 4.20
4004 5384 7.041098 ACGCTCTTATATTTTCTTTATGCAGGG 60.041 37.037 0.00 0.00 0.00 4.45
4005 5385 7.865707 ACGCTCTTATATTTTCTTTATGCAGG 58.134 34.615 0.00 0.00 0.00 4.85
4006 5386 9.722056 AAACGCTCTTATATTTTCTTTATGCAG 57.278 29.630 0.00 0.00 0.00 4.41
4016 5396 9.601217 ACAGTGATCTAAACGCTCTTATATTTT 57.399 29.630 0.00 0.00 0.00 1.82
4017 5397 9.601217 AACAGTGATCTAAACGCTCTTATATTT 57.399 29.630 0.00 0.00 0.00 1.40
4023 5403 9.601217 AAATATAACAGTGATCTAAACGCTCTT 57.399 29.630 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.