Multiple sequence alignment - TraesCS2D01G233200

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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 TraesCS2D01G233200 chr2D 100.000 3514 0 0 1 3514 207253460 207249947 0.000000e+00 6490.0
1 TraesCS2D01G233200 chr2D 91.429 595 49 2 2 595 159187551 159186958 0.000000e+00 815.0
2 TraesCS2D01G233200 chr2D 91.081 583 51 1 1 583 401418321 401418902 0.000000e+00 787.0
3 TraesCS2D01G233200 chr2D 90.741 54 4 1 1004 1057 367225293 367225345 1.750000e-08 71.3
4 TraesCS2D01G233200 chr2B 91.573 1424 39 25 1685 3091 260638776 260640135 0.000000e+00 1890.0
5 TraesCS2D01G233200 chr2B 98.174 438 7 1 3077 3514 260640219 260640655 0.000000e+00 763.0
6 TraesCS2D01G233200 chr2B 94.737 133 7 0 596 728 260623429 260623561 1.280000e-49 207.0
7 TraesCS2D01G233200 chr2A 97.400 846 22 0 2669 3514 257854766 257855611 0.000000e+00 1441.0
8 TraesCS2D01G233200 chr2A 90.774 1008 30 13 1642 2634 257853804 257854763 0.000000e+00 1288.0
9 TraesCS2D01G233200 chr2A 93.214 280 15 3 1345 1622 257791234 257791511 3.270000e-110 409.0
10 TraesCS2D01G233200 chr2A 91.327 196 15 2 985 1178 257785607 257785802 2.080000e-67 267.0
11 TraesCS2D01G233200 chr2A 93.233 133 9 0 596 728 257785458 257785590 2.770000e-46 196.0
12 TraesCS2D01G233200 chr2A 93.333 120 5 2 1167 1286 257786446 257786562 1.300000e-39 174.0
13 TraesCS2D01G233200 chr1D 91.062 593 51 2 1 592 79497588 79498179 0.000000e+00 800.0
14 TraesCS2D01G233200 chr5D 90.801 587 54 0 9 595 181519019 181519605 0.000000e+00 785.0
15 TraesCS2D01G233200 chr5D 86.975 238 17 10 985 1210 154330621 154330386 4.500000e-64 255.0
16 TraesCS2D01G233200 chr5D 85.776 232 23 10 985 1210 225525870 225525643 1.630000e-58 237.0
17 TraesCS2D01G233200 chr5D 85.776 232 23 10 985 1210 225574119 225573892 1.630000e-58 237.0
18 TraesCS2D01G233200 chr7D 90.436 596 55 2 1 595 257570409 257571003 0.000000e+00 784.0
19 TraesCS2D01G233200 chr7D 90.909 275 22 3 715 988 500619042 500619314 1.990000e-97 366.0
20 TraesCS2D01G233200 chr7D 85.502 269 37 2 720 987 46993827 46993560 2.670000e-71 279.0
21 TraesCS2D01G233200 chr3D 90.420 595 57 0 1 595 164498800 164499394 0.000000e+00 784.0
22 TraesCS2D01G233200 chr3D 90.101 596 57 2 1 595 98079716 98080310 0.000000e+00 773.0
23 TraesCS2D01G233200 chr4D 90.268 596 56 2 1 595 242879717 242880311 0.000000e+00 778.0
24 TraesCS2D01G233200 chr7A 89.848 591 60 0 4 594 336198609 336198019 0.000000e+00 760.0
25 TraesCS2D01G233200 chr7A 86.100 259 36 0 730 988 92768261 92768519 2.670000e-71 279.0
26 TraesCS2D01G233200 chr6D 85.558 547 58 12 1903 2441 461387683 461388216 1.430000e-153 553.0
27 TraesCS2D01G233200 chr6D 85.593 236 22 9 985 1210 209633039 209633272 1.630000e-58 237.0
28 TraesCS2D01G233200 chr6D 92.258 155 7 5 1675 1827 461387169 461387320 7.640000e-52 215.0
29 TraesCS2D01G233200 chr6D 81.818 77 6 4 1538 1606 461386932 461387008 1.360000e-04 58.4
30 TraesCS2D01G233200 chr6A 84.954 545 71 7 1903 2441 608073815 608074354 3.090000e-150 542.0
31 TraesCS2D01G233200 chr6A 85.496 262 38 0 730 991 596891573 596891834 1.240000e-69 274.0
32 TraesCS2D01G233200 chr6A 96.850 127 4 0 1701 1827 608073348 608073474 2.750000e-51 213.0
33 TraesCS2D01G233200 chr6A 83.333 222 20 11 1002 1210 271823276 271823059 4.630000e-44 189.0
34 TraesCS2D01G233200 chr6B 84.142 536 57 16 1911 2441 703147084 703147596 8.760000e-136 494.0
35 TraesCS2D01G233200 chr6B 86.100 259 36 0 730 988 2044365 2044107 2.670000e-71 279.0
36 TraesCS2D01G233200 chr6B 94.444 144 5 3 1686 1829 703146339 703146479 5.910000e-53 219.0
37 TraesCS2D01G233200 chr5A 92.520 254 19 0 730 983 536370212 536369959 7.170000e-97 364.0
38 TraesCS2D01G233200 chr5A 85.659 258 37 0 730 987 404561125 404560868 4.470000e-69 272.0
39 TraesCS2D01G233200 chr5A 85.659 258 37 0 730 987 487842952 487842695 4.470000e-69 272.0
40 TraesCS2D01G233200 chr5A 81.974 233 27 10 986 1206 208199542 208199313 2.150000e-42 183.0
41 TraesCS2D01G233200 chr3B 85.659 258 37 0 730 987 2110161 2110418 4.470000e-69 272.0


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 TraesCS2D01G233200 chr2D 207249947 207253460 3513 True 6490.000000 6490 100.000000 1 3514 1 chr2D.!!$R2 3513
1 TraesCS2D01G233200 chr2D 159186958 159187551 593 True 815.000000 815 91.429000 2 595 1 chr2D.!!$R1 593
2 TraesCS2D01G233200 chr2D 401418321 401418902 581 False 787.000000 787 91.081000 1 583 1 chr2D.!!$F2 582
3 TraesCS2D01G233200 chr2B 260638776 260640655 1879 False 1326.500000 1890 94.873500 1685 3514 2 chr2B.!!$F2 1829
4 TraesCS2D01G233200 chr2A 257853804 257855611 1807 False 1364.500000 1441 94.087000 1642 3514 2 chr2A.!!$F3 1872
5 TraesCS2D01G233200 chr2A 257785458 257786562 1104 False 212.333333 267 92.631000 596 1286 3 chr2A.!!$F2 690
6 TraesCS2D01G233200 chr1D 79497588 79498179 591 False 800.000000 800 91.062000 1 592 1 chr1D.!!$F1 591
7 TraesCS2D01G233200 chr5D 181519019 181519605 586 False 785.000000 785 90.801000 9 595 1 chr5D.!!$F1 586
8 TraesCS2D01G233200 chr7D 257570409 257571003 594 False 784.000000 784 90.436000 1 595 1 chr7D.!!$F1 594
9 TraesCS2D01G233200 chr3D 164498800 164499394 594 False 784.000000 784 90.420000 1 595 1 chr3D.!!$F2 594
10 TraesCS2D01G233200 chr3D 98079716 98080310 594 False 773.000000 773 90.101000 1 595 1 chr3D.!!$F1 594
11 TraesCS2D01G233200 chr4D 242879717 242880311 594 False 778.000000 778 90.268000 1 595 1 chr4D.!!$F1 594
12 TraesCS2D01G233200 chr7A 336198019 336198609 590 True 760.000000 760 89.848000 4 594 1 chr7A.!!$R1 590
13 TraesCS2D01G233200 chr6D 461386932 461388216 1284 False 275.466667 553 86.544667 1538 2441 3 chr6D.!!$F2 903
14 TraesCS2D01G233200 chr6A 608073348 608074354 1006 False 377.500000 542 90.902000 1701 2441 2 chr6A.!!$F2 740
15 TraesCS2D01G233200 chr6B 703146339 703147596 1257 False 356.500000 494 89.293000 1686 2441 2 chr6B.!!$F1 755


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
601 602 1.020861 TCATCAGCCACACACATCGC 61.021 55.0 0.00 0.00 0.0 4.58 F
1436 2092 0.104120 TCTGTTGACTGGTCCACGTG 59.896 55.0 9.08 9.08 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 2104 0.027979 CTATTTGGCGCGTGGTGATG 59.972 55.0 8.43 0.0 0.0 3.07 R
2822 4307 0.387929 TTCGGTTGTGCGTTCTCTCT 59.612 50.0 0.00 0.0 0.0 3.10 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
83 84 3.003230 CCCTTGGTTCCCGGCATA 58.997 61.111 0.00 0.00 0.00 3.14
210 211 2.342279 CCTCACGGCGGAAGTGAA 59.658 61.111 13.24 0.00 46.43 3.18
227 228 2.476997 GTGAACTTTGTCTCCGAAGAGC 59.523 50.000 0.00 0.00 40.22 4.09
239 240 5.239744 GTCTCCGAAGAGCACATCTATCTTA 59.760 44.000 0.00 0.00 40.22 2.10
293 294 3.346315 CACAATGCCATGGAAGACAGTA 58.654 45.455 18.40 0.00 0.00 2.74
381 382 1.151668 GCTGCTACCGCCATCTATTG 58.848 55.000 0.00 0.00 34.43 1.90
501 502 1.227674 CGGCTCCAACTGATAGGCC 60.228 63.158 0.00 0.00 36.60 5.19
524 525 1.073964 CAGACCAGTGCATGAACTCG 58.926 55.000 2.28 0.00 0.00 4.18
601 602 1.020861 TCATCAGCCACACACATCGC 61.021 55.000 0.00 0.00 0.00 4.58
613 614 4.443725 CACACACATCGCAGATCTAGAATC 59.556 45.833 0.00 0.00 45.12 2.52
707 708 1.557099 TAGAGTCCATCAACGCCACT 58.443 50.000 0.00 0.00 0.00 4.00
718 719 2.159448 TCAACGCCACTGACAAAAGTTG 60.159 45.455 0.00 0.00 38.87 3.16
728 729 7.456253 CCACTGACAAAAGTTGAATATAGACG 58.544 38.462 0.00 0.00 0.00 4.18
731 732 7.331193 ACTGACAAAAGTTGAATATAGACGTCC 59.669 37.037 13.01 0.00 0.00 4.79
732 733 6.592607 TGACAAAAGTTGAATATAGACGTCCC 59.407 38.462 13.01 0.00 0.00 4.46
733 734 6.708285 ACAAAAGTTGAATATAGACGTCCCT 58.292 36.000 13.01 1.94 0.00 4.20
734 735 6.817140 ACAAAAGTTGAATATAGACGTCCCTC 59.183 38.462 13.01 2.61 0.00 4.30
735 736 6.793505 AAAGTTGAATATAGACGTCCCTCT 57.206 37.500 13.01 0.00 0.00 3.69
736 737 5.776173 AGTTGAATATAGACGTCCCTCTG 57.224 43.478 13.01 0.00 0.00 3.35
737 738 5.202004 AGTTGAATATAGACGTCCCTCTGT 58.798 41.667 13.01 0.00 0.00 3.41
739 740 5.769484 TGAATATAGACGTCCCTCTGTTC 57.231 43.478 13.01 9.98 0.00 3.18
740 741 4.583489 TGAATATAGACGTCCCTCTGTTCC 59.417 45.833 13.01 0.00 0.00 3.62
743 744 2.526888 AGACGTCCCTCTGTTCCATA 57.473 50.000 13.01 0.00 0.00 2.74
744 745 2.816411 AGACGTCCCTCTGTTCCATAA 58.184 47.619 13.01 0.00 0.00 1.90
745 746 3.170717 AGACGTCCCTCTGTTCCATAAA 58.829 45.455 13.01 0.00 0.00 1.40
746 747 3.581332 AGACGTCCCTCTGTTCCATAAAA 59.419 43.478 13.01 0.00 0.00 1.52
747 748 4.225267 AGACGTCCCTCTGTTCCATAAAAT 59.775 41.667 13.01 0.00 0.00 1.82
748 749 5.424252 AGACGTCCCTCTGTTCCATAAAATA 59.576 40.000 13.01 0.00 0.00 1.40
749 750 5.671493 ACGTCCCTCTGTTCCATAAAATAG 58.329 41.667 0.00 0.00 0.00 1.73
750 751 5.189145 ACGTCCCTCTGTTCCATAAAATAGT 59.811 40.000 0.00 0.00 0.00 2.12
751 752 5.523916 CGTCCCTCTGTTCCATAAAATAGTG 59.476 44.000 0.00 0.00 0.00 2.74
752 753 5.297029 GTCCCTCTGTTCCATAAAATAGTGC 59.703 44.000 0.00 0.00 0.00 4.40
753 754 5.191722 TCCCTCTGTTCCATAAAATAGTGCT 59.808 40.000 0.00 0.00 0.00 4.40
754 755 5.888161 CCCTCTGTTCCATAAAATAGTGCTT 59.112 40.000 0.00 0.00 0.00 3.91
755 756 6.183360 CCCTCTGTTCCATAAAATAGTGCTTG 60.183 42.308 0.00 0.00 0.00 4.01
756 757 6.375455 CCTCTGTTCCATAAAATAGTGCTTGT 59.625 38.462 0.00 0.00 0.00 3.16
757 758 7.552687 CCTCTGTTCCATAAAATAGTGCTTGTA 59.447 37.037 0.00 0.00 0.00 2.41
758 759 8.492673 TCTGTTCCATAAAATAGTGCTTGTAG 57.507 34.615 0.00 0.00 0.00 2.74
759 760 8.318412 TCTGTTCCATAAAATAGTGCTTGTAGA 58.682 33.333 0.00 0.00 0.00 2.59
760 761 9.113838 CTGTTCCATAAAATAGTGCTTGTAGAT 57.886 33.333 0.00 0.00 0.00 1.98
761 762 9.461312 TGTTCCATAAAATAGTGCTTGTAGATT 57.539 29.630 0.00 0.00 0.00 2.40
793 794 8.528917 AAAGTCAAACTTTACAAACTTTGACC 57.471 30.769 22.51 13.06 45.75 4.02
794 795 7.222000 AGTCAAACTTTACAAACTTTGACCA 57.778 32.000 22.51 2.11 44.13 4.02
795 796 7.662897 AGTCAAACTTTACAAACTTTGACCAA 58.337 30.769 22.51 0.00 44.13 3.67
796 797 7.812669 AGTCAAACTTTACAAACTTTGACCAAG 59.187 33.333 22.51 8.83 44.13 3.61
874 875 9.453572 ACATCACAAGACATACTTTCATATTGT 57.546 29.630 0.00 0.00 36.61 2.71
937 938 9.830975 ATAAATTTGGTCAAAGTTTGTAAAGCT 57.169 25.926 15.08 8.92 39.89 3.74
982 983 5.740290 ACACTATATTATGGAACGGAGGG 57.260 43.478 0.00 0.00 0.00 4.30
983 984 5.399991 ACACTATATTATGGAACGGAGGGA 58.600 41.667 0.00 0.00 0.00 4.20
1007 1008 9.837525 GGAGTATCACTTATTCGACGTATAAAT 57.162 33.333 8.07 0.00 36.25 1.40
1054 1055 4.379394 CCACAAGGGTCAATACGTTGAATG 60.379 45.833 0.00 0.00 45.38 2.67
1057 1058 6.093495 CACAAGGGTCAATACGTTGAATGTAT 59.907 38.462 4.28 4.28 45.38 2.29
1066 1069 4.404507 ACGTTGAATGTATGCAAGTCAC 57.595 40.909 0.00 0.00 0.00 3.67
1067 1070 3.812609 ACGTTGAATGTATGCAAGTCACA 59.187 39.130 0.00 0.00 0.00 3.58
1085 1088 9.684448 CAAGTCACACTAGGTATGATATAACAG 57.316 37.037 0.00 0.00 0.00 3.16
1140 1143 4.044336 TGAATGTGGTTGTTTTGCAGAG 57.956 40.909 0.00 0.00 0.00 3.35
1152 1155 6.207691 TGTTTTGCAGAGAAGCTAACTTTT 57.792 33.333 0.00 0.00 35.82 2.27
1168 1171 7.988028 AGCTAACTTTTCCCTGATAACTACATC 59.012 37.037 0.00 0.00 0.00 3.06
1231 1887 7.970061 ACATAATGTCAAAATCTCAACCATTCG 59.030 33.333 0.00 0.00 0.00 3.34
1243 1899 2.154567 ACCATTCGTAGTGGCTAGGA 57.845 50.000 0.00 0.00 40.49 2.94
1251 1907 2.292016 CGTAGTGGCTAGGATCACTGAG 59.708 54.545 6.27 0.00 43.24 3.35
1297 1953 5.803020 CCTTTAGGTGTTTTAGCTAGCAG 57.197 43.478 18.83 0.00 40.24 4.24
1298 1954 4.095036 CCTTTAGGTGTTTTAGCTAGCAGC 59.905 45.833 18.83 4.43 40.24 5.25
1299 1955 2.115343 AGGTGTTTTAGCTAGCAGCC 57.885 50.000 18.83 7.67 43.77 4.85
1300 1956 1.351017 AGGTGTTTTAGCTAGCAGCCA 59.649 47.619 18.83 3.00 43.77 4.75
1301 1957 2.159382 GGTGTTTTAGCTAGCAGCCAA 58.841 47.619 18.83 2.18 43.77 4.52
1302 1958 2.755103 GGTGTTTTAGCTAGCAGCCAAT 59.245 45.455 18.83 0.00 43.77 3.16
1303 1959 3.428045 GGTGTTTTAGCTAGCAGCCAATG 60.428 47.826 18.83 0.00 43.77 2.82
1304 1960 3.440173 GTGTTTTAGCTAGCAGCCAATGA 59.560 43.478 18.83 0.00 43.77 2.57
1305 1961 3.440173 TGTTTTAGCTAGCAGCCAATGAC 59.560 43.478 18.83 5.00 43.77 3.06
1306 1962 3.634397 TTTAGCTAGCAGCCAATGACT 57.366 42.857 18.83 0.00 43.77 3.41
1307 1963 2.898729 TAGCTAGCAGCCAATGACTC 57.101 50.000 18.83 0.00 43.77 3.36
1308 1964 1.202330 AGCTAGCAGCCAATGACTCT 58.798 50.000 18.83 0.00 43.77 3.24
1309 1965 1.558756 AGCTAGCAGCCAATGACTCTT 59.441 47.619 18.83 0.00 43.77 2.85
1310 1966 2.026449 AGCTAGCAGCCAATGACTCTTT 60.026 45.455 18.83 0.00 43.77 2.52
1311 1967 2.354199 GCTAGCAGCCAATGACTCTTTC 59.646 50.000 10.63 0.00 34.48 2.62
1312 1968 1.831580 AGCAGCCAATGACTCTTTCC 58.168 50.000 0.00 0.00 0.00 3.13
1313 1969 0.813821 GCAGCCAATGACTCTTTCCC 59.186 55.000 0.00 0.00 0.00 3.97
1314 1970 1.615384 GCAGCCAATGACTCTTTCCCT 60.615 52.381 0.00 0.00 0.00 4.20
1315 1971 2.363683 CAGCCAATGACTCTTTCCCTC 58.636 52.381 0.00 0.00 0.00 4.30
1316 1972 2.026449 CAGCCAATGACTCTTTCCCTCT 60.026 50.000 0.00 0.00 0.00 3.69
1317 1973 2.238395 AGCCAATGACTCTTTCCCTCTC 59.762 50.000 0.00 0.00 0.00 3.20
1318 1974 2.682269 GCCAATGACTCTTTCCCTCTCC 60.682 54.545 0.00 0.00 0.00 3.71
1319 1975 2.573462 CCAATGACTCTTTCCCTCTCCA 59.427 50.000 0.00 0.00 0.00 3.86
1320 1976 3.201708 CCAATGACTCTTTCCCTCTCCAT 59.798 47.826 0.00 0.00 0.00 3.41
1321 1977 4.450053 CAATGACTCTTTCCCTCTCCATC 58.550 47.826 0.00 0.00 0.00 3.51
1322 1978 2.103373 TGACTCTTTCCCTCTCCATCG 58.897 52.381 0.00 0.00 0.00 3.84
1323 1979 0.827368 ACTCTTTCCCTCTCCATCGC 59.173 55.000 0.00 0.00 0.00 4.58
1324 1980 0.826715 CTCTTTCCCTCTCCATCGCA 59.173 55.000 0.00 0.00 0.00 5.10
1325 1981 1.208052 CTCTTTCCCTCTCCATCGCAA 59.792 52.381 0.00 0.00 0.00 4.85
1326 1982 1.628340 TCTTTCCCTCTCCATCGCAAA 59.372 47.619 0.00 0.00 0.00 3.68
1327 1983 2.039746 TCTTTCCCTCTCCATCGCAAAA 59.960 45.455 0.00 0.00 0.00 2.44
1328 1984 2.577606 TTCCCTCTCCATCGCAAAAA 57.422 45.000 0.00 0.00 0.00 1.94
1369 2025 3.582714 AAAAAGCTAGCAGCCAATGAC 57.417 42.857 18.83 0.00 43.77 3.06
1370 2026 2.503895 AAAGCTAGCAGCCAATGACT 57.496 45.000 18.83 0.00 43.77 3.41
1371 2027 2.503895 AAGCTAGCAGCCAATGACTT 57.496 45.000 18.83 0.00 43.77 3.01
1372 2028 2.035530 AGCTAGCAGCCAATGACTTC 57.964 50.000 18.83 0.00 43.77 3.01
1373 2029 1.020437 GCTAGCAGCCAATGACTTCC 58.980 55.000 10.63 0.00 34.48 3.46
1374 2030 1.673168 CTAGCAGCCAATGACTTCCC 58.327 55.000 0.00 0.00 0.00 3.97
1375 2031 0.255890 TAGCAGCCAATGACTTCCCC 59.744 55.000 0.00 0.00 0.00 4.81
1376 2032 1.000396 GCAGCCAATGACTTCCCCT 60.000 57.895 0.00 0.00 0.00 4.79
1377 2033 0.255890 GCAGCCAATGACTTCCCCTA 59.744 55.000 0.00 0.00 0.00 3.53
1378 2034 1.340991 GCAGCCAATGACTTCCCCTAA 60.341 52.381 0.00 0.00 0.00 2.69
1379 2035 2.883888 GCAGCCAATGACTTCCCCTAAA 60.884 50.000 0.00 0.00 0.00 1.85
1380 2036 3.430453 CAGCCAATGACTTCCCCTAAAA 58.570 45.455 0.00 0.00 0.00 1.52
1381 2037 3.831911 CAGCCAATGACTTCCCCTAAAAA 59.168 43.478 0.00 0.00 0.00 1.94
1400 2056 3.582714 AAAAAGCTAGCAGCCAATGAC 57.417 42.857 18.83 0.00 43.77 3.06
1401 2057 2.205022 AAAGCTAGCAGCCAATGACA 57.795 45.000 18.83 0.00 43.77 3.58
1402 2058 1.747709 AAGCTAGCAGCCAATGACAG 58.252 50.000 18.83 0.00 43.77 3.51
1403 2059 0.617413 AGCTAGCAGCCAATGACAGT 59.383 50.000 18.83 0.00 43.77 3.55
1404 2060 0.731417 GCTAGCAGCCAATGACAGTG 59.269 55.000 10.63 0.00 34.48 3.66
1405 2061 1.376543 CTAGCAGCCAATGACAGTGG 58.623 55.000 17.60 17.60 39.33 4.00
1406 2062 0.983467 TAGCAGCCAATGACAGTGGA 59.017 50.000 25.55 0.81 38.54 4.02
1407 2063 0.607489 AGCAGCCAATGACAGTGGAC 60.607 55.000 25.55 15.75 38.54 4.02
1408 2064 1.589716 GCAGCCAATGACAGTGGACC 61.590 60.000 25.55 8.70 38.54 4.46
1409 2065 0.962356 CAGCCAATGACAGTGGACCC 60.962 60.000 25.55 7.96 38.54 4.46
1410 2066 2.040544 GCCAATGACAGTGGACCCG 61.041 63.158 25.55 0.00 38.54 5.28
1411 2067 1.377202 CCAATGACAGTGGACCCGG 60.377 63.158 17.01 0.00 38.54 5.73
1412 2068 2.040544 CAATGACAGTGGACCCGGC 61.041 63.158 0.00 0.00 0.00 6.13
1413 2069 3.605749 AATGACAGTGGACCCGGCG 62.606 63.158 0.00 0.00 0.00 6.46
1422 2078 4.681978 GACCCGGCGCACTCTGTT 62.682 66.667 10.83 0.00 0.00 3.16
1423 2079 4.988598 ACCCGGCGCACTCTGTTG 62.989 66.667 10.83 0.00 0.00 3.33
1424 2080 4.680237 CCCGGCGCACTCTGTTGA 62.680 66.667 10.83 0.00 0.00 3.18
1425 2081 3.414700 CCGGCGCACTCTGTTGAC 61.415 66.667 10.83 0.00 0.00 3.18
1426 2082 2.356313 CGGCGCACTCTGTTGACT 60.356 61.111 10.83 0.00 0.00 3.41
1427 2083 2.661566 CGGCGCACTCTGTTGACTG 61.662 63.158 10.83 0.00 0.00 3.51
1428 2084 2.320587 GGCGCACTCTGTTGACTGG 61.321 63.158 10.83 0.00 0.00 4.00
1429 2085 1.595382 GCGCACTCTGTTGACTGGT 60.595 57.895 0.30 0.00 0.00 4.00
1430 2086 1.560860 GCGCACTCTGTTGACTGGTC 61.561 60.000 0.30 0.00 0.00 4.02
1431 2087 0.946221 CGCACTCTGTTGACTGGTCC 60.946 60.000 0.00 0.00 0.00 4.46
1432 2088 0.106708 GCACTCTGTTGACTGGTCCA 59.893 55.000 0.00 0.00 0.00 4.02
1433 2089 1.871080 CACTCTGTTGACTGGTCCAC 58.129 55.000 0.00 0.00 0.00 4.02
1434 2090 0.389391 ACTCTGTTGACTGGTCCACG 59.611 55.000 0.00 0.00 0.00 4.94
1435 2091 0.389391 CTCTGTTGACTGGTCCACGT 59.611 55.000 0.00 0.00 0.00 4.49
1436 2092 0.104120 TCTGTTGACTGGTCCACGTG 59.896 55.000 9.08 9.08 0.00 4.49
1437 2093 0.104120 CTGTTGACTGGTCCACGTGA 59.896 55.000 19.30 0.00 0.00 4.35
1438 2094 0.179094 TGTTGACTGGTCCACGTGAC 60.179 55.000 19.30 13.01 43.67 3.67
1446 2102 3.390003 GTCCACGTGACCCTTTTGA 57.610 52.632 19.30 0.00 38.09 2.69
1447 2103 0.942252 GTCCACGTGACCCTTTTGAC 59.058 55.000 19.30 9.32 38.09 3.18
1448 2104 0.179040 TCCACGTGACCCTTTTGACC 60.179 55.000 19.30 0.00 0.00 4.02
1449 2105 0.464735 CCACGTGACCCTTTTGACCA 60.465 55.000 19.30 0.00 0.00 4.02
1450 2106 1.604604 CACGTGACCCTTTTGACCAT 58.395 50.000 10.90 0.00 0.00 3.55
1451 2107 1.535462 CACGTGACCCTTTTGACCATC 59.465 52.381 10.90 0.00 0.00 3.51
1452 2108 1.142060 ACGTGACCCTTTTGACCATCA 59.858 47.619 0.00 0.00 0.00 3.07
1453 2109 1.535462 CGTGACCCTTTTGACCATCAC 59.465 52.381 0.00 0.00 34.46 3.06
1454 2110 1.886542 GTGACCCTTTTGACCATCACC 59.113 52.381 0.00 0.00 32.18 4.02
1455 2111 1.496857 TGACCCTTTTGACCATCACCA 59.503 47.619 0.00 0.00 0.00 4.17
1456 2112 1.886542 GACCCTTTTGACCATCACCAC 59.113 52.381 0.00 0.00 0.00 4.16
1457 2113 0.881118 CCCTTTTGACCATCACCACG 59.119 55.000 0.00 0.00 0.00 4.94
1458 2114 0.240945 CCTTTTGACCATCACCACGC 59.759 55.000 0.00 0.00 0.00 5.34
1459 2115 0.110238 CTTTTGACCATCACCACGCG 60.110 55.000 3.53 3.53 0.00 6.01
1460 2116 2.123988 TTTTGACCATCACCACGCGC 62.124 55.000 5.73 0.00 0.00 6.86
1463 2119 4.634703 ACCATCACCACGCGCCAA 62.635 61.111 5.73 0.00 0.00 4.52
1464 2120 3.361158 CCATCACCACGCGCCAAA 61.361 61.111 5.73 0.00 0.00 3.28
1465 2121 2.699768 CCATCACCACGCGCCAAAT 61.700 57.895 5.73 0.00 0.00 2.32
1466 2122 1.372838 CCATCACCACGCGCCAAATA 61.373 55.000 5.73 0.00 0.00 1.40
1467 2123 0.027979 CATCACCACGCGCCAAATAG 59.972 55.000 5.73 0.00 0.00 1.73
1468 2124 0.392461 ATCACCACGCGCCAAATAGT 60.392 50.000 5.73 0.00 0.00 2.12
1469 2125 0.604243 TCACCACGCGCCAAATAGTT 60.604 50.000 5.73 0.00 0.00 2.24
1470 2126 0.239879 CACCACGCGCCAAATAGTTT 59.760 50.000 5.73 0.00 0.00 2.66
1471 2127 0.519961 ACCACGCGCCAAATAGTTTC 59.480 50.000 5.73 0.00 0.00 2.78
1472 2128 0.802494 CCACGCGCCAAATAGTTTCT 59.198 50.000 5.73 0.00 0.00 2.52
1473 2129 1.465689 CCACGCGCCAAATAGTTTCTG 60.466 52.381 5.73 0.00 0.00 3.02
1474 2130 0.802494 ACGCGCCAAATAGTTTCTGG 59.198 50.000 5.73 0.00 0.00 3.86
1522 2178 6.699575 ATATAAATGTGGCACTTGTTCTCC 57.300 37.500 19.83 0.00 0.00 3.71
1523 2179 2.664402 AATGTGGCACTTGTTCTCCT 57.336 45.000 19.83 0.00 0.00 3.69
1524 2180 3.788227 AATGTGGCACTTGTTCTCCTA 57.212 42.857 19.83 0.00 0.00 2.94
1525 2181 3.788227 ATGTGGCACTTGTTCTCCTAA 57.212 42.857 19.83 0.00 0.00 2.69
1526 2182 3.569194 TGTGGCACTTGTTCTCCTAAA 57.431 42.857 19.83 0.00 0.00 1.85
1527 2183 3.892284 TGTGGCACTTGTTCTCCTAAAA 58.108 40.909 19.83 0.00 0.00 1.52
1528 2184 4.274147 TGTGGCACTTGTTCTCCTAAAAA 58.726 39.130 19.83 0.00 0.00 1.94
1529 2185 4.097286 TGTGGCACTTGTTCTCCTAAAAAC 59.903 41.667 19.83 0.00 0.00 2.43
1530 2186 4.097286 GTGGCACTTGTTCTCCTAAAAACA 59.903 41.667 11.13 0.00 33.74 2.83
1531 2187 4.707448 TGGCACTTGTTCTCCTAAAAACAA 59.293 37.500 0.00 0.00 41.67 2.83
1532 2188 5.041287 GGCACTTGTTCTCCTAAAAACAAC 58.959 41.667 0.00 0.00 39.70 3.32
1533 2189 4.733405 GCACTTGTTCTCCTAAAAACAACG 59.267 41.667 0.00 0.00 39.70 4.10
1534 2190 5.270853 CACTTGTTCTCCTAAAAACAACGG 58.729 41.667 0.00 0.00 39.70 4.44
1535 2191 5.065474 CACTTGTTCTCCTAAAAACAACGGA 59.935 40.000 0.00 0.00 39.70 4.69
1536 2192 5.296035 ACTTGTTCTCCTAAAAACAACGGAG 59.704 40.000 0.00 0.00 39.70 4.63
1541 2197 3.681593 TCCTAAAAACAACGGAGATGGG 58.318 45.455 0.00 0.00 33.36 4.00
1570 2226 7.548427 CGATGGATATGAGCAGTTCAGAAATAT 59.452 37.037 0.00 0.00 39.68 1.28
1573 2229 8.316946 TGGATATGAGCAGTTCAGAAATATAGG 58.683 37.037 0.00 0.00 39.68 2.57
1579 2243 4.024809 GCAGTTCAGAAATATAGGGCGTTC 60.025 45.833 0.00 0.00 0.00 3.95
1580 2244 4.209288 CAGTTCAGAAATATAGGGCGTTCG 59.791 45.833 0.00 0.00 0.00 3.95
1582 2246 5.068198 AGTTCAGAAATATAGGGCGTTCGTA 59.932 40.000 0.00 0.00 0.00 3.43
1584 2248 4.581824 TCAGAAATATAGGGCGTTCGTAGT 59.418 41.667 0.00 0.00 0.00 2.73
1585 2249 5.068198 TCAGAAATATAGGGCGTTCGTAGTT 59.932 40.000 0.00 0.00 0.00 2.24
1589 2253 1.477553 TAGGGCGTTCGTAGTTGGAT 58.522 50.000 0.00 0.00 0.00 3.41
1634 2348 3.264947 GCTAATTTTAACGACTCCCCGT 58.735 45.455 0.00 0.00 45.64 5.28
1641 2356 2.047560 CGACTCCCCGTGTTTCCC 60.048 66.667 0.00 0.00 0.00 3.97
1652 2367 2.741211 GTTTCCCCCACTCGCGTC 60.741 66.667 5.77 0.00 0.00 5.19
1946 3393 9.847224 AGTGAAGTCCGGTATCAAATATAAATT 57.153 29.630 0.00 0.00 0.00 1.82
2223 3683 2.165437 AGAGTTCAGCATCCTCGACTTC 59.835 50.000 0.00 0.00 0.00 3.01
2327 3792 1.153489 CCACCGAGAGCCACATCAG 60.153 63.158 0.00 0.00 0.00 2.90
2339 3804 2.677902 GCCACATCAGATGGAAAGACGA 60.678 50.000 15.13 0.00 39.87 4.20
2491 3972 3.953612 TGCTTTCTGTGACTGGAATGTTT 59.046 39.130 0.00 0.00 0.00 2.83
2505 3986 3.569701 GGAATGTTTGCTTCCTCTGTGAA 59.430 43.478 0.00 0.00 39.30 3.18
2719 4204 2.838202 TCCCAGTTGACAATACTCCCTC 59.162 50.000 0.00 0.00 0.00 4.30
2819 4304 2.422479 ACAGCAGCATTAACTCAGCATG 59.578 45.455 0.00 0.00 37.54 4.06
2822 4307 1.746787 CAGCATTAACTCAGCATGCCA 59.253 47.619 15.66 0.00 43.75 4.92
3014 4499 2.146073 CTTGCTGCAAAACGGGAGGG 62.146 60.000 16.74 0.00 0.00 4.30
3015 4500 3.373565 GCTGCAAAACGGGAGGGG 61.374 66.667 0.00 0.00 0.00 4.79
3311 4894 2.699251 GTTTGTAAGCCTCCCAAACG 57.301 50.000 4.16 0.00 38.74 3.60
3347 4930 7.639113 TTAAGACAAACAGGAACTCAAATGT 57.361 32.000 0.00 0.00 34.60 2.71
3454 5037 6.310711 GTGGGTTCTTACTTGAATCTAACTCG 59.689 42.308 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 6.243900 CCATTATGCCTACCTCAAGATGAAT 58.756 40.000 0.00 0.00 0.00 2.57
121 122 1.520342 CGGTCAGCTCTAGCCAAGC 60.520 63.158 0.00 0.00 43.38 4.01
136 137 2.365635 ATGTGCTCCTAGGCCGGT 60.366 61.111 2.96 0.00 0.00 5.28
210 211 1.412710 TGTGCTCTTCGGAGACAAAGT 59.587 47.619 0.00 0.00 44.41 2.66
227 228 7.664082 AATCGGCAAGATTAAGATAGATGTG 57.336 36.000 5.04 0.00 46.99 3.21
293 294 2.270205 CAGCTCCAGCCCAATCGT 59.730 61.111 0.00 0.00 43.38 3.73
381 382 1.478510 TGCTCGTTTCTCCCAGATCTC 59.521 52.381 0.00 0.00 0.00 2.75
473 474 3.113514 TTGGAGCCGTGCAGACCAA 62.114 57.895 13.37 13.37 36.69 3.67
501 502 2.028294 AGTTCATGCACTGGTCTGAGAG 60.028 50.000 0.00 0.00 0.00 3.20
636 637 9.793252 ATAATTTGTTTGTATGCTAGCTTTCAG 57.207 29.630 17.23 0.00 0.00 3.02
692 693 0.602638 TGTCAGTGGCGTTGATGGAC 60.603 55.000 0.00 0.00 0.00 4.02
707 708 6.592607 GGGACGTCTATATTCAACTTTTGTCA 59.407 38.462 16.46 0.00 0.00 3.58
718 719 4.583489 TGGAACAGAGGGACGTCTATATTC 59.417 45.833 16.46 11.40 0.00 1.75
848 849 9.453572 ACAATATGAAAGTATGTCTTGTGATGT 57.546 29.630 0.00 0.00 36.40 3.06
911 912 9.830975 AGCTTTACAAACTTTGACCAAATTTAT 57.169 25.926 8.55 0.00 0.00 1.40
912 913 9.660180 AAGCTTTACAAACTTTGACCAAATTTA 57.340 25.926 8.55 0.00 0.00 1.40
913 914 8.450180 CAAGCTTTACAAACTTTGACCAAATTT 58.550 29.630 8.55 0.00 0.00 1.82
914 915 7.821846 TCAAGCTTTACAAACTTTGACCAAATT 59.178 29.630 8.55 0.00 0.00 1.82
915 916 7.277760 GTCAAGCTTTACAAACTTTGACCAAAT 59.722 33.333 8.55 0.00 0.00 2.32
916 917 6.588373 GTCAAGCTTTACAAACTTTGACCAAA 59.412 34.615 8.55 4.99 0.00 3.28
917 918 6.071616 AGTCAAGCTTTACAAACTTTGACCAA 60.072 34.615 13.07 0.00 0.00 3.67
918 919 5.417580 AGTCAAGCTTTACAAACTTTGACCA 59.582 36.000 13.07 0.00 0.00 4.02
919 920 5.891451 AGTCAAGCTTTACAAACTTTGACC 58.109 37.500 13.07 0.00 0.00 4.02
920 921 7.812309 AAAGTCAAGCTTTACAAACTTTGAC 57.188 32.000 13.07 6.64 44.90 3.18
921 922 9.915629 TTAAAAGTCAAGCTTTACAAACTTTGA 57.084 25.926 13.07 7.17 45.91 2.69
956 957 9.144298 CCCTCCGTTCCATAATATAGTGTATAT 57.856 37.037 0.00 0.00 32.90 0.86
957 958 8.338493 TCCCTCCGTTCCATAATATAGTGTATA 58.662 37.037 0.00 0.00 0.00 1.47
958 959 7.186972 TCCCTCCGTTCCATAATATAGTGTAT 58.813 38.462 0.00 0.00 0.00 2.29
959 960 6.554784 TCCCTCCGTTCCATAATATAGTGTA 58.445 40.000 0.00 0.00 0.00 2.90
960 961 5.399991 TCCCTCCGTTCCATAATATAGTGT 58.600 41.667 0.00 0.00 0.00 3.55
961 962 5.480772 ACTCCCTCCGTTCCATAATATAGTG 59.519 44.000 0.00 0.00 0.00 2.74
962 963 5.652324 ACTCCCTCCGTTCCATAATATAGT 58.348 41.667 0.00 0.00 0.00 2.12
963 964 7.560262 TGATACTCCCTCCGTTCCATAATATAG 59.440 40.741 0.00 0.00 0.00 1.31
964 965 7.341256 GTGATACTCCCTCCGTTCCATAATATA 59.659 40.741 0.00 0.00 0.00 0.86
965 966 6.154706 GTGATACTCCCTCCGTTCCATAATAT 59.845 42.308 0.00 0.00 0.00 1.28
966 967 5.479375 GTGATACTCCCTCCGTTCCATAATA 59.521 44.000 0.00 0.00 0.00 0.98
967 968 4.283722 GTGATACTCCCTCCGTTCCATAAT 59.716 45.833 0.00 0.00 0.00 1.28
968 969 3.640029 GTGATACTCCCTCCGTTCCATAA 59.360 47.826 0.00 0.00 0.00 1.90
969 970 3.117246 AGTGATACTCCCTCCGTTCCATA 60.117 47.826 0.00 0.00 0.00 2.74
970 971 2.040178 GTGATACTCCCTCCGTTCCAT 58.960 52.381 0.00 0.00 0.00 3.41
971 972 1.006758 AGTGATACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
972 973 1.777941 AGTGATACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
973 974 5.530712 GAATAAGTGATACTCCCTCCGTTC 58.469 45.833 0.00 0.00 0.00 3.95
974 975 4.037684 CGAATAAGTGATACTCCCTCCGTT 59.962 45.833 0.00 0.00 0.00 4.44
975 976 3.568853 CGAATAAGTGATACTCCCTCCGT 59.431 47.826 0.00 0.00 0.00 4.69
976 977 3.819337 TCGAATAAGTGATACTCCCTCCG 59.181 47.826 0.00 0.00 0.00 4.63
977 978 4.320348 CGTCGAATAAGTGATACTCCCTCC 60.320 50.000 0.00 0.00 0.00 4.30
978 979 4.275443 ACGTCGAATAAGTGATACTCCCTC 59.725 45.833 0.00 0.00 0.00 4.30
979 980 4.205587 ACGTCGAATAAGTGATACTCCCT 58.794 43.478 0.00 0.00 0.00 4.20
980 981 4.564940 ACGTCGAATAAGTGATACTCCC 57.435 45.455 0.00 0.00 0.00 4.30
981 982 9.837525 ATTTATACGTCGAATAAGTGATACTCC 57.162 33.333 0.00 0.00 0.00 3.85
994 995 7.650104 TCATGTTGCAGATATTTATACGTCGAA 59.350 33.333 0.00 0.00 0.00 3.71
1007 1008 9.183368 TGGTTGTAATTTATCATGTTGCAGATA 57.817 29.630 0.00 0.00 0.00 1.98
1043 1044 5.641636 TGTGACTTGCATACATTCAACGTAT 59.358 36.000 0.00 0.00 0.00 3.06
1054 1055 5.902681 TCATACCTAGTGTGACTTGCATAC 58.097 41.667 0.00 0.00 38.74 2.39
1057 1058 6.731292 ATATCATACCTAGTGTGACTTGCA 57.269 37.500 0.00 0.00 36.58 4.08
1066 1069 9.516546 TGTAGGTCTGTTATATCATACCTAGTG 57.483 37.037 20.45 0.00 43.11 2.74
1085 1088 4.408182 ACCTTGCATGTAGATGTAGGTC 57.592 45.455 17.45 0.00 40.13 3.85
1140 1143 7.822822 TGTAGTTATCAGGGAAAAGTTAGCTTC 59.177 37.037 0.00 0.00 33.01 3.86
1231 1887 2.625790 CCTCAGTGATCCTAGCCACTAC 59.374 54.545 9.38 0.00 41.26 2.73
1243 1899 1.066143 CCACGGCTAAACCTCAGTGAT 60.066 52.381 0.00 0.00 35.61 3.06
1251 1907 0.606096 AAAATGGCCACGGCTAAACC 59.394 50.000 8.16 0.00 41.60 3.27
1286 1942 3.198635 AGAGTCATTGGCTGCTAGCTAAA 59.801 43.478 17.23 5.41 44.77 1.85
1287 1943 2.768527 AGAGTCATTGGCTGCTAGCTAA 59.231 45.455 17.23 8.80 45.66 3.09
1288 1944 2.392662 AGAGTCATTGGCTGCTAGCTA 58.607 47.619 17.23 1.31 41.99 3.32
1289 1945 1.202330 AGAGTCATTGGCTGCTAGCT 58.798 50.000 17.23 0.00 41.99 3.32
1290 1946 2.035530 AAGAGTCATTGGCTGCTAGC 57.964 50.000 8.10 8.10 41.46 3.42
1291 1947 2.941720 GGAAAGAGTCATTGGCTGCTAG 59.058 50.000 0.00 0.00 0.00 3.42
1292 1948 2.356125 GGGAAAGAGTCATTGGCTGCTA 60.356 50.000 0.00 0.00 0.00 3.49
1293 1949 1.615384 GGGAAAGAGTCATTGGCTGCT 60.615 52.381 0.00 0.00 0.00 4.24
1294 1950 0.813821 GGGAAAGAGTCATTGGCTGC 59.186 55.000 0.00 0.00 0.00 5.25
1295 1951 2.026449 AGAGGGAAAGAGTCATTGGCTG 60.026 50.000 0.00 0.00 0.00 4.85
1296 1952 2.238395 GAGAGGGAAAGAGTCATTGGCT 59.762 50.000 0.00 0.00 0.00 4.75
1297 1953 2.637947 GAGAGGGAAAGAGTCATTGGC 58.362 52.381 0.00 0.00 0.00 4.52
1298 1954 2.573462 TGGAGAGGGAAAGAGTCATTGG 59.427 50.000 0.00 0.00 0.00 3.16
1299 1955 3.988976 TGGAGAGGGAAAGAGTCATTG 57.011 47.619 0.00 0.00 0.00 2.82
1300 1956 3.133721 CGATGGAGAGGGAAAGAGTCATT 59.866 47.826 0.00 0.00 0.00 2.57
1301 1957 2.697751 CGATGGAGAGGGAAAGAGTCAT 59.302 50.000 0.00 0.00 0.00 3.06
1302 1958 2.103373 CGATGGAGAGGGAAAGAGTCA 58.897 52.381 0.00 0.00 0.00 3.41
1303 1959 1.202475 GCGATGGAGAGGGAAAGAGTC 60.202 57.143 0.00 0.00 0.00 3.36
1304 1960 0.827368 GCGATGGAGAGGGAAAGAGT 59.173 55.000 0.00 0.00 0.00 3.24
1305 1961 0.826715 TGCGATGGAGAGGGAAAGAG 59.173 55.000 0.00 0.00 0.00 2.85
1306 1962 1.275666 TTGCGATGGAGAGGGAAAGA 58.724 50.000 0.00 0.00 0.00 2.52
1307 1963 2.113860 TTTGCGATGGAGAGGGAAAG 57.886 50.000 0.00 0.00 0.00 2.62
1308 1964 2.577606 TTTTGCGATGGAGAGGGAAA 57.422 45.000 0.00 0.00 0.00 3.13
1309 1965 2.577606 TTTTTGCGATGGAGAGGGAA 57.422 45.000 0.00 0.00 0.00 3.97
1349 2005 3.160269 AGTCATTGGCTGCTAGCTTTTT 58.840 40.909 17.23 0.00 41.99 1.94
1350 2006 2.800250 AGTCATTGGCTGCTAGCTTTT 58.200 42.857 17.23 0.00 41.99 2.27
1351 2007 2.503895 AGTCATTGGCTGCTAGCTTT 57.496 45.000 17.23 0.00 41.99 3.51
1352 2008 2.363683 GAAGTCATTGGCTGCTAGCTT 58.636 47.619 17.23 0.00 41.99 3.74
1353 2009 1.407989 GGAAGTCATTGGCTGCTAGCT 60.408 52.381 17.23 0.00 41.99 3.32
1354 2010 1.020437 GGAAGTCATTGGCTGCTAGC 58.980 55.000 8.10 8.10 41.46 3.42
1355 2011 1.673168 GGGAAGTCATTGGCTGCTAG 58.327 55.000 0.00 0.00 0.00 3.42
1356 2012 0.255890 GGGGAAGTCATTGGCTGCTA 59.744 55.000 0.00 0.00 0.00 3.49
1357 2013 1.000396 GGGGAAGTCATTGGCTGCT 60.000 57.895 0.00 0.00 0.00 4.24
1358 2014 0.255890 TAGGGGAAGTCATTGGCTGC 59.744 55.000 0.00 0.00 0.00 5.25
1359 2015 2.806945 TTAGGGGAAGTCATTGGCTG 57.193 50.000 0.00 0.00 0.00 4.85
1360 2016 3.825908 TTTTAGGGGAAGTCATTGGCT 57.174 42.857 0.00 0.00 0.00 4.75
1380 2036 2.892852 TGTCATTGGCTGCTAGCTTTTT 59.107 40.909 17.23 0.00 41.99 1.94
1381 2037 2.490903 CTGTCATTGGCTGCTAGCTTTT 59.509 45.455 17.23 0.00 41.99 2.27
1382 2038 2.089980 CTGTCATTGGCTGCTAGCTTT 58.910 47.619 17.23 0.00 41.99 3.51
1383 2039 1.004044 ACTGTCATTGGCTGCTAGCTT 59.996 47.619 17.23 0.00 41.99 3.74
1384 2040 0.617413 ACTGTCATTGGCTGCTAGCT 59.383 50.000 17.23 0.00 41.99 3.32
1385 2041 0.731417 CACTGTCATTGGCTGCTAGC 59.269 55.000 8.10 8.10 41.46 3.42
1386 2042 1.065926 TCCACTGTCATTGGCTGCTAG 60.066 52.381 4.33 0.00 33.71 3.42
1387 2043 0.983467 TCCACTGTCATTGGCTGCTA 59.017 50.000 4.33 0.00 33.71 3.49
1388 2044 0.607489 GTCCACTGTCATTGGCTGCT 60.607 55.000 4.33 0.00 33.71 4.24
1389 2045 1.589716 GGTCCACTGTCATTGGCTGC 61.590 60.000 4.33 0.00 33.71 5.25
1390 2046 0.962356 GGGTCCACTGTCATTGGCTG 60.962 60.000 4.33 0.00 33.71 4.85
1391 2047 1.380302 GGGTCCACTGTCATTGGCT 59.620 57.895 4.33 0.00 33.71 4.75
1392 2048 2.040544 CGGGTCCACTGTCATTGGC 61.041 63.158 4.33 0.58 33.71 4.52
1393 2049 1.377202 CCGGGTCCACTGTCATTGG 60.377 63.158 2.77 2.77 35.18 3.16
1394 2050 2.040544 GCCGGGTCCACTGTCATTG 61.041 63.158 2.18 0.00 0.00 2.82
1395 2051 2.351276 GCCGGGTCCACTGTCATT 59.649 61.111 2.18 0.00 0.00 2.57
1396 2052 4.082523 CGCCGGGTCCACTGTCAT 62.083 66.667 2.18 0.00 0.00 3.06
1405 2061 4.681978 AACAGAGTGCGCCGGGTC 62.682 66.667 4.18 0.00 0.00 4.46
1406 2062 4.988598 CAACAGAGTGCGCCGGGT 62.989 66.667 4.18 0.00 0.00 5.28
1407 2063 4.680237 TCAACAGAGTGCGCCGGG 62.680 66.667 4.18 0.00 0.00 5.73
1408 2064 3.414700 GTCAACAGAGTGCGCCGG 61.415 66.667 4.18 0.00 0.00 6.13
1409 2065 2.356313 AGTCAACAGAGTGCGCCG 60.356 61.111 4.18 0.00 0.00 6.46
1410 2066 2.320587 CCAGTCAACAGAGTGCGCC 61.321 63.158 4.18 0.00 32.51 6.53
1411 2067 1.560860 GACCAGTCAACAGAGTGCGC 61.561 60.000 0.00 0.00 32.51 6.09
1412 2068 0.946221 GGACCAGTCAACAGAGTGCG 60.946 60.000 0.00 0.00 32.51 5.34
1413 2069 0.106708 TGGACCAGTCAACAGAGTGC 59.893 55.000 0.00 0.00 32.51 4.40
1414 2070 1.869754 CGTGGACCAGTCAACAGAGTG 60.870 57.143 6.16 0.00 33.09 3.51
1415 2071 0.389391 CGTGGACCAGTCAACAGAGT 59.611 55.000 6.16 0.00 33.09 3.24
1416 2072 0.389391 ACGTGGACCAGTCAACAGAG 59.611 55.000 6.16 0.00 33.09 3.35
1417 2073 0.104120 CACGTGGACCAGTCAACAGA 59.896 55.000 7.95 0.00 33.09 3.41
1418 2074 0.104120 TCACGTGGACCAGTCAACAG 59.896 55.000 17.00 1.80 33.09 3.16
1419 2075 0.179094 GTCACGTGGACCAGTCAACA 60.179 55.000 17.00 0.00 40.83 3.33
1420 2076 2.601562 GTCACGTGGACCAGTCAAC 58.398 57.895 17.00 0.00 40.83 3.18
1428 2084 0.942252 GTCAAAAGGGTCACGTGGAC 59.058 55.000 17.00 12.21 46.20 4.02
1429 2085 0.179040 GGTCAAAAGGGTCACGTGGA 60.179 55.000 17.00 0.00 0.00 4.02
1430 2086 0.464735 TGGTCAAAAGGGTCACGTGG 60.465 55.000 17.00 0.00 0.00 4.94
1431 2087 1.535462 GATGGTCAAAAGGGTCACGTG 59.465 52.381 9.94 9.94 0.00 4.49
1432 2088 1.142060 TGATGGTCAAAAGGGTCACGT 59.858 47.619 0.00 0.00 0.00 4.49
1433 2089 1.535462 GTGATGGTCAAAAGGGTCACG 59.465 52.381 0.00 0.00 0.00 4.35
1434 2090 1.886542 GGTGATGGTCAAAAGGGTCAC 59.113 52.381 0.00 0.00 36.22 3.67
1435 2091 1.496857 TGGTGATGGTCAAAAGGGTCA 59.503 47.619 0.00 0.00 0.00 4.02
1436 2092 1.886542 GTGGTGATGGTCAAAAGGGTC 59.113 52.381 0.00 0.00 0.00 4.46
1437 2093 1.817740 CGTGGTGATGGTCAAAAGGGT 60.818 52.381 0.00 0.00 0.00 4.34
1438 2094 0.881118 CGTGGTGATGGTCAAAAGGG 59.119 55.000 0.00 0.00 0.00 3.95
1439 2095 0.240945 GCGTGGTGATGGTCAAAAGG 59.759 55.000 0.00 0.00 0.00 3.11
1440 2096 0.110238 CGCGTGGTGATGGTCAAAAG 60.110 55.000 0.00 0.00 0.00 2.27
1441 2097 1.945522 CGCGTGGTGATGGTCAAAA 59.054 52.632 0.00 0.00 0.00 2.44
1442 2098 2.612567 GCGCGTGGTGATGGTCAAA 61.613 57.895 8.43 0.00 0.00 2.69
1443 2099 3.047280 GCGCGTGGTGATGGTCAA 61.047 61.111 8.43 0.00 0.00 3.18
1446 2102 3.986739 TATTTGGCGCGTGGTGATGGT 62.987 52.381 8.43 0.00 0.00 3.55
1447 2103 1.372838 TATTTGGCGCGTGGTGATGG 61.373 55.000 8.43 0.00 0.00 3.51
1448 2104 0.027979 CTATTTGGCGCGTGGTGATG 59.972 55.000 8.43 0.00 0.00 3.07
1449 2105 0.392461 ACTATTTGGCGCGTGGTGAT 60.392 50.000 8.43 0.00 0.00 3.06
1450 2106 0.604243 AACTATTTGGCGCGTGGTGA 60.604 50.000 8.43 0.00 0.00 4.02
1451 2107 0.239879 AAACTATTTGGCGCGTGGTG 59.760 50.000 8.43 0.00 0.00 4.17
1452 2108 0.519961 GAAACTATTTGGCGCGTGGT 59.480 50.000 8.43 0.00 0.00 4.16
1453 2109 0.802494 AGAAACTATTTGGCGCGTGG 59.198 50.000 8.43 0.00 0.00 4.94
1454 2110 1.465689 CCAGAAACTATTTGGCGCGTG 60.466 52.381 8.43 0.00 0.00 5.34
1455 2111 0.802494 CCAGAAACTATTTGGCGCGT 59.198 50.000 8.43 0.00 0.00 6.01
1456 2112 0.523335 GCCAGAAACTATTTGGCGCG 60.523 55.000 0.00 0.00 46.82 6.86
1457 2113 3.329114 GCCAGAAACTATTTGGCGC 57.671 52.632 0.00 0.00 46.82 6.53
1496 2152 8.850156 GGAGAACAAGTGCCACATTTATATATT 58.150 33.333 0.00 0.00 0.00 1.28
1497 2153 8.220559 AGGAGAACAAGTGCCACATTTATATAT 58.779 33.333 0.00 0.00 0.00 0.86
1498 2154 7.573710 AGGAGAACAAGTGCCACATTTATATA 58.426 34.615 0.00 0.00 0.00 0.86
1499 2155 6.426587 AGGAGAACAAGTGCCACATTTATAT 58.573 36.000 0.00 0.00 0.00 0.86
1500 2156 5.815581 AGGAGAACAAGTGCCACATTTATA 58.184 37.500 0.00 0.00 0.00 0.98
1501 2157 4.666512 AGGAGAACAAGTGCCACATTTAT 58.333 39.130 0.00 0.00 0.00 1.40
1502 2158 4.098914 AGGAGAACAAGTGCCACATTTA 57.901 40.909 0.00 0.00 0.00 1.40
1503 2159 2.949447 AGGAGAACAAGTGCCACATTT 58.051 42.857 0.00 0.00 0.00 2.32
1504 2160 2.664402 AGGAGAACAAGTGCCACATT 57.336 45.000 0.00 0.00 0.00 2.71
1505 2161 3.788227 TTAGGAGAACAAGTGCCACAT 57.212 42.857 0.00 0.00 0.00 3.21
1506 2162 3.569194 TTTAGGAGAACAAGTGCCACA 57.431 42.857 0.00 0.00 0.00 4.17
1507 2163 4.097286 TGTTTTTAGGAGAACAAGTGCCAC 59.903 41.667 0.00 0.00 33.19 5.01
1508 2164 4.274147 TGTTTTTAGGAGAACAAGTGCCA 58.726 39.130 0.00 0.00 33.19 4.92
1509 2165 4.911514 TGTTTTTAGGAGAACAAGTGCC 57.088 40.909 0.00 0.00 33.19 5.01
1510 2166 4.733405 CGTTGTTTTTAGGAGAACAAGTGC 59.267 41.667 2.25 0.00 43.90 4.40
1511 2167 5.065474 TCCGTTGTTTTTAGGAGAACAAGTG 59.935 40.000 2.25 0.00 43.90 3.16
1512 2168 5.187687 TCCGTTGTTTTTAGGAGAACAAGT 58.812 37.500 2.25 0.00 43.90 3.16
1513 2169 5.744666 TCCGTTGTTTTTAGGAGAACAAG 57.255 39.130 2.25 0.00 43.90 3.16
1520 2176 3.328343 TCCCATCTCCGTTGTTTTTAGGA 59.672 43.478 0.00 0.00 0.00 2.94
1521 2177 3.681593 TCCCATCTCCGTTGTTTTTAGG 58.318 45.455 0.00 0.00 0.00 2.69
1522 2178 4.034048 CGATCCCATCTCCGTTGTTTTTAG 59.966 45.833 0.00 0.00 0.00 1.85
1523 2179 3.936453 CGATCCCATCTCCGTTGTTTTTA 59.064 43.478 0.00 0.00 0.00 1.52
1524 2180 2.747446 CGATCCCATCTCCGTTGTTTTT 59.253 45.455 0.00 0.00 0.00 1.94
1525 2181 2.027561 TCGATCCCATCTCCGTTGTTTT 60.028 45.455 0.00 0.00 0.00 2.43
1526 2182 1.553248 TCGATCCCATCTCCGTTGTTT 59.447 47.619 0.00 0.00 0.00 2.83
1527 2183 1.191535 TCGATCCCATCTCCGTTGTT 58.808 50.000 0.00 0.00 0.00 2.83
1528 2184 1.069204 CATCGATCCCATCTCCGTTGT 59.931 52.381 0.00 0.00 0.00 3.32
1529 2185 1.606480 CCATCGATCCCATCTCCGTTG 60.606 57.143 0.00 0.00 0.00 4.10
1530 2186 0.681733 CCATCGATCCCATCTCCGTT 59.318 55.000 0.00 0.00 0.00 4.44
1531 2187 0.178961 TCCATCGATCCCATCTCCGT 60.179 55.000 0.00 0.00 0.00 4.69
1532 2188 1.189752 ATCCATCGATCCCATCTCCG 58.810 55.000 0.00 0.00 0.00 4.63
1533 2189 3.963374 TCATATCCATCGATCCCATCTCC 59.037 47.826 0.00 0.00 0.00 3.71
1534 2190 4.501229 GCTCATATCCATCGATCCCATCTC 60.501 50.000 0.00 0.00 0.00 2.75
1535 2191 3.387374 GCTCATATCCATCGATCCCATCT 59.613 47.826 0.00 0.00 0.00 2.90
1536 2192 3.133542 TGCTCATATCCATCGATCCCATC 59.866 47.826 0.00 0.00 0.00 3.51
1541 2197 4.814147 TGAACTGCTCATATCCATCGATC 58.186 43.478 0.00 0.00 0.00 3.69
1570 2226 1.135527 CATCCAACTACGAACGCCCTA 59.864 52.381 0.00 0.00 0.00 3.53
1573 2229 0.108520 TCCATCCAACTACGAACGCC 60.109 55.000 0.00 0.00 0.00 5.68
1579 2243 1.418342 CGGCGTTCCATCCAACTACG 61.418 60.000 0.00 0.00 35.48 3.51
1580 2244 1.702491 GCGGCGTTCCATCCAACTAC 61.702 60.000 9.37 0.00 0.00 2.73
1582 2246 2.746277 GCGGCGTTCCATCCAACT 60.746 61.111 9.37 0.00 0.00 3.16
1584 2248 2.435938 GAGCGGCGTTCCATCCAA 60.436 61.111 13.07 0.00 0.00 3.53
1585 2249 4.467084 GGAGCGGCGTTCCATCCA 62.467 66.667 33.58 0.00 37.65 3.41
1606 2270 2.674357 GTCGTTAAAATTAGCGGCCTGA 59.326 45.455 0.00 0.00 36.24 3.86
1608 2272 2.934553 GAGTCGTTAAAATTAGCGGCCT 59.065 45.455 9.82 6.39 41.83 5.19
1609 2273 2.031314 GGAGTCGTTAAAATTAGCGGCC 59.969 50.000 9.82 0.00 41.83 6.13
1610 2274 2.031314 GGGAGTCGTTAAAATTAGCGGC 59.969 50.000 5.99 5.99 41.33 6.53
1613 2277 3.063045 CACGGGGAGTCGTTAAAATTAGC 59.937 47.826 0.00 0.00 41.86 3.09
1614 2278 4.248058 ACACGGGGAGTCGTTAAAATTAG 58.752 43.478 0.00 0.00 41.86 1.73
1616 2280 3.130280 ACACGGGGAGTCGTTAAAATT 57.870 42.857 0.00 0.00 41.86 1.82
1617 2281 2.845363 ACACGGGGAGTCGTTAAAAT 57.155 45.000 0.00 0.00 41.86 1.82
1634 2348 3.552384 ACGCGAGTGGGGGAAACA 61.552 61.111 15.93 0.00 46.97 2.83
1870 2659 0.901827 TTTAGCACTCGATCAGCCCA 59.098 50.000 0.00 0.00 0.00 5.36
1871 2660 2.139118 GATTTAGCACTCGATCAGCCC 58.861 52.381 0.00 0.00 0.00 5.19
1872 2661 3.104843 AGATTTAGCACTCGATCAGCC 57.895 47.619 0.00 0.00 0.00 4.85
1873 2662 6.414890 GTTTTAGATTTAGCACTCGATCAGC 58.585 40.000 0.00 0.00 0.00 4.26
1874 2663 6.291849 CGGTTTTAGATTTAGCACTCGATCAG 60.292 42.308 0.00 0.00 0.00 2.90
1875 2664 5.518847 CGGTTTTAGATTTAGCACTCGATCA 59.481 40.000 0.00 0.00 0.00 2.92
1946 3393 0.250989 GTTCCATTCCGGGTTGGTGA 60.251 55.000 19.21 9.69 39.52 4.02
2327 3792 3.056465 AGAGACCTTGTCGTCTTTCCATC 60.056 47.826 0.00 0.00 43.22 3.51
2339 3804 4.503991 GGACAATGTTCTGAGAGACCTTGT 60.504 45.833 13.54 13.54 0.00 3.16
2491 3972 4.890158 TTCATAGTTCACAGAGGAAGCA 57.110 40.909 0.00 0.00 0.00 3.91
2505 3986 5.354234 CCAGGACGTTGCTTATTTTCATAGT 59.646 40.000 0.00 0.00 0.00 2.12
2551 4032 2.958355 GCATGCCTTACATAACACCCAT 59.042 45.455 6.36 0.00 36.64 4.00
2597 4078 8.082242 GCAGAACCAAAACTATAAACAGACATT 58.918 33.333 0.00 0.00 0.00 2.71
2666 4151 9.828691 TCCAGATCATCCTATTTCTAGTTGATA 57.171 33.333 0.00 0.00 31.30 2.15
2813 4298 1.703438 GCGTTCTCTCTGGCATGCTG 61.703 60.000 18.92 11.12 0.00 4.41
2819 4304 1.569479 GGTTGTGCGTTCTCTCTGGC 61.569 60.000 0.00 0.00 0.00 4.85
2822 4307 0.387929 TTCGGTTGTGCGTTCTCTCT 59.612 50.000 0.00 0.00 0.00 3.10
3347 4930 4.141181 AGCATAAACCCCAATCTAGATGCA 60.141 41.667 5.86 0.00 40.65 3.96



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

AutoCloner maintained by Alex Coulton.