Multiple sequence alignment - TraesCS1A01G422500

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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 TraesCS1A01G422500 chr1A 100.000 3918 0 0 1 3918 577984321 577988238 0.000000e+00 7236.0
1 TraesCS1A01G422500 chr1A 82.723 1366 190 25 1176 2536 578208263 578206939 0.000000e+00 1173.0
2 TraesCS1A01G422500 chr1A 100.000 28 0 0 1508 1535 410156049 410156076 7.000000e-03 52.8
3 TraesCS1A01G422500 chr1D 94.996 2498 100 15 1119 3604 481550665 481553149 0.000000e+00 3897.0
4 TraesCS1A01G422500 chr1D 91.534 2008 133 12 1177 3172 481453708 481451726 0.000000e+00 2732.0
5 TraesCS1A01G422500 chr1D 82.331 1364 195 24 1176 2534 481501629 481500307 0.000000e+00 1142.0
6 TraesCS1A01G422500 chr1D 84.028 576 69 20 389 950 387803208 387802642 2.070000e-147 532.0
7 TraesCS1A01G422500 chr1D 85.593 118 16 1 1247 1364 481489247 481489131 5.320000e-24 122.0
8 TraesCS1A01G422500 chr1D 96.667 60 2 0 3649 3708 257406444 257406385 2.490000e-17 100.0
9 TraesCS1A01G422500 chr1D 100.000 28 0 0 1508 1535 326909113 326909086 7.000000e-03 52.8
10 TraesCS1A01G422500 chr1B 93.640 2044 105 10 994 3032 669922601 669924624 0.000000e+00 3031.0
11 TraesCS1A01G422500 chr1B 85.479 1818 204 25 1176 2962 670159100 670160888 0.000000e+00 1840.0
12 TraesCS1A01G422500 chr1B 83.438 1117 160 17 1176 2287 670142837 670143933 0.000000e+00 1014.0
13 TraesCS1A01G422500 chr1B 85.000 560 65 17 401 951 517914388 517913839 5.720000e-153 551.0
14 TraesCS1A01G422500 chr1B 82.637 622 81 21 344 951 383913609 383914217 3.470000e-145 525.0
15 TraesCS1A01G422500 chr1B 80.866 554 88 13 78 621 517914845 517914300 1.680000e-113 420.0
16 TraesCS1A01G422500 chr1B 80.586 546 92 9 71 611 383913230 383913766 3.640000e-110 409.0
17 TraesCS1A01G422500 chr7A 81.222 884 125 27 72 945 675126780 675125928 0.000000e+00 675.0
18 TraesCS1A01G422500 chr7A 90.455 220 18 2 3218 3435 459003741 459003523 1.780000e-73 287.0
19 TraesCS1A01G422500 chr7A 88.158 228 25 1 3218 3443 74641899 74642126 1.790000e-68 270.0
20 TraesCS1A01G422500 chr7A 95.312 64 3 0 3645 3708 509225250 509225187 6.930000e-18 102.0
21 TraesCS1A01G422500 chr5A 85.612 556 60 16 406 951 417052538 417051993 2.040000e-157 566.0
22 TraesCS1A01G422500 chr5A 92.035 226 15 2 3693 3918 328932895 328933117 8.170000e-82 315.0
23 TraesCS1A01G422500 chr5A 90.171 234 21 1 3218 3449 694506901 694506668 1.770000e-78 303.0
24 TraesCS1A01G422500 chr5A 92.462 199 14 1 3219 3417 22060588 22060785 2.300000e-72 283.0
25 TraesCS1A01G422500 chr5A 88.496 226 12 5 3694 3918 328934008 328934220 1.080000e-65 261.0
26 TraesCS1A01G422500 chr5A 93.407 91 6 0 3828 3918 470764075 470763985 6.830000e-28 135.0
27 TraesCS1A01G422500 chr3D 79.720 858 110 38 76 915 584814494 584813683 2.640000e-156 562.0
28 TraesCS1A01G422500 chr3D 82.474 582 73 10 75 653 537044600 537045155 2.120000e-132 483.0
29 TraesCS1A01G422500 chr7D 84.886 569 70 15 393 950 400194913 400195476 9.510000e-156 560.0
30 TraesCS1A01G422500 chr7D 95.385 65 3 0 3644 3708 119776221 119776157 1.930000e-18 104.0
31 TraesCS1A01G422500 chr7D 92.188 64 5 0 3645 3708 19023216 19023279 1.500000e-14 91.6
32 TraesCS1A01G422500 chr7B 84.838 554 66 15 406 951 590462379 590461836 3.440000e-150 542.0
33 TraesCS1A01G422500 chr7B 84.229 558 69 15 401 950 139161659 139161113 3.470000e-145 525.0
34 TraesCS1A01G422500 chr7B 84.324 555 66 16 406 950 649462407 649462950 1.250000e-144 523.0
35 TraesCS1A01G422500 chr7B 81.212 495 76 11 74 557 485039145 485039633 2.210000e-102 383.0
36 TraesCS1A01G422500 chr7B 81.579 228 37 3 2534 2760 520417958 520418181 2.400000e-42 183.0
37 TraesCS1A01G422500 chr3B 80.576 556 92 12 75 621 15992324 15992872 7.830000e-112 414.0
38 TraesCS1A01G422500 chr3B 89.189 111 12 0 73 183 258165103 258164993 5.280000e-29 139.0
39 TraesCS1A01G422500 chr2B 79.891 552 97 10 78 621 170089759 170089214 3.670000e-105 392.0
40 TraesCS1A01G422500 chr2B 77.083 384 61 14 2122 2499 245130048 245130410 3.090000e-46 196.0
41 TraesCS1A01G422500 chr2B 85.965 114 16 0 2356 2469 245130613 245130726 5.320000e-24 122.0
42 TraesCS1A01G422500 chr4A 92.308 273 15 2 3651 3918 584419351 584419622 2.210000e-102 383.0
43 TraesCS1A01G422500 chr6B 79.603 554 95 14 78 621 494097428 494096883 7.940000e-102 381.0
44 TraesCS1A01G422500 chr6A 93.574 249 12 4 3635 3882 408020507 408020752 6.180000e-98 368.0
45 TraesCS1A01G422500 chr6A 90.351 228 20 1 3218 3443 76667293 76667520 8.230000e-77 298.0
46 TraesCS1A01G422500 chr2D 90.717 237 19 2 3216 3450 407952570 407952805 2.940000e-81 313.0
47 TraesCS1A01G422500 chr2A 88.889 234 24 1 3218 3449 613140178 613139945 1.780000e-73 287.0
48 TraesCS1A01G422500 chr4B 86.383 235 28 3 3218 3449 40607340 40607107 1.810000e-63 254.0
49 TraesCS1A01G422500 chr6D 95.312 64 3 0 3645 3708 8402668 8402731 6.930000e-18 102.0
50 TraesCS1A01G422500 chr6D 95.312 64 3 0 3645 3708 81737005 81736942 6.930000e-18 102.0


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 TraesCS1A01G422500 chr1A 577984321 577988238 3917 False 7236.0 7236 100.0000 1 3918 1 chr1A.!!$F2 3917
1 TraesCS1A01G422500 chr1A 578206939 578208263 1324 True 1173.0 1173 82.7230 1176 2536 1 chr1A.!!$R1 1360
2 TraesCS1A01G422500 chr1D 481550665 481553149 2484 False 3897.0 3897 94.9960 1119 3604 1 chr1D.!!$F1 2485
3 TraesCS1A01G422500 chr1D 481451726 481453708 1982 True 2732.0 2732 91.5340 1177 3172 1 chr1D.!!$R4 1995
4 TraesCS1A01G422500 chr1D 481500307 481501629 1322 True 1142.0 1142 82.3310 1176 2534 1 chr1D.!!$R6 1358
5 TraesCS1A01G422500 chr1D 387802642 387803208 566 True 532.0 532 84.0280 389 950 1 chr1D.!!$R3 561
6 TraesCS1A01G422500 chr1B 669922601 669924624 2023 False 3031.0 3031 93.6400 994 3032 1 chr1B.!!$F1 2038
7 TraesCS1A01G422500 chr1B 670159100 670160888 1788 False 1840.0 1840 85.4790 1176 2962 1 chr1B.!!$F3 1786
8 TraesCS1A01G422500 chr1B 670142837 670143933 1096 False 1014.0 1014 83.4380 1176 2287 1 chr1B.!!$F2 1111
9 TraesCS1A01G422500 chr1B 517913839 517914845 1006 True 485.5 551 82.9330 78 951 2 chr1B.!!$R1 873
10 TraesCS1A01G422500 chr1B 383913230 383914217 987 False 467.0 525 81.6115 71 951 2 chr1B.!!$F4 880
11 TraesCS1A01G422500 chr7A 675125928 675126780 852 True 675.0 675 81.2220 72 945 1 chr7A.!!$R3 873
12 TraesCS1A01G422500 chr5A 417051993 417052538 545 True 566.0 566 85.6120 406 951 1 chr5A.!!$R1 545
13 TraesCS1A01G422500 chr5A 328932895 328934220 1325 False 288.0 315 90.2655 3693 3918 2 chr5A.!!$F2 225
14 TraesCS1A01G422500 chr3D 584813683 584814494 811 True 562.0 562 79.7200 76 915 1 chr3D.!!$R1 839
15 TraesCS1A01G422500 chr3D 537044600 537045155 555 False 483.0 483 82.4740 75 653 1 chr3D.!!$F1 578
16 TraesCS1A01G422500 chr7D 400194913 400195476 563 False 560.0 560 84.8860 393 950 1 chr7D.!!$F2 557
17 TraesCS1A01G422500 chr7B 590461836 590462379 543 True 542.0 542 84.8380 406 951 1 chr7B.!!$R2 545
18 TraesCS1A01G422500 chr7B 139161113 139161659 546 True 525.0 525 84.2290 401 950 1 chr7B.!!$R1 549
19 TraesCS1A01G422500 chr7B 649462407 649462950 543 False 523.0 523 84.3240 406 950 1 chr7B.!!$F3 544
20 TraesCS1A01G422500 chr3B 15992324 15992872 548 False 414.0 414 80.5760 75 621 1 chr3B.!!$F1 546
21 TraesCS1A01G422500 chr2B 170089214 170089759 545 True 392.0 392 79.8910 78 621 1 chr2B.!!$R1 543
22 TraesCS1A01G422500 chr6B 494096883 494097428 545 True 381.0 381 79.6030 78 621 1 chr6B.!!$R1 543

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
982 1155 0.247736 GTGAGGAATCCGTGCTGACT 59.752 55.0 0.0 0.0 28.94 3.41 F
1019 1192 0.105760 ATGAGCCGTCTCCTCCTCAT 60.106 55.0 0.0 0.0 39.51 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2474 2652 0.239347 GCTGAAGTCGCATGCACTTT 59.761 50.000 25.81 14.52 34.10 2.66 R
2973 3203 1.069204 TGACAGCAGAGGATAATCCGC 59.931 52.381 0.00 0.00 42.75 5.54 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
17 18 3.590824 GACATTTGGAGCACCGGG 58.409 61.111 6.32 0.00 39.42 5.73
18 19 1.002624 GACATTTGGAGCACCGGGA 60.003 57.895 6.32 0.00 39.42 5.14
19 20 1.002134 ACATTTGGAGCACCGGGAG 60.002 57.895 6.32 0.00 39.42 4.30
20 21 2.044946 ATTTGGAGCACCGGGAGC 60.045 61.111 6.32 10.14 39.42 4.70
21 22 2.905996 ATTTGGAGCACCGGGAGCA 61.906 57.895 21.10 2.67 39.42 4.26
22 23 3.842925 TTTGGAGCACCGGGAGCAC 62.843 63.158 21.10 15.32 39.42 4.40
42 43 2.859165 CCAAGTTTGGGAGCACTAGA 57.141 50.000 0.00 0.00 44.70 2.43
43 44 3.356529 CCAAGTTTGGGAGCACTAGAT 57.643 47.619 0.00 0.00 44.70 1.98
44 45 4.487714 CCAAGTTTGGGAGCACTAGATA 57.512 45.455 0.00 0.00 44.70 1.98
45 46 5.041191 CCAAGTTTGGGAGCACTAGATAT 57.959 43.478 0.00 0.00 44.70 1.63
46 47 5.440610 CCAAGTTTGGGAGCACTAGATATT 58.559 41.667 0.00 0.00 44.70 1.28
47 48 5.888161 CCAAGTTTGGGAGCACTAGATATTT 59.112 40.000 0.00 0.00 44.70 1.40
48 49 6.378280 CCAAGTTTGGGAGCACTAGATATTTT 59.622 38.462 0.00 0.00 44.70 1.82
49 50 7.415653 CCAAGTTTGGGAGCACTAGATATTTTC 60.416 40.741 0.00 0.00 44.70 2.29
50 51 6.122964 AGTTTGGGAGCACTAGATATTTTCC 58.877 40.000 0.00 0.00 0.00 3.13
51 52 4.706842 TGGGAGCACTAGATATTTTCCC 57.293 45.455 0.00 4.81 42.49 3.97
52 53 3.394606 TGGGAGCACTAGATATTTTCCCC 59.605 47.826 0.00 0.00 41.67 4.81
53 54 3.557264 GGGAGCACTAGATATTTTCCCCG 60.557 52.174 0.00 0.00 37.42 5.73
54 55 3.323979 GGAGCACTAGATATTTTCCCCGA 59.676 47.826 0.00 0.00 0.00 5.14
55 56 4.561105 GAGCACTAGATATTTTCCCCGAG 58.439 47.826 0.00 0.00 0.00 4.63
56 57 3.067833 GCACTAGATATTTTCCCCGAGC 58.932 50.000 0.00 0.00 0.00 5.03
57 58 3.494398 GCACTAGATATTTTCCCCGAGCA 60.494 47.826 0.00 0.00 0.00 4.26
58 59 4.804261 GCACTAGATATTTTCCCCGAGCAT 60.804 45.833 0.00 0.00 0.00 3.79
59 60 4.692625 CACTAGATATTTTCCCCGAGCATG 59.307 45.833 0.00 0.00 0.00 4.06
60 61 3.146104 AGATATTTTCCCCGAGCATGG 57.854 47.619 0.00 0.00 0.00 3.66
61 62 2.711009 AGATATTTTCCCCGAGCATGGA 59.289 45.455 0.00 0.00 0.00 3.41
62 63 3.138283 AGATATTTTCCCCGAGCATGGAA 59.862 43.478 0.00 0.00 38.84 3.53
63 64 1.474330 ATTTTCCCCGAGCATGGAAC 58.526 50.000 0.00 0.00 40.27 3.62
64 65 0.958382 TTTTCCCCGAGCATGGAACG 60.958 55.000 0.00 0.00 40.27 3.95
65 66 1.832719 TTTCCCCGAGCATGGAACGA 61.833 55.000 0.00 0.00 40.27 3.85
66 67 2.511600 CCCCGAGCATGGAACGAC 60.512 66.667 0.00 0.00 0.00 4.34
67 68 2.579201 CCCGAGCATGGAACGACT 59.421 61.111 0.00 0.00 0.00 4.18
68 69 1.079127 CCCGAGCATGGAACGACTT 60.079 57.895 0.00 0.00 0.00 3.01
69 70 1.361668 CCCGAGCATGGAACGACTTG 61.362 60.000 0.00 0.00 0.00 3.16
70 71 1.361668 CCGAGCATGGAACGACTTGG 61.362 60.000 0.00 0.00 0.00 3.61
71 72 1.796796 GAGCATGGAACGACTTGGC 59.203 57.895 0.00 0.00 0.00 4.52
72 73 1.648467 GAGCATGGAACGACTTGGCC 61.648 60.000 0.00 0.00 0.00 5.36
73 74 1.675641 GCATGGAACGACTTGGCCT 60.676 57.895 3.32 0.00 0.00 5.19
101 104 1.686325 CCTATAGGCCGCCTGTGTGT 61.686 60.000 22.95 5.38 34.61 3.72
172 180 2.080693 TCATCACGCCGTAAGCAAAAT 58.919 42.857 0.00 0.00 44.04 1.82
223 232 1.026718 CGAACCTCCAACCTCATGCC 61.027 60.000 0.00 0.00 0.00 4.40
275 284 8.910944 AGTTAGCTACCTCGAACATTCTAAATA 58.089 33.333 0.00 0.00 0.00 1.40
276 285 9.525409 GTTAGCTACCTCGAACATTCTAAATAA 57.475 33.333 0.00 0.00 0.00 1.40
302 312 4.567159 CGCCCAGCTTAAAGTAGAAAGTAG 59.433 45.833 0.00 0.00 0.00 2.57
318 330 6.071320 AGAAAGTAGAGTGGCAAATCCTTTT 58.929 36.000 0.00 0.00 35.26 2.27
319 331 6.551227 AGAAAGTAGAGTGGCAAATCCTTTTT 59.449 34.615 0.00 0.00 35.26 1.94
373 410 9.842444 CGTTGAACAAATTTTAAAATACAGTGG 57.158 29.630 13.68 0.00 0.00 4.00
391 475 7.302350 ACAGTGGTTTTTGTAAAAGAAATGC 57.698 32.000 0.00 0.00 0.00 3.56
567 717 7.546667 ACATGATGGACATTTTTATCTTGCAAC 59.453 33.333 0.00 0.00 37.07 4.17
590 740 9.512287 CAACGTGAACTATTTCATAATATACGC 57.488 33.333 0.00 0.00 43.72 4.42
633 783 5.176407 TGAAGATTTTTGTAACACACGGG 57.824 39.130 0.00 0.00 0.00 5.28
675 831 5.882557 ACGCAATAATGAGAGGAACAGAAAT 59.117 36.000 0.00 0.00 0.00 2.17
769 931 4.246458 CCCGGAACAAAACAACTGAAAAA 58.754 39.130 0.73 0.00 0.00 1.94
849 1021 5.428184 ACCCCACAAGAAACAATGAAAAA 57.572 34.783 0.00 0.00 0.00 1.94
872 1045 3.874543 ACAACAGCGAACAAATCTGTACA 59.125 39.130 0.00 0.00 39.86 2.90
951 1124 2.024414 GCGTCAAATAGGATTTGCCCT 58.976 47.619 6.99 0.00 40.29 5.19
952 1125 2.427095 GCGTCAAATAGGATTTGCCCTT 59.573 45.455 6.99 0.00 37.74 3.95
953 1126 3.734902 GCGTCAAATAGGATTTGCCCTTG 60.735 47.826 6.99 0.00 37.74 3.61
954 1127 3.181487 CGTCAAATAGGATTTGCCCTTGG 60.181 47.826 6.99 0.00 37.74 3.61
964 1137 3.335711 GCCCTTGGCCTGATAGGT 58.664 61.111 3.32 0.00 44.06 3.08
965 1138 1.152881 GCCCTTGGCCTGATAGGTG 60.153 63.158 3.32 1.77 44.06 4.00
966 1139 1.635817 GCCCTTGGCCTGATAGGTGA 61.636 60.000 3.32 0.00 44.06 4.02
967 1140 0.471617 CCCTTGGCCTGATAGGTGAG 59.528 60.000 3.32 0.00 37.80 3.51
968 1141 0.471617 CCTTGGCCTGATAGGTGAGG 59.528 60.000 3.32 0.00 37.80 3.86
969 1142 1.500474 CTTGGCCTGATAGGTGAGGA 58.500 55.000 3.32 0.00 37.80 3.71
970 1143 1.839994 CTTGGCCTGATAGGTGAGGAA 59.160 52.381 3.32 0.00 37.80 3.36
971 1144 2.196742 TGGCCTGATAGGTGAGGAAT 57.803 50.000 3.32 0.00 37.80 3.01
972 1145 2.050144 TGGCCTGATAGGTGAGGAATC 58.950 52.381 3.32 0.00 37.80 2.52
973 1146 1.349357 GGCCTGATAGGTGAGGAATCC 59.651 57.143 0.00 0.00 37.80 3.01
974 1147 1.001406 GCCTGATAGGTGAGGAATCCG 59.999 57.143 0.00 0.00 37.80 4.18
975 1148 2.320781 CCTGATAGGTGAGGAATCCGT 58.679 52.381 0.00 0.00 28.79 4.69
976 1149 2.036475 CCTGATAGGTGAGGAATCCGTG 59.964 54.545 0.00 0.00 28.79 4.94
977 1150 1.412710 TGATAGGTGAGGAATCCGTGC 59.587 52.381 0.00 0.00 0.00 5.34
978 1151 1.689273 GATAGGTGAGGAATCCGTGCT 59.311 52.381 0.00 0.00 0.00 4.40
979 1152 0.824109 TAGGTGAGGAATCCGTGCTG 59.176 55.000 0.00 0.00 0.00 4.41
980 1153 0.904865 AGGTGAGGAATCCGTGCTGA 60.905 55.000 0.00 0.00 0.00 4.26
981 1154 0.741221 GGTGAGGAATCCGTGCTGAC 60.741 60.000 0.00 0.00 30.77 3.51
982 1155 0.247736 GTGAGGAATCCGTGCTGACT 59.752 55.000 0.00 0.00 28.94 3.41
983 1156 0.976641 TGAGGAATCCGTGCTGACTT 59.023 50.000 0.00 0.00 0.00 3.01
984 1157 1.347707 TGAGGAATCCGTGCTGACTTT 59.652 47.619 0.00 0.00 0.00 2.66
985 1158 1.734465 GAGGAATCCGTGCTGACTTTG 59.266 52.381 0.00 0.00 0.00 2.77
986 1159 1.072331 AGGAATCCGTGCTGACTTTGT 59.928 47.619 0.00 0.00 0.00 2.83
987 1160 1.880027 GGAATCCGTGCTGACTTTGTT 59.120 47.619 0.00 0.00 0.00 2.83
988 1161 2.293399 GGAATCCGTGCTGACTTTGTTT 59.707 45.455 0.00 0.00 0.00 2.83
989 1162 3.555518 GAATCCGTGCTGACTTTGTTTC 58.444 45.455 0.00 0.00 0.00 2.78
990 1163 2.325583 TCCGTGCTGACTTTGTTTCT 57.674 45.000 0.00 0.00 0.00 2.52
991 1164 2.639065 TCCGTGCTGACTTTGTTTCTT 58.361 42.857 0.00 0.00 0.00 2.52
992 1165 2.612212 TCCGTGCTGACTTTGTTTCTTC 59.388 45.455 0.00 0.00 0.00 2.87
1004 1177 0.371645 GTTTCTTCGGCGCTGATGAG 59.628 55.000 27.49 20.07 0.00 2.90
1018 1191 0.753479 GATGAGCCGTCTCCTCCTCA 60.753 60.000 0.00 0.00 38.58 3.86
1019 1192 0.105760 ATGAGCCGTCTCCTCCTCAT 60.106 55.000 0.00 0.00 39.51 2.90
1023 1196 1.045911 GCCGTCTCCTCCTCATCCTT 61.046 60.000 0.00 0.00 0.00 3.36
1029 1202 0.757188 TCCTCCTCATCCTTCTCGGC 60.757 60.000 0.00 0.00 0.00 5.54
1044 1217 4.619140 GGCGCTGCATTGCCGATC 62.619 66.667 12.95 0.00 42.22 3.69
1054 1227 2.910199 CATTGCCGATCCTCTTCTTCA 58.090 47.619 0.00 0.00 0.00 3.02
1056 1229 1.561643 TGCCGATCCTCTTCTTCACT 58.438 50.000 0.00 0.00 0.00 3.41
1060 1233 2.763448 CCGATCCTCTTCTTCACTCCTT 59.237 50.000 0.00 0.00 0.00 3.36
1070 1243 3.510459 TCTTCACTCCTTCAGGTGATCA 58.490 45.455 1.86 0.00 41.27 2.92
1071 1244 3.259374 TCTTCACTCCTTCAGGTGATCAC 59.741 47.826 17.91 17.91 41.27 3.06
1093 1266 4.303086 GGAGACGTTTCATTCGGAGATA 57.697 45.455 8.50 0.00 35.04 1.98
1094 1267 4.872664 GGAGACGTTTCATTCGGAGATAT 58.127 43.478 8.50 0.00 35.04 1.63
1095 1268 4.681942 GGAGACGTTTCATTCGGAGATATG 59.318 45.833 8.50 0.00 35.04 1.78
1096 1269 5.263968 AGACGTTTCATTCGGAGATATGT 57.736 39.130 0.00 0.00 35.04 2.29
1097 1270 5.043903 AGACGTTTCATTCGGAGATATGTG 58.956 41.667 0.00 0.00 35.04 3.21
1098 1271 4.755411 ACGTTTCATTCGGAGATATGTGT 58.245 39.130 0.00 0.00 35.04 3.72
1099 1272 4.566759 ACGTTTCATTCGGAGATATGTGTG 59.433 41.667 0.00 0.00 35.04 3.82
1100 1273 4.566759 CGTTTCATTCGGAGATATGTGTGT 59.433 41.667 0.00 0.00 35.04 3.72
1101 1274 5.500771 CGTTTCATTCGGAGATATGTGTGTG 60.501 44.000 0.00 0.00 35.04 3.82
1102 1275 4.736126 TCATTCGGAGATATGTGTGTGT 57.264 40.909 0.00 0.00 35.04 3.72
1103 1276 4.432712 TCATTCGGAGATATGTGTGTGTG 58.567 43.478 0.00 0.00 35.04 3.82
1104 1277 3.953712 TTCGGAGATATGTGTGTGTGT 57.046 42.857 0.00 0.00 35.04 3.72
1105 1278 3.503827 TCGGAGATATGTGTGTGTGTC 57.496 47.619 0.00 0.00 0.00 3.67
1136 1309 1.493772 CGCAGGTGTAGTTTCGTGAA 58.506 50.000 0.00 0.00 0.00 3.18
1137 1310 2.066262 CGCAGGTGTAGTTTCGTGAAT 58.934 47.619 0.00 0.00 0.00 2.57
1138 1311 2.092211 CGCAGGTGTAGTTTCGTGAATC 59.908 50.000 0.00 0.00 0.00 2.52
1139 1312 2.092211 GCAGGTGTAGTTTCGTGAATCG 59.908 50.000 0.00 0.00 41.41 3.34
1140 1313 3.314553 CAGGTGTAGTTTCGTGAATCGT 58.685 45.455 0.00 0.00 40.80 3.73
1141 1314 3.121279 CAGGTGTAGTTTCGTGAATCGTG 59.879 47.826 0.00 0.00 40.80 4.35
1142 1315 3.005050 AGGTGTAGTTTCGTGAATCGTGA 59.995 43.478 0.00 0.00 40.80 4.35
1149 1324 5.651530 AGTTTCGTGAATCGTGATAGTGAT 58.348 37.500 0.00 0.00 40.80 3.06
1555 1730 2.265182 GCGTTGGCTAAACTGGGCA 61.265 57.895 0.00 0.00 36.56 5.36
1842 2017 2.037136 CCTCTTTGACGCCCAGCTG 61.037 63.158 6.78 6.78 0.00 4.24
1872 2047 3.891977 TCTACTATGCGATGGAGAAGCTT 59.108 43.478 0.00 0.00 0.00 3.74
1980 2158 1.076632 AAACAAAGGCCACGGTGGA 60.077 52.632 30.65 0.00 40.96 4.02
2027 2205 0.764271 TTCATGGCTGGTCTCACACA 59.236 50.000 0.00 0.00 0.00 3.72
2058 2236 2.813908 GGTAACTCTGGCACCGCG 60.814 66.667 0.00 0.00 0.00 6.46
2074 2252 4.114997 CGGCCGCAAATGGACACC 62.115 66.667 14.67 0.00 36.54 4.16
2361 2539 1.875963 CGACAACAGGGATGGCAAC 59.124 57.895 0.00 0.00 0.00 4.17
2474 2652 0.320946 CAGAAGAACGGCCGGGTTAA 60.321 55.000 31.76 0.00 0.00 2.01
2478 2656 0.109153 AGAACGGCCGGGTTAAAAGT 59.891 50.000 31.76 0.57 0.00 2.66
2481 2659 2.262303 CGGCCGGGTTAAAAGTGCA 61.262 57.895 20.10 0.00 0.00 4.57
2643 2821 1.568612 CCGCGAACTGCACAGACATT 61.569 55.000 8.23 0.00 46.97 2.71
2774 2952 0.533308 GGCGCCGGTATTATTGTCCA 60.533 55.000 12.58 0.00 0.00 4.02
2828 3018 8.477984 TTTGTGATTCTTGTTTCAAGAAAAGG 57.522 30.769 22.64 0.00 39.43 3.11
2946 3171 1.188863 CCAAGGCCAAGCTTTGCTAT 58.811 50.000 20.64 8.45 42.87 2.97
2949 3174 3.282021 CAAGGCCAAGCTTTGCTATCTA 58.718 45.455 20.64 0.00 38.65 1.98
3028 3258 7.327214 AGTTTTCAAATGTTAGTTTGGCTTGA 58.673 30.769 0.00 0.00 39.10 3.02
3180 3410 7.125391 TGCTCCATTTTAATAAAGGGTCTGAT 58.875 34.615 0.00 0.00 43.83 2.90
3257 3488 4.096382 CGCCAGGCTTTATTTACATTGTCT 59.904 41.667 10.54 0.00 0.00 3.41
3294 3525 6.206829 GGTATAAAATTCAAATCTCCGGGGAG 59.793 42.308 11.27 8.48 43.21 4.30
3311 3542 2.436115 GGCCTAACCAGACACGGC 60.436 66.667 0.00 0.00 38.86 5.68
3315 3546 3.296709 CTAACCAGACACGGCGGCT 62.297 63.158 13.24 2.10 0.00 5.52
3343 3574 1.349627 CGAAAGTGCATGCCTAGCG 59.650 57.895 16.68 13.93 33.85 4.26
3357 3588 1.137872 CCTAGCGAGATTGTGAGCCTT 59.862 52.381 0.00 0.00 0.00 4.35
3363 3594 4.333926 AGCGAGATTGTGAGCCTTAAAATC 59.666 41.667 0.00 0.00 0.00 2.17
3365 3596 4.260375 CGAGATTGTGAGCCTTAAAATCCG 60.260 45.833 0.00 0.00 0.00 4.18
3383 3614 1.757118 CCGAGCTCCTAAACTCATGGA 59.243 52.381 8.47 0.00 32.98 3.41
3395 3626 8.792633 TCCTAAACTCATGGACAAAATTACAAG 58.207 33.333 0.00 0.00 0.00 3.16
3396 3627 7.542130 CCTAAACTCATGGACAAAATTACAAGC 59.458 37.037 0.00 0.00 0.00 4.01
3417 3648 7.280876 ACAAGCAATAAAAGCATTCGATCTCTA 59.719 33.333 0.00 0.00 0.00 2.43
3443 3676 9.970395 ATAATTTCATGTACAATTACTGCATGG 57.030 29.630 0.00 0.00 37.92 3.66
3446 3679 6.832520 TCATGTACAATTACTGCATGGTTT 57.167 33.333 0.00 0.00 37.92 3.27
3521 3754 2.280552 GGACTAGCCCACCACGTCA 61.281 63.158 0.00 0.00 0.00 4.35
3542 3775 8.188139 ACGTCATTCTCTTATTTGTTTGTTTGT 58.812 29.630 0.00 0.00 0.00 2.83
3543 3776 9.019764 CGTCATTCTCTTATTTGTTTGTTTGTT 57.980 29.630 0.00 0.00 0.00 2.83
3590 3823 2.009681 TGGCTTACTGACACTGGAGA 57.990 50.000 0.00 0.00 0.00 3.71
3604 3837 2.494530 GGAGACAGAGGCTAGCGGG 61.495 68.421 9.00 0.20 0.00 6.13
3605 3838 2.443016 AGACAGAGGCTAGCGGGG 60.443 66.667 9.00 0.58 0.00 5.73
3606 3839 4.228567 GACAGAGGCTAGCGGGGC 62.229 72.222 9.00 0.00 0.00 5.80
3633 3866 3.514362 GGGCGGCCCAATTACGTG 61.514 66.667 32.90 0.00 44.65 4.49
3634 3867 2.748647 GGCGGCCCAATTACGTGT 60.749 61.111 8.12 0.00 0.00 4.49
3635 3868 2.337246 GGCGGCCCAATTACGTGTT 61.337 57.895 8.12 0.00 0.00 3.32
3636 3869 1.582461 GCGGCCCAATTACGTGTTT 59.418 52.632 0.00 0.00 0.00 2.83
3637 3870 0.803740 GCGGCCCAATTACGTGTTTA 59.196 50.000 0.00 0.00 0.00 2.01
3638 3871 1.402613 GCGGCCCAATTACGTGTTTAT 59.597 47.619 0.00 0.00 0.00 1.40
3639 3872 2.159352 GCGGCCCAATTACGTGTTTATT 60.159 45.455 0.00 0.00 0.00 1.40
3640 3873 3.687200 CGGCCCAATTACGTGTTTATTC 58.313 45.455 0.00 0.00 0.00 1.75
3641 3874 3.375922 CGGCCCAATTACGTGTTTATTCT 59.624 43.478 0.00 0.00 0.00 2.40
3642 3875 4.142556 CGGCCCAATTACGTGTTTATTCTT 60.143 41.667 0.00 0.00 0.00 2.52
3643 3876 5.620429 CGGCCCAATTACGTGTTTATTCTTT 60.620 40.000 0.00 0.00 0.00 2.52
3644 3877 5.575218 GGCCCAATTACGTGTTTATTCTTTG 59.425 40.000 0.00 0.00 0.00 2.77
3645 3878 5.575218 GCCCAATTACGTGTTTATTCTTTGG 59.425 40.000 0.00 0.00 0.00 3.28
3646 3879 6.096695 CCCAATTACGTGTTTATTCTTTGGG 58.903 40.000 0.00 0.00 43.31 4.12
3647 3880 5.575218 CCAATTACGTGTTTATTCTTTGGGC 59.425 40.000 0.00 0.00 0.00 5.36
3648 3881 5.968528 ATTACGTGTTTATTCTTTGGGCA 57.031 34.783 0.00 0.00 0.00 5.36
3649 3882 3.915437 ACGTGTTTATTCTTTGGGCAG 57.085 42.857 0.00 0.00 0.00 4.85
3650 3883 3.219281 ACGTGTTTATTCTTTGGGCAGT 58.781 40.909 0.00 0.00 0.00 4.40
3651 3884 3.004315 ACGTGTTTATTCTTTGGGCAGTG 59.996 43.478 0.00 0.00 0.00 3.66
3652 3885 3.252215 CGTGTTTATTCTTTGGGCAGTGA 59.748 43.478 0.00 0.00 0.00 3.41
3653 3886 4.082787 CGTGTTTATTCTTTGGGCAGTGAT 60.083 41.667 0.00 0.00 0.00 3.06
3654 3887 5.123186 CGTGTTTATTCTTTGGGCAGTGATA 59.877 40.000 0.00 0.00 0.00 2.15
3655 3888 6.555315 GTGTTTATTCTTTGGGCAGTGATAG 58.445 40.000 0.00 0.00 0.00 2.08
3656 3889 5.652014 TGTTTATTCTTTGGGCAGTGATAGG 59.348 40.000 0.00 0.00 0.00 2.57
3657 3890 2.128771 TTCTTTGGGCAGTGATAGGC 57.871 50.000 0.00 0.00 0.00 3.93
3658 3891 0.107703 TCTTTGGGCAGTGATAGGCG 60.108 55.000 0.00 0.00 0.00 5.52
3659 3892 1.718757 CTTTGGGCAGTGATAGGCGC 61.719 60.000 0.00 0.00 42.61 6.53
3660 3893 3.697439 TTGGGCAGTGATAGGCGCC 62.697 63.158 21.89 21.89 44.10 6.53
3663 3896 4.530857 GCAGTGATAGGCGCCGGT 62.531 66.667 23.20 14.30 0.00 5.28
3664 3897 3.125607 CAGTGATAGGCGCCGGTA 58.874 61.111 23.20 9.71 0.00 4.02
3665 3898 1.007271 CAGTGATAGGCGCCGGTAG 60.007 63.158 23.20 4.75 0.00 3.18
3666 3899 1.455217 AGTGATAGGCGCCGGTAGT 60.455 57.895 23.20 5.39 0.00 2.73
3667 3900 1.007618 GTGATAGGCGCCGGTAGTC 60.008 63.158 23.20 15.73 0.00 2.59
3668 3901 2.198287 TGATAGGCGCCGGTAGTCC 61.198 63.158 23.20 7.88 0.00 3.85
3704 3937 4.840005 GACTAGCCCCAGCCGCAC 62.840 72.222 0.00 0.00 41.25 5.34
3741 3974 2.106684 GACCATAGGATTTCACCCCCTC 59.893 54.545 0.00 0.00 0.00 4.30
3742 3975 1.072331 CCATAGGATTTCACCCCCTCG 59.928 57.143 0.00 0.00 0.00 4.63
3743 3976 0.765510 ATAGGATTTCACCCCCTCGC 59.234 55.000 0.00 0.00 0.00 5.03
3780 4013 1.541233 CGTCTCCTTCCTGCAACAGTT 60.541 52.381 0.00 0.00 0.00 3.16
3782 4015 1.151668 CTCCTTCCTGCAACAGTTCG 58.848 55.000 0.00 0.00 0.00 3.95
3787 4020 2.639286 CTGCAACAGTTCGCCACC 59.361 61.111 0.00 0.00 0.00 4.61
3819 4052 4.386100 TCCCCCTCCCATGGCCTT 62.386 66.667 6.09 0.00 0.00 4.35
3823 4056 2.697644 CCTCCCATGGCCTTCCCT 60.698 66.667 6.09 0.00 0.00 4.20
3839 4072 1.246737 CCCTTTGAAGCTCTGTGGCC 61.247 60.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.002134 CTCCCGGTGCTCCAAATGT 60.002 57.895 0.00 0.00 0.00 2.71
5 6 4.329545 GTGCTCCCGGTGCTCCAA 62.330 66.667 16.01 0.00 0.00 3.53
24 25 7.396540 AAAATATCTAGTGCTCCCAAACTTG 57.603 36.000 0.00 0.00 0.00 3.16
25 26 6.603599 GGAAAATATCTAGTGCTCCCAAACTT 59.396 38.462 0.00 0.00 0.00 2.66
26 27 6.122964 GGAAAATATCTAGTGCTCCCAAACT 58.877 40.000 0.00 0.00 0.00 2.66
27 28 5.299531 GGGAAAATATCTAGTGCTCCCAAAC 59.700 44.000 0.00 0.00 40.72 2.93
28 29 5.445964 GGGAAAATATCTAGTGCTCCCAAA 58.554 41.667 0.00 0.00 40.72 3.28
29 30 4.141251 GGGGAAAATATCTAGTGCTCCCAA 60.141 45.833 6.57 0.00 42.48 4.12
30 31 3.394606 GGGGAAAATATCTAGTGCTCCCA 59.605 47.826 6.57 0.00 42.48 4.37
31 32 3.557264 CGGGGAAAATATCTAGTGCTCCC 60.557 52.174 0.00 0.00 40.37 4.30
32 33 3.323979 TCGGGGAAAATATCTAGTGCTCC 59.676 47.826 0.00 0.00 0.00 4.70
33 34 4.561105 CTCGGGGAAAATATCTAGTGCTC 58.439 47.826 0.00 0.00 0.00 4.26
34 35 3.244249 GCTCGGGGAAAATATCTAGTGCT 60.244 47.826 0.00 0.00 0.00 4.40
35 36 3.067833 GCTCGGGGAAAATATCTAGTGC 58.932 50.000 0.00 0.00 0.00 4.40
36 37 4.336889 TGCTCGGGGAAAATATCTAGTG 57.663 45.455 0.00 0.00 0.00 2.74
37 38 4.263068 CCATGCTCGGGGAAAATATCTAGT 60.263 45.833 0.00 0.00 0.00 2.57
38 39 4.020218 TCCATGCTCGGGGAAAATATCTAG 60.020 45.833 0.00 0.00 0.00 2.43
39 40 3.907474 TCCATGCTCGGGGAAAATATCTA 59.093 43.478 0.00 0.00 0.00 1.98
40 41 2.711009 TCCATGCTCGGGGAAAATATCT 59.289 45.455 0.00 0.00 0.00 1.98
41 42 3.140325 TCCATGCTCGGGGAAAATATC 57.860 47.619 0.00 0.00 0.00 1.63
42 43 3.222603 GTTCCATGCTCGGGGAAAATAT 58.777 45.455 0.00 0.00 44.30 1.28
43 44 2.650322 GTTCCATGCTCGGGGAAAATA 58.350 47.619 0.00 0.00 44.30 1.40
44 45 1.474330 GTTCCATGCTCGGGGAAAAT 58.526 50.000 0.00 0.00 44.30 1.82
45 46 0.958382 CGTTCCATGCTCGGGGAAAA 60.958 55.000 0.00 0.00 44.30 2.29
46 47 1.376683 CGTTCCATGCTCGGGGAAA 60.377 57.895 0.00 0.00 44.30 3.13
47 48 2.267642 CGTTCCATGCTCGGGGAA 59.732 61.111 0.00 0.00 40.75 3.97
48 49 2.682136 TCGTTCCATGCTCGGGGA 60.682 61.111 0.00 0.00 0.00 4.81
49 50 2.511600 GTCGTTCCATGCTCGGGG 60.512 66.667 0.00 0.00 0.00 5.73
50 51 1.079127 AAGTCGTTCCATGCTCGGG 60.079 57.895 0.00 0.00 0.00 5.14
51 52 1.361668 CCAAGTCGTTCCATGCTCGG 61.362 60.000 0.00 0.00 0.00 4.63
52 53 1.970917 GCCAAGTCGTTCCATGCTCG 61.971 60.000 0.00 0.00 0.00 5.03
53 54 1.648467 GGCCAAGTCGTTCCATGCTC 61.648 60.000 0.00 0.00 0.00 4.26
54 55 1.675641 GGCCAAGTCGTTCCATGCT 60.676 57.895 0.00 0.00 0.00 3.79
55 56 1.675641 AGGCCAAGTCGTTCCATGC 60.676 57.895 5.01 0.00 0.00 4.06
56 57 1.308069 CCAGGCCAAGTCGTTCCATG 61.308 60.000 5.01 0.00 0.00 3.66
57 58 1.002134 CCAGGCCAAGTCGTTCCAT 60.002 57.895 5.01 0.00 0.00 3.41
58 59 2.111999 CTCCAGGCCAAGTCGTTCCA 62.112 60.000 5.01 0.00 0.00 3.53
59 60 1.376037 CTCCAGGCCAAGTCGTTCC 60.376 63.158 5.01 0.00 0.00 3.62
60 61 0.390472 CTCTCCAGGCCAAGTCGTTC 60.390 60.000 5.01 0.00 0.00 3.95
61 62 1.674057 CTCTCCAGGCCAAGTCGTT 59.326 57.895 5.01 0.00 0.00 3.85
62 63 2.948720 GCTCTCCAGGCCAAGTCGT 61.949 63.158 5.01 0.00 0.00 4.34
63 64 2.125350 GCTCTCCAGGCCAAGTCG 60.125 66.667 5.01 0.00 0.00 4.18
64 65 1.220477 GAGCTCTCCAGGCCAAGTC 59.780 63.158 5.01 0.00 0.00 3.01
65 66 3.397906 GAGCTCTCCAGGCCAAGT 58.602 61.111 5.01 0.00 0.00 3.16
101 104 0.731514 GAAGTCGCAACGATCGGACA 60.732 55.000 20.98 0.00 38.42 4.02
203 212 0.321653 GCATGAGGTTGGAGGTTCGT 60.322 55.000 0.00 0.00 0.00 3.85
223 232 1.576356 GCTAGCCTCACTGAAATCCG 58.424 55.000 2.29 0.00 0.00 4.18
368 405 7.277539 TCAGCATTTCTTTTACAAAAACCACTG 59.722 33.333 0.00 0.00 0.00 3.66
370 407 7.532682 TCAGCATTTCTTTTACAAAAACCAC 57.467 32.000 0.00 0.00 0.00 4.16
373 410 9.818796 TTTGTTCAGCATTTCTTTTACAAAAAC 57.181 25.926 0.00 0.00 33.02 2.43
549 699 6.636850 AGTTCACGTTGCAAGATAAAAATGTC 59.363 34.615 0.00 0.00 0.00 3.06
560 710 9.935682 ATATTATGAAATAGTTCACGTTGCAAG 57.064 29.630 7.92 0.00 46.40 4.01
567 717 9.124807 TCAGCGTATATTATGAAATAGTTCACG 57.875 33.333 7.92 6.61 46.40 4.35
849 1021 4.334203 TGTACAGATTTGTTCGCTGTTGTT 59.666 37.500 0.00 0.00 42.40 2.83
851 1023 4.466567 TGTACAGATTTGTTCGCTGTTG 57.533 40.909 0.00 0.00 42.40 3.33
852 1024 4.083324 CCATGTACAGATTTGTTCGCTGTT 60.083 41.667 0.33 0.00 42.40 3.16
854 1026 3.181507 CCCATGTACAGATTTGTTCGCTG 60.182 47.826 0.33 0.00 38.76 5.18
855 1027 3.009723 CCCATGTACAGATTTGTTCGCT 58.990 45.455 0.33 0.00 38.76 4.93
857 1029 2.097466 GGCCCATGTACAGATTTGTTCG 59.903 50.000 0.33 0.00 38.76 3.95
858 1030 2.097466 CGGCCCATGTACAGATTTGTTC 59.903 50.000 0.33 0.00 38.76 3.18
859 1031 2.091541 CGGCCCATGTACAGATTTGTT 58.908 47.619 0.33 0.00 38.76 2.83
860 1032 1.681780 CCGGCCCATGTACAGATTTGT 60.682 52.381 0.33 0.00 41.39 2.83
890 1063 0.952984 GCCTTCGCTGAAGCAAGTCT 60.953 55.000 11.33 0.00 42.21 3.24
951 1124 1.965414 TTCCTCACCTATCAGGCCAA 58.035 50.000 5.01 0.00 39.63 4.52
952 1125 2.050144 GATTCCTCACCTATCAGGCCA 58.950 52.381 5.01 0.00 39.63 5.36
953 1126 1.349357 GGATTCCTCACCTATCAGGCC 59.651 57.143 0.00 0.00 39.63 5.19
954 1127 1.001406 CGGATTCCTCACCTATCAGGC 59.999 57.143 0.30 0.00 39.63 4.85
955 1128 2.036475 CACGGATTCCTCACCTATCAGG 59.964 54.545 0.30 0.00 42.49 3.86
956 1129 2.546795 GCACGGATTCCTCACCTATCAG 60.547 54.545 0.30 0.00 0.00 2.90
957 1130 1.412710 GCACGGATTCCTCACCTATCA 59.587 52.381 0.30 0.00 0.00 2.15
958 1131 1.689273 AGCACGGATTCCTCACCTATC 59.311 52.381 0.30 0.00 0.00 2.08
959 1132 1.414181 CAGCACGGATTCCTCACCTAT 59.586 52.381 0.30 0.00 0.00 2.57
960 1133 0.824109 CAGCACGGATTCCTCACCTA 59.176 55.000 0.30 0.00 0.00 3.08
961 1134 0.904865 TCAGCACGGATTCCTCACCT 60.905 55.000 0.30 0.00 0.00 4.00
962 1135 0.741221 GTCAGCACGGATTCCTCACC 60.741 60.000 0.30 0.00 0.00 4.02
963 1136 0.247736 AGTCAGCACGGATTCCTCAC 59.752 55.000 0.30 0.00 0.00 3.51
964 1137 0.976641 AAGTCAGCACGGATTCCTCA 59.023 50.000 0.30 0.00 0.00 3.86
965 1138 1.734465 CAAAGTCAGCACGGATTCCTC 59.266 52.381 0.30 0.00 0.00 3.71
966 1139 1.072331 ACAAAGTCAGCACGGATTCCT 59.928 47.619 0.30 0.00 0.00 3.36
967 1140 1.523758 ACAAAGTCAGCACGGATTCC 58.476 50.000 0.00 0.00 0.00 3.01
968 1141 3.251004 AGAAACAAAGTCAGCACGGATTC 59.749 43.478 0.00 0.00 0.00 2.52
969 1142 3.214328 AGAAACAAAGTCAGCACGGATT 58.786 40.909 0.00 0.00 0.00 3.01
970 1143 2.851195 AGAAACAAAGTCAGCACGGAT 58.149 42.857 0.00 0.00 0.00 4.18
971 1144 2.325583 AGAAACAAAGTCAGCACGGA 57.674 45.000 0.00 0.00 0.00 4.69
972 1145 2.599848 CGAAGAAACAAAGTCAGCACGG 60.600 50.000 0.00 0.00 0.00 4.94
973 1146 2.599848 CCGAAGAAACAAAGTCAGCACG 60.600 50.000 0.00 0.00 0.00 5.34
974 1147 2.854805 GCCGAAGAAACAAAGTCAGCAC 60.855 50.000 0.00 0.00 0.00 4.40
975 1148 1.333619 GCCGAAGAAACAAAGTCAGCA 59.666 47.619 0.00 0.00 0.00 4.41
976 1149 1.660333 CGCCGAAGAAACAAAGTCAGC 60.660 52.381 0.00 0.00 0.00 4.26
977 1150 1.660333 GCGCCGAAGAAACAAAGTCAG 60.660 52.381 0.00 0.00 0.00 3.51
978 1151 0.306533 GCGCCGAAGAAACAAAGTCA 59.693 50.000 0.00 0.00 0.00 3.41
979 1152 0.586802 AGCGCCGAAGAAACAAAGTC 59.413 50.000 2.29 0.00 0.00 3.01
980 1153 0.307760 CAGCGCCGAAGAAACAAAGT 59.692 50.000 2.29 0.00 0.00 2.66
981 1154 0.586319 TCAGCGCCGAAGAAACAAAG 59.414 50.000 2.29 0.00 0.00 2.77
982 1155 1.069296 CATCAGCGCCGAAGAAACAAA 60.069 47.619 2.29 0.00 0.00 2.83
983 1156 0.516877 CATCAGCGCCGAAGAAACAA 59.483 50.000 2.29 0.00 0.00 2.83
984 1157 0.320334 TCATCAGCGCCGAAGAAACA 60.320 50.000 2.29 0.00 0.00 2.83
985 1158 0.371645 CTCATCAGCGCCGAAGAAAC 59.628 55.000 2.29 0.00 0.00 2.78
986 1159 1.361668 GCTCATCAGCGCCGAAGAAA 61.362 55.000 2.29 0.00 35.39 2.52
987 1160 1.811266 GCTCATCAGCGCCGAAGAA 60.811 57.895 2.29 0.00 35.39 2.52
988 1161 2.202797 GCTCATCAGCGCCGAAGA 60.203 61.111 2.29 0.00 35.39 2.87
1004 1177 1.045911 AAGGATGAGGAGGAGACGGC 61.046 60.000 0.00 0.00 0.00 5.68
1008 1181 1.133637 CCGAGAAGGATGAGGAGGAGA 60.134 57.143 0.00 0.00 45.00 3.71
1018 1191 2.599645 AATGCAGCGCCGAGAAGGAT 62.600 55.000 2.29 0.00 45.00 3.24
1019 1192 3.315142 AATGCAGCGCCGAGAAGGA 62.315 57.895 2.29 0.00 45.00 3.36
1029 1202 2.890109 GAGGATCGGCAATGCAGCG 61.890 63.158 7.79 2.10 34.64 5.18
1041 1214 4.141959 CCTGAAGGAGTGAAGAAGAGGATC 60.142 50.000 0.00 0.00 37.39 3.36
1042 1215 3.774216 CCTGAAGGAGTGAAGAAGAGGAT 59.226 47.826 0.00 0.00 37.39 3.24
1044 1217 2.903135 ACCTGAAGGAGTGAAGAAGAGG 59.097 50.000 2.62 0.00 38.94 3.69
1054 1227 0.898320 CCGTGATCACCTGAAGGAGT 59.102 55.000 20.03 0.00 38.94 3.85
1056 1229 1.186200 CTCCGTGATCACCTGAAGGA 58.814 55.000 20.03 17.63 38.94 3.36
1060 1233 2.180674 CGTCTCCGTGATCACCTGA 58.819 57.895 20.03 15.03 0.00 3.86
1071 1244 1.135489 TCTCCGAATGAAACGTCTCCG 60.135 52.381 0.00 0.00 40.83 4.63
1080 1253 4.869861 CACACACACATATCTCCGAATGAA 59.130 41.667 0.00 0.00 0.00 2.57
1081 1254 4.081697 ACACACACACATATCTCCGAATGA 60.082 41.667 0.00 0.00 0.00 2.57
1082 1255 4.183865 ACACACACACATATCTCCGAATG 58.816 43.478 0.00 0.00 0.00 2.67
1083 1256 4.160439 AGACACACACACATATCTCCGAAT 59.840 41.667 0.00 0.00 0.00 3.34
1086 1259 3.510388 AGACACACACACATATCTCCG 57.490 47.619 0.00 0.00 0.00 4.63
1093 1266 7.035612 CGCCATATATATAGACACACACACAT 58.964 38.462 0.00 0.00 0.00 3.21
1094 1267 6.386654 CGCCATATATATAGACACACACACA 58.613 40.000 0.00 0.00 0.00 3.72
1095 1268 5.288712 GCGCCATATATATAGACACACACAC 59.711 44.000 0.00 0.00 0.00 3.82
1096 1269 5.047660 TGCGCCATATATATAGACACACACA 60.048 40.000 4.18 0.00 0.00 3.72
1097 1270 5.407502 TGCGCCATATATATAGACACACAC 58.592 41.667 4.18 0.00 0.00 3.82
1098 1271 5.394115 CCTGCGCCATATATATAGACACACA 60.394 44.000 4.18 0.00 0.00 3.72
1099 1272 5.043903 CCTGCGCCATATATATAGACACAC 58.956 45.833 4.18 0.00 0.00 3.82
1100 1273 4.709886 ACCTGCGCCATATATATAGACACA 59.290 41.667 4.18 0.00 0.00 3.72
1101 1274 5.043903 CACCTGCGCCATATATATAGACAC 58.956 45.833 4.18 0.00 0.00 3.67
1102 1275 4.709886 ACACCTGCGCCATATATATAGACA 59.290 41.667 4.18 0.00 0.00 3.41
1103 1276 5.263968 ACACCTGCGCCATATATATAGAC 57.736 43.478 4.18 0.00 0.00 2.59
1104 1277 6.127101 ACTACACCTGCGCCATATATATAGA 58.873 40.000 4.18 0.00 0.00 1.98
1105 1278 6.392625 ACTACACCTGCGCCATATATATAG 57.607 41.667 4.18 0.00 0.00 1.31
1136 1309 5.168569 ACAAACGTCAATCACTATCACGAT 58.831 37.500 0.00 0.00 34.55 3.73
1137 1310 4.552355 ACAAACGTCAATCACTATCACGA 58.448 39.130 0.00 0.00 34.55 4.35
1138 1311 4.903638 ACAAACGTCAATCACTATCACG 57.096 40.909 0.00 0.00 36.54 4.35
1139 1312 4.846137 GCAACAAACGTCAATCACTATCAC 59.154 41.667 0.00 0.00 0.00 3.06
1140 1313 4.754618 AGCAACAAACGTCAATCACTATCA 59.245 37.500 0.00 0.00 0.00 2.15
1141 1314 5.283060 AGCAACAAACGTCAATCACTATC 57.717 39.130 0.00 0.00 0.00 2.08
1142 1315 5.932303 AGTAGCAACAAACGTCAATCACTAT 59.068 36.000 0.00 0.00 0.00 2.12
1149 1324 2.748461 GCAGTAGCAACAAACGTCAA 57.252 45.000 0.00 0.00 41.58 3.18
1194 1369 2.119832 ACCCTCCCGTAGCACACT 59.880 61.111 0.00 0.00 0.00 3.55
1389 1564 1.135315 CCACTGGAGCGCGAAATTG 59.865 57.895 12.10 0.00 0.00 2.32
1872 2047 3.002583 TGCATGCTGGAGGACGGA 61.003 61.111 20.33 0.00 0.00 4.69
1938 2116 1.163309 TCCTTCCTCCCCATGGTGT 59.837 57.895 11.73 0.00 0.00 4.16
1980 2158 1.816572 GCGTTTTGTGGGGTTCCTACT 60.817 52.381 2.33 0.00 0.00 2.57
2027 2205 0.537371 GTTACCCTGCAGCACTTGGT 60.537 55.000 8.66 12.47 0.00 3.67
2058 2236 4.114997 CGGTGTCCATTTGCGGCC 62.115 66.667 0.00 0.00 0.00 6.13
2271 2449 2.174334 CACGCAATAGCTTGGCTGT 58.826 52.632 0.00 0.00 40.10 4.40
2304 2482 4.755507 TGCAATGCCGCATCCCCA 62.756 61.111 6.27 1.57 36.86 4.96
2337 2515 3.529341 ATCCCTGTTGTCGCACGCA 62.529 57.895 0.00 0.00 0.00 5.24
2474 2652 0.239347 GCTGAAGTCGCATGCACTTT 59.761 50.000 25.81 14.52 34.10 2.66
2478 2656 3.120385 CCGCTGAAGTCGCATGCA 61.120 61.111 19.57 1.73 0.00 3.96
2624 2802 1.568612 AATGTCTGTGCAGTTCGCGG 61.569 55.000 6.13 0.00 46.97 6.46
2774 2952 1.609208 CAACTTACTTGGTGCCTGCT 58.391 50.000 0.00 0.00 0.00 4.24
2828 3018 7.848539 CCATTAACAAACCAAAACGTTCATTTC 59.151 33.333 0.00 0.00 0.00 2.17
2909 3116 4.566488 CCTTGGCTAGTTTCTTCACCTCAT 60.566 45.833 0.00 0.00 0.00 2.90
2946 3171 9.298250 AGGATTATTGCTTAATCTCGTAGTAGA 57.702 33.333 15.18 0.00 43.86 2.59
2949 3174 6.647067 GCAGGATTATTGCTTAATCTCGTAGT 59.353 38.462 15.18 0.00 43.86 2.73
2973 3203 1.069204 TGACAGCAGAGGATAATCCGC 59.931 52.381 0.00 0.00 42.75 5.54
3028 3258 2.568623 AGGCAACGTTCTCAAAGGAT 57.431 45.000 0.00 0.00 46.39 3.24
3219 3449 3.252458 GCCTGGCGAGAAAGTCTTAAAAA 59.748 43.478 1.35 0.00 0.00 1.94
3224 3454 0.398318 AAGCCTGGCGAGAAAGTCTT 59.602 50.000 13.96 0.00 0.00 3.01
3225 3455 0.398318 AAAGCCTGGCGAGAAAGTCT 59.602 50.000 13.96 0.00 0.00 3.24
3226 3456 2.094762 TAAAGCCTGGCGAGAAAGTC 57.905 50.000 13.96 0.00 0.00 3.01
3227 3457 2.789409 ATAAAGCCTGGCGAGAAAGT 57.211 45.000 13.96 0.00 0.00 2.66
3228 3458 4.394920 TGTAAATAAAGCCTGGCGAGAAAG 59.605 41.667 13.96 0.00 0.00 2.62
3229 3459 4.328536 TGTAAATAAAGCCTGGCGAGAAA 58.671 39.130 13.96 0.00 0.00 2.52
3271 3502 6.303839 CCTCCCCGGAGATTTGAATTTTATA 58.696 40.000 12.54 0.00 44.53 0.98
3294 3525 2.436115 GCCGTGTCTGGTTAGGCC 60.436 66.667 0.00 0.00 41.81 5.19
3311 3542 1.693083 CTTTCGCTCGGGTTAAGCCG 61.693 60.000 34.54 34.54 36.36 5.52
3315 3546 0.249953 TGCACTTTCGCTCGGGTTAA 60.250 50.000 0.00 0.00 0.00 2.01
3343 3574 4.876107 TCGGATTTTAAGGCTCACAATCTC 59.124 41.667 10.56 3.45 0.00 2.75
3357 3588 5.670792 TGAGTTTAGGAGCTCGGATTTTA 57.329 39.130 7.83 0.00 36.04 1.52
3363 3594 1.757118 TCCATGAGTTTAGGAGCTCGG 59.243 52.381 7.83 0.00 36.04 4.63
3365 3596 3.895232 TGTCCATGAGTTTAGGAGCTC 57.105 47.619 4.71 4.71 34.08 4.09
3417 3648 9.970395 CCATGCAGTAATTGTACATGAAATTAT 57.030 29.630 0.00 0.00 40.39 1.28
3435 3668 3.996921 AGAGAGATCAAACCATGCAGT 57.003 42.857 0.00 0.00 0.00 4.40
3438 3671 8.317679 AGGTATTATAGAGAGATCAAACCATGC 58.682 37.037 0.00 0.00 0.00 4.06
3616 3849 3.514362 CACGTAATTGGGCCGCCC 61.514 66.667 22.81 22.81 45.71 6.13
3617 3850 1.868987 AAACACGTAATTGGGCCGCC 61.869 55.000 0.00 0.00 0.00 6.13
3618 3851 0.803740 TAAACACGTAATTGGGCCGC 59.196 50.000 0.00 0.00 0.00 6.53
3619 3852 3.375922 AGAATAAACACGTAATTGGGCCG 59.624 43.478 0.00 0.00 0.00 6.13
3620 3853 4.976224 AGAATAAACACGTAATTGGGCC 57.024 40.909 0.00 0.00 0.00 5.80
3621 3854 5.575218 CCAAAGAATAAACACGTAATTGGGC 59.425 40.000 0.00 0.00 32.99 5.36
3622 3855 6.096695 CCCAAAGAATAAACACGTAATTGGG 58.903 40.000 5.44 5.44 45.90 4.12
3623 3856 5.575218 GCCCAAAGAATAAACACGTAATTGG 59.425 40.000 0.00 0.00 35.66 3.16
3624 3857 6.153067 TGCCCAAAGAATAAACACGTAATTG 58.847 36.000 0.00 0.00 0.00 2.32
3625 3858 6.015772 ACTGCCCAAAGAATAAACACGTAATT 60.016 34.615 0.00 0.00 0.00 1.40
3626 3859 5.475564 ACTGCCCAAAGAATAAACACGTAAT 59.524 36.000 0.00 0.00 0.00 1.89
3627 3860 4.822896 ACTGCCCAAAGAATAAACACGTAA 59.177 37.500 0.00 0.00 0.00 3.18
3628 3861 4.214545 CACTGCCCAAAGAATAAACACGTA 59.785 41.667 0.00 0.00 0.00 3.57
3629 3862 3.004315 CACTGCCCAAAGAATAAACACGT 59.996 43.478 0.00 0.00 0.00 4.49
3630 3863 3.252215 TCACTGCCCAAAGAATAAACACG 59.748 43.478 0.00 0.00 0.00 4.49
3631 3864 4.846779 TCACTGCCCAAAGAATAAACAC 57.153 40.909 0.00 0.00 0.00 3.32
3632 3865 5.652014 CCTATCACTGCCCAAAGAATAAACA 59.348 40.000 0.00 0.00 0.00 2.83
3633 3866 5.450550 GCCTATCACTGCCCAAAGAATAAAC 60.451 44.000 0.00 0.00 0.00 2.01
3634 3867 4.644685 GCCTATCACTGCCCAAAGAATAAA 59.355 41.667 0.00 0.00 0.00 1.40
3635 3868 4.207165 GCCTATCACTGCCCAAAGAATAA 58.793 43.478 0.00 0.00 0.00 1.40
3636 3869 3.744214 CGCCTATCACTGCCCAAAGAATA 60.744 47.826 0.00 0.00 0.00 1.75
3637 3870 2.659428 GCCTATCACTGCCCAAAGAAT 58.341 47.619 0.00 0.00 0.00 2.40
3638 3871 1.678728 CGCCTATCACTGCCCAAAGAA 60.679 52.381 0.00 0.00 0.00 2.52
3639 3872 0.107703 CGCCTATCACTGCCCAAAGA 60.108 55.000 0.00 0.00 0.00 2.52
3640 3873 1.718757 GCGCCTATCACTGCCCAAAG 61.719 60.000 0.00 0.00 0.00 2.77
3641 3874 1.748879 GCGCCTATCACTGCCCAAA 60.749 57.895 0.00 0.00 0.00 3.28
3642 3875 2.124736 GCGCCTATCACTGCCCAA 60.125 61.111 0.00 0.00 0.00 4.12
3643 3876 4.175337 GGCGCCTATCACTGCCCA 62.175 66.667 22.15 0.00 41.70 5.36
3646 3879 3.146726 TACCGGCGCCTATCACTGC 62.147 63.158 26.68 0.00 0.00 4.40
3647 3880 1.007271 CTACCGGCGCCTATCACTG 60.007 63.158 26.68 6.56 0.00 3.66
3648 3881 1.453762 GACTACCGGCGCCTATCACT 61.454 60.000 26.68 1.45 0.00 3.41
3649 3882 1.007618 GACTACCGGCGCCTATCAC 60.008 63.158 26.68 7.74 0.00 3.06
3650 3883 2.198287 GGACTACCGGCGCCTATCA 61.198 63.158 26.68 5.76 0.00 2.15
3651 3884 2.649614 GGACTACCGGCGCCTATC 59.350 66.667 26.68 13.74 0.00 2.08
3677 3910 4.484872 GGCTAGTCCGGCCCAACC 62.485 72.222 0.00 0.00 43.49 3.77
3687 3920 4.840005 GTGCGGCTGGGGCTAGTC 62.840 72.222 0.00 0.00 38.73 2.59
3703 3936 3.524606 CTGGGACCCGCGTATCGT 61.525 66.667 5.91 0.00 36.19 3.73
3704 3937 3.214123 TCTGGGACCCGCGTATCG 61.214 66.667 5.91 0.00 38.08 2.92
3725 3958 1.342672 GGCGAGGGGGTGAAATCCTA 61.343 60.000 0.00 0.00 0.00 2.94
3780 4013 3.706373 GAAGCAGGAGGGTGGCGA 61.706 66.667 0.00 0.00 0.00 5.54
3782 4015 4.432741 GGGAAGCAGGAGGGTGGC 62.433 72.222 0.00 0.00 0.00 5.01
3787 4020 3.787001 GGACGGGGAAGCAGGAGG 61.787 72.222 0.00 0.00 0.00 4.30
3819 4052 0.250901 GCCACAGAGCTTCAAAGGGA 60.251 55.000 0.00 0.00 0.00 4.20
3823 4056 0.823356 GGTGGCCACAGAGCTTCAAA 60.823 55.000 35.78 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.