Multiple sequence alignment - TraesCS1D01G082600

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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 TraesCS1D01G082600 chr1D 100.000 6180 0 0 1 6180 64886537 64880358 0.000000e+00 11413
1 TraesCS1D01G082600 chr1D 86.398 2610 260 52 2789 5332 64419789 64417209 0.000000e+00 2765
2 TraesCS1D01G082600 chr1D 85.389 1930 200 45 3443 5339 64140449 64138569 0.000000e+00 1927
3 TraesCS1D01G082600 chr1D 82.786 639 73 23 2789 3396 64141100 64140468 2.540000e-148 536
4 TraesCS1D01G082600 chr1D 83.529 595 45 24 749 1324 64142609 64142049 1.990000e-139 507
5 TraesCS1D01G082600 chr1D 83.139 599 45 25 748 1324 64421543 64420979 4.300000e-136 496
6 TraesCS1D01G082600 chr1B 92.424 5425 281 62 748 6108 105261973 105256615 0.000000e+00 7622
7 TraesCS1D01G082600 chr1B 86.902 1924 189 31 3443 5331 105109635 105107740 0.000000e+00 2098
8 TraesCS1D01G082600 chr1B 86.801 447 45 10 2789 3226 105110290 105109849 2.590000e-133 486
9 TraesCS1D01G082600 chr1B 82.601 592 54 30 748 1324 105111798 105111241 1.560000e-130 477
10 TraesCS1D01G082600 chr1A 91.647 2131 141 12 3227 5332 63743688 63741570 0.000000e+00 2915
11 TraesCS1D01G082600 chr1A 84.780 2615 284 67 2789 5331 63330536 63327964 0.000000e+00 2519
12 TraesCS1D01G082600 chr1A 86.846 1931 186 38 3443 5332 63477794 63475891 0.000000e+00 2097
13 TraesCS1D01G082600 chr1A 92.508 1268 49 21 1965 3226 63744956 63743729 0.000000e+00 1773
14 TraesCS1D01G082600 chr1A 86.154 1690 146 40 4 1639 63748874 63747219 0.000000e+00 1744
15 TraesCS1D01G082600 chr1A 83.993 556 63 12 5396 5928 63741560 63741008 1.540000e-140 510
16 TraesCS1D01G082600 chr1A 87.359 443 49 6 2789 3226 63478448 63478008 9.250000e-138 501
17 TraesCS1D01G082600 chr1A 83.419 585 45 26 749 1310 63332020 63331465 4.300000e-136 496
18 TraesCS1D01G082600 chr1A 85.523 449 45 11 872 1310 63481105 63480667 9.450000e-123 451
19 TraesCS1D01G082600 chr1A 84.722 360 35 14 3411 3751 426230475 426230833 5.930000e-90 342
20 TraesCS1D01G082600 chr1A 91.441 222 9 3 1637 1848 63746945 63746724 4.680000e-76 296
21 TraesCS1D01G082600 chr1A 85.824 261 23 9 489 741 568073915 568073661 1.320000e-66 265
22 TraesCS1D01G082600 chr1A 94.595 74 4 0 750 823 63481194 63481121 1.410000e-21 115
23 TraesCS1D01G082600 chr4B 82.878 549 68 16 3224 3751 69297870 69297327 2.610000e-128 470
24 TraesCS1D01G082600 chr4B 86.179 246 30 4 493 737 86649498 86649740 4.750000e-66 263
25 TraesCS1D01G082600 chr4B 87.857 140 11 4 3088 3224 69298047 69297911 6.410000e-35 159
26 TraesCS1D01G082600 chr5B 85.502 269 33 6 482 749 447183235 447183498 6.100000e-70 276
27 TraesCS1D01G082600 chr5B 84.109 258 36 5 485 741 446430703 446430450 1.720000e-60 244
28 TraesCS1D01G082600 chr4D 85.036 274 34 6 483 754 145579504 145579772 7.890000e-69 272
29 TraesCS1D01G082600 chr4D 86.364 242 28 4 489 729 443208843 443209080 6.150000e-65 259
30 TraesCS1D01G082600 chr4D 84.291 261 32 7 484 741 9306377 9306123 4.780000e-61 246
31 TraesCS1D01G082600 chr6D 85.827 254 31 5 489 741 348087604 348087853 1.320000e-66 265
32 TraesCS1D01G082600 chr3B 84.646 254 34 4 489 741 741566474 741566225 1.330000e-61 248
33 TraesCS1D01G082600 chr6A 95.556 90 3 1 6091 6180 134901329 134901417 6.460000e-30 143
34 TraesCS1D01G082600 chr6A 92.708 96 4 3 6086 6180 283048322 283048415 1.080000e-27 135
35 TraesCS1D01G082600 chr5D 93.684 95 4 2 6087 6180 8276554 8276647 2.320000e-29 141
36 TraesCS1D01G082600 chr2D 95.506 89 3 1 6092 6180 37995226 37995313 2.320000e-29 141
37 TraesCS1D01G082600 chr5A 91.837 98 4 4 6083 6180 673243574 673243667 3.890000e-27 134
38 TraesCS1D01G082600 chrUn 89.623 106 6 4 6078 6180 193551892 193551789 5.030000e-26 130
39 TraesCS1D01G082600 chrUn 89.623 106 6 4 6078 6180 342662914 342663017 5.030000e-26 130
40 TraesCS1D01G082600 chr3A 89.623 106 6 4 6078 6180 212448665 212448562 5.030000e-26 130
41 TraesCS1D01G082600 chr2A 88.889 108 7 4 6074 6180 743960657 743960760 1.810000e-25 128


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 TraesCS1D01G082600 chr1D 64880358 64886537 6179 True 11413.000000 11413 100.000000 1 6180 1 chr1D.!!$R1 6179
1 TraesCS1D01G082600 chr1D 64417209 64421543 4334 True 1630.500000 2765 84.768500 748 5332 2 chr1D.!!$R3 4584
2 TraesCS1D01G082600 chr1D 64138569 64142609 4040 True 990.000000 1927 83.901333 749 5339 3 chr1D.!!$R2 4590
3 TraesCS1D01G082600 chr1B 105256615 105261973 5358 True 7622.000000 7622 92.424000 748 6108 1 chr1B.!!$R1 5360
4 TraesCS1D01G082600 chr1B 105107740 105111798 4058 True 1020.333333 2098 85.434667 748 5331 3 chr1B.!!$R2 4583
5 TraesCS1D01G082600 chr1A 63327964 63332020 4056 True 1507.500000 2519 84.099500 749 5331 2 chr1A.!!$R2 4582
6 TraesCS1D01G082600 chr1A 63741008 63748874 7866 True 1447.600000 2915 89.148600 4 5928 5 chr1A.!!$R4 5924
7 TraesCS1D01G082600 chr1A 63475891 63481194 5303 True 791.000000 2097 88.580750 750 5332 4 chr1A.!!$R3 4582
8 TraesCS1D01G082600 chr4B 69297327 69298047 720 True 314.500000 470 85.367500 3088 3751 2 chr4B.!!$R1 663

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
121 122 0.036671 GGTTAGGGGTTGACTGTCGG 60.037 60.000 2.98 0.0 0.00 4.79 F
803 844 0.106918 TCCAAACACCGAGCAAACCT 60.107 50.000 0.00 0.0 0.00 3.50 F
1830 3603 0.033503 TGACCCGACAGAGGCAGATA 60.034 55.000 0.00 0.0 0.00 1.98 F
2045 5503 1.211949 TCCTTTTTGCGGGAGGATAGG 59.788 52.381 0.00 0.0 34.74 2.57 F
2053 5511 1.272536 GCGGGAGGATAGGACATAGGA 60.273 57.143 0.00 0.0 0.00 2.94 F
3916 7554 1.404035 GGTGCACAAAACCTTCTTCGT 59.596 47.619 20.43 0.0 34.66 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 3603 0.461870 TCGCACGCTGCTAAATGGAT 60.462 50.000 0.00 0.00 42.25 3.41 R
2531 6045 2.123589 TGTCTTCAGGGTTGACCAAGA 58.876 47.619 2.12 0.36 43.89 3.02 R
2932 6458 0.941542 TGTCAAAAAGTTCGCCTCCG 59.058 50.000 0.00 0.00 0.00 4.63 R
3281 6863 2.006888 CTGTAACATGTAACAGCGGGG 58.993 52.381 0.00 0.00 36.96 5.73 R
4002 7640 4.184079 TCATCGTCATCATATGGAGCAG 57.816 45.455 2.13 0.00 0.00 4.24 R
5339 9039 0.107312 CACCCCTTCAGCTGAGGATG 60.107 60.000 26.15 14.37 0.00 3.51 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 3.030652 CGGTGAAGGTTGCCACAC 58.969 61.111 0.00 0.00 35.13 3.82
19 20 1.525077 GGTGAAGGTTGCCACACGA 60.525 57.895 0.00 0.00 35.31 4.35
21 22 1.092921 GTGAAGGTTGCCACACGACA 61.093 55.000 0.00 0.00 33.88 4.35
94 95 3.434319 CACGACATGGTGGGCAGC 61.434 66.667 0.00 0.00 34.27 5.25
107 108 2.094545 GTGGGCAGCAGAAAATGGTTAG 60.095 50.000 0.00 0.00 37.60 2.34
120 121 0.682852 TGGTTAGGGGTTGACTGTCG 59.317 55.000 2.98 0.00 0.00 4.35
121 122 0.036671 GGTTAGGGGTTGACTGTCGG 60.037 60.000 2.98 0.00 0.00 4.79
122 123 0.672711 GTTAGGGGTTGACTGTCGGC 60.673 60.000 2.98 0.00 0.00 5.54
124 125 3.948719 GGGGTTGACTGTCGGCCA 61.949 66.667 17.95 0.00 0.00 5.36
128 129 2.031012 TTGACTGTCGGCCAGCTG 59.969 61.111 6.78 6.78 45.68 4.24
148 149 1.631071 GGGGCAGAGGGAGGAAGAAG 61.631 65.000 0.00 0.00 0.00 2.85
149 150 0.618968 GGGCAGAGGGAGGAAGAAGA 60.619 60.000 0.00 0.00 0.00 2.87
150 151 0.829990 GGCAGAGGGAGGAAGAAGAG 59.170 60.000 0.00 0.00 0.00 2.85
151 152 0.177836 GCAGAGGGAGGAAGAAGAGC 59.822 60.000 0.00 0.00 0.00 4.09
152 153 0.459489 CAGAGGGAGGAAGAAGAGCG 59.541 60.000 0.00 0.00 0.00 5.03
153 154 1.142965 GAGGGAGGAAGAAGAGCGC 59.857 63.158 0.00 0.00 0.00 5.92
155 156 2.888051 GGAGGAAGAAGAGCGCGC 60.888 66.667 26.66 26.66 0.00 6.86
157 158 4.459089 AGGAAGAAGAGCGCGCCC 62.459 66.667 30.33 18.43 0.00 6.13
185 201 3.181533 CGCGCACTAAAAAGGACTTACTC 60.182 47.826 8.75 0.00 0.00 2.59
186 202 3.181533 GCGCACTAAAAAGGACTTACTCG 60.182 47.826 0.30 0.00 0.00 4.18
210 226 2.725203 TAGTTGGGTGACTGCCGTGC 62.725 60.000 0.00 0.00 0.00 5.34
216 232 4.357947 TGACTGCCGTGCGGAGTC 62.358 66.667 23.38 23.38 40.03 3.36
242 258 3.767230 CACCGAGCGAACGTGCAG 61.767 66.667 0.00 0.00 37.31 4.41
250 266 3.414700 GAACGTGCAGCGGGTCTG 61.415 66.667 12.18 0.00 46.52 3.51
260 276 0.249911 AGCGGGTCTGTCTGTTGTTC 60.250 55.000 0.00 0.00 0.00 3.18
269 285 1.274596 GTCTGTTGTTCGTGTGACGT 58.725 50.000 0.00 0.00 43.14 4.34
275 291 2.582728 TGTTCGTGTGACGTAAACCT 57.417 45.000 0.00 0.00 43.14 3.50
277 293 2.159268 TGTTCGTGTGACGTAAACCTGA 60.159 45.455 0.00 0.00 43.14 3.86
308 324 0.737019 GGTGAATTTGCGCCCACATG 60.737 55.000 4.18 0.00 32.25 3.21
321 337 1.374125 CACATGGACACGAAGCGGA 60.374 57.895 0.00 0.00 0.00 5.54
325 341 0.740868 ATGGACACGAAGCGGACATG 60.741 55.000 0.00 0.00 0.00 3.21
328 344 0.438830 GACACGAAGCGGACATGAAC 59.561 55.000 0.00 0.00 0.00 3.18
331 347 0.670546 ACGAAGCGGACATGAACTGG 60.671 55.000 0.00 0.00 0.00 4.00
337 353 0.240945 CGGACATGAACTGGGTTTGC 59.759 55.000 0.00 0.00 0.00 3.68
341 357 0.110238 CATGAACTGGGTTTGCGTCG 60.110 55.000 0.00 0.00 0.00 5.12
363 379 2.028839 TCGCGTTGGGTCTTGATTTCTA 60.029 45.455 5.77 0.00 0.00 2.10
368 384 5.066505 GCGTTGGGTCTTGATTTCTATTCAT 59.933 40.000 0.00 0.00 0.00 2.57
384 400 8.450578 TTCTATTCATGCAGATTTAAACGGAT 57.549 30.769 0.00 0.00 0.00 4.18
389 405 7.857734 TCATGCAGATTTAAACGGATAAAGA 57.142 32.000 0.00 0.00 0.00 2.52
390 406 7.693952 TCATGCAGATTTAAACGGATAAAGAC 58.306 34.615 0.00 0.00 0.00 3.01
391 407 7.335673 TCATGCAGATTTAAACGGATAAAGACA 59.664 33.333 0.00 0.00 0.00 3.41
393 409 6.876789 TGCAGATTTAAACGGATAAAGACAGA 59.123 34.615 0.00 0.00 0.00 3.41
394 410 7.148474 TGCAGATTTAAACGGATAAAGACAGAC 60.148 37.037 0.00 0.00 0.00 3.51
395 411 7.148474 GCAGATTTAAACGGATAAAGACAGACA 60.148 37.037 0.00 0.00 0.00 3.41
396 412 8.717821 CAGATTTAAACGGATAAAGACAGACAA 58.282 33.333 0.00 0.00 0.00 3.18
400 416 9.672086 TTTAAACGGATAAAGACAGACAAAATG 57.328 29.630 0.00 0.00 0.00 2.32
401 417 6.877611 AACGGATAAAGACAGACAAAATGT 57.122 33.333 0.00 0.00 0.00 2.71
402 418 6.241207 ACGGATAAAGACAGACAAAATGTG 57.759 37.500 0.00 0.00 0.00 3.21
410 427 4.389992 AGACAGACAAAATGTGTATCTGCG 59.610 41.667 0.00 0.00 41.96 5.18
425 442 0.605319 CTGCGTTGGAGTTGCCCTAA 60.605 55.000 0.00 0.00 34.97 2.69
462 481 1.009389 AGCTTCTTTCCTCGTTCGCG 61.009 55.000 0.00 0.00 42.98 5.87
467 486 1.615107 CTTTCCTCGTTCGCGTCACC 61.615 60.000 5.77 0.00 42.11 4.02
470 489 2.087009 CCTCGTTCGCGTCACCTTC 61.087 63.158 5.77 0.00 42.11 3.46
473 492 1.947146 CGTTCGCGTCACCTTCACA 60.947 57.895 5.77 0.00 35.57 3.58
474 493 1.853319 GTTCGCGTCACCTTCACAG 59.147 57.895 5.77 0.00 0.00 3.66
482 501 4.150980 CGCGTCACCTTCACAGTAAAAATA 59.849 41.667 0.00 0.00 0.00 1.40
486 505 8.231837 GCGTCACCTTCACAGTAAAAATATTAA 58.768 33.333 0.00 0.00 0.00 1.40
487 506 9.537848 CGTCACCTTCACAGTAAAAATATTAAC 57.462 33.333 0.00 0.00 0.00 2.01
515 551 7.908601 CCTTCCGTTTTTATTTACTCTGCATAC 59.091 37.037 0.00 0.00 0.00 2.39
530 566 7.324178 ACTCTGCATACTAGGTTTGTCTAAAG 58.676 38.462 0.00 0.00 0.00 1.85
632 668 9.772973 AATTCAGCATTGCATATATTTTCACAT 57.227 25.926 11.91 0.00 0.00 3.21
633 669 8.806177 TTCAGCATTGCATATATTTTCACATC 57.194 30.769 11.91 0.00 0.00 3.06
637 673 9.850628 AGCATTGCATATATTTTCACATCATAC 57.149 29.630 11.91 0.00 0.00 2.39
638 674 9.628746 GCATTGCATATATTTTCACATCATACA 57.371 29.630 3.15 0.00 0.00 2.29
723 759 5.244851 TGGCTTCAACCAAAACTAATATGCA 59.755 36.000 0.00 0.00 36.55 3.96
724 760 6.162777 GGCTTCAACCAAAACTAATATGCAA 58.837 36.000 0.00 0.00 0.00 4.08
725 761 6.648725 GGCTTCAACCAAAACTAATATGCAAA 59.351 34.615 0.00 0.00 0.00 3.68
726 762 7.148590 GGCTTCAACCAAAACTAATATGCAAAG 60.149 37.037 0.00 0.00 0.00 2.77
727 763 7.384932 GCTTCAACCAAAACTAATATGCAAAGT 59.615 33.333 0.00 0.00 0.00 2.66
728 764 9.906660 CTTCAACCAAAACTAATATGCAAAGTA 57.093 29.630 0.00 0.00 0.00 2.24
729 765 9.906660 TTCAACCAAAACTAATATGCAAAGTAG 57.093 29.630 0.00 0.00 0.00 2.57
730 766 9.290988 TCAACCAAAACTAATATGCAAAGTAGA 57.709 29.630 0.00 0.00 0.00 2.59
731 767 9.341899 CAACCAAAACTAATATGCAAAGTAGAC 57.658 33.333 0.00 0.00 0.00 2.59
732 768 8.630054 ACCAAAACTAATATGCAAAGTAGACA 57.370 30.769 0.00 0.00 0.00 3.41
733 769 9.073475 ACCAAAACTAATATGCAAAGTAGACAA 57.927 29.630 0.00 0.00 0.00 3.18
734 770 9.906660 CCAAAACTAATATGCAAAGTAGACAAA 57.093 29.630 0.00 0.00 0.00 2.83
741 777 8.986477 AATATGCAAAGTAGACAAAAATGGAC 57.014 30.769 0.00 0.00 0.00 4.02
742 778 5.195001 TGCAAAGTAGACAAAAATGGACC 57.805 39.130 0.00 0.00 0.00 4.46
803 844 0.106918 TCCAAACACCGAGCAAACCT 60.107 50.000 0.00 0.00 0.00 3.50
828 869 1.675972 ACACACAACCGCAACCACA 60.676 52.632 0.00 0.00 0.00 4.17
832 873 2.024022 CAACCGCAACCACACACG 59.976 61.111 0.00 0.00 0.00 4.49
898 942 3.008049 AGAGCTATAAATACGCCCCCTTG 59.992 47.826 0.00 0.00 0.00 3.61
959 1023 1.605058 CTCCGACCCGATTCACCAGT 61.605 60.000 0.00 0.00 0.00 4.00
1332 1434 4.821589 CCCGCCGCTCCTGTTCTC 62.822 72.222 0.00 0.00 0.00 2.87
1342 1444 3.191581 CGCTCCTGTTCTCTTCTGAACTA 59.808 47.826 8.52 0.00 44.63 2.24
1343 1445 4.321304 CGCTCCTGTTCTCTTCTGAACTAA 60.321 45.833 8.52 0.00 44.63 2.24
1344 1446 5.623368 CGCTCCTGTTCTCTTCTGAACTAAT 60.623 44.000 8.52 0.00 44.63 1.73
1346 1448 5.955488 TCCTGTTCTCTTCTGAACTAATCG 58.045 41.667 8.52 0.00 44.63 3.34
1347 1449 4.564769 CCTGTTCTCTTCTGAACTAATCGC 59.435 45.833 8.52 0.00 44.63 4.58
1348 1450 4.166523 TGTTCTCTTCTGAACTAATCGCG 58.833 43.478 0.00 0.00 44.63 5.87
1349 1451 4.082949 TGTTCTCTTCTGAACTAATCGCGA 60.083 41.667 13.09 13.09 44.63 5.87
1350 1452 4.902443 TCTCTTCTGAACTAATCGCGAT 57.098 40.909 17.62 17.62 0.00 4.58
1351 1453 4.849883 TCTCTTCTGAACTAATCGCGATC 58.150 43.478 23.92 11.12 0.00 3.69
1353 1455 4.849883 TCTTCTGAACTAATCGCGATCTC 58.150 43.478 23.92 16.21 0.00 2.75
1354 1456 3.627732 TCTGAACTAATCGCGATCTCC 57.372 47.619 23.92 10.57 0.00 3.71
1377 1484 3.118992 GCTCCTGTTGATTTCATTTCCCC 60.119 47.826 0.00 0.00 0.00 4.81
1400 1507 0.462047 ATCGGCCAGTGGATTCGTTC 60.462 55.000 15.20 0.00 0.00 3.95
1418 1525 3.192922 ACGAATTAGCCGCGTGCC 61.193 61.111 14.64 0.00 42.71 5.01
1419 1526 4.279535 CGAATTAGCCGCGTGCCG 62.280 66.667 14.64 8.01 42.71 5.69
1420 1527 3.192922 GAATTAGCCGCGTGCCGT 61.193 61.111 14.64 1.99 42.71 5.68
1421 1528 3.434566 GAATTAGCCGCGTGCCGTG 62.435 63.158 14.64 1.74 42.71 4.94
1434 1541 0.724549 TGCCGTGCGATGTATGTTTC 59.275 50.000 0.00 0.00 0.00 2.78
1656 2118 9.750125 TCATCGTAATGCTTATCCATATATGTC 57.250 33.333 11.73 0.00 32.58 3.06
1736 3499 8.624776 GTGTTATATACACGTAGGACTAAACCT 58.375 37.037 0.00 0.00 46.94 3.50
1813 3586 1.556373 CCTCAGACATGGGCTGGTGA 61.556 60.000 15.21 0.86 34.20 4.02
1814 3587 0.392193 CTCAGACATGGGCTGGTGAC 60.392 60.000 15.21 0.00 34.20 3.67
1830 3603 0.033503 TGACCCGACAGAGGCAGATA 60.034 55.000 0.00 0.00 0.00 1.98
1864 3637 2.540515 GTGCGATGTATACTGTGCTGT 58.459 47.619 4.17 0.00 0.00 4.40
1885 3658 2.241479 CTGCTGCCTCTCTCCTGGTG 62.241 65.000 0.00 0.00 0.00 4.17
1889 3662 1.610673 GCCTCTCTCCTGGTGGTGA 60.611 63.158 0.00 0.00 34.96 4.02
1906 3679 9.429359 CTGGTGGTGAACTCATATTATTATCTC 57.571 37.037 0.00 0.00 0.00 2.75
2012 5470 3.304861 GGGTTACAAAACATTGACCGGAC 60.305 47.826 9.46 1.07 37.34 4.79
2043 5501 2.193127 TCTCCTTTTTGCGGGAGGATA 58.807 47.619 8.82 0.00 46.51 2.59
2044 5502 2.170607 TCTCCTTTTTGCGGGAGGATAG 59.829 50.000 8.82 0.00 46.51 2.08
2045 5503 1.211949 TCCTTTTTGCGGGAGGATAGG 59.788 52.381 0.00 0.00 34.74 2.57
2046 5504 1.211949 CCTTTTTGCGGGAGGATAGGA 59.788 52.381 0.00 0.00 32.11 2.94
2047 5505 2.289565 CTTTTTGCGGGAGGATAGGAC 58.710 52.381 0.00 0.00 0.00 3.85
2048 5506 1.281419 TTTTGCGGGAGGATAGGACA 58.719 50.000 0.00 0.00 0.00 4.02
2049 5507 1.507140 TTTGCGGGAGGATAGGACAT 58.493 50.000 0.00 0.00 0.00 3.06
2053 5511 1.272536 GCGGGAGGATAGGACATAGGA 60.273 57.143 0.00 0.00 0.00 2.94
2085 5543 4.853924 AAACATGATGACCTGGAACAAC 57.146 40.909 0.00 0.00 38.70 3.32
2282 5786 5.418840 ACAATTATCAACCGCAGATTCCTTT 59.581 36.000 0.00 0.00 0.00 3.11
2304 5810 3.806949 AAAATGGTACTCCTGCTTGGA 57.193 42.857 0.00 0.00 43.86 3.53
2531 6045 7.693969 AGTTCTAGTTGCATAATCTTTGCTT 57.306 32.000 0.00 0.00 40.77 3.91
2601 6115 2.359850 TCCATGCCACGCACTTCC 60.360 61.111 0.00 0.00 43.04 3.46
2614 6129 2.659428 GCACTTCCCCATGCTAAGATT 58.341 47.619 6.85 0.00 38.84 2.40
2932 6458 3.715628 ATGGTGCTTGAGTTTGTCAAC 57.284 42.857 0.00 0.00 40.45 3.18
3204 6737 3.919223 AGGTACTGACGACTGAAGTTC 57.081 47.619 0.00 0.00 37.18 3.01
3281 6863 5.992217 ACTGTTCTGTGTTCTCCTGATTTAC 59.008 40.000 0.00 0.00 0.00 2.01
3285 6867 2.027561 TGTGTTCTCCTGATTTACCCCG 60.028 50.000 0.00 0.00 0.00 5.73
3843 7481 8.715998 CATTCCAATGATACTACTGTTATCTGC 58.284 37.037 0.00 0.00 38.70 4.26
3916 7554 1.404035 GGTGCACAAAACCTTCTTCGT 59.596 47.619 20.43 0.00 34.66 3.85
3917 7555 2.540973 GGTGCACAAAACCTTCTTCGTC 60.541 50.000 20.43 0.00 34.66 4.20
3919 7557 1.595794 GCACAAAACCTTCTTCGTCGA 59.404 47.619 0.00 0.00 0.00 4.20
4002 7640 5.760743 GGTTTCAGAAGGACTATATTCCTGC 59.239 44.000 12.12 10.42 46.06 4.85
4170 7808 4.378978 CGCTGATCGGTGAATTTTGGTTTA 60.379 41.667 9.63 0.00 33.78 2.01
4172 7810 6.457663 CGCTGATCGGTGAATTTTGGTTTATA 60.458 38.462 9.63 0.00 33.78 0.98
4255 7893 2.421424 GCTTTTCAGCTGATCGGAATGT 59.579 45.455 19.04 0.00 43.51 2.71
4333 7982 1.355720 AGTGCCTCCCTTGCTGTATTT 59.644 47.619 0.00 0.00 0.00 1.40
4368 8017 3.126073 CTGCAAAGCTGGGAAGAAAAAC 58.874 45.455 0.00 0.00 0.00 2.43
4398 8047 5.586243 TGCATAGCTTCTGAAGATAAACACC 59.414 40.000 21.06 7.71 32.48 4.16
4438 8087 0.622136 AATCACTGGATGCTGCCTCA 59.378 50.000 7.23 0.00 32.92 3.86
4439 8088 0.107312 ATCACTGGATGCTGCCTCAC 60.107 55.000 7.23 0.00 30.86 3.51
4469 8118 7.770433 CCTTATACAACAACTCATCTGATCCAA 59.230 37.037 0.00 0.00 0.00 3.53
4629 8297 4.697352 GCAGAAGCTTCTCATTGTAAAGGA 59.303 41.667 26.18 0.00 34.74 3.36
4692 8361 4.980590 TGAAAATGATGTGCCGTGTTATC 58.019 39.130 0.00 0.00 0.00 1.75
4848 8518 0.603707 TGCTAACAGCTGTGGTGCTC 60.604 55.000 27.40 14.16 42.97 4.26
4898 8572 0.253044 GCCCCTCTCTGCATGTTGTA 59.747 55.000 0.00 0.00 0.00 2.41
4913 8587 5.625656 GCATGTTGTAGAGCTTAGGAAGTCT 60.626 44.000 0.00 0.00 0.00 3.24
4968 8650 2.426522 AGAGCGCTAACTGAATTTGCA 58.573 42.857 11.50 0.00 38.78 4.08
5012 8694 2.928801 TCTTCAGTGCTGGTGCTTAA 57.071 45.000 0.00 0.00 40.48 1.85
5022 8704 4.635765 GTGCTGGTGCTTAATGAGTGAATA 59.364 41.667 0.00 0.00 40.48 1.75
5089 8774 0.395862 GGATCTCGAGTGACCTGGGA 60.396 60.000 13.13 0.00 0.00 4.37
5113 8798 3.855668 TGACAAGATTTTTGGGATGGGT 58.144 40.909 0.00 0.00 0.00 4.51
5264 8964 6.644248 TGATTGGAAATGATGATGATGGTC 57.356 37.500 0.00 0.00 0.00 4.02
5332 9032 4.279922 TCGAGTGGTGAAACTGACTATCAA 59.720 41.667 0.00 0.00 36.74 2.57
5333 9033 4.623167 CGAGTGGTGAAACTGACTATCAAG 59.377 45.833 0.00 0.00 36.74 3.02
5335 9035 3.437049 GTGGTGAAACTGACTATCAAGGC 59.563 47.826 0.00 0.00 36.74 4.35
5336 9036 3.010420 GGTGAAACTGACTATCAAGGCC 58.990 50.000 0.00 0.00 36.74 5.19
5337 9037 3.559171 GGTGAAACTGACTATCAAGGCCA 60.559 47.826 5.01 0.00 36.74 5.36
5338 9038 4.265073 GTGAAACTGACTATCAAGGCCAT 58.735 43.478 5.01 0.00 0.00 4.40
5339 9039 4.333926 GTGAAACTGACTATCAAGGCCATC 59.666 45.833 5.01 0.00 0.00 3.51
5340 9040 4.019411 TGAAACTGACTATCAAGGCCATCA 60.019 41.667 5.01 0.00 0.00 3.07
5369 9069 1.972660 GAAGGGGTGTGATAGCGGCT 61.973 60.000 7.98 7.98 0.00 5.52
5493 9195 8.974060 AAAAACTACACACAATCTTCCTTCTA 57.026 30.769 0.00 0.00 0.00 2.10
5504 9206 4.207891 TCTTCCTTCTACACTTGCCATC 57.792 45.455 0.00 0.00 0.00 3.51
5524 9226 0.858369 AGGGAAGCTCGATACCCCTA 59.142 55.000 11.64 0.00 45.08 3.53
5549 9252 2.821969 ACATTCCAAACACCATCAGAGC 59.178 45.455 0.00 0.00 0.00 4.09
5576 9279 1.862123 CGTTGTTGACGCAGCAGAT 59.138 52.632 0.00 0.00 45.86 2.90
5614 9317 0.091344 GCGTGAAGATGTCGACAACG 59.909 55.000 26.97 26.97 41.26 4.10
5628 9331 2.096417 CGACAACGACAATCTGGGAAAC 60.096 50.000 0.00 0.00 42.66 2.78
5681 9384 1.364317 TGGTTGGATGACCACCCCAA 61.364 55.000 0.00 0.00 46.45 4.12
5686 9389 1.005805 TGGATGACCACCCCAAATCTG 59.994 52.381 0.00 0.00 41.77 2.90
5709 9412 2.618053 CAAACAGATACGGGGAGACAC 58.382 52.381 0.00 0.00 0.00 3.67
5715 9418 1.553704 GATACGGGGAGACACAACCTT 59.446 52.381 0.00 0.00 0.00 3.50
5742 9445 3.753272 GCTCCTTGACAATGCTGAAACTA 59.247 43.478 0.00 0.00 0.00 2.24
5745 9448 3.755378 CCTTGACAATGCTGAAACTAGCT 59.245 43.478 0.00 0.00 44.01 3.32
5746 9449 4.142730 CCTTGACAATGCTGAAACTAGCTC 60.143 45.833 0.00 0.00 44.01 4.09
5754 9457 4.136796 TGCTGAAACTAGCTCAATGTTGT 58.863 39.130 0.00 0.00 44.01 3.32
5769 9472 2.816411 TGTTGTCGGTTAGAGGAGGAT 58.184 47.619 0.00 0.00 0.00 3.24
5774 9477 2.815503 GTCGGTTAGAGGAGGATCTAGC 59.184 54.545 0.00 0.00 33.44 3.42
5775 9478 2.164338 CGGTTAGAGGAGGATCTAGCC 58.836 57.143 6.58 6.58 45.08 3.93
5776 9479 3.246416 GGTTAGAGGAGGATCTAGCCA 57.754 52.381 10.63 0.00 46.75 4.75
5777 9480 3.785364 GGTTAGAGGAGGATCTAGCCAT 58.215 50.000 10.63 0.00 46.75 4.40
5781 9484 1.899142 GAGGAGGATCTAGCCATCCAC 59.101 57.143 11.90 6.35 44.57 4.02
5782 9485 1.507300 AGGAGGATCTAGCCATCCACT 59.493 52.381 11.90 7.31 44.57 4.00
5783 9486 1.899142 GGAGGATCTAGCCATCCACTC 59.101 57.143 11.90 3.21 44.57 3.51
5785 9488 0.605589 GGATCTAGCCATCCACTCCG 59.394 60.000 5.73 0.00 42.02 4.63
5841 9564 1.046472 AAGACACGACCAGACCCACA 61.046 55.000 0.00 0.00 0.00 4.17
5873 9596 0.896940 TACTGACCACACGACCCCTC 60.897 60.000 0.00 0.00 0.00 4.30
5907 9631 0.186386 CCCTCCTCTAGTCCACCGAT 59.814 60.000 0.00 0.00 0.00 4.18
5941 9665 0.179134 CGAGGTGGACGAGGATTCAC 60.179 60.000 0.00 0.00 0.00 3.18
5943 9667 0.611062 AGGTGGACGAGGATTCACGA 60.611 55.000 0.00 0.00 0.00 4.35
5957 9681 6.273071 AGGATTCACGAAAACCTTTTTCTTG 58.727 36.000 10.19 10.19 30.89 3.02
5958 9682 5.462068 GGATTCACGAAAACCTTTTTCTTGG 59.538 40.000 14.38 2.24 31.23 3.61
5991 9715 0.255890 ACCATCACCACCATAGCACC 59.744 55.000 0.00 0.00 0.00 5.01
5995 9719 1.745115 CACCACCATAGCACCACCG 60.745 63.158 0.00 0.00 0.00 4.94
6011 9735 1.597027 CCGTCAGGGTGCGAACTTT 60.597 57.895 0.00 0.00 0.00 2.66
6022 9746 4.992951 GGGTGCGAACTTTTAACTCTAAGA 59.007 41.667 0.00 0.00 0.00 2.10
6039 9763 3.283259 AAGAGGCCTAAGTACAATGCC 57.717 47.619 4.42 7.42 42.48 4.40
6048 9772 4.334203 CCTAAGTACAATGCCGCAATGTAA 59.666 41.667 20.30 6.99 32.55 2.41
6072 9796 4.854042 GGTCCCCACCCCTTCTAT 57.146 61.111 0.00 0.00 36.54 1.98
6073 9797 2.541177 GGTCCCCACCCCTTCTATC 58.459 63.158 0.00 0.00 36.54 2.08
6108 9833 0.903454 GGAGGAGGGGAGTCGTTGAA 60.903 60.000 0.00 0.00 0.00 2.69
6109 9834 0.533032 GAGGAGGGGAGTCGTTGAAG 59.467 60.000 0.00 0.00 0.00 3.02
6110 9835 0.905337 AGGAGGGGAGTCGTTGAAGG 60.905 60.000 0.00 0.00 0.00 3.46
6111 9836 0.903454 GGAGGGGAGTCGTTGAAGGA 60.903 60.000 0.00 0.00 0.00 3.36
6112 9837 0.974383 GAGGGGAGTCGTTGAAGGAA 59.026 55.000 0.00 0.00 0.00 3.36
6113 9838 1.346722 GAGGGGAGTCGTTGAAGGAAA 59.653 52.381 0.00 0.00 0.00 3.13
6114 9839 1.985895 AGGGGAGTCGTTGAAGGAAAT 59.014 47.619 0.00 0.00 0.00 2.17
6115 9840 3.178865 AGGGGAGTCGTTGAAGGAAATA 58.821 45.455 0.00 0.00 0.00 1.40
6116 9841 3.780850 AGGGGAGTCGTTGAAGGAAATAT 59.219 43.478 0.00 0.00 0.00 1.28
6117 9842 3.877508 GGGGAGTCGTTGAAGGAAATATG 59.122 47.826 0.00 0.00 0.00 1.78
6118 9843 3.312697 GGGAGTCGTTGAAGGAAATATGC 59.687 47.826 0.00 0.00 0.00 3.14
6119 9844 3.312697 GGAGTCGTTGAAGGAAATATGCC 59.687 47.826 0.00 0.00 0.00 4.40
6120 9845 3.279434 AGTCGTTGAAGGAAATATGCCC 58.721 45.455 0.00 0.00 0.00 5.36
6121 9846 3.054361 AGTCGTTGAAGGAAATATGCCCT 60.054 43.478 0.00 0.00 0.00 5.19
6122 9847 4.163458 AGTCGTTGAAGGAAATATGCCCTA 59.837 41.667 0.00 0.00 31.36 3.53
6123 9848 4.272748 GTCGTTGAAGGAAATATGCCCTAC 59.727 45.833 0.00 0.00 31.36 3.18
6124 9849 4.080807 TCGTTGAAGGAAATATGCCCTACA 60.081 41.667 0.00 0.00 31.36 2.74
6125 9850 4.821805 CGTTGAAGGAAATATGCCCTACAT 59.178 41.667 0.00 0.00 43.18 2.29
6126 9851 5.277974 CGTTGAAGGAAATATGCCCTACATG 60.278 44.000 0.00 0.00 40.06 3.21
6127 9852 4.144297 TGAAGGAAATATGCCCTACATGC 58.856 43.478 0.00 0.00 40.06 4.06
6128 9853 3.882102 AGGAAATATGCCCTACATGCA 57.118 42.857 0.00 0.00 43.97 3.96
6129 9854 4.183223 AGGAAATATGCCCTACATGCAA 57.817 40.909 0.00 0.00 42.92 4.08
6130 9855 4.744237 AGGAAATATGCCCTACATGCAAT 58.256 39.130 0.00 0.00 42.92 3.56
6131 9856 5.891198 AGGAAATATGCCCTACATGCAATA 58.109 37.500 0.00 0.00 42.92 1.90
6132 9857 6.314120 AGGAAATATGCCCTACATGCAATAA 58.686 36.000 0.00 0.00 42.92 1.40
6133 9858 6.955851 AGGAAATATGCCCTACATGCAATAAT 59.044 34.615 0.00 0.00 42.92 1.28
6134 9859 8.115384 AGGAAATATGCCCTACATGCAATAATA 58.885 33.333 0.00 0.00 42.92 0.98
6135 9860 8.748412 GGAAATATGCCCTACATGCAATAATAA 58.252 33.333 0.00 0.00 42.92 1.40
6138 9863 8.884124 ATATGCCCTACATGCAATAATAAAGT 57.116 30.769 0.00 0.00 42.92 2.66
6139 9864 7.601705 ATGCCCTACATGCAATAATAAAGTT 57.398 32.000 0.00 0.00 42.92 2.66
6140 9865 6.804677 TGCCCTACATGCAATAATAAAGTTG 58.195 36.000 0.00 0.00 35.40 3.16
6141 9866 6.379703 TGCCCTACATGCAATAATAAAGTTGT 59.620 34.615 0.00 0.00 35.40 3.32
6142 9867 7.093552 TGCCCTACATGCAATAATAAAGTTGTT 60.094 33.333 0.00 0.00 35.40 2.83
6143 9868 8.410141 GCCCTACATGCAATAATAAAGTTGTTA 58.590 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.892334 CGTGTGGCAACCTTCACCG 61.892 63.158 0.00 0.00 33.29 4.94
1 2 1.525077 TCGTGTGGCAACCTTCACC 60.525 57.895 0.00 0.00 33.29 4.02
2 3 1.092921 TGTCGTGTGGCAACCTTCAC 61.093 55.000 0.00 0.00 34.71 3.18
35 36 3.322466 CCACGAGACTGGCCCCTT 61.322 66.667 0.00 0.00 0.00 3.95
43 44 4.702081 GCGCACGACCACGAGACT 62.702 66.667 0.30 0.00 42.66 3.24
45 46 4.400109 GAGCGCACGACCACGAGA 62.400 66.667 11.47 0.00 42.66 4.04
65 66 2.737376 GTCGTGGAAGTGGACGCC 60.737 66.667 0.00 0.00 35.53 5.68
66 67 1.374252 ATGTCGTGGAAGTGGACGC 60.374 57.895 0.00 0.00 35.53 5.19
67 68 2.445274 CATGTCGTGGAAGTGGACG 58.555 57.895 0.00 0.00 36.91 4.79
92 93 3.165071 CAACCCCTAACCATTTTCTGCT 58.835 45.455 0.00 0.00 0.00 4.24
94 95 4.218417 CAGTCAACCCCTAACCATTTTCTG 59.782 45.833 0.00 0.00 0.00 3.02
107 108 3.901797 CTGGCCGACAGTCAACCCC 62.902 68.421 0.00 0.00 42.42 4.95
128 129 3.093172 CTTCCTCCCTCTGCCCCC 61.093 72.222 0.00 0.00 0.00 5.40
157 158 0.729140 CTTTTTAGTGCGCGCTTGGG 60.729 55.000 33.29 11.26 0.00 4.12
158 159 0.729140 CCTTTTTAGTGCGCGCTTGG 60.729 55.000 33.29 18.32 0.00 3.61
159 160 0.237235 TCCTTTTTAGTGCGCGCTTG 59.763 50.000 33.29 13.63 0.00 4.01
160 161 0.237498 GTCCTTTTTAGTGCGCGCTT 59.763 50.000 33.29 22.21 0.00 4.68
161 162 0.602905 AGTCCTTTTTAGTGCGCGCT 60.603 50.000 33.29 28.46 0.00 5.92
163 164 2.735134 AGTAAGTCCTTTTTAGTGCGCG 59.265 45.455 0.00 0.00 0.00 6.86
165 166 3.367025 CCGAGTAAGTCCTTTTTAGTGCG 59.633 47.826 0.00 0.00 0.00 5.34
166 167 4.151867 CACCGAGTAAGTCCTTTTTAGTGC 59.848 45.833 0.00 0.00 0.00 4.40
168 169 4.346127 ACCACCGAGTAAGTCCTTTTTAGT 59.654 41.667 0.00 0.00 0.00 2.24
185 201 0.320421 CAGTCACCCAACTACCACCG 60.320 60.000 0.00 0.00 0.00 4.94
186 202 0.605589 GCAGTCACCCAACTACCACC 60.606 60.000 0.00 0.00 0.00 4.61
210 226 4.436998 GTGTCCGCCCTGACTCCG 62.437 72.222 0.00 0.00 36.21 4.63
242 258 1.557443 CGAACAACAGACAGACCCGC 61.557 60.000 0.00 0.00 0.00 6.13
245 261 1.593006 CACACGAACAACAGACAGACC 59.407 52.381 0.00 0.00 0.00 3.85
247 263 2.536365 GTCACACGAACAACAGACAGA 58.464 47.619 0.00 0.00 0.00 3.41
249 265 1.273688 CGTCACACGAACAACAGACA 58.726 50.000 0.00 0.00 46.05 3.41
250 266 1.274596 ACGTCACACGAACAACAGAC 58.725 50.000 2.48 0.00 46.05 3.51
292 308 0.458370 GTCCATGTGGGCGCAAATTC 60.458 55.000 10.83 0.00 36.21 2.17
308 324 0.669318 TTCATGTCCGCTTCGTGTCC 60.669 55.000 0.00 0.00 0.00 4.02
321 337 0.951558 GACGCAAACCCAGTTCATGT 59.048 50.000 0.00 0.00 0.00 3.21
325 341 1.568025 GACGACGCAAACCCAGTTC 59.432 57.895 0.00 0.00 0.00 3.01
337 353 4.695231 AGACCCAACGCGACGACG 62.695 66.667 15.93 2.12 42.93 5.12
341 357 0.872388 AAATCAAGACCCAACGCGAC 59.128 50.000 15.93 0.00 0.00 5.19
363 379 8.902806 TCTTTATCCGTTTAAATCTGCATGAAT 58.097 29.630 0.00 0.00 0.00 2.57
368 384 6.876789 TCTGTCTTTATCCGTTTAAATCTGCA 59.123 34.615 0.00 0.00 0.00 4.41
384 400 7.360017 CGCAGATACACATTTTGTCTGTCTTTA 60.360 37.037 0.00 0.00 39.91 1.85
388 404 4.152402 ACGCAGATACACATTTTGTCTGTC 59.848 41.667 0.00 0.00 39.91 3.51
389 405 4.065088 ACGCAGATACACATTTTGTCTGT 58.935 39.130 0.00 0.00 39.91 3.41
390 406 4.668576 ACGCAGATACACATTTTGTCTG 57.331 40.909 0.00 0.00 39.91 3.51
391 407 4.083324 CCAACGCAGATACACATTTTGTCT 60.083 41.667 0.00 0.00 39.91 3.41
393 409 3.818210 TCCAACGCAGATACACATTTTGT 59.182 39.130 0.00 0.00 42.84 2.83
394 410 4.083324 ACTCCAACGCAGATACACATTTTG 60.083 41.667 0.00 0.00 0.00 2.44
395 411 4.072131 ACTCCAACGCAGATACACATTTT 58.928 39.130 0.00 0.00 0.00 1.82
396 412 3.674997 ACTCCAACGCAGATACACATTT 58.325 40.909 0.00 0.00 0.00 2.32
399 415 2.412870 CAACTCCAACGCAGATACACA 58.587 47.619 0.00 0.00 0.00 3.72
400 416 1.128692 GCAACTCCAACGCAGATACAC 59.871 52.381 0.00 0.00 0.00 2.90
401 417 1.438651 GCAACTCCAACGCAGATACA 58.561 50.000 0.00 0.00 0.00 2.29
402 418 0.727398 GGCAACTCCAACGCAGATAC 59.273 55.000 0.00 0.00 34.01 2.24
410 427 1.607148 GTGTGTTAGGGCAACTCCAAC 59.393 52.381 0.00 0.00 38.05 3.77
439 456 3.576648 CGAACGAGGAAAGAAGCTAAGT 58.423 45.455 0.00 0.00 0.00 2.24
440 457 2.345942 GCGAACGAGGAAAGAAGCTAAG 59.654 50.000 0.00 0.00 0.00 2.18
444 463 1.282930 ACGCGAACGAGGAAAGAAGC 61.283 55.000 15.93 0.00 43.93 3.86
457 476 0.669619 TACTGTGAAGGTGACGCGAA 59.330 50.000 15.93 0.00 0.00 4.70
462 481 9.836076 GGTTAATATTTTTACTGTGAAGGTGAC 57.164 33.333 0.00 0.00 0.00 3.67
470 489 7.121611 ACGGAAGGGGTTAATATTTTTACTGTG 59.878 37.037 0.00 0.00 0.00 3.66
473 492 8.654485 AAACGGAAGGGGTTAATATTTTTACT 57.346 30.769 0.00 0.00 0.00 2.24
474 493 9.709495 AAAAACGGAAGGGGTTAATATTTTTAC 57.291 29.630 0.00 0.00 0.00 2.01
482 501 8.654485 AGTAAATAAAAACGGAAGGGGTTAAT 57.346 30.769 0.00 0.00 0.00 1.40
486 505 5.708697 CAGAGTAAATAAAAACGGAAGGGGT 59.291 40.000 0.00 0.00 0.00 4.95
487 506 5.392703 GCAGAGTAAATAAAAACGGAAGGGG 60.393 44.000 0.00 0.00 0.00 4.79
612 648 9.628746 TGTATGATGTGAAAATATATGCAATGC 57.371 29.630 0.00 0.00 0.00 3.56
696 732 7.334171 GCATATTAGTTTTGGTTGAAGCCAATT 59.666 33.333 0.00 0.00 46.60 2.32
697 733 6.818142 GCATATTAGTTTTGGTTGAAGCCAAT 59.182 34.615 0.00 0.00 46.60 3.16
705 741 9.341899 GTCTACTTTGCATATTAGTTTTGGTTG 57.658 33.333 0.00 0.00 0.00 3.77
708 744 9.906660 TTTGTCTACTTTGCATATTAGTTTTGG 57.093 29.630 0.00 0.00 0.00 3.28
723 759 6.365520 ACTCTGGTCCATTTTTGTCTACTTT 58.634 36.000 0.00 0.00 0.00 2.66
724 760 5.941788 ACTCTGGTCCATTTTTGTCTACTT 58.058 37.500 0.00 0.00 0.00 2.24
725 761 5.568620 ACTCTGGTCCATTTTTGTCTACT 57.431 39.130 0.00 0.00 0.00 2.57
726 762 7.923414 AATACTCTGGTCCATTTTTGTCTAC 57.077 36.000 0.00 0.00 0.00 2.59
728 764 9.533831 AATAAATACTCTGGTCCATTTTTGTCT 57.466 29.630 0.00 0.00 0.00 3.41
729 765 9.788960 GAATAAATACTCTGGTCCATTTTTGTC 57.211 33.333 0.00 0.00 0.00 3.18
730 766 9.533831 AGAATAAATACTCTGGTCCATTTTTGT 57.466 29.630 0.00 0.00 0.00 2.83
731 767 9.793252 CAGAATAAATACTCTGGTCCATTTTTG 57.207 33.333 0.00 0.00 36.27 2.44
732 768 9.533831 ACAGAATAAATACTCTGGTCCATTTTT 57.466 29.630 4.19 0.00 42.83 1.94
733 769 9.533831 AACAGAATAAATACTCTGGTCCATTTT 57.466 29.630 4.19 0.00 42.83 1.82
734 770 8.960591 CAACAGAATAAATACTCTGGTCCATTT 58.039 33.333 4.19 0.00 42.83 2.32
735 771 7.557719 CCAACAGAATAAATACTCTGGTCCATT 59.442 37.037 4.19 0.00 42.83 3.16
736 772 7.056635 CCAACAGAATAAATACTCTGGTCCAT 58.943 38.462 4.19 0.00 42.83 3.41
737 773 6.414732 CCAACAGAATAAATACTCTGGTCCA 58.585 40.000 4.19 0.00 42.83 4.02
738 774 5.823045 CCCAACAGAATAAATACTCTGGTCC 59.177 44.000 4.19 0.00 42.83 4.46
739 775 5.297029 GCCCAACAGAATAAATACTCTGGTC 59.703 44.000 4.19 0.00 42.83 4.02
740 776 5.044846 AGCCCAACAGAATAAATACTCTGGT 60.045 40.000 4.19 0.00 42.83 4.00
741 777 5.297776 CAGCCCAACAGAATAAATACTCTGG 59.702 44.000 4.19 0.00 42.83 3.86
742 778 5.297776 CCAGCCCAACAGAATAAATACTCTG 59.702 44.000 0.00 0.00 43.90 3.35
803 844 2.109739 GCGGTTGTGTGTGGTGTGA 61.110 57.895 0.00 0.00 0.00 3.58
828 869 1.153329 TTGGTCTTTCCGTGCGTGT 60.153 52.632 0.00 0.00 39.52 4.49
832 873 1.949257 CCACTTGGTCTTTCCGTGC 59.051 57.895 0.00 0.00 39.52 5.34
898 942 1.135689 ACGATGCGATTTGGAAAGTGC 60.136 47.619 0.00 0.00 0.00 4.40
984 1048 4.521062 ATCTGTCGCCTCCGCTGC 62.521 66.667 0.00 0.00 0.00 5.25
985 1049 2.584418 CATCTGTCGCCTCCGCTG 60.584 66.667 0.00 0.00 0.00 5.18
986 1050 3.842923 CCATCTGTCGCCTCCGCT 61.843 66.667 0.00 0.00 0.00 5.52
989 1053 3.866582 CCCCCATCTGTCGCCTCC 61.867 72.222 0.00 0.00 0.00 4.30
994 1058 4.873129 CGTCGCCCCCATCTGTCG 62.873 72.222 0.00 0.00 0.00 4.35
995 1059 4.530857 CCGTCGCCCCCATCTGTC 62.531 72.222 0.00 0.00 0.00 3.51
1280 1367 4.861389 CGGAGATCGCGATTAGTAGTAT 57.139 45.455 24.55 0.00 0.00 2.12
1332 1434 3.978217 GGAGATCGCGATTAGTTCAGAAG 59.022 47.826 24.55 0.00 0.00 2.85
1348 1450 2.611225 AATCAACAGGAGCGGAGATC 57.389 50.000 0.00 0.00 45.39 2.75
1349 1451 2.237143 TGAAATCAACAGGAGCGGAGAT 59.763 45.455 0.00 0.00 0.00 2.75
1350 1452 1.623311 TGAAATCAACAGGAGCGGAGA 59.377 47.619 0.00 0.00 0.00 3.71
1351 1453 2.099141 TGAAATCAACAGGAGCGGAG 57.901 50.000 0.00 0.00 0.00 4.63
1353 1455 3.428045 GGAAATGAAATCAACAGGAGCGG 60.428 47.826 0.00 0.00 0.00 5.52
1354 1456 3.428045 GGGAAATGAAATCAACAGGAGCG 60.428 47.826 0.00 0.00 0.00 5.03
1356 1458 3.129287 CGGGGAAATGAAATCAACAGGAG 59.871 47.826 0.00 0.00 0.00 3.69
1358 1460 2.825532 ACGGGGAAATGAAATCAACAGG 59.174 45.455 0.00 0.00 0.00 4.00
1359 1461 3.505680 TCACGGGGAAATGAAATCAACAG 59.494 43.478 0.00 0.00 0.00 3.16
1360 1462 3.491342 TCACGGGGAAATGAAATCAACA 58.509 40.909 0.00 0.00 0.00 3.33
1361 1463 4.672409 GATCACGGGGAAATGAAATCAAC 58.328 43.478 0.00 0.00 0.00 3.18
1377 1484 1.153369 AATCCACTGGCCGATCACG 60.153 57.895 0.00 0.00 39.43 4.35
1386 1493 3.507597 TCGTGAACGAATCCACTGG 57.492 52.632 2.48 0.00 46.30 4.00
1422 1529 1.004610 CAGGCAGCGAAACATACATCG 60.005 52.381 0.00 0.00 41.81 3.84
1564 1700 1.480954 AGGCTGATAACTGTACCACGG 59.519 52.381 0.00 0.00 0.00 4.94
1567 1739 3.708451 TCTCAGGCTGATAACTGTACCA 58.292 45.455 19.11 0.00 36.17 3.25
1569 1741 5.069781 AGGAATCTCAGGCTGATAACTGTAC 59.930 44.000 19.11 4.26 36.17 2.90
1656 2118 4.127171 CCCTCCAACAATTATGTACGAGG 58.873 47.826 13.43 13.43 45.73 4.63
1731 3494 0.750182 CCAACACCACGTGGAGGTTT 60.750 55.000 40.21 20.50 37.23 3.27
1734 3497 1.597027 GACCAACACCACGTGGAGG 60.597 63.158 40.21 31.93 37.94 4.30
1736 3499 2.318519 CTGGACCAACACCACGTGGA 62.319 60.000 40.21 14.07 37.94 4.02
1813 3586 1.333177 GATATCTGCCTCTGTCGGGT 58.667 55.000 0.00 0.00 0.00 5.28
1814 3587 0.605589 GGATATCTGCCTCTGTCGGG 59.394 60.000 2.05 0.00 0.00 5.14
1817 3590 4.934602 GCTAAATGGATATCTGCCTCTGTC 59.065 45.833 2.05 0.00 0.00 3.51
1830 3603 0.461870 TCGCACGCTGCTAAATGGAT 60.462 50.000 0.00 0.00 42.25 3.41
1864 3637 2.284478 AGGAGAGAGGCAGCAGCA 60.284 61.111 2.65 0.00 44.61 4.41
2043 5501 8.783660 TGTTTAGATATGAACTCCTATGTCCT 57.216 34.615 0.00 0.00 0.00 3.85
2044 5502 9.429359 CATGTTTAGATATGAACTCCTATGTCC 57.571 37.037 0.00 0.00 0.00 4.02
2053 5511 7.935755 CCAGGTCATCATGTTTAGATATGAACT 59.064 37.037 3.65 3.65 43.58 3.01
2085 5543 6.973229 TCGATGATTGTAGCATATGATTGG 57.027 37.500 6.97 0.00 0.00 3.16
2282 5786 5.249780 TCCAAGCAGGAGTACCATTTTTA 57.750 39.130 0.00 0.00 43.07 1.52
2531 6045 2.123589 TGTCTTCAGGGTTGACCAAGA 58.876 47.619 2.12 0.36 43.89 3.02
2601 6115 7.309621 CCAAATCAAGGATAATCTTAGCATGGG 60.310 40.741 0.00 0.00 0.00 4.00
2614 6129 5.892686 TCACATGCAATCCAAATCAAGGATA 59.107 36.000 0.00 0.00 44.94 2.59
2932 6458 0.941542 TGTCAAAAAGTTCGCCTCCG 59.058 50.000 0.00 0.00 0.00 4.63
3281 6863 2.006888 CTGTAACATGTAACAGCGGGG 58.993 52.381 0.00 0.00 36.96 5.73
3715 7346 6.642707 AAAGAACAACCATATTTCGGTCAA 57.357 33.333 0.00 0.00 34.99 3.18
3774 7407 9.366216 AGAAAGAACACCAAATAACACTTTTTC 57.634 29.630 0.00 0.00 0.00 2.29
3843 7481 5.530915 TCACCCTTGAAAATCTACACACAAG 59.469 40.000 0.00 0.00 35.84 3.16
3916 7554 4.320023 TCGGATTTGGTTCAAGAATTCGA 58.680 39.130 0.00 0.00 38.17 3.71
3917 7555 4.678509 TCGGATTTGGTTCAAGAATTCG 57.321 40.909 0.00 0.00 34.02 3.34
3919 7557 6.434028 TCTTCATCGGATTTGGTTCAAGAATT 59.566 34.615 0.00 0.00 0.00 2.17
4002 7640 4.184079 TCATCGTCATCATATGGAGCAG 57.816 45.455 2.13 0.00 0.00 4.24
4255 7893 3.386078 CCTGAAAGATCGAGGGAAGATGA 59.614 47.826 0.00 0.00 34.07 2.92
4333 7982 3.753272 GCTTTGCAGACCAAATCACTCTA 59.247 43.478 0.00 0.00 42.22 2.43
4368 8017 8.999220 TTATCTTCAGAAGCTATGCATATGAG 57.001 34.615 6.92 0.00 0.00 2.90
4438 8087 2.303600 TGAGTTGTTGTATAAGGCCGGT 59.696 45.455 1.90 0.00 0.00 5.28
4439 8088 2.980568 TGAGTTGTTGTATAAGGCCGG 58.019 47.619 0.00 0.00 0.00 6.13
4469 8118 2.624838 CACTCCCTGCAACAAATTCAGT 59.375 45.455 0.00 0.00 0.00 3.41
4629 8297 6.525578 ACTCAATCATGTGATGCTGAAAAT 57.474 33.333 0.00 0.00 34.49 1.82
4692 8361 3.057596 TGCCCGTTATTTTGAGCTGAAAG 60.058 43.478 0.00 0.00 0.00 2.62
4776 8446 2.543777 TCACCGAAGAAAGGTTCAGG 57.456 50.000 0.00 0.00 40.59 3.86
4898 8572 3.450457 CACCATGAGACTTCCTAAGCTCT 59.550 47.826 0.00 3.50 34.72 4.09
4913 8587 3.310727 CACTGCAGTGTCACCATGA 57.689 52.632 34.04 0.00 40.96 3.07
4968 8650 4.755123 GTGTACAGTGAAGTTATGGCAGTT 59.245 41.667 0.00 0.00 0.00 3.16
5012 8694 9.182214 AGCAACATCATTAAGTTATTCACTCAT 57.818 29.630 0.00 0.00 32.94 2.90
5022 8704 7.288810 TCCAAGAAAGCAACATCATTAAGTT 57.711 32.000 0.00 0.00 0.00 2.66
5089 8774 5.310331 ACCCATCCCAAAAATCTTGTCAATT 59.690 36.000 0.00 0.00 0.00 2.32
5264 8964 5.067936 ACACTGTGAGATCCTAATCCTTACG 59.932 44.000 15.86 0.00 31.78 3.18
5332 9032 0.693430 TCAGCTGAGGATGATGGCCT 60.693 55.000 13.74 0.00 38.81 5.19
5333 9033 0.182061 TTCAGCTGAGGATGATGGCC 59.818 55.000 17.43 0.00 37.72 5.36
5335 9035 1.202782 CCCTTCAGCTGAGGATGATGG 60.203 57.143 26.15 14.52 46.27 3.51
5336 9036 1.202782 CCCCTTCAGCTGAGGATGATG 60.203 57.143 26.15 9.46 37.72 3.07
5337 9037 1.138568 CCCCTTCAGCTGAGGATGAT 58.861 55.000 26.15 0.00 37.72 2.45
5338 9038 0.252881 ACCCCTTCAGCTGAGGATGA 60.253 55.000 26.15 6.13 35.97 2.92
5339 9039 0.107312 CACCCCTTCAGCTGAGGATG 60.107 60.000 26.15 14.37 0.00 3.51
5340 9040 0.548682 ACACCCCTTCAGCTGAGGAT 60.549 55.000 26.15 5.10 0.00 3.24
5369 9069 5.697473 TTACATCGCTGAACCATTTTTGA 57.303 34.783 0.00 0.00 0.00 2.69
5493 9195 0.610232 GCTTCCCTGATGGCAAGTGT 60.610 55.000 0.00 0.00 0.00 3.55
5504 9206 0.760945 AGGGGTATCGAGCTTCCCTG 60.761 60.000 14.97 0.00 45.53 4.45
5544 9247 3.802139 TCAACAACGTTTCACTAGCTCTG 59.198 43.478 0.00 0.00 0.00 3.35
5628 9331 4.135153 CTCCGGGGCGACAGTCTG 62.135 72.222 0.00 0.00 0.00 3.51
5686 9389 0.463833 CTCCCCGTATCTGTTTGGCC 60.464 60.000 0.00 0.00 0.00 5.36
5709 9412 3.476552 TGTCAAGGAGCTTACAAGGTTG 58.523 45.455 0.00 0.00 36.78 3.77
5715 9418 3.076621 CAGCATTGTCAAGGAGCTTACA 58.923 45.455 0.42 0.00 32.35 2.41
5742 9445 3.589988 CTCTAACCGACAACATTGAGCT 58.410 45.455 0.00 0.00 0.00 4.09
5745 9448 3.056107 CCTCCTCTAACCGACAACATTGA 60.056 47.826 0.00 0.00 0.00 2.57
5746 9449 3.056107 TCCTCCTCTAACCGACAACATTG 60.056 47.826 0.00 0.00 0.00 2.82
5754 9457 2.224818 GGCTAGATCCTCCTCTAACCGA 60.225 54.545 0.00 0.00 27.46 4.69
5769 9472 2.134287 GGCGGAGTGGATGGCTAGA 61.134 63.158 0.00 0.00 0.00 2.43
5774 9477 1.815421 CTTTCGGCGGAGTGGATGG 60.815 63.158 7.21 0.00 0.00 3.51
5775 9478 0.179073 ATCTTTCGGCGGAGTGGATG 60.179 55.000 7.21 0.00 0.00 3.51
5776 9479 1.068741 GTATCTTTCGGCGGAGTGGAT 59.931 52.381 7.21 6.35 0.00 3.41
5777 9480 0.458669 GTATCTTTCGGCGGAGTGGA 59.541 55.000 7.21 0.00 0.00 4.02
5781 9484 1.787155 CGAATGTATCTTTCGGCGGAG 59.213 52.381 7.21 5.92 41.62 4.63
5782 9485 1.406180 TCGAATGTATCTTTCGGCGGA 59.594 47.619 7.21 0.00 44.55 5.54
5783 9486 1.847818 TCGAATGTATCTTTCGGCGG 58.152 50.000 7.21 0.00 44.55 6.13
5785 9488 3.245519 GGTCTTCGAATGTATCTTTCGGC 59.754 47.826 0.00 0.00 44.55 5.54
5907 9631 3.113386 CTCGGCAGCGACGATCTCA 62.113 63.158 6.94 0.00 44.17 3.27
5995 9719 2.876550 AGTTAAAAGTTCGCACCCTGAC 59.123 45.455 0.00 0.00 0.00 3.51
6004 9728 5.480205 AGGCCTCTTAGAGTTAAAAGTTCG 58.520 41.667 0.00 0.00 0.00 3.95
6011 9735 8.475639 CATTGTACTTAGGCCTCTTAGAGTTAA 58.524 37.037 9.68 6.74 0.00 2.01
6022 9746 0.463833 GCGGCATTGTACTTAGGCCT 60.464 55.000 11.78 11.78 42.43 5.19
6039 9763 2.418060 GGGACCCCAAATTTACATTGCG 60.418 50.000 0.00 0.00 35.81 4.85
6067 9791 1.337071 CTTGCCGCTCTACCGATAGAA 59.663 52.381 0.00 0.00 36.98 2.10
6069 9793 0.669077 ACTTGCCGCTCTACCGATAG 59.331 55.000 0.00 0.00 0.00 2.08
6070 9794 0.384309 CACTTGCCGCTCTACCGATA 59.616 55.000 0.00 0.00 0.00 2.92
6071 9795 1.141881 CACTTGCCGCTCTACCGAT 59.858 57.895 0.00 0.00 0.00 4.18
6072 9796 2.571757 CACTTGCCGCTCTACCGA 59.428 61.111 0.00 0.00 0.00 4.69
6073 9797 2.509336 CCACTTGCCGCTCTACCG 60.509 66.667 0.00 0.00 0.00 4.02
6108 9833 3.882102 TGCATGTAGGGCATATTTCCT 57.118 42.857 0.00 0.00 36.11 3.36
6109 9834 6.588719 TTATTGCATGTAGGGCATATTTCC 57.411 37.500 0.00 0.00 41.58 3.13
6112 9837 9.312904 ACTTTATTATTGCATGTAGGGCATATT 57.687 29.630 0.00 0.00 41.58 1.28
6113 9838 8.884124 ACTTTATTATTGCATGTAGGGCATAT 57.116 30.769 0.00 0.00 41.58 1.78
6114 9839 8.575589 CAACTTTATTATTGCATGTAGGGCATA 58.424 33.333 0.00 0.00 41.58 3.14
6115 9840 7.069826 ACAACTTTATTATTGCATGTAGGGCAT 59.930 33.333 0.00 0.00 41.58 4.40
6116 9841 6.379703 ACAACTTTATTATTGCATGTAGGGCA 59.620 34.615 0.00 0.00 40.00 5.36
6117 9842 6.805713 ACAACTTTATTATTGCATGTAGGGC 58.194 36.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.