Multiple sequence alignment - TraesCS1D01G332600

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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 TraesCS1D01G332600 chr1D 100.000 4083 0 0 1 4083 423044444 423040362 0.000000e+00 7540.0
1 TraesCS1D01G332600 chr1D 92.000 175 10 1 3700 3874 338937381 338937211 4.080000e-60 243.0
2 TraesCS1D01G332600 chr1D 92.857 168 8 1 3706 3873 463381903 463382066 1.470000e-59 241.0
3 TraesCS1D01G332600 chr1D 92.537 67 5 0 3643 3709 141345569 141345635 3.360000e-16 97.1
4 TraesCS1D01G332600 chr1B 92.714 3047 165 29 409 3428 572296170 572293154 0.000000e+00 4344.0
5 TraesCS1D01G332600 chr1B 87.436 390 20 7 1 390 572296485 572296125 4.880000e-114 422.0
6 TraesCS1D01G332600 chr1B 88.950 181 20 0 3903 4083 572292768 572292588 1.480000e-54 224.0
7 TraesCS1D01G332600 chr1B 88.816 152 16 1 3554 3705 572293040 572292890 6.970000e-43 185.0
8 TraesCS1D01G332600 chr1B 100.000 31 0 0 3872 3902 572292887 572292857 1.590000e-04 58.4
9 TraesCS1D01G332600 chr1A 92.974 2021 116 21 798 2804 518974487 518972479 0.000000e+00 2922.0
10 TraesCS1D01G332600 chr1A 93.086 781 39 5 2933 3709 518972467 518971698 0.000000e+00 1129.0
11 TraesCS1D01G332600 chr1A 87.318 481 39 8 1 469 518975615 518975145 7.770000e-147 531.0
12 TraesCS1D01G332600 chr1A 84.819 415 35 10 345 751 518975142 518974748 3.830000e-105 392.0
13 TraesCS1D01G332600 chr1A 96.685 181 6 0 3903 4083 518971580 518971400 6.630000e-78 302.0
14 TraesCS1D01G332600 chr1A 91.083 157 12 2 344 500 518975205 518975051 1.150000e-50 211.0
15 TraesCS1D01G332600 chr1A 97.826 92 2 0 3552 3643 555641226 555641135 4.220000e-35 159.0
16 TraesCS1D01G332600 chr1A 98.361 61 1 0 409 469 518975268 518975208 1.550000e-19 108.0
17 TraesCS1D01G332600 chr1A 94.030 67 4 0 3643 3709 251552583 251552649 7.220000e-18 102.0
18 TraesCS1D01G332600 chr1A 100.000 30 0 0 3871 3900 518971700 518971671 5.700000e-04 56.5
19 TraesCS1D01G332600 chrUn 91.954 174 10 1 3703 3876 96474150 96473981 1.470000e-59 241.0
20 TraesCS1D01G332600 chr3D 91.525 177 10 2 3708 3883 612268449 612268621 5.270000e-59 239.0
21 TraesCS1D01G332600 chr3D 92.353 170 8 2 3708 3877 537154863 537154699 1.900000e-58 237.0
22 TraesCS1D01G332600 chr3D 91.083 157 14 0 1165 1321 418727422 418727578 3.200000e-51 213.0
23 TraesCS1D01G332600 chr3D 95.652 92 4 0 3552 3643 315480460 315480551 9.140000e-32 148.0
24 TraesCS1D01G332600 chr3D 83.571 140 17 5 2953 3089 270439056 270439192 4.280000e-25 126.0
25 TraesCS1D01G332600 chr3D 90.244 82 8 0 2644 2725 270438880 270438961 1.550000e-19 108.0
26 TraesCS1D01G332600 chr3D 92.537 67 5 0 3643 3709 202637070 202637004 3.360000e-16 97.1
27 TraesCS1D01G332600 chr3D 91.045 67 6 0 3643 3709 56125929 56125863 1.560000e-14 91.6
28 TraesCS1D01G332600 chr2A 91.477 176 11 1 3703 3878 148184576 148184747 5.270000e-59 239.0
29 TraesCS1D01G332600 chr2A 92.353 170 8 2 3708 3876 578387555 578387720 1.900000e-58 237.0
30 TraesCS1D01G332600 chr4A 91.860 172 10 1 3703 3874 517406466 517406633 1.900000e-58 237.0
31 TraesCS1D01G332600 chr2D 92.308 169 9 1 3708 3876 362930808 362930972 1.900000e-58 237.0
32 TraesCS1D01G332600 chr2D 91.045 67 6 0 3643 3709 500891757 500891823 1.560000e-14 91.6
33 TraesCS1D01G332600 chr2D 91.045 67 6 0 3643 3709 500892905 500892971 1.560000e-14 91.6
34 TraesCS1D01G332600 chr2D 91.045 67 6 0 3643 3709 634994472 634994406 1.560000e-14 91.6
35 TraesCS1D01G332600 chr3B 91.083 157 14 0 1165 1321 545066482 545066638 3.200000e-51 213.0
36 TraesCS1D01G332600 chr3A 91.083 157 14 0 1165 1321 532451182 532451026 3.200000e-51 213.0
37 TraesCS1D01G332600 chr6D 97.826 92 2 0 3552 3643 221843113 221843022 4.220000e-35 159.0
38 TraesCS1D01G332600 chr6D 95.652 92 4 0 3552 3643 392273107 392273198 9.140000e-32 148.0
39 TraesCS1D01G332600 chr2B 97.826 92 2 0 3552 3643 190023010 190022919 4.220000e-35 159.0
40 TraesCS1D01G332600 chr6A 96.739 92 3 0 3552 3643 263886984 263886893 1.970000e-33 154.0
41 TraesCS1D01G332600 chr6A 96.739 92 3 0 3552 3643 538097712 538097803 1.970000e-33 154.0
42 TraesCS1D01G332600 chr7A 92.683 82 6 0 2644 2725 145768301 145768220 7.170000e-23 119.0
43 TraesCS1D01G332600 chr7A 82.394 142 17 5 2953 3089 145768124 145767986 2.580000e-22 117.0
44 TraesCS1D01G332600 chr7A 80.986 142 19 5 2953 3089 119583980 119583842 5.580000e-19 106.0


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 TraesCS1D01G332600 chr1D 423040362 423044444 4082 True 7540.0000 7540 100.00000 1 4083 1 chr1D.!!$R2 4082
1 TraesCS1D01G332600 chr1B 572292588 572296485 3897 True 1046.6800 4344 91.58320 1 4083 5 chr1B.!!$R1 4082
2 TraesCS1D01G332600 chr1A 518971400 518975615 4215 True 706.4375 2922 93.04075 1 4083 8 chr1A.!!$R2 4082

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
889 1319 0.109597 GCAAATCCGTCACAGCCAAG 60.110 55.0 0.00 0.00 0.00 3.61 F
972 1403 0.179045 CGCCCTAGGGTTCAATCCAG 60.179 60.0 28.96 5.94 37.65 3.86 F
1330 1764 0.183014 CGGAGAGGTAGGTAGAGCCA 59.817 60.0 0.00 0.00 40.61 4.75 F
2352 2800 0.681175 GCAAAAAGGGCATGGTGACT 59.319 50.0 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2689 0.391661 CAGTTACACCGCCAGATGCT 60.392 55.0 0.0 0.0 38.05 3.79 R
2930 3380 0.179140 CAGCAACCACAAAACTGCGT 60.179 50.0 0.0 0.0 39.80 5.24 R
3079 3533 0.824759 ACTGGCGGGAATCAGACTAC 59.175 55.0 0.0 0.0 35.20 2.73 R
3751 4233 0.101759 TTGCTCCGTATGTAGTCCGC 59.898 55.0 0.0 0.0 0.00 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
28 30 2.618816 GCAGTGATGGACCAGATGGAAA 60.619 50.000 5.72 0.00 38.94 3.13
74 76 1.474879 CGGTGAAAAACAAGGTGGTGT 59.525 47.619 0.00 0.00 0.00 4.16
141 148 1.338020 GTTTGCTTCTTGGTGGTGGAG 59.662 52.381 0.00 0.00 0.00 3.86
164 171 4.779486 GGGTGGGGTGGGGGATCT 62.779 72.222 0.00 0.00 0.00 2.75
165 172 2.617215 GGTGGGGTGGGGGATCTT 60.617 66.667 0.00 0.00 0.00 2.40
166 173 2.683475 GTGGGGTGGGGGATCTTG 59.317 66.667 0.00 0.00 0.00 3.02
167 174 2.212761 TGGGGTGGGGGATCTTGT 59.787 61.111 0.00 0.00 0.00 3.16
168 175 1.467190 TGGGGTGGGGGATCTTGTT 60.467 57.895 0.00 0.00 0.00 2.83
200 207 0.536006 GGTGGCAGTGTTGAAGCTCT 60.536 55.000 0.00 0.00 0.00 4.09
203 210 0.871057 GGCAGTGTTGAAGCTCTGTC 59.129 55.000 0.00 0.00 33.84 3.51
237 252 9.210228 TCTATATGCATTGGTGAGATATGAGAT 57.790 33.333 3.54 0.00 0.00 2.75
238 253 9.262358 CTATATGCATTGGTGAGATATGAGATG 57.738 37.037 3.54 0.00 0.00 2.90
239 254 4.648651 TGCATTGGTGAGATATGAGATGG 58.351 43.478 0.00 0.00 0.00 3.51
240 255 4.103627 TGCATTGGTGAGATATGAGATGGT 59.896 41.667 0.00 0.00 0.00 3.55
241 256 5.068636 GCATTGGTGAGATATGAGATGGTT 58.931 41.667 0.00 0.00 0.00 3.67
242 257 6.183361 TGCATTGGTGAGATATGAGATGGTTA 60.183 38.462 0.00 0.00 0.00 2.85
243 258 6.148480 GCATTGGTGAGATATGAGATGGTTAC 59.852 42.308 0.00 0.00 0.00 2.50
244 259 6.806668 TTGGTGAGATATGAGATGGTTACA 57.193 37.500 0.00 0.00 0.00 2.41
245 260 6.161855 TGGTGAGATATGAGATGGTTACAC 57.838 41.667 0.00 0.00 0.00 2.90
246 261 5.660864 TGGTGAGATATGAGATGGTTACACA 59.339 40.000 0.00 0.00 0.00 3.72
247 262 6.327365 TGGTGAGATATGAGATGGTTACACAT 59.673 38.462 0.00 0.00 0.00 3.21
248 263 7.508977 TGGTGAGATATGAGATGGTTACACATA 59.491 37.037 0.00 0.00 0.00 2.29
295 324 3.375299 AGCTTGGTTATGATTTGCGTCTC 59.625 43.478 0.00 0.00 0.00 3.36
306 335 2.386661 TTGCGTCTCCTCTCATTTCC 57.613 50.000 0.00 0.00 0.00 3.13
368 397 3.912820 TTGCGCTGCAAAATCGGGC 62.913 57.895 9.73 5.16 45.96 6.13
369 398 4.120331 GCGCTGCAAAATCGGGCT 62.120 61.111 0.00 0.00 34.28 5.19
370 399 2.568090 CGCTGCAAAATCGGGCTT 59.432 55.556 0.00 0.00 0.00 4.35
371 400 1.080569 CGCTGCAAAATCGGGCTTT 60.081 52.632 0.00 0.00 0.00 3.51
372 401 0.667184 CGCTGCAAAATCGGGCTTTT 60.667 50.000 0.00 0.00 0.00 2.27
373 402 0.792031 GCTGCAAAATCGGGCTTTTG 59.208 50.000 11.80 11.80 44.96 2.44
374 403 1.873486 GCTGCAAAATCGGGCTTTTGT 60.873 47.619 15.30 0.00 44.33 2.83
375 404 2.482864 CTGCAAAATCGGGCTTTTGTT 58.517 42.857 15.30 0.00 44.33 2.83
376 405 2.476241 CTGCAAAATCGGGCTTTTGTTC 59.524 45.455 15.30 5.62 44.33 3.18
377 406 1.798223 GCAAAATCGGGCTTTTGTTCC 59.202 47.619 15.30 0.00 44.33 3.62
378 407 2.547855 GCAAAATCGGGCTTTTGTTCCT 60.548 45.455 15.30 0.00 44.33 3.36
379 408 3.059166 CAAAATCGGGCTTTTGTTCCTG 58.941 45.455 9.28 0.00 39.92 3.86
380 409 1.256812 AATCGGGCTTTTGTTCCTGG 58.743 50.000 0.00 0.00 0.00 4.45
381 410 0.611896 ATCGGGCTTTTGTTCCTGGG 60.612 55.000 0.00 0.00 0.00 4.45
382 411 1.228429 CGGGCTTTTGTTCCTGGGA 60.228 57.895 0.00 0.00 0.00 4.37
383 412 0.825840 CGGGCTTTTGTTCCTGGGAA 60.826 55.000 0.00 0.00 0.00 3.97
384 413 1.644509 GGGCTTTTGTTCCTGGGAAT 58.355 50.000 5.30 0.00 36.45 3.01
385 414 1.977854 GGGCTTTTGTTCCTGGGAATT 59.022 47.619 5.30 0.00 36.45 2.17
386 415 2.371841 GGGCTTTTGTTCCTGGGAATTT 59.628 45.455 5.30 0.00 36.45 1.82
387 416 3.402110 GGCTTTTGTTCCTGGGAATTTG 58.598 45.455 5.30 0.00 36.45 2.32
388 417 3.181455 GGCTTTTGTTCCTGGGAATTTGT 60.181 43.478 5.30 0.00 36.45 2.83
389 418 4.039852 GGCTTTTGTTCCTGGGAATTTGTA 59.960 41.667 5.30 0.00 36.45 2.41
390 419 5.279960 GGCTTTTGTTCCTGGGAATTTGTAT 60.280 40.000 5.30 0.00 36.45 2.29
391 420 5.639082 GCTTTTGTTCCTGGGAATTTGTATG 59.361 40.000 5.30 0.00 36.45 2.39
392 421 6.739331 TTTTGTTCCTGGGAATTTGTATGT 57.261 33.333 5.30 0.00 36.45 2.29
393 422 7.524698 GCTTTTGTTCCTGGGAATTTGTATGTA 60.525 37.037 5.30 0.00 36.45 2.29
394 423 6.827586 TTGTTCCTGGGAATTTGTATGTAC 57.172 37.500 5.30 0.00 36.45 2.90
395 424 4.938832 TGTTCCTGGGAATTTGTATGTACG 59.061 41.667 5.30 0.00 36.45 3.67
396 425 4.145365 TCCTGGGAATTTGTATGTACGG 57.855 45.455 0.00 0.00 0.00 4.02
397 426 3.118186 TCCTGGGAATTTGTATGTACGGG 60.118 47.826 0.00 0.00 0.00 5.28
398 427 3.211045 CTGGGAATTTGTATGTACGGGG 58.789 50.000 0.00 0.00 0.00 5.73
399 428 1.951602 GGGAATTTGTATGTACGGGGC 59.048 52.381 0.00 0.00 0.00 5.80
400 429 1.600485 GGAATTTGTATGTACGGGGCG 59.400 52.381 0.00 0.00 0.00 6.13
401 430 2.553086 GAATTTGTATGTACGGGGCGA 58.447 47.619 0.00 0.00 0.00 5.54
402 431 2.695127 ATTTGTATGTACGGGGCGAA 57.305 45.000 0.00 0.00 0.00 4.70
403 432 1.724429 TTTGTATGTACGGGGCGAAC 58.276 50.000 0.00 0.00 0.00 3.95
404 433 0.896923 TTGTATGTACGGGGCGAACT 59.103 50.000 0.00 0.00 0.00 3.01
405 434 0.896923 TGTATGTACGGGGCGAACTT 59.103 50.000 0.00 0.00 0.00 2.66
406 435 1.135024 TGTATGTACGGGGCGAACTTC 60.135 52.381 0.00 0.00 0.00 3.01
407 436 1.135721 GTATGTACGGGGCGAACTTCT 59.864 52.381 0.00 0.00 0.00 2.85
408 437 0.611714 ATGTACGGGGCGAACTTCTT 59.388 50.000 0.00 0.00 0.00 2.52
409 438 0.393820 TGTACGGGGCGAACTTCTTT 59.606 50.000 0.00 0.00 0.00 2.52
410 439 1.073964 GTACGGGGCGAACTTCTTTC 58.926 55.000 0.00 0.00 0.00 2.62
431 460 4.277593 TTGCGCTGCAAAACCGGG 62.278 61.111 9.73 0.00 45.96 5.73
490 705 1.530441 GCACGCTGTTATCATGTGCAG 60.530 52.381 18.89 0.00 45.99 4.41
512 727 3.181499 GGCAGAGCAAATGACTGAAGATG 60.181 47.826 0.00 0.00 34.07 2.90
538 753 1.027357 ACTTTGACAGCAACAGCAGG 58.973 50.000 0.00 0.00 32.79 4.85
554 769 1.134965 GCAGGCTACTACTCACAGGTG 60.135 57.143 0.00 0.00 0.00 4.00
565 780 0.959553 TCACAGGTGAAGTCTCGACC 59.040 55.000 0.00 0.00 36.53 4.79
762 978 1.609061 CCAACCACTACTCAGCCTGTG 60.609 57.143 0.00 0.00 0.00 3.66
763 979 1.070758 CAACCACTACTCAGCCTGTGT 59.929 52.381 4.66 4.66 0.00 3.72
791 1014 1.002142 GTTAAAAACACGGCGAGGCTT 60.002 47.619 16.62 0.27 0.00 4.35
792 1015 1.310904 TAAAAACACGGCGAGGCTTT 58.689 45.000 16.62 12.14 0.00 3.51
793 1016 0.248866 AAAAACACGGCGAGGCTTTG 60.249 50.000 16.62 1.84 0.00 2.77
794 1017 2.070654 AAAACACGGCGAGGCTTTGG 62.071 55.000 16.62 0.00 0.00 3.28
796 1019 3.726517 CACGGCGAGGCTTTGGTG 61.727 66.667 16.62 0.00 0.00 4.17
845 1275 2.041301 TACCCTCCCCATCACCCG 60.041 66.667 0.00 0.00 0.00 5.28
853 1283 4.181010 CCATCACCCGCCTCCCAG 62.181 72.222 0.00 0.00 0.00 4.45
854 1284 4.181010 CATCACCCGCCTCCCAGG 62.181 72.222 0.00 0.00 38.80 4.45
888 1318 1.523154 GGCAAATCCGTCACAGCCAA 61.523 55.000 0.00 0.00 41.63 4.52
889 1319 0.109597 GCAAATCCGTCACAGCCAAG 60.110 55.000 0.00 0.00 0.00 3.61
969 1400 1.526225 GGCGCCCTAGGGTTCAATC 60.526 63.158 28.96 10.17 37.65 2.67
972 1403 0.179045 CGCCCTAGGGTTCAATCCAG 60.179 60.000 28.96 5.94 37.65 3.86
975 1406 0.179045 CCTAGGGTTCAATCCAGCCG 60.179 60.000 0.00 0.00 36.86 5.52
1314 1748 2.350895 CAGTGCCCCAACATCGGA 59.649 61.111 0.00 0.00 0.00 4.55
1330 1764 0.183014 CGGAGAGGTAGGTAGAGCCA 59.817 60.000 0.00 0.00 40.61 4.75
1334 1768 3.567397 GAGAGGTAGGTAGAGCCAATCA 58.433 50.000 0.00 0.00 40.61 2.57
1415 1849 4.368543 GGTTTGCCTGCTGCTGCC 62.369 66.667 13.47 0.00 42.00 4.85
1545 1979 2.548067 CGTCAAGACCAGTAACAAGCCT 60.548 50.000 0.00 0.00 0.00 4.58
1610 2044 1.065273 CGAGTTGGGGGTACGATCG 59.935 63.158 14.88 14.88 0.00 3.69
1617 2051 1.065928 GGGGTACGATCGCTGACAG 59.934 63.158 16.60 0.00 0.00 3.51
1638 2072 5.581085 ACAGTTATCGGCATGTTAAGAACTC 59.419 40.000 0.00 0.00 0.00 3.01
1639 2073 4.804139 AGTTATCGGCATGTTAAGAACTCG 59.196 41.667 0.00 0.00 0.00 4.18
1640 2074 3.520290 ATCGGCATGTTAAGAACTCGA 57.480 42.857 0.00 0.00 0.00 4.04
1648 2082 6.701841 GGCATGTTAAGAACTCGATAAGATGA 59.298 38.462 13.89 0.00 34.16 2.92
1655 2089 9.684448 TTAAGAACTCGATAAGATGATGTGATC 57.316 33.333 0.00 0.00 0.00 2.92
1656 2090 7.523293 AGAACTCGATAAGATGATGTGATCT 57.477 36.000 0.00 0.00 33.91 2.75
1657 2091 7.369607 AGAACTCGATAAGATGATGTGATCTG 58.630 38.462 0.00 0.00 32.77 2.90
1658 2092 6.890979 ACTCGATAAGATGATGTGATCTGA 57.109 37.500 0.00 0.00 32.77 3.27
1659 2093 6.912082 ACTCGATAAGATGATGTGATCTGAG 58.088 40.000 0.00 7.01 32.77 3.35
1660 2094 6.072008 ACTCGATAAGATGATGTGATCTGAGG 60.072 42.308 10.91 0.00 32.77 3.86
1662 2096 6.491403 TCGATAAGATGATGTGATCTGAGGAA 59.509 38.462 0.00 0.00 32.77 3.36
1663 2097 7.178097 TCGATAAGATGATGTGATCTGAGGAAT 59.822 37.037 0.00 0.00 32.77 3.01
1664 2098 7.275999 CGATAAGATGATGTGATCTGAGGAATG 59.724 40.741 0.00 0.00 32.77 2.67
1665 2099 4.643463 AGATGATGTGATCTGAGGAATGC 58.357 43.478 0.00 0.00 31.14 3.56
1666 2100 4.348461 AGATGATGTGATCTGAGGAATGCT 59.652 41.667 0.00 0.00 31.14 3.79
1667 2101 3.805207 TGATGTGATCTGAGGAATGCTG 58.195 45.455 0.00 0.00 0.00 4.41
1668 2102 3.199289 TGATGTGATCTGAGGAATGCTGT 59.801 43.478 0.00 0.00 0.00 4.40
1669 2103 3.708403 TGTGATCTGAGGAATGCTGTT 57.292 42.857 0.00 0.00 0.00 3.16
1693 2137 2.368548 TGCAGAGTGGACTATGTTGTGT 59.631 45.455 3.52 0.00 37.50 3.72
1704 2148 5.484173 ACTATGTTGTGTTGACAAGTGTG 57.516 39.130 0.00 0.00 42.87 3.82
1771 2215 0.980423 AGTCAGGGCTCTCAAGGTTC 59.020 55.000 0.00 0.00 0.00 3.62
1779 2223 1.257743 CTCTCAAGGTTCGTCCCTGA 58.742 55.000 0.00 0.00 35.57 3.86
1838 2282 5.560722 TGTGATAGTTTTGGGTCTTCTGA 57.439 39.130 0.00 0.00 0.00 3.27
1881 2325 3.380479 TTGGTGGAGTGTCTAACTTCG 57.620 47.619 0.00 0.00 40.07 3.79
2024 2468 5.350091 GGTAATGCACTTCTCTGACTTCTTC 59.650 44.000 0.00 0.00 0.00 2.87
2049 2493 2.426522 TGTTGCTCAGTCTATTGTGCC 58.573 47.619 0.00 0.00 36.90 5.01
2088 2532 9.802039 CATACTAACTAGGAGAGTCCTCTAAAT 57.198 37.037 0.00 0.00 45.66 1.40
2098 2542 7.827236 AGGAGAGTCCTCTAAATCACTATATCG 59.173 40.741 0.00 0.00 45.66 2.92
2153 2598 9.817809 TCATTTACAGTACTCTATGATTTGGTC 57.182 33.333 0.00 0.00 0.00 4.02
2162 2607 5.877012 ACTCTATGATTTGGTCACATGACAC 59.123 40.000 13.77 4.33 46.47 3.67
2188 2633 7.288810 TGTAATTTCAAAACCTGCATCTTCT 57.711 32.000 0.00 0.00 0.00 2.85
2231 2676 6.126863 TCACAGAAGGGAAATCACTAATGT 57.873 37.500 0.00 0.00 30.96 2.71
2232 2677 6.173339 TCACAGAAGGGAAATCACTAATGTC 58.827 40.000 0.98 0.00 29.11 3.06
2233 2678 5.939883 CACAGAAGGGAAATCACTAATGTCA 59.060 40.000 0.98 0.00 29.11 3.58
2239 2687 8.682936 AAGGGAAATCACTAATGTCATCATAC 57.317 34.615 0.00 0.00 33.49 2.39
2241 2689 9.159254 AGGGAAATCACTAATGTCATCATACTA 57.841 33.333 0.00 0.00 33.49 1.82
2252 2700 7.582653 ATGTCATCATACTAGCATCTGGCGG 62.583 48.000 0.00 0.00 39.06 6.13
2275 2723 6.348213 CGGTGTAACTGTTTCCTTATTTCCAG 60.348 42.308 0.00 0.00 38.78 3.86
2286 2734 8.669243 GTTTCCTTATTTCCAGTCTGTTATCTG 58.331 37.037 0.00 0.00 0.00 2.90
2349 2797 1.515081 CTTGCAAAAAGGGCATGGTG 58.485 50.000 0.00 0.00 41.58 4.17
2352 2800 0.681175 GCAAAAAGGGCATGGTGACT 59.319 50.000 0.00 0.00 0.00 3.41
2376 2824 2.362397 GTCCTCGATCATGCTTGGTCTA 59.638 50.000 10.78 0.00 30.22 2.59
2427 2875 1.000396 GGCTGACTTGAGGGCCATT 60.000 57.895 6.18 0.00 43.59 3.16
2481 2929 3.844640 ACAGGTTTGATGTTTAGCCCTT 58.155 40.909 0.00 0.00 0.00 3.95
2690 3140 6.677781 TTAGGATTTGTGTATGTTGCTAGC 57.322 37.500 8.10 8.10 0.00 3.42
2728 3178 6.072286 AGCATTGCATATAGCTGGTTATGTTC 60.072 38.462 11.91 0.00 45.94 3.18
2855 3305 4.060038 TCCTCGATAAAACATGCCTCTC 57.940 45.455 0.00 0.00 0.00 3.20
2897 3347 4.051237 CCACACAAAAGAAAAAGCTAGCC 58.949 43.478 12.13 0.00 0.00 3.93
2922 3372 6.293955 CCTTGTCTTGTTAGTTATTGGTGGTG 60.294 42.308 0.00 0.00 0.00 4.17
2923 3373 5.067273 TGTCTTGTTAGTTATTGGTGGTGG 58.933 41.667 0.00 0.00 0.00 4.61
2924 3374 5.163184 TGTCTTGTTAGTTATTGGTGGTGGA 60.163 40.000 0.00 0.00 0.00 4.02
2925 3375 5.766174 GTCTTGTTAGTTATTGGTGGTGGAA 59.234 40.000 0.00 0.00 0.00 3.53
2926 3376 6.433093 GTCTTGTTAGTTATTGGTGGTGGAAT 59.567 38.462 0.00 0.00 0.00 3.01
2927 3377 6.657541 TCTTGTTAGTTATTGGTGGTGGAATC 59.342 38.462 0.00 0.00 0.00 2.52
2928 3378 4.938832 TGTTAGTTATTGGTGGTGGAATCG 59.061 41.667 0.00 0.00 0.00 3.34
2929 3379 3.713826 AGTTATTGGTGGTGGAATCGT 57.286 42.857 0.00 0.00 0.00 3.73
2930 3380 4.829872 AGTTATTGGTGGTGGAATCGTA 57.170 40.909 0.00 0.00 0.00 3.43
2931 3381 4.510571 AGTTATTGGTGGTGGAATCGTAC 58.489 43.478 0.00 0.00 0.00 3.67
2986 3436 7.873505 ACTACAGGAACTCACTTTTGTATTCTC 59.126 37.037 0.00 0.00 34.60 2.87
2988 3438 5.696724 CAGGAACTCACTTTTGTATTCTCGT 59.303 40.000 0.00 0.00 34.60 4.18
3007 3458 2.064014 GTACTTTTTCAGGTCCGGTCG 58.936 52.381 0.00 0.00 0.00 4.79
3079 3533 1.224075 CCCAGCTTGTATCTGCATCG 58.776 55.000 0.00 0.00 0.00 3.84
3091 3545 3.717400 TCTGCATCGTAGTCTGATTCC 57.283 47.619 0.00 0.00 0.00 3.01
3108 3562 1.048601 TCCCGCCAGTCCATTCTATC 58.951 55.000 0.00 0.00 0.00 2.08
3110 3564 1.051812 CCGCCAGTCCATTCTATCCT 58.948 55.000 0.00 0.00 0.00 3.24
3139 3593 6.990349 CCAGAGTTTTACACAGGAAGAGTTAA 59.010 38.462 0.00 0.00 0.00 2.01
3376 3830 8.314751 GTGCTATATATAGTGGTGTCCTGATTT 58.685 37.037 18.81 0.00 32.96 2.17
3428 3882 4.348168 TCTGCTGGAGTTCCTTTAGAGTTT 59.652 41.667 0.00 0.00 36.82 2.66
3458 3912 4.142469 GCCATTACGTGCCTAAACTGAAAT 60.142 41.667 0.00 0.00 0.00 2.17
3613 4095 3.068024 TGTTTGTTCACTCATTTCAGCCC 59.932 43.478 0.00 0.00 0.00 5.19
3627 4109 3.232720 TCAGCCCGTATGTAGTCCATA 57.767 47.619 0.00 0.00 34.86 2.74
3628 4110 3.774734 TCAGCCCGTATGTAGTCCATAT 58.225 45.455 0.00 0.00 38.29 1.78
3650 4132 9.472361 CATATTGAAATATCCAAAAGGAGCAAG 57.528 33.333 0.00 0.00 29.35 4.01
3706 4188 7.229506 ACCAAGATTTCTGACCTCTTACTTTTG 59.770 37.037 1.76 0.00 0.00 2.44
3707 4189 7.229506 CCAAGATTTCTGACCTCTTACTTTTGT 59.770 37.037 1.76 0.00 0.00 2.83
3708 4190 9.273016 CAAGATTTCTGACCTCTTACTTTTGTA 57.727 33.333 1.76 0.00 0.00 2.41
3709 4191 8.834749 AGATTTCTGACCTCTTACTTTTGTAC 57.165 34.615 0.00 0.00 34.15 2.90
3710 4192 8.652290 AGATTTCTGACCTCTTACTTTTGTACT 58.348 33.333 0.00 0.00 34.15 2.73
3711 4193 8.834749 ATTTCTGACCTCTTACTTTTGTACTC 57.165 34.615 0.00 0.00 34.15 2.59
3712 4194 6.342338 TCTGACCTCTTACTTTTGTACTCC 57.658 41.667 0.00 0.00 34.15 3.85
3713 4195 5.245526 TCTGACCTCTTACTTTTGTACTCCC 59.754 44.000 0.00 0.00 34.15 4.30
3714 4196 5.152934 TGACCTCTTACTTTTGTACTCCCT 58.847 41.667 0.00 0.00 34.15 4.20
3715 4197 5.245526 TGACCTCTTACTTTTGTACTCCCTC 59.754 44.000 0.00 0.00 34.15 4.30
3716 4198 5.404395 ACCTCTTACTTTTGTACTCCCTCT 58.596 41.667 0.00 0.00 34.15 3.69
3717 4199 5.246429 ACCTCTTACTTTTGTACTCCCTCTG 59.754 44.000 0.00 0.00 34.15 3.35
3718 4200 5.246429 CCTCTTACTTTTGTACTCCCTCTGT 59.754 44.000 0.00 0.00 34.15 3.41
3719 4201 6.239629 CCTCTTACTTTTGTACTCCCTCTGTT 60.240 42.308 0.00 0.00 34.15 3.16
3720 4202 6.756221 TCTTACTTTTGTACTCCCTCTGTTC 58.244 40.000 0.00 0.00 34.15 3.18
3721 4203 6.553852 TCTTACTTTTGTACTCCCTCTGTTCT 59.446 38.462 0.00 0.00 34.15 3.01
3722 4204 5.632034 ACTTTTGTACTCCCTCTGTTCTT 57.368 39.130 0.00 0.00 0.00 2.52
3723 4205 6.742559 ACTTTTGTACTCCCTCTGTTCTTA 57.257 37.500 0.00 0.00 0.00 2.10
3724 4206 7.133133 ACTTTTGTACTCCCTCTGTTCTTAA 57.867 36.000 0.00 0.00 0.00 1.85
3725 4207 7.571025 ACTTTTGTACTCCCTCTGTTCTTAAA 58.429 34.615 0.00 0.00 0.00 1.52
3726 4208 8.218488 ACTTTTGTACTCCCTCTGTTCTTAAAT 58.782 33.333 0.00 0.00 0.00 1.40
3727 4209 9.720769 CTTTTGTACTCCCTCTGTTCTTAAATA 57.279 33.333 0.00 0.00 0.00 1.40
3734 4216 9.495382 ACTCCCTCTGTTCTTAAATATAAGTCT 57.505 33.333 0.00 0.00 39.65 3.24
3753 4235 7.873739 AAGTCTTTTTAAAGATTCCAATGCG 57.126 32.000 8.07 0.00 45.83 4.73
3754 4236 6.389906 AGTCTTTTTAAAGATTCCAATGCGG 58.610 36.000 8.07 0.00 45.83 5.69
3755 4237 6.208599 AGTCTTTTTAAAGATTCCAATGCGGA 59.791 34.615 8.07 0.00 45.83 5.54
3756 4238 6.308041 GTCTTTTTAAAGATTCCAATGCGGAC 59.692 38.462 8.07 0.00 45.83 4.79
3757 4239 5.975693 TTTTAAAGATTCCAATGCGGACT 57.024 34.783 0.00 0.00 46.36 3.85
3758 4240 7.392113 TCTTTTTAAAGATTCCAATGCGGACTA 59.608 33.333 0.89 0.00 40.96 2.59
3759 4241 6.431198 TTTAAAGATTCCAATGCGGACTAC 57.569 37.500 0.00 0.00 46.36 2.73
3760 4242 3.627395 AAGATTCCAATGCGGACTACA 57.373 42.857 0.00 0.00 46.36 2.74
3761 4243 3.845781 AGATTCCAATGCGGACTACAT 57.154 42.857 0.00 0.00 46.36 2.29
3762 4244 4.955811 AGATTCCAATGCGGACTACATA 57.044 40.909 0.00 0.00 46.36 2.29
3763 4245 4.632153 AGATTCCAATGCGGACTACATAC 58.368 43.478 0.00 0.00 46.36 2.39
3764 4246 2.502213 TCCAATGCGGACTACATACG 57.498 50.000 0.00 0.00 39.64 3.06
3765 4247 1.067974 TCCAATGCGGACTACATACGG 59.932 52.381 0.00 0.00 39.64 4.02
3766 4248 1.067974 CCAATGCGGACTACATACGGA 59.932 52.381 0.00 0.00 36.56 4.69
3767 4249 2.394708 CAATGCGGACTACATACGGAG 58.605 52.381 0.00 0.00 0.00 4.63
3768 4250 0.314302 ATGCGGACTACATACGGAGC 59.686 55.000 0.00 0.00 0.00 4.70
3769 4251 1.033202 TGCGGACTACATACGGAGCA 61.033 55.000 0.00 0.00 0.00 4.26
3770 4252 0.101759 GCGGACTACATACGGAGCAA 59.898 55.000 0.00 0.00 0.00 3.91
3771 4253 1.470285 GCGGACTACATACGGAGCAAA 60.470 52.381 0.00 0.00 0.00 3.68
3772 4254 2.883574 CGGACTACATACGGAGCAAAA 58.116 47.619 0.00 0.00 0.00 2.44
3773 4255 3.454375 CGGACTACATACGGAGCAAAAT 58.546 45.455 0.00 0.00 0.00 1.82
3774 4256 3.245284 CGGACTACATACGGAGCAAAATG 59.755 47.826 0.00 0.00 0.00 2.32
3775 4257 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
3776 4258 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
3777 4259 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3778 4260 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3779 4261 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3780 4262 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3781 4263 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3782 4264 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3783 4265 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3784 4266 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3785 4267 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3786 4268 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3787 4269 5.295292 CGGAGCAAAATGAGTGAATCTACAT 59.705 40.000 0.00 0.00 0.00 2.29
3788 4270 6.183360 CGGAGCAAAATGAGTGAATCTACATT 60.183 38.462 0.00 0.00 34.99 2.71
3789 4271 7.192232 GGAGCAAAATGAGTGAATCTACATTC 58.808 38.462 0.00 0.00 39.24 2.67
3790 4272 7.066766 GGAGCAAAATGAGTGAATCTACATTCT 59.933 37.037 0.00 0.00 39.49 2.40
3791 4273 9.102757 GAGCAAAATGAGTGAATCTACATTCTA 57.897 33.333 0.00 0.00 39.49 2.10
3792 4274 9.453572 AGCAAAATGAGTGAATCTACATTCTAA 57.546 29.630 0.00 0.00 39.49 2.10
3830 4312 6.880484 ACATCCGTATGTAGTTTGTATTGGA 58.120 36.000 0.00 0.00 44.66 3.53
3831 4313 7.332557 ACATCCGTATGTAGTTTGTATTGGAA 58.667 34.615 0.00 0.00 44.66 3.53
3832 4314 7.990886 ACATCCGTATGTAGTTTGTATTGGAAT 59.009 33.333 0.00 0.00 44.66 3.01
3833 4315 8.495949 CATCCGTATGTAGTTTGTATTGGAATC 58.504 37.037 0.00 0.00 0.00 2.52
3834 4316 7.788026 TCCGTATGTAGTTTGTATTGGAATCT 58.212 34.615 0.00 0.00 0.00 2.40
3835 4317 7.924412 TCCGTATGTAGTTTGTATTGGAATCTC 59.076 37.037 0.00 0.00 0.00 2.75
3836 4318 7.926555 CCGTATGTAGTTTGTATTGGAATCTCT 59.073 37.037 0.00 0.00 0.00 3.10
3837 4319 9.961265 CGTATGTAGTTTGTATTGGAATCTCTA 57.039 33.333 0.00 0.00 0.00 2.43
3867 4349 8.858094 AGACTTATAAGTATTTAGGAACGGAGG 58.142 37.037 18.03 0.00 39.88 4.30
3868 4350 7.960262 ACTTATAAGTATTTAGGAACGGAGGG 58.040 38.462 16.60 0.00 37.52 4.30
3869 4351 7.786464 ACTTATAAGTATTTAGGAACGGAGGGA 59.214 37.037 16.60 0.00 37.52 4.20
3968 4538 7.610580 TTGGATTTCAAATAAAACCCTGAGT 57.389 32.000 0.00 0.00 31.46 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 30 7.892241 GGGAGAAAATAAGGGTTAAAACTAGGT 59.108 37.037 0.00 0.00 0.00 3.08
74 76 3.913445 ACAGCCATTGCCACCCCA 61.913 61.111 0.00 0.00 38.69 4.96
110 112 4.346129 CAAGAAGCAAACACAAGACAGTC 58.654 43.478 0.00 0.00 0.00 3.51
114 116 3.438360 CACCAAGAAGCAAACACAAGAC 58.562 45.455 0.00 0.00 0.00 3.01
155 162 2.176798 ACACAAGAAACAAGATCCCCCA 59.823 45.455 0.00 0.00 0.00 4.96
156 163 2.558359 CACACAAGAAACAAGATCCCCC 59.442 50.000 0.00 0.00 0.00 5.40
157 164 3.486383 TCACACAAGAAACAAGATCCCC 58.514 45.455 0.00 0.00 0.00 4.81
158 165 4.023707 CACTCACACAAGAAACAAGATCCC 60.024 45.833 0.00 0.00 0.00 3.85
159 166 4.023707 CCACTCACACAAGAAACAAGATCC 60.024 45.833 0.00 0.00 0.00 3.36
160 167 4.576463 ACCACTCACACAAGAAACAAGATC 59.424 41.667 0.00 0.00 0.00 2.75
161 168 4.336433 CACCACTCACACAAGAAACAAGAT 59.664 41.667 0.00 0.00 0.00 2.40
162 169 3.689161 CACCACTCACACAAGAAACAAGA 59.311 43.478 0.00 0.00 0.00 3.02
163 170 3.181497 CCACCACTCACACAAGAAACAAG 60.181 47.826 0.00 0.00 0.00 3.16
164 171 2.752354 CCACCACTCACACAAGAAACAA 59.248 45.455 0.00 0.00 0.00 2.83
165 172 2.364632 CCACCACTCACACAAGAAACA 58.635 47.619 0.00 0.00 0.00 2.83
166 173 1.065551 GCCACCACTCACACAAGAAAC 59.934 52.381 0.00 0.00 0.00 2.78
167 174 1.340502 TGCCACCACTCACACAAGAAA 60.341 47.619 0.00 0.00 0.00 2.52
168 175 0.254462 TGCCACCACTCACACAAGAA 59.746 50.000 0.00 0.00 0.00 2.52
200 207 6.212187 ACCAATGCATATAGATAGAGCAGACA 59.788 38.462 0.00 0.00 38.75 3.41
203 210 6.637657 TCACCAATGCATATAGATAGAGCAG 58.362 40.000 0.00 0.00 38.75 4.24
244 259 6.798427 ATAAGAGACCTCACACACATATGT 57.202 37.500 1.41 1.41 40.80 2.29
245 260 7.550551 ACAAATAAGAGACCTCACACACATATG 59.449 37.037 0.00 0.00 0.00 1.78
246 261 7.624549 ACAAATAAGAGACCTCACACACATAT 58.375 34.615 0.00 0.00 0.00 1.78
247 262 7.004555 ACAAATAAGAGACCTCACACACATA 57.995 36.000 0.00 0.00 0.00 2.29
248 263 5.869579 ACAAATAAGAGACCTCACACACAT 58.130 37.500 0.00 0.00 0.00 3.21
295 324 5.591472 TGATGCAACAATAGGAAATGAGAGG 59.409 40.000 0.00 0.00 0.00 3.69
368 397 6.758254 ACATACAAATTCCCAGGAACAAAAG 58.242 36.000 0.07 0.00 36.91 2.27
369 398 6.739331 ACATACAAATTCCCAGGAACAAAA 57.261 33.333 0.07 0.00 36.91 2.44
370 399 6.072397 CGTACATACAAATTCCCAGGAACAAA 60.072 38.462 0.07 0.00 36.91 2.83
371 400 5.413213 CGTACATACAAATTCCCAGGAACAA 59.587 40.000 0.07 0.00 36.91 2.83
372 401 4.938832 CGTACATACAAATTCCCAGGAACA 59.061 41.667 0.07 0.00 36.91 3.18
373 402 4.334481 CCGTACATACAAATTCCCAGGAAC 59.666 45.833 0.07 0.00 36.91 3.62
374 403 4.519213 CCGTACATACAAATTCCCAGGAA 58.481 43.478 0.68 0.68 38.59 3.36
375 404 3.118186 CCCGTACATACAAATTCCCAGGA 60.118 47.826 0.00 0.00 0.00 3.86
376 405 3.211045 CCCGTACATACAAATTCCCAGG 58.789 50.000 0.00 0.00 0.00 4.45
377 406 3.211045 CCCCGTACATACAAATTCCCAG 58.789 50.000 0.00 0.00 0.00 4.45
378 407 2.684334 GCCCCGTACATACAAATTCCCA 60.684 50.000 0.00 0.00 0.00 4.37
379 408 1.951602 GCCCCGTACATACAAATTCCC 59.048 52.381 0.00 0.00 0.00 3.97
380 409 1.600485 CGCCCCGTACATACAAATTCC 59.400 52.381 0.00 0.00 0.00 3.01
381 410 2.553086 TCGCCCCGTACATACAAATTC 58.447 47.619 0.00 0.00 0.00 2.17
382 411 2.679336 GTTCGCCCCGTACATACAAATT 59.321 45.455 0.00 0.00 0.00 1.82
383 412 2.093341 AGTTCGCCCCGTACATACAAAT 60.093 45.455 0.00 0.00 29.93 2.32
384 413 1.275856 AGTTCGCCCCGTACATACAAA 59.724 47.619 0.00 0.00 29.93 2.83
385 414 0.896923 AGTTCGCCCCGTACATACAA 59.103 50.000 0.00 0.00 29.93 2.41
386 415 0.896923 AAGTTCGCCCCGTACATACA 59.103 50.000 0.00 0.00 29.93 2.29
387 416 1.135721 AGAAGTTCGCCCCGTACATAC 59.864 52.381 0.00 0.00 29.93 2.39
388 417 1.477553 AGAAGTTCGCCCCGTACATA 58.522 50.000 0.00 0.00 29.93 2.29
389 418 0.611714 AAGAAGTTCGCCCCGTACAT 59.388 50.000 0.00 0.00 29.93 2.29
390 419 0.393820 AAAGAAGTTCGCCCCGTACA 59.606 50.000 0.00 0.00 29.93 2.90
391 420 1.073964 GAAAGAAGTTCGCCCCGTAC 58.926 55.000 0.00 0.00 0.00 3.67
392 421 3.520187 GAAAGAAGTTCGCCCCGTA 57.480 52.632 0.00 0.00 0.00 4.02
393 422 4.373771 GAAAGAAGTTCGCCCCGT 57.626 55.556 0.00 0.00 0.00 5.28
417 446 2.969677 AAAAGCCCGGTTTTGCAGCG 62.970 55.000 0.00 0.00 46.41 5.18
418 447 1.227527 AAAAGCCCGGTTTTGCAGC 60.228 52.632 0.00 0.00 0.00 5.25
419 448 0.179086 ACAAAAGCCCGGTTTTGCAG 60.179 50.000 24.53 9.67 46.88 4.41
420 449 0.250513 AACAAAAGCCCGGTTTTGCA 59.749 45.000 24.53 0.00 46.88 4.08
421 450 0.934496 GAACAAAAGCCCGGTTTTGC 59.066 50.000 24.53 10.68 46.88 3.68
423 452 1.138069 CAGGAACAAAAGCCCGGTTTT 59.862 47.619 0.00 0.00 0.00 2.43
424 453 0.750249 CAGGAACAAAAGCCCGGTTT 59.250 50.000 0.00 0.00 0.00 3.27
425 454 1.112916 CCAGGAACAAAAGCCCGGTT 61.113 55.000 0.00 0.00 0.00 4.44
426 455 1.530655 CCAGGAACAAAAGCCCGGT 60.531 57.895 0.00 0.00 0.00 5.28
427 456 0.825840 TTCCAGGAACAAAAGCCCGG 60.826 55.000 0.00 0.00 0.00 5.73
428 457 1.036707 TTTCCAGGAACAAAAGCCCG 58.963 50.000 0.00 0.00 0.00 6.13
429 458 3.769739 AATTTCCAGGAACAAAAGCCC 57.230 42.857 0.00 0.00 0.00 5.19
430 459 4.450976 ACAAATTTCCAGGAACAAAAGCC 58.549 39.130 0.00 0.00 0.00 4.35
431 460 6.705825 ACATACAAATTTCCAGGAACAAAAGC 59.294 34.615 0.00 0.00 0.00 3.51
490 705 2.430465 TCTTCAGTCATTTGCTCTGCC 58.570 47.619 0.00 0.00 0.00 4.85
512 727 2.223782 TGTTGCTGTCAAAGTTCATGCC 60.224 45.455 0.00 0.00 33.37 4.40
538 753 3.759618 AGACTTCACCTGTGAGTAGTAGC 59.240 47.826 4.96 0.00 41.13 3.58
554 769 4.461784 GACTGCGGTCGAGACTTC 57.538 61.111 10.53 0.00 32.47 3.01
565 780 0.165944 GGTGACAAAATCCGACTGCG 59.834 55.000 0.00 0.00 37.24 5.18
700 916 4.343323 TGGTGGGTGCGATGGTGG 62.343 66.667 0.00 0.00 0.00 4.61
762 978 4.145756 CGCCGTGTTTTTAACTGAATGAAC 59.854 41.667 0.00 0.00 0.00 3.18
763 979 4.035324 TCGCCGTGTTTTTAACTGAATGAA 59.965 37.500 0.00 0.00 0.00 2.57
791 1014 3.583276 AAGACGGCGATCGCACCAA 62.583 57.895 38.00 0.00 44.11 3.67
792 1015 3.982372 GAAGACGGCGATCGCACCA 62.982 63.158 38.00 0.00 44.11 4.17
793 1016 3.255379 GAAGACGGCGATCGCACC 61.255 66.667 38.00 25.63 44.11 5.01
794 1017 3.255379 GGAAGACGGCGATCGCAC 61.255 66.667 38.00 27.30 44.11 5.34
818 1248 0.473309 GGGGAGGGTAGGATGGGTAC 60.473 65.000 0.00 0.00 0.00 3.34
846 1276 2.042404 GAGATCTGCTGCCTGGGAGG 62.042 65.000 17.41 1.11 38.80 4.30
847 1277 1.335882 TGAGATCTGCTGCCTGGGAG 61.336 60.000 11.32 11.32 0.00 4.30
848 1278 1.306397 TGAGATCTGCTGCCTGGGA 60.306 57.895 0.00 0.00 0.00 4.37
850 1280 1.146485 CCTGAGATCTGCTGCCTGG 59.854 63.158 0.00 0.00 0.00 4.45
851 1281 1.146485 CCCTGAGATCTGCTGCCTG 59.854 63.158 0.00 0.00 0.00 4.85
852 1282 2.071262 CCCCTGAGATCTGCTGCCT 61.071 63.158 0.00 0.00 0.00 4.75
853 1283 2.509916 CCCCTGAGATCTGCTGCC 59.490 66.667 0.00 0.00 0.00 4.85
854 1284 2.203181 GCCCCTGAGATCTGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
855 1285 0.034767 TTTGCCCCTGAGATCTGCTG 60.035 55.000 0.00 0.00 0.00 4.41
856 1286 0.924823 ATTTGCCCCTGAGATCTGCT 59.075 50.000 0.00 0.00 0.00 4.24
857 1287 1.316651 GATTTGCCCCTGAGATCTGC 58.683 55.000 0.00 0.00 0.00 4.26
1314 1748 3.689872 TGATTGGCTCTACCTACCTCT 57.310 47.619 0.00 0.00 40.22 3.69
1330 1764 1.281867 TCCGTGGCAAGAGGATTGATT 59.718 47.619 0.76 0.00 0.00 2.57
1334 1768 1.078143 GCTCCGTGGCAAGAGGATT 60.078 57.895 15.37 0.00 33.04 3.01
1415 1849 3.114616 CTCCGTTCCAGCACTGCG 61.115 66.667 0.00 0.00 0.00 5.18
1449 1883 4.162690 GCGATGCCGTCCCCTTCT 62.163 66.667 0.00 0.00 38.24 2.85
1610 2044 1.656652 ACATGCCGATAACTGTCAGC 58.343 50.000 0.00 0.00 0.00 4.26
1617 2051 4.802039 TCGAGTTCTTAACATGCCGATAAC 59.198 41.667 0.00 0.00 0.00 1.89
1638 2072 6.264841 TCCTCAGATCACATCATCTTATCG 57.735 41.667 0.00 0.00 30.07 2.92
1639 2073 7.064847 GCATTCCTCAGATCACATCATCTTATC 59.935 40.741 0.00 0.00 30.07 1.75
1640 2074 6.879993 GCATTCCTCAGATCACATCATCTTAT 59.120 38.462 0.00 0.00 30.07 1.73
1648 2082 3.928005 ACAGCATTCCTCAGATCACAT 57.072 42.857 0.00 0.00 0.00 3.21
1655 2089 3.005050 TCTGCAAAAACAGCATTCCTCAG 59.995 43.478 0.00 0.00 41.82 3.35
1656 2090 2.957680 TCTGCAAAAACAGCATTCCTCA 59.042 40.909 0.00 0.00 41.82 3.86
1657 2091 3.005155 ACTCTGCAAAAACAGCATTCCTC 59.995 43.478 0.00 0.00 41.82 3.71
1658 2092 2.961062 ACTCTGCAAAAACAGCATTCCT 59.039 40.909 0.00 0.00 41.82 3.36
1659 2093 3.054878 CACTCTGCAAAAACAGCATTCC 58.945 45.455 0.00 0.00 41.82 3.01
1660 2094 3.054878 CCACTCTGCAAAAACAGCATTC 58.945 45.455 0.00 0.00 41.82 2.67
1662 2096 2.035066 GTCCACTCTGCAAAAACAGCAT 59.965 45.455 0.00 0.00 41.82 3.79
1663 2097 1.405105 GTCCACTCTGCAAAAACAGCA 59.595 47.619 0.00 0.00 40.19 4.41
1664 2098 1.678101 AGTCCACTCTGCAAAAACAGC 59.322 47.619 0.00 0.00 37.59 4.40
1665 2099 4.516698 ACATAGTCCACTCTGCAAAAACAG 59.483 41.667 0.00 0.00 39.12 3.16
1666 2100 4.460263 ACATAGTCCACTCTGCAAAAACA 58.540 39.130 0.00 0.00 0.00 2.83
1667 2101 5.215160 CAACATAGTCCACTCTGCAAAAAC 58.785 41.667 0.00 0.00 0.00 2.43
1668 2102 4.887071 ACAACATAGTCCACTCTGCAAAAA 59.113 37.500 0.00 0.00 0.00 1.94
1669 2103 4.275689 CACAACATAGTCCACTCTGCAAAA 59.724 41.667 0.00 0.00 0.00 2.44
1693 2137 3.387699 TCATCTCTGTCCACACTTGTCAA 59.612 43.478 0.00 0.00 0.00 3.18
1779 2223 2.691409 TAATCAGCAAGCTAAGGCGT 57.309 45.000 0.00 0.00 44.37 5.68
1838 2282 2.457598 TCGTAGGCTTCAACTCCTGAT 58.542 47.619 0.00 0.00 32.78 2.90
1881 2325 1.090052 CCAGGTCGCCTCGAAAATCC 61.090 60.000 0.00 0.00 37.72 3.01
2006 2450 3.988819 ACAGAAGAAGTCAGAGAAGTGC 58.011 45.455 0.00 0.00 0.00 4.40
2007 2451 6.686630 ACATACAGAAGAAGTCAGAGAAGTG 58.313 40.000 0.00 0.00 0.00 3.16
2008 2452 6.909550 ACATACAGAAGAAGTCAGAGAAGT 57.090 37.500 0.00 0.00 0.00 3.01
2009 2453 6.090628 GCAACATACAGAAGAAGTCAGAGAAG 59.909 42.308 0.00 0.00 0.00 2.85
2024 2468 5.220548 GCACAATAGACTGAGCAACATACAG 60.221 44.000 0.00 0.00 33.63 2.74
2049 2493 2.687935 GTTAGTATGCACAATGGTGGGG 59.312 50.000 1.53 0.00 45.38 4.96
2088 2532 5.888901 AGGAGGGTATTGACGATATAGTGA 58.111 41.667 0.00 0.00 0.00 3.41
2098 2542 3.181485 CGAACTCAGAGGAGGGTATTGAC 60.181 52.174 1.53 0.00 45.81 3.18
2153 2598 6.420604 GGTTTTGAAATTACAGGTGTCATGTG 59.579 38.462 0.00 0.00 32.02 3.21
2162 2607 6.029346 AGATGCAGGTTTTGAAATTACAGG 57.971 37.500 0.00 0.00 0.00 4.00
2188 2633 9.671279 TCTGTGATTGCTTCTAAAATTATCAGA 57.329 29.630 0.00 0.00 0.00 3.27
2209 2654 5.939883 TGACATTAGTGATTTCCCTTCTGTG 59.060 40.000 0.00 0.00 0.00 3.66
2231 2676 2.232208 CCGCCAGATGCTAGTATGATGA 59.768 50.000 0.00 0.00 38.05 2.92
2232 2677 2.028658 ACCGCCAGATGCTAGTATGATG 60.029 50.000 0.00 0.00 38.05 3.07
2233 2678 2.028658 CACCGCCAGATGCTAGTATGAT 60.029 50.000 0.00 0.00 38.05 2.45
2239 2687 1.137086 AGTTACACCGCCAGATGCTAG 59.863 52.381 0.00 0.00 38.05 3.42
2241 2689 0.391661 CAGTTACACCGCCAGATGCT 60.392 55.000 0.00 0.00 38.05 3.79
2252 2700 7.444487 AGACTGGAAATAAGGAAACAGTTACAC 59.556 37.037 0.00 0.00 39.08 2.90
2255 2703 7.514721 ACAGACTGGAAATAAGGAAACAGTTA 58.485 34.615 7.51 0.00 39.08 2.24
2261 2709 8.383175 ACAGATAACAGACTGGAAATAAGGAAA 58.617 33.333 7.51 0.00 38.30 3.13
2263 2711 7.496346 ACAGATAACAGACTGGAAATAAGGA 57.504 36.000 7.51 0.00 38.30 3.36
2286 2734 6.127479 CCCCTAAGCTCTGATCATATCTGTAC 60.127 46.154 0.00 0.00 0.00 2.90
2349 2797 4.047822 CAAGCATGATCGAGGACTTAGTC 58.952 47.826 3.36 3.36 0.00 2.59
2352 2800 2.766263 ACCAAGCATGATCGAGGACTTA 59.234 45.455 0.00 0.00 0.00 2.24
2376 2824 3.686227 ATCTCCTCATCTGTCTCACCT 57.314 47.619 0.00 0.00 0.00 4.00
2388 2836 4.272489 CCATGGTTTGCTTTATCTCCTCA 58.728 43.478 2.57 0.00 0.00 3.86
2427 2875 3.130633 CAAGGTCAGAATGTCAACGTCA 58.869 45.455 0.00 0.00 37.40 4.35
2529 2979 5.705400 ACAAAGGCAGCAGGGTAATATTAT 58.295 37.500 0.00 0.00 0.00 1.28
2530 2980 5.124036 ACAAAGGCAGCAGGGTAATATTA 57.876 39.130 0.00 0.00 0.00 0.98
2531 2981 3.981212 ACAAAGGCAGCAGGGTAATATT 58.019 40.909 0.00 0.00 0.00 1.28
2690 3140 1.656652 CAATGCTTACCAGAGGTCCG 58.343 55.000 0.00 0.00 37.09 4.79
2855 3305 6.155481 GTGGTTTCACAAGCTGGATAGCAG 62.155 50.000 0.00 0.00 46.28 4.24
2897 3347 5.768164 ACCACCAATAACTAACAAGACAAGG 59.232 40.000 0.00 0.00 0.00 3.61
2922 3372 2.412325 CCACAAAACTGCGTACGATTCC 60.412 50.000 21.65 0.89 0.00 3.01
2923 3373 2.222445 ACCACAAAACTGCGTACGATTC 59.778 45.455 21.65 1.31 0.00 2.52
2924 3374 2.215196 ACCACAAAACTGCGTACGATT 58.785 42.857 21.65 6.75 0.00 3.34
2925 3375 1.873698 ACCACAAAACTGCGTACGAT 58.126 45.000 21.65 0.00 0.00 3.73
2926 3376 1.328069 CAACCACAAAACTGCGTACGA 59.672 47.619 21.65 3.19 0.00 3.43
2927 3377 1.737249 CAACCACAAAACTGCGTACG 58.263 50.000 11.84 11.84 0.00 3.67
2928 3378 1.064952 AGCAACCACAAAACTGCGTAC 59.935 47.619 0.00 0.00 39.80 3.67
2929 3379 1.064803 CAGCAACCACAAAACTGCGTA 59.935 47.619 0.00 0.00 39.80 4.42
2930 3380 0.179140 CAGCAACCACAAAACTGCGT 60.179 50.000 0.00 0.00 39.80 5.24
2931 3381 1.481819 GCAGCAACCACAAAACTGCG 61.482 55.000 0.00 0.00 43.65 5.18
2986 3436 2.064014 GACCGGACCTGAAAAAGTACG 58.936 52.381 9.46 0.00 40.09 3.67
2988 3438 1.688197 ACGACCGGACCTGAAAAAGTA 59.312 47.619 9.46 0.00 0.00 2.24
3079 3533 0.824759 ACTGGCGGGAATCAGACTAC 59.175 55.000 0.00 0.00 35.20 2.73
3091 3545 1.051812 AGGATAGAATGGACTGGCGG 58.948 55.000 0.00 0.00 0.00 6.13
3110 3564 2.171659 TCCTGTGTAAAACTCTGGCACA 59.828 45.455 0.00 0.00 38.23 4.57
3139 3593 1.684386 CGCTCTGGAGGCCTCAGAAT 61.684 60.000 33.29 0.00 40.29 2.40
3613 4095 9.869757 TGGATATTTCAATATGGACTACATACG 57.130 33.333 0.00 0.00 44.41 3.06
3708 4190 9.495382 AGACTTATATTTAAGAACAGAGGGAGT 57.505 33.333 9.58 0.00 38.56 3.85
3727 4209 9.573133 CGCATTGGAATCTTTAAAAAGACTTAT 57.427 29.630 7.29 0.00 46.80 1.73
3728 4210 8.026607 CCGCATTGGAATCTTTAAAAAGACTTA 58.973 33.333 7.29 0.00 43.63 2.24
3729 4211 6.868339 CCGCATTGGAATCTTTAAAAAGACTT 59.132 34.615 7.29 4.18 43.63 3.01
3730 4212 6.208599 TCCGCATTGGAATCTTTAAAAAGACT 59.791 34.615 7.29 0.00 46.38 3.24
3731 4213 6.386654 TCCGCATTGGAATCTTTAAAAAGAC 58.613 36.000 7.29 0.00 46.38 3.01
3732 4214 6.582677 TCCGCATTGGAATCTTTAAAAAGA 57.417 33.333 7.56 7.56 46.38 2.52
3746 4228 1.067974 TCCGTATGTAGTCCGCATTGG 59.932 52.381 0.00 0.00 40.09 3.16
3747 4229 2.394708 CTCCGTATGTAGTCCGCATTG 58.605 52.381 0.00 0.00 0.00 2.82
3748 4230 1.269621 GCTCCGTATGTAGTCCGCATT 60.270 52.381 0.00 0.00 0.00 3.56
3749 4231 0.314302 GCTCCGTATGTAGTCCGCAT 59.686 55.000 0.00 0.00 0.00 4.73
3750 4232 1.033202 TGCTCCGTATGTAGTCCGCA 61.033 55.000 0.00 0.00 0.00 5.69
3751 4233 0.101759 TTGCTCCGTATGTAGTCCGC 59.898 55.000 0.00 0.00 0.00 5.54
3752 4234 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
3753 4235 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
3754 4236 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3755 4237 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3756 4238 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3757 4239 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3758 4240 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3759 4241 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3760 4242 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3761 4243 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3762 4244 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3763 4245 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3764 4246 6.690194 ATGTAGATTCACTCATTTTGCTCC 57.310 37.500 0.00 0.00 0.00 4.70
3765 4247 7.983307 AGAATGTAGATTCACTCATTTTGCTC 58.017 34.615 14.46 0.00 40.59 4.26
3766 4248 7.934855 AGAATGTAGATTCACTCATTTTGCT 57.065 32.000 14.46 0.00 40.59 3.91
3803 4285 9.917129 CCAATACAAACTACATACGGATGTATA 57.083 33.333 20.64 10.32 45.42 1.47
3804 4286 8.644216 TCCAATACAAACTACATACGGATGTAT 58.356 33.333 20.64 8.38 45.42 2.29
3805 4287 8.009622 TCCAATACAAACTACATACGGATGTA 57.990 34.615 19.32 19.32 44.77 2.29
3807 4289 7.780008 TTCCAATACAAACTACATACGGATG 57.220 36.000 5.94 5.94 39.16 3.51
3808 4290 8.429641 AGATTCCAATACAAACTACATACGGAT 58.570 33.333 0.00 0.00 0.00 4.18
3809 4291 7.788026 AGATTCCAATACAAACTACATACGGA 58.212 34.615 0.00 0.00 0.00 4.69
3810 4292 7.926555 AGAGATTCCAATACAAACTACATACGG 59.073 37.037 0.00 0.00 0.00 4.02
3811 4293 8.873215 AGAGATTCCAATACAAACTACATACG 57.127 34.615 0.00 0.00 0.00 3.06
3841 4323 8.858094 CCTCCGTTCCTAAATACTTATAAGTCT 58.142 37.037 21.25 9.50 40.37 3.24
3842 4324 8.087136 CCCTCCGTTCCTAAATACTTATAAGTC 58.913 40.741 21.25 3.55 40.37 3.01
3843 4325 7.786464 TCCCTCCGTTCCTAAATACTTATAAGT 59.214 37.037 21.35 21.35 42.91 2.24
3844 4326 8.186709 TCCCTCCGTTCCTAAATACTTATAAG 57.813 38.462 11.05 11.05 0.00 1.73
3845 4327 7.786464 ACTCCCTCCGTTCCTAAATACTTATAA 59.214 37.037 0.00 0.00 0.00 0.98
3846 4328 7.300658 ACTCCCTCCGTTCCTAAATACTTATA 58.699 38.462 0.00 0.00 0.00 0.98
3847 4329 6.141790 ACTCCCTCCGTTCCTAAATACTTAT 58.858 40.000 0.00 0.00 0.00 1.73
3848 4330 5.522641 ACTCCCTCCGTTCCTAAATACTTA 58.477 41.667 0.00 0.00 0.00 2.24
3849 4331 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
3850 4332 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
3851 4333 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
3852 4334 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3853 4335 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3854 4336 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3855 4337 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3856 4338 4.166725 TCATAACTACTCCCTCCGTTCCTA 59.833 45.833 0.00 0.00 0.00 2.94
3857 4339 3.053095 TCATAACTACTCCCTCCGTTCCT 60.053 47.826 0.00 0.00 0.00 3.36
3858 4340 3.294214 TCATAACTACTCCCTCCGTTCC 58.706 50.000 0.00 0.00 0.00 3.62
3859 4341 4.996788 TTCATAACTACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
3860 4342 5.396436 CCAATTCATAACTACTCCCTCCGTT 60.396 44.000 0.00 0.00 0.00 4.44
3861 4343 4.101119 CCAATTCATAACTACTCCCTCCGT 59.899 45.833 0.00 0.00 0.00 4.69
3862 4344 4.503296 CCCAATTCATAACTACTCCCTCCG 60.503 50.000 0.00 0.00 0.00 4.63
3863 4345 4.202472 CCCCAATTCATAACTACTCCCTCC 60.202 50.000 0.00 0.00 0.00 4.30
3864 4346 4.658901 TCCCCAATTCATAACTACTCCCTC 59.341 45.833 0.00 0.00 0.00 4.30
3865 4347 4.641868 TCCCCAATTCATAACTACTCCCT 58.358 43.478 0.00 0.00 0.00 4.20
3866 4348 5.382664 TTCCCCAATTCATAACTACTCCC 57.617 43.478 0.00 0.00 0.00 4.30
3968 4538 3.117926 TCTGGCATAGAGCTATTTTGCCA 60.118 43.478 26.52 26.52 46.96 4.92


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

AutoCloner maintained by Alex Coulton.