Multiple sequence alignment - TraesCS5D01G442300

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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 TraesCS5D01G442300 chr5D 100.000 2943 0 0 2262 5204 494471044 494473986 0.000000e+00 5435.0
1 TraesCS5D01G442300 chr5D 100.000 1088 0 0 944 2031 494469726 494470813 0.000000e+00 2010.0
2 TraesCS5D01G442300 chr5D 100.000 647 0 0 1 647 494468783 494469429 0.000000e+00 1195.0
3 TraesCS5D01G442300 chr5D 95.425 153 3 1 4615 4763 66765023 66765175 1.870000e-59 241.0
4 TraesCS5D01G442300 chr5D 77.117 437 58 19 4188 4598 494647407 494647827 1.130000e-51 215.0
5 TraesCS5D01G442300 chr5D 91.803 61 3 2 3473 3532 133864693 133864752 3.340000e-12 84.2
6 TraesCS5D01G442300 chr5D 81.188 101 10 3 3366 3465 345100766 345100858 7.230000e-09 73.1
7 TraesCS5D01G442300 chr5B 91.339 2367 123 37 2264 4602 610690800 610693112 0.000000e+00 3160.0
8 TraesCS5D01G442300 chr5B 93.472 1103 41 11 944 2031 610689676 610690762 0.000000e+00 1609.0
9 TraesCS5D01G442300 chr5B 83.564 651 40 25 5 633 610688638 610689243 9.850000e-152 547.0
10 TraesCS5D01G442300 chr5B 81.522 184 25 5 4250 4433 610924191 610924365 5.430000e-30 143.0
11 TraesCS5D01G442300 chr5B 86.154 130 17 1 4203 4332 611047015 611047143 7.030000e-29 139.0
12 TraesCS5D01G442300 chr5B 92.647 68 4 1 3467 3533 21588454 21588521 4.290000e-16 97.1
13 TraesCS5D01G442300 chr5B 90.769 65 3 2 3467 3530 591828457 591828395 3.340000e-12 84.2
14 TraesCS5D01G442300 chr5B 80.392 102 15 3 4195 4295 610878124 610878221 7.230000e-09 73.1
15 TraesCS5D01G442300 chr5A 95.095 1101 29 8 944 2029 617358294 617359384 0.000000e+00 1711.0
16 TraesCS5D01G442300 chr5A 91.997 1237 42 18 2262 3469 617359410 617360618 0.000000e+00 1683.0
17 TraesCS5D01G442300 chr5A 94.958 1071 38 6 3529 4584 617360617 617361686 0.000000e+00 1664.0
18 TraesCS5D01G442300 chr5A 88.391 491 24 19 10 482 617357362 617357837 1.270000e-155 560.0
19 TraesCS5D01G442300 chr5A 91.111 270 11 10 4937 5193 617361967 617362236 2.310000e-93 353.0
20 TraesCS5D01G442300 chr5A 94.702 151 5 1 4616 4763 693639163 693639013 1.130000e-56 231.0
21 TraesCS5D01G442300 chr5A 83.200 250 32 5 4209 4451 618433647 618433893 2.440000e-53 220.0
22 TraesCS5D01G442300 chr5A 88.021 192 9 5 4761 4939 617361693 617361883 1.130000e-51 215.0
23 TraesCS5D01G442300 chr5A 83.182 220 26 5 4217 4433 618431484 618431695 1.910000e-44 191.0
24 TraesCS5D01G442300 chr5A 93.243 74 0 3 506 579 617357838 617357906 2.560000e-18 104.0
25 TraesCS5D01G442300 chr5A 81.522 92 9 3 3370 3461 450365823 450365740 9.350000e-08 69.4
26 TraesCS5D01G442300 chr7A 94.118 153 5 1 4615 4763 162776114 162776266 4.050000e-56 230.0
27 TraesCS5D01G442300 chr7B 92.593 162 7 4 4608 4767 74193696 74193854 1.460000e-55 228.0
28 TraesCS5D01G442300 chr4A 92.121 165 6 2 4605 4763 47137883 47138046 5.240000e-55 226.0
29 TraesCS5D01G442300 chr6A 91.566 166 9 3 4600 4763 147454317 147454479 1.890000e-54 224.0
30 TraesCS5D01G442300 chr2A 92.547 161 5 2 4609 4763 728143966 728144125 1.890000e-54 224.0
31 TraesCS5D01G442300 chr2A 91.617 167 5 4 4605 4763 196517952 196518117 6.780000e-54 222.0
32 TraesCS5D01G442300 chr2A 96.552 58 2 0 3473 3530 751242435 751242378 4.290000e-16 97.1
33 TraesCS5D01G442300 chr2A 90.476 63 4 2 3464 3525 709863053 709863114 1.200000e-11 82.4
34 TraesCS5D01G442300 chr1A 91.667 168 5 4 4604 4763 330766065 330765899 1.890000e-54 224.0
35 TraesCS5D01G442300 chr1A 93.103 58 1 2 3473 3530 558978846 558978792 1.200000e-11 82.4
36 TraesCS5D01G442300 chr1A 79.787 94 4 10 3370 3460 581263907 581263826 3.000000e-03 54.7
37 TraesCS5D01G442300 chr1D 94.915 59 1 1 3473 3531 351255328 351255384 2.000000e-14 91.6
38 TraesCS5D01G442300 chr7D 92.063 63 5 0 3468 3530 63453501 63453563 7.180000e-14 89.8
39 TraesCS5D01G442300 chr4D 91.667 60 4 1 3473 3531 73330333 73330392 1.200000e-11 82.4
40 TraesCS5D01G442300 chr6D 81.522 92 9 3 3370 3461 12491203 12491286 9.350000e-08 69.4
41 TraesCS5D01G442300 chr6D 93.617 47 2 1 3420 3465 36551332 36551378 9.350000e-08 69.4


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 TraesCS5D01G442300 chr5D 494468783 494473986 5203 False 2880.000000 5435 100.000000 1 5204 3 chr5D.!!$F5 5203
1 TraesCS5D01G442300 chr5B 610688638 610693112 4474 False 1772.000000 3160 89.458333 5 4602 3 chr5B.!!$F5 4597
2 TraesCS5D01G442300 chr5A 617357362 617362236 4874 False 898.571429 1711 91.830857 10 5193 7 chr5A.!!$F1 5183
3 TraesCS5D01G442300 chr5A 618431484 618433893 2409 False 205.500000 220 83.191000 4209 4451 2 chr5A.!!$F2 242

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
274 306 0.042188 CCCGCGCAATAATTCACTCG 60.042 55.0 8.75 0.0 0.00 4.18 F
499 531 0.727398 AATTACCAAAGCGAGCGAGC 59.273 50.0 0.00 0.0 37.41 5.03 F
987 1456 0.811616 CTAGCTAGGGTTTGCTGCCG 60.812 60.0 13.32 0.0 40.08 5.69 F
2348 2851 0.029834 CAAGTGAGTTGCTGTGGTGC 59.970 55.0 0.00 0.0 0.00 5.01 F
2538 3042 0.767375 AGTGGTGCCTCAGTGATTGT 59.233 50.0 0.00 0.0 0.00 2.71 F
3525 4058 0.837272 ACACATTATGGGACGGAGGG 59.163 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 2311 0.739112 GCCAGGAGAAGCTGAGAACG 60.739 60.000 0.00 0.00 0.0 3.95 R
2348 2851 2.164219 AGCAATAACCCAAACATCGCTG 59.836 45.455 0.00 0.00 0.0 5.18 R
2460 2964 3.010420 GCCATACTGACCTTGAAAGACC 58.990 50.000 0.00 0.00 0.0 3.85 R
3516 4049 0.183252 AGCTACTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.0 4.79 R
3735 4268 0.392998 TCTCCAATTCTTCCAGCCGC 60.393 55.000 0.00 0.00 0.0 6.53 R
5068 6717 0.886563 AGAATGCCAAGCTTGACTGC 59.113 50.000 28.05 21.56 0.0 4.40 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
33 34 1.004918 GCCAGCGTTACTCACCACT 60.005 57.895 0.00 0.00 0.00 4.00
79 86 0.100503 GTGCGCTGGTTTGTTGAGTT 59.899 50.000 9.73 0.00 0.00 3.01
88 95 3.013921 GGTTTGTTGAGTTGTCAGTGGA 58.986 45.455 0.00 0.00 32.98 4.02
89 96 3.442273 GGTTTGTTGAGTTGTCAGTGGAA 59.558 43.478 0.00 0.00 32.98 3.53
90 97 4.438744 GGTTTGTTGAGTTGTCAGTGGAAG 60.439 45.833 0.00 0.00 32.98 3.46
104 111 4.809426 TCAGTGGAAGAGAGAACGAAAAAC 59.191 41.667 0.00 0.00 0.00 2.43
105 112 4.811557 CAGTGGAAGAGAGAACGAAAAACT 59.188 41.667 0.00 0.00 0.00 2.66
110 120 5.178996 GGAAGAGAGAACGAAAAACTAACCC 59.821 44.000 0.00 0.00 0.00 4.11
118 133 6.261603 AGAACGAAAAACTAACCCCAAAGTAG 59.738 38.462 0.00 0.00 0.00 2.57
130 145 2.939103 CCCAAAGTAGAGCGAAATCAGG 59.061 50.000 0.00 0.00 0.00 3.86
131 146 2.352960 CCAAAGTAGAGCGAAATCAGGC 59.647 50.000 0.00 0.00 0.00 4.85
136 151 1.946745 AGAGCGAAATCAGGCTTAGC 58.053 50.000 0.00 0.00 40.16 3.09
138 153 0.811616 AGCGAAATCAGGCTTAGCGG 60.812 55.000 0.00 0.00 35.61 5.52
141 156 1.471676 CGAAATCAGGCTTAGCGGACT 60.472 52.381 0.00 0.00 0.00 3.85
143 158 3.385577 GAAATCAGGCTTAGCGGACTAG 58.614 50.000 0.00 0.00 0.00 2.57
145 160 2.723322 TCAGGCTTAGCGGACTAGTA 57.277 50.000 0.00 0.00 0.00 1.82
149 164 3.250521 CAGGCTTAGCGGACTAGTACTAC 59.749 52.174 2.99 0.00 0.00 2.73
150 165 3.118112 AGGCTTAGCGGACTAGTACTACA 60.118 47.826 2.99 0.00 0.00 2.74
153 168 5.221204 GGCTTAGCGGACTAGTACTACAATT 60.221 44.000 2.99 0.00 0.00 2.32
154 169 6.016777 GGCTTAGCGGACTAGTACTACAATTA 60.017 42.308 2.99 0.00 0.00 1.40
155 170 7.076983 GCTTAGCGGACTAGTACTACAATTAG 58.923 42.308 2.99 0.00 0.00 1.73
158 173 5.535406 AGCGGACTAGTACTACAATTAGCAT 59.465 40.000 2.99 0.00 0.00 3.79
159 174 6.713903 AGCGGACTAGTACTACAATTAGCATA 59.286 38.462 2.99 0.00 0.00 3.14
160 175 7.393796 AGCGGACTAGTACTACAATTAGCATAT 59.606 37.037 2.99 0.00 0.00 1.78
161 176 7.697291 GCGGACTAGTACTACAATTAGCATATC 59.303 40.741 2.99 0.00 0.00 1.63
173 188 8.567285 ACAATTAGCATATCCATAACTAAGCC 57.433 34.615 0.00 0.00 0.00 4.35
174 189 8.163408 ACAATTAGCATATCCATAACTAAGCCA 58.837 33.333 0.00 0.00 0.00 4.75
175 190 8.454106 CAATTAGCATATCCATAACTAAGCCAC 58.546 37.037 0.00 0.00 0.00 5.01
272 304 1.724582 GCCCCGCGCAATAATTCACT 61.725 55.000 8.75 0.00 37.47 3.41
274 306 0.042188 CCCGCGCAATAATTCACTCG 60.042 55.000 8.75 0.00 0.00 4.18
293 325 3.426568 GCCGCTGTTCCAGAGCAC 61.427 66.667 0.00 0.00 36.12 4.40
406 438 1.629181 CCCCCGGAAAATCCCTACGT 61.629 60.000 0.73 0.00 31.13 3.57
414 446 1.664321 AAATCCCTACGTCGCGCTCT 61.664 55.000 5.56 0.00 0.00 4.09
495 527 3.400505 GTACCAATTACCAAAGCGAGC 57.599 47.619 0.00 0.00 0.00 5.03
496 528 0.802494 ACCAATTACCAAAGCGAGCG 59.198 50.000 0.00 0.00 0.00 5.03
497 529 1.083489 CCAATTACCAAAGCGAGCGA 58.917 50.000 0.00 0.00 0.00 4.93
498 530 1.062587 CCAATTACCAAAGCGAGCGAG 59.937 52.381 0.00 0.00 0.00 5.03
499 531 0.727398 AATTACCAAAGCGAGCGAGC 59.273 50.000 0.00 0.00 37.41 5.03
500 532 1.421410 ATTACCAAAGCGAGCGAGCG 61.421 55.000 0.00 0.00 43.00 5.03
501 533 2.480853 TTACCAAAGCGAGCGAGCGA 62.481 55.000 1.41 0.00 43.00 4.93
502 534 2.867333 TACCAAAGCGAGCGAGCGAG 62.867 60.000 1.41 0.00 43.00 5.03
503 535 4.202196 CAAAGCGAGCGAGCGAGC 62.202 66.667 9.12 9.12 43.00 5.03
554 594 4.067913 TCCTCACATCGCAGCGCA 62.068 61.111 10.87 0.00 0.00 6.09
556 596 4.200851 CTCACATCGCAGCGCACG 62.201 66.667 10.87 14.00 0.00 5.34
987 1456 0.811616 CTAGCTAGGGTTTGCTGCCG 60.812 60.000 13.32 0.00 40.08 5.69
989 1458 3.134127 CTAGGGTTTGCTGCCGCC 61.134 66.667 0.00 0.00 34.43 6.13
1827 2299 1.480545 GAGAAGGAGGACAAGGAGCTC 59.519 57.143 4.71 4.71 0.00 4.09
1839 2311 3.704061 ACAAGGAGCTCTACAAGAGGATC 59.296 47.826 14.64 0.00 42.54 3.36
1842 2314 2.691011 GGAGCTCTACAAGAGGATCGTT 59.309 50.000 14.64 0.00 42.54 3.85
1942 2436 9.377312 GTACTTCATTTCAGCTCTTTTATCTCT 57.623 33.333 0.00 0.00 0.00 3.10
1948 2443 9.545105 CATTTCAGCTCTTTTATCTCTAGATGT 57.455 33.333 2.66 0.00 36.05 3.06
2000 2495 2.343101 AGTAGACGCAGCGCATAAAAA 58.657 42.857 16.61 0.00 0.00 1.94
2333 2836 5.570320 ACTGGTAATTGATAAGCCACAAGT 58.430 37.500 0.00 0.00 0.00 3.16
2335 2838 5.565509 TGGTAATTGATAAGCCACAAGTGA 58.434 37.500 0.94 0.00 0.00 3.41
2348 2851 0.029834 CAAGTGAGTTGCTGTGGTGC 59.970 55.000 0.00 0.00 0.00 5.01
2459 2963 1.539827 GCAAGTGCTGGGAAACGTTAT 59.460 47.619 0.00 0.00 38.21 1.89
2460 2964 2.668279 GCAAGTGCTGGGAAACGTTATG 60.668 50.000 0.00 0.00 38.21 1.90
2538 3042 0.767375 AGTGGTGCCTCAGTGATTGT 59.233 50.000 0.00 0.00 0.00 2.71
2640 3145 6.920569 ATTTCACCGAACGAGCTTTATAAT 57.079 33.333 0.00 0.00 0.00 1.28
2656 3161 9.921637 AGCTTTATAATCATTAGTAGCAGAGTC 57.078 33.333 9.57 0.00 0.00 3.36
2674 3179 3.456277 GAGTCTTATGTGGATTCCCTGGT 59.544 47.826 0.00 0.00 0.00 4.00
2755 3260 4.882842 ATGTTTGGGTTATTGTTGGGAC 57.117 40.909 0.00 0.00 0.00 4.46
2756 3261 3.917300 TGTTTGGGTTATTGTTGGGACT 58.083 40.909 0.00 0.00 0.00 3.85
2757 3262 4.290942 TGTTTGGGTTATTGTTGGGACTT 58.709 39.130 0.00 0.00 0.00 3.01
2758 3263 4.100189 TGTTTGGGTTATTGTTGGGACTTG 59.900 41.667 0.00 0.00 0.00 3.16
2945 3474 7.816031 AGAGTGATGCTTTTTATCAAAACATGG 59.184 33.333 0.00 0.00 36.41 3.66
3056 3586 3.534554 TGATCACGAATGTATGCTGCTT 58.465 40.909 0.00 0.00 0.00 3.91
3064 3594 1.447945 TGTATGCTGCTTGCGCTTTA 58.552 45.000 9.73 0.00 46.63 1.85
3070 3600 1.857602 GCTGCTTGCGCTTTATACAGC 60.858 52.381 9.73 14.89 41.80 4.40
3283 3814 5.885449 ACCTGGAGGATTCTAAGAAGATG 57.115 43.478 0.00 0.00 38.94 2.90
3337 3868 1.285078 GGCCAATCTGGGGTAAGACTT 59.715 52.381 0.00 0.00 38.19 3.01
3347 3878 9.503369 AATCTGGGGTAAGACTTAGTAGTAATT 57.497 33.333 0.00 0.00 33.84 1.40
3352 3883 8.631797 GGGGTAAGACTTAGTAGTAATTCTGAG 58.368 40.741 10.11 0.00 33.84 3.35
3379 3910 1.661112 GTCGCATGCCTGAAAGTCTAC 59.339 52.381 13.15 0.00 0.00 2.59
3380 3911 1.275010 TCGCATGCCTGAAAGTCTACA 59.725 47.619 13.15 0.00 0.00 2.74
3381 3912 2.076100 CGCATGCCTGAAAGTCTACAA 58.924 47.619 13.15 0.00 0.00 2.41
3382 3913 2.094894 CGCATGCCTGAAAGTCTACAAG 59.905 50.000 13.15 0.00 0.00 3.16
3383 3914 3.077359 GCATGCCTGAAAGTCTACAAGT 58.923 45.455 6.36 0.00 0.00 3.16
3384 3915 4.253685 GCATGCCTGAAAGTCTACAAGTA 58.746 43.478 6.36 0.00 0.00 2.24
3385 3916 4.331168 GCATGCCTGAAAGTCTACAAGTAG 59.669 45.833 6.36 0.77 34.56 2.57
3386 3917 5.482908 CATGCCTGAAAGTCTACAAGTAGT 58.517 41.667 7.09 0.00 34.84 2.73
3403 3934 6.321690 ACAAGTAGTCAAGTAGTCTGTCAACT 59.678 38.462 0.00 0.00 0.00 3.16
3428 3959 8.225603 TGGGCTTTCTGAAAGATATACAAATC 57.774 34.615 29.14 10.43 46.36 2.17
3469 4002 4.386711 ACCAGTTTACCTCTGTTTGCTAC 58.613 43.478 0.00 0.00 0.00 3.58
3470 4003 4.102681 ACCAGTTTACCTCTGTTTGCTACT 59.897 41.667 0.00 0.00 0.00 2.57
3471 4004 5.306160 ACCAGTTTACCTCTGTTTGCTACTA 59.694 40.000 0.00 0.00 0.00 1.82
3472 4005 5.638234 CCAGTTTACCTCTGTTTGCTACTAC 59.362 44.000 0.00 0.00 0.00 2.73
3473 4006 6.456501 CAGTTTACCTCTGTTTGCTACTACT 58.543 40.000 0.00 0.00 0.00 2.57
3474 4007 6.586844 CAGTTTACCTCTGTTTGCTACTACTC 59.413 42.308 0.00 0.00 0.00 2.59
3476 4009 2.492484 ACCTCTGTTTGCTACTACTCCG 59.508 50.000 0.00 0.00 0.00 4.63
3477 4010 2.492484 CCTCTGTTTGCTACTACTCCGT 59.508 50.000 0.00 0.00 0.00 4.69
3478 4011 3.427773 CCTCTGTTTGCTACTACTCCGTC 60.428 52.174 0.00 0.00 0.00 4.79
3479 4012 2.490903 TCTGTTTGCTACTACTCCGTCC 59.509 50.000 0.00 0.00 0.00 4.79
3480 4013 1.547372 TGTTTGCTACTACTCCGTCCC 59.453 52.381 0.00 0.00 0.00 4.46
3481 4014 1.547372 GTTTGCTACTACTCCGTCCCA 59.453 52.381 0.00 0.00 0.00 4.37
3483 4016 3.301794 TTGCTACTACTCCGTCCCATA 57.698 47.619 0.00 0.00 0.00 2.74
3485 4018 3.840991 TGCTACTACTCCGTCCCATAAT 58.159 45.455 0.00 0.00 0.00 1.28
3487 4020 3.573110 GCTACTACTCCGTCCCATAATGT 59.427 47.826 0.00 0.00 0.00 2.71
3490 4023 5.786264 ACTACTCCGTCCCATAATGTAAG 57.214 43.478 0.00 0.00 0.00 2.34
3494 4027 4.654262 ACTCCGTCCCATAATGTAAGATGT 59.346 41.667 0.00 0.00 0.00 3.06
3495 4028 5.130477 ACTCCGTCCCATAATGTAAGATGTT 59.870 40.000 0.00 0.00 0.00 2.71
3496 4029 5.996644 TCCGTCCCATAATGTAAGATGTTT 58.003 37.500 0.00 0.00 0.00 2.83
3497 4030 6.419791 TCCGTCCCATAATGTAAGATGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
3498 4031 6.887545 TCCGTCCCATAATGTAAGATGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
3517 4050 5.398603 TTTTTGGCACTACACATTATGGG 57.601 39.130 0.00 0.00 0.00 4.00
3519 4052 3.275617 TGGCACTACACATTATGGGAC 57.724 47.619 0.00 0.00 0.00 4.46
3520 4053 2.210116 GGCACTACACATTATGGGACG 58.790 52.381 0.00 0.00 0.00 4.79
3522 4055 2.159014 GCACTACACATTATGGGACGGA 60.159 50.000 0.00 0.00 0.00 4.69
3524 4057 2.698797 ACTACACATTATGGGACGGAGG 59.301 50.000 0.00 0.00 0.00 4.30
3525 4058 0.837272 ACACATTATGGGACGGAGGG 59.163 55.000 0.00 0.00 0.00 4.30
3526 4059 1.128200 CACATTATGGGACGGAGGGA 58.872 55.000 0.00 0.00 0.00 4.20
3527 4060 1.070758 CACATTATGGGACGGAGGGAG 59.929 57.143 0.00 0.00 0.00 4.30
3528 4061 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3623 4156 7.442969 CGTACCAAATTAGGGTCTAATATTGCA 59.557 37.037 5.07 0.00 39.85 4.08
3636 4169 8.585881 GGTCTAATATTGCATCTCTTGTAGGTA 58.414 37.037 0.00 0.00 0.00 3.08
3654 4187 8.871629 TGTAGGTAAATGCAAATAAGAAGGAA 57.128 30.769 0.00 0.00 0.00 3.36
3828 4361 0.038892 CAAGCAAGCGCATCAAAGGT 60.039 50.000 11.47 0.00 42.27 3.50
3831 4364 0.804989 GCAAGCGCATCAAAGGTAGT 59.195 50.000 11.47 0.00 38.36 2.73
3901 4434 2.045926 GTGCACCATCTTCGCCCT 60.046 61.111 5.22 0.00 0.00 5.19
3903 4436 2.892425 GCACCATCTTCGCCCTCG 60.892 66.667 0.00 0.00 0.00 4.63
4134 4673 1.831286 CTACCCCATCTACGCCGGT 60.831 63.158 1.90 0.00 0.00 5.28
4148 4687 3.428282 CGGTTACAACAGCGGCCC 61.428 66.667 0.00 0.00 33.97 5.80
4393 4951 3.065371 ACTTCCGCACTGAAAACTGAAAG 59.935 43.478 0.00 0.00 42.29 2.62
4451 5068 8.357402 GGACCTTGTGTTGTAATTCAGTTTAAT 58.643 33.333 0.00 0.00 0.00 1.40
4454 5071 7.148983 CCTTGTGTTGTAATTCAGTTTAATGCG 60.149 37.037 0.00 0.00 0.00 4.73
4523 5141 8.379161 CGAGCATTGACTATTAATATCTTCTGC 58.621 37.037 0.00 4.01 0.00 4.26
4598 5216 3.963665 TGTGTGCTTGTTATGCTGTTTC 58.036 40.909 0.00 0.00 0.00 2.78
4602 5220 5.042593 TGTGCTTGTTATGCTGTTTCTTTG 58.957 37.500 0.00 0.00 0.00 2.77
4603 5221 5.043248 GTGCTTGTTATGCTGTTTCTTTGT 58.957 37.500 0.00 0.00 0.00 2.83
4604 5222 6.183360 TGTGCTTGTTATGCTGTTTCTTTGTA 60.183 34.615 0.00 0.00 0.00 2.41
4606 5224 6.862608 TGCTTGTTATGCTGTTTCTTTGTATG 59.137 34.615 0.00 0.00 0.00 2.39
4608 5226 7.382218 GCTTGTTATGCTGTTTCTTTGTATGTT 59.618 33.333 0.00 0.00 0.00 2.71
4616 5234 9.944663 TGCTGTTTCTTTGTATGTTTTACTTAG 57.055 29.630 0.00 0.00 0.00 2.18
4617 5235 9.394477 GCTGTTTCTTTGTATGTTTTACTTAGG 57.606 33.333 0.00 0.00 0.00 2.69
4618 5236 9.893305 CTGTTTCTTTGTATGTTTTACTTAGGG 57.107 33.333 0.00 0.00 0.00 3.53
4619 5237 9.411189 TGTTTCTTTGTATGTTTTACTTAGGGT 57.589 29.630 0.00 0.00 0.00 4.34
4620 5238 9.673454 GTTTCTTTGTATGTTTTACTTAGGGTG 57.327 33.333 0.00 0.00 0.00 4.61
4621 5239 8.983702 TTCTTTGTATGTTTTACTTAGGGTGT 57.016 30.769 0.00 0.00 0.00 4.16
4622 5240 8.385898 TCTTTGTATGTTTTACTTAGGGTGTG 57.614 34.615 0.00 0.00 0.00 3.82
4623 5241 7.994334 TCTTTGTATGTTTTACTTAGGGTGTGT 59.006 33.333 0.00 0.00 0.00 3.72
4624 5242 7.733402 TTGTATGTTTTACTTAGGGTGTGTC 57.267 36.000 0.00 0.00 0.00 3.67
4627 5245 8.308931 TGTATGTTTTACTTAGGGTGTGTCTAG 58.691 37.037 0.00 0.00 0.00 2.43
4628 5246 6.105397 TGTTTTACTTAGGGTGTGTCTAGG 57.895 41.667 0.00 0.00 0.00 3.02
4629 5247 5.012354 TGTTTTACTTAGGGTGTGTCTAGGG 59.988 44.000 0.00 0.00 0.00 3.53
4632 5250 1.207329 CTTAGGGTGTGTCTAGGGCAC 59.793 57.143 10.20 10.20 37.37 5.01
4633 5251 0.115547 TAGGGTGTGTCTAGGGCACA 59.884 55.000 14.22 14.22 43.60 4.57
4634 5252 0.547712 AGGGTGTGTCTAGGGCACAT 60.548 55.000 18.92 5.97 46.66 3.21
4635 5253 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
4636 5254 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
4637 5255 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
4638 5256 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
4639 5257 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
4640 5258 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
4641 5259 3.638627 TGTGTCTAGGGCACATCTAGATG 59.361 47.826 27.63 27.63 43.25 2.90
4666 5284 6.878317 TGCTCTAGTTATTGCACATCTAAGT 58.122 36.000 0.00 0.00 0.00 2.24
4667 5285 6.758416 TGCTCTAGTTATTGCACATCTAAGTG 59.242 38.462 0.00 0.00 42.37 3.16
4668 5286 6.201806 GCTCTAGTTATTGCACATCTAAGTGG 59.798 42.308 0.00 0.00 39.87 4.00
4669 5287 6.582636 TCTAGTTATTGCACATCTAAGTGGG 58.417 40.000 0.00 0.00 39.87 4.61
4670 5288 5.179452 AGTTATTGCACATCTAAGTGGGT 57.821 39.130 0.00 0.00 39.87 4.51
4671 5289 4.943705 AGTTATTGCACATCTAAGTGGGTG 59.056 41.667 0.00 0.00 39.87 4.61
4672 5290 3.719268 ATTGCACATCTAAGTGGGTGA 57.281 42.857 0.00 0.00 39.87 4.02
4673 5291 3.500448 TTGCACATCTAAGTGGGTGAA 57.500 42.857 0.00 0.00 39.87 3.18
4674 5292 3.719268 TGCACATCTAAGTGGGTGAAT 57.281 42.857 0.00 0.00 39.87 2.57
4675 5293 3.609853 TGCACATCTAAGTGGGTGAATC 58.390 45.455 0.00 0.00 39.87 2.52
4676 5294 3.008923 TGCACATCTAAGTGGGTGAATCA 59.991 43.478 0.00 0.00 39.87 2.57
4677 5295 4.009675 GCACATCTAAGTGGGTGAATCAA 58.990 43.478 0.00 0.00 39.87 2.57
4678 5296 4.095483 GCACATCTAAGTGGGTGAATCAAG 59.905 45.833 0.00 0.00 39.87 3.02
4679 5297 5.248640 CACATCTAAGTGGGTGAATCAAGT 58.751 41.667 0.00 0.00 35.88 3.16
4680 5298 6.406370 CACATCTAAGTGGGTGAATCAAGTA 58.594 40.000 0.00 0.00 35.88 2.24
4681 5299 7.050377 CACATCTAAGTGGGTGAATCAAGTAT 58.950 38.462 0.00 0.00 35.88 2.12
4682 5300 8.204160 CACATCTAAGTGGGTGAATCAAGTATA 58.796 37.037 0.00 0.00 35.88 1.47
4683 5301 8.768397 ACATCTAAGTGGGTGAATCAAGTATAA 58.232 33.333 0.00 0.00 0.00 0.98
4684 5302 9.613428 CATCTAAGTGGGTGAATCAAGTATAAA 57.387 33.333 0.00 0.00 0.00 1.40
4685 5303 9.838339 ATCTAAGTGGGTGAATCAAGTATAAAG 57.162 33.333 0.00 0.00 0.00 1.85
4686 5304 9.042450 TCTAAGTGGGTGAATCAAGTATAAAGA 57.958 33.333 0.00 0.00 0.00 2.52
4687 5305 9.319143 CTAAGTGGGTGAATCAAGTATAAAGAG 57.681 37.037 0.00 0.00 0.00 2.85
4688 5306 7.496346 AGTGGGTGAATCAAGTATAAAGAGA 57.504 36.000 0.00 0.00 0.00 3.10
4689 5307 7.918076 AGTGGGTGAATCAAGTATAAAGAGAA 58.082 34.615 0.00 0.00 0.00 2.87
4690 5308 8.383175 AGTGGGTGAATCAAGTATAAAGAGAAA 58.617 33.333 0.00 0.00 0.00 2.52
4691 5309 9.010029 GTGGGTGAATCAAGTATAAAGAGAAAA 57.990 33.333 0.00 0.00 0.00 2.29
4692 5310 9.581289 TGGGTGAATCAAGTATAAAGAGAAAAA 57.419 29.630 0.00 0.00 0.00 1.94
4732 5350 9.987272 ATTCACACGAATCTCAATATAAGATCA 57.013 29.630 0.00 0.00 37.25 2.92
4733 5351 9.816354 TTCACACGAATCTCAATATAAGATCAA 57.184 29.630 0.00 0.00 32.29 2.57
4734 5352 9.987272 TCACACGAATCTCAATATAAGATCAAT 57.013 29.630 0.00 0.00 32.29 2.57
4736 5354 9.987272 ACACGAATCTCAATATAAGATCAATGA 57.013 29.630 0.00 0.00 32.29 2.57
4738 5356 9.987272 ACGAATCTCAATATAAGATCAATGACA 57.013 29.630 0.00 0.00 32.29 3.58
4753 5371 9.708092 AGATCAATGACATATGACTTAGATGTG 57.292 33.333 10.38 0.00 41.09 3.21
4754 5372 7.719778 TCAATGACATATGACTTAGATGTGC 57.280 36.000 10.38 0.00 41.09 4.57
4755 5373 7.274447 TCAATGACATATGACTTAGATGTGCA 58.726 34.615 10.38 0.00 41.09 4.57
4756 5374 7.769970 TCAATGACATATGACTTAGATGTGCAA 59.230 33.333 10.38 0.00 41.09 4.08
4757 5375 8.565416 CAATGACATATGACTTAGATGTGCAAT 58.435 33.333 10.38 0.00 41.09 3.56
4758 5376 9.783081 AATGACATATGACTTAGATGTGCAATA 57.217 29.630 10.38 0.00 41.09 1.90
4759 5377 8.593492 TGACATATGACTTAGATGTGCAATAC 57.407 34.615 10.38 0.00 41.09 1.89
4760 5378 8.424133 TGACATATGACTTAGATGTGCAATACT 58.576 33.333 10.38 0.00 41.09 2.12
4761 5379 9.265901 GACATATGACTTAGATGTGCAATACTT 57.734 33.333 10.38 0.00 41.09 2.24
4777 5395 9.704098 GTGCAATACTTACTAGTTATGCTTTTC 57.296 33.333 0.00 0.00 41.53 2.29
4778 5396 9.667107 TGCAATACTTACTAGTTATGCTTTTCT 57.333 29.630 0.00 0.00 41.53 2.52
4820 5438 8.275015 TGCTATTTATTCAAAGACATCGGAAA 57.725 30.769 0.00 0.00 0.00 3.13
4866 5831 9.599866 CAGACTATATAATTCCACACTTGACAA 57.400 33.333 0.00 0.00 0.00 3.18
4912 6469 3.743521 AGTCAAAACATGAGCAGCACTA 58.256 40.909 0.00 0.00 39.19 2.74
4915 6472 3.748048 TCAAAACATGAGCAGCACTAGTC 59.252 43.478 0.00 0.00 33.04 2.59
4997 6640 2.290260 TGATTAGTGTCCCAACAGCTGG 60.290 50.000 19.93 0.10 45.97 4.85
5068 6717 2.430465 CTTGACATGACCACCTCCTTG 58.570 52.381 0.00 0.00 0.00 3.61
5075 6724 0.108585 GACCACCTCCTTGCAGTCAA 59.891 55.000 0.00 0.00 0.00 3.18
5077 6726 1.239968 CCACCTCCTTGCAGTCAAGC 61.240 60.000 0.00 0.00 46.38 4.01
5078 6727 0.250640 CACCTCCTTGCAGTCAAGCT 60.251 55.000 0.00 0.00 46.38 3.74
5079 6728 0.475906 ACCTCCTTGCAGTCAAGCTT 59.524 50.000 0.00 0.00 46.38 3.74
5080 6729 0.879765 CCTCCTTGCAGTCAAGCTTG 59.120 55.000 20.81 20.81 46.38 4.01
5081 6730 0.879765 CTCCTTGCAGTCAAGCTTGG 59.120 55.000 25.73 11.44 46.38 3.61
5147 6803 0.450583 TTCGACGACCTCCAGATTCG 59.549 55.000 0.00 0.00 38.73 3.34
5175 6831 3.139077 CCGGAAAGAAGTAACAAGCACT 58.861 45.455 0.00 0.00 0.00 4.40
5189 6845 3.028366 GCACTTCCTCGGAAAGCGC 62.028 63.158 0.00 0.00 33.34 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.036577 CTGGCCTGGTCAGACTCTTG 60.037 60.000 23.75 0.00 37.47 3.02
1 2 1.835927 GCTGGCCTGGTCAGACTCTT 61.836 60.000 31.41 0.00 37.47 2.85
2 3 2.289532 GCTGGCCTGGTCAGACTCT 61.290 63.158 31.41 0.00 37.47 3.24
3 4 2.267324 GCTGGCCTGGTCAGACTC 59.733 66.667 31.41 10.52 37.47 3.36
33 34 2.135581 AAAGTCCCACCGACGTCCA 61.136 57.895 10.58 0.00 46.92 4.02
71 74 3.450817 TCTCTTCCACTGACAACTCAACA 59.549 43.478 0.00 0.00 0.00 3.33
74 77 3.566351 TCTCTCTTCCACTGACAACTCA 58.434 45.455 0.00 0.00 0.00 3.41
79 86 2.583143 TCGTTCTCTCTTCCACTGACA 58.417 47.619 0.00 0.00 0.00 3.58
88 95 5.061853 GGGGTTAGTTTTTCGTTCTCTCTT 58.938 41.667 0.00 0.00 0.00 2.85
89 96 4.102054 TGGGGTTAGTTTTTCGTTCTCTCT 59.898 41.667 0.00 0.00 0.00 3.10
90 97 4.383173 TGGGGTTAGTTTTTCGTTCTCTC 58.617 43.478 0.00 0.00 0.00 3.20
104 111 3.604875 TTCGCTCTACTTTGGGGTTAG 57.395 47.619 0.00 0.00 0.00 2.34
105 112 4.020039 TGATTTCGCTCTACTTTGGGGTTA 60.020 41.667 0.00 0.00 0.00 2.85
110 120 2.352960 GCCTGATTTCGCTCTACTTTGG 59.647 50.000 0.00 0.00 0.00 3.28
118 133 0.579156 CGCTAAGCCTGATTTCGCTC 59.421 55.000 0.00 0.00 33.09 5.03
130 145 4.889832 TTGTAGTACTAGTCCGCTAAGC 57.110 45.455 1.87 0.00 0.00 3.09
131 146 7.076983 GCTAATTGTAGTACTAGTCCGCTAAG 58.923 42.308 1.87 0.00 0.00 2.18
136 151 8.182881 GGATATGCTAATTGTAGTACTAGTCCG 58.817 40.741 1.87 0.00 0.00 4.79
149 164 8.454106 GTGGCTTAGTTATGGATATGCTAATTG 58.546 37.037 0.00 0.00 0.00 2.32
150 165 8.386264 AGTGGCTTAGTTATGGATATGCTAATT 58.614 33.333 0.00 0.00 0.00 1.40
153 168 6.935240 AGTGGCTTAGTTATGGATATGCTA 57.065 37.500 0.00 0.00 0.00 3.49
154 169 5.832539 AGTGGCTTAGTTATGGATATGCT 57.167 39.130 0.00 0.00 0.00 3.79
155 170 5.997746 TGAAGTGGCTTAGTTATGGATATGC 59.002 40.000 0.00 0.00 0.00 3.14
158 173 6.409234 CCCTTGAAGTGGCTTAGTTATGGATA 60.409 42.308 0.00 0.00 0.00 2.59
159 174 5.440610 CCTTGAAGTGGCTTAGTTATGGAT 58.559 41.667 0.00 0.00 0.00 3.41
160 175 4.324254 CCCTTGAAGTGGCTTAGTTATGGA 60.324 45.833 0.00 0.00 0.00 3.41
161 176 3.947834 CCCTTGAAGTGGCTTAGTTATGG 59.052 47.826 0.00 0.00 0.00 2.74
164 179 5.514500 AATCCCTTGAAGTGGCTTAGTTA 57.486 39.130 0.00 0.00 0.00 2.24
165 180 4.388577 AATCCCTTGAAGTGGCTTAGTT 57.611 40.909 0.00 0.00 0.00 2.24
166 181 5.717119 ATAATCCCTTGAAGTGGCTTAGT 57.283 39.130 0.00 0.00 0.00 2.24
167 182 6.712547 CCTAATAATCCCTTGAAGTGGCTTAG 59.287 42.308 0.00 0.00 0.00 2.18
168 183 6.601332 CCTAATAATCCCTTGAAGTGGCTTA 58.399 40.000 0.00 0.00 0.00 3.09
169 184 5.449553 CCTAATAATCCCTTGAAGTGGCTT 58.550 41.667 0.00 0.00 0.00 4.35
170 185 4.689983 GCCTAATAATCCCTTGAAGTGGCT 60.690 45.833 0.00 0.00 33.45 4.75
171 186 3.570125 GCCTAATAATCCCTTGAAGTGGC 59.430 47.826 0.00 0.00 0.00 5.01
172 187 5.053978 AGCCTAATAATCCCTTGAAGTGG 57.946 43.478 0.00 0.00 0.00 4.00
173 188 6.831976 ACTAGCCTAATAATCCCTTGAAGTG 58.168 40.000 0.00 0.00 0.00 3.16
174 189 8.011290 TCTACTAGCCTAATAATCCCTTGAAGT 58.989 37.037 0.00 0.00 0.00 3.01
175 190 8.423906 TCTACTAGCCTAATAATCCCTTGAAG 57.576 38.462 0.00 0.00 0.00 3.02
293 325 3.025619 GGCGATTCATTCCGGCTG 58.974 61.111 0.00 0.00 45.94 4.85
398 430 3.200593 GAGAGCGCGACGTAGGGA 61.201 66.667 12.10 0.00 0.00 4.20
482 514 2.092291 CGCTCGCTCGCTTTGGTAA 61.092 57.895 0.00 0.00 0.00 2.85
483 515 2.506217 CGCTCGCTCGCTTTGGTA 60.506 61.111 0.00 0.00 0.00 3.25
484 516 4.357947 TCGCTCGCTCGCTTTGGT 62.358 61.111 0.00 0.00 0.00 3.67
485 517 3.549150 CTCGCTCGCTCGCTTTGG 61.549 66.667 0.00 0.00 0.00 3.28
486 518 4.202196 GCTCGCTCGCTCGCTTTG 62.202 66.667 0.00 0.00 0.00 2.77
500 532 4.897856 GGTCTCGCTCGCTCGCTC 62.898 72.222 0.00 0.00 0.00 5.03
503 535 3.815569 GATGGGTCTCGCTCGCTCG 62.816 68.421 0.00 0.00 0.00 5.03
504 536 2.026879 GATGGGTCTCGCTCGCTC 59.973 66.667 0.00 0.00 0.00 5.03
554 594 3.222354 GAGGGGACGACAAGTGCGT 62.222 63.158 0.00 0.00 45.79 5.24
556 596 2.047179 GGAGGGGACGACAAGTGC 60.047 66.667 0.00 0.00 40.80 4.40
1827 2299 3.380004 AGCTGAGAACGATCCTCTTGTAG 59.620 47.826 0.00 0.00 0.00 2.74
1839 2311 0.739112 GCCAGGAGAAGCTGAGAACG 60.739 60.000 0.00 0.00 0.00 3.95
1842 2314 3.011635 GCGCCAGGAGAAGCTGAGA 62.012 63.158 0.00 0.00 0.00 3.27
2000 2495 2.965831 TCTAAACGCTGGATCTAGCCAT 59.034 45.455 23.65 10.73 40.59 4.40
2333 2836 4.146058 CTGCACCACAGCAACTCA 57.854 55.556 0.00 0.00 45.13 3.41
2348 2851 2.164219 AGCAATAACCCAAACATCGCTG 59.836 45.455 0.00 0.00 0.00 5.18
2459 2963 3.559171 GCCATACTGACCTTGAAAGACCA 60.559 47.826 0.00 0.00 0.00 4.02
2460 2964 3.010420 GCCATACTGACCTTGAAAGACC 58.990 50.000 0.00 0.00 0.00 3.85
2538 3042 3.428664 GGTGGCCCATCCCCATGA 61.429 66.667 0.00 0.00 34.34 3.07
2625 3130 9.193133 TGCTACTAATGATTATAAAGCTCGTTC 57.807 33.333 12.00 0.00 0.00 3.95
2640 3145 6.833933 TCCACATAAGACTCTGCTACTAATGA 59.166 38.462 0.00 0.00 0.00 2.57
2656 3161 5.723295 CAAAAACCAGGGAATCCACATAAG 58.277 41.667 0.09 0.00 34.83 1.73
2658 3163 3.513515 GCAAAAACCAGGGAATCCACATA 59.486 43.478 0.09 0.00 34.83 2.29
2674 3179 3.488778 AACCTCAATGCATGGCAAAAA 57.511 38.095 0.00 0.00 43.62 1.94
2755 3260 3.190878 GCGGACTGCATTCCCAAG 58.809 61.111 16.80 4.96 45.45 3.61
2936 3465 3.143807 ACACACGTGTTCCATGTTTTG 57.856 42.857 20.79 6.18 41.83 2.44
2937 3466 4.966965 TTACACACGTGTTCCATGTTTT 57.033 36.364 20.79 0.00 41.83 2.43
2945 3474 6.034683 GGATAACTGAGATTACACACGTGTTC 59.965 42.308 20.79 14.33 41.83 3.18
2951 3480 8.997621 TTTACTGGATAACTGAGATTACACAC 57.002 34.615 0.00 0.00 0.00 3.82
3056 3586 4.270084 GTGATTACTGCTGTATAAAGCGCA 59.730 41.667 11.47 0.00 46.65 6.09
3064 3594 8.478066 TGATCTACAAAGTGATTACTGCTGTAT 58.522 33.333 4.12 2.47 36.36 2.29
3283 3814 5.500931 GCTCACGTTATCTGAAGTGCAATAC 60.501 44.000 0.00 0.00 34.84 1.89
3337 3868 7.625817 GCGACACTGAACTCAGAATTACTACTA 60.626 40.741 13.61 0.00 46.59 1.82
3347 3878 1.936656 GCATGCGACACTGAACTCAGA 60.937 52.381 13.61 0.00 46.59 3.27
3352 3883 0.950555 TCAGGCATGCGACACTGAAC 60.951 55.000 18.41 0.00 37.06 3.18
3379 3910 6.638873 CAGTTGACAGACTACTTGACTACTTG 59.361 42.308 0.00 0.00 32.79 3.16
3380 3911 6.239064 CCAGTTGACAGACTACTTGACTACTT 60.239 42.308 0.00 0.00 32.79 2.24
3381 3912 5.241949 CCAGTTGACAGACTACTTGACTACT 59.758 44.000 0.00 0.00 32.79 2.57
3382 3913 5.462405 CCAGTTGACAGACTACTTGACTAC 58.538 45.833 0.00 0.00 32.79 2.73
3383 3914 4.523173 CCCAGTTGACAGACTACTTGACTA 59.477 45.833 0.00 0.00 32.79 2.59
3384 3915 3.322254 CCCAGTTGACAGACTACTTGACT 59.678 47.826 0.00 0.00 32.79 3.41
3385 3916 3.654414 CCCAGTTGACAGACTACTTGAC 58.346 50.000 0.00 0.00 32.79 3.18
3386 3917 2.037251 GCCCAGTTGACAGACTACTTGA 59.963 50.000 0.00 0.00 32.79 3.02
3403 3934 8.055181 AGATTTGTATATCTTTCAGAAAGCCCA 58.945 33.333 17.04 5.84 38.39 5.36
3428 3959 5.643777 ACTGGTATAGCTACAACAAGCAAAG 59.356 40.000 10.95 0.00 45.30 2.77
3472 4005 5.215252 ACATCTTACATTATGGGACGGAG 57.785 43.478 0.00 0.00 0.00 4.63
3473 4006 5.623956 AACATCTTACATTATGGGACGGA 57.376 39.130 0.00 0.00 0.00 4.69
3474 4007 6.693315 AAAACATCTTACATTATGGGACGG 57.307 37.500 0.00 0.00 0.00 4.79
3495 4028 5.047660 GTCCCATAATGTGTAGTGCCAAAAA 60.048 40.000 0.00 0.00 0.00 1.94
3496 4029 4.461081 GTCCCATAATGTGTAGTGCCAAAA 59.539 41.667 0.00 0.00 0.00 2.44
3497 4030 4.013728 GTCCCATAATGTGTAGTGCCAAA 58.986 43.478 0.00 0.00 0.00 3.28
3498 4031 3.616219 GTCCCATAATGTGTAGTGCCAA 58.384 45.455 0.00 0.00 0.00 4.52
3499 4032 2.419436 CGTCCCATAATGTGTAGTGCCA 60.419 50.000 0.00 0.00 0.00 4.92
3500 4033 2.210116 CGTCCCATAATGTGTAGTGCC 58.790 52.381 0.00 0.00 0.00 5.01
3501 4034 2.159014 TCCGTCCCATAATGTGTAGTGC 60.159 50.000 0.00 0.00 0.00 4.40
3502 4035 3.492656 CCTCCGTCCCATAATGTGTAGTG 60.493 52.174 0.00 0.00 0.00 2.74
3504 4037 2.037251 CCCTCCGTCCCATAATGTGTAG 59.963 54.545 0.00 0.00 0.00 2.74
3505 4038 2.043992 CCCTCCGTCCCATAATGTGTA 58.956 52.381 0.00 0.00 0.00 2.90
3506 4039 0.837272 CCCTCCGTCCCATAATGTGT 59.163 55.000 0.00 0.00 0.00 3.72
3510 4043 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3511 4044 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3512 4045 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3513 4046 1.145325 CTACTACTCCCTCCGTCCCAT 59.855 57.143 0.00 0.00 0.00 4.00
3515 4048 0.822944 GCTACTACTCCCTCCGTCCC 60.823 65.000 0.00 0.00 0.00 4.46
3516 4049 0.183252 AGCTACTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.00 4.79
3517 4050 2.769893 CTAGCTACTACTCCCTCCGTC 58.230 57.143 0.00 0.00 0.00 4.79
3519 4052 1.202782 TGCTAGCTACTACTCCCTCCG 60.203 57.143 17.23 0.00 0.00 4.63
3520 4053 2.660670 TGCTAGCTACTACTCCCTCC 57.339 55.000 17.23 0.00 0.00 4.30
3522 4055 3.917300 ACAATGCTAGCTACTACTCCCT 58.083 45.455 17.23 0.00 0.00 4.20
3524 4057 9.760077 TTAAAATACAATGCTAGCTACTACTCC 57.240 33.333 17.23 0.00 0.00 3.85
3555 4088 1.732917 CTCGCCAAAGCCACAACAA 59.267 52.632 0.00 0.00 34.57 2.83
3556 4089 2.192861 CCTCGCCAAAGCCACAACA 61.193 57.895 0.00 0.00 34.57 3.33
3623 4156 9.905713 TCTTATTTGCATTTACCTACAAGAGAT 57.094 29.630 0.00 0.00 0.00 2.75
3636 4169 7.373493 CAGACTGTTCCTTCTTATTTGCATTT 58.627 34.615 0.00 0.00 0.00 2.32
3735 4268 0.392998 TCTCCAATTCTTCCAGCCGC 60.393 55.000 0.00 0.00 0.00 6.53
4134 4673 4.708386 CCCGGGCCGCTGTTGTAA 62.708 66.667 23.20 0.00 0.00 2.41
4393 4951 5.050091 CGGCATCCATACTTTACATTCAGTC 60.050 44.000 0.00 0.00 0.00 3.51
4523 5141 1.609061 CCCCATCGCAACCATAGCTAG 60.609 57.143 0.00 0.00 0.00 3.42
4531 5149 4.114997 CAACGCCCCATCGCAACC 62.115 66.667 0.00 0.00 0.00 3.77
4572 5190 2.751259 AGCATAACAAGCACACAGATGG 59.249 45.455 0.00 0.00 0.00 3.51
4598 5216 8.161699 ACACACCCTAAGTAAAACATACAAAG 57.838 34.615 0.00 0.00 0.00 2.77
4602 5220 7.763071 CCTAGACACACCCTAAGTAAAACATAC 59.237 40.741 0.00 0.00 0.00 2.39
4603 5221 7.093201 CCCTAGACACACCCTAAGTAAAACATA 60.093 40.741 0.00 0.00 0.00 2.29
4604 5222 6.296259 CCCTAGACACACCCTAAGTAAAACAT 60.296 42.308 0.00 0.00 0.00 2.71
4606 5224 5.485620 CCCTAGACACACCCTAAGTAAAAC 58.514 45.833 0.00 0.00 0.00 2.43
4608 5226 3.516700 GCCCTAGACACACCCTAAGTAAA 59.483 47.826 0.00 0.00 0.00 2.01
4613 5231 1.272807 GTGCCCTAGACACACCCTAA 58.727 55.000 10.07 0.00 37.96 2.69
4616 5234 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
4620 5238 4.250116 CATCTAGATGTGCCCTAGACAC 57.750 50.000 22.42 8.47 43.57 3.67
4642 5260 6.758416 CACTTAGATGTGCAATAACTAGAGCA 59.242 38.462 0.00 0.00 34.10 4.26
4643 5261 6.201806 CCACTTAGATGTGCAATAACTAGAGC 59.798 42.308 0.00 0.00 36.68 4.09
4644 5262 6.703607 CCCACTTAGATGTGCAATAACTAGAG 59.296 42.308 0.00 0.00 36.68 2.43
4645 5263 6.156256 ACCCACTTAGATGTGCAATAACTAGA 59.844 38.462 0.00 0.00 36.68 2.43
4646 5264 6.258727 CACCCACTTAGATGTGCAATAACTAG 59.741 42.308 0.00 0.00 36.68 2.57
4647 5265 6.070481 TCACCCACTTAGATGTGCAATAACTA 60.070 38.462 0.00 0.00 36.68 2.24
4648 5266 4.943705 CACCCACTTAGATGTGCAATAACT 59.056 41.667 0.00 0.00 36.68 2.24
4649 5267 4.941263 TCACCCACTTAGATGTGCAATAAC 59.059 41.667 0.00 0.00 36.68 1.89
4650 5268 5.172687 TCACCCACTTAGATGTGCAATAA 57.827 39.130 0.00 0.00 36.68 1.40
4651 5269 4.835284 TCACCCACTTAGATGTGCAATA 57.165 40.909 0.00 0.00 36.68 1.90
4652 5270 3.719268 TCACCCACTTAGATGTGCAAT 57.281 42.857 0.00 0.00 36.68 3.56
4653 5271 3.500448 TTCACCCACTTAGATGTGCAA 57.500 42.857 0.00 0.00 36.68 4.08
4654 5272 3.008923 TGATTCACCCACTTAGATGTGCA 59.991 43.478 0.00 0.00 36.68 4.57
4655 5273 3.609853 TGATTCACCCACTTAGATGTGC 58.390 45.455 0.00 0.00 36.68 4.57
4656 5274 5.248640 ACTTGATTCACCCACTTAGATGTG 58.751 41.667 0.00 0.00 37.66 3.21
4657 5275 5.505181 ACTTGATTCACCCACTTAGATGT 57.495 39.130 0.00 0.00 0.00 3.06
4658 5276 9.613428 TTTATACTTGATTCACCCACTTAGATG 57.387 33.333 0.00 0.00 0.00 2.90
4659 5277 9.838339 CTTTATACTTGATTCACCCACTTAGAT 57.162 33.333 0.00 0.00 0.00 1.98
4660 5278 9.042450 TCTTTATACTTGATTCACCCACTTAGA 57.958 33.333 0.00 0.00 0.00 2.10
4661 5279 9.319143 CTCTTTATACTTGATTCACCCACTTAG 57.681 37.037 0.00 0.00 0.00 2.18
4662 5280 9.042450 TCTCTTTATACTTGATTCACCCACTTA 57.958 33.333 0.00 0.00 0.00 2.24
4663 5281 7.918076 TCTCTTTATACTTGATTCACCCACTT 58.082 34.615 0.00 0.00 0.00 3.16
4664 5282 7.496346 TCTCTTTATACTTGATTCACCCACT 57.504 36.000 0.00 0.00 0.00 4.00
4665 5283 8.561738 TTTCTCTTTATACTTGATTCACCCAC 57.438 34.615 0.00 0.00 0.00 4.61
4666 5284 9.581289 TTTTTCTCTTTATACTTGATTCACCCA 57.419 29.630 0.00 0.00 0.00 4.51
4707 5325 9.816354 TTGATCTTATATTGAGATTCGTGTGAA 57.184 29.630 0.00 0.00 38.76 3.18
4708 5326 9.987272 ATTGATCTTATATTGAGATTCGTGTGA 57.013 29.630 0.00 0.00 34.13 3.58
4710 5328 9.987272 TCATTGATCTTATATTGAGATTCGTGT 57.013 29.630 0.00 0.00 34.13 4.49
4712 5330 9.987272 TGTCATTGATCTTATATTGAGATTCGT 57.013 29.630 0.00 0.00 34.13 3.85
4727 5345 9.708092 CACATCTAAGTCATATGTCATTGATCT 57.292 33.333 1.90 0.00 31.60 2.75
4728 5346 8.441608 GCACATCTAAGTCATATGTCATTGATC 58.558 37.037 1.90 0.00 31.60 2.92
4729 5347 7.935210 TGCACATCTAAGTCATATGTCATTGAT 59.065 33.333 1.90 0.00 31.60 2.57
4730 5348 7.274447 TGCACATCTAAGTCATATGTCATTGA 58.726 34.615 1.90 0.00 31.60 2.57
4731 5349 7.486802 TGCACATCTAAGTCATATGTCATTG 57.513 36.000 1.90 0.00 31.60 2.82
4732 5350 8.687292 ATTGCACATCTAAGTCATATGTCATT 57.313 30.769 1.90 0.00 31.60 2.57
4733 5351 9.212641 GTATTGCACATCTAAGTCATATGTCAT 57.787 33.333 1.90 0.00 31.60 3.06
4734 5352 8.424133 AGTATTGCACATCTAAGTCATATGTCA 58.576 33.333 1.90 0.00 31.60 3.58
4735 5353 8.824159 AGTATTGCACATCTAAGTCATATGTC 57.176 34.615 1.90 0.00 31.60 3.06
4740 5358 9.973450 CTAGTAAGTATTGCACATCTAAGTCAT 57.027 33.333 0.00 0.00 30.97 3.06
4741 5359 8.967918 ACTAGTAAGTATTGCACATCTAAGTCA 58.032 33.333 0.00 0.00 32.84 3.41
4742 5360 9.804758 AACTAGTAAGTATTGCACATCTAAGTC 57.195 33.333 0.00 0.00 33.75 3.01
4746 5364 9.692749 GCATAACTAGTAAGTATTGCACATCTA 57.307 33.333 0.00 0.00 40.69 1.98
4747 5365 8.424918 AGCATAACTAGTAAGTATTGCACATCT 58.575 33.333 0.00 0.00 42.19 2.90
4748 5366 8.594881 AGCATAACTAGTAAGTATTGCACATC 57.405 34.615 0.00 0.00 42.19 3.06
4749 5367 8.964476 AAGCATAACTAGTAAGTATTGCACAT 57.036 30.769 0.00 0.00 42.19 3.21
4750 5368 8.786826 AAAGCATAACTAGTAAGTATTGCACA 57.213 30.769 0.00 0.00 42.19 4.57
4751 5369 9.704098 GAAAAGCATAACTAGTAAGTATTGCAC 57.296 33.333 0.00 0.00 42.19 4.57
4752 5370 9.667107 AGAAAAGCATAACTAGTAAGTATTGCA 57.333 29.630 0.00 0.00 42.19 4.08
4758 5376 9.945904 AAGCTAAGAAAAGCATAACTAGTAAGT 57.054 29.630 0.00 0.00 45.30 2.24
4829 5447 9.994432 GGAATTATATAGTCTGCACATTATTGC 57.006 33.333 0.00 0.00 43.31 3.56
4844 5462 9.823647 ACTCTTGTCAAGTGTGGAATTATATAG 57.176 33.333 17.30 3.69 34.25 1.31
4915 6472 2.125552 TGGGCTCATCGAACAGCG 60.126 61.111 11.64 0.00 42.69 5.18
4965 6608 4.263331 GGGACACTAATCAAGGACCTCAAA 60.263 45.833 0.00 0.00 0.00 2.69
4997 6640 3.254892 CGAAGCAAGGAGAAGAACCTAC 58.745 50.000 0.00 0.00 36.67 3.18
5025 6673 1.640917 ACTGTAAGGTGGTGGTCGAT 58.359 50.000 0.00 0.00 39.30 3.59
5068 6717 0.886563 AGAATGCCAAGCTTGACTGC 59.113 50.000 28.05 21.56 0.00 4.40
5075 6724 2.824341 CTGAGGAAAAGAATGCCAAGCT 59.176 45.455 0.00 0.00 0.00 3.74
5077 6726 2.559668 TGCTGAGGAAAAGAATGCCAAG 59.440 45.455 0.00 0.00 0.00 3.61
5078 6727 2.596346 TGCTGAGGAAAAGAATGCCAA 58.404 42.857 0.00 0.00 0.00 4.52
5079 6728 2.291209 TGCTGAGGAAAAGAATGCCA 57.709 45.000 0.00 0.00 0.00 4.92
5080 6729 2.673326 GCTTGCTGAGGAAAAGAATGCC 60.673 50.000 0.00 0.00 0.00 4.40
5081 6730 2.230750 AGCTTGCTGAGGAAAAGAATGC 59.769 45.455 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.