Multiple sequence alignment - TraesCS3D01G311100

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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 TraesCS3D01G311100 chr3D 100.000 3732 0 0 924 4655 425564832 425568563 0.000000e+00 6892.0
1 TraesCS3D01G311100 chr3D 100.000 567 0 0 1 567 425563909 425564475 0.000000e+00 1048.0
2 TraesCS3D01G311100 chr3A 93.610 1565 78 13 1708 3261 562792127 562793680 0.000000e+00 2316.0
3 TraesCS3D01G311100 chr3A 91.608 858 34 12 3384 4215 562793671 562794516 0.000000e+00 1151.0
4 TraesCS3D01G311100 chr3A 93.245 607 31 6 1128 1727 562791574 562792177 0.000000e+00 885.0
5 TraesCS3D01G311100 chr3A 85.558 457 35 14 1 444 562790635 562791073 2.550000e-122 449.0
6 TraesCS3D01G311100 chr3A 92.342 222 13 2 4366 4586 562794801 562795019 3.500000e-81 313.0
7 TraesCS3D01G311100 chr3A 85.938 64 5 4 2153 2214 60524136 60524075 1.080000e-06 65.8
8 TraesCS3D01G311100 chr3A 84.286 70 7 4 2695 2762 293585576 293585643 1.080000e-06 65.8
9 TraesCS3D01G311100 chr3A 100.000 35 0 0 439 473 562791084 562791118 1.080000e-06 65.8
10 TraesCS3D01G311100 chr3A 83.333 72 9 3 2695 2764 429325480 429325410 3.890000e-06 63.9
11 TraesCS3D01G311100 chr3B 92.719 1085 51 13 1715 2784 555545618 555544547 0.000000e+00 1541.0
12 TraesCS3D01G311100 chr3B 91.596 1059 58 24 3078 4122 555544555 555543514 0.000000e+00 1434.0
13 TraesCS3D01G311100 chr3B 93.577 794 36 5 947 1727 555546366 555545575 0.000000e+00 1170.0
14 TraesCS3D01G311100 chr3B 79.381 97 20 0 2153 2249 705917078 705916982 8.360000e-08 69.4
15 TraesCS3D01G311100 chr6A 87.265 746 49 15 3543 4255 318065233 318064501 0.000000e+00 809.0
16 TraesCS3D01G311100 chr6A 92.250 400 17 9 3540 3937 77904684 77905071 5.260000e-154 555.0
17 TraesCS3D01G311100 chr6A 90.500 400 24 8 3540 3937 78045753 78046140 2.480000e-142 516.0
18 TraesCS3D01G311100 chr6A 84.158 101 12 4 2152 2250 472520699 472520797 1.380000e-15 95.3
19 TraesCS3D01G311100 chr1A 92.250 400 16 10 3540 3937 130933818 130934204 1.890000e-153 553.0
20 TraesCS3D01G311100 chr4A 92.000 400 18 9 3543 3940 28768878 28768491 2.450000e-152 549.0
21 TraesCS3D01G311100 chr4A 84.507 71 8 3 2695 2765 472397904 472397971 3.010000e-07 67.6
22 TraesCS3D01G311100 chr2A 91.750 400 19 9 3543 3940 306092195 306091808 1.140000e-150 544.0
23 TraesCS3D01G311100 chr2A 90.323 403 22 10 3543 3940 360683850 360683460 3.210000e-141 512.0
24 TraesCS3D01G311100 chr2A 92.308 52 4 0 2152 2203 67537598 67537649 1.800000e-09 75.0
25 TraesCS3D01G311100 chr2A 86.667 60 7 1 2695 2754 38968475 38968417 1.080000e-06 65.8
26 TraesCS3D01G311100 chr7B 82.353 102 16 2 2153 2253 245070443 245070343 2.310000e-13 87.9
27 TraesCS3D01G311100 chr7B 90.385 52 2 3 72 121 588858172 588858122 1.080000e-06 65.8
28 TraesCS3D01G311100 chr7D 82.000 100 14 2 2153 2250 128787639 128787736 1.070000e-11 82.4
29 TraesCS3D01G311100 chr7D 90.000 50 3 2 72 120 451191678 451191726 3.890000e-06 63.9
30 TraesCS3D01G311100 chr7D 82.192 73 8 4 2113 2181 294047622 294047693 1.810000e-04 58.4
31 TraesCS3D01G311100 chr6B 81.373 102 17 2 2153 2253 574023852 574023752 1.070000e-11 82.4
32 TraesCS3D01G311100 chr2B 93.878 49 2 1 2723 2770 142869574 142869622 6.460000e-09 73.1
33 TraesCS3D01G311100 chr2B 86.667 60 7 1 2695 2754 665189777 665189719 1.080000e-06 65.8
34 TraesCS3D01G311100 chr2D 97.561 41 1 0 69 109 621964507 621964467 2.320000e-08 71.3
35 TraesCS3D01G311100 chr5D 90.385 52 3 2 72 123 6375565 6375516 3.010000e-07 67.6
36 TraesCS3D01G311100 chr5D 86.667 60 7 1 2695 2754 292161343 292161401 1.080000e-06 65.8
37 TraesCS3D01G311100 chr5A 90.385 52 4 1 72 123 169288826 169288876 3.010000e-07 67.6
38 TraesCS3D01G311100 chr5A 90.385 52 2 3 72 123 3296127 3296175 1.080000e-06 65.8
39 TraesCS3D01G311100 chr4B 90.196 51 3 1 72 120 670388338 670388288 1.080000e-06 65.8
40 TraesCS3D01G311100 chr4B 85.714 63 2 6 73 132 627223098 627223156 5.030000e-05 60.2
41 TraesCS3D01G311100 chr7A 88.889 54 3 2 2131 2181 339893136 339893083 3.890000e-06 63.9
42 TraesCS3D01G311100 chr7A 87.037 54 4 2 2131 2181 339753291 339753238 1.810000e-04 58.4
43 TraesCS3D01G311100 chrUn 87.273 55 5 2 72 125 37403276 37403223 1.400000e-05 62.1


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 TraesCS3D01G311100 chr3D 425563909 425568563 4654 False 3970.000000 6892 100.000000 1 4655 2 chr3D.!!$F1 4654
1 TraesCS3D01G311100 chr3A 562790635 562795019 4384 False 863.300000 2316 92.727167 1 4586 6 chr3A.!!$F2 4585
2 TraesCS3D01G311100 chr3B 555543514 555546366 2852 True 1381.666667 1541 92.630667 947 4122 3 chr3B.!!$R2 3175
3 TraesCS3D01G311100 chr6A 318064501 318065233 732 True 809.000000 809 87.265000 3543 4255 1 chr6A.!!$R1 712

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
517 530 0.675522 CAACCCCCGTCGCATAAAGT 60.676 55.0 0.0 0.0 0.0 2.66 F
1675 2157 0.593128 AGTTGAAGCGTGCCATGTTC 59.407 50.0 0.0 0.0 0.0 3.18 F
1881 2367 0.729116 ACATGTGCGTGCTATGCTTC 59.271 50.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2349 1.012086 AGAAGCATAGCACGCACATG 58.988 50.0 0.00 0.0 0.0 3.21 R
3643 4149 0.179084 ATGCGCGCCTACTTATGTGT 60.179 50.0 30.77 0.0 0.0 3.72 R
3757 4265 0.107800 TCTCCGTGGACTCGTCTAGG 60.108 60.0 0.00 0.0 0.0 3.02 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
41 42 2.105821 TCCGGATGAAGGAAGTGTGTTT 59.894 45.455 0.00 0.00 34.33 2.83
101 104 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
190 193 4.482431 GGTAAGCCACCTCCTCCT 57.518 61.111 0.00 0.00 44.79 3.69
191 194 2.213280 GGTAAGCCACCTCCTCCTC 58.787 63.158 0.00 0.00 44.79 3.71
208 211 0.955919 CTCCTCCGGTGCACTTTTCC 60.956 60.000 17.98 0.00 0.00 3.13
210 213 1.971695 CTCCGGTGCACTTTTCCCC 60.972 63.158 17.98 0.00 0.00 4.81
256 261 7.823149 TCTCGTTATAAAAACTCTAACCAGC 57.177 36.000 0.00 0.00 0.00 4.85
257 262 7.380536 TCTCGTTATAAAAACTCTAACCAGCA 58.619 34.615 0.00 0.00 0.00 4.41
258 263 7.330208 TCTCGTTATAAAAACTCTAACCAGCAC 59.670 37.037 0.00 0.00 0.00 4.40
259 264 7.156673 TCGTTATAAAAACTCTAACCAGCACT 58.843 34.615 0.00 0.00 0.00 4.40
260 265 8.306038 TCGTTATAAAAACTCTAACCAGCACTA 58.694 33.333 0.00 0.00 0.00 2.74
261 266 8.928733 CGTTATAAAAACTCTAACCAGCACTAA 58.071 33.333 0.00 0.00 0.00 2.24
273 278 3.055094 ACCAGCACTAATACCTTGACCAG 60.055 47.826 0.00 0.00 0.00 4.00
298 303 8.504005 AGTATAAACGTCCAAGAGAAAACAATG 58.496 33.333 0.00 0.00 0.00 2.82
300 305 3.815809 ACGTCCAAGAGAAAACAATGGA 58.184 40.909 0.00 0.00 37.83 3.41
301 306 3.815401 ACGTCCAAGAGAAAACAATGGAG 59.185 43.478 0.00 0.00 40.65 3.86
302 307 3.815401 CGTCCAAGAGAAAACAATGGAGT 59.185 43.478 0.00 0.00 40.65 3.85
303 308 4.994852 CGTCCAAGAGAAAACAATGGAGTA 59.005 41.667 0.00 0.00 40.65 2.59
304 309 5.120830 CGTCCAAGAGAAAACAATGGAGTAG 59.879 44.000 0.00 0.00 40.65 2.57
305 310 5.998363 GTCCAAGAGAAAACAATGGAGTAGT 59.002 40.000 0.00 0.00 40.65 2.73
331 337 4.867047 ACAACACATCTCGACAGATCATTC 59.133 41.667 0.00 0.00 37.25 2.67
333 339 3.378427 ACACATCTCGACAGATCATTCGA 59.622 43.478 15.46 15.46 41.83 3.71
379 385 2.436542 TCCAACTCTTCCTTCCACGAAA 59.563 45.455 0.00 0.00 0.00 3.46
390 403 3.110178 CACGAAACGGCTCCGGAC 61.110 66.667 13.31 0.00 44.69 4.79
452 465 4.431131 CATCCCACCAGCCGCCTT 62.431 66.667 0.00 0.00 0.00 4.35
453 466 4.115199 ATCCCACCAGCCGCCTTC 62.115 66.667 0.00 0.00 0.00 3.46
459 472 4.033776 CCAGCCGCCTTCCCAGAA 62.034 66.667 0.00 0.00 0.00 3.02
460 473 2.747855 CAGCCGCCTTCCCAGAAC 60.748 66.667 0.00 0.00 0.00 3.01
461 474 4.035102 AGCCGCCTTCCCAGAACC 62.035 66.667 0.00 0.00 0.00 3.62
463 476 4.778143 CCGCCTTCCCAGAACCGG 62.778 72.222 0.00 0.00 0.00 5.28
464 477 3.702048 CGCCTTCCCAGAACCGGA 61.702 66.667 9.46 0.00 0.00 5.14
465 478 2.046217 GCCTTCCCAGAACCGGAC 60.046 66.667 9.46 0.99 0.00 4.79
466 479 2.264794 CCTTCCCAGAACCGGACG 59.735 66.667 9.46 0.00 0.00 4.79
467 480 2.434359 CTTCCCAGAACCGGACGC 60.434 66.667 9.46 0.00 0.00 5.19
468 481 3.234630 CTTCCCAGAACCGGACGCA 62.235 63.158 9.46 0.00 0.00 5.24
469 482 3.524648 TTCCCAGAACCGGACGCAC 62.525 63.158 9.46 0.00 0.00 5.34
513 526 3.788145 CCCAACCCCCGTCGCATA 61.788 66.667 0.00 0.00 0.00 3.14
514 527 2.269562 CCAACCCCCGTCGCATAA 59.730 61.111 0.00 0.00 0.00 1.90
515 528 1.377463 CCAACCCCCGTCGCATAAA 60.377 57.895 0.00 0.00 0.00 1.40
516 529 1.373590 CCAACCCCCGTCGCATAAAG 61.374 60.000 0.00 0.00 0.00 1.85
517 530 0.675522 CAACCCCCGTCGCATAAAGT 60.676 55.000 0.00 0.00 0.00 2.66
518 531 0.675522 AACCCCCGTCGCATAAAGTG 60.676 55.000 0.00 0.00 0.00 3.16
519 532 1.817941 CCCCCGTCGCATAAAGTGG 60.818 63.158 0.00 0.00 0.00 4.00
520 533 2.469516 CCCCGTCGCATAAAGTGGC 61.470 63.158 0.00 0.00 0.00 5.01
521 534 2.469516 CCCGTCGCATAAAGTGGCC 61.470 63.158 0.00 0.00 0.00 5.36
522 535 2.469516 CCGTCGCATAAAGTGGCCC 61.470 63.158 0.00 0.00 0.00 5.80
523 536 2.469516 CGTCGCATAAAGTGGCCCC 61.470 63.158 0.00 0.00 0.00 5.80
524 537 2.124901 TCGCATAAAGTGGCCCCG 60.125 61.111 0.00 0.00 0.00 5.73
525 538 3.887868 CGCATAAAGTGGCCCCGC 61.888 66.667 0.00 0.00 0.00 6.13
535 548 2.030113 GGCCCCGCCGTATAAGAC 59.970 66.667 0.00 0.00 39.62 3.01
536 549 2.030113 GCCCCGCCGTATAAGACC 59.970 66.667 0.00 0.00 0.00 3.85
537 550 2.739132 CCCCGCCGTATAAGACCC 59.261 66.667 0.00 0.00 0.00 4.46
538 551 2.739132 CCCGCCGTATAAGACCCC 59.261 66.667 0.00 0.00 0.00 4.95
539 552 2.739132 CCGCCGTATAAGACCCCC 59.261 66.667 0.00 0.00 0.00 5.40
987 1000 4.444081 CCTCGTCTCCCCCTCCGT 62.444 72.222 0.00 0.00 0.00 4.69
1543 2023 6.516718 ACTCAAGGTACAAATCCATCTATCG 58.483 40.000 0.00 0.00 0.00 2.92
1547 2027 3.921021 GGTACAAATCCATCTATCGCTCG 59.079 47.826 0.00 0.00 0.00 5.03
1549 2029 2.224042 ACAAATCCATCTATCGCTCGCA 60.224 45.455 0.00 0.00 0.00 5.10
1568 2048 3.372954 GCAGTATCTGATCGTTACGCTT 58.627 45.455 0.00 0.00 32.44 4.68
1590 2072 6.365789 GCTTATGTTGATGATCTAGCTGTCTC 59.634 42.308 0.00 0.00 0.00 3.36
1594 2076 2.033927 TGATGATCTAGCTGTCTCGCAC 59.966 50.000 0.00 0.00 0.00 5.34
1607 2089 3.039405 GTCTCGCACTATCTGATCGTTG 58.961 50.000 0.00 0.00 0.00 4.10
1610 2092 1.926510 CGCACTATCTGATCGTTGCAA 59.073 47.619 14.62 0.00 0.00 4.08
1611 2093 2.541346 CGCACTATCTGATCGTTGCAAT 59.459 45.455 0.59 0.00 0.00 3.56
1620 2102 6.252967 TCTGATCGTTGCAATTGTGTTATT 57.747 33.333 0.59 0.00 0.00 1.40
1634 2116 6.741992 TTGTGTTATTGATCTAGCTGTTGG 57.258 37.500 0.00 0.00 0.00 3.77
1646 2128 2.165167 AGCTGTTGGATGGTGTGATTG 58.835 47.619 0.00 0.00 0.00 2.67
1658 2140 3.761218 TGGTGTGATTGTTGTTTGTGAGT 59.239 39.130 0.00 0.00 0.00 3.41
1675 2157 0.593128 AGTTGAAGCGTGCCATGTTC 59.407 50.000 0.00 0.00 0.00 3.18
1677 2159 1.523154 TTGAAGCGTGCCATGTTCCC 61.523 55.000 0.00 0.00 0.00 3.97
1688 2174 3.117888 TGCCATGTTCCCCTTCTATTCTC 60.118 47.826 0.00 0.00 0.00 2.87
1696 2182 3.912528 TCCCCTTCTATTCTCCATCATGG 59.087 47.826 0.00 0.00 39.43 3.66
1724 2210 8.081208 GAATAGATTCGCTCAATTCTTCATCA 57.919 34.615 0.00 0.00 0.00 3.07
1725 2211 8.618702 AATAGATTCGCTCAATTCTTCATCAT 57.381 30.769 0.00 0.00 0.00 2.45
1726 2212 6.301687 AGATTCGCTCAATTCTTCATCATG 57.698 37.500 0.00 0.00 0.00 3.07
1727 2213 6.053650 AGATTCGCTCAATTCTTCATCATGA 58.946 36.000 0.00 0.00 0.00 3.07
1728 2214 6.711194 AGATTCGCTCAATTCTTCATCATGAT 59.289 34.615 1.18 1.18 0.00 2.45
1729 2215 5.919272 TCGCTCAATTCTTCATCATGATC 57.081 39.130 4.86 0.00 0.00 2.92
1730 2216 5.608449 TCGCTCAATTCTTCATCATGATCT 58.392 37.500 4.86 0.00 0.00 2.75
1731 2217 6.752168 TCGCTCAATTCTTCATCATGATCTA 58.248 36.000 4.86 0.00 0.00 1.98
1732 2218 7.212274 TCGCTCAATTCTTCATCATGATCTAA 58.788 34.615 4.86 2.61 0.00 2.10
1733 2219 7.876582 TCGCTCAATTCTTCATCATGATCTAAT 59.123 33.333 4.86 0.80 0.00 1.73
1734 2220 9.148104 CGCTCAATTCTTCATCATGATCTAATA 57.852 33.333 4.86 0.00 0.00 0.98
1741 2227 9.445878 TTCTTCATCATGATCTAATAGATTGGC 57.554 33.333 4.86 0.00 34.53 4.52
1742 2228 8.823794 TCTTCATCATGATCTAATAGATTGGCT 58.176 33.333 4.86 0.00 34.53 4.75
1743 2229 9.100554 CTTCATCATGATCTAATAGATTGGCTC 57.899 37.037 4.86 0.00 34.53 4.70
1744 2230 8.142485 TCATCATGATCTAATAGATTGGCTCA 57.858 34.615 4.86 0.00 34.53 4.26
1745 2231 8.599792 TCATCATGATCTAATAGATTGGCTCAA 58.400 33.333 4.86 0.00 34.53 3.02
1746 2232 9.397280 CATCATGATCTAATAGATTGGCTCAAT 57.603 33.333 4.86 0.67 34.53 2.57
1747 2233 9.976776 ATCATGATCTAATAGATTGGCTCAATT 57.023 29.630 1.18 0.00 34.53 2.32
1748 2234 9.803507 TCATGATCTAATAGATTGGCTCAATTT 57.196 29.630 4.06 0.43 34.53 1.82
1766 2252 7.254319 GCTCAATTTTGCATCATGGTTGAATAG 60.254 37.037 0.00 0.00 34.96 1.73
1767 2253 7.613585 TCAATTTTGCATCATGGTTGAATAGT 58.386 30.769 0.00 0.00 34.96 2.12
1806 2292 9.566530 CGTGTCATAAATTGATATTTGGTTGAA 57.433 29.630 0.00 0.00 36.54 2.69
1820 2306 1.065709 GGTTGAATCCGCCTCTGGTTA 60.066 52.381 0.00 0.00 0.00 2.85
1825 2311 3.964688 TGAATCCGCCTCTGGTTAGATAA 59.035 43.478 0.00 0.00 31.21 1.75
1863 2349 6.408428 GTTGTTCGTTGATTATCATCCGTAC 58.592 40.000 13.38 13.38 0.00 3.67
1864 2350 5.652518 TGTTCGTTGATTATCATCCGTACA 58.347 37.500 16.66 16.66 33.04 2.90
1869 2355 5.612492 CGTTGATTATCATCCGTACATGTGC 60.612 44.000 9.11 6.17 0.00 4.57
1871 2357 3.446310 TTATCATCCGTACATGTGCGT 57.554 42.857 30.01 16.58 36.97 5.24
1881 2367 0.729116 ACATGTGCGTGCTATGCTTC 59.271 50.000 0.00 0.00 0.00 3.86
1886 2372 2.609002 TGTGCGTGCTATGCTTCTATTG 59.391 45.455 0.00 0.00 0.00 1.90
1928 2419 1.137282 TGCAGGTTTCGTAGTCACACA 59.863 47.619 0.00 0.00 0.00 3.72
2138 2630 8.462589 TTGCATATCATGGTGTGTATGTTTAT 57.537 30.769 4.51 0.00 30.82 1.40
2145 2637 6.818142 TCATGGTGTGTATGTTTATGTCAGAG 59.182 38.462 0.00 0.00 0.00 3.35
2220 2712 5.048713 GCAGTACAAATTTGCACTAGGACTT 60.049 40.000 20.97 0.47 33.18 3.01
2339 2836 7.944000 TCACATATATGGCATCCAAATACTTGT 59.056 33.333 16.96 0.00 36.95 3.16
2396 2893 7.254185 CCGGTGTTTACATATATACACACACAC 60.254 40.741 11.47 9.70 42.09 3.82
2537 3034 7.885297 AGCAGTCAAAAGTCATTTGCTAATTA 58.115 30.769 0.00 0.00 46.53 1.40
2706 3204 6.348621 ACTTGCATTTTGTGTTTTGATGAC 57.651 33.333 0.00 0.00 0.00 3.06
2832 3335 7.716799 TGCAACAATCCCTTAACAATCTTAT 57.283 32.000 0.00 0.00 0.00 1.73
2841 3344 7.150447 CCCTTAACAATCTTATAGAAGGGGT 57.850 40.000 8.64 0.00 45.33 4.95
2848 3351 8.721133 ACAATCTTATAGAAGGGGTTTTGTTT 57.279 30.769 0.00 0.00 33.09 2.83
2891 3394 6.830324 AGCATGACTCATTACAAATATGTGGT 59.170 34.615 0.00 0.00 40.84 4.16
2915 3418 6.858478 GTCCTCTTCAAACTTTGTCTTAATGC 59.142 38.462 1.44 0.00 0.00 3.56
2928 3431 5.126067 TGTCTTAATGCCCTCTTAAGATGC 58.874 41.667 16.35 16.35 43.42 3.91
2946 3449 1.271108 TGCTGGTCTTGTTATGCCGAA 60.271 47.619 0.00 0.00 0.00 4.30
2973 3476 2.038952 TCATATACATGCCTGACAGCCC 59.961 50.000 0.00 0.00 31.73 5.19
3007 3510 6.409524 TTGCTGAATTTTCCTCTCAAATGT 57.590 33.333 0.00 0.00 0.00 2.71
3008 3511 7.523293 TTGCTGAATTTTCCTCTCAAATGTA 57.477 32.000 0.00 0.00 0.00 2.29
3046 3549 2.708861 AGTGGGTGTGAATCCAGTGTTA 59.291 45.455 0.00 0.00 35.54 2.41
3079 3582 6.893583 AGAGAAATATGCTGGTAATGACTGT 58.106 36.000 0.00 0.00 0.00 3.55
3080 3583 7.341805 AGAGAAATATGCTGGTAATGACTGTT 58.658 34.615 0.00 0.00 0.00 3.16
3081 3584 7.831193 AGAGAAATATGCTGGTAATGACTGTTT 59.169 33.333 0.00 0.00 0.00 2.83
3082 3585 7.765307 AGAAATATGCTGGTAATGACTGTTTG 58.235 34.615 0.00 0.00 0.00 2.93
3111 3614 2.369394 GGCCATCGAACCTTTCATTCT 58.631 47.619 0.00 0.00 0.00 2.40
3160 3665 6.212955 GTGCAATTTCTGGTTTAAGCACTTA 58.787 36.000 0.00 0.00 45.41 2.24
3227 3732 7.825270 GGTGGTTAATCCCCGAAAAATAAAAAT 59.175 33.333 0.00 0.00 34.77 1.82
3527 4032 3.773860 AAGAAACATGCACACGTTTGA 57.226 38.095 13.67 0.00 35.53 2.69
3643 4149 5.536538 AGCGTCATGGACTCATCTTCTATAA 59.463 40.000 0.00 0.00 0.00 0.98
3672 4178 3.879682 GCGCGCATGCCAGATTGA 61.880 61.111 29.10 0.00 38.08 2.57
3681 4187 3.293337 CATGCCAGATTGATTCCTTCCA 58.707 45.455 0.00 0.00 0.00 3.53
3682 4188 3.008835 TGCCAGATTGATTCCTTCCAG 57.991 47.619 0.00 0.00 0.00 3.86
3748 4256 1.871039 TGAAGCTACAAGACCGCAAAC 59.129 47.619 0.00 0.00 0.00 2.93
3749 4257 1.871039 GAAGCTACAAGACCGCAAACA 59.129 47.619 0.00 0.00 0.00 2.83
3750 4258 2.185004 AGCTACAAGACCGCAAACAT 57.815 45.000 0.00 0.00 0.00 2.71
3751 4259 3.328382 AGCTACAAGACCGCAAACATA 57.672 42.857 0.00 0.00 0.00 2.29
3752 4260 3.000727 AGCTACAAGACCGCAAACATAC 58.999 45.455 0.00 0.00 0.00 2.39
3753 4261 2.222729 GCTACAAGACCGCAAACATACG 60.223 50.000 0.00 0.00 0.00 3.06
3758 4266 3.493213 CCGCAAACATACGGGACC 58.507 61.111 0.00 0.00 45.74 4.46
3767 4275 1.211457 ACATACGGGACCTAGACGAGT 59.789 52.381 0.00 0.00 0.00 4.18
3806 4314 3.008375 TCCTTGTGTATCTTGAGCTGCTT 59.992 43.478 2.53 0.00 0.00 3.91
3836 4344 1.877637 TGGAACGAGACATGGTTGTG 58.122 50.000 0.00 0.00 35.79 3.33
4019 4550 6.477688 TGTTTGTTCTAAACTGACTTCTACCG 59.522 38.462 0.00 0.00 0.00 4.02
4030 4561 4.320870 TGACTTCTACCGCCCTTAAAAAG 58.679 43.478 0.00 0.00 0.00 2.27
4032 4563 2.118313 TCTACCGCCCTTAAAAAGCC 57.882 50.000 0.00 0.00 0.00 4.35
4033 4564 1.100510 CTACCGCCCTTAAAAAGCCC 58.899 55.000 0.00 0.00 0.00 5.19
4160 4694 7.822334 AGTAAAAACATGATGATACCAACTCGA 59.178 33.333 0.00 0.00 0.00 4.04
4209 4743 1.381928 CCACATGCCAGGTGAGATGC 61.382 60.000 11.67 0.00 38.54 3.91
4210 4744 1.450848 ACATGCCAGGTGAGATGCG 60.451 57.895 0.00 0.00 0.00 4.73
4211 4745 1.153309 CATGCCAGGTGAGATGCGA 60.153 57.895 0.00 0.00 0.00 5.10
4213 4747 0.745845 ATGCCAGGTGAGATGCGAAC 60.746 55.000 0.00 0.00 0.00 3.95
4214 4748 1.078848 GCCAGGTGAGATGCGAACT 60.079 57.895 0.00 0.00 0.00 3.01
4218 4752 0.674895 AGGTGAGATGCGAACTTGGC 60.675 55.000 0.00 0.00 0.00 4.52
4219 4753 0.955428 GGTGAGATGCGAACTTGGCA 60.955 55.000 0.51 0.51 45.71 4.92
4226 4760 1.448985 TGCGAACTTGGCATACCTTC 58.551 50.000 0.00 0.00 35.04 3.46
4227 4761 1.271108 TGCGAACTTGGCATACCTTCA 60.271 47.619 0.00 0.00 35.04 3.02
4228 4762 1.130561 GCGAACTTGGCATACCTTCAC 59.869 52.381 0.00 0.00 36.63 3.18
4229 4763 1.737793 CGAACTTGGCATACCTTCACC 59.262 52.381 0.00 0.00 36.63 4.02
4231 4765 3.421844 GAACTTGGCATACCTTCACCTT 58.578 45.455 0.00 0.00 36.63 3.50
4255 4830 4.083862 GGGACCGTGGGAGAGTGC 62.084 72.222 0.00 0.00 0.00 4.40
4256 4831 2.997897 GGACCGTGGGAGAGTGCT 60.998 66.667 0.00 0.00 0.00 4.40
4257 4832 1.681327 GGACCGTGGGAGAGTGCTA 60.681 63.158 0.00 0.00 0.00 3.49
4259 4834 1.668101 GACCGTGGGAGAGTGCTAGG 61.668 65.000 0.00 0.00 0.00 3.02
4265 4865 2.054799 TGGGAGAGTGCTAGGTTTTGT 58.945 47.619 0.00 0.00 0.00 2.83
4268 4868 3.307762 GGGAGAGTGCTAGGTTTTGTGAT 60.308 47.826 0.00 0.00 0.00 3.06
4269 4869 3.935828 GGAGAGTGCTAGGTTTTGTGATC 59.064 47.826 0.00 0.00 0.00 2.92
4270 4870 4.563580 GGAGAGTGCTAGGTTTTGTGATCA 60.564 45.833 0.00 0.00 0.00 2.92
4275 4875 4.757149 GTGCTAGGTTTTGTGATCAACTCT 59.243 41.667 0.00 0.00 32.93 3.24
4331 4978 5.596845 TCTGCCTAACATTTTTGGTGTTTC 58.403 37.500 0.00 0.00 40.13 2.78
4372 5041 6.253746 CGTATGCGTAATACTACTATGGGTC 58.746 44.000 0.00 0.00 39.29 4.46
4391 5060 1.542472 TCTGTTATTGTCGGACTGCGA 59.458 47.619 9.88 0.00 0.00 5.10
4393 5062 1.000052 TGTTATTGTCGGACTGCGACA 60.000 47.619 20.42 20.42 43.45 4.35
4397 5066 0.599060 TTGTCGGACTGCGACATGTA 59.401 50.000 24.06 8.98 44.34 2.29
4398 5067 0.109458 TGTCGGACTGCGACATGTAC 60.109 55.000 20.42 0.00 40.80 2.90
4399 5068 0.109458 GTCGGACTGCGACATGTACA 60.109 55.000 17.24 0.00 36.49 2.90
4409 5078 3.682377 TGCGACATGTACAACACCAATAG 59.318 43.478 0.00 0.00 0.00 1.73
4414 5083 6.254281 ACATGTACAACACCAATAGAAAGC 57.746 37.500 0.00 0.00 0.00 3.51
4425 5094 4.818546 ACCAATAGAAAGCATGGAATCGAG 59.181 41.667 0.00 0.00 36.75 4.04
4447 5116 2.500229 GGTCAAGAAACGGGTGAATGA 58.500 47.619 0.00 0.00 0.00 2.57
4466 5135 6.924612 TGAATGACTGAATTGTTGGTTGAATG 59.075 34.615 0.00 0.00 0.00 2.67
4471 5140 5.107109 TGAATTGTTGGTTGAATGAGACG 57.893 39.130 0.00 0.00 0.00 4.18
4522 5192 2.537143 AGACTTGGGTATGAACTCGGT 58.463 47.619 0.00 0.00 0.00 4.69
4525 5195 2.838202 ACTTGGGTATGAACTCGGTGAT 59.162 45.455 0.00 0.00 0.00 3.06
4591 5261 2.278336 CGACGCGCCGGAGAATTA 60.278 61.111 10.31 0.00 0.00 1.40
4592 5262 2.293627 CGACGCGCCGGAGAATTAG 61.294 63.158 10.31 0.00 0.00 1.73
4593 5263 2.585247 ACGCGCCGGAGAATTAGC 60.585 61.111 10.31 0.00 0.00 3.09
4594 5264 2.584970 CGCGCCGGAGAATTAGCA 60.585 61.111 10.31 0.00 0.00 3.49
4595 5265 2.871427 CGCGCCGGAGAATTAGCAC 61.871 63.158 10.31 0.00 0.00 4.40
4596 5266 2.871427 GCGCCGGAGAATTAGCACG 61.871 63.158 10.31 0.00 0.00 5.34
4597 5267 2.871427 CGCCGGAGAATTAGCACGC 61.871 63.158 5.05 0.00 0.00 5.34
4598 5268 1.521681 GCCGGAGAATTAGCACGCT 60.522 57.895 5.05 0.00 0.00 5.07
4599 5269 1.491505 GCCGGAGAATTAGCACGCTC 61.492 60.000 5.05 0.00 0.00 5.03
4600 5270 1.209275 CCGGAGAATTAGCACGCTCG 61.209 60.000 0.00 0.00 0.00 5.03
4601 5271 1.812214 CGGAGAATTAGCACGCTCGC 61.812 60.000 0.00 0.00 0.00 5.03
4602 5272 0.528684 GGAGAATTAGCACGCTCGCT 60.529 55.000 0.00 2.12 46.26 4.93
4603 5273 0.849579 GAGAATTAGCACGCTCGCTC 59.150 55.000 0.00 0.00 42.62 5.03
4604 5274 0.528684 AGAATTAGCACGCTCGCTCC 60.529 55.000 0.00 0.00 42.62 4.70
4605 5275 1.812214 GAATTAGCACGCTCGCTCCG 61.812 60.000 0.00 0.00 42.62 4.63
4606 5276 2.558554 AATTAGCACGCTCGCTCCGT 62.559 55.000 0.00 0.00 42.62 4.69
4607 5277 2.558554 ATTAGCACGCTCGCTCCGTT 62.559 55.000 0.00 0.00 42.62 4.44
4608 5278 3.678717 TAGCACGCTCGCTCCGTTC 62.679 63.158 0.00 0.00 42.62 3.95
4610 5280 2.483745 CACGCTCGCTCCGTTCTA 59.516 61.111 0.00 0.00 36.69 2.10
4611 5281 1.154093 CACGCTCGCTCCGTTCTAA 60.154 57.895 0.00 0.00 36.69 2.10
4612 5282 0.731514 CACGCTCGCTCCGTTCTAAA 60.732 55.000 0.00 0.00 36.69 1.85
4613 5283 0.731855 ACGCTCGCTCCGTTCTAAAC 60.732 55.000 0.00 0.00 34.96 2.01
4614 5284 0.456312 CGCTCGCTCCGTTCTAAACT 60.456 55.000 0.00 0.00 0.00 2.66
4615 5285 0.992802 GCTCGCTCCGTTCTAAACTG 59.007 55.000 0.00 0.00 0.00 3.16
4616 5286 0.992802 CTCGCTCCGTTCTAAACTGC 59.007 55.000 0.00 0.00 0.00 4.40
4617 5287 0.389426 TCGCTCCGTTCTAAACTGCC 60.389 55.000 0.00 0.00 0.00 4.85
4618 5288 0.389948 CGCTCCGTTCTAAACTGCCT 60.390 55.000 0.00 0.00 0.00 4.75
4619 5289 1.135199 CGCTCCGTTCTAAACTGCCTA 60.135 52.381 0.00 0.00 0.00 3.93
4620 5290 2.269172 GCTCCGTTCTAAACTGCCTAC 58.731 52.381 0.00 0.00 0.00 3.18
4621 5291 2.889852 CTCCGTTCTAAACTGCCTACC 58.110 52.381 0.00 0.00 0.00 3.18
4622 5292 2.232941 CTCCGTTCTAAACTGCCTACCA 59.767 50.000 0.00 0.00 0.00 3.25
4623 5293 2.028748 TCCGTTCTAAACTGCCTACCAC 60.029 50.000 0.00 0.00 0.00 4.16
4624 5294 2.028385 CCGTTCTAAACTGCCTACCACT 60.028 50.000 0.00 0.00 0.00 4.00
4625 5295 3.251571 CGTTCTAAACTGCCTACCACTC 58.748 50.000 0.00 0.00 0.00 3.51
4626 5296 3.305813 CGTTCTAAACTGCCTACCACTCA 60.306 47.826 0.00 0.00 0.00 3.41
4627 5297 4.246458 GTTCTAAACTGCCTACCACTCAG 58.754 47.826 0.00 0.00 0.00 3.35
4628 5298 3.507411 TCTAAACTGCCTACCACTCAGT 58.493 45.455 0.00 0.00 42.28 3.41
4630 5300 2.841442 AACTGCCTACCACTCAGTTC 57.159 50.000 1.47 0.00 44.87 3.01
4631 5301 0.977395 ACTGCCTACCACTCAGTTCC 59.023 55.000 0.00 0.00 37.78 3.62
4632 5302 0.250513 CTGCCTACCACTCAGTTCCC 59.749 60.000 0.00 0.00 0.00 3.97
4633 5303 0.472925 TGCCTACCACTCAGTTCCCA 60.473 55.000 0.00 0.00 0.00 4.37
4634 5304 0.912486 GCCTACCACTCAGTTCCCAT 59.088 55.000 0.00 0.00 0.00 4.00
4635 5305 1.407437 GCCTACCACTCAGTTCCCATG 60.407 57.143 0.00 0.00 0.00 3.66
4636 5306 1.210478 CCTACCACTCAGTTCCCATGG 59.790 57.143 4.14 4.14 36.46 3.66
4637 5307 2.187958 CTACCACTCAGTTCCCATGGA 58.812 52.381 15.22 0.00 34.38 3.41
4638 5308 1.673767 ACCACTCAGTTCCCATGGAT 58.326 50.000 15.22 0.00 34.38 3.41
4639 5309 1.283029 ACCACTCAGTTCCCATGGATG 59.717 52.381 15.22 6.60 34.38 3.51
4640 5310 1.386533 CACTCAGTTCCCATGGATGC 58.613 55.000 15.22 2.03 0.00 3.91
4641 5311 0.107508 ACTCAGTTCCCATGGATGCG 60.108 55.000 15.22 4.09 0.00 4.73
4642 5312 0.178767 CTCAGTTCCCATGGATGCGA 59.821 55.000 15.22 0.00 0.00 5.10
4643 5313 0.617935 TCAGTTCCCATGGATGCGAA 59.382 50.000 15.22 5.07 0.00 4.70
4644 5314 1.212688 TCAGTTCCCATGGATGCGAAT 59.787 47.619 15.22 0.00 28.60 3.34
4645 5315 1.605710 CAGTTCCCATGGATGCGAATC 59.394 52.381 15.22 0.00 28.60 2.52
4646 5316 1.212688 AGTTCCCATGGATGCGAATCA 59.787 47.619 15.22 0.00 28.60 2.57
4647 5317 1.334869 GTTCCCATGGATGCGAATCAC 59.665 52.381 15.22 0.00 28.60 3.06
4648 5318 0.532640 TCCCATGGATGCGAATCACG 60.533 55.000 15.22 0.00 45.66 4.35
4649 5319 1.509644 CCCATGGATGCGAATCACGG 61.510 60.000 15.22 1.87 42.83 4.94
4650 5320 1.280746 CATGGATGCGAATCACGGC 59.719 57.895 5.57 0.00 42.83 5.68
4651 5321 1.893808 ATGGATGCGAATCACGGCC 60.894 57.895 5.57 0.00 42.83 6.13
4652 5322 2.513666 GGATGCGAATCACGGCCA 60.514 61.111 5.57 0.00 42.83 5.36
4653 5323 2.537560 GGATGCGAATCACGGCCAG 61.538 63.158 5.57 0.00 42.83 4.85
4654 5324 1.815421 GATGCGAATCACGGCCAGT 60.815 57.895 2.24 0.00 42.83 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.648092 CACTTCCTTCATCCGGAAATACTTT 59.352 40.000 9.01 0.00 39.86 2.66
21 22 2.185004 AACACACTTCCTTCATCCGG 57.815 50.000 0.00 0.00 0.00 5.14
131 134 7.762588 TTTTTAAACACGGGAATGGATTCTA 57.237 32.000 0.00 0.00 37.00 2.10
157 160 4.698780 GGCTTACCATCGAAGTTTACCTTT 59.301 41.667 0.00 0.00 31.82 3.11
158 161 4.259356 GGCTTACCATCGAAGTTTACCTT 58.741 43.478 0.00 0.00 33.61 3.50
159 162 3.262405 TGGCTTACCATCGAAGTTTACCT 59.738 43.478 0.00 0.00 42.67 3.08
160 163 3.602483 TGGCTTACCATCGAAGTTTACC 58.398 45.455 0.00 0.00 42.67 2.85
208 211 2.158460 AGGAGAGTTGTTCCTTTTGGGG 60.158 50.000 0.00 0.00 42.40 4.96
216 219 4.722361 ACGAGATAAGGAGAGTTGTTCC 57.278 45.455 0.00 0.00 34.83 3.62
217 220 9.798994 TTTATAACGAGATAAGGAGAGTTGTTC 57.201 33.333 0.00 0.00 0.00 3.18
249 254 4.532916 TGGTCAAGGTATTAGTGCTGGTTA 59.467 41.667 0.00 0.00 0.00 2.85
250 255 3.329520 TGGTCAAGGTATTAGTGCTGGTT 59.670 43.478 0.00 0.00 0.00 3.67
252 257 3.055094 ACTGGTCAAGGTATTAGTGCTGG 60.055 47.826 0.00 0.00 0.00 4.85
254 259 7.670605 TTATACTGGTCAAGGTATTAGTGCT 57.329 36.000 0.00 0.00 31.98 4.40
255 260 7.042925 CGTTTATACTGGTCAAGGTATTAGTGC 60.043 40.741 0.00 0.00 31.98 4.40
256 261 7.977853 ACGTTTATACTGGTCAAGGTATTAGTG 59.022 37.037 0.00 0.00 31.98 2.74
257 262 8.071177 ACGTTTATACTGGTCAAGGTATTAGT 57.929 34.615 0.00 0.00 31.98 2.24
258 263 7.650903 GGACGTTTATACTGGTCAAGGTATTAG 59.349 40.741 0.00 0.00 31.98 1.73
259 264 7.123997 TGGACGTTTATACTGGTCAAGGTATTA 59.876 37.037 0.00 0.00 31.98 0.98
260 265 6.070653 TGGACGTTTATACTGGTCAAGGTATT 60.071 38.462 0.00 0.00 31.98 1.89
261 266 5.422970 TGGACGTTTATACTGGTCAAGGTAT 59.577 40.000 0.00 0.00 33.80 2.73
273 278 7.749126 CCATTGTTTTCTCTTGGACGTTTATAC 59.251 37.037 0.00 0.00 0.00 1.47
298 303 5.572126 GTCGAGATGTGTTGTTTACTACTCC 59.428 44.000 0.00 0.00 0.00 3.85
300 305 6.016527 TCTGTCGAGATGTGTTGTTTACTACT 60.017 38.462 0.00 0.00 0.00 2.57
301 306 6.147581 TCTGTCGAGATGTGTTGTTTACTAC 58.852 40.000 0.00 0.00 0.00 2.73
302 307 6.321848 TCTGTCGAGATGTGTTGTTTACTA 57.678 37.500 0.00 0.00 0.00 1.82
303 308 5.196341 TCTGTCGAGATGTGTTGTTTACT 57.804 39.130 0.00 0.00 0.00 2.24
304 309 5.633601 TGATCTGTCGAGATGTGTTGTTTAC 59.366 40.000 0.00 0.00 39.19 2.01
305 310 5.778862 TGATCTGTCGAGATGTGTTGTTTA 58.221 37.500 0.00 0.00 39.19 2.01
354 360 3.744530 CGTGGAAGGAAGAGTTGGAGTTT 60.745 47.826 0.00 0.00 0.00 2.66
390 403 3.353836 CGGTGGCGTGTTGGGAAG 61.354 66.667 0.00 0.00 0.00 3.46
442 455 4.033776 TTCTGGGAAGGCGGCTGG 62.034 66.667 14.21 0.91 0.00 4.85
443 456 2.747855 GTTCTGGGAAGGCGGCTG 60.748 66.667 14.21 0.00 0.00 4.85
444 457 4.035102 GGTTCTGGGAAGGCGGCT 62.035 66.667 5.25 5.25 0.00 5.52
446 459 4.778143 CCGGTTCTGGGAAGGCGG 62.778 72.222 0.00 0.00 0.00 6.13
447 460 3.702048 TCCGGTTCTGGGAAGGCG 61.702 66.667 0.00 0.00 0.00 5.52
448 461 2.046217 GTCCGGTTCTGGGAAGGC 60.046 66.667 0.00 0.00 34.80 4.35
449 462 2.264794 CGTCCGGTTCTGGGAAGG 59.735 66.667 0.00 0.00 34.80 3.46
450 463 2.434359 GCGTCCGGTTCTGGGAAG 60.434 66.667 0.00 0.00 34.80 3.46
451 464 3.235481 TGCGTCCGGTTCTGGGAA 61.235 61.111 0.00 0.00 34.80 3.97
452 465 3.998672 GTGCGTCCGGTTCTGGGA 61.999 66.667 0.00 0.00 0.00 4.37
496 509 2.823376 TTTATGCGACGGGGGTTGGG 62.823 60.000 0.00 0.00 0.00 4.12
497 510 1.373590 CTTTATGCGACGGGGGTTGG 61.374 60.000 0.00 0.00 0.00 3.77
498 511 0.675522 ACTTTATGCGACGGGGGTTG 60.676 55.000 0.00 0.00 0.00 3.77
499 512 0.675522 CACTTTATGCGACGGGGGTT 60.676 55.000 0.00 0.00 0.00 4.11
500 513 1.078708 CACTTTATGCGACGGGGGT 60.079 57.895 0.00 0.00 0.00 4.95
501 514 1.817941 CCACTTTATGCGACGGGGG 60.818 63.158 0.00 0.00 0.00 5.40
502 515 2.469516 GCCACTTTATGCGACGGGG 61.470 63.158 0.00 0.00 0.00 5.73
503 516 2.469516 GGCCACTTTATGCGACGGG 61.470 63.158 0.00 0.00 0.00 5.28
504 517 2.469516 GGGCCACTTTATGCGACGG 61.470 63.158 4.39 0.00 0.00 4.79
505 518 2.469516 GGGGCCACTTTATGCGACG 61.470 63.158 4.39 0.00 0.00 5.12
506 519 2.469516 CGGGGCCACTTTATGCGAC 61.470 63.158 1.96 0.00 0.00 5.19
507 520 2.124901 CGGGGCCACTTTATGCGA 60.125 61.111 1.96 0.00 0.00 5.10
508 521 3.887868 GCGGGGCCACTTTATGCG 61.888 66.667 1.96 0.00 0.00 4.73
518 531 2.030113 GTCTTATACGGCGGGGCC 59.970 66.667 13.24 0.00 46.75 5.80
519 532 2.030113 GGTCTTATACGGCGGGGC 59.970 66.667 13.24 0.00 0.00 5.80
520 533 2.739132 GGGTCTTATACGGCGGGG 59.261 66.667 13.24 0.00 0.00 5.73
521 534 2.739132 GGGGTCTTATACGGCGGG 59.261 66.667 13.24 0.00 0.00 6.13
522 535 2.739132 GGGGGTCTTATACGGCGG 59.261 66.667 13.24 0.00 0.00 6.13
945 958 2.695055 CGTATGCGTGTTGGCTCG 59.305 61.111 0.00 0.00 35.05 5.03
1053 1066 3.447025 GACGCCATCGGGAGGAAGG 62.447 68.421 0.00 0.00 38.47 3.46
1543 2023 2.126914 AACGATCAGATACTGCGAGC 57.873 50.000 0.00 0.00 0.00 5.03
1547 2027 3.001395 AGCGTAACGATCAGATACTGC 57.999 47.619 0.00 4.31 32.47 4.40
1549 2029 6.315091 ACATAAGCGTAACGATCAGATACT 57.685 37.500 0.00 0.00 0.00 2.12
1568 2048 5.563671 GCGAGACAGCTAGATCATCAACATA 60.564 44.000 0.00 0.00 0.00 2.29
1590 2072 1.559831 TGCAACGATCAGATAGTGCG 58.440 50.000 0.00 0.00 0.00 5.34
1594 2076 5.475273 ACACAATTGCAACGATCAGATAG 57.525 39.130 0.00 0.00 0.00 2.08
1607 2089 6.789262 ACAGCTAGATCAATAACACAATTGC 58.211 36.000 5.05 0.00 36.89 3.56
1610 2092 7.112122 TCCAACAGCTAGATCAATAACACAAT 58.888 34.615 0.00 0.00 0.00 2.71
1611 2093 6.472016 TCCAACAGCTAGATCAATAACACAA 58.528 36.000 0.00 0.00 0.00 3.33
1620 2102 2.840038 ACACCATCCAACAGCTAGATCA 59.160 45.455 0.00 0.00 0.00 2.92
1634 2116 4.930963 TCACAAACAACAATCACACCATC 58.069 39.130 0.00 0.00 0.00 3.51
1646 2128 2.845967 CACGCTTCAACTCACAAACAAC 59.154 45.455 0.00 0.00 0.00 3.32
1658 2140 1.523154 GGGAACATGGCACGCTTCAA 61.523 55.000 0.00 0.00 0.00 2.69
1675 2157 3.654806 ACCATGATGGAGAATAGAAGGGG 59.345 47.826 20.11 0.00 40.96 4.79
1677 2159 4.281941 TCGACCATGATGGAGAATAGAAGG 59.718 45.833 20.11 0.00 40.96 3.46
1718 2204 8.599792 TGAGCCAATCTATTAGATCATGATGAA 58.400 33.333 14.30 7.50 32.89 2.57
1719 2205 8.142485 TGAGCCAATCTATTAGATCATGATGA 57.858 34.615 14.30 3.10 32.89 2.92
1720 2206 8.788325 TTGAGCCAATCTATTAGATCATGATG 57.212 34.615 14.30 0.00 32.89 3.07
1721 2207 9.976776 AATTGAGCCAATCTATTAGATCATGAT 57.023 29.630 8.25 8.25 32.89 2.45
1722 2208 9.803507 AAATTGAGCCAATCTATTAGATCATGA 57.196 29.630 6.65 0.00 32.89 3.07
1725 2211 8.355169 GCAAAATTGAGCCAATCTATTAGATCA 58.645 33.333 6.65 0.00 32.89 2.92
1726 2212 8.355169 TGCAAAATTGAGCCAATCTATTAGATC 58.645 33.333 6.65 0.00 32.89 2.75
1727 2213 8.241497 TGCAAAATTGAGCCAATCTATTAGAT 57.759 30.769 0.08 0.08 36.28 1.98
1728 2214 7.643569 TGCAAAATTGAGCCAATCTATTAGA 57.356 32.000 0.00 0.00 33.03 2.10
1729 2215 8.139350 TGATGCAAAATTGAGCCAATCTATTAG 58.861 33.333 0.00 0.00 33.03 1.73
1730 2216 8.009622 TGATGCAAAATTGAGCCAATCTATTA 57.990 30.769 0.00 0.00 33.03 0.98
1731 2217 6.880484 TGATGCAAAATTGAGCCAATCTATT 58.120 32.000 0.00 0.00 35.26 1.73
1732 2218 6.474140 TGATGCAAAATTGAGCCAATCTAT 57.526 33.333 0.00 0.00 32.43 1.98
1733 2219 5.918426 TGATGCAAAATTGAGCCAATCTA 57.082 34.783 0.00 0.00 32.43 1.98
1734 2220 4.811969 TGATGCAAAATTGAGCCAATCT 57.188 36.364 0.00 0.00 32.43 2.40
1735 2221 4.272504 CCATGATGCAAAATTGAGCCAATC 59.727 41.667 0.00 0.00 32.43 2.67
1736 2222 4.196193 CCATGATGCAAAATTGAGCCAAT 58.804 39.130 0.00 0.00 35.39 3.16
1737 2223 3.008157 ACCATGATGCAAAATTGAGCCAA 59.992 39.130 0.00 0.00 0.00 4.52
1738 2224 2.568062 ACCATGATGCAAAATTGAGCCA 59.432 40.909 0.00 0.00 0.00 4.75
1739 2225 3.255969 ACCATGATGCAAAATTGAGCC 57.744 42.857 0.00 0.00 0.00 4.70
1740 2226 4.247258 TCAACCATGATGCAAAATTGAGC 58.753 39.130 0.00 0.00 0.00 4.26
1741 2227 6.978343 ATTCAACCATGATGCAAAATTGAG 57.022 33.333 0.00 0.00 34.96 3.02
1742 2228 7.613585 ACTATTCAACCATGATGCAAAATTGA 58.386 30.769 0.00 0.00 34.96 2.57
1743 2229 7.837202 ACTATTCAACCATGATGCAAAATTG 57.163 32.000 0.00 0.00 34.96 2.32
1744 2230 7.550196 GGAACTATTCAACCATGATGCAAAATT 59.450 33.333 0.00 0.00 34.96 1.82
1745 2231 7.043565 GGAACTATTCAACCATGATGCAAAAT 58.956 34.615 0.00 0.00 34.96 1.82
1746 2232 6.014755 TGGAACTATTCAACCATGATGCAAAA 60.015 34.615 0.00 0.00 34.96 2.44
1747 2233 5.479724 TGGAACTATTCAACCATGATGCAAA 59.520 36.000 0.00 0.00 34.96 3.68
1748 2234 5.015515 TGGAACTATTCAACCATGATGCAA 58.984 37.500 0.00 0.00 34.96 4.08
1766 2252 2.489971 TGACACGGAATCAAGTGGAAC 58.510 47.619 11.54 4.91 42.25 3.62
1767 2253 2.920724 TGACACGGAATCAAGTGGAA 57.079 45.000 11.54 0.00 42.25 3.53
1799 2285 1.299648 CCAGAGGCGGATTCAACCA 59.700 57.895 0.00 0.00 0.00 3.67
1806 2292 5.308825 CAAATTATCTAACCAGAGGCGGAT 58.691 41.667 0.00 0.00 33.22 4.18
1820 2306 6.916360 ACAACCACAATCACCAAATTATCT 57.084 33.333 0.00 0.00 0.00 1.98
1825 2311 3.383185 ACGAACAACCACAATCACCAAAT 59.617 39.130 0.00 0.00 0.00 2.32
1863 2349 1.012086 AGAAGCATAGCACGCACATG 58.988 50.000 0.00 0.00 0.00 3.21
1864 2350 2.602257 TAGAAGCATAGCACGCACAT 57.398 45.000 0.00 0.00 0.00 3.21
1869 2355 1.532868 GGCCAATAGAAGCATAGCACG 59.467 52.381 0.00 0.00 0.00 5.34
1871 2357 1.494296 TGGGCCAATAGAAGCATAGCA 59.506 47.619 2.13 0.00 0.00 3.49
1881 2367 4.526970 ACTAACAGAACATGGGCCAATAG 58.473 43.478 11.89 6.36 0.00 1.73
1886 2372 2.890945 ACAAACTAACAGAACATGGGCC 59.109 45.455 0.00 0.00 0.00 5.80
1944 2435 2.552599 TCCAACAAGCGAACACCATA 57.447 45.000 0.00 0.00 0.00 2.74
1948 2439 1.477105 GCTTTCCAACAAGCGAACAC 58.523 50.000 0.00 0.00 39.92 3.32
1949 2440 3.936585 GCTTTCCAACAAGCGAACA 57.063 47.368 0.00 0.00 39.92 3.18
2138 2630 4.465886 GAGGGAGTATAAGAGCTCTGACA 58.534 47.826 19.06 6.18 32.67 3.58
2145 2637 2.756207 GGATCGGAGGGAGTATAAGAGC 59.244 54.545 0.00 0.00 0.00 4.09
2220 2712 6.551975 TCCCTCCGATACATATTACTTGTCAA 59.448 38.462 0.00 0.00 0.00 3.18
2706 3204 4.504858 AGCGTTTGGGAGTACTTCATAAG 58.495 43.478 2.92 2.17 0.00 1.73
2832 3335 6.800072 AACAATCAAACAAAACCCCTTCTA 57.200 33.333 0.00 0.00 0.00 2.10
2841 3344 6.791887 TGCAGACAAAACAATCAAACAAAA 57.208 29.167 0.00 0.00 0.00 2.44
2848 3351 5.183522 TCATGCTATGCAGACAAAACAATCA 59.816 36.000 0.00 0.00 43.65 2.57
2891 3394 6.016276 GGCATTAAGACAAAGTTTGAAGAGGA 60.016 38.462 22.23 4.08 0.00 3.71
2915 3418 3.054802 ACAAGACCAGCATCTTAAGAGGG 60.055 47.826 18.12 14.42 36.78 4.30
2928 3431 5.811399 TTAATTCGGCATAACAAGACCAG 57.189 39.130 0.00 0.00 0.00 4.00
2946 3449 7.121759 GGCTGTCAGGCATGTATATGAATTAAT 59.878 37.037 20.87 0.00 40.97 1.40
3007 3510 8.768397 ACACCCACTGAGATTTCTTAACATATA 58.232 33.333 0.00 0.00 0.00 0.86
3008 3511 7.554118 CACACCCACTGAGATTTCTTAACATAT 59.446 37.037 0.00 0.00 0.00 1.78
3046 3549 4.583489 CCAGCATATTTCTCTCAGGCATTT 59.417 41.667 0.00 0.00 0.00 2.32
3079 3582 2.115427 TCGATGGCCCTACTGATCAAA 58.885 47.619 0.00 0.00 0.00 2.69
3080 3583 1.788229 TCGATGGCCCTACTGATCAA 58.212 50.000 0.00 0.00 0.00 2.57
3081 3584 1.412710 GTTCGATGGCCCTACTGATCA 59.587 52.381 0.00 0.00 0.00 2.92
3082 3585 1.270358 GGTTCGATGGCCCTACTGATC 60.270 57.143 0.00 0.00 0.00 2.92
3160 3665 5.562298 AACCACACACCAAGAATACTAGT 57.438 39.130 0.00 0.00 0.00 2.57
3227 3732 7.997773 AAGCTATACACATCGACCTCTAATA 57.002 36.000 0.00 0.00 0.00 0.98
3239 3744 7.230510 TGACAAGAAACCAAAAGCTATACACAT 59.769 33.333 0.00 0.00 0.00 3.21
3361 3866 6.313905 CCAATTACTGACAGAATACTGACACC 59.686 42.308 10.08 0.00 46.03 4.16
3527 4032 3.066900 GGCCGATATCACAGCGTATCTAT 59.933 47.826 3.12 0.00 33.06 1.98
3569 4074 5.338632 TGGGTACAAGAAGTGAAGGAGATA 58.661 41.667 0.00 0.00 0.00 1.98
3643 4149 0.179084 ATGCGCGCCTACTTATGTGT 60.179 50.000 30.77 0.00 0.00 3.72
3672 4178 3.995636 TCAGCTAGGTACTGGAAGGAAT 58.004 45.455 0.00 0.00 40.33 3.01
3681 4187 5.228945 ACAAACAACATCAGCTAGGTACT 57.771 39.130 0.00 0.00 46.37 2.73
3682 4188 5.350640 GGTACAAACAACATCAGCTAGGTAC 59.649 44.000 0.00 0.00 0.00 3.34
3748 4256 1.872313 GACTCGTCTAGGTCCCGTATG 59.128 57.143 0.00 0.00 0.00 2.39
3749 4257 1.202746 GGACTCGTCTAGGTCCCGTAT 60.203 57.143 4.92 0.00 44.35 3.06
3750 4258 0.179000 GGACTCGTCTAGGTCCCGTA 59.821 60.000 4.92 0.00 44.35 4.02
3751 4259 1.077858 GGACTCGTCTAGGTCCCGT 60.078 63.158 4.92 0.00 44.35 5.28
3752 4260 3.824810 GGACTCGTCTAGGTCCCG 58.175 66.667 4.92 0.00 44.35 5.14
3755 4263 0.392193 TCCGTGGACTCGTCTAGGTC 60.392 60.000 0.00 0.00 0.00 3.85
3756 4264 0.392729 CTCCGTGGACTCGTCTAGGT 60.393 60.000 0.00 0.00 0.00 3.08
3757 4265 0.107800 TCTCCGTGGACTCGTCTAGG 60.108 60.000 0.00 0.00 0.00 3.02
3758 4266 1.735386 TTCTCCGTGGACTCGTCTAG 58.265 55.000 0.00 0.00 0.00 2.43
3767 4275 1.697432 AGGATGTTGTTTCTCCGTGGA 59.303 47.619 0.00 0.00 34.13 4.02
3836 4344 2.019156 GCTAATCCTGCTGTGTTCCCC 61.019 57.143 0.00 0.00 0.00 4.81
4013 4544 1.340308 GGGCTTTTTAAGGGCGGTAGA 60.340 52.381 0.00 0.00 0.00 2.59
4019 4550 3.981071 ATCAAAGGGCTTTTTAAGGGC 57.019 42.857 0.00 0.00 0.00 5.19
4030 4561 1.824852 CCCTTGGTGTAATCAAAGGGC 59.175 52.381 6.41 0.00 31.22 5.19
4032 4563 6.435904 TGATTAACCCTTGGTGTAATCAAAGG 59.564 38.462 18.20 4.94 39.55 3.11
4033 4564 7.461182 TGATTAACCCTTGGTGTAATCAAAG 57.539 36.000 18.20 0.00 39.55 2.77
4145 4679 6.024664 CGTGAGATATCGAGTTGGTATCATC 58.975 44.000 12.38 7.83 0.00 2.92
4148 4682 5.049612 TCACGTGAGATATCGAGTTGGTATC 60.050 44.000 15.76 2.70 0.00 2.24
4192 4726 1.450848 CGCATCTCACCTGGCATGT 60.451 57.895 0.00 0.00 0.00 3.21
4209 4743 1.737793 GGTGAAGGTATGCCAAGTTCG 59.262 52.381 1.54 0.00 37.19 3.95
4210 4744 3.073274 AGGTGAAGGTATGCCAAGTTC 57.927 47.619 1.54 0.00 37.19 3.01
4211 4745 3.525800 AAGGTGAAGGTATGCCAAGTT 57.474 42.857 1.54 0.00 37.19 2.66
4213 4747 3.573967 ACAAAAGGTGAAGGTATGCCAAG 59.426 43.478 1.54 0.00 37.19 3.61
4214 4748 3.571590 ACAAAAGGTGAAGGTATGCCAA 58.428 40.909 1.54 0.00 37.19 4.52
4227 4761 0.750182 CACGGTCCCACACAAAAGGT 60.750 55.000 0.00 0.00 0.00 3.50
4228 4762 1.452145 CCACGGTCCCACACAAAAGG 61.452 60.000 0.00 0.00 0.00 3.11
4229 4763 1.452145 CCCACGGTCCCACACAAAAG 61.452 60.000 0.00 0.00 0.00 2.27
4231 4765 2.193517 CCCACGGTCCCACACAAA 59.806 61.111 0.00 0.00 0.00 2.83
4312 4959 7.264947 ACAAGAGAAACACCAAAAATGTTAGG 58.735 34.615 0.00 0.00 39.36 2.69
4313 4960 9.965824 ATACAAGAGAAACACCAAAAATGTTAG 57.034 29.630 0.00 0.00 39.36 2.34
4351 4998 5.773680 ACAGACCCATAGTAGTATTACGCAT 59.226 40.000 0.00 0.00 34.88 4.73
4363 5010 4.028131 TCCGACAATAACAGACCCATAGT 58.972 43.478 0.00 0.00 0.00 2.12
4372 5041 1.990799 TCGCAGTCCGACAATAACAG 58.009 50.000 0.40 0.00 41.89 3.16
4382 5051 0.713883 GTTGTACATGTCGCAGTCCG 59.286 55.000 0.00 0.00 38.61 4.79
4391 5060 5.767665 TGCTTTCTATTGGTGTTGTACATGT 59.232 36.000 2.69 2.69 0.00 3.21
4393 5062 6.127647 CCATGCTTTCTATTGGTGTTGTACAT 60.128 38.462 0.00 0.00 0.00 2.29
4397 5066 4.406456 TCCATGCTTTCTATTGGTGTTGT 58.594 39.130 0.00 0.00 0.00 3.32
4398 5067 5.389859 TTCCATGCTTTCTATTGGTGTTG 57.610 39.130 0.00 0.00 0.00 3.33
4399 5068 5.163622 CGATTCCATGCTTTCTATTGGTGTT 60.164 40.000 0.00 0.00 0.00 3.32
4409 5078 0.305922 CCGCTCGATTCCATGCTTTC 59.694 55.000 0.00 0.00 0.00 2.62
4414 5083 0.933097 CTTGACCGCTCGATTCCATG 59.067 55.000 0.00 0.00 0.00 3.66
4425 5094 1.161563 TTCACCCGTTTCTTGACCGC 61.162 55.000 0.00 0.00 0.00 5.68
4447 5116 5.277974 CGTCTCATTCAACCAACAATTCAGT 60.278 40.000 0.00 0.00 0.00 3.41
4466 5135 5.418310 TCAAACAAAAATGTCTCCGTCTC 57.582 39.130 0.00 0.00 0.00 3.36
4471 5140 5.901552 TCCAGTTCAAACAAAAATGTCTCC 58.098 37.500 0.00 0.00 0.00 3.71
4504 5173 2.253610 TCACCGAGTTCATACCCAAGT 58.746 47.619 0.00 0.00 0.00 3.16
4522 5192 3.997319 CGATGAAAGAAACTCGCATCA 57.003 42.857 0.00 0.00 36.13 3.07
4592 5262 3.678717 TAGAACGGAGCGAGCGTGC 62.679 63.158 0.00 0.00 0.00 5.34
4593 5263 0.731514 TTTAGAACGGAGCGAGCGTG 60.732 55.000 0.00 0.00 0.00 5.34
4594 5264 0.731855 GTTTAGAACGGAGCGAGCGT 60.732 55.000 0.00 0.00 0.00 5.07
4595 5265 0.456312 AGTTTAGAACGGAGCGAGCG 60.456 55.000 0.00 0.00 36.23 5.03
4596 5266 0.992802 CAGTTTAGAACGGAGCGAGC 59.007 55.000 0.00 0.00 36.23 5.03
4597 5267 0.992802 GCAGTTTAGAACGGAGCGAG 59.007 55.000 0.00 0.00 36.23 5.03
4598 5268 0.389426 GGCAGTTTAGAACGGAGCGA 60.389 55.000 0.00 0.00 36.23 4.93
4599 5269 0.389948 AGGCAGTTTAGAACGGAGCG 60.390 55.000 0.00 0.00 36.23 5.03
4600 5270 2.269172 GTAGGCAGTTTAGAACGGAGC 58.731 52.381 0.00 0.00 36.23 4.70
4601 5271 2.232941 TGGTAGGCAGTTTAGAACGGAG 59.767 50.000 0.00 0.00 36.23 4.63
4602 5272 2.028748 GTGGTAGGCAGTTTAGAACGGA 60.029 50.000 0.00 0.00 36.23 4.69
4603 5273 2.028385 AGTGGTAGGCAGTTTAGAACGG 60.028 50.000 0.00 0.00 36.23 4.44
4604 5274 3.251571 GAGTGGTAGGCAGTTTAGAACG 58.748 50.000 0.00 0.00 36.23 3.95
4605 5275 4.246458 CTGAGTGGTAGGCAGTTTAGAAC 58.754 47.826 0.00 0.00 0.00 3.01
4606 5276 3.901844 ACTGAGTGGTAGGCAGTTTAGAA 59.098 43.478 0.00 0.00 39.69 2.10
4607 5277 3.507411 ACTGAGTGGTAGGCAGTTTAGA 58.493 45.455 0.00 0.00 39.69 2.10
4608 5278 3.963428 ACTGAGTGGTAGGCAGTTTAG 57.037 47.619 0.00 0.00 39.69 1.85
4612 5282 0.977395 GGAACTGAGTGGTAGGCAGT 59.023 55.000 0.00 0.00 44.15 4.40
4613 5283 0.250513 GGGAACTGAGTGGTAGGCAG 59.749 60.000 0.00 0.00 35.81 4.85
4614 5284 0.472925 TGGGAACTGAGTGGTAGGCA 60.473 55.000 0.00 0.00 0.00 4.75
4615 5285 0.912486 ATGGGAACTGAGTGGTAGGC 59.088 55.000 0.00 0.00 0.00 3.93
4616 5286 1.210478 CCATGGGAACTGAGTGGTAGG 59.790 57.143 2.85 0.00 0.00 3.18
4617 5287 2.187958 TCCATGGGAACTGAGTGGTAG 58.812 52.381 13.02 0.00 0.00 3.18
4618 5288 2.335681 TCCATGGGAACTGAGTGGTA 57.664 50.000 13.02 0.00 0.00 3.25
4619 5289 1.283029 CATCCATGGGAACTGAGTGGT 59.717 52.381 13.02 0.00 34.34 4.16
4620 5290 2.020694 GCATCCATGGGAACTGAGTGG 61.021 57.143 13.02 0.00 34.34 4.00
4621 5291 1.386533 GCATCCATGGGAACTGAGTG 58.613 55.000 13.02 0.05 34.34 3.51
4622 5292 0.107508 CGCATCCATGGGAACTGAGT 60.108 55.000 13.02 0.00 42.66 3.41
4623 5293 0.178767 TCGCATCCATGGGAACTGAG 59.821 55.000 13.02 6.89 45.15 3.35
4624 5294 2.295904 TCGCATCCATGGGAACTGA 58.704 52.632 13.02 1.10 45.15 3.41
4625 5295 4.961637 TCGCATCCATGGGAACTG 57.038 55.556 13.02 6.06 45.15 3.16
4629 5299 0.532640 CGTGATTCGCATCCATGGGA 60.533 55.000 13.02 2.31 46.23 4.37
4630 5300 1.509644 CCGTGATTCGCATCCATGGG 61.510 60.000 13.02 0.00 41.55 4.00
4631 5301 1.944035 CCGTGATTCGCATCCATGG 59.056 57.895 4.97 4.97 38.35 3.66
4632 5302 1.280746 GCCGTGATTCGCATCCATG 59.719 57.895 0.00 0.00 38.35 3.66
4633 5303 1.893808 GGCCGTGATTCGCATCCAT 60.894 57.895 0.00 0.00 38.35 3.41
4634 5304 2.513666 GGCCGTGATTCGCATCCA 60.514 61.111 0.00 0.00 38.35 3.41
4635 5305 2.513666 TGGCCGTGATTCGCATCC 60.514 61.111 0.00 0.00 38.35 3.51
4636 5306 1.815421 ACTGGCCGTGATTCGCATC 60.815 57.895 0.00 0.00 38.35 3.91
4637 5307 2.268920 ACTGGCCGTGATTCGCAT 59.731 55.556 0.00 0.00 38.35 4.73


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

AutoCloner maintained by Alex Coulton.