Multiple sequence alignment - TraesCS5D01G564500

Loading Multiple Alignment...

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 TraesCS5D01G564500 chr5D 100.000 4134 0 0 2343 6476 563400010 563404143 0.000000e+00 7635.0
1 TraesCS5D01G564500 chr5D 100.000 2052 0 0 1 2052 563397668 563399719 0.000000e+00 3790.0
2 TraesCS5D01G564500 chr5D 97.143 35 1 0 3178 3212 563400794 563400828 7.010000e-05 60.2
3 TraesCS5D01G564500 chr5D 97.143 35 1 0 3127 3161 563400845 563400879 7.010000e-05 60.2
4 TraesCS5D01G564500 chr5B 92.393 2629 140 32 3877 6475 705620429 705623027 0.000000e+00 3692.0
5 TraesCS5D01G564500 chr5B 89.264 1127 84 17 27 1143 705616140 705617239 0.000000e+00 1376.0
6 TraesCS5D01G564500 chr5B 91.249 937 44 14 1152 2052 705617299 705618233 0.000000e+00 1242.0
7 TraesCS5D01G564500 chr5B 94.080 777 30 7 2369 3130 705618328 705619103 0.000000e+00 1166.0
8 TraesCS5D01G564500 chr5B 86.676 713 53 9 3155 3856 705619389 705620070 0.000000e+00 752.0
9 TraesCS5D01G564500 chr5B 83.824 340 40 10 3382 3718 170678528 170678855 6.310000e-80 309.0
10 TraesCS5D01G564500 chr5B 86.885 61 8 0 4016 4076 577244740 577244680 1.170000e-07 69.4
11 TraesCS5D01G564500 chr4A 93.123 2530 137 22 3965 6469 609081589 609079072 0.000000e+00 3674.0
12 TraesCS5D01G564500 chr4A 90.785 1096 42 17 730 1770 609085006 609083915 0.000000e+00 1410.0
13 TraesCS5D01G564500 chr4A 91.710 772 27 15 2369 3130 609083353 609082609 0.000000e+00 1037.0
14 TraesCS5D01G564500 chr4A 89.193 694 61 9 1 687 609086544 609085858 0.000000e+00 854.0
15 TraesCS5D01G564500 chr4A 86.427 641 50 13 3161 3789 609082283 609081668 0.000000e+00 667.0
16 TraesCS5D01G564500 chr2B 88.439 346 30 9 3383 3720 9869783 9870126 6.040000e-110 409.0
17 TraesCS5D01G564500 chr1B 87.906 339 35 6 3385 3720 384495783 384496118 1.690000e-105 394.0
18 TraesCS5D01G564500 chr1B 83.721 172 26 2 5505 5675 314565538 314565708 1.870000e-35 161.0
19 TraesCS5D01G564500 chr1A 88.000 325 35 4 3398 3720 520563399 520563721 1.320000e-101 381.0
20 TraesCS5D01G564500 chr4D 85.593 354 33 15 3375 3720 459261232 459260889 7.990000e-94 355.0
21 TraesCS5D01G564500 chr1D 86.405 331 35 9 3396 3720 479201149 479200823 2.870000e-93 353.0
22 TraesCS5D01G564500 chr7B 84.478 335 42 6 3388 3720 674127239 674126913 8.100000e-84 322.0
23 TraesCS5D01G564500 chr7D 84.164 341 39 9 3383 3720 245383792 245384120 3.770000e-82 316.0
24 TraesCS5D01G564500 chr7D 87.097 155 20 0 5503 5657 566026739 566026585 6.670000e-40 176.0
25 TraesCS5D01G564500 chr7D 83.523 176 25 4 5484 5658 454079227 454079399 1.870000e-35 161.0
26 TraesCS5D01G564500 chr5A 83.578 341 45 7 3382 3720 164200882 164201213 6.310000e-80 309.0
27 TraesCS5D01G564500 chr2D 85.714 168 24 0 5504 5671 498473160 498472993 1.860000e-40 178.0
28 TraesCS5D01G564500 chr2D 83.889 180 27 2 5501 5679 560153882 560154060 3.100000e-38 171.0
29 TraesCS5D01G564500 chr2D 79.452 219 38 7 3858 4073 15127617 15127831 1.450000e-31 148.0
30 TraesCS5D01G564500 chr4B 80.603 232 40 4 3847 4076 489674494 489674722 2.400000e-39 174.0
31 TraesCS5D01G564500 chr7A 86.624 157 16 4 5503 5657 652302334 652302181 1.120000e-37 169.0
32 TraesCS5D01G564500 chr3A 83.429 175 26 2 5505 5679 500525142 500524971 6.720000e-35 159.0


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 TraesCS5D01G564500 chr5D 563397668 563404143 6475 False 2886.35 7635 98.5715 1 6476 4 chr5D.!!$F1 6475
1 TraesCS5D01G564500 chr5B 705616140 705623027 6887 False 1645.60 3692 90.7324 27 6475 5 chr5B.!!$F2 6448
2 TraesCS5D01G564500 chr4A 609079072 609086544 7472 True 1528.40 3674 90.2476 1 6469 5 chr4A.!!$R1 6468

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
990 1862 0.618458 GCCTCACCCTCACCATACAA 59.382 55.000 0.00 0.00 0.00 2.41 F
1506 2461 0.321298 GCGAGGTTACCTTTGAGGCA 60.321 55.000 4.99 0.00 39.63 4.75 F
3089 4274 0.035152 CAATGCTACACCCTCTGCCA 60.035 55.000 0.00 0.00 0.00 4.92 F
4529 6373 0.037882 ATCTGTCACCTGCACACGAG 60.038 55.000 0.00 0.00 0.00 4.18 F
4867 6720 2.050168 CCAATGCAGCGCAACGTT 60.050 55.556 11.47 5.65 43.62 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2986 4171 0.034574 CCACCGACCCAAATCATCCA 60.035 55.000 0.0 0.0 0.00 3.41 R
3174 4663 0.035458 ACTTTCCCTCGCACTCTTGG 59.965 55.000 0.0 0.0 0.00 3.61 R
4867 6720 0.179137 CACGAGCGTATCCAGCAAGA 60.179 55.000 0.0 0.0 37.01 3.02 R
5427 7283 1.667724 GAGTAGGCACATGACACATGC 59.332 52.381 0.0 0.0 38.68 4.06 R
5723 7582 2.546789 GTGACTTGGTTTAGTTGGGACG 59.453 50.000 0.0 0.0 0.00 4.79 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
83 85 2.081725 TGTGTATAAAACGAGCGCCA 57.918 45.000 2.29 0.00 0.00 5.69
89 91 1.225376 TAAAACGAGCGCCACACCTG 61.225 55.000 2.29 0.00 0.00 4.00
90 92 3.750373 AAACGAGCGCCACACCTGT 62.750 57.895 2.29 0.00 0.00 4.00
99 101 1.595976 CGCCACACCTGTGTAAAAACG 60.596 52.381 2.05 0.00 42.83 3.60
130 132 3.330701 TGGAGTGAGGACTAAATTTGCCT 59.669 43.478 0.00 4.92 30.16 4.75
134 136 4.288626 AGTGAGGACTAAATTTGCCTGGTA 59.711 41.667 12.14 0.00 0.00 3.25
135 137 5.044846 AGTGAGGACTAAATTTGCCTGGTAT 60.045 40.000 12.14 0.00 0.00 2.73
136 138 5.297029 GTGAGGACTAAATTTGCCTGGTATC 59.703 44.000 12.14 1.72 0.00 2.24
137 139 5.045213 TGAGGACTAAATTTGCCTGGTATCA 60.045 40.000 12.14 3.73 0.00 2.15
184 186 4.041464 TGGATGTAATAGGCTACCCACAA 58.959 43.478 0.00 0.00 0.00 3.33
199 201 4.971939 ACCCACAATGCTGCTTTTATTTT 58.028 34.783 0.00 0.00 0.00 1.82
246 252 4.412858 TCTTGGTAAAACCCTACTCAACCA 59.587 41.667 0.00 0.00 37.50 3.67
275 281 5.967088 AGTGATAAATAGCACGTTGAGACT 58.033 37.500 3.44 0.00 46.41 3.24
307 313 8.121305 AGATGTATCTAAGGATGCTTCTACAG 57.879 38.462 1.37 0.00 42.52 2.74
326 332 3.179830 CAGCGAGGTGTTCACTATGTAC 58.820 50.000 2.98 0.00 0.00 2.90
334 340 6.173339 AGGTGTTCACTATGTACTCCAATTG 58.827 40.000 0.00 0.00 34.91 2.32
335 341 5.163754 GGTGTTCACTATGTACTCCAATTGC 60.164 44.000 0.00 0.00 33.40 3.56
366 373 3.556004 CGCTCCACTCTTCTTCCTCTTTT 60.556 47.826 0.00 0.00 0.00 2.27
417 424 1.813862 CGCCAACTCCTCCTTTTGTCA 60.814 52.381 0.00 0.00 0.00 3.58
436 443 1.228033 CTTTTCCACCGACCCCGTT 60.228 57.895 0.00 0.00 0.00 4.44
439 446 2.679369 TTTCCACCGACCCCGTTTCC 62.679 60.000 0.00 0.00 0.00 3.13
460 467 4.841813 TCCTCATACTTTGACCAACACCTA 59.158 41.667 0.00 0.00 0.00 3.08
474 481 3.619900 ACACCTATGATGAGGCTAGGA 57.380 47.619 5.77 0.00 40.65 2.94
480 487 3.609256 ATGATGAGGCTAGGAGTCAGA 57.391 47.619 0.00 0.00 0.00 3.27
487 494 1.133136 GGCTAGGAGTCAGACCCCATA 60.133 57.143 3.56 0.00 0.00 2.74
494 501 0.839946 GTCAGACCCCATACAGCCAT 59.160 55.000 0.00 0.00 0.00 4.40
504 511 3.562826 CCCATACAGCCATGCCATCTAAT 60.563 47.826 0.00 0.00 0.00 1.73
505 512 3.693085 CCATACAGCCATGCCATCTAATC 59.307 47.826 0.00 0.00 0.00 1.75
515 527 0.673985 CCATCTAATCCGTGGCGAGA 59.326 55.000 0.00 0.00 0.00 4.04
540 552 2.288886 CGTAATTCCTCCTCCCGATTCC 60.289 54.545 0.00 0.00 0.00 3.01
546 558 1.689575 CCTCCTCCCGATTCCTCTTCA 60.690 57.143 0.00 0.00 0.00 3.02
564 576 5.245531 TCTTCATCTCTTTTACGGCAACAT 58.754 37.500 0.00 0.00 0.00 2.71
584 596 3.554692 GACCAGATTGGACGCGCG 61.555 66.667 30.96 30.96 40.96 6.86
589 601 3.861263 GATTGGACGCGCGGGAAC 61.861 66.667 35.22 20.32 0.00 3.62
604 616 1.183549 GGAACGTGCTCTCCCTAAGA 58.816 55.000 0.00 0.00 0.00 2.10
613 625 2.100749 GCTCTCCCTAAGACTGAAGAGC 59.899 54.545 6.44 6.44 40.24 4.09
639 651 4.466370 ACGTTCATTCACTAGATTCTCCCA 59.534 41.667 0.00 0.00 0.00 4.37
669 681 2.155279 GAGGAGTGGTGAAAAGAAGCC 58.845 52.381 0.00 0.00 0.00 4.35
687 699 1.752198 CGGTGAGTGGGAAAGGACA 59.248 57.895 0.00 0.00 0.00 4.02
693 1539 2.708861 TGAGTGGGAAAGGACAAGCTTA 59.291 45.455 0.00 0.00 0.00 3.09
710 1577 2.753247 CTTACCAAGCCCTACTCCTCT 58.247 52.381 0.00 0.00 0.00 3.69
711 1578 2.456073 TACCAAGCCCTACTCCTCTC 57.544 55.000 0.00 0.00 0.00 3.20
712 1579 0.713579 ACCAAGCCCTACTCCTCTCT 59.286 55.000 0.00 0.00 0.00 3.10
713 1580 1.342574 ACCAAGCCCTACTCCTCTCTC 60.343 57.143 0.00 0.00 0.00 3.20
714 1581 1.063266 CCAAGCCCTACTCCTCTCTCT 60.063 57.143 0.00 0.00 0.00 3.10
715 1582 2.306847 CAAGCCCTACTCCTCTCTCTC 58.693 57.143 0.00 0.00 0.00 3.20
716 1583 1.907240 AGCCCTACTCCTCTCTCTCT 58.093 55.000 0.00 0.00 0.00 3.10
717 1584 1.774856 AGCCCTACTCCTCTCTCTCTC 59.225 57.143 0.00 0.00 0.00 3.20
718 1585 1.774856 GCCCTACTCCTCTCTCTCTCT 59.225 57.143 0.00 0.00 0.00 3.10
719 1586 2.224548 GCCCTACTCCTCTCTCTCTCTC 60.225 59.091 0.00 0.00 0.00 3.20
720 1587 3.318313 CCCTACTCCTCTCTCTCTCTCT 58.682 54.545 0.00 0.00 0.00 3.10
721 1588 3.325135 CCCTACTCCTCTCTCTCTCTCTC 59.675 56.522 0.00 0.00 0.00 3.20
722 1589 4.227197 CCTACTCCTCTCTCTCTCTCTCT 58.773 52.174 0.00 0.00 0.00 3.10
723 1590 4.282195 CCTACTCCTCTCTCTCTCTCTCTC 59.718 54.167 0.00 0.00 0.00 3.20
724 1591 4.000928 ACTCCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
725 1592 3.964031 ACTCCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
726 1593 4.222336 CTCCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
727 1594 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
728 1595 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
729 1596 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
730 1597 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
731 1598 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
732 1599 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
733 1600 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
777 1649 2.230653 CCACCATGTCCCTGTCCCA 61.231 63.158 0.00 0.00 0.00 4.37
784 1656 1.745489 GTCCCTGTCCCATTGTCGC 60.745 63.158 0.00 0.00 0.00 5.19
808 1680 5.498862 TTCCTCTCTCTAAATAAGGGGGA 57.501 43.478 0.00 0.00 30.20 4.81
866 1738 1.082117 GTGCCGTAATGTCCTGACCG 61.082 60.000 0.00 0.00 0.00 4.79
931 1803 4.999950 AGTGTGTCCTGAGCTCAAAATAAG 59.000 41.667 18.85 4.57 0.00 1.73
968 1840 2.106332 CCTACACATCCGACCGGC 59.894 66.667 0.00 0.00 34.68 6.13
990 1862 0.618458 GCCTCACCCTCACCATACAA 59.382 55.000 0.00 0.00 0.00 2.41
1062 1949 2.318908 TGAAAAGATTGCCTTGCACCT 58.681 42.857 0.00 0.00 38.71 4.00
1079 1968 0.678395 CCTCAGCAGCGTATCCATCT 59.322 55.000 0.00 0.00 0.00 2.90
1110 1999 3.719268 TTGTGCTCCATTGTCACCTAT 57.281 42.857 0.00 0.00 0.00 2.57
1111 2000 4.835284 TTGTGCTCCATTGTCACCTATA 57.165 40.909 0.00 0.00 0.00 1.31
1119 2008 4.588951 TCCATTGTCACCTATAGCTACCTG 59.411 45.833 0.00 0.00 0.00 4.00
1136 2025 6.047870 GCTACCTGGATATAGCTCATGAATG 58.952 44.000 0.00 0.00 40.59 2.67
1189 2129 4.274008 TCCTGCAAGCTGGCTGCA 62.274 61.111 15.68 13.06 45.94 4.41
1288 2234 4.655649 AGCACAAGACCACTATGGATATGA 59.344 41.667 0.84 0.00 40.96 2.15
1375 2321 0.676466 CAACGCAATGGCCTACTCCA 60.676 55.000 3.32 0.00 40.97 3.86
1506 2461 0.321298 GCGAGGTTACCTTTGAGGCA 60.321 55.000 4.99 0.00 39.63 4.75
1569 2524 1.998444 CTGGTGGATATGGGCTGCCA 61.998 60.000 22.05 7.16 0.00 4.92
1682 2637 4.248842 CTCGCCACCACCACCACA 62.249 66.667 0.00 0.00 0.00 4.17
1761 2722 6.995091 CCTTCGATCCATCCTAATTTCTTTCT 59.005 38.462 0.00 0.00 0.00 2.52
1782 2743 6.707440 TCTTAGCTAAGAGACTTGATCTGG 57.293 41.667 28.47 3.00 38.00 3.86
1822 2783 8.382875 GCTTCAGTATTTTATTTGTCATTTGCC 58.617 33.333 0.00 0.00 0.00 4.52
1824 2785 8.133024 TCAGTATTTTATTTGTCATTTGCCCT 57.867 30.769 0.00 0.00 0.00 5.19
1825 2786 8.250332 TCAGTATTTTATTTGTCATTTGCCCTC 58.750 33.333 0.00 0.00 0.00 4.30
1828 2789 9.087424 GTATTTTATTTGTCATTTGCCCTCTTC 57.913 33.333 0.00 0.00 0.00 2.87
1830 2791 8.415950 TTTTATTTGTCATTTGCCCTCTTCTA 57.584 30.769 0.00 0.00 0.00 2.10
1831 2792 5.904362 ATTTGTCATTTGCCCTCTTCTAC 57.096 39.130 0.00 0.00 0.00 2.59
1832 2793 4.640771 TTGTCATTTGCCCTCTTCTACT 57.359 40.909 0.00 0.00 0.00 2.57
1833 2794 5.755409 TTGTCATTTGCCCTCTTCTACTA 57.245 39.130 0.00 0.00 0.00 1.82
1835 2796 6.121776 TGTCATTTGCCCTCTTCTACTAAA 57.878 37.500 0.00 0.00 0.00 1.85
1854 2817 6.253758 ACTAAAATTTCCCCTTCCCTTACAG 58.746 40.000 0.00 0.00 0.00 2.74
1857 2820 4.759793 ATTTCCCCTTCCCTTACAGTTT 57.240 40.909 0.00 0.00 0.00 2.66
1861 2824 3.010138 TCCCCTTCCCTTACAGTTTCATG 59.990 47.826 0.00 0.00 0.00 3.07
1891 2854 8.623903 TCATGCATGTTCCTATGTAATTTTCTC 58.376 33.333 25.43 0.00 0.00 2.87
1941 3070 9.420118 AGTTATTTCTATGCATTTCCATTGGTA 57.580 29.630 3.54 0.00 0.00 3.25
1956 3085 5.300034 TCCATTGGTACATTTCAGCATCATC 59.700 40.000 1.86 0.00 39.30 2.92
1960 3089 7.936496 TTGGTACATTTCAGCATCATCTTTA 57.064 32.000 0.00 0.00 39.30 1.85
1962 3091 8.523915 TGGTACATTTCAGCATCATCTTTAAT 57.476 30.769 0.00 0.00 0.00 1.40
1963 3092 9.625747 TGGTACATTTCAGCATCATCTTTAATA 57.374 29.630 0.00 0.00 0.00 0.98
1964 3093 9.884465 GGTACATTTCAGCATCATCTTTAATAC 57.116 33.333 0.00 0.00 0.00 1.89
1972 3120 9.842775 TCAGCATCATCTTTAATACTTCTTCAT 57.157 29.630 0.00 0.00 0.00 2.57
1998 3146 5.821995 TCTGTGAAATTGTCATTCTGTGTCA 59.178 36.000 0.00 0.00 38.90 3.58
2002 3150 5.997129 TGAAATTGTCATTCTGTGTCAGCTA 59.003 36.000 0.00 0.00 0.00 3.32
2003 3151 6.656270 TGAAATTGTCATTCTGTGTCAGCTAT 59.344 34.615 0.00 0.00 0.00 2.97
2019 3167 6.183360 TGTCAGCTATACCATGAGTTAACTCC 60.183 42.308 28.43 13.89 42.20 3.85
2035 3183 8.379457 AGTTAACTCCACAGTTCATAGTTTTC 57.621 34.615 1.12 0.00 42.27 2.29
2044 3192 7.255590 CCACAGTTCATAGTTTTCAATTCCTGT 60.256 37.037 0.00 0.00 0.00 4.00
2404 3583 3.668447 TCAAAAGCTCTAACTGCTCTGG 58.332 45.455 0.00 0.00 40.22 3.86
2484 3663 0.608640 ACGATGTGAGGAAGGTGGTC 59.391 55.000 0.00 0.00 0.00 4.02
2565 3744 3.264922 TCTGATCTATGGGCATGGAGA 57.735 47.619 0.00 0.00 31.77 3.71
2633 3812 7.765695 ACTATTGTTTTCATGATCCAGTTGT 57.234 32.000 0.00 0.00 0.00 3.32
2668 3847 4.389374 ACACCTGATGTCTTAGTTTGGTG 58.611 43.478 0.00 0.00 46.28 4.17
2675 3854 5.874810 TGATGTCTTAGTTTGGTGCTGTATC 59.125 40.000 0.00 0.00 0.00 2.24
2700 3879 6.481976 CCGAATAAGTACATGCCTCACATTAA 59.518 38.462 0.00 0.00 36.64 1.40
2752 3936 1.475280 TCCAATTAGGTCGACTGGTCG 59.525 52.381 16.46 15.83 44.87 4.79
2798 3982 5.288232 TGTTTTGCTGTCAACTCAAATTTCG 59.712 36.000 0.00 0.00 30.89 3.46
2904 4089 6.659668 TGGATTGGACGGAAAACACAATATTA 59.340 34.615 0.00 0.00 32.42 0.98
2943 4128 5.070862 GCGTTTACTCATCGTTAGTGTTTG 58.929 41.667 0.00 0.00 0.00 2.93
2950 4135 2.748461 TCGTTAGTGTTTGTTGCAGC 57.252 45.000 0.00 0.00 0.00 5.25
2999 4184 3.099141 GGAACATGTGGATGATTTGGGT 58.901 45.455 0.00 0.00 33.36 4.51
3017 4202 1.270839 GGTCGGTGGGATACATGGATG 60.271 57.143 0.00 0.00 39.74 3.51
3020 4205 1.270839 CGGTGGGATACATGGATGGAC 60.271 57.143 0.00 0.00 39.74 4.02
3022 4207 2.057922 GTGGGATACATGGATGGACCT 58.942 52.381 0.00 0.00 37.81 3.85
3045 4230 7.787904 ACCTACTATGATATGGTGAACAAGGTA 59.212 37.037 0.00 0.00 29.37 3.08
3086 4271 0.391661 ACGCAATGCTACACCCTCTG 60.392 55.000 2.94 0.00 0.00 3.35
3087 4272 1.709147 CGCAATGCTACACCCTCTGC 61.709 60.000 2.94 0.00 0.00 4.26
3088 4273 1.379642 GCAATGCTACACCCTCTGCC 61.380 60.000 0.00 0.00 0.00 4.85
3089 4274 0.035152 CAATGCTACACCCTCTGCCA 60.035 55.000 0.00 0.00 0.00 4.92
3116 4310 0.541863 CACTAAGGCGAGGGTGGAAT 59.458 55.000 0.00 0.00 0.00 3.01
3125 4319 0.521735 GAGGGTGGAATTGCACGTTC 59.478 55.000 21.83 17.36 0.00 3.95
3130 4324 1.873591 GTGGAATTGCACGTTCAGAGT 59.126 47.619 14.63 0.00 0.00 3.24
3138 4332 1.901948 ACGTTCAGAGTGCGAGGGA 60.902 57.895 0.00 0.00 0.00 4.20
3139 4333 1.289066 CGTTCAGAGTGCGAGGGAA 59.711 57.895 0.00 0.00 0.00 3.97
3141 4335 1.433534 GTTCAGAGTGCGAGGGAAAG 58.566 55.000 0.00 0.00 0.00 2.62
3142 4336 1.048601 TTCAGAGTGCGAGGGAAAGT 58.951 50.000 0.00 0.00 0.00 2.66
3143 4337 1.048601 TCAGAGTGCGAGGGAAAGTT 58.951 50.000 0.00 0.00 0.00 2.66
3144 4338 2.244695 TCAGAGTGCGAGGGAAAGTTA 58.755 47.619 0.00 0.00 0.00 2.24
3145 4339 2.631062 TCAGAGTGCGAGGGAAAGTTAA 59.369 45.455 0.00 0.00 0.00 2.01
3146 4340 3.070446 TCAGAGTGCGAGGGAAAGTTAAA 59.930 43.478 0.00 0.00 0.00 1.52
3147 4341 3.813166 CAGAGTGCGAGGGAAAGTTAAAA 59.187 43.478 0.00 0.00 0.00 1.52
3148 4342 4.274950 CAGAGTGCGAGGGAAAGTTAAAAA 59.725 41.667 0.00 0.00 0.00 1.94
3149 4343 5.048713 CAGAGTGCGAGGGAAAGTTAAAAAT 60.049 40.000 0.00 0.00 0.00 1.82
3150 4344 5.048713 AGAGTGCGAGGGAAAGTTAAAAATG 60.049 40.000 0.00 0.00 0.00 2.32
3151 4345 4.022329 AGTGCGAGGGAAAGTTAAAAATGG 60.022 41.667 0.00 0.00 0.00 3.16
3152 4346 3.892588 TGCGAGGGAAAGTTAAAAATGGT 59.107 39.130 0.00 0.00 0.00 3.55
3153 4347 4.234574 GCGAGGGAAAGTTAAAAATGGTG 58.765 43.478 0.00 0.00 0.00 4.17
3171 4660 2.167662 GTGTAAGATGGGTTGGGGTTG 58.832 52.381 0.00 0.00 0.00 3.77
3174 4663 0.831711 AAGATGGGTTGGGGTTGCAC 60.832 55.000 0.00 0.00 0.00 4.57
3195 4684 2.289444 CCAAGAGTGCGAGGGAAAGTTA 60.289 50.000 0.00 0.00 0.00 2.24
3217 4706 8.646900 AGTTAAAAATGGTGTAACATGTTGGAT 58.353 29.630 21.42 0.00 39.98 3.41
3284 4773 1.202417 AGAGTGTGTGGAAGTGTGACG 60.202 52.381 0.00 0.00 0.00 4.35
3304 4793 4.446857 CGTAGGGCGTGTGTATAAATTG 57.553 45.455 0.00 0.00 35.54 2.32
3305 4794 4.114073 CGTAGGGCGTGTGTATAAATTGA 58.886 43.478 0.00 0.00 35.54 2.57
3306 4795 4.026310 CGTAGGGCGTGTGTATAAATTGAC 60.026 45.833 0.00 0.00 35.54 3.18
3307 4796 4.216411 AGGGCGTGTGTATAAATTGACT 57.784 40.909 0.00 0.00 0.00 3.41
3309 4798 5.007682 AGGGCGTGTGTATAAATTGACTTT 58.992 37.500 0.00 0.00 0.00 2.66
3310 4799 5.475564 AGGGCGTGTGTATAAATTGACTTTT 59.524 36.000 0.00 0.00 0.00 2.27
3311 4800 6.655848 AGGGCGTGTGTATAAATTGACTTTTA 59.344 34.615 0.00 0.00 0.00 1.52
3312 4801 7.175293 AGGGCGTGTGTATAAATTGACTTTTAA 59.825 33.333 0.00 0.00 0.00 1.52
3360 4858 4.220382 TGCAAAACATATCAACCAGGGAAG 59.780 41.667 0.00 0.00 0.00 3.46
3458 4957 4.176851 GGAGCGAGGACCGTCGTC 62.177 72.222 10.60 10.60 42.17 4.20
3496 4995 5.639506 CGAAGTGGTACAGATCAGTTTTGAT 59.360 40.000 0.00 0.00 46.61 2.57
3536 5035 9.953565 GTTATATATATCCTTTGTAAGCCACCA 57.046 33.333 0.00 0.00 0.00 4.17
3590 5089 3.497942 GCATTTGTAACCTCCCCCGATAT 60.498 47.826 0.00 0.00 0.00 1.63
3591 5090 4.263156 GCATTTGTAACCTCCCCCGATATA 60.263 45.833 0.00 0.00 0.00 0.86
3592 5091 5.488341 CATTTGTAACCTCCCCCGATATAG 58.512 45.833 0.00 0.00 0.00 1.31
3593 5092 3.909427 TGTAACCTCCCCCGATATAGT 57.091 47.619 0.00 0.00 0.00 2.12
3594 5093 3.503365 TGTAACCTCCCCCGATATAGTG 58.497 50.000 0.00 0.00 0.00 2.74
3595 5094 3.140707 TGTAACCTCCCCCGATATAGTGA 59.859 47.826 0.00 0.00 0.00 3.41
3596 5095 3.339713 AACCTCCCCCGATATAGTGAA 57.660 47.619 0.00 0.00 0.00 3.18
3597 5096 2.890814 ACCTCCCCCGATATAGTGAAG 58.109 52.381 0.00 0.00 0.00 3.02
3598 5097 2.449730 ACCTCCCCCGATATAGTGAAGA 59.550 50.000 0.00 0.00 0.00 2.87
3599 5098 3.077695 ACCTCCCCCGATATAGTGAAGAT 59.922 47.826 0.00 0.00 0.00 2.40
3600 5099 4.097418 CCTCCCCCGATATAGTGAAGATT 58.903 47.826 0.00 0.00 0.00 2.40
3601 5100 4.532521 CCTCCCCCGATATAGTGAAGATTT 59.467 45.833 0.00 0.00 0.00 2.17
3602 5101 5.482908 CTCCCCCGATATAGTGAAGATTTG 58.517 45.833 0.00 0.00 0.00 2.32
3603 5102 4.003648 CCCCCGATATAGTGAAGATTTGC 58.996 47.826 0.00 0.00 0.00 3.68
3604 5103 4.263068 CCCCCGATATAGTGAAGATTTGCT 60.263 45.833 0.00 0.00 0.00 3.91
3605 5104 4.692625 CCCCGATATAGTGAAGATTTGCTG 59.307 45.833 0.00 0.00 0.00 4.41
3606 5105 4.692625 CCCGATATAGTGAAGATTTGCTGG 59.307 45.833 0.00 0.00 0.00 4.85
3607 5106 4.153117 CCGATATAGTGAAGATTTGCTGGC 59.847 45.833 0.00 0.00 0.00 4.85
3633 5132 0.468400 CCGTGGTTTTTCCCCCTTCA 60.468 55.000 0.00 0.00 34.77 3.02
3647 5146 1.549203 CCTTCATGTTGGAGGGGTTG 58.451 55.000 0.00 0.00 30.78 3.77
3655 5154 1.637724 TTGGAGGGGTTGTCCACGTT 61.638 55.000 0.00 0.00 44.06 3.99
3677 5176 1.866015 ATCTCGTGTCCCCTGATTGA 58.134 50.000 0.00 0.00 0.00 2.57
3720 5219 5.592054 TGATTTGCCTGTCGTATCTCTAAG 58.408 41.667 0.00 0.00 0.00 2.18
3767 5266 3.940209 TGACAAATTGAGATTGGTGCC 57.060 42.857 0.00 0.00 29.37 5.01
3799 5298 2.944129 ACAAGCAGGTTTGGCTCTTTA 58.056 42.857 1.07 0.00 41.66 1.85
3801 5300 3.897505 ACAAGCAGGTTTGGCTCTTTATT 59.102 39.130 1.07 0.00 41.66 1.40
3857 5424 7.822600 AGGTTACCTATAGGCCAAATATTTGT 58.177 34.615 23.24 10.41 39.32 2.83
3992 5829 8.922931 TGGTGCATATACTGATATTGATTTGT 57.077 30.769 0.00 0.00 0.00 2.83
4129 5970 9.806203 TCTATTTCATAATTCAACAAGGCATTG 57.194 29.630 10.01 10.01 42.46 2.82
4187 6028 4.702831 TCATTATGCAATCGGCTCTAACA 58.297 39.130 0.00 0.00 45.15 2.41
4190 6031 1.075542 TGCAATCGGCTCTAACAACG 58.924 50.000 0.00 0.00 45.15 4.10
4198 6039 2.213499 GGCTCTAACAACGGGATGATG 58.787 52.381 0.00 0.00 0.00 3.07
4214 6055 8.647796 ACGGGATGATGACATTCTAAAATAGTA 58.352 33.333 0.00 0.00 36.82 1.82
4216 6057 8.926710 GGGATGATGACATTCTAAAATAGTACG 58.073 37.037 0.00 0.00 36.82 3.67
4422 6265 3.056607 CCCTTTTGGCTGGTGAATTACTG 60.057 47.826 0.00 0.00 38.58 2.74
4437 6280 7.189512 GTGAATTACTGAATTGTGTGGCTATC 58.810 38.462 0.00 0.00 35.33 2.08
4529 6373 0.037882 ATCTGTCACCTGCACACGAG 60.038 55.000 0.00 0.00 0.00 4.18
4554 6402 8.825745 AGCACACCAAATTAAATTTAAACACAG 58.174 29.630 14.35 5.93 0.00 3.66
4867 6720 2.050168 CCAATGCAGCGCAACGTT 60.050 55.556 11.47 5.65 43.62 3.99
4968 6821 3.893763 CGCGAGCTCGTCCTCCAT 61.894 66.667 34.46 0.00 42.22 3.41
5053 6906 3.849951 CCGGATAGCACGGCCACT 61.850 66.667 2.24 0.00 45.34 4.00
5144 6997 6.102897 AGTTGGAGACTCATAATAATCCCG 57.897 41.667 4.53 0.00 31.20 5.14
5437 7293 6.996282 TCATGAGAAATATCTGCATGTGTCAT 59.004 34.615 0.00 0.00 39.54 3.06
5438 7294 6.613755 TGAGAAATATCTGCATGTGTCATG 57.386 37.500 5.49 5.49 35.54 3.07
5515 7371 8.100791 ACAAATGCATAGTAACTACTTTCTCCA 58.899 33.333 0.00 0.00 37.73 3.86
5630 7489 8.557592 AATCCGTATGTAGTCTGTATCGAATA 57.442 34.615 0.00 0.00 0.00 1.75
5723 7582 1.134371 GTTGTGGATGCTACTCCCTCC 60.134 57.143 0.00 0.00 34.12 4.30
5752 7612 8.852135 CCCAACTAAACCAAGTCACTTATTTTA 58.148 33.333 4.68 4.18 0.00 1.52
5765 7625 5.104900 TCACTTATTTTAGGACTGAGGGAGC 60.105 44.000 0.00 0.00 0.00 4.70
5894 7757 4.341235 GGCCTAAATTTTGGGAGGATGTAC 59.659 45.833 18.49 0.81 32.08 2.90
6198 8074 9.679661 TTTTCCTATTTGATACATCTTAGCACA 57.320 29.630 0.00 0.00 0.00 4.57
6199 8075 9.679661 TTTCCTATTTGATACATCTTAGCACAA 57.320 29.630 0.00 0.00 0.00 3.33
6205 8081 6.122850 TGATACATCTTAGCACAATGTTGC 57.877 37.500 0.00 0.67 43.34 4.17
6207 8083 4.430137 ACATCTTAGCACAATGTTGCAG 57.570 40.909 9.65 1.46 45.62 4.41
6216 8093 3.120923 GCACAATGTTGCAGAAAATTCCG 60.121 43.478 3.59 0.00 42.49 4.30
6273 8150 7.513190 GTGACGATCTCACTTATTATATGCC 57.487 40.000 14.41 0.00 45.38 4.40
6327 8204 9.825109 TTCGAAAACATCATATGGTGAAGTATA 57.175 29.630 22.80 1.30 37.76 1.47
6328 8205 9.996554 TCGAAAACATCATATGGTGAAGTATAT 57.003 29.630 22.80 0.00 37.76 0.86
6341 8218 6.270000 TGGTGAAGTATATGTAAGCTAGCCAT 59.730 38.462 12.13 10.53 0.00 4.40
6357 8234 4.383931 AGCCATCATTGGAGCAAGATAT 57.616 40.909 0.00 0.00 46.92 1.63
6360 8237 3.126514 CCATCATTGGAGCAAGATATCGC 59.873 47.826 0.00 0.00 46.92 4.58
6396 8273 9.941991 CAAAATATAATTTTGCACTCAAACGAG 57.058 29.630 11.05 0.00 41.48 4.18
6404 8281 6.371809 TTTGCACTCAAACGAGACTAAAAT 57.628 33.333 0.00 0.00 37.28 1.82
6414 8291 9.545105 TCAAACGAGACTAAAATAAGGTAAACA 57.455 29.630 0.00 0.00 0.00 2.83
6444 8321 7.970102 TGGTTAACCACTTAAACTCAGTCTAT 58.030 34.615 23.69 0.00 42.01 1.98
6463 8340 7.594015 CAGTCTATTATCAAATGCTGGCAAATC 59.406 37.037 0.00 0.00 0.00 2.17
6475 8352 8.798859 AATGCTGGCAAATCTACCTATATTAG 57.201 34.615 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 7.148540 GCTCGTTTTATACACATGACAACCTAA 60.149 37.037 0.00 0.00 0.00 2.69
83 85 3.757493 TGAAACCGTTTTTACACAGGTGT 59.243 39.130 10.26 10.26 46.87 4.16
89 91 4.922719 TCCATGTGAAACCGTTTTTACAC 58.077 39.130 5.20 10.61 42.23 2.90
90 92 4.641094 ACTCCATGTGAAACCGTTTTTACA 59.359 37.500 5.54 5.54 43.22 2.41
120 122 8.474025 CCAAACTATTGATACCAGGCAAATTTA 58.526 33.333 0.00 0.00 38.94 1.40
130 132 5.506730 TGGTCACCAAACTATTGATACCA 57.493 39.130 0.00 0.00 38.71 3.25
164 166 4.455877 GCATTGTGGGTAGCCTATTACATC 59.544 45.833 13.11 0.00 0.00 3.06
225 227 4.792513 TGGTTGAGTAGGGTTTTACCAA 57.207 40.909 0.00 0.00 41.02 3.67
239 245 8.363390 TGCTATTTATCACTAGAGATGGTTGAG 58.637 37.037 12.39 5.18 0.00 3.02
246 252 7.941919 TCAACGTGCTATTTATCACTAGAGAT 58.058 34.615 7.83 7.83 0.00 2.75
307 313 3.436496 GAGTACATAGTGAACACCTCGC 58.564 50.000 0.00 0.00 34.52 5.03
326 332 2.163826 CGATGTTCACGCAATTGGAG 57.836 50.000 7.72 0.00 0.00 3.86
335 341 0.109086 AGAGTGGAGCGATGTTCACG 60.109 55.000 0.00 0.00 35.50 4.35
366 373 4.949966 AGGGAAGAGAAGTGTCTAGGTA 57.050 45.455 0.00 0.00 32.80 3.08
417 424 1.986632 AACGGGGTCGGTGGAAAAGT 61.987 55.000 0.00 0.00 41.39 2.66
436 443 4.104102 AGGTGTTGGTCAAAGTATGAGGAA 59.896 41.667 0.00 0.00 39.19 3.36
439 446 6.406370 TCATAGGTGTTGGTCAAAGTATGAG 58.594 40.000 0.00 0.00 39.19 2.90
460 467 3.230134 GTCTGACTCCTAGCCTCATCAT 58.770 50.000 0.00 0.00 0.00 2.45
474 481 0.252696 TGGCTGTATGGGGTCTGACT 60.253 55.000 7.85 0.00 0.00 3.41
480 487 1.658053 ATGGCATGGCTGTATGGGGT 61.658 55.000 21.08 0.00 0.00 4.95
487 494 1.544093 CGGATTAGATGGCATGGCTGT 60.544 52.381 21.08 9.13 0.00 4.40
515 527 1.054978 GGGAGGAGGAATTACGCCCT 61.055 60.000 6.86 5.59 35.02 5.19
540 552 4.690748 TGTTGCCGTAAAAGAGATGAAGAG 59.309 41.667 0.00 0.00 0.00 2.85
546 558 2.095853 CGCATGTTGCCGTAAAAGAGAT 59.904 45.455 0.00 0.00 41.12 2.75
589 601 1.464734 TCAGTCTTAGGGAGAGCACG 58.535 55.000 0.00 0.00 34.31 5.34
604 616 2.440539 ATGAACGTTCGCTCTTCAGT 57.559 45.000 22.48 0.00 0.00 3.41
613 625 5.230306 GGAGAATCTAGTGAATGAACGTTCG 59.770 44.000 22.48 6.52 33.73 3.95
648 660 2.155279 GCTTCTTTTCACCACTCCTCC 58.845 52.381 0.00 0.00 0.00 4.30
669 681 0.107831 TTGTCCTTTCCCACTCACCG 59.892 55.000 0.00 0.00 0.00 4.94
693 1539 0.713579 AGAGAGGAGTAGGGCTTGGT 59.286 55.000 0.00 0.00 0.00 3.67
707 1574 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
708 1575 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
709 1576 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
710 1577 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
711 1578 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
712 1579 5.960811 AGAAAGAGAGAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
713 1580 6.098124 AGAGAAAGAGAGAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
714 1581 5.960811 AGAGAAAGAGAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
715 1582 6.098124 AGAGAGAAAGAGAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
716 1583 5.960811 AGAGAGAAAGAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
717 1584 6.098124 AGAGAGAGAAAGAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
718 1585 5.960811 AGAGAGAGAAAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
719 1586 6.098124 AGAGAGAGAGAAAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
720 1587 5.960811 AGAGAGAGAGAAAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
721 1588 6.098124 AGAGAGAGAGAGAAAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
722 1589 5.960811 AGAGAGAGAGAGAAAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
723 1590 6.098124 AGAGAGAGAGAGAGAAAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
724 1591 5.960811 AGAGAGAGAGAGAGAAAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
725 1592 6.098124 AGAGAGAGAGAGAGAGAAAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
726 1593 5.960811 AGAGAGAGAGAGAGAGAAAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
727 1594 6.127225 TGAGAGAGAGAGAGAGAGAAAGAGAG 60.127 46.154 0.00 0.00 0.00 3.20
728 1595 5.721480 TGAGAGAGAGAGAGAGAGAAAGAGA 59.279 44.000 0.00 0.00 0.00 3.10
729 1596 5.982356 TGAGAGAGAGAGAGAGAGAAAGAG 58.018 45.833 0.00 0.00 0.00 2.85
730 1597 6.566079 ATGAGAGAGAGAGAGAGAGAAAGA 57.434 41.667 0.00 0.00 0.00 2.52
731 1598 7.989741 ACTTATGAGAGAGAGAGAGAGAGAAAG 59.010 40.741 0.00 0.00 0.00 2.62
732 1599 7.770433 CACTTATGAGAGAGAGAGAGAGAGAAA 59.230 40.741 0.00 0.00 0.00 2.52
733 1600 7.275183 CACTTATGAGAGAGAGAGAGAGAGAA 58.725 42.308 0.00 0.00 0.00 2.87
777 1649 5.407407 TTTAGAGAGAGGAAAGCGACAAT 57.593 39.130 0.00 0.00 0.00 2.71
784 1656 5.905913 TCCCCCTTATTTAGAGAGAGGAAAG 59.094 44.000 0.00 0.00 0.00 2.62
808 1680 1.142870 TGCAAGGACTACTGCCTTTGT 59.857 47.619 0.00 0.00 42.99 2.83
866 1738 2.669391 GCTTATTGCACCACAGAACAGC 60.669 50.000 0.00 0.00 42.31 4.40
909 1781 4.757149 ACTTATTTTGAGCTCAGGACACAC 59.243 41.667 17.43 0.00 0.00 3.82
910 1782 4.756642 CACTTATTTTGAGCTCAGGACACA 59.243 41.667 17.43 0.00 0.00 3.72
990 1862 5.700183 TCTGATGGCTATGAGTCTAGTCTT 58.300 41.667 0.00 0.00 0.00 3.01
1052 1939 3.745803 GCTGCTGAGGTGCAAGGC 61.746 66.667 0.00 0.00 42.83 4.35
1062 1949 0.676184 GGAGATGGATACGCTGCTGA 59.324 55.000 0.00 0.00 42.51 4.26
1079 1968 0.899717 GGAGCACAATTTGGCAGGGA 60.900 55.000 10.96 0.00 0.00 4.20
1136 2025 0.743701 CACACTGCCCTGCATCTCTC 60.744 60.000 0.00 0.00 38.13 3.20
1143 2032 2.111878 ACACTCACACTGCCCTGC 59.888 61.111 0.00 0.00 0.00 4.85
1144 2033 1.146930 ACACACTCACACTGCCCTG 59.853 57.895 0.00 0.00 0.00 4.45
1147 2036 0.744414 ACACACACACTCACACTGCC 60.744 55.000 0.00 0.00 0.00 4.85
1189 2129 1.202806 AGCTTAGCCACACACACACAT 60.203 47.619 0.00 0.00 0.00 3.21
1360 2306 1.819632 CGGTGGAGTAGGCCATTGC 60.820 63.158 5.01 0.00 40.68 3.56
1395 2341 4.048470 GAAGGGGGAGGTGGTGGC 62.048 72.222 0.00 0.00 0.00 5.01
1569 2524 4.193893 TGGTGCTGGTGCTGCTGT 62.194 61.111 0.00 0.00 40.48 4.40
1602 2557 1.134877 TGCTCAGAGATCTGGAAAGCG 60.135 52.381 0.00 0.00 41.49 4.68
1682 2637 0.467384 CTGATGATGAGGAGCCGGTT 59.533 55.000 1.90 0.00 0.00 4.44
1735 2696 6.500589 AAGAAATTAGGATGGATCGAAGGA 57.499 37.500 0.00 0.00 0.00 3.36
1761 2722 4.100189 GGCCAGATCAAGTCTCTTAGCTAA 59.900 45.833 5.94 5.94 34.00 3.09
1782 2743 4.773323 ACTGAAGCAACAAAGAATAGGC 57.227 40.909 0.00 0.00 0.00 3.93
1822 2783 6.829298 GGAAGGGGAAATTTTAGTAGAAGAGG 59.171 42.308 0.00 0.00 0.00 3.69
1824 2785 6.507843 AGGGAAGGGGAAATTTTAGTAGAAGA 59.492 38.462 0.00 0.00 0.00 2.87
1825 2786 6.732487 AGGGAAGGGGAAATTTTAGTAGAAG 58.268 40.000 0.00 0.00 0.00 2.85
1828 2789 7.407729 TGTAAGGGAAGGGGAAATTTTAGTAG 58.592 38.462 0.00 0.00 0.00 2.57
1830 2791 6.183361 ACTGTAAGGGAAGGGGAAATTTTAGT 60.183 38.462 0.00 0.00 39.30 2.24
1831 2792 6.253758 ACTGTAAGGGAAGGGGAAATTTTAG 58.746 40.000 0.00 0.00 39.30 1.85
1832 2793 6.222227 ACTGTAAGGGAAGGGGAAATTTTA 57.778 37.500 0.00 0.00 39.30 1.52
1833 2794 5.087923 ACTGTAAGGGAAGGGGAAATTTT 57.912 39.130 0.00 0.00 39.30 1.82
1835 2796 4.759793 AACTGTAAGGGAAGGGGAAATT 57.240 40.909 0.00 0.00 39.30 1.82
1861 2824 6.925610 TTACATAGGAACATGCATGAACTC 57.074 37.500 32.75 22.50 0.00 3.01
1919 3048 7.658525 TGTACCAATGGAAATGCATAGAAAT 57.341 32.000 6.16 0.00 0.00 2.17
1962 3091 9.942850 TGACAATTTCACAGATATGAAGAAGTA 57.057 29.630 0.00 0.00 39.68 2.24
1963 3092 8.853077 TGACAATTTCACAGATATGAAGAAGT 57.147 30.769 0.00 0.00 39.68 3.01
1966 3095 9.676861 AGAATGACAATTTCACAGATATGAAGA 57.323 29.630 0.00 0.00 39.68 2.87
1972 3120 7.661027 TGACACAGAATGACAATTTCACAGATA 59.339 33.333 0.00 0.00 39.69 1.98
1998 3146 5.661312 TGTGGAGTTAACTCATGGTATAGCT 59.339 40.000 31.30 0.00 44.60 3.32
2002 3150 6.013725 TGAACTGTGGAGTTAACTCATGGTAT 60.014 38.462 31.30 16.23 42.80 2.73
2003 3151 5.305902 TGAACTGTGGAGTTAACTCATGGTA 59.694 40.000 31.30 14.76 42.80 3.25
2019 3167 7.651808 ACAGGAATTGAAAACTATGAACTGTG 58.348 34.615 0.00 0.00 33.55 3.66
2404 3583 6.632834 CCGCAATAACTTAATGTAGTGAATGC 59.367 38.462 0.00 0.00 32.09 3.56
2565 3744 2.990740 TGGGTTTCTGGCCATACTTT 57.009 45.000 5.51 0.00 0.00 2.66
2649 3828 3.438087 CAGCACCAAACTAAGACATCAGG 59.562 47.826 0.00 0.00 0.00 3.86
2668 3847 4.389077 GGCATGTACTTATTCGGATACAGC 59.611 45.833 0.00 0.00 31.41 4.40
2675 3854 3.792401 TGTGAGGCATGTACTTATTCGG 58.208 45.455 0.00 0.00 0.00 4.30
2752 3936 9.821662 AAACAGTAAGCTCGTTCAAATTTATAC 57.178 29.630 0.00 0.00 0.00 1.47
2798 3982 3.674753 CGATCAAATGTGGAAAACTTGGC 59.325 43.478 0.00 0.00 0.00 4.52
2904 4089 2.734276 ACGCAACAAACACCAGTTTT 57.266 40.000 0.00 0.00 45.32 2.43
2943 4128 2.979813 CCTAACATTGAAACGCTGCAAC 59.020 45.455 0.00 0.00 0.00 4.17
2950 4135 5.183140 ACATCCCTTTCCTAACATTGAAACG 59.817 40.000 0.00 0.00 0.00 3.60
2986 4171 0.034574 CCACCGACCCAAATCATCCA 60.035 55.000 0.00 0.00 0.00 3.41
2999 4184 1.055849 CCATCCATGTATCCCACCGA 58.944 55.000 0.00 0.00 0.00 4.69
3017 4202 6.665992 TGTTCACCATATCATAGTAGGTCC 57.334 41.667 0.00 0.00 0.00 4.46
3020 4205 7.067496 ACCTTGTTCACCATATCATAGTAGG 57.933 40.000 0.00 0.00 0.00 3.18
3045 4230 1.205893 CTACTCTCCGCCTCAGCTTTT 59.794 52.381 0.00 0.00 36.60 2.27
3086 4271 2.747446 TCGCCTTAGTGAAGAAATTGGC 59.253 45.455 0.00 0.00 34.25 4.52
3087 4272 3.375299 CCTCGCCTTAGTGAAGAAATTGG 59.625 47.826 0.00 0.00 34.25 3.16
3088 4273 3.375299 CCCTCGCCTTAGTGAAGAAATTG 59.625 47.826 0.00 0.00 34.25 2.32
3089 4274 3.009143 ACCCTCGCCTTAGTGAAGAAATT 59.991 43.478 0.00 0.00 34.25 1.82
3125 4319 2.743636 TAACTTTCCCTCGCACTCTG 57.256 50.000 0.00 0.00 0.00 3.35
3130 4324 3.892588 ACCATTTTTAACTTTCCCTCGCA 59.107 39.130 0.00 0.00 0.00 5.10
3132 4326 5.447624 ACACCATTTTTAACTTTCCCTCG 57.552 39.130 0.00 0.00 0.00 4.63
3134 4328 8.585018 CATCTTACACCATTTTTAACTTTCCCT 58.415 33.333 0.00 0.00 0.00 4.20
3135 4329 7.817478 CCATCTTACACCATTTTTAACTTTCCC 59.183 37.037 0.00 0.00 0.00 3.97
3138 4332 8.257602 ACCCATCTTACACCATTTTTAACTTT 57.742 30.769 0.00 0.00 0.00 2.66
3139 4333 7.849322 ACCCATCTTACACCATTTTTAACTT 57.151 32.000 0.00 0.00 0.00 2.66
3141 4335 6.871492 CCAACCCATCTTACACCATTTTTAAC 59.129 38.462 0.00 0.00 0.00 2.01
3142 4336 6.014156 CCCAACCCATCTTACACCATTTTTAA 60.014 38.462 0.00 0.00 0.00 1.52
3143 4337 5.482175 CCCAACCCATCTTACACCATTTTTA 59.518 40.000 0.00 0.00 0.00 1.52
3144 4338 4.285775 CCCAACCCATCTTACACCATTTTT 59.714 41.667 0.00 0.00 0.00 1.94
3145 4339 3.837731 CCCAACCCATCTTACACCATTTT 59.162 43.478 0.00 0.00 0.00 1.82
3146 4340 3.440127 CCCAACCCATCTTACACCATTT 58.560 45.455 0.00 0.00 0.00 2.32
3147 4341 2.292192 CCCCAACCCATCTTACACCATT 60.292 50.000 0.00 0.00 0.00 3.16
3148 4342 1.287739 CCCCAACCCATCTTACACCAT 59.712 52.381 0.00 0.00 0.00 3.55
3149 4343 0.701731 CCCCAACCCATCTTACACCA 59.298 55.000 0.00 0.00 0.00 4.17
3150 4344 0.702316 ACCCCAACCCATCTTACACC 59.298 55.000 0.00 0.00 0.00 4.16
3151 4345 2.167662 CAACCCCAACCCATCTTACAC 58.832 52.381 0.00 0.00 0.00 2.90
3152 4346 1.549037 GCAACCCCAACCCATCTTACA 60.549 52.381 0.00 0.00 0.00 2.41
3153 4347 1.182667 GCAACCCCAACCCATCTTAC 58.817 55.000 0.00 0.00 0.00 2.34
3174 4663 0.035458 ACTTTCCCTCGCACTCTTGG 59.965 55.000 0.00 0.00 0.00 3.61
3183 4672 5.447624 ACACCATTTTTAACTTTCCCTCG 57.552 39.130 0.00 0.00 0.00 4.63
3195 4684 8.189119 AGTATCCAACATGTTACACCATTTTT 57.811 30.769 11.53 0.00 0.00 1.94
3217 4706 1.475751 CCGGACGGCTAGGAAGTAGTA 60.476 57.143 0.00 0.00 0.00 1.82
3284 4773 5.114081 AGTCAATTTATACACACGCCCTAC 58.886 41.667 0.00 0.00 0.00 3.18
3304 4793 4.021456 CCCACCTCCCACAAATTAAAAGTC 60.021 45.833 0.00 0.00 0.00 3.01
3305 4794 3.901222 CCCACCTCCCACAAATTAAAAGT 59.099 43.478 0.00 0.00 0.00 2.66
3306 4795 3.901222 ACCCACCTCCCACAAATTAAAAG 59.099 43.478 0.00 0.00 0.00 2.27
3307 4796 3.898741 GACCCACCTCCCACAAATTAAAA 59.101 43.478 0.00 0.00 0.00 1.52
3309 4798 2.719705 AGACCCACCTCCCACAAATTAA 59.280 45.455 0.00 0.00 0.00 1.40
3310 4799 2.354328 AGACCCACCTCCCACAAATTA 58.646 47.619 0.00 0.00 0.00 1.40
3311 4800 1.158007 AGACCCACCTCCCACAAATT 58.842 50.000 0.00 0.00 0.00 1.82
3312 4801 1.158007 AAGACCCACCTCCCACAAAT 58.842 50.000 0.00 0.00 0.00 2.32
3380 4879 9.426837 CTTGAATTTGGATCACAACATAACAAT 57.573 29.630 0.00 0.00 39.19 2.71
3413 4912 4.563580 GCTCGTTAGAAGTTAGCCTTTCTC 59.436 45.833 0.00 0.00 32.03 2.87
3472 4971 4.988540 TCAAAACTGATCTGTACCACTTCG 59.011 41.667 5.59 0.00 0.00 3.79
3533 5032 2.569853 TGATCAACTTATCCCGTGTGGT 59.430 45.455 0.00 0.00 34.77 4.16
3536 5035 4.253685 CAACTGATCAACTTATCCCGTGT 58.746 43.478 0.00 0.00 0.00 4.49
3590 5089 2.715046 CCAGCCAGCAAATCTTCACTA 58.285 47.619 0.00 0.00 0.00 2.74
3591 5090 1.542492 CCAGCCAGCAAATCTTCACT 58.458 50.000 0.00 0.00 0.00 3.41
3592 5091 0.108945 GCCAGCCAGCAAATCTTCAC 60.109 55.000 0.00 0.00 0.00 3.18
3593 5092 1.588824 CGCCAGCCAGCAAATCTTCA 61.589 55.000 0.00 0.00 0.00 3.02
3594 5093 1.138247 CGCCAGCCAGCAAATCTTC 59.862 57.895 0.00 0.00 0.00 2.87
3595 5094 2.998279 GCGCCAGCCAGCAAATCTT 61.998 57.895 0.00 0.00 37.42 2.40
3596 5095 3.446570 GCGCCAGCCAGCAAATCT 61.447 61.111 0.00 0.00 37.42 2.40
3607 5106 3.551887 GAAAAACCACGGGCGCCAG 62.552 63.158 30.85 28.22 0.00 4.85
3633 5132 0.112412 GTGGACAACCCCTCCAACAT 59.888 55.000 0.00 0.00 39.60 2.71
3655 5154 3.772572 TCAATCAGGGGACACGAGATTTA 59.227 43.478 0.00 0.00 0.00 1.40
3677 5176 1.223187 ACACGGCGAAGAACGAAAAT 58.777 45.000 16.62 0.00 45.77 1.82
3750 5249 5.581874 GGTAAATGGCACCAATCTCAATTTG 59.418 40.000 0.00 0.00 36.01 2.32
3767 5266 3.855689 CCTGCTTGTTCCAGGTAAATG 57.144 47.619 0.00 0.00 43.86 2.32
3799 5298 7.589958 TTGTACATACTTGTTGGGTTTGAAT 57.410 32.000 0.00 0.00 37.28 2.57
3801 5300 6.829298 TCTTTGTACATACTTGTTGGGTTTGA 59.171 34.615 0.00 0.00 37.28 2.69
3875 5442 9.362151 TGGTCAAACTTAGGAATAGTTGATTTT 57.638 29.630 0.00 0.00 36.06 1.82
3878 5715 8.934023 TTTGGTCAAACTTAGGAATAGTTGAT 57.066 30.769 0.00 0.00 36.06 2.57
3967 5804 8.922931 ACAAATCAATATCAGTATATGCACCA 57.077 30.769 0.00 0.00 0.00 4.17
4021 5858 9.748708 CAATGATTTCTAAGTTTGACCAAGAAA 57.251 29.630 0.00 0.00 39.67 2.52
4023 5860 8.567948 GTCAATGATTTCTAAGTTTGACCAAGA 58.432 33.333 0.00 0.00 37.86 3.02
4187 6028 7.993183 ACTATTTTAGAATGTCATCATCCCGTT 59.007 33.333 0.00 0.00 32.56 4.44
4190 6031 8.926710 CGTACTATTTTAGAATGTCATCATCCC 58.073 37.037 0.00 0.00 32.56 3.85
4198 6039 8.126871 TGATGCACGTACTATTTTAGAATGTC 57.873 34.615 0.00 0.00 0.00 3.06
4276 6117 7.041167 TGGACATGTCTTAGTTCAAACATTGAG 60.041 37.037 24.50 0.00 41.38 3.02
4377 6220 9.730705 AGGGAGACATCAATACATACAAATATG 57.269 33.333 0.00 0.00 43.46 1.78
4393 6236 1.272147 ACCAGCCAAAAGGGAGACATC 60.272 52.381 0.00 0.00 40.01 3.06
4422 6265 7.659390 AGCTAGAAATAGATAGCCACACAATTC 59.341 37.037 0.00 0.00 44.45 2.17
4529 6373 8.821894 TCTGTGTTTAAATTTAATTTGGTGTGC 58.178 29.630 11.33 0.99 33.82 4.57
4867 6720 0.179137 CACGAGCGTATCCAGCAAGA 60.179 55.000 0.00 0.00 37.01 3.02
4968 6821 1.847818 CTCGACGTGGAAACTGTTGA 58.152 50.000 0.86 0.00 0.00 3.18
5053 6906 3.716195 CCACCACCATCTCCGGCA 61.716 66.667 0.00 0.00 0.00 5.69
5132 6985 6.566564 GCACTTGTCATCACGGGATTATTATG 60.567 42.308 0.00 0.00 0.00 1.90
5144 6997 2.287915 AGACGTTTGCACTTGTCATCAC 59.712 45.455 12.37 0.00 33.83 3.06
5427 7283 1.667724 GAGTAGGCACATGACACATGC 59.332 52.381 0.00 0.00 38.68 4.06
5437 7293 2.621998 GTTAGCGATAGGAGTAGGCACA 59.378 50.000 0.00 0.00 0.00 4.57
5438 7294 2.621998 TGTTAGCGATAGGAGTAGGCAC 59.378 50.000 0.00 0.00 0.00 5.01
5561 7420 6.712095 AGTGTAGATTCACTCATTTTGCTTCA 59.288 34.615 0.00 0.00 44.07 3.02
5605 7464 6.872628 TTCGATACAGACTACATACGGATT 57.127 37.500 0.00 0.00 0.00 3.01
5609 7468 8.242085 AGAGTATTCGATACAGACTACATACG 57.758 38.462 0.00 0.00 38.21 3.06
5723 7582 2.546789 GTGACTTGGTTTAGTTGGGACG 59.453 50.000 0.00 0.00 0.00 4.79
5752 7612 2.559381 ATTACTGCTCCCTCAGTCCT 57.441 50.000 0.00 0.00 45.32 3.85
5821 7684 3.719268 ATATGCACACAGGTCCAGAAA 57.281 42.857 0.00 0.00 0.00 2.52
6184 8060 5.882000 TCTGCAACATTGTGCTAAGATGTAT 59.118 36.000 10.93 0.00 45.17 2.29
6198 8074 4.764823 TCCTACGGAATTTTCTGCAACATT 59.235 37.500 0.00 0.00 37.06 2.71
6199 8075 4.331968 TCCTACGGAATTTTCTGCAACAT 58.668 39.130 0.00 0.00 37.06 2.71
6253 8130 9.242477 CATACAGGCATATAATAAGTGAGATCG 57.758 37.037 0.00 0.00 0.00 3.69
6289 8166 7.737972 TGATGTTTTCGAAGGAATAAGACAA 57.262 32.000 0.00 0.00 30.88 3.18
6341 8218 2.771089 GGCGATATCTTGCTCCAATGA 58.229 47.619 0.34 0.00 31.87 2.57
6404 8281 7.893124 TGGTTAACCAATGTTGTTTACCTTA 57.107 32.000 25.19 0.00 44.35 2.69
6444 8321 5.893255 AGGTAGATTTGCCAGCATTTGATAA 59.107 36.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.