Multiple sequence alignment - TraesCS6B01G376500

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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 TraesCS6B01G376500 chr6B 100.000 5839 0 0 1 5839 651414571 651420409 0.000000e+00 10783
1 TraesCS6B01G376500 chr6D 94.716 2044 88 9 2850 4887 431462101 431464130 0.000000e+00 3158
2 TraesCS6B01G376500 chr6D 95.245 1367 55 9 1483 2844 431460666 431462027 0.000000e+00 2156
3 TraesCS6B01G376500 chr6D 93.682 918 48 5 4925 5839 431467040 431466130 0.000000e+00 1365
4 TraesCS6B01G376500 chr6D 88.493 869 46 21 49 882 431459158 431460007 0.000000e+00 1002
5 TraesCS6B01G376500 chr6D 87.934 605 41 21 893 1479 431459975 431460565 0.000000e+00 684
6 TraesCS6B01G376500 chrUn 95.023 1768 81 4 4073 5839 74552368 74554129 0.000000e+00 2771
7 TraesCS6B01G376500 chrUn 92.560 1371 72 16 1483 2844 74549793 74551142 0.000000e+00 1940
8 TraesCS6B01G376500 chrUn 92.900 1169 62 6 2850 4015 74551216 74552366 0.000000e+00 1679
9 TraesCS6B01G376500 chrUn 86.887 1510 91 49 25 1479 74548237 74549694 0.000000e+00 1592
10 TraesCS6B01G376500 chr5B 73.464 716 156 24 5106 5813 388540022 388539333 7.560000e-59 239
11 TraesCS6B01G376500 chr5B 75.000 288 45 21 5533 5811 388610276 388610007 2.220000e-19 108
12 TraesCS6B01G376500 chr5A 72.867 715 162 22 5106 5813 433518905 433518216 3.540000e-52 217
13 TraesCS6B01G376500 chr5D 72.765 716 161 24 5106 5813 332509810 332509121 1.650000e-50 211
14 TraesCS6B01G376500 chr1A 73.333 555 104 34 5307 5839 550968354 550968886 1.300000e-36 165
15 TraesCS6B01G376500 chr1B 73.056 553 109 29 5307 5839 629938063 629938595 6.060000e-35 159


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 TraesCS6B01G376500 chr6B 651414571 651420409 5838 False 10783.0 10783 100.0000 1 5839 1 chr6B.!!$F1 5838
1 TraesCS6B01G376500 chr6D 431459158 431464130 4972 False 1750.0 3158 91.5970 49 4887 4 chr6D.!!$F1 4838
2 TraesCS6B01G376500 chr6D 431466130 431467040 910 True 1365.0 1365 93.6820 4925 5839 1 chr6D.!!$R1 914
3 TraesCS6B01G376500 chrUn 74548237 74554129 5892 False 1995.5 2771 91.8425 25 5839 4 chrUn.!!$F1 5814
4 TraesCS6B01G376500 chr5B 388539333 388540022 689 True 239.0 239 73.4640 5106 5813 1 chr5B.!!$R1 707
5 TraesCS6B01G376500 chr5A 433518216 433518905 689 True 217.0 217 72.8670 5106 5813 1 chr5A.!!$R1 707
6 TraesCS6B01G376500 chr5D 332509121 332509810 689 True 211.0 211 72.7650 5106 5813 1 chr5D.!!$R1 707

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
197 200 0.107993 CGATCACACTGGTCATGGCT 60.108 55.0 0.0 0.0 0.00 4.75 F
549 556 0.108138 AATAGCACGACCAGAGCACC 60.108 55.0 0.0 0.0 38.98 5.01 F
1356 1430 0.032515 TCTCTGGGGAATCTGCCGTA 60.033 55.0 0.0 0.0 0.00 4.02 F
1420 1495 0.551396 TGATCTAGTCTCGGGCTGGA 59.449 55.0 0.0 0.0 0.00 3.86 F
1487 1661 0.621862 CCTCTGGGGAAGCTTAGGGT 60.622 60.0 0.0 0.0 37.23 4.34 F
1621 1799 0.738762 TGCTGATTCTCGCTGCTGTC 60.739 55.0 0.0 0.0 0.00 3.51 F
3472 3725 1.235724 AAGGTGTTCTTTGCTACGGC 58.764 50.0 0.0 0.0 39.26 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 1119 0.047176 AGGAGGGAGGAGAGAGGAGA 59.953 60.000 0.00 0.0 0.00 3.71 R
1439 1514 0.109723 AAAACCCTAAGCTGACCGCA 59.890 50.000 0.00 0.0 42.61 5.69 R
2930 3182 1.004044 ACTCCCACCTTCTGCATTCTG 59.996 52.381 0.00 0.0 0.00 3.02 R
3082 3335 4.128925 TCCACAGTGAGAATGATAGTGC 57.871 45.455 0.62 0.0 0.00 4.40 R
3460 3713 1.612442 AGGAGGGCCGTAGCAAAGA 60.612 57.895 0.00 0.0 42.56 2.52 R
3565 3818 2.108250 AGCACCCTCACCAACATACTTT 59.892 45.455 0.00 0.0 0.00 2.66 R
5078 5392 0.675837 GACCCCTAGTTGTTTCGCCC 60.676 60.000 0.00 0.0 0.00 6.13 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
51 52 1.818060 TGTTATGTGACCTGGCATTGC 59.182 47.619 0.00 0.00 0.00 3.56
56 57 1.761784 TGTGACCTGGCATTGCTTTTT 59.238 42.857 8.82 0.00 0.00 1.94
57 58 2.137523 GTGACCTGGCATTGCTTTTTG 58.862 47.619 8.82 0.00 0.00 2.44
65 66 3.068560 GGCATTGCTTTTTGCTCATTCA 58.931 40.909 8.82 0.00 43.37 2.57
67 68 4.155280 GGCATTGCTTTTTGCTCATTCATT 59.845 37.500 8.82 0.00 43.37 2.57
73 74 5.801444 TGCTTTTTGCTCATTCATTACGATG 59.199 36.000 0.00 0.00 43.37 3.84
78 79 3.184986 TGCTCATTCATTACGATGATGCG 59.815 43.478 0.00 0.00 41.71 4.73
99 100 3.301642 CGACCCGAAGTAACATTTACGAC 59.698 47.826 0.00 0.00 0.00 4.34
143 146 1.282875 GTTCAAAGACACGGCAGGC 59.717 57.895 0.00 0.00 0.00 4.85
197 200 0.107993 CGATCACACTGGTCATGGCT 60.108 55.000 0.00 0.00 0.00 4.75
200 203 1.742880 CACACTGGTCATGGCTCCG 60.743 63.158 0.00 0.00 0.00 4.63
213 216 3.247006 TGGCTCCGATCTTCTTGTAAC 57.753 47.619 0.00 0.00 0.00 2.50
239 242 2.510918 GAGCTCGCCGTTAACCCC 60.511 66.667 0.00 0.00 0.00 4.95
250 253 1.093496 GTTAACCCCGCGGAGGAATG 61.093 60.000 31.47 13.91 45.00 2.67
256 259 0.393077 CCCGCGGAGGAATGTCTATT 59.607 55.000 30.73 0.00 45.00 1.73
280 283 5.580691 TGTTCTTGTAGATGAGGCATTAACG 59.419 40.000 0.00 0.00 0.00 3.18
300 303 6.773976 AACGTGAATGGGATGTAATGATTT 57.226 33.333 0.00 0.00 0.00 2.17
310 313 8.815565 TGGGATGTAATGATTTGCTTTTAGTA 57.184 30.769 0.00 0.00 0.00 1.82
356 359 1.340889 GTTCAGTGCTGCCCATTTTGA 59.659 47.619 0.00 0.00 0.00 2.69
357 360 1.927487 TCAGTGCTGCCCATTTTGAT 58.073 45.000 0.00 0.00 0.00 2.57
376 379 4.391155 TGATATGGTGCCCGTATTTTACC 58.609 43.478 7.22 0.00 36.02 2.85
387 390 5.504392 CCCGTATTTTACCGTTGCTATTTC 58.496 41.667 0.00 0.00 0.00 2.17
392 395 4.914312 TTTACCGTTGCTATTTCGACAG 57.086 40.909 0.00 0.00 0.00 3.51
394 397 2.607187 ACCGTTGCTATTTCGACAGAG 58.393 47.619 0.00 0.00 0.00 3.35
403 406 4.274459 GCTATTTCGACAGAGGATGCAAAT 59.726 41.667 0.00 0.00 0.00 2.32
413 416 3.760684 AGAGGATGCAAATGTTGGAGAAC 59.239 43.478 0.00 0.00 33.40 3.01
549 556 0.108138 AATAGCACGACCAGAGCACC 60.108 55.000 0.00 0.00 38.98 5.01
554 561 0.459237 CACGACCAGAGCACCAGATC 60.459 60.000 0.00 0.00 0.00 2.75
556 563 1.326213 CGACCAGAGCACCAGATCCT 61.326 60.000 0.00 0.00 0.00 3.24
557 564 0.908198 GACCAGAGCACCAGATCCTT 59.092 55.000 0.00 0.00 0.00 3.36
558 565 2.111384 GACCAGAGCACCAGATCCTTA 58.889 52.381 0.00 0.00 0.00 2.69
560 567 2.114616 CCAGAGCACCAGATCCTTACT 58.885 52.381 0.00 0.00 0.00 2.24
561 568 2.102252 CCAGAGCACCAGATCCTTACTC 59.898 54.545 0.00 0.00 0.00 2.59
566 590 2.171448 GCACCAGATCCTTACTCACCAT 59.829 50.000 0.00 0.00 0.00 3.55
638 662 0.969149 TTGCCACACAAACCACACAA 59.031 45.000 0.00 0.00 34.56 3.33
641 665 2.027745 TGCCACACAAACCACACAAAAT 60.028 40.909 0.00 0.00 0.00 1.82
642 666 2.607180 GCCACACAAACCACACAAAATC 59.393 45.455 0.00 0.00 0.00 2.17
739 767 0.953727 TGGCACTTGCAGTCATGAAC 59.046 50.000 0.00 0.00 44.36 3.18
754 782 7.489113 GCAGTCATGAACTCAAAAAGAAAGAAA 59.511 33.333 0.00 0.00 35.45 2.52
849 887 4.461781 AGAGAGAAATCCGTTTCCGTCTTA 59.538 41.667 0.00 0.00 43.82 2.10
850 888 5.047519 AGAGAGAAATCCGTTTCCGTCTTAA 60.048 40.000 0.00 0.00 43.82 1.85
876 914 4.458295 ACACGGGTTCTGGATATACTATCG 59.542 45.833 0.00 0.00 0.00 2.92
885 935 5.014860 TCTGGATATACTATCGGACCCTTCA 59.985 44.000 0.00 0.00 0.00 3.02
1058 1119 4.749310 CAGACTCCGCCAGCGCTT 62.749 66.667 7.50 0.00 38.24 4.68
1060 1121 4.443266 GACTCCGCCAGCGCTTCT 62.443 66.667 7.50 0.00 38.24 2.85
1076 1137 0.930726 TTCTCCTCTCTCCTCCCTCC 59.069 60.000 0.00 0.00 0.00 4.30
1077 1138 0.047176 TCTCCTCTCTCCTCCCTCCT 59.953 60.000 0.00 0.00 0.00 3.69
1078 1139 0.478507 CTCCTCTCTCCTCCCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
1188 1257 2.722201 GGACGACATCGCCCTCCTT 61.722 63.158 0.14 0.00 44.43 3.36
1269 1340 3.003478 CGTTTGGCGGCGATCTAC 58.997 61.111 12.98 1.45 36.85 2.59
1335 1406 3.611766 AGTCTAGGGTTTCGGTTCATG 57.388 47.619 0.00 0.00 0.00 3.07
1352 1423 0.473326 ATGCTCTCTGGGGAATCTGC 59.527 55.000 0.00 0.00 0.00 4.26
1356 1430 0.032515 TCTCTGGGGAATCTGCCGTA 60.033 55.000 0.00 0.00 0.00 4.02
1407 1482 5.500234 CCCCTTCTGTGAATTTGTGATCTA 58.500 41.667 0.00 0.00 0.00 1.98
1420 1495 0.551396 TGATCTAGTCTCGGGCTGGA 59.449 55.000 0.00 0.00 0.00 3.86
1467 1543 2.177016 AGCTTAGGGTTTTGGTTCCTGT 59.823 45.455 0.00 0.00 32.46 4.00
1468 1544 2.557056 GCTTAGGGTTTTGGTTCCTGTC 59.443 50.000 0.00 0.00 32.46 3.51
1487 1661 0.621862 CCTCTGGGGAAGCTTAGGGT 60.622 60.000 0.00 0.00 37.23 4.34
1488 1662 0.833949 CTCTGGGGAAGCTTAGGGTC 59.166 60.000 0.00 0.00 0.00 4.46
1530 1704 3.363724 GCCGTTTATTTTGTACTGCTTGC 59.636 43.478 0.00 0.00 0.00 4.01
1557 1731 3.690685 CTGCGGCGGAATTGGGGTA 62.691 63.158 9.78 0.00 0.00 3.69
1561 1735 1.970092 CGGCGGAATTGGGGTATTTA 58.030 50.000 0.00 0.00 0.00 1.40
1579 1756 2.145397 TAGGCGAGATGTGGAGTCTT 57.855 50.000 0.00 0.00 0.00 3.01
1581 1758 1.066573 AGGCGAGATGTGGAGTCTTTG 60.067 52.381 0.00 0.00 0.00 2.77
1596 1773 4.532834 AGTCTTTGTTTAGGGTTTCTGCA 58.467 39.130 0.00 0.00 0.00 4.41
1599 1776 4.097286 TCTTTGTTTAGGGTTTCTGCACAC 59.903 41.667 0.00 0.00 0.00 3.82
1621 1799 0.738762 TGCTGATTCTCGCTGCTGTC 60.739 55.000 0.00 0.00 0.00 3.51
1731 1909 4.895889 CCTATGTGGTGAGTAAGGATCTGA 59.104 45.833 0.00 0.00 0.00 3.27
1734 1912 6.662865 ATGTGGTGAGTAAGGATCTGATAG 57.337 41.667 0.00 0.00 0.00 2.08
1784 1962 3.838565 TGTAGCCCAATTTGTTCCTGAA 58.161 40.909 0.00 0.00 0.00 3.02
1906 2084 7.594714 ACTGAAGATAGTGTGTGTAGTTAGTG 58.405 38.462 0.00 0.00 0.00 2.74
1951 2129 5.878332 TTAAGGTGTATGAATGCACTGTG 57.122 39.130 10.69 2.76 42.11 3.66
1952 2130 3.423539 AGGTGTATGAATGCACTGTGT 57.576 42.857 9.86 0.00 42.11 3.72
1954 2132 2.813754 GGTGTATGAATGCACTGTGTGT 59.186 45.455 9.86 0.00 42.11 3.72
2132 2312 5.046663 TCCATACACTGTGCAGTTTATCTGA 60.047 40.000 7.90 5.90 46.27 3.27
2341 2523 6.975772 TGTTTTCGTACTTCTTCCCAATTTTG 59.024 34.615 0.00 0.00 0.00 2.44
2550 2732 2.450476 CACCAGCCTCCTTATGCTTTT 58.550 47.619 0.00 0.00 35.12 2.27
2558 2740 7.199078 CAGCCTCCTTATGCTTTTATCTTTTC 58.801 38.462 0.00 0.00 35.12 2.29
2756 2938 5.934043 TGTTATAAGGCTGCAGCATATACTG 59.066 40.000 37.63 0.00 44.36 2.74
2797 2979 3.632643 TGCCATCATGTAAGCAGAGAA 57.367 42.857 0.00 0.00 0.00 2.87
2798 2980 3.954200 TGCCATCATGTAAGCAGAGAAA 58.046 40.909 0.00 0.00 0.00 2.52
2844 3026 1.873591 CCAGTGTTTGCTACTGTGACC 59.126 52.381 0.00 0.00 43.05 4.02
2846 3028 2.545526 CAGTGTTTGCTACTGTGACCAG 59.454 50.000 0.00 0.00 44.68 4.00
2905 3157 4.842531 TGTCATCATCTCCTTGGCTTAA 57.157 40.909 0.00 0.00 0.00 1.85
2930 3182 2.262423 AGTTCCTTCTGGTTGCTCAC 57.738 50.000 0.00 0.00 34.23 3.51
3082 3335 3.058293 TGTTATCCTTTTCTGTGCTTGCG 60.058 43.478 0.00 0.00 0.00 4.85
3361 3614 3.963428 TCTAGTCTTGGACCTGCTTTC 57.037 47.619 0.00 0.00 32.18 2.62
3369 3622 3.857157 TGGACCTGCTTTCTTTACTGT 57.143 42.857 0.00 0.00 0.00 3.55
3376 3629 6.564328 ACCTGCTTTCTTTACTGTTTTTCTG 58.436 36.000 0.00 0.00 0.00 3.02
3445 3698 4.579869 AGTTTGTGAAGCTTGGTATCGAT 58.420 39.130 2.10 2.16 0.00 3.59
3451 3704 2.390225 AGCTTGGTATCGATCCTCCT 57.610 50.000 0.00 0.00 0.00 3.69
3460 3713 4.344390 GGTATCGATCCTCCTAAAGGTGTT 59.656 45.833 0.00 0.00 46.32 3.32
3472 3725 1.235724 AAGGTGTTCTTTGCTACGGC 58.764 50.000 0.00 0.00 39.26 5.68
3514 3767 1.736681 CTTCTTGCTAGAGCTGTTGCC 59.263 52.381 14.32 0.00 42.66 4.52
3544 3797 3.758300 GGATGCTTGTTTTATCCGTGTG 58.242 45.455 0.00 0.00 31.89 3.82
3550 3803 4.083003 GCTTGTTTTATCCGTGTGATTGGA 60.083 41.667 0.00 0.00 38.95 3.53
3559 3812 3.501828 TCCGTGTGATTGGAAGTGAATTG 59.498 43.478 0.00 0.00 0.00 2.32
3562 3815 4.613622 CGTGTGATTGGAAGTGAATTGGTC 60.614 45.833 0.00 0.00 0.00 4.02
3587 3840 2.546899 AGTATGTTGGTGAGGGTGCTA 58.453 47.619 0.00 0.00 0.00 3.49
3640 3893 3.131933 CAGCTCTGCAGATAACCTACAGT 59.868 47.826 18.63 0.00 37.50 3.55
3652 3905 7.341256 CAGATAACCTACAGTCTACAGGGTTTA 59.659 40.741 0.00 0.00 37.99 2.01
3666 3919 8.607713 TCTACAGGGTTTAATCTGGTTTATTCA 58.392 33.333 0.00 0.00 35.47 2.57
3671 3924 8.803235 AGGGTTTAATCTGGTTTATTCAACTTC 58.197 33.333 0.00 0.00 35.46 3.01
3683 3936 8.352942 GGTTTATTCAACTTCAATGTTCTGTCT 58.647 33.333 0.00 0.00 35.46 3.41
3687 3940 8.682936 ATTCAACTTCAATGTTCTGTCTTAGT 57.317 30.769 0.00 0.00 0.00 2.24
3740 3993 2.125147 CAGATGGCCCGCTCGAAA 60.125 61.111 0.00 0.00 0.00 3.46
3878 4131 0.679960 ACGGTTTTGATGCTAGGGGC 60.680 55.000 0.00 0.00 42.22 5.80
3914 4167 1.436326 TGGCCACCAACAGGTACTTA 58.564 50.000 0.00 0.00 34.60 2.24
3942 4195 1.155889 TTCGTGCGCATTCTCATGTT 58.844 45.000 15.91 0.00 32.28 2.71
4017 4270 9.950496 AAGCTATTTATAGATGGGACTTGTATG 57.050 33.333 0.97 0.00 32.05 2.39
4018 4271 9.326489 AGCTATTTATAGATGGGACTTGTATGA 57.674 33.333 0.97 0.00 32.05 2.15
4027 4280 8.738645 AGATGGGACTTGTATGATTAAGAAAC 57.261 34.615 0.00 0.00 0.00 2.78
4028 4281 8.552296 AGATGGGACTTGTATGATTAAGAAACT 58.448 33.333 0.00 0.00 0.00 2.66
4029 4282 9.178758 GATGGGACTTGTATGATTAAGAAACTT 57.821 33.333 0.00 0.00 0.00 2.66
4030 4283 8.561738 TGGGACTTGTATGATTAAGAAACTTC 57.438 34.615 0.00 0.00 0.00 3.01
4031 4284 8.160765 TGGGACTTGTATGATTAAGAAACTTCA 58.839 33.333 0.00 0.00 0.00 3.02
4032 4285 8.669243 GGGACTTGTATGATTAAGAAACTTCAG 58.331 37.037 0.00 0.00 0.00 3.02
4033 4286 9.220767 GGACTTGTATGATTAAGAAACTTCAGT 57.779 33.333 0.00 0.00 0.00 3.41
4035 4288 9.003658 ACTTGTATGATTAAGAAACTTCAGTGG 57.996 33.333 0.00 0.00 0.00 4.00
4036 4289 8.918202 TTGTATGATTAAGAAACTTCAGTGGT 57.082 30.769 0.00 0.00 0.00 4.16
4037 4290 8.547967 TGTATGATTAAGAAACTTCAGTGGTC 57.452 34.615 0.00 0.00 0.00 4.02
4038 4291 8.375506 TGTATGATTAAGAAACTTCAGTGGTCT 58.624 33.333 0.00 0.00 0.00 3.85
4039 4292 7.678947 ATGATTAAGAAACTTCAGTGGTCTG 57.321 36.000 0.00 0.00 42.54 3.51
4040 4293 6.591935 TGATTAAGAAACTTCAGTGGTCTGT 58.408 36.000 0.00 0.00 41.91 3.41
4041 4294 6.483307 TGATTAAGAAACTTCAGTGGTCTGTG 59.517 38.462 0.00 0.00 41.91 3.66
4042 4295 3.914426 AGAAACTTCAGTGGTCTGTGT 57.086 42.857 0.00 0.00 41.91 3.72
4043 4296 4.222124 AGAAACTTCAGTGGTCTGTGTT 57.778 40.909 0.00 0.00 41.91 3.32
4044 4297 5.353394 AGAAACTTCAGTGGTCTGTGTTA 57.647 39.130 0.00 0.00 41.91 2.41
4045 4298 5.930135 AGAAACTTCAGTGGTCTGTGTTAT 58.070 37.500 0.00 0.00 41.91 1.89
4046 4299 6.357367 AGAAACTTCAGTGGTCTGTGTTATT 58.643 36.000 0.00 0.00 41.91 1.40
4047 4300 6.828785 AGAAACTTCAGTGGTCTGTGTTATTT 59.171 34.615 0.00 0.00 41.91 1.40
4048 4301 7.990886 AGAAACTTCAGTGGTCTGTGTTATTTA 59.009 33.333 0.00 0.00 41.91 1.40
4049 4302 8.514330 AAACTTCAGTGGTCTGTGTTATTTAA 57.486 30.769 0.00 0.00 41.91 1.52
4050 4303 8.514330 AACTTCAGTGGTCTGTGTTATTTAAA 57.486 30.769 0.00 0.00 41.91 1.52
4051 4304 8.514330 ACTTCAGTGGTCTGTGTTATTTAAAA 57.486 30.769 0.00 0.00 41.91 1.52
4052 4305 8.403236 ACTTCAGTGGTCTGTGTTATTTAAAAC 58.597 33.333 0.00 0.00 41.91 2.43
4053 4306 8.514330 TTCAGTGGTCTGTGTTATTTAAAACT 57.486 30.769 0.00 0.00 41.91 2.66
4054 4307 8.149973 TCAGTGGTCTGTGTTATTTAAAACTC 57.850 34.615 0.00 0.00 41.91 3.01
4055 4308 7.990886 TCAGTGGTCTGTGTTATTTAAAACTCT 59.009 33.333 0.00 0.00 41.91 3.24
4056 4309 8.621286 CAGTGGTCTGTGTTATTTAAAACTCTT 58.379 33.333 0.00 0.00 36.97 2.85
4057 4310 8.837389 AGTGGTCTGTGTTATTTAAAACTCTTC 58.163 33.333 0.00 0.00 0.00 2.87
4058 4311 8.074370 GTGGTCTGTGTTATTTAAAACTCTTCC 58.926 37.037 0.00 0.00 0.00 3.46
4059 4312 7.229907 TGGTCTGTGTTATTTAAAACTCTTCCC 59.770 37.037 0.00 0.00 0.00 3.97
4060 4313 7.295930 GTCTGTGTTATTTAAAACTCTTCCCG 58.704 38.462 0.00 0.00 0.00 5.14
4061 4314 6.993902 TCTGTGTTATTTAAAACTCTTCCCGT 59.006 34.615 0.00 0.00 0.00 5.28
4062 4315 7.172019 TCTGTGTTATTTAAAACTCTTCCCGTC 59.828 37.037 0.00 0.00 0.00 4.79
4063 4316 6.993902 TGTGTTATTTAAAACTCTTCCCGTCT 59.006 34.615 0.00 0.00 0.00 4.18
4064 4317 7.172019 TGTGTTATTTAAAACTCTTCCCGTCTC 59.828 37.037 0.00 0.00 0.00 3.36
4065 4318 7.172019 GTGTTATTTAAAACTCTTCCCGTCTCA 59.828 37.037 0.00 0.00 0.00 3.27
4066 4319 7.716123 TGTTATTTAAAACTCTTCCCGTCTCAA 59.284 33.333 0.00 0.00 0.00 3.02
4067 4320 8.727910 GTTATTTAAAACTCTTCCCGTCTCAAT 58.272 33.333 0.00 0.00 0.00 2.57
4068 4321 6.796705 TTTAAAACTCTTCCCGTCTCAATC 57.203 37.500 0.00 0.00 0.00 2.67
4069 4322 4.351874 AAAACTCTTCCCGTCTCAATCA 57.648 40.909 0.00 0.00 0.00 2.57
4070 4323 3.601443 AACTCTTCCCGTCTCAATCAG 57.399 47.619 0.00 0.00 0.00 2.90
4071 4324 2.808919 ACTCTTCCCGTCTCAATCAGA 58.191 47.619 0.00 0.00 0.00 3.27
4379 4688 4.776532 GTTCGATTTGATTCGACTGTTTCG 59.223 41.667 0.00 0.00 46.94 3.46
4413 4722 4.410099 TCCAGCCTCTGAACAATTTGATT 58.590 39.130 2.79 0.00 32.44 2.57
4610 4919 0.039326 ATTGAGCAAGCAGGCTTCCT 59.961 50.000 3.02 0.00 45.99 3.36
4786 5096 4.977741 TTTCGTAAAGCTTCGTCGAAAT 57.022 36.364 26.45 5.43 42.59 2.17
4908 5219 3.613910 GCTAATGCCCGTTGTGAACAAAT 60.614 43.478 0.00 0.00 37.63 2.32
4909 5220 2.437200 ATGCCCGTTGTGAACAAATG 57.563 45.000 0.00 0.00 37.63 2.32
4914 5225 3.499157 GCCCGTTGTGAACAAATGTAGTA 59.501 43.478 0.00 0.00 37.63 1.82
4938 5249 7.210618 ACTGTACTAGTAGAACATACCCTCT 57.789 40.000 1.87 0.00 38.04 3.69
4945 5256 4.647399 AGTAGAACATACCCTCTGCTCTTC 59.353 45.833 0.00 0.00 29.75 2.87
4952 5263 1.896465 ACCCTCTGCTCTTCTGTGTAC 59.104 52.381 0.00 0.00 0.00 2.90
4957 5268 4.262207 CCTCTGCTCTTCTGTGTACTTTCA 60.262 45.833 0.00 0.00 0.00 2.69
5001 5312 9.683069 CTCAGTTTAATTGTTCATACAAGCTTT 57.317 29.630 0.00 0.00 46.71 3.51
5116 5430 3.739810 GGTCGAACTTGTAGAACTTGGAC 59.260 47.826 0.00 0.80 0.00 4.02
5226 5540 1.444553 CGAACTCGTGGGAGCACTC 60.445 63.158 0.00 0.00 44.48 3.51
5233 5547 3.311110 TGGGAGCACTCGTCCACC 61.311 66.667 0.00 0.00 35.57 4.61
5296 5610 1.229984 CCTGTTCCTCCCCTTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
5572 5886 3.204827 TAGTCGTAGGGCGCGTCC 61.205 66.667 25.39 25.39 41.07 4.79
5641 5955 2.203788 AGGTTCTCCTCGCACCCA 60.204 61.111 0.00 0.00 40.58 4.51
5823 6137 3.437795 CTCGTACACGTCGGCCCT 61.438 66.667 0.00 0.00 40.80 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.515226 AGGTCACATAACATGTATACTTGTTTT 57.485 29.630 30.68 23.57 42.70 2.43
18 19 8.946085 CAGGTCACATAACATGTATACTTGTTT 58.054 33.333 30.68 19.96 42.70 2.83
19 20 7.552687 CCAGGTCACATAACATGTATACTTGTT 59.447 37.037 29.28 29.28 42.70 2.83
20 21 7.047891 CCAGGTCACATAACATGTATACTTGT 58.952 38.462 16.47 16.47 42.70 3.16
21 22 6.017934 GCCAGGTCACATAACATGTATACTTG 60.018 42.308 15.29 15.29 42.70 3.16
22 23 6.055588 GCCAGGTCACATAACATGTATACTT 58.944 40.000 0.00 0.00 42.70 2.24
23 24 5.130311 TGCCAGGTCACATAACATGTATACT 59.870 40.000 0.00 0.00 42.70 2.12
31 32 1.818060 GCAATGCCAGGTCACATAACA 59.182 47.619 0.00 0.00 0.00 2.41
34 35 2.512692 AAGCAATGCCAGGTCACATA 57.487 45.000 0.00 0.00 0.00 2.29
51 52 7.305820 GCATCATCGTAATGAATGAGCAAAAAG 60.306 37.037 0.00 0.00 44.85 2.27
56 57 3.184986 CGCATCATCGTAATGAATGAGCA 59.815 43.478 0.00 0.00 44.85 4.26
57 58 3.429881 TCGCATCATCGTAATGAATGAGC 59.570 43.478 0.00 0.00 44.85 4.26
65 66 0.671796 TCGGGTCGCATCATCGTAAT 59.328 50.000 0.00 0.00 0.00 1.89
67 68 0.030235 CTTCGGGTCGCATCATCGTA 59.970 55.000 0.00 0.00 0.00 3.43
73 74 1.935933 ATGTTACTTCGGGTCGCATC 58.064 50.000 0.00 0.00 0.00 3.91
78 79 4.325472 CAGTCGTAAATGTTACTTCGGGTC 59.675 45.833 0.00 0.00 0.00 4.46
99 100 2.358247 AACCCTGCGGCGTAACAG 60.358 61.111 9.37 7.43 0.00 3.16
105 108 4.473520 ATCTCCAACCCTGCGGCG 62.474 66.667 0.51 0.51 0.00 6.46
140 143 0.181350 GAACATGGATCGAAGGGCCT 59.819 55.000 0.00 0.00 0.00 5.19
143 146 2.988010 TGAGAACATGGATCGAAGGG 57.012 50.000 0.00 0.00 0.00 3.95
197 200 4.019681 ACCAATGGTTACAAGAAGATCGGA 60.020 41.667 0.00 0.00 27.29 4.55
200 203 5.175859 TCGACCAATGGTTACAAGAAGATC 58.824 41.667 6.30 0.00 35.25 2.75
213 216 2.892425 GGCGAGCTCGACCAATGG 60.892 66.667 38.74 8.52 42.67 3.16
239 242 2.225068 ACAATAGACATTCCTCCGCG 57.775 50.000 0.00 0.00 0.00 6.46
246 249 9.039870 CCTCATCTACAAGAACAATAGACATTC 57.960 37.037 0.00 0.00 0.00 2.67
250 253 6.341316 TGCCTCATCTACAAGAACAATAGAC 58.659 40.000 0.00 0.00 0.00 2.59
256 259 5.580691 CGTTAATGCCTCATCTACAAGAACA 59.419 40.000 0.00 0.00 0.00 3.18
280 283 6.152932 AGCAAATCATTACATCCCATTCAC 57.847 37.500 0.00 0.00 0.00 3.18
300 303 9.149225 CAATGTGGCAAAATAATACTAAAAGCA 57.851 29.630 0.00 0.00 0.00 3.91
310 313 7.243604 TCTCCTTTCAATGTGGCAAAATAAT 57.756 32.000 0.00 0.00 0.00 1.28
328 331 0.036022 GCAGCACTGAACCTCTCCTT 59.964 55.000 0.81 0.00 0.00 3.36
376 379 2.876091 TCCTCTGTCGAAATAGCAACG 58.124 47.619 0.00 0.00 0.00 4.10
387 390 2.159476 CCAACATTTGCATCCTCTGTCG 60.159 50.000 0.00 0.00 0.00 4.35
392 395 3.507233 TGTTCTCCAACATTTGCATCCTC 59.493 43.478 0.00 0.00 37.61 3.71
394 397 3.940209 TGTTCTCCAACATTTGCATCC 57.060 42.857 0.00 0.00 37.61 3.51
420 423 8.535335 AGTACATTCTAATCTCTGTCACAACAT 58.465 33.333 0.00 0.00 34.13 2.71
421 424 7.896811 AGTACATTCTAATCTCTGTCACAACA 58.103 34.615 0.00 0.00 0.00 3.33
422 425 8.764524 AAGTACATTCTAATCTCTGTCACAAC 57.235 34.615 0.00 0.00 0.00 3.32
423 426 9.208022 CAAAGTACATTCTAATCTCTGTCACAA 57.792 33.333 0.00 0.00 0.00 3.33
523 530 1.737793 CTGGTCGTGCTATTTTGGGAC 59.262 52.381 0.00 0.00 0.00 4.46
549 556 5.236282 CAGCATATGGTGAGTAAGGATCTG 58.764 45.833 27.06 6.42 45.66 2.90
566 590 8.995027 AAATTAACAGATGATTACCCAGCATA 57.005 30.769 0.00 0.00 0.00 3.14
621 645 2.086054 TTTTGTGTGGTTTGTGTGGC 57.914 45.000 0.00 0.00 0.00 5.01
622 646 3.118811 AGGATTTTGTGTGGTTTGTGTGG 60.119 43.478 0.00 0.00 0.00 4.17
624 648 4.817318 AAGGATTTTGTGTGGTTTGTGT 57.183 36.364 0.00 0.00 0.00 3.72
625 649 5.174395 TCAAAGGATTTTGTGTGGTTTGTG 58.826 37.500 0.56 0.00 43.33 3.33
626 650 5.413309 TCAAAGGATTTTGTGTGGTTTGT 57.587 34.783 0.56 0.00 43.33 2.83
627 651 4.270808 GCTCAAAGGATTTTGTGTGGTTTG 59.729 41.667 0.56 0.00 43.33 2.93
628 652 4.162131 AGCTCAAAGGATTTTGTGTGGTTT 59.838 37.500 0.56 0.00 43.33 3.27
629 653 3.706086 AGCTCAAAGGATTTTGTGTGGTT 59.294 39.130 0.56 0.00 43.33 3.67
630 654 3.068590 CAGCTCAAAGGATTTTGTGTGGT 59.931 43.478 0.00 0.00 43.33 4.16
631 655 3.068590 ACAGCTCAAAGGATTTTGTGTGG 59.931 43.478 0.00 0.00 43.33 4.17
632 656 4.311816 ACAGCTCAAAGGATTTTGTGTG 57.688 40.909 0.00 3.06 43.33 3.82
633 657 4.887071 TGTACAGCTCAAAGGATTTTGTGT 59.113 37.500 0.00 1.38 43.33 3.72
638 662 5.536161 ACACATTGTACAGCTCAAAGGATTT 59.464 36.000 0.00 0.00 40.26 2.17
641 665 3.814842 CACACATTGTACAGCTCAAAGGA 59.185 43.478 0.00 0.00 0.00 3.36
642 666 3.814842 TCACACATTGTACAGCTCAAAGG 59.185 43.478 0.00 0.00 0.00 3.11
754 782 5.650543 CAAGTTTGACAGGCTACACTTTTT 58.349 37.500 0.00 0.00 0.00 1.94
759 787 1.946768 TGCAAGTTTGACAGGCTACAC 59.053 47.619 0.00 0.00 0.00 2.90
760 788 2.340210 TGCAAGTTTGACAGGCTACA 57.660 45.000 0.00 0.00 0.00 2.74
822 855 3.526534 GGAAACGGATTTCTCTCTCAGG 58.473 50.000 0.23 0.00 43.33 3.86
876 914 2.190578 CCGCTCCATGAAGGGTCC 59.809 66.667 0.00 0.00 38.24 4.46
885 935 4.096003 CCCGTGTTCCCGCTCCAT 62.096 66.667 0.00 0.00 0.00 3.41
976 1026 3.971702 GGCCTGCCCTCTGTTGGT 61.972 66.667 0.00 0.00 0.00 3.67
1057 1118 0.930726 GGAGGGAGGAGAGAGGAGAA 59.069 60.000 0.00 0.00 0.00 2.87
1058 1119 0.047176 AGGAGGGAGGAGAGAGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
1060 1121 0.996762 GGAGGAGGGAGGAGAGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1062 1123 0.998945 AGGGAGGAGGGAGGAGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
1063 1124 0.996762 GAGGGAGGAGGGAGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
1188 1257 0.806868 CGGCACTCACGTAGGTCTTA 59.193 55.000 0.00 0.00 0.00 2.10
1335 1406 1.148048 GGCAGATTCCCCAGAGAGC 59.852 63.158 0.00 0.00 0.00 4.09
1352 1423 2.009774 CAAATCCACAGAAGGCTACGG 58.990 52.381 0.00 0.00 0.00 4.02
1356 1430 2.242043 CCAACAAATCCACAGAAGGCT 58.758 47.619 0.00 0.00 0.00 4.58
1395 1470 3.452627 AGCCCGAGACTAGATCACAAATT 59.547 43.478 0.00 0.00 0.00 1.82
1439 1514 0.109723 AAAACCCTAAGCTGACCGCA 59.890 50.000 0.00 0.00 42.61 5.69
1467 1543 0.326618 CCCTAAGCTTCCCCAGAGGA 60.327 60.000 11.56 0.00 45.68 3.71
1468 1544 0.621862 ACCCTAAGCTTCCCCAGAGG 60.622 60.000 0.00 2.47 0.00 3.69
1479 1555 0.815615 CCCGCATCAAGACCCTAAGC 60.816 60.000 0.00 0.00 0.00 3.09
1487 1661 4.812476 CCGTCGCCCGCATCAAGA 62.812 66.667 0.00 0.00 34.38 3.02
1530 1704 1.234615 TTCCGCCGCAGAAAAAGAGG 61.235 55.000 0.00 0.00 0.00 3.69
1557 1731 3.034635 AGACTCCACATCTCGCCTAAAT 58.965 45.455 0.00 0.00 0.00 1.40
1561 1735 1.066573 CAAAGACTCCACATCTCGCCT 60.067 52.381 0.00 0.00 0.00 5.52
1579 1756 3.626930 AGTGTGCAGAAACCCTAAACAA 58.373 40.909 0.00 0.00 0.00 2.83
1581 1758 4.359706 CAAAGTGTGCAGAAACCCTAAAC 58.640 43.478 0.00 0.00 0.00 2.01
1596 1773 1.802960 CAGCGAGAATCAGCAAAGTGT 59.197 47.619 3.83 0.00 37.16 3.55
1599 1776 1.085091 AGCAGCGAGAATCAGCAAAG 58.915 50.000 3.83 0.00 37.16 2.77
1612 1790 1.661509 TCAAGTGTCGACAGCAGCG 60.662 57.895 20.73 6.28 0.00 5.18
1621 1799 1.071471 AAGCCCCTGTCAAGTGTCG 59.929 57.895 0.00 0.00 0.00 4.35
1727 1905 5.530915 CCAAACCAACAAACAGACTATCAGA 59.469 40.000 0.00 0.00 0.00 3.27
1728 1906 5.762045 CCAAACCAACAAACAGACTATCAG 58.238 41.667 0.00 0.00 0.00 2.90
1731 1909 4.215109 AGCCAAACCAACAAACAGACTAT 58.785 39.130 0.00 0.00 0.00 2.12
1734 1912 2.427095 AGAGCCAAACCAACAAACAGAC 59.573 45.455 0.00 0.00 0.00 3.51
1879 2057 8.728833 ACTAACTACACACACTATCTTCAGTAC 58.271 37.037 0.00 0.00 0.00 2.73
1906 2084 7.923414 AAATTCTGAACCACTTACCATACTC 57.077 36.000 0.00 0.00 0.00 2.59
1951 2129 4.085004 GCTAGTCGAGTCTGTCAAAAACAC 60.085 45.833 0.00 0.00 33.24 3.32
1952 2130 4.049186 GCTAGTCGAGTCTGTCAAAAACA 58.951 43.478 0.00 0.00 36.18 2.83
1954 2132 4.316205 TGCTAGTCGAGTCTGTCAAAAA 57.684 40.909 0.00 0.00 0.00 1.94
1968 2146 4.503741 TCAAACAAATGCCTTGCTAGTC 57.496 40.909 0.00 0.00 38.75 2.59
2341 2523 4.701956 ATGCATGCTAAACCACAACTAC 57.298 40.909 20.33 0.00 0.00 2.73
2550 2732 6.265196 ACCACAAACTGCAAGATGAAAAGATA 59.735 34.615 0.00 0.00 37.43 1.98
2558 2740 2.361757 TCCAACCACAAACTGCAAGATG 59.638 45.455 0.00 0.00 37.43 2.90
2756 2938 7.158697 TGGCATATAACACATCCTACATGTAC 58.841 38.462 0.08 0.00 0.00 2.90
2798 2980 6.661805 TCCACTCCTCAGTTTACAAAGTTTTT 59.338 34.615 0.00 0.00 0.00 1.94
2844 3026 9.599322 GATTCAACATGTTCTTAGTTAACACTG 57.401 33.333 8.48 0.00 39.51 3.66
2846 3028 9.813080 GAGATTCAACATGTTCTTAGTTAACAC 57.187 33.333 8.48 0.00 39.51 3.32
2847 3029 9.778741 AGAGATTCAACATGTTCTTAGTTAACA 57.221 29.630 8.48 0.00 40.85 2.41
2930 3182 1.004044 ACTCCCACCTTCTGCATTCTG 59.996 52.381 0.00 0.00 0.00 3.02
3044 3297 5.370880 AGGATAACAATTCTGGGTAGCATCT 59.629 40.000 0.00 0.00 0.00 2.90
3082 3335 4.128925 TCCACAGTGAGAATGATAGTGC 57.871 45.455 0.62 0.00 0.00 4.40
3369 3622 7.639113 ACCTGTGAATAGTTGTTCAGAAAAA 57.361 32.000 0.00 0.00 38.68 1.94
3376 3629 5.706916 TCGACTACCTGTGAATAGTTGTTC 58.293 41.667 0.00 0.00 35.23 3.18
3451 3704 2.809696 GCCGTAGCAAAGAACACCTTTA 59.190 45.455 0.00 0.00 42.88 1.85
3460 3713 1.612442 AGGAGGGCCGTAGCAAAGA 60.612 57.895 0.00 0.00 42.56 2.52
3472 3725 3.933048 CTTGCCAGTGCCAGGAGGG 62.933 68.421 0.00 0.00 40.85 4.30
3535 3788 4.545208 TTCACTTCCAATCACACGGATA 57.455 40.909 0.00 0.00 34.28 2.59
3544 3797 5.467035 TTTGGACCAATTCACTTCCAATC 57.533 39.130 7.99 0.00 45.40 2.67
3550 3803 6.976934 ACATACTTTTGGACCAATTCACTT 57.023 33.333 7.99 0.00 0.00 3.16
3559 3812 3.506067 CCTCACCAACATACTTTTGGACC 59.494 47.826 8.10 0.00 45.69 4.46
3565 3818 2.108250 AGCACCCTCACCAACATACTTT 59.892 45.455 0.00 0.00 0.00 2.66
3583 3836 2.868964 ACTCCCTAACCATCCTAGCA 57.131 50.000 0.00 0.00 0.00 3.49
3587 3840 5.132816 CCTGAAATAACTCCCTAACCATCCT 59.867 44.000 0.00 0.00 0.00 3.24
3640 3893 8.607713 TGAATAAACCAGATTAAACCCTGTAGA 58.392 33.333 0.00 0.00 0.00 2.59
3652 3905 9.696917 GAACATTGAAGTTGAATAAACCAGATT 57.303 29.630 0.00 0.00 39.85 2.40
3666 3919 8.958119 TGTTACTAAGACAGAACATTGAAGTT 57.042 30.769 0.00 0.00 0.00 2.66
3671 3924 8.018677 ACGATTGTTACTAAGACAGAACATTG 57.981 34.615 0.00 0.00 32.19 2.82
3711 3964 2.099756 GGGCCATCTGACAAGCAATAAC 59.900 50.000 4.39 0.00 0.00 1.89
3860 4113 2.106844 GCCCCTAGCATCAAAACCG 58.893 57.895 0.00 0.00 42.97 4.44
3878 4131 4.037208 GTGGCCATGAGAACCTTGATATTG 59.963 45.833 9.72 0.00 0.00 1.90
3914 4167 0.889186 ATGCGCACGAAAGGAAAGGT 60.889 50.000 14.90 0.00 0.00 3.50
3942 4195 3.151554 GAGCATCATGCCATATTGGACA 58.848 45.455 5.84 0.00 46.52 4.02
4015 4268 7.173907 CACAGACCACTGAAGTTTCTTAATCAT 59.826 37.037 0.00 0.00 46.03 2.45
4016 4269 6.483307 CACAGACCACTGAAGTTTCTTAATCA 59.517 38.462 0.00 0.00 46.03 2.57
4017 4270 6.483640 ACACAGACCACTGAAGTTTCTTAATC 59.516 38.462 0.00 0.00 46.03 1.75
4018 4271 6.357367 ACACAGACCACTGAAGTTTCTTAAT 58.643 36.000 0.00 0.00 46.03 1.40
4019 4272 5.741011 ACACAGACCACTGAAGTTTCTTAA 58.259 37.500 0.00 0.00 46.03 1.85
4020 4273 5.353394 ACACAGACCACTGAAGTTTCTTA 57.647 39.130 0.00 0.00 46.03 2.10
4021 4274 4.222124 ACACAGACCACTGAAGTTTCTT 57.778 40.909 0.00 0.00 46.03 2.52
4022 4275 3.914426 ACACAGACCACTGAAGTTTCT 57.086 42.857 0.00 0.00 46.03 2.52
4023 4276 6.619801 AATAACACAGACCACTGAAGTTTC 57.380 37.500 13.76 0.00 46.03 2.78
4024 4277 8.514330 TTAAATAACACAGACCACTGAAGTTT 57.486 30.769 13.76 6.91 46.03 2.66
4025 4278 8.514330 TTTAAATAACACAGACCACTGAAGTT 57.486 30.769 0.00 0.00 46.03 2.66
4026 4279 8.403236 GTTTTAAATAACACAGACCACTGAAGT 58.597 33.333 0.00 0.00 46.03 3.01
4027 4280 8.621286 AGTTTTAAATAACACAGACCACTGAAG 58.379 33.333 0.00 0.00 46.03 3.02
4028 4281 8.514330 AGTTTTAAATAACACAGACCACTGAA 57.486 30.769 0.00 0.00 46.03 3.02
4029 4282 7.990886 AGAGTTTTAAATAACACAGACCACTGA 59.009 33.333 0.00 0.00 46.03 3.41
4031 4284 8.747538 AAGAGTTTTAAATAACACAGACCACT 57.252 30.769 0.00 0.00 0.00 4.00
4032 4285 8.074370 GGAAGAGTTTTAAATAACACAGACCAC 58.926 37.037 0.00 0.00 0.00 4.16
4033 4286 7.229907 GGGAAGAGTTTTAAATAACACAGACCA 59.770 37.037 0.00 0.00 0.00 4.02
4034 4287 7.572539 CGGGAAGAGTTTTAAATAACACAGACC 60.573 40.741 0.00 0.00 0.00 3.85
4035 4288 7.041576 ACGGGAAGAGTTTTAAATAACACAGAC 60.042 37.037 0.00 0.00 0.00 3.51
4036 4289 6.993902 ACGGGAAGAGTTTTAAATAACACAGA 59.006 34.615 0.00 0.00 0.00 3.41
4037 4290 7.172703 AGACGGGAAGAGTTTTAAATAACACAG 59.827 37.037 0.00 0.00 0.00 3.66
4038 4291 6.993902 AGACGGGAAGAGTTTTAAATAACACA 59.006 34.615 0.00 0.00 0.00 3.72
4039 4292 7.172019 TGAGACGGGAAGAGTTTTAAATAACAC 59.828 37.037 0.00 0.00 0.00 3.32
4040 4293 7.218614 TGAGACGGGAAGAGTTTTAAATAACA 58.781 34.615 0.00 0.00 0.00 2.41
4041 4294 7.662604 TGAGACGGGAAGAGTTTTAAATAAC 57.337 36.000 0.00 0.00 0.00 1.89
4042 4295 8.857694 ATTGAGACGGGAAGAGTTTTAAATAA 57.142 30.769 0.00 0.00 0.00 1.40
4043 4296 8.098286 TGATTGAGACGGGAAGAGTTTTAAATA 58.902 33.333 0.00 0.00 0.00 1.40
4044 4297 6.940298 TGATTGAGACGGGAAGAGTTTTAAAT 59.060 34.615 0.00 0.00 0.00 1.40
4045 4298 6.292923 TGATTGAGACGGGAAGAGTTTTAAA 58.707 36.000 0.00 0.00 0.00 1.52
4046 4299 5.860611 TGATTGAGACGGGAAGAGTTTTAA 58.139 37.500 0.00 0.00 0.00 1.52
4047 4300 5.245301 TCTGATTGAGACGGGAAGAGTTTTA 59.755 40.000 0.00 0.00 0.00 1.52
4048 4301 4.040461 TCTGATTGAGACGGGAAGAGTTTT 59.960 41.667 0.00 0.00 0.00 2.43
4049 4302 3.578716 TCTGATTGAGACGGGAAGAGTTT 59.421 43.478 0.00 0.00 0.00 2.66
4050 4303 3.165875 TCTGATTGAGACGGGAAGAGTT 58.834 45.455 0.00 0.00 0.00 3.01
4051 4304 2.808919 TCTGATTGAGACGGGAAGAGT 58.191 47.619 0.00 0.00 0.00 3.24
4052 4305 3.876274 TTCTGATTGAGACGGGAAGAG 57.124 47.619 0.00 0.00 0.00 2.85
4053 4306 4.826274 ATTTCTGATTGAGACGGGAAGA 57.174 40.909 0.00 0.00 0.00 2.87
4054 4307 6.985188 TTAATTTCTGATTGAGACGGGAAG 57.015 37.500 0.00 0.00 0.00 3.46
4055 4308 7.628366 GCAATTAATTTCTGATTGAGACGGGAA 60.628 37.037 0.00 0.00 33.67 3.97
4056 4309 6.183360 GCAATTAATTTCTGATTGAGACGGGA 60.183 38.462 0.00 0.00 33.67 5.14
4057 4310 5.973565 GCAATTAATTTCTGATTGAGACGGG 59.026 40.000 0.00 0.00 33.67 5.28
4058 4311 6.554419 TGCAATTAATTTCTGATTGAGACGG 58.446 36.000 0.00 0.00 33.67 4.79
4059 4312 6.195983 GCTGCAATTAATTTCTGATTGAGACG 59.804 38.462 8.50 0.00 33.67 4.18
4060 4313 7.256286 AGCTGCAATTAATTTCTGATTGAGAC 58.744 34.615 1.02 0.00 33.67 3.36
4061 4314 7.400599 AGCTGCAATTAATTTCTGATTGAGA 57.599 32.000 1.02 0.00 33.67 3.27
4062 4315 9.577110 TTTAGCTGCAATTAATTTCTGATTGAG 57.423 29.630 1.02 0.00 33.67 3.02
4063 4316 9.926158 TTTTAGCTGCAATTAATTTCTGATTGA 57.074 25.926 1.02 0.00 33.67 2.57
4064 4317 9.962759 GTTTTAGCTGCAATTAATTTCTGATTG 57.037 29.630 1.02 0.00 34.67 2.67
4065 4318 9.709495 TGTTTTAGCTGCAATTAATTTCTGATT 57.291 25.926 1.02 0.25 0.00 2.57
4066 4319 9.880157 ATGTTTTAGCTGCAATTAATTTCTGAT 57.120 25.926 1.02 5.12 0.00 2.90
4067 4320 9.357652 GATGTTTTAGCTGCAATTAATTTCTGA 57.642 29.630 1.02 0.00 0.00 3.27
4068 4321 9.142515 TGATGTTTTAGCTGCAATTAATTTCTG 57.857 29.630 1.02 0.00 0.00 3.02
4069 4322 9.880157 ATGATGTTTTAGCTGCAATTAATTTCT 57.120 25.926 1.02 0.00 0.00 2.52
4070 4323 9.910511 CATGATGTTTTAGCTGCAATTAATTTC 57.089 29.630 1.02 0.00 0.00 2.17
4071 4324 8.885722 CCATGATGTTTTAGCTGCAATTAATTT 58.114 29.630 1.02 0.00 0.00 1.82
4379 4688 2.823758 GGCTGGATCCTAGGTGCCC 61.824 68.421 14.23 9.07 34.81 5.36
4387 4696 1.661463 TTGTTCAGAGGCTGGATCCT 58.339 50.000 14.23 0.00 39.67 3.24
4413 4722 4.873259 TGAAACAACAAATCAGACAGTCGA 59.127 37.500 0.00 0.00 0.00 4.20
4610 4919 3.999001 TGCAAACATGCACAGAAACAAAA 59.001 34.783 0.00 0.00 40.23 2.44
4769 5079 5.758570 ACTGTATTTCGACGAAGCTTTAC 57.241 39.130 10.61 11.34 0.00 2.01
4786 5096 1.871039 GCGGACAAGCTGAAAACTGTA 59.129 47.619 0.00 0.00 0.00 2.74
4887 5198 3.634568 TTTGTTCACAACGGGCATTAG 57.365 42.857 0.00 0.00 35.28 1.73
4908 5219 9.823647 GGTATGTTCTACTAGTACAGTACTACA 57.176 37.037 15.43 13.65 40.14 2.74
4909 5220 9.267084 GGGTATGTTCTACTAGTACAGTACTAC 57.733 40.741 15.43 8.82 40.14 2.73
4914 5225 7.055378 CAGAGGGTATGTTCTACTAGTACAGT 58.945 42.308 0.00 0.00 41.62 3.55
4938 5249 4.202357 ACCATGAAAGTACACAGAAGAGCA 60.202 41.667 0.00 0.00 0.00 4.26
4945 5256 7.117812 ACGAAAGATAACCATGAAAGTACACAG 59.882 37.037 0.00 0.00 0.00 3.66
4952 5263 7.011389 TGAGCATACGAAAGATAACCATGAAAG 59.989 37.037 0.00 0.00 0.00 2.62
4957 5268 5.918608 ACTGAGCATACGAAAGATAACCAT 58.081 37.500 0.00 0.00 0.00 3.55
5075 5389 1.450025 CCCTAGTTGTTTCGCCCTTC 58.550 55.000 0.00 0.00 0.00 3.46
5078 5392 0.675837 GACCCCTAGTTGTTTCGCCC 60.676 60.000 0.00 0.00 0.00 6.13
5128 5442 4.385825 TCAAATACTTCAACTTCACCGCT 58.614 39.130 0.00 0.00 0.00 5.52
5296 5610 2.607750 GAGTGGCTGAGGGTGGGA 60.608 66.667 0.00 0.00 0.00 4.37
5416 5730 2.792947 CGGGAGGGGGTACATGTCG 61.793 68.421 0.00 0.00 0.00 4.35
5464 5778 1.038280 GGGAGGACATGTACTACGGG 58.962 60.000 14.46 0.00 0.00 5.28
5517 5831 1.447643 GACATCCTGATCCGGGTGG 59.552 63.158 19.39 5.03 0.00 4.61
5520 5834 1.364171 GACGACATCCTGATCCGGG 59.636 63.158 0.00 0.00 0.00 5.73
5590 5904 2.954753 GCACACCTTCTTCACCGCG 61.955 63.158 0.00 0.00 0.00 6.46
5692 6006 1.153823 CTACAAGGACGACCAGCGG 60.154 63.158 6.71 0.00 46.49 5.52
5767 6081 3.121030 GTGTACGGGCTGCAGCTG 61.121 66.667 35.82 29.16 41.70 4.24


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

AutoCloner maintained by Alex Coulton.