Multiple sequence alignment - TraesCS5D01G135900

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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 TraesCS5D01G135900 chr5D 100.000 6659 0 0 1 6659 216382550 216389208 0.000000e+00 12297.0
1 TraesCS5D01G135900 chr5A 95.564 5884 183 40 167 6003 285996929 286002781 0.000000e+00 9348.0
2 TraesCS5D01G135900 chr5A 94.988 419 17 3 6021 6436 286002766 286003183 0.000000e+00 654.0
3 TraesCS5D01G135900 chr5A 92.982 228 15 1 6433 6659 286012787 286013014 1.380000e-86 331.0
4 TraesCS5D01G135900 chr5A 83.486 109 15 1 1 106 285996822 285996930 1.530000e-16 99.0
5 TraesCS5D01G135900 chr5A 85.507 69 9 1 6569 6637 37406830 37406897 3.330000e-08 71.3
6 TraesCS5D01G135900 chr5B 95.238 4200 152 22 607 4783 232556127 232560301 0.000000e+00 6604.0
7 TraesCS5D01G135900 chr5B 96.975 1223 35 2 4780 6001 232560423 232561644 0.000000e+00 2052.0
8 TraesCS5D01G135900 chr5B 95.041 484 21 2 6021 6501 232561631 232562114 0.000000e+00 758.0
9 TraesCS5D01G135900 chr5B 93.587 421 20 6 153 569 232555405 232555822 7.330000e-174 621.0
10 TraesCS5D01G135900 chr5B 93.642 173 11 0 6487 6659 232576593 232576765 6.620000e-65 259.0
11 TraesCS5D01G135900 chr5B 85.507 69 9 1 6569 6637 48142322 48142255 3.330000e-08 71.3
12 TraesCS5D01G135900 chr3A 81.597 576 56 16 1103 1655 692347255 692347803 1.330000e-116 431.0
13 TraesCS5D01G135900 chr3A 94.286 35 2 0 5048 5082 632608538 632608572 3.000000e-03 54.7
14 TraesCS5D01G135900 chr3A 94.118 34 2 0 5070 5103 689106865 689106898 1.200000e-02 52.8
15 TraesCS5D01G135900 chr1B 79.248 718 72 42 979 1671 547701650 547702315 4.770000e-116 429.0
16 TraesCS5D01G135900 chr1B 95.000 40 2 0 133 172 608052515 608052476 5.570000e-06 63.9
17 TraesCS5D01G135900 chr1D 77.997 709 79 34 988 1667 407296214 407296874 2.270000e-99 374.0
18 TraesCS5D01G135900 chr3B 79.271 521 58 22 1174 1671 658558488 658557995 1.080000e-82 318.0
19 TraesCS5D01G135900 chr3B 94.118 34 2 0 139 172 8054739 8054772 1.200000e-02 52.8
20 TraesCS5D01G135900 chr7D 91.304 46 4 0 127 172 514383438 514383483 5.570000e-06 63.9
21 TraesCS5D01G135900 chr7D 94.737 38 0 2 5039 5075 465577023 465576987 2.590000e-04 58.4
22 TraesCS5D01G135900 chr2B 95.000 40 2 0 133 172 37716835 37716796 5.570000e-06 63.9
23 TraesCS5D01G135900 chrUn 94.737 38 1 1 5042 5078 353978643 353978680 2.590000e-04 58.4
24 TraesCS5D01G135900 chrUn 94.737 38 1 1 5042 5078 367854687 367854650 2.590000e-04 58.4
25 TraesCS5D01G135900 chr4D 100.000 31 0 0 5047 5077 116152450 116152480 2.590000e-04 58.4
26 TraesCS5D01G135900 chr4D 100.000 30 0 0 5046 5075 32941724 32941753 1.000000e-03 56.5
27 TraesCS5D01G135900 chr4B 100.000 31 0 0 5050 5080 576197130 576197160 2.590000e-04 58.4
28 TraesCS5D01G135900 chr2A 100.000 30 0 0 139 168 68245807 68245778 1.000000e-03 56.5
29 TraesCS5D01G135900 chr6D 96.875 32 1 0 99 130 316428588 316428557 3.000000e-03 54.7


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 TraesCS5D01G135900 chr5D 216382550 216389208 6658 False 12297.00 12297 100.00000 1 6659 1 chr5D.!!$F1 6658
1 TraesCS5D01G135900 chr5A 285996822 286003183 6361 False 3367.00 9348 91.34600 1 6436 3 chr5A.!!$F3 6435
2 TraesCS5D01G135900 chr5B 232555405 232562114 6709 False 2508.75 6604 95.21025 153 6501 4 chr5B.!!$F2 6348
3 TraesCS5D01G135900 chr3A 692347255 692347803 548 False 431.00 431 81.59700 1103 1655 1 chr3A.!!$F3 552
4 TraesCS5D01G135900 chr1B 547701650 547702315 665 False 429.00 429 79.24800 979 1671 1 chr1B.!!$F1 692
5 TraesCS5D01G135900 chr1D 407296214 407296874 660 False 374.00 374 77.99700 988 1667 1 chr1D.!!$F1 679

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
405 410 0.163788 CGCTACTTGCAACACCGAAG 59.836 55.000 0.00 0.0 43.06 3.79 F
2083 2448 0.248458 CAAACAAGGACGTGGTGCAC 60.248 55.000 8.80 8.8 0.00 4.57 F
3107 3473 1.602416 CGTGATGCAACCATTGTGCAA 60.602 47.619 6.09 0.0 42.12 4.08 F
4246 4613 1.070914 TGGCAGGTTGATGTTGACGTA 59.929 47.619 0.00 0.0 0.00 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2544 1.127567 CCTGTCAGGACCTGGTGGAA 61.128 60.0 21.56 0.0 37.67 3.53 R
4066 4432 1.035932 AAGCATGGACCAGCATCAGC 61.036 55.0 15.46 6.3 42.56 4.26 R
4313 4680 0.652592 GCTACACAAGCGGCATACAG 59.347 55.0 1.45 0.0 42.53 2.74 R
6019 6513 0.036294 GCCAACGCTAGAAGTTCCCT 60.036 55.0 0.00 0.0 0.00 4.20 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
119 123 9.986157 ATATAATATACTACTCCCTCCGTTTCA 57.014 33.333 0.00 0.00 0.00 2.69
120 124 8.896722 ATAATATACTACTCCCTCCGTTTCAT 57.103 34.615 0.00 0.00 0.00 2.57
121 125 9.986157 ATAATATACTACTCCCTCCGTTTCATA 57.014 33.333 0.00 0.00 0.00 2.15
122 126 8.896722 AATATACTACTCCCTCCGTTTCATAT 57.103 34.615 0.00 0.00 0.00 1.78
123 127 8.896722 ATATACTACTCCCTCCGTTTCATATT 57.103 34.615 0.00 0.00 0.00 1.28
124 128 9.986157 ATATACTACTCCCTCCGTTTCATATTA 57.014 33.333 0.00 0.00 0.00 0.98
125 129 6.402456 ACTACTCCCTCCGTTTCATATTAC 57.598 41.667 0.00 0.00 0.00 1.89
126 130 6.134754 ACTACTCCCTCCGTTTCATATTACT 58.865 40.000 0.00 0.00 0.00 2.24
127 131 5.952347 ACTCCCTCCGTTTCATATTACTT 57.048 39.130 0.00 0.00 0.00 2.24
128 132 7.781693 ACTACTCCCTCCGTTTCATATTACTTA 59.218 37.037 0.00 0.00 0.00 2.24
129 133 7.613551 ACTCCCTCCGTTTCATATTACTTAT 57.386 36.000 0.00 0.00 0.00 1.73
130 134 8.716674 ACTCCCTCCGTTTCATATTACTTATA 57.283 34.615 0.00 0.00 0.00 0.98
131 135 9.322769 ACTCCCTCCGTTTCATATTACTTATAT 57.677 33.333 0.00 0.00 0.00 0.86
260 264 1.211212 TCCAGAATCATCACCCAGCTG 59.789 52.381 6.78 6.78 0.00 4.24
400 405 1.207593 CTGCCGCTACTTGCAACAC 59.792 57.895 0.00 0.00 43.06 3.32
405 410 0.163788 CGCTACTTGCAACACCGAAG 59.836 55.000 0.00 0.00 43.06 3.79
536 552 9.649167 GCAACTTTTTACTACTACCTCATCTAA 57.351 33.333 0.00 0.00 0.00 2.10
628 910 1.736645 GGTGTCGTCATCCGTGTGG 60.737 63.158 0.00 0.00 37.94 4.17
629 911 1.006571 GTGTCGTCATCCGTGTGGT 60.007 57.895 0.00 0.00 37.94 4.16
630 912 1.006688 TGTCGTCATCCGTGTGGTG 60.007 57.895 0.00 0.00 37.94 4.17
631 913 1.006571 GTCGTCATCCGTGTGGTGT 60.007 57.895 0.00 0.00 37.94 4.16
688 970 2.281692 TGCAGCCGTTGATGTGCT 60.282 55.556 0.00 0.00 36.84 4.40
759 1043 2.042333 TGCGAGGGGGCTAGCTAA 60.042 61.111 15.72 0.00 0.00 3.09
763 1047 1.749334 CGAGGGGGCTAGCTAACCTG 61.749 65.000 23.55 14.63 0.00 4.00
916 1208 1.230314 CTTTTCTCCCCCTCCCCCT 60.230 63.158 0.00 0.00 0.00 4.79
917 1209 1.230182 TTTTCTCCCCCTCCCCCTC 60.230 63.158 0.00 0.00 0.00 4.30
918 1210 2.800523 TTTTCTCCCCCTCCCCCTCC 62.801 65.000 0.00 0.00 0.00 4.30
952 1244 0.535553 GCCTACCAACACCAAACCGA 60.536 55.000 0.00 0.00 0.00 4.69
1170 1473 0.392595 GAACCCGGTCCTGTGATTCC 60.393 60.000 0.00 0.00 0.00 3.01
1367 1696 1.961277 CGCTGCGGTTCCACTTTCT 60.961 57.895 15.40 0.00 0.00 2.52
1442 1787 1.425412 GTTTCGGTTCTGCGAGCTAA 58.575 50.000 0.00 0.00 0.00 3.09
1451 1796 1.146637 CTGCGAGCTAATCATCTGCC 58.853 55.000 0.00 0.00 0.00 4.85
1569 1919 7.779754 AGATGAGTATGCATTCTATCTCACT 57.220 36.000 3.54 0.00 35.32 3.41
1635 1997 5.061179 TGGATATGATTGTGATGTGCTCTG 58.939 41.667 0.00 0.00 0.00 3.35
1645 2007 8.962884 ATTGTGATGTGCTCTGTATTGTTATA 57.037 30.769 0.00 0.00 0.00 0.98
1680 2042 8.506083 AGAATAGTTCCAAATATCCCTGTTCAT 58.494 33.333 0.00 0.00 0.00 2.57
1720 2083 6.332630 AGCCTGTTACATATTTGCATTGTTC 58.667 36.000 0.00 0.00 0.00 3.18
1732 2095 2.292845 TGCATTGTTCGCACTGAATTCA 59.707 40.909 8.12 8.12 39.21 2.57
1752 2115 3.947196 TCAGTGCATGGATGTGGAAATAC 59.053 43.478 0.00 0.00 0.00 1.89
1808 2171 5.738619 TGTTAGGAGCAGTAGAATGAACA 57.261 39.130 0.00 0.00 0.00 3.18
1814 2177 5.413833 AGGAGCAGTAGAATGAACACAATTG 59.586 40.000 3.24 3.24 0.00 2.32
1908 2272 5.298276 TGCACTTCCGTTTCTTTCTTGTAAT 59.702 36.000 0.00 0.00 0.00 1.89
2083 2448 0.248458 CAAACAAGGACGTGGTGCAC 60.248 55.000 8.80 8.80 0.00 4.57
2179 2544 2.101582 AGCTGCCTCGTTAAGAATCGAT 59.898 45.455 0.00 0.00 35.57 3.59
2220 2585 4.756135 GGATTTGTGCACCATTGAAAACAT 59.244 37.500 15.69 0.00 0.00 2.71
2356 2722 5.578776 CCTGCCGTGTTTTTAGATAAATCC 58.421 41.667 0.00 0.00 0.00 3.01
2406 2772 9.586435 GCTTTAATTAATTGTCTGTATTGGCTT 57.414 29.630 11.05 0.00 0.00 4.35
2768 3134 8.593679 TCACTGTACAATTTATTCTTCTGAGGA 58.406 33.333 0.00 0.00 0.00 3.71
2801 3167 5.150715 AGCAATATGGTCCTAGACATCAGA 58.849 41.667 0.00 0.00 33.68 3.27
2889 3255 7.160049 AGAGATGCCAACATTCTGATATACTG 58.840 38.462 0.00 0.00 36.35 2.74
2958 3324 6.128742 GCATTTTTGTTCTTCTTACATGCTGG 60.129 38.462 0.00 0.00 29.60 4.85
2979 3345 6.473455 GCTGGCATTCTATTATTTGAACACAC 59.527 38.462 0.00 0.00 0.00 3.82
3107 3473 1.602416 CGTGATGCAACCATTGTGCAA 60.602 47.619 6.09 0.00 42.12 4.08
3175 3541 2.920076 TTATTGTGCCGGGGATGCCC 62.920 60.000 13.41 13.41 44.51 5.36
3437 3803 6.371271 AGCATTTAGTTGTTTGTTTGCACTTT 59.629 30.769 0.00 0.00 0.00 2.66
3645 4011 7.391148 TTTTACTGACTTTATGGAAGGATGC 57.609 36.000 0.00 0.00 39.79 3.91
3889 4255 9.573133 AATTCAAGTTCTTCAGTTGTGTTTTAG 57.427 29.630 0.00 0.00 37.15 1.85
3916 4282 5.957842 TGGTGTTTGGTAGCTTTAGATTG 57.042 39.130 0.00 0.00 0.00 2.67
3923 4289 7.065324 TGTTTGGTAGCTTTAGATTGGTTATCG 59.935 37.037 0.00 0.00 38.36 2.92
3929 4295 7.681939 AGCTTTAGATTGGTTATCGTTTTGA 57.318 32.000 0.00 0.00 38.36 2.69
4066 4432 8.199928 GATGTTCTCATCCTGCTAATTCAGCG 62.200 46.154 0.00 0.00 46.65 5.18
4115 4482 6.012858 AGGCATATTTTCGTTATAGGGATGGA 60.013 38.462 0.00 0.00 0.00 3.41
4118 4485 8.398665 GCATATTTTCGTTATAGGGATGGATTC 58.601 37.037 0.00 0.00 0.00 2.52
4246 4613 1.070914 TGGCAGGTTGATGTTGACGTA 59.929 47.619 0.00 0.00 0.00 3.57
4426 4793 3.614630 GCACATGCATGGTATTGTGTGTT 60.615 43.478 29.41 1.84 41.14 3.32
4430 4797 2.954989 TGCATGGTATTGTGTGTTGTGT 59.045 40.909 0.00 0.00 0.00 3.72
4450 4817 1.341285 TGCTATTCCTGCACATTGGCT 60.341 47.619 0.00 0.00 35.31 4.75
4571 4938 5.479306 AGCACTATTCGTACACATTTGACT 58.521 37.500 0.00 0.00 0.00 3.41
4576 4943 8.373256 CACTATTCGTACACATTTGACTAACTG 58.627 37.037 0.00 0.00 0.00 3.16
4578 4945 7.582435 ATTCGTACACATTTGACTAACTGAG 57.418 36.000 0.00 0.00 0.00 3.35
4627 4994 7.151999 TGCCAAAACTAATATTCACGTGATT 57.848 32.000 20.80 18.27 0.00 2.57
4674 5041 3.610040 TTACATGGGCAGTGACTACAG 57.390 47.619 0.00 0.00 0.00 2.74
4743 5110 5.352016 TCACCGACATAATTTCCCGTAAAAG 59.648 40.000 0.00 0.00 0.00 2.27
4834 5326 4.541085 AGCTGCAAAATTTTGTTCTTGC 57.459 36.364 27.13 22.06 43.52 4.01
4970 5463 3.155501 GACAGGCTAGGTACATATCGGT 58.844 50.000 0.00 0.00 0.00 4.69
5556 6049 5.671329 GCACATTTAGTAACCTTCTTGCTCG 60.671 44.000 0.00 0.00 0.00 5.03
5683 6176 1.525077 TTCTGTGGCGGCTCGTTTT 60.525 52.632 11.43 0.00 0.00 2.43
5713 6206 2.232208 GCCTATGAAGCCTTTTGCACTT 59.768 45.455 0.00 0.00 44.83 3.16
5804 6297 6.540189 GTCTGATGCAGTTATGTTCTATGGTT 59.460 38.462 0.00 0.00 32.61 3.67
5886 6380 1.797537 GGAAAGCATTCACGCGTGC 60.798 57.895 33.63 22.24 41.57 5.34
5960 6454 4.042398 CCAGGTTACGTATGTGAAGATCG 58.958 47.826 0.00 0.00 0.00 3.69
5978 6472 4.627467 AGATCGTGTCTTGCTTAATGTCAC 59.373 41.667 0.00 0.00 31.47 3.67
5986 6480 5.124457 GTCTTGCTTAATGTCACATGGTGAT 59.876 40.000 2.02 0.00 44.63 3.06
5987 6481 4.968812 TGCTTAATGTCACATGGTGATG 57.031 40.909 2.02 0.00 44.63 3.07
5988 6482 3.695556 TGCTTAATGTCACATGGTGATGG 59.304 43.478 2.02 0.00 44.63 3.51
5989 6483 3.067180 GCTTAATGTCACATGGTGATGGG 59.933 47.826 2.02 0.00 44.63 4.00
5990 6484 4.525996 CTTAATGTCACATGGTGATGGGA 58.474 43.478 2.02 0.00 44.63 4.37
5991 6485 3.454719 AATGTCACATGGTGATGGGAA 57.545 42.857 2.02 0.00 43.88 3.97
5992 6486 2.198827 TGTCACATGGTGATGGGAAC 57.801 50.000 2.02 0.00 43.88 3.62
5993 6487 1.704628 TGTCACATGGTGATGGGAACT 59.295 47.619 2.02 0.00 43.88 3.01
5994 6488 2.108075 TGTCACATGGTGATGGGAACTT 59.892 45.455 2.02 0.00 43.88 2.66
5995 6489 2.749621 GTCACATGGTGATGGGAACTTC 59.250 50.000 2.02 0.00 43.88 3.01
5996 6490 2.644299 TCACATGGTGATGGGAACTTCT 59.356 45.455 0.00 0.00 39.17 2.85
5997 6491 3.843619 TCACATGGTGATGGGAACTTCTA 59.156 43.478 0.00 0.00 39.17 2.10
5998 6492 4.080919 TCACATGGTGATGGGAACTTCTAG 60.081 45.833 0.00 0.00 39.17 2.43
5999 6493 3.209410 CATGGTGATGGGAACTTCTAGC 58.791 50.000 0.00 0.00 35.62 3.42
6000 6494 1.207089 TGGTGATGGGAACTTCTAGCG 59.793 52.381 0.00 0.00 35.62 4.26
6001 6495 1.207329 GGTGATGGGAACTTCTAGCGT 59.793 52.381 0.00 0.00 35.62 5.07
6002 6496 2.354805 GGTGATGGGAACTTCTAGCGTT 60.355 50.000 0.00 0.00 35.62 4.84
6003 6497 3.335579 GTGATGGGAACTTCTAGCGTTT 58.664 45.455 0.00 0.00 35.62 3.60
6004 6498 3.751698 GTGATGGGAACTTCTAGCGTTTT 59.248 43.478 0.00 0.00 35.62 2.43
6005 6499 4.215613 GTGATGGGAACTTCTAGCGTTTTT 59.784 41.667 0.00 0.00 35.62 1.94
6102 6597 2.092049 TGGTCTCGGCACTATCTTCCTA 60.092 50.000 0.00 0.00 0.00 2.94
6121 6616 0.542232 ACTCTGGACACGGGCTACTT 60.542 55.000 0.00 0.00 0.00 2.24
6154 6649 2.098607 CCATCAAGTGTGGTGCATGATC 59.901 50.000 0.00 0.00 34.21 2.92
6219 6714 6.365970 ACTTCCTTCATGTGTGTTAGAGAT 57.634 37.500 0.00 0.00 0.00 2.75
6342 6840 3.071023 CACCAACCAGGACAAGACTTCTA 59.929 47.826 0.00 0.00 41.22 2.10
6397 6895 4.284234 CCAACCCATGACAGAAATTTTCCT 59.716 41.667 5.52 0.00 0.00 3.36
6406 6904 2.007608 AGAAATTTTCCTAGACGCCGC 58.992 47.619 5.52 0.00 0.00 6.53
6416 6914 2.402282 TAGACGCCGCGTGGATGATC 62.402 60.000 25.60 6.79 41.37 2.92
6493 6991 6.587990 CCTATTGGTACATGATCGAAGTCATC 59.412 42.308 0.00 0.00 39.30 2.92
6494 6992 5.337578 TTGGTACATGATCGAAGTCATCA 57.662 39.130 0.00 0.00 39.30 3.07
6501 6999 6.634805 ACATGATCGAAGTCATCAAAGTACT 58.365 36.000 0.00 0.00 36.72 2.73
6502 7000 6.533012 ACATGATCGAAGTCATCAAAGTACTG 59.467 38.462 0.00 0.00 36.72 2.74
6503 7001 6.025749 TGATCGAAGTCATCAAAGTACTGT 57.974 37.500 0.00 0.00 0.00 3.55
6504 7002 6.455647 TGATCGAAGTCATCAAAGTACTGTT 58.544 36.000 0.00 0.00 0.00 3.16
6505 7003 6.929049 TGATCGAAGTCATCAAAGTACTGTTT 59.071 34.615 0.00 0.00 0.00 2.83
6506 7004 6.525121 TCGAAGTCATCAAAGTACTGTTTG 57.475 37.500 0.00 0.00 38.55 2.93
6507 7005 6.046593 TCGAAGTCATCAAAGTACTGTTTGT 58.953 36.000 0.00 0.00 38.38 2.83
6508 7006 6.019075 TCGAAGTCATCAAAGTACTGTTTGTG 60.019 38.462 0.00 0.58 38.38 3.33
6509 7007 6.238103 CGAAGTCATCAAAGTACTGTTTGTGT 60.238 38.462 0.00 0.00 38.38 3.72
6510 7008 6.604735 AGTCATCAAAGTACTGTTTGTGTC 57.395 37.500 0.00 0.00 38.38 3.67
6511 7009 5.527582 AGTCATCAAAGTACTGTTTGTGTCC 59.472 40.000 0.00 0.00 38.38 4.02
6512 7010 5.295787 GTCATCAAAGTACTGTTTGTGTCCA 59.704 40.000 0.00 0.00 38.38 4.02
6513 7011 5.883115 TCATCAAAGTACTGTTTGTGTCCAA 59.117 36.000 0.00 0.00 38.38 3.53
6514 7012 6.545666 TCATCAAAGTACTGTTTGTGTCCAAT 59.454 34.615 0.00 0.00 38.38 3.16
6515 7013 6.371809 TCAAAGTACTGTTTGTGTCCAATC 57.628 37.500 0.00 0.00 38.38 2.67
6516 7014 6.119536 TCAAAGTACTGTTTGTGTCCAATCT 58.880 36.000 0.00 0.00 38.38 2.40
6517 7015 6.601613 TCAAAGTACTGTTTGTGTCCAATCTT 59.398 34.615 0.00 0.00 38.38 2.40
6518 7016 7.122055 TCAAAGTACTGTTTGTGTCCAATCTTT 59.878 33.333 0.00 0.00 38.38 2.52
6519 7017 8.402472 CAAAGTACTGTTTGTGTCCAATCTTTA 58.598 33.333 0.00 0.00 33.48 1.85
6520 7018 8.691661 AAGTACTGTTTGTGTCCAATCTTTAT 57.308 30.769 0.00 0.00 0.00 1.40
6521 7019 9.787435 AAGTACTGTTTGTGTCCAATCTTTATA 57.213 29.630 0.00 0.00 0.00 0.98
6522 7020 9.787435 AGTACTGTTTGTGTCCAATCTTTATAA 57.213 29.630 0.00 0.00 0.00 0.98
6531 7029 9.461312 TGTGTCCAATCTTTATAAATTGTAGCT 57.539 29.630 0.00 0.00 32.20 3.32
6532 7030 9.722056 GTGTCCAATCTTTATAAATTGTAGCTG 57.278 33.333 0.00 0.00 32.20 4.24
6533 7031 8.902806 TGTCCAATCTTTATAAATTGTAGCTGG 58.097 33.333 0.00 0.53 32.20 4.85
6534 7032 9.120538 GTCCAATCTTTATAAATTGTAGCTGGA 57.879 33.333 0.00 2.66 32.20 3.86
6535 7033 9.866655 TCCAATCTTTATAAATTGTAGCTGGAT 57.133 29.630 0.00 0.00 32.20 3.41
6539 7037 9.866655 ATCTTTATAAATTGTAGCTGGATTGGA 57.133 29.630 0.00 0.00 0.00 3.53
6540 7038 9.342308 TCTTTATAAATTGTAGCTGGATTGGAG 57.658 33.333 0.00 0.00 0.00 3.86
6541 7039 8.463930 TTTATAAATTGTAGCTGGATTGGAGG 57.536 34.615 0.00 0.00 0.00 4.30
6542 7040 4.591321 AAATTGTAGCTGGATTGGAGGA 57.409 40.909 0.00 0.00 0.00 3.71
6543 7041 4.803329 AATTGTAGCTGGATTGGAGGAT 57.197 40.909 0.00 0.00 0.00 3.24
6544 7042 3.565764 TTGTAGCTGGATTGGAGGATG 57.434 47.619 0.00 0.00 0.00 3.51
6545 7043 2.763039 TGTAGCTGGATTGGAGGATGA 58.237 47.619 0.00 0.00 0.00 2.92
6546 7044 3.114606 TGTAGCTGGATTGGAGGATGAA 58.885 45.455 0.00 0.00 0.00 2.57
6547 7045 2.725221 AGCTGGATTGGAGGATGAAC 57.275 50.000 0.00 0.00 0.00 3.18
6548 7046 1.918262 AGCTGGATTGGAGGATGAACA 59.082 47.619 0.00 0.00 0.00 3.18
6549 7047 2.019984 GCTGGATTGGAGGATGAACAC 58.980 52.381 0.00 0.00 0.00 3.32
6550 7048 2.283298 CTGGATTGGAGGATGAACACG 58.717 52.381 0.00 0.00 0.00 4.49
6551 7049 1.905894 TGGATTGGAGGATGAACACGA 59.094 47.619 0.00 0.00 0.00 4.35
6552 7050 2.304470 TGGATTGGAGGATGAACACGAA 59.696 45.455 0.00 0.00 0.00 3.85
6553 7051 3.244735 TGGATTGGAGGATGAACACGAAA 60.245 43.478 0.00 0.00 0.00 3.46
6554 7052 3.375299 GGATTGGAGGATGAACACGAAAG 59.625 47.826 0.00 0.00 0.00 2.62
6555 7053 2.472695 TGGAGGATGAACACGAAAGG 57.527 50.000 0.00 0.00 0.00 3.11
6556 7054 1.974957 TGGAGGATGAACACGAAAGGA 59.025 47.619 0.00 0.00 0.00 3.36
6557 7055 2.370519 TGGAGGATGAACACGAAAGGAA 59.629 45.455 0.00 0.00 0.00 3.36
6558 7056 3.181449 TGGAGGATGAACACGAAAGGAAA 60.181 43.478 0.00 0.00 0.00 3.13
6559 7057 3.188667 GGAGGATGAACACGAAAGGAAAC 59.811 47.826 0.00 0.00 0.00 2.78
6574 7072 4.009370 AGGAAACTTGAGGACAACTAGC 57.991 45.455 0.00 0.00 37.44 3.42
6575 7073 3.391296 AGGAAACTTGAGGACAACTAGCA 59.609 43.478 0.00 0.00 37.44 3.49
6576 7074 3.498777 GGAAACTTGAGGACAACTAGCAC 59.501 47.826 0.00 0.00 32.27 4.40
6577 7075 3.838244 AACTTGAGGACAACTAGCACA 57.162 42.857 0.00 0.00 32.27 4.57
6578 7076 3.838244 ACTTGAGGACAACTAGCACAA 57.162 42.857 0.00 0.00 32.27 3.33
6579 7077 4.150897 ACTTGAGGACAACTAGCACAAA 57.849 40.909 0.00 0.00 32.27 2.83
6580 7078 4.718961 ACTTGAGGACAACTAGCACAAAT 58.281 39.130 0.00 0.00 32.27 2.32
6581 7079 4.757149 ACTTGAGGACAACTAGCACAAATC 59.243 41.667 0.00 0.00 32.27 2.17
6582 7080 4.350368 TGAGGACAACTAGCACAAATCA 57.650 40.909 0.00 0.00 0.00 2.57
6583 7081 4.713553 TGAGGACAACTAGCACAAATCAA 58.286 39.130 0.00 0.00 0.00 2.57
6584 7082 4.515191 TGAGGACAACTAGCACAAATCAAC 59.485 41.667 0.00 0.00 0.00 3.18
6585 7083 3.498397 AGGACAACTAGCACAAATCAACG 59.502 43.478 0.00 0.00 0.00 4.10
6586 7084 3.226347 GACAACTAGCACAAATCAACGC 58.774 45.455 0.00 0.00 0.00 4.84
6587 7085 2.616376 ACAACTAGCACAAATCAACGCA 59.384 40.909 0.00 0.00 0.00 5.24
6588 7086 2.969443 ACTAGCACAAATCAACGCAC 57.031 45.000 0.00 0.00 0.00 5.34
6589 7087 1.194547 ACTAGCACAAATCAACGCACG 59.805 47.619 0.00 0.00 0.00 5.34
6590 7088 1.194547 CTAGCACAAATCAACGCACGT 59.805 47.619 0.00 0.00 0.00 4.49
6591 7089 1.222300 AGCACAAATCAACGCACGTA 58.778 45.000 0.00 0.00 0.00 3.57
6592 7090 1.194547 AGCACAAATCAACGCACGTAG 59.805 47.619 0.00 0.00 0.00 3.51
6593 7091 1.193650 GCACAAATCAACGCACGTAGA 59.806 47.619 0.00 0.00 0.00 2.59
6594 7092 2.159707 GCACAAATCAACGCACGTAGAT 60.160 45.455 0.00 0.00 0.00 1.98
6595 7093 3.407252 CACAAATCAACGCACGTAGATG 58.593 45.455 0.00 0.00 0.00 2.90
6596 7094 2.159707 ACAAATCAACGCACGTAGATGC 60.160 45.455 0.00 0.00 42.48 3.91
6597 7095 1.720805 AATCAACGCACGTAGATGCA 58.279 45.000 0.00 0.00 46.47 3.96
6598 7096 1.720805 ATCAACGCACGTAGATGCAA 58.279 45.000 0.00 0.00 46.47 4.08
6599 7097 1.720805 TCAACGCACGTAGATGCAAT 58.279 45.000 0.00 0.00 46.47 3.56
6600 7098 2.882324 TCAACGCACGTAGATGCAATA 58.118 42.857 0.00 0.00 46.47 1.90
6601 7099 3.254892 TCAACGCACGTAGATGCAATAA 58.745 40.909 0.00 0.00 46.47 1.40
6602 7100 3.680458 TCAACGCACGTAGATGCAATAAA 59.320 39.130 0.00 0.00 46.47 1.40
6603 7101 4.152580 TCAACGCACGTAGATGCAATAAAA 59.847 37.500 0.00 0.00 46.47 1.52
6604 7102 4.258935 ACGCACGTAGATGCAATAAAAG 57.741 40.909 0.00 0.00 46.47 2.27
6605 7103 3.930229 ACGCACGTAGATGCAATAAAAGA 59.070 39.130 0.00 0.00 46.47 2.52
6606 7104 4.570772 ACGCACGTAGATGCAATAAAAGAT 59.429 37.500 0.00 0.00 46.47 2.40
6607 7105 5.751509 ACGCACGTAGATGCAATAAAAGATA 59.248 36.000 0.00 0.00 46.47 1.98
6608 7106 6.065153 CGCACGTAGATGCAATAAAAGATAC 58.935 40.000 0.00 0.00 46.47 2.24
6609 7107 6.292114 CGCACGTAGATGCAATAAAAGATACA 60.292 38.462 0.00 0.00 46.47 2.29
6610 7108 6.846283 GCACGTAGATGCAATAAAAGATACAC 59.154 38.462 0.00 0.00 45.39 2.90
6611 7109 7.465379 GCACGTAGATGCAATAAAAGATACACA 60.465 37.037 0.00 0.00 45.39 3.72
6612 7110 8.551205 CACGTAGATGCAATAAAAGATACACAT 58.449 33.333 0.00 0.00 0.00 3.21
6613 7111 8.551205 ACGTAGATGCAATAAAAGATACACATG 58.449 33.333 0.00 0.00 0.00 3.21
6614 7112 8.011673 CGTAGATGCAATAAAAGATACACATGG 58.988 37.037 0.00 0.00 0.00 3.66
6615 7113 9.056005 GTAGATGCAATAAAAGATACACATGGA 57.944 33.333 0.00 0.00 0.00 3.41
6616 7114 8.701908 AGATGCAATAAAAGATACACATGGAT 57.298 30.769 0.00 0.00 0.00 3.41
6617 7115 9.797642 AGATGCAATAAAAGATACACATGGATA 57.202 29.630 0.00 0.00 0.00 2.59
6619 7117 9.797642 ATGCAATAAAAGATACACATGGATAGA 57.202 29.630 0.00 0.00 0.00 1.98
6620 7118 9.797642 TGCAATAAAAGATACACATGGATAGAT 57.202 29.630 0.00 0.00 0.00 1.98
6628 7126 9.941325 AAGATACACATGGATAGATTCTTGATC 57.059 33.333 0.00 0.00 34.83 2.92
6629 7127 8.538701 AGATACACATGGATAGATTCTTGATCC 58.461 37.037 8.11 8.11 39.77 3.36
6638 7136 9.730705 TGGATAGATTCTTGATCCAAATCATAC 57.269 33.333 13.54 6.87 44.84 2.39
6639 7137 9.730705 GGATAGATTCTTGATCCAAATCATACA 57.269 33.333 9.67 0.00 41.49 2.29
6642 7140 8.461249 AGATTCTTGATCCAAATCATACAAGG 57.539 34.615 0.00 0.00 41.49 3.61
6643 7141 8.277197 AGATTCTTGATCCAAATCATACAAGGA 58.723 33.333 0.00 0.00 41.49 3.36
6644 7142 7.870509 TTCTTGATCCAAATCATACAAGGAG 57.129 36.000 0.00 0.00 41.49 3.69
6645 7143 6.359804 TCTTGATCCAAATCATACAAGGAGG 58.640 40.000 0.00 0.00 41.49 4.30
6646 7144 5.052693 TGATCCAAATCATACAAGGAGGG 57.947 43.478 0.00 0.00 36.98 4.30
6647 7145 4.726317 TGATCCAAATCATACAAGGAGGGA 59.274 41.667 0.00 0.00 36.98 4.20
6648 7146 4.778213 TCCAAATCATACAAGGAGGGAG 57.222 45.455 0.00 0.00 0.00 4.30
6649 7147 4.370776 TCCAAATCATACAAGGAGGGAGA 58.629 43.478 0.00 0.00 0.00 3.71
6650 7148 4.977739 TCCAAATCATACAAGGAGGGAGAT 59.022 41.667 0.00 0.00 0.00 2.75
6651 7149 5.068636 CCAAATCATACAAGGAGGGAGATG 58.931 45.833 0.00 0.00 0.00 2.90
6652 7150 5.163163 CCAAATCATACAAGGAGGGAGATGA 60.163 44.000 0.00 0.00 0.00 2.92
6653 7151 6.359804 CAAATCATACAAGGAGGGAGATGAA 58.640 40.000 0.00 0.00 0.00 2.57
6654 7152 6.581388 AATCATACAAGGAGGGAGATGAAA 57.419 37.500 0.00 0.00 0.00 2.69
6655 7153 5.359194 TCATACAAGGAGGGAGATGAAAC 57.641 43.478 0.00 0.00 0.00 2.78
6656 7154 4.782691 TCATACAAGGAGGGAGATGAAACA 59.217 41.667 0.00 0.00 0.00 2.83
6657 7155 5.250543 TCATACAAGGAGGGAGATGAAACAA 59.749 40.000 0.00 0.00 0.00 2.83
6658 7156 4.026356 ACAAGGAGGGAGATGAAACAAG 57.974 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 57 8.300286 GGATTTCTCTATGAATCTGACGTCATA 58.700 37.037 20.40 12.98 36.00 2.15
54 58 7.151308 GGATTTCTCTATGAATCTGACGTCAT 58.849 38.462 20.40 3.85 38.10 3.06
97 101 8.896722 ATATGAAACGGAGGGAGTAGTATATT 57.103 34.615 0.00 0.00 0.00 1.28
133 137 9.273016 CCGTTCCATATTACTTATCACTGATTT 57.727 33.333 0.00 0.00 0.00 2.17
134 138 8.647796 TCCGTTCCATATTACTTATCACTGATT 58.352 33.333 0.00 0.00 0.00 2.57
135 139 8.190326 TCCGTTCCATATTACTTATCACTGAT 57.810 34.615 0.00 0.00 0.00 2.90
136 140 7.255836 CCTCCGTTCCATATTACTTATCACTGA 60.256 40.741 0.00 0.00 0.00 3.41
137 141 6.868864 CCTCCGTTCCATATTACTTATCACTG 59.131 42.308 0.00 0.00 0.00 3.66
138 142 6.014499 CCCTCCGTTCCATATTACTTATCACT 60.014 42.308 0.00 0.00 0.00 3.41
139 143 6.014840 TCCCTCCGTTCCATATTACTTATCAC 60.015 42.308 0.00 0.00 0.00 3.06
140 144 6.079336 TCCCTCCGTTCCATATTACTTATCA 58.921 40.000 0.00 0.00 0.00 2.15
141 145 6.210984 ACTCCCTCCGTTCCATATTACTTATC 59.789 42.308 0.00 0.00 0.00 1.75
142 146 6.082707 ACTCCCTCCGTTCCATATTACTTAT 58.917 40.000 0.00 0.00 0.00 1.73
143 147 5.461327 ACTCCCTCCGTTCCATATTACTTA 58.539 41.667 0.00 0.00 0.00 2.24
144 148 4.296056 ACTCCCTCCGTTCCATATTACTT 58.704 43.478 0.00 0.00 0.00 2.24
145 149 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
146 150 4.831710 ACTACTCCCTCCGTTCCATATTAC 59.168 45.833 0.00 0.00 0.00 1.89
147 151 5.070823 ACTACTCCCTCCGTTCCATATTA 57.929 43.478 0.00 0.00 0.00 0.98
148 152 3.924922 ACTACTCCCTCCGTTCCATATT 58.075 45.455 0.00 0.00 0.00 1.28
149 153 3.614568 ACTACTCCCTCCGTTCCATAT 57.385 47.619 0.00 0.00 0.00 1.78
150 154 3.435601 GGTACTACTCCCTCCGTTCCATA 60.436 52.174 0.00 0.00 0.00 2.74
151 155 2.664015 GTACTACTCCCTCCGTTCCAT 58.336 52.381 0.00 0.00 0.00 3.41
260 264 1.078759 CAATCACAGCGGACGGACTC 61.079 60.000 0.00 0.00 0.00 3.36
400 405 2.176273 CCAATGAGCCTCGCTTCGG 61.176 63.158 0.00 0.00 39.88 4.30
405 410 0.308993 GTAATGCCAATGAGCCTCGC 59.691 55.000 0.00 0.00 0.00 5.03
628 910 2.677836 TGCTCTTTTCTGACACACACAC 59.322 45.455 0.00 0.00 0.00 3.82
629 911 2.677836 GTGCTCTTTTCTGACACACACA 59.322 45.455 0.00 0.00 0.00 3.72
630 912 2.285834 CGTGCTCTTTTCTGACACACAC 60.286 50.000 0.00 0.00 0.00 3.82
631 913 1.933181 CGTGCTCTTTTCTGACACACA 59.067 47.619 0.00 0.00 0.00 3.72
688 970 2.280797 GTGCTGACGACCTTGGCA 60.281 61.111 0.00 0.00 0.00 4.92
723 1007 3.620300 CTTGTCCCGTCGCGTGCTA 62.620 63.158 5.77 0.00 0.00 3.49
759 1043 1.825474 CTTCCAGTACGTCATCCAGGT 59.175 52.381 0.00 0.00 0.00 4.00
763 1047 1.134788 CCCACTTCCAGTACGTCATCC 60.135 57.143 0.00 0.00 0.00 3.51
894 1178 1.230182 GGAGGGGGAGAAAAGGGGA 60.230 63.158 0.00 0.00 0.00 4.81
898 1182 1.230314 AGGGGGAGGGGGAGAAAAG 60.230 63.158 0.00 0.00 0.00 2.27
1170 1473 2.169352 CACAGTAGGAGGAACAGGGATG 59.831 54.545 0.00 0.00 0.00 3.51
1285 1612 4.704833 TCGAAGGCAGCACTGGGC 62.705 66.667 0.00 0.00 45.30 5.36
1286 1613 2.743928 GTCGAAGGCAGCACTGGG 60.744 66.667 0.00 0.00 0.00 4.45
1287 1614 2.743928 GGTCGAAGGCAGCACTGG 60.744 66.667 0.00 0.00 0.00 4.00
1288 1615 2.031012 TGGTCGAAGGCAGCACTG 59.969 61.111 0.00 0.00 0.00 3.66
1289 1616 2.044806 AACTGGTCGAAGGCAGCACT 62.045 55.000 0.00 0.00 0.00 4.40
1290 1617 1.166531 AAACTGGTCGAAGGCAGCAC 61.167 55.000 0.00 0.00 0.00 4.40
1291 1618 1.148273 AAACTGGTCGAAGGCAGCA 59.852 52.632 0.00 0.00 0.00 4.41
1367 1696 3.053693 CCCATTATTCAACCCAGTGAGGA 60.054 47.826 4.82 0.00 41.22 3.71
1442 1787 3.580458 AGCTAATCTAACGGGCAGATGAT 59.420 43.478 0.00 0.00 33.03 2.45
1451 1796 3.551863 CCTGAGCTGAGCTAATCTAACGG 60.552 52.174 7.08 0.00 39.88 4.44
1671 2033 2.092212 AGGCCTCAACATATGAACAGGG 60.092 50.000 10.38 6.00 37.67 4.45
1732 2095 2.945008 CGTATTTCCACATCCATGCACT 59.055 45.455 0.00 0.00 0.00 4.40
1752 2115 7.132213 ACTACAACTTCAAATTTGACATGTCG 58.868 34.615 24.64 21.87 36.83 4.35
1918 2282 7.781324 AATTGGTCCTCACTTGTCATTTATT 57.219 32.000 0.00 0.00 0.00 1.40
2083 2448 1.949847 CTGCACTCCCGGTCTGTAGG 61.950 65.000 0.00 0.00 0.00 3.18
2179 2544 1.127567 CCTGTCAGGACCTGGTGGAA 61.128 60.000 21.56 0.00 37.67 3.53
2200 2565 6.519382 TCATATGTTTTCAATGGTGCACAAA 58.481 32.000 20.43 7.20 0.00 2.83
2202 2567 5.718724 TCATATGTTTTCAATGGTGCACA 57.281 34.783 20.43 5.24 0.00 4.57
2220 2585 9.264719 CACATATGAACACAGCTAGAATTCATA 57.735 33.333 10.38 17.39 43.03 2.15
2273 2639 9.705290 CCTGGTTATAAGCACAAAATTTTACTT 57.295 29.630 13.22 10.00 32.29 2.24
2356 2722 6.018098 GCATGAGAAACTCAGAATGGTATCAG 60.018 42.308 0.00 0.00 44.08 2.90
2406 2772 1.246056 GCAGAGGACATTGGCAGCAA 61.246 55.000 0.00 0.00 0.00 3.91
2768 3134 1.066430 ACCATATTGCTTCACGTCGGT 60.066 47.619 0.00 0.00 0.00 4.69
2801 3167 7.620880 TGGTATAAGCAGAACTACTTTGACAT 58.379 34.615 0.00 0.00 0.00 3.06
2958 3324 8.236586 TGAGTGTGTGTTCAAATAATAGAATGC 58.763 33.333 0.00 0.00 0.00 3.56
2979 3345 5.622448 CACGTTTGAAATCATCAGTTGAGTG 59.378 40.000 0.00 0.00 39.77 3.51
3012 3378 9.890629 AGCTGTCTGTGATATAGATTTGTTTTA 57.109 29.630 0.00 0.00 0.00 1.52
3107 3473 3.815401 CCAAACGATCTCCAAAACTCAGT 59.185 43.478 0.00 0.00 0.00 3.41
3415 3781 7.816995 TCTCAAAGTGCAAACAAACAACTAAAT 59.183 29.630 0.00 0.00 0.00 1.40
3437 3803 9.090103 CATACATATACCCTCCTTTACTTCTCA 57.910 37.037 0.00 0.00 0.00 3.27
3889 4255 6.977213 TCTAAAGCTACCAAACACCAAAATC 58.023 36.000 0.00 0.00 0.00 2.17
4066 4432 1.035932 AAGCATGGACCAGCATCAGC 61.036 55.000 15.46 6.30 42.56 4.26
4313 4680 0.652592 GCTACACAAGCGGCATACAG 59.347 55.000 1.45 0.00 42.53 2.74
4417 4784 4.022935 CAGGAATAGCACACAACACACAAT 60.023 41.667 0.00 0.00 0.00 2.71
4430 4797 1.105457 GCCAATGTGCAGGAATAGCA 58.895 50.000 0.00 0.00 40.19 3.49
4571 4938 5.986741 CAGACGATAGCTAGAGACTCAGTTA 59.013 44.000 5.02 3.54 42.67 2.24
4576 4943 3.399330 AGCAGACGATAGCTAGAGACTC 58.601 50.000 0.00 0.00 39.78 3.36
4578 4945 5.627172 CATTAGCAGACGATAGCTAGAGAC 58.373 45.833 0.00 0.00 43.50 3.36
4627 4994 7.310634 ACCCTCCATTATGATACTAGGTAACA 58.689 38.462 0.00 0.00 41.41 2.41
4674 5041 6.174049 ACAAGATAACTAGGCCTCAAGAAAC 58.826 40.000 9.68 0.00 0.00 2.78
4743 5110 5.471456 CCTGCTTATTATGTCAGGTGATTCC 59.529 44.000 0.00 0.00 40.79 3.01
4970 5463 2.363306 ACACAACCAAATCCAGCAGA 57.637 45.000 0.00 0.00 0.00 4.26
5044 5537 2.026641 TGGAACGGAGGGAGTATTACG 58.973 52.381 0.00 0.00 0.00 3.18
5082 5575 3.248024 ACACAATCAACTACTCCCTCCA 58.752 45.455 0.00 0.00 0.00 3.86
5179 5672 9.101655 CAAACCAAGAAAAATCAGAAACAGATT 57.898 29.630 0.00 0.00 37.30 2.40
5556 6049 6.974932 TCAAGAGTTCAATATTGCTGAGAC 57.025 37.500 10.76 4.55 0.00 3.36
5683 6176 1.210478 GGCTTCATAGGCAGGAACTCA 59.790 52.381 0.00 0.00 45.79 3.41
5713 6206 8.539770 TTTGTTTTGCTTACAACAGAAATTGA 57.460 26.923 0.00 0.00 35.39 2.57
5804 6297 2.440147 CCAAGGGCCACATGTCCA 59.560 61.111 6.18 0.00 0.00 4.02
5886 6380 2.035449 TGAACTTACAGACCACACTCGG 59.965 50.000 0.00 0.00 0.00 4.63
5960 6454 4.216257 ACCATGTGACATTAAGCAAGACAC 59.784 41.667 0.00 0.00 0.00 3.67
5967 6461 3.067180 CCCATCACCATGTGACATTAAGC 59.933 47.826 0.00 0.00 45.65 3.09
5971 6465 3.091545 GTTCCCATCACCATGTGACATT 58.908 45.455 0.00 0.00 45.65 2.71
5978 6472 3.209410 GCTAGAAGTTCCCATCACCATG 58.791 50.000 0.00 0.00 0.00 3.66
6008 6502 4.028993 AGAAGTTCCCTATCCGCAAAAA 57.971 40.909 0.00 0.00 0.00 1.94
6009 6503 3.713826 AGAAGTTCCCTATCCGCAAAA 57.286 42.857 0.00 0.00 0.00 2.44
6010 6504 3.431766 GCTAGAAGTTCCCTATCCGCAAA 60.432 47.826 0.00 0.00 0.00 3.68
6011 6505 2.102588 GCTAGAAGTTCCCTATCCGCAA 59.897 50.000 0.00 0.00 0.00 4.85
6012 6506 1.687123 GCTAGAAGTTCCCTATCCGCA 59.313 52.381 0.00 0.00 0.00 5.69
6013 6507 1.336056 CGCTAGAAGTTCCCTATCCGC 60.336 57.143 0.00 0.00 0.00 5.54
6014 6508 1.955080 ACGCTAGAAGTTCCCTATCCG 59.045 52.381 0.00 0.00 0.00 4.18
6015 6509 3.492829 CCAACGCTAGAAGTTCCCTATCC 60.493 52.174 0.00 0.00 0.00 2.59
6016 6510 3.718815 CCAACGCTAGAAGTTCCCTATC 58.281 50.000 0.00 0.00 0.00 2.08
6017 6511 2.158943 GCCAACGCTAGAAGTTCCCTAT 60.159 50.000 0.00 0.00 0.00 2.57
6018 6512 1.206371 GCCAACGCTAGAAGTTCCCTA 59.794 52.381 0.00 0.00 0.00 3.53
6019 6513 0.036294 GCCAACGCTAGAAGTTCCCT 60.036 55.000 0.00 0.00 0.00 4.20
6089 6584 3.954904 TGTCCAGAGTAGGAAGATAGTGC 59.045 47.826 0.00 0.00 39.92 4.40
6102 6597 0.542232 AAGTAGCCCGTGTCCAGAGT 60.542 55.000 0.00 0.00 0.00 3.24
6121 6616 6.013379 ACCACACTTGATGGAGAAGATAGAAA 60.013 38.462 0.00 0.00 39.87 2.52
6154 6649 2.959465 AAAAGTGGAGGTCTGGAAGG 57.041 50.000 0.00 0.00 0.00 3.46
6219 6714 7.994425 TTGCAAAAGATCTATTTGTCTGGTA 57.006 32.000 21.15 7.85 39.42 3.25
6288 6785 6.038050 CCAGGTTTGCTCTAAGATTCAGATTC 59.962 42.308 0.00 0.00 0.00 2.52
6342 6840 2.238847 TAGCATCGCCGAAGCACCTT 62.239 55.000 17.11 0.00 39.83 3.50
6397 6895 2.402282 GATCATCCACGCGGCGTCTA 62.402 60.000 26.96 16.74 38.32 2.59
6406 6904 2.941064 ACAATCTTGCAGATCATCCACG 59.059 45.455 0.00 0.00 32.89 4.94
6416 6914 2.027377 AGTGAGGGAGACAATCTTGCAG 60.027 50.000 0.00 0.00 0.00 4.41
6452 6950 0.991146 TAGGTGCATGGGAAAGAGCA 59.009 50.000 0.00 0.00 34.10 4.26
6493 6991 6.377327 AGATTGGACACAAACAGTACTTTG 57.623 37.500 5.87 5.87 40.55 2.77
6494 6992 7.404671 AAAGATTGGACACAAACAGTACTTT 57.595 32.000 0.00 0.00 40.55 2.66
6505 7003 9.461312 AGCTACAATTTATAAAGATTGGACACA 57.539 29.630 13.48 0.00 37.53 3.72
6506 7004 9.722056 CAGCTACAATTTATAAAGATTGGACAC 57.278 33.333 13.48 2.14 37.53 3.67
6507 7005 8.902806 CCAGCTACAATTTATAAAGATTGGACA 58.097 33.333 13.48 1.83 37.53 4.02
6508 7006 9.120538 TCCAGCTACAATTTATAAAGATTGGAC 57.879 33.333 13.48 5.24 37.53 4.02
6509 7007 9.866655 ATCCAGCTACAATTTATAAAGATTGGA 57.133 29.630 13.48 12.99 37.53 3.53
6513 7011 9.866655 TCCAATCCAGCTACAATTTATAAAGAT 57.133 29.630 3.94 0.00 0.00 2.40
6514 7012 9.342308 CTCCAATCCAGCTACAATTTATAAAGA 57.658 33.333 3.94 0.00 0.00 2.52
6515 7013 8.571336 CCTCCAATCCAGCTACAATTTATAAAG 58.429 37.037 3.94 0.00 0.00 1.85
6516 7014 8.278639 TCCTCCAATCCAGCTACAATTTATAAA 58.721 33.333 0.00 0.00 0.00 1.40
6517 7015 7.811282 TCCTCCAATCCAGCTACAATTTATAA 58.189 34.615 0.00 0.00 0.00 0.98
6518 7016 7.387265 TCCTCCAATCCAGCTACAATTTATA 57.613 36.000 0.00 0.00 0.00 0.98
6519 7017 6.266131 TCCTCCAATCCAGCTACAATTTAT 57.734 37.500 0.00 0.00 0.00 1.40
6520 7018 5.708736 TCCTCCAATCCAGCTACAATTTA 57.291 39.130 0.00 0.00 0.00 1.40
6521 7019 4.591321 TCCTCCAATCCAGCTACAATTT 57.409 40.909 0.00 0.00 0.00 1.82
6522 7020 4.166725 TCATCCTCCAATCCAGCTACAATT 59.833 41.667 0.00 0.00 0.00 2.32
6523 7021 3.718434 TCATCCTCCAATCCAGCTACAAT 59.282 43.478 0.00 0.00 0.00 2.71
6524 7022 3.114606 TCATCCTCCAATCCAGCTACAA 58.885 45.455 0.00 0.00 0.00 2.41
6525 7023 2.763039 TCATCCTCCAATCCAGCTACA 58.237 47.619 0.00 0.00 0.00 2.74
6526 7024 3.118261 TGTTCATCCTCCAATCCAGCTAC 60.118 47.826 0.00 0.00 0.00 3.58
6527 7025 3.114606 TGTTCATCCTCCAATCCAGCTA 58.885 45.455 0.00 0.00 0.00 3.32
6528 7026 1.918262 TGTTCATCCTCCAATCCAGCT 59.082 47.619 0.00 0.00 0.00 4.24
6529 7027 2.019984 GTGTTCATCCTCCAATCCAGC 58.980 52.381 0.00 0.00 0.00 4.85
6530 7028 2.093500 TCGTGTTCATCCTCCAATCCAG 60.093 50.000 0.00 0.00 0.00 3.86
6531 7029 1.905894 TCGTGTTCATCCTCCAATCCA 59.094 47.619 0.00 0.00 0.00 3.41
6532 7030 2.691409 TCGTGTTCATCCTCCAATCC 57.309 50.000 0.00 0.00 0.00 3.01
6533 7031 3.375299 CCTTTCGTGTTCATCCTCCAATC 59.625 47.826 0.00 0.00 0.00 2.67
6534 7032 3.009033 TCCTTTCGTGTTCATCCTCCAAT 59.991 43.478 0.00 0.00 0.00 3.16
6535 7033 2.370519 TCCTTTCGTGTTCATCCTCCAA 59.629 45.455 0.00 0.00 0.00 3.53
6536 7034 1.974957 TCCTTTCGTGTTCATCCTCCA 59.025 47.619 0.00 0.00 0.00 3.86
6537 7035 2.762535 TCCTTTCGTGTTCATCCTCC 57.237 50.000 0.00 0.00 0.00 4.30
6538 7036 4.065789 AGTTTCCTTTCGTGTTCATCCTC 58.934 43.478 0.00 0.00 0.00 3.71
6539 7037 4.086706 AGTTTCCTTTCGTGTTCATCCT 57.913 40.909 0.00 0.00 0.00 3.24
6540 7038 4.274950 TCAAGTTTCCTTTCGTGTTCATCC 59.725 41.667 0.00 0.00 0.00 3.51
6541 7039 5.418310 TCAAGTTTCCTTTCGTGTTCATC 57.582 39.130 0.00 0.00 0.00 2.92
6542 7040 4.275936 CCTCAAGTTTCCTTTCGTGTTCAT 59.724 41.667 0.00 0.00 0.00 2.57
6543 7041 3.625764 CCTCAAGTTTCCTTTCGTGTTCA 59.374 43.478 0.00 0.00 0.00 3.18
6544 7042 3.875134 TCCTCAAGTTTCCTTTCGTGTTC 59.125 43.478 0.00 0.00 0.00 3.18
6545 7043 3.626217 GTCCTCAAGTTTCCTTTCGTGTT 59.374 43.478 0.00 0.00 0.00 3.32
6546 7044 3.203716 GTCCTCAAGTTTCCTTTCGTGT 58.796 45.455 0.00 0.00 0.00 4.49
6547 7045 3.202906 TGTCCTCAAGTTTCCTTTCGTG 58.797 45.455 0.00 0.00 0.00 4.35
6548 7046 3.553828 TGTCCTCAAGTTTCCTTTCGT 57.446 42.857 0.00 0.00 0.00 3.85
6549 7047 3.877508 AGTTGTCCTCAAGTTTCCTTTCG 59.122 43.478 0.00 0.00 33.97 3.46
6550 7048 5.049336 GCTAGTTGTCCTCAAGTTTCCTTTC 60.049 44.000 0.00 0.00 38.13 2.62
6551 7049 4.822350 GCTAGTTGTCCTCAAGTTTCCTTT 59.178 41.667 0.00 0.00 38.13 3.11
6552 7050 4.141482 TGCTAGTTGTCCTCAAGTTTCCTT 60.141 41.667 0.00 0.00 38.13 3.36
6553 7051 3.391296 TGCTAGTTGTCCTCAAGTTTCCT 59.609 43.478 0.00 0.00 38.13 3.36
6554 7052 3.498777 GTGCTAGTTGTCCTCAAGTTTCC 59.501 47.826 0.00 0.00 38.13 3.13
6555 7053 4.127171 TGTGCTAGTTGTCCTCAAGTTTC 58.873 43.478 0.00 0.00 38.13 2.78
6556 7054 4.150897 TGTGCTAGTTGTCCTCAAGTTT 57.849 40.909 0.00 0.00 38.13 2.66
6557 7055 3.838244 TGTGCTAGTTGTCCTCAAGTT 57.162 42.857 0.00 0.00 38.13 2.66
6558 7056 3.838244 TTGTGCTAGTTGTCCTCAAGT 57.162 42.857 0.00 0.00 39.99 3.16
6559 7057 4.756642 TGATTTGTGCTAGTTGTCCTCAAG 59.243 41.667 0.00 0.00 33.97 3.02
6560 7058 4.713553 TGATTTGTGCTAGTTGTCCTCAA 58.286 39.130 0.00 0.00 0.00 3.02
6561 7059 4.350368 TGATTTGTGCTAGTTGTCCTCA 57.650 40.909 0.00 0.00 0.00 3.86
6562 7060 4.377431 CGTTGATTTGTGCTAGTTGTCCTC 60.377 45.833 0.00 0.00 0.00 3.71
6563 7061 3.498397 CGTTGATTTGTGCTAGTTGTCCT 59.502 43.478 0.00 0.00 0.00 3.85
6564 7062 3.810373 CGTTGATTTGTGCTAGTTGTCC 58.190 45.455 0.00 0.00 0.00 4.02
6565 7063 3.226347 GCGTTGATTTGTGCTAGTTGTC 58.774 45.455 0.00 0.00 0.00 3.18
6566 7064 2.616376 TGCGTTGATTTGTGCTAGTTGT 59.384 40.909 0.00 0.00 0.00 3.32
6567 7065 2.973224 GTGCGTTGATTTGTGCTAGTTG 59.027 45.455 0.00 0.00 0.00 3.16
6568 7066 2.349438 CGTGCGTTGATTTGTGCTAGTT 60.349 45.455 0.00 0.00 0.00 2.24
6569 7067 1.194547 CGTGCGTTGATTTGTGCTAGT 59.805 47.619 0.00 0.00 0.00 2.57
6570 7068 1.194547 ACGTGCGTTGATTTGTGCTAG 59.805 47.619 0.00 0.00 0.00 3.42
6571 7069 1.222300 ACGTGCGTTGATTTGTGCTA 58.778 45.000 0.00 0.00 0.00 3.49
6572 7070 1.194547 CTACGTGCGTTGATTTGTGCT 59.805 47.619 1.66 0.00 0.00 4.40
6573 7071 1.193650 TCTACGTGCGTTGATTTGTGC 59.806 47.619 1.66 0.00 0.00 4.57
6574 7072 3.407252 CATCTACGTGCGTTGATTTGTG 58.593 45.455 16.29 6.15 38.21 3.33
6575 7073 2.159707 GCATCTACGTGCGTTGATTTGT 60.160 45.455 16.29 0.00 38.21 2.83
6576 7074 2.430956 GCATCTACGTGCGTTGATTTG 58.569 47.619 16.29 10.73 38.21 2.32
6577 7075 2.806288 GCATCTACGTGCGTTGATTT 57.194 45.000 16.29 0.00 38.21 2.17
6585 7083 6.846283 GTGTATCTTTTATTGCATCTACGTGC 59.154 38.462 0.00 0.00 45.25 5.34
6586 7084 7.905126 TGTGTATCTTTTATTGCATCTACGTG 58.095 34.615 0.00 0.00 0.00 4.49
6587 7085 8.551205 CATGTGTATCTTTTATTGCATCTACGT 58.449 33.333 0.00 0.00 0.00 3.57
6588 7086 8.011673 CCATGTGTATCTTTTATTGCATCTACG 58.988 37.037 0.00 0.00 0.00 3.51
6589 7087 9.056005 TCCATGTGTATCTTTTATTGCATCTAC 57.944 33.333 0.00 0.00 0.00 2.59
6590 7088 9.797642 ATCCATGTGTATCTTTTATTGCATCTA 57.202 29.630 0.00 0.00 0.00 1.98
6591 7089 8.701908 ATCCATGTGTATCTTTTATTGCATCT 57.298 30.769 0.00 0.00 0.00 2.90
6593 7091 9.797642 TCTATCCATGTGTATCTTTTATTGCAT 57.202 29.630 0.00 0.00 0.00 3.96
6594 7092 9.797642 ATCTATCCATGTGTATCTTTTATTGCA 57.202 29.630 0.00 0.00 0.00 4.08
6602 7100 9.941325 GATCAAGAATCTATCCATGTGTATCTT 57.059 33.333 0.00 0.00 0.00 2.40
6603 7101 8.538701 GGATCAAGAATCTATCCATGTGTATCT 58.461 37.037 7.09 0.00 39.24 1.98
6604 7102 8.316946 TGGATCAAGAATCTATCCATGTGTATC 58.683 37.037 9.99 0.00 43.27 2.24
6605 7103 8.211030 TGGATCAAGAATCTATCCATGTGTAT 57.789 34.615 9.99 0.00 43.27 2.29
6606 7104 7.616528 TGGATCAAGAATCTATCCATGTGTA 57.383 36.000 9.99 0.00 43.27 2.90
6607 7105 6.505048 TGGATCAAGAATCTATCCATGTGT 57.495 37.500 9.99 0.00 43.27 3.72
6608 7106 7.812690 TTTGGATCAAGAATCTATCCATGTG 57.187 36.000 13.78 0.00 46.44 3.21
6609 7107 8.222637 TGATTTGGATCAAGAATCTATCCATGT 58.777 33.333 13.78 7.27 46.44 3.21
6610 7108 8.631480 TGATTTGGATCAAGAATCTATCCATG 57.369 34.615 13.78 0.00 46.44 3.66
6612 7110 9.730705 GTATGATTTGGATCAAGAATCTATCCA 57.269 33.333 9.99 9.99 44.96 3.41
6613 7111 9.730705 TGTATGATTTGGATCAAGAATCTATCC 57.269 33.333 5.33 5.33 44.96 2.59
6616 7114 9.565090 CCTTGTATGATTTGGATCAAGAATCTA 57.435 33.333 12.95 4.35 44.96 1.98
6617 7115 8.277197 TCCTTGTATGATTTGGATCAAGAATCT 58.723 33.333 12.95 0.00 44.96 2.40
6618 7116 8.455903 TCCTTGTATGATTTGGATCAAGAATC 57.544 34.615 0.00 1.81 44.96 2.52
6619 7117 7.504911 CCTCCTTGTATGATTTGGATCAAGAAT 59.495 37.037 0.00 0.00 44.96 2.40
6620 7118 6.830324 CCTCCTTGTATGATTTGGATCAAGAA 59.170 38.462 0.00 0.00 44.96 2.52
6621 7119 6.359804 CCTCCTTGTATGATTTGGATCAAGA 58.640 40.000 0.00 0.00 44.96 3.02
6622 7120 5.533903 CCCTCCTTGTATGATTTGGATCAAG 59.466 44.000 0.00 0.00 44.96 3.02
6623 7121 5.193527 TCCCTCCTTGTATGATTTGGATCAA 59.806 40.000 0.00 0.00 44.96 2.57
6624 7122 4.726317 TCCCTCCTTGTATGATTTGGATCA 59.274 41.667 0.00 0.00 45.81 2.92
6625 7123 5.072329 TCTCCCTCCTTGTATGATTTGGATC 59.928 44.000 0.00 0.00 0.00 3.36
6626 7124 4.977739 TCTCCCTCCTTGTATGATTTGGAT 59.022 41.667 0.00 0.00 0.00 3.41
6627 7125 4.370776 TCTCCCTCCTTGTATGATTTGGA 58.629 43.478 0.00 0.00 0.00 3.53
6628 7126 4.778213 TCTCCCTCCTTGTATGATTTGG 57.222 45.455 0.00 0.00 0.00 3.28
6629 7127 5.933617 TCATCTCCCTCCTTGTATGATTTG 58.066 41.667 0.00 0.00 0.00 2.32
6630 7128 6.581388 TTCATCTCCCTCCTTGTATGATTT 57.419 37.500 0.00 0.00 0.00 2.17
6631 7129 6.069440 TGTTTCATCTCCCTCCTTGTATGATT 60.069 38.462 0.00 0.00 0.00 2.57
6632 7130 5.429762 TGTTTCATCTCCCTCCTTGTATGAT 59.570 40.000 0.00 0.00 0.00 2.45
6633 7131 4.782691 TGTTTCATCTCCCTCCTTGTATGA 59.217 41.667 0.00 0.00 0.00 2.15
6634 7132 5.102953 TGTTTCATCTCCCTCCTTGTATG 57.897 43.478 0.00 0.00 0.00 2.39
6635 7133 5.749462 CTTGTTTCATCTCCCTCCTTGTAT 58.251 41.667 0.00 0.00 0.00 2.29
6636 7134 5.165961 CTTGTTTCATCTCCCTCCTTGTA 57.834 43.478 0.00 0.00 0.00 2.41
6637 7135 4.026356 CTTGTTTCATCTCCCTCCTTGT 57.974 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.