Multiple sequence alignment - TraesCS2B01G390700

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 TraesCS2B01G390700 chr2B 100.000 5075 0 0 1 5075 555320220 555325294 0.000000e+00 9372.0
1 TraesCS2B01G390700 chr2D 96.324 2421 64 13 1954 4357 474502940 474505352 0.000000e+00 3954.0
2 TraesCS2B01G390700 chr2D 96.034 1185 22 12 771 1955 474501717 474502876 0.000000e+00 1905.0
3 TraesCS2B01G390700 chr2D 90.061 654 37 13 93 721 474501067 474501717 0.000000e+00 822.0
4 TraesCS2B01G390700 chr2D 96.815 471 8 4 4612 5075 474505345 474505815 0.000000e+00 780.0
5 TraesCS2B01G390700 chr2A 94.079 2449 106 13 1954 4385 616980839 616983265 0.000000e+00 3683.0
6 TraesCS2B01G390700 chr2A 94.103 1204 56 6 775 1964 616979583 616980785 0.000000e+00 1816.0
7 TraesCS2B01G390700 chr2A 95.008 661 30 2 4417 5075 616983268 616983927 0.000000e+00 1035.0
8 TraesCS2B01G390700 chr2A 95.918 49 1 1 723 770 564613434 564613482 1.510000e-10 78.7
9 TraesCS2B01G390700 chr7A 89.899 198 20 0 4357 4554 306225307 306225504 6.520000e-64 255.0
10 TraesCS2B01G390700 chr1A 89.231 195 21 0 4360 4554 514032723 514032917 1.410000e-60 244.0
11 TraesCS2B01G390700 chr1D 88.325 197 22 1 4359 4554 416682890 416683086 8.490000e-58 235.0
12 TraesCS2B01G390700 chr1B 87.831 189 23 0 4360 4548 563471020 563471208 6.610000e-54 222.0
13 TraesCS2B01G390700 chr1B 88.608 79 9 0 4356 4434 55947322 55947400 4.180000e-16 97.1
14 TraesCS2B01G390700 chr1B 88.608 79 9 0 4356 4434 55958384 55958462 4.180000e-16 97.1
15 TraesCS2B01G390700 chr7B 94.444 54 1 2 722 773 707627355 707627408 1.170000e-11 82.4
16 TraesCS2B01G390700 chr4D 100.000 42 0 0 728 769 44373568 44373609 1.510000e-10 78.7
17 TraesCS2B01G390700 chr4B 94.118 51 3 0 723 773 18092853 18092803 1.510000e-10 78.7
18 TraesCS2B01G390700 chr4B 97.727 44 1 0 724 767 639857581 639857538 5.450000e-10 76.8
19 TraesCS2B01G390700 chr5D 94.118 51 2 1 723 773 92120725 92120676 5.450000e-10 76.8
20 TraesCS2B01G390700 chr7D 95.745 47 0 2 724 769 469224891 469224936 1.960000e-09 75.0
21 TraesCS2B01G390700 chr6A 95.745 47 1 1 724 770 56069282 56069237 1.960000e-09 75.0
22 TraesCS2B01G390700 chr3D 94.000 50 1 2 722 769 76394825 76394776 1.960000e-09 75.0


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 TraesCS2B01G390700 chr2B 555320220 555325294 5074 False 9372.00 9372 100.000000 1 5075 1 chr2B.!!$F1 5074
1 TraesCS2B01G390700 chr2D 474501067 474505815 4748 False 1865.25 3954 94.808500 93 5075 4 chr2D.!!$F1 4982
2 TraesCS2B01G390700 chr2A 616979583 616983927 4344 False 2178.00 3683 94.396667 775 5075 3 chr2A.!!$F2 4300

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
47 48 0.322187 GCCACCGGTGACCAGTATTT 60.322 55.0 36.07 0.00 0.00 1.40 F
223 249 0.695924 TGGTGTTACTGGGTCCATGG 59.304 55.0 4.97 4.97 0.00 3.66 F
817 843 0.885879 TGTGCCACCTCGTAGTACTG 59.114 55.0 5.39 0.00 0.00 2.74 F
1669 1708 2.286365 TTCACTGCTACAAAAGGGGG 57.714 50.0 0.00 0.00 0.00 5.40 F
2522 2635 0.622665 CAGGGCAGATTTCCCAGAGT 59.377 55.0 0.48 0.00 46.36 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1096 0.743097 GCTGGAATTGGATGTGAGGC 59.257 55.000 0.00 0.0 0.00 4.70 R
1877 1916 2.030274 GCACAAAAGGCAGAACCGTAAT 60.030 45.455 0.00 0.0 46.52 1.89 R
2354 2467 1.423541 AGTGGTGTACCTTGGCATTCA 59.576 47.619 2.32 0.0 36.82 2.57 R
3200 3324 0.179076 CTGCCATGCCGTATGAGTGA 60.179 55.000 0.00 0.0 39.21 3.41 R
4388 4521 0.255890 GGGGCCTTTGTGAGCATCTA 59.744 55.000 0.84 0.0 34.92 1.98 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
20 21 3.586470 TTGTTGTACCATTGAGGGTGT 57.414 42.857 0.00 0.00 42.39 4.16
21 22 3.586470 TGTTGTACCATTGAGGGTGTT 57.414 42.857 0.00 0.00 42.39 3.32
22 23 3.218453 TGTTGTACCATTGAGGGTGTTG 58.782 45.455 0.00 0.00 42.39 3.33
23 24 3.219281 GTTGTACCATTGAGGGTGTTGT 58.781 45.455 0.00 0.00 42.39 3.32
24 25 2.857483 TGTACCATTGAGGGTGTTGTG 58.143 47.619 0.00 0.00 42.39 3.33
25 26 2.159382 GTACCATTGAGGGTGTTGTGG 58.841 52.381 0.00 0.00 42.39 4.17
26 27 0.850100 ACCATTGAGGGTGTTGTGGA 59.150 50.000 0.00 0.00 43.89 4.02
27 28 1.216678 ACCATTGAGGGTGTTGTGGAA 59.783 47.619 0.00 0.00 43.89 3.53
28 29 1.888512 CCATTGAGGGTGTTGTGGAAG 59.111 52.381 0.00 0.00 0.00 3.46
29 30 1.270550 CATTGAGGGTGTTGTGGAAGC 59.729 52.381 0.00 0.00 0.00 3.86
30 31 0.467290 TTGAGGGTGTTGTGGAAGCC 60.467 55.000 0.00 0.00 0.00 4.35
31 32 1.150536 GAGGGTGTTGTGGAAGCCA 59.849 57.895 0.00 0.00 36.38 4.75
40 41 3.948719 TGGAAGCCACCGGTGACC 61.949 66.667 36.07 28.14 0.00 4.02
41 42 3.948719 GGAAGCCACCGGTGACCA 61.949 66.667 36.07 0.00 0.00 4.02
42 43 2.358737 GAAGCCACCGGTGACCAG 60.359 66.667 36.07 19.68 0.00 4.00
43 44 3.168528 AAGCCACCGGTGACCAGT 61.169 61.111 36.07 9.95 0.00 4.00
44 45 1.823169 GAAGCCACCGGTGACCAGTA 61.823 60.000 36.07 0.00 0.00 2.74
45 46 1.198759 AAGCCACCGGTGACCAGTAT 61.199 55.000 36.07 4.74 0.00 2.12
46 47 1.198759 AGCCACCGGTGACCAGTATT 61.199 55.000 36.07 3.89 0.00 1.89
47 48 0.322187 GCCACCGGTGACCAGTATTT 60.322 55.000 36.07 0.00 0.00 1.40
48 49 1.065998 GCCACCGGTGACCAGTATTTA 60.066 52.381 36.07 0.00 0.00 1.40
49 50 2.420967 GCCACCGGTGACCAGTATTTAT 60.421 50.000 36.07 0.00 0.00 1.40
50 51 3.202906 CCACCGGTGACCAGTATTTATG 58.797 50.000 36.07 10.21 0.00 1.90
51 52 3.370103 CCACCGGTGACCAGTATTTATGT 60.370 47.826 36.07 0.00 0.00 2.29
52 53 4.258543 CACCGGTGACCAGTATTTATGTT 58.741 43.478 31.31 0.00 0.00 2.71
53 54 4.698304 CACCGGTGACCAGTATTTATGTTT 59.302 41.667 31.31 0.00 0.00 2.83
54 55 5.182380 CACCGGTGACCAGTATTTATGTTTT 59.818 40.000 31.31 0.00 0.00 2.43
55 56 6.372103 CACCGGTGACCAGTATTTATGTTTTA 59.628 38.462 31.31 0.00 0.00 1.52
56 57 7.066525 CACCGGTGACCAGTATTTATGTTTTAT 59.933 37.037 31.31 0.00 0.00 1.40
57 58 7.612633 ACCGGTGACCAGTATTTATGTTTTATT 59.387 33.333 6.12 0.00 0.00 1.40
58 59 8.463607 CCGGTGACCAGTATTTATGTTTTATTT 58.536 33.333 1.11 0.00 0.00 1.40
77 78 8.883789 TTTATTTATGCTTTTGTAGTACACGC 57.116 30.769 1.43 6.94 0.00 5.34
78 79 6.737254 ATTTATGCTTTTGTAGTACACGCT 57.263 33.333 1.43 0.50 0.00 5.07
79 80 6.548441 TTTATGCTTTTGTAGTACACGCTT 57.452 33.333 1.43 7.15 0.00 4.68
80 81 6.548441 TTATGCTTTTGTAGTACACGCTTT 57.452 33.333 1.43 2.15 0.00 3.51
81 82 4.461992 TGCTTTTGTAGTACACGCTTTC 57.538 40.909 1.43 0.00 0.00 2.62
82 83 3.249080 TGCTTTTGTAGTACACGCTTTCC 59.751 43.478 1.43 0.00 0.00 3.13
83 84 3.497262 GCTTTTGTAGTACACGCTTTCCT 59.503 43.478 1.43 0.00 0.00 3.36
84 85 4.024302 GCTTTTGTAGTACACGCTTTCCTT 60.024 41.667 1.43 0.00 0.00 3.36
85 86 5.178067 GCTTTTGTAGTACACGCTTTCCTTA 59.822 40.000 1.43 0.00 0.00 2.69
86 87 6.293027 GCTTTTGTAGTACACGCTTTCCTTAA 60.293 38.462 1.43 0.00 0.00 1.85
87 88 7.572539 GCTTTTGTAGTACACGCTTTCCTTAAT 60.573 37.037 1.43 0.00 0.00 1.40
88 89 6.956299 TTGTAGTACACGCTTTCCTTAATC 57.044 37.500 1.43 0.00 0.00 1.75
89 90 6.276832 TGTAGTACACGCTTTCCTTAATCT 57.723 37.500 0.00 0.00 0.00 2.40
90 91 6.327934 TGTAGTACACGCTTTCCTTAATCTC 58.672 40.000 0.00 0.00 0.00 2.75
91 92 4.421948 AGTACACGCTTTCCTTAATCTCG 58.578 43.478 0.00 0.00 0.00 4.04
95 96 2.280628 CGCTTTCCTTAATCTCGCCTT 58.719 47.619 0.00 0.00 0.00 4.35
103 104 4.876107 TCCTTAATCTCGCCTTGTGATTTC 59.124 41.667 0.00 0.00 40.35 2.17
160 162 2.305635 TGCTCTTCACCAGGCAGATTTA 59.694 45.455 0.00 0.00 0.00 1.40
162 164 3.314635 GCTCTTCACCAGGCAGATTTATG 59.685 47.826 0.00 0.00 0.00 1.90
163 165 4.521146 CTCTTCACCAGGCAGATTTATGT 58.479 43.478 0.00 0.00 0.00 2.29
164 166 4.922206 TCTTCACCAGGCAGATTTATGTT 58.078 39.130 0.00 0.00 0.00 2.71
165 167 5.324409 TCTTCACCAGGCAGATTTATGTTT 58.676 37.500 0.00 0.00 0.00 2.83
167 169 6.945435 TCTTCACCAGGCAGATTTATGTTTTA 59.055 34.615 0.00 0.00 0.00 1.52
168 170 7.615365 TCTTCACCAGGCAGATTTATGTTTTAT 59.385 33.333 0.00 0.00 0.00 1.40
169 171 7.716799 TCACCAGGCAGATTTATGTTTTATT 57.283 32.000 0.00 0.00 0.00 1.40
170 172 8.133024 TCACCAGGCAGATTTATGTTTTATTT 57.867 30.769 0.00 0.00 0.00 1.40
171 173 9.249053 TCACCAGGCAGATTTATGTTTTATTTA 57.751 29.630 0.00 0.00 0.00 1.40
174 200 9.480053 CCAGGCAGATTTATGTTTTATTTATGG 57.520 33.333 0.00 0.00 0.00 2.74
220 246 1.134037 GTGTTGGTGTTACTGGGTCCA 60.134 52.381 0.00 0.00 0.00 4.02
223 249 0.695924 TGGTGTTACTGGGTCCATGG 59.304 55.000 4.97 4.97 0.00 3.66
244 270 3.559171 GGAACATTGTACCTCAGGCTTGA 60.559 47.826 0.00 0.00 0.00 3.02
264 290 5.422666 TGAACATGAAAGTGTGTTGCTAG 57.577 39.130 0.00 0.00 38.57 3.42
270 296 7.959940 AACATGAAAGTGTGTTGCTAGGATACT 60.960 37.037 0.00 0.00 43.14 2.12
298 324 8.413229 ACATTTATTACTTACATTGCATGGGTC 58.587 33.333 0.00 0.00 33.60 4.46
300 326 2.489938 ACTTACATTGCATGGGTCGT 57.510 45.000 0.00 0.00 33.60 4.34
317 343 3.364964 GGTCGTGCACCAAATTACTCAAG 60.365 47.826 12.15 0.00 45.98 3.02
318 344 3.250040 GTCGTGCACCAAATTACTCAAGT 59.750 43.478 12.15 0.00 0.00 3.16
425 451 1.133823 TGTGCACATTGGGAACAGACT 60.134 47.619 17.42 0.00 44.54 3.24
431 457 4.389374 CACATTGGGAACAGACTAGTGTT 58.611 43.478 0.00 0.00 44.54 3.32
514 540 3.375299 CCCTTTCGTTCCTTGAATGCTAG 59.625 47.826 0.00 0.00 0.00 3.42
517 543 1.906574 TCGTTCCTTGAATGCTAGGGT 59.093 47.619 0.86 0.00 37.58 4.34
527 553 1.207791 ATGCTAGGGTTCCTGGACAG 58.792 55.000 0.00 0.00 33.74 3.51
550 576 8.646900 ACAGTTGATAAGAAAAATAAAAGCCCA 58.353 29.630 0.00 0.00 0.00 5.36
562 588 3.457610 AAAAGCCCACACATTGTCTTG 57.542 42.857 0.00 0.00 0.00 3.02
574 600 5.471456 ACACATTGTCTTGAAGAACTCATCC 59.529 40.000 0.00 0.00 32.78 3.51
575 601 4.692625 ACATTGTCTTGAAGAACTCATCCG 59.307 41.667 0.00 0.00 32.78 4.18
690 716 9.547753 CAGTTGTAGCACTAACAATAATATCCT 57.452 33.333 0.00 0.00 38.95 3.24
699 725 7.652105 CACTAACAATAATATCCTACACACGCT 59.348 37.037 0.00 0.00 0.00 5.07
702 728 6.346096 ACAATAATATCCTACACACGCTTGT 58.654 36.000 0.00 0.00 35.84 3.16
720 746 6.037172 ACGCTTGTATGATAATTGGTCTGTTC 59.963 38.462 0.00 0.00 0.00 3.18
721 747 6.511767 CGCTTGTATGATAATTGGTCTGTTCC 60.512 42.308 0.00 0.00 0.00 3.62
722 748 6.543831 GCTTGTATGATAATTGGTCTGTTCCT 59.456 38.462 0.00 0.00 0.00 3.36
723 749 7.067494 GCTTGTATGATAATTGGTCTGTTCCTT 59.933 37.037 0.00 0.00 0.00 3.36
724 750 8.877864 TTGTATGATAATTGGTCTGTTCCTTT 57.122 30.769 0.00 0.00 0.00 3.11
725 751 8.877864 TGTATGATAATTGGTCTGTTCCTTTT 57.122 30.769 0.00 0.00 0.00 2.27
726 752 8.956426 TGTATGATAATTGGTCTGTTCCTTTTC 58.044 33.333 0.00 0.00 0.00 2.29
727 753 9.178758 GTATGATAATTGGTCTGTTCCTTTTCT 57.821 33.333 0.00 0.00 0.00 2.52
728 754 8.655935 ATGATAATTGGTCTGTTCCTTTTCTT 57.344 30.769 0.00 0.00 0.00 2.52
729 755 8.477419 TGATAATTGGTCTGTTCCTTTTCTTT 57.523 30.769 0.00 0.00 0.00 2.52
730 756 8.923270 TGATAATTGGTCTGTTCCTTTTCTTTT 58.077 29.630 0.00 0.00 0.00 2.27
731 757 9.764363 GATAATTGGTCTGTTCCTTTTCTTTTT 57.236 29.630 0.00 0.00 0.00 1.94
751 777 5.514274 TTTTGCGAGAAAACTTCCAATCT 57.486 34.783 0.00 0.00 0.00 2.40
752 778 6.627395 TTTTGCGAGAAAACTTCCAATCTA 57.373 33.333 0.00 0.00 0.00 1.98
753 779 6.817765 TTTGCGAGAAAACTTCCAATCTAT 57.182 33.333 0.00 0.00 0.00 1.98
754 780 6.817765 TTGCGAGAAAACTTCCAATCTATT 57.182 33.333 0.00 0.00 0.00 1.73
755 781 6.422776 TGCGAGAAAACTTCCAATCTATTC 57.577 37.500 0.00 0.00 0.00 1.75
756 782 5.937540 TGCGAGAAAACTTCCAATCTATTCA 59.062 36.000 0.00 0.00 0.00 2.57
757 783 6.599244 TGCGAGAAAACTTCCAATCTATTCAT 59.401 34.615 0.00 0.00 0.00 2.57
758 784 7.128976 GCGAGAAAACTTCCAATCTATTCATC 58.871 38.462 0.00 0.00 0.00 2.92
759 785 7.201644 GCGAGAAAACTTCCAATCTATTCATCA 60.202 37.037 0.00 0.00 0.00 3.07
760 786 8.668353 CGAGAAAACTTCCAATCTATTCATCAA 58.332 33.333 0.00 0.00 0.00 2.57
761 787 9.780413 GAGAAAACTTCCAATCTATTCATCAAC 57.220 33.333 0.00 0.00 0.00 3.18
762 788 9.525826 AGAAAACTTCCAATCTATTCATCAACT 57.474 29.630 0.00 0.00 0.00 3.16
763 789 9.565213 GAAAACTTCCAATCTATTCATCAACTG 57.435 33.333 0.00 0.00 0.00 3.16
764 790 8.641498 AAACTTCCAATCTATTCATCAACTGT 57.359 30.769 0.00 0.00 0.00 3.55
765 791 7.856145 ACTTCCAATCTATTCATCAACTGTC 57.144 36.000 0.00 0.00 0.00 3.51
766 792 7.397221 ACTTCCAATCTATTCATCAACTGTCA 58.603 34.615 0.00 0.00 0.00 3.58
767 793 7.884877 ACTTCCAATCTATTCATCAACTGTCAA 59.115 33.333 0.00 0.00 0.00 3.18
768 794 7.854557 TCCAATCTATTCATCAACTGTCAAG 57.145 36.000 0.00 0.00 0.00 3.02
769 795 6.825213 TCCAATCTATTCATCAACTGTCAAGG 59.175 38.462 0.00 0.00 0.00 3.61
817 843 0.885879 TGTGCCACCTCGTAGTACTG 59.114 55.000 5.39 0.00 0.00 2.74
951 985 3.588842 AGAAGAAGTTCATCATGACCCCA 59.411 43.478 10.51 0.00 34.82 4.96
1062 1096 2.675844 TGTTGGTTCACTGAAACTGTCG 59.324 45.455 8.30 0.00 29.52 4.35
1097 1131 6.839124 ATTCCAGCAATCTTGTAACAATGA 57.161 33.333 0.00 0.00 0.00 2.57
1119 1153 4.955811 AGTTATGTTCCTATCCATGCGA 57.044 40.909 0.00 0.00 0.00 5.10
1375 1409 6.706055 TTTACTGAGACTGCACTTTTATCG 57.294 37.500 0.00 0.00 0.00 2.92
1402 1436 5.479306 TCTGTCTGTTGTACTATCTTTGGC 58.521 41.667 0.00 0.00 0.00 4.52
1426 1460 4.913924 GTGATGCACAACTCATTTCTTCAC 59.086 41.667 0.00 0.00 34.08 3.18
1564 1603 8.575454 GTTGTTATTTAGCTCGCATTTAACTTG 58.425 33.333 0.00 0.00 0.00 3.16
1572 1611 4.435651 GCTCGCATTTAACTTGTACCAGTC 60.436 45.833 0.00 0.00 0.00 3.51
1573 1612 3.676172 TCGCATTTAACTTGTACCAGTCG 59.324 43.478 0.00 0.00 0.00 4.18
1669 1708 2.286365 TTCACTGCTACAAAAGGGGG 57.714 50.000 0.00 0.00 0.00 5.40
1714 1753 7.733773 TCATCCTATGTTTCTTGAGAAGGTA 57.266 36.000 0.00 0.00 35.21 3.08
1877 1916 4.322499 GGAACAGACTTCCGAGATAACCAA 60.322 45.833 0.00 0.00 0.00 3.67
1955 1994 5.805994 GTGACTAGCACCTCACTTATGTAAC 59.194 44.000 4.41 0.00 41.78 2.50
2408 2521 4.941263 TGTTGACAAGTAGGGAATATGCAC 59.059 41.667 0.00 0.00 0.00 4.57
2522 2635 0.622665 CAGGGCAGATTTCCCAGAGT 59.377 55.000 0.48 0.00 46.36 3.24
2764 2888 8.784043 GTTAGTCCACATTATGTCAAAGAACTT 58.216 33.333 0.00 0.00 0.00 2.66
2852 2976 8.601047 TGGAATTGTAAATGGAATGGATGTTA 57.399 30.769 0.00 0.00 0.00 2.41
2928 3052 1.276622 GTAAGGCTTCAGTGGGAGGA 58.723 55.000 1.30 0.00 0.00 3.71
2951 3075 5.964958 TTCTCCTCTTTTGCCAGTTATTG 57.035 39.130 0.00 0.00 0.00 1.90
2953 3077 3.495331 TCCTCTTTTGCCAGTTATTGCA 58.505 40.909 0.00 0.00 35.27 4.08
2965 3089 6.207221 TGCCAGTTATTGCAACATATGGATAG 59.793 38.462 20.82 0.00 33.87 2.08
2999 3123 0.883833 AGAGCATTTTTCAGGTGGCG 59.116 50.000 0.00 0.00 0.00 5.69
3032 3156 7.495279 AGAGCTCTCAATAAAGAAATACTGCAG 59.505 37.037 11.45 13.48 0.00 4.41
3250 3374 8.045176 AGAAGATGATTGTTGCTTAGGTAAAC 57.955 34.615 0.00 0.00 0.00 2.01
3253 3377 6.942576 AGATGATTGTTGCTTAGGTAAACTGT 59.057 34.615 0.00 0.00 0.00 3.55
3378 3502 1.404449 CCATTGGCGCACATGATGTTT 60.404 47.619 17.28 0.00 0.00 2.83
3388 3512 0.751277 CATGATGTTTGCCGGGGCTA 60.751 55.000 11.55 0.00 42.51 3.93
3466 3590 4.284490 GGATGAGATATGGAGTGGTAAGCA 59.716 45.833 0.00 0.00 0.00 3.91
3481 3605 2.215907 AAGCATTCCGACTCGATCAG 57.784 50.000 0.00 0.00 0.00 2.90
3484 3608 1.590238 GCATTCCGACTCGATCAGTTG 59.410 52.381 0.00 0.00 34.41 3.16
3763 3887 3.121030 GCAGATGTCGCGGCAGTT 61.121 61.111 21.72 1.90 0.00 3.16
3875 3999 1.168714 GGTGGGCAGAACTGTCAATC 58.831 55.000 8.64 0.00 36.81 2.67
3946 4071 6.794534 ACAAGGGTAAATTGATCCTCTCTTT 58.205 36.000 0.00 0.00 0.00 2.52
4338 4471 1.814772 TTTGTGCCATTTGCCTCCGG 61.815 55.000 0.00 0.00 40.16 5.14
4361 4494 1.821136 CTGCCAAATCAAGAACTCCCC 59.179 52.381 0.00 0.00 0.00 4.81
4385 4518 6.371271 CCCACCAAAATTGCCTAATAAGTTTG 59.629 38.462 0.00 0.00 40.66 2.93
4386 4519 6.934083 CCACCAAAATTGCCTAATAAGTTTGT 59.066 34.615 0.00 0.00 39.86 2.83
4387 4520 7.443879 CCACCAAAATTGCCTAATAAGTTTGTT 59.556 33.333 0.00 0.00 39.86 2.83
4388 4521 8.835439 CACCAAAATTGCCTAATAAGTTTGTTT 58.165 29.630 0.00 0.00 39.86 2.83
4394 4527 9.586435 AATTGCCTAATAAGTTTGTTTAGATGC 57.414 29.630 0.00 0.00 0.00 3.91
4395 4528 7.938140 TGCCTAATAAGTTTGTTTAGATGCT 57.062 32.000 0.00 0.00 0.00 3.79
4396 4529 7.985476 TGCCTAATAAGTTTGTTTAGATGCTC 58.015 34.615 0.00 0.00 0.00 4.26
4397 4530 7.609918 TGCCTAATAAGTTTGTTTAGATGCTCA 59.390 33.333 0.00 0.00 0.00 4.26
4398 4531 7.910683 GCCTAATAAGTTTGTTTAGATGCTCAC 59.089 37.037 0.00 0.00 0.00 3.51
4399 4532 8.946085 CCTAATAAGTTTGTTTAGATGCTCACA 58.054 33.333 0.00 0.00 0.00 3.58
4402 4535 9.683069 AATAAGTTTGTTTAGATGCTCACAAAG 57.317 29.630 0.00 0.00 39.25 2.77
4403 4536 6.076981 AGTTTGTTTAGATGCTCACAAAGG 57.923 37.500 0.00 0.00 39.25 3.11
4404 4537 4.503741 TTGTTTAGATGCTCACAAAGGC 57.496 40.909 0.00 0.00 0.00 4.35
4405 4538 2.819608 TGTTTAGATGCTCACAAAGGCC 59.180 45.455 0.00 0.00 0.00 5.19
4406 4539 2.128771 TTAGATGCTCACAAAGGCCC 57.871 50.000 0.00 0.00 0.00 5.80
4407 4540 0.255890 TAGATGCTCACAAAGGCCCC 59.744 55.000 0.00 0.00 0.00 5.80
4408 4541 1.000396 GATGCTCACAAAGGCCCCT 60.000 57.895 0.00 0.00 0.00 4.79
4409 4542 0.613012 GATGCTCACAAAGGCCCCTT 60.613 55.000 0.00 0.00 37.98 3.95
4410 4543 0.901580 ATGCTCACAAAGGCCCCTTG 60.902 55.000 12.56 12.56 36.26 3.61
4411 4544 2.278330 GCTCACAAAGGCCCCTTGG 61.278 63.158 17.21 0.00 36.26 3.61
4427 4560 3.552890 CCCTTGGCAGTTTAAAGCAAGAC 60.553 47.826 0.00 0.00 0.00 3.01
4446 4579 3.199071 AGACATAGAATAAACCGGCACCA 59.801 43.478 0.00 0.00 0.00 4.17
4452 4585 2.863132 ATAAACCGGCACCACTTGTA 57.137 45.000 0.00 0.00 0.00 2.41
4470 4603 5.885912 ACTTGTACAACAGATTTCACCAGTT 59.114 36.000 3.59 0.00 0.00 3.16
4471 4604 6.038271 ACTTGTACAACAGATTTCACCAGTTC 59.962 38.462 3.59 0.00 0.00 3.01
4480 4613 4.597507 AGATTTCACCAGTTCCTCCTTACA 59.402 41.667 0.00 0.00 0.00 2.41
4481 4614 3.764237 TTCACCAGTTCCTCCTTACAC 57.236 47.619 0.00 0.00 0.00 2.90
4483 4616 0.320697 ACCAGTTCCTCCTTACACGC 59.679 55.000 0.00 0.00 0.00 5.34
4484 4617 0.391263 CCAGTTCCTCCTTACACGCC 60.391 60.000 0.00 0.00 0.00 5.68
4485 4618 0.736325 CAGTTCCTCCTTACACGCCG 60.736 60.000 0.00 0.00 0.00 6.46
4486 4619 1.447314 GTTCCTCCTTACACGCCGG 60.447 63.158 0.00 0.00 0.00 6.13
4506 4639 4.332819 CCGGCGATAAAGTTTTCTCAATCT 59.667 41.667 9.30 0.00 0.00 2.40
4523 4656 8.329346 TCTCAATCTATCCCTTCATCTTTCTT 57.671 34.615 0.00 0.00 0.00 2.52
4534 4667 5.049129 CCTTCATCTTTCTTCACAACCTGTC 60.049 44.000 0.00 0.00 0.00 3.51
4567 4700 7.900782 ACTTGAATGCTTACTATTACGTGTT 57.099 32.000 0.00 0.00 0.00 3.32
4568 4701 7.960793 ACTTGAATGCTTACTATTACGTGTTC 58.039 34.615 0.00 0.00 0.00 3.18
4569 4702 6.897259 TGAATGCTTACTATTACGTGTTCC 57.103 37.500 0.00 0.00 0.00 3.62
4598 4731 2.647299 TGTGAATCAAAGAGGGCCCTAA 59.353 45.455 28.78 8.65 0.00 2.69
4782 4917 7.908082 TGATTGTCGTTTTACTGTCTCAAAAAG 59.092 33.333 0.00 0.00 0.00 2.27
4864 5002 6.467723 AGAAATGACAACGACTCACATAAC 57.532 37.500 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.159382 CCACAACACCCTCAATGGTAC 58.841 52.381 0.00 0.00 36.67 3.34
6 7 2.058705 TCCACAACACCCTCAATGGTA 58.941 47.619 0.00 0.00 36.67 3.25
7 8 0.850100 TCCACAACACCCTCAATGGT 59.150 50.000 0.00 0.00 39.96 3.55
8 9 1.888512 CTTCCACAACACCCTCAATGG 59.111 52.381 0.00 0.00 0.00 3.16
9 10 1.270550 GCTTCCACAACACCCTCAATG 59.729 52.381 0.00 0.00 0.00 2.82
10 11 1.620822 GCTTCCACAACACCCTCAAT 58.379 50.000 0.00 0.00 0.00 2.57
11 12 0.467290 GGCTTCCACAACACCCTCAA 60.467 55.000 0.00 0.00 0.00 3.02
12 13 1.150536 GGCTTCCACAACACCCTCA 59.849 57.895 0.00 0.00 0.00 3.86
13 14 1.150536 TGGCTTCCACAACACCCTC 59.849 57.895 0.00 0.00 0.00 4.30
14 15 3.341270 TGGCTTCCACAACACCCT 58.659 55.556 0.00 0.00 0.00 4.34
23 24 3.948719 GGTCACCGGTGGCTTCCA 61.949 66.667 36.07 13.39 35.13 3.53
24 25 3.901797 CTGGTCACCGGTGGCTTCC 62.902 68.421 36.07 28.00 35.13 3.46
25 26 1.823169 TACTGGTCACCGGTGGCTTC 61.823 60.000 36.07 22.32 43.80 3.86
26 27 1.198759 ATACTGGTCACCGGTGGCTT 61.199 55.000 36.07 23.18 43.80 4.35
27 28 1.198759 AATACTGGTCACCGGTGGCT 61.199 55.000 36.07 20.96 43.80 4.75
28 29 0.322187 AAATACTGGTCACCGGTGGC 60.322 55.000 33.40 32.34 43.80 5.01
29 30 3.202906 CATAAATACTGGTCACCGGTGG 58.797 50.000 33.40 19.88 43.80 4.61
30 31 3.869065 ACATAAATACTGGTCACCGGTG 58.131 45.455 29.26 29.26 43.80 4.94
31 32 4.563140 AACATAAATACTGGTCACCGGT 57.437 40.909 14.40 14.40 46.08 5.28
32 33 5.890424 AAAACATAAATACTGGTCACCGG 57.110 39.130 0.00 0.00 35.68 5.28
51 52 9.332301 GCGTGTACTACAAAAGCATAAATAAAA 57.668 29.630 0.00 0.00 0.00 1.52
52 53 8.723311 AGCGTGTACTACAAAAGCATAAATAAA 58.277 29.630 12.34 0.00 30.97 1.40
53 54 8.259049 AGCGTGTACTACAAAAGCATAAATAA 57.741 30.769 12.34 0.00 30.97 1.40
54 55 7.837202 AGCGTGTACTACAAAAGCATAAATA 57.163 32.000 12.34 0.00 30.97 1.40
55 56 6.737254 AGCGTGTACTACAAAAGCATAAAT 57.263 33.333 12.34 0.00 30.97 1.40
56 57 6.548441 AAGCGTGTACTACAAAAGCATAAA 57.452 33.333 12.34 0.00 30.97 1.40
57 58 6.347888 GGAAAGCGTGTACTACAAAAGCATAA 60.348 38.462 12.34 0.00 30.97 1.90
58 59 5.121142 GGAAAGCGTGTACTACAAAAGCATA 59.879 40.000 12.34 0.00 30.97 3.14
59 60 4.083484 GGAAAGCGTGTACTACAAAAGCAT 60.083 41.667 12.34 1.80 30.97 3.79
60 61 3.249080 GGAAAGCGTGTACTACAAAAGCA 59.751 43.478 12.34 0.00 30.97 3.91
61 62 3.497262 AGGAAAGCGTGTACTACAAAAGC 59.503 43.478 0.00 0.00 0.00 3.51
62 63 5.668558 AAGGAAAGCGTGTACTACAAAAG 57.331 39.130 0.00 0.00 0.00 2.27
63 64 7.658575 AGATTAAGGAAAGCGTGTACTACAAAA 59.341 33.333 0.00 0.00 0.00 2.44
64 65 7.156673 AGATTAAGGAAAGCGTGTACTACAAA 58.843 34.615 0.00 0.00 0.00 2.83
65 66 6.694447 AGATTAAGGAAAGCGTGTACTACAA 58.306 36.000 0.00 0.00 0.00 2.41
66 67 6.276832 AGATTAAGGAAAGCGTGTACTACA 57.723 37.500 0.00 0.00 0.00 2.74
67 68 5.454877 CGAGATTAAGGAAAGCGTGTACTAC 59.545 44.000 0.00 0.00 0.00 2.73
68 69 5.575957 CGAGATTAAGGAAAGCGTGTACTA 58.424 41.667 0.00 0.00 0.00 1.82
69 70 4.421948 CGAGATTAAGGAAAGCGTGTACT 58.578 43.478 0.00 0.00 0.00 2.73
70 71 3.000022 GCGAGATTAAGGAAAGCGTGTAC 60.000 47.826 0.00 0.00 0.00 2.90
71 72 3.184541 GCGAGATTAAGGAAAGCGTGTA 58.815 45.455 0.00 0.00 0.00 2.90
72 73 2.000447 GCGAGATTAAGGAAAGCGTGT 59.000 47.619 0.00 0.00 0.00 4.49
73 74 1.327764 GGCGAGATTAAGGAAAGCGTG 59.672 52.381 0.00 0.00 0.00 5.34
74 75 1.207329 AGGCGAGATTAAGGAAAGCGT 59.793 47.619 0.00 0.00 0.00 5.07
75 76 1.941325 AGGCGAGATTAAGGAAAGCG 58.059 50.000 0.00 0.00 0.00 4.68
76 77 3.010420 ACAAGGCGAGATTAAGGAAAGC 58.990 45.455 0.00 0.00 0.00 3.51
77 78 4.253685 TCACAAGGCGAGATTAAGGAAAG 58.746 43.478 0.00 0.00 0.00 2.62
78 79 4.280436 TCACAAGGCGAGATTAAGGAAA 57.720 40.909 0.00 0.00 0.00 3.13
79 80 3.973206 TCACAAGGCGAGATTAAGGAA 57.027 42.857 0.00 0.00 0.00 3.36
80 81 4.487714 AATCACAAGGCGAGATTAAGGA 57.512 40.909 0.00 0.00 33.70 3.36
81 82 4.260375 CGAAATCACAAGGCGAGATTAAGG 60.260 45.833 0.00 0.00 34.27 2.69
82 83 4.330074 ACGAAATCACAAGGCGAGATTAAG 59.670 41.667 0.00 0.00 34.27 1.85
83 84 4.250464 ACGAAATCACAAGGCGAGATTAA 58.750 39.130 0.00 0.00 34.27 1.40
84 85 3.857052 ACGAAATCACAAGGCGAGATTA 58.143 40.909 0.00 0.00 34.27 1.75
85 86 2.699954 ACGAAATCACAAGGCGAGATT 58.300 42.857 0.00 0.00 36.60 2.40
86 87 2.386661 ACGAAATCACAAGGCGAGAT 57.613 45.000 0.00 0.00 0.00 2.75
87 88 2.163818 AACGAAATCACAAGGCGAGA 57.836 45.000 0.00 0.00 0.00 4.04
88 89 4.600012 AATAACGAAATCACAAGGCGAG 57.400 40.909 0.00 0.00 0.00 5.03
89 90 5.365403 AAAATAACGAAATCACAAGGCGA 57.635 34.783 0.00 0.00 0.00 5.54
90 91 6.579292 TGTAAAAATAACGAAATCACAAGGCG 59.421 34.615 0.00 0.00 0.00 5.52
91 92 7.861176 TGTAAAAATAACGAAATCACAAGGC 57.139 32.000 0.00 0.00 0.00 4.35
95 96 9.605955 CTGACATGTAAAAATAACGAAATCACA 57.394 29.630 0.00 0.00 0.00 3.58
103 104 7.526608 ACACATCCTGACATGTAAAAATAACG 58.473 34.615 0.00 0.00 35.10 3.18
193 219 0.037160 GTAACACCAACACCCCGGAT 59.963 55.000 0.73 0.00 0.00 4.18
200 226 1.134037 TGGACCCAGTAACACCAACAC 60.134 52.381 0.00 0.00 0.00 3.32
203 229 1.074727 CCATGGACCCAGTAACACCAA 59.925 52.381 5.56 0.00 34.28 3.67
220 246 2.578021 AGCCTGAGGTACAATGTTCCAT 59.422 45.455 11.58 0.00 0.00 3.41
223 249 3.674997 TCAAGCCTGAGGTACAATGTTC 58.325 45.455 0.00 0.00 0.00 3.18
244 270 4.460263 TCCTAGCAACACACTTTCATGTT 58.540 39.130 0.00 0.00 39.63 2.71
270 296 8.412456 CCCATGCAATGTAAGTAATAAATGTCA 58.588 33.333 0.00 0.00 44.81 3.58
298 324 3.896648 ACTTGAGTAATTTGGTGCACG 57.103 42.857 11.45 0.00 0.00 5.34
300 326 8.417106 TGAATTTTACTTGAGTAATTTGGTGCA 58.583 29.630 4.57 0.00 39.89 4.57
381 407 8.845227 ACATCAAGTGTTTAACAATGTGATACA 58.155 29.630 16.25 0.00 38.01 2.29
402 428 1.887854 CTGTTCCCAATGTGCACATCA 59.112 47.619 31.45 21.63 35.10 3.07
425 451 3.028850 CCTCCCGATAACCAGAACACTA 58.971 50.000 0.00 0.00 0.00 2.74
431 457 0.325296 ACAGCCTCCCGATAACCAGA 60.325 55.000 0.00 0.00 0.00 3.86
462 488 3.541632 CCAGCCGTTGGTATAGAACAAT 58.458 45.455 0.00 0.00 42.41 2.71
514 540 3.263425 TCTTATCAACTGTCCAGGAACCC 59.737 47.826 0.00 0.00 0.00 4.11
517 543 9.581289 TTATTTTTCTTATCAACTGTCCAGGAA 57.419 29.630 0.00 0.00 0.00 3.36
527 553 8.708742 GTGTGGGCTTTTATTTTTCTTATCAAC 58.291 33.333 0.00 0.00 0.00 3.18
550 576 5.471456 GGATGAGTTCTTCAAGACAATGTGT 59.529 40.000 0.00 0.00 39.77 3.72
562 588 0.729690 GCCTTGCGGATGAGTTCTTC 59.270 55.000 0.00 0.00 0.00 2.87
574 600 2.061028 GAAAGAAACCAATGCCTTGCG 58.939 47.619 0.00 0.00 0.00 4.85
575 601 2.061028 CGAAAGAAACCAATGCCTTGC 58.939 47.619 0.00 0.00 0.00 4.01
618 644 7.929785 GGAAGTTCCATTACGGATATGTTCTAA 59.070 37.037 17.44 0.00 45.80 2.10
631 657 5.468540 AGGCAAAAAGGAAGTTCCATTAC 57.531 39.130 23.87 10.91 39.61 1.89
690 716 6.110033 ACCAATTATCATACAAGCGTGTGTA 58.890 36.000 15.96 7.90 38.82 2.90
699 725 8.877864 AAAGGAACAGACCAATTATCATACAA 57.122 30.769 0.00 0.00 0.00 2.41
702 728 9.753674 AAGAAAAGGAACAGACCAATTATCATA 57.246 29.630 0.00 0.00 0.00 2.15
728 754 5.901552 AGATTGGAAGTTTTCTCGCAAAAA 58.098 33.333 0.00 0.00 0.00 1.94
729 755 5.514274 AGATTGGAAGTTTTCTCGCAAAA 57.486 34.783 0.00 0.00 0.00 2.44
730 756 6.817765 ATAGATTGGAAGTTTTCTCGCAAA 57.182 33.333 0.00 0.00 0.00 3.68
731 757 6.429692 TGAATAGATTGGAAGTTTTCTCGCAA 59.570 34.615 0.00 0.00 0.00 4.85
732 758 5.937540 TGAATAGATTGGAAGTTTTCTCGCA 59.062 36.000 0.00 0.00 0.00 5.10
733 759 6.422776 TGAATAGATTGGAAGTTTTCTCGC 57.577 37.500 0.00 0.00 0.00 5.03
734 760 8.201554 TGATGAATAGATTGGAAGTTTTCTCG 57.798 34.615 0.00 0.00 0.00 4.04
735 761 9.780413 GTTGATGAATAGATTGGAAGTTTTCTC 57.220 33.333 0.00 0.00 0.00 2.87
736 762 9.525826 AGTTGATGAATAGATTGGAAGTTTTCT 57.474 29.630 0.00 0.00 0.00 2.52
737 763 9.565213 CAGTTGATGAATAGATTGGAAGTTTTC 57.435 33.333 0.00 0.00 0.00 2.29
738 764 9.082313 ACAGTTGATGAATAGATTGGAAGTTTT 57.918 29.630 0.00 0.00 0.00 2.43
739 765 8.641498 ACAGTTGATGAATAGATTGGAAGTTT 57.359 30.769 0.00 0.00 0.00 2.66
740 766 7.884877 TGACAGTTGATGAATAGATTGGAAGTT 59.115 33.333 0.00 0.00 0.00 2.66
741 767 7.397221 TGACAGTTGATGAATAGATTGGAAGT 58.603 34.615 0.00 0.00 0.00 3.01
742 768 7.854557 TGACAGTTGATGAATAGATTGGAAG 57.145 36.000 0.00 0.00 0.00 3.46
743 769 7.337689 CCTTGACAGTTGATGAATAGATTGGAA 59.662 37.037 0.00 0.00 0.00 3.53
744 770 6.825213 CCTTGACAGTTGATGAATAGATTGGA 59.175 38.462 0.00 0.00 0.00 3.53
745 771 6.459298 GCCTTGACAGTTGATGAATAGATTGG 60.459 42.308 0.00 0.00 0.00 3.16
746 772 6.094464 TGCCTTGACAGTTGATGAATAGATTG 59.906 38.462 0.00 0.00 0.00 2.67
747 773 6.182627 TGCCTTGACAGTTGATGAATAGATT 58.817 36.000 0.00 0.00 0.00 2.40
748 774 5.748402 TGCCTTGACAGTTGATGAATAGAT 58.252 37.500 0.00 0.00 0.00 1.98
749 775 5.164620 TGCCTTGACAGTTGATGAATAGA 57.835 39.130 0.00 0.00 0.00 1.98
750 776 4.334759 CCTGCCTTGACAGTTGATGAATAG 59.665 45.833 0.00 0.00 35.83 1.73
751 777 4.264253 CCTGCCTTGACAGTTGATGAATA 58.736 43.478 0.00 0.00 35.83 1.75
752 778 3.087031 CCTGCCTTGACAGTTGATGAAT 58.913 45.455 0.00 0.00 35.83 2.57
753 779 2.507484 CCTGCCTTGACAGTTGATGAA 58.493 47.619 0.00 0.00 35.83 2.57
754 780 1.271543 CCCTGCCTTGACAGTTGATGA 60.272 52.381 0.00 0.00 35.83 2.92
755 781 1.171308 CCCTGCCTTGACAGTTGATG 58.829 55.000 0.00 0.00 35.83 3.07
756 782 0.773644 ACCCTGCCTTGACAGTTGAT 59.226 50.000 0.00 0.00 35.83 2.57
757 783 1.429930 TACCCTGCCTTGACAGTTGA 58.570 50.000 0.00 0.00 35.83 3.18
758 784 2.086869 CATACCCTGCCTTGACAGTTG 58.913 52.381 0.00 0.00 35.83 3.16
759 785 1.614317 GCATACCCTGCCTTGACAGTT 60.614 52.381 0.00 0.00 45.66 3.16
760 786 0.035056 GCATACCCTGCCTTGACAGT 60.035 55.000 0.00 0.00 45.66 3.55
761 787 2.785868 GCATACCCTGCCTTGACAG 58.214 57.895 0.00 0.00 45.66 3.51
769 795 4.146071 GCTAACTGCTTGCATACCCTGC 62.146 54.545 0.00 0.00 44.34 4.85
793 819 1.346395 ACTACGAGGTGGCACATGAAA 59.654 47.619 20.82 0.42 44.52 2.69
1062 1096 0.743097 GCTGGAATTGGATGTGAGGC 59.257 55.000 0.00 0.00 0.00 4.70
1097 1131 5.290493 TCGCATGGATAGGAACATAACTT 57.710 39.130 0.00 0.00 0.00 2.66
1107 1141 5.056480 TGTGTCTTATTTCGCATGGATAGG 58.944 41.667 0.00 0.00 0.00 2.57
1108 1142 5.333645 GCTGTGTCTTATTTCGCATGGATAG 60.334 44.000 0.00 0.00 0.00 2.08
1119 1153 2.584835 TGGCCAGCTGTGTCTTATTT 57.415 45.000 13.81 0.00 0.00 1.40
1314 1348 4.689345 AGAATTAACAGTACGTGACAAGGC 59.311 41.667 0.00 0.00 0.00 4.35
1375 1409 3.702045 AGATAGTACAACAGACAGAGGGC 59.298 47.826 0.00 0.00 0.00 5.19
1402 1436 3.818961 AGAAATGAGTTGTGCATCACG 57.181 42.857 0.00 0.00 37.14 4.35
1516 1550 7.826744 ACAACACCCAACAAATCAACTAAAAAT 59.173 29.630 0.00 0.00 0.00 1.82
1572 1611 7.635423 TGTTTTTAGCATATATAACACCAGCG 58.365 34.615 0.00 0.00 0.00 5.18
1573 1612 8.621286 ACTGTTTTTAGCATATATAACACCAGC 58.379 33.333 0.00 0.00 0.00 4.85
1669 1708 5.277825 TGATCAACAAAAACACGATCAACC 58.722 37.500 0.00 0.00 39.49 3.77
1877 1916 2.030274 GCACAAAAGGCAGAACCGTAAT 60.030 45.455 0.00 0.00 46.52 1.89
1955 1994 4.394729 TCAGCTAAAACAAGGGTTGGTAG 58.605 43.478 0.00 0.00 37.30 3.18
2354 2467 1.423541 AGTGGTGTACCTTGGCATTCA 59.576 47.619 2.32 0.00 36.82 2.57
2408 2521 4.780815 TCTGTGGAGCATAAAACCTATGG 58.219 43.478 0.00 0.00 0.00 2.74
2522 2635 7.386848 CAGGTAAATTAAGAAGTTCGAAGTCCA 59.613 37.037 5.84 0.00 0.00 4.02
2638 2762 6.239008 GCCTGCACACAATTATGGTATATGTT 60.239 38.462 0.00 0.00 0.00 2.71
2764 2888 1.909302 CCTTTCTCTGGGCCAGAAGTA 59.091 52.381 34.25 20.85 40.18 2.24
2852 2976 4.346730 TCTGTTGCTGGATTCCAATCAAT 58.653 39.130 17.75 0.00 37.15 2.57
2928 3052 5.105595 GCAATAACTGGCAAAAGAGGAGAAT 60.106 40.000 0.00 0.00 0.00 2.40
2951 3075 8.979574 GTAAGTACTGAACTATCCATATGTTGC 58.020 37.037 0.00 0.00 37.50 4.17
2965 3089 7.659652 AAAATGCTCTCTGTAAGTACTGAAC 57.340 36.000 0.00 0.00 34.46 3.18
3032 3156 0.529378 CAGGCAATCCAACTTCAGCC 59.471 55.000 0.00 0.00 42.31 4.85
3200 3324 0.179076 CTGCCATGCCGTATGAGTGA 60.179 55.000 0.00 0.00 39.21 3.41
3250 3374 2.094286 TGCCCTGAAAAACACAACACAG 60.094 45.455 0.00 0.00 0.00 3.66
3253 3377 1.895798 TGTGCCCTGAAAAACACAACA 59.104 42.857 0.00 0.00 39.91 3.33
3378 3502 2.738587 TTATGAAATTAGCCCCGGCA 57.261 45.000 8.74 0.00 44.88 5.69
3466 3590 2.100197 TCCAACTGATCGAGTCGGAAT 58.900 47.619 13.54 0.00 34.57 3.01
3481 3605 2.975193 GCGGTCAAATTTAACGTCCAAC 59.025 45.455 0.00 0.00 0.00 3.77
3484 3608 2.031857 TGTGCGGTCAAATTTAACGTCC 60.032 45.455 0.00 0.00 0.00 4.79
3513 3637 2.911928 TGTGTCAACAGGGGCGAA 59.088 55.556 0.00 0.00 0.00 4.70
3521 3645 6.764379 TGTAATATCAAGGACTGTGTCAACA 58.236 36.000 0.07 0.00 33.68 3.33
3598 3722 1.153628 GAATCCGGTGACACCCTCG 60.154 63.158 19.11 7.36 33.75 4.63
3684 3808 4.142665 GCTATCAATCATCAATGCATCGCT 60.143 41.667 0.00 0.00 0.00 4.93
3685 3809 4.096311 GCTATCAATCATCAATGCATCGC 58.904 43.478 0.00 0.00 0.00 4.58
3763 3887 1.418373 CTCGTGTGACATTCGAAGCA 58.582 50.000 3.35 0.00 33.32 3.91
3875 3999 8.801882 TCATGTTAAGGGTAAATAGGAACTTG 57.198 34.615 0.00 0.00 41.75 3.16
3928 4053 7.672983 TCACACAAAGAGAGGATCAATTTAC 57.327 36.000 0.00 0.00 37.82 2.01
3946 4071 2.290287 CCGGTCCCTGGATCACACA 61.290 63.158 0.00 0.00 0.00 3.72
4195 4320 6.839124 AGGATGCATACTTGTTGAAATTCA 57.161 33.333 5.29 0.00 0.00 2.57
4196 4321 9.241317 CATAAGGATGCATACTTGTTGAAATTC 57.759 33.333 30.77 0.00 32.11 2.17
4197 4322 8.752187 ACATAAGGATGCATACTTGTTGAAATT 58.248 29.630 30.77 11.51 36.43 1.82
4198 4323 8.297470 ACATAAGGATGCATACTTGTTGAAAT 57.703 30.769 30.77 14.44 36.43 2.17
4199 4324 7.701539 ACATAAGGATGCATACTTGTTGAAA 57.298 32.000 30.77 12.76 36.43 2.69
4200 4325 8.437360 CTACATAAGGATGCATACTTGTTGAA 57.563 34.615 30.77 13.48 36.43 2.69
4338 4471 3.057245 GGGAGTTCTTGATTTGGCAGAAC 60.057 47.826 6.88 6.88 39.12 3.01
4361 4494 6.934083 ACAAACTTATTAGGCAATTTTGGTGG 59.066 34.615 0.00 0.00 29.46 4.61
4385 4518 2.164422 GGGCCTTTGTGAGCATCTAAAC 59.836 50.000 0.84 0.00 34.92 2.01
4386 4519 2.446435 GGGCCTTTGTGAGCATCTAAA 58.554 47.619 0.84 0.00 34.92 1.85
4387 4520 1.340991 GGGGCCTTTGTGAGCATCTAA 60.341 52.381 0.84 0.00 34.92 2.10
4388 4521 0.255890 GGGGCCTTTGTGAGCATCTA 59.744 55.000 0.84 0.00 34.92 1.98
4389 4522 1.000396 GGGGCCTTTGTGAGCATCT 60.000 57.895 0.84 0.00 34.92 2.90
4390 4523 0.613012 AAGGGGCCTTTGTGAGCATC 60.613 55.000 0.84 0.00 31.29 3.91
4391 4524 0.901580 CAAGGGGCCTTTGTGAGCAT 60.902 55.000 19.49 0.00 33.42 3.79
4392 4525 1.531365 CAAGGGGCCTTTGTGAGCA 60.531 57.895 19.49 0.00 33.42 4.26
4393 4526 2.278330 CCAAGGGGCCTTTGTGAGC 61.278 63.158 24.68 0.00 33.42 4.26
4394 4527 4.102113 CCAAGGGGCCTTTGTGAG 57.898 61.111 24.68 8.04 33.42 3.51
4404 4537 1.337118 TGCTTTAAACTGCCAAGGGG 58.663 50.000 0.00 0.00 37.18 4.79
4405 4538 2.627699 TCTTGCTTTAAACTGCCAAGGG 59.372 45.455 10.66 0.00 0.00 3.95
4406 4539 3.068024 TGTCTTGCTTTAAACTGCCAAGG 59.932 43.478 10.66 0.00 0.00 3.61
4407 4540 4.305989 TGTCTTGCTTTAAACTGCCAAG 57.694 40.909 0.00 0.00 0.00 3.61
4408 4541 4.935352 ATGTCTTGCTTTAAACTGCCAA 57.065 36.364 0.00 0.00 0.00 4.52
4409 4542 5.312895 TCTATGTCTTGCTTTAAACTGCCA 58.687 37.500 0.00 0.00 0.00 4.92
4410 4543 5.880054 TCTATGTCTTGCTTTAAACTGCC 57.120 39.130 0.00 0.00 0.00 4.85
4411 4544 9.840427 TTTATTCTATGTCTTGCTTTAAACTGC 57.160 29.630 0.00 0.00 0.00 4.40
4414 4547 9.274065 CGGTTTATTCTATGTCTTGCTTTAAAC 57.726 33.333 0.00 0.00 0.00 2.01
4415 4548 8.455682 CCGGTTTATTCTATGTCTTGCTTTAAA 58.544 33.333 0.00 0.00 0.00 1.52
4427 4560 3.541632 AGTGGTGCCGGTTTATTCTATG 58.458 45.455 1.90 0.00 0.00 2.23
4446 4579 5.437060 ACTGGTGAAATCTGTTGTACAAGT 58.563 37.500 8.98 0.00 0.00 3.16
4452 4585 4.137543 GAGGAACTGGTGAAATCTGTTGT 58.862 43.478 0.00 0.00 41.55 3.32
4470 4603 3.766691 GCCGGCGTGTAAGGAGGA 61.767 66.667 12.58 0.00 0.00 3.71
4480 4613 0.445043 GAAAACTTTATCGCCGGCGT 59.555 50.000 44.16 32.95 40.74 5.68
4481 4614 0.725117 AGAAAACTTTATCGCCGGCG 59.275 50.000 42.13 42.13 41.35 6.46
4483 4616 4.332819 AGATTGAGAAAACTTTATCGCCGG 59.667 41.667 0.00 0.00 31.34 6.13
4484 4617 5.470845 AGATTGAGAAAACTTTATCGCCG 57.529 39.130 0.00 0.00 31.34 6.46
4485 4618 7.308049 GGGATAGATTGAGAAAACTTTATCGCC 60.308 40.741 0.00 0.00 31.34 5.54
4486 4619 7.442666 AGGGATAGATTGAGAAAACTTTATCGC 59.557 37.037 0.00 0.00 31.34 4.58
4506 4639 6.012508 AGGTTGTGAAGAAAGATGAAGGGATA 60.013 38.462 0.00 0.00 0.00 2.59
4516 4649 5.496556 TGAAAGACAGGTTGTGAAGAAAGA 58.503 37.500 0.00 0.00 0.00 2.52
4523 4656 5.353394 AGTACTTGAAAGACAGGTTGTGA 57.647 39.130 0.00 0.00 39.48 3.58
4567 4700 4.893608 TCTTTGATTCACACATTCTCGGA 58.106 39.130 0.00 0.00 0.00 4.55
4568 4701 4.093998 CCTCTTTGATTCACACATTCTCGG 59.906 45.833 0.00 0.00 0.00 4.63
4569 4702 4.093998 CCCTCTTTGATTCACACATTCTCG 59.906 45.833 0.00 0.00 0.00 4.04
4864 5002 0.166814 GGCTAGCTTTGCGTGTCTTG 59.833 55.000 15.72 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.