Multiple sequence alignment - TraesCS6B01G248200

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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 TraesCS6B01G248200 chr6B 100.000 6107 0 0 590 6696 444904050 444910156 0.000000e+00 11278.0
1 TraesCS6B01G248200 chr6B 100.000 244 0 0 1 244 444903461 444903704 1.020000e-122 451.0
2 TraesCS6B01G248200 chr6B 90.698 172 16 0 73 244 694656501 694656330 5.220000e-56 230.0
3 TraesCS6B01G248200 chr6B 90.173 173 16 1 72 244 41602270 41602441 2.430000e-54 224.0
4 TraesCS6B01G248200 chr6D 96.001 3576 107 14 2571 6113 284391653 284395225 0.000000e+00 5779.0
5 TraesCS6B01G248200 chr6D 90.628 1195 49 20 590 1747 284389735 284390903 0.000000e+00 1528.0
6 TraesCS6B01G248200 chr6D 93.898 803 35 5 1756 2557 284390880 284391669 0.000000e+00 1199.0
7 TraesCS6B01G248200 chr6D 92.593 189 4 3 6407 6585 284395490 284395678 5.150000e-66 263.0
8 TraesCS6B01G248200 chr6D 90.116 172 16 1 73 244 284389488 284389658 8.740000e-54 222.0
9 TraesCS6B01G248200 chr6D 89.535 172 18 0 73 244 273221991 273222162 1.130000e-52 219.0
10 TraesCS6B01G248200 chr6A 93.833 2627 90 16 4131 6691 404687798 404690418 0.000000e+00 3888.0
11 TraesCS6B01G248200 chr6A 95.102 1572 63 5 2571 4133 404686150 404687716 0.000000e+00 2464.0
12 TraesCS6B01G248200 chr6A 95.533 806 26 5 1756 2559 404685371 404686168 0.000000e+00 1280.0
13 TraesCS6B01G248200 chr6A 94.391 731 18 5 955 1680 404684643 404685355 0.000000e+00 1101.0
14 TraesCS6B01G248200 chr6A 92.969 128 9 0 834 961 404684396 404684523 3.190000e-43 187.0
15 TraesCS6B01G248200 chr5D 90.698 172 16 0 73 244 14533887 14534058 5.220000e-56 230.0
16 TraesCS6B01G248200 chr7D 90.116 172 17 0 73 244 25074640 25074469 2.430000e-54 224.0
17 TraesCS6B01G248200 chr7D 96.774 62 2 0 5836 5897 551735567 551735506 3.300000e-18 104.0
18 TraesCS6B01G248200 chr7D 90.476 63 4 2 5841 5902 597043667 597043606 1.550000e-11 82.4
19 TraesCS6B01G248200 chr7B 90.116 172 17 0 73 244 745760236 745760407 2.430000e-54 224.0
20 TraesCS6B01G248200 chr7B 93.220 59 2 2 5841 5898 750584053 750583996 1.200000e-12 86.1
21 TraesCS6B01G248200 chr2B 90.116 172 17 0 73 244 178862203 178862374 2.430000e-54 224.0
22 TraesCS6B01G248200 chr2B 93.151 73 5 0 1 73 311895406 311895334 2.550000e-19 108.0
23 TraesCS6B01G248200 chr2B 89.231 65 5 2 5838 5901 693231175 693231238 5.570000e-11 80.5
24 TraesCS6B01G248200 chr1D 90.116 172 17 0 73 244 457064914 457064743 2.430000e-54 224.0
25 TraesCS6B01G248200 chr1B 95.890 73 3 0 1 73 193093940 193094012 1.180000e-22 119.0
26 TraesCS6B01G248200 chr1B 96.610 59 2 0 5841 5899 656234060 656234118 1.540000e-16 99.0
27 TraesCS6B01G248200 chr4A 90.411 73 5 1 1 73 463724793 463724863 1.990000e-15 95.3
28 TraesCS6B01G248200 chr4A 89.552 67 7 0 5831 5897 605647197 605647131 1.200000e-12 86.1
29 TraesCS6B01G248200 chr5B 88.060 67 8 0 5831 5897 709582412 709582478 5.570000e-11 80.5
30 TraesCS6B01G248200 chr2D 94.286 35 1 1 6348 6382 267322 267355 1.200000e-02 52.8


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 TraesCS6B01G248200 chr6B 444903461 444910156 6695 False 5864.5 11278 100.0000 1 6696 2 chr6B.!!$F2 6695
1 TraesCS6B01G248200 chr6D 284389488 284395678 6190 False 1798.2 5779 92.6472 73 6585 5 chr6D.!!$F2 6512
2 TraesCS6B01G248200 chr6A 404684396 404690418 6022 False 1784.0 3888 94.3656 834 6691 5 chr6A.!!$F1 5857

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
892 910 0.041312 GTCGTGACACAGCGCAATTT 60.041 50.000 11.47 0.0 0.00 1.82 F
1493 1660 0.178935 ATCTGGTGGTTTGGTTGGGG 60.179 55.000 0.00 0.0 0.00 4.96 F
1773 1943 0.404040 TGAGGGGAAATGAAAGCGGT 59.596 50.000 0.00 0.0 0.00 5.68 F
1776 1946 1.075536 AGGGGAAATGAAAGCGGTTCT 59.924 47.619 0.00 0.0 37.13 3.01 F
2613 2784 1.145803 GTGTTTGGTCACTACGCTCC 58.854 55.000 0.00 0.0 35.68 4.70 F
3978 4162 0.447801 CACGTTGCTCCATTGTAGGC 59.552 55.000 0.00 0.0 0.00 3.93 F
4583 4851 3.072944 AGCAGCAAGTCTGAAGAATCAC 58.927 45.455 0.00 0.0 45.72 3.06 F
5200 5471 2.109799 CGCTGGATCTGGCGGATT 59.890 61.111 10.75 0.0 46.42 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1924 0.404040 ACCGCTTTCATTTCCCCTCA 59.596 50.000 0.00 0.00 0.00 3.86 R
2613 2784 1.568612 GGGACCATGCGCATCATACG 61.569 60.000 22.51 8.96 33.19 3.06 R
2687 2858 3.744660 ACTTTGGGACACAATGAGAGAC 58.255 45.455 10.11 0.00 39.29 3.36 R
3285 3461 4.210331 GCAGAACATCCTTCCAATGGTAT 58.790 43.478 0.00 0.00 0.00 2.73 R
4208 4476 0.977395 ACCAGACTACCAGTCCTTGC 59.023 55.000 2.74 0.00 46.18 4.01 R
5200 5471 0.400213 GTGACCTTGACCCCATGACA 59.600 55.000 0.00 0.00 0.00 3.58 R
5422 5694 0.445436 CACCGATGCAGCTTGACTTC 59.555 55.000 0.00 0.00 0.00 3.01 R
6084 6388 1.153958 GCATCCAAACAAGGCGCTC 60.154 57.895 7.64 0.00 0.00 5.03 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
25 26 7.846644 AATTGATCTAAGTGAAGCAAGAGAG 57.153 36.000 0.00 0.00 0.00 3.20
26 27 5.991933 TGATCTAAGTGAAGCAAGAGAGT 57.008 39.130 0.00 0.00 0.00 3.24
27 28 7.468141 TTGATCTAAGTGAAGCAAGAGAGTA 57.532 36.000 0.00 0.00 0.00 2.59
28 29 7.652524 TGATCTAAGTGAAGCAAGAGAGTAT 57.347 36.000 0.00 0.00 0.00 2.12
29 30 8.753497 TGATCTAAGTGAAGCAAGAGAGTATA 57.247 34.615 0.00 0.00 0.00 1.47
30 31 9.360901 TGATCTAAGTGAAGCAAGAGAGTATAT 57.639 33.333 0.00 0.00 0.00 0.86
36 37 8.940768 AGTGAAGCAAGAGAGTATATTTCTTC 57.059 34.615 0.00 0.00 0.00 2.87
37 38 8.535335 AGTGAAGCAAGAGAGTATATTTCTTCA 58.465 33.333 3.59 3.59 36.19 3.02
38 39 9.155975 GTGAAGCAAGAGAGTATATTTCTTCAA 57.844 33.333 8.43 0.00 39.00 2.69
39 40 9.725019 TGAAGCAAGAGAGTATATTTCTTCAAA 57.275 29.630 5.01 0.00 35.79 2.69
56 57 8.934507 TTCTTCAAAAATTTAACAATCACCGT 57.065 26.923 0.00 0.00 0.00 4.83
57 58 8.346476 TCTTCAAAAATTTAACAATCACCGTG 57.654 30.769 0.00 0.00 0.00 4.94
58 59 6.517914 TCAAAAATTTAACAATCACCGTGC 57.482 33.333 0.00 0.00 0.00 5.34
59 60 6.276847 TCAAAAATTTAACAATCACCGTGCT 58.723 32.000 0.00 0.00 0.00 4.40
60 61 6.419413 TCAAAAATTTAACAATCACCGTGCTC 59.581 34.615 0.00 0.00 0.00 4.26
61 62 5.446143 AAATTTAACAATCACCGTGCTCA 57.554 34.783 0.00 0.00 0.00 4.26
62 63 5.446143 AATTTAACAATCACCGTGCTCAA 57.554 34.783 0.00 0.00 0.00 3.02
63 64 4.902443 TTTAACAATCACCGTGCTCAAA 57.098 36.364 0.00 0.00 0.00 2.69
64 65 4.902443 TTAACAATCACCGTGCTCAAAA 57.098 36.364 0.00 0.00 0.00 2.44
65 66 3.791973 AACAATCACCGTGCTCAAAAA 57.208 38.095 0.00 0.00 0.00 1.94
66 67 3.354089 ACAATCACCGTGCTCAAAAAG 57.646 42.857 0.00 0.00 0.00 2.27
67 68 2.948979 ACAATCACCGTGCTCAAAAAGA 59.051 40.909 0.00 0.00 0.00 2.52
68 69 3.569701 ACAATCACCGTGCTCAAAAAGAT 59.430 39.130 0.00 0.00 0.00 2.40
69 70 4.759693 ACAATCACCGTGCTCAAAAAGATA 59.240 37.500 0.00 0.00 0.00 1.98
70 71 5.415701 ACAATCACCGTGCTCAAAAAGATAT 59.584 36.000 0.00 0.00 0.00 1.63
71 72 6.597672 ACAATCACCGTGCTCAAAAAGATATA 59.402 34.615 0.00 0.00 0.00 0.86
100 101 2.852449 TGATCCCTTTGGTGCTTCCTAT 59.148 45.455 0.00 0.00 37.07 2.57
106 107 3.307691 CCTTTGGTGCTTCCTATGACTGA 60.308 47.826 0.80 0.00 37.07 3.41
116 117 1.402325 CCTATGACTGAACGTGCACGA 60.402 52.381 42.94 21.93 43.02 4.35
117 118 1.649171 CTATGACTGAACGTGCACGAC 59.351 52.381 42.94 32.45 43.02 4.34
125 126 2.126618 CGTGCACGACGGCTTCTA 60.127 61.111 34.93 0.00 44.85 2.10
133 134 1.752501 CGACGGCTTCTATGGCAACG 61.753 60.000 0.00 0.00 42.51 4.10
138 139 2.498167 GGCTTCTATGGCAACGATGAT 58.502 47.619 0.00 0.00 42.51 2.45
141 142 3.470709 CTTCTATGGCAACGATGATGGT 58.529 45.455 0.00 0.00 42.51 3.55
149 150 0.324614 AACGATGATGGTGGTGAGCA 59.675 50.000 0.00 0.00 0.00 4.26
163 164 2.434884 AGCAATGTCGGAGGCGTG 60.435 61.111 0.00 0.00 28.88 5.34
224 225 2.574399 GAGGGTGCCTCGACTGTC 59.426 66.667 0.00 0.00 41.08 3.51
225 226 2.997897 AGGGTGCCTCGACTGTCC 60.998 66.667 1.55 0.00 0.00 4.02
617 618 9.350357 CTAGATTCCTTTGTGATTTCATTGTTG 57.650 33.333 0.00 0.00 0.00 3.33
621 622 5.598005 TCCTTTGTGATTTCATTGTTGGAGT 59.402 36.000 0.00 0.00 0.00 3.85
626 627 4.215399 GTGATTTCATTGTTGGAGTCGGAA 59.785 41.667 0.00 0.00 0.00 4.30
627 628 4.215399 TGATTTCATTGTTGGAGTCGGAAC 59.785 41.667 0.00 0.00 0.00 3.62
636 637 0.601558 GGAGTCGGAACTGCACTGTA 59.398 55.000 0.00 0.00 42.95 2.74
644 645 4.885325 TCGGAACTGCACTGTATAGTATGA 59.115 41.667 0.00 0.00 34.74 2.15
648 649 7.306807 CGGAACTGCACTGTATAGTATGATTTG 60.307 40.741 0.00 0.00 34.74 2.32
653 654 9.696917 CTGCACTGTATAGTATGATTTGTATGA 57.303 33.333 0.00 0.00 34.74 2.15
666 667 2.248280 TGTATGAAGTGTTGTGCCGT 57.752 45.000 0.00 0.00 0.00 5.68
667 668 3.388345 TGTATGAAGTGTTGTGCCGTA 57.612 42.857 0.00 0.00 0.00 4.02
677 678 2.159014 TGTTGTGCCGTAGCTATTAGGG 60.159 50.000 12.72 6.80 40.80 3.53
678 679 1.784358 TGTGCCGTAGCTATTAGGGT 58.216 50.000 12.72 0.00 39.12 4.34
679 680 2.112998 TGTGCCGTAGCTATTAGGGTT 58.887 47.619 12.72 0.00 39.12 4.11
683 684 2.298163 GCCGTAGCTATTAGGGTTGCTA 59.702 50.000 12.72 0.00 39.12 3.49
731 732 6.381420 TCTTTAATCTTCGGATCTTCTGGTCT 59.619 38.462 0.00 0.00 32.82 3.85
735 736 4.856509 TCTTCGGATCTTCTGGTCTTAGA 58.143 43.478 0.00 0.00 0.00 2.10
744 759 8.454894 GGATCTTCTGGTCTTAGAATTGTTTTC 58.545 37.037 0.00 0.00 36.21 2.29
771 789 6.028146 TGCTTGCTGTTATCAATGAAATGT 57.972 33.333 0.00 0.00 0.00 2.71
772 790 7.155655 TGCTTGCTGTTATCAATGAAATGTA 57.844 32.000 0.00 0.00 0.00 2.29
780 798 7.984391 TGTTATCAATGAAATGTAAGCGATGT 58.016 30.769 0.00 0.00 0.00 3.06
790 808 4.944962 TGTAAGCGATGTTGGATCTTTG 57.055 40.909 0.00 0.00 0.00 2.77
791 809 4.574892 TGTAAGCGATGTTGGATCTTTGA 58.425 39.130 0.00 0.00 0.00 2.69
792 810 5.000591 TGTAAGCGATGTTGGATCTTTGAA 58.999 37.500 0.00 0.00 0.00 2.69
793 811 5.471797 TGTAAGCGATGTTGGATCTTTGAAA 59.528 36.000 0.00 0.00 0.00 2.69
794 812 5.452078 AAGCGATGTTGGATCTTTGAAAA 57.548 34.783 0.00 0.00 0.00 2.29
795 813 5.051891 AGCGATGTTGGATCTTTGAAAAG 57.948 39.130 0.00 0.00 37.36 2.27
892 910 0.041312 GTCGTGACACAGCGCAATTT 60.041 50.000 11.47 0.00 0.00 1.82
937 955 1.067071 AGTTTCCCGGAATCGAGACAC 60.067 52.381 0.73 0.00 39.00 3.67
940 958 2.359981 TCCCGGAATCGAGACACTAT 57.640 50.000 0.73 0.00 39.00 2.12
1030 1180 1.902508 TCCCTCTTTTGCATCTCTCGT 59.097 47.619 0.00 0.00 0.00 4.18
1350 1512 0.960364 GCCTGGTCGAATCCTTTGCA 60.960 55.000 0.00 0.00 0.00 4.08
1363 1525 1.613836 CTTTGCAAGAAGAGGTGGCT 58.386 50.000 0.00 0.00 0.00 4.75
1364 1526 1.959282 CTTTGCAAGAAGAGGTGGCTT 59.041 47.619 0.00 0.00 0.00 4.35
1365 1527 1.609208 TTGCAAGAAGAGGTGGCTTC 58.391 50.000 0.00 0.00 43.57 3.86
1436 1598 1.767759 CCTTGGATTCGGCCATTTCT 58.232 50.000 2.24 0.00 37.86 2.52
1476 1643 0.531974 TACGCTTCGGGGCATTCATC 60.532 55.000 0.00 0.00 0.00 2.92
1493 1660 0.178935 ATCTGGTGGTTTGGTTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
1574 1741 6.040878 ACGTCGTTTTCTATAGCTGCTTAAT 58.959 36.000 7.79 0.00 0.00 1.40
1575 1742 7.198390 ACGTCGTTTTCTATAGCTGCTTAATA 58.802 34.615 7.79 0.00 0.00 0.98
1576 1743 7.378995 ACGTCGTTTTCTATAGCTGCTTAATAG 59.621 37.037 7.79 10.20 0.00 1.73
1577 1744 7.378995 CGTCGTTTTCTATAGCTGCTTAATAGT 59.621 37.037 7.79 0.00 0.00 2.12
1578 1745 9.032420 GTCGTTTTCTATAGCTGCTTAATAGTT 57.968 33.333 7.79 0.00 0.00 2.24
1614 1781 1.432270 GGTAGCGCCTGAGAACATGC 61.432 60.000 2.29 0.00 35.02 4.06
1665 1835 5.523916 TCGGCATATCTAGACTTGCTTTTTC 59.476 40.000 21.64 9.13 35.46 2.29
1746 1916 2.427095 GGGCATAATGAAAGCGGTTCTT 59.573 45.455 0.00 0.00 37.13 2.52
1748 1918 4.494484 GGCATAATGAAAGCGGTTCTTTT 58.506 39.130 0.00 0.00 44.58 2.27
1749 1919 4.929211 GGCATAATGAAAGCGGTTCTTTTT 59.071 37.500 0.00 0.00 44.58 1.94
1771 1941 3.658757 TTTTGAGGGGAAATGAAAGCG 57.341 42.857 0.00 0.00 0.00 4.68
1772 1942 1.544724 TTGAGGGGAAATGAAAGCGG 58.455 50.000 0.00 0.00 0.00 5.52
1773 1943 0.404040 TGAGGGGAAATGAAAGCGGT 59.596 50.000 0.00 0.00 0.00 5.68
1774 1944 1.203001 TGAGGGGAAATGAAAGCGGTT 60.203 47.619 0.00 0.00 0.00 4.44
1775 1945 1.472878 GAGGGGAAATGAAAGCGGTTC 59.527 52.381 0.00 0.00 36.70 3.62
1776 1946 1.075536 AGGGGAAATGAAAGCGGTTCT 59.924 47.619 0.00 0.00 37.13 3.01
1870 2040 8.800370 TCTAGCTTATCAGTGAGTATATGGAG 57.200 38.462 0.00 0.00 0.00 3.86
2116 2286 8.696043 ATATTATCTGGCTCTGCATGTTTTAA 57.304 30.769 0.00 0.00 0.00 1.52
2151 2321 8.340618 ACTCAAATGCTGTAATTGTTCTGTAT 57.659 30.769 0.00 0.00 0.00 2.29
2217 2388 7.522073 GCCATGAACAGAAAGTAGATTTGTTGA 60.522 37.037 0.00 0.00 0.00 3.18
2247 2418 2.421775 TGTGCGTTCAGTTGACAACATT 59.578 40.909 20.08 0.00 0.00 2.71
2437 2608 2.362120 ACCTGCTTGCTGATGGCC 60.362 61.111 0.00 0.00 40.92 5.36
2438 2609 2.044252 CCTGCTTGCTGATGGCCT 60.044 61.111 3.32 0.00 40.92 5.19
2580 2751 5.574891 TTTTTGCGGATGTATGCTATGTT 57.425 34.783 0.00 0.00 0.00 2.71
2581 2752 5.574891 TTTTGCGGATGTATGCTATGTTT 57.425 34.783 0.00 0.00 0.00 2.83
2582 2753 5.574891 TTTGCGGATGTATGCTATGTTTT 57.425 34.783 0.00 0.00 0.00 2.43
2583 2754 4.811555 TGCGGATGTATGCTATGTTTTC 57.188 40.909 0.00 0.00 0.00 2.29
2584 2755 3.563808 TGCGGATGTATGCTATGTTTTCC 59.436 43.478 0.00 0.00 0.00 3.13
2585 2756 3.815401 GCGGATGTATGCTATGTTTTCCT 59.185 43.478 0.00 0.00 0.00 3.36
2586 2757 4.275936 GCGGATGTATGCTATGTTTTCCTT 59.724 41.667 0.00 0.00 0.00 3.36
2613 2784 1.145803 GTGTTTGGTCACTACGCTCC 58.854 55.000 0.00 0.00 35.68 4.70
2677 2848 5.222079 TGATCTGTTGTAGTTGCTTGGTA 57.778 39.130 0.00 0.00 0.00 3.25
2687 2858 8.342634 GTTGTAGTTGCTTGGTATTATATGGTG 58.657 37.037 0.00 0.00 0.00 4.17
2690 2861 6.900194 AGTTGCTTGGTATTATATGGTGTCT 58.100 36.000 0.00 0.00 0.00 3.41
2723 2894 2.814336 CCAAAGTTTGTCTAGGAGTGCC 59.186 50.000 14.36 0.00 0.00 5.01
2827 3003 7.004555 AGTACACCAACATCTCTGTATGAAA 57.995 36.000 0.00 0.00 33.36 2.69
2828 3004 6.874134 AGTACACCAACATCTCTGTATGAAAC 59.126 38.462 0.00 0.00 33.36 2.78
2829 3005 5.620206 ACACCAACATCTCTGTATGAAACA 58.380 37.500 0.00 0.00 33.36 2.83
2830 3006 6.240894 ACACCAACATCTCTGTATGAAACAT 58.759 36.000 0.00 0.00 37.50 2.71
2881 3057 1.596260 CGCACATCTAATGCAGGTCAG 59.404 52.381 0.00 0.00 43.57 3.51
3242 3418 4.095932 CCTCCAATTATCCATCATGATGCG 59.904 45.833 27.24 20.24 37.49 4.73
3278 3454 5.039333 GCTCAAAATGATTACAGTCATGCC 58.961 41.667 0.00 0.00 38.76 4.40
3285 3461 8.523915 AAATGATTACAGTCATGCCAGATTAA 57.476 30.769 0.00 0.00 38.76 1.40
3363 3539 6.647212 TGTTTATCAGAAAGACTGCATACG 57.353 37.500 0.00 0.00 45.38 3.06
3565 3749 7.537715 TCAAATTACAATGTGTAAGCATGGAG 58.462 34.615 6.93 0.00 44.89 3.86
3774 3958 5.276440 ACTTATGGTCTGGTCTTCTCAGAT 58.724 41.667 0.00 0.00 42.36 2.90
3978 4162 0.447801 CACGTTGCTCCATTGTAGGC 59.552 55.000 0.00 0.00 0.00 3.93
4013 4197 9.804977 AAGCATAGCTCCTTAATATTCAAGAAT 57.195 29.630 0.00 0.52 38.25 2.40
4062 4246 6.683974 TTAGCTTTCATCTATTGGCAGTTC 57.316 37.500 0.00 0.00 0.00 3.01
4208 4476 6.365520 AGTGCAAGGTATTTAATCCCCTTAG 58.634 40.000 8.04 5.54 35.57 2.18
4255 4523 9.386010 CACATCACCCATTGATTTTCATTTTAT 57.614 29.630 0.00 0.00 42.87 1.40
4434 4702 6.470877 GTGAAAATTGTGCTAGTTTCGAAACA 59.529 34.615 35.29 22.59 41.30 2.83
4486 4754 3.565902 GGTCCAGTTTGAACTTTCCTGAG 59.434 47.826 0.00 0.00 37.08 3.35
4583 4851 3.072944 AGCAGCAAGTCTGAAGAATCAC 58.927 45.455 0.00 0.00 45.72 3.06
4616 4884 6.267699 AGTCATGTGTATATGTTGCTAGCCTA 59.732 38.462 13.29 0.00 0.00 3.93
4657 4925 3.971305 TCCTGTTCTAACCTTCCTGTTGA 59.029 43.478 0.00 0.00 0.00 3.18
5200 5471 2.109799 CGCTGGATCTGGCGGATT 59.890 61.111 10.75 0.00 46.42 3.01
5330 5602 3.870274 CTGATTGCTCTCCTGTGATGAA 58.130 45.455 0.00 0.00 0.00 2.57
5422 5694 2.421424 GCTCAGCACCTGGAACTAATTG 59.579 50.000 0.00 0.00 31.51 2.32
5617 5889 1.748591 GCCTTACAGATGGAAGGGCAG 60.749 57.143 22.54 0.92 42.24 4.85
5817 6113 3.074412 CTGAACAAAAGTACCAGGCGAT 58.926 45.455 0.00 0.00 0.00 4.58
5905 6206 4.202738 GGGATGGAGGGAGTAGTTCTCTAT 60.203 50.000 0.00 0.00 36.51 1.98
5971 6272 5.122869 AGTGACAATGTGATCCTTCAATTCG 59.877 40.000 0.00 0.00 32.48 3.34
6008 6312 2.943036 TTTTCACGGGTAAAGGCTCT 57.057 45.000 0.00 0.00 0.00 4.09
6084 6388 4.083057 GGAGGAGCTAAGTTTTGCTTTCTG 60.083 45.833 2.54 0.00 39.29 3.02
6124 6428 0.695347 CTCTCACCCTCCCTTGCTTT 59.305 55.000 0.00 0.00 0.00 3.51
6299 6607 4.256110 TCCAGACAATCTACTGCAATGTG 58.744 43.478 0.00 0.00 33.40 3.21
6321 6632 2.450502 AGGGGACTTGGTGCACCT 60.451 61.111 34.75 16.98 37.44 4.00
6352 6663 2.224769 GCTGCCAGCCAACCCTATATAA 60.225 50.000 5.06 0.00 34.48 0.98
6533 6929 1.257743 CAGGTCGAGGTGAGGAGAAA 58.742 55.000 0.00 0.00 0.00 2.52
6534 6930 1.203523 CAGGTCGAGGTGAGGAGAAAG 59.796 57.143 0.00 0.00 0.00 2.62
6549 6955 2.569072 GAAAGGTACTCCCCGTCGCC 62.569 65.000 0.00 0.00 38.49 5.54
6578 6984 2.414293 CGATCAGGAAGAAGACGTCGTT 60.414 50.000 10.46 5.21 0.00 3.85
6585 6991 1.659335 GAAGACGTCGTTGTCGCCA 60.659 57.895 10.46 0.00 43.70 5.69
6634 7058 2.184167 CGCGACCGGGCCAATATTT 61.184 57.895 6.32 0.00 0.00 1.40
6663 7087 2.944129 TGGGCTTATTGGAATAGGCAC 58.056 47.619 13.59 11.13 44.79 5.01
6666 7090 2.808543 GGCTTATTGGAATAGGCACGAG 59.191 50.000 13.59 0.00 43.42 4.18
6676 7100 4.083003 GGAATAGGCACGAGAGAGAGTATG 60.083 50.000 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.882271 ACTCTCTTGCTTCACTTAGATCAATTT 59.118 33.333 0.00 0.00 0.00 1.82
1 2 7.393216 ACTCTCTTGCTTCACTTAGATCAATT 58.607 34.615 0.00 0.00 0.00 2.32
2 3 6.945218 ACTCTCTTGCTTCACTTAGATCAAT 58.055 36.000 0.00 0.00 0.00 2.57
3 4 6.352016 ACTCTCTTGCTTCACTTAGATCAA 57.648 37.500 0.00 0.00 0.00 2.57
4 5 5.991933 ACTCTCTTGCTTCACTTAGATCA 57.008 39.130 0.00 0.00 0.00 2.92
10 11 9.377312 GAAGAAATATACTCTCTTGCTTCACTT 57.623 33.333 0.00 0.00 31.95 3.16
11 12 8.535335 TGAAGAAATATACTCTCTTGCTTCACT 58.465 33.333 0.00 0.00 35.62 3.41
12 13 8.709386 TGAAGAAATATACTCTCTTGCTTCAC 57.291 34.615 0.00 0.00 35.62 3.18
13 14 9.725019 TTTGAAGAAATATACTCTCTTGCTTCA 57.275 29.630 0.00 0.00 37.87 3.02
30 31 9.372369 ACGGTGATTGTTAAATTTTTGAAGAAA 57.628 25.926 0.00 0.00 0.00 2.52
31 32 8.812329 CACGGTGATTGTTAAATTTTTGAAGAA 58.188 29.630 0.74 0.00 0.00 2.52
32 33 7.043059 GCACGGTGATTGTTAAATTTTTGAAGA 60.043 33.333 13.29 0.00 0.00 2.87
33 34 7.042791 AGCACGGTGATTGTTAAATTTTTGAAG 60.043 33.333 13.29 0.00 0.00 3.02
34 35 6.758886 AGCACGGTGATTGTTAAATTTTTGAA 59.241 30.769 13.29 0.00 0.00 2.69
35 36 6.276847 AGCACGGTGATTGTTAAATTTTTGA 58.723 32.000 13.29 0.00 0.00 2.69
36 37 6.199908 TGAGCACGGTGATTGTTAAATTTTTG 59.800 34.615 13.29 0.00 0.00 2.44
37 38 6.276847 TGAGCACGGTGATTGTTAAATTTTT 58.723 32.000 13.29 0.00 0.00 1.94
38 39 5.837437 TGAGCACGGTGATTGTTAAATTTT 58.163 33.333 13.29 0.00 0.00 1.82
39 40 5.446143 TGAGCACGGTGATTGTTAAATTT 57.554 34.783 13.29 0.00 0.00 1.82
40 41 5.446143 TTGAGCACGGTGATTGTTAAATT 57.554 34.783 13.29 0.00 0.00 1.82
41 42 5.446143 TTTGAGCACGGTGATTGTTAAAT 57.554 34.783 13.29 0.00 0.00 1.40
42 43 4.902443 TTTGAGCACGGTGATTGTTAAA 57.098 36.364 13.29 3.95 0.00 1.52
43 44 4.902443 TTTTGAGCACGGTGATTGTTAA 57.098 36.364 13.29 0.00 0.00 2.01
44 45 4.576873 TCTTTTTGAGCACGGTGATTGTTA 59.423 37.500 13.29 0.00 0.00 2.41
45 46 3.380004 TCTTTTTGAGCACGGTGATTGTT 59.620 39.130 13.29 0.00 0.00 2.83
46 47 2.948979 TCTTTTTGAGCACGGTGATTGT 59.051 40.909 13.29 0.00 0.00 2.71
47 48 3.624326 TCTTTTTGAGCACGGTGATTG 57.376 42.857 13.29 0.00 0.00 2.67
48 49 7.624360 TTATATCTTTTTGAGCACGGTGATT 57.376 32.000 13.29 0.00 0.00 2.57
49 50 7.552687 TCTTTATATCTTTTTGAGCACGGTGAT 59.447 33.333 13.29 5.12 0.00 3.06
50 51 6.876789 TCTTTATATCTTTTTGAGCACGGTGA 59.123 34.615 13.29 0.00 0.00 4.02
51 52 6.961554 GTCTTTATATCTTTTTGAGCACGGTG 59.038 38.462 3.15 3.15 0.00 4.94
52 53 6.879458 AGTCTTTATATCTTTTTGAGCACGGT 59.121 34.615 0.00 0.00 0.00 4.83
53 54 7.308782 AGTCTTTATATCTTTTTGAGCACGG 57.691 36.000 0.00 0.00 0.00 4.94
54 55 9.055248 CAAAGTCTTTATATCTTTTTGAGCACG 57.945 33.333 0.00 0.00 30.41 5.34
64 65 9.413734 CCAAAGGGATCAAAGTCTTTATATCTT 57.586 33.333 14.76 6.89 35.59 2.40
65 66 8.560903 ACCAAAGGGATCAAAGTCTTTATATCT 58.439 33.333 14.76 2.51 38.05 1.98
66 67 8.624776 CACCAAAGGGATCAAAGTCTTTATATC 58.375 37.037 0.00 4.69 38.05 1.63
67 68 7.068716 GCACCAAAGGGATCAAAGTCTTTATAT 59.931 37.037 0.00 0.00 38.05 0.86
68 69 6.377146 GCACCAAAGGGATCAAAGTCTTTATA 59.623 38.462 0.00 0.00 38.05 0.98
69 70 5.185828 GCACCAAAGGGATCAAAGTCTTTAT 59.814 40.000 0.00 0.00 38.05 1.40
70 71 4.522789 GCACCAAAGGGATCAAAGTCTTTA 59.477 41.667 0.00 0.00 38.05 1.85
71 72 3.321968 GCACCAAAGGGATCAAAGTCTTT 59.678 43.478 0.00 0.00 38.05 2.52
100 101 1.942223 CGTCGTGCACGTTCAGTCA 60.942 57.895 35.74 14.71 44.07 3.41
116 117 0.178068 ATCGTTGCCATAGAAGCCGT 59.822 50.000 0.00 0.00 0.00 5.68
117 118 0.583438 CATCGTTGCCATAGAAGCCG 59.417 55.000 0.00 0.00 0.00 5.52
125 126 0.034186 ACCACCATCATCGTTGCCAT 60.034 50.000 0.00 0.00 0.00 4.40
133 134 2.357009 GACATTGCTCACCACCATCATC 59.643 50.000 0.00 0.00 0.00 2.92
138 139 1.302431 CCGACATTGCTCACCACCA 60.302 57.895 0.00 0.00 0.00 4.17
141 142 1.296392 CCTCCGACATTGCTCACCA 59.704 57.895 0.00 0.00 0.00 4.17
149 150 4.778143 GGCCACGCCTCCGACATT 62.778 66.667 0.00 0.00 46.69 2.71
163 164 0.462047 CGACTACCATGACCAAGGCC 60.462 60.000 0.00 0.00 0.00 5.19
173 174 2.691011 GAGAAGAAGAGCCGACTACCAT 59.309 50.000 0.00 0.00 0.00 3.55
174 175 2.093106 GAGAAGAAGAGCCGACTACCA 58.907 52.381 0.00 0.00 0.00 3.25
208 209 2.997897 GGACAGTCGAGGCACCCT 60.998 66.667 0.00 0.00 36.03 4.34
210 211 3.222354 AACGGACAGTCGAGGCACC 62.222 63.158 0.00 0.00 0.00 5.01
211 212 2.022129 CAACGGACAGTCGAGGCAC 61.022 63.158 0.00 0.00 0.00 5.01
212 213 2.023414 AACAACGGACAGTCGAGGCA 62.023 55.000 0.00 0.00 0.00 4.75
213 214 1.300697 AACAACGGACAGTCGAGGC 60.301 57.895 0.00 0.00 0.00 4.70
224 225 2.645628 CTTCGACTTCACAACAACGG 57.354 50.000 0.00 0.00 0.00 4.44
602 603 3.501828 CCGACTCCAACAATGAAATCACA 59.498 43.478 0.00 0.00 0.00 3.58
610 611 1.197721 GCAGTTCCGACTCCAACAATG 59.802 52.381 0.00 0.00 32.54 2.82
612 613 0.179234 TGCAGTTCCGACTCCAACAA 59.821 50.000 0.00 0.00 32.54 2.83
613 614 0.531974 GTGCAGTTCCGACTCCAACA 60.532 55.000 0.00 0.00 32.54 3.33
617 618 0.601558 TACAGTGCAGTTCCGACTCC 59.398 55.000 0.00 0.00 32.54 3.85
621 622 4.885325 TCATACTATACAGTGCAGTTCCGA 59.115 41.667 0.00 0.00 36.14 4.55
626 627 9.481340 CATACAAATCATACTATACAGTGCAGT 57.519 33.333 0.00 0.00 36.14 4.40
627 628 9.696917 TCATACAAATCATACTATACAGTGCAG 57.303 33.333 0.00 0.00 36.14 4.41
644 645 3.568007 ACGGCACAACACTTCATACAAAT 59.432 39.130 0.00 0.00 0.00 2.32
648 649 2.093783 GCTACGGCACAACACTTCATAC 59.906 50.000 0.00 0.00 38.54 2.39
653 654 2.762535 ATAGCTACGGCACAACACTT 57.237 45.000 0.00 0.00 41.70 3.16
697 698 9.726438 AGATCCGAAGATTAAAGAAAAAGAAGA 57.274 29.630 0.00 0.00 30.90 2.87
701 702 9.766277 CAGAAGATCCGAAGATTAAAGAAAAAG 57.234 33.333 0.00 0.00 30.90 2.27
711 712 5.894393 TCTAAGACCAGAAGATCCGAAGATT 59.106 40.000 0.00 0.00 30.90 2.40
725 726 5.941948 ACGGAAAACAATTCTAAGACCAG 57.058 39.130 0.00 0.00 0.00 4.00
731 732 4.742659 GCAAGCAACGGAAAACAATTCTAA 59.257 37.500 0.00 0.00 0.00 2.10
735 736 2.865551 CAGCAAGCAACGGAAAACAATT 59.134 40.909 0.00 0.00 0.00 2.32
744 759 2.987413 TTGATAACAGCAAGCAACGG 57.013 45.000 0.00 0.00 0.00 4.44
771 789 6.429692 TCTTTTCAAAGATCCAACATCGCTTA 59.570 34.615 0.00 0.00 39.95 3.09
772 790 5.241506 TCTTTTCAAAGATCCAACATCGCTT 59.758 36.000 0.00 0.00 39.95 4.68
780 798 9.717942 TTTTGAGTTTTCTTTTCAAAGATCCAA 57.282 25.926 2.83 2.05 43.92 3.53
812 830 8.057011 TCTTTTGAGTTTCTTTTAGGGGTAGTT 58.943 33.333 0.00 0.00 0.00 2.24
872 890 2.158058 AATTGCGCTGTGTCACGACG 62.158 55.000 9.73 11.83 0.00 5.12
873 891 0.041312 AAATTGCGCTGTGTCACGAC 60.041 50.000 9.73 0.00 0.00 4.34
879 897 0.386731 GCCGTAAAATTGCGCTGTGT 60.387 50.000 9.73 0.00 34.89 3.72
892 910 1.904865 ACTGACGAGTGGGCCGTAA 60.905 57.895 0.00 0.00 40.67 3.18
1363 1525 3.519510 CCCCAGATCACCAAGAACTAGAA 59.480 47.826 0.00 0.00 0.00 2.10
1364 1526 3.107601 CCCCAGATCACCAAGAACTAGA 58.892 50.000 0.00 0.00 0.00 2.43
1365 1527 2.420687 GCCCCAGATCACCAAGAACTAG 60.421 54.545 0.00 0.00 0.00 2.57
1366 1528 1.559682 GCCCCAGATCACCAAGAACTA 59.440 52.381 0.00 0.00 0.00 2.24
1367 1529 0.329596 GCCCCAGATCACCAAGAACT 59.670 55.000 0.00 0.00 0.00 3.01
1368 1530 0.038166 TGCCCCAGATCACCAAGAAC 59.962 55.000 0.00 0.00 0.00 3.01
1436 1598 6.762661 GCGTAATAGTAGTACCAAAATCCCAA 59.237 38.462 2.34 0.00 0.00 4.12
1476 1643 0.689412 AACCCCAACCAAACCACCAG 60.689 55.000 0.00 0.00 0.00 4.00
1493 1660 1.270678 ACCGTCAACCTTCCAGCTAAC 60.271 52.381 0.00 0.00 0.00 2.34
1574 1741 5.242434 ACCTCAAATCACACGCATTAACTA 58.758 37.500 0.00 0.00 0.00 2.24
1575 1742 4.072131 ACCTCAAATCACACGCATTAACT 58.928 39.130 0.00 0.00 0.00 2.24
1576 1743 4.419522 ACCTCAAATCACACGCATTAAC 57.580 40.909 0.00 0.00 0.00 2.01
1577 1744 4.094294 GCTACCTCAAATCACACGCATTAA 59.906 41.667 0.00 0.00 0.00 1.40
1578 1745 3.621268 GCTACCTCAAATCACACGCATTA 59.379 43.478 0.00 0.00 0.00 1.90
1579 1746 2.420022 GCTACCTCAAATCACACGCATT 59.580 45.455 0.00 0.00 0.00 3.56
1580 1747 2.009774 GCTACCTCAAATCACACGCAT 58.990 47.619 0.00 0.00 0.00 4.73
1614 1781 5.277490 CGGTGACAACAATCATAGGCTATTG 60.277 44.000 3.76 5.61 38.71 1.90
1665 1835 7.985476 TCCAAAATAGGATAGCGAAAAGAAAG 58.015 34.615 0.00 0.00 31.23 2.62
1750 1920 3.244044 CCGCTTTCATTTCCCCTCAAAAA 60.244 43.478 0.00 0.00 0.00 1.94
1751 1921 2.298729 CCGCTTTCATTTCCCCTCAAAA 59.701 45.455 0.00 0.00 0.00 2.44
1752 1922 1.892474 CCGCTTTCATTTCCCCTCAAA 59.108 47.619 0.00 0.00 0.00 2.69
1753 1923 1.203001 ACCGCTTTCATTTCCCCTCAA 60.203 47.619 0.00 0.00 0.00 3.02
1754 1924 0.404040 ACCGCTTTCATTTCCCCTCA 59.596 50.000 0.00 0.00 0.00 3.86
1755 1925 1.472878 GAACCGCTTTCATTTCCCCTC 59.527 52.381 0.00 0.00 33.94 4.30
1756 1926 1.075536 AGAACCGCTTTCATTTCCCCT 59.924 47.619 0.00 0.00 36.57 4.79
1757 1927 1.545841 AGAACCGCTTTCATTTCCCC 58.454 50.000 0.00 0.00 36.57 4.81
1758 1928 2.556622 TCAAGAACCGCTTTCATTTCCC 59.443 45.455 0.00 0.00 36.57 3.97
1759 1929 3.004315 TGTCAAGAACCGCTTTCATTTCC 59.996 43.478 0.00 0.00 36.57 3.13
1760 1930 3.975035 GTGTCAAGAACCGCTTTCATTTC 59.025 43.478 0.00 0.00 36.57 2.17
1761 1931 3.380004 TGTGTCAAGAACCGCTTTCATTT 59.620 39.130 0.00 0.00 36.57 2.32
1762 1932 2.948979 TGTGTCAAGAACCGCTTTCATT 59.051 40.909 0.00 0.00 36.57 2.57
1763 1933 2.571212 TGTGTCAAGAACCGCTTTCAT 58.429 42.857 0.00 0.00 36.57 2.57
1764 1934 2.031258 TGTGTCAAGAACCGCTTTCA 57.969 45.000 0.00 0.00 36.57 2.69
1765 1935 4.946784 ATATGTGTCAAGAACCGCTTTC 57.053 40.909 0.00 0.00 33.60 2.62
1766 1936 6.349300 AGATATATGTGTCAAGAACCGCTTT 58.651 36.000 0.00 0.00 33.60 3.51
1767 1937 5.918608 AGATATATGTGTCAAGAACCGCTT 58.081 37.500 0.00 0.00 37.29 4.68
1768 1938 5.537300 AGATATATGTGTCAAGAACCGCT 57.463 39.130 0.00 0.00 0.00 5.52
1769 1939 5.753438 TGAAGATATATGTGTCAAGAACCGC 59.247 40.000 0.00 0.00 0.00 5.68
1770 1940 7.653311 TGATGAAGATATATGTGTCAAGAACCG 59.347 37.037 0.00 0.00 0.00 4.44
1771 1941 8.768955 GTGATGAAGATATATGTGTCAAGAACC 58.231 37.037 0.00 0.00 0.00 3.62
1772 1942 9.539825 AGTGATGAAGATATATGTGTCAAGAAC 57.460 33.333 0.00 0.00 0.00 3.01
1775 1945 9.138062 GCTAGTGATGAAGATATATGTGTCAAG 57.862 37.037 0.00 0.00 0.00 3.02
1776 1946 8.641541 TGCTAGTGATGAAGATATATGTGTCAA 58.358 33.333 0.00 0.00 0.00 3.18
1870 2040 5.760743 AGTTAGCTTTCAAGAGTGTCCTTTC 59.239 40.000 0.00 0.00 0.00 2.62
2164 2334 7.660112 TCATGCTGAACTAAATTGTGATTGTT 58.340 30.769 0.00 0.00 0.00 2.83
2191 2362 6.259550 ACAAATCTACTTTCTGTTCATGGC 57.740 37.500 0.00 0.00 0.00 4.40
2192 2363 7.874940 TCAACAAATCTACTTTCTGTTCATGG 58.125 34.615 0.00 0.00 0.00 3.66
2193 2364 9.390795 CTTCAACAAATCTACTTTCTGTTCATG 57.609 33.333 0.00 0.00 0.00 3.07
2194 2365 8.078596 GCTTCAACAAATCTACTTTCTGTTCAT 58.921 33.333 0.00 0.00 0.00 2.57
2195 2366 7.066887 TGCTTCAACAAATCTACTTTCTGTTCA 59.933 33.333 0.00 0.00 0.00 3.18
2196 2367 7.417612 TGCTTCAACAAATCTACTTTCTGTTC 58.582 34.615 0.00 0.00 0.00 3.18
2197 2368 7.333528 TGCTTCAACAAATCTACTTTCTGTT 57.666 32.000 0.00 0.00 0.00 3.16
2198 2369 6.942532 TGCTTCAACAAATCTACTTTCTGT 57.057 33.333 0.00 0.00 0.00 3.41
2217 2388 1.949525 ACTGAACGCACAAGATTGCTT 59.050 42.857 0.00 0.00 40.62 3.91
2247 2418 5.913137 AAGAACAACTGACCAAATCAACA 57.087 34.783 0.00 0.00 36.69 3.33
2288 2459 8.354711 TGCAGATATCTAACTATTAGGTCAGG 57.645 38.462 4.54 0.00 34.00 3.86
2300 2471 8.356657 ACATACTGAGAACTGCAGATATCTAAC 58.643 37.037 23.35 10.01 36.86 2.34
2437 2608 7.984050 TCCTGAAGCATAATGAGAGTAAAGAAG 59.016 37.037 0.00 0.00 0.00 2.85
2438 2609 7.851228 TCCTGAAGCATAATGAGAGTAAAGAA 58.149 34.615 0.00 0.00 0.00 2.52
2558 2729 5.574891 AACATAGCATACATCCGCAAAAA 57.425 34.783 0.00 0.00 0.00 1.94
2559 2730 5.574891 AAACATAGCATACATCCGCAAAA 57.425 34.783 0.00 0.00 0.00 2.44
2560 2731 5.449862 GGAAAACATAGCATACATCCGCAAA 60.450 40.000 0.00 0.00 0.00 3.68
2561 2732 4.036262 GGAAAACATAGCATACATCCGCAA 59.964 41.667 0.00 0.00 0.00 4.85
2562 2733 3.563808 GGAAAACATAGCATACATCCGCA 59.436 43.478 0.00 0.00 0.00 5.69
2563 2734 3.815401 AGGAAAACATAGCATACATCCGC 59.185 43.478 0.00 0.00 0.00 5.54
2564 2735 6.377327 AAAGGAAAACATAGCATACATCCG 57.623 37.500 0.00 0.00 0.00 4.18
2568 2739 9.853555 CACAATAAAAGGAAAACATAGCATACA 57.146 29.630 0.00 0.00 0.00 2.29
2569 2740 9.855021 ACACAATAAAAGGAAAACATAGCATAC 57.145 29.630 0.00 0.00 0.00 2.39
2570 2741 9.853555 CACACAATAAAAGGAAAACATAGCATA 57.146 29.630 0.00 0.00 0.00 3.14
2571 2742 8.367156 ACACACAATAAAAGGAAAACATAGCAT 58.633 29.630 0.00 0.00 0.00 3.79
2572 2743 7.721402 ACACACAATAAAAGGAAAACATAGCA 58.279 30.769 0.00 0.00 0.00 3.49
2573 2744 8.587952 AACACACAATAAAAGGAAAACATAGC 57.412 30.769 0.00 0.00 0.00 2.97
2575 2746 9.319143 CCAAACACACAATAAAAGGAAAACATA 57.681 29.630 0.00 0.00 0.00 2.29
2576 2747 7.826744 ACCAAACACACAATAAAAGGAAAACAT 59.173 29.630 0.00 0.00 0.00 2.71
2577 2748 7.162082 ACCAAACACACAATAAAAGGAAAACA 58.838 30.769 0.00 0.00 0.00 2.83
2578 2749 7.332182 TGACCAAACACACAATAAAAGGAAAAC 59.668 33.333 0.00 0.00 0.00 2.43
2579 2750 7.332182 GTGACCAAACACACAATAAAAGGAAAA 59.668 33.333 0.00 0.00 40.11 2.29
2580 2751 6.814146 GTGACCAAACACACAATAAAAGGAAA 59.186 34.615 0.00 0.00 40.11 3.13
2581 2752 6.153680 AGTGACCAAACACACAATAAAAGGAA 59.846 34.615 0.00 0.00 42.45 3.36
2582 2753 5.654650 AGTGACCAAACACACAATAAAAGGA 59.345 36.000 0.00 0.00 42.45 3.36
2583 2754 5.901552 AGTGACCAAACACACAATAAAAGG 58.098 37.500 0.00 0.00 42.45 3.11
2584 2755 6.631238 CGTAGTGACCAAACACACAATAAAAG 59.369 38.462 0.00 0.00 42.45 2.27
2585 2756 6.487960 CGTAGTGACCAAACACACAATAAAA 58.512 36.000 0.00 0.00 42.45 1.52
2586 2757 5.504337 GCGTAGTGACCAAACACACAATAAA 60.504 40.000 0.00 0.00 42.45 1.40
2613 2784 1.568612 GGGACCATGCGCATCATACG 61.569 60.000 22.51 8.96 33.19 3.06
2663 2834 7.570132 ACACCATATAATACCAAGCAACTACA 58.430 34.615 0.00 0.00 0.00 2.74
2677 2848 7.220030 GGACACAATGAGAGACACCATATAAT 58.780 38.462 0.00 0.00 0.00 1.28
2687 2858 3.744660 ACTTTGGGACACAATGAGAGAC 58.255 45.455 10.11 0.00 39.29 3.36
2690 2861 4.277476 ACAAACTTTGGGACACAATGAGA 58.723 39.130 10.11 0.00 39.29 3.27
2881 3057 8.361592 AGCAGAATATGATTAAAATTTGCAGC 57.638 30.769 0.00 0.00 0.00 5.25
2941 3117 8.555166 TGTAAGTAAAAAGAACAGCAAAATCG 57.445 30.769 0.00 0.00 0.00 3.34
3242 3418 4.746115 TCATTTTGAGCATTGCTGACAAAC 59.254 37.500 17.51 0.48 39.88 2.93
3278 3454 8.469309 AACATCCTTCCAATGGTATTAATCTG 57.531 34.615 0.00 0.00 0.00 2.90
3285 3461 4.210331 GCAGAACATCCTTCCAATGGTAT 58.790 43.478 0.00 0.00 0.00 2.73
3418 3594 7.919313 AATATGCAGCAATTTTCAGTATTCG 57.081 32.000 0.00 0.00 0.00 3.34
3687 3871 6.142818 TGTCATAAAACAAACAGTTGAGGG 57.857 37.500 0.00 0.00 41.19 4.30
3699 3883 8.932945 TTTGTAAGTGCAATTGTCATAAAACA 57.067 26.923 10.14 0.00 0.00 2.83
3774 3958 5.968254 TGTAGGATGAAATAACAGTGCGTA 58.032 37.500 0.00 0.00 0.00 4.42
3978 4162 2.939103 AGGAGCTATGCTTGCTTTAACG 59.061 45.455 0.00 0.00 39.88 3.18
4013 4197 6.796426 TCGAATTTTAAATTGTGTGTGGTGA 58.204 32.000 7.72 0.00 0.00 4.02
4062 4246 4.122143 ACCAACACACAAGAACCAATTG 57.878 40.909 0.00 0.00 0.00 2.32
4170 4438 6.500589 ACCTTGCACTACAGTCCAATATAT 57.499 37.500 0.00 0.00 0.00 0.86
4208 4476 0.977395 ACCAGACTACCAGTCCTTGC 59.023 55.000 2.74 0.00 46.18 4.01
4255 4523 5.688823 CAATCGACATGTCAAAACTGCTTA 58.311 37.500 24.93 0.00 0.00 3.09
4434 4702 6.038936 ACTGTAAAACCGCTTATTCAACACTT 59.961 34.615 0.00 0.00 0.00 3.16
4486 4754 9.153721 TCCAATTTGCATCATTATTTTTCACTC 57.846 29.630 0.00 0.00 0.00 3.51
4583 4851 7.359849 GCAACATATACACATGACTAGCTGATG 60.360 40.741 0.00 0.00 0.00 3.07
5200 5471 0.400213 GTGACCTTGACCCCATGACA 59.600 55.000 0.00 0.00 0.00 3.58
5274 5545 4.983671 AAAAAGACGCAAGAGGAAAACT 57.016 36.364 0.00 0.00 43.62 2.66
5422 5694 0.445436 CACCGATGCAGCTTGACTTC 59.555 55.000 0.00 0.00 0.00 3.01
5617 5889 0.529773 TCAGGTTCACGACACAGCAC 60.530 55.000 0.00 0.00 0.00 4.40
5817 6113 1.985473 ATGTTTGAGCAAGGACAGCA 58.015 45.000 0.00 0.00 0.00 4.41
5876 6172 4.844348 ACTACTCCCTCCATCCCATAATT 58.156 43.478 0.00 0.00 0.00 1.40
5886 6187 3.205507 AGCATAGAGAACTACTCCCTCCA 59.794 47.826 0.00 0.00 45.96 3.86
5905 6206 3.389983 ACCCACTTACTACTGAAACAGCA 59.610 43.478 0.00 0.00 34.37 4.41
5992 6293 4.563140 ATTTTAGAGCCTTTACCCGTGA 57.437 40.909 0.00 0.00 0.00 4.35
5995 6296 5.890424 TGAAATTTTAGAGCCTTTACCCG 57.110 39.130 0.00 0.00 0.00 5.28
6008 6312 6.545666 ACTGCACCCATCGATATGAAATTTTA 59.454 34.615 0.00 0.00 34.84 1.52
6084 6388 1.153958 GCATCCAAACAAGGCGCTC 60.154 57.895 7.64 0.00 0.00 5.03
6124 6428 6.524101 ACAGGAAAAGAACTGTAAAAAGCA 57.476 33.333 0.00 0.00 45.45 3.91
6204 6512 8.771920 ATTTCTTCCCACCGAATTTTTAATTC 57.228 30.769 2.75 2.75 0.00 2.17
6207 6515 7.156000 GGAATTTCTTCCCACCGAATTTTTAA 58.844 34.615 0.00 0.00 44.56 1.52
6299 6607 2.763902 CACCAAGTCCCCTTCCCC 59.236 66.667 0.00 0.00 0.00 4.81
6379 6690 9.920826 GATTCCAAAAATGTTTCAAAGACTTTC 57.079 29.630 0.00 0.00 0.00 2.62
6381 6692 9.447157 TTGATTCCAAAAATGTTTCAAAGACTT 57.553 25.926 0.00 0.00 0.00 3.01
6382 6693 9.447157 TTTGATTCCAAAAATGTTTCAAAGACT 57.553 25.926 0.00 0.00 39.15 3.24
6422 6818 2.032550 GCTCCGCTGTGTATACGAGTAA 59.967 50.000 0.00 0.00 0.00 2.24
6634 7058 2.782925 TCCAATAAGCCCAAGATAGCCA 59.217 45.455 0.00 0.00 0.00 4.75
6663 7087 1.606668 GCCCTGTCATACTCTCTCTCG 59.393 57.143 0.00 0.00 0.00 4.04
6666 7090 1.606668 CGAGCCCTGTCATACTCTCTC 59.393 57.143 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.