Multiple sequence alignment - TraesCS6A01G293300

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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 TraesCS6A01G293300 chr6A 100.000 6019 0 0 1 6019 524763090 524769108 0.000000e+00 11116.0
1 TraesCS6A01G293300 chr6D 94.608 5286 160 59 54 5262 382620536 382625773 0.000000e+00 8067.0
2 TraesCS6A01G293300 chr6D 90.186 377 22 6 5647 6013 382626130 382626501 1.520000e-130 477.0
3 TraesCS6A01G293300 chr6D 89.243 251 19 7 1732 1978 291388422 291388176 2.110000e-79 307.0
4 TraesCS6A01G293300 chr6D 85.492 193 15 7 5263 5452 382625868 382626050 7.960000e-44 189.0
5 TraesCS6A01G293300 chr6D 94.595 37 2 0 1 37 3303084 3303048 2.340000e-04 58.4
6 TraesCS6A01G293300 chr6B 94.851 1612 61 12 2044 3651 572402802 572404395 0.000000e+00 2497.0
7 TraesCS6A01G293300 chr6B 94.451 1622 71 14 3650 5262 572404477 572406088 0.000000e+00 2479.0
8 TraesCS6A01G293300 chr6B 90.130 1540 85 27 222 1716 572401293 572402810 0.000000e+00 1940.0
9 TraesCS6A01G293300 chr6B 87.712 236 18 3 5793 6019 572406462 572406695 1.290000e-66 265.0
10 TraesCS6A01G293300 chr6B 94.891 137 7 0 5632 5768 572406329 572406465 1.310000e-51 215.0
11 TraesCS6A01G293300 chr6B 95.455 88 4 0 5263 5350 572406181 572406268 2.260000e-29 141.0
12 TraesCS6A01G293300 chr1B 82.420 1058 125 26 4191 5215 171619508 171620537 0.000000e+00 867.0
13 TraesCS6A01G293300 chr1B 86.022 744 79 19 986 1714 171617309 171618042 0.000000e+00 774.0
14 TraesCS6A01G293300 chr1B 90.890 483 36 4 3288 3769 171618988 171619463 5.090000e-180 641.0
15 TraesCS6A01G293300 chr1B 80.822 438 50 22 2705 3135 171618497 171618907 4.530000e-81 313.0
16 TraesCS6A01G293300 chr1D 82.216 1074 118 36 4191 5226 112353680 112354718 0.000000e+00 857.0
17 TraesCS6A01G293300 chr1D 85.850 735 75 20 986 1701 112351309 112352033 0.000000e+00 754.0
18 TraesCS6A01G293300 chr1D 90.244 492 37 7 3288 3775 112353157 112353641 3.060000e-177 632.0
19 TraesCS6A01G293300 chr1D 80.549 437 53 20 2705 3135 112352666 112353076 2.110000e-79 307.0
20 TraesCS6A01G293300 chr1D 97.059 34 1 0 1 34 455761359 455761326 2.340000e-04 58.4
21 TraesCS6A01G293300 chr1A 84.030 933 106 16 4330 5228 119495941 119496864 0.000000e+00 857.0
22 TraesCS6A01G293300 chr1A 85.752 751 75 20 986 1714 119493661 119494401 0.000000e+00 765.0
23 TraesCS6A01G293300 chr1A 90.309 485 36 8 3292 3769 119495345 119495825 5.120000e-175 625.0
24 TraesCS6A01G293300 chr1A 79.512 410 52 19 2705 3108 119494854 119495237 4.630000e-66 263.0
25 TraesCS6A01G293300 chr5B 86.997 323 28 11 1718 2028 111709332 111709012 9.600000e-93 351.0
26 TraesCS6A01G293300 chr5B 97.059 34 1 0 1 34 291840732 291840765 2.340000e-04 58.4
27 TraesCS6A01G293300 chr4D 87.582 306 28 5 1732 2028 9304139 9304443 4.470000e-91 346.0
28 TraesCS6A01G293300 chr2D 86.420 324 25 9 1718 2028 476025030 476025347 2.690000e-88 337.0
29 TraesCS6A01G293300 chr4A 90.763 249 19 3 1732 1978 594145025 594144779 4.500000e-86 329.0
30 TraesCS6A01G293300 chr7A 85.846 325 27 7 1718 2028 96155899 96155580 1.620000e-85 327.0
31 TraesCS6A01G293300 chr7A 78.700 277 37 11 1706 1975 16716795 16717056 1.340000e-36 165.0
32 TraesCS6A01G293300 chr7A 88.506 87 5 2 5544 5627 547332396 547332312 3.840000e-17 100.0
33 TraesCS6A01G293300 chr3D 84.348 345 28 14 1717 2043 567145958 567146294 1.260000e-81 315.0
34 TraesCS6A01G293300 chr3A 84.663 326 30 11 1718 2028 684415437 684415117 2.110000e-79 307.0
35 TraesCS6A01G293300 chr7D 80.317 315 33 14 1750 2035 566017602 566017916 1.700000e-50 211.0
36 TraesCS6A01G293300 chr7D 100.000 34 0 0 1 34 102964998 102965031 5.040000e-06 63.9
37 TraesCS6A01G293300 chr7D 97.059 34 1 0 1 34 2869919 2869952 2.340000e-04 58.4
38 TraesCS6A01G293300 chr3B 86.885 61 5 2 5545 5602 4537776 4537836 1.400000e-06 65.8
39 TraesCS6A01G293300 chr5D 100.000 32 0 0 1 32 543708611 543708642 6.510000e-05 60.2
40 TraesCS6A01G293300 chrUn 100.000 31 0 0 5 35 302653248 302653278 2.340000e-04 58.4
41 TraesCS6A01G293300 chrUn 100.000 31 0 0 5 35 304066449 304066479 2.340000e-04 58.4
42 TraesCS6A01G293300 chrUn 100.000 31 0 0 5 35 304070853 304070883 2.340000e-04 58.4


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 TraesCS6A01G293300 chr6A 524763090 524769108 6018 False 11116.000000 11116 100.000000 1 6019 1 chr6A.!!$F1 6018
1 TraesCS6A01G293300 chr6D 382620536 382626501 5965 False 2911.000000 8067 90.095333 54 6013 3 chr6D.!!$F1 5959
2 TraesCS6A01G293300 chr6B 572401293 572406695 5402 False 1256.166667 2497 92.915000 222 6019 6 chr6B.!!$F1 5797
3 TraesCS6A01G293300 chr1B 171617309 171620537 3228 False 648.750000 867 85.038500 986 5215 4 chr1B.!!$F1 4229
4 TraesCS6A01G293300 chr1D 112351309 112354718 3409 False 637.500000 857 84.714750 986 5226 4 chr1D.!!$F1 4240
5 TraesCS6A01G293300 chr1A 119493661 119496864 3203 False 627.500000 857 84.900750 986 5228 4 chr1A.!!$F1 4242

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
129 130 0.179015 TTTGGGGCAGCTAAACGTGA 60.179 50.000 0.00 0.00 0.00 4.35 F
1166 1286 0.320421 GCTCTTTGTGTAGGTGGCGA 60.320 55.000 0.00 0.00 0.00 5.54 F
2386 2703 1.062047 TAGCTCTCAACTACGCGCG 59.938 57.895 30.96 30.96 0.00 6.86 F
2402 2719 1.993370 GCGCGACAGATCACTTTAAGT 59.007 47.619 12.10 0.00 0.00 2.24 F
2616 2936 3.349006 GGTGTGCTCTGTGCGTGG 61.349 66.667 0.00 0.00 46.63 4.94 F
4237 4692 5.381757 TGGGTGTTTATTGCCCTATATGAC 58.618 41.667 0.00 0.00 42.77 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 1626 0.948678 TTAACACTCGCAAAGCACCC 59.051 50.000 0.00 0.0 0.00 4.61 R
2616 2936 2.005451 CTGTGGCACTATGTCTGCTTC 58.995 52.381 19.83 0.0 34.84 3.86 R
4033 4485 0.536006 AGGAGTGCAGAGTTTGTGGC 60.536 55.000 0.00 0.0 0.00 5.01 R
4237 4692 2.778187 GCAGGAAGCTAGGTACTACG 57.222 55.000 0.00 0.0 41.75 3.51 R
4326 4784 4.120331 GCGTCCTGCATGTTGCCC 62.120 66.667 0.00 0.0 44.23 5.36 R
5485 6145 0.176219 TACGCCCCGTATTTCCACTG 59.824 55.000 0.00 0.0 41.54 3.66 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
24 25 6.718294 ACAAATATTTAGAAACGGAGGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
25 26 7.854337 ACAAATATTTAGAAACGGAGGGAGTA 58.146 34.615 0.00 0.00 0.00 2.59
26 27 8.491958 ACAAATATTTAGAAACGGAGGGAGTAT 58.508 33.333 0.00 0.00 0.00 2.12
27 28 9.338622 CAAATATTTAGAAACGGAGGGAGTATT 57.661 33.333 0.00 0.00 0.00 1.89
28 29 9.916360 AAATATTTAGAAACGGAGGGAGTATTT 57.084 29.630 0.00 0.00 0.00 1.40
31 32 6.475596 TTAGAAACGGAGGGAGTATTTAGG 57.524 41.667 0.00 0.00 0.00 2.69
32 33 4.617593 AGAAACGGAGGGAGTATTTAGGA 58.382 43.478 0.00 0.00 0.00 2.94
33 34 5.028131 AGAAACGGAGGGAGTATTTAGGAA 58.972 41.667 0.00 0.00 0.00 3.36
34 35 5.666265 AGAAACGGAGGGAGTATTTAGGAAT 59.334 40.000 0.00 0.00 0.00 3.01
35 36 6.842807 AGAAACGGAGGGAGTATTTAGGAATA 59.157 38.462 0.00 0.00 0.00 1.75
36 37 6.667558 AACGGAGGGAGTATTTAGGAATAG 57.332 41.667 0.00 0.00 0.00 1.73
37 38 5.961897 ACGGAGGGAGTATTTAGGAATAGA 58.038 41.667 0.00 0.00 0.00 1.98
38 39 5.774184 ACGGAGGGAGTATTTAGGAATAGAC 59.226 44.000 0.00 0.00 0.00 2.59
39 40 5.106237 CGGAGGGAGTATTTAGGAATAGACG 60.106 48.000 0.00 0.00 0.00 4.18
40 41 6.008960 GGAGGGAGTATTTAGGAATAGACGA 58.991 44.000 0.00 0.00 0.00 4.20
41 42 6.664384 GGAGGGAGTATTTAGGAATAGACGAT 59.336 42.308 0.00 0.00 0.00 3.73
42 43 7.833183 GGAGGGAGTATTTAGGAATAGACGATA 59.167 40.741 0.00 0.00 0.00 2.92
43 44 8.578448 AGGGAGTATTTAGGAATAGACGATAC 57.422 38.462 0.00 0.00 0.00 2.24
44 45 8.168725 AGGGAGTATTTAGGAATAGACGATACA 58.831 37.037 0.00 0.00 0.00 2.29
45 46 8.460428 GGGAGTATTTAGGAATAGACGATACAG 58.540 40.741 0.00 0.00 0.00 2.74
46 47 9.012161 GGAGTATTTAGGAATAGACGATACAGT 57.988 37.037 0.00 0.00 0.00 3.55
49 50 9.327529 GTATTTAGGAATAGACGATACAGTTCG 57.672 37.037 0.00 4.27 44.56 3.95
50 51 4.226113 AGGAATAGACGATACAGTTCGC 57.774 45.455 0.00 0.73 42.82 4.70
51 52 3.884091 AGGAATAGACGATACAGTTCGCT 59.116 43.478 0.00 6.33 42.82 4.93
66 67 4.530857 GCTGGGGATCCGACGTGG 62.531 72.222 5.45 0.00 40.09 4.94
70 71 3.861797 GGGATCCGACGTGGCCAT 61.862 66.667 9.72 0.00 37.80 4.40
84 85 2.441532 CCATTGGCTGAGCTGGGG 60.442 66.667 3.72 0.00 0.00 4.96
102 103 0.465278 GGCCTGATTCTTGGAGGAGC 60.465 60.000 0.00 0.00 0.00 4.70
125 126 1.591703 GGCTTTGGGGCAGCTAAAC 59.408 57.895 0.00 0.00 40.53 2.01
129 130 0.179015 TTTGGGGCAGCTAAACGTGA 60.179 50.000 0.00 0.00 0.00 4.35
149 150 1.203013 AGTTCTGGGCCAGTTTTACCC 60.203 52.381 31.60 13.09 44.52 3.69
155 156 2.940158 GGGCCAGTTTTACCCGATATT 58.060 47.619 4.39 0.00 32.92 1.28
166 167 2.649531 CCCGATATTTGGGCCAGTTA 57.350 50.000 6.23 2.87 40.47 2.24
168 169 3.081804 CCCGATATTTGGGCCAGTTATC 58.918 50.000 19.99 19.99 40.47 1.75
169 170 3.244911 CCCGATATTTGGGCCAGTTATCT 60.245 47.826 23.98 8.71 40.47 1.98
170 171 4.019681 CCCGATATTTGGGCCAGTTATCTA 60.020 45.833 23.98 2.62 40.47 1.98
171 172 5.339200 CCCGATATTTGGGCCAGTTATCTAT 60.339 44.000 23.98 11.37 40.47 1.98
172 173 6.126883 CCCGATATTTGGGCCAGTTATCTATA 60.127 42.308 23.98 10.55 40.47 1.31
173 174 7.335627 CCGATATTTGGGCCAGTTATCTATAA 58.664 38.462 23.98 9.30 0.00 0.98
174 175 7.280205 CCGATATTTGGGCCAGTTATCTATAAC 59.720 40.741 23.98 4.95 42.19 1.89
229 255 3.207669 CCCAGCTGAATCCTGCGC 61.208 66.667 17.39 0.00 41.42 6.09
241 267 3.197790 CTGCGCCAGGATTCGTGG 61.198 66.667 18.91 18.91 41.71 4.94
245 271 1.443407 CGCCAGGATTCGTGGAGAT 59.557 57.895 25.67 0.00 40.60 2.75
261 287 2.544069 GGAGATGAATCCGACCGAAGAC 60.544 54.545 0.00 0.00 0.00 3.01
262 288 1.065701 AGATGAATCCGACCGAAGACG 59.934 52.381 0.00 0.00 39.43 4.18
313 344 5.277345 GCTGACGATCGCCAGTTAATATTTT 60.277 40.000 28.39 0.00 33.19 1.82
330 361 6.699575 ATATTTTCCCAAAATCTCACCGAG 57.300 37.500 0.00 0.00 41.16 4.63
459 518 2.812619 CCCCTGCCCTCGAGAATCC 61.813 68.421 15.71 0.00 0.00 3.01
581 640 0.813210 GGGAAGAGAAGCATCAGCCG 60.813 60.000 0.00 0.00 43.56 5.52
619 678 3.684788 CCCTTCAAGGTATATATGCGCAC 59.315 47.826 14.90 0.00 31.93 5.34
631 690 3.505184 GCGCACACCCATTACCCG 61.505 66.667 0.30 0.00 0.00 5.28
642 701 1.523758 CATTACCCGATAAGCTGCCC 58.476 55.000 0.00 0.00 0.00 5.36
648 707 0.868406 CCGATAAGCTGCCCGAATTC 59.132 55.000 0.00 0.00 0.00 2.17
675 734 3.005554 GAGCCCGTGATATCCAATCATG 58.994 50.000 0.00 1.07 35.42 3.07
736 795 7.005380 CGAATTGATGTTGAAGATTTTTGTGC 58.995 34.615 0.00 0.00 0.00 4.57
745 804 2.758009 AGATTTTTGTGCCATGTGTGC 58.242 42.857 0.00 0.00 0.00 4.57
746 805 1.456544 GATTTTTGTGCCATGTGTGCG 59.543 47.619 0.00 0.00 0.00 5.34
747 806 1.150567 TTTTTGTGCCATGTGTGCGC 61.151 50.000 0.00 0.00 39.63 6.09
748 807 2.014064 TTTTGTGCCATGTGTGCGCT 62.014 50.000 9.73 0.00 39.88 5.92
749 808 2.014064 TTTGTGCCATGTGTGCGCTT 62.014 50.000 9.73 0.00 39.88 4.68
750 809 2.429571 GTGCCATGTGTGCGCTTG 60.430 61.111 9.73 0.00 36.34 4.01
751 810 4.345962 TGCCATGTGTGCGCTTGC 62.346 61.111 9.73 0.00 39.78 4.01
829 930 3.367992 TGTGTGTGGCATTCAAATCAC 57.632 42.857 0.00 0.00 0.00 3.06
863 964 9.087871 ACAGTGATAGCTAGTCTTCATGAATAT 57.912 33.333 8.96 1.91 0.00 1.28
939 1040 8.752005 AATTTGTATGCAACAGTGGTATCTAT 57.248 30.769 0.00 0.00 39.87 1.98
940 1041 9.845740 AATTTGTATGCAACAGTGGTATCTATA 57.154 29.630 0.00 0.00 39.87 1.31
1080 1193 3.906846 CAGGTATCTATTCCCTGCCTTCT 59.093 47.826 0.00 0.00 39.36 2.85
1142 1256 2.426381 GTGCGAAGGGTAGCTAACTAGT 59.574 50.000 9.06 0.00 0.00 2.57
1166 1286 0.320421 GCTCTTTGTGTAGGTGGCGA 60.320 55.000 0.00 0.00 0.00 5.54
1197 1320 2.176889 CAAGAAGGGTACTCGGAGGAA 58.823 52.381 10.23 0.00 0.00 3.36
1254 1377 1.153823 CCGGTCGAATCAGACGCTT 60.154 57.895 0.00 0.00 41.81 4.68
1325 1449 5.174037 TGGGTAACTACTTTGCTTGCTAT 57.826 39.130 0.00 0.00 0.00 2.97
1503 1627 2.267045 GCTTGTGGCAAGGTAAGGG 58.733 57.895 10.38 0.00 41.35 3.95
1569 1694 1.891150 GTTCCGAGGTAGTCCTGACAA 59.109 52.381 0.00 0.00 45.24 3.18
1570 1695 2.496470 GTTCCGAGGTAGTCCTGACAAT 59.504 50.000 0.00 0.00 45.24 2.71
1736 2040 3.979101 TGGAAATTCAATTTGGCTCCC 57.021 42.857 0.00 0.00 31.47 4.30
1919 2229 2.355481 ACCGACGAAACACCGCTC 60.355 61.111 0.00 0.00 0.00 5.03
1924 2234 2.342279 CGAAACACCGCTCCTCCA 59.658 61.111 0.00 0.00 0.00 3.86
1981 2291 6.128282 ACACCAACACGATCATCTACAATTTC 60.128 38.462 0.00 0.00 0.00 2.17
2034 2345 3.361977 CACCCGGGAGCCAAAACG 61.362 66.667 32.02 0.00 0.00 3.60
2116 2427 7.669722 AGGTTTTTCCATCTCTGTAATGCTTTA 59.330 33.333 0.00 0.00 39.02 1.85
2169 2480 2.756760 AGGGCAGATTTGTACATTGCTG 59.243 45.455 16.54 14.58 35.23 4.41
2364 2680 5.046878 TCGCTTTTGATTTCCTCACTACCTA 60.047 40.000 0.00 0.00 32.17 3.08
2386 2703 1.062047 TAGCTCTCAACTACGCGCG 59.938 57.895 30.96 30.96 0.00 6.86
2402 2719 1.993370 GCGCGACAGATCACTTTAAGT 59.007 47.619 12.10 0.00 0.00 2.24
2616 2936 3.349006 GGTGTGCTCTGTGCGTGG 61.349 66.667 0.00 0.00 46.63 4.94
2794 3114 8.328758 TCACATCACCAGGAAGAATATACTTTT 58.671 33.333 0.00 0.00 0.00 2.27
2795 3115 8.960591 CACATCACCAGGAAGAATATACTTTTT 58.039 33.333 0.00 0.00 0.00 1.94
4127 4579 9.236006 ACATTCTTTGTGAATAGTATGAAGCTT 57.764 29.630 0.00 0.00 43.00 3.74
4136 4588 9.331282 GTGAATAGTATGAAGCTTACATCCTTT 57.669 33.333 12.69 3.04 0.00 3.11
4237 4692 5.381757 TGGGTGTTTATTGCCCTATATGAC 58.618 41.667 0.00 0.00 42.77 3.06
4643 5102 6.655003 AGAACTTCCATGAATTTGTACACGAT 59.345 34.615 0.00 0.00 0.00 3.73
4861 5341 5.049749 GCATTTGTTTTGCGGAAGGTATTTT 60.050 36.000 0.00 0.00 0.00 1.82
4879 5359 8.421002 AGGTATTTTTCATGCTGTTAACAACTT 58.579 29.630 10.03 0.50 0.00 2.66
4894 5374 0.179078 AACTTAACCACACGCGGTCA 60.179 50.000 12.47 0.00 38.76 4.02
5056 5548 6.675413 TCCTGGAGCTTACTAACAACTTAA 57.325 37.500 0.00 0.00 0.00 1.85
5057 5549 7.253905 TCCTGGAGCTTACTAACAACTTAAT 57.746 36.000 0.00 0.00 0.00 1.40
5288 5878 2.095059 CACCGCCTTTCTCTTCAATTGG 60.095 50.000 5.42 0.00 0.00 3.16
5342 5932 4.938226 AGGAGCTTGTTAATCAACTACAGC 59.062 41.667 0.00 0.00 35.56 4.40
5363 5979 6.014156 ACAGCATTAATCTAGGGCTAGTTAGG 60.014 42.308 0.00 0.00 34.84 2.69
5367 5983 8.373220 GCATTAATCTAGGGCTAGTTAGGTTTA 58.627 37.037 0.00 0.00 34.84 2.01
5399 6015 6.764877 CTCGTTAAGCAAAGAACAGTAAGA 57.235 37.500 0.00 0.00 0.00 2.10
5401 6017 5.694910 TCGTTAAGCAAAGAACAGTAAGAGG 59.305 40.000 0.00 0.00 0.00 3.69
5402 6018 5.107065 CGTTAAGCAAAGAACAGTAAGAGGG 60.107 44.000 0.00 0.00 0.00 4.30
5404 6020 1.813178 GCAAAGAACAGTAAGAGGGGC 59.187 52.381 0.00 0.00 0.00 5.80
5405 6021 2.437413 CAAAGAACAGTAAGAGGGGCC 58.563 52.381 0.00 0.00 0.00 5.80
5407 6023 1.221021 GAACAGTAAGAGGGGCCGG 59.779 63.158 0.00 0.00 0.00 6.13
5409 6025 3.480133 CAGTAAGAGGGGCCGGGG 61.480 72.222 2.18 0.00 0.00 5.73
5429 6045 4.947147 TTCTGGTGCCACGTGCCC 62.947 66.667 10.91 10.02 40.16 5.36
5452 6068 1.871408 GCTCACCTGCACCTGATATCG 60.871 57.143 0.00 0.00 0.00 2.92
5469 6129 1.300620 CGAAGACAGGGTTCGTGCA 60.301 57.895 0.00 0.00 41.50 4.57
5478 6138 0.310854 GGGTTCGTGCAGTGGAAAAG 59.689 55.000 0.00 0.00 0.00 2.27
5479 6139 0.317854 GGTTCGTGCAGTGGAAAAGC 60.318 55.000 0.00 0.00 0.00 3.51
5480 6140 0.380378 GTTCGTGCAGTGGAAAAGCA 59.620 50.000 0.00 0.00 35.63 3.91
5482 6142 0.662619 TCGTGCAGTGGAAAAGCAAG 59.337 50.000 0.00 0.00 40.35 4.01
5483 6143 0.381801 CGTGCAGTGGAAAAGCAAGT 59.618 50.000 0.00 0.00 40.35 3.16
5484 6144 1.843992 GTGCAGTGGAAAAGCAAGTG 58.156 50.000 0.00 0.00 40.35 3.16
5485 6145 0.102844 TGCAGTGGAAAAGCAAGTGC 59.897 50.000 0.00 0.00 40.05 4.40
5486 6146 0.102844 GCAGTGGAAAAGCAAGTGCA 59.897 50.000 6.00 0.00 45.16 4.57
5487 6147 1.866880 GCAGTGGAAAAGCAAGTGCAG 60.867 52.381 6.00 0.00 45.16 4.41
5488 6148 1.406539 CAGTGGAAAAGCAAGTGCAGT 59.593 47.619 6.00 0.00 45.16 4.40
5489 6149 1.406539 AGTGGAAAAGCAAGTGCAGTG 59.593 47.619 6.00 0.00 45.16 3.66
5490 6150 0.746063 TGGAAAAGCAAGTGCAGTGG 59.254 50.000 6.00 0.00 45.16 4.00
5491 6151 1.032014 GGAAAAGCAAGTGCAGTGGA 58.968 50.000 0.00 0.00 45.16 4.02
5492 6152 1.408702 GGAAAAGCAAGTGCAGTGGAA 59.591 47.619 0.00 0.00 45.16 3.53
5493 6153 2.159114 GGAAAAGCAAGTGCAGTGGAAA 60.159 45.455 0.00 0.00 45.16 3.13
5494 6154 3.493176 GGAAAAGCAAGTGCAGTGGAAAT 60.493 43.478 0.00 0.00 45.16 2.17
5495 6155 4.261994 GGAAAAGCAAGTGCAGTGGAAATA 60.262 41.667 0.00 0.00 45.16 1.40
5496 6156 3.923017 AAGCAAGTGCAGTGGAAATAC 57.077 42.857 0.00 0.00 45.16 1.89
5497 6157 1.806542 AGCAAGTGCAGTGGAAATACG 59.193 47.619 0.00 0.00 45.16 3.06
5498 6158 1.135689 GCAAGTGCAGTGGAAATACGG 60.136 52.381 0.00 0.00 41.59 4.02
5499 6159 1.468520 CAAGTGCAGTGGAAATACGGG 59.531 52.381 0.00 0.00 0.00 5.28
5500 6160 0.035439 AGTGCAGTGGAAATACGGGG 60.035 55.000 0.00 0.00 0.00 5.73
5501 6161 1.377987 TGCAGTGGAAATACGGGGC 60.378 57.895 0.00 0.00 0.00 5.80
5502 6162 2.469516 GCAGTGGAAATACGGGGCG 61.470 63.158 0.00 0.00 0.00 6.13
5503 6163 1.078708 CAGTGGAAATACGGGGCGT 60.079 57.895 0.00 0.00 44.35 5.68
5504 6164 0.176219 CAGTGGAAATACGGGGCGTA 59.824 55.000 0.00 0.00 46.28 4.42
5527 6187 7.148222 CGTATATGAACCCTACGATTCTGATCT 60.148 40.741 0.00 0.00 40.38 2.75
5535 6195 1.827344 ACGATTCTGATCTGTGGCTCA 59.173 47.619 0.00 0.00 0.00 4.26
5536 6196 2.159128 ACGATTCTGATCTGTGGCTCAG 60.159 50.000 10.23 10.23 44.85 3.35
5540 6200 1.552337 TCTGATCTGTGGCTCAGGAAC 59.448 52.381 15.86 8.61 43.76 3.62
5541 6201 1.277273 CTGATCTGTGGCTCAGGAACA 59.723 52.381 15.86 12.02 43.76 3.18
5545 6205 3.228188 TCTGTGGCTCAGGAACATTTT 57.772 42.857 15.86 0.00 43.76 1.82
5569 6229 7.901874 TTTTTAATCGAAACGGAGACAAAAG 57.098 32.000 0.00 0.00 0.00 2.27
5570 6230 6.847956 TTTAATCGAAACGGAGACAAAAGA 57.152 33.333 0.00 0.00 0.00 2.52
5571 6231 7.429636 TTTAATCGAAACGGAGACAAAAGAT 57.570 32.000 0.00 0.00 0.00 2.40
5572 6232 5.941948 AATCGAAACGGAGACAAAAGATT 57.058 34.783 0.00 0.00 0.00 2.40
5573 6233 5.941948 ATCGAAACGGAGACAAAAGATTT 57.058 34.783 0.00 0.00 0.00 2.17
5574 6234 5.090652 TCGAAACGGAGACAAAAGATTTG 57.909 39.130 1.47 1.47 0.00 2.32
5575 6235 4.573201 TCGAAACGGAGACAAAAGATTTGT 59.427 37.500 8.11 8.11 34.97 2.83
5576 6236 4.904154 CGAAACGGAGACAAAAGATTTGTC 59.096 41.667 22.17 22.17 46.71 3.18
5619 6279 9.708092 AATAGAGTTTTAGAGTGTTACAAGACC 57.292 33.333 0.00 0.00 0.00 3.85
5620 6280 6.522946 AGAGTTTTAGAGTGTTACAAGACCC 58.477 40.000 0.00 0.00 0.00 4.46
5621 6281 5.618236 AGTTTTAGAGTGTTACAAGACCCC 58.382 41.667 0.00 0.00 0.00 4.95
5622 6282 5.131475 AGTTTTAGAGTGTTACAAGACCCCA 59.869 40.000 0.00 0.00 0.00 4.96
5623 6283 4.612264 TTAGAGTGTTACAAGACCCCAC 57.388 45.455 0.00 0.00 0.00 4.61
5624 6284 2.690840 AGAGTGTTACAAGACCCCACT 58.309 47.619 0.00 0.00 38.98 4.00
5625 6285 2.368875 AGAGTGTTACAAGACCCCACTG 59.631 50.000 0.00 0.00 36.56 3.66
5626 6286 2.367567 GAGTGTTACAAGACCCCACTGA 59.632 50.000 0.00 0.00 36.56 3.41
5627 6287 2.775384 AGTGTTACAAGACCCCACTGAA 59.225 45.455 0.00 0.00 35.20 3.02
5628 6288 3.201266 AGTGTTACAAGACCCCACTGAAA 59.799 43.478 0.00 0.00 35.20 2.69
5629 6289 3.314357 GTGTTACAAGACCCCACTGAAAC 59.686 47.826 0.00 0.00 0.00 2.78
5630 6290 3.201266 TGTTACAAGACCCCACTGAAACT 59.799 43.478 0.00 0.00 0.00 2.66
5631 6291 4.204799 GTTACAAGACCCCACTGAAACTT 58.795 43.478 0.00 0.00 0.00 2.66
5632 6292 3.382083 ACAAGACCCCACTGAAACTTT 57.618 42.857 0.00 0.00 0.00 2.66
5633 6293 3.708451 ACAAGACCCCACTGAAACTTTT 58.292 40.909 0.00 0.00 0.00 2.27
5634 6294 3.447229 ACAAGACCCCACTGAAACTTTTG 59.553 43.478 0.00 0.00 0.00 2.44
5635 6295 3.382083 AGACCCCACTGAAACTTTTGT 57.618 42.857 0.00 0.00 0.00 2.83
5636 6296 3.708451 AGACCCCACTGAAACTTTTGTT 58.292 40.909 0.00 0.00 45.94 2.83
5637 6297 3.699538 AGACCCCACTGAAACTTTTGTTC 59.300 43.478 0.00 0.00 42.67 3.18
5638 6298 3.436243 ACCCCACTGAAACTTTTGTTCA 58.564 40.909 0.00 0.00 42.67 3.18
5745 6405 9.256477 CCACGTTTGATGCTTATACTAATCTAA 57.744 33.333 0.00 0.00 0.00 2.10
5764 6424 5.859495 TCTAATTTGGCAAAATTTTCCCGT 58.141 33.333 16.82 0.00 42.14 5.28
5791 6451 0.666374 GTGCGTGCCTTTTACCTGTT 59.334 50.000 0.00 0.00 0.00 3.16
5792 6452 1.066454 GTGCGTGCCTTTTACCTGTTT 59.934 47.619 0.00 0.00 0.00 2.83
5793 6453 1.066303 TGCGTGCCTTTTACCTGTTTG 59.934 47.619 0.00 0.00 0.00 2.93
5794 6454 1.066454 GCGTGCCTTTTACCTGTTTGT 59.934 47.619 0.00 0.00 0.00 2.83
5809 6469 6.215845 ACCTGTTTGTTTGTTCATATGCTTC 58.784 36.000 0.00 0.00 0.00 3.86
5885 6545 1.080093 GTGATCCGAGGTTGCACGA 60.080 57.895 0.00 0.00 0.00 4.35
5909 6569 2.555123 GCAATCGCCTCAAGTTCCA 58.445 52.632 0.00 0.00 0.00 3.53
5926 6595 2.256306 TCCAACCATGAGCAGTAGTCA 58.744 47.619 0.00 0.00 0.00 3.41
5944 6614 2.715005 CGACGGGTCGCCGTATTA 59.285 61.111 8.40 0.00 46.81 0.98
5970 6640 5.484290 AGGATCTACGGGTAAATCTAATGGG 59.516 44.000 0.00 0.00 0.00 4.00
5978 6648 4.215109 GGTAAATCTAATGGGCCACATGT 58.785 43.478 9.28 0.00 40.44 3.21
5981 6651 2.715749 TCTAATGGGCCACATGTGAG 57.284 50.000 27.46 17.31 40.44 3.51
5983 6653 2.779430 TCTAATGGGCCACATGTGAGAT 59.221 45.455 27.46 9.81 40.44 2.75
5986 6656 1.077212 GGGCCACATGTGAGATGCT 60.077 57.895 27.46 0.00 0.00 3.79
5993 6663 0.741927 CATGTGAGATGCTGCGGACA 60.742 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.718294 ACTCCCTCCGTTTCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
1 2 8.904099 ATACTCCCTCCGTTTCTAAATATTTG 57.096 34.615 11.05 1.65 0.00 2.32
2 3 9.916360 AAATACTCCCTCCGTTTCTAAATATTT 57.084 29.630 5.89 5.89 0.00 1.40
5 6 8.645110 CCTAAATACTCCCTCCGTTTCTAAATA 58.355 37.037 0.00 0.00 0.00 1.40
6 7 7.346436 TCCTAAATACTCCCTCCGTTTCTAAAT 59.654 37.037 0.00 0.00 0.00 1.40
7 8 6.669154 TCCTAAATACTCCCTCCGTTTCTAAA 59.331 38.462 0.00 0.00 0.00 1.85
8 9 6.197168 TCCTAAATACTCCCTCCGTTTCTAA 58.803 40.000 0.00 0.00 0.00 2.10
9 10 5.769835 TCCTAAATACTCCCTCCGTTTCTA 58.230 41.667 0.00 0.00 0.00 2.10
10 11 4.617593 TCCTAAATACTCCCTCCGTTTCT 58.382 43.478 0.00 0.00 0.00 2.52
11 12 5.349061 TTCCTAAATACTCCCTCCGTTTC 57.651 43.478 0.00 0.00 0.00 2.78
12 13 5.970501 ATTCCTAAATACTCCCTCCGTTT 57.029 39.130 0.00 0.00 0.00 3.60
13 14 6.267242 GTCTATTCCTAAATACTCCCTCCGTT 59.733 42.308 0.00 0.00 0.00 4.44
14 15 5.774184 GTCTATTCCTAAATACTCCCTCCGT 59.226 44.000 0.00 0.00 0.00 4.69
15 16 5.106237 CGTCTATTCCTAAATACTCCCTCCG 60.106 48.000 0.00 0.00 0.00 4.63
16 17 6.008960 TCGTCTATTCCTAAATACTCCCTCC 58.991 44.000 0.00 0.00 0.00 4.30
17 18 7.706100 ATCGTCTATTCCTAAATACTCCCTC 57.294 40.000 0.00 0.00 0.00 4.30
18 19 8.168725 TGTATCGTCTATTCCTAAATACTCCCT 58.831 37.037 0.00 0.00 0.00 4.20
19 20 8.345724 TGTATCGTCTATTCCTAAATACTCCC 57.654 38.462 0.00 0.00 0.00 4.30
20 21 9.012161 ACTGTATCGTCTATTCCTAAATACTCC 57.988 37.037 0.00 0.00 0.00 3.85
23 24 9.327529 CGAACTGTATCGTCTATTCCTAAATAC 57.672 37.037 4.84 0.00 38.01 1.89
24 25 8.019669 GCGAACTGTATCGTCTATTCCTAAATA 58.980 37.037 11.80 0.00 44.49 1.40
25 26 6.862090 GCGAACTGTATCGTCTATTCCTAAAT 59.138 38.462 11.80 0.00 44.49 1.40
26 27 6.039047 AGCGAACTGTATCGTCTATTCCTAAA 59.961 38.462 11.80 0.00 44.49 1.85
27 28 5.530171 AGCGAACTGTATCGTCTATTCCTAA 59.470 40.000 11.80 0.00 44.49 2.69
28 29 5.049612 CAGCGAACTGTATCGTCTATTCCTA 60.050 44.000 11.80 0.00 44.49 2.94
29 30 3.884091 AGCGAACTGTATCGTCTATTCCT 59.116 43.478 11.80 0.37 44.49 3.36
30 31 3.975670 CAGCGAACTGTATCGTCTATTCC 59.024 47.826 11.80 0.00 44.49 3.01
31 32 3.975670 CCAGCGAACTGTATCGTCTATTC 59.024 47.826 11.80 0.00 44.49 1.75
32 33 3.243434 CCCAGCGAACTGTATCGTCTATT 60.243 47.826 11.80 0.00 44.49 1.73
33 34 2.293677 CCCAGCGAACTGTATCGTCTAT 59.706 50.000 11.80 0.00 44.49 1.98
34 35 1.674441 CCCAGCGAACTGTATCGTCTA 59.326 52.381 11.80 0.00 44.49 2.59
35 36 0.456221 CCCAGCGAACTGTATCGTCT 59.544 55.000 11.80 8.04 44.49 4.18
36 37 0.527817 CCCCAGCGAACTGTATCGTC 60.528 60.000 11.80 6.52 44.49 4.20
37 38 0.968901 TCCCCAGCGAACTGTATCGT 60.969 55.000 11.80 0.76 44.49 3.73
38 39 0.389391 ATCCCCAGCGAACTGTATCG 59.611 55.000 7.64 7.64 42.81 2.92
39 40 1.270358 GGATCCCCAGCGAACTGTATC 60.270 57.143 0.00 0.00 42.81 2.24
40 41 0.759346 GGATCCCCAGCGAACTGTAT 59.241 55.000 0.00 0.00 42.81 2.29
41 42 1.672854 CGGATCCCCAGCGAACTGTA 61.673 60.000 6.06 0.00 42.81 2.74
42 43 2.990479 GGATCCCCAGCGAACTGT 59.010 61.111 0.00 0.00 42.81 3.55
43 44 2.202932 CGGATCCCCAGCGAACTG 60.203 66.667 6.06 0.00 44.05 3.16
44 45 2.363795 TCGGATCCCCAGCGAACT 60.364 61.111 6.06 0.00 0.00 3.01
45 46 2.202892 GTCGGATCCCCAGCGAAC 60.203 66.667 6.06 0.00 0.00 3.95
46 47 3.833645 CGTCGGATCCCCAGCGAA 61.834 66.667 6.06 0.00 33.09 4.70
48 49 4.873129 CACGTCGGATCCCCAGCG 62.873 72.222 6.06 8.16 36.00 5.18
49 50 4.530857 CCACGTCGGATCCCCAGC 62.531 72.222 6.06 0.00 36.56 4.85
50 51 4.530857 GCCACGTCGGATCCCCAG 62.531 72.222 6.06 0.00 36.56 4.45
75 76 1.210204 AAGAATCAGGCCCCAGCTCA 61.210 55.000 0.00 0.00 39.73 4.26
84 85 0.254178 TGCTCCTCCAAGAATCAGGC 59.746 55.000 0.00 0.00 0.00 4.85
102 103 2.983791 CTGCCCCAAAGCCCATTG 59.016 61.111 0.00 0.00 0.00 2.82
112 113 1.003839 CTCACGTTTAGCTGCCCCA 60.004 57.895 0.00 0.00 0.00 4.96
125 126 0.535102 AAACTGGCCCAGAACTCACG 60.535 55.000 19.90 0.00 35.18 4.35
129 130 1.203013 GGGTAAAACTGGCCCAGAACT 60.203 52.381 19.90 3.03 41.93 3.01
149 150 8.197988 GTTATAGATAACTGGCCCAAATATCG 57.802 38.462 0.00 0.00 39.53 2.92
168 169 9.855361 CACGCAAAATCTTCTGAATAGTTATAG 57.145 33.333 0.00 0.00 0.00 1.31
169 170 8.826710 CCACGCAAAATCTTCTGAATAGTTATA 58.173 33.333 0.00 0.00 0.00 0.98
170 171 7.201732 CCCACGCAAAATCTTCTGAATAGTTAT 60.202 37.037 0.00 0.00 0.00 1.89
171 172 6.093495 CCCACGCAAAATCTTCTGAATAGTTA 59.907 38.462 0.00 0.00 0.00 2.24
172 173 5.106157 CCCACGCAAAATCTTCTGAATAGTT 60.106 40.000 0.00 0.00 0.00 2.24
173 174 4.396166 CCCACGCAAAATCTTCTGAATAGT 59.604 41.667 0.00 0.00 0.00 2.12
174 175 4.731773 GCCCACGCAAAATCTTCTGAATAG 60.732 45.833 0.00 0.00 34.03 1.73
175 176 3.128589 GCCCACGCAAAATCTTCTGAATA 59.871 43.478 0.00 0.00 34.03 1.75
176 177 2.094545 GCCCACGCAAAATCTTCTGAAT 60.095 45.455 0.00 0.00 34.03 2.57
177 178 1.269448 GCCCACGCAAAATCTTCTGAA 59.731 47.619 0.00 0.00 34.03 3.02
178 179 0.881118 GCCCACGCAAAATCTTCTGA 59.119 50.000 0.00 0.00 34.03 3.27
179 180 0.883833 AGCCCACGCAAAATCTTCTG 59.116 50.000 0.00 0.00 37.52 3.02
180 181 0.883833 CAGCCCACGCAAAATCTTCT 59.116 50.000 0.00 0.00 37.52 2.85
181 182 0.109132 CCAGCCCACGCAAAATCTTC 60.109 55.000 0.00 0.00 37.52 2.87
182 183 1.535204 CCCAGCCCACGCAAAATCTT 61.535 55.000 0.00 0.00 37.52 2.40
206 207 2.440980 GATTCAGCTGGGCCACCC 60.441 66.667 15.13 0.00 45.71 4.61
207 208 2.440980 GGATTCAGCTGGGCCACC 60.441 66.667 15.13 0.00 37.24 4.61
229 255 2.988010 TTCATCTCCACGAATCCTGG 57.012 50.000 0.00 0.00 0.00 4.45
241 267 2.733517 GTCTTCGGTCGGATTCATCTC 58.266 52.381 0.00 0.00 0.00 2.75
262 288 3.682292 ATTTCGCAGCGAGTCCCCC 62.682 63.158 18.62 0.00 37.14 5.40
267 293 0.179124 GGAGAGATTTCGCAGCGAGT 60.179 55.000 18.62 11.08 37.14 4.18
268 294 0.102120 AGGAGAGATTTCGCAGCGAG 59.898 55.000 18.62 0.00 37.14 5.03
313 344 0.391130 CGCTCGGTGAGATTTTGGGA 60.391 55.000 0.00 0.00 0.00 4.37
532 591 2.190578 CTGCACTTCCCGGATCCC 59.809 66.667 0.73 0.00 0.00 3.85
581 640 2.671682 GGAGGGGGTCTTGCTGAC 59.328 66.667 2.51 2.51 44.63 3.51
619 678 2.494059 CAGCTTATCGGGTAATGGGTG 58.506 52.381 0.00 0.00 0.00 4.61
631 690 3.002759 GTCAAGAATTCGGGCAGCTTATC 59.997 47.826 0.00 0.00 0.00 1.75
642 701 1.999051 CGGGCTCGTCAAGAATTCG 59.001 57.895 0.00 0.00 0.00 3.34
667 726 2.299582 TCCAGCCAACAAACATGATTGG 59.700 45.455 18.61 16.26 44.84 3.16
675 734 3.056607 AGCAACATATCCAGCCAACAAAC 60.057 43.478 0.00 0.00 0.00 2.93
745 804 0.244450 ACCAACATGGATTGCAAGCG 59.756 50.000 8.86 0.00 40.96 4.68
746 805 3.806625 ATACCAACATGGATTGCAAGC 57.193 42.857 6.04 6.04 40.96 4.01
747 806 5.010314 AGCATATACCAACATGGATTGCAAG 59.990 40.000 4.94 0.00 40.96 4.01
748 807 4.894705 AGCATATACCAACATGGATTGCAA 59.105 37.500 0.00 0.00 40.96 4.08
749 808 4.278919 CAGCATATACCAACATGGATTGCA 59.721 41.667 2.85 0.00 40.96 4.08
750 809 4.801891 CAGCATATACCAACATGGATTGC 58.198 43.478 2.85 6.48 40.96 3.56
751 810 4.521639 AGCAGCATATACCAACATGGATTG 59.478 41.667 2.85 0.00 40.96 2.67
752 811 4.521639 CAGCAGCATATACCAACATGGATT 59.478 41.667 2.85 0.00 40.96 3.01
753 812 4.077108 CAGCAGCATATACCAACATGGAT 58.923 43.478 2.85 0.00 40.96 3.41
754 813 3.479489 CAGCAGCATATACCAACATGGA 58.521 45.455 2.85 0.00 40.96 3.41
755 814 2.030540 GCAGCAGCATATACCAACATGG 60.031 50.000 0.00 0.00 41.68 3.66
756 815 2.882761 AGCAGCAGCATATACCAACATG 59.117 45.455 3.17 0.00 45.49 3.21
757 816 2.882761 CAGCAGCAGCATATACCAACAT 59.117 45.455 3.17 0.00 45.49 2.71
758 817 2.291365 CAGCAGCAGCATATACCAACA 58.709 47.619 3.17 0.00 45.49 3.33
759 818 2.289002 GACAGCAGCAGCATATACCAAC 59.711 50.000 3.17 0.00 45.49 3.77
760 819 2.564771 GACAGCAGCAGCATATACCAA 58.435 47.619 3.17 0.00 45.49 3.67
829 930 6.730175 AGACTAGCTATCACTGTTGTATTCG 58.270 40.000 0.00 0.00 0.00 3.34
942 1043 8.493787 TGGGTGGTGGTTTATAATTAAAAACT 57.506 30.769 0.00 0.00 36.17 2.66
943 1044 8.586744 TCTGGGTGGTGGTTTATAATTAAAAAC 58.413 33.333 0.00 0.00 35.34 2.43
1142 1256 2.948979 CCACCTACACAAAGAGCAAACA 59.051 45.455 0.00 0.00 0.00 2.83
1148 1262 1.000955 AGTCGCCACCTACACAAAGAG 59.999 52.381 0.00 0.00 0.00 2.85
1166 1286 1.216990 CCCTTCTTGCTCCCCATAGT 58.783 55.000 0.00 0.00 0.00 2.12
1254 1377 1.290324 GCTGTTCTCACGCTCCTCA 59.710 57.895 0.00 0.00 0.00 3.86
1325 1449 4.387437 GGTTTTAGGGGATGAATGGATGGA 60.387 45.833 0.00 0.00 0.00 3.41
1399 1523 5.441718 AAGGTGAGATTGGAAGATTAGCA 57.558 39.130 0.00 0.00 0.00 3.49
1502 1626 0.948678 TTAACACTCGCAAAGCACCC 59.051 50.000 0.00 0.00 0.00 4.61
1503 1627 2.989422 ATTAACACTCGCAAAGCACC 57.011 45.000 0.00 0.00 0.00 5.01
1716 2004 2.233431 CGGGAGCCAAATTGAATTTCCA 59.767 45.455 0.00 0.00 0.00 3.53
1919 2229 4.186159 GCAATTTTCATGTGGAATGGAGG 58.814 43.478 0.00 0.00 34.91 4.30
1924 2234 4.004982 GCTTGGCAATTTTCATGTGGAAT 58.995 39.130 0.00 0.00 34.91 3.01
2022 2333 2.982744 GAGCAGCGTTTTGGCTCCC 61.983 63.158 0.00 0.00 46.35 4.30
2082 2393 5.997746 CAGAGATGGAAAAACCTAACTCACA 59.002 40.000 0.00 0.00 39.86 3.58
2169 2480 8.807581 GTTACAAAATAATATCTGCCAAACAGC 58.192 33.333 0.00 0.00 46.76 4.40
2272 2583 8.364894 GGTTTTACCAAGGACACTGATAAAAAT 58.635 33.333 0.00 0.00 38.42 1.82
2364 2680 2.798680 CGCGTAGTTGAGAGCTACAAT 58.201 47.619 0.00 2.74 38.87 2.71
2402 2719 9.177608 CTCCAACACATCAAAGGAGATTATAAA 57.822 33.333 0.00 0.00 46.89 1.40
2616 2936 2.005451 CTGTGGCACTATGTCTGCTTC 58.995 52.381 19.83 0.00 34.84 3.86
2794 3114 8.339720 ACTGATAAACATATGGGGTAAGGTAA 57.660 34.615 7.80 0.00 0.00 2.85
2795 3115 7.792736 AGACTGATAAACATATGGGGTAAGGTA 59.207 37.037 7.80 0.00 0.00 3.08
2812 3132 7.791029 TGAGCACCACAATAATAGACTGATAA 58.209 34.615 0.00 0.00 0.00 1.75
3226 3560 7.202038 CCAGACATTCTAAATCTCCTGATGGTA 60.202 40.741 0.00 0.00 32.44 3.25
3230 3564 7.291885 TCATCCAGACATTCTAAATCTCCTGAT 59.708 37.037 0.00 0.00 33.70 2.90
3955 4407 7.233632 TGAAGCTGAATAAGGGCACATAATAT 58.766 34.615 0.00 0.00 0.00 1.28
4033 4485 0.536006 AGGAGTGCAGAGTTTGTGGC 60.536 55.000 0.00 0.00 0.00 5.01
4127 4579 7.149202 AGATAAGGGCAATACAAAGGATGTA 57.851 36.000 0.00 0.00 43.63 2.29
4237 4692 2.778187 GCAGGAAGCTAGGTACTACG 57.222 55.000 0.00 0.00 41.75 3.51
4326 4784 4.120331 GCGTCCTGCATGTTGCCC 62.120 66.667 0.00 0.00 44.23 5.36
4643 5102 2.584835 ACTCTGGCCTTTGCACATAA 57.415 45.000 3.32 0.00 40.13 1.90
4861 5341 6.095580 TGTGGTTAAGTTGTTAACAGCATGAA 59.904 34.615 22.32 11.19 46.87 2.57
4879 5359 1.079681 GGATGACCGCGTGTGGTTA 60.080 57.895 4.92 2.77 44.01 2.85
4894 5374 3.630769 CAGCATGTCAGCAAACATAGGAT 59.369 43.478 3.93 0.00 37.78 3.24
5032 5524 5.763876 AAGTTGTTAGTAAGCTCCAGGAT 57.236 39.130 0.00 0.00 0.00 3.24
5056 5548 7.503230 TCACCACAATGTGAAGCATATAATCAT 59.497 33.333 15.91 0.00 42.06 2.45
5057 5549 6.827762 TCACCACAATGTGAAGCATATAATCA 59.172 34.615 15.91 0.00 42.06 2.57
5237 5733 4.363138 CGCATAGAACTTGTGAGCTATCA 58.637 43.478 0.00 0.00 0.00 2.15
5246 5742 5.057149 GTGGAATATCCGCATAGAACTTGT 58.943 41.667 5.11 0.00 46.03 3.16
5275 5865 6.547141 AGTGTTTGATGTCCAATTGAAGAGAA 59.453 34.615 7.12 0.00 34.23 2.87
5308 5898 4.357918 AACAAGCTCCTGTACAACTGAT 57.642 40.909 0.00 0.00 0.00 2.90
5350 5966 6.925934 TCCTGTATAAACCTAACTAGCCCTA 58.074 40.000 0.00 0.00 0.00 3.53
5385 6001 2.437413 GGCCCCTCTTACTGTTCTTTG 58.563 52.381 0.00 0.00 0.00 2.77
5386 6002 1.003233 CGGCCCCTCTTACTGTTCTTT 59.997 52.381 0.00 0.00 0.00 2.52
5389 6005 1.221021 CCGGCCCCTCTTACTGTTC 59.779 63.158 0.00 0.00 0.00 3.18
5409 6025 4.012895 CACGTGGCACCAGAACGC 62.013 66.667 12.86 0.00 40.90 4.84
5410 6026 4.012895 GCACGTGGCACCAGAACG 62.013 66.667 18.88 1.19 43.97 3.95
5429 6045 2.236223 ATCAGGTGCAGGTGAGCTCG 62.236 60.000 9.64 0.00 34.99 5.03
5430 6046 0.826715 TATCAGGTGCAGGTGAGCTC 59.173 55.000 6.82 6.82 34.99 4.09
5452 6068 0.249911 ACTGCACGAACCCTGTCTTC 60.250 55.000 0.00 0.00 0.00 2.87
5469 6129 1.406539 CACTGCACTTGCTTTTCCACT 59.593 47.619 2.33 0.00 42.66 4.00
5478 6138 1.135689 CCGTATTTCCACTGCACTTGC 60.136 52.381 0.00 0.00 42.50 4.01
5479 6139 1.468520 CCCGTATTTCCACTGCACTTG 59.531 52.381 0.00 0.00 0.00 3.16
5480 6140 1.613255 CCCCGTATTTCCACTGCACTT 60.613 52.381 0.00 0.00 0.00 3.16
5482 6142 1.654023 GCCCCGTATTTCCACTGCAC 61.654 60.000 0.00 0.00 0.00 4.57
5483 6143 1.377987 GCCCCGTATTTCCACTGCA 60.378 57.895 0.00 0.00 0.00 4.41
5484 6144 2.469516 CGCCCCGTATTTCCACTGC 61.470 63.158 0.00 0.00 0.00 4.40
5485 6145 0.176219 TACGCCCCGTATTTCCACTG 59.824 55.000 0.00 0.00 41.54 3.66
5486 6146 2.594342 TACGCCCCGTATTTCCACT 58.406 52.632 0.00 0.00 41.54 4.00
5494 6154 0.968405 GGGTTCATATACGCCCCGTA 59.032 55.000 0.00 0.00 46.28 4.02
5495 6155 0.761702 AGGGTTCATATACGCCCCGT 60.762 55.000 0.00 0.00 41.99 5.28
5496 6156 1.067354 GTAGGGTTCATATACGCCCCG 60.067 57.143 0.00 0.00 41.99 5.73
5497 6157 1.067354 CGTAGGGTTCATATACGCCCC 60.067 57.143 0.00 0.00 41.99 5.80
5498 6158 1.888512 TCGTAGGGTTCATATACGCCC 59.111 52.381 0.00 0.00 41.47 6.13
5499 6159 3.863142 ATCGTAGGGTTCATATACGCC 57.137 47.619 0.00 0.00 41.47 5.68
5500 6160 4.857588 CAGAATCGTAGGGTTCATATACGC 59.142 45.833 10.83 0.00 41.47 4.42
5501 6161 6.250344 TCAGAATCGTAGGGTTCATATACG 57.750 41.667 10.83 0.00 42.70 3.06
5502 6162 7.971168 CAGATCAGAATCGTAGGGTTCATATAC 59.029 40.741 10.83 0.00 36.97 1.47
5503 6163 7.670140 ACAGATCAGAATCGTAGGGTTCATATA 59.330 37.037 10.83 0.00 36.97 0.86
5504 6164 6.495181 ACAGATCAGAATCGTAGGGTTCATAT 59.505 38.462 10.83 3.69 36.97 1.78
5505 6165 5.833667 ACAGATCAGAATCGTAGGGTTCATA 59.166 40.000 10.83 0.00 36.97 2.15
5506 6166 4.651503 ACAGATCAGAATCGTAGGGTTCAT 59.348 41.667 10.83 0.00 36.97 2.57
5507 6167 4.023980 ACAGATCAGAATCGTAGGGTTCA 58.976 43.478 10.83 0.00 36.97 3.18
5508 6168 4.363999 CACAGATCAGAATCGTAGGGTTC 58.636 47.826 0.00 0.00 36.97 3.62
5509 6169 3.133003 CCACAGATCAGAATCGTAGGGTT 59.867 47.826 0.00 0.00 36.97 4.11
5510 6170 2.695666 CCACAGATCAGAATCGTAGGGT 59.304 50.000 0.00 0.00 36.97 4.34
5511 6171 2.546795 GCCACAGATCAGAATCGTAGGG 60.547 54.545 0.00 0.00 36.97 3.53
5512 6172 2.363680 AGCCACAGATCAGAATCGTAGG 59.636 50.000 0.00 0.00 36.97 3.18
5545 6205 7.695820 TCTTTTGTCTCCGTTTCGATTAAAAA 58.304 30.769 0.00 0.00 0.00 1.94
5548 6208 7.429636 AATCTTTTGTCTCCGTTTCGATTAA 57.570 32.000 0.00 0.00 0.00 1.40
5550 6210 5.941948 AATCTTTTGTCTCCGTTTCGATT 57.058 34.783 0.00 0.00 0.00 3.34
5551 6211 5.238650 ACAAATCTTTTGTCTCCGTTTCGAT 59.761 36.000 0.00 0.00 0.00 3.59
5552 6212 4.573201 ACAAATCTTTTGTCTCCGTTTCGA 59.427 37.500 0.00 0.00 0.00 3.71
5553 6213 4.844267 ACAAATCTTTTGTCTCCGTTTCG 58.156 39.130 0.00 0.00 0.00 3.46
5593 6253 9.708092 GGTCTTGTAACACTCTAAAACTCTATT 57.292 33.333 0.00 0.00 0.00 1.73
5594 6254 8.312564 GGGTCTTGTAACACTCTAAAACTCTAT 58.687 37.037 0.00 0.00 0.00 1.98
5595 6255 7.256083 GGGGTCTTGTAACACTCTAAAACTCTA 60.256 40.741 0.00 0.00 0.00 2.43
5596 6256 6.464039 GGGGTCTTGTAACACTCTAAAACTCT 60.464 42.308 0.00 0.00 0.00 3.24
5597 6257 5.699915 GGGGTCTTGTAACACTCTAAAACTC 59.300 44.000 0.00 0.00 0.00 3.01
5598 6258 5.131475 TGGGGTCTTGTAACACTCTAAAACT 59.869 40.000 0.00 0.00 0.00 2.66
5599 6259 5.237996 GTGGGGTCTTGTAACACTCTAAAAC 59.762 44.000 0.00 0.00 0.00 2.43
5600 6260 5.131475 AGTGGGGTCTTGTAACACTCTAAAA 59.869 40.000 0.00 0.00 37.86 1.52
5601 6261 4.657039 AGTGGGGTCTTGTAACACTCTAAA 59.343 41.667 0.00 0.00 37.86 1.85
5602 6262 4.039973 CAGTGGGGTCTTGTAACACTCTAA 59.960 45.833 0.00 0.00 40.14 2.10
5603 6263 3.576982 CAGTGGGGTCTTGTAACACTCTA 59.423 47.826 0.00 0.00 40.14 2.43
5604 6264 2.368875 CAGTGGGGTCTTGTAACACTCT 59.631 50.000 0.00 0.00 40.14 3.24
5605 6265 2.367567 TCAGTGGGGTCTTGTAACACTC 59.632 50.000 0.00 0.00 40.14 3.51
5606 6266 2.404559 TCAGTGGGGTCTTGTAACACT 58.595 47.619 0.00 0.00 42.62 3.55
5607 6267 2.922740 TCAGTGGGGTCTTGTAACAC 57.077 50.000 0.00 0.00 0.00 3.32
5608 6268 3.201266 AGTTTCAGTGGGGTCTTGTAACA 59.799 43.478 0.00 0.00 0.00 2.41
5609 6269 3.816994 AGTTTCAGTGGGGTCTTGTAAC 58.183 45.455 0.00 0.00 0.00 2.50
5610 6270 4.513406 AAGTTTCAGTGGGGTCTTGTAA 57.487 40.909 0.00 0.00 0.00 2.41
5611 6271 4.513406 AAAGTTTCAGTGGGGTCTTGTA 57.487 40.909 0.00 0.00 0.00 2.41
5612 6272 3.382083 AAAGTTTCAGTGGGGTCTTGT 57.618 42.857 0.00 0.00 0.00 3.16
5613 6273 3.447229 ACAAAAGTTTCAGTGGGGTCTTG 59.553 43.478 0.00 0.00 0.00 3.02
5614 6274 3.708451 ACAAAAGTTTCAGTGGGGTCTT 58.292 40.909 0.00 0.00 0.00 3.01
5615 6275 3.382083 ACAAAAGTTTCAGTGGGGTCT 57.618 42.857 0.00 0.00 0.00 3.85
5616 6276 3.445805 TGAACAAAAGTTTCAGTGGGGTC 59.554 43.478 0.00 0.00 0.00 4.46
5617 6277 3.436243 TGAACAAAAGTTTCAGTGGGGT 58.564 40.909 0.00 0.00 0.00 4.95
5618 6278 4.464069 TTGAACAAAAGTTTCAGTGGGG 57.536 40.909 0.00 0.00 34.50 4.96
5619 6279 6.256321 CAGATTTGAACAAAAGTTTCAGTGGG 59.744 38.462 4.12 0.00 34.50 4.61
5620 6280 7.035004 TCAGATTTGAACAAAAGTTTCAGTGG 58.965 34.615 4.12 0.00 34.50 4.00
5621 6281 7.253883 GCTCAGATTTGAACAAAAGTTTCAGTG 60.254 37.037 4.12 0.00 34.50 3.66
5622 6282 6.753744 GCTCAGATTTGAACAAAAGTTTCAGT 59.246 34.615 4.12 0.00 34.50 3.41
5623 6283 6.075205 CGCTCAGATTTGAACAAAAGTTTCAG 60.075 38.462 4.12 0.00 34.50 3.02
5624 6284 5.743398 CGCTCAGATTTGAACAAAAGTTTCA 59.257 36.000 4.12 0.00 33.56 2.69
5625 6285 5.743872 ACGCTCAGATTTGAACAAAAGTTTC 59.256 36.000 4.12 0.00 33.56 2.78
5626 6286 5.650543 ACGCTCAGATTTGAACAAAAGTTT 58.349 33.333 4.12 0.00 33.56 2.66
5627 6287 5.248870 ACGCTCAGATTTGAACAAAAGTT 57.751 34.783 4.12 0.00 33.56 2.66
5628 6288 4.900635 ACGCTCAGATTTGAACAAAAGT 57.099 36.364 4.12 0.00 33.56 2.66
5629 6289 5.747565 TGTACGCTCAGATTTGAACAAAAG 58.252 37.500 4.12 0.00 33.56 2.27
5630 6290 5.743026 TGTACGCTCAGATTTGAACAAAA 57.257 34.783 4.12 0.00 33.56 2.44
5631 6291 5.700832 AGATGTACGCTCAGATTTGAACAAA 59.299 36.000 2.48 2.48 31.69 2.83
5632 6292 5.237815 AGATGTACGCTCAGATTTGAACAA 58.762 37.500 0.00 0.00 31.69 2.83
5633 6293 4.820897 AGATGTACGCTCAGATTTGAACA 58.179 39.130 0.00 0.00 31.69 3.18
5634 6294 5.105752 AGAGATGTACGCTCAGATTTGAAC 58.894 41.667 15.36 0.00 34.85 3.18
5635 6295 5.126222 AGAGAGATGTACGCTCAGATTTGAA 59.874 40.000 15.36 0.00 45.53 2.69
5636 6296 4.642437 AGAGAGATGTACGCTCAGATTTGA 59.358 41.667 15.36 0.00 45.53 2.69
5637 6297 4.930963 AGAGAGATGTACGCTCAGATTTG 58.069 43.478 15.36 0.00 45.53 2.32
5638 6298 4.887071 AGAGAGAGATGTACGCTCAGATTT 59.113 41.667 15.36 0.00 45.53 2.17
5678 6338 2.088950 ATTAGTACACGCCGTTGCTT 57.911 45.000 0.00 0.00 34.43 3.91
5756 6416 3.186817 CACGCACTTATAACACGGGAAAA 59.813 43.478 0.00 0.00 0.00 2.29
5764 6424 4.154556 GGTAAAAGGCACGCACTTATAACA 59.845 41.667 0.00 0.00 0.00 2.41
5791 6451 5.183713 CCCTCAGAAGCATATGAACAAACAA 59.816 40.000 6.97 0.00 0.00 2.83
5792 6452 4.701651 CCCTCAGAAGCATATGAACAAACA 59.298 41.667 6.97 0.00 0.00 2.83
5793 6453 4.439289 GCCCTCAGAAGCATATGAACAAAC 60.439 45.833 6.97 0.00 0.00 2.93
5794 6454 3.696051 GCCCTCAGAAGCATATGAACAAA 59.304 43.478 6.97 0.00 0.00 2.83
5909 6569 1.893137 TCGTGACTACTGCTCATGGTT 59.107 47.619 0.00 0.00 0.00 3.67
5944 6614 6.437793 CCATTAGATTTACCCGTAGATCCTCT 59.562 42.308 2.63 0.00 29.70 3.69
5961 6631 2.779430 TCTCACATGTGGCCCATTAGAT 59.221 45.455 25.16 0.00 0.00 1.98
5970 6640 1.432251 GCAGCATCTCACATGTGGC 59.568 57.895 25.16 19.46 0.00 5.01
5978 6648 0.538584 AGATTGTCCGCAGCATCTCA 59.461 50.000 0.00 0.00 0.00 3.27
5981 6651 0.302890 CGAAGATTGTCCGCAGCATC 59.697 55.000 0.00 0.00 0.00 3.91
5983 6653 3.874873 CGAAGATTGTCCGCAGCA 58.125 55.556 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.