Multiple sequence alignment - TraesCS2D01G547100

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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 TraesCS2D01G547100 chr2D 100.000 3902 0 0 1 3902 623500009 623496108 0.000000e+00 7206.0
1 TraesCS2D01G547100 chr2D 83.032 554 83 9 2125 2677 616626639 616626096 3.500000e-135 492.0
2 TraesCS2D01G547100 chr2D 82.332 549 93 4 2125 2671 623791241 623791787 1.270000e-129 473.0
3 TraesCS2D01G547100 chr2D 79.921 254 36 8 1088 1332 623498190 623497943 5.180000e-39 172.0
4 TraesCS2D01G547100 chr2D 79.921 254 36 8 1820 2067 623498922 623498678 5.180000e-39 172.0
5 TraesCS2D01G547100 chr2D 89.916 119 12 0 2782 2900 623791864 623791982 1.880000e-33 154.0
6 TraesCS2D01G547100 chr2D 84.397 141 19 2 1894 2034 623790827 623790964 6.800000e-28 135.0
7 TraesCS2D01G547100 chr2D 89.655 87 9 0 2817 2903 616626002 616625916 1.150000e-20 111.0
8 TraesCS2D01G547100 chr2A 93.657 2822 153 14 1097 3902 754710706 754707895 0.000000e+00 4196.0
9 TraesCS2D01G547100 chr2A 85.149 909 121 10 964 1863 754712031 754711128 0.000000e+00 918.0
10 TraesCS2D01G547100 chr2A 93.596 406 25 1 1094 1499 754711530 754711126 4.310000e-169 604.0
11 TraesCS2D01G547100 chr2A 80.987 689 110 14 1394 2073 754710775 754710099 9.600000e-146 527.0
12 TraesCS2D01G547100 chr2A 86.815 493 37 10 110 594 754712884 754712412 3.450000e-145 525.0
13 TraesCS2D01G547100 chr2A 82.878 549 90 4 2125 2671 755060902 755061448 1.260000e-134 490.0
14 TraesCS2D01G547100 chr2A 80.128 624 104 15 1097 1707 754710340 754709724 7.690000e-122 448.0
15 TraesCS2D01G547100 chr2A 78.469 627 112 10 1463 2077 754711898 754711283 4.730000e-104 388.0
16 TraesCS2D01G547100 chr2A 79.830 352 48 16 597 938 754712363 754712025 6.520000e-58 235.0
17 TraesCS2D01G547100 chr2A 79.128 321 50 10 1764 2077 754710771 754710461 5.110000e-49 206.0
18 TraesCS2D01G547100 chr2A 79.528 254 40 6 1088 1332 754709983 754709733 1.860000e-38 171.0
19 TraesCS2D01G547100 chr2A 84.722 144 15 3 2767 2903 746840019 746839876 1.890000e-28 137.0
20 TraesCS2D01G547100 chr2A 86.111 108 15 0 1936 2043 746840860 746840753 2.460000e-22 117.0
21 TraesCS2D01G547100 chr2A 86.667 105 14 0 1571 1675 755060663 755060767 2.460000e-22 117.0
22 TraesCS2D01G547100 chr2A 82.759 116 13 2 2784 2895 755061537 755061649 3.210000e-16 97.1
23 TraesCS2D01G547100 chr2B 93.233 1995 122 5 1099 3082 765488556 765486564 0.000000e+00 2924.0
24 TraesCS2D01G547100 chr2B 85.141 996 105 29 1094 2065 765488937 765487961 0.000000e+00 979.0
25 TraesCS2D01G547100 chr2B 82.363 1134 156 30 964 2069 765489438 765488321 0.000000e+00 946.0
26 TraesCS2D01G547100 chr2B 91.648 455 35 3 3128 3580 765486554 765486101 9.200000e-176 627.0
27 TraesCS2D01G547100 chr2B 79.795 782 122 26 2125 2900 765562144 765562895 1.600000e-148 536.0
28 TraesCS2D01G547100 chr2B 83.755 554 88 2 2125 2677 751603745 751603193 1.240000e-144 523.0
29 TraesCS2D01G547100 chr2B 80.259 618 99 14 1099 1703 765488192 765487585 9.950000e-121 444.0
30 TraesCS2D01G547100 chr2B 83.567 499 36 14 111 595 765490276 765489810 3.600000e-115 425.0
31 TraesCS2D01G547100 chr2B 79.620 579 118 0 2096 2674 183211782 183212360 2.170000e-112 416.0
32 TraesCS2D01G547100 chr2B 77.567 633 119 13 1463 2077 765489305 765488678 1.030000e-95 361.0
33 TraesCS2D01G547100 chr2B 79.290 338 52 14 597 923 765489770 765489440 1.830000e-53 220.0
34 TraesCS2D01G547100 chr2B 93.496 123 7 1 3719 3840 765486014 765485892 8.610000e-42 182.0
35 TraesCS2D01G547100 chr2B 82.895 152 17 3 2767 2909 751603144 751602993 1.140000e-25 128.0
36 TraesCS2D01G547100 chr2B 86.139 101 14 0 1574 1674 765561899 765561999 4.120000e-20 110.0
37 TraesCS2D01G547100 chr7D 84.153 549 81 6 2125 2670 534655108 534654563 9.600000e-146 527.0
38 TraesCS2D01G547100 chr7D 87.619 105 13 0 1570 1674 534655369 534655265 5.290000e-24 122.0
39 TraesCS2D01G547100 chr7D 88.636 88 10 0 2816 2903 534654460 534654373 1.480000e-19 108.0
40 TraesCS2D01G547100 chr3D 85.069 288 28 9 3556 3832 609085971 609085688 2.970000e-71 279.0
41 TraesCS2D01G547100 chr3A 83.562 292 29 11 3556 3832 742440604 742440317 5.000000e-64 255.0
42 TraesCS2D01G547100 chr3B 82.313 294 31 12 3556 3832 819789049 819788760 6.520000e-58 235.0
43 TraesCS2D01G547100 chr3B 92.593 54 2 1 3832 3885 819788742 819788691 4.180000e-10 76.8


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 TraesCS2D01G547100 chr2D 623496108 623500009 3901 True 2516.666667 7206 86.614000 1 3902 3 chr2D.!!$R2 3901
1 TraesCS2D01G547100 chr2D 616625916 616626639 723 True 301.500000 492 86.343500 2125 2903 2 chr2D.!!$R1 778
2 TraesCS2D01G547100 chr2D 623790827 623791982 1155 False 254.000000 473 85.548333 1894 2900 3 chr2D.!!$F1 1006
3 TraesCS2D01G547100 chr2A 754707895 754712884 4989 True 821.800000 4196 83.728700 110 3902 10 chr2A.!!$R2 3792
4 TraesCS2D01G547100 chr2A 755060663 755061649 986 False 234.700000 490 84.101333 1571 2895 3 chr2A.!!$F1 1324
5 TraesCS2D01G547100 chr2B 765485892 765490276 4384 True 789.777778 2924 85.173778 111 3840 9 chr2B.!!$R2 3729
6 TraesCS2D01G547100 chr2B 183211782 183212360 578 False 416.000000 416 79.620000 2096 2674 1 chr2B.!!$F1 578
7 TraesCS2D01G547100 chr2B 751602993 751603745 752 True 325.500000 523 83.325000 2125 2909 2 chr2B.!!$R1 784
8 TraesCS2D01G547100 chr2B 765561899 765562895 996 False 323.000000 536 82.967000 1574 2900 2 chr2B.!!$F2 1326
9 TraesCS2D01G547100 chr7D 534654373 534655369 996 True 252.333333 527 86.802667 1570 2903 3 chr7D.!!$R1 1333

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
961 1048 0.110238 CAACGTCGCCATCAAACCAG 60.110 55.0 0.0 0.0 0.00 4.00 F
2316 3817 0.106066 GCCATGACATCATTCCCCCA 60.106 55.0 0.0 0.0 33.61 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2865 4426 0.525761 TGCAGAAATGGTTTAGCGCC 59.474 50.0 2.29 0.00 0.0 6.53 R
3730 5339 0.102844 TGTTTGCAGCAAGCTGAACC 59.897 50.0 25.03 8.84 46.3 3.62 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
22 23 4.637574 TTGCGAAAATATTTTTGGCACG 57.362 36.364 26.77 20.06 38.61 5.34
23 24 2.410053 TGCGAAAATATTTTTGGCACGC 59.590 40.909 25.22 25.22 42.98 5.34
24 25 2.410053 GCGAAAATATTTTTGGCACGCA 59.590 40.909 26.22 0.00 42.39 5.24
25 26 3.120854 GCGAAAATATTTTTGGCACGCAA 60.121 39.130 26.22 0.00 42.39 4.85
26 27 4.951174 GCGAAAATATTTTTGGCACGCAAG 60.951 41.667 26.22 8.58 42.39 4.01
27 28 4.384247 CGAAAATATTTTTGGCACGCAAGA 59.616 37.500 17.33 0.00 43.62 3.02
28 29 5.590104 AAAATATTTTTGGCACGCAAGAC 57.410 34.783 7.64 0.00 43.62 3.01
29 30 3.932545 ATATTTTTGGCACGCAAGACA 57.067 38.095 0.00 0.00 43.62 3.41
30 31 2.818130 ATTTTTGGCACGCAAGACAT 57.182 40.000 0.00 0.00 43.62 3.06
31 32 3.932545 ATTTTTGGCACGCAAGACATA 57.067 38.095 0.00 0.00 43.62 2.29
32 33 3.717400 TTTTTGGCACGCAAGACATAA 57.283 38.095 0.00 0.00 43.62 1.90
33 34 3.932545 TTTTGGCACGCAAGACATAAT 57.067 38.095 0.00 0.00 43.62 1.28
34 35 3.932545 TTTGGCACGCAAGACATAATT 57.067 38.095 0.00 0.00 43.62 1.40
35 36 3.485947 TTGGCACGCAAGACATAATTC 57.514 42.857 0.00 0.00 43.62 2.17
36 37 2.710377 TGGCACGCAAGACATAATTCT 58.290 42.857 0.00 0.00 43.62 2.40
37 38 3.081061 TGGCACGCAAGACATAATTCTT 58.919 40.909 0.00 0.00 43.62 2.52
38 39 3.505680 TGGCACGCAAGACATAATTCTTT 59.494 39.130 0.00 0.00 43.62 2.52
39 40 4.022416 TGGCACGCAAGACATAATTCTTTT 60.022 37.500 0.00 0.00 43.62 2.27
40 41 4.923281 GGCACGCAAGACATAATTCTTTTT 59.077 37.500 0.00 0.00 43.62 1.94
66 67 9.899226 TTTTAATTGGTGTTTTTGTTTTTGAGG 57.101 25.926 0.00 0.00 0.00 3.86
67 68 8.848474 TTAATTGGTGTTTTTGTTTTTGAGGA 57.152 26.923 0.00 0.00 0.00 3.71
68 69 7.751768 AATTGGTGTTTTTGTTTTTGAGGAA 57.248 28.000 0.00 0.00 0.00 3.36
69 70 6.546972 TTGGTGTTTTTGTTTTTGAGGAAC 57.453 33.333 0.00 0.00 0.00 3.62
70 71 5.611374 TGGTGTTTTTGTTTTTGAGGAACA 58.389 33.333 0.00 0.00 35.36 3.18
71 72 6.055588 TGGTGTTTTTGTTTTTGAGGAACAA 58.944 32.000 0.00 0.00 43.16 2.83
72 73 6.712547 TGGTGTTTTTGTTTTTGAGGAACAAT 59.287 30.769 3.59 0.00 43.96 2.71
73 74 7.229506 TGGTGTTTTTGTTTTTGAGGAACAATT 59.770 29.630 3.59 0.00 43.96 2.32
74 75 7.536964 GGTGTTTTTGTTTTTGAGGAACAATTG 59.463 33.333 3.24 3.24 43.96 2.32
75 76 7.536964 GTGTTTTTGTTTTTGAGGAACAATTGG 59.463 33.333 10.83 0.00 43.96 3.16
76 77 7.229506 TGTTTTTGTTTTTGAGGAACAATTGGT 59.770 29.630 10.83 1.89 43.96 3.67
77 78 6.734104 TTTGTTTTTGAGGAACAATTGGTG 57.266 33.333 10.83 0.00 43.96 4.17
78 79 4.764172 TGTTTTTGAGGAACAATTGGTGG 58.236 39.130 10.83 0.00 38.36 4.61
79 80 4.223923 TGTTTTTGAGGAACAATTGGTGGT 59.776 37.500 10.83 0.00 38.36 4.16
80 81 4.399004 TTTTGAGGAACAATTGGTGGTG 57.601 40.909 10.83 0.00 38.36 4.17
81 82 3.304911 TTGAGGAACAATTGGTGGTGA 57.695 42.857 10.83 0.00 33.18 4.02
82 83 3.304911 TGAGGAACAATTGGTGGTGAA 57.695 42.857 10.83 0.00 0.00 3.18
83 84 3.843422 TGAGGAACAATTGGTGGTGAAT 58.157 40.909 10.83 0.00 0.00 2.57
84 85 3.826157 TGAGGAACAATTGGTGGTGAATC 59.174 43.478 10.83 0.00 0.00 2.52
85 86 4.082125 GAGGAACAATTGGTGGTGAATCT 58.918 43.478 10.83 0.00 0.00 2.40
86 87 4.482990 AGGAACAATTGGTGGTGAATCTT 58.517 39.130 10.83 0.00 0.00 2.40
87 88 4.901250 AGGAACAATTGGTGGTGAATCTTT 59.099 37.500 10.83 0.00 0.00 2.52
88 89 5.011023 AGGAACAATTGGTGGTGAATCTTTC 59.989 40.000 10.83 0.00 0.00 2.62
89 90 5.011023 GGAACAATTGGTGGTGAATCTTTCT 59.989 40.000 10.83 0.00 0.00 2.52
90 91 5.712152 ACAATTGGTGGTGAATCTTTCTC 57.288 39.130 10.83 0.00 0.00 2.87
91 92 4.216257 ACAATTGGTGGTGAATCTTTCTCG 59.784 41.667 10.83 0.00 0.00 4.04
92 93 2.472695 TGGTGGTGAATCTTTCTCGG 57.527 50.000 0.00 0.00 0.00 4.63
93 94 1.087501 GGTGGTGAATCTTTCTCGGC 58.912 55.000 0.00 0.00 0.00 5.54
94 95 1.339151 GGTGGTGAATCTTTCTCGGCT 60.339 52.381 0.00 0.00 0.00 5.52
95 96 2.003301 GTGGTGAATCTTTCTCGGCTC 58.997 52.381 0.00 0.00 0.00 4.70
96 97 1.902508 TGGTGAATCTTTCTCGGCTCT 59.097 47.619 0.00 0.00 0.00 4.09
97 98 2.303022 TGGTGAATCTTTCTCGGCTCTT 59.697 45.455 0.00 0.00 0.00 2.85
98 99 3.244561 TGGTGAATCTTTCTCGGCTCTTT 60.245 43.478 0.00 0.00 0.00 2.52
99 100 4.020573 TGGTGAATCTTTCTCGGCTCTTTA 60.021 41.667 0.00 0.00 0.00 1.85
100 101 4.330347 GGTGAATCTTTCTCGGCTCTTTAC 59.670 45.833 0.00 0.00 0.00 2.01
101 102 4.330347 GTGAATCTTTCTCGGCTCTTTACC 59.670 45.833 0.00 0.00 0.00 2.85
102 103 3.545366 ATCTTTCTCGGCTCTTTACCC 57.455 47.619 0.00 0.00 0.00 3.69
103 104 1.553704 TCTTTCTCGGCTCTTTACCCC 59.446 52.381 0.00 0.00 0.00 4.95
104 105 1.555533 CTTTCTCGGCTCTTTACCCCT 59.444 52.381 0.00 0.00 0.00 4.79
105 106 0.902531 TTCTCGGCTCTTTACCCCTG 59.097 55.000 0.00 0.00 0.00 4.45
106 107 0.252103 TCTCGGCTCTTTACCCCTGT 60.252 55.000 0.00 0.00 0.00 4.00
107 108 1.006281 TCTCGGCTCTTTACCCCTGTA 59.994 52.381 0.00 0.00 0.00 2.74
108 109 2.040178 CTCGGCTCTTTACCCCTGTAT 58.960 52.381 0.00 0.00 0.00 2.29
129 130 1.022451 TGTATGTTTCGGCCCGAAGC 61.022 55.000 23.70 23.70 46.43 3.86
214 216 4.446413 CCTACCCACGCGTCCCAC 62.446 72.222 9.86 0.00 0.00 4.61
215 217 3.379445 CTACCCACGCGTCCCACT 61.379 66.667 9.86 0.00 0.00 4.00
216 218 3.352338 CTACCCACGCGTCCCACTC 62.352 68.421 9.86 0.00 0.00 3.51
271 280 4.880537 CGTCCCGCTAGCTGGCTG 62.881 72.222 20.56 13.63 0.00 4.85
308 317 3.861797 CGCCATTCCCCTACCGCT 61.862 66.667 0.00 0.00 0.00 5.52
309 318 2.595655 GCCATTCCCCTACCGCTT 59.404 61.111 0.00 0.00 0.00 4.68
310 319 1.526225 GCCATTCCCCTACCGCTTC 60.526 63.158 0.00 0.00 0.00 3.86
311 320 1.148498 CCATTCCCCTACCGCTTCC 59.852 63.158 0.00 0.00 0.00 3.46
312 321 1.632018 CCATTCCCCTACCGCTTCCA 61.632 60.000 0.00 0.00 0.00 3.53
347 356 2.608988 CCAGCCTCACCCCTCTGT 60.609 66.667 0.00 0.00 0.00 3.41
380 396 4.193334 CGATCTCGCTCCGGTGCA 62.193 66.667 26.64 13.55 0.00 4.57
424 446 1.025812 CCTGCTACTCCACTCGGTAG 58.974 60.000 0.00 0.00 38.60 3.18
454 476 3.486542 GGCTGATGAAATTGCTTCGAGAC 60.487 47.826 0.00 0.00 36.78 3.36
487 509 2.037136 CAGCTAGTGGTGGTGCTGC 61.037 63.158 0.00 0.00 44.72 5.25
500 522 2.045926 GCTGCTGTAGGTGGTGGG 60.046 66.667 0.00 0.00 0.00 4.61
504 526 2.580601 GCTGTAGGTGGTGGGTCGT 61.581 63.158 0.00 0.00 0.00 4.34
511 533 0.391263 GGTGGTGGGTCGTTCTGATC 60.391 60.000 0.00 0.00 0.00 2.92
537 559 2.124403 GGTGCTGATCCAGGGCAG 60.124 66.667 6.01 6.01 36.62 4.85
546 569 4.748144 CCAGGGCAGCTTGGGACC 62.748 72.222 8.22 0.00 0.00 4.46
633 709 4.731961 GCATAGTGCATTGAATCTCGTTTG 59.268 41.667 0.00 0.00 44.26 2.93
634 710 5.447683 GCATAGTGCATTGAATCTCGTTTGA 60.448 40.000 0.00 0.00 44.26 2.69
637 713 4.516698 AGTGCATTGAATCTCGTTTGAACT 59.483 37.500 0.00 0.00 0.00 3.01
666 742 6.735678 TGAACTGAAATTATGTGTATGCGT 57.264 33.333 0.00 0.00 0.00 5.24
678 756 3.615056 TGTGTATGCGTTGGATTTACTCG 59.385 43.478 0.00 0.00 0.00 4.18
692 770 5.244178 GGATTTACTCGGATCTACACATCCT 59.756 44.000 0.00 0.00 40.45 3.24
693 771 6.433404 GGATTTACTCGGATCTACACATCCTA 59.567 42.308 0.00 0.00 40.45 2.94
697 775 9.529823 TTTACTCGGATCTACACATCCTATTAT 57.470 33.333 0.00 0.00 40.45 1.28
703 781 7.858382 CGGATCTACACATCCTATTATCGATTC 59.142 40.741 1.71 0.00 40.45 2.52
706 784 8.056407 TCTACACATCCTATTATCGATTCCAG 57.944 38.462 1.71 0.00 0.00 3.86
711 789 8.470002 CACATCCTATTATCGATTCCAGTCATA 58.530 37.037 1.71 0.00 0.00 2.15
712 790 9.206690 ACATCCTATTATCGATTCCAGTCATAT 57.793 33.333 1.71 0.00 0.00 1.78
740 822 7.487822 TTGTAGAACAGAAGATGGAGAGATT 57.512 36.000 0.00 0.00 0.00 2.40
743 825 5.743117 AGAACAGAAGATGGAGAGATTTGG 58.257 41.667 0.00 0.00 0.00 3.28
745 827 6.441924 AGAACAGAAGATGGAGAGATTTGGTA 59.558 38.462 0.00 0.00 0.00 3.25
749 831 6.098124 CAGAAGATGGAGAGATTTGGTACTCT 59.902 42.308 0.00 0.00 44.68 3.24
762 844 8.552296 AGATTTGGTACTCTTTTGTATCTCCAT 58.448 33.333 0.00 0.00 0.00 3.41
766 848 7.782049 TGGTACTCTTTTGTATCTCCATACTG 58.218 38.462 0.00 0.00 36.55 2.74
774 856 9.965824 CTTTTGTATCTCCATACTGTTGTTTTT 57.034 29.630 0.00 0.00 36.55 1.94
790 872 1.543607 TTTTTCATCTGCCGCATGGA 58.456 45.000 0.00 0.00 37.49 3.41
791 873 1.766494 TTTTCATCTGCCGCATGGAT 58.234 45.000 0.00 0.00 37.49 3.41
792 874 1.311859 TTTCATCTGCCGCATGGATC 58.688 50.000 0.00 0.00 37.49 3.36
793 875 0.471191 TTCATCTGCCGCATGGATCT 59.529 50.000 0.00 0.00 37.49 2.75
795 877 1.001293 TCATCTGCCGCATGGATCTAC 59.999 52.381 0.00 0.00 37.49 2.59
796 878 1.051008 ATCTGCCGCATGGATCTACA 58.949 50.000 0.00 0.00 37.49 2.74
808 893 7.073883 CGCATGGATCTACACATCTATTTTTG 58.926 38.462 0.00 0.00 0.00 2.44
821 906 7.489113 CACATCTATTTTTGTGGATTGTTAGCC 59.511 37.037 0.00 0.00 39.61 3.93
822 907 7.178274 ACATCTATTTTTGTGGATTGTTAGCCA 59.822 33.333 0.00 0.00 37.54 4.75
824 909 7.546358 TCTATTTTTGTGGATTGTTAGCCATG 58.454 34.615 0.00 0.00 42.82 3.66
825 910 5.798125 TTTTTGTGGATTGTTAGCCATGA 57.202 34.783 0.00 0.00 42.82 3.07
874 960 3.685214 CTTCCGTCCTGACTCCGCG 62.685 68.421 0.00 0.00 0.00 6.46
924 1011 1.312815 GCTTCTGGTTGAGCTGTGTT 58.687 50.000 0.00 0.00 0.00 3.32
927 1014 0.819259 TCTGGTTGAGCTGTGTTGCC 60.819 55.000 0.00 0.00 0.00 4.52
932 1019 0.746204 TTGAGCTGTGTTGCCGTGAA 60.746 50.000 0.00 0.00 0.00 3.18
933 1020 1.159713 TGAGCTGTGTTGCCGTGAAG 61.160 55.000 0.00 0.00 0.00 3.02
934 1021 2.050985 GCTGTGTTGCCGTGAAGC 60.051 61.111 0.00 0.00 0.00 3.86
935 1022 2.546494 GCTGTGTTGCCGTGAAGCT 61.546 57.895 0.00 0.00 0.00 3.74
936 1023 1.280746 CTGTGTTGCCGTGAAGCTG 59.719 57.895 0.00 0.00 0.00 4.24
937 1024 2.050985 GTGTTGCCGTGAAGCTGC 60.051 61.111 0.00 0.00 0.00 5.25
938 1025 3.648982 TGTTGCCGTGAAGCTGCG 61.649 61.111 0.00 0.00 0.00 5.18
954 1041 4.505217 CGCAGCAACGTCGCCATC 62.505 66.667 0.00 0.00 0.00 3.51
955 1042 3.422303 GCAGCAACGTCGCCATCA 61.422 61.111 0.00 0.00 0.00 3.07
956 1043 2.965147 GCAGCAACGTCGCCATCAA 61.965 57.895 0.00 0.00 0.00 2.57
957 1044 1.573932 CAGCAACGTCGCCATCAAA 59.426 52.632 0.00 0.00 0.00 2.69
958 1045 0.725784 CAGCAACGTCGCCATCAAAC 60.726 55.000 0.00 0.00 0.00 2.93
959 1046 1.442017 GCAACGTCGCCATCAAACC 60.442 57.895 0.00 0.00 0.00 3.27
960 1047 1.945522 CAACGTCGCCATCAAACCA 59.054 52.632 0.00 0.00 0.00 3.67
961 1048 0.110238 CAACGTCGCCATCAAACCAG 60.110 55.000 0.00 0.00 0.00 4.00
962 1049 0.534203 AACGTCGCCATCAAACCAGT 60.534 50.000 0.00 0.00 0.00 4.00
987 1074 2.281070 CGCCGAATCATCCCCCAG 60.281 66.667 0.00 0.00 0.00 4.45
1047 1134 1.340889 TCCTGCACTTGGTTCATTTGC 59.659 47.619 0.00 0.00 0.00 3.68
1082 1169 5.163723 ACAGATCACGGAAATGTATTTGCTG 60.164 40.000 7.16 0.00 36.17 4.41
1115 1202 9.636789 ATGTACTCAAAATTACCCCTTTATACC 57.363 33.333 0.00 0.00 0.00 2.73
1299 1768 1.797933 CGACCACGACTTCTGCTCG 60.798 63.158 0.00 0.00 42.66 5.03
1309 1778 0.600557 CTTCTGCTCGAGGTGTGTCT 59.399 55.000 15.58 0.00 0.00 3.41
1330 1799 1.302752 ATGAAGCTGCGCCAGAACA 60.303 52.632 4.18 0.00 32.44 3.18
1332 1801 0.890542 TGAAGCTGCGCCAGAACATT 60.891 50.000 4.18 0.00 32.44 2.71
1334 1803 0.890542 AAGCTGCGCCAGAACATTGA 60.891 50.000 4.18 0.00 32.44 2.57
1336 1805 1.580845 GCTGCGCCAGAACATTGACT 61.581 55.000 4.18 0.00 32.44 3.41
1424 1893 1.001378 AGTTTTACTGCCTTGCGCTTG 60.001 47.619 9.73 0.33 38.78 4.01
1427 1896 0.591170 TTACTGCCTTGCGCTTGTTC 59.409 50.000 9.73 0.00 38.78 3.18
1466 2391 1.262151 CACGGTGTAACGAACCCAAAG 59.738 52.381 0.00 0.00 38.12 2.77
1533 2824 2.380064 TTGCCCCTTTGTTCATCACT 57.620 45.000 0.00 0.00 0.00 3.41
1630 2921 2.712057 GCCATGTGCATGTATAAGGC 57.288 50.000 10.66 10.66 40.77 4.35
1644 2935 0.847373 TAAGGCCCAACTTCACCACA 59.153 50.000 0.00 0.00 32.02 4.17
1785 3076 2.668279 GCGGTGAGTTTTACATGCTTGG 60.668 50.000 4.44 0.00 0.00 3.61
1999 3293 0.874390 GCCATGTGCATGTATACGGG 59.126 55.000 10.76 0.00 40.77 5.28
2072 3535 0.596083 CTAGGCCAGAACATCGCTCG 60.596 60.000 5.01 0.00 0.00 5.03
2074 3537 2.815211 GCCAGAACATCGCTCGCA 60.815 61.111 0.00 0.00 0.00 5.10
2088 3551 1.989165 GCTCGCATCGGATATTCTGAC 59.011 52.381 0.00 0.00 34.08 3.51
2127 3628 7.634671 TGATGATCTGTTCTATTGCAACATT 57.365 32.000 0.00 0.00 33.30 2.71
2154 3655 1.760875 GATGGTGGCGAGGACCCTA 60.761 63.158 0.00 0.00 31.84 3.53
2178 3679 2.029073 AGCGTCAACTCGTGTGGG 59.971 61.111 0.00 0.00 0.00 4.61
2218 3719 1.411246 GTATCACCCAGTACATCGCCA 59.589 52.381 0.00 0.00 0.00 5.69
2241 3742 2.566833 AGCTGGACAACAATGTAGCA 57.433 45.000 7.69 0.00 41.56 3.49
2263 3764 1.002624 GTCGAATGCCCTGACCCAA 60.003 57.895 0.00 0.00 0.00 4.12
2316 3817 0.106066 GCCATGACATCATTCCCCCA 60.106 55.000 0.00 0.00 33.61 4.96
2358 3859 2.036571 CCTGCTGTGCGAATCTGCA 61.037 57.895 0.00 0.00 43.95 4.41
2382 3883 5.387113 TTGGCACCAAGAGGATATATTGT 57.613 39.130 0.00 0.00 38.69 2.71
2851 4412 4.521075 GCTTCTGCTACCGATGCA 57.479 55.556 0.00 0.00 38.81 3.96
2854 4415 0.179137 CTTCTGCTACCGATGCACGA 60.179 55.000 9.75 0.00 45.77 4.35
2933 4494 3.029570 GGGGTGTAGAGACCTACGAATT 58.970 50.000 0.00 0.00 46.37 2.17
2981 4545 8.397906 CAGTTCTGTTTGTGTATATATGGGTTG 58.602 37.037 0.00 0.00 0.00 3.77
3011 4575 3.976169 TCTTTTGGTTATTGCAGTGCAC 58.024 40.909 19.58 9.40 38.71 4.57
3092 4664 1.812571 GGTTGTCGCTCAAATGGATGT 59.187 47.619 0.00 0.00 37.81 3.06
3096 4668 4.406648 TGTCGCTCAAATGGATGTATCT 57.593 40.909 0.00 0.00 0.00 1.98
3108 4680 3.144506 GGATGTATCTGTGGCTTGGATG 58.855 50.000 0.00 0.00 0.00 3.51
3119 4691 1.901833 GGCTTGGATGTTTCAATGGGT 59.098 47.619 0.00 0.00 0.00 4.51
3120 4692 3.096092 GGCTTGGATGTTTCAATGGGTA 58.904 45.455 0.00 0.00 0.00 3.69
3149 4721 7.440556 CCAGAATTGTACAATGTATCAGAGGAG 59.559 40.741 21.46 4.01 0.00 3.69
3191 4763 2.125912 CACTTGAGCGTCGGAGGG 60.126 66.667 0.00 0.00 0.00 4.30
3216 4788 0.693092 ACACCTACCACACCACCACT 60.693 55.000 0.00 0.00 0.00 4.00
3271 4849 7.095910 CACTATAGATGATCGATTCTGGCTTT 58.904 38.462 6.78 0.00 0.00 3.51
3278 4856 0.804989 CGATTCTGGCTTTGTCCCAC 59.195 55.000 0.00 0.00 0.00 4.61
3363 4941 2.878406 GAGTAGGCTGCTGTTTTTGTGA 59.122 45.455 10.69 0.00 0.00 3.58
3429 5008 3.775661 AGTTTTACTTGTGGTGTGTGC 57.224 42.857 0.00 0.00 0.00 4.57
3434 5013 2.826287 TTGTGGTGTGTGCGGGTG 60.826 61.111 0.00 0.00 0.00 4.61
3446 5025 2.383527 GCGGGTGAAGTGCGAAGAG 61.384 63.158 0.00 0.00 0.00 2.85
3623 5232 0.679640 CAAAGTGGCCCGCTATTGGA 60.680 55.000 0.00 0.00 0.00 3.53
3637 5246 4.550831 CGCTATTGGACAAAGACGCATAAG 60.551 45.833 0.00 0.00 0.00 1.73
3655 5264 2.273776 GAGGCCCTTCTCCTTGCC 59.726 66.667 0.00 0.00 44.35 4.52
3662 5271 0.695347 CCTTCTCCTTGCCTGAGGTT 59.305 55.000 0.00 0.00 38.04 3.50
3713 5322 1.328279 GAACAACAAGGTTCAGGGGG 58.672 55.000 0.00 0.00 45.07 5.40
3727 5336 4.097218 GGGGGCCTCTTGAACAAC 57.903 61.111 0.52 0.00 0.00 3.32
3728 5337 1.152830 GGGGGCCTCTTGAACAACA 59.847 57.895 0.52 0.00 0.00 3.33
3729 5338 0.469144 GGGGGCCTCTTGAACAACAA 60.469 55.000 0.52 0.00 36.97 2.83
3752 5388 0.319211 TCAGCTTGCTGCAAACATGC 60.319 50.000 16.74 15.37 45.94 4.06
3808 5444 1.126846 GTGGAGAGACGTTGAAATGCG 59.873 52.381 0.00 0.00 0.00 4.73
3868 5504 2.342910 CAGCCTAAAAACTGCTGCTG 57.657 50.000 4.89 4.89 45.09 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.120854 GCGTGCCAAAAATATTTTCGCAA 60.121 39.130 26.22 14.62 37.20 4.85
2 3 2.410053 GCGTGCCAAAAATATTTTCGCA 59.590 40.909 26.22 24.32 40.63 5.10
3 4 2.410053 TGCGTGCCAAAAATATTTTCGC 59.590 40.909 25.22 25.22 41.17 4.70
4 5 4.384247 TCTTGCGTGCCAAAAATATTTTCG 59.616 37.500 13.68 12.84 31.94 3.46
6 7 5.053145 TGTCTTGCGTGCCAAAAATATTTT 58.947 33.333 7.64 7.64 31.94 1.82
9 10 3.932545 TGTCTTGCGTGCCAAAAATAT 57.067 38.095 0.00 0.00 31.94 1.28
10 11 3.932545 ATGTCTTGCGTGCCAAAAATA 57.067 38.095 0.00 0.00 31.94 1.40
11 12 2.818130 ATGTCTTGCGTGCCAAAAAT 57.182 40.000 0.00 0.00 31.94 1.82
12 13 3.717400 TTATGTCTTGCGTGCCAAAAA 57.283 38.095 0.00 0.00 31.94 1.94
13 14 3.932545 ATTATGTCTTGCGTGCCAAAA 57.067 38.095 0.00 0.00 31.94 2.44
14 15 3.505680 AGAATTATGTCTTGCGTGCCAAA 59.494 39.130 0.00 0.00 31.94 3.28
15 16 3.081061 AGAATTATGTCTTGCGTGCCAA 58.919 40.909 0.00 0.00 0.00 4.52
16 17 2.710377 AGAATTATGTCTTGCGTGCCA 58.290 42.857 0.00 0.00 0.00 4.92
17 18 3.764885 AAGAATTATGTCTTGCGTGCC 57.235 42.857 0.00 0.00 36.48 5.01
40 41 9.899226 CCTCAAAAACAAAAACACCAATTAAAA 57.101 25.926 0.00 0.00 0.00 1.52
41 42 9.284968 TCCTCAAAAACAAAAACACCAATTAAA 57.715 25.926 0.00 0.00 0.00 1.52
42 43 8.848474 TCCTCAAAAACAAAAACACCAATTAA 57.152 26.923 0.00 0.00 0.00 1.40
43 44 8.722394 GTTCCTCAAAAACAAAAACACCAATTA 58.278 29.630 0.00 0.00 0.00 1.40
44 45 7.229506 TGTTCCTCAAAAACAAAAACACCAATT 59.770 29.630 0.00 0.00 33.86 2.32
45 46 6.712547 TGTTCCTCAAAAACAAAAACACCAAT 59.287 30.769 0.00 0.00 33.86 3.16
46 47 6.055588 TGTTCCTCAAAAACAAAAACACCAA 58.944 32.000 0.00 0.00 33.86 3.67
47 48 5.611374 TGTTCCTCAAAAACAAAAACACCA 58.389 33.333 0.00 0.00 33.86 4.17
48 49 6.546972 TTGTTCCTCAAAAACAAAAACACC 57.453 33.333 0.00 0.00 42.09 4.16
49 50 7.536964 CCAATTGTTCCTCAAAAACAAAAACAC 59.463 33.333 4.43 0.00 46.38 3.32
50 51 7.229506 ACCAATTGTTCCTCAAAAACAAAAACA 59.770 29.630 4.43 0.00 46.38 2.83
51 52 7.536964 CACCAATTGTTCCTCAAAAACAAAAAC 59.463 33.333 4.43 0.00 46.38 2.43
52 53 7.308830 CCACCAATTGTTCCTCAAAAACAAAAA 60.309 33.333 4.43 0.00 46.38 1.94
53 54 6.150140 CCACCAATTGTTCCTCAAAAACAAAA 59.850 34.615 4.43 0.00 46.38 2.44
54 55 5.645497 CCACCAATTGTTCCTCAAAAACAAA 59.355 36.000 4.43 0.00 46.38 2.83
56 57 4.223923 ACCACCAATTGTTCCTCAAAAACA 59.776 37.500 4.43 0.00 39.62 2.83
57 58 4.570369 CACCACCAATTGTTCCTCAAAAAC 59.430 41.667 4.43 0.00 39.62 2.43
58 59 4.467795 TCACCACCAATTGTTCCTCAAAAA 59.532 37.500 4.43 0.00 39.62 1.94
59 60 4.026744 TCACCACCAATTGTTCCTCAAAA 58.973 39.130 4.43 0.00 39.62 2.44
60 61 3.636679 TCACCACCAATTGTTCCTCAAA 58.363 40.909 4.43 0.00 39.62 2.69
61 62 3.304911 TCACCACCAATTGTTCCTCAA 57.695 42.857 4.43 0.00 40.53 3.02
62 63 3.304911 TTCACCACCAATTGTTCCTCA 57.695 42.857 4.43 0.00 0.00 3.86
63 64 4.082125 AGATTCACCACCAATTGTTCCTC 58.918 43.478 4.43 0.00 0.00 3.71
64 65 4.118168 AGATTCACCACCAATTGTTCCT 57.882 40.909 4.43 0.00 0.00 3.36
65 66 4.871933 AAGATTCACCACCAATTGTTCC 57.128 40.909 4.43 0.00 0.00 3.62
66 67 6.089249 AGAAAGATTCACCACCAATTGTTC 57.911 37.500 4.43 0.00 0.00 3.18
67 68 5.278463 CGAGAAAGATTCACCACCAATTGTT 60.278 40.000 4.43 0.00 0.00 2.83
68 69 4.216257 CGAGAAAGATTCACCACCAATTGT 59.784 41.667 4.43 0.00 0.00 2.71
69 70 4.379813 CCGAGAAAGATTCACCACCAATTG 60.380 45.833 0.00 0.00 0.00 2.32
70 71 3.758554 CCGAGAAAGATTCACCACCAATT 59.241 43.478 0.00 0.00 0.00 2.32
71 72 3.347216 CCGAGAAAGATTCACCACCAAT 58.653 45.455 0.00 0.00 0.00 3.16
72 73 2.778299 CCGAGAAAGATTCACCACCAA 58.222 47.619 0.00 0.00 0.00 3.67
73 74 1.610624 GCCGAGAAAGATTCACCACCA 60.611 52.381 0.00 0.00 0.00 4.17
74 75 1.087501 GCCGAGAAAGATTCACCACC 58.912 55.000 0.00 0.00 0.00 4.61
75 76 2.003301 GAGCCGAGAAAGATTCACCAC 58.997 52.381 0.00 0.00 0.00 4.16
76 77 1.902508 AGAGCCGAGAAAGATTCACCA 59.097 47.619 0.00 0.00 0.00 4.17
77 78 2.682155 AGAGCCGAGAAAGATTCACC 57.318 50.000 0.00 0.00 0.00 4.02
78 79 4.330347 GGTAAAGAGCCGAGAAAGATTCAC 59.670 45.833 0.00 0.00 0.00 3.18
79 80 4.504858 GGTAAAGAGCCGAGAAAGATTCA 58.495 43.478 0.00 0.00 0.00 2.57
80 81 3.872182 GGGTAAAGAGCCGAGAAAGATTC 59.128 47.826 0.00 0.00 32.39 2.52
81 82 3.370633 GGGGTAAAGAGCCGAGAAAGATT 60.371 47.826 0.00 0.00 44.86 2.40
82 83 2.170817 GGGGTAAAGAGCCGAGAAAGAT 59.829 50.000 0.00 0.00 44.86 2.40
83 84 1.553704 GGGGTAAAGAGCCGAGAAAGA 59.446 52.381 0.00 0.00 44.86 2.52
84 85 1.555533 AGGGGTAAAGAGCCGAGAAAG 59.444 52.381 0.00 0.00 44.86 2.62
85 86 1.278127 CAGGGGTAAAGAGCCGAGAAA 59.722 52.381 0.00 0.00 44.86 2.52
86 87 0.902531 CAGGGGTAAAGAGCCGAGAA 59.097 55.000 0.00 0.00 44.86 2.87
87 88 0.252103 ACAGGGGTAAAGAGCCGAGA 60.252 55.000 0.00 0.00 44.86 4.04
88 89 1.481871 TACAGGGGTAAAGAGCCGAG 58.518 55.000 0.00 0.00 44.86 4.63
89 90 2.170012 ATACAGGGGTAAAGAGCCGA 57.830 50.000 0.00 0.00 44.86 5.54
90 91 3.323979 ACATATACAGGGGTAAAGAGCCG 59.676 47.826 0.00 0.00 44.86 5.52
91 92 4.976540 ACATATACAGGGGTAAAGAGCC 57.023 45.455 0.00 0.00 43.02 4.70
92 93 7.005709 ACATACATATACAGGGGTAAAGAGC 57.994 40.000 0.00 0.00 32.19 4.09
93 94 9.490379 GAAACATACATATACAGGGGTAAAGAG 57.510 37.037 0.00 0.00 32.19 2.85
94 95 8.145767 CGAAACATACATATACAGGGGTAAAGA 58.854 37.037 0.00 0.00 32.19 2.52
95 96 7.386848 CCGAAACATACATATACAGGGGTAAAG 59.613 40.741 0.00 0.00 32.19 1.85
96 97 7.218614 CCGAAACATACATATACAGGGGTAAA 58.781 38.462 0.00 0.00 32.19 2.01
97 98 6.742082 GCCGAAACATACATATACAGGGGTAA 60.742 42.308 0.00 0.00 32.19 2.85
98 99 5.279607 GCCGAAACATACATATACAGGGGTA 60.280 44.000 0.00 0.00 0.00 3.69
99 100 4.504340 GCCGAAACATACATATACAGGGGT 60.504 45.833 0.00 0.00 0.00 4.95
100 101 4.000988 GCCGAAACATACATATACAGGGG 58.999 47.826 0.00 0.00 0.00 4.79
101 102 4.000988 GGCCGAAACATACATATACAGGG 58.999 47.826 0.00 0.00 0.00 4.45
102 103 4.000988 GGGCCGAAACATACATATACAGG 58.999 47.826 0.00 0.00 0.00 4.00
103 104 3.678072 CGGGCCGAAACATACATATACAG 59.322 47.826 24.41 0.00 0.00 2.74
104 105 3.321396 TCGGGCCGAAACATACATATACA 59.679 43.478 29.11 0.00 31.06 2.29
105 106 3.916761 TCGGGCCGAAACATACATATAC 58.083 45.455 29.11 0.00 31.06 1.47
106 107 4.562082 CTTCGGGCCGAAACATACATATA 58.438 43.478 37.48 14.96 45.23 0.86
107 108 3.399330 CTTCGGGCCGAAACATACATAT 58.601 45.455 37.48 0.00 45.23 1.78
108 109 2.828877 CTTCGGGCCGAAACATACATA 58.171 47.619 37.48 16.22 45.23 2.29
129 130 1.379044 CAGTTGGGCTGGGCTAAGG 60.379 63.158 0.00 0.00 41.42 2.69
213 215 1.270732 ACTAGGTCGTGAGTCGTGAGT 60.271 52.381 0.00 0.00 40.80 3.41
214 216 1.440708 ACTAGGTCGTGAGTCGTGAG 58.559 55.000 0.00 0.00 40.80 3.51
215 217 1.534163 CAACTAGGTCGTGAGTCGTGA 59.466 52.381 0.00 0.00 40.80 4.35
216 218 1.965083 CAACTAGGTCGTGAGTCGTG 58.035 55.000 0.00 0.00 40.80 4.35
217 219 0.240411 GCAACTAGGTCGTGAGTCGT 59.760 55.000 0.00 0.00 40.80 4.34
218 220 0.522180 AGCAACTAGGTCGTGAGTCG 59.478 55.000 0.00 0.00 41.41 4.18
219 221 2.265647 GAGCAACTAGGTCGTGAGTC 57.734 55.000 0.00 0.00 34.67 3.36
271 280 4.828925 GAGGCAGACGCAGGGAGC 62.829 72.222 0.00 0.00 41.24 4.70
424 446 1.089920 ATTTCATCAGCCGACACAGC 58.910 50.000 0.00 0.00 0.00 4.40
454 476 2.758089 GCTGATCGCCTGTGCTTGG 61.758 63.158 0.00 0.00 34.43 3.61
487 509 0.037605 GAACGACCCACCACCTACAG 60.038 60.000 0.00 0.00 0.00 2.74
500 522 2.266554 CTGAAGCAGGATCAGAACGAC 58.733 52.381 0.00 0.00 45.74 4.34
599 675 0.751643 GCACTATGCATCCGGGGTTT 60.752 55.000 0.19 0.00 44.26 3.27
615 691 4.787598 AGTTCAAACGAGATTCAATGCAC 58.212 39.130 0.00 0.00 0.00 4.57
625 701 8.203937 TCAGTTCAATTTTAGTTCAAACGAGA 57.796 30.769 0.00 0.00 0.00 4.04
626 702 8.835467 TTCAGTTCAATTTTAGTTCAAACGAG 57.165 30.769 0.00 0.00 0.00 4.18
627 703 9.796120 ATTTCAGTTCAATTTTAGTTCAAACGA 57.204 25.926 0.00 0.00 0.00 3.85
646 722 5.645929 TCCAACGCATACACATAATTTCAGT 59.354 36.000 0.00 0.00 0.00 3.41
666 742 5.925506 TGTGTAGATCCGAGTAAATCCAA 57.074 39.130 0.00 0.00 0.00 3.53
678 756 8.138712 GGAATCGATAATAGGATGTGTAGATCC 58.861 40.741 0.00 0.00 42.21 3.36
711 789 9.829507 CTCTCCATCTTCTGTTCTACAATAAAT 57.170 33.333 0.00 0.00 0.00 1.40
712 790 9.035890 TCTCTCCATCTTCTGTTCTACAATAAA 57.964 33.333 0.00 0.00 0.00 1.40
713 791 8.595362 TCTCTCCATCTTCTGTTCTACAATAA 57.405 34.615 0.00 0.00 0.00 1.40
714 792 8.774546 ATCTCTCCATCTTCTGTTCTACAATA 57.225 34.615 0.00 0.00 0.00 1.90
715 793 7.673641 ATCTCTCCATCTTCTGTTCTACAAT 57.326 36.000 0.00 0.00 0.00 2.71
716 794 7.487822 AATCTCTCCATCTTCTGTTCTACAA 57.512 36.000 0.00 0.00 0.00 2.41
724 806 6.098124 AGAGTACCAAATCTCTCCATCTTCTG 59.902 42.308 0.00 0.00 36.45 3.02
733 815 9.308318 GAGATACAAAAGAGTACCAAATCTCTC 57.692 37.037 0.00 0.00 39.70 3.20
740 822 8.258007 CAGTATGGAGATACAAAAGAGTACCAA 58.742 37.037 0.00 0.00 37.50 3.67
743 825 9.088512 CAACAGTATGGAGATACAAAAGAGTAC 57.911 37.037 0.00 0.00 43.62 2.73
745 827 7.680730 ACAACAGTATGGAGATACAAAAGAGT 58.319 34.615 0.00 0.00 43.62 3.24
774 856 0.471191 AGATCCATGCGGCAGATGAA 59.529 50.000 9.25 0.00 0.00 2.57
776 858 1.270465 TGTAGATCCATGCGGCAGATG 60.270 52.381 9.25 2.35 0.00 2.90
777 859 1.051008 TGTAGATCCATGCGGCAGAT 58.949 50.000 9.25 6.63 0.00 2.90
778 860 0.104855 GTGTAGATCCATGCGGCAGA 59.895 55.000 9.25 1.00 0.00 4.26
779 861 0.179076 TGTGTAGATCCATGCGGCAG 60.179 55.000 9.25 0.51 0.00 4.85
780 862 0.469494 ATGTGTAGATCCATGCGGCA 59.531 50.000 4.58 4.58 0.00 5.69
781 863 1.151668 GATGTGTAGATCCATGCGGC 58.848 55.000 0.00 0.00 0.00 6.53
782 864 2.827800 AGATGTGTAGATCCATGCGG 57.172 50.000 0.00 0.00 0.00 5.69
783 865 6.791887 AAAATAGATGTGTAGATCCATGCG 57.208 37.500 0.00 0.00 0.00 4.73
784 866 7.859377 CACAAAAATAGATGTGTAGATCCATGC 59.141 37.037 0.00 0.00 41.51 4.06
788 870 8.682936 ATCCACAAAAATAGATGTGTAGATCC 57.317 34.615 5.32 0.00 44.21 3.36
789 871 9.941664 CAATCCACAAAAATAGATGTGTAGATC 57.058 33.333 5.32 0.00 44.21 2.75
790 872 9.466497 ACAATCCACAAAAATAGATGTGTAGAT 57.534 29.630 5.32 0.00 44.21 1.98
791 873 8.862325 ACAATCCACAAAAATAGATGTGTAGA 57.138 30.769 5.32 0.00 44.21 2.59
795 877 7.489113 GGCTAACAATCCACAAAAATAGATGTG 59.511 37.037 0.00 0.00 45.06 3.21
796 878 7.178274 TGGCTAACAATCCACAAAAATAGATGT 59.822 33.333 0.00 0.00 0.00 3.06
808 893 4.458989 TGAACTTCATGGCTAACAATCCAC 59.541 41.667 0.00 0.00 34.81 4.02
874 960 2.671396 CTGAAGGTGTGCCGTATACAAC 59.329 50.000 3.32 0.00 40.50 3.32
902 989 1.302033 CAGCTCAACCAGAAGCGGT 60.302 57.895 0.00 0.00 42.71 5.68
905 992 1.002033 CAACACAGCTCAACCAGAAGC 60.002 52.381 0.00 0.00 0.00 3.86
937 1024 4.505217 GATGGCGACGTTGCTGCG 62.505 66.667 26.31 8.53 37.94 5.18
938 1025 2.456594 TTTGATGGCGACGTTGCTGC 62.457 55.000 26.31 15.97 34.52 5.25
939 1026 0.725784 GTTTGATGGCGACGTTGCTG 60.726 55.000 26.31 0.65 34.52 4.41
940 1027 1.574428 GTTTGATGGCGACGTTGCT 59.426 52.632 26.31 8.58 34.52 3.91
941 1028 1.442017 GGTTTGATGGCGACGTTGC 60.442 57.895 19.96 19.96 0.00 4.17
942 1029 0.110238 CTGGTTTGATGGCGACGTTG 60.110 55.000 0.00 0.00 0.00 4.10
943 1030 0.534203 ACTGGTTTGATGGCGACGTT 60.534 50.000 0.00 0.00 0.00 3.99
944 1031 1.070786 ACTGGTTTGATGGCGACGT 59.929 52.632 0.00 0.00 0.00 4.34
945 1032 0.948623 TCACTGGTTTGATGGCGACG 60.949 55.000 0.00 0.00 0.00 5.12
946 1033 0.798776 CTCACTGGTTTGATGGCGAC 59.201 55.000 0.00 0.00 0.00 5.19
947 1034 0.955428 GCTCACTGGTTTGATGGCGA 60.955 55.000 0.00 0.00 0.00 5.54
948 1035 0.957395 AGCTCACTGGTTTGATGGCG 60.957 55.000 0.00 0.00 0.00 5.69
949 1036 0.524862 CAGCTCACTGGTTTGATGGC 59.475 55.000 0.00 0.00 40.48 4.40
950 1037 0.524862 GCAGCTCACTGGTTTGATGG 59.475 55.000 0.00 0.00 44.63 3.51
951 1038 0.524862 GGCAGCTCACTGGTTTGATG 59.475 55.000 0.00 0.00 44.63 3.07
952 1039 0.957395 CGGCAGCTCACTGGTTTGAT 60.957 55.000 0.00 0.00 44.63 2.57
953 1040 1.597854 CGGCAGCTCACTGGTTTGA 60.598 57.895 0.00 0.00 44.63 2.69
954 1041 2.949106 CGGCAGCTCACTGGTTTG 59.051 61.111 0.00 0.00 44.63 2.93
955 1042 2.980233 GCGGCAGCTCACTGGTTT 60.980 61.111 0.00 0.00 44.63 3.27
960 1047 4.087892 ATTCGGCGGCAGCTCACT 62.088 61.111 10.53 0.00 44.37 3.41
961 1048 3.567797 GATTCGGCGGCAGCTCAC 61.568 66.667 10.53 0.00 44.37 3.51
962 1049 3.390183 ATGATTCGGCGGCAGCTCA 62.390 57.895 10.53 8.29 44.37 4.26
973 1060 1.056700 AGGTCCTGGGGGATGATTCG 61.057 60.000 0.00 0.00 44.33 3.34
987 1074 2.737830 GCCATAGCGAGGAGGTCC 59.262 66.667 0.00 0.00 0.00 4.46
1061 1148 4.601019 CCAGCAAATACATTTCCGTGATC 58.399 43.478 0.00 0.00 0.00 2.92
1082 1169 5.407502 GGTAATTTTGAGTACATTGTGGCC 58.592 41.667 0.00 0.00 0.00 5.36
1115 1202 2.025887 AGTAGGATTGTTTGAGGCCTGG 60.026 50.000 12.00 0.00 0.00 4.45
1336 1805 2.560981 TCTCTCCAGTACATTTGACGCA 59.439 45.455 0.00 0.00 0.00 5.24
1424 1893 4.179298 GTGGTAGTAGGAACGAATGGAAC 58.821 47.826 0.00 0.00 0.00 3.62
1427 1896 3.518590 GTGTGGTAGTAGGAACGAATGG 58.481 50.000 0.00 0.00 0.00 3.16
1466 2391 3.715315 AGGCCTGAGTATAAAGGGGTAAC 59.285 47.826 3.11 0.00 33.87 2.50
1533 2824 2.684374 CGGTGAATCTTCATTGCCATCA 59.316 45.455 0.00 0.00 39.73 3.07
1569 2860 0.961019 AAAAGAAGCGCTTGCCATCA 59.039 45.000 30.47 0.00 40.41 3.07
1630 2921 0.888736 TCGCATGTGGTGAAGTTGGG 60.889 55.000 6.39 0.00 31.83 4.12
1644 2935 0.251354 AGCAGAAGTCATGGTCGCAT 59.749 50.000 0.00 0.00 0.00 4.73
1760 3051 1.136085 CATGTAAAACTCACCGCACCG 60.136 52.381 0.00 0.00 0.00 4.94
1785 3076 5.859205 AATAGGAATGAATGAACCAAGCC 57.141 39.130 0.00 0.00 0.00 4.35
1929 3223 0.529773 GCTTACCATCGCCGATGTCA 60.530 55.000 24.09 9.74 38.28 3.58
1999 3293 0.955428 TCGCACATCCTGAAGTTGGC 60.955 55.000 0.00 0.00 0.00 4.52
2072 3535 2.061773 CACCGTCAGAATATCCGATGC 58.938 52.381 0.00 0.00 0.00 3.91
2074 3537 2.558795 CCTCACCGTCAGAATATCCGAT 59.441 50.000 0.00 0.00 0.00 4.18
2088 3551 0.528466 CATCATCACCGTCCTCACCG 60.528 60.000 0.00 0.00 0.00 4.94
2127 3628 1.750018 CGCCACCATCTCCATGCAA 60.750 57.895 0.00 0.00 0.00 4.08
2154 3655 1.593006 CACGAGTTGACGCTGAACTTT 59.407 47.619 0.00 0.00 33.71 2.66
2178 3679 2.440569 GCTCGAGCAGAAGACGTGC 61.441 63.158 31.91 0.17 41.59 5.34
2218 3719 1.967319 ACATTGTTGTCCAGCTTCGT 58.033 45.000 0.00 0.00 0.00 3.85
2241 3742 4.063967 TCAGGGCATTCGACGCGT 62.064 61.111 13.85 13.85 0.00 6.01
2316 3817 0.905357 CCCATTTGTCGAGGAGGTCT 59.095 55.000 0.00 0.00 0.00 3.85
2379 3880 3.430790 CCGAGCATTCTCTGTATGGACAA 60.431 47.826 0.00 0.00 37.19 3.18
2382 3883 1.069204 GCCGAGCATTCTCTGTATGGA 59.931 52.381 0.00 0.00 37.19 3.41
2854 4415 0.533308 TTTAGCGCCGACAACTTGGT 60.533 50.000 2.29 0.00 0.00 3.67
2865 4426 0.525761 TGCAGAAATGGTTTAGCGCC 59.474 50.000 2.29 0.00 0.00 6.53
2895 4456 3.381272 CACCCCAAATAAATCATCAGCGT 59.619 43.478 0.00 0.00 0.00 5.07
2933 4494 6.327626 ACTGAAGCTATTCAAGGAGGCTATAA 59.672 38.462 0.00 0.00 44.68 0.98
2981 4545 8.520351 ACTGCAATAACCAAAAGATACCTTAAC 58.480 33.333 0.00 0.00 31.15 2.01
3011 4575 7.604164 ACAATCAAGTAGTAACAATCTCCAGTG 59.396 37.037 0.00 0.00 0.00 3.66
3057 4629 1.133606 ACAACCATTTTGGGACGGAGT 60.134 47.619 0.00 0.00 43.37 3.85
3092 4664 4.299586 TGAAACATCCAAGCCACAGATA 57.700 40.909 0.00 0.00 0.00 1.98
3096 4668 2.299582 CCATTGAAACATCCAAGCCACA 59.700 45.455 0.00 0.00 0.00 4.17
3108 4680 6.935167 ACAATTCTGGATTACCCATTGAAAC 58.065 36.000 0.00 0.00 45.57 2.78
3120 4692 9.334947 CTCTGATACATTGTACAATTCTGGATT 57.665 33.333 18.50 0.19 0.00 3.01
3126 4698 9.817809 TTACTCCTCTGATACATTGTACAATTC 57.182 33.333 18.50 13.95 0.00 2.17
3191 4763 1.165270 GGTGTGGTAGGTGTTCATGC 58.835 55.000 0.00 0.00 0.00 4.06
3216 4788 2.942376 CCGTGCATGCACCTTATAGAAA 59.058 45.455 37.92 3.42 43.49 2.52
3271 4849 4.034258 GTCGCGACTCGTGGGACA 62.034 66.667 31.12 0.00 45.52 4.02
3278 4856 1.226323 CAACTAGGGTCGCGACTCG 60.226 63.158 35.50 23.69 36.76 4.18
3323 4901 0.685458 CCCCCAATTCCCAGCTTCTG 60.685 60.000 0.00 0.00 0.00 3.02
3324 4902 0.850883 TCCCCCAATTCCCAGCTTCT 60.851 55.000 0.00 0.00 0.00 2.85
3363 4941 2.711009 TGTTCCATGGTCTCTGTTTCCT 59.289 45.455 12.58 0.00 0.00 3.36
3423 5002 2.899838 GCACTTCACCCGCACACA 60.900 61.111 0.00 0.00 0.00 3.72
3429 5008 2.383527 GCTCTTCGCACTTCACCCG 61.384 63.158 0.00 0.00 38.92 5.28
3623 5232 1.679032 GGCCTCCTTATGCGTCTTTGT 60.679 52.381 0.00 0.00 0.00 2.83
3655 5264 2.507992 CGAGCGCCTCAACCTCAG 60.508 66.667 2.29 0.00 0.00 3.35
3662 5271 4.742201 GCTTCCACGAGCGCCTCA 62.742 66.667 2.29 0.00 32.23 3.86
3711 5320 3.125520 TTGTTGTTCAAGAGGCCCC 57.874 52.632 0.00 0.00 0.00 5.80
3721 5330 2.099756 AGCAAGCTGAACCTTGTTGTTC 59.900 45.455 0.00 0.00 43.17 3.18
3722 5331 2.102578 AGCAAGCTGAACCTTGTTGTT 58.897 42.857 0.00 0.00 43.17 2.83
3723 5332 1.406539 CAGCAAGCTGAACCTTGTTGT 59.593 47.619 16.75 0.00 44.18 3.32
3724 5333 2.129823 CAGCAAGCTGAACCTTGTTG 57.870 50.000 16.75 4.76 46.30 3.33
3725 5334 0.386838 GCAGCAAGCTGAACCTTGTT 59.613 50.000 25.03 0.00 46.30 2.83
3726 5335 0.752743 TGCAGCAAGCTGAACCTTGT 60.753 50.000 25.03 0.00 46.30 3.16
3727 5336 0.386476 TTGCAGCAAGCTGAACCTTG 59.614 50.000 25.03 0.00 46.30 3.61
3728 5337 1.113788 TTTGCAGCAAGCTGAACCTT 58.886 45.000 25.03 0.00 46.30 3.50
3729 5338 0.386838 GTTTGCAGCAAGCTGAACCT 59.613 50.000 25.03 0.00 46.30 3.50
3730 5339 0.102844 TGTTTGCAGCAAGCTGAACC 59.897 50.000 25.03 8.84 46.30 3.62
3731 5340 1.790623 CATGTTTGCAGCAAGCTGAAC 59.209 47.619 25.03 19.63 46.30 3.18
3732 5341 2.143008 CATGTTTGCAGCAAGCTGAA 57.857 45.000 25.03 12.84 46.30 3.02
3733 5342 3.877874 CATGTTTGCAGCAAGCTGA 57.122 47.368 25.03 8.02 46.30 4.26
3752 5388 4.521146 ACCAAGAGGCAACATAATGAGAG 58.479 43.478 0.00 0.00 39.06 3.20
3808 5444 0.921347 ATCAGTATTGTCGAACGCGC 59.079 50.000 5.73 0.00 37.46 6.86
3879 5515 3.533606 AGTAGCTGACAGTAGGCAATG 57.466 47.619 3.99 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.