Multiple sequence alignment - TraesCS2D01G153600

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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 TraesCS2D01G153600 chr2D 100.000 3163 0 0 1 3163 96678665 96681827 0.000000e+00 5842.0
1 TraesCS2D01G153600 chr2D 96.691 2025 38 18 522 2525 96748965 96750981 0.000000e+00 3341.0
2 TraesCS2D01G153600 chr2D 84.556 259 31 8 162 418 96748579 96748830 6.770000e-62 248.0
3 TraesCS2D01G153600 chr2D 88.889 162 18 0 1 162 404458356 404458195 1.920000e-47 200.0
4 TraesCS2D01G153600 chr2D 88.281 128 15 0 1149 1276 95772686 95772813 1.520000e-33 154.0
5 TraesCS2D01G153600 chr2D 95.082 61 3 0 1216 1276 96774906 96774966 2.600000e-16 97.1
6 TraesCS2D01G153600 chr2D 94.545 55 2 1 1220 1273 90309632 90309578 2.020000e-12 84.2
7 TraesCS2D01G153600 chr2D 97.826 46 1 0 422 467 96748867 96748912 2.620000e-11 80.5
8 TraesCS2D01G153600 chr2A 92.544 2119 105 16 422 2525 95157422 95159502 0.000000e+00 2988.0
9 TraesCS2D01G153600 chr2A 93.040 1997 96 10 422 2408 95272130 95274093 0.000000e+00 2878.0
10 TraesCS2D01G153600 chr2A 89.264 652 58 11 2517 3163 634111363 634110719 0.000000e+00 806.0
11 TraesCS2D01G153600 chr2A 77.060 789 168 12 1381 2163 95259753 95260534 2.900000e-120 442.0
12 TraesCS2D01G153600 chr2A 86.806 144 3 10 2398 2532 95274257 95274393 2.540000e-31 147.0
13 TraesCS2D01G153600 chr2B 88.779 2121 158 44 422 2523 147829458 147831517 0.000000e+00 2525.0
14 TraesCS2D01G153600 chr2B 88.779 2121 158 44 422 2523 147869211 147871270 0.000000e+00 2525.0
15 TraesCS2D01G153600 chr2B 93.282 1176 68 6 1353 2524 148037099 148038267 0.000000e+00 1724.0
16 TraesCS2D01G153600 chr2B 91.978 910 56 9 422 1318 148036090 148036995 0.000000e+00 1260.0
17 TraesCS2D01G153600 chr2B 84.867 641 72 18 2524 3158 682866651 682867272 9.630000e-175 623.0
18 TraesCS2D01G153600 chr2B 89.697 165 17 0 1 165 554191038 554190874 8.890000e-51 211.0
19 TraesCS2D01G153600 chr7D 89.401 651 60 3 2521 3162 430934454 430935104 0.000000e+00 811.0
20 TraesCS2D01G153600 chr7D 87.805 164 20 0 2 165 20055530 20055693 3.220000e-45 193.0
21 TraesCS2D01G153600 chr7D 75.000 416 94 9 1403 1813 506882893 506883303 1.940000e-42 183.0
22 TraesCS2D01G153600 chr5D 89.147 645 54 9 2522 3163 322820795 322821426 0.000000e+00 789.0
23 TraesCS2D01G153600 chr5D 89.820 167 16 1 1 167 277067143 277066978 2.470000e-51 213.0
24 TraesCS2D01G153600 chr5D 90.000 160 14 1 1 160 277067677 277067834 4.140000e-49 206.0
25 TraesCS2D01G153600 chr5D 88.095 168 18 2 1 167 405402279 405402113 6.920000e-47 198.0
26 TraesCS2D01G153600 chr5D 100.000 38 0 0 1242 1279 124857772 124857735 1.570000e-08 71.3
27 TraesCS2D01G153600 chr1D 88.992 645 54 15 2522 3163 493898176 493897546 0.000000e+00 782.0
28 TraesCS2D01G153600 chr1D 90.062 161 16 0 1 161 61810122 61809962 3.200000e-50 209.0
29 TraesCS2D01G153600 chr1D 87.425 167 20 1 1 166 445592244 445592078 1.160000e-44 191.0
30 TraesCS2D01G153600 chr1D 86.842 152 20 0 1 152 220843648 220843497 1.510000e-38 171.0
31 TraesCS2D01G153600 chr6D 90.598 585 53 2 2580 3163 408698221 408697638 0.000000e+00 774.0
32 TraesCS2D01G153600 chr6D 79.690 709 92 25 587 1279 409871809 409872481 6.180000e-127 464.0
33 TraesCS2D01G153600 chr6D 77.907 172 28 3 1 162 38003087 38003258 7.220000e-17 99.0
34 TraesCS2D01G153600 chr6D 77.143 175 30 3 1 165 28899921 28899747 3.360000e-15 93.5
35 TraesCS2D01G153600 chr6D 98.113 53 1 0 1223 1275 409882474 409882526 3.360000e-15 93.5
36 TraesCS2D01G153600 chr6D 76.744 172 30 3 1 162 232697231 232697402 1.560000e-13 87.9
37 TraesCS2D01G153600 chr6D 76.163 172 31 1 1 162 56756554 56756383 7.270000e-12 82.4
38 TraesCS2D01G153600 chr1A 86.862 647 76 8 2522 3163 252327484 252326842 0.000000e+00 715.0
39 TraesCS2D01G153600 chr1A 88.667 150 17 0 1 150 433802055 433801906 1.940000e-42 183.0
40 TraesCS2D01G153600 chr1A 84.524 168 26 0 1 168 388785908 388785741 1.950000e-37 167.0
41 TraesCS2D01G153600 chr1A 85.714 154 22 0 1 154 109280576 109280729 2.520000e-36 163.0
42 TraesCS2D01G153600 chr3D 86.536 661 60 18 2514 3163 241669574 241670216 0.000000e+00 701.0
43 TraesCS2D01G153600 chr3D 89.308 159 17 0 1 159 247985001 247985159 1.920000e-47 200.0
44 TraesCS2D01G153600 chr3D 86.885 61 8 0 1217 1277 419515699 419515759 5.660000e-08 69.4
45 TraesCS2D01G153600 chr1B 84.839 653 77 11 2524 3160 144912393 144913039 3.440000e-179 638.0
46 TraesCS2D01G153600 chr5B 83.956 642 85 15 2524 3158 562266700 562267330 1.620000e-167 599.0
47 TraesCS2D01G153600 chr5B 89.506 162 17 0 1 162 97890188 97890027 4.140000e-49 206.0
48 TraesCS2D01G153600 chr5B 88.889 162 18 0 1 162 666192960 666192799 1.920000e-47 200.0
49 TraesCS2D01G153600 chr5B 88.095 168 19 1 1 167 486372860 486372693 6.920000e-47 198.0
50 TraesCS2D01G153600 chr5B 100.000 38 0 0 1242 1279 137671935 137671898 1.570000e-08 71.3
51 TraesCS2D01G153600 chr6B 76.877 1159 156 66 480 1608 616431261 616430185 1.280000e-153 553.0
52 TraesCS2D01G153600 chr6B 77.376 663 108 28 971 1608 616380885 616381530 3.880000e-94 355.0
53 TraesCS2D01G153600 chrUn 76.738 791 169 13 1381 2164 17365105 17365887 8.110000e-116 427.0
54 TraesCS2D01G153600 chrUn 95.833 48 2 0 1229 1276 17364995 17365042 9.410000e-11 78.7
55 TraesCS2D01G153600 chr6A 81.931 321 43 9 971 1279 555323170 555323487 1.130000e-64 257.0
56 TraesCS2D01G153600 chr5A 89.697 165 16 1 1 165 115489079 115489242 3.200000e-50 209.0
57 TraesCS2D01G153600 chr4D 88.344 163 19 0 1 163 316834823 316834985 2.490000e-46 196.0
58 TraesCS2D01G153600 chr4D 87.425 167 21 0 1 167 115219687 115219853 3.220000e-45 193.0
59 TraesCS2D01G153600 chr4D 77.326 172 29 1 1 162 65711249 65711078 3.360000e-15 93.5
60 TraesCS2D01G153600 chr4D 77.326 172 29 3 1 162 141578048 141578219 3.360000e-15 93.5
61 TraesCS2D01G153600 chr4B 87.805 164 20 0 1 164 230260946 230261109 3.220000e-45 193.0
62 TraesCS2D01G153600 chr4B 86.923 130 16 1 3 132 294607048 294607176 9.140000e-31 145.0
63 TraesCS2D01G153600 chr4B 78.808 151 16 4 1 151 344973940 344973806 1.560000e-13 87.9
64 TraesCS2D01G153600 chr7B 75.117 426 93 10 1406 1823 535518372 535518792 1.500000e-43 187.0
65 TraesCS2D01G153600 chr7B 74.825 429 95 10 1403 1823 535506327 535506750 6.970000e-42 182.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G153600 chr2D 96678665 96681827 3162 False 5842.000000 5842 100.000000 1 3163 1 chr2D.!!$F2 3162
1 TraesCS2D01G153600 chr2D 96748579 96750981 2402 False 1223.166667 3341 93.024333 162 2525 3 chr2D.!!$F4 2363
2 TraesCS2D01G153600 chr2A 95157422 95159502 2080 False 2988.000000 2988 92.544000 422 2525 1 chr2A.!!$F1 2103
3 TraesCS2D01G153600 chr2A 95272130 95274393 2263 False 1512.500000 2878 89.923000 422 2532 2 chr2A.!!$F3 2110
4 TraesCS2D01G153600 chr2A 634110719 634111363 644 True 806.000000 806 89.264000 2517 3163 1 chr2A.!!$R1 646
5 TraesCS2D01G153600 chr2A 95259753 95260534 781 False 442.000000 442 77.060000 1381 2163 1 chr2A.!!$F2 782
6 TraesCS2D01G153600 chr2B 147829458 147831517 2059 False 2525.000000 2525 88.779000 422 2523 1 chr2B.!!$F1 2101
7 TraesCS2D01G153600 chr2B 147869211 147871270 2059 False 2525.000000 2525 88.779000 422 2523 1 chr2B.!!$F2 2101
8 TraesCS2D01G153600 chr2B 148036090 148038267 2177 False 1492.000000 1724 92.630000 422 2524 2 chr2B.!!$F4 2102
9 TraesCS2D01G153600 chr2B 682866651 682867272 621 False 623.000000 623 84.867000 2524 3158 1 chr2B.!!$F3 634
10 TraesCS2D01G153600 chr7D 430934454 430935104 650 False 811.000000 811 89.401000 2521 3162 1 chr7D.!!$F2 641
11 TraesCS2D01G153600 chr5D 322820795 322821426 631 False 789.000000 789 89.147000 2522 3163 1 chr5D.!!$F2 641
12 TraesCS2D01G153600 chr1D 493897546 493898176 630 True 782.000000 782 88.992000 2522 3163 1 chr1D.!!$R4 641
13 TraesCS2D01G153600 chr6D 408697638 408698221 583 True 774.000000 774 90.598000 2580 3163 1 chr6D.!!$R3 583
14 TraesCS2D01G153600 chr6D 409871809 409872481 672 False 464.000000 464 79.690000 587 1279 1 chr6D.!!$F3 692
15 TraesCS2D01G153600 chr1A 252326842 252327484 642 True 715.000000 715 86.862000 2522 3163 1 chr1A.!!$R1 641
16 TraesCS2D01G153600 chr3D 241669574 241670216 642 False 701.000000 701 86.536000 2514 3163 1 chr3D.!!$F1 649
17 TraesCS2D01G153600 chr1B 144912393 144913039 646 False 638.000000 638 84.839000 2524 3160 1 chr1B.!!$F1 636
18 TraesCS2D01G153600 chr5B 562266700 562267330 630 False 599.000000 599 83.956000 2524 3158 1 chr5B.!!$F1 634
19 TraesCS2D01G153600 chr6B 616430185 616431261 1076 True 553.000000 553 76.877000 480 1608 1 chr6B.!!$R1 1128
20 TraesCS2D01G153600 chr6B 616380885 616381530 645 False 355.000000 355 77.376000 971 1608 1 chr6B.!!$F1 637
21 TraesCS2D01G153600 chrUn 17364995 17365887 892 False 252.850000 427 86.285500 1229 2164 2 chrUn.!!$F1 935

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
44 45 0.034574 TGTGTATGTCATGTGGGGCC 60.035 55.0 0.0 0.0 0.0 5.80 F
319 320 0.470766 TACCCGTGTGCCTTGTCTTT 59.529 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1717 0.951040 CCACCGCACTCCTTCTCAAC 60.951 60.000 0.0 0.0 0.0 3.18 R
2289 2482 8.545229 TGCAAAAATGGACCAATAATACAAAG 57.455 30.769 0.0 0.0 0.0 2.77 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
42 43 6.522625 TTTTTATGTGTATGTCATGTGGGG 57.477 37.500 0.00 0.00 0.00 4.96
43 44 2.057137 ATGTGTATGTCATGTGGGGC 57.943 50.000 0.00 0.00 0.00 5.80
44 45 0.034574 TGTGTATGTCATGTGGGGCC 60.035 55.000 0.00 0.00 0.00 5.80
45 46 0.751643 GTGTATGTCATGTGGGGCCC 60.752 60.000 18.17 18.17 0.00 5.80
46 47 0.918799 TGTATGTCATGTGGGGCCCT 60.919 55.000 25.93 0.00 0.00 5.19
47 48 1.136828 GTATGTCATGTGGGGCCCTA 58.863 55.000 25.93 14.71 0.00 3.53
48 49 1.072331 GTATGTCATGTGGGGCCCTAG 59.928 57.143 25.93 10.88 0.00 3.02
49 50 0.624500 ATGTCATGTGGGGCCCTAGT 60.625 55.000 25.93 4.08 0.00 2.57
50 51 1.224592 GTCATGTGGGGCCCTAGTG 59.775 63.158 25.93 17.60 0.00 2.74
51 52 1.229820 TCATGTGGGGCCCTAGTGT 60.230 57.895 25.93 0.58 0.00 3.55
52 53 1.077501 CATGTGGGGCCCTAGTGTG 60.078 63.158 25.93 10.87 0.00 3.82
53 54 2.308722 ATGTGGGGCCCTAGTGTGG 61.309 63.158 25.93 0.00 0.00 4.17
59 60 2.751837 GCCCTAGTGTGGCTTGCC 60.752 66.667 4.43 4.43 45.70 4.52
60 61 3.081554 CCCTAGTGTGGCTTGCCT 58.918 61.111 13.18 0.00 0.00 4.75
61 62 1.910580 GCCCTAGTGTGGCTTGCCTA 61.911 60.000 13.18 0.00 45.70 3.93
62 63 0.618458 CCCTAGTGTGGCTTGCCTAA 59.382 55.000 13.18 0.00 0.00 2.69
63 64 1.407437 CCCTAGTGTGGCTTGCCTAAG 60.407 57.143 13.18 3.40 36.97 2.18
64 65 1.555075 CCTAGTGTGGCTTGCCTAAGA 59.445 52.381 13.18 0.00 35.92 2.10
65 66 2.171448 CCTAGTGTGGCTTGCCTAAGAT 59.829 50.000 13.18 0.00 35.92 2.40
66 67 2.119801 AGTGTGGCTTGCCTAAGATG 57.880 50.000 13.18 0.00 35.92 2.90
67 68 1.352352 AGTGTGGCTTGCCTAAGATGT 59.648 47.619 13.18 0.00 35.92 3.06
68 69 1.470098 GTGTGGCTTGCCTAAGATGTG 59.530 52.381 13.18 0.00 35.92 3.21
69 70 1.350684 TGTGGCTTGCCTAAGATGTGA 59.649 47.619 13.18 0.00 35.92 3.58
70 71 1.740025 GTGGCTTGCCTAAGATGTGAC 59.260 52.381 13.18 0.00 35.92 3.67
71 72 1.630369 TGGCTTGCCTAAGATGTGACT 59.370 47.619 13.18 0.00 35.92 3.41
72 73 2.040278 TGGCTTGCCTAAGATGTGACTT 59.960 45.455 13.18 0.00 35.92 3.01
73 74 2.421424 GGCTTGCCTAAGATGTGACTTG 59.579 50.000 4.11 0.00 35.92 3.16
74 75 3.338249 GCTTGCCTAAGATGTGACTTGA 58.662 45.455 0.00 0.00 35.92 3.02
75 76 3.753272 GCTTGCCTAAGATGTGACTTGAA 59.247 43.478 0.00 0.00 35.92 2.69
76 77 4.378874 GCTTGCCTAAGATGTGACTTGAAC 60.379 45.833 0.00 0.00 35.92 3.18
77 78 4.623932 TGCCTAAGATGTGACTTGAACT 57.376 40.909 0.00 0.00 0.00 3.01
78 79 5.738619 TGCCTAAGATGTGACTTGAACTA 57.261 39.130 0.00 0.00 0.00 2.24
79 80 6.109156 TGCCTAAGATGTGACTTGAACTAA 57.891 37.500 0.00 0.00 0.00 2.24
80 81 6.530120 TGCCTAAGATGTGACTTGAACTAAA 58.470 36.000 0.00 0.00 0.00 1.85
81 82 6.426937 TGCCTAAGATGTGACTTGAACTAAAC 59.573 38.462 0.00 0.00 0.00 2.01
82 83 6.426937 GCCTAAGATGTGACTTGAACTAAACA 59.573 38.462 0.00 0.00 0.00 2.83
83 84 7.571428 GCCTAAGATGTGACTTGAACTAAACAC 60.571 40.741 0.00 0.00 0.00 3.32
84 85 7.657761 CCTAAGATGTGACTTGAACTAAACACT 59.342 37.037 0.00 0.00 31.42 3.55
85 86 7.484035 AAGATGTGACTTGAACTAAACACTC 57.516 36.000 0.00 0.00 31.42 3.51
86 87 6.582636 AGATGTGACTTGAACTAAACACTCA 58.417 36.000 0.00 0.00 31.42 3.41
87 88 7.220030 AGATGTGACTTGAACTAAACACTCAT 58.780 34.615 0.00 0.00 31.42 2.90
88 89 6.844696 TGTGACTTGAACTAAACACTCATC 57.155 37.500 0.00 0.00 31.42 2.92
89 90 6.582636 TGTGACTTGAACTAAACACTCATCT 58.417 36.000 0.00 0.00 31.42 2.90
90 91 7.722363 TGTGACTTGAACTAAACACTCATCTA 58.278 34.615 0.00 0.00 31.42 1.98
91 92 8.201464 TGTGACTTGAACTAAACACTCATCTAA 58.799 33.333 0.00 0.00 31.42 2.10
92 93 8.704234 GTGACTTGAACTAAACACTCATCTAAG 58.296 37.037 0.00 0.00 0.00 2.18
93 94 8.421784 TGACTTGAACTAAACACTCATCTAAGT 58.578 33.333 0.00 0.00 0.00 2.24
94 95 9.262358 GACTTGAACTAAACACTCATCTAAGTT 57.738 33.333 0.00 0.00 0.00 2.66
95 96 9.046296 ACTTGAACTAAACACTCATCTAAGTTG 57.954 33.333 0.00 0.00 0.00 3.16
96 97 7.962964 TGAACTAAACACTCATCTAAGTTGG 57.037 36.000 0.00 0.00 0.00 3.77
97 98 7.506114 TGAACTAAACACTCATCTAAGTTGGT 58.494 34.615 0.00 0.00 0.00 3.67
98 99 7.656137 TGAACTAAACACTCATCTAAGTTGGTC 59.344 37.037 0.00 0.00 0.00 4.02
99 100 7.062749 ACTAAACACTCATCTAAGTTGGTCA 57.937 36.000 0.00 0.00 0.00 4.02
100 101 7.506114 ACTAAACACTCATCTAAGTTGGTCAA 58.494 34.615 0.00 0.00 0.00 3.18
101 102 7.990886 ACTAAACACTCATCTAAGTTGGTCAAA 59.009 33.333 0.00 0.00 0.00 2.69
102 103 6.619801 AACACTCATCTAAGTTGGTCAAAC 57.380 37.500 0.00 0.00 39.24 2.93
114 115 5.847111 GTTGGTCAAACTTTCCTAACCTT 57.153 39.130 0.00 0.00 35.75 3.50
115 116 6.216801 GTTGGTCAAACTTTCCTAACCTTT 57.783 37.500 0.00 0.00 35.75 3.11
116 117 5.845391 TGGTCAAACTTTCCTAACCTTTG 57.155 39.130 0.00 0.00 0.00 2.77
117 118 5.511363 TGGTCAAACTTTCCTAACCTTTGA 58.489 37.500 0.00 0.00 0.00 2.69
118 119 6.133356 TGGTCAAACTTTCCTAACCTTTGAT 58.867 36.000 0.00 0.00 34.33 2.57
119 120 6.040391 TGGTCAAACTTTCCTAACCTTTGATG 59.960 38.462 0.00 0.00 34.33 3.07
120 121 6.040504 GGTCAAACTTTCCTAACCTTTGATGT 59.959 38.462 0.00 0.00 34.33 3.06
121 122 7.229907 GGTCAAACTTTCCTAACCTTTGATGTA 59.770 37.037 0.00 0.00 34.33 2.29
122 123 8.290325 GTCAAACTTTCCTAACCTTTGATGTAG 58.710 37.037 0.00 0.00 34.33 2.74
123 124 6.819397 AACTTTCCTAACCTTTGATGTAGC 57.181 37.500 0.00 0.00 0.00 3.58
124 125 5.876357 ACTTTCCTAACCTTTGATGTAGCA 58.124 37.500 0.00 0.00 0.00 3.49
125 126 6.303839 ACTTTCCTAACCTTTGATGTAGCAA 58.696 36.000 0.00 0.00 0.00 3.91
126 127 6.206829 ACTTTCCTAACCTTTGATGTAGCAAC 59.793 38.462 0.00 0.00 0.00 4.17
127 128 4.585879 TCCTAACCTTTGATGTAGCAACC 58.414 43.478 0.00 0.00 0.00 3.77
128 129 4.288626 TCCTAACCTTTGATGTAGCAACCT 59.711 41.667 0.00 0.00 0.00 3.50
129 130 5.010282 CCTAACCTTTGATGTAGCAACCTT 58.990 41.667 0.00 0.00 0.00 3.50
130 131 5.476945 CCTAACCTTTGATGTAGCAACCTTT 59.523 40.000 0.00 0.00 0.00 3.11
131 132 4.853924 ACCTTTGATGTAGCAACCTTTG 57.146 40.909 0.00 0.00 0.00 2.77
132 133 4.469657 ACCTTTGATGTAGCAACCTTTGA 58.530 39.130 0.00 0.00 0.00 2.69
133 134 4.278419 ACCTTTGATGTAGCAACCTTTGAC 59.722 41.667 0.00 0.00 0.00 3.18
134 135 4.278170 CCTTTGATGTAGCAACCTTTGACA 59.722 41.667 0.00 0.00 0.00 3.58
135 136 5.221224 CCTTTGATGTAGCAACCTTTGACAA 60.221 40.000 0.00 0.00 0.00 3.18
136 137 5.843673 TTGATGTAGCAACCTTTGACAAA 57.156 34.783 0.00 0.00 0.00 2.83
137 138 5.437289 TGATGTAGCAACCTTTGACAAAG 57.563 39.130 19.20 19.20 38.24 2.77
138 139 4.887071 TGATGTAGCAACCTTTGACAAAGT 59.113 37.500 23.07 11.02 36.77 2.66
139 140 5.359576 TGATGTAGCAACCTTTGACAAAGTT 59.640 36.000 23.07 15.39 36.77 2.66
140 141 4.992688 TGTAGCAACCTTTGACAAAGTTG 58.007 39.130 23.07 23.67 36.77 3.16
141 142 3.525268 AGCAACCTTTGACAAAGTTGG 57.475 42.857 26.57 16.00 36.77 3.77
142 143 2.831526 AGCAACCTTTGACAAAGTTGGT 59.168 40.909 25.40 25.40 36.44 3.67
143 144 3.119137 AGCAACCTTTGACAAAGTTGGTC 60.119 43.478 25.40 17.61 36.48 4.02
144 145 3.367910 GCAACCTTTGACAAAGTTGGTCA 60.368 43.478 26.57 9.13 43.12 4.02
145 146 4.680440 GCAACCTTTGACAAAGTTGGTCAT 60.680 41.667 26.57 0.00 44.11 3.06
146 147 5.451242 GCAACCTTTGACAAAGTTGGTCATA 60.451 40.000 26.57 8.49 44.11 2.15
147 148 6.568869 CAACCTTTGACAAAGTTGGTCATAA 58.431 36.000 23.07 9.95 44.11 1.90
148 149 6.783708 ACCTTTGACAAAGTTGGTCATAAA 57.216 33.333 23.07 5.73 44.11 1.40
149 150 6.569780 ACCTTTGACAAAGTTGGTCATAAAC 58.430 36.000 23.07 0.00 44.11 2.01
150 151 5.983118 CCTTTGACAAAGTTGGTCATAAACC 59.017 40.000 23.07 0.00 44.11 3.27
151 152 6.406400 CCTTTGACAAAGTTGGTCATAAACCA 60.406 38.462 23.07 0.00 45.25 3.67
164 165 6.408107 GTCATAAACCAAACAACCCCTAAA 57.592 37.500 0.00 0.00 0.00 1.85
165 166 6.999950 GTCATAAACCAAACAACCCCTAAAT 58.000 36.000 0.00 0.00 0.00 1.40
166 167 7.446769 GTCATAAACCAAACAACCCCTAAATT 58.553 34.615 0.00 0.00 0.00 1.82
167 168 7.386573 GTCATAAACCAAACAACCCCTAAATTG 59.613 37.037 0.00 0.00 0.00 2.32
208 209 5.545063 TCAACAAGATCACAAGACACCTA 57.455 39.130 0.00 0.00 0.00 3.08
211 212 4.836825 ACAAGATCACAAGACACCTATGG 58.163 43.478 0.00 0.00 0.00 2.74
248 249 6.813649 TGTTCATACATGAGAGAACAACTAGC 59.186 38.462 20.66 3.07 45.01 3.42
258 259 3.100671 AGAACAACTAGCAGGAGTAGGG 58.899 50.000 0.00 0.00 0.00 3.53
259 260 2.625282 ACAACTAGCAGGAGTAGGGT 57.375 50.000 0.00 0.00 0.00 4.34
260 261 2.180276 ACAACTAGCAGGAGTAGGGTG 58.820 52.381 0.00 0.00 0.00 4.61
261 262 2.180276 CAACTAGCAGGAGTAGGGTGT 58.820 52.381 0.00 0.00 0.00 4.16
262 263 2.567615 CAACTAGCAGGAGTAGGGTGTT 59.432 50.000 0.00 0.00 0.00 3.32
263 264 3.752359 ACTAGCAGGAGTAGGGTGTTA 57.248 47.619 0.00 0.00 0.00 2.41
264 265 3.363627 ACTAGCAGGAGTAGGGTGTTAC 58.636 50.000 0.00 0.00 0.00 2.50
265 266 1.569653 AGCAGGAGTAGGGTGTTACC 58.430 55.000 0.00 0.00 37.60 2.85
274 275 2.666812 GGTGTTACCCCCAGTCGG 59.333 66.667 0.00 0.00 30.04 4.79
288 289 0.546747 AGTCGGGGTTGGGAATCTCA 60.547 55.000 0.00 0.00 0.00 3.27
299 300 2.899900 TGGGAATCTCATACCTGGATCG 59.100 50.000 0.00 0.00 0.00 3.69
303 304 4.082136 GGAATCTCATACCTGGATCGTACC 60.082 50.000 0.00 0.00 0.00 3.34
310 311 1.518572 CTGGATCGTACCCGTGTGC 60.519 63.158 0.00 0.00 35.01 4.57
319 320 0.470766 TACCCGTGTGCCTTGTCTTT 59.529 50.000 0.00 0.00 0.00 2.52
321 322 0.872388 CCCGTGTGCCTTGTCTTTAC 59.128 55.000 0.00 0.00 0.00 2.01
322 323 1.542547 CCCGTGTGCCTTGTCTTTACT 60.543 52.381 0.00 0.00 0.00 2.24
336 337 7.224557 CCTTGTCTTTACTTGGAATTGGTTTTG 59.775 37.037 0.00 0.00 0.00 2.44
344 346 7.245419 ACTTGGAATTGGTTTTGATTTTTCG 57.755 32.000 0.00 0.00 0.00 3.46
349 351 7.119846 TGGAATTGGTTTTGATTTTTCGTGTTT 59.880 29.630 0.00 0.00 0.00 2.83
353 355 6.100004 TGGTTTTGATTTTTCGTGTTTGCTA 58.900 32.000 0.00 0.00 0.00 3.49
360 362 7.421599 TGATTTTTCGTGTTTGCTATTCTTCA 58.578 30.769 0.00 0.00 0.00 3.02
366 368 2.742053 TGTTTGCTATTCTTCAGACGCC 59.258 45.455 0.00 0.00 0.00 5.68
372 374 4.181578 GCTATTCTTCAGACGCCTGTAAA 58.818 43.478 0.00 0.00 41.16 2.01
418 420 7.817962 TCTCTTGGTTAAAGAATTCGGAGTAAG 59.182 37.037 0.00 1.54 44.38 2.34
419 421 6.877322 TCTTGGTTAAAGAATTCGGAGTAAGG 59.123 38.462 0.00 0.00 42.09 2.69
420 422 6.117975 TGGTTAAAGAATTCGGAGTAAGGT 57.882 37.500 0.00 0.00 0.00 3.50
582 623 1.544825 CCTCGCTCTCTGTCCCCAAA 61.545 60.000 0.00 0.00 0.00 3.28
938 1008 1.133699 TCACCCATGCATCCATCTTCC 60.134 52.381 0.00 0.00 0.00 3.46
945 1015 2.485659 TGCATCCATCTTCCTCCTCTT 58.514 47.619 0.00 0.00 0.00 2.85
1161 1254 4.079096 ACCCTGGACTACTACAGCTATTCT 60.079 45.833 0.00 0.00 33.43 2.40
1577 1767 1.781555 CGCTGACATCGTCGCTTTT 59.218 52.632 8.51 0.00 34.95 2.27
1993 2183 7.814107 ACTCGACCGTAAAGTGTTATTCAAATA 59.186 33.333 0.00 0.00 0.00 1.40
2289 2482 5.108027 CGTTGCTGTTTATTTGCTACCAAAC 60.108 40.000 0.00 0.00 43.20 2.93
2314 2510 8.153550 ACTTTGTATTATTGGTCCATTTTTGCA 58.846 29.630 0.00 0.00 0.00 4.08
2340 2541 8.956533 TCACATCTGTATCGAAAATATTTGGA 57.043 30.769 0.39 3.22 0.00 3.53
2502 2895 4.197107 GCATACGTTGCCTTGTCTTATC 57.803 45.455 10.43 0.00 46.15 1.75
2604 3004 1.614241 AAATCGGCCTAGTCGTGCCT 61.614 55.000 0.00 0.00 45.71 4.75
2632 3034 4.254721 TTTTTCGCCGGTTTGGGA 57.745 50.000 1.90 0.00 38.63 4.37
2997 3438 2.784356 GCCACACAAAGCAGCACCA 61.784 57.895 0.00 0.00 0.00 4.17
3025 3466 2.813474 CCGCCGACGAGCAAATGA 60.813 61.111 0.00 0.00 43.93 2.57
3047 3488 3.692406 GAGGTTCCCAGGCGACGT 61.692 66.667 0.00 0.00 0.00 4.34
3050 3491 4.353437 GTTCCCAGGCGACGTCGT 62.353 66.667 35.48 17.33 42.22 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.105554 GCCCCACATGACATACACATAAAAA 60.106 40.000 0.00 0.00 0.00 1.94
20 21 4.400884 GCCCCACATGACATACACATAAAA 59.599 41.667 0.00 0.00 0.00 1.52
21 22 3.951037 GCCCCACATGACATACACATAAA 59.049 43.478 0.00 0.00 0.00 1.40
22 23 3.550820 GCCCCACATGACATACACATAA 58.449 45.455 0.00 0.00 0.00 1.90
23 24 2.158682 GGCCCCACATGACATACACATA 60.159 50.000 0.00 0.00 0.00 2.29
24 25 1.410083 GGCCCCACATGACATACACAT 60.410 52.381 0.00 0.00 0.00 3.21
25 26 0.034574 GGCCCCACATGACATACACA 60.035 55.000 0.00 0.00 0.00 3.72
26 27 0.751643 GGGCCCCACATGACATACAC 60.752 60.000 12.23 0.00 0.00 2.90
27 28 0.918799 AGGGCCCCACATGACATACA 60.919 55.000 21.43 0.00 0.00 2.29
28 29 1.072331 CTAGGGCCCCACATGACATAC 59.928 57.143 21.43 0.00 0.00 2.39
29 30 1.345009 ACTAGGGCCCCACATGACATA 60.345 52.381 21.43 0.00 0.00 2.29
30 31 0.624500 ACTAGGGCCCCACATGACAT 60.625 55.000 21.43 0.00 0.00 3.06
31 32 1.229820 ACTAGGGCCCCACATGACA 60.230 57.895 21.43 0.00 0.00 3.58
32 33 1.224592 CACTAGGGCCCCACATGAC 59.775 63.158 21.43 0.00 0.00 3.06
33 34 1.229820 ACACTAGGGCCCCACATGA 60.230 57.895 21.43 0.00 0.00 3.07
34 35 1.077501 CACACTAGGGCCCCACATG 60.078 63.158 21.43 14.87 0.00 3.21
35 36 2.308722 CCACACTAGGGCCCCACAT 61.309 63.158 21.43 1.11 0.00 3.21
36 37 2.933287 CCACACTAGGGCCCCACA 60.933 66.667 21.43 2.52 0.00 4.17
37 38 4.426313 GCCACACTAGGGCCCCAC 62.426 72.222 21.43 0.00 45.87 4.61
43 44 0.618458 TTAGGCAAGCCACACTAGGG 59.382 55.000 14.40 0.00 38.92 3.53
44 45 1.555075 TCTTAGGCAAGCCACACTAGG 59.445 52.381 14.40 0.00 38.92 3.02
45 46 3.201290 CATCTTAGGCAAGCCACACTAG 58.799 50.000 14.40 3.14 38.92 2.57
46 47 2.571653 ACATCTTAGGCAAGCCACACTA 59.428 45.455 14.40 0.00 38.92 2.74
47 48 1.352352 ACATCTTAGGCAAGCCACACT 59.648 47.619 14.40 0.00 38.92 3.55
48 49 1.470098 CACATCTTAGGCAAGCCACAC 59.530 52.381 14.40 0.00 38.92 3.82
49 50 1.350684 TCACATCTTAGGCAAGCCACA 59.649 47.619 14.40 0.00 38.92 4.17
50 51 1.740025 GTCACATCTTAGGCAAGCCAC 59.260 52.381 14.40 0.00 38.92 5.01
51 52 1.630369 AGTCACATCTTAGGCAAGCCA 59.370 47.619 14.40 0.00 38.92 4.75
52 53 2.409948 AGTCACATCTTAGGCAAGCC 57.590 50.000 2.02 2.02 0.00 4.35
53 54 3.338249 TCAAGTCACATCTTAGGCAAGC 58.662 45.455 0.00 0.00 0.00 4.01
54 55 4.999950 AGTTCAAGTCACATCTTAGGCAAG 59.000 41.667 0.00 0.00 0.00 4.01
55 56 4.973168 AGTTCAAGTCACATCTTAGGCAA 58.027 39.130 0.00 0.00 0.00 4.52
56 57 4.623932 AGTTCAAGTCACATCTTAGGCA 57.376 40.909 0.00 0.00 0.00 4.75
57 58 6.426937 TGTTTAGTTCAAGTCACATCTTAGGC 59.573 38.462 0.00 0.00 0.00 3.93
58 59 7.657761 AGTGTTTAGTTCAAGTCACATCTTAGG 59.342 37.037 0.00 0.00 0.00 2.69
59 60 8.594881 AGTGTTTAGTTCAAGTCACATCTTAG 57.405 34.615 0.00 0.00 0.00 2.18
60 61 8.201464 TGAGTGTTTAGTTCAAGTCACATCTTA 58.799 33.333 0.00 0.00 0.00 2.10
61 62 7.047891 TGAGTGTTTAGTTCAAGTCACATCTT 58.952 34.615 0.00 0.00 0.00 2.40
62 63 6.582636 TGAGTGTTTAGTTCAAGTCACATCT 58.417 36.000 0.00 0.00 0.00 2.90
63 64 6.844696 TGAGTGTTTAGTTCAAGTCACATC 57.155 37.500 0.00 0.00 0.00 3.06
64 65 7.220030 AGATGAGTGTTTAGTTCAAGTCACAT 58.780 34.615 0.00 0.00 0.00 3.21
65 66 6.582636 AGATGAGTGTTTAGTTCAAGTCACA 58.417 36.000 0.00 0.00 0.00 3.58
66 67 8.589335 TTAGATGAGTGTTTAGTTCAAGTCAC 57.411 34.615 0.00 0.00 0.00 3.67
67 68 8.421784 ACTTAGATGAGTGTTTAGTTCAAGTCA 58.578 33.333 0.00 0.00 0.00 3.41
68 69 8.819643 ACTTAGATGAGTGTTTAGTTCAAGTC 57.180 34.615 0.00 0.00 0.00 3.01
69 70 9.046296 CAACTTAGATGAGTGTTTAGTTCAAGT 57.954 33.333 0.00 0.00 0.00 3.16
70 71 8.499162 CCAACTTAGATGAGTGTTTAGTTCAAG 58.501 37.037 0.00 0.00 0.00 3.02
71 72 7.990886 ACCAACTTAGATGAGTGTTTAGTTCAA 59.009 33.333 0.00 0.00 0.00 2.69
72 73 7.506114 ACCAACTTAGATGAGTGTTTAGTTCA 58.494 34.615 0.00 0.00 0.00 3.18
73 74 7.656137 TGACCAACTTAGATGAGTGTTTAGTTC 59.344 37.037 0.00 0.00 0.00 3.01
74 75 7.506114 TGACCAACTTAGATGAGTGTTTAGTT 58.494 34.615 0.00 0.00 0.00 2.24
75 76 7.062749 TGACCAACTTAGATGAGTGTTTAGT 57.937 36.000 0.00 0.00 0.00 2.24
76 77 7.962964 TTGACCAACTTAGATGAGTGTTTAG 57.037 36.000 0.00 0.00 0.00 1.85
77 78 7.990886 AGTTTGACCAACTTAGATGAGTGTTTA 59.009 33.333 0.00 0.00 43.89 2.01
78 79 6.828785 AGTTTGACCAACTTAGATGAGTGTTT 59.171 34.615 0.00 0.00 43.89 2.83
79 80 6.357367 AGTTTGACCAACTTAGATGAGTGTT 58.643 36.000 0.00 0.00 43.89 3.32
80 81 5.930135 AGTTTGACCAACTTAGATGAGTGT 58.070 37.500 0.00 0.00 43.89 3.55
92 93 5.847111 AAGGTTAGGAAAGTTTGACCAAC 57.153 39.130 0.00 0.00 35.32 3.77
93 94 5.952947 TCAAAGGTTAGGAAAGTTTGACCAA 59.047 36.000 0.00 0.00 33.33 3.67
94 95 5.511363 TCAAAGGTTAGGAAAGTTTGACCA 58.489 37.500 0.00 0.00 33.33 4.02
95 96 6.040504 ACATCAAAGGTTAGGAAAGTTTGACC 59.959 38.462 0.00 0.00 39.31 4.02
96 97 7.039313 ACATCAAAGGTTAGGAAAGTTTGAC 57.961 36.000 0.00 0.00 39.31 3.18
97 98 7.040686 GCTACATCAAAGGTTAGGAAAGTTTGA 60.041 37.037 0.00 0.00 40.42 2.69
98 99 7.084486 GCTACATCAAAGGTTAGGAAAGTTTG 58.916 38.462 0.00 0.00 0.00 2.93
99 100 6.775629 TGCTACATCAAAGGTTAGGAAAGTTT 59.224 34.615 0.00 0.00 0.00 2.66
100 101 6.303839 TGCTACATCAAAGGTTAGGAAAGTT 58.696 36.000 0.00 0.00 0.00 2.66
101 102 5.876357 TGCTACATCAAAGGTTAGGAAAGT 58.124 37.500 0.00 0.00 0.00 2.66
102 103 6.349363 GGTTGCTACATCAAAGGTTAGGAAAG 60.349 42.308 0.00 0.00 0.00 2.62
103 104 5.475564 GGTTGCTACATCAAAGGTTAGGAAA 59.524 40.000 0.00 0.00 0.00 3.13
104 105 5.007682 GGTTGCTACATCAAAGGTTAGGAA 58.992 41.667 0.00 0.00 0.00 3.36
105 106 4.288626 AGGTTGCTACATCAAAGGTTAGGA 59.711 41.667 0.00 0.00 0.00 2.94
106 107 4.589908 AGGTTGCTACATCAAAGGTTAGG 58.410 43.478 0.00 0.00 0.00 2.69
107 108 6.206634 TCAAAGGTTGCTACATCAAAGGTTAG 59.793 38.462 0.00 0.00 0.00 2.34
108 109 6.016610 GTCAAAGGTTGCTACATCAAAGGTTA 60.017 38.462 0.00 0.00 0.00 2.85
109 110 4.892934 TCAAAGGTTGCTACATCAAAGGTT 59.107 37.500 0.00 0.00 0.00 3.50
110 111 4.278419 GTCAAAGGTTGCTACATCAAAGGT 59.722 41.667 0.00 0.00 0.00 3.50
111 112 4.278170 TGTCAAAGGTTGCTACATCAAAGG 59.722 41.667 0.00 0.00 0.00 3.11
112 113 5.437289 TGTCAAAGGTTGCTACATCAAAG 57.563 39.130 0.00 0.00 0.00 2.77
113 114 5.843673 TTGTCAAAGGTTGCTACATCAAA 57.156 34.783 0.00 0.00 0.00 2.69
114 115 5.359576 ACTTTGTCAAAGGTTGCTACATCAA 59.640 36.000 25.38 0.00 42.82 2.57
115 116 4.887071 ACTTTGTCAAAGGTTGCTACATCA 59.113 37.500 25.38 0.00 42.82 3.07
116 117 5.438761 ACTTTGTCAAAGGTTGCTACATC 57.561 39.130 25.38 0.00 42.82 3.06
117 118 5.451798 CCAACTTTGTCAAAGGTTGCTACAT 60.452 40.000 25.38 2.45 46.58 2.29
118 119 4.142271 CCAACTTTGTCAAAGGTTGCTACA 60.142 41.667 25.38 0.00 46.58 2.74
119 120 4.142249 ACCAACTTTGTCAAAGGTTGCTAC 60.142 41.667 25.38 0.00 46.58 3.58
120 121 4.020543 ACCAACTTTGTCAAAGGTTGCTA 58.979 39.130 25.38 0.00 46.58 3.49
121 122 2.831526 ACCAACTTTGTCAAAGGTTGCT 59.168 40.909 25.38 13.43 46.58 3.91
122 123 3.186909 GACCAACTTTGTCAAAGGTTGC 58.813 45.455 25.38 9.87 46.58 4.17
124 125 6.783708 TTATGACCAACTTTGTCAAAGGTT 57.216 33.333 25.38 15.57 42.82 3.50
125 126 6.569780 GTTTATGACCAACTTTGTCAAAGGT 58.430 36.000 25.38 18.81 42.82 3.50
141 142 6.408107 TTTAGGGGTTGTTTGGTTTATGAC 57.592 37.500 0.00 0.00 0.00 3.06
142 143 7.071321 ACAATTTAGGGGTTGTTTGGTTTATGA 59.929 33.333 0.00 0.00 35.13 2.15
143 144 7.220740 ACAATTTAGGGGTTGTTTGGTTTATG 58.779 34.615 0.00 0.00 35.13 1.90
144 145 7.381789 ACAATTTAGGGGTTGTTTGGTTTAT 57.618 32.000 0.00 0.00 35.13 1.40
145 146 6.809976 ACAATTTAGGGGTTGTTTGGTTTA 57.190 33.333 0.00 0.00 35.13 2.01
146 147 5.702065 ACAATTTAGGGGTTGTTTGGTTT 57.298 34.783 0.00 0.00 35.13 3.27
147 148 6.041182 GTCTACAATTTAGGGGTTGTTTGGTT 59.959 38.462 0.00 0.00 39.18 3.67
148 149 5.537295 GTCTACAATTTAGGGGTTGTTTGGT 59.463 40.000 0.00 0.00 39.18 3.67
149 150 5.536916 TGTCTACAATTTAGGGGTTGTTTGG 59.463 40.000 0.00 0.00 39.18 3.28
150 151 6.642707 TGTCTACAATTTAGGGGTTGTTTG 57.357 37.500 0.00 0.00 39.18 2.93
151 152 7.343574 AGTTTGTCTACAATTTAGGGGTTGTTT 59.656 33.333 0.00 0.00 39.18 2.83
152 153 6.837048 AGTTTGTCTACAATTTAGGGGTTGTT 59.163 34.615 0.00 0.00 39.18 2.83
153 154 6.370453 AGTTTGTCTACAATTTAGGGGTTGT 58.630 36.000 0.00 0.00 41.16 3.32
154 155 6.488683 TGAGTTTGTCTACAATTTAGGGGTTG 59.511 38.462 0.00 0.00 35.55 3.77
155 156 6.607019 TGAGTTTGTCTACAATTTAGGGGTT 58.393 36.000 0.00 0.00 35.55 4.11
156 157 6.195600 TGAGTTTGTCTACAATTTAGGGGT 57.804 37.500 0.00 0.00 35.55 4.95
157 158 7.703058 ATTGAGTTTGTCTACAATTTAGGGG 57.297 36.000 0.00 0.00 35.55 4.79
158 159 8.028938 CCAATTGAGTTTGTCTACAATTTAGGG 58.971 37.037 7.12 0.00 39.74 3.53
159 160 8.576442 ACCAATTGAGTTTGTCTACAATTTAGG 58.424 33.333 7.12 0.00 39.74 2.69
160 161 9.965824 AACCAATTGAGTTTGTCTACAATTTAG 57.034 29.630 7.12 0.00 39.74 1.85
161 162 9.959749 GAACCAATTGAGTTTGTCTACAATTTA 57.040 29.630 7.12 0.00 39.74 1.40
162 163 8.474025 TGAACCAATTGAGTTTGTCTACAATTT 58.526 29.630 7.12 0.00 39.74 1.82
163 164 8.006298 TGAACCAATTGAGTTTGTCTACAATT 57.994 30.769 7.12 0.00 41.53 2.32
164 165 7.581213 TGAACCAATTGAGTTTGTCTACAAT 57.419 32.000 7.12 0.00 35.55 2.71
165 166 7.094162 TGTTGAACCAATTGAGTTTGTCTACAA 60.094 33.333 7.12 6.23 0.00 2.41
166 167 6.375736 TGTTGAACCAATTGAGTTTGTCTACA 59.624 34.615 7.12 8.24 0.00 2.74
167 168 6.791303 TGTTGAACCAATTGAGTTTGTCTAC 58.209 36.000 7.12 6.09 0.00 2.59
208 209 6.007076 TGTATGAACAATGTGGTTACACCAT 58.993 36.000 0.00 0.00 40.96 3.55
211 212 7.119116 TCTCATGTATGAACAATGTGGTTACAC 59.881 37.037 5.19 0.00 42.77 2.90
232 233 4.093011 ACTCCTGCTAGTTGTTCTCTCAT 58.907 43.478 0.00 0.00 0.00 2.90
268 269 0.107654 GAGATTCCCAACCCCGACTG 60.108 60.000 0.00 0.00 0.00 3.51
269 270 0.546747 TGAGATTCCCAACCCCGACT 60.547 55.000 0.00 0.00 0.00 4.18
270 271 0.546598 ATGAGATTCCCAACCCCGAC 59.453 55.000 0.00 0.00 0.00 4.79
271 272 1.766496 GTATGAGATTCCCAACCCCGA 59.234 52.381 0.00 0.00 0.00 5.14
274 275 2.158608 CCAGGTATGAGATTCCCAACCC 60.159 54.545 0.00 0.00 0.00 4.11
276 277 4.646572 GATCCAGGTATGAGATTCCCAAC 58.353 47.826 0.00 0.00 0.00 3.77
277 278 3.324846 CGATCCAGGTATGAGATTCCCAA 59.675 47.826 0.00 0.00 0.00 4.12
278 279 2.899900 CGATCCAGGTATGAGATTCCCA 59.100 50.000 0.00 0.00 0.00 4.37
279 280 2.900546 ACGATCCAGGTATGAGATTCCC 59.099 50.000 0.00 0.00 0.00 3.97
280 281 4.082136 GGTACGATCCAGGTATGAGATTCC 60.082 50.000 0.00 0.00 0.00 3.01
281 282 4.082136 GGGTACGATCCAGGTATGAGATTC 60.082 50.000 0.00 0.00 0.00 2.52
288 289 1.325355 CACGGGTACGATCCAGGTAT 58.675 55.000 0.00 0.00 44.60 2.73
299 300 0.250166 AAGACAAGGCACACGGGTAC 60.250 55.000 0.00 0.00 0.00 3.34
303 304 1.878953 AGTAAAGACAAGGCACACGG 58.121 50.000 0.00 0.00 0.00 4.94
310 311 6.405278 AACCAATTCCAAGTAAAGACAAGG 57.595 37.500 0.00 0.00 0.00 3.61
319 320 7.982354 ACGAAAAATCAAAACCAATTCCAAGTA 59.018 29.630 0.00 0.00 0.00 2.24
321 322 7.125113 CACGAAAAATCAAAACCAATTCCAAG 58.875 34.615 0.00 0.00 0.00 3.61
322 323 6.595716 ACACGAAAAATCAAAACCAATTCCAA 59.404 30.769 0.00 0.00 0.00 3.53
336 337 7.803189 TCTGAAGAATAGCAAACACGAAAAATC 59.197 33.333 0.00 0.00 0.00 2.17
342 344 3.673338 CGTCTGAAGAATAGCAAACACGA 59.327 43.478 0.00 0.00 0.00 4.35
344 346 3.424962 GGCGTCTGAAGAATAGCAAACAC 60.425 47.826 0.00 0.00 0.00 3.32
349 351 1.550524 ACAGGCGTCTGAAGAATAGCA 59.449 47.619 26.48 0.00 43.49 3.49
372 374 5.711976 AGAGACGTCATTTCATGGGAATTTT 59.288 36.000 19.50 0.00 31.93 1.82
375 377 4.494091 AGAGACGTCATTTCATGGGAAT 57.506 40.909 19.50 0.00 31.93 3.01
382 384 6.285224 TCTTTAACCAAGAGACGTCATTTCA 58.715 36.000 19.50 0.00 36.51 2.69
400 402 8.857694 ATTTCACCTTACTCCGAATTCTTTAA 57.142 30.769 3.52 0.00 0.00 1.52
403 405 7.119846 CAGAATTTCACCTTACTCCGAATTCTT 59.880 37.037 3.52 0.00 0.00 2.52
508 549 3.495670 TTGGTTTTCTGGTCGTTGTTG 57.504 42.857 0.00 0.00 0.00 3.33
509 550 4.729227 AATTGGTTTTCTGGTCGTTGTT 57.271 36.364 0.00 0.00 0.00 2.83
541 582 2.156917 CAATGTCCTGCTTCTCTTGCA 58.843 47.619 0.00 0.00 38.81 4.08
582 623 6.151817 GGAAGGATGCAGTTCTGTTCTTTTAT 59.848 38.462 0.00 0.00 0.00 1.40
895 963 0.249031 GAACTTGGTGTTGTGCAGGC 60.249 55.000 0.00 0.00 39.30 4.85
938 1008 5.393678 GCCGGCTTATATCTAGAAAGAGGAG 60.394 48.000 22.15 5.03 34.49 3.69
945 1015 3.507411 ACAGGCCGGCTTATATCTAGAA 58.493 45.455 28.56 0.00 0.00 2.10
975 1052 5.171476 GTTGCAATGAACTCTACAGCTAGA 58.829 41.667 0.59 0.00 0.00 2.43
1161 1254 2.124320 GCCTCCGCATTAGGGCAA 60.124 61.111 0.00 0.00 43.59 4.52
1527 1717 0.951040 CCACCGCACTCCTTCTCAAC 60.951 60.000 0.00 0.00 0.00 3.18
2289 2482 8.545229 TGCAAAAATGGACCAATAATACAAAG 57.455 30.769 0.00 0.00 0.00 2.77
2314 2510 9.559732 TCCAAATATTTTCGATACAGATGTGAT 57.440 29.630 0.00 0.00 0.00 3.06
2495 2888 6.690098 TGAAAGTGTTATAGACGCGATAAGAC 59.310 38.462 15.93 15.06 43.57 3.01
2498 2891 9.177304 CTTATGAAAGTGTTATAGACGCGATAA 57.823 33.333 15.93 3.48 43.57 1.75
2499 2892 8.562052 TCTTATGAAAGTGTTATAGACGCGATA 58.438 33.333 15.93 5.56 43.57 2.92
2500 2893 7.423199 TCTTATGAAAGTGTTATAGACGCGAT 58.577 34.615 15.93 2.85 43.57 4.58
2501 2894 6.788243 TCTTATGAAAGTGTTATAGACGCGA 58.212 36.000 15.93 0.00 43.57 5.87
2502 2895 6.345093 GCTCTTATGAAAGTGTTATAGACGCG 60.345 42.308 3.53 3.53 43.57 6.01
2594 2994 2.052690 GCTCCTGGAGGCACGACTA 61.053 63.158 24.43 0.00 34.44 2.59
2682 3093 2.728015 CAAAAACGCGTTCCCGGC 60.728 61.111 26.77 0.00 33.68 6.13
2683 3094 1.369568 GTCAAAAACGCGTTCCCGG 60.370 57.895 26.77 14.96 33.68 5.73
2684 3095 0.926628 GTGTCAAAAACGCGTTCCCG 60.927 55.000 26.77 15.87 37.07 5.14
2809 3245 0.883814 GAGGCATCGATGAAGGCTGG 60.884 60.000 29.20 0.00 36.36 4.85


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

AutoCloner maintained by Alex Coulton.