Multiple sequence alignment - TraesCS7D01G121000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G121000 chr7D 100.000 6234 0 0 1 6234 75068179 75061946 0.000000e+00 11513.0
1 TraesCS7D01G121000 chr7D 82.375 783 105 21 3126 3898 75129449 75128690 0.000000e+00 651.0
2 TraesCS7D01G121000 chr7D 82.876 765 83 17 2157 2893 75130296 75129552 1.460000e-180 643.0
3 TraesCS7D01G121000 chr7D 89.137 313 15 3 1422 1716 63446874 63446563 7.630000e-99 372.0
4 TraesCS7D01G121000 chr7D 88.356 146 17 0 2947 3092 75129586 75129441 6.420000e-40 176.0
5 TraesCS7D01G121000 chr7D 92.157 51 3 1 2074 2123 29945895 29945845 3.120000e-08 71.3
6 TraesCS7D01G121000 chr7D 100.000 32 0 0 460 491 470275572 470275541 6.750000e-05 60.2
7 TraesCS7D01G121000 chr7B 96.805 5290 156 8 951 6233 19948304 19943021 0.000000e+00 8820.0
8 TraesCS7D01G121000 chr7B 92.159 1505 118 0 3393 4897 20058234 20056730 0.000000e+00 2126.0
9 TraesCS7D01G121000 chr7B 93.725 494 23 3 2922 3408 20060687 20060195 0.000000e+00 734.0
10 TraesCS7D01G121000 chr7B 83.703 767 81 18 2157 2893 20631815 20631063 0.000000e+00 684.0
11 TraesCS7D01G121000 chr7B 82.930 785 92 25 3129 3898 20630957 20630200 0.000000e+00 669.0
12 TraesCS7D01G121000 chr7B 86.519 586 47 11 2291 2850 20061379 20060800 3.190000e-172 616.0
13 TraesCS7D01G121000 chr7B 79.859 710 89 32 284 949 19949166 19948467 2.630000e-128 470.0
14 TraesCS7D01G121000 chr7B 93.392 227 13 1 1490 1714 740381078 740380852 1.000000e-87 335.0
15 TraesCS7D01G121000 chr7B 92.982 228 14 1 1490 1715 740170790 740170563 1.300000e-86 331.0
16 TraesCS7D01G121000 chr7B 82.656 369 58 6 4941 5308 20056714 20056351 7.800000e-84 322.0
17 TraesCS7D01G121000 chr7B 77.600 125 15 5 5433 5544 20056333 20056209 5.220000e-06 63.9
18 TraesCS7D01G121000 chr7A 96.361 3820 93 16 1720 5514 78718645 78714847 0.000000e+00 6242.0
19 TraesCS7D01G121000 chr7A 92.537 1983 139 4 2922 4897 78836607 78834627 0.000000e+00 2833.0
20 TraesCS7D01G121000 chr7A 86.497 748 78 11 2157 2900 78837462 78836734 0.000000e+00 800.0
21 TraesCS7D01G121000 chr7A 90.556 593 47 5 5643 6234 78714826 78714242 0.000000e+00 776.0
22 TraesCS7D01G121000 chr7A 90.741 486 25 7 958 1426 78719156 78718674 1.140000e-176 630.0
23 TraesCS7D01G121000 chr7A 82.656 369 58 5 4939 5306 78834613 78834250 7.800000e-84 322.0
24 TraesCS7D01G121000 chr7A 79.443 287 38 9 1881 2151 78837812 78837531 3.840000e-42 183.0
25 TraesCS7D01G121000 chrUn 82.409 739 82 21 2157 2862 155967375 155968098 8.940000e-168 601.0
26 TraesCS7D01G121000 chrUn 84.794 559 61 10 3340 3895 155968166 155968703 1.980000e-149 540.0
27 TraesCS7D01G121000 chrUn 87.859 313 20 2 1424 1718 103114080 103114392 9.940000e-93 351.0
28 TraesCS7D01G121000 chrUn 87.960 299 18 2 1421 1701 332581547 332581845 2.780000e-88 337.0
29 TraesCS7D01G121000 chrUn 92.308 52 4 0 4896 4947 71203255 71203204 2.410000e-09 75.0
30 TraesCS7D01G121000 chrUn 92.308 52 4 0 4896 4947 326194389 326194338 2.410000e-09 75.0
31 TraesCS7D01G121000 chr4D 89.320 309 15 2 1423 1713 464509059 464509367 7.630000e-99 372.0
32 TraesCS7D01G121000 chr4D 84.038 213 32 2 1972 2184 134267633 134267843 2.950000e-48 204.0
33 TraesCS7D01G121000 chr4D 97.727 44 1 0 4896 4939 497058712 497058755 6.700000e-10 76.8
34 TraesCS7D01G121000 chr4D 95.455 44 2 0 4895 4938 504090795 504090752 3.120000e-08 71.3
35 TraesCS7D01G121000 chr5D 87.164 335 18 8 1421 1735 45488306 45487977 2.140000e-94 357.0
36 TraesCS7D01G121000 chr5D 80.000 425 71 8 2314 2736 45594004 45593592 1.020000e-77 302.0
37 TraesCS7D01G121000 chr5D 92.453 53 2 1 4888 4940 122198425 122198475 2.410000e-09 75.0
38 TraesCS7D01G121000 chr5D 93.182 44 3 0 535 578 305894206 305894163 1.450000e-06 65.8
39 TraesCS7D01G121000 chr5D 100.000 30 0 0 462 491 349873148 349873119 8.730000e-04 56.5
40 TraesCS7D01G121000 chr1D 88.387 310 17 4 1422 1713 487951457 487951765 7.690000e-94 355.0
41 TraesCS7D01G121000 chr1D 97.674 43 1 0 4896 4938 78965909 78965867 2.410000e-09 75.0
42 TraesCS7D01G121000 chr5A 87.987 308 18 5 1424 1712 679143396 679143703 4.630000e-91 346.0
43 TraesCS7D01G121000 chr6A 93.805 226 12 1 1490 1713 123460218 123459993 7.740000e-89 339.0
44 TraesCS7D01G121000 chr6A 85.342 307 27 2 1422 1710 569997542 569997236 1.020000e-77 302.0
45 TraesCS7D01G121000 chr3D 87.960 299 18 2 1421 1701 30415964 30415666 2.780000e-88 337.0
46 TraesCS7D01G121000 chr3D 97.297 37 1 0 455 491 348919847 348919811 5.220000e-06 63.9
47 TraesCS7D01G121000 chr3A 87.960 299 18 2 1421 1701 43293763 43293465 2.780000e-88 337.0
48 TraesCS7D01G121000 chr5B 93.333 225 13 1 1491 1713 488119986 488120210 1.300000e-86 331.0
49 TraesCS7D01G121000 chr2D 86.131 137 3 1 1421 1541 521875696 521875832 3.920000e-27 134.0
50 TraesCS7D01G121000 chr4B 89.583 96 10 0 2403 2498 670058035 670057940 8.490000e-24 122.0
51 TraesCS7D01G121000 chr4A 95.652 46 2 0 4893 4938 647209302 647209347 2.410000e-09 75.0
52 TraesCS7D01G121000 chr3B 96.970 33 1 0 765 797 381025185 381025217 8.730000e-04 56.5


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 TraesCS7D01G121000 chr7D 75061946 75068179 6233 True 11513.000000 11513 100.000000 1 6234 1 chr7D.!!$R3 6233
1 TraesCS7D01G121000 chr7D 75128690 75130296 1606 True 490.000000 651 84.535667 2157 3898 3 chr7D.!!$R5 1741
2 TraesCS7D01G121000 chr7B 19943021 19949166 6145 True 4645.000000 8820 88.332000 284 6233 2 chr7B.!!$R3 5949
3 TraesCS7D01G121000 chr7B 20056209 20061379 5170 True 772.380000 2126 86.531800 2291 5544 5 chr7B.!!$R4 3253
4 TraesCS7D01G121000 chr7B 20630200 20631815 1615 True 676.500000 684 83.316500 2157 3898 2 chr7B.!!$R5 1741
5 TraesCS7D01G121000 chr7A 78714242 78719156 4914 True 2549.333333 6242 92.552667 958 6234 3 chr7A.!!$R1 5276
6 TraesCS7D01G121000 chr7A 78834250 78837812 3562 True 1034.500000 2833 85.283250 1881 5306 4 chr7A.!!$R2 3425
7 TraesCS7D01G121000 chrUn 155967375 155968703 1328 False 570.500000 601 83.601500 2157 3895 2 chrUn.!!$F3 1738

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
121 122 0.105709 GAAGAGAGGGGAGAGGGAGG 60.106 65.000 0.00 0.00 0.00 4.30 F
124 125 0.114364 GAGAGGGGAGAGGGAGGATC 59.886 65.000 0.00 0.00 0.00 3.36 F
126 127 0.114364 GAGGGGAGAGGGAGGATCTC 59.886 65.000 0.00 0.00 42.08 2.75 F
1331 1548 0.244994 CTTATCCCTCGCAGGATCCG 59.755 60.000 5.98 2.47 43.48 4.18 F
2613 2938 1.414550 GAGGTAGCATTCCAGTCCTCC 59.585 57.143 0.00 0.00 36.46 4.30 F
3262 3820 1.056700 ATCTAACTGGAGGGCCGCAT 61.057 55.000 10.15 0.00 36.79 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1534 2.202932 CAACGGATCCTGCGAGGG 60.203 66.667 10.75 0.00 35.59 4.30 R
2057 2297 2.888594 TGTTCACAGCTTCGGTATAGC 58.111 47.619 0.00 0.00 38.93 2.97 R
2613 2938 6.146216 TGTTATAATGTCAACAAGGCAAACG 58.854 36.000 0.00 0.00 34.09 3.60 R
3262 3820 3.773560 ACCAATAGGGCTACTTTGCAAA 58.226 40.909 12.14 12.14 42.05 3.68 R
4960 7530 4.338682 ACGAGTGCCTAGAAATAGACGAAT 59.661 41.667 0.00 0.00 0.00 3.34 R
5343 7913 1.198637 AGTACTACGCAGTTGACGGAC 59.801 52.381 0.00 0.00 37.78 4.79 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
18 19 4.971125 GCCCACCTAGCCGCGATC 62.971 72.222 8.23 0.00 0.00 3.69
19 20 4.301027 CCCACCTAGCCGCGATCC 62.301 72.222 8.23 0.00 0.00 3.36
20 21 4.301027 CCACCTAGCCGCGATCCC 62.301 72.222 8.23 0.00 0.00 3.85
21 22 4.301027 CACCTAGCCGCGATCCCC 62.301 72.222 8.23 0.00 0.00 4.81
22 23 4.541648 ACCTAGCCGCGATCCCCT 62.542 66.667 8.23 0.00 0.00 4.79
23 24 2.282958 CCTAGCCGCGATCCCCTA 60.283 66.667 8.23 0.00 0.00 3.53
24 25 1.682684 CCTAGCCGCGATCCCCTAT 60.683 63.158 8.23 0.00 0.00 2.57
25 26 1.668101 CCTAGCCGCGATCCCCTATC 61.668 65.000 8.23 0.00 0.00 2.08
26 27 1.668101 CTAGCCGCGATCCCCTATCC 61.668 65.000 8.23 0.00 0.00 2.59
27 28 4.083862 GCCGCGATCCCCTATCCC 62.084 72.222 8.23 0.00 0.00 3.85
28 29 2.603473 CCGCGATCCCCTATCCCA 60.603 66.667 8.23 0.00 0.00 4.37
29 30 2.650116 CCGCGATCCCCTATCCCAG 61.650 68.421 8.23 0.00 0.00 4.45
30 31 2.650116 CGCGATCCCCTATCCCAGG 61.650 68.421 0.00 0.00 45.07 4.45
55 56 4.063967 TGGCTACTCCACGCGGTG 62.064 66.667 12.47 6.37 40.72 4.94
56 57 3.755628 GGCTACTCCACGCGGTGA 61.756 66.667 12.47 5.22 35.23 4.02
57 58 2.506438 GCTACTCCACGCGGTGAC 60.506 66.667 12.47 0.00 35.23 3.67
69 70 4.436998 GGTGACGACGAGGCCCAG 62.437 72.222 0.00 0.00 0.00 4.45
72 73 4.803426 GACGACGAGGCCCAGCTG 62.803 72.222 6.78 6.78 0.00 4.24
92 93 2.124695 GGTGGCCCGGATCTTGAC 60.125 66.667 0.73 0.00 0.00 3.18
93 94 2.124695 GTGGCCCGGATCTTGACC 60.125 66.667 0.73 0.00 0.00 4.02
110 111 1.435515 CCGAAGGCGAGAAGAGAGG 59.564 63.158 0.00 0.00 46.14 3.69
111 112 1.435515 CGAAGGCGAGAAGAGAGGG 59.564 63.158 0.00 0.00 40.82 4.30
112 113 1.819905 GAAGGCGAGAAGAGAGGGG 59.180 63.158 0.00 0.00 0.00 4.79
113 114 0.684805 GAAGGCGAGAAGAGAGGGGA 60.685 60.000 0.00 0.00 0.00 4.81
114 115 0.686112 AAGGCGAGAAGAGAGGGGAG 60.686 60.000 0.00 0.00 0.00 4.30
115 116 1.076632 GGCGAGAAGAGAGGGGAGA 60.077 63.158 0.00 0.00 0.00 3.71
116 117 1.106944 GGCGAGAAGAGAGGGGAGAG 61.107 65.000 0.00 0.00 0.00 3.20
117 118 1.106944 GCGAGAAGAGAGGGGAGAGG 61.107 65.000 0.00 0.00 0.00 3.69
118 119 0.467290 CGAGAAGAGAGGGGAGAGGG 60.467 65.000 0.00 0.00 0.00 4.30
119 120 0.930726 GAGAAGAGAGGGGAGAGGGA 59.069 60.000 0.00 0.00 0.00 4.20
120 121 0.933700 AGAAGAGAGGGGAGAGGGAG 59.066 60.000 0.00 0.00 0.00 4.30
121 122 0.105709 GAAGAGAGGGGAGAGGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
122 123 0.556380 AAGAGAGGGGAGAGGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
123 124 0.330431 AGAGAGGGGAGAGGGAGGAT 60.330 60.000 0.00 0.00 0.00 3.24
124 125 0.114364 GAGAGGGGAGAGGGAGGATC 59.886 65.000 0.00 0.00 0.00 3.36
125 126 0.330431 AGAGGGGAGAGGGAGGATCT 60.330 60.000 0.00 0.00 33.73 2.75
126 127 0.114364 GAGGGGAGAGGGAGGATCTC 59.886 65.000 0.00 0.00 42.08 2.75
134 135 3.934962 GGAGGATCTCCCCGCAGC 61.935 72.222 2.65 0.00 44.36 5.25
135 136 3.934962 GAGGATCTCCCCGCAGCC 61.935 72.222 0.00 0.00 36.42 4.85
229 230 4.308458 CGTGTCGCCCAAGGTGGA 62.308 66.667 0.00 0.00 40.96 4.02
230 231 2.668550 GTGTCGCCCAAGGTGGAC 60.669 66.667 0.00 0.00 40.96 4.02
231 232 4.308458 TGTCGCCCAAGGTGGACG 62.308 66.667 0.00 0.00 40.96 4.79
232 233 3.998672 GTCGCCCAAGGTGGACGA 61.999 66.667 1.26 1.26 40.96 4.20
233 234 3.998672 TCGCCCAAGGTGGACGAC 61.999 66.667 1.26 0.00 40.96 4.34
236 237 4.308458 CCCAAGGTGGACGACGCA 62.308 66.667 0.00 0.00 40.96 5.24
237 238 2.738521 CCAAGGTGGACGACGCAG 60.739 66.667 0.00 0.00 40.96 5.18
238 239 2.738521 CAAGGTGGACGACGCAGG 60.739 66.667 0.00 0.00 0.00 4.85
239 240 2.915659 AAGGTGGACGACGCAGGA 60.916 61.111 0.00 0.00 0.00 3.86
240 241 2.932234 AAGGTGGACGACGCAGGAG 61.932 63.158 0.00 0.00 0.00 3.69
241 242 3.681835 GGTGGACGACGCAGGAGT 61.682 66.667 0.00 0.00 0.00 3.85
242 243 2.338984 GTGGACGACGCAGGAGTT 59.661 61.111 0.00 0.00 0.00 3.01
243 244 2.022129 GTGGACGACGCAGGAGTTG 61.022 63.158 0.00 0.00 0.00 3.16
244 245 2.338984 GGACGACGCAGGAGTTGT 59.661 61.111 0.00 0.00 41.16 3.32
245 246 1.300697 GGACGACGCAGGAGTTGTT 60.301 57.895 0.00 0.00 38.75 2.83
246 247 1.282930 GGACGACGCAGGAGTTGTTC 61.283 60.000 0.00 0.00 38.75 3.18
270 271 1.324383 TTTTTGTTCTCGCTTCCCCC 58.676 50.000 0.00 0.00 0.00 5.40
271 272 0.887387 TTTTGTTCTCGCTTCCCCCG 60.887 55.000 0.00 0.00 0.00 5.73
272 273 1.760479 TTTGTTCTCGCTTCCCCCGA 61.760 55.000 0.00 0.00 0.00 5.14
273 274 1.550130 TTGTTCTCGCTTCCCCCGAT 61.550 55.000 0.00 0.00 33.83 4.18
274 275 1.227292 GTTCTCGCTTCCCCCGATC 60.227 63.158 0.00 0.00 33.83 3.69
275 276 2.432300 TTCTCGCTTCCCCCGATCC 61.432 63.158 0.00 0.00 33.83 3.36
276 277 3.930012 CTCGCTTCCCCCGATCCC 61.930 72.222 0.00 0.00 33.83 3.85
279 280 3.242291 GCTTCCCCCGATCCCGAT 61.242 66.667 0.00 0.00 38.22 4.18
280 281 3.060866 CTTCCCCCGATCCCGATC 58.939 66.667 0.00 0.00 38.22 3.69
281 282 1.534235 CTTCCCCCGATCCCGATCT 60.534 63.158 3.35 0.00 38.22 2.75
282 283 1.821061 CTTCCCCCGATCCCGATCTG 61.821 65.000 3.35 0.00 38.22 2.90
295 296 7.138081 CGATCCCGATCTGATCATAAAGATAG 58.862 42.308 17.19 7.83 38.83 2.08
298 299 9.874195 ATCCCGATCTGATCATAAAGATAGATA 57.126 33.333 17.19 0.00 37.00 1.98
409 410 5.790593 AGACAAGTCTCGTATTTAAGGCAA 58.209 37.500 0.00 0.00 34.17 4.52
410 411 5.869888 AGACAAGTCTCGTATTTAAGGCAAG 59.130 40.000 0.00 0.00 34.17 4.01
465 466 0.251354 TGCCCTGAGACATCTTGAGC 59.749 55.000 0.00 0.00 0.00 4.26
472 473 0.534412 AGACATCTTGAGCGTGGAGG 59.466 55.000 0.00 0.00 0.00 4.30
475 476 0.392193 CATCTTGAGCGTGGAGGCTT 60.392 55.000 0.00 0.00 44.93 4.35
476 477 0.392193 ATCTTGAGCGTGGAGGCTTG 60.392 55.000 0.00 0.00 44.93 4.01
503 524 0.249398 GGTCCGGTATGCACAGACTT 59.751 55.000 0.00 0.00 0.00 3.01
504 525 1.641577 GTCCGGTATGCACAGACTTC 58.358 55.000 0.00 0.00 0.00 3.01
506 527 2.426024 GTCCGGTATGCACAGACTTCTA 59.574 50.000 0.00 0.00 0.00 2.10
508 529 2.223829 CCGGTATGCACAGACTTCTAGG 60.224 54.545 0.00 0.00 0.00 3.02
517 538 6.516718 TGCACAGACTTCTAGGCTAATATTC 58.483 40.000 0.00 0.00 26.27 1.75
521 542 9.255304 CACAGACTTCTAGGCTAATATTCTTTC 57.745 37.037 0.00 0.00 26.27 2.62
522 543 8.982723 ACAGACTTCTAGGCTAATATTCTTTCA 58.017 33.333 0.00 0.00 26.27 2.69
530 551 7.771927 AGGCTAATATTCTTTCATGATTGGG 57.228 36.000 0.00 0.00 0.00 4.12
531 552 6.723052 AGGCTAATATTCTTTCATGATTGGGG 59.277 38.462 0.00 0.00 0.00 4.96
532 553 6.494835 GGCTAATATTCTTTCATGATTGGGGT 59.505 38.462 0.00 0.00 0.00 4.95
533 554 7.669722 GGCTAATATTCTTTCATGATTGGGGTA 59.330 37.037 0.00 0.00 0.00 3.69
549 571 7.722285 TGATTGGGGTATAAAAACTAGCCATAC 59.278 37.037 0.00 0.00 38.27 2.39
553 575 7.058525 GGGGTATAAAAACTAGCCATACTTGT 58.941 38.462 0.00 0.00 38.27 3.16
554 576 7.228108 GGGGTATAAAAACTAGCCATACTTGTC 59.772 40.741 0.00 0.00 38.27 3.18
557 579 9.043079 GTATAAAAACTAGCCATACTTGTCTCC 57.957 37.037 0.00 0.00 32.87 3.71
563 585 4.640771 AGCCATACTTGTCTCCTTTTGA 57.359 40.909 0.00 0.00 0.00 2.69
564 586 5.184892 AGCCATACTTGTCTCCTTTTGAT 57.815 39.130 0.00 0.00 0.00 2.57
571 593 6.566197 ACTTGTCTCCTTTTGATTGTGATC 57.434 37.500 0.00 0.00 0.00 2.92
577 599 3.053693 TCCTTTTGATTGTGATCGGGGAT 60.054 43.478 0.00 0.00 34.91 3.85
583 605 3.117926 TGATTGTGATCGGGGATTGATGT 60.118 43.478 0.00 0.00 34.91 3.06
594 616 1.845809 GATTGATGTGATCCGGCGCC 61.846 60.000 19.07 19.07 0.00 6.53
610 632 1.964373 GCCCGTGTTGTGACCGAAT 60.964 57.895 0.00 0.00 0.00 3.34
614 636 1.438651 CGTGTTGTGACCGAATGGAT 58.561 50.000 0.00 0.00 39.21 3.41
619 641 3.501828 TGTTGTGACCGAATGGATTTGAG 59.498 43.478 0.00 0.00 39.21 3.02
623 645 4.215399 TGTGACCGAATGGATTTGAGTTTC 59.785 41.667 0.00 0.00 39.21 2.78
636 658 3.907894 TGAGTTTCAAATTGCCCGTAC 57.092 42.857 0.00 0.00 0.00 3.67
641 663 4.822896 AGTTTCAAATTGCCCGTACTAACA 59.177 37.500 0.00 0.00 0.00 2.41
644 666 5.968528 TCAAATTGCCCGTACTAACAAAT 57.031 34.783 0.00 0.00 0.00 2.32
645 667 5.704888 TCAAATTGCCCGTACTAACAAATG 58.295 37.500 0.00 0.00 0.00 2.32
653 675 5.490159 CCCGTACTAACAAATGTTTAGGGA 58.510 41.667 14.07 0.00 39.31 4.20
657 679 8.823818 CCGTACTAACAAATGTTTAGGGAATAG 58.176 37.037 3.85 0.00 39.31 1.73
659 681 7.316544 ACTAACAAATGTTTAGGGAATAGCG 57.683 36.000 3.85 0.00 39.31 4.26
665 687 3.602483 TGTTTAGGGAATAGCGTTGGAC 58.398 45.455 0.00 0.00 0.00 4.02
672 694 1.880819 AATAGCGTTGGACGACCGGT 61.881 55.000 6.92 6.92 46.05 5.28
674 696 2.086251 TAGCGTTGGACGACCGGTTT 62.086 55.000 9.42 0.00 46.05 3.27
675 697 2.946752 GCGTTGGACGACCGGTTTC 61.947 63.158 9.42 8.75 46.05 2.78
676 698 1.300388 CGTTGGACGACCGGTTTCT 60.300 57.895 9.42 0.00 46.05 2.52
677 699 1.554042 CGTTGGACGACCGGTTTCTG 61.554 60.000 9.42 1.53 46.05 3.02
678 700 1.595929 TTGGACGACCGGTTTCTGC 60.596 57.895 9.42 0.00 39.42 4.26
681 703 1.359459 GGACGACCGGTTTCTGCATC 61.359 60.000 9.42 0.00 0.00 3.91
683 705 1.375396 CGACCGGTTTCTGCATCCA 60.375 57.895 9.42 0.00 0.00 3.41
685 707 0.734889 GACCGGTTTCTGCATCCATG 59.265 55.000 9.42 0.00 0.00 3.66
687 709 0.734889 CCGGTTTCTGCATCCATGTC 59.265 55.000 0.00 0.00 0.00 3.06
689 711 1.838112 GGTTTCTGCATCCATGTCCA 58.162 50.000 0.00 0.00 0.00 4.02
692 714 3.018856 GTTTCTGCATCCATGTCCATGA 58.981 45.455 8.82 0.00 41.20 3.07
694 716 3.588210 TCTGCATCCATGTCCATGAAT 57.412 42.857 8.82 0.00 41.20 2.57
696 718 5.051409 TCTGCATCCATGTCCATGAATTA 57.949 39.130 8.82 0.00 41.20 1.40
697 719 5.447757 TCTGCATCCATGTCCATGAATTAA 58.552 37.500 8.82 0.00 41.20 1.40
700 722 5.244402 TGCATCCATGTCCATGAATTAATCC 59.756 40.000 8.82 0.00 41.20 3.01
701 723 5.620654 GCATCCATGTCCATGAATTAATCCG 60.621 44.000 8.82 0.00 41.20 4.18
702 724 5.303259 TCCATGTCCATGAATTAATCCGA 57.697 39.130 8.82 0.00 41.20 4.55
704 726 5.071653 TCCATGTCCATGAATTAATCCGAGA 59.928 40.000 8.82 0.00 41.20 4.04
705 727 5.942236 CCATGTCCATGAATTAATCCGAGAT 59.058 40.000 8.82 0.00 41.20 2.75
707 729 4.756642 TGTCCATGAATTAATCCGAGATGC 59.243 41.667 0.00 0.00 0.00 3.91
708 730 3.996363 TCCATGAATTAATCCGAGATGCG 59.004 43.478 0.00 0.00 40.47 4.73
709 731 3.748048 CCATGAATTAATCCGAGATGCGT 59.252 43.478 0.00 0.00 38.67 5.24
713 755 5.838529 TGAATTAATCCGAGATGCGTTAGA 58.161 37.500 0.00 0.00 38.67 2.10
729 771 5.123936 GCGTTAGATAAAAATGGAGGGAGT 58.876 41.667 0.00 0.00 0.00 3.85
731 773 6.424207 GCGTTAGATAAAAATGGAGGGAGTAG 59.576 42.308 0.00 0.00 0.00 2.57
732 774 6.929606 CGTTAGATAAAAATGGAGGGAGTAGG 59.070 42.308 0.00 0.00 0.00 3.18
746 788 4.162509 AGGGAGTAGGTAGCATTCACTTTC 59.837 45.833 0.00 0.00 0.00 2.62
747 789 4.443621 GGAGTAGGTAGCATTCACTTTCC 58.556 47.826 0.00 0.00 0.00 3.13
783 825 1.872952 CAGTGGTCAAATCAGCGTTGA 59.127 47.619 3.86 3.86 37.81 3.18
807 849 0.321996 GCTCCTTCCCGTTCTGTTCT 59.678 55.000 0.00 0.00 0.00 3.01
836 878 3.012518 CAGCAATAACTGGTCTCCCTTG 58.987 50.000 0.00 0.00 31.85 3.61
851 893 0.605319 CCTTGGAGCGGCAAACACTA 60.605 55.000 1.45 0.00 0.00 2.74
853 895 1.234615 TTGGAGCGGCAAACACTAGC 61.235 55.000 1.45 0.00 0.00 3.42
854 896 1.671054 GGAGCGGCAAACACTAGCA 60.671 57.895 1.45 0.00 0.00 3.49
855 897 1.639298 GGAGCGGCAAACACTAGCAG 61.639 60.000 1.45 0.00 0.00 4.24
856 898 0.670546 GAGCGGCAAACACTAGCAGA 60.671 55.000 1.45 0.00 0.00 4.26
857 899 0.671781 AGCGGCAAACACTAGCAGAG 60.672 55.000 1.45 0.00 0.00 3.35
860 902 0.606401 GGCAAACACTAGCAGAGGCA 60.606 55.000 0.00 0.00 44.61 4.75
861 903 0.801251 GCAAACACTAGCAGAGGCAG 59.199 55.000 0.00 0.00 44.61 4.85
862 904 1.609061 GCAAACACTAGCAGAGGCAGA 60.609 52.381 0.00 0.00 44.61 4.26
863 905 2.344950 CAAACACTAGCAGAGGCAGAG 58.655 52.381 0.00 0.00 44.61 3.35
864 906 0.248843 AACACTAGCAGAGGCAGAGC 59.751 55.000 0.00 0.00 44.61 4.09
888 930 2.668144 AGGGGTCGGTTTGAAATTCA 57.332 45.000 0.00 0.00 0.00 2.57
949 992 2.042843 GGAGCCTCTTCCCCGAGA 60.043 66.667 0.00 0.00 32.74 4.04
951 994 2.756283 AGCCTCTTCCCCGAGACG 60.756 66.667 0.00 0.00 32.74 4.18
952 995 3.069318 GCCTCTTCCCCGAGACGT 61.069 66.667 0.00 0.00 32.74 4.34
954 997 2.416432 CCTCTTCCCCGAGACGTCC 61.416 68.421 13.01 2.76 32.74 4.79
957 1000 2.993264 TTCCCCGAGACGTCCACC 60.993 66.667 13.01 0.76 0.00 4.61
958 1001 3.813606 TTCCCCGAGACGTCCACCA 62.814 63.158 13.01 0.00 0.00 4.17
959 1002 4.065281 CCCCGAGACGTCCACCAC 62.065 72.222 13.01 0.00 0.00 4.16
960 1003 3.299977 CCCGAGACGTCCACCACA 61.300 66.667 13.01 0.00 0.00 4.17
961 1004 2.049433 CCGAGACGTCCACCACAC 60.049 66.667 13.01 0.00 0.00 3.82
962 1005 2.049433 CGAGACGTCCACCACACC 60.049 66.667 13.01 0.00 0.00 4.16
963 1006 2.342648 GAGACGTCCACCACACCC 59.657 66.667 13.01 0.00 0.00 4.61
964 1007 3.569049 GAGACGTCCACCACACCCG 62.569 68.421 13.01 0.00 0.00 5.28
1146 1354 2.306847 GAGAGCTCGAGGAAGGAGATT 58.693 52.381 15.58 0.00 33.27 2.40
1247 1455 8.588290 ATCTGTGAAGTTGATTAGTCTCTACT 57.412 34.615 0.00 0.00 39.91 2.57
1317 1534 4.035675 GCCTACATGGTGCTTGTTCTTATC 59.964 45.833 0.00 0.00 38.35 1.75
1331 1548 0.244994 CTTATCCCTCGCAGGATCCG 59.755 60.000 5.98 2.47 43.48 4.18
1828 2050 6.596869 AATTAGGGGAGAAATCAATCAGGA 57.403 37.500 0.00 0.00 0.00 3.86
1850 2072 7.068348 CAGGAGCTAAATTGGTACTACTACTCA 59.932 40.741 0.00 0.00 0.00 3.41
2613 2938 1.414550 GAGGTAGCATTCCAGTCCTCC 59.585 57.143 0.00 0.00 36.46 4.30
3181 3737 6.018262 TGGAATCTGAACAAACAGTAAGTTCG 60.018 38.462 11.41 7.85 43.36 3.95
3262 3820 1.056700 ATCTAACTGGAGGGCCGCAT 61.057 55.000 10.15 0.00 36.79 4.73
3939 6505 1.670811 ACGCTCACAGTTTGAACAAGG 59.329 47.619 0.00 0.00 32.21 3.61
5005 7575 6.373495 TCGTGTGATGTTAGTAGCTCTCTTAA 59.627 38.462 0.00 0.00 0.00 1.85
5326 7896 1.413118 ACCAAAAGCTTGAACCTGGG 58.587 50.000 0.00 0.00 34.14 4.45
5343 7913 0.739112 GGGAGACAGAAGAGCAAGCG 60.739 60.000 0.00 0.00 0.00 4.68
5495 8078 0.685097 TGGTCAGTGGAGTAGTTGCC 59.315 55.000 0.00 0.00 0.00 4.52
5561 8144 5.344066 CAGCTACATGTACAAGTACTCAGG 58.656 45.833 6.85 0.00 37.00 3.86
5710 8298 0.165944 CCGACAATCGTCAACTTGGC 59.834 55.000 0.00 0.00 42.74 4.52
5767 8355 7.664552 ATGAGCCATCATTTTCCTAAAATCA 57.335 32.000 0.00 0.00 43.92 2.57
5812 8400 2.496871 TGGGCTTGGTATTCTGCAATTG 59.503 45.455 0.00 0.00 0.00 2.32
5819 8407 5.172687 TGGTATTCTGCAATTGTAGGTGA 57.827 39.130 21.43 9.91 0.00 4.02
5859 8447 4.395959 TCAAGCGACCGATAATTAAGGT 57.604 40.909 13.77 13.77 41.63 3.50
5860 8448 5.518848 TCAAGCGACCGATAATTAAGGTA 57.481 39.130 13.84 0.00 38.57 3.08
5912 8501 4.152223 GGTTGCCTAAAATTGCACACATTC 59.848 41.667 0.00 0.00 37.18 2.67
5930 8519 0.313672 TCGGCACAAATTTGCACTCC 59.686 50.000 18.12 12.10 44.94 3.85
5944 8534 5.895636 TTGCACTCCATTAAAGTGTATGG 57.104 39.130 7.44 0.00 44.79 2.74
5956 8546 8.519526 CATTAAAGTGTATGGCCTTTTTAGTGA 58.480 33.333 3.32 0.00 33.24 3.41
5962 8552 5.830991 TGTATGGCCTTTTTAGTGACAACTT 59.169 36.000 3.32 0.00 37.88 2.66
5980 8570 9.607988 TGACAACTTGTAATTTTTAGTCTCAGA 57.392 29.630 0.00 0.00 0.00 3.27
6023 8613 4.068599 AGTTCAGGCTTTGCTCTCTAAAC 58.931 43.478 0.00 0.00 0.00 2.01
6051 8641 3.976701 ATTTCGCCGTGGCCCTGAG 62.977 63.158 5.08 0.00 37.98 3.35
6095 8685 7.822161 TGAACAATATATGATCAAGGTTGGG 57.178 36.000 0.00 0.00 37.83 4.12
6096 8686 6.777091 TGAACAATATATGATCAAGGTTGGGG 59.223 38.462 0.00 0.00 37.83 4.96
6124 8714 1.328279 AGCTAGGTGTTTTTGGTGCC 58.672 50.000 0.00 0.00 0.00 5.01
6187 8777 5.296748 TGTCGTTGGATGTGATATGGTATG 58.703 41.667 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.971125 GATCGCGGCTAGGTGGGC 62.971 72.222 6.13 0.00 0.00 5.36
3 4 4.301027 GGGATCGCGGCTAGGTGG 62.301 72.222 6.13 0.00 0.00 4.61
4 5 4.301027 GGGGATCGCGGCTAGGTG 62.301 72.222 6.13 0.00 0.00 4.00
5 6 2.442519 ATAGGGGATCGCGGCTAGGT 62.443 60.000 6.13 0.00 0.00 3.08
6 7 1.668101 GATAGGGGATCGCGGCTAGG 61.668 65.000 6.13 0.00 0.00 3.02
7 8 1.668101 GGATAGGGGATCGCGGCTAG 61.668 65.000 6.13 0.00 35.12 3.42
8 9 1.681327 GGATAGGGGATCGCGGCTA 60.681 63.158 6.13 1.22 35.12 3.93
9 10 2.997897 GGATAGGGGATCGCGGCT 60.998 66.667 6.13 0.00 35.12 5.52
10 11 4.083862 GGGATAGGGGATCGCGGC 62.084 72.222 6.13 0.00 37.71 6.53
13 14 3.393360 CCTGGGATAGGGGATCGC 58.607 66.667 0.06 0.06 45.56 4.58
38 39 4.063967 CACCGCGTGGAGTAGCCA 62.064 66.667 24.59 0.00 46.96 4.75
39 40 3.755628 TCACCGCGTGGAGTAGCC 61.756 66.667 24.59 0.00 39.21 3.93
40 41 2.506438 GTCACCGCGTGGAGTAGC 60.506 66.667 24.59 5.40 39.21 3.58
41 42 2.202440 CGTCACCGCGTGGAGTAG 60.202 66.667 24.59 8.69 39.21 2.57
42 43 2.669229 TCGTCACCGCGTGGAGTA 60.669 61.111 24.59 3.03 39.21 2.59
43 44 4.338539 GTCGTCACCGCGTGGAGT 62.339 66.667 24.59 0.00 39.21 3.85
52 53 4.436998 CTGGGCCTCGTCGTCACC 62.437 72.222 4.53 0.00 0.00 4.02
55 56 4.803426 CAGCTGGGCCTCGTCGTC 62.803 72.222 5.57 0.00 0.00 4.20
75 76 2.124695 GTCAAGATCCGGGCCACC 60.125 66.667 4.39 0.00 0.00 4.61
76 77 2.124695 GGTCAAGATCCGGGCCAC 60.125 66.667 4.39 0.00 0.00 5.01
77 78 3.781307 CGGTCAAGATCCGGGCCA 61.781 66.667 4.39 0.00 43.68 5.36
78 79 2.925162 CTTCGGTCAAGATCCGGGCC 62.925 65.000 0.00 0.00 46.82 5.80
79 80 1.521681 CTTCGGTCAAGATCCGGGC 60.522 63.158 0.00 0.00 46.82 6.13
80 81 1.144057 CCTTCGGTCAAGATCCGGG 59.856 63.158 0.00 0.00 46.82 5.73
81 82 1.521681 GCCTTCGGTCAAGATCCGG 60.522 63.158 0.00 0.00 46.82 5.14
83 84 0.528684 CTCGCCTTCGGTCAAGATCC 60.529 60.000 0.00 0.00 33.29 3.36
84 85 0.456221 TCTCGCCTTCGGTCAAGATC 59.544 55.000 0.00 0.00 33.29 2.75
85 86 0.895530 TTCTCGCCTTCGGTCAAGAT 59.104 50.000 0.00 0.00 33.29 2.40
86 87 0.243907 CTTCTCGCCTTCGGTCAAGA 59.756 55.000 0.00 0.00 33.29 3.02
87 88 0.243907 TCTTCTCGCCTTCGGTCAAG 59.756 55.000 0.00 0.00 36.13 3.02
88 89 0.243907 CTCTTCTCGCCTTCGGTCAA 59.756 55.000 0.00 0.00 36.13 3.18
89 90 0.608308 TCTCTTCTCGCCTTCGGTCA 60.608 55.000 0.00 0.00 36.13 4.02
90 91 0.099791 CTCTCTTCTCGCCTTCGGTC 59.900 60.000 0.00 0.00 36.13 4.79
91 92 1.316706 CCTCTCTTCTCGCCTTCGGT 61.317 60.000 0.00 0.00 36.13 4.69
92 93 1.435515 CCTCTCTTCTCGCCTTCGG 59.564 63.158 0.00 0.00 36.13 4.30
93 94 1.435515 CCCTCTCTTCTCGCCTTCG 59.564 63.158 0.00 0.00 0.00 3.79
94 95 0.684805 TCCCCTCTCTTCTCGCCTTC 60.685 60.000 0.00 0.00 0.00 3.46
95 96 0.686112 CTCCCCTCTCTTCTCGCCTT 60.686 60.000 0.00 0.00 0.00 4.35
96 97 1.076339 CTCCCCTCTCTTCTCGCCT 60.076 63.158 0.00 0.00 0.00 5.52
97 98 1.076632 TCTCCCCTCTCTTCTCGCC 60.077 63.158 0.00 0.00 0.00 5.54
98 99 1.106944 CCTCTCCCCTCTCTTCTCGC 61.107 65.000 0.00 0.00 0.00 5.03
99 100 0.467290 CCCTCTCCCCTCTCTTCTCG 60.467 65.000 0.00 0.00 0.00 4.04
100 101 0.930726 TCCCTCTCCCCTCTCTTCTC 59.069 60.000 0.00 0.00 0.00 2.87
101 102 0.933700 CTCCCTCTCCCCTCTCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
102 103 0.105709 CCTCCCTCTCCCCTCTCTTC 60.106 65.000 0.00 0.00 0.00 2.87
103 104 0.556380 TCCTCCCTCTCCCCTCTCTT 60.556 60.000 0.00 0.00 0.00 2.85
104 105 0.330431 ATCCTCCCTCTCCCCTCTCT 60.330 60.000 0.00 0.00 0.00 3.10
105 106 0.114364 GATCCTCCCTCTCCCCTCTC 59.886 65.000 0.00 0.00 0.00 3.20
106 107 0.330431 AGATCCTCCCTCTCCCCTCT 60.330 60.000 0.00 0.00 0.00 3.69
107 108 0.114364 GAGATCCTCCCTCTCCCCTC 59.886 65.000 0.00 0.00 34.34 4.30
108 109 2.260619 GAGATCCTCCCTCTCCCCT 58.739 63.158 0.00 0.00 34.34 4.79
109 110 4.966247 GAGATCCTCCCTCTCCCC 57.034 66.667 0.00 0.00 34.34 4.81
118 119 3.934962 GGCTGCGGGGAGATCCTC 61.935 72.222 0.00 0.00 35.95 3.71
212 213 4.308458 TCCACCTTGGGCGACACG 62.308 66.667 0.00 0.00 38.32 4.49
213 214 2.668550 GTCCACCTTGGGCGACAC 60.669 66.667 0.00 0.00 38.32 3.67
219 220 4.308458 TGCGTCGTCCACCTTGGG 62.308 66.667 0.00 0.00 38.32 4.12
220 221 2.738521 CTGCGTCGTCCACCTTGG 60.739 66.667 0.00 0.00 39.43 3.61
221 222 2.738521 CCTGCGTCGTCCACCTTG 60.739 66.667 0.00 0.00 0.00 3.61
222 223 2.915659 TCCTGCGTCGTCCACCTT 60.916 61.111 0.00 0.00 0.00 3.50
223 224 3.374402 CTCCTGCGTCGTCCACCT 61.374 66.667 0.00 0.00 0.00 4.00
224 225 3.222354 AACTCCTGCGTCGTCCACC 62.222 63.158 0.00 0.00 0.00 4.61
225 226 2.022129 CAACTCCTGCGTCGTCCAC 61.022 63.158 0.00 0.00 0.00 4.02
226 227 2.023414 AACAACTCCTGCGTCGTCCA 62.023 55.000 0.00 0.00 0.00 4.02
227 228 1.282930 GAACAACTCCTGCGTCGTCC 61.283 60.000 0.00 0.00 0.00 4.79
228 229 1.282930 GGAACAACTCCTGCGTCGTC 61.283 60.000 0.00 0.00 41.61 4.20
229 230 1.300697 GGAACAACTCCTGCGTCGT 60.301 57.895 0.00 0.00 41.61 4.34
230 231 3.550656 GGAACAACTCCTGCGTCG 58.449 61.111 0.00 0.00 41.61 5.12
251 252 1.324383 GGGGGAAGCGAGAACAAAAA 58.676 50.000 0.00 0.00 0.00 1.94
252 253 0.887387 CGGGGGAAGCGAGAACAAAA 60.887 55.000 0.00 0.00 0.00 2.44
253 254 1.302192 CGGGGGAAGCGAGAACAAA 60.302 57.895 0.00 0.00 0.00 2.83
254 255 1.550130 ATCGGGGGAAGCGAGAACAA 61.550 55.000 0.00 0.00 0.00 2.83
255 256 1.956629 GATCGGGGGAAGCGAGAACA 61.957 60.000 0.00 0.00 0.00 3.18
256 257 1.227292 GATCGGGGGAAGCGAGAAC 60.227 63.158 0.00 0.00 0.00 3.01
257 258 2.432300 GGATCGGGGGAAGCGAGAA 61.432 63.158 0.00 0.00 0.00 2.87
258 259 2.838225 GGATCGGGGGAAGCGAGA 60.838 66.667 0.00 0.00 0.00 4.04
259 260 3.930012 GGGATCGGGGGAAGCGAG 61.930 72.222 0.00 0.00 0.00 5.03
262 263 3.241515 GATCGGGATCGGGGGAAGC 62.242 68.421 0.00 0.00 36.95 3.86
263 264 1.534235 AGATCGGGATCGGGGGAAG 60.534 63.158 3.19 0.00 42.48 3.46
264 265 1.837051 CAGATCGGGATCGGGGGAA 60.837 63.158 3.19 0.00 42.48 3.97
265 266 2.094170 ATCAGATCGGGATCGGGGGA 62.094 60.000 8.58 4.17 42.48 4.81
266 267 1.608717 GATCAGATCGGGATCGGGGG 61.609 65.000 12.62 0.00 42.48 5.40
267 268 0.900182 TGATCAGATCGGGATCGGGG 60.900 60.000 19.11 1.59 43.21 5.73
268 269 1.189752 ATGATCAGATCGGGATCGGG 58.810 55.000 19.11 3.71 43.21 5.14
269 270 4.158579 TCTTTATGATCAGATCGGGATCGG 59.841 45.833 19.11 3.02 43.21 4.18
270 271 5.316327 TCTTTATGATCAGATCGGGATCG 57.684 43.478 19.11 9.42 43.21 3.69
271 272 8.231692 TCTATCTTTATGATCAGATCGGGATC 57.768 38.462 18.18 18.18 41.20 3.36
272 273 8.780616 ATCTATCTTTATGATCAGATCGGGAT 57.219 34.615 0.09 3.00 36.65 3.85
273 274 9.126151 GTATCTATCTTTATGATCAGATCGGGA 57.874 37.037 0.09 0.57 36.65 5.14
274 275 8.907885 TGTATCTATCTTTATGATCAGATCGGG 58.092 37.037 0.09 0.00 36.65 5.14
373 374 5.175856 CGAGACTTGTCTACAGGAAACTTTG 59.824 44.000 3.00 0.00 40.21 2.77
380 381 7.148120 CCTTAAATACGAGACTTGTCTACAGGA 60.148 40.741 3.00 0.00 0.00 3.86
382 383 6.472808 GCCTTAAATACGAGACTTGTCTACAG 59.527 42.308 3.00 1.79 0.00 2.74
383 384 6.071784 TGCCTTAAATACGAGACTTGTCTACA 60.072 38.462 3.00 0.00 0.00 2.74
384 385 6.327934 TGCCTTAAATACGAGACTTGTCTAC 58.672 40.000 3.00 0.00 0.00 2.59
436 437 5.310068 AGATGTCTCAGGGCAATCTTGATAT 59.690 40.000 0.00 0.00 0.00 1.63
437 438 4.657504 AGATGTCTCAGGGCAATCTTGATA 59.342 41.667 0.00 0.00 0.00 2.15
438 439 3.458857 AGATGTCTCAGGGCAATCTTGAT 59.541 43.478 0.00 0.00 0.00 2.57
439 440 2.842496 AGATGTCTCAGGGCAATCTTGA 59.158 45.455 0.00 0.00 0.00 3.02
440 441 3.278668 AGATGTCTCAGGGCAATCTTG 57.721 47.619 0.00 0.00 0.00 3.02
442 443 2.842496 TCAAGATGTCTCAGGGCAATCT 59.158 45.455 0.00 0.00 0.00 2.40
443 444 3.204526 CTCAAGATGTCTCAGGGCAATC 58.795 50.000 0.00 0.00 0.00 2.67
444 445 2.683152 GCTCAAGATGTCTCAGGGCAAT 60.683 50.000 3.32 0.00 30.60 3.56
446 447 0.251354 GCTCAAGATGTCTCAGGGCA 59.749 55.000 3.32 0.00 30.60 5.36
447 448 0.809241 CGCTCAAGATGTCTCAGGGC 60.809 60.000 0.00 0.00 0.00 5.19
449 450 1.638133 CACGCTCAAGATGTCTCAGG 58.362 55.000 0.00 0.00 0.00 3.86
465 466 3.190878 GCAATCCAAGCCTCCACG 58.809 61.111 0.00 0.00 0.00 4.94
472 473 3.508840 CGGACCGGCAATCCAAGC 61.509 66.667 5.81 0.00 35.83 4.01
486 487 1.557099 AGAAGTCTGTGCATACCGGA 58.443 50.000 9.46 0.00 0.00 5.14
490 491 3.810310 AGCCTAGAAGTCTGTGCATAC 57.190 47.619 0.00 0.00 0.00 2.39
491 492 7.782897 ATATTAGCCTAGAAGTCTGTGCATA 57.217 36.000 0.00 0.00 0.00 3.14
492 493 6.678568 ATATTAGCCTAGAAGTCTGTGCAT 57.321 37.500 0.00 0.00 0.00 3.96
493 494 6.325028 AGAATATTAGCCTAGAAGTCTGTGCA 59.675 38.462 0.00 0.00 0.00 4.57
498 519 9.995003 CATGAAAGAATATTAGCCTAGAAGTCT 57.005 33.333 0.00 0.00 0.00 3.24
503 524 9.730705 CCAATCATGAAAGAATATTAGCCTAGA 57.269 33.333 0.00 0.00 0.00 2.43
504 525 8.954350 CCCAATCATGAAAGAATATTAGCCTAG 58.046 37.037 0.00 0.00 0.00 3.02
506 527 6.723052 CCCCAATCATGAAAGAATATTAGCCT 59.277 38.462 0.00 0.00 0.00 4.58
508 529 7.530426 ACCCCAATCATGAAAGAATATTAGC 57.470 36.000 0.00 0.00 0.00 3.09
521 542 6.549364 TGGCTAGTTTTTATACCCCAATCATG 59.451 38.462 0.00 0.00 0.00 3.07
522 543 6.678547 TGGCTAGTTTTTATACCCCAATCAT 58.321 36.000 0.00 0.00 0.00 2.45
526 547 7.215743 AGTATGGCTAGTTTTTATACCCCAA 57.784 36.000 0.00 0.00 0.00 4.12
527 548 6.835029 AGTATGGCTAGTTTTTATACCCCA 57.165 37.500 0.00 0.00 0.00 4.96
530 551 8.959705 AGACAAGTATGGCTAGTTTTTATACC 57.040 34.615 0.00 0.00 45.56 2.73
549 571 5.391310 CCGATCACAATCAAAAGGAGACAAG 60.391 44.000 0.00 0.00 31.76 3.16
553 575 3.609853 CCCGATCACAATCAAAAGGAGA 58.390 45.455 0.00 0.00 31.76 3.71
554 576 2.684881 CCCCGATCACAATCAAAAGGAG 59.315 50.000 0.00 0.00 31.76 3.69
557 579 4.398988 TCAATCCCCGATCACAATCAAAAG 59.601 41.667 0.00 0.00 31.76 2.27
563 585 3.117926 TCACATCAATCCCCGATCACAAT 60.118 43.478 0.00 0.00 0.00 2.71
564 586 2.238395 TCACATCAATCCCCGATCACAA 59.762 45.455 0.00 0.00 0.00 3.33
571 593 0.603707 CCGGATCACATCAATCCCCG 60.604 60.000 0.00 0.00 39.71 5.73
577 599 2.513666 GGCGCCGGATCACATCAA 60.514 61.111 12.58 0.00 0.00 2.57
594 616 0.601576 TCCATTCGGTCACAACACGG 60.602 55.000 0.00 0.00 0.00 4.94
596 618 3.252215 TCAAATCCATTCGGTCACAACAC 59.748 43.478 0.00 0.00 0.00 3.32
619 641 5.110940 TGTTAGTACGGGCAATTTGAAAC 57.889 39.130 0.00 0.00 0.00 2.78
623 645 5.465935 ACATTTGTTAGTACGGGCAATTTG 58.534 37.500 0.00 0.00 0.00 2.32
636 658 7.316544 ACGCTATTCCCTAAACATTTGTTAG 57.683 36.000 0.00 0.00 37.25 2.34
641 663 5.124936 GTCCAACGCTATTCCCTAAACATTT 59.875 40.000 0.00 0.00 0.00 2.32
644 666 3.602483 GTCCAACGCTATTCCCTAAACA 58.398 45.455 0.00 0.00 0.00 2.83
645 667 2.606272 CGTCCAACGCTATTCCCTAAAC 59.394 50.000 0.00 0.00 33.65 2.01
653 675 1.153706 CCGGTCGTCCAACGCTATT 60.154 57.895 0.00 0.00 42.21 1.73
657 679 2.946752 GAAACCGGTCGTCCAACGC 61.947 63.158 8.04 0.00 42.21 4.84
659 681 1.838568 GCAGAAACCGGTCGTCCAAC 61.839 60.000 8.04 0.00 0.00 3.77
665 687 0.744414 ATGGATGCAGAAACCGGTCG 60.744 55.000 8.04 0.00 0.00 4.79
672 694 3.369242 TCATGGACATGGATGCAGAAA 57.631 42.857 11.98 0.00 39.24 2.52
674 696 3.588210 ATTCATGGACATGGATGCAGA 57.412 42.857 11.98 0.00 35.74 4.26
675 697 5.777850 TTAATTCATGGACATGGATGCAG 57.222 39.130 11.98 0.00 37.12 4.41
676 698 5.244402 GGATTAATTCATGGACATGGATGCA 59.756 40.000 11.98 0.00 37.12 3.96
677 699 5.620654 CGGATTAATTCATGGACATGGATGC 60.621 44.000 11.98 1.29 37.12 3.91
678 700 5.706833 TCGGATTAATTCATGGACATGGATG 59.293 40.000 11.98 0.00 37.12 3.51
681 703 5.308014 TCTCGGATTAATTCATGGACATGG 58.692 41.667 11.98 0.00 39.24 3.66
683 705 5.413833 GCATCTCGGATTAATTCATGGACAT 59.586 40.000 0.00 0.00 0.00 3.06
685 707 4.143030 CGCATCTCGGATTAATTCATGGAC 60.143 45.833 0.00 0.00 33.78 4.02
687 709 3.748048 ACGCATCTCGGATTAATTCATGG 59.252 43.478 0.00 0.00 43.86 3.66
689 711 6.455647 TCTAACGCATCTCGGATTAATTCAT 58.544 36.000 0.00 0.00 43.86 2.57
692 714 8.827177 TTTATCTAACGCATCTCGGATTAATT 57.173 30.769 0.00 0.00 43.86 1.40
694 716 8.651391 TTTTTATCTAACGCATCTCGGATTAA 57.349 30.769 0.00 0.00 43.86 1.40
696 718 7.307989 CCATTTTTATCTAACGCATCTCGGATT 60.308 37.037 0.00 0.00 43.86 3.01
697 719 6.147821 CCATTTTTATCTAACGCATCTCGGAT 59.852 38.462 0.00 0.00 43.86 4.18
700 722 6.346919 CCTCCATTTTTATCTAACGCATCTCG 60.347 42.308 0.00 0.00 45.38 4.04
701 723 6.073003 CCCTCCATTTTTATCTAACGCATCTC 60.073 42.308 0.00 0.00 0.00 2.75
702 724 5.765182 CCCTCCATTTTTATCTAACGCATCT 59.235 40.000 0.00 0.00 0.00 2.90
704 726 5.690865 TCCCTCCATTTTTATCTAACGCAT 58.309 37.500 0.00 0.00 0.00 4.73
705 727 5.105567 TCCCTCCATTTTTATCTAACGCA 57.894 39.130 0.00 0.00 0.00 5.24
707 729 6.929606 CCTACTCCCTCCATTTTTATCTAACG 59.070 42.308 0.00 0.00 0.00 3.18
708 730 7.803131 ACCTACTCCCTCCATTTTTATCTAAC 58.197 38.462 0.00 0.00 0.00 2.34
709 731 9.155785 CTACCTACTCCCTCCATTTTTATCTAA 57.844 37.037 0.00 0.00 0.00 2.10
713 755 5.670361 TGCTACCTACTCCCTCCATTTTTAT 59.330 40.000 0.00 0.00 0.00 1.40
729 771 3.430374 GCTCGGAAAGTGAATGCTACCTA 60.430 47.826 0.00 0.00 0.00 3.08
731 773 1.666189 GCTCGGAAAGTGAATGCTACC 59.334 52.381 0.00 0.00 0.00 3.18
732 774 2.622436 AGCTCGGAAAGTGAATGCTAC 58.378 47.619 0.00 0.00 0.00 3.58
747 789 3.506059 CTGGCCGATGGGTAGCTCG 62.506 68.421 0.00 0.00 34.97 5.03
761 803 1.237285 ACGCTGATTTGACCACTGGC 61.237 55.000 0.00 0.00 0.00 4.85
783 825 1.186267 AGAACGGGAAGGAGCGACTT 61.186 55.000 0.00 0.00 0.00 3.01
807 849 1.026182 CAGTTATTGCTGCCGCTGGA 61.026 55.000 0.70 0.00 36.97 3.86
836 878 1.639298 CTGCTAGTGTTTGCCGCTCC 61.639 60.000 0.00 0.00 35.05 4.70
845 887 0.248843 GCTCTGCCTCTGCTAGTGTT 59.751 55.000 0.00 0.00 38.71 3.32
860 902 1.716028 AACCGACCCCTTTTGGCTCT 61.716 55.000 0.00 0.00 38.58 4.09
861 903 0.826256 AAACCGACCCCTTTTGGCTC 60.826 55.000 0.00 0.00 38.58 4.70
862 904 1.112916 CAAACCGACCCCTTTTGGCT 61.113 55.000 0.00 0.00 38.58 4.75
863 905 1.110518 TCAAACCGACCCCTTTTGGC 61.111 55.000 0.00 0.00 38.58 4.52
864 906 1.404843 TTCAAACCGACCCCTTTTGG 58.595 50.000 0.00 0.00 39.97 3.28
865 907 3.744238 ATTTCAAACCGACCCCTTTTG 57.256 42.857 0.00 0.00 0.00 2.44
866 908 3.707102 TGAATTTCAAACCGACCCCTTTT 59.293 39.130 0.00 0.00 0.00 2.27
966 1009 3.551407 GGAGGATGGAGGACGGGC 61.551 72.222 0.00 0.00 0.00 6.13
967 1010 2.844839 GGGAGGATGGAGGACGGG 60.845 72.222 0.00 0.00 0.00 5.28
969 1012 2.041922 TGGGGAGGATGGAGGACG 60.042 66.667 0.00 0.00 0.00 4.79
970 1013 2.447714 GCTGGGGAGGATGGAGGAC 61.448 68.421 0.00 0.00 0.00 3.85
1080 1285 3.706373 GCCCCGACCTTGCTCTCA 61.706 66.667 0.00 0.00 0.00 3.27
1131 1339 2.622942 CTCCTCAATCTCCTTCCTCGAG 59.377 54.545 5.13 5.13 0.00 4.04
1317 1534 2.202932 CAACGGATCCTGCGAGGG 60.203 66.667 10.75 0.00 35.59 4.30
1828 2050 9.203163 AGATTGAGTAGTAGTACCAATTTAGCT 57.797 33.333 17.97 11.63 33.61 3.32
2057 2297 2.888594 TGTTCACAGCTTCGGTATAGC 58.111 47.619 0.00 0.00 38.93 2.97
2613 2938 6.146216 TGTTATAATGTCAACAAGGCAAACG 58.854 36.000 0.00 0.00 34.09 3.60
3262 3820 3.773560 ACCAATAGGGCTACTTTGCAAA 58.226 40.909 12.14 12.14 42.05 3.68
4960 7530 4.338682 ACGAGTGCCTAGAAATAGACGAAT 59.661 41.667 0.00 0.00 0.00 3.34
5005 7575 8.627208 ATGACAAAAGATGATTAGTCACAAGT 57.373 30.769 0.00 0.00 38.62 3.16
5326 7896 1.345410 GACGCTTGCTCTTCTGTCTC 58.655 55.000 0.00 0.00 0.00 3.36
5343 7913 1.198637 AGTACTACGCAGTTGACGGAC 59.801 52.381 0.00 0.00 37.78 4.79
5495 8078 8.027771 AGACTTAACCGTAGTTCTACAAGAATG 58.972 37.037 10.05 0.26 36.50 2.67
5561 8144 5.992729 TGCTTTAAAACTCCAATACACGTC 58.007 37.500 0.00 0.00 0.00 4.34
5710 8298 6.211515 AGGTTAAGTTATATAGGTTGCGACG 58.788 40.000 0.00 0.00 0.00 5.12
5767 8355 5.442405 AAAGTGCACTTTACGAAGACGTGT 61.442 41.667 37.07 13.68 43.73 4.49
5787 8375 2.562298 TGCAGAATACCAAGCCCAAAAG 59.438 45.455 0.00 0.00 0.00 2.27
5812 8400 9.660180 AATCTTTTTAGAATCTCAGTCACCTAC 57.340 33.333 0.00 0.00 0.00 3.18
5819 8407 7.604164 TCGCTTGAATCTTTTTAGAATCTCAGT 59.396 33.333 0.00 0.00 0.00 3.41
5866 8454 7.731054 ACCAAGAAATAGCAAAATGGTTACAA 58.269 30.769 0.00 0.00 36.32 2.41
5912 8501 0.031857 TGGAGTGCAAATTTGTGCCG 59.968 50.000 19.03 0.00 44.26 5.69
5930 8519 8.519526 TCACTAAAAAGGCCATACACTTTAATG 58.480 33.333 5.01 0.00 35.99 1.90
5944 8534 8.642908 AAATTACAAGTTGTCACTAAAAAGGC 57.357 30.769 12.82 0.00 30.68 4.35
5956 8546 9.391006 TGTCTGAGACTAAAAATTACAAGTTGT 57.609 29.630 14.42 14.05 33.15 3.32
5975 8565 8.994429 AAGTCAAACATATAGTTCTGTCTGAG 57.006 34.615 0.00 0.00 40.26 3.35
6023 8613 1.234615 ACGGCGAAATCACACCAAGG 61.235 55.000 16.62 0.00 0.00 3.61
6051 8641 4.300803 TCATTTCAAACAGCATTGCAGTC 58.699 39.130 11.91 0.00 0.00 3.51
6093 8683 2.442126 ACACCTAGCTAATTTAGGCCCC 59.558 50.000 0.00 0.00 41.16 5.80
6095 8685 6.330278 CAAAAACACCTAGCTAATTTAGGCC 58.670 40.000 0.00 0.00 41.16 5.19
6096 8686 6.071560 ACCAAAAACACCTAGCTAATTTAGGC 60.072 38.462 5.61 0.00 41.16 3.93
6124 8714 6.771076 TCTGCTTTGCATAAGTAACATTACG 58.229 36.000 9.40 0.00 38.13 3.18


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

AutoCloner maintained by Alex Coulton.