Multiple sequence alignment - TraesCS6D01G288600

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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 TraesCS6D01G288600 chr6D 100.000 7507 0 0 1 7507 399012345 399019851 0.000000e+00 13863.0
1 TraesCS6D01G288600 chr6D 90.419 167 12 1 3468 3634 399015641 399015803 4.560000e-52 217.0
2 TraesCS6D01G288600 chr6D 90.419 167 12 1 3297 3459 399015812 399015978 4.560000e-52 217.0
3 TraesCS6D01G288600 chr6A 95.233 1741 58 10 3649 5381 545109711 545111434 0.000000e+00 2732.0
4 TraesCS6D01G288600 chr6A 95.674 1618 57 6 1 1608 545106014 545107628 0.000000e+00 2588.0
5 TraesCS6D01G288600 chr6A 91.930 1834 85 24 5373 7199 545111455 545113232 0.000000e+00 2508.0
6 TraesCS6D01G288600 chr6A 94.455 1605 63 11 1635 3227 545107624 545109214 0.000000e+00 2447.0
7 TraesCS6D01G288600 chr6A 96.270 429 15 1 3222 3650 545109247 545109674 0.000000e+00 702.0
8 TraesCS6D01G288600 chr6A 79.167 216 34 10 2189 2398 494477025 494477235 1.020000e-28 139.0
9 TraesCS6D01G288600 chr6A 81.765 170 12 10 7198 7365 545113283 545113435 2.840000e-24 124.0
10 TraesCS6D01G288600 chr6B 91.089 1773 102 29 3649 5379 597078281 597080039 0.000000e+00 2348.0
11 TraesCS6D01G288600 chr6B 90.882 1327 97 11 5763 7080 597080716 597082027 0.000000e+00 1759.0
12 TraesCS6D01G288600 chr6B 88.170 1437 84 27 1847 3227 597076378 597077784 0.000000e+00 1633.0
13 TraesCS6D01G288600 chr6B 95.472 1016 30 6 827 1827 597075374 597076388 0.000000e+00 1607.0
14 TraesCS6D01G288600 chr6B 92.972 811 53 3 1 810 597074581 597075388 0.000000e+00 1179.0
15 TraesCS6D01G288600 chr6B 94.186 430 21 3 3222 3650 597077817 597078243 0.000000e+00 652.0
16 TraesCS6D01G288600 chr6B 90.864 405 28 6 5376 5773 597080090 597080492 1.110000e-147 534.0
17 TraesCS6D01G288600 chr6B 92.216 167 8 2 3468 3634 597077893 597078054 1.630000e-56 231.0
18 TraesCS6D01G288600 chr7A 79.371 509 73 26 6425 6915 540048276 540048770 5.620000e-86 329.0
19 TraesCS6D01G288600 chr7A 78.198 344 50 18 2200 2523 725463125 725462787 5.940000e-46 196.0
20 TraesCS6D01G288600 chr5A 81.842 380 38 20 2101 2455 185651479 185651106 2.650000e-74 291.0
21 TraesCS6D01G288600 chr5A 78.163 490 74 24 6425 6906 34329916 34329452 1.590000e-71 281.0
22 TraesCS6D01G288600 chr5D 80.054 371 34 11 2101 2455 137973303 137973649 9.730000e-59 239.0
23 TraesCS6D01G288600 chr5D 79.321 324 39 15 2228 2524 423490952 423490630 1.280000e-47 202.0
24 TraesCS6D01G288600 chr5D 85.714 133 10 4 1922 2045 137973168 137973300 1.700000e-26 132.0
25 TraesCS6D01G288600 chr2A 88.265 196 21 2 1918 2111 122148111 122148306 4.530000e-57 233.0
26 TraesCS6D01G288600 chr5B 79.614 363 29 16 2101 2445 187044662 187044997 1.270000e-52 219.0
27 TraesCS6D01G288600 chr5B 88.679 106 10 2 1942 2045 187044554 187044659 2.200000e-25 128.0
28 TraesCS6D01G288600 chr3A 85.246 61 9 0 146 206 595441331 595441271 6.290000e-06 63.9
29 TraesCS6D01G288600 chr3A 94.872 39 2 0 173 211 729969996 729969958 2.260000e-05 62.1
30 TraesCS6D01G288600 chrUn 94.872 39 2 0 173 211 195674668 195674630 2.260000e-05 62.1
31 TraesCS6D01G288600 chrUn 94.872 39 2 0 173 211 204057301 204057263 2.260000e-05 62.1
32 TraesCS6D01G288600 chrUn 72.727 187 49 2 26 211 233817558 233817743 2.260000e-05 62.1
33 TraesCS6D01G288600 chrUn 72.727 187 49 2 26 211 348677155 348677340 2.260000e-05 62.1
34 TraesCS6D01G288600 chr4D 94.872 39 2 0 173 211 307261088 307261050 2.260000e-05 62.1
35 TraesCS6D01G288600 chr4A 94.737 38 1 1 2484 2521 680954180 680954216 2.930000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G288600 chr6D 399012345 399019851 7506 False 13863.000000 13863 100.000000 1 7507 1 chr6D.!!$F1 7506
1 TraesCS6D01G288600 chr6A 545106014 545113435 7421 False 1850.166667 2732 92.554500 1 7365 6 chr6A.!!$F2 7364
2 TraesCS6D01G288600 chr6B 597074581 597082027 7446 False 1242.875000 2348 91.981375 1 7080 8 chr6B.!!$F1 7079

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
888 897 0.401395 TCCCCACCTGTTCTCCACTT 60.401 55.000 0.00 0.00 0.00 3.16 F
1147 1165 0.041090 TCCCAAATCCCCCTTTGCTC 59.959 55.000 0.00 0.00 35.28 4.26 F
2502 2561 0.605319 ATGTGTGTACCCCGTTGCAG 60.605 55.000 0.00 0.00 0.00 4.41 F
3065 3154 0.317519 GTTTCTTTTCGTGCCACCCG 60.318 55.000 0.00 0.00 0.00 5.28 F
4054 4230 1.425066 TCTGTCTGCCAATGGAAACCT 59.575 47.619 2.05 0.00 0.00 3.50 F
4636 4845 0.534873 AAGTGCGGTTTGTTTTGGCT 59.465 45.000 0.00 0.00 0.00 4.75 F
5022 5240 0.953727 GGTTCTCACACTGCATGCAA 59.046 50.000 22.88 5.23 0.00 4.08 F
6282 6805 0.973632 AGGTTCGTGTATGCAGTCCA 59.026 50.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 2427 0.840722 TTCTCCACCAACCCCTCTCC 60.841 60.000 0.00 0.0 0.00 3.71 R
2964 3052 0.871722 TTTGTATGTGCTGCCGTGTC 59.128 50.000 0.00 0.0 0.00 3.67 R
3333 3461 2.016905 ACCTAGGTGGGCTATGCTAG 57.983 55.000 15.42 0.0 41.11 3.42 R
4329 4509 3.323691 ACAGCCAAAGAACCCAAATAACC 59.676 43.478 0.00 0.0 0.00 2.85 R
5859 6374 0.178995 TGTTTCAGCACTCCATGGCA 60.179 50.000 6.96 0.0 0.00 4.92 R
6212 6735 1.067295 ATGAACTGGAAGCCTGGTGA 58.933 50.000 0.00 0.0 37.60 4.02 R
6448 6971 1.311859 TTCAAAGTCCAGCTGTGCAG 58.688 50.000 13.81 0.0 32.40 4.41 R
7169 7696 0.105778 CAACGCAACCCAACCCAATT 59.894 50.000 0.00 0.0 0.00 2.32 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
31 32 7.984422 TGTGATTCAATGTACATGACTTCTT 57.016 32.000 9.63 0.00 0.00 2.52
143 144 1.296392 CCGAGGGCTTCATCACACA 59.704 57.895 0.00 0.00 0.00 3.72
218 219 2.114616 CATCACCCTCTCCTAGTTGCT 58.885 52.381 0.00 0.00 0.00 3.91
245 246 4.261994 GCAAAAGAACTGAAGGGTATGCAA 60.262 41.667 0.00 0.00 0.00 4.08
255 256 9.474313 AACTGAAGGGTATGCAAATTATCTTTA 57.526 29.630 0.00 0.00 0.00 1.85
278 279 4.591321 AGGGCCTAAATTTCACATCTCA 57.409 40.909 2.82 0.00 0.00 3.27
294 295 1.030457 CTCAAGCCAGATTCCATGCC 58.970 55.000 0.00 0.00 0.00 4.40
322 323 6.038050 CCTCATATTCTTGAAGAACCAAGCTC 59.962 42.308 10.18 0.00 42.34 4.09
381 382 3.706373 CACCTAGTGGCAGCCGGT 61.706 66.667 7.03 4.76 36.63 5.28
531 532 1.202627 GCGCTCTTCTCCATCTGGAAT 60.203 52.381 0.00 0.00 44.91 3.01
651 652 3.495100 GCAAGGATCAACCCGTATCATCT 60.495 47.826 0.00 0.00 40.05 2.90
699 700 3.006537 CAGGGAACAAGGAAACTCTACGA 59.993 47.826 0.00 0.00 42.68 3.43
759 760 1.688735 AGGGAAACTTTTGAGGCTTGC 59.311 47.619 0.00 0.00 0.00 4.01
830 832 8.444783 AGGCCCATATACACAAGAAATATACAA 58.555 33.333 0.00 0.00 0.00 2.41
888 897 0.401395 TCCCCACCTGTTCTCCACTT 60.401 55.000 0.00 0.00 0.00 3.16
1147 1165 0.041090 TCCCAAATCCCCCTTTGCTC 59.959 55.000 0.00 0.00 35.28 4.26
1150 1168 0.977627 CAAATCCCCCTTTGCTCCCC 60.978 60.000 0.00 0.00 30.06 4.81
1372 1390 2.031163 GGCTGTGTGCTCGACCTT 59.969 61.111 0.00 0.00 42.39 3.50
1570 1593 6.863126 CCACAACATTGTTTTGGATTCTAGTC 59.137 38.462 24.25 0.00 39.91 2.59
1746 1771 7.387948 GGACAAGAAAGTGATAGCAAGTAAAGA 59.612 37.037 0.00 0.00 0.00 2.52
1829 1854 5.991933 TGCCACACATTTGGTTATATTGT 57.008 34.783 0.00 0.00 39.09 2.71
1840 1865 6.656632 TTGGTTATATTGTGTTTGAAGGCA 57.343 33.333 0.00 0.00 0.00 4.75
1943 1971 9.725206 TCTCTACTATTAAAGGGGAGTTTGTAT 57.275 33.333 0.00 0.00 32.91 2.29
2053 2082 5.934625 GGTAAGTGTTGATTCAGTCACATCT 59.065 40.000 18.97 10.19 36.32 2.90
2169 2200 2.365617 ACCAGCCGATTCACTACCATAG 59.634 50.000 0.00 0.00 0.00 2.23
2305 2341 2.263540 GAAAGCCGACCCGCTACA 59.736 61.111 0.00 0.00 38.44 2.74
2409 2445 1.229529 GGAGAGGGGTTGGTGGAGA 60.230 63.158 0.00 0.00 0.00 3.71
2431 2470 8.683615 GGAGAAGGAATTATTTGACGGTAAATT 58.316 33.333 4.78 0.00 32.79 1.82
2448 2487 6.194508 CGGTAAATTGAATCAACAATACTGCG 59.805 38.462 0.00 0.00 39.19 5.18
2459 2498 7.285783 TCAACAATACTGCGTAATGTTAGAC 57.714 36.000 16.33 0.00 39.26 2.59
2502 2561 0.605319 ATGTGTGTACCCCGTTGCAG 60.605 55.000 0.00 0.00 0.00 4.41
2537 2597 9.677567 CAATTAGCTAGTATGAGAGAGAAGTTC 57.322 37.037 0.00 0.00 0.00 3.01
2556 2616 8.749354 AGAAGTTCTTAAACATTTCTTTGGTGT 58.251 29.630 0.00 0.00 37.88 4.16
2589 2650 2.039613 GCATAGGAGGGCTAGCAATTCT 59.960 50.000 18.24 10.64 0.00 2.40
2664 2725 1.411977 CCAGTCACAAAACATGGCCAA 59.588 47.619 10.96 0.00 0.00 4.52
2828 2890 9.529823 CACTCCATAACTAGATTGGGTACTATA 57.470 37.037 0.00 0.00 0.00 1.31
2829 2891 9.531158 ACTCCATAACTAGATTGGGTACTATAC 57.469 37.037 0.00 0.00 0.00 1.47
2830 2892 9.756571 CTCCATAACTAGATTGGGTACTATACT 57.243 37.037 0.00 0.00 0.00 2.12
2946 3009 8.912988 TGTACACACACATCTCATAGATTGATA 58.087 33.333 0.00 0.00 31.32 2.15
2987 3075 2.418280 CACGGCAGCACATACAAATGTA 59.582 45.455 0.00 0.00 44.70 2.29
3065 3154 0.317519 GTTTCTTTTCGTGCCACCCG 60.318 55.000 0.00 0.00 0.00 5.28
3089 3178 4.402829 TGGTGACCAAAATAAGCAGCTTA 58.597 39.130 17.35 17.35 0.00 3.09
3280 3408 3.515901 AGATCTCACTTGGGTAGGTTGTC 59.484 47.826 0.00 0.00 0.00 3.18
3333 3461 5.059404 ACAGTGCAATATTTGGCTGTTAC 57.941 39.130 8.79 0.00 34.02 2.50
3552 3680 7.338440 TGATGATGAATCATATCGTTTCGAC 57.662 36.000 5.78 0.00 46.84 4.20
3644 3772 9.177608 TGGAAGAATTTAGAACTGGTATTGATG 57.822 33.333 0.00 0.00 0.00 3.07
3676 3843 6.573434 GGAAATTCAGTTGTTTCCTTTCTGT 58.427 36.000 9.09 0.00 46.26 3.41
3727 3894 5.949354 TGTATTGGCCTTGTTTGTAGCTAAT 59.051 36.000 3.32 0.00 39.39 1.73
3767 3934 4.730613 GCGACGCAAAAGTGGATTGATAAT 60.731 41.667 16.42 0.00 0.00 1.28
3816 3983 4.896562 TGCTACGTGTCATTTTAGAACG 57.103 40.909 0.00 0.00 40.00 3.95
3818 3985 3.122278 GCTACGTGTCATTTTAGAACGCA 59.878 43.478 0.00 0.00 37.76 5.24
3839 4006 5.007921 CGCATGACTGAATTGATCATGGTTA 59.992 40.000 18.14 0.00 46.46 2.85
3909 4078 6.902771 TCTGATTAAGGATAGTAGCCTCAC 57.097 41.667 7.58 0.85 33.76 3.51
4054 4230 1.425066 TCTGTCTGCCAATGGAAACCT 59.575 47.619 2.05 0.00 0.00 3.50
4309 4489 4.696877 CACACTACAGCAGATCCAAATTCA 59.303 41.667 0.00 0.00 0.00 2.57
4329 4509 5.437289 TCAATTCACAACTTTAGCCACTG 57.563 39.130 0.00 0.00 0.00 3.66
4387 4567 8.316946 AGATGACATTTGATTTCAGACTCAGTA 58.683 33.333 0.00 0.00 0.00 2.74
4436 4616 6.650807 TCTTTGCGAGTTGATGAAAATCTACT 59.349 34.615 3.06 3.06 38.86 2.57
4543 4752 4.458295 AGATGGAGAAGTGTGCAGAAAATG 59.542 41.667 0.00 0.00 0.00 2.32
4555 4764 6.198403 GTGTGCAGAAAATGAATAGCATCATG 59.802 38.462 0.00 0.00 39.90 3.07
4600 4809 4.004982 GCATTTGTTTCCCTGCATTGAAT 58.995 39.130 0.00 0.00 34.77 2.57
4636 4845 0.534873 AAGTGCGGTTTGTTTTGGCT 59.465 45.000 0.00 0.00 0.00 4.75
4690 4899 7.648908 TGCAAATTCTGACAACAACTGATTTAG 59.351 33.333 0.00 0.00 0.00 1.85
4721 4931 4.993705 AGGTATGACTTTTGAGGGTGAA 57.006 40.909 0.00 0.00 0.00 3.18
5022 5240 0.953727 GGTTCTCACACTGCATGCAA 59.046 50.000 22.88 5.23 0.00 4.08
5164 5382 6.885918 TCTCTTGGATATTCATGCTTTTGACA 59.114 34.615 0.00 0.00 0.00 3.58
5165 5383 6.855836 TCTTGGATATTCATGCTTTTGACAC 58.144 36.000 0.00 0.00 0.00 3.67
5176 5394 5.452078 TGCTTTTGACACTTTTCCTATGG 57.548 39.130 0.00 0.00 0.00 2.74
5190 5408 4.553330 TCCTATGGATCGGCCTTTATTC 57.447 45.455 0.00 0.00 37.63 1.75
5200 5418 3.516300 TCGGCCTTTATTCTTGTACTCCA 59.484 43.478 0.00 0.00 0.00 3.86
5326 5544 2.015456 TAGTGATGCGGGATCCTGAT 57.985 50.000 25.54 14.22 0.00 2.90
5340 5558 5.213868 GATCCTGATCCCCTCTCCTTATA 57.786 47.826 0.00 0.00 31.76 0.98
5371 5589 3.140144 ACTCTTCTTTTCATTCCCCACCA 59.860 43.478 0.00 0.00 0.00 4.17
5430 5705 4.021981 AGGAAAGTAAATGTGCAAGCCTTC 60.022 41.667 0.00 0.00 0.00 3.46
5435 5710 5.917462 AGTAAATGTGCAAGCCTTCTTTTT 58.083 33.333 0.00 0.00 0.00 1.94
5649 5924 8.778358 GTGTCTCAGTATGTTCTTTGATTTTCT 58.222 33.333 0.00 0.00 37.40 2.52
5717 5992 2.910688 TCTGACGAAGCCAAGAAAGT 57.089 45.000 0.00 0.00 0.00 2.66
5755 6036 6.491745 TGTGTCATATAAAGGTGCAAAAAGGA 59.508 34.615 0.00 0.00 0.00 3.36
5756 6037 7.178274 TGTGTCATATAAAGGTGCAAAAAGGAT 59.822 33.333 0.00 0.00 0.00 3.24
5799 6314 7.345653 TGGAAATGAGATATGACTAGAACCAGT 59.654 37.037 0.00 0.00 0.00 4.00
5804 6319 8.628630 TGAGATATGACTAGAACCAGTATCAG 57.371 38.462 0.00 0.00 0.00 2.90
5812 6327 2.906389 AGAACCAGTATCAGCCTTGTCA 59.094 45.455 0.00 0.00 0.00 3.58
5837 6352 8.877779 CACTGAGAAATAATTGTGGTAAGAGAG 58.122 37.037 0.00 0.00 0.00 3.20
5859 6374 5.526434 AGGCTGTGTAGGTATTAGGTAAGT 58.474 41.667 0.00 0.00 0.00 2.24
5865 6380 5.989777 GTGTAGGTATTAGGTAAGTGCCATG 59.010 44.000 0.00 0.00 0.00 3.66
5868 6383 4.348168 AGGTATTAGGTAAGTGCCATGGAG 59.652 45.833 18.40 0.00 0.00 3.86
5898 6413 8.342634 TGAAACATTCTGTACTTTAGTCAAAGC 58.657 33.333 0.00 0.00 44.27 3.51
5999 6521 5.940192 TTGCTACAATTTGTCCACACTAG 57.060 39.130 5.07 0.00 0.00 2.57
6077 6600 2.892374 TGGAGATGCTGTGTGTATTCG 58.108 47.619 0.00 0.00 0.00 3.34
6212 6735 9.543783 GTCAATAAATAACGGAGTCTATTTCCT 57.456 33.333 0.49 0.00 45.00 3.36
6282 6805 0.973632 AGGTTCGTGTATGCAGTCCA 59.026 50.000 0.00 0.00 0.00 4.02
6347 6870 4.815846 TGAACGGGTTAAGAAAGTGGTAAC 59.184 41.667 0.00 0.00 0.00 2.50
6366 6889 7.919621 GTGGTAACGCTTCTATACTTGTAGATT 59.080 37.037 0.00 0.00 46.04 2.40
6411 6934 4.153655 GTCGGAACCAGGAAAATGACTAAC 59.846 45.833 0.00 0.00 0.00 2.34
6419 6942 5.449304 CAGGAAAATGACTAACCGTTGTTC 58.551 41.667 0.00 0.00 35.87 3.18
6420 6943 5.008217 CAGGAAAATGACTAACCGTTGTTCA 59.992 40.000 0.00 0.00 35.87 3.18
6422 6945 4.823790 AAATGACTAACCGTTGTTCACC 57.176 40.909 0.00 0.00 35.87 4.02
6423 6946 2.243602 TGACTAACCGTTGTTCACCC 57.756 50.000 0.00 0.00 35.87 4.61
6427 6950 2.092807 ACTAACCGTTGTTCACCCTTGT 60.093 45.455 0.00 0.00 35.87 3.16
6429 6952 1.842052 ACCGTTGTTCACCCTTGTTT 58.158 45.000 0.00 0.00 0.00 2.83
6430 6953 2.172679 ACCGTTGTTCACCCTTGTTTT 58.827 42.857 0.00 0.00 0.00 2.43
6431 6954 2.164827 ACCGTTGTTCACCCTTGTTTTC 59.835 45.455 0.00 0.00 0.00 2.29
6432 6955 2.425668 CCGTTGTTCACCCTTGTTTTCT 59.574 45.455 0.00 0.00 0.00 2.52
6433 6956 3.119280 CCGTTGTTCACCCTTGTTTTCTT 60.119 43.478 0.00 0.00 0.00 2.52
6434 6957 4.490743 CGTTGTTCACCCTTGTTTTCTTT 58.509 39.130 0.00 0.00 0.00 2.52
6435 6958 4.326009 CGTTGTTCACCCTTGTTTTCTTTG 59.674 41.667 0.00 0.00 0.00 2.77
6440 6963 3.835395 TCACCCTTGTTTTCTTTGGTGTT 59.165 39.130 6.40 0.00 42.92 3.32
6467 6990 1.134128 TCTGCACAGCTGGACTTTGAA 60.134 47.619 19.93 0.00 0.00 2.69
6522 7045 7.391786 CCAATTCTAACTTATTCGACTTGACG 58.608 38.462 0.00 0.00 27.64 4.35
6569 7093 5.874810 TGATCTGTTTCTAAATCCGACCTTG 59.125 40.000 0.00 0.00 0.00 3.61
6573 7097 5.369833 TGTTTCTAAATCCGACCTTGTTCA 58.630 37.500 0.00 0.00 0.00 3.18
6575 7099 6.488683 TGTTTCTAAATCCGACCTTGTTCATT 59.511 34.615 0.00 0.00 0.00 2.57
6618 7142 9.768662 ATTTTCTAAAAATCTGTTTCAGCATGT 57.231 25.926 0.00 0.00 37.40 3.21
6619 7143 9.598517 TTTTCTAAAAATCTGTTTCAGCATGTT 57.401 25.926 0.00 0.00 37.40 2.71
6620 7144 8.801715 TTCTAAAAATCTGTTTCAGCATGTTC 57.198 30.769 0.00 0.00 37.40 3.18
6621 7145 8.169977 TCTAAAAATCTGTTTCAGCATGTTCT 57.830 30.769 0.00 0.00 37.40 3.01
6646 7170 5.128171 TGTTCTCACAAACTACCACACTAGT 59.872 40.000 0.00 0.00 0.00 2.57
6647 7171 5.864418 TCTCACAAACTACCACACTAGTT 57.136 39.130 0.00 0.00 38.39 2.24
6666 7190 8.138074 CACTAGTTAGCTTATTGATACTCTGCA 58.862 37.037 0.00 0.00 0.00 4.41
6667 7191 8.138712 ACTAGTTAGCTTATTGATACTCTGCAC 58.861 37.037 0.00 0.00 0.00 4.57
6955 7481 2.680841 TGGTATTGGACATGTAAAGCGC 59.319 45.455 0.00 0.00 0.00 5.92
6966 7493 2.679450 TGTAAAGCGCAATCGTGTAGT 58.321 42.857 11.47 0.00 38.14 2.73
6982 7509 5.872617 TCGTGTAGTTTTATTGGTGAGATGG 59.127 40.000 0.00 0.00 0.00 3.51
6986 7513 9.174166 GTGTAGTTTTATTGGTGAGATGGTATT 57.826 33.333 0.00 0.00 0.00 1.89
6994 7521 3.135712 TGGTGAGATGGTATTATGGCGTT 59.864 43.478 0.00 0.00 0.00 4.84
6995 7522 4.345547 TGGTGAGATGGTATTATGGCGTTA 59.654 41.667 0.00 0.00 0.00 3.18
6998 7525 6.430000 GGTGAGATGGTATTATGGCGTTATTT 59.570 38.462 0.00 0.00 0.00 1.40
6999 7526 7.040686 GGTGAGATGGTATTATGGCGTTATTTT 60.041 37.037 0.00 0.00 0.00 1.82
7013 7540 5.277058 GGCGTTATTTTGTTCATGTTTTGCA 60.277 36.000 0.00 0.00 0.00 4.08
7016 7543 7.058241 GCGTTATTTTGTTCATGTTTTGCAATC 59.942 33.333 0.00 0.00 0.00 2.67
7017 7544 8.060679 CGTTATTTTGTTCATGTTTTGCAATCA 58.939 29.630 0.00 3.46 0.00 2.57
7018 7545 9.372541 GTTATTTTGTTCATGTTTTGCAATCAG 57.627 29.630 0.00 0.00 0.00 2.90
7038 7565 4.639755 TCAGATGCACAAAGAACTGTTTGA 59.360 37.500 6.35 0.00 39.40 2.69
7080 7607 3.371102 TCTATTGATGCGTAGTGGAGC 57.629 47.619 0.00 0.00 0.00 4.70
7093 7620 3.906720 AGTGGAGCGTTTATATGGTGT 57.093 42.857 0.00 0.00 0.00 4.16
7095 7622 4.690122 AGTGGAGCGTTTATATGGTGTAC 58.310 43.478 0.00 0.00 0.00 2.90
7096 7623 4.160814 AGTGGAGCGTTTATATGGTGTACA 59.839 41.667 0.00 0.00 0.00 2.90
7101 7628 7.225145 TGGAGCGTTTATATGGTGTACAATTAC 59.775 37.037 0.00 0.00 0.00 1.89
7102 7629 7.225145 GGAGCGTTTATATGGTGTACAATTACA 59.775 37.037 0.00 0.00 35.75 2.41
7128 7655 3.773860 TTTTTCAAGCAGAGTCGCAAA 57.226 38.095 9.14 0.24 0.00 3.68
7129 7656 3.988379 TTTTCAAGCAGAGTCGCAAAT 57.012 38.095 9.14 0.00 0.00 2.32
7130 7657 5.431420 TTTTTCAAGCAGAGTCGCAAATA 57.569 34.783 9.14 0.00 0.00 1.40
7131 7658 4.404507 TTTCAAGCAGAGTCGCAAATAC 57.595 40.909 9.14 0.00 0.00 1.89
7132 7659 3.038788 TCAAGCAGAGTCGCAAATACA 57.961 42.857 9.14 0.00 0.00 2.29
7133 7660 3.398406 TCAAGCAGAGTCGCAAATACAA 58.602 40.909 9.14 0.00 0.00 2.41
7134 7661 3.433274 TCAAGCAGAGTCGCAAATACAAG 59.567 43.478 9.14 0.00 0.00 3.16
7135 7662 1.734465 AGCAGAGTCGCAAATACAAGC 59.266 47.619 9.14 0.00 0.00 4.01
7180 7708 2.179427 GAGAAGGGAAATTGGGTTGGG 58.821 52.381 0.00 0.00 0.00 4.12
7199 7727 2.163412 GGGTTGCGTTGCATCAATCTAA 59.837 45.455 0.00 0.00 38.76 2.10
7229 7809 5.292765 ACTTATATCTTGCGGTGATGACTG 58.707 41.667 0.00 0.00 0.00 3.51
7231 7811 2.479566 ATCTTGCGGTGATGACTGTT 57.520 45.000 0.00 0.00 0.00 3.16
7232 7812 1.795768 TCTTGCGGTGATGACTGTTC 58.204 50.000 0.00 0.00 0.00 3.18
7233 7813 1.069978 TCTTGCGGTGATGACTGTTCA 59.930 47.619 0.00 0.00 35.73 3.18
7234 7814 2.079158 CTTGCGGTGATGACTGTTCAT 58.921 47.619 0.00 0.00 45.78 2.57
7247 7827 6.012658 TGACTGTTCATCAACCTATTTTGC 57.987 37.500 0.00 0.00 0.00 3.68
7248 7828 5.769662 TGACTGTTCATCAACCTATTTTGCT 59.230 36.000 0.00 0.00 0.00 3.91
7249 7829 6.265196 TGACTGTTCATCAACCTATTTTGCTT 59.735 34.615 0.00 0.00 0.00 3.91
7252 7832 7.014615 ACTGTTCATCAACCTATTTTGCTTCTT 59.985 33.333 0.00 0.00 0.00 2.52
7269 7849 7.572523 TGCTTCTTGTATAAGATTCCATTGG 57.427 36.000 2.46 0.00 42.25 3.16
7274 7854 7.872138 TCTTGTATAAGATTCCATTGGTTCCT 58.128 34.615 1.86 0.00 37.99 3.36
7275 7855 7.993183 TCTTGTATAAGATTCCATTGGTTCCTC 59.007 37.037 1.86 0.00 37.99 3.71
7276 7856 6.601332 TGTATAAGATTCCATTGGTTCCTCC 58.399 40.000 1.86 0.00 0.00 4.30
7277 7857 6.389869 TGTATAAGATTCCATTGGTTCCTCCT 59.610 38.462 1.86 0.00 37.07 3.69
7321 7908 1.067071 GGAGGGCGAAAGATATACGGG 60.067 57.143 0.00 0.00 0.00 5.28
7323 7910 0.034337 GGGCGAAAGATATACGGGCA 59.966 55.000 0.00 0.00 0.00 5.36
7325 7912 2.093869 GGGCGAAAGATATACGGGCATA 60.094 50.000 0.00 0.00 0.00 3.14
7327 7914 2.597305 GCGAAAGATATACGGGCATACG 59.403 50.000 0.00 0.00 40.31 3.06
7328 7915 3.176708 CGAAAGATATACGGGCATACGG 58.823 50.000 0.00 0.00 38.39 4.02
7329 7916 2.667473 AAGATATACGGGCATACGGC 57.333 50.000 0.00 0.00 43.74 5.68
7339 7926 3.329114 GCATACGGCCTTGCTTTTC 57.671 52.632 13.22 0.00 35.95 2.29
7351 7938 2.806945 TGCTTTTCCCCACCTATCTG 57.193 50.000 0.00 0.00 0.00 2.90
7353 7940 2.239654 TGCTTTTCCCCACCTATCTGAG 59.760 50.000 0.00 0.00 0.00 3.35
7365 7952 3.041946 CCTATCTGAGTAGTTGGCCCTT 58.958 50.000 0.00 0.00 0.00 3.95
7366 7953 4.223953 CCTATCTGAGTAGTTGGCCCTTA 58.776 47.826 0.00 0.00 0.00 2.69
7367 7954 4.282195 CCTATCTGAGTAGTTGGCCCTTAG 59.718 50.000 0.00 0.00 0.00 2.18
7368 7955 3.468071 TCTGAGTAGTTGGCCCTTAGA 57.532 47.619 0.00 0.00 0.00 2.10
7369 7956 3.366396 TCTGAGTAGTTGGCCCTTAGAG 58.634 50.000 0.00 0.00 0.00 2.43
7370 7957 3.011369 TCTGAGTAGTTGGCCCTTAGAGA 59.989 47.826 0.00 0.00 0.00 3.10
7371 7958 3.097614 TGAGTAGTTGGCCCTTAGAGAC 58.902 50.000 0.00 0.00 0.00 3.36
7372 7959 2.099427 GAGTAGTTGGCCCTTAGAGACG 59.901 54.545 0.00 0.00 0.00 4.18
7373 7960 1.136500 GTAGTTGGCCCTTAGAGACGG 59.864 57.143 0.00 0.00 0.00 4.79
7374 7961 0.252103 AGTTGGCCCTTAGAGACGGA 60.252 55.000 0.00 0.00 0.00 4.69
7375 7962 0.175989 GTTGGCCCTTAGAGACGGAG 59.824 60.000 0.00 0.00 0.00 4.63
7393 7980 5.661458 ACGGAGTTGAGTCATGTATTTAGG 58.339 41.667 0.00 0.00 37.78 2.69
7394 7981 5.187186 ACGGAGTTGAGTCATGTATTTAGGT 59.813 40.000 0.00 0.00 37.78 3.08
7395 7982 5.520288 CGGAGTTGAGTCATGTATTTAGGTG 59.480 44.000 0.00 0.00 0.00 4.00
7396 7983 6.627287 CGGAGTTGAGTCATGTATTTAGGTGA 60.627 42.308 0.00 0.00 0.00 4.02
7397 7984 7.275920 GGAGTTGAGTCATGTATTTAGGTGAT 58.724 38.462 0.00 0.00 0.00 3.06
7398 7985 8.421784 GGAGTTGAGTCATGTATTTAGGTGATA 58.578 37.037 0.00 0.00 0.00 2.15
7399 7986 9.250624 GAGTTGAGTCATGTATTTAGGTGATAC 57.749 37.037 0.00 0.00 0.00 2.24
7400 7987 8.204836 AGTTGAGTCATGTATTTAGGTGATACC 58.795 37.037 0.00 0.00 38.99 2.73
7401 7988 7.669089 TGAGTCATGTATTTAGGTGATACCA 57.331 36.000 0.28 0.00 41.95 3.25
7402 7989 8.262601 TGAGTCATGTATTTAGGTGATACCAT 57.737 34.615 0.28 0.00 41.95 3.55
7403 7990 9.374711 TGAGTCATGTATTTAGGTGATACCATA 57.625 33.333 0.28 0.00 41.95 2.74
7404 7991 9.862371 GAGTCATGTATTTAGGTGATACCATAG 57.138 37.037 0.28 0.00 41.95 2.23
7405 7992 9.381038 AGTCATGTATTTAGGTGATACCATAGT 57.619 33.333 0.28 0.00 41.95 2.12
7408 7995 9.871238 CATGTATTTAGGTGATACCATAGTACC 57.129 37.037 0.28 0.00 41.95 3.34
7409 7996 8.114331 TGTATTTAGGTGATACCATAGTACCG 57.886 38.462 0.28 0.00 41.95 4.02
7410 7997 6.600882 ATTTAGGTGATACCATAGTACCGG 57.399 41.667 0.00 0.00 41.95 5.28
7411 7998 2.885616 AGGTGATACCATAGTACCGGG 58.114 52.381 6.32 0.00 41.95 5.73
7412 7999 1.274447 GGTGATACCATAGTACCGGGC 59.726 57.143 6.32 0.00 38.42 6.13
7413 8000 1.068055 GTGATACCATAGTACCGGGCG 60.068 57.143 6.32 0.00 0.00 6.13
7414 8001 0.108945 GATACCATAGTACCGGGCGC 60.109 60.000 6.32 0.00 0.00 6.53
7415 8002 0.828762 ATACCATAGTACCGGGCGCA 60.829 55.000 10.83 0.00 0.00 6.09
7416 8003 1.737355 TACCATAGTACCGGGCGCAC 61.737 60.000 10.83 3.71 0.00 5.34
7417 8004 2.657296 CATAGTACCGGGCGCACG 60.657 66.667 28.36 28.36 0.00 5.34
7426 8013 3.834799 GGGCGCACGGTAGCTACT 61.835 66.667 22.74 1.53 0.00 2.57
7427 8014 2.484062 GGGCGCACGGTAGCTACTA 61.484 63.158 22.74 0.00 0.00 1.82
7428 8015 1.434696 GGCGCACGGTAGCTACTAA 59.565 57.895 22.74 0.00 0.00 2.24
7429 8016 0.594284 GGCGCACGGTAGCTACTAAG 60.594 60.000 22.74 16.17 0.00 2.18
7430 8017 0.379669 GCGCACGGTAGCTACTAAGA 59.620 55.000 22.74 0.00 0.00 2.10
7431 8018 1.001597 GCGCACGGTAGCTACTAAGAT 60.002 52.381 22.74 2.39 0.00 2.40
7432 8019 2.543238 GCGCACGGTAGCTACTAAGATT 60.543 50.000 22.74 0.00 0.00 2.40
7433 8020 3.043586 CGCACGGTAGCTACTAAGATTG 58.956 50.000 22.74 11.73 0.00 2.67
7434 8021 3.488721 CGCACGGTAGCTACTAAGATTGT 60.489 47.826 22.74 7.99 0.00 2.71
7435 8022 4.260907 CGCACGGTAGCTACTAAGATTGTA 60.261 45.833 22.74 0.00 0.00 2.41
7436 8023 5.213675 GCACGGTAGCTACTAAGATTGTAG 58.786 45.833 22.74 0.00 40.05 2.74
7437 8024 5.008415 GCACGGTAGCTACTAAGATTGTAGA 59.992 44.000 22.74 0.00 39.61 2.59
7438 8025 6.459298 GCACGGTAGCTACTAAGATTGTAGAA 60.459 42.308 22.74 0.00 39.61 2.10
7439 8026 7.478322 CACGGTAGCTACTAAGATTGTAGAAA 58.522 38.462 22.74 0.00 39.61 2.52
7440 8027 7.431668 CACGGTAGCTACTAAGATTGTAGAAAC 59.568 40.741 22.74 0.20 39.61 2.78
7441 8028 7.121759 ACGGTAGCTACTAAGATTGTAGAAACA 59.878 37.037 22.74 0.00 39.61 2.83
7442 8029 8.136165 CGGTAGCTACTAAGATTGTAGAAACAT 58.864 37.037 22.74 0.00 39.61 2.71
7443 8030 9.465985 GGTAGCTACTAAGATTGTAGAAACATC 57.534 37.037 22.74 0.00 39.61 3.06
7446 8033 8.972127 AGCTACTAAGATTGTAGAAACATCTGA 58.028 33.333 5.25 0.00 39.61 3.27
7447 8034 9.757227 GCTACTAAGATTGTAGAAACATCTGAT 57.243 33.333 5.25 0.00 39.61 2.90
7457 8044 9.942850 TTGTAGAAACATCTGATCATAAACAGA 57.057 29.630 0.00 0.00 45.19 3.41
7460 8047 8.362860 AGAAACATCTGATCATAAACAGATCG 57.637 34.615 0.00 0.00 46.59 3.69
7461 8048 7.984050 AGAAACATCTGATCATAAACAGATCGT 59.016 33.333 0.00 0.00 46.59 3.73
7462 8049 9.249457 GAAACATCTGATCATAAACAGATCGTA 57.751 33.333 0.00 0.00 46.59 3.43
7463 8050 9.599866 AAACATCTGATCATAAACAGATCGTAA 57.400 29.630 0.00 0.00 46.59 3.18
7464 8051 9.770097 AACATCTGATCATAAACAGATCGTAAT 57.230 29.630 0.00 0.00 46.59 1.89
7479 8066 9.817809 ACAGATCGTAATATGATTTGTTGTACT 57.182 29.630 11.48 0.00 36.04 2.73
7506 8093 7.908193 AAAAGTTCGTATCAAAACACATCAC 57.092 32.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 6.206829 CACAGTCATCATTGCTCCATATGATT 59.793 38.462 3.65 0.00 38.97 2.57
218 219 2.091885 ACCCTTCAGTTCTTTTGCCTCA 60.092 45.455 0.00 0.00 0.00 3.86
255 256 5.332743 TGAGATGTGAAATTTAGGCCCTTT 58.667 37.500 0.00 0.00 0.00 3.11
278 279 1.188863 GTTGGCATGGAATCTGGCTT 58.811 50.000 0.00 0.00 39.72 4.35
294 295 7.452880 TTGGTTCTTCAAGAATATGAGGTTG 57.547 36.000 2.39 0.00 36.50 3.77
381 382 4.454504 GTCTTTAATGAAAAGGAGGCGTCA 59.545 41.667 8.91 0.00 44.10 4.35
503 504 1.372997 GAGAAGAGCGCACCGTCAA 60.373 57.895 11.47 0.00 0.00 3.18
531 532 6.183360 CCGATCTAGTTTCATCAGGTTAGGAA 60.183 42.308 0.00 0.00 0.00 3.36
651 652 1.280998 GTTCCTTCCCCCTCGATTTGA 59.719 52.381 0.00 0.00 0.00 2.69
712 713 3.028094 AGGGTTATAGTTCTCTCGGCA 57.972 47.619 0.00 0.00 0.00 5.69
759 760 3.377172 AGGCATTTTAATTCGTTCTCCGG 59.623 43.478 0.00 0.00 37.11 5.14
802 804 3.576078 TTCTTGTGTATATGGGCCTGG 57.424 47.619 4.53 0.00 0.00 4.45
830 832 0.947244 CGTTTGCAGTGCTTTCCTCT 59.053 50.000 17.60 0.00 0.00 3.69
1150 1168 4.899239 GGCATGGAGACGGAGGCG 62.899 72.222 0.00 0.00 0.00 5.52
1486 1509 4.278170 ACCGCATCTCAAATTCAAACAAGA 59.722 37.500 0.00 0.00 0.00 3.02
1570 1593 8.800231 TCAAACATGAATTCACATTTACAGTG 57.200 30.769 11.07 4.34 38.32 3.66
1746 1771 7.546358 GCTCAAGTCAGCTATATCAGTATCAT 58.454 38.462 0.00 0.00 36.38 2.45
1840 1865 6.670695 ATTTGCATTAGAACCAAAGAAGGT 57.329 33.333 0.00 0.00 45.91 3.50
1943 1971 2.273179 CCCTGGGAGACGAACGACA 61.273 63.158 7.01 0.00 0.00 4.35
1972 2000 2.171448 AGAATGGTGGGAAGATCCTTCG 59.829 50.000 0.00 0.00 36.57 3.79
2169 2200 8.794553 AGAAGATAGATTGATTGATTTGCCATC 58.205 33.333 0.00 0.00 0.00 3.51
2184 2215 7.728083 AGGCAGTGTAGATGTAGAAGATAGATT 59.272 37.037 0.00 0.00 0.00 2.40
2225 2260 3.127030 CGAAGGTTGAGCTAAATGGGAAC 59.873 47.826 0.00 0.00 0.00 3.62
2235 2270 1.668151 GGCGAACGAAGGTTGAGCT 60.668 57.895 0.00 0.00 36.24 4.09
2305 2341 1.896660 GGATGTGCGTGTGTGGGTT 60.897 57.895 0.00 0.00 0.00 4.11
2391 2427 0.840722 TTCTCCACCAACCCCTCTCC 60.841 60.000 0.00 0.00 0.00 3.71
2502 2561 2.105960 CTAGCTAATTGCCCGTGCGC 62.106 60.000 0.00 0.00 44.23 6.09
2537 2597 7.924103 GGTACACACCAAAGAAATGTTTAAG 57.076 36.000 0.00 0.00 45.04 1.85
2589 2650 1.474478 CAGTTTAGAGCGAGGAGAGCA 59.526 52.381 0.00 0.00 37.01 4.26
2828 2890 9.614792 GACTAATTTGGAAATGACCATAGTAGT 57.385 33.333 15.72 15.72 46.53 2.73
2829 2891 9.838339 AGACTAATTTGGAAATGACCATAGTAG 57.162 33.333 0.00 0.00 41.53 2.57
2831 2893 9.178758 GAAGACTAATTTGGAAATGACCATAGT 57.821 33.333 0.00 0.00 39.82 2.12
2832 2894 9.177608 TGAAGACTAATTTGGAAATGACCATAG 57.822 33.333 0.00 0.00 39.82 2.23
2833 2895 9.699410 ATGAAGACTAATTTGGAAATGACCATA 57.301 29.630 0.00 0.00 39.82 2.74
2834 2896 8.599624 ATGAAGACTAATTTGGAAATGACCAT 57.400 30.769 0.00 0.00 39.82 3.55
2835 2897 7.890127 AGATGAAGACTAATTTGGAAATGACCA 59.110 33.333 0.00 0.00 38.24 4.02
2946 3009 6.100004 CCGTGTCAGTGAAGTATGTCTAAAT 58.900 40.000 0.00 0.00 0.00 1.40
2964 3052 0.871722 TTTGTATGTGCTGCCGTGTC 59.128 50.000 0.00 0.00 0.00 3.67
2987 3075 7.387265 AATCCAACCTGGTTCCTAAATTTTT 57.613 32.000 9.62 0.00 39.03 1.94
2997 3085 5.637809 GATTCGTAAAATCCAACCTGGTTC 58.362 41.667 9.62 0.00 39.03 3.62
3065 3154 3.005791 AGCTGCTTATTTTGGTCACCAAC 59.994 43.478 9.45 0.00 43.82 3.77
3089 3178 7.235804 TCTTAAAAGGTGTTATTGGGCTAGTT 58.764 34.615 0.00 0.00 0.00 2.24
3199 3288 1.003580 GGATCAAGAGTTGCAGGTCCA 59.996 52.381 0.00 0.00 0.00 4.02
3280 3408 1.407656 TTATGAGGCCCGCCACTAGG 61.408 60.000 8.74 0.00 38.92 3.02
3333 3461 2.016905 ACCTAGGTGGGCTATGCTAG 57.983 55.000 15.42 0.00 41.11 3.42
3414 3542 6.303054 TCCTTGGTTACACATTCAATCTCAA 58.697 36.000 0.00 0.00 0.00 3.02
3552 3680 4.869297 GCTGGAATATCATCTTCAGATCCG 59.131 45.833 0.00 0.00 31.21 4.18
3644 3772 4.045636 ACAACTGAATTTCCAACACAGC 57.954 40.909 0.00 0.00 32.67 4.40
3767 3934 5.675684 TGTCAGTTATACATCTGCCAGAA 57.324 39.130 0.00 0.00 0.00 3.02
3816 3983 4.913335 ACCATGATCAATTCAGTCATGC 57.087 40.909 0.00 0.00 44.84 4.06
3839 4006 3.260632 CCCGAACCCAGATCCAAATTTTT 59.739 43.478 0.00 0.00 0.00 1.94
4028 4204 6.454795 GTTTCCATTGGCAGACAGATTAAAA 58.545 36.000 0.00 0.00 0.00 1.52
4029 4205 5.047377 GGTTTCCATTGGCAGACAGATTAAA 60.047 40.000 0.00 0.00 0.00 1.52
4030 4206 4.462483 GGTTTCCATTGGCAGACAGATTAA 59.538 41.667 0.00 0.00 0.00 1.40
4031 4207 4.016444 GGTTTCCATTGGCAGACAGATTA 58.984 43.478 0.00 0.00 0.00 1.75
4054 4230 7.996788 TGGTAGGAATATGTGAGAGATAGGTA 58.003 38.462 0.00 0.00 0.00 3.08
4309 4489 4.215109 ACCAGTGGCTAAAGTTGTGAATT 58.785 39.130 9.78 0.00 0.00 2.17
4329 4509 3.323691 ACAGCCAAAGAACCCAAATAACC 59.676 43.478 0.00 0.00 0.00 2.85
4387 4567 7.831193 AGACAATCCAAATGCTAGTAACTCAAT 59.169 33.333 0.00 0.00 0.00 2.57
4501 4683 3.995199 TCTAAGTTCACCTGTTGAGCTG 58.005 45.455 0.00 0.00 44.53 4.24
4543 4752 6.630444 ATGGAAGTGTTCATGATGCTATTC 57.370 37.500 0.00 0.00 0.00 1.75
4555 4764 7.367285 TGCATAGTGTTAAAATGGAAGTGTTC 58.633 34.615 0.00 0.00 0.00 3.18
4600 4809 5.233902 CCGCACTTGTCATTTTCATTTTGAA 59.766 36.000 0.00 0.00 34.03 2.69
4721 4931 3.914426 ATAACATCTTCCAGGAAGCGT 57.086 42.857 23.08 18.66 39.29 5.07
5129 5347 9.163899 CATGAATATCCAAGAGAGACATAATGG 57.836 37.037 0.00 0.00 0.00 3.16
5164 5382 2.127708 AGGCCGATCCATAGGAAAAGT 58.872 47.619 0.00 0.00 34.34 2.66
5165 5383 2.938956 AGGCCGATCCATAGGAAAAG 57.061 50.000 0.00 0.00 34.34 2.27
5176 5394 4.750598 GGAGTACAAGAATAAAGGCCGATC 59.249 45.833 0.00 0.00 0.00 3.69
5190 5408 9.226606 TCAAATTTGGTAACTATGGAGTACAAG 57.773 33.333 17.90 0.00 33.58 3.16
5326 5544 8.718217 AGTCTATTATCTATAAGGAGAGGGGA 57.282 38.462 0.00 0.00 0.00 4.81
5410 5682 5.535753 AAGAAGGCTTGCACATTTACTTT 57.464 34.783 3.46 0.00 31.83 2.66
5435 5710 7.653311 CACAACCAGAAGATTCGATATCATACA 59.347 37.037 3.12 0.00 0.00 2.29
5649 5924 5.854010 AGTCTTACACAGAGAAACAGACA 57.146 39.130 0.00 0.00 33.11 3.41
5755 6036 8.212312 TCATTTCCAGGCAAATGCAAAATATAT 58.788 29.630 7.80 0.00 41.65 0.86
5756 6037 7.563020 TCATTTCCAGGCAAATGCAAAATATA 58.437 30.769 7.80 0.00 41.65 0.86
5799 6314 4.890158 TTTCTCAGTGACAAGGCTGATA 57.110 40.909 0.00 0.00 40.45 2.15
5804 6319 6.088824 CACAATTATTTCTCAGTGACAAGGC 58.911 40.000 0.00 0.00 0.00 4.35
5812 6327 8.043710 CCTCTCTTACCACAATTATTTCTCAGT 58.956 37.037 0.00 0.00 0.00 3.41
5837 6352 5.598769 CACTTACCTAATACCTACACAGCC 58.401 45.833 0.00 0.00 0.00 4.85
5859 6374 0.178995 TGTTTCAGCACTCCATGGCA 60.179 50.000 6.96 0.00 0.00 4.92
6077 6600 3.056465 CCCTGACTGGTAGAGAAACTGAC 60.056 52.174 0.00 0.00 0.00 3.51
6190 6713 8.148999 GGTGAGGAAATAGACTCCGTTATTTAT 58.851 37.037 0.00 0.00 38.08 1.40
6212 6735 1.067295 ATGAACTGGAAGCCTGGTGA 58.933 50.000 0.00 0.00 37.60 4.02
6375 6898 5.163622 CCTGGTTCCGACGTTTAGAAGTATA 60.164 44.000 0.00 0.00 0.00 1.47
6376 6899 4.381292 CCTGGTTCCGACGTTTAGAAGTAT 60.381 45.833 0.00 0.00 0.00 2.12
6377 6900 3.057315 CCTGGTTCCGACGTTTAGAAGTA 60.057 47.826 0.00 0.00 0.00 2.24
6382 6905 2.443887 TTCCTGGTTCCGACGTTTAG 57.556 50.000 0.00 0.00 0.00 1.85
6391 6914 3.439129 CGGTTAGTCATTTTCCTGGTTCC 59.561 47.826 0.00 0.00 0.00 3.62
6411 6934 2.425668 AGAAAACAAGGGTGAACAACGG 59.574 45.455 0.00 0.00 0.00 4.44
6420 6943 4.901197 AAACACCAAAGAAAACAAGGGT 57.099 36.364 0.00 0.00 0.00 4.34
6445 6968 1.677576 CAAAGTCCAGCTGTGCAGAAA 59.322 47.619 13.81 0.00 0.00 2.52
6448 6971 1.311859 TTCAAAGTCCAGCTGTGCAG 58.688 50.000 13.81 0.00 32.40 4.41
6451 6974 2.575532 TCCTTTCAAAGTCCAGCTGTG 58.424 47.619 13.81 3.77 33.66 3.66
6452 6975 3.297134 TTCCTTTCAAAGTCCAGCTGT 57.703 42.857 13.81 0.00 0.00 4.40
6467 6990 2.687935 ACGCACATGTTGTCTTTTCCTT 59.312 40.909 0.00 0.00 0.00 3.36
6522 7045 3.190118 CAGCAGGAGTTGAGGTGAAAATC 59.810 47.826 0.00 0.00 32.85 2.17
6618 7142 5.353123 GTGTGGTAGTTTGTGAGAACAAGAA 59.647 40.000 0.00 0.00 31.94 2.52
6619 7143 4.873827 GTGTGGTAGTTTGTGAGAACAAGA 59.126 41.667 0.00 0.00 31.94 3.02
6620 7144 4.876107 AGTGTGGTAGTTTGTGAGAACAAG 59.124 41.667 0.00 0.00 31.94 3.16
6621 7145 4.839121 AGTGTGGTAGTTTGTGAGAACAA 58.161 39.130 0.00 0.00 31.94 2.83
6646 7170 8.465273 TCTAGTGCAGAGTATCAATAAGCTAA 57.535 34.615 0.00 0.00 37.82 3.09
6647 7171 8.518702 CATCTAGTGCAGAGTATCAATAAGCTA 58.481 37.037 0.00 0.00 36.48 3.32
6676 7201 5.221303 GCTGCAATTATTCACCACCACATAT 60.221 40.000 0.00 0.00 0.00 1.78
6720 7245 4.012374 CACAACCTTTCACTATCAGCCAT 58.988 43.478 0.00 0.00 0.00 4.40
6904 7430 4.925646 GCAAGGGAAGCAAAAGAATACAAG 59.074 41.667 0.00 0.00 0.00 3.16
6951 7477 4.436852 CCAATAAAACTACACGATTGCGCT 60.437 41.667 9.73 0.00 42.48 5.92
6955 7481 7.359262 TCTCACCAATAAAACTACACGATTG 57.641 36.000 0.00 0.00 0.00 2.67
6966 7493 7.040755 CGCCATAATACCATCTCACCAATAAAA 60.041 37.037 0.00 0.00 0.00 1.52
6982 7509 8.850454 ACATGAACAAAATAACGCCATAATAC 57.150 30.769 0.00 0.00 0.00 1.89
6986 7513 7.359598 GCAAAACATGAACAAAATAACGCCATA 60.360 33.333 0.00 0.00 0.00 2.74
6988 7515 5.277058 GCAAAACATGAACAAAATAACGCCA 60.277 36.000 0.00 0.00 0.00 5.69
6994 7521 8.883954 TCTGATTGCAAAACATGAACAAAATA 57.116 26.923 1.71 0.00 0.00 1.40
6995 7522 7.789273 TCTGATTGCAAAACATGAACAAAAT 57.211 28.000 1.71 0.00 0.00 1.82
6998 7525 5.177881 GCATCTGATTGCAAAACATGAACAA 59.822 36.000 1.71 0.00 42.31 2.83
6999 7526 4.687018 GCATCTGATTGCAAAACATGAACA 59.313 37.500 1.71 0.00 42.31 3.18
7013 7540 5.779529 AACAGTTCTTTGTGCATCTGATT 57.220 34.783 0.00 0.00 0.00 2.57
7016 7543 4.923893 TCAAACAGTTCTTTGTGCATCTG 58.076 39.130 0.00 0.00 33.54 2.90
7017 7544 5.126061 AGTTCAAACAGTTCTTTGTGCATCT 59.874 36.000 0.00 0.00 33.54 2.90
7018 7545 5.343249 AGTTCAAACAGTTCTTTGTGCATC 58.657 37.500 0.00 0.00 33.54 3.91
7059 7586 3.717707 GCTCCACTACGCATCAATAGAA 58.282 45.455 0.00 0.00 0.00 2.10
7110 7637 3.812609 TGTATTTGCGACTCTGCTTGAAA 59.187 39.130 0.00 0.00 35.36 2.69
7116 7643 1.202076 GGCTTGTATTTGCGACTCTGC 60.202 52.381 0.00 0.00 0.00 4.26
7117 7644 2.076100 TGGCTTGTATTTGCGACTCTG 58.924 47.619 0.00 0.00 0.00 3.35
7118 7645 2.472695 TGGCTTGTATTTGCGACTCT 57.527 45.000 0.00 0.00 0.00 3.24
7119 7646 3.552604 TTTGGCTTGTATTTGCGACTC 57.447 42.857 0.00 0.00 0.00 3.36
7120 7647 4.236935 CATTTTGGCTTGTATTTGCGACT 58.763 39.130 0.00 0.00 0.00 4.18
7121 7648 3.987220 ACATTTTGGCTTGTATTTGCGAC 59.013 39.130 0.00 0.00 0.00 5.19
7122 7649 3.986572 CACATTTTGGCTTGTATTTGCGA 59.013 39.130 0.00 0.00 0.00 5.10
7123 7650 3.986572 TCACATTTTGGCTTGTATTTGCG 59.013 39.130 0.00 0.00 0.00 4.85
7124 7651 5.106987 CCTTCACATTTTGGCTTGTATTTGC 60.107 40.000 0.00 0.00 0.00 3.68
7125 7652 6.222389 TCCTTCACATTTTGGCTTGTATTTG 58.778 36.000 0.00 0.00 0.00 2.32
7126 7653 6.418057 TCCTTCACATTTTGGCTTGTATTT 57.582 33.333 0.00 0.00 0.00 1.40
7127 7654 6.610075 ATCCTTCACATTTTGGCTTGTATT 57.390 33.333 0.00 0.00 0.00 1.89
7128 7655 7.118723 TCTATCCTTCACATTTTGGCTTGTAT 58.881 34.615 0.00 0.00 0.00 2.29
7129 7656 6.480763 TCTATCCTTCACATTTTGGCTTGTA 58.519 36.000 0.00 0.00 0.00 2.41
7130 7657 5.324409 TCTATCCTTCACATTTTGGCTTGT 58.676 37.500 0.00 0.00 0.00 3.16
7131 7658 5.902613 TCTATCCTTCACATTTTGGCTTG 57.097 39.130 0.00 0.00 0.00 4.01
7132 7659 7.364144 GGAAATCTATCCTTCACATTTTGGCTT 60.364 37.037 0.00 0.00 36.50 4.35
7133 7660 6.097412 GGAAATCTATCCTTCACATTTTGGCT 59.903 38.462 0.00 0.00 36.50 4.75
7134 7661 6.276091 GGAAATCTATCCTTCACATTTTGGC 58.724 40.000 0.00 0.00 36.50 4.52
7135 7662 6.460123 CGGGAAATCTATCCTTCACATTTTGG 60.460 42.308 0.00 0.00 39.57 3.28
7169 7696 0.105778 CAACGCAACCCAACCCAATT 59.894 50.000 0.00 0.00 0.00 2.32
7180 7708 5.722051 GCAAATTAGATTGATGCAACGCAAC 60.722 40.000 0.00 0.00 43.62 4.17
7210 7790 3.827008 ACAGTCATCACCGCAAGATAT 57.173 42.857 0.00 0.00 43.02 1.63
7229 7809 7.147976 ACAAGAAGCAAAATAGGTTGATGAAC 58.852 34.615 0.00 0.00 0.00 3.18
7231 7811 6.899393 ACAAGAAGCAAAATAGGTTGATGA 57.101 33.333 0.00 0.00 0.00 2.92
7234 7814 9.733556 TCTTATACAAGAAGCAAAATAGGTTGA 57.266 29.630 0.00 0.00 37.85 3.18
7242 7822 9.859427 CAATGGAATCTTATACAAGAAGCAAAA 57.141 29.630 0.00 0.00 43.89 2.44
7243 7823 8.469200 CCAATGGAATCTTATACAAGAAGCAAA 58.531 33.333 0.00 0.00 43.89 3.68
7244 7824 7.615365 ACCAATGGAATCTTATACAAGAAGCAA 59.385 33.333 6.16 0.00 43.89 3.91
7245 7825 7.118723 ACCAATGGAATCTTATACAAGAAGCA 58.881 34.615 6.16 0.00 43.89 3.91
7246 7826 7.573968 ACCAATGGAATCTTATACAAGAAGC 57.426 36.000 6.16 0.00 43.89 3.86
7247 7827 8.624776 GGAACCAATGGAATCTTATACAAGAAG 58.375 37.037 6.16 0.00 43.89 2.85
7248 7828 8.336235 AGGAACCAATGGAATCTTATACAAGAA 58.664 33.333 6.16 0.00 43.89 2.52
7249 7829 7.872138 AGGAACCAATGGAATCTTATACAAGA 58.128 34.615 6.16 0.00 44.77 3.02
7252 7832 6.389869 AGGAGGAACCAATGGAATCTTATACA 59.610 38.462 6.16 0.00 42.04 2.29
7269 7849 2.960688 AAGCTGGCCGAGGAGGAAC 61.961 63.158 0.00 0.00 45.00 3.62
7274 7854 3.249189 AACCAAGCTGGCCGAGGA 61.249 61.111 0.00 0.00 42.67 3.71
7275 7855 2.747855 GAACCAAGCTGGCCGAGG 60.748 66.667 0.00 0.00 42.67 4.63
7276 7856 2.747855 GGAACCAAGCTGGCCGAG 60.748 66.667 0.00 0.00 42.67 4.63
7277 7857 2.424842 AATGGAACCAAGCTGGCCGA 62.425 55.000 0.00 0.00 42.67 5.54
7321 7908 0.179137 GGAAAAGCAAGGCCGTATGC 60.179 55.000 19.59 19.59 42.87 3.14
7323 7910 0.683179 GGGGAAAAGCAAGGCCGTAT 60.683 55.000 0.00 0.00 0.00 3.06
7325 7912 2.600470 GGGGAAAAGCAAGGCCGT 60.600 61.111 0.00 0.00 0.00 5.68
7327 7914 2.583441 GGTGGGGAAAAGCAAGGCC 61.583 63.158 0.00 0.00 0.00 5.19
7328 7915 0.251608 TAGGTGGGGAAAAGCAAGGC 60.252 55.000 0.00 0.00 0.00 4.35
7329 7916 2.024941 AGATAGGTGGGGAAAAGCAAGG 60.025 50.000 0.00 0.00 0.00 3.61
7330 7917 3.019564 CAGATAGGTGGGGAAAAGCAAG 58.980 50.000 0.00 0.00 0.00 4.01
7331 7918 2.647299 TCAGATAGGTGGGGAAAAGCAA 59.353 45.455 0.00 0.00 0.00 3.91
7332 7919 2.239654 CTCAGATAGGTGGGGAAAAGCA 59.760 50.000 0.00 0.00 0.00 3.91
7333 7920 2.239907 ACTCAGATAGGTGGGGAAAAGC 59.760 50.000 0.00 0.00 0.00 3.51
7334 7921 4.717280 ACTACTCAGATAGGTGGGGAAAAG 59.283 45.833 0.00 0.00 0.00 2.27
7335 7922 4.695606 ACTACTCAGATAGGTGGGGAAAA 58.304 43.478 0.00 0.00 0.00 2.29
7351 7938 2.099427 CGTCTCTAAGGGCCAACTACTC 59.901 54.545 6.18 0.00 0.00 2.59
7353 7940 1.136500 CCGTCTCTAAGGGCCAACTAC 59.864 57.143 6.18 0.00 0.00 2.73
7365 7952 3.687125 ACATGACTCAACTCCGTCTCTA 58.313 45.455 0.00 0.00 0.00 2.43
7366 7953 2.520069 ACATGACTCAACTCCGTCTCT 58.480 47.619 0.00 0.00 0.00 3.10
7367 7954 4.640789 ATACATGACTCAACTCCGTCTC 57.359 45.455 0.00 0.00 0.00 3.36
7368 7955 5.407407 AAATACATGACTCAACTCCGTCT 57.593 39.130 0.00 0.00 0.00 4.18
7369 7956 5.749109 CCTAAATACATGACTCAACTCCGTC 59.251 44.000 0.00 0.00 0.00 4.79
7370 7957 5.187186 ACCTAAATACATGACTCAACTCCGT 59.813 40.000 0.00 0.00 0.00 4.69
7371 7958 5.520288 CACCTAAATACATGACTCAACTCCG 59.480 44.000 0.00 0.00 0.00 4.63
7372 7959 6.640518 TCACCTAAATACATGACTCAACTCC 58.359 40.000 0.00 0.00 0.00 3.85
7373 7960 9.250624 GTATCACCTAAATACATGACTCAACTC 57.749 37.037 0.00 0.00 31.30 3.01
7374 7961 8.204836 GGTATCACCTAAATACATGACTCAACT 58.795 37.037 0.00 0.00 34.73 3.16
7375 7962 7.985184 TGGTATCACCTAAATACATGACTCAAC 59.015 37.037 0.00 0.00 39.58 3.18
7376 7963 8.084985 TGGTATCACCTAAATACATGACTCAA 57.915 34.615 0.00 0.00 39.58 3.02
7377 7964 7.669089 TGGTATCACCTAAATACATGACTCA 57.331 36.000 0.00 0.00 39.58 3.41
7378 7965 9.862371 CTATGGTATCACCTAAATACATGACTC 57.138 37.037 0.00 0.00 39.58 3.36
7379 7966 9.381038 ACTATGGTATCACCTAAATACATGACT 57.619 33.333 0.00 0.00 39.58 3.41
7382 7969 9.871238 GGTACTATGGTATCACCTAAATACATG 57.129 37.037 0.00 0.00 39.58 3.21
7383 7970 8.746530 CGGTACTATGGTATCACCTAAATACAT 58.253 37.037 0.07 0.00 39.58 2.29
7384 7971 7.177216 CCGGTACTATGGTATCACCTAAATACA 59.823 40.741 0.07 0.00 39.58 2.29
7385 7972 7.363268 CCCGGTACTATGGTATCACCTAAATAC 60.363 44.444 0.00 0.00 39.58 1.89
7386 7973 6.664816 CCCGGTACTATGGTATCACCTAAATA 59.335 42.308 0.00 0.00 39.58 1.40
7387 7974 5.482878 CCCGGTACTATGGTATCACCTAAAT 59.517 44.000 0.00 0.00 39.58 1.40
7388 7975 4.834496 CCCGGTACTATGGTATCACCTAAA 59.166 45.833 0.00 0.00 39.58 1.85
7389 7976 4.410099 CCCGGTACTATGGTATCACCTAA 58.590 47.826 0.00 0.00 39.58 2.69
7390 7977 3.815396 GCCCGGTACTATGGTATCACCTA 60.815 52.174 0.00 0.00 39.58 3.08
7391 7978 2.885616 CCCGGTACTATGGTATCACCT 58.114 52.381 0.00 0.00 39.58 4.00
7392 7979 1.274447 GCCCGGTACTATGGTATCACC 59.726 57.143 0.00 0.00 39.22 4.02
7393 7980 1.068055 CGCCCGGTACTATGGTATCAC 60.068 57.143 0.00 0.00 0.00 3.06
7394 7981 1.250328 CGCCCGGTACTATGGTATCA 58.750 55.000 0.00 0.00 0.00 2.15
7395 7982 0.108945 GCGCCCGGTACTATGGTATC 60.109 60.000 0.00 0.00 0.00 2.24
7396 7983 0.828762 TGCGCCCGGTACTATGGTAT 60.829 55.000 4.18 0.00 0.00 2.73
7397 7984 1.455402 TGCGCCCGGTACTATGGTA 60.455 57.895 4.18 0.00 0.00 3.25
7398 7985 2.760799 TGCGCCCGGTACTATGGT 60.761 61.111 4.18 0.00 0.00 3.55
7399 7986 2.279918 GTGCGCCCGGTACTATGG 60.280 66.667 4.18 0.00 0.00 2.74
7400 7987 2.657296 CGTGCGCCCGGTACTATG 60.657 66.667 3.71 0.00 0.00 2.23
7401 7988 3.908081 CCGTGCGCCCGGTACTAT 61.908 66.667 23.86 0.00 43.07 2.12
7409 7996 2.008268 TTAGTAGCTACCGTGCGCCC 62.008 60.000 20.31 0.00 38.13 6.13
7410 7997 0.594284 CTTAGTAGCTACCGTGCGCC 60.594 60.000 20.31 0.00 38.13 6.53
7411 7998 0.379669 TCTTAGTAGCTACCGTGCGC 59.620 55.000 20.31 0.00 38.13 6.09
7412 7999 3.043586 CAATCTTAGTAGCTACCGTGCG 58.956 50.000 20.31 5.25 38.13 5.34
7413 8000 4.043037 ACAATCTTAGTAGCTACCGTGC 57.957 45.455 20.31 0.00 0.00 5.34
7414 8001 6.615264 TCTACAATCTTAGTAGCTACCGTG 57.385 41.667 20.31 10.29 39.00 4.94
7415 8002 7.121759 TGTTTCTACAATCTTAGTAGCTACCGT 59.878 37.037 20.31 5.56 39.00 4.83
7416 8003 7.478322 TGTTTCTACAATCTTAGTAGCTACCG 58.522 38.462 20.31 9.40 39.00 4.02
7417 8004 9.465985 GATGTTTCTACAATCTTAGTAGCTACC 57.534 37.037 20.31 2.81 39.00 3.18
7420 8007 8.972127 TCAGATGTTTCTACAATCTTAGTAGCT 58.028 33.333 0.00 0.00 39.00 3.32
7421 8008 9.757227 ATCAGATGTTTCTACAATCTTAGTAGC 57.243 33.333 0.00 0.00 39.00 3.58
7431 8018 9.942850 TCTGTTTATGATCAGATGTTTCTACAA 57.057 29.630 0.09 0.00 37.91 2.41
7434 8021 9.468532 CGATCTGTTTATGATCAGATGTTTCTA 57.531 33.333 14.01 0.00 46.92 2.10
7435 8022 7.984050 ACGATCTGTTTATGATCAGATGTTTCT 59.016 33.333 14.01 0.00 46.92 2.52
7436 8023 8.136057 ACGATCTGTTTATGATCAGATGTTTC 57.864 34.615 14.01 2.51 46.92 2.78
7437 8024 9.599866 TTACGATCTGTTTATGATCAGATGTTT 57.400 29.630 14.01 3.33 46.92 2.83
7438 8025 9.770097 ATTACGATCTGTTTATGATCAGATGTT 57.230 29.630 14.01 5.26 46.92 2.71
7453 8040 9.817809 AGTACAACAAATCATATTACGATCTGT 57.182 29.630 0.00 0.00 0.00 3.41
7480 8067 9.607285 GTGATGTGTTTTGATACGAACTTTTAT 57.393 29.630 0.00 0.00 0.00 1.40
7481 8068 8.996988 GTGATGTGTTTTGATACGAACTTTTA 57.003 30.769 0.00 0.00 0.00 1.52
7482 8069 7.908193 GTGATGTGTTTTGATACGAACTTTT 57.092 32.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.