Multiple sequence alignment - TraesCS2A01G507200

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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 TraesCS2A01G507200 chr2A 100.000 6459 0 0 1 6459 734623602 734630060 0.000000e+00 11928.0
1 TraesCS2A01G507200 chr2A 98.185 1543 18 5 973 2509 734523313 734521775 0.000000e+00 2686.0
2 TraesCS2A01G507200 chr2A 95.619 913 30 4 1 907 734524218 734523310 0.000000e+00 1456.0
3 TraesCS2A01G507200 chr2A 99.630 540 2 0 2691 3230 734521760 734521221 0.000000e+00 987.0
4 TraesCS2A01G507200 chr2A 75.256 683 116 30 5797 6443 734634066 734634731 6.380000e-70 276.0
5 TraesCS2A01G507200 chr2D 92.478 2898 150 38 2691 5543 601203208 601206082 0.000000e+00 4082.0
6 TraesCS2A01G507200 chr2D 93.086 1620 67 20 907 2509 601201603 601203194 0.000000e+00 2329.0
7 TraesCS2A01G507200 chr2D 90.549 455 28 7 5539 5978 601206217 601206671 7.210000e-164 588.0
8 TraesCS2A01G507200 chr2D 87.760 433 24 11 6037 6459 601206700 601207113 4.530000e-131 479.0
9 TraesCS2A01G507200 chr2D 78.245 809 112 39 5670 6456 601244984 601245750 1.640000e-125 460.0
10 TraesCS2A01G507200 chr2D 89.041 292 25 3 1 286 601184822 601185112 7.970000e-94 355.0
11 TraesCS2A01G507200 chr2D 88.584 219 20 3 513 730 601188905 601189119 1.790000e-65 261.0
12 TraesCS2A01G507200 chr2D 75.000 688 110 35 5800 6456 601212183 601212839 1.790000e-65 261.0
13 TraesCS2A01G507200 chr2D 88.571 140 12 3 729 865 601201503 601201641 4.010000e-37 167.0
14 TraesCS2A01G507200 chr2D 91.176 102 9 0 5827 5928 601398803 601398904 8.730000e-29 139.0
15 TraesCS2A01G507200 chr2B 91.387 1428 84 18 907 2318 731339932 731341336 0.000000e+00 1919.0
16 TraesCS2A01G507200 chr2B 91.358 810 44 15 4751 5546 731342516 731343313 0.000000e+00 1085.0
17 TraesCS2A01G507200 chr2B 88.369 662 69 4 1 656 731313127 731313786 0.000000e+00 789.0
18 TraesCS2A01G507200 chr2B 89.066 439 37 6 5539 5971 731343446 731343879 9.530000e-148 534.0
19 TraesCS2A01G507200 chr2B 78.630 847 105 51 5644 6456 731460470 731461274 5.820000e-135 492.0
20 TraesCS2A01G507200 chr2B 84.577 402 50 10 4044 4437 731341794 731342191 7.850000e-104 388.0
21 TraesCS2A01G507200 chr2B 89.098 266 15 6 6020 6276 731343892 731344152 1.050000e-82 318.0
22 TraesCS2A01G507200 chr2B 80.405 148 26 3 2363 2509 181060281 181060136 6.850000e-20 110.0
23 TraesCS2A01G507200 chr2B 74.830 294 48 12 6154 6443 731351016 731351287 6.850000e-20 110.0
24 TraesCS2A01G507200 chr2B 88.636 88 7 1 3800 3884 731457216 731457303 3.190000e-18 104.0
25 TraesCS2A01G507200 chr2B 100.000 47 0 0 6413 6459 731344506 731344552 3.210000e-13 87.9
26 TraesCS2A01G507200 chr2B 78.689 122 21 4 2921 3042 609961483 609961599 6.940000e-10 76.8
27 TraesCS2A01G507200 chr3A 100.000 190 0 0 2506 2695 403210302 403210113 1.030000e-92 351.0
28 TraesCS2A01G507200 chr7B 99.482 193 0 1 2503 2695 380068873 380069064 3.710000e-92 350.0
29 TraesCS2A01G507200 chr7B 97.059 204 2 4 2497 2699 570905339 570905539 2.230000e-89 340.0
30 TraesCS2A01G507200 chr7B 80.405 148 26 3 2363 2509 268063834 268063689 6.850000e-20 110.0
31 TraesCS2A01G507200 chr3B 99.479 192 1 0 2506 2697 129724836 129725027 3.710000e-92 350.0
32 TraesCS2A01G507200 chr3B 98.974 195 0 2 2498 2692 157236452 157236644 1.330000e-91 348.0
33 TraesCS2A01G507200 chr3B 81.481 108 20 0 2921 3028 758458922 758459029 8.920000e-14 89.8
34 TraesCS2A01G507200 chr3B 87.500 72 9 0 2921 2992 238319934 238320005 4.150000e-12 84.2
35 TraesCS2A01G507200 chr6A 98.974 195 1 1 2506 2699 233342397 233342591 1.330000e-91 348.0
36 TraesCS2A01G507200 chr6A 99.474 190 1 0 2503 2692 189563474 189563663 4.790000e-91 346.0
37 TraesCS2A01G507200 chr4B 98.974 195 0 2 2498 2691 421859338 421859145 1.330000e-91 348.0
38 TraesCS2A01G507200 chr4A 98.969 194 2 0 2505 2698 443844961 443844768 1.330000e-91 348.0
39 TraesCS2A01G507200 chr5B 72.039 608 127 26 37 610 629936475 629937073 2.430000e-29 141.0
40 TraesCS2A01G507200 chr5B 81.081 148 25 3 2363 2509 506578723 506578578 1.470000e-21 115.0
41 TraesCS2A01G507200 chr5A 83.088 136 22 1 2925 3060 539071652 539071786 8.790000e-24 122.0
42 TraesCS2A01G507200 chr6D 81.081 148 25 3 2363 2509 339854023 339853878 1.470000e-21 115.0
43 TraesCS2A01G507200 chr6D 80.808 99 18 1 2921 3018 403660713 403660811 6.940000e-10 76.8
44 TraesCS2A01G507200 chr1D 81.119 143 24 3 2368 2509 218666019 218666159 1.900000e-20 111.0
45 TraesCS2A01G507200 chr1D 81.119 143 24 3 2368 2509 234149388 234149528 1.900000e-20 111.0
46 TraesCS2A01G507200 chr1D 80.405 148 25 4 2363 2509 373485541 373485397 6.850000e-20 110.0
47 TraesCS2A01G507200 chr1D 83.333 120 17 3 2920 3039 365430056 365429940 2.460000e-19 108.0
48 TraesCS2A01G507200 chr1B 82.569 109 14 4 2927 3034 312555262 312555366 2.480000e-14 91.6
49 TraesCS2A01G507200 chr1B 94.595 37 2 0 549 585 32557445 32557481 2.520000e-04 58.4
50 TraesCS2A01G507200 chr1A 94.444 36 2 0 549 584 21614234 21614269 1.000000e-03 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 TraesCS2A01G507200 chr2A 734623602 734630060 6458 False 11928.000000 11928 100.000000 1 6459 1 chr2A.!!$F1 6458
1 TraesCS2A01G507200 chr2A 734521221 734524218 2997 True 1709.666667 2686 97.811333 1 3230 3 chr2A.!!$R1 3229
2 TraesCS2A01G507200 chr2A 734634066 734634731 665 False 276.000000 276 75.256000 5797 6443 1 chr2A.!!$F2 646
3 TraesCS2A01G507200 chr2D 601201503 601207113 5610 False 1529.000000 4082 90.488800 729 6459 5 chr2D.!!$F5 5730
4 TraesCS2A01G507200 chr2D 601244984 601245750 766 False 460.000000 460 78.245000 5670 6456 1 chr2D.!!$F2 786
5 TraesCS2A01G507200 chr2D 601184822 601189119 4297 False 308.000000 355 88.812500 1 730 2 chr2D.!!$F4 729
6 TraesCS2A01G507200 chr2D 601212183 601212839 656 False 261.000000 261 75.000000 5800 6456 1 chr2D.!!$F1 656
7 TraesCS2A01G507200 chr2B 731313127 731313786 659 False 789.000000 789 88.369000 1 656 1 chr2B.!!$F2 655
8 TraesCS2A01G507200 chr2B 731339932 731344552 4620 False 721.983333 1919 90.914333 907 6459 6 chr2B.!!$F4 5552
9 TraesCS2A01G507200 chr2B 731457216 731461274 4058 False 298.000000 492 83.633000 3800 6456 2 chr2B.!!$F5 2656

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
147 153 0.546122 TGGTCTGCTTGTTGTGTCCT 59.454 50.000 0.00 0.00 0.00 3.85 F
299 305 0.609131 CTTGGGCCGTCACCTTTCAT 60.609 55.000 0.00 0.00 0.00 2.57 F
942 4522 0.986019 AGGACACACCCACTGAACCA 60.986 55.000 0.00 0.00 40.05 3.67 F
1603 5193 2.492773 GCTGGTGCAGGTGCTTGTT 61.493 57.895 3.18 0.00 42.66 2.83 F
2517 6133 0.039618 TTTGGTCATGAAGGGGAGCC 59.960 55.000 0.00 0.00 0.00 4.70 F
2544 6160 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35 F
2546 6162 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16 F
2547 6163 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33 F
2614 6230 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67 F
2615 6231 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73 F
2641 6257 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46 F
3539 7167 0.743097 GATCTGATGCCCAAACCAGC 59.257 55.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 5638 0.604578 ACATGCACCATTGGCACTTC 59.395 50.000 1.54 0.0 45.23 3.01 R
2388 6000 2.208431 CAATTCGTGGGCAAGCAAAAA 58.792 42.857 0.00 0.0 0.00 1.94 R
2390 6002 0.033228 CCAATTCGTGGGCAAGCAAA 59.967 50.000 0.00 0.0 44.64 3.68 R
2538 6154 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.0 44.78 4.85 R
3363 6982 0.249868 CGTCTTTCTGGTCAGTGGCA 60.250 55.000 0.00 0.0 0.00 4.92 R
3474 7102 0.474660 ACCCCCTCCATCTCTATGCC 60.475 60.000 0.00 0.0 0.00 4.40 R
4143 7853 0.537828 TGCATGGCTGAGCAAACAGA 60.538 50.000 6.82 0.0 39.94 3.41 R
4572 8334 3.213506 TGTTTCAGGACAGGACACATTG 58.786 45.455 0.00 0.0 0.00 2.82 R
4656 8421 7.888021 TGTAAAGCAAGAAAATGGAGGATAAGA 59.112 33.333 0.00 0.0 0.00 2.10 R
4729 8500 6.935741 AAGCATGTTTAAGATATAACCGCA 57.064 33.333 0.00 0.0 0.00 5.69 R
4890 8819 9.865321 ATGAAGATAATTGAACAAATGAAGGTG 57.135 29.630 0.00 0.0 0.00 4.00 R
5759 11968 1.140312 GGGGGAGAATACATCCTGCA 58.860 55.000 0.00 0.0 37.01 4.41 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
78 79 1.333619 GCGTTCCTTTTCTGAAGTGCA 59.666 47.619 0.00 0.00 0.00 4.57
101 107 3.353836 GTGGTCGTGCAATGGCGT 61.354 61.111 0.00 0.00 45.35 5.68
147 153 0.546122 TGGTCTGCTTGTTGTGTCCT 59.454 50.000 0.00 0.00 0.00 3.85
299 305 0.609131 CTTGGGCCGTCACCTTTCAT 60.609 55.000 0.00 0.00 0.00 2.57
480 3764 3.392947 TCTGAGGTTGTTTGACCATGGTA 59.607 43.478 19.80 0.00 42.35 3.25
481 3765 3.750371 TGAGGTTGTTTGACCATGGTAG 58.250 45.455 19.80 0.00 42.35 3.18
482 3766 3.137544 TGAGGTTGTTTGACCATGGTAGT 59.862 43.478 19.80 0.00 42.35 2.73
526 4101 3.825585 TGCTTGCAAGTGGTTGATCATTA 59.174 39.130 26.55 0.00 35.46 1.90
545 4120 7.880160 TCATTATAATTCTGTCTGGGGTTTG 57.120 36.000 0.00 0.00 0.00 2.93
610 4188 5.159209 TCGGACGATGTCTTCTTCTAAAAC 58.841 41.667 0.00 0.00 32.47 2.43
627 4205 9.442047 CTTCTAAAACAAGGACTCTGACAATAT 57.558 33.333 0.00 0.00 0.00 1.28
634 4212 7.495901 ACAAGGACTCTGACAATATACATCTG 58.504 38.462 0.00 0.00 0.00 2.90
656 4234 5.632959 TGAACGTGAAAAACAACCAACTAG 58.367 37.500 0.00 0.00 0.00 2.57
813 4393 3.547468 GCAAATTTCCAATCGATCAACGG 59.453 43.478 0.00 0.00 42.82 4.44
852 4432 3.357079 CGCTGGGCAAGACACACC 61.357 66.667 0.00 0.00 0.00 4.16
873 4453 4.578928 ACCCATTAAACTGTGTGTCTTGTC 59.421 41.667 0.00 0.00 0.00 3.18
942 4522 0.986019 AGGACACACCCACTGAACCA 60.986 55.000 0.00 0.00 40.05 3.67
1509 5095 5.586643 GGTATTGGAGTTTCTTTCTAGCCAG 59.413 44.000 0.00 0.00 0.00 4.85
1603 5193 2.492773 GCTGGTGCAGGTGCTTGTT 61.493 57.895 3.18 0.00 42.66 2.83
1672 5262 4.629634 TGCAGGTAACACATTTCAGTATCG 59.370 41.667 0.00 0.00 41.41 2.92
1696 5286 6.238484 CGGGATTGGCTAAGAATAGAAACTTG 60.238 42.308 0.00 0.00 0.00 3.16
2042 5638 5.281693 TGTTTTCTATGAACATGTCTGCG 57.718 39.130 0.00 0.00 32.44 5.18
2514 6130 5.226194 CAAAATTTTGGTCATGAAGGGGA 57.774 39.130 21.00 0.00 34.59 4.81
2515 6131 5.240121 CAAAATTTTGGTCATGAAGGGGAG 58.760 41.667 21.00 0.00 34.59 4.30
2516 6132 1.923356 TTTTGGTCATGAAGGGGAGC 58.077 50.000 0.00 0.00 0.00 4.70
2517 6133 0.039618 TTTGGTCATGAAGGGGAGCC 59.960 55.000 0.00 0.00 0.00 4.70
2519 6135 0.846427 TGGTCATGAAGGGGAGCCTT 60.846 55.000 0.00 0.00 0.00 4.35
2522 6138 1.755783 CATGAAGGGGAGCCTTGGC 60.756 63.158 2.97 2.97 0.00 4.52
2523 6139 3.350031 ATGAAGGGGAGCCTTGGCG 62.350 63.158 5.95 0.00 0.00 5.69
2531 6147 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2532 6148 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2533 6149 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2534 6150 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2535 6151 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2536 6152 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2537 6153 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2542 6158 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2543 6159 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2544 6160 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2545 6161 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2546 6162 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2547 6163 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2548 6164 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2549 6165 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2550 6166 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2551 6167 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2552 6168 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2553 6169 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2554 6170 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2555 6171 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2556 6172 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2571 6187 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
2572 6188 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
2573 6189 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
2574 6190 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
2575 6191 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
2576 6192 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
2577 6193 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
2578 6194 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
2579 6195 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
2580 6196 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
2594 6210 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2595 6211 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2596 6212 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2597 6213 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2598 6214 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2599 6215 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2600 6216 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2601 6217 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2602 6218 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2603 6219 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2604 6220 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2605 6221 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2606 6222 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2607 6223 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2608 6224 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2609 6225 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2610 6226 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2611 6227 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2612 6228 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2613 6229 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2614 6230 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2615 6231 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2616 6232 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2617 6233 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2618 6234 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2619 6235 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2620 6236 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2621 6237 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2622 6238 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2623 6239 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2624 6240 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2625 6241 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2626 6242 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2627 6243 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2628 6244 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2629 6245 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2630 6246 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2631 6247 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2636 6252 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2637 6253 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2638 6254 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2639 6255 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2640 6256 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2641 6257 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2642 6258 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2643 6259 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2644 6260 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2645 6261 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2646 6262 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2647 6263 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2648 6264 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2649 6265 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2650 6266 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2651 6267 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2652 6268 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2653 6269 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2654 6270 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2655 6271 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2680 6296 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2681 6297 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2682 6298 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2683 6299 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2684 6300 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2685 6301 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2686 6302 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2687 6303 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2688 6304 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2689 6305 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
3238 6857 2.265739 GGCCAGTCAGCATGTCGA 59.734 61.111 0.00 0.00 37.40 4.20
3267 6886 4.411540 AGTCAAGATGATAATGGCTCACCT 59.588 41.667 0.00 0.00 36.63 4.00
3268 6887 4.514441 GTCAAGATGATAATGGCTCACCTG 59.486 45.833 0.00 0.00 36.63 4.00
3381 7000 1.202698 ACTGCCACTGACCAGAAAGAC 60.203 52.381 3.76 0.00 33.40 3.01
3403 7022 3.243002 CGGATAGGTTACGTCCAAGACTC 60.243 52.174 0.00 0.00 32.23 3.36
3408 7029 4.597004 AGGTTACGTCCAAGACTCTGATA 58.403 43.478 0.00 0.00 0.00 2.15
3441 7062 8.019669 GCAGCTTTAGTATACAATCCATGAATG 58.980 37.037 5.50 0.00 0.00 2.67
3503 7131 1.307866 GGAGGGGGTGAGGGAATGA 60.308 63.158 0.00 0.00 0.00 2.57
3539 7167 0.743097 GATCTGATGCCCAAACCAGC 59.257 55.000 0.00 0.00 0.00 4.85
3557 7185 1.592064 GCTGGCTGCTTCTCCTAATC 58.408 55.000 9.31 0.00 38.95 1.75
3563 7191 2.685388 GCTGCTTCTCCTAATCCCAAAC 59.315 50.000 0.00 0.00 0.00 2.93
3579 7207 5.852827 TCCCAAACTGGAATTGTCATTTTC 58.147 37.500 0.00 0.00 40.96 2.29
3621 7249 7.776030 AGATGGTATATTCTATAGTGTCTCCCG 59.224 40.741 0.00 0.00 0.00 5.14
3641 7269 4.202284 CCCGTAATACCTAAGCCAGCTTTA 60.202 45.833 10.64 0.00 37.47 1.85
3652 7280 6.823689 CCTAAGCCAGCTTTACTTCTTTATCA 59.176 38.462 10.64 0.00 37.47 2.15
3745 7386 6.127925 GCAATGTCCAAATGTTGATCTCTGTA 60.128 38.462 0.00 0.00 0.00 2.74
3757 7398 1.357137 TCTCTGTACCCATGCCAACA 58.643 50.000 0.00 0.00 0.00 3.33
3768 7409 3.006110 CCCATGCCAACAAGCCAATATAG 59.994 47.826 0.00 0.00 0.00 1.31
3797 7438 3.087031 CAGATTTGATTGGCCAGACAGT 58.913 45.455 5.11 3.46 0.00 3.55
3829 7473 6.517864 GCACTCTAGGTACCAAAGTAAACTCA 60.518 42.308 15.94 0.00 0.00 3.41
3943 7595 2.664402 AGGTGGTTGCTTGAACTCAT 57.336 45.000 0.00 0.00 34.66 2.90
4068 7775 6.611613 TTAGAAGTGGATGAGTGATCACTT 57.388 37.500 28.46 14.70 42.66 3.16
4143 7853 9.554395 CTAATTATGGTTGGTTGTTTCCTTTTT 57.446 29.630 0.00 0.00 0.00 1.94
4255 7965 6.433404 AGCTACTTCTGCTGTTTGTACTAGTA 59.567 38.462 0.00 0.00 39.56 1.82
4399 8112 9.258826 TGTTTTACAAGTAAGTATTCTGCGTTA 57.741 29.630 0.00 0.00 0.00 3.18
4424 8137 4.218200 TGTTCACTGGCACATTAATCTTGG 59.782 41.667 0.00 0.00 38.20 3.61
4446 8191 3.553828 ACCACCTTGGGTATATCAACG 57.446 47.619 0.00 0.00 43.37 4.10
4611 8373 7.438757 CCTGAAACATCAACAACAATTTCATCA 59.561 33.333 0.00 0.00 35.97 3.07
4656 8421 8.695456 ACTTGAAACATTTGATTCTTACTTGGT 58.305 29.630 2.83 0.00 0.00 3.67
4670 8437 7.510675 TCTTACTTGGTCTTATCCTCCATTT 57.489 36.000 0.00 0.00 0.00 2.32
4675 8442 6.660949 ACTTGGTCTTATCCTCCATTTTCTTG 59.339 38.462 0.00 0.00 0.00 3.02
4676 8443 4.949856 TGGTCTTATCCTCCATTTTCTTGC 59.050 41.667 0.00 0.00 0.00 4.01
4678 8445 5.654209 GGTCTTATCCTCCATTTTCTTGCTT 59.346 40.000 0.00 0.00 0.00 3.91
4679 8446 6.153510 GGTCTTATCCTCCATTTTCTTGCTTT 59.846 38.462 0.00 0.00 0.00 3.51
4681 8448 8.184848 GTCTTATCCTCCATTTTCTTGCTTTAC 58.815 37.037 0.00 0.00 0.00 2.01
4732 8503 6.582437 AAACAAAATGGAAGTAAGTTTGCG 57.418 33.333 0.00 0.00 33.46 4.85
4886 8815 3.681897 CACAGATTGCACCTAGTGAGTTC 59.318 47.826 0.00 0.00 35.23 3.01
4890 8819 5.121454 CAGATTGCACCTAGTGAGTTCTTTC 59.879 44.000 0.00 0.00 35.23 2.62
4892 8821 3.728845 TGCACCTAGTGAGTTCTTTCAC 58.271 45.455 0.00 0.00 46.14 3.18
4901 8830 6.382869 AGTGAGTTCTTTCACCTTCATTTG 57.617 37.500 2.76 0.00 46.81 2.32
4902 8831 5.888161 AGTGAGTTCTTTCACCTTCATTTGT 59.112 36.000 2.76 0.00 46.81 2.83
4903 8832 6.378280 AGTGAGTTCTTTCACCTTCATTTGTT 59.622 34.615 2.76 0.00 46.81 2.83
4907 8836 7.785033 AGTTCTTTCACCTTCATTTGTTCAAT 58.215 30.769 0.00 0.00 0.00 2.57
4908 8837 8.260114 AGTTCTTTCACCTTCATTTGTTCAATT 58.740 29.630 0.00 0.00 0.00 2.32
4909 8838 9.528018 GTTCTTTCACCTTCATTTGTTCAATTA 57.472 29.630 0.00 0.00 0.00 1.40
4911 8840 9.912634 TCTTTCACCTTCATTTGTTCAATTATC 57.087 29.630 0.00 0.00 0.00 1.75
4912 8841 9.918630 CTTTCACCTTCATTTGTTCAATTATCT 57.081 29.630 0.00 0.00 0.00 1.98
4996 10262 5.604231 AGATTCCAGAACAGTCATGGCTATA 59.396 40.000 0.00 0.00 33.92 1.31
5026 10292 7.812191 GGTAAGTTACATGCATGATTTTCACAA 59.188 33.333 32.75 9.90 0.00 3.33
5158 10424 4.870991 GGTGGTCTGAAGCTCTTATAACAC 59.129 45.833 0.00 0.00 0.00 3.32
5186 10453 7.389053 ACTTCAACATCTCAAACATAGGAGTTC 59.611 37.037 0.00 0.00 32.93 3.01
5212 10479 3.071479 AGCAATGCTGGAATTTTGCAAG 58.929 40.909 7.07 6.45 45.26 4.01
5213 10480 2.413634 GCAATGCTGGAATTTTGCAAGC 60.414 45.455 0.00 0.00 43.00 4.01
5214 10481 1.717194 ATGCTGGAATTTTGCAAGCG 58.283 45.000 0.00 0.00 40.24 4.68
5388 11021 2.692709 TTTTCTCTGGATTTGGGGCA 57.307 45.000 0.00 0.00 0.00 5.36
5414 11050 6.106673 AGTAGTTAATGAACCGTTCTCCATG 58.893 40.000 12.43 0.00 36.08 3.66
5420 11056 2.028476 TGAACCGTTCTCCATGTGTAGG 60.028 50.000 12.43 0.00 0.00 3.18
5467 11245 3.230976 GGTGTTTCCCTTCCATGAACTT 58.769 45.455 0.00 0.00 0.00 2.66
5469 11247 4.501400 GGTGTTTCCCTTCCATGAACTTTG 60.501 45.833 0.00 0.00 0.00 2.77
5546 11535 3.286353 TGTCTGATTTTGCACACTGGAA 58.714 40.909 0.00 0.00 0.00 3.53
5639 11843 7.534723 AATCAGTACACCACCATATACGTAT 57.465 36.000 13.54 13.54 0.00 3.06
5682 11886 3.184683 GCAGCAGCGACTCGAAGG 61.185 66.667 1.63 0.00 0.00 3.46
5705 11913 4.332819 GCGCTTTGGTGGATGGATATATAC 59.667 45.833 0.00 0.00 0.00 1.47
5755 11964 4.130118 GGTGAAGCTATAACATGGTCAGG 58.870 47.826 0.00 0.00 0.00 3.86
5759 11968 2.774234 AGCTATAACATGGTCAGGCAGT 59.226 45.455 0.00 0.00 0.00 4.40
5768 11980 1.002868 GTCAGGCAGTGCAGGATGT 60.003 57.895 18.61 0.00 39.31 3.06
5769 11981 0.250234 GTCAGGCAGTGCAGGATGTA 59.750 55.000 18.61 0.00 39.31 2.29
5770 11982 1.134280 GTCAGGCAGTGCAGGATGTAT 60.134 52.381 18.61 0.00 39.31 2.29
5772 11984 1.945394 CAGGCAGTGCAGGATGTATTC 59.055 52.381 18.61 0.00 39.31 1.75
5773 11985 1.842562 AGGCAGTGCAGGATGTATTCT 59.157 47.619 18.61 0.00 39.31 2.40
5774 11986 2.158842 AGGCAGTGCAGGATGTATTCTC 60.159 50.000 18.61 0.00 39.31 2.87
5777 11990 1.771255 AGTGCAGGATGTATTCTCCCC 59.229 52.381 0.00 0.00 39.31 4.81
5967 12184 2.002586 CTCATCGCACTCGTTCCAAAT 58.997 47.619 0.00 0.00 36.96 2.32
5987 12204 7.031372 CCAAATGAACCACAATCAATCACTAG 58.969 38.462 0.00 0.00 0.00 2.57
5998 12215 8.058328 CACAATCAATCACTAGTTAAGCATACG 58.942 37.037 0.00 0.00 0.00 3.06
5999 12216 7.979537 ACAATCAATCACTAGTTAAGCATACGA 59.020 33.333 0.00 0.00 0.00 3.43
6156 12410 4.551388 GTCAGCCTCTGAACCTATATTCG 58.449 47.826 0.00 0.00 42.46 3.34
6165 12419 6.119536 TCTGAACCTATATTCGGTTTTGCAT 58.880 36.000 9.65 0.00 44.41 3.96
6193 12447 3.986277 TGGATCATCGTCATGACTGATG 58.014 45.455 32.25 32.25 42.05 3.07
6258 12515 0.617249 CCTCCCACTGCTTCTCCTCT 60.617 60.000 0.00 0.00 0.00 3.69
6279 12536 2.294078 GGACCAGTCCTCCTGTGGG 61.294 68.421 9.67 0.00 46.16 4.61
6280 12537 1.536662 GACCAGTCCTCCTGTGGGT 60.537 63.158 0.00 0.00 39.74 4.51
6281 12538 0.252103 GACCAGTCCTCCTGTGGGTA 60.252 60.000 0.00 0.00 39.74 3.69
6282 12539 0.192566 ACCAGTCCTCCTGTGGGTAA 59.807 55.000 0.00 0.00 39.74 2.85
6283 12540 0.905357 CCAGTCCTCCTGTGGGTAAG 59.095 60.000 0.00 0.00 39.74 2.34
6284 12541 1.552486 CCAGTCCTCCTGTGGGTAAGA 60.552 57.143 0.00 0.00 39.74 2.10
6285 12542 2.257207 CAGTCCTCCTGTGGGTAAGAA 58.743 52.381 0.00 0.00 36.37 2.52
6286 12543 2.637872 CAGTCCTCCTGTGGGTAAGAAA 59.362 50.000 0.00 0.00 36.37 2.52
6291 12548 3.583086 CCTCCTGTGGGTAAGAAAGAGAA 59.417 47.826 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 1.070786 ATTGCACGACCACGAACCT 59.929 52.632 0.00 0.00 42.66 3.50
101 107 0.609406 CTCCACCAGAGGTCTGTCGA 60.609 60.000 6.25 0.00 42.27 4.20
147 153 3.727258 CCGGGAGCACCATGGGAA 61.727 66.667 18.09 0.00 40.22 3.97
452 3208 2.933906 GTCAAACAACCTCAGACGACAA 59.066 45.455 0.00 0.00 0.00 3.18
500 3785 2.030371 TCAACCACTTGCAAGCATCAA 58.970 42.857 26.27 5.20 0.00 2.57
526 4101 3.336694 ACCCAAACCCCAGACAGAATTAT 59.663 43.478 0.00 0.00 0.00 1.28
545 4120 2.704464 AGCCCGACTTACAATTACCC 57.296 50.000 0.00 0.00 0.00 3.69
582 4157 0.526524 GAAGACATCGTCCGAGCCTG 60.527 60.000 0.00 0.00 32.18 4.85
610 4188 7.720442 TCAGATGTATATTGTCAGAGTCCTTG 58.280 38.462 0.00 0.00 0.00 3.61
627 4205 5.354513 TGGTTGTTTTTCACGTTCAGATGTA 59.645 36.000 0.00 0.00 0.00 2.29
634 4212 5.633927 ACTAGTTGGTTGTTTTTCACGTTC 58.366 37.500 0.00 0.00 0.00 3.95
813 4393 1.868987 ATGGTTTGGTAAACGCGCCC 61.869 55.000 5.73 1.19 42.29 6.13
852 4432 4.578516 TGGACAAGACACACAGTTTAATGG 59.421 41.667 0.00 0.00 0.00 3.16
904 4484 3.601685 CCCAGCGGCGTGGTTTTT 61.602 61.111 21.25 0.00 35.60 1.94
925 4505 1.238439 CATGGTTCAGTGGGTGTGTC 58.762 55.000 0.00 0.00 0.00 3.67
1509 5095 2.028385 TCCGAGTAAAGGGAAGAAGTGC 60.028 50.000 0.00 0.00 0.00 4.40
1603 5193 3.554960 CCATCTTCAGGTCGTTTCTCACA 60.555 47.826 0.00 0.00 0.00 3.58
1672 5262 6.460261 GCAAGTTTCTATTCTTAGCCAATCCC 60.460 42.308 0.00 0.00 0.00 3.85
1696 5286 3.192844 TCGATATCGGTTCCCAATCTAGC 59.807 47.826 24.12 0.00 40.29 3.42
1813 5403 1.568597 ACAGGTATGCCAGCCCAATAA 59.431 47.619 1.54 0.00 37.19 1.40
2042 5638 0.604578 ACATGCACCATTGGCACTTC 59.395 50.000 1.54 0.00 45.23 3.01
2388 6000 2.208431 CAATTCGTGGGCAAGCAAAAA 58.792 42.857 0.00 0.00 0.00 1.94
2389 6001 1.539929 CCAATTCGTGGGCAAGCAAAA 60.540 47.619 0.00 0.00 44.64 2.44
2390 6002 0.033228 CCAATTCGTGGGCAAGCAAA 59.967 50.000 0.00 0.00 44.64 3.68
2513 6129 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2514 6130 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2515 6131 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2516 6132 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2517 6133 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2519 6135 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2524 6140 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2525 6141 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2526 6142 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2527 6143 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2528 6144 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2529 6145 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2530 6146 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2531 6147 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2532 6148 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2533 6149 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2534 6150 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2535 6151 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2536 6152 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2537 6153 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2538 6154 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2539 6155 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2551 6167 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
2552 6168 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
2553 6169 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
2554 6170 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
2555 6171 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
2556 6172 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
2557 6173 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
2558 6174 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
2559 6175 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
2560 6176 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
2561 6177 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2562 6178 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2563 6179 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2564 6180 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2565 6181 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2566 6182 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2567 6183 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2568 6184 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2569 6185 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2570 6186 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2571 6187 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2572 6188 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2584 6200 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2585 6201 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2586 6202 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2587 6203 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2588 6204 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2589 6205 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2590 6206 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2591 6207 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2592 6208 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2593 6209 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2594 6210 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2595 6211 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2596 6212 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2597 6213 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2598 6214 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2599 6215 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2600 6216 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2601 6217 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2602 6218 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2603 6219 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2604 6220 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2605 6221 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2606 6222 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2607 6223 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2608 6224 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2609 6225 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2610 6226 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2620 6236 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2621 6237 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2622 6238 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2623 6239 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2624 6240 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2625 6241 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2626 6242 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2627 6243 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2628 6244 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2629 6245 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2630 6246 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2631 6247 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2632 6248 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2633 6249 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2634 6250 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2635 6251 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2636 6252 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2637 6253 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2638 6254 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2650 6266 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2653 6269 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2654 6270 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2655 6271 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2656 6272 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2662 6278 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2663 6279 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2664 6280 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2665 6281 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2666 6282 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2687 6303 3.137176 TGGATGGTGGCCAAAATCAAAAA 59.863 39.130 23.59 8.96 36.95 1.94
2688 6304 2.707791 TGGATGGTGGCCAAAATCAAAA 59.292 40.909 23.59 10.84 36.95 2.44
2689 6305 2.333069 TGGATGGTGGCCAAAATCAAA 58.667 42.857 23.59 12.75 36.95 2.69
3238 6857 5.068636 GCCATTATCATCTTGACTGGATGT 58.931 41.667 0.00 0.00 40.76 3.06
3363 6982 0.249868 CGTCTTTCTGGTCAGTGGCA 60.250 55.000 0.00 0.00 0.00 4.92
3381 7000 2.686915 AGTCTTGGACGTAACCTATCCG 59.313 50.000 0.00 0.00 37.67 4.18
3403 7022 9.743057 GTATACTAAAGCTGCAGGATATATCAG 57.257 37.037 17.12 7.44 0.00 2.90
3408 7029 8.043710 GGATTGTATACTAAAGCTGCAGGATAT 58.956 37.037 17.12 2.43 0.00 1.63
3441 7062 6.632035 CGTAAGACGTAAGGAATACAGATCAC 59.368 42.308 0.00 0.00 46.39 3.06
3471 7099 2.061061 CCCCTCCATCTCTATGCCTTT 58.939 52.381 0.00 0.00 0.00 3.11
3474 7102 0.474660 ACCCCCTCCATCTCTATGCC 60.475 60.000 0.00 0.00 0.00 4.40
3475 7103 0.689623 CACCCCCTCCATCTCTATGC 59.310 60.000 0.00 0.00 0.00 3.14
3503 7131 8.031277 GCATCAGATCAAACCAAAATAGTCTTT 58.969 33.333 0.00 0.00 0.00 2.52
3539 7167 1.202746 GGGATTAGGAGAAGCAGCCAG 60.203 57.143 0.00 0.00 0.00 4.85
3557 7185 5.857268 AGAAAATGACAATTCCAGTTTGGG 58.143 37.500 7.31 0.00 38.32 4.12
3605 7233 6.845908 AGGTATTACGGGAGACACTATAGAA 58.154 40.000 6.78 0.00 0.00 2.10
3621 7249 7.273712 AGAAGTAAAGCTGGCTTAGGTATTAC 58.726 38.462 8.30 6.41 35.72 1.89
3652 7280 6.295292 GGAGCACCAAATGAAACCTTATCTTT 60.295 38.462 0.00 0.00 35.97 2.52
3685 7326 5.816777 ACGCAATAAGCATTAAATTTGCCAT 59.183 32.000 0.00 0.00 46.13 4.40
3715 7356 4.378774 TCAACATTTGGACATTGCAAAGG 58.621 39.130 1.71 0.89 43.39 3.11
3745 7386 2.200930 TGGCTTGTTGGCATGGGT 59.799 55.556 0.00 0.00 46.76 4.51
3757 7398 8.636213 CAAATCTGATGGAAACTATATTGGCTT 58.364 33.333 0.00 0.00 0.00 4.35
3768 7409 4.081531 TGGCCAATCAAATCTGATGGAAAC 60.082 41.667 0.61 0.00 41.66 2.78
3797 7438 1.063867 GGTACCTAGAGTGCTCCCTCA 60.064 57.143 4.06 0.00 33.75 3.86
3829 7473 3.992999 TGCCATCATAGGGGTGAAAAAT 58.007 40.909 0.00 0.00 0.00 1.82
4104 7811 2.280308 TAATTAGCCCACCACTCCCT 57.720 50.000 0.00 0.00 0.00 4.20
4143 7853 0.537828 TGCATGGCTGAGCAAACAGA 60.538 50.000 6.82 0.00 39.94 3.41
4255 7965 6.478129 TCCCGTTTAGGAAACTTGATTATGT 58.522 36.000 1.02 0.00 45.00 2.29
4292 8005 8.956426 TCCCATCTGTACAAGATAAAAATGAAC 58.044 33.333 0.00 0.00 44.24 3.18
4396 8109 7.538575 AGATTAATGTGCCAGTGAACAATAAC 58.461 34.615 0.00 4.67 27.55 1.89
4399 8112 6.392354 CAAGATTAATGTGCCAGTGAACAAT 58.608 36.000 0.00 0.00 0.00 2.71
4424 8137 3.875134 CGTTGATATACCCAAGGTGGTTC 59.125 47.826 0.00 0.00 39.91 3.62
4446 8191 7.653311 AGAGCAAATTGTTTAATGACTGGTTTC 59.347 33.333 0.00 0.00 0.00 2.78
4572 8334 3.213506 TGTTTCAGGACAGGACACATTG 58.786 45.455 0.00 0.00 0.00 2.82
4631 8393 9.185192 GACCAAGTAAGAATCAAATGTTTCAAG 57.815 33.333 6.91 0.00 0.00 3.02
4632 8394 8.912988 AGACCAAGTAAGAATCAAATGTTTCAA 58.087 29.630 6.91 0.00 0.00 2.69
4656 8421 7.888021 TGTAAAGCAAGAAAATGGAGGATAAGA 59.112 33.333 0.00 0.00 0.00 2.10
4729 8500 6.935741 AAGCATGTTTAAGATATAACCGCA 57.064 33.333 0.00 0.00 0.00 5.69
4886 8815 9.918630 AGATAATTGAACAAATGAAGGTGAAAG 57.081 29.630 0.00 0.00 0.00 2.62
4890 8819 9.865321 ATGAAGATAATTGAACAAATGAAGGTG 57.135 29.630 0.00 0.00 0.00 4.00
4892 8821 9.525409 GGATGAAGATAATTGAACAAATGAAGG 57.475 33.333 0.00 0.00 0.00 3.46
4909 8838 9.911788 ACAGACATAATTAAACTGGATGAAGAT 57.088 29.630 15.87 0.00 33.57 2.40
4910 8839 9.739276 AACAGACATAATTAAACTGGATGAAGA 57.261 29.630 15.87 0.00 33.57 2.87
4996 10262 7.466746 AAATCATGCATGTAACTTACCAAGT 57.533 32.000 25.43 0.00 45.46 3.16
5026 10292 9.467258 CACAAATTCTGAAAAACATGATACACT 57.533 29.630 0.00 0.00 0.00 3.55
5158 10424 5.869344 TCCTATGTTTGAGATGTTGAAGTCG 59.131 40.000 0.00 0.00 0.00 4.18
5186 10453 4.378046 GCAAAATTCCAGCATTGCTCTTTG 60.378 41.667 8.54 13.28 43.58 2.77
5212 10479 2.101582 AGACCAGTGGAAGTATCATCGC 59.898 50.000 18.40 0.00 0.00 4.58
5213 10480 3.243569 GGAGACCAGTGGAAGTATCATCG 60.244 52.174 18.40 0.00 0.00 3.84
5214 10481 3.964031 AGGAGACCAGTGGAAGTATCATC 59.036 47.826 18.40 0.00 0.00 2.92
5374 11006 1.839994 CTACTCTGCCCCAAATCCAGA 59.160 52.381 0.00 0.00 34.68 3.86
5388 11021 5.479375 TGGAGAACGGTTCATTAACTACTCT 59.521 40.000 21.86 0.00 35.81 3.24
5414 11050 8.738645 ATCCTTTTCAGATTTGTATCCTACAC 57.261 34.615 0.00 0.00 38.63 2.90
5420 11056 9.173939 CGCATTTATCCTTTTCAGATTTGTATC 57.826 33.333 0.00 0.00 0.00 2.24
5504 11493 9.698309 CAGACAAGAGAGTTCAGATAGTTTTTA 57.302 33.333 0.00 0.00 0.00 1.52
5562 11695 8.880991 TCCTCTTCACTTTCAGTATAAGTACT 57.119 34.615 0.00 0.00 41.84 2.73
5578 11711 7.667043 TTGTATTGTGTTGTATCCTCTTCAC 57.333 36.000 0.00 0.00 0.00 3.18
5639 11843 6.542005 AGCAAATCATTGTATCCGTATGAACA 59.458 34.615 0.00 0.00 38.85 3.18
5648 11852 3.378339 GCTGCAGCAAATCATTGTATCC 58.622 45.455 33.36 0.00 41.59 2.59
5682 11886 1.609208 ATATCCATCCACCAAAGCGC 58.391 50.000 0.00 0.00 0.00 5.92
5705 11913 8.506140 AATCACGAATTCGCAATTATATTTGG 57.494 30.769 27.03 0.00 44.43 3.28
5716 11924 2.550180 TCACCAAAATCACGAATTCGCA 59.450 40.909 27.03 14.73 44.43 5.10
5755 11964 2.216898 GGAGAATACATCCTGCACTGC 58.783 52.381 0.00 0.00 33.77 4.40
5759 11968 1.140312 GGGGGAGAATACATCCTGCA 58.860 55.000 0.00 0.00 37.01 4.41
5777 11990 4.728534 TGCAATTTCGTCGAAATTAAGGG 58.271 39.130 33.85 25.29 46.37 3.95
5967 12184 7.094805 GCTTAACTAGTGATTGATTGTGGTTCA 60.095 37.037 0.00 0.00 0.00 3.18
5981 12198 8.851960 CATACTTTCGTATGCTTAACTAGTGA 57.148 34.615 0.00 0.00 44.50 3.41
6009 12226 9.698309 GGAGATCGTCAATAAGAATGAATTAGA 57.302 33.333 0.00 0.00 0.00 2.10
6010 12227 9.703892 AGGAGATCGTCAATAAGAATGAATTAG 57.296 33.333 0.00 0.00 0.00 1.73
6013 12230 7.810282 CGTAGGAGATCGTCAATAAGAATGAAT 59.190 37.037 0.00 0.00 0.00 2.57
6014 12231 7.139392 CGTAGGAGATCGTCAATAAGAATGAA 58.861 38.462 0.00 0.00 0.00 2.57
6016 12233 6.919687 CGTAGGAGATCGTCAATAAGAATG 57.080 41.667 0.00 0.00 0.00 2.67
6029 12246 4.806964 CCTTAGGAGGTACCGTAGGAGATC 60.807 54.167 6.18 0.00 45.05 2.75
6031 12248 2.441001 CCTTAGGAGGTACCGTAGGAGA 59.559 54.545 6.18 0.00 45.05 3.71
6032 12249 2.861274 CCTTAGGAGGTACCGTAGGAG 58.139 57.143 6.18 3.60 45.05 3.69
6156 12410 3.448301 TGATCCATTCCAGATGCAAAACC 59.552 43.478 0.00 0.00 0.00 3.27
6165 12419 3.642848 TCATGACGATGATCCATTCCAGA 59.357 43.478 0.00 0.00 33.40 3.86
6193 12447 0.804156 GCTGACAAGTAGGCTCGCTC 60.804 60.000 0.00 0.00 0.00 5.03
6194 12448 1.216710 GCTGACAAGTAGGCTCGCT 59.783 57.895 0.00 0.00 0.00 4.93
6196 12450 2.161486 GCGCTGACAAGTAGGCTCG 61.161 63.158 0.00 0.00 0.00 5.03
6279 12536 7.772332 TTGACTGAGTTGTTCTCTTTCTTAC 57.228 36.000 0.00 0.00 43.13 2.34
6280 12537 8.786826 TTTTGACTGAGTTGTTCTCTTTCTTA 57.213 30.769 0.00 0.00 43.13 2.10
6281 12538 7.687941 TTTTGACTGAGTTGTTCTCTTTCTT 57.312 32.000 0.00 0.00 43.13 2.52
6282 12539 7.554118 TGATTTTGACTGAGTTGTTCTCTTTCT 59.446 33.333 0.00 0.00 43.13 2.52
6283 12540 7.641802 GTGATTTTGACTGAGTTGTTCTCTTTC 59.358 37.037 0.00 0.00 43.13 2.62
6284 12541 7.337942 AGTGATTTTGACTGAGTTGTTCTCTTT 59.662 33.333 0.00 0.00 43.13 2.52
6285 12542 6.825721 AGTGATTTTGACTGAGTTGTTCTCTT 59.174 34.615 0.00 0.00 43.13 2.85
6286 12543 6.352516 AGTGATTTTGACTGAGTTGTTCTCT 58.647 36.000 0.00 0.00 43.13 3.10
6291 12548 5.297776 CCTTGAGTGATTTTGACTGAGTTGT 59.702 40.000 0.00 0.00 0.00 3.32
6324 12584 0.450583 ATTGCAGCATCACTTCAGCG 59.549 50.000 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.