Multiple sequence alignment - TraesCS7D01G360500

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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 TraesCS7D01G360500 chr7D 100.000 5514 0 0 1 5514 463260603 463266116 0.000000e+00 10183
1 TraesCS7D01G360500 chr7A 89.341 2533 145 37 4 2472 536985260 536982789 0.000000e+00 3066
2 TraesCS7D01G360500 chr7A 89.618 2042 106 29 3528 5514 536981655 536979665 0.000000e+00 2499
3 TraesCS7D01G360500 chr7A 95.238 462 20 1 3070 3529 536982201 536981740 0.000000e+00 730
4 TraesCS7D01G360500 chr7A 93.534 464 26 3 2554 3016 536982790 536982330 0.000000e+00 688
5 TraesCS7D01G360500 chr7B 88.828 2023 111 33 3528 5514 488411808 488409865 0.000000e+00 2377
6 TraesCS7D01G360500 chr7B 89.417 1682 83 26 143 1758 488415315 488413663 0.000000e+00 2032
7 TraesCS7D01G360500 chr7B 91.235 1004 57 8 2554 3529 488412870 488411870 0.000000e+00 1338
8 TraesCS7D01G360500 chr7B 94.796 711 34 3 1764 2472 488413578 488412869 0.000000e+00 1105
9 TraesCS7D01G360500 chr7B 90.625 160 14 1 3 162 488415482 488415324 1.560000e-50 211
10 TraesCS7D01G360500 chr3D 93.519 108 4 3 1689 1793 315480532 315480425 2.060000e-34 158
11 TraesCS7D01G360500 chr3D 90.991 111 8 2 1689 1798 73853134 73853243 1.240000e-31 148
12 TraesCS7D01G360500 chr3D 96.471 85 3 0 2471 2555 602205164 602205248 2.070000e-29 141
13 TraesCS7D01G360500 chr3D 90.816 98 8 1 2468 2565 437189806 437189902 4.480000e-26 130
14 TraesCS7D01G360500 chr6D 93.396 106 6 1 1689 1793 221843041 221843146 7.400000e-34 156
15 TraesCS7D01G360500 chr6D 94.318 88 5 0 2469 2556 325727709 325727796 9.630000e-28 135
16 TraesCS7D01G360500 chr6D 90.196 102 8 2 2468 2569 39676412 39676511 1.250000e-26 132
17 TraesCS7D01G360500 chr6A 93.333 105 7 0 1689 1793 184388281 184388177 7.400000e-34 156
18 TraesCS7D01G360500 chr6A 93.396 106 6 1 1689 1793 263886912 263887017 7.400000e-34 156
19 TraesCS7D01G360500 chr6A 94.318 88 5 0 2469 2556 464514427 464514514 9.630000e-28 135
20 TraesCS7D01G360500 chr2B 93.333 105 6 1 1689 1793 251374916 251374813 2.660000e-33 154
21 TraesCS7D01G360500 chr2B 95.349 86 4 0 2471 2556 14834325 14834410 2.680000e-28 137
22 TraesCS7D01G360500 chr2D 91.150 113 8 2 1689 1801 195294990 195294880 9.570000e-33 152
23 TraesCS7D01G360500 chr4B 96.471 85 3 0 2471 2555 656162703 656162619 2.070000e-29 141
24 TraesCS7D01G360500 chr5D 96.471 85 2 1 2471 2555 122198431 122198514 7.450000e-29 139
25 TraesCS7D01G360500 chr4D 93.684 95 3 3 2462 2555 504090803 504090711 7.450000e-29 139


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 TraesCS7D01G360500 chr7D 463260603 463266116 5513 False 10183.00 10183 100.00000 1 5514 1 chr7D.!!$F1 5513
1 TraesCS7D01G360500 chr7A 536979665 536985260 5595 True 1745.75 3066 91.93275 4 5514 4 chr7A.!!$R1 5510
2 TraesCS7D01G360500 chr7B 488409865 488415482 5617 True 1412.60 2377 90.98020 3 5514 5 chr7B.!!$R1 5511


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
789 826 0.532862 CGTGTGCTCCAAACTCCAGT 60.533 55.0 0.00 0.0 0.00 4.00 F
1416 1523 0.035915 GAAGGCCACCTGGAGAAGAC 60.036 60.0 5.01 0.0 37.39 3.01 F
1465 1572 0.617413 AGGAAGATCTGCTGGTGGTG 59.383 55.0 0.00 0.0 0.00 4.17 F
2098 2295 0.671251 GGTTTCACCATTGTTCGGCA 59.329 50.0 0.00 0.0 38.42 5.69 F
2835 3032 0.677288 TACACCTGTGGACCGTCAAG 59.323 55.0 0.00 0.0 34.19 3.02 F
4267 4662 0.251341 GCCCTGAAGGTGTGGTGATT 60.251 55.0 0.00 0.0 38.26 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2241 0.033109 TCGCCCATCCTCTCTCAAGA 60.033 55.0 0.00 0.0 0.00 3.02 R
2848 3045 0.176680 AGTCAGAGCATAACCAGCCG 59.823 55.0 0.00 0.0 0.00 5.52 R
2875 3072 2.260844 ATCCTGGACCACATATTGCG 57.739 50.0 0.00 0.0 0.00 4.85 R
3863 4238 2.160822 GATCACCATCCAGGATGTCG 57.839 55.0 25.35 16.6 41.22 4.35 R
4337 4732 0.034670 ACAGAATGCAGGAGAAGCCC 60.035 55.0 0.00 0.0 42.53 5.19 R
5459 5891 0.037697 GGAAAATGACCCCGTTTGGC 60.038 55.0 0.00 0.0 32.24 4.52 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
38 39 6.601613 TCACAGCTTTAAGTCCTGAAGAAAAA 59.398 34.615 6.60 0.00 0.00 1.94
50 51 8.143835 AGTCCTGAAGAAAAATGGTAAAATGTG 58.856 33.333 0.00 0.00 0.00 3.21
57 58 8.472007 AGAAAAATGGTAAAATGTGGTCAGTA 57.528 30.769 0.00 0.00 0.00 2.74
72 73 6.661805 TGTGGTCAGTAGATACACAACAGATA 59.338 38.462 0.00 0.00 39.74 1.98
91 92 2.279582 ACTGATTCCGTTCACGCTAG 57.720 50.000 0.00 0.00 38.18 3.42
195 226 6.034256 GTCAATTTACATTCAGAACAGCATGC 59.966 38.462 10.51 10.51 42.53 4.06
329 360 4.136051 TGAGAATCACAAGTCACAATGCA 58.864 39.130 0.00 0.00 42.56 3.96
749 786 2.939460 ATTTTACATTCAGCCACCGC 57.061 45.000 0.00 0.00 0.00 5.68
789 826 0.532862 CGTGTGCTCCAAACTCCAGT 60.533 55.000 0.00 0.00 0.00 4.00
826 876 4.297299 AGCGATGCAAATATCCAACTTG 57.703 40.909 0.00 0.00 0.00 3.16
851 901 3.931578 AGCACTCTCTCGCAAAAAGTAT 58.068 40.909 0.00 0.00 0.00 2.12
1011 1106 2.491022 CCTCGGGATGTCCTCGTCC 61.491 68.421 0.00 0.00 46.10 4.79
1145 1251 1.066587 GGAGATGCTCCTCCGTTCG 59.933 63.158 6.23 0.00 46.41 3.95
1147 1253 2.586357 GATGCTCCTCCGTTCGCC 60.586 66.667 0.00 0.00 0.00 5.54
1148 1254 4.162690 ATGCTCCTCCGTTCGCCC 62.163 66.667 0.00 0.00 0.00 6.13
1173 1280 0.756903 CCCCGATCACCCGTTAATCT 59.243 55.000 0.00 0.00 0.00 2.40
1175 1282 1.217882 CCGATCACCCGTTAATCTGC 58.782 55.000 0.00 0.00 0.00 4.26
1239 1346 2.771639 CGACATCGCCTTCCTCGGA 61.772 63.158 0.00 0.00 0.00 4.55
1282 1389 1.977293 GCTTCCCGCCTCTTCTCCAT 61.977 60.000 0.00 0.00 0.00 3.41
1284 1391 0.617535 TTCCCGCCTCTTCTCCATCA 60.618 55.000 0.00 0.00 0.00 3.07
1315 1422 1.103803 ACATAGACGTGCATCGGACT 58.896 50.000 12.18 12.11 44.69 3.85
1316 1423 1.202302 ACATAGACGTGCATCGGACTG 60.202 52.381 12.18 7.19 44.69 3.51
1319 1426 1.080772 GACGTGCATCGGACTGTGA 60.081 57.895 12.18 0.00 44.69 3.58
1342 1449 2.432456 GCGCGTCCTGTGATGTGA 60.432 61.111 8.43 0.00 39.84 3.58
1416 1523 0.035915 GAAGGCCACCTGGAGAAGAC 60.036 60.000 5.01 0.00 37.39 3.01
1417 1524 1.831652 AAGGCCACCTGGAGAAGACG 61.832 60.000 5.01 0.00 37.39 4.18
1420 1527 2.125912 CACCTGGAGAAGACGCGG 60.126 66.667 12.47 0.00 0.00 6.46
1465 1572 0.617413 AGGAAGATCTGCTGGTGGTG 59.383 55.000 0.00 0.00 0.00 4.17
1495 1602 8.553459 ACAATCTGTTTTCACTAGGTTCATAG 57.447 34.615 0.00 0.00 0.00 2.23
1526 1633 8.839310 TTTTGTTCCTTTTGATTTTTGTCTCA 57.161 26.923 0.00 0.00 0.00 3.27
1527 1634 9.447157 TTTTGTTCCTTTTGATTTTTGTCTCAT 57.553 25.926 0.00 0.00 0.00 2.90
1528 1635 8.647143 TTGTTCCTTTTGATTTTTGTCTCATC 57.353 30.769 0.00 0.00 0.00 2.92
1529 1636 7.209475 TGTTCCTTTTGATTTTTGTCTCATCC 58.791 34.615 0.00 0.00 0.00 3.51
1530 1637 6.345096 TCCTTTTGATTTTTGTCTCATCCC 57.655 37.500 0.00 0.00 0.00 3.85
1531 1638 5.245977 TCCTTTTGATTTTTGTCTCATCCCC 59.754 40.000 0.00 0.00 0.00 4.81
1532 1639 5.246883 CCTTTTGATTTTTGTCTCATCCCCT 59.753 40.000 0.00 0.00 0.00 4.79
1539 1646 7.728083 TGATTTTTGTCTCATCCCCTTTTAAGA 59.272 33.333 0.00 0.00 0.00 2.10
1579 1686 2.738521 CAGGTTCACACGGAGGCG 60.739 66.667 0.00 0.00 0.00 5.52
1596 1703 1.071605 GCGTACTTGAACAGCCTCAG 58.928 55.000 0.00 0.00 0.00 3.35
1632 1739 1.905894 TGCAGCCATTGTAGAGGTACA 59.094 47.619 0.00 0.00 37.38 2.90
1659 1766 3.500343 CTCAGGGGAAGTTGAATTGGTT 58.500 45.455 0.00 0.00 0.00 3.67
1662 1769 1.970640 GGGGAAGTTGAATTGGTTGCT 59.029 47.619 0.00 0.00 0.00 3.91
1680 1795 3.114606 TGCTTGATTGATACTCCCTCCA 58.885 45.455 0.00 0.00 0.00 3.86
1805 2000 4.022589 CGGAGGGAGTAGCAAATTACGATA 60.023 45.833 0.00 0.00 0.00 2.92
1974 2169 1.485895 GGTGCATAATTTGGGTGCCAT 59.514 47.619 0.00 0.00 38.06 4.40
1997 2192 2.704572 CCAGGGAAACTCTGTAAGCTG 58.295 52.381 0.00 0.00 0.00 4.24
2044 2241 6.127619 GGTCCATTTTATCAGCTAAACTTGCT 60.128 38.462 0.00 0.00 42.06 3.91
2098 2295 0.671251 GGTTTCACCATTGTTCGGCA 59.329 50.000 0.00 0.00 38.42 5.69
2125 2322 2.519691 AGGGGGAGGATTTTGTGCATAT 59.480 45.455 0.00 0.00 0.00 1.78
2142 2339 4.628766 TGCATATGCTGATATTTCGCTCTC 59.371 41.667 27.13 0.00 42.66 3.20
2197 2394 3.689872 AGGTGAGAAGCCTATACTGGA 57.310 47.619 0.00 0.00 33.97 3.86
2275 2472 4.034048 GCTTATACAACGTATGTGCTTGCT 59.966 41.667 11.90 0.00 43.77 3.91
2327 2524 5.738619 TCTGTGTTGTTAAGCATCCTCTA 57.261 39.130 0.00 0.00 0.00 2.43
2358 2555 5.574970 ATCTTGCTTTATTCCCTAGGGAG 57.425 43.478 29.40 18.87 46.06 4.30
2359 2556 4.631234 TCTTGCTTTATTCCCTAGGGAGA 58.369 43.478 29.40 20.41 46.06 3.71
2364 2561 4.446311 GCTTTATTCCCTAGGGAGATTGCA 60.446 45.833 29.40 15.18 46.06 4.08
2374 2571 2.901839 AGGGAGATTGCAATGCTTGTTT 59.098 40.909 18.59 0.00 0.00 2.83
2460 2657 4.487948 CAAGGATGCAAACCAATGTGTAG 58.512 43.478 14.25 0.00 0.00 2.74
2470 2667 6.570378 GCAAACCAATGTGTAGATTGCTTACT 60.570 38.462 0.00 0.00 38.79 2.24
2471 2668 7.361713 GCAAACCAATGTGTAGATTGCTTACTA 60.362 37.037 0.00 0.00 38.79 1.82
2472 2669 7.611213 AACCAATGTGTAGATTGCTTACTAC 57.389 36.000 0.00 0.00 39.27 2.73
2473 2670 6.947464 ACCAATGTGTAGATTGCTTACTACT 58.053 36.000 0.00 0.00 39.46 2.57
2474 2671 7.042335 ACCAATGTGTAGATTGCTTACTACTC 58.958 38.462 0.00 0.00 39.46 2.59
2475 2672 6.480320 CCAATGTGTAGATTGCTTACTACTCC 59.520 42.308 0.00 0.00 39.46 3.85
2476 2673 5.593679 TGTGTAGATTGCTTACTACTCCC 57.406 43.478 0.00 0.00 39.46 4.30
2477 2674 5.269991 TGTGTAGATTGCTTACTACTCCCT 58.730 41.667 0.00 0.00 39.46 4.20
2478 2675 5.360144 TGTGTAGATTGCTTACTACTCCCTC 59.640 44.000 0.00 0.00 39.46 4.30
2479 2676 4.894114 TGTAGATTGCTTACTACTCCCTCC 59.106 45.833 0.00 0.00 39.46 4.30
2480 2677 2.959707 AGATTGCTTACTACTCCCTCCG 59.040 50.000 0.00 0.00 0.00 4.63
2481 2678 2.226962 TTGCTTACTACTCCCTCCGT 57.773 50.000 0.00 0.00 0.00 4.69
2482 2679 1.760192 TGCTTACTACTCCCTCCGTC 58.240 55.000 0.00 0.00 0.00 4.79
2483 2680 1.031235 GCTTACTACTCCCTCCGTCC 58.969 60.000 0.00 0.00 0.00 4.79
2484 2681 1.689984 CTTACTACTCCCTCCGTCCC 58.310 60.000 0.00 0.00 0.00 4.46
2485 2682 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2486 2683 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2487 2684 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2488 2685 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2489 2686 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2490 2687 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2491 2688 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2492 2689 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2493 2690 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2494 2691 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2495 2692 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2496 2693 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
2497 2694 5.897824 TCCCTCCGTCCCATAATATAAGATC 59.102 44.000 0.00 0.00 0.00 2.75
2498 2695 5.221263 CCCTCCGTCCCATAATATAAGATCG 60.221 48.000 0.00 0.00 0.00 3.69
2499 2696 5.360144 CCTCCGTCCCATAATATAAGATCGT 59.640 44.000 0.00 0.00 0.00 3.73
2500 2697 6.127423 CCTCCGTCCCATAATATAAGATCGTT 60.127 42.308 0.00 0.00 0.00 3.85
2501 2698 7.235935 TCCGTCCCATAATATAAGATCGTTT 57.764 36.000 0.00 0.00 0.00 3.60
2502 2699 7.673180 TCCGTCCCATAATATAAGATCGTTTT 58.327 34.615 0.00 0.00 0.00 2.43
2503 2700 7.601130 TCCGTCCCATAATATAAGATCGTTTTG 59.399 37.037 0.00 0.00 0.00 2.44
2504 2701 7.234384 CGTCCCATAATATAAGATCGTTTTGC 58.766 38.462 0.00 0.00 0.00 3.68
2505 2702 7.234384 GTCCCATAATATAAGATCGTTTTGCG 58.766 38.462 0.00 0.00 43.01 4.85
2516 2713 3.247563 TCGTTTTGCGAGCTAAAACAG 57.752 42.857 18.63 12.95 45.68 3.16
2517 2714 2.601266 TCGTTTTGCGAGCTAAAACAGC 60.601 45.455 18.63 5.74 45.68 4.40
2534 2731 9.846248 CTAAAACAGCTTGCAAAACTATCTTAT 57.154 29.630 0.00 0.00 0.00 1.73
2542 2739 9.846248 GCTTGCAAAACTATCTTATATTATGGG 57.154 33.333 0.00 0.00 0.00 4.00
2545 2742 9.214957 TGCAAAACTATCTTATATTATGGGACG 57.785 33.333 0.00 0.00 0.00 4.79
2546 2743 8.665685 GCAAAACTATCTTATATTATGGGACGG 58.334 37.037 0.00 0.00 0.00 4.79
2547 2744 9.938280 CAAAACTATCTTATATTATGGGACGGA 57.062 33.333 0.00 0.00 0.00 4.69
2549 2746 7.899648 ACTATCTTATATTATGGGACGGAGG 57.100 40.000 0.00 0.00 0.00 4.30
2550 2747 6.839657 ACTATCTTATATTATGGGACGGAGGG 59.160 42.308 0.00 0.00 0.00 4.30
2551 2748 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2552 2749 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2673 2870 6.491403 AGGATTTTGCTAATGATGGTATGTCC 59.509 38.462 0.00 0.00 0.00 4.02
2705 2902 7.159437 TGTTCTTGTATGCATTTTGTTTTCG 57.841 32.000 3.54 0.00 0.00 3.46
2706 2903 6.754209 TGTTCTTGTATGCATTTTGTTTTCGT 59.246 30.769 3.54 0.00 0.00 3.85
2828 3025 5.063880 AGAATTCTTGTTACACCTGTGGAC 58.936 41.667 0.88 1.25 34.19 4.02
2835 3032 0.677288 TACACCTGTGGACCGTCAAG 59.323 55.000 0.00 0.00 34.19 3.02
2875 3072 4.404715 TGGTTATGCTCTGACTACCCTTAC 59.595 45.833 0.00 0.00 0.00 2.34
2888 3085 2.914059 ACCCTTACGCAATATGTGGTC 58.086 47.619 0.00 0.00 30.87 4.02
2889 3086 2.218603 CCCTTACGCAATATGTGGTCC 58.781 52.381 0.00 0.00 30.87 4.46
2921 3118 8.934697 TGCTTATGGTGTAGAGGTTATTTATCT 58.065 33.333 0.00 0.00 0.00 1.98
2969 3168 6.430000 TGTTGAGCATAAGTTTTCTTCCCTAC 59.570 38.462 0.00 0.00 40.91 3.18
2973 3172 4.533815 CATAAGTTTTCTTCCCTACCCCC 58.466 47.826 0.00 0.00 40.91 5.40
2980 3179 3.519370 TCTTCCCTACCCCCTAAATGT 57.481 47.619 0.00 0.00 0.00 2.71
2981 3180 3.120108 TCTTCCCTACCCCCTAAATGTG 58.880 50.000 0.00 0.00 0.00 3.21
2991 3191 6.645884 ACCCCCTAAATGTGTTTCTACATA 57.354 37.500 0.00 0.00 40.24 2.29
3017 3217 9.520515 AATGTTTTTGAAGATACCATACAGTCT 57.479 29.630 0.00 0.00 0.00 3.24
3040 3297 7.175641 GTCTAGATGGTGCAAATAGGCATTTAT 59.824 37.037 0.00 0.00 46.92 1.40
3043 3300 5.929058 TGGTGCAAATAGGCATTTATCAA 57.071 34.783 0.00 0.00 46.92 2.57
3088 3366 7.387122 CACAGCTGTGTTGCTATGATATCTATT 59.613 37.037 34.04 0.00 39.61 1.73
3116 3394 4.859798 CCACTGTTCGAAGATTAGTCTGTC 59.140 45.833 0.00 0.00 35.04 3.51
3125 3403 7.310664 TCGAAGATTAGTCTGTCGTTATTGTT 58.689 34.615 14.55 0.00 36.86 2.83
3280 3559 6.342338 AGTCGAGTTAGTTGTAAGTTGGAT 57.658 37.500 0.00 0.00 0.00 3.41
3338 3617 7.458409 AATTCAAATATGAGTTGAGTGCACT 57.542 32.000 21.88 21.88 34.57 4.40
3399 3678 1.339438 TGGATCAGCTTGACAAGGCTC 60.339 52.381 16.80 2.59 36.59 4.70
3412 3691 2.711547 ACAAGGCTCTGAAGGTACCTTT 59.288 45.455 27.72 12.12 38.67 3.11
3430 3711 6.903340 ACCTTTACACTTATAGATGGGGTT 57.097 37.500 0.00 0.00 0.00 4.11
3436 3717 3.069586 CACTTATAGATGGGGTTCTCGCA 59.930 47.826 0.00 0.00 42.62 5.10
3482 3763 3.273434 TGTCCTATGCACTGCAATTCTC 58.727 45.455 8.03 0.39 43.62 2.87
3488 3769 1.093159 GCACTGCAATTCTCAGGGAG 58.907 55.000 9.94 0.00 37.13 4.30
3510 3791 7.255277 GGGAGAAATAGGTGAAAGATGTTATGC 60.255 40.741 0.00 0.00 0.00 3.14
3525 3806 8.553085 AGATGTTATGCTAGGTGCCATATATA 57.447 34.615 0.00 0.00 42.00 0.86
3579 3947 6.620877 ATGTAAACTGGACATAGAGGTGAA 57.379 37.500 0.00 0.00 35.75 3.18
3585 3953 8.567285 AAACTGGACATAGAGGTGAATTTTAG 57.433 34.615 0.00 0.00 0.00 1.85
3673 4041 6.154363 TGTTCAACTGAAAAGGAGGTTTGAAT 59.846 34.615 0.00 0.00 35.58 2.57
3674 4042 6.147864 TCAACTGAAAAGGAGGTTTGAATG 57.852 37.500 0.00 0.00 0.00 2.67
3731 4100 4.441495 GCAATTGGCACTATCCCTTTAACC 60.441 45.833 7.72 0.00 43.97 2.85
3802 4177 4.938575 TTAGAGTTCCTTTTGGGGCATA 57.061 40.909 0.00 0.00 40.87 3.14
3863 4238 8.462016 CAGCTTATTATTTATAATGCTGGGACC 58.538 37.037 18.16 0.00 41.32 4.46
3903 4278 2.896685 CCATTGGGCAACTTGAAGGTAA 59.103 45.455 0.00 0.00 0.00 2.85
4182 4576 4.727507 TGCCTTTGTTTTGCTTCTGTTA 57.272 36.364 0.00 0.00 0.00 2.41
4233 4628 1.280133 TGCTACTGCATGCTTTCTCCT 59.720 47.619 20.33 0.00 45.31 3.69
4267 4662 0.251341 GCCCTGAAGGTGTGGTGATT 60.251 55.000 0.00 0.00 38.26 2.57
4378 4773 1.604604 TTTTTGTTCCTCTCCTGCGG 58.395 50.000 0.00 0.00 0.00 5.69
4481 4878 5.652452 TCGATTACCAATCTCTCACAGAAGA 59.348 40.000 0.00 0.00 35.73 2.87
4487 4884 4.694509 CCAATCTCTCACAGAAGAACTTGG 59.305 45.833 0.00 0.00 33.62 3.61
4492 4889 6.042093 ATCTCTCACAGAAGAACTTGGTACAA 59.958 38.462 0.00 0.00 38.08 2.41
4540 4937 2.433446 CTCTGCCACCCACAAGCT 59.567 61.111 0.00 0.00 0.00 3.74
4650 5056 7.448748 AAAATCTTGTCACCTTGTACATACC 57.551 36.000 0.00 0.00 0.00 2.73
4678 5084 3.225940 AGGCCTTTGTTTCCAAGAAGAG 58.774 45.455 0.00 0.00 0.00 2.85
4679 5085 2.288457 GGCCTTTGTTTCCAAGAAGAGC 60.288 50.000 0.00 0.00 0.00 4.09
4681 5087 3.551659 GCCTTTGTTTCCAAGAAGAGCAG 60.552 47.826 0.00 0.00 0.00 4.24
4763 5173 6.340962 TCCCCATCGTCAAACTATACTATG 57.659 41.667 0.00 0.00 0.00 2.23
4769 5179 9.823098 CCATCGTCAAACTATACTATGTACTAC 57.177 37.037 0.00 0.00 0.00 2.73
4849 5264 7.885399 AGTTTGCACTATAGATCTTGAAGGTTT 59.115 33.333 6.78 0.00 0.00 3.27
4872 5290 9.875675 GTTTTCAAGAGATATAGCATGATGTTC 57.124 33.333 0.00 0.00 0.00 3.18
4939 5358 0.515564 CGTCGGTTTGTTGGATGGTC 59.484 55.000 0.00 0.00 0.00 4.02
4949 5368 7.107542 GGTTTGTTGGATGGTCTACAGTTATA 58.892 38.462 0.00 0.00 0.00 0.98
4950 5369 7.280205 GGTTTGTTGGATGGTCTACAGTTATAG 59.720 40.741 0.00 0.00 0.00 1.31
4996 5415 2.942641 GAACTTTGGTTCCTCCCCG 58.057 57.895 0.00 0.00 44.24 5.73
5125 5544 0.179062 ACCGAGCTTCATCATCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
5129 5548 0.755079 AGCTTCATCATCCAGCGCTA 59.245 50.000 10.99 0.00 38.66 4.26
5162 5581 4.835056 GCCAGGCTATTCCTTTCCAATAAT 59.165 41.667 3.29 0.00 44.75 1.28
5163 5582 6.010219 GCCAGGCTATTCCTTTCCAATAATA 58.990 40.000 3.29 0.00 44.75 0.98
5164 5583 6.493458 GCCAGGCTATTCCTTTCCAATAATAA 59.507 38.462 3.29 0.00 44.75 1.40
5165 5584 7.523873 GCCAGGCTATTCCTTTCCAATAATAAC 60.524 40.741 3.29 0.00 44.75 1.89
5197 5616 1.957877 CCTAGAGCCCTAGACCTTTCG 59.042 57.143 3.42 0.00 44.00 3.46
5198 5617 1.338655 CTAGAGCCCTAGACCTTTCGC 59.661 57.143 0.00 0.00 44.00 4.70
5199 5618 1.144276 GAGCCCTAGACCTTTCGCC 59.856 63.158 0.00 0.00 0.00 5.54
5212 5631 1.457303 CTTTCGCCGCTCATATACTGC 59.543 52.381 0.00 0.00 0.00 4.40
5266 5687 6.918892 AAAAAGGAAAATTCAGAAAACCGG 57.081 33.333 0.00 0.00 0.00 5.28
5272 5693 5.989168 GGAAAATTCAGAAAACCGGTTCATT 59.011 36.000 22.53 12.63 0.00 2.57
5391 5821 4.612264 TCTAGACCCAACACTACCAAAC 57.388 45.455 0.00 0.00 0.00 2.93
5400 5830 4.202010 CCAACACTACCAAACCTCAACAAG 60.202 45.833 0.00 0.00 0.00 3.16
5408 5838 4.173256 CCAAACCTCAACAAGACAACAAC 58.827 43.478 0.00 0.00 0.00 3.32
5432 5862 7.429633 ACATACATGGATAAAAGACGAGAGAG 58.570 38.462 0.00 0.00 0.00 3.20
5511 5943 1.070786 GCTCCCTGACACGGTCAAA 59.929 57.895 7.90 0.00 42.26 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.769044 GTGTATCTACTGACCACATTTTACCAT 59.231 37.037 0.00 0.00 31.53 3.55
50 51 7.067129 TCAGTATCTGTTGTGTATCTACTGACC 59.933 40.741 5.63 0.00 38.89 4.02
57 58 6.096987 ACGGAATCAGTATCTGTTGTGTATCT 59.903 38.462 0.00 0.00 32.52 1.98
72 73 1.816835 TCTAGCGTGAACGGAATCAGT 59.183 47.619 4.84 0.00 40.23 3.41
91 92 8.388484 ACCACATAAGATTATTCATGCTTCTC 57.612 34.615 0.00 0.00 0.00 2.87
97 98 8.671921 GCAGGATACCACATAAGATTATTCATG 58.328 37.037 0.00 0.00 37.17 3.07
195 226 8.075574 TGTTATCAGTGCTTTGTAAAGATTGTG 58.924 33.333 8.47 0.71 38.28 3.33
329 360 4.591924 TCCTCCTCTTAGTTTCGGTTTCTT 59.408 41.667 0.00 0.00 0.00 2.52
508 539 1.137675 CCTGCTGACGATCCAATCTGA 59.862 52.381 0.00 0.00 0.00 3.27
693 727 1.439644 GGAATTCGCTCTCGCTCCT 59.560 57.895 0.00 0.00 35.26 3.69
694 728 1.592939 GGGAATTCGCTCTCGCTCC 60.593 63.158 14.84 0.00 35.26 4.70
728 765 3.691498 GCGGTGGCTGAATGTAAAATAC 58.309 45.455 0.00 0.00 35.83 1.89
749 786 4.266976 ACGAATACAATTTACGCGGAAGAG 59.733 41.667 12.47 4.36 0.00 2.85
789 826 0.759436 CGCTAGCCCTCCTTCCCTTA 60.759 60.000 9.66 0.00 0.00 2.69
990 1067 3.551407 GAGGACATCCCGAGGGCC 61.551 72.222 2.58 0.00 41.55 5.80
1145 1251 3.556306 TGATCGGGGATTCGGGGC 61.556 66.667 0.00 0.00 0.00 5.80
1147 1253 2.426023 GGTGATCGGGGATTCGGG 59.574 66.667 0.00 0.00 0.00 5.14
1148 1254 2.426023 GGGTGATCGGGGATTCGG 59.574 66.667 0.00 0.00 0.00 4.30
1149 1255 2.029073 CGGGTGATCGGGGATTCG 59.971 66.667 0.00 0.00 0.00 3.34
1150 1256 0.754472 TAACGGGTGATCGGGGATTC 59.246 55.000 0.00 0.00 0.00 2.52
1151 1257 1.205966 TTAACGGGTGATCGGGGATT 58.794 50.000 0.00 0.00 0.00 3.01
1152 1258 1.346722 GATTAACGGGTGATCGGGGAT 59.653 52.381 0.00 0.00 0.00 3.85
1153 1259 0.754472 GATTAACGGGTGATCGGGGA 59.246 55.000 0.00 0.00 0.00 4.81
1239 1346 2.168106 AGCAGCTCACATCTTCTCGATT 59.832 45.455 0.00 0.00 0.00 3.34
1282 1389 3.741075 CGTCTATGTGGCTAGGCAAATGA 60.741 47.826 27.81 20.05 0.00 2.57
1284 1391 2.170607 ACGTCTATGTGGCTAGGCAAAT 59.829 45.455 24.10 24.10 0.00 2.32
1315 1422 2.429571 GGACGCGCGTAAGTCACA 60.430 61.111 37.91 0.00 39.01 3.58
1316 1423 2.126580 AGGACGCGCGTAAGTCAC 60.127 61.111 37.91 22.01 39.01 3.67
1319 1426 2.209064 ATCACAGGACGCGCGTAAGT 62.209 55.000 37.91 29.17 41.68 2.24
1342 1449 0.112412 AGGAATCAAACGGGTGCCTT 59.888 50.000 0.00 0.00 0.00 4.35
1446 1553 0.617413 CACCACCAGCAGATCTTCCT 59.383 55.000 0.00 0.00 0.00 3.36
1501 1608 8.839310 TGAGACAAAAATCAAAAGGAACAAAA 57.161 26.923 0.00 0.00 0.00 2.44
1502 1609 9.097257 GATGAGACAAAAATCAAAAGGAACAAA 57.903 29.630 0.00 0.00 0.00 2.83
1504 1611 7.209475 GGATGAGACAAAAATCAAAAGGAACA 58.791 34.615 0.00 0.00 0.00 3.18
1505 1612 6.646653 GGGATGAGACAAAAATCAAAAGGAAC 59.353 38.462 0.00 0.00 0.00 3.62
1506 1613 6.239572 GGGGATGAGACAAAAATCAAAAGGAA 60.240 38.462 0.00 0.00 0.00 3.36
1507 1614 5.245977 GGGGATGAGACAAAAATCAAAAGGA 59.754 40.000 0.00 0.00 0.00 3.36
1508 1615 5.246883 AGGGGATGAGACAAAAATCAAAAGG 59.753 40.000 0.00 0.00 0.00 3.11
1509 1616 6.350629 AGGGGATGAGACAAAAATCAAAAG 57.649 37.500 0.00 0.00 0.00 2.27
1510 1617 6.745794 AAGGGGATGAGACAAAAATCAAAA 57.254 33.333 0.00 0.00 0.00 2.44
1511 1618 6.745794 AAAGGGGATGAGACAAAAATCAAA 57.254 33.333 0.00 0.00 0.00 2.69
1512 1619 6.745794 AAAAGGGGATGAGACAAAAATCAA 57.254 33.333 0.00 0.00 0.00 2.57
1513 1620 7.728083 TCTTAAAAGGGGATGAGACAAAAATCA 59.272 33.333 0.00 0.00 0.00 2.57
1514 1621 8.122472 TCTTAAAAGGGGATGAGACAAAAATC 57.878 34.615 0.00 0.00 0.00 2.17
1515 1622 8.670521 ATCTTAAAAGGGGATGAGACAAAAAT 57.329 30.769 0.00 0.00 0.00 1.82
1516 1623 8.367156 CAATCTTAAAAGGGGATGAGACAAAAA 58.633 33.333 0.00 0.00 0.00 1.94
1517 1624 7.508977 ACAATCTTAAAAGGGGATGAGACAAAA 59.491 33.333 0.00 0.00 0.00 2.44
1518 1625 7.010160 ACAATCTTAAAAGGGGATGAGACAAA 58.990 34.615 0.00 0.00 0.00 2.83
1519 1626 6.552008 ACAATCTTAAAAGGGGATGAGACAA 58.448 36.000 0.00 0.00 0.00 3.18
1520 1627 6.139679 ACAATCTTAAAAGGGGATGAGACA 57.860 37.500 0.00 0.00 0.00 3.41
1521 1628 6.095580 GGAACAATCTTAAAAGGGGATGAGAC 59.904 42.308 0.00 0.00 0.00 3.36
1522 1629 6.187682 GGAACAATCTTAAAAGGGGATGAGA 58.812 40.000 0.00 0.00 0.00 3.27
1523 1630 5.951747 TGGAACAATCTTAAAAGGGGATGAG 59.048 40.000 0.00 0.00 31.92 2.90
1524 1631 5.898120 TGGAACAATCTTAAAAGGGGATGA 58.102 37.500 0.00 0.00 31.92 2.92
1579 1686 2.933056 GCTCCTGAGGCTGTTCAAGTAC 60.933 54.545 0.00 0.00 0.00 2.73
1596 1703 2.338785 GCAACCCTGAAGCTGCTCC 61.339 63.158 1.00 0.00 0.00 4.70
1632 1739 1.494721 TCAACTTCCCCTGAGCAACTT 59.505 47.619 0.00 0.00 0.00 2.66
1637 1744 1.821136 CCAATTCAACTTCCCCTGAGC 59.179 52.381 0.00 0.00 0.00 4.26
1659 1766 3.114606 TGGAGGGAGTATCAATCAAGCA 58.885 45.455 0.00 0.00 36.25 3.91
1662 1769 5.191522 TGTGAATGGAGGGAGTATCAATCAA 59.808 40.000 0.00 0.00 36.25 2.57
1680 1795 7.387119 TCAGTACGTATGTAGTCTTGTGAAT 57.613 36.000 0.00 0.00 31.76 2.57
1762 1878 8.721478 CCCTCCGTTCATAAATATAAGATGTTG 58.279 37.037 0.00 0.00 0.00 3.33
1974 2169 2.814097 GCTTACAGAGTTTCCCTGGCAA 60.814 50.000 0.00 0.00 36.03 4.52
2044 2241 0.033109 TCGCCCATCCTCTCTCAAGA 60.033 55.000 0.00 0.00 0.00 3.02
2098 2295 1.925959 CAAAATCCTCCCCCTTCCTCT 59.074 52.381 0.00 0.00 0.00 3.69
2125 2322 3.758755 ATGGAGAGCGAAATATCAGCA 57.241 42.857 0.00 0.00 0.00 4.41
2142 2339 2.393764 GGACAAACGCAAACTGAATGG 58.606 47.619 0.00 0.00 0.00 3.16
2197 2394 8.135382 ACATAGTTTCTACAGTTACAGTCCAT 57.865 34.615 0.00 0.00 0.00 3.41
2275 2472 7.269316 TGACAGAATATATTTACAGCCGTCAA 58.731 34.615 0.00 0.00 0.00 3.18
2314 2511 4.980339 TGGCATGATAGAGGATGCTTAA 57.020 40.909 0.00 0.00 43.77 1.85
2327 2524 5.221581 GGGAATAAAGCAAGATTGGCATGAT 60.222 40.000 0.00 0.00 0.00 2.45
2374 2571 2.775911 AGAGTGCTTGCTAAGATGCA 57.224 45.000 0.00 0.00 41.65 3.96
2391 2588 3.181465 GGTAACTAGCCAAGCAGCATAGA 60.181 47.826 0.00 0.00 34.23 1.98
2460 2657 2.694109 ACGGAGGGAGTAGTAAGCAATC 59.306 50.000 0.00 0.00 0.00 2.67
2470 2667 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2471 2668 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2472 2669 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2473 2670 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2474 2671 5.221263 CGATCTTATATTATGGGACGGAGGG 60.221 48.000 0.00 0.00 0.00 4.30
2475 2672 5.360144 ACGATCTTATATTATGGGACGGAGG 59.640 44.000 0.00 0.00 0.00 4.30
2476 2673 6.452494 ACGATCTTATATTATGGGACGGAG 57.548 41.667 0.00 0.00 0.00 4.63
2477 2674 6.845758 AACGATCTTATATTATGGGACGGA 57.154 37.500 0.00 0.00 0.00 4.69
2478 2675 7.623506 GCAAAACGATCTTATATTATGGGACGG 60.624 40.741 0.00 0.00 0.00 4.79
2479 2676 7.234384 GCAAAACGATCTTATATTATGGGACG 58.766 38.462 0.00 0.00 0.00 4.79
2508 2705 9.846248 ATAAGATAGTTTTGCAAGCTGTTTTAG 57.154 29.630 13.66 0.00 0.00 1.85
2516 2713 9.846248 CCCATAATATAAGATAGTTTTGCAAGC 57.154 33.333 0.00 0.00 0.00 4.01
2519 2716 9.214957 CGTCCCATAATATAAGATAGTTTTGCA 57.785 33.333 0.00 0.00 0.00 4.08
2520 2717 8.665685 CCGTCCCATAATATAAGATAGTTTTGC 58.334 37.037 0.00 0.00 0.00 3.68
2521 2718 9.938280 TCCGTCCCATAATATAAGATAGTTTTG 57.062 33.333 0.00 0.00 0.00 2.44
2523 2720 8.759782 CCTCCGTCCCATAATATAAGATAGTTT 58.240 37.037 0.00 0.00 0.00 2.66
2524 2721 7.344871 CCCTCCGTCCCATAATATAAGATAGTT 59.655 40.741 0.00 0.00 0.00 2.24
2525 2722 6.839657 CCCTCCGTCCCATAATATAAGATAGT 59.160 42.308 0.00 0.00 0.00 2.12
2526 2723 7.067421 TCCCTCCGTCCCATAATATAAGATAG 58.933 42.308 0.00 0.00 0.00 2.08
2527 2724 6.988725 TCCCTCCGTCCCATAATATAAGATA 58.011 40.000 0.00 0.00 0.00 1.98
2528 2725 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
2529 2726 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2530 2727 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2531 2728 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2532 2729 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2533 2730 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2534 2731 4.140853 AGTTACTCCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
2535 2732 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
2536 2733 2.023695 AGTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
2537 2734 1.572415 AGTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
2538 2735 0.338814 AGTTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2539 2736 1.002069 TAGTTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2540 2737 2.378378 ATAGTTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
2541 2738 4.750021 AAAATAGTTACTCCCTCCGTCC 57.250 45.455 0.00 0.00 0.00 4.79
2542 2739 5.068855 AGCTAAAATAGTTACTCCCTCCGTC 59.931 44.000 0.00 0.00 0.00 4.79
2543 2740 4.961099 AGCTAAAATAGTTACTCCCTCCGT 59.039 41.667 0.00 0.00 0.00 4.69
2544 2741 5.532664 AGCTAAAATAGTTACTCCCTCCG 57.467 43.478 0.00 0.00 0.00 4.63
2545 2742 6.885922 TGAAGCTAAAATAGTTACTCCCTCC 58.114 40.000 0.00 0.00 0.00 4.30
2705 2902 2.348666 GGCATCACTGTGTCATCGTAAC 59.651 50.000 7.79 0.00 0.00 2.50
2706 2903 2.028567 TGGCATCACTGTGTCATCGTAA 60.029 45.455 7.79 0.00 0.00 3.18
2799 2996 9.653287 CACAGGTGTAACAAGAATTCTAGATTA 57.347 33.333 8.75 5.27 39.98 1.75
2816 3013 0.677288 CTTGACGGTCCACAGGTGTA 59.323 55.000 5.55 0.00 0.00 2.90
2841 3038 1.882311 CATAACCAGCCGCAGCAAA 59.118 52.632 0.00 0.00 43.56 3.68
2842 3039 2.699768 GCATAACCAGCCGCAGCAA 61.700 57.895 0.00 0.00 43.56 3.91
2848 3045 0.176680 AGTCAGAGCATAACCAGCCG 59.823 55.000 0.00 0.00 0.00 5.52
2849 3046 2.483889 GGTAGTCAGAGCATAACCAGCC 60.484 54.545 0.00 0.00 0.00 4.85
2850 3047 2.483889 GGGTAGTCAGAGCATAACCAGC 60.484 54.545 0.00 0.00 0.00 4.85
2851 3048 3.034635 AGGGTAGTCAGAGCATAACCAG 58.965 50.000 0.00 0.00 0.00 4.00
2875 3072 2.260844 ATCCTGGACCACATATTGCG 57.739 50.000 0.00 0.00 0.00 4.85
2888 3085 4.384056 CTCTACACCATAAGCAATCCTGG 58.616 47.826 0.00 0.00 34.84 4.45
2889 3086 4.141620 ACCTCTACACCATAAGCAATCCTG 60.142 45.833 0.00 0.00 0.00 3.86
2969 3168 7.559897 ACATTATGTAGAAACACATTTAGGGGG 59.440 37.037 0.00 0.00 39.77 5.40
2991 3191 9.520515 AGACTGTATGGTATCTTCAAAAACATT 57.479 29.630 0.00 0.00 0.00 2.71
2999 3199 7.767250 CCATCTAGACTGTATGGTATCTTCA 57.233 40.000 0.00 0.00 36.26 3.02
3011 3211 4.684485 GCCTATTTGCACCATCTAGACTGT 60.684 45.833 0.00 0.00 0.00 3.55
3016 3216 5.779529 AAATGCCTATTTGCACCATCTAG 57.220 39.130 0.00 0.00 45.48 2.43
3017 3217 7.003482 TGATAAATGCCTATTTGCACCATCTA 58.997 34.615 0.00 0.00 45.48 1.98
3040 3297 8.780846 TGTGACTACTGTTCTTTTAGTTTTGA 57.219 30.769 0.00 0.00 0.00 2.69
3043 3300 7.011482 CAGCTGTGACTACTGTTCTTTTAGTTT 59.989 37.037 5.25 0.00 0.00 2.66
3063 3320 5.287674 AGATATCATAGCAACACAGCTGT 57.712 39.130 15.25 15.25 46.11 4.40
3088 3366 4.525487 ACTAATCTTCGAACAGTGGGTGTA 59.475 41.667 0.00 0.00 39.03 2.90
3125 3403 6.204688 CACAATGACTGAAGTTAAAGCTGGTA 59.795 38.462 0.00 0.00 0.00 3.25
3212 3491 7.651027 AGCAGCATGATCCTAAAATAAAGTT 57.349 32.000 0.00 0.00 39.69 2.66
3280 3559 7.966246 AAAATATGATCAACAGCTTGCAAAA 57.034 28.000 0.00 0.00 0.00 2.44
3338 3617 4.458989 GTCCCACTCTGAAAATGCACAATA 59.541 41.667 0.00 0.00 0.00 1.90
3399 3678 9.751542 CATCTATAAGTGTAAAGGTACCTTCAG 57.248 37.037 27.24 12.41 34.84 3.02
3412 3691 4.280174 GCGAGAACCCCATCTATAAGTGTA 59.720 45.833 0.00 0.00 0.00 2.90
3482 3763 5.749462 ACATCTTTCACCTATTTCTCCCTG 58.251 41.667 0.00 0.00 0.00 4.45
3488 3769 8.778358 CCTAGCATAACATCTTTCACCTATTTC 58.222 37.037 0.00 0.00 0.00 2.17
3554 3921 7.108841 TCACCTCTATGTCCAGTTTACATAC 57.891 40.000 0.00 0.00 38.49 2.39
3558 3925 7.923414 AAATTCACCTCTATGTCCAGTTTAC 57.077 36.000 0.00 0.00 0.00 2.01
3645 4013 7.340743 TCAAACCTCCTTTTCAGTTGAACATAA 59.659 33.333 0.00 0.00 33.13 1.90
3689 4058 7.011669 CCAATTGCTTTGAAGTTTGAACTCATT 59.988 33.333 0.00 0.00 37.53 2.57
3701 4070 4.427312 GGATAGTGCCAATTGCTTTGAAG 58.573 43.478 0.00 0.00 42.00 3.02
3702 4071 3.195396 GGGATAGTGCCAATTGCTTTGAA 59.805 43.478 0.00 0.00 42.00 2.69
3703 4072 2.760092 GGGATAGTGCCAATTGCTTTGA 59.240 45.455 0.00 0.00 42.00 2.69
3704 4073 2.762327 AGGGATAGTGCCAATTGCTTTG 59.238 45.455 0.00 0.00 42.00 2.77
3705 4074 3.105959 AGGGATAGTGCCAATTGCTTT 57.894 42.857 0.00 0.00 42.00 3.51
3706 4075 2.834638 AGGGATAGTGCCAATTGCTT 57.165 45.000 0.00 0.00 42.00 3.91
3707 4076 2.834638 AAGGGATAGTGCCAATTGCT 57.165 45.000 0.00 0.00 42.00 3.91
3711 4080 4.601406 TGGTTAAAGGGATAGTGCCAAT 57.399 40.909 0.00 0.00 0.00 3.16
3720 4089 7.454380 TGAACAAGAATGAATGGTTAAAGGGAT 59.546 33.333 0.00 0.00 0.00 3.85
3863 4238 2.160822 GATCACCATCCAGGATGTCG 57.839 55.000 25.35 16.60 41.22 4.35
4217 4612 2.574006 TTGAGGAGAAAGCATGCAGT 57.426 45.000 21.98 6.66 0.00 4.40
4233 4628 6.158695 ACCTTCAGGGCTTATCTAGAATTTGA 59.841 38.462 0.00 0.00 40.27 2.69
4267 4662 7.326454 CAAATCTGAACACCTTCTCATCTCTA 58.674 38.462 0.00 0.00 0.00 2.43
4336 4731 0.255318 CAGAATGCAGGAGAAGCCCT 59.745 55.000 0.00 0.00 37.37 5.19
4337 4732 0.034670 ACAGAATGCAGGAGAAGCCC 60.035 55.000 0.00 0.00 42.53 5.19
4378 4773 4.612259 GCATGAGCAAATCGGTATGTGATC 60.612 45.833 0.00 0.00 36.46 2.92
4481 4878 3.905591 TGGCTACCTAGTTGTACCAAGTT 59.094 43.478 0.00 0.00 0.00 2.66
4487 4884 1.829222 TGGCTGGCTACCTAGTTGTAC 59.171 52.381 2.00 0.00 0.00 2.90
4492 4889 0.336737 AGTCTGGCTGGCTACCTAGT 59.663 55.000 0.00 0.00 0.00 2.57
4540 4937 2.238521 GATGTGCCCTTCAGGTTGAAA 58.761 47.619 0.00 0.00 35.73 2.69
4575 4978 6.214399 AGAACTGTAAACCTCTTCTTACACG 58.786 40.000 0.00 0.00 34.02 4.49
4629 5035 4.222145 ACGGTATGTACAAGGTGACAAGAT 59.778 41.667 0.00 0.00 0.00 2.40
4650 5056 2.817258 TGGAAACAAAGGCCTTATGACG 59.183 45.455 20.84 7.79 37.44 4.35
4678 5084 1.078567 CTCTCAGCTTCCCCACTGC 60.079 63.158 0.00 0.00 33.80 4.40
4679 5085 1.078567 GCTCTCAGCTTCCCCACTG 60.079 63.158 0.00 0.00 38.45 3.66
4681 5087 2.125350 CGCTCTCAGCTTCCCCAC 60.125 66.667 0.00 0.00 39.60 4.61
4763 5173 6.502136 AGTAACTGAAACCCGTAGTAGTAC 57.498 41.667 0.00 0.00 0.00 2.73
4769 5179 8.440833 CAAGAAAATAGTAACTGAAACCCGTAG 58.559 37.037 0.00 0.00 0.00 3.51
4849 5264 9.842775 AAAGAACATCATGCTATATCTCTTGAA 57.157 29.630 0.00 0.00 0.00 2.69
4856 5271 9.608617 CATGACAAAAGAACATCATGCTATATC 57.391 33.333 0.51 0.00 41.31 1.63
4872 5290 1.669795 GGAAAGCCGGCATGACAAAAG 60.670 52.381 31.54 0.00 0.00 2.27
4916 5335 1.130373 CATCCAACAAACCGACGATGG 59.870 52.381 0.00 0.00 0.00 3.51
4949 5368 8.603304 AGTACCAGGAATTACAAAACAGATACT 58.397 33.333 0.00 0.00 0.00 2.12
4950 5369 8.788325 AGTACCAGGAATTACAAAACAGATAC 57.212 34.615 0.00 0.00 0.00 2.24
4992 5411 2.614057 GCTGTCATGATTCTAAACGGGG 59.386 50.000 0.00 0.00 0.00 5.73
4996 5415 4.505922 CCGAGAGCTGTCATGATTCTAAAC 59.494 45.833 11.90 0.00 0.00 2.01
5086 5505 2.544726 GCTCAGTGCCAACTACCAC 58.455 57.895 0.00 0.00 33.79 4.16
5125 5544 1.002033 GCCTGGCATCAAATTCTAGCG 60.002 52.381 15.17 0.00 0.00 4.26
5129 5548 3.893813 GGAATAGCCTGGCATCAAATTCT 59.106 43.478 22.65 0.00 0.00 2.40
5162 5581 2.093890 TCTAGGCACCGACGAATGTTA 58.906 47.619 0.00 0.00 0.00 2.41
5163 5582 0.892755 TCTAGGCACCGACGAATGTT 59.107 50.000 0.00 0.00 0.00 2.71
5164 5583 0.456221 CTCTAGGCACCGACGAATGT 59.544 55.000 0.00 0.00 0.00 2.71
5165 5584 0.872021 GCTCTAGGCACCGACGAATG 60.872 60.000 0.00 0.00 41.35 2.67
5272 5693 5.259832 TGATGTTGCAGTTTTGACATGAA 57.740 34.783 0.00 0.00 33.21 2.57
5391 5821 5.749596 TGTATGTTGTTGTCTTGTTGAGG 57.250 39.130 0.00 0.00 0.00 3.86
5400 5830 7.692291 CGTCTTTTATCCATGTATGTTGTTGTC 59.308 37.037 0.00 0.00 0.00 3.18
5408 5838 7.652727 TCTCTCTCGTCTTTTATCCATGTATG 58.347 38.462 0.00 0.00 0.00 2.39
5432 5862 0.238553 GCGCCCTGTCTGTTTTTCTC 59.761 55.000 0.00 0.00 0.00 2.87
5459 5891 0.037697 GGAAAATGACCCCGTTTGGC 60.038 55.000 0.00 0.00 32.24 4.52
5466 5898 0.684479 GGAGGCAGGAAAATGACCCC 60.684 60.000 0.00 0.00 0.00 4.95
5468 5900 2.095461 GAAGGAGGCAGGAAAATGACC 58.905 52.381 0.00 0.00 0.00 4.02



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

AutoCloner maintained by Alex Coulton.