Multiple sequence alignment - TraesCS3A01G298100

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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 TraesCS3A01G298100 chr3A 100.000 2438 0 0 1 2438 532487254 532489691 0.000000e+00 4503.0
1 TraesCS3A01G298100 chr3A 90.342 673 46 3 1766 2438 306917296 306917949 0.000000e+00 865.0
2 TraesCS3A01G298100 chr3A 87.538 329 31 4 998 1326 532644458 532644776 2.960000e-99 372.0
3 TraesCS3A01G298100 chr3A 77.586 406 67 17 1043 1427 719360744 719360342 8.770000e-55 224.0
4 TraesCS3A01G298100 chr3A 89.189 185 10 3 611 794 532644174 532644349 3.160000e-54 222.0
5 TraesCS3A01G298100 chr3A 76.528 409 69 20 1043 1427 719354021 719353616 5.320000e-47 198.0
6 TraesCS3A01G298100 chr3A 75.291 429 76 22 1024 1427 719337281 719336858 6.930000e-41 178.0
7 TraesCS3A01G298100 chr3A 75.000 428 79 20 1024 1427 719350037 719349614 3.220000e-39 172.0
8 TraesCS3A01G298100 chr3A 85.906 149 13 3 614 759 534167869 534167726 4.200000e-33 152.0
9 TraesCS3A01G298100 chr3D 92.650 898 49 5 638 1523 418705984 418705092 0.000000e+00 1277.0
10 TraesCS3A01G298100 chr3D 94.545 550 18 1 64 601 418706538 418705989 0.000000e+00 839.0
11 TraesCS3A01G298100 chr3D 92.890 436 26 3 1090 1524 418482627 418482196 1.590000e-176 628.0
12 TraesCS3A01G298100 chr3D 90.649 385 27 3 1056 1432 418410759 418410376 1.010000e-138 503.0
13 TraesCS3A01G298100 chr3D 84.220 545 40 15 50 583 416403423 416403932 2.820000e-134 488.0
14 TraesCS3A01G298100 chr3D 83.570 493 62 9 611 1094 418483313 418482831 6.190000e-121 444.0
15 TraesCS3A01G298100 chr3D 92.674 273 20 0 1160 1432 416404365 416404637 6.320000e-106 394.0
16 TraesCS3A01G298100 chr3D 85.000 240 18 6 611 841 418411101 418410871 6.780000e-56 228.0
17 TraesCS3A01G298100 chr3D 78.780 377 40 16 182 552 416481139 416481481 1.470000e-52 217.0
18 TraesCS3A01G298100 chr3D 75.309 405 78 13 1043 1427 589417690 589417288 8.960000e-40 174.0
19 TraesCS3A01G298100 chr3D 81.967 183 29 4 1247 1427 589432507 589432327 4.200000e-33 152.0
20 TraesCS3A01G298100 chr3D 92.857 70 5 0 1 70 418713709 418713640 4.290000e-18 102.0
21 TraesCS3A01G298100 chr3B 94.670 788 34 3 740 1524 545009205 545008423 0.000000e+00 1216.0
22 TraesCS3A01G298100 chr3B 87.393 936 77 18 611 1524 544922694 544921778 0.000000e+00 1037.0
23 TraesCS3A01G298100 chr3B 88.938 678 51 5 1765 2438 342915744 342915087 0.000000e+00 815.0
24 TraesCS3A01G298100 chr3B 97.608 209 5 0 1 209 545044853 545044645 2.300000e-95 359.0
25 TraesCS3A01G298100 chr3B 84.762 210 18 7 638 841 544821532 544821331 5.320000e-47 198.0
26 TraesCS3A01G298100 chr3B 96.552 116 4 0 209 324 545043742 545043627 2.470000e-45 193.0
27 TraesCS3A01G298100 chr3B 91.912 136 10 1 1297 1432 544819027 544818893 3.200000e-44 189.0
28 TraesCS3A01G298100 chr3B 90.780 141 9 3 552 689 545013377 545013238 4.140000e-43 185.0
29 TraesCS3A01G298100 chr3B 88.816 152 4 3 425 563 545028322 545028171 8.960000e-40 174.0
30 TraesCS3A01G298100 chr3B 96.923 65 2 0 368 432 545043378 545043314 2.560000e-20 110.0
31 TraesCS3A01G298100 chr1A 92.399 671 32 2 1768 2438 515658331 515657680 0.000000e+00 939.0
32 TraesCS3A01G298100 chr2A 91.246 674 35 6 1765 2438 22024697 22025346 0.000000e+00 896.0
33 TraesCS3A01G298100 chr2D 89.583 672 49 7 1768 2438 179682392 179681741 0.000000e+00 833.0
34 TraesCS3A01G298100 chr2D 87.928 671 48 9 1768 2438 73827508 73828145 0.000000e+00 760.0
35 TraesCS3A01G298100 chr2D 88.327 514 39 8 1768 2280 255615133 255614640 4.490000e-167 597.0
36 TraesCS3A01G298100 chr2B 89.222 668 50 9 1773 2438 489018047 489018694 0.000000e+00 815.0
37 TraesCS3A01G298100 chr7D 88.839 672 44 11 1767 2438 618056963 618057603 0.000000e+00 797.0
38 TraesCS3A01G298100 chr7D 71.463 410 93 19 53 444 611467657 611468060 1.200000e-13 87.9
39 TraesCS3A01G298100 chr5D 88.806 670 42 11 1769 2438 238780533 238781169 0.000000e+00 791.0
40 TraesCS3A01G298100 chr5D 88.690 672 45 8 1767 2438 543429286 543428646 0.000000e+00 791.0
41 TraesCS3A01G298100 chr5D 89.650 628 34 8 1811 2438 327642171 327641575 0.000000e+00 771.0
42 TraesCS3A01G298100 chr6D 88.393 672 47 8 1767 2438 78765098 78765738 0.000000e+00 780.0
43 TraesCS3A01G298100 chr5A 93.990 416 24 1 2023 2438 75341290 75341704 1.590000e-176 628.0
44 TraesCS3A01G298100 chr4D 92.784 194 13 1 1764 1957 58390446 58390254 1.850000e-71 279.0
45 TraesCS3A01G298100 chr4B 85.088 114 12 5 1525 1636 546024901 546025011 7.130000e-21 111.0
46 TraesCS3A01G298100 chr7A 76.571 175 33 6 274 444 701459063 701459233 3.340000e-14 89.8


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 TraesCS3A01G298100 chr3A 532487254 532489691 2437 False 4503.000000 4503 100.000000 1 2438 1 chr3A.!!$F2 2437
1 TraesCS3A01G298100 chr3A 306917296 306917949 653 False 865.000000 865 90.342000 1766 2438 1 chr3A.!!$F1 672
2 TraesCS3A01G298100 chr3A 532644174 532644776 602 False 297.000000 372 88.363500 611 1326 2 chr3A.!!$F3 715
3 TraesCS3A01G298100 chr3D 418705092 418706538 1446 True 1058.000000 1277 93.597500 64 1523 2 chr3D.!!$R6 1459
4 TraesCS3A01G298100 chr3D 418482196 418483313 1117 True 536.000000 628 88.230000 611 1524 2 chr3D.!!$R5 913
5 TraesCS3A01G298100 chr3D 416403423 416404637 1214 False 441.000000 488 88.447000 50 1432 2 chr3D.!!$F2 1382
6 TraesCS3A01G298100 chr3D 418410376 418411101 725 True 365.500000 503 87.824500 611 1432 2 chr3D.!!$R4 821
7 TraesCS3A01G298100 chr3B 545008423 545009205 782 True 1216.000000 1216 94.670000 740 1524 1 chr3B.!!$R3 784
8 TraesCS3A01G298100 chr3B 544921778 544922694 916 True 1037.000000 1037 87.393000 611 1524 1 chr3B.!!$R2 913
9 TraesCS3A01G298100 chr3B 342915087 342915744 657 True 815.000000 815 88.938000 1765 2438 1 chr3B.!!$R1 673
10 TraesCS3A01G298100 chr3B 545043314 545044853 1539 True 220.666667 359 97.027667 1 432 3 chr3B.!!$R7 431
11 TraesCS3A01G298100 chr1A 515657680 515658331 651 True 939.000000 939 92.399000 1768 2438 1 chr1A.!!$R1 670
12 TraesCS3A01G298100 chr2A 22024697 22025346 649 False 896.000000 896 91.246000 1765 2438 1 chr2A.!!$F1 673
13 TraesCS3A01G298100 chr2D 179681741 179682392 651 True 833.000000 833 89.583000 1768 2438 1 chr2D.!!$R1 670
14 TraesCS3A01G298100 chr2D 73827508 73828145 637 False 760.000000 760 87.928000 1768 2438 1 chr2D.!!$F1 670
15 TraesCS3A01G298100 chr2B 489018047 489018694 647 False 815.000000 815 89.222000 1773 2438 1 chr2B.!!$F1 665
16 TraesCS3A01G298100 chr7D 618056963 618057603 640 False 797.000000 797 88.839000 1767 2438 1 chr7D.!!$F2 671
17 TraesCS3A01G298100 chr5D 238780533 238781169 636 False 791.000000 791 88.806000 1769 2438 1 chr5D.!!$F1 669
18 TraesCS3A01G298100 chr5D 543428646 543429286 640 True 791.000000 791 88.690000 1767 2438 1 chr5D.!!$R2 671
19 TraesCS3A01G298100 chr5D 327641575 327642171 596 True 771.000000 771 89.650000 1811 2438 1 chr5D.!!$R1 627
20 TraesCS3A01G298100 chr6D 78765098 78765738 640 False 780.000000 780 88.393000 1767 2438 1 chr6D.!!$F1 671

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
608 1736 0.31836 CGTACGTGTGCCACTGAAGA 60.318 55.0 7.22 0.0 31.34 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 3025 0.029035 CGCGCGGACAGAACTATACT 59.971 55.0 24.84 0.0 0.0 2.12 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
508 1636 2.261671 GACTGATGCGTGGACGGT 59.738 61.111 0.71 0.00 40.23 4.83
604 1732 3.762992 CGCGTACGTGTGCCACTG 61.763 66.667 20.36 0.00 31.34 3.66
605 1733 2.355363 GCGTACGTGTGCCACTGA 60.355 61.111 17.90 0.00 31.34 3.41
606 1734 1.952133 GCGTACGTGTGCCACTGAA 60.952 57.895 17.90 0.00 31.34 3.02
607 1735 1.886861 GCGTACGTGTGCCACTGAAG 61.887 60.000 17.90 0.00 31.34 3.02
608 1736 0.318360 CGTACGTGTGCCACTGAAGA 60.318 55.000 7.22 0.00 31.34 2.87
609 1737 1.668919 CGTACGTGTGCCACTGAAGAT 60.669 52.381 7.22 0.00 31.34 2.40
723 1882 1.488705 AACCCATGGTTCTCGCCTCA 61.489 55.000 11.73 0.00 43.05 3.86
778 1941 9.753674 TTTCACTCATTTTATTTATCCTGGTCT 57.246 29.630 0.00 0.00 0.00 3.85
832 2005 2.480224 TGCGGTACTACGTGCTAATC 57.520 50.000 0.00 0.00 35.98 1.75
843 2016 0.577269 GTGCTAATCGGCTAGTTGCG 59.423 55.000 0.00 0.00 44.05 4.85
1005 2210 3.709633 AGGCGACTCAGCATGGCA 61.710 61.111 0.00 0.00 39.27 4.92
1022 2227 0.801251 GCAGCATCAGGTGAGTTCAC 59.199 55.000 3.67 3.67 45.95 3.18
1054 2259 4.351938 CGTTCGACCAGGACGGCA 62.352 66.667 11.55 0.00 39.03 5.69
1233 2646 3.717294 GCCGGCCAGGAGGAAGAA 61.717 66.667 18.11 0.00 45.00 2.52
1472 2901 7.280356 ACTGAACTTTGTATACTTTGTCTGGT 58.720 34.615 4.17 0.00 0.00 4.00
1473 2902 7.773690 ACTGAACTTTGTATACTTTGTCTGGTT 59.226 33.333 4.17 0.00 0.00 3.67
1474 2903 7.925993 TGAACTTTGTATACTTTGTCTGGTTG 58.074 34.615 4.17 0.00 0.00 3.77
1475 2904 7.771361 TGAACTTTGTATACTTTGTCTGGTTGA 59.229 33.333 4.17 0.00 0.00 3.18
1524 2954 2.061773 CGATTAGCGGCAGATACAAGG 58.938 52.381 1.45 0.00 36.03 3.61
1525 2955 2.417719 GATTAGCGGCAGATACAAGGG 58.582 52.381 1.45 0.00 0.00 3.95
1526 2956 0.468226 TTAGCGGCAGATACAAGGGG 59.532 55.000 1.45 0.00 0.00 4.79
1527 2957 0.397957 TAGCGGCAGATACAAGGGGA 60.398 55.000 1.45 0.00 0.00 4.81
1528 2958 1.223487 GCGGCAGATACAAGGGGAA 59.777 57.895 0.00 0.00 0.00 3.97
1529 2959 0.393808 GCGGCAGATACAAGGGGAAA 60.394 55.000 0.00 0.00 0.00 3.13
1530 2960 1.750682 GCGGCAGATACAAGGGGAAAT 60.751 52.381 0.00 0.00 0.00 2.17
1531 2961 2.486548 GCGGCAGATACAAGGGGAAATA 60.487 50.000 0.00 0.00 0.00 1.40
1532 2962 3.139077 CGGCAGATACAAGGGGAAATAC 58.861 50.000 0.00 0.00 0.00 1.89
1533 2963 3.181454 CGGCAGATACAAGGGGAAATACT 60.181 47.826 0.00 0.00 0.00 2.12
1534 2964 4.390264 GGCAGATACAAGGGGAAATACTC 58.610 47.826 0.00 0.00 0.00 2.59
1535 2965 4.141482 GGCAGATACAAGGGGAAATACTCA 60.141 45.833 0.00 0.00 0.00 3.41
1536 2966 5.456763 GGCAGATACAAGGGGAAATACTCAT 60.457 44.000 0.00 0.00 0.00 2.90
1537 2967 6.064717 GCAGATACAAGGGGAAATACTCATT 58.935 40.000 0.00 0.00 0.00 2.57
1538 2968 6.016777 GCAGATACAAGGGGAAATACTCATTG 60.017 42.308 0.00 0.00 44.96 2.82
1539 2969 6.488006 CAGATACAAGGGGAAATACTCATTGG 59.512 42.308 0.00 0.00 43.91 3.16
1540 2970 4.675063 ACAAGGGGAAATACTCATTGGT 57.325 40.909 0.00 0.00 43.91 3.67
1541 2971 5.010708 ACAAGGGGAAATACTCATTGGTT 57.989 39.130 0.00 0.00 43.91 3.67
1542 2972 5.016831 ACAAGGGGAAATACTCATTGGTTC 58.983 41.667 0.00 0.00 43.91 3.62
1543 2973 4.251103 AGGGGAAATACTCATTGGTTCC 57.749 45.455 0.00 0.00 37.59 3.62
1544 2974 3.858638 AGGGGAAATACTCATTGGTTCCT 59.141 43.478 0.00 0.00 38.25 3.36
1545 2975 3.954258 GGGGAAATACTCATTGGTTCCTG 59.046 47.826 0.00 0.00 38.25 3.86
1546 2976 3.954258 GGGAAATACTCATTGGTTCCTGG 59.046 47.826 0.00 0.00 38.25 4.45
1547 2977 3.954258 GGAAATACTCATTGGTTCCTGGG 59.046 47.826 0.00 0.00 35.80 4.45
1548 2978 4.325030 GGAAATACTCATTGGTTCCTGGGA 60.325 45.833 0.00 0.00 35.80 4.37
1549 2979 3.933861 ATACTCATTGGTTCCTGGGAC 57.066 47.619 0.00 0.00 0.00 4.46
1550 2980 1.444933 ACTCATTGGTTCCTGGGACA 58.555 50.000 7.57 0.00 0.00 4.02
1551 2981 1.995542 ACTCATTGGTTCCTGGGACAT 59.004 47.619 7.57 0.00 38.20 3.06
1552 2982 2.025887 ACTCATTGGTTCCTGGGACATC 60.026 50.000 7.57 0.00 38.20 3.06
1553 2983 2.240667 CTCATTGGTTCCTGGGACATCT 59.759 50.000 7.57 0.00 38.20 2.90
1554 2984 2.025981 TCATTGGTTCCTGGGACATCTG 60.026 50.000 7.57 0.80 38.20 2.90
1555 2985 1.444933 TTGGTTCCTGGGACATCTGT 58.555 50.000 7.57 0.00 38.20 3.41
1556 2986 0.984230 TGGTTCCTGGGACATCTGTC 59.016 55.000 7.57 1.59 44.04 3.51
1567 2997 3.363341 GACATCTGTCCTCGGAATCTC 57.637 52.381 0.00 0.00 39.07 2.75
1568 2998 1.678627 ACATCTGTCCTCGGAATCTCG 59.321 52.381 0.00 0.00 32.29 4.04
1569 2999 0.671251 ATCTGTCCTCGGAATCTCGC 59.329 55.000 0.00 0.00 32.29 5.03
1570 3000 1.066587 CTGTCCTCGGAATCTCGCC 59.933 63.158 0.00 0.00 0.00 5.54
1576 3006 2.586079 CGGAATCTCGCCGCACAT 60.586 61.111 0.00 0.00 42.55 3.21
1577 3007 2.589492 CGGAATCTCGCCGCACATC 61.589 63.158 0.00 0.00 42.55 3.06
1578 3008 2.247437 GGAATCTCGCCGCACATCC 61.247 63.158 0.00 0.00 0.00 3.51
1579 3009 2.586079 AATCTCGCCGCACATCCG 60.586 61.111 0.00 0.00 0.00 4.18
1589 3019 2.584064 CACATCCGCACCTGCCTA 59.416 61.111 0.00 0.00 37.91 3.93
1590 3020 1.146930 CACATCCGCACCTGCCTAT 59.853 57.895 0.00 0.00 37.91 2.57
1591 3021 0.464373 CACATCCGCACCTGCCTATT 60.464 55.000 0.00 0.00 37.91 1.73
1592 3022 1.128200 ACATCCGCACCTGCCTATTA 58.872 50.000 0.00 0.00 37.91 0.98
1593 3023 1.699634 ACATCCGCACCTGCCTATTAT 59.300 47.619 0.00 0.00 37.91 1.28
1594 3024 2.106511 ACATCCGCACCTGCCTATTATT 59.893 45.455 0.00 0.00 37.91 1.40
1595 3025 3.326588 ACATCCGCACCTGCCTATTATTA 59.673 43.478 0.00 0.00 37.91 0.98
1596 3026 3.678056 TCCGCACCTGCCTATTATTAG 57.322 47.619 0.00 0.00 37.91 1.73
1597 3027 2.969950 TCCGCACCTGCCTATTATTAGT 59.030 45.455 0.00 0.00 37.91 2.24
1598 3028 4.154176 TCCGCACCTGCCTATTATTAGTA 58.846 43.478 0.00 0.00 37.91 1.82
1599 3029 4.775780 TCCGCACCTGCCTATTATTAGTAT 59.224 41.667 0.00 0.00 37.91 2.12
1600 3030 5.953548 TCCGCACCTGCCTATTATTAGTATA 59.046 40.000 0.00 0.00 37.91 1.47
1601 3031 6.096423 TCCGCACCTGCCTATTATTAGTATAG 59.904 42.308 0.00 0.00 37.91 1.31
1602 3032 6.127423 CCGCACCTGCCTATTATTAGTATAGT 60.127 42.308 0.00 0.00 37.91 2.12
1603 3033 7.321153 CGCACCTGCCTATTATTAGTATAGTT 58.679 38.462 0.00 0.00 37.91 2.24
1604 3034 7.488471 CGCACCTGCCTATTATTAGTATAGTTC 59.512 40.741 0.00 0.00 37.91 3.01
1605 3035 8.532819 GCACCTGCCTATTATTAGTATAGTTCT 58.467 37.037 0.00 0.00 34.31 3.01
1606 3036 9.862371 CACCTGCCTATTATTAGTATAGTTCTG 57.138 37.037 0.00 0.00 0.00 3.02
1607 3037 9.603189 ACCTGCCTATTATTAGTATAGTTCTGT 57.397 33.333 0.00 0.00 0.00 3.41
1610 3040 8.737175 TGCCTATTATTAGTATAGTTCTGTCCG 58.263 37.037 0.00 0.00 0.00 4.79
1611 3041 7.701501 GCCTATTATTAGTATAGTTCTGTCCGC 59.298 40.741 0.00 0.00 0.00 5.54
1612 3042 7.909121 CCTATTATTAGTATAGTTCTGTCCGCG 59.091 40.741 0.00 0.00 0.00 6.46
1613 3043 3.344904 TTAGTATAGTTCTGTCCGCGC 57.655 47.619 0.00 0.00 0.00 6.86
1614 3044 0.029035 AGTATAGTTCTGTCCGCGCG 59.971 55.000 25.67 25.67 0.00 6.86
1615 3045 0.248377 GTATAGTTCTGTCCGCGCGT 60.248 55.000 29.95 10.01 0.00 6.01
1616 3046 0.452987 TATAGTTCTGTCCGCGCGTT 59.547 50.000 29.95 5.86 0.00 4.84
1617 3047 0.389426 ATAGTTCTGTCCGCGCGTTT 60.389 50.000 29.95 6.92 0.00 3.60
1618 3048 1.005294 TAGTTCTGTCCGCGCGTTTC 61.005 55.000 29.95 18.02 0.00 2.78
1619 3049 3.399770 TTCTGTCCGCGCGTTTCG 61.400 61.111 29.95 13.63 42.12 3.46
1620 3050 4.634133 TCTGTCCGCGCGTTTCGT 62.634 61.111 29.95 0.00 41.07 3.85
1621 3051 2.730006 TTCTGTCCGCGCGTTTCGTA 62.730 55.000 29.95 6.92 41.07 3.43
1622 3052 2.126385 TGTCCGCGCGTTTCGTAT 60.126 55.556 29.95 0.00 41.07 3.06
1623 3053 1.680105 CTGTCCGCGCGTTTCGTATT 61.680 55.000 29.95 0.00 41.07 1.89
1624 3054 1.295645 GTCCGCGCGTTTCGTATTG 60.296 57.895 29.95 9.95 41.07 1.90
1625 3055 2.643485 CCGCGCGTTTCGTATTGC 60.643 61.111 29.95 0.00 41.07 3.56
1626 3056 2.094910 CGCGCGTTTCGTATTGCA 59.905 55.556 24.19 0.00 41.07 4.08
1627 3057 1.508126 CGCGCGTTTCGTATTGCAA 60.508 52.632 24.19 0.00 41.07 4.08
1628 3058 1.707463 CGCGCGTTTCGTATTGCAAC 61.707 55.000 24.19 0.00 41.07 4.17
1629 3059 0.452122 GCGCGTTTCGTATTGCAACT 60.452 50.000 8.43 0.00 41.07 3.16
1630 3060 1.510007 CGCGTTTCGTATTGCAACTC 58.490 50.000 0.00 0.00 0.00 3.01
1631 3061 1.126113 CGCGTTTCGTATTGCAACTCT 59.874 47.619 0.00 0.00 0.00 3.24
1632 3062 2.759038 GCGTTTCGTATTGCAACTCTC 58.241 47.619 0.00 0.00 0.00 3.20
1633 3063 2.412089 GCGTTTCGTATTGCAACTCTCT 59.588 45.455 0.00 0.00 0.00 3.10
1634 3064 3.482112 GCGTTTCGTATTGCAACTCTCTC 60.482 47.826 0.00 0.00 0.00 3.20
1635 3065 3.060895 CGTTTCGTATTGCAACTCTCTCC 59.939 47.826 0.00 0.00 0.00 3.71
1636 3066 2.561733 TCGTATTGCAACTCTCTCCG 57.438 50.000 0.00 0.00 0.00 4.63
1637 3067 0.924090 CGTATTGCAACTCTCTCCGC 59.076 55.000 0.00 0.00 0.00 5.54
1638 3068 1.735700 CGTATTGCAACTCTCTCCGCA 60.736 52.381 0.00 0.00 0.00 5.69
1639 3069 1.929836 GTATTGCAACTCTCTCCGCAG 59.070 52.381 0.00 0.00 35.47 5.18
1640 3070 1.023513 ATTGCAACTCTCTCCGCAGC 61.024 55.000 0.00 0.00 35.47 5.25
1641 3071 2.104572 TTGCAACTCTCTCCGCAGCT 62.105 55.000 0.00 0.00 35.47 4.24
1642 3072 2.099431 GCAACTCTCTCCGCAGCTG 61.099 63.158 10.11 10.11 0.00 4.24
1643 3073 2.099431 CAACTCTCTCCGCAGCTGC 61.099 63.158 29.12 29.12 37.78 5.25
1644 3074 2.282039 AACTCTCTCCGCAGCTGCT 61.282 57.895 34.22 12.13 39.32 4.24
1645 3075 2.202770 CTCTCTCCGCAGCTGCTG 60.203 66.667 34.22 28.58 39.32 4.41
1646 3076 2.993840 TCTCTCCGCAGCTGCTGT 60.994 61.111 34.22 0.00 39.32 4.40
1647 3077 2.047465 CTCTCCGCAGCTGCTGTT 60.047 61.111 34.22 0.00 39.32 3.16
1648 3078 2.047844 TCTCCGCAGCTGCTGTTC 60.048 61.111 34.22 13.55 39.32 3.18
1649 3079 2.047465 CTCCGCAGCTGCTGTTCT 60.047 61.111 34.22 0.00 39.32 3.01
1650 3080 2.047844 TCCGCAGCTGCTGTTCTC 60.048 61.111 34.22 12.51 39.32 2.87
1651 3081 3.485431 CCGCAGCTGCTGTTCTCG 61.485 66.667 34.22 22.21 39.32 4.04
1652 3082 2.736236 CGCAGCTGCTGTTCTCGT 60.736 61.111 34.22 0.00 39.32 4.18
1653 3083 1.444383 CGCAGCTGCTGTTCTCGTA 60.444 57.895 34.22 0.00 39.32 3.43
1654 3084 0.803768 CGCAGCTGCTGTTCTCGTAT 60.804 55.000 34.22 0.00 39.32 3.06
1655 3085 1.363744 GCAGCTGCTGTTCTCGTATT 58.636 50.000 31.33 0.00 38.21 1.89
1656 3086 1.734465 GCAGCTGCTGTTCTCGTATTT 59.266 47.619 31.33 0.00 38.21 1.40
1657 3087 2.222908 GCAGCTGCTGTTCTCGTATTTC 60.223 50.000 31.33 5.70 38.21 2.17
1658 3088 2.995939 CAGCTGCTGTTCTCGTATTTCA 59.004 45.455 21.21 0.00 0.00 2.69
1659 3089 3.061831 CAGCTGCTGTTCTCGTATTTCAG 59.938 47.826 21.21 0.00 0.00 3.02
1660 3090 2.996621 GCTGCTGTTCTCGTATTTCAGT 59.003 45.455 0.00 0.00 0.00 3.41
1661 3091 3.061429 GCTGCTGTTCTCGTATTTCAGTC 59.939 47.826 0.00 0.00 0.00 3.51
1662 3092 3.585862 TGCTGTTCTCGTATTTCAGTCC 58.414 45.455 0.00 0.00 0.00 3.85
1663 3093 3.258372 TGCTGTTCTCGTATTTCAGTCCT 59.742 43.478 0.00 0.00 0.00 3.85
1664 3094 3.860536 GCTGTTCTCGTATTTCAGTCCTC 59.139 47.826 0.00 0.00 0.00 3.71
1665 3095 4.425520 CTGTTCTCGTATTTCAGTCCTCC 58.574 47.826 0.00 0.00 0.00 4.30
1666 3096 3.830178 TGTTCTCGTATTTCAGTCCTCCA 59.170 43.478 0.00 0.00 0.00 3.86
1667 3097 4.174762 GTTCTCGTATTTCAGTCCTCCAC 58.825 47.826 0.00 0.00 0.00 4.02
1668 3098 3.427573 TCTCGTATTTCAGTCCTCCACA 58.572 45.455 0.00 0.00 0.00 4.17
1669 3099 3.192844 TCTCGTATTTCAGTCCTCCACAC 59.807 47.826 0.00 0.00 0.00 3.82
1670 3100 2.232941 TCGTATTTCAGTCCTCCACACC 59.767 50.000 0.00 0.00 0.00 4.16
1671 3101 2.233922 CGTATTTCAGTCCTCCACACCT 59.766 50.000 0.00 0.00 0.00 4.00
1672 3102 2.867109 ATTTCAGTCCTCCACACCTG 57.133 50.000 0.00 0.00 0.00 4.00
1673 3103 1.507140 TTTCAGTCCTCCACACCTGT 58.493 50.000 0.00 0.00 0.00 4.00
1674 3104 1.048601 TTCAGTCCTCCACACCTGTC 58.951 55.000 0.00 0.00 0.00 3.51
1675 3105 0.832135 TCAGTCCTCCACACCTGTCC 60.832 60.000 0.00 0.00 0.00 4.02
1676 3106 1.536662 AGTCCTCCACACCTGTCCC 60.537 63.158 0.00 0.00 0.00 4.46
1677 3107 2.603473 TCCTCCACACCTGTCCCG 60.603 66.667 0.00 0.00 0.00 5.14
1678 3108 4.394712 CCTCCACACCTGTCCCGC 62.395 72.222 0.00 0.00 0.00 6.13
1679 3109 3.625897 CTCCACACCTGTCCCGCA 61.626 66.667 0.00 0.00 0.00 5.69
1680 3110 3.883744 CTCCACACCTGTCCCGCAC 62.884 68.421 0.00 0.00 0.00 5.34
1684 3114 4.704833 CACCTGTCCCGCACCCTG 62.705 72.222 0.00 0.00 0.00 4.45
1692 3122 4.875713 CCGCACCCTGCCCCATAC 62.876 72.222 0.00 0.00 41.12 2.39
1693 3123 4.875713 CGCACCCTGCCCCATACC 62.876 72.222 0.00 0.00 41.12 2.73
1694 3124 4.522975 GCACCCTGCCCCATACCC 62.523 72.222 0.00 0.00 37.42 3.69
1695 3125 3.020647 CACCCTGCCCCATACCCA 61.021 66.667 0.00 0.00 0.00 4.51
1696 3126 2.046163 ACCCTGCCCCATACCCAT 59.954 61.111 0.00 0.00 0.00 4.00
1697 3127 1.625565 ACCCTGCCCCATACCCATT 60.626 57.895 0.00 0.00 0.00 3.16
1698 3128 1.228215 ACCCTGCCCCATACCCATTT 61.228 55.000 0.00 0.00 0.00 2.32
1699 3129 0.856982 CCCTGCCCCATACCCATTTA 59.143 55.000 0.00 0.00 0.00 1.40
1700 3130 1.480498 CCCTGCCCCATACCCATTTAC 60.480 57.143 0.00 0.00 0.00 2.01
1701 3131 1.480498 CCTGCCCCATACCCATTTACC 60.480 57.143 0.00 0.00 0.00 2.85
1702 3132 1.499007 CTGCCCCATACCCATTTACCT 59.501 52.381 0.00 0.00 0.00 3.08
1703 3133 2.714250 CTGCCCCATACCCATTTACCTA 59.286 50.000 0.00 0.00 0.00 3.08
1704 3134 2.444010 TGCCCCATACCCATTTACCTAC 59.556 50.000 0.00 0.00 0.00 3.18
1705 3135 2.224942 GCCCCATACCCATTTACCTACC 60.225 54.545 0.00 0.00 0.00 3.18
1706 3136 2.377531 CCCCATACCCATTTACCTACCC 59.622 54.545 0.00 0.00 0.00 3.69
1707 3137 3.057586 CCCATACCCATTTACCTACCCA 58.942 50.000 0.00 0.00 0.00 4.51
1708 3138 3.181437 CCCATACCCATTTACCTACCCAC 60.181 52.174 0.00 0.00 0.00 4.61
1709 3139 3.181437 CCATACCCATTTACCTACCCACC 60.181 52.174 0.00 0.00 0.00 4.61
1710 3140 2.371391 ACCCATTTACCTACCCACCT 57.629 50.000 0.00 0.00 0.00 4.00
1711 3141 2.202707 ACCCATTTACCTACCCACCTC 58.797 52.381 0.00 0.00 0.00 3.85
1712 3142 1.493446 CCCATTTACCTACCCACCTCC 59.507 57.143 0.00 0.00 0.00 4.30
1713 3143 2.488836 CCATTTACCTACCCACCTCCT 58.511 52.381 0.00 0.00 0.00 3.69
1714 3144 2.438392 CCATTTACCTACCCACCTCCTC 59.562 54.545 0.00 0.00 0.00 3.71
1715 3145 2.259014 TTTACCTACCCACCTCCTCC 57.741 55.000 0.00 0.00 0.00 4.30
1716 3146 0.340908 TTACCTACCCACCTCCTCCC 59.659 60.000 0.00 0.00 0.00 4.30
1717 3147 1.596955 TACCTACCCACCTCCTCCCC 61.597 65.000 0.00 0.00 0.00 4.81
1718 3148 2.784984 CTACCCACCTCCTCCCCA 59.215 66.667 0.00 0.00 0.00 4.96
1719 3149 1.082206 CTACCCACCTCCTCCCCAA 59.918 63.158 0.00 0.00 0.00 4.12
1720 3150 1.229723 TACCCACCTCCTCCCCAAC 60.230 63.158 0.00 0.00 0.00 3.77
1721 3151 1.757508 TACCCACCTCCTCCCCAACT 61.758 60.000 0.00 0.00 0.00 3.16
1722 3152 2.606587 CCCACCTCCTCCCCAACTG 61.607 68.421 0.00 0.00 0.00 3.16
1723 3153 1.847968 CCACCTCCTCCCCAACTGT 60.848 63.158 0.00 0.00 0.00 3.55
1724 3154 1.679898 CACCTCCTCCCCAACTGTC 59.320 63.158 0.00 0.00 0.00 3.51
1725 3155 1.539124 ACCTCCTCCCCAACTGTCC 60.539 63.158 0.00 0.00 0.00 4.02
1726 3156 2.301738 CCTCCTCCCCAACTGTCCC 61.302 68.421 0.00 0.00 0.00 4.46
1727 3157 1.229658 CTCCTCCCCAACTGTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
1728 3158 1.538876 TCCTCCCCAACTGTCCCTG 60.539 63.158 0.00 0.00 0.00 4.45
1729 3159 1.538876 CCTCCCCAACTGTCCCTGA 60.539 63.158 0.00 0.00 0.00 3.86
1730 3160 0.916358 CCTCCCCAACTGTCCCTGAT 60.916 60.000 0.00 0.00 0.00 2.90
1731 3161 0.995024 CTCCCCAACTGTCCCTGATT 59.005 55.000 0.00 0.00 0.00 2.57
1732 3162 0.698238 TCCCCAACTGTCCCTGATTG 59.302 55.000 0.00 0.00 0.00 2.67
1733 3163 0.698238 CCCCAACTGTCCCTGATTGA 59.302 55.000 0.00 0.00 0.00 2.57
1734 3164 1.614317 CCCCAACTGTCCCTGATTGAC 60.614 57.143 0.00 0.00 0.00 3.18
1735 3165 1.352352 CCCAACTGTCCCTGATTGACT 59.648 52.381 0.00 0.00 33.83 3.41
1736 3166 2.224867 CCCAACTGTCCCTGATTGACTT 60.225 50.000 0.00 0.00 33.83 3.01
1737 3167 3.490348 CCAACTGTCCCTGATTGACTTT 58.510 45.455 0.00 0.00 33.83 2.66
1738 3168 3.254166 CCAACTGTCCCTGATTGACTTTG 59.746 47.826 0.00 0.00 33.83 2.77
1739 3169 2.508526 ACTGTCCCTGATTGACTTTGC 58.491 47.619 0.00 0.00 33.83 3.68
1740 3170 1.466167 CTGTCCCTGATTGACTTTGCG 59.534 52.381 0.00 0.00 33.83 4.85
1741 3171 1.202758 TGTCCCTGATTGACTTTGCGT 60.203 47.619 0.00 0.00 33.83 5.24
1742 3172 1.197721 GTCCCTGATTGACTTTGCGTG 59.802 52.381 0.00 0.00 0.00 5.34
1743 3173 1.202758 TCCCTGATTGACTTTGCGTGT 60.203 47.619 0.00 0.00 0.00 4.49
1744 3174 2.037902 TCCCTGATTGACTTTGCGTGTA 59.962 45.455 0.00 0.00 0.00 2.90
1745 3175 2.416547 CCCTGATTGACTTTGCGTGTAG 59.583 50.000 0.00 0.00 0.00 2.74
1746 3176 3.325870 CCTGATTGACTTTGCGTGTAGA 58.674 45.455 0.00 0.00 0.00 2.59
1747 3177 3.935203 CCTGATTGACTTTGCGTGTAGAT 59.065 43.478 0.00 0.00 0.00 1.98
1748 3178 4.201753 CCTGATTGACTTTGCGTGTAGATG 60.202 45.833 0.00 0.00 0.00 2.90
1749 3179 3.125146 TGATTGACTTTGCGTGTAGATGC 59.875 43.478 0.00 0.00 34.35 3.91
1750 3180 2.162319 TGACTTTGCGTGTAGATGCA 57.838 45.000 1.99 1.99 42.59 3.96
1758 3188 4.661993 TGCGTGTAGATGCAAAAAGTAG 57.338 40.909 3.93 0.00 41.30 2.57
1759 3189 3.120338 TGCGTGTAGATGCAAAAAGTAGC 60.120 43.478 3.93 0.00 41.30 3.58
1760 3190 3.125316 GCGTGTAGATGCAAAAAGTAGCT 59.875 43.478 0.00 0.00 33.89 3.32
1761 3191 4.641954 CGTGTAGATGCAAAAAGTAGCTG 58.358 43.478 0.00 0.00 29.24 4.24
1762 3192 4.406943 GTGTAGATGCAAAAAGTAGCTGC 58.593 43.478 0.00 0.00 36.60 5.25
1763 3193 3.440173 TGTAGATGCAAAAAGTAGCTGCC 59.560 43.478 0.00 0.00 35.13 4.85
1771 3201 2.437085 AAAGTAGCTGCCCATTACCC 57.563 50.000 0.00 0.00 0.00 3.69
1803 3233 8.468720 GCTTTCGCCCAACTTTATAAATAAAA 57.531 30.769 0.00 0.00 32.39 1.52
1843 3273 7.119846 GCACATAGAAGGACTAGTTCAAAACAT 59.880 37.037 3.42 0.00 34.35 2.71
1877 3311 8.637099 CAAGTCTCACAATAATAGATCCAGAGA 58.363 37.037 0.00 0.00 0.00 3.10
2063 3513 3.060020 GACGGCCATCGAACGGAGA 62.060 63.158 2.24 0.00 42.43 3.71
2090 3540 3.077556 AAGGCGGAGATGGCGTCT 61.078 61.111 9.44 9.44 40.81 4.18
2191 3641 0.960364 GGGGAGCGCTGAATCACAAA 60.960 55.000 18.48 0.00 0.00 2.83
2327 3777 1.228862 GCACCAATCCCCACCAACT 60.229 57.895 0.00 0.00 0.00 3.16
2370 3824 0.319040 GAACTGAGCAGACACGCAGA 60.319 55.000 4.21 0.00 39.55 4.26
2392 3846 7.468631 GCAGAAGAAGAAAATGTGGTTCAAGTA 60.469 37.037 0.00 0.00 0.00 2.24
2393 3847 7.857885 CAGAAGAAGAAAATGTGGTTCAAGTAC 59.142 37.037 0.00 0.00 0.00 2.73
2406 3860 3.323774 TCAAGTACTCGGGGGTATCAT 57.676 47.619 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.032634 CCGTGTGCGTGCTTGGTAT 61.033 57.895 0.00 0.00 36.15 2.73
9 10 2.352229 CAACCGTGTGCGTGCTTG 60.352 61.111 0.00 0.00 36.15 4.01
34 35 1.823041 GGACTCGTAGGGGACTCCG 60.823 68.421 0.00 0.00 41.75 4.63
278 1189 1.682257 AGGAGTTCCTGAAGCTGGC 59.318 57.895 0.00 0.00 46.55 4.85
435 1551 1.205893 GTGCCTTCTCATCCTTCGACT 59.794 52.381 0.00 0.00 0.00 4.18
475 1603 4.067972 TCAGTCCAACACCAGTTAACTC 57.932 45.455 4.77 0.00 35.85 3.01
508 1636 0.319469 TCGCTCACACAAGCATCGAA 60.319 50.000 0.00 0.00 42.62 3.71
598 1726 2.485814 GGTGAGTTCAATCTTCAGTGGC 59.514 50.000 0.00 0.00 0.00 5.01
599 1727 2.738846 CGGTGAGTTCAATCTTCAGTGG 59.261 50.000 0.00 0.00 0.00 4.00
600 1728 3.653344 TCGGTGAGTTCAATCTTCAGTG 58.347 45.455 0.00 0.00 0.00 3.66
601 1729 4.310769 CTTCGGTGAGTTCAATCTTCAGT 58.689 43.478 0.00 0.00 0.00 3.41
602 1730 3.124297 GCTTCGGTGAGTTCAATCTTCAG 59.876 47.826 0.00 0.00 0.00 3.02
603 1731 3.067106 GCTTCGGTGAGTTCAATCTTCA 58.933 45.455 0.00 0.00 0.00 3.02
604 1732 2.092838 CGCTTCGGTGAGTTCAATCTTC 59.907 50.000 0.00 0.00 0.00 2.87
605 1733 2.069273 CGCTTCGGTGAGTTCAATCTT 58.931 47.619 0.00 0.00 0.00 2.40
606 1734 1.714794 CGCTTCGGTGAGTTCAATCT 58.285 50.000 0.00 0.00 0.00 2.40
607 1735 0.095417 GCGCTTCGGTGAGTTCAATC 59.905 55.000 0.00 0.00 0.00 2.67
608 1736 1.298859 GGCGCTTCGGTGAGTTCAAT 61.299 55.000 7.64 0.00 0.00 2.57
609 1737 1.959226 GGCGCTTCGGTGAGTTCAA 60.959 57.895 7.64 0.00 0.00 2.69
723 1882 8.500753 TTTGACGGAATATATAGCACAACTTT 57.499 30.769 0.00 0.00 0.00 2.66
778 1941 6.483974 TGACACCAAGAGCGAGTTAAATTTTA 59.516 34.615 0.00 0.00 0.00 1.52
832 2005 0.669318 TCAAGTTCCGCAACTAGCCG 60.669 55.000 0.00 0.00 42.45 5.52
843 2016 3.304458 GGAACGGTGTTTGATCAAGTTCC 60.304 47.826 27.37 27.37 43.15 3.62
1005 2210 0.671781 GCGTGAACTCACCTGATGCT 60.672 55.000 4.30 0.00 43.66 3.79
1233 2646 4.270153 TCCCTGCACCTGTCCCCT 62.270 66.667 0.00 0.00 0.00 4.79
1395 2816 0.596577 TGAACTCGTCGAAGGTGAGG 59.403 55.000 0.00 0.00 34.03 3.86
1524 2954 3.954258 CCAGGAACCAATGAGTATTTCCC 59.046 47.826 0.00 0.00 0.00 3.97
1525 2955 3.954258 CCCAGGAACCAATGAGTATTTCC 59.046 47.826 0.00 0.00 0.00 3.13
1526 2956 4.640647 GTCCCAGGAACCAATGAGTATTTC 59.359 45.833 0.00 0.00 0.00 2.17
1527 2957 4.044065 TGTCCCAGGAACCAATGAGTATTT 59.956 41.667 0.00 0.00 0.00 1.40
1528 2958 3.591527 TGTCCCAGGAACCAATGAGTATT 59.408 43.478 0.00 0.00 0.00 1.89
1529 2959 3.189606 TGTCCCAGGAACCAATGAGTAT 58.810 45.455 0.00 0.00 0.00 2.12
1530 2960 2.626785 TGTCCCAGGAACCAATGAGTA 58.373 47.619 0.00 0.00 0.00 2.59
1531 2961 1.444933 TGTCCCAGGAACCAATGAGT 58.555 50.000 0.00 0.00 0.00 3.41
1532 2962 2.240667 AGATGTCCCAGGAACCAATGAG 59.759 50.000 0.00 0.00 0.00 2.90
1533 2963 2.025981 CAGATGTCCCAGGAACCAATGA 60.026 50.000 0.00 0.00 0.00 2.57
1534 2964 2.291153 ACAGATGTCCCAGGAACCAATG 60.291 50.000 0.00 0.00 0.00 2.82
1535 2965 1.995542 ACAGATGTCCCAGGAACCAAT 59.004 47.619 0.00 0.00 0.00 3.16
1536 2966 1.351017 GACAGATGTCCCAGGAACCAA 59.649 52.381 1.33 0.00 39.07 3.67
1537 2967 0.984230 GACAGATGTCCCAGGAACCA 59.016 55.000 1.33 0.00 39.07 3.67
1538 2968 3.863407 GACAGATGTCCCAGGAACC 57.137 57.895 1.33 0.00 39.07 3.62
1547 2977 2.287308 CGAGATTCCGAGGACAGATGTC 60.287 54.545 4.33 4.33 44.04 3.06
1548 2978 1.678627 CGAGATTCCGAGGACAGATGT 59.321 52.381 0.00 0.00 0.00 3.06
1549 2979 1.601663 GCGAGATTCCGAGGACAGATG 60.602 57.143 0.00 0.00 0.00 2.90
1550 2980 0.671251 GCGAGATTCCGAGGACAGAT 59.329 55.000 0.00 0.00 0.00 2.90
1551 2981 1.384989 GGCGAGATTCCGAGGACAGA 61.385 60.000 0.00 0.00 0.00 3.41
1552 2982 1.066587 GGCGAGATTCCGAGGACAG 59.933 63.158 0.00 0.00 0.00 3.51
1553 2983 3.207354 GGCGAGATTCCGAGGACA 58.793 61.111 0.00 0.00 0.00 4.02
1560 2990 2.247437 GGATGTGCGGCGAGATTCC 61.247 63.158 12.98 7.39 0.00 3.01
1561 2991 2.589492 CGGATGTGCGGCGAGATTC 61.589 63.158 12.98 0.94 0.00 2.52
1562 2992 2.586079 CGGATGTGCGGCGAGATT 60.586 61.111 12.98 0.00 0.00 2.40
1571 3001 2.947938 ATAGGCAGGTGCGGATGTGC 62.948 60.000 5.08 5.08 43.26 4.57
1572 3002 0.464373 AATAGGCAGGTGCGGATGTG 60.464 55.000 0.00 0.00 43.26 3.21
1573 3003 1.128200 TAATAGGCAGGTGCGGATGT 58.872 50.000 0.00 0.00 43.26 3.06
1574 3004 2.479566 ATAATAGGCAGGTGCGGATG 57.520 50.000 0.00 0.00 43.26 3.51
1575 3005 3.583086 ACTAATAATAGGCAGGTGCGGAT 59.417 43.478 0.00 0.00 43.26 4.18
1576 3006 2.969950 ACTAATAATAGGCAGGTGCGGA 59.030 45.455 0.00 0.00 43.26 5.54
1577 3007 3.402628 ACTAATAATAGGCAGGTGCGG 57.597 47.619 0.00 0.00 43.26 5.69
1578 3008 6.864342 ACTATACTAATAATAGGCAGGTGCG 58.136 40.000 0.00 0.00 43.26 5.34
1579 3009 8.532819 AGAACTATACTAATAATAGGCAGGTGC 58.467 37.037 0.00 0.00 41.14 5.01
1580 3010 9.862371 CAGAACTATACTAATAATAGGCAGGTG 57.138 37.037 0.00 0.00 32.26 4.00
1581 3011 9.603189 ACAGAACTATACTAATAATAGGCAGGT 57.397 33.333 0.00 0.00 32.26 4.00
1584 3014 8.737175 CGGACAGAACTATACTAATAATAGGCA 58.263 37.037 0.00 0.00 32.26 4.75
1585 3015 7.701501 GCGGACAGAACTATACTAATAATAGGC 59.298 40.741 0.00 0.00 32.26 3.93
1586 3016 7.909121 CGCGGACAGAACTATACTAATAATAGG 59.091 40.741 0.00 0.00 32.26 2.57
1587 3017 7.428761 GCGCGGACAGAACTATACTAATAATAG 59.571 40.741 8.83 0.00 33.87 1.73
1588 3018 7.246311 GCGCGGACAGAACTATACTAATAATA 58.754 38.462 8.83 0.00 0.00 0.98
1589 3019 6.091437 GCGCGGACAGAACTATACTAATAAT 58.909 40.000 8.83 0.00 0.00 1.28
1590 3020 5.455392 GCGCGGACAGAACTATACTAATAA 58.545 41.667 8.83 0.00 0.00 1.40
1591 3021 4.377738 CGCGCGGACAGAACTATACTAATA 60.378 45.833 24.84 0.00 0.00 0.98
1592 3022 3.608707 CGCGCGGACAGAACTATACTAAT 60.609 47.826 24.84 0.00 0.00 1.73
1593 3023 2.286595 CGCGCGGACAGAACTATACTAA 60.287 50.000 24.84 0.00 0.00 2.24
1594 3024 1.262417 CGCGCGGACAGAACTATACTA 59.738 52.381 24.84 0.00 0.00 1.82
1595 3025 0.029035 CGCGCGGACAGAACTATACT 59.971 55.000 24.84 0.00 0.00 2.12
1596 3026 0.248377 ACGCGCGGACAGAACTATAC 60.248 55.000 35.22 0.00 0.00 1.47
1597 3027 0.452987 AACGCGCGGACAGAACTATA 59.547 50.000 35.22 0.00 0.00 1.31
1598 3028 0.389426 AAACGCGCGGACAGAACTAT 60.389 50.000 35.22 5.42 0.00 2.12
1599 3029 1.005294 GAAACGCGCGGACAGAACTA 61.005 55.000 35.22 0.00 0.00 2.24
1600 3030 2.279918 AAACGCGCGGACAGAACT 60.280 55.556 35.22 7.19 0.00 3.01
1601 3031 2.170273 GAAACGCGCGGACAGAAC 59.830 61.111 35.22 13.54 0.00 3.01
1602 3032 2.730006 TACGAAACGCGCGGACAGAA 62.730 55.000 35.22 12.48 46.04 3.02
1603 3033 2.531927 ATACGAAACGCGCGGACAGA 62.532 55.000 35.22 14.80 46.04 3.41
1604 3034 1.680105 AATACGAAACGCGCGGACAG 61.680 55.000 35.22 23.41 46.04 3.51
1605 3035 1.733758 AATACGAAACGCGCGGACA 60.734 52.632 35.22 12.86 46.04 4.02
1606 3036 1.295645 CAATACGAAACGCGCGGAC 60.296 57.895 35.22 22.07 46.04 4.79
1607 3037 3.073874 GCAATACGAAACGCGCGGA 62.074 57.895 35.22 11.89 46.04 5.54
1608 3038 2.643485 GCAATACGAAACGCGCGG 60.643 61.111 35.22 18.70 46.04 6.46
1609 3039 1.508126 TTGCAATACGAAACGCGCG 60.508 52.632 30.96 30.96 46.04 6.86
1610 3040 0.452122 AGTTGCAATACGAAACGCGC 60.452 50.000 5.73 0.00 46.04 6.86
1612 3042 2.412089 AGAGAGTTGCAATACGAAACGC 59.588 45.455 0.59 0.00 0.00 4.84
1613 3043 3.060895 GGAGAGAGTTGCAATACGAAACG 59.939 47.826 0.59 0.00 0.00 3.60
1614 3044 3.060895 CGGAGAGAGTTGCAATACGAAAC 59.939 47.826 0.59 0.00 0.00 2.78
1615 3045 3.250744 CGGAGAGAGTTGCAATACGAAA 58.749 45.455 0.59 0.00 0.00 3.46
1616 3046 2.876091 CGGAGAGAGTTGCAATACGAA 58.124 47.619 0.59 0.00 0.00 3.85
1617 3047 1.469251 GCGGAGAGAGTTGCAATACGA 60.469 52.381 0.59 0.00 0.00 3.43
1618 3048 0.924090 GCGGAGAGAGTTGCAATACG 59.076 55.000 0.59 0.00 0.00 3.06
1619 3049 1.929836 CTGCGGAGAGAGTTGCAATAC 59.070 52.381 0.59 0.00 36.82 1.89
1620 3050 1.740380 GCTGCGGAGAGAGTTGCAATA 60.740 52.381 8.65 0.00 36.82 1.90
1621 3051 1.023513 GCTGCGGAGAGAGTTGCAAT 61.024 55.000 8.65 0.00 36.82 3.56
1622 3052 1.669115 GCTGCGGAGAGAGTTGCAA 60.669 57.895 8.65 0.00 36.82 4.08
1623 3053 2.047844 GCTGCGGAGAGAGTTGCA 60.048 61.111 8.65 0.00 35.75 4.08
1624 3054 2.099431 CAGCTGCGGAGAGAGTTGC 61.099 63.158 8.65 0.00 0.00 4.17
1625 3055 2.099431 GCAGCTGCGGAGAGAGTTG 61.099 63.158 25.23 0.00 0.00 3.16
1626 3056 2.264166 GCAGCTGCGGAGAGAGTT 59.736 61.111 25.23 0.00 0.00 3.01
1636 3066 1.363744 AATACGAGAACAGCAGCTGC 58.636 50.000 31.53 31.53 42.49 5.25
1637 3067 2.995939 TGAAATACGAGAACAGCAGCTG 59.004 45.455 21.54 21.54 37.52 4.24
1638 3068 3.257393 CTGAAATACGAGAACAGCAGCT 58.743 45.455 0.00 0.00 0.00 4.24
1639 3069 2.996621 ACTGAAATACGAGAACAGCAGC 59.003 45.455 0.00 0.00 32.67 5.25
1640 3070 3.614616 GGACTGAAATACGAGAACAGCAG 59.385 47.826 0.00 0.00 32.67 4.24
1641 3071 3.258372 AGGACTGAAATACGAGAACAGCA 59.742 43.478 0.00 0.00 32.67 4.41
1642 3072 3.851098 AGGACTGAAATACGAGAACAGC 58.149 45.455 0.00 0.00 32.67 4.40
1643 3073 4.082190 TGGAGGACTGAAATACGAGAACAG 60.082 45.833 0.00 0.00 35.14 3.16
1644 3074 3.830178 TGGAGGACTGAAATACGAGAACA 59.170 43.478 0.00 0.00 0.00 3.18
1645 3075 4.174762 GTGGAGGACTGAAATACGAGAAC 58.825 47.826 0.00 0.00 0.00 3.01
1646 3076 3.830178 TGTGGAGGACTGAAATACGAGAA 59.170 43.478 0.00 0.00 0.00 2.87
1647 3077 3.192844 GTGTGGAGGACTGAAATACGAGA 59.807 47.826 0.00 0.00 0.00 4.04
1648 3078 3.512680 GTGTGGAGGACTGAAATACGAG 58.487 50.000 0.00 0.00 0.00 4.18
1649 3079 2.232941 GGTGTGGAGGACTGAAATACGA 59.767 50.000 0.00 0.00 0.00 3.43
1650 3080 2.233922 AGGTGTGGAGGACTGAAATACG 59.766 50.000 0.00 0.00 0.00 3.06
1651 3081 3.008049 ACAGGTGTGGAGGACTGAAATAC 59.992 47.826 0.00 0.00 35.08 1.89
1652 3082 3.248024 ACAGGTGTGGAGGACTGAAATA 58.752 45.455 0.00 0.00 35.08 1.40
1653 3083 2.039084 GACAGGTGTGGAGGACTGAAAT 59.961 50.000 0.00 0.00 35.08 2.17
1654 3084 1.416401 GACAGGTGTGGAGGACTGAAA 59.584 52.381 0.00 0.00 35.08 2.69
1655 3085 1.048601 GACAGGTGTGGAGGACTGAA 58.951 55.000 0.00 0.00 35.08 3.02
1656 3086 0.832135 GGACAGGTGTGGAGGACTGA 60.832 60.000 0.00 0.00 35.08 3.41
1657 3087 1.674057 GGACAGGTGTGGAGGACTG 59.326 63.158 0.00 0.00 37.01 3.51
1658 3088 1.536662 GGGACAGGTGTGGAGGACT 60.537 63.158 0.00 0.00 0.00 3.85
1659 3089 2.943978 CGGGACAGGTGTGGAGGAC 61.944 68.421 0.00 0.00 0.00 3.85
1660 3090 2.603473 CGGGACAGGTGTGGAGGA 60.603 66.667 0.00 0.00 0.00 3.71
1661 3091 4.394712 GCGGGACAGGTGTGGAGG 62.395 72.222 0.00 0.00 0.00 4.30
1662 3092 3.625897 TGCGGGACAGGTGTGGAG 61.626 66.667 0.00 0.00 0.00 3.86
1663 3093 3.936203 GTGCGGGACAGGTGTGGA 61.936 66.667 0.00 0.00 0.00 4.02
1667 3097 4.704833 CAGGGTGCGGGACAGGTG 62.705 72.222 1.14 0.00 0.00 4.00
1675 3105 4.875713 GTATGGGGCAGGGTGCGG 62.876 72.222 0.00 0.00 46.21 5.69
1676 3106 4.875713 GGTATGGGGCAGGGTGCG 62.876 72.222 0.00 0.00 46.21 5.34
1677 3107 4.522975 GGGTATGGGGCAGGGTGC 62.523 72.222 0.00 0.00 44.08 5.01
1678 3108 1.948403 AATGGGTATGGGGCAGGGTG 61.948 60.000 0.00 0.00 0.00 4.61
1679 3109 1.228215 AAATGGGTATGGGGCAGGGT 61.228 55.000 0.00 0.00 0.00 4.34
1680 3110 0.856982 TAAATGGGTATGGGGCAGGG 59.143 55.000 0.00 0.00 0.00 4.45
1681 3111 1.480498 GGTAAATGGGTATGGGGCAGG 60.480 57.143 0.00 0.00 0.00 4.85
1682 3112 1.499007 AGGTAAATGGGTATGGGGCAG 59.501 52.381 0.00 0.00 0.00 4.85
1683 3113 1.614449 AGGTAAATGGGTATGGGGCA 58.386 50.000 0.00 0.00 0.00 5.36
1684 3114 2.224942 GGTAGGTAAATGGGTATGGGGC 60.225 54.545 0.00 0.00 0.00 5.80
1685 3115 2.377531 GGGTAGGTAAATGGGTATGGGG 59.622 54.545 0.00 0.00 0.00 4.96
1686 3116 3.057586 TGGGTAGGTAAATGGGTATGGG 58.942 50.000 0.00 0.00 0.00 4.00
1687 3117 3.181437 GGTGGGTAGGTAAATGGGTATGG 60.181 52.174 0.00 0.00 0.00 2.74
1688 3118 3.720002 AGGTGGGTAGGTAAATGGGTATG 59.280 47.826 0.00 0.00 0.00 2.39
1689 3119 3.978672 GAGGTGGGTAGGTAAATGGGTAT 59.021 47.826 0.00 0.00 0.00 2.73
1690 3120 3.387012 GAGGTGGGTAGGTAAATGGGTA 58.613 50.000 0.00 0.00 0.00 3.69
1691 3121 2.202707 GAGGTGGGTAGGTAAATGGGT 58.797 52.381 0.00 0.00 0.00 4.51
1692 3122 1.493446 GGAGGTGGGTAGGTAAATGGG 59.507 57.143 0.00 0.00 0.00 4.00
1693 3123 2.438392 GAGGAGGTGGGTAGGTAAATGG 59.562 54.545 0.00 0.00 0.00 3.16
1694 3124 2.438392 GGAGGAGGTGGGTAGGTAAATG 59.562 54.545 0.00 0.00 0.00 2.32
1695 3125 2.631540 GGGAGGAGGTGGGTAGGTAAAT 60.632 54.545 0.00 0.00 0.00 1.40
1696 3126 1.274011 GGGAGGAGGTGGGTAGGTAAA 60.274 57.143 0.00 0.00 0.00 2.01
1697 3127 0.340908 GGGAGGAGGTGGGTAGGTAA 59.659 60.000 0.00 0.00 0.00 2.85
1698 3128 1.596955 GGGGAGGAGGTGGGTAGGTA 61.597 65.000 0.00 0.00 0.00 3.08
1699 3129 2.785703 GGGAGGAGGTGGGTAGGT 59.214 66.667 0.00 0.00 0.00 3.08
1700 3130 2.040779 GGGGAGGAGGTGGGTAGG 60.041 72.222 0.00 0.00 0.00 3.18
1701 3131 1.082206 TTGGGGAGGAGGTGGGTAG 59.918 63.158 0.00 0.00 0.00 3.18
1702 3132 1.229723 GTTGGGGAGGAGGTGGGTA 60.230 63.158 0.00 0.00 0.00 3.69
1703 3133 2.531942 GTTGGGGAGGAGGTGGGT 60.532 66.667 0.00 0.00 0.00 4.51
1704 3134 2.204151 AGTTGGGGAGGAGGTGGG 60.204 66.667 0.00 0.00 0.00 4.61
1705 3135 1.842381 GACAGTTGGGGAGGAGGTGG 61.842 65.000 0.00 0.00 0.00 4.61
1706 3136 1.679898 GACAGTTGGGGAGGAGGTG 59.320 63.158 0.00 0.00 0.00 4.00
1707 3137 1.539124 GGACAGTTGGGGAGGAGGT 60.539 63.158 0.00 0.00 0.00 3.85
1708 3138 2.301738 GGGACAGTTGGGGAGGAGG 61.302 68.421 0.00 0.00 0.00 4.30
1709 3139 1.229658 AGGGACAGTTGGGGAGGAG 60.230 63.158 0.00 0.00 0.00 3.69
1710 3140 1.538876 CAGGGACAGTTGGGGAGGA 60.539 63.158 0.00 0.00 0.00 3.71
1711 3141 0.916358 ATCAGGGACAGTTGGGGAGG 60.916 60.000 0.00 0.00 0.00 4.30
1712 3142 0.995024 AATCAGGGACAGTTGGGGAG 59.005 55.000 0.00 0.00 0.00 4.30
1713 3143 0.698238 CAATCAGGGACAGTTGGGGA 59.302 55.000 0.00 0.00 0.00 4.81
1714 3144 0.698238 TCAATCAGGGACAGTTGGGG 59.302 55.000 0.00 0.00 0.00 4.96
1715 3145 1.352352 AGTCAATCAGGGACAGTTGGG 59.648 52.381 0.00 0.00 37.74 4.12
1716 3146 2.867109 AGTCAATCAGGGACAGTTGG 57.133 50.000 0.00 0.00 37.74 3.77
1717 3147 3.304928 GCAAAGTCAATCAGGGACAGTTG 60.305 47.826 0.00 0.00 37.74 3.16
1718 3148 2.887152 GCAAAGTCAATCAGGGACAGTT 59.113 45.455 0.00 0.00 37.74 3.16
1719 3149 2.508526 GCAAAGTCAATCAGGGACAGT 58.491 47.619 0.00 0.00 37.74 3.55
1720 3150 1.466167 CGCAAAGTCAATCAGGGACAG 59.534 52.381 0.00 0.00 37.74 3.51
1721 3151 1.202758 ACGCAAAGTCAATCAGGGACA 60.203 47.619 0.00 0.00 37.74 4.02
1722 3152 1.197721 CACGCAAAGTCAATCAGGGAC 59.802 52.381 0.00 0.00 35.50 4.46
1723 3153 1.202758 ACACGCAAAGTCAATCAGGGA 60.203 47.619 0.00 0.00 0.00 4.20
1724 3154 1.238439 ACACGCAAAGTCAATCAGGG 58.762 50.000 0.00 0.00 0.00 4.45
1725 3155 3.325870 TCTACACGCAAAGTCAATCAGG 58.674 45.455 0.00 0.00 0.00 3.86
1726 3156 4.726021 GCATCTACACGCAAAGTCAATCAG 60.726 45.833 0.00 0.00 0.00 2.90
1727 3157 3.125146 GCATCTACACGCAAAGTCAATCA 59.875 43.478 0.00 0.00 0.00 2.57
1728 3158 3.125146 TGCATCTACACGCAAAGTCAATC 59.875 43.478 0.00 0.00 34.59 2.67
1729 3159 3.073678 TGCATCTACACGCAAAGTCAAT 58.926 40.909 0.00 0.00 34.59 2.57
1730 3160 2.488952 TGCATCTACACGCAAAGTCAA 58.511 42.857 0.00 0.00 34.59 3.18
1731 3161 2.162319 TGCATCTACACGCAAAGTCA 57.838 45.000 0.00 0.00 34.59 3.41
1736 3166 3.980646 ACTTTTTGCATCTACACGCAA 57.019 38.095 0.00 0.00 45.93 4.85
1737 3167 3.120338 GCTACTTTTTGCATCTACACGCA 60.120 43.478 0.00 0.00 36.05 5.24
1738 3168 3.125316 AGCTACTTTTTGCATCTACACGC 59.875 43.478 0.00 0.00 0.00 5.34
1739 3169 4.641954 CAGCTACTTTTTGCATCTACACG 58.358 43.478 0.00 0.00 0.00 4.49
1740 3170 4.406943 GCAGCTACTTTTTGCATCTACAC 58.593 43.478 0.00 0.00 37.75 2.90
1741 3171 3.440173 GGCAGCTACTTTTTGCATCTACA 59.560 43.478 0.00 0.00 39.54 2.74
1742 3172 3.181496 GGGCAGCTACTTTTTGCATCTAC 60.181 47.826 0.00 0.00 39.54 2.59
1743 3173 3.016736 GGGCAGCTACTTTTTGCATCTA 58.983 45.455 0.00 0.00 39.54 1.98
1744 3174 1.821136 GGGCAGCTACTTTTTGCATCT 59.179 47.619 0.00 0.00 39.54 2.90
1745 3175 1.545582 TGGGCAGCTACTTTTTGCATC 59.454 47.619 0.00 0.00 39.54 3.91
1746 3176 1.631405 TGGGCAGCTACTTTTTGCAT 58.369 45.000 0.00 0.00 39.54 3.96
1747 3177 1.631405 ATGGGCAGCTACTTTTTGCA 58.369 45.000 0.00 0.00 39.54 4.08
1748 3178 2.749280 AATGGGCAGCTACTTTTTGC 57.251 45.000 0.00 0.00 37.11 3.68
1749 3179 3.119137 GGGTAATGGGCAGCTACTTTTTG 60.119 47.826 0.00 0.00 0.00 2.44
1750 3180 3.096852 GGGTAATGGGCAGCTACTTTTT 58.903 45.455 0.00 0.00 0.00 1.94
1751 3181 2.042433 TGGGTAATGGGCAGCTACTTTT 59.958 45.455 0.00 0.00 0.00 2.27
1752 3182 1.638589 TGGGTAATGGGCAGCTACTTT 59.361 47.619 0.00 0.00 0.00 2.66
1753 3183 1.295020 TGGGTAATGGGCAGCTACTT 58.705 50.000 0.00 0.00 0.00 2.24
1754 3184 1.295020 TTGGGTAATGGGCAGCTACT 58.705 50.000 0.00 0.00 0.00 2.57
1755 3185 2.137810 TTTGGGTAATGGGCAGCTAC 57.862 50.000 0.00 0.00 0.00 3.58
1756 3186 2.909504 TTTTGGGTAATGGGCAGCTA 57.090 45.000 0.00 0.00 0.00 3.32
1757 3187 1.901833 CTTTTTGGGTAATGGGCAGCT 59.098 47.619 0.00 0.00 0.00 4.24
1758 3188 1.066215 CCTTTTTGGGTAATGGGCAGC 60.066 52.381 0.00 0.00 0.00 5.25
1759 3189 1.066215 GCCTTTTTGGGTAATGGGCAG 60.066 52.381 0.00 0.00 35.29 4.85
1760 3190 0.980423 GCCTTTTTGGGTAATGGGCA 59.020 50.000 0.00 0.00 35.29 5.36
1761 3191 1.275666 AGCCTTTTTGGGTAATGGGC 58.724 50.000 0.00 0.00 46.10 5.36
1824 3254 7.307811 GGTGTGTATGTTTTGAACTAGTCCTTC 60.308 40.741 0.00 0.00 0.00 3.46
1843 3273 5.554437 TTATTGTGAGACTTGGGTGTGTA 57.446 39.130 0.00 0.00 0.00 2.90
2063 3513 3.506059 CTCCGCCTTCATCGCCGAT 62.506 63.158 0.00 0.00 0.00 4.18
2191 3641 4.496341 CGCTCTGGACGATTTGCAATAAAT 60.496 41.667 0.00 0.00 0.00 1.40
2327 3777 0.539051 GGAGCTGCTTTAGAGAGGCA 59.461 55.000 2.53 0.00 34.66 4.75
2370 3824 7.254795 CGAGTACTTGAACCACATTTTCTTCTT 60.255 37.037 3.81 0.00 0.00 2.52
2392 3846 2.335933 CCCTTTATGATACCCCCGAGT 58.664 52.381 0.00 0.00 0.00 4.18
2393 3847 1.628846 CCCCTTTATGATACCCCCGAG 59.371 57.143 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.