Multiple sequence alignment - TraesCS2B01G153500

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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 TraesCS2B01G153500 chr2B 100.000 4389 0 0 1 4389 121514153 121509765 0.000000e+00 8010.0
1 TraesCS2B01G153500 chr2B 98.684 608 7 1 1 607 45561311 45561918 0.000000e+00 1077.0
2 TraesCS2B01G153500 chr2B 97.321 112 3 0 635 746 768556643 768556532 1.610000e-44 191.0
3 TraesCS2B01G153500 chr2B 90.826 109 8 2 744 851 561009911 561009804 1.270000e-30 145.0
4 TraesCS2B01G153500 chr2B 80.625 160 22 6 1040 1193 121513078 121512922 9.980000e-22 115.0
5 TraesCS2B01G153500 chr2B 80.625 160 22 6 1076 1232 121513114 121512961 9.980000e-22 115.0
6 TraesCS2B01G153500 chr2B 90.000 50 5 0 4216 4265 121509888 121509839 1.020000e-06 65.8
7 TraesCS2B01G153500 chr2B 90.000 50 5 0 4266 4315 121509938 121509889 1.020000e-06 65.8
8 TraesCS2B01G153500 chr2D 93.031 2181 107 22 2105 4265 78523778 78521623 0.000000e+00 3144.0
9 TraesCS2B01G153500 chr2D 89.789 568 21 16 850 1381 78525092 78524526 0.000000e+00 693.0
10 TraesCS2B01G153500 chr2D 90.385 468 29 8 1477 1940 78524235 78523780 6.280000e-168 601.0
11 TraesCS2B01G153500 chr2D 97.619 168 4 0 1940 2107 420278322 420278155 5.550000e-74 289.0
12 TraesCS2B01G153500 chr2D 89.130 92 6 4 2528 2618 78523688 78523600 1.290000e-20 111.0
13 TraesCS2B01G153500 chr2D 76.042 192 29 12 3471 3656 630633945 630634125 2.810000e-12 84.2
14 TraesCS2B01G153500 chr2D 75.622 201 25 18 3464 3656 629727406 629727590 1.310000e-10 78.7
15 TraesCS2B01G153500 chr2D 75.622 201 25 18 3464 3656 630089916 630089732 1.310000e-10 78.7
16 TraesCS2B01G153500 chr2D 74.242 198 34 11 3464 3656 629989542 629989357 2.830000e-07 67.6
17 TraesCS2B01G153500 chr2A 91.847 1153 54 15 3129 4265 78804380 78803252 0.000000e+00 1572.0
18 TraesCS2B01G153500 chr2A 94.033 1039 49 6 2103 3133 78805520 78804487 0.000000e+00 1563.0
19 TraesCS2B01G153500 chr2A 90.645 930 58 14 856 1757 78806706 78805778 0.000000e+00 1208.0
20 TraesCS2B01G153500 chr2A 94.611 167 7 1 3716 3882 78802594 78802430 1.570000e-64 257.0
21 TraesCS2B01G153500 chr2A 93.789 161 8 1 1782 1942 78805676 78805518 1.580000e-59 241.0
22 TraesCS2B01G153500 chr2A 76.000 175 21 15 3489 3656 760508074 760507914 2.190000e-08 71.3
23 TraesCS2B01G153500 chr1B 98.852 610 4 3 1 608 678131849 678131241 0.000000e+00 1085.0
24 TraesCS2B01G153500 chr1B 98.851 609 4 3 1 608 545472315 545472921 0.000000e+00 1083.0
25 TraesCS2B01G153500 chr1B 98.680 606 7 1 4 608 529476981 529476376 0.000000e+00 1074.0
26 TraesCS2B01G153500 chr1B 98.358 609 8 2 1 608 57622098 57621491 0.000000e+00 1068.0
27 TraesCS2B01G153500 chr1B 92.308 208 8 3 635 841 678131087 678130887 5.550000e-74 289.0
28 TraesCS2B01G153500 chr1B 95.000 180 8 1 1941 2119 322414904 322414725 9.290000e-72 281.0
29 TraesCS2B01G153500 chr1B 97.436 117 3 0 635 751 545473064 545473180 2.680000e-47 200.0
30 TraesCS2B01G153500 chr1B 98.214 112 2 0 635 746 57621337 57621226 3.460000e-46 196.0
31 TraesCS2B01G153500 chr1B 97.321 112 3 0 635 746 667544459 667544348 1.610000e-44 191.0
32 TraesCS2B01G153500 chr1B 94.231 104 4 2 749 851 57621193 57621091 1.630000e-34 158.0
33 TraesCS2B01G153500 chr1B 91.429 105 7 2 749 852 545473208 545473311 4.580000e-30 143.0
34 TraesCS2B01G153500 chr1B 88.732 71 7 1 2642 2711 653056193 653056123 7.820000e-13 86.1
35 TraesCS2B01G153500 chr6B 98.843 605 7 0 4 608 521045037 521044433 0.000000e+00 1079.0
36 TraesCS2B01G153500 chr6B 98.835 601 7 0 4 604 593939686 593939086 0.000000e+00 1072.0
37 TraesCS2B01G153500 chr6B 98.358 609 9 1 1 608 89123018 89123626 0.000000e+00 1068.0
38 TraesCS2B01G153500 chr6B 98.214 112 2 0 635 746 89132720 89132831 3.460000e-46 196.0
39 TraesCS2B01G153500 chr5B 98.361 610 8 1 1 608 489520861 489521470 0.000000e+00 1070.0
40 TraesCS2B01G153500 chr5B 80.717 586 61 26 2107 2671 544764271 544764825 4.090000e-110 409.0
41 TraesCS2B01G153500 chr5B 95.429 175 7 1 1931 2105 649699903 649700076 1.200000e-70 278.0
42 TraesCS2B01G153500 chr5B 82.759 319 24 10 2715 3032 544764932 544765220 5.630000e-64 255.0
43 TraesCS2B01G153500 chr5B 84.711 242 27 8 1202 1434 544763449 544763689 2.640000e-57 233.0
44 TraesCS2B01G153500 chr5B 93.137 102 4 3 749 849 593655369 593655468 3.540000e-31 147.0
45 TraesCS2B01G153500 chr5B 93.137 102 4 3 749 849 670703908 670704007 3.540000e-31 147.0
46 TraesCS2B01G153500 chr5B 92.157 102 6 2 750 850 422366818 422366918 4.580000e-30 143.0
47 TraesCS2B01G153500 chr5B 95.745 47 2 0 1792 1838 544809958 544810004 4.710000e-10 76.8
48 TraesCS2B01G153500 chr5A 80.895 581 58 26 2105 2671 564532257 564532798 4.090000e-110 409.0
49 TraesCS2B01G153500 chr5A 85.246 244 21 11 1202 1434 564531457 564531696 2.040000e-58 237.0
50 TraesCS2B01G153500 chr5A 80.791 177 17 9 3499 3664 564588909 564589079 5.960000e-24 122.0
51 TraesCS2B01G153500 chr5A 95.122 41 2 0 3624 3664 564579635 564579675 1.020000e-06 65.8
52 TraesCS2B01G153500 chr1A 79.397 597 83 25 3081 3660 564090466 564089893 6.890000e-103 385.0
53 TraesCS2B01G153500 chr1A 82.175 331 43 13 2712 3036 564090870 564090550 2.010000e-68 270.0
54 TraesCS2B01G153500 chr1A 76.882 186 23 8 2127 2302 564091313 564091138 2.170000e-13 87.9
55 TraesCS2B01G153500 chr5D 80.222 541 61 23 2195 2708 446682717 446683238 8.970000e-97 364.0
56 TraesCS2B01G153500 chr5D 97.605 167 4 0 1941 2107 445106488 445106654 2.000000e-73 287.0
57 TraesCS2B01G153500 chr5D 80.833 360 44 13 1170 1505 446570045 446570403 4.350000e-65 259.0
58 TraesCS2B01G153500 chr5D 81.921 177 15 8 3499 3664 446741893 446742063 2.750000e-27 134.0
59 TraesCS2B01G153500 chr5D 77.397 146 18 6 3474 3608 370441005 370441146 6.090000e-09 73.1
60 TraesCS2B01G153500 chr5D 85.135 74 7 3 3464 3535 446683606 446683677 6.090000e-09 73.1
61 TraesCS2B01G153500 chr5D 76.871 147 20 11 3474 3608 314524152 314524008 2.190000e-08 71.3
62 TraesCS2B01G153500 chr5D 86.441 59 8 0 3606 3664 446683720 446683778 1.020000e-06 65.8
63 TraesCS2B01G153500 chr6A 97.076 171 5 0 1940 2110 458217709 458217879 5.550000e-74 289.0
64 TraesCS2B01G153500 chr1D 97.041 169 4 1 1941 2109 128530637 128530470 2.580000e-72 283.0
65 TraesCS2B01G153500 chr1D 97.006 167 5 0 1940 2106 286391232 286391066 9.290000e-72 281.0
66 TraesCS2B01G153500 chr3D 95.977 174 6 1 1933 2105 556141151 556140978 9.290000e-72 281.0
67 TraesCS2B01G153500 chr3B 93.085 188 12 1 1935 2122 123027156 123027342 1.560000e-69 274.0
68 TraesCS2B01G153500 chr3B 97.321 112 3 0 635 746 708513396 708513507 1.610000e-44 191.0
69 TraesCS2B01G153500 chr3B 88.182 110 9 2 3555 3664 222329606 222329711 1.280000e-25 128.0
70 TraesCS2B01G153500 chr3B 85.455 110 12 2 3555 3664 725393381 725393486 1.290000e-20 111.0
71 TraesCS2B01G153500 chr4B 98.214 112 2 0 635 746 621033621 621033732 3.460000e-46 196.0
72 TraesCS2B01G153500 chr4B 97.321 112 3 0 635 746 552576907 552577018 1.610000e-44 191.0
73 TraesCS2B01G153500 chr4B 94.175 103 3 3 749 850 447793867 447793967 2.110000e-33 154.0
74 TraesCS2B01G153500 chr4B 92.381 105 5 3 749 852 445267226 445267124 3.540000e-31 147.0
75 TraesCS2B01G153500 chr7B 92.381 105 6 2 749 853 118975691 118975793 9.830000e-32 148.0


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 TraesCS2B01G153500 chr2B 121509765 121514153 4388 True 8010.000000 8010 100.000000 1 4389 1 chr2B.!!$R1 4388
1 TraesCS2B01G153500 chr2B 45561311 45561918 607 False 1077.000000 1077 98.684000 1 607 1 chr2B.!!$F1 606
2 TraesCS2B01G153500 chr2D 78521623 78525092 3469 True 1137.250000 3144 90.583750 850 4265 4 chr2D.!!$R4 3415
3 TraesCS2B01G153500 chr2A 78802430 78806706 4276 True 968.200000 1572 92.985000 856 4265 5 chr2A.!!$R2 3409
4 TraesCS2B01G153500 chr1B 529476376 529476981 605 True 1074.000000 1074 98.680000 4 608 1 chr1B.!!$R2 604
5 TraesCS2B01G153500 chr1B 678130887 678131849 962 True 687.000000 1085 95.580000 1 841 2 chr1B.!!$R6 840
6 TraesCS2B01G153500 chr1B 545472315 545473311 996 False 475.333333 1083 95.905333 1 852 3 chr1B.!!$F1 851
7 TraesCS2B01G153500 chr1B 57621091 57622098 1007 True 474.000000 1068 96.934333 1 851 3 chr1B.!!$R5 850
8 TraesCS2B01G153500 chr6B 521044433 521045037 604 True 1079.000000 1079 98.843000 4 608 1 chr6B.!!$R1 604
9 TraesCS2B01G153500 chr6B 593939086 593939686 600 True 1072.000000 1072 98.835000 4 604 1 chr6B.!!$R2 600
10 TraesCS2B01G153500 chr6B 89123018 89123626 608 False 1068.000000 1068 98.358000 1 608 1 chr6B.!!$F1 607
11 TraesCS2B01G153500 chr5B 489520861 489521470 609 False 1070.000000 1070 98.361000 1 608 1 chr5B.!!$F2 607
12 TraesCS2B01G153500 chr5B 544763449 544765220 1771 False 299.000000 409 82.729000 1202 3032 3 chr5B.!!$F7 1830
13 TraesCS2B01G153500 chr5A 564531457 564532798 1341 False 323.000000 409 83.070500 1202 2671 2 chr5A.!!$F3 1469
14 TraesCS2B01G153500 chr1A 564089893 564091313 1420 True 247.633333 385 79.484667 2127 3660 3 chr1A.!!$R1 1533

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
964 1136 0.179181 TGAACTCTAAGTACGGCGCG 60.179 55.0 6.9 0.0 0.00 6.86 F
1951 2613 0.106819 ATAGCACGTACTCCCTCCGT 60.107 55.0 0.0 0.0 34.71 4.69 F
1952 2614 0.322816 TAGCACGTACTCCCTCCGTT 60.323 55.0 0.0 0.0 31.46 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 3115 0.464373 ACCATAATGGCAGAGTGCGG 60.464 55.0 0.0 0.0 46.21 5.69 R
3172 4127 0.463204 CAGTGACCTGCCGATGAGAT 59.537 55.0 0.0 0.0 0.00 2.75 R
3614 4579 0.674895 CAAGTAGCCCACCAGTCAGC 60.675 60.0 0.0 0.0 0.00 4.26 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
953 1125 1.199327 CGTCGTTGGCTCTGAACTCTA 59.801 52.381 0.00 0.00 0.00 2.43
964 1136 0.179181 TGAACTCTAAGTACGGCGCG 60.179 55.000 6.90 0.00 0.00 6.86
981 1153 2.335712 CGAGGGAGCAGTTTTGGGC 61.336 63.158 0.00 0.00 0.00 5.36
1422 1626 3.411517 CCCCTCCCGCTCCACATT 61.412 66.667 0.00 0.00 0.00 2.71
1488 1880 5.043903 CGAAAGCAGATCGATTTCTCCTTA 58.956 41.667 18.81 0.00 45.80 2.69
1534 1926 2.012051 GCTGTATGAGGTGGGGTTTCG 61.012 57.143 0.00 0.00 0.00 3.46
1562 1960 7.571428 CGTTTTCAGTTAAAGTCTTCAGGGATC 60.571 40.741 0.00 0.00 0.00 3.36
1575 1977 7.955185 AGTCTTCAGGGATCTCATATGTATCTT 59.045 37.037 15.61 6.64 0.00 2.40
1692 2102 1.985473 TGTTGCCTTGAGTGCAGATT 58.015 45.000 0.00 0.00 40.35 2.40
1731 2144 2.373335 TTGTGCCACCCAGTAACAAT 57.627 45.000 0.00 0.00 0.00 2.71
1792 2454 8.894768 AATGCTAATTTCTGCTACTAAGTAGG 57.105 34.615 0.00 0.00 36.71 3.18
1882 2544 4.090642 GCACAGAGTTTCAGATCAACGTAG 59.909 45.833 0.00 0.00 0.00 3.51
1939 2601 3.892552 GCGTATTAGCGAAAAATAGCACG 59.107 43.478 0.00 0.00 33.94 5.34
1940 2602 4.549489 GCGTATTAGCGAAAAATAGCACGT 60.549 41.667 0.00 0.00 33.54 4.49
1941 2603 5.331756 GCGTATTAGCGAAAAATAGCACGTA 60.332 40.000 0.00 0.00 33.54 3.57
1942 2604 6.054569 CGTATTAGCGAAAAATAGCACGTAC 58.945 40.000 0.00 0.00 35.48 3.67
1943 2605 6.075205 CGTATTAGCGAAAAATAGCACGTACT 60.075 38.462 0.00 0.00 35.48 2.73
1944 2606 5.691508 TTAGCGAAAAATAGCACGTACTC 57.308 39.130 0.00 0.00 35.48 2.59
1945 2607 2.928116 AGCGAAAAATAGCACGTACTCC 59.072 45.455 0.00 0.00 35.48 3.85
1946 2608 2.030091 GCGAAAAATAGCACGTACTCCC 59.970 50.000 0.00 0.00 0.00 4.30
1947 2609 3.518590 CGAAAAATAGCACGTACTCCCT 58.481 45.455 0.00 0.00 0.00 4.20
1948 2610 3.550678 CGAAAAATAGCACGTACTCCCTC 59.449 47.826 0.00 0.00 0.00 4.30
1949 2611 3.538634 AAAATAGCACGTACTCCCTCC 57.461 47.619 0.00 0.00 0.00 4.30
1950 2612 1.030457 AATAGCACGTACTCCCTCCG 58.970 55.000 0.00 0.00 0.00 4.63
1951 2613 0.106819 ATAGCACGTACTCCCTCCGT 60.107 55.000 0.00 0.00 34.71 4.69
1952 2614 0.322816 TAGCACGTACTCCCTCCGTT 60.323 55.000 0.00 0.00 31.46 4.44
1953 2615 1.153881 GCACGTACTCCCTCCGTTC 60.154 63.158 0.00 0.00 31.46 3.95
1954 2616 1.509923 CACGTACTCCCTCCGTTCC 59.490 63.158 0.00 0.00 31.46 3.62
1955 2617 0.964358 CACGTACTCCCTCCGTTCCT 60.964 60.000 0.00 0.00 31.46 3.36
1956 2618 0.620556 ACGTACTCCCTCCGTTCCTA 59.379 55.000 0.00 0.00 0.00 2.94
1957 2619 1.004745 ACGTACTCCCTCCGTTCCTAA 59.995 52.381 0.00 0.00 0.00 2.69
1958 2620 2.094675 CGTACTCCCTCCGTTCCTAAA 58.905 52.381 0.00 0.00 0.00 1.85
1959 2621 2.692041 CGTACTCCCTCCGTTCCTAAAT 59.308 50.000 0.00 0.00 0.00 1.40
1960 2622 3.885297 CGTACTCCCTCCGTTCCTAAATA 59.115 47.826 0.00 0.00 0.00 1.40
1961 2623 4.522022 CGTACTCCCTCCGTTCCTAAATAT 59.478 45.833 0.00 0.00 0.00 1.28
1962 2624 5.707298 CGTACTCCCTCCGTTCCTAAATATA 59.293 44.000 0.00 0.00 0.00 0.86
1963 2625 6.207417 CGTACTCCCTCCGTTCCTAAATATAA 59.793 42.308 0.00 0.00 0.00 0.98
1964 2626 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1965 2627 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1966 2628 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1967 2629 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1968 2630 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1969 2631 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1970 2632 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1971 2633 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
1987 2649 8.753497 AAGTCTTTTTAGAGATTCCAACAAGT 57.247 30.769 0.00 0.00 0.00 3.16
1988 2650 8.159344 AGTCTTTTTAGAGATTCCAACAAGTG 57.841 34.615 0.00 0.00 0.00 3.16
1999 2661 2.006888 CCAACAAGTGGCTACATACGG 58.993 52.381 2.02 0.00 41.72 4.02
2000 2662 2.354303 CCAACAAGTGGCTACATACGGA 60.354 50.000 2.02 0.00 41.72 4.69
2001 2663 2.930040 CAACAAGTGGCTACATACGGAG 59.070 50.000 2.02 0.00 0.00 4.63
2002 2664 1.134788 ACAAGTGGCTACATACGGAGC 60.135 52.381 2.02 0.00 38.00 4.70
2003 2665 1.134818 CAAGTGGCTACATACGGAGCA 60.135 52.381 2.02 0.00 40.64 4.26
2004 2666 1.191535 AGTGGCTACATACGGAGCAA 58.808 50.000 2.02 0.00 40.64 3.91
2005 2667 1.553248 AGTGGCTACATACGGAGCAAA 59.447 47.619 2.02 0.00 40.64 3.68
2006 2668 2.027561 AGTGGCTACATACGGAGCAAAA 60.028 45.455 2.02 0.00 40.64 2.44
2007 2669 2.943033 GTGGCTACATACGGAGCAAAAT 59.057 45.455 0.00 0.00 40.64 1.82
2008 2670 2.942376 TGGCTACATACGGAGCAAAATG 59.058 45.455 0.00 0.00 40.64 2.32
2009 2671 3.202906 GGCTACATACGGAGCAAAATGA 58.797 45.455 0.00 0.00 40.64 2.57
2010 2672 3.248602 GGCTACATACGGAGCAAAATGAG 59.751 47.826 0.00 0.00 40.64 2.90
2011 2673 3.871594 GCTACATACGGAGCAAAATGAGT 59.128 43.478 0.00 0.00 38.62 3.41
2012 2674 4.260375 GCTACATACGGAGCAAAATGAGTG 60.260 45.833 0.00 0.00 38.62 3.51
2013 2675 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2014 2676 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2015 2677 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2016 2678 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2017 2679 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2018 2680 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2019 2681 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2020 2682 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2021 2683 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2060 2722 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
2061 2723 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
2062 2724 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
2063 2725 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
2064 2726 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
2065 2727 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
2066 2728 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
2067 2729 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
2068 2730 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
2069 2731 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
2070 2732 6.468956 CGTATGTTGTAGTCCATTTGAAATGC 59.531 38.462 12.26 0.23 0.00 3.56
2071 2733 5.132897 TGTTGTAGTCCATTTGAAATGCC 57.867 39.130 12.26 5.23 0.00 4.40
2072 2734 4.832266 TGTTGTAGTCCATTTGAAATGCCT 59.168 37.500 12.26 11.73 0.00 4.75
2073 2735 6.007076 TGTTGTAGTCCATTTGAAATGCCTA 58.993 36.000 12.26 10.85 0.00 3.93
2074 2736 6.491745 TGTTGTAGTCCATTTGAAATGCCTAA 59.508 34.615 12.26 1.00 0.00 2.69
2075 2737 7.014711 TGTTGTAGTCCATTTGAAATGCCTAAA 59.985 33.333 12.26 6.93 0.00 1.85
2076 2738 7.531857 TGTAGTCCATTTGAAATGCCTAAAA 57.468 32.000 12.26 4.58 0.00 1.52
2077 2739 7.957002 TGTAGTCCATTTGAAATGCCTAAAAA 58.043 30.769 12.26 2.62 0.00 1.94
2078 2740 8.087750 TGTAGTCCATTTGAAATGCCTAAAAAG 58.912 33.333 12.26 0.00 0.00 2.27
2079 2741 7.301868 AGTCCATTTGAAATGCCTAAAAAGA 57.698 32.000 12.26 0.00 0.00 2.52
2080 2742 7.154656 AGTCCATTTGAAATGCCTAAAAAGAC 58.845 34.615 12.26 10.86 0.00 3.01
2081 2743 7.015584 AGTCCATTTGAAATGCCTAAAAAGACT 59.984 33.333 12.26 12.67 31.00 3.24
2082 2744 7.657354 GTCCATTTGAAATGCCTAAAAAGACTT 59.343 33.333 12.26 0.00 0.00 3.01
2083 2745 8.865090 TCCATTTGAAATGCCTAAAAAGACTTA 58.135 29.630 12.26 0.00 0.00 2.24
2084 2746 9.657419 CCATTTGAAATGCCTAAAAAGACTTAT 57.343 29.630 12.26 0.00 0.00 1.73
2099 2761 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2100 2762 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2101 2763 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2174 2844 5.330455 AGAGAAATGCTCATACTCGTTCA 57.670 39.130 0.00 0.00 46.45 3.18
2287 2974 1.093159 GTCTCCTTGGATGCAGCAAG 58.907 55.000 3.51 5.75 0.00 4.01
2306 2993 3.797559 AGTTTTAGCTTGAGCCTTCCT 57.202 42.857 0.00 0.00 43.38 3.36
2336 3046 3.909732 TGTCTCCCCAGTTTGATGTTTT 58.090 40.909 0.00 0.00 0.00 2.43
2348 3058 7.148705 CCAGTTTGATGTTTTCATGCATAGTTG 60.149 37.037 0.00 0.00 41.05 3.16
2399 3115 3.936453 TGTGTATGCCGATAAGTTTGGTC 59.064 43.478 0.00 0.00 0.00 4.02
2414 3130 1.220749 GGTCCGCACTCTGCCATTA 59.779 57.895 0.00 0.00 41.12 1.90
2435 3151 7.362920 CCATTATGGTTATGGGATTTCGGAATC 60.363 40.741 8.00 8.00 39.11 2.52
2527 3246 3.243367 GCAAGTGCATCCAGTGTTTTACA 60.243 43.478 0.00 0.00 41.59 2.41
2691 3412 7.962918 GTGATTGTTGTAATGTACATTCCTGAC 59.037 37.037 24.00 16.60 38.68 3.51
2763 3558 4.569761 TCTGTGGTGCGATTAGATAGTC 57.430 45.455 0.00 0.00 0.00 2.59
2935 3731 4.377021 ACATCTACGCACTTCTTGTCAAA 58.623 39.130 0.00 0.00 0.00 2.69
2936 3732 4.814234 ACATCTACGCACTTCTTGTCAAAA 59.186 37.500 0.00 0.00 0.00 2.44
2951 3747 1.160137 CAAAAGCTCCTTCCGGACAG 58.840 55.000 1.83 5.06 34.92 3.51
2954 3750 3.394836 GCTCCTTCCGGACAGCCT 61.395 66.667 1.83 0.00 34.92 4.58
3061 3898 1.080230 CTGTGGACTCACTCCTGCG 60.080 63.158 0.00 0.00 43.94 5.18
3163 4118 3.432326 GCATAGATTCGGTTCTGACCCTT 60.432 47.826 0.00 0.00 43.42 3.95
3452 4410 8.671921 GTGGCGCATCTAATATAGTTAGTACTA 58.328 37.037 10.83 0.00 40.96 1.82
3453 4411 8.671921 TGGCGCATCTAATATAGTTAGTACTAC 58.328 37.037 10.83 0.00 39.59 2.73
3525 4486 2.162681 GATGTTCAGAAGGGTGGTTGG 58.837 52.381 0.00 0.00 0.00 3.77
3614 4579 3.005554 GTGGTTGTGATCTGGTGATGAG 58.994 50.000 0.00 0.00 32.19 2.90
3622 4591 0.900421 TCTGGTGATGAGCTGACTGG 59.100 55.000 0.00 0.00 0.00 4.00
3671 4640 3.387050 TGCTGATGATATGCTCAGTCTGT 59.613 43.478 11.06 0.00 40.80 3.41
3672 4641 4.141779 TGCTGATGATATGCTCAGTCTGTT 60.142 41.667 11.06 0.00 40.80 3.16
3673 4642 4.815308 GCTGATGATATGCTCAGTCTGTTT 59.185 41.667 11.06 0.00 40.80 2.83
3674 4643 5.277393 GCTGATGATATGCTCAGTCTGTTTG 60.277 44.000 11.06 0.00 40.80 2.93
3675 4644 4.573607 TGATGATATGCTCAGTCTGTTTGC 59.426 41.667 0.00 4.30 37.28 3.68
3676 4645 4.212143 TGATATGCTCAGTCTGTTTGCT 57.788 40.909 0.00 0.00 0.00 3.91
3677 4646 4.186926 TGATATGCTCAGTCTGTTTGCTC 58.813 43.478 0.00 0.00 0.00 4.26
3678 4647 2.556144 ATGCTCAGTCTGTTTGCTCA 57.444 45.000 0.00 0.00 0.00 4.26
3679 4648 1.875009 TGCTCAGTCTGTTTGCTCAG 58.125 50.000 0.00 0.00 36.85 3.35
3680 4649 1.139654 TGCTCAGTCTGTTTGCTCAGT 59.860 47.619 0.00 0.00 36.85 3.41
3681 4650 1.797635 GCTCAGTCTGTTTGCTCAGTC 59.202 52.381 0.00 0.00 36.85 3.51
3682 4651 2.547642 GCTCAGTCTGTTTGCTCAGTCT 60.548 50.000 0.00 0.00 36.85 3.24
3683 4652 3.058450 CTCAGTCTGTTTGCTCAGTCTG 58.942 50.000 17.26 17.26 45.58 3.51
3745 4714 5.020132 CCAGATCTTAGTCCCCGAGATTAT 58.980 45.833 0.00 0.00 30.64 1.28
3758 4727 1.396996 GAGATTATTTGCGCCGTGTGT 59.603 47.619 4.18 0.00 0.00 3.72
3759 4728 1.130373 AGATTATTTGCGCCGTGTGTG 59.870 47.619 4.18 0.00 0.00 3.82
3807 4776 5.181748 CCCTTGGTTCTTCTTCTATGTGAG 58.818 45.833 0.00 0.00 0.00 3.51
3856 4834 7.284074 TCAGTGTTATTACTTGGTCAAGGAAA 58.716 34.615 11.83 7.59 43.80 3.13
3866 4844 3.909732 TGGTCAAGGAAATTCTGTTGGT 58.090 40.909 8.15 0.00 0.00 3.67
4047 5029 6.480981 CCAAAATGGTGCAATAAATCATCTCC 59.519 38.462 0.00 0.00 31.35 3.71
4071 5053 1.876156 GATGGGTCGAATTCAGCATCC 59.124 52.381 6.22 0.00 0.00 3.51
4198 5183 1.070038 GCCATTGATTTGCGTTGTGG 58.930 50.000 0.00 0.00 0.00 4.17
4207 5192 0.820074 TTGCGTTGTGGTCCGGAAAT 60.820 50.000 5.23 0.00 31.42 2.17
4254 5239 8.184192 TGAAAAGAGATGAAAACTCAGAAACAC 58.816 33.333 0.00 0.00 38.36 3.32
4256 5241 4.212214 AGAGATGAAAACTCAGAAACACGC 59.788 41.667 0.00 0.00 38.36 5.34
4260 5245 3.380004 TGAAAACTCAGAAACACGCCAAT 59.620 39.130 0.00 0.00 0.00 3.16
4261 5246 4.576873 TGAAAACTCAGAAACACGCCAATA 59.423 37.500 0.00 0.00 0.00 1.90
4262 5247 4.483476 AAACTCAGAAACACGCCAATAC 57.517 40.909 0.00 0.00 0.00 1.89
4263 5248 2.066262 ACTCAGAAACACGCCAATACG 58.934 47.619 0.00 0.00 39.50 3.06
4264 5249 2.288579 ACTCAGAAACACGCCAATACGA 60.289 45.455 0.00 0.00 36.70 3.43
4265 5250 2.333926 TCAGAAACACGCCAATACGAG 58.666 47.619 0.00 0.00 36.70 4.18
4266 5251 1.076332 AGAAACACGCCAATACGAGC 58.924 50.000 0.00 0.00 36.70 5.03
4274 5259 2.825086 GCCAATACGAGCGTGAAATT 57.175 45.000 5.69 0.00 0.00 1.82
4275 5260 3.131240 GCCAATACGAGCGTGAAATTT 57.869 42.857 5.69 0.00 0.00 1.82
4276 5261 3.098636 GCCAATACGAGCGTGAAATTTC 58.901 45.455 11.41 11.41 0.00 2.17
4277 5262 3.680789 CCAATACGAGCGTGAAATTTCC 58.319 45.455 15.48 6.21 0.00 3.13
4278 5263 3.374058 CCAATACGAGCGTGAAATTTCCT 59.626 43.478 15.48 5.50 0.00 3.36
4279 5264 4.334443 CAATACGAGCGTGAAATTTCCTG 58.666 43.478 15.48 8.80 0.00 3.86
4280 5265 2.163818 ACGAGCGTGAAATTTCCTGA 57.836 45.000 15.48 0.00 0.00 3.86
4281 5266 2.489971 ACGAGCGTGAAATTTCCTGAA 58.510 42.857 15.48 0.00 0.00 3.02
4282 5267 2.875933 ACGAGCGTGAAATTTCCTGAAA 59.124 40.909 15.48 0.00 34.46 2.69
4283 5268 3.314080 ACGAGCGTGAAATTTCCTGAAAA 59.686 39.130 15.48 0.00 33.56 2.29
4284 5269 3.908382 CGAGCGTGAAATTTCCTGAAAAG 59.092 43.478 15.48 0.40 33.56 2.27
4285 5270 4.319477 CGAGCGTGAAATTTCCTGAAAAGA 60.319 41.667 15.48 0.00 33.56 2.52
4286 5271 5.113502 AGCGTGAAATTTCCTGAAAAGAG 57.886 39.130 15.48 0.00 33.56 2.85
4287 5272 4.821805 AGCGTGAAATTTCCTGAAAAGAGA 59.178 37.500 15.48 0.00 33.56 3.10
4288 5273 5.474876 AGCGTGAAATTTCCTGAAAAGAGAT 59.525 36.000 15.48 0.00 33.56 2.75
4289 5274 5.570589 GCGTGAAATTTCCTGAAAAGAGATG 59.429 40.000 15.48 0.00 33.56 2.90
4290 5275 6.568462 GCGTGAAATTTCCTGAAAAGAGATGA 60.568 38.462 15.48 0.00 33.56 2.92
4291 5276 7.362662 CGTGAAATTTCCTGAAAAGAGATGAA 58.637 34.615 15.48 0.00 33.56 2.57
4292 5277 7.862372 CGTGAAATTTCCTGAAAAGAGATGAAA 59.138 33.333 15.48 0.00 33.56 2.69
4293 5278 9.533253 GTGAAATTTCCTGAAAAGAGATGAAAA 57.467 29.630 15.48 0.00 33.56 2.29
4294 5279 9.533253 TGAAATTTCCTGAAAAGAGATGAAAAC 57.467 29.630 15.48 0.00 33.56 2.43
4295 5280 9.755804 GAAATTTCCTGAAAAGAGATGAAAACT 57.244 29.630 6.95 0.00 33.56 2.66
4296 5281 9.755804 AAATTTCCTGAAAAGAGATGAAAACTC 57.244 29.630 0.00 0.00 32.18 3.01
4297 5282 7.880160 TTTCCTGAAAAGAGATGAAAACTCA 57.120 32.000 0.00 0.00 38.36 3.41
4298 5283 7.502120 TTCCTGAAAAGAGATGAAAACTCAG 57.498 36.000 0.00 0.00 38.36 3.35
4299 5284 6.000219 TCCTGAAAAGAGATGAAAACTCAGG 59.000 40.000 8.21 8.21 46.65 3.86
4301 5286 7.502120 CTGAAAAGAGATGAAAACTCAGGAA 57.498 36.000 0.00 0.00 38.36 3.36
4302 5287 7.264373 TGAAAAGAGATGAAAACTCAGGAAC 57.736 36.000 0.00 0.00 38.36 3.62
4303 5288 7.056635 TGAAAAGAGATGAAAACTCAGGAACT 58.943 34.615 0.00 0.00 38.36 3.01
4304 5289 7.557719 TGAAAAGAGATGAAAACTCAGGAACTT 59.442 33.333 0.00 0.00 38.36 2.66
4305 5290 6.874288 AAGAGATGAAAACTCAGGAACTTG 57.126 37.500 0.00 0.00 38.36 3.16
4306 5291 5.934781 AGAGATGAAAACTCAGGAACTTGT 58.065 37.500 0.00 0.00 38.36 3.16
4307 5292 5.994668 AGAGATGAAAACTCAGGAACTTGTC 59.005 40.000 0.00 0.00 38.36 3.18
4308 5293 5.684704 AGATGAAAACTCAGGAACTTGTCA 58.315 37.500 0.00 0.00 34.60 3.58
4309 5294 5.762218 AGATGAAAACTCAGGAACTTGTCAG 59.238 40.000 0.00 0.00 34.60 3.51
4319 5304 4.569162 CAGGAACTTGTCAGTACGAAACAA 59.431 41.667 9.41 9.41 34.60 2.83
4364 5349 7.094933 ACTGAAATACTACGTCCAACCATTTTC 60.095 37.037 0.00 0.00 0.00 2.29
4372 5357 2.801679 GTCCAACCATTTTCGTACGTCA 59.198 45.455 16.05 0.00 0.00 4.35
4384 5369 2.352651 TCGTACGTCATTTCCCTCTACG 59.647 50.000 16.05 0.00 39.37 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 8.034215 TGTTGTTGGAGGAATATGCTTAAAATG 58.966 33.333 0.00 0.00 0.00 2.32
173 177 9.643693 ATGATATGAAGATGTTGTTTGGAAAAC 57.356 29.630 0.00 0.00 0.00 2.43
753 914 0.696501 ACCCTTTTGTCTACCGCCAT 59.303 50.000 0.00 0.00 0.00 4.40
763 924 5.845391 TTTTCGAGATTTGACCCTTTTGT 57.155 34.783 0.00 0.00 0.00 2.83
789 950 5.779241 TCAAGATCTGACCCCTGTTTAAT 57.221 39.130 0.00 0.00 0.00 1.40
791 952 5.576563 TTTCAAGATCTGACCCCTGTTTA 57.423 39.130 0.00 0.00 32.21 2.01
953 1125 3.823330 CTCCCTCGCGCCGTACTT 61.823 66.667 0.00 0.00 0.00 2.24
964 1136 1.979155 GGCCCAAAACTGCTCCCTC 60.979 63.158 0.00 0.00 0.00 4.30
973 1145 0.591659 GTGAAGAGTCGGCCCAAAAC 59.408 55.000 0.00 0.00 0.00 2.43
981 1153 4.796231 CCGCCGGTGAAGAGTCGG 62.796 72.222 18.79 7.63 45.84 4.79
1434 1638 2.289133 GGAAATGGATCGAGACCCTAGC 60.289 54.545 8.60 0.00 0.00 3.42
1488 1880 6.070656 TCATCTGTTCTGTTCCAAATTTCCT 58.929 36.000 0.00 0.00 0.00 3.36
1534 1926 6.419771 CCTGAAGACTTTAACTGAAAACGAC 58.580 40.000 0.00 0.00 0.00 4.34
1713 2126 3.730215 ATATTGTTACTGGGTGGCACA 57.270 42.857 20.82 0.00 0.00 4.57
1777 2356 7.832685 TGTGAAATACTCCTACTTAGTAGCAGA 59.167 37.037 16.42 7.59 35.06 4.26
1780 2359 8.083462 GGATGTGAAATACTCCTACTTAGTAGC 58.917 40.741 13.54 0.00 35.06 3.58
1792 2454 5.065731 CCTTCAGCTTGGATGTGAAATACTC 59.934 44.000 0.00 0.00 30.00 2.59
1882 2544 3.303593 CGTATCATTCATTGGCAGCTGTC 60.304 47.826 12.53 12.53 0.00 3.51
1913 2575 6.515340 GTGCTATTTTTCGCTAATACGCATAC 59.485 38.462 0.00 0.00 31.18 2.39
1939 2601 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
1940 2602 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
1941 2603 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
1942 2604 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1943 2605 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1944 2606 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1945 2607 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
1961 2623 9.847224 ACTTGTTGGAATCTCTAAAAAGACTTA 57.153 29.630 9.03 0.00 35.06 2.24
1962 2624 8.624776 CACTTGTTGGAATCTCTAAAAAGACTT 58.375 33.333 9.03 0.00 35.06 3.01
1963 2625 8.159344 CACTTGTTGGAATCTCTAAAAAGACT 57.841 34.615 9.03 0.00 35.06 3.24
1980 2642 2.930040 CTCCGTATGTAGCCACTTGTTG 59.070 50.000 0.00 0.00 0.00 3.33
1981 2643 2.677037 GCTCCGTATGTAGCCACTTGTT 60.677 50.000 0.00 0.00 32.40 2.83
1982 2644 1.134788 GCTCCGTATGTAGCCACTTGT 60.135 52.381 0.00 0.00 32.40 3.16
1983 2645 1.134818 TGCTCCGTATGTAGCCACTTG 60.135 52.381 0.00 0.00 37.97 3.16
1984 2646 1.191535 TGCTCCGTATGTAGCCACTT 58.808 50.000 0.00 0.00 37.97 3.16
1985 2647 1.191535 TTGCTCCGTATGTAGCCACT 58.808 50.000 0.00 0.00 37.97 4.00
1986 2648 2.018542 TTTGCTCCGTATGTAGCCAC 57.981 50.000 0.00 0.00 37.97 5.01
1987 2649 2.772077 TTTTGCTCCGTATGTAGCCA 57.228 45.000 0.00 0.00 37.97 4.75
1988 2650 3.202906 TCATTTTGCTCCGTATGTAGCC 58.797 45.455 0.00 0.00 37.97 3.93
1989 2651 3.871594 ACTCATTTTGCTCCGTATGTAGC 59.128 43.478 0.00 0.00 39.25 3.58
1990 2652 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1991 2653 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1992 2654 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1993 2655 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1994 2656 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1995 2657 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1996 2658 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1997 2659 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1998 2660 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1999 2661 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2038 2700 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
2039 2701 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
2041 2703 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
2042 2704 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
2043 2705 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
2044 2706 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
2045 2707 6.468956 GCATTTCAAATGGACTACAACATACG 59.531 38.462 12.14 0.00 0.00 3.06
2046 2708 6.751888 GGCATTTCAAATGGACTACAACATAC 59.248 38.462 12.14 0.00 0.00 2.39
2047 2709 6.663093 AGGCATTTCAAATGGACTACAACATA 59.337 34.615 12.14 0.00 0.00 2.29
2048 2710 5.481473 AGGCATTTCAAATGGACTACAACAT 59.519 36.000 12.14 0.00 0.00 2.71
2049 2711 4.832266 AGGCATTTCAAATGGACTACAACA 59.168 37.500 12.14 0.00 0.00 3.33
2050 2712 5.391312 AGGCATTTCAAATGGACTACAAC 57.609 39.130 12.14 0.00 0.00 3.32
2051 2713 7.531857 TTTAGGCATTTCAAATGGACTACAA 57.468 32.000 12.14 1.11 0.00 2.41
2052 2714 7.531857 TTTTAGGCATTTCAAATGGACTACA 57.468 32.000 12.14 0.00 0.00 2.74
2053 2715 8.303876 TCTTTTTAGGCATTTCAAATGGACTAC 58.696 33.333 12.14 0.00 0.00 2.73
2054 2716 8.303876 GTCTTTTTAGGCATTTCAAATGGACTA 58.696 33.333 12.14 2.16 0.00 2.59
2055 2717 7.015584 AGTCTTTTTAGGCATTTCAAATGGACT 59.984 33.333 12.14 9.71 0.00 3.85
2056 2718 7.154656 AGTCTTTTTAGGCATTTCAAATGGAC 58.845 34.615 12.14 7.77 0.00 4.02
2057 2719 7.301868 AGTCTTTTTAGGCATTTCAAATGGA 57.698 32.000 12.14 0.00 0.00 3.41
2058 2720 7.967890 AAGTCTTTTTAGGCATTTCAAATGG 57.032 32.000 12.14 0.00 0.00 3.16
2073 2735 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2074 2736 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2075 2737 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2076 2738 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2077 2739 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2078 2740 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2079 2741 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2080 2742 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2081 2743 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2082 2744 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2083 2745 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2084 2746 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2085 2747 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2086 2748 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2087 2749 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
2088 2750 3.359950 GAAACTACTCCCTCCGTTCCTA 58.640 50.000 0.00 0.00 0.00 2.94
2089 2751 2.177734 GAAACTACTCCCTCCGTTCCT 58.822 52.381 0.00 0.00 0.00 3.36
2090 2752 1.206610 GGAAACTACTCCCTCCGTTCC 59.793 57.143 0.00 0.00 0.00 3.62
2091 2753 1.897802 TGGAAACTACTCCCTCCGTTC 59.102 52.381 0.00 0.00 34.22 3.95
2092 2754 1.900486 CTGGAAACTACTCCCTCCGTT 59.100 52.381 0.00 0.00 34.22 4.44
2093 2755 1.203149 ACTGGAAACTACTCCCTCCGT 60.203 52.381 0.00 0.00 34.22 4.69
2094 2756 1.558233 ACTGGAAACTACTCCCTCCG 58.442 55.000 0.00 0.00 34.22 4.63
2095 2757 3.978610 TCTACTGGAAACTACTCCCTCC 58.021 50.000 0.00 0.00 34.22 4.30
2096 2758 5.997384 TTTCTACTGGAAACTACTCCCTC 57.003 43.478 0.00 0.00 38.81 4.30
2097 2759 6.272558 ACAATTTCTACTGGAAACTACTCCCT 59.727 38.462 0.00 0.00 45.29 4.20
2098 2760 6.473758 ACAATTTCTACTGGAAACTACTCCC 58.526 40.000 0.00 0.00 45.29 4.30
2099 2761 7.981102 AACAATTTCTACTGGAAACTACTCC 57.019 36.000 0.00 0.00 45.29 3.85
2142 2812 4.927049 TGAGCATTTCTCTTTGGAGGATT 58.073 39.130 0.00 0.00 42.38 3.01
2143 2813 4.581309 TGAGCATTTCTCTTTGGAGGAT 57.419 40.909 0.00 0.00 42.38 3.24
2144 2814 4.581309 ATGAGCATTTCTCTTTGGAGGA 57.419 40.909 0.00 0.00 42.38 3.71
2200 2876 1.821136 CTCTTTCAGGATGCCAAACCC 59.179 52.381 0.00 0.00 34.76 4.11
2287 2974 4.855715 AAAGGAAGGCTCAAGCTAAAAC 57.144 40.909 1.46 0.00 41.70 2.43
2399 3115 0.464373 ACCATAATGGCAGAGTGCGG 60.464 55.000 0.00 0.00 46.21 5.69
2414 3130 4.072131 CGATTCCGAAATCCCATAACCAT 58.928 43.478 0.00 0.00 38.46 3.55
2527 3246 5.884792 CCTCTTTCAAGATGCCAGACTAATT 59.115 40.000 0.00 0.00 33.93 1.40
2763 3558 8.514594 TCTGAAAGCAACATCCTAATACAAAAG 58.485 33.333 0.00 0.00 0.00 2.27
2951 3747 3.703001 ATATATGGTGGTAGCACAGGC 57.297 47.619 25.23 9.79 41.61 4.85
2954 3750 4.202419 GGTGGAATATATGGTGGTAGCACA 60.202 45.833 25.23 12.59 0.00 4.57
3121 3964 8.424918 TCTATGCATACTTCTTTAGGAGAAAGG 58.575 37.037 1.16 0.00 43.56 3.11
3163 4118 3.233980 CGATGAGATGCCGGGGGA 61.234 66.667 2.18 0.00 0.00 4.81
3172 4127 0.463204 CAGTGACCTGCCGATGAGAT 59.537 55.000 0.00 0.00 0.00 2.75
3452 4410 6.992063 ATCGATAATATACCGGTCGTTAGT 57.008 37.500 12.40 3.68 34.24 2.24
3453 4411 9.941664 AAATATCGATAATATACCGGTCGTTAG 57.058 33.333 12.40 0.00 34.24 2.34
3455 4413 8.680903 AGAAATATCGATAATATACCGGTCGTT 58.319 33.333 12.40 7.36 34.24 3.85
3525 4486 3.620821 GGAGATAAAGTGCAGAGCTTCAC 59.379 47.826 6.60 6.60 0.00 3.18
3614 4579 0.674895 CAAGTAGCCCACCAGTCAGC 60.675 60.000 0.00 0.00 0.00 4.26
3622 4591 1.550976 AGCTCTACACAAGTAGCCCAC 59.449 52.381 0.00 0.00 45.90 4.61
3671 4640 4.152402 GCGAAATAGAACAGACTGAGCAAA 59.848 41.667 10.08 0.00 0.00 3.68
3672 4641 3.679980 GCGAAATAGAACAGACTGAGCAA 59.320 43.478 10.08 0.00 0.00 3.91
3673 4642 3.254060 GCGAAATAGAACAGACTGAGCA 58.746 45.455 10.08 0.00 0.00 4.26
3674 4643 2.280183 CGCGAAATAGAACAGACTGAGC 59.720 50.000 10.08 0.15 0.00 4.26
3675 4644 3.502920 ACGCGAAATAGAACAGACTGAG 58.497 45.455 15.93 0.00 0.00 3.35
3676 4645 3.190744 AGACGCGAAATAGAACAGACTGA 59.809 43.478 15.93 0.00 0.00 3.41
3677 4646 3.502920 AGACGCGAAATAGAACAGACTG 58.497 45.455 15.93 0.00 0.00 3.51
3678 4647 3.851976 AGACGCGAAATAGAACAGACT 57.148 42.857 15.93 0.00 0.00 3.24
3679 4648 4.488889 CGAAAGACGCGAAATAGAACAGAC 60.489 45.833 15.93 0.00 34.51 3.51
3680 4649 3.606777 CGAAAGACGCGAAATAGAACAGA 59.393 43.478 15.93 0.00 34.51 3.41
3681 4650 3.364023 ACGAAAGACGCGAAATAGAACAG 59.636 43.478 15.93 0.00 46.94 3.16
3682 4651 3.311106 ACGAAAGACGCGAAATAGAACA 58.689 40.909 15.93 0.00 46.94 3.18
3683 4652 3.967080 ACGAAAGACGCGAAATAGAAC 57.033 42.857 15.93 0.00 46.94 3.01
3724 4693 6.519213 GCAAATAATCTCGGGGACTAAGATCT 60.519 42.308 0.00 0.00 31.58 2.75
3758 4727 5.227569 ACTGAATGAACCCATATATCGCA 57.772 39.130 0.00 0.00 31.59 5.10
3759 4728 5.812642 CCTACTGAATGAACCCATATATCGC 59.187 44.000 0.00 0.00 31.59 4.58
3768 4737 0.919710 AGGGCCTACTGAATGAACCC 59.080 55.000 2.82 0.00 36.04 4.11
3807 4776 4.873827 TGGTTCTAACGTCTATTGGCATTC 59.126 41.667 0.00 0.00 0.00 2.67
3856 4834 7.595819 TTTTTCCTTATCACACCAACAGAAT 57.404 32.000 0.00 0.00 0.00 2.40
3866 4844 6.325919 ACGAAATGCTTTTTCCTTATCACA 57.674 33.333 0.00 0.00 0.00 3.58
3904 4885 9.992910 CGAATTGAATTACTGAATCAAATCTCA 57.007 29.630 0.00 0.00 0.00 3.27
3925 4906 1.474077 GCCTTCATTGTGGCTCGAATT 59.526 47.619 13.42 0.00 45.26 2.17
4047 5029 2.208431 GCTGAATTCGACCCATCTCTG 58.792 52.381 0.04 0.00 0.00 3.35
4071 5053 5.598769 CCTTCCTAGGTTTTAGTACGGATG 58.401 45.833 9.08 0.00 36.74 3.51
4169 5151 3.524541 CAAATCAATGGCTTTAGGTGGC 58.475 45.455 0.00 0.00 0.00 5.01
4198 5183 1.323791 CGCGAAACAAATTTCCGGAC 58.676 50.000 1.83 0.00 41.12 4.79
4207 5192 3.794028 CAGGAAATTTCACGCGAAACAAA 59.206 39.130 15.93 6.04 43.75 2.83
4256 5241 3.374058 AGGAAATTTCACGCTCGTATTGG 59.626 43.478 19.49 0.00 0.00 3.16
4260 5245 3.306917 TCAGGAAATTTCACGCTCGTA 57.693 42.857 19.49 0.00 0.00 3.43
4261 5246 2.163818 TCAGGAAATTTCACGCTCGT 57.836 45.000 19.49 0.00 0.00 4.18
4262 5247 3.536158 TTTCAGGAAATTTCACGCTCG 57.464 42.857 19.49 1.74 0.00 5.03
4263 5248 5.049405 TCTCTTTTCAGGAAATTTCACGCTC 60.049 40.000 19.49 2.14 0.00 5.03
4264 5249 4.821805 TCTCTTTTCAGGAAATTTCACGCT 59.178 37.500 19.49 5.17 0.00 5.07
4265 5250 5.108385 TCTCTTTTCAGGAAATTTCACGC 57.892 39.130 19.49 2.86 0.00 5.34
4266 5251 6.902341 TCATCTCTTTTCAGGAAATTTCACG 58.098 36.000 19.49 9.73 0.00 4.35
4267 5252 9.533253 TTTTCATCTCTTTTCAGGAAATTTCAC 57.467 29.630 19.49 9.16 0.00 3.18
4268 5253 9.533253 GTTTTCATCTCTTTTCAGGAAATTTCA 57.467 29.630 19.49 0.00 0.00 2.69
4269 5254 9.755804 AGTTTTCATCTCTTTTCAGGAAATTTC 57.244 29.630 9.83 9.83 0.00 2.17
4270 5255 9.755804 GAGTTTTCATCTCTTTTCAGGAAATTT 57.244 29.630 0.00 0.00 0.00 1.82
4271 5256 8.917088 TGAGTTTTCATCTCTTTTCAGGAAATT 58.083 29.630 0.00 0.00 33.59 1.82
4272 5257 8.469309 TGAGTTTTCATCTCTTTTCAGGAAAT 57.531 30.769 0.00 0.00 33.59 2.17
4273 5258 7.880160 TGAGTTTTCATCTCTTTTCAGGAAA 57.120 32.000 0.00 0.00 33.59 3.13
4274 5259 7.502120 CTGAGTTTTCATCTCTTTTCAGGAA 57.498 36.000 0.00 0.00 31.68 3.36
4276 5261 6.251655 CCTGAGTTTTCATCTCTTTTCAGG 57.748 41.667 3.13 3.13 42.96 3.86
4277 5262 7.228308 AGTTCCTGAGTTTTCATCTCTTTTCAG 59.772 37.037 0.00 0.00 31.68 3.02
4278 5263 7.056635 AGTTCCTGAGTTTTCATCTCTTTTCA 58.943 34.615 0.00 0.00 31.68 2.69
4279 5264 7.503521 AGTTCCTGAGTTTTCATCTCTTTTC 57.496 36.000 0.00 0.00 31.68 2.29
4280 5265 7.340487 ACAAGTTCCTGAGTTTTCATCTCTTTT 59.660 33.333 0.00 0.00 31.68 2.27
4281 5266 6.830838 ACAAGTTCCTGAGTTTTCATCTCTTT 59.169 34.615 0.00 0.00 31.68 2.52
4282 5267 6.360618 ACAAGTTCCTGAGTTTTCATCTCTT 58.639 36.000 0.00 0.00 31.68 2.85
4283 5268 5.934781 ACAAGTTCCTGAGTTTTCATCTCT 58.065 37.500 0.00 0.00 31.68 3.10
4284 5269 5.760253 TGACAAGTTCCTGAGTTTTCATCTC 59.240 40.000 0.00 0.00 31.68 2.75
4285 5270 5.684704 TGACAAGTTCCTGAGTTTTCATCT 58.315 37.500 0.00 0.00 31.68 2.90
4286 5271 5.529060 ACTGACAAGTTCCTGAGTTTTCATC 59.471 40.000 0.00 0.00 30.14 2.92
4287 5272 5.440610 ACTGACAAGTTCCTGAGTTTTCAT 58.559 37.500 0.00 0.00 30.14 2.57
4288 5273 4.843728 ACTGACAAGTTCCTGAGTTTTCA 58.156 39.130 0.00 0.00 30.14 2.69
4289 5274 5.050972 CGTACTGACAAGTTCCTGAGTTTTC 60.051 44.000 0.00 0.00 37.88 2.29
4290 5275 4.809426 CGTACTGACAAGTTCCTGAGTTTT 59.191 41.667 0.00 0.00 37.88 2.43
4291 5276 4.098960 TCGTACTGACAAGTTCCTGAGTTT 59.901 41.667 0.00 0.00 37.88 2.66
4292 5277 3.635373 TCGTACTGACAAGTTCCTGAGTT 59.365 43.478 0.00 0.00 37.88 3.01
4293 5278 3.220110 TCGTACTGACAAGTTCCTGAGT 58.780 45.455 0.00 0.00 37.88 3.41
4294 5279 3.917329 TCGTACTGACAAGTTCCTGAG 57.083 47.619 0.00 0.00 37.88 3.35
4295 5280 4.142116 TGTTTCGTACTGACAAGTTCCTGA 60.142 41.667 0.00 0.00 37.88 3.86
4296 5281 4.116961 TGTTTCGTACTGACAAGTTCCTG 58.883 43.478 0.00 0.00 37.88 3.86
4297 5282 4.395959 TGTTTCGTACTGACAAGTTCCT 57.604 40.909 0.00 0.00 37.88 3.36
4298 5283 4.330620 TGTTGTTTCGTACTGACAAGTTCC 59.669 41.667 6.00 0.00 37.88 3.62
4299 5284 5.163933 TGTGTTGTTTCGTACTGACAAGTTC 60.164 40.000 6.00 2.57 37.88 3.01
4300 5285 4.691685 TGTGTTGTTTCGTACTGACAAGTT 59.308 37.500 6.00 0.00 37.88 2.66
4301 5286 4.092383 GTGTGTTGTTTCGTACTGACAAGT 59.908 41.667 6.00 0.00 40.67 3.16
4302 5287 4.092237 TGTGTGTTGTTTCGTACTGACAAG 59.908 41.667 6.00 0.00 34.29 3.16
4303 5288 3.995048 TGTGTGTTGTTTCGTACTGACAA 59.005 39.130 0.00 0.00 0.00 3.18
4304 5289 3.586892 TGTGTGTTGTTTCGTACTGACA 58.413 40.909 0.00 0.00 0.00 3.58
4305 5290 4.033587 ACATGTGTGTTGTTTCGTACTGAC 59.966 41.667 0.00 0.00 34.01 3.51
4306 5291 4.185394 ACATGTGTGTTGTTTCGTACTGA 58.815 39.130 0.00 0.00 34.01 3.41
4307 5292 4.530094 ACATGTGTGTTGTTTCGTACTG 57.470 40.909 0.00 0.00 34.01 2.74
4349 5334 1.794116 CGTACGAAAATGGTTGGACGT 59.206 47.619 10.44 0.00 37.68 4.34
4364 5349 2.096496 ACGTAGAGGGAAATGACGTACG 59.904 50.000 15.01 15.01 44.30 3.67


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

AutoCloner maintained by Alex Coulton.