Multiple sequence alignment - TraesCS1D01G403300

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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 TraesCS1D01G403300 chr1D 100.000 3896 0 0 1 3896 467864460 467860565 0.000000e+00 7195.0
1 TraesCS1D01G403300 chr1D 87.849 930 76 11 1053 1981 467852765 467853658 0.000000e+00 1057.0
2 TraesCS1D01G403300 chr1D 84.239 920 121 8 1057 1976 467848503 467849398 0.000000e+00 874.0
3 TraesCS1D01G403300 chr1D 79.589 730 134 10 2249 2969 467849584 467850307 3.470000e-140 508.0
4 TraesCS1D01G403300 chr1D 98.755 241 3 0 1 241 100603091 100602851 2.780000e-116 429.0
5 TraesCS1D01G403300 chr1D 98.750 240 3 0 1 240 464182084 464181845 1.000000e-115 427.0
6 TraesCS1D01G403300 chr1D 97.177 248 7 0 1 248 250349701 250349948 1.670000e-113 420.0
7 TraesCS1D01G403300 chr1D 96.109 257 9 1 1 256 445167814 445167558 6.020000e-113 418.0
8 TraesCS1D01G403300 chr1D 84.762 105 9 6 700 800 58756162 58756263 8.910000e-17 99.0
9 TraesCS1D01G403300 chr1D 83.019 106 10 5 700 800 58756375 58756477 5.360000e-14 89.8
10 TraesCS1D01G403300 chr1D 80.583 103 16 4 700 800 478978060 478978160 4.170000e-10 76.8
11 TraesCS1D01G403300 chr1D 79.808 104 16 5 700 800 441035315 441035416 1.940000e-08 71.3
12 TraesCS1D01G403300 chr1B 92.043 1307 70 9 1739 3045 645947948 645946676 0.000000e+00 1807.0
13 TraesCS1D01G403300 chr1B 87.565 965 74 19 1037 1982 645896511 645895574 0.000000e+00 1075.0
14 TraesCS1D01G403300 chr1B 84.908 921 113 10 1057 1976 645886703 645887598 0.000000e+00 907.0
15 TraesCS1D01G403300 chr1B 88.747 471 41 9 3075 3541 645933175 645932713 2.030000e-157 566.0
16 TraesCS1D01G403300 chr1B 78.562 793 153 13 2244 3030 645895367 645894586 1.250000e-139 507.0
17 TraesCS1D01G403300 chr1B 91.471 340 20 4 3532 3864 645931667 645931330 3.550000e-125 459.0
18 TraesCS1D01G403300 chr1B 78.468 692 140 7 2249 2934 645906258 645905570 9.930000e-121 444.0
19 TraesCS1D01G403300 chr1B 88.688 221 25 0 237 457 645958665 645958445 1.780000e-68 270.0
20 TraesCS1D01G403300 chr1B 89.796 49 5 0 2153 2201 278722029 278721981 3.250000e-06 63.9
21 TraesCS1D01G403300 chr1A 91.960 1306 51 13 804 2106 560881850 560880596 0.000000e+00 1781.0
22 TraesCS1D01G403300 chr1A 89.559 929 70 14 1045 1973 560840379 560841280 0.000000e+00 1153.0
23 TraesCS1D01G403300 chr1A 83.696 920 126 8 1057 1976 560837456 560838351 0.000000e+00 846.0
24 TraesCS1D01G403300 chr1A 86.443 686 85 6 2271 2949 560880235 560879551 0.000000e+00 745.0
25 TraesCS1D01G403300 chr1A 89.371 461 40 6 3075 3534 560878439 560877987 4.370000e-159 571.0
26 TraesCS1D01G403300 chr1A 80.055 732 134 9 2244 2969 560841473 560842198 2.060000e-147 532.0
27 TraesCS1D01G403300 chr1A 87.363 364 44 2 237 599 560883304 560882942 2.170000e-112 416.0
28 TraesCS1D01G403300 chr1A 88.561 271 9 1 3613 3883 560877816 560877568 3.780000e-80 309.0
29 TraesCS1D01G403300 chr1A 94.203 69 3 1 732 800 560882419 560882352 1.910000e-18 104.0
30 TraesCS1D01G403300 chr1A 92.958 71 1 1 3013 3079 560878800 560878730 2.480000e-17 100.0
31 TraesCS1D01G403300 chr1A 80.808 99 17 1 2103 2199 557490504 557490406 4.170000e-10 76.8
32 TraesCS1D01G403300 chr7B 81.888 911 137 22 1075 1974 705110046 705110939 0.000000e+00 743.0
33 TraesCS1D01G403300 chr5B 83.375 794 117 10 1169 1956 586534337 586535121 0.000000e+00 721.0
34 TraesCS1D01G403300 chr5B 88.000 50 4 2 700 748 553341894 553341942 1.510000e-04 58.4
35 TraesCS1D01G403300 chr2B 82.882 812 121 8 1177 1979 764109529 764108727 0.000000e+00 713.0
36 TraesCS1D01G403300 chr2B 95.000 200 8 2 3697 3895 59758115 59758313 2.920000e-81 313.0
37 TraesCS1D01G403300 chr2B 93.939 198 12 0 3686 3883 695581907 695581710 2.280000e-77 300.0
38 TraesCS1D01G403300 chr2B 83.957 187 21 4 3348 3534 59757552 59757729 1.860000e-38 171.0
39 TraesCS1D01G403300 chr2B 78.899 109 20 3 2096 2203 786027164 786027270 1.940000e-08 71.3
40 TraesCS1D01G403300 chr2B 100.000 29 0 0 1076 1104 764109603 764109575 2.000000e-03 54.7
41 TraesCS1D01G403300 chr4D 81.660 807 116 17 1180 1976 366974294 366975078 3.280000e-180 641.0
42 TraesCS1D01G403300 chr4D 90.566 53 5 0 2147 2199 46199443 46199391 1.940000e-08 71.3
43 TraesCS1D01G403300 chr3A 80.099 809 137 14 1177 1976 142878817 142879610 7.260000e-162 580.0
44 TraesCS1D01G403300 chr3A 91.304 46 4 0 2154 2199 95018393 95018348 3.250000e-06 63.9
45 TraesCS1D01G403300 chr2D 98.745 239 3 0 1 239 537484891 537485129 3.600000e-115 425.0
46 TraesCS1D01G403300 chr2D 97.581 248 5 1 1 247 561494131 561493884 1.290000e-114 424.0
47 TraesCS1D01G403300 chr2D 96.813 251 5 3 1 250 587909948 587910196 2.170000e-112 416.0
48 TraesCS1D01G403300 chr2D 95.000 200 8 2 3697 3895 36283003 36282805 2.920000e-81 313.0
49 TraesCS1D01G403300 chr2D 94.444 198 11 0 3686 3883 578602818 578602621 4.890000e-79 305.0
50 TraesCS1D01G403300 chr2D 84.492 187 20 4 3348 3534 36283553 36283376 4.000000e-40 176.0
51 TraesCS1D01G403300 chr7D 97.200 250 5 2 1 249 502437452 502437700 4.650000e-114 422.0
52 TraesCS1D01G403300 chr5D 97.200 250 6 1 1 250 557625100 557624852 4.650000e-114 422.0
53 TraesCS1D01G403300 chr5D 96.491 57 2 0 3443 3499 403569883 403569827 1.150000e-15 95.3
54 TraesCS1D01G403300 chr4A 87.847 288 25 5 1177 1462 97987524 97987245 2.900000e-86 329.0
55 TraesCS1D01G403300 chr4A 78.338 397 81 4 2390 2782 602226780 602227175 6.460000e-63 252.0
56 TraesCS1D01G403300 chr2A 95.000 200 8 2 3697 3895 39705289 39705487 2.920000e-81 313.0
57 TraesCS1D01G403300 chr2A 92.417 211 12 3 3686 3895 716179010 716178803 8.180000e-77 298.0
58 TraesCS1D01G403300 chr2A 89.474 171 18 0 3117 3287 716180012 716179842 2.360000e-52 217.0
59 TraesCS1D01G403300 chr2A 84.043 188 21 4 3348 3534 39704743 39704922 5.180000e-39 172.0
60 TraesCS1D01G403300 chr2A 83.654 104 12 5 700 800 420682798 420682899 4.140000e-15 93.5
61 TraesCS1D01G403300 chr2A 83.019 106 9 6 700 800 670676545 670676444 1.930000e-13 87.9
62 TraesCS1D01G403300 chr2A 89.130 46 5 0 2163 2208 67080031 67079986 1.510000e-04 58.4
63 TraesCS1D01G403300 chr6B 82.474 97 13 4 706 800 703939217 703939123 8.970000e-12 82.4
64 TraesCS1D01G403300 chr4B 80.583 103 15 5 700 800 85732288 85732189 1.500000e-09 75.0
65 TraesCS1D01G403300 chr7A 100.000 39 0 0 2163 2201 572871397 572871435 5.400000e-09 73.1
66 TraesCS1D01G403300 chr3D 86.154 65 9 0 2135 2199 608238741 608238805 1.940000e-08 71.3
67 TraesCS1D01G403300 chr3B 86.154 65 9 0 2135 2199 541579904 541579968 1.940000e-08 71.3


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 TraesCS1D01G403300 chr1D 467860565 467864460 3895 True 7195.000000 7195 100.000000 1 3896 1 chr1D.!!$R4 3895
1 TraesCS1D01G403300 chr1D 467848503 467853658 5155 False 813.000000 1057 83.892333 1053 2969 3 chr1D.!!$F5 1916
2 TraesCS1D01G403300 chr1B 645946676 645947948 1272 True 1807.000000 1807 92.043000 1739 3045 1 chr1B.!!$R3 1306
3 TraesCS1D01G403300 chr1B 645886703 645887598 895 False 907.000000 907 84.908000 1057 1976 1 chr1B.!!$F1 919
4 TraesCS1D01G403300 chr1B 645894586 645896511 1925 True 791.000000 1075 83.063500 1037 3030 2 chr1B.!!$R5 1993
5 TraesCS1D01G403300 chr1B 645931330 645933175 1845 True 512.500000 566 90.109000 3075 3864 2 chr1B.!!$R6 789
6 TraesCS1D01G403300 chr1B 645905570 645906258 688 True 444.000000 444 78.468000 2249 2934 1 chr1B.!!$R2 685
7 TraesCS1D01G403300 chr1A 560837456 560842198 4742 False 843.666667 1153 84.436667 1045 2969 3 chr1A.!!$F1 1924
8 TraesCS1D01G403300 chr1A 560877568 560883304 5736 True 575.142857 1781 90.122714 237 3883 7 chr1A.!!$R2 3646
9 TraesCS1D01G403300 chr7B 705110046 705110939 893 False 743.000000 743 81.888000 1075 1974 1 chr7B.!!$F1 899
10 TraesCS1D01G403300 chr5B 586534337 586535121 784 False 721.000000 721 83.375000 1169 1956 1 chr5B.!!$F2 787
11 TraesCS1D01G403300 chr2B 764108727 764109603 876 True 383.850000 713 91.441000 1076 1979 2 chr2B.!!$R2 903
12 TraesCS1D01G403300 chr2B 59757552 59758313 761 False 242.000000 313 89.478500 3348 3895 2 chr2B.!!$F2 547
13 TraesCS1D01G403300 chr4D 366974294 366975078 784 False 641.000000 641 81.660000 1180 1976 1 chr4D.!!$F1 796
14 TraesCS1D01G403300 chr3A 142878817 142879610 793 False 580.000000 580 80.099000 1177 1976 1 chr3A.!!$F1 799
15 TraesCS1D01G403300 chr2D 36282805 36283553 748 True 244.500000 313 89.746000 3348 3895 2 chr2D.!!$R3 547
16 TraesCS1D01G403300 chr2A 716178803 716180012 1209 True 257.500000 298 90.945500 3117 3895 2 chr2A.!!$R3 778
17 TraesCS1D01G403300 chr2A 39704743 39705487 744 False 242.500000 313 89.521500 3348 3895 2 chr2A.!!$F2 547

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
824 1742 0.251634 TGTGTCTGTGGAGTGCACAA 59.748 50.0 21.04 7.18 35.14 3.33 F
826 1744 0.541392 TGTCTGTGGAGTGCACAAGT 59.459 50.0 21.04 0.00 31.61 3.16 F
2547 9097 0.179121 GATACGATGTGCCACGTGGA 60.179 55.0 38.30 18.34 42.61 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 9097 0.506932 CGTTGACGATCACTTGCGTT 59.493 50.000 0.0 0.0 41.34 4.84 R
2641 9191 3.041940 AAAGTCCGACGCCGCTTG 61.042 61.111 0.0 0.0 0.00 4.01 R
3487 11187 1.165270 GTGACGGGGTTGATTTGGAG 58.835 55.000 0.0 0.0 0.00 3.86 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
22 23 5.597813 GATGTGATCCCGTTATCAATGAC 57.402 43.478 0.00 0.00 37.61 3.06
23 24 4.479786 TGTGATCCCGTTATCAATGACA 57.520 40.909 0.00 0.00 37.61 3.58
24 25 5.034852 TGTGATCCCGTTATCAATGACAT 57.965 39.130 0.00 0.00 37.61 3.06
25 26 5.056480 TGTGATCCCGTTATCAATGACATC 58.944 41.667 0.00 0.00 37.61 3.06
26 27 4.452455 GTGATCCCGTTATCAATGACATCC 59.548 45.833 0.00 0.00 37.61 3.51
27 28 4.102367 TGATCCCGTTATCAATGACATCCA 59.898 41.667 0.00 0.00 32.97 3.41
28 29 4.495690 TCCCGTTATCAATGACATCCAA 57.504 40.909 0.00 0.00 0.00 3.53
30 31 4.821260 TCCCGTTATCAATGACATCCAATG 59.179 41.667 0.00 0.00 0.00 2.82
42 43 4.428294 ACATCCAATGTCCATAGTCAGG 57.572 45.455 0.00 0.00 39.92 3.86
43 44 4.040047 ACATCCAATGTCCATAGTCAGGA 58.960 43.478 0.00 0.00 39.92 3.86
44 45 4.474651 ACATCCAATGTCCATAGTCAGGAA 59.525 41.667 0.00 0.00 39.92 3.36
45 46 5.044919 ACATCCAATGTCCATAGTCAGGAAA 60.045 40.000 0.00 0.00 39.92 3.13
46 47 4.843728 TCCAATGTCCATAGTCAGGAAAC 58.156 43.478 0.00 0.00 36.80 2.78
48 49 4.567537 CCAATGTCCATAGTCAGGAAACCA 60.568 45.833 0.00 0.00 36.80 3.67
49 50 5.195940 CAATGTCCATAGTCAGGAAACCAT 58.804 41.667 0.00 0.00 36.80 3.55
50 51 4.220693 TGTCCATAGTCAGGAAACCATG 57.779 45.455 0.00 0.00 36.80 3.66
51 52 3.843619 TGTCCATAGTCAGGAAACCATGA 59.156 43.478 0.00 0.00 36.80 3.07
60 61 5.491982 GTCAGGAAACCATGACTATCTGTT 58.508 41.667 0.00 0.00 42.06 3.16
61 62 5.352569 GTCAGGAAACCATGACTATCTGTTG 59.647 44.000 0.00 0.00 42.06 3.33
62 63 5.248248 TCAGGAAACCATGACTATCTGTTGA 59.752 40.000 0.00 0.00 0.00 3.18
64 65 6.259608 CAGGAAACCATGACTATCTGTTGATC 59.740 42.308 0.00 0.00 34.32 2.92
65 66 6.070021 AGGAAACCATGACTATCTGTTGATCA 60.070 38.462 0.00 0.00 34.32 2.92
66 67 6.599244 GGAAACCATGACTATCTGTTGATCAA 59.401 38.462 3.38 3.38 34.32 2.57
67 68 6.992063 AACCATGACTATCTGTTGATCAAC 57.008 37.500 28.10 28.10 41.50 3.18
69 70 5.105351 ACCATGACTATCTGTTGATCAACGA 60.105 40.000 28.55 26.46 43.94 3.85
70 71 5.461407 CCATGACTATCTGTTGATCAACGAG 59.539 44.000 28.55 24.84 43.94 4.18
71 72 4.424626 TGACTATCTGTTGATCAACGAGC 58.575 43.478 28.55 18.56 43.94 5.03
72 73 4.158579 TGACTATCTGTTGATCAACGAGCT 59.841 41.667 28.55 20.51 43.94 4.09
73 74 5.357032 TGACTATCTGTTGATCAACGAGCTA 59.643 40.000 28.55 20.52 43.94 3.32
75 76 4.727507 ATCTGTTGATCAACGAGCTAGT 57.272 40.909 28.55 13.33 43.94 2.57
77 78 3.506067 TCTGTTGATCAACGAGCTAGTCA 59.494 43.478 28.55 10.88 43.94 3.41
78 79 4.022329 TCTGTTGATCAACGAGCTAGTCAA 60.022 41.667 28.55 10.18 43.94 3.18
79 80 3.987868 TGTTGATCAACGAGCTAGTCAAC 59.012 43.478 28.55 16.99 43.94 3.18
80 81 4.238514 GTTGATCAACGAGCTAGTCAACT 58.761 43.478 22.09 0.00 41.13 3.16
81 82 5.048294 TGTTGATCAACGAGCTAGTCAACTA 60.048 40.000 28.55 7.59 43.38 2.24
83 84 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
87 88 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
89 90 3.283751 GAGCTAGTCAACTAGAGGCTCA 58.716 50.000 18.26 1.80 46.80 4.26
90 91 3.020984 AGCTAGTCAACTAGAGGCTCAC 58.979 50.000 18.26 4.72 46.80 3.51
91 92 3.020984 GCTAGTCAACTAGAGGCTCACT 58.979 50.000 18.26 12.32 46.80 3.41
92 93 4.080243 AGCTAGTCAACTAGAGGCTCACTA 60.080 45.833 18.26 12.80 46.80 2.74
93 94 4.274950 GCTAGTCAACTAGAGGCTCACTAG 59.725 50.000 23.14 23.14 46.80 2.57
95 96 2.691011 GTCAACTAGAGGCTCACTAGGG 59.309 54.545 18.26 7.64 40.86 3.53
96 97 2.581246 TCAACTAGAGGCTCACTAGGGA 59.419 50.000 18.26 9.66 40.86 4.20
97 98 2.691011 CAACTAGAGGCTCACTAGGGAC 59.309 54.545 18.26 0.00 40.86 4.46
98 99 1.923850 ACTAGAGGCTCACTAGGGACA 59.076 52.381 18.26 0.00 40.86 4.02
99 100 2.516277 ACTAGAGGCTCACTAGGGACAT 59.484 50.000 18.26 0.00 40.86 3.06
100 101 1.786937 AGAGGCTCACTAGGGACATG 58.213 55.000 18.26 0.00 0.00 3.21
102 103 1.834263 GAGGCTCACTAGGGACATGTT 59.166 52.381 10.25 0.00 0.00 2.71
103 104 1.556911 AGGCTCACTAGGGACATGTTG 59.443 52.381 0.00 0.00 0.00 3.33
104 105 1.279271 GGCTCACTAGGGACATGTTGT 59.721 52.381 0.00 0.00 0.00 3.32
105 106 2.350522 GCTCACTAGGGACATGTTGTG 58.649 52.381 0.00 5.31 0.00 3.33
106 107 2.936993 GCTCACTAGGGACATGTTGTGG 60.937 54.545 0.00 0.00 0.00 4.17
108 109 2.301870 TCACTAGGGACATGTTGTGGTC 59.698 50.000 0.00 0.00 0.00 4.02
109 110 2.303022 CACTAGGGACATGTTGTGGTCT 59.697 50.000 0.00 0.00 34.49 3.85
110 111 3.513912 CACTAGGGACATGTTGTGGTCTA 59.486 47.826 0.00 0.00 34.49 2.59
111 112 4.162320 CACTAGGGACATGTTGTGGTCTAT 59.838 45.833 0.00 0.00 34.49 1.98
112 113 3.634397 AGGGACATGTTGTGGTCTATG 57.366 47.619 0.00 0.00 34.49 2.23
113 114 2.912956 AGGGACATGTTGTGGTCTATGT 59.087 45.455 0.00 0.00 36.54 2.29
114 115 4.101114 AGGGACATGTTGTGGTCTATGTA 58.899 43.478 0.00 0.00 34.18 2.29
115 116 4.721776 AGGGACATGTTGTGGTCTATGTAT 59.278 41.667 0.00 0.00 34.18 2.29
116 117 5.191722 AGGGACATGTTGTGGTCTATGTATT 59.808 40.000 0.00 0.00 34.18 1.89
117 118 5.527582 GGGACATGTTGTGGTCTATGTATTC 59.472 44.000 0.00 0.00 34.18 1.75
118 119 6.112734 GGACATGTTGTGGTCTATGTATTCA 58.887 40.000 0.00 0.00 34.18 2.57
119 120 6.258727 GGACATGTTGTGGTCTATGTATTCAG 59.741 42.308 0.00 0.00 34.18 3.02
120 121 6.946340 ACATGTTGTGGTCTATGTATTCAGA 58.054 36.000 0.00 0.00 32.41 3.27
121 122 6.818644 ACATGTTGTGGTCTATGTATTCAGAC 59.181 38.462 0.00 0.00 40.40 3.51
122 123 6.353404 TGTTGTGGTCTATGTATTCAGACA 57.647 37.500 4.32 0.00 42.45 3.41
123 124 6.946340 TGTTGTGGTCTATGTATTCAGACAT 58.054 36.000 4.32 0.00 42.45 3.06
124 125 6.818142 TGTTGTGGTCTATGTATTCAGACATG 59.182 38.462 4.32 0.00 42.45 3.21
125 126 5.359756 TGTGGTCTATGTATTCAGACATGC 58.640 41.667 0.00 0.00 42.45 4.06
126 127 5.104982 TGTGGTCTATGTATTCAGACATGCA 60.105 40.000 0.00 0.00 42.45 3.96
127 128 5.994054 GTGGTCTATGTATTCAGACATGCAT 59.006 40.000 0.00 0.00 42.45 3.96
129 130 7.657354 GTGGTCTATGTATTCAGACATGCATTA 59.343 37.037 0.00 0.00 42.45 1.90
131 132 7.148738 GGTCTATGTATTCAGACATGCATTACG 60.149 40.741 0.00 0.00 42.45 3.18
132 133 7.595130 GTCTATGTATTCAGACATGCATTACGA 59.405 37.037 0.00 0.00 40.31 3.43
133 134 8.306761 TCTATGTATTCAGACATGCATTACGAT 58.693 33.333 0.00 0.00 40.31 3.73
135 136 7.552458 TGTATTCAGACATGCATTACGATTT 57.448 32.000 0.00 0.00 0.00 2.17
136 137 7.630026 TGTATTCAGACATGCATTACGATTTC 58.370 34.615 0.00 0.00 0.00 2.17
137 138 5.484173 TTCAGACATGCATTACGATTTCC 57.516 39.130 0.00 0.00 0.00 3.13
138 139 3.555547 TCAGACATGCATTACGATTTCCG 59.444 43.478 0.00 0.00 45.44 4.30
140 141 2.869801 GACATGCATTACGATTTCCGGA 59.130 45.455 0.00 0.00 43.93 5.14
141 142 3.476552 ACATGCATTACGATTTCCGGAT 58.523 40.909 4.15 0.00 43.93 4.18
143 144 5.060506 ACATGCATTACGATTTCCGGATAA 58.939 37.500 4.15 0.00 43.93 1.75
145 146 4.443621 TGCATTACGATTTCCGGATAACA 58.556 39.130 4.15 0.00 43.93 2.41
146 147 4.271533 TGCATTACGATTTCCGGATAACAC 59.728 41.667 4.15 0.00 43.93 3.32
147 148 4.271533 GCATTACGATTTCCGGATAACACA 59.728 41.667 4.15 0.00 43.93 3.72
148 149 5.220700 GCATTACGATTTCCGGATAACACAA 60.221 40.000 4.15 0.00 43.93 3.33
149 150 6.512741 GCATTACGATTTCCGGATAACACAAT 60.513 38.462 4.15 0.00 43.93 2.71
150 151 6.988622 TTACGATTTCCGGATAACACAATT 57.011 33.333 4.15 0.00 43.93 2.32
151 152 8.552865 CATTACGATTTCCGGATAACACAATTA 58.447 33.333 4.15 0.00 43.93 1.40
152 153 8.665643 TTACGATTTCCGGATAACACAATTAT 57.334 30.769 4.15 0.00 43.93 1.28
153 154 9.761504 TTACGATTTCCGGATAACACAATTATA 57.238 29.630 4.15 0.00 43.93 0.98
154 155 8.665643 ACGATTTCCGGATAACACAATTATAA 57.334 30.769 4.15 0.00 43.93 0.98
155 156 8.553696 ACGATTTCCGGATAACACAATTATAAC 58.446 33.333 4.15 0.00 43.93 1.89
156 157 8.552865 CGATTTCCGGATAACACAATTATAACA 58.447 33.333 4.15 0.00 33.91 2.41
159 160 8.966069 TTCCGGATAACACAATTATAACATGA 57.034 30.769 4.15 0.00 0.00 3.07
160 161 8.966069 TCCGGATAACACAATTATAACATGAA 57.034 30.769 0.00 0.00 0.00 2.57
161 162 8.832521 TCCGGATAACACAATTATAACATGAAC 58.167 33.333 0.00 0.00 0.00 3.18
163 164 9.995957 CGGATAACACAATTATAACATGAACAA 57.004 29.630 0.00 0.00 0.00 2.83
186 187 9.685276 ACAATAGACAATTATCATGAACAAGGA 57.315 29.630 0.00 0.00 0.00 3.36
235 236 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
236 237 4.792068 CCTCTAGGGCATATTTCCAACAA 58.208 43.478 0.00 0.00 0.00 2.83
237 238 5.388654 CCTCTAGGGCATATTTCCAACAAT 58.611 41.667 0.00 0.00 0.00 2.71
239 240 5.385198 TCTAGGGCATATTTCCAACAATCC 58.615 41.667 0.00 0.00 0.00 3.01
247 248 1.323412 TTCCAACAATCCGGTGGTTG 58.677 50.000 20.86 20.86 41.10 3.77
255 256 2.748058 ATCCGGTGGTTGGCAGTGTC 62.748 60.000 0.00 0.00 0.00 3.67
264 265 0.973632 TTGGCAGTGTCGATGGTACT 59.026 50.000 0.00 0.00 0.00 2.73
309 310 3.011566 TGGCGAAGAGAAGAGAGAGAT 57.988 47.619 0.00 0.00 0.00 2.75
324 325 4.802307 AGAGAGATAGAGGAATGAGCACA 58.198 43.478 0.00 0.00 0.00 4.57
337 338 0.462759 GAGCACAATCGGGAGGAAGG 60.463 60.000 0.00 0.00 0.00 3.46
347 348 0.903454 GGGAGGAAGGAGACGGTCAA 60.903 60.000 11.27 0.00 0.00 3.18
354 355 3.288964 GAAGGAGACGGTCAAGATCCTA 58.711 50.000 14.80 0.00 39.48 2.94
421 422 1.522580 GGGACGCTGCTGAAGATCC 60.523 63.158 0.00 0.00 33.73 3.36
447 448 1.519719 GGCCCACTGCACAACAAAA 59.480 52.632 0.00 0.00 43.89 2.44
458 459 2.287547 GCACAACAAAATCGCCTCTTGA 60.288 45.455 0.00 0.00 0.00 3.02
459 460 3.795150 GCACAACAAAATCGCCTCTTGAA 60.795 43.478 0.00 0.00 0.00 2.69
464 465 3.383185 ACAAAATCGCCTCTTGAACCAAA 59.617 39.130 0.00 0.00 0.00 3.28
481 482 1.305930 AAAACCCGCTGATCTTCGCC 61.306 55.000 0.00 0.00 0.00 5.54
522 523 1.880027 GTCTTCGGCCAACACAAGAAT 59.120 47.619 2.24 0.00 0.00 2.40
529 530 2.622942 GGCCAACACAAGAATGAAGACA 59.377 45.455 0.00 0.00 0.00 3.41
547 549 1.111116 CATCCCTTCGGCCAATGCAT 61.111 55.000 2.24 0.00 40.13 3.96
548 550 1.111116 ATCCCTTCGGCCAATGCATG 61.111 55.000 2.24 0.00 40.13 4.06
581 583 4.636648 TCTCTCTTCGTTCTACATGAGGAC 59.363 45.833 0.00 0.00 0.00 3.85
643 1058 1.541588 GCAGCAGGGAAAACGAAGAAT 59.458 47.619 0.00 0.00 0.00 2.40
650 1065 4.209080 CAGGGAAAACGAAGAATTGTTTGC 59.791 41.667 2.51 0.00 38.26 3.68
660 1075 3.236816 AGAATTGTTTGCGCGAATGAAG 58.763 40.909 14.34 0.00 0.00 3.02
667 1082 5.027737 TGTTTGCGCGAATGAAGAATATTC 58.972 37.500 14.34 7.41 0.00 1.75
695 1114 7.893124 AAATCTAGTGCAATGGATTTCTCAT 57.107 32.000 26.42 9.92 34.56 2.90
696 1115 7.893124 AATCTAGTGCAATGGATTTCTCATT 57.107 32.000 18.48 0.00 35.45 2.57
812 1730 5.234329 ACTTTGAATCAACTACGTGTGTCTG 59.766 40.000 0.00 0.00 0.00 3.51
815 1733 2.502213 TCAACTACGTGTGTCTGTGG 57.498 50.000 0.00 0.00 0.00 4.17
822 1740 1.490693 CGTGTGTCTGTGGAGTGCAC 61.491 60.000 9.40 9.40 0.00 4.57
823 1741 0.461870 GTGTGTCTGTGGAGTGCACA 60.462 55.000 21.04 17.16 35.44 4.57
824 1742 0.251634 TGTGTCTGTGGAGTGCACAA 59.748 50.000 21.04 7.18 35.14 3.33
826 1744 0.541392 TGTCTGTGGAGTGCACAAGT 59.459 50.000 21.04 0.00 31.61 3.16
827 1745 1.065491 TGTCTGTGGAGTGCACAAGTT 60.065 47.619 21.04 0.00 31.61 2.66
828 1746 2.169561 TGTCTGTGGAGTGCACAAGTTA 59.830 45.455 21.04 3.08 31.61 2.24
831 1749 3.814842 TCTGTGGAGTGCACAAGTTAATG 59.185 43.478 21.04 5.34 31.61 1.90
844 1762 6.587226 GCACAAGTTAATGCTCAATTTCATCA 59.413 34.615 4.42 0.00 38.84 3.07
878 1796 5.049167 TGCACAAAATTCCACAAATCAGTC 58.951 37.500 0.00 0.00 0.00 3.51
888 1806 3.368843 CCACAAATCAGTCGAGACAGGAT 60.369 47.826 5.99 5.48 31.76 3.24
889 1807 4.248859 CACAAATCAGTCGAGACAGGATT 58.751 43.478 13.62 13.62 38.41 3.01
890 1808 5.410924 CACAAATCAGTCGAGACAGGATTA 58.589 41.667 17.33 0.00 36.93 1.75
891 1809 6.045318 CACAAATCAGTCGAGACAGGATTAT 58.955 40.000 17.33 10.21 36.93 1.28
892 1810 6.199908 CACAAATCAGTCGAGACAGGATTATC 59.800 42.308 17.33 0.00 36.93 1.75
893 1811 6.097554 ACAAATCAGTCGAGACAGGATTATCT 59.902 38.462 17.33 5.92 36.93 1.98
894 1812 5.703978 ATCAGTCGAGACAGGATTATCTG 57.296 43.478 5.99 0.00 40.40 2.90
896 1814 4.950475 TCAGTCGAGACAGGATTATCTGTT 59.050 41.667 5.99 0.00 46.76 3.16
897 1815 5.039984 CAGTCGAGACAGGATTATCTGTTG 58.960 45.833 5.99 0.00 46.76 3.33
898 1816 4.098654 AGTCGAGACAGGATTATCTGTTGG 59.901 45.833 5.99 0.00 46.76 3.77
903 1821 6.405953 CGAGACAGGATTATCTGTTGGTAGTT 60.406 42.308 0.00 0.00 46.76 2.24
959 1877 2.823154 TCCACATCACTGTCATCACGTA 59.177 45.455 0.00 0.00 31.62 3.57
960 1878 3.119495 TCCACATCACTGTCATCACGTAG 60.119 47.826 0.00 0.00 31.62 3.51
1012 1930 9.369904 GGTACGTAACTTAAATGACTAAATCCA 57.630 33.333 2.57 0.00 0.00 3.41
1107 2990 3.589639 CGTAGCTCTCGTGTCACTC 57.410 57.895 0.65 0.00 0.00 3.51
1336 3237 4.918278 TGGTGGTGTCGTCCCGGA 62.918 66.667 0.73 0.00 0.00 5.14
1464 3365 2.440796 TACGGGGACTACTGGCGG 60.441 66.667 0.00 0.00 0.00 6.13
1858 8038 0.689080 GGAGCACCTGGAGAGGATGA 60.689 60.000 0.00 0.00 42.93 2.92
2106 8363 9.321590 GTGTACGGTTTTATCAAAATGTTACTC 57.678 33.333 0.00 0.00 32.22 2.59
2107 8364 8.505625 TGTACGGTTTTATCAAAATGTTACTCC 58.494 33.333 0.00 0.00 32.22 3.85
2108 8365 6.916440 ACGGTTTTATCAAAATGTTACTCCC 58.084 36.000 0.00 0.00 32.22 4.30
2109 8366 6.717997 ACGGTTTTATCAAAATGTTACTCCCT 59.282 34.615 0.00 0.00 32.22 4.20
2110 8367 7.094506 ACGGTTTTATCAAAATGTTACTCCCTC 60.095 37.037 0.00 0.00 32.22 4.30
2111 8368 7.544622 GGTTTTATCAAAATGTTACTCCCTCC 58.455 38.462 0.00 0.00 32.22 4.30
2112 8369 6.995511 TTTATCAAAATGTTACTCCCTCCG 57.004 37.500 0.00 0.00 0.00 4.63
2113 8370 3.343941 TCAAAATGTTACTCCCTCCGG 57.656 47.619 0.00 0.00 0.00 5.14
2114 8371 2.640826 TCAAAATGTTACTCCCTCCGGT 59.359 45.455 0.00 0.00 0.00 5.28
2121 8378 2.077687 TACTCCCTCCGGTCCATAAC 57.922 55.000 0.00 0.00 0.00 1.89
2163 8420 9.976511 AAAGTAAAGTTAAATTAACCTTGGCTC 57.023 29.630 11.83 0.81 39.47 4.70
2164 8421 8.700439 AGTAAAGTTAAATTAACCTTGGCTCA 57.300 30.769 11.83 0.00 39.47 4.26
2165 8422 9.138596 AGTAAAGTTAAATTAACCTTGGCTCAA 57.861 29.630 11.83 0.00 39.47 3.02
2166 8423 9.752961 GTAAAGTTAAATTAACCTTGGCTCAAA 57.247 29.630 11.83 0.00 39.47 2.69
2169 8426 8.018537 AGTTAAATTAACCTTGGCTCAAAACT 57.981 30.769 11.83 0.00 39.47 2.66
2170 8427 7.926018 AGTTAAATTAACCTTGGCTCAAAACTG 59.074 33.333 11.83 0.00 39.47 3.16
2171 8428 3.726291 TTAACCTTGGCTCAAAACTGC 57.274 42.857 0.00 0.00 0.00 4.40
2172 8429 1.484038 AACCTTGGCTCAAAACTGCA 58.516 45.000 0.00 0.00 0.00 4.41
2173 8430 1.484038 ACCTTGGCTCAAAACTGCAA 58.516 45.000 0.00 0.00 0.00 4.08
2174 8431 1.136891 ACCTTGGCTCAAAACTGCAAC 59.863 47.619 0.00 0.00 0.00 4.17
2175 8432 1.136695 CCTTGGCTCAAAACTGCAACA 59.863 47.619 0.00 0.00 0.00 3.33
2176 8433 2.195922 CTTGGCTCAAAACTGCAACAC 58.804 47.619 0.00 0.00 0.00 3.32
2177 8434 1.473258 TGGCTCAAAACTGCAACACT 58.527 45.000 0.00 0.00 0.00 3.55
2188 8445 7.437862 TCAAAACTGCAACACTTATTTTGGATC 59.562 33.333 7.24 0.00 37.53 3.36
2190 8447 4.082787 ACTGCAACACTTATTTTGGATCGG 60.083 41.667 0.00 0.00 0.00 4.18
2207 8464 2.641305 TCGGAGGAAGTACTGTCTAGC 58.359 52.381 0.00 0.00 0.00 3.42
2231 8488 5.665916 ATGGTTAATTTTGCTTCCCTCAG 57.334 39.130 0.00 0.00 0.00 3.35
2232 8489 4.479158 TGGTTAATTTTGCTTCCCTCAGT 58.521 39.130 0.00 0.00 0.00 3.41
2239 8785 2.770164 TGCTTCCCTCAGTTTCTAGC 57.230 50.000 0.00 0.00 0.00 3.42
2240 8786 1.279271 TGCTTCCCTCAGTTTCTAGCC 59.721 52.381 0.00 0.00 0.00 3.93
2423 8973 1.281899 GTGACCGAGCATGCTCTAAC 58.718 55.000 37.44 27.89 40.69 2.34
2547 9097 0.179121 GATACGATGTGCCACGTGGA 60.179 55.000 38.30 18.34 42.61 4.02
2567 9117 2.141781 CGCAAGTGATCGTCAACGT 58.858 52.632 2.09 0.00 40.80 3.99
2641 9191 2.434359 CAGAACGGTTCGAGGGGC 60.434 66.667 14.70 0.00 34.02 5.80
2771 9330 1.153667 CGAGCCTGCTCTTCCACTC 60.154 63.158 16.45 0.00 40.69 3.51
2890 9452 1.227823 CGTGTGCCTGTTCCCAGAA 60.228 57.895 0.00 0.00 41.50 3.02
2904 9468 8.091449 CCTGTTCCCAGAATCTAGTTGATATAC 58.909 40.741 0.00 0.00 41.50 1.47
2905 9469 8.547481 TGTTCCCAGAATCTAGTTGATATACA 57.453 34.615 0.00 0.00 34.45 2.29
2954 9519 5.808042 AAAGCTGTAACTATGCTCACATG 57.192 39.130 0.00 0.00 37.04 3.21
2996 9561 6.090898 GCCTTCTGGTGTAGCATATAATAACG 59.909 42.308 0.00 0.00 35.27 3.18
3061 10333 0.973632 ACAGACACCATCGCCAACTA 59.026 50.000 0.00 0.00 0.00 2.24
3091 10658 5.359194 AACCACATATACAGAGGACTTGG 57.641 43.478 0.00 0.00 0.00 3.61
3139 10706 3.317993 ACACTTGGTTGCCTCATTTGTAC 59.682 43.478 0.00 0.00 0.00 2.90
3157 10724 5.712217 TGTACAAGTCAAAGTCTGTTTCG 57.288 39.130 0.00 0.00 0.00 3.46
3306 10995 9.113838 CACAATGTTACTCTTTGGAGCTTATAT 57.886 33.333 0.00 0.00 42.98 0.86
3383 11072 9.331282 CTAACTAATCCGAGGAGATGAAATTTT 57.669 33.333 0.00 0.00 0.00 1.82
3413 11108 3.444034 TGCAGTAGTACAAGCGAAGATCT 59.556 43.478 2.52 0.00 0.00 2.75
3427 11124 5.866633 AGCGAAGATCTAAAGACTGTTTCAG 59.133 40.000 0.00 0.00 37.52 3.02
3487 11187 2.228059 TCCGGTCTCGAGACATAATCC 58.772 52.381 38.52 23.60 46.47 3.01
3500 11200 5.449553 AGACATAATCCTCCAAATCAACCC 58.550 41.667 0.00 0.00 0.00 4.11
3513 11213 0.391597 TCAACCCCGTCACTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
3534 11234 6.068670 AGTCCATTTTAGCAGTACAAACCTT 58.931 36.000 0.00 0.00 0.00 3.50
3535 11235 6.016276 AGTCCATTTTAGCAGTACAAACCTTG 60.016 38.462 0.00 0.00 0.00 3.61
3537 11237 6.322712 TCCATTTTAGCAGTACAAACCTTGTT 59.677 34.615 0.00 0.00 42.22 2.83
3539 11239 8.138712 CCATTTTAGCAGTACAAACCTTGTTAA 58.861 33.333 0.00 0.00 42.22 2.01
3546 12354 6.238538 GCAGTACAAACCTTGTTAAGCACTAA 60.239 38.462 0.00 0.00 42.22 2.24
3805 12760 1.078848 ACGCAACAGAGCAGGATCC 60.079 57.895 2.48 2.48 0.00 3.36
3847 12802 5.067283 GGTCGCCATTATAACCTTCACATTT 59.933 40.000 0.00 0.00 0.00 2.32
3877 12832 5.144832 TGATCAAATCCATCCATCTGCATT 58.855 37.500 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.056480 TGTCATTGATAACGGGATCACATC 58.944 41.667 0.00 0.00 35.56 3.06
4 5 4.102367 TGGATGTCATTGATAACGGGATCA 59.898 41.667 0.00 0.00 33.96 2.92
5 6 4.641396 TGGATGTCATTGATAACGGGATC 58.359 43.478 0.00 0.00 0.00 3.36
6 7 4.705110 TGGATGTCATTGATAACGGGAT 57.295 40.909 0.00 0.00 0.00 3.85
7 8 4.495690 TTGGATGTCATTGATAACGGGA 57.504 40.909 0.00 0.00 0.00 5.14
8 9 4.580167 ACATTGGATGTCATTGATAACGGG 59.420 41.667 0.00 0.00 39.92 5.28
22 23 4.694760 TCCTGACTATGGACATTGGATG 57.305 45.455 0.00 0.00 0.00 3.51
23 24 5.440610 GTTTCCTGACTATGGACATTGGAT 58.559 41.667 0.00 0.00 32.65 3.41
24 25 4.324254 GGTTTCCTGACTATGGACATTGGA 60.324 45.833 0.00 0.00 32.65 3.53
25 26 3.947834 GGTTTCCTGACTATGGACATTGG 59.052 47.826 0.00 0.00 32.65 3.16
26 27 4.588899 TGGTTTCCTGACTATGGACATTG 58.411 43.478 0.00 0.00 32.65 2.82
27 28 4.927267 TGGTTTCCTGACTATGGACATT 57.073 40.909 0.00 0.00 32.65 2.71
28 29 4.474651 TCATGGTTTCCTGACTATGGACAT 59.525 41.667 0.00 0.00 38.56 3.06
30 31 4.192317 GTCATGGTTTCCTGACTATGGAC 58.808 47.826 0.00 0.00 38.56 4.02
31 32 4.487714 GTCATGGTTTCCTGACTATGGA 57.512 45.455 0.00 0.00 38.56 3.41
38 39 5.248248 TCAACAGATAGTCATGGTTTCCTGA 59.752 40.000 10.65 0.00 0.00 3.86
39 40 5.491070 TCAACAGATAGTCATGGTTTCCTG 58.509 41.667 0.00 0.00 0.00 3.86
40 41 5.762179 TCAACAGATAGTCATGGTTTCCT 57.238 39.130 0.00 0.00 0.00 3.36
41 42 6.115446 TGATCAACAGATAGTCATGGTTTCC 58.885 40.000 0.00 0.00 0.00 3.13
42 43 7.467623 GTTGATCAACAGATAGTCATGGTTTC 58.532 38.462 29.43 0.00 40.84 2.78
43 44 6.092670 CGTTGATCAACAGATAGTCATGGTTT 59.907 38.462 32.06 0.00 41.20 3.27
44 45 5.582269 CGTTGATCAACAGATAGTCATGGTT 59.418 40.000 32.06 0.00 41.20 3.67
45 46 5.105351 TCGTTGATCAACAGATAGTCATGGT 60.105 40.000 32.06 0.00 41.20 3.55
46 47 5.351458 TCGTTGATCAACAGATAGTCATGG 58.649 41.667 32.06 15.04 41.20 3.66
48 49 5.046529 GCTCGTTGATCAACAGATAGTCAT 58.953 41.667 32.06 0.00 41.20 3.06
49 50 4.158579 AGCTCGTTGATCAACAGATAGTCA 59.841 41.667 32.06 11.38 41.20 3.41
50 51 4.677584 AGCTCGTTGATCAACAGATAGTC 58.322 43.478 32.06 19.15 41.20 2.59
51 52 4.727507 AGCTCGTTGATCAACAGATAGT 57.272 40.909 32.06 16.47 41.20 2.12
54 55 4.158579 TGACTAGCTCGTTGATCAACAGAT 59.841 41.667 32.06 26.87 41.20 2.90
55 56 3.506067 TGACTAGCTCGTTGATCAACAGA 59.494 43.478 32.06 26.81 41.20 3.41
56 57 3.838120 TGACTAGCTCGTTGATCAACAG 58.162 45.455 32.06 26.93 41.20 3.16
57 58 3.934457 TGACTAGCTCGTTGATCAACA 57.066 42.857 32.06 20.24 41.20 3.33
58 59 4.238514 AGTTGACTAGCTCGTTGATCAAC 58.761 43.478 25.68 25.68 43.94 3.18
60 61 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
61 62 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
62 63 4.336993 CCTCTAGTTGACTAGCTCGTTGAT 59.663 45.833 12.30 0.00 44.24 2.57
64 65 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
65 66 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
66 67 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
67 68 2.289547 GAGCCTCTAGTTGACTAGCTCG 59.710 54.545 12.30 0.00 44.24 5.03
69 70 3.020984 GTGAGCCTCTAGTTGACTAGCT 58.979 50.000 12.30 7.92 44.24 3.32
70 71 3.020984 AGTGAGCCTCTAGTTGACTAGC 58.979 50.000 12.30 3.61 44.24 3.42
71 72 4.819630 CCTAGTGAGCCTCTAGTTGACTAG 59.180 50.000 11.14 11.14 45.57 2.57
72 73 4.385421 CCCTAGTGAGCCTCTAGTTGACTA 60.385 50.000 0.00 0.00 34.72 2.59
73 74 3.626222 CCCTAGTGAGCCTCTAGTTGACT 60.626 52.174 0.00 0.00 34.72 3.41
75 76 2.581246 TCCCTAGTGAGCCTCTAGTTGA 59.419 50.000 0.00 4.76 34.72 3.18
77 78 2.312140 TGTCCCTAGTGAGCCTCTAGTT 59.688 50.000 0.00 0.00 34.72 2.24
78 79 1.923850 TGTCCCTAGTGAGCCTCTAGT 59.076 52.381 0.00 0.00 34.72 2.57
79 80 2.738587 TGTCCCTAGTGAGCCTCTAG 57.261 55.000 0.00 0.00 35.86 2.43
80 81 2.245028 ACATGTCCCTAGTGAGCCTCTA 59.755 50.000 0.00 0.00 0.00 2.43
81 82 1.007721 ACATGTCCCTAGTGAGCCTCT 59.992 52.381 0.00 0.00 0.00 3.69
83 84 1.556911 CAACATGTCCCTAGTGAGCCT 59.443 52.381 0.00 0.00 0.00 4.58
87 88 2.301870 GACCACAACATGTCCCTAGTGA 59.698 50.000 0.00 0.00 0.00 3.41
89 90 2.621070 AGACCACAACATGTCCCTAGT 58.379 47.619 0.00 0.00 31.76 2.57
90 91 4.162320 ACATAGACCACAACATGTCCCTAG 59.838 45.833 0.00 0.00 31.76 3.02
91 92 4.101114 ACATAGACCACAACATGTCCCTA 58.899 43.478 0.00 0.00 31.76 3.53
92 93 2.912956 ACATAGACCACAACATGTCCCT 59.087 45.455 0.00 0.00 31.76 4.20
93 94 3.350219 ACATAGACCACAACATGTCCC 57.650 47.619 0.00 0.00 31.76 4.46
95 96 7.010552 GTCTGAATACATAGACCACAACATGTC 59.989 40.741 0.00 0.00 37.85 3.06
96 97 6.818644 GTCTGAATACATAGACCACAACATGT 59.181 38.462 0.00 0.00 37.85 3.21
97 98 6.818142 TGTCTGAATACATAGACCACAACATG 59.182 38.462 0.00 0.00 41.99 3.21
98 99 6.946340 TGTCTGAATACATAGACCACAACAT 58.054 36.000 0.00 0.00 41.99 2.71
99 100 6.353404 TGTCTGAATACATAGACCACAACA 57.647 37.500 0.00 0.00 41.99 3.33
100 101 6.238211 GCATGTCTGAATACATAGACCACAAC 60.238 42.308 0.00 0.00 41.99 3.32
102 103 5.104982 TGCATGTCTGAATACATAGACCACA 60.105 40.000 0.00 0.00 41.99 4.17
103 104 5.359756 TGCATGTCTGAATACATAGACCAC 58.640 41.667 0.00 0.00 41.99 4.16
104 105 5.612725 TGCATGTCTGAATACATAGACCA 57.387 39.130 0.00 0.00 41.99 4.02
105 106 7.148738 CGTAATGCATGTCTGAATACATAGACC 60.149 40.741 0.00 0.00 41.99 3.85
106 107 7.595130 TCGTAATGCATGTCTGAATACATAGAC 59.405 37.037 0.00 0.00 42.77 2.59
108 109 7.873739 TCGTAATGCATGTCTGAATACATAG 57.126 36.000 0.00 0.00 38.01 2.23
109 110 8.831715 AATCGTAATGCATGTCTGAATACATA 57.168 30.769 0.00 0.00 38.01 2.29
110 111 7.734924 AATCGTAATGCATGTCTGAATACAT 57.265 32.000 0.00 0.00 40.75 2.29
111 112 7.254761 GGAAATCGTAATGCATGTCTGAATACA 60.255 37.037 0.00 0.00 0.00 2.29
112 113 7.072030 GGAAATCGTAATGCATGTCTGAATAC 58.928 38.462 0.00 0.00 0.00 1.89
113 114 6.073819 CGGAAATCGTAATGCATGTCTGAATA 60.074 38.462 0.00 0.00 0.00 1.75
114 115 5.277490 CGGAAATCGTAATGCATGTCTGAAT 60.277 40.000 0.00 0.00 0.00 2.57
115 116 4.033932 CGGAAATCGTAATGCATGTCTGAA 59.966 41.667 0.00 0.00 0.00 3.02
116 117 3.555547 CGGAAATCGTAATGCATGTCTGA 59.444 43.478 0.00 0.00 0.00 3.27
117 118 3.303329 CCGGAAATCGTAATGCATGTCTG 60.303 47.826 0.00 0.00 37.11 3.51
118 119 2.872245 CCGGAAATCGTAATGCATGTCT 59.128 45.455 0.00 0.00 37.11 3.41
119 120 2.869801 TCCGGAAATCGTAATGCATGTC 59.130 45.455 0.00 0.00 37.11 3.06
120 121 2.912771 TCCGGAAATCGTAATGCATGT 58.087 42.857 0.00 0.00 37.11 3.21
121 122 5.049749 TGTTATCCGGAAATCGTAATGCATG 60.050 40.000 9.01 0.00 37.11 4.06
122 123 5.049680 GTGTTATCCGGAAATCGTAATGCAT 60.050 40.000 9.01 0.00 37.11 3.96
123 124 4.271533 GTGTTATCCGGAAATCGTAATGCA 59.728 41.667 9.01 0.00 37.11 3.96
124 125 4.271533 TGTGTTATCCGGAAATCGTAATGC 59.728 41.667 9.01 0.34 37.11 3.56
125 126 5.977171 TGTGTTATCCGGAAATCGTAATG 57.023 39.130 9.01 0.00 37.11 1.90
126 127 7.562454 AATTGTGTTATCCGGAAATCGTAAT 57.438 32.000 9.01 3.30 37.11 1.89
127 128 6.988622 AATTGTGTTATCCGGAAATCGTAA 57.011 33.333 9.01 0.00 37.11 3.18
129 130 8.553696 GTTATAATTGTGTTATCCGGAAATCGT 58.446 33.333 9.01 0.00 37.11 3.73
133 134 9.397280 TCATGTTATAATTGTGTTATCCGGAAA 57.603 29.630 9.01 0.99 0.00 3.13
135 136 8.832521 GTTCATGTTATAATTGTGTTATCCGGA 58.167 33.333 6.61 6.61 0.00 5.14
136 137 8.616942 TGTTCATGTTATAATTGTGTTATCCGG 58.383 33.333 0.00 0.00 0.00 5.14
137 138 9.995957 TTGTTCATGTTATAATTGTGTTATCCG 57.004 29.630 0.00 0.00 0.00 4.18
160 161 9.685276 TCCTTGTTCATGATAATTGTCTATTGT 57.315 29.630 0.00 0.00 0.00 2.71
196 197 9.533831 CCCTAGAGGCAATAATAAAATGGTTAT 57.466 33.333 0.00 0.00 0.00 1.89
198 199 7.839680 CCCTAGAGGCAATAATAAAATGGTT 57.160 36.000 0.00 0.00 0.00 3.67
216 217 5.385198 GGATTGTTGGAAATATGCCCTAGA 58.615 41.667 0.00 0.00 0.00 2.43
217 218 4.216257 CGGATTGTTGGAAATATGCCCTAG 59.784 45.833 0.00 0.00 0.00 3.02
218 219 4.141287 CGGATTGTTGGAAATATGCCCTA 58.859 43.478 0.00 0.00 0.00 3.53
219 220 2.958355 CGGATTGTTGGAAATATGCCCT 59.042 45.455 0.00 0.00 0.00 5.19
221 222 2.693074 ACCGGATTGTTGGAAATATGCC 59.307 45.455 9.46 0.00 0.00 4.40
224 225 3.976015 ACCACCGGATTGTTGGAAATAT 58.024 40.909 9.46 0.00 0.00 1.28
225 226 3.443145 ACCACCGGATTGTTGGAAATA 57.557 42.857 9.46 0.00 0.00 1.40
226 227 2.298729 CAACCACCGGATTGTTGGAAAT 59.701 45.455 9.46 0.00 36.57 2.17
228 229 1.323412 CAACCACCGGATTGTTGGAA 58.677 50.000 9.46 0.00 36.57 3.53
229 230 3.028916 CAACCACCGGATTGTTGGA 57.971 52.632 9.46 0.00 36.57 3.53
231 232 1.288752 GCCAACCACCGGATTGTTG 59.711 57.895 9.46 17.45 39.20 3.33
232 233 1.152652 TGCCAACCACCGGATTGTT 60.153 52.632 9.46 5.20 0.00 2.83
233 234 1.603455 CTGCCAACCACCGGATTGT 60.603 57.895 9.46 0.00 0.00 2.71
235 236 1.603455 CACTGCCAACCACCGGATT 60.603 57.895 9.46 0.00 0.00 3.01
236 237 2.034066 CACTGCCAACCACCGGAT 59.966 61.111 9.46 0.00 0.00 4.18
237 238 3.469863 GACACTGCCAACCACCGGA 62.470 63.158 9.46 0.00 0.00 5.14
239 240 3.345808 CGACACTGCCAACCACCG 61.346 66.667 0.00 0.00 0.00 4.94
247 248 2.953466 TTAGTACCATCGACACTGCC 57.047 50.000 0.00 0.00 0.00 4.85
255 256 3.132289 TCCAGCTCCTTTTAGTACCATCG 59.868 47.826 0.00 0.00 0.00 3.84
264 265 0.322187 GCCGGTTCCAGCTCCTTTTA 60.322 55.000 1.90 0.00 0.00 1.52
283 284 3.254060 TCTCTTCTCTTCGCCATTTTCG 58.746 45.455 0.00 0.00 0.00 3.46
284 285 4.499183 TCTCTCTTCTCTTCGCCATTTTC 58.501 43.478 0.00 0.00 0.00 2.29
297 298 6.006449 GCTCATTCCTCTATCTCTCTCTTCT 58.994 44.000 0.00 0.00 0.00 2.85
309 310 2.103094 CCCGATTGTGCTCATTCCTCTA 59.897 50.000 5.38 0.00 0.00 2.43
324 325 1.043673 CCGTCTCCTTCCTCCCGATT 61.044 60.000 0.00 0.00 0.00 3.34
337 338 3.892588 AGGATTAGGATCTTGACCGTCTC 59.107 47.826 0.00 0.00 32.66 3.36
347 348 4.148838 CGAAGAGTCCAGGATTAGGATCT 58.851 47.826 0.00 0.00 37.52 2.75
354 355 1.893801 ACGAACGAAGAGTCCAGGATT 59.106 47.619 0.14 0.00 0.00 3.01
400 401 1.888436 ATCTTCAGCAGCGTCCCGAA 61.888 55.000 0.00 0.00 0.00 4.30
421 422 2.743928 GCAGTGGGCCGAAGACAG 60.744 66.667 0.00 0.00 36.11 3.51
429 430 0.106521 ATTTTGTTGTGCAGTGGGCC 59.893 50.000 0.00 0.00 43.89 5.80
447 448 1.886542 GGTTTTGGTTCAAGAGGCGAT 59.113 47.619 0.00 0.00 0.00 4.58
458 459 1.886542 GAAGATCAGCGGGTTTTGGTT 59.113 47.619 0.00 0.00 0.00 3.67
459 460 1.534729 GAAGATCAGCGGGTTTTGGT 58.465 50.000 0.00 0.00 0.00 3.67
464 465 2.125106 GGCGAAGATCAGCGGGTT 60.125 61.111 8.91 0.00 0.00 4.11
481 482 1.741770 CTCTTCGGTCGCCTTTGGG 60.742 63.158 0.00 0.00 0.00 4.12
513 514 4.647564 AGGGATGTCTTCATTCTTGTGT 57.352 40.909 0.00 0.00 34.06 3.72
560 562 3.374367 CGTCCTCATGTAGAACGAAGAGA 59.626 47.826 0.00 0.00 33.40 3.10
567 569 2.159226 CCAGGTCGTCCTCATGTAGAAC 60.159 54.545 0.00 0.00 43.07 3.01
581 583 3.062099 CGTAAACATGAATGACCAGGTCG 59.938 47.826 15.24 1.76 34.95 4.79
613 1028 0.966875 TCCCTGCTGCGCAATCAAAT 60.967 50.000 13.05 0.00 38.41 2.32
631 1046 3.655556 CGCGCAAACAATTCTTCGTTTTC 60.656 43.478 8.75 0.00 33.14 2.29
643 1058 2.765108 TTCTTCATTCGCGCAAACAA 57.235 40.000 8.75 0.00 0.00 2.83
650 1065 8.920665 AGATTTCTAGAATATTCTTCATTCGCG 58.079 33.333 22.60 0.00 38.70 5.87
677 1096 7.893124 ATTCTAATGAGAAATCCATTGCACT 57.107 32.000 0.00 0.00 44.85 4.40
712 1131 9.905171 TTTCGTTGTTTGATTCATATGATTGAA 57.095 25.926 6.17 0.66 39.77 2.69
800 1219 1.930817 GCACTCCACAGACACACGTAG 60.931 57.143 0.00 0.00 0.00 3.51
801 1220 0.031585 GCACTCCACAGACACACGTA 59.968 55.000 0.00 0.00 0.00 3.57
804 1223 2.311294 GTGCACTCCACAGACACAC 58.689 57.895 10.32 0.00 44.06 3.82
805 1224 4.855105 GTGCACTCCACAGACACA 57.145 55.556 10.32 0.00 44.06 3.72
812 1730 2.554032 AGCATTAACTTGTGCACTCCAC 59.446 45.455 19.41 0.00 43.63 4.02
815 1733 4.488126 TTGAGCATTAACTTGTGCACTC 57.512 40.909 19.41 3.39 43.63 3.51
822 1740 8.752766 AACTGATGAAATTGAGCATTAACTTG 57.247 30.769 0.00 0.00 0.00 3.16
823 1741 8.579006 TGAACTGATGAAATTGAGCATTAACTT 58.421 29.630 0.00 0.00 0.00 2.66
824 1742 8.114331 TGAACTGATGAAATTGAGCATTAACT 57.886 30.769 0.00 0.00 0.00 2.24
826 1744 8.741841 TCATGAACTGATGAAATTGAGCATTAA 58.258 29.630 0.00 0.00 29.11 1.40
827 1745 8.283699 TCATGAACTGATGAAATTGAGCATTA 57.716 30.769 0.00 0.00 29.11 1.90
828 1746 7.165460 TCATGAACTGATGAAATTGAGCATT 57.835 32.000 0.00 0.00 29.11 3.56
831 1749 5.125097 ACCTCATGAACTGATGAAATTGAGC 59.875 40.000 0.00 0.00 31.90 4.26
844 1762 4.262164 GGAATTTTGTGCACCTCATGAACT 60.262 41.667 15.69 0.00 37.80 3.01
878 1796 4.392921 ACCAACAGATAATCCTGTCTCG 57.607 45.455 0.00 0.00 45.82 4.04
909 1827 1.689813 TGCTTGGAACTACCGACAGAA 59.310 47.619 0.00 0.00 42.61 3.02
959 1877 2.098607 TCTCTTCGTGTGTTTCGTGTCT 59.901 45.455 0.00 0.00 0.00 3.41
960 1878 2.456989 TCTCTTCGTGTGTTTCGTGTC 58.543 47.619 0.00 0.00 0.00 3.67
965 1883 4.025145 ACCGAATTTCTCTTCGTGTGTTTC 60.025 41.667 5.61 0.00 44.98 2.78
966 1884 3.875134 ACCGAATTTCTCTTCGTGTGTTT 59.125 39.130 5.61 0.00 44.98 2.83
968 1886 3.107642 ACCGAATTTCTCTTCGTGTGT 57.892 42.857 5.61 0.00 44.98 3.72
969 1887 3.059044 CGTACCGAATTTCTCTTCGTGTG 59.941 47.826 5.61 0.00 44.98 3.82
970 1888 3.240069 CGTACCGAATTTCTCTTCGTGT 58.760 45.455 5.61 5.79 44.98 4.49
971 1889 3.240069 ACGTACCGAATTTCTCTTCGTG 58.760 45.455 5.61 0.77 44.98 4.35
973 1891 5.091431 AGTTACGTACCGAATTTCTCTTCG 58.909 41.667 0.00 0.00 45.79 3.79
999 1917 4.142600 GCGTTGCTTCTGGATTTAGTCATT 60.143 41.667 0.00 0.00 0.00 2.57
1012 1930 2.359230 GGAGCCAGCGTTGCTTCT 60.359 61.111 0.00 0.00 39.69 2.85
1464 3365 2.964389 GCGATCTTCCGGAGCTGC 60.964 66.667 3.34 2.14 0.00 5.25
1722 7899 4.016706 AGGTCGGCCGGGTTGAAG 62.017 66.667 27.83 0.00 40.50 3.02
1872 8052 2.282251 AGCAGGTCCTCGTCGTGA 60.282 61.111 0.00 0.00 0.00 4.35
2078 8335 5.148568 ACATTTTGATAAAACCGTACACGC 58.851 37.500 0.00 0.00 33.23 5.34
2108 8365 3.605634 TGACATTTGTTATGGACCGGAG 58.394 45.455 9.46 0.00 0.00 4.63
2109 8366 3.704800 TGACATTTGTTATGGACCGGA 57.295 42.857 9.46 0.00 0.00 5.14
2110 8367 5.588648 ACTTATGACATTTGTTATGGACCGG 59.411 40.000 0.00 0.00 0.00 5.28
2111 8368 6.677781 ACTTATGACATTTGTTATGGACCG 57.322 37.500 0.00 0.00 0.00 4.79
2140 8397 9.752961 TTTGAGCCAAGGTTAATTTAACTTTAC 57.247 29.630 16.64 11.61 36.05 2.01
2159 8416 2.584492 AAGTGTTGCAGTTTTGAGCC 57.416 45.000 0.00 0.00 0.00 4.70
2160 8417 6.413269 CAAAATAAGTGTTGCAGTTTTGAGC 58.587 36.000 0.00 0.00 38.26 4.26
2161 8418 6.756074 TCCAAAATAAGTGTTGCAGTTTTGAG 59.244 34.615 9.26 2.00 38.26 3.02
2163 8420 6.900568 TCCAAAATAAGTGTTGCAGTTTTG 57.099 33.333 0.00 0.00 36.70 2.44
2164 8421 6.420604 CGATCCAAAATAAGTGTTGCAGTTTT 59.579 34.615 0.00 0.00 0.00 2.43
2165 8422 5.920273 CGATCCAAAATAAGTGTTGCAGTTT 59.080 36.000 0.00 0.00 0.00 2.66
2166 8423 5.460646 CGATCCAAAATAAGTGTTGCAGTT 58.539 37.500 0.00 0.00 0.00 3.16
2169 8426 4.075682 TCCGATCCAAAATAAGTGTTGCA 58.924 39.130 0.00 0.00 0.00 4.08
2170 8427 4.438744 CCTCCGATCCAAAATAAGTGTTGC 60.439 45.833 0.00 0.00 0.00 4.17
2171 8428 4.941263 TCCTCCGATCCAAAATAAGTGTTG 59.059 41.667 0.00 0.00 0.00 3.33
2172 8429 5.174037 TCCTCCGATCCAAAATAAGTGTT 57.826 39.130 0.00 0.00 0.00 3.32
2173 8430 4.837093 TCCTCCGATCCAAAATAAGTGT 57.163 40.909 0.00 0.00 0.00 3.55
2174 8431 5.186198 ACTTCCTCCGATCCAAAATAAGTG 58.814 41.667 0.00 0.00 0.00 3.16
2175 8432 5.437191 ACTTCCTCCGATCCAAAATAAGT 57.563 39.130 0.00 0.00 0.00 2.24
2176 8433 6.480320 CAGTACTTCCTCCGATCCAAAATAAG 59.520 42.308 0.00 0.00 0.00 1.73
2177 8434 6.070424 ACAGTACTTCCTCCGATCCAAAATAA 60.070 38.462 0.00 0.00 0.00 1.40
2188 8445 2.366533 TGCTAGACAGTACTTCCTCCG 58.633 52.381 0.00 0.00 0.00 4.63
2190 8447 4.160626 ACCATTGCTAGACAGTACTTCCTC 59.839 45.833 0.00 0.00 0.00 3.71
2207 8464 5.792741 TGAGGGAAGCAAAATTAACCATTG 58.207 37.500 0.00 0.00 0.00 2.82
2423 8973 3.561143 AGGTGTAGATAGGTGAGCTCTG 58.439 50.000 16.19 0.00 0.00 3.35
2433 8983 4.822350 TCTCGGATGACAAGGTGTAGATAG 59.178 45.833 0.00 0.00 0.00 2.08
2547 9097 0.506932 CGTTGACGATCACTTGCGTT 59.493 50.000 0.00 0.00 41.34 4.84
2641 9191 3.041940 AAAGTCCGACGCCGCTTG 61.042 61.111 0.00 0.00 0.00 4.01
2730 9289 3.345808 GCGAGCTCAACGTTGGCA 61.346 61.111 30.26 14.73 0.00 4.92
2771 9330 4.087892 CTGCCCACTCCCAGTCGG 62.088 72.222 0.00 0.00 28.96 4.79
2954 9519 3.778954 AGGCTATGCAGTTTATCTCCC 57.221 47.619 0.00 0.00 0.00 4.30
3061 10333 6.386927 TCCTCTGTATATGTGGTTCCAATCTT 59.613 38.462 0.00 0.00 0.00 2.40
3091 10658 7.962917 TGAAAAGAGAATGCTTTGTTTTCAAC 58.037 30.769 13.39 0.00 39.73 3.18
3139 10706 2.287009 GCCCGAAACAGACTTTGACTTG 60.287 50.000 0.00 0.00 0.00 3.16
3157 10724 1.235281 GGACCAACGTCAAGAAGCCC 61.235 60.000 0.00 0.00 41.13 5.19
3241 10808 0.390735 CTGCAATTTGCCAGGAAGCC 60.391 55.000 18.27 0.00 44.23 4.35
3262 10830 8.583810 ACATTGTGTCATTTCTTTTTCAGATG 57.416 30.769 0.00 0.00 0.00 2.90
3312 11001 5.987777 TCCTCTAGTCTCGAAACTTATCG 57.012 43.478 0.00 0.00 44.04 2.92
3367 11056 7.130917 CAGCATAAGAAAATTTCATCTCCTCG 58.869 38.462 8.55 0.00 0.00 4.63
3383 11072 4.433615 GCTTGTACTACTGCAGCATAAGA 58.566 43.478 15.27 0.00 0.00 2.10
3413 11108 8.886719 CATCTCATTATGCTGAAACAGTCTTTA 58.113 33.333 0.00 0.00 33.43 1.85
3427 11124 3.208594 TGTGAGTGCCATCTCATTATGC 58.791 45.455 6.63 0.00 44.59 3.14
3487 11187 1.165270 GTGACGGGGTTGATTTGGAG 58.835 55.000 0.00 0.00 0.00 3.86
3500 11200 3.125316 GCTAAAATGGACTTGAGTGACGG 59.875 47.826 0.00 0.00 0.00 4.79
3513 11213 6.084326 ACAAGGTTTGTACTGCTAAAATGG 57.916 37.500 0.00 0.00 43.27 3.16
3569 12381 7.115520 CAGTCATTATCTTTAGTACATGGCTCG 59.884 40.741 0.00 0.00 0.00 5.03
3805 12760 1.414181 ACCAATCGGGCAGATACTCTG 59.586 52.381 0.00 0.00 40.76 3.35
3847 12802 5.955961 TGGATGGATTTGATCAGACAGTA 57.044 39.130 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.