Multiple sequence alignment - TraesCS7B01G404500

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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 TraesCS7B01G404500 chr7B 100.000 3529 0 0 1 3529 672769881 672773409 0.000000e+00 6517
1 TraesCS7B01G404500 chr7B 81.609 1691 227 41 218 1878 701457533 701459169 0.000000e+00 1323
2 TraesCS7B01G404500 chr7B 79.420 690 114 16 567 1241 701646000 701646676 2.480000e-126 462
3 TraesCS7B01G404500 chr7B 82.974 464 55 16 2510 2963 701460138 701460587 7.100000e-107 398
4 TraesCS7B01G404500 chr7B 93.452 168 10 1 2 169 58715087 58715253 7.560000e-62 248
5 TraesCS7B01G404500 chr7A 92.810 3185 167 22 168 3315 688345350 688348509 0.000000e+00 4556
6 TraesCS7B01G404500 chr7A 87.869 1797 186 16 218 1993 702610773 702612558 0.000000e+00 2082
7 TraesCS7B01G404500 chr7A 81.872 1699 256 31 218 1878 702407442 702409126 0.000000e+00 1384
8 TraesCS7B01G404500 chr7A 80.564 1312 188 35 595 1878 702237726 702238998 0.000000e+00 948
9 TraesCS7B01G404500 chr7A 76.428 823 108 36 2510 3315 702239979 702240732 2.000000e-97 366
10 TraesCS7B01G404500 chr7A 88.129 278 24 7 2013 2286 702612545 702612817 4.390000e-84 322
11 TraesCS7B01G404500 chr7A 80.737 353 43 15 2510 2852 702620741 702621078 5.850000e-63 252
12 TraesCS7B01G404500 chr7A 88.557 201 20 2 2314 2511 702983296 702983096 1.270000e-59 241
13 TraesCS7B01G404500 chr7A 80.000 260 44 7 1821 2076 703545801 703546056 6.020000e-43 185
14 TraesCS7B01G404500 chr7D 93.785 1625 78 13 168 1789 595346680 595348284 0.000000e+00 2420
15 TraesCS7B01G404500 chr7D 92.862 1625 76 14 931 2552 595348281 595349868 0.000000e+00 2322
16 TraesCS7B01G404500 chr7D 88.180 1802 177 18 218 1987 612403683 612405480 0.000000e+00 2115
17 TraesCS7B01G404500 chr7D 82.362 1990 259 49 563 2511 612428100 612430038 0.000000e+00 1646
18 TraesCS7B01G404500 chr7D 82.256 1702 245 32 218 1878 612325795 612327480 0.000000e+00 1417
19 TraesCS7B01G404500 chr7D 81.609 1691 237 36 218 1878 611857528 611855882 0.000000e+00 1332
20 TraesCS7B01G404500 chr7D 80.536 1305 189 32 595 1870 611871144 611869876 0.000000e+00 942
21 TraesCS7B01G404500 chr7D 91.037 569 30 9 2765 3315 595350066 595350631 0.000000e+00 749
22 TraesCS7B01G404500 chr7D 78.546 839 163 15 1248 2076 612708062 612708893 1.440000e-148 536
23 TraesCS7B01G404500 chr7D 77.805 820 94 34 2513 3315 611854901 611854153 3.260000e-115 425
24 TraesCS7B01G404500 chr7D 85.230 413 40 14 2028 2421 612405481 612405891 4.240000e-109 405
25 TraesCS7B01G404500 chr7D 76.942 824 103 45 2510 3315 612289314 612290068 4.270000e-104 388
26 TraesCS7B01G404500 chr7D 87.147 319 41 0 224 542 612427797 612428115 2.590000e-96 363
27 TraesCS7B01G404500 chr7D 76.444 658 138 14 1236 1879 612935777 612936431 1.210000e-89 340
28 TraesCS7B01G404500 chr7D 76.502 566 94 23 302 859 612826456 612826990 4.490000e-69 272
29 TraesCS7B01G404500 chr7D 82.424 330 37 11 2510 2831 612430118 612430434 5.810000e-68 268
30 TraesCS7B01G404500 chr7D 85.227 264 21 11 218 481 612286734 612286979 4.520000e-64 255
31 TraesCS7B01G404500 chr7D 78.189 486 42 27 2512 2980 612328404 612328842 5.850000e-63 252
32 TraesCS7B01G404500 chr7D 94.393 107 6 0 2874 2980 611868562 611868456 7.840000e-37 165
33 TraesCS7B01G404500 chr2D 74.348 1610 331 50 303 1888 420739305 420740856 8.380000e-171 610
34 TraesCS7B01G404500 chr2D 92.814 167 10 2 2 167 597962672 597962837 1.270000e-59 241
35 TraesCS7B01G404500 chrUn 81.681 464 54 19 2510 2958 368812154 368812601 1.200000e-94 357
36 TraesCS7B01G404500 chr4A 94.048 168 9 1 2 169 669675003 669674837 1.630000e-63 254
37 TraesCS7B01G404500 chr1D 93.491 169 10 1 2 170 328819238 328819071 2.100000e-62 250
38 TraesCS7B01G404500 chr5B 92.899 169 10 2 2 170 563165685 563165851 9.790000e-61 244
39 TraesCS7B01G404500 chr4B 92.899 169 10 2 2 170 50838979 50838813 9.790000e-61 244
40 TraesCS7B01G404500 chr1A 92.899 169 11 1 2 170 425685368 425685201 9.790000e-61 244
41 TraesCS7B01G404500 chr2B 92.857 168 11 1 2 169 93397090 93396924 3.520000e-60 243
42 TraesCS7B01G404500 chr3D 92.308 169 12 1 2 170 428958582 428958749 4.550000e-59 239


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 TraesCS7B01G404500 chr7B 672769881 672773409 3528 False 6517.000000 6517 100.000000 1 3529 1 chr7B.!!$F2 3528
1 TraesCS7B01G404500 chr7B 701457533 701460587 3054 False 860.500000 1323 82.291500 218 2963 2 chr7B.!!$F4 2745
2 TraesCS7B01G404500 chr7B 701646000 701646676 676 False 462.000000 462 79.420000 567 1241 1 chr7B.!!$F3 674
3 TraesCS7B01G404500 chr7A 688345350 688348509 3159 False 4556.000000 4556 92.810000 168 3315 1 chr7A.!!$F1 3147
4 TraesCS7B01G404500 chr7A 702407442 702409126 1684 False 1384.000000 1384 81.872000 218 1878 1 chr7A.!!$F2 1660
5 TraesCS7B01G404500 chr7A 702610773 702612817 2044 False 1202.000000 2082 87.999000 218 2286 2 chr7A.!!$F6 2068
6 TraesCS7B01G404500 chr7A 702237726 702240732 3006 False 657.000000 948 78.496000 595 3315 2 chr7A.!!$F5 2720
7 TraesCS7B01G404500 chr7D 595346680 595350631 3951 False 1830.333333 2420 92.561333 168 3315 3 chr7D.!!$F4 3147
8 TraesCS7B01G404500 chr7D 612403683 612405891 2208 False 1260.000000 2115 86.705000 218 2421 2 chr7D.!!$F7 2203
9 TraesCS7B01G404500 chr7D 611854153 611857528 3375 True 878.500000 1332 79.707000 218 3315 2 chr7D.!!$R1 3097
10 TraesCS7B01G404500 chr7D 612325795 612328842 3047 False 834.500000 1417 80.222500 218 2980 2 chr7D.!!$F6 2762
11 TraesCS7B01G404500 chr7D 612427797 612430434 2637 False 759.000000 1646 83.977667 224 2831 3 chr7D.!!$F8 2607
12 TraesCS7B01G404500 chr7D 611868456 611871144 2688 True 553.500000 942 87.464500 595 2980 2 chr7D.!!$R2 2385
13 TraesCS7B01G404500 chr7D 612708062 612708893 831 False 536.000000 536 78.546000 1248 2076 1 chr7D.!!$F1 828
14 TraesCS7B01G404500 chr7D 612935777 612936431 654 False 340.000000 340 76.444000 1236 1879 1 chr7D.!!$F3 643
15 TraesCS7B01G404500 chr7D 612286734 612290068 3334 False 321.500000 388 81.084500 218 3315 2 chr7D.!!$F5 3097
16 TraesCS7B01G404500 chr7D 612826456 612826990 534 False 272.000000 272 76.502000 302 859 1 chr7D.!!$F2 557
17 TraesCS7B01G404500 chr2D 420739305 420740856 1551 False 610.000000 610 74.348000 303 1888 1 chr2D.!!$F1 1585

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
27 28 0.170339 CGGTGAGATGACGTGCTACA 59.830 55.0 0.00 0.0 0.0 2.74 F
128 129 0.678950 TGTTGCATGGTCGACTGAGA 59.321 50.0 16.46 0.0 0.0 3.27 F
1284 1386 0.934496 TGCTTTTTCAGGACACGTCG 59.066 50.0 0.00 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 1577 1.758936 TCGGAGCAGAGAATTACCGA 58.241 50.000 0.00 0.00 45.36 4.69 R
1738 2727 2.689471 GTGCATCCATCATTACTTGCCA 59.311 45.455 0.00 0.00 0.00 4.92 R
3254 4794 0.459585 TTCGAAGGATCCGAAAGCCG 60.460 55.000 5.98 5.25 42.18 5.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.955145 ATTGCAACCGGTGAGATGA 57.045 47.368 8.52 0.00 0.00 2.92
19 20 1.453155 ATTGCAACCGGTGAGATGAC 58.547 50.000 8.52 0.00 0.00 3.06
20 21 0.948623 TTGCAACCGGTGAGATGACG 60.949 55.000 8.52 0.00 0.00 4.35
21 22 1.374252 GCAACCGGTGAGATGACGT 60.374 57.895 8.52 0.00 0.00 4.34
22 23 1.626654 GCAACCGGTGAGATGACGTG 61.627 60.000 8.52 0.00 0.00 4.49
23 24 1.374252 AACCGGTGAGATGACGTGC 60.374 57.895 8.52 0.00 0.00 5.34
24 25 1.816863 AACCGGTGAGATGACGTGCT 61.817 55.000 8.52 0.00 0.00 4.40
25 26 0.963856 ACCGGTGAGATGACGTGCTA 60.964 55.000 6.12 0.00 0.00 3.49
26 27 0.525668 CCGGTGAGATGACGTGCTAC 60.526 60.000 0.00 0.00 0.00 3.58
27 28 0.170339 CGGTGAGATGACGTGCTACA 59.830 55.000 0.00 0.00 0.00 2.74
28 29 1.402325 CGGTGAGATGACGTGCTACAA 60.402 52.381 0.00 0.00 0.00 2.41
29 30 2.683968 GGTGAGATGACGTGCTACAAA 58.316 47.619 0.00 0.00 0.00 2.83
30 31 3.262420 GGTGAGATGACGTGCTACAAAT 58.738 45.455 0.00 0.00 0.00 2.32
31 32 3.062639 GGTGAGATGACGTGCTACAAATG 59.937 47.826 0.00 0.00 0.00 2.32
32 33 3.926527 GTGAGATGACGTGCTACAAATGA 59.073 43.478 0.00 0.00 0.00 2.57
33 34 4.032217 GTGAGATGACGTGCTACAAATGAG 59.968 45.833 0.00 0.00 0.00 2.90
34 35 3.525537 AGATGACGTGCTACAAATGAGG 58.474 45.455 0.00 0.00 0.00 3.86
35 36 3.195610 AGATGACGTGCTACAAATGAGGA 59.804 43.478 0.00 0.00 0.00 3.71
36 37 2.959516 TGACGTGCTACAAATGAGGAG 58.040 47.619 0.00 0.00 0.00 3.69
37 38 2.271800 GACGTGCTACAAATGAGGAGG 58.728 52.381 0.00 0.00 0.00 4.30
38 39 1.066143 ACGTGCTACAAATGAGGAGGG 60.066 52.381 0.00 0.00 0.00 4.30
39 40 1.207089 CGTGCTACAAATGAGGAGGGA 59.793 52.381 0.00 0.00 0.00 4.20
40 41 2.158900 CGTGCTACAAATGAGGAGGGAT 60.159 50.000 0.00 0.00 0.00 3.85
41 42 3.209410 GTGCTACAAATGAGGAGGGATG 58.791 50.000 0.00 0.00 0.00 3.51
42 43 3.114606 TGCTACAAATGAGGAGGGATGA 58.885 45.455 0.00 0.00 0.00 2.92
43 44 3.118261 TGCTACAAATGAGGAGGGATGAC 60.118 47.826 0.00 0.00 0.00 3.06
44 45 3.118261 GCTACAAATGAGGAGGGATGACA 60.118 47.826 0.00 0.00 0.00 3.58
45 46 4.445448 GCTACAAATGAGGAGGGATGACAT 60.445 45.833 0.00 0.00 0.00 3.06
46 47 3.894759 ACAAATGAGGAGGGATGACATG 58.105 45.455 0.00 0.00 0.00 3.21
47 48 2.621998 CAAATGAGGAGGGATGACATGC 59.378 50.000 0.00 0.00 0.00 4.06
48 49 1.817087 ATGAGGAGGGATGACATGCT 58.183 50.000 6.91 0.00 0.00 3.79
49 50 1.588239 TGAGGAGGGATGACATGCTT 58.412 50.000 6.91 0.00 0.00 3.91
50 51 1.487976 TGAGGAGGGATGACATGCTTC 59.512 52.381 10.16 10.16 0.00 3.86
51 52 1.487976 GAGGAGGGATGACATGCTTCA 59.512 52.381 18.53 0.00 0.00 3.02
52 53 1.918262 AGGAGGGATGACATGCTTCAA 59.082 47.619 18.53 0.00 0.00 2.69
53 54 2.019984 GGAGGGATGACATGCTTCAAC 58.980 52.381 18.53 1.36 0.00 3.18
54 55 2.019984 GAGGGATGACATGCTTCAACC 58.980 52.381 13.21 4.54 37.65 3.77
55 56 1.355381 AGGGATGACATGCTTCAACCA 59.645 47.619 12.73 0.00 39.62 3.67
56 57 2.170166 GGGATGACATGCTTCAACCAA 58.830 47.619 12.73 0.00 39.62 3.67
57 58 2.094545 GGGATGACATGCTTCAACCAAC 60.095 50.000 12.73 0.00 39.62 3.77
58 59 2.557924 GGATGACATGCTTCAACCAACA 59.442 45.455 7.50 0.00 38.14 3.33
59 60 3.005684 GGATGACATGCTTCAACCAACAA 59.994 43.478 7.50 0.00 38.14 2.83
60 61 4.501229 GGATGACATGCTTCAACCAACAAA 60.501 41.667 7.50 0.00 38.14 2.83
61 62 4.462508 TGACATGCTTCAACCAACAAAA 57.537 36.364 0.00 0.00 0.00 2.44
62 63 4.180057 TGACATGCTTCAACCAACAAAAC 58.820 39.130 0.00 0.00 0.00 2.43
63 64 4.081752 TGACATGCTTCAACCAACAAAACT 60.082 37.500 0.00 0.00 0.00 2.66
64 65 5.126222 TGACATGCTTCAACCAACAAAACTA 59.874 36.000 0.00 0.00 0.00 2.24
65 66 5.971763 ACATGCTTCAACCAACAAAACTAA 58.028 33.333 0.00 0.00 0.00 2.24
66 67 6.581712 ACATGCTTCAACCAACAAAACTAAT 58.418 32.000 0.00 0.00 0.00 1.73
67 68 6.479660 ACATGCTTCAACCAACAAAACTAATG 59.520 34.615 0.00 0.00 0.00 1.90
68 69 5.971763 TGCTTCAACCAACAAAACTAATGT 58.028 33.333 0.00 0.00 0.00 2.71
69 70 6.402222 TGCTTCAACCAACAAAACTAATGTT 58.598 32.000 0.00 0.00 41.50 2.71
77 78 3.712187 ACAAAACTAATGTTGCAACCGG 58.288 40.909 26.14 15.05 36.39 5.28
78 79 3.131400 ACAAAACTAATGTTGCAACCGGT 59.869 39.130 26.14 15.64 36.39 5.28
79 80 4.338682 ACAAAACTAATGTTGCAACCGGTA 59.661 37.500 26.14 14.02 36.39 4.02
80 81 5.010213 ACAAAACTAATGTTGCAACCGGTAT 59.990 36.000 26.14 10.57 36.39 2.73
81 82 4.695217 AACTAATGTTGCAACCGGTATG 57.305 40.909 26.14 10.06 34.71 2.39
82 83 3.945346 ACTAATGTTGCAACCGGTATGA 58.055 40.909 26.14 6.55 0.00 2.15
83 84 4.328536 ACTAATGTTGCAACCGGTATGAA 58.671 39.130 26.14 5.77 0.00 2.57
84 85 4.762765 ACTAATGTTGCAACCGGTATGAAA 59.237 37.500 26.14 6.81 0.00 2.69
85 86 4.592485 AATGTTGCAACCGGTATGAAAA 57.408 36.364 26.14 4.24 0.00 2.29
86 87 4.592485 ATGTTGCAACCGGTATGAAAAA 57.408 36.364 26.14 5.13 0.00 1.94
108 109 8.649973 AAAAATGTTGCATACGGTTAAAGAAA 57.350 26.923 0.00 0.00 0.00 2.52
109 110 8.825667 AAAATGTTGCATACGGTTAAAGAAAT 57.174 26.923 0.00 0.00 0.00 2.17
110 111 7.810766 AATGTTGCATACGGTTAAAGAAATG 57.189 32.000 0.00 0.00 0.00 2.32
111 112 6.320494 TGTTGCATACGGTTAAAGAAATGT 57.680 33.333 0.00 0.00 0.00 2.71
112 113 6.740110 TGTTGCATACGGTTAAAGAAATGTT 58.260 32.000 0.00 0.00 0.00 2.71
113 114 6.638873 TGTTGCATACGGTTAAAGAAATGTTG 59.361 34.615 0.00 0.00 0.00 3.33
114 115 5.157781 TGCATACGGTTAAAGAAATGTTGC 58.842 37.500 0.00 0.00 0.00 4.17
115 116 5.157781 GCATACGGTTAAAGAAATGTTGCA 58.842 37.500 0.00 0.00 0.00 4.08
116 117 5.804979 GCATACGGTTAAAGAAATGTTGCAT 59.195 36.000 0.00 0.00 0.00 3.96
117 118 6.237542 GCATACGGTTAAAGAAATGTTGCATG 60.238 38.462 0.00 0.00 0.00 4.06
118 119 4.555262 ACGGTTAAAGAAATGTTGCATGG 58.445 39.130 0.00 0.00 0.00 3.66
119 120 4.038642 ACGGTTAAAGAAATGTTGCATGGT 59.961 37.500 0.00 0.00 0.00 3.55
120 121 4.621034 CGGTTAAAGAAATGTTGCATGGTC 59.379 41.667 0.00 0.00 0.00 4.02
121 122 4.621034 GGTTAAAGAAATGTTGCATGGTCG 59.379 41.667 0.00 0.00 0.00 4.79
122 123 5.457140 GTTAAAGAAATGTTGCATGGTCGA 58.543 37.500 0.00 0.00 0.00 4.20
123 124 3.559238 AAGAAATGTTGCATGGTCGAC 57.441 42.857 7.13 7.13 0.00 4.20
124 125 2.783135 AGAAATGTTGCATGGTCGACT 58.217 42.857 16.46 0.00 0.00 4.18
125 126 2.485426 AGAAATGTTGCATGGTCGACTG 59.515 45.455 16.46 8.03 0.00 3.51
126 127 2.183478 AATGTTGCATGGTCGACTGA 57.817 45.000 16.46 2.65 0.00 3.41
127 128 1.730501 ATGTTGCATGGTCGACTGAG 58.269 50.000 16.46 6.42 0.00 3.35
128 129 0.678950 TGTTGCATGGTCGACTGAGA 59.321 50.000 16.46 0.00 0.00 3.27
129 130 1.071605 GTTGCATGGTCGACTGAGAC 58.928 55.000 16.46 5.53 40.25 3.36
130 131 0.969149 TTGCATGGTCGACTGAGACT 59.031 50.000 16.46 0.00 40.76 3.24
131 132 0.969149 TGCATGGTCGACTGAGACTT 59.031 50.000 16.46 0.00 40.76 3.01
132 133 1.344438 TGCATGGTCGACTGAGACTTT 59.656 47.619 16.46 0.00 40.76 2.66
133 134 1.728971 GCATGGTCGACTGAGACTTTG 59.271 52.381 16.46 3.37 40.76 2.77
134 135 2.868044 GCATGGTCGACTGAGACTTTGT 60.868 50.000 16.46 0.00 40.76 2.83
135 136 3.393800 CATGGTCGACTGAGACTTTGTT 58.606 45.455 16.46 0.00 40.76 2.83
136 137 4.556233 CATGGTCGACTGAGACTTTGTTA 58.444 43.478 16.46 0.00 40.76 2.41
137 138 4.659111 TGGTCGACTGAGACTTTGTTAA 57.341 40.909 16.46 0.00 40.76 2.01
138 139 5.013568 TGGTCGACTGAGACTTTGTTAAA 57.986 39.130 16.46 0.00 40.76 1.52
139 140 5.607477 TGGTCGACTGAGACTTTGTTAAAT 58.393 37.500 16.46 0.00 40.76 1.40
140 141 5.465390 TGGTCGACTGAGACTTTGTTAAATG 59.535 40.000 16.46 0.00 40.76 2.32
141 142 5.465724 GGTCGACTGAGACTTTGTTAAATGT 59.534 40.000 16.46 0.00 40.76 2.71
142 143 6.346678 GGTCGACTGAGACTTTGTTAAATGTC 60.347 42.308 16.46 0.00 40.76 3.06
143 144 6.200286 GTCGACTGAGACTTTGTTAAATGTCA 59.800 38.462 8.70 0.00 40.96 3.58
144 145 6.420903 TCGACTGAGACTTTGTTAAATGTCAG 59.579 38.462 7.10 0.00 40.96 3.51
145 146 6.201044 CGACTGAGACTTTGTTAAATGTCAGT 59.799 38.462 2.87 2.87 40.96 3.41
146 147 7.484035 ACTGAGACTTTGTTAAATGTCAGTC 57.516 36.000 0.00 0.00 40.96 3.51
147 148 7.047891 ACTGAGACTTTGTTAAATGTCAGTCA 58.952 34.615 0.00 3.28 40.96 3.41
148 149 7.225538 ACTGAGACTTTGTTAAATGTCAGTCAG 59.774 37.037 15.01 15.01 41.92 3.51
149 150 7.272244 TGAGACTTTGTTAAATGTCAGTCAGA 58.728 34.615 0.00 0.00 40.96 3.27
153 154 6.260936 ACTTTGTTAAATGTCAGTCAGACTGG 59.739 38.462 27.15 11.34 45.94 4.00
154 155 5.290493 TGTTAAATGTCAGTCAGACTGGT 57.710 39.130 27.15 13.06 45.94 4.00
155 156 5.680619 TGTTAAATGTCAGTCAGACTGGTT 58.319 37.500 27.15 17.43 45.94 3.67
156 157 6.119536 TGTTAAATGTCAGTCAGACTGGTTT 58.880 36.000 27.15 24.06 45.94 3.27
157 158 6.601613 TGTTAAATGTCAGTCAGACTGGTTTT 59.398 34.615 27.15 23.11 45.94 2.43
158 159 7.122055 TGTTAAATGTCAGTCAGACTGGTTTTT 59.878 33.333 27.15 22.84 45.94 1.94
159 160 8.617809 GTTAAATGTCAGTCAGACTGGTTTTTA 58.382 33.333 27.15 22.04 45.94 1.52
160 161 6.867662 AATGTCAGTCAGACTGGTTTTTAG 57.132 37.500 27.15 2.55 45.94 1.85
161 162 4.127171 TGTCAGTCAGACTGGTTTTTAGC 58.873 43.478 27.15 10.20 45.94 3.09
162 163 4.127171 GTCAGTCAGACTGGTTTTTAGCA 58.873 43.478 27.15 4.86 45.94 3.49
163 164 4.212214 GTCAGTCAGACTGGTTTTTAGCAG 59.788 45.833 27.15 3.05 45.94 4.24
164 165 3.499918 CAGTCAGACTGGTTTTTAGCAGG 59.500 47.826 21.46 0.00 42.35 4.85
165 166 2.226674 GTCAGACTGGTTTTTAGCAGGC 59.773 50.000 1.81 5.77 0.00 4.85
166 167 1.541588 CAGACTGGTTTTTAGCAGGCC 59.458 52.381 6.58 0.00 0.00 5.19
463 464 2.131709 CGTGCCCTTCCCCTCGATA 61.132 63.158 0.00 0.00 0.00 2.92
644 669 1.430228 GAGCCGGAGAGTCTCGAAC 59.570 63.158 13.97 5.54 0.00 3.95
741 788 3.003173 CTGGACTTCGCCTCCCCA 61.003 66.667 0.00 0.00 0.00 4.96
753 803 2.040884 TCCCCATTCTCCCTCCGG 60.041 66.667 0.00 0.00 0.00 5.14
963 1023 2.858868 CTCAGCTTGACACAGCGC 59.141 61.111 0.00 0.00 45.24 5.92
1150 1225 1.560860 GCAGACGGCAGACAGACAAC 61.561 60.000 0.00 0.00 43.97 3.32
1158 1233 3.664107 GGCAGACAGACAACAACAGATA 58.336 45.455 0.00 0.00 0.00 1.98
1159 1234 4.256920 GGCAGACAGACAACAACAGATAT 58.743 43.478 0.00 0.00 0.00 1.63
1284 1386 0.934496 TGCTTTTTCAGGACACGTCG 59.066 50.000 0.00 0.00 0.00 5.12
1453 1559 2.238437 GCTACGCGGAGGCTTAAGC 61.238 63.158 22.20 19.53 41.14 3.09
1471 1577 3.788227 AGCTCGTCCTAGAGAGATCAT 57.212 47.619 12.10 0.00 40.57 2.45
1488 1594 3.735237 TCATCGGTAATTCTCTGCTCC 57.265 47.619 0.00 0.00 0.00 4.70
1738 2727 2.435805 TGAAGCTGTCACAAGAGACCTT 59.564 45.455 0.00 0.00 37.73 3.50
1914 3126 7.252965 TGTGTAAGATTCGTCAAAAATGTGA 57.747 32.000 0.00 0.00 0.00 3.58
2156 3376 4.096682 TGCCCTACTGTTTTGTGTTTGTAC 59.903 41.667 0.00 0.00 0.00 2.90
2178 3400 7.665559 TGTACTTGATTTTCTTGGTTAGCTGAT 59.334 33.333 0.00 0.00 0.00 2.90
2210 3433 1.078490 TGAATTCATTGGCCTTGGGGA 59.922 47.619 3.38 0.00 33.58 4.81
2485 3786 1.734465 CACTGATCGGAGCTTGTTTCC 59.266 52.381 9.00 0.00 0.00 3.13
2599 4044 7.129457 AGGTGCTCAGATAAATCTTGTATGA 57.871 36.000 0.00 0.00 34.22 2.15
2674 4127 6.926272 AGTCAATTACTCGAAGCTGATTATCC 59.074 38.462 0.00 0.00 30.33 2.59
2677 4130 5.854010 TTACTCGAAGCTGATTATCCTGT 57.146 39.130 0.00 0.00 0.00 4.00
2678 4131 4.744795 ACTCGAAGCTGATTATCCTGTT 57.255 40.909 0.00 0.00 0.00 3.16
2679 4132 5.854010 ACTCGAAGCTGATTATCCTGTTA 57.146 39.130 0.00 0.00 0.00 2.41
2680 4133 6.222038 ACTCGAAGCTGATTATCCTGTTAA 57.778 37.500 0.00 0.00 0.00 2.01
2681 4134 6.276847 ACTCGAAGCTGATTATCCTGTTAAG 58.723 40.000 0.00 0.00 0.00 1.85
2682 4135 5.050490 TCGAAGCTGATTATCCTGTTAAGC 58.950 41.667 0.00 0.00 0.00 3.09
2709 4169 3.522553 CCTATGGTTTCAGTTCCTCGTC 58.477 50.000 0.00 0.00 0.00 4.20
2740 4202 0.380378 ACGACGCACTGCATGTTTTT 59.620 45.000 1.11 0.00 0.00 1.94
2840 4340 6.294787 CCAAACGGCTCTGTGAGATATATAGT 60.295 42.308 0.00 0.00 0.00 2.12
2935 4440 5.230726 GCATCTTTGTGTCACTTCTGTTTTG 59.769 40.000 4.27 0.00 0.00 2.44
2981 4486 1.286880 GCAACAGGAGCATTGCGTT 59.713 52.632 2.38 0.00 41.61 4.84
3020 4540 1.663643 TGATTATTGGCGACGCTTGTC 59.336 47.619 20.77 9.93 39.33 3.18
3034 4554 0.368227 CTTGTCGCTCGAGTGCAATC 59.632 55.000 25.28 3.54 0.00 2.67
3075 4595 1.734465 CTGCCGTTGATTCAGAACTCC 59.266 52.381 0.00 0.00 0.00 3.85
3101 4623 4.212143 AGCTCTGATTGCTGATACAACA 57.788 40.909 0.00 0.00 39.56 3.33
3115 4637 2.184167 CAACACCGACGGCAAAGGT 61.184 57.895 15.39 1.69 39.12 3.50
3173 4709 4.448210 AGATGAGTTTGTAACACCGTTGT 58.552 39.130 0.00 0.00 37.67 3.32
3207 4747 2.805353 CTCCGCTGAACACCGTCG 60.805 66.667 0.00 0.00 0.00 5.12
3254 4794 5.305585 TCTTTTGTGAAGGGAGACATGTAC 58.694 41.667 0.00 0.00 0.00 2.90
3296 4836 3.091545 CCTTTGTGTATGCCCATGAACT 58.908 45.455 0.00 0.00 0.00 3.01
3318 4858 3.966979 TCATTAGGCAATGAAGCTTCCA 58.033 40.909 23.42 11.98 45.93 3.53
3319 4859 3.949754 TCATTAGGCAATGAAGCTTCCAG 59.050 43.478 23.42 13.73 45.93 3.86
3320 4860 3.719268 TTAGGCAATGAAGCTTCCAGA 57.281 42.857 23.42 5.68 34.17 3.86
3321 4861 1.831580 AGGCAATGAAGCTTCCAGAC 58.168 50.000 23.42 14.82 34.17 3.51
3322 4862 1.353694 AGGCAATGAAGCTTCCAGACT 59.646 47.619 23.42 16.78 34.17 3.24
3323 4863 1.471684 GGCAATGAAGCTTCCAGACTG 59.528 52.381 23.42 13.41 34.17 3.51
3324 4864 1.135460 GCAATGAAGCTTCCAGACTGC 60.135 52.381 23.42 18.48 0.00 4.40
3325 4865 2.156917 CAATGAAGCTTCCAGACTGCA 58.843 47.619 23.42 3.26 0.00 4.41
3326 4866 2.555325 CAATGAAGCTTCCAGACTGCAA 59.445 45.455 23.42 1.79 0.00 4.08
3327 4867 1.597742 TGAAGCTTCCAGACTGCAAC 58.402 50.000 23.42 0.00 0.00 4.17
3328 4868 0.877743 GAAGCTTCCAGACTGCAACC 59.122 55.000 15.97 0.00 0.00 3.77
3329 4869 0.183492 AAGCTTCCAGACTGCAACCA 59.817 50.000 0.00 0.00 0.00 3.67
3330 4870 0.183492 AGCTTCCAGACTGCAACCAA 59.817 50.000 0.00 0.00 0.00 3.67
3331 4871 0.312102 GCTTCCAGACTGCAACCAAC 59.688 55.000 0.00 0.00 0.00 3.77
3332 4872 0.954452 CTTCCAGACTGCAACCAACC 59.046 55.000 0.00 0.00 0.00 3.77
3333 4873 0.817634 TTCCAGACTGCAACCAACCG 60.818 55.000 0.00 0.00 0.00 4.44
3334 4874 1.227823 CCAGACTGCAACCAACCGA 60.228 57.895 0.00 0.00 0.00 4.69
3335 4875 1.230635 CCAGACTGCAACCAACCGAG 61.231 60.000 0.00 0.00 0.00 4.63
3336 4876 0.249868 CAGACTGCAACCAACCGAGA 60.250 55.000 0.00 0.00 0.00 4.04
3337 4877 0.687354 AGACTGCAACCAACCGAGAT 59.313 50.000 0.00 0.00 0.00 2.75
3338 4878 1.899814 AGACTGCAACCAACCGAGATA 59.100 47.619 0.00 0.00 0.00 1.98
3339 4879 2.301870 AGACTGCAACCAACCGAGATAA 59.698 45.455 0.00 0.00 0.00 1.75
3340 4880 3.071479 GACTGCAACCAACCGAGATAAA 58.929 45.455 0.00 0.00 0.00 1.40
3341 4881 2.812011 ACTGCAACCAACCGAGATAAAC 59.188 45.455 0.00 0.00 0.00 2.01
3342 4882 2.811431 CTGCAACCAACCGAGATAAACA 59.189 45.455 0.00 0.00 0.00 2.83
3343 4883 3.215151 TGCAACCAACCGAGATAAACAA 58.785 40.909 0.00 0.00 0.00 2.83
3344 4884 3.632604 TGCAACCAACCGAGATAAACAAA 59.367 39.130 0.00 0.00 0.00 2.83
3345 4885 3.978855 GCAACCAACCGAGATAAACAAAC 59.021 43.478 0.00 0.00 0.00 2.93
3346 4886 4.498345 GCAACCAACCGAGATAAACAAACA 60.498 41.667 0.00 0.00 0.00 2.83
3347 4887 5.212194 CAACCAACCGAGATAAACAAACAG 58.788 41.667 0.00 0.00 0.00 3.16
3348 4888 3.818773 ACCAACCGAGATAAACAAACAGG 59.181 43.478 0.00 0.00 0.00 4.00
3349 4889 3.190535 CCAACCGAGATAAACAAACAGGG 59.809 47.826 0.00 0.00 0.00 4.45
3350 4890 2.433436 ACCGAGATAAACAAACAGGGC 58.567 47.619 0.00 0.00 0.00 5.19
3351 4891 2.224670 ACCGAGATAAACAAACAGGGCA 60.225 45.455 0.00 0.00 0.00 5.36
3352 4892 2.161609 CCGAGATAAACAAACAGGGCAC 59.838 50.000 0.00 0.00 0.00 5.01
3353 4893 2.811431 CGAGATAAACAAACAGGGCACA 59.189 45.455 0.00 0.00 0.00 4.57
3354 4894 3.252215 CGAGATAAACAAACAGGGCACAA 59.748 43.478 0.00 0.00 0.00 3.33
3355 4895 4.613622 CGAGATAAACAAACAGGGCACAAG 60.614 45.833 0.00 0.00 0.00 3.16
3356 4896 4.215109 AGATAAACAAACAGGGCACAAGT 58.785 39.130 0.00 0.00 0.00 3.16
3357 4897 5.381757 AGATAAACAAACAGGGCACAAGTA 58.618 37.500 0.00 0.00 0.00 2.24
3358 4898 3.793797 AAACAAACAGGGCACAAGTAC 57.206 42.857 0.00 0.00 0.00 2.73
3359 4899 2.428544 ACAAACAGGGCACAAGTACA 57.571 45.000 0.00 0.00 0.00 2.90
3360 4900 2.729194 ACAAACAGGGCACAAGTACAA 58.271 42.857 0.00 0.00 0.00 2.41
3361 4901 2.687935 ACAAACAGGGCACAAGTACAAG 59.312 45.455 0.00 0.00 0.00 3.16
3362 4902 2.687935 CAAACAGGGCACAAGTACAAGT 59.312 45.455 0.00 0.00 0.00 3.16
3363 4903 1.967319 ACAGGGCACAAGTACAAGTG 58.033 50.000 11.94 11.94 38.74 3.16
3369 4909 0.593128 CACAAGTACAAGTGCTGGGC 59.407 55.000 5.00 0.00 0.00 5.36
3370 4910 0.182537 ACAAGTACAAGTGCTGGGCA 59.817 50.000 0.00 0.00 35.60 5.36
3392 4932 4.460948 CCATTTGGTGATCCTCCTTTTG 57.539 45.455 5.78 1.70 34.23 2.44
3393 4933 3.834231 CCATTTGGTGATCCTCCTTTTGT 59.166 43.478 5.78 0.00 34.23 2.83
3394 4934 4.284234 CCATTTGGTGATCCTCCTTTTGTT 59.716 41.667 5.78 0.00 34.23 2.83
3395 4935 5.473039 CATTTGGTGATCCTCCTTTTGTTC 58.527 41.667 5.78 0.00 34.23 3.18
3396 4936 3.874383 TGGTGATCCTCCTTTTGTTCA 57.126 42.857 5.78 0.00 34.23 3.18
3397 4937 4.387026 TGGTGATCCTCCTTTTGTTCAT 57.613 40.909 5.78 0.00 34.23 2.57
3398 4938 5.512942 TGGTGATCCTCCTTTTGTTCATA 57.487 39.130 5.78 0.00 34.23 2.15
3399 4939 6.078456 TGGTGATCCTCCTTTTGTTCATAT 57.922 37.500 5.78 0.00 34.23 1.78
3400 4940 6.493166 TGGTGATCCTCCTTTTGTTCATATT 58.507 36.000 5.78 0.00 34.23 1.28
3401 4941 6.953520 TGGTGATCCTCCTTTTGTTCATATTT 59.046 34.615 5.78 0.00 34.23 1.40
3402 4942 7.093814 TGGTGATCCTCCTTTTGTTCATATTTG 60.094 37.037 5.78 0.00 34.23 2.32
3403 4943 6.753744 GTGATCCTCCTTTTGTTCATATTTGC 59.246 38.462 0.00 0.00 0.00 3.68
3404 4944 6.664816 TGATCCTCCTTTTGTTCATATTTGCT 59.335 34.615 0.00 0.00 0.00 3.91
3405 4945 7.833682 TGATCCTCCTTTTGTTCATATTTGCTA 59.166 33.333 0.00 0.00 0.00 3.49
3406 4946 8.593945 ATCCTCCTTTTGTTCATATTTGCTAA 57.406 30.769 0.00 0.00 0.00 3.09
3407 4947 8.415950 TCCTCCTTTTGTTCATATTTGCTAAA 57.584 30.769 0.00 0.00 0.00 1.85
3408 4948 8.865090 TCCTCCTTTTGTTCATATTTGCTAAAA 58.135 29.630 0.00 0.00 0.00 1.52
3409 4949 9.657419 CCTCCTTTTGTTCATATTTGCTAAAAT 57.343 29.630 0.00 0.00 39.38 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.374125 CGTCATCTCACCGGTTGCA 60.374 57.895 2.97 0.00 0.00 4.08
3 4 1.374252 ACGTCATCTCACCGGTTGC 60.374 57.895 2.97 0.00 0.00 4.17
4 5 1.626654 GCACGTCATCTCACCGGTTG 61.627 60.000 2.97 0.00 0.00 3.77
5 6 1.374252 GCACGTCATCTCACCGGTT 60.374 57.895 2.97 0.00 0.00 4.44
6 7 0.963856 TAGCACGTCATCTCACCGGT 60.964 55.000 0.00 0.00 0.00 5.28
7 8 0.525668 GTAGCACGTCATCTCACCGG 60.526 60.000 0.00 0.00 0.00 5.28
8 9 0.170339 TGTAGCACGTCATCTCACCG 59.830 55.000 0.00 0.00 0.00 4.94
9 10 2.363788 TTGTAGCACGTCATCTCACC 57.636 50.000 0.00 0.00 0.00 4.02
10 11 3.926527 TCATTTGTAGCACGTCATCTCAC 59.073 43.478 0.00 0.00 0.00 3.51
11 12 4.176271 CTCATTTGTAGCACGTCATCTCA 58.824 43.478 0.00 0.00 0.00 3.27
12 13 3.553511 CCTCATTTGTAGCACGTCATCTC 59.446 47.826 0.00 0.00 0.00 2.75
13 14 3.195610 TCCTCATTTGTAGCACGTCATCT 59.804 43.478 0.00 0.00 0.00 2.90
14 15 3.521560 TCCTCATTTGTAGCACGTCATC 58.478 45.455 0.00 0.00 0.00 2.92
15 16 3.525537 CTCCTCATTTGTAGCACGTCAT 58.474 45.455 0.00 0.00 0.00 3.06
16 17 2.353704 CCTCCTCATTTGTAGCACGTCA 60.354 50.000 0.00 0.00 0.00 4.35
17 18 2.271800 CCTCCTCATTTGTAGCACGTC 58.728 52.381 0.00 0.00 0.00 4.34
18 19 1.066143 CCCTCCTCATTTGTAGCACGT 60.066 52.381 0.00 0.00 0.00 4.49
19 20 1.207089 TCCCTCCTCATTTGTAGCACG 59.793 52.381 0.00 0.00 0.00 5.34
20 21 3.118261 TCATCCCTCCTCATTTGTAGCAC 60.118 47.826 0.00 0.00 0.00 4.40
21 22 3.114606 TCATCCCTCCTCATTTGTAGCA 58.885 45.455 0.00 0.00 0.00 3.49
22 23 3.118261 TGTCATCCCTCCTCATTTGTAGC 60.118 47.826 0.00 0.00 0.00 3.58
23 24 4.760530 TGTCATCCCTCCTCATTTGTAG 57.239 45.455 0.00 0.00 0.00 2.74
24 25 4.686944 GCATGTCATCCCTCCTCATTTGTA 60.687 45.833 0.00 0.00 0.00 2.41
25 26 3.894759 CATGTCATCCCTCCTCATTTGT 58.105 45.455 0.00 0.00 0.00 2.83
26 27 2.621998 GCATGTCATCCCTCCTCATTTG 59.378 50.000 0.00 0.00 0.00 2.32
27 28 2.512896 AGCATGTCATCCCTCCTCATTT 59.487 45.455 0.00 0.00 0.00 2.32
28 29 2.133520 AGCATGTCATCCCTCCTCATT 58.866 47.619 0.00 0.00 0.00 2.57
29 30 1.817087 AGCATGTCATCCCTCCTCAT 58.183 50.000 0.00 0.00 0.00 2.90
30 31 1.487976 GAAGCATGTCATCCCTCCTCA 59.512 52.381 0.00 0.00 0.00 3.86
31 32 1.487976 TGAAGCATGTCATCCCTCCTC 59.512 52.381 0.00 0.00 0.00 3.71
32 33 1.588239 TGAAGCATGTCATCCCTCCT 58.412 50.000 0.00 0.00 0.00 3.69
33 34 2.019984 GTTGAAGCATGTCATCCCTCC 58.980 52.381 0.00 0.00 0.00 4.30
34 35 2.019984 GGTTGAAGCATGTCATCCCTC 58.980 52.381 0.00 0.00 33.08 4.30
35 36 1.355381 TGGTTGAAGCATGTCATCCCT 59.645 47.619 9.71 0.00 36.80 4.20
36 37 1.838112 TGGTTGAAGCATGTCATCCC 58.162 50.000 9.71 4.23 36.80 3.85
37 38 2.557924 TGTTGGTTGAAGCATGTCATCC 59.442 45.455 0.00 6.51 37.73 3.51
38 39 3.921119 TGTTGGTTGAAGCATGTCATC 57.079 42.857 0.00 0.00 0.00 2.92
39 40 4.669206 TTTGTTGGTTGAAGCATGTCAT 57.331 36.364 0.00 0.00 0.00 3.06
40 41 4.081752 AGTTTTGTTGGTTGAAGCATGTCA 60.082 37.500 0.00 0.00 0.00 3.58
41 42 4.432712 AGTTTTGTTGGTTGAAGCATGTC 58.567 39.130 0.00 0.00 0.00 3.06
42 43 4.470334 AGTTTTGTTGGTTGAAGCATGT 57.530 36.364 0.00 0.00 0.00 3.21
43 44 6.479660 ACATTAGTTTTGTTGGTTGAAGCATG 59.520 34.615 0.00 0.00 0.00 4.06
44 45 6.581712 ACATTAGTTTTGTTGGTTGAAGCAT 58.418 32.000 0.00 0.00 0.00 3.79
45 46 5.971763 ACATTAGTTTTGTTGGTTGAAGCA 58.028 33.333 0.00 0.00 0.00 3.91
46 47 6.704819 CAACATTAGTTTTGTTGGTTGAAGC 58.295 36.000 8.33 0.00 46.46 3.86
55 56 4.116238 CCGGTTGCAACATTAGTTTTGTT 58.884 39.130 29.55 0.00 37.79 2.83
56 57 3.131400 ACCGGTTGCAACATTAGTTTTGT 59.869 39.130 29.55 10.27 35.28 2.83
57 58 3.712187 ACCGGTTGCAACATTAGTTTTG 58.288 40.909 29.55 9.70 35.28 2.44
58 59 5.241949 TCATACCGGTTGCAACATTAGTTTT 59.758 36.000 29.55 9.87 35.28 2.43
59 60 4.762765 TCATACCGGTTGCAACATTAGTTT 59.237 37.500 29.55 13.16 35.28 2.66
60 61 4.328536 TCATACCGGTTGCAACATTAGTT 58.671 39.130 29.55 9.86 38.88 2.24
61 62 3.945346 TCATACCGGTTGCAACATTAGT 58.055 40.909 29.55 21.08 0.00 2.24
62 63 4.955925 TTCATACCGGTTGCAACATTAG 57.044 40.909 29.55 16.86 0.00 1.73
63 64 5.707242 TTTTCATACCGGTTGCAACATTA 57.293 34.783 29.55 17.17 0.00 1.90
64 65 4.592485 TTTTCATACCGGTTGCAACATT 57.408 36.364 29.55 15.62 0.00 2.71
65 66 4.592485 TTTTTCATACCGGTTGCAACAT 57.408 36.364 29.55 17.03 0.00 2.71
83 84 8.649973 TTTCTTTAACCGTATGCAACATTTTT 57.350 26.923 0.00 0.00 0.00 1.94
84 85 8.707839 CATTTCTTTAACCGTATGCAACATTTT 58.292 29.630 0.00 0.00 0.00 1.82
85 86 7.870445 ACATTTCTTTAACCGTATGCAACATTT 59.130 29.630 0.00 0.00 0.00 2.32
86 87 7.375053 ACATTTCTTTAACCGTATGCAACATT 58.625 30.769 0.00 0.00 0.00 2.71
87 88 6.919721 ACATTTCTTTAACCGTATGCAACAT 58.080 32.000 0.00 0.00 0.00 2.71
88 89 6.320494 ACATTTCTTTAACCGTATGCAACA 57.680 33.333 0.00 0.00 0.00 3.33
89 90 6.399564 GCAACATTTCTTTAACCGTATGCAAC 60.400 38.462 0.00 0.00 0.00 4.17
90 91 5.631512 GCAACATTTCTTTAACCGTATGCAA 59.368 36.000 0.00 0.00 0.00 4.08
91 92 5.157781 GCAACATTTCTTTAACCGTATGCA 58.842 37.500 0.00 0.00 0.00 3.96
92 93 5.157781 TGCAACATTTCTTTAACCGTATGC 58.842 37.500 0.00 0.00 0.00 3.14
93 94 6.253298 CCATGCAACATTTCTTTAACCGTATG 59.747 38.462 0.00 0.00 0.00 2.39
94 95 6.071616 ACCATGCAACATTTCTTTAACCGTAT 60.072 34.615 0.00 0.00 0.00 3.06
95 96 5.241949 ACCATGCAACATTTCTTTAACCGTA 59.758 36.000 0.00 0.00 0.00 4.02
96 97 4.038642 ACCATGCAACATTTCTTTAACCGT 59.961 37.500 0.00 0.00 0.00 4.83
97 98 4.555262 ACCATGCAACATTTCTTTAACCG 58.445 39.130 0.00 0.00 0.00 4.44
98 99 4.621034 CGACCATGCAACATTTCTTTAACC 59.379 41.667 0.00 0.00 0.00 2.85
99 100 5.342259 GTCGACCATGCAACATTTCTTTAAC 59.658 40.000 3.51 0.00 0.00 2.01
100 101 5.240623 AGTCGACCATGCAACATTTCTTTAA 59.759 36.000 13.01 0.00 0.00 1.52
101 102 4.759693 AGTCGACCATGCAACATTTCTTTA 59.240 37.500 13.01 0.00 0.00 1.85
102 103 3.569701 AGTCGACCATGCAACATTTCTTT 59.430 39.130 13.01 0.00 0.00 2.52
103 104 3.058016 CAGTCGACCATGCAACATTTCTT 60.058 43.478 13.01 0.00 0.00 2.52
104 105 2.485426 CAGTCGACCATGCAACATTTCT 59.515 45.455 13.01 0.00 0.00 2.52
105 106 2.483877 TCAGTCGACCATGCAACATTTC 59.516 45.455 13.01 0.00 0.00 2.17
106 107 2.485426 CTCAGTCGACCATGCAACATTT 59.515 45.455 13.01 0.00 0.00 2.32
107 108 2.079158 CTCAGTCGACCATGCAACATT 58.921 47.619 13.01 0.00 0.00 2.71
108 109 1.276138 TCTCAGTCGACCATGCAACAT 59.724 47.619 13.01 0.00 0.00 2.71
109 110 0.678950 TCTCAGTCGACCATGCAACA 59.321 50.000 13.01 0.00 0.00 3.33
110 111 1.071605 GTCTCAGTCGACCATGCAAC 58.928 55.000 13.01 3.16 0.00 4.17
111 112 0.969149 AGTCTCAGTCGACCATGCAA 59.031 50.000 13.01 0.00 34.46 4.08
112 113 0.969149 AAGTCTCAGTCGACCATGCA 59.031 50.000 13.01 0.00 34.46 3.96
113 114 1.728971 CAAAGTCTCAGTCGACCATGC 59.271 52.381 13.01 0.00 34.46 4.06
114 115 3.032017 ACAAAGTCTCAGTCGACCATG 57.968 47.619 13.01 5.07 34.46 3.66
115 116 3.753294 AACAAAGTCTCAGTCGACCAT 57.247 42.857 13.01 0.00 34.46 3.55
116 117 4.659111 TTAACAAAGTCTCAGTCGACCA 57.341 40.909 13.01 0.00 34.46 4.02
117 118 5.465724 ACATTTAACAAAGTCTCAGTCGACC 59.534 40.000 13.01 0.00 34.46 4.79
118 119 6.200286 TGACATTTAACAAAGTCTCAGTCGAC 59.800 38.462 7.70 7.70 32.41 4.20
119 120 6.277605 TGACATTTAACAAAGTCTCAGTCGA 58.722 36.000 0.00 0.00 32.41 4.20
120 121 6.201044 ACTGACATTTAACAAAGTCTCAGTCG 59.799 38.462 0.00 0.00 33.46 4.18
121 122 7.484035 ACTGACATTTAACAAAGTCTCAGTC 57.516 36.000 0.00 0.00 33.46 3.51
122 123 7.047891 TGACTGACATTTAACAAAGTCTCAGT 58.952 34.615 0.00 0.00 39.79 3.41
123 124 7.439356 TCTGACTGACATTTAACAAAGTCTCAG 59.561 37.037 0.00 0.00 35.94 3.35
124 125 7.224753 GTCTGACTGACATTTAACAAAGTCTCA 59.775 37.037 7.54 0.00 44.73 3.27
125 126 7.568433 GTCTGACTGACATTTAACAAAGTCTC 58.432 38.462 7.54 0.00 44.73 3.36
126 127 7.484035 GTCTGACTGACATTTAACAAAGTCT 57.516 36.000 7.54 0.00 44.73 3.24
142 143 3.499918 CCTGCTAAAAACCAGTCTGACTG 59.500 47.826 26.94 26.94 45.53 3.51
143 144 3.744660 CCTGCTAAAAACCAGTCTGACT 58.255 45.455 4.06 4.06 0.00 3.41
144 145 2.226674 GCCTGCTAAAAACCAGTCTGAC 59.773 50.000 0.00 0.00 0.00 3.51
145 146 2.504367 GCCTGCTAAAAACCAGTCTGA 58.496 47.619 0.00 0.00 0.00 3.27
146 147 1.541588 GGCCTGCTAAAAACCAGTCTG 59.458 52.381 0.00 0.00 0.00 3.51
147 148 1.547901 GGGCCTGCTAAAAACCAGTCT 60.548 52.381 0.84 0.00 0.00 3.24
148 149 0.888619 GGGCCTGCTAAAAACCAGTC 59.111 55.000 0.84 0.00 0.00 3.51
149 150 0.893727 CGGGCCTGCTAAAAACCAGT 60.894 55.000 0.84 0.00 0.00 4.00
150 151 0.893727 ACGGGCCTGCTAAAAACCAG 60.894 55.000 12.89 0.00 0.00 4.00
151 152 0.400975 TACGGGCCTGCTAAAAACCA 59.599 50.000 12.89 0.00 0.00 3.67
152 153 0.806868 GTACGGGCCTGCTAAAAACC 59.193 55.000 12.89 0.00 0.00 3.27
153 154 1.817357 AGTACGGGCCTGCTAAAAAC 58.183 50.000 12.89 0.49 0.00 2.43
154 155 2.156098 CAAGTACGGGCCTGCTAAAAA 58.844 47.619 12.89 0.00 0.00 1.94
155 156 1.816074 CAAGTACGGGCCTGCTAAAA 58.184 50.000 12.89 0.00 0.00 1.52
156 157 0.675522 GCAAGTACGGGCCTGCTAAA 60.676 55.000 12.89 0.00 0.00 1.85
157 158 1.078708 GCAAGTACGGGCCTGCTAA 60.079 57.895 12.89 0.00 0.00 3.09
158 159 1.956629 GAGCAAGTACGGGCCTGCTA 61.957 60.000 16.23 0.11 32.34 3.49
159 160 3.316573 GAGCAAGTACGGGCCTGCT 62.317 63.158 16.21 16.21 35.13 4.24
160 161 2.820037 GAGCAAGTACGGGCCTGC 60.820 66.667 12.89 8.05 0.00 4.85
161 162 1.448540 CTGAGCAAGTACGGGCCTG 60.449 63.158 11.02 11.02 0.00 4.85
162 163 1.608717 CTCTGAGCAAGTACGGGCCT 61.609 60.000 0.84 0.00 0.00 5.19
163 164 1.153549 CTCTGAGCAAGTACGGGCC 60.154 63.158 0.00 0.00 0.00 5.80
164 165 0.737715 CACTCTGAGCAAGTACGGGC 60.738 60.000 4.19 3.91 0.00 6.13
165 166 0.888619 TCACTCTGAGCAAGTACGGG 59.111 55.000 4.19 0.00 0.00 5.28
166 167 1.813178 TCTCACTCTGAGCAAGTACGG 59.187 52.381 4.19 0.00 43.95 4.02
187 188 0.664767 GACTGTGCAGTCGACCACTC 60.665 60.000 20.75 11.86 46.93 3.51
189 190 3.938112 GACTGTGCAGTCGACCAC 58.062 61.111 13.01 14.53 46.93 4.16
507 508 1.379977 ACGCGGATCTTGAGGAGGA 60.380 57.895 12.47 0.00 0.00 3.71
554 561 0.178964 TGCTTCTTGGGGTTGGGAAG 60.179 55.000 0.00 0.00 38.42 3.46
680 726 1.443407 CGAGGCAGGTCGATGGAAT 59.557 57.895 0.00 0.00 42.85 3.01
682 728 3.838271 GCGAGGCAGGTCGATGGA 61.838 66.667 6.55 0.00 42.85 3.41
717 764 3.188786 GCGAAGTCCAGCGCGATT 61.189 61.111 12.10 0.00 43.96 3.34
1150 1225 4.309933 TGCAGCGAGGATAATATCTGTTG 58.690 43.478 0.00 1.36 0.00 3.33
1158 1233 4.558095 GCATGAATTTGCAGCGAGGATAAT 60.558 41.667 0.00 0.00 42.31 1.28
1159 1234 3.243168 GCATGAATTTGCAGCGAGGATAA 60.243 43.478 0.00 0.00 42.31 1.75
1453 1559 3.000041 CCGATGATCTCTCTAGGACGAG 59.000 54.545 0.00 0.00 0.00 4.18
1471 1577 1.758936 TCGGAGCAGAGAATTACCGA 58.241 50.000 0.00 0.00 45.36 4.69
1592 2581 3.448301 CAGCCAAGCAGATAATTTGGGAA 59.552 43.478 4.82 0.00 41.28 3.97
1738 2727 2.689471 GTGCATCCATCATTACTTGCCA 59.311 45.455 0.00 0.00 0.00 4.92
1816 2813 4.469586 TGCCAAACATATACTCACCAGAGA 59.530 41.667 0.00 0.00 44.98 3.10
1881 3084 7.821595 TGACGAATCTTACACAACGATTAAT 57.178 32.000 0.00 0.00 0.00 1.40
1914 3126 5.428253 ACTCTATAATTGGCATGTCAACGT 58.572 37.500 16.33 9.08 0.00 3.99
2156 3376 6.917533 ACATCAGCTAACCAAGAAAATCAAG 58.082 36.000 0.00 0.00 0.00 3.02
2210 3433 4.973168 TGCAGAAGAGAGTTTGTACCAAT 58.027 39.130 0.00 0.00 0.00 3.16
2307 3550 7.041508 ACTGTCTTTTTGCTACAGAATTCAGAG 60.042 37.037 8.44 2.74 42.59 3.35
2312 3555 8.000780 AGAAACTGTCTTTTTGCTACAGAATT 57.999 30.769 8.57 3.64 42.59 2.17
2599 4044 2.684001 TGGTCGAACGGCATAGAAAT 57.316 45.000 0.00 0.00 0.00 2.17
2674 4127 6.374333 TGAAACCATAGGCTTAAGCTTAACAG 59.626 38.462 25.88 16.91 41.70 3.16
2677 4130 6.481643 ACTGAAACCATAGGCTTAAGCTTAA 58.518 36.000 25.88 17.71 41.70 1.85
2678 4131 6.062258 ACTGAAACCATAGGCTTAAGCTTA 57.938 37.500 25.88 22.97 41.70 3.09
2679 4132 4.923415 ACTGAAACCATAGGCTTAAGCTT 58.077 39.130 25.88 21.50 41.70 3.74
2680 4133 4.576330 ACTGAAACCATAGGCTTAAGCT 57.424 40.909 25.88 14.65 41.70 3.74
2681 4134 4.096532 GGAACTGAAACCATAGGCTTAAGC 59.903 45.833 19.53 19.53 41.14 3.09
2682 4135 5.501156 AGGAACTGAAACCATAGGCTTAAG 58.499 41.667 0.00 0.00 37.18 1.85
2709 4169 4.302765 CGTCGTCGCAATGAAACG 57.697 55.556 2.15 2.15 37.74 3.60
2740 4202 3.133901 TGCAGATCATTTTACTCCCGCTA 59.866 43.478 0.00 0.00 0.00 4.26
2872 4372 7.885922 TCATATAAGGTGCAGTAGTTGGAAAAA 59.114 33.333 0.00 0.00 0.00 1.94
2935 4440 3.126514 CACAAGATGACACAGATTCTGCC 59.873 47.826 13.64 4.27 34.37 4.85
2981 4486 4.299586 TCAACTTCCACCTTGCATATCA 57.700 40.909 0.00 0.00 0.00 2.15
3020 4540 1.135046 CCATAGATTGCACTCGAGCG 58.865 55.000 13.61 3.64 37.31 5.03
3034 4554 0.811915 CCGGATACCTCTCGCCATAG 59.188 60.000 0.00 0.00 0.00 2.23
3075 4595 4.874396 TGTATCAGCAATCAGAGCTTCAAG 59.126 41.667 0.00 0.00 41.14 3.02
3101 4623 2.590575 CACACCTTTGCCGTCGGT 60.591 61.111 13.94 0.00 0.00 4.69
3115 4637 2.037902 TCACTCAAGCCGAATAACCACA 59.962 45.455 0.00 0.00 0.00 4.17
3173 4709 0.963962 GAGTCCACGTTGTACCAGGA 59.036 55.000 0.00 0.00 0.00 3.86
3186 4726 2.741092 GGTGTTCAGCGGAGTCCA 59.259 61.111 10.49 0.00 0.00 4.02
3207 4747 2.811431 GGCACAAAATTTTACAAGGCCC 59.189 45.455 2.44 0.00 32.89 5.80
3254 4794 0.459585 TTCGAAGGATCCGAAAGCCG 60.460 55.000 5.98 5.25 42.18 5.52
3315 4855 1.227823 CGGTTGGTTGCAGTCTGGA 60.228 57.895 1.14 0.00 0.00 3.86
3316 4856 1.227823 TCGGTTGGTTGCAGTCTGG 60.228 57.895 1.14 0.00 0.00 3.86
3317 4857 0.249868 TCTCGGTTGGTTGCAGTCTG 60.250 55.000 0.00 0.00 0.00 3.51
3318 4858 0.687354 ATCTCGGTTGGTTGCAGTCT 59.313 50.000 0.00 0.00 0.00 3.24
3319 4859 2.380084 TATCTCGGTTGGTTGCAGTC 57.620 50.000 0.00 0.00 0.00 3.51
3320 4860 2.812011 GTTTATCTCGGTTGGTTGCAGT 59.188 45.455 0.00 0.00 0.00 4.40
3321 4861 2.811431 TGTTTATCTCGGTTGGTTGCAG 59.189 45.455 0.00 0.00 0.00 4.41
3322 4862 2.852449 TGTTTATCTCGGTTGGTTGCA 58.148 42.857 0.00 0.00 0.00 4.08
3323 4863 3.907894 TTGTTTATCTCGGTTGGTTGC 57.092 42.857 0.00 0.00 0.00 4.17
3324 4864 5.176407 TGTTTGTTTATCTCGGTTGGTTG 57.824 39.130 0.00 0.00 0.00 3.77
3325 4865 4.277423 CCTGTTTGTTTATCTCGGTTGGTT 59.723 41.667 0.00 0.00 0.00 3.67
3326 4866 3.818773 CCTGTTTGTTTATCTCGGTTGGT 59.181 43.478 0.00 0.00 0.00 3.67
3327 4867 3.190535 CCCTGTTTGTTTATCTCGGTTGG 59.809 47.826 0.00 0.00 0.00 3.77
3328 4868 3.365969 GCCCTGTTTGTTTATCTCGGTTG 60.366 47.826 0.00 0.00 0.00 3.77
3329 4869 2.817844 GCCCTGTTTGTTTATCTCGGTT 59.182 45.455 0.00 0.00 0.00 4.44
3330 4870 2.224670 TGCCCTGTTTGTTTATCTCGGT 60.225 45.455 0.00 0.00 0.00 4.69
3331 4871 2.161609 GTGCCCTGTTTGTTTATCTCGG 59.838 50.000 0.00 0.00 0.00 4.63
3332 4872 2.811431 TGTGCCCTGTTTGTTTATCTCG 59.189 45.455 0.00 0.00 0.00 4.04
3333 4873 4.278419 ACTTGTGCCCTGTTTGTTTATCTC 59.722 41.667 0.00 0.00 0.00 2.75
3334 4874 4.215109 ACTTGTGCCCTGTTTGTTTATCT 58.785 39.130 0.00 0.00 0.00 1.98
3335 4875 4.584327 ACTTGTGCCCTGTTTGTTTATC 57.416 40.909 0.00 0.00 0.00 1.75
3336 4876 4.890581 TGTACTTGTGCCCTGTTTGTTTAT 59.109 37.500 0.00 0.00 0.00 1.40
3337 4877 4.270834 TGTACTTGTGCCCTGTTTGTTTA 58.729 39.130 0.00 0.00 0.00 2.01
3338 4878 3.093057 TGTACTTGTGCCCTGTTTGTTT 58.907 40.909 0.00 0.00 0.00 2.83
3339 4879 2.729194 TGTACTTGTGCCCTGTTTGTT 58.271 42.857 0.00 0.00 0.00 2.83
3340 4880 2.428544 TGTACTTGTGCCCTGTTTGT 57.571 45.000 0.00 0.00 0.00 2.83
3341 4881 2.687935 ACTTGTACTTGTGCCCTGTTTG 59.312 45.455 0.00 0.00 0.00 2.93
3342 4882 2.687935 CACTTGTACTTGTGCCCTGTTT 59.312 45.455 6.03 0.00 0.00 2.83
3343 4883 2.297701 CACTTGTACTTGTGCCCTGTT 58.702 47.619 6.03 0.00 0.00 3.16
3344 4884 1.967319 CACTTGTACTTGTGCCCTGT 58.033 50.000 6.03 0.00 0.00 4.00
3350 4890 0.593128 GCCCAGCACTTGTACTTGTG 59.407 55.000 12.34 12.34 37.26 3.33
3351 4891 0.182537 TGCCCAGCACTTGTACTTGT 59.817 50.000 0.00 0.00 31.71 3.16
3352 4892 3.019964 TGCCCAGCACTTGTACTTG 57.980 52.632 0.00 0.00 31.71 3.16
3371 4911 3.834231 ACAAAAGGAGGATCACCAAATGG 59.166 43.478 10.13 0.00 38.94 3.16
3372 4912 5.010922 TGAACAAAAGGAGGATCACCAAATG 59.989 40.000 10.13 7.76 38.94 2.32
3373 4913 5.147032 TGAACAAAAGGAGGATCACCAAAT 58.853 37.500 10.13 0.00 38.94 2.32
3374 4914 4.541705 TGAACAAAAGGAGGATCACCAAA 58.458 39.130 10.13 0.00 38.94 3.28
3375 4915 4.177537 TGAACAAAAGGAGGATCACCAA 57.822 40.909 10.13 0.00 38.94 3.67
3376 4916 3.874383 TGAACAAAAGGAGGATCACCA 57.126 42.857 10.13 0.00 38.94 4.17
3377 4917 7.260603 CAAATATGAACAAAAGGAGGATCACC 58.739 38.462 0.00 0.00 36.25 4.02
3378 4918 6.753744 GCAAATATGAACAAAAGGAGGATCAC 59.246 38.462 0.00 0.00 36.25 3.06
3379 4919 6.664816 AGCAAATATGAACAAAAGGAGGATCA 59.335 34.615 0.00 0.00 36.25 2.92
3380 4920 7.105241 AGCAAATATGAACAAAAGGAGGATC 57.895 36.000 0.00 0.00 0.00 3.36
3381 4921 8.593945 TTAGCAAATATGAACAAAAGGAGGAT 57.406 30.769 0.00 0.00 0.00 3.24
3382 4922 8.415950 TTTAGCAAATATGAACAAAAGGAGGA 57.584 30.769 0.00 0.00 0.00 3.71
3383 4923 9.657419 ATTTTAGCAAATATGAACAAAAGGAGG 57.343 29.630 0.00 0.00 30.22 4.30


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

AutoCloner maintained by Alex Coulton.