Multiple sequence alignment - TraesCS6B01G083200

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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 TraesCS6B01G083200 chr6B 100.000 5292 0 0 877 6168 60090977 60085686 0.000000e+00 9773.0
1 TraesCS6B01G083200 chr6B 100.000 535 0 0 1 535 60091853 60091319 0.000000e+00 989.0
2 TraesCS6B01G083200 chr6B 82.462 325 44 12 3229 3548 79299949 79299633 7.880000e-69 272.0
3 TraesCS6B01G083200 chr6B 83.019 265 35 9 3309 3572 59827146 59826891 1.340000e-56 231.0
4 TraesCS6B01G083200 chr6B 90.000 150 15 0 4428 4577 66917583 66917434 1.750000e-45 195.0
5 TraesCS6B01G083200 chr6B 90.000 150 15 0 4428 4577 66942173 66942024 1.750000e-45 195.0
6 TraesCS6B01G083200 chr6B 72.129 714 153 38 1472 2160 79555157 79554465 2.290000e-39 174.0
7 TraesCS6B01G083200 chr6B 91.057 123 11 0 877 999 75514494 75514372 3.820000e-37 167.0
8 TraesCS6B01G083200 chr6B 87.248 149 14 2 4429 4577 66859710 66859567 1.380000e-36 165.0
9 TraesCS6B01G083200 chr6B 89.516 124 13 0 877 1000 75423393 75423270 2.300000e-34 158.0
10 TraesCS6B01G083200 chr6B 71.709 714 155 38 1472 2160 79437664 79436973 8.280000e-34 156.0
11 TraesCS6B01G083200 chr6B 71.589 711 156 37 1472 2160 79641482 79640796 1.070000e-32 152.0
12 TraesCS6B01G083200 chr6B 81.657 169 23 5 4600 4767 62122386 62122547 3.880000e-27 134.0
13 TraesCS6B01G083200 chr6B 91.250 80 6 1 2599 2677 78619418 78619497 2.350000e-19 108.0
14 TraesCS6B01G083200 chr6B 81.301 123 21 2 3876 3997 79298963 79298842 1.410000e-16 99.0
15 TraesCS6B01G083200 chr6B 70.872 539 123 29 1474 1993 61790596 61791119 1.830000e-15 95.3
16 TraesCS6B01G083200 chr6B 87.500 56 5 2 4271 4324 82009418 82009473 5.160000e-06 63.9
17 TraesCS6B01G083200 chr6A 95.159 2417 89 9 877 3280 33188359 33185958 0.000000e+00 3790.0
18 TraesCS6B01G083200 chr6A 93.527 1375 55 7 4271 5614 33185253 33183882 0.000000e+00 2015.0
19 TraesCS6B01G083200 chr6A 95.527 626 27 1 3314 3938 33185962 33185337 0.000000e+00 1000.0
20 TraesCS6B01G083200 chr6A 91.011 356 13 10 83 422 33188863 33188511 4.360000e-126 462.0
21 TraesCS6B01G083200 chr6A 79.643 560 79 23 3234 3786 45870904 45871435 2.720000e-98 370.0
22 TraesCS6B01G083200 chr6A 78.092 566 73 23 3229 3786 46114626 46114104 1.670000e-80 311.0
23 TraesCS6B01G083200 chr6A 78.092 566 73 23 3229 3786 46116407 46115885 1.670000e-80 311.0
24 TraesCS6B01G083200 chr6A 83.083 266 34 10 3309 3572 33014843 33014587 1.340000e-56 231.0
25 TraesCS6B01G083200 chr6A 77.322 366 76 6 1638 1998 33016498 33016135 6.270000e-50 209.0
26 TraesCS6B01G083200 chr6A 75.974 462 74 21 1956 2392 45981869 45981420 2.910000e-48 204.0
27 TraesCS6B01G083200 chr6A 90.476 147 14 0 4431 4577 36053028 36052882 1.750000e-45 195.0
28 TraesCS6B01G083200 chr6A 73.774 530 107 20 877 1390 40543198 40542685 4.910000e-41 180.0
29 TraesCS6B01G083200 chr6A 72.207 716 149 39 1472 2160 46295806 46295114 2.290000e-39 174.0
30 TraesCS6B01G083200 chr6A 88.710 124 14 0 877 1000 39877911 39877788 1.070000e-32 152.0
31 TraesCS6B01G083200 chr6A 81.657 169 23 5 4600 4767 34012637 34012798 3.880000e-27 134.0
32 TraesCS6B01G083200 chr6A 92.063 63 5 0 2598 2660 45869134 45869196 8.520000e-14 89.8
33 TraesCS6B01G083200 chr6A 90.909 66 6 0 2598 2663 46118173 46118108 8.520000e-14 89.8
34 TraesCS6B01G083200 chr6A 90.909 66 6 0 2598 2663 46146292 46146227 8.520000e-14 89.8
35 TraesCS6B01G083200 chr6A 86.567 67 9 0 3873 3939 45872091 45872157 2.380000e-09 75.0
36 TraesCS6B01G083200 chr6A 88.136 59 7 0 2983 3041 29490491 29490549 3.080000e-08 71.3
37 TraesCS6B01G083200 chr6D 96.154 1794 62 4 877 2665 29205219 29207010 0.000000e+00 2924.0
38 TraesCS6B01G083200 chr6D 95.366 1230 45 7 4278 5500 29228703 29229927 0.000000e+00 1945.0
39 TraesCS6B01G083200 chr6D 92.798 972 49 6 3308 4273 29222220 29223176 0.000000e+00 1387.0
40 TraesCS6B01G083200 chr6D 94.333 600 22 4 2693 3280 29221631 29222230 0.000000e+00 909.0
41 TraesCS6B01G083200 chr6D 91.561 237 16 2 84 316 29204767 29205003 2.140000e-84 324.0
42 TraesCS6B01G083200 chr6D 97.619 126 3 0 5489 5614 29229945 29230070 3.740000e-52 217.0
43 TraesCS6B01G083200 chr6D 73.996 523 113 20 877 1392 35667420 35666914 2.270000e-44 191.0
44 TraesCS6B01G083200 chr6D 89.516 124 13 0 877 1000 36106011 36105888 2.300000e-34 158.0
45 TraesCS6B01G083200 chr6D 88.800 125 14 0 877 1001 36074083 36073959 2.980000e-33 154.0
46 TraesCS6B01G083200 chr6D 81.065 169 20 7 4600 4767 28663279 28663122 2.330000e-24 124.0
47 TraesCS6B01G083200 chr6D 91.566 83 3 3 455 534 29205057 29205138 1.820000e-20 111.0
48 TraesCS6B01G083200 chr6D 95.652 46 2 0 376 421 29205012 29205057 2.380000e-09 75.0
49 TraesCS6B01G083200 chr1B 97.302 556 15 0 5613 6168 607151042 607150487 0.000000e+00 944.0
50 TraesCS6B01G083200 chr1B 96.057 558 20 1 5613 6168 403400162 403400719 0.000000e+00 907.0
51 TraesCS6B01G083200 chr1B 96.050 557 21 1 5613 6168 454925017 454925573 0.000000e+00 905.0
52 TraesCS6B01G083200 chr7B 97.122 556 12 3 5613 6168 92810705 92810154 0.000000e+00 935.0
53 TraesCS6B01G083200 chr7B 96.763 556 18 0 5613 6168 84110548 84109993 0.000000e+00 928.0
54 TraesCS6B01G083200 chr5B 96.043 556 20 2 5613 6168 692471928 692472481 0.000000e+00 904.0
55 TraesCS6B01G083200 chr5B 71.170 718 157 32 1472 2158 697030024 697029326 3.880000e-27 134.0
56 TraesCS6B01G083200 chr4A 95.528 559 22 1 5613 6168 739511197 739510639 0.000000e+00 891.0
57 TraesCS6B01G083200 chr2B 95.374 562 20 3 5613 6168 585753309 585753870 0.000000e+00 889.0
58 TraesCS6B01G083200 chr2B 95.341 558 23 2 5613 6167 12935300 12935857 0.000000e+00 883.0
59 TraesCS6B01G083200 chrUn 82.576 396 47 15 3250 3638 27971624 27971244 4.610000e-86 329.0
60 TraesCS6B01G083200 chrUn 79.070 430 47 15 4734 5122 27970550 27970123 7.930000e-64 255.0
61 TraesCS6B01G083200 chrUn 72.419 649 135 34 1472 2098 112303837 112303211 3.820000e-37 167.0
62 TraesCS6B01G083200 chrUn 86.000 150 21 0 4428 4577 100623233 100623382 1.780000e-35 161.0
63 TraesCS6B01G083200 chrUn 90.000 120 12 0 4430 4549 344892826 344892945 8.280000e-34 156.0
64 TraesCS6B01G083200 chrUn 90.909 66 6 0 2598 2663 314026613 314026548 8.520000e-14 89.8
65 TraesCS6B01G083200 chrUn 82.692 104 10 6 4600 4702 112599071 112599167 1.100000e-12 86.1
66 TraesCS6B01G083200 chrUn 87.719 57 4 2 4271 4324 27078191 27078247 5.160000e-06 63.9
67 TraesCS6B01G083200 chrUn 94.872 39 1 1 1908 1945 105552856 105552894 6.680000e-05 60.2
68 TraesCS6B01G083200 chr1D 91.935 62 4 1 1 62 340899614 340899554 1.100000e-12 86.1
69 TraesCS6B01G083200 chr2A 90.566 53 3 2 4272 4324 50691923 50691973 1.110000e-07 69.4
70 TraesCS6B01G083200 chr1A 97.436 39 1 0 4286 4324 410687868 410687830 3.990000e-07 67.6
71 TraesCS6B01G083200 chr1A 97.436 39 1 0 4286 4324 412353804 412353842 3.990000e-07 67.6
72 TraesCS6B01G083200 chr1A 97.436 39 1 0 4286 4324 567414445 567414483 3.990000e-07 67.6
73 TraesCS6B01G083200 chr1A 97.436 39 1 0 4286 4324 580612418 580612380 3.990000e-07 67.6


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 TraesCS6B01G083200 chr6B 60085686 60091853 6167 True 5381.000000 9773 100.000000 1 6168 2 chr6B.!!$R10 6167
1 TraesCS6B01G083200 chr6A 33183882 33188863 4981 True 1816.750000 3790 93.806000 83 5614 4 chr6A.!!$R8 5531
2 TraesCS6B01G083200 chr6A 46114104 46118173 4069 True 237.266667 311 82.364333 2598 3786 3 chr6A.!!$R9 1188
3 TraesCS6B01G083200 chr6A 33014587 33016498 1911 True 220.000000 231 80.202500 1638 3572 2 chr6A.!!$R7 1934
4 TraesCS6B01G083200 chr6D 29221631 29223176 1545 False 1148.000000 1387 93.565500 2693 4273 2 chr6D.!!$F2 1580
5 TraesCS6B01G083200 chr6D 29228703 29230070 1367 False 1081.000000 1945 96.492500 4278 5614 2 chr6D.!!$F3 1336
6 TraesCS6B01G083200 chr6D 29204767 29207010 2243 False 858.500000 2924 93.733250 84 2665 4 chr6D.!!$F1 2581
7 TraesCS6B01G083200 chr1B 607150487 607151042 555 True 944.000000 944 97.302000 5613 6168 1 chr1B.!!$R1 555
8 TraesCS6B01G083200 chr1B 403400162 403400719 557 False 907.000000 907 96.057000 5613 6168 1 chr1B.!!$F1 555
9 TraesCS6B01G083200 chr1B 454925017 454925573 556 False 905.000000 905 96.050000 5613 6168 1 chr1B.!!$F2 555
10 TraesCS6B01G083200 chr7B 92810154 92810705 551 True 935.000000 935 97.122000 5613 6168 1 chr7B.!!$R2 555
11 TraesCS6B01G083200 chr7B 84109993 84110548 555 True 928.000000 928 96.763000 5613 6168 1 chr7B.!!$R1 555
12 TraesCS6B01G083200 chr5B 692471928 692472481 553 False 904.000000 904 96.043000 5613 6168 1 chr5B.!!$F1 555
13 TraesCS6B01G083200 chr4A 739510639 739511197 558 True 891.000000 891 95.528000 5613 6168 1 chr4A.!!$R1 555
14 TraesCS6B01G083200 chr2B 585753309 585753870 561 False 889.000000 889 95.374000 5613 6168 1 chr2B.!!$F2 555
15 TraesCS6B01G083200 chr2B 12935300 12935857 557 False 883.000000 883 95.341000 5613 6167 1 chr2B.!!$F1 554
16 TraesCS6B01G083200 chrUn 27970123 27971624 1501 True 292.000000 329 80.823000 3250 5122 2 chrUn.!!$R3 1872

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
53 54 0.031994 CCAGCCTTCGGTTTGGTTTG 59.968 55.0 0.00 0.00 0.00 2.93 F
68 69 0.037734 GTTTGATTCACCCCCGGAGT 59.962 55.0 0.73 0.00 0.00 3.85 F
76 77 0.251073 CACCCCCGGAGTTTATCGTT 59.749 55.0 0.73 0.00 0.00 3.85 F
1573 1599 0.315568 CAGCCTAGCCGTGATACCTC 59.684 60.0 0.00 0.00 0.00 3.85 F
2713 2881 0.394080 AAAGCTCTGAGATGGCTGCC 60.394 55.0 12.87 12.87 36.37 4.85 F
3724 5274 0.620556 CTTTTCTCCAGGCCCTGCTA 59.379 55.0 4.81 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1287 0.896940 AGGAAGTGGCGGTCGTCTAA 60.897 55.000 0.00 0.0 0.00 2.10 R
1417 1443 1.322442 GGTGGCAAGTCTTCTGCTTT 58.678 50.000 0.00 0.0 0.00 3.51 R
1600 1626 1.659098 CCGCATAACCGAGAAGTTGAC 59.341 52.381 0.00 0.0 0.00 3.18 R
3147 4029 0.108186 TGAGGCACGAACTAGCATGG 60.108 55.000 0.00 0.0 0.00 3.66 R
4242 6067 0.177141 GGCACACCTATAAGTCCGCA 59.823 55.000 0.00 0.0 0.00 5.69 R
5449 7860 0.462581 TGCCTATCAGCGCAAAGAGG 60.463 55.000 11.47 14.3 34.65 3.69 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
27 28 4.261701 CTAGCTAGCAGGGGACGT 57.738 61.111 18.83 0.00 0.00 4.34
37 38 3.414486 AGGGGACGTGAAAAACCAG 57.586 52.632 0.00 0.00 0.00 4.00
38 39 0.822121 AGGGGACGTGAAAAACCAGC 60.822 55.000 0.00 0.00 0.00 4.85
39 40 1.658114 GGGACGTGAAAAACCAGCC 59.342 57.895 0.00 0.00 0.00 4.85
40 41 0.822121 GGGACGTGAAAAACCAGCCT 60.822 55.000 0.00 0.00 0.00 4.58
41 42 1.029681 GGACGTGAAAAACCAGCCTT 58.970 50.000 0.00 0.00 0.00 4.35
42 43 1.001706 GGACGTGAAAAACCAGCCTTC 60.002 52.381 0.00 0.00 0.00 3.46
43 44 0.661020 ACGTGAAAAACCAGCCTTCG 59.339 50.000 0.00 0.00 0.00 3.79
44 45 0.040425 CGTGAAAAACCAGCCTTCGG 60.040 55.000 0.00 0.00 0.00 4.30
45 46 1.029681 GTGAAAAACCAGCCTTCGGT 58.970 50.000 0.00 0.00 38.85 4.69
49 50 4.174305 AACCAGCCTTCGGTTTGG 57.826 55.556 0.00 0.00 44.46 3.28
50 51 1.229076 AACCAGCCTTCGGTTTGGT 59.771 52.632 5.69 5.69 44.46 3.67
51 52 0.396556 AACCAGCCTTCGGTTTGGTT 60.397 50.000 14.20 14.20 44.46 3.67
52 53 0.396556 ACCAGCCTTCGGTTTGGTTT 60.397 50.000 5.69 0.00 38.81 3.27
53 54 0.031994 CCAGCCTTCGGTTTGGTTTG 59.968 55.000 0.00 0.00 0.00 2.93
54 55 1.028905 CAGCCTTCGGTTTGGTTTGA 58.971 50.000 0.00 0.00 0.00 2.69
55 56 1.613437 CAGCCTTCGGTTTGGTTTGAT 59.387 47.619 0.00 0.00 0.00 2.57
56 57 2.035832 CAGCCTTCGGTTTGGTTTGATT 59.964 45.455 0.00 0.00 0.00 2.57
57 58 2.296190 AGCCTTCGGTTTGGTTTGATTC 59.704 45.455 0.00 0.00 0.00 2.52
58 59 2.035321 GCCTTCGGTTTGGTTTGATTCA 59.965 45.455 0.00 0.00 0.00 2.57
59 60 3.638484 CCTTCGGTTTGGTTTGATTCAC 58.362 45.455 0.00 0.00 0.00 3.18
60 61 3.552068 CCTTCGGTTTGGTTTGATTCACC 60.552 47.826 0.00 0.00 34.52 4.02
61 62 1.957877 TCGGTTTGGTTTGATTCACCC 59.042 47.619 0.00 0.00 32.71 4.61
62 63 1.000394 CGGTTTGGTTTGATTCACCCC 60.000 52.381 0.00 0.00 32.71 4.95
63 64 1.346395 GGTTTGGTTTGATTCACCCCC 59.654 52.381 0.00 0.00 32.71 5.40
64 65 1.000394 GTTTGGTTTGATTCACCCCCG 60.000 52.381 0.00 0.00 32.71 5.73
65 66 0.540830 TTGGTTTGATTCACCCCCGG 60.541 55.000 0.00 0.00 32.71 5.73
66 67 1.381076 GGTTTGATTCACCCCCGGA 59.619 57.895 0.73 0.00 0.00 5.14
67 68 0.679960 GGTTTGATTCACCCCCGGAG 60.680 60.000 0.73 0.00 0.00 4.63
68 69 0.037734 GTTTGATTCACCCCCGGAGT 59.962 55.000 0.73 0.00 0.00 3.85
69 70 0.774908 TTTGATTCACCCCCGGAGTT 59.225 50.000 0.73 0.00 0.00 3.01
70 71 0.774908 TTGATTCACCCCCGGAGTTT 59.225 50.000 0.73 0.00 0.00 2.66
71 72 1.659022 TGATTCACCCCCGGAGTTTA 58.341 50.000 0.73 0.00 0.00 2.01
72 73 2.201830 TGATTCACCCCCGGAGTTTAT 58.798 47.619 0.73 0.00 0.00 1.40
73 74 2.171870 TGATTCACCCCCGGAGTTTATC 59.828 50.000 0.73 5.96 0.00 1.75
74 75 0.538118 TTCACCCCCGGAGTTTATCG 59.462 55.000 0.73 0.00 0.00 2.92
75 76 0.615544 TCACCCCCGGAGTTTATCGT 60.616 55.000 0.73 0.00 0.00 3.73
76 77 0.251073 CACCCCCGGAGTTTATCGTT 59.749 55.000 0.73 0.00 0.00 3.85
77 78 1.481772 CACCCCCGGAGTTTATCGTTA 59.518 52.381 0.73 0.00 0.00 3.18
78 79 2.093553 CACCCCCGGAGTTTATCGTTAA 60.094 50.000 0.73 0.00 0.00 2.01
79 80 2.169144 ACCCCCGGAGTTTATCGTTAAG 59.831 50.000 0.73 0.00 0.00 1.85
80 81 2.169144 CCCCCGGAGTTTATCGTTAAGT 59.831 50.000 0.73 0.00 0.00 2.24
81 82 3.369787 CCCCCGGAGTTTATCGTTAAGTT 60.370 47.826 0.73 0.00 0.00 2.66
82 83 4.256110 CCCCGGAGTTTATCGTTAAGTTT 58.744 43.478 0.73 0.00 0.00 2.66
154 160 5.947228 ATTTGCTATTATGGATCCACACG 57.053 39.130 18.99 5.31 0.00 4.49
274 283 7.838079 TCCTTTGGAATTTCTTCAATCTTCA 57.162 32.000 0.00 0.00 32.70 3.02
304 322 2.099756 GGGGCTGGAATTTCTTCAATCG 59.900 50.000 0.00 0.00 32.70 3.34
362 381 2.050350 CCATTGTCCAGCCCAGCAG 61.050 63.158 0.00 0.00 0.00 4.24
363 382 2.362120 ATTGTCCAGCCCAGCAGC 60.362 61.111 0.00 0.00 0.00 5.25
364 383 3.214190 ATTGTCCAGCCCAGCAGCA 62.214 57.895 0.00 0.00 34.23 4.41
404 423 0.598065 GGGCGCACTTCATTTCAGTT 59.402 50.000 10.83 0.00 0.00 3.16
422 448 3.197333 CAGTTCATCAGATCCACTCCACT 59.803 47.826 0.00 0.00 0.00 4.00
423 449 3.843027 AGTTCATCAGATCCACTCCACTT 59.157 43.478 0.00 0.00 0.00 3.16
424 450 4.081198 AGTTCATCAGATCCACTCCACTTC 60.081 45.833 0.00 0.00 0.00 3.01
425 451 2.768527 TCATCAGATCCACTCCACTTCC 59.231 50.000 0.00 0.00 0.00 3.46
426 452 2.630889 TCAGATCCACTCCACTTCCT 57.369 50.000 0.00 0.00 0.00 3.36
427 453 2.461695 TCAGATCCACTCCACTTCCTC 58.538 52.381 0.00 0.00 0.00 3.71
428 454 2.182827 CAGATCCACTCCACTTCCTCA 58.817 52.381 0.00 0.00 0.00 3.86
429 455 2.568956 CAGATCCACTCCACTTCCTCAA 59.431 50.000 0.00 0.00 0.00 3.02
430 456 3.008375 CAGATCCACTCCACTTCCTCAAA 59.992 47.826 0.00 0.00 0.00 2.69
431 457 3.652869 AGATCCACTCCACTTCCTCAAAA 59.347 43.478 0.00 0.00 0.00 2.44
432 458 3.943671 TCCACTCCACTTCCTCAAAAA 57.056 42.857 0.00 0.00 0.00 1.94
469 495 1.448540 CAGATCCACTCCACCGCAC 60.449 63.158 0.00 0.00 0.00 5.34
495 521 3.226777 GAGCAAGTAGGGCAGATCTAGA 58.773 50.000 0.00 0.00 0.00 2.43
496 522 3.639094 GAGCAAGTAGGGCAGATCTAGAA 59.361 47.826 0.00 0.00 0.00 2.10
1003 1029 1.067142 TCCTCGGTTTCTTCGACATGG 60.067 52.381 0.00 0.00 32.86 3.66
1034 1060 2.202756 CTTCGTGCCTACCCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
1035 1061 3.718210 CTTCGTGCCTACCCTCGCC 62.718 68.421 0.00 0.00 0.00 5.54
1096 1122 2.804090 GCGACGACGACTGGTTCC 60.804 66.667 12.29 0.00 42.66 3.62
1200 1226 0.823356 ACAAGCACTGGATTGCCGTT 60.823 50.000 0.00 0.00 44.08 4.44
1229 1255 2.354188 CGAGTGCGACACCGACAA 60.354 61.111 6.39 0.00 40.82 3.18
1261 1287 4.749310 CGGTGCTTCGCTCTGCCT 62.749 66.667 0.00 0.00 0.00 4.75
1271 1297 1.226717 GCTCTGCCTTAGACGACCG 60.227 63.158 0.00 0.00 0.00 4.79
1417 1443 1.378531 CGAATCCCGCTTCCAATTGA 58.621 50.000 7.12 0.00 0.00 2.57
1438 1464 2.328099 GCAGAAGACTTGCCACCGG 61.328 63.158 0.00 0.00 0.00 5.28
1463 1489 6.618287 TGAATGTCCGACCATGATTTATTC 57.382 37.500 0.00 0.00 0.00 1.75
1464 1490 5.236263 TGAATGTCCGACCATGATTTATTCG 59.764 40.000 0.00 0.00 0.00 3.34
1518 1544 0.617820 ACTGGTGGCTTCGGGATAGT 60.618 55.000 0.00 0.00 0.00 2.12
1573 1599 0.315568 CAGCCTAGCCGTGATACCTC 59.684 60.000 0.00 0.00 0.00 3.85
1597 1623 2.607187 CGGTGGACTTGTATGACAGTC 58.393 52.381 0.00 0.00 0.00 3.51
1600 1626 3.935203 GGTGGACTTGTATGACAGTCATG 59.065 47.826 24.15 11.05 37.70 3.07
1671 1697 9.817365 CTATTTGTATCAAAGTTCAGTGTTCAG 57.183 33.333 1.67 0.00 0.00 3.02
1736 1763 4.808895 GGTGTTGGGAAGAACAATTGAAAC 59.191 41.667 13.59 2.96 37.58 2.78
2086 2116 5.813080 TTGATGCTTGATGACATCTTCAG 57.187 39.130 16.25 10.34 42.57 3.02
2126 2159 7.609532 AGCTATGAGTTCTTTTCTTATGCTTGT 59.390 33.333 0.00 0.00 0.00 3.16
2221 2378 0.873743 AACACCAACCATTTTGCGCG 60.874 50.000 0.00 0.00 0.00 6.86
2362 2519 1.002430 TGTCTTCCTCCTGCACATGTC 59.998 52.381 0.00 0.00 0.00 3.06
2385 2542 0.914551 CGTAATCCGTGCGTGAGAAG 59.085 55.000 0.00 0.00 0.00 2.85
2427 2584 4.772624 AGGCCCACTTTTTCCTTCTTAATC 59.227 41.667 0.00 0.00 0.00 1.75
2487 2645 2.093128 GGTTTCCCTCCTTAATCTCGCA 60.093 50.000 0.00 0.00 0.00 5.10
2573 2731 2.261729 TGTTATGTAGCCAGGTGGTGA 58.738 47.619 0.00 0.00 37.57 4.02
2641 2803 3.753272 TCAAGTCAGACCTAGCAAATTGC 59.247 43.478 10.41 10.41 45.46 3.56
2713 2881 0.394080 AAAGCTCTGAGATGGCTGCC 60.394 55.000 12.87 12.87 36.37 4.85
2746 2914 2.421529 GGACGCTGGATTAATTCCCTGT 60.422 50.000 0.00 0.00 44.77 4.00
2760 2928 2.662596 CTGTCGCAGCCCCAGTTA 59.337 61.111 0.00 0.00 0.00 2.24
2824 2993 4.335647 CCGGACCCTGTGCAAGCT 62.336 66.667 0.00 0.00 0.00 3.74
2895 3067 6.129717 CGTTTCTGTTTTATTGAGTTTCAGCG 60.130 38.462 0.00 0.00 0.00 5.18
2920 3092 3.565307 TGAACTTTTGGGTCATCTTGCT 58.435 40.909 0.00 0.00 0.00 3.91
2998 3172 9.866655 AATGGATACTAAGATTGGCAAATTCTA 57.133 29.630 3.01 0.00 37.61 2.10
3055 3236 7.513132 CCTGTGTATTGATGTATGCGAAATAG 58.487 38.462 0.00 0.00 0.00 1.73
3063 3244 4.053469 TGTATGCGAAATAGTGCAGCTA 57.947 40.909 0.00 0.00 45.52 3.32
3099 3280 7.847096 TGCTACTAATCAAGTCAGGTTATTCA 58.153 34.615 0.00 0.00 39.80 2.57
3147 4029 5.206159 TGTTCTGAAACCAGCATTAGCGC 62.206 47.826 0.00 0.00 39.21 5.92
3276 4778 9.961264 TTGTTTGTGTATCCCTAATGTTGTATA 57.039 29.630 0.00 0.00 0.00 1.47
3307 4809 8.816640 ATTTATTTTTGTAACTCAGCTGTTGG 57.183 30.769 14.67 7.99 0.00 3.77
3395 4941 3.423539 TGCTTGACTTCTTATGCCTGT 57.576 42.857 0.00 0.00 0.00 4.00
3451 4997 4.325972 TGATCTCTTGCACAGCACATAAA 58.674 39.130 0.00 0.00 38.71 1.40
3618 5168 4.085357 TGCAAGCAAGGACTCTTAAGAA 57.915 40.909 6.63 0.00 0.00 2.52
3644 5194 2.893489 TCTACACTCTTTGCTCTGCTGA 59.107 45.455 0.00 0.00 0.00 4.26
3699 5249 2.223900 GCTTTGATGCCAGGCTAAATCC 60.224 50.000 14.15 3.00 0.00 3.01
3724 5274 0.620556 CTTTTCTCCAGGCCCTGCTA 59.379 55.000 4.81 0.00 0.00 3.49
3791 5343 6.603201 CCTTTAAATTGCTGATCTTCTACCCA 59.397 38.462 0.00 0.00 0.00 4.51
3809 5362 4.290093 ACCCATCTCTACTGAATGTGCTA 58.710 43.478 0.00 0.00 0.00 3.49
3866 5419 4.096984 GCTTACGCTTTACCTCCTACAGTA 59.903 45.833 0.00 0.00 0.00 2.74
3872 5425 5.764192 CGCTTTACCTCCTACAGTATACTCT 59.236 44.000 1.26 0.00 0.00 3.24
3975 5528 7.658525 TCCCTATTTGTGCAAATATTGATGT 57.341 32.000 15.16 0.00 41.02 3.06
3993 5546 5.742063 TGATGTCTGCTCAGAGATGAAAAT 58.258 37.500 13.32 0.00 40.93 1.82
3994 5547 5.585047 TGATGTCTGCTCAGAGATGAAAATG 59.415 40.000 13.32 0.00 40.93 2.32
3995 5548 3.688185 TGTCTGCTCAGAGATGAAAATGC 59.312 43.478 0.00 0.00 38.27 3.56
3997 5550 5.114780 GTCTGCTCAGAGATGAAAATGCTA 58.885 41.667 0.00 0.00 38.27 3.49
4039 5597 2.584835 TGCTTTCATGCTAGGTGGTT 57.415 45.000 0.00 0.00 0.00 3.67
4044 5602 4.379499 GCTTTCATGCTAGGTGGTTGTAAC 60.379 45.833 0.00 0.00 0.00 2.50
4070 5628 7.446769 TGAACTACTAATCCTTTGTTGTGCTA 58.553 34.615 0.00 0.00 0.00 3.49
4084 5642 5.686753 TGTTGTGCTACCGGGATATATTTT 58.313 37.500 6.32 0.00 0.00 1.82
4098 5656 8.987890 CGGGATATATTTTTATTTTGCCTTTGG 58.012 33.333 0.00 0.00 0.00 3.28
4125 5684 4.584325 TGCTGAATTGCCTTTAACTTCTGT 59.416 37.500 0.00 0.00 0.00 3.41
4126 5685 5.068987 TGCTGAATTGCCTTTAACTTCTGTT 59.931 36.000 0.00 0.00 39.98 3.16
4127 5686 5.985530 GCTGAATTGCCTTTAACTTCTGTTT 59.014 36.000 0.00 0.00 37.59 2.83
4128 5687 6.479990 GCTGAATTGCCTTTAACTTCTGTTTT 59.520 34.615 0.00 0.00 37.59 2.43
4129 5688 7.011389 GCTGAATTGCCTTTAACTTCTGTTTTT 59.989 33.333 0.00 0.00 37.59 1.94
4185 5744 4.630644 AGTGTGATCTGAATGTTGTCCT 57.369 40.909 0.00 0.00 0.00 3.85
4211 5805 7.280876 TGTCTTCATAAGTGATTGATAACTGCC 59.719 37.037 0.00 0.00 33.56 4.85
4380 6742 7.276658 TGATTCTATCACTAATGCCGGTTTTA 58.723 34.615 1.90 0.36 33.59 1.52
4381 6743 7.771361 TGATTCTATCACTAATGCCGGTTTTAA 59.229 33.333 1.90 0.00 33.59 1.52
4383 6745 7.925043 TCTATCACTAATGCCGGTTTTAAAA 57.075 32.000 1.90 0.00 0.00 1.52
4384 6746 8.338072 TCTATCACTAATGCCGGTTTTAAAAA 57.662 30.769 1.90 0.00 0.00 1.94
4436 6801 4.154195 GTGGTGAATGTATCGAAACTGCTT 59.846 41.667 0.00 0.00 0.00 3.91
4562 6927 3.152261 TCGTTCAAAATTTGCCGTGTT 57.848 38.095 14.01 0.00 0.00 3.32
4595 6960 5.503927 ACTCTGAATGTATTGCTTGATGGT 58.496 37.500 0.00 0.00 0.00 3.55
4671 7037 3.878237 AGATGATGCATGATCCCTTGT 57.122 42.857 20.76 1.00 0.00 3.16
4706 7073 8.358895 TGTACTGCAAGAATTTGATGAAAATCA 58.641 29.630 0.00 0.00 35.72 2.57
4724 7091 5.886960 AATCAATTTGTCAGTGACTAGCC 57.113 39.130 23.29 0.00 33.15 3.93
4757 7124 6.350949 GCATTCCTAAAAAGTATGCCCAAGAA 60.351 38.462 0.00 0.00 36.48 2.52
4804 7171 1.067821 AGCCTCTACGCATAAGAGTGC 59.932 52.381 6.30 8.42 39.09 4.40
4959 7361 7.523293 ACAATTGTGATGGTTTGAGTCATAA 57.477 32.000 11.07 0.00 0.00 1.90
5111 7521 4.278669 TCGAGTATAGTTCCTTCCATCTGC 59.721 45.833 0.00 0.00 0.00 4.26
5205 7615 5.736338 CATTTTAGTTTGTGCATGCGTTTT 58.264 33.333 14.09 0.00 0.00 2.43
5241 7651 1.873591 GTATCAGCATCGCGGGATTTT 59.126 47.619 12.94 0.81 32.02 1.82
5331 7742 8.684386 TTTGGTTACTTGTGACTAATGAATGA 57.316 30.769 0.00 0.00 0.00 2.57
5415 7826 0.537143 TGCTTCCTTTGCGATGGTGT 60.537 50.000 5.80 0.00 0.00 4.16
5449 7860 2.742774 AGTTGGCGAACTTTTTGATGC 58.257 42.857 8.47 0.00 39.56 3.91
5458 7873 3.017265 ACTTTTTGATGCCTCTTTGCG 57.983 42.857 0.00 0.00 0.00 4.85
5538 7982 4.787598 CAGAACACATTTTACAGCTGACC 58.212 43.478 23.35 0.00 0.00 4.02
5594 8038 4.701956 AATTTCTGGACACAATAAGCCG 57.298 40.909 0.00 0.00 0.00 5.52
5632 8076 1.271926 ACTAGGAAAATTGCCCGTGCT 60.272 47.619 0.00 0.00 38.71 4.40
5720 8168 5.221864 GGATTATACTCCCTCCGTTCCAAAT 60.222 44.000 0.00 0.00 0.00 2.32
5773 8221 3.951680 ACAAAGTTGTACCAAGGTTGAGG 59.048 43.478 0.00 0.00 40.16 3.86
5784 8232 4.280929 ACCAAGGTTGAGGCACTTATTTTC 59.719 41.667 0.00 0.00 41.55 2.29
5980 8442 3.560481 TGGTTCGAATAAAGTTGTTCGCA 59.440 39.130 15.49 4.92 46.74 5.10
5992 8454 1.890876 TGTTCGCACTACCATTGCTT 58.109 45.000 0.00 0.00 37.87 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.752009 TCACGTCCCCTGCTAGCTAG 60.752 60.000 16.84 16.84 0.00 3.42
11 12 0.323999 TTCACGTCCCCTGCTAGCTA 60.324 55.000 17.23 1.31 0.00 3.32
12 13 1.192146 TTTCACGTCCCCTGCTAGCT 61.192 55.000 17.23 0.00 0.00 3.32
13 14 0.321298 TTTTCACGTCCCCTGCTAGC 60.321 55.000 8.10 8.10 0.00 3.42
14 15 1.804748 GTTTTTCACGTCCCCTGCTAG 59.195 52.381 0.00 0.00 0.00 3.42
15 16 1.543871 GGTTTTTCACGTCCCCTGCTA 60.544 52.381 0.00 0.00 0.00 3.49
16 17 0.822121 GGTTTTTCACGTCCCCTGCT 60.822 55.000 0.00 0.00 0.00 4.24
17 18 1.104577 TGGTTTTTCACGTCCCCTGC 61.105 55.000 0.00 0.00 0.00 4.85
18 19 0.951558 CTGGTTTTTCACGTCCCCTG 59.048 55.000 0.00 0.00 0.00 4.45
19 20 0.822121 GCTGGTTTTTCACGTCCCCT 60.822 55.000 0.00 0.00 0.00 4.79
20 21 1.658114 GCTGGTTTTTCACGTCCCC 59.342 57.895 0.00 0.00 0.00 4.81
21 22 0.822121 AGGCTGGTTTTTCACGTCCC 60.822 55.000 0.00 0.00 0.00 4.46
22 23 1.001706 GAAGGCTGGTTTTTCACGTCC 60.002 52.381 0.00 0.00 0.00 4.79
23 24 1.333791 CGAAGGCTGGTTTTTCACGTC 60.334 52.381 0.00 0.00 0.00 4.34
24 25 0.661020 CGAAGGCTGGTTTTTCACGT 59.339 50.000 0.00 0.00 0.00 4.49
25 26 0.040425 CCGAAGGCTGGTTTTTCACG 60.040 55.000 0.00 0.00 46.14 4.35
26 27 3.865700 CCGAAGGCTGGTTTTTCAC 57.134 52.632 0.00 0.00 46.14 3.18
38 39 3.552068 GGTGAATCAAACCAAACCGAAGG 60.552 47.826 0.00 0.00 46.12 3.46
39 40 3.552068 GGGTGAATCAAACCAAACCGAAG 60.552 47.826 0.96 0.00 39.65 3.79
40 41 2.362717 GGGTGAATCAAACCAAACCGAA 59.637 45.455 0.96 0.00 39.65 4.30
41 42 1.957877 GGGTGAATCAAACCAAACCGA 59.042 47.619 0.96 0.00 39.65 4.69
42 43 1.000394 GGGGTGAATCAAACCAAACCG 60.000 52.381 7.41 0.00 39.65 4.44
43 44 1.346395 GGGGGTGAATCAAACCAAACC 59.654 52.381 7.41 0.00 39.65 3.27
44 45 1.000394 CGGGGGTGAATCAAACCAAAC 60.000 52.381 7.41 0.00 39.65 2.93
45 46 1.333177 CGGGGGTGAATCAAACCAAA 58.667 50.000 7.41 0.00 39.65 3.28
46 47 0.540830 CCGGGGGTGAATCAAACCAA 60.541 55.000 0.00 0.00 39.65 3.67
47 48 1.075836 CCGGGGGTGAATCAAACCA 59.924 57.895 0.00 0.00 39.65 3.67
48 49 0.679960 CTCCGGGGGTGAATCAAACC 60.680 60.000 0.00 0.00 36.94 3.27
49 50 0.037734 ACTCCGGGGGTGAATCAAAC 59.962 55.000 6.13 0.00 0.00 2.93
50 51 0.774908 AACTCCGGGGGTGAATCAAA 59.225 50.000 6.13 0.00 0.00 2.69
51 52 0.774908 AAACTCCGGGGGTGAATCAA 59.225 50.000 6.13 0.00 0.00 2.57
52 53 1.659022 TAAACTCCGGGGGTGAATCA 58.341 50.000 6.13 0.00 0.00 2.57
53 54 2.805657 CGATAAACTCCGGGGGTGAATC 60.806 54.545 6.13 5.49 0.00 2.52
54 55 1.140252 CGATAAACTCCGGGGGTGAAT 59.860 52.381 6.13 0.00 0.00 2.57
55 56 0.538118 CGATAAACTCCGGGGGTGAA 59.462 55.000 6.13 0.00 0.00 3.18
56 57 0.615544 ACGATAAACTCCGGGGGTGA 60.616 55.000 6.13 0.00 0.00 4.02
57 58 0.251073 AACGATAAACTCCGGGGGTG 59.749 55.000 6.13 0.00 0.00 4.61
58 59 1.864669 TAACGATAAACTCCGGGGGT 58.135 50.000 6.13 0.00 0.00 4.95
59 60 2.169144 ACTTAACGATAAACTCCGGGGG 59.831 50.000 6.13 0.00 0.00 5.40
60 61 3.531934 ACTTAACGATAAACTCCGGGG 57.468 47.619 0.00 0.00 0.00 5.73
61 62 7.543947 AATAAACTTAACGATAAACTCCGGG 57.456 36.000 0.00 0.00 0.00 5.73
62 63 9.269415 CAAAATAAACTTAACGATAAACTCCGG 57.731 33.333 0.00 0.00 0.00 5.14
63 64 9.269415 CCAAAATAAACTTAACGATAAACTCCG 57.731 33.333 0.00 0.00 0.00 4.63
64 65 9.563898 CCCAAAATAAACTTAACGATAAACTCC 57.436 33.333 0.00 0.00 0.00 3.85
65 66 9.069078 GCCCAAAATAAACTTAACGATAAACTC 57.931 33.333 0.00 0.00 0.00 3.01
66 67 8.799367 AGCCCAAAATAAACTTAACGATAAACT 58.201 29.630 0.00 0.00 0.00 2.66
67 68 8.975410 AGCCCAAAATAAACTTAACGATAAAC 57.025 30.769 0.00 0.00 0.00 2.01
71 72 9.398538 TGTATAGCCCAAAATAAACTTAACGAT 57.601 29.630 0.00 0.00 0.00 3.73
72 73 8.789825 TGTATAGCCCAAAATAAACTTAACGA 57.210 30.769 0.00 0.00 0.00 3.85
73 74 9.843334 TTTGTATAGCCCAAAATAAACTTAACG 57.157 29.630 0.00 0.00 0.00 3.18
77 78 9.923143 GTTCTTTGTATAGCCCAAAATAAACTT 57.077 29.630 0.00 0.00 31.86 2.66
78 79 9.084533 TGTTCTTTGTATAGCCCAAAATAAACT 57.915 29.630 0.00 0.00 31.86 2.66
79 80 9.699703 TTGTTCTTTGTATAGCCCAAAATAAAC 57.300 29.630 0.00 0.00 31.86 2.01
282 291 1.937191 TTGAAGAAATTCCAGCCCCC 58.063 50.000 0.00 0.00 0.00 5.40
326 344 0.464735 GGGCCACGGTATACAATGCA 60.465 55.000 4.39 0.00 0.00 3.96
362 381 2.413453 GTGAAAGTGACGGAAGAGATGC 59.587 50.000 0.00 0.00 0.00 3.91
363 382 2.663602 CGTGAAAGTGACGGAAGAGATG 59.336 50.000 0.00 0.00 33.08 2.90
364 383 2.947852 CGTGAAAGTGACGGAAGAGAT 58.052 47.619 0.00 0.00 33.08 2.75
404 423 2.768527 GGAAGTGGAGTGGATCTGATGA 59.231 50.000 0.00 0.00 0.00 2.92
445 471 3.347216 CGGTGGAGTGGATCTGATTTTT 58.653 45.455 0.00 0.00 0.00 1.94
446 472 2.941415 GCGGTGGAGTGGATCTGATTTT 60.941 50.000 0.00 0.00 0.00 1.82
447 473 1.407437 GCGGTGGAGTGGATCTGATTT 60.407 52.381 0.00 0.00 0.00 2.17
448 474 0.179000 GCGGTGGAGTGGATCTGATT 59.821 55.000 0.00 0.00 0.00 2.57
449 475 0.977627 TGCGGTGGAGTGGATCTGAT 60.978 55.000 0.00 0.00 0.00 2.90
450 476 1.609210 TGCGGTGGAGTGGATCTGA 60.609 57.895 0.00 0.00 0.00 3.27
451 477 1.448540 GTGCGGTGGAGTGGATCTG 60.449 63.158 0.00 0.00 0.00 2.90
452 478 2.660064 GGTGCGGTGGAGTGGATCT 61.660 63.158 0.00 0.00 0.00 2.75
453 479 2.125106 GGTGCGGTGGAGTGGATC 60.125 66.667 0.00 0.00 0.00 3.36
454 480 2.927856 TGGTGCGGTGGAGTGGAT 60.928 61.111 0.00 0.00 0.00 3.41
455 481 3.625897 CTGGTGCGGTGGAGTGGA 61.626 66.667 0.00 0.00 0.00 4.02
456 482 3.941188 ACTGGTGCGGTGGAGTGG 61.941 66.667 0.00 0.00 0.00 4.00
457 483 2.666190 CACTGGTGCGGTGGAGTG 60.666 66.667 0.00 0.00 37.12 3.51
458 484 2.842462 TCACTGGTGCGGTGGAGT 60.842 61.111 0.00 0.00 40.76 3.85
459 485 2.047844 CTCACTGGTGCGGTGGAG 60.048 66.667 0.00 0.00 40.76 3.86
460 486 4.314440 GCTCACTGGTGCGGTGGA 62.314 66.667 0.00 0.00 40.76 4.02
461 487 4.624364 TGCTCACTGGTGCGGTGG 62.624 66.667 0.00 0.00 40.76 4.61
464 490 1.005037 TACTTGCTCACTGGTGCGG 60.005 57.895 0.00 0.00 36.33 5.69
469 495 0.392193 CTGCCCTACTTGCTCACTGG 60.392 60.000 0.00 0.00 0.00 4.00
1096 1122 3.952628 GACGGCTTCCAAGGGACCG 62.953 68.421 11.46 11.46 43.90 4.79
1261 1287 0.896940 AGGAAGTGGCGGTCGTCTAA 60.897 55.000 0.00 0.00 0.00 2.10
1356 1382 8.367911 GGTGTTGAGATTATATCACTCCATGTA 58.632 37.037 0.00 0.00 0.00 2.29
1417 1443 1.322442 GGTGGCAAGTCTTCTGCTTT 58.678 50.000 0.00 0.00 0.00 3.51
1438 1464 4.701956 AAATCATGGTCGGACATTCAAC 57.298 40.909 10.76 0.00 0.00 3.18
1518 1544 5.309638 TCAAATTGGAGGATGTTGTACGAA 58.690 37.500 0.00 0.00 0.00 3.85
1597 1623 3.242091 CGCATAACCGAGAAGTTGACATG 60.242 47.826 0.00 0.00 0.00 3.21
1600 1626 1.659098 CCGCATAACCGAGAAGTTGAC 59.341 52.381 0.00 0.00 0.00 3.18
1671 1697 2.234300 TGACCTTCGTCTTCCACAAC 57.766 50.000 0.00 0.00 39.94 3.32
2086 2116 2.288729 TCATAGCTTCATCGCAACATGC 59.711 45.455 0.00 0.00 40.69 4.06
2212 2369 0.958822 ACCCTTCTTTCGCGCAAAAT 59.041 45.000 8.75 0.00 0.00 1.82
2221 2378 4.217836 ACCTTTCCGATACCCTTCTTTC 57.782 45.455 0.00 0.00 0.00 2.62
2385 2542 2.818274 CGCTTTACACCCCTCCGC 60.818 66.667 0.00 0.00 0.00 5.54
2427 2584 0.741221 GTTTACCCCTGAGCGCAGAG 60.741 60.000 19.95 12.09 45.17 3.35
2487 2645 6.889301 TGAAAGAAAAGCATGAGATCTTGT 57.111 33.333 0.00 0.00 31.14 3.16
2573 2731 6.232581 AGCTTAGCAGTAGATCAGTGAATT 57.767 37.500 7.07 0.00 0.00 2.17
2678 2846 5.293814 CAGAGCTTTGTCTCTATCCATTGTG 59.706 44.000 0.00 0.00 41.22 3.33
2746 2914 2.124736 GCATAACTGGGGCTGCGA 60.125 61.111 0.00 0.00 0.00 5.10
2895 3067 5.523369 CAAGATGACCCAAAAGTTCAAGAC 58.477 41.667 0.00 0.00 0.00 3.01
2920 3092 4.572795 TGACGTTGTGCATTAGAAGAAACA 59.427 37.500 0.00 0.00 0.00 2.83
3055 3236 2.542411 GCAAAGGCATGTATAGCTGCAC 60.542 50.000 1.02 0.00 40.18 4.57
3063 3244 7.056635 ACTTGATTAGTAGCAAAGGCATGTAT 58.943 34.615 0.00 0.00 44.61 2.29
3099 3280 0.249699 TGTCGGCGATTGTCACAAGT 60.250 50.000 14.79 0.00 0.00 3.16
3147 4029 0.108186 TGAGGCACGAACTAGCATGG 60.108 55.000 0.00 0.00 0.00 3.66
3281 4783 9.906660 CCAACAGCTGAGTTACAAAAATAAATA 57.093 29.630 23.35 0.00 0.00 1.40
3282 4784 8.421002 ACCAACAGCTGAGTTACAAAAATAAAT 58.579 29.630 23.35 0.00 0.00 1.40
3283 4785 7.777095 ACCAACAGCTGAGTTACAAAAATAAA 58.223 30.769 23.35 0.00 0.00 1.40
3286 4788 5.852282 ACCAACAGCTGAGTTACAAAAAT 57.148 34.783 23.35 0.00 0.00 1.82
3287 4789 5.652994 AACCAACAGCTGAGTTACAAAAA 57.347 34.783 23.35 0.00 0.00 1.94
3292 4794 7.900782 TTTAGATAACCAACAGCTGAGTTAC 57.099 36.000 23.35 16.50 0.00 2.50
3294 4796 8.322091 ACTATTTAGATAACCAACAGCTGAGTT 58.678 33.333 23.35 21.07 0.00 3.01
3295 4797 7.852263 ACTATTTAGATAACCAACAGCTGAGT 58.148 34.615 23.35 11.83 0.00 3.41
3296 4798 9.988815 ATACTATTTAGATAACCAACAGCTGAG 57.011 33.333 23.35 12.34 0.00 3.35
3395 4941 2.890311 CCACCACCAATGCTTGTTTCTA 59.110 45.455 0.00 0.00 0.00 2.10
3451 4997 8.950210 CATAGCATATCTAACCGGAAAATCATT 58.050 33.333 9.46 0.00 0.00 2.57
3590 5138 2.297033 GAGTCCTTGCTTGCAATTTGGA 59.703 45.455 8.55 9.22 0.00 3.53
3618 5168 4.934602 GCAGAGCAAAGAGTGTAGAGAAAT 59.065 41.667 0.00 0.00 0.00 2.17
3644 5194 3.785887 TGGCTAGGTGGGAAATAACAGAT 59.214 43.478 0.00 0.00 0.00 2.90
3699 5249 2.025510 AGGGCCTGGAGAAAAGATTCAG 60.026 50.000 4.50 0.00 38.06 3.02
3724 5274 2.158784 GCTGCTGAGGAAGGAATGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
3791 5343 8.798859 AACAAAATAGCACATTCAGTAGAGAT 57.201 30.769 0.00 0.00 0.00 2.75
3809 5362 3.037549 TGGAAGTGAGGGCAAACAAAAT 58.962 40.909 0.00 0.00 0.00 1.82
3866 5419 6.893005 ACTACCAGCAAGAACTTAGAGAGTAT 59.107 38.462 0.00 0.00 37.72 2.12
3872 5425 3.260884 CCCACTACCAGCAAGAACTTAGA 59.739 47.826 0.00 0.00 0.00 2.10
3975 5528 4.217836 AGCATTTTCATCTCTGAGCAGA 57.782 40.909 0.00 0.00 35.85 4.26
4009 5567 4.270834 AGCATGAAAGCATTCTGATCTGT 58.729 39.130 0.00 0.00 36.48 3.41
4015 5573 3.066342 CCACCTAGCATGAAAGCATTCTG 59.934 47.826 0.00 0.73 36.48 3.02
4039 5597 9.268268 CAACAAAGGATTAGTAGTTCAGTTACA 57.732 33.333 0.00 0.00 0.00 2.41
4044 5602 6.428159 AGCACAACAAAGGATTAGTAGTTCAG 59.572 38.462 0.00 0.00 0.00 3.02
4070 5628 7.849322 AGGCAAAATAAAAATATATCCCGGT 57.151 32.000 0.00 0.00 0.00 5.28
4084 5642 4.343526 TCAGCAAGACCAAAGGCAAAATAA 59.656 37.500 0.00 0.00 0.00 1.40
4098 5656 5.126396 AGTTAAAGGCAATTCAGCAAGAC 57.874 39.130 0.00 0.00 35.83 3.01
4185 5744 7.280876 GGCAGTTATCAATCACTTATGAAGACA 59.719 37.037 0.00 0.00 38.69 3.41
4211 5805 7.429636 AAGAAATTTGAAACCAGATGCATTG 57.570 32.000 0.00 1.14 0.00 2.82
4242 6067 0.177141 GGCACACCTATAAGTCCGCA 59.823 55.000 0.00 0.00 0.00 5.69
4436 6801 1.067142 GGGCAGAAGTATCGTGTGTGA 60.067 52.381 0.00 0.00 0.00 3.58
4562 6927 6.426025 GCAATACATTCAGAGTCATGCTATGA 59.574 38.462 9.46 9.46 42.98 2.15
4614 6980 5.388654 ACTTCCTTCAGTCCAACATGATTT 58.611 37.500 0.00 0.00 0.00 2.17
4706 7073 3.077359 GCTGGCTAGTCACTGACAAATT 58.923 45.455 11.80 0.00 34.60 1.82
4724 7091 3.259123 ACTTTTTAGGAATGCAAGGGCTG 59.741 43.478 0.00 0.00 41.91 4.85
4757 7124 6.143915 TGGAGTAGGATAGCAGGTTTCTAAT 58.856 40.000 0.00 0.00 0.00 1.73
5205 7615 6.941857 TGCTGATACAACACAGAAGGTAATA 58.058 36.000 0.00 0.00 36.38 0.98
5241 7651 2.939756 ACACGCACAAAGTACAACATCA 59.060 40.909 0.00 0.00 0.00 3.07
5314 7724 7.283807 TGGGATTCATCATTCATTAGTCACAAG 59.716 37.037 0.00 0.00 0.00 3.16
5331 7742 2.848694 AGGTCACACTGATGGGATTCAT 59.151 45.455 0.00 0.00 41.43 2.57
5415 7826 1.821666 GCCAACTTACCCAAGCCTTCA 60.822 52.381 0.00 0.00 34.94 3.02
5445 7856 1.530293 CTATCAGCGCAAAGAGGCATC 59.470 52.381 11.47 0.00 0.00 3.91
5446 7857 1.590932 CTATCAGCGCAAAGAGGCAT 58.409 50.000 11.47 0.00 0.00 4.40
5448 7859 1.780025 GCCTATCAGCGCAAAGAGGC 61.780 60.000 25.36 25.36 42.45 4.70
5449 7860 0.462581 TGCCTATCAGCGCAAAGAGG 60.463 55.000 11.47 14.30 34.65 3.69
5538 7982 3.257393 AGTTAGCAAGTCATCTGCTTCG 58.743 45.455 2.22 0.00 39.79 3.79
5594 8038 5.053145 CCTAGTGTCTTTATCATGCCAGTC 58.947 45.833 0.00 0.00 0.00 3.51
5610 8054 2.159382 CACGGGCAATTTTCCTAGTGT 58.841 47.619 11.10 0.00 32.17 3.55
5632 8076 1.112315 AGCATGTTCCCCGTTGCAAA 61.112 50.000 0.00 0.00 37.56 3.68
5763 8211 4.475944 CGAAAATAAGTGCCTCAACCTTG 58.524 43.478 0.00 0.00 0.00 3.61
5773 8221 2.031683 CCATCCGTCCGAAAATAAGTGC 59.968 50.000 0.00 0.00 0.00 4.40
5784 8232 0.744874 ACACATACTCCATCCGTCCG 59.255 55.000 0.00 0.00 0.00 4.79
5980 8442 8.432013 TGAGATTATATGACAAGCAATGGTAGT 58.568 33.333 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.