Multiple sequence alignment - TraesCS4D01G276300

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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 TraesCS4D01G276300 chr4D 100.000 6049 0 0 1 6049 447345741 447339693 0.000000e+00 11171.0
1 TraesCS4D01G276300 chr4D 91.581 2031 119 31 71 2070 417655102 417653093 0.000000e+00 2756.0
2 TraesCS4D01G276300 chr4D 92.220 1928 117 22 165 2074 460719408 460717496 0.000000e+00 2699.0
3 TraesCS4D01G276300 chr4D 90.900 2033 135 31 71 2075 401138436 401136426 0.000000e+00 2684.0
4 TraesCS4D01G276300 chr4D 92.958 71 5 0 4468 4538 297209711 297209641 2.980000e-18 104.0
5 TraesCS4D01G276300 chr1D 93.158 2017 116 13 71 2074 286620694 286622701 0.000000e+00 2940.0
6 TraesCS4D01G276300 chr1D 91.313 2026 139 34 71 2074 270155569 270157579 0.000000e+00 2732.0
7 TraesCS4D01G276300 chr1D 88.839 2007 183 35 71 2053 57470063 57472052 0.000000e+00 2427.0
8 TraesCS4D01G276300 chr1D 98.611 72 1 0 1 72 192270698 192270627 1.770000e-25 128.0
9 TraesCS4D01G276300 chr1D 89.286 56 5 1 2502 2556 270507886 270507831 1.090000e-07 69.4
10 TraesCS4D01G276300 chr2D 91.111 2025 144 24 71 2073 433405094 433407104 0.000000e+00 2710.0
11 TraesCS4D01G276300 chr2D 77.681 345 64 11 3860 4196 534956310 534955971 1.330000e-46 198.0
12 TraesCS4D01G276300 chr2D 97.297 74 2 0 1 74 440100533 440100606 6.360000e-25 126.0
13 TraesCS4D01G276300 chr2D 77.863 131 29 0 2520 2650 440606980 440607110 1.400000e-11 82.4
14 TraesCS4D01G276300 chr2D 97.500 40 1 0 4173 4212 585076853 585076892 1.090000e-07 69.4
15 TraesCS4D01G276300 chr6D 90.094 2029 155 37 71 2074 352644301 352646308 0.000000e+00 2591.0
16 TraesCS4D01G276300 chr6D 91.954 87 4 2 1 84 37707185 37707271 1.070000e-22 119.0
17 TraesCS4D01G276300 chr6D 95.349 43 2 0 4173 4215 428449024 428448982 1.090000e-07 69.4
18 TraesCS4D01G276300 chr6D 79.487 78 16 0 2520 2597 117392590 117392667 8.470000e-04 56.5
19 TraesCS4D01G276300 chr7A 90.059 2022 162 27 72 2074 543744882 543742881 0.000000e+00 2584.0
20 TraesCS4D01G276300 chr4B 97.200 1250 30 3 4804 6049 559857585 559856337 0.000000e+00 2109.0
21 TraesCS4D01G276300 chr4B 93.810 937 46 7 3829 4758 559867057 559866126 0.000000e+00 1399.0
22 TraesCS4D01G276300 chr4B 92.598 743 43 6 3100 3832 559868224 559867484 0.000000e+00 1057.0
23 TraesCS4D01G276300 chr4B 84.236 831 76 27 2075 2880 559870200 559869400 0.000000e+00 758.0
24 TraesCS4D01G276300 chr4B 91.667 72 6 0 4468 4539 531092537 531092608 3.860000e-17 100.0
25 TraesCS4D01G276300 chr4B 97.297 37 1 0 4754 4790 559857621 559857585 5.060000e-06 63.9
26 TraesCS4D01G276300 chr4A 88.417 941 75 16 4450 5372 19657238 19658162 0.000000e+00 1103.0
27 TraesCS4D01G276300 chr4A 94.374 551 26 4 5500 6049 19658220 19658766 0.000000e+00 841.0
28 TraesCS4D01G276300 chr4A 85.077 650 66 11 2075 2693 19653964 19654613 8.550000e-178 634.0
29 TraesCS4D01G276300 chr4A 91.260 389 30 4 3831 4215 19656852 19657240 1.490000e-145 527.0
30 TraesCS4D01G276300 chr4A 92.388 289 12 6 2697 2984 19655292 19655571 2.630000e-108 403.0
31 TraesCS4D01G276300 chr4A 88.298 282 23 7 3532 3812 19656303 19656575 4.520000e-86 329.0
32 TraesCS4D01G276300 chr4A 89.796 245 22 3 3291 3534 19655839 19656081 1.640000e-80 311.0
33 TraesCS4D01G276300 chr4A 88.085 235 20 7 1850 2081 201646714 201646485 7.730000e-69 272.0
34 TraesCS4D01G276300 chr4A 93.496 123 3 2 2973 3092 19655592 19655712 1.730000e-40 178.0
35 TraesCS4D01G276300 chr4A 86.923 130 14 2 3124 3250 19655711 19655840 6.320000e-30 143.0
36 TraesCS4D01G276300 chr1B 86.709 474 43 10 1611 2074 653180173 653180636 5.410000e-140 508.0
37 TraesCS4D01G276300 chr2A 86.939 245 23 4 1848 2084 530152187 530151944 3.590000e-67 267.0
38 TraesCS4D01G276300 chr2A 79.023 348 53 16 3860 4196 678191052 678190714 2.840000e-53 220.0
39 TraesCS4D01G276300 chr2A 97.297 74 2 0 1 74 583415750 583415823 6.360000e-25 126.0
40 TraesCS4D01G276300 chr2A 80.000 90 11 6 2509 2595 135889269 135889184 6.550000e-05 60.2
41 TraesCS4D01G276300 chr5A 87.773 229 20 3 1853 2075 220641562 220641336 1.670000e-65 261.0
42 TraesCS4D01G276300 chr5A 84.615 65 10 0 4214 4278 216954223 216954287 1.410000e-06 65.8
43 TraesCS4D01G276300 chr2B 78.488 344 56 11 3860 4196 636209888 636209556 6.140000e-50 209.0
44 TraesCS4D01G276300 chr2B 79.907 214 33 7 4236 4446 181121334 181121128 1.360000e-31 148.0
45 TraesCS4D01G276300 chr2B 97.297 74 2 0 1 74 517760651 517760724 6.360000e-25 126.0
46 TraesCS4D01G276300 chr3D 80.252 238 38 7 4220 4452 558297747 558297980 2.900000e-38 171.0
47 TraesCS4D01G276300 chr3D 94.937 79 3 1 1 79 479490662 479490585 8.230000e-24 122.0
48 TraesCS4D01G276300 chr3D 93.902 82 4 1 1 82 494049126 494049046 8.230000e-24 122.0
49 TraesCS4D01G276300 chr3D 93.750 48 3 0 2528 2575 112387795 112387748 8.410000e-09 73.1
50 TraesCS4D01G276300 chr3D 95.455 44 2 0 4172 4215 316545535 316545492 3.020000e-08 71.3
51 TraesCS4D01G276300 chr7D 100.000 70 0 0 1 70 401178294 401178225 4.920000e-26 130.0
52 TraesCS4D01G276300 chr7D 93.056 72 5 0 4468 4539 507232135 507232064 8.290000e-19 106.0
53 TraesCS4D01G276300 chr7D 90.278 72 7 0 4468 4539 19026101 19026030 1.790000e-15 95.3
54 TraesCS4D01G276300 chr7D 90.278 72 7 0 4468 4539 498414356 498414427 1.790000e-15 95.3
55 TraesCS4D01G276300 chr7D 88.889 72 8 0 4468 4539 549660551 549660622 8.350000e-14 89.8
56 TraesCS4D01G276300 chr6A 100.000 70 0 0 1 70 225835613 225835682 4.920000e-26 130.0
57 TraesCS4D01G276300 chr6A 91.667 72 6 0 4468 4539 162191228 162191299 3.860000e-17 100.0
58 TraesCS4D01G276300 chr5B 94.444 72 4 0 4468 4539 692442524 692442595 1.780000e-20 111.0
59 TraesCS4D01G276300 chr5B 93.056 72 5 0 4141 4212 506665268 506665339 8.290000e-19 106.0
60 TraesCS4D01G276300 chr5B 93.056 72 5 0 4141 4212 643312659 643312730 8.290000e-19 106.0
61 TraesCS4D01G276300 chr5B 93.056 72 5 0 4141 4212 712185471 712185542 8.290000e-19 106.0
62 TraesCS4D01G276300 chr3B 93.151 73 5 0 4467 4539 763244460 763244532 2.310000e-19 108.0
63 TraesCS4D01G276300 chr3B 93.056 72 5 0 4468 4539 82361578 82361507 8.290000e-19 106.0
64 TraesCS4D01G276300 chr3B 88.462 52 5 1 2520 2571 716142883 716142833 1.820000e-05 62.1
65 TraesCS4D01G276300 chr5D 93.056 72 5 0 4468 4539 90695692 90695763 8.290000e-19 106.0
66 TraesCS4D01G276300 chr5D 91.667 72 6 0 4468 4539 117886277 117886206 3.860000e-17 100.0
67 TraesCS4D01G276300 chr5D 88.889 72 7 1 4468 4539 275204446 275204376 3.000000e-13 87.9
68 TraesCS4D01G276300 chr5D 100.000 28 0 0 5183 5210 522494658 522494685 1.100000e-02 52.8
69 TraesCS4D01G276300 chrUn 91.667 72 6 0 4468 4539 306723319 306723390 3.860000e-17 100.0
70 TraesCS4D01G276300 chr6B 91.667 72 6 0 4468 4539 612981293 612981364 3.860000e-17 100.0
71 TraesCS4D01G276300 chr6B 97.297 37 1 0 2519 2555 9036976 9037012 5.060000e-06 63.9


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 TraesCS4D01G276300 chr4D 447339693 447345741 6048 True 11171.000000 11171 100.000000 1 6049 1 chr4D.!!$R4 6048
1 TraesCS4D01G276300 chr4D 417653093 417655102 2009 True 2756.000000 2756 91.581000 71 2070 1 chr4D.!!$R3 1999
2 TraesCS4D01G276300 chr4D 460717496 460719408 1912 True 2699.000000 2699 92.220000 165 2074 1 chr4D.!!$R5 1909
3 TraesCS4D01G276300 chr4D 401136426 401138436 2010 True 2684.000000 2684 90.900000 71 2075 1 chr4D.!!$R2 2004
4 TraesCS4D01G276300 chr1D 286620694 286622701 2007 False 2940.000000 2940 93.158000 71 2074 1 chr1D.!!$F3 2003
5 TraesCS4D01G276300 chr1D 270155569 270157579 2010 False 2732.000000 2732 91.313000 71 2074 1 chr1D.!!$F2 2003
6 TraesCS4D01G276300 chr1D 57470063 57472052 1989 False 2427.000000 2427 88.839000 71 2053 1 chr1D.!!$F1 1982
7 TraesCS4D01G276300 chr2D 433405094 433407104 2010 False 2710.000000 2710 91.111000 71 2073 1 chr2D.!!$F1 2002
8 TraesCS4D01G276300 chr6D 352644301 352646308 2007 False 2591.000000 2591 90.094000 71 2074 1 chr6D.!!$F3 2003
9 TraesCS4D01G276300 chr7A 543742881 543744882 2001 True 2584.000000 2584 90.059000 72 2074 1 chr7A.!!$R1 2002
10 TraesCS4D01G276300 chr4B 559856337 559857621 1284 True 1086.450000 2109 97.248500 4754 6049 2 chr4B.!!$R1 1295
11 TraesCS4D01G276300 chr4B 559866126 559870200 4074 True 1071.333333 1399 90.214667 2075 4758 3 chr4B.!!$R2 2683
12 TraesCS4D01G276300 chr4A 19653964 19658766 4802 False 496.555556 1103 90.003222 2075 6049 9 chr4A.!!$F1 3974

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 0.766288 GCCCTTGAGCCTCCTCCTAT 60.766 60.0 0.00 0.0 37.29 2.57 F
1392 1400 0.851469 TCGGAGTACCAGGAGGCTAT 59.149 55.0 0.00 0.0 39.06 2.97 F
2288 2380 0.179108 ATACGAGCCCGAAAGCAGTC 60.179 55.0 0.00 0.0 39.50 3.51 F
2603 2705 0.108804 AGCATCGTCCGTTACACCAG 60.109 55.0 0.00 0.0 0.00 4.00 F
3118 4852 0.721718 GTCATCCTTTCTGTTCGGCG 59.278 55.0 0.00 0.0 0.00 6.46 F
3901 6373 0.478072 ACAGGAAGTGCCCATTCACA 59.522 50.0 0.00 0.0 39.35 3.58 F
4491 6972 0.893270 TCAATTCTGTTGGCCCACCG 60.893 55.0 4.19 0.0 39.70 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1908 0.965866 TCAGCTCGATGACGTCCCTT 60.966 55.000 14.12 0.00 40.69 3.95 R
2584 2686 0.108804 CTGGTGTAACGGACGATGCT 60.109 55.000 0.00 0.00 38.12 3.79 R
3151 4885 0.248661 CCGCATCGTCGTCATCTTCT 60.249 55.000 0.00 0.00 0.00 2.85 R
3771 5740 1.063174 CATGCTTCCGCTCTGTTTAGC 59.937 52.381 0.00 0.00 39.21 3.09 R
4795 7277 0.179001 CCCAGTTTCTGAAACCCCGT 60.179 55.000 25.22 8.07 42.34 5.28 R
4796 7278 0.179001 ACCCAGTTTCTGAAACCCCG 60.179 55.000 25.22 16.25 42.34 5.73 R
5697 8205 0.320771 TCTTCAAGCTTGAGACGCCC 60.321 55.000 27.02 0.00 38.61 6.13 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
17 18 2.674380 CCACCAGTGCCCTTGAGC 60.674 66.667 0.00 0.00 0.00 4.26
18 19 2.674380 CACCAGTGCCCTTGAGCC 60.674 66.667 0.00 0.00 0.00 4.70
19 20 2.856000 ACCAGTGCCCTTGAGCCT 60.856 61.111 0.00 0.00 0.00 4.58
20 21 2.045536 CCAGTGCCCTTGAGCCTC 60.046 66.667 0.00 0.00 0.00 4.70
21 22 2.045536 CAGTGCCCTTGAGCCTCC 60.046 66.667 0.00 0.00 0.00 4.30
22 23 2.204059 AGTGCCCTTGAGCCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
23 24 2.270527 GTGCCCTTGAGCCTCCTC 59.729 66.667 0.00 0.00 38.62 3.71
24 25 3.011517 TGCCCTTGAGCCTCCTCC 61.012 66.667 0.00 0.00 37.29 4.30
25 26 2.690510 GCCCTTGAGCCTCCTCCT 60.691 66.667 0.00 0.00 37.29 3.69
26 27 1.383248 GCCCTTGAGCCTCCTCCTA 60.383 63.158 0.00 0.00 37.29 2.94
27 28 0.766288 GCCCTTGAGCCTCCTCCTAT 60.766 60.000 0.00 0.00 37.29 2.57
28 29 1.347062 CCCTTGAGCCTCCTCCTATC 58.653 60.000 0.00 0.00 37.29 2.08
29 30 1.132881 CCCTTGAGCCTCCTCCTATCT 60.133 57.143 0.00 0.00 37.29 1.98
30 31 2.688477 CCTTGAGCCTCCTCCTATCTT 58.312 52.381 0.00 0.00 37.29 2.40
31 32 3.044894 CCTTGAGCCTCCTCCTATCTTT 58.955 50.000 0.00 0.00 37.29 2.52
32 33 4.227197 CCTTGAGCCTCCTCCTATCTTTA 58.773 47.826 0.00 0.00 37.29 1.85
33 34 4.283212 CCTTGAGCCTCCTCCTATCTTTAG 59.717 50.000 0.00 0.00 37.29 1.85
34 35 3.235200 TGAGCCTCCTCCTATCTTTAGC 58.765 50.000 0.00 0.00 37.29 3.09
35 36 2.565391 GAGCCTCCTCCTATCTTTAGCC 59.435 54.545 0.00 0.00 31.68 3.93
36 37 2.090494 AGCCTCCTCCTATCTTTAGCCA 60.090 50.000 0.00 0.00 0.00 4.75
37 38 2.909662 GCCTCCTCCTATCTTTAGCCAT 59.090 50.000 0.00 0.00 0.00 4.40
38 39 3.055458 GCCTCCTCCTATCTTTAGCCATC 60.055 52.174 0.00 0.00 0.00 3.51
39 40 3.517500 CCTCCTCCTATCTTTAGCCATCC 59.482 52.174 0.00 0.00 0.00 3.51
40 41 3.517500 CTCCTCCTATCTTTAGCCATCCC 59.482 52.174 0.00 0.00 0.00 3.85
41 42 3.144894 TCCTCCTATCTTTAGCCATCCCT 59.855 47.826 0.00 0.00 0.00 4.20
42 43 3.913163 CCTCCTATCTTTAGCCATCCCTT 59.087 47.826 0.00 0.00 0.00 3.95
43 44 4.263243 CCTCCTATCTTTAGCCATCCCTTG 60.263 50.000 0.00 0.00 0.00 3.61
51 52 3.851955 CCATCCCTTGGCATCTGC 58.148 61.111 0.00 0.00 39.09 4.26
122 123 2.096442 GCAATTGCCTTGGCGAAGC 61.096 57.895 20.06 9.38 45.27 3.86
240 241 1.089920 ACGGATCTGAATGTTGCAGC 58.910 50.000 9.00 0.00 33.45 5.25
366 367 4.785376 AGTGGGAGACTGAAGGAAATATGT 59.215 41.667 0.00 0.00 31.75 2.29
381 382 7.454225 AGGAAATATGTCCTAGAGGCAATAAC 58.546 38.462 13.25 0.00 46.69 1.89
469 470 5.217978 TCCGGAAACTTAGTACATGTGTT 57.782 39.130 9.11 0.09 0.00 3.32
565 568 6.013725 AGTTTCCTGACCATAGACATGTGTTA 60.014 38.462 1.15 0.00 0.00 2.41
595 598 3.466836 TGAACGGGATCACATCATTAGC 58.533 45.455 0.00 0.00 0.00 3.09
671 674 9.554724 TTAGTTTTATTGCTATTGCTTTCTTCG 57.445 29.630 0.00 0.00 40.48 3.79
695 698 7.040617 TCGTGACTTATACATATTCCTCTGACC 60.041 40.741 0.00 0.00 0.00 4.02
795 798 3.380471 AGATGCTCTACAGGTGTCTCT 57.620 47.619 0.00 0.00 0.00 3.10
806 809 3.054361 ACAGGTGTCTCTGAAGGTGTTTT 60.054 43.478 0.00 0.00 38.11 2.43
1045 1049 2.128771 ACCGATGACAAAGGGAATGG 57.871 50.000 4.83 0.00 0.00 3.16
1151 1156 7.131302 GGTTATTGACCCGAGATGTGTCTCT 62.131 48.000 4.18 0.00 43.61 3.10
1178 1183 4.338012 TGTCTACATAGTTCTCGAACCCA 58.662 43.478 6.20 0.00 42.06 4.51
1181 1186 6.604396 TGTCTACATAGTTCTCGAACCCATAA 59.396 38.462 6.20 0.00 42.06 1.90
1182 1187 7.123098 TGTCTACATAGTTCTCGAACCCATAAA 59.877 37.037 6.20 0.00 42.06 1.40
1191 1196 1.816074 GAACCCATAAAGTCCGCACA 58.184 50.000 0.00 0.00 0.00 4.57
1233 1239 9.676195 TGATTTGTATTATGAGTTGTGTGTTTG 57.324 29.630 0.00 0.00 0.00 2.93
1389 1397 1.700955 TTATCGGAGTACCAGGAGGC 58.299 55.000 0.00 0.00 39.06 4.70
1392 1400 0.851469 TCGGAGTACCAGGAGGCTAT 59.149 55.000 0.00 0.00 39.06 2.97
1421 1432 2.176045 CCGGGAAAGTTAATGGGCTTT 58.824 47.619 0.00 0.00 37.60 3.51
1440 1451 3.344535 TTATGGGCCATAGTGGAGAGA 57.655 47.619 24.42 6.28 40.96 3.10
1441 1452 1.727062 ATGGGCCATAGTGGAGAGAG 58.273 55.000 19.68 0.00 40.96 3.20
1447 1458 1.501170 CCATAGTGGAGAGAGGGAGGA 59.499 57.143 0.00 0.00 40.96 3.71
1695 1759 4.695455 GCACAACAGTTATTCTCTTAGCCA 59.305 41.667 0.00 0.00 0.00 4.75
1775 1839 2.514592 CCCTGCGCGGATCACATT 60.515 61.111 20.25 0.00 33.16 2.71
1844 1908 4.026744 CCCTCTACTGGATCAAGAGTTCA 58.973 47.826 3.42 0.00 35.93 3.18
1878 1942 0.588252 GCTGAACGTGTGCTGAACAT 59.412 50.000 0.00 0.00 41.97 2.71
1908 1972 3.492421 GTACGTTCGGTACTTGGATCA 57.508 47.619 0.00 0.00 46.50 2.92
1926 1990 2.621338 TCAGTTGGATCGTGAAGATGC 58.379 47.619 0.00 0.00 46.40 3.91
1929 1993 2.234661 AGTTGGATCGTGAAGATGCTCA 59.765 45.455 1.50 0.00 46.37 4.26
2007 2077 0.968901 TCCCCGTCTCGTTGCTATGT 60.969 55.000 0.00 0.00 0.00 2.29
2086 2156 1.409521 CCCCAACAGAACCACACTTCA 60.410 52.381 0.00 0.00 0.00 3.02
2087 2157 2.586425 CCCAACAGAACCACACTTCAT 58.414 47.619 0.00 0.00 0.00 2.57
2104 2174 4.724074 TTCATGGTGGATGAAGAAATGC 57.276 40.909 0.00 0.00 44.65 3.56
2142 2212 3.619038 GTCCTAACTCGGCATCAAAGAAG 59.381 47.826 0.00 0.00 0.00 2.85
2150 2220 2.679837 CGGCATCAAAGAAGTGCTATGT 59.320 45.455 0.00 0.00 38.83 2.29
2154 2224 5.163581 GGCATCAAAGAAGTGCTATGTCAAT 60.164 40.000 0.00 0.00 38.83 2.57
2157 2227 7.681304 GCATCAAAGAAGTGCTATGTCAATGAT 60.681 37.037 0.00 0.00 36.02 2.45
2163 2233 5.045012 AGTGCTATGTCAATGATGGATGT 57.955 39.130 0.00 0.00 0.00 3.06
2191 2279 1.007319 GCGACGTCGAAGAAATAGCAC 60.007 52.381 39.74 14.61 43.02 4.40
2210 2302 1.005215 ACCAATGAAGCCCTTCTCTGG 59.995 52.381 18.93 18.93 42.50 3.86
2288 2380 0.179108 ATACGAGCCCGAAAGCAGTC 60.179 55.000 0.00 0.00 39.50 3.51
2296 2388 2.605580 GCCCGAAAGCAGTCAAAAGAAG 60.606 50.000 0.00 0.00 0.00 2.85
2406 2501 3.291585 GCATTCAAGAAACACGTGTCAG 58.708 45.455 23.61 10.25 0.00 3.51
2451 2553 3.063997 GCTCGGAACAGTGATTAATGTGG 59.936 47.826 0.00 0.00 34.96 4.17
2510 2612 5.762045 CAATTTCTTCACCGACAAGAACAT 58.238 37.500 3.68 0.69 39.15 2.71
2513 2615 3.390135 TCTTCACCGACAAGAACATGAC 58.610 45.455 0.00 0.00 0.00 3.06
2556 2658 4.791069 TGGAGTACCCGCCTCCCC 62.791 72.222 4.12 0.00 46.64 4.81
2602 2704 0.389296 CAGCATCGTCCGTTACACCA 60.389 55.000 0.00 0.00 0.00 4.17
2603 2705 0.108804 AGCATCGTCCGTTACACCAG 60.109 55.000 0.00 0.00 0.00 4.00
2693 2795 6.625081 GCCCGTTAGAAAGCTTTATCACAATT 60.625 38.462 12.68 0.00 0.00 2.32
2695 2797 8.455682 CCCGTTAGAAAGCTTTATCACAATTTA 58.544 33.333 12.68 0.00 0.00 1.40
2814 3592 4.928661 AACTTCATGACGCACTGAATAC 57.071 40.909 0.00 0.00 31.39 1.89
2818 3596 5.412594 ACTTCATGACGCACTGAATACAATT 59.587 36.000 0.00 0.00 31.39 2.32
2825 3603 7.045416 TGACGCACTGAATACAATTATAAGGT 58.955 34.615 0.00 0.00 0.00 3.50
2898 3676 2.103601 GCCCAGTAGCCGAAATTACCTA 59.896 50.000 0.00 0.00 0.00 3.08
2916 4095 2.299013 CCTAAAGGGGAACAAGCAAACC 59.701 50.000 0.00 0.00 0.00 3.27
2967 4146 1.586564 CTAAGGCGCTCGAAGTCCG 60.587 63.158 7.64 0.00 40.25 4.79
3096 4770 2.730672 GGCACGTAAGCTGCACTCG 61.731 63.158 1.02 5.65 43.16 4.18
3097 4771 2.772189 CACGTAAGCTGCACTCGC 59.228 61.111 1.02 0.00 45.62 5.03
3098 4772 1.734477 CACGTAAGCTGCACTCGCT 60.734 57.895 1.02 0.00 45.62 4.93
3115 4849 1.391485 CGCTGTCATCCTTTCTGTTCG 59.609 52.381 0.00 0.00 0.00 3.95
3118 4852 0.721718 GTCATCCTTTCTGTTCGGCG 59.278 55.000 0.00 0.00 0.00 6.46
3151 4885 4.771356 CCGCGCGTCTCTTCCGAA 62.771 66.667 29.95 0.00 0.00 4.30
3165 4899 1.445871 TCCGAAGAAGATGACGACGA 58.554 50.000 0.00 0.00 0.00 4.20
3166 4900 2.014857 TCCGAAGAAGATGACGACGAT 58.985 47.619 0.00 0.00 0.00 3.73
3175 4909 2.809601 GACGACGATGCGGCAACT 60.810 61.111 6.82 0.00 39.62 3.16
3272 5009 3.700970 TGATGGAGAACGCGGGCA 61.701 61.111 12.47 0.00 0.00 5.36
3306 5043 4.691860 ATTTTCGGCATGAGAAGTTGAG 57.308 40.909 0.00 0.00 0.00 3.02
3407 5150 2.045280 CATCCCGAGCCCTCTACTG 58.955 63.158 0.00 0.00 0.00 2.74
3429 5173 4.521256 TGTTGGGGATTTTCTTAAGGTTCG 59.479 41.667 1.85 0.00 0.00 3.95
3451 5195 4.561734 CGGGGTTAGAGAGAAATCTATGGC 60.562 50.000 0.00 0.00 31.96 4.40
3462 5206 5.727630 AGAAATCTATGGCTAGGGTTCCTA 58.272 41.667 0.00 0.00 34.61 2.94
3554 5522 9.152595 GACTAATAACCAGAAAAACAGTAGGAG 57.847 37.037 0.00 0.00 0.00 3.69
3634 5603 9.160496 CACTTAATCATGAAGATTAGGCCTATC 57.840 37.037 14.74 13.01 46.77 2.08
3642 5611 5.538813 TGAAGATTAGGCCTATCGCTTAAGA 59.461 40.000 14.74 0.00 41.78 2.10
3664 5633 3.498774 AATAGCATCAAGGTAGGCCTG 57.501 47.619 17.99 0.00 46.33 4.85
3670 5639 3.181450 GCATCAAGGTAGGCCTGATTAGT 60.181 47.826 17.99 0.00 46.33 2.24
3679 5648 6.268847 AGGTAGGCCTGATTAGTATTCTCAAG 59.731 42.308 17.99 0.00 45.05 3.02
3713 5682 5.280676 GGGGCTCATGATACCAATGATAGAA 60.281 44.000 14.92 0.00 0.00 2.10
3771 5740 5.410924 TCTTGACCTCATGATTAGAACACG 58.589 41.667 0.00 0.00 0.00 4.49
3850 6322 8.517062 AAACTAGGGAGAATGAAATCAGATTG 57.483 34.615 0.00 0.00 0.00 2.67
3901 6373 0.478072 ACAGGAAGTGCCCATTCACA 59.522 50.000 0.00 0.00 39.35 3.58
3929 6402 8.635765 AACTGTTTTATCAGAGGCAGAATTAA 57.364 30.769 0.00 0.00 38.63 1.40
4223 6702 4.251103 TCTAGCTGATGTACTTCCTCCA 57.749 45.455 0.00 0.00 0.00 3.86
4239 6718 5.779241 TCCTCCATTCTAATGAACAAGGT 57.221 39.130 4.25 0.00 38.70 3.50
4284 6763 6.549912 ACTTTGACCGTAAATTAGACCAAC 57.450 37.500 0.00 0.00 0.00 3.77
4285 6764 5.471116 ACTTTGACCGTAAATTAGACCAACC 59.529 40.000 0.00 0.00 0.00 3.77
4286 6765 4.620589 TGACCGTAAATTAGACCAACCA 57.379 40.909 0.00 0.00 0.00 3.67
4287 6766 4.970711 TGACCGTAAATTAGACCAACCAA 58.029 39.130 0.00 0.00 0.00 3.67
4349 6828 8.870160 TTTGTATTGGAAAGAAGTGTTCAATG 57.130 30.769 0.00 0.00 0.00 2.82
4409 6888 8.330466 TGATGTAATTTACGGTCAAAGTTGAT 57.670 30.769 10.33 0.00 39.73 2.57
4415 6894 7.617533 ATTTACGGTCAAAGTTGATTTTTCG 57.382 32.000 0.00 0.94 39.73 3.46
4421 6900 5.458779 GGTCAAAGTTGATTTTTCGGAAGTG 59.541 40.000 0.00 0.00 39.73 3.16
4458 6939 2.370189 GGGATGGAGGGAGTATTGTCTG 59.630 54.545 0.00 0.00 0.00 3.51
4488 6969 3.237746 TGATTTCAATTCTGTTGGCCCA 58.762 40.909 0.00 0.00 0.00 5.36
4491 6972 0.893270 TCAATTCTGTTGGCCCACCG 60.893 55.000 4.19 0.00 39.70 4.94
4603 7084 8.830201 TGATTTTACAAATGAAGGGAAACATG 57.170 30.769 0.00 0.00 0.00 3.21
4703 7184 3.274288 TGATGTATGCGTTGTATTGCCA 58.726 40.909 0.00 0.00 0.00 4.92
4784 7266 8.092687 ACTCTTATGTGACAACCGTAAGTTTAT 58.907 33.333 0.00 0.00 36.18 1.40
4790 7272 9.834628 ATGTGACAACCGTAAGTTTATTAAATG 57.165 29.630 0.00 0.00 36.18 2.32
4795 7277 8.136165 ACAACCGTAAGTTTATTAAATGCACAA 58.864 29.630 0.00 0.00 36.18 3.33
4796 7278 8.421701 CAACCGTAAGTTTATTAAATGCACAAC 58.578 33.333 0.00 0.00 36.18 3.32
4803 7285 5.470047 TTATTAAATGCACAACGGGGTTT 57.530 34.783 0.00 0.00 0.00 3.27
5170 7655 6.529220 AGCCCTCTGTCATTTATCTGAATAC 58.471 40.000 0.00 0.00 0.00 1.89
5391 7899 1.028905 CCTTTTTGCCGACCTCACAA 58.971 50.000 0.00 0.00 0.00 3.33
5490 7998 6.100004 TGTTATCTGTTGTCCGAAAGAGATC 58.900 40.000 7.90 0.00 38.91 2.75
5697 8205 3.127533 GGGCTACTGGCTTGTGCG 61.128 66.667 0.00 0.00 41.46 5.34
5840 8350 2.499289 AGTGAGACTTCCAGCCATACAG 59.501 50.000 0.00 0.00 0.00 2.74
5931 8441 4.457603 TCAATAACCCAACCACTTCATTCG 59.542 41.667 0.00 0.00 0.00 3.34
5962 8472 1.610522 GCTTGATCTTGCAACACCACT 59.389 47.619 0.00 0.00 0.00 4.00
5978 8488 6.590234 ACACCACTCCTTCCATTTAATTTC 57.410 37.500 0.00 0.00 0.00 2.17
6027 8537 0.526739 TCGCCATCGTGGTTCGTATG 60.527 55.000 6.02 0.00 40.46 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.674380 GCTCAAGGGCACTGGTGG 60.674 66.667 0.00 0.00 0.00 4.61
1 2 2.674380 GGCTCAAGGGCACTGGTG 60.674 66.667 0.00 0.00 40.53 4.17
2 3 2.856000 AGGCTCAAGGGCACTGGT 60.856 61.111 0.00 0.00 43.56 4.00
3 4 2.045536 GAGGCTCAAGGGCACTGG 60.046 66.667 10.25 0.00 43.56 4.00
4 5 2.045536 GGAGGCTCAAGGGCACTG 60.046 66.667 17.69 0.00 43.56 3.66
5 6 2.204059 AGGAGGCTCAAGGGCACT 60.204 61.111 17.69 0.00 43.56 4.40
6 7 2.270527 GAGGAGGCTCAAGGGCAC 59.729 66.667 17.69 0.00 43.56 5.01
7 8 2.181523 TAGGAGGAGGCTCAAGGGCA 62.182 60.000 17.69 0.00 43.56 5.36
8 9 0.766288 ATAGGAGGAGGCTCAAGGGC 60.766 60.000 17.69 0.00 41.20 5.19
9 10 1.132881 AGATAGGAGGAGGCTCAAGGG 60.133 57.143 17.69 0.00 0.00 3.95
10 11 2.397044 AGATAGGAGGAGGCTCAAGG 57.603 55.000 17.69 0.00 0.00 3.61
11 12 4.262420 GCTAAAGATAGGAGGAGGCTCAAG 60.262 50.000 17.69 0.00 0.00 3.02
12 13 3.643792 GCTAAAGATAGGAGGAGGCTCAA 59.356 47.826 17.69 0.00 0.00 3.02
13 14 3.235200 GCTAAAGATAGGAGGAGGCTCA 58.765 50.000 17.69 0.00 0.00 4.26
14 15 2.565391 GGCTAAAGATAGGAGGAGGCTC 59.435 54.545 5.78 5.78 0.00 4.70
15 16 2.090494 TGGCTAAAGATAGGAGGAGGCT 60.090 50.000 0.00 0.00 0.00 4.58
16 17 2.330216 TGGCTAAAGATAGGAGGAGGC 58.670 52.381 0.00 0.00 0.00 4.70
17 18 3.517500 GGATGGCTAAAGATAGGAGGAGG 59.482 52.174 0.00 0.00 0.00 4.30
18 19 3.517500 GGGATGGCTAAAGATAGGAGGAG 59.482 52.174 0.00 0.00 0.00 3.69
19 20 3.144894 AGGGATGGCTAAAGATAGGAGGA 59.855 47.826 0.00 0.00 0.00 3.71
20 21 3.525862 AGGGATGGCTAAAGATAGGAGG 58.474 50.000 0.00 0.00 0.00 4.30
21 22 4.263243 CCAAGGGATGGCTAAAGATAGGAG 60.263 50.000 0.00 0.00 43.80 3.69
22 23 3.652869 CCAAGGGATGGCTAAAGATAGGA 59.347 47.826 0.00 0.00 43.80 2.94
23 24 4.026356 CCAAGGGATGGCTAAAGATAGG 57.974 50.000 0.00 0.00 43.80 2.57
57 58 4.699522 GACCCTGTCGTGGTGGGC 62.700 72.222 0.00 0.00 44.56 5.36
58 59 4.016706 GGACCCTGTCGTGGTGGG 62.017 72.222 0.00 0.00 46.07 4.61
59 60 2.124507 ATTGGACCCTGTCGTGGTGG 62.125 60.000 0.00 0.00 35.85 4.61
60 61 0.955428 CATTGGACCCTGTCGTGGTG 60.955 60.000 0.00 0.00 35.85 4.17
61 62 1.125093 TCATTGGACCCTGTCGTGGT 61.125 55.000 0.00 0.00 39.32 4.16
62 63 0.036164 TTCATTGGACCCTGTCGTGG 59.964 55.000 0.00 0.00 32.65 4.94
63 64 1.890876 TTTCATTGGACCCTGTCGTG 58.109 50.000 0.00 0.00 32.65 4.35
64 65 2.649531 TTTTCATTGGACCCTGTCGT 57.350 45.000 0.00 0.00 32.65 4.34
65 66 3.347216 AGATTTTCATTGGACCCTGTCG 58.653 45.455 0.00 0.00 32.65 4.35
66 67 5.728637 AAAGATTTTCATTGGACCCTGTC 57.271 39.130 0.00 0.00 0.00 3.51
67 68 5.366477 ACAAAAGATTTTCATTGGACCCTGT 59.634 36.000 0.00 0.00 0.00 4.00
68 69 5.697633 CACAAAAGATTTTCATTGGACCCTG 59.302 40.000 0.00 0.00 0.00 4.45
69 70 5.602145 TCACAAAAGATTTTCATTGGACCCT 59.398 36.000 0.00 0.00 0.00 4.34
122 123 5.474532 TGGTTCTCTTGTGAAATCTGGATTG 59.525 40.000 0.00 0.00 0.00 2.67
240 241 0.613777 AAGAGGCTTAGTCAACGGGG 59.386 55.000 0.00 0.00 0.00 5.73
366 367 5.876357 ACAACTTTGTTATTGCCTCTAGGA 58.124 37.500 0.00 0.00 38.47 2.94
447 448 4.877378 ACACATGTACTAAGTTTCCGGA 57.123 40.909 0.00 0.00 0.00 5.14
469 470 9.431887 GGACACTCTGTTTTTGTCTATGTATTA 57.568 33.333 0.00 0.00 39.72 0.98
483 485 3.197983 GGCATACTAGGGACACTCTGTTT 59.802 47.826 0.00 0.00 0.00 2.83
484 486 2.766828 GGCATACTAGGGACACTCTGTT 59.233 50.000 0.00 0.00 0.00 3.16
565 568 4.525996 TGTGATCCCGTTCATCAAATGAT 58.474 39.130 0.00 0.00 39.39 2.45
595 598 3.310774 GGTCTTGTCCATCACATCATTCG 59.689 47.826 0.00 0.00 33.90 3.34
671 674 7.952671 TGGTCAGAGGAATATGTATAAGTCAC 58.047 38.462 0.00 0.00 0.00 3.67
695 698 3.732212 TCGGGAGTTGCATAATCTCATG 58.268 45.455 0.00 0.00 0.00 3.07
736 739 3.188460 ACGTTGTGACATTTGATAGCACC 59.812 43.478 0.00 0.00 0.00 5.01
748 751 1.481363 TCACCCAGTTACGTTGTGACA 59.519 47.619 0.00 0.00 31.45 3.58
806 809 4.314522 TCTTGATCTATGCCAACCCAAA 57.685 40.909 0.00 0.00 0.00 3.28
1045 1049 2.817538 AACCGCATAACAACATACGC 57.182 45.000 0.00 0.00 0.00 4.42
1138 1143 9.274096 ATGTAGACATGACAGAGACACATCTCG 62.274 44.444 0.00 0.00 44.52 4.04
1151 1156 6.404403 GGTTCGAGAACTATGTAGACATGACA 60.404 42.308 14.62 0.00 40.94 3.58
1178 1183 3.656559 ACGTTAAGTGTGCGGACTTTAT 58.343 40.909 8.99 0.00 37.38 1.40
1181 1186 1.862827 GAACGTTAAGTGTGCGGACTT 59.137 47.619 8.99 5.58 39.54 3.01
1182 1187 1.494824 GAACGTTAAGTGTGCGGACT 58.505 50.000 8.99 0.00 0.00 3.85
1191 1196 6.721571 ACAAATCATCATCGAACGTTAAGT 57.278 33.333 0.00 0.00 0.00 2.24
1225 1230 2.365582 ACTTCAGTCACCCAAACACAC 58.634 47.619 0.00 0.00 0.00 3.82
1233 1239 1.602377 CCGAACAAACTTCAGTCACCC 59.398 52.381 0.00 0.00 0.00 4.61
1421 1432 2.493500 CCTCTCTCCACTATGGCCCATA 60.494 54.545 2.87 2.87 37.47 2.74
1472 1491 4.750695 TCGGATTGGGCAGGGGGA 62.751 66.667 0.00 0.00 0.00 4.81
1775 1839 1.587568 CGTGGTGACGGTGATGGTA 59.412 57.895 0.00 0.00 42.18 3.25
1844 1908 0.965866 TCAGCTCGATGACGTCCCTT 60.966 55.000 14.12 0.00 40.69 3.95
1878 1942 2.652530 GAACGTACGGCACCTCCA 59.347 61.111 21.06 0.00 34.01 3.86
1908 1972 2.234661 TGAGCATCTTCACGATCCAACT 59.765 45.455 0.00 0.00 34.92 3.16
1924 1988 2.224185 ACGTGGTTGATGTAGTTGAGCA 60.224 45.455 0.00 0.00 0.00 4.26
1926 1990 5.107220 GGTTAACGTGGTTGATGTAGTTGAG 60.107 44.000 0.00 0.00 0.00 3.02
1929 1993 4.964593 AGGTTAACGTGGTTGATGTAGTT 58.035 39.130 0.00 0.00 0.00 2.24
1976 2046 1.458777 ACGGGGAGAGTGTGTCCAA 60.459 57.895 0.00 0.00 35.57 3.53
2007 2077 6.712276 TCACGCAAGATCTATCTAGGAGATA 58.288 40.000 0.00 0.00 37.14 1.98
2086 2156 5.687166 ATTTGCATTTCTTCATCCACCAT 57.313 34.783 0.00 0.00 0.00 3.55
2087 2157 5.486735 AATTTGCATTTCTTCATCCACCA 57.513 34.783 0.00 0.00 0.00 4.17
2104 2174 2.250924 AGGACTCAAGGGGCAAATTTG 58.749 47.619 14.03 14.03 0.00 2.32
2142 2212 4.023450 CCACATCCATCATTGACATAGCAC 60.023 45.833 0.00 0.00 0.00 4.40
2150 2220 3.634504 CTTTCCCCACATCCATCATTGA 58.365 45.455 0.00 0.00 0.00 2.57
2154 2224 0.394216 CGCTTTCCCCACATCCATCA 60.394 55.000 0.00 0.00 0.00 3.07
2157 2227 1.002624 GTCGCTTTCCCCACATCCA 60.003 57.895 0.00 0.00 0.00 3.41
2163 2233 2.758770 CTTCGACGTCGCTTTCCCCA 62.759 60.000 32.19 10.45 39.60 4.96
2191 2279 1.760192 CCAGAGAAGGGCTTCATTGG 58.240 55.000 0.00 0.00 41.84 3.16
2210 2302 1.783416 CGCAACTGATTTCTTCGTCGC 60.783 52.381 0.00 0.00 0.00 5.19
2270 2362 1.214589 GACTGCTTTCGGGCTCGTA 59.785 57.895 5.57 0.00 37.69 3.43
2288 2380 4.156664 TCTCGTCGTAGTCCTTCTTTTG 57.843 45.455 0.00 0.00 0.00 2.44
2296 2388 0.179000 TACCCCTCTCGTCGTAGTCC 59.821 60.000 0.00 0.00 0.00 3.85
2406 2501 6.366630 GCTCATCGCTTGGATAAGTATTTTC 58.633 40.000 0.00 0.00 36.27 2.29
2433 2528 4.641989 AGATGCCACATTAATCACTGTTCC 59.358 41.667 0.00 0.00 0.00 3.62
2451 2553 4.644103 ATGTTCAACTATTGGCAGATGC 57.356 40.909 0.00 0.00 41.14 3.91
2482 2584 4.582701 TGTCGGTGAAGAAATTGCAAAT 57.417 36.364 1.71 0.00 0.00 2.32
2584 2686 0.108804 CTGGTGTAACGGACGATGCT 60.109 55.000 0.00 0.00 38.12 3.79
2586 2688 0.459585 CCCTGGTGTAACGGACGATG 60.460 60.000 0.00 0.00 38.12 3.84
2587 2689 1.895238 CCCTGGTGTAACGGACGAT 59.105 57.895 0.00 0.00 38.12 3.73
2665 2767 0.881796 AAAGCTTTCTAACGGGCTGC 59.118 50.000 5.69 0.00 35.08 5.25
2814 3592 9.855021 AAATGAACTTTTCGGACCTTATAATTG 57.145 29.630 0.00 0.00 0.00 2.32
2844 3622 1.298859 GGCTACAGTCGCCTTTGTGG 61.299 60.000 8.90 0.00 44.17 4.17
2898 3676 1.872773 TGGTTTGCTTGTTCCCCTTT 58.127 45.000 0.00 0.00 0.00 3.11
2949 4128 1.586564 CGGACTTCGAGCGCCTTAG 60.587 63.158 2.29 0.00 42.43 2.18
2967 4146 3.790437 TAGGCTGGGCTGCTGCTC 61.790 66.667 15.64 12.43 40.87 4.26
2970 4149 4.845580 CGGTAGGCTGGGCTGCTG 62.846 72.222 11.32 9.04 0.00 4.41
3013 4684 2.359107 CGGCAGCTTTCCTCAGCA 60.359 61.111 0.00 0.00 42.84 4.41
3092 4766 1.620819 ACAGAAAGGATGACAGCGAGT 59.379 47.619 0.00 0.00 0.00 4.18
3093 4767 2.376808 ACAGAAAGGATGACAGCGAG 57.623 50.000 0.00 0.00 0.00 5.03
3094 4768 2.688507 GAACAGAAAGGATGACAGCGA 58.311 47.619 0.00 0.00 0.00 4.93
3096 4770 1.734465 CCGAACAGAAAGGATGACAGC 59.266 52.381 0.00 0.00 0.00 4.40
3097 4771 1.734465 GCCGAACAGAAAGGATGACAG 59.266 52.381 0.00 0.00 0.00 3.51
3098 4772 1.808411 GCCGAACAGAAAGGATGACA 58.192 50.000 0.00 0.00 0.00 3.58
3145 4879 1.808343 TCGTCGTCATCTTCTTCGGAA 59.192 47.619 0.00 0.00 0.00 4.30
3151 4885 0.248661 CCGCATCGTCGTCATCTTCT 60.249 55.000 0.00 0.00 0.00 2.85
3162 4896 2.034879 CCTCAAGTTGCCGCATCGT 61.035 57.895 0.00 0.00 0.00 3.73
3165 4899 3.434319 CGCCTCAAGTTGCCGCAT 61.434 61.111 12.61 0.00 0.00 4.73
3261 4998 3.296709 AAGACGATGCCCGCGTTCT 62.297 57.895 4.92 0.00 42.77 3.01
3272 5009 4.258543 TGCCGAAAATTAAGGAAGACGAT 58.741 39.130 0.00 0.00 0.00 3.73
3407 5150 4.082408 CCGAACCTTAAGAAAATCCCCAAC 60.082 45.833 3.36 0.00 0.00 3.77
3429 5173 4.595350 AGCCATAGATTTCTCTCTAACCCC 59.405 45.833 0.00 0.00 31.75 4.95
3451 5195 4.873724 TTCCCCAATTTAGGAACCCTAG 57.126 45.455 2.39 0.00 37.42 3.02
3462 5206 3.962063 ACCGTACAAGTTTTCCCCAATTT 59.038 39.130 0.00 0.00 0.00 1.82
3554 5522 2.356135 TCCCGAGTGCTTGAAATTAGC 58.644 47.619 0.00 0.00 39.10 3.09
3634 5603 6.124088 ACCTTGATGCTATTTTCTTAAGCG 57.876 37.500 0.00 0.00 39.14 4.68
3679 5648 2.045524 TCATGAGCCCCTTGATCTCTC 58.954 52.381 0.00 0.00 0.00 3.20
3691 5660 7.934855 ATTTCTATCATTGGTATCATGAGCC 57.065 36.000 11.09 11.09 0.00 4.70
3771 5740 1.063174 CATGCTTCCGCTCTGTTTAGC 59.937 52.381 0.00 0.00 39.21 3.09
3901 6373 4.287067 TCTGCCTCTGATAAAACAGTTCCT 59.713 41.667 0.00 0.00 38.79 3.36
3929 6402 1.206132 CATTGTGGCATGTTCCAGCAT 59.794 47.619 0.00 0.00 36.67 3.79
4223 6702 5.182001 GTGTGAGCACCTTGTTCATTAGAAT 59.818 40.000 0.00 0.00 39.69 2.40
4239 6718 5.304101 AGTTAAATTTTGGGATGTGTGAGCA 59.696 36.000 0.00 0.00 0.00 4.26
4256 6735 9.287373 TGGTCTAATTTACGGTCAAAGTTAAAT 57.713 29.630 0.00 0.00 0.00 1.40
4326 6805 6.549364 ACCATTGAACACTTCTTTCCAATACA 59.451 34.615 0.00 0.00 0.00 2.29
4327 6806 6.981722 ACCATTGAACACTTCTTTCCAATAC 58.018 36.000 0.00 0.00 0.00 1.89
4396 6875 4.217754 TCCGAAAAATCAACTTTGACCG 57.782 40.909 0.00 0.00 40.49 4.79
4409 6888 1.757682 AGGCACACACTTCCGAAAAA 58.242 45.000 0.00 0.00 0.00 1.94
4414 6893 2.422597 TGAATAAGGCACACACTTCCG 58.577 47.619 0.00 0.00 0.00 4.30
4415 6894 4.380867 CCAATGAATAAGGCACACACTTCC 60.381 45.833 0.00 0.00 0.00 3.46
4421 6900 3.068590 CCATCCCAATGAATAAGGCACAC 59.931 47.826 0.00 0.00 34.61 3.82
4458 6939 9.143631 CCAACAGAATTGAAATCATAAAGAACC 57.856 33.333 0.00 0.00 0.00 3.62
4488 6969 6.005198 TCACATTCCCAAGTAATTTTACGGT 58.995 36.000 0.00 0.00 38.65 4.83
4491 6972 6.152831 AGCCTCACATTCCCAAGTAATTTTAC 59.847 38.462 0.00 0.00 0.00 2.01
4637 7118 8.197439 GGGAAATGACAAACTATTTTCCCATAG 58.803 37.037 22.15 2.56 36.38 2.23
4675 7156 4.465632 ACAACGCATACATCAAGGACTA 57.534 40.909 0.00 0.00 0.00 2.59
4679 7160 4.282068 GCAATACAACGCATACATCAAGG 58.718 43.478 0.00 0.00 0.00 3.61
4703 7184 6.909550 TTAAGGTTGCTTGGTTATGACAAT 57.090 33.333 0.00 0.00 0.00 2.71
4784 7266 2.693591 TGAAACCCCGTTGTGCATTTAA 59.306 40.909 0.00 0.00 0.00 1.52
4790 7272 0.741915 TTTCTGAAACCCCGTTGTGC 59.258 50.000 0.00 0.00 0.00 4.57
4795 7277 0.179001 CCCAGTTTCTGAAACCCCGT 60.179 55.000 25.22 8.07 42.34 5.28
4796 7278 0.179001 ACCCAGTTTCTGAAACCCCG 60.179 55.000 25.22 16.25 42.34 5.73
4803 7285 4.513406 AAAGTAACCACCCAGTTTCTGA 57.487 40.909 0.00 0.00 32.44 3.27
4939 7422 1.377725 GGCCTGCAGCACATACAGT 60.378 57.895 8.66 0.00 46.50 3.55
5015 7500 3.243367 TGAATGTTTTCTTTCCAGTGCCG 60.243 43.478 0.00 0.00 34.40 5.69
5093 7578 4.657436 AGCTAGACGAATTCTAAGTGGG 57.343 45.455 3.52 0.00 36.32 4.61
5297 7798 6.014242 ACCATCACAAGACAGAGATAAACAGA 60.014 38.462 0.00 0.00 0.00 3.41
5306 7807 2.288457 ACGTCACCATCACAAGACAGAG 60.288 50.000 0.00 0.00 0.00 3.35
5490 7998 3.193263 CGAAAGAGGTGTGAGGATGATG 58.807 50.000 0.00 0.00 0.00 3.07
5697 8205 0.320771 TCTTCAAGCTTGAGACGCCC 60.321 55.000 27.02 0.00 38.61 6.13
5840 8350 1.099879 AGATGGCTTTGGCGCTCATC 61.100 55.000 7.64 11.03 39.81 2.92
5931 8441 2.292103 AGATCAAGCAGAGCTCGAAC 57.708 50.000 8.37 1.55 39.11 3.95
5962 8472 8.950007 AACTGTAAGGAAATTAAATGGAAGGA 57.050 30.769 0.00 0.00 39.30 3.36
6027 8537 1.936547 GAAATCATCACAGAGCGGGTC 59.063 52.381 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.