Multiple sequence alignment - TraesCS1A01G249100

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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 TraesCS1A01G249100 chr1A 100.000 6033 0 0 1 6033 441106522 441112554 0.000000e+00 11141.0
1 TraesCS1A01G249100 chr1A 97.345 113 3 0 1 113 28695967 28695855 6.170000e-45 193.0
2 TraesCS1A01G249100 chr1A 89.431 123 10 2 5914 6033 441183994 441184116 1.050000e-32 152.0
3 TraesCS1A01G249100 chr1A 94.000 50 3 0 5448 5497 279731635 279731586 6.480000e-10 76.8
4 TraesCS1A01G249100 chr1B 95.523 3038 83 15 2350 5360 457318682 457321693 0.000000e+00 4807.0
5 TraesCS1A01G249100 chr1B 90.021 1884 83 28 503 2330 457316710 457318544 0.000000e+00 2340.0
6 TraesCS1A01G249100 chr1B 91.957 373 26 4 101 472 497990184 497990553 2.490000e-143 520.0
7 TraesCS1A01G249100 chr1B 88.603 272 13 5 5779 6033 457322090 457322360 1.260000e-81 315.0
8 TraesCS1A01G249100 chr1B 83.598 189 7 5 5494 5666 457321809 457321989 8.100000e-34 156.0
9 TraesCS1A01G249100 chr1B 82.400 125 13 6 5567 5686 457378373 457378493 3.850000e-17 100.0
10 TraesCS1A01G249100 chr1D 97.615 1677 37 3 2332 4008 341474270 341475943 0.000000e+00 2872.0
11 TraesCS1A01G249100 chr1D 96.177 1334 40 5 4028 5360 341475934 341477257 0.000000e+00 2170.0
12 TraesCS1A01G249100 chr1D 91.656 1546 75 12 817 2313 341472740 341474280 0.000000e+00 2091.0
13 TraesCS1A01G249100 chr1D 84.300 586 30 20 5494 6033 341477366 341477935 3.220000e-142 516.0
14 TraesCS1A01G249100 chr1D 84.021 194 22 6 5844 6031 341494164 341494354 1.730000e-40 178.0
15 TraesCS1A01G249100 chr1D 91.589 107 4 4 503 604 341472271 341472377 6.300000e-30 143.0
16 TraesCS1A01G249100 chr1D 95.238 42 2 0 472 513 341472224 341472265 3.900000e-07 67.6
17 TraesCS1A01G249100 chr1D 96.970 33 1 0 5358 5390 341477291 341477323 8.450000e-04 56.5
18 TraesCS1A01G249100 chrUn 99.799 995 2 0 128 1122 452954166 452955160 0.000000e+00 1827.0
19 TraesCS1A01G249100 chr5D 92.800 375 23 4 101 472 481941440 481941813 1.910000e-149 540.0
20 TraesCS1A01G249100 chr5D 85.465 172 19 2 3265 3436 18185863 18185698 2.240000e-39 174.0
21 TraesCS1A01G249100 chr6D 92.348 379 22 5 101 476 377549356 377548982 3.200000e-147 532.0
22 TraesCS1A01G249100 chr7D 92.267 375 22 5 101 472 495328456 495328826 5.360000e-145 525.0
23 TraesCS1A01G249100 chr7D 91.711 374 25 5 103 472 631906177 631906548 1.160000e-141 514.0
24 TraesCS1A01G249100 chr7D 91.489 376 23 7 101 473 29683270 29683639 5.390000e-140 508.0
25 TraesCS1A01G249100 chr5A 91.429 385 26 6 101 480 633276252 633275870 6.930000e-144 521.0
26 TraesCS1A01G249100 chr5A 100.000 107 0 0 1 107 535202628 535202734 1.330000e-46 198.0
27 TraesCS1A01G249100 chr5A 100.000 107 0 0 1 107 535212286 535212392 1.330000e-46 198.0
28 TraesCS1A01G249100 chr4A 90.862 383 28 5 94 473 61593001 61592623 1.940000e-139 507.0
29 TraesCS1A01G249100 chr4B 82.162 555 65 25 3115 3663 428477245 428476719 4.290000e-121 446.0
30 TraesCS1A01G249100 chr6A 81.004 558 71 25 3115 3663 602188036 602187505 1.560000e-110 411.0
31 TraesCS1A01G249100 chr6A 80.859 559 71 24 3115 3663 602183243 602182711 2.020000e-109 407.0
32 TraesCS1A01G249100 chr6A 80.680 559 72 27 3115 3663 602209481 602210013 9.420000e-108 401.0
33 TraesCS1A01G249100 chr6A 97.414 116 3 0 1 116 59753495 59753380 1.330000e-46 198.0
34 TraesCS1A01G249100 chr6A 95.833 120 4 1 1 120 479941132 479941014 6.170000e-45 193.0
35 TraesCS1A01G249100 chr2A 85.588 340 37 8 3115 3446 160036129 160035794 4.480000e-91 346.0
36 TraesCS1A01G249100 chr2A 94.737 57 3 0 5448 5504 750268783 750268727 8.330000e-14 89.8
37 TraesCS1A01G249100 chr2A 96.000 50 2 0 5448 5497 721107403 721107354 1.390000e-11 82.4
38 TraesCS1A01G249100 chr2A 94.118 51 3 0 5448 5498 41761035 41760985 1.800000e-10 78.7
39 TraesCS1A01G249100 chr7A 83.618 293 29 12 3019 3310 28510828 28510554 2.160000e-64 257.0
40 TraesCS1A01G249100 chr7A 83.276 293 30 12 3019 3310 218924079 218924353 1.000000e-62 252.0
41 TraesCS1A01G249100 chr7A 96.610 118 2 2 1 116 89005373 89005490 1.720000e-45 195.0
42 TraesCS1A01G249100 chr7A 97.345 113 3 0 1 113 686486361 686486249 6.170000e-45 193.0
43 TraesCS1A01G249100 chr7A 85.207 169 19 2 3265 3433 623427268 623427430 1.040000e-37 169.0
44 TraesCS1A01G249100 chr7A 96.000 50 2 0 5448 5497 154386428 154386379 1.390000e-11 82.4
45 TraesCS1A01G249100 chr3B 82.692 260 39 5 2493 2748 808792418 808792161 6.080000e-55 226.0
46 TraesCS1A01G249100 chr3B 96.000 50 2 0 5448 5497 705143394 705143443 1.390000e-11 82.4
47 TraesCS1A01G249100 chr3A 100.000 108 0 0 1 108 653503218 653503325 3.690000e-47 200.0
48 TraesCS1A01G249100 chr3A 95.041 121 5 1 1 121 608806314 608806433 7.980000e-44 189.0
49 TraesCS1A01G249100 chr3A 86.275 153 16 3 5886 6033 31808328 31808480 1.740000e-35 161.0
50 TraesCS1A01G249100 chr3A 94.000 50 3 0 5448 5497 646682889 646682938 6.480000e-10 76.8
51 TraesCS1A01G249100 chr7B 95.745 47 2 0 5452 5498 494751188 494751142 6.480000e-10 76.8
52 TraesCS1A01G249100 chr5B 94.000 50 3 0 5448 5497 244414240 244414289 6.480000e-10 76.8


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 TraesCS1A01G249100 chr1A 441106522 441112554 6032 False 11141.000000 11141 100.000000 1 6033 1 chr1A.!!$F1 6032
1 TraesCS1A01G249100 chr1B 457316710 457322360 5650 False 1904.500000 4807 89.436250 503 6033 4 chr1B.!!$F3 5530
2 TraesCS1A01G249100 chr1D 341472224 341477935 5711 False 1130.871429 2872 93.363571 472 6033 7 chr1D.!!$F2 5561
3 TraesCS1A01G249100 chrUn 452954166 452955160 994 False 1827.000000 1827 99.799000 128 1122 1 chrUn.!!$F1 994
4 TraesCS1A01G249100 chr4B 428476719 428477245 526 True 446.000000 446 82.162000 3115 3663 1 chr4B.!!$R1 548
5 TraesCS1A01G249100 chr6A 602187505 602188036 531 True 411.000000 411 81.004000 3115 3663 1 chr6A.!!$R4 548
6 TraesCS1A01G249100 chr6A 602182711 602183243 532 True 407.000000 407 80.859000 3115 3663 1 chr6A.!!$R3 548
7 TraesCS1A01G249100 chr6A 602209481 602210013 532 False 401.000000 401 80.680000 3115 3663 1 chr6A.!!$F1 548

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
113 114 0.251742 TTTCCAACAGGGGGCATCTG 60.252 55.000 5.03 5.03 37.22 2.90 F
125 126 1.153958 GCATCTGCACCCGCTTTTC 60.154 57.895 0.00 0.00 41.59 2.29 F
1526 1725 1.520590 GCGCTCAGATCTCGTGAATTC 59.479 52.381 0.00 0.00 0.00 2.17 F
1668 1869 0.038159 GTCTTATCCCATCTCCGCGG 60.038 60.000 22.12 22.12 0.00 6.46 F
1895 2125 0.179018 AGGAGTGTGCACCAAGGTTC 60.179 55.000 15.69 2.84 0.00 3.62 F
2867 3215 0.182537 TGGTGTGTGGGAGAAACTGG 59.817 55.000 0.00 0.00 0.00 4.00 F
3284 3635 0.332632 TTATTGCTGCCCTTGCCTCT 59.667 50.000 0.00 0.00 36.33 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1283 1482 0.314935 ATTGCTTGCAAACAGGACCG 59.685 50.000 12.17 0.0 0.00 4.79 R
1618 1819 0.623194 TGATCCCCGAATTCCTGCAA 59.377 50.000 0.00 0.0 0.00 4.08 R
3088 3436 0.690762 GGTGACCCTAACCAAGCTGA 59.309 55.000 0.00 0.0 37.65 4.26 R
3284 3635 4.522405 CGATATGGGATGTGGGCATTTTTA 59.478 41.667 0.00 0.0 35.07 1.52 R
3349 3700 6.539103 GGGTATGCTTCTTTTAGTAACTGAGG 59.461 42.308 0.00 0.0 0.00 3.86 R
4727 5097 0.392193 CTGCTGCCGAACTCCATTCT 60.392 55.000 0.00 0.0 34.88 2.40 R
5141 5536 0.467290 TCAACACAAGTTCCCAGCCC 60.467 55.000 0.00 0.0 35.28 5.19 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
25 26 8.635765 ATTTCCGGATAACACAATTATAGCAT 57.364 30.769 4.15 0.00 0.00 3.79
26 27 7.433708 TTCCGGATAACACAATTATAGCATG 57.566 36.000 4.15 0.00 0.00 4.06
27 28 6.764379 TCCGGATAACACAATTATAGCATGA 58.236 36.000 0.00 0.00 0.00 3.07
28 29 7.220740 TCCGGATAACACAATTATAGCATGAA 58.779 34.615 0.00 0.00 0.00 2.57
29 30 7.882791 TCCGGATAACACAATTATAGCATGAAT 59.117 33.333 0.00 0.00 0.00 2.57
30 31 9.161629 CCGGATAACACAATTATAGCATGAATA 57.838 33.333 0.00 0.00 0.00 1.75
89 90 7.530426 AATGCTTTTATTATTGCCTCTAGGG 57.470 36.000 0.00 0.00 35.18 3.53
102 103 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
103 104 4.392940 CCTCTAGGGCATATTTCCAACAG 58.607 47.826 0.00 0.00 0.00 3.16
104 105 4.392940 CTCTAGGGCATATTTCCAACAGG 58.607 47.826 0.00 0.00 0.00 4.00
105 106 2.459555 AGGGCATATTTCCAACAGGG 57.540 50.000 0.00 0.00 38.37 4.45
106 107 1.062962 AGGGCATATTTCCAACAGGGG 60.063 52.381 0.00 0.00 37.22 4.79
107 108 1.413118 GGCATATTTCCAACAGGGGG 58.587 55.000 0.00 0.00 37.22 5.40
108 109 0.752658 GCATATTTCCAACAGGGGGC 59.247 55.000 0.00 0.00 37.22 5.80
109 110 1.964344 GCATATTTCCAACAGGGGGCA 60.964 52.381 0.00 0.00 37.22 5.36
110 111 2.681422 CATATTTCCAACAGGGGGCAT 58.319 47.619 0.00 0.00 37.22 4.40
111 112 2.452600 TATTTCCAACAGGGGGCATC 57.547 50.000 0.00 0.00 37.22 3.91
112 113 0.712380 ATTTCCAACAGGGGGCATCT 59.288 50.000 0.00 0.00 37.22 2.90
113 114 0.251742 TTTCCAACAGGGGGCATCTG 60.252 55.000 5.03 5.03 37.22 2.90
114 115 2.757099 CCAACAGGGGGCATCTGC 60.757 66.667 6.29 0.00 41.14 4.26
115 116 2.036098 CAACAGGGGGCATCTGCA 59.964 61.111 4.33 0.00 44.36 4.41
116 117 2.036256 AACAGGGGGCATCTGCAC 59.964 61.111 4.33 0.00 45.53 4.57
123 124 3.064324 GGCATCTGCACCCGCTTT 61.064 61.111 4.33 0.00 44.36 3.51
124 125 2.639327 GGCATCTGCACCCGCTTTT 61.639 57.895 4.33 0.00 44.36 2.27
125 126 1.153958 GCATCTGCACCCGCTTTTC 60.154 57.895 0.00 0.00 41.59 2.29
126 127 1.865788 GCATCTGCACCCGCTTTTCA 61.866 55.000 0.00 0.00 41.59 2.69
1351 1550 2.359354 CGGTGCGGGATTTGTCCA 60.359 61.111 0.00 0.00 0.00 4.02
1480 1679 3.731653 GAGGCTCTCCGCAGCTTCC 62.732 68.421 7.40 0.00 39.12 3.46
1491 1690 2.612115 AGCTTCCTGGAGGTGGGG 60.612 66.667 7.71 0.00 36.34 4.96
1526 1725 1.520590 GCGCTCAGATCTCGTGAATTC 59.479 52.381 0.00 0.00 0.00 2.17
1528 1727 2.123342 GCTCAGATCTCGTGAATTCCG 58.877 52.381 2.27 6.50 0.00 4.30
1539 1740 2.706890 GTGAATTCCGGCTCCTAACAA 58.293 47.619 2.27 0.00 0.00 2.83
1542 1743 4.879545 GTGAATTCCGGCTCCTAACAATTA 59.120 41.667 2.27 0.00 0.00 1.40
1544 1745 6.708949 GTGAATTCCGGCTCCTAACAATTATA 59.291 38.462 2.27 0.00 0.00 0.98
1547 1748 8.528044 AATTCCGGCTCCTAACAATTATAAAA 57.472 30.769 0.00 0.00 0.00 1.52
1556 1757 8.691661 TCCTAACAATTATAAAATCCTGAGCC 57.308 34.615 0.00 0.00 0.00 4.70
1565 1766 2.566708 AATCCTGAGCCTTCTCTCCT 57.433 50.000 0.00 0.00 40.03 3.69
1569 1770 3.100671 TCCTGAGCCTTCTCTCCTTTAC 58.899 50.000 0.00 0.00 40.03 2.01
1582 1783 2.954318 CTCCTTTACATCTGGCCCATTG 59.046 50.000 0.00 0.00 0.00 2.82
1618 1819 8.763984 ATGCCAATGATTTCTAGATTTCTTCT 57.236 30.769 0.00 0.00 38.57 2.85
1641 1842 0.179045 AGGAATTCGGGGATCAAGCG 60.179 55.000 0.00 0.00 0.00 4.68
1644 1845 0.463833 AATTCGGGGATCAAGCGGAC 60.464 55.000 0.00 0.00 0.00 4.79
1651 1852 0.931005 GGATCAAGCGGACGATTGTC 59.069 55.000 20.03 16.04 41.63 3.18
1668 1869 0.038159 GTCTTATCCCATCTCCGCGG 60.038 60.000 22.12 22.12 0.00 6.46
1725 1926 3.716872 CCCTCCAATTCCTAGGTACACAT 59.283 47.826 9.08 0.00 0.00 3.21
1737 1938 5.934625 CCTAGGTACACATCCAAGCATAATC 59.065 44.000 0.00 0.00 0.00 1.75
1739 1940 4.413520 AGGTACACATCCAAGCATAATCCT 59.586 41.667 0.00 0.00 0.00 3.24
1740 1941 5.103940 AGGTACACATCCAAGCATAATCCTT 60.104 40.000 0.00 0.00 0.00 3.36
1741 1942 5.239525 GGTACACATCCAAGCATAATCCTTC 59.760 44.000 0.00 0.00 0.00 3.46
1743 1944 4.079558 ACACATCCAAGCATAATCCTTCCT 60.080 41.667 0.00 0.00 0.00 3.36
1745 1946 6.064060 CACATCCAAGCATAATCCTTCCTTA 58.936 40.000 0.00 0.00 0.00 2.69
1746 1947 6.718454 CACATCCAAGCATAATCCTTCCTTAT 59.282 38.462 0.00 0.00 0.00 1.73
1786 1993 7.153985 ACTTATTTGCTTAATTGCTTGCAGAA 58.846 30.769 0.00 0.00 36.75 3.02
1895 2125 0.179018 AGGAGTGTGCACCAAGGTTC 60.179 55.000 15.69 2.84 0.00 3.62
1910 2140 2.704572 AGGTTCGATGGCTTGAAGAAG 58.295 47.619 0.00 0.00 0.00 2.85
1921 2151 2.157863 GCTTGAAGAAGAAGTACACGGC 59.842 50.000 0.00 0.00 0.00 5.68
2190 2420 6.378745 TCTGCTTGACATATACCCTAACCTA 58.621 40.000 0.00 0.00 0.00 3.08
2194 2424 7.097834 GCTTGACATATACCCTAACCTATGTC 58.902 42.308 12.39 12.39 45.42 3.06
2244 2474 3.244422 TGGAGGTTAATCGCATATCCCAC 60.244 47.826 0.00 0.00 0.00 4.61
2456 2804 2.262915 CTGCCAGTCGTGAGGTCC 59.737 66.667 0.00 0.00 0.00 4.46
2459 2807 2.567049 CCAGTCGTGAGGTCCGTC 59.433 66.667 0.00 0.00 0.00 4.79
2687 3035 5.704515 CCTTCTTGATGACAACTCTGAACAT 59.295 40.000 0.00 0.00 32.27 2.71
2733 3081 9.487790 CCTTTCTTATCATTTATCCTGACTCTC 57.512 37.037 0.00 0.00 0.00 3.20
2867 3215 0.182537 TGGTGTGTGGGAGAAACTGG 59.817 55.000 0.00 0.00 0.00 4.00
2946 3294 3.654414 GCTCCCATAGGTATCGTTTCTG 58.346 50.000 0.00 0.00 0.00 3.02
3057 3405 9.903682 ATAGTAATGACATTATTTCAGCAATGC 57.096 29.630 10.99 0.00 35.91 3.56
3088 3436 7.907389 TGATATCTGGACTTCTGTTGTACTTT 58.093 34.615 3.98 0.00 0.00 2.66
3284 3635 0.332632 TTATTGCTGCCCTTGCCTCT 59.667 50.000 0.00 0.00 36.33 3.69
3349 3700 2.490903 ACATGCTTCAACATCTGCCTTC 59.509 45.455 0.00 0.00 0.00 3.46
3374 3727 6.539103 CCTCAGTTACTAAAAGAAGCATACCC 59.461 42.308 0.00 0.00 0.00 3.69
4008 4374 7.881775 AACTGACAGACTAAAAACCAATTCT 57.118 32.000 10.08 0.00 0.00 2.40
4011 4377 8.749354 ACTGACAGACTAAAAACCAATTCTTTT 58.251 29.630 10.08 0.00 0.00 2.27
4012 4378 9.586435 CTGACAGACTAAAAACCAATTCTTTTT 57.414 29.630 0.00 7.79 35.49 1.94
4174 4541 2.110901 CAAGCCTGCAGAACTCATCT 57.889 50.000 17.39 0.00 39.68 2.90
4288 4655 1.668047 GCGAGGGATACGGGTAAATCG 60.668 57.143 0.00 0.00 37.60 3.34
4459 4826 2.886862 TCCCTACGACGAACAAAACA 57.113 45.000 0.00 0.00 0.00 2.83
4461 4828 2.865551 TCCCTACGACGAACAAAACAAC 59.134 45.455 0.00 0.00 0.00 3.32
4606 4973 2.596904 TATTTCCCGAGAAGAAGGCG 57.403 50.000 0.00 0.00 32.35 5.52
4717 5087 1.406614 GCAACTCCAGATGTCAGAGGG 60.407 57.143 0.00 0.00 31.70 4.30
4727 5097 5.046304 CCAGATGTCAGAGGGAAGTTTAGAA 60.046 44.000 0.00 0.00 0.00 2.10
4728 5098 6.105333 CAGATGTCAGAGGGAAGTTTAGAAG 58.895 44.000 0.00 0.00 0.00 2.85
4729 5099 6.019748 AGATGTCAGAGGGAAGTTTAGAAGA 58.980 40.000 0.00 0.00 0.00 2.87
4834 5207 0.534412 AGAGGTTGAGGATGCAGTCG 59.466 55.000 0.00 0.00 0.00 4.18
4882 5255 3.126686 GCTTCAGCATCCAGAAAAGAGTC 59.873 47.826 0.00 0.00 41.59 3.36
4960 5333 0.321346 TTGATCCAGCTCTGCGTGAA 59.679 50.000 0.00 0.00 0.00 3.18
4963 5336 0.035317 ATCCAGCTCTGCGTGAACAA 59.965 50.000 0.00 0.00 0.00 2.83
4972 5345 3.081061 TCTGCGTGAACAAATAATGGCT 58.919 40.909 0.00 0.00 0.00 4.75
4981 5354 5.721000 TGAACAAATAATGGCTGGGAGATTT 59.279 36.000 0.00 0.00 0.00 2.17
5023 5396 1.270907 ACGGCAAGAGGAGAATGTCT 58.729 50.000 0.00 0.00 0.00 3.41
5060 5455 1.369625 AGATCGGTTCGGAATGTTGC 58.630 50.000 0.00 0.00 0.00 4.17
5167 5562 4.651778 TGGGAACTTGTGTTGATAAGAGG 58.348 43.478 0.00 0.00 36.39 3.69
5217 5612 6.603237 TGGCGATGATAAATGTCTACTTTG 57.397 37.500 0.00 0.00 0.00 2.77
5232 5627 7.913789 TGTCTACTTTGAGGGTTGTGTATAAT 58.086 34.615 0.00 0.00 0.00 1.28
5233 5628 8.380099 TGTCTACTTTGAGGGTTGTGTATAATT 58.620 33.333 0.00 0.00 0.00 1.40
5360 5755 9.014297 AGAAAACTTAGGTTCCAGTTATTCATG 57.986 33.333 0.00 0.00 34.14 3.07
5391 5822 4.652421 TTCTGACTTGAATTTGCTTGCA 57.348 36.364 0.00 0.00 0.00 4.08
5398 5829 4.986659 ACTTGAATTTGCTTGCATCTGAAC 59.013 37.500 0.00 0.00 0.00 3.18
5421 5855 4.161565 CAGTAGTCTGTTGCCTATGGGTTA 59.838 45.833 0.00 0.00 36.97 2.85
5439 5873 5.941647 TGGGTTATGTTTCCTTGCTAAGTAC 59.058 40.000 0.00 0.00 0.00 2.73
5440 5874 6.178324 GGGTTATGTTTCCTTGCTAAGTACT 58.822 40.000 0.00 0.00 0.00 2.73
5441 5875 6.315642 GGGTTATGTTTCCTTGCTAAGTACTC 59.684 42.308 0.00 0.00 0.00 2.59
5442 5876 6.315642 GGTTATGTTTCCTTGCTAAGTACTCC 59.684 42.308 0.00 0.00 0.00 3.85
5445 5879 4.020485 TGTTTCCTTGCTAAGTACTCCCTC 60.020 45.833 0.00 0.00 0.00 4.30
5446 5880 2.748388 TCCTTGCTAAGTACTCCCTCC 58.252 52.381 0.00 0.00 0.00 4.30
5447 5881 1.409427 CCTTGCTAAGTACTCCCTCCG 59.591 57.143 0.00 0.00 0.00 4.63
5448 5882 2.100989 CTTGCTAAGTACTCCCTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
5449 5883 2.226962 TGCTAAGTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
5450 5884 2.532843 TGCTAAGTACTCCCTCCGTTT 58.467 47.619 0.00 0.00 0.00 3.60
5451 5885 2.901839 TGCTAAGTACTCCCTCCGTTTT 59.098 45.455 0.00 0.00 0.00 2.43
5452 5886 4.088634 TGCTAAGTACTCCCTCCGTTTTA 58.911 43.478 0.00 0.00 0.00 1.52
5453 5887 4.159135 TGCTAAGTACTCCCTCCGTTTTAG 59.841 45.833 0.00 0.00 0.00 1.85
5454 5888 4.400567 GCTAAGTACTCCCTCCGTTTTAGA 59.599 45.833 0.00 0.00 0.00 2.10
5455 5889 5.068855 GCTAAGTACTCCCTCCGTTTTAGAT 59.931 44.000 0.00 0.00 0.00 1.98
5456 5890 6.264067 GCTAAGTACTCCCTCCGTTTTAGATA 59.736 42.308 0.00 0.00 0.00 1.98
5457 5891 6.462552 AAGTACTCCCTCCGTTTTAGATAC 57.537 41.667 0.00 0.00 0.00 2.24
5458 5892 5.513233 AGTACTCCCTCCGTTTTAGATACA 58.487 41.667 0.00 0.00 0.00 2.29
5459 5893 6.134754 AGTACTCCCTCCGTTTTAGATACAT 58.865 40.000 0.00 0.00 0.00 2.29
5460 5894 5.532664 ACTCCCTCCGTTTTAGATACATC 57.467 43.478 0.00 0.00 0.00 3.06
5461 5895 4.344390 ACTCCCTCCGTTTTAGATACATCC 59.656 45.833 0.00 0.00 0.00 3.51
5462 5896 4.291792 TCCCTCCGTTTTAGATACATCCA 58.708 43.478 0.00 0.00 0.00 3.41
5463 5897 4.905456 TCCCTCCGTTTTAGATACATCCAT 59.095 41.667 0.00 0.00 0.00 3.41
5464 5898 6.079336 TCCCTCCGTTTTAGATACATCCATA 58.921 40.000 0.00 0.00 0.00 2.74
5465 5899 6.729100 TCCCTCCGTTTTAGATACATCCATAT 59.271 38.462 0.00 0.00 0.00 1.78
5466 5900 7.236847 TCCCTCCGTTTTAGATACATCCATATT 59.763 37.037 0.00 0.00 0.00 1.28
5467 5901 7.549488 CCCTCCGTTTTAGATACATCCATATTC 59.451 40.741 0.00 0.00 0.00 1.75
5468 5902 7.275779 CCTCCGTTTTAGATACATCCATATTCG 59.724 40.741 0.00 0.00 0.00 3.34
5469 5903 7.888424 TCCGTTTTAGATACATCCATATTCGA 58.112 34.615 0.00 0.00 0.00 3.71
5470 5904 8.027189 TCCGTTTTAGATACATCCATATTCGAG 58.973 37.037 0.00 0.00 0.00 4.04
5471 5905 8.027189 CCGTTTTAGATACATCCATATTCGAGA 58.973 37.037 0.00 0.00 0.00 4.04
5472 5906 8.851416 CGTTTTAGATACATCCATATTCGAGAC 58.149 37.037 0.00 0.00 0.00 3.36
5473 5907 9.692749 GTTTTAGATACATCCATATTCGAGACA 57.307 33.333 0.00 0.00 0.00 3.41
5482 5916 9.003658 ACATCCATATTCGAGACAAATAATTCC 57.996 33.333 0.00 0.00 0.00 3.01
5483 5917 9.002600 CATCCATATTCGAGACAAATAATTCCA 57.997 33.333 0.00 0.00 0.00 3.53
5484 5918 8.972458 TCCATATTCGAGACAAATAATTCCAA 57.028 30.769 0.00 0.00 0.00 3.53
5485 5919 9.402320 TCCATATTCGAGACAAATAATTCCAAA 57.598 29.630 0.00 0.00 0.00 3.28
5486 5920 9.450807 CCATATTCGAGACAAATAATTCCAAAC 57.549 33.333 0.00 0.00 0.00 2.93
5487 5921 9.158364 CATATTCGAGACAAATAATTCCAAACG 57.842 33.333 0.00 0.00 0.00 3.60
5488 5922 5.539582 TCGAGACAAATAATTCCAAACGG 57.460 39.130 0.00 0.00 0.00 4.44
5489 5923 5.239351 TCGAGACAAATAATTCCAAACGGA 58.761 37.500 0.00 0.00 0.00 4.69
5490 5924 5.350365 TCGAGACAAATAATTCCAAACGGAG 59.650 40.000 0.00 0.00 32.88 4.63
5491 5925 5.447279 CGAGACAAATAATTCCAAACGGAGG 60.447 44.000 0.00 0.00 32.88 4.30
5492 5926 4.705023 AGACAAATAATTCCAAACGGAGGG 59.295 41.667 0.00 0.00 32.88 4.30
5503 5940 4.286549 TCCAAACGGAGGGAGTAATTTGTA 59.713 41.667 0.00 0.00 0.00 2.41
5561 5998 6.682861 GCCAATTTGTTAGTTCTTGGTTCACT 60.683 38.462 0.00 0.00 38.85 3.41
5645 6103 4.147321 ACACAAGCCATCAACAGATCTTT 58.853 39.130 0.00 0.00 0.00 2.52
5701 6159 6.767524 TGGCAACATATAAGTTAAACCCTG 57.232 37.500 0.00 0.00 46.17 4.45
5702 6160 5.654650 TGGCAACATATAAGTTAAACCCTGG 59.345 40.000 0.00 0.00 46.17 4.45
5703 6161 5.655090 GGCAACATATAAGTTAAACCCTGGT 59.345 40.000 0.00 0.00 0.00 4.00
5704 6162 6.829811 GGCAACATATAAGTTAAACCCTGGTA 59.170 38.462 0.00 0.00 0.00 3.25
5705 6163 7.201758 GGCAACATATAAGTTAAACCCTGGTAC 60.202 40.741 0.00 0.00 0.00 3.34
5706 6164 7.555195 GCAACATATAAGTTAAACCCTGGTACT 59.445 37.037 0.00 0.00 0.00 2.73
5707 6165 8.889717 CAACATATAAGTTAAACCCTGGTACTG 58.110 37.037 0.00 0.00 0.00 2.74
5762 6220 6.650390 GGTGGTGCAAATTTAAACAGATGAAT 59.350 34.615 0.00 0.00 0.00 2.57
5769 6227 7.412237 GCAAATTTAAACAGATGAATGGACTGC 60.412 37.037 0.00 0.00 35.38 4.40
5899 6392 3.133003 CACTGGCACTACCACTATAGCTT 59.867 47.826 0.00 0.00 46.36 3.74
5900 6393 3.133003 ACTGGCACTACCACTATAGCTTG 59.867 47.826 0.00 0.00 46.36 4.01
5939 6434 0.958091 CAATGAACCTGAACCGGCAA 59.042 50.000 0.00 0.00 0.00 4.52
5945 6440 1.568504 ACCTGAACCGGCAATCTCTA 58.431 50.000 0.00 0.00 0.00 2.43
5994 6491 3.690745 GCAGCAGCTCCCAAATGT 58.309 55.556 0.00 0.00 37.91 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.514594 CATGCTATAATTGTGTTATCCGGAAAT 58.485 33.333 9.01 0.00 0.00 2.17
1 2 7.717436 TCATGCTATAATTGTGTTATCCGGAAA 59.283 33.333 9.01 0.99 0.00 3.13
3 4 6.764379 TCATGCTATAATTGTGTTATCCGGA 58.236 36.000 6.61 6.61 0.00 5.14
4 5 7.433708 TTCATGCTATAATTGTGTTATCCGG 57.566 36.000 0.00 0.00 0.00 5.14
63 64 9.247861 CCCTAGAGGCAATAATAAAAGCATTAT 57.752 33.333 0.00 0.00 33.46 1.28
64 65 8.635765 CCCTAGAGGCAATAATAAAAGCATTA 57.364 34.615 0.00 0.00 0.00 1.90
65 66 7.530426 CCCTAGAGGCAATAATAAAAGCATT 57.470 36.000 0.00 0.00 0.00 3.56
81 82 4.392940 CTGTTGGAAATATGCCCTAGAGG 58.607 47.826 0.00 0.00 39.47 3.69
82 83 4.392940 CCTGTTGGAAATATGCCCTAGAG 58.607 47.826 0.00 0.00 34.57 2.43
83 84 3.138283 CCCTGTTGGAAATATGCCCTAGA 59.862 47.826 0.00 0.00 35.39 2.43
84 85 3.490348 CCCTGTTGGAAATATGCCCTAG 58.510 50.000 0.00 0.00 35.39 3.02
85 86 2.176798 CCCCTGTTGGAAATATGCCCTA 59.823 50.000 0.00 0.00 35.39 3.53
86 87 1.062962 CCCCTGTTGGAAATATGCCCT 60.063 52.381 0.00 0.00 35.39 5.19
87 88 1.413118 CCCCTGTTGGAAATATGCCC 58.587 55.000 0.00 0.00 35.39 5.36
88 89 1.413118 CCCCCTGTTGGAAATATGCC 58.587 55.000 0.00 0.00 35.39 4.40
89 90 0.752658 GCCCCCTGTTGGAAATATGC 59.247 55.000 0.00 0.00 35.39 3.14
90 91 2.157640 TGCCCCCTGTTGGAAATATG 57.842 50.000 0.00 0.00 35.39 1.78
91 92 2.519691 AGATGCCCCCTGTTGGAAATAT 59.480 45.455 0.00 0.00 35.39 1.28
92 93 1.929494 AGATGCCCCCTGTTGGAAATA 59.071 47.619 0.00 0.00 35.39 1.40
93 94 0.712380 AGATGCCCCCTGTTGGAAAT 59.288 50.000 0.00 0.00 35.39 2.17
94 95 0.251742 CAGATGCCCCCTGTTGGAAA 60.252 55.000 0.00 0.00 35.39 3.13
95 96 1.383799 CAGATGCCCCCTGTTGGAA 59.616 57.895 0.00 0.00 35.39 3.53
96 97 3.089838 CAGATGCCCCCTGTTGGA 58.910 61.111 0.00 0.00 35.39 3.53
97 98 2.757099 GCAGATGCCCCCTGTTGG 60.757 66.667 0.00 0.00 34.29 3.77
98 99 2.036098 TGCAGATGCCCCCTGTTG 59.964 61.111 1.72 0.00 41.18 3.33
99 100 2.036256 GTGCAGATGCCCCCTGTT 59.964 61.111 1.72 0.00 41.18 3.16
100 101 4.052518 GGTGCAGATGCCCCCTGT 62.053 66.667 1.72 0.00 41.18 4.00
106 107 2.548127 GAAAAGCGGGTGCAGATGCC 62.548 60.000 1.72 0.00 46.23 4.40
107 108 1.153958 GAAAAGCGGGTGCAGATGC 60.154 57.895 0.00 0.00 46.23 3.91
108 109 0.597568 TTGAAAAGCGGGTGCAGATG 59.402 50.000 0.00 0.00 46.23 2.90
109 110 1.327303 TTTGAAAAGCGGGTGCAGAT 58.673 45.000 0.00 0.00 46.23 2.90
110 111 1.107114 TTTTGAAAAGCGGGTGCAGA 58.893 45.000 0.00 0.00 46.23 4.26
111 112 1.933247 TTTTTGAAAAGCGGGTGCAG 58.067 45.000 0.00 0.00 46.23 4.41
112 113 2.208431 CATTTTTGAAAAGCGGGTGCA 58.792 42.857 0.00 0.00 46.23 4.57
113 114 2.209273 ACATTTTTGAAAAGCGGGTGC 58.791 42.857 0.00 0.00 43.24 5.01
114 115 4.616953 AGTACATTTTTGAAAAGCGGGTG 58.383 39.130 0.00 0.00 0.00 4.61
115 116 4.929819 AGTACATTTTTGAAAAGCGGGT 57.070 36.364 0.00 0.00 0.00 5.28
116 117 6.597262 AAAAGTACATTTTTGAAAAGCGGG 57.403 33.333 0.00 0.00 37.89 6.13
1283 1482 0.314935 ATTGCTTGCAAACAGGACCG 59.685 50.000 12.17 0.00 0.00 4.79
1351 1550 2.920645 CGTCCTCGCCTGACACTGT 61.921 63.158 0.00 0.00 32.91 3.55
1480 1679 1.560505 CCAAAATTCCCCACCTCCAG 58.439 55.000 0.00 0.00 0.00 3.86
1491 1690 2.288152 TGAGCGCAAGAACCCAAAATTC 60.288 45.455 11.47 0.00 43.02 2.17
1526 1725 6.715264 AGGATTTTATAATTGTTAGGAGCCGG 59.285 38.462 0.00 0.00 0.00 6.13
1528 1727 8.691661 TCAGGATTTTATAATTGTTAGGAGCC 57.308 34.615 0.00 0.00 0.00 4.70
1539 1740 7.294482 AGGAGAGAAGGCTCAGGATTTTATAAT 59.706 37.037 0.00 0.00 43.81 1.28
1542 1743 4.974501 AGGAGAGAAGGCTCAGGATTTTAT 59.025 41.667 0.00 0.00 43.81 1.40
1544 1745 3.188773 AGGAGAGAAGGCTCAGGATTTT 58.811 45.455 0.00 0.00 43.81 1.82
1547 1748 2.566708 AAGGAGAGAAGGCTCAGGAT 57.433 50.000 0.00 0.00 43.81 3.24
1556 1757 3.432890 GGGCCAGATGTAAAGGAGAGAAG 60.433 52.174 4.39 0.00 0.00 2.85
1565 1766 3.900601 ACAAACAATGGGCCAGATGTAAA 59.099 39.130 23.30 0.00 0.00 2.01
1569 1770 1.619827 ACACAAACAATGGGCCAGATG 59.380 47.619 13.78 16.23 35.04 2.90
1582 1783 7.092716 AGAAATCATTGGCATAGAACACAAAC 58.907 34.615 0.00 0.00 0.00 2.93
1618 1819 0.623194 TGATCCCCGAATTCCTGCAA 59.377 50.000 0.00 0.00 0.00 4.08
1641 1842 4.561105 GAGATGGGATAAGACAATCGTCC 58.439 47.826 0.00 0.00 43.73 4.79
1644 1845 3.579709 CGGAGATGGGATAAGACAATCG 58.420 50.000 0.00 0.00 0.00 3.34
1651 1852 1.374758 GCCGCGGAGATGGGATAAG 60.375 63.158 33.48 0.00 0.00 1.73
1668 1869 1.078143 AGTTGCGATCCCCTTCAGC 60.078 57.895 0.00 0.00 0.00 4.26
1725 1926 5.372363 TCCATAAGGAAGGATTATGCTTGGA 59.628 40.000 3.16 1.08 42.23 3.53
1741 1942 8.940397 ATAAGTTTTACCATCCATCCATAAGG 57.060 34.615 0.00 0.00 0.00 2.69
1745 1946 7.345392 AGCAAATAAGTTTTACCATCCATCCAT 59.655 33.333 0.00 0.00 0.00 3.41
1746 1947 6.667414 AGCAAATAAGTTTTACCATCCATCCA 59.333 34.615 0.00 0.00 0.00 3.41
1786 1993 9.677567 GTACAACAAACAAGATCAAATGTATGT 57.322 29.630 0.00 4.46 0.00 2.29
1832 2062 3.133003 GCTTGTACTTCTCCATCAGGCTA 59.867 47.826 0.00 0.00 33.74 3.93
1895 2125 4.092091 GTGTACTTCTTCTTCAAGCCATCG 59.908 45.833 0.00 0.00 0.00 3.84
1910 2140 1.007336 CACACTCCGCCGTGTACTTC 61.007 60.000 7.50 0.00 45.74 3.01
2338 2568 8.964533 ATCATGTACTCCCTCTATGAACTAAT 57.035 34.615 0.00 0.00 32.21 1.73
2341 2571 6.613271 ACAATCATGTACTCCCTCTATGAACT 59.387 38.462 0.00 0.00 38.24 3.01
2342 2572 6.821388 ACAATCATGTACTCCCTCTATGAAC 58.179 40.000 0.00 0.00 38.24 3.18
2368 2716 7.415989 CCCATTAGATTCAACATCCTTCAACTG 60.416 40.741 0.00 0.00 0.00 3.16
2456 2804 5.513376 CATACATTGAAACCATCCATGACG 58.487 41.667 0.00 0.00 35.32 4.35
2459 2807 5.265350 TGCATACATTGAAACCATCCATG 57.735 39.130 0.00 0.00 37.25 3.66
2743 3091 6.774170 AGATGCAACATGATATTAAGCTCCAA 59.226 34.615 0.00 0.00 0.00 3.53
2946 3294 3.318017 AGAACGAGTGTCATACAAGTGC 58.682 45.455 0.00 0.00 0.00 4.40
2987 3335 6.492007 TCTAGGAGTAGTTGTTAACAGTCG 57.508 41.667 8.56 0.00 0.00 4.18
3057 3405 7.869937 ACAACAGAAGTCCAGATATCATTATCG 59.130 37.037 5.32 0.00 39.42 2.92
3088 3436 0.690762 GGTGACCCTAACCAAGCTGA 59.309 55.000 0.00 0.00 37.65 4.26
3284 3635 4.522405 CGATATGGGATGTGGGCATTTTTA 59.478 41.667 0.00 0.00 35.07 1.52
3349 3700 6.539103 GGGTATGCTTCTTTTAGTAACTGAGG 59.461 42.308 0.00 0.00 0.00 3.86
3976 4342 7.803659 GGTTTTTAGTCTGTCAGTTAGCAATTC 59.196 37.037 0.00 0.00 0.00 2.17
4056 4422 8.914328 TCTGTTGCACAAAATTCATATATGTG 57.086 30.769 12.42 5.77 43.17 3.21
4069 4436 4.072131 GTCTCCCTTATCTGTTGCACAAA 58.928 43.478 0.00 0.00 0.00 2.83
4174 4541 4.535781 ACCAGCATAGGAAAATACATGCA 58.464 39.130 8.00 0.00 44.90 3.96
4459 4826 1.475751 CCAGCAGTCTTGTCCACAGTT 60.476 52.381 0.00 0.00 0.00 3.16
4461 4828 1.233285 GCCAGCAGTCTTGTCCACAG 61.233 60.000 0.00 0.00 0.00 3.66
4486 4853 1.591619 GGAACTAAAGATACACGCCGC 59.408 52.381 0.00 0.00 0.00 6.53
4555 4922 2.955660 CTCTCTCTCGCTTGGTAGGATT 59.044 50.000 0.00 0.00 0.00 3.01
4717 5087 5.163844 GCCGAACTCCATTCTTCTAAACTTC 60.164 44.000 0.00 0.00 34.88 3.01
4727 5097 0.392193 CTGCTGCCGAACTCCATTCT 60.392 55.000 0.00 0.00 34.88 2.40
4728 5098 1.986575 GCTGCTGCCGAACTCCATTC 61.987 60.000 3.85 0.00 0.00 2.67
4729 5099 2.042831 GCTGCTGCCGAACTCCATT 61.043 57.895 3.85 0.00 0.00 3.16
4867 5240 3.244033 AGAGCGACTCTTTTCTGGATG 57.756 47.619 3.88 0.00 37.60 3.51
4882 5255 1.294659 GAGCAGGTGAACCAAGAGCG 61.295 60.000 1.62 0.00 38.89 5.03
4960 5333 4.406649 CCAAATCTCCCAGCCATTATTTGT 59.593 41.667 0.00 0.00 34.20 2.83
4963 5336 2.967887 GCCAAATCTCCCAGCCATTATT 59.032 45.455 0.00 0.00 0.00 1.40
4972 5345 1.947597 GCGCATTGCCAAATCTCCCA 61.948 55.000 0.30 0.00 37.76 4.37
5023 5396 4.399618 CGATCTTCTTCACCTTAGAGGACA 59.600 45.833 0.07 0.00 37.67 4.02
5138 5533 1.604593 CACAAGTTCCCAGCCCCAG 60.605 63.158 0.00 0.00 0.00 4.45
5139 5534 1.943730 AACACAAGTTCCCAGCCCCA 61.944 55.000 0.00 0.00 30.46 4.96
5140 5535 1.152546 AACACAAGTTCCCAGCCCC 60.153 57.895 0.00 0.00 30.46 5.80
5141 5536 0.467290 TCAACACAAGTTCCCAGCCC 60.467 55.000 0.00 0.00 35.28 5.19
5167 5562 6.053650 AGAACCCTAACACAAGTTACAAGTC 58.946 40.000 0.00 0.00 39.15 3.01
5341 5736 7.252612 TGAGTCATGAATAACTGGAACCTAA 57.747 36.000 0.00 0.00 0.00 2.69
5360 5755 9.070149 GCAAATTCAAGTCAGAATAATTGAGTC 57.930 33.333 0.00 0.00 37.24 3.36
5398 5829 2.501723 ACCCATAGGCAACAGACTACTG 59.498 50.000 0.00 0.00 42.77 2.74
5414 5848 5.580022 ACTTAGCAAGGAAACATAACCCAT 58.420 37.500 0.00 0.00 0.00 4.00
5416 5850 6.178324 AGTACTTAGCAAGGAAACATAACCC 58.822 40.000 0.00 0.00 0.00 4.11
5421 5855 4.536489 AGGGAGTACTTAGCAAGGAAACAT 59.464 41.667 0.00 0.00 0.00 2.71
5439 5873 4.344102 TGGATGTATCTAAAACGGAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
5440 5874 4.291792 TGGATGTATCTAAAACGGAGGGA 58.708 43.478 0.00 0.00 0.00 4.20
5441 5875 4.682778 TGGATGTATCTAAAACGGAGGG 57.317 45.455 0.00 0.00 0.00 4.30
5442 5876 7.275779 CGAATATGGATGTATCTAAAACGGAGG 59.724 40.741 0.00 0.00 0.00 4.30
5445 5879 8.027189 TCTCGAATATGGATGTATCTAAAACGG 58.973 37.037 0.00 0.00 0.00 4.44
5446 5880 8.851416 GTCTCGAATATGGATGTATCTAAAACG 58.149 37.037 0.00 0.00 0.00 3.60
5447 5881 9.692749 TGTCTCGAATATGGATGTATCTAAAAC 57.307 33.333 0.00 0.00 0.00 2.43
5456 5890 9.003658 GGAATTATTTGTCTCGAATATGGATGT 57.996 33.333 0.00 0.00 0.00 3.06
5457 5891 9.002600 TGGAATTATTTGTCTCGAATATGGATG 57.997 33.333 0.00 0.00 0.00 3.51
5458 5892 9.573166 TTGGAATTATTTGTCTCGAATATGGAT 57.427 29.630 0.00 0.00 0.00 3.41
5459 5893 8.972458 TTGGAATTATTTGTCTCGAATATGGA 57.028 30.769 0.00 0.00 0.00 3.41
5460 5894 9.450807 GTTTGGAATTATTTGTCTCGAATATGG 57.549 33.333 0.00 0.00 0.00 2.74
5461 5895 9.158364 CGTTTGGAATTATTTGTCTCGAATATG 57.842 33.333 0.00 0.00 0.00 1.78
5462 5896 8.342634 CCGTTTGGAATTATTTGTCTCGAATAT 58.657 33.333 0.00 0.00 37.49 1.28
5463 5897 7.549842 TCCGTTTGGAATTATTTGTCTCGAATA 59.450 33.333 0.00 0.00 42.85 1.75
5464 5898 6.373216 TCCGTTTGGAATTATTTGTCTCGAAT 59.627 34.615 0.00 0.00 42.85 3.34
5465 5899 5.701750 TCCGTTTGGAATTATTTGTCTCGAA 59.298 36.000 0.00 0.00 42.85 3.71
5466 5900 5.239351 TCCGTTTGGAATTATTTGTCTCGA 58.761 37.500 0.00 0.00 42.85 4.04
5467 5901 5.447279 CCTCCGTTTGGAATTATTTGTCTCG 60.447 44.000 0.00 0.00 45.87 4.04
5468 5902 5.163652 CCCTCCGTTTGGAATTATTTGTCTC 60.164 44.000 0.00 0.00 45.87 3.36
5469 5903 4.705023 CCCTCCGTTTGGAATTATTTGTCT 59.295 41.667 0.00 0.00 45.87 3.41
5470 5904 4.703093 TCCCTCCGTTTGGAATTATTTGTC 59.297 41.667 0.00 0.00 45.87 3.18
5471 5905 4.668636 TCCCTCCGTTTGGAATTATTTGT 58.331 39.130 0.00 0.00 45.87 2.83
5472 5906 4.705023 ACTCCCTCCGTTTGGAATTATTTG 59.295 41.667 0.00 0.00 45.87 2.32
5473 5907 4.930696 ACTCCCTCCGTTTGGAATTATTT 58.069 39.130 0.00 0.00 45.87 1.40
5474 5908 4.586306 ACTCCCTCCGTTTGGAATTATT 57.414 40.909 0.00 0.00 45.87 1.40
5475 5909 5.703730 TTACTCCCTCCGTTTGGAATTAT 57.296 39.130 0.00 0.00 45.87 1.28
5476 5910 5.703730 ATTACTCCCTCCGTTTGGAATTA 57.296 39.130 0.00 0.00 45.87 1.40
5477 5911 4.586306 ATTACTCCCTCCGTTTGGAATT 57.414 40.909 0.00 0.00 45.87 2.17
5478 5912 4.586306 AATTACTCCCTCCGTTTGGAAT 57.414 40.909 0.00 0.00 45.87 3.01
5479 5913 4.076394 CAAATTACTCCCTCCGTTTGGAA 58.924 43.478 0.00 0.00 45.87 3.53
5480 5914 3.073356 ACAAATTACTCCCTCCGTTTGGA 59.927 43.478 0.00 0.00 43.88 3.53
5481 5915 3.418047 ACAAATTACTCCCTCCGTTTGG 58.582 45.455 0.00 0.00 32.46 3.28
5482 5916 5.296035 GGATACAAATTACTCCCTCCGTTTG 59.704 44.000 0.00 0.00 33.92 2.93
5483 5917 5.434408 GGATACAAATTACTCCCTCCGTTT 58.566 41.667 0.00 0.00 0.00 3.60
5484 5918 5.032327 GGATACAAATTACTCCCTCCGTT 57.968 43.478 0.00 0.00 0.00 4.44
5485 5919 4.684484 GGATACAAATTACTCCCTCCGT 57.316 45.455 0.00 0.00 0.00 4.69
5503 5940 2.505407 TGCAACCAGTAGTAGCATGGAT 59.495 45.455 0.00 0.00 37.54 3.41
5561 5998 3.284617 CAGGATCTGTGATGATTGGCAA 58.715 45.455 0.68 0.68 0.00 4.52
5667 6125 6.767902 ACTTATATGTTGCCAAGTATCCTGTG 59.232 38.462 0.00 0.00 29.67 3.66
5680 6138 6.769134 ACCAGGGTTTAACTTATATGTTGC 57.231 37.500 12.91 4.79 0.00 4.17
5681 6139 8.889717 CAGTACCAGGGTTTAACTTATATGTTG 58.110 37.037 12.91 0.00 0.00 3.33
5682 6140 8.608598 ACAGTACCAGGGTTTAACTTATATGTT 58.391 33.333 8.83 8.83 0.00 2.71
5685 6143 8.383374 TGACAGTACCAGGGTTTAACTTATAT 57.617 34.615 0.00 0.00 0.00 0.86
5689 6147 5.578157 ATGACAGTACCAGGGTTTAACTT 57.422 39.130 0.00 0.00 0.00 2.66
5717 6175 3.326880 ACCGAGTTGGGAAACAGTATTCT 59.673 43.478 0.24 0.00 44.64 2.40
5798 6277 7.920160 TCTTGTATATCTGAATGTTTGTGCA 57.080 32.000 0.00 0.00 0.00 4.57
5939 6434 1.550524 TGCAGCGGTTTCACTAGAGAT 59.449 47.619 0.00 0.00 0.00 2.75
5945 6440 1.032014 AAACATGCAGCGGTTTCACT 58.968 45.000 8.73 0.00 32.00 3.41
5994 6491 1.072331 GGCTGAAAGTGAACCTGGAGA 59.928 52.381 0.00 0.00 35.30 3.71


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

AutoCloner maintained by Alex Coulton.