Multiple sequence alignment - TraesCS7B01G057900

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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 TraesCS7B01G057900 chr7B 100.000 5701 0 0 1 5701 60095140 60089440 0.000000e+00 10528.0
1 TraesCS7B01G057900 chr7B 87.007 3117 336 36 1878 4966 59824242 59821167 0.000000e+00 3448.0
2 TraesCS7B01G057900 chr7B 86.857 2625 277 34 2523 5122 60497039 60494458 0.000000e+00 2874.0
3 TraesCS7B01G057900 chr7B 86.683 1682 171 20 1878 3551 60065143 60063507 0.000000e+00 1816.0
4 TraesCS7B01G057900 chr7B 83.619 1923 252 45 2574 4456 60566488 60564589 0.000000e+00 1748.0
5 TraesCS7B01G057900 chr7B 77.526 2385 416 91 2603 4936 59668399 59666084 0.000000e+00 1325.0
6 TraesCS7B01G057900 chr7B 79.430 1896 322 57 2596 4457 60605451 60603590 0.000000e+00 1279.0
7 TraesCS7B01G057900 chr7B 86.753 1155 61 29 382 1474 59826043 59824919 0.000000e+00 1201.0
8 TraesCS7B01G057900 chr7B 79.111 1417 245 34 3311 4702 60030686 60029296 0.000000e+00 929.0
9 TraesCS7B01G057900 chr7B 84.434 893 116 12 3537 4418 60060327 60059447 0.000000e+00 857.0
10 TraesCS7B01G057900 chr7B 85.968 677 74 8 4405 5078 60051913 60051255 0.000000e+00 704.0
11 TraesCS7B01G057900 chr7B 83.224 459 39 19 864 1321 60065758 60065337 2.490000e-103 387.0
12 TraesCS7B01G057900 chr7B 84.615 403 42 14 5310 5701 60494274 60493881 3.220000e-102 383.0
13 TraesCS7B01G057900 chr7B 89.041 292 27 5 94 383 59826400 59826112 1.950000e-94 357.0
14 TraesCS7B01G057900 chr7B 85.337 341 30 6 961 1286 60500115 60499780 9.150000e-88 335.0
15 TraesCS7B01G057900 chr7B 76.158 583 94 24 4492 5056 60564583 60564028 1.220000e-66 265.0
16 TraesCS7B01G057900 chr7B 81.471 340 35 13 968 1287 60570223 60569892 2.640000e-63 254.0
17 TraesCS7B01G057900 chr7B 86.747 166 15 4 5541 5700 60047458 60047294 1.630000e-40 178.0
18 TraesCS7B01G057900 chr7B 86.747 166 13 4 335 496 60077959 60078119 5.870000e-40 176.0
19 TraesCS7B01G057900 chr7B 86.755 151 11 4 5408 5549 60050834 60050684 5.910000e-35 159.0
20 TraesCS7B01G057900 chr7B 87.234 94 5 4 2 95 36733810 36733896 3.630000e-17 100.0
21 TraesCS7B01G057900 chr7B 85.859 99 6 6 1 98 92323121 92323212 1.310000e-16 99.0
22 TraesCS7B01G057900 chr7A 88.397 3051 245 51 2519 5537 106995269 106992296 0.000000e+00 3572.0
23 TraesCS7B01G057900 chr7A 86.431 2631 292 38 2523 5122 107153591 107150995 0.000000e+00 2820.0
24 TraesCS7B01G057900 chr7A 84.994 2639 299 46 2352 4966 106745583 106743018 0.000000e+00 2590.0
25 TraesCS7B01G057900 chr7A 81.798 1802 240 56 3121 4883 107322404 107320652 0.000000e+00 1430.0
26 TraesCS7B01G057900 chr7A 77.630 1949 341 64 2530 4441 107603621 107601731 0.000000e+00 1096.0
27 TraesCS7B01G057900 chr7A 85.569 984 80 27 1295 2269 106773195 106772265 0.000000e+00 974.0
28 TraesCS7B01G057900 chr7A 87.033 910 47 18 452 1321 106749261 106748383 0.000000e+00 961.0
29 TraesCS7B01G057900 chr7A 89.171 434 37 5 864 1297 106773938 106773515 3.020000e-147 532.0
30 TraesCS7B01G057900 chr7A 86.683 398 39 10 5310 5701 107150812 107150423 4.080000e-116 429.0
31 TraesCS7B01G057900 chr7A 82.927 492 61 13 1842 2324 106748235 106747758 6.830000e-114 422.0
32 TraesCS7B01G057900 chr7A 91.749 303 18 2 461 763 106749706 106749411 1.140000e-111 414.0
33 TraesCS7B01G057900 chr7A 84.615 364 47 3 94 455 106750339 106749983 2.530000e-93 353.0
34 TraesCS7B01G057900 chr7A 84.751 341 32 6 961 1286 107155828 107155493 1.980000e-84 324.0
35 TraesCS7B01G057900 chr7A 94.505 182 10 0 5520 5701 106985319 106985138 1.210000e-71 281.0
36 TraesCS7B01G057900 chr7A 84.314 306 24 8 339 632 106775354 106775061 1.560000e-70 278.0
37 TraesCS7B01G057900 chr7A 81.682 333 33 15 975 1287 107339183 107338859 9.480000e-63 252.0
38 TraesCS7B01G057900 chr7A 77.644 416 55 19 968 1360 106999361 106998961 9.620000e-53 219.0
39 TraesCS7B01G057900 chr7A 86.567 134 9 3 733 865 106774093 106773968 7.700000e-29 139.0
40 TraesCS7B01G057900 chr7A 88.889 90 3 6 1 90 216420791 216420709 2.810000e-18 104.0
41 TraesCS7B01G057900 chr7A 90.667 75 6 1 5426 5499 106741641 106741567 1.310000e-16 99.0
42 TraesCS7B01G057900 chr7D 78.261 2139 398 56 2596 4702 102578594 102576491 0.000000e+00 1312.0
43 TraesCS7B01G057900 chr7D 92.453 53 2 2 2458 2509 351553662 351553611 2.200000e-09 75.0
44 TraesCS7B01G057900 chr2B 90.076 262 22 4 94 351 629486996 629486735 2.540000e-88 337.0
45 TraesCS7B01G057900 chr2A 88.142 253 23 7 94 342 13833524 13833275 1.550000e-75 294.0
46 TraesCS7B01G057900 chr6D 87.500 248 29 2 94 339 319661772 319662019 9.350000e-73 285.0
47 TraesCS7B01G057900 chr6D 90.909 55 5 0 2457 2511 18907207 18907261 2.200000e-09 75.0
48 TraesCS7B01G057900 chr1B 87.402 254 25 7 94 342 90467264 90467515 9.350000e-73 285.0
49 TraesCS7B01G057900 chr1B 86.957 253 31 2 94 344 470484296 470484044 3.360000e-72 283.0
50 TraesCS7B01G057900 chr5A 87.200 250 30 2 94 341 131403864 131404113 3.360000e-72 283.0
51 TraesCS7B01G057900 chr4B 86.770 257 31 3 94 348 27302067 27301812 3.360000e-72 283.0
52 TraesCS7B01G057900 chr4A 86.735 98 6 4 1 98 352496997 352496907 1.010000e-17 102.0
53 TraesCS7B01G057900 chr1D 86.139 101 7 4 1 101 132854070 132853977 1.010000e-17 102.0
54 TraesCS7B01G057900 chr1D 83.186 113 9 7 1 112 415983117 415983014 1.690000e-15 95.3
55 TraesCS7B01G057900 chr5B 85.437 103 7 6 2 103 360418530 360418435 3.630000e-17 100.0
56 TraesCS7B01G057900 chrUn 86.458 96 6 4 2 97 207766772 207766860 1.310000e-16 99.0
57 TraesCS7B01G057900 chr4D 86.458 96 6 4 2 97 62463961 62463873 1.310000e-16 99.0
58 TraesCS7B01G057900 chr3A 76.111 180 26 13 2335 2509 59465779 59465612 1.700000e-10 78.7


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 TraesCS7B01G057900 chr7B 60089440 60095140 5700 True 10528.000000 10528 100.000000 1 5701 1 chr7B.!!$R3 5700
1 TraesCS7B01G057900 chr7B 59821167 59826400 5233 True 1668.666667 3448 87.600333 94 4966 3 chr7B.!!$R5 4872
2 TraesCS7B01G057900 chr7B 59666084 59668399 2315 True 1325.000000 1325 77.526000 2603 4936 1 chr7B.!!$R1 2333
3 TraesCS7B01G057900 chr7B 60603590 60605451 1861 True 1279.000000 1279 79.430000 2596 4457 1 chr7B.!!$R4 1861
4 TraesCS7B01G057900 chr7B 60493881 60500115 6234 True 1197.333333 2874 85.603000 961 5701 3 chr7B.!!$R8 4740
5 TraesCS7B01G057900 chr7B 60059447 60065758 6311 True 1020.000000 1816 84.780333 864 4418 3 chr7B.!!$R7 3554
6 TraesCS7B01G057900 chr7B 60029296 60030686 1390 True 929.000000 929 79.111000 3311 4702 1 chr7B.!!$R2 1391
7 TraesCS7B01G057900 chr7B 60564028 60570223 6195 True 755.666667 1748 80.416000 968 5056 3 chr7B.!!$R9 4088
8 TraesCS7B01G057900 chr7B 60047294 60051913 4619 True 347.000000 704 86.490000 4405 5700 3 chr7B.!!$R6 1295
9 TraesCS7B01G057900 chr7A 106992296 106999361 7065 True 1895.500000 3572 83.020500 968 5537 2 chr7A.!!$R8 4569
10 TraesCS7B01G057900 chr7A 107320652 107322404 1752 True 1430.000000 1430 81.798000 3121 4883 1 chr7A.!!$R2 1762
11 TraesCS7B01G057900 chr7A 107150423 107155828 5405 True 1191.000000 2820 85.955000 961 5701 3 chr7A.!!$R9 4740
12 TraesCS7B01G057900 chr7A 107601731 107603621 1890 True 1096.000000 1096 77.630000 2530 4441 1 chr7A.!!$R4 1911
13 TraesCS7B01G057900 chr7A 106741567 106750339 8772 True 806.500000 2590 86.997500 94 5499 6 chr7A.!!$R6 5405
14 TraesCS7B01G057900 chr7A 106772265 106775354 3089 True 480.750000 974 86.405250 339 2269 4 chr7A.!!$R7 1930
15 TraesCS7B01G057900 chr7D 102576491 102578594 2103 True 1312.000000 1312 78.261000 2596 4702 1 chr7D.!!$R1 2106

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
935 2648 0.108662 CGATGTAGGAGTGCAGTGCA 60.109 55.0 15.37 15.37 35.6 4.57 F
1880 9322 0.108329 CGCTTCCCTCATACAACCGT 60.108 55.0 0.00 0.00 0.0 4.83 F
2801 12946 0.034186 CAGTTCCTTGGGGCTATGCA 60.034 55.0 0.00 0.00 0.0 3.96 F
4146 17541 0.250234 GTATGCTGCAGTCTGGACCA 59.750 55.0 16.64 2.74 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 9839 0.108396 AAAATTTTGCCCTGCCGCTT 59.892 45.000 1.75 0.00 0.00 4.68 R
3309 13475 0.036732 CACCAGGCTGTGTGTATGGT 59.963 55.000 21.00 6.48 45.00 3.55 R
4548 17965 0.405198 TTGCCAGCTTCATGGAAGGA 59.595 50.000 7.97 0.00 43.57 3.36 R
5653 23700 1.134699 CGTTCCCAGATCAGCTAAGCA 60.135 52.381 0.00 0.00 0.00 3.91 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
74 75 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
81 82 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
82 83 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
83 84 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
84 85 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
85 86 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
86 87 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
87 88 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
88 89 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
89 90 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
90 91 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
91 92 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
92 93 3.521947 AGTATTTTCGGACGGAGGAAG 57.478 47.619 0.00 0.00 0.00 3.46
217 218 8.841300 TGACACAAAGTAGTGCAACATTTAATA 58.159 29.630 0.00 0.00 43.23 0.98
218 219 9.840427 GACACAAAGTAGTGCAACATTTAATAT 57.160 29.630 0.00 0.00 43.23 1.28
245 254 8.672823 ATGCATGATATGATATGATACCACAC 57.327 34.615 0.00 0.00 0.00 3.82
324 334 4.011023 ACGATAGCGCTTATGATACTCCT 58.989 43.478 18.68 0.00 42.48 3.69
330 340 5.881447 AGCGCTTATGATACTCCTATTACG 58.119 41.667 2.64 0.00 0.00 3.18
398 478 2.801063 GAACATGCATGTGCCATGTAC 58.199 47.619 31.98 12.39 41.61 2.90
431 514 0.392998 CCTAAAGCCCACGCAGACAT 60.393 55.000 0.00 0.00 37.52 3.06
488 842 7.343057 AGGATCTATATATGTCCATTCTTGCGA 59.657 37.037 13.24 0.00 33.12 5.10
550 904 4.800993 CCTAGCGAACATTCTACTTGACAG 59.199 45.833 0.00 0.00 0.00 3.51
626 988 0.670546 CTGGACACACTCGCCGAATT 60.671 55.000 0.00 0.00 0.00 2.17
635 1807 0.389817 CTCGCCGAATTGTGAGGACA 60.390 55.000 0.00 0.00 38.83 4.02
666 1838 2.437281 ACCGAAGATGATCCATCAAGCT 59.563 45.455 9.30 0.00 42.72 3.74
674 1846 1.140452 GATCCATCAAGCTGCTGAGGA 59.860 52.381 1.35 8.93 31.51 3.71
682 1854 2.394563 GCTGCTGAGGACGCCTTTC 61.395 63.158 0.00 0.00 31.76 2.62
684 1856 2.347490 GCTGAGGACGCCTTTCCA 59.653 61.111 0.00 0.00 38.25 3.53
763 1993 2.505819 ACAGAGAGAGGGAGAGAGAGAC 59.494 54.545 0.00 0.00 0.00 3.36
809 2485 5.793817 TCTAGAGAACTTGCTTGCATACAA 58.206 37.500 0.00 0.00 0.00 2.41
841 2517 2.598565 CGAGGATGAGGAGGATTACCA 58.401 52.381 0.00 0.00 38.94 3.25
928 2641 9.163899 ACAGTATATATACACGATGTAGGAGTG 57.836 37.037 22.00 10.67 36.14 3.51
933 2646 1.067565 ACACGATGTAGGAGTGCAGTG 60.068 52.381 0.00 0.00 39.31 3.66
935 2648 0.108662 CGATGTAGGAGTGCAGTGCA 60.109 55.000 15.37 15.37 35.60 4.57
936 2649 1.649664 GATGTAGGAGTGCAGTGCAG 58.350 55.000 20.42 0.00 40.08 4.41
937 2650 0.979665 ATGTAGGAGTGCAGTGCAGT 59.020 50.000 25.33 25.33 45.60 4.40
943 2656 1.674057 AGTGCAGTGCAGTCCTACC 59.326 57.895 20.42 4.62 37.74 3.18
944 2657 1.738099 GTGCAGTGCAGTCCTACCG 60.738 63.158 20.42 0.00 40.08 4.02
945 2658 2.207229 TGCAGTGCAGTCCTACCGT 61.207 57.895 15.37 0.00 33.32 4.83
946 2659 0.896479 TGCAGTGCAGTCCTACCGTA 60.896 55.000 15.37 0.00 33.32 4.02
947 2660 0.460311 GCAGTGCAGTCCTACCGTAT 59.540 55.000 11.09 0.00 0.00 3.06
948 2661 1.536284 GCAGTGCAGTCCTACCGTATC 60.536 57.143 11.09 0.00 0.00 2.24
949 2662 1.067212 CAGTGCAGTCCTACCGTATCC 59.933 57.143 0.00 0.00 0.00 2.59
950 2663 1.108776 GTGCAGTCCTACCGTATCCA 58.891 55.000 0.00 0.00 0.00 3.41
951 2664 1.108776 TGCAGTCCTACCGTATCCAC 58.891 55.000 0.00 0.00 0.00 4.02
953 2666 1.386533 CAGTCCTACCGTATCCACGT 58.613 55.000 0.00 0.00 46.96 4.49
986 2701 4.142966 GGACAGCAAACTACACCGAATTAC 60.143 45.833 0.00 0.00 0.00 1.89
987 2702 4.382291 ACAGCAAACTACACCGAATTACA 58.618 39.130 0.00 0.00 0.00 2.41
988 2703 4.451096 ACAGCAAACTACACCGAATTACAG 59.549 41.667 0.00 0.00 0.00 2.74
1044 2767 2.499205 CCGGCAGCAAGGATCGTA 59.501 61.111 0.00 0.00 0.00 3.43
1048 2771 1.806247 CGGCAGCAAGGATCGTAATCA 60.806 52.381 0.00 0.00 33.21 2.57
1361 4019 1.764723 TCTCACCCCTGCATGTATCTG 59.235 52.381 0.00 0.00 0.00 2.90
1363 4021 0.820891 CACCCCTGCATGTATCTGGC 60.821 60.000 0.00 0.00 0.00 4.85
1364 4022 1.281199 ACCCCTGCATGTATCTGGCA 61.281 55.000 0.00 0.00 35.96 4.92
1365 4023 0.111832 CCCCTGCATGTATCTGGCAT 59.888 55.000 0.00 0.00 36.87 4.40
1366 4024 1.479942 CCCCTGCATGTATCTGGCATT 60.480 52.381 0.00 0.00 36.87 3.56
1368 4026 2.488528 CCCTGCATGTATCTGGCATTCT 60.489 50.000 0.00 0.00 36.87 2.40
1369 4027 2.552743 CCTGCATGTATCTGGCATTCTG 59.447 50.000 0.00 0.00 36.87 3.02
1370 4028 2.552743 CTGCATGTATCTGGCATTCTGG 59.447 50.000 0.00 0.00 36.87 3.86
1371 4029 1.268899 GCATGTATCTGGCATTCTGGC 59.731 52.381 0.00 0.00 44.03 4.85
1539 5211 4.870426 ACACACACTTAATATCTCCGCAAG 59.130 41.667 0.00 0.00 0.00 4.01
1540 5212 5.109210 CACACACTTAATATCTCCGCAAGA 58.891 41.667 0.00 0.00 43.02 3.02
1702 7594 4.822026 TCGGTTTTTCCTTTGAGCAAAAA 58.178 34.783 0.00 0.00 0.00 1.94
1742 7634 0.320697 CCCTAAATCGATCGGGTCCC 59.679 60.000 16.41 0.00 31.89 4.46
1743 7635 1.339097 CCTAAATCGATCGGGTCCCT 58.661 55.000 16.41 0.00 0.00 4.20
1766 7661 0.955178 CAATGTTGGCCCACGTAACA 59.045 50.000 7.93 7.93 38.52 2.41
1771 7666 3.045492 GGCCCACGTAACACACCG 61.045 66.667 0.00 0.00 0.00 4.94
1868 9310 0.804989 CAAACATCCACTCGCTTCCC 59.195 55.000 0.00 0.00 0.00 3.97
1869 9311 0.693049 AAACATCCACTCGCTTCCCT 59.307 50.000 0.00 0.00 0.00 4.20
1870 9312 0.250513 AACATCCACTCGCTTCCCTC 59.749 55.000 0.00 0.00 0.00 4.30
1871 9313 0.904865 ACATCCACTCGCTTCCCTCA 60.905 55.000 0.00 0.00 0.00 3.86
1872 9314 0.467384 CATCCACTCGCTTCCCTCAT 59.533 55.000 0.00 0.00 0.00 2.90
1873 9315 1.688735 CATCCACTCGCTTCCCTCATA 59.311 52.381 0.00 0.00 0.00 2.15
1874 9316 1.112113 TCCACTCGCTTCCCTCATAC 58.888 55.000 0.00 0.00 0.00 2.39
1875 9317 0.824109 CCACTCGCTTCCCTCATACA 59.176 55.000 0.00 0.00 0.00 2.29
1876 9318 1.207089 CCACTCGCTTCCCTCATACAA 59.793 52.381 0.00 0.00 0.00 2.41
1877 9319 2.271800 CACTCGCTTCCCTCATACAAC 58.728 52.381 0.00 0.00 0.00 3.32
1878 9320 1.207329 ACTCGCTTCCCTCATACAACC 59.793 52.381 0.00 0.00 0.00 3.77
1879 9321 0.174845 TCGCTTCCCTCATACAACCG 59.825 55.000 0.00 0.00 0.00 4.44
1880 9322 0.108329 CGCTTCCCTCATACAACCGT 60.108 55.000 0.00 0.00 0.00 4.83
1982 9633 0.832135 TGAGTCCTTCCTCCGCTTGT 60.832 55.000 0.00 0.00 0.00 3.16
1987 9638 3.302347 CTTCCTCCGCTTGTCGCCT 62.302 63.158 0.00 0.00 36.73 5.52
1994 9645 2.980233 GCTTGTCGCCTTGCCACT 60.980 61.111 0.00 0.00 0.00 4.00
2116 9788 1.340502 GGCAAAGCCTCCTTAGCTCTT 60.341 52.381 0.00 0.00 46.69 2.85
2167 9839 0.838554 TGGCTGGCTAGTGGGTACAA 60.839 55.000 2.00 0.00 0.00 2.41
2306 10285 4.963318 TGCTGATAATCCCTTACTCTGG 57.037 45.455 0.00 0.00 0.00 3.86
2307 10286 3.071602 TGCTGATAATCCCTTACTCTGGC 59.928 47.826 0.00 0.00 0.00 4.85
2321 10300 2.159014 ACTCTGGCGTGAAACTACAACA 60.159 45.455 0.00 0.00 31.75 3.33
2332 10340 8.318876 GCGTGAAACTACAACATATAGTGTAAG 58.681 37.037 0.76 0.00 35.24 2.34
2455 12581 5.763204 GGTTTTGTAATAGCCAGCTATAGCA 59.237 40.000 26.07 11.13 45.16 3.49
2482 12611 0.618458 TTGGAGGACCGCTGCTATTT 59.382 50.000 0.00 0.00 39.42 1.40
2483 12612 0.618458 TGGAGGACCGCTGCTATTTT 59.382 50.000 0.00 0.00 39.42 1.82
2506 12635 4.036262 TGCATAGCCCGCTATTTAAAACAG 59.964 41.667 6.48 0.00 37.16 3.16
2567 12696 6.633856 CCTATTTGCTTGCTTAATTGTTCCT 58.366 36.000 0.00 0.00 0.00 3.36
2631 12767 2.365617 GCCGAGGACCTGATCAAGAATA 59.634 50.000 0.00 0.00 0.00 1.75
2677 12813 1.270625 CCCTGCGACACTAACCAAAGA 60.271 52.381 0.00 0.00 0.00 2.52
2762 12904 1.202758 TCTCCAACATCGTGTGCCTTT 60.203 47.619 0.00 0.00 0.00 3.11
2790 12935 4.576879 GGAAGATTCCGTAACAGTTCCTT 58.423 43.478 0.00 0.00 37.65 3.36
2801 12946 0.034186 CAGTTCCTTGGGGCTATGCA 60.034 55.000 0.00 0.00 0.00 3.96
2804 12949 1.899142 GTTCCTTGGGGCTATGCAAAA 59.101 47.619 0.00 0.00 0.00 2.44
2847 12995 9.668497 GAAATGACAGTATAACCTTTCCTAACT 57.332 33.333 0.00 0.00 0.00 2.24
2850 12998 7.609056 TGACAGTATAACCTTTCCTAACTCAC 58.391 38.462 0.00 0.00 0.00 3.51
2921 13072 3.583086 AGAGTTGCAGAGGTAAAAGGCTA 59.417 43.478 0.00 0.00 0.00 3.93
2939 13090 1.917782 TAAAGATTGCCGTGCCGCAC 61.918 55.000 13.81 13.81 38.83 5.34
2965 13116 5.234752 ACCAGGTTTTCAAGTTTTTGTGAC 58.765 37.500 0.00 0.00 35.73 3.67
2973 13124 9.615295 GTTTTCAAGTTTTTGTGACTGTTACTA 57.385 29.630 4.30 0.00 35.73 1.82
3060 13211 0.600782 TTTACAACCTCGTCCGTGCC 60.601 55.000 0.00 0.00 0.00 5.01
3074 13225 2.289274 TCCGTGCCATAAATATGTTGCG 59.711 45.455 0.16 1.71 31.82 4.85
3153 13308 3.118629 TCCTACACCACTTGCATCTCATC 60.119 47.826 0.00 0.00 0.00 2.92
3154 13309 2.119801 ACACCACTTGCATCTCATCC 57.880 50.000 0.00 0.00 0.00 3.51
3229 13392 8.489489 ACCTTTTCATCTCTGCTAATTATCTGA 58.511 33.333 0.00 0.00 0.00 3.27
3278 13444 0.461339 GGCGATGTGACCATAACCGT 60.461 55.000 0.00 0.00 0.00 4.83
3283 13449 2.932855 TGTGACCATAACCGTGGAAA 57.067 45.000 0.00 0.00 42.02 3.13
3287 13453 2.901192 TGACCATAACCGTGGAAAGAGA 59.099 45.455 0.00 0.00 42.02 3.10
3288 13454 3.056107 TGACCATAACCGTGGAAAGAGAG 60.056 47.826 0.00 0.00 42.02 3.20
3294 13460 2.816411 ACCGTGGAAAGAGAGACCATA 58.184 47.619 0.00 0.00 36.09 2.74
3309 13475 2.426024 GACCATAGCCGACTTCACAGTA 59.574 50.000 0.00 0.00 31.22 2.74
3322 13488 3.313012 TCACAGTACCATACACACAGC 57.687 47.619 0.00 0.00 0.00 4.40
3346 13512 2.160417 GGTGTGTCTATGCTTGTGCTTC 59.840 50.000 0.00 0.00 40.48 3.86
3348 13514 2.038952 TGTGTCTATGCTTGTGCTTCCT 59.961 45.455 0.00 0.00 40.48 3.36
3355 13521 1.908619 TGCTTGTGCTTCCTGAGGATA 59.091 47.619 0.04 0.00 40.48 2.59
3358 13524 3.758554 GCTTGTGCTTCCTGAGGATAAAA 59.241 43.478 0.04 0.00 36.03 1.52
3364 13530 5.065731 GTGCTTCCTGAGGATAAAACAGATG 59.934 44.000 0.04 0.00 0.00 2.90
3366 13532 4.842531 TCCTGAGGATAAAACAGATGCA 57.157 40.909 0.00 0.00 0.00 3.96
3367 13533 5.178096 TCCTGAGGATAAAACAGATGCAA 57.822 39.130 0.00 0.00 0.00 4.08
3368 13534 5.759059 TCCTGAGGATAAAACAGATGCAAT 58.241 37.500 0.00 0.00 0.00 3.56
3373 13539 8.985315 TGAGGATAAAACAGATGCAATAATCT 57.015 30.769 0.00 0.00 37.39 2.40
3451 13617 6.605471 TCTTCTTCTATACTGGCTTTGTCA 57.395 37.500 0.00 0.00 0.00 3.58
3453 13619 7.624549 TCTTCTTCTATACTGGCTTTGTCATT 58.375 34.615 0.00 0.00 0.00 2.57
3498 13664 3.107601 TCAGGAGTACCAAGGATCAAGG 58.892 50.000 0.00 0.00 38.94 3.61
3501 13667 2.838202 GGAGTACCAAGGATCAAGGTCA 59.162 50.000 6.27 0.00 36.87 4.02
3567 16927 4.022589 ACATTTTCTCATGGTCAGCACTTG 60.023 41.667 0.00 0.00 0.00 3.16
3570 16930 3.490439 TCTCATGGTCAGCACTTGAAA 57.510 42.857 0.00 0.00 37.61 2.69
3577 16937 3.378112 TGGTCAGCACTTGAAACTTGAAG 59.622 43.478 0.00 0.00 37.61 3.02
3583 16943 4.336713 AGCACTTGAAACTTGAAGTTCCTC 59.663 41.667 11.44 6.91 37.47 3.71
3584 16944 4.336713 GCACTTGAAACTTGAAGTTCCTCT 59.663 41.667 11.44 0.00 37.47 3.69
3791 17168 0.603975 GACTGCAAAGAGGCTCCGTT 60.604 55.000 11.71 2.78 34.04 4.44
3828 17211 0.965866 CTCCGGCAGAGTGGTGACTA 60.966 60.000 0.00 0.00 37.87 2.59
3878 17267 3.314635 GCGATCCTTCTTGCTGAATCATT 59.685 43.478 0.00 0.00 33.71 2.57
3892 17281 7.532571 TGCTGAATCATTACATCAGTGAAAAG 58.467 34.615 0.00 0.00 42.00 2.27
3904 17293 6.712547 ACATCAGTGAAAAGAGGTTAAGGAAG 59.287 38.462 0.00 0.00 0.00 3.46
3937 17326 7.094805 ACGAAAGAAGAATATGCTGTTGCTTTA 60.095 33.333 0.00 0.00 40.48 1.85
3938 17327 7.217070 CGAAAGAAGAATATGCTGTTGCTTTAC 59.783 37.037 0.00 0.00 40.48 2.01
4000 17389 8.552034 GTTGATGAGATCCCTTATTTAACTTCG 58.448 37.037 0.00 0.00 0.00 3.79
4013 17402 2.708386 AACTTCGTTCCTCTCTGACG 57.292 50.000 0.00 0.00 38.09 4.35
4035 17424 7.958567 TGACGATCGGTACAAAAATGATTTTAC 59.041 33.333 20.98 0.00 36.62 2.01
4036 17425 8.036273 ACGATCGGTACAAAAATGATTTTACT 57.964 30.769 20.98 0.00 36.62 2.24
4145 17540 0.807667 CGTATGCTGCAGTCTGGACC 60.808 60.000 16.64 0.00 0.00 4.46
4146 17541 0.250234 GTATGCTGCAGTCTGGACCA 59.750 55.000 16.64 2.74 0.00 4.02
4151 17546 1.269257 GCTGCAGTCTGGACCAAAAAC 60.269 52.381 16.64 0.00 0.00 2.43
4208 17607 3.802948 TTTCATCTAGGTTCTCCGCTC 57.197 47.619 0.00 0.00 39.05 5.03
4306 17705 2.809446 CACAACTTCATCGCCGATAGA 58.191 47.619 0.00 0.00 39.76 1.98
4334 17733 3.678289 CACAATCCCAGACACTGATTCA 58.322 45.455 0.00 0.00 32.44 2.57
4548 17965 0.032813 CCCCAGCCCTGATCAACAAT 60.033 55.000 0.00 0.00 0.00 2.71
4951 18420 3.246416 AGACAGGTACAGTCCTCAACT 57.754 47.619 12.46 0.00 46.45 3.16
5007 18586 2.754946 TACAACCCTGAATGTCCGAC 57.245 50.000 0.00 0.00 0.00 4.79
5064 18644 0.611714 AACCGAACGGAGGCAGTATT 59.388 50.000 20.14 0.00 38.96 1.89
5065 18645 1.477553 ACCGAACGGAGGCAGTATTA 58.522 50.000 20.14 0.00 38.96 0.98
5066 18646 1.135721 ACCGAACGGAGGCAGTATTAC 59.864 52.381 20.14 0.00 38.96 1.89
5184 19963 9.825109 TGAATTGGATATAAACAGTCGTATTCA 57.175 29.630 0.00 0.00 0.00 2.57
5209 19988 9.003658 CATCCCTATCTCTTTTGCGTATTAAAT 57.996 33.333 0.00 0.00 0.00 1.40
5223 20002 8.598202 TGCGTATTAAATATATACTCCCTCCA 57.402 34.615 0.00 0.00 0.00 3.86
5224 20003 9.038072 TGCGTATTAAATATATACTCCCTCCAA 57.962 33.333 0.00 0.00 0.00 3.53
5248 20027 8.842280 CAACCTATAATATAAGGGCGTTTTTGA 58.158 33.333 0.00 0.00 37.18 2.69
5249 20028 8.387190 ACCTATAATATAAGGGCGTTTTTGAC 57.613 34.615 0.00 0.00 37.18 3.18
5250 20029 7.994334 ACCTATAATATAAGGGCGTTTTTGACA 59.006 33.333 0.00 0.00 37.18 3.58
5251 20030 8.287503 CCTATAATATAAGGGCGTTTTTGACAC 58.712 37.037 0.00 0.00 0.00 3.67
5252 20031 7.875327 ATAATATAAGGGCGTTTTTGACACT 57.125 32.000 0.00 0.00 0.00 3.55
5253 20032 6.584185 AATATAAGGGCGTTTTTGACACTT 57.416 33.333 0.00 0.00 0.00 3.16
5254 20033 4.929819 ATAAGGGCGTTTTTGACACTTT 57.070 36.364 0.00 0.00 0.00 2.66
5255 20034 7.690952 ATATAAGGGCGTTTTTGACACTTTA 57.309 32.000 0.00 0.00 0.00 1.85
5256 20035 4.722361 AAGGGCGTTTTTGACACTTTAA 57.278 36.364 0.00 0.00 0.00 1.52
5257 20036 4.301637 AGGGCGTTTTTGACACTTTAAG 57.698 40.909 0.00 0.00 0.00 1.85
5258 20037 3.949113 AGGGCGTTTTTGACACTTTAAGA 59.051 39.130 0.00 0.00 0.00 2.10
5259 20038 4.036380 AGGGCGTTTTTGACACTTTAAGAG 59.964 41.667 0.00 0.00 0.00 2.85
5260 20039 4.201980 GGGCGTTTTTGACACTTTAAGAGT 60.202 41.667 0.00 0.00 39.89 3.24
5399 20190 5.464168 CAGCTCCTTTATGGACAGTTTTTG 58.536 41.667 0.00 0.00 40.56 2.44
5505 20308 7.907389 ACTTTCAGATGAACTTATCAGTACCA 58.093 34.615 0.00 0.00 42.53 3.25
5553 23594 7.209471 ACGGTACTGCTTTCATTTAATCAAA 57.791 32.000 0.23 0.00 0.00 2.69
5608 23649 8.621532 AACAGTCAAAGTTAGAGAATTATGCA 57.378 30.769 0.00 0.00 0.00 3.96
5610 23651 9.890629 ACAGTCAAAGTTAGAGAATTATGCATA 57.109 29.630 1.16 1.16 0.00 3.14
5653 23700 7.174426 ACGCTAAGTTTGGTTCTTTAATTAGCT 59.826 33.333 10.72 0.00 40.90 3.32
5658 23706 8.404107 AGTTTGGTTCTTTAATTAGCTGCTTA 57.596 30.769 7.79 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
56 57 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
57 58 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
58 59 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
59 60 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
60 61 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
61 62 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
62 63 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
63 64 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
64 65 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
65 66 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
66 67 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
67 68 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
68 69 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
69 70 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
70 71 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
71 72 3.260128 ACTTCCTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
72 73 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
73 74 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
74 75 4.019174 AGTACTTCCTCCGTCCGAAAATA 58.981 43.478 0.00 0.00 0.00 1.40
75 76 2.830321 AGTACTTCCTCCGTCCGAAAAT 59.170 45.455 0.00 0.00 0.00 1.82
76 77 2.242043 AGTACTTCCTCCGTCCGAAAA 58.758 47.619 0.00 0.00 0.00 2.29
77 78 1.915141 AGTACTTCCTCCGTCCGAAA 58.085 50.000 0.00 0.00 0.00 3.46
78 79 2.026822 ACTAGTACTTCCTCCGTCCGAA 60.027 50.000 0.00 0.00 0.00 4.30
79 80 1.556911 ACTAGTACTTCCTCCGTCCGA 59.443 52.381 0.00 0.00 0.00 4.55
80 81 2.035530 ACTAGTACTTCCTCCGTCCG 57.964 55.000 0.00 0.00 0.00 4.79
81 82 4.712476 TGATACTAGTACTTCCTCCGTCC 58.288 47.826 4.31 0.00 0.00 4.79
82 83 5.335035 GCATGATACTAGTACTTCCTCCGTC 60.335 48.000 4.31 0.00 0.00 4.79
83 84 4.519730 GCATGATACTAGTACTTCCTCCGT 59.480 45.833 4.31 0.00 0.00 4.69
84 85 4.519350 TGCATGATACTAGTACTTCCTCCG 59.481 45.833 4.31 0.00 0.00 4.63
85 86 6.597832 ATGCATGATACTAGTACTTCCTCC 57.402 41.667 4.31 0.00 0.00 4.30
86 87 8.961634 TCATATGCATGATACTAGTACTTCCTC 58.038 37.037 10.16 0.00 36.22 3.71
87 88 8.885693 TCATATGCATGATACTAGTACTTCCT 57.114 34.615 10.16 0.00 36.22 3.36
219 220 9.117183 GTGTGGTATCATATCATATCATGCATT 57.883 33.333 0.00 0.00 0.00 3.56
220 221 7.718314 GGTGTGGTATCATATCATATCATGCAT 59.282 37.037 0.00 0.00 0.00 3.96
221 222 7.049754 GGTGTGGTATCATATCATATCATGCA 58.950 38.462 0.00 0.00 0.00 3.96
222 223 7.049754 TGGTGTGGTATCATATCATATCATGC 58.950 38.462 0.00 0.00 0.00 4.06
223 224 9.269453 GATGGTGTGGTATCATATCATATCATG 57.731 37.037 5.20 0.00 36.23 3.07
230 231 7.379059 AAAGAGATGGTGTGGTATCATATCA 57.621 36.000 0.00 0.00 39.95 2.15
280 290 8.272545 TCGTGCATACTAACTAGACTTTTAGA 57.727 34.615 0.00 0.00 0.00 2.10
297 307 6.947635 GAGTATCATAAGCGCTATCGTGCATA 60.948 42.308 12.05 0.00 41.71 3.14
303 313 4.624336 AGGAGTATCATAAGCGCTATCG 57.376 45.455 12.05 1.11 36.25 2.92
308 318 5.877031 TCGTAATAGGAGTATCATAAGCGC 58.123 41.667 0.00 0.00 33.84 5.92
324 334 4.214971 GGTCGACTAAGGCTGATCGTAATA 59.785 45.833 16.46 0.00 36.03 0.98
330 340 1.002251 CGAGGTCGACTAAGGCTGATC 60.002 57.143 16.46 0.00 43.02 2.92
398 478 2.032675 GCTTTAGGGAGGTCGTACGTAG 59.967 54.545 16.05 0.00 0.00 3.51
431 514 2.304761 AGTAGCAGAACCGAAATCCCAA 59.695 45.455 0.00 0.00 0.00 4.12
505 859 4.998033 GGGTAACTGAAGCATAGATAAGGC 59.002 45.833 0.00 0.00 0.00 4.35
626 988 1.070758 GTCTCTTGGCTTGTCCTCACA 59.929 52.381 0.00 0.00 35.26 3.58
635 1807 1.902508 TCATCTTCGGTCTCTTGGCTT 59.097 47.619 0.00 0.00 0.00 4.35
666 1838 2.050836 TTGGAAAGGCGTCCTCAGCA 62.051 55.000 10.97 0.00 38.62 4.41
674 1846 2.275380 GGCACCATTGGAAAGGCGT 61.275 57.895 10.37 0.00 0.00 5.68
682 1854 1.526575 AAGAAGCGTGGCACCATTGG 61.527 55.000 12.86 0.00 0.00 3.16
684 1856 1.959085 CAAGAAGCGTGGCACCATT 59.041 52.632 12.86 6.88 0.00 3.16
711 1883 2.050144 AGCCTCAAGAAGTCACTTGGA 58.950 47.619 0.00 0.00 44.84 3.53
763 1993 1.599071 TGCAGCGAAAGTCTGAAAGTG 59.401 47.619 0.00 0.00 37.41 3.16
809 2485 1.209504 TCATCCTCGGGCGAAATTTCT 59.790 47.619 15.92 0.00 0.00 2.52
841 2517 2.696759 CCGGCGGCGAAATTTCCTT 61.697 57.895 34.49 0.00 0.00 3.36
868 2576 2.016318 ACATTGATGTGTATGCACCGG 58.984 47.619 11.66 0.00 44.65 5.28
886 2594 0.171679 CTGTCCGCCGTGTATGTACA 59.828 55.000 0.00 0.00 0.00 2.90
887 2595 0.171903 ACTGTCCGCCGTGTATGTAC 59.828 55.000 0.00 0.00 0.00 2.90
891 2599 5.882000 TGTATATATACTGTCCGCCGTGTAT 59.118 40.000 20.80 0.00 34.41 2.29
928 2641 0.460311 ATACGGTAGGACTGCACTGC 59.540 55.000 0.00 0.00 0.00 4.40
933 2646 0.030369 CGTGGATACGGTAGGACTGC 59.970 60.000 0.00 0.00 46.23 4.40
952 2665 2.737376 GCTGTCCGTCCGTGGAAC 60.737 66.667 0.00 0.00 40.44 3.62
953 2666 2.313051 TTTGCTGTCCGTCCGTGGAA 62.313 55.000 0.00 0.00 40.44 3.53
986 2701 2.103263 GGTGGCATTCTCCCTACTACTG 59.897 54.545 0.00 0.00 0.00 2.74
987 2702 2.399580 GGTGGCATTCTCCCTACTACT 58.600 52.381 0.00 0.00 0.00 2.57
988 2703 1.068741 CGGTGGCATTCTCCCTACTAC 59.931 57.143 0.00 0.00 0.00 2.73
1039 2762 4.920640 AAGTGACGAGGATGATTACGAT 57.079 40.909 0.00 0.00 0.00 3.73
1044 2767 3.265791 GAGCAAAGTGACGAGGATGATT 58.734 45.455 0.00 0.00 0.00 2.57
1048 2771 1.670087 CGTGAGCAAAGTGACGAGGAT 60.670 52.381 0.00 0.00 33.64 3.24
1361 4019 1.020437 GCTCAAGTAGCCAGAATGCC 58.980 55.000 0.00 0.00 46.25 4.40
1396 4200 5.741982 CCGAATTTGGATCGTATGGAAAAAC 59.258 40.000 5.72 0.00 38.60 2.43
1702 7594 5.773176 AGGGTTTATGAAACGAACCAGAATT 59.227 36.000 6.80 0.00 43.59 2.17
1706 7598 6.563222 TTTAGGGTTTATGAAACGAACCAG 57.437 37.500 6.80 0.00 43.59 4.00
1742 7634 1.005867 GTGGGCCAACATTGCACAG 60.006 57.895 8.40 0.00 44.08 3.66
1743 7635 2.854401 CGTGGGCCAACATTGCACA 61.854 57.895 8.40 0.00 40.50 4.57
1803 7698 1.988956 GGTGCATGGGCCCAATTGA 60.989 57.895 32.58 10.62 40.13 2.57
1868 9310 2.533266 GGGTTACGACGGTTGTATGAG 58.467 52.381 8.99 0.00 0.00 2.90
1869 9311 1.204467 GGGGTTACGACGGTTGTATGA 59.796 52.381 8.99 0.00 0.00 2.15
1870 9312 1.067000 TGGGGTTACGACGGTTGTATG 60.067 52.381 8.99 0.00 0.00 2.39
1871 9313 1.205417 CTGGGGTTACGACGGTTGTAT 59.795 52.381 8.99 0.00 0.00 2.29
1872 9314 0.602562 CTGGGGTTACGACGGTTGTA 59.397 55.000 4.08 4.08 0.00 2.41
1873 9315 1.368579 CTGGGGTTACGACGGTTGT 59.631 57.895 6.24 6.24 0.00 3.32
1874 9316 2.030958 GCTGGGGTTACGACGGTTG 61.031 63.158 0.00 0.00 0.00 3.77
1875 9317 2.344872 GCTGGGGTTACGACGGTT 59.655 61.111 0.00 0.00 0.00 4.44
1876 9318 2.918802 TGCTGGGGTTACGACGGT 60.919 61.111 0.00 0.00 0.00 4.83
1877 9319 2.433664 GTGCTGGGGTTACGACGG 60.434 66.667 0.00 0.00 0.00 4.79
1878 9320 2.433664 GGTGCTGGGGTTACGACG 60.434 66.667 0.00 0.00 0.00 5.12
1879 9321 2.433664 CGGTGCTGGGGTTACGAC 60.434 66.667 0.00 0.00 0.00 4.34
1880 9322 4.382320 GCGGTGCTGGGGTTACGA 62.382 66.667 0.00 0.00 0.00 3.43
1917 9391 0.693049 GTGTCTGGACATTGAGGGGT 59.307 55.000 6.71 0.00 43.97 4.95
1982 9633 2.662596 CCAGTAGTGGCAAGGCGA 59.337 61.111 2.97 0.00 36.89 5.54
2081 9746 3.854459 GCCGCTAGCTGCAACGAC 61.854 66.667 24.24 0.00 43.06 4.34
2116 9788 2.038557 GAGAAAGAGTACCTTGTGGGCA 59.961 50.000 0.00 0.00 39.10 5.36
2167 9839 0.108396 AAAATTTTGCCCTGCCGCTT 59.892 45.000 1.75 0.00 0.00 4.68
2210 9883 6.621316 TTTTGCTTTCGTAACTTCCATACA 57.379 33.333 0.00 0.00 0.00 2.29
2211 9884 6.581166 CCTTTTTGCTTTCGTAACTTCCATAC 59.419 38.462 0.00 0.00 0.00 2.39
2212 9885 6.487331 TCCTTTTTGCTTTCGTAACTTCCATA 59.513 34.615 0.00 0.00 0.00 2.74
2213 9886 5.300792 TCCTTTTTGCTTTCGTAACTTCCAT 59.699 36.000 0.00 0.00 0.00 3.41
2223 9896 5.287035 GCATAACAGATCCTTTTTGCTTTCG 59.713 40.000 10.33 0.00 0.00 3.46
2306 10285 6.642683 ACACTATATGTTGTAGTTTCACGC 57.357 37.500 0.00 0.00 38.98 5.34
2307 10286 9.350357 ACTTACACTATATGTTGTAGTTTCACG 57.650 33.333 0.00 0.00 43.19 4.35
2332 10340 4.919754 CAGCTGGCTATTCAAAACTTTGAC 59.080 41.667 5.57 0.00 45.99 3.18
2343 10351 1.202417 TGACGCTACAGCTGGCTATTC 60.202 52.381 19.93 9.14 39.32 1.75
2351 10359 2.351835 CCGCTATAATGACGCTACAGCT 60.352 50.000 0.00 0.00 39.32 4.24
2360 12486 3.871594 ACTGCTCAAACCGCTATAATGAC 59.128 43.478 0.00 0.00 0.00 3.06
2422 12548 7.414762 GCTGGCTATTACAAAACCTTATCGAAA 60.415 37.037 0.00 0.00 0.00 3.46
2424 12550 5.526111 GCTGGCTATTACAAAACCTTATCGA 59.474 40.000 0.00 0.00 0.00 3.59
2435 12561 4.997395 GCTTGCTATAGCTGGCTATTACAA 59.003 41.667 24.61 18.93 42.66 2.41
2455 12581 0.678048 GCGGTCCTCCAAATCAGCTT 60.678 55.000 0.00 0.00 0.00 3.74
2482 12611 4.399618 TGTTTTAAATAGCGGGCTATGCAA 59.600 37.500 13.53 8.17 39.03 4.08
2483 12612 3.948473 TGTTTTAAATAGCGGGCTATGCA 59.052 39.130 13.53 0.00 39.03 3.96
2567 12696 4.722220 AGCCAAGCAAATAGCATGATCTA 58.278 39.130 0.00 0.00 44.41 1.98
2677 12813 2.290514 CCCAGGTGTGTGACATGATCTT 60.291 50.000 0.00 0.00 38.73 2.40
2720 12856 0.473694 TGCTGGGGAAGGAGAGAACA 60.474 55.000 0.00 0.00 0.00 3.18
2775 12917 0.688487 CCCCAAGGAACTGTTACGGA 59.312 55.000 0.00 0.00 40.86 4.69
2790 12935 1.065564 GCCAAATTTTGCATAGCCCCA 60.066 47.619 9.26 0.00 0.00 4.96
2801 12946 7.772757 TCATTTCCAAGTGTAAAGCCAAATTTT 59.227 29.630 0.00 0.00 0.00 1.82
2804 12949 6.183360 TGTCATTTCCAAGTGTAAAGCCAAAT 60.183 34.615 0.00 0.00 0.00 2.32
2847 12995 6.769134 TCTGTATCTTCTATCGGTTTGTGA 57.231 37.500 0.00 0.00 0.00 3.58
2850 12998 8.703604 TTTCTTCTGTATCTTCTATCGGTTTG 57.296 34.615 0.00 0.00 0.00 2.93
2897 13045 3.057946 GCCTTTTACCTCTGCAACTCTTG 60.058 47.826 0.00 0.00 0.00 3.02
2939 13090 6.203723 TCACAAAAACTTGAAAACCTGGTTTG 59.796 34.615 24.47 14.47 35.80 2.93
2944 13095 5.925969 ACAGTCACAAAAACTTGAAAACCTG 59.074 36.000 0.00 0.00 0.00 4.00
2973 13124 8.193953 ACATGTTGTTTCTTGGAATTAGGATT 57.806 30.769 0.00 0.00 0.00 3.01
3060 13211 4.200827 CCGTCGAACGCAACATATTTATG 58.799 43.478 0.00 0.00 40.91 1.90
3074 13225 3.729716 GCTCATCATAAGTACCGTCGAAC 59.270 47.826 0.00 0.00 0.00 3.95
3224 13387 1.975680 ACACCTGTTTACCCGTCAGAT 59.024 47.619 0.00 0.00 0.00 2.90
3229 13392 3.370103 CCATCATACACCTGTTTACCCGT 60.370 47.826 0.00 0.00 0.00 5.28
3278 13444 1.757118 CGGCTATGGTCTCTCTTTCCA 59.243 52.381 0.00 0.00 35.64 3.53
3283 13449 2.303175 GAAGTCGGCTATGGTCTCTCT 58.697 52.381 0.00 0.00 0.00 3.10
3287 13453 1.478510 CTGTGAAGTCGGCTATGGTCT 59.521 52.381 0.00 0.00 0.00 3.85
3288 13454 1.204941 ACTGTGAAGTCGGCTATGGTC 59.795 52.381 0.00 0.00 0.00 4.02
3294 13460 1.267121 ATGGTACTGTGAAGTCGGCT 58.733 50.000 0.00 0.00 0.00 5.52
3309 13475 0.036732 CACCAGGCTGTGTGTATGGT 59.963 55.000 21.00 6.48 45.00 3.55
3322 13488 2.079158 CACAAGCATAGACACACCAGG 58.921 52.381 0.00 0.00 0.00 4.45
3346 13512 7.572523 TTATTGCATCTGTTTTATCCTCAGG 57.427 36.000 0.00 0.00 0.00 3.86
3348 13514 8.843262 CAGATTATTGCATCTGTTTTATCCTCA 58.157 33.333 6.85 0.00 43.67 3.86
3364 13530 4.506758 ACAAATGCCCAACAGATTATTGC 58.493 39.130 0.00 0.00 0.00 3.56
3366 13532 6.818142 GCTTTACAAATGCCCAACAGATTATT 59.182 34.615 0.00 0.00 0.00 1.40
3367 13533 6.340522 GCTTTACAAATGCCCAACAGATTAT 58.659 36.000 0.00 0.00 0.00 1.28
3368 13534 5.337169 GGCTTTACAAATGCCCAACAGATTA 60.337 40.000 5.48 0.00 40.71 1.75
3373 13539 2.042464 TGGCTTTACAAATGCCCAACA 58.958 42.857 12.44 0.00 45.56 3.33
3379 13545 4.485163 CCTGTTAGTGGCTTTACAAATGC 58.515 43.478 0.00 0.00 0.00 3.56
3399 13565 1.138859 GTTGCAAACCAAAGCTTCCCT 59.861 47.619 0.00 0.00 42.21 4.20
3451 13617 6.078456 TCTGGGTAGTTCAATCATCCAAAT 57.922 37.500 0.00 0.00 0.00 2.32
3453 13619 5.512942 TTCTGGGTAGTTCAATCATCCAA 57.487 39.130 0.00 0.00 0.00 3.53
3567 16927 6.625873 ATTGTGAGAGGAACTTCAAGTTTC 57.374 37.500 3.76 1.56 41.55 2.78
3570 16930 7.939039 TCAAATATTGTGAGAGGAACTTCAAGT 59.061 33.333 0.00 0.00 41.55 3.16
3577 16937 6.441093 TGCATCAAATATTGTGAGAGGAAC 57.559 37.500 0.00 0.00 0.00 3.62
3767 17144 2.169352 GGAGCCTCTTTGCAGTCAGATA 59.831 50.000 0.00 0.00 0.00 1.98
3768 17145 1.065564 GGAGCCTCTTTGCAGTCAGAT 60.066 52.381 0.00 0.00 0.00 2.90
3791 17168 3.748048 CGGAGCTTCTCAAAATCTGTCAA 59.252 43.478 0.00 0.00 31.08 3.18
3878 17267 7.311092 TCCTTAACCTCTTTTCACTGATGTA 57.689 36.000 0.00 0.00 0.00 2.29
3892 17281 3.256631 TCGTGGTGTACTTCCTTAACCTC 59.743 47.826 8.61 0.33 0.00 3.85
3904 17293 5.581085 AGCATATTCTTCTTTCGTGGTGTAC 59.419 40.000 0.00 0.00 0.00 2.90
4000 17389 1.096416 ACCGATCGTCAGAGAGGAAC 58.904 55.000 15.09 0.00 33.08 3.62
4035 17424 7.619050 AGTCTTGTATATGGATCCAAGCATAG 58.381 38.462 20.67 11.99 35.42 2.23
4036 17425 7.310671 GGAGTCTTGTATATGGATCCAAGCATA 60.311 40.741 20.67 13.49 35.42 3.14
4145 17540 7.899330 CACAAAGTCAGCAACTAATTGTTTTTG 59.101 33.333 6.60 1.27 37.00 2.44
4146 17541 7.602265 ACACAAAGTCAGCAACTAATTGTTTTT 59.398 29.630 6.60 0.00 37.00 1.94
4151 17546 6.498304 AGAACACAAAGTCAGCAACTAATTG 58.502 36.000 0.00 0.00 37.17 2.32
4208 17607 5.295431 TGGCAGTTGAAAGATTATGAACG 57.705 39.130 0.00 0.00 0.00 3.95
4334 17733 3.055747 AGCTTTCTAAAGTAAGAGGCGCT 60.056 43.478 7.64 0.00 38.28 5.92
4548 17965 0.405198 TTGCCAGCTTCATGGAAGGA 59.595 50.000 7.97 0.00 43.57 3.36
5007 18586 3.726291 AAAACATGAACTTCCCCAACG 57.274 42.857 0.00 0.00 0.00 4.10
5218 19997 5.189145 ACGCCCTTATATTATAGGTTGGAGG 59.811 44.000 0.00 0.00 0.00 4.30
5223 20002 8.843262 GTCAAAAACGCCCTTATATTATAGGTT 58.157 33.333 0.00 0.00 0.00 3.50
5224 20003 7.994334 TGTCAAAAACGCCCTTATATTATAGGT 59.006 33.333 0.00 0.00 0.00 3.08
5263 20042 8.822855 CAACTGTGTACATCACTAGTGTAAAAA 58.177 33.333 21.99 3.12 46.27 1.94
5264 20043 7.982919 ACAACTGTGTACATCACTAGTGTAAAA 59.017 33.333 21.99 3.51 46.27 1.52
5265 20044 7.494211 ACAACTGTGTACATCACTAGTGTAAA 58.506 34.615 21.99 3.90 46.27 2.01
5266 20045 7.013942 AGACAACTGTGTACATCACTAGTGTAA 59.986 37.037 21.99 4.68 46.27 2.41
5267 20046 6.489022 AGACAACTGTGTACATCACTAGTGTA 59.511 38.462 21.99 9.79 46.27 2.90
5399 20190 7.086376 TCAACTGTCTATAAAGGACACGTAAC 58.914 38.462 0.00 0.00 38.57 2.50
5602 23643 7.418337 TCTCCTGTTAGTCTGTTATGCATAA 57.582 36.000 15.21 15.21 0.00 1.90
5608 23649 4.463186 AGCGTTCTCCTGTTAGTCTGTTAT 59.537 41.667 0.00 0.00 0.00 1.89
5610 23651 2.628657 AGCGTTCTCCTGTTAGTCTGTT 59.371 45.455 0.00 0.00 0.00 3.16
5611 23652 2.240279 AGCGTTCTCCTGTTAGTCTGT 58.760 47.619 0.00 0.00 0.00 3.41
5612 23653 4.082679 ACTTAGCGTTCTCCTGTTAGTCTG 60.083 45.833 0.00 0.00 0.00 3.51
5613 23654 4.080687 ACTTAGCGTTCTCCTGTTAGTCT 58.919 43.478 0.00 0.00 0.00 3.24
5614 23655 4.437772 ACTTAGCGTTCTCCTGTTAGTC 57.562 45.455 0.00 0.00 0.00 2.59
5617 23658 4.202284 ACCAAACTTAGCGTTCTCCTGTTA 60.202 41.667 0.00 0.00 33.90 2.41
5618 23659 3.139077 CCAAACTTAGCGTTCTCCTGTT 58.861 45.455 0.00 0.00 33.90 3.16
5653 23700 1.134699 CGTTCCCAGATCAGCTAAGCA 60.135 52.381 0.00 0.00 0.00 3.91
5658 23706 2.088104 TATCCGTTCCCAGATCAGCT 57.912 50.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.