Multiple sequence alignment - TraesCS2A01G222300

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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 TraesCS2A01G222300 chr2A 100.000 3173 0 0 2786 5958 213112439 213109267 0.000000e+00 5860.0
1 TraesCS2A01G222300 chr2A 100.000 2552 0 0 1 2552 213115224 213112673 0.000000e+00 4713.0
2 TraesCS2A01G222300 chr2A 93.663 505 22 2 2850 3344 775054309 775054813 0.000000e+00 747.0
3 TraesCS2A01G222300 chr1A 95.635 1260 45 2 2826 4075 534238496 534237237 0.000000e+00 2013.0
4 TraesCS2A01G222300 chr1A 93.721 1290 64 10 2802 4078 369277610 369278895 0.000000e+00 1917.0
5 TraesCS2A01G222300 chr1A 84.839 310 43 4 1394 1701 13973238 13973545 5.800000e-80 309.0
6 TraesCS2A01G222300 chr4A 95.178 1265 50 6 2826 4080 617356636 617355373 0.000000e+00 1988.0
7 TraesCS2A01G222300 chr6A 95.091 1263 50 4 2826 4078 158467962 158466702 0.000000e+00 1978.0
8 TraesCS2A01G222300 chr6A 94.159 1267 61 7 2826 4080 185246387 185247652 0.000000e+00 1917.0
9 TraesCS2A01G222300 chr2D 95.414 1243 32 10 958 2189 196860518 196859290 0.000000e+00 1956.0
10 TraesCS2A01G222300 chr2D 91.615 644 38 5 4077 4717 196858680 196858050 0.000000e+00 876.0
11 TraesCS2A01G222300 chr2D 91.446 643 26 13 5317 5958 196856052 196855438 0.000000e+00 856.0
12 TraesCS2A01G222300 chr2D 96.919 357 5 5 4703 5055 196856604 196856250 1.430000e-165 593.0
13 TraesCS2A01G222300 chr2D 97.059 272 8 0 2279 2550 196859057 196858786 5.440000e-125 459.0
14 TraesCS2A01G222300 chr2D 91.481 270 10 7 640 906 196860775 196860516 5.680000e-95 359.0
15 TraesCS2A01G222300 chr2D 94.512 164 9 0 5028 5191 196856250 196856087 2.760000e-63 254.0
16 TraesCS2A01G222300 chr3A 95.153 1238 48 8 2850 4077 11816442 11817677 0.000000e+00 1943.0
17 TraesCS2A01G222300 chr3A 94.220 1263 62 7 2826 4077 550712640 550711378 0.000000e+00 1917.0
18 TraesCS2A01G222300 chr3A 75.926 486 113 4 1394 1877 724484269 724484752 4.610000e-61 246.0
19 TraesCS2A01G222300 chr7A 94.851 1243 53 7 2826 4058 106984733 106983492 0.000000e+00 1930.0
20 TraesCS2A01G222300 chrUn 94.649 1252 53 8 2837 4076 64108274 64109523 0.000000e+00 1929.0
21 TraesCS2A01G222300 chrUn 93.551 1287 73 7 2803 4080 124698506 124699791 0.000000e+00 1908.0
22 TraesCS2A01G222300 chrUn 78.019 646 130 12 1394 2033 108369416 108368777 4.330000e-106 396.0
23 TraesCS2A01G222300 chr2B 94.378 1263 57 8 2826 4078 23320877 23319619 0.000000e+00 1927.0
24 TraesCS2A01G222300 chr2B 93.986 1297 33 16 941 2204 254288914 254287630 0.000000e+00 1921.0
25 TraesCS2A01G222300 chr2B 93.097 1101 51 14 4077 5162 254287153 254286063 0.000000e+00 1589.0
26 TraesCS2A01G222300 chr2B 86.384 874 71 25 70 911 254289770 254288913 0.000000e+00 911.0
27 TraesCS2A01G222300 chr2B 88.034 585 35 21 5383 5958 254282883 254282325 0.000000e+00 660.0
28 TraesCS2A01G222300 chr2B 95.238 315 15 0 2238 2552 254287553 254287239 3.210000e-137 499.0
29 TraesCS2A01G222300 chr2B 87.805 164 11 3 5167 5323 254284886 254284725 3.670000e-42 183.0
30 TraesCS2A01G222300 chr5A 94.364 1242 57 10 2850 4080 105432023 105430784 0.000000e+00 1893.0
31 TraesCS2A01G222300 chr5A 94.283 1242 59 4 2850 4080 708587637 708586397 0.000000e+00 1890.0
32 TraesCS2A01G222300 chr5A 94.265 1238 59 6 2850 4077 107456041 107454806 0.000000e+00 1882.0
33 TraesCS2A01G222300 chr5A 77.898 647 129 13 1394 2033 705822896 705823535 2.010000e-104 390.0
34 TraesCS2A01G222300 chr4B 94.270 1239 60 6 2850 4078 662026093 662024856 0.000000e+00 1884.0
35 TraesCS2A01G222300 chr4B 78.638 646 126 12 1394 2033 665855317 665855956 9.240000e-113 418.0
36 TraesCS2A01G222300 chr3D 76.420 581 125 9 1393 1967 593216061 593216635 2.700000e-78 303.0
37 TraesCS2A01G222300 chr3D 94.118 68 4 0 4154 4221 152542541 152542608 2.940000e-18 104.0
38 TraesCS2A01G222300 chr3B 82.201 309 53 2 1394 1701 731484977 731485284 1.270000e-66 265.0
39 TraesCS2A01G222300 chr7B 100.000 28 0 0 910 937 665505603 665505576 1.100000e-02 52.8
40 TraesCS2A01G222300 chr5B 100.000 28 0 0 911 938 610021531 610021504 1.100000e-02 52.8


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 TraesCS2A01G222300 chr2A 213109267 213115224 5957 True 5286.500000 5860 100.000000 1 5958 2 chr2A.!!$R1 5957
1 TraesCS2A01G222300 chr2A 775054309 775054813 504 False 747.000000 747 93.663000 2850 3344 1 chr2A.!!$F1 494
2 TraesCS2A01G222300 chr1A 534237237 534238496 1259 True 2013.000000 2013 95.635000 2826 4075 1 chr1A.!!$R1 1249
3 TraesCS2A01G222300 chr1A 369277610 369278895 1285 False 1917.000000 1917 93.721000 2802 4078 1 chr1A.!!$F2 1276
4 TraesCS2A01G222300 chr4A 617355373 617356636 1263 True 1988.000000 1988 95.178000 2826 4080 1 chr4A.!!$R1 1254
5 TraesCS2A01G222300 chr6A 158466702 158467962 1260 True 1978.000000 1978 95.091000 2826 4078 1 chr6A.!!$R1 1252
6 TraesCS2A01G222300 chr6A 185246387 185247652 1265 False 1917.000000 1917 94.159000 2826 4080 1 chr6A.!!$F1 1254
7 TraesCS2A01G222300 chr2D 196855438 196860775 5337 True 764.714286 1956 94.063714 640 5958 7 chr2D.!!$R1 5318
8 TraesCS2A01G222300 chr3A 11816442 11817677 1235 False 1943.000000 1943 95.153000 2850 4077 1 chr3A.!!$F1 1227
9 TraesCS2A01G222300 chr3A 550711378 550712640 1262 True 1917.000000 1917 94.220000 2826 4077 1 chr3A.!!$R1 1251
10 TraesCS2A01G222300 chr7A 106983492 106984733 1241 True 1930.000000 1930 94.851000 2826 4058 1 chr7A.!!$R1 1232
11 TraesCS2A01G222300 chrUn 64108274 64109523 1249 False 1929.000000 1929 94.649000 2837 4076 1 chrUn.!!$F1 1239
12 TraesCS2A01G222300 chrUn 124698506 124699791 1285 False 1908.000000 1908 93.551000 2803 4080 1 chrUn.!!$F2 1277
13 TraesCS2A01G222300 chrUn 108368777 108369416 639 True 396.000000 396 78.019000 1394 2033 1 chrUn.!!$R1 639
14 TraesCS2A01G222300 chr2B 23319619 23320877 1258 True 1927.000000 1927 94.378000 2826 4078 1 chr2B.!!$R1 1252
15 TraesCS2A01G222300 chr2B 254282325 254289770 7445 True 960.500000 1921 90.757333 70 5958 6 chr2B.!!$R2 5888
16 TraesCS2A01G222300 chr5A 105430784 105432023 1239 True 1893.000000 1893 94.364000 2850 4080 1 chr5A.!!$R1 1230
17 TraesCS2A01G222300 chr5A 708586397 708587637 1240 True 1890.000000 1890 94.283000 2850 4080 1 chr5A.!!$R3 1230
18 TraesCS2A01G222300 chr5A 107454806 107456041 1235 True 1882.000000 1882 94.265000 2850 4077 1 chr5A.!!$R2 1227
19 TraesCS2A01G222300 chr5A 705822896 705823535 639 False 390.000000 390 77.898000 1394 2033 1 chr5A.!!$F1 639
20 TraesCS2A01G222300 chr4B 662024856 662026093 1237 True 1884.000000 1884 94.270000 2850 4078 1 chr4B.!!$R1 1228
21 TraesCS2A01G222300 chr4B 665855317 665855956 639 False 418.000000 418 78.638000 1394 2033 1 chr4B.!!$F1 639
22 TraesCS2A01G222300 chr3D 593216061 593216635 574 False 303.000000 303 76.420000 1393 1967 1 chr3D.!!$F2 574

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
932 961 0.036765 AAATTGCTAGGCGTGGACGA 60.037 50.000 2.73 0.00 43.02 4.20 F
956 985 0.452784 GCGGCTGCTTCAGTAAAACG 60.453 55.000 11.21 0.00 38.39 3.60 F
959 988 0.591170 GCTGCTTCAGTAAAACGCCA 59.409 50.000 0.00 0.00 33.43 5.69 F
1281 1311 0.682209 ACGGCCTCATGGTACGTAGT 60.682 55.000 0.00 0.00 43.34 2.73 F
1282 1312 1.311859 CGGCCTCATGGTACGTAGTA 58.688 55.000 0.00 0.00 45.11 1.82 F
3239 3518 2.060980 GGACCGGTGAGGAGATGCT 61.061 63.158 14.63 0.00 45.00 3.79 F
3425 3705 1.170442 TCGTCGTTGCAGGTCTCATA 58.830 50.000 0.00 0.00 0.00 2.15 F
4270 4590 1.066303 CTCTCAAGCTAGTACCGCTGG 59.934 57.143 7.91 5.55 37.87 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2336 2.239400 TCCCGACGATTATGCTGATCT 58.761 47.619 0.00 0.0 0.00 2.75 R
2219 2338 2.289072 CCTTCCCGACGATTATGCTGAT 60.289 50.000 0.00 0.0 0.00 2.90 R
2956 3233 2.142761 CCTCAGATGGGATCCGCCA 61.143 63.158 5.45 0.0 38.95 5.69 R
3239 3518 1.621992 GATACTCCGGCAGAGATCCA 58.378 55.000 4.40 0.0 46.50 3.41 R
3257 3536 4.463597 GACGTATGTTGCCGTCGA 57.536 55.556 0.00 0.0 43.22 4.20 R
4100 4419 0.405585 ACACCTTCATTGGGTCAGGG 59.594 55.000 0.00 0.0 34.44 4.45 R
4482 4813 0.621082 GGCTTGCTCCTACCTCCTTT 59.379 55.000 0.00 0.0 0.00 3.11 R
5512 10318 0.106819 CCTTGGATCCTTCCTGGCTG 60.107 60.000 14.23 0.0 43.07 4.85 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 8.702163 AAGAAAATCACAAATCTGAAAACGTT 57.298 26.923 0.00 0.00 0.00 3.99
26 27 8.118893 AGAAAATCACAAATCTGAAAACGTTG 57.881 30.769 0.00 0.00 0.00 4.10
27 28 7.973388 AGAAAATCACAAATCTGAAAACGTTGA 59.027 29.630 0.00 0.00 0.00 3.18
28 29 8.472683 AAAATCACAAATCTGAAAACGTTGAA 57.527 26.923 0.00 0.00 0.00 2.69
29 30 8.647143 AAATCACAAATCTGAAAACGTTGAAT 57.353 26.923 0.00 0.00 0.00 2.57
30 31 9.743057 AAATCACAAATCTGAAAACGTTGAATA 57.257 25.926 0.00 0.00 0.00 1.75
31 32 9.912634 AATCACAAATCTGAAAACGTTGAATAT 57.087 25.926 0.00 0.00 0.00 1.28
73 74 7.485418 TGTGCATATATTTTACAACTACCCG 57.515 36.000 0.00 0.00 0.00 5.28
75 76 7.011576 TGTGCATATATTTTACAACTACCCGTG 59.988 37.037 0.00 0.00 0.00 4.94
81 82 5.692613 TTTTACAACTACCCGTGGATTTG 57.307 39.130 0.00 0.00 0.00 2.32
87 88 4.841443 ACTACCCGTGGATTTGAAAAAC 57.159 40.909 0.00 0.00 0.00 2.43
91 92 4.627058 ACCCGTGGATTTGAAAAACATTC 58.373 39.130 0.00 0.00 0.00 2.67
122 123 9.898152 TTTTTGAAATTCCATGTTACCTTTTCT 57.102 25.926 0.00 0.00 0.00 2.52
185 186 5.398603 TCACTTCTCCTCAAGATCAACTC 57.601 43.478 0.00 0.00 32.82 3.01
191 192 1.554392 CTCAAGATCAACTCGCGGAG 58.446 55.000 6.13 5.03 35.52 4.63
197 198 5.416013 TCAAGATCAACTCGCGGAGATATAT 59.584 40.000 6.13 0.00 33.32 0.86
200 201 3.418047 TCAACTCGCGGAGATATATCCA 58.582 45.455 16.44 0.00 39.53 3.41
201 202 3.440522 TCAACTCGCGGAGATATATCCAG 59.559 47.826 16.44 8.65 39.53 3.86
204 206 3.275143 CTCGCGGAGATATATCCAGACT 58.725 50.000 16.44 0.00 39.53 3.24
216 218 1.776662 TCCAGACTAGCTATGCCGTT 58.223 50.000 0.00 0.00 0.00 4.44
217 219 1.681793 TCCAGACTAGCTATGCCGTTC 59.318 52.381 0.00 0.00 0.00 3.95
240 242 6.148948 TCTTTGTTCGTCTAAAATGCAATGG 58.851 36.000 0.00 0.00 0.00 3.16
260 263 1.450312 AGCATTGGCCGTAGTGCTC 60.450 57.895 15.55 0.00 43.97 4.26
277 280 3.067461 GTGCTCGAGATCTTGGAGTATGT 59.933 47.826 18.75 0.00 0.00 2.29
300 303 4.911390 AGAAAGATAGACTTGGGGTTGTG 58.089 43.478 0.00 0.00 38.98 3.33
310 313 0.251832 TGGGGTTGTGTGGTTTGTGT 60.252 50.000 0.00 0.00 0.00 3.72
312 315 1.470051 GGGTTGTGTGGTTTGTGTCT 58.530 50.000 0.00 0.00 0.00 3.41
327 330 2.304470 TGTGTCTATGTTAGCCTTGCCA 59.696 45.455 0.00 0.00 0.00 4.92
331 334 3.248602 GTCTATGTTAGCCTTGCCAATCG 59.751 47.826 0.00 0.00 0.00 3.34
362 365 5.105392 TGAGAAATAATTGGCGCTGGATTTT 60.105 36.000 7.64 0.75 0.00 1.82
365 368 0.173255 AATTGGCGCTGGATTTTCCG 59.827 50.000 7.64 0.00 40.17 4.30
374 377 2.404186 GGATTTTCCGACCCACGCC 61.404 63.158 0.00 0.00 41.07 5.68
405 408 1.815003 GTTGGCTGAGAATGGAACTGG 59.185 52.381 0.00 0.00 0.00 4.00
410 413 2.617532 GCTGAGAATGGAACTGGAGCTT 60.618 50.000 0.00 0.00 0.00 3.74
411 414 3.269178 CTGAGAATGGAACTGGAGCTTC 58.731 50.000 0.00 0.00 0.00 3.86
413 416 1.065854 AGAATGGAACTGGAGCTTCCG 60.066 52.381 0.00 0.00 40.17 4.30
415 418 0.693049 ATGGAACTGGAGCTTCCGTT 59.307 50.000 0.75 0.75 40.17 4.44
416 419 0.250295 TGGAACTGGAGCTTCCGTTG 60.250 55.000 6.53 0.00 40.17 4.10
462 465 1.582610 CCCCATCCAAACGAACACCG 61.583 60.000 0.00 0.00 45.44 4.94
463 466 1.582610 CCCATCCAAACGAACACCGG 61.583 60.000 0.00 0.00 43.93 5.28
465 468 1.302993 ATCCAAACGAACACCGGGG 60.303 57.895 0.00 0.00 43.93 5.73
466 469 2.757980 ATCCAAACGAACACCGGGGG 62.758 60.000 9.50 0.00 43.93 5.40
467 470 3.666253 CAAACGAACACCGGGGGC 61.666 66.667 9.50 0.00 43.93 5.80
468 471 3.881104 AAACGAACACCGGGGGCT 61.881 61.111 9.50 0.00 43.93 5.19
469 472 4.636435 AACGAACACCGGGGGCTG 62.636 66.667 9.50 0.00 43.93 4.85
490 501 5.600696 CTGGGTAACATCCAATATTTTGGC 58.399 41.667 9.87 0.00 45.88 4.52
491 502 5.026121 TGGGTAACATCCAATATTTTGGCA 58.974 37.500 9.87 0.70 45.88 4.92
492 503 5.128499 TGGGTAACATCCAATATTTTGGCAG 59.872 40.000 9.87 7.32 45.88 4.85
493 504 5.453198 GGGTAACATCCAATATTTTGGCAGG 60.453 44.000 9.87 4.82 45.88 4.85
494 505 7.817900 GGGTAACATCCAATATTTTGGCAGGT 61.818 42.308 9.87 6.22 45.88 4.00
495 506 8.560647 GGGTAACATCCAATATTTTGGCAGGTA 61.561 40.741 9.87 5.35 45.88 3.08
506 520 0.913934 TGGCAGGTATCTCAGGGCAA 60.914 55.000 0.00 0.00 0.00 4.52
522 543 2.423538 GGGCAACGAATAGCAAGTTGAT 59.576 45.455 7.16 2.05 45.66 2.57
536 557 4.204573 GCAAGTTGATACGTACGTGAGATC 59.795 45.833 30.25 23.56 0.00 2.75
546 567 8.789825 ATACGTACGTGAGATCTATAGGATTT 57.210 34.615 30.25 0.00 34.33 2.17
579 600 6.458232 ACAAACTTGTAACAACCTTGCATA 57.542 33.333 0.00 0.00 40.16 3.14
583 604 7.753309 AACTTGTAACAACCTTGCATACATA 57.247 32.000 0.00 0.00 35.27 2.29
584 605 7.141100 ACTTGTAACAACCTTGCATACATAC 57.859 36.000 0.00 0.00 35.27 2.39
585 606 6.712998 ACTTGTAACAACCTTGCATACATACA 59.287 34.615 0.00 0.00 35.27 2.29
586 607 7.393234 ACTTGTAACAACCTTGCATACATACAT 59.607 33.333 0.00 0.00 35.27 2.29
587 608 7.082700 TGTAACAACCTTGCATACATACATG 57.917 36.000 0.00 0.00 32.38 3.21
588 609 6.657117 TGTAACAACCTTGCATACATACATGT 59.343 34.615 2.69 2.69 44.48 3.21
590 611 6.194796 ACAACCTTGCATACATACATGTTC 57.805 37.500 2.30 0.00 41.97 3.18
591 612 5.709631 ACAACCTTGCATACATACATGTTCA 59.290 36.000 2.30 0.00 41.97 3.18
594 615 6.798482 ACCTTGCATACATACATGTTCAATG 58.202 36.000 2.30 4.43 41.97 2.82
702 724 3.955771 TTAACGCGTGCTTCTTTTCTT 57.044 38.095 14.98 0.00 0.00 2.52
707 730 0.517316 CGTGCTTCTTTTCTTCCCCG 59.483 55.000 0.00 0.00 0.00 5.73
732 756 0.749818 TGCAGAACGCCAGGACAAAA 60.750 50.000 0.00 0.00 41.33 2.44
748 772 4.852650 GGACAAAAGAAACGACAAAACGAA 59.147 37.500 0.00 0.00 37.03 3.85
759 783 4.151689 ACGACAAAACGAATCATACACCAG 59.848 41.667 0.00 0.00 37.03 4.00
760 784 4.151689 CGACAAAACGAATCATACACCAGT 59.848 41.667 0.00 0.00 35.09 4.00
761 785 5.346551 CGACAAAACGAATCATACACCAGTA 59.653 40.000 0.00 0.00 35.09 2.74
762 786 6.476243 ACAAAACGAATCATACACCAGTAC 57.524 37.500 0.00 0.00 31.96 2.73
763 787 6.228258 ACAAAACGAATCATACACCAGTACT 58.772 36.000 0.00 0.00 31.96 2.73
772 796 5.786311 TCATACACCAGTACTGTACAAACC 58.214 41.667 21.18 0.00 31.96 3.27
800 824 2.852495 TTCCTGGTTCCGATCGCAGC 62.852 60.000 10.32 8.65 0.00 5.25
801 825 3.257561 CTGGTTCCGATCGCAGCG 61.258 66.667 9.06 9.06 0.00 5.18
802 826 3.699955 CTGGTTCCGATCGCAGCGA 62.700 63.158 22.06 22.06 41.13 4.93
803 827 2.956964 GGTTCCGATCGCAGCGAG 60.957 66.667 24.08 10.42 39.91 5.03
846 870 2.622436 CCATCTCGTCCTCACCTTTTC 58.378 52.381 0.00 0.00 0.00 2.29
851 875 3.067833 CTCGTCCTCACCTTTTCCTTTC 58.932 50.000 0.00 0.00 0.00 2.62
852 876 2.436542 TCGTCCTCACCTTTTCCTTTCA 59.563 45.455 0.00 0.00 0.00 2.69
853 877 3.072476 TCGTCCTCACCTTTTCCTTTCAT 59.928 43.478 0.00 0.00 0.00 2.57
854 878 3.437049 CGTCCTCACCTTTTCCTTTCATC 59.563 47.826 0.00 0.00 0.00 2.92
908 937 0.602638 TAGTGAAGCGCCAACCACAG 60.603 55.000 2.29 0.00 32.35 3.66
909 938 2.594303 TGAAGCGCCAACCACAGG 60.594 61.111 2.29 0.00 0.00 4.00
915 944 2.909965 GCCAACCACAGGCGGAAA 60.910 61.111 0.00 0.00 43.15 3.13
916 945 2.275380 GCCAACCACAGGCGGAAAT 61.275 57.895 0.00 0.00 43.15 2.17
917 946 1.815817 GCCAACCACAGGCGGAAATT 61.816 55.000 0.00 0.00 43.15 1.82
918 947 0.038343 CCAACCACAGGCGGAAATTG 60.038 55.000 0.00 0.00 0.00 2.32
919 948 0.667184 CAACCACAGGCGGAAATTGC 60.667 55.000 0.00 0.00 0.00 3.56
920 949 0.827507 AACCACAGGCGGAAATTGCT 60.828 50.000 0.00 0.00 0.00 3.91
921 950 0.037590 ACCACAGGCGGAAATTGCTA 59.962 50.000 0.00 0.00 0.00 3.49
922 951 0.734889 CCACAGGCGGAAATTGCTAG 59.265 55.000 0.00 0.00 0.00 3.42
923 952 0.734889 CACAGGCGGAAATTGCTAGG 59.265 55.000 0.00 0.00 0.00 3.02
924 953 1.032114 ACAGGCGGAAATTGCTAGGC 61.032 55.000 0.00 0.00 0.00 3.93
925 954 1.819632 AGGCGGAAATTGCTAGGCG 60.820 57.895 0.00 0.00 0.00 5.52
926 955 2.112815 GGCGGAAATTGCTAGGCGT 61.113 57.895 0.00 0.00 0.00 5.68
927 956 1.062525 GCGGAAATTGCTAGGCGTG 59.937 57.895 0.00 0.00 0.00 5.34
928 957 1.721487 CGGAAATTGCTAGGCGTGG 59.279 57.895 0.00 0.00 0.00 4.94
929 958 0.742990 CGGAAATTGCTAGGCGTGGA 60.743 55.000 0.00 0.00 0.00 4.02
930 959 0.733150 GGAAATTGCTAGGCGTGGAC 59.267 55.000 0.00 0.00 0.00 4.02
931 960 0.373716 GAAATTGCTAGGCGTGGACG 59.626 55.000 0.00 0.00 43.27 4.79
932 961 0.036765 AAATTGCTAGGCGTGGACGA 60.037 50.000 2.73 0.00 43.02 4.20
933 962 0.460284 AATTGCTAGGCGTGGACGAG 60.460 55.000 2.73 0.00 43.02 4.18
934 963 2.907897 ATTGCTAGGCGTGGACGAGC 62.908 60.000 2.73 3.97 43.02 5.03
935 964 3.827898 GCTAGGCGTGGACGAGCT 61.828 66.667 2.73 0.00 43.02 4.09
936 965 2.409651 CTAGGCGTGGACGAGCTC 59.590 66.667 2.73 2.73 43.02 4.09
937 966 3.456431 CTAGGCGTGGACGAGCTCG 62.456 68.421 33.45 33.45 43.02 5.03
956 985 0.452784 GCGGCTGCTTCAGTAAAACG 60.453 55.000 11.21 0.00 38.39 3.60
959 988 0.591170 GCTGCTTCAGTAAAACGCCA 59.409 50.000 0.00 0.00 33.43 5.69
960 989 1.663161 GCTGCTTCAGTAAAACGCCAC 60.663 52.381 0.00 0.00 33.43 5.01
995 1025 1.484444 CCCCCTGGATCGAGGAATCC 61.484 65.000 24.24 0.00 44.73 3.01
1020 1050 2.589540 GGTCCGGGTGATCATGCA 59.410 61.111 0.00 0.00 0.00 3.96
1023 1053 2.203252 CCGGGTGATCATGCAGGG 60.203 66.667 0.00 0.00 0.00 4.45
1280 1310 1.311859 TACGGCCTCATGGTACGTAG 58.688 55.000 0.00 0.00 43.34 3.51
1281 1311 0.682209 ACGGCCTCATGGTACGTAGT 60.682 55.000 0.00 0.00 43.34 2.73
1282 1312 1.311859 CGGCCTCATGGTACGTAGTA 58.688 55.000 0.00 0.00 45.11 1.82
1309 1339 2.291411 ACTCCACTCCACCGTATGTACT 60.291 50.000 0.00 0.00 0.00 2.73
1310 1340 2.758979 CTCCACTCCACCGTATGTACTT 59.241 50.000 0.00 0.00 0.00 2.24
1311 1341 3.949754 CTCCACTCCACCGTATGTACTTA 59.050 47.826 0.00 0.00 0.00 2.24
1312 1342 3.696051 TCCACTCCACCGTATGTACTTAC 59.304 47.826 8.51 8.51 0.00 2.34
1385 1415 4.450122 CGTGCACGACTGCCATGC 62.450 66.667 34.93 0.00 43.51 4.06
2018 2059 2.349590 CCACAGATCGCACTTGATTCA 58.650 47.619 0.00 0.00 0.00 2.57
2069 2124 2.187707 CGAACCGTTTTATCCGTCGAT 58.812 47.619 0.00 0.00 0.00 3.59
2073 2128 4.637483 ACCGTTTTATCCGTCGATTCTA 57.363 40.909 0.00 0.00 0.00 2.10
2074 2129 4.604976 ACCGTTTTATCCGTCGATTCTAG 58.395 43.478 0.00 0.00 0.00 2.43
2082 2144 3.571571 TCCGTCGATTCTAGTGTGTTTG 58.428 45.455 0.00 0.00 0.00 2.93
2090 2152 5.812127 CGATTCTAGTGTGTTTGGATGATCA 59.188 40.000 0.00 0.00 0.00 2.92
2098 2160 3.009026 TGTTTGGATGATCATGTGACCG 58.991 45.455 14.30 0.00 0.00 4.79
2163 2225 4.243008 TCCGTGGGCTTCAACGCA 62.243 61.111 0.00 0.00 0.00 5.24
2198 2260 5.095490 GGTGCATTGCATACAACTAAACTC 58.905 41.667 15.49 0.00 41.91 3.01
2204 2323 7.361713 GCATTGCATACAACTAAACTCTGGTTA 60.362 37.037 3.15 0.00 38.99 2.85
2205 2324 8.677300 CATTGCATACAACTAAACTCTGGTTAT 58.323 33.333 0.00 0.00 38.99 1.89
2206 2325 9.899661 ATTGCATACAACTAAACTCTGGTTATA 57.100 29.630 0.00 0.00 38.99 0.98
2207 2326 8.712285 TGCATACAACTAAACTCTGGTTATAC 57.288 34.615 0.00 0.00 34.90 1.47
2208 2327 8.315482 TGCATACAACTAAACTCTGGTTATACA 58.685 33.333 0.00 0.00 34.90 2.29
2209 2328 8.818057 GCATACAACTAAACTCTGGTTATACAG 58.182 37.037 0.00 0.00 39.84 2.74
2210 2329 9.871238 CATACAACTAAACTCTGGTTATACAGT 57.129 33.333 0.00 0.00 39.48 3.55
2213 2332 8.863086 ACAACTAAACTCTGGTTATACAGTACA 58.137 33.333 0.00 0.00 39.48 2.90
2214 2333 9.701098 CAACTAAACTCTGGTTATACAGTACAA 57.299 33.333 0.00 0.00 39.48 2.41
2215 2334 9.702494 AACTAAACTCTGGTTATACAGTACAAC 57.298 33.333 0.00 0.00 39.48 3.32
2216 2335 9.086758 ACTAAACTCTGGTTATACAGTACAACT 57.913 33.333 1.78 0.00 39.48 3.16
2219 2338 8.874744 AACTCTGGTTATACAGTACAACTAGA 57.125 34.615 14.97 14.97 37.42 2.43
2231 2350 7.142021 ACAGTACAACTAGATCAGCATAATCG 58.858 38.462 0.00 0.00 0.00 3.34
2234 2353 5.215903 ACAACTAGATCAGCATAATCGTCG 58.784 41.667 0.00 0.00 0.00 5.12
2235 2354 4.427096 ACTAGATCAGCATAATCGTCGG 57.573 45.455 0.00 0.00 0.00 4.79
2401 2667 3.026879 CCGCGCTCATAGCAGTCG 61.027 66.667 5.56 0.00 42.58 4.18
2535 2801 2.906458 CTCTGCGGAATCCAGCCT 59.094 61.111 12.15 0.00 0.00 4.58
2803 3069 3.462678 GACCCTCTCGCACCCCTC 61.463 72.222 0.00 0.00 0.00 4.30
3185 3464 2.666207 CCCCGTTTGGATCCGTCA 59.334 61.111 7.39 0.00 37.49 4.35
3239 3518 2.060980 GGACCGGTGAGGAGATGCT 61.061 63.158 14.63 0.00 45.00 3.79
3257 3536 1.626686 CTGGATCTCTGCCGGAGTAT 58.373 55.000 5.05 0.00 42.40 2.12
3399 3679 3.188048 GTCTCAGACGTCGTTTCCTTCTA 59.812 47.826 10.46 0.00 0.00 2.10
3425 3705 1.170442 TCGTCGTTGCAGGTCTCATA 58.830 50.000 0.00 0.00 0.00 2.15
3725 4006 1.214589 CCAAGGTTGATGCAGCAGC 59.785 57.895 10.63 10.63 42.57 5.25
3938 4219 6.287589 CCTACATCAACTGGATAGGGATAC 57.712 45.833 0.00 0.00 33.95 2.24
4100 4419 3.809905 AGTCTTGACCAGTGTCCTTTTC 58.190 45.455 0.00 0.00 41.01 2.29
4101 4420 2.879026 GTCTTGACCAGTGTCCTTTTCC 59.121 50.000 0.00 0.00 41.01 3.13
4197 4517 1.259142 TTCATCGGCGTACCCCTTGA 61.259 55.000 6.85 0.00 0.00 3.02
4239 4559 6.106673 AGTTTGACTATGGAATCAAGGTACG 58.893 40.000 0.00 0.00 36.26 3.67
4240 4560 5.670792 TTGACTATGGAATCAAGGTACGT 57.329 39.130 0.00 0.00 31.29 3.57
4241 4561 6.778834 TTGACTATGGAATCAAGGTACGTA 57.221 37.500 0.00 0.00 31.29 3.57
4242 4562 6.140303 TGACTATGGAATCAAGGTACGTAC 57.860 41.667 17.56 17.56 0.00 3.67
4243 4563 5.889853 TGACTATGGAATCAAGGTACGTACT 59.110 40.000 24.07 8.57 0.00 2.73
4244 4564 6.145338 ACTATGGAATCAAGGTACGTACTG 57.855 41.667 24.07 15.85 0.00 2.74
4245 4565 5.655532 ACTATGGAATCAAGGTACGTACTGT 59.344 40.000 24.07 10.16 0.00 3.55
4246 4566 4.877378 TGGAATCAAGGTACGTACTGTT 57.123 40.909 24.07 15.23 0.00 3.16
4264 4584 7.481169 CGTACTGTTTTACTCTCAAGCTAGTAC 59.519 40.741 0.00 0.00 35.61 2.73
4270 4590 1.066303 CTCTCAAGCTAGTACCGCTGG 59.934 57.143 7.91 5.55 37.87 4.85
4317 4642 3.018856 TGGCAGAATCACCATTCATGTC 58.981 45.455 0.00 0.00 41.03 3.06
4358 4683 7.421530 TGTCAACTGTCAGTAAATTAGCTTC 57.578 36.000 5.77 0.00 0.00 3.86
4398 4723 4.101430 TGCACTGATGATAGAGGTTGCATA 59.899 41.667 0.00 0.00 0.00 3.14
4404 4735 2.705658 TGATAGAGGTTGCATACAGGGG 59.294 50.000 0.00 0.00 0.00 4.79
4476 4807 5.169992 TGTGGATCACATTCAGAACTGAT 57.830 39.130 5.34 5.23 39.62 2.90
4480 4811 4.337555 GGATCACATTCAGAACTGATTGGG 59.662 45.833 22.06 19.88 42.54 4.12
4482 4813 4.984295 TCACATTCAGAACTGATTGGGAA 58.016 39.130 21.42 10.73 45.06 3.97
4499 4833 2.356227 GGGAAAAGGAGGTAGGAGCAAG 60.356 54.545 0.00 0.00 0.00 4.01
4507 4841 2.969262 GAGGTAGGAGCAAGCCTTATCT 59.031 50.000 0.00 0.00 39.50 1.98
4510 4844 3.389656 GGTAGGAGCAAGCCTTATCTCTT 59.610 47.826 0.00 2.22 39.50 2.85
4521 4855 8.716909 GCAAGCCTTATCTCTTATTGTTAGATC 58.283 37.037 0.00 0.00 32.39 2.75
4531 4865 7.644157 TCTCTTATTGTTAGATCATCACGTTCG 59.356 37.037 0.00 0.00 0.00 3.95
4562 4896 0.670546 CCAGGCCGTTACACTGTCAG 60.671 60.000 0.00 0.00 0.00 3.51
4644 4978 0.994263 GCAATCATTTCGCCAAGTGC 59.006 50.000 0.00 0.00 0.00 4.40
4778 6574 8.093307 GCATCCTTCTATGATCATCACTTCTTA 58.907 37.037 12.53 0.00 0.00 2.10
4831 6627 2.552743 GGTTAGGCTGTTTCAGTTGTCC 59.447 50.000 0.00 0.00 33.43 4.02
4874 6670 9.730420 ATAAAGTATATTGCGAATTTTGTGTCC 57.270 29.630 0.00 0.00 0.00 4.02
4933 6729 4.430423 GACGACGCAAAGCAGCCG 62.430 66.667 0.00 0.00 0.00 5.52
4964 6760 4.159901 TGCAGCGATGATGCCCGA 62.160 61.111 4.02 0.00 44.94 5.14
5070 6895 3.426695 GGAAATGTTGAGCATCGTCCTTG 60.427 47.826 5.17 0.00 38.07 3.61
5073 6898 0.716108 GTTGAGCATCGTCCTTGTCG 59.284 55.000 0.00 0.00 38.61 4.35
5162 6987 4.125703 CACATGCTATTCTGAACTCTCCC 58.874 47.826 0.00 0.00 0.00 4.30
5164 6989 2.832838 TGCTATTCTGAACTCTCCCCA 58.167 47.619 0.00 0.00 0.00 4.96
5225 8222 8.176814 TGTTGTTTTACTAGAAATATCGACCG 57.823 34.615 0.00 0.00 0.00 4.79
5236 8233 7.242914 AGAAATATCGACCGATGGTTTTTAC 57.757 36.000 14.42 5.23 35.25 2.01
5276 8280 9.816354 AAACAGTTAAGCACAAAGACAATAAAT 57.184 25.926 0.00 0.00 0.00 1.40
5277 8281 9.463443 AACAGTTAAGCACAAAGACAATAAATC 57.537 29.630 0.00 0.00 0.00 2.17
5281 8285 3.505680 AGCACAAAGACAATAAATCCGCA 59.494 39.130 0.00 0.00 0.00 5.69
5282 8286 4.022416 AGCACAAAGACAATAAATCCGCAA 60.022 37.500 0.00 0.00 0.00 4.85
5323 8327 1.122227 AAATGTGCAACTGGCCTTGT 58.878 45.000 3.32 0.00 43.89 3.16
5324 8328 1.122227 AATGTGCAACTGGCCTTGTT 58.878 45.000 3.32 6.59 43.89 2.83
5325 8329 1.122227 ATGTGCAACTGGCCTTGTTT 58.878 45.000 3.32 0.00 43.89 2.83
5326 8330 0.175302 TGTGCAACTGGCCTTGTTTG 59.825 50.000 3.32 3.01 43.89 2.93
5327 8331 0.175531 GTGCAACTGGCCTTGTTTGT 59.824 50.000 3.32 0.00 43.89 2.83
5328 8332 1.407258 GTGCAACTGGCCTTGTTTGTA 59.593 47.619 3.32 0.00 43.89 2.41
5512 10318 2.785258 GTCCGTTGATCCTTGCGC 59.215 61.111 0.00 0.00 0.00 6.09
5580 10388 2.620115 AGGCATTATTCAGCATCCAACG 59.380 45.455 0.00 0.00 0.00 4.10
5613 10421 4.533919 TTTCGGACCTAATCAAACGGTA 57.466 40.909 0.00 0.00 0.00 4.02
5614 10422 4.533919 TTCGGACCTAATCAAACGGTAA 57.466 40.909 0.00 0.00 0.00 2.85
5681 10490 1.893808 AGGCTGCCACGTTGAACTG 60.894 57.895 22.65 0.00 0.00 3.16
5687 10496 2.671396 CTGCCACGTTGAACTGGTATAC 59.329 50.000 12.93 0.00 0.00 1.47
5688 10497 2.004733 GCCACGTTGAACTGGTATACC 58.995 52.381 15.50 15.50 0.00 2.73
5689 10498 2.624636 CCACGTTGAACTGGTATACCC 58.375 52.381 19.42 4.24 34.29 3.69
5720 10529 5.638657 CAGAAATCACTGACTTTCCTCTCTG 59.361 44.000 0.00 0.00 39.94 3.35
5721 10530 4.550076 AATCACTGACTTTCCTCTCTGG 57.450 45.455 0.00 0.00 37.10 3.86
5739 10549 8.619546 CCTCTCTGGAAAAATAATCATGAACTC 58.380 37.037 0.00 0.00 38.35 3.01
5753 10563 6.806120 TCATGAACTCGATTACATGTTACG 57.194 37.500 2.30 8.12 40.32 3.18
5767 10579 2.883574 TGTTACGTATTTCCCTGCGAG 58.116 47.619 0.00 0.00 0.00 5.03
5916 10732 2.017559 CTCCGCCGGTTCTTCCTAGG 62.018 65.000 1.63 0.82 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.594687 CAACGTTTTCAGATTTGTGATTTTCTT 58.405 29.630 0.00 0.00 0.00 2.52
1 2 7.973388 TCAACGTTTTCAGATTTGTGATTTTCT 59.027 29.630 0.00 0.00 0.00 2.52
3 4 8.472683 TTCAACGTTTTCAGATTTGTGATTTT 57.527 26.923 0.00 0.00 0.00 1.82
5 6 9.912634 ATATTCAACGTTTTCAGATTTGTGATT 57.087 25.926 0.00 0.00 0.00 2.57
47 48 8.564574 CGGGTAGTTGTAAAATATATGCACATT 58.435 33.333 0.00 0.00 0.00 2.71
48 49 7.717875 ACGGGTAGTTGTAAAATATATGCACAT 59.282 33.333 0.00 0.00 0.00 3.21
49 50 7.011576 CACGGGTAGTTGTAAAATATATGCACA 59.988 37.037 0.00 0.00 0.00 4.57
50 51 7.349711 CACGGGTAGTTGTAAAATATATGCAC 58.650 38.462 0.00 0.00 0.00 4.57
51 52 6.483974 CCACGGGTAGTTGTAAAATATATGCA 59.516 38.462 0.00 0.00 0.00 3.96
52 53 6.707161 TCCACGGGTAGTTGTAAAATATATGC 59.293 38.462 0.00 0.00 0.00 3.14
53 54 8.842358 ATCCACGGGTAGTTGTAAAATATATG 57.158 34.615 0.00 0.00 0.00 1.78
54 55 9.856162 AAATCCACGGGTAGTTGTAAAATATAT 57.144 29.630 0.00 0.00 0.00 0.86
55 56 9.111613 CAAATCCACGGGTAGTTGTAAAATATA 57.888 33.333 0.00 0.00 0.00 0.86
56 57 7.830201 TCAAATCCACGGGTAGTTGTAAAATAT 59.170 33.333 0.00 0.00 0.00 1.28
57 58 7.166851 TCAAATCCACGGGTAGTTGTAAAATA 58.833 34.615 0.00 0.00 0.00 1.40
58 59 6.005198 TCAAATCCACGGGTAGTTGTAAAAT 58.995 36.000 0.00 0.00 0.00 1.82
59 60 5.374921 TCAAATCCACGGGTAGTTGTAAAA 58.625 37.500 0.00 0.00 0.00 1.52
60 61 4.970711 TCAAATCCACGGGTAGTTGTAAA 58.029 39.130 0.00 0.00 0.00 2.01
61 62 4.620589 TCAAATCCACGGGTAGTTGTAA 57.379 40.909 0.00 0.00 0.00 2.41
62 63 4.620589 TTCAAATCCACGGGTAGTTGTA 57.379 40.909 0.00 0.00 0.00 2.41
63 64 3.495434 TTCAAATCCACGGGTAGTTGT 57.505 42.857 0.00 0.00 0.00 3.32
64 65 4.839668 TTTTCAAATCCACGGGTAGTTG 57.160 40.909 0.00 0.00 0.00 3.16
65 66 4.645588 TGTTTTTCAAATCCACGGGTAGTT 59.354 37.500 0.00 0.00 0.00 2.24
66 67 4.208746 TGTTTTTCAAATCCACGGGTAGT 58.791 39.130 0.00 0.00 0.00 2.73
67 68 4.839668 TGTTTTTCAAATCCACGGGTAG 57.160 40.909 0.00 0.00 0.00 3.18
68 69 5.302059 TGAATGTTTTTCAAATCCACGGGTA 59.698 36.000 0.00 0.00 0.00 3.69
73 74 9.786105 AAAATTGTGAATGTTTTTCAAATCCAC 57.214 25.926 0.00 0.00 0.00 4.02
87 88 9.953697 AACATGGAATTTCAAAAATTGTGAATG 57.046 25.926 0.00 0.00 35.03 2.67
91 92 9.054922 AGGTAACATGGAATTTCAAAAATTGTG 57.945 29.630 0.00 2.64 41.41 3.33
100 101 7.831691 TCAGAAAAGGTAACATGGAATTTCA 57.168 32.000 0.00 0.00 41.41 2.69
150 151 3.312697 GGAGAAGTGAACTGCGAGTTTTT 59.687 43.478 3.56 0.80 38.80 1.94
152 153 2.103263 AGGAGAAGTGAACTGCGAGTTT 59.897 45.455 3.56 0.00 38.80 2.66
185 186 3.002862 GCTAGTCTGGATATATCTCCGCG 59.997 52.174 12.42 0.00 38.21 6.46
191 192 5.533154 ACGGCATAGCTAGTCTGGATATATC 59.467 44.000 3.96 3.96 0.00 1.63
197 198 1.681793 GAACGGCATAGCTAGTCTGGA 59.318 52.381 0.00 0.00 0.00 3.86
200 201 3.195825 ACAAAGAACGGCATAGCTAGTCT 59.804 43.478 0.00 0.00 0.00 3.24
201 202 3.522553 ACAAAGAACGGCATAGCTAGTC 58.477 45.455 0.00 0.00 0.00 2.59
204 206 2.927477 CGAACAAAGAACGGCATAGCTA 59.073 45.455 0.00 0.00 0.00 3.32
216 218 6.148948 CCATTGCATTTTAGACGAACAAAGA 58.851 36.000 0.00 0.00 0.00 2.52
217 219 5.164061 GCCATTGCATTTTAGACGAACAAAG 60.164 40.000 0.00 0.00 37.47 2.77
242 244 2.671070 AGCACTACGGCCAATGCT 59.329 55.556 12.85 12.85 43.50 3.79
251 254 1.671328 TCCAAGATCTCGAGCACTACG 59.329 52.381 7.81 4.66 0.00 3.51
260 263 7.265647 TCTTTCTACATACTCCAAGATCTCG 57.734 40.000 0.00 0.00 0.00 4.04
277 280 5.546499 ACACAACCCCAAGTCTATCTTTCTA 59.454 40.000 0.00 0.00 33.63 2.10
300 303 4.324267 AGGCTAACATAGACACAAACCAC 58.676 43.478 0.00 0.00 35.81 4.16
310 313 3.118408 ACGATTGGCAAGGCTAACATAGA 60.118 43.478 5.96 0.00 30.71 1.98
312 315 2.942376 CACGATTGGCAAGGCTAACATA 59.058 45.455 5.96 0.00 30.71 2.29
327 330 5.163519 CCAATTATTTCTCAAGCCCACGATT 60.164 40.000 0.00 0.00 0.00 3.34
331 334 3.734902 CGCCAATTATTTCTCAAGCCCAC 60.735 47.826 0.00 0.00 0.00 4.61
340 343 5.343307 AAAATCCAGCGCCAATTATTTCT 57.657 34.783 2.29 0.00 0.00 2.52
341 344 4.507756 GGAAAATCCAGCGCCAATTATTTC 59.492 41.667 2.29 8.60 36.28 2.17
365 368 3.124686 TTTTTGCAGGCGTGGGTC 58.875 55.556 8.72 0.00 0.00 4.46
390 393 3.269178 GAAGCTCCAGTTCCATTCTCAG 58.731 50.000 0.00 0.00 0.00 3.35
393 396 1.065854 CGGAAGCTCCAGTTCCATTCT 60.066 52.381 2.43 0.00 43.35 2.40
398 401 0.034896 TCAACGGAAGCTCCAGTTCC 59.965 55.000 0.00 0.00 40.25 3.62
405 408 2.048127 ACGGCTCAACGGAAGCTC 60.048 61.111 6.02 0.00 38.39 4.09
444 447 1.582610 CCGGTGTTCGTTTGGATGGG 61.583 60.000 0.00 0.00 37.11 4.00
448 451 2.111460 CCCCGGTGTTCGTTTGGA 59.889 61.111 0.00 0.00 37.11 3.53
449 452 2.981350 CCCCCGGTGTTCGTTTGG 60.981 66.667 0.00 0.00 37.11 3.28
462 465 2.601299 GGATGTTACCCAGCCCCC 59.399 66.667 0.00 0.00 44.19 5.40
490 501 0.824109 TCGTTGCCCTGAGATACCTG 59.176 55.000 0.00 0.00 0.00 4.00
491 502 1.568504 TTCGTTGCCCTGAGATACCT 58.431 50.000 0.00 0.00 0.00 3.08
492 503 2.622064 ATTCGTTGCCCTGAGATACC 57.378 50.000 0.00 0.00 0.00 2.73
493 504 3.060602 GCTATTCGTTGCCCTGAGATAC 58.939 50.000 0.00 0.00 0.00 2.24
494 505 2.698274 TGCTATTCGTTGCCCTGAGATA 59.302 45.455 0.00 0.00 0.00 1.98
495 506 1.486310 TGCTATTCGTTGCCCTGAGAT 59.514 47.619 0.00 0.00 0.00 2.75
506 520 4.731961 CGTACGTATCAACTTGCTATTCGT 59.268 41.667 7.22 0.00 0.00 3.85
522 543 9.710900 TTAAATCCTATAGATCTCACGTACGTA 57.289 33.333 22.34 6.15 32.47 3.57
546 567 7.921745 GGTTGTTACAAGTTTGTTAGGCAATTA 59.078 33.333 0.00 0.00 42.35 1.40
550 571 4.951094 AGGTTGTTACAAGTTTGTTAGGCA 59.049 37.500 0.00 0.00 42.35 4.75
568 589 6.193514 TGAACATGTATGTATGCAAGGTTG 57.806 37.500 0.00 0.00 40.80 3.77
579 600 8.862325 TTCTCCTTTACATTGAACATGTATGT 57.138 30.769 15.24 15.24 44.20 2.29
583 604 6.006449 AGCTTCTCCTTTACATTGAACATGT 58.994 36.000 0.00 0.00 36.13 3.21
584 605 6.320171 CAGCTTCTCCTTTACATTGAACATG 58.680 40.000 0.00 0.00 0.00 3.21
585 606 5.105997 GCAGCTTCTCCTTTACATTGAACAT 60.106 40.000 0.00 0.00 0.00 2.71
586 607 4.216257 GCAGCTTCTCCTTTACATTGAACA 59.784 41.667 0.00 0.00 0.00 3.18
587 608 4.379918 GGCAGCTTCTCCTTTACATTGAAC 60.380 45.833 0.00 0.00 0.00 3.18
588 609 3.758554 GGCAGCTTCTCCTTTACATTGAA 59.241 43.478 0.00 0.00 0.00 2.69
590 611 2.096496 CGGCAGCTTCTCCTTTACATTG 59.904 50.000 0.00 0.00 0.00 2.82
591 612 2.359900 CGGCAGCTTCTCCTTTACATT 58.640 47.619 0.00 0.00 0.00 2.71
594 615 0.036294 ACCGGCAGCTTCTCCTTTAC 60.036 55.000 0.00 0.00 0.00 2.01
732 756 6.360329 GTGTATGATTCGTTTTGTCGTTTCT 58.640 36.000 0.00 0.00 0.00 2.52
748 772 6.212791 AGGTTTGTACAGTACTGGTGTATGAT 59.787 38.462 26.12 5.75 33.08 2.45
759 783 4.234530 ACACGAGAGGTTTGTACAGTAC 57.765 45.455 3.49 3.49 0.00 2.73
760 784 4.924305 AACACGAGAGGTTTGTACAGTA 57.076 40.909 0.00 0.00 0.00 2.74
761 785 3.814005 AACACGAGAGGTTTGTACAGT 57.186 42.857 0.00 0.00 0.00 3.55
762 786 3.493503 GGAAACACGAGAGGTTTGTACAG 59.506 47.826 0.00 0.00 38.50 2.74
763 787 3.133362 AGGAAACACGAGAGGTTTGTACA 59.867 43.478 0.00 0.00 38.50 2.90
772 796 1.797025 GGAACCAGGAAACACGAGAG 58.203 55.000 0.00 0.00 0.00 3.20
800 824 2.033424 TGAAGTGACACTGTCTCACTCG 59.967 50.000 17.22 0.00 46.26 4.18
801 825 3.376540 GTGAAGTGACACTGTCTCACTC 58.623 50.000 23.00 11.87 46.26 3.51
803 827 2.101582 AGGTGAAGTGACACTGTCTCAC 59.898 50.000 22.51 22.51 40.22 3.51
846 870 3.255642 TCTTCCCGCAAAAAGATGAAAGG 59.744 43.478 0.00 0.00 0.00 3.11
851 875 4.418392 CAAGATCTTCCCGCAAAAAGATG 58.582 43.478 4.57 0.00 41.20 2.90
852 876 3.119352 GCAAGATCTTCCCGCAAAAAGAT 60.119 43.478 4.57 4.60 43.23 2.40
853 877 2.228822 GCAAGATCTTCCCGCAAAAAGA 59.771 45.455 4.57 0.00 36.05 2.52
854 878 2.599659 GCAAGATCTTCCCGCAAAAAG 58.400 47.619 4.57 0.00 0.00 2.27
908 937 2.112815 ACGCCTAGCAATTTCCGCC 61.113 57.895 0.00 0.00 0.00 6.13
909 938 1.062525 CACGCCTAGCAATTTCCGC 59.937 57.895 0.00 0.00 0.00 5.54
910 939 0.742990 TCCACGCCTAGCAATTTCCG 60.743 55.000 0.00 0.00 0.00 4.30
911 940 0.733150 GTCCACGCCTAGCAATTTCC 59.267 55.000 0.00 0.00 0.00 3.13
912 941 0.373716 CGTCCACGCCTAGCAATTTC 59.626 55.000 0.00 0.00 0.00 2.17
913 942 0.036765 TCGTCCACGCCTAGCAATTT 60.037 50.000 0.00 0.00 39.60 1.82
914 943 0.460284 CTCGTCCACGCCTAGCAATT 60.460 55.000 0.00 0.00 39.60 2.32
915 944 1.141881 CTCGTCCACGCCTAGCAAT 59.858 57.895 0.00 0.00 39.60 3.56
916 945 2.571757 CTCGTCCACGCCTAGCAA 59.428 61.111 0.00 0.00 39.60 3.91
917 946 4.129737 GCTCGTCCACGCCTAGCA 62.130 66.667 6.45 0.00 36.91 3.49
918 947 3.759766 GAGCTCGTCCACGCCTAGC 62.760 68.421 0.00 3.71 39.60 3.42
919 948 2.409651 GAGCTCGTCCACGCCTAG 59.590 66.667 0.00 0.00 39.60 3.02
920 949 3.506096 CGAGCTCGTCCACGCCTA 61.506 66.667 27.79 0.00 39.60 3.93
933 962 3.989698 TACTGAAGCAGCCGCGAGC 62.990 63.158 8.23 9.98 45.49 5.03
934 963 1.014044 TTTACTGAAGCAGCCGCGAG 61.014 55.000 8.23 0.00 45.49 5.03
935 964 0.601576 TTTTACTGAAGCAGCCGCGA 60.602 50.000 8.23 0.00 45.49 5.87
936 965 0.452784 GTTTTACTGAAGCAGCCGCG 60.453 55.000 0.00 0.00 45.49 6.46
937 966 0.452784 CGTTTTACTGAAGCAGCCGC 60.453 55.000 0.00 0.00 34.37 6.53
938 967 0.452784 GCGTTTTACTGAAGCAGCCG 60.453 55.000 0.00 0.00 34.37 5.52
939 968 0.109735 GGCGTTTTACTGAAGCAGCC 60.110 55.000 0.00 0.00 34.37 4.85
943 972 2.766970 TTGTGGCGTTTTACTGAAGC 57.233 45.000 0.00 0.00 0.00 3.86
995 1025 2.252072 ATCACCCGGACCCATTCACG 62.252 60.000 0.73 0.00 0.00 4.35
1140 1170 0.036164 TCAGCATGTACACCACCACC 59.964 55.000 0.00 0.00 37.40 4.61
1280 1310 0.896226 GTGGAGTGGAGTGGAGGTAC 59.104 60.000 0.00 0.00 0.00 3.34
1281 1311 0.252103 GGTGGAGTGGAGTGGAGGTA 60.252 60.000 0.00 0.00 0.00 3.08
1282 1312 1.536662 GGTGGAGTGGAGTGGAGGT 60.537 63.158 0.00 0.00 0.00 3.85
1283 1313 2.650116 CGGTGGAGTGGAGTGGAGG 61.650 68.421 0.00 0.00 0.00 4.30
1284 1314 0.611062 TACGGTGGAGTGGAGTGGAG 60.611 60.000 0.00 0.00 0.00 3.86
1285 1315 0.040646 ATACGGTGGAGTGGAGTGGA 59.959 55.000 0.00 0.00 0.00 4.02
1286 1316 0.175760 CATACGGTGGAGTGGAGTGG 59.824 60.000 0.00 0.00 0.00 4.00
1287 1317 0.895530 ACATACGGTGGAGTGGAGTG 59.104 55.000 0.00 0.00 0.00 3.51
1288 1318 2.097825 GTACATACGGTGGAGTGGAGT 58.902 52.381 0.00 0.00 0.00 3.85
1309 1339 4.109766 CGGATGCGTAGAAATGACTGTAA 58.890 43.478 0.00 0.00 0.00 2.41
1310 1340 3.129813 ACGGATGCGTAGAAATGACTGTA 59.870 43.478 11.73 0.00 0.00 2.74
1311 1341 2.094182 ACGGATGCGTAGAAATGACTGT 60.094 45.455 11.73 0.00 0.00 3.55
1312 1342 2.540515 ACGGATGCGTAGAAATGACTG 58.459 47.619 11.73 0.00 0.00 3.51
1344 1374 0.733566 TTACTTTAGACACGCGCCCG 60.734 55.000 5.73 0.00 41.14 6.13
1389 1430 3.200593 CATCCCGAGCTGCAGCAC 61.201 66.667 38.24 31.25 45.16 4.40
2060 2115 4.174009 CAAACACACTAGAATCGACGGAT 58.826 43.478 0.00 0.00 0.00 4.18
2069 2124 6.372381 CACATGATCATCCAAACACACTAGAA 59.628 38.462 4.86 0.00 0.00 2.10
2073 2128 4.456911 GTCACATGATCATCCAAACACACT 59.543 41.667 4.86 0.00 0.00 3.55
2074 2129 4.379813 GGTCACATGATCATCCAAACACAC 60.380 45.833 4.86 0.00 0.00 3.82
2082 2144 2.546795 GGAGTCGGTCACATGATCATCC 60.547 54.545 4.86 3.04 0.00 3.51
2090 2152 2.813754 CAAAACATGGAGTCGGTCACAT 59.186 45.455 0.00 0.00 0.00 3.21
2198 2260 7.863375 GCTGATCTAGTTGTACTGTATAACCAG 59.137 40.741 19.63 18.53 38.45 4.00
2205 2324 8.290325 CGATTATGCTGATCTAGTTGTACTGTA 58.710 37.037 0.00 0.00 0.00 2.74
2206 2325 7.142021 CGATTATGCTGATCTAGTTGTACTGT 58.858 38.462 0.00 0.00 0.00 3.55
2207 2326 7.142021 ACGATTATGCTGATCTAGTTGTACTG 58.858 38.462 0.00 0.00 0.00 2.74
2208 2327 7.278461 ACGATTATGCTGATCTAGTTGTACT 57.722 36.000 0.00 0.00 0.00 2.73
2209 2328 6.303496 CGACGATTATGCTGATCTAGTTGTAC 59.697 42.308 0.00 0.00 0.00 2.90
2210 2329 6.371389 CGACGATTATGCTGATCTAGTTGTA 58.629 40.000 0.00 0.00 0.00 2.41
2211 2330 5.215903 CGACGATTATGCTGATCTAGTTGT 58.784 41.667 0.00 0.00 0.00 3.32
2212 2331 4.618912 CCGACGATTATGCTGATCTAGTTG 59.381 45.833 0.00 0.00 0.00 3.16
2213 2332 4.321304 CCCGACGATTATGCTGATCTAGTT 60.321 45.833 0.00 0.00 0.00 2.24
2214 2333 3.191581 CCCGACGATTATGCTGATCTAGT 59.808 47.826 0.00 0.00 0.00 2.57
2215 2334 3.440522 TCCCGACGATTATGCTGATCTAG 59.559 47.826 0.00 0.00 0.00 2.43
2216 2335 3.418047 TCCCGACGATTATGCTGATCTA 58.582 45.455 0.00 0.00 0.00 1.98
2217 2336 2.239400 TCCCGACGATTATGCTGATCT 58.761 47.619 0.00 0.00 0.00 2.75
2218 2337 2.724977 TCCCGACGATTATGCTGATC 57.275 50.000 0.00 0.00 0.00 2.92
2219 2338 2.289072 CCTTCCCGACGATTATGCTGAT 60.289 50.000 0.00 0.00 0.00 2.90
2231 2350 4.099573 TCAGATAAACAGATCCTTCCCGAC 59.900 45.833 0.00 0.00 0.00 4.79
2234 2353 7.888250 AAATTCAGATAAACAGATCCTTCCC 57.112 36.000 0.00 0.00 0.00 3.97
2267 2533 9.717892 CATCAACATTGATCAACTCTATTCTTG 57.282 33.333 11.07 4.34 45.62 3.02
2271 2537 9.017509 ACAACATCAACATTGATCAACTCTATT 57.982 29.630 11.07 0.00 45.62 1.73
2298 2564 3.233980 ACCCTCACGCTGCAGTCA 61.234 61.111 16.64 0.00 0.00 3.41
2401 2667 2.502692 AAGACCAGAACGCCGGCTAC 62.503 60.000 26.68 15.23 0.00 3.58
2786 3052 3.462678 GAGGGGTGCGAGAGGGTC 61.463 72.222 0.00 0.00 0.00 4.46
2956 3233 2.142761 CCTCAGATGGGATCCGCCA 61.143 63.158 5.45 0.00 38.95 5.69
3116 3395 2.856000 AGCAGGACAGCCCACCTT 60.856 61.111 0.00 0.00 37.41 3.50
3239 3518 1.621992 GATACTCCGGCAGAGATCCA 58.378 55.000 4.40 0.00 46.50 3.41
3257 3536 4.463597 GACGTATGTTGCCGTCGA 57.536 55.556 0.00 0.00 43.22 4.20
3296 3575 2.270205 CTCGTGGCTGGCTGGAAT 59.730 61.111 2.00 0.00 0.00 3.01
3399 3679 1.446792 CTGCAACGACGATGCCTCT 60.447 57.895 24.68 0.00 43.16 3.69
3425 3705 2.491675 GGAACTTCCCGATCAGGTTT 57.508 50.000 0.00 0.00 38.74 3.27
3725 4006 3.931468 ACGAATTCATCTTCAGAGCTGTG 59.069 43.478 4.05 4.05 0.00 3.66
3938 4219 3.548014 CCAAACTAAGCAACAACTGTCGG 60.548 47.826 0.00 0.00 0.00 4.79
4089 4408 0.771755 GGGTCAGGGAAAAGGACACT 59.228 55.000 0.00 0.00 32.29 3.55
4100 4419 0.405585 ACACCTTCATTGGGTCAGGG 59.594 55.000 0.00 0.00 34.44 4.45
4101 4420 1.888512 CAACACCTTCATTGGGTCAGG 59.111 52.381 0.00 0.00 34.44 3.86
4150 4470 4.212716 AGCATCCAATGTTGATGTATGCT 58.787 39.130 13.81 13.81 42.65 3.79
4239 4559 7.754475 GGTACTAGCTTGAGAGTAAAACAGTAC 59.246 40.741 1.04 4.26 35.85 2.73
4240 4560 7.361542 CGGTACTAGCTTGAGAGTAAAACAGTA 60.362 40.741 1.04 0.00 30.15 2.74
4241 4561 6.569994 CGGTACTAGCTTGAGAGTAAAACAGT 60.570 42.308 1.04 0.00 30.15 3.55
4242 4562 5.800941 CGGTACTAGCTTGAGAGTAAAACAG 59.199 44.000 1.04 0.00 30.15 3.16
4243 4563 5.706916 CGGTACTAGCTTGAGAGTAAAACA 58.293 41.667 1.04 0.00 30.15 2.83
4244 4564 4.562000 GCGGTACTAGCTTGAGAGTAAAAC 59.438 45.833 1.04 0.00 30.15 2.43
4245 4565 4.461781 AGCGGTACTAGCTTGAGAGTAAAA 59.538 41.667 1.04 0.00 43.24 1.52
4246 4566 4.015084 AGCGGTACTAGCTTGAGAGTAAA 58.985 43.478 1.04 0.00 43.24 2.01
4270 4590 3.701241 TGGTGAATCAACGCTTTGAAAC 58.299 40.909 9.92 8.59 45.01 2.78
4317 4642 3.642705 TGACAACTGATGAGTCAACTCG 58.357 45.455 0.00 0.00 45.72 4.18
4358 4683 1.538075 TGCAGTTCATCACACATGCAG 59.462 47.619 0.00 0.00 38.64 4.41
4398 4723 2.858974 CCTCCCCACAACCCCTGT 60.859 66.667 0.00 0.00 39.56 4.00
4404 4735 0.819582 CAATCATGCCTCCCCACAAC 59.180 55.000 0.00 0.00 0.00 3.32
4476 4807 1.633945 GCTCCTACCTCCTTTTCCCAA 59.366 52.381 0.00 0.00 0.00 4.12
4480 4811 2.360844 GCTTGCTCCTACCTCCTTTTC 58.639 52.381 0.00 0.00 0.00 2.29
4482 4813 0.621082 GGCTTGCTCCTACCTCCTTT 59.379 55.000 0.00 0.00 0.00 3.11
4499 4833 9.935241 TGATGATCTAACAATAAGAGATAAGGC 57.065 33.333 0.00 0.00 30.01 4.35
4507 4841 7.255569 ACGAACGTGATGATCTAACAATAAGA 58.744 34.615 0.00 0.00 0.00 2.10
4510 4844 5.679792 CGACGAACGTGATGATCTAACAATA 59.320 40.000 4.19 0.00 37.22 1.90
4531 4865 1.087771 CGGCCTGGATGGTTAACGAC 61.088 60.000 0.00 0.00 38.35 4.34
4562 4896 2.691409 TGTGAGATTGGGGAATCGTC 57.309 50.000 0.00 0.00 34.47 4.20
4644 4978 3.064408 AGTGATCATACAAAGCATGCACG 59.936 43.478 21.98 9.99 0.00 5.34
4646 4980 3.310501 CGAGTGATCATACAAAGCATGCA 59.689 43.478 21.98 0.00 0.00 3.96
4738 6532 5.271598 AGAAGGATGCATTTGGGTGAATAA 58.728 37.500 0.00 0.00 0.00 1.40
4740 6534 3.716431 AGAAGGATGCATTTGGGTGAAT 58.284 40.909 0.00 0.00 0.00 2.57
4778 6574 9.428097 GATGACAGAAGCCAATTTTCTAAAAAT 57.572 29.630 0.00 0.00 33.30 1.82
4831 6627 5.715070 ACTTTATCAGTGAAGTTCGAGAGG 58.285 41.667 0.00 0.00 30.76 3.69
4874 6670 1.720301 CCTCCTCGACCTACGTTCG 59.280 63.158 0.00 0.00 43.13 3.95
4964 6760 6.546395 CAGCAGCATAAACGTTAATCTTCTT 58.454 36.000 0.00 0.00 0.00 2.52
5162 6987 3.069729 CCCCGAGAGACTATTTTAGGTGG 59.930 52.174 0.00 0.00 0.00 4.61
5164 6989 3.306613 CCCCCGAGAGACTATTTTAGGT 58.693 50.000 0.00 0.00 0.00 3.08
5220 8217 4.845621 AATACGTAAAAACCATCGGTCG 57.154 40.909 0.00 0.00 33.12 4.79
5225 8222 9.453325 TTCACAAAGAAATACGTAAAAACCATC 57.547 29.630 0.00 0.00 32.05 3.51
5291 8295 5.120519 AGTTGCACATTTTGTTGTCTTTGTG 59.879 36.000 0.00 0.00 37.96 3.33
5302 8306 1.868498 CAAGGCCAGTTGCACATTTTG 59.132 47.619 5.01 0.00 43.89 2.44
5311 8315 5.705609 ATTACTACAAACAAGGCCAGTTG 57.294 39.130 13.53 8.63 0.00 3.16
5325 8329 9.309516 CGGATTACTTTGCTCTTTATTACTACA 57.690 33.333 0.00 0.00 0.00 2.74
5326 8330 8.762426 CCGGATTACTTTGCTCTTTATTACTAC 58.238 37.037 0.00 0.00 0.00 2.73
5327 8331 8.480501 ACCGGATTACTTTGCTCTTTATTACTA 58.519 33.333 9.46 0.00 0.00 1.82
5328 8332 7.280205 CACCGGATTACTTTGCTCTTTATTACT 59.720 37.037 9.46 0.00 0.00 2.24
5512 10318 0.106819 CCTTGGATCCTTCCTGGCTG 60.107 60.000 14.23 0.00 43.07 4.85
5530 10338 5.051153 GGCTAGTTACTGCTAAATCTGTCC 58.949 45.833 0.00 0.00 0.00 4.02
5563 10371 4.422073 TCCTCGTTGGATGCTGAATAAT 57.578 40.909 0.00 0.00 40.56 1.28
5564 10372 3.904800 TCCTCGTTGGATGCTGAATAA 57.095 42.857 0.00 0.00 40.56 1.40
5602 10410 3.572255 AGCATTGGTGTTACCGTTTGATT 59.428 39.130 0.00 0.00 42.58 2.57
5681 10490 5.465724 GTGATTTCTGACGAATGGGTATACC 59.534 44.000 13.99 13.99 40.81 2.73
5687 10496 3.599343 TCAGTGATTTCTGACGAATGGG 58.401 45.455 0.00 0.00 39.20 4.00
5727 10537 8.964150 CGTAACATGTAATCGAGTTCATGATTA 58.036 33.333 30.50 22.13 39.68 1.75
5739 10549 6.563381 GCAGGGAAATACGTAACATGTAATCG 60.563 42.308 0.00 7.22 0.00 3.34
5746 10556 3.131577 TCTCGCAGGGAAATACGTAACAT 59.868 43.478 0.00 0.00 0.00 2.71
5748 10558 3.155093 TCTCGCAGGGAAATACGTAAC 57.845 47.619 0.00 0.00 0.00 2.50
5749 10559 3.429822 CCTTCTCGCAGGGAAATACGTAA 60.430 47.826 0.00 0.00 0.00 3.18
5750 10560 2.100252 CCTTCTCGCAGGGAAATACGTA 59.900 50.000 0.00 0.00 0.00 3.57
5751 10561 1.134788 CCTTCTCGCAGGGAAATACGT 60.135 52.381 0.00 0.00 0.00 3.57
5752 10562 1.136305 TCCTTCTCGCAGGGAAATACG 59.864 52.381 0.00 0.00 34.24 3.06
5753 10563 2.981859 TCCTTCTCGCAGGGAAATAC 57.018 50.000 0.00 0.00 34.24 1.89
5767 10579 1.086634 AGCTCGATTGCGCTTCCTTC 61.087 55.000 9.73 0.00 30.31 3.46
5823 10638 9.567776 TGGAATCGGTGAATTAATTATGTATGT 57.432 29.630 0.00 0.00 0.00 2.29
5824 10639 9.825972 GTGGAATCGGTGAATTAATTATGTATG 57.174 33.333 0.00 0.00 0.00 2.39
5916 10732 2.919494 CGCTTCCCACCTGTTTGGC 61.919 63.158 0.00 0.00 40.22 4.52


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

AutoCloner maintained by Alex Coulton.