Multiple sequence alignment - TraesCS5B01G503900

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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 TraesCS5B01G503900 chr5B 100.000 2812 0 0 1 2812 670119210 670116399 0.000000e+00 5193.0
1 TraesCS5B01G503900 chr5B 85.938 384 42 5 363 736 680543298 680543679 1.570000e-107 399.0
2 TraesCS5B01G503900 chr4A 88.661 1367 95 26 991 2324 641400889 641402228 0.000000e+00 1611.0
3 TraesCS5B01G503900 chr4A 83.571 420 34 11 2397 2806 641402231 641402625 7.400000e-96 361.0
4 TraesCS5B01G503900 chr4A 89.212 241 21 2 1 240 641398271 641398507 2.120000e-76 296.0
5 TraesCS5B01G503900 chr4A 89.437 142 12 2 2493 2633 641398361 641398500 2.880000e-40 176.0
6 TraesCS5B01G503900 chr5D 86.160 1250 83 30 267 1494 530874828 530873647 0.000000e+00 1267.0
7 TraesCS5B01G503900 chr5D 86.092 870 80 23 1484 2324 530873629 530872772 0.000000e+00 898.0
8 TraesCS5B01G503900 chr5D 93.436 259 14 1 1 259 530908287 530908032 5.680000e-102 381.0
9 TraesCS5B01G503900 chr5D 76.991 226 46 6 363 584 416844342 416844565 1.060000e-24 124.0
10 TraesCS5B01G503900 chr2A 88.991 327 18 10 994 1305 683014794 683014471 3.400000e-104 388.0
11 TraesCS5B01G503900 chr2A 77.746 692 75 44 1420 2053 683014270 683013600 4.460000e-93 351.0
12 TraesCS5B01G503900 chr2A 90.361 166 14 2 455 620 341917609 341917446 1.700000e-52 217.0
13 TraesCS5B01G503900 chr2A 92.000 50 4 0 2348 2397 706752954 706753003 1.400000e-08 71.3
14 TraesCS5B01G503900 chr2D 88.720 328 19 9 994 1306 539430242 539429918 4.390000e-103 385.0
15 TraesCS5B01G503900 chr2D 77.858 691 76 37 1420 2053 539429713 539429043 9.580000e-95 357.0
16 TraesCS5B01G503900 chr2D 81.853 259 37 8 431 686 79532390 79532641 2.840000e-50 209.0
17 TraesCS5B01G503900 chr2D 92.000 50 4 0 2348 2397 566989051 566989100 1.400000e-08 71.3
18 TraesCS5B01G503900 chr2D 88.462 52 5 1 2348 2399 533660229 533660179 8.410000e-06 62.1
19 TraesCS5B01G503900 chr2B 87.387 333 18 11 994 1305 643685963 643685634 7.400000e-96 361.0
20 TraesCS5B01G503900 chr2B 77.437 718 82 40 1391 2053 643685475 643684783 3.450000e-94 355.0
21 TraesCS5B01G503900 chr2B 92.000 50 4 0 2348 2397 679898299 679898348 1.400000e-08 71.3
22 TraesCS5B01G503900 chr2B 90.385 52 5 0 2348 2399 633269626 633269575 5.030000e-08 69.4
23 TraesCS5B01G503900 chr7D 94.737 95 5 0 273 367 463109041 463109135 6.280000e-32 148.0
24 TraesCS5B01G503900 chr7D 96.591 88 3 0 273 360 535726802 535726715 2.260000e-31 147.0
25 TraesCS5B01G503900 chr7D 93.000 100 6 1 267 365 131620129 131620228 8.120000e-31 145.0
26 TraesCS5B01G503900 chr7D 81.765 170 26 4 368 534 76408747 76408914 1.360000e-28 137.0
27 TraesCS5B01G503900 chr1B 94.737 95 4 1 271 365 117282832 117282739 2.260000e-31 147.0
28 TraesCS5B01G503900 chrUn 92.929 99 7 0 269 367 37006454 37006356 8.120000e-31 145.0
29 TraesCS5B01G503900 chrUn 92.929 99 7 0 269 367 38258675 38258577 8.120000e-31 145.0
30 TraesCS5B01G503900 chrUn 92.929 99 7 0 269 367 196709555 196709653 8.120000e-31 145.0
31 TraesCS5B01G503900 chrUn 90.385 52 5 0 2348 2399 26140734 26140683 5.030000e-08 69.4
32 TraesCS5B01G503900 chr7B 93.000 100 6 1 269 367 487811866 487811767 8.120000e-31 145.0
33 TraesCS5B01G503900 chr7B 80.556 180 30 4 358 534 22748139 22748316 1.760000e-27 134.0
34 TraesCS5B01G503900 chr7B 81.176 170 27 4 368 534 22627596 22627763 6.320000e-27 132.0
35 TraesCS5B01G503900 chr7B 81.176 170 27 4 368 534 22806665 22806832 6.320000e-27 132.0
36 TraesCS5B01G503900 chr7B 81.287 171 25 6 368 534 22914430 22914597 6.320000e-27 132.0
37 TraesCS5B01G503900 chr4D 97.778 45 1 0 2677 2721 93392391 93392347 8.350000e-11 78.7
38 TraesCS5B01G503900 chr5A 95.652 46 2 0 2351 2396 402024640 402024595 1.080000e-09 75.0
39 TraesCS5B01G503900 chr6B 92.000 50 2 2 2354 2402 555856442 555856394 5.030000e-08 69.4
40 TraesCS5B01G503900 chr3D 90.000 50 5 0 2348 2397 524715677 524715628 6.500000e-07 65.8


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 TraesCS5B01G503900 chr5B 670116399 670119210 2811 True 5193.0 5193 100.00000 1 2812 1 chr5B.!!$R1 2811
1 TraesCS5B01G503900 chr4A 641398271 641402625 4354 False 611.0 1611 87.72025 1 2806 4 chr4A.!!$F1 2805
2 TraesCS5B01G503900 chr5D 530872772 530874828 2056 True 1082.5 1267 86.12600 267 2324 2 chr5D.!!$R2 2057
3 TraesCS5B01G503900 chr2A 683013600 683014794 1194 True 369.5 388 83.36850 994 2053 2 chr2A.!!$R2 1059
4 TraesCS5B01G503900 chr2D 539429043 539430242 1199 True 371.0 385 83.28900 994 2053 2 chr2D.!!$R2 1059
5 TraesCS5B01G503900 chr2B 643684783 643685963 1180 True 358.0 361 82.41200 994 2053 2 chr2B.!!$R2 1059

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
865 2588 0.040603 GACACCGTCTCGAACTCGTT 60.041 55.0 0.0 0.0 40.8 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2520 4529 0.106819 GCAGGGAGGCATCATCTGTT 60.107 55.0 17.79 0.0 33.44 3.16 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
29 30 8.934697 AGCCATTAGTAAGATAGATACCACAAA 58.065 33.333 0.00 0.00 0.00 2.83
30 31 9.726438 GCCATTAGTAAGATAGATACCACAAAT 57.274 33.333 0.00 0.00 0.00 2.32
50 51 8.777413 CACAAATAATATGATTGACACCGATCT 58.223 33.333 0.00 0.00 34.83 2.75
51 52 9.342308 ACAAATAATATGATTGACACCGATCTT 57.658 29.630 0.00 0.00 34.83 2.40
55 56 7.664082 AATATGATTGACACCGATCTTGATC 57.336 36.000 0.78 0.78 34.83 2.92
68 70 5.005203 CCGATCTTGATCAGAAACGAAGAAG 59.995 44.000 10.69 7.71 37.48 2.85
72 74 4.257267 TGATCAGAAACGAAGAAGCAGA 57.743 40.909 0.00 0.00 0.00 4.26
89 91 1.214062 GAGGACGGTGCAGAGACAG 59.786 63.158 1.61 0.00 0.00 3.51
101 103 3.260128 TGCAGAGACAGTCAGATTGATGT 59.740 43.478 2.66 0.00 0.00 3.06
109 111 4.687948 ACAGTCAGATTGATGTTGTCTTCG 59.312 41.667 0.00 0.00 0.00 3.79
119 121 6.066054 TGATGTTGTCTTCGTTTATTTGCA 57.934 33.333 0.00 0.00 0.00 4.08
141 143 0.627451 AGATGATGCCTCCCTGCAAA 59.373 50.000 0.00 0.00 45.84 3.68
144 146 0.178967 TGATGCCTCCCTGCAAACAA 60.179 50.000 0.00 0.00 45.84 2.83
211 213 5.086104 ACTTCAGCGTCACCATAATTACT 57.914 39.130 0.00 0.00 0.00 2.24
220 222 6.128795 GCGTCACCATAATTACTGCTCTAATC 60.129 42.308 0.00 0.00 0.00 1.75
224 226 7.388776 TCACCATAATTACTGCTCTAATCATGC 59.611 37.037 0.00 0.00 0.00 4.06
233 235 4.132336 TGCTCTAATCATGCTTGGATGTC 58.868 43.478 0.00 0.00 0.00 3.06
235 237 4.375272 CTCTAATCATGCTTGGATGTCGT 58.625 43.478 0.00 0.00 0.00 4.34
240 242 0.107508 ATGCTTGGATGTCGTCAGGG 60.108 55.000 0.00 0.00 0.00 4.45
242 244 0.535335 GCTTGGATGTCGTCAGGGTA 59.465 55.000 0.00 0.00 0.00 3.69
243 245 1.471676 GCTTGGATGTCGTCAGGGTAG 60.472 57.143 0.00 0.00 0.00 3.18
245 247 1.182667 TGGATGTCGTCAGGGTAGTG 58.817 55.000 0.00 0.00 0.00 2.74
249 251 1.171308 TGTCGTCAGGGTAGTGTAGC 58.829 55.000 0.00 0.00 0.00 3.58
250 252 1.271762 TGTCGTCAGGGTAGTGTAGCT 60.272 52.381 0.00 0.00 0.00 3.32
251 253 1.132643 GTCGTCAGGGTAGTGTAGCTG 59.867 57.143 0.00 0.00 0.00 4.24
252 254 1.003928 TCGTCAGGGTAGTGTAGCTGA 59.996 52.381 0.00 0.00 0.00 4.26
253 255 1.132643 CGTCAGGGTAGTGTAGCTGAC 59.867 57.143 0.00 0.00 38.15 3.51
254 256 2.168496 GTCAGGGTAGTGTAGCTGACA 58.832 52.381 0.00 0.00 40.36 3.58
255 257 2.761208 GTCAGGGTAGTGTAGCTGACAT 59.239 50.000 0.00 0.00 41.14 3.06
257 259 4.585162 GTCAGGGTAGTGTAGCTGACATAT 59.415 45.833 0.00 0.00 41.14 1.78
258 260 4.827835 TCAGGGTAGTGTAGCTGACATATC 59.172 45.833 0.00 0.00 41.14 1.63
259 261 4.021894 CAGGGTAGTGTAGCTGACATATCC 60.022 50.000 0.00 0.00 41.14 2.59
261 263 4.262079 GGGTAGTGTAGCTGACATATCCAC 60.262 50.000 0.00 0.00 41.14 4.02
262 264 4.341235 GGTAGTGTAGCTGACATATCCACA 59.659 45.833 0.00 0.00 41.14 4.17
264 266 4.026744 AGTGTAGCTGACATATCCACACT 58.973 43.478 7.20 7.20 41.14 3.55
265 267 4.098654 AGTGTAGCTGACATATCCACACTC 59.901 45.833 7.20 0.00 40.70 3.51
287 289 6.666980 ACTCTTTATTTAGTACTCCCTCCGTT 59.333 38.462 0.00 0.00 0.00 4.44
290 292 2.905415 TTAGTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
321 323 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
322 324 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
369 371 7.842887 AGGATAGAGGGAGTATGTTTTAGTC 57.157 40.000 0.00 0.00 0.00 2.59
371 373 8.734763 AGGATAGAGGGAGTATGTTTTAGTCTA 58.265 37.037 0.00 0.00 0.00 2.59
373 375 6.718522 AGAGGGAGTATGTTTTAGTCTAGC 57.281 41.667 0.00 0.00 0.00 3.42
383 387 5.925509 TGTTTTAGTCTAGCCACACTCTTT 58.074 37.500 0.00 0.00 0.00 2.52
427 432 7.843760 AGGTTCATGGGGATAAATTTATGTTCA 59.156 33.333 15.39 10.04 0.00 3.18
429 434 7.838079 TCATGGGGATAAATTTATGTTCAGG 57.162 36.000 15.39 11.07 0.00 3.86
459 464 1.555075 AGCCACATATGACGTCCAACT 59.445 47.619 14.12 0.00 0.00 3.16
460 465 1.665679 GCCACATATGACGTCCAACTG 59.334 52.381 14.12 7.93 0.00 3.16
464 469 4.454161 CCACATATGACGTCCAACTGAAAA 59.546 41.667 14.12 0.00 0.00 2.29
485 490 0.312416 CCTAGAGCGTGCTTAGCGAT 59.688 55.000 0.00 0.00 40.04 4.58
615 864 2.613977 CGTGCCTTCCTTCAAGTCATCT 60.614 50.000 0.00 0.00 0.00 2.90
630 879 3.264193 AGTCATCTACCACATCCTTGCAA 59.736 43.478 0.00 0.00 0.00 4.08
634 883 1.942657 CTACCACATCCTTGCAATCCG 59.057 52.381 0.00 0.00 0.00 4.18
636 885 1.064463 ACCACATCCTTGCAATCCGAT 60.064 47.619 0.00 0.00 0.00 4.18
643 1238 4.271696 TCCTTGCAATCCGATACTATGG 57.728 45.455 0.00 0.00 0.00 2.74
659 1254 1.956869 ATGGTCACATGTGAGAGGGA 58.043 50.000 28.54 11.12 40.75 4.20
664 1259 2.165437 GTCACATGTGAGAGGGAGAGAC 59.835 54.545 28.54 9.80 40.75 3.36
719 1434 2.640316 AATTGCCGGGTCTAAGATCC 57.360 50.000 2.18 0.00 0.00 3.36
721 1436 1.342672 TTGCCGGGTCTAAGATCCCC 61.343 60.000 2.18 0.00 40.54 4.81
730 1445 5.246307 GGGTCTAAGATCCCCGAATATTTG 58.754 45.833 0.00 0.00 37.89 2.32
734 1449 7.173390 GGTCTAAGATCCCCGAATATTTGAAAG 59.827 40.741 4.10 0.00 0.00 2.62
739 1936 2.362077 CCCCGAATATTTGAAAGCCTGG 59.638 50.000 4.10 0.00 0.00 4.45
744 1941 6.340522 CCGAATATTTGAAAGCCTGGATTTT 58.659 36.000 11.72 3.90 0.00 1.82
865 2588 0.040603 GACACCGTCTCGAACTCGTT 60.041 55.000 0.00 0.00 40.80 3.85
974 2700 4.612412 TTTCGCCTGAACCGCCGT 62.612 61.111 0.00 0.00 32.71 5.68
1353 3151 4.250305 CCGGGCGAAGGGTATGGG 62.250 72.222 0.00 0.00 0.00 4.00
1356 3154 2.509422 GGCGAAGGGTATGGGTCC 59.491 66.667 0.00 0.00 0.00 4.46
1363 3161 1.296002 AGGGTATGGGTCCAAGAACC 58.704 55.000 9.66 9.66 40.41 3.62
1372 3170 2.213499 GGTCCAAGAACCGCTCATATG 58.787 52.381 0.00 0.00 0.00 1.78
1373 3171 2.420129 GGTCCAAGAACCGCTCATATGT 60.420 50.000 1.90 0.00 0.00 2.29
1412 3284 2.111384 GAAGGAGGCCAGTGACAGATA 58.889 52.381 5.01 0.00 0.00 1.98
1441 3321 2.458951 TGCGTTCATGTGCAAGTTTTC 58.541 42.857 7.41 0.00 38.34 2.29
1486 3366 7.395190 TGTTGGAGGATATTCACATTGAAAG 57.605 36.000 0.00 0.00 40.12 2.62
1495 3375 9.970395 GGATATTCACATTGAAAGCATAATTGA 57.030 29.630 0.00 0.00 40.12 2.57
1507 3416 8.246180 TGAAAGCATAATTGACTCCTGAATTTC 58.754 33.333 0.00 0.00 0.00 2.17
1571 3514 6.374333 TGAAGCATAATCTTGGTTTCCTGTAC 59.626 38.462 0.00 0.00 37.44 2.90
1618 3564 6.210784 TGCAGTTGTATCTTCTGTTAGGTAGT 59.789 38.462 0.00 0.00 0.00 2.73
1631 3577 4.217550 TGTTAGGTAGTTTGGCAATGCTTC 59.782 41.667 4.82 0.77 0.00 3.86
1663 3611 6.271159 AGAAGGTAAACTCTTCTCAGGTTCAT 59.729 38.462 0.00 0.00 45.35 2.57
1667 3615 2.625639 ACTCTTCTCAGGTTCATGGGT 58.374 47.619 0.00 0.00 0.00 4.51
1669 3617 4.366267 ACTCTTCTCAGGTTCATGGGTAT 58.634 43.478 0.00 0.00 0.00 2.73
1759 3707 1.345741 TGCTGAGGTTGGACAGAAGAG 59.654 52.381 0.00 0.00 36.38 2.85
1762 3710 2.634940 CTGAGGTTGGACAGAAGAGGAA 59.365 50.000 0.00 0.00 36.38 3.36
1805 3765 1.212935 CTTGTACCTGGGAAGGATGGG 59.787 57.143 0.00 0.00 0.00 4.00
1815 3775 2.308866 GGGAAGGATGGGTTCTGAAGAA 59.691 50.000 0.00 0.00 0.00 2.52
1816 3776 3.615155 GGAAGGATGGGTTCTGAAGAAG 58.385 50.000 0.00 0.00 34.27 2.85
1817 3777 3.264450 GGAAGGATGGGTTCTGAAGAAGA 59.736 47.826 0.00 0.00 34.27 2.87
1829 3789 6.348868 GGTTCTGAAGAAGAATGTTGGACATC 60.349 42.308 0.00 0.00 46.53 3.06
1840 3800 3.588955 TGTTGGACATCGATGTTCAGAG 58.411 45.455 32.44 7.31 46.27 3.35
1842 3802 1.550072 TGGACATCGATGTTCAGAGCA 59.450 47.619 31.39 12.11 41.21 4.26
1849 3809 1.998315 CGATGTTCAGAGCAACAGGAG 59.002 52.381 0.00 0.00 39.63 3.69
1859 3819 1.203100 AGCAACAGGAGGGCTTTCAAT 60.203 47.619 0.00 0.00 33.21 2.57
1860 3827 1.620323 GCAACAGGAGGGCTTTCAATT 59.380 47.619 0.00 0.00 0.00 2.32
1868 3835 5.067805 CAGGAGGGCTTTCAATTATGGTAAC 59.932 44.000 0.00 0.00 0.00 2.50
1883 3861 2.756760 TGGTAACAGGCGTAGAGTAAGG 59.243 50.000 0.00 0.00 46.17 2.69
1917 3904 2.649190 TGGCAACAGCACAAGTTCTAA 58.351 42.857 0.00 0.00 46.17 2.10
1922 3909 4.555511 GCAACAGCACAAGTTCTAAGAAGG 60.556 45.833 0.00 0.00 0.00 3.46
1995 3982 3.305720 AGAAAAGGGGGAAAGAAACACC 58.694 45.455 0.00 0.00 0.00 4.16
2128 4115 3.321682 TGCTAAAACTTGGCTTGATGCTT 59.678 39.130 0.00 0.00 42.39 3.91
2141 4128 4.641989 GCTTGATGCTTATTTCAGAAGGGA 59.358 41.667 0.00 0.00 38.95 4.20
2143 4130 5.698741 TGATGCTTATTTCAGAAGGGAGA 57.301 39.130 0.00 0.00 0.00 3.71
2144 4131 6.257994 TGATGCTTATTTCAGAAGGGAGAT 57.742 37.500 0.00 0.00 0.00 2.75
2146 4133 6.769822 TGATGCTTATTTCAGAAGGGAGATTC 59.230 38.462 0.00 0.00 0.00 2.52
2147 4134 5.118990 TGCTTATTTCAGAAGGGAGATTCG 58.881 41.667 0.00 0.00 34.27 3.34
2148 4135 5.104941 TGCTTATTTCAGAAGGGAGATTCGA 60.105 40.000 0.00 0.00 34.27 3.71
2149 4136 5.994668 GCTTATTTCAGAAGGGAGATTCGAT 59.005 40.000 0.00 0.00 34.27 3.59
2150 4137 6.147000 GCTTATTTCAGAAGGGAGATTCGATC 59.853 42.308 0.00 0.00 34.27 3.69
2151 4138 5.620738 ATTTCAGAAGGGAGATTCGATCA 57.379 39.130 0.00 0.00 34.27 2.92
2152 4139 5.620738 TTTCAGAAGGGAGATTCGATCAT 57.379 39.130 0.00 0.00 34.27 2.45
2153 4140 5.620738 TTCAGAAGGGAGATTCGATCATT 57.379 39.130 0.00 0.00 34.27 2.57
2154 4141 5.620738 TCAGAAGGGAGATTCGATCATTT 57.379 39.130 0.00 0.00 34.27 2.32
2155 4142 5.363101 TCAGAAGGGAGATTCGATCATTTG 58.637 41.667 0.00 0.00 34.27 2.32
2156 4143 4.024218 CAGAAGGGAGATTCGATCATTTGC 60.024 45.833 0.00 0.00 34.27 3.68
2157 4144 2.856222 AGGGAGATTCGATCATTTGCC 58.144 47.619 0.00 0.00 0.00 4.52
2158 4145 1.882623 GGGAGATTCGATCATTTGCCC 59.117 52.381 0.00 0.00 0.00 5.36
2161 4148 0.040067 GATTCGATCATTTGCCCCGC 60.040 55.000 0.00 0.00 0.00 6.13
2162 4149 0.751277 ATTCGATCATTTGCCCCGCA 60.751 50.000 0.00 0.00 36.47 5.69
2163 4150 0.751277 TTCGATCATTTGCCCCGCAT 60.751 50.000 0.00 0.00 38.76 4.73
2164 4151 0.751277 TCGATCATTTGCCCCGCATT 60.751 50.000 0.00 0.00 38.76 3.56
2167 4154 2.030007 CGATCATTTGCCCCGCATTATT 60.030 45.455 0.00 0.00 38.76 1.40
2169 4156 3.176552 TCATTTGCCCCGCATTATTTG 57.823 42.857 0.00 0.00 38.76 2.32
2171 4158 0.539051 TTTGCCCCGCATTATTTGGG 59.461 50.000 0.00 0.00 38.76 4.12
2173 4160 3.947173 CCCCGCATTATTTGGGCA 58.053 55.556 0.00 0.00 41.88 5.36
2174 4161 1.441311 CCCCGCATTATTTGGGCAC 59.559 57.895 0.00 0.00 41.88 5.01
2218 4220 3.173953 TGGGGACTTGATCATTTGCTT 57.826 42.857 0.00 0.00 0.00 3.91
2270 4272 5.931724 CCCCATTTTACTTGGATTTGTTGAC 59.068 40.000 0.00 0.00 36.26 3.18
2340 4342 9.942526 ATTCCAGATACTCCCTTTAATTCAAAT 57.057 29.630 0.00 0.00 0.00 2.32
2341 4343 9.768215 TTCCAGATACTCCCTTTAATTCAAATT 57.232 29.630 0.00 0.00 0.00 1.82
2368 4370 8.702163 ATTTTACAAAATTGTACTATGGCTGC 57.298 30.769 5.53 0.00 42.84 5.25
2369 4371 4.355543 ACAAAATTGTACTATGGCTGCG 57.644 40.909 0.00 0.00 40.16 5.18
2370 4372 4.006989 ACAAAATTGTACTATGGCTGCGA 58.993 39.130 0.00 0.00 40.16 5.10
2371 4373 4.142687 ACAAAATTGTACTATGGCTGCGAC 60.143 41.667 0.00 0.00 40.16 5.19
2372 4374 2.979814 ATTGTACTATGGCTGCGACA 57.020 45.000 0.00 0.00 0.00 4.35
2373 4375 2.753055 TTGTACTATGGCTGCGACAA 57.247 45.000 0.00 0.00 0.00 3.18
2374 4376 2.979814 TGTACTATGGCTGCGACAAT 57.020 45.000 0.00 0.00 0.00 2.71
2375 4377 3.260475 TGTACTATGGCTGCGACAATT 57.740 42.857 0.00 0.00 0.00 2.32
2376 4378 4.394439 TGTACTATGGCTGCGACAATTA 57.606 40.909 0.00 0.00 0.00 1.40
2377 4379 4.760878 TGTACTATGGCTGCGACAATTAA 58.239 39.130 0.00 0.00 0.00 1.40
2378 4380 5.364778 TGTACTATGGCTGCGACAATTAAT 58.635 37.500 0.00 0.00 0.00 1.40
2379 4381 5.820423 TGTACTATGGCTGCGACAATTAATT 59.180 36.000 0.00 0.00 0.00 1.40
2380 4382 5.835113 ACTATGGCTGCGACAATTAATTT 57.165 34.783 0.00 0.00 0.00 1.82
2381 4383 5.581605 ACTATGGCTGCGACAATTAATTTG 58.418 37.500 0.00 0.00 41.36 2.32
2382 4384 3.229276 TGGCTGCGACAATTAATTTGG 57.771 42.857 0.00 0.00 39.80 3.28
2383 4385 2.822561 TGGCTGCGACAATTAATTTGGA 59.177 40.909 0.00 0.00 39.80 3.53
2384 4386 3.446873 TGGCTGCGACAATTAATTTGGAT 59.553 39.130 0.00 0.00 39.80 3.41
2385 4387 4.081752 TGGCTGCGACAATTAATTTGGATT 60.082 37.500 0.00 0.00 39.80 3.01
2386 4388 4.268405 GGCTGCGACAATTAATTTGGATTG 59.732 41.667 0.00 7.11 39.80 2.67
2387 4389 4.268405 GCTGCGACAATTAATTTGGATTGG 59.732 41.667 0.00 0.00 39.80 3.16
2388 4390 5.649557 CTGCGACAATTAATTTGGATTGGA 58.350 37.500 0.00 0.00 39.80 3.53
2389 4391 5.649557 TGCGACAATTAATTTGGATTGGAG 58.350 37.500 0.00 7.25 39.80 3.86
2390 4392 5.043248 GCGACAATTAATTTGGATTGGAGG 58.957 41.667 0.00 0.00 39.80 4.30
2391 4393 5.591099 CGACAATTAATTTGGATTGGAGGG 58.409 41.667 0.00 0.00 39.80 4.30
2392 4394 5.451798 CGACAATTAATTTGGATTGGAGGGG 60.452 44.000 0.00 0.00 39.80 4.79
2393 4395 4.721274 ACAATTAATTTGGATTGGAGGGGG 59.279 41.667 0.00 0.00 39.80 5.40
2394 4396 4.642489 ATTAATTTGGATTGGAGGGGGT 57.358 40.909 0.00 0.00 0.00 4.95
2395 4397 5.759773 ATTAATTTGGATTGGAGGGGGTA 57.240 39.130 0.00 0.00 0.00 3.69
2396 4398 5.554034 TTAATTTGGATTGGAGGGGGTAA 57.446 39.130 0.00 0.00 0.00 2.85
2397 4399 2.911552 TTTGGATTGGAGGGGGTAAC 57.088 50.000 0.00 0.00 0.00 2.50
2398 4400 1.761711 TTGGATTGGAGGGGGTAACA 58.238 50.000 0.00 0.00 39.74 2.41
2399 4401 1.994399 TGGATTGGAGGGGGTAACAT 58.006 50.000 0.00 0.00 39.74 2.71
2400 4402 3.153043 TGGATTGGAGGGGGTAACATA 57.847 47.619 0.00 0.00 39.74 2.29
2401 4403 3.687045 TGGATTGGAGGGGGTAACATAT 58.313 45.455 0.00 0.00 39.74 1.78
2402 4404 3.397618 TGGATTGGAGGGGGTAACATATG 59.602 47.826 0.00 0.00 39.74 1.78
2429 4438 5.170748 CACCTTTTGCAATTCCTTGTATCC 58.829 41.667 0.00 0.00 34.69 2.59
2437 4446 5.655974 TGCAATTCCTTGTATCCATTTGCTA 59.344 36.000 0.00 0.00 39.08 3.49
2447 4456 6.829849 TGTATCCATTTGCTACAGATGATGA 58.170 36.000 0.05 0.00 28.98 2.92
2451 4460 5.945191 TCCATTTGCTACAGATGATGAACAA 59.055 36.000 0.05 0.00 28.98 2.83
2455 4464 9.229784 CATTTGCTACAGATGATGAACAAATAC 57.770 33.333 0.00 0.00 37.23 1.89
2473 4482 7.879070 ACAAATACCATGATATGATTGACAGC 58.121 34.615 0.00 0.00 0.00 4.40
2490 4499 3.048602 CGACCAAGAGGACGGTGT 58.951 61.111 0.00 0.00 46.84 4.16
2536 4545 3.281727 TTGTAACAGATGATGCCTCCC 57.718 47.619 0.00 0.00 0.00 4.30
2542 4551 0.851469 AGATGATGCCTCCCTGCAAT 59.149 50.000 0.00 0.00 45.84 3.56
2565 4574 2.719798 GCACGTTTATGCAAGCTATGG 58.280 47.619 0.00 0.00 45.39 2.74
2583 4592 0.884704 GGGCGTGTTGCTCTGAAAGA 60.885 55.000 0.00 0.00 42.52 2.52
2586 4595 2.404215 GCGTGTTGCTCTGAAAGACTA 58.596 47.619 0.00 0.00 38.67 2.59
2594 4603 6.597672 TGTTGCTCTGAAAGACTAAAACTTCA 59.402 34.615 0.00 0.00 38.67 3.02
2603 4612 2.132762 ACTAAAACTTCAGCGTCACCG 58.867 47.619 0.00 0.00 37.07 4.94
2632 4641 5.256474 ACTGCTCTAATAATGCTTGGTTGT 58.744 37.500 0.00 0.00 0.00 3.32
2634 4643 5.252547 TGCTCTAATAATGCTTGGTTGTCA 58.747 37.500 0.00 0.00 0.00 3.58
2640 4649 1.180029 ATGCTTGGTTGTCATCAGCC 58.820 50.000 0.00 0.00 43.74 4.85
2673 4682 5.531287 GGACCAATCAGTGTATCCCAATTAC 59.469 44.000 0.00 0.00 0.00 1.89
2674 4683 6.327386 ACCAATCAGTGTATCCCAATTACT 57.673 37.500 0.00 0.00 0.00 2.24
2675 4684 6.122277 ACCAATCAGTGTATCCCAATTACTG 58.878 40.000 0.00 0.00 39.95 2.74
2676 4685 5.532406 CCAATCAGTGTATCCCAATTACTGG 59.468 44.000 0.00 0.00 45.97 4.00
2677 4686 5.975988 ATCAGTGTATCCCAATTACTGGT 57.024 39.130 0.00 0.00 44.76 4.00
2678 4687 5.097742 TCAGTGTATCCCAATTACTGGTG 57.902 43.478 0.00 0.00 44.76 4.17
2679 4688 4.534500 TCAGTGTATCCCAATTACTGGTGT 59.466 41.667 0.00 0.00 44.76 4.16
2680 4689 5.722441 TCAGTGTATCCCAATTACTGGTGTA 59.278 40.000 0.00 0.00 44.76 2.90
2681 4690 6.385759 TCAGTGTATCCCAATTACTGGTGTAT 59.614 38.462 0.00 0.00 44.76 2.29
2682 4691 6.706270 CAGTGTATCCCAATTACTGGTGTATC 59.294 42.308 0.00 0.00 44.76 2.24
2683 4692 6.615726 AGTGTATCCCAATTACTGGTGTATCT 59.384 38.462 0.00 0.00 44.76 1.98
2684 4693 6.929606 GTGTATCCCAATTACTGGTGTATCTC 59.070 42.308 0.00 0.00 44.76 2.75
2685 4694 6.844388 TGTATCCCAATTACTGGTGTATCTCT 59.156 38.462 0.00 0.00 44.76 3.10
2686 4695 6.831664 ATCCCAATTACTGGTGTATCTCTT 57.168 37.500 0.00 0.00 44.76 2.85
2687 4696 7.931015 ATCCCAATTACTGGTGTATCTCTTA 57.069 36.000 0.00 0.00 44.76 2.10
2745 4754 6.205658 ACTCCTATCTTTCAGAAAACAAGCAC 59.794 38.462 0.00 0.00 0.00 4.40
2774 4783 8.153479 TGCATTACTGTGTACATATGAATTCC 57.847 34.615 10.38 0.00 0.00 3.01
2783 4792 7.655732 TGTGTACATATGAATTCCGTAATCAGG 59.344 37.037 10.38 0.00 0.00 3.86
2788 4797 9.003658 ACATATGAATTCCGTAATCAGGATTTC 57.996 33.333 10.38 10.98 43.25 2.17
2798 4807 4.460948 AATCAGGATTTCACATGCCAAC 57.539 40.909 0.00 0.00 0.00 3.77
2801 4810 3.640498 TCAGGATTTCACATGCCAACAAA 59.360 39.130 0.00 0.00 0.00 2.83
2802 4811 3.991773 CAGGATTTCACATGCCAACAAAG 59.008 43.478 0.00 0.00 0.00 2.77
2804 4813 4.021719 AGGATTTCACATGCCAACAAAGAG 60.022 41.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.376075 GATCAAGATCGGTGTCAATCATATTAT 57.624 33.333 0.00 0.00 0.00 1.28
30 31 8.367156 TGATCAAGATCGGTGTCAATCATATTA 58.633 33.333 0.00 0.00 40.63 0.98
31 32 7.219322 TGATCAAGATCGGTGTCAATCATATT 58.781 34.615 0.00 0.00 40.63 1.28
32 33 6.762333 TGATCAAGATCGGTGTCAATCATAT 58.238 36.000 0.00 0.00 40.63 1.78
50 51 4.631131 TCTGCTTCTTCGTTTCTGATCAA 58.369 39.130 0.00 0.00 0.00 2.57
51 52 4.240888 CTCTGCTTCTTCGTTTCTGATCA 58.759 43.478 0.00 0.00 0.00 2.92
55 56 2.734079 GTCCTCTGCTTCTTCGTTTCTG 59.266 50.000 0.00 0.00 0.00 3.02
68 70 2.125753 CTCTGCACCGTCCTCTGC 60.126 66.667 0.00 0.00 0.00 4.26
72 74 1.528292 GACTGTCTCTGCACCGTCCT 61.528 60.000 0.00 0.00 0.00 3.85
89 91 5.597813 AACGAAGACAACATCAATCTGAC 57.402 39.130 0.00 0.00 0.00 3.51
101 103 6.125327 TCTGTTGCAAATAAACGAAGACAA 57.875 33.333 0.00 0.00 0.00 3.18
109 111 5.413499 AGGCATCATCTGTTGCAAATAAAC 58.587 37.500 0.00 0.00 41.26 2.01
119 121 0.106819 GCAGGGAGGCATCATCTGTT 60.107 55.000 17.79 0.00 33.44 3.16
141 143 1.953686 AGCTTGGCATAAACGTGTTGT 59.046 42.857 0.00 0.00 0.00 3.32
144 146 3.605634 TGATAGCTTGGCATAAACGTGT 58.394 40.909 0.00 0.00 0.00 4.49
184 186 0.032130 TGGTGACGCTGAAGTCTCAC 59.968 55.000 5.56 0.00 41.47 3.51
186 188 2.941453 TATGGTGACGCTGAAGTCTC 57.059 50.000 5.56 2.50 41.47 3.36
188 190 5.005779 CAGTAATTATGGTGACGCTGAAGTC 59.994 44.000 0.00 0.00 41.30 3.01
211 213 4.132336 GACATCCAAGCATGATTAGAGCA 58.868 43.478 0.00 0.00 0.00 4.26
220 222 1.012086 CCTGACGACATCCAAGCATG 58.988 55.000 0.00 0.00 0.00 4.06
224 226 1.825474 ACTACCCTGACGACATCCAAG 59.175 52.381 0.00 0.00 0.00 3.61
233 235 1.132643 GTCAGCTACACTACCCTGACG 59.867 57.143 4.17 0.00 43.02 4.35
235 237 2.597578 TGTCAGCTACACTACCCTGA 57.402 50.000 0.00 0.00 31.43 3.86
240 242 5.067936 AGTGTGGATATGTCAGCTACACTAC 59.932 44.000 15.73 7.10 43.64 2.73
242 244 4.026744 AGTGTGGATATGTCAGCTACACT 58.973 43.478 13.11 13.11 42.09 3.55
243 245 4.098654 AGAGTGTGGATATGTCAGCTACAC 59.901 45.833 0.00 0.00 42.09 2.90
245 247 4.927978 AGAGTGTGGATATGTCAGCTAC 57.072 45.455 0.00 0.00 0.00 3.58
249 251 9.823647 ACTAAATAAAGAGTGTGGATATGTCAG 57.176 33.333 0.00 0.00 0.00 3.51
255 257 8.921205 GGGAGTACTAAATAAAGAGTGTGGATA 58.079 37.037 0.00 0.00 0.00 2.59
257 259 6.958192 AGGGAGTACTAAATAAAGAGTGTGGA 59.042 38.462 0.00 0.00 0.00 4.02
258 260 7.184067 AGGGAGTACTAAATAAAGAGTGTGG 57.816 40.000 0.00 0.00 0.00 4.17
259 261 7.266400 GGAGGGAGTACTAAATAAAGAGTGTG 58.734 42.308 0.00 0.00 0.00 3.82
261 263 6.096564 ACGGAGGGAGTACTAAATAAAGAGTG 59.903 42.308 0.00 0.00 0.00 3.51
262 264 6.193504 ACGGAGGGAGTACTAAATAAAGAGT 58.806 40.000 0.00 0.00 0.00 3.24
264 266 6.097412 GGAACGGAGGGAGTACTAAATAAAGA 59.903 42.308 0.00 0.00 0.00 2.52
265 267 6.127253 TGGAACGGAGGGAGTACTAAATAAAG 60.127 42.308 0.00 0.00 0.00 1.85
312 314 8.707938 AAGAACGTTTTTAACACTACACTAGT 57.292 30.769 0.46 0.00 40.28 2.57
349 351 6.776603 GGCTAGACTAAAACATACTCCCTCTA 59.223 42.308 0.00 0.00 0.00 2.43
350 352 5.599242 GGCTAGACTAAAACATACTCCCTCT 59.401 44.000 0.00 0.00 0.00 3.69
366 368 8.079211 TCATTAATAAAGAGTGTGGCTAGACT 57.921 34.615 0.00 0.00 32.31 3.24
367 369 8.894768 ATCATTAATAAAGAGTGTGGCTAGAC 57.105 34.615 0.00 0.00 0.00 2.59
369 371 8.893219 TGATCATTAATAAAGAGTGTGGCTAG 57.107 34.615 0.00 0.00 0.00 3.42
371 373 9.851686 TTATGATCATTAATAAAGAGTGTGGCT 57.148 29.630 14.65 0.00 0.00 4.75
427 432 5.013183 GTCATATGTGGCTCCTTAATACCCT 59.987 44.000 1.90 0.00 0.00 4.34
429 434 4.929808 CGTCATATGTGGCTCCTTAATACC 59.070 45.833 1.90 0.00 0.00 2.73
459 464 3.334583 AAGCACGCTCTAGGATTTTCA 57.665 42.857 0.00 0.00 0.00 2.69
460 465 3.246463 GCTAAGCACGCTCTAGGATTTTC 59.754 47.826 0.00 0.00 0.00 2.29
464 469 0.312416 CGCTAAGCACGCTCTAGGAT 59.688 55.000 0.00 0.00 0.00 3.24
485 490 5.063204 GCACCAATATTGAGGCACATAGTA 58.937 41.667 17.23 0.00 0.00 1.82
615 864 1.557371 TCGGATTGCAAGGATGTGGTA 59.443 47.619 4.94 0.00 0.00 3.25
630 879 4.832823 TCACATGTGACCATAGTATCGGAT 59.167 41.667 24.56 0.00 34.14 4.18
634 883 5.279206 CCCTCTCACATGTGACCATAGTATC 60.279 48.000 24.56 0.00 35.46 2.24
636 885 3.960755 CCCTCTCACATGTGACCATAGTA 59.039 47.826 24.56 1.83 35.46 1.82
643 1238 2.165437 GTCTCTCCCTCTCACATGTGAC 59.835 54.545 24.56 7.77 35.46 3.67
659 1254 3.960102 CCTATCTCTTGCCTTGAGTCTCT 59.040 47.826 0.65 0.00 33.59 3.10
664 1259 1.767681 AGCCCTATCTCTTGCCTTGAG 59.232 52.381 0.00 0.00 0.00 3.02
697 1300 3.699538 GGATCTTAGACCCGGCAATTTTT 59.300 43.478 0.00 0.00 0.00 1.94
699 1414 2.422945 GGGATCTTAGACCCGGCAATTT 60.423 50.000 0.00 0.00 36.56 1.82
719 1434 3.287222 TCCAGGCTTTCAAATATTCGGG 58.713 45.455 0.00 0.00 0.00 5.14
721 1436 7.832503 AAAAATCCAGGCTTTCAAATATTCG 57.167 32.000 0.00 0.00 0.00 3.34
773 1970 8.649591 TGTGTGTACAAAGGGTTCTACTAAATA 58.350 33.333 0.00 0.00 32.88 1.40
806 2529 1.248101 AAAAAGATTCGGGTGGGCCG 61.248 55.000 0.00 0.00 34.97 6.13
865 2588 5.548056 TGGGCCTGATTTTATTTTTACCCAA 59.452 36.000 4.53 0.00 40.57 4.12
946 2672 1.004277 TCAGGCGAAACCCTATGCTTT 59.996 47.619 0.00 0.00 40.58 3.51
1353 3151 2.906354 ACATATGAGCGGTTCTTGGAC 58.094 47.619 10.38 0.00 0.00 4.02
1383 3181 2.026449 ACTGGCCTCCTTCTCAGAATTG 60.026 50.000 3.32 0.00 0.00 2.32
1412 3284 2.339418 CACATGAACGCATTGCCAAAT 58.661 42.857 0.00 0.00 30.68 2.32
1422 3302 2.458951 TGAAAACTTGCACATGAACGC 58.541 42.857 0.00 0.00 0.00 4.84
1441 3321 7.148639 CCAACAGCAAATGAAGAAATCAGATTG 60.149 37.037 0.00 0.00 42.53 2.67
1486 3366 5.066505 ACCGAAATTCAGGAGTCAATTATGC 59.933 40.000 10.02 0.00 0.00 3.14
1507 3416 4.091509 GCTACAAGTTGTCATACTGAACCG 59.908 45.833 12.82 0.00 0.00 4.44
1618 3564 1.702182 TGTCAGGAAGCATTGCCAAA 58.298 45.000 4.70 0.00 36.97 3.28
1631 3577 5.859495 AGAAGAGTTTACCTTCTTGTCAGG 58.141 41.667 0.00 0.00 45.71 3.86
1663 3611 1.281199 ATGGTGGCTCTGCATACCCA 61.281 55.000 10.95 0.00 36.80 4.51
1667 3615 0.179076 CGACATGGTGGCTCTGCATA 60.179 55.000 0.00 0.00 0.00 3.14
1669 3617 2.046988 CGACATGGTGGCTCTGCA 60.047 61.111 0.00 0.00 0.00 4.41
1759 3707 2.329379 CACTGTCTACTTGAGCGTTCC 58.671 52.381 0.00 0.00 0.00 3.62
1762 3710 0.603569 CCCACTGTCTACTTGAGCGT 59.396 55.000 0.00 0.00 0.00 5.07
1805 3765 6.566197 ATGTCCAACATTCTTCTTCAGAAC 57.434 37.500 0.00 0.00 44.70 3.01
1815 3775 4.578871 TGAACATCGATGTCCAACATTCT 58.421 39.130 30.06 12.18 39.27 2.40
1816 3776 4.631377 TCTGAACATCGATGTCCAACATTC 59.369 41.667 30.06 21.25 39.27 2.67
1817 3777 4.578871 TCTGAACATCGATGTCCAACATT 58.421 39.130 30.06 13.69 39.27 2.71
1829 3789 1.998315 CTCCTGTTGCTCTGAACATCG 59.002 52.381 0.00 0.00 35.32 3.84
1840 3800 1.260544 ATTGAAAGCCCTCCTGTTGC 58.739 50.000 0.00 0.00 0.00 4.17
1842 3802 4.026052 CCATAATTGAAAGCCCTCCTGTT 58.974 43.478 0.00 0.00 0.00 3.16
1849 3809 4.441495 GCCTGTTACCATAATTGAAAGCCC 60.441 45.833 0.00 0.00 0.00 5.19
1859 3819 5.068198 CCTTACTCTACGCCTGTTACCATAA 59.932 44.000 0.00 0.00 0.00 1.90
1860 3827 4.581824 CCTTACTCTACGCCTGTTACCATA 59.418 45.833 0.00 0.00 0.00 2.74
1868 3835 1.481871 TTCCCCTTACTCTACGCCTG 58.518 55.000 0.00 0.00 0.00 4.85
1870 3837 3.339253 TTTTTCCCCTTACTCTACGCC 57.661 47.619 0.00 0.00 0.00 5.68
1899 3877 4.531332 CTTCTTAGAACTTGTGCTGTTGC 58.469 43.478 0.00 0.00 40.20 4.17
1917 3904 3.393687 TCATACCCATGCTTACCCTTCT 58.606 45.455 0.00 0.00 31.73 2.85
1922 3909 4.973168 TCTGAATCATACCCATGCTTACC 58.027 43.478 0.00 0.00 31.73 2.85
2128 4115 6.731292 TGATCGAATCTCCCTTCTGAAATA 57.269 37.500 0.00 0.00 0.00 1.40
2141 4128 1.597742 CGGGGCAAATGATCGAATCT 58.402 50.000 0.00 0.00 0.00 2.40
2143 4130 0.751277 TGCGGGGCAAATGATCGAAT 60.751 50.000 0.00 0.00 34.76 3.34
2144 4131 0.751277 ATGCGGGGCAAATGATCGAA 60.751 50.000 0.00 0.00 43.62 3.71
2146 4133 0.950836 TAATGCGGGGCAAATGATCG 59.049 50.000 0.00 0.00 43.62 3.69
2147 4134 3.665745 AATAATGCGGGGCAAATGATC 57.334 42.857 0.00 0.00 43.62 2.92
2148 4135 3.494749 CCAAATAATGCGGGGCAAATGAT 60.495 43.478 0.00 0.00 43.62 2.45
2149 4136 2.158986 CCAAATAATGCGGGGCAAATGA 60.159 45.455 0.00 0.00 43.62 2.57
2150 4137 2.211806 CCAAATAATGCGGGGCAAATG 58.788 47.619 0.00 0.00 43.62 2.32
2151 4138 1.140652 CCCAAATAATGCGGGGCAAAT 59.859 47.619 0.00 0.00 43.62 2.32
2152 4139 0.539051 CCCAAATAATGCGGGGCAAA 59.461 50.000 0.00 0.00 43.62 3.68
2153 4140 2.206635 CCCAAATAATGCGGGGCAA 58.793 52.632 0.00 0.00 43.62 4.52
2154 4141 3.947173 CCCAAATAATGCGGGGCA 58.053 55.556 0.00 0.00 44.86 5.36
2156 4143 1.042559 AGTGCCCAAATAATGCGGGG 61.043 55.000 0.00 0.00 43.72 5.73
2157 4144 0.823460 AAGTGCCCAAATAATGCGGG 59.177 50.000 0.00 0.00 43.42 6.13
2158 4145 1.476085 TCAAGTGCCCAAATAATGCGG 59.524 47.619 0.00 0.00 0.00 5.69
2161 4148 6.238266 GCAAATGATCAAGTGCCCAAATAATG 60.238 38.462 18.64 0.00 0.00 1.90
2162 4149 5.818857 GCAAATGATCAAGTGCCCAAATAAT 59.181 36.000 18.64 0.00 0.00 1.28
2163 4150 5.177326 GCAAATGATCAAGTGCCCAAATAA 58.823 37.500 18.64 0.00 0.00 1.40
2164 4151 4.757594 GCAAATGATCAAGTGCCCAAATA 58.242 39.130 18.64 0.00 0.00 1.40
2167 4154 2.747396 GCAAATGATCAAGTGCCCAA 57.253 45.000 18.64 0.00 0.00 4.12
2171 4158 0.179129 CGGGGCAAATGATCAAGTGC 60.179 55.000 20.36 20.36 36.24 4.40
2173 4160 0.611618 TGCGGGGCAAATGATCAAGT 60.612 50.000 0.00 0.00 34.76 3.16
2174 4161 0.748450 ATGCGGGGCAAATGATCAAG 59.252 50.000 0.00 0.00 43.62 3.02
2270 4272 5.619132 AAATTGAGGAATAGGGCAAATGG 57.381 39.130 0.00 0.00 0.00 3.16
2342 4344 9.150348 GCAGCCATAGTACAATTTTGTAAAATT 57.850 29.630 8.99 8.99 46.42 1.82
2343 4345 7.487829 CGCAGCCATAGTACAATTTTGTAAAAT 59.512 33.333 4.79 0.00 44.46 1.82
2344 4346 6.804295 CGCAGCCATAGTACAATTTTGTAAAA 59.196 34.615 4.79 0.00 44.46 1.52
2345 4347 6.149640 TCGCAGCCATAGTACAATTTTGTAAA 59.850 34.615 4.79 0.00 44.46 2.01
2346 4348 5.644206 TCGCAGCCATAGTACAATTTTGTAA 59.356 36.000 4.79 0.00 44.46 2.41
2347 4349 5.064198 GTCGCAGCCATAGTACAATTTTGTA 59.936 40.000 0.00 0.00 42.35 2.41
2348 4350 4.006989 TCGCAGCCATAGTACAATTTTGT 58.993 39.130 1.08 1.08 44.86 2.83
2349 4351 4.142708 TGTCGCAGCCATAGTACAATTTTG 60.143 41.667 0.00 0.00 0.00 2.44
2350 4352 4.006989 TGTCGCAGCCATAGTACAATTTT 58.993 39.130 0.00 0.00 0.00 1.82
2351 4353 3.605634 TGTCGCAGCCATAGTACAATTT 58.394 40.909 0.00 0.00 0.00 1.82
2352 4354 3.260475 TGTCGCAGCCATAGTACAATT 57.740 42.857 0.00 0.00 0.00 2.32
2353 4355 2.979814 TGTCGCAGCCATAGTACAAT 57.020 45.000 0.00 0.00 0.00 2.71
2354 4356 2.753055 TTGTCGCAGCCATAGTACAA 57.247 45.000 0.00 0.00 0.00 2.41
2355 4357 2.979814 ATTGTCGCAGCCATAGTACA 57.020 45.000 0.00 0.00 0.00 2.90
2356 4358 5.924475 ATTAATTGTCGCAGCCATAGTAC 57.076 39.130 0.00 0.00 0.00 2.73
2357 4359 6.238621 CCAAATTAATTGTCGCAGCCATAGTA 60.239 38.462 0.39 0.00 37.32 1.82
2358 4360 5.450412 CCAAATTAATTGTCGCAGCCATAGT 60.450 40.000 0.39 0.00 37.32 2.12
2359 4361 4.977963 CCAAATTAATTGTCGCAGCCATAG 59.022 41.667 0.39 0.00 37.32 2.23
2360 4362 4.642437 TCCAAATTAATTGTCGCAGCCATA 59.358 37.500 0.39 0.00 37.32 2.74
2361 4363 3.446873 TCCAAATTAATTGTCGCAGCCAT 59.553 39.130 0.39 0.00 37.32 4.40
2362 4364 2.822561 TCCAAATTAATTGTCGCAGCCA 59.177 40.909 0.39 0.00 37.32 4.75
2363 4365 3.502191 TCCAAATTAATTGTCGCAGCC 57.498 42.857 0.39 0.00 37.32 4.85
2364 4366 4.268405 CCAATCCAAATTAATTGTCGCAGC 59.732 41.667 0.39 0.00 37.32 5.25
2365 4367 5.649557 TCCAATCCAAATTAATTGTCGCAG 58.350 37.500 0.39 0.00 37.32 5.18
2366 4368 5.394005 CCTCCAATCCAAATTAATTGTCGCA 60.394 40.000 0.39 0.00 37.32 5.10
2367 4369 5.043248 CCTCCAATCCAAATTAATTGTCGC 58.957 41.667 0.39 0.00 37.32 5.19
2368 4370 5.451798 CCCCTCCAATCCAAATTAATTGTCG 60.452 44.000 0.39 0.00 37.32 4.35
2369 4371 5.163311 CCCCCTCCAATCCAAATTAATTGTC 60.163 44.000 0.39 0.00 37.32 3.18
2370 4372 4.721274 CCCCCTCCAATCCAAATTAATTGT 59.279 41.667 0.39 0.00 37.32 2.71
2371 4373 4.721274 ACCCCCTCCAATCCAAATTAATTG 59.279 41.667 0.39 0.00 38.84 2.32
2372 4374 4.971661 ACCCCCTCCAATCCAAATTAATT 58.028 39.130 0.00 0.00 0.00 1.40
2373 4375 4.642489 ACCCCCTCCAATCCAAATTAAT 57.358 40.909 0.00 0.00 0.00 1.40
2374 4376 5.222568 TGTTACCCCCTCCAATCCAAATTAA 60.223 40.000 0.00 0.00 0.00 1.40
2375 4377 4.295238 TGTTACCCCCTCCAATCCAAATTA 59.705 41.667 0.00 0.00 0.00 1.40
2376 4378 3.078305 TGTTACCCCCTCCAATCCAAATT 59.922 43.478 0.00 0.00 0.00 1.82
2377 4379 2.657459 TGTTACCCCCTCCAATCCAAAT 59.343 45.455 0.00 0.00 0.00 2.32
2378 4380 2.074579 TGTTACCCCCTCCAATCCAAA 58.925 47.619 0.00 0.00 0.00 3.28
2379 4381 1.761711 TGTTACCCCCTCCAATCCAA 58.238 50.000 0.00 0.00 0.00 3.53
2380 4382 1.994399 ATGTTACCCCCTCCAATCCA 58.006 50.000 0.00 0.00 0.00 3.41
2381 4383 3.397955 ACATATGTTACCCCCTCCAATCC 59.602 47.826 1.41 0.00 0.00 3.01
2382 4384 4.398319 CACATATGTTACCCCCTCCAATC 58.602 47.826 5.37 0.00 0.00 2.67
2383 4385 3.140144 CCACATATGTTACCCCCTCCAAT 59.860 47.826 5.37 0.00 0.00 3.16
2384 4386 2.512056 CCACATATGTTACCCCCTCCAA 59.488 50.000 5.37 0.00 0.00 3.53
2385 4387 2.131854 CCACATATGTTACCCCCTCCA 58.868 52.381 5.37 0.00 0.00 3.86
2386 4388 1.202891 GCCACATATGTTACCCCCTCC 60.203 57.143 5.37 0.00 0.00 4.30
2387 4389 1.493022 TGCCACATATGTTACCCCCTC 59.507 52.381 5.37 0.00 0.00 4.30
2388 4390 1.214424 GTGCCACATATGTTACCCCCT 59.786 52.381 5.37 0.00 0.00 4.79
2389 4391 1.687563 GTGCCACATATGTTACCCCC 58.312 55.000 5.37 0.00 0.00 5.40
2390 4392 1.214424 AGGTGCCACATATGTTACCCC 59.786 52.381 21.47 12.04 32.81 4.95
2391 4393 2.729028 AGGTGCCACATATGTTACCC 57.271 50.000 21.47 13.29 32.81 3.69
2392 4394 4.743493 CAAAAGGTGCCACATATGTTACC 58.257 43.478 19.12 19.12 32.65 2.85
2429 4438 9.229784 GTATTTGTTCATCATCTGTAGCAAATG 57.770 33.333 0.00 0.00 35.46 2.32
2437 4446 9.803507 ATATCATGGTATTTGTTCATCATCTGT 57.196 29.630 0.00 0.00 0.00 3.41
2447 4456 8.355169 GCTGTCAATCATATCATGGTATTTGTT 58.645 33.333 9.28 0.00 0.00 2.83
2451 4460 6.369890 GTCGCTGTCAATCATATCATGGTATT 59.630 38.462 0.00 0.00 0.00 1.89
2455 4464 3.434641 GGTCGCTGTCAATCATATCATGG 59.565 47.826 0.00 0.00 0.00 3.66
2473 4482 1.372997 CACACCGTCCTCTTGGTCG 60.373 63.158 0.00 0.00 42.85 4.79
2520 4529 0.106819 GCAGGGAGGCATCATCTGTT 60.107 55.000 17.79 0.00 33.44 3.16
2525 4534 0.554305 TGATTGCAGGGAGGCATCAT 59.446 50.000 0.00 0.00 44.48 2.45
2526 4535 0.106868 CTGATTGCAGGGAGGCATCA 60.107 55.000 0.00 0.00 44.48 3.07
2527 4536 1.453762 GCTGATTGCAGGGAGGCATC 61.454 60.000 0.00 0.00 44.48 3.91
2528 4537 1.455217 GCTGATTGCAGGGAGGCAT 60.455 57.895 0.00 0.00 44.48 4.40
2542 4551 1.522668 AGCTTGCATAAACGTGCTGA 58.477 45.000 0.00 0.00 45.27 4.26
2564 4573 0.884704 TCTTTCAGAGCAACACGCCC 60.885 55.000 0.00 0.00 44.04 6.13
2565 4574 0.235926 GTCTTTCAGAGCAACACGCC 59.764 55.000 0.00 0.00 44.04 5.68
2603 4612 9.057089 ACCAAGCATTATTAGAGCAGTAATTAC 57.943 33.333 7.57 7.57 0.00 1.89
2632 4641 2.158445 GGTCCCTAGACTAGGCTGATGA 60.158 54.545 21.54 10.97 44.86 2.92
2634 4643 1.860240 TGGTCCCTAGACTAGGCTGAT 59.140 52.381 21.54 0.00 44.86 2.90
2640 4649 4.282496 ACACTGATTGGTCCCTAGACTAG 58.718 47.826 2.18 2.18 43.05 2.57
2673 4682 5.536538 TGGTAGCTGATAAGAGATACACCAG 59.463 44.000 0.00 0.00 36.70 4.00
2674 4683 5.454966 TGGTAGCTGATAAGAGATACACCA 58.545 41.667 0.00 0.00 36.70 4.17
2675 4684 6.406692 TTGGTAGCTGATAAGAGATACACC 57.593 41.667 0.00 0.00 36.70 4.16
2676 4685 8.768955 CATTTTGGTAGCTGATAAGAGATACAC 58.231 37.037 0.00 0.00 36.70 2.90
2677 4686 8.704668 TCATTTTGGTAGCTGATAAGAGATACA 58.295 33.333 0.00 0.00 36.70 2.29
2678 4687 9.717942 ATCATTTTGGTAGCTGATAAGAGATAC 57.282 33.333 0.00 0.00 34.66 2.24
2687 4696 8.995027 TGGTTTATATCATTTTGGTAGCTGAT 57.005 30.769 0.00 0.00 33.21 2.90
2721 4730 6.205464 TGTGCTTGTTTTCTGAAAGATAGGAG 59.795 38.462 2.75 0.00 46.36 3.69
2722 4731 6.061441 TGTGCTTGTTTTCTGAAAGATAGGA 58.939 36.000 2.75 1.21 46.36 2.94
2723 4732 6.205464 TCTGTGCTTGTTTTCTGAAAGATAGG 59.795 38.462 2.75 0.00 46.36 2.57
2724 4733 7.194607 TCTGTGCTTGTTTTCTGAAAGATAG 57.805 36.000 2.75 3.64 46.36 2.08
2725 4734 7.587629 CATCTGTGCTTGTTTTCTGAAAGATA 58.412 34.615 2.75 0.00 46.36 1.98
2726 4735 6.444633 CATCTGTGCTTGTTTTCTGAAAGAT 58.555 36.000 2.75 0.00 46.36 2.40
2727 4736 5.824429 CATCTGTGCTTGTTTTCTGAAAGA 58.176 37.500 2.75 0.00 44.68 2.52
2745 4754 7.951530 TCATATGTACACAGTAATGCATCTG 57.048 36.000 12.58 12.58 37.65 2.90
2751 4760 8.365399 ACGGAATTCATATGTACACAGTAATG 57.635 34.615 7.93 0.00 0.00 1.90
2762 4771 8.924511 AAATCCTGATTACGGAATTCATATGT 57.075 30.769 7.93 2.72 33.55 2.29
2763 4772 9.002600 TGAAATCCTGATTACGGAATTCATATG 57.997 33.333 7.93 0.00 42.51 1.78
2764 4773 9.003658 GTGAAATCCTGATTACGGAATTCATAT 57.996 33.333 7.93 0.00 46.42 1.78
2766 4775 6.828273 TGTGAAATCCTGATTACGGAATTCAT 59.172 34.615 7.93 0.00 46.42 2.57
2767 4776 6.176896 TGTGAAATCCTGATTACGGAATTCA 58.823 36.000 7.93 5.67 44.18 2.57
2774 4783 3.627123 TGGCATGTGAAATCCTGATTACG 59.373 43.478 0.00 0.00 0.00 3.18
2778 4787 3.433343 TGTTGGCATGTGAAATCCTGAT 58.567 40.909 0.00 0.00 0.00 2.90
2783 4792 4.240096 CCTCTTTGTTGGCATGTGAAATC 58.760 43.478 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.