Multiple sequence alignment - TraesCS2B01G622500

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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 TraesCS2B01G622500 chr2B 100.000 5114 0 0 1 5114 796601632 796596519 0.000000e+00 9444.0
1 TraesCS2B01G622500 chr2B 82.635 501 75 7 1859 2350 789260350 789260847 2.830000e-117 433.0
2 TraesCS2B01G622500 chr2B 83.425 362 50 8 2281 2634 795757304 795756945 1.370000e-85 327.0
3 TraesCS2B01G622500 chr2B 77.500 480 104 4 2363 2840 796024840 796025317 8.380000e-73 285.0
4 TraesCS2B01G622500 chr2B 86.190 210 15 11 4535 4740 796583331 796583132 1.120000e-51 215.0
5 TraesCS2B01G622500 chr2B 78.543 247 36 13 4762 4994 796532739 796532496 4.130000e-31 147.0
6 TraesCS2B01G622500 chr2B 79.736 227 26 13 4172 4389 796622321 796622536 4.130000e-31 147.0
7 TraesCS2B01G622500 chr2B 83.916 143 11 7 4762 4904 796623030 796623160 5.380000e-25 126.0
8 TraesCS2B01G622500 chr2D 94.925 3645 142 20 504 4118 637901018 637904649 0.000000e+00 5666.0
9 TraesCS2B01G622500 chr2D 87.925 588 34 16 4166 4740 637905010 637905573 0.000000e+00 658.0
10 TraesCS2B01G622500 chr2D 80.140 856 164 5 1865 2720 640024486 640025335 7.220000e-178 634.0
11 TraesCS2B01G622500 chr2D 86.312 263 33 3 3 264 637900507 637900767 3.010000e-72 283.0
12 TraesCS2B01G622500 chr2D 82.591 247 16 11 4779 5014 637906703 637906933 5.230000e-45 193.0
13 TraesCS2B01G622500 chr2D 82.558 172 29 1 1277 1448 22816480 22816310 3.190000e-32 150.0
14 TraesCS2B01G622500 chr2D 76.056 355 47 23 4040 4389 637892685 637892364 3.190000e-32 150.0
15 TraesCS2B01G622500 chr2D 88.298 94 8 2 379 472 637900929 637901019 5.410000e-20 110.0
16 TraesCS2B01G622500 chr2D 79.412 170 15 12 4193 4352 637969578 637969737 9.060000e-18 102.0
17 TraesCS2B01G622500 chr2D 92.000 50 3 1 4732 4780 637905706 637905755 9.190000e-08 69.4
18 TraesCS2B01G622500 chr2A 93.396 3831 173 34 696 4467 761304316 761308125 0.000000e+00 5600.0
19 TraesCS2B01G622500 chr2A 84.004 919 147 0 1850 2768 761856926 761856008 0.000000e+00 883.0
20 TraesCS2B01G622500 chr2A 83.025 972 154 5 2783 3744 761521330 761522300 0.000000e+00 870.0
21 TraesCS2B01G622500 chr2A 82.775 865 131 7 1866 2730 761898617 761897771 0.000000e+00 756.0
22 TraesCS2B01G622500 chr2A 77.910 1177 232 16 2887 4049 761897552 761896390 0.000000e+00 708.0
23 TraesCS2B01G622500 chr2A 83.788 697 103 7 3049 3735 761622501 761621805 0.000000e+00 652.0
24 TraesCS2B01G622500 chr2A 85.202 446 64 2 2279 2722 761520869 761521314 1.680000e-124 457.0
25 TraesCS2B01G622500 chr2A 77.778 594 88 18 2624 3195 761674528 761673957 4.940000e-85 326.0
26 TraesCS2B01G622500 chr2A 80.052 386 45 19 4740 5113 761308544 761308909 1.830000e-64 257.0
27 TraesCS2B01G622500 chr2A 83.774 265 20 17 4477 4741 761308168 761308409 3.980000e-56 230.0
28 TraesCS2B01G622500 chr2A 77.083 384 51 28 4040 4414 761315434 761315789 2.430000e-43 187.0
29 TraesCS2B01G622500 chr2A 77.341 331 58 13 939 1258 764189351 764189675 4.070000e-41 180.0
30 TraesCS2B01G622500 chr2A 96.000 75 3 0 4762 4836 761316259 761316333 6.950000e-24 122.0
31 TraesCS2B01G622500 chr1D 85.916 2265 294 12 1865 4118 6542212 6539962 0.000000e+00 2392.0
32 TraesCS2B01G622500 chr1A 85.595 2277 306 14 1850 4115 7811142 7813407 0.000000e+00 2368.0
33 TraesCS2B01G622500 chr1A 79.649 285 49 6 3841 4118 7799733 7799451 4.040000e-46 196.0
34 TraesCS2B01G622500 chrUn 86.416 1038 120 4 1850 2887 22435518 22436534 0.000000e+00 1116.0
35 TraesCS2B01G622500 chrUn 83.408 898 128 13 2889 3780 22436750 22437632 0.000000e+00 813.0
36 TraesCS2B01G622500 chrUn 80.000 605 85 16 2605 3195 22521337 22521919 1.020000e-111 414.0
37 TraesCS2B01G622500 chrUn 81.466 491 82 8 1852 2334 22421771 22422260 1.330000e-105 394.0
38 TraesCS2B01G622500 chrUn 79.577 426 52 22 4249 4662 266576134 266576536 6.520000e-69 272.0
39 TraesCS2B01G622500 chrUn 78.405 301 39 17 4762 5045 266576828 266577119 6.810000e-39 172.0
40 TraesCS2B01G622500 chr5B 79.820 1110 198 22 2965 4054 644446234 644445131 0.000000e+00 785.0
41 TraesCS2B01G622500 chr5A 79.855 1102 195 22 2965 4045 641215546 641214451 0.000000e+00 780.0
42 TraesCS2B01G622500 chr5D 80.374 856 142 20 3209 4045 513536119 513535271 1.210000e-175 627.0
43 TraesCS2B01G622500 chr7D 77.601 942 195 15 3143 4076 511326202 511327135 1.610000e-154 556.0
44 TraesCS2B01G622500 chr7D 86.667 150 18 2 2967 3115 511325978 511326126 1.140000e-36 165.0
45 TraesCS2B01G622500 chr6D 81.625 517 74 9 1485 1999 456099048 456098551 4.770000e-110 409.0
46 TraesCS2B01G622500 chr6D 73.648 1017 187 67 2969 3934 456790023 456791009 8.260000e-83 318.0
47 TraesCS2B01G622500 chr6A 73.425 1016 195 63 2967 3934 603405273 603406261 1.380000e-80 311.0
48 TraesCS2B01G622500 chr7A 86.000 150 19 2 2967 3115 583872721 583872869 5.300000e-35 159.0
49 TraesCS2B01G622500 chr7B 85.000 80 12 0 1369 1448 665726360 665726281 1.180000e-11 82.4


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 TraesCS2B01G622500 chr2B 796596519 796601632 5113 True 9444.000000 9444 100.000000 1 5114 1 chr2B.!!$R4 5113
1 TraesCS2B01G622500 chr2D 637900507 637906933 6426 False 1163.233333 5666 88.675167 3 5014 6 chr2D.!!$F3 5011
2 TraesCS2B01G622500 chr2D 640024486 640025335 849 False 634.000000 634 80.140000 1865 2720 1 chr2D.!!$F2 855
3 TraesCS2B01G622500 chr2A 761304316 761308909 4593 False 2029.000000 5600 85.740667 696 5113 3 chr2A.!!$F2 4417
4 TraesCS2B01G622500 chr2A 761856008 761856926 918 True 883.000000 883 84.004000 1850 2768 1 chr2A.!!$R3 918
5 TraesCS2B01G622500 chr2A 761896390 761898617 2227 True 732.000000 756 80.342500 1866 4049 2 chr2A.!!$R4 2183
6 TraesCS2B01G622500 chr2A 761520869 761522300 1431 False 663.500000 870 84.113500 2279 3744 2 chr2A.!!$F4 1465
7 TraesCS2B01G622500 chr2A 761621805 761622501 696 True 652.000000 652 83.788000 3049 3735 1 chr2A.!!$R1 686
8 TraesCS2B01G622500 chr2A 761673957 761674528 571 True 326.000000 326 77.778000 2624 3195 1 chr2A.!!$R2 571
9 TraesCS2B01G622500 chr1D 6539962 6542212 2250 True 2392.000000 2392 85.916000 1865 4118 1 chr1D.!!$R1 2253
10 TraesCS2B01G622500 chr1A 7811142 7813407 2265 False 2368.000000 2368 85.595000 1850 4115 1 chr1A.!!$F1 2265
11 TraesCS2B01G622500 chrUn 22435518 22437632 2114 False 964.500000 1116 84.912000 1850 3780 2 chrUn.!!$F3 1930
12 TraesCS2B01G622500 chrUn 22521337 22521919 582 False 414.000000 414 80.000000 2605 3195 1 chrUn.!!$F2 590
13 TraesCS2B01G622500 chrUn 266576134 266577119 985 False 222.000000 272 78.991000 4249 5045 2 chrUn.!!$F4 796
14 TraesCS2B01G622500 chr5B 644445131 644446234 1103 True 785.000000 785 79.820000 2965 4054 1 chr5B.!!$R1 1089
15 TraesCS2B01G622500 chr5A 641214451 641215546 1095 True 780.000000 780 79.855000 2965 4045 1 chr5A.!!$R1 1080
16 TraesCS2B01G622500 chr5D 513535271 513536119 848 True 627.000000 627 80.374000 3209 4045 1 chr5D.!!$R1 836
17 TraesCS2B01G622500 chr7D 511325978 511327135 1157 False 360.500000 556 82.134000 2967 4076 2 chr7D.!!$F1 1109
18 TraesCS2B01G622500 chr6D 456790023 456791009 986 False 318.000000 318 73.648000 2969 3934 1 chr6D.!!$F1 965
19 TraesCS2B01G622500 chr6A 603405273 603406261 988 False 311.000000 311 73.425000 2967 3934 1 chr6A.!!$F1 967

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
174 175 0.108138 CAGCTCCTTTAGGACACCCG 60.108 60.000 0.00 0.0 39.78 5.28 F
783 876 0.319813 CGCCCAGGCCAAAAGAAAAG 60.320 55.000 5.01 0.0 37.98 2.27 F
985 1085 0.839277 CATCCATACCTCACAGCCCA 59.161 55.000 0.00 0.0 0.00 5.36 F
988 1088 1.153369 CATACCTCACAGCCCACGG 60.153 63.158 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1679 1.003597 CTGAGGCAGAAGCAGCTGT 60.004 57.895 16.64 0.0 44.61 4.40 R
1598 1710 1.541368 CTCTTCCCCTTGGTCCCCA 60.541 63.158 0.00 0.0 0.00 4.96 R
2844 2974 1.511464 GTAGTGCGTGGACTCGTCG 60.511 63.158 0.00 0.0 0.00 5.12 R
4127 4699 8.682936 ACTCTATGCAAAAAGAAGAAGAAAGA 57.317 30.769 0.00 0.0 0.00 2.52 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
22 23 5.981088 TCACCAAATCATGCACATACTTT 57.019 34.783 0.00 0.00 0.00 2.66
24 25 5.104374 CACCAAATCATGCACATACTTTCC 58.896 41.667 0.00 0.00 0.00 3.13
43 44 6.774656 ACTTTCCAAGAAAGATCACAGTCATT 59.225 34.615 20.77 0.00 0.00 2.57
86 87 2.158623 ACACAGTTCAGGAATGGCAAGA 60.159 45.455 0.00 0.00 0.00 3.02
97 98 0.396435 ATGGCAAGAACCGAGTGACA 59.604 50.000 0.00 0.00 34.03 3.58
100 101 1.295792 GCAAGAACCGAGTGACACAA 58.704 50.000 8.59 0.00 0.00 3.33
137 138 3.140325 TCTCAACTCACCAAACCATCC 57.860 47.619 0.00 0.00 0.00 3.51
138 139 2.441375 TCTCAACTCACCAAACCATCCA 59.559 45.455 0.00 0.00 0.00 3.41
174 175 0.108138 CAGCTCCTTTAGGACACCCG 60.108 60.000 0.00 0.00 39.78 5.28
175 176 0.544595 AGCTCCTTTAGGACACCCGT 60.545 55.000 0.00 0.00 39.78 5.28
177 178 1.551883 GCTCCTTTAGGACACCCGTTA 59.448 52.381 0.00 0.00 39.78 3.18
180 181 4.439968 CTCCTTTAGGACACCCGTTATTC 58.560 47.826 0.00 0.00 39.78 1.75
181 182 3.839490 TCCTTTAGGACACCCGTTATTCA 59.161 43.478 0.00 0.00 39.78 2.57
186 187 2.304761 AGGACACCCGTTATTCACATGT 59.695 45.455 0.00 0.00 37.58 3.21
190 191 5.181622 GGACACCCGTTATTCACATGTTTTA 59.818 40.000 0.00 0.00 0.00 1.52
194 195 7.435784 ACACCCGTTATTCACATGTTTTAAAAC 59.564 33.333 21.66 21.66 39.33 2.43
264 266 6.254589 CAGGCTTACGTTTTATCTTGAGAGAG 59.745 42.308 0.00 0.00 34.85 3.20
266 268 5.005875 GCTTACGTTTTATCTTGAGAGAGCC 59.994 44.000 0.00 0.00 34.85 4.70
268 270 3.260884 ACGTTTTATCTTGAGAGAGCCCA 59.739 43.478 0.00 0.00 34.85 5.36
270 272 3.914426 TTTATCTTGAGAGAGCCCACC 57.086 47.619 0.00 0.00 34.85 4.61
274 276 2.902608 TCTTGAGAGAGCCCACCTTAA 58.097 47.619 0.00 0.00 0.00 1.85
275 277 2.834549 TCTTGAGAGAGCCCACCTTAAG 59.165 50.000 0.00 0.00 0.00 1.85
285 364 3.330998 AGCCCACCTTAAGTAAAAGCTCT 59.669 43.478 0.97 0.00 0.00 4.09
290 369 5.515008 CCACCTTAAGTAAAAGCTCTTCCCT 60.515 44.000 0.97 0.00 0.00 4.20
303 382 5.432645 AGCTCTTCCCTATTTTTAGTGAGC 58.567 41.667 0.00 0.00 43.01 4.26
304 383 5.045578 AGCTCTTCCCTATTTTTAGTGAGCA 60.046 40.000 12.56 0.00 44.49 4.26
305 384 5.648092 GCTCTTCCCTATTTTTAGTGAGCAA 59.352 40.000 0.00 0.00 42.46 3.91
307 386 7.499232 GCTCTTCCCTATTTTTAGTGAGCAATA 59.501 37.037 0.00 0.00 42.46 1.90
308 387 9.396022 CTCTTCCCTATTTTTAGTGAGCAATAA 57.604 33.333 0.00 0.00 0.00 1.40
309 388 9.920946 TCTTCCCTATTTTTAGTGAGCAATAAT 57.079 29.630 0.00 0.00 0.00 1.28
310 389 9.956720 CTTCCCTATTTTTAGTGAGCAATAATG 57.043 33.333 0.00 0.00 0.00 1.90
362 441 8.794335 AAGTTACATTATTTCCTCTCTCAACC 57.206 34.615 0.00 0.00 0.00 3.77
363 442 7.918076 AGTTACATTATTTCCTCTCTCAACCA 58.082 34.615 0.00 0.00 0.00 3.67
364 443 8.383175 AGTTACATTATTTCCTCTCTCAACCAA 58.617 33.333 0.00 0.00 0.00 3.67
365 444 9.178758 GTTACATTATTTCCTCTCTCAACCAAT 57.821 33.333 0.00 0.00 0.00 3.16
367 446 8.970859 ACATTATTTCCTCTCTCAACCAATAG 57.029 34.615 0.00 0.00 0.00 1.73
368 447 8.772250 ACATTATTTCCTCTCTCAACCAATAGA 58.228 33.333 0.00 0.00 0.00 1.98
369 448 9.790344 CATTATTTCCTCTCTCAACCAATAGAT 57.210 33.333 0.00 0.00 0.00 1.98
370 449 9.790344 ATTATTTCCTCTCTCAACCAATAGATG 57.210 33.333 0.00 0.00 0.00 2.90
371 450 4.679373 TCCTCTCTCAACCAATAGATGC 57.321 45.455 0.00 0.00 0.00 3.91
372 451 4.033009 TCCTCTCTCAACCAATAGATGCA 58.967 43.478 0.00 0.00 0.00 3.96
373 452 4.125703 CCTCTCTCAACCAATAGATGCAC 58.874 47.826 0.00 0.00 0.00 4.57
374 453 4.141756 CCTCTCTCAACCAATAGATGCACT 60.142 45.833 0.00 0.00 0.00 4.40
375 454 4.763073 TCTCTCAACCAATAGATGCACTG 58.237 43.478 0.00 0.00 0.00 3.66
376 455 4.223700 TCTCTCAACCAATAGATGCACTGT 59.776 41.667 0.00 0.00 0.00 3.55
377 456 4.910195 TCTCAACCAATAGATGCACTGTT 58.090 39.130 0.00 0.00 0.00 3.16
385 464 0.593128 AGATGCACTGTTGGCGTTTC 59.407 50.000 0.00 0.00 0.00 2.78
398 477 2.370189 TGGCGTTTCATTCCCCAAATTT 59.630 40.909 0.00 0.00 0.00 1.82
428 507 5.704053 AGTATCCTGACGTTTAAGTTTTGGG 59.296 40.000 0.00 0.00 0.00 4.12
430 509 4.131596 TCCTGACGTTTAAGTTTTGGGAG 58.868 43.478 0.00 0.00 0.00 4.30
461 540 6.160459 AGAGATGTCCCAAGGTGGTAATTTAT 59.840 38.462 0.00 0.00 35.17 1.40
471 550 7.759433 CCAAGGTGGTAATTTATTGTCACAATC 59.241 37.037 6.21 0.00 31.35 2.67
472 551 8.303156 CAAGGTGGTAATTTATTGTCACAATCA 58.697 33.333 6.21 0.00 0.00 2.57
473 552 8.593945 AGGTGGTAATTTATTGTCACAATCAT 57.406 30.769 6.21 0.00 0.00 2.45
474 553 8.686334 AGGTGGTAATTTATTGTCACAATCATC 58.314 33.333 6.21 0.00 0.00 2.92
475 554 7.643764 GGTGGTAATTTATTGTCACAATCATCG 59.356 37.037 6.21 0.00 0.00 3.84
476 555 7.165812 GTGGTAATTTATTGTCACAATCATCGC 59.834 37.037 6.21 0.00 0.00 4.58
477 556 7.148171 TGGTAATTTATTGTCACAATCATCGCA 60.148 33.333 6.21 0.00 0.00 5.10
478 557 7.862372 GGTAATTTATTGTCACAATCATCGCAT 59.138 33.333 6.21 0.00 0.00 4.73
479 558 9.236691 GTAATTTATTGTCACAATCATCGCATT 57.763 29.630 6.21 0.00 0.00 3.56
480 559 7.688478 ATTTATTGTCACAATCATCGCATTG 57.312 32.000 6.21 0.00 39.35 2.82
481 560 4.968812 ATTGTCACAATCATCGCATTGA 57.031 36.364 0.00 0.00 37.24 2.57
482 561 3.745332 TGTCACAATCATCGCATTGAC 57.255 42.857 8.13 0.00 37.24 3.18
483 562 2.419673 TGTCACAATCATCGCATTGACC 59.580 45.455 8.13 0.00 37.24 4.02
484 563 2.419673 GTCACAATCATCGCATTGACCA 59.580 45.455 8.13 0.00 37.24 4.02
485 564 2.679336 TCACAATCATCGCATTGACCAG 59.321 45.455 8.13 0.00 37.24 4.00
486 565 1.402968 ACAATCATCGCATTGACCAGC 59.597 47.619 8.13 0.00 37.24 4.85
487 566 1.674441 CAATCATCGCATTGACCAGCT 59.326 47.619 0.00 0.00 36.03 4.24
488 567 2.874086 CAATCATCGCATTGACCAGCTA 59.126 45.455 0.00 0.00 36.03 3.32
489 568 2.916702 TCATCGCATTGACCAGCTAT 57.083 45.000 0.00 0.00 0.00 2.97
490 569 4.541973 ATCATCGCATTGACCAGCTATA 57.458 40.909 0.00 0.00 0.00 1.31
491 570 3.653344 TCATCGCATTGACCAGCTATAC 58.347 45.455 0.00 0.00 0.00 1.47
492 571 3.069443 TCATCGCATTGACCAGCTATACA 59.931 43.478 0.00 0.00 0.00 2.29
493 572 3.097877 TCGCATTGACCAGCTATACAG 57.902 47.619 0.00 0.00 0.00 2.74
533 612 9.333724 GTTATCCCTTTAATCTCGGTTATTTGA 57.666 33.333 0.00 0.00 0.00 2.69
537 616 8.050325 TCCCTTTAATCTCGGTTATTTGATCAA 58.950 33.333 3.38 3.38 0.00 2.57
596 676 7.201384 GCAGCTAGTATTTTGCAATGAAAAGAC 60.201 37.037 0.00 0.00 37.32 3.01
603 695 9.294030 GTATTTTGCAATGAAAAGACTGGATAG 57.706 33.333 0.00 0.00 35.24 2.08
654 746 8.519799 AGAAGACACTTCACTTTAAAAATGGA 57.480 30.769 12.86 0.00 0.00 3.41
673 765 5.839262 TGGATGAATAGCGCGTATAAAAG 57.161 39.130 8.43 0.00 0.00 2.27
674 766 5.534407 TGGATGAATAGCGCGTATAAAAGA 58.466 37.500 8.43 0.00 0.00 2.52
675 767 6.163476 TGGATGAATAGCGCGTATAAAAGAT 58.837 36.000 8.43 0.00 0.00 2.40
676 768 7.317390 TGGATGAATAGCGCGTATAAAAGATA 58.683 34.615 8.43 0.00 0.00 1.98
677 769 7.274904 TGGATGAATAGCGCGTATAAAAGATAC 59.725 37.037 8.43 0.00 0.00 2.24
680 772 3.360249 AGCGCGTATAAAAGATACGGT 57.640 42.857 8.43 0.00 45.17 4.83
681 773 3.047796 AGCGCGTATAAAAGATACGGTG 58.952 45.455 8.43 7.24 45.17 4.94
682 774 3.044986 GCGCGTATAAAAGATACGGTGA 58.955 45.455 8.43 0.00 45.17 4.02
683 775 3.121563 GCGCGTATAAAAGATACGGTGAC 60.122 47.826 8.43 2.10 45.17 3.67
722 815 0.812412 AATAAACCCCGCCGACGATG 60.812 55.000 0.00 0.00 43.93 3.84
783 876 0.319813 CGCCCAGGCCAAAAGAAAAG 60.320 55.000 5.01 0.00 37.98 2.27
788 881 4.522114 CCCAGGCCAAAAGAAAAGAAAAA 58.478 39.130 5.01 0.00 0.00 1.94
789 882 4.335315 CCCAGGCCAAAAGAAAAGAAAAAC 59.665 41.667 5.01 0.00 0.00 2.43
790 883 5.185454 CCAGGCCAAAAGAAAAGAAAAACT 58.815 37.500 5.01 0.00 0.00 2.66
791 884 6.345298 CCAGGCCAAAAGAAAAGAAAAACTA 58.655 36.000 5.01 0.00 0.00 2.24
792 885 6.257849 CCAGGCCAAAAGAAAAGAAAAACTAC 59.742 38.462 5.01 0.00 0.00 2.73
793 886 7.041721 CAGGCCAAAAGAAAAGAAAAACTACT 58.958 34.615 5.01 0.00 0.00 2.57
794 887 8.194769 CAGGCCAAAAGAAAAGAAAAACTACTA 58.805 33.333 5.01 0.00 0.00 1.82
795 888 8.414003 AGGCCAAAAGAAAAGAAAAACTACTAG 58.586 33.333 5.01 0.00 0.00 2.57
832 925 8.365647 AGATTATCGGTATTATAAATAGCGGGG 58.634 37.037 23.20 4.46 43.25 5.73
878 971 4.127171 TCGTCTTCACTTCTTTCCCAAAG 58.873 43.478 0.00 0.00 39.88 2.77
896 989 1.377333 GCAGAGCACCTACCAACCC 60.377 63.158 0.00 0.00 0.00 4.11
955 1055 1.536676 CAAACCCCGGCCATCCTAT 59.463 57.895 2.24 0.00 0.00 2.57
985 1085 0.839277 CATCCATACCTCACAGCCCA 59.161 55.000 0.00 0.00 0.00 5.36
988 1088 1.153369 CATACCTCACAGCCCACGG 60.153 63.158 0.00 0.00 0.00 4.94
989 1089 1.305802 ATACCTCACAGCCCACGGA 60.306 57.895 0.00 0.00 0.00 4.69
992 1092 4.742201 CTCACAGCCCACGGACGG 62.742 72.222 0.00 0.00 0.00 4.79
1245 1345 1.885388 CCTCAACGACCACAACGCA 60.885 57.895 0.00 0.00 0.00 5.24
1344 1444 3.121030 CGCTTCCCGCTGGACAAG 61.121 66.667 0.00 0.00 41.57 3.16
1396 1496 3.597728 CGCTCCGGCTCTACCTCC 61.598 72.222 0.00 0.00 35.61 4.30
1494 1606 2.282674 CAGCAGCAGCCTTCCCAA 60.283 61.111 0.00 0.00 43.56 4.12
1554 1666 3.453679 GTCTTCTCCGGCGAGGCT 61.454 66.667 9.30 0.00 40.77 4.58
1555 1667 2.680352 TCTTCTCCGGCGAGGCTT 60.680 61.111 9.30 0.00 40.77 4.35
1653 1765 3.711814 TTCCGCTCCATTCCGGCA 61.712 61.111 0.00 0.00 44.01 5.69
1899 2014 1.667724 CCGATGTCGTACCTCTACGTT 59.332 52.381 0.00 0.00 45.14 3.99
2205 2320 2.507102 CAGTGGTACAGCCTCGCG 60.507 66.667 0.00 0.00 41.80 5.87
2691 2820 1.949257 CAACGACCTTGCCAAGTCC 59.051 57.895 3.37 0.00 0.00 3.85
2844 2974 3.741476 ACGGCGTACCACGTCCTC 61.741 66.667 12.58 0.00 44.43 3.71
2925 3402 4.194720 ATCGGCGTGCTCGAGGTC 62.195 66.667 15.58 0.00 40.09 3.85
3891 4463 4.113815 CTGGCGATGCAGGGGGAA 62.114 66.667 0.00 0.00 0.00 3.97
4118 4690 3.434167 GGTGACATGCTCCTATGACCATT 60.434 47.826 0.00 0.00 29.75 3.16
4119 4691 4.202357 GGTGACATGCTCCTATGACCATTA 60.202 45.833 0.00 0.00 29.75 1.90
4120 4692 5.513788 GGTGACATGCTCCTATGACCATTAT 60.514 44.000 0.00 0.00 29.75 1.28
4121 4693 5.410746 GTGACATGCTCCTATGACCATTATG 59.589 44.000 0.00 0.00 0.00 1.90
4123 4695 6.269769 TGACATGCTCCTATGACCATTATGTA 59.730 38.462 0.00 0.00 0.00 2.29
4124 4696 7.078249 ACATGCTCCTATGACCATTATGTAA 57.922 36.000 0.00 0.00 0.00 2.41
4126 4698 7.998383 ACATGCTCCTATGACCATTATGTAAAA 59.002 33.333 0.00 0.00 0.00 1.52
4127 4699 9.017509 CATGCTCCTATGACCATTATGTAAAAT 57.982 33.333 0.00 0.00 0.00 1.82
4128 4700 8.621532 TGCTCCTATGACCATTATGTAAAATC 57.378 34.615 0.00 0.00 0.00 2.17
4129 4701 8.439971 TGCTCCTATGACCATTATGTAAAATCT 58.560 33.333 0.00 0.00 0.00 2.40
4201 5098 3.187227 ACACTGCACAATCGATCACTTTC 59.813 43.478 0.00 0.00 0.00 2.62
4226 5123 7.763071 TCTGTTTGTGTGATCAGAGAATCATAG 59.237 37.037 12.16 3.78 37.93 2.23
4290 5187 3.679389 TGAACATTCAGAAGCTTCCTCC 58.321 45.455 22.81 0.00 32.50 4.30
4292 5189 1.988107 ACATTCAGAAGCTTCCTCCCA 59.012 47.619 22.81 3.48 0.00 4.37
4293 5190 2.376518 ACATTCAGAAGCTTCCTCCCAA 59.623 45.455 22.81 8.91 0.00 4.12
4294 5191 3.011032 ACATTCAGAAGCTTCCTCCCAAT 59.989 43.478 22.81 10.69 0.00 3.16
4295 5192 3.356529 TTCAGAAGCTTCCTCCCAATC 57.643 47.619 22.81 0.00 0.00 2.67
4296 5193 2.555664 TCAGAAGCTTCCTCCCAATCT 58.444 47.619 22.81 0.00 0.00 2.40
4297 5194 2.503356 TCAGAAGCTTCCTCCCAATCTC 59.497 50.000 22.81 0.00 0.00 2.75
4298 5195 2.238144 CAGAAGCTTCCTCCCAATCTCA 59.762 50.000 22.81 0.00 0.00 3.27
4299 5196 2.915604 AGAAGCTTCCTCCCAATCTCAA 59.084 45.455 22.81 0.00 0.00 3.02
4300 5197 3.526841 AGAAGCTTCCTCCCAATCTCAAT 59.473 43.478 22.81 0.00 0.00 2.57
4389 5311 4.065088 CCACTACATTCCATTCCATACCG 58.935 47.826 0.00 0.00 0.00 4.02
4391 5313 4.511454 CACTACATTCCATTCCATACCGTG 59.489 45.833 0.00 0.00 0.00 4.94
4552 5513 5.041940 GTCGACCAAGCTAACGAGAATAAT 58.958 41.667 3.51 0.00 35.52 1.28
4602 5566 1.841663 CTCCGGCGACTGTTGTTTGG 61.842 60.000 9.30 0.00 0.00 3.28
4607 5571 0.592247 GCGACTGTTGTTTGGCACAG 60.592 55.000 0.94 0.94 42.39 3.66
4608 5572 0.732571 CGACTGTTGTTTGGCACAGT 59.267 50.000 7.34 7.34 42.39 3.55
4684 5653 7.366847 AGCATCAAGGTGAAGTGTATATACT 57.633 36.000 13.89 0.00 0.00 2.12
4685 5654 8.478775 AGCATCAAGGTGAAGTGTATATACTA 57.521 34.615 13.89 0.00 0.00 1.82
4686 5655 8.361139 AGCATCAAGGTGAAGTGTATATACTAC 58.639 37.037 13.89 10.05 0.00 2.73
4717 5686 9.383519 CATTCTAAAAGTAGCTTGTCCTAATCA 57.616 33.333 0.00 0.00 0.00 2.57
4741 5821 4.433615 TGTCCGAATTAGCATGTCTCTTC 58.566 43.478 0.00 0.00 0.00 2.87
4746 5974 6.092670 TCCGAATTAGCATGTCTCTTCTTTTG 59.907 38.462 0.00 0.00 0.00 2.44
4749 5977 7.269937 CGAATTAGCATGTCTCTTCTTTTGTTG 59.730 37.037 0.00 0.00 0.00 3.33
4839 7016 5.949354 TGTCCACTCGGATTATCCAAAATTT 59.051 36.000 12.17 0.00 45.33 1.82
4844 7021 8.345565 CCACTCGGATTATCCAAAATTTTAGAG 58.654 37.037 12.17 8.43 35.91 2.43
4853 7030 5.772521 TCCAAAATTTTAGAGTGCTCAAGC 58.227 37.500 2.44 0.00 42.50 4.01
4854 7031 5.536161 TCCAAAATTTTAGAGTGCTCAAGCT 59.464 36.000 2.44 0.00 42.66 3.74
4855 7032 5.860716 CCAAAATTTTAGAGTGCTCAAGCTC 59.139 40.000 2.44 0.00 42.66 4.09
4857 7034 6.639632 AAATTTTAGAGTGCTCAAGCTCAA 57.360 33.333 3.32 0.00 42.66 3.02
4858 7035 5.876612 ATTTTAGAGTGCTCAAGCTCAAG 57.123 39.130 3.32 0.00 42.66 3.02
4859 7036 4.342862 TTTAGAGTGCTCAAGCTCAAGT 57.657 40.909 3.32 0.00 42.66 3.16
4860 7037 5.468540 TTTAGAGTGCTCAAGCTCAAGTA 57.531 39.130 3.32 0.00 42.66 2.24
4861 7038 5.468540 TTAGAGTGCTCAAGCTCAAGTAA 57.531 39.130 3.32 0.00 42.66 2.24
4862 7039 3.658709 AGAGTGCTCAAGCTCAAGTAAC 58.341 45.455 3.32 0.00 42.66 2.50
4953 7158 6.690530 CATTGGCCATCTTTTTCTTTCACTA 58.309 36.000 6.09 0.00 0.00 2.74
4968 7179 9.773328 TTTCTTTCACTAATTTCATAGATTGCG 57.227 29.630 0.00 0.00 0.00 4.85
4969 7180 7.409697 TCTTTCACTAATTTCATAGATTGCGC 58.590 34.615 0.00 0.00 0.00 6.09
4970 7181 6.676237 TTCACTAATTTCATAGATTGCGCA 57.324 33.333 5.66 5.66 0.00 6.09
5001 7222 5.341617 CATTTTCTAGGTAGGTCAGACGTC 58.658 45.833 7.70 7.70 0.00 4.34
5030 7251 1.888215 TTGCAGTGCAAGAGAGGAAG 58.112 50.000 26.36 0.00 43.99 3.46
5037 7258 1.352352 TGCAAGAGAGGAAGGGAAAGG 59.648 52.381 0.00 0.00 0.00 3.11
5052 7273 2.403259 GAAAGGTTGTTTGATTGGGCG 58.597 47.619 0.00 0.00 0.00 6.13
5057 7278 1.035923 TTGTTTGATTGGGCGCTCAA 58.964 45.000 27.44 27.44 0.00 3.02
5062 7283 4.247781 ATTGGGCGCTCAATCAGG 57.752 55.556 29.57 0.00 32.42 3.86
5079 7300 5.871396 ATCAGGCCGTCGGAATATATTAT 57.129 39.130 17.49 0.00 0.00 1.28
5081 7302 6.045072 TCAGGCCGTCGGAATATATTATTT 57.955 37.500 17.49 0.00 0.00 1.40
5082 7303 5.872617 TCAGGCCGTCGGAATATATTATTTG 59.127 40.000 17.49 0.00 0.00 2.32
5091 7312 9.234384 GTCGGAATATATTATTTGATCGATCGT 57.766 33.333 20.03 11.23 0.00 3.73
5102 7323 3.431856 TGATCGATCGTACGTTGGAAAG 58.568 45.455 20.03 1.68 34.70 2.62
5105 7326 1.576246 CGATCGTACGTTGGAAAGACG 59.424 52.381 16.05 0.00 45.46 4.18
5113 7334 0.586802 GTTGGAAAGACGGTGAGTGC 59.413 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.105797 GGAAAGTATGTGCATGATTTGGTGA 60.106 40.000 0.00 0.00 0.00 4.02
1 2 5.104374 GGAAAGTATGTGCATGATTTGGTG 58.896 41.667 0.00 0.00 0.00 4.17
22 23 4.456911 GCAATGACTGTGATCTTTCTTGGA 59.543 41.667 0.00 0.00 0.00 3.53
24 25 5.152097 GTGCAATGACTGTGATCTTTCTTG 58.848 41.667 0.00 0.00 0.00 3.02
43 44 1.338960 TGATTGCAGATTCTCGGTGCA 60.339 47.619 0.00 0.00 45.30 4.57
70 71 1.200020 CGGTTCTTGCCATTCCTGAAC 59.800 52.381 0.00 0.00 37.04 3.18
86 87 2.980568 TGACTTTTGTGTCACTCGGTT 58.019 42.857 4.27 0.00 41.43 4.44
97 98 7.060383 TGAGAAGAGAAGAGATGACTTTTGT 57.940 36.000 0.00 0.00 0.00 2.83
100 101 7.015098 TGAGTTGAGAAGAGAAGAGATGACTTT 59.985 37.037 0.00 0.00 0.00 2.66
154 155 1.276622 GGGTGTCCTAAAGGAGCTGA 58.723 55.000 0.00 0.00 46.49 4.26
156 157 0.544595 ACGGGTGTCCTAAAGGAGCT 60.545 55.000 0.00 0.00 46.49 4.09
194 195 9.748708 TTCCAAAAGAAATTATGTTCTTCTGTG 57.251 29.630 0.95 1.44 45.09 3.66
217 219 9.860898 GCCTGGAAATATTTATCATAACATTCC 57.139 33.333 0.00 0.00 35.50 3.01
231 233 8.747538 AGATAAAACGTAAGCCTGGAAATATT 57.252 30.769 0.00 0.00 45.62 1.28
236 238 5.553123 TCAAGATAAAACGTAAGCCTGGAA 58.447 37.500 0.00 0.00 45.62 3.53
242 244 5.005875 GGCTCTCTCAAGATAAAACGTAAGC 59.994 44.000 0.00 0.00 45.62 3.09
247 249 3.619038 GTGGGCTCTCTCAAGATAAAACG 59.381 47.826 0.00 0.00 0.00 3.60
253 255 1.963985 AAGGTGGGCTCTCTCAAGAT 58.036 50.000 0.00 0.00 0.00 2.40
255 257 2.569404 ACTTAAGGTGGGCTCTCTCAAG 59.431 50.000 7.53 0.00 0.00 3.02
264 266 3.687125 AGAGCTTTTACTTAAGGTGGGC 58.313 45.455 7.53 4.73 36.09 5.36
266 268 4.700692 GGGAAGAGCTTTTACTTAAGGTGG 59.299 45.833 7.53 0.00 36.09 4.61
268 270 5.844773 AGGGAAGAGCTTTTACTTAAGGT 57.155 39.130 7.53 0.00 38.48 3.50
274 276 9.232473 CACTAAAAATAGGGAAGAGCTTTTACT 57.768 33.333 0.00 0.00 0.00 2.24
275 277 9.227777 TCACTAAAAATAGGGAAGAGCTTTTAC 57.772 33.333 0.00 0.00 0.00 2.01
285 364 8.413229 GCATTATTGCTCACTAAAAATAGGGAA 58.587 33.333 2.33 0.00 45.77 3.97
337 416 8.383175 TGGTTGAGAGAGGAAATAATGTAACTT 58.617 33.333 0.00 0.00 0.00 2.66
338 417 7.918076 TGGTTGAGAGAGGAAATAATGTAACT 58.082 34.615 0.00 0.00 0.00 2.24
339 418 8.561738 TTGGTTGAGAGAGGAAATAATGTAAC 57.438 34.615 0.00 0.00 0.00 2.50
343 422 9.790344 ATCTATTGGTTGAGAGAGGAAATAATG 57.210 33.333 0.00 0.00 0.00 1.90
344 423 9.790344 CATCTATTGGTTGAGAGAGGAAATAAT 57.210 33.333 0.00 0.00 0.00 1.28
346 425 7.147497 TGCATCTATTGGTTGAGAGAGGAAATA 60.147 37.037 0.00 0.00 0.00 1.40
347 426 6.060788 GCATCTATTGGTTGAGAGAGGAAAT 58.939 40.000 0.00 0.00 0.00 2.17
348 427 5.045651 TGCATCTATTGGTTGAGAGAGGAAA 60.046 40.000 0.00 0.00 0.00 3.13
349 428 4.471025 TGCATCTATTGGTTGAGAGAGGAA 59.529 41.667 0.00 0.00 0.00 3.36
350 429 4.033009 TGCATCTATTGGTTGAGAGAGGA 58.967 43.478 0.00 0.00 0.00 3.71
351 430 4.125703 GTGCATCTATTGGTTGAGAGAGG 58.874 47.826 0.00 0.00 0.00 3.69
352 431 4.809958 CAGTGCATCTATTGGTTGAGAGAG 59.190 45.833 0.00 0.00 0.00 3.20
353 432 4.223700 ACAGTGCATCTATTGGTTGAGAGA 59.776 41.667 0.00 0.00 0.00 3.10
354 433 4.511527 ACAGTGCATCTATTGGTTGAGAG 58.488 43.478 0.00 0.00 0.00 3.20
355 434 4.558226 ACAGTGCATCTATTGGTTGAGA 57.442 40.909 0.00 0.00 0.00 3.27
356 435 4.142534 CCAACAGTGCATCTATTGGTTGAG 60.143 45.833 14.53 5.49 43.53 3.02
357 436 3.758023 CCAACAGTGCATCTATTGGTTGA 59.242 43.478 14.53 0.00 43.53 3.18
358 437 4.100707 CCAACAGTGCATCTATTGGTTG 57.899 45.455 14.53 11.42 43.53 3.77
362 441 1.739466 ACGCCAACAGTGCATCTATTG 59.261 47.619 0.00 0.00 31.07 1.90
363 442 2.113860 ACGCCAACAGTGCATCTATT 57.886 45.000 0.00 0.00 0.00 1.73
364 443 2.113860 AACGCCAACAGTGCATCTAT 57.886 45.000 0.00 0.00 0.00 1.98
365 444 1.804151 GAAACGCCAACAGTGCATCTA 59.196 47.619 0.00 0.00 0.00 1.98
366 445 0.593128 GAAACGCCAACAGTGCATCT 59.407 50.000 0.00 0.00 0.00 2.90
367 446 0.310543 TGAAACGCCAACAGTGCATC 59.689 50.000 0.00 0.00 0.00 3.91
368 447 0.961019 ATGAAACGCCAACAGTGCAT 59.039 45.000 0.00 0.00 0.00 3.96
369 448 0.743688 AATGAAACGCCAACAGTGCA 59.256 45.000 0.00 0.00 0.00 4.57
370 449 1.408422 GAATGAAACGCCAACAGTGC 58.592 50.000 0.00 0.00 0.00 4.40
371 450 1.335872 GGGAATGAAACGCCAACAGTG 60.336 52.381 0.00 0.00 0.00 3.66
372 451 0.958822 GGGAATGAAACGCCAACAGT 59.041 50.000 0.00 0.00 0.00 3.55
373 452 0.243636 GGGGAATGAAACGCCAACAG 59.756 55.000 0.00 0.00 39.61 3.16
374 453 0.468214 TGGGGAATGAAACGCCAACA 60.468 50.000 0.00 0.00 44.96 3.33
375 454 2.346597 TGGGGAATGAAACGCCAAC 58.653 52.632 0.00 0.00 44.96 3.77
376 455 4.932060 TGGGGAATGAAACGCCAA 57.068 50.000 0.00 0.00 44.96 4.52
377 456 1.638529 ATTTGGGGAATGAAACGCCA 58.361 45.000 0.00 0.00 45.94 5.69
405 484 5.702209 TCCCAAAACTTAAACGTCAGGATAC 59.298 40.000 0.00 0.00 0.00 2.24
406 485 5.867330 TCCCAAAACTTAAACGTCAGGATA 58.133 37.500 0.00 0.00 0.00 2.59
407 486 4.721132 TCCCAAAACTTAAACGTCAGGAT 58.279 39.130 0.00 0.00 0.00 3.24
412 491 2.555325 CCCCTCCCAAAACTTAAACGTC 59.445 50.000 0.00 0.00 0.00 4.34
414 493 1.271379 GCCCCTCCCAAAACTTAAACG 59.729 52.381 0.00 0.00 0.00 3.60
415 494 2.605257 AGCCCCTCCCAAAACTTAAAC 58.395 47.619 0.00 0.00 0.00 2.01
421 500 1.286248 TCTCTAGCCCCTCCCAAAAC 58.714 55.000 0.00 0.00 0.00 2.43
428 507 0.105453 TGGGACATCTCTAGCCCCTC 60.105 60.000 0.00 0.00 39.93 4.30
430 509 0.761802 CTTGGGACATCTCTAGCCCC 59.238 60.000 0.00 0.00 39.93 5.80
461 540 3.119884 GGTCAATGCGATGATTGTGACAA 60.120 43.478 0.00 0.00 37.66 3.18
471 550 3.392882 TGTATAGCTGGTCAATGCGATG 58.607 45.455 0.00 0.00 0.00 3.84
472 551 3.657634 CTGTATAGCTGGTCAATGCGAT 58.342 45.455 0.00 0.00 0.00 4.58
473 552 2.803133 GCTGTATAGCTGGTCAATGCGA 60.803 50.000 3.91 0.00 46.57 5.10
474 553 1.528586 GCTGTATAGCTGGTCAATGCG 59.471 52.381 3.91 0.00 46.57 4.73
488 567 9.196139 GGGATAACTAGAGAATCATAGCTGTAT 57.804 37.037 0.00 0.00 37.82 2.29
489 568 8.394822 AGGGATAACTAGAGAATCATAGCTGTA 58.605 37.037 0.00 0.00 37.82 2.74
490 569 7.245292 AGGGATAACTAGAGAATCATAGCTGT 58.755 38.462 0.00 0.00 37.82 4.40
491 570 7.716799 AGGGATAACTAGAGAATCATAGCTG 57.283 40.000 0.00 0.00 37.82 4.24
492 571 8.734593 AAAGGGATAACTAGAGAATCATAGCT 57.265 34.615 0.00 0.00 37.82 3.32
498 577 9.849166 CGAGATTAAAGGGATAACTAGAGAATC 57.151 37.037 0.00 0.00 0.00 2.52
499 578 8.808092 CCGAGATTAAAGGGATAACTAGAGAAT 58.192 37.037 0.00 0.00 0.00 2.40
500 579 7.783596 ACCGAGATTAAAGGGATAACTAGAGAA 59.216 37.037 0.00 0.00 0.00 2.87
501 580 7.296098 ACCGAGATTAAAGGGATAACTAGAGA 58.704 38.462 0.00 0.00 0.00 3.10
502 581 7.527568 ACCGAGATTAAAGGGATAACTAGAG 57.472 40.000 0.00 0.00 0.00 2.43
503 582 7.909485 AACCGAGATTAAAGGGATAACTAGA 57.091 36.000 0.00 0.00 0.00 2.43
507 586 9.333724 TCAAATAACCGAGATTAAAGGGATAAC 57.666 33.333 0.00 0.00 0.00 1.89
519 598 9.613428 TCACTTTATTGATCAAATAACCGAGAT 57.387 29.630 13.09 0.00 39.84 2.75
523 602 9.277565 CACTTCACTTTATTGATCAAATAACCG 57.722 33.333 13.09 7.92 39.84 4.44
531 610 5.705441 GGGACACACTTCACTTTATTGATCA 59.295 40.000 0.00 0.00 0.00 2.92
533 612 5.010282 GGGGACACACTTCACTTTATTGAT 58.990 41.667 0.00 0.00 0.00 2.57
537 616 2.986728 AGGGGGACACACTTCACTTTAT 59.013 45.455 0.00 0.00 0.00 1.40
566 645 7.514784 TCATTGCAAAATACTAGCTGCATAT 57.485 32.000 1.71 0.00 43.83 1.78
577 657 9.294030 CTATCCAGTCTTTTCATTGCAAAATAC 57.706 33.333 1.71 0.00 0.00 1.89
578 658 9.241919 TCTATCCAGTCTTTTCATTGCAAAATA 57.758 29.630 1.71 0.00 0.00 1.40
579 659 8.125978 TCTATCCAGTCTTTTCATTGCAAAAT 57.874 30.769 1.71 0.00 0.00 1.82
580 660 7.523293 TCTATCCAGTCTTTTCATTGCAAAA 57.477 32.000 1.71 0.00 0.00 2.44
581 661 7.523293 TTCTATCCAGTCTTTTCATTGCAAA 57.477 32.000 1.71 0.00 0.00 3.68
596 676 7.540299 AGAAGAACGTCTAACTTTCTATCCAG 58.460 38.462 0.00 0.00 35.93 3.86
603 695 7.230466 TGTTGAAGAAGAACGTCTAACTTTC 57.770 36.000 0.00 0.00 0.00 2.62
633 725 9.696917 ATTCATCCATTTTTAAAGTGAAGTGTC 57.303 29.630 1.70 0.00 0.00 3.67
654 746 6.252869 CCGTATCTTTTATACGCGCTATTCAT 59.747 38.462 5.73 0.00 44.10 2.57
673 765 1.870901 GTCACGCCGTCACCGTATC 60.871 63.158 0.00 0.00 37.12 2.24
674 766 2.180017 GTCACGCCGTCACCGTAT 59.820 61.111 0.00 0.00 37.12 3.06
675 767 4.388080 CGTCACGCCGTCACCGTA 62.388 66.667 0.00 0.00 37.12 4.02
684 776 4.322385 GTTGGTTGCCGTCACGCC 62.322 66.667 0.00 0.00 0.00 5.68
685 777 4.322385 GGTTGGTTGCCGTCACGC 62.322 66.667 0.00 0.00 0.00 5.34
686 778 1.791103 ATTGGTTGGTTGCCGTCACG 61.791 55.000 0.00 0.00 0.00 4.35
722 815 1.372623 GGTCAGACCAACGTCGACC 60.373 63.158 15.43 14.12 45.98 4.79
729 822 2.032071 CCCACGGGTCAGACCAAC 59.968 66.667 21.75 3.82 41.02 3.77
783 876 4.648651 TGAGGGGTTGCTAGTAGTTTTTC 58.351 43.478 0.00 0.00 0.00 2.29
788 881 3.185880 TCTTGAGGGGTTGCTAGTAGT 57.814 47.619 0.00 0.00 0.00 2.73
789 882 4.762289 AATCTTGAGGGGTTGCTAGTAG 57.238 45.455 0.00 0.00 0.00 2.57
790 883 5.010719 CGATAATCTTGAGGGGTTGCTAGTA 59.989 44.000 0.00 0.00 0.00 1.82
791 884 4.202264 CGATAATCTTGAGGGGTTGCTAGT 60.202 45.833 0.00 0.00 0.00 2.57
792 885 4.310769 CGATAATCTTGAGGGGTTGCTAG 58.689 47.826 0.00 0.00 0.00 3.42
793 886 3.071023 CCGATAATCTTGAGGGGTTGCTA 59.929 47.826 0.00 0.00 0.00 3.49
794 887 2.158755 CCGATAATCTTGAGGGGTTGCT 60.159 50.000 0.00 0.00 0.00 3.91
795 888 2.222027 CCGATAATCTTGAGGGGTTGC 58.778 52.381 0.00 0.00 0.00 4.17
828 921 0.173935 TGTGTCGTAATAGTGCCCCG 59.826 55.000 0.00 0.00 0.00 5.73
832 925 0.293723 CGCGTGTGTCGTAATAGTGC 59.706 55.000 0.00 0.00 42.13 4.40
878 971 1.377333 GGGTTGGTAGGTGCTCTGC 60.377 63.158 0.00 0.00 0.00 4.26
896 989 1.153529 CTCTGCTCTGCTCTGGCTG 60.154 63.158 0.00 0.00 39.59 4.85
955 1055 6.126911 TGTGAGGTATGGATGTTTATGTGCTA 60.127 38.462 0.00 0.00 0.00 3.49
985 1085 1.798234 TTCATCGTGTCACCGTCCGT 61.798 55.000 0.00 0.00 0.00 4.69
988 1088 0.388649 AGCTTCATCGTGTCACCGTC 60.389 55.000 0.00 0.00 0.00 4.79
989 1089 0.033504 AAGCTTCATCGTGTCACCGT 59.966 50.000 0.00 0.00 0.00 4.83
992 1092 0.166814 GGCAAGCTTCATCGTGTCAC 59.833 55.000 0.00 0.00 0.00 3.67
993 1093 1.291184 CGGCAAGCTTCATCGTGTCA 61.291 55.000 0.00 0.00 0.00 3.58
995 1095 1.301716 ACGGCAAGCTTCATCGTGT 60.302 52.632 14.74 0.00 32.60 4.49
1057 1157 2.379634 CGAACGCGTTGCATGAGGA 61.380 57.895 31.89 0.00 0.00 3.71
1344 1444 2.791868 GCGGGAGAAGAGCCCTCTC 61.792 68.421 0.00 0.00 43.72 3.20
1509 1621 1.271840 CCATCCTCTCGGGGTCCAAA 61.272 60.000 0.00 0.00 35.33 3.28
1567 1679 1.003597 CTGAGGCAGAAGCAGCTGT 60.004 57.895 16.64 0.00 44.61 4.40
1598 1710 1.541368 CTCTTCCCCTTGGTCCCCA 60.541 63.158 0.00 0.00 0.00 4.96
1599 1711 2.985116 GCTCTTCCCCTTGGTCCCC 61.985 68.421 0.00 0.00 0.00 4.81
1601 1713 2.269241 CGCTCTTCCCCTTGGTCC 59.731 66.667 0.00 0.00 0.00 4.46
1899 2014 4.764336 CGCGCCTTGACGACGGTA 62.764 66.667 0.00 0.00 34.06 4.02
2589 2718 1.592223 GACCTTCTCCTCCACGGTG 59.408 63.158 0.00 0.00 0.00 4.94
2841 2971 3.733960 TGCGTGGACTCGTCGAGG 61.734 66.667 25.25 8.93 33.35 4.63
2844 2974 1.511464 GTAGTGCGTGGACTCGTCG 60.511 63.158 0.00 0.00 0.00 5.12
4120 4692 9.868277 TGCAAAAAGAAGAAGAAAGATTTTACA 57.132 25.926 0.00 0.00 0.00 2.41
4126 4698 9.294614 ACTCTATGCAAAAAGAAGAAGAAAGAT 57.705 29.630 0.00 0.00 0.00 2.40
4127 4699 8.682936 ACTCTATGCAAAAAGAAGAAGAAAGA 57.317 30.769 0.00 0.00 0.00 2.52
4133 4705 9.410556 GCAATTAACTCTATGCAAAAAGAAGAA 57.589 29.630 0.00 0.00 38.63 2.52
4184 5071 4.410492 AACAGAAAGTGATCGATTGTGC 57.590 40.909 0.00 0.00 0.00 4.57
4201 5098 6.738832 ATGATTCTCTGATCACACAAACAG 57.261 37.500 0.00 0.00 38.75 3.16
4241 5138 4.163427 TCTATCCACTCCATTCCATCCTC 58.837 47.826 0.00 0.00 0.00 3.71
4245 5142 6.865834 GAGTATCTATCCACTCCATTCCAT 57.134 41.667 0.00 0.00 36.06 3.41
4294 5191 9.862149 GTTCCCTCCCTTTAATTATTATTGAGA 57.138 33.333 0.00 0.00 0.00 3.27
4295 5192 9.640952 TGTTCCCTCCCTTTAATTATTATTGAG 57.359 33.333 0.00 0.00 0.00 3.02
4296 5193 9.998752 TTGTTCCCTCCCTTTAATTATTATTGA 57.001 29.630 0.00 0.00 0.00 2.57
4299 5196 8.924303 GCTTTGTTCCCTCCCTTTAATTATTAT 58.076 33.333 0.00 0.00 0.00 1.28
4300 5197 7.067737 CGCTTTGTTCCCTCCCTTTAATTATTA 59.932 37.037 0.00 0.00 0.00 0.98
4316 5232 1.153958 GCATCTGCCGCTTTGTTCC 60.154 57.895 0.00 0.00 34.31 3.62
4389 5311 2.051345 CCGCACCGACAAAAGCAC 60.051 61.111 0.00 0.00 0.00 4.40
4391 5313 2.051345 CACCGCACCGACAAAAGC 60.051 61.111 0.00 0.00 0.00 3.51
4474 5402 8.887717 CAAAGAAGAAGAAGAAGAAGAAGAACA 58.112 33.333 0.00 0.00 0.00 3.18
4566 5527 4.836825 CCGGAGATGGAATACAATAGCAT 58.163 43.478 0.00 0.00 0.00 3.79
4602 5566 7.816513 TGAATGAATATCTATCTAGCACTGTGC 59.183 37.037 24.59 24.59 45.46 4.57
4638 5604 5.240403 GCTGCTTTCTGAATAAGATAAGGGG 59.760 44.000 0.00 0.00 33.93 4.79
4681 5650 8.218338 AGCTACTTTTAGAATGCTACGTAGTA 57.782 34.615 22.98 19.62 45.11 1.82
4683 5652 7.488471 ACAAGCTACTTTTAGAATGCTACGTAG 59.512 37.037 18.47 18.47 31.70 3.51
4684 5653 7.318141 ACAAGCTACTTTTAGAATGCTACGTA 58.682 34.615 0.00 0.00 0.00 3.57
4685 5654 6.164176 ACAAGCTACTTTTAGAATGCTACGT 58.836 36.000 0.00 0.00 0.00 3.57
4686 5655 6.237861 GGACAAGCTACTTTTAGAATGCTACG 60.238 42.308 0.00 0.00 0.00 3.51
4717 5686 5.028549 AGAGACATGCTAATTCGGACAAT 57.971 39.130 0.00 0.00 0.00 2.71
4741 5821 5.745294 CACTTCACCACTTGATCAACAAAAG 59.255 40.000 3.38 5.58 38.08 2.27
4746 5974 2.554032 CCCACTTCACCACTTGATCAAC 59.446 50.000 3.38 0.00 32.84 3.18
4749 5977 1.168714 GCCCACTTCACCACTTGATC 58.831 55.000 0.00 0.00 32.84 2.92
4839 7016 5.221441 TGTTACTTGAGCTTGAGCACTCTAA 60.221 40.000 5.70 0.00 45.16 2.10
4844 7021 3.134458 ACTGTTACTTGAGCTTGAGCAC 58.866 45.455 5.70 0.00 45.16 4.40
4853 7030 7.171678 ACAAAGCTAGCTTTACTGTTACTTGAG 59.828 37.037 35.73 22.63 43.56 3.02
4854 7031 6.990349 ACAAAGCTAGCTTTACTGTTACTTGA 59.010 34.615 35.73 0.00 43.56 3.02
4855 7032 7.190920 ACAAAGCTAGCTTTACTGTTACTTG 57.809 36.000 35.73 24.19 43.56 3.16
4857 7034 7.813627 GTCTACAAAGCTAGCTTTACTGTTACT 59.186 37.037 35.73 13.77 43.56 2.24
4858 7035 7.597743 TGTCTACAAAGCTAGCTTTACTGTTAC 59.402 37.037 35.73 28.04 43.56 2.50
4859 7036 7.663827 TGTCTACAAAGCTAGCTTTACTGTTA 58.336 34.615 35.73 21.05 43.56 2.41
4860 7037 6.522054 TGTCTACAAAGCTAGCTTTACTGTT 58.478 36.000 35.73 21.56 43.56 3.16
4861 7038 6.097915 TGTCTACAAAGCTAGCTTTACTGT 57.902 37.500 35.73 31.22 43.56 3.55
4862 7039 6.813649 TGATGTCTACAAAGCTAGCTTTACTG 59.186 38.462 35.73 27.96 43.56 2.74
4953 7158 3.645884 GCCATGCGCAATCTATGAAATT 58.354 40.909 17.11 0.00 37.47 1.82
4969 7180 4.022589 CCTACCTAGAAAATGCATGCCATG 60.023 45.833 16.68 0.00 33.49 3.66
4970 7181 4.147321 CCTACCTAGAAAATGCATGCCAT 58.853 43.478 16.68 6.01 35.06 4.40
5001 7222 0.534877 TGCACTGCAACCACCTACTG 60.535 55.000 0.00 0.00 34.76 2.74
5023 7244 3.204382 TCAAACAACCTTTCCCTTCCTCT 59.796 43.478 0.00 0.00 0.00 3.69
5024 7245 3.562182 TCAAACAACCTTTCCCTTCCTC 58.438 45.455 0.00 0.00 0.00 3.71
5025 7246 3.680777 TCAAACAACCTTTCCCTTCCT 57.319 42.857 0.00 0.00 0.00 3.36
5026 7247 4.503123 CCAATCAAACAACCTTTCCCTTCC 60.503 45.833 0.00 0.00 0.00 3.46
5030 7251 2.549992 GCCCAATCAAACAACCTTTCCC 60.550 50.000 0.00 0.00 0.00 3.97
5037 7258 0.313672 TGAGCGCCCAATCAAACAAC 59.686 50.000 2.29 0.00 0.00 3.32
5052 7273 2.852495 TTCCGACGGCCTGATTGAGC 62.852 60.000 9.66 0.00 0.00 4.26
5057 7278 5.871396 ATAATATATTCCGACGGCCTGAT 57.129 39.130 9.66 3.21 0.00 2.90
5061 7282 6.292168 CGATCAAATAATATATTCCGACGGCC 60.292 42.308 9.66 0.00 0.00 6.13
5062 7283 6.474427 TCGATCAAATAATATATTCCGACGGC 59.526 38.462 9.66 0.00 0.00 5.68
5064 7285 8.410436 CGATCGATCAAATAATATATTCCGACG 58.590 37.037 24.40 1.05 0.00 5.12
5079 7300 3.490800 TCCAACGTACGATCGATCAAA 57.509 42.857 24.34 9.25 34.70 2.69
5081 7302 3.127376 TCTTTCCAACGTACGATCGATCA 59.873 43.478 24.34 3.68 34.70 2.92
5082 7303 3.481388 GTCTTTCCAACGTACGATCGATC 59.519 47.826 24.34 15.68 34.70 3.69
5091 7312 1.682854 ACTCACCGTCTTTCCAACGTA 59.317 47.619 0.00 0.00 38.44 3.57


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

AutoCloner maintained by Alex Coulton.