Multiple sequence alignment - TraesCS4A01G438900

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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 TraesCS4A01G438900 chr4A 100.000 2694 0 0 1 2694 708597078 708594385 0.000000e+00 4975.0
1 TraesCS4A01G438900 chr4A 79.271 439 70 12 349 770 708585468 708585034 1.220000e-73 287.0
2 TraesCS4A01G438900 chr4A 83.067 313 47 4 463 770 708584426 708584115 2.040000e-71 279.0
3 TraesCS4A01G438900 chr7A 93.499 846 37 8 847 1682 25859029 25859866 0.000000e+00 1242.0
4 TraesCS4A01G438900 chr7A 82.449 490 76 7 349 828 25872245 25872734 1.150000e-113 420.0
5 TraesCS4A01G438900 chr7A 86.224 196 16 6 113 298 25857127 25857321 4.550000e-48 202.0
6 TraesCS4A01G438900 chr7A 89.744 117 8 2 349 461 25866906 25867022 2.160000e-31 147.0
7 TraesCS4A01G438900 chr7A 93.878 98 5 1 2269 2365 705448841 705448744 2.160000e-31 147.0
8 TraesCS4A01G438900 chr7A 95.604 91 3 1 2 92 25856916 25857005 7.770000e-31 145.0
9 TraesCS4A01G438900 chr7A 92.941 85 5 1 310 393 25858236 25858320 3.640000e-24 122.0
10 TraesCS4A01G438900 chr7D 94.312 756 38 2 996 1747 25008618 25009372 0.000000e+00 1153.0
11 TraesCS4A01G438900 chr7D 86.948 498 21 18 1745 2221 25009881 25010355 1.110000e-143 520.0
12 TraesCS4A01G438900 chr7D 93.878 245 15 0 2357 2601 25010392 25010636 1.180000e-98 370.0
13 TraesCS4A01G438900 chr7D 81.579 228 36 4 1472 1693 25032616 25032843 1.650000e-42 183.0
14 TraesCS4A01G438900 chr7D 90.625 128 11 1 171 298 24979946 24980072 4.610000e-38 169.0
15 TraesCS4A01G438900 chr7D 90.551 127 8 3 2 128 24979751 24979873 5.970000e-37 165.0
16 TraesCS4A01G438900 chr2D 96.809 94 3 0 2272 2365 592140598 592140691 9.980000e-35 158.0
17 TraesCS4A01G438900 chr7B 94.792 96 4 1 2264 2359 432933332 432933238 6.010000e-32 148.0
18 TraesCS4A01G438900 chr5B 93.939 99 5 1 2272 2369 45261634 45261732 6.010000e-32 148.0
19 TraesCS4A01G438900 chr5B 90.000 110 9 1 2255 2362 631894500 631894609 1.010000e-29 141.0
20 TraesCS4A01G438900 chr1D 97.674 86 2 0 2273 2358 474055591 474055676 6.010000e-32 148.0
21 TraesCS4A01G438900 chr1D 93.000 100 5 1 2272 2371 69615700 69615603 7.770000e-31 145.0
22 TraesCS4A01G438900 chr1D 95.122 41 2 0 2623 2663 238073879 238073919 6.230000e-07 65.8
23 TraesCS4A01G438900 chr4D 96.591 88 3 0 2271 2358 16403450 16403537 2.160000e-31 147.0
24 TraesCS4A01G438900 chr6B 82.877 146 18 7 2273 2414 116281106 116281248 1.010000e-24 124.0
25 TraesCS4A01G438900 chr1B 94.737 57 3 0 2607 2663 336205718 336205662 3.690000e-14 89.8


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 TraesCS4A01G438900 chr4A 708594385 708597078 2693 True 4975.00 4975 100.000000 1 2694 1 chr4A.!!$R1 2693
1 TraesCS4A01G438900 chr4A 708584115 708585468 1353 True 283.00 287 81.169000 349 770 2 chr4A.!!$R2 421
2 TraesCS4A01G438900 chr7A 25856916 25859866 2950 False 427.75 1242 92.067000 2 1682 4 chr7A.!!$F3 1680
3 TraesCS4A01G438900 chr7D 25008618 25010636 2018 False 681.00 1153 91.712667 996 2601 3 chr7D.!!$F3 1605

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
468 1487 0.033601 TCCACAAACCAGGTGCAACT 60.034 50.0 0.00 0.0 36.74 3.16 F
526 1546 0.381801 CCGCACTGCACAAGTTTCTT 59.618 50.0 1.11 0.0 36.83 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 3637 0.104855 TGAACGTGCACAAGAGAGCT 59.895 50.0 18.64 0.0 32.15 4.09 R
2139 4705 0.170561 CATCACCTTGCTGCTGCTTC 59.829 55.0 17.00 0.0 40.48 3.86 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
57 58 8.184192 AGCTATCGTTTTTGTTTCCATCATTAG 58.816 33.333 0.00 0.00 0.00 1.73
92 93 8.861086 TGCACTTCCATTTTTACACCTTATTAA 58.139 29.630 0.00 0.00 0.00 1.40
93 94 9.869757 GCACTTCCATTTTTACACCTTATTAAT 57.130 29.630 0.00 0.00 0.00 1.40
132 234 7.159372 AGAAACTGTAGTTAACCACATACTGG 58.841 38.462 7.33 0.00 40.90 4.00
136 238 3.067684 AGTTAACCACATACTGGCACC 57.932 47.619 0.88 0.00 45.32 5.01
151 253 0.532115 GCACCACAAATGATCCCCAC 59.468 55.000 0.00 0.00 0.00 4.61
153 255 1.545582 CACCACAAATGATCCCCACAC 59.454 52.381 0.00 0.00 0.00 3.82
171 283 2.242926 CACCACCAACTCTCTCTCTCA 58.757 52.381 0.00 0.00 0.00 3.27
183 295 5.131977 ACTCTCTCTCTCACTCATAAGCCTA 59.868 44.000 0.00 0.00 0.00 3.93
184 296 6.183361 ACTCTCTCTCTCACTCATAAGCCTAT 60.183 42.308 0.00 0.00 0.00 2.57
204 316 0.792640 CACCGTCGTCACGTACTAGT 59.207 55.000 0.00 0.00 45.17 2.57
256 368 4.578871 TGATCCACACACTTTGTCCTATG 58.421 43.478 0.00 0.00 35.67 2.23
258 370 3.738982 TCCACACACTTTGTCCTATGTG 58.261 45.455 1.81 1.81 46.32 3.21
283 395 9.042008 TGGAAAATACGAGAAAATCTATACTGC 57.958 33.333 0.00 0.00 0.00 4.40
308 1308 7.274250 GCACTAATTCCATAAGCAAGAACAAAG 59.726 37.037 0.00 0.00 0.00 2.77
339 1354 2.788786 CACTTTGTGCCGTTGATTTGAC 59.211 45.455 0.00 0.00 0.00 3.18
406 1422 3.655276 TTCCCTCGTGTCACTTTAGTC 57.345 47.619 0.65 0.00 0.00 2.59
420 1439 8.777413 TGTCACTTTAGTCATCTTCTTCAAATG 58.223 33.333 0.00 0.00 0.00 2.32
425 1444 8.884124 TTTAGTCATCTTCTTCAAATGGGATT 57.116 30.769 0.00 0.00 0.00 3.01
429 1448 7.068348 AGTCATCTTCTTCAAATGGGATTGATG 59.932 37.037 0.00 0.00 38.98 3.07
440 1459 0.179045 GGATTGATGGCTAGGCACGT 60.179 55.000 22.77 6.62 0.00 4.49
441 1460 1.668419 GATTGATGGCTAGGCACGTT 58.332 50.000 22.77 5.76 0.00 3.99
442 1461 1.599542 GATTGATGGCTAGGCACGTTC 59.400 52.381 22.77 15.79 0.00 3.95
444 1463 1.264749 TGATGGCTAGGCACGTTCCT 61.265 55.000 22.77 12.49 40.21 3.36
445 1464 0.750850 GATGGCTAGGCACGTTCCTA 59.249 55.000 22.77 13.51 37.66 2.94
446 1465 0.464452 ATGGCTAGGCACGTTCCTAC 59.536 55.000 22.77 7.45 37.66 3.18
453 1472 1.154197 GGCACGTTCCTACTTTCCAC 58.846 55.000 0.00 0.00 0.00 4.02
458 1477 3.002965 CACGTTCCTACTTTCCACAAACC 59.997 47.826 0.00 0.00 0.00 3.27
461 1480 3.502123 TCCTACTTTCCACAAACCAGG 57.498 47.619 0.00 0.00 0.00 4.45
462 1481 2.781174 TCCTACTTTCCACAAACCAGGT 59.219 45.455 0.00 0.00 0.00 4.00
463 1482 2.884639 CCTACTTTCCACAAACCAGGTG 59.115 50.000 0.00 0.00 36.03 4.00
464 1483 1.111277 ACTTTCCACAAACCAGGTGC 58.889 50.000 0.00 0.00 34.94 5.01
465 1484 1.110442 CTTTCCACAAACCAGGTGCA 58.890 50.000 0.00 0.00 34.94 4.57
466 1485 1.480137 CTTTCCACAAACCAGGTGCAA 59.520 47.619 0.00 0.00 34.94 4.08
467 1486 0.820871 TTCCACAAACCAGGTGCAAC 59.179 50.000 0.00 0.00 34.94 4.17
468 1487 0.033601 TCCACAAACCAGGTGCAACT 60.034 50.000 0.00 0.00 36.74 3.16
470 1489 2.158534 TCCACAAACCAGGTGCAACTAT 60.159 45.455 2.54 0.00 36.74 2.12
472 1491 3.823873 CCACAAACCAGGTGCAACTATTA 59.176 43.478 2.54 0.00 36.74 0.98
473 1492 4.320935 CCACAAACCAGGTGCAACTATTAC 60.321 45.833 2.54 0.00 36.74 1.89
474 1493 4.277174 CACAAACCAGGTGCAACTATTACA 59.723 41.667 2.54 0.00 36.74 2.41
475 1494 4.518970 ACAAACCAGGTGCAACTATTACAG 59.481 41.667 2.54 0.00 36.74 2.74
478 1497 4.579869 ACCAGGTGCAACTATTACAGAAG 58.420 43.478 2.54 0.00 36.74 2.85
480 1499 5.003804 CCAGGTGCAACTATTACAGAAGTT 58.996 41.667 2.54 0.00 36.38 2.66
483 1502 7.148407 CCAGGTGCAACTATTACAGAAGTTAAG 60.148 40.741 2.54 0.00 34.23 1.85
484 1503 7.602644 CAGGTGCAACTATTACAGAAGTTAAGA 59.397 37.037 2.54 0.00 34.23 2.10
485 1504 7.603024 AGGTGCAACTATTACAGAAGTTAAGAC 59.397 37.037 0.00 0.00 34.23 3.01
488 1507 9.635520 TGCAACTATTACAGAAGTTAAGACTAC 57.364 33.333 0.00 0.00 34.23 2.73
517 1537 1.083489 TAATTAGCACCGCACTGCAC 58.917 50.000 1.11 0.00 39.86 4.57
518 1538 0.888736 AATTAGCACCGCACTGCACA 60.889 50.000 1.11 0.00 39.86 4.57
524 1544 0.592247 CACCGCACTGCACAAGTTTC 60.592 55.000 1.11 0.00 36.83 2.78
526 1546 0.381801 CCGCACTGCACAAGTTTCTT 59.618 50.000 1.11 0.00 36.83 2.52
531 1551 2.164219 CACTGCACAAGTTTCTTGGTGT 59.836 45.455 12.95 4.55 36.83 4.16
533 1553 1.748493 TGCACAAGTTTCTTGGTGTCC 59.252 47.619 12.95 0.00 33.88 4.02
540 1560 4.706842 AGTTTCTTGGTGTCCTGTATGT 57.293 40.909 0.00 0.00 0.00 2.29
544 1564 3.146066 TCTTGGTGTCCTGTATGTTTGC 58.854 45.455 0.00 0.00 0.00 3.68
548 1568 2.413837 GTGTCCTGTATGTTTGCGTCT 58.586 47.619 0.00 0.00 0.00 4.18
553 1573 5.703592 TGTCCTGTATGTTTGCGTCTTAATT 59.296 36.000 0.00 0.00 0.00 1.40
555 1575 7.148540 TGTCCTGTATGTTTGCGTCTTAATTAC 60.149 37.037 0.00 0.00 0.00 1.89
562 1586 6.130723 TGTTTGCGTCTTAATTACGAACTTG 58.869 36.000 13.04 0.00 42.90 3.16
575 1599 1.203052 CGAACTTGCAATCCTGGCATT 59.797 47.619 0.00 0.00 41.58 3.56
576 1600 2.353011 CGAACTTGCAATCCTGGCATTT 60.353 45.455 0.00 0.00 41.58 2.32
617 1641 9.804758 AACTATGTCTTAGTGTAGCATTTCTAC 57.195 33.333 0.00 0.00 46.17 2.59
634 1658 9.241317 GCATTTCTACATCTGGTCAAAATATTG 57.759 33.333 0.00 0.00 37.92 1.90
635 1659 9.740239 CATTTCTACATCTGGTCAAAATATTGG 57.260 33.333 0.00 0.00 37.15 3.16
646 1670 6.211184 TGGTCAAAATATTGGCATCTTGTTCT 59.789 34.615 0.00 0.00 43.07 3.01
763 2711 6.528537 TCCCATCATTAATTGTTCCTTGTG 57.471 37.500 0.00 0.00 0.00 3.33
780 2728 4.202202 CCTTGTGCTTCCATTTTTACACCA 60.202 41.667 0.00 0.00 0.00 4.17
812 2760 7.918562 CCTAGAACTAGAACTCAAGCTAATCAC 59.081 40.741 10.04 0.00 35.21 3.06
815 2763 8.972127 AGAACTAGAACTCAAGCTAATCACATA 58.028 33.333 0.00 0.00 0.00 2.29
822 2770 5.039920 TCAAGCTAATCACATAGTGGCAT 57.960 39.130 0.00 0.00 33.87 4.40
823 2771 4.818005 TCAAGCTAATCACATAGTGGCATG 59.182 41.667 0.00 0.00 33.87 4.06
828 2776 5.066375 GCTAATCACATAGTGGCATGACAAA 59.934 40.000 0.58 0.00 33.87 2.83
835 2783 2.880443 AGTGGCATGACAAACAATCCT 58.120 42.857 0.58 0.00 0.00 3.24
842 2790 4.217118 GCATGACAAACAATCCTCTCTGTT 59.783 41.667 0.00 0.00 37.36 3.16
932 2970 2.286197 GTCCCCAAGGCCCTAGGT 60.286 66.667 8.29 0.00 0.00 3.08
938 2976 2.065799 CCCAAGGCCCTAGGTCATAAT 58.934 52.381 8.29 0.00 0.00 1.28
941 2979 3.650942 CCAAGGCCCTAGGTCATAATACA 59.349 47.826 8.29 0.00 0.00 2.29
954 2992 8.998277 AGGTCATAATACAAGCTAGAACTAGA 57.002 34.615 12.33 0.00 35.21 2.43
955 2993 9.422681 AGGTCATAATACAAGCTAGAACTAGAA 57.577 33.333 12.33 0.00 35.21 2.10
956 2994 9.685828 GGTCATAATACAAGCTAGAACTAGAAG 57.314 37.037 12.33 4.22 35.21 2.85
957 2995 9.187455 GTCATAATACAAGCTAGAACTAGAAGC 57.813 37.037 12.33 0.00 35.21 3.86
958 2996 8.361139 TCATAATACAAGCTAGAACTAGAAGCC 58.639 37.037 12.33 0.00 36.92 4.35
983 3021 1.063649 CACCGAGTATCACCGACCG 59.936 63.158 0.00 0.00 33.17 4.79
985 3023 1.820906 CCGAGTATCACCGACCGGA 60.821 63.158 16.07 0.00 39.31 5.14
986 3024 1.354506 CGAGTATCACCGACCGGAC 59.645 63.158 16.07 0.00 38.96 4.79
987 3025 1.732308 GAGTATCACCGACCGGACC 59.268 63.158 16.07 0.00 38.96 4.46
1052 3094 1.069765 CCGATGTAGCGGCCATCTT 59.930 57.895 2.24 0.00 45.38 2.40
1164 3206 2.740714 GACCTGCACGATGTTCGCC 61.741 63.158 0.00 0.00 45.12 5.54
1247 3289 3.757270 CCTATGTCCTGTCCGAGATAGT 58.243 50.000 0.00 0.00 35.39 2.12
1360 3406 1.154131 CGTCACTCACTCTGCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
1408 3454 9.101655 TGATGAATTCACTGTGTAATGTGATAG 57.898 33.333 11.07 0.00 41.93 2.08
1409 3455 7.848223 TGAATTCACTGTGTAATGTGATAGG 57.152 36.000 3.38 0.00 41.93 2.57
1410 3456 7.394016 TGAATTCACTGTGTAATGTGATAGGT 58.606 34.615 3.38 0.00 41.93 3.08
1420 3469 2.842462 TGATAGGTGGCGGCGGAT 60.842 61.111 9.78 0.00 0.00 4.18
1455 3504 1.135257 CGTGAAGAATGACGAGGAGCT 60.135 52.381 0.00 0.00 37.81 4.09
1519 3568 1.238625 TTTTCATTGGGTCGGCGTCC 61.239 55.000 14.92 14.92 0.00 4.79
1557 3606 7.651808 TCTTTCATTCTTTTCAAGTGTGGATC 58.348 34.615 0.00 0.00 0.00 3.36
1588 3637 2.882876 GACCTTCTCGGCTACGCA 59.117 61.111 0.00 0.00 40.69 5.24
1703 3752 2.887568 CAGAGTAGCCCTTGCGCG 60.888 66.667 0.00 0.00 44.33 6.86
1727 3776 6.445475 GGGATCATCGACTTACTAAGGTAAC 58.555 44.000 0.00 0.00 34.61 2.50
1747 3796 8.622948 GGTAACTGGCATTAAGCTAAGATAAT 57.377 34.615 0.00 0.00 44.79 1.28
1792 4350 7.174426 TCTCTCGTCTCAACTTGAAACACTATA 59.826 37.037 0.00 0.00 0.00 1.31
1793 4351 7.082602 TCTCGTCTCAACTTGAAACACTATAC 58.917 38.462 0.00 0.00 0.00 1.47
1867 4425 6.765036 CAGTTGGTAGAAGATGATGCAAGTAT 59.235 38.462 0.00 0.00 0.00 2.12
1889 4447 6.619801 ATTGTTCAAGTCAAGTAGTGGAAC 57.380 37.500 0.00 0.00 35.09 3.62
1892 4450 3.973657 TCAAGTCAAGTAGTGGAACGTC 58.026 45.455 0.00 0.00 45.86 4.34
1898 4456 3.004419 TCAAGTAGTGGAACGTCTCAGTG 59.996 47.826 8.21 0.00 45.86 3.66
1899 4457 2.584236 AGTAGTGGAACGTCTCAGTGT 58.416 47.619 8.21 0.00 45.86 3.55
1952 4518 3.876914 TGTTGTCTTCAGTCATCACCAAC 59.123 43.478 0.00 0.00 33.40 3.77
1955 4521 3.070018 GTCTTCAGTCATCACCAACCAG 58.930 50.000 0.00 0.00 0.00 4.00
1987 4553 4.801891 TCTTGTAGTACTAAACTGCCACG 58.198 43.478 3.61 0.00 39.88 4.94
2010 4576 4.218635 GCGATGGTAGAGATTGATAGGACA 59.781 45.833 0.00 0.00 0.00 4.02
2011 4577 5.621104 GCGATGGTAGAGATTGATAGGACAG 60.621 48.000 0.00 0.00 0.00 3.51
2012 4578 5.475220 CGATGGTAGAGATTGATAGGACAGT 59.525 44.000 0.00 0.00 0.00 3.55
2013 4579 6.655425 CGATGGTAGAGATTGATAGGACAGTA 59.345 42.308 0.00 0.00 0.00 2.74
2014 4580 7.175119 CGATGGTAGAGATTGATAGGACAGTAA 59.825 40.741 0.00 0.00 0.00 2.24
2015 4581 8.964533 ATGGTAGAGATTGATAGGACAGTAAT 57.035 34.615 0.00 0.00 0.00 1.89
2017 4583 9.877222 TGGTAGAGATTGATAGGACAGTAATAA 57.123 33.333 0.00 0.00 0.00 1.40
2113 4679 6.094325 TGTTGACACAAGTTCGTCCTTTAATT 59.906 34.615 0.61 0.00 0.00 1.40
2116 4682 4.578928 ACACAAGTTCGTCCTTTAATTGCT 59.421 37.500 0.00 0.00 0.00 3.91
2139 4705 2.793946 CGCAGGATTTCAAGCCGG 59.206 61.111 0.00 0.00 40.07 6.13
2166 4737 1.078426 GCAAGGTGATGGGCTACGT 60.078 57.895 0.00 0.00 0.00 3.57
2193 4772 1.069358 GGAGCGCTGCTATTTCCTACT 59.931 52.381 22.85 0.00 39.88 2.57
2206 4785 6.319911 GCTATTTCCTACTTCCTTTGATGCTT 59.680 38.462 0.00 0.00 0.00 3.91
2221 4800 8.517878 CCTTTGATGCTTTTCTGAATAAAGAGA 58.482 33.333 6.12 0.00 35.16 3.10
2223 4802 9.850628 TTTGATGCTTTTCTGAATAAAGAGATG 57.149 29.630 6.12 0.00 35.16 2.90
2224 4803 7.993101 TGATGCTTTTCTGAATAAAGAGATGG 58.007 34.615 6.12 0.00 35.16 3.51
2225 4804 7.830697 TGATGCTTTTCTGAATAAAGAGATGGA 59.169 33.333 6.12 0.00 35.16 3.41
2226 4805 7.383102 TGCTTTTCTGAATAAAGAGATGGAC 57.617 36.000 6.12 0.00 35.16 4.02
2227 4806 6.942005 TGCTTTTCTGAATAAAGAGATGGACA 59.058 34.615 6.12 0.00 35.16 4.02
2228 4807 7.613022 TGCTTTTCTGAATAAAGAGATGGACAT 59.387 33.333 6.12 0.00 35.16 3.06
2229 4808 7.914346 GCTTTTCTGAATAAAGAGATGGACATG 59.086 37.037 6.12 0.00 35.16 3.21
2230 4809 6.932356 TTCTGAATAAAGAGATGGACATGC 57.068 37.500 0.00 0.00 0.00 4.06
2242 4821 1.378882 GGACATGCATGCCGTGTGAT 61.379 55.000 26.53 4.08 43.58 3.06
2243 4822 0.248336 GACATGCATGCCGTGTGATG 60.248 55.000 26.53 18.09 43.58 3.07
2244 4823 0.961857 ACATGCATGCCGTGTGATGT 60.962 50.000 26.53 16.54 42.01 3.06
2253 4832 2.036089 TGCCGTGTGATGTTGTGTAGTA 59.964 45.455 0.00 0.00 0.00 1.82
2276 4855 9.959749 AGTAATCTACTACGTAGTACAGTACTC 57.040 37.037 29.42 16.06 45.11 2.59
2277 4856 9.187455 GTAATCTACTACGTAGTACAGTACTCC 57.813 40.741 27.07 12.07 45.11 3.85
2278 4857 6.150396 TCTACTACGTAGTACAGTACTCCC 57.850 45.833 27.51 8.17 45.11 4.30
2279 4858 5.894393 TCTACTACGTAGTACAGTACTCCCT 59.106 44.000 27.51 5.20 45.11 4.20
2280 4859 5.017294 ACTACGTAGTACAGTACTCCCTC 57.983 47.826 26.36 5.93 45.11 4.30
2281 4860 3.274095 ACGTAGTACAGTACTCCCTCC 57.726 52.381 16.91 1.21 41.94 4.30
2282 4861 2.208431 CGTAGTACAGTACTCCCTCCG 58.792 57.143 16.91 8.88 40.14 4.63
2283 4862 2.419297 CGTAGTACAGTACTCCCTCCGT 60.419 54.545 16.91 0.00 40.14 4.69
2284 4863 2.895242 AGTACAGTACTCCCTCCGTT 57.105 50.000 7.48 0.00 32.47 4.44
2285 4864 2.720915 AGTACAGTACTCCCTCCGTTC 58.279 52.381 7.48 0.00 32.47 3.95
2286 4865 1.747924 GTACAGTACTCCCTCCGTTCC 59.252 57.143 3.19 0.00 0.00 3.62
2287 4866 0.964358 ACAGTACTCCCTCCGTTCCG 60.964 60.000 0.00 0.00 0.00 4.30
2288 4867 0.679002 CAGTACTCCCTCCGTTCCGA 60.679 60.000 0.00 0.00 0.00 4.55
2289 4868 0.258194 AGTACTCCCTCCGTTCCGAT 59.742 55.000 0.00 0.00 0.00 4.18
2290 4869 1.109609 GTACTCCCTCCGTTCCGATT 58.890 55.000 0.00 0.00 0.00 3.34
2291 4870 1.479730 GTACTCCCTCCGTTCCGATTT 59.520 52.381 0.00 0.00 0.00 2.17
2292 4871 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
2293 4872 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
2294 4873 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
2295 4874 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2297 4876 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
2298 4877 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
2299 4878 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
2300 4879 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
2301 4880 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
2302 4881 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
2303 4882 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
2304 4883 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
2305 4884 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
2306 4885 2.733026 CCGATTTACTCGTCGTGGTTTT 59.267 45.455 0.00 0.00 46.18 2.43
2307 4886 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
2308 4887 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
2309 4888 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
2310 4889 5.117592 CGATTTACTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 42.56 2.24
2311 4890 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
2312 4891 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2313 4892 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2314 4893 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2315 4894 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2316 4895 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2317 4896 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2318 4897 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2319 4898 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2320 4899 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
2334 4913 8.848474 TTCAAATTTGAACTAAAACCACCAAA 57.152 26.923 26.01 2.16 41.88 3.28
2335 4914 8.848474 TCAAATTTGAACTAAAACCACCAAAA 57.152 26.923 18.45 0.00 33.55 2.44
2336 4915 8.940952 TCAAATTTGAACTAAAACCACCAAAAG 58.059 29.630 18.45 0.00 33.55 2.27
2337 4916 8.726068 CAAATTTGAACTAAAACCACCAAAAGT 58.274 29.630 13.08 0.00 0.00 2.66
2338 4917 9.945904 AAATTTGAACTAAAACCACCAAAAGTA 57.054 25.926 0.00 0.00 0.00 2.24
2339 4918 9.945904 AATTTGAACTAAAACCACCAAAAGTAA 57.054 25.926 0.00 0.00 0.00 2.24
2340 4919 9.945904 ATTTGAACTAAAACCACCAAAAGTAAA 57.054 25.926 0.00 0.00 0.00 2.01
2341 4920 9.945904 TTTGAACTAAAACCACCAAAAGTAAAT 57.054 25.926 0.00 0.00 0.00 1.40
2342 4921 9.589111 TTGAACTAAAACCACCAAAAGTAAATC 57.411 29.630 0.00 0.00 0.00 2.17
2343 4922 7.916450 TGAACTAAAACCACCAAAAGTAAATCG 59.084 33.333 0.00 0.00 0.00 3.34
2344 4923 6.741109 ACTAAAACCACCAAAAGTAAATCGG 58.259 36.000 0.00 0.00 0.00 4.18
2345 4924 5.855740 AAAACCACCAAAAGTAAATCGGA 57.144 34.783 0.00 0.00 0.00 4.55
2346 4925 5.855740 AAACCACCAAAAGTAAATCGGAA 57.144 34.783 0.00 0.00 0.00 4.30
2347 4926 4.841443 ACCACCAAAAGTAAATCGGAAC 57.159 40.909 0.00 0.00 0.00 3.62
2448 5027 2.882229 GCTATGGTGGCTTTGGTTGGTA 60.882 50.000 0.00 0.00 0.00 3.25
2468 5047 2.169330 AGTTACTCTGAACCGGACCTC 58.831 52.381 9.46 1.67 0.00 3.85
2481 5060 6.040166 TGAACCGGACCTCTATCTAACATAAC 59.960 42.308 9.46 0.00 0.00 1.89
2495 5074 1.810151 ACATAACGATTTGTGCCGCTT 59.190 42.857 0.00 0.00 0.00 4.68
2497 5076 1.803334 TAACGATTTGTGCCGCTTCT 58.197 45.000 0.00 0.00 0.00 2.85
2528 5107 3.111853 ACGTGCCCATACATATGACTG 57.888 47.619 10.38 6.04 35.75 3.51
2529 5108 2.434336 ACGTGCCCATACATATGACTGT 59.566 45.455 10.38 0.00 35.75 3.55
2533 5112 2.993899 GCCCATACATATGACTGTACGC 59.006 50.000 10.38 4.16 34.59 4.42
2547 5126 1.202405 TGTACGCACGATCTGATGCAT 60.202 47.619 0.00 0.00 42.17 3.96
2551 5130 0.795085 GCACGATCTGATGCATAGCC 59.205 55.000 0.00 0.00 41.65 3.93
2561 5140 4.020751 TCTGATGCATAGCCTCCATTCTAC 60.021 45.833 0.00 0.00 0.00 2.59
2597 5176 6.769134 AGCATTTTTACCGCCTATAACTTT 57.231 33.333 0.00 0.00 0.00 2.66
2601 5180 7.627726 GCATTTTTACCGCCTATAACTTTGTCT 60.628 37.037 0.00 0.00 0.00 3.41
2602 5181 6.730960 TTTTACCGCCTATAACTTTGTCTG 57.269 37.500 0.00 0.00 0.00 3.51
2603 5182 5.664294 TTACCGCCTATAACTTTGTCTGA 57.336 39.130 0.00 0.00 0.00 3.27
2604 5183 4.755266 ACCGCCTATAACTTTGTCTGAT 57.245 40.909 0.00 0.00 0.00 2.90
2605 5184 4.442706 ACCGCCTATAACTTTGTCTGATG 58.557 43.478 0.00 0.00 0.00 3.07
2606 5185 3.248602 CCGCCTATAACTTTGTCTGATGC 59.751 47.826 0.00 0.00 0.00 3.91
2607 5186 3.871006 CGCCTATAACTTTGTCTGATGCA 59.129 43.478 0.00 0.00 0.00 3.96
2608 5187 4.332543 CGCCTATAACTTTGTCTGATGCAA 59.667 41.667 0.00 0.00 0.00 4.08
2609 5188 5.008019 CGCCTATAACTTTGTCTGATGCAAT 59.992 40.000 0.00 0.00 0.00 3.56
2610 5189 6.433766 GCCTATAACTTTGTCTGATGCAATC 58.566 40.000 0.00 0.00 45.83 2.67
2621 5200 2.245159 GATGCAATCGATGGTGGAGA 57.755 50.000 0.00 0.00 31.13 3.71
2622 5201 2.141517 GATGCAATCGATGGTGGAGAG 58.858 52.381 0.00 0.00 31.13 3.20
2623 5202 0.178767 TGCAATCGATGGTGGAGAGG 59.821 55.000 0.00 0.00 0.00 3.69
2624 5203 1.162800 GCAATCGATGGTGGAGAGGC 61.163 60.000 0.00 0.00 0.00 4.70
2625 5204 0.533755 CAATCGATGGTGGAGAGGCC 60.534 60.000 0.00 0.00 37.10 5.19
2626 5205 0.982852 AATCGATGGTGGAGAGGCCA 60.983 55.000 5.01 0.00 46.96 5.36
2636 5215 3.857157 TGGAGAGGCCATTATAACCAC 57.143 47.619 5.01 0.00 43.33 4.16
2637 5216 3.119319 TGGAGAGGCCATTATAACCACA 58.881 45.455 5.01 0.00 43.33 4.17
2638 5217 3.721575 TGGAGAGGCCATTATAACCACAT 59.278 43.478 5.01 0.00 43.33 3.21
2639 5218 4.202461 TGGAGAGGCCATTATAACCACATC 60.202 45.833 5.01 0.00 43.33 3.06
2640 5219 4.042187 GGAGAGGCCATTATAACCACATCT 59.958 45.833 5.01 0.00 36.34 2.90
2641 5220 5.456763 GGAGAGGCCATTATAACCACATCTT 60.457 44.000 5.01 0.00 36.34 2.40
2642 5221 6.239887 GGAGAGGCCATTATAACCACATCTTA 60.240 42.308 5.01 0.00 36.34 2.10
2643 5222 7.149202 AGAGGCCATTATAACCACATCTTAA 57.851 36.000 5.01 0.00 0.00 1.85
2644 5223 7.582719 AGAGGCCATTATAACCACATCTTAAA 58.417 34.615 5.01 0.00 0.00 1.52
2645 5224 7.502561 AGAGGCCATTATAACCACATCTTAAAC 59.497 37.037 5.01 0.00 0.00 2.01
2646 5225 7.122715 AGGCCATTATAACCACATCTTAAACA 58.877 34.615 5.01 0.00 0.00 2.83
2647 5226 7.617723 AGGCCATTATAACCACATCTTAAACAA 59.382 33.333 5.01 0.00 0.00 2.83
2648 5227 8.254508 GGCCATTATAACCACATCTTAAACAAA 58.745 33.333 0.00 0.00 0.00 2.83
2649 5228 9.646427 GCCATTATAACCACATCTTAAACAAAA 57.354 29.630 0.00 0.00 0.00 2.44
2668 5247 9.880157 AAACAAAATAAAGATCATGAGGAATGG 57.120 29.630 0.09 0.00 36.86 3.16
2669 5248 7.495055 ACAAAATAAAGATCATGAGGAATGGC 58.505 34.615 0.09 0.00 36.86 4.40
2670 5249 7.343833 ACAAAATAAAGATCATGAGGAATGGCT 59.656 33.333 0.09 0.00 36.86 4.75
2671 5250 7.909485 AAATAAAGATCATGAGGAATGGCTT 57.091 32.000 0.09 0.00 36.86 4.35
2672 5251 7.521871 AATAAAGATCATGAGGAATGGCTTC 57.478 36.000 0.09 0.00 36.86 3.86
2673 5252 3.123157 AGATCATGAGGAATGGCTTCG 57.877 47.619 0.09 0.00 36.86 3.79
2674 5253 2.702478 AGATCATGAGGAATGGCTTCGA 59.298 45.455 0.09 0.00 36.86 3.71
2675 5254 2.609427 TCATGAGGAATGGCTTCGAG 57.391 50.000 0.00 0.00 36.86 4.04
2676 5255 0.942962 CATGAGGAATGGCTTCGAGC 59.057 55.000 0.00 0.00 41.46 5.03
2677 5256 0.531532 ATGAGGAATGGCTTCGAGCG 60.532 55.000 0.00 0.00 43.62 5.03
2678 5257 1.884926 GAGGAATGGCTTCGAGCGG 60.885 63.158 0.00 0.00 43.62 5.52
2679 5258 3.577313 GGAATGGCTTCGAGCGGC 61.577 66.667 0.00 0.00 43.62 6.53
2680 5259 3.929948 GAATGGCTTCGAGCGGCG 61.930 66.667 0.51 0.51 43.62 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 5.959618 AAAATGGAAGTGCAAGGTACTAC 57.040 39.130 0.00 0.00 38.49 2.73
97 98 8.476447 GGTTAACTACAGTTTCTATTCTAGGCT 58.524 37.037 5.42 0.00 39.31 4.58
99 100 9.583765 GTGGTTAACTACAGTTTCTATTCTAGG 57.416 37.037 16.42 0.00 39.31 3.02
105 106 9.871238 CAGTATGTGGTTAACTACAGTTTCTAT 57.129 33.333 25.96 12.64 40.64 1.98
107 108 7.159372 CCAGTATGTGGTTAACTACAGTTTCT 58.841 38.462 25.96 18.02 40.64 2.52
108 109 7.360575 CCAGTATGTGGTTAACTACAGTTTC 57.639 40.000 25.96 16.49 40.64 2.78
129 231 0.819582 GGGATCATTTGTGGTGCCAG 59.180 55.000 0.00 0.00 0.00 4.85
132 234 0.532115 GTGGGGATCATTTGTGGTGC 59.468 55.000 0.00 0.00 0.00 5.01
136 238 1.545582 GTGGTGTGGGGATCATTTGTG 59.454 52.381 0.00 0.00 0.00 3.33
151 253 2.029470 GTGAGAGAGAGAGTTGGTGGTG 60.029 54.545 0.00 0.00 0.00 4.17
153 255 2.491693 GAGTGAGAGAGAGAGTTGGTGG 59.508 54.545 0.00 0.00 0.00 4.61
171 283 2.293677 CGACGGTGATAGGCTTATGAGT 59.706 50.000 0.00 0.00 0.00 3.41
204 316 7.170965 AGAGGTTCTTGCATTGATTTCTCTTA 58.829 34.615 0.00 0.00 0.00 2.10
258 370 9.042008 TGCAGTATAGATTTTCTCGTATTTTCC 57.958 33.333 0.00 0.00 0.00 3.13
259 371 9.851043 GTGCAGTATAGATTTTCTCGTATTTTC 57.149 33.333 0.00 0.00 0.00 2.29
266 378 8.704234 GGAATTAGTGCAGTATAGATTTTCTCG 58.296 37.037 1.17 0.00 0.00 4.04
273 385 8.597167 TGCTTATGGAATTAGTGCAGTATAGAT 58.403 33.333 1.17 0.00 0.00 1.98
274 386 7.962441 TGCTTATGGAATTAGTGCAGTATAGA 58.038 34.615 1.17 0.00 0.00 1.98
283 395 7.756722 CCTTTGTTCTTGCTTATGGAATTAGTG 59.243 37.037 0.00 0.00 0.00 2.74
327 1342 4.387559 TGTTCTCATACGTCAAATCAACGG 59.612 41.667 0.00 0.00 44.21 4.44
328 1343 5.509605 TGTTCTCATACGTCAAATCAACG 57.490 39.130 0.00 0.00 45.37 4.10
339 1354 7.816513 AGAATGGTGATATGATGTTCTCATACG 59.183 37.037 0.00 0.00 46.92 3.06
384 1399 4.039973 TGACTAAAGTGACACGAGGGAAAT 59.960 41.667 0.00 0.00 0.00 2.17
385 1400 3.385433 TGACTAAAGTGACACGAGGGAAA 59.615 43.478 0.00 0.00 0.00 3.13
386 1401 2.960384 TGACTAAAGTGACACGAGGGAA 59.040 45.455 0.00 0.00 0.00 3.97
406 1422 6.513180 CCATCAATCCCATTTGAAGAAGATG 58.487 40.000 0.00 0.00 38.98 2.90
420 1439 0.886490 CGTGCCTAGCCATCAATCCC 60.886 60.000 0.00 0.00 0.00 3.85
425 1444 1.220749 GGAACGTGCCTAGCCATCA 59.779 57.895 4.88 0.00 0.00 3.07
429 1448 0.535797 AAGTAGGAACGTGCCTAGCC 59.464 55.000 23.47 12.21 41.05 3.93
440 1459 3.203487 ACCTGGTTTGTGGAAAGTAGGAA 59.797 43.478 0.00 0.00 32.93 3.36
441 1460 2.781174 ACCTGGTTTGTGGAAAGTAGGA 59.219 45.455 0.00 0.00 32.93 2.94
442 1461 2.884639 CACCTGGTTTGTGGAAAGTAGG 59.115 50.000 0.00 0.00 34.02 3.18
444 1463 2.303175 GCACCTGGTTTGTGGAAAGTA 58.697 47.619 0.00 0.00 34.27 2.24
445 1464 1.111277 GCACCTGGTTTGTGGAAAGT 58.889 50.000 0.00 0.00 34.27 2.66
446 1465 1.110442 TGCACCTGGTTTGTGGAAAG 58.890 50.000 0.00 0.00 34.27 2.62
453 1472 4.759693 TCTGTAATAGTTGCACCTGGTTTG 59.240 41.667 0.00 0.00 0.00 2.93
458 1477 7.602644 TCTTAACTTCTGTAATAGTTGCACCTG 59.397 37.037 0.00 0.00 36.16 4.00
461 1480 8.535690 AGTCTTAACTTCTGTAATAGTTGCAC 57.464 34.615 0.00 0.00 36.16 4.57
462 1481 9.635520 GTAGTCTTAACTTCTGTAATAGTTGCA 57.364 33.333 0.00 0.00 36.92 4.08
463 1482 9.857957 AGTAGTCTTAACTTCTGTAATAGTTGC 57.142 33.333 0.00 0.00 36.92 4.17
494 1514 3.192422 TGCAGTGCGGTGCTAATTAATTT 59.808 39.130 11.20 0.00 44.32 1.82
496 1516 2.097466 GTGCAGTGCGGTGCTAATTAAT 59.903 45.455 11.20 0.00 44.32 1.40
507 1527 0.381801 AAGAAACTTGTGCAGTGCGG 59.618 50.000 11.20 3.25 35.12 5.69
508 1528 1.469917 CAAGAAACTTGTGCAGTGCG 58.530 50.000 11.20 0.00 35.12 5.34
514 1534 2.024414 AGGACACCAAGAAACTTGTGC 58.976 47.619 9.99 0.00 0.00 4.57
517 1537 4.821805 ACATACAGGACACCAAGAAACTTG 59.178 41.667 4.73 4.73 0.00 3.16
518 1538 5.048846 ACATACAGGACACCAAGAAACTT 57.951 39.130 0.00 0.00 0.00 2.66
524 1544 2.095768 CGCAAACATACAGGACACCAAG 60.096 50.000 0.00 0.00 0.00 3.61
526 1546 1.202710 ACGCAAACATACAGGACACCA 60.203 47.619 0.00 0.00 0.00 4.17
531 1551 6.035220 CGTAATTAAGACGCAAACATACAGGA 59.965 38.462 0.31 0.00 32.89 3.86
533 1553 6.985013 TCGTAATTAAGACGCAAACATACAG 58.015 36.000 7.62 0.00 40.14 2.74
540 1560 5.141568 GCAAGTTCGTAATTAAGACGCAAA 58.858 37.500 0.17 0.00 40.14 3.68
544 1564 5.957796 GGATTGCAAGTTCGTAATTAAGACG 59.042 40.000 4.94 6.40 41.69 4.18
548 1568 5.392595 GCCAGGATTGCAAGTTCGTAATTAA 60.393 40.000 4.94 0.00 0.00 1.40
553 1573 1.271108 TGCCAGGATTGCAAGTTCGTA 60.271 47.619 4.94 0.00 35.40 3.43
555 1575 0.813184 ATGCCAGGATTGCAAGTTCG 59.187 50.000 4.94 0.00 42.92 3.95
588 1612 9.372369 GAAATGCTACACTAAGACATAGTTTCT 57.628 33.333 0.00 0.00 42.31 2.52
617 1641 6.401047 AGATGCCAATATTTTGACCAGATG 57.599 37.500 0.00 0.00 34.60 2.90
646 1670 9.961265 CCATGACGAGTGTATTTATCTTTAGTA 57.039 33.333 0.00 0.00 0.00 1.82
737 2681 7.877097 CACAAGGAACAATTAATGATGGGAAAA 59.123 33.333 0.00 0.00 0.00 2.29
754 2702 5.462068 GTGTAAAAATGGAAGCACAAGGAAC 59.538 40.000 0.00 0.00 0.00 3.62
763 2711 5.102313 GCACTATGGTGTAAAAATGGAAGC 58.898 41.667 11.18 0.00 44.65 3.86
780 2728 6.183360 GCTTGAGTTCTAGTTCTAGGCACTAT 60.183 42.308 6.96 0.00 41.70 2.12
795 2743 6.344500 CCACTATGTGATTAGCTTGAGTTCT 58.656 40.000 0.00 0.00 35.23 3.01
796 2744 5.007136 GCCACTATGTGATTAGCTTGAGTTC 59.993 44.000 0.00 0.00 35.23 3.01
812 2760 4.400251 AGGATTGTTTGTCATGCCACTATG 59.600 41.667 0.00 0.00 0.00 2.23
815 2763 2.821969 GAGGATTGTTTGTCATGCCACT 59.178 45.455 0.00 0.00 0.00 4.00
822 2770 4.058124 CGAACAGAGAGGATTGTTTGTCA 58.942 43.478 0.00 0.00 37.63 3.58
823 2771 4.058817 ACGAACAGAGAGGATTGTTTGTC 58.941 43.478 4.79 0.00 44.57 3.18
828 2776 4.703897 TCAAAACGAACAGAGAGGATTGT 58.296 39.130 0.00 0.00 0.00 2.71
932 2970 8.361139 GGCTTCTAGTTCTAGCTTGTATTATGA 58.639 37.037 0.00 0.00 35.30 2.15
938 2976 5.624738 GCTTGGCTTCTAGTTCTAGCTTGTA 60.625 44.000 0.00 0.00 35.30 2.41
941 2979 3.369997 GGCTTGGCTTCTAGTTCTAGCTT 60.370 47.826 0.00 0.00 35.30 3.74
954 2992 1.764571 TACTCGGTGTGGCTTGGCTT 61.765 55.000 0.00 0.00 0.00 4.35
955 2993 1.553690 ATACTCGGTGTGGCTTGGCT 61.554 55.000 0.00 0.00 0.00 4.75
956 2994 1.078426 ATACTCGGTGTGGCTTGGC 60.078 57.895 0.00 0.00 0.00 4.52
957 2995 0.249120 TGATACTCGGTGTGGCTTGG 59.751 55.000 0.00 0.00 0.00 3.61
958 2996 1.359848 GTGATACTCGGTGTGGCTTG 58.640 55.000 0.00 0.00 0.00 4.01
983 3021 1.021390 CATCGCCAGTGAAGTGGTCC 61.021 60.000 6.06 0.00 40.09 4.46
985 3023 0.320771 GTCATCGCCAGTGAAGTGGT 60.321 55.000 6.06 0.00 40.09 4.16
986 3024 0.320683 TGTCATCGCCAGTGAAGTGG 60.321 55.000 0.00 0.00 41.01 4.00
987 3025 0.792640 GTGTCATCGCCAGTGAAGTG 59.207 55.000 0.00 0.00 0.00 3.16
1116 3158 2.109304 GGAGAGGTAGACTAGGGCATCT 59.891 54.545 0.00 0.00 0.00 2.90
1221 3263 1.760875 GGACAGGACATAGGCCGGA 60.761 63.158 5.05 0.00 0.00 5.14
1247 3289 4.215908 GACAGGTGTGGATAGATAGTCCA 58.784 47.826 0.00 0.00 43.26 4.02
1360 3406 0.321653 ATCACGGGAAGCAGAACCAC 60.322 55.000 0.00 0.00 0.00 4.16
1420 3469 2.755876 ACGATGAGGCTCTCCGCA 60.756 61.111 22.20 2.52 46.18 5.69
1455 3504 1.588082 GACGGCGACAGAAGGGTTA 59.412 57.895 16.62 0.00 0.00 2.85
1519 3568 5.198965 AGAATGAAAGAGATGGTTCCCATG 58.801 41.667 0.00 0.00 45.26 3.66
1588 3637 0.104855 TGAACGTGCACAAGAGAGCT 59.895 50.000 18.64 0.00 32.15 4.09
1703 3752 6.264970 AGTTACCTTAGTAAGTCGATGATCCC 59.735 42.308 9.05 0.00 37.53 3.85
1765 4323 4.442733 GTGTTTCAAGTTGAGACGAGAGAG 59.557 45.833 18.59 0.00 34.57 3.20
1792 4350 7.169308 GTGAACGACGAAATTATATCAGGATGT 59.831 37.037 0.00 0.00 37.40 3.06
1793 4351 7.359264 GGTGAACGACGAAATTATATCAGGATG 60.359 40.741 0.00 0.00 37.54 3.51
1867 4425 4.569162 CGTTCCACTACTTGACTTGAACAA 59.431 41.667 0.00 0.00 32.30 2.83
1889 4447 4.055360 TGATACCAAACAACACTGAGACG 58.945 43.478 0.00 0.00 0.00 4.18
1892 4450 5.527214 TCAGTTGATACCAAACAACACTGAG 59.473 40.000 0.00 0.00 45.70 3.35
1937 4503 1.142667 TGCTGGTTGGTGATGACTGAA 59.857 47.619 0.00 0.00 0.00 3.02
1987 4553 4.218635 TGTCCTATCAATCTCTACCATCGC 59.781 45.833 0.00 0.00 0.00 4.58
2066 4632 6.985117 ACATCAATGTCATTTGCAGTTTACT 58.015 32.000 0.00 0.00 35.87 2.24
2067 4633 7.381948 TCAACATCAATGTCATTTGCAGTTTAC 59.618 33.333 0.00 0.00 40.80 2.01
2113 4679 0.744414 GAAATCCTGCGCACCTAGCA 60.744 55.000 5.66 0.00 46.13 3.49
2116 4682 1.737838 CTTGAAATCCTGCGCACCTA 58.262 50.000 5.66 0.00 0.00 3.08
2139 4705 0.170561 CATCACCTTGCTGCTGCTTC 59.829 55.000 17.00 0.00 40.48 3.86
2144 4710 1.565390 TAGCCCATCACCTTGCTGCT 61.565 55.000 0.00 0.00 35.34 4.24
2145 4711 1.077501 TAGCCCATCACCTTGCTGC 60.078 57.895 0.00 0.00 35.34 5.25
2146 4712 1.091771 CGTAGCCCATCACCTTGCTG 61.092 60.000 0.00 0.00 35.34 4.41
2147 4713 1.221840 CGTAGCCCATCACCTTGCT 59.778 57.895 0.00 0.00 37.84 3.91
2148 4714 0.177141 TACGTAGCCCATCACCTTGC 59.823 55.000 0.00 0.00 0.00 4.01
2184 4755 7.452813 AGAAAAGCATCAAAGGAAGTAGGAAAT 59.547 33.333 0.00 0.00 0.00 2.17
2193 4772 8.859090 TCTTTATTCAGAAAAGCATCAAAGGAA 58.141 29.630 0.00 0.00 34.58 3.36
2206 4785 6.885918 TGCATGTCCATCTCTTTATTCAGAAA 59.114 34.615 0.00 0.00 0.00 2.52
2221 4800 1.378911 ACACGGCATGCATGTCCAT 60.379 52.632 28.15 17.79 0.00 3.41
2222 4801 2.033911 ACACGGCATGCATGTCCA 59.966 55.556 28.15 0.00 0.00 4.02
2223 4802 1.378882 ATCACACGGCATGCATGTCC 61.379 55.000 24.92 23.65 0.00 4.02
2224 4803 0.248336 CATCACACGGCATGCATGTC 60.248 55.000 26.79 24.28 0.00 3.06
2225 4804 0.961857 ACATCACACGGCATGCATGT 60.962 50.000 26.79 19.63 32.58 3.21
2226 4805 0.171679 AACATCACACGGCATGCATG 59.828 50.000 22.70 22.70 0.00 4.06
2227 4806 0.171679 CAACATCACACGGCATGCAT 59.828 50.000 21.36 3.56 0.00 3.96
2228 4807 1.171549 ACAACATCACACGGCATGCA 61.172 50.000 21.36 0.00 0.00 3.96
2229 4808 0.730155 CACAACATCACACGGCATGC 60.730 55.000 9.90 9.90 0.00 4.06
2230 4809 0.592637 ACACAACATCACACGGCATG 59.407 50.000 0.00 0.00 0.00 4.06
2262 4841 2.208431 CGGAGGGAGTACTGTACTACG 58.792 57.143 20.86 15.43 40.68 3.51
2263 4842 3.274095 ACGGAGGGAGTACTGTACTAC 57.726 52.381 19.80 19.80 39.59 2.73
2264 4843 3.370953 GGAACGGAGGGAGTACTGTACTA 60.371 52.174 19.73 0.00 39.59 1.82
2265 4844 2.620108 GGAACGGAGGGAGTACTGTACT 60.620 54.545 19.79 19.79 42.86 2.73
2266 4845 1.747924 GGAACGGAGGGAGTACTGTAC 59.252 57.143 9.93 9.93 0.00 2.90
2267 4846 2.134789 GGAACGGAGGGAGTACTGTA 57.865 55.000 0.00 0.00 0.00 2.74
2268 4847 2.973148 GGAACGGAGGGAGTACTGT 58.027 57.895 0.00 0.00 0.00 3.55
2287 4866 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
2288 4867 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
2289 4868 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
2290 4869 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2291 4870 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2292 4871 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2293 4872 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2294 4873 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2295 4874 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2296 4875 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2309 4888 8.848474 TTTGGTGGTTTTAGTTCAAATTTGAA 57.152 26.923 26.01 26.01 44.31 2.69
2310 4889 8.848474 TTTTGGTGGTTTTAGTTCAAATTTGA 57.152 26.923 16.91 16.91 34.92 2.69
2311 4890 8.726068 ACTTTTGGTGGTTTTAGTTCAAATTTG 58.274 29.630 12.15 12.15 0.00 2.32
2312 4891 8.856153 ACTTTTGGTGGTTTTAGTTCAAATTT 57.144 26.923 0.00 0.00 0.00 1.82
2313 4892 9.945904 TTACTTTTGGTGGTTTTAGTTCAAATT 57.054 25.926 0.00 0.00 0.00 1.82
2314 4893 9.945904 TTTACTTTTGGTGGTTTTAGTTCAAAT 57.054 25.926 0.00 0.00 0.00 2.32
2315 4894 9.945904 ATTTACTTTTGGTGGTTTTAGTTCAAA 57.054 25.926 0.00 0.00 0.00 2.69
2316 4895 9.589111 GATTTACTTTTGGTGGTTTTAGTTCAA 57.411 29.630 0.00 0.00 0.00 2.69
2317 4896 7.916450 CGATTTACTTTTGGTGGTTTTAGTTCA 59.084 33.333 0.00 0.00 0.00 3.18
2318 4897 7.380333 CCGATTTACTTTTGGTGGTTTTAGTTC 59.620 37.037 0.00 0.00 0.00 3.01
2319 4898 7.068470 TCCGATTTACTTTTGGTGGTTTTAGTT 59.932 33.333 0.00 0.00 0.00 2.24
2320 4899 6.546772 TCCGATTTACTTTTGGTGGTTTTAGT 59.453 34.615 0.00 0.00 0.00 2.24
2321 4900 6.972722 TCCGATTTACTTTTGGTGGTTTTAG 58.027 36.000 0.00 0.00 0.00 1.85
2322 4901 6.956202 TCCGATTTACTTTTGGTGGTTTTA 57.044 33.333 0.00 0.00 0.00 1.52
2323 4902 5.855740 TCCGATTTACTTTTGGTGGTTTT 57.144 34.783 0.00 0.00 0.00 2.43
2324 4903 5.593968 GTTCCGATTTACTTTTGGTGGTTT 58.406 37.500 0.00 0.00 0.00 3.27
2325 4904 4.261280 CGTTCCGATTTACTTTTGGTGGTT 60.261 41.667 0.00 0.00 0.00 3.67
2326 4905 3.251487 CGTTCCGATTTACTTTTGGTGGT 59.749 43.478 0.00 0.00 0.00 4.16
2327 4906 3.365565 CCGTTCCGATTTACTTTTGGTGG 60.366 47.826 0.00 0.00 0.00 4.61
2328 4907 3.499157 TCCGTTCCGATTTACTTTTGGTG 59.501 43.478 0.00 0.00 0.00 4.17
2329 4908 3.742385 TCCGTTCCGATTTACTTTTGGT 58.258 40.909 0.00 0.00 0.00 3.67
2330 4909 3.126343 CCTCCGTTCCGATTTACTTTTGG 59.874 47.826 0.00 0.00 0.00 3.28
2331 4910 3.126343 CCCTCCGTTCCGATTTACTTTTG 59.874 47.826 0.00 0.00 0.00 2.44
2332 4911 3.008266 TCCCTCCGTTCCGATTTACTTTT 59.992 43.478 0.00 0.00 0.00 2.27
2333 4912 2.568509 TCCCTCCGTTCCGATTTACTTT 59.431 45.455 0.00 0.00 0.00 2.66
2334 4913 2.167900 CTCCCTCCGTTCCGATTTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2335 4914 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
2336 4915 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
2337 4916 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
2338 4917 1.479730 GTACTCCCTCCGTTCCGATTT 59.520 52.381 0.00 0.00 0.00 2.17
2339 4918 1.109609 GTACTCCCTCCGTTCCGATT 58.890 55.000 0.00 0.00 0.00 3.34
2340 4919 0.258194 AGTACTCCCTCCGTTCCGAT 59.742 55.000 0.00 0.00 0.00 4.18
2341 4920 0.911769 TAGTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
2342 4921 1.307097 CTAGTACTCCCTCCGTTCCG 58.693 60.000 0.00 0.00 0.00 4.30
2343 4922 1.031235 GCTAGTACTCCCTCCGTTCC 58.969 60.000 0.00 0.00 0.00 3.62
2344 4923 2.055684 AGCTAGTACTCCCTCCGTTC 57.944 55.000 0.00 0.00 0.00 3.95
2345 4924 2.509131 ACTAGCTAGTACTCCCTCCGTT 59.491 50.000 24.97 0.00 34.13 4.44
2346 4925 2.126057 ACTAGCTAGTACTCCCTCCGT 58.874 52.381 24.97 0.00 34.13 4.69
2347 4926 2.934886 ACTAGCTAGTACTCCCTCCG 57.065 55.000 24.97 0.00 34.13 4.63
2348 4927 4.980339 ACTACTAGCTAGTACTCCCTCC 57.020 50.000 26.36 0.00 37.73 4.30
2349 4928 7.243604 TCATACTACTAGCTAGTACTCCCTC 57.756 44.000 26.36 0.00 40.18 4.30
2350 4929 7.630005 TTCATACTACTAGCTAGTACTCCCT 57.370 40.000 26.36 11.06 40.18 4.20
2351 4930 6.372381 GCTTCATACTACTAGCTAGTACTCCC 59.628 46.154 26.36 8.57 40.18 4.30
2352 4931 7.163441 AGCTTCATACTACTAGCTAGTACTCC 58.837 42.308 26.36 10.89 41.87 3.85
2353 4932 8.500773 CAAGCTTCATACTACTAGCTAGTACTC 58.499 40.741 26.36 11.00 42.79 2.59
2354 4933 7.040961 GCAAGCTTCATACTACTAGCTAGTACT 60.041 40.741 26.36 20.07 42.79 2.73
2355 4934 7.040961 AGCAAGCTTCATACTACTAGCTAGTAC 60.041 40.741 26.36 15.38 42.79 2.73
2426 5005 0.171007 CAACCAAAGCCACCATAGCG 59.829 55.000 0.00 0.00 34.64 4.26
2435 5014 3.751698 CAGAGTAACTACCAACCAAAGCC 59.248 47.826 0.00 0.00 0.00 4.35
2448 5027 2.169330 GAGGTCCGGTTCAGAGTAACT 58.831 52.381 0.00 0.00 0.00 2.24
2468 5047 6.581370 CGGCACAAATCGTTATGTTAGATAG 58.419 40.000 0.00 0.00 0.00 2.08
2481 5060 3.405170 AAATAGAAGCGGCACAAATCG 57.595 42.857 1.45 0.00 0.00 3.34
2495 5074 3.098377 TGGGCACGTACTGGTAAATAGA 58.902 45.455 0.00 0.00 0.00 1.98
2497 5076 4.405036 TGTATGGGCACGTACTGGTAAATA 59.595 41.667 18.88 0.00 39.36 1.40
2528 5107 1.491670 ATGCATCAGATCGTGCGTAC 58.508 50.000 11.97 0.00 44.11 3.67
2529 5108 2.922335 GCTATGCATCAGATCGTGCGTA 60.922 50.000 0.19 16.47 44.11 4.42
2533 5112 2.335752 GAGGCTATGCATCAGATCGTG 58.664 52.381 0.19 0.00 39.28 4.35
2547 5126 3.227614 TGCATACGTAGAATGGAGGCTA 58.772 45.455 0.08 0.00 0.00 3.93
2551 5130 7.545615 TGCTATTATTGCATACGTAGAATGGAG 59.454 37.037 0.08 1.29 35.31 3.86
2597 5176 2.282407 CACCATCGATTGCATCAGACA 58.718 47.619 0.00 0.00 0.00 3.41
2601 5180 1.485895 TCTCCACCATCGATTGCATCA 59.514 47.619 0.00 0.00 0.00 3.07
2602 5181 2.141517 CTCTCCACCATCGATTGCATC 58.858 52.381 0.00 0.00 0.00 3.91
2603 5182 1.202734 CCTCTCCACCATCGATTGCAT 60.203 52.381 0.00 0.00 0.00 3.96
2604 5183 0.178767 CCTCTCCACCATCGATTGCA 59.821 55.000 0.00 0.00 0.00 4.08
2605 5184 1.162800 GCCTCTCCACCATCGATTGC 61.163 60.000 0.00 0.00 0.00 3.56
2606 5185 0.533755 GGCCTCTCCACCATCGATTG 60.534 60.000 0.00 0.00 34.01 2.67
2607 5186 0.982852 TGGCCTCTCCACCATCGATT 60.983 55.000 3.32 0.00 40.72 3.34
2608 5187 1.383109 TGGCCTCTCCACCATCGAT 60.383 57.895 3.32 0.00 40.72 3.59
2609 5188 2.038813 TGGCCTCTCCACCATCGA 59.961 61.111 3.32 0.00 40.72 3.59
2617 5196 3.857157 TGTGGTTATAATGGCCTCTCC 57.143 47.619 3.32 0.00 0.00 3.71
2618 5197 5.234466 AGATGTGGTTATAATGGCCTCTC 57.766 43.478 3.32 0.00 0.00 3.20
2619 5198 5.653255 AAGATGTGGTTATAATGGCCTCT 57.347 39.130 3.32 0.00 0.00 3.69
2620 5199 7.284489 TGTTTAAGATGTGGTTATAATGGCCTC 59.716 37.037 3.32 0.00 0.00 4.70
2621 5200 7.122715 TGTTTAAGATGTGGTTATAATGGCCT 58.877 34.615 3.32 0.00 0.00 5.19
2622 5201 7.341445 TGTTTAAGATGTGGTTATAATGGCC 57.659 36.000 0.00 0.00 0.00 5.36
2623 5202 9.646427 TTTTGTTTAAGATGTGGTTATAATGGC 57.354 29.630 0.00 0.00 0.00 4.40
2642 5221 9.880157 CCATTCCTCATGATCTTTATTTTGTTT 57.120 29.630 0.00 0.00 34.31 2.83
2643 5222 7.983484 GCCATTCCTCATGATCTTTATTTTGTT 59.017 33.333 0.00 0.00 34.31 2.83
2644 5223 7.343833 AGCCATTCCTCATGATCTTTATTTTGT 59.656 33.333 0.00 0.00 34.31 2.83
2645 5224 7.723324 AGCCATTCCTCATGATCTTTATTTTG 58.277 34.615 0.00 0.00 34.31 2.44
2646 5225 7.909485 AGCCATTCCTCATGATCTTTATTTT 57.091 32.000 0.00 0.00 34.31 1.82
2647 5226 7.255381 CGAAGCCATTCCTCATGATCTTTATTT 60.255 37.037 0.00 0.00 34.31 1.40
2648 5227 6.206243 CGAAGCCATTCCTCATGATCTTTATT 59.794 38.462 0.00 0.00 34.31 1.40
2649 5228 5.704515 CGAAGCCATTCCTCATGATCTTTAT 59.295 40.000 0.00 0.00 34.31 1.40
2650 5229 5.059161 CGAAGCCATTCCTCATGATCTTTA 58.941 41.667 0.00 0.00 34.31 1.85
2651 5230 3.881688 CGAAGCCATTCCTCATGATCTTT 59.118 43.478 0.00 0.00 34.31 2.52
2652 5231 3.135348 TCGAAGCCATTCCTCATGATCTT 59.865 43.478 0.00 0.00 34.31 2.40
2653 5232 2.702478 TCGAAGCCATTCCTCATGATCT 59.298 45.455 0.00 0.00 34.31 2.75
2654 5233 3.065655 CTCGAAGCCATTCCTCATGATC 58.934 50.000 0.00 0.00 34.31 2.92
2655 5234 2.809665 GCTCGAAGCCATTCCTCATGAT 60.810 50.000 0.00 0.00 34.48 2.45
2656 5235 1.473965 GCTCGAAGCCATTCCTCATGA 60.474 52.381 0.00 0.00 34.48 3.07
2657 5236 0.942962 GCTCGAAGCCATTCCTCATG 59.057 55.000 0.00 0.00 34.48 3.07
2658 5237 0.531532 CGCTCGAAGCCATTCCTCAT 60.532 55.000 0.00 0.00 38.18 2.90
2659 5238 1.153568 CGCTCGAAGCCATTCCTCA 60.154 57.895 0.00 0.00 38.18 3.86
2660 5239 1.884926 CCGCTCGAAGCCATTCCTC 60.885 63.158 0.00 0.00 38.18 3.71
2661 5240 2.187946 CCGCTCGAAGCCATTCCT 59.812 61.111 0.00 0.00 38.18 3.36
2662 5241 3.577313 GCCGCTCGAAGCCATTCC 61.577 66.667 0.00 0.00 38.18 3.01
2663 5242 3.929948 CGCCGCTCGAAGCCATTC 61.930 66.667 0.00 0.00 38.18 2.67
2664 5243 4.451150 TCGCCGCTCGAAGCCATT 62.451 61.111 0.00 0.00 45.36 3.16
2676 5255 4.933064 GGATCGCCTGTCTCGCCG 62.933 72.222 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.