Multiple sequence alignment - TraesCS6A01G389000

Loading Multiple Alignment...

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 TraesCS6A01G389000 chr6A 100.000 5472 0 0 1 5472 604611875 604606404 0.000000e+00 10105
1 TraesCS6A01G389000 chr6A 99.585 963 2 1 1 961 590107599 590108561 0.000000e+00 1755
2 TraesCS6A01G389000 chr6A 83.610 543 62 19 4003 4542 604852337 604851819 8.240000e-133 484
3 TraesCS6A01G389000 chr6B 90.225 3509 300 22 961 4439 696251257 696247762 0.000000e+00 4540
4 TraesCS6A01G389000 chr6B 85.068 3402 429 43 991 4335 696152504 696149125 0.000000e+00 3395
5 TraesCS6A01G389000 chr6B 86.582 2437 267 36 2313 4719 696343047 696340641 0.000000e+00 2634
6 TraesCS6A01G389000 chr6B 84.187 2694 317 54 1885 4511 696177878 696175227 0.000000e+00 2514
7 TraesCS6A01G389000 chr6B 85.793 2351 275 29 2380 4719 696303532 696301230 0.000000e+00 2436
8 TraesCS6A01G389000 chr6B 91.392 848 65 2 961 1800 696345311 696344464 0.000000e+00 1155
9 TraesCS6A01G389000 chr6B 87.093 829 104 1 991 1819 696179058 696178233 0.000000e+00 935
10 TraesCS6A01G389000 chr6B 88.571 700 45 13 4567 5243 696145555 696144868 0.000000e+00 817
11 TraesCS6A01G389000 chr6B 97.059 68 1 1 5347 5413 696144837 696144770 4.480000e-21 113
12 TraesCS6A01G389000 chr6D 84.683 3395 436 52 991 4333 458019432 458016070 0.000000e+00 3312
13 TraesCS6A01G389000 chr6D 86.624 2669 286 36 2084 4722 458027654 458025027 0.000000e+00 2885
14 TraesCS6A01G389000 chr6D 88.553 2315 242 18 2144 4446 457697730 457695427 0.000000e+00 2785
15 TraesCS6A01G389000 chr6D 88.498 2017 228 3 2450 4463 458057306 458055291 0.000000e+00 2436
16 TraesCS6A01G389000 chr6D 90.345 1564 140 6 2035 3594 458012203 458010647 0.000000e+00 2041
17 TraesCS6A01G389000 chr6D 87.508 1617 182 16 2355 3966 458049527 458047926 0.000000e+00 1849
18 TraesCS6A01G389000 chr6D 90.972 864 75 2 961 1824 458060332 458059472 0.000000e+00 1160
19 TraesCS6A01G389000 chr6D 88.452 840 93 3 991 1829 457699966 457699130 0.000000e+00 1011
20 TraesCS6A01G389000 chr6D 88.519 810 91 2 991 1799 458028985 458028177 0.000000e+00 979
21 TraesCS6A01G389000 chr6D 84.304 962 125 12 3582 4542 458009823 458008887 0.000000e+00 917
22 TraesCS6A01G389000 chr6D 85.714 602 83 1 987 1588 458050125 458049527 2.780000e-177 632
23 TraesCS6A01G389000 chr6D 84.293 573 64 13 1402 1948 458012794 458012222 2.240000e-148 536
24 TraesCS6A01G389000 chr6D 83.914 373 50 3 3961 4333 458045264 458044902 1.130000e-91 348
25 TraesCS6A01G389000 chr6D 78.492 358 49 15 4367 4721 458016006 458015674 5.550000e-50 209
26 TraesCS6A01G389000 chr2A 99.274 964 4 2 1 962 775203003 775203965 0.000000e+00 1738
27 TraesCS6A01G389000 chr2A 98.344 966 8 2 1 961 755085186 755086148 0.000000e+00 1688
28 TraesCS6A01G389000 chr4B 98.962 963 8 1 1 961 489663301 489664263 0.000000e+00 1722
29 TraesCS6A01G389000 chr5B 98.127 961 15 3 1 961 684778587 684777630 0.000000e+00 1672
30 TraesCS6A01G389000 chr1B 97.720 965 17 5 1 964 603286345 603285385 0.000000e+00 1655
31 TraesCS6A01G389000 chr1B 96.674 962 23 5 1 961 681028540 681029493 0.000000e+00 1591
32 TraesCS6A01G389000 chr2B 97.713 962 15 6 1 961 632378016 632378971 0.000000e+00 1648
33 TraesCS6A01G389000 chr7A 97.508 963 19 4 1 963 34442597 34441640 0.000000e+00 1640


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 TraesCS6A01G389000 chr6A 604606404 604611875 5471 True 10105.000000 10105 100.000000 1 5472 1 chr6A.!!$R1 5471
1 TraesCS6A01G389000 chr6A 590107599 590108561 962 False 1755.000000 1755 99.585000 1 961 1 chr6A.!!$F1 960
2 TraesCS6A01G389000 chr6A 604851819 604852337 518 True 484.000000 484 83.610000 4003 4542 1 chr6A.!!$R2 539
3 TraesCS6A01G389000 chr6B 696247762 696251257 3495 True 4540.000000 4540 90.225000 961 4439 1 chr6B.!!$R1 3478
4 TraesCS6A01G389000 chr6B 696301230 696303532 2302 True 2436.000000 2436 85.793000 2380 4719 1 chr6B.!!$R2 2339
5 TraesCS6A01G389000 chr6B 696340641 696345311 4670 True 1894.500000 2634 88.987000 961 4719 2 chr6B.!!$R5 3758
6 TraesCS6A01G389000 chr6B 696175227 696179058 3831 True 1724.500000 2514 85.640000 991 4511 2 chr6B.!!$R4 3520
7 TraesCS6A01G389000 chr6B 696144770 696152504 7734 True 1441.666667 3395 90.232667 991 5413 3 chr6B.!!$R3 4422
8 TraesCS6A01G389000 chr6D 458025027 458028985 3958 True 1932.000000 2885 87.571500 991 4722 2 chr6D.!!$R3 3731
9 TraesCS6A01G389000 chr6D 457695427 457699966 4539 True 1898.000000 2785 88.502500 991 4446 2 chr6D.!!$R1 3455
10 TraesCS6A01G389000 chr6D 458055291 458060332 5041 True 1798.000000 2436 89.735000 961 4463 2 chr6D.!!$R5 3502
11 TraesCS6A01G389000 chr6D 458008887 458019432 10545 True 1403.000000 3312 84.423400 991 4721 5 chr6D.!!$R2 3730
12 TraesCS6A01G389000 chr6D 458044902 458050125 5223 True 943.000000 1849 85.712000 987 4333 3 chr6D.!!$R4 3346
13 TraesCS6A01G389000 chr2A 775203003 775203965 962 False 1738.000000 1738 99.274000 1 962 1 chr2A.!!$F2 961
14 TraesCS6A01G389000 chr2A 755085186 755086148 962 False 1688.000000 1688 98.344000 1 961 1 chr2A.!!$F1 960
15 TraesCS6A01G389000 chr4B 489663301 489664263 962 False 1722.000000 1722 98.962000 1 961 1 chr4B.!!$F1 960
16 TraesCS6A01G389000 chr5B 684777630 684778587 957 True 1672.000000 1672 98.127000 1 961 1 chr5B.!!$R1 960
17 TraesCS6A01G389000 chr1B 603285385 603286345 960 True 1655.000000 1655 97.720000 1 964 1 chr1B.!!$R1 963
18 TraesCS6A01G389000 chr1B 681028540 681029493 953 False 1591.000000 1591 96.674000 1 961 1 chr1B.!!$F1 960
19 TraesCS6A01G389000 chr2B 632378016 632378971 955 False 1648.000000 1648 97.713000 1 961 1 chr2B.!!$F1 960
20 TraesCS6A01G389000 chr7A 34441640 34442597 957 True 1640.000000 1640 97.508000 1 963 1 chr7A.!!$R1 962

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
724 727 6.128634 GGAGAGTAAACCTTACGTGAATTGTG 60.129 42.308 0.00 0.0 0.00 3.33 F
1568 1584 0.110192 GAAAAAGGCTCGACCAAGCG 60.110 55.000 6.78 0.0 43.45 4.68 F
1627 1643 0.179067 AAAAACGACACTGGCGAGGA 60.179 50.000 12.34 0.0 0.00 3.71 F
3270 6040 0.807496 GACCAAGAGCTTGCATCCAC 59.193 55.000 4.72 0.0 39.16 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1736 0.531532 CGCAAGGTAGCTGGGAGATG 60.532 60.000 0.00 0.00 0.00 2.90 R
3196 5966 1.001487 TCACGCTTTGCCAAATCAGTG 60.001 47.619 11.23 11.23 0.00 3.66 R
3596 6366 3.191371 GGATCACGGAAAAAGCATCTTGT 59.809 43.478 0.00 0.00 0.00 3.16 R
5244 21117 0.033504 GGACGTTGCTGGAGTCTCAA 59.966 55.000 1.47 0.00 35.42 3.02 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
724 727 6.128634 GGAGAGTAAACCTTACGTGAATTGTG 60.129 42.308 0.00 0.00 0.00 3.33
969 978 6.881065 TCAGATCAAAACCAACAATAGAGAGG 59.119 38.462 0.00 0.00 0.00 3.69
1212 1228 1.216444 GTGGATGTCGCTGCTGAGA 59.784 57.895 0.00 0.00 0.00 3.27
1257 1273 4.206477 TGTCATCGACAAGTTCATCCAT 57.794 40.909 0.00 0.00 39.78 3.41
1270 1286 0.879400 CATCCATCAGCTCGGCACTC 60.879 60.000 0.00 0.00 0.00 3.51
1271 1287 2.037620 ATCCATCAGCTCGGCACTCC 62.038 60.000 0.00 0.00 0.00 3.85
1285 1301 4.659172 CTCCCGGCCACCAGCAAA 62.659 66.667 2.24 0.00 46.50 3.68
1542 1558 2.691526 TGATCTTGCCAATTGGATGCTC 59.308 45.455 29.02 16.27 37.39 4.26
1554 1570 5.902613 ATTGGATGCTCGAAGATGAAAAA 57.097 34.783 0.00 0.00 33.89 1.94
1568 1584 0.110192 GAAAAAGGCTCGACCAAGCG 60.110 55.000 6.78 0.00 43.45 4.68
1627 1643 0.179067 AAAAACGACACTGGCGAGGA 60.179 50.000 12.34 0.00 0.00 3.71
1680 1696 1.134220 TGTCAGGCTTTTGTCTCGGTT 60.134 47.619 0.00 0.00 27.72 4.44
1836 1854 5.736616 AGATAAGAGGTATTTCAAACCCCCT 59.263 40.000 0.00 0.00 37.77 4.79
1881 2357 7.718314 AGGTTAATTCCTTAATAAGCCTAACGG 59.282 37.037 0.00 0.00 33.52 4.44
1883 2359 9.112725 GTTAATTCCTTAATAAGCCTAACGGAA 57.887 33.333 0.00 0.00 34.22 4.30
1934 2426 8.157476 AGGTTAAAGATCAGTGTTGTACTCAAT 58.843 33.333 0.00 0.00 37.60 2.57
1939 2431 5.934625 AGATCAGTGTTGTACTCAATTGACC 59.065 40.000 3.38 0.00 37.60 4.02
1981 2473 9.899226 GATCCTTTAAAGCATGAATAACATACC 57.101 33.333 9.86 0.00 37.46 2.73
2006 2498 9.554395 CCCATATGTTGTTGTAACATGAGTATA 57.446 33.333 13.79 0.00 40.70 1.47
2225 3686 2.689471 TGGCAACATAAGCAATAGGCAG 59.311 45.455 0.00 0.00 45.17 4.85
2249 3739 4.638304 TGGTAGACCTTAACTTGTTGAGC 58.362 43.478 0.00 0.00 36.82 4.26
2265 3755 5.009631 TGTTGAGCACTTGCACCTTATATT 58.990 37.500 3.62 0.00 45.16 1.28
2266 3756 5.106197 TGTTGAGCACTTGCACCTTATATTG 60.106 40.000 3.62 0.00 45.16 1.90
2291 3781 8.892723 TGTGCTTAGATTATCATGGTTTACTTG 58.107 33.333 0.00 0.00 0.00 3.16
2340 3834 3.242804 CGATCCTCTTGGAGTTCGTAGTC 60.243 52.174 0.00 0.00 46.91 2.59
2342 3836 4.564782 TCCTCTTGGAGTTCGTAGTCTA 57.435 45.455 0.00 0.00 37.46 2.59
2343 3837 4.260170 TCCTCTTGGAGTTCGTAGTCTAC 58.740 47.826 0.00 0.00 37.46 2.59
2524 5294 6.560003 TCAAGTATGCTTTCCCAGAGAATA 57.440 37.500 0.00 0.00 33.44 1.75
2675 5445 6.294361 TGAGAAGAATATTTGGTTCCGAGA 57.706 37.500 0.00 0.00 0.00 4.04
2704 5474 3.612479 GCCCTGATGTGCTAAAACAAGTG 60.612 47.826 0.00 0.00 32.81 3.16
2842 5612 4.686191 TGGTTCTGCATTGGACAAAAAT 57.314 36.364 0.00 0.00 0.00 1.82
3136 5906 3.275999 TCAAGTCCATGACATGATGCTG 58.724 45.455 17.24 8.70 35.75 4.41
3196 5966 1.880819 CTTTGGCAGGCCATGGTCAC 61.881 60.000 20.74 10.18 46.64 3.67
3270 6040 0.807496 GACCAAGAGCTTGCATCCAC 59.193 55.000 4.72 0.00 39.16 4.02
3324 6094 6.920210 CGATCTCTGACAGTTATAGCATCAAA 59.080 38.462 1.59 0.00 0.00 2.69
3577 6347 7.494625 CCTACTGGAATTATTCAGCTCGTAAAA 59.505 37.037 7.29 0.00 34.57 1.52
3604 6374 7.545362 ACAACATCTACTCATTACAAGATGC 57.455 36.000 10.30 0.00 45.98 3.91
3607 6377 8.671921 CAACATCTACTCATTACAAGATGCTTT 58.328 33.333 10.30 0.00 45.98 3.51
3609 6379 9.236006 ACATCTACTCATTACAAGATGCTTTTT 57.764 29.630 10.30 0.00 45.98 1.94
3610 6380 9.713740 CATCTACTCATTACAAGATGCTTTTTC 57.286 33.333 0.00 0.00 39.03 2.29
3611 6381 8.268850 TCTACTCATTACAAGATGCTTTTTCC 57.731 34.615 0.00 0.00 0.00 3.13
3704 6477 8.283291 CGGGCTTTAATATTATGAAGAGTTCAC 58.717 37.037 9.99 0.00 43.48 3.18
3722 6495 4.558226 TCACTATGTGCAGTCAAGGAAT 57.442 40.909 0.00 0.00 32.98 3.01
3734 6507 3.026694 GTCAAGGAATTGGGGAATCTGG 58.973 50.000 0.00 0.00 0.00 3.86
3737 6510 0.262876 GGAATTGGGGAATCTGGCCT 59.737 55.000 3.32 0.00 0.00 5.19
3749 6522 4.321527 GGAATCTGGCCTGTTTGAAAGAAG 60.322 45.833 10.37 0.00 0.00 2.85
3751 6524 2.951642 TCTGGCCTGTTTGAAAGAAGTG 59.048 45.455 3.32 0.00 0.00 3.16
3770 6543 2.939103 GTGCATCTACAGTTGGATGGTC 59.061 50.000 14.27 3.98 39.52 4.02
3864 6637 8.383619 CAAACTTCAGTCTTTACGGATATTCTG 58.616 37.037 0.00 0.00 29.59 3.02
3875 6648 5.207110 ACGGATATTCTGTCCTGATTCAG 57.793 43.478 6.70 6.70 27.61 3.02
3882 6655 0.036732 TGTCCTGATTCAGCACCCAC 59.963 55.000 8.23 0.68 0.00 4.61
3919 6692 3.004126 TGGTCCCCTCTGCCATATAAT 57.996 47.619 0.00 0.00 0.00 1.28
3935 6708 8.814931 TGCCATATAATCTCCAAATATTTTGGG 58.185 33.333 16.72 9.27 39.96 4.12
3993 16421 2.552155 GGATTGTACCAGCACTCACCAA 60.552 50.000 0.00 0.00 0.00 3.67
4031 16459 9.322773 TGAACATTAATTTGATTGAAGCAACAA 57.677 25.926 0.00 0.00 0.00 2.83
4046 16474 1.815003 CAACAAAGGAGGATCTGTGGC 59.185 52.381 0.00 0.00 33.73 5.01
4073 16501 3.202097 GGAGAGATGCCTGCTTTACTTC 58.798 50.000 0.00 0.00 0.00 3.01
4075 16503 2.497675 AGAGATGCCTGCTTTACTTCGA 59.502 45.455 0.00 0.00 0.00 3.71
4285 16713 2.124411 GCCTATGGGTTCTACTTGGGA 58.876 52.381 0.00 0.00 34.45 4.37
4341 16773 5.464168 AGTTACTCTTTGCAATGATGTTGC 58.536 37.500 14.72 5.85 45.11 4.17
4372 16804 0.886563 AAATCAAGTCTGCTGCAGCC 59.113 50.000 34.64 20.05 41.18 4.85
4399 16831 5.634118 TCTATAAGGAATGAGGCAAATGGG 58.366 41.667 0.00 0.00 0.00 4.00
4446 16899 2.758979 TCCAGGACAGAACGGAAGATAC 59.241 50.000 0.00 0.00 0.00 2.24
4451 16904 3.952967 GGACAGAACGGAAGATACCTACT 59.047 47.826 0.00 0.00 0.00 2.57
4459 16912 4.096081 ACGGAAGATACCTACTTTGACGAG 59.904 45.833 0.00 0.00 0.00 4.18
4463 16916 6.183360 GGAAGATACCTACTTTGACGAGGAAT 60.183 42.308 0.00 0.00 34.24 3.01
4464 16917 6.150396 AGATACCTACTTTGACGAGGAATG 57.850 41.667 0.00 0.00 34.24 2.67
4467 16920 3.056035 ACCTACTTTGACGAGGAATGGAC 60.056 47.826 0.00 0.00 34.24 4.02
4522 16975 3.146066 TCACAACCAATGCAAGAGGTAC 58.854 45.455 8.30 0.00 34.63 3.34
4528 16981 4.442706 ACCAATGCAAGAGGTACTAATCG 58.557 43.478 6.32 0.00 41.55 3.34
4569 20418 5.051153 TCGTACATTACTTTCTGTGTGCAA 58.949 37.500 0.00 0.00 0.00 4.08
4621 20470 2.004583 ACCCATACGTGACATGTTCG 57.995 50.000 18.16 18.16 0.00 3.95
4660 20510 3.428589 GGGATCTTCTGTTGAATGCAAGC 60.429 47.826 0.00 0.00 34.01 4.01
4663 20513 2.224079 TCTTCTGTTGAATGCAAGCGTC 59.776 45.455 0.00 0.00 34.01 5.19
4706 20556 0.880441 TGGAATGTTGTGGTGATGCG 59.120 50.000 0.00 0.00 0.00 4.73
4724 20574 0.798776 CGTGAACCATGAAGCTGGAC 59.201 55.000 0.00 0.00 39.73 4.02
4737 20587 4.202357 TGAAGCTGGACTGATTAGTTGTGT 60.202 41.667 0.00 0.00 37.25 3.72
4747 20597 3.814842 TGATTAGTTGTGTGTGGAAGCTG 59.185 43.478 0.00 0.00 0.00 4.24
4755 20605 5.437289 TGTGTGTGGAAGCTGAAATAAAG 57.563 39.130 0.00 0.00 0.00 1.85
4762 20612 3.127030 GGAAGCTGAAATAAAGGTGTCCG 59.873 47.826 0.00 0.00 0.00 4.79
4764 20614 3.600388 AGCTGAAATAAAGGTGTCCGAG 58.400 45.455 0.00 0.00 0.00 4.63
4775 20625 1.070289 GGTGTCCGAGAAGAAGTGGTT 59.930 52.381 0.00 0.00 0.00 3.67
4776 20626 2.484947 GGTGTCCGAGAAGAAGTGGTTT 60.485 50.000 0.00 0.00 0.00 3.27
4832 20684 2.290323 GGGACTGTTGTGCTACCAGATT 60.290 50.000 0.00 0.00 34.78 2.40
4847 20699 5.294734 ACCAGATTTTGTTGCCTTGATTT 57.705 34.783 0.00 0.00 0.00 2.17
4861 20713 8.458843 GTTGCCTTGATTTACTATTGCTAAGAA 58.541 33.333 0.00 0.00 0.00 2.52
4896 20748 2.038387 AGGTGAAGTTTCGCTGTTGT 57.962 45.000 5.51 0.00 37.80 3.32
4897 20749 2.365582 AGGTGAAGTTTCGCTGTTGTT 58.634 42.857 5.51 0.00 37.80 2.83
4898 20750 2.752903 AGGTGAAGTTTCGCTGTTGTTT 59.247 40.909 5.51 0.00 37.80 2.83
4899 20751 3.942748 AGGTGAAGTTTCGCTGTTGTTTA 59.057 39.130 5.51 0.00 37.80 2.01
4947 20799 6.714810 TGTAACTTAATTTGATGGACTGCTGT 59.285 34.615 0.00 0.00 0.00 4.40
4975 20827 7.840931 TGAGATATGTGTACATTCAGTTGAGT 58.159 34.615 0.00 0.00 37.76 3.41
4988 20840 2.945008 CAGTTGAGTTGAAACAGCTGGA 59.055 45.455 19.93 0.00 40.08 3.86
4991 20843 4.037208 AGTTGAGTTGAAACAGCTGGATTG 59.963 41.667 19.93 0.00 0.00 2.67
4992 20844 3.819368 TGAGTTGAAACAGCTGGATTGA 58.181 40.909 19.93 4.01 0.00 2.57
4993 20845 3.817084 TGAGTTGAAACAGCTGGATTGAG 59.183 43.478 19.93 0.00 0.00 3.02
4994 20846 4.067896 GAGTTGAAACAGCTGGATTGAGA 58.932 43.478 19.93 0.00 0.00 3.27
4995 20847 3.817647 AGTTGAAACAGCTGGATTGAGAC 59.182 43.478 19.93 7.64 0.00 3.36
4996 20848 3.777106 TGAAACAGCTGGATTGAGACT 57.223 42.857 19.93 0.00 0.00 3.24
4997 20849 4.090761 TGAAACAGCTGGATTGAGACTT 57.909 40.909 19.93 0.00 0.00 3.01
4998 20850 3.817084 TGAAACAGCTGGATTGAGACTTG 59.183 43.478 19.93 0.00 0.00 3.16
4999 20851 3.777106 AACAGCTGGATTGAGACTTGA 57.223 42.857 19.93 0.00 0.00 3.02
5004 20856 4.032310 AGCTGGATTGAGACTTGAGAGAT 58.968 43.478 0.00 0.00 0.00 2.75
5027 20879 8.874156 AGATATATATGCTGTCAGGTTTCAGAA 58.126 33.333 0.00 0.00 34.02 3.02
5028 20880 8.839310 ATATATATGCTGTCAGGTTTCAGAAC 57.161 34.615 1.14 0.00 34.02 3.01
5039 20891 4.150098 CAGGTTTCAGAACTGTAGTAACGC 59.850 45.833 1.73 0.00 36.03 4.84
5041 20893 4.748600 GGTTTCAGAACTGTAGTAACGCTT 59.251 41.667 1.73 0.00 36.03 4.68
5051 20903 3.732219 TGTAGTAACGCTTTTGTCACTCG 59.268 43.478 0.00 0.00 0.00 4.18
5070 20922 2.426024 TCGTATACTCTGAACCAGTGGC 59.574 50.000 9.78 0.00 32.61 5.01
5097 20949 3.319122 GGAGGATTTGCACAATGGGTATC 59.681 47.826 0.00 0.00 0.00 2.24
5111 20963 3.631250 TGGGTATCCATCCAAGAAAAGC 58.369 45.455 0.00 0.00 38.32 3.51
5112 20964 3.011144 TGGGTATCCATCCAAGAAAAGCA 59.989 43.478 0.00 0.00 38.32 3.91
5121 20973 5.299148 CATCCAAGAAAAGCAAATTCACCA 58.701 37.500 0.00 0.00 0.00 4.17
5123 20975 5.927819 TCCAAGAAAAGCAAATTCACCAAT 58.072 33.333 0.00 0.00 0.00 3.16
5183 21056 8.854614 AAGTGCATAGACTGAAGAAAATTAGT 57.145 30.769 0.00 0.00 0.00 2.24
5185 21058 7.276658 AGTGCATAGACTGAAGAAAATTAGTCG 59.723 37.037 0.00 0.00 43.19 4.18
5192 21065 6.760291 ACTGAAGAAAATTAGTCGAAGGAGT 58.240 36.000 0.00 0.00 0.00 3.85
5194 21067 8.532819 ACTGAAGAAAATTAGTCGAAGGAGTAT 58.467 33.333 0.00 0.00 0.00 2.12
5227 21100 1.079681 TTTATGTCGCCGCTTCCGT 60.080 52.632 0.00 0.00 0.00 4.69
5243 21116 2.741092 GTCCTGGACGTTGCTGGA 59.259 61.111 11.71 0.00 33.72 3.86
5244 21117 1.296715 GTCCTGGACGTTGCTGGAT 59.703 57.895 11.71 0.00 38.03 3.41
5247 21120 0.321564 CCTGGACGTTGCTGGATTGA 60.322 55.000 0.00 0.00 0.00 2.57
5248 21121 1.081892 CTGGACGTTGCTGGATTGAG 58.918 55.000 0.00 0.00 0.00 3.02
5251 21124 1.338200 GGACGTTGCTGGATTGAGACT 60.338 52.381 0.00 0.00 0.00 3.24
5252 21125 1.996191 GACGTTGCTGGATTGAGACTC 59.004 52.381 0.00 0.00 0.00 3.36
5253 21126 1.338200 ACGTTGCTGGATTGAGACTCC 60.338 52.381 0.00 0.00 0.00 3.85
5254 21127 1.338105 CGTTGCTGGATTGAGACTCCA 60.338 52.381 0.00 0.00 40.49 3.86
5260 21133 1.338105 TGGATTGAGACTCCAGCAACG 60.338 52.381 0.00 0.00 37.87 4.10
5261 21134 1.338200 GGATTGAGACTCCAGCAACGT 60.338 52.381 0.00 0.00 32.72 3.99
5264 21137 1.112916 TGAGACTCCAGCAACGTCCA 61.113 55.000 0.00 0.00 0.00 4.02
5265 21138 0.389166 GAGACTCCAGCAACGTCCAG 60.389 60.000 0.00 0.00 0.00 3.86
5266 21139 1.374758 GACTCCAGCAACGTCCAGG 60.375 63.158 0.00 0.00 0.00 4.45
5267 21140 1.816863 GACTCCAGCAACGTCCAGGA 61.817 60.000 0.00 0.00 0.00 3.86
5285 21158 3.919163 ACGGAAGTGGCGACATAAA 57.081 47.368 0.00 0.00 46.97 1.40
5286 21159 1.722011 ACGGAAGTGGCGACATAAAG 58.278 50.000 0.00 0.00 46.97 1.85
5287 21160 1.006832 CGGAAGTGGCGACATAAAGG 58.993 55.000 0.00 0.00 46.14 3.11
5288 21161 1.674817 CGGAAGTGGCGACATAAAGGT 60.675 52.381 0.00 0.00 46.14 3.50
5289 21162 1.737793 GGAAGTGGCGACATAAAGGTG 59.262 52.381 0.00 0.00 46.14 4.00
5290 21163 2.614481 GGAAGTGGCGACATAAAGGTGA 60.614 50.000 0.00 0.00 46.14 4.02
5291 21164 2.386661 AGTGGCGACATAAAGGTGAG 57.613 50.000 0.00 0.00 46.14 3.51
5292 21165 1.066143 AGTGGCGACATAAAGGTGAGG 60.066 52.381 0.00 0.00 46.14 3.86
5293 21166 1.066430 GTGGCGACATAAAGGTGAGGA 60.066 52.381 0.00 0.00 46.14 3.71
5294 21167 1.837439 TGGCGACATAAAGGTGAGGAT 59.163 47.619 0.00 0.00 33.40 3.24
5295 21168 2.158957 TGGCGACATAAAGGTGAGGATC 60.159 50.000 0.00 0.00 33.40 3.36
5296 21169 2.128035 GCGACATAAAGGTGAGGATCG 58.872 52.381 0.00 0.00 38.61 3.69
5298 21171 2.223829 CGACATAAAGGTGAGGATCGCT 60.224 50.000 0.00 0.00 46.91 4.93
5299 21172 3.126831 GACATAAAGGTGAGGATCGCTG 58.873 50.000 0.00 0.00 46.91 5.18
5300 21173 2.766263 ACATAAAGGTGAGGATCGCTGA 59.234 45.455 0.00 0.00 46.91 4.26
5301 21174 3.181471 ACATAAAGGTGAGGATCGCTGAG 60.181 47.826 0.00 0.00 46.91 3.35
5302 21175 0.107945 AAAGGTGAGGATCGCTGAGC 60.108 55.000 0.00 0.00 46.91 4.26
5303 21176 1.965754 AAGGTGAGGATCGCTGAGCC 61.966 60.000 0.00 4.93 46.91 4.70
5304 21177 2.107953 GTGAGGATCGCTGAGCCC 59.892 66.667 0.00 0.00 43.69 5.19
5305 21178 3.157252 TGAGGATCGCTGAGCCCC 61.157 66.667 0.00 0.00 39.17 5.80
5306 21179 3.934962 GAGGATCGCTGAGCCCCC 61.935 72.222 0.00 0.00 39.17 5.40
5309 21182 3.849951 GATCGCTGAGCCCCCGAA 61.850 66.667 0.00 0.00 34.42 4.30
5310 21183 3.798954 GATCGCTGAGCCCCCGAAG 62.799 68.421 0.00 0.00 34.42 3.79
5320 21193 4.215742 CCCCGAAGCGGCGACATA 62.216 66.667 12.98 0.00 46.86 2.29
5321 21194 2.029073 CCCGAAGCGGCGACATAT 59.971 61.111 12.98 0.00 46.86 1.78
5322 21195 1.287815 CCCGAAGCGGCGACATATA 59.712 57.895 12.98 0.00 46.86 0.86
5323 21196 0.108804 CCCGAAGCGGCGACATATAT 60.109 55.000 12.98 0.00 46.86 0.86
5324 21197 1.133598 CCCGAAGCGGCGACATATATA 59.866 52.381 12.98 0.00 46.86 0.86
5325 21198 2.223735 CCCGAAGCGGCGACATATATAT 60.224 50.000 12.98 0.00 46.86 0.86
5326 21199 3.444916 CCGAAGCGGCGACATATATATT 58.555 45.455 12.98 0.00 41.17 1.28
5327 21200 3.242944 CCGAAGCGGCGACATATATATTG 59.757 47.826 12.98 0.00 41.17 1.90
5328 21201 3.301835 CGAAGCGGCGACATATATATTGC 60.302 47.826 12.98 0.00 0.00 3.56
5329 21202 3.526931 AGCGGCGACATATATATTGCT 57.473 42.857 12.98 0.00 0.00 3.91
5330 21203 3.190079 AGCGGCGACATATATATTGCTG 58.810 45.455 12.98 7.59 0.00 4.41
5331 21204 2.285220 GCGGCGACATATATATTGCTGG 59.715 50.000 12.98 3.12 0.00 4.85
5332 21205 3.521560 CGGCGACATATATATTGCTGGT 58.478 45.455 0.00 0.00 0.00 4.00
5333 21206 3.551890 CGGCGACATATATATTGCTGGTC 59.448 47.826 0.00 6.31 0.00 4.02
5334 21207 3.871594 GGCGACATATATATTGCTGGTCC 59.128 47.826 3.27 0.00 0.00 4.46
5335 21208 3.871594 GCGACATATATATTGCTGGTCCC 59.128 47.826 0.00 0.00 0.00 4.46
5336 21209 4.112634 CGACATATATATTGCTGGTCCCG 58.887 47.826 0.00 0.00 0.00 5.14
5337 21210 4.442706 GACATATATATTGCTGGTCCCGG 58.557 47.826 0.00 0.00 0.00 5.73
5412 21285 4.007644 CTGCGGCTGTGTCTCCCA 62.008 66.667 0.00 0.00 0.00 4.37
5413 21286 3.320879 CTGCGGCTGTGTCTCCCAT 62.321 63.158 0.00 0.00 0.00 4.00
5414 21287 2.821366 GCGGCTGTGTCTCCCATG 60.821 66.667 0.00 0.00 0.00 3.66
5415 21288 2.981302 CGGCTGTGTCTCCCATGA 59.019 61.111 0.00 0.00 0.00 3.07
5416 21289 1.524002 CGGCTGTGTCTCCCATGAT 59.476 57.895 0.00 0.00 0.00 2.45
5417 21290 0.107508 CGGCTGTGTCTCCCATGATT 60.108 55.000 0.00 0.00 0.00 2.57
5418 21291 1.138859 CGGCTGTGTCTCCCATGATTA 59.861 52.381 0.00 0.00 0.00 1.75
5419 21292 2.224378 CGGCTGTGTCTCCCATGATTAT 60.224 50.000 0.00 0.00 0.00 1.28
5420 21293 3.745480 CGGCTGTGTCTCCCATGATTATT 60.745 47.826 0.00 0.00 0.00 1.40
5421 21294 4.210331 GGCTGTGTCTCCCATGATTATTT 58.790 43.478 0.00 0.00 0.00 1.40
5422 21295 4.276926 GGCTGTGTCTCCCATGATTATTTC 59.723 45.833 0.00 0.00 0.00 2.17
5423 21296 5.128919 GCTGTGTCTCCCATGATTATTTCT 58.871 41.667 0.00 0.00 0.00 2.52
5424 21297 5.238214 GCTGTGTCTCCCATGATTATTTCTC 59.762 44.000 0.00 0.00 0.00 2.87
5425 21298 6.312141 TGTGTCTCCCATGATTATTTCTCA 57.688 37.500 0.00 0.00 0.00 3.27
5426 21299 6.115446 TGTGTCTCCCATGATTATTTCTCAC 58.885 40.000 0.00 0.00 0.00 3.51
5427 21300 5.529060 GTGTCTCCCATGATTATTTCTCACC 59.471 44.000 0.00 0.00 0.00 4.02
5428 21301 5.191522 TGTCTCCCATGATTATTTCTCACCA 59.808 40.000 0.00 0.00 0.00 4.17
5429 21302 6.122277 GTCTCCCATGATTATTTCTCACCAA 58.878 40.000 0.00 0.00 0.00 3.67
5430 21303 6.038714 GTCTCCCATGATTATTTCTCACCAAC 59.961 42.308 0.00 0.00 0.00 3.77
5431 21304 5.825532 TCCCATGATTATTTCTCACCAACA 58.174 37.500 0.00 0.00 0.00 3.33
5432 21305 5.887598 TCCCATGATTATTTCTCACCAACAG 59.112 40.000 0.00 0.00 0.00 3.16
5433 21306 5.450965 CCCATGATTATTTCTCACCAACAGC 60.451 44.000 0.00 0.00 0.00 4.40
5434 21307 4.944962 TGATTATTTCTCACCAACAGCG 57.055 40.909 0.00 0.00 0.00 5.18
5435 21308 3.689161 TGATTATTTCTCACCAACAGCGG 59.311 43.478 0.00 0.00 0.00 5.52
5436 21309 2.107950 TATTTCTCACCAACAGCGGG 57.892 50.000 0.00 0.00 0.00 6.13
5437 21310 1.244019 ATTTCTCACCAACAGCGGGC 61.244 55.000 0.00 0.00 0.00 6.13
5438 21311 4.680237 TCTCACCAACAGCGGGCG 62.680 66.667 0.00 0.00 0.00 6.13
5439 21312 4.988598 CTCACCAACAGCGGGCGT 62.989 66.667 0.00 0.00 0.00 5.68
5442 21315 4.329545 ACCAACAGCGGGCGTGAT 62.330 61.111 0.00 0.00 0.00 3.06
5443 21316 3.055719 CCAACAGCGGGCGTGATT 61.056 61.111 0.00 0.00 0.00 2.57
5444 21317 2.176546 CAACAGCGGGCGTGATTG 59.823 61.111 0.00 0.00 0.00 2.67
5445 21318 3.055719 AACAGCGGGCGTGATTGG 61.056 61.111 0.00 0.00 0.00 3.16
5446 21319 3.842925 AACAGCGGGCGTGATTGGT 62.843 57.895 0.00 0.00 0.00 3.67
5447 21320 3.803082 CAGCGGGCGTGATTGGTG 61.803 66.667 0.00 0.00 0.00 4.17
5450 21323 3.124921 CGGGCGTGATTGGTGGAC 61.125 66.667 0.00 0.00 0.00 4.02
5451 21324 2.351276 GGGCGTGATTGGTGGACT 59.649 61.111 0.00 0.00 0.00 3.85
5452 21325 2.040544 GGGCGTGATTGGTGGACTG 61.041 63.158 0.00 0.00 0.00 3.51
5453 21326 2.040544 GGCGTGATTGGTGGACTGG 61.041 63.158 0.00 0.00 0.00 4.00
5454 21327 2.690778 GCGTGATTGGTGGACTGGC 61.691 63.158 0.00 0.00 0.00 4.85
5455 21328 1.003355 CGTGATTGGTGGACTGGCT 60.003 57.895 0.00 0.00 0.00 4.75
5456 21329 1.300971 CGTGATTGGTGGACTGGCTG 61.301 60.000 0.00 0.00 0.00 4.85
5457 21330 1.303561 TGATTGGTGGACTGGCTGC 60.304 57.895 0.00 0.00 0.00 5.25
5458 21331 1.001641 GATTGGTGGACTGGCTGCT 60.002 57.895 0.00 0.00 0.00 4.24
5459 21332 1.303888 ATTGGTGGACTGGCTGCTG 60.304 57.895 0.00 0.00 0.00 4.41
5460 21333 2.776370 ATTGGTGGACTGGCTGCTGG 62.776 60.000 0.00 0.00 0.00 4.85
5461 21334 4.729918 GGTGGACTGGCTGCTGGG 62.730 72.222 0.00 0.00 0.00 4.45
5462 21335 3.640407 GTGGACTGGCTGCTGGGA 61.640 66.667 0.00 0.00 0.00 4.37
5463 21336 2.853542 TGGACTGGCTGCTGGGAA 60.854 61.111 0.00 0.00 0.00 3.97
5464 21337 2.436109 GGACTGGCTGCTGGGAAA 59.564 61.111 0.00 0.00 0.00 3.13
5465 21338 1.000396 GGACTGGCTGCTGGGAAAT 60.000 57.895 0.00 0.00 0.00 2.17
5466 21339 0.613012 GGACTGGCTGCTGGGAAATT 60.613 55.000 0.00 0.00 0.00 1.82
5467 21340 1.340991 GGACTGGCTGCTGGGAAATTA 60.341 52.381 0.00 0.00 0.00 1.40
5468 21341 2.446435 GACTGGCTGCTGGGAAATTAA 58.554 47.619 0.00 0.00 0.00 1.40
5469 21342 3.026694 GACTGGCTGCTGGGAAATTAAT 58.973 45.455 0.00 0.00 0.00 1.40
5470 21343 3.444029 ACTGGCTGCTGGGAAATTAATT 58.556 40.909 0.00 0.00 0.00 1.40
5471 21344 3.196254 ACTGGCTGCTGGGAAATTAATTG 59.804 43.478 0.39 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1212 1228 2.884012 CTCGATGTCATAGGTCAGCTCT 59.116 50.000 0.00 0.00 0.00 4.09
1270 1286 3.683937 CTTTTGCTGGTGGCCGGG 61.684 66.667 2.18 0.00 40.92 5.73
1271 1287 3.683937 CCTTTTGCTGGTGGCCGG 61.684 66.667 0.00 0.00 40.92 6.13
1284 1300 0.853530 ACTCCTTGAAGCCACCCTTT 59.146 50.000 0.00 0.00 32.78 3.11
1285 1301 0.853530 AACTCCTTGAAGCCACCCTT 59.146 50.000 0.00 0.00 36.19 3.95
1435 1451 2.355412 CCACAGATGAATGCTGACAGGA 60.355 50.000 4.26 0.73 36.86 3.86
1505 1521 2.709934 AGATCATCCCTTGGACCATCAG 59.290 50.000 0.00 0.00 32.98 2.90
1542 1558 2.094417 GGTCGAGCCTTTTTCATCTTCG 59.906 50.000 2.39 0.00 0.00 3.79
1627 1643 1.568504 TGGATCTTGCGGTAGACCTT 58.431 50.000 0.00 0.00 0.00 3.50
1719 1736 0.531532 CGCAAGGTAGCTGGGAGATG 60.532 60.000 0.00 0.00 0.00 2.90
1858 2313 9.112725 GTTCCGTTAGGCTTATTAAGGAATTAA 57.887 33.333 5.61 0.00 38.55 1.40
1934 2426 6.094881 GGATCACGAGAAATATTTTGGGTCAA 59.905 38.462 1.43 0.00 0.00 3.18
2155 3609 6.375455 ACACTTTAGCCATAGTTGGAATTCAG 59.625 38.462 7.93 0.00 46.92 3.02
2179 3640 9.813080 CATCTGTAGTTTGCTTACTTAAGAAAC 57.187 33.333 10.09 8.85 35.72 2.78
2182 3643 6.594159 GCCATCTGTAGTTTGCTTACTTAAGA 59.406 38.462 10.09 2.37 35.33 2.10
2183 3644 6.371548 TGCCATCTGTAGTTTGCTTACTTAAG 59.628 38.462 0.00 0.00 36.40 1.85
2225 3686 5.351740 GCTCAACAAGTTAAGGTCTACCATC 59.648 44.000 1.26 0.00 38.89 3.51
2265 3755 8.892723 CAAGTAAACCATGATAATCTAAGCACA 58.107 33.333 0.00 0.00 0.00 4.57
2266 3756 7.857885 GCAAGTAAACCATGATAATCTAAGCAC 59.142 37.037 0.00 0.00 0.00 4.40
2319 3812 3.949113 AGACTACGAACTCCAAGAGGATC 59.051 47.826 0.00 0.00 44.70 3.36
2365 3862 6.305272 AGATACCAATGTCATGTCAGAAGT 57.695 37.500 0.00 0.00 0.00 3.01
2369 3866 5.027293 TGGAGATACCAATGTCATGTCAG 57.973 43.478 0.00 0.00 46.75 3.51
2652 5422 6.294361 TCTCGGAACCAAATATTCTTCTCA 57.706 37.500 0.00 0.00 0.00 3.27
2653 5423 6.037281 GGTTCTCGGAACCAAATATTCTTCTC 59.963 42.308 23.09 0.06 40.03 2.87
2655 5425 5.220605 CGGTTCTCGGAACCAAATATTCTTC 60.221 44.000 25.64 4.78 40.28 2.87
2675 5445 2.268076 GCACATCAGGGCAACGGTT 61.268 57.895 0.00 0.00 37.60 4.44
2772 5542 5.765677 TCATCTTTGATCACCGGTTTTGTTA 59.234 36.000 2.97 0.00 0.00 2.41
2775 5545 4.216257 ACTCATCTTTGATCACCGGTTTTG 59.784 41.667 2.97 0.00 0.00 2.44
2776 5546 4.216257 CACTCATCTTTGATCACCGGTTTT 59.784 41.667 2.97 0.00 0.00 2.43
2842 5612 7.272244 TGTTATTCATTCCATCTAAGCTTCGA 58.728 34.615 0.00 1.57 0.00 3.71
2888 5658 5.012893 GGTCTTGAGATTGGGTGAAAGATT 58.987 41.667 0.00 0.00 0.00 2.40
3079 5849 7.277396 CCTTTCCATCATAGCCAATTTCAATT 58.723 34.615 0.00 0.00 0.00 2.32
3080 5850 6.687139 GCCTTTCCATCATAGCCAATTTCAAT 60.687 38.462 0.00 0.00 0.00 2.57
3136 5906 6.136541 ACCGATTTTGAAATAATGAGCTCC 57.863 37.500 12.15 0.00 0.00 4.70
3196 5966 1.001487 TCACGCTTTGCCAAATCAGTG 60.001 47.619 11.23 11.23 0.00 3.66
3270 6040 5.163488 TGGCTTAGATCTTCATTTGCCAATG 60.163 40.000 0.00 4.13 44.86 2.82
3324 6094 4.761975 CCTAGGCAATTGTTTGATGCAAT 58.238 39.130 7.40 0.00 41.80 3.56
3577 6347 9.809096 CATCTTGTAATGAGTAGATGTTGTAGT 57.191 33.333 0.00 0.00 39.27 2.73
3596 6366 3.191371 GGATCACGGAAAAAGCATCTTGT 59.809 43.478 0.00 0.00 0.00 3.16
3670 6443 7.676004 TCATAATATTAAAGCCCGAGATCACA 58.324 34.615 0.00 0.00 0.00 3.58
3704 6477 3.379372 CCCAATTCCTTGACTGCACATAG 59.621 47.826 0.00 0.00 34.04 2.23
3722 6495 0.486879 AAACAGGCCAGATTCCCCAA 59.513 50.000 5.01 0.00 0.00 4.12
3734 6507 2.869233 TGCACTTCTTTCAAACAGGC 57.131 45.000 0.00 0.00 0.00 4.85
3737 6510 5.822519 ACTGTAGATGCACTTCTTTCAAACA 59.177 36.000 0.00 0.00 0.00 2.83
3749 6522 2.939103 GACCATCCAACTGTAGATGCAC 59.061 50.000 12.79 7.15 38.85 4.57
3751 6524 2.159099 TCGACCATCCAACTGTAGATGC 60.159 50.000 12.79 3.22 38.85 3.91
3770 6543 4.022416 CCTCTTGTATTCCTGAGATCCTCG 60.022 50.000 0.00 0.00 32.35 4.63
3813 6586 1.003464 TGCCAAGCTTGCATAGTGAGA 59.997 47.619 21.43 0.00 32.85 3.27
3875 6648 0.690762 TCTAAGAACTGGGTGGGTGC 59.309 55.000 0.00 0.00 0.00 5.01
3882 6655 4.518249 GGACCAAGAATCTAAGAACTGGG 58.482 47.826 2.00 0.00 0.00 4.45
3919 6692 4.770010 GTGGTCACCCAAAATATTTGGAGA 59.230 41.667 20.56 15.11 44.15 3.71
3935 6708 4.081309 TGGTAAATAGTAGCCAGTGGTCAC 60.081 45.833 11.74 9.02 0.00 3.67
3993 16421 8.970020 TCAAATTAATGTTCAGGTATGCAAGAT 58.030 29.630 0.00 0.00 0.00 2.40
4031 16459 2.503356 CAAGTAGCCACAGATCCTCCTT 59.497 50.000 0.00 0.00 0.00 3.36
4046 16474 1.761784 AGCAGGCATCTCTCCAAGTAG 59.238 52.381 0.00 0.00 0.00 2.57
4073 16501 5.974158 CAGTCCTGAATGTTATACTCAGTCG 59.026 44.000 0.00 0.00 35.78 4.18
4075 16503 6.127310 GGACAGTCCTGAATGTTATACTCAGT 60.127 42.308 12.94 0.00 39.96 3.41
4126 16554 1.689984 TCAAACACAGGAATGCAGCA 58.310 45.000 0.00 0.00 0.00 4.41
4285 16713 2.142292 GACATGGGAGGTGGCCAAGT 62.142 60.000 7.24 0.00 0.00 3.16
4341 16773 4.093998 CAGACTTGATTTCGGAAGATGTGG 59.906 45.833 0.00 0.00 41.60 4.17
4376 16808 5.634118 CCCATTTGCCTCATTCCTTATAGA 58.366 41.667 0.00 0.00 0.00 1.98
4387 16819 1.381599 GGGATGCCCATTTGCCTCA 60.382 57.895 0.00 0.00 44.65 3.86
4399 16831 3.515602 AACCTAGGATGATTGGGATGC 57.484 47.619 17.98 0.00 0.00 3.91
4414 16846 5.768662 CGTTCTGTCCTGGATAGATAACCTA 59.231 44.000 21.77 5.23 30.42 3.08
4446 16899 3.522553 GTCCATTCCTCGTCAAAGTAGG 58.477 50.000 0.00 0.00 0.00 3.18
4451 16904 2.093658 GCTAGGTCCATTCCTCGTCAAA 60.094 50.000 0.00 0.00 38.86 2.69
4459 16912 1.139853 CCTGACAGCTAGGTCCATTCC 59.860 57.143 0.00 0.00 36.97 3.01
4463 16916 0.116342 TTCCCTGACAGCTAGGTCCA 59.884 55.000 0.00 0.00 36.97 4.02
4464 16917 1.501582 ATTCCCTGACAGCTAGGTCC 58.498 55.000 0.00 0.00 36.97 4.46
4467 16920 3.356529 AACAATTCCCTGACAGCTAGG 57.643 47.619 0.00 0.00 35.01 3.02
4505 16958 4.876107 CGATTAGTACCTCTTGCATTGGTT 59.124 41.667 10.37 0.00 35.48 3.67
4553 17006 9.612066 TCATGATATATTGCACACAGAAAGTAA 57.388 29.630 0.00 0.00 0.00 2.24
4554 17007 9.045223 GTCATGATATATTGCACACAGAAAGTA 57.955 33.333 0.00 0.00 0.00 2.24
4564 17018 9.902196 TTGATGAAATGTCATGATATATTGCAC 57.098 29.630 2.15 5.21 44.83 4.57
4565 17019 9.902196 GTTGATGAAATGTCATGATATATTGCA 57.098 29.630 2.15 8.94 44.83 4.08
4602 20451 2.004583 CGAACATGTCACGTATGGGT 57.995 50.000 14.43 0.00 0.00 4.51
4621 20470 2.057922 TCCCCTGAATAGATGAAGGGC 58.942 52.381 0.78 0.00 46.97 5.19
4660 20510 1.375140 AGCAGCACACCATCAGACG 60.375 57.895 0.00 0.00 0.00 4.18
4663 20513 0.892358 AACCAGCAGCACACCATCAG 60.892 55.000 0.00 0.00 0.00 2.90
4706 20556 1.808945 CAGTCCAGCTTCATGGTTCAC 59.191 52.381 0.00 0.00 41.43 3.18
4724 20574 4.067896 AGCTTCCACACACAACTAATCAG 58.932 43.478 0.00 0.00 0.00 2.90
4737 20587 4.469657 ACACCTTTATTTCAGCTTCCACA 58.530 39.130 0.00 0.00 0.00 4.17
4747 20597 5.932883 ACTTCTTCTCGGACACCTTTATTTC 59.067 40.000 0.00 0.00 0.00 2.17
4755 20605 0.680061 ACCACTTCTTCTCGGACACC 59.320 55.000 0.00 0.00 0.00 4.16
4762 20612 6.261158 AGAGCAAGTAAAAACCACTTCTTCTC 59.739 38.462 0.00 0.00 33.99 2.87
4764 20614 6.202226 CAGAGCAAGTAAAAACCACTTCTTC 58.798 40.000 0.00 0.00 33.99 2.87
4775 20625 9.667107 AATAGTAACATAGCAGAGCAAGTAAAA 57.333 29.630 0.00 0.00 0.00 1.52
4776 20626 9.667107 AAATAGTAACATAGCAGAGCAAGTAAA 57.333 29.630 0.00 0.00 0.00 2.01
4826 20678 6.458210 AGTAAATCAAGGCAACAAAATCTGG 58.542 36.000 0.00 0.00 41.41 3.86
4832 20684 6.991938 AGCAATAGTAAATCAAGGCAACAAA 58.008 32.000 0.00 0.00 41.41 2.83
4861 20713 3.428532 TCACCTAGAGGCGAACTTAAGT 58.571 45.455 1.12 1.12 39.32 2.24
4921 20773 7.023575 CAGCAGTCCATCAAATTAAGTTACAC 58.976 38.462 0.00 0.00 0.00 2.90
4947 20799 8.093927 TCAACTGAATGTACACATATCTCAACA 58.906 33.333 0.00 0.00 35.10 3.33
4975 20827 4.090761 AGTCTCAATCCAGCTGTTTCAA 57.909 40.909 13.81 0.00 0.00 2.69
4991 20843 8.955388 TGACAGCATATATATCTCTCAAGTCTC 58.045 37.037 0.00 0.00 0.00 3.36
4992 20844 8.876303 TGACAGCATATATATCTCTCAAGTCT 57.124 34.615 0.00 0.00 0.00 3.24
4993 20845 8.190122 CCTGACAGCATATATATCTCTCAAGTC 58.810 40.741 0.00 0.00 0.00 3.01
4994 20846 7.673504 ACCTGACAGCATATATATCTCTCAAGT 59.326 37.037 0.00 0.00 0.00 3.16
4995 20847 8.065473 ACCTGACAGCATATATATCTCTCAAG 57.935 38.462 0.00 0.00 0.00 3.02
4996 20848 8.427902 AACCTGACAGCATATATATCTCTCAA 57.572 34.615 0.00 0.00 0.00 3.02
4997 20849 8.427902 AAACCTGACAGCATATATATCTCTCA 57.572 34.615 0.00 0.00 0.00 3.27
4998 20850 8.526978 TGAAACCTGACAGCATATATATCTCTC 58.473 37.037 0.00 0.00 0.00 3.20
4999 20851 8.427902 TGAAACCTGACAGCATATATATCTCT 57.572 34.615 0.00 0.00 0.00 3.10
5004 20856 7.928167 CAGTTCTGAAACCTGACAGCATATATA 59.072 37.037 0.00 0.00 35.92 0.86
5027 20879 4.690122 AGTGACAAAAGCGTTACTACAGT 58.310 39.130 0.00 0.00 34.27 3.55
5028 20880 4.143597 CGAGTGACAAAAGCGTTACTACAG 60.144 45.833 0.00 0.00 36.00 2.74
5039 20891 6.308282 GGTTCAGAGTATACGAGTGACAAAAG 59.692 42.308 0.00 0.00 0.00 2.27
5041 20893 5.242171 TGGTTCAGAGTATACGAGTGACAAA 59.758 40.000 0.00 0.00 0.00 2.83
5051 20903 2.481449 CCGCCACTGGTTCAGAGTATAC 60.481 54.545 1.59 0.00 35.18 1.47
5070 20922 3.508840 GTGCAAATCCTCCGCCCG 61.509 66.667 0.00 0.00 0.00 6.13
5076 20928 3.319122 GGATACCCATTGTGCAAATCCTC 59.681 47.826 0.00 0.00 0.00 3.71
5097 20949 4.692155 GGTGAATTTGCTTTTCTTGGATGG 59.308 41.667 0.00 0.00 0.00 3.51
5110 20962 6.441093 TCAGTCTATGATTGGTGAATTTGC 57.559 37.500 0.00 0.00 31.12 3.68
5111 20963 8.272545 TCTTCAGTCTATGATTGGTGAATTTG 57.727 34.615 0.00 0.00 37.89 2.32
5112 20964 9.118300 GATCTTCAGTCTATGATTGGTGAATTT 57.882 33.333 0.00 0.00 37.89 1.82
5121 20973 7.295322 TCAATCGGATCTTCAGTCTATGATT 57.705 36.000 0.00 0.00 37.89 2.57
5123 20975 6.294955 CCATCAATCGGATCTTCAGTCTATGA 60.295 42.308 0.00 0.00 32.57 2.15
5183 21056 3.574396 GTGGATCATGGATACTCCTTCGA 59.426 47.826 0.00 0.00 37.46 3.71
5185 21058 4.503991 GGTGTGGATCATGGATACTCCTTC 60.504 50.000 0.00 0.00 37.46 3.46
5192 21065 6.514012 ACATAAAGGTGTGGATCATGGATA 57.486 37.500 0.00 0.00 0.00 2.59
5194 21067 4.683129 CGACATAAAGGTGTGGATCATGGA 60.683 45.833 0.00 0.00 30.43 3.41
5204 21077 0.321298 AAGCGGCGACATAAAGGTGT 60.321 50.000 12.98 0.00 34.39 4.16
5227 21100 0.321564 CAATCCAGCAACGTCCAGGA 60.322 55.000 0.00 0.00 0.00 3.86
5233 21106 1.338200 GGAGTCTCAATCCAGCAACGT 60.338 52.381 1.47 0.00 36.79 3.99
5243 21116 1.338200 GGACGTTGCTGGAGTCTCAAT 60.338 52.381 1.47 0.00 35.42 2.57
5244 21117 0.033504 GGACGTTGCTGGAGTCTCAA 59.966 55.000 1.47 0.00 35.42 3.02
5247 21120 1.668294 CTGGACGTTGCTGGAGTCT 59.332 57.895 0.00 0.00 35.42 3.24
5248 21121 1.374758 CCTGGACGTTGCTGGAGTC 60.375 63.158 0.00 0.00 0.00 3.36
5251 21124 2.741092 GTCCTGGACGTTGCTGGA 59.259 61.111 11.71 0.00 33.72 3.86
5264 21137 0.968901 TATGTCGCCACTTCCGTCCT 60.969 55.000 0.00 0.00 0.00 3.85
5265 21138 0.108520 TTATGTCGCCACTTCCGTCC 60.109 55.000 0.00 0.00 0.00 4.79
5266 21139 1.659098 CTTTATGTCGCCACTTCCGTC 59.341 52.381 0.00 0.00 0.00 4.79
5267 21140 1.674817 CCTTTATGTCGCCACTTCCGT 60.675 52.381 0.00 0.00 0.00 4.69
5269 21142 1.737793 CACCTTTATGTCGCCACTTCC 59.262 52.381 0.00 0.00 0.00 3.46
5271 21144 2.615493 CCTCACCTTTATGTCGCCACTT 60.615 50.000 0.00 0.00 0.00 3.16
5272 21145 1.066143 CCTCACCTTTATGTCGCCACT 60.066 52.381 0.00 0.00 0.00 4.00
5273 21146 1.066430 TCCTCACCTTTATGTCGCCAC 60.066 52.381 0.00 0.00 0.00 5.01
5274 21147 1.271856 TCCTCACCTTTATGTCGCCA 58.728 50.000 0.00 0.00 0.00 5.69
5275 21148 2.484889 GATCCTCACCTTTATGTCGCC 58.515 52.381 0.00 0.00 0.00 5.54
5276 21149 2.128035 CGATCCTCACCTTTATGTCGC 58.872 52.381 0.00 0.00 0.00 5.19
5277 21150 2.128035 GCGATCCTCACCTTTATGTCG 58.872 52.381 0.00 0.00 0.00 4.35
5278 21151 3.126831 CAGCGATCCTCACCTTTATGTC 58.873 50.000 0.00 0.00 0.00 3.06
5279 21152 2.766263 TCAGCGATCCTCACCTTTATGT 59.234 45.455 0.00 0.00 0.00 2.29
5280 21153 3.388308 CTCAGCGATCCTCACCTTTATG 58.612 50.000 0.00 0.00 0.00 1.90
5281 21154 2.224161 GCTCAGCGATCCTCACCTTTAT 60.224 50.000 0.00 0.00 0.00 1.40
5282 21155 1.137086 GCTCAGCGATCCTCACCTTTA 59.863 52.381 0.00 0.00 0.00 1.85
5283 21156 0.107945 GCTCAGCGATCCTCACCTTT 60.108 55.000 0.00 0.00 0.00 3.11
5284 21157 1.519719 GCTCAGCGATCCTCACCTT 59.480 57.895 0.00 0.00 0.00 3.50
5285 21158 2.430610 GGCTCAGCGATCCTCACCT 61.431 63.158 0.00 0.00 0.00 4.00
5286 21159 2.107953 GGCTCAGCGATCCTCACC 59.892 66.667 0.00 0.00 0.00 4.02
5287 21160 2.107953 GGGCTCAGCGATCCTCAC 59.892 66.667 0.00 0.00 0.00 3.51
5288 21161 3.157252 GGGGCTCAGCGATCCTCA 61.157 66.667 0.00 0.00 0.00 3.86
5289 21162 3.934962 GGGGGCTCAGCGATCCTC 61.935 72.222 0.00 0.00 0.00 3.71
5292 21165 3.798954 CTTCGGGGGCTCAGCGATC 62.799 68.421 0.00 0.00 0.00 3.69
5293 21166 3.854669 CTTCGGGGGCTCAGCGAT 61.855 66.667 0.00 0.00 0.00 4.58
5306 21179 3.301835 GCAATATATATGTCGCCGCTTCG 60.302 47.826 0.00 0.00 0.00 3.79
5307 21180 3.865745 AGCAATATATATGTCGCCGCTTC 59.134 43.478 0.00 0.00 0.00 3.86
5308 21181 3.618594 CAGCAATATATATGTCGCCGCTT 59.381 43.478 0.00 0.00 0.00 4.68
5309 21182 3.190079 CAGCAATATATATGTCGCCGCT 58.810 45.455 0.00 0.00 0.00 5.52
5310 21183 2.285220 CCAGCAATATATATGTCGCCGC 59.715 50.000 0.00 0.00 0.00 6.53
5311 21184 3.521560 ACCAGCAATATATATGTCGCCG 58.478 45.455 0.00 0.00 0.00 6.46
5312 21185 3.871594 GGACCAGCAATATATATGTCGCC 59.128 47.826 0.00 0.00 0.00 5.54
5313 21186 3.871594 GGGACCAGCAATATATATGTCGC 59.128 47.826 9.82 9.82 0.00 5.19
5314 21187 4.112634 CGGGACCAGCAATATATATGTCG 58.887 47.826 0.00 0.00 0.00 4.35
5315 21188 4.442706 CCGGGACCAGCAATATATATGTC 58.557 47.826 0.00 0.00 0.00 3.06
5316 21189 3.370527 GCCGGGACCAGCAATATATATGT 60.371 47.826 2.18 0.00 0.00 2.29
5317 21190 3.206150 GCCGGGACCAGCAATATATATG 58.794 50.000 2.18 0.00 0.00 1.78
5318 21191 2.158957 CGCCGGGACCAGCAATATATAT 60.159 50.000 2.18 0.00 0.00 0.86
5319 21192 1.206132 CGCCGGGACCAGCAATATATA 59.794 52.381 2.18 0.00 0.00 0.86
5320 21193 0.036388 CGCCGGGACCAGCAATATAT 60.036 55.000 2.18 0.00 0.00 0.86
5321 21194 1.116536 TCGCCGGGACCAGCAATATA 61.117 55.000 2.18 0.00 0.00 0.86
5322 21195 1.768684 ATCGCCGGGACCAGCAATAT 61.769 55.000 2.18 0.00 0.00 1.28
5323 21196 1.978455 AATCGCCGGGACCAGCAATA 61.978 55.000 2.18 0.00 0.00 1.90
5324 21197 3.344137 AATCGCCGGGACCAGCAAT 62.344 57.895 2.18 0.00 0.00 3.56
5325 21198 3.969250 GAATCGCCGGGACCAGCAA 62.969 63.158 2.18 0.00 0.00 3.91
5326 21199 4.467084 GAATCGCCGGGACCAGCA 62.467 66.667 2.18 0.00 0.00 4.41
5328 21201 4.891727 CCGAATCGCCGGGACCAG 62.892 72.222 2.18 0.00 45.43 4.00
5410 21283 5.585390 GCTGTTGGTGAGAAATAATCATGG 58.415 41.667 0.00 0.00 0.00 3.66
5412 21285 4.336433 CCGCTGTTGGTGAGAAATAATCAT 59.664 41.667 0.00 0.00 0.00 2.45
5413 21286 3.689161 CCGCTGTTGGTGAGAAATAATCA 59.311 43.478 0.00 0.00 0.00 2.57
5414 21287 3.065371 CCCGCTGTTGGTGAGAAATAATC 59.935 47.826 0.00 0.00 0.00 1.75
5415 21288 3.016736 CCCGCTGTTGGTGAGAAATAAT 58.983 45.455 0.00 0.00 0.00 1.28
5416 21289 2.432444 CCCGCTGTTGGTGAGAAATAA 58.568 47.619 0.00 0.00 0.00 1.40
5417 21290 1.948611 GCCCGCTGTTGGTGAGAAATA 60.949 52.381 0.00 0.00 0.00 1.40
5418 21291 1.244019 GCCCGCTGTTGGTGAGAAAT 61.244 55.000 0.00 0.00 0.00 2.17
5419 21292 1.896660 GCCCGCTGTTGGTGAGAAA 60.897 57.895 0.00 0.00 0.00 2.52
5420 21293 2.281484 GCCCGCTGTTGGTGAGAA 60.281 61.111 0.00 0.00 0.00 2.87
5421 21294 4.680237 CGCCCGCTGTTGGTGAGA 62.680 66.667 0.00 0.00 35.32 3.27
5422 21295 4.988598 ACGCCCGCTGTTGGTGAG 62.989 66.667 5.38 0.00 36.85 3.51
5425 21298 3.842925 AATCACGCCCGCTGTTGGT 62.843 57.895 0.00 0.00 0.00 3.67
5426 21299 3.055719 AATCACGCCCGCTGTTGG 61.056 61.111 0.00 0.00 0.00 3.77
5427 21300 2.176546 CAATCACGCCCGCTGTTG 59.823 61.111 0.00 0.00 0.00 3.33
5428 21301 3.055719 CCAATCACGCCCGCTGTT 61.056 61.111 0.00 0.00 0.00 3.16
5429 21302 4.329545 ACCAATCACGCCCGCTGT 62.330 61.111 0.00 0.00 0.00 4.40
5430 21303 3.803082 CACCAATCACGCCCGCTG 61.803 66.667 0.00 0.00 0.00 5.18
5433 21306 3.124921 GTCCACCAATCACGCCCG 61.125 66.667 0.00 0.00 0.00 6.13
5434 21307 2.040544 CAGTCCACCAATCACGCCC 61.041 63.158 0.00 0.00 0.00 6.13
5435 21308 2.040544 CCAGTCCACCAATCACGCC 61.041 63.158 0.00 0.00 0.00 5.68
5436 21309 2.690778 GCCAGTCCACCAATCACGC 61.691 63.158 0.00 0.00 0.00 5.34
5437 21310 1.003355 AGCCAGTCCACCAATCACG 60.003 57.895 0.00 0.00 0.00 4.35
5438 21311 1.589716 GCAGCCAGTCCACCAATCAC 61.590 60.000 0.00 0.00 0.00 3.06
5439 21312 1.303561 GCAGCCAGTCCACCAATCA 60.304 57.895 0.00 0.00 0.00 2.57
5440 21313 1.001641 AGCAGCCAGTCCACCAATC 60.002 57.895 0.00 0.00 0.00 2.67
5441 21314 1.303888 CAGCAGCCAGTCCACCAAT 60.304 57.895 0.00 0.00 0.00 3.16
5442 21315 2.113774 CAGCAGCCAGTCCACCAA 59.886 61.111 0.00 0.00 0.00 3.67
5443 21316 3.957586 CCAGCAGCCAGTCCACCA 61.958 66.667 0.00 0.00 0.00 4.17
5444 21317 4.729918 CCCAGCAGCCAGTCCACC 62.730 72.222 0.00 0.00 0.00 4.61
5445 21318 2.697147 TTTCCCAGCAGCCAGTCCAC 62.697 60.000 0.00 0.00 0.00 4.02
5446 21319 1.792757 ATTTCCCAGCAGCCAGTCCA 61.793 55.000 0.00 0.00 0.00 4.02
5447 21320 0.613012 AATTTCCCAGCAGCCAGTCC 60.613 55.000 0.00 0.00 0.00 3.85
5448 21321 2.128771 TAATTTCCCAGCAGCCAGTC 57.871 50.000 0.00 0.00 0.00 3.51
5449 21322 2.603075 TTAATTTCCCAGCAGCCAGT 57.397 45.000 0.00 0.00 0.00 4.00
5450 21323 3.788937 CAATTAATTTCCCAGCAGCCAG 58.211 45.455 0.00 0.00 0.00 4.85
5451 21324 3.891422 CAATTAATTTCCCAGCAGCCA 57.109 42.857 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.