Multiple sequence alignment - TraesCS4A01G359000

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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 TraesCS4A01G359000 chr4A 100.000 7482 0 0 1 7482 631956060 631963541 0.000000e+00 13817.0
1 TraesCS4A01G359000 chr4A 84.397 141 17 5 3968 4108 715806676 715806541 4.710000e-27 134.0
2 TraesCS4A01G359000 chr5D 95.278 3325 135 17 4166 7482 537758604 537761914 0.000000e+00 5251.0
3 TraesCS4A01G359000 chr5D 90.491 1283 70 25 684 1955 537754806 537756047 0.000000e+00 1646.0
4 TraesCS4A01G359000 chr5D 92.732 1142 50 12 1973 3083 537756030 537757169 0.000000e+00 1618.0
5 TraesCS4A01G359000 chr5D 92.522 896 28 5 3079 3958 537757632 537758504 0.000000e+00 1247.0
6 TraesCS4A01G359000 chr5D 93.520 679 36 4 22 696 537754087 537754761 0.000000e+00 1003.0
7 TraesCS4A01G359000 chr5D 91.919 99 8 0 3989 4087 509429464 509429366 1.010000e-28 139.0
8 TraesCS4A01G359000 chr5B 95.188 1704 75 7 4086 5787 678509492 678511190 0.000000e+00 2686.0
9 TraesCS4A01G359000 chr5B 93.416 1701 82 12 5788 7482 678511304 678512980 0.000000e+00 2494.0
10 TraesCS4A01G359000 chr5B 92.489 1105 31 17 1989 3063 678507377 678508459 0.000000e+00 1533.0
11 TraesCS4A01G359000 chr5B 86.698 1293 87 44 686 1956 678506062 678507291 0.000000e+00 1356.0
12 TraesCS4A01G359000 chr5B 91.441 888 44 13 3079 3958 678508582 678509445 0.000000e+00 1190.0
13 TraesCS4A01G359000 chr5B 91.993 587 32 8 2 586 678493952 678494525 0.000000e+00 809.0
14 TraesCS4A01G359000 chr5B 93.000 100 6 1 3991 4090 680856569 680856471 2.180000e-30 145.0
15 TraesCS4A01G359000 chrUn 89.178 499 34 5 6572 7069 332035095 332034616 8.300000e-169 604.0
16 TraesCS4A01G359000 chrUn 88.978 499 35 5 6572 7069 60686130 60685651 3.860000e-167 599.0
17 TraesCS4A01G359000 chrUn 88.978 499 35 5 6572 7069 60692635 60692156 3.860000e-167 599.0
18 TraesCS4A01G359000 chrUn 88.978 499 35 5 6572 7069 340605678 340606157 3.860000e-167 599.0
19 TraesCS4A01G359000 chrUn 88.978 499 35 5 6572 7069 351584965 351584486 3.860000e-167 599.0
20 TraesCS4A01G359000 chrUn 88.778 499 36 5 6572 7069 60743882 60743403 1.800000e-165 593.0
21 TraesCS4A01G359000 chrUn 88.778 499 36 6 6572 7069 224196083 224195604 1.800000e-165 593.0
22 TraesCS4A01G359000 chrUn 89.212 482 32 5 6589 7069 221985954 221986416 1.080000e-162 584.0
23 TraesCS4A01G359000 chrUn 85.609 271 19 6 6572 6841 375249043 375249294 4.450000e-67 267.0
24 TraesCS4A01G359000 chr4B 88.778 499 36 6 6572 7069 656332646 656332167 1.800000e-165 593.0
25 TraesCS4A01G359000 chr4B 91.753 97 8 0 3992 4088 654204884 654204980 1.310000e-27 135.0
26 TraesCS4A01G359000 chr1D 91.453 234 17 3 496 726 451647422 451647189 1.210000e-82 318.0
27 TraesCS4A01G359000 chr1D 91.064 235 17 3 496 726 451665012 451664778 1.570000e-81 315.0
28 TraesCS4A01G359000 chr1A 91.342 231 17 2 498 726 299726972 299726743 5.640000e-81 313.0
29 TraesCS4A01G359000 chr1A 89.855 207 19 2 496 700 546226647 546226441 1.600000e-66 265.0
30 TraesCS4A01G359000 chr4D 89.177 231 23 1 496 724 462844985 462844755 3.420000e-73 287.0
31 TraesCS4A01G359000 chr7A 80.337 356 41 20 3295 3626 715758934 715759284 7.500000e-60 243.0
32 TraesCS4A01G359000 chr1B 80.337 356 41 20 3295 3626 633784147 633784497 7.500000e-60 243.0
33 TraesCS4A01G359000 chr1B 84.722 216 29 3 512 726 8857078 8857290 5.880000e-51 213.0
34 TraesCS4A01G359000 chr3B 80.130 307 32 12 2653 2942 754719009 754718715 1.270000e-47 202.0
35 TraesCS4A01G359000 chr3B 90.196 102 8 1 3991 4092 605016271 605016370 1.690000e-26 132.0
36 TraesCS4A01G359000 chr3B 86.957 115 14 1 3974 4087 659588183 659588069 2.190000e-25 128.0
37 TraesCS4A01G359000 chr2D 92.000 100 8 0 3988 4087 445896308 445896407 2.810000e-29 141.0
38 TraesCS4A01G359000 chr2A 91.837 98 8 0 3991 4088 657520831 657520734 3.640000e-28 137.0
39 TraesCS4A01G359000 chr6B 90.099 101 10 0 3987 4087 129450871 129450971 1.690000e-26 132.0
40 TraesCS4A01G359000 chr6B 81.967 122 20 1 496 615 184762182 184762061 1.330000e-17 102.0
41 TraesCS4A01G359000 chr7B 79.348 184 29 7 496 672 379204363 379204182 3.670000e-23 121.0
42 TraesCS4A01G359000 chr6D 88.312 77 6 2 497 571 470955058 470954983 1.030000e-13 89.8
43 TraesCS4A01G359000 chr6D 97.143 35 1 0 620 654 466782165 466782131 8.110000e-05 60.2


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 TraesCS4A01G359000 chr4A 631956060 631963541 7481 False 13817.0 13817 100.0000 1 7482 1 chr4A.!!$F1 7481
1 TraesCS4A01G359000 chr5D 537754087 537761914 7827 False 2153.0 5251 92.9086 22 7482 5 chr5D.!!$F1 7460
2 TraesCS4A01G359000 chr5B 678506062 678512980 6918 False 1851.8 2686 91.8464 686 7482 5 chr5B.!!$F2 6796
3 TraesCS4A01G359000 chr5B 678493952 678494525 573 False 809.0 809 91.9930 2 586 1 chr5B.!!$F1 584

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
726 787 1.077930 CCCATGTGCTCCCTGACTG 60.078 63.158 0.00 0.00 0.00 3.51 F
1289 1370 0.106719 CCCCTCCCGCATGTTGTATT 60.107 55.000 0.00 0.00 0.00 1.89 F
1547 1631 0.166814 CCAGTCGCTAGCAGCAAAAC 59.833 55.000 16.45 2.66 42.58 2.43 F
2397 2587 0.833949 CTCCTTGCCCTCCTCCTTAC 59.166 60.000 0.00 0.00 0.00 2.34 F
2680 2871 0.961019 TCCAACTTCCAAGCACATGC 59.039 50.000 0.00 0.00 42.49 4.06 F
3161 3931 1.568123 TGGGACATTGGATGCATACCA 59.432 47.619 6.42 9.96 35.47 3.25 F
4624 5412 0.322816 ATGTGGCCACTGTGTCCATC 60.323 55.000 34.75 8.40 31.83 3.51 F
6432 7341 0.036010 CCTGGCTTACCCACACAGAG 60.036 60.000 0.00 0.00 39.18 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1973 0.251916 CTTCACCGGCCTCATTGGTA 59.748 55.000 0.00 0.00 38.35 3.25 R
3188 3958 1.463674 AAATCACGGGGAACATCTGC 58.536 50.000 0.00 0.00 0.00 4.26 R
3433 4217 5.124776 AGTTGTTCCAAAATCGTTTGTCTGA 59.875 36.000 0.00 0.00 42.26 3.27 R
4179 4967 1.006337 GCACCCAATTTCGCTGCAA 60.006 52.632 0.00 0.00 0.00 4.08 R
4589 5377 3.848726 CCACATGGTTACATTGAAAGGC 58.151 45.455 0.00 0.00 34.35 4.35 R
5021 5810 0.246635 GTCTACTGCAAAGCCCGAGA 59.753 55.000 0.00 0.00 0.00 4.04 R
6438 7347 0.037303 AGGTGTCATGGAGTTGGCTG 59.963 55.000 0.00 0.00 0.00 4.85 R
7301 8213 3.498774 ATCATGACCATGGAAGGCTAC 57.501 47.619 21.47 1.27 39.24 3.58 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
177 179 3.181486 ACAGCTCACATGGTAGTATGTCG 60.181 47.826 0.00 0.00 39.17 4.35
192 194 8.774586 GGTAGTATGTCGCAATGAGATTTTATT 58.225 33.333 0.00 0.00 32.00 1.40
290 292 1.542472 GGCTCTAATACGCCTCTCTCC 59.458 57.143 0.00 0.00 42.98 3.71
306 308 8.713271 CGCCTCTCTCCTGTAAATAATATTTTC 58.287 37.037 3.36 0.00 0.00 2.29
380 382 5.448768 CGTTGATAGATAGACGGTCACTTGT 60.449 44.000 11.27 0.00 32.29 3.16
615 619 4.889409 TCAAGAGAATGTGAAAACTTGGCT 59.111 37.500 0.00 0.00 36.45 4.75
616 620 5.360714 TCAAGAGAATGTGAAAACTTGGCTT 59.639 36.000 0.00 0.00 36.45 4.35
723 784 1.133181 TGTTCCCATGTGCTCCCTGA 61.133 55.000 0.00 0.00 0.00 3.86
726 787 1.077930 CCCATGTGCTCCCTGACTG 60.078 63.158 0.00 0.00 0.00 3.51
842 903 4.298626 TCCAGGCCTATTTAGAGTGACAT 58.701 43.478 3.98 0.00 0.00 3.06
1042 1123 3.056328 GTGGGTTTCTGGCTCGCC 61.056 66.667 0.00 0.00 0.00 5.54
1068 1149 0.872388 GTTTTCGCTCGATTGTGGGT 59.128 50.000 0.00 0.00 0.00 4.51
1069 1150 1.265905 GTTTTCGCTCGATTGTGGGTT 59.734 47.619 0.00 0.00 0.00 4.11
1071 1152 0.320374 TTCGCTCGATTGTGGGTTCT 59.680 50.000 0.00 0.00 0.00 3.01
1119 1200 3.137459 CTCTCCGTCTCTGCGCCT 61.137 66.667 4.18 0.00 0.00 5.52
1262 1343 3.948086 CTGGTGAGTCGCCGTCGTC 62.948 68.421 17.76 0.00 36.72 4.20
1289 1370 0.106719 CCCCTCCCGCATGTTGTATT 60.107 55.000 0.00 0.00 0.00 1.89
1297 1378 1.267334 CGCATGTTGTATTCCGTTCCG 60.267 52.381 0.00 0.00 0.00 4.30
1306 1387 1.379527 ATTCCGTTCCGCTTGGATTC 58.620 50.000 0.00 0.00 42.75 2.52
1337 1421 3.331002 TTGTGCTGCAACCGGATTA 57.669 47.368 9.46 0.00 31.07 1.75
1488 1572 2.094597 GCTTGAGCATATGCCAACACAA 60.095 45.455 23.96 18.62 43.38 3.33
1498 1582 6.237996 GCATATGCCAACACAATTTTCATCTG 60.238 38.462 17.26 0.00 34.31 2.90
1522 1606 3.844211 TCTATTTTGTGTAGGAGGCAGGT 59.156 43.478 0.00 0.00 0.00 4.00
1547 1631 0.166814 CCAGTCGCTAGCAGCAAAAC 59.833 55.000 16.45 2.66 42.58 2.43
1574 1658 8.075574 TGCAATGTTGAGAGTGTAAATTAACAG 58.924 33.333 0.00 0.00 31.16 3.16
1614 1724 3.441572 GTGCAAGCTTTCCATATGTCAGT 59.558 43.478 0.00 0.00 0.00 3.41
1615 1725 4.081406 TGCAAGCTTTCCATATGTCAGTT 58.919 39.130 0.00 0.00 0.00 3.16
1616 1726 4.082625 TGCAAGCTTTCCATATGTCAGTTG 60.083 41.667 0.00 0.00 0.00 3.16
1617 1727 4.676196 GCAAGCTTTCCATATGTCAGTTGG 60.676 45.833 0.00 0.00 0.00 3.77
1618 1728 3.019564 AGCTTTCCATATGTCAGTTGGC 58.980 45.455 1.24 0.00 0.00 4.52
1623 1733 5.999205 TTCCATATGTCAGTTGGCAAAAT 57.001 34.783 0.00 0.00 31.21 1.82
1663 1773 6.819146 ACTGTTAGTTTTAGCTCTCCTTATGC 59.181 38.462 0.00 0.00 0.00 3.14
1725 1837 4.279671 TCGCTGGTAAACAATTCCATTTGT 59.720 37.500 0.00 0.00 41.49 2.83
1727 1839 4.152223 GCTGGTAAACAATTCCATTTGTGC 59.848 41.667 0.00 0.00 39.68 4.57
1801 1913 1.607628 CATCTGCTTGCCTTATCTGCC 59.392 52.381 0.00 0.00 0.00 4.85
1813 1925 4.567159 GCCTTATCTGCCGTATAATACTGC 59.433 45.833 0.00 0.00 39.06 4.40
1893 2005 3.403936 GTGAAGTCACAAGGCCAGT 57.596 52.632 5.01 0.00 45.75 4.00
1894 2006 0.947244 GTGAAGTCACAAGGCCAGTG 59.053 55.000 19.17 19.17 45.75 3.66
1895 2007 0.836606 TGAAGTCACAAGGCCAGTGA 59.163 50.000 22.64 22.64 43.23 3.41
1912 2024 3.747529 CAGTGAAAATTGTTTGCCCATCC 59.252 43.478 0.00 0.00 0.00 3.51
1933 2045 8.875803 CCATCCATTTGTTTATCTGAAATGTTG 58.124 33.333 0.00 0.00 35.98 3.33
2120 2288 4.025401 GCCGGTTGGTCGCTGTTG 62.025 66.667 1.90 0.00 37.67 3.33
2139 2307 7.308435 GCTGTTGATTTCTTGCTTACTGTAAT 58.692 34.615 0.00 0.00 0.00 1.89
2141 2309 9.121517 CTGTTGATTTCTTGCTTACTGTAATTG 57.878 33.333 0.00 0.00 0.00 2.32
2146 2314 6.554334 TTCTTGCTTACTGTAATTGACACC 57.446 37.500 0.00 0.00 33.31 4.16
2309 2478 5.963176 ACACATGCTTTGACATATGTTCA 57.037 34.783 10.30 6.83 34.03 3.18
2372 2541 6.757237 AGATCTTCATAGTGCTATTGAGGTG 58.243 40.000 0.00 0.00 0.00 4.00
2397 2587 0.833949 CTCCTTGCCCTCCTCCTTAC 59.166 60.000 0.00 0.00 0.00 2.34
2426 2616 4.358851 TGCTTCTGTATTTGTTGTGTTGC 58.641 39.130 0.00 0.00 0.00 4.17
2639 2830 5.868043 TGTCTGCAAACTCAGTATCATTG 57.132 39.130 0.00 0.00 35.63 2.82
2641 2832 5.409520 TGTCTGCAAACTCAGTATCATTGTC 59.590 40.000 0.00 0.00 35.63 3.18
2680 2871 0.961019 TCCAACTTCCAAGCACATGC 59.039 50.000 0.00 0.00 42.49 4.06
2868 3064 5.856126 CATTGATGTGCTTTTTCAATGCT 57.144 34.783 10.78 0.00 45.51 3.79
2904 3100 6.349243 TGGAACATTCAGAATCTTTTGCAT 57.651 33.333 0.00 0.00 0.00 3.96
2996 3192 8.037758 TCTGCCTCAAATCTAAGTTCTCTTAAG 58.962 37.037 0.00 0.00 35.98 1.85
3068 3264 3.679389 CCTAGAAACTGTTCAGGCATGT 58.321 45.455 0.00 0.00 36.09 3.21
3160 3930 2.363306 TGGGACATTGGATGCATACC 57.637 50.000 6.42 7.32 0.00 2.73
3161 3931 1.568123 TGGGACATTGGATGCATACCA 59.432 47.619 6.42 9.96 35.47 3.25
3162 3932 1.956477 GGGACATTGGATGCATACCAC 59.044 52.381 6.42 1.42 37.13 4.16
3163 3933 2.653726 GGACATTGGATGCATACCACA 58.346 47.619 6.42 0.00 37.13 4.17
3164 3934 3.225104 GGACATTGGATGCATACCACAT 58.775 45.455 6.42 6.71 37.13 3.21
3165 3935 3.005050 GGACATTGGATGCATACCACATG 59.995 47.826 21.51 21.51 37.13 3.21
3166 3936 3.884693 GACATTGGATGCATACCACATGA 59.115 43.478 25.19 13.41 37.13 3.07
3167 3937 3.887110 ACATTGGATGCATACCACATGAG 59.113 43.478 25.19 15.27 37.13 2.90
3168 3938 3.650281 TTGGATGCATACCACATGAGT 57.350 42.857 6.42 0.00 37.13 3.41
3169 3939 4.769345 TTGGATGCATACCACATGAGTA 57.231 40.909 6.42 0.79 37.13 2.59
3177 3947 5.221441 TGCATACCACATGAGTAGTGATACC 60.221 44.000 0.00 0.00 39.30 2.73
3188 3958 5.028549 AGTAGTGATACCTTGGCAATCAG 57.971 43.478 0.00 0.00 30.58 2.90
3257 4027 2.220313 GATTGGGCTCTGCTTCTCATC 58.780 52.381 0.00 0.00 0.00 2.92
3336 4120 4.584325 TGGCTTTCATGAGCTTTACTGTTT 59.416 37.500 6.87 0.00 42.32 2.83
3445 4229 2.479566 AGGTGCATCAGACAAACGAT 57.520 45.000 0.00 0.00 0.00 3.73
3450 4234 3.670055 GTGCATCAGACAAACGATTTTGG 59.330 43.478 0.00 0.00 45.65 3.28
3453 4237 4.382754 GCATCAGACAAACGATTTTGGAAC 59.617 41.667 3.86 0.00 45.65 3.62
3504 4288 7.765307 AGCATGACTTAACTGTATTTCATTGG 58.235 34.615 0.00 0.00 0.00 3.16
3727 4513 3.720002 AGGTTTTGGAGGAACTTGGACTA 59.280 43.478 0.00 0.00 41.55 2.59
3735 4521 4.010349 GAGGAACTTGGACTAACAATGGG 58.990 47.826 0.00 0.00 41.55 4.00
3757 4543 6.127168 TGGGTCAGTTCATCGACTTATGTATT 60.127 38.462 0.00 0.00 32.57 1.89
3813 4599 6.699575 AGGTTTACCTGCATCATATGTTTC 57.300 37.500 0.00 0.00 46.55 2.78
3878 4664 8.284945 TGTAGCTCTTCATGATTTGCTTAAAT 57.715 30.769 17.71 0.00 32.72 1.40
3887 4673 6.746822 TCATGATTTGCTTAAATAGTTGCACG 59.253 34.615 0.00 0.00 35.01 5.34
3958 4746 8.156165 TCATGCATGGACACAATATACTCAATA 58.844 33.333 25.97 0.00 0.00 1.90
3959 4747 8.953313 CATGCATGGACACAATATACTCAATAT 58.047 33.333 19.40 0.00 31.75 1.28
3961 4749 9.435688 TGCATGGACACAATATACTCAATATAC 57.564 33.333 0.00 0.00 30.19 1.47
4003 4791 6.672266 TGATTCATAATACTCCCTCTGTCC 57.328 41.667 0.00 0.00 0.00 4.02
4004 4792 5.544176 TGATTCATAATACTCCCTCTGTCCC 59.456 44.000 0.00 0.00 0.00 4.46
4005 4793 4.552883 TCATAATACTCCCTCTGTCCCA 57.447 45.455 0.00 0.00 0.00 4.37
4006 4794 4.890988 TCATAATACTCCCTCTGTCCCAA 58.109 43.478 0.00 0.00 0.00 4.12
4007 4795 5.285401 TCATAATACTCCCTCTGTCCCAAA 58.715 41.667 0.00 0.00 0.00 3.28
4008 4796 5.729229 TCATAATACTCCCTCTGTCCCAAAA 59.271 40.000 0.00 0.00 0.00 2.44
4009 4797 6.389869 TCATAATACTCCCTCTGTCCCAAAAT 59.610 38.462 0.00 0.00 0.00 1.82
4011 4799 6.652205 AATACTCCCTCTGTCCCAAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
4012 4800 4.302559 ACTCCCTCTGTCCCAAAATAAC 57.697 45.455 0.00 0.00 0.00 1.89
4014 4802 4.263506 ACTCCCTCTGTCCCAAAATAACTG 60.264 45.833 0.00 0.00 0.00 3.16
4015 4803 3.655777 TCCCTCTGTCCCAAAATAACTGT 59.344 43.478 0.00 0.00 0.00 3.55
4016 4804 4.010349 CCCTCTGTCCCAAAATAACTGTC 58.990 47.826 0.00 0.00 0.00 3.51
4017 4805 3.684788 CCTCTGTCCCAAAATAACTGTCG 59.315 47.826 0.00 0.00 0.00 4.35
4018 4806 4.315803 CTCTGTCCCAAAATAACTGTCGT 58.684 43.478 0.00 0.00 0.00 4.34
4019 4807 4.710324 TCTGTCCCAAAATAACTGTCGTT 58.290 39.130 0.00 0.00 37.15 3.85
4020 4808 4.513692 TCTGTCCCAAAATAACTGTCGTTG 59.486 41.667 0.00 0.00 34.59 4.10
4021 4809 4.452825 TGTCCCAAAATAACTGTCGTTGA 58.547 39.130 0.00 0.00 34.59 3.18
4022 4810 5.067273 TGTCCCAAAATAACTGTCGTTGAT 58.933 37.500 0.00 0.00 34.59 2.57
4023 4811 5.533154 TGTCCCAAAATAACTGTCGTTGATT 59.467 36.000 0.00 0.00 34.59 2.57
4024 4812 6.039941 TGTCCCAAAATAACTGTCGTTGATTT 59.960 34.615 0.00 0.00 34.59 2.17
4025 4813 7.228906 TGTCCCAAAATAACTGTCGTTGATTTA 59.771 33.333 0.00 0.00 34.59 1.40
4026 4814 7.749126 GTCCCAAAATAACTGTCGTTGATTTAG 59.251 37.037 0.00 0.00 34.59 1.85
4027 4815 7.446013 TCCCAAAATAACTGTCGTTGATTTAGT 59.554 33.333 0.00 0.00 34.59 2.24
4028 4816 8.723311 CCCAAAATAACTGTCGTTGATTTAGTA 58.277 33.333 0.00 0.00 34.59 1.82
4029 4817 9.537848 CCAAAATAACTGTCGTTGATTTAGTAC 57.462 33.333 0.00 0.00 34.59 2.73
4033 4821 9.485206 AATAACTGTCGTTGATTTAGTACAACT 57.515 29.630 0.00 0.00 42.53 3.16
4034 4822 7.781548 AACTGTCGTTGATTTAGTACAACTT 57.218 32.000 0.00 0.00 42.53 2.66
4035 4823 7.781548 ACTGTCGTTGATTTAGTACAACTTT 57.218 32.000 0.00 0.00 42.53 2.66
4036 4824 7.627340 ACTGTCGTTGATTTAGTACAACTTTG 58.373 34.615 0.00 0.00 42.53 2.77
4037 4825 7.279313 ACTGTCGTTGATTTAGTACAACTTTGT 59.721 33.333 0.00 0.00 42.53 2.83
4038 4826 8.645730 TGTCGTTGATTTAGTACAACTTTGTA 57.354 30.769 0.00 0.00 42.53 2.41
4075 4863 8.919145 ACTAAATCAACAACACTTATTTTGGGA 58.081 29.630 0.00 0.00 0.00 4.37
4076 4864 9.191995 CTAAATCAACAACACTTATTTTGGGAC 57.808 33.333 0.00 0.00 0.00 4.46
4077 4865 5.176407 TCAACAACACTTATTTTGGGACG 57.824 39.130 0.00 0.00 0.00 4.79
4078 4866 4.036971 TCAACAACACTTATTTTGGGACGG 59.963 41.667 0.00 0.00 0.00 4.79
4079 4867 3.822940 ACAACACTTATTTTGGGACGGA 58.177 40.909 0.00 0.00 0.00 4.69
4080 4868 3.818773 ACAACACTTATTTTGGGACGGAG 59.181 43.478 0.00 0.00 0.00 4.63
4081 4869 3.067684 ACACTTATTTTGGGACGGAGG 57.932 47.619 0.00 0.00 0.00 4.30
4082 4870 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4083 4871 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4084 4872 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4121 4909 8.638565 GCGTTCACCATATATGATTTAAAATGC 58.361 33.333 14.54 11.29 0.00 3.56
4131 4919 5.664294 TGATTTAAAATGCATGCTCCTGT 57.336 34.783 20.33 3.04 0.00 4.00
4132 4920 5.653507 TGATTTAAAATGCATGCTCCTGTC 58.346 37.500 20.33 7.45 0.00 3.51
4150 4938 8.017946 GCTCCTGTCAACTAAAAAGTGAATTAG 58.982 37.037 0.00 0.00 35.67 1.73
4156 4944 9.651718 GTCAACTAAAAAGTGAATTAGTGTCAG 57.348 33.333 0.00 0.00 40.51 3.51
4179 4967 9.995003 TCAGTTGAATTTTGGTTTTGCTTATAT 57.005 25.926 0.00 0.00 0.00 0.86
4207 4995 4.555262 CGAAATTGGGTGCTGTTTATGTT 58.445 39.130 0.00 0.00 0.00 2.71
4238 5026 9.263538 CCATTTTTGAATCTTGACAAATCTTCA 57.736 29.630 0.00 0.00 36.21 3.02
4266 5054 8.840833 ATACATTAACAAAATGGGTCCAAAAC 57.159 30.769 0.00 0.00 32.14 2.43
4307 5095 2.294979 GTCGGACTTTGGTCTTGGTTT 58.705 47.619 0.00 0.00 41.82 3.27
4432 5220 4.764172 AGTGTTTTATGTTGGCAGCAAAA 58.236 34.783 8.44 7.71 0.00 2.44
4468 5256 8.515414 ACTCTTTTTGCAGTCCATCTATTTAAC 58.485 33.333 0.00 0.00 0.00 2.01
4532 5320 4.826733 ACACTAGGCACACATTTTGAATGA 59.173 37.500 7.59 0.00 0.00 2.57
4536 5324 8.192774 CACTAGGCACACATTTTGAATGATAAT 58.807 33.333 7.59 0.00 0.00 1.28
4587 5375 6.172630 TCTGAGCATGCTAAAACACTGATAA 58.827 36.000 22.74 0.00 0.00 1.75
4589 5377 6.845302 TGAGCATGCTAAAACACTGATAAAG 58.155 36.000 22.74 0.00 0.00 1.85
4624 5412 0.322816 ATGTGGCCACTGTGTCCATC 60.323 55.000 34.75 8.40 31.83 3.51
4690 5478 2.038557 ACTACTCCTGTTGCCATTTCGT 59.961 45.455 0.00 0.00 0.00 3.85
4741 5529 0.538057 CCACTGTGGTGTTCCTGCAT 60.538 55.000 18.76 0.00 41.53 3.96
4773 5561 1.709147 CGTATTGCTCCTGTGCTGCC 61.709 60.000 0.00 0.00 0.00 4.85
4794 5582 0.979665 TTCTCTCTGACCCTGCCTTG 59.020 55.000 0.00 0.00 0.00 3.61
4946 5735 4.398044 CGGTGGGCAATTGTTTATTACTCT 59.602 41.667 7.40 0.00 0.00 3.24
5024 5813 8.877808 ATTTTGACCAGAACTTTGAATTTCTC 57.122 30.769 0.00 0.00 29.23 2.87
5069 5858 5.850614 TGTCTAGTTTTGACAAGGTACTCC 58.149 41.667 0.00 0.00 40.89 3.85
5081 5870 6.380274 TGACAAGGTACTCCCAAGTAATCTAG 59.620 42.308 0.00 0.00 38.49 2.43
5161 5950 0.392595 GGCCTTACCAGGAAGTTCGG 60.393 60.000 0.00 0.00 44.19 4.30
5264 6053 8.817092 TGATAACTCATATCATACGGTCCATA 57.183 34.615 0.00 0.00 44.30 2.74
5276 6065 6.317642 TCATACGGTCCATATTTTTCCACAAG 59.682 38.462 0.00 0.00 0.00 3.16
5293 6082 4.379186 CCACAAGCTGATAGTTGCTTTCTG 60.379 45.833 0.00 0.00 45.91 3.02
5315 6104 2.397044 TCCAGGGCCTTGTGAATTTT 57.603 45.000 14.60 0.00 0.00 1.82
5647 6436 6.333168 ACCTATCAGGATCTACAGAGAAGGTA 59.667 42.308 0.00 0.00 37.67 3.08
5698 6487 5.132502 TGTCTCACATGGTTCAAATTGACT 58.867 37.500 0.00 0.00 0.00 3.41
5784 6573 5.272402 TCTCTTCTCTCTCTCTCTCTCTCA 58.728 45.833 0.00 0.00 0.00 3.27
5785 6574 5.901853 TCTCTTCTCTCTCTCTCTCTCTCAT 59.098 44.000 0.00 0.00 0.00 2.90
5987 6893 1.291877 GACTCGCGGCACAGTGAAAT 61.292 55.000 6.13 0.00 0.00 2.17
6090 6996 5.535030 ACCATTAACTGAGGGTGAAAAGTTC 59.465 40.000 0.00 0.00 34.76 3.01
6214 7121 8.162878 ACAATAATAGCCAATTCAGACTCATG 57.837 34.615 0.00 0.00 0.00 3.07
6227 7134 9.926158 AATTCAGACTCATGTATATCTGCTAAG 57.074 33.333 11.11 0.00 38.77 2.18
6259 7166 4.741321 ATTGAACAATTGATCCCGCAAT 57.259 36.364 13.59 3.66 40.04 3.56
6303 7210 4.992688 TGAAGGCTAACAATTAAATGCCG 58.007 39.130 0.00 0.00 44.42 5.69
6351 7259 7.013274 ACAAAATGTATCTATCCGTGAATTGGG 59.987 37.037 0.00 0.00 0.00 4.12
6364 7272 2.410322 AATTGGGCTCCGCTCACACA 62.410 55.000 0.00 0.00 39.49 3.72
6432 7341 0.036010 CCTGGCTTACCCACACAGAG 60.036 60.000 0.00 0.00 39.18 3.35
6438 7347 0.322456 TTACCCACACAGAGGCATGC 60.322 55.000 9.90 9.90 0.00 4.06
6456 7365 1.589716 GCAGCCAACTCCATGACACC 61.590 60.000 0.00 0.00 0.00 4.16
6526 7435 8.762645 TGGTAGATTGTCTCTTCAGATATTTGT 58.237 33.333 0.00 0.00 35.28 2.83
6559 7468 1.428448 TCGTCATTTCTTCTGGCGTG 58.572 50.000 0.00 0.00 42.13 5.34
6567 7476 0.612174 TCTTCTGGCGTGGAGTAGCT 60.612 55.000 0.00 0.00 0.00 3.32
6577 7486 0.976641 TGGAGTAGCTGAGTGTTGGG 59.023 55.000 0.00 0.00 0.00 4.12
6628 7537 7.670009 TTCTGGGCATGTTTTGAATTTTATG 57.330 32.000 0.00 0.00 0.00 1.90
6684 7593 6.632834 CGTGTACAATTCTGAAAACCAAGAAG 59.367 38.462 0.00 0.00 0.00 2.85
6689 7598 4.637483 TTCTGAAAACCAAGAAGCACTG 57.363 40.909 0.00 0.00 0.00 3.66
6695 7604 3.923017 AACCAAGAAGCACTGTAATGC 57.077 42.857 0.00 0.00 46.50 3.56
6714 7623 4.193826 TGCTGATCCTTATCTTATCCGC 57.806 45.455 0.00 0.00 32.93 5.54
6944 7853 6.174049 GCTTTGGTTCTCAAGATTACCTAGT 58.826 40.000 3.27 0.00 36.62 2.57
6954 7863 4.744795 AGATTACCTAGTGAAGCTGTGG 57.255 45.455 0.00 0.00 0.00 4.17
6990 7899 5.912149 AGAATAGATGGCCACTTGGAATA 57.088 39.130 8.16 0.00 37.39 1.75
7070 7979 6.208204 AGCTTCAATGCTTCAACTTATTCACT 59.792 34.615 0.00 0.00 40.93 3.41
7106 8015 0.807667 GCTAGAGTGTCGCATGGTGG 60.808 60.000 0.00 0.00 0.00 4.61
7109 8018 3.899981 GAGTGTCGCATGGTGGCCA 62.900 63.158 0.00 0.00 38.19 5.36
7155 8064 7.885297 TGGCTATAATATGGAAAATTGTCAGC 58.115 34.615 0.00 0.00 0.00 4.26
7157 8066 7.094805 GGCTATAATATGGAAAATTGTCAGCGA 60.095 37.037 0.00 0.00 0.00 4.93
7161 8070 0.179189 GGAAAATTGTCAGCGAGCCG 60.179 55.000 0.00 0.00 0.00 5.52
7206 8116 7.771506 ATACATATACCCCTTGCATTATCCT 57.228 36.000 0.00 0.00 0.00 3.24
7218 8128 5.894298 TGCATTATCCTGAACTGGAGTAT 57.106 39.130 6.58 0.78 39.78 2.12
7229 8139 8.598916 TCCTGAACTGGAGTATATGTTTTGTTA 58.401 33.333 0.00 0.00 0.00 2.41
7237 8147 8.516234 TGGAGTATATGTTTTGTTAAAATGCGT 58.484 29.630 0.00 0.00 32.22 5.24
7301 8213 2.234661 TCATGGAGCAGAGGTTGTACAG 59.765 50.000 0.00 0.00 0.00 2.74
7314 8226 3.270877 GTTGTACAGTAGCCTTCCATGG 58.729 50.000 4.97 4.97 0.00 3.66
7328 8240 5.746952 GCCTTCCATGGTCATGATATTCAGA 60.747 44.000 12.58 0.00 41.20 3.27
7334 8246 8.222637 TCCATGGTCATGATATTCAGAAAATCT 58.777 33.333 12.58 0.00 41.20 2.40
7387 8299 3.436704 ACGTATCTTTGATGTTGGCTGTG 59.563 43.478 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 7.044181 TGTTTGCTGTTTTCAAATCCATGTAA 58.956 30.769 0.00 0.00 36.06 2.41
252 254 2.433446 CAAGCTCTGGTGGGCACT 59.567 61.111 0.00 0.00 0.00 4.40
366 368 3.064207 GCATTTCACAAGTGACCGTCTA 58.936 45.455 1.73 0.00 39.66 2.59
367 369 1.873591 GCATTTCACAAGTGACCGTCT 59.126 47.619 1.73 0.00 39.66 4.18
368 370 1.873591 AGCATTTCACAAGTGACCGTC 59.126 47.619 1.73 0.00 39.66 4.79
369 371 1.967319 AGCATTTCACAAGTGACCGT 58.033 45.000 1.73 0.00 39.66 4.83
577 581 1.065199 TCTTGATCAGGGGTGACATGC 60.065 52.381 4.83 0.00 0.00 4.06
676 680 7.162973 TCAGGGAGATTAATAGTAGGTCTCA 57.837 40.000 13.29 0.00 37.61 3.27
705 766 0.678048 GTCAGGGAGCACATGGGAAC 60.678 60.000 0.00 0.00 0.00 3.62
723 784 2.781174 TGTCTTTTACCAGTTCCCCAGT 59.219 45.455 0.00 0.00 0.00 4.00
726 787 3.245122 TGGATGTCTTTTACCAGTTCCCC 60.245 47.826 0.00 0.00 0.00 4.81
729 790 5.048013 CCCTTTGGATGTCTTTTACCAGTTC 60.048 44.000 0.00 0.00 33.85 3.01
735 796 4.462483 TGATGCCCTTTGGATGTCTTTTAC 59.538 41.667 0.00 0.00 0.00 2.01
799 860 5.408604 TGGAAGATTTTAGCTCTTGTTCGTC 59.591 40.000 0.00 0.00 33.18 4.20
842 903 0.459585 GACGGCTAGAACCATTCGCA 60.460 55.000 0.00 0.00 34.02 5.10
889 959 6.377146 TGAAGTGGATAATAGACTTTTTGGGC 59.623 38.462 0.00 0.00 30.01 5.36
890 960 7.148069 GGTGAAGTGGATAATAGACTTTTTGGG 60.148 40.741 0.00 0.00 30.01 4.12
893 964 6.598064 CCGGTGAAGTGGATAATAGACTTTTT 59.402 38.462 0.00 0.00 30.01 1.94
989 1070 2.063541 GATTCCCATTGCTTCGGCGG 62.064 60.000 7.21 0.00 45.37 6.13
990 1071 1.356624 GATTCCCATTGCTTCGGCG 59.643 57.895 0.00 0.00 45.37 6.46
991 1072 0.817013 TTGATTCCCATTGCTTCGGC 59.183 50.000 0.00 0.00 42.19 5.54
992 1073 1.406539 CCTTGATTCCCATTGCTTCGG 59.593 52.381 0.00 0.00 0.00 4.30
993 1074 2.094675 ACCTTGATTCCCATTGCTTCG 58.905 47.619 0.00 0.00 0.00 3.79
994 1075 4.273318 AGTACCTTGATTCCCATTGCTTC 58.727 43.478 0.00 0.00 0.00 3.86
995 1076 4.018050 AGAGTACCTTGATTCCCATTGCTT 60.018 41.667 0.00 0.00 0.00 3.91
996 1077 3.525199 AGAGTACCTTGATTCCCATTGCT 59.475 43.478 0.00 0.00 0.00 3.91
1037 1118 3.488090 GAAAACGGGAGCGGCGAG 61.488 66.667 12.98 0.00 0.00 5.03
1042 1123 3.838795 CGAGCGAAAACGGGAGCG 61.839 66.667 0.00 0.00 34.34 5.03
1068 1149 0.965866 AGAGGCCGTCACATCGAGAA 60.966 55.000 0.00 0.00 0.00 2.87
1069 1150 1.377366 GAGAGGCCGTCACATCGAGA 61.377 60.000 0.00 0.00 0.00 4.04
1071 1152 2.415608 GGAGAGGCCGTCACATCGA 61.416 63.158 10.03 0.00 0.00 3.59
1119 1200 4.058732 TCAAACCCTAGCGCGCGA 62.059 61.111 37.18 21.03 0.00 5.87
1297 1378 2.700773 GCACCACCCGAATCCAAGC 61.701 63.158 0.00 0.00 0.00 4.01
1306 1387 3.345808 CACAACTCGCACCACCCG 61.346 66.667 0.00 0.00 0.00 5.28
1330 1414 1.605712 GGCATCTCCGAACTAATCCGG 60.606 57.143 0.00 0.00 46.57 5.14
1337 1421 2.420687 GGAAGAATGGCATCTCCGAACT 60.421 50.000 0.00 0.00 37.80 3.01
1488 1572 8.960591 CCTACACAAAATAGACCAGATGAAAAT 58.039 33.333 0.00 0.00 0.00 1.82
1498 1582 4.192317 CTGCCTCCTACACAAAATAGACC 58.808 47.826 0.00 0.00 0.00 3.85
1522 1606 2.786539 CTGCTAGCGACTGGCAACCA 62.787 60.000 10.77 0.00 46.52 3.67
1547 1631 8.075574 TGTTAATTTACACTCTCAACATTGCAG 58.924 33.333 0.00 0.00 0.00 4.41
1574 1658 6.912591 GCTTGCACATGGTAATTTACTGTATC 59.087 38.462 6.52 1.72 0.00 2.24
1614 1724 5.946942 TTATAAGCATCCCATTTTGCCAA 57.053 34.783 0.00 0.00 39.72 4.52
1615 1725 6.782000 AGTATTATAAGCATCCCATTTTGCCA 59.218 34.615 0.00 0.00 39.72 4.92
1616 1726 7.092716 CAGTATTATAAGCATCCCATTTTGCC 58.907 38.462 0.00 0.00 39.72 4.52
1617 1727 7.661040 ACAGTATTATAAGCATCCCATTTTGC 58.339 34.615 0.00 0.00 39.17 3.68
1623 1733 9.914834 AAAACTAACAGTATTATAAGCATCCCA 57.085 29.630 0.00 0.00 0.00 4.37
1647 1757 5.420725 TTGTCAGCATAAGGAGAGCTAAA 57.579 39.130 0.00 0.00 36.73 1.85
1662 1772 5.468540 AATAAGAAACCCCTTTTGTCAGC 57.531 39.130 0.00 0.00 0.00 4.26
1663 1773 7.761038 ACTAATAAGAAACCCCTTTTGTCAG 57.239 36.000 0.00 0.00 0.00 3.51
1696 1806 5.095490 GGAATTGTTTACCAGCGAATTCTG 58.905 41.667 3.52 0.00 34.72 3.02
1725 1837 8.630054 ACAATACAATAAACAAAGGAGTAGCA 57.370 30.769 0.00 0.00 0.00 3.49
1801 1913 7.155328 AGAGAAATGGGAAGCAGTATTATACG 58.845 38.462 0.00 0.00 0.00 3.06
1813 1925 4.263506 ACCACAACCTAGAGAAATGGGAAG 60.264 45.833 0.00 0.00 0.00 3.46
1861 1973 0.251916 CTTCACCGGCCTCATTGGTA 59.748 55.000 0.00 0.00 38.35 3.25
1890 2002 3.747529 GGATGGGCAAACAATTTTCACTG 59.252 43.478 0.00 0.00 0.00 3.66
1893 2005 4.637387 ATGGATGGGCAAACAATTTTCA 57.363 36.364 0.00 0.00 0.00 2.69
1894 2006 5.241285 ACAAATGGATGGGCAAACAATTTTC 59.759 36.000 0.00 0.00 0.00 2.29
1895 2007 5.139001 ACAAATGGATGGGCAAACAATTTT 58.861 33.333 0.00 0.00 0.00 1.82
1963 2075 1.001020 ATCATGACTTGCCCCGCAA 60.001 52.632 0.00 0.00 46.80 4.85
1965 2077 1.315257 AACATCATGACTTGCCCCGC 61.315 55.000 0.00 0.00 0.00 6.13
1968 2080 5.300286 AGCTAATAAACATCATGACTTGCCC 59.700 40.000 0.00 0.00 0.00 5.36
1969 2081 6.038603 TGAGCTAATAAACATCATGACTTGCC 59.961 38.462 0.00 0.00 0.00 4.52
1970 2082 7.019774 TGAGCTAATAAACATCATGACTTGC 57.980 36.000 0.00 0.00 0.00 4.01
1974 2086 9.224267 ACCATATGAGCTAATAAACATCATGAC 57.776 33.333 3.65 0.00 32.99 3.06
2120 2288 7.750903 GGTGTCAATTACAGTAAGCAAGAAATC 59.249 37.037 0.00 0.00 39.29 2.17
2146 2314 1.798813 GTTCAGCAGTTAACCCTGTCG 59.201 52.381 18.15 2.93 34.84 4.35
2309 2478 6.410540 CCTCTTCAAAGACCTAATAAGCAGT 58.589 40.000 0.00 0.00 0.00 4.40
2397 2587 5.106948 ACAACAAATACAGAAGCATGACGAG 60.107 40.000 0.00 0.00 0.00 4.18
2639 2830 4.273148 ACCACTTCAGAACATGGTAGAC 57.727 45.455 11.34 0.00 43.72 2.59
2641 2832 4.003648 GGAACCACTTCAGAACATGGTAG 58.996 47.826 12.87 0.00 44.80 3.18
2687 2878 6.833416 TGATCTGGAAAGAGAAGGAACAAAAA 59.167 34.615 0.00 0.00 0.00 1.94
2868 3064 7.632861 TCTGAATGTTCCATTAAATCTCCTCA 58.367 34.615 0.00 0.00 0.00 3.86
2951 3147 2.042979 AGATTTAAGGCCTCCCAAGCAA 59.957 45.455 5.23 0.00 0.00 3.91
2996 3192 6.595716 ACTGAGAAAACATTATCAGCCTACAC 59.404 38.462 11.83 0.00 42.33 2.90
3000 3196 5.809001 TGACTGAGAAAACATTATCAGCCT 58.191 37.500 11.83 0.00 42.33 4.58
3068 3264 2.057137 AGACAAGGTTGCAAGCTGAA 57.943 45.000 30.27 0.00 36.76 3.02
3153 3923 5.221441 GGTATCACTACTCATGTGGTATGCA 60.221 44.000 0.00 0.00 35.67 3.96
3154 3924 5.011125 AGGTATCACTACTCATGTGGTATGC 59.989 44.000 0.00 0.00 35.67 3.14
3155 3925 6.656632 AGGTATCACTACTCATGTGGTATG 57.343 41.667 0.00 0.00 35.67 2.39
3156 3926 6.042093 CCAAGGTATCACTACTCATGTGGTAT 59.958 42.308 0.00 0.00 35.67 2.73
3157 3927 5.362717 CCAAGGTATCACTACTCATGTGGTA 59.637 44.000 0.00 1.12 35.67 3.25
3158 3928 4.162320 CCAAGGTATCACTACTCATGTGGT 59.838 45.833 0.00 0.00 38.46 4.16
3159 3929 4.697514 CCAAGGTATCACTACTCATGTGG 58.302 47.826 0.00 0.00 36.21 4.17
3160 3930 4.122776 GCCAAGGTATCACTACTCATGTG 58.877 47.826 0.00 0.00 36.82 3.21
3161 3931 3.774766 TGCCAAGGTATCACTACTCATGT 59.225 43.478 0.00 0.00 0.00 3.21
3162 3932 4.406648 TGCCAAGGTATCACTACTCATG 57.593 45.455 0.00 0.00 0.00 3.07
3163 3933 5.130975 TGATTGCCAAGGTATCACTACTCAT 59.869 40.000 3.08 0.00 0.00 2.90
3164 3934 4.469586 TGATTGCCAAGGTATCACTACTCA 59.530 41.667 3.08 0.00 0.00 3.41
3165 3935 5.023533 TGATTGCCAAGGTATCACTACTC 57.976 43.478 3.08 0.00 0.00 2.59
3166 3936 4.684485 GCTGATTGCCAAGGTATCACTACT 60.684 45.833 3.08 0.00 35.15 2.57
3167 3937 3.561725 GCTGATTGCCAAGGTATCACTAC 59.438 47.826 3.08 0.00 35.15 2.73
3168 3938 3.199727 TGCTGATTGCCAAGGTATCACTA 59.800 43.478 3.08 0.00 42.00 2.74
3169 3939 2.025981 TGCTGATTGCCAAGGTATCACT 60.026 45.455 3.08 0.00 42.00 3.41
3177 3947 2.159282 GGAACATCTGCTGATTGCCAAG 60.159 50.000 2.92 0.00 42.00 3.61
3188 3958 1.463674 AAATCACGGGGAACATCTGC 58.536 50.000 0.00 0.00 0.00 4.26
3197 3967 5.941948 GTGATATTTCCTAAATCACGGGG 57.058 43.478 0.00 0.00 39.90 5.73
3257 4027 7.479916 GCTGTTCATTTAGAAGAATTTCACTCG 59.520 37.037 0.00 0.00 36.78 4.18
3433 4217 5.124776 AGTTGTTCCAAAATCGTTTGTCTGA 59.875 36.000 0.00 0.00 42.26 3.27
3450 4234 9.444600 TTGGGTAATAAAGATACAGAGTTGTTC 57.555 33.333 0.00 0.00 38.76 3.18
3727 4513 3.074412 GTCGATGAACTGACCCATTGTT 58.926 45.455 0.00 0.00 0.00 2.83
3735 4521 8.635877 AAGAATACATAAGTCGATGAACTGAC 57.364 34.615 0.00 0.00 35.33 3.51
3757 4543 3.128764 CGCAGTAGTCACATCCACTAAGA 59.871 47.826 0.00 0.00 0.00 2.10
3878 4664 2.248280 TTTTCAGAGCCGTGCAACTA 57.752 45.000 0.00 0.00 31.75 2.24
3887 4673 8.246871 AGAAACAGCTTTAATATTTTCAGAGCC 58.753 33.333 0.00 0.00 0.00 4.70
3975 4763 9.386122 ACAGAGGGAGTATTATGAATCAACTAT 57.614 33.333 0.00 0.00 0.00 2.12
3976 4764 8.783660 ACAGAGGGAGTATTATGAATCAACTA 57.216 34.615 0.00 0.00 0.00 2.24
3977 4765 7.202047 GGACAGAGGGAGTATTATGAATCAACT 60.202 40.741 0.00 0.00 0.00 3.16
3978 4766 6.931840 GGACAGAGGGAGTATTATGAATCAAC 59.068 42.308 0.00 0.00 0.00 3.18
3979 4767 6.043243 GGGACAGAGGGAGTATTATGAATCAA 59.957 42.308 0.00 0.00 0.00 2.57
3980 4768 5.544176 GGGACAGAGGGAGTATTATGAATCA 59.456 44.000 0.00 0.00 0.00 2.57
3981 4769 5.544176 TGGGACAGAGGGAGTATTATGAATC 59.456 44.000 0.00 0.00 0.00 2.52
3982 4770 5.476983 TGGGACAGAGGGAGTATTATGAAT 58.523 41.667 0.00 0.00 0.00 2.57
3984 4772 4.552883 TGGGACAGAGGGAGTATTATGA 57.447 45.455 0.00 0.00 0.00 2.15
3985 4773 5.630415 TTTGGGACAGAGGGAGTATTATG 57.370 43.478 0.00 0.00 42.39 1.90
3987 4775 7.404980 AGTTATTTTGGGACAGAGGGAGTATTA 59.595 37.037 0.00 0.00 42.39 0.98
3988 4776 6.217693 AGTTATTTTGGGACAGAGGGAGTATT 59.782 38.462 0.00 0.00 42.39 1.89
3990 4778 5.045869 CAGTTATTTTGGGACAGAGGGAGTA 60.046 44.000 0.00 0.00 42.39 2.59
3991 4779 3.916989 AGTTATTTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
3992 4780 4.263506 ACAGTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
3993 4781 3.655777 ACAGTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
3995 4783 3.684788 CGACAGTTATTTTGGGACAGAGG 59.315 47.826 0.00 0.00 42.39 3.69
3996 4784 4.315803 ACGACAGTTATTTTGGGACAGAG 58.684 43.478 0.00 0.00 42.39 3.35
3998 4786 4.513692 TCAACGACAGTTATTTTGGGACAG 59.486 41.667 0.00 0.00 38.02 3.51
4000 4788 5.622770 ATCAACGACAGTTATTTTGGGAC 57.377 39.130 0.00 0.00 38.79 4.46
4003 4791 9.537848 GTACTAAATCAACGACAGTTATTTTGG 57.462 33.333 0.00 0.00 38.79 3.28
4007 4795 9.485206 AGTTGTACTAAATCAACGACAGTTATT 57.515 29.630 0.00 0.00 45.56 1.40
4008 4796 9.485206 AAGTTGTACTAAATCAACGACAGTTAT 57.515 29.630 0.00 0.00 45.56 1.89
4009 4797 8.876275 AAGTTGTACTAAATCAACGACAGTTA 57.124 30.769 0.00 0.00 45.56 2.24
4011 4799 7.279313 ACAAAGTTGTACTAAATCAACGACAGT 59.721 33.333 0.00 0.00 45.56 3.55
4012 4800 7.627340 ACAAAGTTGTACTAAATCAACGACAG 58.373 34.615 0.00 0.00 45.56 3.51
4049 4837 8.919145 TCCCAAAATAAGTGTTGTTGATTTAGT 58.081 29.630 0.00 0.00 0.00 2.24
4050 4838 9.191995 GTCCCAAAATAAGTGTTGTTGATTTAG 57.808 33.333 0.00 0.00 0.00 1.85
4051 4839 7.863375 CGTCCCAAAATAAGTGTTGTTGATTTA 59.137 33.333 0.00 0.00 0.00 1.40
4052 4840 6.699642 CGTCCCAAAATAAGTGTTGTTGATTT 59.300 34.615 0.00 0.00 0.00 2.17
4053 4841 6.212955 CGTCCCAAAATAAGTGTTGTTGATT 58.787 36.000 0.00 0.00 0.00 2.57
4054 4842 5.278758 CCGTCCCAAAATAAGTGTTGTTGAT 60.279 40.000 0.00 0.00 0.00 2.57
4055 4843 4.036971 CCGTCCCAAAATAAGTGTTGTTGA 59.963 41.667 0.00 0.00 0.00 3.18
4056 4844 4.036971 TCCGTCCCAAAATAAGTGTTGTTG 59.963 41.667 0.00 0.00 0.00 3.33
4057 4845 4.208746 TCCGTCCCAAAATAAGTGTTGTT 58.791 39.130 0.00 0.00 0.00 2.83
4058 4846 3.818773 CTCCGTCCCAAAATAAGTGTTGT 59.181 43.478 0.00 0.00 0.00 3.32
4059 4847 3.190535 CCTCCGTCCCAAAATAAGTGTTG 59.809 47.826 0.00 0.00 0.00 3.33
4060 4848 3.418047 CCTCCGTCCCAAAATAAGTGTT 58.582 45.455 0.00 0.00 0.00 3.32
4061 4849 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
4062 4850 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4063 4851 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4064 4852 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4065 4853 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4066 4854 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4067 4855 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4068 4856 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4069 4857 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
4070 4858 2.969950 CAATATACTCCCTCCGTCCCAA 59.030 50.000 0.00 0.00 0.00 4.12
4071 4859 2.090943 ACAATATACTCCCTCCGTCCCA 60.091 50.000 0.00 0.00 0.00 4.37
4072 4860 2.606378 ACAATATACTCCCTCCGTCCC 58.394 52.381 0.00 0.00 0.00 4.46
4073 4861 4.377897 CAAACAATATACTCCCTCCGTCC 58.622 47.826 0.00 0.00 0.00 4.79
4074 4862 3.808174 GCAAACAATATACTCCCTCCGTC 59.192 47.826 0.00 0.00 0.00 4.79
4075 4863 3.740141 CGCAAACAATATACTCCCTCCGT 60.740 47.826 0.00 0.00 0.00 4.69
4076 4864 2.800544 CGCAAACAATATACTCCCTCCG 59.199 50.000 0.00 0.00 0.00 4.63
4077 4865 3.805207 ACGCAAACAATATACTCCCTCC 58.195 45.455 0.00 0.00 0.00 4.30
4078 4866 4.873827 TGAACGCAAACAATATACTCCCTC 59.126 41.667 0.00 0.00 0.00 4.30
4079 4867 4.634443 GTGAACGCAAACAATATACTCCCT 59.366 41.667 0.00 0.00 0.00 4.20
4080 4868 4.201881 GGTGAACGCAAACAATATACTCCC 60.202 45.833 0.00 0.00 0.00 4.30
4081 4869 4.393680 TGGTGAACGCAAACAATATACTCC 59.606 41.667 0.00 0.00 0.00 3.85
4082 4870 5.539582 TGGTGAACGCAAACAATATACTC 57.460 39.130 0.00 0.00 0.00 2.59
4083 4871 7.801716 ATATGGTGAACGCAAACAATATACT 57.198 32.000 0.00 0.00 0.00 2.12
4084 4872 9.541724 CATATATGGTGAACGCAAACAATATAC 57.458 33.333 4.68 0.00 0.00 1.47
4121 4909 5.239306 TCACTTTTTAGTTGACAGGAGCATG 59.761 40.000 0.00 0.00 0.00 4.06
4131 4919 9.391006 ACTGACACTAATTCACTTTTTAGTTGA 57.609 29.630 0.00 0.00 36.71 3.18
4150 4938 5.351189 AGCAAAACCAAAATTCAACTGACAC 59.649 36.000 0.00 0.00 0.00 3.67
4156 4944 9.328721 GCAATATAAGCAAAACCAAAATTCAAC 57.671 29.630 0.00 0.00 0.00 3.18
4179 4967 1.006337 GCACCCAATTTCGCTGCAA 60.006 52.632 0.00 0.00 0.00 4.08
4207 4995 8.783833 TTTGTCAAGATTCAAAAATGGAAACA 57.216 26.923 0.00 0.00 36.29 2.83
4307 5095 4.791334 TCTTTGTCCCCCAATACCTATTCA 59.209 41.667 0.00 0.00 31.81 2.57
4432 5220 7.665559 TGGACTGCAAAAAGAGTGTCTTAATAT 59.334 33.333 0.00 0.00 35.27 1.28
4468 5256 4.216902 TCAATGAGGAGTTTGATTGCACAG 59.783 41.667 0.00 0.00 0.00 3.66
4567 5355 5.393461 GGCTTTATCAGTGTTTTAGCATGCT 60.393 40.000 25.99 25.99 0.00 3.79
4587 5375 4.021192 CCACATGGTTACATTGAAAGGCTT 60.021 41.667 0.00 0.00 34.35 4.35
4589 5377 3.848726 CCACATGGTTACATTGAAAGGC 58.151 45.455 0.00 0.00 34.35 4.35
4624 5412 6.372659 ACAGAAGCTGTTTAGGATGTATGTTG 59.627 38.462 0.00 0.00 42.59 3.33
4741 5529 2.158827 AGCAATACGGTGGCATGACATA 60.159 45.455 3.50 0.00 0.00 2.29
4773 5561 1.216710 GGCAGGGTCAGAGAGAACG 59.783 63.158 0.00 0.00 33.56 3.95
4907 5696 5.297278 TGCCCACCGAAATGTTATGTTATAC 59.703 40.000 0.00 0.00 0.00 1.47
4924 5713 5.914898 AGAGTAATAAACAATTGCCCACC 57.085 39.130 5.05 0.00 31.01 4.61
4946 5735 7.458397 AGAATTAACTACCACCTTGACATCAA 58.542 34.615 0.00 0.00 0.00 2.57
5012 5801 2.989166 GCAAAGCCCGAGAAATTCAAAG 59.011 45.455 0.00 0.00 0.00 2.77
5021 5810 0.246635 GTCTACTGCAAAGCCCGAGA 59.753 55.000 0.00 0.00 0.00 4.04
5024 5813 0.517316 GTTGTCTACTGCAAAGCCCG 59.483 55.000 0.00 0.00 0.00 6.13
5060 5849 8.487028 CATTTCTAGATTACTTGGGAGTACCTT 58.513 37.037 0.00 0.00 38.07 3.50
5161 5950 6.327279 ACATTAGGTTGCTTAAACAAGGTC 57.673 37.500 0.00 0.00 40.86 3.85
5264 6053 5.244626 AGCAACTATCAGCTTGTGGAAAAAT 59.755 36.000 0.00 0.00 38.01 1.82
5276 6065 4.216257 TGGAAACAGAAAGCAACTATCAGC 59.784 41.667 0.00 0.00 35.01 4.26
5293 6082 1.632589 ATTCACAAGGCCCTGGAAAC 58.367 50.000 6.25 0.00 0.00 2.78
5315 6104 5.336150 TGAAACTGTTTTCAAATGCCAGA 57.664 34.783 7.28 0.00 46.59 3.86
5580 6369 8.662781 AAGCTTCGCTCTGATACAATAAAATA 57.337 30.769 0.00 0.00 38.25 1.40
5581 6370 7.559590 AAGCTTCGCTCTGATACAATAAAAT 57.440 32.000 0.00 0.00 38.25 1.82
5698 6487 4.431158 ACCCTACTAAGAAGGAAGGGAA 57.569 45.455 17.34 0.00 46.21 3.97
5766 6555 8.491045 TTGTATATGAGAGAGAGAGAGAGAGA 57.509 38.462 0.00 0.00 0.00 3.10
5807 6713 5.108187 ACTTCCACGGACTGTAGATACTA 57.892 43.478 0.00 0.00 0.00 1.82
5809 6715 4.715527 AACTTCCACGGACTGTAGATAC 57.284 45.455 0.00 0.00 0.00 2.24
5811 6717 3.446516 GGTAACTTCCACGGACTGTAGAT 59.553 47.826 0.00 0.00 0.00 1.98
5870 6776 3.505680 TGCTCAAACTAATTTGCCGACAT 59.494 39.130 0.00 0.00 44.22 3.06
5987 6893 1.638070 TGCCCCATTCATGAACACCTA 59.362 47.619 11.07 0.00 0.00 3.08
6090 6996 4.078639 AGAATTTAGCTTCTCCCATCGG 57.921 45.455 0.00 0.00 29.38 4.18
6120 7027 7.094549 CGGTTTCAAAAGGACATCTTATTACCA 60.095 37.037 0.00 0.00 34.78 3.25
6121 7028 7.120138 TCGGTTTCAAAAGGACATCTTATTACC 59.880 37.037 0.00 0.00 34.78 2.85
6227 7134 9.346725 GGATCAATTGTTCAATTCTAAAGTGTC 57.653 33.333 16.38 2.16 0.00 3.67
6364 7272 1.206132 TCGTGGATAAGAACACCGCAT 59.794 47.619 0.00 0.00 34.18 4.73
6371 7279 3.809832 CACATGGGATCGTGGATAAGAAC 59.190 47.826 0.00 0.00 34.31 3.01
6438 7347 0.037303 AGGTGTCATGGAGTTGGCTG 59.963 55.000 0.00 0.00 0.00 4.85
6456 7365 7.188834 TCAAAGTTGCATAAATAATCTGCGAG 58.811 34.615 0.00 0.00 38.75 5.03
6526 7435 9.878599 GAAGAAATGACGAATACTTGAAGAAAA 57.121 29.630 0.00 0.00 0.00 2.29
6529 7438 7.331934 CCAGAAGAAATGACGAATACTTGAAGA 59.668 37.037 0.00 0.00 0.00 2.87
6559 7468 0.977395 ACCCAACACTCAGCTACTCC 59.023 55.000 0.00 0.00 0.00 3.85
6648 7557 6.096282 TCAGAATTGTACACGACTGGATATCA 59.904 38.462 16.79 0.00 0.00 2.15
6649 7558 6.504398 TCAGAATTGTACACGACTGGATATC 58.496 40.000 16.79 0.00 0.00 1.63
6654 7563 5.440685 GTTTTCAGAATTGTACACGACTGG 58.559 41.667 16.79 0.00 0.00 4.00
6684 7593 5.303971 AGATAAGGATCAGCATTACAGTGC 58.696 41.667 0.00 0.00 45.38 4.40
6689 7598 6.256757 GCGGATAAGATAAGGATCAGCATTAC 59.743 42.308 0.00 0.00 39.60 1.89
6695 7604 4.156922 ACGAGCGGATAAGATAAGGATCAG 59.843 45.833 0.00 0.00 34.17 2.90
6714 7623 8.888579 ATTCCTGTTATCCAGTAAAATACGAG 57.111 34.615 0.00 0.00 39.74 4.18
6790 7699 5.053145 GCTTGAGCTACTGCATACTTGTAT 58.947 41.667 0.00 0.00 42.74 2.29
6944 7853 0.606401 GTAGCTTGGCCACAGCTTCA 60.606 55.000 32.96 20.84 39.79 3.02
6954 7863 4.408182 TCTATTCTTCCTGTAGCTTGGC 57.592 45.455 0.00 0.00 0.00 4.52
6990 7899 5.012239 ACAACCATAGCATTCACTTGACAT 58.988 37.500 0.00 0.00 0.00 3.06
7070 7979 2.840974 GCAGGAAGCAGCGTTAGAA 58.159 52.632 0.00 0.00 44.79 2.10
7106 8015 0.179163 GCGACCAAATACTTGCTGGC 60.179 55.000 0.00 0.00 33.19 4.85
7109 8018 2.200373 AAGGCGACCAAATACTTGCT 57.800 45.000 0.00 0.00 0.00 3.91
7155 8064 3.041940 AGCGAAAACACCGGCTCG 61.042 61.111 0.00 3.57 0.00 5.03
7157 8066 1.098712 TTTCAGCGAAAACACCGGCT 61.099 50.000 0.00 0.00 35.84 5.52
7218 8128 7.810282 ACATAGCACGCATTTTAACAAAACATA 59.190 29.630 0.00 0.00 32.37 2.29
7229 8139 4.700268 TGATCAACATAGCACGCATTTT 57.300 36.364 0.00 0.00 0.00 1.82
7233 8143 5.170748 CCTATATGATCAACATAGCACGCA 58.829 41.667 16.78 0.00 43.48 5.24
7237 8147 9.276590 CTGAAAACCTATATGATCAACATAGCA 57.723 33.333 16.78 10.77 43.48 3.49
7301 8213 3.498774 ATCATGACCATGGAAGGCTAC 57.501 47.619 21.47 1.27 39.24 3.58
7328 8240 8.454106 CGGTTCAAATGATACTTCTCAGATTTT 58.546 33.333 0.00 0.00 0.00 1.82
7334 8246 4.574892 TGCGGTTCAAATGATACTTCTCA 58.425 39.130 0.00 0.00 0.00 3.27
7387 8299 7.066307 AGAATCCAATAATAACCCAAATGGC 57.934 36.000 0.00 0.00 37.83 4.40


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

AutoCloner maintained by Alex Coulton.