Multiple sequence alignment - TraesCS3A01G366400

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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 TraesCS3A01G366400 chr3A 100.000 7844 0 0 1 7844 615708600 615700757 0.000000e+00 14486.0
1 TraesCS3A01G366400 chr3A 92.976 2292 104 29 4650 6935 615276707 615274467 0.000000e+00 3288.0
2 TraesCS3A01G366400 chr3A 87.698 2024 146 48 2637 4614 615278802 615276836 0.000000e+00 2263.0
3 TraesCS3A01G366400 chr3A 93.655 788 42 7 1964 2744 615279535 615278749 0.000000e+00 1171.0
4 TraesCS3A01G366400 chr3A 86.241 814 54 34 927 1710 615280445 615279660 0.000000e+00 830.0
5 TraesCS3A01G366400 chr3A 86.641 262 35 0 7502 7763 290448581 290448320 2.770000e-74 291.0
6 TraesCS3A01G366400 chr3A 80.755 265 41 3 7577 7841 708557439 708557693 1.730000e-46 198.0
7 TraesCS3A01G366400 chr3D 95.714 6066 213 27 1800 7844 473441833 473435794 0.000000e+00 9718.0
8 TraesCS3A01G366400 chr3D 89.550 2000 132 36 2794 4761 472949862 472947908 0.000000e+00 2464.0
9 TraesCS3A01G366400 chr3D 93.885 1390 69 8 4793 6177 472947905 472946527 0.000000e+00 2082.0
10 TraesCS3A01G366400 chr3D 90.577 1231 71 31 600 1799 473443267 473442051 0.000000e+00 1589.0
11 TraesCS3A01G366400 chr3D 92.822 808 48 8 1964 2764 472950661 472949857 0.000000e+00 1162.0
12 TraesCS3A01G366400 chr3D 84.273 1011 71 37 722 1723 472951666 472950735 0.000000e+00 905.0
13 TraesCS3A01G366400 chr3D 89.683 630 35 10 6279 6908 472946523 472945924 0.000000e+00 776.0
14 TraesCS3A01G366400 chr3D 93.000 100 5 1 3925 4024 570265025 570265122 2.280000e-30 145.0
15 TraesCS3A01G366400 chr3D 85.185 81 12 0 45 125 473443771 473443691 5.040000e-12 84.2
16 TraesCS3A01G366400 chr3B 95.868 5494 191 17 1800 7276 628402063 628396589 0.000000e+00 8855.0
17 TraesCS3A01G366400 chr3B 94.177 2284 89 19 3910 6177 628120032 628117777 0.000000e+00 3441.0
18 TraesCS3A01G366400 chr3B 88.582 1953 128 43 1951 3852 628121935 628120027 0.000000e+00 2283.0
19 TraesCS3A01G366400 chr3B 90.371 997 51 21 669 1636 628403411 628402431 0.000000e+00 1267.0
20 TraesCS3A01G366400 chr3B 88.602 658 44 7 6279 6935 628117773 628117146 0.000000e+00 771.0
21 TraesCS3A01G366400 chr3B 82.822 815 57 53 722 1502 628122696 628121931 0.000000e+00 652.0
22 TraesCS3A01G366400 chr3B 92.197 346 25 1 7501 7844 628396512 628396167 9.150000e-134 488.0
23 TraesCS3A01G366400 chr3B 95.480 177 7 1 1631 1806 628402388 628402212 1.670000e-71 281.0
24 TraesCS3A01G366400 chr3B 80.377 265 43 2 7577 7841 763650144 763649889 8.030000e-45 193.0
25 TraesCS3A01G366400 chr3B 85.119 168 17 3 28 194 628404848 628404688 1.750000e-36 165.0
26 TraesCS3A01G366400 chr3B 94.643 56 3 0 7316 7371 628396590 628396535 3.900000e-13 87.9
27 TraesCS3A01G366400 chr2B 85.970 335 45 2 7501 7834 296017461 296017794 2.690000e-94 357.0
28 TraesCS3A01G366400 chr2B 90.123 81 8 0 7603 7683 55195328 55195408 1.080000e-18 106.0
29 TraesCS3A01G366400 chr2B 97.917 48 1 0 2846 2893 282847248 282847201 5.040000e-12 84.2
30 TraesCS3A01G366400 chr5A 92.784 97 5 1 3931 4027 552861673 552861579 1.060000e-28 139.0


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 TraesCS3A01G366400 chr3A 615700757 615708600 7843 True 14486.000000 14486 100.000000 1 7844 1 chr3A.!!$R2 7843
1 TraesCS3A01G366400 chr3A 615274467 615280445 5978 True 1888.000000 3288 90.142500 927 6935 4 chr3A.!!$R3 6008
2 TraesCS3A01G366400 chr3D 473435794 473443771 7977 True 3797.066667 9718 90.492000 45 7844 3 chr3D.!!$R2 7799
3 TraesCS3A01G366400 chr3D 472945924 472951666 5742 True 1477.800000 2464 90.042600 722 6908 5 chr3D.!!$R1 6186
4 TraesCS3A01G366400 chr3B 628396167 628404848 8681 True 1857.316667 8855 92.279667 28 7844 6 chr3B.!!$R3 7816
5 TraesCS3A01G366400 chr3B 628117146 628122696 5550 True 1786.750000 3441 88.545750 722 6935 4 chr3B.!!$R2 6213

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
472 1097 0.193321 TGCTCCCTCTGCCCCATATA 59.807 55.000 0.00 0.00 0.00 0.86 F
675 1539 0.249447 CGGTCTGTTGTGCTCACTCA 60.249 55.000 1.47 1.03 0.00 3.41 F
877 1766 0.876342 GAATCGTTAGCCTCGCCCAG 60.876 60.000 0.00 0.00 0.00 4.45 F
1373 2287 1.757699 CCCAAGCAGACCTACTACCTC 59.242 57.143 0.00 0.00 0.00 3.85 F
1953 3150 1.344953 TTCATGGCACCGGGATAGCT 61.345 55.000 6.32 0.00 0.00 3.32 F
2175 3707 2.342650 GCGCATTGCCAAGGAAGGA 61.343 57.895 0.30 0.00 37.76 3.36 F
2410 3949 2.500098 GGACACCTGGACAAGTGCTATA 59.500 50.000 0.00 0.00 37.51 1.31 F
2411 3950 3.055385 GGACACCTGGACAAGTGCTATAA 60.055 47.826 0.00 0.00 37.51 0.98 F
4074 5762 3.087031 CACTCATCCAACTCTTGCCATT 58.913 45.455 0.00 0.00 0.00 3.16 F
4356 6045 2.277084 GGGTAACTGTCAAGCCGTATG 58.723 52.381 0.00 0.00 0.00 2.39 F
5373 7180 3.486383 ACTGGTGTTACAATTGACCCAG 58.514 45.455 20.90 20.90 38.79 4.45 F
6346 8167 2.032681 AAGCCAGACCCACGCTTC 59.967 61.111 0.00 0.00 38.44 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1373 2287 0.467384 CCTGCAGGTACTCCATGGAG 59.533 60.000 35.55 35.55 46.91 3.86 R
1773 2751 1.376037 GCACCTTCTACGCCTTGCT 60.376 57.895 0.00 0.00 0.00 3.91 R
1846 3041 2.189594 TGTCAATCTTGCAGACCCTG 57.810 50.000 1.06 0.00 34.12 4.45 R
3184 4837 0.462759 GGCTATCACACAGGGCAGAC 60.463 60.000 0.00 0.00 0.00 3.51 R
3185 4838 0.909133 TGGCTATCACACAGGGCAGA 60.909 55.000 0.00 0.00 0.00 4.26 R
4059 5747 1.704628 TCAGGAATGGCAAGAGTTGGA 59.295 47.619 0.00 0.00 0.00 3.53 R
4204 5893 0.608130 CGTCCTGGACCATGAGACAA 59.392 55.000 20.68 0.00 0.00 3.18 R
4244 5933 3.007398 TCTCAAGAGCTTCAGGAAGAACC 59.993 47.826 13.01 1.32 40.79 3.62 R
5384 7191 7.224949 TCGTGGATGCGTTTAATTTGTATATCA 59.775 33.333 0.00 0.00 0.00 2.15 R
6315 8136 3.126000 GTCTGGCTTGAACTGTTCATAGC 59.874 47.826 29.17 29.17 39.84 2.97 R
6802 8625 0.179012 TGCCACGCATCATCATCCAT 60.179 50.000 0.00 0.00 31.71 3.41 R
7702 9568 1.073763 GGTATCATGCCATACCTGCCA 59.926 52.381 13.80 0.00 43.63 4.92 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
20 21 3.990959 AAAGAGGCCCTTAGTCTTGAG 57.009 47.619 0.00 0.00 34.00 3.02
21 22 1.199615 AGAGGCCCTTAGTCTTGAGC 58.800 55.000 0.00 0.00 0.00 4.26
22 23 1.199615 GAGGCCCTTAGTCTTGAGCT 58.800 55.000 0.00 0.00 0.00 4.09
23 24 2.023888 AGAGGCCCTTAGTCTTGAGCTA 60.024 50.000 0.00 0.00 0.00 3.32
24 25 2.364002 GAGGCCCTTAGTCTTGAGCTAG 59.636 54.545 0.00 0.00 0.00 3.42
25 26 2.112190 GGCCCTTAGTCTTGAGCTAGT 58.888 52.381 0.00 0.00 0.00 2.57
26 27 2.101750 GGCCCTTAGTCTTGAGCTAGTC 59.898 54.545 0.00 0.00 0.00 2.59
50 51 3.791245 CATGGCAAGTCTAGAGTCCTTC 58.209 50.000 0.00 0.00 0.00 3.46
60 61 2.100605 AGAGTCCTTCCGAAACATGC 57.899 50.000 0.00 0.00 0.00 4.06
62 63 1.464997 GAGTCCTTCCGAAACATGCAC 59.535 52.381 0.00 0.00 0.00 4.57
85 86 6.422701 CACAAAAATGCATGTGTTCTTCATCT 59.577 34.615 0.00 0.00 41.51 2.90
92 93 3.319137 TGTGTTCTTCATCTCTTCGGG 57.681 47.619 0.00 0.00 0.00 5.14
131 132 6.218019 TCTTTGCAACATTGAGAAGAAATGG 58.782 36.000 0.00 0.00 38.98 3.16
154 155 5.994668 GGACCATCTGATCAAAAGGAGATAC 59.005 44.000 12.46 0.73 0.00 2.24
158 159 4.686972 TCTGATCAAAAGGAGATACGCTG 58.313 43.478 0.00 0.00 0.00 5.18
160 161 2.024176 TCAAAAGGAGATACGCTGCC 57.976 50.000 0.00 0.00 35.18 4.85
170 171 1.676678 ATACGCTGCCGAGTCCACAT 61.677 55.000 0.00 0.00 38.29 3.21
194 195 4.067896 TGAGAATTTTGCTCTCCAGTCAC 58.932 43.478 0.00 0.00 38.89 3.67
196 197 4.070716 AGAATTTTGCTCTCCAGTCACAG 58.929 43.478 0.00 0.00 0.00 3.66
214 364 8.773645 CAGTCACAGAATTTAGTTACAATGTCA 58.226 33.333 0.00 0.00 0.00 3.58
215 365 9.507329 AGTCACAGAATTTAGTTACAATGTCAT 57.493 29.630 0.00 0.00 0.00 3.06
224 374 4.832248 AGTTACAATGTCATGGTGATCGT 58.168 39.130 2.83 0.00 0.00 3.73
231 381 2.009774 GTCATGGTGATCGTTCCCTTG 58.990 52.381 0.00 9.02 0.00 3.61
244 394 3.917985 CGTTCCCTTGGCGAAAATTTAAG 59.082 43.478 0.00 0.00 0.00 1.85
247 402 3.761752 TCCCTTGGCGAAAATTTAAGAGG 59.238 43.478 0.00 0.00 0.00 3.69
275 430 2.673368 CGCTAGATTGAAGGTGGTGAAC 59.327 50.000 0.00 0.00 0.00 3.18
312 932 5.859205 TGTGCATATATAGCCTCGATGAT 57.141 39.130 0.00 0.00 0.00 2.45
313 933 5.836347 TGTGCATATATAGCCTCGATGATC 58.164 41.667 0.00 0.00 0.00 2.92
335 955 3.430895 CGTTTTCTTCTTAGCAAGGCGTA 59.569 43.478 0.00 0.00 0.00 4.42
343 963 3.702548 TCTTAGCAAGGCGTATGGACTTA 59.297 43.478 0.00 0.00 44.21 2.24
372 992 2.758736 AGCTAGATCGGCCATTGATC 57.241 50.000 2.24 7.32 42.04 2.92
378 998 1.876156 GATCGGCCATTGATCTTGGAC 59.124 52.381 16.61 13.51 39.30 4.02
385 1010 2.615447 CCATTGATCTTGGACGTCATGG 59.385 50.000 18.91 14.57 36.26 3.66
398 1023 3.010627 TCATGGTCCATGAGGCTCA 57.989 52.632 27.61 21.19 44.60 4.26
399 1024 1.288188 TCATGGTCCATGAGGCTCAA 58.712 50.000 27.61 6.75 44.60 3.02
400 1025 1.065199 TCATGGTCCATGAGGCTCAAC 60.065 52.381 27.61 15.05 44.60 3.18
403 1028 1.028868 GGTCCATGAGGCTCAACAGC 61.029 60.000 22.84 13.48 46.06 4.40
405 1030 1.208052 GTCCATGAGGCTCAACAGCTA 59.792 52.381 22.84 1.32 46.03 3.32
413 1038 1.528129 GCTCAACAGCTAGGCTTGTT 58.472 50.000 0.00 0.00 43.09 2.83
417 1042 3.817647 CTCAACAGCTAGGCTTGTTTCTT 59.182 43.478 0.38 0.00 36.40 2.52
431 1056 5.234972 GCTTGTTTCTTGGTTTTCATTCTGG 59.765 40.000 0.00 0.00 0.00 3.86
442 1067 9.541143 TTGGTTTTCATTCTGGTCTTATTTTTC 57.459 29.630 0.00 0.00 0.00 2.29
443 1068 8.923270 TGGTTTTCATTCTGGTCTTATTTTTCT 58.077 29.630 0.00 0.00 0.00 2.52
467 1092 0.615827 AAAAATGCTCCCTCTGCCCC 60.616 55.000 0.00 0.00 0.00 5.80
470 1095 0.698886 AATGCTCCCTCTGCCCCATA 60.699 55.000 0.00 0.00 0.00 2.74
472 1097 0.193321 TGCTCCCTCTGCCCCATATA 59.807 55.000 0.00 0.00 0.00 0.86
475 1100 3.115390 GCTCCCTCTGCCCCATATAATA 58.885 50.000 0.00 0.00 0.00 0.98
477 1102 4.907875 GCTCCCTCTGCCCCATATAATATA 59.092 45.833 0.00 0.00 0.00 0.86
479 1104 6.465035 GCTCCCTCTGCCCCATATAATATAAG 60.465 46.154 0.00 0.00 0.00 1.73
482 1107 7.293299 TCCCTCTGCCCCATATAATATAAGATG 59.707 40.741 0.00 0.00 0.00 2.90
483 1108 7.072961 CCCTCTGCCCCATATAATATAAGATGT 59.927 40.741 0.00 0.00 0.00 3.06
509 1134 3.674997 ACAATCGGTTGTAACAGCATCT 58.325 40.909 13.52 0.00 46.37 2.90
510 1135 4.072131 ACAATCGGTTGTAACAGCATCTT 58.928 39.130 13.52 0.00 46.37 2.40
512 1137 5.880332 ACAATCGGTTGTAACAGCATCTTAT 59.120 36.000 13.52 0.00 46.37 1.73
515 1140 8.559536 CAATCGGTTGTAACAGCATCTTATATT 58.440 33.333 0.00 0.00 0.00 1.28
517 1142 9.944376 ATCGGTTGTAACAGCATCTTATATTAT 57.056 29.630 0.00 0.00 0.00 1.28
549 1413 9.476202 GAAATGTTTTAATTTGGTAGTTGAGCT 57.524 29.630 0.00 0.00 29.89 4.09
550 1414 9.476202 AAATGTTTTAATTTGGTAGTTGAGCTC 57.524 29.630 6.82 6.82 0.00 4.09
573 1437 7.372451 TCGTATCTCGATTTTCATTTGGTTT 57.628 32.000 0.00 0.00 44.01 3.27
574 1438 7.812648 TCGTATCTCGATTTTCATTTGGTTTT 58.187 30.769 0.00 0.00 44.01 2.43
575 1439 8.293867 TCGTATCTCGATTTTCATTTGGTTTTT 58.706 29.630 0.00 0.00 44.01 1.94
640 1504 4.421058 GTTGAACCACCACAAAGAAACTC 58.579 43.478 0.00 0.00 0.00 3.01
647 1511 5.891551 ACCACCACAAAGAAACTCTACATTT 59.108 36.000 0.00 0.00 0.00 2.32
649 1513 6.183360 CCACCACAAAGAAACTCTACATTTGT 60.183 38.462 0.00 0.00 42.99 2.83
656 1520 9.612620 CAAAGAAACTCTACATTTGTGTATTCC 57.387 33.333 0.00 0.00 0.00 3.01
657 1521 7.596749 AGAAACTCTACATTTGTGTATTCCG 57.403 36.000 0.00 0.00 0.00 4.30
658 1522 6.594159 AGAAACTCTACATTTGTGTATTCCGG 59.406 38.462 0.00 0.00 0.00 5.14
660 1524 5.416947 ACTCTACATTTGTGTATTCCGGTC 58.583 41.667 0.00 0.00 0.00 4.79
661 1525 5.187186 ACTCTACATTTGTGTATTCCGGTCT 59.813 40.000 0.00 0.00 0.00 3.85
665 1529 4.215399 ACATTTGTGTATTCCGGTCTGTTG 59.785 41.667 0.00 0.00 0.00 3.33
671 1535 0.396435 ATTCCGGTCTGTTGTGCTCA 59.604 50.000 0.00 0.00 0.00 4.26
672 1536 0.531974 TTCCGGTCTGTTGTGCTCAC 60.532 55.000 0.00 0.00 0.00 3.51
674 1538 0.946221 CCGGTCTGTTGTGCTCACTC 60.946 60.000 0.00 0.00 0.00 3.51
675 1539 0.249447 CGGTCTGTTGTGCTCACTCA 60.249 55.000 1.47 1.03 0.00 3.41
677 1541 1.473257 GGTCTGTTGTGCTCACTCACA 60.473 52.381 1.47 4.04 44.39 3.58
706 1580 5.127682 CCCTATTGACCCTTTCATGGAAAAG 59.872 44.000 0.00 0.00 36.26 2.27
707 1581 5.951747 CCTATTGACCCTTTCATGGAAAAGA 59.048 40.000 8.15 0.00 38.30 2.52
709 1583 4.722526 TGACCCTTTCATGGAAAAGAGA 57.277 40.909 8.15 0.00 38.30 3.10
714 1588 5.184711 CCCTTTCATGGAAAAGAGAGAGAG 58.815 45.833 8.15 0.00 38.30 3.20
715 1589 5.046014 CCCTTTCATGGAAAAGAGAGAGAGA 60.046 44.000 8.15 0.00 38.30 3.10
716 1590 6.108015 CCTTTCATGGAAAAGAGAGAGAGAG 58.892 44.000 8.15 0.00 38.30 3.20
717 1591 6.070881 CCTTTCATGGAAAAGAGAGAGAGAGA 60.071 42.308 8.15 0.00 38.30 3.10
718 1592 6.528537 TTCATGGAAAAGAGAGAGAGAGAG 57.471 41.667 0.00 0.00 0.00 3.20
719 1593 4.402155 TCATGGAAAAGAGAGAGAGAGAGC 59.598 45.833 0.00 0.00 0.00 4.09
720 1594 3.772387 TGGAAAAGAGAGAGAGAGAGCA 58.228 45.455 0.00 0.00 0.00 4.26
743 1617 6.978080 GCAGAAAATAACCTCACAAAACAAGA 59.022 34.615 0.00 0.00 0.00 3.02
763 1637 6.207614 ACAAGAAGCCAAAGAAAGAACTATCC 59.792 38.462 0.00 0.00 0.00 2.59
807 1681 1.809869 GCGCCCTTCATTTTCTCCC 59.190 57.895 0.00 0.00 0.00 4.30
814 1689 3.761752 CCCTTCATTTTCTCCCGCTTTTA 59.238 43.478 0.00 0.00 0.00 1.52
815 1690 4.380550 CCCTTCATTTTCTCCCGCTTTTAC 60.381 45.833 0.00 0.00 0.00 2.01
834 1722 7.175119 GCTTTTACTCCTCTACCACTGAAAAAT 59.825 37.037 0.00 0.00 0.00 1.82
866 1755 3.973206 TGGAGCTTCCAAGAATCGTTA 57.027 42.857 2.78 0.00 45.00 3.18
868 1757 2.609916 GGAGCTTCCAAGAATCGTTAGC 59.390 50.000 0.00 0.00 36.28 3.09
877 1766 0.876342 GAATCGTTAGCCTCGCCCAG 60.876 60.000 0.00 0.00 0.00 4.45
924 1814 3.538841 GTGAGCCACGTGAACTCG 58.461 61.111 24.33 8.74 32.98 4.18
925 1815 2.022129 GTGAGCCACGTGAACTCGG 61.022 63.158 24.33 8.22 32.98 4.63
1005 1899 3.158648 TTATCGCCACCTCCCCCG 61.159 66.667 0.00 0.00 0.00 5.73
1373 2287 1.757699 CCCAAGCAGACCTACTACCTC 59.242 57.143 0.00 0.00 0.00 3.85
1773 2751 6.039605 TCACTGCATGTCTCAAAAAGAATTGA 59.960 34.615 0.00 0.00 35.21 2.57
1803 2843 5.647589 CGTAGAAGGTGCACTATACAAGAA 58.352 41.667 17.98 0.00 0.00 2.52
1846 3041 2.231215 ATAGCAACACGAGCAGATCC 57.769 50.000 0.00 0.00 0.00 3.36
1889 3085 3.402628 TTCTCCTCTGTTAAGCACCAC 57.597 47.619 0.00 0.00 0.00 4.16
1953 3150 1.344953 TTCATGGCACCGGGATAGCT 61.345 55.000 6.32 0.00 0.00 3.32
2175 3707 2.342650 GCGCATTGCCAAGGAAGGA 61.343 57.895 0.30 0.00 37.76 3.36
2410 3949 2.500098 GGACACCTGGACAAGTGCTATA 59.500 50.000 0.00 0.00 37.51 1.31
2411 3950 3.055385 GGACACCTGGACAAGTGCTATAA 60.055 47.826 0.00 0.00 37.51 0.98
2478 4017 6.924111 ACGTGATGCCTTCTAAATTCAAAAT 58.076 32.000 0.00 0.00 0.00 1.82
2555 4097 7.566879 AGATTTAGGATCTTCTGTACTCCATGT 59.433 37.037 0.00 0.00 0.00 3.21
2558 4100 5.983540 AGGATCTTCTGTACTCCATGTTTC 58.016 41.667 0.00 0.00 0.00 2.78
2567 4109 7.223584 TCTGTACTCCATGTTTCTTTGATCAA 58.776 34.615 3.38 3.38 0.00 2.57
2682 4245 3.121944 GCAGAGTTGTTGTACATCAGACG 59.878 47.826 6.71 0.00 0.00 4.18
2817 4439 7.068716 GCCTTTTTGTGTCCCTCTAATTGATAT 59.931 37.037 0.00 0.00 0.00 1.63
2818 4440 8.408601 CCTTTTTGTGTCCCTCTAATTGATATG 58.591 37.037 0.00 0.00 0.00 1.78
3182 4835 6.432107 TGTTTAAAGCAAGAACGTCCAATAC 58.568 36.000 0.00 0.00 0.00 1.89
3184 4837 4.749245 AAAGCAAGAACGTCCAATACAG 57.251 40.909 0.00 0.00 0.00 2.74
3185 4838 3.402628 AGCAAGAACGTCCAATACAGT 57.597 42.857 0.00 0.00 0.00 3.55
3334 4992 8.319057 ACTATAAGTGAGGTGTTAATCCATCA 57.681 34.615 3.19 0.00 0.00 3.07
3396 5068 7.046033 TGTCATCTGCTATCAATGCCTATATG 58.954 38.462 0.00 0.00 0.00 1.78
3400 5072 9.043079 CATCTGCTATCAATGCCTATATGTAAG 57.957 37.037 0.00 0.00 0.00 2.34
3425 5097 6.961554 GCCAGAAATAACTGTCGTATCTTTTG 59.038 38.462 0.00 0.00 36.30 2.44
3452 5124 7.573096 GCTCCAGTTTCGTCTTTCATGAATTAA 60.573 37.037 9.40 0.00 29.66 1.40
3508 5188 5.736951 AGATATGTGCTGTTCTCTATCCC 57.263 43.478 0.00 0.00 0.00 3.85
3590 5270 4.273480 GCGCATCACTTCAGGTAATTATGT 59.727 41.667 0.30 0.00 0.00 2.29
3696 5377 9.661187 GAAATGATGTTAGAGATACTTGCATTG 57.339 33.333 0.00 0.00 0.00 2.82
3697 5378 8.743085 AATGATGTTAGAGATACTTGCATTGT 57.257 30.769 0.00 0.00 0.00 2.71
3700 5381 9.098355 TGATGTTAGAGATACTTGCATTGTTAC 57.902 33.333 0.00 0.00 0.00 2.50
3701 5382 9.098355 GATGTTAGAGATACTTGCATTGTTACA 57.902 33.333 0.00 0.00 0.00 2.41
3786 5473 7.276438 GCATGATCAAGGTTCATTAAGAAAACC 59.724 37.037 0.00 7.88 42.27 3.27
3905 5592 9.760660 ATTTCGTCTTTTCTCAATATCTTTTCG 57.239 29.630 0.00 0.00 0.00 3.46
4059 5747 5.242171 TGCTGTTCAAATGAATGACACTCAT 59.758 36.000 0.00 0.00 39.09 2.90
4074 5762 3.087031 CACTCATCCAACTCTTGCCATT 58.913 45.455 0.00 0.00 0.00 3.16
4244 5933 2.350388 GGTTGCTTACACCAATCACACG 60.350 50.000 0.00 0.00 0.00 4.49
4356 6045 2.277084 GGGTAACTGTCAAGCCGTATG 58.723 52.381 0.00 0.00 0.00 2.39
4366 6055 4.021807 TGTCAAGCCGTATGTACTCTTTCA 60.022 41.667 0.00 0.00 0.00 2.69
4597 6286 9.158233 CTGCATCCTGTTATTTCATTTTTCATT 57.842 29.630 0.00 0.00 0.00 2.57
4631 6421 4.147653 CGTTACACGGTAGTTTTGTCTCTG 59.852 45.833 0.00 0.00 38.08 3.35
4703 6493 6.326970 AGGCATAGTGAATATCCTCCTACTT 58.673 40.000 0.00 0.00 0.00 2.24
4789 6585 6.524101 ACGTTGCTTGTAATCCCATTATTT 57.476 33.333 0.00 0.00 0.00 1.40
4791 6587 6.811170 ACGTTGCTTGTAATCCCATTATTTTG 59.189 34.615 0.00 0.00 0.00 2.44
4856 6660 5.347342 TGTAATTTATGGGCGCTTCAATTG 58.653 37.500 7.64 0.00 0.00 2.32
5373 7180 3.486383 ACTGGTGTTACAATTGACCCAG 58.514 45.455 20.90 20.90 38.79 4.45
5384 7191 5.086621 ACAATTGACCCAGATAGCCTTTTT 58.913 37.500 13.59 0.00 0.00 1.94
5765 7573 3.990469 ACTGTACAGCATTCACTTCTTCG 59.010 43.478 22.90 0.00 0.00 3.79
5775 7583 4.647424 TTCACTTCTTCGTTGGCAATTT 57.353 36.364 1.92 0.00 0.00 1.82
6071 7887 5.163205 TGTTGAAATCAGAGAAGAAGTGGGA 60.163 40.000 0.00 0.00 0.00 4.37
6164 7981 5.903010 TGGCTTGGTAAGATATCTTCCAGTA 59.097 40.000 21.17 12.56 35.85 2.74
6181 7998 6.216801 TCCAGTAGATTGCGTGTTAGTTAT 57.783 37.500 0.00 0.00 0.00 1.89
6183 8000 7.423199 TCCAGTAGATTGCGTGTTAGTTATAG 58.577 38.462 0.00 0.00 0.00 1.31
6194 8011 7.927092 TGCGTGTTAGTTATAGGCAATATTACA 59.073 33.333 0.00 0.00 32.98 2.41
6209 8026 7.556275 GGCAATATTACAATATTAGGCTAGCCA 59.444 37.037 34.70 16.70 39.84 4.75
6282 8100 7.649057 TCAGTATATATTCTCACCAAGTCACG 58.351 38.462 0.00 0.00 0.00 4.35
6315 8136 7.494625 TGGGCTATTAACTTATTCTTTGTCTCG 59.505 37.037 0.00 0.00 0.00 4.04
6346 8167 2.032681 AAGCCAGACCCACGCTTC 59.967 61.111 0.00 0.00 38.44 3.86
6472 8293 4.729868 ACTTCCTTGTTGGCTATGACTTT 58.270 39.130 0.00 0.00 35.26 2.66
6556 8378 3.803186 ATCCCTTCTATTGGGCTGATG 57.197 47.619 0.00 0.00 44.23 3.07
6668 8491 3.084786 GACAGGGACAAGAAGAAATGGG 58.915 50.000 0.00 0.00 0.00 4.00
6802 8625 1.819288 GGAGACGTGATCAAGAGGTGA 59.181 52.381 15.90 0.00 41.67 4.02
7233 9059 3.993081 GCCATCCAGAAAGACTCATATCG 59.007 47.826 0.00 0.00 0.00 2.92
7274 9137 2.234414 GGCAGGATTTGAAGAAATGGCA 59.766 45.455 0.00 0.00 31.58 4.92
7275 9138 3.306919 GGCAGGATTTGAAGAAATGGCAA 60.307 43.478 0.00 0.00 31.58 4.52
7276 9139 4.510571 GCAGGATTTGAAGAAATGGCAAT 58.489 39.130 0.00 0.00 31.58 3.56
7277 9140 4.939439 GCAGGATTTGAAGAAATGGCAATT 59.061 37.500 0.00 0.00 31.58 2.32
7278 9141 5.163794 GCAGGATTTGAAGAAATGGCAATTG 60.164 40.000 0.00 0.00 31.58 2.32
7279 9142 6.167685 CAGGATTTGAAGAAATGGCAATTGA 58.832 36.000 10.34 0.00 31.58 2.57
7280 9143 6.312918 CAGGATTTGAAGAAATGGCAATTGAG 59.687 38.462 10.34 0.00 31.58 3.02
7281 9144 5.064325 GGATTTGAAGAAATGGCAATTGAGC 59.936 40.000 10.34 0.00 31.58 4.26
7282 9145 4.603989 TTGAAGAAATGGCAATTGAGCA 57.396 36.364 10.34 0.00 35.83 4.26
7283 9146 4.811969 TGAAGAAATGGCAATTGAGCAT 57.188 36.364 10.34 0.00 35.83 3.79
7284 9147 5.155278 TGAAGAAATGGCAATTGAGCATT 57.845 34.783 10.34 0.00 35.83 3.56
7285 9148 4.932799 TGAAGAAATGGCAATTGAGCATTG 59.067 37.500 10.34 0.00 44.79 2.82
7297 9160 4.627611 TTGAGCATTGCTAGAATGAAGC 57.372 40.909 11.96 0.00 39.88 3.86
7298 9161 3.882444 TGAGCATTGCTAGAATGAAGCT 58.118 40.909 11.96 6.77 39.88 3.74
7299 9162 3.875727 TGAGCATTGCTAGAATGAAGCTC 59.124 43.478 11.96 13.74 45.40 4.09
7300 9163 3.212685 AGCATTGCTAGAATGAAGCTCC 58.787 45.455 10.00 0.00 40.73 4.70
7301 9164 3.117963 AGCATTGCTAGAATGAAGCTCCT 60.118 43.478 10.00 3.48 40.73 3.69
7302 9165 4.102210 AGCATTGCTAGAATGAAGCTCCTA 59.898 41.667 10.00 0.00 40.73 2.94
7303 9166 4.818546 GCATTGCTAGAATGAAGCTCCTAA 59.181 41.667 15.05 0.00 40.73 2.69
7304 9167 5.472820 GCATTGCTAGAATGAAGCTCCTAAT 59.527 40.000 15.05 0.00 40.73 1.73
7305 9168 6.652481 GCATTGCTAGAATGAAGCTCCTAATA 59.348 38.462 15.05 0.00 40.73 0.98
7306 9169 7.173907 GCATTGCTAGAATGAAGCTCCTAATAA 59.826 37.037 15.05 0.00 40.73 1.40
7307 9170 8.719648 CATTGCTAGAATGAAGCTCCTAATAAG 58.280 37.037 0.00 0.00 40.73 1.73
7308 9171 7.366847 TGCTAGAATGAAGCTCCTAATAAGT 57.633 36.000 0.00 0.00 40.73 2.24
7309 9172 8.478775 TGCTAGAATGAAGCTCCTAATAAGTA 57.521 34.615 0.00 0.00 40.73 2.24
7310 9173 8.924303 TGCTAGAATGAAGCTCCTAATAAGTAA 58.076 33.333 0.00 0.00 40.73 2.24
7311 9174 9.418045 GCTAGAATGAAGCTCCTAATAAGTAAG 57.582 37.037 0.00 0.00 37.01 2.34
7314 9177 8.763601 AGAATGAAGCTCCTAATAAGTAAGTGT 58.236 33.333 0.00 0.00 0.00 3.55
7512 9376 5.473066 AGTTTTTCAATACCAGCTGCAAT 57.527 34.783 8.66 0.06 0.00 3.56
7519 9383 2.874648 TACCAGCTGCAATGCCTCGG 62.875 60.000 8.66 0.36 0.00 4.63
7606 9470 1.338200 GGCGTTGGACTGTTGAGAGAT 60.338 52.381 0.00 0.00 0.00 2.75
7638 9502 4.275508 CTGCAGCACCACCCCTGT 62.276 66.667 0.00 0.00 0.00 4.00
7673 9539 0.803768 CAGGAACCAGAGACGATGCG 60.804 60.000 0.00 0.00 0.00 4.73
7702 9568 0.693049 AGTTTCATGCCCCTTCTCGT 59.307 50.000 0.00 0.00 0.00 4.18
7742 9608 3.852578 ACCCTTGTCTGGTTAAGGATGAT 59.147 43.478 4.66 0.00 44.98 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.026729 GCTCAAGACTAAGGGCCTCTTT 60.027 50.000 6.46 0.00 36.93 2.52
2 3 1.199615 GCTCAAGACTAAGGGCCTCT 58.800 55.000 6.46 0.00 0.00 3.69
3 4 1.199615 AGCTCAAGACTAAGGGCCTC 58.800 55.000 6.46 0.00 0.00 4.70
5 6 2.101750 GACTAGCTCAAGACTAAGGGCC 59.898 54.545 0.00 0.00 0.00 5.80
6 7 2.761208 TGACTAGCTCAAGACTAAGGGC 59.239 50.000 0.00 0.00 0.00 5.19
7 8 3.181480 GCTGACTAGCTCAAGACTAAGGG 60.181 52.174 0.00 0.00 46.57 3.95
8 9 4.040445 GCTGACTAGCTCAAGACTAAGG 57.960 50.000 0.00 0.00 46.57 2.69
21 22 2.687700 AGACTTGCCATGCTGACTAG 57.312 50.000 0.00 0.00 0.00 2.57
22 23 3.365472 TCTAGACTTGCCATGCTGACTA 58.635 45.455 0.00 0.00 0.00 2.59
23 24 2.168106 CTCTAGACTTGCCATGCTGACT 59.832 50.000 0.00 0.00 0.00 3.41
24 25 2.093764 ACTCTAGACTTGCCATGCTGAC 60.094 50.000 0.00 0.00 0.00 3.51
25 26 2.167281 GACTCTAGACTTGCCATGCTGA 59.833 50.000 0.00 0.00 0.00 4.26
26 27 2.548875 GACTCTAGACTTGCCATGCTG 58.451 52.381 0.00 0.00 0.00 4.41
31 32 2.180276 GGAAGGACTCTAGACTTGCCA 58.820 52.381 0.00 0.00 0.00 4.92
50 51 3.172000 GCATTTTTGTGCATGTTTCGG 57.828 42.857 0.00 0.00 44.43 4.30
60 61 5.970140 TGAAGAACACATGCATTTTTGTG 57.030 34.783 14.99 14.99 46.76 3.33
62 63 6.866770 AGAGATGAAGAACACATGCATTTTTG 59.133 34.615 0.00 0.00 0.00 2.44
85 86 2.882137 GGTTCACATGTTTTCCCGAAGA 59.118 45.455 0.00 0.00 0.00 2.87
92 93 4.681744 TGCAAAGAGGTTCACATGTTTTC 58.318 39.130 0.00 0.00 0.00 2.29
131 132 5.694006 CGTATCTCCTTTTGATCAGATGGTC 59.306 44.000 15.35 0.00 0.00 4.02
154 155 2.034879 AAATGTGGACTCGGCAGCG 61.035 57.895 0.00 0.00 0.00 5.18
158 159 1.808411 TTCTCAAATGTGGACTCGGC 58.192 50.000 0.00 0.00 0.00 5.54
160 161 4.618489 GCAAAATTCTCAAATGTGGACTCG 59.382 41.667 0.00 0.00 0.00 4.18
170 171 5.009010 GTGACTGGAGAGCAAAATTCTCAAA 59.991 40.000 4.82 0.00 42.26 2.69
194 195 8.729756 TCACCATGACATTGTAACTAAATTCTG 58.270 33.333 0.00 0.00 0.00 3.02
196 197 9.722056 GATCACCATGACATTGTAACTAAATTC 57.278 33.333 0.00 0.00 0.00 2.17
214 364 0.394352 GCCAAGGGAACGATCACCAT 60.394 55.000 0.00 0.00 0.00 3.55
215 365 1.002624 GCCAAGGGAACGATCACCA 60.003 57.895 0.00 0.00 0.00 4.17
224 374 4.219725 CCTCTTAAATTTTCGCCAAGGGAA 59.780 41.667 0.00 0.00 32.81 3.97
231 381 1.741145 TCCGCCTCTTAAATTTTCGCC 59.259 47.619 0.00 0.00 0.00 5.54
275 430 0.248743 GCACAATGTCGCCATCATGG 60.249 55.000 0.00 0.00 41.55 3.66
276 431 0.452585 TGCACAATGTCGCCATCATG 59.547 50.000 5.61 0.00 0.00 3.07
283 903 3.935203 AGGCTATATATGCACAATGTCGC 59.065 43.478 0.00 0.00 0.00 5.19
298 918 5.707242 AGAAAACGATCATCGAGGCTATA 57.293 39.130 15.60 0.00 43.74 1.31
299 919 4.592485 AGAAAACGATCATCGAGGCTAT 57.408 40.909 15.60 0.00 43.74 2.97
300 920 4.098044 AGAAGAAAACGATCATCGAGGCTA 59.902 41.667 15.60 0.00 43.74 3.93
301 921 2.969628 AGAAAACGATCATCGAGGCT 57.030 45.000 15.60 2.41 43.74 4.58
312 932 2.478894 CGCCTTGCTAAGAAGAAAACGA 59.521 45.455 0.00 0.00 0.00 3.85
313 933 2.223377 ACGCCTTGCTAAGAAGAAAACG 59.777 45.455 0.00 0.00 0.00 3.60
335 955 3.115390 AGCTACCCACACATAAGTCCAT 58.885 45.455 0.00 0.00 0.00 3.41
343 963 1.964223 CCGATCTAGCTACCCACACAT 59.036 52.381 0.00 0.00 0.00 3.21
378 998 0.531532 GAGCCTCATGGACCATGACG 60.532 60.000 29.67 25.62 44.60 4.35
385 1010 2.475666 GCTGTTGAGCCTCATGGAC 58.524 57.895 0.00 0.00 39.57 4.02
395 1020 3.406764 AGAAACAAGCCTAGCTGTTGAG 58.593 45.455 0.00 0.00 39.62 3.02
397 1022 3.304928 CCAAGAAACAAGCCTAGCTGTTG 60.305 47.826 0.00 0.00 39.62 3.33
398 1023 2.887152 CCAAGAAACAAGCCTAGCTGTT 59.113 45.455 0.00 0.00 39.62 3.16
399 1024 2.158608 ACCAAGAAACAAGCCTAGCTGT 60.159 45.455 0.00 0.00 39.62 4.40
400 1025 2.508526 ACCAAGAAACAAGCCTAGCTG 58.491 47.619 0.00 0.00 39.62 4.24
403 1028 5.514274 TGAAAACCAAGAAACAAGCCTAG 57.486 39.130 0.00 0.00 0.00 3.02
405 1030 5.129320 AGAATGAAAACCAAGAAACAAGCCT 59.871 36.000 0.00 0.00 0.00 4.58
413 1038 8.477419 AATAAGACCAGAATGAAAACCAAGAA 57.523 30.769 0.00 0.00 39.69 2.52
417 1042 8.923270 AGAAAAATAAGACCAGAATGAAAACCA 58.077 29.630 0.00 0.00 39.69 3.67
449 1074 1.000866 GGGGCAGAGGGAGCATTTT 59.999 57.895 0.00 0.00 0.00 1.82
454 1079 1.362224 TTATATGGGGCAGAGGGAGC 58.638 55.000 0.00 0.00 0.00 4.70
477 1102 9.221933 TGTTACAACCGATTGTTATAACATCTT 57.778 29.630 18.69 7.42 46.54 2.40
489 1114 4.685169 AAGATGCTGTTACAACCGATTG 57.315 40.909 0.00 0.00 41.98 2.67
490 1115 8.677148 AATATAAGATGCTGTTACAACCGATT 57.323 30.769 0.00 0.00 0.00 3.34
491 1116 9.944376 ATAATATAAGATGCTGTTACAACCGAT 57.056 29.630 0.00 0.00 0.00 4.18
497 1122 9.626045 CGACTCATAATATAAGATGCTGTTACA 57.374 33.333 0.00 0.00 0.00 2.41
498 1123 9.841880 TCGACTCATAATATAAGATGCTGTTAC 57.158 33.333 0.00 0.00 0.00 2.50
500 1125 9.764363 TTTCGACTCATAATATAAGATGCTGTT 57.236 29.630 0.00 0.00 0.00 3.16
517 1142 8.842280 ACTACCAAATTAAAACATTTCGACTCA 58.158 29.630 0.00 0.00 0.00 3.41
522 1386 8.424731 GCTCAACTACCAAATTAAAACATTTCG 58.575 33.333 0.00 0.00 0.00 3.46
533 1397 5.978814 AGATACGAGCTCAACTACCAAATT 58.021 37.500 15.40 0.00 0.00 1.82
550 1414 8.447787 AAAAACCAAATGAAAATCGAGATACG 57.552 30.769 0.00 0.00 44.09 3.06
607 1471 4.330074 GTGGTGGTTCAACGATCTCATTAG 59.670 45.833 0.00 0.00 0.00 1.73
618 1482 4.157840 AGAGTTTCTTTGTGGTGGTTCAAC 59.842 41.667 0.00 0.00 0.00 3.18
619 1483 4.340617 AGAGTTTCTTTGTGGTGGTTCAA 58.659 39.130 0.00 0.00 0.00 2.69
640 1504 5.175859 ACAGACCGGAATACACAAATGTAG 58.824 41.667 9.46 0.00 44.51 2.74
647 1511 2.761559 CACAACAGACCGGAATACACA 58.238 47.619 9.46 0.00 0.00 3.72
649 1513 1.346395 AGCACAACAGACCGGAATACA 59.654 47.619 9.46 0.00 0.00 2.29
654 1518 1.069090 GTGAGCACAACAGACCGGA 59.931 57.895 9.46 0.00 0.00 5.14
655 1519 0.946221 GAGTGAGCACAACAGACCGG 60.946 60.000 0.00 0.00 0.00 5.28
656 1520 0.249447 TGAGTGAGCACAACAGACCG 60.249 55.000 3.19 0.00 0.00 4.79
657 1521 1.221414 GTGAGTGAGCACAACAGACC 58.779 55.000 3.19 0.00 38.63 3.85
658 1522 1.939974 TGTGAGTGAGCACAACAGAC 58.060 50.000 3.19 0.00 45.08 3.51
665 1529 2.024414 AGGGTTTTTGTGAGTGAGCAC 58.976 47.619 0.00 0.00 39.22 4.40
671 1535 4.141018 AGGGTCAATAGGGTTTTTGTGAGT 60.141 41.667 0.00 0.00 0.00 3.41
672 1536 4.407365 AGGGTCAATAGGGTTTTTGTGAG 58.593 43.478 0.00 0.00 0.00 3.51
674 1538 5.069781 TGAAAGGGTCAATAGGGTTTTTGTG 59.930 40.000 0.00 0.00 31.51 3.33
675 1539 5.212745 TGAAAGGGTCAATAGGGTTTTTGT 58.787 37.500 0.00 0.00 31.51 2.83
677 1541 5.248248 CCATGAAAGGGTCAATAGGGTTTTT 59.752 40.000 0.00 0.00 40.50 1.94
678 1542 4.777366 CCATGAAAGGGTCAATAGGGTTTT 59.223 41.667 0.00 0.00 40.50 2.43
679 1543 4.045334 TCCATGAAAGGGTCAATAGGGTTT 59.955 41.667 0.00 0.00 40.01 3.27
680 1544 3.596046 TCCATGAAAGGGTCAATAGGGTT 59.404 43.478 0.00 0.00 40.01 4.11
681 1545 3.197983 TCCATGAAAGGGTCAATAGGGT 58.802 45.455 0.00 0.00 40.01 4.34
682 1546 3.951563 TCCATGAAAGGGTCAATAGGG 57.048 47.619 0.00 0.00 40.01 3.53
706 1580 6.096846 AGGTTATTTTCTGCTCTCTCTCTCTC 59.903 42.308 0.00 0.00 0.00 3.20
707 1581 5.957774 AGGTTATTTTCTGCTCTCTCTCTCT 59.042 40.000 0.00 0.00 0.00 3.10
709 1583 5.719085 TGAGGTTATTTTCTGCTCTCTCTCT 59.281 40.000 0.00 0.00 0.00 3.10
714 1588 6.560253 TTTGTGAGGTTATTTTCTGCTCTC 57.440 37.500 0.00 0.00 0.00 3.20
715 1589 6.321181 TGTTTTGTGAGGTTATTTTCTGCTCT 59.679 34.615 0.00 0.00 0.00 4.09
716 1590 6.503524 TGTTTTGTGAGGTTATTTTCTGCTC 58.496 36.000 0.00 0.00 0.00 4.26
717 1591 6.463995 TGTTTTGTGAGGTTATTTTCTGCT 57.536 33.333 0.00 0.00 0.00 4.24
718 1592 6.978080 TCTTGTTTTGTGAGGTTATTTTCTGC 59.022 34.615 0.00 0.00 0.00 4.26
719 1593 8.925161 TTCTTGTTTTGTGAGGTTATTTTCTG 57.075 30.769 0.00 0.00 0.00 3.02
720 1594 7.706607 GCTTCTTGTTTTGTGAGGTTATTTTCT 59.293 33.333 0.00 0.00 0.00 2.52
743 1617 5.478332 CCTTGGATAGTTCTTTCTTTGGCTT 59.522 40.000 0.00 0.00 0.00 4.35
763 1637 0.178964 TGTTTTCTGGGCTCCCCTTG 60.179 55.000 1.89 0.00 45.70 3.61
807 1681 3.192844 TCAGTGGTAGAGGAGTAAAAGCG 59.807 47.826 0.00 0.00 0.00 4.68
814 1689 8.990163 TTTTTATTTTTCAGTGGTAGAGGAGT 57.010 30.769 0.00 0.00 0.00 3.85
847 1735 2.609916 GCTAACGATTCTTGGAAGCTCC 59.390 50.000 0.00 0.00 36.96 4.70
862 1751 1.359459 GAAACTGGGCGAGGCTAACG 61.359 60.000 0.51 0.00 0.00 3.18
866 1755 2.665603 GAGAAACTGGGCGAGGCT 59.334 61.111 0.51 0.00 0.00 4.58
868 1757 1.961180 ATCCGAGAAACTGGGCGAGG 61.961 60.000 0.51 0.00 29.20 4.63
907 1797 2.022129 CCGAGTTCACGTGGCTCAC 61.022 63.158 27.60 16.37 0.00 3.51
908 1798 1.174078 TACCGAGTTCACGTGGCTCA 61.174 55.000 27.60 14.41 0.00 4.26
909 1799 0.731855 GTACCGAGTTCACGTGGCTC 60.732 60.000 22.44 22.44 0.00 4.70
910 1800 1.288127 GTACCGAGTTCACGTGGCT 59.712 57.895 17.00 14.20 0.00 4.75
911 1801 0.598158 TTGTACCGAGTTCACGTGGC 60.598 55.000 17.00 9.29 0.00 5.01
914 1804 2.101249 TCCTTTTGTACCGAGTTCACGT 59.899 45.455 0.00 0.00 0.00 4.49
916 1806 2.479275 GCTCCTTTTGTACCGAGTTCAC 59.521 50.000 0.00 0.00 0.00 3.18
917 1807 2.549349 GGCTCCTTTTGTACCGAGTTCA 60.549 50.000 0.00 0.00 0.00 3.18
918 1808 2.074576 GGCTCCTTTTGTACCGAGTTC 58.925 52.381 0.00 0.00 0.00 3.01
919 1809 1.271217 GGGCTCCTTTTGTACCGAGTT 60.271 52.381 0.00 0.00 0.00 3.01
920 1810 0.323957 GGGCTCCTTTTGTACCGAGT 59.676 55.000 0.00 0.00 0.00 4.18
921 1811 0.392595 GGGGCTCCTTTTGTACCGAG 60.393 60.000 0.00 0.00 0.00 4.63
922 1812 1.681076 GGGGCTCCTTTTGTACCGA 59.319 57.895 0.00 0.00 0.00 4.69
924 1814 4.757773 GGGGGCTCCTTTTGTACC 57.242 61.111 0.52 0.00 0.00 3.34
1373 2287 0.467384 CCTGCAGGTACTCCATGGAG 59.533 60.000 35.55 35.55 46.91 3.86
1740 2717 1.478105 AGACATGCAGTGATCTACGCA 59.522 47.619 0.00 6.07 40.88 5.24
1773 2751 1.376037 GCACCTTCTACGCCTTGCT 60.376 57.895 0.00 0.00 0.00 3.91
1846 3041 2.189594 TGTCAATCTTGCAGACCCTG 57.810 50.000 1.06 0.00 34.12 4.45
1953 3150 9.897744 CAGATGTTTCAGTCAAAAGCTTTATTA 57.102 29.630 13.10 0.00 0.00 0.98
2172 3704 3.685139 TCAGCGATTTCTTCTTGTCCT 57.315 42.857 0.00 0.00 0.00 3.85
2175 3707 5.106396 CCAATCTTCAGCGATTTCTTCTTGT 60.106 40.000 0.00 0.00 31.52 3.16
2252 3789 6.142818 ACAGCATAGCTATTATCGAGATCC 57.857 41.667 2.64 0.00 36.40 3.36
2478 4017 7.986889 TGCAGTTAAAGAAGCATCATACTATCA 59.013 33.333 0.00 0.00 31.05 2.15
2533 4072 7.400339 AGAAACATGGAGTACAGAAGATCCTAA 59.600 37.037 0.00 0.00 32.79 2.69
2713 4334 8.053355 TCCAGTCTATGTACAAGAACTCTGATA 58.947 37.037 0.00 0.00 0.00 2.15
2790 4412 3.586470 TTAGAGGGACACAAAAAGGCA 57.414 42.857 0.00 0.00 0.00 4.75
2817 4439 8.028354 CCTATCACATGATAAAGCAAACAAACA 58.972 33.333 0.00 0.00 36.66 2.83
2818 4440 7.009540 GCCTATCACATGATAAAGCAAACAAAC 59.990 37.037 0.00 0.00 36.66 2.93
3038 4660 3.495001 GTGACTCAGTTTAGGACTTGCAC 59.505 47.826 0.00 0.00 36.10 4.57
3157 4810 4.545823 TGGACGTTCTTGCTTTAAACAG 57.454 40.909 0.00 0.00 0.00 3.16
3171 4824 1.338769 GGGCAGACTGTATTGGACGTT 60.339 52.381 3.99 0.00 0.00 3.99
3182 4835 1.741732 GCTATCACACAGGGCAGACTG 60.742 57.143 0.00 0.00 44.03 3.51
3184 4837 0.462759 GGCTATCACACAGGGCAGAC 60.463 60.000 0.00 0.00 0.00 3.51
3185 4838 0.909133 TGGCTATCACACAGGGCAGA 60.909 55.000 0.00 0.00 0.00 4.26
3396 5068 6.979238 AGATACGACAGTTATTTCTGGCTTAC 59.021 38.462 0.00 0.00 40.96 2.34
3400 5072 6.663944 AAAGATACGACAGTTATTTCTGGC 57.336 37.500 0.00 0.00 39.84 4.85
3425 5097 1.878953 TGAAAGACGAAACTGGAGCC 58.121 50.000 0.00 0.00 0.00 4.70
3508 5188 2.544685 CCTTCTTCTGTAGCATCACCG 58.455 52.381 0.00 0.00 0.00 4.94
3590 5270 9.747898 AACCATCATACCAAATGAAACTAACTA 57.252 29.630 0.00 0.00 0.00 2.24
3607 5287 7.827236 CACCTTCCTTTTACAGTAACCATCATA 59.173 37.037 0.00 0.00 0.00 2.15
3701 5382 4.554723 GCGTGCAACAATACAAGAAGACTT 60.555 41.667 0.00 0.00 35.74 3.01
4059 5747 1.704628 TCAGGAATGGCAAGAGTTGGA 59.295 47.619 0.00 0.00 0.00 3.53
4074 5762 2.191400 AGCAACCTCATTAGCTCAGGA 58.809 47.619 7.71 0.00 30.05 3.86
4204 5893 0.608130 CGTCCTGGACCATGAGACAA 59.392 55.000 20.68 0.00 0.00 3.18
4244 5933 3.007398 TCTCAAGAGCTTCAGGAAGAACC 59.993 47.826 13.01 1.32 40.79 3.62
4366 6055 4.079980 TGTGCCATAACTGTTGTGTACT 57.920 40.909 14.81 0.00 0.00 2.73
4631 6421 6.290294 TGTAAAATGGTCCAGTAGGAGTAC 57.710 41.667 0.00 0.00 46.92 2.73
4789 6585 5.964958 AGTTAGCATAAAGAAGCAAGCAA 57.035 34.783 0.00 0.00 0.00 3.91
4791 6587 4.560427 GCAAGTTAGCATAAAGAAGCAAGC 59.440 41.667 0.00 0.00 0.00 4.01
4856 6660 1.899142 AGAACAGAGAGCTCCAGAACC 59.101 52.381 10.93 0.00 0.00 3.62
5384 7191 7.224949 TCGTGGATGCGTTTAATTTGTATATCA 59.775 33.333 0.00 0.00 0.00 2.15
6164 7981 5.018539 TGCCTATAACTAACACGCAATCT 57.981 39.130 0.00 0.00 0.00 2.40
6181 7998 9.832445 GCTAGCCTAATATTGTAATATTGCCTA 57.168 33.333 16.32 12.61 40.70 3.93
6183 8000 7.556275 TGGCTAGCCTAATATTGTAATATTGCC 59.444 37.037 33.07 18.07 40.70 4.52
6194 8011 4.103153 TGCAAGTCTGGCTAGCCTAATATT 59.897 41.667 33.07 18.30 36.94 1.28
6282 8100 9.732130 AAGAATAAGTTAATAGCCCATCTGATC 57.268 33.333 0.00 0.00 0.00 2.92
6315 8136 3.126000 GTCTGGCTTGAACTGTTCATAGC 59.874 47.826 29.17 29.17 39.84 2.97
6346 8167 3.436704 TGATAAACTGCTTGGCTTCTTCG 59.563 43.478 0.00 0.00 0.00 3.79
6472 8293 3.011818 CTGTGCATCAATGTAGCTTGGA 58.988 45.455 0.00 0.00 0.00 3.53
6602 8424 6.048073 TCAGCATTACGATATTCAGCAAAC 57.952 37.500 0.00 0.00 0.00 2.93
6802 8625 0.179012 TGCCACGCATCATCATCCAT 60.179 50.000 0.00 0.00 31.71 3.41
7233 9059 4.818546 TGCCTAAGAGATTTCAGCTTATGC 59.181 41.667 0.00 0.00 36.74 3.14
7274 9137 5.360144 AGCTTCATTCTAGCAATGCTCAATT 59.640 36.000 12.53 0.00 41.11 2.32
7275 9138 4.888239 AGCTTCATTCTAGCAATGCTCAAT 59.112 37.500 12.53 8.79 41.11 2.57
7276 9139 4.267536 AGCTTCATTCTAGCAATGCTCAA 58.732 39.130 12.53 6.50 41.11 3.02
7277 9140 3.875727 GAGCTTCATTCTAGCAATGCTCA 59.124 43.478 12.53 0.00 43.33 4.26
7278 9141 3.250521 GGAGCTTCATTCTAGCAATGCTC 59.749 47.826 12.53 0.00 43.18 4.26
7279 9142 3.117963 AGGAGCTTCATTCTAGCAATGCT 60.118 43.478 13.92 13.92 41.11 3.79
7280 9143 3.212685 AGGAGCTTCATTCTAGCAATGC 58.787 45.455 0.00 0.00 41.11 3.56
7281 9144 8.613060 TTATTAGGAGCTTCATTCTAGCAATG 57.387 34.615 0.00 7.99 41.11 2.82
7282 9145 8.435982 ACTTATTAGGAGCTTCATTCTAGCAAT 58.564 33.333 0.00 0.00 41.11 3.56
7283 9146 7.796054 ACTTATTAGGAGCTTCATTCTAGCAA 58.204 34.615 0.00 0.00 41.11 3.91
7284 9147 7.366847 ACTTATTAGGAGCTTCATTCTAGCA 57.633 36.000 0.00 0.00 41.11 3.49
7285 9148 9.418045 CTTACTTATTAGGAGCTTCATTCTAGC 57.582 37.037 0.00 0.00 38.93 3.42
7288 9151 8.763601 ACACTTACTTATTAGGAGCTTCATTCT 58.236 33.333 0.00 0.00 0.00 2.40
7289 9152 8.950208 ACACTTACTTATTAGGAGCTTCATTC 57.050 34.615 0.00 0.00 0.00 2.67
7291 9154 9.819267 GTTACACTTACTTATTAGGAGCTTCAT 57.181 33.333 0.00 0.00 0.00 2.57
7292 9155 8.809066 TGTTACACTTACTTATTAGGAGCTTCA 58.191 33.333 0.00 0.00 0.00 3.02
7293 9156 9.649167 TTGTTACACTTACTTATTAGGAGCTTC 57.351 33.333 0.00 0.00 0.00 3.86
7294 9157 9.654663 CTTGTTACACTTACTTATTAGGAGCTT 57.345 33.333 0.00 0.00 0.00 3.74
7295 9158 8.258708 CCTTGTTACACTTACTTATTAGGAGCT 58.741 37.037 0.00 0.00 0.00 4.09
7296 9159 8.039538 ACCTTGTTACACTTACTTATTAGGAGC 58.960 37.037 0.00 0.00 0.00 4.70
7297 9160 9.583765 GACCTTGTTACACTTACTTATTAGGAG 57.416 37.037 0.00 0.00 0.00 3.69
7298 9161 9.092338 TGACCTTGTTACACTTACTTATTAGGA 57.908 33.333 0.00 0.00 0.00 2.94
7299 9162 9.886132 ATGACCTTGTTACACTTACTTATTAGG 57.114 33.333 0.00 0.00 0.00 2.69
7302 9165 9.569122 ACAATGACCTTGTTACACTTACTTATT 57.431 29.630 0.00 0.00 45.98 1.40
7334 9197 6.051074 GGCCTCAATTCCTCCAAATTATTTG 58.949 40.000 10.46 10.46 40.32 2.32
7439 9303 3.596066 AATGTCGAGGCGCTGCAGT 62.596 57.895 16.64 0.00 0.00 4.40
7475 9339 3.971245 AAAACTTCACTTTTGGTGGCA 57.029 38.095 0.00 0.00 45.38 4.92
7486 9350 4.681483 GCAGCTGGTATTGAAAAACTTCAC 59.319 41.667 17.12 0.00 0.00 3.18
7498 9362 1.396653 GAGGCATTGCAGCTGGTATT 58.603 50.000 17.12 0.00 34.17 1.89
7519 9383 2.167075 CCCAGGTCTTCCAAATCAATGC 59.833 50.000 0.00 0.00 35.89 3.56
7527 9391 4.344865 GGCGCCCAGGTCTTCCAA 62.345 66.667 18.11 0.00 35.89 3.53
7588 9452 2.158449 GCAATCTCTCAACAGTCCAACG 59.842 50.000 0.00 0.00 0.00 4.10
7638 9502 2.203084 TGGTCGCAAAGGACGCAA 60.203 55.556 0.00 0.00 37.82 4.85
7673 9539 2.289565 GGCATGAAACTAGTAGGTGGC 58.710 52.381 0.00 2.13 0.00 5.01
7702 9568 1.073763 GGTATCATGCCATACCTGCCA 59.926 52.381 13.80 0.00 43.63 4.92
7716 9582 4.431378 TCCTTAACCAGACAAGGGTATCA 58.569 43.478 0.79 0.00 41.47 2.15
7742 9608 1.369692 CGGTTAGGTGGTCTGCACA 59.630 57.895 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.