Multiple sequence alignment - TraesCS7D01G112800

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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 TraesCS7D01G112800 chr7D 100.000 4365 0 0 1 4365 69040594 69044958 0.000000e+00 8061.0
1 TraesCS7D01G112800 chr7D 84.349 1214 134 28 808 2018 66348491 66347331 0.000000e+00 1138.0
2 TraesCS7D01G112800 chr7D 92.761 746 32 8 930 1662 65940372 65939636 0.000000e+00 1059.0
3 TraesCS7D01G112800 chr7D 88.802 768 62 8 921 1666 66105615 66104850 0.000000e+00 920.0
4 TraesCS7D01G112800 chr7D 96.552 551 12 3 3405 3950 65937279 65936731 0.000000e+00 905.0
5 TraesCS7D01G112800 chr7D 95.992 499 17 3 2911 3406 65937817 65937319 0.000000e+00 808.0
6 TraesCS7D01G112800 chr7D 87.367 657 31 21 1692 2322 65939561 65938931 0.000000e+00 706.0
7 TraesCS7D01G112800 chr7D 94.524 420 19 3 3948 4363 16184359 16184778 0.000000e+00 645.0
8 TraesCS7D01G112800 chr7D 84.028 576 75 13 2843 3407 85346826 85347395 4.970000e-149 538.0
9 TraesCS7D01G112800 chr7D 86.768 461 53 5 2955 3407 83600651 83600191 1.400000e-139 507.0
10 TraesCS7D01G112800 chr7D 79.971 699 99 23 948 1624 548812956 548812277 1.100000e-130 477.0
11 TraesCS7D01G112800 chr7D 89.024 82 6 3 757 838 66348511 66348433 9.990000e-17 99.0
12 TraesCS7D01G112800 chr7D 94.643 56 3 0 2194 2249 66346658 66346603 2.160000e-13 87.9
13 TraesCS7D01G112800 chr7B 90.519 2215 112 42 169 2334 10880154 10882319 0.000000e+00 2837.0
14 TraesCS7D01G112800 chr7B 89.389 999 46 25 1370 2334 10893589 10894561 0.000000e+00 1203.0
15 TraesCS7D01G112800 chr7B 92.308 624 20 14 754 1377 10891800 10892395 0.000000e+00 861.0
16 TraesCS7D01G112800 chr7B 96.450 507 16 2 2902 3406 10895224 10895730 0.000000e+00 835.0
17 TraesCS7D01G112800 chr7B 93.628 565 17 4 3405 3950 10883507 10884071 0.000000e+00 826.0
18 TraesCS7D01G112800 chr7B 87.793 598 20 11 3405 3950 10895812 10896408 0.000000e+00 651.0
19 TraesCS7D01G112800 chr7B 87.202 461 52 4 2944 3403 10069544 10069998 6.470000e-143 518.0
20 TraesCS7D01G112800 chr7B 94.074 135 7 1 855 989 10819944 10820077 2.060000e-48 204.0
21 TraesCS7D01G112800 chr7B 83.217 143 15 4 2065 2206 10069240 10069374 5.930000e-24 122.0
22 TraesCS7D01G112800 chrUn 90.285 1616 67 34 754 2334 305654129 305655689 0.000000e+00 2032.0
23 TraesCS7D01G112800 chrUn 90.770 1311 59 27 1062 2337 308151910 308150627 0.000000e+00 1694.0
24 TraesCS7D01G112800 chrUn 90.770 1311 59 27 1062 2337 308156018 308154735 0.000000e+00 1694.0
25 TraesCS7D01G112800 chrUn 93.628 565 17 4 3405 3950 308149442 308148878 0.000000e+00 826.0
26 TraesCS7D01G112800 chrUn 93.628 565 17 4 3405 3950 308153550 308152986 0.000000e+00 826.0
27 TraesCS7D01G112800 chrUn 96.748 123 4 0 3405 3527 305656877 305656999 5.720000e-49 206.0
28 TraesCS7D01G112800 chr7A 95.343 1224 37 2 2331 3534 74686203 74687426 0.000000e+00 1927.0
29 TraesCS7D01G112800 chr7A 97.086 755 20 2 2331 3083 714924342 714925096 0.000000e+00 1271.0
30 TraesCS7D01G112800 chr7A 84.351 1278 127 30 757 2018 70767559 70766339 0.000000e+00 1184.0
31 TraesCS7D01G112800 chr7A 92.911 663 13 7 754 1411 74684428 74685061 0.000000e+00 933.0
32 TraesCS7D01G112800 chr7A 90.145 690 48 10 855 1543 70737293 70736623 0.000000e+00 880.0
33 TraesCS7D01G112800 chr7A 93.229 576 25 8 2845 3407 70734835 70734261 0.000000e+00 835.0
34 TraesCS7D01G112800 chr7A 88.244 672 26 22 1685 2329 74685249 74685894 0.000000e+00 754.0
35 TraesCS7D01G112800 chr7A 89.076 595 37 10 1685 2251 70735576 70734982 0.000000e+00 713.0
36 TraesCS7D01G112800 chr7A 88.966 580 47 6 847 1417 70754457 70753886 0.000000e+00 701.0
37 TraesCS7D01G112800 chr7A 92.654 422 24 4 3948 4363 19848916 19848496 6.250000e-168 601.0
38 TraesCS7D01G112800 chr7A 90.196 459 44 1 2945 3403 74594170 74594627 8.080000e-167 597.0
39 TraesCS7D01G112800 chr7A 85.739 568 60 13 2849 3407 85197426 85196871 8.140000e-162 580.0
40 TraesCS7D01G112800 chr7A 92.935 368 12 7 3405 3758 70734222 70733855 1.390000e-144 523.0
41 TraesCS7D01G112800 chr7A 79.349 707 103 25 948 1616 634349476 634348775 1.430000e-124 457.0
42 TraesCS7D01G112800 chr7A 90.726 248 5 3 3530 3759 74687450 74687697 9.110000e-82 315.0
43 TraesCS7D01G112800 chr7A 77.798 545 74 21 1696 2205 74593202 74593734 4.270000e-75 292.0
44 TraesCS7D01G112800 chr7A 92.929 198 7 3 3759 3950 74697130 74697326 9.240000e-72 281.0
45 TraesCS7D01G112800 chr7A 94.245 139 3 1 3817 3950 70733835 70733697 1.590000e-49 207.0
46 TraesCS7D01G112800 chr7A 91.195 159 2 4 1542 1691 70735763 70735608 5.720000e-49 206.0
47 TraesCS7D01G112800 chr7A 75.839 447 84 18 1083 1511 77731837 77732277 5.720000e-49 206.0
48 TraesCS7D01G112800 chr7A 91.045 134 0 4 1567 1691 74685084 74685214 2.090000e-38 171.0
49 TraesCS7D01G112800 chr7A 81.690 142 15 4 2067 2206 74593839 74593971 1.660000e-19 108.0
50 TraesCS7D01G112800 chr7A 89.231 65 3 3 777 838 70767520 70767457 1.300000e-10 78.7
51 TraesCS7D01G112800 chr6A 97.086 755 20 2 2331 3083 527455265 527456019 0.000000e+00 1271.0
52 TraesCS7D01G112800 chr6A 96.821 755 22 2 2331 3083 527378472 527379226 0.000000e+00 1260.0
53 TraesCS7D01G112800 chr6A 93.571 420 23 3 3948 4363 286335428 286335847 1.330000e-174 623.0
54 TraesCS7D01G112800 chr2A 96.821 755 21 3 2331 3083 11111464 11112217 0.000000e+00 1258.0
55 TraesCS7D01G112800 chr2A 96.291 755 26 2 2331 3083 11166975 11167729 0.000000e+00 1238.0
56 TraesCS7D01G112800 chr2A 79.459 185 25 7 2070 2251 51387977 51387803 7.670000e-23 119.0
57 TraesCS7D01G112800 chr1A 97.527 728 17 1 2331 3057 8508059 8508786 0.000000e+00 1243.0
58 TraesCS7D01G112800 chr1A 97.527 728 16 2 2331 3057 539260625 539261351 0.000000e+00 1243.0
59 TraesCS7D01G112800 chr5A 95.894 755 27 3 2331 3083 615622922 615622170 0.000000e+00 1219.0
60 TraesCS7D01G112800 chr6D 93.846 715 34 7 45 750 409783757 409784470 0.000000e+00 1068.0
61 TraesCS7D01G112800 chr6D 92.697 712 40 10 45 748 59818426 59819133 0.000000e+00 1016.0
62 TraesCS7D01G112800 chr6D 92.577 714 41 11 48 753 147988131 147987422 0.000000e+00 1014.0
63 TraesCS7D01G112800 chr6D 94.048 420 12 5 3948 4363 10676577 10676167 3.710000e-175 625.0
64 TraesCS7D01G112800 chr6D 93.349 421 24 3 3946 4363 455521438 455521019 1.720000e-173 619.0
65 TraesCS7D01G112800 chr6D 93.285 417 24 3 3946 4358 420556798 420557214 2.890000e-171 612.0
66 TraesCS7D01G112800 chr2D 93.706 715 34 9 48 754 499159365 499158654 0.000000e+00 1061.0
67 TraesCS7D01G112800 chr2D 92.458 716 41 10 48 753 12334923 12334211 0.000000e+00 1011.0
68 TraesCS7D01G112800 chr3D 92.372 721 37 15 45 754 456106710 456107423 0.000000e+00 1011.0
69 TraesCS7D01G112800 chr3D 94.643 56 2 1 1 55 319484150 319484095 7.780000e-13 86.1
70 TraesCS7D01G112800 chr5D 92.211 719 43 10 45 753 527244019 527244734 0.000000e+00 1005.0
71 TraesCS7D01G112800 chr1D 92.190 717 46 8 45 753 33732397 33733111 0.000000e+00 1005.0
72 TraesCS7D01G112800 chr1D 94.524 420 12 4 3946 4363 425566816 425566406 4.760000e-179 638.0
73 TraesCS7D01G112800 chr1D 93.587 421 23 3 3946 4363 432632914 432633333 3.710000e-175 625.0
74 TraesCS7D01G112800 chr1D 93.220 59 2 2 1 58 86952164 86952107 7.780000e-13 86.1
75 TraesCS7D01G112800 chr6B 87.162 740 40 23 1625 2337 360922870 360922159 0.000000e+00 789.0
76 TraesCS7D01G112800 chr4D 94.563 423 18 4 3945 4363 28420238 28419817 0.000000e+00 649.0
77 TraesCS7D01G112800 chr2B 81.152 191 24 6 2065 2251 76516162 76515980 4.550000e-30 143.0
78 TraesCS7D01G112800 chr2B 94.828 58 1 2 1 57 162607701 162607757 6.010000e-14 89.8
79 TraesCS7D01G112800 chr2B 94.737 57 2 1 1 57 210498706 210498761 2.160000e-13 87.9
80 TraesCS7D01G112800 chr4A 90.141 71 7 0 2101 2171 415170478 415170548 4.650000e-15 93.5
81 TraesCS7D01G112800 chr4A 78.443 167 16 11 2073 2223 656493636 656493474 1.670000e-14 91.6
82 TraesCS7D01G112800 chr4A 94.828 58 1 2 1 57 99374758 99374814 6.010000e-14 89.8
83 TraesCS7D01G112800 chr5B 94.828 58 1 2 1 57 227434523 227434467 6.010000e-14 89.8
84 TraesCS7D01G112800 chr5B 96.296 54 1 1 1 53 23958319 23958266 2.160000e-13 87.9
85 TraesCS7D01G112800 chr4B 94.828 58 1 2 1 57 40816744 40816688 6.010000e-14 89.8
86 TraesCS7D01G112800 chr3B 94.737 57 0 2 1 55 106328119 106328174 7.780000e-13 86.1


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 TraesCS7D01G112800 chr7D 69040594 69044958 4364 False 8061.000000 8061 100.000000 1 4365 1 chr7D.!!$F2 4364
1 TraesCS7D01G112800 chr7D 66104850 66105615 765 True 920.000000 920 88.802000 921 1666 1 chr7D.!!$R1 745
2 TraesCS7D01G112800 chr7D 65936731 65940372 3641 True 869.500000 1059 93.168000 930 3950 4 chr7D.!!$R4 3020
3 TraesCS7D01G112800 chr7D 85346826 85347395 569 False 538.000000 538 84.028000 2843 3407 1 chr7D.!!$F3 564
4 TraesCS7D01G112800 chr7D 548812277 548812956 679 True 477.000000 477 79.971000 948 1624 1 chr7D.!!$R3 676
5 TraesCS7D01G112800 chr7D 66346603 66348511 1908 True 441.633333 1138 89.338667 757 2249 3 chr7D.!!$R5 1492
6 TraesCS7D01G112800 chr7B 10880154 10884071 3917 False 1831.500000 2837 92.073500 169 3950 2 chr7B.!!$F3 3781
7 TraesCS7D01G112800 chr7B 10891800 10896408 4608 False 887.500000 1203 91.485000 754 3950 4 chr7B.!!$F4 3196
8 TraesCS7D01G112800 chr7B 10069240 10069998 758 False 320.000000 518 85.209500 2065 3403 2 chr7B.!!$F2 1338
9 TraesCS7D01G112800 chrUn 308148878 308156018 7140 True 1260.000000 1694 92.199000 1062 3950 4 chrUn.!!$R1 2888
10 TraesCS7D01G112800 chrUn 305654129 305656999 2870 False 1119.000000 2032 93.516500 754 3527 2 chrUn.!!$F1 2773
11 TraesCS7D01G112800 chr7A 714924342 714925096 754 False 1271.000000 1271 97.086000 2331 3083 1 chr7A.!!$F3 752
12 TraesCS7D01G112800 chr7A 74684428 74687697 3269 False 820.000000 1927 91.653800 754 3759 5 chr7A.!!$F5 3005
13 TraesCS7D01G112800 chr7A 70753886 70754457 571 True 701.000000 701 88.966000 847 1417 1 chr7A.!!$R2 570
14 TraesCS7D01G112800 chr7A 70766339 70767559 1220 True 631.350000 1184 86.791000 757 2018 2 chr7A.!!$R6 1261
15 TraesCS7D01G112800 chr7A 85196871 85197426 555 True 580.000000 580 85.739000 2849 3407 1 chr7A.!!$R3 558
16 TraesCS7D01G112800 chr7A 70733697 70737293 3596 True 560.666667 880 91.804167 855 3950 6 chr7A.!!$R5 3095
17 TraesCS7D01G112800 chr7A 634348775 634349476 701 True 457.000000 457 79.349000 948 1616 1 chr7A.!!$R4 668
18 TraesCS7D01G112800 chr7A 74593202 74594627 1425 False 332.333333 597 83.228000 1696 3403 3 chr7A.!!$F4 1707
19 TraesCS7D01G112800 chr6A 527455265 527456019 754 False 1271.000000 1271 97.086000 2331 3083 1 chr6A.!!$F3 752
20 TraesCS7D01G112800 chr6A 527378472 527379226 754 False 1260.000000 1260 96.821000 2331 3083 1 chr6A.!!$F2 752
21 TraesCS7D01G112800 chr2A 11111464 11112217 753 False 1258.000000 1258 96.821000 2331 3083 1 chr2A.!!$F1 752
22 TraesCS7D01G112800 chr2A 11166975 11167729 754 False 1238.000000 1238 96.291000 2331 3083 1 chr2A.!!$F2 752
23 TraesCS7D01G112800 chr1A 8508059 8508786 727 False 1243.000000 1243 97.527000 2331 3057 1 chr1A.!!$F1 726
24 TraesCS7D01G112800 chr1A 539260625 539261351 726 False 1243.000000 1243 97.527000 2331 3057 1 chr1A.!!$F2 726
25 TraesCS7D01G112800 chr5A 615622170 615622922 752 True 1219.000000 1219 95.894000 2331 3083 1 chr5A.!!$R1 752
26 TraesCS7D01G112800 chr6D 409783757 409784470 713 False 1068.000000 1068 93.846000 45 750 1 chr6D.!!$F2 705
27 TraesCS7D01G112800 chr6D 59818426 59819133 707 False 1016.000000 1016 92.697000 45 748 1 chr6D.!!$F1 703
28 TraesCS7D01G112800 chr6D 147987422 147988131 709 True 1014.000000 1014 92.577000 48 753 1 chr6D.!!$R2 705
29 TraesCS7D01G112800 chr2D 499158654 499159365 711 True 1061.000000 1061 93.706000 48 754 1 chr2D.!!$R2 706
30 TraesCS7D01G112800 chr2D 12334211 12334923 712 True 1011.000000 1011 92.458000 48 753 1 chr2D.!!$R1 705
31 TraesCS7D01G112800 chr3D 456106710 456107423 713 False 1011.000000 1011 92.372000 45 754 1 chr3D.!!$F1 709
32 TraesCS7D01G112800 chr5D 527244019 527244734 715 False 1005.000000 1005 92.211000 45 753 1 chr5D.!!$F1 708
33 TraesCS7D01G112800 chr1D 33732397 33733111 714 False 1005.000000 1005 92.190000 45 753 1 chr1D.!!$F1 708
34 TraesCS7D01G112800 chr6B 360922159 360922870 711 True 789.000000 789 87.162000 1625 2337 1 chr6B.!!$R1 712

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
691 713 0.461548 CTCCCTGCTCGTTGCTATGA 59.538 55.0 5.00 0.0 43.37 2.15 F
1452 2753 0.526662 AGAAGTCTACCTCCGCAACG 59.473 55.0 0.00 0.0 0.00 4.10 F
2252 4586 0.755327 GCCGGCTGGGTTTATGGAAT 60.755 55.0 22.15 0.0 38.44 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 2825 1.135489 GCTGATGTTGTCGAGGTCGTA 60.135 52.381 0.00 0.00 40.80 3.43 R
3098 10375 2.368221 GGGCATCTCTCTACTCTGCATT 59.632 50.000 0.00 0.00 34.56 3.56 R
4006 11435 0.026285 CAACTATACTGGTTGCGCGC 59.974 55.000 27.26 27.26 37.76 6.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.537728 AAAGATTCATATATTGGAAGGTTGCA 57.462 30.769 0.00 0.00 0.00 4.08
35 36 8.716674 AAGATTCATATATTGGAAGGTTGCAT 57.283 30.769 0.00 0.00 0.00 3.96
36 37 8.716674 AGATTCATATATTGGAAGGTTGCATT 57.283 30.769 0.00 0.00 0.00 3.56
37 38 9.151177 AGATTCATATATTGGAAGGTTGCATTT 57.849 29.630 0.00 0.00 0.00 2.32
38 39 9.199982 GATTCATATATTGGAAGGTTGCATTTG 57.800 33.333 0.00 0.00 0.00 2.32
39 40 7.053316 TCATATATTGGAAGGTTGCATTTGG 57.947 36.000 0.00 0.00 0.00 3.28
40 41 6.838090 TCATATATTGGAAGGTTGCATTTGGA 59.162 34.615 0.00 0.00 0.00 3.53
41 42 3.683365 ATTGGAAGGTTGCATTTGGAC 57.317 42.857 0.00 0.00 0.00 4.02
42 43 2.079170 TGGAAGGTTGCATTTGGACA 57.921 45.000 0.00 0.00 0.00 4.02
43 44 2.607499 TGGAAGGTTGCATTTGGACAT 58.393 42.857 0.00 0.00 0.00 3.06
46 47 2.198827 AGGTTGCATTTGGACATCGA 57.801 45.000 0.00 0.00 0.00 3.59
234 241 1.339151 CCTCCGGTGGAAGAAAGGAAG 60.339 57.143 17.99 0.00 0.00 3.46
339 359 3.323979 CCTCCTTTATATACGTGGCCAGT 59.676 47.826 5.11 9.57 0.00 4.00
459 481 1.024579 CCTGCGGCGGTAACTTCATT 61.025 55.000 9.78 0.00 0.00 2.57
474 496 2.998316 TCATTATCACCATCGCCACA 57.002 45.000 0.00 0.00 0.00 4.17
479 501 2.463589 ATCACCATCGCCACACCGTT 62.464 55.000 0.00 0.00 0.00 4.44
677 699 2.652590 GTACGTGGACATACTCTCCCT 58.347 52.381 0.00 0.00 0.00 4.20
691 713 0.461548 CTCCCTGCTCGTTGCTATGA 59.538 55.000 5.00 0.00 43.37 2.15
925 958 1.844289 TCCAACGGCCCACCTAGTT 60.844 57.895 0.00 0.00 0.00 2.24
937 970 2.093447 CCACCTAGTTCCGAAAGCTGAT 60.093 50.000 0.00 0.00 0.00 2.90
940 973 2.432510 CCTAGTTCCGAAAGCTGATCCT 59.567 50.000 0.00 0.00 0.00 3.24
1016 1058 2.096248 TCTCGCTTCTTCTCTTCTCCC 58.904 52.381 0.00 0.00 0.00 4.30
1436 2737 2.497675 CCTGTCAGAATCCGAGGAAGAA 59.502 50.000 0.00 0.00 0.00 2.52
1452 2753 0.526662 AGAAGTCTACCTCCGCAACG 59.473 55.000 0.00 0.00 0.00 4.10
1518 2825 2.952245 CCACCGTCGACTTCGTCT 59.048 61.111 14.70 0.00 40.80 4.18
1890 4149 1.523938 GCGCCCCATGGTAGACTTC 60.524 63.158 11.73 0.00 0.00 3.01
2058 4332 6.248433 TCCTTTGGCAAGAAACTCATATTCT 58.752 36.000 0.00 0.00 38.75 2.40
2109 4436 4.211374 CCGGTGTAGTCTGAAACTTTTGAG 59.789 45.833 0.00 0.00 39.55 3.02
2123 4450 8.739039 TGAAACTTTTGAGAATCTGTTTCAGAA 58.261 29.630 16.72 1.69 44.04 3.02
2139 4466 7.930217 TGTTTCAGAATTTCAGTTAGGAGTTG 58.070 34.615 0.00 0.00 0.00 3.16
2164 4491 4.265073 ACATGGAAATAGTCTGAACTGCC 58.735 43.478 0.00 0.00 36.92 4.85
2167 4494 3.512329 TGGAAATAGTCTGAACTGCCGTA 59.488 43.478 0.00 0.00 36.92 4.02
2171 4498 2.089980 TAGTCTGAACTGCCGTAGGAC 58.910 52.381 0.00 0.00 44.12 3.85
2172 4499 2.290768 TAGTCTGAACTGCCGTAGGACT 60.291 50.000 12.47 12.47 44.12 3.85
2186 4513 5.888691 CGTAGGACTATAGACATCAGCAT 57.111 43.478 6.78 0.00 0.00 3.79
2192 4519 8.256356 AGGACTATAGACATCAGCATAAGTTT 57.744 34.615 6.78 0.00 0.00 2.66
2252 4586 0.755327 GCCGGCTGGGTTTATGGAAT 60.755 55.000 22.15 0.00 38.44 3.01
2253 4587 1.318576 CCGGCTGGGTTTATGGAATC 58.681 55.000 2.57 0.00 0.00 2.52
2254 4588 1.133792 CCGGCTGGGTTTATGGAATCT 60.134 52.381 2.57 0.00 0.00 2.40
2255 4589 2.222027 CGGCTGGGTTTATGGAATCTC 58.778 52.381 0.00 0.00 0.00 2.75
2882 10099 5.620206 TCAAAATCAGTTCAGTCTGCCTAA 58.380 37.500 0.00 0.00 35.63 2.69
2969 10244 6.264832 CACAGCACTTTACATTGTTTTGAGA 58.735 36.000 0.00 0.00 0.00 3.27
2985 10260 7.140705 TGTTTTGAGATTTTGTACATCAGCTG 58.859 34.615 7.63 7.63 0.00 4.24
3026 10303 1.967319 AACTGTTGCAGTACCTGTGG 58.033 50.000 1.97 0.00 44.62 4.17
3444 10814 9.326339 CCGCTTAAAGTTTTGTTATTCTCTTAC 57.674 33.333 0.00 0.00 0.00 2.34
3520 10890 1.624487 CGTACACGACTTGCTGCATA 58.376 50.000 1.84 0.00 43.02 3.14
3609 11007 6.979238 ACGATACTGTAAGAATGCTAGTTTCC 59.021 38.462 0.00 0.00 37.43 3.13
3950 11379 4.477780 GTTCGACTCTTCACCTGTTAGAG 58.522 47.826 0.00 0.00 40.91 2.43
3951 11380 2.488545 TCGACTCTTCACCTGTTAGAGC 59.511 50.000 0.00 0.00 39.17 4.09
3952 11381 2.229062 CGACTCTTCACCTGTTAGAGCA 59.771 50.000 0.00 0.00 39.17 4.26
3953 11382 3.119316 CGACTCTTCACCTGTTAGAGCAT 60.119 47.826 0.00 0.00 39.17 3.79
3954 11383 4.429108 GACTCTTCACCTGTTAGAGCATC 58.571 47.826 0.00 0.00 39.17 3.91
3965 11394 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
3966 11395 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
3967 11396 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
3968 11397 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
3973 11402 4.999939 CCAACAGCCGCGCCAAAC 63.000 66.667 0.00 0.00 0.00 2.93
3974 11403 3.964875 CAACAGCCGCGCCAAACT 61.965 61.111 0.00 0.00 0.00 2.66
3975 11404 2.281208 AACAGCCGCGCCAAACTA 60.281 55.556 0.00 0.00 0.00 2.24
3976 11405 2.325082 AACAGCCGCGCCAAACTAG 61.325 57.895 0.00 0.00 0.00 2.57
3977 11406 4.166011 CAGCCGCGCCAAACTAGC 62.166 66.667 0.00 0.00 0.00 3.42
4007 11436 1.125930 CAAAATTGCCCGTTTTAGCGC 59.874 47.619 0.00 0.00 0.00 5.92
4008 11437 0.731174 AAATTGCCCGTTTTAGCGCG 60.731 50.000 0.00 0.00 0.00 6.86
4009 11438 3.677099 ATTGCCCGTTTTAGCGCGC 62.677 57.895 26.66 26.66 36.35 6.86
4021 11450 3.259020 GCGCGCGCAACCAGTATA 61.259 61.111 46.11 0.00 41.49 1.47
4022 11451 2.920869 CGCGCGCAACCAGTATAG 59.079 61.111 32.61 6.38 0.00 1.31
4023 11452 1.876714 CGCGCGCAACCAGTATAGT 60.877 57.895 32.61 0.00 0.00 2.12
4024 11453 1.418342 CGCGCGCAACCAGTATAGTT 61.418 55.000 32.61 0.00 0.00 2.24
4025 11454 0.026285 GCGCGCAACCAGTATAGTTG 59.974 55.000 29.10 0.00 45.92 3.16
4032 11461 2.939103 CAACCAGTATAGTTGCTCCAGC 59.061 50.000 0.00 0.00 38.31 4.85
4033 11462 1.137086 ACCAGTATAGTTGCTCCAGCG 59.863 52.381 0.00 0.00 45.83 5.18
4034 11463 1.539065 CCAGTATAGTTGCTCCAGCGG 60.539 57.143 0.00 0.00 45.83 5.52
4035 11464 0.753262 AGTATAGTTGCTCCAGCGGG 59.247 55.000 0.00 0.00 45.83 6.13
4036 11465 0.880718 GTATAGTTGCTCCAGCGGGC 60.881 60.000 0.00 0.00 45.83 6.13
4037 11466 2.363711 TATAGTTGCTCCAGCGGGCG 62.364 60.000 0.00 0.00 45.83 6.13
4066 11495 4.409588 CGCGCGCGGCATATGTAC 62.410 66.667 43.28 10.21 43.84 2.90
4067 11496 3.036084 GCGCGCGGCATATGTACT 61.036 61.111 33.06 0.00 42.87 2.73
4068 11497 2.594962 GCGCGCGGCATATGTACTT 61.595 57.895 33.06 0.00 42.87 2.24
4069 11498 1.487231 CGCGCGGCATATGTACTTC 59.513 57.895 24.84 0.00 0.00 3.01
4070 11499 1.212455 CGCGCGGCATATGTACTTCA 61.212 55.000 24.84 0.00 0.00 3.02
4071 11500 0.508641 GCGCGGCATATGTACTTCAG 59.491 55.000 8.83 0.00 0.00 3.02
4072 11501 0.508641 CGCGGCATATGTACTTCAGC 59.491 55.000 4.29 0.00 0.00 4.26
4073 11502 0.508641 GCGGCATATGTACTTCAGCG 59.491 55.000 4.29 0.00 0.00 5.18
4074 11503 0.508641 CGGCATATGTACTTCAGCGC 59.491 55.000 0.00 0.00 0.00 5.92
4075 11504 0.508641 GGCATATGTACTTCAGCGCG 59.491 55.000 0.00 0.00 0.00 6.86
4076 11505 0.111089 GCATATGTACTTCAGCGCGC 60.111 55.000 26.66 26.66 0.00 6.86
4077 11506 0.159554 CATATGTACTTCAGCGCGCG 59.840 55.000 28.44 28.44 0.00 6.86
4078 11507 0.939577 ATATGTACTTCAGCGCGCGG 60.940 55.000 33.06 26.50 0.00 6.46
4079 11508 2.947118 TATGTACTTCAGCGCGCGGG 62.947 60.000 33.06 23.76 0.00 6.13
4091 11520 3.124921 CGCGGGCCGAAACTCAAT 61.125 61.111 33.44 0.00 40.02 2.57
4092 11521 2.791927 GCGGGCCGAAACTCAATC 59.208 61.111 33.44 4.02 0.00 2.67
4093 11522 3.089784 CGGGCCGAAACTCAATCG 58.910 61.111 24.41 0.00 39.92 3.34
4094 11523 1.740296 CGGGCCGAAACTCAATCGT 60.740 57.895 24.41 0.00 38.60 3.73
4095 11524 1.794222 GGGCCGAAACTCAATCGTG 59.206 57.895 0.00 0.00 38.60 4.35
4096 11525 1.134694 GGCCGAAACTCAATCGTGC 59.865 57.895 0.00 0.00 38.60 5.34
4097 11526 1.225745 GCCGAAACTCAATCGTGCG 60.226 57.895 0.00 0.00 38.60 5.34
4098 11527 1.225745 CCGAAACTCAATCGTGCGC 60.226 57.895 0.00 0.00 38.60 6.09
4099 11528 1.225745 CGAAACTCAATCGTGCGCC 60.226 57.895 4.18 0.00 35.64 6.53
4100 11529 1.225745 GAAACTCAATCGTGCGCCG 60.226 57.895 4.18 8.64 38.13 6.46
4101 11530 3.308878 AAACTCAATCGTGCGCCGC 62.309 57.895 4.18 0.00 36.19 6.53
4102 11531 4.742201 ACTCAATCGTGCGCCGCT 62.742 61.111 11.67 0.00 36.19 5.52
4103 11532 3.490759 CTCAATCGTGCGCCGCTT 61.491 61.111 11.67 3.00 36.19 4.68
4104 11533 2.125872 TCAATCGTGCGCCGCTTA 60.126 55.556 11.67 0.00 36.19 3.09
4105 11534 1.490693 CTCAATCGTGCGCCGCTTAT 61.491 55.000 11.67 0.00 36.19 1.73
4106 11535 1.087202 TCAATCGTGCGCCGCTTATT 61.087 50.000 11.67 4.46 36.19 1.40
4107 11536 0.248054 CAATCGTGCGCCGCTTATTT 60.248 50.000 11.67 0.00 36.19 1.40
4108 11537 0.248054 AATCGTGCGCCGCTTATTTG 60.248 50.000 11.67 0.00 36.19 2.32
4109 11538 2.646799 ATCGTGCGCCGCTTATTTGC 62.647 55.000 11.67 0.00 36.19 3.68
4110 11539 2.485122 GTGCGCCGCTTATTTGCT 59.515 55.556 11.67 0.00 0.00 3.91
4111 11540 1.869132 GTGCGCCGCTTATTTGCTG 60.869 57.895 11.67 0.00 0.00 4.41
4112 11541 2.951227 GCGCCGCTTATTTGCTGC 60.951 61.111 0.00 0.00 39.28 5.25
4116 11545 2.793946 CGCTTATTTGCTGCGCCT 59.206 55.556 4.18 0.00 43.08 5.52
4117 11546 1.584483 CGCTTATTTGCTGCGCCTG 60.584 57.895 4.18 0.00 43.08 4.85
4118 11547 1.875364 GCTTATTTGCTGCGCCTGC 60.875 57.895 14.38 14.38 43.20 4.85
4119 11548 1.805254 CTTATTTGCTGCGCCTGCT 59.195 52.632 20.27 6.11 43.34 4.24
4120 11549 0.171903 CTTATTTGCTGCGCCTGCTT 59.828 50.000 20.27 9.98 43.34 3.91
4121 11550 0.171007 TTATTTGCTGCGCCTGCTTC 59.829 50.000 20.27 0.00 43.34 3.86
4122 11551 1.656818 TATTTGCTGCGCCTGCTTCC 61.657 55.000 20.27 0.00 43.34 3.46
4148 11577 4.468615 GACTCTCGCGCGCTCACT 62.469 66.667 30.48 7.23 0.00 3.41
4149 11578 4.468615 ACTCTCGCGCGCTCACTC 62.469 66.667 30.48 0.00 0.00 3.51
4158 11587 2.811317 CGCTCACTCGCAACTCCC 60.811 66.667 0.00 0.00 0.00 4.30
4159 11588 2.343758 GCTCACTCGCAACTCCCA 59.656 61.111 0.00 0.00 0.00 4.37
4160 11589 2.029844 GCTCACTCGCAACTCCCAC 61.030 63.158 0.00 0.00 0.00 4.61
4161 11590 1.374758 CTCACTCGCAACTCCCACC 60.375 63.158 0.00 0.00 0.00 4.61
4162 11591 2.358737 CACTCGCAACTCCCACCC 60.359 66.667 0.00 0.00 0.00 4.61
4163 11592 3.637273 ACTCGCAACTCCCACCCC 61.637 66.667 0.00 0.00 0.00 4.95
4164 11593 4.410400 CTCGCAACTCCCACCCCC 62.410 72.222 0.00 0.00 0.00 5.40
4231 11660 4.990553 GCGCTTCCCCGGCCTATC 62.991 72.222 0.00 0.00 0.00 2.08
4232 11661 4.315941 CGCTTCCCCGGCCTATCC 62.316 72.222 0.00 0.00 0.00 2.59
4233 11662 3.955044 GCTTCCCCGGCCTATCCC 61.955 72.222 0.00 0.00 0.00 3.85
4234 11663 3.249961 CTTCCCCGGCCTATCCCC 61.250 72.222 0.00 0.00 0.00 4.81
4352 11781 3.907927 CGCAAGGTGTTCGACAAAA 57.092 47.368 0.00 0.00 0.00 2.44
4353 11782 1.462791 CGCAAGGTGTTCGACAAAAC 58.537 50.000 0.00 0.00 0.00 2.43
4354 11783 1.462791 GCAAGGTGTTCGACAAAACG 58.537 50.000 0.00 0.00 31.58 3.60
4355 11784 1.462791 CAAGGTGTTCGACAAAACGC 58.537 50.000 0.00 0.00 38.60 4.84
4359 11788 2.572173 GTGTTCGACAAAACGCCTAG 57.428 50.000 0.00 0.00 34.35 3.02
4360 11789 2.129607 GTGTTCGACAAAACGCCTAGA 58.870 47.619 0.00 0.00 34.35 2.43
4361 11790 2.540931 GTGTTCGACAAAACGCCTAGAA 59.459 45.455 0.00 0.00 34.35 2.10
4362 11791 2.798283 TGTTCGACAAAACGCCTAGAAG 59.202 45.455 0.00 0.00 31.58 2.85
4363 11792 3.054878 GTTCGACAAAACGCCTAGAAGA 58.945 45.455 0.00 0.00 0.00 2.87
4364 11793 3.587797 TCGACAAAACGCCTAGAAGAT 57.412 42.857 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.639563 TGCAACCTTCCAATATATGAATCTTTA 57.360 29.630 0.00 0.00 0.00 1.85
9 10 8.537728 TGCAACCTTCCAATATATGAATCTTT 57.462 30.769 0.00 0.00 0.00 2.52
10 11 8.716674 ATGCAACCTTCCAATATATGAATCTT 57.283 30.769 0.00 0.00 0.00 2.40
11 12 8.716674 AATGCAACCTTCCAATATATGAATCT 57.283 30.769 0.00 0.00 0.00 2.40
12 13 9.199982 CAAATGCAACCTTCCAATATATGAATC 57.800 33.333 0.00 0.00 0.00 2.52
13 14 8.152246 CCAAATGCAACCTTCCAATATATGAAT 58.848 33.333 0.00 0.00 0.00 2.57
14 15 7.344093 TCCAAATGCAACCTTCCAATATATGAA 59.656 33.333 0.00 0.00 0.00 2.57
15 16 6.838090 TCCAAATGCAACCTTCCAATATATGA 59.162 34.615 0.00 0.00 0.00 2.15
16 17 6.925165 GTCCAAATGCAACCTTCCAATATATG 59.075 38.462 0.00 0.00 0.00 1.78
17 18 6.610830 TGTCCAAATGCAACCTTCCAATATAT 59.389 34.615 0.00 0.00 0.00 0.86
18 19 5.954752 TGTCCAAATGCAACCTTCCAATATA 59.045 36.000 0.00 0.00 0.00 0.86
19 20 4.776837 TGTCCAAATGCAACCTTCCAATAT 59.223 37.500 0.00 0.00 0.00 1.28
20 21 4.155709 TGTCCAAATGCAACCTTCCAATA 58.844 39.130 0.00 0.00 0.00 1.90
21 22 2.971330 TGTCCAAATGCAACCTTCCAAT 59.029 40.909 0.00 0.00 0.00 3.16
22 23 2.392662 TGTCCAAATGCAACCTTCCAA 58.607 42.857 0.00 0.00 0.00 3.53
23 24 2.079170 TGTCCAAATGCAACCTTCCA 57.921 45.000 0.00 0.00 0.00 3.53
24 25 2.415893 CGATGTCCAAATGCAACCTTCC 60.416 50.000 0.00 0.00 0.00 3.46
25 26 2.487762 TCGATGTCCAAATGCAACCTTC 59.512 45.455 0.00 0.00 0.00 3.46
26 27 2.489329 CTCGATGTCCAAATGCAACCTT 59.511 45.455 0.00 0.00 0.00 3.50
27 28 2.086869 CTCGATGTCCAAATGCAACCT 58.913 47.619 0.00 0.00 0.00 3.50
28 29 2.083774 TCTCGATGTCCAAATGCAACC 58.916 47.619 0.00 0.00 0.00 3.77
29 30 2.096496 CCTCTCGATGTCCAAATGCAAC 59.904 50.000 0.00 0.00 0.00 4.17
30 31 2.290260 ACCTCTCGATGTCCAAATGCAA 60.290 45.455 0.00 0.00 0.00 4.08
31 32 1.278985 ACCTCTCGATGTCCAAATGCA 59.721 47.619 0.00 0.00 0.00 3.96
32 33 2.029838 ACCTCTCGATGTCCAAATGC 57.970 50.000 0.00 0.00 0.00 3.56
33 34 3.871594 GGTAACCTCTCGATGTCCAAATG 59.128 47.826 0.00 0.00 0.00 2.32
34 35 3.430374 CGGTAACCTCTCGATGTCCAAAT 60.430 47.826 0.00 0.00 0.00 2.32
35 36 2.094390 CGGTAACCTCTCGATGTCCAAA 60.094 50.000 0.00 0.00 0.00 3.28
36 37 1.475280 CGGTAACCTCTCGATGTCCAA 59.525 52.381 0.00 0.00 0.00 3.53
37 38 1.100510 CGGTAACCTCTCGATGTCCA 58.899 55.000 0.00 0.00 0.00 4.02
38 39 0.384669 CCGGTAACCTCTCGATGTCC 59.615 60.000 0.00 0.00 0.00 4.02
39 40 1.386533 TCCGGTAACCTCTCGATGTC 58.613 55.000 0.00 0.00 0.00 3.06
40 41 1.475682 GTTCCGGTAACCTCTCGATGT 59.524 52.381 0.00 0.00 31.38 3.06
41 42 2.205307 GTTCCGGTAACCTCTCGATG 57.795 55.000 0.00 0.00 31.38 3.84
65 66 2.778270 ACTAGGCCCAATACTTCCTTCC 59.222 50.000 0.00 0.00 0.00 3.46
67 68 2.509964 CCACTAGGCCCAATACTTCCTT 59.490 50.000 0.00 0.00 0.00 3.36
68 69 2.127708 CCACTAGGCCCAATACTTCCT 58.872 52.381 0.00 0.00 0.00 3.36
69 70 1.143073 CCCACTAGGCCCAATACTTCC 59.857 57.143 0.00 0.00 0.00 3.46
100 101 0.178891 TGTGGCCCTTTCTCCTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
139 144 0.676736 TCCAATTCGGTTTGGGCAAC 59.323 50.000 14.68 0.00 45.21 4.17
302 318 2.623431 AGGGAGGGAGAGAGGCCT 60.623 66.667 3.86 3.86 0.00 5.19
446 468 4.084537 CGATGGTGATAATGAAGTTACCGC 60.085 45.833 0.00 0.00 0.00 5.68
459 481 1.142965 CGGTGTGGCGATGGTGATA 59.857 57.895 0.00 0.00 0.00 2.15
474 496 0.461339 AGTTTCGTCAGCACAACGGT 60.461 50.000 5.83 0.00 40.45 4.83
479 501 0.033504 GGGAGAGTTTCGTCAGCACA 59.966 55.000 0.00 0.00 0.00 4.57
571 593 1.375396 CCGATCCAAGCACCGAACA 60.375 57.895 0.00 0.00 0.00 3.18
638 660 1.651240 CCCTCGTAGACCGAAAGCGA 61.651 60.000 0.00 0.00 46.75 4.93
677 699 2.432146 AGGAGAATCATAGCAACGAGCA 59.568 45.455 7.30 0.00 41.80 4.26
691 713 6.007076 TCACGCAAGATCTATCTAGGAGAAT 58.993 40.000 0.00 0.00 43.62 2.40
925 958 3.417069 TTCAAAGGATCAGCTTTCGGA 57.583 42.857 0.00 0.00 0.00 4.55
937 970 6.603201 CCAAGGCAGAGTATTTATTCAAAGGA 59.397 38.462 0.00 0.00 0.00 3.36
940 973 5.163663 CGCCAAGGCAGAGTATTTATTCAAA 60.164 40.000 12.19 0.00 42.06 2.69
979 1013 2.297701 GAGAGCTGTTGGTTGGTTGAA 58.702 47.619 0.00 0.00 0.00 2.69
1436 2737 1.881602 GACGTTGCGGAGGTAGACT 59.118 57.895 0.00 0.00 0.00 3.24
1518 2825 1.135489 GCTGATGTTGTCGAGGTCGTA 60.135 52.381 0.00 0.00 40.80 3.43
1852 4105 2.513204 CCGCCTGACCAGCTGATG 60.513 66.667 17.39 1.02 0.00 3.07
1890 4149 3.488978 ACGAGCTCGGAGTCGTCG 61.489 66.667 36.93 20.05 46.17 5.12
2073 4400 4.625028 ACTACACCGGTTTCAGTAAACTC 58.375 43.478 2.97 0.00 43.76 3.01
2109 4436 9.003658 TCCTAACTGAAATTCTGAAACAGATTC 57.996 33.333 20.65 5.49 40.39 2.52
2123 4450 6.013379 TCCATGTCTCAACTCCTAACTGAAAT 60.013 38.462 0.00 0.00 0.00 2.17
2139 4466 5.293079 GCAGTTCAGACTATTTCCATGTCTC 59.707 44.000 0.00 0.00 38.80 3.36
2164 4491 5.888691 ATGCTGATGTCTATAGTCCTACG 57.111 43.478 0.00 0.00 0.00 3.51
2167 4494 7.847711 AACTTATGCTGATGTCTATAGTCCT 57.152 36.000 0.00 0.00 0.00 3.85
2171 4498 9.755804 TTCAGAAACTTATGCTGATGTCTATAG 57.244 33.333 0.00 0.00 38.35 1.31
2192 4519 7.252612 TGACCACCTACTGATTTAATTCAGA 57.747 36.000 26.35 13.46 44.88 3.27
2252 4586 6.317893 TGTCTATAATCGTACTGCAGTTGAGA 59.682 38.462 27.06 20.91 0.00 3.27
2253 4587 6.495706 TGTCTATAATCGTACTGCAGTTGAG 58.504 40.000 27.06 16.31 0.00 3.02
2254 4588 6.445357 TGTCTATAATCGTACTGCAGTTGA 57.555 37.500 27.06 22.73 0.00 3.18
2255 4589 6.918022 TGATGTCTATAATCGTACTGCAGTTG 59.082 38.462 27.06 18.05 0.00 3.16
2969 10244 9.846248 GATAAAAAGACAGCTGATGTACAAAAT 57.154 29.630 23.35 3.16 44.17 1.82
3098 10375 2.368221 GGGCATCTCTCTACTCTGCATT 59.632 50.000 0.00 0.00 34.56 3.56
3609 11007 3.787634 GCTCATGAACAATGTAATGTGCG 59.212 43.478 15.35 6.10 37.56 5.34
3875 11296 5.021033 ACTCCATAAGATTGCAGAGTCAG 57.979 43.478 0.00 0.00 28.69 3.51
3950 11379 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
3951 11380 3.869272 GCGCGGCTGTTGGAGATG 61.869 66.667 8.83 0.00 0.00 2.90
3956 11385 4.999939 GTTTGGCGCGGCTGTTGG 63.000 66.667 33.23 0.00 0.00 3.77
3957 11386 2.513065 CTAGTTTGGCGCGGCTGTTG 62.513 60.000 33.23 14.34 0.00 3.33
3958 11387 2.281208 TAGTTTGGCGCGGCTGTT 60.281 55.556 33.23 17.83 0.00 3.16
3959 11388 2.742372 CTAGTTTGGCGCGGCTGT 60.742 61.111 33.23 16.80 0.00 4.40
3960 11389 4.166011 GCTAGTTTGGCGCGGCTG 62.166 66.667 33.23 16.16 0.00 4.85
3987 11416 1.125930 GCGCTAAAACGGGCAATTTTG 59.874 47.619 0.00 0.00 41.86 2.44
3988 11417 1.424403 GCGCTAAAACGGGCAATTTT 58.576 45.000 0.00 3.81 41.86 1.82
3989 11418 0.731174 CGCGCTAAAACGGGCAATTT 60.731 50.000 5.56 0.00 42.32 1.82
3990 11419 1.154112 CGCGCTAAAACGGGCAATT 60.154 52.632 5.56 0.00 42.32 2.32
3991 11420 2.483288 CGCGCTAAAACGGGCAAT 59.517 55.556 5.56 0.00 42.32 3.56
4004 11433 3.210419 CTATACTGGTTGCGCGCGC 62.210 63.158 45.02 45.02 42.35 6.86
4005 11434 1.418342 AACTATACTGGTTGCGCGCG 61.418 55.000 28.44 28.44 0.00 6.86
4006 11435 0.026285 CAACTATACTGGTTGCGCGC 59.974 55.000 27.26 27.26 37.76 6.86
4011 11440 2.939103 GCTGGAGCAACTATACTGGTTG 59.061 50.000 0.00 0.00 44.60 3.77
4012 11441 2.418746 CGCTGGAGCAACTATACTGGTT 60.419 50.000 0.00 0.00 42.21 3.67
4013 11442 1.137086 CGCTGGAGCAACTATACTGGT 59.863 52.381 0.00 0.00 42.21 4.00
4014 11443 1.539065 CCGCTGGAGCAACTATACTGG 60.539 57.143 0.00 0.00 42.21 4.00
4015 11444 1.539065 CCCGCTGGAGCAACTATACTG 60.539 57.143 0.00 0.00 42.21 2.74
4016 11445 0.753262 CCCGCTGGAGCAACTATACT 59.247 55.000 0.00 0.00 42.21 2.12
4017 11446 0.880718 GCCCGCTGGAGCAACTATAC 60.881 60.000 0.00 0.00 42.21 1.47
4018 11447 1.445942 GCCCGCTGGAGCAACTATA 59.554 57.895 0.00 0.00 42.21 1.31
4019 11448 2.190578 GCCCGCTGGAGCAACTAT 59.809 61.111 0.00 0.00 42.21 2.12
4020 11449 4.451150 CGCCCGCTGGAGCAACTA 62.451 66.667 0.00 0.00 42.21 2.24
4049 11478 4.409588 GTACATATGCCGCGCGCG 62.410 66.667 43.73 43.73 42.08 6.86
4050 11479 2.480426 GAAGTACATATGCCGCGCGC 62.480 60.000 27.36 23.91 38.31 6.86
4051 11480 1.212455 TGAAGTACATATGCCGCGCG 61.212 55.000 25.67 25.67 0.00 6.86
4052 11481 0.508641 CTGAAGTACATATGCCGCGC 59.491 55.000 0.00 0.00 0.00 6.86
4053 11482 0.508641 GCTGAAGTACATATGCCGCG 59.491 55.000 1.58 0.00 0.00 6.46
4054 11483 0.508641 CGCTGAAGTACATATGCCGC 59.491 55.000 1.58 0.00 0.00 6.53
4055 11484 0.508641 GCGCTGAAGTACATATGCCG 59.491 55.000 0.00 0.00 0.00 5.69
4056 11485 0.508641 CGCGCTGAAGTACATATGCC 59.491 55.000 5.56 0.00 0.00 4.40
4057 11486 0.111089 GCGCGCTGAAGTACATATGC 60.111 55.000 26.67 0.00 0.00 3.14
4058 11487 0.159554 CGCGCGCTGAAGTACATATG 59.840 55.000 30.48 4.24 0.00 1.78
4059 11488 0.939577 CCGCGCGCTGAAGTACATAT 60.940 55.000 30.48 0.00 0.00 1.78
4060 11489 1.587876 CCGCGCGCTGAAGTACATA 60.588 57.895 30.48 0.00 0.00 2.29
4061 11490 2.885644 CCGCGCGCTGAAGTACAT 60.886 61.111 30.48 0.00 0.00 2.29
4074 11503 3.095898 GATTGAGTTTCGGCCCGCG 62.096 63.158 0.00 0.00 0.00 6.46
4075 11504 2.791927 GATTGAGTTTCGGCCCGC 59.208 61.111 0.00 0.00 0.00 6.13
4076 11505 1.740296 ACGATTGAGTTTCGGCCCG 60.740 57.895 0.00 0.00 40.83 6.13
4077 11506 1.794222 CACGATTGAGTTTCGGCCC 59.206 57.895 0.00 0.00 40.83 5.80
4078 11507 1.134694 GCACGATTGAGTTTCGGCC 59.865 57.895 0.00 0.00 40.83 6.13
4079 11508 1.225745 CGCACGATTGAGTTTCGGC 60.226 57.895 0.00 0.00 40.83 5.54
4080 11509 1.225745 GCGCACGATTGAGTTTCGG 60.226 57.895 0.30 0.00 40.83 4.30
4081 11510 1.225745 GGCGCACGATTGAGTTTCG 60.226 57.895 10.83 0.00 42.20 3.46
4082 11511 4.745549 GGCGCACGATTGAGTTTC 57.254 55.556 10.83 0.00 0.00 2.78
4093 11522 1.869132 CAGCAAATAAGCGGCGCAC 60.869 57.895 35.02 13.31 40.15 5.34
4094 11523 2.484662 CAGCAAATAAGCGGCGCA 59.515 55.556 35.02 15.48 40.15 6.09
4095 11524 2.951227 GCAGCAAATAAGCGGCGC 60.951 61.111 26.86 26.86 45.03 6.53
4131 11560 4.468615 AGTGAGCGCGCGAGAGTC 62.469 66.667 37.18 22.83 0.00 3.36
4132 11561 4.468615 GAGTGAGCGCGCGAGAGT 62.469 66.667 37.18 18.58 0.00 3.24
4141 11570 2.811317 GGGAGTTGCGAGTGAGCG 60.811 66.667 0.00 0.00 40.67 5.03
4142 11571 2.029844 GTGGGAGTTGCGAGTGAGC 61.030 63.158 0.00 0.00 37.71 4.26
4143 11572 1.374758 GGTGGGAGTTGCGAGTGAG 60.375 63.158 0.00 0.00 0.00 3.51
4144 11573 2.741092 GGTGGGAGTTGCGAGTGA 59.259 61.111 0.00 0.00 0.00 3.41
4145 11574 2.358737 GGGTGGGAGTTGCGAGTG 60.359 66.667 0.00 0.00 0.00 3.51
4146 11575 3.637273 GGGGTGGGAGTTGCGAGT 61.637 66.667 0.00 0.00 0.00 4.18
4147 11576 4.410400 GGGGGTGGGAGTTGCGAG 62.410 72.222 0.00 0.00 0.00 5.03
4214 11643 4.990553 GATAGGCCGGGGAAGCGC 62.991 72.222 2.18 0.00 0.00 5.92
4215 11644 4.315941 GGATAGGCCGGGGAAGCG 62.316 72.222 2.18 0.00 0.00 4.68
4216 11645 3.955044 GGGATAGGCCGGGGAAGC 61.955 72.222 2.18 0.00 37.63 3.86
4217 11646 3.249961 GGGGATAGGCCGGGGAAG 61.250 72.222 2.18 0.00 37.63 3.46
4290 11719 4.838486 CGCTGCTCGTCGGAGGAC 62.838 72.222 0.00 0.00 40.80 3.85
4331 11760 3.723348 GTCGAACACCTTGCGGGC 61.723 66.667 0.00 0.00 39.10 6.13
4332 11761 1.440938 TTTGTCGAACACCTTGCGGG 61.441 55.000 0.00 0.00 41.89 6.13
4333 11762 0.378962 TTTTGTCGAACACCTTGCGG 59.621 50.000 0.00 0.00 0.00 5.69
4334 11763 1.462791 GTTTTGTCGAACACCTTGCG 58.537 50.000 0.00 0.00 0.00 4.85
4335 11764 1.462791 CGTTTTGTCGAACACCTTGC 58.537 50.000 0.00 0.00 0.00 4.01
4336 11765 1.462791 GCGTTTTGTCGAACACCTTG 58.537 50.000 0.00 0.00 0.00 3.61
4337 11766 0.379316 GGCGTTTTGTCGAACACCTT 59.621 50.000 0.00 0.00 30.80 3.50
4338 11767 0.463116 AGGCGTTTTGTCGAACACCT 60.463 50.000 0.00 0.00 37.27 4.00
4339 11768 1.193874 CTAGGCGTTTTGTCGAACACC 59.806 52.381 0.00 0.00 33.03 4.16
4340 11769 2.129607 TCTAGGCGTTTTGTCGAACAC 58.870 47.619 0.00 0.00 0.00 3.32
4341 11770 2.512485 TCTAGGCGTTTTGTCGAACA 57.488 45.000 0.00 0.00 0.00 3.18
4342 11771 3.054878 TCTTCTAGGCGTTTTGTCGAAC 58.945 45.455 0.00 0.00 0.00 3.95
4343 11772 3.374220 TCTTCTAGGCGTTTTGTCGAA 57.626 42.857 0.00 0.00 0.00 3.71
4344 11773 3.587797 ATCTTCTAGGCGTTTTGTCGA 57.412 42.857 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.