Multiple sequence alignment - TraesCS3A01G468100

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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 TraesCS3A01G468100 chr3A 100.000 4317 0 0 1 4317 701121216 701125532 0.000000e+00 7973.0
1 TraesCS3A01G468100 chr3A 87.134 785 67 21 2582 3340 700893612 700894388 0.000000e+00 859.0
2 TraesCS3A01G468100 chr3A 90.329 517 30 8 2059 2574 700953175 700953672 0.000000e+00 660.0
3 TraesCS3A01G468100 chr3A 81.698 754 111 21 2591 3342 700945542 700946270 1.720000e-168 603.0
4 TraesCS3A01G468100 chr3A 90.167 478 26 4 2582 3057 700953836 700954294 1.720000e-168 603.0
5 TraesCS3A01G468100 chr3A 83.598 567 67 9 2742 3284 701140477 701141041 3.850000e-140 508.0
6 TraesCS3A01G468100 chr3A 84.902 510 46 15 2091 2574 700960662 700961166 1.800000e-133 486.0
7 TraesCS3A01G468100 chr3A 88.636 396 20 17 933 1307 700959237 700959628 3.930000e-125 459.0
8 TraesCS3A01G468100 chr3A 82.047 557 52 27 686 1202 700907381 700907929 8.580000e-117 431.0
9 TraesCS3A01G468100 chr3A 82.828 495 65 13 2088 2570 701139724 701140210 3.990000e-115 425.0
10 TraesCS3A01G468100 chr3A 84.855 449 18 13 876 1304 700891047 700891465 1.450000e-109 407.0
11 TraesCS3A01G468100 chr3A 83.333 444 61 9 295 733 700948712 700949147 8.700000e-107 398.0
12 TraesCS3A01G468100 chr3A 84.596 396 20 19 934 1302 700952155 700952536 5.310000e-94 355.0
13 TraesCS3A01G468100 chr3A 85.886 333 25 15 876 1192 701137975 701138301 6.920000e-88 335.0
14 TraesCS3A01G468100 chr3A 78.341 434 73 16 222 643 700854942 700855366 1.190000e-65 261.0
15 TraesCS3A01G468100 chr3A 97.727 44 1 0 1557 1600 701139226 701139269 4.630000e-10 76.8
16 TraesCS3A01G468100 chr3A 84.848 66 3 2 865 930 700890989 700891047 4.660000e-05 60.2
17 TraesCS3A01G468100 chr3B 98.077 780 14 1 2278 3057 755770979 755771757 0.000000e+00 1356.0
18 TraesCS3A01G468100 chr3B 88.209 882 55 20 923 1780 755769534 755770390 0.000000e+00 1007.0
19 TraesCS3A01G468100 chr3B 86.515 749 66 18 2617 3340 755575769 755576507 0.000000e+00 791.0
20 TraesCS3A01G468100 chr3B 94.118 510 26 2 2059 2568 754720017 754720522 0.000000e+00 773.0
21 TraesCS3A01G468100 chr3B 81.506 903 87 38 2582 3423 755660143 755661026 0.000000e+00 669.0
22 TraesCS3A01G468100 chr3B 90.057 523 26 9 2059 2574 755605113 755605616 0.000000e+00 654.0
23 TraesCS3A01G468100 chr3B 81.507 730 79 31 686 1374 755603813 755604527 2.270000e-152 549.0
24 TraesCS3A01G468100 chr3B 88.813 438 37 8 2146 2574 754770975 754771409 1.060000e-145 527.0
25 TraesCS3A01G468100 chr3B 88.053 452 35 1 2606 3057 754722096 754722528 6.400000e-143 518.0
26 TraesCS3A01G468100 chr3B 83.363 565 64 11 2748 3284 756082109 756081547 3.000000e-136 496.0
27 TraesCS3A01G468100 chr3B 93.313 329 21 1 2730 3057 755606046 755606374 6.490000e-133 484.0
28 TraesCS3A01G468100 chr3B 88.482 382 30 7 2198 2574 755575223 755575595 2.370000e-122 449.0
29 TraesCS3A01G468100 chr3B 81.404 527 46 32 876 1366 755707934 755708444 2.440000e-102 383.0
30 TraesCS3A01G468100 chr3B 85.390 397 25 15 933 1298 754718145 754718539 8.760000e-102 381.0
31 TraesCS3A01G468100 chr3B 90.136 294 26 3 1773 2064 754719259 754719551 3.150000e-101 379.0
32 TraesCS3A01G468100 chr3B 94.359 195 11 0 449 643 755768142 755768336 2.520000e-77 300.0
33 TraesCS3A01G468100 chr3B 94.972 179 9 0 2059 2237 755770803 755770981 9.140000e-72 281.0
34 TraesCS3A01G468100 chr3B 93.571 140 5 2 643 780 755769400 755769537 5.660000e-49 206.0
35 TraesCS3A01G468100 chr3B 81.503 173 19 7 1894 2064 755709264 755709425 3.500000e-26 130.0
36 TraesCS3A01G468100 chr3B 100.000 29 0 0 2587 2615 754720698 754720726 2.000000e-03 54.7
37 TraesCS3A01G468100 chr3D 96.683 814 26 1 1773 2585 566301062 566300249 0.000000e+00 1352.0
38 TraesCS3A01G468100 chr3D 94.228 589 28 5 192 780 566302648 566302066 0.000000e+00 894.0
39 TraesCS3A01G468100 chr3D 88.811 715 52 18 2588 3284 566422600 566421896 0.000000e+00 852.0
40 TraesCS3A01G468100 chr3D 95.174 518 20 5 2059 2574 566131993 566131479 0.000000e+00 813.0
41 TraesCS3A01G468100 chr3D 94.444 486 17 5 2582 3060 566300130 566299648 0.000000e+00 739.0
42 TraesCS3A01G468100 chr3D 80.378 846 80 41 2597 3379 566392581 566391759 8.100000e-157 564.0
43 TraesCS3A01G468100 chr3D 93.072 332 21 2 2730 3060 566129640 566129310 6.490000e-133 484.0
44 TraesCS3A01G468100 chr3D 80.263 684 83 30 645 1309 566104024 566103374 6.540000e-128 468.0
45 TraesCS3A01G468100 chr3D 86.937 444 20 18 876 1311 566423883 566423470 8.460000e-127 464.0
46 TraesCS3A01G468100 chr3D 84.061 527 33 23 923 1423 566302069 566301568 1.090000e-125 460.0
47 TraesCS3A01G468100 chr3D 83.333 474 33 25 933 1368 566394941 566394476 3.130000e-106 396.0
48 TraesCS3A01G468100 chr3D 89.701 301 26 5 1767 2064 566132754 566132456 3.150000e-101 379.0
49 TraesCS3A01G468100 chr3D 88.679 318 18 10 1003 1305 566138596 566138282 5.270000e-99 372.0
50 TraesCS3A01G468100 chr3D 94.545 165 9 0 1476 1640 566301572 566301408 5.540000e-64 255.0
51 TraesCS3A01G468100 chr3D 92.222 180 13 1 1 180 566349983 566349805 1.990000e-63 254.0
52 TraesCS3A01G468100 chr3D 91.667 144 11 1 3141 3284 566100800 566100658 9.470000e-47 198.0
53 TraesCS3A01G468100 chr3D 89.041 146 13 1 3114 3259 566129188 566129046 1.230000e-40 178.0
54 TraesCS3A01G468100 chr3D 92.727 55 4 0 2653 2707 566129698 566129644 3.580000e-11 80.5
55 TraesCS3A01G468100 chr3D 84.058 69 4 2 862 930 566423944 566423883 4.660000e-05 60.2
56 TraesCS3A01G468100 chr3D 94.595 37 2 0 2582 2618 566131314 566131278 1.680000e-04 58.4
57 TraesCS3A01G468100 chrUn 83.187 571 66 15 2742 3284 408040739 408041307 3.000000e-136 496.0
58 TraesCS3A01G468100 chrUn 80.000 330 44 13 3995 4317 255307845 255308159 1.560000e-54 224.0
59 TraesCS3A01G468100 chrUn 80.000 330 44 13 3995 4317 255318560 255318874 1.560000e-54 224.0
60 TraesCS3A01G468100 chrUn 74.231 683 104 36 3419 4055 255307210 255307866 2.020000e-53 220.0
61 TraesCS3A01G468100 chrUn 74.085 683 105 36 3419 4055 255317925 255318581 9.400000e-52 215.0
62 TraesCS3A01G468100 chrUn 83.429 175 25 4 3419 3590 86981733 86981906 4.470000e-35 159.0
63 TraesCS3A01G468100 chr7A 75.667 937 139 61 3429 4311 71071860 71072761 6.770000e-103 385.0
64 TraesCS3A01G468100 chr7A 78.209 592 72 28 3764 4317 165444851 165445423 4.160000e-85 326.0
65 TraesCS3A01G468100 chr7A 80.511 313 41 8 4010 4317 15710902 15711199 5.620000e-54 222.0
66 TraesCS3A01G468100 chr6D 76.567 670 113 27 3421 4055 308923467 308924127 1.160000e-85 327.0
67 TraesCS3A01G468100 chr1A 75.898 668 90 41 3432 4055 308212183 308211543 4.250000e-70 276.0
68 TraesCS3A01G468100 chr1A 75.542 646 90 36 3438 4048 531022350 531021738 5.540000e-64 255.0
69 TraesCS3A01G468100 chr1A 72.615 650 104 44 3421 4050 7063978 7064573 3.480000e-31 147.0
70 TraesCS3A01G468100 chr7D 83.766 308 30 11 4015 4317 41696828 41696536 1.530000e-69 274.0
71 TraesCS3A01G468100 chr5B 75.382 654 108 32 3427 4042 13502495 13503133 2.560000e-67 267.0
72 TraesCS3A01G468100 chr5B 80.255 314 42 10 4010 4317 4554072 4554371 7.270000e-53 219.0
73 TraesCS3A01G468100 chr4D 73.881 827 125 52 3559 4317 398543292 398544095 3.330000e-61 246.0
74 TraesCS3A01G468100 chr4D 87.786 131 16 0 1070 1200 503639118 503639248 2.080000e-33 154.0
75 TraesCS3A01G468100 chr5D 80.363 331 40 14 3995 4317 17478832 17479145 1.210000e-55 228.0
76 TraesCS3A01G468100 chr5D 80.528 303 44 6 4015 4314 20759139 20758849 7.270000e-53 219.0
77 TraesCS3A01G468100 chr5D 74.719 178 39 3 413 587 415653691 415653865 1.660000e-09 75.0
78 TraesCS3A01G468100 chr5D 89.130 46 3 2 512 556 376685238 376685282 6.030000e-04 56.5
79 TraesCS3A01G468100 chr2B 74.247 664 113 34 3422 4055 755340641 755340006 4.340000e-55 226.0
80 TraesCS3A01G468100 chr2B 88.623 167 18 1 1050 1215 704575111 704575277 7.320000e-48 202.0
81 TraesCS3A01G468100 chr2D 88.957 163 16 2 1047 1207 584624673 584624835 2.630000e-47 200.0
82 TraesCS3A01G468100 chr2D 73.054 668 120 45 3426 4061 32064028 32063389 9.540000e-42 182.0
83 TraesCS3A01G468100 chr2D 77.049 244 47 7 374 614 524574467 524574704 9.740000e-27 132.0
84 TraesCS3A01G468100 chr1B 78.431 306 57 8 3424 3723 641687838 641688140 1.580000e-44 191.0
85 TraesCS3A01G468100 chr4B 87.013 154 14 5 1050 1200 649490467 649490617 7.420000e-38 169.0
86 TraesCS3A01G468100 chr4B 84.211 171 23 3 1776 1943 649491108 649491277 3.450000e-36 163.0
87 TraesCS3A01G468100 chr5A 88.235 136 14 2 1066 1200 688242472 688242606 1.240000e-35 161.0
88 TraesCS3A01G468100 chr5A 83.908 87 14 0 513 599 115099369 115099455 2.770000e-12 84.2


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 TraesCS3A01G468100 chr3A 701121216 701125532 4316 False 7973.000000 7973 100.000000 1 4317 1 chr3A.!!$F3 4316
1 TraesCS3A01G468100 chr3A 700945542 700954294 8752 False 523.800000 660 86.024600 295 3342 5 chr3A.!!$F5 3047
2 TraesCS3A01G468100 chr3A 700959237 700961166 1929 False 472.500000 486 86.769000 933 2574 2 chr3A.!!$F6 1641
3 TraesCS3A01G468100 chr3A 700890989 700894388 3399 False 442.066667 859 85.612333 865 3340 3 chr3A.!!$F4 2475
4 TraesCS3A01G468100 chr3A 700907381 700907929 548 False 431.000000 431 82.047000 686 1202 1 chr3A.!!$F2 516
5 TraesCS3A01G468100 chr3A 701137975 701141041 3066 False 336.200000 508 87.509750 876 3284 4 chr3A.!!$F7 2408
6 TraesCS3A01G468100 chr3B 755660143 755661026 883 False 669.000000 669 81.506000 2582 3423 1 chr3B.!!$F2 841
7 TraesCS3A01G468100 chr3B 755768142 755771757 3615 False 630.000000 1356 93.837600 449 3057 5 chr3B.!!$F7 2608
8 TraesCS3A01G468100 chr3B 755575223 755576507 1284 False 620.000000 791 87.498500 2198 3340 2 chr3B.!!$F4 1142
9 TraesCS3A01G468100 chr3B 755603813 755606374 2561 False 562.333333 654 88.292333 686 3057 3 chr3B.!!$F5 2371
10 TraesCS3A01G468100 chr3B 756081547 756082109 562 True 496.000000 496 83.363000 2748 3284 1 chr3B.!!$R1 536
11 TraesCS3A01G468100 chr3B 754718145 754722528 4383 False 421.140000 773 91.539400 933 3057 5 chr3B.!!$F3 2124
12 TraesCS3A01G468100 chr3B 755707934 755709425 1491 False 256.500000 383 81.453500 876 2064 2 chr3B.!!$F6 1188
13 TraesCS3A01G468100 chr3D 566299648 566302648 3000 True 740.000000 1352 92.792200 192 3060 5 chr3D.!!$R5 2868
14 TraesCS3A01G468100 chr3D 566391759 566394941 3182 True 480.000000 564 81.855500 933 3379 2 chr3D.!!$R6 2446
15 TraesCS3A01G468100 chr3D 566421896 566423944 2048 True 458.733333 852 86.602000 862 3284 3 chr3D.!!$R7 2422
16 TraesCS3A01G468100 chr3D 566100658 566104024 3366 True 333.000000 468 85.965000 645 3284 2 chr3D.!!$R3 2639
17 TraesCS3A01G468100 chr3D 566129046 566132754 3708 True 332.150000 813 92.385000 1767 3259 6 chr3D.!!$R4 1492
18 TraesCS3A01G468100 chrUn 408040739 408041307 568 False 496.000000 496 83.187000 2742 3284 1 chrUn.!!$F2 542
19 TraesCS3A01G468100 chrUn 255307210 255308159 949 False 222.000000 224 77.115500 3419 4317 2 chrUn.!!$F3 898
20 TraesCS3A01G468100 chrUn 255317925 255318874 949 False 219.500000 224 77.042500 3419 4317 2 chrUn.!!$F4 898
21 TraesCS3A01G468100 chr7A 71071860 71072761 901 False 385.000000 385 75.667000 3429 4311 1 chr7A.!!$F2 882
22 TraesCS3A01G468100 chr7A 165444851 165445423 572 False 326.000000 326 78.209000 3764 4317 1 chr7A.!!$F3 553
23 TraesCS3A01G468100 chr6D 308923467 308924127 660 False 327.000000 327 76.567000 3421 4055 1 chr6D.!!$F1 634
24 TraesCS3A01G468100 chr1A 308211543 308212183 640 True 276.000000 276 75.898000 3432 4055 1 chr1A.!!$R1 623
25 TraesCS3A01G468100 chr1A 531021738 531022350 612 True 255.000000 255 75.542000 3438 4048 1 chr1A.!!$R2 610
26 TraesCS3A01G468100 chr5B 13502495 13503133 638 False 267.000000 267 75.382000 3427 4042 1 chr5B.!!$F2 615
27 TraesCS3A01G468100 chr4D 398543292 398544095 803 False 246.000000 246 73.881000 3559 4317 1 chr4D.!!$F1 758
28 TraesCS3A01G468100 chr2B 755340006 755340641 635 True 226.000000 226 74.247000 3422 4055 1 chr2B.!!$R1 633

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
137 138 0.107897 CCCATCCGGACGTTCATCAA 60.108 55.0 6.12 0.0 0.00 2.57 F
1167 8066 0.041238 TCTTCTCCATGGTCTCCGGT 59.959 55.0 12.58 0.0 0.00 5.28 F
1725 9281 0.682209 CCTTCCAAGCAGGGTGATGG 60.682 60.0 0.00 0.0 38.24 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 8939 1.742411 GCTAATGCTCAACCGCCAGTA 60.742 52.381 0.0 0.0 36.03 2.74 R
3134 17286 1.026182 GTGATGAAGGATGCGTGCCA 61.026 55.000 0.0 0.0 0.00 4.92 R
3446 17621 1.616725 CCACAAGAAGCAATAGCCCCA 60.617 52.381 0.0 0.0 43.56 4.96 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
24 25 6.632909 TCAAATTGCCATTAACTTCTCCATG 58.367 36.000 0.00 0.00 0.00 3.66
26 27 5.841957 ATTGCCATTAACTTCTCCATGTC 57.158 39.130 0.00 0.00 0.00 3.06
27 28 3.620488 TGCCATTAACTTCTCCATGTCC 58.380 45.455 0.00 0.00 0.00 4.02
28 29 3.266772 TGCCATTAACTTCTCCATGTCCT 59.733 43.478 0.00 0.00 0.00 3.85
30 31 4.122776 CCATTAACTTCTCCATGTCCTCG 58.877 47.826 0.00 0.00 0.00 4.63
31 32 3.887621 TTAACTTCTCCATGTCCTCGG 57.112 47.619 0.00 0.00 0.00 4.63
32 33 1.645710 AACTTCTCCATGTCCTCGGT 58.354 50.000 0.00 0.00 0.00 4.69
33 34 2.526888 ACTTCTCCATGTCCTCGGTA 57.473 50.000 0.00 0.00 0.00 4.02
34 35 3.033659 ACTTCTCCATGTCCTCGGTAT 57.966 47.619 0.00 0.00 0.00 2.73
35 36 3.375699 ACTTCTCCATGTCCTCGGTATT 58.624 45.455 0.00 0.00 0.00 1.89
37 38 4.225267 ACTTCTCCATGTCCTCGGTATTTT 59.775 41.667 0.00 0.00 0.00 1.82
38 39 4.137116 TCTCCATGTCCTCGGTATTTTG 57.863 45.455 0.00 0.00 0.00 2.44
39 40 3.517901 TCTCCATGTCCTCGGTATTTTGT 59.482 43.478 0.00 0.00 0.00 2.83
41 42 4.258543 TCCATGTCCTCGGTATTTTGTTC 58.741 43.478 0.00 0.00 0.00 3.18
43 44 4.332819 CCATGTCCTCGGTATTTTGTTCTC 59.667 45.833 0.00 0.00 0.00 2.87
44 45 4.884668 TGTCCTCGGTATTTTGTTCTCT 57.115 40.909 0.00 0.00 0.00 3.10
46 47 4.282449 TGTCCTCGGTATTTTGTTCTCTCA 59.718 41.667 0.00 0.00 0.00 3.27
47 48 5.221561 TGTCCTCGGTATTTTGTTCTCTCAA 60.222 40.000 0.00 0.00 0.00 3.02
48 49 5.875359 GTCCTCGGTATTTTGTTCTCTCAAT 59.125 40.000 0.00 0.00 0.00 2.57
49 50 6.371825 GTCCTCGGTATTTTGTTCTCTCAATT 59.628 38.462 0.00 0.00 0.00 2.32
50 51 7.548075 GTCCTCGGTATTTTGTTCTCTCAATTA 59.452 37.037 0.00 0.00 0.00 1.40
51 52 7.548075 TCCTCGGTATTTTGTTCTCTCAATTAC 59.452 37.037 0.00 0.00 0.00 1.89
53 54 8.475331 TCGGTATTTTGTTCTCTCAATTACTC 57.525 34.615 0.00 0.00 0.00 2.59
54 55 7.548075 TCGGTATTTTGTTCTCTCAATTACTCC 59.452 37.037 0.00 0.00 0.00 3.85
55 56 7.464178 CGGTATTTTGTTCTCTCAATTACTCCG 60.464 40.741 0.00 0.00 0.00 4.63
57 58 4.884668 TTGTTCTCTCAATTACTCCGGT 57.115 40.909 0.00 0.00 0.00 5.28
58 59 4.451629 TGTTCTCTCAATTACTCCGGTC 57.548 45.455 0.00 0.00 0.00 4.79
62 63 6.209986 TGTTCTCTCAATTACTCCGGTCTAAA 59.790 38.462 0.00 0.00 0.00 1.85
65 66 5.717119 TCTCAATTACTCCGGTCTAAACAC 58.283 41.667 0.00 0.00 0.00 3.32
67 68 4.529377 TCAATTACTCCGGTCTAAACACCT 59.471 41.667 0.00 0.00 33.77 4.00
68 69 5.012354 TCAATTACTCCGGTCTAAACACCTT 59.988 40.000 0.00 0.00 33.77 3.50
69 70 4.525912 TTACTCCGGTCTAAACACCTTC 57.474 45.455 0.00 0.00 33.77 3.46
72 73 1.345415 TCCGGTCTAAACACCTTCACC 59.655 52.381 0.00 0.00 33.77 4.02
73 74 1.071071 CCGGTCTAAACACCTTCACCA 59.929 52.381 0.00 0.00 33.77 4.17
74 75 2.140717 CGGTCTAAACACCTTCACCAC 58.859 52.381 0.00 0.00 33.77 4.16
75 76 2.484065 CGGTCTAAACACCTTCACCACA 60.484 50.000 0.00 0.00 33.77 4.17
76 77 3.139077 GGTCTAAACACCTTCACCACAG 58.861 50.000 0.00 0.00 33.08 3.66
78 79 4.058817 GTCTAAACACCTTCACCACAGAG 58.941 47.826 0.00 0.00 0.00 3.35
79 80 3.709653 TCTAAACACCTTCACCACAGAGT 59.290 43.478 0.00 0.00 0.00 3.24
81 82 3.753294 AACACCTTCACCACAGAGTAG 57.247 47.619 0.00 0.00 0.00 2.57
83 84 2.628657 ACACCTTCACCACAGAGTAGAC 59.371 50.000 0.00 0.00 0.00 2.59
84 85 2.628178 CACCTTCACCACAGAGTAGACA 59.372 50.000 0.00 0.00 0.00 3.41
85 86 3.069586 CACCTTCACCACAGAGTAGACAA 59.930 47.826 0.00 0.00 0.00 3.18
86 87 3.709653 ACCTTCACCACAGAGTAGACAAA 59.290 43.478 0.00 0.00 0.00 2.83
87 88 4.348168 ACCTTCACCACAGAGTAGACAAAT 59.652 41.667 0.00 0.00 0.00 2.32
90 91 6.073003 CCTTCACCACAGAGTAGACAAATTTC 60.073 42.308 0.00 0.00 0.00 2.17
91 92 5.924356 TCACCACAGAGTAGACAAATTTCA 58.076 37.500 0.00 0.00 0.00 2.69
92 93 5.758296 TCACCACAGAGTAGACAAATTTCAC 59.242 40.000 0.00 0.00 0.00 3.18
94 95 5.063204 CCACAGAGTAGACAAATTTCACCA 58.937 41.667 0.00 0.00 0.00 4.17
95 96 5.707298 CCACAGAGTAGACAAATTTCACCAT 59.293 40.000 0.00 0.00 0.00 3.55
96 97 6.348786 CCACAGAGTAGACAAATTTCACCATG 60.349 42.308 0.00 0.00 0.00 3.66
98 99 4.702131 AGAGTAGACAAATTTCACCATGGC 59.298 41.667 13.04 0.00 0.00 4.40
99 100 3.440173 AGTAGACAAATTTCACCATGGCG 59.560 43.478 13.04 1.26 0.00 5.69
100 101 2.238521 AGACAAATTTCACCATGGCGT 58.761 42.857 13.04 0.00 0.00 5.68
101 102 2.228822 AGACAAATTTCACCATGGCGTC 59.771 45.455 13.04 5.92 0.00 5.19
104 105 3.006752 ACAAATTTCACCATGGCGTCAAT 59.993 39.130 13.04 2.33 0.00 2.57
106 107 0.243365 TTTCACCATGGCGTCAATGC 59.757 50.000 13.04 0.00 0.00 3.56
107 108 0.892814 TTCACCATGGCGTCAATGCA 60.893 50.000 13.04 0.00 36.28 3.96
111 112 1.023502 CCATGGCGTCAATGCATGTA 58.976 50.000 0.00 0.00 36.28 2.29
112 113 1.268692 CCATGGCGTCAATGCATGTAC 60.269 52.381 0.00 0.19 36.28 2.90
114 115 1.368641 TGGCGTCAATGCATGTACTC 58.631 50.000 0.00 0.00 36.28 2.59
119 120 3.119291 CGTCAATGCATGTACTCTCTCC 58.881 50.000 0.00 0.00 0.00 3.71
125 126 1.000283 GCATGTACTCTCTCCCATCCG 60.000 57.143 0.00 0.00 0.00 4.18
126 127 1.615883 CATGTACTCTCTCCCATCCGG 59.384 57.143 0.00 0.00 0.00 5.14
128 129 1.320507 GTACTCTCTCCCATCCGGAC 58.679 60.000 6.12 0.00 34.86 4.79
129 130 0.179026 TACTCTCTCCCATCCGGACG 60.179 60.000 6.12 0.00 34.86 4.79
131 132 1.000019 TCTCTCCCATCCGGACGTT 60.000 57.895 6.12 0.00 34.86 3.99
132 133 1.035932 TCTCTCCCATCCGGACGTTC 61.036 60.000 6.12 0.00 34.86 3.95
133 134 1.304630 TCTCCCATCCGGACGTTCA 60.305 57.895 6.12 0.00 34.86 3.18
134 135 0.686441 TCTCCCATCCGGACGTTCAT 60.686 55.000 6.12 0.00 34.86 2.57
137 138 0.107897 CCCATCCGGACGTTCATCAA 60.108 55.000 6.12 0.00 0.00 2.57
139 140 1.674519 CCATCCGGACGTTCATCAACA 60.675 52.381 6.12 0.00 32.14 3.33
140 141 2.279741 CATCCGGACGTTCATCAACAT 58.720 47.619 6.12 0.00 32.14 2.71
141 142 2.004583 TCCGGACGTTCATCAACATC 57.995 50.000 0.00 0.00 32.14 3.06
142 143 1.273886 TCCGGACGTTCATCAACATCA 59.726 47.619 0.00 0.00 32.14 3.07
143 144 2.093711 TCCGGACGTTCATCAACATCAT 60.094 45.455 0.00 0.00 32.14 2.45
144 145 2.285220 CCGGACGTTCATCAACATCATC 59.715 50.000 0.00 0.00 32.14 2.92
145 146 3.190079 CGGACGTTCATCAACATCATCT 58.810 45.455 0.00 0.00 32.14 2.90
146 147 3.000623 CGGACGTTCATCAACATCATCTG 59.999 47.826 0.00 0.00 32.14 2.90
147 148 3.935203 GGACGTTCATCAACATCATCTGT 59.065 43.478 0.00 0.00 40.84 3.41
149 150 3.686241 ACGTTCATCAACATCATCTGTGG 59.314 43.478 0.00 0.00 38.39 4.17
150 151 3.486375 CGTTCATCAACATCATCTGTGGC 60.486 47.826 0.00 0.00 38.39 5.01
152 153 3.959293 TCATCAACATCATCTGTGGCTT 58.041 40.909 0.00 0.00 38.39 4.35
153 154 4.338012 TCATCAACATCATCTGTGGCTTT 58.662 39.130 0.00 0.00 38.39 3.51
155 156 5.355071 TCATCAACATCATCTGTGGCTTTAC 59.645 40.000 0.00 0.00 38.39 2.01
156 157 4.009675 TCAACATCATCTGTGGCTTTACC 58.990 43.478 0.00 0.00 38.39 2.85
171 172 4.459337 GGCTTTACCATATGCAAGTATCCC 59.541 45.833 0.00 0.00 38.86 3.85
172 173 4.459337 GCTTTACCATATGCAAGTATCCCC 59.541 45.833 0.00 0.00 0.00 4.81
173 174 5.630121 CTTTACCATATGCAAGTATCCCCA 58.370 41.667 0.00 0.00 0.00 4.96
174 175 3.795688 ACCATATGCAAGTATCCCCAG 57.204 47.619 0.00 0.00 0.00 4.45
175 176 3.326521 ACCATATGCAAGTATCCCCAGA 58.673 45.455 0.00 0.00 0.00 3.86
176 177 3.328931 ACCATATGCAAGTATCCCCAGAG 59.671 47.826 0.00 0.00 0.00 3.35
177 178 3.584406 CCATATGCAAGTATCCCCAGAGA 59.416 47.826 0.00 0.00 0.00 3.10
178 179 4.042062 CCATATGCAAGTATCCCCAGAGAA 59.958 45.833 0.00 0.00 0.00 2.87
179 180 3.853355 ATGCAAGTATCCCCAGAGAAG 57.147 47.619 0.00 0.00 0.00 2.85
181 182 1.475930 GCAAGTATCCCCAGAGAAGGC 60.476 57.143 0.00 0.00 0.00 4.35
182 183 1.123928 AAGTATCCCCAGAGAAGGCG 58.876 55.000 0.00 0.00 0.00 5.52
183 184 1.069935 GTATCCCCAGAGAAGGCGC 59.930 63.158 0.00 0.00 0.00 6.53
184 185 2.498941 TATCCCCAGAGAAGGCGCG 61.499 63.158 0.00 0.00 0.00 6.86
187 188 4.845580 CCCAGAGAAGGCGCGCAT 62.846 66.667 34.42 26.01 0.00 4.73
188 189 2.821366 CCAGAGAAGGCGCGCATT 60.821 61.111 32.64 32.64 0.00 3.56
190 191 1.061570 CAGAGAAGGCGCGCATTTC 59.938 57.895 32.57 30.51 0.00 2.17
250 251 4.576463 AGGGATCATAATTCTTCACAACGC 59.424 41.667 0.00 0.00 0.00 4.84
310 3188 2.056906 GCCTCATGGAATACCGGGCT 62.057 60.000 6.32 0.00 39.42 5.19
311 3189 0.250467 CCTCATGGAATACCGGGCTG 60.250 60.000 6.32 0.00 39.42 4.85
329 3207 2.288886 GCTGGGTTTGAAGTAGTCGTCT 60.289 50.000 0.00 0.00 0.00 4.18
331 3209 2.030540 TGGGTTTGAAGTAGTCGTCTCG 60.031 50.000 0.00 0.00 0.00 4.04
333 3211 2.606308 GGTTTGAAGTAGTCGTCTCGCA 60.606 50.000 0.00 0.00 0.00 5.10
357 3235 2.760092 GAGCCTTTGCACCAATTATCCA 59.240 45.455 0.00 0.00 41.13 3.41
373 3251 0.975887 TCCAATTTGGGGCAAAGAGC 59.024 50.000 15.37 0.00 38.32 4.09
447 3325 2.029623 CCCATTTCTTCCTGGATGCTG 58.970 52.381 0.00 0.00 34.24 4.41
497 3375 5.527214 TGTCGTCATCATTGTCTGAAAAACT 59.473 36.000 0.00 0.00 37.44 2.66
587 3465 8.030082 GATGAATCCATCGTTTGCCAACAAAC 62.030 42.308 10.81 10.81 46.19 2.93
599 3477 4.664188 TGCCAACAAACGAGTAAAAGAAC 58.336 39.130 0.00 0.00 0.00 3.01
629 3507 7.106890 TCCATCATTTGACTTTGTATCGGTTA 58.893 34.615 0.00 0.00 0.00 2.85
641 3519 4.769688 TGTATCGGTTAGGACGAAGAGTA 58.230 43.478 0.00 0.00 44.20 2.59
677 4622 1.266211 CGTGCGCAGAAATGTACGTAC 60.266 52.381 18.90 18.90 37.70 3.67
734 4691 1.079503 GAAGTTTCCAGGTGCTAGCG 58.920 55.000 10.77 0.00 0.00 4.26
797 7555 1.994779 CCTGCGTTCCATTTGCATTTC 59.005 47.619 0.00 0.00 38.07 2.17
798 7556 2.609984 CCTGCGTTCCATTTGCATTTCA 60.610 45.455 0.00 0.00 38.07 2.69
834 7600 0.320697 AAACACGAGGCAGAGGTACC 59.679 55.000 2.73 2.73 0.00 3.34
837 7603 3.155167 CGAGGCAGAGGTACCCCC 61.155 72.222 8.74 4.30 0.00 5.40
838 7604 2.040606 GAGGCAGAGGTACCCCCA 59.959 66.667 8.74 0.00 34.66 4.96
839 7605 2.285442 AGGCAGAGGTACCCCCAC 60.285 66.667 8.74 0.00 34.66 4.61
841 7607 3.408853 GCAGAGGTACCCCCACCC 61.409 72.222 8.74 0.00 39.62 4.61
842 7608 3.081409 CAGAGGTACCCCCACCCG 61.081 72.222 8.74 0.00 39.62 5.28
843 7609 4.410033 AGAGGTACCCCCACCCGG 62.410 72.222 8.74 0.00 39.62 5.73
870 7646 1.473965 CCATCTCATCCTGGTTCGTGG 60.474 57.143 0.00 0.00 0.00 4.94
899 7675 0.818296 ACCTTTCCCATCTCGTCTCG 59.182 55.000 0.00 0.00 0.00 4.04
978 7821 1.517257 CTCCACACGAGCTAAGCGG 60.517 63.158 0.00 0.00 0.00 5.52
1167 8066 0.041238 TCTTCTCCATGGTCTCCGGT 59.959 55.000 12.58 0.00 0.00 5.28
1224 8657 2.039084 CCTCCCCTCCCTAATTTCATCG 59.961 54.545 0.00 0.00 0.00 3.84
1254 8687 7.318893 GCAAATGCTATTTCTCTTTCTTCCTT 58.681 34.615 0.00 0.00 38.21 3.36
1388 8873 2.223249 CGGTGTGTGAAGTGAAACCAAG 60.223 50.000 0.00 0.00 37.80 3.61
1422 8939 2.104963 GGAGTCTTTCCAGTGTCTTGGT 59.895 50.000 0.00 0.00 46.01 3.67
1503 9020 2.258109 AGGTTGGGTGAGTCTTACTCC 58.742 52.381 4.69 0.00 44.44 3.85
1631 9176 7.010771 AGGCTTAAAACTTACAAGGGAAATCT 58.989 34.615 0.00 0.00 0.00 2.40
1725 9281 0.682209 CCTTCCAAGCAGGGTGATGG 60.682 60.000 0.00 0.00 38.24 3.51
1765 9322 3.073274 AGGCTGGCGATTACTCTTTTT 57.927 42.857 0.00 0.00 0.00 1.94
1886 12422 2.661675 CCACAAACTCGACATCGTACAG 59.338 50.000 0.54 0.00 40.80 2.74
1972 12846 2.304180 AGAGCTGATTGTGCTGTTACCT 59.696 45.455 0.00 0.00 41.30 3.08
2015 12889 9.495754 GTGAATGACTAGAGATACAATTTTTGC 57.504 33.333 0.00 0.00 0.00 3.68
2018 12892 7.849804 TGACTAGAGATACAATTTTTGCCTC 57.150 36.000 0.00 0.00 0.00 4.70
2048 12922 5.163963 CGAGCTGCAACATTTTAATTTTCCC 60.164 40.000 1.02 0.00 0.00 3.97
2343 14514 4.155826 CAGGAACTCAAGTGTGTTTTGTCA 59.844 41.667 0.72 0.00 34.60 3.58
2746 16788 4.708177 AGTTGTTACATCTCACAAGCACT 58.292 39.130 0.00 0.00 33.55 4.40
3028 17104 1.401199 GCTGCATCTTCTTTCTCTGGC 59.599 52.381 0.00 0.00 0.00 4.85
3057 17133 4.858140 GCTACTGGTTTCGTTCTTCTAGTC 59.142 45.833 0.00 0.00 0.00 2.59
3064 17145 3.934457 TCGTTCTTCTAGTCATGTGCA 57.066 42.857 0.00 0.00 0.00 4.57
3078 17184 2.106477 TGTGCACATAATCGCAGGAA 57.894 45.000 17.42 0.00 39.20 3.36
3092 17205 2.644676 GCAGGAATCAGGAGGGTAAAC 58.355 52.381 0.00 0.00 0.00 2.01
3108 17221 3.243602 GGTAAACCGGTTGAAATGTGCTT 60.244 43.478 23.08 3.02 0.00 3.91
3110 17223 1.686355 ACCGGTTGAAATGTGCTTGA 58.314 45.000 0.00 0.00 0.00 3.02
3120 17272 1.242076 ATGTGCTTGAGACACTTGCC 58.758 50.000 0.00 0.00 38.86 4.52
3134 17286 6.006449 AGACACTTGCCAGATTTCAGTTATT 58.994 36.000 0.00 0.00 0.00 1.40
3186 17338 9.202273 GATAGATGGATTGTCTGTTTGATAGTC 57.798 37.037 0.00 0.00 0.00 2.59
3192 17344 3.838120 TGTCTGTTTGATAGTCGCTCAG 58.162 45.455 0.00 0.00 0.00 3.35
3210 17362 5.665459 GCTCAGCTTTATTCTAGGAGTTGA 58.335 41.667 0.00 0.00 0.00 3.18
3227 17379 4.323417 AGTTGATTATGAACGCCTTGTGA 58.677 39.130 0.00 0.00 0.00 3.58
3263 17416 5.579047 TGTTTAGGTGATGTGGGATCATTT 58.421 37.500 0.00 0.00 0.00 2.32
3312 17481 6.124088 GGTACCTGAATAATGCTCTGTTTG 57.876 41.667 4.06 0.00 0.00 2.93
3324 17493 2.129607 CTCTGTTTGTTGTGCAATGGC 58.870 47.619 0.00 0.00 36.89 4.40
3370 17545 4.568152 AAAAGTTGAAGACAATGTCGGG 57.432 40.909 7.83 0.00 37.67 5.14
3398 17573 3.857157 TCAGTTTAGTCTTTGCCCTGT 57.143 42.857 0.00 0.00 0.00 4.00
3401 17576 4.137543 CAGTTTAGTCTTTGCCCTGTTCT 58.862 43.478 0.00 0.00 0.00 3.01
3423 17598 9.614792 GTTCTATAGTTTCAACCTGGTTCATAT 57.385 33.333 9.62 6.46 0.00 1.78
3485 17660 3.190535 GTGGTATGTCACGAAAATTGCCT 59.809 43.478 0.00 0.00 0.00 4.75
3599 17792 3.695606 GACCTCCTGCGTGCTGGA 61.696 66.667 17.91 17.91 40.90 3.86
3600 17793 3.240134 GACCTCCTGCGTGCTGGAA 62.240 63.158 19.16 6.00 42.20 3.53
3601 17794 2.435586 CCTCCTGCGTGCTGGAAG 60.436 66.667 19.16 11.16 42.20 3.46
3602 17795 2.659016 CTCCTGCGTGCTGGAAGA 59.341 61.111 19.16 0.52 42.20 2.87
3604 17797 1.294659 CTCCTGCGTGCTGGAAGAAC 61.295 60.000 19.16 0.00 42.20 3.01
3664 17877 5.901336 GCAACCTGCTTTTTAAATTTCGTTG 59.099 36.000 0.00 0.00 40.96 4.10
3737 17962 5.310409 TGGGACTTCAAAGAAGTTCTGAT 57.690 39.130 15.63 0.00 0.00 2.90
3741 17966 6.920210 GGGACTTCAAAGAAGTTCTGATTTTG 59.080 38.462 15.63 7.38 0.00 2.44
3937 18205 7.322664 ACATTGAATAAAATGTCGCCAATTCT 58.677 30.769 0.00 0.00 45.47 2.40
4102 18428 7.687941 ATGTTCGTCCATTCTAGAAATGTTT 57.312 32.000 9.71 0.00 0.00 2.83
4106 18432 4.438744 CGTCCATTCTAGAAATGTTTGCCC 60.439 45.833 9.71 0.00 0.00 5.36
4285 18637 9.467258 ACAGTTTCAAATATGTTCATGAGTTTG 57.533 29.630 0.00 4.73 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.879892 GAGGACATGGAGAAGTTAATGGC 59.120 47.826 0.00 0.00 0.00 4.40
9 10 4.122776 CCGAGGACATGGAGAAGTTAATG 58.877 47.826 0.00 0.00 0.00 1.90
13 14 1.645710 ACCGAGGACATGGAGAAGTT 58.354 50.000 0.00 0.00 0.00 2.66
15 16 4.408182 AAATACCGAGGACATGGAGAAG 57.592 45.455 0.00 0.00 0.00 2.85
17 18 3.517901 ACAAAATACCGAGGACATGGAGA 59.482 43.478 0.00 0.00 0.00 3.71
18 19 3.873910 ACAAAATACCGAGGACATGGAG 58.126 45.455 0.00 0.00 0.00 3.86
19 20 3.992943 ACAAAATACCGAGGACATGGA 57.007 42.857 0.00 0.00 0.00 3.41
20 21 4.261801 AGAACAAAATACCGAGGACATGG 58.738 43.478 0.00 0.00 0.00 3.66
21 22 5.178797 AGAGAACAAAATACCGAGGACATG 58.821 41.667 0.00 0.00 0.00 3.21
24 25 4.817517 TGAGAGAACAAAATACCGAGGAC 58.182 43.478 0.00 0.00 0.00 3.85
26 27 6.743575 AATTGAGAGAACAAAATACCGAGG 57.256 37.500 0.00 0.00 33.44 4.63
27 28 8.480643 AGTAATTGAGAGAACAAAATACCGAG 57.519 34.615 0.00 0.00 32.10 4.63
28 29 7.548075 GGAGTAATTGAGAGAACAAAATACCGA 59.452 37.037 0.00 0.00 32.10 4.69
30 31 7.201617 CCGGAGTAATTGAGAGAACAAAATACC 60.202 40.741 0.00 0.00 32.10 2.73
31 32 7.333672 ACCGGAGTAATTGAGAGAACAAAATAC 59.666 37.037 9.46 0.00 33.44 1.89
32 33 7.391620 ACCGGAGTAATTGAGAGAACAAAATA 58.608 34.615 9.46 0.00 33.44 1.40
33 34 6.238648 ACCGGAGTAATTGAGAGAACAAAAT 58.761 36.000 9.46 0.00 33.44 1.82
34 35 5.617252 ACCGGAGTAATTGAGAGAACAAAA 58.383 37.500 9.46 0.00 33.44 2.44
35 36 5.011738 AGACCGGAGTAATTGAGAGAACAAA 59.988 40.000 9.46 0.00 33.44 2.83
37 38 4.087182 AGACCGGAGTAATTGAGAGAACA 58.913 43.478 9.46 0.00 0.00 3.18
38 39 4.722361 AGACCGGAGTAATTGAGAGAAC 57.278 45.455 9.46 0.00 0.00 3.01
39 40 6.209986 TGTTTAGACCGGAGTAATTGAGAGAA 59.790 38.462 9.46 0.00 0.00 2.87
41 42 5.805994 GTGTTTAGACCGGAGTAATTGAGAG 59.194 44.000 9.46 0.00 0.00 3.20
43 44 4.868734 GGTGTTTAGACCGGAGTAATTGAG 59.131 45.833 9.46 0.00 0.00 3.02
44 45 4.529377 AGGTGTTTAGACCGGAGTAATTGA 59.471 41.667 9.46 0.00 41.35 2.57
46 47 5.012354 TGAAGGTGTTTAGACCGGAGTAATT 59.988 40.000 9.46 0.00 41.35 1.40
47 48 4.529377 TGAAGGTGTTTAGACCGGAGTAAT 59.471 41.667 9.46 0.00 41.35 1.89
48 49 3.896888 TGAAGGTGTTTAGACCGGAGTAA 59.103 43.478 9.46 1.70 41.35 2.24
49 50 3.256631 GTGAAGGTGTTTAGACCGGAGTA 59.743 47.826 9.46 0.00 41.35 2.59
50 51 2.036862 GTGAAGGTGTTTAGACCGGAGT 59.963 50.000 9.46 0.00 41.35 3.85
51 52 2.612221 GGTGAAGGTGTTTAGACCGGAG 60.612 54.545 9.46 0.00 41.35 4.63
53 54 1.071071 TGGTGAAGGTGTTTAGACCGG 59.929 52.381 0.00 0.00 41.35 5.28
54 55 2.140717 GTGGTGAAGGTGTTTAGACCG 58.859 52.381 0.00 0.00 41.35 4.79
55 56 3.139077 CTGTGGTGAAGGTGTTTAGACC 58.861 50.000 0.00 0.00 36.09 3.85
57 58 3.709653 ACTCTGTGGTGAAGGTGTTTAGA 59.290 43.478 0.00 0.00 0.00 2.10
58 59 4.073293 ACTCTGTGGTGAAGGTGTTTAG 57.927 45.455 0.00 0.00 0.00 1.85
62 63 2.628657 GTCTACTCTGTGGTGAAGGTGT 59.371 50.000 0.00 0.00 0.00 4.16
65 66 4.336889 TTTGTCTACTCTGTGGTGAAGG 57.663 45.455 0.00 0.00 0.00 3.46
67 68 6.260050 GTGAAATTTGTCTACTCTGTGGTGAA 59.740 38.462 0.00 0.00 0.00 3.18
68 69 5.758296 GTGAAATTTGTCTACTCTGTGGTGA 59.242 40.000 0.00 0.00 0.00 4.02
69 70 5.049405 GGTGAAATTTGTCTACTCTGTGGTG 60.049 44.000 0.00 0.00 0.00 4.17
72 73 6.348786 CCATGGTGAAATTTGTCTACTCTGTG 60.349 42.308 2.57 0.00 0.00 3.66
73 74 5.707298 CCATGGTGAAATTTGTCTACTCTGT 59.293 40.000 2.57 0.00 0.00 3.41
74 75 5.392380 GCCATGGTGAAATTTGTCTACTCTG 60.392 44.000 14.67 0.00 0.00 3.35
75 76 4.702131 GCCATGGTGAAATTTGTCTACTCT 59.298 41.667 14.67 0.00 0.00 3.24
76 77 4.437390 CGCCATGGTGAAATTTGTCTACTC 60.437 45.833 21.19 0.00 0.00 2.59
78 79 3.190535 ACGCCATGGTGAAATTTGTCTAC 59.809 43.478 31.66 0.00 0.00 2.59
79 80 3.417101 ACGCCATGGTGAAATTTGTCTA 58.583 40.909 31.66 0.00 0.00 2.59
81 82 2.030363 TGACGCCATGGTGAAATTTGTC 60.030 45.455 31.66 16.44 0.00 3.18
83 84 2.721274 TGACGCCATGGTGAAATTTG 57.279 45.000 31.66 5.22 0.00 2.32
84 85 3.587923 CATTGACGCCATGGTGAAATTT 58.412 40.909 31.66 8.83 0.00 1.82
85 86 2.674747 GCATTGACGCCATGGTGAAATT 60.675 45.455 31.66 9.25 0.00 1.82
86 87 1.135024 GCATTGACGCCATGGTGAAAT 60.135 47.619 31.66 24.11 0.00 2.17
87 88 0.243365 GCATTGACGCCATGGTGAAA 59.757 50.000 31.66 23.06 0.00 2.69
90 91 0.526739 CATGCATTGACGCCATGGTG 60.527 55.000 23.88 23.88 0.00 4.17
91 92 0.966875 ACATGCATTGACGCCATGGT 60.967 50.000 14.67 0.00 0.00 3.55
92 93 1.023502 TACATGCATTGACGCCATGG 58.976 50.000 7.63 7.63 0.00 3.66
94 95 1.942657 GAGTACATGCATTGACGCCAT 59.057 47.619 0.00 0.00 0.00 4.40
95 96 1.066215 AGAGTACATGCATTGACGCCA 60.066 47.619 0.00 0.00 0.00 5.69
96 97 1.594862 GAGAGTACATGCATTGACGCC 59.405 52.381 0.00 0.00 0.00 5.68
98 99 3.119291 GGAGAGAGTACATGCATTGACG 58.881 50.000 0.00 0.00 0.00 4.35
99 100 3.118629 TGGGAGAGAGTACATGCATTGAC 60.119 47.826 0.00 0.00 0.00 3.18
100 101 3.106827 TGGGAGAGAGTACATGCATTGA 58.893 45.455 0.00 0.00 0.00 2.57
101 102 3.548745 TGGGAGAGAGTACATGCATTG 57.451 47.619 0.00 0.00 0.00 2.82
104 105 2.042464 GGATGGGAGAGAGTACATGCA 58.958 52.381 0.00 0.00 32.77 3.96
106 107 1.615883 CCGGATGGGAGAGAGTACATG 59.384 57.143 0.00 0.00 38.47 3.21
107 108 1.499438 TCCGGATGGGAGAGAGTACAT 59.501 52.381 0.00 0.00 40.94 2.29
119 120 1.006832 GTTGATGAACGTCCGGATGG 58.993 55.000 27.02 15.61 0.00 3.51
125 126 3.935203 ACAGATGATGTTGATGAACGTCC 59.065 43.478 13.74 0.92 44.50 4.79
126 127 4.201753 CCACAGATGATGTTGATGAACGTC 60.202 45.833 10.02 10.02 45.09 4.34
128 129 3.486375 GCCACAGATGATGTTGATGAACG 60.486 47.826 0.00 0.00 41.41 3.95
129 130 3.693085 AGCCACAGATGATGTTGATGAAC 59.307 43.478 0.00 0.00 41.41 3.18
131 132 3.639672 AGCCACAGATGATGTTGATGA 57.360 42.857 0.00 0.00 41.41 2.92
132 133 4.713824 AAAGCCACAGATGATGTTGATG 57.286 40.909 0.00 0.00 41.41 3.07
133 134 4.641989 GGTAAAGCCACAGATGATGTTGAT 59.358 41.667 0.00 0.00 41.41 2.57
134 135 4.009675 GGTAAAGCCACAGATGATGTTGA 58.990 43.478 0.00 0.00 41.41 3.18
137 138 3.719268 TGGTAAAGCCACAGATGATGT 57.281 42.857 0.00 0.00 43.61 3.06
149 150 4.459337 GGGGATACTTGCATATGGTAAAGC 59.541 45.833 4.56 0.00 0.00 3.51
150 151 5.630121 TGGGGATACTTGCATATGGTAAAG 58.370 41.667 4.56 0.00 0.00 1.85
152 153 4.910913 TCTGGGGATACTTGCATATGGTAA 59.089 41.667 4.56 0.00 0.00 2.85
153 154 4.498493 TCTGGGGATACTTGCATATGGTA 58.502 43.478 4.56 0.00 0.00 3.25
155 156 3.584406 TCTCTGGGGATACTTGCATATGG 59.416 47.826 4.56 0.00 0.00 2.74
156 157 4.897509 TCTCTGGGGATACTTGCATATG 57.102 45.455 0.00 0.00 0.00 1.78
157 158 4.288105 CCTTCTCTGGGGATACTTGCATAT 59.712 45.833 0.00 0.00 0.00 1.78
158 159 3.648067 CCTTCTCTGGGGATACTTGCATA 59.352 47.826 0.00 0.00 0.00 3.14
159 160 2.441001 CCTTCTCTGGGGATACTTGCAT 59.559 50.000 0.00 0.00 0.00 3.96
160 161 1.839994 CCTTCTCTGGGGATACTTGCA 59.160 52.381 0.00 0.00 0.00 4.08
161 162 1.475930 GCCTTCTCTGGGGATACTTGC 60.476 57.143 0.00 0.00 0.00 4.01
162 163 1.202580 CGCCTTCTCTGGGGATACTTG 60.203 57.143 0.00 0.00 41.89 3.16
163 164 1.123928 CGCCTTCTCTGGGGATACTT 58.876 55.000 0.00 0.00 41.89 2.24
164 165 1.403687 GCGCCTTCTCTGGGGATACT 61.404 60.000 0.00 0.00 41.89 2.12
166 167 2.498941 CGCGCCTTCTCTGGGGATA 61.499 63.158 0.00 0.00 41.89 2.59
171 172 2.315038 GAAATGCGCGCCTTCTCTGG 62.315 60.000 30.77 0.00 0.00 3.86
172 173 1.061570 GAAATGCGCGCCTTCTCTG 59.938 57.895 30.77 0.00 0.00 3.35
173 174 1.078848 AGAAATGCGCGCCTTCTCT 60.079 52.632 29.48 24.23 0.00 3.10
174 175 1.061570 CAGAAATGCGCGCCTTCTC 59.938 57.895 31.26 23.76 0.00 2.87
175 176 3.044059 GCAGAAATGCGCGCCTTCT 62.044 57.895 29.48 29.48 0.00 2.85
176 177 2.577911 GCAGAAATGCGCGCCTTC 60.578 61.111 30.77 28.31 0.00 3.46
177 178 1.375853 TATGCAGAAATGCGCGCCTT 61.376 50.000 30.77 23.25 37.69 4.35
178 179 1.779025 CTATGCAGAAATGCGCGCCT 61.779 55.000 30.77 17.59 37.69 5.52
179 180 1.369689 CTATGCAGAAATGCGCGCC 60.370 57.895 30.77 13.41 37.69 6.53
181 182 1.191868 CTCTCTATGCAGAAATGCGCG 59.808 52.381 0.00 0.00 37.69 6.86
182 183 1.070041 GCTCTCTATGCAGAAATGCGC 60.070 52.381 0.00 0.00 37.69 6.09
183 184 2.207590 TGCTCTCTATGCAGAAATGCG 58.792 47.619 0.00 0.00 35.31 4.73
184 185 3.376234 TGTTGCTCTCTATGCAGAAATGC 59.624 43.478 0.00 0.00 41.71 3.56
185 186 5.556355 TTGTTGCTCTCTATGCAGAAATG 57.444 39.130 0.00 0.00 41.71 2.32
186 187 6.120905 AGATTGTTGCTCTCTATGCAGAAAT 58.879 36.000 0.00 0.00 41.71 2.17
187 188 5.494724 AGATTGTTGCTCTCTATGCAGAAA 58.505 37.500 0.00 0.00 41.71 2.52
188 189 5.095145 AGATTGTTGCTCTCTATGCAGAA 57.905 39.130 0.00 0.00 41.71 3.02
190 191 5.570344 CAAAGATTGTTGCTCTCTATGCAG 58.430 41.667 0.00 0.00 41.71 4.41
250 251 3.751175 TCATTTTTCTTGCGTCTAGTGGG 59.249 43.478 0.00 0.00 0.00 4.61
298 299 1.035385 CAAACCCAGCCCGGTATTCC 61.035 60.000 0.00 0.00 33.98 3.01
310 3188 2.030540 CGAGACGACTACTTCAAACCCA 60.031 50.000 0.00 0.00 0.00 4.51
311 3189 2.593257 CGAGACGACTACTTCAAACCC 58.407 52.381 0.00 0.00 0.00 4.11
329 3207 1.669115 GTGCAAAGGCTCTCTGCGA 60.669 57.895 10.45 0.20 44.05 5.10
331 3209 1.174712 TTGGTGCAAAGGCTCTCTGC 61.175 55.000 8.73 8.73 41.91 4.26
333 3211 2.299326 AATTGGTGCAAAGGCTCTCT 57.701 45.000 0.00 0.00 41.91 3.10
357 3235 3.711863 TGATAGCTCTTTGCCCCAAATT 58.288 40.909 0.00 0.00 44.23 1.82
373 3251 7.294017 AGGGTTCAATAAATGGCATTGATAG 57.706 36.000 14.47 5.16 40.94 2.08
447 3325 3.538591 TGCTGAGATGATGATGGTGAAC 58.461 45.455 0.00 0.00 0.00 3.18
587 3465 3.040147 TGGAGCTGGTTCTTTTACTCG 57.960 47.619 0.00 0.00 0.00 4.18
599 3477 3.508793 ACAAAGTCAAATGATGGAGCTGG 59.491 43.478 0.00 0.00 0.00 4.85
629 3507 3.305199 CGTCACCTTTTACTCTTCGTCCT 60.305 47.826 0.00 0.00 0.00 3.85
641 3519 3.326109 CGCCGTTCGTCACCTTTT 58.674 55.556 0.00 0.00 0.00 2.27
768 4728 2.380084 TGGAACGCAGGTAATCACTC 57.620 50.000 0.00 0.00 0.00 3.51
841 7607 3.482232 GATGAGATGGGGGTGGCCG 62.482 68.421 0.00 0.00 0.00 6.13
842 7608 2.517919 GATGAGATGGGGGTGGCC 59.482 66.667 0.00 0.00 0.00 5.36
843 7609 2.081161 AGGATGAGATGGGGGTGGC 61.081 63.158 0.00 0.00 0.00 5.01
870 7646 2.806945 TGGGAAAGGTGATGGATGAC 57.193 50.000 0.00 0.00 0.00 3.06
899 7675 1.227943 TGCCTGGCTTGTGTGAGAC 60.228 57.895 21.03 0.00 0.00 3.36
978 7821 1.198637 GATCTGTGGCAGTTGCTGTTC 59.801 52.381 3.88 0.00 41.70 3.18
1167 8066 2.353406 GCTGTAGTTGGAGTAGCCGAAA 60.353 50.000 0.00 0.00 40.66 3.46
1254 8687 5.983540 AGAAAACACACAAAGGGCATTTTA 58.016 33.333 0.00 0.00 0.00 1.52
1256 8689 4.486125 AGAAAACACACAAAGGGCATTT 57.514 36.364 0.00 0.00 0.00 2.32
1257 8690 4.190772 CAAGAAAACACACAAAGGGCATT 58.809 39.130 0.00 0.00 0.00 3.56
1258 8691 3.795877 CAAGAAAACACACAAAGGGCAT 58.204 40.909 0.00 0.00 0.00 4.40
1259 8692 2.676463 GCAAGAAAACACACAAAGGGCA 60.676 45.455 0.00 0.00 0.00 5.36
1388 8873 2.594592 ACTCCAACCACTTGCGGC 60.595 61.111 0.00 0.00 0.00 6.53
1422 8939 1.742411 GCTAATGCTCAACCGCCAGTA 60.742 52.381 0.00 0.00 36.03 2.74
1450 8967 5.243954 AGCCTTGAAAGACCCAAATTAACTC 59.756 40.000 0.00 0.00 0.00 3.01
1620 9165 2.229784 GGCAAGTGTGAGATTTCCCTTG 59.770 50.000 0.00 0.00 34.03 3.61
1631 9176 2.260844 CCTTTCTCAGGCAAGTGTGA 57.739 50.000 0.00 0.00 35.13 3.58
1765 9322 4.280929 TCACCGAATGAAGTCTCTTGAGAA 59.719 41.667 1.51 0.00 33.02 2.87
1769 9326 3.919216 AGTCACCGAATGAAGTCTCTTG 58.081 45.455 0.00 0.00 39.72 3.02
1770 9327 4.561105 GAAGTCACCGAATGAAGTCTCTT 58.439 43.478 0.00 0.00 39.72 2.85
1886 12422 9.438291 CAGATTATCGACAATTGAACATAAACC 57.562 33.333 13.59 7.30 0.00 3.27
1963 12827 8.968242 CAGAAAACATTAAAAGAAGGTAACAGC 58.032 33.333 0.00 0.00 41.41 4.40
2048 12922 6.072508 CCAATATTCTGATTCCCAATACCACG 60.073 42.308 0.00 0.00 0.00 4.94
2086 13525 3.322369 TGGCTTCGTTACACATACACAG 58.678 45.455 0.00 0.00 0.00 3.66
2184 13640 6.311445 CAGTCAAGACATGTATGTTGACCTAC 59.689 42.308 28.11 15.03 44.02 3.18
2272 14423 7.061557 GTCAAGAAATTGAAGACTTTATGCAGC 59.938 37.037 0.00 0.00 32.04 5.25
2343 14514 8.489489 ACCAGAATACACTCATTAGATGATGTT 58.511 33.333 9.55 0.00 38.85 2.71
3028 17104 2.457366 ACGAAACCAGTAGCCAGAAG 57.543 50.000 0.00 0.00 0.00 2.85
3057 17133 1.941975 TCCTGCGATTATGTGCACATG 59.058 47.619 36.72 23.22 37.15 3.21
3064 17145 3.244353 CCTCCTGATTCCTGCGATTATGT 60.244 47.826 0.00 0.00 0.00 2.29
3078 17184 1.280998 CAACCGGTTTACCCTCCTGAT 59.719 52.381 19.55 0.00 0.00 2.90
3092 17205 1.879380 TCTCAAGCACATTTCAACCGG 59.121 47.619 0.00 0.00 0.00 5.28
3108 17221 3.181451 ACTGAAATCTGGCAAGTGTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
3110 17223 3.498774 ACTGAAATCTGGCAAGTGTCT 57.501 42.857 0.00 0.00 0.00 3.41
3120 17272 3.119884 TGCGTGCCAATAACTGAAATCTG 60.120 43.478 0.00 0.00 0.00 2.90
3134 17286 1.026182 GTGATGAAGGATGCGTGCCA 61.026 55.000 0.00 0.00 0.00 4.92
3186 17338 4.314740 ACTCCTAGAATAAAGCTGAGCG 57.685 45.455 0.00 0.00 0.00 5.03
3210 17362 3.884895 TCCATCACAAGGCGTTCATAAT 58.115 40.909 0.00 0.00 0.00 1.28
3269 17422 9.393786 AGGTACCCACATCATATATTACTCTTT 57.606 33.333 8.74 0.00 0.00 2.52
3284 17437 4.413520 AGAGCATTATTCAGGTACCCACAT 59.586 41.667 8.74 0.10 0.00 3.21
3285 17438 3.780294 AGAGCATTATTCAGGTACCCACA 59.220 43.478 8.74 0.00 0.00 4.17
3287 17440 3.780294 ACAGAGCATTATTCAGGTACCCA 59.220 43.478 8.74 0.00 0.00 4.51
3299 17468 4.645762 TTGCACAACAAACAGAGCATTA 57.354 36.364 0.00 0.00 34.56 1.90
3355 17530 1.639722 TCCTCCCGACATTGTCTTCA 58.360 50.000 14.54 0.00 0.00 3.02
3363 17538 1.645710 ACTGAACTTCCTCCCGACAT 58.354 50.000 0.00 0.00 0.00 3.06
3365 17540 2.545537 AAACTGAACTTCCTCCCGAC 57.454 50.000 0.00 0.00 0.00 4.79
3370 17545 5.049336 GGCAAAGACTAAACTGAACTTCCTC 60.049 44.000 0.00 0.00 0.00 3.71
3446 17621 1.616725 CCACAAGAAGCAATAGCCCCA 60.617 52.381 0.00 0.00 43.56 4.96
3485 17660 6.931840 GGTGGGTAATATTTTGCAACTTTGAA 59.068 34.615 0.00 0.00 0.00 2.69
3563 17744 4.181010 CTACTGCATGGGCCGGCT 62.181 66.667 28.56 2.77 40.13 5.52
3643 17839 7.603963 AAACAACGAAATTTAAAAAGCAGGT 57.396 28.000 0.00 0.00 0.00 4.00
3709 17934 9.231297 CAGAACTTCTTTGAAGTCCCAAATATA 57.769 33.333 12.53 0.00 35.72 0.86
3710 17935 7.944554 TCAGAACTTCTTTGAAGTCCCAAATAT 59.055 33.333 12.53 0.00 35.72 1.28
3711 17936 7.287061 TCAGAACTTCTTTGAAGTCCCAAATA 58.713 34.615 12.53 0.00 35.72 1.40
3913 18181 7.760131 AGAATTGGCGACATTTTATTCAATG 57.240 32.000 14.28 0.00 42.32 2.82
4042 18313 8.688747 ATTGGTGGAGCAATTTTAAAATTCAA 57.311 26.923 20.71 18.60 36.52 2.69
4050 18321 8.511604 TTTTGAAAATTGGTGGAGCAATTTTA 57.488 26.923 28.82 18.46 45.39 1.52
4058 18383 8.434661 CGAACATTATTTTGAAAATTGGTGGAG 58.565 33.333 8.60 0.00 0.00 3.86
4076 18401 8.786826 AACATTTCTAGAATGGACGAACATTA 57.213 30.769 5.89 0.00 40.92 1.90
4102 18428 8.511604 TTTTTAACAATTTTCTTGAATGGGCA 57.488 26.923 0.00 0.00 0.00 5.36
4184 18518 9.833894 CAAACGTTTTCTAAAATCAAGAACATG 57.166 29.630 11.66 0.00 32.81 3.21


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

AutoCloner maintained by Alex Coulton.