Multiple sequence alignment - TraesCS7A01G267600

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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 TraesCS7A01G267600 chr7A 100.000 9603 0 0 1 9603 270891312 270881710 0.000000e+00 17734
1 TraesCS7A01G267600 chr7A 96.633 3950 116 10 3749 7692 379802737 379806675 0.000000e+00 6541
2 TraesCS7A01G267600 chr7A 95.294 3952 164 14 3749 7692 71873229 71877166 0.000000e+00 6248
3 TraesCS7A01G267600 chr7A 95.313 3947 164 16 3749 7687 71995210 71999143 0.000000e+00 6244
4 TraesCS7A01G267600 chr7A 94.947 3958 158 27 3749 7692 343937427 343933498 0.000000e+00 6163
5 TraesCS7A01G267600 chr7A 94.923 3959 157 27 3749 7692 343946308 343942379 0.000000e+00 6157
6 TraesCS7A01G267600 chr7A 94.534 3952 170 17 3749 7687 479772654 479776572 0.000000e+00 6059
7 TraesCS7A01G267600 chr7A 94.008 3972 175 38 3749 7692 392307321 392303385 0.000000e+00 5958
8 TraesCS7A01G267600 chr7A 95.971 2209 80 5 1537 3744 527906306 527908506 0.000000e+00 3578
9 TraesCS7A01G267600 chr7A 93.764 1732 75 14 7694 9419 527908510 527910214 0.000000e+00 2569
10 TraesCS7A01G267600 chr7A 95.352 1506 63 3 1 1505 527904817 527906316 0.000000e+00 2386
11 TraesCS7A01G267600 chr7A 86.329 2231 256 30 1535 3748 461484275 461482077 0.000000e+00 2385
12 TraesCS7A01G267600 chr7A 96.575 730 23 2 2937 3665 734698272 734699000 0.000000e+00 1208
13 TraesCS7A01G267600 chr7A 89.003 291 31 1 3408 3697 622252206 622252496 9.170000e-95 359
14 TraesCS7A01G267600 chr7A 96.667 180 4 2 9420 9598 270863404 270863226 2.030000e-76 298
15 TraesCS7A01G267600 chr7A 95.000 180 7 2 9420 9598 270850930 270850752 2.040000e-71 281
16 TraesCS7A01G267600 chr7A 93.011 186 11 2 9420 9603 212917190 212917375 4.420000e-68 270
17 TraesCS7A01G267600 chr1A 95.371 3953 156 16 3749 7687 302426932 302422993 0.000000e+00 6261
18 TraesCS7A01G267600 chr1A 91.935 186 13 2 9420 9603 185377228 185377043 9.570000e-65 259
19 TraesCS7A01G267600 chr3A 95.182 3964 151 11 3746 7692 98157321 98161261 0.000000e+00 6226
20 TraesCS7A01G267600 chr3A 93.323 3954 232 22 3751 7692 29978927 29974994 0.000000e+00 5810
21 TraesCS7A01G267600 chr3A 94.773 1014 39 7 3749 4761 98177631 98178631 0.000000e+00 1567
22 TraesCS7A01G267600 chr3A 84.883 1495 174 30 7966 9420 352091206 352092688 0.000000e+00 1461
23 TraesCS7A01G267600 chr3A 89.216 918 79 9 7732 8641 707859174 707860079 0.000000e+00 1129
24 TraesCS7A01G267600 chr3A 84.567 1121 148 16 8307 9419 554370181 554371284 0.000000e+00 1088
25 TraesCS7A01G267600 chr3A 83.188 1029 134 22 8387 9414 163166438 163165448 0.000000e+00 905
26 TraesCS7A01G267600 chr3A 86.099 446 41 7 7962 8388 163167042 163166599 2.440000e-125 460
27 TraesCS7A01G267600 chr3A 83.978 362 39 6 7966 8308 554369716 554370077 7.190000e-86 329
28 TraesCS7A01G267600 chr1D 88.115 3761 377 45 1 3742 162594225 162597934 0.000000e+00 4405
29 TraesCS7A01G267600 chr1D 87.526 2421 234 40 1339 3748 485426492 485424129 0.000000e+00 2736
30 TraesCS7A01G267600 chr1D 88.571 1540 158 12 1 1531 42044147 42042617 0.000000e+00 1853
31 TraesCS7A01G267600 chr1D 82.565 998 127 25 8055 9013 485424045 485423056 0.000000e+00 835
32 TraesCS7A01G267600 chr1D 82.371 1004 124 25 8055 9013 42040377 42039382 0.000000e+00 824
33 TraesCS7A01G267600 chr1D 81.665 1009 121 35 8055 9013 424879705 424878711 0.000000e+00 780
34 TraesCS7A01G267600 chr1D 88.462 442 49 2 8978 9419 485423054 485422615 5.110000e-147 532
35 TraesCS7A01G267600 chr5A 97.463 2207 55 1 1541 3746 553299052 553296846 0.000000e+00 3764
36 TraesCS7A01G267600 chr5A 96.998 1732 50 2 7690 9420 553296848 553295118 0.000000e+00 2909
37 TraesCS7A01G267600 chr5A 88.367 2192 204 36 1564 3742 617310922 617308769 0.000000e+00 2588
38 TraesCS7A01G267600 chr5A 96.811 1505 42 4 1 1503 553300544 553299044 0.000000e+00 2508
39 TraesCS7A01G267600 chr5A 81.972 1004 121 32 8057 9013 370094093 370095083 0.000000e+00 797
40 TraesCS7A01G267600 chr5A 96.610 177 4 2 9422 9596 311106708 311106532 9.430000e-75 292
41 TraesCS7A01G267600 chr5A 96.023 176 5 2 9422 9596 311096708 311096534 1.580000e-72 285
42 TraesCS7A01G267600 chr6D 96.930 2215 57 5 1535 3746 6824631 6826837 0.000000e+00 3703
43 TraesCS7A01G267600 chr6D 94.825 1739 71 9 7690 9419 6826835 6828563 0.000000e+00 2695
44 TraesCS7A01G267600 chr6D 88.235 2210 205 40 1551 3748 360751653 360749487 0.000000e+00 2590
45 TraesCS7A01G267600 chr6D 96.291 1510 48 4 1 1509 6823143 6824645 0.000000e+00 2471
46 TraesCS7A01G267600 chr6D 82.851 1003 120 27 8055 9013 360749403 360748409 0.000000e+00 852
47 TraesCS7A01G267600 chr2D 96.707 1913 57 2 1628 3539 649294990 649296897 0.000000e+00 3179
48 TraesCS7A01G267600 chr2D 97.277 1836 42 4 1537 3370 12730102 12728273 0.000000e+00 3107
49 TraesCS7A01G267600 chr2D 95.172 1740 63 11 7690 9419 12727954 12726226 0.000000e+00 2728
50 TraesCS7A01G267600 chr2D 82.517 1001 120 25 8055 9013 417245713 417244726 0.000000e+00 828
51 TraesCS7A01G267600 chr2A 88.311 2652 255 36 3749 6383 711165185 711162572 0.000000e+00 3129
52 TraesCS7A01G267600 chr2A 88.504 2192 201 37 1564 3742 171836712 171838865 0.000000e+00 2604
53 TraesCS7A01G267600 chr3D 92.053 1963 134 9 1545 3498 573207412 573209361 0.000000e+00 2741
54 TraesCS7A01G267600 chr3D 89.033 1468 126 13 7732 9185 573209692 573211138 0.000000e+00 1786
55 TraesCS7A01G267600 chr5D 86.957 2231 223 37 1540 3748 201706441 201704257 0.000000e+00 2446
56 TraesCS7A01G267600 chr4B 90.148 1482 136 8 1 1474 622887767 622886288 0.000000e+00 1919
57 TraesCS7A01G267600 chr4B 89.939 1481 139 8 1 1474 445327872 445329349 0.000000e+00 1901
58 TraesCS7A01G267600 chr3B 90.142 1481 137 7 1 1474 777040625 777039147 0.000000e+00 1917
59 TraesCS7A01G267600 chr6A 89.818 1483 139 9 1 1474 46108757 46110236 0.000000e+00 1892
60 TraesCS7A01G267600 chr6A 72.573 649 130 34 8800 9423 532634918 532634293 1.660000e-37 169
61 TraesCS7A01G267600 chr2B 84.621 1476 168 26 7966 9398 726916038 726914579 0.000000e+00 1413
62 TraesCS7A01G267600 chr2B 85.761 927 100 20 2829 3742 726917175 726916268 0.000000e+00 952
63 TraesCS7A01G267600 chr7D 82.762 992 130 19 8055 9013 608289858 608288875 0.000000e+00 846
64 TraesCS7A01G267600 chr7D 88.688 442 48 2 8978 9419 346625190 346624751 1.100000e-148 538
65 TraesCS7A01G267600 chrUn 81.149 801 106 22 8055 8815 269558593 269559388 1.380000e-167 601
66 TraesCS7A01G267600 chrUn 73.239 568 118 18 8803 9363 326892309 326891769 9.910000e-40 176
67 TraesCS7A01G267600 chr4A 94.086 186 9 2 9420 9603 217664735 217664550 2.040000e-71 281
68 TraesCS7A01G267600 chr4A 93.548 186 9 3 9420 9602 441204566 441204381 3.420000e-69 274
69 TraesCS7A01G267600 chr4A 92.021 188 9 4 9420 9603 299745915 299746100 9.570000e-65 259


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 TraesCS7A01G267600 chr7A 270881710 270891312 9602 True 17734.000000 17734 100.000000 1 9603 1 chr7A.!!$R3 9602
1 TraesCS7A01G267600 chr7A 379802737 379806675 3938 False 6541.000000 6541 96.633000 3749 7692 1 chr7A.!!$F4 3943
2 TraesCS7A01G267600 chr7A 71873229 71877166 3937 False 6248.000000 6248 95.294000 3749 7692 1 chr7A.!!$F1 3943
3 TraesCS7A01G267600 chr7A 71995210 71999143 3933 False 6244.000000 6244 95.313000 3749 7687 1 chr7A.!!$F2 3938
4 TraesCS7A01G267600 chr7A 343933498 343937427 3929 True 6163.000000 6163 94.947000 3749 7692 1 chr7A.!!$R4 3943
5 TraesCS7A01G267600 chr7A 343942379 343946308 3929 True 6157.000000 6157 94.923000 3749 7692 1 chr7A.!!$R5 3943
6 TraesCS7A01G267600 chr7A 479772654 479776572 3918 False 6059.000000 6059 94.534000 3749 7687 1 chr7A.!!$F5 3938
7 TraesCS7A01G267600 chr7A 392303385 392307321 3936 True 5958.000000 5958 94.008000 3749 7692 1 chr7A.!!$R6 3943
8 TraesCS7A01G267600 chr7A 527904817 527910214 5397 False 2844.333333 3578 95.029000 1 9419 3 chr7A.!!$F8 9418
9 TraesCS7A01G267600 chr7A 461482077 461484275 2198 True 2385.000000 2385 86.329000 1535 3748 1 chr7A.!!$R7 2213
10 TraesCS7A01G267600 chr7A 734698272 734699000 728 False 1208.000000 1208 96.575000 2937 3665 1 chr7A.!!$F7 728
11 TraesCS7A01G267600 chr1A 302422993 302426932 3939 True 6261.000000 6261 95.371000 3749 7687 1 chr1A.!!$R2 3938
12 TraesCS7A01G267600 chr3A 98157321 98161261 3940 False 6226.000000 6226 95.182000 3746 7692 1 chr3A.!!$F1 3946
13 TraesCS7A01G267600 chr3A 29974994 29978927 3933 True 5810.000000 5810 93.323000 3751 7692 1 chr3A.!!$R1 3941
14 TraesCS7A01G267600 chr3A 98177631 98178631 1000 False 1567.000000 1567 94.773000 3749 4761 1 chr3A.!!$F2 1012
15 TraesCS7A01G267600 chr3A 352091206 352092688 1482 False 1461.000000 1461 84.883000 7966 9420 1 chr3A.!!$F3 1454
16 TraesCS7A01G267600 chr3A 707859174 707860079 905 False 1129.000000 1129 89.216000 7732 8641 1 chr3A.!!$F4 909
17 TraesCS7A01G267600 chr3A 554369716 554371284 1568 False 708.500000 1088 84.272500 7966 9419 2 chr3A.!!$F5 1453
18 TraesCS7A01G267600 chr3A 163165448 163167042 1594 True 682.500000 905 84.643500 7962 9414 2 chr3A.!!$R2 1452
19 TraesCS7A01G267600 chr1D 162594225 162597934 3709 False 4405.000000 4405 88.115000 1 3742 1 chr1D.!!$F1 3741
20 TraesCS7A01G267600 chr1D 485422615 485426492 3877 True 1367.666667 2736 86.184333 1339 9419 3 chr1D.!!$R3 8080
21 TraesCS7A01G267600 chr1D 42039382 42044147 4765 True 1338.500000 1853 85.471000 1 9013 2 chr1D.!!$R2 9012
22 TraesCS7A01G267600 chr1D 424878711 424879705 994 True 780.000000 780 81.665000 8055 9013 1 chr1D.!!$R1 958
23 TraesCS7A01G267600 chr5A 553295118 553300544 5426 True 3060.333333 3764 97.090667 1 9420 3 chr5A.!!$R4 9419
24 TraesCS7A01G267600 chr5A 617308769 617310922 2153 True 2588.000000 2588 88.367000 1564 3742 1 chr5A.!!$R3 2178
25 TraesCS7A01G267600 chr5A 370094093 370095083 990 False 797.000000 797 81.972000 8057 9013 1 chr5A.!!$F1 956
26 TraesCS7A01G267600 chr6D 6823143 6828563 5420 False 2956.333333 3703 96.015333 1 9419 3 chr6D.!!$F1 9418
27 TraesCS7A01G267600 chr6D 360748409 360751653 3244 True 1721.000000 2590 85.543000 1551 9013 2 chr6D.!!$R1 7462
28 TraesCS7A01G267600 chr2D 649294990 649296897 1907 False 3179.000000 3179 96.707000 1628 3539 1 chr2D.!!$F1 1911
29 TraesCS7A01G267600 chr2D 12726226 12730102 3876 True 2917.500000 3107 96.224500 1537 9419 2 chr2D.!!$R2 7882
30 TraesCS7A01G267600 chr2D 417244726 417245713 987 True 828.000000 828 82.517000 8055 9013 1 chr2D.!!$R1 958
31 TraesCS7A01G267600 chr2A 711162572 711165185 2613 True 3129.000000 3129 88.311000 3749 6383 1 chr2A.!!$R1 2634
32 TraesCS7A01G267600 chr2A 171836712 171838865 2153 False 2604.000000 2604 88.504000 1564 3742 1 chr2A.!!$F1 2178
33 TraesCS7A01G267600 chr3D 573207412 573211138 3726 False 2263.500000 2741 90.543000 1545 9185 2 chr3D.!!$F1 7640
34 TraesCS7A01G267600 chr5D 201704257 201706441 2184 True 2446.000000 2446 86.957000 1540 3748 1 chr5D.!!$R1 2208
35 TraesCS7A01G267600 chr4B 622886288 622887767 1479 True 1919.000000 1919 90.148000 1 1474 1 chr4B.!!$R1 1473
36 TraesCS7A01G267600 chr4B 445327872 445329349 1477 False 1901.000000 1901 89.939000 1 1474 1 chr4B.!!$F1 1473
37 TraesCS7A01G267600 chr3B 777039147 777040625 1478 True 1917.000000 1917 90.142000 1 1474 1 chr3B.!!$R1 1473
38 TraesCS7A01G267600 chr6A 46108757 46110236 1479 False 1892.000000 1892 89.818000 1 1474 1 chr6A.!!$F1 1473
39 TraesCS7A01G267600 chr2B 726914579 726917175 2596 True 1182.500000 1413 85.191000 2829 9398 2 chr2B.!!$R1 6569
40 TraesCS7A01G267600 chr7D 608288875 608289858 983 True 846.000000 846 82.762000 8055 9013 1 chr7D.!!$R2 958
41 TraesCS7A01G267600 chrUn 269558593 269559388 795 False 601.000000 601 81.149000 8055 8815 1 chrUn.!!$F1 760

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
696 702 3.982475 GAGCATGACTCGGAATATGACA 58.018 45.455 0.00 0.00 35.18 3.58 F
1021 1029 0.179018 GGGCCGCTTGAATCATAGGT 60.179 55.000 0.00 0.00 0.00 3.08 F
1427 1437 0.253327 CCCTGGCCCAGAAGTAAGAC 59.747 60.000 13.74 0.00 32.44 3.01 F
2109 2150 1.745653 GTGGTGCTGAATTTAGAGGGC 59.254 52.381 0.58 0.00 0.00 5.19 F
2375 2419 1.822114 TTTGCATCGAGGGACCGACA 61.822 55.000 0.00 0.00 41.70 4.35 F
3746 3857 2.666272 TGGTTGGACCATGTTTGCTA 57.334 45.000 0.00 0.00 44.79 3.49 F
4444 4570 0.469144 ATTCCTCTCCTCTCCCTCGC 60.469 60.000 0.00 0.00 0.00 5.03 F
5600 5733 0.539051 ACCTATCAGTGGAGCAGTGC 59.461 55.000 7.13 7.13 35.04 4.40 F
7292 7440 1.053835 TCAGGACACTTGACTGGCCA 61.054 55.000 4.71 4.71 42.70 5.36 F
7499 7647 3.007635 GTTAGCACCGCTTTAGGTTCAT 58.992 45.455 0.00 0.00 43.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2027 2.752903 GCCAACGGTTACCATTCTCATT 59.247 45.455 1.13 0.00 0.00 2.57 R
2134 2175 5.216622 AGACTGTATCCCCATTAGCAAGTA 58.783 41.667 0.00 0.00 0.00 2.24 R
2375 2419 6.949352 TCTTTGACTGCAAATCTTCTCTTT 57.051 33.333 0.00 0.00 42.66 2.52 R
3747 3858 3.454858 ACCAGAACTAGGGATGTGACAT 58.545 45.455 0.00 0.00 0.00 3.06 R
4423 4549 1.410932 CGAGGGAGAGGAGAGGAATGT 60.411 57.143 0.00 0.00 0.00 2.71 R
4866 4994 0.244721 GGTTTGCGTCTACGGGTAGT 59.755 55.000 4.49 0.00 40.23 2.73 R
6217 6353 0.251832 ACCTCGCCGGATGGATCTAT 60.252 55.000 5.05 0.00 37.49 1.98 R
7390 7538 0.976641 CACTGGGCTAACAGGACTCA 59.023 55.000 8.13 0.00 42.75 3.41 R
8339 8657 1.002087 CAAGTGACCTACAGGGACCAC 59.998 57.143 0.00 5.15 40.01 4.16 R
9535 10115 0.036010 AGAGTCCAAATGAGGTGCGG 60.036 55.000 0.00 0.00 0.00 5.69 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
72 75 5.083122 TGTCTTCCTTCATCTCAGAGACTT 58.917 41.667 0.91 0.00 0.00 3.01
86 89 8.815565 TCTCAGAGACTTAACATCTTGAGTAT 57.184 34.615 0.00 0.00 35.33 2.12
98 101 8.668510 AACATCTTGAGTATTATGGTGTCATC 57.331 34.615 0.00 0.00 34.96 2.92
464 467 8.637986 AGTTTTTCTGTAGATGTTGGCAAATTA 58.362 29.630 0.00 0.00 0.00 1.40
465 468 9.423061 GTTTTTCTGTAGATGTTGGCAAATTAT 57.577 29.630 0.00 0.00 0.00 1.28
475 478 8.316214 AGATGTTGGCAAATTATTTGATGAGTT 58.684 29.630 20.37 1.83 43.26 3.01
480 483 7.609960 TGGCAAATTATTTGATGAGTTTGCTA 58.390 30.769 20.37 10.54 46.25 3.49
696 702 3.982475 GAGCATGACTCGGAATATGACA 58.018 45.455 0.00 0.00 35.18 3.58
701 707 5.107182 GCATGACTCGGAATATGACAATGAG 60.107 44.000 0.00 0.00 0.00 2.90
913 919 9.559958 CTGTTACATAACATTTCATGTCCTTTC 57.440 33.333 4.98 0.00 44.34 2.62
1021 1029 0.179018 GGGCCGCTTGAATCATAGGT 60.179 55.000 0.00 0.00 0.00 3.08
1038 1046 2.609747 AGGTGTTTCTCAGTGCCTAGA 58.390 47.619 0.00 0.00 0.00 2.43
1044 1052 2.836636 TCTCAGTGCCTAGACTGGAT 57.163 50.000 10.73 0.00 43.16 3.41
1215 1223 9.946165 GTGTAAGTATTAAATATTCCAACTGCC 57.054 33.333 0.00 0.00 28.70 4.85
1216 1224 9.127277 TGTAAGTATTAAATATTCCAACTGCCC 57.873 33.333 0.00 0.00 28.70 5.36
1254 1262 9.090692 GCAATATTCATGTGCTAACAATCTTTT 57.909 29.630 0.00 0.00 40.46 2.27
1427 1437 0.253327 CCCTGGCCCAGAAGTAAGAC 59.747 60.000 13.74 0.00 32.44 3.01
1986 2027 4.100344 TGCCTACACAACTAACAGAAGTGA 59.900 41.667 0.00 0.00 34.47 3.41
2109 2150 1.745653 GTGGTGCTGAATTTAGAGGGC 59.254 52.381 0.58 0.00 0.00 5.19
2134 2175 7.554476 GCTATCCTTAAGAAACAAGAGGAACAT 59.446 37.037 3.36 0.00 39.74 2.71
2375 2419 1.822114 TTTGCATCGAGGGACCGACA 61.822 55.000 0.00 0.00 41.70 4.35
3539 3646 5.799936 GCTCTTATTTCTTATGCGCAAAACA 59.200 36.000 17.11 0.00 0.00 2.83
3746 3857 2.666272 TGGTTGGACCATGTTTGCTA 57.334 45.000 0.00 0.00 44.79 3.49
3747 3858 2.950781 TGGTTGGACCATGTTTGCTAA 58.049 42.857 0.00 0.00 44.79 3.09
4423 4549 1.979155 CCTCTCACTCTCCCGTGCA 60.979 63.158 0.00 0.00 34.92 4.57
4444 4570 0.469144 ATTCCTCTCCTCTCCCTCGC 60.469 60.000 0.00 0.00 0.00 5.03
4445 4571 1.576368 TTCCTCTCCTCTCCCTCGCT 61.576 60.000 0.00 0.00 0.00 4.93
4446 4572 1.528309 CCTCTCCTCTCCCTCGCTC 60.528 68.421 0.00 0.00 0.00 5.03
4447 4573 1.531748 CTCTCCTCTCCCTCGCTCT 59.468 63.158 0.00 0.00 0.00 4.09
4823 4951 1.194495 CGCCGTCGATTTAGTACACC 58.806 55.000 0.00 0.00 38.10 4.16
4866 4994 0.815095 TAGATGCGCGAGACCTTCAA 59.185 50.000 12.10 0.00 0.00 2.69
4972 5102 2.847234 AACTCCGGTGGGCTGACA 60.847 61.111 8.63 0.00 0.00 3.58
5013 5143 1.880941 ATCACCACTAACCCCTCTCC 58.119 55.000 0.00 0.00 0.00 3.71
5048 5178 2.739132 GGGCCCCGTAATAGGTCG 59.261 66.667 12.23 0.00 0.00 4.79
5063 5193 1.909302 AGGTCGAATCCCAGTCAACAT 59.091 47.619 0.00 0.00 0.00 2.71
5600 5733 0.539051 ACCTATCAGTGGAGCAGTGC 59.461 55.000 7.13 7.13 35.04 4.40
5926 6062 2.029020 TGCTGAGAGTTAAGCGTGTGAT 60.029 45.455 0.00 0.00 42.54 3.06
6217 6353 2.281208 GGCACGGTGTACCAAGCA 60.281 61.111 10.24 0.00 37.23 3.91
6328 6465 3.233507 ACCCGAATAGGCGATAAACCTA 58.766 45.455 0.00 0.00 43.80 3.08
6333 6470 5.154932 CGAATAGGCGATAAACCTAGACTG 58.845 45.833 0.00 0.00 42.94 3.51
6593 6730 1.565759 TGAGTGCTATGGATGGCCTTT 59.434 47.619 3.32 0.00 32.80 3.11
6774 6911 8.377799 TGATACAAGTGCATGTATGATAGGATT 58.622 33.333 15.90 0.00 44.44 3.01
6924 7071 2.694109 GTTGTAGATAGTCGGGCTCCTT 59.306 50.000 0.00 0.00 0.00 3.36
7146 7294 1.939934 CGTGTATTGCTATGTGTGGGG 59.060 52.381 0.00 0.00 0.00 4.96
7243 7391 2.509336 CTGCTACAGCCCGGTTCG 60.509 66.667 0.00 0.00 41.18 3.95
7292 7440 1.053835 TCAGGACACTTGACTGGCCA 61.054 55.000 4.71 4.71 42.70 5.36
7390 7538 4.342086 TACAGCCCGGGTTCCCCT 62.342 66.667 24.63 7.12 42.67 4.79
7499 7647 3.007635 GTTAGCACCGCTTTAGGTTCAT 58.992 45.455 0.00 0.00 43.00 2.57
7701 7849 3.494332 GTCCCGATAGCTAAACCCTCTA 58.506 50.000 0.00 0.00 0.00 2.43
7704 7852 5.892686 GTCCCGATAGCTAAACCCTCTATAT 59.107 44.000 0.00 0.00 0.00 0.86
7763 7930 6.319658 ACACATGCAGCTAGTATATGCTTTTT 59.680 34.615 0.00 0.00 40.62 1.94
7792 7959 5.283294 TGTTTGAAACAAGATCACATGCAG 58.717 37.500 8.51 0.00 38.72 4.41
7832 8007 8.276252 ACTTTACAAACTTGAGCTAAACTGAA 57.724 30.769 0.00 0.00 0.00 3.02
8272 8480 6.439692 AGGATCAAAAGGAAAATCAGCAATCT 59.560 34.615 0.00 0.00 0.00 2.40
8432 8913 2.046507 GCAGGACTGGAGGCAGTG 60.047 66.667 0.00 0.00 35.23 3.66
8470 8951 6.318112 TGATGATGAGGATGACTACTATGGT 58.682 40.000 0.00 0.00 0.00 3.55
8795 9317 4.746535 TCGGATGCAACTCAATACCTTA 57.253 40.909 0.00 0.00 0.00 2.69
8910 9454 2.238898 GGTGAGTAATGCCCTAAGGTGT 59.761 50.000 0.00 0.00 34.57 4.16
9168 9748 4.324991 GCCCGACCAGGAACCGTT 62.325 66.667 0.00 0.00 45.00 4.44
9426 10006 7.598759 TGAAATATCTAGTAGTGGAGGAACC 57.401 40.000 0.00 0.00 39.54 3.62
9427 10007 6.264744 TGAAATATCTAGTAGTGGAGGAACCG 59.735 42.308 0.00 0.00 42.61 4.44
9428 10008 3.666345 ATCTAGTAGTGGAGGAACCGT 57.334 47.619 0.00 0.00 42.61 4.83
9429 10009 4.785346 ATCTAGTAGTGGAGGAACCGTA 57.215 45.455 0.00 0.00 42.61 4.02
9430 10010 4.574674 TCTAGTAGTGGAGGAACCGTAA 57.425 45.455 0.00 0.00 42.61 3.18
9431 10011 4.922206 TCTAGTAGTGGAGGAACCGTAAA 58.078 43.478 0.00 0.00 42.61 2.01
9432 10012 4.946157 TCTAGTAGTGGAGGAACCGTAAAG 59.054 45.833 0.00 0.00 42.61 1.85
9434 10014 0.323957 AGTGGAGGAACCGTAAAGGC 59.676 55.000 0.00 0.00 46.52 4.35
9435 10015 0.675837 GTGGAGGAACCGTAAAGGCC 60.676 60.000 0.00 0.00 46.52 5.19
9436 10016 0.838987 TGGAGGAACCGTAAAGGCCT 60.839 55.000 0.00 0.00 46.52 5.19
9437 10017 0.107800 GGAGGAACCGTAAAGGCCTC 60.108 60.000 5.23 0.00 44.15 4.70
9438 10018 0.459759 GAGGAACCGTAAAGGCCTCG 60.460 60.000 5.23 5.32 46.52 4.63
9439 10019 1.190178 AGGAACCGTAAAGGCCTCGT 61.190 55.000 5.23 0.00 46.52 4.18
9440 10020 1.017701 GGAACCGTAAAGGCCTCGTG 61.018 60.000 5.23 2.46 46.52 4.35
9441 10021 0.320160 GAACCGTAAAGGCCTCGTGT 60.320 55.000 5.23 3.13 46.52 4.49
9442 10022 0.601841 AACCGTAAAGGCCTCGTGTG 60.602 55.000 5.23 0.00 46.52 3.82
9443 10023 1.005394 CCGTAAAGGCCTCGTGTGT 60.005 57.895 5.23 0.00 0.00 3.72
9444 10024 1.289109 CCGTAAAGGCCTCGTGTGTG 61.289 60.000 5.23 0.00 0.00 3.82
9445 10025 0.599204 CGTAAAGGCCTCGTGTGTGT 60.599 55.000 5.23 0.00 0.00 3.72
9446 10026 1.589803 GTAAAGGCCTCGTGTGTGTT 58.410 50.000 5.23 0.00 0.00 3.32
9447 10027 1.263217 GTAAAGGCCTCGTGTGTGTTG 59.737 52.381 5.23 0.00 0.00 3.33
9448 10028 1.724582 AAAGGCCTCGTGTGTGTTGC 61.725 55.000 5.23 0.00 0.00 4.17
9449 10029 2.884997 AAGGCCTCGTGTGTGTTGCA 62.885 55.000 5.23 0.00 0.00 4.08
9450 10030 2.633657 GCCTCGTGTGTGTTGCAG 59.366 61.111 0.00 0.00 0.00 4.41
9451 10031 2.633657 CCTCGTGTGTGTTGCAGC 59.366 61.111 0.00 0.00 0.00 5.25
9452 10032 2.633657 CTCGTGTGTGTTGCAGCC 59.366 61.111 0.00 0.00 0.00 4.85
9453 10033 2.896801 CTCGTGTGTGTTGCAGCCC 61.897 63.158 0.00 0.00 0.00 5.19
9454 10034 3.208383 CGTGTGTGTTGCAGCCCA 61.208 61.111 0.00 0.00 0.00 5.36
9455 10035 2.769539 CGTGTGTGTTGCAGCCCAA 61.770 57.895 0.00 0.00 0.00 4.12
9462 10042 3.831637 TTGCAGCCCAACACCCCT 61.832 61.111 0.00 0.00 0.00 4.79
9463 10043 3.808218 TTGCAGCCCAACACCCCTC 62.808 63.158 0.00 0.00 0.00 4.30
9465 10045 3.579302 CAGCCCAACACCCCTCCA 61.579 66.667 0.00 0.00 0.00 3.86
9466 10046 2.780924 AGCCCAACACCCCTCCAA 60.781 61.111 0.00 0.00 0.00 3.53
9467 10047 2.200092 GCCCAACACCCCTCCAAA 59.800 61.111 0.00 0.00 0.00 3.28
9468 10048 1.908299 GCCCAACACCCCTCCAAAG 60.908 63.158 0.00 0.00 0.00 2.77
9469 10049 1.541672 CCCAACACCCCTCCAAAGT 59.458 57.895 0.00 0.00 0.00 2.66
9470 10050 0.827507 CCCAACACCCCTCCAAAGTG 60.828 60.000 0.00 0.00 37.53 3.16
9471 10051 0.827507 CCAACACCCCTCCAAAGTGG 60.828 60.000 0.00 0.00 39.43 4.00
9472 10052 1.152546 AACACCCCTCCAAAGTGGC 60.153 57.895 0.00 0.00 37.47 5.01
9473 10053 2.283173 CACCCCTCCAAAGTGGCC 60.283 66.667 0.00 0.00 37.47 5.36
9474 10054 3.590574 ACCCCTCCAAAGTGGCCC 61.591 66.667 0.00 0.00 37.47 5.80
9475 10055 3.589542 CCCCTCCAAAGTGGCCCA 61.590 66.667 0.00 0.00 37.47 5.36
9476 10056 2.525592 CCCTCCAAAGTGGCCCAA 59.474 61.111 0.00 0.00 37.47 4.12
9477 10057 1.152355 CCCTCCAAAGTGGCCCAAA 60.152 57.895 0.00 0.00 37.47 3.28
9478 10058 0.762461 CCCTCCAAAGTGGCCCAAAA 60.762 55.000 0.00 0.00 37.47 2.44
9479 10059 0.392706 CCTCCAAAGTGGCCCAAAAC 59.607 55.000 0.00 0.00 37.47 2.43
9480 10060 0.392706 CTCCAAAGTGGCCCAAAACC 59.607 55.000 0.00 0.00 37.47 3.27
9481 10061 1.051556 TCCAAAGTGGCCCAAAACCC 61.052 55.000 0.00 0.00 37.47 4.11
9482 10062 1.053835 CCAAAGTGGCCCAAAACCCT 61.054 55.000 0.00 0.00 0.00 4.34
9483 10063 0.392706 CAAAGTGGCCCAAAACCCTC 59.607 55.000 0.00 0.00 0.00 4.30
9484 10064 0.264657 AAAGTGGCCCAAAACCCTCT 59.735 50.000 0.00 0.00 0.00 3.69
9485 10065 1.154430 AAGTGGCCCAAAACCCTCTA 58.846 50.000 0.00 0.00 0.00 2.43
9486 10066 1.154430 AGTGGCCCAAAACCCTCTAA 58.846 50.000 0.00 0.00 0.00 2.10
9487 10067 1.501604 AGTGGCCCAAAACCCTCTAAA 59.498 47.619 0.00 0.00 0.00 1.85
9488 10068 1.616865 GTGGCCCAAAACCCTCTAAAC 59.383 52.381 0.00 0.00 0.00 2.01
9489 10069 1.263356 GGCCCAAAACCCTCTAAACC 58.737 55.000 0.00 0.00 0.00 3.27
9490 10070 1.263356 GCCCAAAACCCTCTAAACCC 58.737 55.000 0.00 0.00 0.00 4.11
9491 10071 1.933021 CCCAAAACCCTCTAAACCCC 58.067 55.000 0.00 0.00 0.00 4.95
9492 10072 1.551560 CCCAAAACCCTCTAAACCCCC 60.552 57.143 0.00 0.00 0.00 5.40
9493 10073 1.431633 CCAAAACCCTCTAAACCCCCT 59.568 52.381 0.00 0.00 0.00 4.79
9494 10074 2.556782 CCAAAACCCTCTAAACCCCCTC 60.557 54.545 0.00 0.00 0.00 4.30
9495 10075 1.379776 AAACCCTCTAAACCCCCTCC 58.620 55.000 0.00 0.00 0.00 4.30
9496 10076 0.197661 AACCCTCTAAACCCCCTCCA 59.802 55.000 0.00 0.00 0.00 3.86
9497 10077 0.426022 ACCCTCTAAACCCCCTCCAT 59.574 55.000 0.00 0.00 0.00 3.41
9498 10078 1.141185 CCCTCTAAACCCCCTCCATC 58.859 60.000 0.00 0.00 0.00 3.51
9499 10079 1.141185 CCTCTAAACCCCCTCCATCC 58.859 60.000 0.00 0.00 0.00 3.51
9500 10080 1.345526 CCTCTAAACCCCCTCCATCCT 60.346 57.143 0.00 0.00 0.00 3.24
9501 10081 2.050918 CTCTAAACCCCCTCCATCCTC 58.949 57.143 0.00 0.00 0.00 3.71
9502 10082 1.657162 TCTAAACCCCCTCCATCCTCT 59.343 52.381 0.00 0.00 0.00 3.69
9503 10083 2.050918 CTAAACCCCCTCCATCCTCTC 58.949 57.143 0.00 0.00 0.00 3.20
9504 10084 0.983378 AAACCCCCTCCATCCTCTCG 60.983 60.000 0.00 0.00 0.00 4.04
9505 10085 2.525381 CCCCCTCCATCCTCTCGG 60.525 72.222 0.00 0.00 0.00 4.63
9506 10086 3.237741 CCCCTCCATCCTCTCGGC 61.238 72.222 0.00 0.00 0.00 5.54
9507 10087 3.237741 CCCTCCATCCTCTCGGCC 61.238 72.222 0.00 0.00 0.00 6.13
9508 10088 3.610669 CCTCCATCCTCTCGGCCG 61.611 72.222 22.12 22.12 0.00 6.13
9509 10089 2.835431 CTCCATCCTCTCGGCCGT 60.835 66.667 27.15 0.06 0.00 5.68
9510 10090 2.363795 TCCATCCTCTCGGCCGTT 60.364 61.111 27.15 1.18 0.00 4.44
9511 10091 2.107141 CCATCCTCTCGGCCGTTC 59.893 66.667 27.15 0.00 0.00 3.95
9512 10092 2.278857 CATCCTCTCGGCCGTTCG 60.279 66.667 27.15 14.97 0.00 3.95
9513 10093 2.439701 ATCCTCTCGGCCGTTCGA 60.440 61.111 27.15 18.37 37.60 3.71
9514 10094 1.828660 ATCCTCTCGGCCGTTCGAT 60.829 57.895 27.15 17.97 38.55 3.59
9515 10095 1.797211 ATCCTCTCGGCCGTTCGATC 61.797 60.000 27.15 0.00 38.55 3.69
9516 10096 2.771639 CCTCTCGGCCGTTCGATCA 61.772 63.158 27.15 1.93 38.55 2.92
9517 10097 1.586564 CTCTCGGCCGTTCGATCAC 60.587 63.158 27.15 0.00 38.55 3.06
9518 10098 2.949678 CTCGGCCGTTCGATCACG 60.950 66.667 27.15 2.65 38.55 4.35
9534 10114 3.556625 CGATCACGTGGCCGAAAA 58.443 55.556 17.00 0.00 37.88 2.29
9535 10115 1.131826 CGATCACGTGGCCGAAAAC 59.868 57.895 17.00 0.00 37.88 2.43
9536 10116 1.500396 GATCACGTGGCCGAAAACC 59.500 57.895 17.00 0.00 37.88 3.27
9537 10117 2.235536 GATCACGTGGCCGAAAACCG 62.236 60.000 17.00 0.00 37.88 4.44
9538 10118 4.676586 CACGTGGCCGAAAACCGC 62.677 66.667 7.95 0.00 37.88 5.68
9540 10120 4.676586 CGTGGCCGAAAACCGCAC 62.677 66.667 0.00 0.00 37.56 5.34
9541 10121 4.337060 GTGGCCGAAAACCGCACC 62.337 66.667 0.00 0.00 37.64 5.01
9542 10122 4.572571 TGGCCGAAAACCGCACCT 62.573 61.111 0.00 0.00 35.02 4.00
9543 10123 3.733960 GGCCGAAAACCGCACCTC 61.734 66.667 0.00 0.00 36.84 3.85
9544 10124 2.975799 GCCGAAAACCGCACCTCA 60.976 61.111 0.00 0.00 36.84 3.86
9545 10125 2.332654 GCCGAAAACCGCACCTCAT 61.333 57.895 0.00 0.00 36.84 2.90
9546 10126 1.862602 GCCGAAAACCGCACCTCATT 61.863 55.000 0.00 0.00 36.84 2.57
9547 10127 0.596082 CCGAAAACCGCACCTCATTT 59.404 50.000 0.00 0.00 36.84 2.32
9548 10128 1.665735 CCGAAAACCGCACCTCATTTG 60.666 52.381 0.00 0.00 36.84 2.32
9549 10129 1.665735 CGAAAACCGCACCTCATTTGG 60.666 52.381 0.00 0.00 0.00 3.28
9550 10130 1.611491 GAAAACCGCACCTCATTTGGA 59.389 47.619 0.00 0.00 0.00 3.53
9551 10131 0.958822 AAACCGCACCTCATTTGGAC 59.041 50.000 0.00 0.00 0.00 4.02
9552 10132 0.110486 AACCGCACCTCATTTGGACT 59.890 50.000 0.00 0.00 0.00 3.85
9553 10133 0.321653 ACCGCACCTCATTTGGACTC 60.322 55.000 0.00 0.00 0.00 3.36
9554 10134 0.036010 CCGCACCTCATTTGGACTCT 60.036 55.000 0.00 0.00 0.00 3.24
9555 10135 1.363744 CGCACCTCATTTGGACTCTC 58.636 55.000 0.00 0.00 0.00 3.20
9556 10136 1.743996 GCACCTCATTTGGACTCTCC 58.256 55.000 0.00 0.00 36.96 3.71
9557 10137 1.280421 GCACCTCATTTGGACTCTCCT 59.720 52.381 0.00 0.00 37.46 3.69
9558 10138 2.501723 GCACCTCATTTGGACTCTCCTA 59.498 50.000 0.00 0.00 37.46 2.94
9559 10139 3.431486 GCACCTCATTTGGACTCTCCTAG 60.431 52.174 0.00 0.00 37.46 3.02
9560 10140 2.769095 ACCTCATTTGGACTCTCCTAGC 59.231 50.000 0.00 0.00 37.46 3.42
9561 10141 3.037549 CCTCATTTGGACTCTCCTAGCT 58.962 50.000 0.00 0.00 37.46 3.32
9562 10142 3.069443 CCTCATTTGGACTCTCCTAGCTC 59.931 52.174 0.00 0.00 37.46 4.09
9563 10143 3.960102 CTCATTTGGACTCTCCTAGCTCT 59.040 47.826 0.00 0.00 37.46 4.09
9564 10144 5.130705 TCATTTGGACTCTCCTAGCTCTA 57.869 43.478 0.00 0.00 37.46 2.43
9565 10145 5.519808 TCATTTGGACTCTCCTAGCTCTAA 58.480 41.667 0.00 0.00 37.46 2.10
9566 10146 5.596361 TCATTTGGACTCTCCTAGCTCTAAG 59.404 44.000 0.00 0.00 37.46 2.18
9567 10147 4.864483 TTGGACTCTCCTAGCTCTAAGA 57.136 45.455 0.00 0.00 37.46 2.10
9568 10148 4.864483 TGGACTCTCCTAGCTCTAAGAA 57.136 45.455 0.00 0.00 37.46 2.52
9569 10149 4.528920 TGGACTCTCCTAGCTCTAAGAAC 58.471 47.826 0.00 0.00 37.46 3.01
9570 10150 3.887110 GGACTCTCCTAGCTCTAAGAACC 59.113 52.174 0.00 0.00 32.53 3.62
9571 10151 4.385977 GGACTCTCCTAGCTCTAAGAACCT 60.386 50.000 0.00 0.00 32.53 3.50
9572 10152 5.163174 GGACTCTCCTAGCTCTAAGAACCTA 60.163 48.000 0.00 0.00 32.53 3.08
9573 10153 6.466759 GGACTCTCCTAGCTCTAAGAACCTAT 60.467 46.154 0.00 0.00 32.53 2.57
9574 10154 7.256763 GGACTCTCCTAGCTCTAAGAACCTATA 60.257 44.444 0.00 0.00 32.53 1.31
9575 10155 8.048016 ACTCTCCTAGCTCTAAGAACCTATAA 57.952 38.462 0.00 0.00 0.00 0.98
9576 10156 8.504409 ACTCTCCTAGCTCTAAGAACCTATAAA 58.496 37.037 0.00 0.00 0.00 1.40
9577 10157 9.528489 CTCTCCTAGCTCTAAGAACCTATAAAT 57.472 37.037 0.00 0.00 0.00 1.40
9585 10165 9.549078 GCTCTAAGAACCTATAAATATATGCCC 57.451 37.037 0.00 0.00 0.00 5.36
9587 10167 8.999895 TCTAAGAACCTATAAATATATGCCCCC 58.000 37.037 0.00 0.00 0.00 5.40
9602 10182 1.311059 CCCCCTCCAAAATCCTGGG 59.689 63.158 0.00 0.00 37.06 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 9.764363 GATGACACCATAATACTCAAGATGTTA 57.236 33.333 0.00 0.00 32.09 2.41
86 89 7.505258 TGATTATTTCCTCGATGACACCATAA 58.495 34.615 0.00 0.00 32.09 1.90
282 285 7.867909 CGAGGATGCATACTTCAAGTAATAAGA 59.132 37.037 14.07 0.00 33.89 2.10
464 467 5.477984 TCTTGGCTTAGCAAACTCATCAAAT 59.522 36.000 6.53 0.00 0.00 2.32
465 468 4.826733 TCTTGGCTTAGCAAACTCATCAAA 59.173 37.500 6.53 0.00 0.00 2.69
475 478 3.181445 TGACTCCTTTCTTGGCTTAGCAA 60.181 43.478 6.53 0.00 0.00 3.91
480 483 3.328931 TCATCTGACTCCTTTCTTGGCTT 59.671 43.478 0.00 0.00 0.00 4.35
913 919 5.382618 AAAGGCATGCAAGTAGAAGAAAG 57.617 39.130 21.36 0.00 0.00 2.62
983 991 3.118038 GCCCATCCTGTTTACATAGTGGA 60.118 47.826 8.33 0.00 0.00 4.02
1021 1029 2.300152 CCAGTCTAGGCACTGAGAAACA 59.700 50.000 12.07 0.00 45.92 2.83
1038 1046 4.647399 GCACTAGAAGAAGACCTATCCAGT 59.353 45.833 0.00 0.00 0.00 4.00
1044 1052 3.011369 TGGAGGCACTAGAAGAAGACCTA 59.989 47.826 0.00 0.00 41.55 3.08
1215 1223 6.319658 ACATGAATATTGCTCCAACAAGTAGG 59.680 38.462 0.00 0.00 31.96 3.18
1216 1224 7.191551 CACATGAATATTGCTCCAACAAGTAG 58.808 38.462 0.00 0.00 31.96 2.57
1427 1437 2.409975 CACAATTTTGGAAGCTGCTGG 58.590 47.619 1.35 0.00 0.00 4.85
1763 1799 6.262944 AGTGCATTTGTGAAAGTGAGAATACA 59.737 34.615 0.00 0.00 0.00 2.29
1986 2027 2.752903 GCCAACGGTTACCATTCTCATT 59.247 45.455 1.13 0.00 0.00 2.57
2134 2175 5.216622 AGACTGTATCCCCATTAGCAAGTA 58.783 41.667 0.00 0.00 0.00 2.24
2375 2419 6.949352 TCTTTGACTGCAAATCTTCTCTTT 57.051 33.333 0.00 0.00 42.66 2.52
3520 3627 9.847706 TTTATCTTGTTTTGCGCATAAGAAATA 57.152 25.926 20.25 16.85 31.89 1.40
3539 3646 8.946085 TCGAATTAACATGCTTCAGTTTATCTT 58.054 29.630 0.00 0.00 0.00 2.40
3746 3857 3.846588 ACCAGAACTAGGGATGTGACATT 59.153 43.478 0.00 0.00 0.00 2.71
3747 3858 3.454858 ACCAGAACTAGGGATGTGACAT 58.545 45.455 0.00 0.00 0.00 3.06
4423 4549 1.410932 CGAGGGAGAGGAGAGGAATGT 60.411 57.143 0.00 0.00 0.00 2.71
4444 4570 0.378257 GCGCAGTGAGAGAGAGAGAG 59.622 60.000 0.30 0.00 0.00 3.20
4445 4571 1.029408 GGCGCAGTGAGAGAGAGAGA 61.029 60.000 10.83 0.00 0.00 3.10
4446 4572 1.433064 GGCGCAGTGAGAGAGAGAG 59.567 63.158 10.83 0.00 0.00 3.20
4447 4573 2.049185 GGGCGCAGTGAGAGAGAGA 61.049 63.158 10.83 0.00 0.00 3.10
4866 4994 0.244721 GGTTTGCGTCTACGGGTAGT 59.755 55.000 4.49 0.00 40.23 2.73
4972 5102 1.206371 AGCGCCTAACTAAACGTCCAT 59.794 47.619 2.29 0.00 0.00 3.41
5013 5143 1.224069 CCGCCTGTCAGTGTCTGTTG 61.224 60.000 0.00 0.00 32.61 3.33
5042 5172 2.531771 TGTTGACTGGGATTCGACCTA 58.468 47.619 0.00 0.00 0.00 3.08
5926 6062 3.255725 CGCTACCTTTACCAAATCGTGA 58.744 45.455 0.00 0.00 0.00 4.35
6071 6207 6.049149 TCAAGTTGGCTAATAAATCGAGAGG 58.951 40.000 2.34 0.00 0.00 3.69
6171 6307 2.683768 CTAGTCTATCCCAAGCCCACT 58.316 52.381 0.00 0.00 0.00 4.00
6184 6320 1.275291 GTGCCACTTGTGCCTAGTCTA 59.725 52.381 0.00 0.00 0.00 2.59
6217 6353 0.251832 ACCTCGCCGGATGGATCTAT 60.252 55.000 5.05 0.00 37.49 1.98
6333 6470 3.555168 CCTGACTAACCACACAAGACTCC 60.555 52.174 0.00 0.00 0.00 3.85
6593 6730 2.449464 TCATTCCCGTCTTCCTACGAA 58.551 47.619 0.00 0.00 45.68 3.85
6774 6911 5.246203 AGGTACTCAGCAAGACTTACATCAA 59.754 40.000 0.00 0.00 0.00 2.57
7119 7267 5.119434 CACACATAGCAATACACGTTACACA 59.881 40.000 0.00 0.00 0.00 3.72
7243 7391 4.228567 GGCTAGCAGGACTCCGGC 62.229 72.222 18.24 11.99 44.77 6.13
7292 7440 2.290641 GGAACGAAGTGAAACACATGCT 59.709 45.455 4.75 0.00 45.00 3.79
7390 7538 0.976641 CACTGGGCTAACAGGACTCA 59.023 55.000 8.13 0.00 42.75 3.41
7418 7566 4.634004 GTCGGTCAACAACATATGAATCCA 59.366 41.667 10.38 0.00 0.00 3.41
7492 7640 2.159043 CGACATGGCTAGTCATGAACCT 60.159 50.000 37.32 19.39 45.30 3.50
7518 7666 5.121380 AGCATCCATATGACAAAGAACCT 57.879 39.130 3.65 0.00 34.84 3.50
7687 7835 6.479006 TGCGTCTATATAGAGGGTTTAGCTA 58.521 40.000 26.01 0.00 38.33 3.32
7704 7852 9.817809 AAGAGTATTCTAATTGAAATGCGTCTA 57.182 29.630 0.00 0.00 38.29 2.59
7763 7930 9.247126 CATGTGATCTTGTTTCAAACAACAATA 57.753 29.630 11.83 2.98 45.79 1.90
7832 8007 9.487790 GTTGATCTTTAAGAGATATAGCAAGCT 57.512 33.333 0.03 0.00 45.17 3.74
8339 8657 1.002087 CAAGTGACCTACAGGGACCAC 59.998 57.143 0.00 5.15 40.01 4.16
8432 8913 2.924757 TCATCATCTCCATGACTGGC 57.075 50.000 0.00 0.00 42.05 4.85
8470 8951 2.666272 AGTCATCATCTCCCTCGCTA 57.334 50.000 0.00 0.00 0.00 4.26
8698 9219 5.991606 TGAGATAGGTCATATTTTGCGAAGG 59.008 40.000 0.00 0.00 0.00 3.46
8795 9317 7.553760 TCAAATACATCTCATACACACAAGCAT 59.446 33.333 0.00 0.00 0.00 3.79
8910 9454 4.061357 TGTGTAACCGAGACATTTGTGA 57.939 40.909 0.00 0.00 34.36 3.58
9168 9748 2.631062 AGCCCGACGACATTTATATCCA 59.369 45.455 0.00 0.00 0.00 3.41
9320 9900 3.958822 GACGGTACACTGTCGGCCG 62.959 68.421 22.12 22.12 46.83 6.13
9370 9950 5.296283 CGAGGATCTAATTACCGTCGGATAT 59.704 44.000 20.51 7.68 0.00 1.63
9420 10000 1.190178 ACGAGGCCTTTACGGTTCCT 61.190 55.000 6.77 0.00 34.25 3.36
9421 10001 1.017701 CACGAGGCCTTTACGGTTCC 61.018 60.000 6.77 0.00 34.25 3.62
9422 10002 0.320160 ACACGAGGCCTTTACGGTTC 60.320 55.000 6.77 0.00 34.25 3.62
9423 10003 0.601841 CACACGAGGCCTTTACGGTT 60.602 55.000 6.77 0.00 34.25 4.44
9424 10004 1.005394 CACACGAGGCCTTTACGGT 60.005 57.895 6.77 3.67 34.25 4.83
9425 10005 1.005394 ACACACGAGGCCTTTACGG 60.005 57.895 6.77 3.00 0.00 4.02
9426 10006 0.599204 ACACACACGAGGCCTTTACG 60.599 55.000 6.77 9.10 0.00 3.18
9427 10007 1.263217 CAACACACACGAGGCCTTTAC 59.737 52.381 6.77 0.00 0.00 2.01
9428 10008 1.588674 CAACACACACGAGGCCTTTA 58.411 50.000 6.77 0.00 0.00 1.85
9429 10009 1.724582 GCAACACACACGAGGCCTTT 61.725 55.000 6.77 0.00 0.00 3.11
9430 10010 2.186826 GCAACACACACGAGGCCTT 61.187 57.895 6.77 0.00 0.00 4.35
9431 10011 2.591715 GCAACACACACGAGGCCT 60.592 61.111 3.86 3.86 0.00 5.19
9432 10012 2.896801 CTGCAACACACACGAGGCC 61.897 63.158 0.00 0.00 0.00 5.19
9433 10013 2.633657 CTGCAACACACACGAGGC 59.366 61.111 0.00 0.00 0.00 4.70
9434 10014 2.633657 GCTGCAACACACACGAGG 59.366 61.111 0.00 0.00 0.00 4.63
9435 10015 2.633657 GGCTGCAACACACACGAG 59.366 61.111 0.50 0.00 0.00 4.18
9436 10016 2.899838 GGGCTGCAACACACACGA 60.900 61.111 0.50 0.00 0.00 4.35
9437 10017 2.769539 TTGGGCTGCAACACACACG 61.770 57.895 0.50 0.00 0.00 4.49
9438 10018 1.226945 GTTGGGCTGCAACACACAC 60.227 57.895 0.50 0.00 33.13 3.82
9439 10019 1.680314 TGTTGGGCTGCAACACACA 60.680 52.632 0.50 5.04 37.59 3.72
9440 10020 3.205395 TGTTGGGCTGCAACACAC 58.795 55.556 0.50 2.70 37.59 3.82
9443 10023 2.837291 GGGTGTTGGGCTGCAACA 60.837 61.111 0.50 5.38 39.86 3.33
9444 10024 3.615709 GGGGTGTTGGGCTGCAAC 61.616 66.667 0.50 0.00 0.00 4.17
9445 10025 3.808218 GAGGGGTGTTGGGCTGCAA 62.808 63.158 0.50 0.00 0.00 4.08
9446 10026 4.284550 GAGGGGTGTTGGGCTGCA 62.285 66.667 0.50 0.00 0.00 4.41
9448 10028 2.655077 TTTGGAGGGGTGTTGGGCTG 62.655 60.000 0.00 0.00 0.00 4.85
9449 10029 2.371897 CTTTGGAGGGGTGTTGGGCT 62.372 60.000 0.00 0.00 0.00 5.19
9450 10030 1.908299 CTTTGGAGGGGTGTTGGGC 60.908 63.158 0.00 0.00 0.00 5.36
9451 10031 0.827507 CACTTTGGAGGGGTGTTGGG 60.828 60.000 0.00 0.00 0.00 4.12
9452 10032 0.827507 CCACTTTGGAGGGGTGTTGG 60.828 60.000 0.00 0.00 41.91 3.77
9453 10033 2.732289 CCACTTTGGAGGGGTGTTG 58.268 57.895 0.00 0.00 41.91 3.33
9459 10039 0.762461 TTTTGGGCCACTTTGGAGGG 60.762 55.000 5.23 0.00 40.96 4.30
9460 10040 0.392706 GTTTTGGGCCACTTTGGAGG 59.607 55.000 5.23 0.00 40.96 4.30
9461 10041 0.392706 GGTTTTGGGCCACTTTGGAG 59.607 55.000 5.23 0.00 40.96 3.86
9462 10042 1.051556 GGGTTTTGGGCCACTTTGGA 61.052 55.000 5.23 0.00 40.96 3.53
9463 10043 1.053835 AGGGTTTTGGGCCACTTTGG 61.054 55.000 5.23 0.00 41.55 3.28
9464 10044 0.392706 GAGGGTTTTGGGCCACTTTG 59.607 55.000 5.23 0.00 0.00 2.77
9465 10045 0.264657 AGAGGGTTTTGGGCCACTTT 59.735 50.000 5.23 0.00 0.00 2.66
9466 10046 1.154430 TAGAGGGTTTTGGGCCACTT 58.846 50.000 5.23 0.00 0.00 3.16
9467 10047 1.154430 TTAGAGGGTTTTGGGCCACT 58.846 50.000 5.23 0.00 0.00 4.00
9468 10048 1.616865 GTTTAGAGGGTTTTGGGCCAC 59.383 52.381 5.23 0.00 0.00 5.01
9469 10049 1.481615 GGTTTAGAGGGTTTTGGGCCA 60.482 52.381 0.00 0.00 0.00 5.36
9470 10050 1.263356 GGTTTAGAGGGTTTTGGGCC 58.737 55.000 0.00 0.00 0.00 5.80
9471 10051 1.263356 GGGTTTAGAGGGTTTTGGGC 58.737 55.000 0.00 0.00 0.00 5.36
9472 10052 1.551560 GGGGGTTTAGAGGGTTTTGGG 60.552 57.143 0.00 0.00 0.00 4.12
9473 10053 1.431633 AGGGGGTTTAGAGGGTTTTGG 59.568 52.381 0.00 0.00 0.00 3.28
9474 10054 2.556782 GGAGGGGGTTTAGAGGGTTTTG 60.557 54.545 0.00 0.00 0.00 2.44
9475 10055 1.714787 GGAGGGGGTTTAGAGGGTTTT 59.285 52.381 0.00 0.00 0.00 2.43
9476 10056 1.379776 GGAGGGGGTTTAGAGGGTTT 58.620 55.000 0.00 0.00 0.00 3.27
9477 10057 0.197661 TGGAGGGGGTTTAGAGGGTT 59.802 55.000 0.00 0.00 0.00 4.11
9478 10058 0.426022 ATGGAGGGGGTTTAGAGGGT 59.574 55.000 0.00 0.00 0.00 4.34
9479 10059 1.141185 GATGGAGGGGGTTTAGAGGG 58.859 60.000 0.00 0.00 0.00 4.30
9480 10060 1.141185 GGATGGAGGGGGTTTAGAGG 58.859 60.000 0.00 0.00 0.00 3.69
9481 10061 2.050918 GAGGATGGAGGGGGTTTAGAG 58.949 57.143 0.00 0.00 0.00 2.43
9482 10062 1.657162 AGAGGATGGAGGGGGTTTAGA 59.343 52.381 0.00 0.00 0.00 2.10
9483 10063 2.050918 GAGAGGATGGAGGGGGTTTAG 58.949 57.143 0.00 0.00 0.00 1.85
9484 10064 1.691482 CGAGAGGATGGAGGGGGTTTA 60.691 57.143 0.00 0.00 0.00 2.01
9485 10065 0.983378 CGAGAGGATGGAGGGGGTTT 60.983 60.000 0.00 0.00 0.00 3.27
9486 10066 1.383248 CGAGAGGATGGAGGGGGTT 60.383 63.158 0.00 0.00 0.00 4.11
9487 10067 2.283809 CGAGAGGATGGAGGGGGT 59.716 66.667 0.00 0.00 0.00 4.95
9499 10079 1.586564 GTGATCGAACGGCCGAGAG 60.587 63.158 35.90 21.37 42.21 3.20
9500 10080 2.488355 GTGATCGAACGGCCGAGA 59.512 61.111 35.90 26.59 42.21 4.04
9501 10081 2.949678 CGTGATCGAACGGCCGAG 60.950 66.667 35.90 22.14 42.21 4.63
9502 10082 3.433453 TCGTGATCGAACGGCCGA 61.433 61.111 35.90 10.13 43.34 5.54
9517 10097 1.131826 GTTTTCGGCCACGTGATCG 59.868 57.895 19.30 19.36 41.85 3.69
9518 10098 1.500396 GGTTTTCGGCCACGTGATC 59.500 57.895 19.30 8.22 41.85 2.92
9519 10099 2.322081 CGGTTTTCGGCCACGTGAT 61.322 57.895 19.30 0.00 41.85 3.06
9520 10100 2.968156 CGGTTTTCGGCCACGTGA 60.968 61.111 19.30 0.00 41.85 4.35
9521 10101 4.676586 GCGGTTTTCGGCCACGTG 62.677 66.667 9.08 9.08 41.85 4.49
9523 10103 4.676586 GTGCGGTTTTCGGCCACG 62.677 66.667 2.24 0.00 43.96 4.94
9524 10104 4.337060 GGTGCGGTTTTCGGCCAC 62.337 66.667 2.24 0.00 43.96 5.01
9525 10105 4.572571 AGGTGCGGTTTTCGGCCA 62.573 61.111 2.24 0.00 43.96 5.36
9526 10106 3.733960 GAGGTGCGGTTTTCGGCC 61.734 66.667 0.00 0.00 43.96 6.13
9527 10107 1.862602 AATGAGGTGCGGTTTTCGGC 61.863 55.000 0.00 0.00 44.67 5.54
9528 10108 0.596082 AAATGAGGTGCGGTTTTCGG 59.404 50.000 0.00 0.00 39.69 4.30
9529 10109 1.665735 CCAAATGAGGTGCGGTTTTCG 60.666 52.381 0.00 0.00 42.76 3.46
9530 10110 1.611491 TCCAAATGAGGTGCGGTTTTC 59.389 47.619 0.00 0.00 0.00 2.29
9531 10111 1.339929 GTCCAAATGAGGTGCGGTTTT 59.660 47.619 0.00 0.00 0.00 2.43
9532 10112 0.958822 GTCCAAATGAGGTGCGGTTT 59.041 50.000 0.00 0.00 0.00 3.27
9533 10113 0.110486 AGTCCAAATGAGGTGCGGTT 59.890 50.000 0.00 0.00 0.00 4.44
9534 10114 0.321653 GAGTCCAAATGAGGTGCGGT 60.322 55.000 0.00 0.00 0.00 5.68
9535 10115 0.036010 AGAGTCCAAATGAGGTGCGG 60.036 55.000 0.00 0.00 0.00 5.69
9536 10116 1.363744 GAGAGTCCAAATGAGGTGCG 58.636 55.000 0.00 0.00 0.00 5.34
9537 10117 1.280421 AGGAGAGTCCAAATGAGGTGC 59.720 52.381 0.00 0.00 39.61 5.01
9538 10118 3.431486 GCTAGGAGAGTCCAAATGAGGTG 60.431 52.174 0.00 0.00 39.61 4.00
9539 10119 2.769095 GCTAGGAGAGTCCAAATGAGGT 59.231 50.000 0.00 0.00 39.61 3.85
9540 10120 3.037549 AGCTAGGAGAGTCCAAATGAGG 58.962 50.000 0.00 0.00 39.61 3.86
9541 10121 3.960102 AGAGCTAGGAGAGTCCAAATGAG 59.040 47.826 0.00 0.00 39.61 2.90
9542 10122 3.987745 AGAGCTAGGAGAGTCCAAATGA 58.012 45.455 0.00 0.00 39.61 2.57
9543 10123 5.596361 TCTTAGAGCTAGGAGAGTCCAAATG 59.404 44.000 0.00 0.00 39.61 2.32
9544 10124 5.772004 TCTTAGAGCTAGGAGAGTCCAAAT 58.228 41.667 0.00 0.00 39.61 2.32
9545 10125 5.194473 TCTTAGAGCTAGGAGAGTCCAAA 57.806 43.478 0.00 0.00 39.61 3.28
9546 10126 4.864483 TCTTAGAGCTAGGAGAGTCCAA 57.136 45.455 0.00 0.00 39.61 3.53
9547 10127 4.528920 GTTCTTAGAGCTAGGAGAGTCCA 58.471 47.826 0.00 0.00 39.61 4.02
9548 10128 3.887110 GGTTCTTAGAGCTAGGAGAGTCC 59.113 52.174 0.00 0.00 36.58 3.85
9549 10129 4.788679 AGGTTCTTAGAGCTAGGAGAGTC 58.211 47.826 0.00 0.00 0.00 3.36
9550 10130 4.873724 AGGTTCTTAGAGCTAGGAGAGT 57.126 45.455 0.00 0.00 0.00 3.24
9551 10131 8.927675 TTTATAGGTTCTTAGAGCTAGGAGAG 57.072 38.462 0.00 0.00 33.58 3.20
9559 10139 9.549078 GGGCATATATTTATAGGTTCTTAGAGC 57.451 37.037 0.00 0.00 0.00 4.09
9561 10141 8.999895 GGGGGCATATATTTATAGGTTCTTAGA 58.000 37.037 0.00 0.00 0.00 2.10
9584 10164 1.311059 CCCAGGATTTTGGAGGGGG 59.689 63.158 0.00 0.00 40.87 5.40


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

AutoCloner maintained by Alex Coulton.