Multiple sequence alignment - TraesCS4A01G349100

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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 TraesCS4A01G349100 chr4A 100.000 4652 0 0 1992 6643 626066805 626062154 0.000000e+00 8591.0
1 TraesCS4A01G349100 chr4A 100.000 1166 0 0 333 1498 626068464 626067299 0.000000e+00 2154.0
2 TraesCS4A01G349100 chr4A 80.220 2270 337 61 2582 4792 626049845 626047629 0.000000e+00 1602.0
3 TraesCS4A01G349100 chr4A 79.671 2312 335 75 2757 4988 626014463 626012207 0.000000e+00 1541.0
4 TraesCS4A01G349100 chr4A 83.196 1696 256 21 3276 4960 626022079 626020402 0.000000e+00 1526.0
5 TraesCS4A01G349100 chr4A 79.694 458 79 6 4845 5295 626064042 626063592 1.070000e-82 318.0
6 TraesCS4A01G349100 chr4A 76.964 560 94 22 2624 3156 626077361 626076810 3.030000e-73 287.0
7 TraesCS4A01G349100 chr4A 100.000 127 0 0 1 127 626068796 626068670 1.110000e-57 235.0
8 TraesCS4A01G349100 chr4A 87.059 85 4 2 2106 2190 626066383 626066306 9.180000e-14 89.8
9 TraesCS4A01G349100 chr4A 87.059 85 4 2 2414 2491 626066691 626066607 9.180000e-14 89.8
10 TraesCS4A01G349100 chr5D 94.349 3274 158 10 2039 5290 543098884 543102152 0.000000e+00 4996.0
11 TraesCS4A01G349100 chr5D 80.809 2350 357 58 2491 4790 543092121 543094426 0.000000e+00 1755.0
12 TraesCS4A01G349100 chr5D 81.148 2196 334 44 2789 4936 543213333 543215496 0.000000e+00 1688.0
13 TraesCS4A01G349100 chr5D 80.460 2262 357 47 2757 4988 543229349 543231555 0.000000e+00 1650.0
14 TraesCS4A01G349100 chr5D 83.929 1680 250 12 3287 4957 543223763 543225431 0.000000e+00 1589.0
15 TraesCS4A01G349100 chr5D 90.771 1116 80 7 4755 5859 543101701 543102804 0.000000e+00 1469.0
16 TraesCS4A01G349100 chr5D 80.019 2057 335 50 2764 4794 543067899 543069905 0.000000e+00 1452.0
17 TraesCS4A01G349100 chr5D 80.599 1402 221 34 2633 4009 543235305 543236680 0.000000e+00 1035.0
18 TraesCS4A01G349100 chr5D 76.564 1519 294 45 3308 4785 542109506 542111003 0.000000e+00 776.0
19 TraesCS4A01G349100 chr5D 83.087 881 119 14 3993 4865 543236727 543237585 0.000000e+00 774.0
20 TraesCS4A01G349100 chr5D 94.614 427 18 1 1074 1495 543098252 543098678 0.000000e+00 656.0
21 TraesCS4A01G349100 chr5D 88.889 522 44 6 353 861 543097458 543097978 1.220000e-176 630.0
22 TraesCS4A01G349100 chr5D 90.200 449 27 6 5416 5859 543105693 543106129 2.690000e-158 569.0
23 TraesCS4A01G349100 chr5D 75.075 1332 275 42 3474 4775 543334012 543335316 9.670000e-158 568.0
24 TraesCS4A01G349100 chr5D 89.978 449 28 6 5416 5859 543106167 543106603 1.250000e-156 564.0
25 TraesCS4A01G349100 chr5D 89.978 449 28 6 5416 5859 543108067 543108503 1.250000e-156 564.0
26 TraesCS4A01G349100 chr5D 89.755 449 29 7 5416 5859 543103318 543103754 5.820000e-155 558.0
27 TraesCS4A01G349100 chr5D 89.755 449 29 6 5416 5859 543105218 543105654 5.820000e-155 558.0
28 TraesCS4A01G349100 chr5D 89.755 449 29 7 5416 5859 543110915 543111351 5.820000e-155 558.0
29 TraesCS4A01G349100 chr5D 89.755 449 29 7 5416 5859 543113290 543113726 5.820000e-155 558.0
30 TraesCS4A01G349100 chr5D 89.532 449 29 7 5416 5859 543109492 543109927 2.710000e-153 553.0
31 TraesCS4A01G349100 chr5D 89.532 449 30 7 5416 5859 543113765 543114201 2.710000e-153 553.0
32 TraesCS4A01G349100 chr5D 89.310 449 31 6 5416 5859 543107592 543108028 1.260000e-151 547.0
33 TraesCS4A01G349100 chr5D 89.087 449 32 7 5416 5859 543103793 543104229 5.860000e-150 542.0
34 TraesCS4A01G349100 chr5D 73.045 1343 294 50 3482 4775 543306168 543307491 4.790000e-111 412.0
35 TraesCS4A01G349100 chr5D 78.193 642 114 19 3308 3937 542204295 542204922 2.910000e-103 387.0
36 TraesCS4A01G349100 chr5D 79.431 457 88 2 4755 5205 543101791 543102247 1.070000e-82 318.0
37 TraesCS4A01G349100 chr5D 89.677 155 9 5 5835 5985 543114879 543115030 2.450000e-44 191.0
38 TraesCS4A01G349100 chr5D 82.090 201 33 1 4845 5045 543225232 543225429 1.150000e-37 169.0
39 TraesCS4A01G349100 chr5D 81.429 210 27 7 2464 2663 543222886 543223093 1.920000e-35 161.0
40 TraesCS4A01G349100 chr5D 88.043 92 4 1 2106 2190 543099257 543099348 1.180000e-17 102.0
41 TraesCS4A01G349100 chr5D 100.000 53 0 0 1992 2044 543098794 543098846 1.520000e-16 99.0
42 TraesCS4A01G349100 chr5D 79.866 149 12 7 2222 2370 543098826 543098956 7.090000e-15 93.5
43 TraesCS4A01G349100 chr5B 92.955 2910 152 26 2312 5205 684603515 684606387 0.000000e+00 4189.0
44 TraesCS4A01G349100 chr5B 79.676 2529 372 66 2464 4935 684610210 684612653 0.000000e+00 1692.0
45 TraesCS4A01G349100 chr5B 78.738 2314 374 71 2531 4794 684577715 684579960 0.000000e+00 1439.0
46 TraesCS4A01G349100 chr5B 80.104 1729 261 41 2722 4413 684690241 684691923 0.000000e+00 1210.0
47 TraesCS4A01G349100 chr5B 93.061 735 48 1 4845 5579 684605937 684606668 0.000000e+00 1072.0
48 TraesCS4A01G349100 chr5B 81.624 1170 178 24 3815 4957 684614782 684615941 0.000000e+00 935.0
49 TraesCS4A01G349100 chr5B 79.028 1173 191 28 2849 3993 684628896 684630041 0.000000e+00 752.0
50 TraesCS4A01G349100 chr5B 79.028 1173 191 28 2849 3993 684642599 684643744 0.000000e+00 752.0
51 TraesCS4A01G349100 chr5B 88.943 615 40 13 909 1496 684602900 684603513 0.000000e+00 734.0
52 TraesCS4A01G349100 chr5B 92.810 306 16 4 5680 5985 684606669 684606968 7.910000e-119 438.0
53 TraesCS4A01G349100 chr5B 79.796 490 97 2 3474 3962 557350332 557350820 8.190000e-94 355.0
54 TraesCS4A01G349100 chr5B 80.879 455 66 13 4411 4865 684693913 684694346 8.250000e-89 339.0
55 TraesCS4A01G349100 chr5A 96.229 663 24 1 5982 6643 345362503 345363165 0.000000e+00 1085.0
56 TraesCS4A01G349100 chr5A 95.000 660 30 2 5985 6643 435249293 435248636 0.000000e+00 1033.0
57 TraesCS4A01G349100 chr5A 94.268 663 35 2 5982 6643 631629218 631628558 0.000000e+00 1011.0
58 TraesCS4A01G349100 chr1A 95.606 660 27 2 5985 6643 61035709 61035051 0.000000e+00 1057.0
59 TraesCS4A01G349100 chr1A 94.681 658 33 2 5985 6641 325031752 325031096 0.000000e+00 1020.0
60 TraesCS4A01G349100 chr1A 81.443 291 39 9 584 861 560243147 560242859 2.410000e-54 224.0
61 TraesCS4A01G349100 chr2A 95.152 660 30 2 5985 6643 38223368 38224026 0.000000e+00 1040.0
62 TraesCS4A01G349100 chr2A 79.152 283 46 7 584 859 770212520 770212796 4.090000e-42 183.0
63 TraesCS4A01G349100 chr2A 76.712 292 43 19 2336 2612 250829751 250829470 8.980000e-29 139.0
64 TraesCS4A01G349100 chr6A 94.586 665 34 2 5980 6643 593936762 593937425 0.000000e+00 1027.0
65 TraesCS4A01G349100 chr6A 94.545 660 31 2 5985 6643 133808978 133808323 0.000000e+00 1014.0
66 TraesCS4A01G349100 chr6A 82.390 318 44 7 586 891 31740535 31740218 3.950000e-67 267.0
67 TraesCS4A01G349100 chr6A 82.684 231 30 10 581 806 101829312 101829537 5.260000e-46 196.0
68 TraesCS4A01G349100 chr7A 94.003 667 35 3 5978 6643 554482553 554483215 0.000000e+00 1005.0
69 TraesCS4A01G349100 chr7A 83.439 314 44 6 586 891 27864164 27863851 1.090000e-72 285.0
70 TraesCS4A01G349100 chr4B 84.227 317 41 7 584 891 32430481 32430797 3.890000e-77 300.0
71 TraesCS4A01G349100 chr7D 82.637 311 45 6 584 890 30923254 30923559 3.950000e-67 267.0
72 TraesCS4A01G349100 chr2B 82.515 326 36 13 585 893 668011120 668011441 3.950000e-67 267.0
73 TraesCS4A01G349100 chr1D 82.428 313 42 9 588 890 68853031 68853340 1.840000e-65 261.0
74 TraesCS4A01G349100 chr6D 82.909 275 38 7 584 849 468927125 468926851 8.610000e-59 239.0
75 TraesCS4A01G349100 chr4D 79.240 342 45 13 2281 2608 117419768 117419439 1.450000e-51 215.0
76 TraesCS4A01G349100 chr4D 78.070 342 49 13 2281 2608 151095315 151095644 6.800000e-45 193.0
77 TraesCS4A01G349100 chr3D 83.478 230 35 3 584 812 388779081 388778854 1.880000e-50 211.0
78 TraesCS4A01G349100 chr3A 95.726 117 4 1 11 127 572139755 572139870 3.160000e-43 187.0
79 TraesCS4A01G349100 chr3B 81.221 213 25 11 2463 2667 761146240 761146445 2.480000e-34 158.0
80 TraesCS4A01G349100 chr3B 81.221 213 25 8 2463 2667 761170605 761170810 2.480000e-34 158.0
81 TraesCS4A01G349100 chr2D 75.460 326 50 14 2298 2610 498401098 498401406 1.500000e-26 132.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G349100 chr4A 626062154 626068796 6642 True 1912.933333 8591 92.302000 1 6643 6 chr4A.!!$R5 6642
1 TraesCS4A01G349100 chr4A 626047629 626049845 2216 True 1602.000000 1602 80.220000 2582 4792 1 chr4A.!!$R3 2210
2 TraesCS4A01G349100 chr4A 626012207 626014463 2256 True 1541.000000 1541 79.671000 2757 4988 1 chr4A.!!$R1 2231
3 TraesCS4A01G349100 chr4A 626020402 626022079 1677 True 1526.000000 1526 83.196000 3276 4960 1 chr4A.!!$R2 1684
4 TraesCS4A01G349100 chr4A 626076810 626077361 551 True 287.000000 287 76.964000 2624 3156 1 chr4A.!!$R4 532
5 TraesCS4A01G349100 chr5D 543213333 543215496 2163 False 1688.000000 1688 81.148000 2789 4936 1 chr5D.!!$F4 2147
6 TraesCS4A01G349100 chr5D 543067899 543069905 2006 False 1452.000000 1452 80.019000 2764 4794 1 chr5D.!!$F3 2030
7 TraesCS4A01G349100 chr5D 543222886 543237585 14699 False 896.333333 1650 81.932333 2464 5045 6 chr5D.!!$F8 2581
8 TraesCS4A01G349100 chr5D 543092121 543115030 22909 False 782.547619 4996 89.194571 353 5985 21 chr5D.!!$F7 5632
9 TraesCS4A01G349100 chr5D 542109506 542111003 1497 False 776.000000 776 76.564000 3308 4785 1 chr5D.!!$F1 1477
10 TraesCS4A01G349100 chr5D 543334012 543335316 1304 False 568.000000 568 75.075000 3474 4775 1 chr5D.!!$F6 1301
11 TraesCS4A01G349100 chr5D 543306168 543307491 1323 False 412.000000 412 73.045000 3482 4775 1 chr5D.!!$F5 1293
12 TraesCS4A01G349100 chr5D 542204295 542204922 627 False 387.000000 387 78.193000 3308 3937 1 chr5D.!!$F2 629
13 TraesCS4A01G349100 chr5B 684602900 684615941 13041 False 1510.000000 4189 88.178167 909 5985 6 chr5B.!!$F5 5076
14 TraesCS4A01G349100 chr5B 684577715 684579960 2245 False 1439.000000 1439 78.738000 2531 4794 1 chr5B.!!$F2 2263
15 TraesCS4A01G349100 chr5B 684690241 684694346 4105 False 774.500000 1210 80.491500 2722 4865 2 chr5B.!!$F6 2143
16 TraesCS4A01G349100 chr5B 684628896 684630041 1145 False 752.000000 752 79.028000 2849 3993 1 chr5B.!!$F3 1144
17 TraesCS4A01G349100 chr5B 684642599 684643744 1145 False 752.000000 752 79.028000 2849 3993 1 chr5B.!!$F4 1144
18 TraesCS4A01G349100 chr5A 345362503 345363165 662 False 1085.000000 1085 96.229000 5982 6643 1 chr5A.!!$F1 661
19 TraesCS4A01G349100 chr5A 435248636 435249293 657 True 1033.000000 1033 95.000000 5985 6643 1 chr5A.!!$R1 658
20 TraesCS4A01G349100 chr5A 631628558 631629218 660 True 1011.000000 1011 94.268000 5982 6643 1 chr5A.!!$R2 661
21 TraesCS4A01G349100 chr1A 61035051 61035709 658 True 1057.000000 1057 95.606000 5985 6643 1 chr1A.!!$R1 658
22 TraesCS4A01G349100 chr1A 325031096 325031752 656 True 1020.000000 1020 94.681000 5985 6641 1 chr1A.!!$R2 656
23 TraesCS4A01G349100 chr2A 38223368 38224026 658 False 1040.000000 1040 95.152000 5985 6643 1 chr2A.!!$F1 658
24 TraesCS4A01G349100 chr6A 593936762 593937425 663 False 1027.000000 1027 94.586000 5980 6643 1 chr6A.!!$F2 663
25 TraesCS4A01G349100 chr6A 133808323 133808978 655 True 1014.000000 1014 94.545000 5985 6643 1 chr6A.!!$R2 658
26 TraesCS4A01G349100 chr7A 554482553 554483215 662 False 1005.000000 1005 94.003000 5978 6643 1 chr7A.!!$F1 665

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
92 93 0.040067 GCTGAAAGTCCACGCCTTTG 60.040 55.0 0.0 0.0 35.30 2.77 F
985 6105 0.184933 CCCTGTTTCCTGGTCAACCA 59.815 55.0 1.2 1.2 45.30 3.67 F
2041 7226 0.320374 TAGCTTGTCCCTGTCCAACG 59.680 55.0 0.0 0.0 0.00 4.10 F
2090 7275 0.659957 GCAGGGCATTTCAGATCGAC 59.340 55.0 0.0 0.0 0.00 4.20 F
3048 8386 0.383491 CTTGACAACTTCTGTGCGCG 60.383 55.0 0.0 0.0 38.84 6.86 F
4805 34353 1.410004 TTGACAGGACGACAAGGAGT 58.590 50.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 6454 0.037326 AACCGATTGCAGCTTCGAGA 60.037 50.000 16.85 0.00 37.55 4.04 R
2388 7573 0.096976 CGCAGCCCGTGAATTAAGTG 59.903 55.000 0.00 0.00 0.00 3.16 R
2995 8316 1.001745 GTTTGCGGGTAAAAGCGCAG 61.002 55.000 11.47 0.00 38.60 5.18 R
3859 28046 1.842920 TCCAGGCCTGACAAGAGCA 60.843 57.895 34.91 4.03 0.00 4.26 R
4839 34480 0.036858 GGTCACCAGTGAGAGAAGGC 60.037 60.000 0.00 0.00 40.75 4.35 R
6450 48193 0.534412 CTGTGGAGTCATCGCTTCCT 59.466 55.000 0.00 0.00 0.00 3.36 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
17 18 2.045926 AATCAGGGCGTGCCTGTC 60.046 61.111 11.25 0.00 36.73 3.51
25 26 3.706140 CGTGCCTGTCGCTAATCC 58.294 61.111 0.00 0.00 38.78 3.01
27 28 1.148157 CGTGCCTGTCGCTAATCCTG 61.148 60.000 0.00 0.00 38.78 3.86
29 30 1.889573 GCCTGTCGCTAATCCTGCC 60.890 63.158 0.00 0.00 0.00 4.85
30 31 1.592669 CCTGTCGCTAATCCTGCCG 60.593 63.158 0.00 0.00 0.00 5.69
32 33 2.202878 GTCGCTAATCCTGCCGCA 60.203 61.111 0.00 0.00 0.00 5.69
33 34 2.106938 TCGCTAATCCTGCCGCAG 59.893 61.111 13.82 13.82 0.00 5.18
34 35 3.643978 CGCTAATCCTGCCGCAGC 61.644 66.667 15.36 2.30 40.48 5.25
35 36 2.203126 GCTAATCCTGCCGCAGCT 60.203 61.111 15.36 4.14 40.80 4.24
36 37 2.541120 GCTAATCCTGCCGCAGCTG 61.541 63.158 15.36 10.11 40.80 4.24
37 38 2.514592 TAATCCTGCCGCAGCTGC 60.515 61.111 29.12 29.12 40.80 5.25
38 39 2.937379 CTAATCCTGCCGCAGCTGCT 62.937 60.000 34.22 16.84 40.80 4.24
39 40 2.930385 TAATCCTGCCGCAGCTGCTC 62.930 60.000 34.22 25.23 40.80 4.26
42 43 3.054503 CTGCCGCAGCTGCTCTTT 61.055 61.111 34.22 0.00 40.80 2.52
44 45 4.157958 GCCGCAGCTGCTCTTTCG 62.158 66.667 34.22 18.46 39.32 3.46
48 49 2.331132 GCAGCTGCTCTTTCGGCTT 61.331 57.895 31.33 0.00 45.80 4.35
49 50 1.500844 CAGCTGCTCTTTCGGCTTG 59.499 57.895 0.00 0.00 45.80 4.01
50 51 2.177778 GCTGCTCTTTCGGCTTGC 59.822 61.111 0.00 0.00 35.53 4.01
51 52 2.477845 CTGCTCTTTCGGCTTGCG 59.522 61.111 0.00 0.00 0.00 4.85
54 55 1.349973 GCTCTTTCGGCTTGCGATC 59.650 57.895 0.00 0.00 0.00 3.69
56 57 0.460987 CTCTTTCGGCTTGCGATCCT 60.461 55.000 0.00 0.00 0.00 3.24
57 58 0.740868 TCTTTCGGCTTGCGATCCTG 60.741 55.000 0.00 0.00 0.00 3.86
58 59 1.003839 TTTCGGCTTGCGATCCTGT 60.004 52.632 0.00 0.00 0.00 4.00
60 61 3.869272 CGGCTTGCGATCCTGTGC 61.869 66.667 0.00 0.00 0.00 4.57
61 62 2.747460 GGCTTGCGATCCTGTGCA 60.747 61.111 0.00 0.00 39.81 4.57
64 65 1.651240 GCTTGCGATCCTGTGCATGT 61.651 55.000 0.00 0.00 41.42 3.21
66 67 1.328680 CTTGCGATCCTGTGCATGTAC 59.671 52.381 7.03 7.03 41.42 2.90
67 68 0.805711 TGCGATCCTGTGCATGTACG 60.806 55.000 9.48 4.38 35.90 3.67
68 69 0.806102 GCGATCCTGTGCATGTACGT 60.806 55.000 9.48 0.00 0.00 3.57
70 71 1.469079 CGATCCTGTGCATGTACGTGA 60.469 52.381 19.38 8.36 0.00 4.35
71 72 2.616960 GATCCTGTGCATGTACGTGAA 58.383 47.619 19.38 5.27 0.00 3.18
72 73 2.078849 TCCTGTGCATGTACGTGAAG 57.921 50.000 19.38 11.61 0.00 3.02
73 74 1.078709 CCTGTGCATGTACGTGAAGG 58.921 55.000 19.38 16.22 0.00 3.46
74 75 0.443869 CTGTGCATGTACGTGAAGGC 59.556 55.000 19.38 3.71 0.00 4.35
76 77 0.443869 GTGCATGTACGTGAAGGCTG 59.556 55.000 19.38 0.00 0.00 4.85
77 78 0.320050 TGCATGTACGTGAAGGCTGA 59.680 50.000 19.38 0.00 0.00 4.26
78 79 1.270571 TGCATGTACGTGAAGGCTGAA 60.271 47.619 19.38 0.00 0.00 3.02
80 81 2.159653 GCATGTACGTGAAGGCTGAAAG 60.160 50.000 19.38 0.00 0.00 2.62
81 82 2.902705 TGTACGTGAAGGCTGAAAGT 57.097 45.000 0.00 0.00 35.30 2.66
82 83 2.750948 TGTACGTGAAGGCTGAAAGTC 58.249 47.619 0.00 0.00 40.46 3.01
84 85 0.468226 ACGTGAAGGCTGAAAGTCCA 59.532 50.000 0.00 0.00 41.78 4.02
85 86 0.868406 CGTGAAGGCTGAAAGTCCAC 59.132 55.000 0.00 0.00 41.78 4.02
86 87 0.868406 GTGAAGGCTGAAAGTCCACG 59.132 55.000 0.00 0.00 41.78 4.94
87 88 0.884704 TGAAGGCTGAAAGTCCACGC 60.885 55.000 0.00 0.00 41.78 5.34
88 89 1.578206 GAAGGCTGAAAGTCCACGCC 61.578 60.000 0.00 0.00 41.78 5.68
89 90 2.032681 GGCTGAAAGTCCACGCCT 59.967 61.111 0.00 0.00 37.76 5.52
91 92 1.172812 GGCTGAAAGTCCACGCCTTT 61.173 55.000 0.00 0.00 37.76 3.11
92 93 0.040067 GCTGAAAGTCCACGCCTTTG 60.040 55.000 0.00 0.00 35.30 2.77
93 94 1.593196 CTGAAAGTCCACGCCTTTGA 58.407 50.000 0.00 0.00 32.47 2.69
94 95 1.264288 CTGAAAGTCCACGCCTTTGAC 59.736 52.381 0.00 0.00 32.47 3.18
95 96 1.134220 TGAAAGTCCACGCCTTTGACT 60.134 47.619 0.00 0.00 40.94 3.41
96 97 2.103432 TGAAAGTCCACGCCTTTGACTA 59.897 45.455 0.00 0.00 38.36 2.59
97 98 3.244422 TGAAAGTCCACGCCTTTGACTAT 60.244 43.478 0.00 0.00 38.36 2.12
98 99 3.418684 AAGTCCACGCCTTTGACTATT 57.581 42.857 0.00 0.00 38.36 1.73
99 100 3.418684 AGTCCACGCCTTTGACTATTT 57.581 42.857 0.00 0.00 37.58 1.40
100 101 3.751518 AGTCCACGCCTTTGACTATTTT 58.248 40.909 0.00 0.00 37.58 1.82
101 102 4.142038 AGTCCACGCCTTTGACTATTTTT 58.858 39.130 0.00 0.00 37.58 1.94
122 123 6.494893 TTTTTCTGACATGTGCATAGTACC 57.505 37.500 1.15 0.00 0.00 3.34
124 125 6.538945 TTTCTGACATGTGCATAGTACCTA 57.461 37.500 1.15 0.00 0.00 3.08
125 126 5.515797 TCTGACATGTGCATAGTACCTAC 57.484 43.478 1.15 0.00 0.00 3.18
126 127 4.953579 TCTGACATGTGCATAGTACCTACA 59.046 41.667 1.15 0.00 0.00 2.74
370 5356 2.608998 CCTGGCTATGATGCTACGTCTG 60.609 54.545 0.00 0.00 0.00 3.51
376 5362 3.733443 ATGATGCTACGTCTGTATGCA 57.267 42.857 0.00 0.00 38.31 3.96
377 5363 2.809446 TGATGCTACGTCTGTATGCAC 58.191 47.619 0.00 0.00 37.46 4.57
378 5364 2.128035 GATGCTACGTCTGTATGCACC 58.872 52.381 0.00 0.00 37.46 5.01
397 5383 4.121317 CACCATGCATCTTTTGTTGTTGT 58.879 39.130 0.00 0.00 0.00 3.32
406 5392 6.562640 GCATCTTTTGTTGTTGTTGCTATGTG 60.563 38.462 0.00 0.00 0.00 3.21
409 5395 6.870965 TCTTTTGTTGTTGTTGCTATGTGTTT 59.129 30.769 0.00 0.00 0.00 2.83
434 5420 9.889128 TTGTATGATGAGATCAATGTAGTTTCA 57.111 29.630 0.00 0.00 43.50 2.69
439 5425 9.538508 TGATGAGATCAATGTAGTTTCATACAG 57.461 33.333 0.00 0.00 35.31 2.74
441 5427 7.275183 TGAGATCAATGTAGTTTCATACAGGG 58.725 38.462 0.00 0.00 38.96 4.45
457 5443 1.138859 CAGGGTGCTCGGATAACATGA 59.861 52.381 0.00 0.00 0.00 3.07
486 5472 1.732259 GACATGACTTAAGGCACACGG 59.268 52.381 14.74 6.37 0.00 4.94
523 5519 1.073125 ACCATCCATGTCCGTGAACAA 59.927 47.619 0.00 0.00 31.81 2.83
524 5520 1.739466 CCATCCATGTCCGTGAACAAG 59.261 52.381 0.00 0.00 31.81 3.16
539 5535 1.875488 ACAAGGCCGGATTAGGTAGT 58.125 50.000 5.05 0.00 0.00 2.73
545 5541 2.143925 GCCGGATTAGGTAGTGAATGC 58.856 52.381 5.05 0.00 0.00 3.56
579 5575 6.935771 ACTACGATCATGGTAGTACTCCTAAG 59.064 42.308 10.55 0.00 46.43 2.18
598 5594 1.689959 GCATGAGTGCGAAGTTTTGG 58.310 50.000 0.00 0.00 42.28 3.28
611 5607 2.525124 TTTTGGAGGCCGAGCTCCA 61.525 57.895 8.47 7.35 46.84 3.86
724 5723 7.428761 CCACAAGAACGTGTTAAATTTCGTTTA 59.571 33.333 14.25 0.00 44.47 2.01
726 5725 9.339492 ACAAGAACGTGTTAAATTTCGTTTAAA 57.661 25.926 14.25 0.00 44.47 1.52
745 5744 9.039500 CGTTTAAAAATATTGTGATTTGCAAGC 57.961 29.630 0.00 0.00 0.00 4.01
774 5773 2.524569 AAAAATCGGCCCAACAACAG 57.475 45.000 0.00 0.00 0.00 3.16
785 5784 3.745975 GCCCAACAACAGAAATAAAAGGC 59.254 43.478 0.00 0.00 0.00 4.35
799 5798 8.739039 AGAAATAAAAGGCCCATTTAAAAATGC 58.261 29.630 13.58 0.57 43.38 3.56
819 5818 7.527084 AATGCGTATTTCTCTTTCTCTGTAC 57.473 36.000 0.00 0.00 0.00 2.90
824 5823 4.537135 TTTCTCTTTCTCTGTACGCCAT 57.463 40.909 0.00 0.00 0.00 4.40
841 5840 4.941263 ACGCCATGTGTGAAAGTATAATGT 59.059 37.500 0.00 0.00 0.00 2.71
842 5841 5.064707 ACGCCATGTGTGAAAGTATAATGTC 59.935 40.000 0.00 0.00 0.00 3.06
861 5860 5.431420 TGTCGTGAAATTTTGCACATACT 57.569 34.783 9.82 0.00 34.78 2.12
862 5861 5.826586 TGTCGTGAAATTTTGCACATACTT 58.173 33.333 9.82 0.00 34.78 2.24
863 5862 5.685068 TGTCGTGAAATTTTGCACATACTTG 59.315 36.000 9.82 0.00 34.78 3.16
864 5863 5.116983 GTCGTGAAATTTTGCACATACTTGG 59.883 40.000 9.82 0.00 34.78 3.61
865 5864 4.981674 CGTGAAATTTTGCACATACTTGGT 59.018 37.500 9.82 0.00 34.78 3.67
866 5865 6.017026 TCGTGAAATTTTGCACATACTTGGTA 60.017 34.615 9.82 0.00 34.78 3.25
867 5866 6.806249 CGTGAAATTTTGCACATACTTGGTAT 59.194 34.615 9.82 0.00 34.78 2.73
868 5867 7.965655 CGTGAAATTTTGCACATACTTGGTATA 59.034 33.333 9.82 0.00 34.78 1.47
869 5868 9.072294 GTGAAATTTTGCACATACTTGGTATAC 57.928 33.333 5.40 0.00 35.19 1.47
870 5869 8.797438 TGAAATTTTGCACATACTTGGTATACA 58.203 29.630 5.01 0.00 0.00 2.29
871 5870 9.801873 GAAATTTTGCACATACTTGGTATACAT 57.198 29.630 5.01 0.00 0.00 2.29
872 5871 9.585099 AAATTTTGCACATACTTGGTATACATG 57.415 29.630 5.01 2.09 0.00 3.21
903 5995 5.931146 TGTGTCCACAAATATTGGCATTTTC 59.069 36.000 0.00 0.00 38.56 2.29
922 6019 2.674420 TCGGTCCTAAACATCCCCTAG 58.326 52.381 0.00 0.00 0.00 3.02
955 6062 2.564947 GCCCACATTTCCAACCACAATA 59.435 45.455 0.00 0.00 0.00 1.90
985 6105 0.184933 CCCTGTTTCCTGGTCAACCA 59.815 55.000 1.20 1.20 45.30 3.67
1042 6163 3.181476 CCAAAAAGACCTTGACCTTGGTG 60.181 47.826 0.00 0.00 36.59 4.17
1052 6173 0.666577 GACCTTGGTGTCGAGAACCG 60.667 60.000 11.57 2.02 40.86 4.44
1097 6218 2.038952 TCCCACCAATGTCAAGACTCAG 59.961 50.000 1.53 0.00 0.00 3.35
1330 6454 3.330720 CCCGCCTGGAAACCCTCT 61.331 66.667 0.00 0.00 37.49 3.69
1332 6456 2.294078 CCGCCTGGAAACCCTCTCT 61.294 63.158 0.00 0.00 37.49 3.10
1496 6638 2.478539 GCAGAGAAATGCGGGTCAAATC 60.479 50.000 0.00 0.00 36.28 2.17
1497 6639 3.012518 CAGAGAAATGCGGGTCAAATCT 58.987 45.455 0.00 0.00 0.00 2.40
2041 7226 0.320374 TAGCTTGTCCCTGTCCAACG 59.680 55.000 0.00 0.00 0.00 4.10
2067 7252 1.603456 TTTCCGATGCTGAAACTGCA 58.397 45.000 5.87 5.87 42.03 4.41
2090 7275 0.659957 GCAGGGCATTTCAGATCGAC 59.340 55.000 0.00 0.00 0.00 4.20
2109 7294 3.179048 GACGCCACTTGATTTATTTGCC 58.821 45.455 0.00 0.00 0.00 4.52
2132 7317 4.282068 GTCGCCGTTGTCGAATATAGTTA 58.718 43.478 0.00 0.00 37.73 2.24
2134 7319 4.913345 TCGCCGTTGTCGAATATAGTTATG 59.087 41.667 0.00 0.00 39.71 1.90
2144 7329 8.033038 TGTCGAATATAGTTATGCTATCCAACC 58.967 37.037 0.00 0.00 40.61 3.77
2150 7335 3.389983 AGTTATGCTATCCAACCGGCTTA 59.610 43.478 0.00 0.00 0.00 3.09
2182 7367 1.134753 TGTTTGTCACAGGCTGCAAAG 59.865 47.619 15.89 2.29 31.04 2.77
2239 7424 2.736670 AAGCTTGTTCCTGTCCAACT 57.263 45.000 0.00 0.00 0.00 3.16
2240 7425 3.857157 AAGCTTGTTCCTGTCCAACTA 57.143 42.857 0.00 0.00 0.00 2.24
2248 7433 5.362263 TGTTCCTGTCCAACTAAACACTAC 58.638 41.667 0.00 0.00 0.00 2.73
2306 7491 2.754002 TGATGCATTTCCGATGCTGAAA 59.246 40.909 0.00 0.00 44.79 2.69
2360 7545 3.548745 TCAGATCGATGCCACTTGATT 57.451 42.857 0.54 0.00 0.00 2.57
2364 7549 5.467735 TCAGATCGATGCCACTTGATTTATG 59.532 40.000 0.54 0.00 0.00 1.90
2388 7573 2.791927 GGTTGCCGATTTCGAGCC 59.208 61.111 0.67 0.00 43.02 4.70
2403 7589 0.733150 GAGCCACTTAATTCACGGGC 59.267 55.000 0.00 0.00 41.65 6.13
2628 7841 6.123045 ACTACAAGGCTTGGTTGTTATACT 57.877 37.500 29.26 8.37 38.98 2.12
2734 8005 2.125310 CTGTATTCCACCGCGCCA 60.125 61.111 0.00 0.00 0.00 5.69
2796 8072 5.565592 TTATTGCTTAACTGATGCAGGTG 57.434 39.130 0.00 0.00 39.23 4.00
2816 8092 2.434336 TGGCGTGCTTAGGAATCTACAT 59.566 45.455 0.00 0.00 0.00 2.29
2828 8104 4.586841 AGGAATCTACATCAGAGGTACTGC 59.413 45.833 0.00 0.00 45.38 4.40
2906 8212 6.602278 TCTTTCTAACGAGATCCATAGGAGA 58.398 40.000 0.00 0.00 34.05 3.71
2908 8214 4.328536 TCTAACGAGATCCATAGGAGAGC 58.671 47.826 0.00 0.00 34.05 4.09
2927 8233 4.971924 AGAGCCCCAGAAAGAGTTATACAT 59.028 41.667 0.00 0.00 0.00 2.29
2995 8316 5.239087 ACGCTTGCTAGTTAGGAGTAGTATC 59.761 44.000 0.00 0.00 32.39 2.24
3048 8386 0.383491 CTTGACAACTTCTGTGCGCG 60.383 55.000 0.00 0.00 38.84 6.86
3284 8683 9.065871 CAAATTCGATGGTTTGAAAGAAGTATC 57.934 33.333 11.01 0.00 37.48 2.24
3859 28046 1.763968 TGCCGCAGTCACTAGATAGT 58.236 50.000 0.00 0.00 36.90 2.12
4242 31764 5.506686 AGTCGATGGTGATATCCGATATG 57.493 43.478 5.59 0.00 0.00 1.78
4501 34027 1.411977 CTGGTGCCTCATCTGACCTAG 59.588 57.143 0.00 0.00 0.00 3.02
4805 34353 1.410004 TTGACAGGACGACAAGGAGT 58.590 50.000 0.00 0.00 0.00 3.85
4839 34480 0.109132 GCCAGCAAAATCAGGGAACG 60.109 55.000 0.00 0.00 0.00 3.95
5058 34699 7.153217 TGACGAGATCACAAAACTAGTATCA 57.847 36.000 0.00 0.00 29.99 2.15
5059 34700 7.027760 TGACGAGATCACAAAACTAGTATCAC 58.972 38.462 0.00 0.00 29.99 3.06
5118 34769 2.433970 GGGAACATCTTCTCTCTCTGGG 59.566 54.545 0.00 0.00 0.00 4.45
5139 34790 2.096496 GGACGAGAGCACCAAATCAATG 59.904 50.000 0.00 0.00 0.00 2.82
5149 34800 4.682860 GCACCAAATCAATGTCAACAGAAG 59.317 41.667 0.00 0.00 0.00 2.85
5153 34804 6.096705 ACCAAATCAATGTCAACAGAAGAACA 59.903 34.615 0.00 0.00 0.00 3.18
5176 34827 0.543749 AGATGGTCCTAACAGCAGCC 59.456 55.000 0.00 0.00 30.31 4.85
5203 34854 0.033503 TCAGGGAGCACCGTCTATCA 60.034 55.000 0.00 0.00 46.96 2.15
5223 34874 0.607489 CTGGTGAGGAGGCCACAAAG 60.607 60.000 5.01 0.00 36.31 2.77
5231 34882 2.158460 AGGAGGCCACAAAGCTAGTTTT 60.158 45.455 5.01 0.00 0.00 2.43
5239 34890 5.273944 CCACAAAGCTAGTTTTGACAGAAC 58.726 41.667 31.20 0.62 39.79 3.01
5247 34898 4.782019 AGTTTTGACAGAACAACAAGCA 57.218 36.364 11.10 0.00 0.00 3.91
5251 34902 6.318648 AGTTTTGACAGAACAACAAGCAGATA 59.681 34.615 11.10 0.00 0.00 1.98
5269 34920 3.444388 AGATAGTTATAGCGGTAGCCAGC 59.556 47.826 0.00 0.00 46.67 4.85
5270 34921 1.410004 AGTTATAGCGGTAGCCAGCA 58.590 50.000 0.00 0.00 46.67 4.41
5305 34956 1.740332 TTCTGTCACCCGCAACGAGA 61.740 55.000 0.00 0.00 0.00 4.04
5306 34957 1.734477 CTGTCACCCGCAACGAGAG 60.734 63.158 0.00 0.00 0.00 3.20
5324 34975 3.059982 CGCCAACCAGTGAGGAGA 58.940 61.111 0.00 0.00 41.22 3.71
5340 34991 1.339151 GGAGATCAAGAAACGGGTGCT 60.339 52.381 0.00 0.00 0.00 4.40
5342 34993 0.721718 GATCAAGAAACGGGTGCTCG 59.278 55.000 0.00 0.00 0.00 5.03
5343 34994 0.034896 ATCAAGAAACGGGTGCTCGT 59.965 50.000 0.00 0.00 46.08 4.18
5345 34996 1.597027 AAGAAACGGGTGCTCGTGG 60.597 57.895 0.00 0.00 43.07 4.94
5362 35013 2.357034 GTGAGAGCGGCGAACCAA 60.357 61.111 12.98 0.00 34.57 3.67
5367 35018 3.083600 GAGCGGCGAACCAATGACG 62.084 63.158 12.98 0.00 34.57 4.35
5371 35022 0.806102 CGGCGAACCAATGACGAGAT 60.806 55.000 0.00 0.00 34.57 2.75
5386 35037 2.224209 ACGAGATCAAGAAACGGGTGTT 60.224 45.455 0.00 0.00 40.98 3.32
5423 35074 4.508551 AGATGATGCTAACAATGGGTCA 57.491 40.909 0.00 0.00 0.00 4.02
5457 38907 2.107141 CCTTCTTCGCCCTAGCCG 59.893 66.667 0.00 0.00 34.57 5.52
5501 40376 7.698628 GGAGTATTCCTTTTGCTGATACTTTC 58.301 38.462 0.00 0.00 40.58 2.62
5515 40390 1.597742 ACTTTCGTTGCATGCAGACT 58.402 45.000 21.50 3.61 0.00 3.24
5550 40425 3.306780 CGATGTGTAGGGTCTGGAGTTTT 60.307 47.826 0.00 0.00 0.00 2.43
5552 40427 2.370849 TGTGTAGGGTCTGGAGTTTTCC 59.629 50.000 0.00 0.00 44.31 3.13
5557 40432 1.271434 GGGTCTGGAGTTTTCCCTGAC 60.271 57.143 0.00 0.00 43.33 3.51
5572 40447 2.880890 CCCTGACTTGTGTTTCTGAAGG 59.119 50.000 0.00 0.00 0.00 3.46
5616 40966 6.825284 TTTGTACTTTTGCATGATGTGTTG 57.175 33.333 0.00 0.00 0.00 3.33
5617 40967 4.297510 TGTACTTTTGCATGATGTGTTGC 58.702 39.130 0.00 0.00 39.33 4.17
5632 40982 2.356695 GTGTTGCGAACCAGTAAAACCT 59.643 45.455 0.00 0.00 0.00 3.50
5633 40983 2.614983 TGTTGCGAACCAGTAAAACCTC 59.385 45.455 0.00 0.00 0.00 3.85
5634 40984 1.886886 TGCGAACCAGTAAAACCTCC 58.113 50.000 0.00 0.00 0.00 4.30
5636 40986 1.804748 GCGAACCAGTAAAACCTCCTG 59.195 52.381 0.00 0.00 0.00 3.86
5637 40987 2.809299 GCGAACCAGTAAAACCTCCTGT 60.809 50.000 0.00 0.00 0.00 4.00
5638 40988 3.473625 CGAACCAGTAAAACCTCCTGTT 58.526 45.455 0.00 0.00 39.43 3.16
5639 40989 4.634199 CGAACCAGTAAAACCTCCTGTTA 58.366 43.478 0.00 0.00 35.67 2.41
5642 40992 4.918588 ACCAGTAAAACCTCCTGTTATGG 58.081 43.478 0.00 0.00 35.67 2.74
5643 40993 4.263771 ACCAGTAAAACCTCCTGTTATGGG 60.264 45.833 0.00 0.00 35.67 4.00
5720 42048 7.112397 GTGTAAATGCAATGCAATTTCATACG 58.888 34.615 13.45 0.00 39.24 3.06
5726 42054 5.693555 TGCAATGCAATTTCATACGTTTTCA 59.306 32.000 5.01 0.00 34.76 2.69
5761 43477 7.706281 AACAATGCAATTTCATACGTTTTCA 57.294 28.000 0.00 0.00 31.22 2.69
5777 43493 2.798976 TTCACCAGCTGCAAAACATC 57.201 45.000 8.66 0.00 0.00 3.06
5909 47649 7.386025 CGAAATCAGCAATCCTATGAGTGAATA 59.614 37.037 0.00 0.00 38.86 1.75
5943 47683 5.762218 ACAAGGCAGATTGTAGAGCATATTC 59.238 40.000 0.00 0.00 41.53 1.75
5950 47690 7.215789 CAGATTGTAGAGCATATTCAGGAACT 58.784 38.462 0.00 0.00 43.88 3.01
5966 47709 4.022329 CAGGAACTTGGTACCATCCAAAAC 60.022 45.833 27.40 11.91 45.26 2.43
6450 48193 2.441375 TGTTCCTCATTGGTGTCTTCCA 59.559 45.455 0.00 0.00 37.07 3.53
6556 48300 1.581954 CTCGTCAGTGAGAAGCCGT 59.418 57.895 0.00 0.00 38.28 5.68
6620 48364 1.740380 CGGCGAAGTTCATGTCCTGAT 60.740 52.381 0.00 0.00 32.72 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.592669 CGGCAGGATTAGCGACAGG 60.593 63.158 0.00 0.00 0.00 4.00
14 15 2.202878 GCGGCAGGATTAGCGACA 60.203 61.111 0.00 0.00 0.00 4.35
16 17 2.106938 CTGCGGCAGGATTAGCGA 59.893 61.111 22.11 0.00 0.00 4.93
17 18 3.643978 GCTGCGGCAGGATTAGCG 61.644 66.667 29.44 4.68 38.54 4.26
30 31 2.331132 AAGCCGAAAGAGCAGCTGC 61.331 57.895 31.53 31.53 42.49 5.25
32 33 2.331132 GCAAGCCGAAAGAGCAGCT 61.331 57.895 0.00 0.00 37.10 4.24
33 34 2.177778 GCAAGCCGAAAGAGCAGC 59.822 61.111 0.00 0.00 0.00 5.25
34 35 2.029288 TCGCAAGCCGAAAGAGCAG 61.029 57.895 0.00 0.00 44.21 4.24
35 36 2.030412 TCGCAAGCCGAAAGAGCA 59.970 55.556 0.00 0.00 44.21 4.26
44 45 2.117156 ATGCACAGGATCGCAAGCC 61.117 57.895 0.00 0.00 42.37 4.35
48 49 0.805711 CGTACATGCACAGGATCGCA 60.806 55.000 0.00 0.00 43.45 5.10
49 50 0.806102 ACGTACATGCACAGGATCGC 60.806 55.000 0.00 0.00 0.00 4.58
50 51 0.923403 CACGTACATGCACAGGATCG 59.077 55.000 0.00 0.00 0.00 3.69
51 52 2.293677 TCACGTACATGCACAGGATC 57.706 50.000 0.00 0.00 0.00 3.36
54 55 1.078709 CCTTCACGTACATGCACAGG 58.921 55.000 0.00 0.00 0.00 4.00
56 57 0.034756 AGCCTTCACGTACATGCACA 59.965 50.000 0.00 0.00 0.00 4.57
57 58 0.443869 CAGCCTTCACGTACATGCAC 59.556 55.000 0.00 0.00 0.00 4.57
58 59 0.320050 TCAGCCTTCACGTACATGCA 59.680 50.000 0.00 0.00 0.00 3.96
60 61 3.067106 ACTTTCAGCCTTCACGTACATG 58.933 45.455 0.00 0.00 0.00 3.21
61 62 3.326747 GACTTTCAGCCTTCACGTACAT 58.673 45.455 0.00 0.00 0.00 2.29
64 65 1.689813 TGGACTTTCAGCCTTCACGTA 59.310 47.619 0.00 0.00 0.00 3.57
66 67 0.868406 GTGGACTTTCAGCCTTCACG 59.132 55.000 0.00 0.00 0.00 4.35
67 68 0.868406 CGTGGACTTTCAGCCTTCAC 59.132 55.000 0.00 0.00 0.00 3.18
68 69 0.884704 GCGTGGACTTTCAGCCTTCA 60.885 55.000 0.00 0.00 0.00 3.02
70 71 1.600916 GGCGTGGACTTTCAGCCTT 60.601 57.895 0.00 0.00 44.06 4.35
71 72 2.032681 GGCGTGGACTTTCAGCCT 59.967 61.111 0.00 0.00 44.06 4.58
72 73 1.172812 AAAGGCGTGGACTTTCAGCC 61.173 55.000 0.00 0.00 35.83 4.85
73 74 0.040067 CAAAGGCGTGGACTTTCAGC 60.040 55.000 0.00 0.00 39.06 4.26
74 75 1.264288 GTCAAAGGCGTGGACTTTCAG 59.736 52.381 0.26 0.00 39.06 3.02
76 77 1.594331 AGTCAAAGGCGTGGACTTTC 58.406 50.000 4.50 0.00 39.06 2.62
77 78 2.922740 TAGTCAAAGGCGTGGACTTT 57.077 45.000 15.70 0.00 42.19 2.66
78 79 3.418684 AATAGTCAAAGGCGTGGACTT 57.581 42.857 15.70 1.87 41.74 3.01
80 81 4.499037 AAAAATAGTCAAAGGCGTGGAC 57.501 40.909 0.00 0.00 0.00 4.02
99 100 6.237901 AGGTACTATGCACATGTCAGAAAAA 58.762 36.000 0.00 0.00 36.02 1.94
100 101 5.804639 AGGTACTATGCACATGTCAGAAAA 58.195 37.500 0.00 0.00 36.02 2.29
101 102 5.420725 AGGTACTATGCACATGTCAGAAA 57.579 39.130 0.00 0.00 36.02 2.52
102 103 5.420739 TGTAGGTACTATGCACATGTCAGAA 59.579 40.000 0.00 0.00 45.60 3.02
103 104 4.953579 TGTAGGTACTATGCACATGTCAGA 59.046 41.667 0.00 0.00 45.60 3.27
104 105 5.262588 TGTAGGTACTATGCACATGTCAG 57.737 43.478 0.00 0.00 45.60 3.51
344 345 2.033141 CATCATAGCCAGGGCCGG 59.967 66.667 6.70 9.66 43.17 6.13
345 346 1.830587 TAGCATCATAGCCAGGGCCG 61.831 60.000 6.70 0.00 43.17 6.13
346 347 0.322008 GTAGCATCATAGCCAGGGCC 60.322 60.000 6.70 0.00 43.17 5.80
348 349 0.681733 ACGTAGCATCATAGCCAGGG 59.318 55.000 0.00 0.00 34.23 4.45
349 350 1.615883 AGACGTAGCATCATAGCCAGG 59.384 52.381 0.00 0.00 34.23 4.45
351 352 2.031870 ACAGACGTAGCATCATAGCCA 58.968 47.619 0.00 0.00 34.23 4.75
352 353 2.802787 ACAGACGTAGCATCATAGCC 57.197 50.000 0.00 0.00 34.23 3.93
354 355 4.618912 GTGCATACAGACGTAGCATCATAG 59.381 45.833 0.00 0.00 35.59 2.23
355 356 4.546570 GTGCATACAGACGTAGCATCATA 58.453 43.478 0.00 0.00 35.59 2.15
356 357 3.384668 GTGCATACAGACGTAGCATCAT 58.615 45.455 0.00 0.00 35.59 2.45
376 5362 4.405116 ACAACAACAAAAGATGCATGGT 57.595 36.364 2.46 0.00 0.00 3.55
377 5363 4.553156 GCAACAACAACAAAAGATGCATGG 60.553 41.667 2.46 0.00 33.00 3.66
378 5364 4.271533 AGCAACAACAACAAAAGATGCATG 59.728 37.500 2.46 0.00 35.11 4.06
397 5383 7.769970 TGATCTCATCATACAAACACATAGCAA 59.230 33.333 0.00 0.00 33.59 3.91
426 5412 3.187700 CGAGCACCCTGTATGAAACTAC 58.812 50.000 0.00 0.00 0.00 2.73
434 5420 2.394632 TGTTATCCGAGCACCCTGTAT 58.605 47.619 0.00 0.00 0.00 2.29
439 5425 2.325583 TTCATGTTATCCGAGCACCC 57.674 50.000 0.00 0.00 0.00 4.61
441 5427 5.484173 TCAAATTCATGTTATCCGAGCAC 57.516 39.130 0.00 0.00 0.00 4.40
457 5443 4.706962 GCCTTAAGTCATGTCCCTCAAATT 59.293 41.667 0.97 0.00 0.00 1.82
486 5472 1.250840 GGTCACCCCTCAAATGCACC 61.251 60.000 0.00 0.00 0.00 5.01
510 5506 1.671054 CGGCCTTGTTCACGGACAT 60.671 57.895 0.00 0.00 0.00 3.06
511 5507 2.280524 CGGCCTTGTTCACGGACA 60.281 61.111 0.00 0.00 0.00 4.02
523 5519 2.170012 TTCACTACCTAATCCGGCCT 57.830 50.000 0.00 0.00 0.00 5.19
524 5520 2.767505 CATTCACTACCTAATCCGGCC 58.232 52.381 0.00 0.00 0.00 6.13
539 5535 9.196552 CATGATCGTAGTTTATTAGAGCATTCA 57.803 33.333 0.00 0.00 36.04 2.57
556 5552 5.704515 GCTTAGGAGTACTACCATGATCGTA 59.295 44.000 0.00 0.00 0.00 3.43
558 5554 4.519350 TGCTTAGGAGTACTACCATGATCG 59.481 45.833 0.00 0.00 0.00 3.69
598 5594 3.077556 TCCTTGGAGCTCGGCCTC 61.078 66.667 7.83 0.00 0.00 4.70
611 5607 3.440522 GCTTTCAAAATACCGAGCTCCTT 59.559 43.478 8.47 0.00 0.00 3.36
612 5608 3.010420 GCTTTCAAAATACCGAGCTCCT 58.990 45.455 8.47 0.00 0.00 3.69
700 5699 8.892887 TTAAACGAAATTTAACACGTTCTTGT 57.107 26.923 13.64 3.91 45.71 3.16
724 5723 7.733402 ACAGCTTGCAAATCACAATATTTTT 57.267 28.000 0.00 0.00 0.00 1.94
726 5725 7.377398 TGTACAGCTTGCAAATCACAATATTT 58.623 30.769 0.00 0.00 0.00 1.40
733 5732 5.964887 TTTTTGTACAGCTTGCAAATCAC 57.035 34.783 0.00 0.00 39.28 3.06
759 5758 1.923356 ATTTCTGTTGTTGGGCCGAT 58.077 45.000 0.00 0.00 0.00 4.18
760 5759 2.570415 TATTTCTGTTGTTGGGCCGA 57.430 45.000 0.00 0.00 0.00 5.54
774 5773 8.909708 GCATTTTTAAATGGGCCTTTTATTTC 57.090 30.769 21.21 7.84 44.54 2.17
799 5798 4.499758 GGCGTACAGAGAAAGAGAAATACG 59.500 45.833 0.00 0.00 37.73 3.06
812 5811 2.078849 TTCACACATGGCGTACAGAG 57.921 50.000 0.00 0.00 0.00 3.35
819 5818 5.484173 ACATTATACTTTCACACATGGCG 57.516 39.130 0.00 0.00 0.00 5.69
824 5823 7.716768 TTTCACGACATTATACTTTCACACA 57.283 32.000 0.00 0.00 0.00 3.72
841 5840 5.218885 CCAAGTATGTGCAAAATTTCACGA 58.781 37.500 0.00 0.00 36.06 4.35
842 5841 4.981674 ACCAAGTATGTGCAAAATTTCACG 59.018 37.500 0.00 0.00 36.06 4.35
861 5860 6.167685 GGACACACTTACACATGTATACCAA 58.832 40.000 0.00 0.00 0.00 3.67
862 5861 5.246429 TGGACACACTTACACATGTATACCA 59.754 40.000 0.00 0.00 0.00 3.25
863 5862 5.579511 GTGGACACACTTACACATGTATACC 59.420 44.000 0.00 0.00 44.29 2.73
864 5863 6.642683 GTGGACACACTTACACATGTATAC 57.357 41.667 0.00 0.00 44.29 1.47
903 5995 2.674420 TCTAGGGGATGTTTAGGACCG 58.326 52.381 0.00 0.00 0.00 4.79
940 6037 4.531732 ACTTGGCATATTGTGGTTGGAAAT 59.468 37.500 0.00 0.00 0.00 2.17
1017 6138 4.647399 CCAAGGTCAAGGTCTTTTTGGTAA 59.353 41.667 0.00 0.00 31.33 2.85
1052 6173 9.244799 GGATTTCCGTTCCAAAAATATATTGTC 57.755 33.333 0.00 0.00 33.21 3.18
1056 6177 7.201965 GGTGGGATTTCCGTTCCAAAAATATAT 60.202 37.037 0.00 0.00 38.76 0.86
1057 6178 6.097129 GGTGGGATTTCCGTTCCAAAAATATA 59.903 38.462 0.00 0.00 38.76 0.86
1060 6181 3.007506 GGTGGGATTTCCGTTCCAAAAAT 59.992 43.478 0.00 0.00 38.76 1.82
1063 6184 1.133450 TGGTGGGATTTCCGTTCCAAA 60.133 47.619 4.37 0.00 38.76 3.28
1330 6454 0.037326 AACCGATTGCAGCTTCGAGA 60.037 50.000 16.85 0.00 37.55 4.04
1332 6456 0.037326 AGAACCGATTGCAGCTTCGA 60.037 50.000 16.85 0.00 37.55 3.71
2041 7226 1.311859 TCAGCATCGGAAATGCATCC 58.688 50.000 12.12 0.00 46.77 3.51
2132 7317 3.508845 ATTAAGCCGGTTGGATAGCAT 57.491 42.857 1.90 0.00 37.49 3.79
2134 7319 4.649088 AAAATTAAGCCGGTTGGATAGC 57.351 40.909 1.90 0.00 37.49 2.97
2144 7329 7.168302 TGACAAACACACATAAAAATTAAGCCG 59.832 33.333 0.00 0.00 0.00 5.52
2221 7406 3.857157 TTAGTTGGACAGGAACAAGCT 57.143 42.857 0.00 0.00 0.00 3.74
2228 7413 3.553508 GCGTAGTGTTTAGTTGGACAGGA 60.554 47.826 0.00 0.00 0.00 3.86
2275 7460 8.236586 GCATCGGAAATGCATCAATTAAGTATA 58.763 33.333 0.00 0.00 44.00 1.47
2326 7511 2.632377 GATCTGAAATGCGGGACAGAA 58.368 47.619 0.00 0.00 41.57 3.02
2360 7545 2.685829 CGGCAACCGCAGCACATAA 61.686 57.895 0.00 0.00 41.17 1.90
2388 7573 0.096976 CGCAGCCCGTGAATTAAGTG 59.903 55.000 0.00 0.00 0.00 3.16
2403 7589 1.299316 CAACAGCAACCAACCGCAG 60.299 57.895 0.00 0.00 0.00 5.18
2628 7841 1.755959 AGTTTGCAGTTGCCACATCAA 59.244 42.857 1.06 0.00 41.18 2.57
2734 8005 4.887071 TCAGTAGCAACAGTCAACCAAAAT 59.113 37.500 0.00 0.00 0.00 1.82
2796 8072 2.596904 TGTAGATTCCTAAGCACGCC 57.403 50.000 0.00 0.00 0.00 5.68
2816 8092 1.930251 AGCTTGAGCAGTACCTCTGA 58.070 50.000 5.70 0.00 46.27 3.27
2828 8104 2.551459 CCTCTGACCAACAAAGCTTGAG 59.449 50.000 0.00 0.00 0.00 3.02
2906 8212 6.592870 GTTATGTATAACTCTTTCTGGGGCT 58.407 40.000 7.36 0.00 39.53 5.19
2927 8233 5.697633 ACCTCGATTTAGCGTTTTGAAGTTA 59.302 36.000 0.00 0.00 0.00 2.24
2995 8316 1.001745 GTTTGCGGGTAAAAGCGCAG 61.002 55.000 11.47 0.00 38.60 5.18
3048 8386 4.808364 GCATAGAGAATAGAATCCATCCGC 59.192 45.833 0.00 0.00 0.00 5.54
3284 8683 3.366679 CCTTGTGCTTAAATCTGTGGCTG 60.367 47.826 0.00 0.00 0.00 4.85
3746 27930 2.181021 CGGCCTCTGTGACGGTAC 59.819 66.667 0.00 0.00 0.00 3.34
3859 28046 1.842920 TCCAGGCCTGACAAGAGCA 60.843 57.895 34.91 4.03 0.00 4.26
4032 28308 4.536090 ACATCCTTGGATTTACTCACCTGA 59.464 41.667 0.00 0.00 0.00 3.86
4242 31764 3.935828 GGTATGCAGTCCTCTTCTTTGAC 59.064 47.826 0.00 0.00 0.00 3.18
4449 33975 5.371526 CCTGCTTCTCCAAATATAAGCTCA 58.628 41.667 7.35 0.00 43.69 4.26
4501 34027 0.308993 GCATATCGAGTTGCCTTGCC 59.691 55.000 10.44 0.00 32.66 4.52
4775 34323 4.210746 GTCGTCCTGTCAAAACTAGTTTCC 59.789 45.833 20.78 12.26 31.45 3.13
4805 34353 2.047274 GGCTGCTGCTACGACCAA 60.047 61.111 15.64 0.00 39.59 3.67
4839 34480 0.036858 GGTCACCAGTGAGAGAAGGC 60.037 60.000 0.00 0.00 40.75 4.35
4950 34591 4.143305 CCTGTCGAAACTCGTTTCTTGATC 60.143 45.833 17.45 0.00 44.93 2.92
5058 34699 2.979678 ACCATCTACTTGTTGGTCTGGT 59.020 45.455 0.00 0.00 43.26 4.00
5059 34700 3.338249 CACCATCTACTTGTTGGTCTGG 58.662 50.000 0.00 0.00 44.50 3.86
5080 34721 3.746045 TCCCTGATCGCTATTGTTACC 57.254 47.619 0.00 0.00 0.00 2.85
5081 34722 4.439057 TGTTCCCTGATCGCTATTGTTAC 58.561 43.478 0.00 0.00 0.00 2.50
5118 34769 1.808411 TTGATTTGGTGCTCTCGTCC 58.192 50.000 0.00 0.00 0.00 4.79
5139 34790 4.453819 CCATCTCCTTGTTCTTCTGTTGAC 59.546 45.833 0.00 0.00 0.00 3.18
5172 34823 1.893544 CTCCCTGATTATGCTGGCTG 58.106 55.000 0.00 0.00 0.00 4.85
5176 34827 1.602311 GGTGCTCCCTGATTATGCTG 58.398 55.000 0.00 0.00 0.00 4.41
5203 34854 1.352622 TTTGTGGCCTCCTCACCAGT 61.353 55.000 3.32 0.00 36.38 4.00
5223 34874 4.735338 GCTTGTTGTTCTGTCAAAACTAGC 59.265 41.667 5.38 5.38 41.57 3.42
5231 34882 4.960938 ACTATCTGCTTGTTGTTCTGTCA 58.039 39.130 0.00 0.00 0.00 3.58
5239 34890 5.050490 ACCGCTATAACTATCTGCTTGTTG 58.950 41.667 0.00 0.00 0.00 3.33
5247 34898 3.444388 GCTGGCTACCGCTATAACTATCT 59.556 47.826 0.00 0.00 36.09 1.98
5251 34902 1.341531 CTGCTGGCTACCGCTATAACT 59.658 52.381 0.00 0.00 36.09 2.24
5269 34920 1.912043 AGAAGGTGTTCCCTGATCCTG 59.088 52.381 0.00 0.00 45.47 3.86
5270 34921 1.912043 CAGAAGGTGTTCCCTGATCCT 59.088 52.381 0.00 0.00 45.47 3.24
5290 34941 3.112709 GCTCTCGTTGCGGGTGAC 61.113 66.667 0.00 0.00 0.00 3.67
5305 34956 3.241530 TCCTCACTGGTTGGCGCT 61.242 61.111 7.64 0.00 37.07 5.92
5306 34957 2.527951 ATCTCCTCACTGGTTGGCGC 62.528 60.000 0.00 0.00 37.07 6.53
5310 34961 3.969287 TCTTGATCTCCTCACTGGTTG 57.031 47.619 0.00 0.00 37.07 3.77
5324 34975 0.034896 ACGAGCACCCGTTTCTTGAT 59.965 50.000 0.00 0.00 40.17 2.57
5342 34993 3.112709 GTTCGCCGCTCTCACCAC 61.113 66.667 0.00 0.00 0.00 4.16
5343 34994 4.373116 GGTTCGCCGCTCTCACCA 62.373 66.667 0.00 0.00 0.00 4.17
5345 34996 1.741770 ATTGGTTCGCCGCTCTCAC 60.742 57.895 0.00 0.00 41.18 3.51
5356 35007 5.622378 GTTTCTTGATCTCGTCATTGGTTC 58.378 41.667 0.00 0.00 36.54 3.62
5362 35013 2.233922 ACCCGTTTCTTGATCTCGTCAT 59.766 45.455 0.00 0.00 36.54 3.06
5367 35018 3.186613 GTCAACACCCGTTTCTTGATCTC 59.813 47.826 0.00 0.00 31.13 2.75
5371 35022 1.292061 CGTCAACACCCGTTTCTTGA 58.708 50.000 0.00 0.00 31.13 3.02
5386 35037 2.068519 CATCTACTTGTTGCTGCGTCA 58.931 47.619 0.00 0.00 0.00 4.35
5423 35074 0.548682 AGGTGTTCCCTCATCCTGCT 60.549 55.000 0.00 0.00 40.71 4.24
5457 38907 1.079503 CTTCCTGTAAGCGTCTTGGC 58.920 55.000 2.86 0.00 0.00 4.52
5460 38910 2.249139 ACTCCTTCCTGTAAGCGTCTT 58.751 47.619 0.00 0.00 33.49 3.01
5501 40376 1.891178 CATTCAGTCTGCATGCAACG 58.109 50.000 22.88 11.39 0.00 4.10
5515 40390 1.066645 ACACATCGCTCTCTGCATTCA 60.067 47.619 0.00 0.00 43.06 2.57
5537 40412 1.064825 TCAGGGAAAACTCCAGACCC 58.935 55.000 0.00 0.00 40.71 4.46
5550 40425 3.433598 CCTTCAGAAACACAAGTCAGGGA 60.434 47.826 0.00 0.00 0.00 4.20
5552 40427 3.545703 ACCTTCAGAAACACAAGTCAGG 58.454 45.455 0.00 0.00 0.00 3.86
5557 40432 4.119862 TCTTCGACCTTCAGAAACACAAG 58.880 43.478 0.00 0.00 0.00 3.16
5572 40447 1.135746 ACACGTCGGATTCTCTTCGAC 60.136 52.381 0.00 0.00 46.52 4.20
5616 40966 1.804748 CAGGAGGTTTTACTGGTTCGC 59.195 52.381 0.00 0.00 0.00 4.70
5617 40967 3.121738 ACAGGAGGTTTTACTGGTTCG 57.878 47.619 0.00 0.00 36.57 3.95
5632 40982 2.265367 TGCTTGAGACCCATAACAGGA 58.735 47.619 0.00 0.00 0.00 3.86
5633 40983 2.787473 TGCTTGAGACCCATAACAGG 57.213 50.000 0.00 0.00 0.00 4.00
5634 40984 3.877559 TCATGCTTGAGACCCATAACAG 58.122 45.455 0.00 0.00 0.00 3.16
5636 40986 4.641989 ACATTCATGCTTGAGACCCATAAC 59.358 41.667 2.23 0.00 32.27 1.89
5637 40987 4.858850 ACATTCATGCTTGAGACCCATAA 58.141 39.130 2.23 0.00 32.27 1.90
5638 40988 4.508551 ACATTCATGCTTGAGACCCATA 57.491 40.909 2.23 0.00 32.27 2.74
5639 40989 3.377253 ACATTCATGCTTGAGACCCAT 57.623 42.857 2.23 0.00 32.27 4.00
5642 40992 2.945668 GGGTACATTCATGCTTGAGACC 59.054 50.000 2.23 8.81 32.27 3.85
5643 40993 2.945668 GGGGTACATTCATGCTTGAGAC 59.054 50.000 2.23 1.07 32.27 3.36
5720 42048 2.615869 TGTTTTGCAGCTGGTGAAAAC 58.384 42.857 24.28 24.28 32.90 2.43
5726 42054 3.294079 GCATTGTTTTGCAGCTGGT 57.706 47.368 17.12 0.00 42.31 4.00
5755 43471 2.615869 TGTTTTGCAGCTGGTGAAAAC 58.384 42.857 24.28 24.28 32.90 2.43
5761 43477 4.870123 TTTATGATGTTTTGCAGCTGGT 57.130 36.364 17.12 0.00 34.02 4.00
5777 43493 6.149633 GGAAGCGCCTAATGGTATTTTTATG 58.850 40.000 2.29 0.00 35.27 1.90
5859 45950 5.185249 GTGGGAACTGACTTACTGATAGACA 59.815 44.000 0.00 0.00 0.00 3.41
5860 45951 5.652518 GTGGGAACTGACTTACTGATAGAC 58.347 45.833 0.00 0.00 0.00 2.59
5861 45952 4.398358 CGTGGGAACTGACTTACTGATAGA 59.602 45.833 0.00 0.00 0.00 1.98
5865 45956 2.589720 TCGTGGGAACTGACTTACTGA 58.410 47.619 0.00 0.00 0.00 3.41
5866 45957 3.380479 TTCGTGGGAACTGACTTACTG 57.620 47.619 0.00 0.00 0.00 2.74
5867 45958 4.039973 TGATTTCGTGGGAACTGACTTACT 59.960 41.667 0.00 0.00 0.00 2.24
5943 47683 3.433306 TTGGATGGTACCAAGTTCCTG 57.567 47.619 26.26 0.00 43.79 3.86
5950 47690 2.243810 GCTGGTTTTGGATGGTACCAA 58.756 47.619 20.76 0.00 46.44 3.67
5966 47709 3.674682 GCTCTTAGTACACACTCTGCTGG 60.675 52.174 0.00 0.00 36.14 4.85
6360 48103 1.950007 CCGACTATCGCGAGGACAT 59.050 57.895 16.66 0.00 38.82 3.06
6450 48193 0.534412 CTGTGGAGTCATCGCTTCCT 59.466 55.000 0.00 0.00 0.00 3.36
6556 48300 1.072505 GGAGTTGACGCCTTTCCCA 59.927 57.895 0.00 0.00 32.72 4.37
6567 48311 4.299547 AGCGCGCACAGGAGTTGA 62.300 61.111 35.10 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.