Multiple sequence alignment - TraesCS7D01G008300

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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 TraesCS7D01G008300 chr7D 100.000 6986 0 0 1 6986 4018650 4011665 0.000000e+00 12901.0
1 TraesCS7D01G008300 chr7D 84.224 1198 125 35 3854 5021 3565440 3564277 0.000000e+00 1107.0
2 TraesCS7D01G008300 chr7D 82.916 679 82 21 3128 3787 2664446 2663783 1.310000e-161 580.0
3 TraesCS7D01G008300 chr7D 82.504 663 60 19 2385 3037 3621223 3620607 1.330000e-146 531.0
4 TraesCS7D01G008300 chr7D 83.221 596 73 14 6149 6721 3563561 3562970 8.030000e-144 521.0
5 TraesCS7D01G008300 chr7D 79.965 574 73 21 1867 2438 2881532 2880999 1.100000e-102 385.0
6 TraesCS7D01G008300 chr7D 86.325 351 34 2 2862 3211 2507672 2507335 3.080000e-98 370.0
7 TraesCS7D01G008300 chr7D 80.819 464 56 15 3125 3580 2675975 2675537 4.040000e-87 333.0
8 TraesCS7D01G008300 chr7D 83.030 330 44 8 3107 3425 3420189 3419861 8.870000e-74 289.0
9 TraesCS7D01G008300 chr7D 90.141 71 7 0 4106 4176 3608474 3608404 7.460000e-15 93.5
10 TraesCS7D01G008300 chr7A 95.571 4109 133 19 2671 6746 3849415 3845323 0.000000e+00 6534.0
11 TraesCS7D01G008300 chr7A 92.312 3824 231 29 2162 5965 3539359 3535579 0.000000e+00 5374.0
12 TraesCS7D01G008300 chr7A 84.633 1705 152 69 869 2516 3851114 3849463 0.000000e+00 1596.0
13 TraesCS7D01G008300 chr7A 82.571 700 95 22 3107 3787 3800867 3800176 6.030000e-165 592.0
14 TraesCS7D01G008300 chr7A 80.807 719 76 35 1 684 3851983 3851292 2.250000e-139 507.0
15 TraesCS7D01G008300 chr7A 87.352 253 6 11 6744 6986 3845294 3845058 4.150000e-67 267.0
16 TraesCS7D01G008300 chr7A 92.667 150 11 0 2289 2438 2658064 2657915 4.240000e-52 217.0
17 TraesCS7D01G008300 chr4A 93.174 2300 109 17 2765 5052 741412386 741410123 0.000000e+00 3334.0
18 TraesCS7D01G008300 chr4A 93.517 1342 59 6 3119 4452 741367998 741366677 0.000000e+00 1971.0
19 TraesCS7D01G008300 chr4A 94.062 1280 44 11 3780 5052 742012791 742014045 0.000000e+00 1914.0
20 TraesCS7D01G008300 chr4A 83.457 1614 148 63 1025 2592 739595610 739597150 0.000000e+00 1391.0
21 TraesCS7D01G008300 chr4A 83.561 1539 162 51 3518 5021 739598030 739599512 0.000000e+00 1356.0
22 TraesCS7D01G008300 chr4A 91.677 829 53 6 5132 5946 742014042 742014868 0.000000e+00 1134.0
23 TraesCS7D01G008300 chr4A 94.992 599 17 5 4457 5052 741366609 741366021 0.000000e+00 928.0
24 TraesCS7D01G008300 chr4A 86.795 674 71 11 5338 5999 739599516 739600183 0.000000e+00 736.0
25 TraesCS7D01G008300 chr4A 90.761 552 43 7 2668 3216 739597157 739597703 0.000000e+00 730.0
26 TraesCS7D01G008300 chr4A 85.693 678 70 19 5338 5999 740154256 740153590 0.000000e+00 689.0
27 TraesCS7D01G008300 chr4A 93.981 432 23 2 5132 5562 741366024 741365595 0.000000e+00 651.0
28 TraesCS7D01G008300 chr4A 93.981 432 23 2 5132 5562 741410126 741409697 0.000000e+00 651.0
29 TraesCS7D01G008300 chr4A 80.195 924 112 37 5857 6717 741181268 741182183 1.650000e-175 627.0
30 TraesCS7D01G008300 chr4A 81.783 785 85 31 5994 6746 739600236 739600994 7.750000e-169 604.0
31 TraesCS7D01G008300 chr4A 82.821 716 78 22 5994 6669 741365387 741364677 3.610000e-167 599.0
32 TraesCS7D01G008300 chr4A 82.821 716 78 22 5994 6669 741409489 741408779 3.610000e-167 599.0
33 TraesCS7D01G008300 chr4A 82.994 688 86 16 3107 3787 733809448 733810111 1.680000e-165 593.0
34 TraesCS7D01G008300 chr4A 82.759 696 90 19 3107 3787 739610438 739611118 1.680000e-165 593.0
35 TraesCS7D01G008300 chr4A 79.137 973 115 47 5994 6911 742014998 742015937 6.030000e-165 592.0
36 TraesCS7D01G008300 chr4A 81.014 690 98 21 3119 3787 739758024 739757347 1.040000e-142 518.0
37 TraesCS7D01G008300 chr4A 85.161 465 62 6 3327 3787 742024681 742025142 2.950000e-128 470.0
38 TraesCS7D01G008300 chr4A 81.865 579 73 18 1874 2438 741776646 741776086 6.390000e-125 459.0
39 TraesCS7D01G008300 chr4A 85.194 412 42 11 2162 2573 741412795 741412403 8.440000e-109 405.0
40 TraesCS7D01G008300 chr4A 93.534 232 14 1 2934 3164 741178258 741178489 1.870000e-90 344.0
41 TraesCS7D01G008300 chr4A 90.076 262 21 2 2141 2397 740601533 740601272 1.120000e-87 335.0
42 TraesCS7D01G008300 chr4A 80.260 461 52 16 245 680 739594855 739595301 1.890000e-80 311.0
43 TraesCS7D01G008300 chr4A 96.855 159 5 0 5841 5999 741365598 741365440 4.150000e-67 267.0
44 TraesCS7D01G008300 chr4A 96.855 159 5 0 5841 5999 741409700 741409542 4.150000e-67 267.0
45 TraesCS7D01G008300 chr4A 87.444 223 26 1 4802 5024 740154477 740154257 8.990000e-64 255.0
46 TraesCS7D01G008300 chr4A 88.095 210 16 4 6744 6947 739603294 739603500 2.520000e-59 241.0
47 TraesCS7D01G008300 chr4A 96.552 145 5 0 5855 5999 739997050 739996906 2.520000e-59 241.0
48 TraesCS7D01G008300 chr4A 78.195 399 57 19 1867 2255 741047988 741048366 1.960000e-55 228.0
49 TraesCS7D01G008300 chr4A 88.333 180 17 3 3110 3286 740498621 740498799 5.490000e-51 213.0
50 TraesCS7D01G008300 chr4A 85.204 196 28 1 1 196 739594659 739594853 4.270000e-47 200.0
51 TraesCS7D01G008300 chr4A 92.523 107 5 3 5041 5145 35625884 35625779 4.370000e-32 150.0
52 TraesCS7D01G008300 chr4A 80.702 171 22 5 4882 5052 741785213 741785054 9.520000e-24 122.0
53 TraesCS7D01G008300 chr4A 90.476 84 7 1 6744 6827 741182313 741182395 7.410000e-20 110.0
54 TraesCS7D01G008300 chr4A 89.610 77 1 4 852 928 688787157 688787088 2.680000e-14 91.6
55 TraesCS7D01G008300 chrUn 100.000 395 0 0 5077 5471 479299730 479300124 0.000000e+00 730.0
56 TraesCS7D01G008300 chr4B 95.876 97 4 0 5049 5145 252979310 252979214 2.610000e-34 158.0
57 TraesCS7D01G008300 chr3D 95.876 97 4 0 5048 5144 30979382 30979286 2.610000e-34 158.0
58 TraesCS7D01G008300 chr6A 95.000 100 3 2 5046 5145 172113269 172113172 9.380000e-34 156.0
59 TraesCS7D01G008300 chr3B 91.964 112 7 2 5030 5140 15111127 15111017 9.380000e-34 156.0
60 TraesCS7D01G008300 chr6B 91.150 113 9 1 5032 5144 12465864 12465753 1.210000e-32 152.0
61 TraesCS7D01G008300 chr1D 97.619 84 2 0 5137 5220 225405130 225405047 2.030000e-30 145.0
62 TraesCS7D01G008300 chr2A 93.684 95 4 2 5125 5218 515955457 515955364 2.630000e-29 141.0
63 TraesCS7D01G008300 chr5D 94.505 91 3 2 5128 5218 535711526 535711614 9.450000e-29 139.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G008300 chr7D 4011665 4018650 6985 True 12901.000000 12901 100.000000 1 6986 1 chr7D.!!$R8 6985
1 TraesCS7D01G008300 chr7D 3562970 3565440 2470 True 814.000000 1107 83.722500 3854 6721 2 chr7D.!!$R9 2867
2 TraesCS7D01G008300 chr7D 2663783 2664446 663 True 580.000000 580 82.916000 3128 3787 1 chr7D.!!$R2 659
3 TraesCS7D01G008300 chr7D 3620607 3621223 616 True 531.000000 531 82.504000 2385 3037 1 chr7D.!!$R7 652
4 TraesCS7D01G008300 chr7D 2880999 2881532 533 True 385.000000 385 79.965000 1867 2438 1 chr7D.!!$R4 571
5 TraesCS7D01G008300 chr7A 3535579 3539359 3780 True 5374.000000 5374 92.312000 2162 5965 1 chr7A.!!$R2 3803
6 TraesCS7D01G008300 chr7A 3845058 3851983 6925 True 2226.000000 6534 87.090750 1 6986 4 chr7A.!!$R4 6985
7 TraesCS7D01G008300 chr7A 3800176 3800867 691 True 592.000000 592 82.571000 3107 3787 1 chr7A.!!$R3 680
8 TraesCS7D01G008300 chr4A 742012791 742015937 3146 False 1213.333333 1914 88.292000 3780 6911 3 chr4A.!!$F8 3131
9 TraesCS7D01G008300 chr4A 741408779 741412795 4016 True 1051.200000 3334 90.405000 2162 6669 5 chr4A.!!$R10 4507
10 TraesCS7D01G008300 chr4A 741364677 741367998 3321 True 883.200000 1971 92.433200 3119 6669 5 chr4A.!!$R9 3550
11 TraesCS7D01G008300 chr4A 739594659 739603500 8841 False 696.125000 1391 84.989500 1 6947 8 chr4A.!!$F6 6946
12 TraesCS7D01G008300 chr4A 733809448 733810111 663 False 593.000000 593 82.994000 3107 3787 1 chr4A.!!$F1 680
13 TraesCS7D01G008300 chr4A 739610438 739611118 680 False 593.000000 593 82.759000 3107 3787 1 chr4A.!!$F2 680
14 TraesCS7D01G008300 chr4A 739757347 739758024 677 True 518.000000 518 81.014000 3119 3787 1 chr4A.!!$R3 668
15 TraesCS7D01G008300 chr4A 740153590 740154477 887 True 472.000000 689 86.568500 4802 5999 2 chr4A.!!$R8 1197
16 TraesCS7D01G008300 chr4A 741776086 741776646 560 True 459.000000 459 81.865000 1874 2438 1 chr4A.!!$R6 564
17 TraesCS7D01G008300 chr4A 741178258 741182395 4137 False 360.333333 627 88.068333 2934 6827 3 chr4A.!!$F7 3893

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
815 902 0.030908 GATCCGAGGGTAGAAGCACG 59.969 60.000 0.00 0.00 0.00 5.34 F
2353 2556 0.030908 GGTATTCGACCGAGAGCCAG 59.969 60.000 0.00 0.00 38.87 4.85 F
2356 2559 0.457851 ATTCGACCGAGAGCCAGAAG 59.542 55.000 0.00 0.00 0.00 2.85 F
3907 6292 0.606401 ACCATGAAGGACCTTGCGTG 60.606 55.000 12.68 13.77 41.22 5.34 F
4407 6824 3.850122 TCAGTACTGACAATCTGACGG 57.150 47.619 21.74 0.00 34.14 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2443 2649 1.006998 TCATTGGTCCATTTCCCCAGG 59.993 52.381 0.0 0.0 0.00 4.45 R
3888 6273 0.606401 CACGCAAGGTCCTTCATGGT 60.606 55.000 0.0 0.0 46.39 3.55 R
4046 6439 0.680921 ATGAGCATCCCAAACCCACG 60.681 55.000 0.0 0.0 0.00 4.94 R
5886 8494 1.142097 GGAGGAGCTGCCGTTAGTC 59.858 63.158 0.0 0.0 43.43 2.59 R
6295 9005 1.609208 ATTCCCACTTGTCTGCACAC 58.391 50.000 0.0 0.0 29.76 3.82 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
133 134 2.110967 CCTGCTCATGGGTTCTGCG 61.111 63.158 0.00 0.00 0.00 5.18
134 135 2.046023 TGCTCATGGGTTCTGCGG 60.046 61.111 0.00 0.00 0.00 5.69
145 146 1.656652 GTTCTGCGGCAGATGTGTAT 58.343 50.000 31.20 0.00 40.39 2.29
150 151 3.118775 TCTGCGGCAGATGTGTATTAAGT 60.119 43.478 27.76 0.00 35.39 2.24
152 153 3.621268 TGCGGCAGATGTGTATTAAGTTC 59.379 43.478 0.00 0.00 0.00 3.01
156 157 5.186198 GGCAGATGTGTATTAAGTTCCTGT 58.814 41.667 0.00 0.00 0.00 4.00
158 159 6.821665 GGCAGATGTGTATTAAGTTCCTGTAA 59.178 38.462 0.00 0.00 0.00 2.41
159 160 7.499232 GGCAGATGTGTATTAAGTTCCTGTAAT 59.501 37.037 0.00 0.00 0.00 1.89
161 162 9.383519 CAGATGTGTATTAAGTTCCTGTAATGT 57.616 33.333 0.00 0.00 0.00 2.71
176 177 6.070251 TCCTGTAATGTAGAGGAAATGCAGAA 60.070 38.462 0.00 0.00 44.37 3.02
183 184 8.845413 ATGTAGAGGAAATGCAGAAGATTATC 57.155 34.615 0.00 0.00 0.00 1.75
196 197 6.073331 GCAGAAGATTATCAAGCCAGATGTAC 60.073 42.308 0.00 0.00 0.00 2.90
197 198 7.215789 CAGAAGATTATCAAGCCAGATGTACT 58.784 38.462 0.00 0.00 0.00 2.73
198 199 8.363390 CAGAAGATTATCAAGCCAGATGTACTA 58.637 37.037 0.00 0.00 0.00 1.82
199 200 8.364142 AGAAGATTATCAAGCCAGATGTACTAC 58.636 37.037 0.00 0.00 0.00 2.73
200 201 6.998802 AGATTATCAAGCCAGATGTACTACC 58.001 40.000 0.00 0.00 0.00 3.18
201 202 6.554982 AGATTATCAAGCCAGATGTACTACCA 59.445 38.462 0.00 0.00 0.00 3.25
204 205 3.774766 TCAAGCCAGATGTACTACCATGT 59.225 43.478 0.00 0.00 0.00 3.21
211 212 6.450545 CCAGATGTACTACCATGTATGACAG 58.549 44.000 0.00 0.00 0.00 3.51
289 296 4.389687 GCATAACAGCCTGATTGTTTTTGG 59.610 41.667 0.00 0.00 39.36 3.28
294 301 2.827921 AGCCTGATTGTTTTTGGCCTAG 59.172 45.455 3.32 0.00 44.19 3.02
311 320 4.813697 GGCCTAGCAGTCTAAGAAAAGATG 59.186 45.833 0.00 0.00 0.00 2.90
335 344 7.506114 TGTGATTCACCTAACAGGGTAATATC 58.494 38.462 14.05 0.00 40.58 1.63
336 345 7.126573 TGTGATTCACCTAACAGGGTAATATCA 59.873 37.037 14.05 0.00 40.58 2.15
337 346 8.157476 GTGATTCACCTAACAGGGTAATATCAT 58.843 37.037 5.44 0.00 40.58 2.45
338 347 8.723365 TGATTCACCTAACAGGGTAATATCATT 58.277 33.333 0.00 0.00 40.58 2.57
368 377 3.428045 GCTAGCCTGAATGAAAATTGCGT 60.428 43.478 2.29 0.00 0.00 5.24
369 378 3.221964 AGCCTGAATGAAAATTGCGTC 57.778 42.857 0.00 0.00 0.00 5.19
388 397 3.628017 GTCGTGGAACTTGTGAAAATGG 58.372 45.455 0.00 0.00 31.75 3.16
392 401 1.001974 GGAACTTGTGAAAATGGGGGC 59.998 52.381 0.00 0.00 0.00 5.80
402 412 3.245948 TGAAAATGGGGGCCTCTATTTGT 60.246 43.478 26.01 16.16 0.00 2.83
414 424 5.707764 GGCCTCTATTTGTATTTGAGATCCC 59.292 44.000 0.00 0.00 0.00 3.85
451 464 2.528564 AGCCCACAATACAATGCAACT 58.471 42.857 0.00 0.00 0.00 3.16
452 465 2.231964 AGCCCACAATACAATGCAACTG 59.768 45.455 0.00 0.00 0.00 3.16
453 466 2.674747 GCCCACAATACAATGCAACTGG 60.675 50.000 0.00 0.00 0.00 4.00
455 468 3.257873 CCCACAATACAATGCAACTGGAA 59.742 43.478 0.00 0.00 0.00 3.53
457 470 4.022068 CCACAATACAATGCAACTGGAACT 60.022 41.667 0.00 0.00 0.00 3.01
485 518 1.549170 AGTCGGTTCTAGAATTGGCGT 59.451 47.619 8.75 0.00 0.00 5.68
496 529 3.270877 AGAATTGGCGTTGTCCTACATC 58.729 45.455 0.00 0.00 0.00 3.06
497 530 2.779755 ATTGGCGTTGTCCTACATCA 57.220 45.000 0.00 0.00 0.00 3.07
498 531 1.803334 TTGGCGTTGTCCTACATCAC 58.197 50.000 0.00 0.00 0.00 3.06
499 532 0.682292 TGGCGTTGTCCTACATCACA 59.318 50.000 0.00 0.00 0.00 3.58
500 533 1.277842 TGGCGTTGTCCTACATCACAT 59.722 47.619 0.00 0.00 0.00 3.21
501 534 1.665679 GGCGTTGTCCTACATCACATG 59.334 52.381 0.00 0.00 0.00 3.21
503 536 2.935238 GCGTTGTCCTACATCACATGGT 60.935 50.000 0.00 0.00 33.60 3.55
553 586 4.686554 GCAAAGTGTCTACTCAGTAACAGG 59.313 45.833 1.44 0.00 35.69 4.00
569 602 5.838521 AGTAACAGGAATGGACCAATTTTGT 59.161 36.000 0.00 0.00 0.00 2.83
570 603 5.628797 AACAGGAATGGACCAATTTTGTT 57.371 34.783 0.00 5.19 0.00 2.83
571 604 4.959723 ACAGGAATGGACCAATTTTGTTG 58.040 39.130 0.00 0.00 0.00 3.33
595 628 5.742926 GGACTCGTTAGTAATCACTAGCAAC 59.257 44.000 0.00 0.00 38.11 4.17
601 641 4.281898 AGTAATCACTAGCAACCGGTTT 57.718 40.909 19.55 6.97 31.45 3.27
651 692 1.611519 GGAGCTAGCTACAGATCCGT 58.388 55.000 22.69 0.00 41.01 4.69
653 694 2.287909 GGAGCTAGCTACAGATCCGTTG 60.288 54.545 22.69 0.00 41.01 4.10
654 695 1.683917 AGCTAGCTACAGATCCGTTGG 59.316 52.381 17.69 0.00 0.00 3.77
659 700 2.644555 CTACAGATCCGTTGGGGGCG 62.645 65.000 0.00 0.00 36.01 6.13
794 881 1.201429 TTGGCTGAGGGGAGGAGAAC 61.201 60.000 0.00 0.00 0.00 3.01
795 882 2.726351 GGCTGAGGGGAGGAGAACG 61.726 68.421 0.00 0.00 0.00 3.95
797 884 1.000486 CTGAGGGGAGGAGAACGGA 60.000 63.158 0.00 0.00 0.00 4.69
798 885 0.397816 CTGAGGGGAGGAGAACGGAT 60.398 60.000 0.00 0.00 0.00 4.18
799 886 0.397254 TGAGGGGAGGAGAACGGATC 60.397 60.000 0.00 0.00 0.00 3.36
800 887 1.075151 AGGGGAGGAGAACGGATCC 60.075 63.158 0.00 0.00 37.07 3.36
801 888 2.499827 GGGGAGGAGAACGGATCCG 61.500 68.421 32.20 32.20 42.02 4.18
802 889 1.455217 GGGAGGAGAACGGATCCGA 60.455 63.158 39.55 0.00 42.02 4.55
803 890 1.457009 GGGAGGAGAACGGATCCGAG 61.457 65.000 39.55 13.42 42.02 4.63
804 891 1.457009 GGAGGAGAACGGATCCGAGG 61.457 65.000 39.55 12.61 42.02 4.63
805 892 1.455959 AGGAGAACGGATCCGAGGG 60.456 63.158 39.55 12.21 42.02 4.30
806 893 1.757340 GGAGAACGGATCCGAGGGT 60.757 63.158 39.55 20.90 42.83 4.34
807 894 0.466922 GGAGAACGGATCCGAGGGTA 60.467 60.000 39.55 0.00 42.83 3.69
808 895 0.953003 GAGAACGGATCCGAGGGTAG 59.047 60.000 39.55 10.20 42.83 3.18
809 896 0.549950 AGAACGGATCCGAGGGTAGA 59.450 55.000 39.55 0.00 42.83 2.59
810 897 1.064166 AGAACGGATCCGAGGGTAGAA 60.064 52.381 39.55 0.00 42.83 2.10
811 898 1.337387 GAACGGATCCGAGGGTAGAAG 59.663 57.143 39.55 7.81 42.83 2.85
812 899 1.108132 ACGGATCCGAGGGTAGAAGC 61.108 60.000 39.55 0.00 42.83 3.86
813 900 1.107538 CGGATCCGAGGGTAGAAGCA 61.108 60.000 30.62 0.00 42.83 3.91
814 901 0.389757 GGATCCGAGGGTAGAAGCAC 59.610 60.000 0.00 0.00 0.00 4.40
815 902 0.030908 GATCCGAGGGTAGAAGCACG 59.969 60.000 0.00 0.00 0.00 5.34
816 903 0.395311 ATCCGAGGGTAGAAGCACGA 60.395 55.000 0.00 0.00 0.00 4.35
817 904 1.030488 TCCGAGGGTAGAAGCACGAG 61.030 60.000 0.00 0.00 0.00 4.18
818 905 1.433879 CGAGGGTAGAAGCACGAGG 59.566 63.158 0.00 0.00 0.00 4.63
819 906 1.030488 CGAGGGTAGAAGCACGAGGA 61.030 60.000 0.00 0.00 0.00 3.71
820 907 0.741915 GAGGGTAGAAGCACGAGGAG 59.258 60.000 0.00 0.00 0.00 3.69
821 908 0.684805 AGGGTAGAAGCACGAGGAGG 60.685 60.000 0.00 0.00 0.00 4.30
822 909 1.142097 GGTAGAAGCACGAGGAGGC 59.858 63.158 0.00 0.00 0.00 4.70
823 910 1.226717 GTAGAAGCACGAGGAGGCG 60.227 63.158 0.00 0.00 34.54 5.52
824 911 3.064987 TAGAAGCACGAGGAGGCGC 62.065 63.158 0.00 0.00 34.54 6.53
855 942 3.036959 GAGGGAGAGGGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
859 946 3.036959 GAGAGGGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
860 947 3.369388 AGAGGGGGAGGGAGGGAC 61.369 72.222 0.00 0.00 0.00 4.46
937 1029 4.888325 CGGGCAGAGGGGGAGGAT 62.888 72.222 0.00 0.00 0.00 3.24
938 1030 2.368878 GGGCAGAGGGGGAGGATT 60.369 66.667 0.00 0.00 0.00 3.01
940 1032 2.761465 GGCAGAGGGGGAGGATTGG 61.761 68.421 0.00 0.00 0.00 3.16
943 1035 3.502875 GAGGGGGAGGATTGGGGC 61.503 72.222 0.00 0.00 0.00 5.80
944 1036 4.058505 AGGGGGAGGATTGGGGCT 62.059 66.667 0.00 0.00 0.00 5.19
945 1037 3.825623 GGGGGAGGATTGGGGCTG 61.826 72.222 0.00 0.00 0.00 4.85
946 1038 3.825623 GGGGAGGATTGGGGCTGG 61.826 72.222 0.00 0.00 0.00 4.85
947 1039 2.696125 GGGAGGATTGGGGCTGGA 60.696 66.667 0.00 0.00 0.00 3.86
948 1040 2.087461 GGGAGGATTGGGGCTGGAT 61.087 63.158 0.00 0.00 0.00 3.41
949 1041 1.152368 GGAGGATTGGGGCTGGATG 59.848 63.158 0.00 0.00 0.00 3.51
950 1042 1.649271 GGAGGATTGGGGCTGGATGT 61.649 60.000 0.00 0.00 0.00 3.06
951 1043 0.466922 GAGGATTGGGGCTGGATGTG 60.467 60.000 0.00 0.00 0.00 3.21
952 1044 1.456331 GGATTGGGGCTGGATGTGG 60.456 63.158 0.00 0.00 0.00 4.17
979 1096 2.920912 TGGACTCGGGCCTTTCGT 60.921 61.111 0.84 0.00 0.00 3.85
1073 1206 2.590859 GCGGGGGCGTTATCCTTC 60.591 66.667 0.00 0.00 0.00 3.46
1075 1208 2.110420 GGGGGCGTTATCCTTCGG 59.890 66.667 0.00 0.00 0.00 4.30
1098 1231 2.280321 ACCCGTTCCGTTCCGTTG 60.280 61.111 0.00 0.00 0.00 4.10
1099 1232 3.045492 CCCGTTCCGTTCCGTTGG 61.045 66.667 0.00 0.00 0.00 3.77
1100 1233 2.280321 CCGTTCCGTTCCGTTGGT 60.280 61.111 0.00 0.00 0.00 3.67
1102 1235 1.566077 CGTTCCGTTCCGTTGGTTC 59.434 57.895 0.00 0.00 0.00 3.62
1104 1237 2.246042 TTCCGTTCCGTTGGTTCGC 61.246 57.895 0.00 0.00 0.00 4.70
1105 1238 4.067016 CCGTTCCGTTGGTTCGCG 62.067 66.667 0.00 0.00 0.00 5.87
1106 1239 4.712873 CGTTCCGTTGGTTCGCGC 62.713 66.667 0.00 0.00 0.00 6.86
1108 1241 4.912485 TTCCGTTGGTTCGCGCCA 62.912 61.111 0.00 0.00 36.62 5.69
1109 1242 4.912485 TCCGTTGGTTCGCGCCAA 62.912 61.111 13.34 13.34 45.37 4.52
1118 1262 3.599285 TTCGCGCCAACGAAGGGAT 62.599 57.895 0.00 0.00 46.39 3.85
1120 1264 4.179579 GCGCCAACGAAGGGATGC 62.180 66.667 0.00 0.00 43.93 3.91
1125 1269 1.651240 CCAACGAAGGGATGCTGCTG 61.651 60.000 0.00 0.00 0.00 4.41
1128 1272 2.178890 CGAAGGGATGCTGCTGCTC 61.179 63.158 17.00 11.01 40.48 4.26
1130 1274 2.547640 GAAGGGATGCTGCTGCTCCA 62.548 60.000 24.53 6.50 37.86 3.86
1131 1275 2.827642 GGGATGCTGCTGCTCCAC 60.828 66.667 24.53 12.86 37.86 4.02
1132 1276 3.200593 GGATGCTGCTGCTCCACG 61.201 66.667 21.00 0.00 40.48 4.94
1224 1371 1.132495 ACCAGTAGGATCCCCATACCC 60.132 57.143 8.55 0.00 38.69 3.69
1230 1377 0.905337 GGATCCCCATACCCTCCTCG 60.905 65.000 0.00 0.00 0.00 4.63
1337 1496 2.670148 CCCCCTTCTCCCAAGACGG 61.670 68.421 0.00 0.00 39.97 4.79
1338 1497 2.269241 CCCTTCTCCCAAGACGGC 59.731 66.667 0.00 0.00 39.16 5.68
1339 1498 2.125512 CCTTCTCCCAAGACGGCG 60.126 66.667 4.80 4.80 34.48 6.46
1340 1499 2.657237 CTTCTCCCAAGACGGCGT 59.343 61.111 14.65 14.65 0.00 5.68
1341 1500 1.446272 CTTCTCCCAAGACGGCGTC 60.446 63.158 31.33 31.33 0.00 5.19
1342 1501 3.277211 TTCTCCCAAGACGGCGTCG 62.277 63.158 31.59 19.59 37.67 5.12
1343 1502 4.796231 CTCCCAAGACGGCGTCGG 62.796 72.222 31.59 26.53 41.39 4.79
1345 1504 4.796231 CCCAAGACGGCGTCGGAG 62.796 72.222 31.59 24.03 41.39 4.63
1346 1505 4.052229 CCAAGACGGCGTCGGAGT 62.052 66.667 31.59 17.00 41.39 3.85
1347 1506 2.049433 CAAGACGGCGTCGGAGTT 60.049 61.111 31.59 19.03 41.39 3.01
1348 1507 1.663702 CAAGACGGCGTCGGAGTTT 60.664 57.895 31.59 18.67 41.39 2.66
1385 1544 3.936653 CGAGCAGCAAGAACACGA 58.063 55.556 0.00 0.00 0.00 4.35
1393 1552 1.224069 GCAAGAACACGAGCAGCAGA 61.224 55.000 0.00 0.00 0.00 4.26
1394 1553 0.510359 CAAGAACACGAGCAGCAGAC 59.490 55.000 0.00 0.00 0.00 3.51
1423 1585 1.993391 GGGAAGGATGGGGACGACA 60.993 63.158 0.00 0.00 0.00 4.35
1514 1682 2.040359 CTCCCTCTTCCCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
1516 1684 4.089757 CCCTCTTCCCCTCCCCGA 62.090 72.222 0.00 0.00 0.00 5.14
1582 1754 3.467226 CGCCCCTCCTCCGCTAAA 61.467 66.667 0.00 0.00 0.00 1.85
1584 1756 1.301954 GCCCCTCCTCCGCTAAAAA 59.698 57.895 0.00 0.00 0.00 1.94
1606 1783 5.791336 AAAGATCGGCATGTGTAGATAGA 57.209 39.130 0.00 0.00 0.00 1.98
1607 1784 5.791336 AAGATCGGCATGTGTAGATAGAA 57.209 39.130 0.00 0.00 0.00 2.10
1608 1785 5.991933 AGATCGGCATGTGTAGATAGAAT 57.008 39.130 0.00 0.00 0.00 2.40
1609 1786 5.718146 AGATCGGCATGTGTAGATAGAATG 58.282 41.667 0.00 0.00 0.00 2.67
1610 1787 4.257267 TCGGCATGTGTAGATAGAATGG 57.743 45.455 0.00 0.00 0.00 3.16
1611 1788 3.006859 TCGGCATGTGTAGATAGAATGGG 59.993 47.826 0.00 0.00 0.00 4.00
1612 1789 3.679389 GGCATGTGTAGATAGAATGGGG 58.321 50.000 0.00 0.00 0.00 4.96
1613 1790 3.560025 GGCATGTGTAGATAGAATGGGGG 60.560 52.174 0.00 0.00 0.00 5.40
1915 2098 1.121407 CACCGGATCCAGCTCCCATA 61.121 60.000 9.46 0.00 31.04 2.74
1930 2113 1.978580 CCCATATCTCCCACCAGGTAC 59.021 57.143 0.00 0.00 36.75 3.34
1947 2132 7.711339 CACCAGGTACTAAAATCCACTCTAATC 59.289 40.741 0.00 0.00 36.02 1.75
1948 2133 7.147532 ACCAGGTACTAAAATCCACTCTAATCC 60.148 40.741 0.00 0.00 36.02 3.01
1958 2143 9.807921 AAAATCCACTCTAATCCTCTTTTGTTA 57.192 29.630 0.00 0.00 0.00 2.41
1959 2144 9.981460 AAATCCACTCTAATCCTCTTTTGTTAT 57.019 29.630 0.00 0.00 0.00 1.89
1960 2145 9.981460 AATCCACTCTAATCCTCTTTTGTTATT 57.019 29.630 0.00 0.00 0.00 1.40
1962 2147 9.886132 TCCACTCTAATCCTCTTTTGTTATTAC 57.114 33.333 0.00 0.00 0.00 1.89
1963 2148 9.667107 CCACTCTAATCCTCTTTTGTTATTACA 57.333 33.333 0.00 0.00 0.00 2.41
2027 2219 4.290942 ACTAGCTAGCTAACCATGGTTCT 58.709 43.478 33.06 25.34 39.31 3.01
2043 2235 3.503363 TGGTTCTTGCTTGTGTGATGATC 59.497 43.478 0.00 0.00 0.00 2.92
2124 2316 2.765122 GCACAGTTTGAAGAGCTCTCT 58.235 47.619 18.55 6.36 42.75 3.10
2127 2319 2.075338 CAGTTTGAAGAGCTCTCTGCC 58.925 52.381 18.55 7.51 44.23 4.85
2299 2501 2.812658 CAAAAGGGAAATGGAGCTCCT 58.187 47.619 32.28 13.87 36.82 3.69
2353 2556 0.030908 GGTATTCGACCGAGAGCCAG 59.969 60.000 0.00 0.00 38.87 4.85
2356 2559 0.457851 ATTCGACCGAGAGCCAGAAG 59.542 55.000 0.00 0.00 0.00 2.85
2501 2707 4.275810 CCCTCATGACAGTCCATTTGATT 58.724 43.478 0.00 0.00 0.00 2.57
2509 2716 5.068234 ACAGTCCATTTGATTGCATTCTG 57.932 39.130 9.81 0.67 34.21 3.02
2527 2734 3.435275 TCTGTATGTCTTGCTCACCTCT 58.565 45.455 0.00 0.00 0.00 3.69
2544 2751 6.720309 TCACCTCTCATTTAATCACATTCCA 58.280 36.000 0.00 0.00 0.00 3.53
2547 2754 7.121759 CACCTCTCATTTAATCACATTCCAACT 59.878 37.037 0.00 0.00 0.00 3.16
2578 2793 3.393089 AGTCGCACTCTGACTGAATTT 57.607 42.857 0.00 0.00 44.69 1.82
2580 2795 4.489810 AGTCGCACTCTGACTGAATTTAG 58.510 43.478 0.00 0.00 44.69 1.85
2616 2831 3.865745 CCCTTAGATAGTTGTGAACTGCG 59.134 47.826 0.00 0.00 42.84 5.18
2634 2849 4.142816 ACTGCGCTGTCAAGAATATTCAAC 60.143 41.667 14.78 12.14 0.00 3.18
2640 2855 6.535150 CGCTGTCAAGAATATTCAACTTAGGA 59.465 38.462 17.56 1.83 0.00 2.94
2642 2857 9.547753 GCTGTCAAGAATATTCAACTTAGGATA 57.452 33.333 17.56 2.46 0.00 2.59
2673 2888 5.673337 ATACTGTGGTAATTTATGCAGCG 57.327 39.130 0.00 0.00 0.00 5.18
2674 2889 3.605634 ACTGTGGTAATTTATGCAGCGA 58.394 40.909 0.00 0.00 0.00 4.93
2675 2890 4.006989 ACTGTGGTAATTTATGCAGCGAA 58.993 39.130 0.00 0.00 0.00 4.70
2692 2907 4.335315 CAGCGAATTTCCTAACATGGCTAA 59.665 41.667 0.00 0.00 0.00 3.09
2694 2909 5.594317 AGCGAATTTCCTAACATGGCTAAAT 59.406 36.000 0.00 0.00 0.00 1.40
2700 2915 4.131596 TCCTAACATGGCTAAATAACGCC 58.868 43.478 0.00 0.00 46.46 5.68
2718 2933 5.734855 ACGCCAAATACACTGATATTCAC 57.265 39.130 0.00 0.00 0.00 3.18
2755 2971 7.117285 TGTCTGAACTCATAATGACTGCTAT 57.883 36.000 0.00 0.00 0.00 2.97
2762 2978 6.987386 ACTCATAATGACTGCTATACCTGTC 58.013 40.000 0.00 0.00 35.16 3.51
2782 2998 6.485648 CCTGTCATTTCTATGATTCAGCATGA 59.514 38.462 0.00 0.00 42.51 3.07
2784 3000 7.052248 TGTCATTTCTATGATTCAGCATGACT 58.948 34.615 17.94 0.00 40.95 3.41
2932 3150 1.586422 TGCAGAGAACTCACTGTTGC 58.414 50.000 4.64 5.53 39.30 4.17
2985 3203 2.225019 GCCAGATCAATTACCAGATGCG 59.775 50.000 0.00 0.00 0.00 4.73
3479 3818 7.939784 AAATTCATACTACAGGGTTTTCCTC 57.060 36.000 0.00 0.00 46.12 3.71
3717 4147 8.506168 TTGGTATTTGATATCTGAACACCTTC 57.494 34.615 15.91 0.00 0.00 3.46
3846 4278 9.761504 CTATTATATCATCGAATCCTGCTTCAT 57.238 33.333 0.00 0.00 0.00 2.57
3888 6273 7.522889 GCTTGCACTCTGTAGTCTCATATATGA 60.523 40.741 14.64 14.64 31.97 2.15
3897 6282 8.127150 TGTAGTCTCATATATGACCATGAAGG 57.873 38.462 11.49 0.09 45.67 3.46
3907 6292 0.606401 ACCATGAAGGACCTTGCGTG 60.606 55.000 12.68 13.77 41.22 5.34
3929 6314 7.358066 CGTGATGAAGCATAAGCATAAGAAAT 58.642 34.615 0.00 0.00 45.49 2.17
3964 6356 7.862512 AAACAAATCATGGACACAACATTTT 57.137 28.000 0.00 0.00 0.00 1.82
4318 6727 6.376018 GGCACATTTGGTTTACCTACATCTAA 59.624 38.462 0.00 0.00 36.82 2.10
4334 6743 9.416794 CCTACATCTAAAGTACAATGCTCATAG 57.583 37.037 0.00 0.00 0.00 2.23
4407 6824 3.850122 TCAGTACTGACAATCTGACGG 57.150 47.619 21.74 0.00 34.14 4.79
4516 6998 4.720649 TCTGCGTTAAGAGAATAGTGCT 57.279 40.909 0.00 0.00 0.00 4.40
4614 7114 8.115490 ACAGTAATTCCCTCTTGAATCTTTTG 57.885 34.615 0.00 0.00 33.91 2.44
5050 7630 7.148373 GGACAGACATAGCTAGTATGCTAGTAC 60.148 44.444 17.77 3.92 46.89 2.73
5075 7655 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
6107 8798 6.795114 CGCTACAAATCGAGTTTTGTTTGTAT 59.205 34.615 19.17 0.30 45.14 2.29
6171 8876 6.005823 TCTGATTTTGCTTGATCTCTCCAAA 58.994 36.000 0.00 0.00 0.00 3.28
6218 8923 9.238368 AGGAAAAATATTCTACCGAATTTCACA 57.762 29.630 7.10 0.00 40.28 3.58
6295 9005 9.978044 TTGTTGATAGACAATATGATCTCTCTG 57.022 33.333 0.00 0.00 40.76 3.35
6428 9177 2.337849 ACATGCCACAAAGGGGAATTT 58.662 42.857 0.00 0.00 38.09 1.82
6585 9340 4.380444 CCATTTCCGACCAGGTGTTATTTG 60.380 45.833 0.00 0.00 41.99 2.32
6733 9493 7.538303 TTGGAACTTTCAGAAAATTTCAAGC 57.462 32.000 6.69 0.00 36.35 4.01
6815 11876 7.095017 GGAGAAGTTGAAGGAAACATACTCTTG 60.095 40.741 0.00 0.00 32.13 3.02
6823 11884 8.912988 TGAAGGAAACATACTCTTGTGAATTTT 58.087 29.630 0.00 0.00 0.00 1.82
6825 11886 7.886338 AGGAAACATACTCTTGTGAATTTTCC 58.114 34.615 0.00 0.00 0.00 3.13
6826 11887 7.505585 AGGAAACATACTCTTGTGAATTTTCCA 59.494 33.333 10.91 0.00 0.00 3.53
6952 12020 9.520515 ACAAAAGATAAAAATAGAGAGCCTTCA 57.479 29.630 0.00 0.00 0.00 3.02
6955 12023 8.744568 AAGATAAAAATAGAGAGCCTTCAAGG 57.255 34.615 0.00 0.00 38.80 3.61
6983 12052 3.739300 GCCATGCTTGCAATTCATGATAC 59.261 43.478 28.79 19.24 39.80 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 0.391130 TACACATCTGCCGCAGAACC 60.391 55.000 26.30 0.00 44.04 3.62
127 128 2.401583 AATACACATCTGCCGCAGAA 57.598 45.000 26.30 10.55 44.04 3.02
133 134 5.186198 ACAGGAACTTAATACACATCTGCC 58.814 41.667 0.00 0.00 34.60 4.85
134 135 7.843490 TTACAGGAACTTAATACACATCTGC 57.157 36.000 0.00 0.00 34.60 4.26
145 146 9.667107 CATTTCCTCTACATTACAGGAACTTAA 57.333 33.333 0.00 0.00 44.41 1.85
150 151 6.061022 TGCATTTCCTCTACATTACAGGAA 57.939 37.500 0.00 0.00 43.30 3.36
152 153 5.674525 TCTGCATTTCCTCTACATTACAGG 58.325 41.667 0.00 0.00 0.00 4.00
158 159 8.435187 TGATAATCTTCTGCATTTCCTCTACAT 58.565 33.333 0.00 0.00 0.00 2.29
159 160 7.795047 TGATAATCTTCTGCATTTCCTCTACA 58.205 34.615 0.00 0.00 0.00 2.74
161 162 7.443575 GCTTGATAATCTTCTGCATTTCCTCTA 59.556 37.037 0.00 0.00 0.00 2.43
176 177 6.554982 TGGTAGTACATCTGGCTTGATAATCT 59.445 38.462 2.06 0.00 0.00 2.40
183 184 4.142609 ACATGGTAGTACATCTGGCTTG 57.857 45.455 2.06 0.00 0.00 4.01
196 197 3.574396 ACCGATCCTGTCATACATGGTAG 59.426 47.826 0.00 0.00 0.00 3.18
197 198 3.320826 CACCGATCCTGTCATACATGGTA 59.679 47.826 0.00 0.00 0.00 3.25
198 199 2.103094 CACCGATCCTGTCATACATGGT 59.897 50.000 0.00 0.00 0.00 3.55
199 200 2.548707 CCACCGATCCTGTCATACATGG 60.549 54.545 0.00 0.00 0.00 3.66
200 201 2.365293 TCCACCGATCCTGTCATACATG 59.635 50.000 0.00 0.00 0.00 3.21
201 202 2.677914 TCCACCGATCCTGTCATACAT 58.322 47.619 0.00 0.00 0.00 2.29
204 205 1.970640 CCATCCACCGATCCTGTCATA 59.029 52.381 0.00 0.00 0.00 2.15
211 212 4.878878 GGTTCCATCCACCGATCC 57.121 61.111 0.00 0.00 0.00 3.36
231 232 1.298859 GCTTTGCCAGTACCTGTCCG 61.299 60.000 0.00 0.00 0.00 4.79
250 251 1.873698 ATGCTTTGCTTGCCAGTTTG 58.126 45.000 0.00 0.00 0.00 2.93
289 296 5.293079 CACATCTTTTCTTAGACTGCTAGGC 59.707 44.000 0.00 0.00 0.00 3.93
294 301 7.239972 GTGAATCACATCTTTTCTTAGACTGC 58.760 38.462 8.74 0.00 34.08 4.40
311 320 7.506114 TGATATTACCCTGTTAGGTGAATCAC 58.494 38.462 4.51 4.51 41.42 3.06
335 344 6.226052 TCATTCAGGCTAGCACTACATAATG 58.774 40.000 18.24 14.37 0.00 1.90
336 345 6.425210 TCATTCAGGCTAGCACTACATAAT 57.575 37.500 18.24 3.26 0.00 1.28
337 346 5.869649 TCATTCAGGCTAGCACTACATAA 57.130 39.130 18.24 0.90 0.00 1.90
338 347 5.869649 TTCATTCAGGCTAGCACTACATA 57.130 39.130 18.24 0.00 0.00 2.29
339 348 4.760530 TTCATTCAGGCTAGCACTACAT 57.239 40.909 18.24 4.16 0.00 2.29
368 377 2.621055 CCCATTTTCACAAGTTCCACGA 59.379 45.455 0.00 0.00 0.00 4.35
369 378 2.288152 CCCCATTTTCACAAGTTCCACG 60.288 50.000 0.00 0.00 0.00 4.94
388 397 5.048846 TCTCAAATACAAATAGAGGCCCC 57.951 43.478 0.00 0.00 0.00 5.80
392 401 6.759272 TCGGGATCTCAAATACAAATAGAGG 58.241 40.000 0.00 0.00 0.00 3.69
457 470 0.038251 CTAGAACCGACTGCACAGCA 60.038 55.000 0.00 0.00 36.92 4.41
496 529 3.510753 TCACAATTTCCCATCACCATGTG 59.489 43.478 0.00 0.00 38.54 3.21
497 530 3.765511 CTCACAATTTCCCATCACCATGT 59.234 43.478 0.00 0.00 0.00 3.21
498 531 3.765511 ACTCACAATTTCCCATCACCATG 59.234 43.478 0.00 0.00 0.00 3.66
499 532 4.051661 ACTCACAATTTCCCATCACCAT 57.948 40.909 0.00 0.00 0.00 3.55
500 533 3.524095 ACTCACAATTTCCCATCACCA 57.476 42.857 0.00 0.00 0.00 4.17
501 534 4.142381 GCTAACTCACAATTTCCCATCACC 60.142 45.833 0.00 0.00 0.00 4.02
503 536 4.661222 TGCTAACTCACAATTTCCCATCA 58.339 39.130 0.00 0.00 0.00 3.07
506 539 2.819608 GCTGCTAACTCACAATTTCCCA 59.180 45.455 0.00 0.00 0.00 4.37
507 540 2.819608 TGCTGCTAACTCACAATTTCCC 59.180 45.455 0.00 0.00 0.00 3.97
508 541 4.479619 CTTGCTGCTAACTCACAATTTCC 58.520 43.478 0.00 0.00 0.00 3.13
509 542 3.916776 GCTTGCTGCTAACTCACAATTTC 59.083 43.478 0.00 0.00 38.95 2.17
510 543 3.318839 TGCTTGCTGCTAACTCACAATTT 59.681 39.130 0.00 0.00 43.37 1.82
511 544 2.886523 TGCTTGCTGCTAACTCACAATT 59.113 40.909 0.00 0.00 43.37 2.32
512 545 2.507484 TGCTTGCTGCTAACTCACAAT 58.493 42.857 0.00 0.00 43.37 2.71
513 546 1.965935 TGCTTGCTGCTAACTCACAA 58.034 45.000 0.00 0.00 43.37 3.33
534 567 5.186021 CCATTCCTGTTACTGAGTAGACACT 59.814 44.000 0.00 0.00 37.87 3.55
553 586 5.213891 AGTCCAACAAAATTGGTCCATTC 57.786 39.130 5.62 0.00 40.40 2.67
569 602 5.416639 TGCTAGTGATTACTAACGAGTCCAA 59.583 40.000 0.00 0.00 38.85 3.53
570 603 4.945543 TGCTAGTGATTACTAACGAGTCCA 59.054 41.667 0.00 0.00 38.85 4.02
571 604 5.496133 TGCTAGTGATTACTAACGAGTCC 57.504 43.478 0.00 0.00 38.85 3.85
595 628 4.634004 TCTGTATTGCATTACTGAAACCGG 59.366 41.667 19.72 0.00 30.14 5.28
601 641 6.820335 AGTGCTATCTGTATTGCATTACTGA 58.180 36.000 22.47 22.47 43.93 3.41
640 681 1.146263 GCCCCCAACGGATCTGTAG 59.854 63.158 7.83 2.56 0.00 2.74
703 772 3.803162 GCTCCTCTCCTTGCCCCC 61.803 72.222 0.00 0.00 0.00 5.40
785 872 1.457009 CCTCGGATCCGTTCTCCTCC 61.457 65.000 32.15 0.00 40.74 4.30
787 874 1.455959 CCCTCGGATCCGTTCTCCT 60.456 63.158 32.15 0.00 40.74 3.69
794 881 1.107538 TGCTTCTACCCTCGGATCCG 61.108 60.000 28.62 28.62 41.35 4.18
795 882 0.389757 GTGCTTCTACCCTCGGATCC 59.610 60.000 0.00 0.00 0.00 3.36
797 884 0.395311 TCGTGCTTCTACCCTCGGAT 60.395 55.000 0.00 0.00 0.00 4.18
798 885 1.001764 TCGTGCTTCTACCCTCGGA 60.002 57.895 0.00 0.00 0.00 4.55
799 886 1.433879 CTCGTGCTTCTACCCTCGG 59.566 63.158 0.00 0.00 0.00 4.63
800 887 1.030488 TCCTCGTGCTTCTACCCTCG 61.030 60.000 0.00 0.00 0.00 4.63
801 888 0.741915 CTCCTCGTGCTTCTACCCTC 59.258 60.000 0.00 0.00 0.00 4.30
802 889 0.684805 CCTCCTCGTGCTTCTACCCT 60.685 60.000 0.00 0.00 0.00 4.34
803 890 1.817209 CCTCCTCGTGCTTCTACCC 59.183 63.158 0.00 0.00 0.00 3.69
804 891 1.142097 GCCTCCTCGTGCTTCTACC 59.858 63.158 0.00 0.00 0.00 3.18
805 892 1.226717 CGCCTCCTCGTGCTTCTAC 60.227 63.158 0.00 0.00 0.00 2.59
806 893 3.064987 GCGCCTCCTCGTGCTTCTA 62.065 63.158 0.00 0.00 36.32 2.10
807 894 4.443266 GCGCCTCCTCGTGCTTCT 62.443 66.667 0.00 0.00 36.32 2.85
837 924 4.548513 CCCTCCCCCTCTCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
838 925 3.036959 TCCCTCCCCCTCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
839 926 3.039526 CTCCCTCCCCCTCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
840 927 4.179599 CCTCCCTCCCCCTCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
841 928 4.179599 CCCTCCCTCCCCCTCTCC 62.180 77.778 0.00 0.00 0.00 3.71
842 929 3.036959 TCCCTCCCTCCCCCTCTC 61.037 72.222 0.00 0.00 0.00 3.20
843 930 3.369388 GTCCCTCCCTCCCCCTCT 61.369 72.222 0.00 0.00 0.00 3.69
844 931 4.862823 CGTCCCTCCCTCCCCCTC 62.863 77.778 0.00 0.00 0.00 4.30
847 934 3.768833 TATGCGTCCCTCCCTCCCC 62.769 68.421 0.00 0.00 0.00 4.81
848 935 2.122989 TATGCGTCCCTCCCTCCC 60.123 66.667 0.00 0.00 0.00 4.30
851 938 2.838225 CGGTATGCGTCCCTCCCT 60.838 66.667 0.00 0.00 0.00 4.20
855 942 4.157120 GCCACGGTATGCGTCCCT 62.157 66.667 0.00 0.00 0.00 4.20
890 982 0.528033 CCGTGATCTGCTCTGCTCTG 60.528 60.000 0.00 0.00 0.00 3.35
891 983 0.969917 ACCGTGATCTGCTCTGCTCT 60.970 55.000 0.00 0.00 0.00 4.09
924 1016 2.081161 CCCCAATCCTCCCCCTCTG 61.081 68.421 0.00 0.00 0.00 3.35
927 1019 4.058505 AGCCCCAATCCTCCCCCT 62.059 66.667 0.00 0.00 0.00 4.79
928 1020 3.825623 CAGCCCCAATCCTCCCCC 61.826 72.222 0.00 0.00 0.00 5.40
931 1023 1.152368 CATCCAGCCCCAATCCTCC 59.848 63.158 0.00 0.00 0.00 4.30
932 1024 0.466922 CACATCCAGCCCCAATCCTC 60.467 60.000 0.00 0.00 0.00 3.71
937 1029 4.380945 GGCCACATCCAGCCCCAA 62.381 66.667 0.00 0.00 43.76 4.12
961 1053 2.125512 CGAAAGGCCCGAGTCCAG 60.126 66.667 0.00 0.00 0.00 3.86
964 1056 3.119096 GCACGAAAGGCCCGAGTC 61.119 66.667 6.90 0.00 0.00 3.36
996 1113 3.399181 TGGACGGAGCCCATCACC 61.399 66.667 0.00 0.00 0.00 4.02
997 1114 2.125106 GTGGACGGAGCCCATCAC 60.125 66.667 0.00 0.00 35.91 3.06
1098 1231 4.084888 CCTTCGTTGGCGCGAACC 62.085 66.667 26.43 11.30 44.55 3.62
1099 1232 4.084888 CCCTTCGTTGGCGCGAAC 62.085 66.667 23.48 23.48 44.55 3.95
1100 1233 3.599285 ATCCCTTCGTTGGCGCGAA 62.599 57.895 12.10 14.23 46.78 4.70
1102 1235 3.864686 CATCCCTTCGTTGGCGCG 61.865 66.667 0.00 0.00 38.14 6.86
1104 1237 2.436646 AGCATCCCTTCGTTGGCG 60.437 61.111 0.00 0.00 39.92 5.69
1105 1238 3.056313 GCAGCATCCCTTCGTTGGC 62.056 63.158 0.00 0.00 0.00 4.52
1106 1239 1.377725 AGCAGCATCCCTTCGTTGG 60.378 57.895 0.00 0.00 0.00 3.77
1108 1241 2.042831 GCAGCAGCATCCCTTCGTT 61.043 57.895 0.00 0.00 41.58 3.85
1109 1242 2.437359 GCAGCAGCATCCCTTCGT 60.437 61.111 0.00 0.00 41.58 3.85
1110 1243 2.124819 AGCAGCAGCATCCCTTCG 60.125 61.111 3.17 0.00 45.49 3.79
1111 1244 1.823041 GGAGCAGCAGCATCCCTTC 60.823 63.158 3.17 0.00 45.49 3.46
1112 1245 2.274760 GGAGCAGCAGCATCCCTT 59.725 61.111 3.17 0.00 45.49 3.95
1113 1246 3.013327 TGGAGCAGCAGCATCCCT 61.013 61.111 3.17 0.00 45.49 4.20
1114 1247 2.827642 GTGGAGCAGCAGCATCCC 60.828 66.667 3.17 2.03 45.49 3.85
1193 1340 0.179145 CCTACTGGTGTAAGACGGCG 60.179 60.000 4.80 4.80 0.00 6.46
1224 1371 2.182030 GCGGTGGAGAACGAGGAG 59.818 66.667 0.00 0.00 0.00 3.69
1319 1478 2.670148 CCGTCTTGGGAGAAGGGGG 61.670 68.421 1.11 0.00 44.79 5.40
1320 1479 2.990479 CCGTCTTGGGAGAAGGGG 59.010 66.667 1.11 0.00 44.79 4.79
1328 1487 4.796231 CTCCGACGCCGTCTTGGG 62.796 72.222 16.07 9.44 38.63 4.12
1371 1530 1.206072 CTGCTCGTGTTCTTGCTGC 59.794 57.895 0.00 0.00 0.00 5.25
1372 1531 1.206072 GCTGCTCGTGTTCTTGCTG 59.794 57.895 0.00 0.00 0.00 4.41
1516 1684 4.736896 GAAGTCTTCGGCGGCGGT 62.737 66.667 31.73 9.77 0.00 5.68
1582 1754 6.582636 TCTATCTACACATGCCGATCTTTTT 58.417 36.000 0.00 0.00 0.00 1.94
1584 1756 5.791336 TCTATCTACACATGCCGATCTTT 57.209 39.130 0.00 0.00 0.00 2.52
1586 1758 5.337089 CCATTCTATCTACACATGCCGATCT 60.337 44.000 0.00 0.00 0.00 2.75
1610 1787 4.717313 GGCCGTGTCAGTTCCCCC 62.717 72.222 0.00 0.00 0.00 5.40
1611 1788 3.192103 AAGGCCGTGTCAGTTCCCC 62.192 63.158 0.00 0.00 0.00 4.81
1612 1789 1.966451 CAAGGCCGTGTCAGTTCCC 60.966 63.158 10.93 0.00 0.00 3.97
1613 1790 2.617274 GCAAGGCCGTGTCAGTTCC 61.617 63.158 20.23 0.00 0.00 3.62
1614 1791 1.598130 AGCAAGGCCGTGTCAGTTC 60.598 57.895 20.23 2.08 0.00 3.01
1616 1793 2.281070 CAGCAAGGCCGTGTCAGT 60.281 61.111 20.23 0.01 0.00 3.41
1617 1794 3.052082 CCAGCAAGGCCGTGTCAG 61.052 66.667 20.23 9.91 0.00 3.51
1638 1815 3.052082 CGTCCAAGCACCTGCAGG 61.052 66.667 31.60 31.60 45.16 4.85
1781 1964 4.115199 GGAGCCCCTGCCGTTCAT 62.115 66.667 0.00 0.00 38.69 2.57
1915 2098 4.412528 GGATTTTAGTACCTGGTGGGAGAT 59.587 45.833 10.23 0.00 38.76 2.75
1930 2113 9.454859 ACAAAAGAGGATTAGAGTGGATTTTAG 57.545 33.333 0.00 0.00 0.00 1.85
1958 2143 9.899661 TTGGTTGAGCAAGTATATAAGTGTAAT 57.100 29.630 0.00 0.00 0.00 1.89
1959 2144 9.899661 ATTGGTTGAGCAAGTATATAAGTGTAA 57.100 29.630 1.96 0.00 0.00 2.41
1960 2145 9.899661 AATTGGTTGAGCAAGTATATAAGTGTA 57.100 29.630 1.96 0.00 0.00 2.90
1961 2146 8.677300 CAATTGGTTGAGCAAGTATATAAGTGT 58.323 33.333 0.00 0.00 37.53 3.55
1962 2147 8.892723 TCAATTGGTTGAGCAAGTATATAAGTG 58.107 33.333 5.42 0.00 39.36 3.16
1963 2148 9.461312 TTCAATTGGTTGAGCAAGTATATAAGT 57.539 29.630 5.42 0.00 44.62 2.24
1967 2152 9.590451 CAATTTCAATTGGTTGAGCAAGTATAT 57.410 29.630 5.42 0.00 44.62 0.86
2001 2186 4.585162 ACCATGGTTAGCTAGCTAGTAGTG 59.415 45.833 23.03 18.96 0.00 2.74
2067 2259 3.401243 GAAGGCGCGCTGGAAATGG 62.401 63.158 32.29 0.00 0.00 3.16
2112 2304 1.263342 CCTGGGCAGAGAGCTCTTCA 61.263 60.000 19.36 10.44 46.80 3.02
2272 2468 4.278419 GCTCCATTTCCCTTTTGCGTATAT 59.722 41.667 0.00 0.00 0.00 0.86
2299 2501 4.525487 AGGTCAAGAATTAGTCGTACCACA 59.475 41.667 0.00 0.00 32.54 4.17
2443 2649 1.006998 TCATTGGTCCATTTCCCCAGG 59.993 52.381 0.00 0.00 0.00 4.45
2501 2707 3.686241 GTGAGCAAGACATACAGAATGCA 59.314 43.478 0.00 0.00 42.53 3.96
2509 2716 3.876274 TGAGAGGTGAGCAAGACATAC 57.124 47.619 0.00 0.00 0.00 2.39
2544 2751 4.632153 AGTGCGACTGAATGAGTTAAGTT 58.368 39.130 0.00 0.00 33.83 2.66
2547 2754 4.022329 TCAGAGTGCGACTGAATGAGTTAA 60.022 41.667 0.00 0.00 40.70 2.01
2592 2807 5.488341 GCAGTTCACAACTATCTAAGGGAA 58.512 41.667 0.00 0.00 40.46 3.97
2616 2831 7.849804 TCCTAAGTTGAATATTCTTGACAGC 57.150 36.000 16.24 0.00 0.00 4.40
2653 2868 3.605634 TCGCTGCATAAATTACCACAGT 58.394 40.909 0.00 0.00 0.00 3.55
2664 2879 5.221028 CCATGTTAGGAAATTCGCTGCATAA 60.221 40.000 0.00 0.00 0.00 1.90
2665 2880 4.275689 CCATGTTAGGAAATTCGCTGCATA 59.724 41.667 0.00 0.00 0.00 3.14
2666 2881 3.067180 CCATGTTAGGAAATTCGCTGCAT 59.933 43.478 0.00 0.00 0.00 3.96
2667 2882 2.423185 CCATGTTAGGAAATTCGCTGCA 59.577 45.455 0.00 0.00 0.00 4.41
2668 2883 2.796032 GCCATGTTAGGAAATTCGCTGC 60.796 50.000 0.00 0.00 0.00 5.25
2669 2884 2.684881 AGCCATGTTAGGAAATTCGCTG 59.315 45.455 0.00 0.00 0.00 5.18
2670 2885 3.004752 AGCCATGTTAGGAAATTCGCT 57.995 42.857 0.00 0.00 0.00 4.93
2671 2886 4.893424 TTAGCCATGTTAGGAAATTCGC 57.107 40.909 0.00 0.00 0.00 4.70
2672 2887 7.586300 CGTTATTTAGCCATGTTAGGAAATTCG 59.414 37.037 0.00 0.00 0.00 3.34
2673 2888 7.378728 GCGTTATTTAGCCATGTTAGGAAATTC 59.621 37.037 0.00 0.00 0.00 2.17
2674 2889 7.200455 GCGTTATTTAGCCATGTTAGGAAATT 58.800 34.615 0.00 0.00 0.00 1.82
2675 2890 6.735130 GCGTTATTTAGCCATGTTAGGAAAT 58.265 36.000 0.00 0.00 0.00 2.17
2692 2907 8.342634 GTGAATATCAGTGTATTTGGCGTTATT 58.657 33.333 0.00 0.00 0.00 1.40
2694 2909 6.019398 CGTGAATATCAGTGTATTTGGCGTTA 60.019 38.462 0.00 0.00 0.00 3.18
2718 2933 8.864069 ATGAGTTCAGACAAGAGAATAATACG 57.136 34.615 0.00 0.00 0.00 3.06
2755 2971 6.888105 TGCTGAATCATAGAAATGACAGGTA 58.112 36.000 0.00 0.00 44.79 3.08
2782 2998 1.546961 AGCTAAGAGTGCGGTACAGT 58.453 50.000 0.00 0.00 35.28 3.55
2784 3000 4.081862 ACAATTAGCTAAGAGTGCGGTACA 60.082 41.667 12.54 0.00 35.28 2.90
2789 3005 5.748630 TCACATACAATTAGCTAAGAGTGCG 59.251 40.000 18.68 13.27 35.28 5.34
2790 3006 7.721286 ATCACATACAATTAGCTAAGAGTGC 57.279 36.000 18.68 0.00 0.00 4.40
2847 3063 2.610532 GAAATCCCGGGCTCCCTGTC 62.611 65.000 18.49 1.81 0.00 3.51
2907 3124 5.984695 ACAGTGAGTTCTCTGCATAAGTA 57.015 39.130 10.26 0.00 40.14 2.24
2922 3140 7.840342 ATAGTTTTCTATCAGCAACAGTGAG 57.160 36.000 0.00 0.00 38.62 3.51
2932 3150 4.991687 GCCCCGAGAATAGTTTTCTATCAG 59.008 45.833 0.00 0.00 41.71 2.90
3105 3324 2.300152 CAGTGTTGCCTCTGGTAGAGAA 59.700 50.000 7.39 0.00 45.07 2.87
3111 3330 2.107204 AGATTTCAGTGTTGCCTCTGGT 59.893 45.455 0.00 0.00 33.88 4.00
3479 3818 4.808364 CCAAATATGCACCCCAAATAAACG 59.192 41.667 0.00 0.00 0.00 3.60
3846 4278 2.030007 GCAAGCCAGTTCTATTTGCACA 60.030 45.455 2.93 0.00 42.63 4.57
3888 6273 0.606401 CACGCAAGGTCCTTCATGGT 60.606 55.000 0.00 0.00 46.39 3.55
3897 6282 1.089920 ATGCTTCATCACGCAAGGTC 58.910 50.000 0.00 0.00 46.39 3.85
4038 6431 1.347378 TCCCAAACCCACGGTAAGTAC 59.653 52.381 0.00 0.00 33.12 2.73
4046 6439 0.680921 ATGAGCATCCCAAACCCACG 60.681 55.000 0.00 0.00 0.00 4.94
4318 6727 8.704849 AGATAGAGACTATGAGCATTGTACTT 57.295 34.615 0.00 0.00 0.00 2.24
4407 6824 2.214387 GCATAGGCTTTTGGATGCAC 57.786 50.000 13.00 0.00 43.36 4.57
4461 6943 9.831737 CATTTCTCTTGTGTTTTCTCGAAATAT 57.168 29.630 0.00 0.00 31.08 1.28
4531 7016 1.965643 ACCACCTGTAGACAAGCGTAA 59.034 47.619 0.00 0.00 0.00 3.18
4535 7032 2.552743 GGAAAACCACCTGTAGACAAGC 59.447 50.000 0.00 0.00 0.00 4.01
4543 7040 0.923358 TGTGAGGGAAAACCACCTGT 59.077 50.000 0.00 0.00 43.89 4.00
4614 7114 7.981789 AGGAGTGAAAAATGAAAAGGAGAAAAC 59.018 33.333 0.00 0.00 0.00 2.43
4836 7339 4.165950 ACCTGCATTACATACCATGGAAGA 59.834 41.667 21.47 3.16 36.34 2.87
5050 7630 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
5886 8494 1.142097 GGAGGAGCTGCCGTTAGTC 59.858 63.158 0.00 0.00 43.43 2.59
6107 8798 2.027192 ACTGAGATTTTGCCTTCCGCTA 60.027 45.455 0.00 0.00 38.78 4.26
6124 8815 3.056107 GGCCACATACTTGACTACACTGA 60.056 47.826 0.00 0.00 0.00 3.41
6171 8876 2.313317 TCAACTTCTCCGGTGTACACT 58.687 47.619 24.55 0.00 0.00 3.55
6295 9005 1.609208 ATTCCCACTTGTCTGCACAC 58.391 50.000 0.00 0.00 29.76 3.82
6377 9126 7.164171 CACGCTGAACATTTTCCGAATAAATAG 59.836 37.037 0.00 0.00 0.00 1.73
6428 9177 3.530265 AACCATGCGTAATTCTCGGTA 57.470 42.857 5.39 0.00 0.00 4.02
6565 9320 2.554893 GCAAATAACACCTGGTCGGAAA 59.445 45.455 0.00 0.00 36.31 3.13
6686 9445 3.944055 TCCTCAAGTCTGAGTTACTGC 57.056 47.619 0.00 0.00 46.71 4.40
6732 9492 8.457238 AAACTTAGAGAGGAAATTATGGATGC 57.543 34.615 0.00 0.00 0.00 3.91
6733 9493 9.618890 TGAAACTTAGAGAGGAAATTATGGATG 57.381 33.333 0.00 0.00 0.00 3.51
6955 12023 0.108329 ATTGCAAGCATGGCTCAAGC 60.108 50.000 4.94 0.00 38.25 4.01
6956 12024 2.268298 GAATTGCAAGCATGGCTCAAG 58.732 47.619 4.94 0.00 38.25 3.02
6957 12025 1.619332 TGAATTGCAAGCATGGCTCAA 59.381 42.857 4.94 0.00 38.25 3.02
6958 12026 1.258676 TGAATTGCAAGCATGGCTCA 58.741 45.000 4.94 0.00 38.25 4.26


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

AutoCloner maintained by Alex Coulton.