Multiple sequence alignment - TraesCS3D01G070700

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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 TraesCS3D01G070700 chr3D 100.000 4487 0 0 3662 8148 31719063 31723549 0.000000e+00 8287
1 TraesCS3D01G070700 chr3D 96.148 4491 156 10 3667 8144 19949334 19953820 0.000000e+00 7319
2 TraesCS3D01G070700 chr3D 100.000 3311 0 0 1 3311 31715402 31718712 0.000000e+00 6115
3 TraesCS3D01G070700 chr3D 96.614 2953 79 11 3662 6600 564303822 564300877 0.000000e+00 4879
4 TraesCS3D01G070700 chr3D 96.716 2893 81 8 3662 6540 301439074 301436182 0.000000e+00 4804
5 TraesCS3D01G070700 chr3D 100.000 1496 0 0 8418 9913 31723819 31725314 0.000000e+00 2763
6 TraesCS3D01G070700 chr3D 96.995 366 9 1 2941 3306 564304685 564304322 1.830000e-171 614
7 TraesCS3D01G070700 chr3D 95.299 234 7 4 317 548 31712159 31711928 1.570000e-97 368
8 TraesCS3D01G070700 chr3D 85.000 140 12 6 9774 9912 415538603 415538734 6.250000e-27 134
9 TraesCS3D01G070700 chr1D 97.531 4496 92 9 3662 8148 226462765 226467250 0.000000e+00 7670
10 TraesCS3D01G070700 chr1D 97.119 4478 115 7 3683 8147 456923169 456918693 0.000000e+00 7542
11 TraesCS3D01G070700 chr1D 97.225 4397 96 13 3773 8148 452230120 452234511 0.000000e+00 7420
12 TraesCS3D01G070700 chr1D 97.424 4347 99 9 3811 8148 495120371 495116029 0.000000e+00 7395
13 TraesCS3D01G070700 chr1D 97.105 4353 103 12 3807 8148 470879914 470875574 0.000000e+00 7319
14 TraesCS3D01G070700 chr1D 96.584 322 11 0 2990 3311 226461778 226462099 1.470000e-147 534
15 TraesCS3D01G070700 chr1D 90.808 359 12 2 2939 3297 495121264 495120927 2.520000e-125 460
16 TraesCS3D01G070700 chr1D 98.000 100 2 0 8418 8517 226467308 226467407 3.680000e-39 174
17 TraesCS3D01G070700 chr1D 98.000 100 2 0 8418 8517 452234568 452234667 3.680000e-39 174
18 TraesCS3D01G070700 chr1D 98.958 96 1 0 8422 8517 452229528 452229623 1.320000e-38 172
19 TraesCS3D01G070700 chr1D 95.000 100 5 0 8418 8517 3522713 3522812 3.710000e-34 158
20 TraesCS3D01G070700 chr7D 97.050 4508 105 14 3662 8148 496104959 496100459 0.000000e+00 7563
21 TraesCS3D01G070700 chr7D 97.078 4381 104 13 3788 8148 23676159 23680535 0.000000e+00 7360
22 TraesCS3D01G070700 chr7D 94.851 369 19 0 2941 3309 580052398 580052766 2.400000e-160 577
23 TraesCS3D01G070700 chr7D 90.808 359 15 2 2940 3298 109422357 109422697 1.950000e-126 464
24 TraesCS3D01G070700 chr7D 98.020 101 2 0 8418 8518 496100398 496100298 1.020000e-39 176
25 TraesCS3D01G070700 chr7D 98.000 100 2 0 8418 8517 580057705 580057804 3.680000e-39 174
26 TraesCS3D01G070700 chr7D 97.000 100 3 0 8418 8517 109431344 109431443 1.710000e-37 169
27 TraesCS3D01G070700 chr2D 97.027 4507 104 16 3662 8148 36681863 36686359 0.000000e+00 7553
28 TraesCS3D01G070700 chr2D 95.773 4306 138 17 3667 7941 5707757 5703465 0.000000e+00 6903
29 TraesCS3D01G070700 chr2D 95.266 1014 37 7 3662 4664 605084082 605083069 0.000000e+00 1596
30 TraesCS3D01G070700 chr2D 97.721 351 8 0 2940 3290 301367572 301367922 1.100000e-168 604
31 TraesCS3D01G070700 chr2D 94.444 324 13 4 2964 3286 5708496 5708177 2.490000e-135 494
32 TraesCS3D01G070700 chr2D 94.643 112 4 1 8418 8527 346286361 346286472 1.320000e-38 172
33 TraesCS3D01G070700 chr2D 97.980 99 1 1 8419 8517 36686419 36686516 4.760000e-38 171
34 TraesCS3D01G070700 chr2D 97.938 97 2 0 8421 8517 301367571 301367667 1.710000e-37 169
35 TraesCS3D01G070700 chr6D 97.346 4409 104 9 3749 8148 38578056 38582460 0.000000e+00 7481
36 TraesCS3D01G070700 chr6D 92.183 371 9 1 2941 3311 24841453 24841103 3.190000e-139 507
37 TraesCS3D01G070700 chr6D 93.694 111 5 2 8423 8531 90888544 90888434 2.220000e-36 165
38 TraesCS3D01G070700 chr6D 93.636 110 5 2 8418 8526 24836270 24836162 7.970000e-36 163
39 TraesCS3D01G070700 chr6D 96.842 95 3 0 8423 8517 24841453 24841359 1.030000e-34 159
40 TraesCS3D01G070700 chr6D 95.050 101 4 1 8418 8518 38582519 38582618 3.710000e-34 158
41 TraesCS3D01G070700 chr6D 95.000 100 5 0 8418 8517 90883736 90883637 3.710000e-34 158
42 TraesCS3D01G070700 chr6D 94.000 100 5 1 8423 8522 38577389 38577487 6.200000e-32 150
43 TraesCS3D01G070700 chr6D 93.878 49 3 0 8441 8489 11065831 11065879 3.840000e-09 75
44 TraesCS3D01G070700 chrUn 97.195 4385 109 9 3773 8148 96239856 96235477 0.000000e+00 7404
45 TraesCS3D01G070700 chrUn 96.196 552 15 3 1 547 89687850 89688400 0.000000e+00 898
46 TraesCS3D01G070700 chrUn 91.870 369 10 2 2941 3309 101052843 101052495 1.920000e-136 497
47 TraesCS3D01G070700 chrUn 93.636 110 3 2 8418 8527 96235421 96235316 2.870000e-35 161
48 TraesCS3D01G070700 chrUn 95.789 95 4 0 8423 8517 101052843 101052749 4.790000e-33 154
49 TraesCS3D01G070700 chrUn 93.684 95 4 1 8423 8517 96240641 96240549 3.730000e-29 141
50 TraesCS3D01G070700 chr3A 94.858 2392 78 19 574 2940 44428586 44430957 0.000000e+00 3694
51 TraesCS3D01G070700 chr3A 92.979 1410 56 16 8518 9913 44430953 44432333 0.000000e+00 2015
52 TraesCS3D01G070700 chr3A 90.000 100 5 3 9814 9912 535002648 535002553 3.760000e-24 124
53 TraesCS3D01G070700 chr3B 94.983 2292 79 18 673 2940 53812486 53814765 0.000000e+00 3563
54 TraesCS3D01G070700 chr3B 94.841 756 35 3 8518 9273 53814761 53815512 0.000000e+00 1177
55 TraesCS3D01G070700 chr1A 95.298 553 20 4 1 547 478571468 478570916 0.000000e+00 872
56 TraesCS3D01G070700 chr1A 93.309 553 30 5 1 547 543040202 543040753 0.000000e+00 809
57 TraesCS3D01G070700 chr1A 93.939 66 2 2 8441 8505 80706278 80706342 2.280000e-16 99
58 TraesCS3D01G070700 chr7B 94.234 555 24 5 1 547 23662248 23662802 0.000000e+00 841
59 TraesCS3D01G070700 chr5B 93.333 555 29 5 1 549 692673165 692672613 0.000000e+00 813
60 TraesCS3D01G070700 chr5B 91.741 557 39 4 1 550 16404296 16404852 0.000000e+00 767
61 TraesCS3D01G070700 chr5B 90.336 238 21 2 319 554 16395706 16395469 2.690000e-80 311
62 TraesCS3D01G070700 chr2A 92.665 559 28 6 1 547 630069257 630068700 0.000000e+00 793
63 TraesCS3D01G070700 chr5D 94.370 373 16 3 2941 3308 510654410 510654038 1.440000e-157 568
64 TraesCS3D01G070700 chr5D 82.957 399 47 15 158 547 502112385 502111999 3.430000e-89 340
65 TraesCS3D01G070700 chr5D 98.000 100 2 0 8418 8517 432796439 432796538 3.680000e-39 174
66 TraesCS3D01G070700 chr5D 94.000 100 6 0 8418 8517 510649074 510648975 1.720000e-32 152
67 TraesCS3D01G070700 chr4B 96.842 95 3 0 8423 8517 625982940 625983034 1.030000e-34 159


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 TraesCS3D01G070700 chr3D 31715402 31725314 9912 False 5721.666667 8287 100.000000 1 9913 3 chr3D.!!$F3 9912
1 TraesCS3D01G070700 chr3D 19949334 19953820 4486 False 7319.000000 7319 96.148000 3667 8144 1 chr3D.!!$F1 4477
2 TraesCS3D01G070700 chr3D 301436182 301439074 2892 True 4804.000000 4804 96.716000 3662 6540 1 chr3D.!!$R2 2878
3 TraesCS3D01G070700 chr3D 564300877 564304685 3808 True 2746.500000 4879 96.804500 2941 6600 2 chr3D.!!$R3 3659
4 TraesCS3D01G070700 chr1D 456918693 456923169 4476 True 7542.000000 7542 97.119000 3683 8147 1 chr1D.!!$R1 4464
5 TraesCS3D01G070700 chr1D 470875574 470879914 4340 True 7319.000000 7319 97.105000 3807 8148 1 chr1D.!!$R2 4341
6 TraesCS3D01G070700 chr1D 495116029 495121264 5235 True 3927.500000 7395 94.116000 2939 8148 2 chr1D.!!$R3 5209
7 TraesCS3D01G070700 chr1D 226461778 226467407 5629 False 2792.666667 7670 97.371667 2990 8517 3 chr1D.!!$F2 5527
8 TraesCS3D01G070700 chr1D 452229528 452234667 5139 False 2588.666667 7420 98.061000 3773 8517 3 chr1D.!!$F3 4744
9 TraesCS3D01G070700 chr7D 23676159 23680535 4376 False 7360.000000 7360 97.078000 3788 8148 1 chr7D.!!$F1 4360
10 TraesCS3D01G070700 chr7D 496100298 496104959 4661 True 3869.500000 7563 97.535000 3662 8518 2 chr7D.!!$R1 4856
11 TraesCS3D01G070700 chr2D 36681863 36686516 4653 False 3862.000000 7553 97.503500 3662 8517 2 chr2D.!!$F2 4855
12 TraesCS3D01G070700 chr2D 5703465 5708496 5031 True 3698.500000 6903 95.108500 2964 7941 2 chr2D.!!$R2 4977
13 TraesCS3D01G070700 chr2D 605083069 605084082 1013 True 1596.000000 1596 95.266000 3662 4664 1 chr2D.!!$R1 1002
14 TraesCS3D01G070700 chr6D 38577389 38582618 5229 False 2596.333333 7481 95.465333 3749 8522 3 chr6D.!!$F2 4773
15 TraesCS3D01G070700 chrUn 96235316 96240641 5325 True 2568.666667 7404 94.838333 3773 8527 3 chrUn.!!$R1 4754
16 TraesCS3D01G070700 chrUn 89687850 89688400 550 False 898.000000 898 96.196000 1 547 1 chrUn.!!$F1 546
17 TraesCS3D01G070700 chr3A 44428586 44432333 3747 False 2854.500000 3694 93.918500 574 9913 2 chr3A.!!$F1 9339
18 TraesCS3D01G070700 chr3B 53812486 53815512 3026 False 2370.000000 3563 94.912000 673 9273 2 chr3B.!!$F1 8600
19 TraesCS3D01G070700 chr1A 478570916 478571468 552 True 872.000000 872 95.298000 1 547 1 chr1A.!!$R1 546
20 TraesCS3D01G070700 chr1A 543040202 543040753 551 False 809.000000 809 93.309000 1 547 1 chr1A.!!$F2 546
21 TraesCS3D01G070700 chr7B 23662248 23662802 554 False 841.000000 841 94.234000 1 547 1 chr7B.!!$F1 546
22 TraesCS3D01G070700 chr5B 692672613 692673165 552 True 813.000000 813 93.333000 1 549 1 chr5B.!!$R2 548
23 TraesCS3D01G070700 chr5B 16404296 16404852 556 False 767.000000 767 91.741000 1 550 1 chr5B.!!$F1 549
24 TraesCS3D01G070700 chr2A 630068700 630069257 557 True 793.000000 793 92.665000 1 547 1 chr2A.!!$R1 546

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
573 584 0.609131 AGGGCATCGGTGGTTCTTTG 60.609 55.000 0.00 0.00 0.00 2.77 F
574 585 0.893727 GGGCATCGGTGGTTCTTTGT 60.894 55.000 0.00 0.00 0.00 2.83 F
576 587 1.467342 GGCATCGGTGGTTCTTTGTAC 59.533 52.381 0.00 0.00 0.00 2.90 F
1284 1317 2.182284 CCCACATCCGCGACGTAA 59.818 61.111 8.23 0.00 0.00 3.18 F
2614 2678 0.462759 GCAAGGGTTCGATGCTAGCT 60.463 55.000 17.23 0.83 37.12 3.32 F
2801 2865 0.251742 TTTGGGGCATTCTGGACAGG 60.252 55.000 0.00 0.00 0.00 4.00 F
4664 5911 1.214175 TGTGGTTCCATCAGTGTTGGT 59.786 47.619 17.85 0.00 35.64 3.67 F
4908 6156 0.891373 CGTCACTCACTGACCAGGAT 59.109 55.000 0.00 0.00 46.01 3.24 F
5995 7243 0.179034 GATTGCCGCTTCTCTCCCAT 60.179 55.000 0.00 0.00 0.00 4.00 F
6575 7826 0.975556 TGATGCGCCTTCCACCTCTA 60.976 55.000 4.18 0.00 0.00 2.43 F
6702 7953 1.486211 CCCACTTCCTATCGGACTGT 58.514 55.000 0.00 0.00 39.60 3.55 F
7050 8302 1.880894 CGAGTTGCGTGAGGAGGTA 59.119 57.895 0.00 0.00 34.64 3.08 F
8840 10102 1.301401 TCAAAGCACCGGGAAGACG 60.301 57.895 6.32 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1729 1.548582 CCAACAGCCTGGAGAATTGGT 60.549 52.381 0.00 0.00 38.96 3.67 R
1861 1913 1.665679 GAAGATGCAAAATCGCCTCGA 59.334 47.619 0.00 0.00 41.13 4.04 R
1886 1938 3.239449 TGAAGGAACTGTCTAGGCAGAA 58.761 45.455 30.51 4.32 40.86 3.02 R
2786 2850 0.251341 AACACCTGTCCAGAATGCCC 60.251 55.000 0.00 0.00 31.97 5.36 R
4211 5458 0.867746 CGCAGTAAGAACAGCAGCAA 59.132 50.000 0.00 0.00 37.97 3.91 R
4733 5980 1.134367 CAGCATAAGAAGGACGACCGA 59.866 52.381 0.00 0.00 41.83 4.69 R
5950 7198 0.388134 GCACGAGCCGTCTCAAGTAA 60.388 55.000 0.00 0.00 38.32 2.24 R
6575 7826 0.610232 GGCATGAAAGGAGGTGCACT 60.610 55.000 17.98 2.27 39.27 4.40 R
7050 8302 0.036732 CCGGTGGTGGCTGCATATAT 59.963 55.000 0.50 0.00 0.00 0.86 R
8570 9832 0.257328 AGGAGAGCGATGAGACAGGA 59.743 55.000 0.00 0.00 0.00 3.86 R
8571 9833 1.110442 AAGGAGAGCGATGAGACAGG 58.890 55.000 0.00 0.00 0.00 4.00 R
8898 10160 0.322975 ATCCGTCAGCTGCAAAGACT 59.677 50.000 9.47 0.00 0.00 3.24 R
9843 11117 0.618393 CCTGGGGCATGGACCAAAAT 60.618 55.000 0.00 0.00 36.09 1.82 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
281 285 4.376170 GCGGTGGGATTTGGGGGT 62.376 66.667 0.00 0.00 0.00 4.95
557 568 8.614469 TTTTGCAATTTACTCCAAAAATAGGG 57.386 30.769 0.00 0.00 35.11 3.53
558 569 5.729510 TGCAATTTACTCCAAAAATAGGGC 58.270 37.500 0.00 0.00 0.00 5.19
559 570 5.247110 TGCAATTTACTCCAAAAATAGGGCA 59.753 36.000 0.00 0.00 31.41 5.36
560 571 6.070309 TGCAATTTACTCCAAAAATAGGGCAT 60.070 34.615 0.00 0.00 30.13 4.40
561 572 6.479990 GCAATTTACTCCAAAAATAGGGCATC 59.520 38.462 0.00 0.00 0.00 3.91
562 573 5.828299 TTTACTCCAAAAATAGGGCATCG 57.172 39.130 0.00 0.00 0.00 3.84
563 574 2.654863 ACTCCAAAAATAGGGCATCGG 58.345 47.619 0.00 0.00 0.00 4.18
564 575 2.025321 ACTCCAAAAATAGGGCATCGGT 60.025 45.455 0.00 0.00 0.00 4.69
565 576 2.358898 CTCCAAAAATAGGGCATCGGTG 59.641 50.000 0.00 0.00 0.00 4.94
566 577 1.408702 CCAAAAATAGGGCATCGGTGG 59.591 52.381 0.00 0.00 0.00 4.61
567 578 2.099405 CAAAAATAGGGCATCGGTGGT 58.901 47.619 0.00 0.00 0.00 4.16
568 579 2.495669 CAAAAATAGGGCATCGGTGGTT 59.504 45.455 0.00 0.00 0.00 3.67
569 580 2.052782 AAATAGGGCATCGGTGGTTC 57.947 50.000 0.00 0.00 0.00 3.62
570 581 1.213296 AATAGGGCATCGGTGGTTCT 58.787 50.000 0.00 0.00 0.00 3.01
571 582 1.213296 ATAGGGCATCGGTGGTTCTT 58.787 50.000 0.00 0.00 0.00 2.52
572 583 0.988832 TAGGGCATCGGTGGTTCTTT 59.011 50.000 0.00 0.00 0.00 2.52
573 584 0.609131 AGGGCATCGGTGGTTCTTTG 60.609 55.000 0.00 0.00 0.00 2.77
574 585 0.893727 GGGCATCGGTGGTTCTTTGT 60.894 55.000 0.00 0.00 0.00 2.83
575 586 1.612199 GGGCATCGGTGGTTCTTTGTA 60.612 52.381 0.00 0.00 0.00 2.41
576 587 1.467342 GGCATCGGTGGTTCTTTGTAC 59.533 52.381 0.00 0.00 0.00 2.90
693 704 2.975410 TCTTGTCAATTTCTGCAGCG 57.025 45.000 9.47 0.00 0.00 5.18
827 840 2.520741 GCCTCTCCCTCTCCTCCG 60.521 72.222 0.00 0.00 0.00 4.63
1266 1299 2.679287 GAGAACCCCCTCGTCGGT 60.679 66.667 0.00 0.00 0.00 4.69
1282 1315 4.430765 GTCCCACATCCGCGACGT 62.431 66.667 8.23 0.00 0.00 4.34
1283 1316 2.751036 TCCCACATCCGCGACGTA 60.751 61.111 8.23 0.00 0.00 3.57
1284 1317 2.182284 CCCACATCCGCGACGTAA 59.818 61.111 8.23 0.00 0.00 3.18
1379 1418 3.374988 TGGTTCAGATTTGAGCTAATGCG 59.625 43.478 0.20 0.00 45.42 4.73
1400 1439 3.325870 GCTTTGCTTTCGGCCTAAATTT 58.674 40.909 2.45 0.00 40.92 1.82
1443 1482 7.119699 CACCTTCAAGTAATTCAGCTGTTATCA 59.880 37.037 14.67 0.00 0.00 2.15
1509 1548 4.016444 GACATCCATTGGCCTTTCTTACA 58.984 43.478 3.32 0.00 0.00 2.41
1515 1554 6.964464 TCCATTGGCCTTTCTTACATTACTA 58.036 36.000 3.32 0.00 0.00 1.82
1717 1769 2.556559 GGAAATGGGGGCACTAGAAACA 60.557 50.000 0.00 0.00 0.00 2.83
1731 1783 5.298276 CACTAGAAACAGGTAAAGTTGCCAA 59.702 40.000 0.00 0.00 35.15 4.52
1801 1853 4.142469 GGTGTTATCCACATACTTGCCAAC 60.142 45.833 0.00 0.00 46.44 3.77
1861 1913 4.841443 GGAATTTGGTTTCCGTAAGTGT 57.159 40.909 0.00 0.00 36.12 3.55
1883 1935 2.789092 CGAGGCGATTTTGCATCTTCAC 60.789 50.000 3.26 0.00 43.12 3.18
1886 1938 3.256631 AGGCGATTTTGCATCTTCACTTT 59.743 39.130 0.00 0.00 36.28 2.66
1910 1962 2.303022 TGCCTAGACAGTTCCTTCAAGG 59.697 50.000 0.00 0.00 36.46 3.61
1911 1963 2.937433 GCCTAGACAGTTCCTTCAAGGC 60.937 54.545 0.00 0.00 41.27 4.35
1912 1964 2.569404 CCTAGACAGTTCCTTCAAGGCT 59.431 50.000 0.00 0.00 34.61 4.58
1913 1965 3.008485 CCTAGACAGTTCCTTCAAGGCTT 59.992 47.826 0.00 0.00 34.61 4.35
1914 1966 3.133141 AGACAGTTCCTTCAAGGCTTC 57.867 47.619 0.00 0.00 34.61 3.86
1915 1967 2.439507 AGACAGTTCCTTCAAGGCTTCA 59.560 45.455 0.00 0.00 34.61 3.02
1916 1968 3.117888 AGACAGTTCCTTCAAGGCTTCAA 60.118 43.478 0.00 0.00 34.61 2.69
1917 1969 3.217626 ACAGTTCCTTCAAGGCTTCAAG 58.782 45.455 3.61 3.61 34.61 3.02
2016 2072 1.216178 GGTCGGCGGTAGCTTGTTA 59.784 57.895 7.21 0.00 44.37 2.41
2132 2188 7.598759 ACTGGACAATATACGAGAATAAGGT 57.401 36.000 0.00 0.00 0.00 3.50
2230 2287 2.704725 AAATACAGTGTGCGGCTTTG 57.295 45.000 5.88 0.00 0.00 2.77
2252 2309 9.552114 CTTTGTTGACTCTTGTTATGATCATTC 57.448 33.333 14.65 8.42 0.00 2.67
2510 2567 2.563179 TCCCTGTCAGCAGAAGAGTAAC 59.437 50.000 0.00 0.00 45.28 2.50
2614 2678 0.462759 GCAAGGGTTCGATGCTAGCT 60.463 55.000 17.23 0.83 37.12 3.32
2684 2748 3.008157 TGGGACTGTAATAAAGCACCGAA 59.992 43.478 0.00 0.00 0.00 4.30
2786 2850 5.559035 GCAGTTGCGTATATAGCTTCTTTGG 60.559 44.000 0.00 0.00 35.28 3.28
2801 2865 0.251742 TTTGGGGCATTCTGGACAGG 60.252 55.000 0.00 0.00 0.00 4.00
2934 2999 1.561076 ACCAGTGCATCCTGCTATGAA 59.439 47.619 0.00 0.00 45.31 2.57
2967 3032 6.975196 AGATGTGTATAGTCTCTCTTGCAT 57.025 37.500 0.00 0.00 0.00 3.96
2982 3047 8.264347 TCTCTCTTGCATTTTACCATACACATA 58.736 33.333 0.00 0.00 0.00 2.29
3772 4970 2.507944 CCCCTGCTTCCTCCATCG 59.492 66.667 0.00 0.00 0.00 3.84
3773 4971 2.507944 CCCTGCTTCCTCCATCGG 59.492 66.667 0.00 0.00 0.00 4.18
3774 4972 2.507944 CCTGCTTCCTCCATCGGG 59.492 66.667 0.00 0.00 0.00 5.14
3775 4973 2.507944 CTGCTTCCTCCATCGGGG 59.492 66.667 0.00 0.00 38.37 5.73
3776 4974 3.764160 CTGCTTCCTCCATCGGGGC 62.764 68.421 0.00 0.00 36.21 5.80
4143 5389 4.824479 TCAACAGATGTCAGCCTATTCA 57.176 40.909 0.00 0.00 0.00 2.57
4208 5455 1.746787 GTGGTGCAATGATGATGCTCA 59.253 47.619 0.00 0.00 44.14 4.26
4211 5458 2.361119 GGTGCAATGATGATGCTCATGT 59.639 45.455 3.76 0.00 44.14 3.21
4303 5550 3.119291 GCGATGTGGTCTTATCTCTGTG 58.881 50.000 0.00 0.00 0.00 3.66
4406 5653 8.122472 TCTGTTGATGAGTTCTATTCACAGTA 57.878 34.615 0.00 0.00 0.00 2.74
4416 5663 5.939764 TCTATTCACAGTACTCTGCCATT 57.060 39.130 0.00 0.00 44.77 3.16
4634 5881 3.450115 GACCCGCCTACGCTCTGT 61.450 66.667 0.00 0.00 38.22 3.41
4664 5911 1.214175 TGTGGTTCCATCAGTGTTGGT 59.786 47.619 17.85 0.00 35.64 3.67
4728 5975 3.306902 CCTGCCTACTCCTTCAGGA 57.693 57.895 1.09 0.00 46.80 3.86
4799 6047 0.898320 TTCTGTGGCTACTGCTCTCC 59.102 55.000 0.64 0.00 39.59 3.71
4908 6156 0.891373 CGTCACTCACTGACCAGGAT 59.109 55.000 0.00 0.00 46.01 3.24
5025 6273 4.737946 GCATCTACACAGTCAGGTACATCC 60.738 50.000 0.00 0.00 0.00 3.51
5059 6307 3.631227 GGATTCTGGAGCCTCTTTTCATG 59.369 47.826 0.00 0.00 0.00 3.07
5061 6309 4.908601 TTCTGGAGCCTCTTTTCATGTA 57.091 40.909 0.00 0.00 0.00 2.29
5103 6351 2.162809 GTCTTCTCTCCGACCTCTTGAC 59.837 54.545 0.00 0.00 0.00 3.18
5119 6367 5.142061 TCTTGACTCGCCTGTTAATGTTA 57.858 39.130 0.00 0.00 0.00 2.41
5126 6374 4.757594 TCGCCTGTTAATGTTATTACCGT 58.242 39.130 0.00 0.00 0.00 4.83
5277 6525 4.929808 GGTTGTCGTGTCATTCTTGATACT 59.070 41.667 2.21 0.00 40.67 2.12
5293 6541 5.426689 TGATACTGACTCTTGCTCCATTT 57.573 39.130 0.00 0.00 0.00 2.32
5448 6696 1.301716 GTCTGCGTCCTTCCAGCAA 60.302 57.895 0.00 0.00 40.63 3.91
5524 6772 1.062810 AGGGCCTCTTAGGGTCTGTAG 60.063 57.143 0.00 0.00 35.37 2.74
5950 7198 1.924524 CCGAACGTAAGCATCGTCATT 59.075 47.619 5.92 0.00 45.16 2.57
5995 7243 0.179034 GATTGCCGCTTCTCTCCCAT 60.179 55.000 0.00 0.00 0.00 4.00
6013 7261 2.459644 CATCCCATTTTTGGGCTGAGA 58.540 47.619 8.84 0.00 45.51 3.27
6064 7312 1.253593 ACAGCCATCGACTGCTCTGA 61.254 55.000 7.51 0.00 38.79 3.27
6333 7584 2.756207 GTCCTTCTACCTCGAGCTTCTT 59.244 50.000 6.99 0.00 0.00 2.52
6529 7780 4.985409 CCATTTCCTCTTCACTATACTCGC 59.015 45.833 0.00 0.00 0.00 5.03
6575 7826 0.975556 TGATGCGCCTTCCACCTCTA 60.976 55.000 4.18 0.00 0.00 2.43
6591 7842 2.503356 CCTCTAGTGCACCTCCTTTCAT 59.497 50.000 14.63 0.00 0.00 2.57
6702 7953 1.486211 CCCACTTCCTATCGGACTGT 58.514 55.000 0.00 0.00 39.60 3.55
6799 8051 2.284699 CCCTCCCTTCCGGTGTCT 60.285 66.667 0.00 0.00 0.00 3.41
6856 8108 3.357203 ACTCGCTCTGATGGTTCTCTTA 58.643 45.455 0.00 0.00 0.00 2.10
7050 8302 1.880894 CGAGTTGCGTGAGGAGGTA 59.119 57.895 0.00 0.00 34.64 3.08
7235 8493 3.812019 CGTCTCCTCGTGGTCGGG 61.812 72.222 2.99 0.00 37.69 5.14
7300 8558 4.778579 ACGACTCTGACTACATAGCCTTA 58.221 43.478 0.00 0.00 0.00 2.69
7347 8606 2.158842 CCTCATGACTGATCTTGGTCCC 60.159 54.545 0.00 0.00 32.18 4.46
7390 8649 3.648545 TGAGATCTCCTCGACCTCTGATA 59.351 47.826 20.03 0.00 44.92 2.15
7579 8840 3.127376 TGTCTATCTTGCTGTTACGCGTA 59.873 43.478 16.41 16.41 0.00 4.42
8520 9782 2.375174 AGTTGCCCATTCCTAACACTGA 59.625 45.455 0.00 0.00 0.00 3.41
8521 9783 3.010584 AGTTGCCCATTCCTAACACTGAT 59.989 43.478 0.00 0.00 0.00 2.90
8527 9789 5.687441 GCCCATTCCTAACACTGATCACATA 60.687 44.000 0.00 0.00 0.00 2.29
8553 9815 2.136026 ACAGTCAAAAGGTTCCCTCCT 58.864 47.619 0.00 0.00 39.84 3.69
8559 9821 2.432174 AAAGGTTCCCTCCTGCTGGC 62.432 60.000 4.42 0.00 37.93 4.85
8569 9831 2.079925 CTCCTGCTGGCTTTCAACTAC 58.920 52.381 4.42 0.00 0.00 2.73
8570 9832 1.699634 TCCTGCTGGCTTTCAACTACT 59.300 47.619 4.42 0.00 0.00 2.57
8571 9833 2.079925 CCTGCTGGCTTTCAACTACTC 58.920 52.381 0.00 0.00 0.00 2.59
8572 9834 2.079925 CTGCTGGCTTTCAACTACTCC 58.920 52.381 0.00 0.00 0.00 3.85
8574 9836 2.079925 GCTGGCTTTCAACTACTCCTG 58.920 52.381 0.00 0.00 0.00 3.86
8575 9837 2.551071 GCTGGCTTTCAACTACTCCTGT 60.551 50.000 0.00 0.00 0.00 4.00
8576 9838 3.330267 CTGGCTTTCAACTACTCCTGTC 58.670 50.000 0.00 0.00 0.00 3.51
8655 9917 5.156355 GGACTCGTCTGTTTCATTTACGTA 58.844 41.667 0.00 0.00 35.21 3.57
8665 9927 9.790389 TCTGTTTCATTTACGTAAAACAAATGT 57.210 25.926 23.49 3.65 40.10 2.71
8699 9961 4.329462 TTGTTGCTACATTTTGGAACCC 57.671 40.909 0.81 0.00 34.36 4.11
8712 9974 5.576563 TTTGGAACCCTATTTCAGTCTGA 57.423 39.130 0.00 0.00 0.00 3.27
8763 10025 8.188799 AGTTTTACTTACTTGCCTGAAGTTTTC 58.811 33.333 0.00 0.00 42.70 2.29
8840 10102 1.301401 TCAAAGCACCGGGAAGACG 60.301 57.895 6.32 0.00 0.00 4.18
8898 10160 2.489971 CGGTTAAGCACCTTTGTCTCA 58.510 47.619 5.38 0.00 44.69 3.27
8900 10162 3.477530 GGTTAAGCACCTTTGTCTCAGT 58.522 45.455 0.00 0.00 43.29 3.41
8913 10175 1.797635 GTCTCAGTCTTTGCAGCTGAC 59.202 52.381 20.43 9.67 35.65 3.51
8999 10262 5.376625 AGTAGAAGCCTTTGTTCACAATGA 58.623 37.500 7.05 0.00 35.55 2.57
9012 10275 1.174712 ACAATGAGTGTGGCCTGTGC 61.175 55.000 3.32 0.00 39.72 4.57
9013 10276 1.151221 AATGAGTGTGGCCTGTGCA 59.849 52.632 3.32 0.00 40.13 4.57
9041 10304 7.048512 GCTTTTGGGCTTCTATAGTTCTCTTA 58.951 38.462 0.00 0.00 0.00 2.10
9127 10390 4.034975 GCAGTAGTTCCTGAAATCTCATGC 59.965 45.833 0.00 0.00 34.23 4.06
9235 10498 8.942338 AAGAAAATTTAACAGAAAACCTCACC 57.058 30.769 0.00 0.00 0.00 4.02
9269 10532 7.600752 GTGCATGAAGAGGAAGTATATAGAACC 59.399 40.741 0.00 0.00 0.00 3.62
9291 10554 1.205655 TCTGTTCTCATTCAGGAGCCG 59.794 52.381 0.00 0.00 34.84 5.52
9302 10565 1.687146 AGGAGCCGGAGCAATCTGA 60.687 57.895 5.05 0.00 43.56 3.27
9303 10566 1.227497 GGAGCCGGAGCAATCTGAG 60.227 63.158 5.05 0.00 43.56 3.35
9304 10567 1.680522 GGAGCCGGAGCAATCTGAGA 61.681 60.000 5.05 0.00 43.56 3.27
9305 10568 0.529555 GAGCCGGAGCAATCTGAGAC 60.530 60.000 5.05 0.00 43.56 3.36
9306 10569 1.880340 GCCGGAGCAATCTGAGACG 60.880 63.158 5.05 0.00 39.53 4.18
9307 10570 1.227089 CCGGAGCAATCTGAGACGG 60.227 63.158 0.00 0.00 0.00 4.79
9310 10573 0.247736 GGAGCAATCTGAGACGGTGT 59.752 55.000 0.00 0.00 0.00 4.16
9369 10632 4.951254 TGAACTACATTGTTGGAACGAGA 58.049 39.130 0.00 0.00 0.00 4.04
9370 10633 4.988540 TGAACTACATTGTTGGAACGAGAG 59.011 41.667 0.00 0.00 0.00 3.20
9372 10635 1.523758 ACATTGTTGGAACGAGAGCC 58.476 50.000 0.00 0.00 0.00 4.70
9373 10636 1.072331 ACATTGTTGGAACGAGAGCCT 59.928 47.619 0.00 0.00 0.00 4.58
9376 10639 0.895530 TGTTGGAACGAGAGCCTAGG 59.104 55.000 3.67 3.67 0.00 3.02
9377 10640 0.896226 GTTGGAACGAGAGCCTAGGT 59.104 55.000 11.31 0.00 0.00 3.08
9380 10643 1.272536 TGGAACGAGAGCCTAGGTCTT 60.273 52.381 11.31 0.00 40.67 3.01
9381 10644 1.135333 GGAACGAGAGCCTAGGTCTTG 59.865 57.143 19.36 19.36 44.43 3.02
9382 10645 1.135333 GAACGAGAGCCTAGGTCTTGG 59.865 57.143 22.47 16.02 43.52 3.61
9383 10646 0.331954 ACGAGAGCCTAGGTCTTGGA 59.668 55.000 22.47 0.00 43.52 3.53
9384 10647 0.741915 CGAGAGCCTAGGTCTTGGAC 59.258 60.000 11.31 0.16 40.67 4.02
9385 10648 1.683629 CGAGAGCCTAGGTCTTGGACT 60.684 57.143 11.31 0.00 40.67 3.85
9386 10649 2.028876 GAGAGCCTAGGTCTTGGACTC 58.971 57.143 11.31 6.43 40.67 3.36
9387 10650 0.741915 GAGCCTAGGTCTTGGACTCG 59.258 60.000 11.31 0.00 32.47 4.18
9388 10651 0.039911 AGCCTAGGTCTTGGACTCGT 59.960 55.000 11.31 0.00 32.47 4.18
9389 10652 1.284198 AGCCTAGGTCTTGGACTCGTA 59.716 52.381 11.31 0.00 32.47 3.43
9390 10653 1.404748 GCCTAGGTCTTGGACTCGTAC 59.595 57.143 11.31 0.00 32.47 3.67
9391 10654 2.719739 CCTAGGTCTTGGACTCGTACA 58.280 52.381 0.00 0.00 32.47 2.90
9392 10655 3.087031 CCTAGGTCTTGGACTCGTACAA 58.913 50.000 0.00 0.00 32.47 2.41
9393 10656 3.508793 CCTAGGTCTTGGACTCGTACAAA 59.491 47.826 0.00 0.00 32.14 2.83
9394 10657 3.662247 AGGTCTTGGACTCGTACAAAG 57.338 47.619 0.00 0.00 32.14 2.77
9395 10658 3.228453 AGGTCTTGGACTCGTACAAAGA 58.772 45.455 0.00 0.00 32.14 2.52
9396 10659 3.640029 AGGTCTTGGACTCGTACAAAGAA 59.360 43.478 0.00 0.00 32.14 2.52
9397 10660 3.739810 GGTCTTGGACTCGTACAAAGAAC 59.260 47.826 0.00 0.00 32.14 3.01
9406 10669 6.424207 GGACTCGTACAAAGAACTTCAATCTT 59.576 38.462 0.00 0.00 38.75 2.40
9425 10688 8.292448 TCAATCTTAAAGCTCTGTTGAAACATC 58.708 33.333 0.00 0.00 38.41 3.06
9436 10699 3.698539 TGTTGAAACATCTCAAAGGTGCA 59.301 39.130 0.00 0.00 37.08 4.57
9452 10715 3.044059 GCAGATCGGCAGCACAACC 62.044 63.158 13.30 0.00 0.00 3.77
9471 10736 7.262048 CACAACCGCCATTATTACCTAAAAAT 58.738 34.615 0.00 0.00 0.00 1.82
9615 10889 8.703743 AGCAAGAGAGAACTCAATAGACAATAT 58.296 33.333 4.64 0.00 44.79 1.28
9642 10916 3.418684 ACAACTACTGGTCCACATTCC 57.581 47.619 0.00 0.00 0.00 3.01
9653 10927 0.536233 CCACATTCCGGGTCACACAA 60.536 55.000 0.00 0.00 0.00 3.33
9665 10939 5.336372 CCGGGTCACACAAACATAAATGATT 60.336 40.000 0.00 0.00 0.00 2.57
9725 10999 6.668541 AAGAGATTGTGTAAACATGATCGG 57.331 37.500 0.00 0.00 0.00 4.18
9742 11016 3.955771 TCGGGCATTATTTTTAGACGC 57.044 42.857 0.00 0.00 0.00 5.19
9807 11081 2.371841 TCCACTGCATATATGGTCCACC 59.628 50.000 14.51 0.00 34.89 4.61
9836 11110 3.515502 TCATCTCAGAACATCCGGAAGTT 59.484 43.478 24.17 24.17 0.00 2.66
9843 11117 3.072476 AGAACATCCGGAAGTTTCCTCAA 59.928 43.478 24.64 0.00 45.33 3.02
9885 11159 4.760204 GCGTTTTGGCCTTATATCCTACAT 59.240 41.667 3.32 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 285 2.961893 CGGTCGACCATTCCCCCAA 61.962 63.158 32.80 0.00 35.14 4.12
547 558 2.099405 ACCACCGATGCCCTATTTTTG 58.901 47.619 0.00 0.00 0.00 2.44
548 559 2.525105 ACCACCGATGCCCTATTTTT 57.475 45.000 0.00 0.00 0.00 1.94
549 560 2.025321 AGAACCACCGATGCCCTATTTT 60.025 45.455 0.00 0.00 0.00 1.82
550 561 1.564348 AGAACCACCGATGCCCTATTT 59.436 47.619 0.00 0.00 0.00 1.40
551 562 1.213296 AGAACCACCGATGCCCTATT 58.787 50.000 0.00 0.00 0.00 1.73
552 563 1.213296 AAGAACCACCGATGCCCTAT 58.787 50.000 0.00 0.00 0.00 2.57
553 564 0.988832 AAAGAACCACCGATGCCCTA 59.011 50.000 0.00 0.00 0.00 3.53
554 565 0.609131 CAAAGAACCACCGATGCCCT 60.609 55.000 0.00 0.00 0.00 5.19
555 566 0.893727 ACAAAGAACCACCGATGCCC 60.894 55.000 0.00 0.00 0.00 5.36
556 567 1.467342 GTACAAAGAACCACCGATGCC 59.533 52.381 0.00 0.00 0.00 4.40
557 568 1.467342 GGTACAAAGAACCACCGATGC 59.533 52.381 0.00 0.00 36.96 3.91
558 569 2.773487 TGGTACAAAGAACCACCGATG 58.227 47.619 0.00 0.00 42.10 3.84
564 575 2.506231 TGTCCAGTGGTACAAAGAACCA 59.494 45.455 9.54 0.00 44.16 3.67
565 576 3.202829 TGTCCAGTGGTACAAAGAACC 57.797 47.619 9.54 0.00 44.16 3.62
566 577 5.519722 CAAATGTCCAGTGGTACAAAGAAC 58.480 41.667 9.54 0.00 44.16 3.01
567 578 4.037446 GCAAATGTCCAGTGGTACAAAGAA 59.963 41.667 9.54 0.00 44.16 2.52
568 579 3.568007 GCAAATGTCCAGTGGTACAAAGA 59.432 43.478 9.54 0.00 44.16 2.52
569 580 3.609175 CGCAAATGTCCAGTGGTACAAAG 60.609 47.826 9.54 7.75 44.16 2.77
570 581 2.292016 CGCAAATGTCCAGTGGTACAAA 59.708 45.455 9.54 0.00 44.16 2.83
571 582 1.876799 CGCAAATGTCCAGTGGTACAA 59.123 47.619 9.54 0.00 44.16 2.41
572 583 1.202710 ACGCAAATGTCCAGTGGTACA 60.203 47.619 9.54 12.48 0.00 2.90
573 584 1.463444 GACGCAAATGTCCAGTGGTAC 59.537 52.381 9.54 6.92 32.61 3.34
574 585 1.803334 GACGCAAATGTCCAGTGGTA 58.197 50.000 9.54 0.00 32.61 3.25
575 586 2.629002 GACGCAAATGTCCAGTGGT 58.371 52.632 9.54 0.00 32.61 4.16
640 651 9.185192 CTTATTCTTTGCGAGAAGAAATTTGTT 57.815 29.630 14.81 0.00 46.99 2.83
648 659 5.046591 TCCCTTCTTATTCTTTGCGAGAAGA 60.047 40.000 11.75 2.28 46.99 2.87
651 662 4.819105 TCCCTTCTTATTCTTTGCGAGA 57.181 40.909 0.00 0.00 0.00 4.04
693 704 7.938563 TGTGCATTTGTATTTCTTTTACACC 57.061 32.000 0.00 0.00 29.60 4.16
827 840 2.609491 GGAAAATGAGACGGTTTTGGGC 60.609 50.000 0.00 0.00 0.00 5.36
1266 1299 2.274232 CTTACGTCGCGGATGTGGGA 62.274 60.000 6.13 0.00 33.52 4.37
1281 1314 1.520120 GGGCCGGCGTCTTACTTAC 60.520 63.158 22.54 1.26 0.00 2.34
1282 1315 1.543065 TTGGGCCGGCGTCTTACTTA 61.543 55.000 22.54 0.00 0.00 2.24
1283 1316 2.400269 TTTGGGCCGGCGTCTTACTT 62.400 55.000 22.54 0.00 0.00 2.24
1284 1317 2.798148 CTTTGGGCCGGCGTCTTACT 62.798 60.000 22.54 0.00 0.00 2.24
1379 1418 2.654749 ATTTAGGCCGAAAGCAAAGC 57.345 45.000 16.45 0.00 46.50 3.51
1419 1458 7.335422 ACTGATAACAGCTGAATTACTTGAAGG 59.665 37.037 23.35 0.00 46.95 3.46
1668 1720 4.625324 GCCTGGAGAATTGGTACACATGTA 60.625 45.833 0.00 0.00 39.29 2.29
1677 1729 1.548582 CCAACAGCCTGGAGAATTGGT 60.549 52.381 0.00 0.00 38.96 3.67
1717 1769 2.956333 GTGGTCTTTGGCAACTTTACCT 59.044 45.455 16.04 0.00 37.61 3.08
1801 1853 4.575236 CCAATCATCAGGAGACTCAACATG 59.425 45.833 4.53 2.97 40.21 3.21
1861 1913 1.665679 GAAGATGCAAAATCGCCTCGA 59.334 47.619 0.00 0.00 41.13 4.04
1883 1935 4.278975 AGGAACTGTCTAGGCAGAAAAG 57.721 45.455 30.51 5.08 37.18 2.27
1886 1938 3.239449 TGAAGGAACTGTCTAGGCAGAA 58.761 45.455 30.51 4.32 40.86 3.02
1934 1990 5.841810 ACAAACATTTACACATGGTCAAGG 58.158 37.500 0.00 0.00 0.00 3.61
2016 2072 4.558226 TGACACCATAAACAGAGCAGAT 57.442 40.909 0.00 0.00 0.00 2.90
2181 2238 7.944729 ACAAGAATGAAATTAGGCACAGTAT 57.055 32.000 0.00 0.00 36.07 2.12
2441 2498 4.460382 CACCAAAGCAATCACCAAGAGTAT 59.540 41.667 0.00 0.00 0.00 2.12
2510 2567 4.177026 CCTAGAGACCGAACAGAACATTG 58.823 47.826 0.00 0.00 0.00 2.82
2614 2678 2.284754 TGGCACCAAGAACATTGCTA 57.715 45.000 0.00 0.00 35.24 3.49
2684 2748 5.148651 AGAACTTACGAGGCAATAGTTGT 57.851 39.130 0.00 0.00 0.00 3.32
2735 2799 1.411246 CCGATATTTCAGGGGACGACA 59.589 52.381 0.00 0.00 0.00 4.35
2786 2850 0.251341 AACACCTGTCCAGAATGCCC 60.251 55.000 0.00 0.00 31.97 5.36
2801 2865 5.968848 TCATTTCGTTTGCTGTTAGAAACAC 59.031 36.000 0.00 0.00 36.25 3.32
2902 2966 1.001974 TGCACTGGTTGACGCTCTAAT 59.998 47.619 0.00 0.00 0.00 1.73
2934 2999 9.415008 AGAGACTATACACATCTAACAATCAGT 57.585 33.333 0.00 0.00 0.00 3.41
3760 4958 3.483869 AGCCCCGATGGAGGAAGC 61.484 66.667 0.00 0.00 35.39 3.86
3762 4960 3.089874 CCAGCCCCGATGGAGGAA 61.090 66.667 0.00 0.00 42.34 3.36
3767 4965 3.231889 CTCGATCCAGCCCCGATGG 62.232 68.421 0.00 0.00 40.92 3.51
3769 4967 3.620785 GCTCGATCCAGCCCCGAT 61.621 66.667 0.05 0.00 32.76 4.18
4125 5371 4.743045 GCATCTGAATAGGCTGACATCTGT 60.743 45.833 0.00 0.00 0.00 3.41
4143 5389 1.071385 CGATAGGCAGAAAGGGCATCT 59.929 52.381 0.00 0.00 35.46 2.90
4208 5455 2.227388 GCAGTAAGAACAGCAGCAACAT 59.773 45.455 0.00 0.00 37.99 2.71
4211 5458 0.867746 CGCAGTAAGAACAGCAGCAA 59.132 50.000 0.00 0.00 37.97 3.91
4634 5881 3.117474 TGATGGAACCACAAGTAACCCAA 60.117 43.478 0.00 0.00 0.00 4.12
4664 5911 3.606662 GCATAGGAGCTCGGGCGA 61.607 66.667 7.83 0.00 44.37 5.54
4728 5975 2.679287 GAAGGACGACCGACCCCT 60.679 66.667 7.25 2.85 41.83 4.79
4732 5979 1.134560 AGCATAAGAAGGACGACCGAC 59.865 52.381 0.00 0.00 41.83 4.79
4733 5980 1.134367 CAGCATAAGAAGGACGACCGA 59.866 52.381 0.00 0.00 41.83 4.69
4734 5981 1.134367 TCAGCATAAGAAGGACGACCG 59.866 52.381 0.00 0.00 41.83 4.79
4860 6108 1.218196 GAGGATCCAGGAGTCCCACTA 59.782 57.143 15.82 0.00 35.00 2.74
4908 6156 3.891977 AGAGACGCTTGAGCCTCATAATA 59.108 43.478 0.00 0.00 37.91 0.98
5025 6273 1.406069 CCAGAATCCAGAACCCACGAG 60.406 57.143 0.00 0.00 0.00 4.18
5059 6307 4.505922 CAGCACGGAAGAATCAGAAGATAC 59.494 45.833 0.00 0.00 33.08 2.24
5061 6309 3.055530 ACAGCACGGAAGAATCAGAAGAT 60.056 43.478 0.00 0.00 35.53 2.40
5103 6351 4.807304 ACGGTAATAACATTAACAGGCGAG 59.193 41.667 0.00 0.00 0.00 5.03
5119 6367 1.004277 AGGTGTGCCATCAACGGTAAT 59.996 47.619 0.00 0.00 37.19 1.89
5126 6374 1.067295 AGGAAGAGGTGTGCCATCAA 58.933 50.000 0.00 0.00 37.19 2.57
5293 6541 0.968901 ACCTTGGTGCGACGATCCTA 60.969 55.000 0.00 0.00 0.00 2.94
5524 6772 6.259550 ACAATGTAAAGAAACATCTCCAGC 57.740 37.500 0.00 0.00 39.16 4.85
5950 7198 0.388134 GCACGAGCCGTCTCAAGTAA 60.388 55.000 0.00 0.00 38.32 2.24
6013 7261 3.521126 AGATAGGTGGATGCAGAAACAGT 59.479 43.478 0.00 0.00 0.00 3.55
6064 7312 3.716872 CACTCCATAGGAATACCACCCTT 59.283 47.826 0.00 0.00 38.94 3.95
6333 7584 6.055588 AGAAGAAAAGAAAGATCGTCCACAA 58.944 36.000 0.00 0.00 0.00 3.33
6575 7826 0.610232 GGCATGAAAGGAGGTGCACT 60.610 55.000 17.98 2.27 39.27 4.40
6591 7842 1.616930 TTATGAACCGGGGGAGGCA 60.617 57.895 6.32 0.00 33.69 4.75
6702 7953 2.704464 CCATTCAGGCTGAGTCATGA 57.296 50.000 23.01 7.84 0.00 3.07
7050 8302 0.036732 CCGGTGGTGGCTGCATATAT 59.963 55.000 0.50 0.00 0.00 0.86
7189 8445 1.290203 ACAACGCGATCATGATCACC 58.710 50.000 30.13 20.44 37.69 4.02
7235 8493 3.131933 TCAACATAGAGAAGGAGCAGAGC 59.868 47.826 0.00 0.00 0.00 4.09
7317 8576 2.608623 TCAGTCATGAGGAACTGGTCA 58.391 47.619 11.22 0.00 41.55 4.02
7347 8606 4.640201 TCAATCCCAAGAAAATAGCGAAGG 59.360 41.667 0.00 0.00 0.00 3.46
7390 8649 5.505181 TTTTCTTGGGAGATGTAGAAGCT 57.495 39.130 0.00 0.00 0.00 3.74
7579 8840 9.420118 GATATGAACAGGATAGGAGATATCAGT 57.580 37.037 5.32 0.00 41.94 3.41
8421 9683 9.534565 GCAAGAGAGATTATACACATCTAACAA 57.465 33.333 0.00 0.00 30.70 2.83
8437 9699 6.109359 GTGTATGGTAAAGTGCAAGAGAGAT 58.891 40.000 0.00 0.00 0.00 2.75
8553 9815 1.699634 AGGAGTAGTTGAAAGCCAGCA 59.300 47.619 0.00 0.00 0.00 4.41
8559 9821 5.098893 CGATGAGACAGGAGTAGTTGAAAG 58.901 45.833 0.00 0.00 0.00 2.62
8569 9831 0.667993 GGAGAGCGATGAGACAGGAG 59.332 60.000 0.00 0.00 0.00 3.69
8570 9832 0.257328 AGGAGAGCGATGAGACAGGA 59.743 55.000 0.00 0.00 0.00 3.86
8571 9833 1.110442 AAGGAGAGCGATGAGACAGG 58.890 55.000 0.00 0.00 0.00 4.00
8572 9834 2.426738 AGAAAGGAGAGCGATGAGACAG 59.573 50.000 0.00 0.00 0.00 3.51
8574 9836 3.378742 TGTAGAAAGGAGAGCGATGAGAC 59.621 47.826 0.00 0.00 0.00 3.36
8575 9837 3.621558 TGTAGAAAGGAGAGCGATGAGA 58.378 45.455 0.00 0.00 0.00 3.27
8576 9838 4.582701 ATGTAGAAAGGAGAGCGATGAG 57.417 45.455 0.00 0.00 0.00 2.90
8634 9896 7.010367 TGTTTTACGTAAATGAAACAGACGAGT 59.990 33.333 20.72 0.00 37.15 4.18
8665 9927 3.540314 AGCAACAAAAACAATGGCAGA 57.460 38.095 0.00 0.00 0.00 4.26
8699 9961 9.809096 TCTAGTTATGCTTTCAGACTGAAATAG 57.191 33.333 26.66 21.79 44.37 1.73
8750 10012 2.297701 GTGTCAGGAAAACTTCAGGCA 58.702 47.619 0.00 0.00 0.00 4.75
8763 10025 0.689623 AGGAGAAGCTTGGTGTCAGG 59.310 55.000 2.10 0.00 0.00 3.86
8840 10102 3.002348 GGCTGCTGATAACGTATGTTTCC 59.998 47.826 5.48 0.00 39.54 3.13
8846 10108 2.838736 CTTGGGCTGCTGATAACGTAT 58.161 47.619 0.00 0.00 0.00 3.06
8898 10160 0.322975 ATCCGTCAGCTGCAAAGACT 59.677 50.000 9.47 0.00 0.00 3.24
8900 10162 1.159285 CAATCCGTCAGCTGCAAAGA 58.841 50.000 9.47 3.35 0.00 2.52
8913 10175 3.349972 CGCATACATTCGCAATCCG 57.650 52.632 0.00 0.00 38.61 4.18
8999 10262 2.567497 GCATTGCACAGGCCACACT 61.567 57.895 5.01 0.00 40.13 3.55
9012 10275 5.841957 ACTATAGAAGCCCAAAAGCATTG 57.158 39.130 6.78 0.00 34.23 2.82
9013 10276 6.190587 AGAACTATAGAAGCCCAAAAGCATT 58.809 36.000 6.78 0.00 34.23 3.56
9041 10304 7.871973 ACATTTGCAATGTACAACATACAACAT 59.128 29.630 0.00 0.00 37.97 2.71
9056 10319 1.202166 TGCCGATCGACATTTGCAATG 60.202 47.619 18.66 3.61 0.00 2.82
9127 10390 7.824704 AGATATATAAGAATGCAAGCACTCG 57.175 36.000 0.00 0.00 0.00 4.18
9235 10498 2.022195 CCTCTTCATGCACAAGATGGG 58.978 52.381 9.78 5.95 0.00 4.00
9269 10532 2.419851 GGCTCCTGAATGAGAACAGAGG 60.420 54.545 0.00 0.00 36.38 3.69
9285 10548 1.227497 CTCAGATTGCTCCGGCTCC 60.227 63.158 0.00 0.00 39.59 4.70
9291 10554 0.247736 ACACCGTCTCAGATTGCTCC 59.752 55.000 0.00 0.00 0.00 4.70
9306 10569 4.732106 GATCGGATCGGTCACACC 57.268 61.111 1.62 0.00 36.93 4.16
9324 10587 5.957842 TCTTTCAATGGTTGGTGATACAC 57.042 39.130 0.00 0.00 0.00 2.90
9369 10632 0.039911 ACGAGTCCAAGACCTAGGCT 59.960 55.000 9.30 4.10 32.18 4.58
9370 10633 1.404748 GTACGAGTCCAAGACCTAGGC 59.595 57.143 9.30 1.39 32.18 3.93
9372 10635 4.458295 TCTTTGTACGAGTCCAAGACCTAG 59.542 45.833 0.00 0.00 32.18 3.02
9373 10636 4.401022 TCTTTGTACGAGTCCAAGACCTA 58.599 43.478 0.00 0.00 32.18 3.08
9376 10639 4.618965 AGTTCTTTGTACGAGTCCAAGAC 58.381 43.478 0.00 0.00 0.00 3.01
9377 10640 4.931661 AGTTCTTTGTACGAGTCCAAGA 57.068 40.909 0.00 0.00 0.00 3.02
9380 10643 4.659111 TGAAGTTCTTTGTACGAGTCCA 57.341 40.909 4.17 0.00 0.00 4.02
9381 10644 5.927115 AGATTGAAGTTCTTTGTACGAGTCC 59.073 40.000 4.17 0.00 0.00 3.85
9382 10645 7.409465 AAGATTGAAGTTCTTTGTACGAGTC 57.591 36.000 4.17 0.00 29.12 3.36
9383 10646 8.882415 TTAAGATTGAAGTTCTTTGTACGAGT 57.118 30.769 4.17 0.00 35.19 4.18
9384 10647 9.798885 CTTTAAGATTGAAGTTCTTTGTACGAG 57.201 33.333 4.17 0.00 35.19 4.18
9385 10648 8.280497 GCTTTAAGATTGAAGTTCTTTGTACGA 58.720 33.333 4.17 0.00 35.19 3.43
9386 10649 8.283291 AGCTTTAAGATTGAAGTTCTTTGTACG 58.717 33.333 4.17 0.00 35.19 3.67
9387 10650 9.600646 GAGCTTTAAGATTGAAGTTCTTTGTAC 57.399 33.333 4.17 0.00 33.37 2.90
9388 10651 9.561069 AGAGCTTTAAGATTGAAGTTCTTTGTA 57.439 29.630 9.62 0.00 39.90 2.41
9389 10652 8.348507 CAGAGCTTTAAGATTGAAGTTCTTTGT 58.651 33.333 11.89 0.00 39.90 2.83
9390 10653 8.348507 ACAGAGCTTTAAGATTGAAGTTCTTTG 58.651 33.333 11.89 7.34 39.90 2.77
9391 10654 8.457238 ACAGAGCTTTAAGATTGAAGTTCTTT 57.543 30.769 11.89 5.60 39.90 2.52
9392 10655 8.348507 CAACAGAGCTTTAAGATTGAAGTTCTT 58.651 33.333 11.89 0.00 39.90 2.52
9393 10656 7.716998 TCAACAGAGCTTTAAGATTGAAGTTCT 59.283 33.333 9.62 9.62 42.23 3.01
9394 10657 7.865707 TCAACAGAGCTTTAAGATTGAAGTTC 58.134 34.615 0.00 6.01 35.32 3.01
9395 10658 7.807977 TCAACAGAGCTTTAAGATTGAAGTT 57.192 32.000 0.00 0.00 0.00 2.66
9396 10659 7.807977 TTCAACAGAGCTTTAAGATTGAAGT 57.192 32.000 0.00 0.00 32.43 3.01
9397 10660 8.131100 TGTTTCAACAGAGCTTTAAGATTGAAG 58.869 33.333 0.00 0.00 36.33 3.02
9406 10669 7.255242 CCTTTGAGATGTTTCAACAGAGCTTTA 60.255 37.037 0.00 0.00 43.04 1.85
9425 10688 0.674581 TGCCGATCTGCACCTTTGAG 60.675 55.000 7.83 0.00 36.04 3.02
9452 10715 6.399639 ACCCATTTTTAGGTAATAATGGCG 57.600 37.500 19.08 15.78 45.43 5.69
9453 10716 6.921307 CGAACCCATTTTTAGGTAATAATGGC 59.079 38.462 19.08 10.04 45.43 4.40
9457 10720 7.122501 GGTTCCGAACCCATTTTTAGGTAATAA 59.877 37.037 18.32 0.00 46.12 1.40
9484 10749 4.481072 GTCCTCTAACCCTCTAGGCAATA 58.519 47.826 0.00 0.00 40.58 1.90
9488 10753 1.218450 AGGTCCTCTAACCCTCTAGGC 59.782 57.143 0.00 0.00 40.42 3.93
9567 10832 5.181690 TGCAAAGTTTTGTGATGTAGGTC 57.818 39.130 6.48 0.00 40.24 3.85
9615 10889 2.640332 TGGACCAGTAGTTGTAATGCCA 59.360 45.455 0.00 0.00 0.00 4.92
9642 10916 4.757799 TCATTTATGTTTGTGTGACCCG 57.242 40.909 0.00 0.00 0.00 5.28
9725 10999 6.972328 TCAATCAAGCGTCTAAAAATAATGCC 59.028 34.615 0.00 0.00 0.00 4.40
9742 11016 2.100252 GGACACCATGGCATCAATCAAG 59.900 50.000 13.04 0.00 0.00 3.02
9836 11110 2.566724 GGCATGGACCAAAATTGAGGAA 59.433 45.455 0.00 0.00 0.00 3.36
9843 11117 0.618393 CCTGGGGCATGGACCAAAAT 60.618 55.000 0.00 0.00 36.09 1.82
9885 11159 9.138062 GTGCATGACATTTCAATTGTTAACATA 57.862 29.630 9.56 1.09 34.61 2.29


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

AutoCloner maintained by Alex Coulton.