Multiple sequence alignment - TraesCS6D01G163700

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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 TraesCS6D01G163700 chr6D 100.000 5899 0 0 1 5899 142927023 142921125 0.000000e+00 10894.0
1 TraesCS6D01G163700 chr6D 81.476 637 86 19 1007 1627 142868806 142868186 1.480000e-135 494.0
2 TraesCS6D01G163700 chr6D 87.079 356 34 9 1226 1579 142858090 142857745 5.540000e-105 392.0
3 TraesCS6D01G163700 chr6D 90.426 282 23 4 3885 4163 142847934 142847654 9.340000e-98 368.0
4 TraesCS6D01G163700 chr6D 81.759 307 28 15 3883 4163 142867535 142867231 1.280000e-56 231.0
5 TraesCS6D01G163700 chr6D 86.957 161 20 1 4595 4754 142847108 142846948 4.700000e-41 180.0
6 TraesCS6D01G163700 chr6B 94.085 1268 70 5 3775 5040 248506119 248504855 0.000000e+00 1921.0
7 TraesCS6D01G163700 chr6B 91.417 1235 64 21 736 1932 248509817 248508587 0.000000e+00 1655.0
8 TraesCS6D01G163700 chr6B 90.326 889 63 5 1995 2877 248508583 248507712 0.000000e+00 1144.0
9 TraesCS6D01G163700 chr6B 95.423 721 24 4 5182 5899 148683465 148684179 0.000000e+00 1140.0
10 TraesCS6D01G163700 chr6B 88.960 942 58 18 2883 3780 248507093 248506154 0.000000e+00 1122.0
11 TraesCS6D01G163700 chr6B 83.306 605 83 13 1040 1633 248390378 248389781 5.200000e-150 542.0
12 TraesCS6D01G163700 chr6B 92.199 282 18 4 3885 4163 248373737 248373457 4.280000e-106 396.0
13 TraesCS6D01G163700 chr6B 85.000 360 43 5 1222 1579 248387134 248386784 7.270000e-94 355.0
14 TraesCS6D01G163700 chr6B 81.759 307 28 17 3883 4163 248389136 248388832 1.280000e-56 231.0
15 TraesCS6D01G163700 chr6B 86.335 161 21 1 4595 4754 248372911 248372751 2.190000e-39 174.0
16 TraesCS6D01G163700 chr6B 97.297 37 1 0 3734 3770 686811984 686811948 4.940000e-06 63.9
17 TraesCS6D01G163700 chr6A 92.937 1246 70 9 699 1932 187975363 187974124 0.000000e+00 1797.0
18 TraesCS6D01G163700 chr6A 90.372 1101 86 11 1995 3080 187974120 187973025 0.000000e+00 1428.0
19 TraesCS6D01G163700 chr6A 93.604 813 50 2 4229 5040 187969605 187968794 0.000000e+00 1212.0
20 TraesCS6D01G163700 chr6A 95.944 715 28 1 5185 5899 363823296 363822583 0.000000e+00 1158.0
21 TraesCS6D01G163700 chr6A 94.251 661 32 3 3126 3780 187972727 187972067 0.000000e+00 1005.0
22 TraesCS6D01G163700 chr6A 95.279 466 19 3 3775 4237 187972032 187971567 0.000000e+00 736.0
23 TraesCS6D01G163700 chr6A 82.537 607 74 19 1040 1627 187912377 187911784 6.820000e-139 505.0
24 TraesCS6D01G163700 chr6A 92.199 282 18 4 3885 4163 187905505 187905225 4.280000e-106 396.0
25 TraesCS6D01G163700 chr6A 82.222 360 38 18 1222 1579 187909306 187908971 2.690000e-73 287.0
26 TraesCS6D01G163700 chr6A 82.085 307 27 17 3883 4163 187911128 187910824 2.750000e-58 237.0
27 TraesCS6D01G163700 chr6A 85.714 161 22 1 4595 4754 187904672 187904512 1.020000e-37 169.0
28 TraesCS6D01G163700 chr6A 85.311 177 7 9 5069 5226 175442125 175441949 1.320000e-36 165.0
29 TraesCS6D01G163700 chr6A 84.328 134 16 4 5068 5199 52561981 52561851 6.210000e-25 126.0
30 TraesCS6D01G163700 chr2D 94.131 852 24 4 5069 5899 102961220 102960374 0.000000e+00 1273.0
31 TraesCS6D01G163700 chr2D 96.379 718 22 2 5185 5899 642403762 642403046 0.000000e+00 1179.0
32 TraesCS6D01G163700 chr2D 95.839 721 23 2 5185 5899 569782301 569781582 0.000000e+00 1158.0
33 TraesCS6D01G163700 chr2D 91.237 582 44 4 1 580 385668329 385667753 0.000000e+00 785.0
34 TraesCS6D01G163700 chr2D 85.714 133 15 3 5068 5196 470244214 470244346 2.870000e-28 137.0
35 TraesCS6D01G163700 chr5D 95.822 718 26 2 5185 5899 478988083 478987367 0.000000e+00 1157.0
36 TraesCS6D01G163700 chr5D 91.738 581 42 2 1 580 29336325 29335750 0.000000e+00 802.0
37 TraesCS6D01G163700 chr7D 95.804 715 29 1 5185 5899 76658967 76658254 0.000000e+00 1153.0
38 TraesCS6D01G163700 chrUn 95.304 724 26 4 5182 5899 70675434 70676155 0.000000e+00 1142.0
39 TraesCS6D01G163700 chrUn 92.069 580 42 3 1 579 24446107 24445531 0.000000e+00 813.0
40 TraesCS6D01G163700 chr7B 95.000 720 33 2 5182 5899 436422414 436423132 0.000000e+00 1127.0
41 TraesCS6D01G163700 chr7B 90.449 534 35 9 5142 5667 480127307 480127832 0.000000e+00 689.0
42 TraesCS6D01G163700 chr7B 90.130 537 34 10 5142 5667 133766214 133765686 0.000000e+00 680.0
43 TraesCS6D01G163700 chr7B 84.211 133 13 5 5069 5196 158348473 158348344 8.030000e-24 122.0
44 TraesCS6D01G163700 chr3B 93.127 582 38 2 1 581 247575152 247574572 0.000000e+00 852.0
45 TraesCS6D01G163700 chr3B 83.957 187 10 3 5057 5224 784395459 784395644 1.700000e-35 161.0
46 TraesCS6D01G163700 chr3B 95.833 72 2 1 5059 5130 72240917 72240987 1.340000e-21 115.0
47 TraesCS6D01G163700 chr4A 91.897 580 39 4 1 579 474788289 474787717 0.000000e+00 804.0
48 TraesCS6D01G163700 chr4D 91.595 583 42 4 1 580 71529134 71528556 0.000000e+00 798.0
49 TraesCS6D01G163700 chr4D 91.237 582 44 3 1 579 71461660 71461083 0.000000e+00 785.0
50 TraesCS6D01G163700 chr7A 91.424 583 44 3 1 582 569236446 569235869 0.000000e+00 795.0
51 TraesCS6D01G163700 chr7A 77.033 209 39 8 3499 3703 507168650 507168853 1.740000e-20 111.0
52 TraesCS6D01G163700 chr3D 91.379 580 45 4 1 579 63148443 63149018 0.000000e+00 789.0
53 TraesCS6D01G163700 chr3D 89.013 628 32 12 5069 5667 606339143 606338524 0.000000e+00 743.0
54 TraesCS6D01G163700 chr3D 90.824 534 33 9 5142 5667 567400454 567400979 0.000000e+00 701.0
55 TraesCS6D01G163700 chr3D 93.182 44 2 1 3736 3779 591609342 591609384 4.940000e-06 63.9
56 TraesCS6D01G163700 chr2A 88.604 623 46 12 5069 5672 577202541 577201925 0.000000e+00 734.0
57 TraesCS6D01G163700 chr2A 88.264 622 45 9 5069 5667 714178611 714177995 0.000000e+00 719.0
58 TraesCS6D01G163700 chr5B 87.821 624 43 11 5069 5667 594429638 594430253 0.000000e+00 701.0
59 TraesCS6D01G163700 chr5B 75.309 162 28 8 3500 3653 8189442 8189599 3.820000e-07 67.6
60 TraesCS6D01G163700 chr1B 90.824 534 33 9 5142 5667 183070653 183071178 0.000000e+00 701.0
61 TraesCS6D01G163700 chr1B 85.057 174 8 6 5069 5224 558045892 558045719 1.700000e-35 161.0
62 TraesCS6D01G163700 chr2B 86.667 135 13 3 5065 5194 787729884 787729750 1.710000e-30 145.0
63 TraesCS6D01G163700 chr4B 97.101 69 1 1 5063 5130 496781460 496781528 1.340000e-21 115.0
64 TraesCS6D01G163700 chr3A 100.000 32 0 0 3739 3770 722498229 722498198 6.380000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G163700 chr6D 142921125 142927023 5898 True 10894.0 10894 100.0000 1 5899 1 chr6D.!!$R2 5898
1 TraesCS6D01G163700 chr6D 142867231 142868806 1575 True 362.5 494 81.6175 1007 4163 2 chr6D.!!$R4 3156
2 TraesCS6D01G163700 chr6D 142846948 142847934 986 True 274.0 368 88.6915 3885 4754 2 chr6D.!!$R3 869
3 TraesCS6D01G163700 chr6B 248504855 248509817 4962 True 1460.5 1921 91.1970 736 5040 4 chr6B.!!$R4 4304
4 TraesCS6D01G163700 chr6B 148683465 148684179 714 False 1140.0 1140 95.4230 5182 5899 1 chr6B.!!$F1 717
5 TraesCS6D01G163700 chr6B 248386784 248390378 3594 True 376.0 542 83.3550 1040 4163 3 chr6B.!!$R3 3123
6 TraesCS6D01G163700 chr6B 248372751 248373737 986 True 285.0 396 89.2670 3885 4754 2 chr6B.!!$R2 869
7 TraesCS6D01G163700 chr6A 187968794 187975363 6569 True 1235.6 1797 93.2886 699 5040 5 chr6A.!!$R5 4341
8 TraesCS6D01G163700 chr6A 363822583 363823296 713 True 1158.0 1158 95.9440 5185 5899 1 chr6A.!!$R3 714
9 TraesCS6D01G163700 chr6A 187904512 187912377 7865 True 318.8 505 84.9514 1040 4754 5 chr6A.!!$R4 3714
10 TraesCS6D01G163700 chr2D 102960374 102961220 846 True 1273.0 1273 94.1310 5069 5899 1 chr2D.!!$R1 830
11 TraesCS6D01G163700 chr2D 642403046 642403762 716 True 1179.0 1179 96.3790 5185 5899 1 chr2D.!!$R4 714
12 TraesCS6D01G163700 chr2D 569781582 569782301 719 True 1158.0 1158 95.8390 5185 5899 1 chr2D.!!$R3 714
13 TraesCS6D01G163700 chr2D 385667753 385668329 576 True 785.0 785 91.2370 1 580 1 chr2D.!!$R2 579
14 TraesCS6D01G163700 chr5D 478987367 478988083 716 True 1157.0 1157 95.8220 5185 5899 1 chr5D.!!$R2 714
15 TraesCS6D01G163700 chr5D 29335750 29336325 575 True 802.0 802 91.7380 1 580 1 chr5D.!!$R1 579
16 TraesCS6D01G163700 chr7D 76658254 76658967 713 True 1153.0 1153 95.8040 5185 5899 1 chr7D.!!$R1 714
17 TraesCS6D01G163700 chrUn 70675434 70676155 721 False 1142.0 1142 95.3040 5182 5899 1 chrUn.!!$F1 717
18 TraesCS6D01G163700 chrUn 24445531 24446107 576 True 813.0 813 92.0690 1 579 1 chrUn.!!$R1 578
19 TraesCS6D01G163700 chr7B 436422414 436423132 718 False 1127.0 1127 95.0000 5182 5899 1 chr7B.!!$F1 717
20 TraesCS6D01G163700 chr7B 480127307 480127832 525 False 689.0 689 90.4490 5142 5667 1 chr7B.!!$F2 525
21 TraesCS6D01G163700 chr7B 133765686 133766214 528 True 680.0 680 90.1300 5142 5667 1 chr7B.!!$R1 525
22 TraesCS6D01G163700 chr3B 247574572 247575152 580 True 852.0 852 93.1270 1 581 1 chr3B.!!$R1 580
23 TraesCS6D01G163700 chr4A 474787717 474788289 572 True 804.0 804 91.8970 1 579 1 chr4A.!!$R1 578
24 TraesCS6D01G163700 chr4D 71528556 71529134 578 True 798.0 798 91.5950 1 580 1 chr4D.!!$R2 579
25 TraesCS6D01G163700 chr4D 71461083 71461660 577 True 785.0 785 91.2370 1 579 1 chr4D.!!$R1 578
26 TraesCS6D01G163700 chr7A 569235869 569236446 577 True 795.0 795 91.4240 1 582 1 chr7A.!!$R1 581
27 TraesCS6D01G163700 chr3D 63148443 63149018 575 False 789.0 789 91.3790 1 579 1 chr3D.!!$F1 578
28 TraesCS6D01G163700 chr3D 606338524 606339143 619 True 743.0 743 89.0130 5069 5667 1 chr3D.!!$R1 598
29 TraesCS6D01G163700 chr3D 567400454 567400979 525 False 701.0 701 90.8240 5142 5667 1 chr3D.!!$F2 525
30 TraesCS6D01G163700 chr2A 577201925 577202541 616 True 734.0 734 88.6040 5069 5672 1 chr2A.!!$R1 603
31 TraesCS6D01G163700 chr2A 714177995 714178611 616 True 719.0 719 88.2640 5069 5667 1 chr2A.!!$R2 598
32 TraesCS6D01G163700 chr5B 594429638 594430253 615 False 701.0 701 87.8210 5069 5667 1 chr5B.!!$F2 598
33 TraesCS6D01G163700 chr1B 183070653 183071178 525 False 701.0 701 90.8240 5142 5667 1 chr1B.!!$F1 525

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
585 599 0.108019 ACGTTTCCCAACAGAGTCCC 59.892 55.0 0.00 0.00 32.54 4.46 F
652 666 0.179073 CGGTGCAGGTCCCAGATTAG 60.179 60.0 0.00 0.00 0.00 1.73 F
653 667 0.181350 GGTGCAGGTCCCAGATTAGG 59.819 60.0 0.00 0.00 0.00 2.69 F
681 695 0.250513 GCCTTTCTCCTCGACCATGT 59.749 55.0 0.00 0.00 0.00 3.21 F
2404 2642 0.249489 GGTGTGATGCCTAGCGGTAG 60.249 60.0 14.73 14.73 0.00 3.18 F
3085 3976 0.105778 GAGAGGAGGGAAAGATGGCG 59.894 60.0 0.00 0.00 0.00 5.69 F
4438 13251 0.179045 CATGCTTCCCTTACCCGAGG 60.179 60.0 0.00 0.00 36.52 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2326 0.099436 CCCGCATTAAGTTGAGCTGC 59.901 55.0 0.0 0.00 0.00 5.25 R
2289 2520 0.893727 AGCCGGTGTGATTTGGGTTC 60.894 55.0 1.9 0.00 0.00 3.62 R
2312 2543 1.029681 GGTGGTTGTCCTTGGTGTTC 58.970 55.0 0.0 0.00 34.23 3.18 R
2515 2753 1.567504 GGGACATACGACGACAATGG 58.432 55.0 0.0 0.00 0.00 3.16 R
3678 4817 2.094026 GCATGGGAAAAGATTCACCACC 60.094 50.0 0.0 0.00 38.24 4.61 R
4763 13797 1.560860 GCACGATAGATTGCGGCCTC 61.561 60.0 0.0 0.00 41.38 4.70 R
5419 14775 0.879090 GGTGAAAGAACCGCGGATTT 59.121 50.0 35.9 27.05 0.00 2.17 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
35 36 0.800239 TCCCTCCTCTTTCCTTCCCT 59.200 55.000 0.00 0.00 0.00 4.20
36 37 1.154434 TCCCTCCTCTTTCCTTCCCTT 59.846 52.381 0.00 0.00 0.00 3.95
76 79 1.001393 GGCGAATTGGGGAGGAACA 60.001 57.895 0.00 0.00 0.00 3.18
88 91 3.381335 GGGAGGAACACCAAGTAGGATA 58.619 50.000 0.00 0.00 42.29 2.59
143 146 4.015163 CCCTCTCCCTCCCACCTATATATT 60.015 50.000 0.00 0.00 0.00 1.28
148 153 5.350547 TCCCTCCCACCTATATATTTGAGG 58.649 45.833 0.00 0.00 38.27 3.86
149 154 5.700402 CCTCCCACCTATATATTTGAGGG 57.300 47.826 5.25 7.40 35.57 4.30
150 155 4.475016 CCTCCCACCTATATATTTGAGGGG 59.525 50.000 13.26 6.19 35.57 4.79
189 201 6.112734 AGAACACACAACAACATCTGTTAGA 58.887 36.000 0.00 0.00 46.91 2.10
318 330 3.258372 TGCTGACGGAACTCATCTACTTT 59.742 43.478 0.00 0.00 0.00 2.66
359 371 2.248248 AGAGTTTGAGGGACGTCATCA 58.752 47.619 18.91 17.35 0.00 3.07
443 456 4.866508 AGAAGTTCGACTACATCAACCA 57.133 40.909 0.00 0.00 0.00 3.67
444 457 5.407407 AGAAGTTCGACTACATCAACCAT 57.593 39.130 0.00 0.00 0.00 3.55
455 468 5.592282 ACTACATCAACCATGTTGTCAAACA 59.408 36.000 6.83 0.00 45.09 2.83
485 498 3.558931 TCGGTCTATGAGGGTACGTAA 57.441 47.619 0.00 0.00 0.00 3.18
582 596 3.547054 TGTTACGTTTCCCAACAGAGT 57.453 42.857 0.00 0.00 32.54 3.24
583 597 3.460103 TGTTACGTTTCCCAACAGAGTC 58.540 45.455 0.00 0.00 32.54 3.36
584 598 2.804527 GTTACGTTTCCCAACAGAGTCC 59.195 50.000 0.00 0.00 32.54 3.85
585 599 0.108019 ACGTTTCCCAACAGAGTCCC 59.892 55.000 0.00 0.00 32.54 4.46
586 600 0.605589 CGTTTCCCAACAGAGTCCCC 60.606 60.000 0.00 0.00 32.54 4.81
587 601 0.605589 GTTTCCCAACAGAGTCCCCG 60.606 60.000 0.00 0.00 32.54 5.73
588 602 1.774894 TTTCCCAACAGAGTCCCCGG 61.775 60.000 0.00 0.00 0.00 5.73
589 603 4.410400 CCCAACAGAGTCCCCGGC 62.410 72.222 0.00 0.00 0.00 6.13
590 604 4.410400 CCAACAGAGTCCCCGGCC 62.410 72.222 0.00 0.00 0.00 6.13
591 605 4.760047 CAACAGAGTCCCCGGCCG 62.760 72.222 21.04 21.04 0.00 6.13
609 623 4.212913 GGAGGCATGCGAGCTCGA 62.213 66.667 38.74 23.38 43.02 4.04
610 624 2.959071 GAGGCATGCGAGCTCGAC 60.959 66.667 38.74 27.87 43.02 4.20
611 625 3.423162 GAGGCATGCGAGCTCGACT 62.423 63.158 38.74 24.90 43.02 4.18
612 626 3.260483 GGCATGCGAGCTCGACTG 61.260 66.667 38.74 30.91 43.02 3.51
613 627 3.922893 GCATGCGAGCTCGACTGC 61.923 66.667 38.74 35.25 43.02 4.40
614 628 2.507769 CATGCGAGCTCGACTGCA 60.508 61.111 38.74 26.24 43.02 4.41
615 629 1.881709 CATGCGAGCTCGACTGCAT 60.882 57.895 38.74 27.22 41.09 3.96
616 630 1.153489 ATGCGAGCTCGACTGCATT 60.153 52.632 38.74 13.78 38.91 3.56
617 631 1.426816 ATGCGAGCTCGACTGCATTG 61.427 55.000 38.74 7.73 38.91 2.82
618 632 2.806856 GCGAGCTCGACTGCATTGG 61.807 63.158 38.74 6.94 43.02 3.16
619 633 2.806856 CGAGCTCGACTGCATTGGC 61.807 63.158 32.06 0.00 43.02 4.52
620 634 2.437359 AGCTCGACTGCATTGGCC 60.437 61.111 0.00 0.00 40.13 5.36
621 635 2.747460 GCTCGACTGCATTGGCCA 60.747 61.111 0.00 0.00 40.13 5.36
622 636 2.758089 GCTCGACTGCATTGGCCAG 61.758 63.158 5.11 0.00 40.13 4.85
623 637 2.046023 TCGACTGCATTGGCCAGG 60.046 61.111 5.11 3.42 40.13 4.45
624 638 3.136123 CGACTGCATTGGCCAGGG 61.136 66.667 5.11 2.99 40.13 4.45
625 639 2.356278 GACTGCATTGGCCAGGGA 59.644 61.111 5.11 2.60 40.13 4.20
626 640 1.751927 GACTGCATTGGCCAGGGAG 60.752 63.158 21.32 21.32 40.13 4.30
627 641 2.441532 CTGCATTGGCCAGGGAGG 60.442 66.667 17.00 1.88 40.13 4.30
628 642 3.267233 TGCATTGGCCAGGGAGGT 61.267 61.111 5.11 0.00 40.61 3.85
629 643 2.757099 GCATTGGCCAGGGAGGTG 60.757 66.667 5.11 0.78 40.61 4.00
630 644 2.043652 CATTGGCCAGGGAGGTGG 60.044 66.667 5.11 0.00 40.61 4.61
631 645 3.350163 ATTGGCCAGGGAGGTGGG 61.350 66.667 5.11 0.00 40.61 4.61
649 663 4.101448 GCGGTGCAGGTCCCAGAT 62.101 66.667 0.00 0.00 0.00 2.90
650 664 2.671070 CGGTGCAGGTCCCAGATT 59.329 61.111 0.00 0.00 0.00 2.40
651 665 1.904771 CGGTGCAGGTCCCAGATTA 59.095 57.895 0.00 0.00 0.00 1.75
652 666 0.179073 CGGTGCAGGTCCCAGATTAG 60.179 60.000 0.00 0.00 0.00 1.73
653 667 0.181350 GGTGCAGGTCCCAGATTAGG 59.819 60.000 0.00 0.00 0.00 2.69
654 668 0.464554 GTGCAGGTCCCAGATTAGGC 60.465 60.000 0.00 0.00 0.00 3.93
655 669 1.149401 GCAGGTCCCAGATTAGGCC 59.851 63.158 0.00 0.00 0.00 5.19
656 670 1.447643 CAGGTCCCAGATTAGGCCG 59.552 63.158 0.00 0.00 0.00 6.13
657 671 2.111251 GGTCCCAGATTAGGCCGC 59.889 66.667 0.00 0.00 0.00 6.53
658 672 2.742116 GGTCCCAGATTAGGCCGCA 61.742 63.158 0.00 0.00 0.00 5.69
659 673 1.523938 GTCCCAGATTAGGCCGCAC 60.524 63.158 0.00 0.00 0.00 5.34
660 674 2.588877 CCCAGATTAGGCCGCACG 60.589 66.667 0.00 0.00 0.00 5.34
661 675 2.499205 CCAGATTAGGCCGCACGA 59.501 61.111 0.00 0.00 0.00 4.35
662 676 1.592669 CCAGATTAGGCCGCACGAG 60.593 63.158 0.00 0.00 0.00 4.18
663 677 2.107141 AGATTAGGCCGCACGAGC 59.893 61.111 0.00 0.00 37.42 5.03
670 684 3.491652 GCCGCACGAGCCTTTCTC 61.492 66.667 0.00 0.00 37.52 2.87
671 685 2.815647 CCGCACGAGCCTTTCTCC 60.816 66.667 0.00 0.00 38.62 3.71
672 686 2.262915 CGCACGAGCCTTTCTCCT 59.737 61.111 0.00 0.00 38.62 3.69
673 687 1.807573 CGCACGAGCCTTTCTCCTC 60.808 63.158 0.00 0.00 38.62 3.71
678 692 2.277858 GAGCCTTTCTCCTCGACCA 58.722 57.895 0.00 0.00 35.77 4.02
679 693 0.827368 GAGCCTTTCTCCTCGACCAT 59.173 55.000 0.00 0.00 35.77 3.55
680 694 0.539051 AGCCTTTCTCCTCGACCATG 59.461 55.000 0.00 0.00 0.00 3.66
681 695 0.250513 GCCTTTCTCCTCGACCATGT 59.749 55.000 0.00 0.00 0.00 3.21
682 696 1.740718 GCCTTTCTCCTCGACCATGTC 60.741 57.143 0.00 0.00 0.00 3.06
683 697 1.827969 CCTTTCTCCTCGACCATGTCT 59.172 52.381 0.00 0.00 0.00 3.41
684 698 2.234908 CCTTTCTCCTCGACCATGTCTT 59.765 50.000 0.00 0.00 0.00 3.01
685 699 3.307059 CCTTTCTCCTCGACCATGTCTTT 60.307 47.826 0.00 0.00 0.00 2.52
686 700 4.319177 CTTTCTCCTCGACCATGTCTTTT 58.681 43.478 0.00 0.00 0.00 2.27
687 701 4.351874 TTCTCCTCGACCATGTCTTTTT 57.648 40.909 0.00 0.00 0.00 1.94
718 732 1.449726 ATACCTCGTATGTCGCCGCA 61.450 55.000 0.00 0.00 39.67 5.69
748 762 7.816995 ACCGCTTGCAATATTTCAAAAGATTTA 59.183 29.630 0.00 0.00 28.13 1.40
750 764 9.464248 CGCTTGCAATATTTCAAAAGATTTAAC 57.536 29.630 0.00 0.00 28.13 2.01
761 775 6.198687 TCAAAAGATTTAACTGTGTGAAGCG 58.801 36.000 0.00 0.00 0.00 4.68
893 909 1.202417 GGTCGCATTTCCGAGAGATGA 60.202 52.381 8.09 0.00 37.99 2.92
986 1006 1.852895 CCGCGTCTTAACACTATCAGC 59.147 52.381 4.92 0.00 0.00 4.26
1129 1162 2.749044 CCAGCGCACCATGCTCTT 60.749 61.111 11.47 0.00 36.10 2.85
1171 1204 4.814294 CCAGGCTACGCGGACACC 62.814 72.222 12.47 3.85 0.00 4.16
1220 1265 2.203938 TGGGCGGTTCCTCCTCTT 60.204 61.111 0.00 0.00 34.39 2.85
1291 1336 2.824041 GGGCGCATCGTGGACATT 60.824 61.111 10.83 0.00 0.00 2.71
1294 1339 1.087202 GGCGCATCGTGGACATTACA 61.087 55.000 10.83 0.00 0.00 2.41
1566 1626 3.508793 CCAAGCTTTGGTGATCTTGTCAT 59.491 43.478 0.00 0.00 45.93 3.06
1593 1653 1.655885 CCTGCCATATGTGCGCACAA 61.656 55.000 43.14 31.17 45.41 3.33
1878 2102 5.412594 TCACCTTGCTAGCAAACTTCTTATG 59.587 40.000 28.95 17.25 35.33 1.90
1924 2152 7.716612 ACATGACACGAGAATATGAGATACAA 58.283 34.615 0.00 0.00 0.00 2.41
1925 2153 7.864882 ACATGACACGAGAATATGAGATACAAG 59.135 37.037 0.00 0.00 0.00 3.16
1926 2154 7.334844 TGACACGAGAATATGAGATACAAGT 57.665 36.000 0.00 0.00 0.00 3.16
1927 2155 8.446599 TGACACGAGAATATGAGATACAAGTA 57.553 34.615 0.00 0.00 0.00 2.24
1929 2157 9.900710 GACACGAGAATATGAGATACAAGTATT 57.099 33.333 0.00 0.00 0.00 1.89
1970 2198 6.657836 ACAAGTATTTTACTCGTATGGTGC 57.342 37.500 0.00 0.00 38.26 5.01
1971 2199 6.167685 ACAAGTATTTTACTCGTATGGTGCA 58.832 36.000 0.00 0.00 38.26 4.57
1972 2200 6.821665 ACAAGTATTTTACTCGTATGGTGCAT 59.178 34.615 0.00 0.00 38.26 3.96
1973 2201 7.335924 ACAAGTATTTTACTCGTATGGTGCATT 59.664 33.333 0.00 0.00 38.26 3.56
1974 2202 7.478520 AGTATTTTACTCGTATGGTGCATTC 57.521 36.000 0.00 0.00 32.47 2.67
1975 2203 7.272978 AGTATTTTACTCGTATGGTGCATTCT 58.727 34.615 0.00 0.00 32.47 2.40
1976 2204 7.769044 AGTATTTTACTCGTATGGTGCATTCTT 59.231 33.333 0.00 0.00 32.47 2.52
1977 2205 6.811253 TTTTACTCGTATGGTGCATTCTTT 57.189 33.333 0.00 0.00 0.00 2.52
1978 2206 6.811253 TTTACTCGTATGGTGCATTCTTTT 57.189 33.333 0.00 0.00 0.00 2.27
1979 2207 6.811253 TTACTCGTATGGTGCATTCTTTTT 57.189 33.333 0.00 0.00 0.00 1.94
2001 2229 2.547299 TTTTTCGGGTGACGTATGGT 57.453 45.000 0.00 0.00 44.69 3.55
2002 2230 1.798283 TTTTCGGGTGACGTATGGTG 58.202 50.000 0.00 0.00 44.69 4.17
2003 2231 0.671163 TTTCGGGTGACGTATGGTGC 60.671 55.000 0.00 0.00 44.69 5.01
2098 2326 1.669115 CTTGGGACGAGCACACCAG 60.669 63.158 0.00 0.00 33.96 4.00
2115 2343 1.202110 CCAGCAGCTCAACTTAATGCG 60.202 52.381 0.00 0.00 41.69 4.73
2125 2353 1.580059 ACTTAATGCGGGGAGAAGGA 58.420 50.000 0.00 0.00 0.00 3.36
2205 2436 2.642171 AAGGGAGGAGTGTCATACCA 57.358 50.000 0.00 0.00 0.00 3.25
2219 2450 4.042809 TGTCATACCAAACCAAGGTGATCT 59.957 41.667 0.00 0.00 40.26 2.75
2254 2485 8.342634 TCAAAACTTGCTAAACTAACTAGCTTG 58.657 33.333 0.00 0.00 41.96 4.01
2289 2520 1.517242 GCCTAGCCTCCATTTGATCG 58.483 55.000 0.00 0.00 0.00 3.69
2303 2534 4.497473 TTTGATCGAACCCAAATCACAC 57.503 40.909 0.00 0.00 0.00 3.82
2312 2543 1.308069 CCAAATCACACCGGCTGAGG 61.308 60.000 0.00 0.00 37.30 3.86
2321 2552 1.672356 CCGGCTGAGGAACACCAAG 60.672 63.158 0.00 0.00 0.00 3.61
2355 2593 1.516110 ACTAGTAGTCCCTCCGGCTA 58.484 55.000 0.00 0.00 0.00 3.93
2392 2630 2.286935 AGACCCCCAATAGGTGTGAT 57.713 50.000 0.00 0.00 37.88 3.06
2402 2640 0.686441 TAGGTGTGATGCCTAGCGGT 60.686 55.000 0.00 0.00 37.54 5.68
2403 2641 0.686441 AGGTGTGATGCCTAGCGGTA 60.686 55.000 0.00 0.00 33.97 4.02
2404 2642 0.249489 GGTGTGATGCCTAGCGGTAG 60.249 60.000 14.73 14.73 0.00 3.18
2430 2668 6.239543 GCATCATTTTCTGATCTCCTAGAGGA 60.240 42.308 0.00 0.00 42.91 3.71
2567 2805 4.102113 GCATGGGCTTCACTTGGT 57.898 55.556 0.00 0.00 36.96 3.67
2608 2846 2.305927 CCCTAGGCTTTGAAAGAGTCCA 59.694 50.000 9.48 0.00 0.00 4.02
2622 2860 1.122019 AGTCCAGTCAGACCACCACC 61.122 60.000 0.00 0.00 37.49 4.61
2670 2908 1.488812 ACCCCATGCGCAATAAGTAGA 59.511 47.619 17.11 0.00 0.00 2.59
2695 2933 4.630644 AGTCATCACTGGAACAAGATGT 57.369 40.909 0.00 0.00 45.31 3.06
2736 2974 1.620819 AGTCAGACCATCTTGTCGCTT 59.379 47.619 0.00 0.00 40.26 4.68
2752 2990 1.166531 GCTTCTCGCAACACCAACCT 61.167 55.000 0.00 0.00 38.92 3.50
2777 3015 1.125093 TGCTTCCTCCCCGACTTTCA 61.125 55.000 0.00 0.00 0.00 2.69
2859 3100 2.342650 ATGCACCCACATTCGCCAC 61.343 57.895 0.00 0.00 0.00 5.01
2878 3119 2.607635 CACCGCAACCGCCATATATATC 59.392 50.000 0.00 0.00 33.11 1.63
2880 3121 3.702548 ACCGCAACCGCCATATATATCTA 59.297 43.478 0.00 0.00 33.11 1.98
2971 3833 2.405594 CGACGAGAAGAGCCTCCG 59.594 66.667 0.00 0.00 0.00 4.63
3006 3868 4.733542 GGCCGCCACCTTGCCTTA 62.734 66.667 3.91 0.00 42.01 2.69
3021 3883 2.499693 TGCCTTATGTCGATGTTCTCCA 59.500 45.455 0.00 0.00 0.00 3.86
3025 3887 5.509840 GCCTTATGTCGATGTTCTCCACTAT 60.510 44.000 0.00 0.00 0.00 2.12
3054 3916 4.473520 CCGGATGCGGCAAGAGGT 62.474 66.667 14.38 0.00 0.00 3.85
3065 3927 1.484444 GCAAGAGGTGGGTGGAGAGT 61.484 60.000 0.00 0.00 0.00 3.24
3071 3933 1.261238 GGTGGGTGGAGAGTGAGAGG 61.261 65.000 0.00 0.00 0.00 3.69
3072 3934 0.251832 GTGGGTGGAGAGTGAGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
3081 3972 3.629796 GGAGAGTGAGAGGAGGGAAAGAT 60.630 52.174 0.00 0.00 0.00 2.40
3085 3976 0.105778 GAGAGGAGGGAAAGATGGCG 59.894 60.000 0.00 0.00 0.00 5.69
3102 3993 1.595357 CGGTGGGTAGACTTGGACC 59.405 63.158 0.00 0.00 34.75 4.46
3109 4001 3.549433 TAGACTTGGACCCCCGCCA 62.549 63.158 0.00 0.00 34.29 5.69
3184 4317 4.418013 TGCAGTTGTTTGATATGAACCG 57.582 40.909 0.00 0.00 0.00 4.44
3193 4326 2.080693 TGATATGAACCGTTGCACACC 58.919 47.619 0.00 0.00 0.00 4.16
3425 4559 6.642540 GGTTGGATTTTTAGCTGAGTCTTTTG 59.357 38.462 0.00 0.00 0.00 2.44
3531 4669 9.071276 GATGATACCCTGAACATTGTTATGAAT 57.929 33.333 1.15 0.00 35.65 2.57
3532 4670 8.821686 TGATACCCTGAACATTGTTATGAATT 57.178 30.769 1.15 0.00 35.65 2.17
3787 4966 9.209175 AGATAAATAGAATTAGTGTTCGCCATC 57.791 33.333 0.00 0.00 33.36 3.51
3880 5063 1.794714 AGCATCCGGTAGGTGATTCT 58.205 50.000 0.00 0.00 39.05 2.40
4191 11022 9.912634 CTTGTTTTTGGAATTACATATGACACT 57.087 29.630 10.38 0.00 0.00 3.55
4353 13165 6.373759 TCTGCAGGTCTGGACTATTTATCTA 58.626 40.000 15.13 0.00 0.00 1.98
4374 13186 1.085893 TGCATCATTTGATCACGCGT 58.914 45.000 5.58 5.58 31.21 6.01
4438 13251 0.179045 CATGCTTCCCTTACCCGAGG 60.179 60.000 0.00 0.00 36.52 4.63
4439 13252 0.620700 ATGCTTCCCTTACCCGAGGT 60.621 55.000 1.14 1.14 40.16 3.85
4454 13267 4.577693 ACCCGAGGTCAAAAAGAAGTAAAC 59.422 41.667 0.00 0.00 0.00 2.01
4541 13358 9.331282 CCTATTTCCCTAATCTACTGACAAAAG 57.669 37.037 0.00 0.00 0.00 2.27
4763 13797 4.115401 TCAAGTGATCACATCTTCTCGG 57.885 45.455 27.02 2.51 0.00 4.63
4831 13865 5.918011 ACCTGTGTAATTTAAACGTTGCATG 59.082 36.000 0.00 0.00 0.00 4.06
4899 13951 9.733556 TGACAACAAAAGGTGTATCATTACTAT 57.266 29.630 0.00 0.00 40.60 2.12
4925 13977 2.378038 AGTCACAGGTGCAACACAAAT 58.622 42.857 3.64 0.00 39.98 2.32
4992 14327 7.136119 GGCTAAATTTACATTACGCTTATGCA 58.864 34.615 1.16 0.00 39.64 3.96
5034 14369 7.240167 TCATGGGATAAAATGGCTTCATATGA 58.760 34.615 0.00 0.00 0.00 2.15
5037 14372 6.071221 TGGGATAAAATGGCTTCATATGATGC 60.071 38.462 27.26 27.26 42.42 3.91
5040 14375 8.689061 GGATAAAATGGCTTCATATGATGCATA 58.311 33.333 32.54 24.46 44.21 3.14
5042 14377 9.865321 ATAAAATGGCTTCATATGATGCATAAC 57.135 29.630 32.54 21.00 44.21 1.89
5043 14378 5.909621 ATGGCTTCATATGATGCATAACC 57.090 39.130 32.54 20.73 44.21 2.85
5044 14379 4.989277 TGGCTTCATATGATGCATAACCT 58.011 39.130 32.54 0.00 44.21 3.50
5045 14380 5.387788 TGGCTTCATATGATGCATAACCTT 58.612 37.500 32.54 0.00 44.21 3.50
5046 14381 6.541907 TGGCTTCATATGATGCATAACCTTA 58.458 36.000 32.54 13.57 44.21 2.69
5047 14382 7.003482 TGGCTTCATATGATGCATAACCTTAA 58.997 34.615 32.54 12.38 44.21 1.85
5048 14383 7.670979 TGGCTTCATATGATGCATAACCTTAAT 59.329 33.333 32.54 0.00 44.21 1.40
5049 14384 7.972277 GGCTTCATATGATGCATAACCTTAATG 59.028 37.037 32.54 0.00 44.21 1.90
5050 14385 8.517878 GCTTCATATGATGCATAACCTTAATGT 58.482 33.333 29.16 0.00 42.61 2.71
5052 14387 9.571816 TTCATATGATGCATAACCTTAATGTCA 57.428 29.630 6.17 0.00 29.74 3.58
5053 14388 9.571816 TCATATGATGCATAACCTTAATGTCAA 57.428 29.630 0.00 0.00 29.74 3.18
5095 14430 2.552367 AGGGAAAAGCCTAGCAGTAGT 58.448 47.619 0.00 0.00 36.66 2.73
5211 14567 0.820871 AGCGCTTTCCAAAACAACCA 59.179 45.000 2.64 0.00 0.00 3.67
5384 14740 2.821378 TCAAGTGCATGGATCCAAAGTG 59.179 45.455 20.67 14.11 0.00 3.16
5388 14744 1.355381 TGCATGGATCCAAAGTGACCT 59.645 47.619 20.67 0.00 0.00 3.85
5389 14745 2.225091 TGCATGGATCCAAAGTGACCTT 60.225 45.455 20.67 0.00 0.00 3.50
5448 14804 3.366273 CGGTTCTTTCACCCAATGACATG 60.366 47.826 0.00 0.00 36.92 3.21
5623 15013 9.508642 TCATAGTACTCATAATCACTACTCCTG 57.491 37.037 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.696187 CCCTTTCCTTTTTCACCGGAAA 59.304 45.455 9.46 0.00 42.70 3.13
36 37 2.312390 CCCTTTCCTTTTTCACCGGAA 58.688 47.619 9.46 0.00 35.16 4.30
76 79 2.761786 TAGGCCGTATCCTACTTGGT 57.238 50.000 0.00 0.00 37.66 3.67
143 146 4.760220 GCCTCCCCTCCCCCTCAA 62.760 72.222 0.00 0.00 0.00 3.02
150 155 4.541648 TCTAGGCGCCTCCCCTCC 62.542 72.222 36.73 0.00 33.88 4.30
151 156 2.444140 TTCTAGGCGCCTCCCCTC 60.444 66.667 36.73 0.00 33.88 4.30
152 157 2.764547 GTTCTAGGCGCCTCCCCT 60.765 66.667 36.73 12.19 36.47 4.79
189 201 4.722700 GGGAGGCACCGCACATGT 62.723 66.667 0.00 0.00 40.11 3.21
318 330 1.618343 TGATCCAGCAAAGTGTCGAGA 59.382 47.619 0.00 0.00 0.00 4.04
359 371 0.657840 GTTCTGCACACGTTCAGCTT 59.342 50.000 5.40 0.00 0.00 3.74
443 456 4.989279 AAGCTGAAGTGTTTGACAACAT 57.011 36.364 0.00 0.00 44.85 2.71
444 457 4.671508 CGAAAGCTGAAGTGTTTGACAACA 60.672 41.667 0.00 0.00 40.82 3.33
455 468 3.118956 CCTCATAGACCGAAAGCTGAAGT 60.119 47.826 0.00 0.00 0.00 3.01
460 473 1.867363 ACCCTCATAGACCGAAAGCT 58.133 50.000 0.00 0.00 0.00 3.74
485 498 0.969894 CGAGAAGGGGAGAGTGTGTT 59.030 55.000 0.00 0.00 0.00 3.32
553 567 4.950050 TGGGAAACGTAACATGCAATTTT 58.050 34.783 0.00 0.00 0.00 1.82
564 578 2.224354 GGGACTCTGTTGGGAAACGTAA 60.224 50.000 0.00 0.00 0.00 3.18
592 606 4.212913 TCGAGCTCGCATGCCTCC 62.213 66.667 30.97 0.00 39.60 4.30
593 607 2.959071 GTCGAGCTCGCATGCCTC 60.959 66.667 30.97 12.01 39.60 4.70
594 608 3.456365 AGTCGAGCTCGCATGCCT 61.456 61.111 30.97 16.85 39.60 4.75
595 609 3.260483 CAGTCGAGCTCGCATGCC 61.260 66.667 30.97 14.97 39.60 4.40
596 610 3.922893 GCAGTCGAGCTCGCATGC 61.923 66.667 33.91 33.91 40.93 4.06
597 611 1.426816 AATGCAGTCGAGCTCGCATG 61.427 55.000 30.97 28.29 39.80 4.06
598 612 1.153489 AATGCAGTCGAGCTCGCAT 60.153 52.632 30.97 23.61 40.80 4.73
599 613 2.096442 CAATGCAGTCGAGCTCGCA 61.096 57.895 30.97 22.43 39.60 5.10
600 614 2.699809 CAATGCAGTCGAGCTCGC 59.300 61.111 30.97 24.09 39.60 5.03
601 615 2.806856 GCCAATGCAGTCGAGCTCG 61.807 63.158 30.03 30.03 37.89 5.03
602 616 2.467826 GGCCAATGCAGTCGAGCTC 61.468 63.158 2.73 2.73 40.13 4.09
603 617 2.437359 GGCCAATGCAGTCGAGCT 60.437 61.111 0.00 0.00 40.13 4.09
604 618 2.747460 TGGCCAATGCAGTCGAGC 60.747 61.111 0.61 0.00 40.13 5.03
605 619 2.110967 CCTGGCCAATGCAGTCGAG 61.111 63.158 7.01 0.00 40.13 4.04
606 620 2.046023 CCTGGCCAATGCAGTCGA 60.046 61.111 7.01 0.00 40.13 4.20
607 621 3.136123 CCCTGGCCAATGCAGTCG 61.136 66.667 7.01 0.00 40.13 4.18
608 622 1.751927 CTCCCTGGCCAATGCAGTC 60.752 63.158 7.01 0.00 40.13 3.51
609 623 2.357836 CTCCCTGGCCAATGCAGT 59.642 61.111 7.01 0.00 40.13 4.40
610 624 2.441532 CCTCCCTGGCCAATGCAG 60.442 66.667 7.01 0.00 40.13 4.41
611 625 3.267233 ACCTCCCTGGCCAATGCA 61.267 61.111 7.01 0.00 40.22 3.96
612 626 2.757099 CACCTCCCTGGCCAATGC 60.757 66.667 7.01 0.00 40.22 3.56
613 627 2.043652 CCACCTCCCTGGCCAATG 60.044 66.667 7.01 0.00 40.22 2.82
614 628 3.350163 CCCACCTCCCTGGCCAAT 61.350 66.667 7.01 0.00 40.22 3.16
632 646 2.252072 TAATCTGGGACCTGCACCGC 62.252 60.000 0.00 0.00 0.00 5.68
633 647 0.179073 CTAATCTGGGACCTGCACCG 60.179 60.000 0.00 0.00 0.00 4.94
634 648 0.181350 CCTAATCTGGGACCTGCACC 59.819 60.000 0.00 0.00 0.00 5.01
635 649 0.464554 GCCTAATCTGGGACCTGCAC 60.465 60.000 0.00 0.00 0.00 4.57
636 650 1.635817 GGCCTAATCTGGGACCTGCA 61.636 60.000 0.00 0.00 0.00 4.41
637 651 1.149401 GGCCTAATCTGGGACCTGC 59.851 63.158 0.00 0.00 0.00 4.85
638 652 1.447643 CGGCCTAATCTGGGACCTG 59.552 63.158 0.00 0.00 0.00 4.00
639 653 2.444256 GCGGCCTAATCTGGGACCT 61.444 63.158 0.00 0.00 0.00 3.85
640 654 2.111251 GCGGCCTAATCTGGGACC 59.889 66.667 0.00 0.00 0.00 4.46
641 655 1.523938 GTGCGGCCTAATCTGGGAC 60.524 63.158 0.00 0.00 0.00 4.46
642 656 2.908015 GTGCGGCCTAATCTGGGA 59.092 61.111 0.00 0.00 0.00 4.37
643 657 2.588877 CGTGCGGCCTAATCTGGG 60.589 66.667 0.00 0.00 0.00 4.45
644 658 1.592669 CTCGTGCGGCCTAATCTGG 60.593 63.158 0.00 0.00 0.00 3.86
645 659 2.240500 GCTCGTGCGGCCTAATCTG 61.241 63.158 0.00 0.00 0.00 2.90
646 660 2.107141 GCTCGTGCGGCCTAATCT 59.893 61.111 0.00 0.00 0.00 2.40
647 661 2.967615 GGCTCGTGCGGCCTAATC 60.968 66.667 0.00 0.00 45.57 1.75
653 667 3.491652 GAGAAAGGCTCGTGCGGC 61.492 66.667 3.02 0.00 40.82 6.53
654 668 2.815647 GGAGAAAGGCTCGTGCGG 60.816 66.667 3.02 0.00 44.91 5.69
655 669 1.807573 GAGGAGAAAGGCTCGTGCG 60.808 63.158 3.02 0.00 44.91 5.34
656 670 1.807573 CGAGGAGAAAGGCTCGTGC 60.808 63.158 0.00 0.00 44.91 5.34
657 671 0.456995 GTCGAGGAGAAAGGCTCGTG 60.457 60.000 0.00 0.00 44.91 4.35
658 672 1.596895 GGTCGAGGAGAAAGGCTCGT 61.597 60.000 0.00 0.00 44.91 4.18
659 673 1.139947 GGTCGAGGAGAAAGGCTCG 59.860 63.158 0.00 0.00 44.91 5.03
660 674 0.827368 ATGGTCGAGGAGAAAGGCTC 59.173 55.000 0.00 0.00 43.17 4.70
661 675 0.539051 CATGGTCGAGGAGAAAGGCT 59.461 55.000 0.00 0.00 0.00 4.58
662 676 0.250513 ACATGGTCGAGGAGAAAGGC 59.749 55.000 0.00 0.00 0.00 4.35
663 677 1.827969 AGACATGGTCGAGGAGAAAGG 59.172 52.381 0.00 0.00 37.67 3.11
664 678 3.601443 AAGACATGGTCGAGGAGAAAG 57.399 47.619 0.00 0.00 37.67 2.62
665 679 4.351874 AAAAGACATGGTCGAGGAGAAA 57.648 40.909 0.00 0.00 37.67 2.52
666 680 4.351874 AAAAAGACATGGTCGAGGAGAA 57.648 40.909 0.00 0.00 37.67 2.87
694 708 0.886563 CGACATACGAGGTATCCCCC 59.113 60.000 0.00 0.00 45.77 5.40
695 709 0.243095 GCGACATACGAGGTATCCCC 59.757 60.000 0.00 0.00 45.77 4.81
696 710 0.243095 GGCGACATACGAGGTATCCC 59.757 60.000 0.00 0.00 45.77 3.85
697 711 0.109873 CGGCGACATACGAGGTATCC 60.110 60.000 0.00 0.00 45.77 2.59
723 737 6.651755 AATCTTTTGAAATATTGCAAGCGG 57.348 33.333 8.87 4.39 0.00 5.52
741 755 4.814234 TCACGCTTCACACAGTTAAATCTT 59.186 37.500 0.00 0.00 0.00 2.40
748 762 5.238432 TCAAATATTCACGCTTCACACAGTT 59.762 36.000 0.00 0.00 0.00 3.16
750 764 5.281693 TCAAATATTCACGCTTCACACAG 57.718 39.130 0.00 0.00 0.00 3.66
866 882 0.575390 CGGAAATGCGACCATACGTC 59.425 55.000 0.00 0.00 38.21 4.34
893 909 0.386476 TCTACTTGTGCGGTCGTGTT 59.614 50.000 0.00 0.00 0.00 3.32
986 1006 1.803519 GCTCTGCTTCTCACGTCGG 60.804 63.158 0.00 0.00 0.00 4.79
1044 1077 2.203280 CCCACTTGGTGTGCCGAA 60.203 61.111 0.00 0.00 44.92 4.30
1053 1086 2.751436 CCATGGTCGCCCACTTGG 60.751 66.667 2.57 0.00 45.65 3.61
1169 1202 3.681835 GCAGGTGTCGGTCTCGGT 61.682 66.667 0.00 0.00 36.95 4.69
1373 1418 1.000171 GTTGTAGTCCGACCCGTTCTT 60.000 52.381 0.00 0.00 0.00 2.52
1566 1626 1.344953 ACATATGGCAGGCCGGAGAA 61.345 55.000 5.05 0.00 39.42 2.87
1593 1653 7.673926 ACCATTTTAACCAAGATGATTGTACCT 59.326 33.333 0.00 0.00 29.71 3.08
1675 1840 9.941325 ACAAATCATTTACAAGCCATCATTTTA 57.059 25.926 0.00 0.00 0.00 1.52
1680 1845 7.701539 AGTACAAATCATTTACAAGCCATCA 57.298 32.000 0.00 0.00 0.00 3.07
1930 2158 3.264104 CTTGTATCTACCCCGCGAAAAA 58.736 45.455 8.23 0.00 0.00 1.94
1932 2160 1.826720 ACTTGTATCTACCCCGCGAAA 59.173 47.619 8.23 0.00 0.00 3.46
1934 2162 2.346766 TACTTGTATCTACCCCGCGA 57.653 50.000 8.23 0.00 0.00 5.87
1935 2163 3.655276 AATACTTGTATCTACCCCGCG 57.345 47.619 0.00 0.00 0.00 6.46
1936 2164 6.519382 AGTAAAATACTTGTATCTACCCCGC 58.481 40.000 0.00 0.00 34.86 6.13
1937 2165 6.860023 CGAGTAAAATACTTGTATCTACCCCG 59.140 42.308 0.00 3.73 39.59 5.73
1982 2210 2.144730 CACCATACGTCACCCGAAAAA 58.855 47.619 0.00 0.00 40.70 1.94
1983 2211 1.798283 CACCATACGTCACCCGAAAA 58.202 50.000 0.00 0.00 40.70 2.29
1984 2212 0.671163 GCACCATACGTCACCCGAAA 60.671 55.000 0.00 0.00 40.70 3.46
1985 2213 1.079681 GCACCATACGTCACCCGAA 60.080 57.895 0.00 0.00 40.70 4.30
1986 2214 1.609635 ATGCACCATACGTCACCCGA 61.610 55.000 0.00 0.00 40.70 5.14
1987 2215 0.742990 AATGCACCATACGTCACCCG 60.743 55.000 0.00 0.00 44.03 5.28
1988 2216 1.014352 GAATGCACCATACGTCACCC 58.986 55.000 0.00 0.00 0.00 4.61
1989 2217 1.732941 TGAATGCACCATACGTCACC 58.267 50.000 0.00 0.00 0.00 4.02
1990 2218 4.097714 CAATTGAATGCACCATACGTCAC 58.902 43.478 0.00 0.00 0.00 3.67
1991 2219 3.755905 ACAATTGAATGCACCATACGTCA 59.244 39.130 13.59 0.00 0.00 4.35
1992 2220 4.355543 ACAATTGAATGCACCATACGTC 57.644 40.909 13.59 0.00 0.00 4.34
1993 2221 4.484236 CAACAATTGAATGCACCATACGT 58.516 39.130 13.59 0.00 0.00 3.57
1994 2222 3.858812 CCAACAATTGAATGCACCATACG 59.141 43.478 13.59 0.00 0.00 3.06
1995 2223 4.819769 ACCAACAATTGAATGCACCATAC 58.180 39.130 13.59 0.00 0.00 2.39
1996 2224 5.480642 AACCAACAATTGAATGCACCATA 57.519 34.783 13.59 0.00 0.00 2.74
1997 2225 4.354893 AACCAACAATTGAATGCACCAT 57.645 36.364 13.59 0.00 0.00 3.55
1998 2226 3.834489 AACCAACAATTGAATGCACCA 57.166 38.095 13.59 0.00 0.00 4.17
1999 2227 5.931146 TGATAAACCAACAATTGAATGCACC 59.069 36.000 13.59 0.00 0.00 5.01
2000 2228 6.867816 TCTGATAAACCAACAATTGAATGCAC 59.132 34.615 13.59 0.00 0.00 4.57
2001 2229 6.990798 TCTGATAAACCAACAATTGAATGCA 58.009 32.000 13.59 0.00 0.00 3.96
2002 2230 7.887996 TTCTGATAAACCAACAATTGAATGC 57.112 32.000 13.59 0.00 0.00 3.56
2003 2231 9.642327 TGATTCTGATAAACCAACAATTGAATG 57.358 29.630 13.59 10.43 0.00 2.67
2098 2326 0.099436 CCCGCATTAAGTTGAGCTGC 59.901 55.000 0.00 0.00 0.00 5.25
2115 2343 5.773176 TGAGTTTATGTTTTTCCTTCTCCCC 59.227 40.000 0.00 0.00 0.00 4.81
2125 2353 8.188139 CCAACGCCTATATGAGTTTATGTTTTT 58.812 33.333 0.00 0.00 0.00 1.94
2157 2387 1.335872 GGTGTTTTCAGATGGCAACCG 60.336 52.381 0.00 0.00 0.00 4.44
2205 2436 2.982488 ACTCCTCAGATCACCTTGGTTT 59.018 45.455 0.00 0.00 0.00 3.27
2219 2450 7.224297 AGTTTAGCAAGTTTTGATACTCCTCA 58.776 34.615 0.00 0.00 30.20 3.86
2254 2485 3.612955 GCTAGGCCTGACGTTATCATCTC 60.613 52.174 17.99 0.00 36.48 2.75
2289 2520 0.893727 AGCCGGTGTGATTTGGGTTC 60.894 55.000 1.90 0.00 0.00 3.62
2303 2534 1.672356 CTTGGTGTTCCTCAGCCGG 60.672 63.158 0.00 0.00 43.10 6.13
2312 2543 1.029681 GGTGGTTGTCCTTGGTGTTC 58.970 55.000 0.00 0.00 34.23 3.18
2321 2552 3.975168 ACTAGTATGTGGTGGTTGTCC 57.025 47.619 0.00 0.00 0.00 4.02
2403 2641 9.106291 CCTCTAGGAGATCAGAAAATGATGCCT 62.106 44.444 11.43 11.43 45.28 4.75
2404 2642 7.019621 CCTCTAGGAGATCAGAAAATGATGCC 61.020 46.154 0.00 0.00 42.76 4.40
2447 2685 2.589157 CCACTGTCCGGGGCAACTA 61.589 63.158 1.61 0.00 0.00 2.24
2515 2753 1.567504 GGGACATACGACGACAATGG 58.432 55.000 0.00 0.00 0.00 3.16
2519 2757 1.647545 GACCGGGACATACGACGACA 61.648 60.000 6.32 0.00 0.00 4.35
2608 2846 2.524394 AGCGGTGGTGGTCTGACT 60.524 61.111 7.85 0.00 0.00 3.41
2670 2908 5.745312 TCTTGTTCCAGTGATGACTATGT 57.255 39.130 0.00 0.00 0.00 2.29
2695 2933 1.685765 CTGTGGATCTGGGTCCCGA 60.686 63.158 2.65 4.11 37.48 5.14
2736 2974 1.070786 GGAGGTTGGTGTTGCGAGA 59.929 57.895 0.00 0.00 0.00 4.04
2752 2990 2.066393 CGGGGAGGAAGCAGATGGA 61.066 63.158 0.00 0.00 0.00 3.41
2777 3015 0.391793 GGCTTTGCTCTAGCGTTCCT 60.392 55.000 0.00 0.00 45.83 3.36
2859 3100 3.179443 AGATATATATGGCGGTTGCGG 57.821 47.619 0.00 0.00 44.10 5.69
2880 3121 1.306226 GGTCTAGGTCCCAGTGCCT 60.306 63.158 0.00 0.00 38.81 4.75
2971 3833 1.742768 CCTAGGTCGTGGATCTGGC 59.257 63.158 0.00 0.00 0.00 4.85
3006 3868 4.122776 GCAATAGTGGAGAACATCGACAT 58.877 43.478 0.00 0.00 39.00 3.06
3021 3883 0.107456 CCGGATGAGGCAGCAATAGT 59.893 55.000 0.00 0.00 0.00 2.12
3025 3887 1.153107 CATCCGGATGAGGCAGCAA 60.153 57.895 36.42 0.00 41.20 3.91
3054 3916 0.040351 CTCCTCTCACTCTCCACCCA 59.960 60.000 0.00 0.00 0.00 4.51
3065 3927 1.207791 GCCATCTTTCCCTCCTCTCA 58.792 55.000 0.00 0.00 0.00 3.27
3071 3933 1.452108 CCACCGCCATCTTTCCCTC 60.452 63.158 0.00 0.00 0.00 4.30
3072 3934 2.677228 CCACCGCCATCTTTCCCT 59.323 61.111 0.00 0.00 0.00 4.20
3081 3972 2.589157 CCAAGTCTACCCACCGCCA 61.589 63.158 0.00 0.00 0.00 5.69
3102 3993 3.302344 CTTTGTTGGGTGGCGGGG 61.302 66.667 0.00 0.00 0.00 5.73
3109 4001 0.385390 CGCTTTGCTCTTTGTTGGGT 59.615 50.000 0.00 0.00 0.00 4.51
3184 4317 5.874810 TCATCTAGTAATCTTGGTGTGCAAC 59.125 40.000 0.00 0.00 31.42 4.17
3193 4326 6.015350 ACACGGGGTATCATCTAGTAATCTTG 60.015 42.308 0.00 0.00 0.00 3.02
3392 4526 4.522789 AGCTAAAAATCCAACCACGAATGT 59.477 37.500 0.00 0.00 0.00 2.71
3425 4559 2.491152 CATGCAACCGTGGATGCC 59.509 61.111 17.16 1.94 45.17 4.40
3678 4817 2.094026 GCATGGGAAAAGATTCACCACC 60.094 50.000 0.00 0.00 38.24 4.61
3873 5056 6.609237 TGCATAGAATTAGTGCAGAATCAC 57.391 37.500 7.54 0.00 43.30 3.06
3880 5063 4.141233 TCAGCTGCATAGAATTAGTGCA 57.859 40.909 9.47 10.34 45.69 4.57
4054 10885 2.370189 CCTTCCACATGAGTCCCCTATC 59.630 54.545 0.00 0.00 0.00 2.08
4212 11043 8.906867 ACAGAAAATATACACCAAATCATGAGG 58.093 33.333 0.09 0.00 0.00 3.86
4251 13054 5.531659 TCACCAAGCGAAAAGGTTATACAAA 59.468 36.000 0.00 0.00 38.72 2.83
4353 13165 2.097954 ACGCGTGATCAAATGATGCAAT 59.902 40.909 12.93 0.00 34.37 3.56
4374 13186 2.352422 GACCACATGGGCAGAGCA 59.648 61.111 0.00 0.00 44.76 4.26
4438 13251 6.530181 CCAACCACTGTTTACTTCTTTTTGAC 59.470 38.462 0.00 0.00 30.42 3.18
4439 13252 6.626302 CCAACCACTGTTTACTTCTTTTTGA 58.374 36.000 0.00 0.00 30.42 2.69
4454 13267 2.228822 GGTTAACTGATGCCAACCACTG 59.771 50.000 5.42 0.00 40.17 3.66
4541 13358 8.289618 TGCAAAGTAAGTTCATTGAGAATGTAC 58.710 33.333 0.00 0.00 38.76 2.90
4583 13588 6.406370 AGTGAATCAACCGATGACTTCAATA 58.594 36.000 12.64 0.00 41.93 1.90
4763 13797 1.560860 GCACGATAGATTGCGGCCTC 61.561 60.000 0.00 0.00 41.38 4.70
4823 13857 7.739022 AAACATATTTACATGACATGCAACG 57.261 32.000 15.49 4.41 0.00 4.10
4873 13925 9.733556 ATAGTAATGATACACCTTTTGTTGTCA 57.266 29.630 0.00 0.00 39.91 3.58
4884 13936 9.680315 GTGACTTGTCTATAGTAATGATACACC 57.320 37.037 0.00 0.00 34.29 4.16
4890 13942 7.630728 GCACCTGTGACTTGTCTATAGTAATGA 60.631 40.741 0.51 0.00 0.00 2.57
4899 13951 2.169561 TGTTGCACCTGTGACTTGTCTA 59.830 45.455 0.51 0.00 0.00 2.59
5042 14377 9.937175 GCTAGCTTAGTTAAATTGACATTAAGG 57.063 33.333 7.70 0.00 0.00 2.69
5045 14380 9.667107 AGTGCTAGCTTAGTTAAATTGACATTA 57.333 29.630 17.23 0.00 0.00 1.90
5046 14381 8.567285 AGTGCTAGCTTAGTTAAATTGACATT 57.433 30.769 17.23 0.00 0.00 2.71
5047 14382 9.099454 GTAGTGCTAGCTTAGTTAAATTGACAT 57.901 33.333 17.23 0.00 0.00 3.06
5048 14383 8.311836 AGTAGTGCTAGCTTAGTTAAATTGACA 58.688 33.333 17.23 0.00 0.00 3.58
5049 14384 8.705048 AGTAGTGCTAGCTTAGTTAAATTGAC 57.295 34.615 17.23 0.35 0.00 3.18
5051 14386 9.250624 CCTAGTAGTGCTAGCTTAGTTAAATTG 57.749 37.037 17.23 0.00 44.47 2.32
5052 14387 8.422566 CCCTAGTAGTGCTAGCTTAGTTAAATT 58.577 37.037 17.23 0.00 44.47 1.82
5053 14388 7.783596 TCCCTAGTAGTGCTAGCTTAGTTAAAT 59.216 37.037 17.23 0.00 44.47 1.40
5054 14389 7.121382 TCCCTAGTAGTGCTAGCTTAGTTAAA 58.879 38.462 17.23 0.00 44.47 1.52
5055 14390 6.666678 TCCCTAGTAGTGCTAGCTTAGTTAA 58.333 40.000 17.23 0.00 44.47 2.01
5056 14391 6.257994 TCCCTAGTAGTGCTAGCTTAGTTA 57.742 41.667 17.23 2.79 44.47 2.24
5057 14392 5.126699 TCCCTAGTAGTGCTAGCTTAGTT 57.873 43.478 17.23 1.67 44.47 2.24
5058 14393 4.792513 TCCCTAGTAGTGCTAGCTTAGT 57.207 45.455 17.23 13.17 44.47 2.24
5059 14394 6.466885 TTTTCCCTAGTAGTGCTAGCTTAG 57.533 41.667 17.23 9.44 44.47 2.18
5060 14395 5.163437 GCTTTTCCCTAGTAGTGCTAGCTTA 60.163 44.000 17.23 5.86 44.47 3.09
5061 14396 4.383226 GCTTTTCCCTAGTAGTGCTAGCTT 60.383 45.833 17.23 6.91 44.47 3.74
5062 14397 3.133183 GCTTTTCCCTAGTAGTGCTAGCT 59.867 47.826 17.23 0.00 44.47 3.32
5063 14398 3.459145 GCTTTTCCCTAGTAGTGCTAGC 58.541 50.000 8.10 8.10 44.47 3.42
5064 14399 3.707102 AGGCTTTTCCCTAGTAGTGCTAG 59.293 47.826 8.22 8.22 45.21 3.42
5065 14400 3.721021 AGGCTTTTCCCTAGTAGTGCTA 58.279 45.455 0.00 0.00 32.11 3.49
5066 14401 2.552367 AGGCTTTTCCCTAGTAGTGCT 58.448 47.619 0.00 0.00 32.11 4.40
5067 14402 4.061357 CTAGGCTTTTCCCTAGTAGTGC 57.939 50.000 0.00 0.00 46.16 4.40
5095 14430 2.170166 CTGATAGGCCAAAAACCAGCA 58.830 47.619 5.01 0.00 0.00 4.41
5342 14698 6.554334 TGAAACTAATCCAAGGTTCTTTCG 57.446 37.500 3.56 0.00 42.58 3.46
5384 14740 4.403734 TGGATCCAAAGTAACCAAAGGTC 58.596 43.478 13.46 0.00 33.12 3.85
5419 14775 0.879090 GGTGAAAGAACCGCGGATTT 59.121 50.000 35.90 27.05 0.00 2.17
5623 15013 1.669779 GACTTGATGGTGATGCTGAGC 59.330 52.381 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.