Multiple sequence alignment - TraesCS1D01G030100

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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 TraesCS1D01G030100 chr1D 100.000 3003 0 0 1 3003 11701837 11704839 0.000000e+00 5546.0
1 TraesCS1D01G030100 chr1D 83.680 625 75 14 141 749 3761600 3762213 5.620000e-157 564.0
2 TraesCS1D01G030100 chr1D 80.286 700 78 34 1277 1936 40326011 40326690 9.740000e-130 473.0
3 TraesCS1D01G030100 chr1D 80.912 592 90 17 169 749 399935984 399935405 2.120000e-121 446.0
4 TraesCS1D01G030100 chr1D 84.471 425 41 14 1445 1853 58816846 58817261 2.170000e-106 396.0
5 TraesCS1D01G030100 chr1A 87.426 1360 86 44 645 1944 13830057 13831391 0.000000e+00 1485.0
6 TraesCS1D01G030100 chr1A 83.546 705 60 23 1970 2664 13831454 13832112 2.560000e-170 608.0
7 TraesCS1D01G030100 chr1A 87.713 293 34 2 2712 3003 13832115 13832406 1.030000e-89 340.0
8 TraesCS1D01G030100 chr1B 85.208 1298 107 41 872 2092 17574552 17575841 0.000000e+00 1254.0
9 TraesCS1D01G030100 chr1B 78.603 687 89 31 1277 1936 59927250 59927905 4.660000e-108 401.0
10 TraesCS1D01G030100 chrUn 81.573 928 96 39 1093 1989 71523377 71524260 0.000000e+00 697.0
11 TraesCS1D01G030100 chrUn 80.894 984 103 42 1096 2048 300096125 300095196 0.000000e+00 697.0
12 TraesCS1D01G030100 chrUn 80.894 984 103 42 1096 2048 310994039 310993110 0.000000e+00 697.0
13 TraesCS1D01G030100 chrUn 82.503 743 78 24 1093 1808 379511403 379512120 3.310000e-169 604.0
14 TraesCS1D01G030100 chrUn 82.568 740 75 27 1096 1808 428990682 428989970 1.190000e-168 603.0
15 TraesCS1D01G030100 chrUn 84.103 585 56 22 1096 1653 436748213 436747639 5.700000e-147 531.0
16 TraesCS1D01G030100 chrUn 79.087 679 86 30 1283 1936 335950655 335950008 1.670000e-112 416.0
17 TraesCS1D01G030100 chrUn 79.880 333 32 12 1495 1808 345161457 345161141 8.430000e-51 211.0
18 TraesCS1D01G030100 chrUn 84.932 146 20 2 2504 2648 96471038 96471182 2.410000e-31 147.0
19 TraesCS1D01G030100 chr6D 82.876 765 84 22 1066 1808 25534000 25533261 0.000000e+00 643.0
20 TraesCS1D01G030100 chr6D 84.393 519 68 7 226 739 24828122 24828632 5.780000e-137 497.0
21 TraesCS1D01G030100 chr6A 81.842 771 87 24 1066 1808 23480721 23479976 1.540000e-167 599.0
22 TraesCS1D01G030100 chr6A 83.688 141 15 8 2506 2643 229086092 229085957 3.140000e-25 126.0
23 TraesCS1D01G030100 chr7B 84.715 615 68 13 140 749 78241880 78242473 2.580000e-165 592.0
24 TraesCS1D01G030100 chr7B 84.058 345 49 3 406 749 663255942 663256281 8.030000e-86 327.0
25 TraesCS1D01G030100 chr2D 83.721 559 75 9 185 742 613218783 613218240 5.740000e-142 514.0
26 TraesCS1D01G030100 chr2D 83.206 524 55 15 255 750 513025350 513025868 1.640000e-122 449.0
27 TraesCS1D01G030100 chr6B 82.155 566 87 9 173 736 713474467 713473914 9.740000e-130 473.0
28 TraesCS1D01G030100 chr6B 83.217 143 16 8 2504 2643 304893834 304893971 1.130000e-24 124.0
29 TraesCS1D01G030100 chr4A 81.336 584 86 13 173 749 674361727 674361160 1.270000e-123 453.0
30 TraesCS1D01G030100 chr4A 81.321 530 75 14 239 749 601217491 601218015 2.790000e-110 409.0
31 TraesCS1D01G030100 chr4A 77.477 111 22 2 2539 2648 497020384 497020492 2.500000e-06 63.9
32 TraesCS1D01G030100 chr4B 80.750 613 81 21 169 759 624724748 624725345 7.640000e-121 444.0
33 TraesCS1D01G030100 chr4B 80.066 607 84 22 173 760 530237300 530236712 1.670000e-112 416.0
34 TraesCS1D01G030100 chr4B 79.398 631 90 17 142 749 661881677 661882290 2.790000e-110 409.0
35 TraesCS1D01G030100 chr4B 83.761 351 45 5 406 752 455413739 455413397 3.730000e-84 322.0
36 TraesCS1D01G030100 chr4D 81.034 580 84 13 184 750 67289811 67289245 3.550000e-119 438.0
37 TraesCS1D01G030100 chr5B 79.796 589 92 14 172 749 676509289 676508717 1.300000e-108 403.0
38 TraesCS1D01G030100 chr5B 85.315 143 19 2 2502 2643 68901356 68901215 2.410000e-31 147.0
39 TraesCS1D01G030100 chr5A 81.273 534 61 18 140 641 510497885 510498411 2.170000e-106 396.0
40 TraesCS1D01G030100 chr5A 84.615 143 20 2 2502 2643 51688982 51689123 1.120000e-29 141.0
41 TraesCS1D01G030100 chr2A 79.693 586 90 11 184 752 158244807 158244234 2.170000e-106 396.0
42 TraesCS1D01G030100 chr3A 80.380 474 79 9 275 742 13002099 13002564 6.160000e-92 348.0
43 TraesCS1D01G030100 chr3B 72.807 570 102 32 180 714 577529955 577529404 8.680000e-31 145.0
44 TraesCS1D01G030100 chr3B 84.444 135 17 4 2518 2649 659582916 659582783 2.430000e-26 130.0
45 TraesCS1D01G030100 chr3B 91.111 45 4 0 2508 2552 434987198 434987242 8.990000e-06 62.1
46 TraesCS1D01G030100 chr5D 84.615 143 20 2 2502 2643 61713926 61714067 1.120000e-29 141.0


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 TraesCS1D01G030100 chr1D 11701837 11704839 3002 False 5546 5546 100.000000 1 3003 1 chr1D.!!$F2 3002
1 TraesCS1D01G030100 chr1D 3761600 3762213 613 False 564 564 83.680000 141 749 1 chr1D.!!$F1 608
2 TraesCS1D01G030100 chr1D 40326011 40326690 679 False 473 473 80.286000 1277 1936 1 chr1D.!!$F3 659
3 TraesCS1D01G030100 chr1D 399935405 399935984 579 True 446 446 80.912000 169 749 1 chr1D.!!$R1 580
4 TraesCS1D01G030100 chr1A 13830057 13832406 2349 False 811 1485 86.228333 645 3003 3 chr1A.!!$F1 2358
5 TraesCS1D01G030100 chr1B 17574552 17575841 1289 False 1254 1254 85.208000 872 2092 1 chr1B.!!$F1 1220
6 TraesCS1D01G030100 chr1B 59927250 59927905 655 False 401 401 78.603000 1277 1936 1 chr1B.!!$F2 659
7 TraesCS1D01G030100 chrUn 71523377 71524260 883 False 697 697 81.573000 1093 1989 1 chrUn.!!$F1 896
8 TraesCS1D01G030100 chrUn 300095196 300096125 929 True 697 697 80.894000 1096 2048 1 chrUn.!!$R1 952
9 TraesCS1D01G030100 chrUn 310993110 310994039 929 True 697 697 80.894000 1096 2048 1 chrUn.!!$R2 952
10 TraesCS1D01G030100 chrUn 379511403 379512120 717 False 604 604 82.503000 1093 1808 1 chrUn.!!$F3 715
11 TraesCS1D01G030100 chrUn 428989970 428990682 712 True 603 603 82.568000 1096 1808 1 chrUn.!!$R5 712
12 TraesCS1D01G030100 chrUn 436747639 436748213 574 True 531 531 84.103000 1096 1653 1 chrUn.!!$R6 557
13 TraesCS1D01G030100 chrUn 335950008 335950655 647 True 416 416 79.087000 1283 1936 1 chrUn.!!$R3 653
14 TraesCS1D01G030100 chr6D 25533261 25534000 739 True 643 643 82.876000 1066 1808 1 chr6D.!!$R1 742
15 TraesCS1D01G030100 chr6D 24828122 24828632 510 False 497 497 84.393000 226 739 1 chr6D.!!$F1 513
16 TraesCS1D01G030100 chr6A 23479976 23480721 745 True 599 599 81.842000 1066 1808 1 chr6A.!!$R1 742
17 TraesCS1D01G030100 chr7B 78241880 78242473 593 False 592 592 84.715000 140 749 1 chr7B.!!$F1 609
18 TraesCS1D01G030100 chr2D 613218240 613218783 543 True 514 514 83.721000 185 742 1 chr2D.!!$R1 557
19 TraesCS1D01G030100 chr2D 513025350 513025868 518 False 449 449 83.206000 255 750 1 chr2D.!!$F1 495
20 TraesCS1D01G030100 chr6B 713473914 713474467 553 True 473 473 82.155000 173 736 1 chr6B.!!$R1 563
21 TraesCS1D01G030100 chr4A 674361160 674361727 567 True 453 453 81.336000 173 749 1 chr4A.!!$R1 576
22 TraesCS1D01G030100 chr4A 601217491 601218015 524 False 409 409 81.321000 239 749 1 chr4A.!!$F2 510
23 TraesCS1D01G030100 chr4B 624724748 624725345 597 False 444 444 80.750000 169 759 1 chr4B.!!$F1 590
24 TraesCS1D01G030100 chr4B 530236712 530237300 588 True 416 416 80.066000 173 760 1 chr4B.!!$R2 587
25 TraesCS1D01G030100 chr4B 661881677 661882290 613 False 409 409 79.398000 142 749 1 chr4B.!!$F2 607
26 TraesCS1D01G030100 chr4D 67289245 67289811 566 True 438 438 81.034000 184 750 1 chr4D.!!$R1 566
27 TraesCS1D01G030100 chr5B 676508717 676509289 572 True 403 403 79.796000 172 749 1 chr5B.!!$R2 577
28 TraesCS1D01G030100 chr5A 510497885 510498411 526 False 396 396 81.273000 140 641 1 chr5A.!!$F2 501
29 TraesCS1D01G030100 chr2A 158244234 158244807 573 True 396 396 79.693000 184 752 1 chr2A.!!$R1 568

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
223 236 0.179020 CATGGTGGCGTGGTGGATAT 60.179 55.0 0.0 0.0 0.0 1.63 F
558 638 0.383231 ACGACGACTTTCCGACTGTT 59.617 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1061 1181 0.183971 AGAGGGAGATGTCGATCGGT 59.816 55.0 16.41 1.44 33.34 4.69 R
2073 2391 0.387929 AACTTCAGACCGAACGCTGA 59.612 50.0 0.00 0.00 39.24 4.26 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
20 21 3.155093 GTTCATACATGCTTGGCTTGG 57.845 47.619 4.44 0.00 37.90 3.61
21 22 1.105457 TCATACATGCTTGGCTTGGC 58.895 50.000 4.44 0.00 37.90 4.52
22 23 1.108776 CATACATGCTTGGCTTGGCT 58.891 50.000 4.44 0.00 37.90 4.75
23 24 1.066605 CATACATGCTTGGCTTGGCTC 59.933 52.381 4.44 0.00 37.90 4.70
24 25 0.329261 TACATGCTTGGCTTGGCTCT 59.671 50.000 4.44 0.00 37.90 4.09
25 26 1.248785 ACATGCTTGGCTTGGCTCTG 61.249 55.000 4.44 0.00 37.90 3.35
26 27 1.681327 ATGCTTGGCTTGGCTCTGG 60.681 57.895 0.00 0.00 0.00 3.86
27 28 3.756727 GCTTGGCTTGGCTCTGGC 61.757 66.667 0.00 0.00 37.82 4.85
28 29 2.035312 CTTGGCTTGGCTCTGGCT 59.965 61.111 0.00 0.00 38.73 4.75
29 30 2.282674 TTGGCTTGGCTCTGGCTG 60.283 61.111 0.00 0.00 38.73 4.85
30 31 3.137385 TTGGCTTGGCTCTGGCTGT 62.137 57.895 0.00 0.00 38.73 4.40
31 32 3.060615 GGCTTGGCTCTGGCTGTG 61.061 66.667 0.00 0.00 38.73 3.66
32 33 3.060615 GCTTGGCTCTGGCTGTGG 61.061 66.667 0.00 0.00 38.73 4.17
33 34 2.752358 CTTGGCTCTGGCTGTGGA 59.248 61.111 0.00 0.00 38.73 4.02
34 35 1.376942 CTTGGCTCTGGCTGTGGAG 60.377 63.158 0.00 0.00 38.73 3.86
53 54 3.400590 GACGACGGTGTTGGCGAC 61.401 66.667 0.00 0.00 0.00 5.19
71 72 4.575973 GCGCCATCAGCCCATCCT 62.576 66.667 0.00 0.00 38.78 3.24
72 73 2.593725 CGCCATCAGCCCATCCTG 60.594 66.667 0.00 0.00 38.78 3.86
73 74 2.910994 GCCATCAGCCCATCCTGC 60.911 66.667 0.00 0.00 34.35 4.85
74 75 2.593725 CCATCAGCCCATCCTGCG 60.594 66.667 0.00 0.00 32.87 5.18
75 76 2.593725 CATCAGCCCATCCTGCGG 60.594 66.667 0.00 0.00 32.87 5.69
81 82 4.802051 CCCATCCTGCGGGTGGTG 62.802 72.222 23.55 15.98 39.05 4.17
82 83 4.033776 CCATCCTGCGGGTGGTGT 62.034 66.667 19.59 0.00 32.70 4.16
83 84 2.436646 CATCCTGCGGGTGGTGTC 60.437 66.667 12.43 0.00 0.00 3.67
84 85 3.717294 ATCCTGCGGGTGGTGTCC 61.717 66.667 12.43 0.00 0.00 4.02
85 86 4.954118 TCCTGCGGGTGGTGTCCT 62.954 66.667 12.43 0.00 0.00 3.85
86 87 4.394712 CCTGCGGGTGGTGTCCTC 62.395 72.222 2.29 0.00 0.00 3.71
87 88 4.394712 CTGCGGGTGGTGTCCTCC 62.395 72.222 0.00 0.00 36.52 4.30
88 89 4.954118 TGCGGGTGGTGTCCTCCT 62.954 66.667 6.81 0.00 37.34 3.69
89 90 3.637273 GCGGGTGGTGTCCTCCTT 61.637 66.667 6.81 0.00 37.34 3.36
90 91 2.288025 GCGGGTGGTGTCCTCCTTA 61.288 63.158 6.81 0.00 37.34 2.69
91 92 1.833787 GCGGGTGGTGTCCTCCTTAA 61.834 60.000 6.81 0.00 37.34 1.85
92 93 0.909623 CGGGTGGTGTCCTCCTTAAT 59.090 55.000 6.81 0.00 37.34 1.40
93 94 2.112998 CGGGTGGTGTCCTCCTTAATA 58.887 52.381 6.81 0.00 37.34 0.98
94 95 2.159000 CGGGTGGTGTCCTCCTTAATAC 60.159 54.545 6.81 0.00 37.34 1.89
95 96 3.113043 GGGTGGTGTCCTCCTTAATACT 58.887 50.000 6.81 0.00 37.34 2.12
96 97 3.522343 GGGTGGTGTCCTCCTTAATACTT 59.478 47.826 6.81 0.00 37.34 2.24
97 98 4.514401 GGTGGTGTCCTCCTTAATACTTG 58.486 47.826 0.31 0.00 34.62 3.16
98 99 4.019591 GGTGGTGTCCTCCTTAATACTTGT 60.020 45.833 0.31 0.00 34.62 3.16
99 100 5.514310 GGTGGTGTCCTCCTTAATACTTGTT 60.514 44.000 0.31 0.00 34.62 2.83
100 101 6.296030 GGTGGTGTCCTCCTTAATACTTGTTA 60.296 42.308 0.31 0.00 34.62 2.41
101 102 7.336396 GTGGTGTCCTCCTTAATACTTGTTAT 58.664 38.462 0.00 0.00 0.00 1.89
102 103 7.827729 GTGGTGTCCTCCTTAATACTTGTTATT 59.172 37.037 0.00 0.00 34.55 1.40
103 104 8.387813 TGGTGTCCTCCTTAATACTTGTTATTT 58.612 33.333 0.00 0.00 32.31 1.40
104 105 9.239551 GGTGTCCTCCTTAATACTTGTTATTTT 57.760 33.333 0.00 0.00 32.31 1.82
129 130 9.729281 TTTTTCTTGTTATTAGGGGTACTGTAG 57.271 33.333 0.00 0.00 0.00 2.74
130 131 7.427989 TTCTTGTTATTAGGGGTACTGTAGG 57.572 40.000 0.00 0.00 0.00 3.18
131 132 6.505754 TCTTGTTATTAGGGGTACTGTAGGT 58.494 40.000 0.00 0.00 0.00 3.08
132 133 6.381994 TCTTGTTATTAGGGGTACTGTAGGTG 59.618 42.308 0.00 0.00 0.00 4.00
133 134 4.964262 TGTTATTAGGGGTACTGTAGGTGG 59.036 45.833 0.00 0.00 0.00 4.61
134 135 3.790022 ATTAGGGGTACTGTAGGTGGT 57.210 47.619 0.00 0.00 0.00 4.16
135 136 2.537633 TAGGGGTACTGTAGGTGGTG 57.462 55.000 0.00 0.00 0.00 4.17
136 137 0.788383 AGGGGTACTGTAGGTGGTGA 59.212 55.000 0.00 0.00 0.00 4.02
137 138 1.365028 AGGGGTACTGTAGGTGGTGAT 59.635 52.381 0.00 0.00 0.00 3.06
138 139 2.193993 GGGGTACTGTAGGTGGTGATT 58.806 52.381 0.00 0.00 0.00 2.57
175 188 3.827898 CCTCTGTCTCCCGTCGGC 61.828 72.222 5.50 0.00 0.00 5.54
176 189 2.752238 CTCTGTCTCCCGTCGGCT 60.752 66.667 5.50 0.00 0.00 5.52
177 190 2.750637 TCTGTCTCCCGTCGGCTC 60.751 66.667 5.50 0.00 0.00 4.70
222 235 1.223211 CATGGTGGCGTGGTGGATA 59.777 57.895 0.00 0.00 0.00 2.59
223 236 0.179020 CATGGTGGCGTGGTGGATAT 60.179 55.000 0.00 0.00 0.00 1.63
224 237 1.071542 CATGGTGGCGTGGTGGATATA 59.928 52.381 0.00 0.00 0.00 0.86
250 264 3.953775 CCTTGCCGGTGGGAGTGT 61.954 66.667 1.90 0.00 34.06 3.55
251 265 2.358737 CTTGCCGGTGGGAGTGTC 60.359 66.667 1.90 0.00 34.06 3.67
370 393 1.538687 CCTAGTCCCCGTTTCGGTGT 61.539 60.000 7.40 0.00 46.80 4.16
387 410 2.159476 GGTGTTGCGTCTAGTATCGTCA 60.159 50.000 0.00 0.00 0.00 4.35
392 415 1.938577 GCGTCTAGTATCGTCAGTGGA 59.061 52.381 0.00 0.00 0.00 4.02
393 416 2.286301 GCGTCTAGTATCGTCAGTGGAC 60.286 54.545 0.00 0.00 40.77 4.02
430 485 1.160329 CGGTGGATTTGCTCGGATCC 61.160 60.000 0.00 0.00 41.78 3.36
441 496 2.232941 TGCTCGGATCCTTTCGTAGTTT 59.767 45.455 10.75 0.00 0.00 2.66
475 538 2.093658 GCGTCTTCAGGTTGGATCCTTA 60.094 50.000 14.23 0.00 35.37 2.69
480 543 6.239317 CGTCTTCAGGTTGGATCCTTATGATA 60.239 42.308 14.23 1.74 35.37 2.15
558 638 0.383231 ACGACGACTTTCCGACTGTT 59.617 50.000 0.00 0.00 0.00 3.16
560 640 1.856597 CGACGACTTTCCGACTGTTTT 59.143 47.619 0.00 0.00 0.00 2.43
669 752 1.139058 GGTGCGTGGTCTATGGATCTT 59.861 52.381 0.00 0.00 0.00 2.40
760 849 6.627395 TTTTCGGAAAAACTATGAGCTTCA 57.373 33.333 13.20 0.00 29.44 3.02
761 850 5.862924 TTCGGAAAAACTATGAGCTTCAG 57.137 39.130 0.00 0.00 0.00 3.02
774 863 1.083242 GCTTCAGGCTCTCTTCGCAG 61.083 60.000 0.00 0.00 38.06 5.18
808 898 6.624021 AGGTTTTATAGGTAGAATGGGTCCAT 59.376 38.462 0.00 0.00 38.46 3.41
835 925 5.517411 CACATGTACGTACGTATCACCAAAT 59.483 40.000 29.05 12.65 32.82 2.32
857 949 3.342377 TCCATCACCAATCGCAAAGTA 57.658 42.857 0.00 0.00 0.00 2.24
860 952 1.434555 TCACCAATCGCAAAGTACCG 58.565 50.000 0.00 0.00 0.00 4.02
929 1023 1.390123 CGCGTGTGTTCGATCATTTCT 59.610 47.619 0.00 0.00 0.00 2.52
930 1024 2.532973 CGCGTGTGTTCGATCATTTCTC 60.533 50.000 0.00 0.00 0.00 2.87
931 1025 2.222819 GCGTGTGTTCGATCATTTCTCC 60.223 50.000 0.00 0.00 0.00 3.71
932 1026 3.254060 CGTGTGTTCGATCATTTCTCCT 58.746 45.455 0.00 0.00 0.00 3.69
933 1027 4.421058 CGTGTGTTCGATCATTTCTCCTA 58.579 43.478 0.00 0.00 0.00 2.94
934 1028 4.500837 CGTGTGTTCGATCATTTCTCCTAG 59.499 45.833 0.00 0.00 0.00 3.02
940 1035 3.827302 TCGATCATTTCTCCTAGCCTACC 59.173 47.826 0.00 0.00 0.00 3.18
999 1102 4.111016 CACATGCACAGCGGGCAG 62.111 66.667 10.96 6.27 45.68 4.85
1042 1162 2.006062 CGCATCGTCGTCTCCATCG 61.006 63.158 0.00 0.00 0.00 3.84
1051 1171 0.460284 CGTCTCCATCGAACAAGGGG 60.460 60.000 0.00 0.00 0.00 4.79
1052 1172 0.902531 GTCTCCATCGAACAAGGGGA 59.097 55.000 0.00 0.00 0.00 4.81
1053 1173 1.278127 GTCTCCATCGAACAAGGGGAA 59.722 52.381 0.00 0.00 32.76 3.97
1054 1174 1.555075 TCTCCATCGAACAAGGGGAAG 59.445 52.381 0.00 0.00 0.00 3.46
1055 1175 0.618458 TCCATCGAACAAGGGGAAGG 59.382 55.000 0.00 0.00 0.00 3.46
1056 1176 0.394352 CCATCGAACAAGGGGAAGGG 60.394 60.000 0.00 0.00 0.00 3.95
1057 1177 0.618458 CATCGAACAAGGGGAAGGGA 59.382 55.000 0.00 0.00 0.00 4.20
1058 1178 1.212935 CATCGAACAAGGGGAAGGGAT 59.787 52.381 0.00 0.00 0.00 3.85
1059 1179 0.909623 TCGAACAAGGGGAAGGGATC 59.090 55.000 0.00 0.00 0.00 3.36
1061 1181 2.116238 CGAACAAGGGGAAGGGATCTA 58.884 52.381 0.00 0.00 0.00 1.98
1062 1182 2.158943 CGAACAAGGGGAAGGGATCTAC 60.159 54.545 0.00 0.00 0.00 2.59
1273 1401 4.720902 TGCTGGTGTCCGCCATGG 62.721 66.667 7.63 7.63 37.96 3.66
1521 1692 3.685214 CTCCGTCGAACGCTGGGAG 62.685 68.421 0.00 11.22 40.91 4.30
1638 1845 1.032014 GCTGGGACTTGCACAAGAAA 58.968 50.000 16.95 0.00 40.79 2.52
1685 1898 0.905357 AAGCCGCCTCAGACTAACAT 59.095 50.000 0.00 0.00 0.00 2.71
1698 1932 0.907837 CTAACATGACAGCGACGACG 59.092 55.000 0.00 2.12 42.93 5.12
1773 2010 2.599597 CTCCCCATGCCCTCCTTG 59.400 66.667 0.00 0.00 0.00 3.61
1818 2067 7.572724 CGTGCACTCTGTACTAGTAACTAAGTT 60.573 40.741 16.19 0.00 30.49 2.66
1899 2175 4.019174 AGGGTGTGGAATTCAATCACATC 58.981 43.478 15.96 15.30 42.34 3.06
1902 2179 5.593909 GGGTGTGGAATTCAATCACATCATA 59.406 40.000 20.95 0.78 42.46 2.15
1903 2180 6.266103 GGGTGTGGAATTCAATCACATCATAT 59.734 38.462 20.95 0.00 42.46 1.78
1946 2226 3.193479 TCTCAGCTAGTGAAAAGCATCGA 59.807 43.478 0.00 0.00 42.62 3.59
1975 2292 0.583438 CATTTGGCCGATGCTACTCG 59.417 55.000 0.00 0.00 37.74 4.18
1983 2300 0.992072 CGATGCTACTCGTGGTGTTG 59.008 55.000 0.00 0.00 34.00 3.33
2058 2376 3.565307 TCAGGGTCATTTTTCTGCAAGT 58.435 40.909 0.00 0.00 33.76 3.16
2096 2414 1.458445 GCGTTCGGTCTGAAGTTAACC 59.542 52.381 0.88 0.00 37.23 2.85
2099 2417 3.556775 CGTTCGGTCTGAAGTTAACCAAA 59.443 43.478 0.88 0.00 37.23 3.28
2103 2421 6.790285 TCGGTCTGAAGTTAACCAAATAAC 57.210 37.500 0.88 0.00 36.28 1.89
2109 2431 8.192110 GTCTGAAGTTAACCAAATAACAAACCA 58.808 33.333 0.88 0.00 38.07 3.67
2112 2434 8.478877 TGAAGTTAACCAAATAACAAACCACAT 58.521 29.630 0.88 0.00 38.07 3.21
2152 2474 9.358872 GTACTACCAGTACCAAACAGTATTTAC 57.641 37.037 5.35 0.00 43.96 2.01
2168 2490 8.881743 ACAGTATTTACGCAAATAACCGAATTA 58.118 29.630 2.38 0.00 38.13 1.40
2172 2494 6.729987 ATTTACGCAAATAACCGAATTACCGG 60.730 38.462 0.00 0.00 42.55 5.28
2197 2519 4.994852 GGCACAACCGTATATATGTGTCAT 59.005 41.667 11.97 0.00 45.26 3.06
2208 2530 7.093902 CGTATATATGTGTCATGGGGTAGAAGT 60.094 40.741 0.00 0.00 0.00 3.01
2218 2540 3.186283 TGGGGTAGAAGTAGAAATGGCA 58.814 45.455 0.00 0.00 0.00 4.92
2219 2541 3.054655 TGGGGTAGAAGTAGAAATGGCAC 60.055 47.826 0.00 0.00 0.00 5.01
2237 2563 4.035441 TGGCACAAAACTAACGTTAAGACC 59.965 41.667 9.68 3.69 31.92 3.85
2244 2570 4.037858 ACTAACGTTAAGACCGCCATAG 57.962 45.455 9.68 0.00 0.00 2.23
2254 2580 2.766263 AGACCGCCATAGAACAGATCAA 59.234 45.455 0.00 0.00 0.00 2.57
2259 2585 3.303593 CGCCATAGAACAGATCAATGCAC 60.304 47.826 0.00 0.00 0.00 4.57
2267 2593 1.332686 CAGATCAATGCACATCCCACG 59.667 52.381 0.00 0.00 0.00 4.94
2280 2606 4.952704 CCACGCACATGGGATACA 57.047 55.556 0.00 0.00 35.95 2.29
2281 2607 2.393557 CCACGCACATGGGATACAC 58.606 57.895 0.00 0.00 35.95 2.90
2282 2608 0.392327 CCACGCACATGGGATACACA 60.392 55.000 0.00 0.00 35.95 3.72
2283 2609 1.447945 CACGCACATGGGATACACAA 58.552 50.000 0.00 0.00 39.74 3.33
2284 2610 1.809547 CACGCACATGGGATACACAAA 59.190 47.619 0.00 0.00 39.74 2.83
2285 2611 2.227626 CACGCACATGGGATACACAAAA 59.772 45.455 0.00 0.00 39.74 2.44
2286 2612 2.887783 ACGCACATGGGATACACAAAAA 59.112 40.909 0.00 0.00 39.74 1.94
2287 2613 3.509575 ACGCACATGGGATACACAAAAAT 59.490 39.130 0.00 0.00 39.74 1.82
2288 2614 4.104776 CGCACATGGGATACACAAAAATC 58.895 43.478 0.00 0.00 39.74 2.17
2289 2615 4.380339 CGCACATGGGATACACAAAAATCA 60.380 41.667 0.00 0.00 39.74 2.57
2290 2616 5.104374 GCACATGGGATACACAAAAATCAG 58.896 41.667 0.00 0.00 39.74 2.90
2291 2617 5.105797 GCACATGGGATACACAAAAATCAGA 60.106 40.000 0.00 0.00 39.74 3.27
2292 2618 6.406177 GCACATGGGATACACAAAAATCAGAT 60.406 38.462 0.00 0.00 39.74 2.90
2293 2619 7.198390 CACATGGGATACACAAAAATCAGATC 58.802 38.462 0.00 0.00 39.74 2.75
2294 2620 6.322201 ACATGGGATACACAAAAATCAGATCC 59.678 38.462 0.00 0.00 39.74 3.36
2295 2621 5.825532 TGGGATACACAAAAATCAGATCCA 58.174 37.500 0.00 0.00 34.31 3.41
2296 2622 5.887598 TGGGATACACAAAAATCAGATCCAG 59.112 40.000 0.00 0.00 34.31 3.86
2297 2623 5.221126 GGGATACACAAAAATCAGATCCAGC 60.221 44.000 0.00 0.00 34.31 4.85
2298 2624 5.357878 GGATACACAAAAATCAGATCCAGCA 59.642 40.000 0.00 0.00 33.12 4.41
2299 2625 6.127647 GGATACACAAAAATCAGATCCAGCAA 60.128 38.462 0.00 0.00 33.12 3.91
2300 2626 5.130292 ACACAAAAATCAGATCCAGCAAG 57.870 39.130 0.00 0.00 0.00 4.01
2399 2725 6.326064 ACCCATGCCATAAAAACTTGCATATA 59.674 34.615 0.00 0.00 40.46 0.86
2400 2726 6.646240 CCCATGCCATAAAAACTTGCATATAC 59.354 38.462 0.00 0.00 40.46 1.47
2424 2750 3.523606 ATTGCATGCGCCTTTTTATGA 57.476 38.095 14.09 0.00 37.32 2.15
2427 2753 2.992543 TGCATGCGCCTTTTTATGAAAC 59.007 40.909 14.09 0.00 37.32 2.78
2428 2754 3.253230 GCATGCGCCTTTTTATGAAACT 58.747 40.909 4.18 0.00 0.00 2.66
2429 2755 3.304293 GCATGCGCCTTTTTATGAAACTC 59.696 43.478 4.18 0.00 0.00 3.01
2431 2757 3.896122 TGCGCCTTTTTATGAAACTCAC 58.104 40.909 4.18 0.00 0.00 3.51
2432 2758 3.568007 TGCGCCTTTTTATGAAACTCACT 59.432 39.130 4.18 0.00 0.00 3.41
2433 2759 3.914364 GCGCCTTTTTATGAAACTCACTG 59.086 43.478 0.00 0.00 0.00 3.66
2434 2760 4.556699 GCGCCTTTTTATGAAACTCACTGT 60.557 41.667 0.00 0.00 0.00 3.55
2463 2789 3.053831 GTGCAAGCACTCCCTAAACTA 57.946 47.619 17.37 0.00 43.12 2.24
2470 2796 6.407202 CAAGCACTCCCTAAACTAACTACAT 58.593 40.000 0.00 0.00 0.00 2.29
2502 2828 6.995686 AGTACAGTGTCATCCAATTTTGTACA 59.004 34.615 0.00 0.00 41.06 2.90
2509 2839 4.822350 TCATCCAATTTTGTACACCGTTCA 59.178 37.500 0.00 0.00 0.00 3.18
2521 2851 8.780846 TTGTACACCGTTCACAAATATAAGAT 57.219 30.769 0.00 0.00 0.00 2.40
2526 2856 8.020819 ACACCGTTCACAAATATAAGATGTTTG 58.979 33.333 7.02 7.02 44.03 2.93
2544 2874 9.775854 AGATGTTTGAGATATTTCACTATGGAG 57.224 33.333 0.00 0.00 0.00 3.86
2565 2895 2.322355 ACATACTGGCTGACATGAGC 57.678 50.000 0.00 0.00 38.34 4.26
2576 2907 3.129109 CTGACATGAGCGAGCAACATAT 58.871 45.455 0.00 0.00 0.00 1.78
2585 2916 5.083136 AGCGAGCAACATATTAAATCGTG 57.917 39.130 0.00 0.00 0.00 4.35
2586 2917 4.024893 AGCGAGCAACATATTAAATCGTGG 60.025 41.667 0.00 0.00 0.00 4.94
2601 2932 9.998106 ATTAAATCGTGGCTATATATATCCCAC 57.002 33.333 23.29 23.29 41.87 4.61
2602 2933 7.676683 AAATCGTGGCTATATATATCCCACT 57.323 36.000 26.73 15.92 42.83 4.00
2603 2934 6.902771 ATCGTGGCTATATATATCCCACTC 57.097 41.667 26.73 13.52 42.83 3.51
2604 2935 5.762279 TCGTGGCTATATATATCCCACTCA 58.238 41.667 26.73 17.81 42.83 3.41
2605 2936 5.828328 TCGTGGCTATATATATCCCACTCAG 59.172 44.000 26.73 18.41 42.83 3.35
2606 2937 5.828328 CGTGGCTATATATATCCCACTCAGA 59.172 44.000 26.73 3.24 42.83 3.27
2607 2938 6.321435 CGTGGCTATATATATCCCACTCAGAA 59.679 42.308 26.73 2.71 42.83 3.02
2608 2939 7.147897 CGTGGCTATATATATCCCACTCAGAAA 60.148 40.741 26.73 2.19 42.83 2.52
2609 2940 8.540388 GTGGCTATATATATCCCACTCAGAAAA 58.460 37.037 24.65 0.00 41.99 2.29
2610 2941 9.111519 TGGCTATATATATCCCACTCAGAAAAA 57.888 33.333 9.61 0.00 0.00 1.94
2653 2984 5.499139 TGTGAACAAAGGAAGTAGCTTTG 57.501 39.130 0.00 0.00 42.01 2.77
2654 2985 4.338118 TGTGAACAAAGGAAGTAGCTTTGG 59.662 41.667 1.40 0.00 40.99 3.28
2664 2995 7.394144 AGGAAGTAGCTTTGGTCCAATATAT 57.606 36.000 4.80 0.00 0.00 0.86
2665 2996 8.506196 AGGAAGTAGCTTTGGTCCAATATATA 57.494 34.615 4.80 0.00 0.00 0.86
2668 2999 9.726438 GAAGTAGCTTTGGTCCAATATATACAT 57.274 33.333 4.80 0.42 0.00 2.29
2697 3028 8.814931 ACATTGATGGACAAGAAAATATTTCCA 58.185 29.630 0.10 4.01 42.02 3.53
2698 3029 9.309516 CATTGATGGACAAGAAAATATTTCCAG 57.690 33.333 9.54 1.01 42.02 3.86
2699 3030 8.421249 TTGATGGACAAGAAAATATTTCCAGT 57.579 30.769 9.54 3.69 36.60 4.00
2700 3031 9.527157 TTGATGGACAAGAAAATATTTCCAGTA 57.473 29.630 9.54 0.54 36.60 2.74
2701 3032 9.699410 TGATGGACAAGAAAATATTTCCAGTAT 57.301 29.630 9.54 0.00 36.60 2.12
2706 3037 9.937175 GACAAGAAAATATTTCCAGTATAGTGC 57.063 33.333 0.10 0.00 0.00 4.40
2707 3038 8.903820 ACAAGAAAATATTTCCAGTATAGTGCC 58.096 33.333 0.10 0.00 0.00 5.01
2708 3039 8.902806 CAAGAAAATATTTCCAGTATAGTGCCA 58.097 33.333 0.10 0.00 0.00 4.92
2709 3040 9.646522 AAGAAAATATTTCCAGTATAGTGCCAT 57.353 29.630 0.10 0.00 0.00 4.40
2710 3041 9.289782 AGAAAATATTTCCAGTATAGTGCCATC 57.710 33.333 0.10 0.00 0.00 3.51
2711 3042 8.409358 AAAATATTTCCAGTATAGTGCCATCC 57.591 34.615 0.10 0.00 0.00 3.51
2712 3043 6.702449 ATATTTCCAGTATAGTGCCATCCA 57.298 37.500 1.67 0.00 0.00 3.41
2713 3044 4.853468 TTTCCAGTATAGTGCCATCCAA 57.147 40.909 1.67 0.00 0.00 3.53
2714 3045 5.387113 TTTCCAGTATAGTGCCATCCAAT 57.613 39.130 1.67 0.00 0.00 3.16
2741 3072 6.706055 TTAAACTAGAAATCGTGTCAGCAG 57.294 37.500 0.00 0.00 0.00 4.24
2747 3078 4.380531 AGAAATCGTGTCAGCAGAAAGAA 58.619 39.130 0.00 0.00 0.00 2.52
2753 3084 4.574421 TCGTGTCAGCAGAAAGAAAAATCA 59.426 37.500 0.00 0.00 0.00 2.57
2754 3085 5.065859 TCGTGTCAGCAGAAAGAAAAATCAA 59.934 36.000 0.00 0.00 0.00 2.57
2761 3092 6.199719 CAGCAGAAAGAAAAATCAACCAAGAC 59.800 38.462 0.00 0.00 0.00 3.01
2783 3114 6.827251 AGACTACATATTTCGTCTCCTGTGTA 59.173 38.462 0.00 0.00 31.51 2.90
2798 3129 4.081642 TCCTGTGTATTCTAGTGCTTGTCC 60.082 45.833 0.00 0.00 0.00 4.02
2802 3133 2.279582 ATTCTAGTGCTTGTCCGTCG 57.720 50.000 0.00 0.00 0.00 5.12
2806 3137 2.089887 TAGTGCTTGTCCGTCGCCAA 62.090 55.000 0.00 0.00 0.00 4.52
2812 3143 1.225376 TTGTCCGTCGCCAATGTGAC 61.225 55.000 0.00 0.00 46.30 3.67
2815 3146 1.216977 CCGTCGCCAATGTGACCTA 59.783 57.895 1.09 0.00 46.93 3.08
2818 3149 1.076332 GTCGCCAATGTGACCTACAC 58.924 55.000 0.00 0.00 44.50 2.90
2832 3163 7.689953 GTGACCTACACTACAAATTATACCG 57.310 40.000 0.00 0.00 45.13 4.02
2856 3187 7.391016 CGAACAAAGAAAAATTGAGTGGTTTC 58.609 34.615 0.00 0.00 0.00 2.78
2857 3188 7.275560 CGAACAAAGAAAAATTGAGTGGTTTCT 59.724 33.333 0.00 0.00 41.02 2.52
2891 3222 2.826128 GGGTCCATTTTCACCTTCCTTC 59.174 50.000 0.00 0.00 32.69 3.46
2926 3257 2.808543 ACGAAGATCACAAGAGCAAACC 59.191 45.455 0.00 0.00 30.99 3.27
2945 3276 4.841443 ACCAACCAAACGGAAAGAATAC 57.159 40.909 0.00 0.00 0.00 1.89
2946 3277 3.570975 ACCAACCAAACGGAAAGAATACC 59.429 43.478 0.00 0.00 0.00 2.73
2948 3279 4.082949 CCAACCAAACGGAAAGAATACCTC 60.083 45.833 0.00 0.00 0.00 3.85
2984 3315 7.719871 AGTATGACACTAAGTACCATCTTGT 57.280 36.000 0.00 0.00 34.98 3.16
2997 3328 3.181434 ACCATCTTGTAGCCAGGTTTTGA 60.181 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.477700 GCCAAGCCAAGCATGTATGAA 59.522 47.619 0.00 0.00 0.00 2.57
2 3 1.105457 GCCAAGCCAAGCATGTATGA 58.895 50.000 0.00 0.00 0.00 2.15
3 4 1.066605 GAGCCAAGCCAAGCATGTATG 59.933 52.381 0.00 0.00 0.00 2.39
5 6 0.329261 AGAGCCAAGCCAAGCATGTA 59.671 50.000 0.00 0.00 0.00 2.29
7 8 1.511305 CAGAGCCAAGCCAAGCATG 59.489 57.895 0.00 0.00 0.00 4.06
8 9 1.681327 CCAGAGCCAAGCCAAGCAT 60.681 57.895 0.00 0.00 0.00 3.79
9 10 2.282674 CCAGAGCCAAGCCAAGCA 60.283 61.111 0.00 0.00 0.00 3.91
10 11 3.756727 GCCAGAGCCAAGCCAAGC 61.757 66.667 0.00 0.00 0.00 4.01
11 12 2.035312 AGCCAGAGCCAAGCCAAG 59.965 61.111 0.00 0.00 41.25 3.61
12 13 2.282674 CAGCCAGAGCCAAGCCAA 60.283 61.111 0.00 0.00 41.25 4.52
13 14 3.573229 ACAGCCAGAGCCAAGCCA 61.573 61.111 0.00 0.00 41.25 4.75
14 15 3.060615 CACAGCCAGAGCCAAGCC 61.061 66.667 0.00 0.00 41.25 4.35
15 16 3.060615 CCACAGCCAGAGCCAAGC 61.061 66.667 0.00 0.00 41.25 4.01
16 17 1.376942 CTCCACAGCCAGAGCCAAG 60.377 63.158 0.00 0.00 41.25 3.61
17 18 2.752358 CTCCACAGCCAGAGCCAA 59.248 61.111 0.00 0.00 41.25 4.52
21 22 2.125753 GTCGCTCCACAGCCAGAG 60.126 66.667 0.00 0.00 43.56 3.35
22 23 4.056125 CGTCGCTCCACAGCCAGA 62.056 66.667 0.00 0.00 43.56 3.86
23 24 4.056125 TCGTCGCTCCACAGCCAG 62.056 66.667 0.00 0.00 43.56 4.85
24 25 4.357947 GTCGTCGCTCCACAGCCA 62.358 66.667 0.00 0.00 43.56 4.75
27 28 4.039357 ACCGTCGTCGCTCCACAG 62.039 66.667 0.00 0.00 35.54 3.66
28 29 4.337060 CACCGTCGTCGCTCCACA 62.337 66.667 0.00 0.00 35.54 4.17
29 30 3.836176 AACACCGTCGTCGCTCCAC 62.836 63.158 0.00 0.00 35.54 4.02
30 31 3.598715 AACACCGTCGTCGCTCCA 61.599 61.111 0.00 0.00 35.54 3.86
31 32 3.103911 CAACACCGTCGTCGCTCC 61.104 66.667 0.00 0.00 35.54 4.70
32 33 3.103911 CCAACACCGTCGTCGCTC 61.104 66.667 0.00 0.00 35.54 5.03
35 36 4.986587 TCGCCAACACCGTCGTCG 62.987 66.667 0.00 0.00 0.00 5.12
36 37 3.400590 GTCGCCAACACCGTCGTC 61.401 66.667 0.00 0.00 0.00 4.20
55 56 2.593725 CAGGATGGGCTGATGGCG 60.594 66.667 0.00 0.00 42.94 5.69
56 57 2.910994 GCAGGATGGGCTGATGGC 60.911 66.667 0.00 0.00 36.98 4.40
57 58 2.593725 CGCAGGATGGGCTGATGG 60.594 66.667 0.00 0.00 43.90 3.51
70 71 4.394712 GGAGGACACCACCCGCAG 62.395 72.222 0.00 0.00 0.00 5.18
71 72 4.954118 AGGAGGACACCACCCGCA 62.954 66.667 0.00 0.00 34.74 5.69
72 73 1.833787 TTAAGGAGGACACCACCCGC 61.834 60.000 0.00 0.00 34.74 6.13
73 74 0.909623 ATTAAGGAGGACACCACCCG 59.090 55.000 0.00 0.00 34.74 5.28
74 75 3.113043 AGTATTAAGGAGGACACCACCC 58.887 50.000 0.00 0.00 34.74 4.61
75 76 4.019591 ACAAGTATTAAGGAGGACACCACC 60.020 45.833 0.00 0.00 34.40 4.61
76 77 5.161943 ACAAGTATTAAGGAGGACACCAC 57.838 43.478 0.00 0.00 0.00 4.16
77 78 5.836024 AACAAGTATTAAGGAGGACACCA 57.164 39.130 0.00 0.00 0.00 4.17
78 79 8.803397 AAATAACAAGTATTAAGGAGGACACC 57.197 34.615 0.00 0.00 31.82 4.16
103 104 9.729281 CTACAGTACCCCTAATAACAAGAAAAA 57.271 33.333 0.00 0.00 0.00 1.94
104 105 8.323567 CCTACAGTACCCCTAATAACAAGAAAA 58.676 37.037 0.00 0.00 0.00 2.29
105 106 7.458806 ACCTACAGTACCCCTAATAACAAGAAA 59.541 37.037 0.00 0.00 0.00 2.52
106 107 6.961721 ACCTACAGTACCCCTAATAACAAGAA 59.038 38.462 0.00 0.00 0.00 2.52
107 108 6.381994 CACCTACAGTACCCCTAATAACAAGA 59.618 42.308 0.00 0.00 0.00 3.02
108 109 6.407752 CCACCTACAGTACCCCTAATAACAAG 60.408 46.154 0.00 0.00 0.00 3.16
109 110 5.426185 CCACCTACAGTACCCCTAATAACAA 59.574 44.000 0.00 0.00 0.00 2.83
110 111 4.964262 CCACCTACAGTACCCCTAATAACA 59.036 45.833 0.00 0.00 0.00 2.41
111 112 4.964897 ACCACCTACAGTACCCCTAATAAC 59.035 45.833 0.00 0.00 0.00 1.89
112 113 4.964262 CACCACCTACAGTACCCCTAATAA 59.036 45.833 0.00 0.00 0.00 1.40
113 114 4.232587 TCACCACCTACAGTACCCCTAATA 59.767 45.833 0.00 0.00 0.00 0.98
114 115 3.013188 TCACCACCTACAGTACCCCTAAT 59.987 47.826 0.00 0.00 0.00 1.73
115 116 2.382993 TCACCACCTACAGTACCCCTAA 59.617 50.000 0.00 0.00 0.00 2.69
116 117 2.002315 TCACCACCTACAGTACCCCTA 58.998 52.381 0.00 0.00 0.00 3.53
117 118 0.788383 TCACCACCTACAGTACCCCT 59.212 55.000 0.00 0.00 0.00 4.79
118 119 1.875488 ATCACCACCTACAGTACCCC 58.125 55.000 0.00 0.00 0.00 4.95
119 120 2.835764 TCAATCACCACCTACAGTACCC 59.164 50.000 0.00 0.00 0.00 3.69
120 121 4.546829 TTCAATCACCACCTACAGTACC 57.453 45.455 0.00 0.00 0.00 3.34
121 122 6.870971 TTTTTCAATCACCACCTACAGTAC 57.129 37.500 0.00 0.00 0.00 2.73
222 235 3.161557 GGCAAGGCCGGGATCTAT 58.838 61.111 2.18 0.00 39.62 1.98
248 262 3.170717 AGGAACATCTAAAGACGGGACA 58.829 45.455 0.00 0.00 0.00 4.02
250 264 3.835978 TGAAGGAACATCTAAAGACGGGA 59.164 43.478 0.00 0.00 0.00 5.14
251 265 4.202245 TGAAGGAACATCTAAAGACGGG 57.798 45.455 0.00 0.00 0.00 5.28
370 393 2.096980 CCACTGACGATACTAGACGCAA 59.903 50.000 0.00 0.00 0.00 4.85
387 410 1.066430 ACACACTTTCACACGTCCACT 60.066 47.619 0.00 0.00 0.00 4.00
392 415 1.801395 CGGAGACACACTTTCACACGT 60.801 52.381 0.00 0.00 0.00 4.49
393 416 0.852777 CGGAGACACACTTTCACACG 59.147 55.000 0.00 0.00 0.00 4.49
401 426 1.056660 AAATCCACCGGAGACACACT 58.943 50.000 9.46 0.00 34.05 3.55
430 485 6.955963 GCATGAACATAGACAAACTACGAAAG 59.044 38.462 0.00 0.00 33.62 2.62
441 496 4.176271 CTGAAGACGCATGAACATAGACA 58.824 43.478 0.00 0.00 0.00 3.41
475 538 7.363880 CCGCTGTTGAAGGGTAGTATATATCAT 60.364 40.741 0.00 0.00 37.13 2.45
480 543 3.965347 ACCGCTGTTGAAGGGTAGTATAT 59.035 43.478 0.00 0.00 37.13 0.86
497 572 1.580845 GCAGCAGAACATCAACCGCT 61.581 55.000 0.00 0.00 0.00 5.52
558 638 3.628487 CCGGACAAACCTTGTTGTAGAAA 59.372 43.478 0.00 0.00 45.52 2.52
560 640 2.841215 CCGGACAAACCTTGTTGTAGA 58.159 47.619 0.00 0.00 45.52 2.59
626 708 5.925397 CCTAGCAATGACTATAAGCACTGAG 59.075 44.000 0.00 0.00 0.00 3.35
760 849 2.550830 TTTTTCTGCGAAGAGAGCCT 57.449 45.000 0.00 0.00 0.00 4.58
783 873 5.974370 TGGACCCATTCTACCTATAAAACCT 59.026 40.000 0.00 0.00 0.00 3.50
808 898 4.438608 GGTGATACGTACGTACATGTGGAA 60.439 45.833 28.99 7.24 33.01 3.53
811 901 4.018649 TGGTGATACGTACGTACATGTG 57.981 45.455 28.99 11.15 33.01 3.21
812 902 4.700268 TTGGTGATACGTACGTACATGT 57.300 40.909 28.99 14.34 33.01 3.21
835 925 3.884895 ACTTTGCGATTGGTGATGGATA 58.115 40.909 0.00 0.00 0.00 2.59
860 952 1.202371 TGTCGTATCCAATCCGCACTC 60.202 52.381 0.00 0.00 0.00 3.51
915 1009 3.706594 AGGCTAGGAGAAATGATCGAACA 59.293 43.478 0.00 0.00 0.00 3.18
929 1023 0.784495 ATCCGATGGGTAGGCTAGGA 59.216 55.000 0.00 0.00 33.83 2.94
930 1024 1.550976 GAATCCGATGGGTAGGCTAGG 59.449 57.143 0.00 0.00 33.83 3.02
931 1025 1.202582 CGAATCCGATGGGTAGGCTAG 59.797 57.143 0.00 0.00 38.22 3.42
932 1026 1.254026 CGAATCCGATGGGTAGGCTA 58.746 55.000 0.00 0.00 38.22 3.93
933 1027 1.472662 CCGAATCCGATGGGTAGGCT 61.473 60.000 0.00 0.00 38.22 4.58
934 1028 1.004918 CCGAATCCGATGGGTAGGC 60.005 63.158 0.00 0.00 38.22 3.93
940 1035 1.595382 GCCTGTCCGAATCCGATGG 60.595 63.158 0.00 0.00 38.22 3.51
980 1083 4.107051 GCCCGCTGTGCATGTGTC 62.107 66.667 0.00 0.00 0.00 3.67
999 1102 1.336755 CCTGGGGCACGTATTTATTGC 59.663 52.381 0.00 0.00 35.40 3.56
1042 1162 2.172930 GGTAGATCCCTTCCCCTTGTTC 59.827 54.545 0.00 0.00 0.00 3.18
1057 1177 2.040545 AGGGAGATGTCGATCGGTAGAT 59.959 50.000 16.41 0.04 40.38 1.98
1058 1178 1.420514 AGGGAGATGTCGATCGGTAGA 59.579 52.381 16.41 0.00 33.34 2.59
1059 1179 1.807742 GAGGGAGATGTCGATCGGTAG 59.192 57.143 16.41 0.00 33.34 3.18
1061 1181 0.183971 AGAGGGAGATGTCGATCGGT 59.816 55.000 16.41 1.44 33.34 4.69
1062 1182 0.878416 GAGAGGGAGATGTCGATCGG 59.122 60.000 16.41 0.00 33.34 4.18
1115 1243 4.170062 CTGCCGCCATTGCTGACG 62.170 66.667 0.00 0.00 34.43 4.35
1521 1692 2.601804 GAGGTCTCGAGTTTCTTGCTC 58.398 52.381 13.13 3.86 0.00 4.26
1550 1739 4.552365 CATGGCGGCCACGATCCT 62.552 66.667 26.48 3.86 44.60 3.24
1722 1956 4.021925 GAGGCGTGGAAGCTGGGT 62.022 66.667 0.00 0.00 37.29 4.51
1773 2010 2.946762 GGACGTGCCAGCAGAAAC 59.053 61.111 0.00 0.00 36.34 2.78
1818 2067 0.892755 AAACTAGATCGCCGTGGTGA 59.107 50.000 4.36 4.36 39.09 4.02
1902 2179 9.851686 TGAGATGAAATAAAAGGCACTACATAT 57.148 29.630 0.00 0.00 38.49 1.78
1903 2180 9.330063 CTGAGATGAAATAAAAGGCACTACATA 57.670 33.333 0.00 0.00 38.49 2.29
1909 2189 5.573337 AGCTGAGATGAAATAAAAGGCAC 57.427 39.130 0.00 0.00 0.00 5.01
1911 2191 6.540189 TCACTAGCTGAGATGAAATAAAAGGC 59.460 38.462 0.00 0.00 0.00 4.35
1946 2226 1.526575 CGGCCAAATGCTGTGGAGTT 61.527 55.000 2.24 0.00 41.73 3.01
1975 2292 5.219633 GTTACATTGGAATCACAACACCAC 58.780 41.667 0.00 0.00 32.39 4.16
1983 2300 9.965824 CCTATATTTTGGTTACATTGGAATCAC 57.034 33.333 0.00 0.00 0.00 3.06
2035 2353 4.405358 ACTTGCAGAAAAATGACCCTGAAA 59.595 37.500 0.00 0.00 0.00 2.69
2067 2385 0.892358 AGACCGAACGCTGAGGTACA 60.892 55.000 0.00 0.00 38.57 2.90
2073 2391 0.387929 AACTTCAGACCGAACGCTGA 59.612 50.000 0.00 0.00 39.24 4.26
2082 2400 7.650504 GGTTTGTTATTTGGTTAACTTCAGACC 59.349 37.037 5.42 6.03 33.99 3.85
2096 2414 7.932120 TTCGGTAAATGTGGTTTGTTATTTG 57.068 32.000 0.00 0.00 0.00 2.32
2099 2417 7.309920 GTCATTCGGTAAATGTGGTTTGTTAT 58.690 34.615 0.00 0.00 44.36 1.89
2103 2421 4.481463 GGTCATTCGGTAAATGTGGTTTG 58.519 43.478 0.00 0.00 44.36 2.93
2109 2431 4.460948 AGTACGGTCATTCGGTAAATGT 57.539 40.909 0.00 0.00 44.36 2.71
2112 2434 3.761218 TGGTAGTACGGTCATTCGGTAAA 59.239 43.478 0.00 0.00 34.51 2.01
2152 2474 2.976729 CCGGTAATTCGGTTATTTGCG 58.023 47.619 0.00 0.00 44.60 4.85
2172 2494 4.628074 ACACATATATACGGTTGTGCCTC 58.372 43.478 12.17 0.00 42.45 4.70
2179 2501 4.595781 ACCCCATGACACATATATACGGTT 59.404 41.667 0.00 0.00 0.00 4.44
2197 2519 3.054655 GTGCCATTTCTACTTCTACCCCA 60.055 47.826 0.00 0.00 0.00 4.96
2208 2530 6.380095 AACGTTAGTTTTGTGCCATTTCTA 57.620 33.333 0.00 0.00 37.26 2.10
2218 2540 3.248363 GGCGGTCTTAACGTTAGTTTTGT 59.752 43.478 8.23 0.00 41.49 2.83
2219 2541 3.248125 TGGCGGTCTTAACGTTAGTTTTG 59.752 43.478 8.23 1.84 41.49 2.44
2233 2557 2.388735 TGATCTGTTCTATGGCGGTCT 58.611 47.619 0.00 0.00 0.00 3.85
2237 2563 2.874086 TGCATTGATCTGTTCTATGGCG 59.126 45.455 10.61 0.00 37.84 5.69
2244 2570 3.018856 TGGGATGTGCATTGATCTGTTC 58.981 45.455 0.00 0.00 0.00 3.18
2254 2580 1.378911 ATGTGCGTGGGATGTGCAT 60.379 52.632 0.00 0.00 41.23 3.96
2267 2593 5.070770 TGATTTTTGTGTATCCCATGTGC 57.929 39.130 0.00 0.00 0.00 4.57
2275 2601 6.441093 TGCTGGATCTGATTTTTGTGTATC 57.559 37.500 0.00 0.00 0.00 2.24
2277 2603 5.183713 CCTTGCTGGATCTGATTTTTGTGTA 59.816 40.000 0.00 0.00 38.35 2.90
2278 2604 4.021719 CCTTGCTGGATCTGATTTTTGTGT 60.022 41.667 0.00 0.00 38.35 3.72
2279 2605 4.021719 ACCTTGCTGGATCTGATTTTTGTG 60.022 41.667 3.40 0.00 39.71 3.33
2280 2606 4.154942 ACCTTGCTGGATCTGATTTTTGT 58.845 39.130 3.40 0.00 39.71 2.83
2281 2607 4.796038 ACCTTGCTGGATCTGATTTTTG 57.204 40.909 3.40 0.00 39.71 2.44
2282 2608 4.221482 GGAACCTTGCTGGATCTGATTTTT 59.779 41.667 3.40 0.00 37.71 1.94
2283 2609 3.766051 GGAACCTTGCTGGATCTGATTTT 59.234 43.478 3.40 0.00 37.71 1.82
2284 2610 3.011032 AGGAACCTTGCTGGATCTGATTT 59.989 43.478 3.40 0.00 37.71 2.17
2285 2611 2.579860 AGGAACCTTGCTGGATCTGATT 59.420 45.455 3.40 0.00 37.71 2.57
2286 2612 2.172293 GAGGAACCTTGCTGGATCTGAT 59.828 50.000 3.40 0.00 37.71 2.90
2287 2613 1.556911 GAGGAACCTTGCTGGATCTGA 59.443 52.381 3.40 0.00 37.71 3.27
2288 2614 1.280133 TGAGGAACCTTGCTGGATCTG 59.720 52.381 3.40 0.00 37.71 2.90
2289 2615 1.661463 TGAGGAACCTTGCTGGATCT 58.339 50.000 3.40 0.00 37.71 2.75
2290 2616 2.087646 GTTGAGGAACCTTGCTGGATC 58.912 52.381 3.40 1.30 39.71 3.36
2291 2617 1.425066 TGTTGAGGAACCTTGCTGGAT 59.575 47.619 3.40 0.00 39.71 3.41
2292 2618 0.843309 TGTTGAGGAACCTTGCTGGA 59.157 50.000 3.40 0.00 39.71 3.86
2293 2619 1.915141 ATGTTGAGGAACCTTGCTGG 58.085 50.000 0.00 0.00 42.93 4.85
2294 2620 2.886523 TGAATGTTGAGGAACCTTGCTG 59.113 45.455 0.00 0.00 0.00 4.41
2295 2621 3.228188 TGAATGTTGAGGAACCTTGCT 57.772 42.857 0.00 0.00 0.00 3.91
2296 2622 3.068024 TGTTGAATGTTGAGGAACCTTGC 59.932 43.478 0.00 0.00 0.00 4.01
2297 2623 4.916983 TGTTGAATGTTGAGGAACCTTG 57.083 40.909 0.00 0.00 0.00 3.61
2298 2624 5.139727 TCATGTTGAATGTTGAGGAACCTT 58.860 37.500 0.00 0.00 0.00 3.50
2299 2625 4.728772 TCATGTTGAATGTTGAGGAACCT 58.271 39.130 0.00 0.00 0.00 3.50
2300 2626 5.393461 GGATCATGTTGAATGTTGAGGAACC 60.393 44.000 0.00 0.00 0.00 3.62
2353 2679 5.221126 GGGTTGCTTATCAATGGATCTTGTC 60.221 44.000 0.00 0.00 36.99 3.18
2357 2683 4.524802 TGGGTTGCTTATCAATGGATCT 57.475 40.909 0.00 0.00 36.99 2.75
2399 2725 1.881591 AAAGGCGCATGCAATTTTGT 58.118 40.000 19.57 0.00 45.35 2.83
2400 2726 2.973419 AAAAGGCGCATGCAATTTTG 57.027 40.000 19.57 0.51 45.35 2.44
2431 2757 1.610038 TGCTTGCACTGAAATCCACAG 59.390 47.619 0.00 0.00 40.68 3.66
2432 2758 1.337703 GTGCTTGCACTGAAATCCACA 59.662 47.619 17.36 0.00 0.00 4.17
2433 2759 1.610522 AGTGCTTGCACTGAAATCCAC 59.389 47.619 25.00 0.00 33.58 4.02
2434 2760 1.881973 GAGTGCTTGCACTGAAATCCA 59.118 47.619 29.60 0.00 35.23 3.41
2449 2775 8.959705 AAATATGTAGTTAGTTTAGGGAGTGC 57.040 34.615 0.00 0.00 0.00 4.40
2463 2789 9.944376 ATGACACTGTACTGAAAATATGTAGTT 57.056 29.630 6.77 0.00 0.00 2.24
2470 2796 8.862325 AATTGGATGACACTGTACTGAAAATA 57.138 30.769 6.77 0.00 0.00 1.40
2484 2810 4.138290 ACGGTGTACAAAATTGGATGACA 58.862 39.130 0.00 0.00 0.00 3.58
2486 2812 4.822350 TGAACGGTGTACAAAATTGGATGA 59.178 37.500 0.00 0.00 0.00 2.92
2502 2828 8.330466 TCAAACATCTTATATTTGTGAACGGT 57.670 30.769 0.00 0.00 35.33 4.83
2521 2851 9.817809 GTACTCCATAGTGAAATATCTCAAACA 57.182 33.333 0.00 0.00 36.36 2.83
2544 2874 3.126831 GCTCATGTCAGCCAGTATGTAC 58.873 50.000 0.00 0.00 32.76 2.90
2551 2881 2.172372 GCTCGCTCATGTCAGCCAG 61.172 63.158 1.10 0.00 35.84 4.85
2552 2882 2.125391 GCTCGCTCATGTCAGCCA 60.125 61.111 1.10 0.00 35.84 4.75
2565 2895 4.024893 AGCCACGATTTAATATGTTGCTCG 60.025 41.667 0.00 0.00 28.32 5.03
2576 2907 9.209048 AGTGGGATATATATAGCCACGATTTAA 57.791 33.333 24.71 1.50 40.52 1.52
2623 2954 9.774742 GCTACTTCCTTTGTTCACAAATATAAG 57.225 33.333 5.59 11.04 43.92 1.73
2671 3002 8.814931 TGGAAATATTTTCTTGTCCATCAATGT 58.185 29.630 7.98 0.00 35.35 2.71
2672 3003 9.309516 CTGGAAATATTTTCTTGTCCATCAATG 57.690 33.333 7.98 0.00 34.75 2.82
2673 3004 9.039165 ACTGGAAATATTTTCTTGTCCATCAAT 57.961 29.630 7.98 0.00 34.75 2.57
2674 3005 8.421249 ACTGGAAATATTTTCTTGTCCATCAA 57.579 30.769 7.98 0.00 34.75 2.57
2675 3006 9.699410 ATACTGGAAATATTTTCTTGTCCATCA 57.301 29.630 7.98 0.00 34.75 3.07
2680 3011 9.937175 GCACTATACTGGAAATATTTTCTTGTC 57.063 33.333 7.98 0.00 0.00 3.18
2681 3012 8.903820 GGCACTATACTGGAAATATTTTCTTGT 58.096 33.333 7.98 8.88 0.00 3.16
2682 3013 8.902806 TGGCACTATACTGGAAATATTTTCTTG 58.097 33.333 7.98 3.80 0.00 3.02
2683 3014 9.646522 ATGGCACTATACTGGAAATATTTTCTT 57.353 29.630 7.98 0.00 0.00 2.52
2684 3015 9.289782 GATGGCACTATACTGGAAATATTTTCT 57.710 33.333 7.98 0.00 0.00 2.52
2685 3016 8.515414 GGATGGCACTATACTGGAAATATTTTC 58.485 37.037 1.43 0.11 0.00 2.29
2686 3017 8.004215 TGGATGGCACTATACTGGAAATATTTT 58.996 33.333 1.43 0.00 0.00 1.82
2687 3018 7.526041 TGGATGGCACTATACTGGAAATATTT 58.474 34.615 0.00 0.00 0.00 1.40
2688 3019 7.090319 TGGATGGCACTATACTGGAAATATT 57.910 36.000 0.00 0.00 0.00 1.28
2689 3020 6.702449 TGGATGGCACTATACTGGAAATAT 57.298 37.500 0.00 0.00 0.00 1.28
2690 3021 6.508030 TTGGATGGCACTATACTGGAAATA 57.492 37.500 0.00 0.00 0.00 1.40
2691 3022 5.387113 TTGGATGGCACTATACTGGAAAT 57.613 39.130 0.00 0.00 0.00 2.17
2692 3023 4.853468 TTGGATGGCACTATACTGGAAA 57.147 40.909 0.00 0.00 0.00 3.13
2693 3024 5.387113 AATTGGATGGCACTATACTGGAA 57.613 39.130 0.00 0.00 0.00 3.53
2694 3025 5.387113 AAATTGGATGGCACTATACTGGA 57.613 39.130 0.00 0.00 0.00 3.86
2695 3026 6.469782 AAAAATTGGATGGCACTATACTGG 57.530 37.500 0.00 0.00 0.00 4.00
2731 3062 4.847633 TGATTTTTCTTTCTGCTGACACG 58.152 39.130 0.00 0.00 0.00 4.49
2734 3065 5.591099 TGGTTGATTTTTCTTTCTGCTGAC 58.409 37.500 0.00 0.00 0.00 3.51
2737 3068 6.097412 AGTCTTGGTTGATTTTTCTTTCTGCT 59.903 34.615 0.00 0.00 0.00 4.24
2747 3078 9.010029 ACGAAATATGTAGTCTTGGTTGATTTT 57.990 29.630 0.00 0.00 0.00 1.82
2753 3084 6.154706 AGGAGACGAAATATGTAGTCTTGGTT 59.845 38.462 9.74 0.00 43.17 3.67
2754 3085 5.657302 AGGAGACGAAATATGTAGTCTTGGT 59.343 40.000 9.74 0.00 43.17 3.67
2761 3092 8.353684 AGAATACACAGGAGACGAAATATGTAG 58.646 37.037 0.00 0.00 0.00 2.74
2768 3099 5.621555 GCACTAGAATACACAGGAGACGAAA 60.622 44.000 0.00 0.00 0.00 3.46
2783 3114 1.736032 GCGACGGACAAGCACTAGAAT 60.736 52.381 0.00 0.00 0.00 2.40
2798 3129 0.389296 TGTAGGTCACATTGGCGACG 60.389 55.000 0.00 0.00 32.74 5.12
2812 3143 8.706492 TTGTTCGGTATAATTTGTAGTGTAGG 57.294 34.615 0.00 0.00 0.00 3.18
2815 3146 8.836268 TCTTTGTTCGGTATAATTTGTAGTGT 57.164 30.769 0.00 0.00 0.00 3.55
2828 3159 6.095720 ACCACTCAATTTTTCTTTGTTCGGTA 59.904 34.615 0.00 0.00 0.00 4.02
2831 3162 6.885735 AACCACTCAATTTTTCTTTGTTCG 57.114 33.333 0.00 0.00 0.00 3.95
2832 3163 8.479313 AGAAACCACTCAATTTTTCTTTGTTC 57.521 30.769 0.00 0.00 35.26 3.18
2846 3177 6.183360 CCGGAATAAGGTATAGAAACCACTCA 60.183 42.308 0.00 0.00 42.40 3.41
2856 3187 5.757099 AATGGACCCGGAATAAGGTATAG 57.243 43.478 0.73 0.00 36.17 1.31
2857 3188 6.101442 TGAAAATGGACCCGGAATAAGGTATA 59.899 38.462 0.73 0.00 36.17 1.47
2865 3196 1.357761 AGGTGAAAATGGACCCGGAAT 59.642 47.619 0.73 0.00 32.03 3.01
2868 3199 1.173913 GAAGGTGAAAATGGACCCGG 58.826 55.000 0.00 0.00 32.03 5.73
2891 3222 4.387559 TGATCTTCGTTTGTCATGGTAACG 59.612 41.667 16.48 16.48 44.26 3.18
2926 3257 4.760204 AGAGGTATTCTTTCCGTTTGGTTG 59.240 41.667 0.00 0.00 31.56 3.77
2961 3292 7.648510 GCTACAAGATGGTACTTAGTGTCATAC 59.351 40.741 0.00 0.00 0.00 2.39
2964 3295 5.105473 GGCTACAAGATGGTACTTAGTGTCA 60.105 44.000 0.00 0.00 0.00 3.58
2965 3296 5.105473 TGGCTACAAGATGGTACTTAGTGTC 60.105 44.000 0.00 0.00 0.00 3.67
2966 3297 4.775780 TGGCTACAAGATGGTACTTAGTGT 59.224 41.667 0.00 0.00 0.00 3.55
2973 3304 3.629142 AACCTGGCTACAAGATGGTAC 57.371 47.619 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.