Multiple sequence alignment - TraesCS7A01G134100

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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 TraesCS7A01G134100 chr7A 100.000 4989 0 0 1 4989 85916156 85911168 0.000000e+00 9214.0
1 TraesCS7A01G134100 chr7A 91.971 137 10 1 4828 4964 727614157 727614022 1.830000e-44 191.0
2 TraesCS7A01G134100 chr7A 85.965 114 6 6 4633 4746 727614459 727614356 4.080000e-21 113.0
3 TraesCS7A01G134100 chr7D 92.378 3595 168 45 734 4306 84604181 84600671 0.000000e+00 5024.0
4 TraesCS7A01G134100 chr7D 85.782 211 19 7 4628 4838 90761833 90761634 3.910000e-51 213.0
5 TraesCS7A01G134100 chr7D 86.139 202 17 7 4628 4829 93792543 93792733 1.820000e-49 207.0
6 TraesCS7A01G134100 chr7D 92.701 137 10 0 4828 4964 90761504 90761368 1.100000e-46 198.0
7 TraesCS7A01G134100 chr7D 92.701 137 10 0 4828 4964 93792872 93793008 1.100000e-46 198.0
8 TraesCS7A01G134100 chr7D 88.489 139 11 5 4306 4441 90748211 90748347 4.000000e-36 163.0
9 TraesCS7A01G134100 chr7D 88.119 101 8 3 4880 4980 528781341 528781245 3.160000e-22 117.0
10 TraesCS7A01G134100 chr7D 90.385 52 5 0 2195 2246 631898562 631898613 8.960000e-08 69.4
11 TraesCS7A01G134100 chr7B 92.641 3411 172 30 769 4145 34390456 34387091 0.000000e+00 4835.0
12 TraesCS7A01G134100 chr7B 83.387 620 75 20 7 606 34391169 34390558 2.630000e-152 549.0
13 TraesCS7A01G134100 chr7B 83.333 240 34 5 1167 1406 23663990 23664223 3.020000e-52 217.0
14 TraesCS7A01G134100 chr7B 89.634 164 11 3 4143 4306 34387000 34386843 2.350000e-48 204.0
15 TraesCS7A01G134100 chr6A 82.746 1078 108 42 1504 2563 250071944 250072961 0.000000e+00 889.0
16 TraesCS7A01G134100 chr4A 98.400 375 5 1 4616 4989 608586361 608586735 0.000000e+00 658.0
17 TraesCS7A01G134100 chr4A 97.059 374 11 0 4616 4989 45367304 45367677 9.110000e-177 630.0
18 TraesCS7A01G134100 chr4A 97.806 319 6 1 4306 4624 608586110 608586427 2.630000e-152 549.0
19 TraesCS7A01G134100 chr4A 95.963 322 13 0 4303 4624 45367049 45367370 1.590000e-144 523.0
20 TraesCS7A01G134100 chr4A 95.775 142 6 0 4300 4441 608599948 608599807 3.880000e-56 230.0
21 TraesCS7A01G134100 chr4A 95.000 120 6 0 4322 4441 45372260 45372141 6.590000e-44 189.0
22 TraesCS7A01G134100 chr2A 97.581 372 5 1 4618 4989 150919803 150920170 7.050000e-178 634.0
23 TraesCS7A01G134100 chr2A 95.639 321 9 3 4305 4624 150919551 150919867 1.240000e-140 510.0
24 TraesCS7A01G134100 chr2A 86.256 211 18 7 4628 4838 22185611 22185412 8.410000e-53 219.0
25 TraesCS7A01G134100 chr2A 95.588 136 6 0 4306 4441 150924772 150924637 8.410000e-53 219.0
26 TraesCS7A01G134100 chr2A 91.304 138 11 1 4828 4964 22185282 22185145 2.370000e-43 187.0
27 TraesCS7A01G134100 chr3D 75.646 735 140 27 2101 2823 69855713 69856420 3.720000e-86 329.0
28 TraesCS7A01G134100 chr3D 76.611 419 54 26 4304 4694 441245235 441245637 1.830000e-44 191.0
29 TraesCS7A01G134100 chr3D 90.196 102 7 3 4880 4980 441245873 441245972 4.050000e-26 130.0
30 TraesCS7A01G134100 chr3B 74.932 734 150 24 2110 2832 115782711 115782001 6.270000e-79 305.0
31 TraesCS7A01G134100 chr3A 74.286 735 153 25 2101 2823 81477557 81478267 1.370000e-70 278.0
32 TraesCS7A01G134100 chrUn 88.489 139 11 5 4306 4441 477347605 477347741 4.000000e-36 163.0


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 TraesCS7A01G134100 chr7A 85911168 85916156 4988 True 9214.000000 9214 100.000 1 4989 1 chr7A.!!$R1 4988
1 TraesCS7A01G134100 chr7D 84600671 84604181 3510 True 5024.000000 5024 92.378 734 4306 1 chr7D.!!$R1 3572
2 TraesCS7A01G134100 chr7B 34386843 34391169 4326 True 1862.666667 4835 88.554 7 4306 3 chr7B.!!$R1 4299
3 TraesCS7A01G134100 chr6A 250071944 250072961 1017 False 889.000000 889 82.746 1504 2563 1 chr6A.!!$F1 1059
4 TraesCS7A01G134100 chr4A 608586110 608586735 625 False 603.500000 658 98.103 4306 4989 2 chr4A.!!$F2 683
5 TraesCS7A01G134100 chr4A 45367049 45367677 628 False 576.500000 630 96.511 4303 4989 2 chr4A.!!$F1 686
6 TraesCS7A01G134100 chr2A 150919551 150920170 619 False 572.000000 634 96.610 4305 4989 2 chr2A.!!$F1 684
7 TraesCS7A01G134100 chr3D 69855713 69856420 707 False 329.000000 329 75.646 2101 2823 1 chr3D.!!$F1 722
8 TraesCS7A01G134100 chr3B 115782001 115782711 710 True 305.000000 305 74.932 2110 2832 1 chr3B.!!$R1 722
9 TraesCS7A01G134100 chr3A 81477557 81478267 710 False 278.000000 278 74.286 2101 2823 1 chr3A.!!$F1 722

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
239 248 0.036765 CCGAAAAGATGGACCACGGA 60.037 55.000 12.41 0.0 41.09 4.69 F
1206 1264 0.109781 GTCGGTGCGTGCATTTCATT 60.110 50.000 0.00 0.0 0.00 2.57 F
1208 1266 0.109827 CGGTGCGTGCATTTCATTGA 60.110 50.000 0.00 0.0 0.00 2.57 F
1638 1715 0.375454 TTCTGTGCGTTTGTTCGGTG 59.625 50.000 0.00 0.0 0.00 4.94 F
1683 1760 0.905357 TTGGTTTTGGGTTGGTGTGG 59.095 50.000 0.00 0.0 0.00 4.17 F
2842 2935 1.134560 CGCCCTCTACTGGTAAGACAC 59.865 57.143 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1372 0.035820 ACCGCCGCAAGAATCCTAAA 60.036 50.000 0.00 0.0 43.02 1.85 R
2318 2411 0.400213 TGTTCTCCTTGATGCCGGTT 59.600 50.000 1.90 0.0 0.00 4.44 R
2902 2995 1.202336 GCGGAGATTTGGCAGAAATGG 60.202 52.381 0.00 0.0 0.00 3.16 R
2906 2999 2.398554 GCGCGGAGATTTGGCAGAA 61.399 57.895 8.83 0.0 0.00 3.02 R
3663 3759 1.398390 GCAGTCCACGGTGATCATTTC 59.602 52.381 10.28 0.0 0.00 2.17 R
4145 4352 0.250513 GAGAACCAGGTAGGCAGGTG 59.749 60.000 0.00 0.0 43.14 4.00 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
22 23 0.249197 TGAGGAGCATCGATTCTGCG 60.249 55.000 10.58 0.00 44.38 5.18
31 32 1.173913 TCGATTCTGCGAGGAGACAA 58.826 50.000 0.00 0.00 35.01 3.18
33 34 1.272781 GATTCTGCGAGGAGACAACG 58.727 55.000 0.00 0.00 35.96 4.10
70 71 8.102484 AGGGGACACATGTATAAGATAAAAGT 57.898 34.615 0.00 0.00 0.00 2.66
74 75 8.827677 GGACACATGTATAAGATAAAAGTCCAC 58.172 37.037 15.05 0.00 40.15 4.02
75 76 8.732746 ACACATGTATAAGATAAAAGTCCACC 57.267 34.615 0.00 0.00 0.00 4.61
84 85 1.129058 AAAAGTCCACCGAGACCACT 58.871 50.000 0.00 0.00 37.49 4.00
86 87 1.186267 AAGTCCACCGAGACCACTCC 61.186 60.000 0.00 0.00 39.76 3.85
87 88 1.906824 GTCCACCGAGACCACTCCA 60.907 63.158 0.00 0.00 39.76 3.86
88 89 1.078528 TCCACCGAGACCACTCCAT 59.921 57.895 0.00 0.00 39.76 3.41
89 90 1.219124 CCACCGAGACCACTCCATG 59.781 63.158 0.00 0.00 39.76 3.66
90 91 1.448540 CACCGAGACCACTCCATGC 60.449 63.158 0.00 0.00 39.76 4.06
91 92 2.187946 CCGAGACCACTCCATGCC 59.812 66.667 0.00 0.00 39.76 4.40
92 93 2.659063 CCGAGACCACTCCATGCCA 61.659 63.158 0.00 0.00 39.76 4.92
94 95 1.607801 CGAGACCACTCCATGCCAGA 61.608 60.000 0.00 0.00 39.76 3.86
95 96 0.177604 GAGACCACTCCATGCCAGAG 59.822 60.000 0.00 0.00 37.19 3.35
139 140 2.942376 TCAAAACATGCACAGAGTCGTT 59.058 40.909 0.00 0.00 0.00 3.85
140 141 3.038017 CAAAACATGCACAGAGTCGTTG 58.962 45.455 0.00 0.00 0.00 4.10
157 158 2.672478 CGTTGTCCTGTTGCAACCAAAA 60.672 45.455 26.14 9.18 41.16 2.44
158 159 3.530535 GTTGTCCTGTTGCAACCAAAAT 58.469 40.909 26.14 0.00 39.07 1.82
161 162 2.102252 GTCCTGTTGCAACCAAAATGGA 59.898 45.455 26.14 18.60 40.96 3.41
169 170 0.525761 AACCAAAATGGACCGATGCG 59.474 50.000 2.85 0.00 40.96 4.73
170 171 1.226660 CCAAAATGGACCGATGCGC 60.227 57.895 0.00 0.00 40.96 6.09
177 178 2.511373 GACCGATGCGCCATGACA 60.511 61.111 4.18 0.00 0.00 3.58
178 179 2.046411 ACCGATGCGCCATGACAA 60.046 55.556 4.18 0.00 0.00 3.18
180 181 2.397754 CCGATGCGCCATGACAACA 61.398 57.895 4.18 0.00 0.00 3.33
186 192 2.117206 GCCATGACAACACCCCCA 59.883 61.111 0.00 0.00 0.00 4.96
202 208 2.571548 CCAAGAGGGTGACAATGCC 58.428 57.895 0.00 0.00 0.00 4.40
206 212 0.994247 AGAGGGTGACAATGCCATGA 59.006 50.000 0.00 0.00 0.00 3.07
207 213 1.064906 AGAGGGTGACAATGCCATGAG 60.065 52.381 0.00 0.00 0.00 2.90
209 215 0.682209 GGGTGACAATGCCATGAGCT 60.682 55.000 0.00 0.00 44.23 4.09
229 238 1.376609 GCCGCCATGTCCGAAAAGAT 61.377 55.000 4.76 0.00 0.00 2.40
231 240 0.378257 CGCCATGTCCGAAAAGATGG 59.622 55.000 0.00 0.00 41.77 3.51
237 246 3.525619 TCCGAAAAGATGGACCACG 57.474 52.632 0.00 0.00 0.00 4.94
239 248 0.036765 CCGAAAAGATGGACCACGGA 60.037 55.000 12.41 0.00 41.09 4.69
244 263 2.124695 GATGGACCACGGAAGCCC 60.125 66.667 0.00 0.00 0.00 5.19
246 265 2.198304 GATGGACCACGGAAGCCCTT 62.198 60.000 0.00 0.00 0.00 3.95
297 317 0.671781 CAAGAGGGAAGCGACACCTG 60.672 60.000 0.00 0.00 34.02 4.00
298 318 1.831652 AAGAGGGAAGCGACACCTGG 61.832 60.000 0.00 0.00 34.02 4.45
299 319 2.526873 AGGGAAGCGACACCTGGT 60.527 61.111 0.00 0.00 32.26 4.00
306 326 2.347114 CGACACCTGGTGGCATCA 59.653 61.111 30.84 0.00 42.59 3.07
316 336 4.758251 TGGCATCACCGTCGCTGG 62.758 66.667 0.00 0.00 43.94 4.85
319 339 3.490759 CATCACCGTCGCTGGCAC 61.491 66.667 0.00 0.00 0.00 5.01
334 354 3.121030 CACAGAGCTTTCGCCCGG 61.121 66.667 0.00 0.00 36.60 5.73
420 440 0.831288 CCATCTCGAGGCCTCCAGAT 60.831 60.000 30.77 30.77 37.92 2.90
424 444 1.001631 TCGAGGCCTCCAGATCCAA 59.998 57.895 27.20 0.00 0.00 3.53
427 447 0.620556 GAGGCCTCCAGATCCAAACA 59.379 55.000 23.19 0.00 0.00 2.83
430 450 1.467920 GCCTCCAGATCCAAACAAGG 58.532 55.000 0.00 0.00 0.00 3.61
449 469 4.473520 AGCCGCCACCATCGAAGG 62.474 66.667 4.85 4.85 0.00 3.46
459 479 4.402192 ATCGAAGGCACGACGATG 57.598 55.556 0.00 0.00 45.21 3.84
469 489 0.249615 CACGACGATGGCAGGATCAT 60.250 55.000 0.00 0.00 0.00 2.45
479 499 3.171388 AGGATCATCCGCCACCCC 61.171 66.667 0.00 0.00 42.75 4.95
484 504 3.866582 CATCCGCCACCCCTCCTC 61.867 72.222 0.00 0.00 0.00 3.71
505 525 0.930742 CGCTACGAGGACTCATTCGC 60.931 60.000 0.00 0.00 40.32 4.70
508 528 2.735762 GCTACGAGGACTCATTCGCTTT 60.736 50.000 0.00 0.00 40.32 3.51
509 529 2.457366 ACGAGGACTCATTCGCTTTT 57.543 45.000 0.00 0.00 40.32 2.27
510 530 2.767505 ACGAGGACTCATTCGCTTTTT 58.232 42.857 0.00 0.00 40.32 1.94
535 555 8.980481 TTTAGGGAGGATTTCTACATGATTTC 57.020 34.615 0.00 0.00 0.00 2.17
573 593 3.627395 TCAATGGGTAGCATTCGTCTT 57.373 42.857 0.00 0.00 0.00 3.01
579 599 3.119245 TGGGTAGCATTCGTCTTACAGTC 60.119 47.826 0.00 0.00 0.00 3.51
627 647 5.664294 AAAAATTGCACATATGGAGCTGA 57.336 34.783 19.08 10.88 0.00 4.26
628 648 5.664294 AAAATTGCACATATGGAGCTGAA 57.336 34.783 19.08 9.64 0.00 3.02
629 649 5.864418 AAATTGCACATATGGAGCTGAAT 57.136 34.783 19.08 11.09 0.00 2.57
630 650 5.449107 AATTGCACATATGGAGCTGAATC 57.551 39.130 19.08 0.00 0.00 2.52
631 651 2.854963 TGCACATATGGAGCTGAATCC 58.145 47.619 19.08 0.00 40.03 3.01
632 652 2.440627 TGCACATATGGAGCTGAATCCT 59.559 45.455 19.08 0.00 40.29 3.24
633 653 3.117776 TGCACATATGGAGCTGAATCCTT 60.118 43.478 19.08 0.00 40.29 3.36
634 654 4.102996 TGCACATATGGAGCTGAATCCTTA 59.897 41.667 19.08 0.00 40.29 2.69
635 655 5.065914 GCACATATGGAGCTGAATCCTTAA 58.934 41.667 7.80 0.00 40.29 1.85
636 656 5.709164 GCACATATGGAGCTGAATCCTTAAT 59.291 40.000 7.80 0.00 40.29 1.40
637 657 6.881065 GCACATATGGAGCTGAATCCTTAATA 59.119 38.462 7.80 0.00 40.29 0.98
638 658 7.391554 GCACATATGGAGCTGAATCCTTAATAA 59.608 37.037 7.80 0.00 40.29 1.40
639 659 9.288576 CACATATGGAGCTGAATCCTTAATAAA 57.711 33.333 7.80 0.00 40.29 1.40
640 660 9.866655 ACATATGGAGCTGAATCCTTAATAAAA 57.133 29.630 7.80 0.00 40.29 1.52
644 664 9.652114 ATGGAGCTGAATCCTTAATAAAATTCT 57.348 29.630 0.00 0.00 40.29 2.40
645 665 9.479549 TGGAGCTGAATCCTTAATAAAATTCTT 57.520 29.630 0.00 0.00 40.29 2.52
663 683 8.664211 AAATTCTTAACATTAGACGAGATCCC 57.336 34.615 0.00 0.00 0.00 3.85
664 684 5.786264 TCTTAACATTAGACGAGATCCCC 57.214 43.478 0.00 0.00 0.00 4.81
665 685 5.455872 TCTTAACATTAGACGAGATCCCCT 58.544 41.667 0.00 0.00 0.00 4.79
666 686 6.607970 TCTTAACATTAGACGAGATCCCCTA 58.392 40.000 0.00 0.00 0.00 3.53
667 687 6.715718 TCTTAACATTAGACGAGATCCCCTAG 59.284 42.308 0.00 0.00 0.00 3.02
668 688 4.726035 ACATTAGACGAGATCCCCTAGA 57.274 45.455 0.00 0.00 0.00 2.43
669 689 5.063017 ACATTAGACGAGATCCCCTAGAA 57.937 43.478 0.00 0.00 0.00 2.10
670 690 5.455872 ACATTAGACGAGATCCCCTAGAAA 58.544 41.667 0.00 0.00 0.00 2.52
671 691 5.897824 ACATTAGACGAGATCCCCTAGAAAA 59.102 40.000 0.00 0.00 0.00 2.29
672 692 6.555360 ACATTAGACGAGATCCCCTAGAAAAT 59.445 38.462 0.00 0.00 0.00 1.82
673 693 4.946478 AGACGAGATCCCCTAGAAAATG 57.054 45.455 0.00 0.00 0.00 2.32
674 694 3.070302 AGACGAGATCCCCTAGAAAATGC 59.930 47.826 0.00 0.00 0.00 3.56
675 695 2.771943 ACGAGATCCCCTAGAAAATGCA 59.228 45.455 0.00 0.00 0.00 3.96
676 696 3.392616 ACGAGATCCCCTAGAAAATGCAT 59.607 43.478 0.00 0.00 0.00 3.96
677 697 4.593206 ACGAGATCCCCTAGAAAATGCATA 59.407 41.667 0.00 0.00 0.00 3.14
678 698 5.071788 ACGAGATCCCCTAGAAAATGCATAA 59.928 40.000 0.00 0.00 0.00 1.90
679 699 5.997746 CGAGATCCCCTAGAAAATGCATAAA 59.002 40.000 0.00 0.00 0.00 1.40
680 700 6.148480 CGAGATCCCCTAGAAAATGCATAAAG 59.852 42.308 0.00 0.00 0.00 1.85
681 701 7.154191 AGATCCCCTAGAAAATGCATAAAGA 57.846 36.000 0.00 0.00 0.00 2.52
682 702 7.763613 AGATCCCCTAGAAAATGCATAAAGAT 58.236 34.615 0.00 0.00 0.00 2.40
683 703 8.230306 AGATCCCCTAGAAAATGCATAAAGATT 58.770 33.333 0.00 0.00 0.00 2.40
684 704 7.587037 TCCCCTAGAAAATGCATAAAGATTG 57.413 36.000 0.00 0.00 0.00 2.67
685 705 6.040842 TCCCCTAGAAAATGCATAAAGATTGC 59.959 38.462 0.00 0.00 40.55 3.56
694 714 5.063180 TGCATAAAGATTGCAGTTTGAGG 57.937 39.130 0.00 0.00 44.73 3.86
695 715 4.523943 TGCATAAAGATTGCAGTTTGAGGT 59.476 37.500 0.00 0.00 44.73 3.85
696 716 5.709631 TGCATAAAGATTGCAGTTTGAGGTA 59.290 36.000 0.00 0.00 44.73 3.08
697 717 6.377996 TGCATAAAGATTGCAGTTTGAGGTAT 59.622 34.615 0.00 0.00 44.73 2.73
698 718 6.694411 GCATAAAGATTGCAGTTTGAGGTATG 59.306 38.462 0.00 0.00 39.90 2.39
699 719 7.629222 GCATAAAGATTGCAGTTTGAGGTATGT 60.629 37.037 0.00 0.00 39.90 2.29
700 720 5.886960 AAGATTGCAGTTTGAGGTATGTC 57.113 39.130 0.00 0.00 0.00 3.06
701 721 5.171339 AGATTGCAGTTTGAGGTATGTCT 57.829 39.130 0.00 0.00 0.00 3.41
702 722 4.940046 AGATTGCAGTTTGAGGTATGTCTG 59.060 41.667 0.00 0.00 0.00 3.51
703 723 4.350368 TTGCAGTTTGAGGTATGTCTGA 57.650 40.909 0.00 0.00 0.00 3.27
704 724 4.350368 TGCAGTTTGAGGTATGTCTGAA 57.650 40.909 0.00 0.00 0.00 3.02
705 725 4.910195 TGCAGTTTGAGGTATGTCTGAAT 58.090 39.130 0.00 0.00 0.00 2.57
706 726 4.937620 TGCAGTTTGAGGTATGTCTGAATC 59.062 41.667 0.00 0.00 0.00 2.52
708 728 5.645497 GCAGTTTGAGGTATGTCTGAATCTT 59.355 40.000 0.00 0.00 0.00 2.40
717 737 7.955918 AGGTATGTCTGAATCTTTTGCTTTTT 58.044 30.769 0.00 0.00 0.00 1.94
718 738 9.077885 AGGTATGTCTGAATCTTTTGCTTTTTA 57.922 29.630 0.00 0.00 0.00 1.52
788 842 2.362503 TCGTGTGGCGAGGAGGAT 60.363 61.111 0.00 0.00 45.68 3.24
791 845 1.068250 GTGTGGCGAGGAGGATAGC 59.932 63.158 0.00 0.00 0.00 2.97
879 933 1.654220 CCACCAAACAGCCAACGAG 59.346 57.895 0.00 0.00 0.00 4.18
914 968 1.758592 CCACTTCCCCGTCTTCCAA 59.241 57.895 0.00 0.00 0.00 3.53
992 1046 0.251742 ATTTAACAGCCAGCCAGCCA 60.252 50.000 0.00 0.00 0.00 4.75
993 1047 0.895100 TTTAACAGCCAGCCAGCCAG 60.895 55.000 0.00 0.00 0.00 4.85
1174 1232 4.880426 GCCTCCTCCCCGATCCCA 62.880 72.222 0.00 0.00 0.00 4.37
1177 1235 1.527370 CTCCTCCCCGATCCCAAAC 59.473 63.158 0.00 0.00 0.00 2.93
1202 1260 2.663520 TCGTCGGTGCGTGCATTT 60.664 55.556 0.00 0.00 0.00 2.32
1204 1262 2.942879 GTCGGTGCGTGCATTTCA 59.057 55.556 0.00 0.00 0.00 2.69
1205 1263 1.501741 GTCGGTGCGTGCATTTCAT 59.498 52.632 0.00 0.00 0.00 2.57
1206 1264 0.109781 GTCGGTGCGTGCATTTCATT 60.110 50.000 0.00 0.00 0.00 2.57
1208 1266 0.109827 CGGTGCGTGCATTTCATTGA 60.110 50.000 0.00 0.00 0.00 2.57
1209 1267 1.467883 CGGTGCGTGCATTTCATTGAT 60.468 47.619 0.00 0.00 0.00 2.57
1211 1269 2.187707 GTGCGTGCATTTCATTGATCC 58.812 47.619 0.00 0.00 0.00 3.36
1212 1270 2.093890 TGCGTGCATTTCATTGATCCT 58.906 42.857 0.00 0.00 0.00 3.24
1215 1273 2.033801 CGTGCATTTCATTGATCCTCCC 59.966 50.000 0.00 0.00 0.00 4.30
1270 1339 0.584396 TGTTGCGTTCGCCTTGTTAG 59.416 50.000 14.44 0.00 0.00 2.34
1276 1345 1.797025 GTTCGCCTTGTTAGCTGACT 58.203 50.000 10.29 0.00 0.00 3.41
1302 1372 1.068127 GGTCTGTGTGTAGGTGTTCGT 59.932 52.381 0.00 0.00 0.00 3.85
1306 1376 4.443394 GTCTGTGTGTAGGTGTTCGTTTAG 59.557 45.833 0.00 0.00 0.00 1.85
1309 1379 4.039488 TGTGTGTAGGTGTTCGTTTAGGAT 59.961 41.667 0.00 0.00 0.00 3.24
1371 1441 2.131067 GCGAGGGAGGAGAAGGAGG 61.131 68.421 0.00 0.00 0.00 4.30
1372 1442 1.615814 CGAGGGAGGAGAAGGAGGA 59.384 63.158 0.00 0.00 0.00 3.71
1612 1683 0.468214 TGCGATCTCGGAGGAGGAAT 60.468 55.000 4.96 0.00 40.85 3.01
1626 1697 0.739813 AGGAATACGCGGTTCTGTGC 60.740 55.000 20.75 8.64 0.00 4.57
1638 1715 0.375454 TTCTGTGCGTTTGTTCGGTG 59.625 50.000 0.00 0.00 0.00 4.94
1683 1760 0.905357 TTGGTTTTGGGTTGGTGTGG 59.095 50.000 0.00 0.00 0.00 4.17
1686 1763 2.427245 TTTTGGGTTGGTGTGGGCG 61.427 57.895 0.00 0.00 0.00 6.13
1687 1764 3.663815 TTTGGGTTGGTGTGGGCGT 62.664 57.895 0.00 0.00 0.00 5.68
1688 1765 4.885270 TGGGTTGGTGTGGGCGTG 62.885 66.667 0.00 0.00 0.00 5.34
1841 1918 1.525077 CGAGGAGGAGGAGGACGAG 60.525 68.421 0.00 0.00 0.00 4.18
2261 2348 3.239253 ACCGACAAACCGAGCCCT 61.239 61.111 0.00 0.00 0.00 5.19
2360 2453 2.759973 TTCCAGAGCGGCGAGGAT 60.760 61.111 12.98 0.00 33.14 3.24
2842 2935 1.134560 CGCCCTCTACTGGTAAGACAC 59.865 57.143 0.00 0.00 0.00 3.67
2859 2952 3.054802 AGACACAACTCAATCCCTCCATC 60.055 47.826 0.00 0.00 0.00 3.51
2860 2953 2.644299 ACACAACTCAATCCCTCCATCA 59.356 45.455 0.00 0.00 0.00 3.07
2862 2955 4.081406 CACAACTCAATCCCTCCATCAAA 58.919 43.478 0.00 0.00 0.00 2.69
2863 2956 4.523943 CACAACTCAATCCCTCCATCAAAA 59.476 41.667 0.00 0.00 0.00 2.44
2864 2957 5.186409 CACAACTCAATCCCTCCATCAAAAT 59.814 40.000 0.00 0.00 0.00 1.82
2866 2959 5.463051 ACTCAATCCCTCCATCAAAATCT 57.537 39.130 0.00 0.00 0.00 2.40
2869 2962 5.829986 TCAATCCCTCCATCAAAATCTTCA 58.170 37.500 0.00 0.00 0.00 3.02
2871 2964 6.153340 TCAATCCCTCCATCAAAATCTTCAAC 59.847 38.462 0.00 0.00 0.00 3.18
2874 2967 6.018469 TCCCTCCATCAAAATCTTCAACATT 58.982 36.000 0.00 0.00 0.00 2.71
2880 2973 8.090214 TCCATCAAAATCTTCAACATTTTCTCC 58.910 33.333 0.00 0.00 32.25 3.71
2881 2974 7.332678 CCATCAAAATCTTCAACATTTTCTCCC 59.667 37.037 0.00 0.00 32.25 4.30
2882 2975 7.601705 TCAAAATCTTCAACATTTTCTCCCT 57.398 32.000 0.00 0.00 32.25 4.20
2890 2983 6.975196 TCAACATTTTCTCCCTGAAATTCA 57.025 33.333 0.00 0.00 43.34 2.57
2891 2984 7.543359 TCAACATTTTCTCCCTGAAATTCAT 57.457 32.000 0.00 0.00 43.34 2.57
2892 2985 7.605449 TCAACATTTTCTCCCTGAAATTCATC 58.395 34.615 0.00 0.00 43.34 2.92
2893 2986 7.233144 TCAACATTTTCTCCCTGAAATTCATCA 59.767 33.333 0.00 0.00 43.34 3.07
2894 2987 6.928520 ACATTTTCTCCCTGAAATTCATCAC 58.071 36.000 0.00 0.00 43.34 3.06
2895 2988 5.982890 TTTTCTCCCTGAAATTCATCACC 57.017 39.130 0.00 0.00 43.34 4.02
2896 2989 4.656100 TTCTCCCTGAAATTCATCACCA 57.344 40.909 0.00 0.00 0.00 4.17
2897 2990 4.868172 TCTCCCTGAAATTCATCACCAT 57.132 40.909 0.00 0.00 0.00 3.55
2898 2991 4.529897 TCTCCCTGAAATTCATCACCATG 58.470 43.478 0.00 0.00 0.00 3.66
2899 2992 4.227982 TCTCCCTGAAATTCATCACCATGA 59.772 41.667 0.00 0.00 37.24 3.07
2902 2995 4.142315 CCCTGAAATTCATCACCATGACAC 60.142 45.833 0.00 0.00 38.86 3.67
2906 2999 5.481122 TGAAATTCATCACCATGACACCATT 59.519 36.000 0.00 0.00 38.86 3.16
2912 3005 1.203052 CACCATGACACCATTTCTGCC 59.797 52.381 0.00 0.00 0.00 4.85
2913 3006 1.203038 ACCATGACACCATTTCTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
2919 3012 3.507233 TGACACCATTTCTGCCAAATCTC 59.493 43.478 0.00 0.00 0.00 2.75
2922 3015 1.202336 CCATTTCTGCCAAATCTCCGC 60.202 52.381 0.00 0.00 0.00 5.54
3080 3173 2.606519 TTCCACTCCCTCCACCCG 60.607 66.667 0.00 0.00 0.00 5.28
3550 3643 4.767255 GCTGCCCGTGTCCCTCAG 62.767 72.222 0.00 0.00 0.00 3.35
3594 3687 1.215647 GTGTCGCCGATCAAGGTCT 59.784 57.895 0.00 0.00 0.00 3.85
3640 3736 2.234300 ACTTGTGGACGGTACAGTTG 57.766 50.000 0.00 0.00 0.00 3.16
3663 3759 4.993584 GCCTTCTGTATATGTGGACTGATG 59.006 45.833 0.00 0.00 0.00 3.07
3766 3862 4.021925 GCGGTGGAAGGCCTGACT 62.022 66.667 5.69 0.00 34.31 3.41
3778 3874 0.176910 GCCTGACTTACAGCCTCCTC 59.823 60.000 0.00 0.00 44.52 3.71
3880 3976 3.537206 GAGGAGTTGCACGCTGGGT 62.537 63.158 0.00 0.00 0.00 4.51
3883 3979 1.598130 GAGTTGCACGCTGGGTTCT 60.598 57.895 0.00 0.00 0.00 3.01
3884 3980 1.152963 AGTTGCACGCTGGGTTCTT 60.153 52.632 0.00 0.00 0.00 2.52
3886 3982 1.148273 TTGCACGCTGGGTTCTTCT 59.852 52.632 0.00 0.00 0.00 2.85
3891 3987 2.943978 CGCTGGGTTCTTCTCCGGT 61.944 63.158 0.00 0.00 0.00 5.28
3934 4033 0.879400 GCATGGTGATCCTCGAGCTG 60.879 60.000 6.99 0.00 34.23 4.24
3969 4068 1.620822 CCCAAGGAAAGGGTTCACAG 58.379 55.000 0.00 0.00 41.61 3.66
4012 4112 1.269958 TTTAGCTCCTCTGCTCTGCA 58.730 50.000 0.00 0.00 42.97 4.41
4036 4136 5.367937 AGTCCATGGATAGTGTATGCTTTCT 59.632 40.000 19.62 1.53 0.00 2.52
4145 4352 2.985847 GCCTCCAGTGTTGTGGGC 60.986 66.667 0.00 0.00 38.26 5.36
4171 4378 2.379972 CCTACCTGGTTCTCTGACGAT 58.620 52.381 3.84 0.00 0.00 3.73
4173 4380 2.223803 ACCTGGTTCTCTGACGATCT 57.776 50.000 0.00 0.00 0.00 2.75
4208 4415 1.056660 CTACCTACCGGCAATGGGAT 58.943 55.000 0.00 0.00 0.00 3.85
4209 4416 0.762418 TACCTACCGGCAATGGGATG 59.238 55.000 0.00 0.00 0.00 3.51
4210 4417 1.898574 CCTACCGGCAATGGGATGC 60.899 63.158 0.00 0.00 45.67 3.91
4256 4463 2.046892 GCGCTTTGGCAGAGGAGA 60.047 61.111 7.20 0.00 38.60 3.71
4257 4464 2.394563 GCGCTTTGGCAGAGGAGAC 61.395 63.158 7.20 0.00 38.60 3.36
4258 4465 1.743252 CGCTTTGGCAGAGGAGACC 60.743 63.158 7.20 0.00 38.60 3.85
4260 4467 1.975327 CTTTGGCAGAGGAGACCGA 59.025 57.895 0.00 0.00 0.00 4.69
4369 4577 2.573869 CCGGACGTCATCTGCTGT 59.426 61.111 18.91 0.00 31.52 4.40
4552 4760 1.336440 CTAGACTCTGCGCACATAGCT 59.664 52.381 5.66 8.59 42.61 3.32
4671 4879 4.776322 CCGCCACTGGGAATCGCA 62.776 66.667 0.00 0.00 35.59 5.10
4672 4880 2.514592 CGCCACTGGGAATCGCAT 60.515 61.111 0.00 0.00 35.59 4.73
4673 4881 2.537560 CGCCACTGGGAATCGCATC 61.538 63.158 0.00 0.00 35.59 3.91
4674 4882 2.537560 GCCACTGGGAATCGCATCG 61.538 63.158 0.00 0.00 35.59 3.84
4675 4883 2.537560 CCACTGGGAATCGCATCGC 61.538 63.158 0.00 0.00 35.59 4.58
4676 4884 2.203070 ACTGGGAATCGCATCGCC 60.203 61.111 0.00 0.00 0.00 5.54
4677 4885 3.341043 CTGGGAATCGCATCGCCG 61.341 66.667 0.00 0.00 0.00 6.46
4796 5004 4.260670 CGTACGCAAGATGTAATTTTCCG 58.739 43.478 0.52 0.00 43.62 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.596727 GCAGAATCGATGCTCCTCAAC 59.403 52.381 1.74 0.00 40.59 3.18
2 3 1.803998 CGCAGAATCGATGCTCCTCAA 60.804 52.381 1.74 0.00 41.61 3.02
4 5 0.031314 TCGCAGAATCGATGCTCCTC 59.969 55.000 1.74 0.00 41.61 3.71
5 6 0.031857 CTCGCAGAATCGATGCTCCT 59.968 55.000 1.74 0.00 41.61 3.69
11 12 1.393603 TGTCTCCTCGCAGAATCGAT 58.606 50.000 0.00 0.00 37.87 3.59
17 18 0.605589 TCTCGTTGTCTCCTCGCAGA 60.606 55.000 0.00 0.00 0.00 4.26
22 23 0.879765 TCGGTTCTCGTTGTCTCCTC 59.120 55.000 0.00 0.00 40.32 3.71
31 32 0.541296 TCCCCTTTCTCGGTTCTCGT 60.541 55.000 0.00 0.00 40.32 4.18
33 34 0.974383 TGTCCCCTTTCTCGGTTCTC 59.026 55.000 0.00 0.00 0.00 2.87
70 71 1.078528 ATGGAGTGGTCTCGGTGGA 59.921 57.895 0.00 0.00 41.26 4.02
74 75 2.187946 GGCATGGAGTGGTCTCGG 59.812 66.667 0.00 0.00 41.26 4.63
75 76 1.153489 CTGGCATGGAGTGGTCTCG 60.153 63.158 0.00 0.00 41.26 4.04
89 90 4.828925 GGCGTCCTCTGCTCTGGC 62.829 72.222 0.00 0.00 39.26 4.85
90 91 3.385384 TGGCGTCCTCTGCTCTGG 61.385 66.667 0.00 0.00 0.00 3.86
91 92 2.125753 GTGGCGTCCTCTGCTCTG 60.126 66.667 0.00 0.00 0.00 3.35
92 93 1.986757 ATGTGGCGTCCTCTGCTCT 60.987 57.895 0.00 0.00 0.00 4.09
94 95 2.267006 CATGTGGCGTCCTCTGCT 59.733 61.111 0.00 0.00 0.00 4.24
95 96 3.503363 GCATGTGGCGTCCTCTGC 61.503 66.667 0.00 0.00 0.00 4.26
119 120 3.038017 CAACGACTCTGTGCATGTTTTG 58.962 45.455 0.00 0.00 0.00 2.44
123 124 1.502231 GACAACGACTCTGTGCATGT 58.498 50.000 0.00 0.00 0.00 3.21
139 140 2.158986 CCATTTTGGTTGCAACAGGACA 60.159 45.455 29.55 16.06 31.35 4.02
140 141 2.102252 TCCATTTTGGTTGCAACAGGAC 59.898 45.455 29.55 13.62 39.03 3.85
157 158 2.592574 CATGGCGCATCGGTCCAT 60.593 61.111 10.83 0.00 40.98 3.41
158 159 3.780173 TCATGGCGCATCGGTCCA 61.780 61.111 10.83 0.00 0.00 4.02
161 162 2.046411 TTGTCATGGCGCATCGGT 60.046 55.556 10.83 0.00 0.00 4.69
169 170 1.532794 TTGGGGGTGTTGTCATGGC 60.533 57.895 0.00 0.00 0.00 4.40
170 171 0.112218 TCTTGGGGGTGTTGTCATGG 59.888 55.000 0.00 0.00 0.00 3.66
186 192 1.355381 TCATGGCATTGTCACCCTCTT 59.645 47.619 0.00 0.00 0.00 2.85
209 215 2.281831 TTTTCGGACATGGCGGCA 60.282 55.556 16.34 16.34 0.00 5.69
229 238 2.852075 AAGGGCTTCCGTGGTCCA 60.852 61.111 0.00 0.00 35.17 4.02
234 243 1.376812 GGTACCAAGGGCTTCCGTG 60.377 63.158 7.15 0.00 39.31 4.94
235 244 2.951101 CGGTACCAAGGGCTTCCGT 61.951 63.158 13.54 0.00 35.17 4.69
237 246 1.376812 CACGGTACCAAGGGCTTCC 60.377 63.158 13.54 0.00 0.00 3.46
239 248 1.677552 CTCACGGTACCAAGGGCTT 59.322 57.895 13.54 0.00 0.00 4.35
244 263 1.595357 GTCCCCTCACGGTACCAAG 59.405 63.158 13.54 5.85 0.00 3.61
246 265 2.284112 GGTCCCCTCACGGTACCA 60.284 66.667 13.54 0.00 35.51 3.25
249 268 2.284112 GTGGGTCCCCTCACGGTA 60.284 66.667 5.13 0.00 36.94 4.02
285 305 3.050275 GCCACCAGGTGTCGCTTC 61.050 66.667 18.82 0.00 37.19 3.86
290 310 3.987404 GTGATGCCACCAGGTGTC 58.013 61.111 18.82 6.21 37.33 3.67
298 318 3.490759 CAGCGACGGTGATGCCAC 61.491 66.667 21.96 0.00 42.46 5.01
299 319 4.758251 CCAGCGACGGTGATGCCA 62.758 66.667 27.42 0.00 36.97 4.92
306 326 4.363990 CTCTGTGCCAGCGACGGT 62.364 66.667 0.00 0.00 0.00 4.83
309 329 1.905922 GAAAGCTCTGTGCCAGCGAC 61.906 60.000 0.00 0.00 44.23 5.19
311 331 2.866028 GAAAGCTCTGTGCCAGCG 59.134 61.111 0.00 0.00 44.23 5.18
334 354 1.664965 GGTGACACGAGTGAGGTGC 60.665 63.158 10.50 0.00 38.98 5.01
343 363 2.563798 GGTACCACGGGTGACACGA 61.564 63.158 16.69 0.00 36.19 4.35
420 440 2.282180 GCGGCTCCCTTGTTTGGA 60.282 61.111 0.00 0.00 0.00 3.53
424 444 4.660938 GGTGGCGGCTCCCTTGTT 62.661 66.667 18.61 0.00 0.00 2.83
427 447 4.115199 GATGGTGGCGGCTCCCTT 62.115 66.667 25.14 15.35 0.00 3.95
430 450 4.467084 TTCGATGGTGGCGGCTCC 62.467 66.667 22.04 22.04 0.00 4.70
449 469 2.202932 ATCCTGCCATCGTCGTGC 60.203 61.111 0.00 0.00 0.00 5.34
469 489 4.779733 GAGAGGAGGGGTGGCGGA 62.780 72.222 0.00 0.00 0.00 5.54
508 528 9.768215 AAATCATGTAGAAATCCTCCCTAAAAA 57.232 29.630 0.00 0.00 0.00 1.94
509 529 9.408648 GAAATCATGTAGAAATCCTCCCTAAAA 57.591 33.333 0.00 0.00 0.00 1.52
510 530 7.998964 GGAAATCATGTAGAAATCCTCCCTAAA 59.001 37.037 0.00 0.00 34.12 1.85
513 533 5.433051 TGGAAATCATGTAGAAATCCTCCCT 59.567 40.000 0.00 0.00 36.51 4.20
551 571 3.950397 AGACGAATGCTACCCATTGAAA 58.050 40.909 0.00 0.00 44.02 2.69
552 572 3.627395 AGACGAATGCTACCCATTGAA 57.373 42.857 0.00 0.00 44.02 2.69
553 573 3.627395 AAGACGAATGCTACCCATTGA 57.373 42.857 0.00 0.00 44.02 2.57
606 626 5.664294 TTCAGCTCCATATGTGCAATTTT 57.336 34.783 16.72 0.00 35.92 1.82
607 627 5.221382 GGATTCAGCTCCATATGTGCAATTT 60.221 40.000 16.72 3.28 35.92 1.82
609 629 3.825014 GGATTCAGCTCCATATGTGCAAT 59.175 43.478 16.72 10.28 35.92 3.56
610 630 3.117776 AGGATTCAGCTCCATATGTGCAA 60.118 43.478 16.72 6.85 37.81 4.08
611 631 2.440627 AGGATTCAGCTCCATATGTGCA 59.559 45.455 16.72 0.00 37.81 4.57
612 632 3.137446 AGGATTCAGCTCCATATGTGC 57.863 47.619 1.24 5.94 37.81 4.57
613 633 8.853077 TTATTAAGGATTCAGCTCCATATGTG 57.147 34.615 1.24 0.00 37.81 3.21
614 634 9.866655 TTTTATTAAGGATTCAGCTCCATATGT 57.133 29.630 1.24 0.00 37.81 2.29
618 638 9.652114 AGAATTTTATTAAGGATTCAGCTCCAT 57.348 29.630 12.94 0.00 37.81 3.41
619 639 9.479549 AAGAATTTTATTAAGGATTCAGCTCCA 57.520 29.630 12.94 0.00 37.81 3.86
637 657 9.110502 GGGATCTCGTCTAATGTTAAGAATTTT 57.889 33.333 0.00 0.00 0.00 1.82
638 658 7.715686 GGGGATCTCGTCTAATGTTAAGAATTT 59.284 37.037 0.00 0.00 0.00 1.82
639 659 7.071321 AGGGGATCTCGTCTAATGTTAAGAATT 59.929 37.037 0.00 0.00 0.00 2.17
640 660 6.555360 AGGGGATCTCGTCTAATGTTAAGAAT 59.445 38.462 0.00 0.00 0.00 2.40
641 661 5.897824 AGGGGATCTCGTCTAATGTTAAGAA 59.102 40.000 0.00 0.00 0.00 2.52
642 662 5.455872 AGGGGATCTCGTCTAATGTTAAGA 58.544 41.667 0.00 0.00 0.00 2.10
643 663 5.793030 AGGGGATCTCGTCTAATGTTAAG 57.207 43.478 0.00 0.00 0.00 1.85
644 664 6.607970 TCTAGGGGATCTCGTCTAATGTTAA 58.392 40.000 0.00 0.00 0.00 2.01
645 665 6.196918 TCTAGGGGATCTCGTCTAATGTTA 57.803 41.667 0.00 0.00 0.00 2.41
646 666 5.063017 TCTAGGGGATCTCGTCTAATGTT 57.937 43.478 0.00 0.00 0.00 2.71
647 667 4.726035 TCTAGGGGATCTCGTCTAATGT 57.274 45.455 0.00 0.00 0.00 2.71
648 668 6.406692 TTTTCTAGGGGATCTCGTCTAATG 57.593 41.667 0.00 0.00 0.00 1.90
649 669 6.519213 GCATTTTCTAGGGGATCTCGTCTAAT 60.519 42.308 0.00 0.00 0.00 1.73
650 670 5.221461 GCATTTTCTAGGGGATCTCGTCTAA 60.221 44.000 0.00 0.00 0.00 2.10
651 671 4.281182 GCATTTTCTAGGGGATCTCGTCTA 59.719 45.833 0.00 0.00 0.00 2.59
652 672 3.070302 GCATTTTCTAGGGGATCTCGTCT 59.930 47.826 0.00 0.00 0.00 4.18
653 673 3.181465 TGCATTTTCTAGGGGATCTCGTC 60.181 47.826 0.00 0.00 0.00 4.20
654 674 2.771943 TGCATTTTCTAGGGGATCTCGT 59.228 45.455 0.00 0.00 0.00 4.18
655 675 3.475566 TGCATTTTCTAGGGGATCTCG 57.524 47.619 0.00 0.00 0.00 4.04
656 676 7.227156 TCTTTATGCATTTTCTAGGGGATCTC 58.773 38.462 3.54 0.00 0.00 2.75
657 677 7.154191 TCTTTATGCATTTTCTAGGGGATCT 57.846 36.000 3.54 0.00 0.00 2.75
658 678 8.302438 CAATCTTTATGCATTTTCTAGGGGATC 58.698 37.037 3.54 0.00 0.00 3.36
659 679 7.256083 GCAATCTTTATGCATTTTCTAGGGGAT 60.256 37.037 3.54 0.00 43.29 3.85
660 680 6.040842 GCAATCTTTATGCATTTTCTAGGGGA 59.959 38.462 3.54 0.00 43.29 4.81
661 681 6.218746 GCAATCTTTATGCATTTTCTAGGGG 58.781 40.000 3.54 0.00 43.29 4.79
673 693 5.064441 ACCTCAAACTGCAATCTTTATGC 57.936 39.130 0.00 0.00 44.08 3.14
674 694 7.765307 ACATACCTCAAACTGCAATCTTTATG 58.235 34.615 0.00 0.00 0.00 1.90
675 695 7.831193 AGACATACCTCAAACTGCAATCTTTAT 59.169 33.333 0.00 0.00 0.00 1.40
676 696 7.119699 CAGACATACCTCAAACTGCAATCTTTA 59.880 37.037 0.00 0.00 0.00 1.85
677 697 6.006449 AGACATACCTCAAACTGCAATCTTT 58.994 36.000 0.00 0.00 0.00 2.52
678 698 5.413833 CAGACATACCTCAAACTGCAATCTT 59.586 40.000 0.00 0.00 0.00 2.40
679 699 4.940046 CAGACATACCTCAAACTGCAATCT 59.060 41.667 0.00 0.00 0.00 2.40
680 700 4.937620 TCAGACATACCTCAAACTGCAATC 59.062 41.667 0.00 0.00 0.00 2.67
681 701 4.910195 TCAGACATACCTCAAACTGCAAT 58.090 39.130 0.00 0.00 0.00 3.56
682 702 4.350368 TCAGACATACCTCAAACTGCAA 57.650 40.909 0.00 0.00 0.00 4.08
683 703 4.350368 TTCAGACATACCTCAAACTGCA 57.650 40.909 0.00 0.00 0.00 4.41
684 704 5.181748 AGATTCAGACATACCTCAAACTGC 58.818 41.667 0.00 0.00 0.00 4.40
685 705 7.678947 AAAGATTCAGACATACCTCAAACTG 57.321 36.000 0.00 0.00 0.00 3.16
686 706 7.308830 GCAAAAGATTCAGACATACCTCAAACT 60.309 37.037 0.00 0.00 0.00 2.66
687 707 6.803807 GCAAAAGATTCAGACATACCTCAAAC 59.196 38.462 0.00 0.00 0.00 2.93
688 708 6.716628 AGCAAAAGATTCAGACATACCTCAAA 59.283 34.615 0.00 0.00 0.00 2.69
689 709 6.240894 AGCAAAAGATTCAGACATACCTCAA 58.759 36.000 0.00 0.00 0.00 3.02
690 710 5.809001 AGCAAAAGATTCAGACATACCTCA 58.191 37.500 0.00 0.00 0.00 3.86
691 711 6.749923 AAGCAAAAGATTCAGACATACCTC 57.250 37.500 0.00 0.00 0.00 3.85
692 712 7.530426 AAAAGCAAAAGATTCAGACATACCT 57.470 32.000 0.00 0.00 0.00 3.08
693 713 9.860898 ATAAAAAGCAAAAGATTCAGACATACC 57.139 29.630 0.00 0.00 0.00 2.73
729 749 8.021396 GGTTCGCAGAACTTTCAAATTAGTTAT 58.979 33.333 16.93 0.00 45.90 1.89
731 751 6.206498 GGTTCGCAGAACTTTCAAATTAGTT 58.794 36.000 16.93 0.00 45.90 2.24
732 752 5.560183 CGGTTCGCAGAACTTTCAAATTAGT 60.560 40.000 16.93 0.00 45.90 2.24
744 783 1.390463 GACTCATTCGGTTCGCAGAAC 59.610 52.381 11.42 11.42 45.90 3.01
750 790 1.927174 GGACATGACTCATTCGGTTCG 59.073 52.381 0.00 0.00 0.00 3.95
787 841 4.489771 GTGCACGGGCCTGGCTAT 62.490 66.667 19.68 1.00 40.13 2.97
840 894 3.558411 GCCTTGTCGCTAGCGCTG 61.558 66.667 31.82 19.20 39.59 5.18
879 933 3.360340 GGCTGCTGACAGTGTGCC 61.360 66.667 15.77 15.77 46.30 5.01
914 968 1.500736 GAGATGGGATGGGATTGGGTT 59.499 52.381 0.00 0.00 0.00 4.11
998 1052 3.660422 ATCACGGGTGGGGGCATTG 62.660 63.158 0.00 0.00 0.00 2.82
999 1053 3.346734 ATCACGGGTGGGGGCATT 61.347 61.111 0.00 0.00 0.00 3.56
1000 1054 4.127744 CATCACGGGTGGGGGCAT 62.128 66.667 0.00 0.00 0.00 4.40
1072 1130 2.560119 CGCGAGGAGAGGATGAGGG 61.560 68.421 0.00 0.00 0.00 4.30
1074 1132 2.334653 GCGCGAGGAGAGGATGAG 59.665 66.667 12.10 0.00 0.00 2.90
1174 1232 3.057337 CCGACGAGGAGTGGGTTT 58.943 61.111 0.00 0.00 42.90 3.27
1202 1260 2.571653 ACAAGAACGGGAGGATCAATGA 59.428 45.455 0.00 0.00 36.25 2.57
1204 1262 3.264450 AGAACAAGAACGGGAGGATCAAT 59.736 43.478 0.00 0.00 36.25 2.57
1205 1263 2.637872 AGAACAAGAACGGGAGGATCAA 59.362 45.455 0.00 0.00 36.25 2.57
1206 1264 2.257207 AGAACAAGAACGGGAGGATCA 58.743 47.619 0.00 0.00 36.25 2.92
1208 1266 2.372172 ACAAGAACAAGAACGGGAGGAT 59.628 45.455 0.00 0.00 0.00 3.24
1209 1267 1.766496 ACAAGAACAAGAACGGGAGGA 59.234 47.619 0.00 0.00 0.00 3.71
1211 1269 3.467803 AGAACAAGAACAAGAACGGGAG 58.532 45.455 0.00 0.00 0.00 4.30
1212 1270 3.553828 AGAACAAGAACAAGAACGGGA 57.446 42.857 0.00 0.00 0.00 5.14
1215 1273 6.033513 GGAAAACAAGAACAAGAACAAGAACG 59.966 38.462 0.00 0.00 0.00 3.95
1270 1339 2.017049 ACACAGACCAACAAAGTCAGC 58.983 47.619 0.00 0.00 36.68 4.26
1276 1345 3.275143 CACCTACACACAGACCAACAAA 58.725 45.455 0.00 0.00 0.00 2.83
1302 1372 0.035820 ACCGCCGCAAGAATCCTAAA 60.036 50.000 0.00 0.00 43.02 1.85
1306 1376 1.982073 CTTGACCGCCGCAAGAATCC 61.982 60.000 0.00 0.00 44.16 3.01
1309 1379 2.668212 CCTTGACCGCCGCAAGAA 60.668 61.111 6.11 0.00 44.16 2.52
1371 1441 1.193650 CGACTCGATCGTCATCTCCTC 59.806 57.143 15.94 0.00 46.25 3.71
1372 1442 1.222300 CGACTCGATCGTCATCTCCT 58.778 55.000 15.94 0.00 46.25 3.69
1626 1697 1.189446 CGAGACTTCACCGAACAAACG 59.811 52.381 0.00 0.00 0.00 3.60
1628 1705 2.875087 TCGAGACTTCACCGAACAAA 57.125 45.000 0.00 0.00 0.00 2.83
1629 1706 2.667448 CGATCGAGACTTCACCGAACAA 60.667 50.000 10.26 0.00 35.87 2.83
1638 1715 2.209838 TCAATGCCGATCGAGACTTC 57.790 50.000 18.66 0.00 0.00 3.01
1825 1902 3.011885 CCTCGTCCTCCTCCTCCT 58.988 66.667 0.00 0.00 0.00 3.69
1960 2037 3.119096 GGTCGAAGGAACTGGCGC 61.119 66.667 0.00 0.00 40.86 6.53
2254 2341 3.303189 AGTCCATGTCAGGGCTCG 58.697 61.111 0.00 0.00 40.24 5.03
2261 2348 2.687200 CCGGGGGAGTCCATGTCA 60.687 66.667 12.30 0.00 37.22 3.58
2315 2408 1.860641 TCTCCTTGATGCCGGTTAGA 58.139 50.000 1.90 0.00 0.00 2.10
2318 2411 0.400213 TGTTCTCCTTGATGCCGGTT 59.600 50.000 1.90 0.00 0.00 4.44
2371 2464 4.492160 GCGTCTCGATGCCCGTGA 62.492 66.667 0.00 0.00 38.30 4.35
2842 2935 5.655532 AGATTTTGATGGAGGGATTGAGTTG 59.344 40.000 0.00 0.00 0.00 3.16
2859 2952 7.436118 TCAGGGAGAAAATGTTGAAGATTTTG 58.564 34.615 16.36 3.72 34.00 2.44
2860 2953 7.601705 TCAGGGAGAAAATGTTGAAGATTTT 57.398 32.000 12.11 12.11 36.04 1.82
2862 2955 7.601705 TTTCAGGGAGAAAATGTTGAAGATT 57.398 32.000 0.00 0.00 43.00 2.40
2874 2967 6.750640 TCATGGTGATGAATTTCAGGGAGAAA 60.751 38.462 5.21 0.00 40.76 2.52
2880 2973 4.142315 GGTGTCATGGTGATGAATTTCAGG 60.142 45.833 5.21 0.00 40.39 3.86
2881 2974 4.460034 TGGTGTCATGGTGATGAATTTCAG 59.540 41.667 5.21 0.00 40.39 3.02
2882 2975 4.405548 TGGTGTCATGGTGATGAATTTCA 58.594 39.130 0.75 0.75 40.39 2.69
2890 2983 2.756760 GCAGAAATGGTGTCATGGTGAT 59.243 45.455 0.00 0.00 33.18 3.06
2891 2984 2.161855 GCAGAAATGGTGTCATGGTGA 58.838 47.619 0.00 0.00 33.18 4.02
2892 2985 1.203052 GGCAGAAATGGTGTCATGGTG 59.797 52.381 0.00 0.00 33.18 4.17
2893 2986 1.203038 TGGCAGAAATGGTGTCATGGT 60.203 47.619 0.00 0.00 33.18 3.55
2894 2987 1.548081 TGGCAGAAATGGTGTCATGG 58.452 50.000 0.00 0.00 33.18 3.66
2895 2988 3.663995 TTTGGCAGAAATGGTGTCATG 57.336 42.857 0.00 0.00 33.18 3.07
2896 2989 4.091549 AGATTTGGCAGAAATGGTGTCAT 58.908 39.130 0.00 0.00 34.56 3.06
2897 2990 3.499338 AGATTTGGCAGAAATGGTGTCA 58.501 40.909 0.00 0.00 0.00 3.58
2898 2991 3.119352 GGAGATTTGGCAGAAATGGTGTC 60.119 47.826 0.00 0.00 0.00 3.67
2899 2992 2.827921 GGAGATTTGGCAGAAATGGTGT 59.172 45.455 0.00 0.00 0.00 4.16
2902 2995 1.202336 GCGGAGATTTGGCAGAAATGG 60.202 52.381 0.00 0.00 0.00 3.16
2906 2999 2.398554 GCGCGGAGATTTGGCAGAA 61.399 57.895 8.83 0.00 0.00 3.02
2912 3005 2.705826 GAGCTGCGCGGAGATTTG 59.294 61.111 32.75 5.49 0.00 2.32
2913 3006 2.835701 TTCGAGCTGCGCGGAGATTT 62.836 55.000 32.75 15.54 40.61 2.17
2922 3015 3.540014 CGTCTGCTTCGAGCTGCG 61.540 66.667 0.00 0.00 42.97 5.18
3550 3643 4.436998 CGTCGTGCTCCAGGACCC 62.437 72.222 11.13 0.00 43.56 4.46
3640 3736 4.672587 TCAGTCCACATATACAGAAGGC 57.327 45.455 0.00 0.00 0.00 4.35
3663 3759 1.398390 GCAGTCCACGGTGATCATTTC 59.602 52.381 10.28 0.00 0.00 2.17
3766 3862 2.361992 TCGGCGAGGAGGCTGTAA 60.362 61.111 4.99 0.00 44.22 2.41
3934 4033 2.129785 GGGCAATGGCATGGACTCC 61.130 63.158 7.84 0.73 43.71 3.85
3969 4068 1.506493 CTACAGCTCAATGGCGATCC 58.494 55.000 0.00 0.00 37.29 3.36
4012 4112 5.367937 AGAAAGCATACACTATCCATGGACT 59.632 40.000 18.99 9.21 0.00 3.85
4013 4113 5.615289 AGAAAGCATACACTATCCATGGAC 58.385 41.667 18.99 0.14 0.00 4.02
4072 4172 1.600957 GGCAGATGATCAATGTGACCG 59.399 52.381 0.00 0.00 31.07 4.79
4145 4352 0.250513 GAGAACCAGGTAGGCAGGTG 59.749 60.000 0.00 0.00 43.14 4.00
4171 4378 1.263356 AGGTGTCCGGATCGAAAAGA 58.737 50.000 7.81 0.00 0.00 2.52
4173 4380 1.205417 GGTAGGTGTCCGGATCGAAAA 59.795 52.381 7.81 0.00 0.00 2.29
4178 4385 1.326328 GGTAGGTAGGTGTCCGGATC 58.674 60.000 7.81 3.98 0.00 3.36
4208 4415 2.390599 GGAGAAATCTGTGCGCGCA 61.391 57.895 33.09 33.09 0.00 6.09
4209 4416 2.029904 GAGGAGAAATCTGTGCGCGC 62.030 60.000 27.26 27.26 0.00 6.86
4210 4417 0.459237 AGAGGAGAAATCTGTGCGCG 60.459 55.000 0.00 0.00 0.00 6.86
4258 4465 2.514592 ACCAGATGCCCGCATTCG 60.515 61.111 3.24 0.00 36.70 3.34
4260 4467 2.124151 GGACCAGATGCCCGCATT 60.124 61.111 3.24 0.00 36.70 3.56
4369 4577 0.747852 TTGTCCAGCTGTACACGTGA 59.252 50.000 25.01 2.68 0.00 4.35
4427 4635 2.435938 GTGCCGATTGGAGCCGAA 60.436 61.111 1.98 0.00 37.49 4.30
4654 4862 4.776322 TGCGATTCCCAGTGGCGG 62.776 66.667 2.61 0.00 0.00 6.13
4655 4863 2.514592 ATGCGATTCCCAGTGGCG 60.515 61.111 2.61 2.75 0.00 5.69
4656 4864 2.537560 CGATGCGATTCCCAGTGGC 61.538 63.158 2.61 0.00 0.00 5.01
4657 4865 2.537560 GCGATGCGATTCCCAGTGG 61.538 63.158 0.63 0.63 0.00 4.00
4658 4866 2.537560 GGCGATGCGATTCCCAGTG 61.538 63.158 0.00 0.00 0.00 3.66
4659 4867 2.203070 GGCGATGCGATTCCCAGT 60.203 61.111 0.00 0.00 0.00 4.00
4660 4868 3.341043 CGGCGATGCGATTCCCAG 61.341 66.667 0.00 0.00 0.00 4.45
4765 4973 2.138355 CTTGCGTACGCGAGTTTGA 58.862 52.632 38.06 18.19 46.40 2.69
4796 5004 2.690510 AAGGAGGAGAGCTGGCCC 60.691 66.667 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.