Multiple sequence alignment - TraesCS4A01G334300

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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 TraesCS4A01G334300 chr4A 100.000 2882 0 0 1 2882 617359412 617362293 0.000000e+00 5323.0
1 TraesCS4A01G334300 chr4A 86.886 1426 154 17 770 2175 617281366 617282778 0.000000e+00 1567.0
2 TraesCS4A01G334300 chr4A 83.998 1631 192 33 770 2343 617288824 617290442 0.000000e+00 1502.0
3 TraesCS4A01G334300 chr4A 83.532 1676 201 30 770 2388 617348893 617350550 0.000000e+00 1496.0
4 TraesCS4A01G334300 chr4A 94.361 266 14 1 504 769 474005142 474005406 9.610000e-110 407.0
5 TraesCS4A01G334300 chr4A 93.985 266 15 1 504 769 192982775 192983039 4.470000e-108 401.0
6 TraesCS4A01G334300 chr5D 92.479 1662 82 16 770 2400 550301226 550299577 0.000000e+00 2337.0
7 TraesCS4A01G334300 chr5D 83.056 1623 186 42 770 2343 550374641 550373059 0.000000e+00 1391.0
8 TraesCS4A01G334300 chr5D 84.935 1394 158 28 770 2149 550402714 550401359 0.000000e+00 1363.0
9 TraesCS4A01G334300 chr5D 90.000 510 34 13 1 506 550301731 550301235 0.000000e+00 643.0
10 TraesCS4A01G334300 chr5D 88.043 184 8 8 2712 2882 550299082 550298900 3.760000e-49 206.0
11 TraesCS4A01G334300 chr5D 100.000 31 0 0 2649 2679 550299184 550299154 1.120000e-04 58.4
12 TraesCS4A01G334300 chr5D 100.000 31 0 0 265 295 550374807 550374777 1.120000e-04 58.4
13 TraesCS4A01G334300 chr5B 92.154 1657 89 14 770 2400 702479565 702477924 0.000000e+00 2302.0
14 TraesCS4A01G334300 chr5B 85.446 1436 173 23 770 2181 702552818 702551395 0.000000e+00 1461.0
15 TraesCS4A01G334300 chr5B 82.734 1668 192 47 770 2391 702558064 702556447 0.000000e+00 1397.0
16 TraesCS4A01G334300 chr5B 90.934 364 21 10 147 506 702479929 702479574 2.010000e-131 479.0
17 TraesCS4A01G334300 chr5B 83.557 298 32 7 2395 2679 702477899 702477606 2.200000e-66 263.0
18 TraesCS4A01G334300 chr5B 86.486 185 10 7 2712 2882 702477513 702477330 3.790000e-44 189.0
19 TraesCS4A01G334300 chr5B 93.258 89 6 0 15 103 702480014 702479926 6.480000e-27 132.0
20 TraesCS4A01G334300 chr5B 100.000 31 0 0 265 295 702552984 702552954 1.120000e-04 58.4
21 TraesCS4A01G334300 chr5A 97.318 261 6 1 504 764 546521295 546521554 2.640000e-120 442.0
22 TraesCS4A01G334300 chr5A 94.361 266 14 1 504 769 179967861 179968125 9.610000e-110 407.0
23 TraesCS4A01G334300 chr5A 93.985 266 15 1 504 769 151650528 151650792 4.470000e-108 401.0
24 TraesCS4A01G334300 chr1A 94.737 266 13 1 504 769 92312443 92312179 2.070000e-111 412.0
25 TraesCS4A01G334300 chr1A 94.361 266 14 1 504 769 369171727 369171991 9.610000e-110 407.0
26 TraesCS4A01G334300 chr7B 95.019 261 12 1 504 764 124540350 124540609 2.670000e-110 409.0
27 TraesCS4A01G334300 chr2A 94.361 266 14 1 504 769 589517532 589517268 9.610000e-110 407.0


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 TraesCS4A01G334300 chr4A 617359412 617362293 2881 False 5323.000000 5323 100.000000 1 2882 1 chr4A.!!$F6 2881
1 TraesCS4A01G334300 chr4A 617281366 617282778 1412 False 1567.000000 1567 86.886000 770 2175 1 chr4A.!!$F3 1405
2 TraesCS4A01G334300 chr4A 617288824 617290442 1618 False 1502.000000 1502 83.998000 770 2343 1 chr4A.!!$F4 1573
3 TraesCS4A01G334300 chr4A 617348893 617350550 1657 False 1496.000000 1496 83.532000 770 2388 1 chr4A.!!$F5 1618
4 TraesCS4A01G334300 chr5D 550401359 550402714 1355 True 1363.000000 1363 84.935000 770 2149 1 chr5D.!!$R1 1379
5 TraesCS4A01G334300 chr5D 550298900 550301731 2831 True 811.100000 2337 92.630500 1 2882 4 chr5D.!!$R2 2881
6 TraesCS4A01G334300 chr5D 550373059 550374807 1748 True 724.700000 1391 91.528000 265 2343 2 chr5D.!!$R3 2078
7 TraesCS4A01G334300 chr5B 702551395 702558064 6669 True 972.133333 1461 89.393333 265 2391 3 chr5B.!!$R2 2126
8 TraesCS4A01G334300 chr5B 702477330 702480014 2684 True 673.000000 2302 89.277800 15 2882 5 chr5B.!!$R1 2867

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
144 193 0.109179 GATGCACATGCCGCAAGAAA 60.109 50.0 13.76 0.0 43.84 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 7327 0.839277 ATCGTCCCTTCCATGCATGA 59.161 50.0 28.31 11.26 0.0 3.07 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
54 55 3.357203 CCTAGACTAGAACCAGAGTGCA 58.643 50.000 11.27 0.00 0.00 4.57
103 152 3.465990 GGTTAAACCCTAGGTCGCC 57.534 57.895 8.29 0.00 33.12 5.54
104 153 0.460811 GGTTAAACCCTAGGTCGCCG 60.461 60.000 8.29 0.00 33.12 6.46
105 154 1.086067 GTTAAACCCTAGGTCGCCGC 61.086 60.000 8.29 0.00 33.12 6.53
106 155 2.242797 TTAAACCCTAGGTCGCCGCC 62.243 60.000 8.29 0.00 33.12 6.13
129 178 4.811761 GCGGTGTTTCGGCGATGC 62.812 66.667 11.76 7.39 33.07 3.91
130 179 3.418913 CGGTGTTTCGGCGATGCA 61.419 61.111 11.76 10.27 0.00 3.96
131 180 2.175811 GGTGTTTCGGCGATGCAC 59.824 61.111 25.75 25.75 0.00 4.57
132 181 2.612567 GGTGTTTCGGCGATGCACA 61.613 57.895 30.68 22.47 0.00 4.57
133 182 1.501741 GTGTTTCGGCGATGCACAT 59.498 52.632 27.51 0.00 0.00 3.21
134 183 0.794229 GTGTTTCGGCGATGCACATG 60.794 55.000 27.51 0.00 0.00 3.21
135 184 1.869132 GTTTCGGCGATGCACATGC 60.869 57.895 11.76 0.00 42.50 4.06
136 185 3.050166 TTTCGGCGATGCACATGCC 62.050 57.895 11.76 14.11 45.39 4.40
140 189 4.479542 GCGATGCACATGCCGCAA 62.480 61.111 18.52 0.00 46.05 4.85
141 190 2.277692 CGATGCACATGCCGCAAG 60.278 61.111 13.76 7.99 43.84 4.01
142 191 2.752939 CGATGCACATGCCGCAAGA 61.753 57.895 13.76 0.00 43.84 3.02
143 192 1.507630 GATGCACATGCCGCAAGAA 59.492 52.632 13.76 0.00 43.84 2.52
144 193 0.109179 GATGCACATGCCGCAAGAAA 60.109 50.000 13.76 0.00 43.84 2.52
145 194 0.388907 ATGCACATGCCGCAAGAAAC 60.389 50.000 13.76 0.00 43.84 2.78
161 210 4.537135 AGAAACTCGCTAATCCAAGTCA 57.463 40.909 0.00 0.00 0.00 3.41
217 267 5.063564 GCCAGAAGATTAACTTAACTCGGTG 59.936 44.000 0.00 0.00 39.13 4.94
224 274 6.653320 AGATTAACTTAACTCGGTGAAATGCA 59.347 34.615 0.00 0.00 0.00 3.96
225 275 4.749245 AACTTAACTCGGTGAAATGCAG 57.251 40.909 0.00 0.00 0.00 4.41
226 276 3.074412 ACTTAACTCGGTGAAATGCAGG 58.926 45.455 0.00 0.00 0.00 4.85
227 277 3.244422 ACTTAACTCGGTGAAATGCAGGA 60.244 43.478 0.00 0.00 0.00 3.86
228 278 2.496899 AACTCGGTGAAATGCAGGAT 57.503 45.000 0.00 0.00 0.00 3.24
229 279 2.029838 ACTCGGTGAAATGCAGGATC 57.970 50.000 0.00 0.00 0.00 3.36
231 281 0.461870 TCGGTGAAATGCAGGATCCG 60.462 55.000 5.98 11.88 34.69 4.18
232 282 1.439353 CGGTGAAATGCAGGATCCGG 61.439 60.000 7.64 7.64 31.04 5.14
233 283 0.394352 GGTGAAATGCAGGATCCGGT 60.394 55.000 13.75 0.00 0.00 5.28
234 284 1.017387 GTGAAATGCAGGATCCGGTC 58.983 55.000 13.75 6.57 0.00 4.79
242 292 2.441532 GGATCCGGTCCGAGTCCA 60.442 66.667 22.54 0.88 37.23 4.02
243 293 2.491022 GGATCCGGTCCGAGTCCAG 61.491 68.421 22.54 3.78 37.23 3.86
245 295 0.465097 GATCCGGTCCGAGTCCAGTA 60.465 60.000 14.39 0.00 0.00 2.74
246 296 0.750911 ATCCGGTCCGAGTCCAGTAC 60.751 60.000 14.39 0.00 0.00 2.73
247 297 2.758089 CCGGTCCGAGTCCAGTACG 61.758 68.421 14.39 0.00 0.00 3.67
248 298 2.037136 CGGTCCGAGTCCAGTACGT 61.037 63.158 4.91 0.00 0.00 3.57
249 299 0.740868 CGGTCCGAGTCCAGTACGTA 60.741 60.000 4.91 0.00 0.00 3.57
250 300 0.729690 GGTCCGAGTCCAGTACGTAC 59.270 60.000 18.10 18.10 0.00 3.67
435 514 4.307432 TCTCTGTTTAGTGCTGTGCTAAC 58.693 43.478 0.00 0.00 0.00 2.34
438 517 3.138304 TGTTTAGTGCTGTGCTAACTGG 58.862 45.455 0.00 0.00 0.00 4.00
506 585 3.130164 TGCATGGCAATTGCGTATTTACT 59.870 39.130 23.48 0.00 43.10 2.24
507 586 3.730715 GCATGGCAATTGCGTATTTACTC 59.269 43.478 23.48 7.40 43.26 2.59
508 587 4.290155 CATGGCAATTGCGTATTTACTCC 58.710 43.478 23.48 6.69 43.26 3.85
511 590 3.003378 GGCAATTGCGTATTTACTCCCTC 59.997 47.826 23.48 1.22 43.26 4.30
513 592 2.589798 TTGCGTATTTACTCCCTCCG 57.410 50.000 0.00 0.00 0.00 4.63
514 593 1.477553 TGCGTATTTACTCCCTCCGT 58.522 50.000 0.00 0.00 0.00 4.69
515 594 1.406539 TGCGTATTTACTCCCTCCGTC 59.593 52.381 0.00 0.00 0.00 4.79
516 595 1.269465 GCGTATTTACTCCCTCCGTCC 60.269 57.143 0.00 0.00 0.00 4.79
517 596 2.026641 CGTATTTACTCCCTCCGTCCA 58.973 52.381 0.00 0.00 0.00 4.02
518 597 2.626743 CGTATTTACTCCCTCCGTCCAT 59.373 50.000 0.00 0.00 0.00 3.41
519 598 3.822735 CGTATTTACTCCCTCCGTCCATA 59.177 47.826 0.00 0.00 0.00 2.74
520 599 4.279169 CGTATTTACTCCCTCCGTCCATAA 59.721 45.833 0.00 0.00 0.00 1.90
521 600 5.221303 CGTATTTACTCCCTCCGTCCATAAA 60.221 44.000 0.00 0.00 0.00 1.40
522 601 5.906772 ATTTACTCCCTCCGTCCATAAAT 57.093 39.130 0.00 0.00 0.00 1.40
523 602 7.309377 CGTATTTACTCCCTCCGTCCATAAATA 60.309 40.741 0.00 0.00 0.00 1.40
524 603 6.811634 TTTACTCCCTCCGTCCATAAATAA 57.188 37.500 0.00 0.00 0.00 1.40
525 604 4.957684 ACTCCCTCCGTCCATAAATAAG 57.042 45.455 0.00 0.00 0.00 1.73
526 605 4.296056 ACTCCCTCCGTCCATAAATAAGT 58.704 43.478 0.00 0.00 0.00 2.24
527 606 4.101119 ACTCCCTCCGTCCATAAATAAGTG 59.899 45.833 0.00 0.00 0.00 3.16
528 607 4.035112 TCCCTCCGTCCATAAATAAGTGT 58.965 43.478 0.00 0.00 0.00 3.55
529 608 4.127171 CCCTCCGTCCATAAATAAGTGTG 58.873 47.826 0.00 0.00 0.00 3.82
530 609 3.560068 CCTCCGTCCATAAATAAGTGTGC 59.440 47.826 0.00 0.00 0.00 4.57
531 610 4.442706 CTCCGTCCATAAATAAGTGTGCT 58.557 43.478 0.00 0.00 0.00 4.40
532 611 4.839121 TCCGTCCATAAATAAGTGTGCTT 58.161 39.130 0.00 0.00 38.66 3.91
533 612 4.873827 TCCGTCCATAAATAAGTGTGCTTC 59.126 41.667 0.00 0.00 36.22 3.86
534 613 4.876107 CCGTCCATAAATAAGTGTGCTTCT 59.124 41.667 0.00 0.00 36.22 2.85
535 614 6.046593 CCGTCCATAAATAAGTGTGCTTCTA 58.953 40.000 0.00 0.00 36.22 2.10
536 615 6.537301 CCGTCCATAAATAAGTGTGCTTCTAA 59.463 38.462 0.00 0.00 36.22 2.10
537 616 7.399523 CGTCCATAAATAAGTGTGCTTCTAAC 58.600 38.462 0.00 0.00 36.22 2.34
538 617 7.277981 CGTCCATAAATAAGTGTGCTTCTAACT 59.722 37.037 0.00 0.00 36.22 2.24
539 618 8.947115 GTCCATAAATAAGTGTGCTTCTAACTT 58.053 33.333 0.00 0.00 37.82 2.66
540 619 9.515226 TCCATAAATAAGTGTGCTTCTAACTTT 57.485 29.630 0.00 0.00 35.77 2.66
545 624 8.451908 AATAAGTGTGCTTCTAACTTTTGTCT 57.548 30.769 0.00 0.00 35.77 3.41
546 625 6.759497 AAGTGTGCTTCTAACTTTTGTCTT 57.241 33.333 0.00 0.00 29.98 3.01
547 626 7.859325 AAGTGTGCTTCTAACTTTTGTCTTA 57.141 32.000 0.00 0.00 29.98 2.10
548 627 7.859325 AGTGTGCTTCTAACTTTTGTCTTAA 57.141 32.000 0.00 0.00 0.00 1.85
549 628 7.920738 AGTGTGCTTCTAACTTTTGTCTTAAG 58.079 34.615 0.00 0.00 0.00 1.85
550 629 7.553044 AGTGTGCTTCTAACTTTTGTCTTAAGT 59.447 33.333 1.63 0.00 37.43 2.24
551 630 7.851472 GTGTGCTTCTAACTTTTGTCTTAAGTC 59.149 37.037 1.63 0.00 34.88 3.01
552 631 7.551262 TGTGCTTCTAACTTTTGTCTTAAGTCA 59.449 33.333 1.63 0.00 34.88 3.41
553 632 8.395633 GTGCTTCTAACTTTTGTCTTAAGTCAA 58.604 33.333 10.54 10.54 34.88 3.18
554 633 8.952278 TGCTTCTAACTTTTGTCTTAAGTCAAA 58.048 29.630 19.60 19.60 34.88 2.69
555 634 9.783256 GCTTCTAACTTTTGTCTTAAGTCAAAA 57.217 29.630 27.41 27.41 39.44 2.44
606 685 6.909550 AAAAAGGTGGCAGTATTTATGACA 57.090 33.333 0.00 0.00 31.73 3.58
616 695 9.899661 TGGCAGTATTTATGACACTAAATTAGT 57.100 29.630 0.00 0.00 40.28 2.24
736 815 9.788960 AAAACTTTGACTTAGAACAAAAGCTAG 57.211 29.630 0.00 0.00 35.95 3.42
737 816 8.732746 AACTTTGACTTAGAACAAAAGCTAGA 57.267 30.769 0.00 0.00 35.95 2.43
738 817 8.732746 ACTTTGACTTAGAACAAAAGCTAGAA 57.267 30.769 0.00 0.00 35.95 2.10
739 818 8.831550 ACTTTGACTTAGAACAAAAGCTAGAAG 58.168 33.333 0.00 0.00 35.95 2.85
740 819 8.732746 TTTGACTTAGAACAAAAGCTAGAAGT 57.267 30.769 0.00 0.00 33.90 3.01
741 820 9.826574 TTTGACTTAGAACAAAAGCTAGAAGTA 57.173 29.630 0.00 0.00 33.90 2.24
742 821 8.813643 TGACTTAGAACAAAAGCTAGAAGTAC 57.186 34.615 0.00 0.00 0.00 2.73
743 822 8.418662 TGACTTAGAACAAAAGCTAGAAGTACA 58.581 33.333 0.00 0.00 0.00 2.90
744 823 8.590719 ACTTAGAACAAAAGCTAGAAGTACAC 57.409 34.615 0.00 0.00 0.00 2.90
745 824 8.422566 ACTTAGAACAAAAGCTAGAAGTACACT 58.577 33.333 0.00 0.00 0.00 3.55
746 825 9.262358 CTTAGAACAAAAGCTAGAAGTACACTT 57.738 33.333 0.00 0.00 39.23 3.16
749 828 9.780186 AGAACAAAAGCTAGAAGTACACTTATT 57.220 29.630 0.00 0.00 36.11 1.40
751 830 8.240883 ACAAAAGCTAGAAGTACACTTATTCG 57.759 34.615 0.00 0.00 36.11 3.34
752 831 7.871463 ACAAAAGCTAGAAGTACACTTATTCGT 59.129 33.333 0.00 0.00 36.11 3.85
753 832 7.813852 AAAGCTAGAAGTACACTTATTCGTG 57.186 36.000 0.00 0.00 40.67 4.35
754 833 5.892568 AGCTAGAAGTACACTTATTCGTGG 58.107 41.667 0.00 0.00 39.19 4.94
755 834 5.651139 AGCTAGAAGTACACTTATTCGTGGA 59.349 40.000 0.00 0.00 39.19 4.02
756 835 5.742926 GCTAGAAGTACACTTATTCGTGGAC 59.257 44.000 0.00 0.00 46.77 4.02
759 838 3.492421 GTACACTTATTCGTGGACGGA 57.508 47.619 0.00 0.00 38.82 4.69
760 839 2.649331 ACACTTATTCGTGGACGGAG 57.351 50.000 0.00 0.00 39.19 4.63
761 840 1.203994 ACACTTATTCGTGGACGGAGG 59.796 52.381 0.00 0.00 39.19 4.30
762 841 0.822164 ACTTATTCGTGGACGGAGGG 59.178 55.000 0.00 0.00 40.29 4.30
763 842 1.108776 CTTATTCGTGGACGGAGGGA 58.891 55.000 0.00 0.00 40.29 4.20
764 843 1.479323 CTTATTCGTGGACGGAGGGAA 59.521 52.381 0.00 0.00 40.29 3.97
765 844 1.784358 TATTCGTGGACGGAGGGAAT 58.216 50.000 0.00 0.00 40.29 3.01
766 845 1.784358 ATTCGTGGACGGAGGGAATA 58.216 50.000 0.00 0.00 40.29 1.75
767 846 0.819582 TTCGTGGACGGAGGGAATAC 59.180 55.000 0.00 0.00 40.29 1.89
768 847 0.323633 TCGTGGACGGAGGGAATACA 60.324 55.000 0.00 0.00 40.29 2.29
812 899 8.999220 TCTAGATCGATATATACAGTCAACGT 57.001 34.615 0.00 0.00 0.00 3.99
854 941 9.868277 GATCATAGGAAACTTCTCATCGAATAT 57.132 33.333 0.00 0.00 43.67 1.28
858 945 7.604657 AGGAAACTTCTCATCGAATATACCT 57.395 36.000 0.00 0.00 37.44 3.08
860 947 7.928706 AGGAAACTTCTCATCGAATATACCTTG 59.071 37.037 0.00 0.00 37.44 3.61
862 949 5.542779 ACTTCTCATCGAATATACCTTGCC 58.457 41.667 0.00 0.00 0.00 4.52
866 953 4.385825 TCATCGAATATACCTTGCCAACC 58.614 43.478 0.00 0.00 0.00 3.77
868 955 2.775384 TCGAATATACCTTGCCAACCCT 59.225 45.455 0.00 0.00 0.00 4.34
869 956 3.139077 CGAATATACCTTGCCAACCCTC 58.861 50.000 0.00 0.00 0.00 4.30
871 958 4.390264 GAATATACCTTGCCAACCCTCTC 58.610 47.826 0.00 0.00 0.00 3.20
872 959 1.972588 ATACCTTGCCAACCCTCTCT 58.027 50.000 0.00 0.00 0.00 3.10
958 1053 2.632763 AGCCAACCCTCTCTACTCTT 57.367 50.000 0.00 0.00 0.00 2.85
984 1086 0.673985 CAACTCGTCTCACTCCACCA 59.326 55.000 0.00 0.00 0.00 4.17
985 1087 0.962489 AACTCGTCTCACTCCACCAG 59.038 55.000 0.00 0.00 0.00 4.00
986 1088 1.214062 CTCGTCTCACTCCACCAGC 59.786 63.158 0.00 0.00 0.00 4.85
989 1091 1.214062 GTCTCACTCCACCAGCTCG 59.786 63.158 0.00 0.00 0.00 5.03
990 1092 1.074951 TCTCACTCCACCAGCTCGA 59.925 57.895 0.00 0.00 0.00 4.04
1056 1158 2.229792 GTTGTCCTTGTGAGCATTGGA 58.770 47.619 0.00 0.00 0.00 3.53
1091 1193 1.479573 AAGGATGCTCGCTAGCTCCTA 60.480 52.381 22.57 2.47 46.69 2.94
1116 1221 2.367648 TCAGGTGGTGGTGGTGGT 60.368 61.111 0.00 0.00 0.00 4.16
1280 1385 4.467084 TGGCGGCGGAGGATCAAC 62.467 66.667 9.78 0.00 36.25 3.18
1338 1443 1.532078 TGGTAGCGGTGTGAGTGGA 60.532 57.895 0.00 0.00 0.00 4.02
1350 1455 3.069980 GAGTGGATCTGCGTCGGCT 62.070 63.158 0.00 0.00 40.82 5.52
1869 7223 1.306997 ATCCGGATCTGGTGGTGGT 60.307 57.895 20.32 0.00 0.00 4.16
1901 7255 7.206687 CACTAAATTACCCTTTGTTGAGCAAA 58.793 34.615 0.00 0.00 44.05 3.68
1904 7258 4.911514 TTACCCTTTGTTGAGCAAACTC 57.088 40.909 4.22 0.00 41.68 3.01
1972 7327 5.775686 CATTTCACATCAAAGGACACATGT 58.224 37.500 0.00 0.00 0.00 3.21
2083 7448 4.157656 GCAGGTTTGTGCCAATAGACATAA 59.842 41.667 0.00 0.00 37.49 1.90
2084 7449 5.163519 GCAGGTTTGTGCCAATAGACATAAT 60.164 40.000 0.00 0.00 37.49 1.28
2085 7450 6.039270 GCAGGTTTGTGCCAATAGACATAATA 59.961 38.462 0.00 0.00 37.49 0.98
2086 7451 7.416213 GCAGGTTTGTGCCAATAGACATAATAA 60.416 37.037 0.00 0.00 37.49 1.40
2087 7452 8.632679 CAGGTTTGTGCCAATAGACATAATAAT 58.367 33.333 0.00 0.00 0.00 1.28
2131 7497 8.948631 TGTAGCCTTTTCTATCTCAAATAGTG 57.051 34.615 0.00 0.00 0.00 2.74
2178 7553 6.310956 TGTTTGCAATGTCTTTCTGAGTTTTG 59.689 34.615 0.00 0.00 0.00 2.44
2250 7643 4.965119 GGTCTATACCAACCTTGCTTTG 57.035 45.455 0.00 0.00 45.98 2.77
2269 7662 8.593945 TGCTTTGTATTTGAAATATTCCCTCT 57.406 30.769 0.43 0.00 0.00 3.69
2279 7673 8.561738 TTGAAATATTCCCTCTGTGTTAGTTC 57.438 34.615 0.00 0.00 0.00 3.01
2393 7796 6.581542 GGACCTATCGTAGAAAATGTCATACG 59.418 42.308 0.00 0.00 43.58 3.06
2401 7834 6.887763 CGTAGAAAATGTCATACGAAAGAACG 59.112 38.462 0.00 0.00 42.66 3.95
2418 7851 6.737254 AAGAACGGTAACATGTAAATGAGG 57.263 37.500 0.00 0.00 0.00 3.86
2436 7869 0.322187 GGTTTGGGCAGTGTCGGTAT 60.322 55.000 0.00 0.00 0.00 2.73
2439 7872 1.268066 TTGGGCAGTGTCGGTATACA 58.732 50.000 5.01 0.00 0.00 2.29
2457 7890 9.374960 CGGTATACACGACTTTAAATCTAGTAC 57.625 37.037 5.01 0.00 0.00 2.73
2461 7902 7.138692 ACACGACTTTAAATCTAGTACTCGT 57.861 36.000 0.00 0.00 0.00 4.18
2463 7904 7.118971 ACACGACTTTAAATCTAGTACTCGTCT 59.881 37.037 0.00 0.00 0.00 4.18
2472 7913 5.654317 TCTAGTACTCGTCTATCAAAGCG 57.346 43.478 0.00 0.00 0.00 4.68
2480 7921 3.932710 TCGTCTATCAAAGCGCAAAGAAT 59.067 39.130 11.47 0.00 0.00 2.40
2492 7933 4.081087 AGCGCAAAGAATAAGAGGTTCCTA 60.081 41.667 11.47 0.00 0.00 2.94
2501 7942 7.001073 AGAATAAGAGGTTCCTAATGAATGCC 58.999 38.462 0.00 0.00 34.90 4.40
2525 7966 5.010516 CGGCCCCAATTTATTATCATGTCAA 59.989 40.000 0.00 0.00 0.00 3.18
2529 7970 7.687592 GCCCCAATTTATTATCATGTCAAGCTT 60.688 37.037 0.00 0.00 0.00 3.74
2545 7986 8.001881 TGTCAAGCTTTTGGTTCTTATTACAA 57.998 30.769 0.00 0.00 38.17 2.41
2546 7987 8.470805 TGTCAAGCTTTTGGTTCTTATTACAAA 58.529 29.630 0.00 0.00 38.17 2.83
2584 8025 4.265073 GGTCTTGGCTGATACATCTTGTT 58.735 43.478 0.00 0.00 0.00 2.83
2591 8032 7.734924 TGGCTGATACATCTTGTTATTGATC 57.265 36.000 0.00 0.00 0.00 2.92
2597 8038 9.423061 TGATACATCTTGTTATTGATCGGTATG 57.577 33.333 0.00 0.00 0.00 2.39
2607 8048 7.180229 TGTTATTGATCGGTATGGGAGATGTAT 59.820 37.037 0.00 0.00 0.00 2.29
2608 8049 5.661056 TTGATCGGTATGGGAGATGTATC 57.339 43.478 0.00 0.00 0.00 2.24
2609 8050 4.935578 TGATCGGTATGGGAGATGTATCT 58.064 43.478 0.00 0.00 40.50 1.98
2610 8051 5.333581 TGATCGGTATGGGAGATGTATCTT 58.666 41.667 0.00 0.00 37.25 2.40
2611 8052 5.185828 TGATCGGTATGGGAGATGTATCTTG 59.814 44.000 0.00 0.00 37.25 3.02
2612 8053 3.258372 TCGGTATGGGAGATGTATCTTGC 59.742 47.826 0.00 0.00 37.25 4.01
2613 8054 3.006859 CGGTATGGGAGATGTATCTTGCA 59.993 47.826 0.00 0.00 37.25 4.08
2615 8056 2.602257 TGGGAGATGTATCTTGCACG 57.398 50.000 0.00 0.00 37.25 5.34
2617 8058 2.700371 TGGGAGATGTATCTTGCACGAT 59.300 45.455 10.84 10.84 37.25 3.73
2620 8061 2.478134 GAGATGTATCTTGCACGATGGC 59.522 50.000 15.50 8.84 37.25 4.40
2628 8069 2.246841 TGCACGATGGCAAACAGAG 58.753 52.632 0.00 0.00 41.65 3.35
2629 8070 1.236616 TGCACGATGGCAAACAGAGG 61.237 55.000 0.00 0.00 41.65 3.69
2631 8072 1.238439 CACGATGGCAAACAGAGGTT 58.762 50.000 0.00 0.00 39.43 3.50
2699 8246 4.522114 TGTTTGGTCAGAAACATCTCACA 58.478 39.130 0.00 0.00 40.18 3.58
2700 8247 4.576053 TGTTTGGTCAGAAACATCTCACAG 59.424 41.667 0.00 0.00 40.18 3.66
2702 8249 4.263018 TGGTCAGAAACATCTCACAGAG 57.737 45.455 0.00 0.00 0.00 3.35
2703 8250 3.643320 TGGTCAGAAACATCTCACAGAGT 59.357 43.478 0.00 0.00 0.00 3.24
2704 8251 4.101585 TGGTCAGAAACATCTCACAGAGTT 59.898 41.667 0.00 0.00 0.00 3.01
2752 8359 0.790814 GGAAAAGCGACGTGAGGAAG 59.209 55.000 0.00 0.00 0.00 3.46
2754 8361 1.721926 GAAAAGCGACGTGAGGAAGAG 59.278 52.381 0.00 0.00 0.00 2.85
2771 8378 4.397417 GGAAGAGGATCATGTTTGGTTCAG 59.603 45.833 0.00 0.00 37.82 3.02
2781 8388 4.149511 TGTTTGGTTCAGACACATCTCA 57.850 40.909 0.00 0.00 30.42 3.27
2805 8413 6.929049 CACAGGTAACACTGATTACAAGAAGA 59.071 38.462 0.00 0.00 40.97 2.87
2832 8440 5.477291 TCAACAAAGGAGAGAACTAGATCGT 59.523 40.000 0.00 0.00 0.00 3.73
2836 8444 6.015350 ACAAAGGAGAGAACTAGATCGTTTCA 60.015 38.462 0.00 0.00 29.93 2.69
2848 8469 4.626042 AGATCGTTTCATGTGCTATCTCC 58.374 43.478 0.00 0.00 0.00 3.71
2873 8494 1.898472 ACATGCCTCTATCCATCTCCG 59.102 52.381 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.863049 CATGCAAATTTACAACAAGATAAGTCC 58.137 33.333 0.00 0.00 0.00 3.85
8 9 6.183360 GCGCATGCAAATTTACAACAAGATAA 60.183 34.615 19.57 0.00 42.15 1.75
14 15 2.064762 GGCGCATGCAAATTTACAACA 58.935 42.857 19.57 0.00 45.35 3.33
20 21 2.094675 AGTCTAGGCGCATGCAAATTT 58.905 42.857 19.57 0.40 45.35 1.82
54 55 4.632153 ACAACTTTGACTGAGCGAGTAAT 58.368 39.130 0.00 0.00 33.83 1.89
111 160 4.499023 CATCGCCGAAACACCGCG 62.499 66.667 0.00 0.00 0.00 6.46
112 161 4.811761 GCATCGCCGAAACACCGC 62.812 66.667 0.00 0.00 0.00 5.68
113 162 3.418913 TGCATCGCCGAAACACCG 61.419 61.111 0.00 0.00 0.00 4.94
114 163 1.922135 ATGTGCATCGCCGAAACACC 61.922 55.000 16.92 3.87 0.00 4.16
115 164 0.794229 CATGTGCATCGCCGAAACAC 60.794 55.000 13.91 13.91 0.00 3.32
116 165 1.501292 CATGTGCATCGCCGAAACA 59.499 52.632 0.00 0.00 0.00 2.83
117 166 1.869132 GCATGTGCATCGCCGAAAC 60.869 57.895 0.00 0.00 41.59 2.78
118 167 2.484662 GCATGTGCATCGCCGAAA 59.515 55.556 0.00 0.00 41.59 3.46
119 168 3.507924 GGCATGTGCATCGCCGAA 61.508 61.111 7.36 0.00 44.36 4.30
123 172 4.479542 TTGCGGCATGTGCATCGC 62.480 61.111 17.62 17.62 46.63 4.58
124 173 2.255994 TTCTTGCGGCATGTGCATCG 62.256 55.000 14.19 9.53 42.84 3.84
125 174 0.109179 TTTCTTGCGGCATGTGCATC 60.109 50.000 14.19 0.00 42.84 3.91
126 175 0.388907 GTTTCTTGCGGCATGTGCAT 60.389 50.000 14.19 0.00 42.84 3.96
127 176 1.007502 GTTTCTTGCGGCATGTGCA 60.008 52.632 14.53 10.20 44.36 4.57
128 177 0.730494 GAGTTTCTTGCGGCATGTGC 60.730 55.000 14.53 5.27 41.14 4.57
129 178 0.453282 CGAGTTTCTTGCGGCATGTG 60.453 55.000 14.53 4.14 0.00 3.21
130 179 1.868997 CGAGTTTCTTGCGGCATGT 59.131 52.632 14.53 0.00 0.00 3.21
131 180 1.512734 GCGAGTTTCTTGCGGCATG 60.513 57.895 2.28 6.50 30.77 4.06
132 181 0.391130 TAGCGAGTTTCTTGCGGCAT 60.391 50.000 2.28 0.00 44.91 4.40
133 182 0.601576 TTAGCGAGTTTCTTGCGGCA 60.602 50.000 0.00 0.00 44.91 5.69
134 183 0.727398 ATTAGCGAGTTTCTTGCGGC 59.273 50.000 0.00 0.00 44.91 6.53
135 184 1.327764 GGATTAGCGAGTTTCTTGCGG 59.672 52.381 3.74 0.00 44.91 5.69
136 185 1.999735 TGGATTAGCGAGTTTCTTGCG 59.000 47.619 3.74 0.00 44.91 4.85
137 186 3.437049 ACTTGGATTAGCGAGTTTCTTGC 59.563 43.478 1.15 1.15 40.93 4.01
138 187 4.690748 TGACTTGGATTAGCGAGTTTCTTG 59.309 41.667 0.00 0.00 0.00 3.02
139 188 4.894784 TGACTTGGATTAGCGAGTTTCTT 58.105 39.130 0.00 0.00 0.00 2.52
140 189 4.537135 TGACTTGGATTAGCGAGTTTCT 57.463 40.909 0.00 0.00 0.00 2.52
141 190 5.049680 TGTTTGACTTGGATTAGCGAGTTTC 60.050 40.000 0.00 0.00 0.00 2.78
142 191 4.819630 TGTTTGACTTGGATTAGCGAGTTT 59.180 37.500 0.00 0.00 0.00 2.66
143 192 4.213482 GTGTTTGACTTGGATTAGCGAGTT 59.787 41.667 0.00 0.00 0.00 3.01
144 193 3.746492 GTGTTTGACTTGGATTAGCGAGT 59.254 43.478 0.00 0.00 0.00 4.18
145 194 3.745975 TGTGTTTGACTTGGATTAGCGAG 59.254 43.478 0.00 0.00 0.00 5.03
217 267 1.160329 CGGACCGGATCCTGCATTTC 61.160 60.000 9.46 0.00 46.69 2.17
224 274 2.123812 GGACTCGGACCGGATCCT 60.124 66.667 22.92 0.00 46.69 3.24
225 275 2.441532 TGGACTCGGACCGGATCC 60.442 66.667 23.25 23.25 45.20 3.36
226 276 0.465097 TACTGGACTCGGACCGGATC 60.465 60.000 15.25 11.67 37.25 3.36
227 277 0.750911 GTACTGGACTCGGACCGGAT 60.751 60.000 15.25 1.69 37.25 4.18
228 278 1.377725 GTACTGGACTCGGACCGGA 60.378 63.158 15.25 0.00 37.25 5.14
229 279 2.758089 CGTACTGGACTCGGACCGG 61.758 68.421 15.25 0.00 39.46 5.28
231 281 0.729690 GTACGTACTGGACTCGGACC 59.270 60.000 18.47 0.00 33.03 4.46
232 282 0.371645 CGTACGTACTGGACTCGGAC 59.628 60.000 22.55 0.00 35.42 4.79
233 283 0.037326 ACGTACGTACTGGACTCGGA 60.037 55.000 21.41 0.00 0.00 4.55
234 284 1.324736 GTACGTACGTACTGGACTCGG 59.675 57.143 38.40 7.67 45.30 4.63
235 285 1.007011 CGTACGTACGTACTGGACTCG 60.007 57.143 40.05 28.08 46.22 4.18
236 286 2.703190 CGTACGTACGTACTGGACTC 57.297 55.000 40.05 22.55 46.22 3.36
305 355 1.964552 CATCAAGATGGAGGCCTCAC 58.035 55.000 33.29 22.31 35.24 3.51
406 485 3.055819 CAGCACTAAACAGAGAAGGCCTA 60.056 47.826 5.16 0.00 0.00 3.93
435 514 6.461110 AATTTATTGATTGAGGCAGACCAG 57.539 37.500 0.00 0.00 39.06 4.00
438 517 8.125448 GTCAGTAATTTATTGATTGAGGCAGAC 58.875 37.037 5.10 0.00 0.00 3.51
498 577 5.796424 TTATGGACGGAGGGAGTAAATAC 57.204 43.478 0.00 0.00 0.00 1.89
506 585 4.035112 ACACTTATTTATGGACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
507 586 4.127171 CACACTTATTTATGGACGGAGGG 58.873 47.826 0.00 0.00 0.00 4.30
508 587 3.560068 GCACACTTATTTATGGACGGAGG 59.440 47.826 0.00 0.00 0.00 4.30
511 590 4.876107 AGAAGCACACTTATTTATGGACGG 59.124 41.667 0.00 0.00 35.82 4.79
513 592 8.494016 AGTTAGAAGCACACTTATTTATGGAC 57.506 34.615 0.00 0.00 35.82 4.02
514 593 9.515226 AAAGTTAGAAGCACACTTATTTATGGA 57.485 29.630 0.00 0.00 35.82 3.41
519 598 8.903820 AGACAAAAGTTAGAAGCACACTTATTT 58.096 29.630 0.00 0.00 35.82 1.40
520 599 8.451908 AGACAAAAGTTAGAAGCACACTTATT 57.548 30.769 0.00 0.00 35.82 1.40
521 600 8.451908 AAGACAAAAGTTAGAAGCACACTTAT 57.548 30.769 0.00 0.00 35.82 1.73
522 601 7.859325 AAGACAAAAGTTAGAAGCACACTTA 57.141 32.000 0.00 0.00 35.82 2.24
523 602 6.759497 AAGACAAAAGTTAGAAGCACACTT 57.241 33.333 0.00 0.00 39.43 3.16
524 603 7.553044 ACTTAAGACAAAAGTTAGAAGCACACT 59.447 33.333 10.09 0.00 33.39 3.55
525 604 7.694886 ACTTAAGACAAAAGTTAGAAGCACAC 58.305 34.615 10.09 0.00 33.39 3.82
526 605 7.551262 TGACTTAAGACAAAAGTTAGAAGCACA 59.449 33.333 10.09 0.00 37.31 4.57
527 606 7.916552 TGACTTAAGACAAAAGTTAGAAGCAC 58.083 34.615 10.09 0.00 37.31 4.40
528 607 8.500753 TTGACTTAAGACAAAAGTTAGAAGCA 57.499 30.769 16.33 0.00 37.31 3.91
529 608 9.783256 TTTTGACTTAAGACAAAAGTTAGAAGC 57.217 29.630 29.42 0.00 41.83 3.86
583 662 6.493458 AGTGTCATAAATACTGCCACCTTTTT 59.507 34.615 0.00 0.00 0.00 1.94
584 663 6.010219 AGTGTCATAAATACTGCCACCTTTT 58.990 36.000 0.00 0.00 0.00 2.27
585 664 5.570320 AGTGTCATAAATACTGCCACCTTT 58.430 37.500 0.00 0.00 0.00 3.11
586 665 5.179452 AGTGTCATAAATACTGCCACCTT 57.821 39.130 0.00 0.00 0.00 3.50
587 666 4.844349 AGTGTCATAAATACTGCCACCT 57.156 40.909 0.00 0.00 0.00 4.00
588 667 6.995511 TTTAGTGTCATAAATACTGCCACC 57.004 37.500 0.00 0.00 31.02 4.61
590 669 9.899661 ACTAATTTAGTGTCATAAATACTGCCA 57.100 29.630 8.27 0.00 37.69 4.92
614 693 9.436957 ACAATTCAAAACGAATCTAGTGATACT 57.563 29.630 0.00 0.00 43.83 2.12
710 789 9.788960 CTAGCTTTTGTTCTAAGTCAAAGTTTT 57.211 29.630 0.00 0.00 35.47 2.43
711 790 9.174166 TCTAGCTTTTGTTCTAAGTCAAAGTTT 57.826 29.630 0.00 0.00 35.47 2.66
712 791 8.732746 TCTAGCTTTTGTTCTAAGTCAAAGTT 57.267 30.769 0.00 0.00 35.47 2.66
713 792 8.732746 TTCTAGCTTTTGTTCTAAGTCAAAGT 57.267 30.769 0.00 0.00 35.47 2.66
714 793 8.831550 ACTTCTAGCTTTTGTTCTAAGTCAAAG 58.168 33.333 0.00 0.00 35.47 2.77
715 794 8.732746 ACTTCTAGCTTTTGTTCTAAGTCAAA 57.267 30.769 0.00 0.00 32.75 2.69
716 795 9.257651 GTACTTCTAGCTTTTGTTCTAAGTCAA 57.742 33.333 0.00 0.00 0.00 3.18
717 796 8.418662 TGTACTTCTAGCTTTTGTTCTAAGTCA 58.581 33.333 0.00 0.00 0.00 3.41
718 797 8.701540 GTGTACTTCTAGCTTTTGTTCTAAGTC 58.298 37.037 0.00 0.00 0.00 3.01
719 798 8.422566 AGTGTACTTCTAGCTTTTGTTCTAAGT 58.577 33.333 0.00 0.00 0.00 2.24
720 799 8.819643 AGTGTACTTCTAGCTTTTGTTCTAAG 57.180 34.615 0.00 0.00 0.00 2.18
723 802 9.780186 AATAAGTGTACTTCTAGCTTTTGTTCT 57.220 29.630 0.00 0.00 37.40 3.01
725 804 8.709646 CGAATAAGTGTACTTCTAGCTTTTGTT 58.290 33.333 0.00 0.00 37.40 2.83
726 805 7.871463 ACGAATAAGTGTACTTCTAGCTTTTGT 59.129 33.333 0.00 0.00 37.40 2.83
727 806 8.162880 CACGAATAAGTGTACTTCTAGCTTTTG 58.837 37.037 0.00 0.00 37.40 2.44
728 807 7.331193 CCACGAATAAGTGTACTTCTAGCTTTT 59.669 37.037 0.00 0.00 40.33 2.27
729 808 6.812160 CCACGAATAAGTGTACTTCTAGCTTT 59.188 38.462 0.00 0.00 40.33 3.51
730 809 6.152323 TCCACGAATAAGTGTACTTCTAGCTT 59.848 38.462 0.00 0.00 40.33 3.74
731 810 5.651139 TCCACGAATAAGTGTACTTCTAGCT 59.349 40.000 0.00 0.00 40.33 3.32
732 811 5.742926 GTCCACGAATAAGTGTACTTCTAGC 59.257 44.000 0.00 0.00 40.33 3.42
733 812 5.964168 CGTCCACGAATAAGTGTACTTCTAG 59.036 44.000 0.00 0.00 43.02 2.43
734 813 5.163723 CCGTCCACGAATAAGTGTACTTCTA 60.164 44.000 0.00 0.00 43.02 2.10
735 814 4.380233 CCGTCCACGAATAAGTGTACTTCT 60.380 45.833 0.00 0.00 43.02 2.85
736 815 3.855950 CCGTCCACGAATAAGTGTACTTC 59.144 47.826 0.00 0.00 43.02 3.01
737 816 3.507233 TCCGTCCACGAATAAGTGTACTT 59.493 43.478 0.00 2.51 43.02 2.24
738 817 3.084039 TCCGTCCACGAATAAGTGTACT 58.916 45.455 0.00 0.00 43.02 2.73
739 818 3.432782 CTCCGTCCACGAATAAGTGTAC 58.567 50.000 0.00 0.00 43.02 2.90
740 819 2.424601 CCTCCGTCCACGAATAAGTGTA 59.575 50.000 0.00 0.00 43.02 2.90
741 820 1.203994 CCTCCGTCCACGAATAAGTGT 59.796 52.381 0.00 0.00 43.02 3.55
742 821 1.470979 CCCTCCGTCCACGAATAAGTG 60.471 57.143 0.00 0.00 43.02 3.16
743 822 0.822164 CCCTCCGTCCACGAATAAGT 59.178 55.000 0.00 0.00 43.02 2.24
744 823 1.108776 TCCCTCCGTCCACGAATAAG 58.891 55.000 0.00 0.00 43.02 1.73
745 824 1.559368 TTCCCTCCGTCCACGAATAA 58.441 50.000 0.00 0.00 43.02 1.40
746 825 1.784358 ATTCCCTCCGTCCACGAATA 58.216 50.000 0.00 0.00 43.02 1.75
747 826 1.411612 GTATTCCCTCCGTCCACGAAT 59.588 52.381 0.00 0.00 43.02 3.34
748 827 0.819582 GTATTCCCTCCGTCCACGAA 59.180 55.000 0.00 0.00 43.02 3.85
749 828 0.323633 TGTATTCCCTCCGTCCACGA 60.324 55.000 0.00 0.00 43.02 4.35
750 829 0.750850 ATGTATTCCCTCCGTCCACG 59.249 55.000 0.00 0.00 39.44 4.94
751 830 2.561569 CAATGTATTCCCTCCGTCCAC 58.438 52.381 0.00 0.00 0.00 4.02
752 831 1.134220 GCAATGTATTCCCTCCGTCCA 60.134 52.381 0.00 0.00 0.00 4.02
753 832 1.141053 AGCAATGTATTCCCTCCGTCC 59.859 52.381 0.00 0.00 0.00 4.79
754 833 2.622064 AGCAATGTATTCCCTCCGTC 57.378 50.000 0.00 0.00 0.00 4.79
755 834 2.224305 GCTAGCAATGTATTCCCTCCGT 60.224 50.000 10.63 0.00 0.00 4.69
756 835 2.417719 GCTAGCAATGTATTCCCTCCG 58.582 52.381 10.63 0.00 0.00 4.63
757 836 2.417719 CGCTAGCAATGTATTCCCTCC 58.582 52.381 16.45 0.00 0.00 4.30
758 837 2.417719 CCGCTAGCAATGTATTCCCTC 58.582 52.381 16.45 0.00 0.00 4.30
759 838 1.543429 GCCGCTAGCAATGTATTCCCT 60.543 52.381 16.45 0.00 42.97 4.20
760 839 0.875059 GCCGCTAGCAATGTATTCCC 59.125 55.000 16.45 0.00 42.97 3.97
812 899 8.664669 TCCTATGATCATAATGCCAGTAGTAA 57.335 34.615 16.08 0.00 0.00 2.24
854 941 0.984230 CAGAGAGGGTTGGCAAGGTA 59.016 55.000 0.00 0.00 0.00 3.08
855 942 1.763770 CAGAGAGGGTTGGCAAGGT 59.236 57.895 0.00 0.00 0.00 3.50
858 945 1.376466 GAGCAGAGAGGGTTGGCAA 59.624 57.895 0.00 0.00 0.00 4.52
860 947 1.965754 ATCGAGCAGAGAGGGTTGGC 61.966 60.000 0.00 0.00 0.00 4.52
862 949 0.248825 CGATCGAGCAGAGAGGGTTG 60.249 60.000 10.26 0.00 0.00 3.77
866 953 0.521291 GATCCGATCGAGCAGAGAGG 59.479 60.000 18.66 0.00 0.00 3.69
914 1009 4.896482 GGTATATATAGTGCTGGAGGGGAG 59.104 50.000 0.00 0.00 0.00 4.30
958 1053 0.601558 GTGAGACGAGTTGGGTGCTA 59.398 55.000 0.00 0.00 0.00 3.49
984 1086 1.741732 GCCATTGTGAGTGATCGAGCT 60.742 52.381 0.90 0.00 0.00 4.09
985 1087 0.654683 GCCATTGTGAGTGATCGAGC 59.345 55.000 0.00 0.00 0.00 5.03
986 1088 2.306341 AGCCATTGTGAGTGATCGAG 57.694 50.000 0.00 0.00 0.00 4.04
989 1091 2.939103 GTGGTAGCCATTGTGAGTGATC 59.061 50.000 0.00 0.00 35.28 2.92
990 1092 2.356125 GGTGGTAGCCATTGTGAGTGAT 60.356 50.000 0.00 0.00 35.28 3.06
1035 1137 1.069022 CCAATGCTCACAAGGACAACG 60.069 52.381 0.00 0.00 0.00 4.10
1091 1193 2.822637 CCACCACCTGAGGCACTGT 61.823 63.158 0.00 0.00 41.55 3.55
1280 1385 2.735772 CCAGACCCAGATCCACCCG 61.736 68.421 0.00 0.00 0.00 5.28
1338 1443 1.454111 ACTAGGAGCCGACGCAGAT 60.454 57.895 0.00 0.00 37.52 2.90
1350 1455 4.041464 TGGCATAACCATTACCACTAGGA 58.959 43.478 0.00 0.00 46.36 2.94
1508 1613 3.291584 TCAGAGTAGCTGGTACCATCAG 58.708 50.000 16.75 6.78 44.98 2.90
1684 1789 3.116091 CAACACTTGGGCCTTCAGT 57.884 52.632 4.53 0.90 0.00 3.41
1869 7223 7.034967 ACAAAGGGTAATTTAGTGGTATCCA 57.965 36.000 0.00 0.00 0.00 3.41
1904 7258 7.421530 AAAATACATATCGAGGTCCAATTCG 57.578 36.000 0.00 0.00 38.13 3.34
1972 7327 0.839277 ATCGTCCCTTCCATGCATGA 59.161 50.000 28.31 11.26 0.00 3.07
2038 7393 5.422214 CCTGAACAGGTGTAGGAGTTAAT 57.578 43.478 12.21 0.00 43.61 1.40
2131 7497 2.877043 ATGGCGGAATCAAGCAATTC 57.123 45.000 2.74 0.00 35.35 2.17
2178 7553 6.373779 CACAAGAAACATACTTGGACATGTC 58.626 40.000 17.91 17.91 45.92 3.06
2269 7662 2.600470 AACGAACCCGAACTAACACA 57.400 45.000 0.00 0.00 39.50 3.72
2276 7670 4.996062 TGATTCTAAAACGAACCCGAAC 57.004 40.909 0.00 0.00 39.50 3.95
2279 7673 7.524065 ACTATTTTGATTCTAAAACGAACCCG 58.476 34.615 0.00 0.00 42.50 5.28
2393 7796 7.094933 ACCTCATTTACATGTTACCGTTCTTTC 60.095 37.037 2.30 0.00 0.00 2.62
2401 7834 5.623596 GCCCAAACCTCATTTACATGTTACC 60.624 44.000 2.30 0.00 0.00 2.85
2418 7851 2.004733 GTATACCGACACTGCCCAAAC 58.995 52.381 0.00 0.00 0.00 2.93
2436 7869 8.256611 ACGAGTACTAGATTTAAAGTCGTGTA 57.743 34.615 10.22 3.86 42.73 2.90
2439 7872 7.608308 AGACGAGTACTAGATTTAAAGTCGT 57.392 36.000 10.22 4.11 45.86 4.34
2440 7873 9.796062 GATAGACGAGTACTAGATTTAAAGTCG 57.204 37.037 10.22 0.73 38.60 4.18
2457 7890 2.923655 TCTTTGCGCTTTGATAGACGAG 59.076 45.455 9.73 0.00 0.00 4.18
2461 7902 6.258727 CCTCTTATTCTTTGCGCTTTGATAGA 59.741 38.462 9.73 0.00 0.00 1.98
2463 7904 5.880332 ACCTCTTATTCTTTGCGCTTTGATA 59.120 36.000 9.73 0.00 0.00 2.15
2472 7913 7.865706 TCATTAGGAACCTCTTATTCTTTGC 57.134 36.000 0.00 0.00 0.00 3.68
2480 7921 4.444306 CCGGCATTCATTAGGAACCTCTTA 60.444 45.833 0.00 0.00 38.60 2.10
2492 7933 0.982326 AATTGGGGCCGGCATTCATT 60.982 50.000 30.85 17.31 0.00 2.57
2501 7942 4.522405 TGACATGATAATAAATTGGGGCCG 59.478 41.667 0.00 0.00 0.00 6.13
2545 7986 6.051717 CCAAGACCGATCACTGAGAATAATT 58.948 40.000 0.00 0.00 0.00 1.40
2546 7987 5.605534 CCAAGACCGATCACTGAGAATAAT 58.394 41.667 0.00 0.00 0.00 1.28
2550 7991 1.066858 GCCAAGACCGATCACTGAGAA 60.067 52.381 0.00 0.00 0.00 2.87
2554 7995 0.247460 TCAGCCAAGACCGATCACTG 59.753 55.000 0.00 0.00 0.00 3.66
2584 8025 7.126061 AGATACATCTCCCATACCGATCAATA 58.874 38.462 0.00 0.00 29.30 1.90
2591 8032 3.006859 TGCAAGATACATCTCCCATACCG 59.993 47.826 0.00 0.00 35.76 4.02
2597 8038 2.890808 TCGTGCAAGATACATCTCCC 57.109 50.000 0.00 0.00 35.76 4.30
2610 8051 1.236616 CCTCTGTTTGCCATCGTGCA 61.237 55.000 0.00 0.00 40.07 4.57
2611 8052 1.237285 ACCTCTGTTTGCCATCGTGC 61.237 55.000 0.00 0.00 0.00 5.34
2612 8053 1.197721 GAACCTCTGTTTGCCATCGTG 59.802 52.381 0.00 0.00 33.97 4.35
2613 8054 1.072331 AGAACCTCTGTTTGCCATCGT 59.928 47.619 0.00 0.00 33.97 3.73
2615 8056 3.064900 AGAGAACCTCTGTTTGCCATC 57.935 47.619 0.00 0.00 39.62 3.51
2617 8058 2.172505 TCAAGAGAACCTCTGTTTGCCA 59.827 45.455 0.00 0.00 40.28 4.92
2620 8061 8.327941 TCATATTTCAAGAGAACCTCTGTTTG 57.672 34.615 0.00 0.00 40.28 2.93
2624 8065 6.111382 TGCTCATATTTCAAGAGAACCTCTG 58.889 40.000 0.00 0.00 40.28 3.35
2625 8066 6.305272 TGCTCATATTTCAAGAGAACCTCT 57.695 37.500 0.00 0.00 43.37 3.69
2626 8067 7.712639 TGTATGCTCATATTTCAAGAGAACCTC 59.287 37.037 0.00 0.00 32.39 3.85
2628 8069 7.712639 TCTGTATGCTCATATTTCAAGAGAACC 59.287 37.037 0.00 0.00 32.39 3.62
2629 8070 8.654230 TCTGTATGCTCATATTTCAAGAGAAC 57.346 34.615 0.00 0.00 32.39 3.01
2631 8072 8.016301 ACTCTGTATGCTCATATTTCAAGAGA 57.984 34.615 15.35 0.00 0.00 3.10
2679 8226 5.034852 TCTGTGAGATGTTTCTGACCAAA 57.965 39.130 0.00 0.00 35.45 3.28
2680 8227 4.101585 ACTCTGTGAGATGTTTCTGACCAA 59.898 41.667 1.25 0.00 35.45 3.67
2681 8228 3.643320 ACTCTGTGAGATGTTTCTGACCA 59.357 43.478 1.25 0.00 35.45 4.02
2682 8229 4.264460 ACTCTGTGAGATGTTTCTGACC 57.736 45.455 1.25 0.00 35.45 4.02
2683 8230 6.364706 CACTAACTCTGTGAGATGTTTCTGAC 59.635 42.308 1.25 0.00 36.71 3.51
2685 8232 6.450545 TCACTAACTCTGTGAGATGTTTCTG 58.549 40.000 1.25 0.00 39.23 3.02
2687 8234 7.095439 CCTTTCACTAACTCTGTGAGATGTTTC 60.095 40.741 1.25 0.00 43.98 2.78
2689 8236 6.042093 TCCTTTCACTAACTCTGTGAGATGTT 59.958 38.462 1.25 0.00 43.98 2.71
2690 8237 5.540337 TCCTTTCACTAACTCTGTGAGATGT 59.460 40.000 1.25 0.00 43.98 3.06
2691 8238 6.030548 TCCTTTCACTAACTCTGTGAGATG 57.969 41.667 1.25 0.00 43.98 2.90
2692 8239 6.212388 ACATCCTTTCACTAACTCTGTGAGAT 59.788 38.462 1.25 0.00 43.98 2.75
2693 8240 5.540337 ACATCCTTTCACTAACTCTGTGAGA 59.460 40.000 1.25 0.00 43.98 3.27
2694 8241 5.788450 ACATCCTTTCACTAACTCTGTGAG 58.212 41.667 0.00 0.00 43.98 3.51
2695 8242 5.540337 AGACATCCTTTCACTAACTCTGTGA 59.460 40.000 0.00 0.00 41.94 3.58
2696 8243 5.788450 AGACATCCTTTCACTAACTCTGTG 58.212 41.667 0.00 0.00 36.82 3.66
2697 8244 6.426646 AAGACATCCTTTCACTAACTCTGT 57.573 37.500 0.00 0.00 0.00 3.41
2739 8346 0.248702 GATCCTCTTCCTCACGTCGC 60.249 60.000 0.00 0.00 0.00 5.19
2752 8359 4.154918 GTGTCTGAACCAAACATGATCCTC 59.845 45.833 0.00 0.00 0.00 3.71
2754 8361 3.820467 TGTGTCTGAACCAAACATGATCC 59.180 43.478 0.00 0.00 0.00 3.36
2771 8378 3.990469 CAGTGTTACCTGTGAGATGTGTC 59.010 47.826 0.00 0.00 0.00 3.67
2781 8388 7.062749 TCTTCTTGTAATCAGTGTTACCTGT 57.937 36.000 10.92 0.00 34.43 4.00
2805 8413 7.547370 CGATCTAGTTCTCTCCTTTGTTGATTT 59.453 37.037 0.00 0.00 0.00 2.17
2832 8440 2.239402 TGCCTGGAGATAGCACATGAAA 59.761 45.455 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.