Multiple sequence alignment - TraesCS6A01G403900

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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 TraesCS6A01G403900 chr6A 100.000 4394 0 0 1 4394 610934962 610930569 0.000000e+00 8115.0
1 TraesCS6A01G403900 chr6A 82.702 2457 378 27 1013 3436 610946031 610943589 0.000000e+00 2139.0
2 TraesCS6A01G403900 chr6B 90.656 3264 247 25 250 3465 708182973 708179720 0.000000e+00 4285.0
3 TraesCS6A01G403900 chr6B 89.241 2333 217 24 1025 3342 708099123 708096810 0.000000e+00 2887.0
4 TraesCS6A01G403900 chr6B 88.018 2387 244 27 1019 3391 708105588 708103230 0.000000e+00 2785.0
5 TraesCS6A01G403900 chr6B 87.723 1572 187 4 1001 2571 708073897 708072331 0.000000e+00 1829.0
6 TraesCS6A01G403900 chr6B 84.343 1635 237 16 998 2623 708067339 708065715 0.000000e+00 1583.0
7 TraesCS6A01G403900 chr6B 88.671 865 87 8 2613 3473 708072186 708071329 0.000000e+00 1044.0
8 TraesCS6A01G403900 chr6B 84.894 801 109 11 2670 3465 708055680 708054887 0.000000e+00 798.0
9 TraesCS6A01G403900 chr6B 92.545 389 27 2 463 851 708074643 708074257 1.380000e-154 556.0
10 TraesCS6A01G403900 chr6B 87.419 461 32 12 1 436 708075093 708074634 1.410000e-139 507.0
11 TraesCS6A01G403900 chr6B 82.599 454 58 12 3806 4256 708107773 708107338 8.920000e-102 381.0
12 TraesCS6A01G403900 chr6B 87.879 231 24 4 3951 4180 708070709 708070482 7.240000e-68 268.0
13 TraesCS6A01G403900 chr6B 84.211 228 28 7 3642 3862 708047949 708047723 9.570000e-52 215.0
14 TraesCS6A01G403900 chr6B 79.638 221 20 11 360 557 708106310 708106092 7.670000e-28 135.0
15 TraesCS6A01G403900 chr6D 90.285 2347 204 16 1127 3465 464348431 464346101 0.000000e+00 3049.0
16 TraesCS6A01G403900 chr6D 81.931 2413 377 44 1013 3391 464433088 464430701 0.000000e+00 1986.0
17 TraesCS6A01G403900 chr6D 84.921 1638 236 9 982 2615 464405628 464403998 0.000000e+00 1646.0
18 TraesCS6A01G403900 chr6D 86.290 1043 95 22 2372 3391 464398260 464397243 0.000000e+00 1090.0
19 TraesCS6A01G403900 chr6D 87.690 658 68 13 3560 4207 464345876 464345222 0.000000e+00 754.0
20 TraesCS6A01G403900 chr6D 82.959 845 96 35 2644 3465 464403307 464402488 0.000000e+00 719.0
21 TraesCS6A01G403900 chr6D 84.874 238 23 9 4023 4256 464400790 464400562 1.230000e-55 228.0
22 TraesCS6A01G403900 chr6D 87.209 86 11 0 344 429 464433698 464433613 1.010000e-16 99.0
23 TraesCS6A01G403900 chr7A 76.468 1993 377 69 1046 2986 732936366 732934414 0.000000e+00 998.0
24 TraesCS6A01G403900 chr7B 77.342 1580 319 34 1001 2559 750148596 750150157 0.000000e+00 898.0
25 TraesCS6A01G403900 chr7B 75.706 177 35 5 3137 3309 750220088 750220260 1.010000e-11 82.4
26 TraesCS6A01G403900 chr2B 75.308 2029 403 74 1001 2985 118323088 118325062 0.000000e+00 881.0


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 TraesCS6A01G403900 chr6A 610930569 610934962 4393 True 8115.000000 8115 100.000000 1 4394 1 chr6A.!!$R1 4393
1 TraesCS6A01G403900 chr6A 610943589 610946031 2442 True 2139.000000 2139 82.702000 1013 3436 1 chr6A.!!$R2 2423
2 TraesCS6A01G403900 chr6B 708179720 708182973 3253 True 4285.000000 4285 90.656000 250 3465 1 chr6B.!!$R4 3215
3 TraesCS6A01G403900 chr6B 708096810 708099123 2313 True 2887.000000 2887 89.241000 1025 3342 1 chr6B.!!$R3 2317
4 TraesCS6A01G403900 chr6B 708103230 708107773 4543 True 1100.333333 2785 83.418333 360 4256 3 chr6B.!!$R6 3896
5 TraesCS6A01G403900 chr6B 708065715 708075093 9378 True 964.500000 1829 88.096667 1 4180 6 chr6B.!!$R5 4179
6 TraesCS6A01G403900 chr6B 708054887 708055680 793 True 798.000000 798 84.894000 2670 3465 1 chr6B.!!$R2 795
7 TraesCS6A01G403900 chr6D 464345222 464348431 3209 True 1901.500000 3049 88.987500 1127 4207 2 chr6D.!!$R1 3080
8 TraesCS6A01G403900 chr6D 464430701 464433698 2997 True 1042.500000 1986 84.570000 344 3391 2 chr6D.!!$R3 3047
9 TraesCS6A01G403900 chr6D 464397243 464405628 8385 True 920.750000 1646 84.761000 982 4256 4 chr6D.!!$R2 3274
10 TraesCS6A01G403900 chr7A 732934414 732936366 1952 True 998.000000 998 76.468000 1046 2986 1 chr7A.!!$R1 1940
11 TraesCS6A01G403900 chr7B 750148596 750150157 1561 False 898.000000 898 77.342000 1001 2559 1 chr7B.!!$F1 1558
12 TraesCS6A01G403900 chr2B 118323088 118325062 1974 False 881.000000 881 75.308000 1001 2985 1 chr2B.!!$F1 1984

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
931 2177 0.181587 TTTTTGCTCCCGTCAGGTCA 59.818 50.0 0.0 0.00 36.75 4.02 F
2179 3663 0.036732 ACAAGCATGGACCGATGTGT 59.963 50.0 0.0 1.99 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 3682 1.131883 GCATCATCTGTGTGTCCTTGC 59.868 52.381 0.00 0.0 0.00 4.01 R
3915 11789 0.037697 CCGTACAGTTACTGCAGCCA 60.038 55.000 15.27 0.0 34.37 4.75 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
42 43 2.432146 TGCTCACCATGGATCTGTCTAC 59.568 50.000 21.47 0.00 0.00 2.59
78 79 0.319900 GAGCTGACTGAACGAAGGCA 60.320 55.000 0.00 0.00 32.97 4.75
83 88 1.495584 GACTGAACGAAGGCACGCAA 61.496 55.000 0.00 0.00 36.70 4.85
131 155 1.760192 AATCCATCAACAGAGCAGGC 58.240 50.000 0.00 0.00 0.00 4.85
142 166 3.080319 ACAGAGCAGGCTTTTCATTCTC 58.920 45.455 0.00 0.00 0.00 2.87
157 181 5.073311 TCATTCTCGAGTTTCCTTAGTGG 57.927 43.478 13.13 0.00 37.10 4.00
169 193 4.178956 TCCTTAGTGGAAGCACCTTTTT 57.821 40.909 1.91 0.00 42.94 1.94
182 206 5.052481 AGCACCTTTTTCTTCTTTGATTGC 58.948 37.500 0.00 0.00 0.00 3.56
193 217 0.887247 TTTGATTGCGTGTGGATGGG 59.113 50.000 0.00 0.00 0.00 4.00
230 254 1.270971 GCATATTTGCCTGCACAACG 58.729 50.000 0.00 0.00 43.38 4.10
241 265 1.876263 GCACAACGTTGCCACCAAC 60.876 57.895 27.61 6.15 46.15 3.77
282 306 5.523916 CACATCCAACGGGTAGATTTCTAAG 59.476 44.000 0.00 0.00 34.93 2.18
320 344 9.169592 GTGGAGCCTCTAGTAATAGTAAGATAG 57.830 40.741 0.00 0.00 0.00 2.08
435 1542 3.719268 TCAGCCACCATAATGTCTTGT 57.281 42.857 0.00 0.00 0.00 3.16
472 1604 5.640357 TGTTCATTAAGATGGGTACGTTGTC 59.360 40.000 0.00 0.00 33.93 3.18
473 1605 4.426416 TCATTAAGATGGGTACGTTGTCG 58.574 43.478 0.00 0.00 37.19 4.35
563 1695 3.827876 ACCATGACTCATTCACATTTGCA 59.172 39.130 0.00 0.00 36.92 4.08
649 1855 6.334989 TGGACTTTACACATAACATACGAGG 58.665 40.000 0.00 0.00 0.00 4.63
836 2058 1.219124 GAAGGCATCACGCTCCAGA 59.781 57.895 0.00 0.00 41.91 3.86
861 2083 0.343372 ATCCCCCTGGCAAGTCTCTA 59.657 55.000 0.00 0.00 0.00 2.43
869 2091 3.318839 CCTGGCAAGTCTCTATCTCTCTG 59.681 52.174 0.00 0.00 0.00 3.35
876 2098 5.552870 AGTCTCTATCTCTCTGTCTCTCC 57.447 47.826 0.00 0.00 0.00 3.71
881 2106 5.722290 TCTATCTCTCTGTCTCTCCCTCTA 58.278 45.833 0.00 0.00 0.00 2.43
887 2126 4.724293 TCTCTGTCTCTCCCTCTATCTGAA 59.276 45.833 0.00 0.00 0.00 3.02
900 2146 2.486472 ATCTGAACTGAACTGGCCTG 57.514 50.000 8.29 8.29 0.00 4.85
907 2153 0.673022 CTGAACTGGCCTGCTCACTC 60.673 60.000 11.33 1.41 0.00 3.51
908 2154 1.372683 GAACTGGCCTGCTCACTCA 59.627 57.895 9.95 0.00 0.00 3.41
931 2177 0.181587 TTTTTGCTCCCGTCAGGTCA 59.818 50.000 0.00 0.00 36.75 4.02
973 2220 8.967918 GCTGGAAGGTAATTAAAAAGAGGTTAT 58.032 33.333 0.00 0.00 0.00 1.89
999 2431 2.481952 CTGCTTGCTGTTAGAGTGAACC 59.518 50.000 0.00 0.00 0.00 3.62
1105 2537 4.038402 CACTTGAAGTGGCCTTCTTGAAAT 59.962 41.667 17.27 4.08 46.07 2.17
1423 2861 9.837525 GCTTGAATATTGATTTGGATAGTGATC 57.162 33.333 0.00 0.00 0.00 2.92
1741 3225 1.799403 TGAGTGACGAAGACGAGTCTC 59.201 52.381 6.19 0.00 39.39 3.36
1774 3258 4.445453 TGACATGAATGAGTATGAGGTGC 58.555 43.478 0.00 0.00 0.00 5.01
1920 3404 5.813383 TGTAGTAGAGTACTGCTAACCACT 58.187 41.667 0.00 1.07 41.48 4.00
1974 3458 2.233431 GCCAACCCATGTTCATGCTTTA 59.767 45.455 7.21 0.00 30.42 1.85
2002 3486 7.174080 AGAGTTTAGATGAAGAGAAAAGTTGGC 59.826 37.037 0.00 0.00 0.00 4.52
2103 3587 6.319141 AGAAAGCTTACAAGGAAATGTGAC 57.681 37.500 0.00 0.00 34.75 3.67
2179 3663 0.036732 ACAAGCATGGACCGATGTGT 59.963 50.000 0.00 1.99 0.00 3.72
2198 3682 2.884012 TGTTACTGTGTTGGCCATCAAG 59.116 45.455 18.06 17.65 35.80 3.02
2304 3788 0.889186 TTGCTGCTTTTCCCGAGGAC 60.889 55.000 0.00 0.00 0.00 3.85
2439 3923 4.032703 TCAAAGAAGCTTTGTGCAAGTC 57.967 40.909 16.70 0.00 45.94 3.01
2465 3949 9.715123 CGTTCAAACAAGCATTATACATGAATA 57.285 29.630 0.00 0.00 0.00 1.75
2544 10009 5.556915 ACGAAAGATGGTTTCCTTGATGTA 58.443 37.500 0.00 0.00 0.00 2.29
2712 10351 6.124340 AGTTGGTGCATCATCATCTCATAAA 58.876 36.000 10.56 0.00 0.00 1.40
2715 10354 5.887035 TGGTGCATCATCATCTCATAAACAA 59.113 36.000 0.00 0.00 0.00 2.83
2739 10378 9.922305 CAAATATTCTATCGTTCTTCTTTCCAC 57.078 33.333 0.00 0.00 0.00 4.02
2793 10435 4.946157 CCTAATCTCAGAGCATTGTTTGGT 59.054 41.667 0.00 0.00 39.22 3.67
2794 10436 4.778534 AATCTCAGAGCATTGTTTGGTG 57.221 40.909 0.00 0.00 35.82 4.17
2875 10532 3.701532 ACTCGAGCCTAGAGAATTTCG 57.298 47.619 13.61 0.00 38.97 3.46
2929 10586 2.093764 CACCTGAGGTTGAGAGGATGTC 60.094 54.545 0.00 0.00 31.02 3.06
3013 10694 7.023575 GCCAAATTTATATGTATCAAGCTCCG 58.976 38.462 0.00 0.00 0.00 4.63
3109 10790 0.314302 CCTACGGGAGCTTCGTATGG 59.686 60.000 18.85 17.37 41.39 2.74
3115 10796 3.579066 GAGCTTCGTATGGCTCCTC 57.421 57.895 3.87 0.00 46.32 3.71
3116 10797 0.747255 GAGCTTCGTATGGCTCCTCA 59.253 55.000 3.87 0.00 46.32 3.86
3135 10816 4.827835 CCTCATGATGATGAAGCTGGAAAT 59.172 41.667 0.00 0.00 38.17 2.17
3153 10834 0.541998 ATGACCCGATGCCGATCCTA 60.542 55.000 0.00 0.00 38.22 2.94
3188 10869 0.664761 CTTGTGGTGCTGGAGTTGTG 59.335 55.000 0.00 0.00 0.00 3.33
3191 10872 1.148273 TGGTGCTGGAGTTGTGGTC 59.852 57.895 0.00 0.00 0.00 4.02
3203 10884 3.340928 AGTTGTGGTCTTATAAACCCGC 58.659 45.455 11.79 9.36 35.84 6.13
3235 10916 2.526110 GTGCCCAAGGGTTCCCTT 59.474 61.111 16.55 16.55 46.38 3.95
3244 10926 0.555769 AGGGTTCCCTTGTCTGCAAA 59.444 50.000 4.31 0.00 33.73 3.68
3265 10947 3.644884 AGTTACGACTTGAGGACTGTG 57.355 47.619 0.00 0.00 29.87 3.66
3266 10948 2.957006 AGTTACGACTTGAGGACTGTGT 59.043 45.455 0.00 0.00 29.87 3.72
3376 11068 2.133281 TGGATTCTGCACCTTCCATG 57.867 50.000 3.24 0.00 33.40 3.66
3383 11075 2.413142 GCACCTTCCATGCCTCAGC 61.413 63.158 0.00 0.00 37.08 4.26
3391 11083 1.486310 TCCATGCCTCAGCTTCGTATT 59.514 47.619 0.00 0.00 40.80 1.89
3397 11089 3.117046 GCCTCAGCTTCGTATTAGTGAC 58.883 50.000 0.00 0.00 35.50 3.67
3402 11097 4.155462 TCAGCTTCGTATTAGTGACTCGTT 59.845 41.667 0.00 0.00 0.00 3.85
3405 11100 5.572126 AGCTTCGTATTAGTGACTCGTTTTC 59.428 40.000 0.00 0.00 0.00 2.29
3407 11102 6.452611 GCTTCGTATTAGTGACTCGTTTTCTG 60.453 42.308 0.00 0.00 0.00 3.02
3465 11160 3.412386 AGACACAAAGGATGCAAGGTAC 58.588 45.455 0.00 0.00 0.00 3.34
3473 11169 1.209504 GGATGCAAGGTACTGCTACCA 59.790 52.381 8.39 0.00 44.75 3.25
3474 11170 2.555199 GATGCAAGGTACTGCTACCAG 58.445 52.381 8.39 0.00 44.75 4.00
3483 11179 3.352447 CTGCTACCAGTGATGGACG 57.648 57.895 0.31 0.00 34.31 4.79
3484 11180 0.532573 CTGCTACCAGTGATGGACGT 59.467 55.000 0.31 0.00 34.31 4.34
3486 11182 0.530744 GCTACCAGTGATGGACGTGA 59.469 55.000 0.00 0.00 0.00 4.35
3488 11184 2.881074 CTACCAGTGATGGACGTGAAG 58.119 52.381 0.00 0.00 0.00 3.02
3489 11185 1.338107 ACCAGTGATGGACGTGAAGA 58.662 50.000 0.00 0.00 0.00 2.87
3490 11186 1.273606 ACCAGTGATGGACGTGAAGAG 59.726 52.381 0.00 0.00 0.00 2.85
3491 11187 1.354040 CAGTGATGGACGTGAAGAGC 58.646 55.000 0.00 0.00 0.00 4.09
3492 11188 0.969149 AGTGATGGACGTGAAGAGCA 59.031 50.000 0.00 0.00 0.00 4.26
3506 11202 6.768029 GTGAAGAGCACAAATTTTAATGCA 57.232 33.333 16.94 0.00 46.91 3.96
3507 11203 7.176285 GTGAAGAGCACAAATTTTAATGCAA 57.824 32.000 16.94 0.61 46.91 4.08
3508 11204 7.285788 GTGAAGAGCACAAATTTTAATGCAAG 58.714 34.615 16.94 0.00 46.91 4.01
3523 11321 9.657419 TTTTAATGCAAGGTACTACTAGTTACC 57.343 33.333 13.80 13.80 38.49 2.85
3526 11324 6.029346 TGCAAGGTACTACTAGTTACCAAC 57.971 41.667 20.86 12.37 38.49 3.77
3535 11333 7.104043 ACTACTAGTTACCAACGCATTATGA 57.896 36.000 0.00 0.00 36.23 2.15
3545 11343 4.154737 CCAACGCATTATGATCCTATGGTG 59.845 45.833 0.00 0.00 0.00 4.17
3546 11344 4.890158 ACGCATTATGATCCTATGGTGA 57.110 40.909 0.00 0.00 0.00 4.02
3558 11356 4.960938 TCCTATGGTGAATGCATGTCTAC 58.039 43.478 0.00 0.00 0.00 2.59
3682 11547 7.478322 ACAATTATCAGCTCATGTTGTTCATC 58.522 34.615 0.00 0.00 34.09 2.92
3696 11561 5.069648 TGTTGTTCATCTTATTTGGGCACAA 59.930 36.000 0.00 0.00 34.07 3.33
3720 11585 1.825090 TGAGCAATCACTTCCGCAAT 58.175 45.000 0.00 0.00 0.00 3.56
3750 11615 4.749598 CGCCTTGTGCAGTGATATTGTATA 59.250 41.667 0.00 0.00 41.33 1.47
3753 11618 7.080099 GCCTTGTGCAGTGATATTGTATAATG 58.920 38.462 0.00 0.00 40.77 1.90
3778 11643 8.717821 TGATTATTATTGTATCAAGTAAGGCGC 58.282 33.333 0.00 0.00 0.00 6.53
3780 11645 3.560636 ATTGTATCAAGTAAGGCGCCT 57.439 42.857 27.08 27.08 0.00 5.52
3781 11646 3.343941 TTGTATCAAGTAAGGCGCCTT 57.656 42.857 41.05 41.05 39.83 4.35
3782 11647 2.627945 TGTATCAAGTAAGGCGCCTTG 58.372 47.619 44.36 31.58 39.50 3.61
3783 11648 2.027561 TGTATCAAGTAAGGCGCCTTGT 60.028 45.455 44.36 31.00 39.25 3.16
3785 11650 1.210155 CAAGTAAGGCGCCTTGTGC 59.790 57.895 44.36 32.94 37.47 4.57
3786 11651 1.228124 AAGTAAGGCGCCTTGTGCA 60.228 52.632 44.36 26.82 41.25 4.57
3788 11653 0.609131 AGTAAGGCGCCTTGTGCAAT 60.609 50.000 44.36 25.75 41.25 3.56
3792 11657 0.527565 AGGCGCCTTGTGCAATAAAG 59.472 50.000 27.08 0.00 41.25 1.85
3793 11658 0.243636 GGCGCCTTGTGCAATAAAGT 59.756 50.000 22.15 0.00 41.25 2.66
3811 11681 4.640771 AAGTCCCTAGCTTGAATGACAA 57.359 40.909 0.00 0.00 36.97 3.18
3818 11688 6.267471 TCCCTAGCTTGAATGACAACAATTTT 59.733 34.615 0.00 0.00 34.56 1.82
3821 11691 5.916318 AGCTTGAATGACAACAATTTTGGA 58.084 33.333 0.00 0.00 34.56 3.53
3827 11697 3.791245 TGACAACAATTTTGGAACCAGC 58.209 40.909 0.00 0.00 0.00 4.85
3834 11704 1.198713 TTTTGGAACCAGCTTGGCAA 58.801 45.000 0.00 0.00 42.67 4.52
3838 11708 0.032540 GGAACCAGCTTGGCAAGTTG 59.967 55.000 30.13 30.13 42.67 3.16
3839 11709 0.746659 GAACCAGCTTGGCAAGTTGT 59.253 50.000 32.70 20.97 42.67 3.32
3912 11786 4.778579 AGTCTTGTGCTCATAGATGCATT 58.221 39.130 0.00 0.00 41.45 3.56
3914 11788 4.024218 GTCTTGTGCTCATAGATGCATTCC 60.024 45.833 0.00 0.00 41.45 3.01
3915 11789 3.851458 TGTGCTCATAGATGCATTCCT 57.149 42.857 0.00 0.00 41.45 3.36
3917 11791 2.812591 GTGCTCATAGATGCATTCCTGG 59.187 50.000 0.00 0.00 41.45 4.45
3918 11792 1.811359 GCTCATAGATGCATTCCTGGC 59.189 52.381 0.00 0.00 0.00 4.85
3919 11793 2.552591 GCTCATAGATGCATTCCTGGCT 60.553 50.000 0.00 0.00 0.00 4.75
3920 11794 3.075148 CTCATAGATGCATTCCTGGCTG 58.925 50.000 0.00 0.00 0.00 4.85
3921 11795 1.540267 CATAGATGCATTCCTGGCTGC 59.460 52.381 0.00 12.46 38.87 5.25
3924 11798 2.437449 TGCATTCCTGGCTGCAGT 59.563 55.556 16.64 0.00 43.11 4.40
3925 11799 1.684629 TGCATTCCTGGCTGCAGTA 59.315 52.632 16.64 4.03 43.11 2.74
3926 11800 0.038021 TGCATTCCTGGCTGCAGTAA 59.962 50.000 16.64 2.75 43.11 2.24
3927 11801 0.453390 GCATTCCTGGCTGCAGTAAC 59.547 55.000 16.64 6.91 38.28 2.50
3928 11802 1.952367 GCATTCCTGGCTGCAGTAACT 60.952 52.381 16.64 0.00 38.28 2.24
3929 11803 1.741706 CATTCCTGGCTGCAGTAACTG 59.258 52.381 16.64 9.87 34.12 3.16
3930 11804 0.764890 TTCCTGGCTGCAGTAACTGT 59.235 50.000 16.64 0.00 33.43 3.55
3931 11805 1.639722 TCCTGGCTGCAGTAACTGTA 58.360 50.000 16.64 0.00 33.43 2.74
3932 11806 1.275291 TCCTGGCTGCAGTAACTGTAC 59.725 52.381 16.64 0.00 33.43 2.90
3933 11807 1.350193 CTGGCTGCAGTAACTGTACG 58.650 55.000 16.64 0.00 35.20 3.67
3934 11808 0.037697 TGGCTGCAGTAACTGTACGG 60.038 55.000 16.64 0.00 35.20 4.02
3935 11809 0.037605 GGCTGCAGTAACTGTACGGT 60.038 55.000 16.64 0.04 35.20 4.83
3936 11810 1.203052 GGCTGCAGTAACTGTACGGTA 59.797 52.381 16.64 0.00 35.20 4.02
3937 11811 2.527100 GCTGCAGTAACTGTACGGTAG 58.473 52.381 16.64 1.59 39.79 3.18
3938 11812 2.094854 GCTGCAGTAACTGTACGGTAGT 60.095 50.000 16.64 0.00 39.28 2.73
3939 11813 3.499048 CTGCAGTAACTGTACGGTAGTG 58.501 50.000 8.00 9.98 34.83 2.74
3940 11814 3.148412 TGCAGTAACTGTACGGTAGTGA 58.852 45.455 8.00 0.00 35.20 3.41
3941 11815 3.569277 TGCAGTAACTGTACGGTAGTGAA 59.431 43.478 8.00 1.20 35.20 3.18
3942 11816 4.219070 TGCAGTAACTGTACGGTAGTGAAT 59.781 41.667 8.00 0.00 35.20 2.57
3943 11817 5.415389 TGCAGTAACTGTACGGTAGTGAATA 59.585 40.000 8.00 0.00 35.20 1.75
3944 11818 5.741040 GCAGTAACTGTACGGTAGTGAATAC 59.259 44.000 8.00 5.92 35.20 1.89
3945 11819 6.623549 GCAGTAACTGTACGGTAGTGAATACA 60.624 42.308 8.00 0.00 35.20 2.29
3946 11820 6.965500 CAGTAACTGTACGGTAGTGAATACAG 59.035 42.308 8.00 8.36 46.53 2.74
3947 11821 6.881065 AGTAACTGTACGGTAGTGAATACAGA 59.119 38.462 8.00 0.00 44.81 3.41
3948 11822 6.770746 AACTGTACGGTAGTGAATACAGAT 57.229 37.500 8.00 2.81 44.81 2.90
3949 11823 6.374565 ACTGTACGGTAGTGAATACAGATC 57.625 41.667 5.26 0.00 44.81 2.75
3950 11824 5.007430 ACTGTACGGTAGTGAATACAGATCG 59.993 44.000 5.26 0.00 44.81 3.69
3951 11825 3.351020 ACGGTAGTGAATACAGATCGC 57.649 47.619 0.00 0.00 35.96 4.58
3952 11826 2.950309 ACGGTAGTGAATACAGATCGCT 59.050 45.455 0.00 0.00 40.53 4.93
3953 11827 4.132336 ACGGTAGTGAATACAGATCGCTA 58.868 43.478 0.00 0.00 38.51 4.26
3976 11884 1.546476 AGTAGCAGTTCAGGAACGGAG 59.454 52.381 14.97 7.09 45.50 4.63
3987 11895 3.325425 TCAGGAACGGAGACACCAAAATA 59.675 43.478 0.00 0.00 38.90 1.40
4020 11928 3.750130 ACTTCTGTTACTGCATCTGCTTG 59.250 43.478 3.53 0.00 42.66 4.01
4121 12030 9.823647 TCTGGAACAAAATTATCTACAGAGATC 57.176 33.333 0.00 0.00 39.05 2.75
4185 12094 2.554370 ATTTGCATGTTGCTTTGGCT 57.446 40.000 0.75 0.00 45.31 4.75
4207 12116 0.734253 GCTTCAGTCACGACTCGCAT 60.734 55.000 0.00 0.00 40.20 4.73
4208 12117 1.263776 CTTCAGTCACGACTCGCATC 58.736 55.000 0.00 0.00 40.20 3.91
4210 12119 2.202492 AGTCACGACTCGCATCGC 60.202 61.111 7.90 0.00 46.22 4.58
4211 12120 2.504026 GTCACGACTCGCATCGCA 60.504 61.111 7.90 0.00 46.22 5.10
4212 12121 2.202479 TCACGACTCGCATCGCAG 60.202 61.111 7.90 2.39 46.22 5.18
4213 12122 3.906649 CACGACTCGCATCGCAGC 61.907 66.667 7.90 0.00 46.22 5.25
4214 12123 4.419939 ACGACTCGCATCGCAGCA 62.420 61.111 7.90 0.00 46.22 4.41
4215 12124 3.614659 CGACTCGCATCGCAGCAG 61.615 66.667 0.00 0.00 34.90 4.24
4216 12125 3.922893 GACTCGCATCGCAGCAGC 61.923 66.667 0.00 0.00 37.42 5.25
4219 12128 4.765449 TCGCATCGCAGCAGCCTT 62.765 61.111 0.00 0.00 37.52 4.35
4220 12129 4.233635 CGCATCGCAGCAGCCTTC 62.234 66.667 0.00 0.00 37.52 3.46
4221 12130 3.885521 GCATCGCAGCAGCCTTCC 61.886 66.667 0.00 0.00 37.52 3.46
4222 12131 3.207669 CATCGCAGCAGCCTTCCC 61.208 66.667 0.00 0.00 37.52 3.97
4223 12132 4.496336 ATCGCAGCAGCCTTCCCC 62.496 66.667 0.00 0.00 37.52 4.81
4226 12135 4.811364 GCAGCAGCCTTCCCCTCC 62.811 72.222 0.00 0.00 33.58 4.30
4227 12136 4.479993 CAGCAGCCTTCCCCTCCG 62.480 72.222 0.00 0.00 0.00 4.63
4230 12139 4.479993 CAGCCTTCCCCTCCGCAG 62.480 72.222 0.00 0.00 0.00 5.18
4244 12153 2.899339 GCAGGAATCTCCAGCGGC 60.899 66.667 0.00 0.00 39.26 6.53
4245 12154 2.587194 CAGGAATCTCCAGCGGCG 60.587 66.667 0.51 0.51 39.61 6.46
4246 12155 3.077556 AGGAATCTCCAGCGGCGT 61.078 61.111 9.37 0.00 39.61 5.68
4247 12156 2.892425 GGAATCTCCAGCGGCGTG 60.892 66.667 9.37 5.60 36.28 5.34
4248 12157 2.892425 GAATCTCCAGCGGCGTGG 60.892 66.667 18.41 18.41 39.19 4.94
4255 12164 4.465512 CAGCGGCGTGGCATTGAC 62.466 66.667 9.37 0.00 34.64 3.18
4280 12189 1.153628 CGTTCCCCTGTCCGACATC 60.154 63.158 0.62 0.00 0.00 3.06
4291 12200 2.351322 CGACATCGCCTCGACGAG 60.351 66.667 18.08 18.08 46.69 4.18
4300 12209 3.203412 CTCGACGAGGACGGAGGG 61.203 72.222 17.27 0.00 44.46 4.30
4303 12212 3.519930 GACGAGGACGGAGGGCTC 61.520 72.222 0.00 0.00 44.46 4.70
4304 12213 3.999297 GACGAGGACGGAGGGCTCT 62.999 68.421 0.00 0.00 44.46 4.09
4305 12214 3.213402 CGAGGACGGAGGGCTCTC 61.213 72.222 4.50 4.50 39.25 3.20
4313 12222 3.627690 GAGGGCTCTCCACTCCTG 58.372 66.667 0.57 0.00 38.24 3.86
4314 12223 1.000993 GAGGGCTCTCCACTCCTGA 59.999 63.158 0.57 0.00 38.24 3.86
4315 12224 1.305718 AGGGCTCTCCACTCCTGAC 60.306 63.158 0.00 0.00 38.24 3.51
4316 12225 2.716017 GGGCTCTCCACTCCTGACG 61.716 68.421 0.00 0.00 35.00 4.35
4317 12226 2.183046 GCTCTCCACTCCTGACGC 59.817 66.667 0.00 0.00 0.00 5.19
4318 12227 2.487428 CTCTCCACTCCTGACGCG 59.513 66.667 3.53 3.53 0.00 6.01
4319 12228 3.057547 CTCTCCACTCCTGACGCGG 62.058 68.421 12.47 0.00 0.00 6.46
4320 12229 4.803426 CTCCACTCCTGACGCGGC 62.803 72.222 12.47 8.67 0.00 6.53
4341 12250 1.153765 CGTCATCTTCTCAGCGCCA 60.154 57.895 2.29 0.00 0.00 5.69
4343 12252 0.108424 GTCATCTTCTCAGCGCCACT 60.108 55.000 2.29 0.00 0.00 4.00
4353 12262 4.681978 GCGCCACTCCACGGACTT 62.682 66.667 0.00 0.00 0.00 3.01
4354 12263 2.432628 CGCCACTCCACGGACTTC 60.433 66.667 0.00 0.00 0.00 3.01
4355 12264 2.932234 CGCCACTCCACGGACTTCT 61.932 63.158 0.00 0.00 0.00 2.85
4356 12265 1.079750 GCCACTCCACGGACTTCTC 60.080 63.158 0.00 0.00 0.00 2.87
4357 12266 1.816863 GCCACTCCACGGACTTCTCA 61.817 60.000 0.00 0.00 0.00 3.27
4358 12267 0.244994 CCACTCCACGGACTTCTCAG 59.755 60.000 0.00 0.00 0.00 3.35
4359 12268 0.389166 CACTCCACGGACTTCTCAGC 60.389 60.000 0.00 0.00 0.00 4.26
4360 12269 1.153939 CTCCACGGACTTCTCAGCG 60.154 63.158 0.00 0.00 0.00 5.18
4361 12270 1.867919 CTCCACGGACTTCTCAGCGT 61.868 60.000 0.00 0.00 0.00 5.07
4362 12271 1.444553 CCACGGACTTCTCAGCGTC 60.445 63.158 0.00 0.00 0.00 5.19
4363 12272 1.285950 CACGGACTTCTCAGCGTCA 59.714 57.895 0.00 0.00 31.88 4.35
4364 12273 0.109086 CACGGACTTCTCAGCGTCAT 60.109 55.000 0.00 0.00 31.88 3.06
4377 13402 3.056536 TCAGCGTCATCTACTCTGCTTTT 60.057 43.478 0.00 0.00 40.16 2.27
4390 13415 8.612619 TCTACTCTGCTTTTTAAACTCTGTTTG 58.387 33.333 6.01 0.00 0.00 2.93
4391 13416 7.391148 ACTCTGCTTTTTAAACTCTGTTTGA 57.609 32.000 6.01 0.00 0.00 2.69
4392 13417 8.000780 ACTCTGCTTTTTAAACTCTGTTTGAT 57.999 30.769 6.01 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.100510 CCATGGTGAGCATGTTCTGG 58.899 55.000 21.47 5.40 0.00 3.86
42 43 3.005554 AGCTCAACATTTCCGTCATCTG 58.994 45.455 0.00 0.00 0.00 2.90
78 79 1.178276 TTGGTTTCACCTGTTTGCGT 58.822 45.000 0.00 0.00 39.58 5.24
83 88 4.099419 GGTTCTCATTTGGTTTCACCTGTT 59.901 41.667 0.00 0.00 39.58 3.16
106 111 6.270815 CCTGCTCTGTTGATGGATTTAAATG 58.729 40.000 5.17 0.00 0.00 2.32
107 112 5.163478 GCCTGCTCTGTTGATGGATTTAAAT 60.163 40.000 0.00 0.00 0.00 1.40
108 113 4.158394 GCCTGCTCTGTTGATGGATTTAAA 59.842 41.667 0.00 0.00 0.00 1.52
109 114 3.696051 GCCTGCTCTGTTGATGGATTTAA 59.304 43.478 0.00 0.00 0.00 1.52
111 116 2.097825 GCCTGCTCTGTTGATGGATTT 58.902 47.619 0.00 0.00 0.00 2.17
112 117 1.284198 AGCCTGCTCTGTTGATGGATT 59.716 47.619 0.00 0.00 0.00 3.01
131 155 7.360438 CCACTAAGGAAACTCGAGAATGAAAAG 60.360 40.741 21.68 10.92 42.68 2.27
157 181 6.292542 GCAATCAAAGAAGAAAAAGGTGCTTC 60.293 38.462 0.00 0.00 38.58 3.86
160 184 4.084900 CGCAATCAAAGAAGAAAAAGGTGC 60.085 41.667 0.00 0.00 0.00 5.01
169 193 2.844946 TCCACACGCAATCAAAGAAGA 58.155 42.857 0.00 0.00 0.00 2.87
193 217 3.560636 TGCTTCAGATAGTAAAGCCCC 57.439 47.619 4.09 0.00 43.71 5.80
230 254 1.665442 GATGGGTGTTGGTGGCAAC 59.335 57.895 0.00 0.00 35.75 4.17
241 265 1.413812 TGTGAGATCGATGGATGGGTG 59.586 52.381 0.54 0.00 31.51 4.61
282 306 1.765314 AGGCTCCACACTGATCCATAC 59.235 52.381 0.00 0.00 0.00 2.39
320 344 1.084370 CGAGTTGACCGGCTGAATCC 61.084 60.000 0.00 0.00 0.00 3.01
435 1542 7.984422 TCTTAATGAACAGATTCTTGCAAGA 57.016 32.000 25.16 25.16 35.69 3.02
446 1553 5.670792 ACGTACCCATCTTAATGAACAGA 57.329 39.130 0.00 0.00 34.61 3.41
452 1584 4.426416 TCGACAACGTACCCATCTTAATG 58.574 43.478 0.00 0.00 40.69 1.90
472 1604 4.264614 GCATGTGATTCTTTGAATGCTTCG 59.735 41.667 0.00 0.00 37.89 3.79
473 1605 5.408356 AGCATGTGATTCTTTGAATGCTTC 58.592 37.500 2.25 0.00 46.32 3.86
563 1695 7.852263 AGGCTCAAGTGTAGTGAATTAATAGT 58.148 34.615 0.00 0.00 0.00 2.12
649 1855 4.210331 ACTTTGGAGATTGGGCATATCAC 58.790 43.478 1.69 0.00 0.00 3.06
780 2002 1.215382 CCGCTCATCTGTTCCGTCA 59.785 57.895 0.00 0.00 0.00 4.35
836 2058 2.220786 CTTGCCAGGGGGATTGAGCT 62.221 60.000 0.00 0.00 35.59 4.09
861 2083 5.013495 CAGATAGAGGGAGAGACAGAGAGAT 59.987 48.000 0.00 0.00 0.00 2.75
869 2091 4.787551 TCAGTTCAGATAGAGGGAGAGAC 58.212 47.826 0.00 0.00 0.00 3.36
876 2098 3.431486 GGCCAGTTCAGTTCAGATAGAGG 60.431 52.174 0.00 0.00 0.00 3.69
881 2106 1.612726 GCAGGCCAGTTCAGTTCAGAT 60.613 52.381 5.01 0.00 0.00 2.90
887 2126 1.072159 GTGAGCAGGCCAGTTCAGT 59.928 57.895 15.03 0.00 29.11 3.41
900 2146 3.311966 GGAGCAAAAACAATGAGTGAGC 58.688 45.455 0.00 0.00 0.00 4.26
907 2153 2.607771 CCTGACGGGAGCAAAAACAATG 60.608 50.000 0.00 0.00 37.23 2.82
908 2154 1.613437 CCTGACGGGAGCAAAAACAAT 59.387 47.619 0.00 0.00 37.23 2.71
931 2177 3.021695 TCCAGCTACGTACACTAGCAAT 58.978 45.455 17.62 0.68 39.36 3.56
973 2220 4.065088 CACTCTAACAGCAAGCAGGTTTA 58.935 43.478 7.29 0.00 0.00 2.01
1105 2537 1.070289 CTGCAGCCTGATCAGCTCATA 59.930 52.381 17.76 2.45 38.95 2.15
1423 2861 9.722184 ATCTTCTACAGAATCATCCATAACATG 57.278 33.333 0.00 0.00 34.16 3.21
1425 2863 9.551734 CAATCTTCTACAGAATCATCCATAACA 57.448 33.333 0.00 0.00 34.16 2.41
1645 3128 4.552166 CAGTTACCCAAACAAGTGACTG 57.448 45.455 1.43 1.43 42.04 3.51
1695 3178 8.246871 AGTATTTGCTTCAAAATCTCCTTTAGC 58.753 33.333 0.00 0.00 36.90 3.09
1741 3225 9.811995 ATACTCATTCATGTCATCAATTTTTGG 57.188 29.630 0.00 0.00 0.00 3.28
1774 3258 6.695429 TGAGGATATCATGGATCTTCTTTCG 58.305 40.000 16.26 0.00 32.22 3.46
2103 3587 1.135689 GCAAGTGCAAGTGGTAATCCG 60.136 52.381 0.00 0.00 41.59 4.18
2179 3663 1.885887 GCTTGATGGCCAACACAGTAA 59.114 47.619 16.33 0.00 0.00 2.24
2198 3682 1.131883 GCATCATCTGTGTGTCCTTGC 59.868 52.381 0.00 0.00 0.00 4.01
2304 3788 6.260870 AGAGCCGACACAGATATTATGTAG 57.739 41.667 0.00 0.00 0.00 2.74
2439 3923 8.619146 ATTCATGTATAATGCTTGTTTGAACG 57.381 30.769 0.00 0.00 0.00 3.95
2524 9989 6.953520 TGGATTACATCAAGGAAACCATCTTT 59.046 34.615 0.00 0.00 0.00 2.52
2544 10009 6.620877 TCACCACTAGTAGTTTCATGGATT 57.379 37.500 10.02 0.00 0.00 3.01
2712 10351 9.667107 TGGAAAGAAGAACGATAGAATATTTGT 57.333 29.630 0.00 0.00 41.38 2.83
2715 10354 9.667107 TTGTGGAAAGAAGAACGATAGAATATT 57.333 29.630 0.00 0.00 41.38 1.28
2739 10378 7.524912 CATGTAAGATCTTTCCACTCAAGTTG 58.475 38.462 14.36 0.00 0.00 3.16
2751 10390 4.307032 AGGTGGTGCATGTAAGATCTTT 57.693 40.909 14.36 0.00 0.00 2.52
2752 10391 5.435686 TTAGGTGGTGCATGTAAGATCTT 57.564 39.130 13.56 13.56 0.00 2.40
2793 10435 7.606456 GGTAAAGATACTGATGAAAGTCCAACA 59.394 37.037 0.00 0.00 32.36 3.33
2794 10436 7.824779 AGGTAAAGATACTGATGAAAGTCCAAC 59.175 37.037 0.00 0.00 32.36 3.77
2832 10489 7.957002 AGTTCTCAACATGAAGAACTCTTAGA 58.043 34.615 24.26 4.84 38.88 2.10
2875 10532 1.734163 CACCCACCAATTACCTCGTC 58.266 55.000 0.00 0.00 0.00 4.20
2929 10586 4.931601 TGAAGAAGGAACAATCATGTCTCG 59.068 41.667 0.00 0.00 39.40 4.04
3109 10790 2.809119 CAGCTTCATCATCATGAGGAGC 59.191 50.000 16.08 12.95 38.49 4.70
3115 10796 5.507482 GGTCATTTCCAGCTTCATCATCATG 60.507 44.000 0.00 0.00 0.00 3.07
3116 10797 4.583489 GGTCATTTCCAGCTTCATCATCAT 59.417 41.667 0.00 0.00 0.00 2.45
3135 10816 1.152631 TAGGATCGGCATCGGGTCA 60.153 57.895 0.00 0.00 36.95 4.02
3153 10834 3.558746 CCACAAGACAAGGAAGCATCTCT 60.559 47.826 0.00 0.00 0.00 3.10
3188 10869 4.157105 ACATTGTTGCGGGTTTATAAGACC 59.843 41.667 7.79 7.79 36.41 3.85
3191 10872 4.398044 AGGACATTGTTGCGGGTTTATAAG 59.602 41.667 0.00 0.00 0.00 1.73
3203 10884 2.153366 GGCACCAAAGGACATTGTTG 57.847 50.000 0.00 0.00 0.00 3.33
3235 10916 4.185394 TCAAGTCGTAACTTTTGCAGACA 58.815 39.130 1.93 0.00 43.28 3.41
3244 10926 3.383825 ACACAGTCCTCAAGTCGTAACTT 59.616 43.478 0.00 0.00 46.80 2.66
3265 10947 4.312443 TCCATCGTCCACTTGTTAAAGAC 58.688 43.478 0.00 0.00 36.84 3.01
3266 10948 4.562757 CCTCCATCGTCCACTTGTTAAAGA 60.563 45.833 0.00 0.00 36.84 2.52
3304 10989 4.337274 TGAAAATGACAGGCATGATAGCTG 59.663 41.667 4.84 0.00 37.28 4.24
3376 11068 3.117046 GTCACTAATACGAAGCTGAGGC 58.883 50.000 0.00 0.00 39.06 4.70
3383 11075 6.800408 TCAGAAAACGAGTCACTAATACGAAG 59.200 38.462 0.00 0.00 0.00 3.79
3391 11083 9.706691 AATAATCTTTCAGAAAACGAGTCACTA 57.293 29.630 0.00 0.00 0.00 2.74
3397 11089 9.203668 CATTCGAATAATCTTTCAGAAAACGAG 57.796 33.333 10.97 0.00 0.00 4.18
3402 11097 9.825972 GTTGTCATTCGAATAATCTTTCAGAAA 57.174 29.630 10.97 0.00 0.00 2.52
3405 11100 7.423598 CGTGTTGTCATTCGAATAATCTTTCAG 59.576 37.037 10.97 0.00 0.00 3.02
3407 11102 6.192863 GCGTGTTGTCATTCGAATAATCTTTC 59.807 38.462 10.97 0.00 0.00 2.62
3440 11135 2.936919 TGCATCCTTTGTGTCTCAGT 57.063 45.000 0.00 0.00 0.00 3.41
3465 11160 0.532573 ACGTCCATCACTGGTAGCAG 59.467 55.000 20.16 20.16 43.61 4.24
3466 11161 0.246360 CACGTCCATCACTGGTAGCA 59.754 55.000 0.00 0.00 43.61 3.49
3473 11169 0.969149 TGCTCTTCACGTCCATCACT 59.031 50.000 0.00 0.00 0.00 3.41
3474 11170 1.071605 GTGCTCTTCACGTCCATCAC 58.928 55.000 0.00 0.00 35.76 3.06
3475 11171 3.514777 GTGCTCTTCACGTCCATCA 57.485 52.632 0.00 0.00 35.76 3.07
3483 11179 6.768029 TGCATTAAAATTTGTGCTCTTCAC 57.232 33.333 18.43 0.00 45.82 3.18
3484 11180 6.424509 CCTTGCATTAAAATTTGTGCTCTTCA 59.575 34.615 18.43 2.45 38.37 3.02
3486 11182 6.290605 ACCTTGCATTAAAATTTGTGCTCTT 58.709 32.000 18.43 4.49 38.37 2.85
3488 11184 6.868339 AGTACCTTGCATTAAAATTTGTGCTC 59.132 34.615 18.43 0.86 38.37 4.26
3489 11185 6.758254 AGTACCTTGCATTAAAATTTGTGCT 58.242 32.000 18.43 5.17 38.37 4.40
3490 11186 7.812669 AGTAGTACCTTGCATTAAAATTTGTGC 59.187 33.333 13.53 13.53 38.05 4.57
3497 11193 9.657419 GGTAACTAGTAGTACCTTGCATTAAAA 57.343 33.333 14.23 0.00 0.00 1.52
3498 11194 8.814931 TGGTAACTAGTAGTACCTTGCATTAAA 58.185 33.333 19.81 0.00 33.90 1.52
3501 11197 6.862469 TGGTAACTAGTAGTACCTTGCATT 57.138 37.500 19.81 2.07 33.90 3.56
3502 11198 6.626623 CGTTGGTAACTAGTAGTACCTTGCAT 60.627 42.308 19.81 2.63 33.90 3.96
3503 11199 5.335897 CGTTGGTAACTAGTAGTACCTTGCA 60.336 44.000 19.81 2.53 33.90 4.08
3504 11200 5.098211 CGTTGGTAACTAGTAGTACCTTGC 58.902 45.833 19.81 11.40 33.90 4.01
3505 11201 5.098211 GCGTTGGTAACTAGTAGTACCTTG 58.902 45.833 19.81 12.57 33.90 3.61
3506 11202 4.766891 TGCGTTGGTAACTAGTAGTACCTT 59.233 41.667 19.81 4.62 33.90 3.50
3507 11203 4.335416 TGCGTTGGTAACTAGTAGTACCT 58.665 43.478 19.81 4.91 33.90 3.08
3508 11204 4.701956 TGCGTTGGTAACTAGTAGTACC 57.298 45.455 14.52 14.52 37.61 3.34
3523 11321 4.996758 TCACCATAGGATCATAATGCGTTG 59.003 41.667 0.08 0.00 0.00 4.10
3526 11324 5.448225 GCATTCACCATAGGATCATAATGCG 60.448 44.000 7.32 0.31 38.75 4.73
3535 11333 4.719026 AGACATGCATTCACCATAGGAT 57.281 40.909 0.00 0.00 0.00 3.24
3545 11343 3.428045 GCCAAACTGGTAGACATGCATTC 60.428 47.826 0.00 0.00 40.46 2.67
3546 11344 2.493278 GCCAAACTGGTAGACATGCATT 59.507 45.455 0.00 0.00 40.46 3.56
3606 11471 4.341235 TCCCAATCGAGGAACAGTACATAG 59.659 45.833 0.00 0.00 0.00 2.23
3621 11486 5.036737 GCTTGTTTGTGATAATCCCAATCG 58.963 41.667 0.00 0.00 0.00 3.34
3682 11547 6.339730 TGCTCATTAATTGTGCCCAAATAAG 58.660 36.000 0.00 0.00 42.79 1.73
3696 11561 3.947196 TGCGGAAGTGATTGCTCATTAAT 59.053 39.130 0.00 0.00 32.98 1.40
3753 11618 8.175716 GGCGCCTTACTTGATACAATAATAATC 58.824 37.037 22.15 0.00 0.00 1.75
3757 11622 5.621193 AGGCGCCTTACTTGATACAATAAT 58.379 37.500 27.08 0.00 0.00 1.28
3758 11623 5.031066 AGGCGCCTTACTTGATACAATAA 57.969 39.130 27.08 0.00 0.00 1.40
3778 11643 3.378427 GCTAGGGACTTTATTGCACAAGG 59.622 47.826 0.00 0.00 41.75 3.61
3780 11645 4.301072 AGCTAGGGACTTTATTGCACAA 57.699 40.909 0.00 0.00 41.75 3.33
3781 11646 4.009675 CAAGCTAGGGACTTTATTGCACA 58.990 43.478 0.00 0.00 41.75 4.57
3782 11647 4.261801 TCAAGCTAGGGACTTTATTGCAC 58.738 43.478 0.00 0.00 41.75 4.57
3783 11648 4.568072 TCAAGCTAGGGACTTTATTGCA 57.432 40.909 0.00 0.00 41.75 4.08
3785 11650 6.599244 TGTCATTCAAGCTAGGGACTTTATTG 59.401 38.462 0.00 0.00 41.75 1.90
3786 11651 6.721318 TGTCATTCAAGCTAGGGACTTTATT 58.279 36.000 0.00 0.00 41.75 1.40
3788 11653 5.755409 TGTCATTCAAGCTAGGGACTTTA 57.245 39.130 0.00 0.00 41.75 1.85
3792 11657 3.674997 TGTTGTCATTCAAGCTAGGGAC 58.325 45.455 0.00 0.00 36.66 4.46
3793 11658 4.365514 TTGTTGTCATTCAAGCTAGGGA 57.634 40.909 0.00 0.00 36.66 4.20
3811 11681 2.485302 GCCAAGCTGGTTCCAAAATTGT 60.485 45.455 0.00 0.00 40.46 2.71
3818 11688 0.396974 AACTTGCCAAGCTGGTTCCA 60.397 50.000 3.88 0.00 40.46 3.53
3821 11691 1.194218 AACAACTTGCCAAGCTGGTT 58.806 45.000 12.15 7.75 40.46 3.67
3889 11763 4.212143 TGCATCTATGAGCACAAGACTT 57.788 40.909 0.00 0.00 35.51 3.01
3894 11768 3.881089 CAGGAATGCATCTATGAGCACAA 59.119 43.478 0.00 0.00 44.49 3.33
3901 11775 1.540267 GCAGCCAGGAATGCATCTATG 59.460 52.381 11.33 0.00 42.11 2.23
3912 11786 1.275291 GTACAGTTACTGCAGCCAGGA 59.725 52.381 15.27 0.00 43.53 3.86
3914 11788 1.350193 CGTACAGTTACTGCAGCCAG 58.650 55.000 15.27 1.99 44.80 4.85
3915 11789 0.037697 CCGTACAGTTACTGCAGCCA 60.038 55.000 15.27 0.00 34.37 4.75
3917 11791 2.094854 ACTACCGTACAGTTACTGCAGC 60.095 50.000 15.27 0.00 34.37 5.25
3918 11792 3.189910 TCACTACCGTACAGTTACTGCAG 59.810 47.826 13.48 13.48 34.37 4.41
3919 11793 3.148412 TCACTACCGTACAGTTACTGCA 58.852 45.455 12.80 0.00 34.37 4.41
3920 11794 3.837213 TCACTACCGTACAGTTACTGC 57.163 47.619 12.80 0.00 34.37 4.40
3921 11795 6.845302 TGTATTCACTACCGTACAGTTACTG 58.155 40.000 11.21 11.21 37.52 2.74
3922 11796 6.881065 TCTGTATTCACTACCGTACAGTTACT 59.119 38.462 10.18 0.00 42.73 2.24
3923 11797 7.076842 TCTGTATTCACTACCGTACAGTTAC 57.923 40.000 10.18 0.00 42.73 2.50
3924 11798 7.254556 CGATCTGTATTCACTACCGTACAGTTA 60.255 40.741 10.18 0.00 42.73 2.24
3925 11799 6.457934 CGATCTGTATTCACTACCGTACAGTT 60.458 42.308 10.18 3.74 42.73 3.16
3926 11800 5.007430 CGATCTGTATTCACTACCGTACAGT 59.993 44.000 10.18 0.00 42.73 3.55
3927 11801 5.441543 CGATCTGTATTCACTACCGTACAG 58.558 45.833 5.30 5.30 43.25 2.74
3928 11802 4.260907 GCGATCTGTATTCACTACCGTACA 60.261 45.833 0.00 0.00 0.00 2.90
3929 11803 4.024218 AGCGATCTGTATTCACTACCGTAC 60.024 45.833 0.00 0.00 0.00 3.67
3930 11804 4.132336 AGCGATCTGTATTCACTACCGTA 58.868 43.478 0.00 0.00 0.00 4.02
3931 11805 2.950309 AGCGATCTGTATTCACTACCGT 59.050 45.455 0.00 0.00 0.00 4.83
3932 11806 3.627732 AGCGATCTGTATTCACTACCG 57.372 47.619 0.00 0.00 0.00 4.02
3933 11807 4.023107 TGCTAGCGATCTGTATTCACTACC 60.023 45.833 10.77 0.00 0.00 3.18
3934 11808 5.109662 TGCTAGCGATCTGTATTCACTAC 57.890 43.478 10.77 0.00 0.00 2.73
3935 11809 4.822350 ACTGCTAGCGATCTGTATTCACTA 59.178 41.667 10.77 0.00 0.00 2.74
3936 11810 3.634448 ACTGCTAGCGATCTGTATTCACT 59.366 43.478 10.77 0.00 0.00 3.41
3937 11811 3.971150 ACTGCTAGCGATCTGTATTCAC 58.029 45.455 10.77 0.00 0.00 3.18
3938 11812 4.320567 GCTACTGCTAGCGATCTGTATTCA 60.321 45.833 10.77 0.00 36.26 2.57
3939 11813 4.162812 GCTACTGCTAGCGATCTGTATTC 58.837 47.826 10.77 0.89 36.26 1.75
3940 11814 4.167554 GCTACTGCTAGCGATCTGTATT 57.832 45.455 10.77 0.00 36.26 1.89
3941 11815 3.840890 GCTACTGCTAGCGATCTGTAT 57.159 47.619 10.77 0.00 36.26 2.29
3950 11824 1.478510 TCCTGAACTGCTACTGCTAGC 59.521 52.381 8.10 8.10 45.19 3.42
3951 11825 3.516615 GTTCCTGAACTGCTACTGCTAG 58.483 50.000 2.80 0.00 40.48 3.42
3952 11826 2.094700 CGTTCCTGAACTGCTACTGCTA 60.095 50.000 8.28 0.00 39.08 3.49
3953 11827 1.337260 CGTTCCTGAACTGCTACTGCT 60.337 52.381 8.28 0.00 39.08 4.24
3969 11843 6.018180 GGATATGTATTTTGGTGTCTCCGTTC 60.018 42.308 0.00 0.00 39.52 3.95
3976 11884 7.865706 AGTTCAGGATATGTATTTTGGTGTC 57.134 36.000 0.00 0.00 0.00 3.67
3987 11895 6.109359 GCAGTAACAGAAGTTCAGGATATGT 58.891 40.000 5.50 0.00 39.15 2.29
4045 11953 3.017442 CACAGTTCTCTGACCGAGGATA 58.983 50.000 0.00 0.00 43.76 2.59
4046 11954 1.821753 CACAGTTCTCTGACCGAGGAT 59.178 52.381 0.00 0.00 43.76 3.24
4047 11955 1.202891 TCACAGTTCTCTGACCGAGGA 60.203 52.381 0.00 0.00 43.76 3.71
4121 12030 8.919661 GCTCCATAATTTGTTCTTTCAGAAAAG 58.080 33.333 0.00 0.00 42.77 2.27
4137 12046 3.036091 AGCAATTGCAGGCTCCATAATT 58.964 40.909 30.89 3.64 45.16 1.40
4185 12094 1.371758 GAGTCGTGACTGAAGCGCA 60.372 57.895 11.47 0.00 42.66 6.09
4209 12118 4.811364 GGAGGGGAAGGCTGCTGC 62.811 72.222 7.10 7.10 38.76 5.25
4210 12119 4.479993 CGGAGGGGAAGGCTGCTG 62.480 72.222 0.00 0.00 0.00 4.41
4213 12122 4.479993 CTGCGGAGGGGAAGGCTG 62.480 72.222 0.00 0.00 0.00 4.85
4216 12125 2.330924 GATTCCTGCGGAGGGGAAGG 62.331 65.000 24.01 0.00 43.64 3.46
4217 12126 1.147153 GATTCCTGCGGAGGGGAAG 59.853 63.158 24.01 0.00 43.64 3.46
4218 12127 1.306997 AGATTCCTGCGGAGGGGAA 60.307 57.895 24.01 11.75 44.37 3.97
4219 12128 1.762460 GAGATTCCTGCGGAGGGGA 60.762 63.158 24.01 12.67 40.25 4.81
4220 12129 2.812619 GGAGATTCCTGCGGAGGGG 61.813 68.421 24.01 0.00 40.25 4.79
4221 12130 2.037620 CTGGAGATTCCTGCGGAGGG 62.038 65.000 24.01 4.51 39.21 4.30
4222 12131 1.445095 CTGGAGATTCCTGCGGAGG 59.555 63.158 18.34 18.34 39.21 4.30
4228 12137 2.587194 CGCCGCTGGAGATTCCTG 60.587 66.667 0.00 0.00 37.46 3.86
4229 12138 3.077556 ACGCCGCTGGAGATTCCT 61.078 61.111 5.46 0.00 37.46 3.36
4230 12139 2.892425 CACGCCGCTGGAGATTCC 60.892 66.667 5.46 0.00 36.96 3.01
4231 12140 2.892425 CCACGCCGCTGGAGATTC 60.892 66.667 5.46 0.00 32.30 2.52
4238 12147 4.465512 GTCAATGCCACGCCGCTG 62.466 66.667 0.00 0.00 0.00 5.18
4260 12169 4.754667 GTCGGACAGGGGAACGCC 62.755 72.222 2.62 0.00 44.92 5.68
4261 12170 3.310860 ATGTCGGACAGGGGAACGC 62.311 63.158 16.84 0.00 43.76 4.84
4262 12171 1.153628 GATGTCGGACAGGGGAACG 60.154 63.158 16.84 0.00 0.00 3.95
4263 12172 1.153628 CGATGTCGGACAGGGGAAC 60.154 63.158 16.84 3.27 35.37 3.62
4264 12173 3.014085 GCGATGTCGGACAGGGGAA 62.014 63.158 16.84 0.00 40.23 3.97
4265 12174 3.458163 GCGATGTCGGACAGGGGA 61.458 66.667 16.84 0.00 40.23 4.81
4266 12175 4.530857 GGCGATGTCGGACAGGGG 62.531 72.222 16.84 8.91 40.23 4.79
4267 12176 3.432051 GAGGCGATGTCGGACAGGG 62.432 68.421 16.84 11.29 40.23 4.45
4268 12177 2.105128 GAGGCGATGTCGGACAGG 59.895 66.667 16.84 11.64 40.23 4.00
4269 12178 2.278206 CGAGGCGATGTCGGACAG 60.278 66.667 16.84 5.04 40.23 3.51
4270 12179 2.748647 TCGAGGCGATGTCGGACA 60.749 61.111 14.01 14.01 40.23 4.02
4271 12180 2.278013 GTCGAGGCGATGTCGGAC 60.278 66.667 0.00 0.00 38.42 4.79
4274 12183 2.351322 CTCGTCGAGGCGATGTCG 60.351 66.667 14.68 0.00 42.61 4.35
4300 12209 2.183046 GCGTCAGGAGTGGAGAGC 59.817 66.667 0.00 0.00 0.00 4.09
4301 12210 2.487428 CGCGTCAGGAGTGGAGAG 59.513 66.667 0.00 0.00 0.00 3.20
4302 12211 3.062466 CCGCGTCAGGAGTGGAGA 61.062 66.667 4.92 0.00 41.54 3.71
4303 12212 4.803426 GCCGCGTCAGGAGTGGAG 62.803 72.222 4.92 0.00 41.54 3.86
4316 12225 2.510238 AGAAGATGACGCTGCCGC 60.510 61.111 0.00 0.00 38.22 6.53
4317 12226 1.144565 CTGAGAAGATGACGCTGCCG 61.145 60.000 0.00 0.00 41.14 5.69
4318 12227 1.427592 GCTGAGAAGATGACGCTGCC 61.428 60.000 0.00 0.00 0.00 4.85
4319 12228 1.750572 CGCTGAGAAGATGACGCTGC 61.751 60.000 0.00 0.00 0.00 5.25
4320 12229 1.750572 GCGCTGAGAAGATGACGCTG 61.751 60.000 0.00 0.00 42.81 5.18
4321 12230 1.518133 GCGCTGAGAAGATGACGCT 60.518 57.895 0.00 0.00 42.81 5.07
4322 12231 2.520904 GGCGCTGAGAAGATGACGC 61.521 63.158 7.64 0.00 45.19 5.19
4323 12232 1.153765 TGGCGCTGAGAAGATGACG 60.154 57.895 7.64 0.00 0.00 4.35
4324 12233 0.108424 AGTGGCGCTGAGAAGATGAC 60.108 55.000 7.64 0.00 0.00 3.06
4325 12234 0.174389 GAGTGGCGCTGAGAAGATGA 59.826 55.000 4.71 0.00 0.00 2.92
4341 12250 1.867919 CGCTGAGAAGTCCGTGGAGT 61.868 60.000 0.00 0.00 0.00 3.85
4343 12252 1.863662 GACGCTGAGAAGTCCGTGGA 61.864 60.000 0.00 0.00 33.63 4.02
4349 12258 3.625764 AGAGTAGATGACGCTGAGAAGTC 59.374 47.826 2.28 2.28 36.75 3.01
4350 12259 3.616219 AGAGTAGATGACGCTGAGAAGT 58.384 45.455 0.00 0.00 36.75 3.01
4357 12266 3.601443 AAAAGCAGAGTAGATGACGCT 57.399 42.857 0.00 0.00 39.00 5.07
4358 12267 5.779806 TTAAAAAGCAGAGTAGATGACGC 57.220 39.130 0.00 0.00 0.00 5.19
4359 12268 7.329717 AGAGTTTAAAAAGCAGAGTAGATGACG 59.670 37.037 0.00 0.00 0.00 4.35
4360 12269 8.439286 CAGAGTTTAAAAAGCAGAGTAGATGAC 58.561 37.037 0.00 0.00 0.00 3.06
4361 12270 8.150945 ACAGAGTTTAAAAAGCAGAGTAGATGA 58.849 33.333 0.00 0.00 0.00 2.92
4362 12271 8.316640 ACAGAGTTTAAAAAGCAGAGTAGATG 57.683 34.615 0.00 0.00 0.00 2.90
4363 12272 8.910351 AACAGAGTTTAAAAAGCAGAGTAGAT 57.090 30.769 0.00 0.00 0.00 1.98
4364 12273 8.612619 CAAACAGAGTTTAAAAAGCAGAGTAGA 58.387 33.333 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.