Multiple sequence alignment - TraesCS5A01G099200

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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 TraesCS5A01G099200 chr5A 100.000 6897 0 0 1 6897 141883304 141876408 0.000000e+00 12737.0
1 TraesCS5A01G099200 chr5A 86.111 324 22 7 4436 4738 287614009 287614330 1.850000e-85 327.0
2 TraesCS5A01G099200 chr5A 84.862 218 23 10 3122 3332 229505334 229505120 1.950000e-50 211.0
3 TraesCS5A01G099200 chr5A 78.006 341 35 28 2993 3301 218605343 218605011 1.980000e-40 178.0
4 TraesCS5A01G099200 chr5A 87.671 73 6 3 2248 2319 338287880 338287810 1.590000e-11 82.4
5 TraesCS5A01G099200 chr5A 97.368 38 1 0 2963 3000 141880312 141880275 1.610000e-06 65.8
6 TraesCS5A01G099200 chr5A 97.368 38 1 0 2993 3030 141880342 141880305 1.610000e-06 65.8
7 TraesCS5A01G099200 chr5D 95.387 4747 157 29 1 4733 126574665 126569967 0.000000e+00 7496.0
8 TraesCS5A01G099200 chr5D 96.280 2312 41 14 4619 6897 126569949 126567650 0.000000e+00 3751.0
9 TraesCS5A01G099200 chr5D 83.486 218 23 11 3122 3332 190492029 190492240 2.540000e-44 191.0
10 TraesCS5A01G099200 chr5D 75.964 441 63 36 2876 3301 167035803 167036215 3.280000e-43 187.0
11 TraesCS5A01G099200 chr5D 88.732 71 6 2 2248 2317 255076531 255076462 1.230000e-12 86.1
12 TraesCS5A01G099200 chr5B 95.144 2430 74 19 531 2940 139351768 139349363 0.000000e+00 3794.0
13 TraesCS5A01G099200 chr5B 96.816 2073 43 8 2993 5062 139343812 139341760 0.000000e+00 3441.0
14 TraesCS5A01G099200 chr5B 96.741 1074 18 4 5109 6173 139341758 139340693 0.000000e+00 1773.0
15 TraesCS5A01G099200 chr5B 92.640 625 19 10 6238 6838 139340372 139339751 0.000000e+00 874.0
16 TraesCS5A01G099200 chr5B 89.624 559 42 10 1 551 139352900 139352350 0.000000e+00 697.0
17 TraesCS5A01G099200 chr5B 96.429 56 2 0 2945 3000 139343830 139343775 7.370000e-15 93.5
18 TraesCS5A01G099200 chr5B 98.077 52 1 0 6172 6223 139340410 139340359 2.650000e-14 91.6
19 TraesCS5A01G099200 chr4A 88.235 323 16 8 4437 4740 45682457 45682776 3.930000e-97 366.0
20 TraesCS5A01G099200 chr4B 88.312 308 31 3 4437 4741 22911199 22911504 1.410000e-96 364.0
21 TraesCS5A01G099200 chr4B 81.860 215 26 12 3047 3255 212147488 212147695 1.190000e-37 169.0
22 TraesCS5A01G099200 chr4B 81.395 215 27 12 3047 3255 212118830 212119037 5.540000e-36 163.0
23 TraesCS5A01G099200 chr4B 81.429 210 27 11 3051 3255 212089699 212089901 1.990000e-35 161.0
24 TraesCS5A01G099200 chr3B 87.267 322 18 6 4438 4738 342869957 342869638 5.120000e-91 346.0
25 TraesCS5A01G099200 chr1A 87.037 324 19 6 4440 4743 208883814 208884134 1.840000e-90 344.0
26 TraesCS5A01G099200 chr1A 96.491 171 5 1 4437 4607 292773762 292773931 1.460000e-71 281.0
27 TraesCS5A01G099200 chr1A 91.304 69 2 2 2253 2317 398460993 398460925 2.650000e-14 91.6
28 TraesCS5A01G099200 chr6A 87.372 293 15 12 4431 4706 61027789 61027502 4.010000e-82 316.0
29 TraesCS5A01G099200 chr6A 80.769 130 14 9 3005 3129 153772266 153772389 2.650000e-14 91.6
30 TraesCS5A01G099200 chr1B 87.031 293 15 7 4432 4704 424541268 424541557 6.720000e-80 309.0
31 TraesCS5A01G099200 chr1B 95.833 168 7 0 4436 4603 216492763 216492596 8.810000e-69 272.0
32 TraesCS5A01G099200 chr1B 91.304 138 8 3 4602 4738 309493678 309493812 1.180000e-42 185.0
33 TraesCS5A01G099200 chr1B 90.769 65 6 0 2253 2317 565664563 565664627 3.430000e-13 87.9
34 TraesCS5A01G099200 chr6D 84.211 323 15 17 4437 4738 101258250 101258557 1.460000e-71 281.0
35 TraesCS5A01G099200 chr7B 85.714 245 9 8 4516 4738 511301835 511302075 1.160000e-57 235.0
36 TraesCS5A01G099200 chr7B 83.735 166 24 3 3715 3878 261051751 261051915 3.330000e-33 154.0
37 TraesCS5A01G099200 chr7A 83.636 165 24 3 3716 3878 309411633 309411796 1.200000e-32 152.0
38 TraesCS5A01G099200 chr6B 83.186 113 15 4 3164 3276 691636923 691636815 4.400000e-17 100.0
39 TraesCS5A01G099200 chr3D 80.451 133 15 8 3002 3129 320640549 320640675 2.650000e-14 91.6
40 TraesCS5A01G099200 chr2D 90.769 65 6 0 2253 2317 394525198 394525134 3.430000e-13 87.9
41 TraesCS5A01G099200 chr2B 90.769 65 6 0 2253 2317 466165306 466165242 3.430000e-13 87.9
42 TraesCS5A01G099200 chr1D 89.855 69 3 2 2253 2317 317439597 317439529 1.230000e-12 86.1


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 TraesCS5A01G099200 chr5A 141876408 141883304 6896 True 4289.533333 12737 98.245333 1 6897 3 chr5A.!!$R4 6896
1 TraesCS5A01G099200 chr5D 126567650 126574665 7015 True 5623.500000 7496 95.833500 1 6897 2 chr5D.!!$R2 6896
2 TraesCS5A01G099200 chr5B 139349363 139352900 3537 True 2245.500000 3794 92.384000 1 2940 2 chr5B.!!$R2 2939
3 TraesCS5A01G099200 chr5B 139339751 139343830 4079 True 1254.620000 3441 96.140600 2945 6838 5 chr5B.!!$R1 3893

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
970 1593 1.512734 CAGAAATTCTGCACGCGCC 60.513 57.895 10.30 0.0 37.72 6.53 F
1494 2128 2.159382 CCGTTGCCATGTTAACCTCTT 58.841 47.619 2.48 0.0 0.00 2.85 F
2020 2659 3.025322 TCTTTTCCTGGGCTTTGTTCA 57.975 42.857 0.00 0.0 0.00 3.18 F
2939 3595 0.693049 AGGTGGATCTGGGTGACAAC 59.307 55.000 0.00 0.0 0.00 3.32 F
3679 4337 0.695347 CCTTCCTTGCTTCTCCAGGT 59.305 55.000 0.00 0.0 0.00 4.00 F
4871 5664 1.203162 TCCCCATGGCATGTTTCTTGT 60.203 47.619 24.80 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2882 0.392595 GGAACGCGGGAAGGAATTCT 60.393 55.000 12.47 0.00 0.00 2.40 R
2844 3489 2.573941 GCATTGGCAGGAAGAACATC 57.426 50.000 0.00 0.00 40.72 3.06 R
3794 4452 0.247736 GATGACAAGAGCTCACCCGT 59.752 55.000 17.77 6.77 0.00 5.28 R
3799 4457 0.532573 GGACCGATGACAAGAGCTCA 59.467 55.000 17.77 0.00 0.00 4.26 R
5111 5904 0.442310 CAGCGACAATACCACAACGG 59.558 55.000 0.00 0.00 42.50 4.44 R
6819 7943 1.067250 GACAGCAGAGCGGAGGATC 59.933 63.158 0.00 0.00 0.00 3.36 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
202 209 5.650703 TCGAGACACTAATCTGTTGGTCATA 59.349 40.000 0.00 0.00 0.00 2.15
399 407 3.433306 TTAAGAAGGGTGACATGGGTG 57.567 47.619 0.00 0.00 0.00 4.61
414 422 4.892934 ACATGGGTGTCTTTCTAAAAGCAA 59.107 37.500 0.00 0.00 31.41 3.91
421 429 7.039993 GGGTGTCTTTCTAAAAGCAATTTCCTA 60.040 37.037 0.00 0.00 32.27 2.94
423 431 9.346725 GTGTCTTTCTAAAAGCAATTTCCTATG 57.653 33.333 0.00 0.00 32.27 2.23
557 565 5.699143 AGATTTCCTCTATGGTTCCCAATG 58.301 41.667 0.00 0.00 36.95 2.82
765 1387 5.651139 CACAGAATCCATCATCAGTTTTCCT 59.349 40.000 0.00 0.00 0.00 3.36
766 1388 5.651139 ACAGAATCCATCATCAGTTTTCCTG 59.349 40.000 0.00 0.00 42.97 3.86
782 1404 2.057922 TCCTGCTGGAGGACTTTCTTT 58.942 47.619 14.48 0.00 46.96 2.52
785 1407 4.006319 CCTGCTGGAGGACTTTCTTTAAG 58.994 47.826 10.00 0.00 46.33 1.85
962 1585 4.452455 ACCTCAAACTACGCAGAAATTCTG 59.548 41.667 18.02 18.02 46.90 3.02
969 1592 4.047030 CAGAAATTCTGCACGCGC 57.953 55.556 10.30 0.00 37.72 6.86
970 1593 1.512734 CAGAAATTCTGCACGCGCC 60.513 57.895 10.30 0.00 37.72 6.53
971 1594 2.202479 GAAATTCTGCACGCGCCC 60.202 61.111 5.73 0.00 37.32 6.13
972 1595 4.101790 AAATTCTGCACGCGCCCG 62.102 61.111 5.73 0.00 37.32 6.13
1021 1644 2.359975 GCACCACCGAGGGAAAGG 60.360 66.667 0.00 0.00 43.89 3.11
1055 1678 4.593864 GGAGGAGATGGCGCGGTC 62.594 72.222 8.83 1.23 0.00 4.79
1204 1838 2.478539 GGACCGCAATCTTTGAATGAGC 60.479 50.000 0.00 0.00 0.00 4.26
1205 1839 2.161855 ACCGCAATCTTTGAATGAGCA 58.838 42.857 0.00 0.00 0.00 4.26
1206 1840 2.557924 ACCGCAATCTTTGAATGAGCAA 59.442 40.909 0.00 0.00 0.00 3.91
1207 1841 3.194116 ACCGCAATCTTTGAATGAGCAAT 59.806 39.130 0.00 0.00 0.00 3.56
1208 1842 3.795101 CCGCAATCTTTGAATGAGCAATC 59.205 43.478 0.00 0.00 0.00 2.67
1209 1843 4.439700 CCGCAATCTTTGAATGAGCAATCT 60.440 41.667 0.00 0.00 0.00 2.40
1210 1844 5.100259 CGCAATCTTTGAATGAGCAATCTT 58.900 37.500 0.00 0.00 0.00 2.40
1211 1845 5.575606 CGCAATCTTTGAATGAGCAATCTTT 59.424 36.000 0.00 0.00 0.00 2.52
1212 1846 6.453791 CGCAATCTTTGAATGAGCAATCTTTG 60.454 38.462 0.00 0.00 0.00 2.77
1213 1847 6.588756 GCAATCTTTGAATGAGCAATCTTTGA 59.411 34.615 0.00 0.00 0.00 2.69
1214 1848 7.201444 GCAATCTTTGAATGAGCAATCTTTGAG 60.201 37.037 0.00 0.00 0.00 3.02
1371 2005 4.405671 TCGCGTCTCCCGGAGTCT 62.406 66.667 14.36 0.00 36.94 3.24
1494 2128 2.159382 CCGTTGCCATGTTAACCTCTT 58.841 47.619 2.48 0.00 0.00 2.85
1498 2132 3.500448 TGCCATGTTAACCTCTTCACA 57.500 42.857 2.48 0.00 0.00 3.58
1553 2187 4.504858 CAGGATAAAAGAAGCGTACCAGT 58.495 43.478 0.00 0.00 0.00 4.00
1689 2323 4.244066 GCTGATAGCCTGATACAGTCATG 58.756 47.826 0.00 0.00 35.97 3.07
1853 2491 5.402054 AGATCCATCTAGTCTCTTGGTCT 57.598 43.478 0.00 0.00 34.85 3.85
2020 2659 3.025322 TCTTTTCCTGGGCTTTGTTCA 57.975 42.857 0.00 0.00 0.00 3.18
2119 2758 5.938125 TGTACCTTTACTTGAGAAATCTGGC 59.062 40.000 0.00 0.00 0.00 4.85
2206 2846 8.187354 TGCATTGCAATTGTGATGTTAAATAG 57.813 30.769 9.83 0.00 34.76 1.73
2374 3018 7.560796 ACCTATCAGGGTATTTCTAATCAGG 57.439 40.000 0.00 0.00 40.58 3.86
2660 3304 6.536224 TCAGTGCTGTAGTTATGATGATTGTG 59.464 38.462 0.00 0.00 0.00 3.33
2844 3489 8.110002 CAGTTGCTTAAAGTTTGCTTTGTTAAG 58.890 33.333 0.00 0.00 44.00 1.85
2846 3491 8.817100 GTTGCTTAAAGTTTGCTTTGTTAAGAT 58.183 29.630 0.00 0.00 44.00 2.40
2939 3595 0.693049 AGGTGGATCTGGGTGACAAC 59.307 55.000 0.00 0.00 0.00 3.32
2976 3632 5.541845 TGAGGAAACACTCACATAGACAAG 58.458 41.667 0.00 0.00 42.26 3.16
2977 3633 5.304357 TGAGGAAACACTCACATAGACAAGA 59.696 40.000 0.00 0.00 42.26 3.02
2978 3634 6.014242 TGAGGAAACACTCACATAGACAAGAT 60.014 38.462 0.00 0.00 42.26 2.40
2979 3635 6.773638 AGGAAACACTCACATAGACAAGATT 58.226 36.000 0.00 0.00 0.00 2.40
2980 3636 6.876257 AGGAAACACTCACATAGACAAGATTC 59.124 38.462 0.00 0.00 0.00 2.52
2981 3637 6.650807 GGAAACACTCACATAGACAAGATTCA 59.349 38.462 0.00 0.00 0.00 2.57
2982 3638 7.360438 GGAAACACTCACATAGACAAGATTCAC 60.360 40.741 0.00 0.00 0.00 3.18
2983 3639 5.482908 ACACTCACATAGACAAGATTCACC 58.517 41.667 0.00 0.00 0.00 4.02
2984 3640 5.012046 ACACTCACATAGACAAGATTCACCA 59.988 40.000 0.00 0.00 0.00 4.17
2985 3641 5.349817 CACTCACATAGACAAGATTCACCAC 59.650 44.000 0.00 0.00 0.00 4.16
2986 3642 4.832248 TCACATAGACAAGATTCACCACC 58.168 43.478 0.00 0.00 0.00 4.61
2987 3643 4.285775 TCACATAGACAAGATTCACCACCA 59.714 41.667 0.00 0.00 0.00 4.17
2988 3644 5.003160 CACATAGACAAGATTCACCACCAA 58.997 41.667 0.00 0.00 0.00 3.67
2989 3645 5.473162 CACATAGACAAGATTCACCACCAAA 59.527 40.000 0.00 0.00 0.00 3.28
2990 3646 5.707298 ACATAGACAAGATTCACCACCAAAG 59.293 40.000 0.00 0.00 0.00 2.77
2991 3647 4.170468 AGACAAGATTCACCACCAAAGT 57.830 40.909 0.00 0.00 0.00 2.66
2992 3648 5.304686 AGACAAGATTCACCACCAAAGTA 57.695 39.130 0.00 0.00 0.00 2.24
2993 3649 5.063880 AGACAAGATTCACCACCAAAGTAC 58.936 41.667 0.00 0.00 0.00 2.73
2994 3650 5.048846 ACAAGATTCACCACCAAAGTACT 57.951 39.130 0.00 0.00 0.00 2.73
2995 3651 5.063880 ACAAGATTCACCACCAAAGTACTC 58.936 41.667 0.00 0.00 0.00 2.59
2996 3652 4.974645 AGATTCACCACCAAAGTACTCA 57.025 40.909 0.00 0.00 0.00 3.41
2997 3653 4.642429 AGATTCACCACCAAAGTACTCAC 58.358 43.478 0.00 0.00 0.00 3.51
2998 3654 3.916359 TTCACCACCAAAGTACTCACA 57.084 42.857 0.00 0.00 0.00 3.58
2999 3655 4.431416 TTCACCACCAAAGTACTCACAT 57.569 40.909 0.00 0.00 0.00 3.21
3000 3656 5.554437 TTCACCACCAAAGTACTCACATA 57.446 39.130 0.00 0.00 0.00 2.29
3001 3657 5.147330 TCACCACCAAAGTACTCACATAG 57.853 43.478 0.00 0.00 0.00 2.23
3002 3658 4.836175 TCACCACCAAAGTACTCACATAGA 59.164 41.667 0.00 0.00 0.00 1.98
3003 3659 4.929808 CACCACCAAAGTACTCACATAGAC 59.070 45.833 0.00 0.00 0.00 2.59
3004 3660 4.591498 ACCACCAAAGTACTCACATAGACA 59.409 41.667 0.00 0.00 0.00 3.41
3005 3661 5.071250 ACCACCAAAGTACTCACATAGACAA 59.929 40.000 0.00 0.00 0.00 3.18
3052 3708 1.163420 ATGCCAAAACGAGACGCACA 61.163 50.000 0.00 0.00 31.17 4.57
3109 3765 6.954352 ACTAGGGTAGTTCTTCCAAATCTT 57.046 37.500 0.00 0.00 34.86 2.40
3356 4012 1.743394 CGGACCTTACCCAAAATCTGC 59.257 52.381 0.00 0.00 0.00 4.26
3432 4088 3.079578 CAATTCTTCAGAGGCTTCAGCA 58.920 45.455 0.00 0.00 44.36 4.41
3464 4120 0.902531 TCTGGTCGATTTGGAGGGTC 59.097 55.000 0.00 0.00 0.00 4.46
3581 4239 2.992114 AGCGCTCTCCCGACTGTT 60.992 61.111 2.64 0.00 0.00 3.16
3656 4314 2.747855 CCTCGCTTGGGACTTGGC 60.748 66.667 0.00 0.00 0.00 4.52
3679 4337 0.695347 CCTTCCTTGCTTCTCCAGGT 59.305 55.000 0.00 0.00 0.00 4.00
3899 4560 1.355720 CCATCTTTGGTCCACCTTCCT 59.644 52.381 0.00 0.00 38.30 3.36
4051 4712 4.926140 TGACAATTTGTTACACATGGCA 57.074 36.364 3.08 0.00 0.00 4.92
4068 4729 7.283127 ACACATGGCATAACAACTATTAGGAAG 59.717 37.037 0.00 0.00 0.00 3.46
4106 4767 1.846712 GCTGAAGGCCAGGTTCTCCT 61.847 60.000 5.01 0.00 46.37 3.69
4135 4796 7.450074 TGGAACTCTTGTTGTGTATGTATTCT 58.550 34.615 0.00 0.00 36.39 2.40
4155 4816 4.808558 TCTGTGATTGGCTTATTGTTTGC 58.191 39.130 0.00 0.00 0.00 3.68
4235 4896 8.326680 AGTATTTTTGGAAAATGCAGAAATGG 57.673 30.769 13.86 0.00 34.41 3.16
4651 5312 4.965532 ACACAAGACCTTAGGCTCTGATAT 59.034 41.667 0.00 0.00 0.00 1.63
4652 5313 6.136857 ACACAAGACCTTAGGCTCTGATATA 58.863 40.000 0.00 0.00 0.00 0.86
4756 5549 8.934023 TTCAACAAATACTTCTACATTCCCTT 57.066 30.769 0.00 0.00 0.00 3.95
4871 5664 1.203162 TCCCCATGGCATGTTTCTTGT 60.203 47.619 24.80 0.00 0.00 3.16
4872 5665 2.042297 TCCCCATGGCATGTTTCTTGTA 59.958 45.455 24.80 0.32 0.00 2.41
5111 5904 5.655532 TGACTGAACATAGGGTAGTAAGACC 59.344 44.000 0.00 0.00 38.93 3.85
5194 5987 7.500992 TGGTAGACATTAAAAGCCTATCTGAG 58.499 38.462 0.00 0.00 0.00 3.35
5590 6383 0.470456 TAGTCTGGTCCGTGGTGGTT 60.470 55.000 0.00 0.00 39.52 3.67
5987 6780 4.437239 GTCCTGTGACCTGTCTGATATTG 58.563 47.826 0.00 0.00 35.34 1.90
6075 6886 5.324409 ACAGCCAGGAAAATCTAAATGACA 58.676 37.500 0.00 0.00 0.00 3.58
6236 7332 7.264947 CAGTGTTACAGATTTTTGGAAAAGGT 58.735 34.615 0.00 0.00 0.00 3.50
6743 7867 7.506599 TGCCATTTCTGTTGGTCAATCATATAT 59.493 33.333 0.00 0.00 36.57 0.86
6886 8010 1.491754 TGGATGCTATCATGCACCAGT 59.508 47.619 0.00 0.00 44.48 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 43 2.811317 GGCACGTCTCCAGCTTCG 60.811 66.667 0.00 0.00 0.00 3.79
165 172 4.079970 AGTGTCTCGATTCACTGAACCTA 58.920 43.478 17.68 0.00 42.30 3.08
276 284 8.425703 TCAATATTCGTGATTAGGACCATGTTA 58.574 33.333 0.00 0.00 0.00 2.41
277 285 7.279615 TCAATATTCGTGATTAGGACCATGTT 58.720 34.615 0.00 0.00 0.00 2.71
399 407 9.561270 GACATAGGAAATTGCTTTTAGAAAGAC 57.439 33.333 4.69 0.00 0.00 3.01
450 458 2.167693 TGGTGAGCTATACCACTTTCCG 59.832 50.000 16.24 0.00 43.00 4.30
505 513 4.409574 TGTAGGGTACAGAAACTGGAAACA 59.590 41.667 0.00 0.00 35.51 2.83
688 1307 6.420638 TCTAGTACAGTACCATGCAGACTAA 58.579 40.000 7.13 0.00 0.00 2.24
696 1315 6.538742 CCAAACCATTCTAGTACAGTACCATG 59.461 42.308 7.13 5.24 0.00 3.66
699 1318 6.290294 TCCAAACCATTCTAGTACAGTACC 57.710 41.667 7.13 0.00 0.00 3.34
765 1387 4.974645 TCTTAAAGAAAGTCCTCCAGCA 57.025 40.909 0.00 0.00 36.51 4.41
766 1388 6.635030 TTTTCTTAAAGAAAGTCCTCCAGC 57.365 37.500 0.00 0.00 44.14 4.85
778 1400 6.040842 AGCAGCCTCAAACATTTTCTTAAAGA 59.959 34.615 0.00 0.00 0.00 2.52
779 1401 6.145048 CAGCAGCCTCAAACATTTTCTTAAAG 59.855 38.462 0.00 0.00 0.00 1.85
782 1404 4.559300 GCAGCAGCCTCAAACATTTTCTTA 60.559 41.667 0.00 0.00 33.58 2.10
785 1407 2.064014 GCAGCAGCCTCAAACATTTTC 58.936 47.619 0.00 0.00 33.58 2.29
970 1593 4.939368 TGGGTGTTGGGCGTTCGG 62.939 66.667 0.00 0.00 0.00 4.30
971 1594 3.656045 GTGGGTGTTGGGCGTTCG 61.656 66.667 0.00 0.00 0.00 3.95
972 1595 3.292159 GGTGGGTGTTGGGCGTTC 61.292 66.667 0.00 0.00 0.00 3.95
973 1596 4.130554 TGGTGGGTGTTGGGCGTT 62.131 61.111 0.00 0.00 0.00 4.84
974 1597 4.887190 GTGGTGGGTGTTGGGCGT 62.887 66.667 0.00 0.00 0.00 5.68
1204 1838 4.857588 GCATCAAAGCTCACTCAAAGATTG 59.142 41.667 0.00 0.00 0.00 2.67
1205 1839 4.379186 CGCATCAAAGCTCACTCAAAGATT 60.379 41.667 0.00 0.00 0.00 2.40
1206 1840 3.126514 CGCATCAAAGCTCACTCAAAGAT 59.873 43.478 0.00 0.00 0.00 2.40
1207 1841 2.481568 CGCATCAAAGCTCACTCAAAGA 59.518 45.455 0.00 0.00 0.00 2.52
1208 1842 2.481568 TCGCATCAAAGCTCACTCAAAG 59.518 45.455 0.00 0.00 0.00 2.77
1209 1843 2.493035 TCGCATCAAAGCTCACTCAAA 58.507 42.857 0.00 0.00 0.00 2.69
1210 1844 2.168326 TCGCATCAAAGCTCACTCAA 57.832 45.000 0.00 0.00 0.00 3.02
1211 1845 2.004733 CATCGCATCAAAGCTCACTCA 58.995 47.619 0.00 0.00 0.00 3.41
1212 1846 2.274437 TCATCGCATCAAAGCTCACTC 58.726 47.619 0.00 0.00 0.00 3.51
1213 1847 2.277969 CTCATCGCATCAAAGCTCACT 58.722 47.619 0.00 0.00 0.00 3.41
1214 1848 1.267932 GCTCATCGCATCAAAGCTCAC 60.268 52.381 0.00 0.00 38.92 3.51
1371 2005 1.301716 GCACGCCTGACTCCAGAAA 60.302 57.895 0.00 0.00 43.02 2.52
1494 2128 4.216902 CAGAGGCTGTGAATGAAAATGTGA 59.783 41.667 5.59 0.00 0.00 3.58
1498 2132 2.494870 GGCAGAGGCTGTGAATGAAAAT 59.505 45.455 16.83 0.00 40.87 1.82
1598 2232 9.209175 GATTCGTCAATATACAGCCTCTAAAAT 57.791 33.333 0.00 0.00 0.00 1.82
1616 2250 7.174080 TCAAATTATCAACAACCTGATTCGTCA 59.826 33.333 0.00 0.00 37.27 4.35
1853 2491 9.747898 ATACAGTAAGGACATCAACCAAAATAA 57.252 29.630 0.00 0.00 0.00 1.40
2020 2659 3.580458 ACCTGTGAAGCTCAGTCACTATT 59.420 43.478 16.02 0.42 44.70 1.73
2162 2802 5.646467 TGCAGAAACGTTTAGAAGTGTAC 57.354 39.130 14.65 0.00 0.00 2.90
2177 2817 4.633175 ACATCACAATTGCAATGCAGAAA 58.367 34.783 13.82 0.00 40.61 2.52
2179 2819 3.945981 ACATCACAATTGCAATGCAGA 57.054 38.095 13.82 11.18 40.61 4.26
2236 2880 2.624636 GAACGCGGGAAGGAATTCTTA 58.375 47.619 12.47 0.00 35.50 2.10
2237 2881 1.450025 GAACGCGGGAAGGAATTCTT 58.550 50.000 12.47 0.00 38.65 2.52
2238 2882 0.392595 GGAACGCGGGAAGGAATTCT 60.393 55.000 12.47 0.00 0.00 2.40
2239 2883 0.675522 TGGAACGCGGGAAGGAATTC 60.676 55.000 12.47 1.71 0.00 2.17
2341 2985 8.925338 AGAAATACCCTGATAGGTACAAAGTAG 58.075 37.037 0.00 0.00 45.08 2.57
2660 3304 3.378427 ACATATTTCTTTCTTCGGGCTGC 59.622 43.478 0.00 0.00 0.00 5.25
2844 3489 2.573941 GCATTGGCAGGAAGAACATC 57.426 50.000 0.00 0.00 40.72 3.06
2939 3595 5.576774 GTGTTTCCTCAAAAGTTTTCCACAG 59.423 40.000 0.00 0.00 0.00 3.66
2976 3632 4.385825 TGTGAGTACTTTGGTGGTGAATC 58.614 43.478 0.00 0.00 0.00 2.52
2977 3633 4.431416 TGTGAGTACTTTGGTGGTGAAT 57.569 40.909 0.00 0.00 0.00 2.57
2978 3634 3.916359 TGTGAGTACTTTGGTGGTGAA 57.084 42.857 0.00 0.00 0.00 3.18
2979 3635 4.836175 TCTATGTGAGTACTTTGGTGGTGA 59.164 41.667 0.00 0.00 0.00 4.02
2980 3636 4.929808 GTCTATGTGAGTACTTTGGTGGTG 59.070 45.833 0.00 0.00 0.00 4.17
2981 3637 4.591498 TGTCTATGTGAGTACTTTGGTGGT 59.409 41.667 0.00 0.00 0.00 4.16
2982 3638 5.147330 TGTCTATGTGAGTACTTTGGTGG 57.853 43.478 0.00 0.00 0.00 4.61
2983 3639 6.455647 TCTTGTCTATGTGAGTACTTTGGTG 58.544 40.000 0.00 0.00 0.00 4.17
2984 3640 6.665992 TCTTGTCTATGTGAGTACTTTGGT 57.334 37.500 0.00 0.00 0.00 3.67
2985 3641 7.819415 TGAATCTTGTCTATGTGAGTACTTTGG 59.181 37.037 0.00 0.00 0.00 3.28
2986 3642 8.651588 GTGAATCTTGTCTATGTGAGTACTTTG 58.348 37.037 0.00 0.00 0.00 2.77
2987 3643 7.819900 GGTGAATCTTGTCTATGTGAGTACTTT 59.180 37.037 0.00 0.00 0.00 2.66
2988 3644 7.039011 TGGTGAATCTTGTCTATGTGAGTACTT 60.039 37.037 0.00 0.00 0.00 2.24
2989 3645 6.437477 TGGTGAATCTTGTCTATGTGAGTACT 59.563 38.462 0.00 0.00 0.00 2.73
2990 3646 6.531948 GTGGTGAATCTTGTCTATGTGAGTAC 59.468 42.308 0.00 0.00 0.00 2.73
2991 3647 6.351033 GGTGGTGAATCTTGTCTATGTGAGTA 60.351 42.308 0.00 0.00 0.00 2.59
2992 3648 5.482908 GTGGTGAATCTTGTCTATGTGAGT 58.517 41.667 0.00 0.00 0.00 3.41
2993 3649 4.872691 GGTGGTGAATCTTGTCTATGTGAG 59.127 45.833 0.00 0.00 0.00 3.51
2994 3650 4.285775 TGGTGGTGAATCTTGTCTATGTGA 59.714 41.667 0.00 0.00 0.00 3.58
2995 3651 4.578871 TGGTGGTGAATCTTGTCTATGTG 58.421 43.478 0.00 0.00 0.00 3.21
2996 3652 4.908601 TGGTGGTGAATCTTGTCTATGT 57.091 40.909 0.00 0.00 0.00 2.29
2997 3653 5.707298 ACTTTGGTGGTGAATCTTGTCTATG 59.293 40.000 0.00 0.00 0.00 2.23
2998 3654 5.880901 ACTTTGGTGGTGAATCTTGTCTAT 58.119 37.500 0.00 0.00 0.00 1.98
2999 3655 5.304686 ACTTTGGTGGTGAATCTTGTCTA 57.695 39.130 0.00 0.00 0.00 2.59
3000 3656 4.170468 ACTTTGGTGGTGAATCTTGTCT 57.830 40.909 0.00 0.00 0.00 3.41
3001 3657 5.063880 AGTACTTTGGTGGTGAATCTTGTC 58.936 41.667 0.00 0.00 0.00 3.18
3002 3658 5.048846 AGTACTTTGGTGGTGAATCTTGT 57.951 39.130 0.00 0.00 0.00 3.16
3003 3659 5.063204 TGAGTACTTTGGTGGTGAATCTTG 58.937 41.667 0.00 0.00 0.00 3.02
3004 3660 5.304686 TGAGTACTTTGGTGGTGAATCTT 57.695 39.130 0.00 0.00 0.00 2.40
3005 3661 4.974645 TGAGTACTTTGGTGGTGAATCT 57.025 40.909 0.00 0.00 0.00 2.40
3052 3708 2.799017 TGTTGCTGCTTGGATCTTGAT 58.201 42.857 0.00 0.00 0.00 2.57
3109 3765 4.230733 TCTCTCAAGACCCATCTCTCCTAA 59.769 45.833 0.00 0.00 32.34 2.69
3356 4012 4.938080 ACTGTCAAGTAGTTCTGTCTGTG 58.062 43.478 0.00 0.00 33.79 3.66
3372 4028 2.891580 GTCCACTCTGACCTAACTGTCA 59.108 50.000 0.00 0.00 42.75 3.58
3432 4088 2.989824 CCAGACTGTCCGGTCGGT 60.990 66.667 13.27 13.27 40.76 4.69
3453 4109 2.998949 GCCCTCGACCCTCCAAAT 59.001 61.111 0.00 0.00 0.00 2.32
3656 4314 1.352352 TGGAGAAGCAAGGAAGGAAGG 59.648 52.381 0.00 0.00 0.00 3.46
3679 4337 7.938490 TGTATGCTTAGATATGAAGGCATGAAA 59.062 33.333 11.62 0.00 35.94 2.69
3794 4452 0.247736 GATGACAAGAGCTCACCCGT 59.752 55.000 17.77 6.77 0.00 5.28
3799 4457 0.532573 GGACCGATGACAAGAGCTCA 59.467 55.000 17.77 0.00 0.00 4.26
4051 4712 8.822805 TGACAAGGTCTTCCTAATAGTTGTTAT 58.177 33.333 0.00 0.00 44.35 1.89
4106 4767 6.061441 ACATACACAACAAGAGTTCCATCAA 58.939 36.000 0.00 0.00 35.28 2.57
4135 4796 3.573598 CGCAAACAATAAGCCAATCACA 58.426 40.909 0.00 0.00 0.00 3.58
4155 4816 1.447317 AACTGCCAAGTGTCAAGCCG 61.447 55.000 0.00 0.00 36.51 5.52
4235 4896 2.743928 CCACAGCGACCTTCCTGC 60.744 66.667 0.00 0.00 32.37 4.85
4433 5094 4.436584 GCTAGTGCATGAAGCTTAACAGTG 60.437 45.833 0.00 0.00 45.94 3.66
4651 5312 6.934645 GCTAGTGCATGAAGGTTAATATGGTA 59.065 38.462 0.00 0.00 39.41 3.25
4652 5313 5.765182 GCTAGTGCATGAAGGTTAATATGGT 59.235 40.000 0.00 0.00 39.41 3.55
4662 5323 1.945394 GTGATGGCTAGTGCATGAAGG 59.055 52.381 0.00 0.00 41.91 3.46
4871 5664 8.762645 CCTTGCACTCCATTCCTAGAATATATA 58.237 37.037 0.00 0.00 0.00 0.86
4872 5665 7.628234 CCTTGCACTCCATTCCTAGAATATAT 58.372 38.462 0.00 0.00 0.00 0.86
5066 5859 6.551601 AGTCATGAACTTAGGTAGACCCATAG 59.448 42.308 0.00 0.00 33.03 2.23
5111 5904 0.442310 CAGCGACAATACCACAACGG 59.558 55.000 0.00 0.00 42.50 4.44
5118 5911 2.603560 GCAGAAGTACAGCGACAATACC 59.396 50.000 0.00 0.00 0.00 2.73
5194 5987 3.131046 CCTGTGGAGGGAACAAATTATGC 59.869 47.826 0.00 0.00 35.40 3.14
5286 6079 3.476552 TCGCAGATTTGACAACCTCTTT 58.523 40.909 0.00 0.00 0.00 2.52
5934 6727 3.806380 ACAGCCAATGCATTTCAAACAA 58.194 36.364 9.83 0.00 41.13 2.83
5943 6736 3.638160 CCAATTACCTACAGCCAATGCAT 59.362 43.478 0.00 0.00 41.13 3.96
6075 6886 7.441157 TGATAAGTCGCTTCCGAAATTATCAAT 59.559 33.333 20.59 1.57 46.96 2.57
6213 7309 6.478673 CCACCTTTTCCAAAAATCTGTAACAC 59.521 38.462 0.00 0.00 0.00 3.32
6236 7332 2.754552 GGATGCATCTTTAACACTGCCA 59.245 45.455 25.28 0.00 33.70 4.92
6625 7749 6.140110 CACGAAACAAGAATTTGTAATCCGT 58.860 36.000 0.00 0.00 46.54 4.69
6792 7916 5.442391 CATGATGATCATGCCCATATGGTA 58.558 41.667 21.08 9.52 46.37 3.25
6819 7943 1.067250 GACAGCAGAGCGGAGGATC 59.933 63.158 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.