Multiple sequence alignment - TraesCS7A01G259800

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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 TraesCS7A01G259800 chr7A 100.000 2205 0 0 1551 3755 251750104 251747900 0.000000e+00 4072.0
1 TraesCS7A01G259800 chr7A 100.000 1186 0 0 1 1186 251751654 251750469 0.000000e+00 2191.0
2 TraesCS7A01G259800 chr7A 100.000 37 0 0 494 530 251751124 251751088 6.730000e-08 69.4
3 TraesCS7A01G259800 chr7A 100.000 37 0 0 531 567 251751161 251751125 6.730000e-08 69.4
4 TraesCS7A01G259800 chr7B 94.485 1106 48 8 1551 2650 213256341 213255243 0.000000e+00 1692.0
5 TraesCS7A01G259800 chr7B 85.529 850 107 10 2914 3755 213253507 213252666 0.000000e+00 874.0
6 TraesCS7A01G259800 chr7B 93.968 431 17 6 762 1186 213256827 213256400 0.000000e+00 643.0
7 TraesCS7A01G259800 chr7B 93.243 148 9 1 2645 2791 213255194 213255047 2.270000e-52 217.0
8 TraesCS7A01G259800 chr7B 86.585 164 19 2 532 694 213266558 213266397 1.070000e-40 178.0
9 TraesCS7A01G259800 chr7D 93.920 1102 45 6 1554 2651 236647225 236646142 0.000000e+00 1644.0
10 TraesCS7A01G259800 chr7D 92.649 925 52 8 1551 2465 429708391 429709309 0.000000e+00 1317.0
11 TraesCS7A01G259800 chr7D 85.464 798 81 9 2979 3755 236645789 236645006 0.000000e+00 798.0
12 TraesCS7A01G259800 chr7D 91.158 475 36 5 1 473 429707059 429707529 1.140000e-179 640.0
13 TraesCS7A01G259800 chr7D 94.118 425 9 6 762 1186 236647692 236647284 1.900000e-177 632.0
14 TraesCS7A01G259800 chr7D 94.065 337 12 3 850 1186 429708004 429708332 4.330000e-139 505.0
15 TraesCS7A01G259800 chr7D 95.406 283 12 1 2369 2651 429709351 429709632 2.060000e-122 449.0
16 TraesCS7A01G259800 chr7D 92.230 296 15 7 2645 2934 236646095 236645802 2.700000e-111 412.0
17 TraesCS7A01G259800 chr7D 90.116 172 14 2 325 493 236649849 236649678 1.760000e-53 220.0
18 TraesCS7A01G259800 chr7D 88.415 164 17 1 531 694 236649608 236649447 2.960000e-46 196.0
19 TraesCS7A01G259800 chr7D 87.879 165 18 1 531 695 429707609 429707771 3.830000e-45 193.0
20 TraesCS7A01G259800 chr7D 97.222 108 2 1 2645 2751 429709679 429709786 8.290000e-42 182.0
21 TraesCS7A01G259800 chr7D 93.878 98 4 2 2369 2465 429709282 429709378 3.020000e-31 147.0
22 TraesCS7A01G259800 chr7D 92.727 55 4 0 269 323 236678557 236678503 3.110000e-11 80.5
23 TraesCS7A01G259800 chr4D 80.682 704 80 31 1970 2649 499292517 499291846 2.610000e-136 496.0
24 TraesCS7A01G259800 chr5A 79.718 710 91 27 1970 2649 680077388 680076702 7.350000e-127 464.0
25 TraesCS7A01G259800 chr5A 81.988 161 25 3 960 1118 680078548 680078390 2.350000e-27 134.0
26 TraesCS7A01G259800 chr5A 86.842 76 9 1 2110 2185 496287828 496287754 2.400000e-12 84.2
27 TraesCS7A01G259800 chr5A 86.842 76 9 1 2110 2185 496572425 496572351 2.400000e-12 84.2
28 TraesCS7A01G259800 chr4B 85.232 237 13 10 960 1182 642088939 642088711 1.360000e-54 224.0
29 TraesCS7A01G259800 chrUn 85.526 76 10 1 2110 2185 359420047 359420121 1.120000e-10 78.7
30 TraesCS7A01G259800 chr5B 85.526 76 10 1 2110 2185 474319611 474319537 1.120000e-10 78.7


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 TraesCS7A01G259800 chr7A 251747900 251751654 3754 True 1600.450000 4072 100.000000 1 3755 4 chr7A.!!$R1 3754
1 TraesCS7A01G259800 chr7B 213252666 213256827 4161 True 856.500000 1692 91.806250 762 3755 4 chr7B.!!$R2 2993
2 TraesCS7A01G259800 chr7D 236645006 236649849 4843 True 650.333333 1644 90.710500 325 3755 6 chr7D.!!$R2 3430
3 TraesCS7A01G259800 chr7D 429707059 429709786 2727 False 490.428571 1317 93.179571 1 2751 7 chr7D.!!$F1 2750
4 TraesCS7A01G259800 chr4D 499291846 499292517 671 True 496.000000 496 80.682000 1970 2649 1 chr4D.!!$R1 679
5 TraesCS7A01G259800 chr5A 680076702 680078548 1846 True 299.000000 464 80.853000 960 2649 2 chr5A.!!$R3 1689

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
972 2765 0.044855 ACAAGGCCATAGTCTCCCCT 59.955 55.0 5.01 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2854 6752 0.25064 ACAAGAGCAGCTGTTGGAGG 60.251 55.0 30.19 10.81 38.76 4.3 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
48 51 6.229561 ACTAGCTTTTTCAATGAACGAGTC 57.770 37.500 0.00 0.00 0.00 3.36
49 52 4.133856 AGCTTTTTCAATGAACGAGTCG 57.866 40.909 11.85 11.85 0.00 4.18
68 71 6.787515 CGAGTCGTTATCACATGCATATTTTC 59.212 38.462 3.82 0.00 0.00 2.29
84 87 6.183360 GCATATTTTCACCTGGTTGATCGTTA 60.183 38.462 0.00 0.00 0.00 3.18
113 116 4.023291 GGGCAATATGGTTTTCAAGGAGA 58.977 43.478 0.00 0.00 0.00 3.71
120 123 3.370104 TGGTTTTCAAGGAGAAAGGCAA 58.630 40.909 0.00 0.00 46.24 4.52
128 131 1.065854 AGGAGAAAGGCAATCCACGAG 60.066 52.381 0.00 0.00 35.45 4.18
144 147 6.123045 TCCACGAGGATATACATCAGAGTA 57.877 41.667 0.00 0.00 39.61 2.59
145 148 6.722328 TCCACGAGGATATACATCAGAGTAT 58.278 40.000 0.00 0.00 39.61 2.12
182 185 7.275888 TCATTTTGTCAACTCTTACAATGCT 57.724 32.000 0.00 0.00 35.64 3.79
218 221 0.329596 AAGACCCAAAGGCTAGCCAG 59.670 55.000 34.70 22.69 38.92 4.85
240 243 3.428870 GCCGATACAAGTTCATGATACCG 59.571 47.826 0.00 0.00 0.00 4.02
248 251 4.927978 AGTTCATGATACCGGAGAGAAG 57.072 45.455 9.46 0.00 0.00 2.85
259 262 0.539518 GGAGAGAAGTGGCTTCCTCC 59.460 60.000 20.10 20.10 43.45 4.30
260 263 1.270907 GAGAGAAGTGGCTTCCTCCA 58.729 55.000 5.38 0.00 40.98 3.86
261 264 1.206849 GAGAGAAGTGGCTTCCTCCAG 59.793 57.143 5.38 0.00 40.98 3.86
262 265 0.251634 GAGAAGTGGCTTCCTCCAGG 59.748 60.000 5.38 0.00 40.98 4.45
268 271 1.301293 GGCTTCCTCCAGGGACAAG 59.699 63.158 0.00 0.00 45.03 3.16
274 277 1.371183 CTCCAGGGACAAGCAACGA 59.629 57.895 0.00 0.00 0.00 3.85
280 283 2.554032 CAGGGACAAGCAACGAGAAAAT 59.446 45.455 0.00 0.00 0.00 1.82
312 315 3.067106 GGAGCTTTCAATCAGAACGACA 58.933 45.455 0.00 0.00 35.56 4.35
344 347 3.552890 CCGCTGCTGCTATATGTAGAACA 60.553 47.826 14.03 0.00 36.97 3.18
345 348 3.672397 CGCTGCTGCTATATGTAGAACAG 59.328 47.826 14.03 5.32 36.97 3.16
346 349 4.557496 CGCTGCTGCTATATGTAGAACAGA 60.557 45.833 14.03 0.00 36.97 3.41
347 350 4.922692 GCTGCTGCTATATGTAGAACAGAG 59.077 45.833 8.53 7.81 36.03 3.35
348 351 4.876125 TGCTGCTATATGTAGAACAGAGC 58.124 43.478 0.00 0.00 34.65 4.09
367 373 3.084786 AGCAAGGAGTTTATGTTGGAGC 58.915 45.455 0.00 0.00 0.00 4.70
391 397 0.721718 GCGATTGTGGTGCAGAGTAC 59.278 55.000 0.00 0.00 0.00 2.73
484 492 5.934625 TCTCTCAAGAATAGTTGTTGCTTCC 59.065 40.000 0.00 0.00 34.25 3.46
490 498 3.764885 ATAGTTGTTGCTTCCGATTGC 57.235 42.857 0.00 0.00 0.00 3.56
498 576 1.766143 GCTTCCGATTGCAGCGTAGG 61.766 60.000 9.67 0.50 0.00 3.18
505 583 2.545526 CGATTGCAGCGTAGGAATCATT 59.454 45.455 18.07 0.00 43.84 2.57
506 584 3.002656 CGATTGCAGCGTAGGAATCATTT 59.997 43.478 18.07 0.00 43.84 2.32
507 585 4.496341 CGATTGCAGCGTAGGAATCATTTT 60.496 41.667 18.07 0.00 43.84 1.82
508 586 4.782019 TTGCAGCGTAGGAATCATTTTT 57.218 36.364 0.00 0.00 0.00 1.94
509 587 4.355543 TGCAGCGTAGGAATCATTTTTC 57.644 40.909 0.00 0.00 0.00 2.29
510 588 3.755905 TGCAGCGTAGGAATCATTTTTCA 59.244 39.130 0.00 0.00 0.00 2.69
511 589 4.217334 TGCAGCGTAGGAATCATTTTTCAA 59.783 37.500 0.00 0.00 0.00 2.69
512 590 4.558860 GCAGCGTAGGAATCATTTTTCAAC 59.441 41.667 0.00 0.00 0.00 3.18
513 591 5.698832 CAGCGTAGGAATCATTTTTCAACA 58.301 37.500 0.00 0.00 0.00 3.33
514 592 6.148948 CAGCGTAGGAATCATTTTTCAACAA 58.851 36.000 0.00 0.00 0.00 2.83
515 593 6.306356 CAGCGTAGGAATCATTTTTCAACAAG 59.694 38.462 0.00 0.00 0.00 3.16
516 594 6.016276 AGCGTAGGAATCATTTTTCAACAAGT 60.016 34.615 0.00 0.00 0.00 3.16
517 595 7.174253 AGCGTAGGAATCATTTTTCAACAAGTA 59.826 33.333 0.00 0.00 0.00 2.24
518 596 7.968405 GCGTAGGAATCATTTTTCAACAAGTAT 59.032 33.333 0.00 0.00 0.00 2.12
554 632 8.385898 ACGTAGGAATCATTTTTCAACAAGTA 57.614 30.769 0.00 0.00 0.00 2.24
626 704 5.237561 TCGCAAAGCACACTGTTAATTTAGA 59.762 36.000 0.00 0.00 0.00 2.10
640 718 9.337396 CTGTTAATTTAGATGTTGGTAGGCATA 57.663 33.333 0.00 0.00 0.00 3.14
867 2660 3.289836 CTTCTGATCTCTGAGCTCTCCA 58.710 50.000 16.19 3.12 0.00 3.86
899 2692 1.066143 CATGGACTACTTTCAGCCCGT 60.066 52.381 0.00 0.00 0.00 5.28
972 2765 0.044855 ACAAGGCCATAGTCTCCCCT 59.955 55.000 5.01 0.00 0.00 4.79
1660 3482 0.469917 CTTGGTGTGCCTCCGGATAT 59.530 55.000 3.57 0.00 35.27 1.63
1729 3559 0.538287 GCTTTTCCCTGCAGAGGTGT 60.538 55.000 17.39 0.00 37.73 4.16
1928 4216 8.638565 CATGTTTTTAGCTTTATCCTTTTCGTG 58.361 33.333 0.00 0.00 0.00 4.35
1942 4230 3.889196 TTTCGTGGTGTTTGTATCTGC 57.111 42.857 0.00 0.00 0.00 4.26
2026 4315 0.168128 GGCGAATTCGGGAACAACAG 59.832 55.000 27.78 0.00 40.23 3.16
2057 4347 5.412526 TTGAGTAAAAATCAAGACGCGTT 57.587 34.783 15.53 0.00 32.96 4.84
2193 4504 8.087982 TCTTTTGTATGTGAGAGTTCAATGAC 57.912 34.615 0.00 0.00 34.49 3.06
2200 4511 4.241681 GTGAGAGTTCAATGACTGGTCTC 58.758 47.826 2.38 0.00 34.49 3.36
2324 4637 2.565046 TCACTGTGGTGCATCATCAA 57.435 45.000 1.27 0.00 42.72 2.57
2500 4955 8.298854 GCTGATTTATTTTCCCTTTTGCAATTT 58.701 29.630 0.00 0.00 0.00 1.82
2615 5071 5.884792 AGAAGCACTTAGGAAAGGATGATTG 59.115 40.000 0.00 0.00 37.01 2.67
2731 5243 2.666619 GCAACTTCTGCCATGTTCTTCG 60.667 50.000 0.00 0.00 46.13 3.79
2751 5265 1.134877 GGTCTTTACTGGTCTACGCCC 60.135 57.143 0.00 0.00 0.00 6.13
2806 5321 4.917385 TCTCCAACAGCAGCCTATTTTAA 58.083 39.130 0.00 0.00 0.00 1.52
2807 5322 5.509498 TCTCCAACAGCAGCCTATTTTAAT 58.491 37.500 0.00 0.00 0.00 1.40
2809 5324 4.114794 CCAACAGCAGCCTATTTTAATGC 58.885 43.478 0.00 0.00 37.15 3.56
2810 5325 4.381825 CCAACAGCAGCCTATTTTAATGCA 60.382 41.667 0.00 0.00 39.34 3.96
2839 5354 1.377690 TATGAGCTTTTGGACCCCCA 58.622 50.000 0.00 0.00 41.64 4.96
2861 6759 0.756294 CCCCCACAAAAACCTCCAAC 59.244 55.000 0.00 0.00 0.00 3.77
2879 6777 2.057137 ACAGCTGCTCTTGTTGGAAA 57.943 45.000 15.27 0.00 0.00 3.13
2880 6778 2.378038 ACAGCTGCTCTTGTTGGAAAA 58.622 42.857 15.27 0.00 0.00 2.29
2938 6869 2.100216 GCCGGCTGTGTATTTGCG 59.900 61.111 22.15 0.00 0.00 4.85
3017 6948 2.361104 GGAACATTCCCGCAGCCA 60.361 61.111 0.00 0.00 41.62 4.75
3021 6952 0.975887 AACATTCCCGCAGCCAATTT 59.024 45.000 0.00 0.00 0.00 1.82
3033 6964 2.438434 CAATTTCCCTCCCGCGCT 60.438 61.111 5.56 0.00 0.00 5.92
3067 6998 2.501610 GATCCAGACACTCCCGCC 59.498 66.667 0.00 0.00 0.00 6.13
3069 7000 2.579684 GATCCAGACACTCCCGCCAC 62.580 65.000 0.00 0.00 0.00 5.01
3085 7016 0.036105 CCACAGCTGCACTACCATGA 60.036 55.000 15.27 0.00 0.00 3.07
3088 7019 1.280133 ACAGCTGCACTACCATGATGT 59.720 47.619 15.27 0.00 0.00 3.06
3091 7022 1.134280 GCTGCACTACCATGATGTCCT 60.134 52.381 0.00 0.00 0.00 3.85
3098 7029 4.100653 CACTACCATGATGTCCTGATCTGT 59.899 45.833 0.00 0.00 0.00 3.41
3102 7033 3.379240 CATGATGTCCTGATCTGTCGTC 58.621 50.000 0.00 1.48 0.00 4.20
3120 7051 2.770048 CCCCTCCTCCAATCGGCT 60.770 66.667 0.00 0.00 0.00 5.52
3150 7081 1.703411 CACAACACCCATTTCCACCT 58.297 50.000 0.00 0.00 0.00 4.00
3182 7113 1.451387 ATCGCCCCACCGACAAATC 60.451 57.895 0.00 0.00 40.40 2.17
3193 7124 0.870393 CGACAAATCTGCACTGCTGT 59.130 50.000 1.98 0.00 0.00 4.40
3242 7173 2.309528 ACGTGTGAAGAGCAAGTTCA 57.690 45.000 0.00 0.00 0.00 3.18
3250 7181 0.969894 AGAGCAAGTTCAGCTACCGT 59.030 50.000 0.00 0.00 43.58 4.83
3251 7182 1.071605 GAGCAAGTTCAGCTACCGTG 58.928 55.000 0.00 0.00 43.58 4.94
3257 7188 1.070105 TTCAGCTACCGTGGCGTTT 59.930 52.632 0.69 0.00 34.52 3.60
3296 7228 2.723010 CGTTTCAGCATCGAGTTTCAGC 60.723 50.000 0.00 0.00 0.00 4.26
3382 7314 1.069765 CGTTGTGTGGAGGCTCAGT 59.930 57.895 17.69 0.00 0.00 3.41
3387 7319 3.386237 GTGGAGGCTCAGTCGGCT 61.386 66.667 17.69 0.00 43.13 5.52
3398 7330 4.357947 GTCGGCTGTGGCACGAGA 62.358 66.667 13.77 6.60 40.02 4.04
3420 7352 2.231478 TCAACTTCCTGGTGATCGAGAC 59.769 50.000 0.00 0.00 37.49 3.36
3468 7400 1.290324 CAGTGACCAGTGAGTCCCG 59.710 63.158 8.66 0.00 35.83 5.14
3522 7454 1.262640 TAGAGGGACGCCAGGGAAAC 61.263 60.000 0.00 0.00 0.00 2.78
3555 7487 3.056328 GGCAAGGTTCACGAGGGC 61.056 66.667 0.00 0.00 0.00 5.19
3608 7540 3.107642 TCTGAAAGAGGGACAACGAAC 57.892 47.619 0.00 0.00 38.67 3.95
3609 7541 2.432874 TCTGAAAGAGGGACAACGAACA 59.567 45.455 0.00 0.00 38.67 3.18
3618 7550 1.002792 GGACAACGAACACAAGAAGGC 60.003 52.381 0.00 0.00 0.00 4.35
3636 7568 2.125350 GGAGCGCAAGACAGAGGG 60.125 66.667 11.47 0.00 43.02 4.30
3637 7569 2.650116 GGAGCGCAAGACAGAGGGA 61.650 63.158 11.47 0.00 43.02 4.20
3638 7570 1.446966 GAGCGCAAGACAGAGGGAC 60.447 63.158 11.47 0.00 43.02 4.46
3640 7572 1.301716 GCGCAAGACAGAGGGACAA 60.302 57.895 0.30 0.00 43.02 3.18
3655 7607 0.784778 GACAACAAGCTCGAGTTCGG 59.215 55.000 15.13 6.82 40.29 4.30
3657 7609 1.069090 AACAAGCTCGAGTTCGGCA 59.931 52.632 15.13 0.00 40.29 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.107453 CGACTCGTTCATTGAAAAAGCTAGT 60.107 40.000 0.00 0.00 0.00 2.57
26 27 5.107453 ACGACTCGTTCATTGAAAAAGCTAG 60.107 40.000 0.00 0.00 36.35 3.42
28 29 3.560068 ACGACTCGTTCATTGAAAAAGCT 59.440 39.130 0.00 0.00 36.35 3.74
43 46 5.829233 AATATGCATGTGATAACGACTCG 57.171 39.130 10.16 0.00 0.00 4.18
48 51 6.634035 CAGGTGAAAATATGCATGTGATAACG 59.366 38.462 10.16 0.00 0.00 3.18
49 52 6.919662 CCAGGTGAAAATATGCATGTGATAAC 59.080 38.462 10.16 1.23 0.00 1.89
56 59 5.327616 TCAACCAGGTGAAAATATGCATG 57.672 39.130 10.16 0.00 0.00 4.06
68 71 3.594603 AGAGTAACGATCAACCAGGTG 57.405 47.619 0.00 0.00 0.00 4.00
84 87 5.765510 TGAAAACCATATTGCCCATAGAGT 58.234 37.500 0.00 0.00 0.00 3.24
155 158 7.809331 GCATTGTAAGAGTTGACAAAATGATGA 59.191 33.333 9.59 0.00 38.94 2.92
194 197 3.371595 GGCTAGCCTTTGGGTCTTGAATA 60.372 47.826 27.17 0.00 34.28 1.75
202 205 2.356667 GCTGGCTAGCCTTTGGGT 59.643 61.111 33.07 0.00 44.33 4.51
218 221 3.428870 CGGTATCATGAACTTGTATCGGC 59.571 47.826 0.00 0.00 0.00 5.54
240 243 0.539518 GGAGGAAGCCACTTCTCTCC 59.460 60.000 19.79 19.79 43.45 3.71
259 262 1.593196 TTTCTCGTTGCTTGTCCCTG 58.407 50.000 0.00 0.00 0.00 4.45
260 263 2.341846 TTTTCTCGTTGCTTGTCCCT 57.658 45.000 0.00 0.00 0.00 4.20
261 264 3.643159 AATTTTCTCGTTGCTTGTCCC 57.357 42.857 0.00 0.00 0.00 4.46
262 265 5.516090 TGTTAATTTTCTCGTTGCTTGTCC 58.484 37.500 0.00 0.00 0.00 4.02
268 271 7.693952 TCCATCTATGTTAATTTTCTCGTTGC 58.306 34.615 0.00 0.00 0.00 4.17
274 277 9.466497 TGAAAGCTCCATCTATGTTAATTTTCT 57.534 29.630 0.00 0.00 0.00 2.52
280 283 8.267183 TCTGATTGAAAGCTCCATCTATGTTAA 58.733 33.333 0.00 0.00 0.00 2.01
344 347 4.583871 CTCCAACATAAACTCCTTGCTCT 58.416 43.478 0.00 0.00 0.00 4.09
345 348 3.127721 GCTCCAACATAAACTCCTTGCTC 59.872 47.826 0.00 0.00 0.00 4.26
346 349 3.084786 GCTCCAACATAAACTCCTTGCT 58.915 45.455 0.00 0.00 0.00 3.91
347 350 2.164422 GGCTCCAACATAAACTCCTTGC 59.836 50.000 0.00 0.00 0.00 4.01
348 351 3.690460 AGGCTCCAACATAAACTCCTTG 58.310 45.455 0.00 0.00 0.00 3.61
367 373 3.499737 GCACCACAATCGCCGAGG 61.500 66.667 0.00 0.00 0.00 4.63
391 397 0.918983 TAGGCTTGATGGGTCCTTGG 59.081 55.000 0.00 0.00 0.00 3.61
426 432 1.903877 GCTAGTGCAAGGCCCTCTCA 61.904 60.000 0.00 0.00 39.41 3.27
484 492 1.570813 TGATTCCTACGCTGCAATCG 58.429 50.000 0.00 6.49 0.00 3.34
490 498 5.698832 TGTTGAAAAATGATTCCTACGCTG 58.301 37.500 0.00 0.00 0.00 5.18
524 602 8.842280 TGTTGAAAAATGATTCCTACGTAAACT 58.158 29.630 0.00 0.00 0.00 2.66
525 603 9.453325 TTGTTGAAAAATGATTCCTACGTAAAC 57.547 29.630 0.00 0.00 0.00 2.01
526 604 9.672086 CTTGTTGAAAAATGATTCCTACGTAAA 57.328 29.630 0.00 0.00 0.00 2.01
527 605 8.842280 ACTTGTTGAAAAATGATTCCTACGTAA 58.158 29.630 0.00 0.00 0.00 3.18
528 606 8.385898 ACTTGTTGAAAAATGATTCCTACGTA 57.614 30.769 0.00 0.00 0.00 3.57
529 607 7.272037 ACTTGTTGAAAAATGATTCCTACGT 57.728 32.000 0.00 0.00 0.00 3.57
570 648 8.742777 TGAGCATCAAAATTAAAGCTTCTACAT 58.257 29.630 0.00 0.00 45.97 2.29
571 649 8.109705 TGAGCATCAAAATTAAAGCTTCTACA 57.890 30.769 0.00 0.00 45.97 2.74
626 704 3.638160 CAGCCAAATATGCCTACCAACAT 59.362 43.478 0.00 0.00 0.00 2.71
640 718 5.140454 GTCATAAGGTATTCCCAGCCAAAT 58.860 41.667 0.00 0.00 34.66 2.32
867 2660 1.372501 AGTCCATGGGCCTTAACTGT 58.627 50.000 14.18 0.00 0.00 3.55
1590 3395 1.676967 ACAGGGCTAAGCTGCTTGC 60.677 57.895 24.35 22.31 43.29 4.01
1591 3396 1.930908 GCACAGGGCTAAGCTGCTTG 61.931 60.000 24.35 14.78 40.25 4.01
1621 3426 2.067766 GAGCTGCAACAGAGAGAAGTG 58.932 52.381 1.02 0.00 32.44 3.16
1866 3730 5.008415 CCTCAGTACTGGATCAATTGCATTC 59.992 44.000 22.48 0.00 0.00 2.67
1928 4216 6.677913 ACAATAACAAGCAGATACAAACACC 58.322 36.000 0.00 0.00 0.00 4.16
1942 4230 6.093219 CCACAGATCCTTCAGACAATAACAAG 59.907 42.308 0.00 0.00 0.00 3.16
2026 4315 7.329471 GTCTTGATTTTTACTCAAATGGCCTTC 59.671 37.037 3.32 0.00 32.53 3.46
2074 4364 4.209080 GCAATTGTTTGAACTAACCTGTGC 59.791 41.667 7.40 0.00 34.60 4.57
2168 4464 7.933577 AGTCATTGAACTCTCACATACAAAAGA 59.066 33.333 0.00 0.00 0.00 2.52
2189 4500 2.760092 GAGAGCTTCAGAGACCAGTCAT 59.240 50.000 0.00 0.00 0.00 3.06
2193 4504 0.455410 CGGAGAGCTTCAGAGACCAG 59.545 60.000 0.00 0.00 0.00 4.00
2200 4511 4.991687 AGTTTTCTTAACGGAGAGCTTCAG 59.008 41.667 0.00 0.00 0.00 3.02
2315 4628 2.226437 ACGACACCTTTGTTGATGATGC 59.774 45.455 0.00 0.00 39.28 3.91
2324 4637 3.393800 CTGATTCAGACGACACCTTTGT 58.606 45.455 8.00 0.00 33.88 2.83
2731 5243 2.290531 GGCGTAGACCAGTAAAGACC 57.709 55.000 0.00 0.00 0.00 3.85
2770 5284 5.178096 TGTTGGAGATGCTCTTATTTCCA 57.822 39.130 0.00 0.00 38.97 3.53
2806 5321 5.835113 AAGCTCATAAAACGGTAATGCAT 57.165 34.783 0.00 0.00 0.00 3.96
2807 5322 5.637006 AAAGCTCATAAAACGGTAATGCA 57.363 34.783 0.00 0.00 0.00 3.96
2809 5324 6.526674 GTCCAAAAGCTCATAAAACGGTAATG 59.473 38.462 0.00 0.00 0.00 1.90
2810 5325 6.349860 GGTCCAAAAGCTCATAAAACGGTAAT 60.350 38.462 0.00 0.00 0.00 1.89
2848 6746 1.410153 AGCAGCTGTTGGAGGTTTTTG 59.590 47.619 16.64 0.00 0.00 2.44
2854 6752 0.250640 ACAAGAGCAGCTGTTGGAGG 60.251 55.000 30.19 10.81 38.76 4.30
2856 6754 1.311859 CAACAAGAGCAGCTGTTGGA 58.688 50.000 30.19 0.00 38.76 3.53
2857 6755 3.859650 CAACAAGAGCAGCTGTTGG 57.140 52.632 30.19 14.05 38.76 3.77
2859 6757 2.057137 TTCCAACAAGAGCAGCTGTT 57.943 45.000 16.64 9.79 0.00 3.16
2861 6759 3.655276 ATTTTCCAACAAGAGCAGCTG 57.345 42.857 10.11 10.11 0.00 4.24
2965 6896 3.487202 TTGCGCGTGGCTCGATTC 61.487 61.111 13.77 1.20 44.05 2.52
3047 6978 2.501610 GGGAGTGTCTGGATCCGC 59.498 66.667 7.39 0.31 33.68 5.54
3067 6998 1.669265 CATCATGGTAGTGCAGCTGTG 59.331 52.381 16.64 2.78 0.00 3.66
3069 7000 1.938577 GACATCATGGTAGTGCAGCTG 59.061 52.381 10.11 10.11 0.00 4.24
3085 7016 1.115467 GGGACGACAGATCAGGACAT 58.885 55.000 0.00 0.00 0.00 3.06
3088 7019 1.381327 GGGGGACGACAGATCAGGA 60.381 63.158 0.00 0.00 0.00 3.86
3091 7022 1.381327 GGAGGGGGACGACAGATCA 60.381 63.158 0.00 0.00 0.00 2.92
3098 7029 1.382695 GATTGGAGGAGGGGGACGA 60.383 63.158 0.00 0.00 0.00 4.20
3102 7033 3.878667 GCCGATTGGAGGAGGGGG 61.879 72.222 1.98 0.00 37.49 5.40
3178 7109 1.601162 CGCAAACAGCAGTGCAGATTT 60.601 47.619 19.20 11.33 46.13 2.17
3182 7113 2.728383 GCGCAAACAGCAGTGCAG 60.728 61.111 19.20 12.56 46.13 4.41
3193 7124 3.787676 CGACAGATGCGGCGCAAA 61.788 61.111 39.46 17.80 43.62 3.68
3215 7146 1.750351 CTCTTCACACGTTTCGACGA 58.250 50.000 5.91 0.00 36.85 4.20
3242 7173 1.447314 GCTAAACGCCACGGTAGCT 60.447 57.895 14.10 0.00 39.63 3.32
3257 7188 2.656069 GGCCGAACTCCAGTGGCTA 61.656 63.158 3.51 0.00 46.72 3.93
3264 7195 1.301401 CTGAAACGGCCGAACTCCA 60.301 57.895 35.90 19.45 0.00 3.86
3276 7207 2.723010 CGCTGAAACTCGATGCTGAAAC 60.723 50.000 0.00 0.00 0.00 2.78
3296 7228 1.153901 AATACAGTCGGCCGTCACG 60.154 57.895 27.15 17.01 0.00 4.35
3309 7241 0.392461 GAAGGTGCCGAGCCAATACA 60.392 55.000 0.00 0.00 0.00 2.29
3358 7290 1.626654 GCCTCCACACAACGATGTCG 61.627 60.000 0.00 0.11 46.33 4.35
3367 7299 2.574018 CCGACTGAGCCTCCACACA 61.574 63.158 0.00 0.00 0.00 3.72
3382 7314 3.356639 GATCTCGTGCCACAGCCGA 62.357 63.158 0.00 0.00 38.70 5.54
3387 7319 1.608025 GGAAGTTGATCTCGTGCCACA 60.608 52.381 0.00 0.00 0.00 4.17
3398 7330 3.099905 TCTCGATCACCAGGAAGTTGAT 58.900 45.455 0.00 0.00 0.00 2.57
3468 7400 0.673956 GGTCTTCCTCTTTGTCGGGC 60.674 60.000 0.00 0.00 0.00 6.13
3512 7444 1.607801 GCCTCATTGGTTTCCCTGGC 61.608 60.000 0.00 0.00 38.35 4.85
3522 7454 2.484062 GCCATCACCGCCTCATTGG 61.484 63.158 0.00 0.00 39.35 3.16
3524 7456 1.001020 TTGCCATCACCGCCTCATT 60.001 52.632 0.00 0.00 0.00 2.57
3555 7487 2.568090 GCATGAGGTGCGGGTTTG 59.432 61.111 0.00 0.00 45.23 2.93
3565 7497 0.392193 ACTCCTTCGCTTGCATGAGG 60.392 55.000 3.33 1.77 0.00 3.86
3607 7539 2.357517 CGCTCCGCCTTCTTGTGT 60.358 61.111 0.00 0.00 0.00 3.72
3618 7550 2.507992 CCTCTGTCTTGCGCTCCG 60.508 66.667 9.73 0.00 0.00 4.63
3624 7556 1.876156 CTTGTTGTCCCTCTGTCTTGC 59.124 52.381 0.00 0.00 0.00 4.01
3636 7568 0.784778 CCGAACTCGAGCTTGTTGTC 59.215 55.000 13.61 0.00 43.02 3.18
3637 7569 1.222115 GCCGAACTCGAGCTTGTTGT 61.222 55.000 13.61 0.00 43.02 3.32
3638 7570 1.221466 TGCCGAACTCGAGCTTGTTG 61.221 55.000 13.61 0.00 43.02 3.33
3640 7572 1.069090 TTGCCGAACTCGAGCTTGT 59.931 52.632 13.61 0.00 43.02 3.16
3655 7607 1.576421 CCGAGCTCAACCTTGTTGC 59.424 57.895 15.40 0.00 0.00 4.17
3657 7609 1.961277 CGCCGAGCTCAACCTTGTT 60.961 57.895 15.40 0.00 0.00 2.83
3681 7633 0.386858 ATGTTGTCGGACTCGTCACG 60.387 55.000 9.88 0.00 34.54 4.35


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

AutoCloner maintained by Alex Coulton.