Multiple sequence alignment - TraesCS2A01G510900

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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 TraesCS2A01G510900 chr2A 100.000 5503 0 0 1 5503 735774549 735780051 0.000000e+00 10163.0
1 TraesCS2A01G510900 chr2B 93.792 3447 129 35 928 4326 734123910 734127319 0.000000e+00 5101.0
2 TraesCS2A01G510900 chr2B 94.916 1554 64 6 2550 4095 734187109 734188655 0.000000e+00 2418.0
3 TraesCS2A01G510900 chr2B 83.006 865 96 34 2 840 734123028 734123867 0.000000e+00 736.0
4 TraesCS2A01G510900 chr2B 88.020 601 45 14 4327 4909 734188879 734189470 0.000000e+00 686.0
5 TraesCS2A01G510900 chr2B 93.264 193 11 2 4327 4517 734127369 734127561 3.250000e-72 283.0
6 TraesCS2A01G510900 chr2B 97.006 167 5 0 2312 2478 734186613 734186779 1.170000e-71 281.0
7 TraesCS2A01G510900 chr2B 95.808 167 5 1 2075 2241 734186450 734186614 9.090000e-68 268.0
8 TraesCS2A01G510900 chr2B 93.662 142 9 0 4185 4326 734188688 734188829 4.320000e-51 213.0
9 TraesCS2A01G510900 chr2B 100.000 34 0 0 4138 4171 734188656 734188689 4.600000e-06 63.9
10 TraesCS2A01G510900 chr2D 94.139 3344 159 24 1449 4770 603601946 603605274 0.000000e+00 5055.0
11 TraesCS2A01G510900 chr2D 93.114 2280 107 19 2089 4326 603639438 603641709 0.000000e+00 3295.0
12 TraesCS2A01G510900 chr2D 86.156 1423 117 29 65 1437 603600516 603601908 0.000000e+00 1463.0
13 TraesCS2A01G510900 chr2D 89.447 597 38 15 4327 4909 603641759 603642344 0.000000e+00 730.0
14 TraesCS2A01G510900 chr7A 97.822 597 9 3 4909 5503 80531580 80532174 0.000000e+00 1027.0
15 TraesCS2A01G510900 chr7A 95.966 595 17 3 4910 5503 14176617 14177205 0.000000e+00 959.0
16 TraesCS2A01G510900 chr3A 97.152 597 13 3 4909 5503 163104827 163104233 0.000000e+00 1005.0
17 TraesCS2A01G510900 chr5A 96.494 599 18 2 4906 5503 535651561 535652157 0.000000e+00 987.0
18 TraesCS2A01G510900 chr5A 96.296 594 18 3 4912 5503 2092870 2093461 0.000000e+00 972.0
19 TraesCS2A01G510900 chr4A 95.960 594 20 3 4910 5501 5738488 5739079 0.000000e+00 961.0
20 TraesCS2A01G510900 chr4A 89.666 329 32 2 3400 3727 327608361 327608688 8.530000e-113 418.0
21 TraesCS2A01G510900 chr6A 95.101 592 20 4 4913 5503 600273660 600274243 0.000000e+00 924.0
22 TraesCS2A01G510900 chr6A 94.764 592 20 6 4913 5503 600249819 600250400 0.000000e+00 911.0
23 TraesCS2A01G510900 chr5B 93.489 599 32 4 4910 5503 479635887 479636483 0.000000e+00 883.0
24 TraesCS2A01G510900 chr7D 89.123 285 31 0 3400 3684 410894541 410894825 6.780000e-94 355.0
25 TraesCS2A01G510900 chr7D 88.070 285 34 0 3400 3684 315166717 315166433 6.830000e-89 339.0
26 TraesCS2A01G510900 chr3D 88.070 285 32 1 3400 3684 25285311 25285593 2.460000e-88 337.0
27 TraesCS2A01G510900 chr7B 87.018 285 37 0 3400 3684 325472725 325473009 6.880000e-84 322.0


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 TraesCS2A01G510900 chr2A 735774549 735780051 5502 False 10163.000000 10163 100.000000 1 5503 1 chr2A.!!$F1 5502
1 TraesCS2A01G510900 chr2B 734123028 734127561 4533 False 2040.000000 5101 90.020667 2 4517 3 chr2B.!!$F1 4515
2 TraesCS2A01G510900 chr2B 734186450 734189470 3020 False 654.983333 2418 94.902000 2075 4909 6 chr2B.!!$F2 2834
3 TraesCS2A01G510900 chr2D 603600516 603605274 4758 False 3259.000000 5055 90.147500 65 4770 2 chr2D.!!$F1 4705
4 TraesCS2A01G510900 chr2D 603639438 603642344 2906 False 2012.500000 3295 91.280500 2089 4909 2 chr2D.!!$F2 2820
5 TraesCS2A01G510900 chr7A 80531580 80532174 594 False 1027.000000 1027 97.822000 4909 5503 1 chr7A.!!$F2 594
6 TraesCS2A01G510900 chr7A 14176617 14177205 588 False 959.000000 959 95.966000 4910 5503 1 chr7A.!!$F1 593
7 TraesCS2A01G510900 chr3A 163104233 163104827 594 True 1005.000000 1005 97.152000 4909 5503 1 chr3A.!!$R1 594
8 TraesCS2A01G510900 chr5A 535651561 535652157 596 False 987.000000 987 96.494000 4906 5503 1 chr5A.!!$F2 597
9 TraesCS2A01G510900 chr5A 2092870 2093461 591 False 972.000000 972 96.296000 4912 5503 1 chr5A.!!$F1 591
10 TraesCS2A01G510900 chr4A 5738488 5739079 591 False 961.000000 961 95.960000 4910 5501 1 chr4A.!!$F1 591
11 TraesCS2A01G510900 chr6A 600273660 600274243 583 False 924.000000 924 95.101000 4913 5503 1 chr6A.!!$F2 590
12 TraesCS2A01G510900 chr6A 600249819 600250400 581 False 911.000000 911 94.764000 4913 5503 1 chr6A.!!$F1 590
13 TraesCS2A01G510900 chr5B 479635887 479636483 596 False 883.000000 883 93.489000 4910 5503 1 chr5B.!!$F1 593

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
768 793 0.179073 CTTGGGCCGAAGATGATCGT 60.179 55.000 22.08 0.0 41.16 3.73 F
1234 1289 0.881118 TCCGCGTACCTTCGTACTTT 59.119 50.000 4.92 0.0 42.38 2.66 F
2405 2507 0.595095 CCCTGAAAGCTGTTGCAGAC 59.405 55.000 0.00 0.0 41.54 3.51 F
3073 3442 2.034843 TATTGGTGCCGCAAGCCA 59.965 55.556 0.00 0.0 42.71 4.75 F
3666 4039 0.037232 GCCAAGAGACTAAGGTGCGT 60.037 55.000 0.00 0.0 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1675 0.107654 AGGCGAACATTACCTGCTCC 60.108 55.0 0.00 0.0 30.82 4.70 R
3065 3434 0.532573 TCTAAGAGGACTGGCTTGCG 59.467 55.0 0.00 0.0 0.00 4.85 R
3238 3611 0.454600 ATCCATGCTTGAGCTTTGCG 59.545 50.0 4.44 0.0 42.66 4.85 R
4267 4640 0.958822 AACCCTTCCATGCGAACAAC 59.041 50.0 0.00 0.0 0.00 3.32 R
4887 5337 2.087857 ATGAAAAAGGTGGCGGGGGA 62.088 55.0 0.00 0.0 0.00 4.81 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
61 62 6.765403 TCTAGCTACCATGTTGTTTAACTGT 58.235 36.000 0.00 0.00 37.68 3.55
117 118 7.938140 TTTAGAAAGTTCATGAATCCGGATT 57.062 32.000 29.60 29.60 0.00 3.01
125 126 8.525290 AGTTCATGAATCCGGATTAAATTCTT 57.475 30.769 29.28 12.81 31.99 2.52
207 208 9.506018 TTTGTGAATTTGAGAGAAGTCATGATA 57.494 29.630 0.00 0.00 36.23 2.15
371 376 8.634475 ATGAGAACGAAAAAGGAAAGAAAAAG 57.366 30.769 0.00 0.00 0.00 2.27
372 377 7.033185 TGAGAACGAAAAAGGAAAGAAAAAGG 58.967 34.615 0.00 0.00 0.00 3.11
373 378 6.338146 AGAACGAAAAAGGAAAGAAAAAGGG 58.662 36.000 0.00 0.00 0.00 3.95
376 381 6.703319 ACGAAAAAGGAAAGAAAAAGGGAAA 58.297 32.000 0.00 0.00 0.00 3.13
377 382 7.162761 ACGAAAAAGGAAAGAAAAAGGGAAAA 58.837 30.769 0.00 0.00 0.00 2.29
405 415 8.664669 ATCTAGGGAAAGCCAAAAATAGAAAA 57.335 30.769 0.00 0.00 35.15 2.29
425 435 5.476091 AAAAACTGGTTGGAAGTTTCACA 57.524 34.783 2.32 0.00 44.93 3.58
426 436 5.476091 AAAACTGGTTGGAAGTTTCACAA 57.524 34.783 2.32 0.00 44.93 3.33
427 437 5.476091 AAACTGGTTGGAAGTTTCACAAA 57.524 34.783 0.00 0.00 42.75 2.83
428 438 5.476091 AACTGGTTGGAAGTTTCACAAAA 57.524 34.783 0.00 0.00 34.16 2.44
437 447 5.186797 TGGAAGTTTCACAAAATCAGTTGGT 59.813 36.000 0.00 0.00 32.50 3.67
438 448 6.106003 GGAAGTTTCACAAAATCAGTTGGTT 58.894 36.000 0.00 0.00 32.50 3.67
448 458 7.693120 CACAAAATCAGTTGGTTGTTTCATTTG 59.307 33.333 0.00 0.00 31.98 2.32
483 493 7.724061 ACTGTAACTTCATTCATACCCAAAACT 59.276 33.333 0.00 0.00 0.00 2.66
632 657 4.623932 AGTAAGAGACTGCAATTGGACA 57.376 40.909 7.72 0.00 36.87 4.02
639 664 5.104193 AGAGACTGCAATTGGACAGGAATAT 60.104 40.000 14.97 0.00 38.25 1.28
667 692 3.807538 GCTCAGCCACATGCACGG 61.808 66.667 0.00 0.00 44.83 4.94
669 694 1.450848 CTCAGCCACATGCACGGAT 60.451 57.895 2.87 0.00 44.83 4.18
707 732 4.711846 AGGTTTTTGAAAGCCTCTTGAGTT 59.288 37.500 6.10 0.00 45.03 3.01
758 783 3.545124 ATGAACGTGCTTGGGCCGA 62.545 57.895 0.00 0.00 37.74 5.54
767 792 1.502163 GCTTGGGCCGAAGATGATCG 61.502 60.000 29.58 4.01 42.37 3.69
768 793 0.179073 CTTGGGCCGAAGATGATCGT 60.179 55.000 22.08 0.00 41.16 3.73
772 797 1.340248 GGGCCGAAGATGATCGTCTAA 59.660 52.381 17.79 0.00 41.16 2.10
819 844 1.132453 GCCCTGTAGGAACGAAAATGC 59.868 52.381 0.00 0.00 38.24 3.56
845 871 4.202090 GGCGTGTACCAGTAAGCTAGTATT 60.202 45.833 0.00 0.00 0.00 1.89
847 873 5.231568 GCGTGTACCAGTAAGCTAGTATTTG 59.768 44.000 0.00 0.00 0.00 2.32
852 878 3.458189 CAGTAAGCTAGTATTTGGCGCT 58.542 45.455 7.64 0.00 0.00 5.92
858 884 4.514401 AGCTAGTATTTGGCGCTTTAAGT 58.486 39.130 7.64 0.02 0.00 2.24
888 914 2.230660 GCTTTTCCGCTATTATGGGCT 58.769 47.619 0.00 0.00 0.00 5.19
903 929 2.264455 TGGGCTGTTAATGGGCAAATT 58.736 42.857 6.55 0.00 0.00 1.82
980 1015 4.473520 CGGCCATCTTCCCGTGCT 62.474 66.667 2.24 0.00 39.67 4.40
1092 1127 1.304217 AAGAGAAGGCCGTCCGAGA 60.304 57.895 15.64 0.00 37.47 4.04
1222 1277 2.357009 GGTCTGTCTCTTATTCCGCGTA 59.643 50.000 4.92 0.00 0.00 4.42
1224 1279 2.357009 TCTGTCTCTTATTCCGCGTACC 59.643 50.000 4.92 0.00 0.00 3.34
1227 1282 3.181493 TGTCTCTTATTCCGCGTACCTTC 60.181 47.826 4.92 0.00 0.00 3.46
1234 1289 0.881118 TCCGCGTACCTTCGTACTTT 59.119 50.000 4.92 0.00 42.38 2.66
1391 1446 3.482783 GTGCTGCTCGCGTTCCTC 61.483 66.667 5.77 0.00 43.27 3.71
1422 1477 7.448469 CCTTCTCCAAAGATTTTCAGAAGGTAA 59.552 37.037 21.50 3.01 42.29 2.85
1438 1493 9.658799 TCAGAAGGTAATACTTTGATTCAGAAG 57.341 33.333 0.00 6.90 0.00 2.85
1439 1494 8.887717 CAGAAGGTAATACTTTGATTCAGAAGG 58.112 37.037 0.00 0.00 0.00 3.46
1440 1495 8.606830 AGAAGGTAATACTTTGATTCAGAAGGT 58.393 33.333 0.00 0.00 0.00 3.50
1479 1560 1.820906 CATCCGGACCATGGCACTG 60.821 63.158 13.04 11.39 0.00 3.66
1492 1573 2.494059 TGGCACTGACAGTTTTAGAGC 58.506 47.619 5.04 5.06 0.00 4.09
1594 1675 1.448985 TTTCCGGCAAGATTTCTCCG 58.551 50.000 0.00 1.73 41.41 4.63
1619 1700 1.906574 AGGTAATGTTCGCCTTCCTGA 59.093 47.619 0.00 0.00 0.00 3.86
1658 1739 5.835113 ATTGGGTTGCTGTATTCATGTAC 57.165 39.130 0.00 0.00 0.00 2.90
1670 1754 7.905493 GCTGTATTCATGTACTAGTTTTCAAGC 59.095 37.037 0.00 0.00 0.00 4.01
1750 1834 2.219674 GCTTGTTCAGTTGACGACAGAG 59.780 50.000 0.00 0.00 0.00 3.35
1799 1883 6.739331 ACTTCCCATCTTATCAAGAGGTAG 57.261 41.667 0.57 1.19 41.61 3.18
1856 1941 2.730183 TCTTGCACGTTTTTCTGTCG 57.270 45.000 0.00 0.00 0.00 4.35
1955 2040 8.495949 CATCGCGTAGGATTCTTTATACAAAAT 58.504 33.333 5.77 0.00 0.00 1.82
1998 2083 4.273480 TGTCTAAGTTGCAAAGCTCAAGAC 59.727 41.667 17.21 17.21 0.00 3.01
2006 2091 4.870363 TGCAAAGCTCAAGACCAATTTAC 58.130 39.130 0.00 0.00 0.00 2.01
2021 2108 7.400339 AGACCAATTTACAGTCTCATCTCCTTA 59.600 37.037 0.00 0.00 36.06 2.69
2390 2492 5.110814 TGGATACACTTGTAAATCCCCTG 57.889 43.478 8.19 0.00 46.17 4.45
2405 2507 0.595095 CCCTGAAAGCTGTTGCAGAC 59.405 55.000 0.00 0.00 41.54 3.51
2495 2628 9.547753 GATATTCAGGTATGTTGTCTGTACAAT 57.452 33.333 0.00 0.00 46.84 2.71
2496 2629 9.905713 ATATTCAGGTATGTTGTCTGTACAATT 57.094 29.630 0.00 0.00 46.84 2.32
2506 2639 8.109705 TGTTGTCTGTACAATTATCTTGCATT 57.890 30.769 0.00 0.00 46.84 3.56
2543 2679 6.590292 CCTTCGTGTGAGTTATATTTGTGTCT 59.410 38.462 0.00 0.00 0.00 3.41
2827 3194 8.652810 TCTTTAAGTATGCGAATTTACCTACC 57.347 34.615 0.00 0.00 0.00 3.18
3016 3384 6.324819 AGTAATGTTTGATTTCAGGATTGCG 58.675 36.000 0.00 0.00 0.00 4.85
3073 3442 2.034843 TATTGGTGCCGCAAGCCA 59.965 55.556 0.00 0.00 42.71 4.75
3086 3455 2.801342 CGCAAGCCAGTCCTCTTAGATC 60.801 54.545 0.00 0.00 0.00 2.75
3238 3611 3.983741 AGCTGCGATGAATCTAGTTACC 58.016 45.455 0.00 0.00 0.00 2.85
3352 3725 6.992063 ATTCAAGTTGCTACCTGACTTATG 57.008 37.500 0.00 0.00 32.69 1.90
3353 3726 5.738619 TCAAGTTGCTACCTGACTTATGA 57.261 39.130 0.00 0.00 32.69 2.15
3435 3808 4.282195 CAGTCTACCTTCCTTGTCAAGAGT 59.718 45.833 14.42 8.14 0.00 3.24
3507 3880 2.783832 GAGCTTTTGTTGCTTGTTCGAC 59.216 45.455 0.00 0.00 41.30 4.20
3514 3887 3.497118 TGTTGCTTGTTCGACAAACTTG 58.503 40.909 0.00 0.00 37.69 3.16
3663 4036 2.503356 AGATGGCCAAGAGACTAAGGTG 59.497 50.000 10.96 0.00 0.00 4.00
3666 4039 0.037232 GCCAAGAGACTAAGGTGCGT 60.037 55.000 0.00 0.00 0.00 5.24
3693 4066 5.350640 GACTTCATAGTTTGGTTCCTTACCG 59.649 44.000 0.00 0.00 41.69 4.02
3724 4097 8.125978 TGCTTATTCAACTGAATTTCTGGATT 57.874 30.769 10.08 0.00 41.64 3.01
3740 4113 4.299586 TGGATTGCACCAGTCTGAATTA 57.700 40.909 0.00 0.00 34.77 1.40
3826 4199 0.310854 CAGTGGGCGACTCCAAAAAC 59.689 55.000 0.00 0.00 38.72 2.43
3956 4329 3.372206 CCTATTGAGAACACGGAGCAAAG 59.628 47.826 0.00 0.00 0.00 2.77
3968 4341 3.077359 CGGAGCAAAGGAAAGAAGATGT 58.923 45.455 0.00 0.00 0.00 3.06
4036 4409 0.955905 GAAAGCAAAGGCACCGGTTA 59.044 50.000 2.97 0.00 44.61 2.85
4074 4447 2.744243 GGAGGGCTGATGCTGAGCT 61.744 63.158 5.83 0.00 39.59 4.09
4096 4469 5.163581 GCTCATCTTGTTACAAATGGATGCT 60.164 40.000 16.18 0.00 33.03 3.79
4097 4470 6.198650 TCATCTTGTTACAAATGGATGCTG 57.801 37.500 16.18 0.88 33.03 4.41
4101 4474 5.945191 TCTTGTTACAAATGGATGCTGATCA 59.055 36.000 0.00 0.00 0.00 2.92
4120 4493 6.237154 TGATCAATTGTATGAGGTGTTGTCA 58.763 36.000 5.13 0.00 31.76 3.58
4247 4620 1.971357 CCCATCTAGGCGGTTGATAGT 59.029 52.381 0.00 0.00 35.39 2.12
4309 4682 5.924475 TGCTAACTGACTTAAACTTGAGC 57.076 39.130 0.00 0.00 0.00 4.26
4310 4683 5.364778 TGCTAACTGACTTAAACTTGAGCA 58.635 37.500 0.00 0.00 34.04 4.26
4351 4773 4.970662 ATTGCTGTTTACTGGTAGCATG 57.029 40.909 0.00 0.00 44.65 4.06
4384 4806 6.210584 CCACTAAATTGGAGGTTGGTAACATT 59.789 38.462 0.00 0.00 43.22 2.71
4385 4807 7.256154 CCACTAAATTGGAGGTTGGTAACATTT 60.256 37.037 0.00 0.00 43.22 2.32
4412 4836 3.810310 ACACTAGCAGGCTATCAGAAC 57.190 47.619 0.81 0.00 0.00 3.01
4432 4856 3.763057 ACTTGGAGGTTGGTGGATTAAC 58.237 45.455 0.00 0.00 0.00 2.01
4439 4863 3.780850 AGGTTGGTGGATTAACTCCTAGG 59.219 47.826 0.82 0.82 45.21 3.02
4443 4867 6.126565 GGTTGGTGGATTAACTCCTAGGTAAT 60.127 42.308 9.08 5.75 45.21 1.89
4518 4942 8.064222 AGATTTTCATTATATCGCAAGTGTTCG 58.936 33.333 0.00 0.00 39.48 3.95
4519 4943 5.651172 TTCATTATATCGCAAGTGTTCGG 57.349 39.130 0.00 0.00 39.48 4.30
4563 4987 6.551385 TGAGATTCTTTTTCTTCTCACTGC 57.449 37.500 0.00 0.00 39.61 4.40
4753 5185 9.613428 AAATATCTCAAAAGATCGAACATACCA 57.387 29.630 0.00 0.00 41.46 3.25
4831 5269 4.201628 CGTTTATCCAAGAGAGCAGAAACG 60.202 45.833 0.00 0.00 41.01 3.60
4832 5270 4.801330 TTATCCAAGAGAGCAGAAACGA 57.199 40.909 0.00 0.00 0.00 3.85
4834 5282 3.685139 TCCAAGAGAGCAGAAACGAAT 57.315 42.857 0.00 0.00 0.00 3.34
4838 5286 2.983229 AGAGAGCAGAAACGAATGCAT 58.017 42.857 0.00 0.00 45.01 3.96
4839 5287 3.341823 AGAGAGCAGAAACGAATGCATT 58.658 40.909 12.83 12.83 45.01 3.56
4840 5288 3.126514 AGAGAGCAGAAACGAATGCATTG 59.873 43.478 18.59 11.63 45.01 2.82
4843 5291 1.387756 GCAGAAACGAATGCATTGCAC 59.612 47.619 18.59 1.12 43.04 4.57
4844 5292 2.663808 CAGAAACGAATGCATTGCACA 58.336 42.857 18.59 0.00 43.04 4.57
4871 5321 7.465353 TCATCTCTGCATTATCTCTCTTAGG 57.535 40.000 0.00 0.00 0.00 2.69
4893 5343 1.003118 TGAAAACACATCTCTCCCCCG 59.997 52.381 0.00 0.00 0.00 5.73
5172 5624 7.716799 ACTCCCTCACAATTTATTTAATGCA 57.283 32.000 0.00 0.00 0.00 3.96
5330 5783 7.716799 TTATAATCACAAACAGAAGCCCAAT 57.283 32.000 0.00 0.00 0.00 3.16
5401 5857 1.451207 AAGCGTGGACACACTGCAA 60.451 52.632 13.76 0.00 45.50 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 9.627123 ATCCGGATTCATGAACTTTCTAAAATA 57.373 29.630 12.38 0.00 0.00 1.40
96 97 7.938140 TTTAATCCGGATTCATGAACTTTCT 57.062 32.000 32.43 7.32 32.50 2.52
97 98 9.237846 GAATTTAATCCGGATTCATGAACTTTC 57.762 33.333 32.43 19.64 31.69 2.62
161 162 9.491675 TCACAAATATACTCTTTAACAAACCGA 57.508 29.630 0.00 0.00 0.00 4.69
346 351 7.706607 CCTTTTTCTTTCCTTTTTCGTTCTCAT 59.293 33.333 0.00 0.00 0.00 2.90
376 381 9.100197 TCTATTTTTGGCTTTCCCTAGATTTTT 57.900 29.630 0.00 0.00 0.00 1.94
377 382 8.664669 TCTATTTTTGGCTTTCCCTAGATTTT 57.335 30.769 0.00 0.00 0.00 1.82
381 386 8.485578 TTTTTCTATTTTTGGCTTTCCCTAGA 57.514 30.769 0.00 0.00 0.00 2.43
405 415 5.476091 TTTGTGAAACTTCCAACCAGTTT 57.524 34.783 0.00 0.00 45.28 2.66
413 423 5.186797 ACCAACTGATTTTGTGAAACTTCCA 59.813 36.000 0.00 0.00 38.04 3.53
419 429 6.931281 TGAAACAACCAACTGATTTTGTGAAA 59.069 30.769 0.00 0.00 32.54 2.69
423 433 7.148272 CCAAATGAAACAACCAACTGATTTTGT 60.148 33.333 0.00 0.00 33.59 2.83
424 434 7.065563 TCCAAATGAAACAACCAACTGATTTTG 59.934 33.333 0.00 0.00 0.00 2.44
425 435 7.108847 TCCAAATGAAACAACCAACTGATTTT 58.891 30.769 0.00 0.00 0.00 1.82
426 436 6.648192 TCCAAATGAAACAACCAACTGATTT 58.352 32.000 0.00 0.00 0.00 2.17
427 437 6.098124 TCTCCAAATGAAACAACCAACTGATT 59.902 34.615 0.00 0.00 0.00 2.57
428 438 5.598005 TCTCCAAATGAAACAACCAACTGAT 59.402 36.000 0.00 0.00 0.00 2.90
438 448 9.959749 GTTACAGTTATTTCTCCAAATGAAACA 57.040 29.630 0.00 0.00 36.43 2.83
511 521 8.587608 TGAGTTGCTTTCCAATTTATTTGATCT 58.412 29.630 0.00 0.00 37.53 2.75
526 536 5.734855 TCTTAGTTGTGTGAGTTGCTTTC 57.265 39.130 0.00 0.00 0.00 2.62
615 639 1.980765 TCCTGTCCAATTGCAGTCTCT 59.019 47.619 10.87 0.00 0.00 3.10
616 640 2.479566 TCCTGTCCAATTGCAGTCTC 57.520 50.000 10.87 0.00 0.00 3.36
629 654 1.221414 GCAGTGGCGATATTCCTGTC 58.779 55.000 0.00 0.00 0.00 3.51
655 680 0.457035 ATCAAATCCGTGCATGTGGC 59.543 50.000 4.96 0.00 45.13 5.01
663 688 9.801873 AAACCTTTATTGATAATCAAATCCGTG 57.198 29.630 0.00 0.00 40.12 4.94
690 715 1.956477 GCCAACTCAAGAGGCTTTCAA 59.044 47.619 1.73 0.00 44.92 2.69
704 729 7.716799 TCTCATTTTTATTGTATGGCCAACT 57.283 32.000 10.96 0.00 0.00 3.16
707 732 6.380846 AGCTTCTCATTTTTATTGTATGGCCA 59.619 34.615 8.56 8.56 0.00 5.36
746 771 0.749454 ATCATCTTCGGCCCAAGCAC 60.749 55.000 5.04 0.00 42.56 4.40
772 797 2.228138 TCTGGTCGTACAGCGTTTTT 57.772 45.000 0.00 0.00 42.13 1.94
779 804 0.248661 CGGCTCATCTGGTCGTACAG 60.249 60.000 0.00 3.27 39.84 2.74
780 805 1.663379 CCGGCTCATCTGGTCGTACA 61.663 60.000 0.00 0.00 36.43 2.90
781 806 1.065928 CCGGCTCATCTGGTCGTAC 59.934 63.158 0.00 0.00 36.43 3.67
788 813 2.374830 CTACAGGGCCGGCTCATCTG 62.375 65.000 31.81 27.91 0.00 2.90
803 828 0.440758 CGCGCATTTTCGTTCCTACA 59.559 50.000 8.75 0.00 0.00 2.74
819 844 2.126385 TTACTGGTACACGCCGCG 60.126 61.111 12.14 12.14 0.00 6.46
847 873 1.064060 CTATGTGGCACTTAAAGCGCC 59.936 52.381 19.83 2.97 43.52 6.53
888 914 5.941058 TCGTAGAAGAATTTGCCCATTAACA 59.059 36.000 0.00 0.00 0.00 2.41
903 929 0.179197 CGACGCAGCTTCGTAGAAGA 60.179 55.000 12.34 0.00 45.90 2.87
937 971 2.112190 GTCCTGCTTCTAGGGCTAGTT 58.888 52.381 9.34 0.00 39.40 2.24
1092 1127 0.901124 TTGTTGGTGCTTGGCTTGTT 59.099 45.000 0.00 0.00 0.00 2.83
1222 1277 1.270678 GCACCTGGAAAGTACGAAGGT 60.271 52.381 0.00 3.19 41.99 3.50
1224 1279 2.338500 GAGCACCTGGAAAGTACGAAG 58.662 52.381 0.00 0.00 0.00 3.79
1227 1282 0.038526 ACGAGCACCTGGAAAGTACG 60.039 55.000 0.00 1.16 0.00 3.67
1234 1289 0.904865 AATCTCCACGAGCACCTGGA 60.905 55.000 0.00 2.26 35.20 3.86
1318 1373 1.214367 GCCGAACTTCTTGTCGTTCA 58.786 50.000 0.00 0.00 39.49 3.18
1391 1446 6.426937 TCTGAAAATCTTTGGAGAAGGTTACG 59.573 38.462 0.00 0.00 35.07 3.18
1437 1492 6.015519 TGCATAAAACAGAGCAACATTTACCT 60.016 34.615 0.00 0.00 33.48 3.08
1438 1493 6.155827 TGCATAAAACAGAGCAACATTTACC 58.844 36.000 0.00 0.00 33.48 2.85
1439 1494 7.009540 GGATGCATAAAACAGAGCAACATTTAC 59.990 37.037 0.00 0.00 40.76 2.01
1440 1495 7.035004 GGATGCATAAAACAGAGCAACATTTA 58.965 34.615 0.00 0.00 40.76 1.40
1442 1497 5.413499 GGATGCATAAAACAGAGCAACATT 58.587 37.500 0.00 0.00 40.76 2.71
1443 1498 4.439153 CGGATGCATAAAACAGAGCAACAT 60.439 41.667 0.00 0.00 40.76 2.71
1444 1499 3.119884 CGGATGCATAAAACAGAGCAACA 60.120 43.478 0.00 0.00 40.76 3.33
1445 1500 3.429085 CGGATGCATAAAACAGAGCAAC 58.571 45.455 0.00 0.00 40.76 4.17
1446 1501 2.423185 CCGGATGCATAAAACAGAGCAA 59.577 45.455 0.00 0.00 40.76 3.91
1492 1573 1.986882 ACTGGAACCAAAAGCAGAGG 58.013 50.000 0.00 0.00 0.00 3.69
1594 1675 0.107654 AGGCGAACATTACCTGCTCC 60.108 55.000 0.00 0.00 30.82 4.70
1619 1700 3.515104 CCCAATTGCTCACATTAACCCTT 59.485 43.478 0.00 0.00 0.00 3.95
1658 1739 9.630098 ACAATGTTTGATATGCTTGAAAACTAG 57.370 29.630 0.00 0.00 33.07 2.57
1670 1754 6.927936 TGGTTCACCAAACAATGTTTGATATG 59.072 34.615 32.93 26.21 44.35 1.78
1750 1834 3.883489 AGTTTTTCCTGTAGTCAAGGTGC 59.117 43.478 0.00 0.00 0.00 5.01
1799 1883 5.220605 GGATCATCGTTTGTTAGCTTGTACC 60.221 44.000 0.00 0.00 0.00 3.34
1856 1941 8.967918 AGTTATTCTGGCCTAAAACCTAATTTC 58.032 33.333 3.32 0.00 0.00 2.17
1955 2040 9.983024 TTAGACAAGGGATAAATATGTTTTGGA 57.017 29.630 0.00 0.00 0.00 3.53
1998 2083 8.834465 CAATAAGGAGATGAGACTGTAAATTGG 58.166 37.037 0.00 0.00 0.00 3.16
2006 2091 9.743057 CTAAAGTACAATAAGGAGATGAGACTG 57.257 37.037 0.00 0.00 0.00 3.51
2131 2218 5.422012 ACTTTCCACCCCTGCAAATAAATAG 59.578 40.000 0.00 0.00 0.00 1.73
2134 2221 3.582164 ACTTTCCACCCCTGCAAATAAA 58.418 40.909 0.00 0.00 0.00 1.40
2357 2459 4.102524 ACAAGTGTATCCAACTTCACCTGA 59.897 41.667 0.00 0.00 35.70 3.86
2390 2492 2.481952 CCTGTAGTCTGCAACAGCTTTC 59.518 50.000 10.23 0.00 41.45 2.62
2405 2507 2.300152 ACCAGTGATGTGTGTCCTGTAG 59.700 50.000 0.00 0.00 0.00 2.74
2523 2659 9.209175 AGAAAGAGACACAAATATAACTCACAC 57.791 33.333 0.00 0.00 0.00 3.82
2827 3194 5.428496 TGTTCAAAGAAGCTGATGAAGTG 57.572 39.130 0.00 0.00 32.85 3.16
2870 3237 1.417890 ACACTGCTATATGGTGCCCTC 59.582 52.381 0.00 0.00 34.70 4.30
3051 3420 1.077787 TTGCGGCACCAATAGGGAG 60.078 57.895 0.05 0.00 41.15 4.30
3052 3421 1.077787 CTTGCGGCACCAATAGGGA 60.078 57.895 0.05 0.00 41.15 4.20
3065 3434 0.532573 TCTAAGAGGACTGGCTTGCG 59.467 55.000 0.00 0.00 0.00 4.85
3073 3442 9.707957 TTTTCTATCTGAAGATCTAAGAGGACT 57.292 33.333 12.26 1.10 35.89 3.85
3086 3455 7.056635 ACATACCATGGGTTTTCTATCTGAAG 58.943 38.462 18.09 0.00 37.09 3.02
3238 3611 0.454600 ATCCATGCTTGAGCTTTGCG 59.545 50.000 4.44 0.00 42.66 4.85
3353 3726 9.293404 GGTTCAGGTACCTAAGAAATAAAAACT 57.707 33.333 15.80 0.00 35.23 2.66
3435 3808 7.386059 GGATTCCCAGAGAAAATTTTAAGCAA 58.614 34.615 2.75 0.00 38.21 3.91
3663 4036 2.806244 ACCAAACTATGAAGTCACACGC 59.194 45.455 0.00 0.00 33.75 5.34
3666 4039 5.304686 AGGAACCAAACTATGAAGTCACA 57.695 39.130 0.00 0.00 33.75 3.58
3693 4066 9.899226 AGAAATTCAGTTGAATAAGCAAACTAC 57.101 29.630 7.72 0.00 43.41 2.73
3724 4097 4.350368 TTCAGTAATTCAGACTGGTGCA 57.650 40.909 1.81 0.00 43.76 4.57
3740 4113 1.898094 TGCCGCTGCATGTTTCAGT 60.898 52.632 0.00 0.00 44.23 3.41
3826 4199 1.153823 CACGCTTCAGGAGTACCGG 60.154 63.158 0.00 0.00 41.83 5.28
3938 4311 1.140052 TCCTTTGCTCCGTGTTCTCAA 59.860 47.619 0.00 0.00 0.00 3.02
3956 4329 3.968265 TCCCCATTGACATCTTCTTTCC 58.032 45.455 0.00 0.00 0.00 3.13
3968 4341 3.699038 CCTTTTTCGCTTATCCCCATTGA 59.301 43.478 0.00 0.00 0.00 2.57
4036 4409 1.480137 CCCTGAAGCTCTTCACTCGAT 59.520 52.381 8.14 0.00 43.90 3.59
4058 4431 1.346479 ATGAGCTCAGCATCAGCCCT 61.346 55.000 22.96 0.00 43.56 5.19
4074 4447 5.945191 TCAGCATCCATTTGTAACAAGATGA 59.055 36.000 0.00 0.00 34.40 2.92
4096 4469 6.237154 TGACAACACCTCATACAATTGATCA 58.763 36.000 13.59 0.00 0.00 2.92
4097 4470 6.372659 ACTGACAACACCTCATACAATTGATC 59.627 38.462 13.59 0.00 0.00 2.92
4101 4474 5.620206 TCACTGACAACACCTCATACAATT 58.380 37.500 0.00 0.00 0.00 2.32
4120 4493 5.936956 GTGTCTGATCTCAAAATCCTTCACT 59.063 40.000 0.00 0.00 0.00 3.41
4247 4620 7.537596 ACAACATTTCATGATCCTTGGTTAA 57.462 32.000 0.00 0.00 0.00 2.01
4267 4640 0.958822 AACCCTTCCATGCGAACAAC 59.041 50.000 0.00 0.00 0.00 3.32
4309 4682 8.350722 AGCAATATCAATTCAGCTGAAAGTATG 58.649 33.333 31.55 24.72 37.61 2.39
4310 4683 8.461249 AGCAATATCAATTCAGCTGAAAGTAT 57.539 30.769 31.55 23.95 37.61 2.12
4392 4816 3.370104 AGTTCTGATAGCCTGCTAGTGT 58.630 45.455 5.00 0.00 31.45 3.55
4412 4836 4.010349 GAGTTAATCCACCAACCTCCAAG 58.990 47.826 0.00 0.00 0.00 3.61
4432 4856 6.650120 ACACAACCACAATATTACCTAGGAG 58.350 40.000 17.98 0.00 0.00 3.69
4439 4863 6.977213 ACCTTGAACACAACCACAATATTAC 58.023 36.000 0.00 0.00 0.00 1.89
4443 4867 4.950475 TGAACCTTGAACACAACCACAATA 59.050 37.500 0.00 0.00 0.00 1.90
4560 4984 5.375417 TGTTTACCACATTTCATGAGCAG 57.625 39.130 0.00 0.00 0.00 4.24
4563 4987 6.420604 GGTTGTTGTTTACCACATTTCATGAG 59.579 38.462 0.00 0.00 34.43 2.90
4596 5021 6.557110 TGCGAGTTTTAGCTAGTTTTGTTTT 58.443 32.000 0.00 0.00 0.00 2.43
4615 5040 8.190888 ACATTTAACTTCTCTAGAAATGCGAG 57.809 34.615 9.83 0.00 39.85 5.03
4753 5185 5.248477 TCTTATAGAGGTTTGAGTTGGCAGT 59.752 40.000 0.00 0.00 0.00 4.40
4831 5269 5.232202 CAGAGATGAAATGTGCAATGCATTC 59.768 40.000 12.38 12.02 41.91 2.67
4832 5270 5.109210 CAGAGATGAAATGTGCAATGCATT 58.891 37.500 12.38 5.99 41.91 3.56
4834 5282 3.674955 GCAGAGATGAAATGTGCAATGCA 60.675 43.478 2.72 2.72 35.60 3.96
4838 5286 4.794278 AATGCAGAGATGAAATGTGCAA 57.206 36.364 1.78 0.00 46.54 4.08
4840 5288 6.205076 AGAGATAATGCAGAGATGAAATGTGC 59.795 38.462 0.00 0.00 34.62 4.57
4843 5291 8.610248 AAGAGAGATAATGCAGAGATGAAATG 57.390 34.615 0.00 0.00 0.00 2.32
4844 5292 9.932207 CTAAGAGAGATAATGCAGAGATGAAAT 57.068 33.333 0.00 0.00 0.00 2.17
4871 5321 2.820197 GGGGGAGAGATGTGTTTTCAAC 59.180 50.000 0.00 0.00 0.00 3.18
4887 5337 2.087857 ATGAAAAAGGTGGCGGGGGA 62.088 55.000 0.00 0.00 0.00 4.81
4893 5343 6.775594 ATTACCTCTTATGAAAAAGGTGGC 57.224 37.500 3.21 0.00 42.08 5.01
5172 5624 7.716799 TTCATTATATTTGAGGGCTTTGTGT 57.283 32.000 0.00 0.00 0.00 3.72
5309 5761 4.321899 GCATTGGGCTTCTGTTTGTGATTA 60.322 41.667 0.00 0.00 40.25 1.75
5310 5762 3.555586 GCATTGGGCTTCTGTTTGTGATT 60.556 43.478 0.00 0.00 40.25 2.57


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

AutoCloner maintained by Alex Coulton.