Multiple sequence alignment - TraesCS2B01G531000

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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 TraesCS2B01G531000 chr2B 100.000 4373 0 0 1 4373 726462232 726466604 0.000000e+00 8076.0
1 TraesCS2B01G531000 chr2B 76.726 1289 225 61 1887 3139 723429454 723430703 0.000000e+00 649.0
2 TraesCS2B01G531000 chr2D 95.203 3023 83 13 1409 4373 598611075 598614093 0.000000e+00 4723.0
3 TraesCS2B01G531000 chr2D 86.581 626 50 24 1 603 598609179 598609793 0.000000e+00 660.0
4 TraesCS2B01G531000 chr2D 76.439 1286 238 53 1887 3139 595508346 595509599 1.720000e-178 636.0
5 TraesCS2B01G531000 chr2D 92.199 423 14 3 980 1402 598610611 598611014 8.150000e-162 580.0
6 TraesCS2B01G531000 chr2D 90.367 218 14 6 456 669 598609601 598609815 3.330000e-71 279.0
7 TraesCS2B01G531000 chr2D 96.907 97 3 0 899 995 598610001 598610097 3.500000e-36 163.0
8 TraesCS2B01G531000 chr2D 93.333 75 5 0 4125 4199 628908015 628908089 1.290000e-20 111.0
9 TraesCS2B01G531000 chr2D 74.306 288 40 24 442 714 564051503 564051771 1.670000e-14 91.6
10 TraesCS2B01G531000 chr2D 74.627 268 37 24 461 714 564051502 564051752 6.020000e-14 89.8
11 TraesCS2B01G531000 chr2D 95.122 41 2 0 4218 4258 169803455 169803415 1.020000e-06 65.8
12 TraesCS2B01G531000 chr2A 95.685 2132 62 10 1408 3524 732545649 732547765 0.000000e+00 3400.0
13 TraesCS2B01G531000 chr2A 96.438 758 27 0 1408 2165 732507982 732508739 0.000000e+00 1251.0
14 TraesCS2B01G531000 chr2A 95.383 758 32 1 1408 2165 732519687 732520441 0.000000e+00 1203.0
15 TraesCS2B01G531000 chr2A 88.546 681 41 15 3688 4336 732547924 732548599 0.000000e+00 791.0
16 TraesCS2B01G531000 chr2A 79.359 998 166 30 2159 3139 729568253 729569227 0.000000e+00 665.0
17 TraesCS2B01G531000 chr2A 86.312 621 52 24 1 602 732506626 732507232 0.000000e+00 645.0
18 TraesCS2B01G531000 chr2A 86.013 622 54 24 1 603 732544291 732544898 1.720000e-178 636.0
19 TraesCS2B01G531000 chr2A 96.633 297 10 0 1106 1402 732545281 732545577 1.090000e-135 494.0
20 TraesCS2B01G531000 chr2A 96.296 297 11 0 1106 1402 732507614 732507910 5.080000e-134 488.0
21 TraesCS2B01G531000 chr2A 95.510 245 11 0 1158 1402 732519371 732519615 4.100000e-105 392.0
22 TraesCS2B01G531000 chr2A 90.233 215 16 4 456 669 732507044 732507254 4.310000e-70 276.0
23 TraesCS2B01G531000 chr2A 97.516 161 4 0 893 1053 732507448 732507608 4.310000e-70 276.0
24 TraesCS2B01G531000 chr2A 90.233 215 16 4 456 669 732544709 732544919 4.310000e-70 276.0
25 TraesCS2B01G531000 chr2A 97.516 161 4 0 893 1053 732545115 732545275 4.310000e-70 276.0
26 TraesCS2B01G531000 chr2A 84.524 252 23 14 574 818 732544785 732545027 7.310000e-58 235.0
27 TraesCS2B01G531000 chr2A 83.730 252 25 14 574 818 732507120 732507362 1.580000e-54 224.0
28 TraesCS2B01G531000 chr2A 90.345 145 6 2 3511 3647 732547782 732547926 2.690000e-42 183.0
29 TraesCS2B01G531000 chr2A 97.778 45 1 0 823 867 732545066 732545110 1.300000e-10 78.7
30 TraesCS2B01G531000 chr2A 94.872 39 2 0 4218 4256 180368500 180368538 1.310000e-05 62.1
31 TraesCS2B01G531000 chr2A 97.222 36 1 0 3083 3118 766003288 766003253 1.310000e-05 62.1
32 TraesCS2B01G531000 chr2A 94.737 38 2 0 3083 3120 138517679 138517642 4.720000e-05 60.2
33 TraesCS2B01G531000 chr7A 90.909 484 34 6 3711 4193 236860432 236859958 3.690000e-180 641.0
34 TraesCS2B01G531000 chr7A 96.522 115 4 0 4199 4313 236811909 236811795 1.610000e-44 191.0
35 TraesCS2B01G531000 chr1A 73.705 1023 220 41 2161 3154 497887781 497886779 1.930000e-93 353.0
36 TraesCS2B01G531000 chr6B 86.765 204 12 5 3837 4026 54416604 54416806 3.430000e-51 213.0
37 TraesCS2B01G531000 chrUn 95.918 98 2 2 4274 4369 19105138 19105235 1.630000e-34 158.0
38 TraesCS2B01G531000 chrUn 100.000 28 0 0 3530 3557 45828162 45828189 8.000000e-03 52.8
39 TraesCS2B01G531000 chrUn 100.000 28 0 0 3530 3557 323578085 323578058 8.000000e-03 52.8
40 TraesCS2B01G531000 chr3D 95.876 97 3 1 4274 4369 265507357 265507453 5.860000e-34 156.0
41 TraesCS2B01G531000 chr3D 90.741 108 8 2 4089 4196 347609793 347609898 4.560000e-30 143.0
42 TraesCS2B01G531000 chr3D 100.000 28 0 0 3530 3557 599436732 599436759 8.000000e-03 52.8
43 TraesCS2B01G531000 chr7B 89.091 110 10 2 4089 4198 160557817 160557924 7.630000e-28 135.0
44 TraesCS2B01G531000 chr5D 88.288 111 12 1 4089 4199 456090716 456090825 9.870000e-27 132.0
45 TraesCS2B01G531000 chr5A 86.792 106 13 1 4094 4199 667760163 667760059 2.760000e-22 117.0
46 TraesCS2B01G531000 chr5A 100.000 28 0 0 840 867 452280412 452280385 8.000000e-03 52.8
47 TraesCS2B01G531000 chr1B 86.792 106 12 2 4094 4199 677934893 677934790 2.760000e-22 117.0
48 TraesCS2B01G531000 chr1B 79.817 109 16 3 3034 3139 540338366 540338261 1.690000e-09 75.0
49 TraesCS2B01G531000 chr5B 95.775 71 2 1 4274 4343 527639287 527639357 3.570000e-21 113.0
50 TraesCS2B01G531000 chr4B 91.549 71 5 1 4274 4343 349759543 349759473 3.600000e-16 97.1


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 TraesCS2B01G531000 chr2B 726462232 726466604 4372 False 8076.000000 8076 100.000000 1 4373 1 chr2B.!!$F2 4372
1 TraesCS2B01G531000 chr2B 723429454 723430703 1249 False 649.000000 649 76.726000 1887 3139 1 chr2B.!!$F1 1252
2 TraesCS2B01G531000 chr2D 598609179 598614093 4914 False 1281.000000 4723 92.251400 1 4373 5 chr2D.!!$F4 4372
3 TraesCS2B01G531000 chr2D 595508346 595509599 1253 False 636.000000 636 76.439000 1887 3139 1 chr2D.!!$F1 1252
4 TraesCS2B01G531000 chr2A 732519371 732520441 1070 False 797.500000 1203 95.446500 1158 2165 2 chr2A.!!$F4 1007
5 TraesCS2B01G531000 chr2A 732544291 732548599 4308 False 707.744444 3400 91.919222 1 4336 9 chr2A.!!$F5 4335
6 TraesCS2B01G531000 chr2A 729568253 729569227 974 False 665.000000 665 79.359000 2159 3139 1 chr2A.!!$F2 980
7 TraesCS2B01G531000 chr2A 732506626 732508739 2113 False 526.666667 1251 91.754167 1 2165 6 chr2A.!!$F3 2164
8 TraesCS2B01G531000 chr1A 497886779 497887781 1002 True 353.000000 353 73.705000 2161 3154 1 chr1A.!!$R1 993

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
887 953 0.468226 CCTACAGCGCCCAATAGGAA 59.532 55.0 15.32 0.00 37.02 3.36 F
1053 1648 0.478789 TTTGCCTTCCCCTTCCCCTA 60.479 55.0 0.00 0.00 0.00 3.53 F
2267 2940 0.526954 CGCATCCCAATTGAAGCTGC 60.527 55.0 7.12 10.16 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2940 0.460311 CTGTAAGGTACTCCCGGCTG 59.540 60.0 0.0 0.0 38.49 4.85 R
2506 3196 1.760192 AGGAATCCTGCAAGCATCAC 58.240 50.0 0.0 0.0 29.57 3.06 R
3813 4568 0.179062 CGCCATGGAGAAAGGAGGAG 60.179 60.0 18.4 0.0 0.00 3.69 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
27 28 4.466827 ACGGACCAAGAACACCTATTTTT 58.533 39.130 0.00 0.00 0.00 1.94
251 260 7.113684 TGTTTTTGAACTATTGTTTAATCCGCG 59.886 33.333 0.00 0.00 36.39 6.46
352 362 7.906160 TCTCTTTTAGTTTGTTCTTCAGTTCG 58.094 34.615 0.00 0.00 0.00 3.95
457 468 9.730705 ATAGATGAACTTTTTCAGTCTCAATGA 57.269 29.630 0.00 0.00 45.07 2.57
458 469 8.455903 AGATGAACTTTTTCAGTCTCAATGAA 57.544 30.769 0.00 0.00 45.07 2.57
459 470 8.348507 AGATGAACTTTTTCAGTCTCAATGAAC 58.651 33.333 0.00 0.00 45.07 3.18
460 471 7.630242 TGAACTTTTTCAGTCTCAATGAACT 57.370 32.000 0.00 0.00 36.79 3.01
461 472 8.055279 TGAACTTTTTCAGTCTCAATGAACTT 57.945 30.769 0.00 0.00 36.79 2.66
462 473 8.522830 TGAACTTTTTCAGTCTCAATGAACTTT 58.477 29.630 0.00 0.00 36.79 2.66
463 474 9.358872 GAACTTTTTCAGTCTCAATGAACTTTT 57.641 29.630 0.00 0.00 36.44 2.27
464 475 9.710900 AACTTTTTCAGTCTCAATGAACTTTTT 57.289 25.926 0.00 0.00 36.44 1.94
465 476 9.358872 ACTTTTTCAGTCTCAATGAACTTTTTC 57.641 29.630 0.00 0.00 36.44 2.29
466 477 8.702163 TTTTTCAGTCTCAATGAACTTTTTCC 57.298 30.769 0.00 0.00 36.44 3.13
467 478 7.403312 TTTCAGTCTCAATGAACTTTTTCCA 57.597 32.000 0.00 0.00 36.44 3.53
468 479 7.403312 TTCAGTCTCAATGAACTTTTTCCAA 57.597 32.000 0.00 0.00 31.86 3.53
469 480 7.403312 TCAGTCTCAATGAACTTTTTCCAAA 57.597 32.000 0.00 0.00 0.00 3.28
470 481 8.010733 TCAGTCTCAATGAACTTTTTCCAAAT 57.989 30.769 0.00 0.00 0.00 2.32
471 482 8.477256 TCAGTCTCAATGAACTTTTTCCAAATT 58.523 29.630 0.00 0.00 0.00 1.82
472 483 8.545420 CAGTCTCAATGAACTTTTTCCAAATTG 58.455 33.333 0.00 0.00 29.71 2.32
473 484 7.712205 AGTCTCAATGAACTTTTTCCAAATTGG 59.288 33.333 5.48 5.48 39.43 3.16
474 485 7.495606 GTCTCAATGAACTTTTTCCAAATTGGT 59.504 33.333 12.28 0.00 39.03 3.67
475 486 8.046107 TCTCAATGAACTTTTTCCAAATTGGTT 58.954 29.630 12.28 0.00 39.03 3.67
476 487 9.323985 CTCAATGAACTTTTTCCAAATTGGTTA 57.676 29.630 12.28 0.00 39.03 2.85
477 488 9.672673 TCAATGAACTTTTTCCAAATTGGTTAA 57.327 25.926 12.28 5.18 39.03 2.01
478 489 9.715123 CAATGAACTTTTTCCAAATTGGTTAAC 57.285 29.630 12.28 0.00 39.03 2.01
479 490 9.679661 AATGAACTTTTTCCAAATTGGTTAACT 57.320 25.926 12.28 0.00 39.03 2.24
480 491 9.679661 ATGAACTTTTTCCAAATTGGTTAACTT 57.320 25.926 12.28 2.34 39.03 2.66
481 492 9.508642 TGAACTTTTTCCAAATTGGTTAACTTT 57.491 25.926 12.28 0.60 39.03 2.66
514 525 7.938563 TGGTTAACTTTTTCCGAAATCAATG 57.061 32.000 5.42 0.00 0.00 2.82
524 535 8.574196 TTTTCCGAAATCAATGAACTTCTTTC 57.426 30.769 0.00 2.70 34.41 2.62
634 649 8.863086 AGATCCAATGAACTCTTTTTCAAATCA 58.137 29.630 0.00 0.00 38.95 2.57
801 817 3.730761 CCTGAACCAGCAGCGCAC 61.731 66.667 11.47 0.00 34.56 5.34
814 831 1.657181 GCGCACCACAACCGAAAAG 60.657 57.895 0.30 0.00 0.00 2.27
819 836 2.794350 GCACCACAACCGAAAAGAAATG 59.206 45.455 0.00 0.00 0.00 2.32
820 837 2.794350 CACCACAACCGAAAAGAAATGC 59.206 45.455 0.00 0.00 0.00 3.56
821 838 2.428890 ACCACAACCGAAAAGAAATGCA 59.571 40.909 0.00 0.00 0.00 3.96
829 879 6.046885 ACCGAAAAGAAATGCAATTGTTTG 57.953 33.333 10.09 1.76 36.10 2.93
863 929 2.510238 CTGCTGGTCGCTGTAGGC 60.510 66.667 0.00 0.00 40.11 3.93
884 950 4.049393 GCCTACAGCGCCCAATAG 57.951 61.111 2.29 0.40 0.00 1.73
885 951 1.598130 GCCTACAGCGCCCAATAGG 60.598 63.158 15.85 15.85 37.79 2.57
886 952 2.040009 GCCTACAGCGCCCAATAGGA 62.040 60.000 21.62 0.00 37.02 2.94
887 953 0.468226 CCTACAGCGCCCAATAGGAA 59.532 55.000 15.32 0.00 37.02 3.36
888 954 1.541233 CCTACAGCGCCCAATAGGAAG 60.541 57.143 15.32 0.00 37.02 3.46
889 955 0.468226 TACAGCGCCCAATAGGAAGG 59.532 55.000 2.29 0.00 38.24 3.46
890 956 1.271840 ACAGCGCCCAATAGGAAGGA 61.272 55.000 2.29 0.00 38.24 3.36
891 957 0.533755 CAGCGCCCAATAGGAAGGAG 60.534 60.000 2.29 0.00 38.24 3.69
1022 1617 4.998672 CCAAACACCGTATCTAGAAAACCA 59.001 41.667 0.00 0.00 0.00 3.67
1024 1619 6.819649 CCAAACACCGTATCTAGAAAACCATA 59.180 38.462 0.00 0.00 0.00 2.74
1053 1648 0.478789 TTTGCCTTCCCCTTCCCCTA 60.479 55.000 0.00 0.00 0.00 3.53
1054 1649 0.478789 TTGCCTTCCCCTTCCCCTAA 60.479 55.000 0.00 0.00 0.00 2.69
1055 1650 0.478789 TGCCTTCCCCTTCCCCTAAA 60.479 55.000 0.00 0.00 0.00 1.85
1075 1670 2.964438 TAAATAGAGCGGCGGCGGTG 62.964 60.000 40.45 9.73 46.35 4.94
1177 1772 0.597898 GGCGAGAATCCGTCCTTAGC 60.598 60.000 0.00 0.00 0.00 3.09
1341 1936 1.449601 TCGGAAAAGATCAGCGGCC 60.450 57.895 0.00 0.00 0.00 6.13
1390 1985 3.055819 GCTAAAGGTGAGATGGACACTGA 60.056 47.826 0.00 0.00 38.20 3.41
1402 1997 0.608640 GACACTGATGGGAGGTCGTT 59.391 55.000 0.00 0.00 0.00 3.85
1405 2000 1.208052 CACTGATGGGAGGTCGTTGAT 59.792 52.381 0.00 0.00 0.00 2.57
1496 2157 4.557205 GCAATCTACCCGAATCGATTAGT 58.443 43.478 11.38 11.38 0.00 2.24
1505 2166 4.700692 CCCGAATCGATTAGTGAGATCCTA 59.299 45.833 11.38 0.00 0.00 2.94
1588 2249 3.503363 GGCAGCGGCAGTGCTAAG 61.503 66.667 16.11 8.17 45.23 2.18
1607 2268 1.308783 GCTTGGGCTTCAGGCTACAC 61.309 60.000 0.00 0.00 44.03 2.90
1895 2556 5.068198 ACACATATGCAAATCTTCCATGGAC 59.932 40.000 15.91 1.03 0.00 4.02
1967 2628 0.586802 GGCACCACAAGAACTTCGAC 59.413 55.000 0.00 0.00 0.00 4.20
2047 2711 4.486125 TCACCTGCTGCATGTTCTTATA 57.514 40.909 7.87 0.00 0.00 0.98
2091 2755 2.028567 GGCCTCTACAGCATGATAGGTC 60.029 54.545 0.00 0.00 39.69 3.85
2267 2940 0.526954 CGCATCCCAATTGAAGCTGC 60.527 55.000 7.12 10.16 0.00 5.25
2662 3352 8.529476 AGTACTTATTTCTTCTACAACGGTGAT 58.471 33.333 7.88 0.00 0.00 3.06
2893 3583 2.622942 TGTGTTGGTTGATTCAGAAGGC 59.377 45.455 0.00 0.00 0.00 4.35
2966 3656 4.523943 TGGTTTCTGTGGAATTGAATGGAG 59.476 41.667 0.00 0.00 0.00 3.86
3009 3699 3.684788 GCCTATTCGACAACACAATCTGT 59.315 43.478 0.00 0.00 32.89 3.41
3040 3733 5.181748 GCTCAAGTCATCTTAATCACACCT 58.818 41.667 0.00 0.00 32.07 4.00
3200 3896 9.994432 GAAAAGATGGTGATATGTGAAAGTTAG 57.006 33.333 0.00 0.00 0.00 2.34
3231 3927 3.610911 GCTGCCTTTCCTGTAGTTATGT 58.389 45.455 0.00 0.00 0.00 2.29
3268 3964 8.952278 TGAACATTTTTAACTGTACTGTCAAGT 58.048 29.630 5.81 0.00 40.67 3.16
3462 4173 5.666969 TGCGACCAAATATTTCGATTAGG 57.333 39.130 11.29 5.54 34.62 2.69
3505 4216 7.769220 AGTAAGAGATCAAATCAAGGCATTTG 58.231 34.615 0.00 3.14 42.77 2.32
3567 4308 3.518068 CCGGAAAAGGATGGCGCC 61.518 66.667 22.73 22.73 0.00 6.53
3638 4387 2.884221 TACCGTCCCCTTCCCCCTT 61.884 63.158 0.00 0.00 0.00 3.95
3639 4388 2.420466 TACCGTCCCCTTCCCCCTTT 62.420 60.000 0.00 0.00 0.00 3.11
3647 4396 0.038310 CCTTCCCCCTTTCTGACCAC 59.962 60.000 0.00 0.00 0.00 4.16
3655 4404 0.946221 CTTTCTGACCACGCTCGCTT 60.946 55.000 0.00 0.00 0.00 4.68
3665 4414 2.437359 GCTCGCTTGCCCACTCAT 60.437 61.111 0.00 0.00 0.00 2.90
3690 4439 3.011517 ACCTCGCAGCTTCCCCAT 61.012 61.111 0.00 0.00 0.00 4.00
3692 4441 3.207669 CTCGCAGCTTCCCCATGC 61.208 66.667 0.00 0.00 36.60 4.06
3693 4442 3.694058 CTCGCAGCTTCCCCATGCT 62.694 63.158 0.00 0.00 40.54 3.79
3694 4443 2.753043 CGCAGCTTCCCCATGCTT 60.753 61.111 0.00 0.00 37.44 3.91
3696 4445 1.679977 GCAGCTTCCCCATGCTTCA 60.680 57.895 0.00 0.00 37.44 3.02
3729 4484 1.609072 GCGCACTTCCCTTCTCTTTTT 59.391 47.619 0.30 0.00 0.00 1.94
3735 4490 0.395312 TCCCTTCTCTTTTTCGCCGT 59.605 50.000 0.00 0.00 0.00 5.68
3742 4497 0.816018 TCTTTTTCGCCGTGCCTCAA 60.816 50.000 0.00 0.00 0.00 3.02
3772 4527 3.394719 AGAAAGCTCAAGGAACGACTTC 58.605 45.455 0.00 0.00 0.00 3.01
3774 4529 2.734276 AGCTCAAGGAACGACTTCTC 57.266 50.000 0.00 0.00 0.00 2.87
3777 4532 1.618837 CTCAAGGAACGACTTCTCCCA 59.381 52.381 0.00 0.00 31.50 4.37
3818 4573 2.420890 CATGCCGAGCTCCTCCTC 59.579 66.667 8.47 0.00 0.00 3.71
3840 4595 0.537188 TTCTCCATGGCGAGTTCCTC 59.463 55.000 6.96 0.00 0.00 3.71
4033 4788 3.321111 TCAGAAAACTTCAGACGTAGCCT 59.679 43.478 0.00 0.00 0.00 4.58
4036 4791 3.963428 AAACTTCAGACGTAGCCTGAT 57.037 42.857 6.30 0.00 40.02 2.90
4092 4848 3.136443 TCTGGAGGCACTTTCTTCTTTCA 59.864 43.478 0.00 0.00 41.55 2.69
4108 4864 7.820648 TCTTCTTTCATCTTTCTAATGGTTGC 58.179 34.615 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.541899 TTAAAGGAAAAATAGGTGTTCTTGGT 57.458 30.769 0.00 0.00 0.00 3.67
109 112 9.262358 GAAAAGACTAGACTTCAAACACATAGT 57.738 33.333 7.92 0.00 0.00 2.12
110 113 9.261180 TGAAAAGACTAGACTTCAAACACATAG 57.739 33.333 7.92 0.00 0.00 2.23
111 114 9.778741 ATGAAAAGACTAGACTTCAAACACATA 57.221 29.630 7.92 0.00 31.94 2.29
446 457 8.545420 CAATTTGGAAAAAGTTCATTGAGACTG 58.455 33.333 3.36 0.00 35.25 3.51
447 458 7.712205 CCAATTTGGAAAAAGTTCATTGAGACT 59.288 33.333 10.03 0.00 40.96 3.24
448 459 7.495606 ACCAATTTGGAAAAAGTTCATTGAGAC 59.504 33.333 22.19 0.00 40.96 3.36
449 460 7.563906 ACCAATTTGGAAAAAGTTCATTGAGA 58.436 30.769 22.19 0.00 40.96 3.27
450 461 7.790823 ACCAATTTGGAAAAAGTTCATTGAG 57.209 32.000 22.19 0.00 40.96 3.02
451 462 9.672673 TTAACCAATTTGGAAAAAGTTCATTGA 57.327 25.926 22.19 0.00 40.96 2.57
452 463 9.715123 GTTAACCAATTTGGAAAAAGTTCATTG 57.285 29.630 22.19 0.00 40.96 2.82
453 464 9.679661 AGTTAACCAATTTGGAAAAAGTTCATT 57.320 25.926 22.19 4.38 40.96 2.57
454 465 9.679661 AAGTTAACCAATTTGGAAAAAGTTCAT 57.320 25.926 22.19 0.00 40.96 2.57
455 466 9.508642 AAAGTTAACCAATTTGGAAAAAGTTCA 57.491 25.926 22.19 0.00 40.96 3.18
459 470 9.781834 GGAAAAAGTTAACCAATTTGGAAAAAG 57.218 29.630 22.19 0.00 40.96 2.27
460 471 9.297037 TGGAAAAAGTTAACCAATTTGGAAAAA 57.703 25.926 22.19 9.57 40.96 1.94
461 472 8.863872 TGGAAAAAGTTAACCAATTTGGAAAA 57.136 26.923 22.19 11.89 40.96 2.29
462 473 8.863872 TTGGAAAAAGTTAACCAATTTGGAAA 57.136 26.923 22.19 12.22 40.96 3.13
463 474 8.863872 TTTGGAAAAAGTTAACCAATTTGGAA 57.136 26.923 22.19 6.78 40.96 3.53
464 475 9.467796 AATTTGGAAAAAGTTAACCAATTTGGA 57.532 25.926 22.19 0.00 40.96 3.53
465 476 9.513727 CAATTTGGAAAAAGTTAACCAATTTGG 57.486 29.630 14.02 14.02 42.91 3.28
466 477 9.513727 CCAATTTGGAAAAAGTTAACCAATTTG 57.486 29.630 10.03 20.91 44.36 2.32
467 478 9.249053 ACCAATTTGGAAAAAGTTAACCAATTT 57.751 25.926 22.19 1.41 40.96 1.82
468 479 8.815565 ACCAATTTGGAAAAAGTTAACCAATT 57.184 26.923 22.19 0.00 40.96 2.32
469 480 8.815565 AACCAATTTGGAAAAAGTTAACCAAT 57.184 26.923 22.19 0.00 40.96 3.16
470 481 9.734984 TTAACCAATTTGGAAAAAGTTAACCAA 57.265 25.926 22.19 0.00 40.96 3.67
471 482 9.163899 GTTAACCAATTTGGAAAAAGTTAACCA 57.836 29.630 22.19 0.00 40.96 3.67
472 483 9.386010 AGTTAACCAATTTGGAAAAAGTTAACC 57.614 29.630 22.19 9.29 40.96 2.85
478 489 9.781834 GGAAAAAGTTAACCAATTTGGAAAAAG 57.218 29.630 22.19 0.00 40.96 2.27
479 490 8.451748 CGGAAAAAGTTAACCAATTTGGAAAAA 58.548 29.630 22.19 9.57 40.96 1.94
480 491 7.822822 TCGGAAAAAGTTAACCAATTTGGAAAA 59.177 29.630 22.19 11.89 40.96 2.29
481 492 7.328737 TCGGAAAAAGTTAACCAATTTGGAAA 58.671 30.769 22.19 12.22 40.96 3.13
482 493 6.875076 TCGGAAAAAGTTAACCAATTTGGAA 58.125 32.000 22.19 6.78 40.96 3.53
483 494 6.466885 TCGGAAAAAGTTAACCAATTTGGA 57.533 33.333 22.19 0.00 40.96 3.53
484 495 7.541122 TTTCGGAAAAAGTTAACCAATTTGG 57.459 32.000 14.02 14.02 45.02 3.28
514 525 5.040635 TCACCAAAAATGCGAAAGAAGTTC 58.959 37.500 0.00 0.00 0.00 3.01
774 790 2.238521 GCTGGTTCAGGAAAATGACCA 58.761 47.619 0.00 0.00 32.82 4.02
779 795 0.883833 CGCTGCTGGTTCAGGAAAAT 59.116 50.000 0.00 0.00 34.74 1.82
801 817 3.090952 TGCATTTCTTTTCGGTTGTGG 57.909 42.857 0.00 0.00 0.00 4.17
814 831 4.456566 AGCCCATTCAAACAATTGCATTTC 59.543 37.500 5.05 0.00 36.45 2.17
819 836 2.923020 CGTAGCCCATTCAAACAATTGC 59.077 45.455 5.05 0.00 36.45 3.56
820 837 3.510719 CCGTAGCCCATTCAAACAATTG 58.489 45.455 3.24 3.24 37.92 2.32
821 838 2.094234 GCCGTAGCCCATTCAAACAATT 60.094 45.455 0.00 0.00 0.00 2.32
867 933 1.598130 CCTATTGGGCGCTGTAGGC 60.598 63.158 7.64 0.00 37.64 3.93
869 935 1.541233 CCTTCCTATTGGGCGCTGTAG 60.541 57.143 7.64 4.73 34.39 2.74
871 937 1.224592 CCTTCCTATTGGGCGCTGT 59.775 57.895 7.64 0.00 34.39 4.40
872 938 0.533755 CTCCTTCCTATTGGGCGCTG 60.534 60.000 7.64 0.00 34.39 5.18
873 939 1.832912 CTCCTTCCTATTGGGCGCT 59.167 57.895 7.64 0.00 34.39 5.92
874 940 1.894282 GCTCCTTCCTATTGGGCGC 60.894 63.158 0.00 0.00 34.39 6.53
875 941 0.250081 GAGCTCCTTCCTATTGGGCG 60.250 60.000 0.87 0.00 34.39 6.13
876 942 0.109532 GGAGCTCCTTCCTATTGGGC 59.890 60.000 26.25 0.00 34.27 5.36
877 943 0.767998 GGGAGCTCCTTCCTATTGGG 59.232 60.000 31.36 0.00 37.40 4.12
878 944 0.767998 GGGGAGCTCCTTCCTATTGG 59.232 60.000 31.36 0.00 37.40 3.16
879 945 0.394565 CGGGGAGCTCCTTCCTATTG 59.605 60.000 31.36 9.19 37.40 1.90
880 946 0.764752 CCGGGGAGCTCCTTCCTATT 60.765 60.000 31.36 0.00 37.40 1.73
881 947 1.152226 CCGGGGAGCTCCTTCCTAT 60.152 63.158 31.36 0.00 37.40 2.57
882 948 2.282446 CCGGGGAGCTCCTTCCTA 59.718 66.667 31.36 0.00 37.40 2.94
953 1019 5.921408 CGTGTTATATACTTTCTCTCAGGCC 59.079 44.000 0.00 0.00 0.00 5.19
1022 1617 3.621558 GGAAGGCAAAGGTAACAGCTAT 58.378 45.455 0.00 0.00 41.41 2.97
1024 1619 1.547901 GGGAAGGCAAAGGTAACAGCT 60.548 52.381 0.00 0.00 41.41 4.24
1053 1648 0.865769 CGCCGCCGCTCTATTTATTT 59.134 50.000 0.00 0.00 0.00 1.40
1054 1649 0.949105 CCGCCGCCGCTCTATTTATT 60.949 55.000 0.00 0.00 0.00 1.40
1055 1650 1.374252 CCGCCGCCGCTCTATTTAT 60.374 57.895 0.00 0.00 0.00 1.40
1177 1772 2.578714 GCCTGATAGAGCTCCCCGG 61.579 68.421 10.93 7.24 0.00 5.73
1212 1807 1.000163 CCCGATCCGGTTGATACTCTG 60.000 57.143 0.00 0.00 46.80 3.35
1356 1951 4.181578 TCACCTTTAGCTTCAATACGAGC 58.818 43.478 0.00 0.00 0.00 5.03
1357 1952 5.651530 TCTCACCTTTAGCTTCAATACGAG 58.348 41.667 0.00 0.00 0.00 4.18
1390 1985 1.224592 GCCATCAACGACCTCCCAT 59.775 57.895 0.00 0.00 0.00 4.00
1402 1997 2.040813 AGCTCCTTTCTTTCTGCCATCA 59.959 45.455 0.00 0.00 0.00 3.07
1405 2000 1.901591 CAGCTCCTTTCTTTCTGCCA 58.098 50.000 0.00 0.00 0.00 4.92
1462 2123 0.680921 TAGATTGCCTGCCTTGCCAC 60.681 55.000 0.00 0.00 0.00 5.01
1496 2157 9.745018 AAATTTCTGAATTTCAGTAGGATCTCA 57.255 29.630 22.44 1.20 44.58 3.27
1505 2166 6.697019 CACCGACAAAATTTCTGAATTTCAGT 59.303 34.615 22.44 4.51 44.58 3.41
1553 2214 1.674057 CTCCTTGCGGGTCTGTTCT 59.326 57.895 0.00 0.00 36.25 3.01
1588 2249 1.002134 TGTAGCCTGAAGCCCAAGC 60.002 57.895 0.00 0.00 45.47 4.01
1607 2268 3.623906 TGGATCTGCTTGGAGAAGAAG 57.376 47.619 0.00 0.00 32.59 2.85
1895 2556 1.098712 CGAACCTCCTCTCCTCCTCG 61.099 65.000 0.00 0.00 0.00 4.63
1967 2628 2.316792 CGTGTTTACTCACTCTGGTCG 58.683 52.381 0.00 0.00 36.33 4.79
2047 2711 9.297037 GGCCAGATTACTTATATGGTACATTTT 57.703 33.333 0.00 0.00 45.60 1.82
2091 2755 7.038659 AGCAGCAGTTAAGTATTGAGTTAGAG 58.961 38.462 0.00 0.00 0.00 2.43
2267 2940 0.460311 CTGTAAGGTACTCCCGGCTG 59.540 60.000 0.00 0.00 38.49 4.85
2420 3093 5.473504 ACCACACATACATTTTCTTCCAGTC 59.526 40.000 0.00 0.00 0.00 3.51
2506 3196 1.760192 AGGAATCCTGCAAGCATCAC 58.240 50.000 0.00 0.00 29.57 3.06
2662 3352 3.395702 ACATGCCCGCCGGAACTA 61.396 61.111 5.05 0.00 0.00 2.24
2908 3598 2.543012 CTCAAGATAGCCATGTTCAGCG 59.457 50.000 0.00 0.00 0.00 5.18
3058 3751 5.529060 AGCATATAGGCTACTTGCAACTTTC 59.471 40.000 24.28 2.66 43.70 2.62
3200 3896 1.077716 AAAGGCAGCCGTATGACCC 60.078 57.895 5.55 0.00 0.00 4.46
3260 3956 7.672983 AATACAGGTTCACATAACTTGACAG 57.327 36.000 6.95 0.00 32.43 3.51
3268 3964 7.260387 TCCCACTTAATACAGGTTCACATAA 57.740 36.000 0.00 0.00 0.00 1.90
3393 4100 3.077359 GAGCCAAAGACTATTGCACACT 58.923 45.455 0.00 0.00 0.00 3.55
3396 4103 3.373439 CAGAGAGCCAAAGACTATTGCAC 59.627 47.826 0.00 0.00 0.00 4.57
3493 4204 5.300286 GCATAGTTCTACCAAATGCCTTGAT 59.700 40.000 0.00 0.00 37.55 2.57
3505 4216 8.144478 TGTAGATCAGATTTGCATAGTTCTACC 58.856 37.037 0.00 0.00 34.71 3.18
3567 4308 8.633237 TTTATTTATTTTGCAAAATTCACGCG 57.367 26.923 35.18 3.53 39.24 6.01
3606 4354 0.609662 ACGGTACTGCGGGTTATGTT 59.390 50.000 0.23 0.00 0.00 2.71
3638 4387 1.664649 CAAGCGAGCGTGGTCAGAA 60.665 57.895 3.12 0.00 0.00 3.02
3639 4388 2.049156 CAAGCGAGCGTGGTCAGA 60.049 61.111 3.12 0.00 0.00 3.27
3721 4476 0.949105 GAGGCACGGCGAAAAAGAGA 60.949 55.000 16.62 0.00 0.00 3.10
3729 4484 4.373116 GGAGTTGAGGCACGGCGA 62.373 66.667 16.62 0.00 0.00 5.54
3755 4510 1.273886 GGAGAAGTCGTTCCTTGAGCT 59.726 52.381 0.00 0.00 32.48 4.09
3772 4527 1.589414 AGGGACTCAAGGAATGGGAG 58.411 55.000 0.00 0.00 32.10 4.30
3805 4560 0.686112 AGAAAGGAGGAGGAGCTCGG 60.686 60.000 7.83 0.00 0.00 4.63
3813 4568 0.179062 CGCCATGGAGAAAGGAGGAG 60.179 60.000 18.40 0.00 0.00 3.69
3818 4573 1.373570 GAACTCGCCATGGAGAAAGG 58.626 55.000 19.39 10.36 37.49 3.11
3840 4595 2.147433 AAAGGAAGGAGGCAGCAGGG 62.147 60.000 0.00 0.00 0.00 4.45
3897 4652 0.182775 ACACTCACCAAGGTCCAACC 59.817 55.000 0.00 0.00 38.99 3.77
4033 4788 9.829507 ATTTGTGTTTGTCAAATTTCCTAATCA 57.170 25.926 0.40 0.00 40.97 2.57
4036 4791 9.311916 CAGATTTGTGTTTGTCAAATTTCCTAA 57.688 29.630 0.40 0.00 42.90 2.69
4092 4848 5.184892 ACAGGAGCAACCATTAGAAAGAT 57.815 39.130 2.96 0.00 42.04 2.40
4108 4864 5.344743 TGTAGAGGAAATTGCTACAGGAG 57.655 43.478 0.00 0.00 39.46 3.69
4347 5132 7.988737 TCGATTACTGATGAAAAGCAATCAAT 58.011 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.