Multiple sequence alignment - TraesCS4A01G180200

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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 TraesCS4A01G180200 chr4A 100.000 3068 0 0 1 3068 454589268 454592335 0.000000e+00 5666.0
1 TraesCS4A01G180200 chr4A 100.000 551 0 0 3269 3819 454592536 454593086 0.000000e+00 1018.0
2 TraesCS4A01G180200 chr4A 85.000 320 41 6 205 518 465772954 465773272 6.160000e-83 318.0
3 TraesCS4A01G180200 chr4D 89.969 1964 91 28 1 1909 119224281 119226193 0.000000e+00 2438.0
4 TraesCS4A01G180200 chr4D 95.034 1168 34 10 1916 3068 119226408 119227566 0.000000e+00 1814.0
5 TraesCS4A01G180200 chr4D 92.145 331 14 5 3478 3798 119228440 119228768 1.250000e-124 457.0
6 TraesCS4A01G180200 chr4D 92.891 211 12 3 3269 3478 119227615 119227823 1.720000e-78 303.0
7 TraesCS4A01G180200 chr4D 90.476 42 3 1 2192 2232 116252126 116252167 2.000000e-03 54.7
8 TraesCS4A01G180200 chr4B 92.213 1387 43 21 551 1909 181428915 181430264 0.000000e+00 1903.0
9 TraesCS4A01G180200 chr4B 91.460 1007 34 9 1916 2907 181430391 181431360 0.000000e+00 1336.0
10 TraesCS4A01G180200 chr4B 90.187 428 34 5 96 518 181427657 181428081 5.580000e-153 551.0
11 TraesCS4A01G180200 chr4B 89.685 349 18 10 3478 3813 181431893 181432236 2.730000e-116 429.0
12 TraesCS4A01G180200 chr4B 82.919 322 45 8 204 518 172324195 172323877 8.080000e-72 281.0
13 TraesCS4A01G180200 chr4B 90.667 75 6 1 1 75 519180183 519180256 8.730000e-17 99.0
14 TraesCS4A01G180200 chr6B 85.570 298 35 7 205 495 715748371 715748075 4.790000e-79 305.0
15 TraesCS4A01G180200 chr3A 85.235 298 36 7 205 495 315537677 315537973 2.230000e-77 300.0
16 TraesCS4A01G180200 chr3A 92.857 42 0 3 2186 2225 556668861 556668901 1.480000e-04 58.4
17 TraesCS4A01G180200 chr5B 83.230 322 44 9 205 518 97518969 97518650 1.740000e-73 287.0
18 TraesCS4A01G180200 chr3B 82.812 320 45 7 205 518 418699001 418699316 1.040000e-70 278.0
19 TraesCS4A01G180200 chr3B 81.560 141 20 6 81 220 325882471 325882336 1.120000e-20 111.0
20 TraesCS4A01G180200 chr3B 92.308 52 4 0 19 70 379926456 379926507 1.470000e-09 75.0
21 TraesCS4A01G180200 chr6D 82.188 320 49 7 205 518 159711811 159711494 6.290000e-68 268.0
22 TraesCS4A01G180200 chr6D 88.983 118 11 2 93 209 455166604 455166720 1.110000e-30 145.0
23 TraesCS4A01G180200 chr6D 83.178 107 11 6 105 209 355111385 355111486 1.460000e-14 91.6
24 TraesCS4A01G180200 chr2D 89.381 113 10 2 97 208 323389097 323388986 1.430000e-29 141.0
25 TraesCS4A01G180200 chr2D 88.496 113 11 2 97 208 323963605 323963494 6.650000e-28 135.0
26 TraesCS4A01G180200 chr2D 79.048 210 31 10 1 208 274476668 274476866 8.610000e-27 132.0
27 TraesCS4A01G180200 chr2D 85.859 99 13 1 1 99 323389237 323389140 1.880000e-18 104.0
28 TraesCS4A01G180200 chr2D 85.859 99 13 1 1 99 323963745 323963648 1.880000e-18 104.0
29 TraesCS4A01G180200 chr2D 94.737 38 0 2 2186 2221 7542669 7542706 1.480000e-04 58.4
30 TraesCS4A01G180200 chr2B 89.286 112 12 0 97 208 391968726 391968615 1.430000e-29 141.0
31 TraesCS4A01G180200 chr2B 90.000 80 7 1 1 80 391968851 391968773 6.750000e-18 102.0
32 TraesCS4A01G180200 chr2B 100.000 30 0 0 2186 2215 397433455 397433484 5.330000e-04 56.5
33 TraesCS4A01G180200 chr2A 78.774 212 28 14 1 208 331350897 331351095 4.010000e-25 126.0
34 TraesCS4A01G180200 chr2A 81.890 127 17 2 93 219 143034643 143034523 6.750000e-18 102.0
35 TraesCS4A01G180200 chr2A 92.857 42 3 0 2907 2948 682625744 682625703 1.150000e-05 62.1
36 TraesCS4A01G180200 chr1A 82.456 114 17 3 96 208 378736670 378736781 3.140000e-16 97.1
37 TraesCS4A01G180200 chr7D 94.595 37 0 2 2186 2220 574274884 574274920 5.330000e-04 56.5
38 TraesCS4A01G180200 chr7A 94.595 37 0 2 2186 2220 663579199 663579235 5.330000e-04 56.5
39 TraesCS4A01G180200 chr1D 100.000 29 0 0 2192 2220 80001467 80001495 2.000000e-03 54.7


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 TraesCS4A01G180200 chr4A 454589268 454593086 3818 False 3342.00 5666 100.00000 1 3819 2 chr4A.!!$F2 3818
1 TraesCS4A01G180200 chr4D 119224281 119228768 4487 False 1253.00 2438 92.50975 1 3798 4 chr4D.!!$F2 3797
2 TraesCS4A01G180200 chr4B 181427657 181432236 4579 False 1054.75 1903 90.88625 96 3813 4 chr4B.!!$F2 3717

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
566 1385 1.066858 TGGGCTCTTTCGCTAGTTCTG 60.067 52.381 0.0 0.0 0.0 3.02 F
1396 2233 0.104144 TTCCTCCCTCCCCAAACTGA 60.104 55.000 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 2257 0.036388 TCAGATTCAAGTGGGTCGGC 60.036 55.0 0.0 0.0 0.00 5.54 R
3279 4384 0.038744 CATGGCAGGTTCACTTCCCT 59.961 55.0 0.0 0.0 30.57 4.20 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
75 87 9.803315 ACATTTTTAAAAGAAGAAGGAGAACAC 57.197 29.630 0.14 0.00 0.00 3.32
78 90 7.568199 TTTAAAAGAAGAAGGAGAACACCTG 57.432 36.000 0.00 0.00 40.49 4.00
127 139 4.894252 AGAGGGGTCTAACAGGTATGTA 57.106 45.455 0.00 0.00 39.29 2.29
383 400 7.531857 TTGTTTAGGATGCAAGGTTAATCAA 57.468 32.000 0.00 0.00 0.00 2.57
443 460 7.903431 CGATCCAAATTAAAAGTAAACTCCTCG 59.097 37.037 0.00 0.00 0.00 4.63
455 472 6.549061 AGTAAACTCCTCGACAAAAACAAAC 58.451 36.000 0.00 0.00 0.00 2.93
462 479 5.588648 TCCTCGACAAAAACAAACTGAAGAT 59.411 36.000 0.00 0.00 0.00 2.40
490 507 5.242393 AGAAACCATCTATAACCATGCATGC 59.758 40.000 21.69 11.82 36.32 4.06
491 508 3.424703 ACCATCTATAACCATGCATGCC 58.575 45.455 21.69 0.00 0.00 4.40
495 512 3.423749 TCTATAACCATGCATGCCCATG 58.576 45.455 21.69 12.99 41.71 3.66
521 554 5.222278 AGGGTGAGAAGAAGGGTAAGATA 57.778 43.478 0.00 0.00 0.00 1.98
541 574 6.306987 AGATATTGAAATAAAGGATGCGGGT 58.693 36.000 0.00 0.00 0.00 5.28
566 1385 1.066858 TGGGCTCTTTCGCTAGTTCTG 60.067 52.381 0.00 0.00 0.00 3.02
587 1406 9.716507 GTTCTGATAAAGTACGTACCGTATAAA 57.283 33.333 21.80 11.24 44.12 1.40
602 1421 7.573968 ACCGTATAAATATATAGTCCGTCCC 57.426 40.000 0.00 0.00 0.00 4.46
603 1422 6.260936 ACCGTATAAATATATAGTCCGTCCCG 59.739 42.308 0.00 0.00 0.00 5.14
604 1423 6.260936 CCGTATAAATATATAGTCCGTCCCGT 59.739 42.308 0.00 0.00 0.00 5.28
605 1424 7.441157 CCGTATAAATATATAGTCCGTCCCGTA 59.559 40.741 0.00 0.00 0.00 4.02
643 1462 8.137437 TGAATTTCAGAGACATCCAAAGTTTTC 58.863 33.333 0.00 0.00 0.00 2.29
645 1464 8.924511 ATTTCAGAGACATCCAAAGTTTTCTA 57.075 30.769 0.00 0.00 0.00 2.10
646 1465 7.969536 TTCAGAGACATCCAAAGTTTTCTAG 57.030 36.000 0.00 0.00 0.00 2.43
732 1559 5.123344 AGTTATTAGCCGCAAGTAAACAAGG 59.877 40.000 0.00 0.00 0.00 3.61
801 1631 6.772605 TGTCAAGATCTCCTTCTGAATTTCA 58.227 36.000 0.00 0.00 31.42 2.69
897 1727 4.324991 GGGACGGAGGGCGTGTTT 62.325 66.667 0.00 0.00 0.00 2.83
929 1759 6.870965 TCCAATCTTCTTCTCTTCTTTTCTCG 59.129 38.462 0.00 0.00 0.00 4.04
949 1779 2.096516 CGTTCTCTTTCTCTTGTGCTGC 60.097 50.000 0.00 0.00 0.00 5.25
983 1814 1.142870 CCCATACATACACCCACCCAG 59.857 57.143 0.00 0.00 0.00 4.45
1028 1865 0.250901 GGAGTGAGGGAAGCAAGCAA 60.251 55.000 0.00 0.00 0.00 3.91
1037 1874 1.543358 GGAAGCAAGCAAGGAAGGAAG 59.457 52.381 0.00 0.00 0.00 3.46
1038 1875 1.543358 GAAGCAAGCAAGGAAGGAAGG 59.457 52.381 0.00 0.00 0.00 3.46
1039 1876 0.251519 AGCAAGCAAGGAAGGAAGGG 60.252 55.000 0.00 0.00 0.00 3.95
1040 1877 0.251341 GCAAGCAAGGAAGGAAGGGA 60.251 55.000 0.00 0.00 0.00 4.20
1357 2194 4.840005 GCCTACCAGCGCAGGTCC 62.840 72.222 29.12 14.02 42.06 4.46
1387 2224 1.645710 TCACACTTCTTCCTCCCTCC 58.354 55.000 0.00 0.00 0.00 4.30
1395 2232 0.329596 CTTCCTCCCTCCCCAAACTG 59.670 60.000 0.00 0.00 0.00 3.16
1396 2233 0.104144 TTCCTCCCTCCCCAAACTGA 60.104 55.000 0.00 0.00 0.00 3.41
1397 2234 0.547712 TCCTCCCTCCCCAAACTGAG 60.548 60.000 0.00 0.00 0.00 3.35
1398 2235 0.547712 CCTCCCTCCCCAAACTGAGA 60.548 60.000 0.00 0.00 0.00 3.27
1405 2242 4.151883 CCTCCCCAAACTGAGAAAATCAA 58.848 43.478 0.00 0.00 37.52 2.57
1420 2257 1.176527 ATCAAACCAATCAGCACCGG 58.823 50.000 0.00 0.00 0.00 5.28
1421 2258 1.080569 CAAACCAATCAGCACCGGC 60.081 57.895 0.00 0.00 41.61 6.13
1422 2259 2.275380 AAACCAATCAGCACCGGCC 61.275 57.895 0.00 0.00 42.56 6.13
1424 2261 4.776322 CCAATCAGCACCGGCCGA 62.776 66.667 30.73 5.29 42.56 5.54
1425 2262 3.499737 CAATCAGCACCGGCCGAC 61.500 66.667 30.73 16.13 42.56 4.79
1426 2263 4.778143 AATCAGCACCGGCCGACC 62.778 66.667 30.73 14.36 42.56 4.79
1664 2501 2.271607 GACAGCGATGCTCTCCGTCA 62.272 60.000 0.00 0.00 36.40 4.35
1831 2674 0.305922 GAGCTCAATTCGAATGGCCG 59.694 55.000 12.25 4.46 0.00 6.13
1909 2758 5.221682 TGTCTCCATTTTGGCATGTCAAATT 60.222 36.000 25.04 18.70 37.47 1.82
1912 2761 5.239351 TCCATTTTGGCATGTCAAATTCTG 58.761 37.500 25.04 20.31 37.47 3.02
1913 2762 5.011840 TCCATTTTGGCATGTCAAATTCTGA 59.988 36.000 25.04 16.22 37.47 3.27
1960 3017 5.221165 GGGGTTGGAAATGATAATACCGTTG 60.221 44.000 0.00 0.00 0.00 4.10
2165 3224 1.205064 CTCGTTTGCAGCAAGTCGG 59.795 57.895 24.35 15.91 0.00 4.79
2292 3357 0.324552 TCTTTGTGATGCCATGGGGG 60.325 55.000 15.13 0.00 40.85 5.40
2343 3408 6.648879 TTCTTTCAATTTGTTACTCAGGGG 57.351 37.500 0.00 0.00 0.00 4.79
2383 3448 1.808945 CCAAGACTTGGCAGATGTGAC 59.191 52.381 21.10 0.00 45.17 3.67
2452 3522 7.173735 TGTTGTTATATGCCATTGCTCATCTAG 59.826 37.037 0.00 0.00 38.71 2.43
2500 3575 5.239306 CAGTTAAGTTGATGCTCACTTGGAA 59.761 40.000 0.00 0.00 0.00 3.53
2501 3576 6.006449 AGTTAAGTTGATGCTCACTTGGAAT 58.994 36.000 0.00 0.00 0.00 3.01
2502 3577 7.119699 CAGTTAAGTTGATGCTCACTTGGAATA 59.880 37.037 0.00 0.00 0.00 1.75
2503 3578 7.335422 AGTTAAGTTGATGCTCACTTGGAATAG 59.665 37.037 0.00 0.00 0.00 1.73
2504 3579 3.944015 AGTTGATGCTCACTTGGAATAGC 59.056 43.478 0.00 0.00 35.51 2.97
2505 3580 2.554142 TGATGCTCACTTGGAATAGCG 58.446 47.619 0.00 0.00 37.80 4.26
2506 3581 2.093500 TGATGCTCACTTGGAATAGCGT 60.093 45.455 0.00 0.00 37.80 5.07
2507 3582 1.725641 TGCTCACTTGGAATAGCGTG 58.274 50.000 0.00 0.00 37.80 5.34
2508 3583 1.009829 GCTCACTTGGAATAGCGTGG 58.990 55.000 0.00 0.00 0.00 4.94
2509 3584 1.405526 GCTCACTTGGAATAGCGTGGA 60.406 52.381 0.00 0.00 0.00 4.02
2510 3585 2.935238 GCTCACTTGGAATAGCGTGGAA 60.935 50.000 0.00 0.00 0.00 3.53
2511 3586 3.334691 CTCACTTGGAATAGCGTGGAAA 58.665 45.455 0.00 0.00 0.00 3.13
2512 3587 3.941483 CTCACTTGGAATAGCGTGGAAAT 59.059 43.478 0.00 0.00 0.00 2.17
2513 3588 3.938963 TCACTTGGAATAGCGTGGAAATC 59.061 43.478 0.00 0.00 0.00 2.17
2514 3589 3.065371 CACTTGGAATAGCGTGGAAATCC 59.935 47.826 0.00 0.00 0.00 3.01
2515 3590 3.054361 ACTTGGAATAGCGTGGAAATCCT 60.054 43.478 0.44 0.00 36.82 3.24
2516 3591 3.644966 TGGAATAGCGTGGAAATCCTT 57.355 42.857 0.44 0.00 36.82 3.36
2517 3592 3.278574 TGGAATAGCGTGGAAATCCTTG 58.721 45.455 0.44 0.00 36.82 3.61
2518 3593 3.279434 GGAATAGCGTGGAAATCCTTGT 58.721 45.455 0.44 0.00 36.82 3.16
2519 3594 3.312697 GGAATAGCGTGGAAATCCTTGTC 59.687 47.826 0.44 0.00 36.82 3.18
2520 3595 3.914426 ATAGCGTGGAAATCCTTGTCT 57.086 42.857 0.44 0.00 36.82 3.41
2521 3596 2.568623 AGCGTGGAAATCCTTGTCTT 57.431 45.000 0.44 0.00 36.82 3.01
2522 3597 2.427506 AGCGTGGAAATCCTTGTCTTC 58.572 47.619 0.44 0.00 36.82 2.87
2523 3598 2.039084 AGCGTGGAAATCCTTGTCTTCT 59.961 45.455 0.44 0.00 36.82 2.85
2524 3599 2.160417 GCGTGGAAATCCTTGTCTTCTG 59.840 50.000 0.44 0.00 36.82 3.02
2529 3629 5.124617 GTGGAAATCCTTGTCTTCTGATTCC 59.875 44.000 0.44 0.00 36.82 3.01
2764 3864 6.340522 AGCACAAACTTTGACTTAGCAATTT 58.659 32.000 8.55 0.00 0.00 1.82
2811 3914 8.144862 TGGTTTGCTAGGGAATAATTTGAAAT 57.855 30.769 0.00 0.00 0.00 2.17
3057 4162 4.917415 GGTGATATGCGGCAAATAATTCAC 59.083 41.667 6.82 12.92 0.00 3.18
3058 4163 5.507149 GGTGATATGCGGCAAATAATTCACA 60.507 40.000 6.82 0.00 34.19 3.58
3369 4474 4.779993 TTACCCAAAGTTTGCCCAAAAT 57.220 36.364 10.25 0.00 31.33 1.82
3408 4513 4.998671 TTTGTTGTCAAATTGAGCTCCA 57.001 36.364 12.15 0.00 38.44 3.86
3410 4515 2.622942 TGTTGTCAAATTGAGCTCCACC 59.377 45.455 12.15 0.00 0.00 4.61
3428 4533 6.266131 TCCACCTATCCTGATTTGCTTTAT 57.734 37.500 0.00 0.00 0.00 1.40
3581 5316 0.603569 GGCTCTCTGAACGAAGGTCA 59.396 55.000 0.00 0.00 0.00 4.02
3607 5342 4.065088 CTCCTGCTGCTAGTCTAGTCTAG 58.935 52.174 16.86 16.86 40.01 2.43
3611 5346 5.105567 TGCTGCTAGTCTAGTCTAGTCTT 57.894 43.478 20.53 0.29 39.44 3.01
3617 5352 6.155565 TGCTAGTCTAGTCTAGTCTTCTCTGT 59.844 42.308 20.53 0.00 39.44 3.41
3691 5426 5.049818 CACATCACACTTCACTCTTTTCCTC 60.050 44.000 0.00 0.00 0.00 3.71
3758 5505 4.067192 CCATCATCACACTTCACAGTTCA 58.933 43.478 0.00 0.00 0.00 3.18
3759 5506 4.153655 CCATCATCACACTTCACAGTTCAG 59.846 45.833 0.00 0.00 0.00 3.02
3768 5517 5.127845 ACACTTCACAGTTCAGAGAGAGAAA 59.872 40.000 0.00 0.00 0.00 2.52
3798 5547 4.423732 GCAGAGAGCTACAAGAAGAAGAG 58.576 47.826 0.00 0.00 41.15 2.85
3799 5548 4.423732 CAGAGAGCTACAAGAAGAAGAGC 58.576 47.826 0.00 0.00 0.00 4.09
3800 5549 4.158394 CAGAGAGCTACAAGAAGAAGAGCT 59.842 45.833 0.00 0.00 45.94 4.09
3803 5552 5.505780 AGAGCTACAAGAAGAAGAGCTAGA 58.494 41.667 0.00 0.00 43.39 2.43
3810 5559 4.601406 AGAAGAAGAGCTAGAAGGAGGA 57.399 45.455 0.00 0.00 0.00 3.71
3811 5560 4.536765 AGAAGAAGAGCTAGAAGGAGGAG 58.463 47.826 0.00 0.00 0.00 3.69
3812 5561 3.312736 AGAAGAGCTAGAAGGAGGAGG 57.687 52.381 0.00 0.00 0.00 4.30
3813 5562 2.091333 AGAAGAGCTAGAAGGAGGAGGG 60.091 54.545 0.00 0.00 0.00 4.30
3814 5563 0.560688 AGAGCTAGAAGGAGGAGGGG 59.439 60.000 0.00 0.00 0.00 4.79
3815 5564 0.471022 GAGCTAGAAGGAGGAGGGGG 60.471 65.000 0.00 0.00 0.00 5.40
3816 5565 0.931757 AGCTAGAAGGAGGAGGGGGA 60.932 60.000 0.00 0.00 0.00 4.81
3817 5566 0.031010 GCTAGAAGGAGGAGGGGGAA 60.031 60.000 0.00 0.00 0.00 3.97
3818 5567 1.415273 GCTAGAAGGAGGAGGGGGAAT 60.415 57.143 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.471116 TGCATTAGAGCATATCATCAACACC 59.529 40.000 0.00 0.00 40.11 4.16
66 67 3.756117 GAACATTTCCAGGTGTTCTCCT 58.244 45.455 12.30 0.00 46.58 3.69
75 87 5.500234 TGAACCTATGAGAACATTTCCAGG 58.500 41.667 0.00 0.00 37.87 4.45
78 90 9.125026 ACATAATGAACCTATGAGAACATTTCC 57.875 33.333 0.00 0.00 37.87 3.13
90 102 7.082972 AGACCCCTCTAACATAATGAACCTAT 58.917 38.462 0.00 0.00 0.00 2.57
91 103 6.449956 AGACCCCTCTAACATAATGAACCTA 58.550 40.000 0.00 0.00 0.00 3.08
127 139 9.976776 AATATGAAGAATCTGAATATGCCATCT 57.023 29.630 0.00 0.00 0.00 2.90
210 222 9.357652 GCATTTGAATATGTCACTAAACAACAT 57.642 29.630 0.00 0.00 35.39 2.71
383 400 3.247006 AGAAAGACGGTCGTGCAATAT 57.753 42.857 4.85 0.00 0.00 1.28
443 460 8.687824 TCTTTCATCTTCAGTTTGTTTTTGTC 57.312 30.769 0.00 0.00 0.00 3.18
462 479 6.889177 TGCATGGTTATAGATGGTTTCTTTCA 59.111 34.615 0.00 0.00 35.79 2.69
491 508 3.341823 CTTCTTCTCACCCTTGTCATGG 58.658 50.000 0.00 0.00 0.00 3.66
495 512 1.700186 ACCCTTCTTCTCACCCTTGTC 59.300 52.381 0.00 0.00 0.00 3.18
521 554 4.536765 AGACCCGCATCCTTTATTTCAAT 58.463 39.130 0.00 0.00 0.00 2.57
535 568 1.271840 AAGAGCCCAATAGACCCGCA 61.272 55.000 0.00 0.00 0.00 5.69
541 574 3.031736 ACTAGCGAAAGAGCCCAATAGA 58.968 45.455 0.00 0.00 38.01 1.98
732 1559 0.101939 CGCTAGGAAACCGGAGTACC 59.898 60.000 9.46 6.01 0.00 3.34
801 1631 4.463891 CCTATTGAAAACCTGGATGCTTGT 59.536 41.667 0.00 0.00 0.00 3.16
844 1674 2.046314 CGCCAACAGAACCCCGAT 60.046 61.111 0.00 0.00 0.00 4.18
895 1725 4.179133 AGAAGAAGATTGGAGGGAGGAAA 58.821 43.478 0.00 0.00 0.00 3.13
897 1727 3.013417 AGAGAAGAAGATTGGAGGGAGGA 59.987 47.826 0.00 0.00 0.00 3.71
929 1759 2.096516 CGCAGCACAAGAGAAAGAGAAC 60.097 50.000 0.00 0.00 0.00 3.01
949 1779 2.535485 TATGGGTCTGGCTTGGCACG 62.535 60.000 0.00 0.00 0.00 5.34
983 1814 2.283101 TGGCAGTGATTGGTGGGC 60.283 61.111 0.00 0.00 0.00 5.36
1028 1865 2.352032 CGAGCGTCCCTTCCTTCCT 61.352 63.158 0.00 0.00 0.00 3.36
1098 1935 1.376466 GCAGAGCACCCAGAGGAAA 59.624 57.895 0.00 0.00 36.73 3.13
1357 2194 4.084328 GGAAGAAGTGTGAAATCAGTGACG 60.084 45.833 0.00 0.00 0.00 4.35
1387 2224 5.275067 TGGTTTGATTTTCTCAGTTTGGG 57.725 39.130 0.00 0.00 34.68 4.12
1395 2232 4.925646 GGTGCTGATTGGTTTGATTTTCTC 59.074 41.667 0.00 0.00 0.00 2.87
1396 2233 4.559300 CGGTGCTGATTGGTTTGATTTTCT 60.559 41.667 0.00 0.00 0.00 2.52
1397 2234 3.674753 CGGTGCTGATTGGTTTGATTTTC 59.325 43.478 0.00 0.00 0.00 2.29
1398 2235 3.554752 CCGGTGCTGATTGGTTTGATTTT 60.555 43.478 0.00 0.00 0.00 1.82
1405 2242 2.676471 GGCCGGTGCTGATTGGTT 60.676 61.111 1.90 0.00 37.74 3.67
1420 2257 0.036388 TCAGATTCAAGTGGGTCGGC 60.036 55.000 0.00 0.00 0.00 5.54
1421 2258 2.472695 TTCAGATTCAAGTGGGTCGG 57.527 50.000 0.00 0.00 0.00 4.79
1422 2259 3.620374 CAGATTCAGATTCAAGTGGGTCG 59.380 47.826 0.00 0.00 0.00 4.79
1423 2260 4.583871 ACAGATTCAGATTCAAGTGGGTC 58.416 43.478 0.00 0.00 0.00 4.46
1424 2261 4.288105 AGACAGATTCAGATTCAAGTGGGT 59.712 41.667 0.00 0.00 0.00 4.51
1425 2262 4.841422 AGACAGATTCAGATTCAAGTGGG 58.159 43.478 0.00 0.00 0.00 4.61
1426 2263 5.391736 GCAAGACAGATTCAGATTCAAGTGG 60.392 44.000 0.00 0.00 0.00 4.00
1427 2264 5.411977 AGCAAGACAGATTCAGATTCAAGTG 59.588 40.000 0.00 0.00 0.00 3.16
1428 2265 5.558818 AGCAAGACAGATTCAGATTCAAGT 58.441 37.500 0.00 0.00 0.00 3.16
1429 2266 6.258287 CCTAGCAAGACAGATTCAGATTCAAG 59.742 42.308 0.00 0.00 0.00 3.02
1430 2267 6.111382 CCTAGCAAGACAGATTCAGATTCAA 58.889 40.000 0.00 0.00 0.00 2.69
1431 2268 5.668471 CCTAGCAAGACAGATTCAGATTCA 58.332 41.667 0.00 0.00 0.00 2.57
1528 2365 2.932130 GATCCACCTTGAGCGAGGGC 62.932 65.000 8.58 0.00 41.31 5.19
1573 2410 0.678950 TGATGACGAAGGTGAGCACA 59.321 50.000 2.75 0.00 0.00 4.57
1664 2501 3.681835 GACGAGGCTGACGGTGGT 61.682 66.667 0.00 0.00 34.93 4.16
1776 2619 2.099756 GGTTGCAGTTCCATGGATAAGC 59.900 50.000 17.06 18.95 0.00 3.09
1909 2758 5.105106 TCCAGTTATTTATGGCTCGTTCAGA 60.105 40.000 0.00 0.00 36.47 3.27
1912 2761 5.049405 CCATCCAGTTATTTATGGCTCGTTC 60.049 44.000 0.00 0.00 36.47 3.95
1913 2762 4.821805 CCATCCAGTTATTTATGGCTCGTT 59.178 41.667 0.00 0.00 36.47 3.85
1960 3017 6.771267 CCCTCCCTAAATTTCCAACACTATAC 59.229 42.308 0.00 0.00 0.00 1.47
2084 3141 5.937975 CCATGAATGGGGTCAAAAGTAAT 57.062 39.130 1.01 0.00 44.31 1.89
2088 3145 4.467082 TCATTCCATGAATGGGGTCAAAAG 59.533 41.667 14.84 0.00 46.43 2.27
2165 3224 2.614057 CGAGGGAGTAACATGGAAATGC 59.386 50.000 0.00 0.00 0.00 3.56
2278 3343 0.324645 AAACTCCCCCATGGCATCAC 60.325 55.000 6.09 0.00 0.00 3.06
2292 3357 5.853282 CACAACTAAGCACAATAGCAAACTC 59.147 40.000 0.00 0.00 36.85 3.01
2343 3408 6.823689 TCTTGGAGGTGCATAAGATAACTTTC 59.176 38.462 0.00 0.00 37.53 2.62
2381 3446 3.307242 GCATCGTCCACTGTTAAGATGTC 59.693 47.826 13.49 6.30 38.11 3.06
2383 3448 3.525537 AGCATCGTCCACTGTTAAGATG 58.474 45.455 9.84 9.84 38.65 2.90
2428 3498 7.226441 ACTAGATGAGCAATGGCATATAACAA 58.774 34.615 0.00 0.00 44.61 2.83
2431 3501 8.253810 GTCTACTAGATGAGCAATGGCATATAA 58.746 37.037 0.00 0.00 44.61 0.98
2500 3575 3.914426 AGACAAGGATTTCCACGCTAT 57.086 42.857 0.00 0.00 38.89 2.97
2501 3576 3.260884 AGAAGACAAGGATTTCCACGCTA 59.739 43.478 0.00 0.00 38.89 4.26
2502 3577 2.039084 AGAAGACAAGGATTTCCACGCT 59.961 45.455 0.00 0.00 38.89 5.07
2503 3578 2.160417 CAGAAGACAAGGATTTCCACGC 59.840 50.000 0.00 0.00 38.89 5.34
2504 3579 3.664107 TCAGAAGACAAGGATTTCCACG 58.336 45.455 0.00 0.00 38.89 4.94
2505 3580 5.124617 GGAATCAGAAGACAAGGATTTCCAC 59.875 44.000 0.00 0.00 38.89 4.02
2506 3581 5.014544 AGGAATCAGAAGACAAGGATTTCCA 59.985 40.000 0.00 0.00 38.89 3.53
2507 3582 5.504853 AGGAATCAGAAGACAAGGATTTCC 58.495 41.667 0.00 0.00 30.60 3.13
2508 3583 6.093357 GTGAGGAATCAGAAGACAAGGATTTC 59.907 42.308 0.00 0.00 30.60 2.17
2509 3584 5.942826 GTGAGGAATCAGAAGACAAGGATTT 59.057 40.000 0.00 0.00 30.60 2.17
2510 3585 5.013495 TGTGAGGAATCAGAAGACAAGGATT 59.987 40.000 0.00 0.00 32.97 3.01
2511 3586 4.533707 TGTGAGGAATCAGAAGACAAGGAT 59.466 41.667 0.00 0.00 0.00 3.24
2512 3587 3.903714 TGTGAGGAATCAGAAGACAAGGA 59.096 43.478 0.00 0.00 0.00 3.36
2513 3588 4.277515 TGTGAGGAATCAGAAGACAAGG 57.722 45.455 0.00 0.00 0.00 3.61
2514 3589 4.634883 CCATGTGAGGAATCAGAAGACAAG 59.365 45.833 0.00 0.00 0.00 3.16
2515 3590 4.042062 ACCATGTGAGGAATCAGAAGACAA 59.958 41.667 0.00 0.00 0.00 3.18
2516 3591 3.584406 ACCATGTGAGGAATCAGAAGACA 59.416 43.478 0.00 0.00 0.00 3.41
2517 3592 4.213564 ACCATGTGAGGAATCAGAAGAC 57.786 45.455 0.00 0.00 0.00 3.01
2518 3593 4.916041 AACCATGTGAGGAATCAGAAGA 57.084 40.909 0.00 0.00 0.00 2.87
2519 3594 4.397417 GGAAACCATGTGAGGAATCAGAAG 59.603 45.833 0.00 0.00 0.00 2.85
2520 3595 4.043310 AGGAAACCATGTGAGGAATCAGAA 59.957 41.667 0.00 0.00 0.00 3.02
2521 3596 3.588842 AGGAAACCATGTGAGGAATCAGA 59.411 43.478 0.00 0.00 0.00 3.27
2522 3597 3.693085 CAGGAAACCATGTGAGGAATCAG 59.307 47.826 0.00 0.00 0.00 2.90
2523 3598 3.074390 ACAGGAAACCATGTGAGGAATCA 59.926 43.478 0.00 0.00 0.00 2.57
2524 3599 3.690460 ACAGGAAACCATGTGAGGAATC 58.310 45.455 0.00 0.00 0.00 2.52
2529 3629 5.063204 TCAGTTAACAGGAAACCATGTGAG 58.937 41.667 8.61 0.00 0.00 3.51
2764 3864 1.125093 TTCGCTTCTTCAGGTCCCCA 61.125 55.000 0.00 0.00 0.00 4.96
3268 4373 1.909302 TCACTTCCCTTCTCATGGTCC 59.091 52.381 0.00 0.00 0.00 4.46
3269 4374 3.339141 GTTCACTTCCCTTCTCATGGTC 58.661 50.000 0.00 0.00 0.00 4.02
3270 4375 2.040412 GGTTCACTTCCCTTCTCATGGT 59.960 50.000 0.00 0.00 0.00 3.55
3271 4376 2.307098 AGGTTCACTTCCCTTCTCATGG 59.693 50.000 0.00 0.00 0.00 3.66
3272 4377 3.341823 CAGGTTCACTTCCCTTCTCATG 58.658 50.000 0.00 0.00 0.00 3.07
3273 4378 2.290577 GCAGGTTCACTTCCCTTCTCAT 60.291 50.000 0.00 0.00 0.00 2.90
3274 4379 1.072331 GCAGGTTCACTTCCCTTCTCA 59.928 52.381 0.00 0.00 0.00 3.27
3275 4380 1.611936 GGCAGGTTCACTTCCCTTCTC 60.612 57.143 0.00 0.00 0.00 2.87
3276 4381 0.402121 GGCAGGTTCACTTCCCTTCT 59.598 55.000 0.00 0.00 0.00 2.85
3277 4382 0.110486 TGGCAGGTTCACTTCCCTTC 59.890 55.000 0.00 0.00 30.57 3.46
3278 4383 0.779997 ATGGCAGGTTCACTTCCCTT 59.220 50.000 0.00 0.00 30.57 3.95
3279 4384 0.038744 CATGGCAGGTTCACTTCCCT 59.961 55.000 0.00 0.00 30.57 4.20
3280 4385 1.598701 GCATGGCAGGTTCACTTCCC 61.599 60.000 0.00 0.00 30.57 3.97
3369 4474 9.387123 GACAACAAAACAAAAGCAAAAATTGTA 57.613 25.926 0.00 0.00 36.33 2.41
3408 4513 8.494433 TGAACTATAAAGCAAATCAGGATAGGT 58.506 33.333 0.00 0.00 0.00 3.08
3428 4533 6.647895 GGGACGAGAACAATAAACTTGAACTA 59.352 38.462 0.00 0.00 0.00 2.24
3462 4575 2.738314 GCCATGCCAAAACAATGAAGAC 59.262 45.455 0.00 0.00 0.00 3.01
3581 5316 0.334676 AGACTAGCAGCAGGAGACCT 59.665 55.000 0.00 0.00 0.00 3.85
3595 5330 9.796180 AAAAACAGAGAAGACTAGACTAGACTA 57.204 33.333 16.55 0.00 30.82 2.59
3691 5426 4.167268 GAGCGTAGTGAAGAGTAAAGTGG 58.833 47.826 0.00 0.00 0.00 4.00
3758 5505 3.577848 TCTGCTGCTTCTTTTCTCTCTCT 59.422 43.478 0.00 0.00 0.00 3.10
3759 5506 3.924144 TCTGCTGCTTCTTTTCTCTCTC 58.076 45.455 0.00 0.00 0.00 3.20
3787 5536 4.709397 TCCTCCTTCTAGCTCTTCTTCTTG 59.291 45.833 0.00 0.00 0.00 3.02
3789 5538 4.536765 CTCCTCCTTCTAGCTCTTCTTCT 58.463 47.826 0.00 0.00 0.00 2.85
3790 5539 3.636764 CCTCCTCCTTCTAGCTCTTCTTC 59.363 52.174 0.00 0.00 0.00 2.87
3791 5540 3.629796 CCCTCCTCCTTCTAGCTCTTCTT 60.630 52.174 0.00 0.00 0.00 2.52
3798 5547 0.031010 TTCCCCCTCCTCCTTCTAGC 60.031 60.000 0.00 0.00 0.00 3.42
3799 5548 2.805290 ATTCCCCCTCCTCCTTCTAG 57.195 55.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.