Multiple sequence alignment - TraesCS1D01G002700

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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 TraesCS1D01G002700 chr1D 100.000 5854 0 0 1 5854 622211 616358 0.000000e+00 10811.0
1 TraesCS1D01G002700 chr1D 86.272 2586 304 28 2308 4882 696764 694219 0.000000e+00 2761.0
2 TraesCS1D01G002700 chr1D 78.329 1269 145 62 4676 5854 450764 451992 0.000000e+00 701.0
3 TraesCS1D01G002700 chr1B 89.710 3926 371 20 1095 5012 4114561 4118461 0.000000e+00 4981.0
4 TraesCS1D01G002700 chr1B 89.348 3680 380 8 1100 4772 4483642 4479968 0.000000e+00 4614.0
5 TraesCS1D01G002700 chr1B 85.842 4351 538 42 345 4639 4094820 4099148 0.000000e+00 4551.0
6 TraesCS1D01G002700 chr1B 87.339 3894 399 40 2006 5854 4560707 4556863 0.000000e+00 4373.0
7 TraesCS1D01G002700 chr1B 87.206 3447 428 10 1100 4540 3951180 3954619 0.000000e+00 3910.0
8 TraesCS1D01G002700 chr1B 86.410 3554 463 14 1095 4639 4510812 4507270 0.000000e+00 3869.0
9 TraesCS1D01G002700 chr1B 85.710 3625 476 20 1030 4636 3964514 3968114 0.000000e+00 3786.0
10 TraesCS1D01G002700 chr1B 86.458 3360 416 28 770 4116 4150487 4153820 0.000000e+00 3648.0
11 TraesCS1D01G002700 chr1B 90.123 2035 186 10 216 2242 4857243 4855216 0.000000e+00 2630.0
12 TraesCS1D01G002700 chr1B 83.867 1531 181 40 3623 5128 4014146 4015635 0.000000e+00 1399.0
13 TraesCS1D01G002700 chr1B 86.244 836 56 21 5051 5854 4479758 4478950 0.000000e+00 852.0
14 TraesCS1D01G002700 chr1B 81.653 605 53 17 5051 5626 4118461 4119036 3.220000e-122 449.0
15 TraesCS1D01G002700 chr1B 87.500 368 35 10 8 367 4094447 4094811 1.170000e-111 414.0
16 TraesCS1D01G002700 chr1B 97.059 204 6 0 4809 5012 4479961 4479758 1.560000e-90 344.0
17 TraesCS1D01G002700 chr1B 78.716 296 41 11 5367 5645 4587778 4587488 1.680000e-40 178.0
18 TraesCS1D01G002700 chr1B 85.455 165 21 3 5602 5765 4015808 4015970 1.010000e-37 169.0
19 TraesCS1D01G002700 chr1B 89.583 48 3 1 511 556 4830433 4830480 6.340000e-05 60.2
20 TraesCS1D01G002700 chr1A 88.142 3989 375 56 1899 5854 3453891 3449968 0.000000e+00 4656.0
21 TraesCS1D01G002700 chr1A 85.300 4517 552 61 81 4540 3504855 3500394 0.000000e+00 4560.0
22 TraesCS1D01G002700 chr1A 88.608 3643 306 40 2255 5854 2975203 2978779 0.000000e+00 4327.0
23 TraesCS1D01G002700 chr1A 88.245 3522 309 39 2230 5710 3680272 3676815 0.000000e+00 4113.0
24 TraesCS1D01G002700 chr1A 85.930 3447 456 18 1030 4469 3672524 3669100 0.000000e+00 3651.0
25 TraesCS1D01G002700 chr1A 89.981 2126 175 27 8 2102 3455878 3453760 0.000000e+00 2712.0
26 TraesCS1D01G002700 chr1A 83.695 1429 204 21 609 2030 2982196 2983602 0.000000e+00 1321.0
27 TraesCS1D01G002700 chr1A 78.730 315 39 16 5367 5665 3487957 3487655 1.000000e-42 185.0
28 TraesCS1D01G002700 chr1A 81.102 254 24 11 5624 5854 3668531 3668279 1.300000e-41 182.0
29 TraesCS1D01G002700 chr3D 79.208 404 45 19 5450 5818 560072677 560072278 1.630000e-60 244.0


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 TraesCS1D01G002700 chr1D 616358 622211 5853 True 10811.000000 10811 100.000000 1 5854 1 chr1D.!!$R1 5853
1 TraesCS1D01G002700 chr1D 694219 696764 2545 True 2761.000000 2761 86.272000 2308 4882 1 chr1D.!!$R2 2574
2 TraesCS1D01G002700 chr1D 450764 451992 1228 False 701.000000 701 78.329000 4676 5854 1 chr1D.!!$F1 1178
3 TraesCS1D01G002700 chr1B 4556863 4560707 3844 True 4373.000000 4373 87.339000 2006 5854 1 chr1B.!!$R2 3848
4 TraesCS1D01G002700 chr1B 3951180 3954619 3439 False 3910.000000 3910 87.206000 1100 4540 1 chr1B.!!$F1 3440
5 TraesCS1D01G002700 chr1B 4507270 4510812 3542 True 3869.000000 3869 86.410000 1095 4639 1 chr1B.!!$R1 3544
6 TraesCS1D01G002700 chr1B 3964514 3968114 3600 False 3786.000000 3786 85.710000 1030 4636 1 chr1B.!!$F2 3606
7 TraesCS1D01G002700 chr1B 4150487 4153820 3333 False 3648.000000 3648 86.458000 770 4116 1 chr1B.!!$F3 3346
8 TraesCS1D01G002700 chr1B 4114561 4119036 4475 False 2715.000000 4981 85.681500 1095 5626 2 chr1B.!!$F7 4531
9 TraesCS1D01G002700 chr1B 4855216 4857243 2027 True 2630.000000 2630 90.123000 216 2242 1 chr1B.!!$R4 2026
10 TraesCS1D01G002700 chr1B 4094447 4099148 4701 False 2482.500000 4551 86.671000 8 4639 2 chr1B.!!$F6 4631
11 TraesCS1D01G002700 chr1B 4478950 4483642 4692 True 1936.666667 4614 90.883667 1100 5854 3 chr1B.!!$R5 4754
12 TraesCS1D01G002700 chr1B 4014146 4015970 1824 False 784.000000 1399 84.661000 3623 5765 2 chr1B.!!$F5 2142
13 TraesCS1D01G002700 chr1A 3500394 3504855 4461 True 4560.000000 4560 85.300000 81 4540 1 chr1A.!!$R2 4459
14 TraesCS1D01G002700 chr1A 3676815 3680272 3457 True 4113.000000 4113 88.245000 2230 5710 1 chr1A.!!$R3 3480
15 TraesCS1D01G002700 chr1A 3449968 3455878 5910 True 3684.000000 4656 89.061500 8 5854 2 chr1A.!!$R4 5846
16 TraesCS1D01G002700 chr1A 2975203 2983602 8399 False 2824.000000 4327 86.151500 609 5854 2 chr1A.!!$F1 5245
17 TraesCS1D01G002700 chr1A 3668279 3672524 4245 True 1916.500000 3651 83.516000 1030 5854 2 chr1A.!!$R5 4824

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
997 1094 2.167281 CCTCATGACAATGGACGAGACT 59.833 50.0 0.00 0.0 34.30 3.24 F
1977 2109 0.460987 CCCAGAACTAGGCAAGCTCG 60.461 60.0 0.00 0.0 0.00 5.03 F
2186 2462 0.393537 CTGTTCCTGCCAGCTTAGGG 60.394 60.0 8.22 0.0 34.76 3.53 F
3274 3552 0.452987 CCAACAACATGGCATCTCCG 59.547 55.0 0.00 0.0 37.80 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2445 0.328258 TTCCCTAAGCTGGCAGGAAC 59.672 55.0 17.64 0.0 33.42 3.62 R
3119 3397 0.813821 GCATCTCCAACTTCCCAAGC 59.186 55.0 0.00 0.0 0.00 4.01 R
3359 3640 0.827507 TCCCTTTTTGGTGAGCAGCC 60.828 55.0 0.00 0.0 0.00 4.85 R
4989 5350 0.107654 AGGTTCGTGGGAGCAATAGC 60.108 55.0 0.00 0.0 42.56 2.97 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
33 34 4.324402 CAGAAAGTGTGTCAAACAGCAAAC 59.676 41.667 0.00 0.00 40.26 2.93
54 57 6.616774 AACGTAGTATGAGTCTACCTTAGC 57.383 41.667 0.00 0.00 45.00 3.09
63 66 4.575236 TGAGTCTACCTTAGCGACTATGTG 59.425 45.833 0.00 0.00 38.07 3.21
67 70 6.038050 AGTCTACCTTAGCGACTATGTGTAAC 59.962 42.308 0.00 0.00 36.33 2.50
68 71 6.038050 GTCTACCTTAGCGACTATGTGTAACT 59.962 42.308 0.00 0.00 38.04 2.24
69 72 7.225538 GTCTACCTTAGCGACTATGTGTAACTA 59.774 40.741 0.00 0.00 38.04 2.24
70 73 6.764308 ACCTTAGCGACTATGTGTAACTAA 57.236 37.500 0.00 0.00 38.04 2.24
71 74 7.344095 ACCTTAGCGACTATGTGTAACTAAT 57.656 36.000 0.00 0.00 38.04 1.73
72 75 7.779073 ACCTTAGCGACTATGTGTAACTAATT 58.221 34.615 0.00 0.00 38.04 1.40
149 165 8.164153 GCAATACTAATCATTTGCACACTTTTG 58.836 33.333 1.89 0.00 43.00 2.44
208 225 3.314541 ACATGGGAAGACGTACAGAAC 57.685 47.619 0.00 0.00 0.00 3.01
997 1094 2.167281 CCTCATGACAATGGACGAGACT 59.833 50.000 0.00 0.00 34.30 3.24
1196 1328 1.774254 TCACTGAGGTCCCAACACATT 59.226 47.619 0.00 0.00 0.00 2.71
1393 1525 3.567478 ACTTGGTGAGCTCAACTTCTT 57.433 42.857 30.87 11.17 33.92 2.52
1439 1571 4.746535 TGACCTCAACAACAACAGTCTA 57.253 40.909 0.00 0.00 0.00 2.59
1446 1578 4.814234 TCAACAACAACAGTCTACATGGTC 59.186 41.667 0.00 0.00 0.00 4.02
1484 1616 9.925545 AATATCAGCTCTCTATCATCACTATCT 57.074 33.333 0.00 0.00 0.00 1.98
1493 1625 9.585369 TCTCTATCATCACTATCTTGTCTTGAT 57.415 33.333 0.00 0.00 0.00 2.57
1508 1640 1.734465 CTTGATCTCGGCTTCAACCAC 59.266 52.381 0.00 0.00 0.00 4.16
1535 1667 7.642186 TCAAAGGGAAAATTCCTCATGAGATA 58.358 34.615 24.62 11.44 46.72 1.98
1540 1672 5.240403 GGAAAATTCCTCATGAGATAGGTGC 59.760 44.000 24.62 8.16 44.11 5.01
1568 1700 0.997932 GTCTCACGCAGCTTGATCTG 59.002 55.000 1.37 0.00 37.15 2.90
1592 1724 5.177696 GTCATTTAACAGACTCACAGGACAC 59.822 44.000 0.00 0.00 0.00 3.67
1634 1766 6.636850 GCAACCTAACAATGTTAACTGTTCTG 59.363 38.462 14.47 10.45 37.05 3.02
1642 1774 5.964958 ATGTTAACTGTTCTGGTCATTGG 57.035 39.130 7.22 0.00 0.00 3.16
1724 1856 3.357203 TCTACAGCTAAGCTACAGCACT 58.643 45.455 19.30 8.37 45.16 4.40
1749 1881 1.203523 GCGGCATGATACCAAAAACCA 59.796 47.619 0.00 0.00 0.00 3.67
1789 1921 6.801862 CAGCTAAATACTTTGTACCTGTTTGC 59.198 38.462 0.00 0.00 0.00 3.68
1835 1967 3.307762 CCCAAGAACTAGGCAAGCTAGTT 60.308 47.826 12.09 12.09 46.53 2.24
1845 1977 3.512724 AGGCAAGCTAGTTCATTTGCAAT 59.487 39.130 0.00 0.00 45.73 3.56
1861 1993 8.565416 TCATTTGCAATATCTTGAGCTTGATAG 58.435 33.333 0.00 0.00 34.04 2.08
1867 1999 8.566260 GCAATATCTTGAGCTTGATAGAAATGT 58.434 33.333 9.68 0.00 34.04 2.71
1944 2076 9.525409 CACTTTTTCTCTTTGACAATCAAATCT 57.475 29.630 4.55 0.00 44.37 2.40
1973 2105 1.580059 TACCCCCAGAACTAGGCAAG 58.420 55.000 0.00 0.00 0.00 4.01
1977 2109 0.460987 CCCAGAACTAGGCAAGCTCG 60.461 60.000 0.00 0.00 0.00 5.03
1989 2121 1.332377 GCAAGCTCGCTATGCTAAACG 60.332 52.381 14.46 0.00 40.22 3.60
1990 2122 1.258982 CAAGCTCGCTATGCTAAACGG 59.741 52.381 0.00 0.00 40.22 4.44
2002 2134 3.849911 TGCTAAACGGACTTGATCTCAG 58.150 45.455 0.00 0.00 0.00 3.35
2022 2298 7.370383 TCTCAGCAAAAATCAAATAACAGGTC 58.630 34.615 0.00 0.00 0.00 3.85
2078 2354 6.024049 GCTCAACGAAATTTTTCTCGATGAT 58.976 36.000 9.68 0.00 43.14 2.45
2081 2357 8.874745 TCAACGAAATTTTTCTCGATGATAAC 57.125 30.769 6.23 0.00 40.51 1.89
2142 2418 5.744171 TGCTGAATCTCCAGTATTTAAGCA 58.256 37.500 0.00 0.00 35.60 3.91
2162 2438 9.715123 TTAAGCATGTACAACAATCAAATATCG 57.285 29.630 0.00 0.00 0.00 2.92
2169 2445 4.336433 ACAACAATCAAATATCGGGCTCTG 59.664 41.667 0.00 0.00 0.00 3.35
2176 2452 0.394565 ATATCGGGCTCTGTTCCTGC 59.605 55.000 0.00 0.00 0.00 4.85
2186 2462 0.393537 CTGTTCCTGCCAGCTTAGGG 60.394 60.000 8.22 0.00 34.76 3.53
2204 2480 7.072581 AGCTTAGGGAATATAACCAAGCTAGTT 59.927 37.037 20.72 7.19 43.15 2.24
2264 2541 2.359143 CCCCCAGGAAATTGGCAATCTA 60.359 50.000 14.04 0.00 36.88 1.98
2434 2711 2.162681 CCTTGTTCAACTTGGGCTAGG 58.837 52.381 0.00 0.00 0.00 3.02
2444 2721 2.305052 ACTTGGGCTAGGTAACAACTCC 59.695 50.000 0.00 0.00 41.41 3.85
2462 2739 2.642807 CTCCCTTTCAGGACCTTTACCA 59.357 50.000 0.00 0.00 37.67 3.25
2594 2871 4.214332 CAGCTTCAGAAGAACCAACTAACC 59.786 45.833 14.86 0.00 0.00 2.85
2712 2989 3.454447 TGCATGTACCCAGCTAACAGTAT 59.546 43.478 0.00 0.00 0.00 2.12
2715 2992 6.183361 TGCATGTACCCAGCTAACAGTATTAT 60.183 38.462 0.00 0.00 0.00 1.28
2716 2993 6.369065 GCATGTACCCAGCTAACAGTATTATC 59.631 42.308 0.00 0.00 0.00 1.75
2726 3003 9.685828 CAGCTAACAGTATTATCTCTAGGAAAC 57.314 37.037 0.00 0.00 0.00 2.78
2781 3058 7.664318 TCCTTTCTAAATTGTCCAACCTAGAAC 59.336 37.037 10.14 0.00 31.76 3.01
2924 3202 3.883669 AGAAAAGCTGAGCAATCTAGGG 58.116 45.455 7.39 0.00 0.00 3.53
2952 3230 1.191535 TATGTCCGGGAACAGACTGG 58.808 55.000 7.51 0.00 34.76 4.00
2969 3247 3.189606 ACTGGGTGGATTGATACCTGAA 58.810 45.455 0.00 0.00 37.15 3.02
3060 3338 0.525761 TGCGGCTGGAAATTTAGCAC 59.474 50.000 13.55 6.74 41.63 4.40
3089 3367 5.238868 GCAGATCATGTTAGATGTGAGCAAT 59.761 40.000 5.41 0.00 40.61 3.56
3178 3456 2.419673 CGCATAATCAGTTCAGTGGCAA 59.580 45.455 0.00 0.00 0.00 4.52
3269 3547 1.259609 CAGTCCCAACAACATGGCAT 58.740 50.000 0.00 0.00 39.26 4.40
3274 3552 0.452987 CCAACAACATGGCATCTCCG 59.547 55.000 0.00 0.00 37.80 4.63
3286 3564 2.283298 GCATCTCCGAAATGCTTCAGA 58.717 47.619 0.00 0.00 44.83 3.27
3289 3567 4.656041 CATCTCCGAAATGCTTCAGAAAC 58.344 43.478 0.00 0.00 0.00 2.78
3311 3589 4.283467 ACTTGGTTTCTTCCCAATAAAGGC 59.717 41.667 0.00 0.00 41.00 4.35
3359 3640 3.255642 CACCTTGTTATTCAACCCCAGTG 59.744 47.826 0.00 0.00 33.41 3.66
3380 3664 1.412343 GCTGCTCACCAAAAAGGGAAA 59.588 47.619 0.00 0.00 43.89 3.13
3430 3714 1.270732 TGTGATGGGTTTTGGCATTGC 60.271 47.619 0.00 0.00 0.00 3.56
3612 3899 4.474651 ACATCATTGGAACAGGAGGATACA 59.525 41.667 0.00 0.00 42.39 2.29
3686 3976 3.764434 AGCTTCATCAGACCGAAGAGTTA 59.236 43.478 13.45 0.00 40.94 2.24
3687 3977 4.220821 AGCTTCATCAGACCGAAGAGTTAA 59.779 41.667 13.45 0.00 40.94 2.01
4342 4633 4.935808 GTGAAAGATATTCTGGACCAACGT 59.064 41.667 0.00 0.00 0.00 3.99
4519 4814 4.083537 CCTTTCAGCGCACTTACATTACAA 60.084 41.667 11.47 0.00 0.00 2.41
4544 4848 2.035066 GGGATGCATGTTGACATAAGGC 59.965 50.000 2.46 0.00 34.26 4.35
4547 4851 2.368439 TGCATGTTGACATAAGGCCTC 58.632 47.619 5.23 0.00 34.26 4.70
4598 4903 3.967203 GCAGAGGCTGATTCAGATTTC 57.033 47.619 17.87 10.35 36.96 2.17
4599 4904 3.543665 GCAGAGGCTGATTCAGATTTCT 58.456 45.455 17.87 12.24 36.96 2.52
4600 4905 3.312973 GCAGAGGCTGATTCAGATTTCTG 59.687 47.826 23.82 23.82 40.18 3.02
4603 4908 5.823570 CAGAGGCTGATTCAGATTTCTGATT 59.176 40.000 23.82 7.75 42.09 2.57
4738 5059 5.529791 ACTATCCGGATACAACAAAGATCG 58.470 41.667 20.49 8.53 0.00 3.69
5016 5385 2.931320 GCTCCCACGAACCTAAAGACTG 60.931 54.545 0.00 0.00 0.00 3.51
5073 5446 6.375455 CCATGTAGTCCTGCTTTATTTGTTCT 59.625 38.462 0.00 0.00 0.00 3.01
5127 5520 3.261580 CAAGCAGGTACGATCACAATGA 58.738 45.455 0.00 0.00 0.00 2.57
5128 5521 3.170791 AGCAGGTACGATCACAATGAG 57.829 47.619 0.00 0.00 0.00 2.90
5135 5528 5.097529 GGTACGATCACAATGAGTAAACGA 58.902 41.667 0.00 0.00 0.00 3.85
5234 5636 4.399483 AGGACTTACAGAGGGTTGTAGA 57.601 45.455 0.00 0.00 35.17 2.59
5261 5665 6.051179 GGAGTATGTAGTCCTTTTCCTTGT 57.949 41.667 6.65 0.00 41.59 3.16
5262 5666 5.875359 GGAGTATGTAGTCCTTTTCCTTGTG 59.125 44.000 6.65 0.00 41.59 3.33
5263 5667 6.295688 GGAGTATGTAGTCCTTTTCCTTGTGA 60.296 42.308 6.65 0.00 41.59 3.58
5264 5668 6.465084 AGTATGTAGTCCTTTTCCTTGTGAC 58.535 40.000 0.00 0.00 0.00 3.67
5265 5669 4.764050 TGTAGTCCTTTTCCTTGTGACA 57.236 40.909 0.00 0.00 0.00 3.58
5266 5670 4.448210 TGTAGTCCTTTTCCTTGTGACAC 58.552 43.478 0.00 0.00 0.00 3.67
5267 5671 3.933861 AGTCCTTTTCCTTGTGACACT 57.066 42.857 7.20 0.00 0.00 3.55
5323 5768 0.825425 TGGAATCCAAAACTGGCGCA 60.825 50.000 10.83 0.00 0.00 6.09
5330 5775 2.163412 TCCAAAACTGGCGCATTATCAC 59.837 45.455 10.83 0.00 0.00 3.06
5347 5792 2.546778 TCACGTCATCCCGCTTTATTC 58.453 47.619 0.00 0.00 0.00 1.75
5410 5879 3.790820 CGATGCATAAACGGAACAAATGG 59.209 43.478 0.00 0.00 0.00 3.16
5414 5883 3.551485 GCATAAACGGAACAAATGGATGC 59.449 43.478 0.00 0.00 0.00 3.91
5438 5907 4.252971 ACACACGGATATAGGTGCATAC 57.747 45.455 0.00 0.00 37.68 2.39
5439 5908 3.895656 ACACACGGATATAGGTGCATACT 59.104 43.478 0.00 0.00 37.68 2.12
5441 5910 5.715279 ACACACGGATATAGGTGCATACTAT 59.285 40.000 15.43 15.43 37.68 2.12
5446 5915 9.084164 CACGGATATAGGTGCATACTATAAAAC 57.916 37.037 18.93 14.40 37.06 2.43
5455 5924 9.297037 AGGTGCATACTATAAAACAAGAAAAGT 57.703 29.630 0.00 0.00 0.00 2.66
5507 5979 1.330521 GTTGTAGGGCACGCATATGTG 59.669 52.381 14.72 14.72 42.81 3.21
5691 6189 5.536260 TGAGATGAGATGATAGGAAAAGCG 58.464 41.667 0.00 0.00 0.00 4.68
5692 6190 5.069648 TGAGATGAGATGATAGGAAAAGCGT 59.930 40.000 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.202639 TGACACACTTTCTGCATCCGT 60.203 47.619 0.00 0.00 0.00 4.69
5 6 3.066621 TGTTTGACACACTTTCTGCATCC 59.933 43.478 0.00 0.00 0.00 3.51
6 7 4.285292 CTGTTTGACACACTTTCTGCATC 58.715 43.478 0.00 0.00 0.00 3.91
33 34 4.987285 TCGCTAAGGTAGACTCATACTACG 59.013 45.833 0.00 0.00 40.47 3.51
63 66 9.891535 GCTTATGTGTACGTGTAAATTAGTTAC 57.108 33.333 0.00 0.00 42.24 2.50
67 70 7.955502 TGTGCTTATGTGTACGTGTAAATTAG 58.044 34.615 0.00 0.00 0.00 1.73
68 71 7.063662 CCTGTGCTTATGTGTACGTGTAAATTA 59.936 37.037 0.00 0.00 0.00 1.40
69 72 6.128391 CCTGTGCTTATGTGTACGTGTAAATT 60.128 38.462 0.00 0.00 0.00 1.82
70 73 5.350365 CCTGTGCTTATGTGTACGTGTAAAT 59.650 40.000 0.00 0.00 0.00 1.40
71 74 4.687018 CCTGTGCTTATGTGTACGTGTAAA 59.313 41.667 0.00 0.00 0.00 2.01
72 75 4.239304 CCTGTGCTTATGTGTACGTGTAA 58.761 43.478 0.00 0.00 0.00 2.41
149 165 7.081976 CCAGCACTTTGTAAATACAAGTAACC 58.918 38.462 6.16 0.00 45.77 2.85
208 225 8.350722 TGGTAATATTCTACTTCTTCTAGCACG 58.649 37.037 0.00 0.00 0.00 5.34
565 646 9.455847 CATAACTGCTTGAATATTTCTTAAGCC 57.544 33.333 17.41 7.24 42.17 4.35
1196 1328 1.463214 TTTCCAGTGGAGGAGGGCA 60.463 57.895 12.67 0.00 39.25 5.36
1339 1471 2.202987 CGTCTGGCAGGGAGATGC 60.203 66.667 15.73 0.00 45.74 3.91
1373 1505 3.209410 CAAGAAGTTGAGCTCACCAAGT 58.791 45.455 18.03 1.54 35.46 3.16
1459 1591 9.925545 AAGATAGTGATGATAGAGAGCTGATAT 57.074 33.333 0.00 0.00 0.00 1.63
1469 1601 9.585369 AGATCAAGACAAGATAGTGATGATAGA 57.415 33.333 0.00 0.00 0.00 1.98
1472 1604 7.369607 CGAGATCAAGACAAGATAGTGATGAT 58.630 38.462 0.00 0.00 0.00 2.45
1484 1616 3.067106 GTTGAAGCCGAGATCAAGACAA 58.933 45.455 0.00 0.00 36.31 3.18
1493 1625 1.118965 TGAGGTGGTTGAAGCCGAGA 61.119 55.000 0.00 0.00 0.00 4.04
1540 1672 1.597854 TGCGTGAGACTTTGCAGGG 60.598 57.895 0.00 0.00 32.73 4.45
1568 1700 5.177696 GTGTCCTGTGAGTCTGTTAAATGAC 59.822 44.000 0.00 2.02 0.00 3.06
1592 1724 0.179048 TGCCCATAGACGCAGGAATG 60.179 55.000 0.00 0.00 0.00 2.67
1605 1737 5.047377 CAGTTAACATTGTTAGGTTGCCCAT 60.047 40.000 8.61 0.00 29.89 4.00
1702 1834 3.380004 AGTGCTGTAGCTTAGCTGTAGAG 59.620 47.826 17.97 6.89 40.10 2.43
1716 1848 1.737236 CATGCCGCTTAAAGTGCTGTA 59.263 47.619 0.00 0.00 0.00 2.74
1724 1856 5.164954 GTTTTTGGTATCATGCCGCTTAAA 58.835 37.500 0.00 0.00 0.00 1.52
1749 1881 8.282256 AGTATTTAGCTGGGTTAGATTTCCAAT 58.718 33.333 0.00 0.00 0.00 3.16
1789 1921 6.070710 GGGTATAGGCCCTGAAAGTAGATTAG 60.071 46.154 0.00 0.00 45.22 1.73
1835 1967 6.762702 TCAAGCTCAAGATATTGCAAATGA 57.237 33.333 1.71 2.84 0.00 2.57
1877 2009 7.620888 AGATTGGTTATGAAGATTGGAATTGGT 59.379 33.333 0.00 0.00 0.00 3.67
1891 2023 8.539544 TGTTCATCTTAGTGAGATTGGTTATGA 58.460 33.333 0.00 0.00 42.55 2.15
1973 2105 0.853419 GTCCGTTTAGCATAGCGAGC 59.147 55.000 0.00 0.00 0.00 5.03
1977 2109 4.372656 AGATCAAGTCCGTTTAGCATAGC 58.627 43.478 0.00 0.00 0.00 2.97
1989 2121 5.633830 TGATTTTTGCTGAGATCAAGTCC 57.366 39.130 0.00 0.00 0.00 3.85
1990 2122 9.630098 TTATTTGATTTTTGCTGAGATCAAGTC 57.370 29.630 0.00 0.00 39.05 3.01
2002 2134 7.671495 ATTGGACCTGTTATTTGATTTTTGC 57.329 32.000 0.00 0.00 0.00 3.68
2022 2298 1.774856 CCCTAGTTCTGGGGGTATTGG 59.225 57.143 12.61 0.00 40.97 3.16
2048 2324 6.797033 CGAGAAAAATTTCGTTGAGCATAGTT 59.203 34.615 0.00 0.00 41.92 2.24
2060 2336 8.667987 TTTGGTTATCATCGAGAAAAATTTCG 57.332 30.769 0.00 0.00 41.92 3.46
2078 2354 5.258051 GGTATTGGACCTGTGATTTGGTTA 58.742 41.667 0.00 0.00 45.89 2.85
2107 2383 2.957006 AGATTCAGCAAGATGCCCAATC 59.043 45.455 12.57 12.57 46.52 2.67
2142 2418 5.827797 AGCCCGATATTTGATTGTTGTACAT 59.172 36.000 0.00 0.00 0.00 2.29
2169 2445 0.328258 TTCCCTAAGCTGGCAGGAAC 59.672 55.000 17.64 0.00 33.42 3.62
2176 2452 4.762251 GCTTGGTTATATTCCCTAAGCTGG 59.238 45.833 0.00 0.00 34.68 4.85
2204 2480 5.630121 TGATTTTCAAAGAGGGCTAGTTGA 58.370 37.500 0.00 0.00 0.00 3.18
2211 2487 6.405176 CCTGTTATCTGATTTTCAAAGAGGGC 60.405 42.308 0.00 0.00 27.63 5.19
2264 2541 6.828785 ACAAGCCTAAATATTCGAGGTTCATT 59.171 34.615 14.73 5.78 32.53 2.57
2462 2739 6.935741 TTGCGACCTAAACATATATTTGCT 57.064 33.333 0.00 0.00 0.00 3.91
2481 2758 6.381801 AGACATGGAGAAATTTAAGTTTGCG 58.618 36.000 0.06 0.00 0.00 4.85
2715 2992 6.270927 CCCCTGATCATATTGTTTCCTAGAGA 59.729 42.308 0.00 0.00 0.00 3.10
2716 2993 6.043706 ACCCCTGATCATATTGTTTCCTAGAG 59.956 42.308 0.00 0.00 0.00 2.43
2726 3003 5.256474 GGTATGGAACCCCTGATCATATTG 58.744 45.833 0.00 0.00 43.16 1.90
2754 3031 7.751646 TCTAGGTTGGACAATTTAGAAAGGAA 58.248 34.615 0.00 0.00 0.00 3.36
2924 3202 3.133362 TGTTCCCGGACATATCAAGGTAC 59.867 47.826 0.73 0.00 0.00 3.34
2936 3214 2.214920 ACCCAGTCTGTTCCCGGAC 61.215 63.158 0.73 0.00 45.71 4.79
2952 3230 5.104259 AGTTCTTCAGGTATCAATCCACC 57.896 43.478 0.00 0.00 34.86 4.61
2969 3247 1.216064 TCATGCATGCCCCTAGTTCT 58.784 50.000 22.25 0.00 0.00 3.01
3046 3324 2.549633 CAGGCGTGCTAAATTTCCAG 57.450 50.000 0.00 0.00 0.00 3.86
3060 3338 2.229675 TCTAACATGATCTGCAGGCG 57.770 50.000 15.13 0.55 0.00 5.52
3089 3367 1.563924 ACACGCCACTGAGGGTATTA 58.436 50.000 0.00 0.00 38.09 0.98
3094 3372 3.357079 GCAACACGCCACTGAGGG 61.357 66.667 0.00 0.00 38.09 4.30
3117 3395 2.363683 CATCTCCAACTTCCCAAGCTC 58.636 52.381 0.00 0.00 0.00 4.09
3119 3397 0.813821 GCATCTCCAACTTCCCAAGC 59.186 55.000 0.00 0.00 0.00 4.01
3158 3436 3.191162 TGTTGCCACTGAACTGATTATGC 59.809 43.478 0.00 0.00 0.00 3.14
3178 3456 2.905415 TGCAAAGGAGGATGGAATGT 57.095 45.000 0.00 0.00 0.00 2.71
3269 3547 4.008074 AGTTTCTGAAGCATTTCGGAGA 57.992 40.909 7.01 0.00 46.51 3.71
3274 3552 6.516478 GAAACCAAGTTTCTGAAGCATTTC 57.484 37.500 11.92 7.11 45.65 2.17
3311 3589 1.276421 CCAGAGAGGTTACCACACAGG 59.724 57.143 3.51 0.00 45.67 4.00
3359 3640 0.827507 TCCCTTTTTGGTGAGCAGCC 60.828 55.000 0.00 0.00 0.00 4.85
3380 3664 4.414337 TGGCAAAAGCAAACCAAGTATT 57.586 36.364 0.00 0.00 0.00 1.89
3430 3714 7.997107 ATTATTATGACAACAATTGCAGCAG 57.003 32.000 5.05 0.00 0.00 4.24
3612 3899 2.618709 GTTGTGCCTTGTAGACTTTGCT 59.381 45.455 0.00 0.00 0.00 3.91
3686 3976 9.219603 TCACTACGAAATCTTCTTTCATCATTT 57.780 29.630 0.00 0.00 0.00 2.32
3687 3977 8.777865 TCACTACGAAATCTTCTTTCATCATT 57.222 30.769 0.00 0.00 0.00 2.57
3935 4225 7.068839 GTGATATCTCGATGGATTATAGGTGGT 59.931 40.741 3.98 0.00 0.00 4.16
4099 4389 2.280628 CGTGAGAAGGAAGGTTATGCC 58.719 52.381 0.00 0.00 37.58 4.40
4342 4633 4.000325 CAGTTGATATTGGTGTTGTCGGA 59.000 43.478 0.00 0.00 0.00 4.55
4446 4737 2.024414 GGATGAGTGTTTGGTATGCCC 58.976 52.381 0.00 0.00 0.00 5.36
4519 4814 2.291209 TGTCAACATGCATCCCTTGT 57.709 45.000 0.00 0.00 33.65 3.16
4544 4848 4.764172 CTGGTTTCTCACTAGGATTGAGG 58.236 47.826 8.53 0.00 40.87 3.86
4621 4938 9.476928 ACAAGAGGTATATATAGGTGGTGTATC 57.523 37.037 0.00 0.00 0.00 2.24
4722 5042 2.277084 ACGGCGATCTTTGTTGTATCC 58.723 47.619 16.62 0.00 0.00 2.59
4989 5350 0.107654 AGGTTCGTGGGAGCAATAGC 60.108 55.000 0.00 0.00 42.56 2.97
5090 5466 6.966534 CCTGCTTGGTCCAAGATATTTATT 57.033 37.500 31.94 0.00 43.42 1.40
5114 5492 6.185852 TCTCGTTTACTCATTGTGATCGTA 57.814 37.500 0.00 0.00 31.88 3.43
5127 5520 9.659830 GTTTACATTCATTTGTTCTCGTTTACT 57.340 29.630 0.00 0.00 0.00 2.24
5128 5521 9.440784 TGTTTACATTCATTTGTTCTCGTTTAC 57.559 29.630 0.00 0.00 0.00 2.01
5196 5598 8.877195 TGTAAGTCCTTTTACTTAGTCCAAGAT 58.123 33.333 5.35 0.00 41.42 2.40
5197 5599 8.253867 TGTAAGTCCTTTTACTTAGTCCAAGA 57.746 34.615 5.35 0.00 41.42 3.02
5198 5600 8.365647 TCTGTAAGTCCTTTTACTTAGTCCAAG 58.634 37.037 0.00 0.00 41.42 3.61
5199 5601 8.253867 TCTGTAAGTCCTTTTACTTAGTCCAA 57.746 34.615 0.00 0.00 41.42 3.53
5200 5602 7.039223 CCTCTGTAAGTCCTTTTACTTAGTCCA 60.039 40.741 0.00 0.00 41.42 4.02
5201 5603 7.321908 CCTCTGTAAGTCCTTTTACTTAGTCC 58.678 42.308 0.00 0.00 41.42 3.85
5202 5604 7.039152 ACCCTCTGTAAGTCCTTTTACTTAGTC 60.039 40.741 0.00 0.00 41.42 2.59
5234 5636 4.162509 GGAAAAGGACTACATACTCCTGCT 59.837 45.833 0.00 0.00 36.97 4.24
5258 5662 5.830991 GGGGGCAATAATAATAGTGTCACAA 59.169 40.000 5.62 0.00 36.87 3.33
5259 5663 5.381757 GGGGGCAATAATAATAGTGTCACA 58.618 41.667 5.62 0.00 36.87 3.58
5260 5664 4.454504 CGGGGGCAATAATAATAGTGTCAC 59.545 45.833 0.00 0.00 34.48 3.67
5261 5665 4.103469 ACGGGGGCAATAATAATAGTGTCA 59.897 41.667 0.00 0.00 33.54 3.58
5262 5666 4.454504 CACGGGGGCAATAATAATAGTGTC 59.545 45.833 0.00 0.00 31.18 3.67
5263 5667 4.103469 TCACGGGGGCAATAATAATAGTGT 59.897 41.667 0.00 0.00 29.96 3.55
5264 5668 4.647611 TCACGGGGGCAATAATAATAGTG 58.352 43.478 0.00 0.00 0.00 2.74
5265 5669 4.986054 TCACGGGGGCAATAATAATAGT 57.014 40.909 0.00 0.00 0.00 2.12
5266 5670 4.457949 GGTTCACGGGGGCAATAATAATAG 59.542 45.833 0.00 0.00 0.00 1.73
5267 5671 4.105057 AGGTTCACGGGGGCAATAATAATA 59.895 41.667 0.00 0.00 0.00 0.98
5319 5764 0.512952 GGGATGACGTGATAATGCGC 59.487 55.000 0.00 0.00 0.00 6.09
5323 5768 2.910688 AAGCGGGATGACGTGATAAT 57.089 45.000 0.00 0.00 35.98 1.28
5330 5775 3.458189 AGAAGAATAAAGCGGGATGACG 58.542 45.455 0.00 0.00 0.00 4.35
5347 5792 8.669243 GTGATTTTACTTTGATACCCAGAGAAG 58.331 37.037 0.00 0.00 31.89 2.85
5410 5879 2.987149 CCTATATCCGTGTGTTCGCATC 59.013 50.000 0.00 0.00 0.00 3.91
5414 5883 2.124903 GCACCTATATCCGTGTGTTCG 58.875 52.381 4.52 0.00 32.40 3.95
5450 5919 9.117183 CCCTTTTACTTAGTACTGTTGACTTTT 57.883 33.333 5.39 0.00 0.00 2.27
5452 5921 6.709397 GCCCTTTTACTTAGTACTGTTGACTT 59.291 38.462 5.39 0.00 0.00 3.01
5453 5922 6.042897 AGCCCTTTTACTTAGTACTGTTGACT 59.957 38.462 5.39 0.00 0.00 3.41
5454 5923 6.228995 AGCCCTTTTACTTAGTACTGTTGAC 58.771 40.000 5.39 0.00 0.00 3.18
5455 5924 6.429521 AGCCCTTTTACTTAGTACTGTTGA 57.570 37.500 5.39 0.00 0.00 3.18
5507 5979 3.745797 GCTCCATCATAAGGACAAGGACC 60.746 52.174 0.00 0.00 0.00 4.46
5587 6071 3.402628 AATCTCGTTACCAGTGCTTGT 57.597 42.857 0.00 0.00 0.00 3.16
5692 6190 3.758755 AGCTCTCATGTTGTCTGTCAA 57.241 42.857 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.