Multiple sequence alignment - TraesCS4D01G241700

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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 TraesCS4D01G241700 chr4D 100.000 9060 0 0 656 9715 404098684 404107743 0.000000e+00 16731.0
1 TraesCS4D01G241700 chr4D 100.000 359 0 0 1 359 404098029 404098387 0.000000e+00 664.0
2 TraesCS4D01G241700 chr4A 95.739 6337 186 26 1473 7744 61584312 61590629 0.000000e+00 10129.0
3 TraesCS4D01G241700 chr4A 93.996 1066 47 9 7889 8942 61590631 61591691 0.000000e+00 1598.0
4 TraesCS4D01G241700 chr4A 97.906 812 14 2 656 1464 61583447 61584258 0.000000e+00 1402.0
5 TraesCS4D01G241700 chr4A 91.667 360 9 9 1 346 61582630 61582982 6.830000e-131 479.0
6 TraesCS4D01G241700 chr4A 84.368 467 39 13 9252 9715 61592003 61592438 2.510000e-115 427.0
7 TraesCS4D01G241700 chr4B 98.175 4493 62 6 1475 5963 500835494 500839970 0.000000e+00 7825.0
8 TraesCS4D01G241700 chr4B 97.531 3119 46 9 5961 9075 500840051 500843142 0.000000e+00 5304.0
9 TraesCS4D01G241700 chr4B 97.531 810 17 2 656 1464 500834631 500835438 0.000000e+00 1382.0
10 TraesCS4D01G241700 chr4B 94.038 520 17 5 9201 9715 500864299 500864809 0.000000e+00 776.0
11 TraesCS4D01G241700 chr4B 95.745 329 7 5 1 326 500834231 500834555 3.110000e-144 523.0
12 TraesCS4D01G241700 chr4B 100.000 32 0 0 9181 9212 500864266 500864297 1.050000e-04 60.2
13 TraesCS4D01G241700 chr2D 81.155 329 33 14 659 979 46209356 46209663 4.540000e-58 237.0
14 TraesCS4D01G241700 chr2D 95.000 60 2 1 9102 9161 549021011 549020953 1.040000e-14 93.5
15 TraesCS4D01G241700 chr2D 92.308 65 3 2 9092 9156 483261161 483261099 3.740000e-14 91.6
16 TraesCS4D01G241700 chr2D 100.000 30 0 0 9067 9096 528624981 528624952 1.000000e-03 56.5
17 TraesCS4D01G241700 chr2B 93.846 65 3 1 9095 9159 721702715 721702778 8.030000e-16 97.1
18 TraesCS4D01G241700 chr1B 92.754 69 2 3 9091 9159 470935519 470935584 8.030000e-16 97.1
19 TraesCS4D01G241700 chr3B 93.750 64 1 3 9097 9159 704132751 704132812 1.040000e-14 93.5
20 TraesCS4D01G241700 chr3B 88.889 72 6 2 9089 9159 379305253 379305183 4.830000e-13 87.9
21 TraesCS4D01G241700 chr3B 97.778 45 1 0 1755 1799 625215660 625215704 2.910000e-10 78.7
22 TraesCS4D01G241700 chr5A 93.548 62 3 1 9099 9160 552746640 552746700 3.740000e-14 91.6
23 TraesCS4D01G241700 chr6D 92.188 64 4 1 9098 9161 90135052 90134990 1.340000e-13 89.8
24 TraesCS4D01G241700 chr7D 92.188 64 2 2 9092 9155 634836449 634836509 4.830000e-13 87.9
25 TraesCS4D01G241700 chr5B 76.027 146 24 10 9575 9715 345507051 345507190 2.260000e-06 65.8
26 TraesCS4D01G241700 chr5B 100.000 30 0 0 9066 9095 574906319 574906348 1.000000e-03 56.5
27 TraesCS4D01G241700 chr2A 100.000 33 0 0 9596 9628 709625904 709625872 2.930000e-05 62.1
28 TraesCS4D01G241700 chr5D 94.595 37 0 2 9061 9096 56445661 56445626 1.000000e-03 56.5
29 TraesCS4D01G241700 chr5D 100.000 30 0 0 9067 9096 230416824 230416853 1.000000e-03 56.5
30 TraesCS4D01G241700 chr3D 100.000 30 0 0 9067 9096 507038749 507038720 1.000000e-03 56.5
31 TraesCS4D01G241700 chr3D 100.000 28 0 0 9069 9096 612268615 612268588 1.800000e-02 52.8
32 TraesCS4D01G241700 chr6A 100.000 29 0 0 9067 9095 589717098 589717070 5.000000e-03 54.7
33 TraesCS4D01G241700 chr3A 96.875 32 1 0 9065 9096 64291117 64291086 5.000000e-03 54.7
34 TraesCS4D01G241700 chr3A 100.000 28 0 0 9069 9096 70732965 70732938 1.800000e-02 52.8


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 TraesCS4D01G241700 chr4D 404098029 404107743 9714 False 8697.5 16731 100.0000 1 9715 2 chr4D.!!$F1 9714
1 TraesCS4D01G241700 chr4A 61582630 61592438 9808 False 2807.0 10129 92.7352 1 9715 5 chr4A.!!$F1 9714
2 TraesCS4D01G241700 chr4B 500834231 500843142 8911 False 3758.5 7825 97.2455 1 9075 4 chr4B.!!$F1 9074
3 TraesCS4D01G241700 chr4B 500864266 500864809 543 False 418.1 776 97.0190 9181 9715 2 chr4B.!!$F2 534

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
163 172 1.269448 GAATCTGCCGAAACCAAAGCA 59.731 47.619 0.00 0.00 0.00 3.91 F
1140 1315 2.104111 CCCGTAATTCTGGCCATACAGA 59.896 50.000 5.51 0.00 45.22 3.41 F
1951 2172 0.774276 TTGTTGGCCCATGGACTACA 59.226 50.000 15.22 15.48 44.05 2.74 F
2195 2416 1.269936 GCATGCAACCAAAAGCTCAGT 60.270 47.619 14.21 0.00 0.00 3.41 F
3535 3785 2.287915 GCATTTGTATCCTGAACGCGAT 59.712 45.455 15.93 0.00 0.00 4.58 F
4095 4345 2.375174 AGGGTACACTTGAATTCTGCCA 59.625 45.455 7.05 0.00 0.00 4.92 F
5155 5406 2.353269 AGAGTCGCTGACTATCGAAGTG 59.647 50.000 10.48 0.00 43.53 3.16 F
5255 5506 5.280654 TGCAGCATATCAGACTAACATGA 57.719 39.130 0.00 0.00 0.00 3.07 F
6084 6422 5.326200 ACTGTACCTGACTAGTGTATTGC 57.674 43.478 0.00 0.00 0.00 3.56 F
6911 7252 8.448615 GGTACTGTTATTTGAGTGGTGAAATAC 58.551 37.037 0.00 0.00 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1142 1317 2.546368 TGTCACCAGCAACAATTACGTC 59.454 45.455 0.00 0.0 0.00 4.34 R
2392 2613 0.109412 AAGAGACGTACGAAAGCCGG 60.109 55.000 24.41 0.0 43.93 6.13 R
3535 3785 8.780846 AAATAGTCATACACGGTCACATTTAA 57.219 30.769 0.00 0.0 0.00 1.52 R
4095 4345 6.069963 ACAAATTCTAGTGGAGGAAGCTGTAT 60.070 38.462 0.00 0.0 0.00 2.29 R
4892 5142 2.218759 GCAAGTAACTGTATCGGCATCG 59.781 50.000 0.00 0.0 37.82 3.84 R
5255 5506 9.277783 CTATAACAGCAGAGGCAAATAAGTAAT 57.722 33.333 0.00 0.0 44.61 1.89 R
6361 6702 1.693606 CACCCCAAAACTCTTGGCATT 59.306 47.619 0.00 0.0 38.23 3.56 R
6981 7322 2.091885 AGAAAGCCAAGACTCACCCAAA 60.092 45.455 0.00 0.0 0.00 3.28 R
7327 7694 3.575687 CCTTGATCAATTAATCCCCAGCC 59.424 47.826 8.96 0.0 0.00 4.85 R
8802 9186 1.267121 AGGAAGCGCAACCTAGAGAA 58.733 50.000 20.79 0.0 34.47 2.87 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
37 38 3.737172 ATGCAAAGTCACGCGGCC 61.737 61.111 12.47 0.00 0.00 6.13
129 138 6.362248 AGCTTAAACAAACAGGACCTTCTTA 58.638 36.000 0.00 0.00 0.00 2.10
130 139 7.004691 AGCTTAAACAAACAGGACCTTCTTAT 58.995 34.615 0.00 0.00 0.00 1.73
132 141 8.235226 GCTTAAACAAACAGGACCTTCTTATAC 58.765 37.037 0.00 0.00 0.00 1.47
135 144 6.681729 ACAAACAGGACCTTCTTATACAGA 57.318 37.500 0.00 0.00 0.00 3.41
136 145 7.074653 ACAAACAGGACCTTCTTATACAGAA 57.925 36.000 0.00 0.00 39.39 3.02
163 172 1.269448 GAATCTGCCGAAACCAAAGCA 59.731 47.619 0.00 0.00 0.00 3.91
1140 1315 2.104111 CCCGTAATTCTGGCCATACAGA 59.896 50.000 5.51 0.00 45.22 3.41
1142 1317 3.748048 CCGTAATTCTGGCCATACAGATG 59.252 47.826 5.51 0.00 46.07 2.90
1465 1641 9.706691 TTCTAGTGTGAAACTTCTATGTTTAGG 57.293 33.333 0.00 0.00 39.86 2.69
1467 1643 6.838382 AGTGTGAAACTTCTATGTTTAGGGT 58.162 36.000 0.00 0.00 39.86 4.34
1469 1645 6.935208 GTGTGAAACTTCTATGTTTAGGGTCT 59.065 38.462 0.00 0.00 39.86 3.85
1471 1647 7.660208 TGTGAAACTTCTATGTTTAGGGTCTTC 59.340 37.037 0.00 0.00 39.86 2.87
1701 1922 7.602517 AGTCATTCCGTGAGATTAAAAAGAG 57.397 36.000 0.00 0.00 37.56 2.85
1914 2135 2.338577 ATGTGGCACCTGCTATTCTC 57.661 50.000 16.26 0.00 41.70 2.87
1951 2172 0.774276 TTGTTGGCCCATGGACTACA 59.226 50.000 15.22 15.48 44.05 2.74
2104 2325 3.100671 AGGGTAGTAGCTGGAGAACTTG 58.899 50.000 0.00 0.00 0.00 3.16
2195 2416 1.269936 GCATGCAACCAAAAGCTCAGT 60.270 47.619 14.21 0.00 0.00 3.41
2276 2497 5.077134 GCTTCCTTTCCAAGCATTTGTAT 57.923 39.130 0.00 0.00 44.87 2.29
3034 3255 9.300681 TGAATACTCTGTTCCATGATTTTTCTT 57.699 29.630 0.00 0.00 0.00 2.52
3162 3383 4.380841 TTCCTGCAAAAGATGATCATGC 57.619 40.909 14.30 12.15 37.52 4.06
3275 3496 8.329502 ACCAATTATAAGCTTCCTCAGTTAACT 58.670 33.333 0.00 1.12 0.00 2.24
3345 3568 5.811190 TGCTTAGTGAATTGGTAAGGCTTA 58.189 37.500 2.04 2.04 0.00 3.09
3535 3785 2.287915 GCATTTGTATCCTGAACGCGAT 59.712 45.455 15.93 0.00 0.00 4.58
3882 4132 7.226720 TCACTAACAGAAATGGAAGTCAGAAAC 59.773 37.037 0.00 0.00 0.00 2.78
4095 4345 2.375174 AGGGTACACTTGAATTCTGCCA 59.625 45.455 7.05 0.00 0.00 4.92
4277 4527 2.926329 ACCCCCACAATACAAGGAAGAT 59.074 45.455 0.00 0.00 0.00 2.40
4809 5059 2.875672 GCAAATGGTCACCTGAGCTACA 60.876 50.000 0.00 0.00 42.60 2.74
5155 5406 2.353269 AGAGTCGCTGACTATCGAAGTG 59.647 50.000 10.48 0.00 43.53 3.16
5255 5506 5.280654 TGCAGCATATCAGACTAACATGA 57.719 39.130 0.00 0.00 0.00 3.07
6084 6422 5.326200 ACTGTACCTGACTAGTGTATTGC 57.674 43.478 0.00 0.00 0.00 3.56
6911 7252 8.448615 GGTACTGTTATTTGAGTGGTGAAATAC 58.551 37.037 0.00 0.00 0.00 1.89
7327 7694 2.692557 CACTCAGTCCTATGGTGAGAGG 59.307 54.545 5.61 0.00 40.21 3.69
7763 8134 2.124024 GGCATGCCATGAGCCTCA 60.124 61.111 32.08 0.00 44.92 3.86
7773 8144 3.308259 GCCATGAGCCTCATCCATCTATT 60.308 47.826 3.68 0.00 34.28 1.73
7823 8194 8.786898 GCATCTGCCTCTTATGTAATAATTCAA 58.213 33.333 0.00 0.00 34.87 2.69
7851 8223 4.576330 AACCTGAAGGATTAGAACTGGG 57.424 45.455 2.62 0.00 38.94 4.45
7852 8224 3.803340 ACCTGAAGGATTAGAACTGGGA 58.197 45.455 2.62 0.00 38.94 4.37
7860 8232 3.933332 GGATTAGAACTGGGAAACACGAG 59.067 47.826 0.00 0.00 0.00 4.18
7881 8253 8.350722 CACGAGTATTACCTCTGTATTGTACAT 58.649 37.037 0.00 0.00 38.15 2.29
8762 9146 5.702209 AGTGATTTCATTCATTTGTTTGGGC 59.298 36.000 0.00 0.00 0.00 5.36
8802 9186 9.216117 GTTAATCTGTACAGTTTGTCCATTAGT 57.784 33.333 23.51 4.66 0.00 2.24
8814 9198 5.086104 TGTCCATTAGTTCTCTAGGTTGC 57.914 43.478 0.00 0.00 0.00 4.17
8828 9212 1.737793 AGGTTGCGCTTCCTTTATTCG 59.262 47.619 9.73 0.00 0.00 3.34
8871 9255 7.187824 TCCTCATCTTAAAGCTGTACAGAAT 57.812 36.000 27.08 11.06 0.00 2.40
8917 9301 8.388484 AGTGTAAATGCAATTTTGGCAATAAA 57.612 26.923 0.00 0.00 46.10 1.40
8968 9352 6.251255 TGGGTGGTAAAGTACTGTAGTTTT 57.749 37.500 21.81 12.33 33.61 2.43
9029 9413 6.481954 AACTTGCTAATAACACACTACTGC 57.518 37.500 0.00 0.00 0.00 4.40
9079 9463 9.640952 AGAGATGCTCTAATAATATCTACTCCC 57.359 37.037 0.00 0.00 39.28 4.30
9080 9464 9.640952 GAGATGCTCTAATAATATCTACTCCCT 57.359 37.037 0.00 0.00 0.00 4.20
9081 9465 9.640952 AGATGCTCTAATAATATCTACTCCCTC 57.359 37.037 0.00 0.00 0.00 4.30
9082 9466 8.776061 ATGCTCTAATAATATCTACTCCCTCC 57.224 38.462 0.00 0.00 0.00 4.30
9083 9467 6.829298 TGCTCTAATAATATCTACTCCCTCCG 59.171 42.308 0.00 0.00 0.00 4.63
9085 9469 7.339976 GCTCTAATAATATCTACTCCCTCCGTT 59.660 40.741 0.00 0.00 0.00 4.44
9086 9470 8.804912 TCTAATAATATCTACTCCCTCCGTTC 57.195 38.462 0.00 0.00 0.00 3.95
9088 9472 4.472690 AATATCTACTCCCTCCGTTCCT 57.527 45.455 0.00 0.00 0.00 3.36
9089 9473 5.595814 AATATCTACTCCCTCCGTTCCTA 57.404 43.478 0.00 0.00 0.00 2.94
9090 9474 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
9091 9475 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
9092 9476 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
9095 9479 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
9096 9480 7.173722 TCTACTCCCTCCGTTCCTAAATATAG 58.826 42.308 0.00 0.00 0.00 1.31
9097 9481 4.527427 ACTCCCTCCGTTCCTAAATATAGC 59.473 45.833 0.00 0.00 0.00 2.97
9099 9483 5.895807 TCCCTCCGTTCCTAAATATAGCTA 58.104 41.667 0.00 0.00 0.00 3.32
9100 9484 5.713861 TCCCTCCGTTCCTAAATATAGCTAC 59.286 44.000 0.00 0.00 0.00 3.58
9101 9485 5.715753 CCCTCCGTTCCTAAATATAGCTACT 59.284 44.000 0.00 0.00 0.00 2.57
9103 9487 6.127675 CCTCCGTTCCTAAATATAGCTACTCC 60.128 46.154 0.00 0.00 0.00 3.85
9105 9489 5.715753 CCGTTCCTAAATATAGCTACTCCCT 59.284 44.000 0.00 0.00 0.00 4.20
9106 9490 6.127675 CCGTTCCTAAATATAGCTACTCCCTC 60.128 46.154 0.00 0.00 0.00 4.30
9107 9491 6.127675 CGTTCCTAAATATAGCTACTCCCTCC 60.128 46.154 0.00 0.00 0.00 4.30
9108 9492 5.507637 TCCTAAATATAGCTACTCCCTCCG 58.492 45.833 0.00 0.00 0.00 4.63
9109 9493 5.014966 TCCTAAATATAGCTACTCCCTCCGT 59.985 44.000 0.00 0.00 0.00 4.69
9110 9494 5.715753 CCTAAATATAGCTACTCCCTCCGTT 59.284 44.000 0.00 0.00 0.00 4.44
9111 9495 5.725325 AAATATAGCTACTCCCTCCGTTC 57.275 43.478 0.00 0.00 0.00 3.95
9112 9496 4.661247 ATATAGCTACTCCCTCCGTTCT 57.339 45.455 0.00 0.00 0.00 3.01
9114 9498 2.822707 AGCTACTCCCTCCGTTCTTA 57.177 50.000 0.00 0.00 0.00 2.10
9115 9499 3.097342 AGCTACTCCCTCCGTTCTTAA 57.903 47.619 0.00 0.00 0.00 1.85
9116 9500 3.438183 AGCTACTCCCTCCGTTCTTAAA 58.562 45.455 0.00 0.00 0.00 1.52
9120 9504 7.008941 AGCTACTCCCTCCGTTCTTAAATATA 58.991 38.462 0.00 0.00 0.00 0.86
9121 9505 7.508296 AGCTACTCCCTCCGTTCTTAAATATAA 59.492 37.037 0.00 0.00 0.00 0.98
9122 9506 7.813627 GCTACTCCCTCCGTTCTTAAATATAAG 59.186 40.741 0.00 0.00 39.97 1.73
9123 9507 7.063934 ACTCCCTCCGTTCTTAAATATAAGG 57.936 40.000 0.00 0.00 39.24 2.69
9124 9508 5.861727 TCCCTCCGTTCTTAAATATAAGGC 58.138 41.667 0.00 0.00 39.24 4.35
9126 9510 6.100714 TCCCTCCGTTCTTAAATATAAGGCTT 59.899 38.462 4.58 4.58 39.24 4.35
9129 9513 8.683615 CCTCCGTTCTTAAATATAAGGCTTTTT 58.316 33.333 4.45 2.60 39.24 1.94
9160 9544 8.839310 ATTTCAATATGGACTACATACAGAGC 57.161 34.615 0.00 0.00 44.41 4.09
9161 9545 6.346477 TCAATATGGACTACATACAGAGCC 57.654 41.667 0.00 0.00 44.41 4.70
9162 9546 6.077993 TCAATATGGACTACATACAGAGCCT 58.922 40.000 0.00 0.00 44.41 4.58
9163 9547 6.554982 TCAATATGGACTACATACAGAGCCTT 59.445 38.462 0.00 0.00 44.41 4.35
9164 9548 7.071196 TCAATATGGACTACATACAGAGCCTTT 59.929 37.037 0.00 0.00 44.41 3.11
9165 9549 5.700402 ATGGACTACATACAGAGCCTTTT 57.300 39.130 0.00 0.00 38.26 2.27
9166 9550 5.499004 TGGACTACATACAGAGCCTTTTT 57.501 39.130 0.00 0.00 0.00 1.94
9232 9635 1.975660 TGGTGGTTTAGTTGGCTCAC 58.024 50.000 0.00 0.00 0.00 3.51
9233 9636 1.213182 TGGTGGTTTAGTTGGCTCACA 59.787 47.619 0.00 0.00 0.00 3.58
9235 9638 1.263217 GTGGTTTAGTTGGCTCACACG 59.737 52.381 0.00 0.00 0.00 4.49
9336 9767 2.399356 GCTCGGTTGGCCAACTAGC 61.399 63.158 37.48 37.48 40.31 3.42
9372 9803 3.308595 TCTGTCACGTGTGCACTTAAAAG 59.691 43.478 19.41 7.23 0.00 2.27
9514 9949 8.908786 TTATATGAAAAATCAGCCTCAGTAGG 57.091 34.615 0.00 0.00 46.76 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.665916 CACTGTGGGAGCTGTCGTG 60.666 63.158 0.00 0.00 0.00 4.35
163 172 2.029828 TGCAAATTGTATCGCCGGTTTT 60.030 40.909 1.90 0.00 0.00 2.43
1140 1315 3.188460 GTCACCAGCAACAATTACGTCAT 59.812 43.478 0.00 0.00 0.00 3.06
1142 1317 2.546368 TGTCACCAGCAACAATTACGTC 59.454 45.455 0.00 0.00 0.00 4.34
1177 1353 4.213513 ACTCATAGTTTAGTAGGGGGTCG 58.786 47.826 0.00 0.00 0.00 4.79
1383 1559 7.312899 CACCAAAAATATTGTCAGGAACCTAC 58.687 38.462 4.51 0.00 0.00 3.18
1464 1640 3.579151 ACTCAGTGAAACCTAGAAGACCC 59.421 47.826 0.00 0.00 37.80 4.46
1465 1641 4.875561 ACTCAGTGAAACCTAGAAGACC 57.124 45.455 0.00 0.00 37.80 3.85
1467 1643 6.211584 AGCAATACTCAGTGAAACCTAGAAGA 59.788 38.462 0.00 0.00 37.80 2.87
1469 1645 6.360370 AGCAATACTCAGTGAAACCTAGAA 57.640 37.500 0.00 0.00 37.80 2.10
1914 2135 7.233689 GCCAACAAAAGAACTGTGTTTAAAAG 58.766 34.615 0.00 0.00 33.27 2.27
2104 2325 3.644966 TCACATCAGGAACCAATACCC 57.355 47.619 0.00 0.00 0.00 3.69
2195 2416 4.524316 ATGCATCACTTTTTGCTGCTAA 57.476 36.364 0.00 0.00 45.87 3.09
2217 2438 7.624360 AACCGCTCAATGAATACAAAGATAA 57.376 32.000 0.00 0.00 0.00 1.75
2392 2613 0.109412 AAGAGACGTACGAAAGCCGG 60.109 55.000 24.41 0.00 43.93 6.13
3162 3383 9.045223 TCATAGAATTTGAAGTGTATTCATCCG 57.955 33.333 0.00 0.00 32.11 4.18
3275 3496 9.200817 CCTCCAGGGAATAATAAAATCAAAAGA 57.799 33.333 0.00 0.00 37.23 2.52
3535 3785 8.780846 AAATAGTCATACACGGTCACATTTAA 57.219 30.769 0.00 0.00 0.00 1.52
3882 4132 9.745323 GTTCAATTTTTCTCTTCTGTTTTGTTG 57.255 29.630 0.00 0.00 0.00 3.33
4095 4345 6.069963 ACAAATTCTAGTGGAGGAAGCTGTAT 60.070 38.462 0.00 0.00 0.00 2.29
4277 4527 7.067372 TCCATAAAAAGTCTTCGACGTAGGATA 59.933 37.037 1.44 0.00 37.67 2.59
4809 5059 6.775708 TGCAAATAGTACTTCCACTTAGGTT 58.224 36.000 0.00 0.00 39.02 3.50
4892 5142 2.218759 GCAAGTAACTGTATCGGCATCG 59.781 50.000 0.00 0.00 37.82 3.84
5155 5406 9.294030 CTGATAATCTTTGGTTCTACAAAATGC 57.706 33.333 0.00 0.00 39.60 3.56
5255 5506 9.277783 CTATAACAGCAGAGGCAAATAAGTAAT 57.722 33.333 0.00 0.00 44.61 1.89
6361 6702 1.693606 CACCCCAAAACTCTTGGCATT 59.306 47.619 0.00 0.00 38.23 3.56
6911 7252 6.026186 AGATCCCATAGACAAATAGGGGTAG 58.974 44.000 3.61 0.00 45.25 3.18
6974 7315 3.244911 CCAAGACTCACCCAAACAGGTAT 60.245 47.826 0.00 0.00 38.39 2.73
6981 7322 2.091885 AGAAAGCCAAGACTCACCCAAA 60.092 45.455 0.00 0.00 0.00 3.28
7327 7694 3.575687 CCTTGATCAATTAATCCCCAGCC 59.424 47.826 8.96 0.00 0.00 4.85
7507 7875 7.994425 TCATGAAGAATTAAACAAGGTAGCA 57.006 32.000 0.00 0.00 0.00 3.49
7823 8194 9.892130 CAGTTCTAATCCTTCAGGTTTAGTAAT 57.108 33.333 17.69 9.27 43.23 1.89
7834 8205 5.313712 GTGTTTCCCAGTTCTAATCCTTCA 58.686 41.667 0.00 0.00 0.00 3.02
7851 8223 7.758528 ACAATACAGAGGTAATACTCGTGTTTC 59.241 37.037 0.00 0.00 42.31 2.78
7852 8224 7.609056 ACAATACAGAGGTAATACTCGTGTTT 58.391 34.615 0.00 0.00 42.31 2.83
8762 9146 8.865978 TGTACAGATTAACAGCTAAATACAACG 58.134 33.333 0.00 0.00 0.00 4.10
8802 9186 1.267121 AGGAAGCGCAACCTAGAGAA 58.733 50.000 20.79 0.00 34.47 2.87
8814 9198 7.908082 TGATAAATCAAACGAATAAAGGAAGCG 59.092 33.333 0.00 0.00 33.08 4.68
8871 9255 6.493802 ACACTCATTCACTCAGTTTACCTCTA 59.506 38.462 0.00 0.00 0.00 2.43
8976 9360 0.912487 ATCCAGTACTTCCCCCGCAA 60.912 55.000 0.00 0.00 0.00 4.85
8977 9361 0.912487 AATCCAGTACTTCCCCCGCA 60.912 55.000 0.00 0.00 0.00 5.69
8978 9362 0.463833 CAATCCAGTACTTCCCCCGC 60.464 60.000 0.00 0.00 0.00 6.13
8979 9363 0.463833 GCAATCCAGTACTTCCCCCG 60.464 60.000 0.00 0.00 0.00 5.73
8980 9364 0.919710 AGCAATCCAGTACTTCCCCC 59.080 55.000 0.00 0.00 0.00 5.40
8982 9366 2.911484 CTGAGCAATCCAGTACTTCCC 58.089 52.381 0.00 0.00 0.00 3.97
8983 9367 2.284190 GCTGAGCAATCCAGTACTTCC 58.716 52.381 0.00 0.00 34.29 3.46
8984 9368 2.284190 GGCTGAGCAATCCAGTACTTC 58.716 52.381 6.82 0.00 34.29 3.01
8986 9370 1.279496 TGGCTGAGCAATCCAGTACT 58.721 50.000 6.82 0.00 34.29 2.73
8988 9372 2.040278 AGTTTGGCTGAGCAATCCAGTA 59.960 45.455 6.82 0.00 34.29 2.74
8990 9374 1.542492 AGTTTGGCTGAGCAATCCAG 58.458 50.000 6.82 0.00 34.88 3.86
9029 9413 3.402628 AGATCCCGAATAACCATTCCG 57.597 47.619 0.00 0.00 37.82 4.30
9067 9451 4.472690 AGGAACGGAGGGAGTAGATATT 57.527 45.455 0.00 0.00 0.00 1.28
9075 9459 4.773149 AGCTATATTTAGGAACGGAGGGAG 59.227 45.833 0.00 0.00 0.00 4.30
9077 9461 5.715753 AGTAGCTATATTTAGGAACGGAGGG 59.284 44.000 0.00 0.00 0.00 4.30
9078 9462 6.127675 GGAGTAGCTATATTTAGGAACGGAGG 60.128 46.154 0.00 0.00 0.00 4.30
9079 9463 6.127675 GGGAGTAGCTATATTTAGGAACGGAG 60.128 46.154 0.00 0.00 0.00 4.63
9080 9464 5.713861 GGGAGTAGCTATATTTAGGAACGGA 59.286 44.000 0.00 0.00 0.00 4.69
9081 9465 5.715753 AGGGAGTAGCTATATTTAGGAACGG 59.284 44.000 0.00 0.00 0.00 4.44
9082 9466 6.127675 GGAGGGAGTAGCTATATTTAGGAACG 60.128 46.154 0.00 0.00 0.00 3.95
9083 9467 6.127675 CGGAGGGAGTAGCTATATTTAGGAAC 60.128 46.154 0.00 0.00 0.00 3.62
9085 9469 5.014966 ACGGAGGGAGTAGCTATATTTAGGA 59.985 44.000 0.00 0.00 0.00 2.94
9086 9470 5.262804 ACGGAGGGAGTAGCTATATTTAGG 58.737 45.833 0.00 0.00 0.00 2.69
9088 9472 6.550163 AGAACGGAGGGAGTAGCTATATTTA 58.450 40.000 0.00 0.00 0.00 1.40
9089 9473 5.395611 AGAACGGAGGGAGTAGCTATATTT 58.604 41.667 0.00 0.00 0.00 1.40
9090 9474 5.000570 AGAACGGAGGGAGTAGCTATATT 57.999 43.478 0.00 0.00 0.00 1.28
9091 9475 4.661247 AGAACGGAGGGAGTAGCTATAT 57.339 45.455 0.00 0.00 0.00 0.86
9092 9476 4.450305 AAGAACGGAGGGAGTAGCTATA 57.550 45.455 0.00 0.00 0.00 1.31
9095 9479 2.822707 TAAGAACGGAGGGAGTAGCT 57.177 50.000 0.00 0.00 0.00 3.32
9096 9480 3.881937 TTTAAGAACGGAGGGAGTAGC 57.118 47.619 0.00 0.00 0.00 3.58
9097 9481 8.305317 CCTTATATTTAAGAACGGAGGGAGTAG 58.695 40.741 4.66 0.00 37.59 2.57
9099 9483 6.464039 GCCTTATATTTAAGAACGGAGGGAGT 60.464 42.308 4.66 0.00 37.59 3.85
9100 9484 5.932883 GCCTTATATTTAAGAACGGAGGGAG 59.067 44.000 4.66 0.00 37.59 4.30
9101 9485 5.605488 AGCCTTATATTTAAGAACGGAGGGA 59.395 40.000 4.66 0.00 37.59 4.20
9103 9487 7.803279 AAAGCCTTATATTTAAGAACGGAGG 57.197 36.000 4.66 0.00 37.59 4.30
9134 9518 9.929180 GCTCTGTATGTAGTCCATATTGAAATA 57.071 33.333 0.00 0.00 38.29 1.40
9135 9519 7.880195 GGCTCTGTATGTAGTCCATATTGAAAT 59.120 37.037 0.00 0.00 38.29 2.17
9136 9520 7.071196 AGGCTCTGTATGTAGTCCATATTGAAA 59.929 37.037 0.00 0.00 38.29 2.69
9138 9522 6.077993 AGGCTCTGTATGTAGTCCATATTGA 58.922 40.000 0.00 0.00 38.29 2.57
9139 9523 6.352016 AGGCTCTGTATGTAGTCCATATTG 57.648 41.667 0.00 0.00 38.29 1.90
9140 9524 7.380423 AAAGGCTCTGTATGTAGTCCATATT 57.620 36.000 0.00 0.00 38.29 1.28
9141 9525 7.380423 AAAAGGCTCTGTATGTAGTCCATAT 57.620 36.000 0.00 0.00 38.29 1.78
9142 9526 6.808321 AAAAGGCTCTGTATGTAGTCCATA 57.192 37.500 0.00 0.00 34.86 2.74
9143 9527 5.700402 AAAAGGCTCTGTATGTAGTCCAT 57.300 39.130 0.00 0.00 37.58 3.41
9144 9528 5.499004 AAAAAGGCTCTGTATGTAGTCCA 57.501 39.130 0.00 0.00 0.00 4.02
9163 9547 5.363939 CCAAGGTTTTGGCTCACATAAAAA 58.636 37.500 0.00 0.00 46.84 1.94
9164 9548 4.954875 CCAAGGTTTTGGCTCACATAAAA 58.045 39.130 0.00 0.00 46.84 1.52
9165 9549 4.599047 CCAAGGTTTTGGCTCACATAAA 57.401 40.909 0.00 0.00 46.84 1.40
9336 9767 3.603857 CGTGACAGAAAAAGTAAGCCACG 60.604 47.826 0.00 0.00 38.75 4.94
9514 9949 0.454196 ACTTTCGCACAAACCACCAC 59.546 50.000 0.00 0.00 0.00 4.16
9685 10121 9.612066 AAAAGAAGTTTGAAGCATGGATTTTTA 57.388 25.926 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.