Multiple sequence alignment - TraesCS7B01G350400

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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 TraesCS7B01G350400 chr7B 100.000 4223 0 0 1 4223 607588841 607593063 0.000000e+00 7799
1 TraesCS7B01G350400 chr7B 95.261 612 15 4 3626 4223 694197999 694198610 0.000000e+00 957
2 TraesCS7B01G350400 chr7B 94.988 419 15 2 3625 4038 65706085 65705668 0.000000e+00 652
3 TraesCS7B01G350400 chr7B 94.634 205 6 3 3614 3816 703111192 703111393 3.170000e-81 313
4 TraesCS7B01G350400 chr7A 91.850 3632 185 38 3 3623 644115347 644118878 0.000000e+00 4964
5 TraesCS7B01G350400 chr7D 94.900 1706 60 16 1864 3566 559452887 559454568 0.000000e+00 2643
6 TraesCS7B01G350400 chr7D 86.090 1747 129 59 3 1711 559451207 559452877 0.000000e+00 1775
7 TraesCS7B01G350400 chr7D 78.947 494 76 18 2249 2737 602268469 602268939 1.140000e-80 311
8 TraesCS7B01G350400 chr4A 95.552 607 18 4 3626 4223 650626220 650626826 0.000000e+00 963
9 TraesCS7B01G350400 chr1B 91.653 611 23 6 3625 4223 31328902 31329496 0.000000e+00 821
10 TraesCS7B01G350400 chr6D 95.465 419 10 4 3814 4223 62899371 62899789 0.000000e+00 660
11 TraesCS7B01G350400 chr4D 95.455 418 11 2 3814 4223 439703039 439703456 0.000000e+00 660
12 TraesCS7B01G350400 chr6B 95.455 418 8 3 3817 4223 646672279 646671862 0.000000e+00 656
13 TraesCS7B01G350400 chr6B 96.875 192 6 0 3625 3816 646672406 646672215 5.270000e-84 322
14 TraesCS7B01G350400 chr3D 95.000 420 11 4 3814 4223 84512305 84512724 0.000000e+00 651
15 TraesCS7B01G350400 chr3D 95.000 420 11 4 3814 4223 613845374 613845793 0.000000e+00 651
16 TraesCS7B01G350400 chr6A 90.588 425 16 10 3616 4017 85131877 85131454 3.710000e-150 542
17 TraesCS7B01G350400 chr2D 95.522 201 8 1 3616 3816 559251101 559251300 1.890000e-83 320
18 TraesCS7B01G350400 chr1D 95.025 201 9 1 3616 3816 196003260 196003459 8.810000e-82 315
19 TraesCS7B01G350400 chr5B 94.554 202 11 0 3615 3816 649459874 649460075 3.170000e-81 313


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 TraesCS7B01G350400 chr7B 607588841 607593063 4222 False 7799 7799 100.000 1 4223 1 chr7B.!!$F1 4222
1 TraesCS7B01G350400 chr7B 694197999 694198610 611 False 957 957 95.261 3626 4223 1 chr7B.!!$F2 597
2 TraesCS7B01G350400 chr7A 644115347 644118878 3531 False 4964 4964 91.850 3 3623 1 chr7A.!!$F1 3620
3 TraesCS7B01G350400 chr7D 559451207 559454568 3361 False 2209 2643 90.495 3 3566 2 chr7D.!!$F2 3563
4 TraesCS7B01G350400 chr4A 650626220 650626826 606 False 963 963 95.552 3626 4223 1 chr4A.!!$F1 597
5 TraesCS7B01G350400 chr1B 31328902 31329496 594 False 821 821 91.653 3625 4223 1 chr1B.!!$F1 598
6 TraesCS7B01G350400 chr6B 646671862 646672406 544 True 489 656 96.165 3625 4223 2 chr6B.!!$R1 598

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
320 329 0.532573 ATATCCTATGGCTCGTGGCG 59.467 55.0 6.55 0.00 42.94 5.69 F
364 374 0.625980 TTGGGGGCACATGGATAGGA 60.626 55.0 0.00 0.00 0.00 2.94 F
1237 1296 0.393132 CGCTCCCCCTTTTCTTCCTC 60.393 60.0 0.00 0.00 0.00 3.71 F
1717 1787 0.107508 TATTCTGCTGGCAGTCTGGC 60.108 55.0 19.16 19.16 43.96 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1237 1296 1.325476 GGCAGGCAAGAGGGGATTTG 61.325 60.000 0.0 0.0 0.00 2.32 R
1288 1347 1.676006 CGTCCTGCATTACCATTTCCC 59.324 52.381 0.0 0.0 0.00 3.97 R
2667 2740 1.060729 TTTCACCCGGTTCATCCTCA 58.939 50.000 0.0 0.0 0.00 3.86 R
3418 3496 0.667184 CGCCCATGCAAAACAGTTCC 60.667 55.000 0.0 0.0 37.32 3.62 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 7.662258 TCTGTTTCAAGACCCAACGAATTATAA 59.338 33.333 0.00 0.00 0.00 0.98
28 29 7.812648 TGTTTCAAGACCCAACGAATTATAAG 58.187 34.615 0.00 0.00 0.00 1.73
72 74 1.366319 AAGATCAGGGGCTCAACAGT 58.634 50.000 0.00 0.00 0.00 3.55
281 290 1.351012 GCGCAGATCAGCACATGTC 59.649 57.895 10.95 0.00 0.00 3.06
282 291 1.088340 GCGCAGATCAGCACATGTCT 61.088 55.000 10.95 0.00 0.00 3.41
283 292 1.366679 CGCAGATCAGCACATGTCTT 58.633 50.000 10.95 0.00 0.00 3.01
284 293 1.062148 CGCAGATCAGCACATGTCTTG 59.938 52.381 10.95 0.00 0.00 3.02
285 294 1.400846 GCAGATCAGCACATGTCTTGG 59.599 52.381 5.05 0.00 0.00 3.61
286 295 2.708051 CAGATCAGCACATGTCTTGGT 58.292 47.619 0.00 0.00 0.00 3.67
287 296 3.865446 CAGATCAGCACATGTCTTGGTA 58.135 45.455 0.00 0.00 0.00 3.25
288 297 4.449131 CAGATCAGCACATGTCTTGGTAT 58.551 43.478 0.00 0.00 0.00 2.73
289 298 4.880120 CAGATCAGCACATGTCTTGGTATT 59.120 41.667 0.00 0.00 0.00 1.89
290 299 5.356190 CAGATCAGCACATGTCTTGGTATTT 59.644 40.000 0.00 0.00 0.00 1.40
291 300 5.587844 AGATCAGCACATGTCTTGGTATTTC 59.412 40.000 0.00 0.00 0.00 2.17
292 301 4.650734 TCAGCACATGTCTTGGTATTTCA 58.349 39.130 0.00 0.00 0.00 2.69
293 302 5.255687 TCAGCACATGTCTTGGTATTTCAT 58.744 37.500 0.00 0.00 0.00 2.57
294 303 5.711506 TCAGCACATGTCTTGGTATTTCATT 59.288 36.000 0.00 0.00 0.00 2.57
295 304 6.209192 TCAGCACATGTCTTGGTATTTCATTT 59.791 34.615 0.00 0.00 0.00 2.32
296 305 6.529125 CAGCACATGTCTTGGTATTTCATTTC 59.471 38.462 0.00 0.00 0.00 2.17
297 306 5.512788 GCACATGTCTTGGTATTTCATTTCG 59.487 40.000 0.00 0.00 0.00 3.46
312 321 7.667043 TTTCATTTCGTGTATATCCTATGGC 57.333 36.000 0.00 0.00 0.00 4.40
320 329 0.532573 ATATCCTATGGCTCGTGGCG 59.467 55.000 6.55 0.00 42.94 5.69
364 374 0.625980 TTGGGGGCACATGGATAGGA 60.626 55.000 0.00 0.00 0.00 2.94
441 451 5.538082 TTTAGGAGAGGAGGATATCGGAT 57.462 43.478 0.00 0.00 0.00 4.18
442 452 3.380471 AGGAGAGGAGGATATCGGATG 57.620 52.381 0.00 0.00 0.00 3.51
473 483 3.266254 CACCCTCCTCCCGTAGATAGATA 59.734 52.174 0.00 0.00 0.00 1.98
474 484 3.524380 ACCCTCCTCCCGTAGATAGATAG 59.476 52.174 0.00 0.00 0.00 2.08
475 485 3.781407 CCCTCCTCCCGTAGATAGATAGA 59.219 52.174 0.00 0.00 0.00 1.98
476 486 4.414182 CCCTCCTCCCGTAGATAGATAGAT 59.586 50.000 0.00 0.00 0.00 1.98
568 600 4.421058 GGAAAAATCACCGTGGATAAAGC 58.579 43.478 0.00 0.00 0.00 3.51
625 658 1.305887 GGGGAAAGAGACGGGGAGA 60.306 63.158 0.00 0.00 0.00 3.71
773 815 2.759973 TGCTTCCGCTCCGAGGAT 60.760 61.111 0.00 0.00 37.65 3.24
871 913 2.525877 GGCCGGGCTGGATACCTA 60.526 66.667 22.87 0.00 42.00 3.08
872 914 2.741747 GCCGGGCTGGATACCTAC 59.258 66.667 18.84 0.00 42.00 3.18
896 949 2.830370 CCCTTTCGGCCCATCAGC 60.830 66.667 0.00 0.00 0.00 4.26
944 998 3.123621 GCATCGAAGCCCATCTATAAACG 59.876 47.826 0.00 0.00 0.00 3.60
946 1000 4.238761 TCGAAGCCCATCTATAAACGAG 57.761 45.455 0.00 0.00 0.00 4.18
947 1001 2.731976 CGAAGCCCATCTATAAACGAGC 59.268 50.000 0.00 0.00 0.00 5.03
948 1002 3.728845 GAAGCCCATCTATAAACGAGCA 58.271 45.455 0.00 0.00 0.00 4.26
953 1007 3.496130 CCCATCTATAAACGAGCAAGCAG 59.504 47.826 0.00 0.00 0.00 4.24
989 1043 1.672854 TTATCCTGTCCGGGAGCACG 61.673 60.000 0.00 0.00 38.92 5.34
1036 1091 1.079956 CTGCTGCTTCTCTGCGAGT 60.080 57.895 0.00 0.00 41.87 4.18
1040 1095 1.077645 CTGCTTCTCTGCGAGTGAGC 61.078 60.000 18.90 18.90 38.92 4.26
1049 1104 2.691771 GCGAGTGAGCGAGTGAGGA 61.692 63.158 0.00 0.00 0.00 3.71
1237 1296 0.393132 CGCTCCCCCTTTTCTTCCTC 60.393 60.000 0.00 0.00 0.00 3.71
1330 1389 3.128845 CGGTAAATGCCCGCCGTT 61.129 61.111 0.00 0.00 38.85 4.44
1382 1441 1.070445 TGCTGCCTTTGTCCCAAATTG 59.930 47.619 0.00 0.00 0.00 2.32
1458 1517 0.320683 TGTGAGTGTCGATTGGGCAG 60.321 55.000 0.00 0.00 0.00 4.85
1461 1520 1.278985 TGAGTGTCGATTGGGCAGATT 59.721 47.619 0.00 0.00 0.00 2.40
1463 1522 1.003580 AGTGTCGATTGGGCAGATTGT 59.996 47.619 0.00 0.00 0.00 2.71
1464 1523 1.131126 GTGTCGATTGGGCAGATTGTG 59.869 52.381 0.00 0.00 0.00 3.33
1465 1524 1.271325 TGTCGATTGGGCAGATTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1467 1526 1.811965 TCGATTGGGCAGATTGTGTTG 59.188 47.619 0.00 0.00 0.00 3.33
1468 1527 1.541147 CGATTGGGCAGATTGTGTTGT 59.459 47.619 0.00 0.00 0.00 3.32
1469 1528 2.414559 CGATTGGGCAGATTGTGTTGTC 60.415 50.000 0.00 0.00 0.00 3.18
1470 1529 2.363306 TTGGGCAGATTGTGTTGTCT 57.637 45.000 0.00 0.00 0.00 3.41
1471 1530 1.896220 TGGGCAGATTGTGTTGTCTC 58.104 50.000 0.00 0.00 0.00 3.36
1472 1531 1.168714 GGGCAGATTGTGTTGTCTCC 58.831 55.000 0.00 0.00 0.00 3.71
1473 1532 1.168714 GGCAGATTGTGTTGTCTCCC 58.831 55.000 0.00 0.00 0.00 4.30
1495 1554 4.019681 CCATGTTTTAGAGTAGGGTCACCA 60.020 45.833 0.00 0.00 40.13 4.17
1498 1557 1.843368 TTAGAGTAGGGTCACCACCG 58.157 55.000 0.00 0.00 44.91 4.94
1711 1781 4.771590 TTTTGTTCTATTCTGCTGGCAG 57.228 40.909 10.94 10.94 44.86 4.85
1712 1782 3.423539 TTGTTCTATTCTGCTGGCAGT 57.576 42.857 17.16 6.69 43.96 4.40
1713 1783 2.977914 TGTTCTATTCTGCTGGCAGTC 58.022 47.619 17.16 9.10 43.96 3.51
1714 1784 2.568956 TGTTCTATTCTGCTGGCAGTCT 59.431 45.455 17.16 12.02 43.96 3.24
1715 1785 2.935201 GTTCTATTCTGCTGGCAGTCTG 59.065 50.000 17.16 12.08 43.96 3.51
1716 1786 1.483827 TCTATTCTGCTGGCAGTCTGG 59.516 52.381 17.16 11.61 43.96 3.86
1717 1787 0.107508 TATTCTGCTGGCAGTCTGGC 60.108 55.000 19.16 19.16 43.96 4.85
1727 1797 2.368439 GGCAGTCTGGCACATATCAAA 58.632 47.619 20.87 0.00 43.14 2.69
1728 1798 2.098117 GGCAGTCTGGCACATATCAAAC 59.902 50.000 20.87 0.00 43.14 2.93
1734 1804 4.637534 GTCTGGCACATATCAAACATGACT 59.362 41.667 0.00 0.00 38.20 3.41
1735 1805 5.124457 GTCTGGCACATATCAAACATGACTT 59.876 40.000 0.00 0.00 38.20 3.01
1768 1838 9.814899 AAACAAATGTTGTATTCATTCTGTCAA 57.185 25.926 0.00 0.00 44.59 3.18
1798 1868 0.109723 TGGAAACTAACGGGCAGCTT 59.890 50.000 0.00 0.00 0.00 3.74
1799 1869 1.348366 TGGAAACTAACGGGCAGCTTA 59.652 47.619 0.00 0.00 0.00 3.09
1804 1874 3.343941 ACTAACGGGCAGCTTAATTCA 57.656 42.857 0.00 0.00 0.00 2.57
1808 1878 1.003118 ACGGGCAGCTTAATTCACTCA 59.997 47.619 0.00 0.00 0.00 3.41
1814 1884 5.008118 GGGCAGCTTAATTCACTCATAAGAC 59.992 44.000 0.00 0.00 0.00 3.01
1817 1887 6.713520 CAGCTTAATTCACTCATAAGACAGC 58.286 40.000 0.00 0.00 0.00 4.40
1858 1928 2.223272 TGCTCGTAGTGTATCAGAAGCG 60.223 50.000 0.00 0.00 0.00 4.68
2028 2100 3.248024 TGACTGAGGAAAAGGAGGCTAA 58.752 45.455 0.00 0.00 0.00 3.09
2083 2156 1.329292 CACGGAAAACAGCGAGACAAA 59.671 47.619 0.00 0.00 0.00 2.83
2097 2170 4.730521 GCGAGACAAAATAATTGCTGCTAC 59.269 41.667 0.00 0.00 0.00 3.58
2118 2191 7.558081 TGCTACTTAAGTGATACAGACAGATCT 59.442 37.037 18.56 0.00 34.57 2.75
2129 2202 7.819415 TGATACAGACAGATCTTTTGGTACTTG 59.181 37.037 0.00 0.00 30.42 3.16
2158 2231 5.872070 AGACACATTTTTGCGAAAAGGAAAA 59.128 32.000 26.18 1.52 46.14 2.29
2246 2319 5.976534 TCTGTGTGATTTTGCAACATAACAC 59.023 36.000 28.46 28.46 37.71 3.32
2411 2484 4.079844 TGCCAATCTGGGTTTATCATCTCA 60.080 41.667 0.00 0.00 38.19 3.27
2412 2485 5.075493 GCCAATCTGGGTTTATCATCTCAT 58.925 41.667 0.00 0.00 38.19 2.90
2413 2486 6.183361 TGCCAATCTGGGTTTATCATCTCATA 60.183 38.462 0.00 0.00 38.19 2.15
2414 2487 6.888632 GCCAATCTGGGTTTATCATCTCATAT 59.111 38.462 0.00 0.00 38.19 1.78
2434 2507 8.183104 TCATATATACTTTGTCAGCTAGCTGT 57.817 34.615 36.99 22.88 43.96 4.40
2547 2620 2.505557 GTTAGGGTCGGCGACACG 60.506 66.667 37.13 0.00 41.43 4.49
2586 2659 2.812011 CCGTGAGAAAGGTAAAGTTGGG 59.188 50.000 0.00 0.00 0.00 4.12
2604 2677 1.137675 GGGGAAGTCGTACGGCTTTAT 59.862 52.381 33.23 14.57 40.49 1.40
2697 2770 1.892474 CCGGGTGAAATTGTCATGGTT 59.108 47.619 0.00 0.00 38.90 3.67
2731 2804 6.867662 TTCTCAAAACTTGTTCTCTCCATC 57.132 37.500 0.00 0.00 0.00 3.51
2733 2806 4.398319 TCAAAACTTGTTCTCTCCATCCC 58.602 43.478 0.00 0.00 0.00 3.85
2734 2807 4.104738 TCAAAACTTGTTCTCTCCATCCCT 59.895 41.667 0.00 0.00 0.00 4.20
2761 2835 3.631686 TGCCTTGTATGCTCGCATATTTT 59.368 39.130 14.03 0.00 40.49 1.82
2978 3052 2.984471 TGAAGTAATCGACAGCGTTGAC 59.016 45.455 6.16 0.00 38.98 3.18
3035 3109 7.231519 TCTGAGTCATCATCGTAGTATGGAAAT 59.768 37.037 0.00 0.00 34.12 2.17
3041 3115 2.469826 TCGTAGTATGGAAATGCTGCG 58.530 47.619 7.70 7.70 41.76 5.18
3057 3131 0.036483 TGCGCATGCTCTCAACCTTA 60.036 50.000 17.13 0.00 43.34 2.69
3111 3185 0.534877 TGGTGCCACTGCTTGTACTG 60.535 55.000 0.00 0.00 38.71 2.74
3197 3272 0.532573 TTTTGCAACGCTTGGTCCAA 59.467 45.000 3.76 3.76 0.00 3.53
3199 3274 1.315981 TTGCAACGCTTGGTCCAACA 61.316 50.000 0.00 0.00 0.00 3.33
3381 3459 1.760613 ACCGGACACATGTATCGGAAT 59.239 47.619 28.51 12.97 43.14 3.01
3390 3468 7.309499 GGACACATGTATCGGAATTAGAGATCT 60.309 40.741 0.00 0.00 0.00 2.75
3418 3496 0.245539 CCATGCCCTGCAAGTTCTTG 59.754 55.000 8.04 8.04 43.62 3.02
3569 3647 3.181530 CGTTCAGATTTAGCACAGTTCCG 60.182 47.826 0.00 0.00 0.00 4.30
3595 3673 3.949113 GGAGACAGTCGAGATAACTTCCT 59.051 47.826 0.00 0.00 0.00 3.36
3596 3674 4.399934 GGAGACAGTCGAGATAACTTCCTT 59.600 45.833 0.00 0.00 0.00 3.36
3623 3701 3.122278 CACGCTTTGATGGCTTTCATTTG 59.878 43.478 0.00 0.00 35.97 2.32
3725 3804 4.641989 GGGTAGTACTCGGATGAAAGTACA 59.358 45.833 13.40 0.00 46.66 2.90
3726 3805 5.301298 GGGTAGTACTCGGATGAAAGTACAT 59.699 44.000 13.40 0.00 46.66 2.29
3748 3827 4.060205 TGAAAGTACTAAAACGAGTGGGC 58.940 43.478 0.00 0.00 0.00 5.36
3777 3856 4.309950 GACAAGGTGGGGACGCGT 62.310 66.667 13.85 13.85 43.50 6.01
3779 3858 2.593436 CAAGGTGGGGACGCGTTT 60.593 61.111 15.53 0.00 45.82 3.60
3780 3859 2.190841 CAAGGTGGGGACGCGTTTT 61.191 57.895 15.53 0.00 45.82 2.43
3781 3860 0.885596 CAAGGTGGGGACGCGTTTTA 60.886 55.000 15.53 0.00 45.82 1.52
3782 3861 0.179023 AAGGTGGGGACGCGTTTTAA 60.179 50.000 15.53 0.00 45.82 1.52
3783 3862 0.037160 AGGTGGGGACGCGTTTTAAT 59.963 50.000 15.53 0.00 43.50 1.40
3784 3863 1.278699 AGGTGGGGACGCGTTTTAATA 59.721 47.619 15.53 0.00 43.50 0.98
3785 3864 2.092807 AGGTGGGGACGCGTTTTAATAT 60.093 45.455 15.53 0.00 43.50 1.28
3786 3865 3.134442 AGGTGGGGACGCGTTTTAATATA 59.866 43.478 15.53 0.00 43.50 0.86
3787 3866 3.495753 GGTGGGGACGCGTTTTAATATAG 59.504 47.826 15.53 0.00 43.50 1.31
3788 3867 3.495753 GTGGGGACGCGTTTTAATATAGG 59.504 47.826 15.53 0.00 0.00 2.57
3789 3868 3.069289 GGGGACGCGTTTTAATATAGGG 58.931 50.000 15.53 0.00 0.00 3.53
3790 3869 3.069289 GGGACGCGTTTTAATATAGGGG 58.931 50.000 15.53 0.00 0.00 4.79
3791 3870 2.481568 GGACGCGTTTTAATATAGGGGC 59.518 50.000 15.53 0.00 0.00 5.80
3792 3871 3.132925 GACGCGTTTTAATATAGGGGCA 58.867 45.455 15.53 0.00 0.00 5.36
3905 4005 1.292541 GCCCCTCTCGTCGAAAACT 59.707 57.895 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.485463 TCGTTGGGTCTTGAAACAGAT 57.515 42.857 0.00 0.00 0.00 2.90
1 2 2.992124 TCGTTGGGTCTTGAAACAGA 57.008 45.000 0.00 0.00 0.00 3.41
27 28 4.925390 AAGATTCTTTGCCTCTCTTCCT 57.075 40.909 0.00 0.00 0.00 3.36
28 29 8.738645 TTATTAAGATTCTTTGCCTCTCTTCC 57.261 34.615 3.86 0.00 0.00 3.46
117 119 4.712425 CCTGCCGTGCAAGCAAGC 62.712 66.667 13.19 10.42 40.35 4.01
158 160 7.289317 CCTTTCCTGTAACTACCATGGATAGTA 59.711 40.741 21.47 6.95 32.47 1.82
242 250 1.823899 CATTCCGGGGCAGTTAGGC 60.824 63.158 0.00 0.00 43.27 3.93
243 251 1.823899 GCATTCCGGGGCAGTTAGG 60.824 63.158 0.00 0.00 0.00 2.69
281 290 9.273016 AGGATATACACGAAATGAAATACCAAG 57.727 33.333 0.00 0.00 0.00 3.61
286 295 9.378551 GCCATAGGATATACACGAAATGAAATA 57.621 33.333 0.00 0.00 0.00 1.40
287 296 8.103305 AGCCATAGGATATACACGAAATGAAAT 58.897 33.333 0.00 0.00 0.00 2.17
288 297 7.450074 AGCCATAGGATATACACGAAATGAAA 58.550 34.615 0.00 0.00 0.00 2.69
289 298 7.004555 AGCCATAGGATATACACGAAATGAA 57.995 36.000 0.00 0.00 0.00 2.57
290 299 6.605471 AGCCATAGGATATACACGAAATGA 57.395 37.500 0.00 0.00 0.00 2.57
291 300 5.516696 CGAGCCATAGGATATACACGAAATG 59.483 44.000 0.00 0.00 0.00 2.32
292 301 5.185249 ACGAGCCATAGGATATACACGAAAT 59.815 40.000 0.00 0.00 0.00 2.17
293 302 4.521639 ACGAGCCATAGGATATACACGAAA 59.478 41.667 0.00 0.00 0.00 3.46
294 303 4.077108 ACGAGCCATAGGATATACACGAA 58.923 43.478 0.00 0.00 0.00 3.85
295 304 3.439129 CACGAGCCATAGGATATACACGA 59.561 47.826 0.00 0.00 0.00 4.35
296 305 3.427638 CCACGAGCCATAGGATATACACG 60.428 52.174 0.00 0.00 0.00 4.49
297 306 3.676324 GCCACGAGCCATAGGATATACAC 60.676 52.174 0.00 0.00 34.35 2.90
312 321 1.933181 TCTGCATTATTTCGCCACGAG 59.067 47.619 0.00 0.00 37.14 4.18
320 329 3.354397 CCGCGTTTCTCTGCATTATTTC 58.646 45.455 4.92 0.00 0.00 2.17
351 361 2.037772 ACTCCGAATCCTATCCATGTGC 59.962 50.000 0.00 0.00 0.00 4.57
352 362 3.576118 AGACTCCGAATCCTATCCATGTG 59.424 47.826 0.00 0.00 0.00 3.21
441 451 3.936203 GGAGGGTGACGTGCCACA 61.936 66.667 9.33 0.00 38.74 4.17
442 452 3.591254 GAGGAGGGTGACGTGCCAC 62.591 68.421 0.00 0.00 37.25 5.01
473 483 1.533711 CGATTCCAGGCCCCAATCT 59.466 57.895 0.00 0.00 0.00 2.40
474 484 2.196245 GCGATTCCAGGCCCCAATC 61.196 63.158 0.00 3.87 0.00 2.67
475 485 2.123726 GCGATTCCAGGCCCCAAT 60.124 61.111 0.00 0.00 0.00 3.16
476 486 2.721803 TTTGCGATTCCAGGCCCCAA 62.722 55.000 0.00 0.00 0.00 4.12
568 600 2.648454 CCGGCAAAAAGTTCCCCG 59.352 61.111 0.00 0.00 38.71 5.73
618 651 2.590114 AAAACCGACCCTCTCCCCG 61.590 63.158 0.00 0.00 0.00 5.73
625 658 1.152756 AAGCAGCAAAACCGACCCT 60.153 52.632 0.00 0.00 0.00 4.34
920 973 4.623932 TTATAGATGGGCTTCGATGCTT 57.376 40.909 21.05 8.16 0.00 3.91
944 998 4.774503 AGCGCCTCCTGCTTGCTC 62.775 66.667 2.29 0.00 40.48 4.26
989 1043 4.029287 GGATAACGAAGCGGCTCC 57.971 61.111 1.45 0.00 0.00 4.70
1036 1091 0.891373 CCTCTTTCCTCACTCGCTCA 59.109 55.000 0.00 0.00 0.00 4.26
1040 1095 0.171455 CCGTCCTCTTTCCTCACTCG 59.829 60.000 0.00 0.00 0.00 4.18
1049 1104 1.153823 CATCGTCGCCGTCCTCTTT 60.154 57.895 0.00 0.00 35.01 2.52
1220 1275 3.525800 TTTGAGGAAGAAAAGGGGGAG 57.474 47.619 0.00 0.00 0.00 4.30
1226 1281 4.928263 AGAGGGGATTTGAGGAAGAAAAG 58.072 43.478 0.00 0.00 0.00 2.27
1237 1296 1.325476 GGCAGGCAAGAGGGGATTTG 61.325 60.000 0.00 0.00 0.00 2.32
1288 1347 1.676006 CGTCCTGCATTACCATTTCCC 59.324 52.381 0.00 0.00 0.00 3.97
1328 1387 3.793144 CAGCGAGCAAGGCGGAAC 61.793 66.667 0.00 0.00 35.00 3.62
1330 1389 4.314440 AACAGCGAGCAAGGCGGA 62.314 61.111 0.00 0.00 35.00 5.54
1382 1441 4.337555 CCACTCAATCCATCCTCACAAATC 59.662 45.833 0.00 0.00 0.00 2.17
1458 1517 4.853924 AAACATGGGAGACAACACAATC 57.146 40.909 0.00 0.00 0.00 2.67
1461 1520 5.042463 TCTAAAACATGGGAGACAACACA 57.958 39.130 0.00 0.00 0.00 3.72
1463 1522 5.304686 ACTCTAAAACATGGGAGACAACA 57.695 39.130 0.00 0.00 0.00 3.33
1464 1523 5.875359 CCTACTCTAAAACATGGGAGACAAC 59.125 44.000 0.00 0.00 0.00 3.32
1465 1524 5.045869 CCCTACTCTAAAACATGGGAGACAA 60.046 44.000 0.00 0.00 35.40 3.18
1467 1526 4.470304 ACCCTACTCTAAAACATGGGAGAC 59.530 45.833 0.00 0.00 37.06 3.36
1468 1527 4.695606 ACCCTACTCTAAAACATGGGAGA 58.304 43.478 0.00 0.00 37.06 3.71
1469 1528 4.469945 TGACCCTACTCTAAAACATGGGAG 59.530 45.833 0.00 0.00 37.06 4.30
1470 1529 4.224370 GTGACCCTACTCTAAAACATGGGA 59.776 45.833 0.00 0.00 37.06 4.37
1471 1530 4.514401 GTGACCCTACTCTAAAACATGGG 58.486 47.826 0.00 0.00 39.06 4.00
1472 1531 4.019681 TGGTGACCCTACTCTAAAACATGG 60.020 45.833 0.00 0.00 0.00 3.66
1473 1532 4.935808 GTGGTGACCCTACTCTAAAACATG 59.064 45.833 0.00 0.00 0.00 3.21
1495 1554 6.017934 CAGCATAAACATAACTATTCTGCGGT 60.018 38.462 0.00 0.00 32.59 5.68
1498 1557 6.728200 TGCAGCATAAACATAACTATTCTGC 58.272 36.000 0.00 6.73 41.95 4.26
1711 1781 4.637534 AGTCATGTTTGATATGTGCCAGAC 59.362 41.667 0.00 0.00 33.56 3.51
1712 1782 4.847198 AGTCATGTTTGATATGTGCCAGA 58.153 39.130 0.00 0.00 33.56 3.86
1713 1783 5.571784 AAGTCATGTTTGATATGTGCCAG 57.428 39.130 0.00 0.00 33.56 4.85
1714 1784 5.243507 ACAAAGTCATGTTTGATATGTGCCA 59.756 36.000 13.93 0.00 39.40 4.92
1715 1785 5.713025 ACAAAGTCATGTTTGATATGTGCC 58.287 37.500 13.93 0.00 39.40 5.01
1716 1786 6.380995 TGACAAAGTCATGTTTGATATGTGC 58.619 36.000 13.93 0.00 39.40 4.57
1717 1787 7.809665 TCTGACAAAGTCATGTTTGATATGTG 58.190 34.615 13.93 0.00 41.94 3.21
1718 1788 7.984422 TCTGACAAAGTCATGTTTGATATGT 57.016 32.000 13.93 2.78 41.94 2.29
1735 1805 9.814899 AATGAATACAACATTTGTTTCTGACAA 57.185 25.926 0.00 0.00 46.19 3.18
1768 1838 6.039382 GCCCGTTAGTTTCCATCATCTTTTAT 59.961 38.462 0.00 0.00 0.00 1.40
1798 1868 8.144478 GTCATAGGCTGTCTTATGAGTGAATTA 58.856 37.037 0.00 0.00 30.59 1.40
1799 1869 6.989169 GTCATAGGCTGTCTTATGAGTGAATT 59.011 38.462 0.00 0.00 30.59 2.17
1804 1874 5.939764 TTGTCATAGGCTGTCTTATGAGT 57.060 39.130 0.00 0.00 30.59 3.41
1808 1878 7.776969 ACAATCATTTGTCATAGGCTGTCTTAT 59.223 33.333 0.00 0.00 42.43 1.73
1880 1950 2.906691 TCAAGTGCCATTTTGGGTTG 57.093 45.000 0.00 0.00 38.19 3.77
1983 2053 9.547753 TCAGGAATTAGCTATGAGTGAAATTAC 57.452 33.333 0.00 0.00 0.00 1.89
2028 2100 7.888021 TGGGACAACTACATTCAGTATGATTTT 59.112 33.333 0.00 0.00 40.44 1.82
2083 2156 9.613428 TGTATCACTTAAGTAGCAGCAATTATT 57.387 29.630 8.04 0.00 0.00 1.40
2097 2170 8.877779 CCAAAAGATCTGTCTGTATCACTTAAG 58.122 37.037 0.00 0.00 34.13 1.85
2178 2251 4.708421 AGAAACTGTAGGGTCGTGCTATAA 59.292 41.667 0.00 0.00 0.00 0.98
2411 2484 8.424918 ACAACAGCTAGCTGACAAAGTATATAT 58.575 33.333 43.42 19.01 46.30 0.86
2412 2485 7.782049 ACAACAGCTAGCTGACAAAGTATATA 58.218 34.615 43.42 0.00 46.30 0.86
2413 2486 6.644347 ACAACAGCTAGCTGACAAAGTATAT 58.356 36.000 43.42 19.70 46.30 0.86
2414 2487 6.037786 ACAACAGCTAGCTGACAAAGTATA 57.962 37.500 43.42 0.00 46.30 1.47
2434 2507 7.723616 TGGAGAAGGATTTCTGACATTTAACAA 59.276 33.333 0.00 0.00 43.63 2.83
2547 2620 2.821366 CCTGCGATGACCTGCACC 60.821 66.667 0.00 0.00 35.90 5.01
2604 2677 2.323968 TCACAGTGCTGTTGTGCTTA 57.676 45.000 1.57 0.00 44.27 3.09
2667 2740 1.060729 TTTCACCCGGTTCATCCTCA 58.939 50.000 0.00 0.00 0.00 3.86
2720 2793 2.158971 GCAAGAGAGGGATGGAGAGAAC 60.159 54.545 0.00 0.00 0.00 3.01
2731 2804 1.211457 AGCATACAAGGCAAGAGAGGG 59.789 52.381 0.00 0.00 0.00 4.30
2733 2806 2.200067 CGAGCATACAAGGCAAGAGAG 58.800 52.381 0.00 0.00 0.00 3.20
2734 2807 1.740380 GCGAGCATACAAGGCAAGAGA 60.740 52.381 0.00 0.00 0.00 3.10
2761 2835 3.055458 TGAATCGATGTTCTTGCCAGGTA 60.055 43.478 0.00 0.00 0.00 3.08
2978 3052 2.051334 TGAACACCTTCACCCAGTTG 57.949 50.000 0.00 0.00 31.00 3.16
3041 3115 1.669779 CAGCTAAGGTTGAGAGCATGC 59.330 52.381 10.51 10.51 38.73 4.06
3197 3272 3.547746 TGTAAAACGAAGGCCTTCTTGT 58.452 40.909 36.30 26.92 37.44 3.16
3199 3274 5.535030 AGAAATGTAAAACGAAGGCCTTCTT 59.465 36.000 36.30 28.24 37.44 2.52
3381 3459 2.742348 TGGCCGGTTACAGATCTCTAA 58.258 47.619 1.90 0.00 0.00 2.10
3418 3496 0.667184 CGCCCATGCAAAACAGTTCC 60.667 55.000 0.00 0.00 37.32 3.62
3569 3647 3.949113 AGTTATCTCGACTGTCTCCCTTC 59.051 47.826 6.21 0.00 0.00 3.46
3582 3660 4.259850 GCGTGCTTAAAGGAAGTTATCTCG 60.260 45.833 0.00 0.00 37.49 4.04
3595 3673 1.885887 AGCCATCAAAGCGTGCTTAAA 59.114 42.857 7.64 0.00 34.84 1.52
3596 3674 1.533625 AGCCATCAAAGCGTGCTTAA 58.466 45.000 7.64 0.00 34.84 1.85
3623 3701 5.106277 GCCCAACCACTCTAAAAGTTGTATC 60.106 44.000 0.00 0.00 38.31 2.24
3725 3804 4.694037 GCCCACTCGTTTTAGTACTTTCAT 59.306 41.667 0.00 0.00 0.00 2.57
3726 3805 4.060205 GCCCACTCGTTTTAGTACTTTCA 58.940 43.478 0.00 0.00 0.00 2.69
3748 3827 0.903454 ACCTTGTCAGGAGTACCGGG 60.903 60.000 6.32 0.00 44.19 5.73
3777 3856 8.109560 AGGACTAAACTGCCCCTATATTAAAA 57.890 34.615 0.00 0.00 0.00 1.52
3778 3857 7.701257 AGGACTAAACTGCCCCTATATTAAA 57.299 36.000 0.00 0.00 0.00 1.52
3779 3858 7.456902 CCTAGGACTAAACTGCCCCTATATTAA 59.543 40.741 1.05 0.00 0.00 1.40
3780 3859 6.958192 CCTAGGACTAAACTGCCCCTATATTA 59.042 42.308 1.05 0.00 0.00 0.98
3781 3860 5.785940 CCTAGGACTAAACTGCCCCTATATT 59.214 44.000 1.05 0.00 0.00 1.28
3782 3861 5.077441 TCCTAGGACTAAACTGCCCCTATAT 59.923 44.000 7.62 0.00 0.00 0.86
3783 3862 4.421231 TCCTAGGACTAAACTGCCCCTATA 59.579 45.833 7.62 0.00 0.00 1.31
3784 3863 3.209152 TCCTAGGACTAAACTGCCCCTAT 59.791 47.826 7.62 0.00 0.00 2.57
3785 3864 2.588720 TCCTAGGACTAAACTGCCCCTA 59.411 50.000 7.62 0.00 0.00 3.53
3786 3865 1.365028 TCCTAGGACTAAACTGCCCCT 59.635 52.381 7.62 0.00 0.00 4.79
3787 3866 1.875488 TCCTAGGACTAAACTGCCCC 58.125 55.000 7.62 0.00 0.00 5.80
3788 3867 3.994931 TTTCCTAGGACTAAACTGCCC 57.005 47.619 12.22 0.00 0.00 5.36
3789 3868 6.621613 CAAATTTTCCTAGGACTAAACTGCC 58.378 40.000 12.22 0.00 0.00 4.85
3790 3869 6.093404 GCAAATTTTCCTAGGACTAAACTGC 58.907 40.000 12.22 17.21 0.00 4.40
3791 3870 7.214467 TGCAAATTTTCCTAGGACTAAACTG 57.786 36.000 12.22 12.04 0.00 3.16
3792 3871 6.434340 CCTGCAAATTTTCCTAGGACTAAACT 59.566 38.462 12.22 0.00 0.00 2.66
3905 4005 3.559511 TTGTAGCACCATGGCGGCA 62.560 57.895 25.69 16.34 39.03 5.69
4033 4142 1.562672 CGATGGAAGAGGGGTTGGGT 61.563 60.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.