Multiple sequence alignment - TraesCS1D01G187900

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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 TraesCS1D01G187900 chr1D 100.000 5718 0 0 1 5718 260324942 260330659 0.000000e+00 10560.0
1 TraesCS1D01G187900 chr1D 79.880 666 111 13 3211 3866 44842 45494 3.120000e-127 466.0
2 TraesCS1D01G187900 chr1A 95.641 3005 108 13 2480 5477 340411803 340408815 0.000000e+00 4802.0
3 TraesCS1D01G187900 chr1A 85.705 1511 90 50 1 1407 340414548 340413060 0.000000e+00 1478.0
4 TraesCS1D01G187900 chr1A 81.697 825 58 34 1409 2172 340413021 340412229 8.200000e-168 601.0
5 TraesCS1D01G187900 chr1A 94.769 325 14 1 5290 5614 340408806 340408485 2.380000e-138 503.0
6 TraesCS1D01G187900 chr1A 91.760 267 13 4 2222 2480 340412231 340411966 4.210000e-96 363.0
7 TraesCS1D01G187900 chr1A 97.222 108 3 0 5611 5718 340408405 340408298 3.520000e-42 183.0
8 TraesCS1D01G187900 chr1B 95.659 2626 93 9 2503 5120 352881195 352878583 0.000000e+00 4198.0
9 TraesCS1D01G187900 chr1B 86.336 1471 108 39 1 1421 352883817 352882390 0.000000e+00 1517.0
10 TraesCS1D01G187900 chr1B 85.028 708 47 16 1424 2098 352882341 352881660 0.000000e+00 665.0
11 TraesCS1D01G187900 chr1B 82.340 453 50 18 4999 5443 352878572 352878142 3.260000e-97 366.0
12 TraesCS1D01G187900 chr1B 89.180 305 18 8 2095 2389 352881500 352881201 3.260000e-97 366.0
13 TraesCS1D01G187900 chr1B 89.394 264 14 2 5455 5718 352877714 352877465 2.570000e-83 320.0
14 TraesCS1D01G187900 chr3D 92.795 1152 53 10 3533 4665 550946565 550945425 0.000000e+00 1640.0
15 TraesCS1D01G187900 chr4D 80.659 1639 276 22 3083 4696 502111034 502109412 0.000000e+00 1232.0
16 TraesCS1D01G187900 chr4B 80.549 1640 276 23 3083 4696 646225235 646223613 0.000000e+00 1221.0
17 TraesCS1D01G187900 chr5A 80.073 1641 282 25 3083 4696 685014235 685012613 0.000000e+00 1177.0
18 TraesCS1D01G187900 chr6B 86.591 798 69 6 3091 3873 664639037 664639811 0.000000e+00 846.0
19 TraesCS1D01G187900 chr3A 83.297 910 57 30 3756 4665 707392809 707391995 0.000000e+00 750.0
20 TraesCS1D01G187900 chr3A 92.035 226 18 0 3466 3691 707393031 707392806 9.250000e-83 318.0
21 TraesCS1D01G187900 chr3A 94.074 135 6 2 3329 3463 707393525 707393393 2.700000e-48 204.0
22 TraesCS1D01G187900 chr7D 87.805 82 7 2 3731 3809 520953040 520952959 6.100000e-15 93.5


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 TraesCS1D01G187900 chr1D 260324942 260330659 5717 False 10560.000000 10560 100.000000 1 5718 1 chr1D.!!$F2 5717
1 TraesCS1D01G187900 chr1D 44842 45494 652 False 466.000000 466 79.880000 3211 3866 1 chr1D.!!$F1 655
2 TraesCS1D01G187900 chr1A 340408298 340414548 6250 True 1321.666667 4802 91.132333 1 5718 6 chr1A.!!$R1 5717
3 TraesCS1D01G187900 chr1B 352877465 352883817 6352 True 1238.666667 4198 87.989500 1 5718 6 chr1B.!!$R1 5717
4 TraesCS1D01G187900 chr3D 550945425 550946565 1140 True 1640.000000 1640 92.795000 3533 4665 1 chr3D.!!$R1 1132
5 TraesCS1D01G187900 chr4D 502109412 502111034 1622 True 1232.000000 1232 80.659000 3083 4696 1 chr4D.!!$R1 1613
6 TraesCS1D01G187900 chr4B 646223613 646225235 1622 True 1221.000000 1221 80.549000 3083 4696 1 chr4B.!!$R1 1613
7 TraesCS1D01G187900 chr5A 685012613 685014235 1622 True 1177.000000 1177 80.073000 3083 4696 1 chr5A.!!$R1 1613
8 TraesCS1D01G187900 chr6B 664639037 664639811 774 False 846.000000 846 86.591000 3091 3873 1 chr6B.!!$F1 782
9 TraesCS1D01G187900 chr3A 707391995 707393525 1530 True 424.000000 750 89.802000 3329 4665 3 chr3A.!!$R1 1336

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
664 721 0.320334 CGCCCCAATTCAAAACACCC 60.320 55.0 0.00 0.0 0.00 4.61 F
1609 1830 0.108804 ACGACAGCTGTATTCACCGG 60.109 55.0 21.73 0.0 0.00 5.28 F
2408 2847 0.533755 CAGCCCCTCTAATGCCGAAG 60.534 60.0 0.00 0.0 0.00 3.79 F
2797 3403 0.541764 AAAGCAATGGAAAGGCCGGA 60.542 50.0 5.05 0.0 40.66 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2783 0.319641 GCCGTCTCAGGAAAGTTCGT 60.320 55.000 0.00 0.0 0.00 3.85 R
2529 3133 0.758734 CGGGATAGATGGCCAAGTGA 59.241 55.000 10.96 0.0 0.00 3.41 R
3411 4026 1.302033 CCGGTCTTGACAAGCAGCT 60.302 57.895 10.50 0.0 0.00 4.24 R
4782 5804 1.483827 TCTGCACTGCCTTCATAGAGG 59.516 52.381 0.00 0.0 39.93 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.549423 CGTGTACGTGGTATACTGGATGG 60.549 52.174 0.00 0.00 29.90 3.51
307 313 7.923888 TGACTTTCTCAGATCAGAAAACTTTG 58.076 34.615 8.95 1.75 40.97 2.77
308 314 7.012704 TGACTTTCTCAGATCAGAAAACTTTGG 59.987 37.037 8.95 1.21 40.97 3.28
309 315 6.830838 ACTTTCTCAGATCAGAAAACTTTGGT 59.169 34.615 8.95 1.69 40.97 3.67
312 318 8.746052 TTCTCAGATCAGAAAACTTTGGTTTA 57.254 30.769 0.00 0.00 43.90 2.01
314 320 9.354673 TCTCAGATCAGAAAACTTTGGTTTATT 57.645 29.630 0.00 0.00 43.90 1.40
316 322 9.748708 TCAGATCAGAAAACTTTGGTTTATTTG 57.251 29.630 0.00 0.00 43.90 2.32
318 324 6.820470 TCAGAAAACTTTGGTTTATTTGCG 57.180 33.333 0.00 0.00 43.90 4.85
319 325 5.751028 TCAGAAAACTTTGGTTTATTTGCGG 59.249 36.000 0.00 0.00 43.90 5.69
320 326 5.050431 CAGAAAACTTTGGTTTATTTGCGGG 60.050 40.000 0.00 0.00 43.90 6.13
322 328 5.532664 AAACTTTGGTTTATTTGCGGGTA 57.467 34.783 0.00 0.00 43.00 3.69
342 368 6.944234 GGTAGAATCCAAAAATACCCTCAG 57.056 41.667 0.00 0.00 31.56 3.35
392 418 2.613730 TCGTCAGATGAGTTCGTGTC 57.386 50.000 0.00 0.00 0.00 3.67
393 419 1.877443 TCGTCAGATGAGTTCGTGTCA 59.123 47.619 0.00 0.00 0.00 3.58
394 420 2.292292 TCGTCAGATGAGTTCGTGTCAA 59.708 45.455 0.00 0.00 0.00 3.18
395 421 2.405357 CGTCAGATGAGTTCGTGTCAAC 59.595 50.000 0.00 0.00 0.00 3.18
396 422 3.381045 GTCAGATGAGTTCGTGTCAACA 58.619 45.455 0.00 0.00 0.00 3.33
397 423 3.182572 GTCAGATGAGTTCGTGTCAACAC 59.817 47.826 3.13 3.13 43.15 3.32
398 424 3.123050 CAGATGAGTTCGTGTCAACACA 58.877 45.455 13.30 0.00 46.75 3.72
430 456 1.968493 AGAAGCACTCGTGGGTAGAAA 59.032 47.619 0.00 0.00 0.00 2.52
475 507 4.285775 GGATTCAATTCAAAAACCCTCCCA 59.714 41.667 0.00 0.00 0.00 4.37
611 658 3.096495 CCCCACCATCCGTCCCAT 61.096 66.667 0.00 0.00 0.00 4.00
616 669 2.271821 CCATCCGTCCCATGTGCA 59.728 61.111 0.00 0.00 0.00 4.57
625 682 3.660571 CCATGTGCACCCCCTCCA 61.661 66.667 15.69 0.00 0.00 3.86
664 721 0.320334 CGCCCCAATTCAAAACACCC 60.320 55.000 0.00 0.00 0.00 4.61
689 746 3.625897 CTCCGCTCCCCACACACA 61.626 66.667 0.00 0.00 0.00 3.72
690 747 2.927856 TCCGCTCCCCACACACAT 60.928 61.111 0.00 0.00 0.00 3.21
739 806 2.548480 CGCCCGGAGAGAAATAAATTCC 59.452 50.000 0.73 0.00 38.94 3.01
830 897 2.744768 GCTCGCTACAAGTGCAGCC 61.745 63.158 0.00 0.00 34.15 4.85
869 939 7.877612 GTGTTTTTGTTAATCATTCCCCAATCT 59.122 33.333 0.00 0.00 0.00 2.40
921 991 2.680352 TCCTCTCACTCCCACGCC 60.680 66.667 0.00 0.00 0.00 5.68
938 1008 3.151022 CCGCACTCCCTCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
939 1009 3.522731 CGCACTCCCTCCTCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
940 1010 3.844090 GCACTCCCTCCTCCTCGC 61.844 72.222 0.00 0.00 0.00 5.03
941 1011 3.151022 CACTCCCTCCTCCTCGCC 61.151 72.222 0.00 0.00 0.00 5.54
942 1012 4.824515 ACTCCCTCCTCCTCGCCG 62.825 72.222 0.00 0.00 0.00 6.46
944 1014 4.507916 TCCCTCCTCCTCGCCGAG 62.508 72.222 7.25 7.25 0.00 4.63
958 1028 3.822192 CGAGGACGCGGGTGATGA 61.822 66.667 10.96 0.00 0.00 2.92
959 1029 2.815308 GAGGACGCGGGTGATGAT 59.185 61.111 10.96 0.00 0.00 2.45
961 1031 0.876342 GAGGACGCGGGTGATGATTC 60.876 60.000 10.96 0.00 0.00 2.52
962 1032 1.153449 GGACGCGGGTGATGATTCA 60.153 57.895 10.96 0.00 0.00 2.57
964 1034 0.861837 GACGCGGGTGATGATTCATC 59.138 55.000 17.97 17.97 40.88 2.92
965 1035 0.465705 ACGCGGGTGATGATTCATCT 59.534 50.000 23.49 2.91 41.06 2.90
966 1036 1.134401 ACGCGGGTGATGATTCATCTT 60.134 47.619 23.49 0.00 41.06 2.40
967 1037 1.528586 CGCGGGTGATGATTCATCTTC 59.471 52.381 23.49 16.80 41.06 2.87
968 1038 2.564771 GCGGGTGATGATTCATCTTCA 58.435 47.619 23.49 7.23 41.06 3.02
969 1039 3.144506 GCGGGTGATGATTCATCTTCAT 58.855 45.455 23.49 0.00 41.21 2.57
970 1040 3.188048 GCGGGTGATGATTCATCTTCATC 59.812 47.826 23.49 9.73 46.30 2.92
976 1046 5.121925 GTGATGATTCATCTTCATCCATCCG 59.878 44.000 23.49 0.00 45.79 4.18
995 1065 3.389656 TCCGTATGATGGGCAACTGATTA 59.610 43.478 0.00 0.00 0.00 1.75
1053 1126 1.509923 GGCGGTACTAGCACTCGTT 59.490 57.895 13.98 0.00 36.08 3.85
1063 1136 2.622064 AGCACTCGTTGGTTTCTTCT 57.378 45.000 0.00 0.00 28.85 2.85
1073 1146 2.742372 TTTCTTCTCGCTGGCGGC 60.742 61.111 14.94 8.64 40.25 6.53
1155 1228 2.349755 GCAGGGCGAGGTAAACCA 59.650 61.111 1.26 0.00 38.89 3.67
1167 1247 3.500343 AGGTAAACCAGCTTGCTTCATT 58.500 40.909 1.26 0.00 38.89 2.57
1246 1335 4.634703 TTTGCTTCCTCGCGGCCA 62.635 61.111 6.13 0.00 0.00 5.36
1326 1422 1.004918 CCTGTGTCCGTCCACCTTC 60.005 63.158 0.00 0.00 34.35 3.46
1395 1505 2.541466 AGGAACGAGAGAGATTTGGGT 58.459 47.619 0.00 0.00 0.00 4.51
1400 1510 1.404181 CGAGAGAGATTTGGGTGCGAA 60.404 52.381 0.00 0.00 0.00 4.70
1403 1513 3.012518 AGAGAGATTTGGGTGCGAATTG 58.987 45.455 0.00 0.00 0.00 2.32
1423 1570 7.995998 CGAATTGTTTTCGAAAATTTACAGGTG 59.004 33.333 24.93 7.66 43.97 4.00
1471 1678 8.583810 TCCGTACTTATTTTCGAAATCTATGG 57.416 34.615 12.12 10.82 0.00 2.74
1485 1692 7.056635 CGAAATCTATGGAGGGGCATTTATAT 58.943 38.462 0.00 0.00 0.00 0.86
1523 1733 2.466846 GGGGCCAGACCACAATAAATT 58.533 47.619 4.39 0.00 43.87 1.82
1609 1830 0.108804 ACGACAGCTGTATTCACCGG 60.109 55.000 21.73 0.00 0.00 5.28
1612 1833 1.819632 CAGCTGTATTCACCGGGCC 60.820 63.158 6.32 0.00 0.00 5.80
1635 1856 4.873129 CTCCCGATGACGCGTGGG 62.873 72.222 20.70 22.10 43.36 4.61
1816 2043 1.368950 CCGATCCGGCTCATGATGT 59.631 57.895 6.06 0.00 41.17 3.06
1844 2071 4.662961 CACCCACGCGCTCACTCA 62.663 66.667 5.73 0.00 0.00 3.41
2042 2302 3.485463 TGGGTCAGGTTAAAGTCTGTG 57.515 47.619 0.00 0.00 33.13 3.66
2057 2317 2.758979 GTCTGTGGGATCTCTTTCCGTA 59.241 50.000 0.00 0.00 36.58 4.02
2098 2358 7.667043 AGAAGCTCGTGATAAAATTTGTACA 57.333 32.000 0.00 0.00 0.00 2.90
2275 2702 9.653287 TGGATTACAATACAAGAAAGTACTCTG 57.347 33.333 0.00 0.00 0.00 3.35
2298 2731 5.647658 TGGCCTAGTGTGAAAATTATGAGTG 59.352 40.000 3.32 0.00 0.00 3.51
2344 2783 3.988976 AGCACTCCAAGCTTAAGATCA 57.011 42.857 6.67 0.00 39.87 2.92
2408 2847 0.533755 CAGCCCCTCTAATGCCGAAG 60.534 60.000 0.00 0.00 0.00 3.79
2428 2868 6.066128 GAAGCAAACGTCGAAAAATATTGG 57.934 37.500 0.00 0.00 0.00 3.16
2526 3130 1.541310 ATCCCGTTCCGTTCTGCTCA 61.541 55.000 0.00 0.00 0.00 4.26
2529 3133 0.670546 CCGTTCCGTTCTGCTCACAT 60.671 55.000 0.00 0.00 0.00 3.21
2543 3147 2.420547 GCTCACATCACTTGGCCATCTA 60.421 50.000 6.09 0.00 0.00 1.98
2630 3234 2.154462 CGGGTCAAAACTCAGAATGCT 58.846 47.619 0.00 0.00 34.76 3.79
2633 3237 3.823304 GGGTCAAAACTCAGAATGCTTCT 59.177 43.478 0.00 0.00 41.70 2.85
2651 3255 6.418101 TGCTTCTAGCCTGAATTTATTCTGT 58.582 36.000 4.29 0.00 41.51 3.41
2652 3256 6.886459 TGCTTCTAGCCTGAATTTATTCTGTT 59.114 34.615 4.29 0.00 41.51 3.16
2653 3257 8.046708 TGCTTCTAGCCTGAATTTATTCTGTTA 58.953 33.333 4.29 0.00 41.51 2.41
2674 3279 1.225855 TACCGAACAGTGCAAAGCAG 58.774 50.000 0.00 0.00 40.08 4.24
2676 3281 1.370900 CGAACAGTGCAAAGCAGGC 60.371 57.895 0.00 0.00 40.08 4.85
2684 3290 1.111116 TGCAAAGCAGGCAGAAAGCT 61.111 50.000 0.00 0.00 41.03 3.74
2708 3314 2.029918 GGAATTTTGATAGGGCCATCGC 60.030 50.000 6.18 0.00 0.00 4.58
2797 3403 0.541764 AAAGCAATGGAAAGGCCGGA 60.542 50.000 5.05 0.00 40.66 5.14
2831 3437 4.615588 AGATTGCTAGATGAGGTTAGCC 57.384 45.455 0.00 0.00 41.19 3.93
2853 3459 1.439679 AGCTTTCCACGACGGATTTC 58.560 50.000 0.00 0.00 45.80 2.17
2855 3461 0.719465 CTTTCCACGACGGATTTCGG 59.281 55.000 0.00 0.00 45.80 4.30
2869 3475 6.536688 ACGGATTTCGGTTCGTTTAAAATAG 58.463 36.000 0.00 0.00 44.45 1.73
2872 3479 3.372869 TCGGTTCGTTTAAAATAGCGC 57.627 42.857 0.00 0.00 0.00 5.92
2923 3530 5.516696 GCTTCTTCTTCGCTGTTTTCTTTTT 59.483 36.000 0.00 0.00 0.00 1.94
2925 3532 5.578776 TCTTCTTCGCTGTTTTCTTTTTCC 58.421 37.500 0.00 0.00 0.00 3.13
2979 3586 1.003718 AGGTGGGAGCGTTGCTAAC 60.004 57.895 0.00 0.00 39.88 2.34
3411 4026 3.691342 CAACCTCCGGGACTGCGA 61.691 66.667 0.00 0.00 36.25 5.10
4081 5087 1.569479 GCCTGCAGAACTTCACGTCC 61.569 60.000 17.39 0.00 0.00 4.79
4201 5207 2.995872 GCTCCGCAACCTCGTCTCT 61.996 63.158 0.00 0.00 0.00 3.10
4782 5804 1.421410 CGCCGTCCTGTGTTCATAGC 61.421 60.000 0.00 0.00 0.00 2.97
4822 5844 2.297597 GACTGCAGAGAGTGGTACTGTT 59.702 50.000 23.35 0.00 34.60 3.16
4851 5873 6.349860 GCCGATTTGAACCTTTTAACATACCT 60.350 38.462 0.00 0.00 0.00 3.08
4996 6026 6.691754 TTGTATTGTCTGCTGAGTTTTGAA 57.308 33.333 0.00 0.00 0.00 2.69
5092 6124 4.033358 GCACGGAAACACTAGAATCTCATG 59.967 45.833 0.00 0.00 0.00 3.07
5126 6285 7.062906 TGAAATAATTGTTGCATGTCATTGC 57.937 32.000 0.00 0.00 43.07 3.56
5184 6360 2.162408 GGGAAGGCGAGTGATTTTTCTG 59.838 50.000 0.00 0.00 0.00 3.02
5189 6365 2.478539 GGCGAGTGATTTTTCTGGATGC 60.479 50.000 0.00 0.00 0.00 3.91
5369 6737 3.455543 TCAGGTGCAGATGATGGTTGATA 59.544 43.478 0.00 0.00 0.00 2.15
5423 6791 6.369890 GCAATCATTGTCTTGACTAAGTCTCA 59.630 38.462 0.00 0.00 35.38 3.27
5424 6792 7.623089 GCAATCATTGTCTTGACTAAGTCTCAC 60.623 40.741 0.00 0.00 35.38 3.51
5453 7237 0.741221 GAAGTGATGAGCCGGTGACC 60.741 60.000 1.90 0.00 0.00 4.02
5479 7263 2.384203 GGACAGGAATCCGCTTTCG 58.616 57.895 0.00 0.00 0.00 3.46
5653 7520 5.833131 AGTGGATGGTCAAAATACAAAGTGT 59.167 36.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.678190 GCAGGATTAGGTGTCAGTGTCC 60.678 54.545 0.00 0.00 0.00 4.02
150 151 1.441729 CGCGCCTCCTTCCAGATAA 59.558 57.895 0.00 0.00 0.00 1.75
151 152 3.129300 CGCGCCTCCTTCCAGATA 58.871 61.111 0.00 0.00 0.00 1.98
157 158 3.869272 CATGTGCGCGCCTCCTTC 61.869 66.667 30.77 12.10 0.00 3.46
177 178 3.112709 GAACAGAGCCCGTCGCAC 61.113 66.667 0.00 0.00 41.38 5.34
285 291 7.269477 ACCAAAGTTTTCTGATCTGAGAAAG 57.731 36.000 7.07 0.00 41.75 2.62
298 304 4.812091 ACCCGCAAATAAACCAAAGTTTTC 59.188 37.500 0.00 0.00 43.82 2.29
301 307 4.828387 TCTACCCGCAAATAAACCAAAGTT 59.172 37.500 0.00 0.00 38.03 2.66
307 313 3.949113 TGGATTCTACCCGCAAATAAACC 59.051 43.478 0.00 0.00 0.00 3.27
308 314 5.570234 TTGGATTCTACCCGCAAATAAAC 57.430 39.130 0.00 0.00 0.00 2.01
309 315 6.591750 TTTTGGATTCTACCCGCAAATAAA 57.408 33.333 0.00 0.00 0.00 1.40
312 318 5.675684 ATTTTTGGATTCTACCCGCAAAT 57.324 34.783 0.00 0.00 0.00 2.32
314 320 4.399934 GGTATTTTTGGATTCTACCCGCAA 59.600 41.667 0.00 0.00 0.00 4.85
316 322 3.317149 GGGTATTTTTGGATTCTACCCGC 59.683 47.826 0.61 0.00 41.46 6.13
319 325 5.299531 GCTGAGGGTATTTTTGGATTCTACC 59.700 44.000 0.00 0.00 0.00 3.18
320 326 5.299531 GGCTGAGGGTATTTTTGGATTCTAC 59.700 44.000 0.00 0.00 0.00 2.59
322 328 4.264352 TGGCTGAGGGTATTTTTGGATTCT 60.264 41.667 0.00 0.00 0.00 2.40
342 368 4.156556 TGAATAAGCTTGACATCTTGTGGC 59.843 41.667 9.86 0.00 35.91 5.01
389 415 4.277423 TCTCGATCTAGTTGTGTGTTGACA 59.723 41.667 0.00 0.00 0.00 3.58
390 416 4.795268 TCTCGATCTAGTTGTGTGTTGAC 58.205 43.478 0.00 0.00 0.00 3.18
391 417 5.447624 TTCTCGATCTAGTTGTGTGTTGA 57.552 39.130 0.00 0.00 0.00 3.18
392 418 4.090642 GCTTCTCGATCTAGTTGTGTGTTG 59.909 45.833 0.00 0.00 0.00 3.33
393 419 4.238514 GCTTCTCGATCTAGTTGTGTGTT 58.761 43.478 0.00 0.00 0.00 3.32
394 420 3.255888 TGCTTCTCGATCTAGTTGTGTGT 59.744 43.478 0.00 0.00 0.00 3.72
395 421 3.610242 GTGCTTCTCGATCTAGTTGTGTG 59.390 47.826 0.00 0.00 0.00 3.82
396 422 3.508012 AGTGCTTCTCGATCTAGTTGTGT 59.492 43.478 0.00 0.00 0.00 3.72
397 423 4.101942 GAGTGCTTCTCGATCTAGTTGTG 58.898 47.826 0.00 0.00 33.25 3.33
398 424 4.364415 GAGTGCTTCTCGATCTAGTTGT 57.636 45.455 0.00 0.00 33.25 3.32
430 456 3.036084 CGCTGCCGTTTCGACTGT 61.036 61.111 0.00 0.00 0.00 3.55
605 652 3.645268 GAGGGGGTGCACATGGGAC 62.645 68.421 20.43 0.00 37.06 4.46
616 669 4.070265 TCGGATCGTGGAGGGGGT 62.070 66.667 0.00 0.00 0.00 4.95
676 733 2.042831 GCAGATGTGTGTGGGGAGC 61.043 63.158 0.00 0.00 0.00 4.70
689 746 1.605992 TGCTTGGCTGCTAGCAGAT 59.394 52.632 41.87 0.00 44.75 2.90
690 747 3.071575 TGCTTGGCTGCTAGCAGA 58.928 55.556 41.87 23.64 44.75 4.26
739 806 3.702048 TTGGGGAGACGGCCTTCG 61.702 66.667 3.18 0.00 45.88 3.79
830 897 4.619227 AACACTCACCACGGCCGG 62.619 66.667 31.76 18.27 0.00 6.13
869 939 1.002868 GGCAGGAGCAAGCAGAGAA 60.003 57.895 0.00 0.00 44.61 2.87
921 991 3.151022 GAGGAGGAGGGAGTGCGG 61.151 72.222 0.00 0.00 0.00 5.69
941 1011 2.629050 AATCATCACCCGCGTCCTCG 62.629 60.000 4.92 0.00 40.37 4.63
942 1012 0.876342 GAATCATCACCCGCGTCCTC 60.876 60.000 4.92 0.00 0.00 3.71
944 1014 0.532862 ATGAATCATCACCCGCGTCC 60.533 55.000 4.92 0.00 38.69 4.79
945 1015 0.861837 GATGAATCATCACCCGCGTC 59.138 55.000 17.60 0.00 40.28 5.19
946 1016 0.465705 AGATGAATCATCACCCGCGT 59.534 50.000 23.41 0.00 42.72 6.01
947 1017 1.528586 GAAGATGAATCATCACCCGCG 59.471 52.381 23.41 0.00 42.72 6.46
948 1018 2.564771 TGAAGATGAATCATCACCCGC 58.435 47.619 23.41 9.23 42.72 6.13
955 1025 5.238624 ACGGATGGATGAAGATGAATCAT 57.761 39.130 0.00 0.00 40.14 2.45
956 1026 4.694760 ACGGATGGATGAAGATGAATCA 57.305 40.909 0.00 0.00 0.00 2.57
957 1027 6.401394 TCATACGGATGGATGAAGATGAATC 58.599 40.000 8.02 0.00 33.49 2.52
958 1028 6.364568 TCATACGGATGGATGAAGATGAAT 57.635 37.500 8.02 0.00 33.49 2.57
959 1029 5.806654 TCATACGGATGGATGAAGATGAA 57.193 39.130 8.02 0.00 33.49 2.57
972 1042 1.768275 TCAGTTGCCCATCATACGGAT 59.232 47.619 0.00 0.00 36.39 4.18
973 1043 1.199615 TCAGTTGCCCATCATACGGA 58.800 50.000 0.00 0.00 0.00 4.69
976 1046 7.275888 TCAATTAATCAGTTGCCCATCATAC 57.724 36.000 0.00 0.00 0.00 2.39
1047 1120 1.068741 AGCGAGAAGAAACCAACGAGT 59.931 47.619 0.00 0.00 0.00 4.18
1053 1126 1.667830 CGCCAGCGAGAAGAAACCA 60.668 57.895 6.06 0.00 42.83 3.67
1139 1212 1.745489 GCTGGTTTACCTCGCCCTG 60.745 63.158 0.00 0.00 36.82 4.45
1152 1225 0.242017 GCGAAATGAAGCAAGCTGGT 59.758 50.000 0.00 0.00 0.00 4.00
1153 1226 0.457337 GGCGAAATGAAGCAAGCTGG 60.457 55.000 0.00 0.00 34.54 4.85
1154 1227 0.524862 AGGCGAAATGAAGCAAGCTG 59.475 50.000 0.00 0.00 34.54 4.24
1155 1228 1.068055 CAAGGCGAAATGAAGCAAGCT 60.068 47.619 0.00 0.00 34.54 3.74
1246 1335 0.537371 CAAGGGAGCACGGGAAAGTT 60.537 55.000 0.00 0.00 0.00 2.66
1326 1422 7.172875 CACTTGCAGGGATATTCTGAAATCTAG 59.827 40.741 0.00 0.00 34.36 2.43
1362 1472 3.506455 TCTCGTTCCTTTCTCGAACTCAT 59.494 43.478 0.00 0.00 37.96 2.90
1364 1474 3.188873 TCTCTCGTTCCTTTCTCGAACTC 59.811 47.826 0.00 0.00 37.96 3.01
1395 1505 7.306283 CCTGTAAATTTTCGAAAACAATTCGCA 60.306 33.333 24.68 17.99 41.30 5.10
1400 1510 6.704050 CCCACCTGTAAATTTTCGAAAACAAT 59.296 34.615 24.68 15.66 0.00 2.71
1403 1513 5.593968 ACCCACCTGTAAATTTTCGAAAAC 58.406 37.500 24.68 13.74 0.00 2.43
1423 1570 5.176592 AGTATCTCGCAAACTTAGAAACCC 58.823 41.667 0.00 0.00 0.00 4.11
1471 1678 7.466746 TGCTAAAATCATATAAATGCCCCTC 57.533 36.000 0.00 0.00 32.76 4.30
1485 1692 3.191791 GCCCCGTACTTTTGCTAAAATCA 59.808 43.478 0.00 0.00 0.00 2.57
1523 1733 3.458163 GGCACGGATGAGGACGGA 61.458 66.667 0.00 0.00 0.00 4.69
1584 1805 0.458669 AATACAGCTGTCGTACCGGG 59.541 55.000 25.56 0.00 0.00 5.73
1586 1807 2.182825 GTGAATACAGCTGTCGTACCG 58.817 52.381 25.56 0.00 0.00 4.02
1587 1808 2.537401 GGTGAATACAGCTGTCGTACC 58.463 52.381 25.56 21.94 40.78 3.34
1588 1809 2.182825 CGGTGAATACAGCTGTCGTAC 58.817 52.381 25.56 17.30 41.65 3.67
1668 1889 0.525311 GCTTTGCTTTCAGAGAGGCC 59.475 55.000 0.00 0.00 0.00 5.19
1840 2067 4.664677 GCCGGCGTGTCAGTGAGT 62.665 66.667 12.58 0.00 0.00 3.41
1879 2106 2.552315 CAACAACTTTCCATAGCGGTGT 59.448 45.455 0.00 0.00 35.57 4.16
1992 2219 6.483405 AACACTAGCTAACTAGAGTACCAGT 58.517 40.000 7.18 0.00 45.90 4.00
1993 2220 8.503458 TTAACACTAGCTAACTAGAGTACCAG 57.497 38.462 7.18 0.00 45.90 4.00
1994 2221 9.118300 GATTAACACTAGCTAACTAGAGTACCA 57.882 37.037 7.18 0.00 45.90 3.25
2002 2229 7.398047 TGACCCAAGATTAACACTAGCTAACTA 59.602 37.037 0.00 0.00 0.00 2.24
2022 2278 2.105821 CCACAGACTTTAACCTGACCCA 59.894 50.000 0.00 0.00 34.65 4.51
2042 2302 2.484889 GCATGTACGGAAAGAGATCCC 58.515 52.381 0.00 0.00 36.00 3.85
2057 2317 1.763968 TCTAGAGTAGCCACGCATGT 58.236 50.000 0.00 0.00 0.00 3.21
2162 2589 2.498941 CGAGCCGATAAGCCCTCCA 61.499 63.158 0.00 0.00 0.00 3.86
2164 2591 1.007154 GACGAGCCGATAAGCCCTC 60.007 63.158 1.50 0.00 0.00 4.30
2200 2627 7.441903 AAAGAATCATGGGGAAATAATTGCT 57.558 32.000 0.00 0.00 0.00 3.91
2274 2701 5.647658 CACTCATAATTTTCACACTAGGCCA 59.352 40.000 5.01 0.00 0.00 5.36
2275 2702 5.449177 GCACTCATAATTTTCACACTAGGCC 60.449 44.000 0.00 0.00 0.00 5.19
2298 2731 2.027837 ACAAAAGGAGCATGATTTGGGC 60.028 45.455 0.00 0.00 37.15 5.36
2344 2783 0.319641 GCCGTCTCAGGAAAGTTCGT 60.320 55.000 0.00 0.00 0.00 3.85
2380 2819 1.112113 TAGAGGGGCTGACTTAAGCG 58.888 55.000 1.29 0.00 44.52 4.68
2408 2847 5.815964 AACCAATATTTTTCGACGTTTGC 57.184 34.783 0.00 0.00 0.00 3.68
2420 2860 7.702348 GCGAGCATTTTCTTCTAACCAATATTT 59.298 33.333 0.00 0.00 0.00 1.40
2423 2863 5.220586 CGCGAGCATTTTCTTCTAACCAATA 60.221 40.000 0.00 0.00 0.00 1.90
2443 2883 1.005037 ATCAAACAGACTGGCGCGA 60.005 52.632 12.10 0.00 0.00 5.87
2526 3130 2.107204 GGGATAGATGGCCAAGTGATGT 59.893 50.000 10.96 0.00 0.00 3.06
2529 3133 0.758734 CGGGATAGATGGCCAAGTGA 59.241 55.000 10.96 0.00 0.00 3.41
2543 3147 8.257306 ACAAATAAATAAATTCAGCAACGGGAT 58.743 29.630 0.00 0.00 0.00 3.85
2633 3237 9.268268 CGGTAATAACAGAATAAATTCAGGCTA 57.732 33.333 5.55 0.00 39.23 3.93
2651 3255 3.815962 TGCTTTGCACTGTTCGGTAATAA 59.184 39.130 0.00 0.00 31.71 1.40
2652 3256 3.403968 TGCTTTGCACTGTTCGGTAATA 58.596 40.909 0.00 0.00 31.71 0.98
2653 3257 2.226330 TGCTTTGCACTGTTCGGTAAT 58.774 42.857 0.00 0.00 31.71 1.89
2674 3279 3.069289 CAAAATTCCCAAGCTTTCTGCC 58.931 45.455 0.00 0.00 44.23 4.85
2676 3281 6.335777 CCTATCAAAATTCCCAAGCTTTCTG 58.664 40.000 0.00 0.00 0.00 3.02
2684 3290 3.481559 TGGCCCTATCAAAATTCCCAA 57.518 42.857 0.00 0.00 0.00 4.12
2797 3403 2.547299 GCAATCTAGCATGCTCTCCT 57.453 50.000 26.57 4.86 39.46 3.69
2831 3437 1.210931 TCCGTCGTGGAAAGCTACG 59.789 57.895 0.21 0.21 46.38 3.51
2853 3459 3.088552 CTGCGCTATTTTAAACGAACCG 58.911 45.455 9.73 0.00 0.00 4.44
2855 3461 4.330740 TCCTGCGCTATTTTAAACGAAC 57.669 40.909 9.73 0.00 0.00 3.95
2886 3493 5.650543 GAAGAAGAAGCTAGAAGGAGACAG 58.349 45.833 0.00 0.00 0.00 3.51
2891 3498 3.093057 AGCGAAGAAGAAGCTAGAAGGA 58.907 45.455 0.00 0.00 39.74 3.36
2923 3530 0.984230 AGAAGCGGACAAATCCTGGA 59.016 50.000 0.00 0.00 43.73 3.86
2925 3532 1.740025 GGAAGAAGCGGACAAATCCTG 59.260 52.381 0.00 0.00 43.73 3.86
2979 3586 0.763652 ATCTGCAGGCATCCACTAGG 59.236 55.000 15.13 0.00 0.00 3.02
3411 4026 1.302033 CCGGTCTTGACAAGCAGCT 60.302 57.895 10.50 0.00 0.00 4.24
4081 5087 2.249309 CGCAGGTTGTCGTTGCTG 59.751 61.111 0.00 0.00 0.00 4.41
4702 5724 5.548406 TCCTTGCTTTACTTCCTAGTGAAC 58.452 41.667 0.00 0.00 35.78 3.18
4782 5804 1.483827 TCTGCACTGCCTTCATAGAGG 59.516 52.381 0.00 0.00 39.93 3.69
4822 5844 3.810310 AAAAGGTTCAAATCGGCAACA 57.190 38.095 0.00 0.00 0.00 3.33
4901 5923 7.011482 AGCCTAAGTTAAAGAACTAATGCATCG 59.989 37.037 0.00 0.00 45.50 3.84
4996 6026 5.383476 CAGAGATCAGAATTGGCCCTAAAT 58.617 41.667 0.00 0.00 0.00 1.40
5092 6124 6.873076 TGCAACAATTATTTCATCAAGGAACC 59.127 34.615 0.00 0.00 0.00 3.62
5126 6285 6.057533 TGTCCCTATCATGCTTTTCATACTG 58.942 40.000 0.00 0.00 33.19 2.74
5173 6349 3.619929 GCAATGGCATCCAGAAAAATCAC 59.380 43.478 0.00 0.00 36.75 3.06
5184 6360 3.585990 CGGACGGCAATGGCATCC 61.586 66.667 12.08 12.08 43.71 3.51
5189 6365 1.153249 ATGTACCGGACGGCAATGG 60.153 57.895 9.46 0.00 39.32 3.16
5351 6719 6.436261 CAGATTTATCAACCATCATCTGCAC 58.564 40.000 0.00 0.00 33.29 4.57
5369 6737 4.141158 ACTGACCTTTCACCTTCCAGATTT 60.141 41.667 0.00 0.00 0.00 2.17
5423 6791 3.755378 GCTCATCACTTCATCAGTTTGGT 59.245 43.478 0.00 0.00 30.92 3.67
5424 6792 3.128242 GGCTCATCACTTCATCAGTTTGG 59.872 47.826 0.00 0.00 30.92 3.28
5453 7237 1.656652 GGATTCCTGTCCGACACATG 58.343 55.000 0.00 0.00 33.23 3.21
5479 7263 2.863658 GTGTTTGCACGTGAGAGATC 57.136 50.000 22.23 0.00 35.75 2.75
5564 7348 7.397192 ACATACATTTTCTTTGCCATCCTTAGT 59.603 33.333 0.00 0.00 0.00 2.24
5565 7349 7.775120 ACATACATTTTCTTTGCCATCCTTAG 58.225 34.615 0.00 0.00 0.00 2.18
5566 7350 7.415095 CGACATACATTTTCTTTGCCATCCTTA 60.415 37.037 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.