Multiple sequence alignment - TraesCS1D01G220500

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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 TraesCS1D01G220500 chr1D 100.000 3497 0 0 1 3497 308260423 308263919 0.000000e+00 6458.0
1 TraesCS1D01G220500 chr1A 92.046 3206 151 44 6 3170 387514546 387517688 0.000000e+00 4412.0
2 TraesCS1D01G220500 chr1A 87.296 307 21 7 3203 3497 387517689 387517989 5.590000e-88 335.0
3 TraesCS1D01G220500 chr1A 88.415 164 17 2 415 577 71070595 71070757 2.750000e-46 196.0
4 TraesCS1D01G220500 chr1B 91.684 2922 154 44 596 3497 417399861 417402713 0.000000e+00 3967.0
5 TraesCS1D01G220500 chr1B 89.130 230 24 1 303 531 417399630 417399859 5.710000e-73 285.0
6 TraesCS1D01G220500 chr5B 92.963 1080 51 12 817 1891 443697343 443698402 0.000000e+00 1550.0
7 TraesCS1D01G220500 chr3B 94.453 685 36 2 1207 1891 400612120 400611438 0.000000e+00 1053.0
8 TraesCS1D01G220500 chr3B 82.302 582 63 19 960 1527 22400972 22401527 5.290000e-128 468.0
9 TraesCS1D01G220500 chr3B 87.135 171 19 2 411 580 474144069 474143901 1.280000e-44 191.0
10 TraesCS1D01G220500 chr3B 75.148 169 39 3 1691 1856 630401498 630401330 3.740000e-10 76.8
11 TraesCS1D01G220500 chr4B 84.388 474 42 19 963 1430 626628964 626628517 1.490000e-118 436.0
12 TraesCS1D01G220500 chr3D 85.149 202 28 2 1657 1857 62329618 62329818 4.580000e-49 206.0
13 TraesCS1D01G220500 chr3D 82.558 86 10 5 1719 1801 23173695 23173612 1.740000e-08 71.3
14 TraesCS1D01G220500 chr3D 73.718 156 37 3 1649 1802 64644466 64644619 1.360000e-04 58.4
15 TraesCS1D01G220500 chr7D 88.690 168 16 2 414 580 454079409 454079244 5.920000e-48 202.0
16 TraesCS1D01G220500 chr3A 84.653 202 29 2 1657 1857 71224690 71224890 2.130000e-47 200.0
17 TraesCS1D01G220500 chrUn 88.485 165 14 5 414 577 96478224 96478384 9.900000e-46 195.0
18 TraesCS1D01G220500 chr6B 87.805 164 16 3 415 577 415731743 415731903 4.610000e-44 189.0
19 TraesCS1D01G220500 chr6B 87.805 164 17 2 415 577 489430688 489430849 4.610000e-44 189.0
20 TraesCS1D01G220500 chr2B 87.425 167 17 3 415 580 76096776 76096613 4.610000e-44 189.0


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 TraesCS1D01G220500 chr1D 308260423 308263919 3496 False 6458.0 6458 100.000 1 3497 1 chr1D.!!$F1 3496
1 TraesCS1D01G220500 chr1A 387514546 387517989 3443 False 2373.5 4412 89.671 6 3497 2 chr1A.!!$F2 3491
2 TraesCS1D01G220500 chr1B 417399630 417402713 3083 False 2126.0 3967 90.407 303 3497 2 chr1B.!!$F1 3194
3 TraesCS1D01G220500 chr5B 443697343 443698402 1059 False 1550.0 1550 92.963 817 1891 1 chr5B.!!$F1 1074
4 TraesCS1D01G220500 chr3B 400611438 400612120 682 True 1053.0 1053 94.453 1207 1891 1 chr3B.!!$R1 684
5 TraesCS1D01G220500 chr3B 22400972 22401527 555 False 468.0 468 82.302 960 1527 1 chr3B.!!$F1 567

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
106 107 0.033601 AGCAGTCTCCGAGATGAGGT 60.034 55.0 0.33 0.0 33.04 3.85 F
386 388 0.179004 TGGTCCACCGTGCAATTTCT 60.179 50.0 0.00 0.0 39.43 2.52 F
1891 2002 0.452184 ACAGCTACGACGATCAGGTG 59.548 55.0 19.00 19.0 42.16 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1765 0.546122 CGGTCCATGGAATCCCTGAA 59.454 55.000 18.20 0.0 0.0 3.02 R
2194 2321 1.135199 CCTGCATCTGGATGTTGTTGC 60.135 52.381 11.52 0.0 40.8 4.17 R
2982 3123 0.173708 GGACCGATGAGTGAGTGGAC 59.826 60.000 0.00 0.0 0.0 4.02 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
67 68 2.365095 CTAAGCCGCGGAGGTTAGGG 62.365 65.000 33.48 8.13 43.70 3.53
76 77 2.817901 CGGAGGTTAGGGACAAATACG 58.182 52.381 0.00 0.00 0.00 3.06
90 91 0.616371 AATACGTAGGTTGGGCAGCA 59.384 50.000 0.08 0.00 0.00 4.41
100 101 3.071206 GGGCAGCAGTCTCCGAGA 61.071 66.667 0.00 0.00 0.00 4.04
106 107 0.033601 AGCAGTCTCCGAGATGAGGT 60.034 55.000 0.33 0.00 33.04 3.85
114 115 3.885976 TCCGAGATGAGGTAGGAGAAT 57.114 47.619 0.00 0.00 0.00 2.40
115 116 4.995624 TCCGAGATGAGGTAGGAGAATA 57.004 45.455 0.00 0.00 0.00 1.75
116 117 5.522315 TCCGAGATGAGGTAGGAGAATAT 57.478 43.478 0.00 0.00 0.00 1.28
118 119 6.416415 TCCGAGATGAGGTAGGAGAATATAC 58.584 44.000 0.00 0.00 0.00 1.47
123 124 8.245929 AGATGAGGTAGGAGAATATACCCTAA 57.754 38.462 0.00 0.00 42.10 2.69
143 144 9.020731 ACCCTAATTTTTGTTACTGGAGTTATG 57.979 33.333 0.00 0.00 0.00 1.90
149 150 5.699097 TTGTTACTGGAGTTATGGTTTGC 57.301 39.130 0.00 0.00 0.00 3.68
221 222 1.117150 GTATGAGGAGGCCAACGGTA 58.883 55.000 5.01 0.00 0.00 4.02
242 243 2.153645 GCAGTGTTGATGGTGATGTCA 58.846 47.619 0.00 0.00 0.00 3.58
245 246 2.039480 AGTGTTGATGGTGATGTCAGCT 59.961 45.455 12.75 0.00 44.12 4.24
272 273 3.945285 GGCGGGAAAATAAGAAGTGATGA 59.055 43.478 0.00 0.00 0.00 2.92
278 279 7.550712 GGGAAAATAAGAAGTGATGATGCTTT 58.449 34.615 0.00 0.00 0.00 3.51
279 280 8.037166 GGGAAAATAAGAAGTGATGATGCTTTT 58.963 33.333 0.00 0.00 0.00 2.27
310 312 5.590259 CAGTGAATAAACGGGGAATGAGAAT 59.410 40.000 0.00 0.00 0.00 2.40
313 315 6.263168 GTGAATAAACGGGGAATGAGAATGAT 59.737 38.462 0.00 0.00 0.00 2.45
321 323 4.141390 GGGGAATGAGAATGATAGTGGTGT 60.141 45.833 0.00 0.00 0.00 4.16
386 388 0.179004 TGGTCCACCGTGCAATTTCT 60.179 50.000 0.00 0.00 39.43 2.52
387 389 0.958822 GGTCCACCGTGCAATTTCTT 59.041 50.000 0.00 0.00 0.00 2.52
388 390 1.068541 GGTCCACCGTGCAATTTCTTC 60.069 52.381 0.00 0.00 0.00 2.87
389 391 1.606668 GTCCACCGTGCAATTTCTTCA 59.393 47.619 0.00 0.00 0.00 3.02
402 408 8.233190 GTGCAATTTCTTCATAGCCTATGTATC 58.767 37.037 11.36 0.00 37.45 2.24
476 486 7.709269 TTCAATAAAGACTACATACGGATGC 57.291 36.000 7.78 0.00 36.43 3.91
527 538 8.902540 TCACTCATTTTGTTCTGTATGTACTT 57.097 30.769 0.00 0.00 0.00 2.24
534 598 6.795098 TTGTTCTGTATGTACTTCGCATTT 57.205 33.333 0.00 0.00 0.00 2.32
535 599 6.795098 TGTTCTGTATGTACTTCGCATTTT 57.205 33.333 0.00 0.00 0.00 1.82
536 600 6.598525 TGTTCTGTATGTACTTCGCATTTTG 58.401 36.000 0.00 0.00 0.00 2.44
537 601 5.794687 TCTGTATGTACTTCGCATTTTGG 57.205 39.130 0.00 0.00 0.00 3.28
538 602 5.483811 TCTGTATGTACTTCGCATTTTGGA 58.516 37.500 0.00 0.00 0.00 3.53
539 603 5.935206 TCTGTATGTACTTCGCATTTTGGAA 59.065 36.000 0.00 0.00 0.00 3.53
540 604 6.597672 TCTGTATGTACTTCGCATTTTGGAAT 59.402 34.615 0.00 0.00 0.00 3.01
541 605 6.781138 TGTATGTACTTCGCATTTTGGAATC 58.219 36.000 0.00 0.00 0.00 2.52
542 606 6.597672 TGTATGTACTTCGCATTTTGGAATCT 59.402 34.615 0.00 0.00 0.00 2.40
543 607 5.545658 TGTACTTCGCATTTTGGAATCTC 57.454 39.130 0.00 0.00 0.00 2.75
544 608 5.245531 TGTACTTCGCATTTTGGAATCTCT 58.754 37.500 0.00 0.00 0.00 3.10
545 609 6.403049 TGTACTTCGCATTTTGGAATCTCTA 58.597 36.000 0.00 0.00 0.00 2.43
546 610 6.876789 TGTACTTCGCATTTTGGAATCTCTAA 59.123 34.615 0.00 0.00 0.00 2.10
547 611 6.817765 ACTTCGCATTTTGGAATCTCTAAA 57.182 33.333 0.00 0.00 0.00 1.85
548 612 6.612306 ACTTCGCATTTTGGAATCTCTAAAC 58.388 36.000 0.00 0.00 0.00 2.01
549 613 6.206634 ACTTCGCATTTTGGAATCTCTAAACA 59.793 34.615 0.00 0.00 0.00 2.83
550 614 6.182039 TCGCATTTTGGAATCTCTAAACAG 57.818 37.500 0.00 0.00 0.00 3.16
551 615 5.937540 TCGCATTTTGGAATCTCTAAACAGA 59.062 36.000 0.00 0.00 0.00 3.41
552 616 6.024049 CGCATTTTGGAATCTCTAAACAGAC 58.976 40.000 0.00 0.00 0.00 3.51
553 617 6.128172 CGCATTTTGGAATCTCTAAACAGACT 60.128 38.462 0.00 0.00 0.00 3.24
554 618 7.573843 CGCATTTTGGAATCTCTAAACAGACTT 60.574 37.037 0.00 0.00 0.00 3.01
555 619 8.730680 GCATTTTGGAATCTCTAAACAGACTTA 58.269 33.333 0.00 0.00 0.00 2.24
572 636 8.888579 ACAGACTTATATTTATGAACGAAGGG 57.111 34.615 0.00 0.00 0.00 3.95
573 637 8.701895 ACAGACTTATATTTATGAACGAAGGGA 58.298 33.333 0.00 0.00 0.00 4.20
574 638 9.197694 CAGACTTATATTTATGAACGAAGGGAG 57.802 37.037 0.00 0.00 0.00 4.30
575 639 8.925338 AGACTTATATTTATGAACGAAGGGAGT 58.075 33.333 0.00 0.00 0.00 3.85
583 647 9.855021 ATTTATGAACGAAGGGAGTAATTTTTG 57.145 29.630 0.00 0.00 0.00 2.44
584 648 8.624367 TTATGAACGAAGGGAGTAATTTTTGA 57.376 30.769 0.00 0.00 0.00 2.69
585 649 6.945938 TGAACGAAGGGAGTAATTTTTGAA 57.054 33.333 0.00 0.00 0.00 2.69
586 650 7.336161 TGAACGAAGGGAGTAATTTTTGAAA 57.664 32.000 0.00 0.00 0.00 2.69
587 651 7.773149 TGAACGAAGGGAGTAATTTTTGAAAA 58.227 30.769 0.00 0.00 0.00 2.29
588 652 8.251721 TGAACGAAGGGAGTAATTTTTGAAAAA 58.748 29.630 5.47 5.47 0.00 1.94
589 653 9.256477 GAACGAAGGGAGTAATTTTTGAAAAAT 57.744 29.630 9.92 9.92 0.00 1.82
590 654 9.607988 AACGAAGGGAGTAATTTTTGAAAAATT 57.392 25.926 25.96 25.96 34.55 1.82
623 687 2.611225 AGGCAGAAGATTAAGGAGCG 57.389 50.000 0.00 0.00 0.00 5.03
656 720 6.588719 TGCTTGTGCTAAAAGTATGGAAAT 57.411 33.333 0.00 0.00 40.48 2.17
784 854 2.283966 AGACGGTAGCAGGTGCCT 60.284 61.111 5.11 0.00 43.38 4.75
840 910 4.747218 GAGTCAGTCTCTCCCGGT 57.253 61.111 0.00 0.00 39.86 5.28
843 913 2.053277 GTCAGTCTCTCCCGGTCCC 61.053 68.421 0.00 0.00 0.00 4.46
844 914 3.141488 CAGTCTCTCCCGGTCCCG 61.141 72.222 0.00 0.00 39.44 5.14
1327 1418 2.180276 TCTTCTACCCTCCTGTCTTGC 58.820 52.381 0.00 0.00 0.00 4.01
1465 1572 2.228822 CGAGTGGAAATTTTGTCCTGGG 59.771 50.000 0.00 0.00 36.03 4.45
1493 1600 9.357652 CAAAGAAATCAAGAAACTGAGTTGAAA 57.642 29.630 0.00 0.00 34.00 2.69
1495 1602 7.484140 AGAAATCAAGAAACTGAGTTGAAACC 58.516 34.615 0.00 0.00 34.00 3.27
1605 1715 2.753452 CTCCGTGTTGCTTCCTAGTAGA 59.247 50.000 0.00 0.00 0.00 2.59
1654 1765 5.278660 GCAAGTGGTTGATTGAGATTCTGTT 60.279 40.000 0.00 0.00 35.46 3.16
1891 2002 0.452184 ACAGCTACGACGATCAGGTG 59.548 55.000 19.00 19.00 42.16 4.00
1903 2014 2.037620 ATCAGGTGCTCGGATCCAGC 62.038 60.000 22.16 22.16 37.40 4.85
1942 2056 1.484653 TCCAAACATCCATCGGATCGT 59.515 47.619 0.00 0.00 40.98 3.73
1997 2112 2.356665 TTGGTTTCAGCTGCCAAGTA 57.643 45.000 17.36 0.00 37.36 2.24
2194 2321 1.751927 GAGGCATCAGGGGCAACAG 60.752 63.158 0.00 0.00 39.74 3.16
2204 2331 0.319813 GGGGCAACAGCAACAACATC 60.320 55.000 0.00 0.00 39.74 3.06
2223 2350 1.565759 TCCAGATGCAGGTAAAGCCAT 59.434 47.619 0.00 0.00 40.61 4.40
2224 2351 2.025037 TCCAGATGCAGGTAAAGCCATT 60.025 45.455 0.00 0.00 40.61 3.16
2226 2353 3.953612 CCAGATGCAGGTAAAGCCATTTA 59.046 43.478 0.00 0.00 40.61 1.40
2227 2354 4.037208 CCAGATGCAGGTAAAGCCATTTAG 59.963 45.833 0.00 0.00 40.61 1.85
2228 2355 3.633986 AGATGCAGGTAAAGCCATTTAGC 59.366 43.478 0.00 2.54 45.55 3.09
2229 2356 2.801483 TGCAGGTAAAGCCATTTAGCA 58.199 42.857 11.25 0.00 46.90 3.49
2230 2357 2.491693 TGCAGGTAAAGCCATTTAGCAC 59.508 45.455 11.25 5.00 46.90 4.40
2231 2358 2.159240 GCAGGTAAAGCCATTTAGCACC 60.159 50.000 11.25 0.00 46.90 5.01
2232 2359 3.356290 CAGGTAAAGCCATTTAGCACCT 58.644 45.455 11.25 1.47 46.90 4.00
2233 2360 3.763897 CAGGTAAAGCCATTTAGCACCTT 59.236 43.478 11.25 0.00 46.90 3.50
2234 2361 4.220602 CAGGTAAAGCCATTTAGCACCTTT 59.779 41.667 11.25 0.00 46.90 3.11
2235 2362 5.417580 CAGGTAAAGCCATTTAGCACCTTTA 59.582 40.000 11.25 0.00 46.90 1.85
2236 2363 5.652452 AGGTAAAGCCATTTAGCACCTTTAG 59.348 40.000 11.25 0.00 46.90 1.85
2247 2374 7.900782 TTTAGCACCTTTAGTTACATCTGAC 57.099 36.000 0.00 0.00 0.00 3.51
2253 2380 7.624344 GCACCTTTAGTTACATCTGACAACATC 60.624 40.741 0.00 0.00 0.00 3.06
2318 2446 0.402121 GGTCCTTTCTTCTGGCAGGT 59.598 55.000 15.73 0.00 0.00 4.00
2322 2450 2.174639 TCCTTTCTTCTGGCAGGTTGAA 59.825 45.455 15.73 13.15 0.00 2.69
2418 2546 0.401356 TGGAGCTGGCAATGTCTTCA 59.599 50.000 0.00 0.00 0.00 3.02
2571 2704 1.456296 CAGCTTAGCTTCATGTGGCA 58.544 50.000 3.00 0.00 36.40 4.92
2597 2730 1.602377 GTTCTTGTTGCCGTGCTAACT 59.398 47.619 0.00 0.00 0.00 2.24
2599 2732 1.871039 TCTTGTTGCCGTGCTAACTTC 59.129 47.619 0.00 0.00 0.00 3.01
2604 2737 0.531090 TGCCGTGCTAACTTCGTTGT 60.531 50.000 0.00 0.00 0.00 3.32
2720 2856 7.255660 CCAGAGAGGATATGTAGTAGGTTTGTC 60.256 44.444 0.00 0.00 41.22 3.18
2740 2876 7.915293 TTGTCTGTAATGTATGGTTACCAAG 57.085 36.000 8.63 0.00 36.95 3.61
2846 2987 2.223089 CGCTCATGAATTGAATCACGCA 60.223 45.455 0.00 0.00 32.78 5.24
2847 2988 3.728566 CGCTCATGAATTGAATCACGCAA 60.729 43.478 0.00 0.00 32.78 4.85
2848 2989 3.789756 GCTCATGAATTGAATCACGCAAG 59.210 43.478 0.00 0.00 37.34 4.01
2920 3061 1.003233 ACGGCTTCTTTCTCTGCCC 60.003 57.895 0.00 0.00 42.15 5.36
2977 3118 0.605860 CTCTGCCTGCACTTTGCTCT 60.606 55.000 0.00 0.00 45.31 4.09
2978 3119 0.604780 TCTGCCTGCACTTTGCTCTC 60.605 55.000 0.00 0.00 45.31 3.20
2982 3123 0.809385 CCTGCACTTTGCTCTCCATG 59.191 55.000 0.00 0.00 45.31 3.66
2983 3124 1.531423 CTGCACTTTGCTCTCCATGT 58.469 50.000 0.00 0.00 45.31 3.21
2984 3125 1.467734 CTGCACTTTGCTCTCCATGTC 59.532 52.381 0.00 0.00 45.31 3.06
2985 3126 0.807496 GCACTTTGCTCTCCATGTCC 59.193 55.000 0.00 0.00 40.96 4.02
2986 3127 1.883638 GCACTTTGCTCTCCATGTCCA 60.884 52.381 0.00 0.00 40.96 4.02
2987 3128 1.808945 CACTTTGCTCTCCATGTCCAC 59.191 52.381 0.00 0.00 0.00 4.02
2988 3129 1.701847 ACTTTGCTCTCCATGTCCACT 59.298 47.619 0.00 0.00 0.00 4.00
2989 3130 2.289945 ACTTTGCTCTCCATGTCCACTC 60.290 50.000 0.00 0.00 0.00 3.51
2990 3131 1.351076 TTGCTCTCCATGTCCACTCA 58.649 50.000 0.00 0.00 0.00 3.41
2991 3132 0.610174 TGCTCTCCATGTCCACTCAC 59.390 55.000 0.00 0.00 0.00 3.51
2992 3133 0.901124 GCTCTCCATGTCCACTCACT 59.099 55.000 0.00 0.00 0.00 3.41
2993 3134 1.134848 GCTCTCCATGTCCACTCACTC 60.135 57.143 0.00 0.00 0.00 3.51
2994 3135 2.174360 CTCTCCATGTCCACTCACTCA 58.826 52.381 0.00 0.00 0.00 3.41
2997 3138 1.478105 TCCATGTCCACTCACTCATCG 59.522 52.381 0.00 0.00 0.00 3.84
3019 3160 1.138036 CATGGCACGGCAACATCAG 59.862 57.895 0.00 0.00 0.00 2.90
3078 3219 1.167851 GGCAGTTGTGATGCTAGCAA 58.832 50.000 23.54 2.55 43.35 3.91
3100 3241 1.202818 GGGAAGTGGACAGAAGCAACT 60.203 52.381 0.00 0.00 0.00 3.16
3115 3256 1.070105 AACTAGCGAAACCGTGCCA 59.930 52.632 0.00 0.00 0.00 4.92
3130 3271 3.308530 CGTGCCAAACTCAGATTTTTCC 58.691 45.455 0.00 0.00 0.00 3.13
3193 3336 3.430862 ATGTGCGCGGCGTGATTT 61.431 55.556 26.40 1.99 0.00 2.17
3207 3350 3.796844 GCGTGATTTCATCATCTCCTCGA 60.797 47.826 0.00 0.00 42.04 4.04
3247 3390 2.063266 CCTCGTCCGTTCATTCGAAAA 58.937 47.619 0.00 0.00 31.43 2.29
3310 3454 0.981277 CTACCCAGTCCCCATTCGGT 60.981 60.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.028476 TCACCACCGAACCACATAAGAG 60.028 50.000 0.00 0.00 0.00 2.85
3 4 1.972075 TCACCACCGAACCACATAAGA 59.028 47.619 0.00 0.00 0.00 2.10
57 58 3.900966 ACGTATTTGTCCCTAACCTCC 57.099 47.619 0.00 0.00 0.00 4.30
67 68 2.676342 CTGCCCAACCTACGTATTTGTC 59.324 50.000 13.28 7.49 0.00 3.18
76 77 0.391793 GAGACTGCTGCCCAACCTAC 60.392 60.000 0.00 0.00 0.00 3.18
90 91 2.105821 CTCCTACCTCATCTCGGAGACT 59.894 54.545 10.41 0.00 43.02 3.24
100 101 9.860393 AAATTAGGGTATATTCTCCTACCTCAT 57.140 33.333 0.00 0.00 37.98 2.90
118 119 8.466798 CCATAACTCCAGTAACAAAAATTAGGG 58.533 37.037 0.00 0.00 0.00 3.53
123 124 7.655732 GCAAACCATAACTCCAGTAACAAAAAT 59.344 33.333 0.00 0.00 0.00 1.82
143 144 0.395173 ATGTACCCCCATCGCAAACC 60.395 55.000 0.00 0.00 0.00 3.27
149 150 0.106708 CTCCACATGTACCCCCATCG 59.893 60.000 0.00 0.00 0.00 3.84
198 199 2.742116 TTGGCCTCCTCATACCCGC 61.742 63.158 3.32 0.00 0.00 6.13
208 209 2.125106 CTGCTACCGTTGGCCTCC 60.125 66.667 3.32 0.00 0.00 4.30
221 222 2.224597 TGACATCACCATCAACACTGCT 60.225 45.455 0.00 0.00 0.00 4.24
242 243 5.562298 TCTTATTTTCCCGCCTATTAGCT 57.438 39.130 0.00 0.00 0.00 3.32
245 246 6.891388 TCACTTCTTATTTTCCCGCCTATTA 58.109 36.000 0.00 0.00 0.00 0.98
272 273 7.754924 CGTTTATTCACTGTATCCAAAAAGCAT 59.245 33.333 0.00 0.00 0.00 3.79
278 279 4.944930 CCCCGTTTATTCACTGTATCCAAA 59.055 41.667 0.00 0.00 0.00 3.28
279 280 4.225492 TCCCCGTTTATTCACTGTATCCAA 59.775 41.667 0.00 0.00 0.00 3.53
295 296 4.444876 CCACTATCATTCTCATTCCCCGTT 60.445 45.833 0.00 0.00 0.00 4.44
299 300 5.041191 ACACCACTATCATTCTCATTCCC 57.959 43.478 0.00 0.00 0.00 3.97
310 312 5.656859 ACTGCACTATAGAACACCACTATCA 59.343 40.000 6.78 0.00 33.43 2.15
313 315 6.096423 CCTTACTGCACTATAGAACACCACTA 59.904 42.308 6.78 0.00 0.00 2.74
321 323 4.743651 GCCATGCCTTACTGCACTATAGAA 60.744 45.833 6.78 0.00 45.48 2.10
386 388 7.611770 ACTTTATGCGATACATAGGCTATGAA 58.388 34.615 34.80 16.75 42.20 2.57
387 389 7.170393 ACTTTATGCGATACATAGGCTATGA 57.830 36.000 34.80 20.96 42.20 2.15
388 390 8.926715 TTACTTTATGCGATACATAGGCTATG 57.073 34.615 28.48 28.48 42.20 2.23
402 408 5.287226 ACGAAGGGAGTATTACTTTATGCG 58.713 41.667 0.00 3.43 0.00 4.73
514 525 5.935206 TCCAAAATGCGAAGTACATACAGAA 59.065 36.000 0.00 0.00 0.00 3.02
517 528 6.597672 AGATTCCAAAATGCGAAGTACATACA 59.402 34.615 0.00 0.00 0.00 2.29
527 538 5.937540 TCTGTTTAGAGATTCCAAAATGCGA 59.062 36.000 0.00 0.00 0.00 5.10
546 610 9.326413 CCCTTCGTTCATAAATATAAGTCTGTT 57.674 33.333 0.00 0.00 0.00 3.16
547 611 8.701895 TCCCTTCGTTCATAAATATAAGTCTGT 58.298 33.333 0.00 0.00 0.00 3.41
548 612 9.197694 CTCCCTTCGTTCATAAATATAAGTCTG 57.802 37.037 0.00 0.00 0.00 3.51
549 613 8.925338 ACTCCCTTCGTTCATAAATATAAGTCT 58.075 33.333 0.00 0.00 0.00 3.24
557 621 9.855021 CAAAAATTACTCCCTTCGTTCATAAAT 57.145 29.630 0.00 0.00 0.00 1.40
558 622 9.069082 TCAAAAATTACTCCCTTCGTTCATAAA 57.931 29.630 0.00 0.00 0.00 1.40
559 623 8.624367 TCAAAAATTACTCCCTTCGTTCATAA 57.376 30.769 0.00 0.00 0.00 1.90
560 624 8.624367 TTCAAAAATTACTCCCTTCGTTCATA 57.376 30.769 0.00 0.00 0.00 2.15
561 625 7.519032 TTCAAAAATTACTCCCTTCGTTCAT 57.481 32.000 0.00 0.00 0.00 2.57
562 626 6.945938 TTCAAAAATTACTCCCTTCGTTCA 57.054 33.333 0.00 0.00 0.00 3.18
563 627 8.637281 TTTTTCAAAAATTACTCCCTTCGTTC 57.363 30.769 0.00 0.00 0.00 3.95
564 628 9.607988 AATTTTTCAAAAATTACTCCCTTCGTT 57.392 25.926 17.55 0.00 0.00 3.85
582 646 9.698309 TGCCTTCGTTTCAATATTAATTTTTCA 57.302 25.926 0.00 0.00 0.00 2.69
584 648 9.921637 TCTGCCTTCGTTTCAATATTAATTTTT 57.078 25.926 0.00 0.00 0.00 1.94
585 649 9.921637 TTCTGCCTTCGTTTCAATATTAATTTT 57.078 25.926 0.00 0.00 0.00 1.82
586 650 9.573133 CTTCTGCCTTCGTTTCAATATTAATTT 57.427 29.630 0.00 0.00 0.00 1.82
587 651 8.956426 TCTTCTGCCTTCGTTTCAATATTAATT 58.044 29.630 0.00 0.00 0.00 1.40
588 652 8.506168 TCTTCTGCCTTCGTTTCAATATTAAT 57.494 30.769 0.00 0.00 0.00 1.40
589 653 7.915293 TCTTCTGCCTTCGTTTCAATATTAA 57.085 32.000 0.00 0.00 0.00 1.40
590 654 8.506168 AATCTTCTGCCTTCGTTTCAATATTA 57.494 30.769 0.00 0.00 0.00 0.98
591 655 7.396540 AATCTTCTGCCTTCGTTTCAATATT 57.603 32.000 0.00 0.00 0.00 1.28
592 656 8.506168 TTAATCTTCTGCCTTCGTTTCAATAT 57.494 30.769 0.00 0.00 0.00 1.28
593 657 7.065803 CCTTAATCTTCTGCCTTCGTTTCAATA 59.934 37.037 0.00 0.00 0.00 1.90
594 658 6.127897 CCTTAATCTTCTGCCTTCGTTTCAAT 60.128 38.462 0.00 0.00 0.00 2.57
595 659 5.181245 CCTTAATCTTCTGCCTTCGTTTCAA 59.819 40.000 0.00 0.00 0.00 2.69
596 660 4.695455 CCTTAATCTTCTGCCTTCGTTTCA 59.305 41.667 0.00 0.00 0.00 2.69
597 661 4.935808 TCCTTAATCTTCTGCCTTCGTTTC 59.064 41.667 0.00 0.00 0.00 2.78
598 662 4.906618 TCCTTAATCTTCTGCCTTCGTTT 58.093 39.130 0.00 0.00 0.00 3.60
599 663 4.508662 CTCCTTAATCTTCTGCCTTCGTT 58.491 43.478 0.00 0.00 0.00 3.85
600 664 3.680196 GCTCCTTAATCTTCTGCCTTCGT 60.680 47.826 0.00 0.00 0.00 3.85
601 665 2.869192 GCTCCTTAATCTTCTGCCTTCG 59.131 50.000 0.00 0.00 0.00 3.79
602 666 2.869192 CGCTCCTTAATCTTCTGCCTTC 59.131 50.000 0.00 0.00 0.00 3.46
603 667 2.501723 TCGCTCCTTAATCTTCTGCCTT 59.498 45.455 0.00 0.00 0.00 4.35
656 720 7.507616 TCTGGAGTAGGCTTTTAATTCCAAAAA 59.492 33.333 0.00 0.00 0.00 1.94
784 854 2.884320 TGTCCTCACTGCCTACTTACA 58.116 47.619 0.00 0.00 0.00 2.41
844 914 3.767044 GAGGGAGGGAGGGAGAGCC 62.767 73.684 0.00 0.00 0.00 4.70
845 915 2.123033 GAGGGAGGGAGGGAGAGC 60.123 72.222 0.00 0.00 0.00 4.09
846 916 2.612251 GGAGGGAGGGAGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
847 917 3.036959 GGGAGGGAGGGAGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
848 918 4.179599 GGGGAGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1142 1227 3.154473 CGGGCAGGAGAATCGGGA 61.154 66.667 0.00 0.00 34.37 5.14
1327 1418 1.178276 AGAGCTCTCTACGGGTTGTG 58.822 55.000 11.45 0.00 38.35 3.33
1436 1543 4.984161 ACAAAATTTCCACTCGCAAATCAG 59.016 37.500 0.00 0.00 0.00 2.90
1444 1551 2.228822 CCCAGGACAAAATTTCCACTCG 59.771 50.000 0.00 0.00 35.33 4.18
1465 1572 8.184192 TCAACTCAGTTTCTTGATTTCTTTGAC 58.816 33.333 0.00 0.00 0.00 3.18
1493 1600 7.748677 TGATGATACATAAAGGTCATGATGGT 58.251 34.615 0.00 0.00 31.86 3.55
1605 1715 5.509840 GGCATGATTCATCGTACTAGGACTT 60.510 44.000 2.99 0.00 0.00 3.01
1654 1765 0.546122 CGGTCCATGGAATCCCTGAA 59.454 55.000 18.20 0.00 0.00 3.02
1867 1978 3.411418 ATCGTCGTAGCTGTGGCCG 62.411 63.158 0.00 0.00 39.73 6.13
1891 2002 2.932130 GAACTGGGCTGGATCCGAGC 62.932 65.000 21.31 21.31 35.64 5.03
1942 2056 3.999001 GAGTGCATATATTAGCTGCTGCA 59.001 43.478 18.42 9.43 42.74 4.41
1962 2076 9.346725 GCTGAAACCAAATTAAATTCAGTAGAG 57.653 33.333 17.35 0.00 45.43 2.43
1974 2089 3.640967 ACTTGGCAGCTGAAACCAAATTA 59.359 39.130 20.43 0.00 42.65 1.40
1997 2112 2.746472 GCTTGGTTCCAACACTCTGAGT 60.746 50.000 4.06 4.06 0.00 3.41
2085 2200 3.904136 AGCAGGAAACAAGATGAAACG 57.096 42.857 0.00 0.00 0.00 3.60
2194 2321 1.135199 CCTGCATCTGGATGTTGTTGC 60.135 52.381 11.52 0.00 40.80 4.17
2204 2331 2.062971 ATGGCTTTACCTGCATCTGG 57.937 50.000 0.00 0.00 40.22 3.86
2223 2350 7.446769 TGTCAGATGTAACTAAAGGTGCTAAA 58.553 34.615 0.00 0.00 0.00 1.85
2224 2351 6.999950 TGTCAGATGTAACTAAAGGTGCTAA 58.000 36.000 0.00 0.00 0.00 3.09
2226 2353 5.483685 TGTCAGATGTAACTAAAGGTGCT 57.516 39.130 0.00 0.00 0.00 4.40
2227 2354 5.468746 TGTTGTCAGATGTAACTAAAGGTGC 59.531 40.000 0.00 0.00 0.00 5.01
2228 2355 7.604164 AGATGTTGTCAGATGTAACTAAAGGTG 59.396 37.037 0.00 0.00 0.00 4.00
2229 2356 7.680730 AGATGTTGTCAGATGTAACTAAAGGT 58.319 34.615 0.00 0.00 0.00 3.50
2230 2357 8.553459 AAGATGTTGTCAGATGTAACTAAAGG 57.447 34.615 0.00 0.00 0.00 3.11
2231 2358 9.429359 AGAAGATGTTGTCAGATGTAACTAAAG 57.571 33.333 0.00 0.00 0.00 1.85
2232 2359 9.208022 CAGAAGATGTTGTCAGATGTAACTAAA 57.792 33.333 0.00 0.00 0.00 1.85
2233 2360 8.585018 TCAGAAGATGTTGTCAGATGTAACTAA 58.415 33.333 0.00 0.00 0.00 2.24
2234 2361 8.122472 TCAGAAGATGTTGTCAGATGTAACTA 57.878 34.615 0.00 0.00 0.00 2.24
2235 2362 6.997655 TCAGAAGATGTTGTCAGATGTAACT 58.002 36.000 0.00 0.00 0.00 2.24
2236 2363 7.682824 CATCAGAAGATGTTGTCAGATGTAAC 58.317 38.462 0.00 0.00 45.28 2.50
2253 2380 5.635280 CACACTGTGGTTACTACATCAGAAG 59.365 44.000 13.09 0.00 33.66 2.85
2264 2391 2.287009 GCTTTGCTCACACTGTGGTTAC 60.287 50.000 13.09 0.00 33.87 2.50
2265 2392 1.946768 GCTTTGCTCACACTGTGGTTA 59.053 47.619 13.09 0.00 33.87 2.85
2269 2396 2.857592 AAAGCTTTGCTCACACTGTG 57.142 45.000 11.80 6.19 38.25 3.66
2318 2446 5.924356 TCACATGGTCAGTTAGTTCTTCAA 58.076 37.500 0.00 0.00 0.00 2.69
2322 2450 5.808366 TCTTCACATGGTCAGTTAGTTCT 57.192 39.130 0.00 0.00 0.00 3.01
2325 2453 5.540337 TCTCTTCTTCACATGGTCAGTTAGT 59.460 40.000 0.00 0.00 0.00 2.24
2571 2704 0.110486 ACGGCAACAAGAACAGGGAT 59.890 50.000 0.00 0.00 0.00 3.85
2740 2876 8.909708 TGCAAGCACTGATAACATTAATTAAC 57.090 30.769 0.00 0.00 0.00 2.01
2794 2931 2.573340 GCCCTTCCAACGCCAATG 59.427 61.111 0.00 0.00 0.00 2.82
2846 2987 3.031013 CAAGAAACCAACCCCACTTCTT 58.969 45.455 0.00 0.00 36.92 2.52
2847 2988 2.024369 ACAAGAAACCAACCCCACTTCT 60.024 45.455 0.00 0.00 0.00 2.85
2848 2989 2.384828 ACAAGAAACCAACCCCACTTC 58.615 47.619 0.00 0.00 0.00 3.01
2920 3061 1.739562 GGAAGCTCAGAGCCACACG 60.740 63.158 19.40 0.00 43.77 4.49
2969 3110 2.289882 TGAGTGGACATGGAGAGCAAAG 60.290 50.000 0.00 0.00 0.00 2.77
2977 3118 1.478105 CGATGAGTGAGTGGACATGGA 59.522 52.381 0.00 0.00 0.00 3.41
2978 3119 1.472201 CCGATGAGTGAGTGGACATGG 60.472 57.143 0.00 0.00 0.00 3.66
2982 3123 0.173708 GGACCGATGAGTGAGTGGAC 59.826 60.000 0.00 0.00 0.00 4.02
2983 3124 0.251608 TGGACCGATGAGTGAGTGGA 60.252 55.000 0.00 0.00 0.00 4.02
2984 3125 0.826715 ATGGACCGATGAGTGAGTGG 59.173 55.000 0.00 0.00 0.00 4.00
2985 3126 1.472201 CCATGGACCGATGAGTGAGTG 60.472 57.143 5.56 0.00 0.00 3.51
2986 3127 0.826715 CCATGGACCGATGAGTGAGT 59.173 55.000 5.56 0.00 0.00 3.41
2987 3128 0.531532 GCCATGGACCGATGAGTGAG 60.532 60.000 18.40 0.00 0.00 3.51
2988 3129 1.264045 TGCCATGGACCGATGAGTGA 61.264 55.000 18.40 0.00 0.00 3.41
2989 3130 1.091771 GTGCCATGGACCGATGAGTG 61.092 60.000 18.40 0.00 0.00 3.51
2990 3131 1.221840 GTGCCATGGACCGATGAGT 59.778 57.895 18.40 0.00 0.00 3.41
2991 3132 1.884464 CGTGCCATGGACCGATGAG 60.884 63.158 18.40 0.00 0.00 2.90
2992 3133 2.186644 CGTGCCATGGACCGATGA 59.813 61.111 18.40 0.00 0.00 2.92
2993 3134 2.896854 CCGTGCCATGGACCGATG 60.897 66.667 18.40 0.74 0.00 3.84
2994 3135 4.856801 GCCGTGCCATGGACCGAT 62.857 66.667 18.40 0.00 0.00 4.18
2997 3138 3.747976 GTTGCCGTGCCATGGACC 61.748 66.667 18.40 3.11 0.00 4.46
3034 3175 0.322975 ACAGGAGGATATCGCATGCC 59.677 55.000 13.15 0.00 30.21 4.40
3078 3219 1.140312 TGCTTCTGTCCACTTCCCTT 58.860 50.000 0.00 0.00 0.00 3.95
3100 3241 0.533308 AGTTTGGCACGGTTTCGCTA 60.533 50.000 0.00 0.00 40.63 4.26
3115 3256 6.225981 ACAGCAAAGGAAAAATCTGAGTTT 57.774 33.333 0.00 0.00 0.00 2.66
3130 3271 2.159476 CCAACATGATCCGACAGCAAAG 60.159 50.000 0.00 0.00 0.00 2.77
3207 3350 4.442706 AGGTTTTGCGATCGTGATTATCT 58.557 39.130 17.81 4.24 0.00 1.98
3247 3390 1.716028 AACCGGGTGGAAGGCTTTCT 61.716 55.000 6.32 0.00 39.21 2.52
3358 3502 2.095919 GTGCGAGTGCCGTAAAATCTTT 60.096 45.455 0.00 0.00 41.78 2.52


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

AutoCloner maintained by Alex Coulton.