Multiple sequence alignment - TraesCS4D01G213600

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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 TraesCS4D01G213600 chr4D 100.000 3481 0 0 1 3481 366325129 366321649 0.000000e+00 6429.0
1 TraesCS4D01G213600 chr4A 95.242 1387 50 7 2105 3481 98600190 98601570 0.000000e+00 2182.0
2 TraesCS4D01G213600 chr4A 86.043 1390 85 44 668 1985 98598586 98599938 0.000000e+00 1391.0
3 TraesCS4D01G213600 chr4A 91.429 350 28 1 3134 3481 56482117 56482466 2.430000e-131 479.0
4 TraesCS4D01G213600 chr4A 98.507 67 1 0 33 99 98598217 98598283 6.100000e-23 119.0
5 TraesCS4D01G213600 chr4B 88.459 1525 69 47 526 1985 450916372 450914890 0.000000e+00 1742.0
6 TraesCS4D01G213600 chr4B 96.429 756 22 3 2117 2871 450914756 450914005 0.000000e+00 1242.0
7 TraesCS4D01G213600 chr4B 92.190 589 21 6 2902 3481 450913879 450913307 0.000000e+00 809.0
8 TraesCS4D01G213600 chr4B 87.023 524 33 14 15 505 450916877 450916356 3.030000e-155 558.0
9 TraesCS4D01G213600 chr3D 94.000 350 19 1 3134 3481 443673035 443673384 2.380000e-146 529.0
10 TraesCS4D01G213600 chr2A 89.459 370 37 1 3114 3481 578017344 578017713 1.890000e-127 466.0
11 TraesCS4D01G213600 chr2A 81.818 88 9 3 2031 2111 532043322 532043409 2.240000e-07 67.6
12 TraesCS4D01G213600 chr6B 92.683 205 14 1 3134 3337 101435522 101435318 9.450000e-76 294.0
13 TraesCS4D01G213600 chr2D 92.045 88 5 2 2027 2113 20663382 20663468 4.720000e-24 122.0
14 TraesCS4D01G213600 chr5A 83.562 73 9 3 2040 2110 448620316 448620245 8.060000e-07 65.8
15 TraesCS4D01G213600 chr3A 100.000 33 0 0 2033 2065 649820030 649820062 1.040000e-05 62.1


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 TraesCS4D01G213600 chr4D 366321649 366325129 3480 True 6429.000000 6429 100.00000 1 3481 1 chr4D.!!$R1 3480
1 TraesCS4D01G213600 chr4A 98598217 98601570 3353 False 1230.666667 2182 93.26400 33 3481 3 chr4A.!!$F2 3448
2 TraesCS4D01G213600 chr4B 450913307 450916877 3570 True 1087.750000 1742 91.02525 15 3481 4 chr4B.!!$R1 3466


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
970 1065 1.302431 CGTCACATCAACCAGGCCA 60.302 57.895 5.01 0.00 0.00 5.36 F
1206 1338 0.037975 TTACTTCCGGGAGACAACGC 60.038 55.000 19.39 0.00 0.00 4.84 F
1283 1415 0.319383 GCGATGTCAGATCTGCGGAT 60.319 55.000 18.36 8.05 34.45 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2065 0.319383 CTAGCTATGCTGACGCCTGG 60.319 60.000 1.96 0.0 40.10 4.45 R
2176 2534 0.809385 CTGCATGTTCTGGAGGCTTG 59.191 55.000 0.00 0.0 39.51 4.01 R
3180 3643 1.003003 TCACTGGATTCCGTTGATGCA 59.997 47.619 0.00 0.0 0.00 3.96 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
209 219 1.340248 CGTACGCCCTCCATTCACTAT 59.660 52.381 0.52 0.00 0.00 2.12
210 220 2.223971 CGTACGCCCTCCATTCACTATT 60.224 50.000 0.52 0.00 0.00 1.73
211 221 2.332063 ACGCCCTCCATTCACTATTG 57.668 50.000 0.00 0.00 0.00 1.90
219 229 6.434028 GCCCTCCATTCACTATTGCATTATAA 59.566 38.462 0.00 0.00 0.00 0.98
285 298 8.828688 AGTAGGTTTGTACACTCATTTTAGTC 57.171 34.615 0.00 0.00 0.00 2.59
286 299 7.876582 AGTAGGTTTGTACACTCATTTTAGTCC 59.123 37.037 0.00 0.00 0.00 3.85
293 306 8.054152 TGTACACTCATTTTAGTCCGTATGTA 57.946 34.615 0.00 0.00 0.00 2.29
296 309 7.609056 ACACTCATTTTAGTCCGTATGTACTT 58.391 34.615 0.00 0.00 0.00 2.24
344 357 1.813513 ACAATGAACGGAAGGAGCAG 58.186 50.000 0.00 0.00 0.00 4.24
500 547 5.851517 CGAATACTAGTAGTCGTTGCTTG 57.148 43.478 33.34 12.81 45.15 4.01
501 548 5.330295 CGAATACTAGTAGTCGTTGCTTGT 58.670 41.667 33.34 1.98 45.15 3.16
502 549 5.227391 CGAATACTAGTAGTCGTTGCTTGTG 59.773 44.000 33.34 11.61 45.15 3.33
503 550 2.673833 ACTAGTAGTCGTTGCTTGTGC 58.326 47.619 0.00 0.00 40.20 4.57
504 551 2.296471 ACTAGTAGTCGTTGCTTGTGCT 59.704 45.455 0.00 0.00 40.48 4.40
505 552 2.240493 AGTAGTCGTTGCTTGTGCTT 57.760 45.000 0.00 0.00 40.48 3.91
506 553 2.561569 AGTAGTCGTTGCTTGTGCTTT 58.438 42.857 0.00 0.00 40.48 3.51
507 554 2.943033 AGTAGTCGTTGCTTGTGCTTTT 59.057 40.909 0.00 0.00 40.48 2.27
508 555 2.939460 AGTCGTTGCTTGTGCTTTTT 57.061 40.000 0.00 0.00 40.48 1.94
532 579 8.857694 TTTTTCTTTGAGGGATAATAGTCGTT 57.142 30.769 0.00 0.00 0.00 3.85
533 580 7.843490 TTTCTTTGAGGGATAATAGTCGTTG 57.157 36.000 0.00 0.00 0.00 4.10
534 581 5.357257 TCTTTGAGGGATAATAGTCGTTGC 58.643 41.667 0.00 0.00 0.00 4.17
535 582 5.128827 TCTTTGAGGGATAATAGTCGTTGCT 59.871 40.000 0.00 0.00 0.00 3.91
536 583 5.353394 TTGAGGGATAATAGTCGTTGCTT 57.647 39.130 0.00 0.00 0.00 3.91
562 609 2.507992 CTTCTCGCGCCAGTCAGG 60.508 66.667 0.00 0.00 41.84 3.86
698 773 2.032799 CACTCGCACAAAAGGCTGTAAA 59.967 45.455 0.00 0.00 0.00 2.01
733 808 2.610433 TCGTTAATGAGCAGAGCACTG 58.390 47.619 6.80 6.80 45.91 3.66
762 837 2.675583 CCTCACCCTCATCTCATCTCA 58.324 52.381 0.00 0.00 0.00 3.27
763 838 3.241156 CCTCACCCTCATCTCATCTCAT 58.759 50.000 0.00 0.00 0.00 2.90
764 839 3.258872 CCTCACCCTCATCTCATCTCATC 59.741 52.174 0.00 0.00 0.00 2.92
765 840 4.154176 CTCACCCTCATCTCATCTCATCT 58.846 47.826 0.00 0.00 0.00 2.90
766 841 4.151121 TCACCCTCATCTCATCTCATCTC 58.849 47.826 0.00 0.00 0.00 2.75
767 842 3.896272 CACCCTCATCTCATCTCATCTCA 59.104 47.826 0.00 0.00 0.00 3.27
768 843 3.896888 ACCCTCATCTCATCTCATCTCAC 59.103 47.826 0.00 0.00 0.00 3.51
769 844 3.258872 CCCTCATCTCATCTCATCTCACC 59.741 52.174 0.00 0.00 0.00 4.02
770 845 4.154176 CCTCATCTCATCTCATCTCACCT 58.846 47.826 0.00 0.00 0.00 4.00
771 846 4.219070 CCTCATCTCATCTCATCTCACCTC 59.781 50.000 0.00 0.00 0.00 3.85
881 956 2.429930 CCCCACGCACCTCAAGAA 59.570 61.111 0.00 0.00 0.00 2.52
970 1065 1.302431 CGTCACATCAACCAGGCCA 60.302 57.895 5.01 0.00 0.00 5.36
988 1083 2.490148 AAGATCAGATCGGCGGCGA 61.490 57.895 36.40 36.40 0.00 5.54
1162 1287 1.202952 TCCCCTCTCGCTCTCTTATCC 60.203 57.143 0.00 0.00 0.00 2.59
1174 1299 3.657727 CTCTCTTATCCCTCTCCCTCTCT 59.342 52.174 0.00 0.00 0.00 3.10
1177 1302 2.542257 TATCCCTCTCCCTCTCTCCT 57.458 55.000 0.00 0.00 0.00 3.69
1190 1322 4.404394 CCCTCTCTCCTCCTCTTCTTTTAC 59.596 50.000 0.00 0.00 0.00 2.01
1206 1338 0.037975 TTACTTCCGGGAGACAACGC 60.038 55.000 19.39 0.00 0.00 4.84
1223 1355 1.469308 ACGCGAGAAGAAGAAGATCGT 59.531 47.619 15.93 0.00 35.87 3.73
1232 1364 4.130286 AGAAGAAGATCGTTGGATGGAC 57.870 45.455 0.00 0.00 31.51 4.02
1243 1375 1.804326 GGATGGACGTCAACGGTCG 60.804 63.158 18.91 0.00 44.95 4.79
1245 1377 1.069378 GATGGACGTCAACGGTCGAC 61.069 60.000 18.91 7.13 44.95 4.20
1283 1415 0.319383 GCGATGTCAGATCTGCGGAT 60.319 55.000 18.36 8.05 34.45 4.18
1311 1443 3.197790 CACGGATCTGGCGCTTGG 61.198 66.667 7.64 0.00 0.00 3.61
1418 1559 7.148340 CCAAGAGAAATAACAATCTGTCTGGAC 60.148 40.741 0.00 0.00 0.00 4.02
1432 1573 4.713553 TGTCTGGACATCTTGTTTTGCTA 58.286 39.130 0.00 0.00 36.21 3.49
1461 1602 3.119424 AGTTTAGCAGCTACTCCTCGTTC 60.119 47.826 0.00 0.00 0.00 3.95
1536 1677 3.492102 AGCTACAACAAGAGCTTCCAA 57.508 42.857 0.00 0.00 46.99 3.53
1633 1792 2.535331 GTTTTGTTTCTTTCAGCCGCA 58.465 42.857 0.00 0.00 0.00 5.69
1700 1862 3.415457 AGCCTGCCTCTTTCTATATGC 57.585 47.619 0.00 0.00 0.00 3.14
1729 1893 2.855728 CTTTGCTGCCGTGCGATTCC 62.856 60.000 0.00 0.00 35.36 3.01
1860 2024 5.069251 ACCCTCTTGAGAAGGTAATATCACG 59.931 44.000 0.00 0.00 37.12 4.35
1893 2062 8.171840 ACCATATTTGTTTTGTTTTGTTTCGTG 58.828 29.630 0.00 0.00 0.00 4.35
1894 2063 8.383619 CCATATTTGTTTTGTTTTGTTTCGTGA 58.616 29.630 0.00 0.00 0.00 4.35
1895 2064 9.193602 CATATTTGTTTTGTTTTGTTTCGTGAC 57.806 29.630 0.00 0.00 0.00 3.67
1896 2065 5.577860 TTGTTTTGTTTTGTTTCGTGACC 57.422 34.783 0.00 0.00 0.00 4.02
1897 2066 3.988517 TGTTTTGTTTTGTTTCGTGACCC 59.011 39.130 0.00 0.00 0.00 4.46
1950 2119 7.439157 TCAGAATTCTGTCATTTCACGAAAT 57.561 32.000 29.80 0.00 44.12 2.17
1981 2150 3.100658 TCGGAATGTGAAAACTGTCGA 57.899 42.857 0.00 0.00 0.00 4.20
1982 2151 3.659786 TCGGAATGTGAAAACTGTCGAT 58.340 40.909 0.00 0.00 0.00 3.59
1984 2153 4.084066 TCGGAATGTGAAAACTGTCGATTG 60.084 41.667 0.00 0.00 0.00 2.67
1986 2155 4.023193 GGAATGTGAAAACTGTCGATTGGT 60.023 41.667 0.00 0.00 0.00 3.67
1987 2156 5.507315 GGAATGTGAAAACTGTCGATTGGTT 60.507 40.000 0.00 0.00 0.00 3.67
2006 2252 4.873827 TGGTTCGATATTTACTTGCACCTC 59.126 41.667 0.00 0.00 0.00 3.85
2009 2255 5.339008 TCGATATTTACTTGCACCTCTGT 57.661 39.130 0.00 0.00 0.00 3.41
2011 2257 7.050970 TCGATATTTACTTGCACCTCTGTAT 57.949 36.000 0.00 0.00 0.00 2.29
2013 2259 8.635328 TCGATATTTACTTGCACCTCTGTATAA 58.365 33.333 0.00 0.00 0.00 0.98
2014 2260 9.424319 CGATATTTACTTGCACCTCTGTATAAT 57.576 33.333 0.00 0.00 0.00 1.28
2018 2264 8.662781 TTTACTTGCACCTCTGTATAATGATC 57.337 34.615 0.00 0.00 0.00 2.92
2023 2269 6.749139 TGCACCTCTGTATAATGATCTGTAC 58.251 40.000 0.00 0.00 0.00 2.90
2024 2270 6.551227 TGCACCTCTGTATAATGATCTGTACT 59.449 38.462 0.00 0.00 0.00 2.73
2025 2271 6.865726 GCACCTCTGTATAATGATCTGTACTG 59.134 42.308 0.00 0.00 0.00 2.74
2026 2272 6.865726 CACCTCTGTATAATGATCTGTACTGC 59.134 42.308 0.00 0.00 0.00 4.40
2032 2285 7.652727 TGTATAATGATCTGTACTGCACTCTC 58.347 38.462 0.00 0.00 0.00 3.20
2045 2298 5.725362 ACTGCACTCTCTGTTCCTAAATAC 58.275 41.667 0.00 0.00 0.00 1.89
2050 2303 6.311690 GCACTCTCTGTTCCTAAATACAAGAC 59.688 42.308 0.00 0.00 0.00 3.01
2052 2305 6.208994 ACTCTCTGTTCCTAAATACAAGACGT 59.791 38.462 0.00 0.00 0.00 4.34
2065 2318 2.097466 ACAAGACGTTTTGGCAGTTCAG 59.903 45.455 21.34 0.00 32.32 3.02
2069 2322 3.942748 AGACGTTTTGGCAGTTCAGTTTA 59.057 39.130 0.00 0.00 0.00 2.01
2131 2489 1.200020 CTTTTAGGCAGCCAACTTCCG 59.800 52.381 15.80 0.00 33.88 4.30
2176 2534 9.620259 ATCAACTTCCTTTTCAGTTATATCCTC 57.380 33.333 0.00 0.00 31.78 3.71
2199 2557 1.681166 GCCTCCAGAACATGCAGATGT 60.681 52.381 0.00 0.00 45.24 3.06
2234 2592 6.322712 AGTTGTTAAACCAAATCTTGCAGGTA 59.677 34.615 0.00 0.00 36.94 3.08
2688 3046 5.772521 AGAAATTGTTGTGCATCAAGTACC 58.227 37.500 0.00 0.00 36.66 3.34
2724 3083 6.570692 TCTGTTCGTTGATATAAGGAGTTCC 58.429 40.000 0.00 0.00 0.00 3.62
2736 3095 0.951040 GGAGTTCCTTGTGTGCCTCG 60.951 60.000 0.00 0.00 0.00 4.63
2872 3233 6.990341 AAAAACACTTTGGACTAACTACGT 57.010 33.333 0.00 0.00 0.00 3.57
2882 3243 9.666626 CTTTGGACTAACTACGTATATCTGAAG 57.333 37.037 0.00 0.00 0.00 3.02
2883 3244 8.969260 TTGGACTAACTACGTATATCTGAAGA 57.031 34.615 0.00 0.00 0.00 2.87
2924 3380 6.636705 TGGAGTACATTGGAACTGTGTATAC 58.363 40.000 0.00 0.00 33.29 1.47
3057 3514 6.234177 CAACATCTCTCAAAGTAAAGTCCCT 58.766 40.000 0.00 0.00 0.00 4.20
3169 3630 6.751425 CAGCACAAAACACATTTCTACAGAAA 59.249 34.615 6.85 6.85 46.60 2.52
3262 3725 2.232399 GTAAACCCCTTCGCTTCCAAA 58.768 47.619 0.00 0.00 0.00 3.28
3318 3781 2.031682 GCACACAGTCATCAAAGACCAC 60.032 50.000 0.00 0.00 39.34 4.16
3337 3800 7.509546 AGACCACTCAAGACAAATTAAGAAGA 58.490 34.615 0.00 0.00 0.00 2.87
3392 3857 4.523083 ACCAATACTTCGGTGCATGTATT 58.477 39.130 0.00 0.00 36.43 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 184 5.467735 GGAGGGCGTACGTATTATTTTGATT 59.532 40.000 17.90 0.00 0.00 2.57
187 197 0.457035 GTGAATGGAGGGCGTACGTA 59.543 55.000 17.90 0.00 0.00 3.57
190 200 3.131396 CAATAGTGAATGGAGGGCGTAC 58.869 50.000 0.00 0.00 0.00 3.67
192 202 1.747206 GCAATAGTGAATGGAGGGCGT 60.747 52.381 0.00 0.00 0.00 5.68
194 204 2.057137 TGCAATAGTGAATGGAGGGC 57.943 50.000 0.00 0.00 0.00 5.19
318 331 5.007724 GCTCCTTCCGTTCATTGTTATAAGG 59.992 44.000 0.00 0.00 34.79 2.69
360 373 8.006298 TGGCATCTTAGACTCAAAAAGAAAAA 57.994 30.769 0.00 0.00 33.26 1.94
361 374 7.285401 ACTGGCATCTTAGACTCAAAAAGAAAA 59.715 33.333 0.00 0.00 33.26 2.29
362 375 6.772716 ACTGGCATCTTAGACTCAAAAAGAAA 59.227 34.615 0.00 0.00 33.26 2.52
364 377 5.869579 ACTGGCATCTTAGACTCAAAAAGA 58.130 37.500 0.00 0.00 34.00 2.52
394 431 7.251321 TGGGCAATCTGTTTTTATTGGTTAT 57.749 32.000 0.00 0.00 34.37 1.89
403 440 5.813513 ATTCTCTTGGGCAATCTGTTTTT 57.186 34.783 0.00 0.00 0.00 1.94
410 447 4.759183 GGTGAGATATTCTCTTGGGCAATC 59.241 45.833 6.13 0.00 43.73 2.67
476 517 3.376234 AGCAACGACTACTAGTATTCGCA 59.624 43.478 31.11 1.94 40.44 5.10
507 554 8.726988 CAACGACTATTATCCCTCAAAGAAAAA 58.273 33.333 0.00 0.00 0.00 1.94
508 555 7.148306 GCAACGACTATTATCCCTCAAAGAAAA 60.148 37.037 0.00 0.00 0.00 2.29
509 556 6.315393 GCAACGACTATTATCCCTCAAAGAAA 59.685 38.462 0.00 0.00 0.00 2.52
510 557 5.815740 GCAACGACTATTATCCCTCAAAGAA 59.184 40.000 0.00 0.00 0.00 2.52
511 558 5.128827 AGCAACGACTATTATCCCTCAAAGA 59.871 40.000 0.00 0.00 0.00 2.52
512 559 5.360591 AGCAACGACTATTATCCCTCAAAG 58.639 41.667 0.00 0.00 0.00 2.77
513 560 5.353394 AGCAACGACTATTATCCCTCAAA 57.647 39.130 0.00 0.00 0.00 2.69
514 561 5.128827 AGAAGCAACGACTATTATCCCTCAA 59.871 40.000 0.00 0.00 0.00 3.02
515 562 4.649674 AGAAGCAACGACTATTATCCCTCA 59.350 41.667 0.00 0.00 0.00 3.86
516 563 4.985409 CAGAAGCAACGACTATTATCCCTC 59.015 45.833 0.00 0.00 0.00 4.30
517 564 4.740934 GCAGAAGCAACGACTATTATCCCT 60.741 45.833 0.00 0.00 41.58 4.20
518 565 3.495001 GCAGAAGCAACGACTATTATCCC 59.505 47.826 0.00 0.00 41.58 3.85
519 566 4.210120 CAGCAGAAGCAACGACTATTATCC 59.790 45.833 0.00 0.00 45.49 2.59
520 567 4.318404 GCAGCAGAAGCAACGACTATTATC 60.318 45.833 0.00 0.00 45.49 1.75
521 568 3.557595 GCAGCAGAAGCAACGACTATTAT 59.442 43.478 0.00 0.00 45.49 1.28
522 569 2.930040 GCAGCAGAAGCAACGACTATTA 59.070 45.455 0.00 0.00 45.49 0.98
523 570 1.734465 GCAGCAGAAGCAACGACTATT 59.266 47.619 0.00 0.00 45.49 1.73
524 571 1.338105 TGCAGCAGAAGCAACGACTAT 60.338 47.619 0.00 0.00 45.49 2.12
525 572 0.033366 TGCAGCAGAAGCAACGACTA 59.967 50.000 0.00 0.00 45.49 2.59
526 573 1.227645 TGCAGCAGAAGCAACGACT 60.228 52.632 0.00 0.00 45.49 4.18
527 574 1.082496 GTGCAGCAGAAGCAACGAC 60.082 57.895 0.00 0.00 44.64 4.34
528 575 0.815213 AAGTGCAGCAGAAGCAACGA 60.815 50.000 0.00 0.00 44.64 3.85
529 576 0.385223 GAAGTGCAGCAGAAGCAACG 60.385 55.000 0.00 0.00 44.64 4.10
530 577 0.950116 AGAAGTGCAGCAGAAGCAAC 59.050 50.000 0.00 0.00 44.64 4.17
531 578 1.233019 GAGAAGTGCAGCAGAAGCAA 58.767 50.000 0.00 0.00 44.64 3.91
532 579 0.947660 CGAGAAGTGCAGCAGAAGCA 60.948 55.000 0.00 0.00 45.49 3.91
533 580 1.786582 CGAGAAGTGCAGCAGAAGC 59.213 57.895 0.00 0.00 42.56 3.86
534 581 1.786582 GCGAGAAGTGCAGCAGAAG 59.213 57.895 0.00 0.00 0.00 2.85
535 582 2.023771 CGCGAGAAGTGCAGCAGAA 61.024 57.895 0.00 0.00 0.00 3.02
536 583 2.431430 CGCGAGAAGTGCAGCAGA 60.431 61.111 0.00 0.00 0.00 4.26
574 639 1.733526 GGAGTGTGTTTGGTGGCAC 59.266 57.895 9.70 9.70 36.26 5.01
630 695 1.080093 GCTGCACGGCTGTACTGTA 60.080 57.895 0.00 0.00 35.54 2.74
631 696 2.357517 GCTGCACGGCTGTACTGT 60.358 61.111 0.00 0.00 38.94 3.55
632 697 3.121030 GGCTGCACGGCTGTACTG 61.121 66.667 0.00 0.00 34.85 2.74
633 698 4.742201 CGGCTGCACGGCTGTACT 62.742 66.667 0.00 0.00 35.72 2.73
677 742 1.225855 TACAGCCTTTTGTGCGAGTG 58.774 50.000 0.00 0.00 32.56 3.51
678 743 1.961793 TTACAGCCTTTTGTGCGAGT 58.038 45.000 0.00 0.00 32.56 4.18
680 745 3.784701 TTTTTACAGCCTTTTGTGCGA 57.215 38.095 0.00 0.00 32.56 5.10
698 773 8.953990 GCTCATTAACGAATACGCAATTAATTT 58.046 29.630 0.00 0.00 43.96 1.82
762 837 2.578480 GGAAAGGAAAGGGAGGTGAGAT 59.422 50.000 0.00 0.00 0.00 2.75
763 838 1.985895 GGAAAGGAAAGGGAGGTGAGA 59.014 52.381 0.00 0.00 0.00 3.27
764 839 1.988846 AGGAAAGGAAAGGGAGGTGAG 59.011 52.381 0.00 0.00 0.00 3.51
765 840 2.133858 AGGAAAGGAAAGGGAGGTGA 57.866 50.000 0.00 0.00 0.00 4.02
766 841 2.555448 GGAAGGAAAGGAAAGGGAGGTG 60.555 54.545 0.00 0.00 0.00 4.00
767 842 1.711375 GGAAGGAAAGGAAAGGGAGGT 59.289 52.381 0.00 0.00 0.00 3.85
768 843 1.006043 GGGAAGGAAAGGAAAGGGAGG 59.994 57.143 0.00 0.00 0.00 4.30
769 844 1.006043 GGGGAAGGAAAGGAAAGGGAG 59.994 57.143 0.00 0.00 0.00 4.30
770 845 1.081481 GGGGAAGGAAAGGAAAGGGA 58.919 55.000 0.00 0.00 0.00 4.20
771 846 0.041238 GGGGGAAGGAAAGGAAAGGG 59.959 60.000 0.00 0.00 0.00 3.95
794 869 2.292916 GGCAACGCACAAACGAAGC 61.293 57.895 0.00 0.00 36.70 3.86
863 938 2.690653 TTTCTTGAGGTGCGTGGGGG 62.691 60.000 0.00 0.00 0.00 5.40
864 939 1.228124 TTTCTTGAGGTGCGTGGGG 60.228 57.895 0.00 0.00 0.00 4.96
865 940 1.515521 GGTTTCTTGAGGTGCGTGGG 61.516 60.000 0.00 0.00 0.00 4.61
866 941 1.841663 CGGTTTCTTGAGGTGCGTGG 61.842 60.000 0.00 0.00 0.00 4.94
868 943 2.251642 GCGGTTTCTTGAGGTGCGT 61.252 57.895 0.00 0.00 0.00 5.24
870 945 1.244019 ATGGCGGTTTCTTGAGGTGC 61.244 55.000 0.00 0.00 0.00 5.01
877 952 3.636764 GGATGGAATTATGGCGGTTTCTT 59.363 43.478 0.00 0.00 0.00 2.52
881 956 2.746279 TGGATGGAATTATGGCGGTT 57.254 45.000 0.00 0.00 0.00 4.44
918 997 3.209097 CCCAAATGGCCGCGTAGG 61.209 66.667 4.92 0.00 44.97 3.18
919 998 3.209097 CCCCAAATGGCCGCGTAG 61.209 66.667 4.92 0.00 0.00 3.51
928 1007 3.814268 CCACGAGCGCCCCAAATG 61.814 66.667 2.29 0.00 0.00 2.32
950 1031 0.605319 GGCCTGGTTGATGTGACGAA 60.605 55.000 0.00 0.00 0.00 3.85
961 1042 1.134280 CGATCTGATCTTGGCCTGGTT 60.134 52.381 15.16 0.00 0.00 3.67
962 1043 0.467384 CGATCTGATCTTGGCCTGGT 59.533 55.000 15.16 0.00 0.00 4.00
970 1065 2.028190 CGCCGCCGATCTGATCTT 59.972 61.111 15.16 0.00 36.29 2.40
988 1083 2.431942 GAACATGGTCGCCGTCGT 60.432 61.111 0.00 0.00 36.96 4.34
1162 1287 0.478507 GAGGAGGAGAGAGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1174 1299 3.514309 CCGGAAGTAAAAGAAGAGGAGGA 59.486 47.826 0.00 0.00 0.00 3.71
1177 1302 3.513517 TCCCGGAAGTAAAAGAAGAGGA 58.486 45.455 0.73 0.00 0.00 3.71
1190 1322 2.809601 CGCGTTGTCTCCCGGAAG 60.810 66.667 0.73 0.00 0.00 3.46
1206 1338 4.098055 TCCAACGATCTTCTTCTTCTCG 57.902 45.455 0.00 0.00 35.56 4.04
1223 1355 0.320073 GACCGTTGACGTCCATCCAA 60.320 55.000 14.12 0.00 37.74 3.53
1243 1375 4.084849 CGCATTTCATTCTACAGATCCGTC 60.085 45.833 0.00 0.00 0.00 4.79
1245 1377 4.051237 TCGCATTTCATTCTACAGATCCG 58.949 43.478 0.00 0.00 0.00 4.18
1311 1443 2.349886 GCACACGATTCTGACAGGAATC 59.650 50.000 1.81 9.45 44.62 2.52
1347 1480 3.557577 TGCGAATTGGACAAAGTCATG 57.442 42.857 0.00 0.00 32.29 3.07
1348 1481 4.789012 AATGCGAATTGGACAAAGTCAT 57.211 36.364 0.00 0.00 32.29 3.06
1418 1559 5.232463 ACTGCCAAATAGCAAAACAAGATG 58.768 37.500 0.00 0.00 43.52 2.90
1432 1573 3.690460 AGTAGCTGCTAAACTGCCAAAT 58.310 40.909 11.57 0.00 43.85 2.32
1536 1677 5.305585 ACTGAAAACCTACGTGATTGTGAT 58.694 37.500 0.00 0.00 0.00 3.06
1633 1792 2.227388 CAGCTTCTCCGTTGCAGATTTT 59.773 45.455 0.00 0.00 0.00 1.82
1682 1844 3.006323 AGACGCATATAGAAAGAGGCAGG 59.994 47.826 0.00 0.00 0.00 4.85
1700 1862 0.514691 GGCAGCAAAGAGACAAGACG 59.485 55.000 0.00 0.00 0.00 4.18
1729 1893 6.128553 ACAGCACATTTCACATAAGACTAACG 60.129 38.462 0.00 0.00 0.00 3.18
1888 2057 3.220999 CTGACGCCTGGGTCACGAA 62.221 63.158 12.40 0.00 41.76 3.85
1889 2058 3.680786 CTGACGCCTGGGTCACGA 61.681 66.667 12.40 0.00 41.76 4.35
1891 2060 2.238847 TATGCTGACGCCTGGGTCAC 62.239 60.000 12.40 10.24 41.76 3.67
1893 2062 1.227380 CTATGCTGACGCCTGGGTC 60.227 63.158 7.35 7.35 37.45 4.46
1894 2063 2.903357 CTATGCTGACGCCTGGGT 59.097 61.111 0.00 0.00 34.43 4.51
1895 2064 1.748329 TAGCTATGCTGACGCCTGGG 61.748 60.000 1.96 0.00 40.10 4.45
1896 2065 0.319383 CTAGCTATGCTGACGCCTGG 60.319 60.000 1.96 0.00 40.10 4.45
1897 2066 0.943359 GCTAGCTATGCTGACGCCTG 60.943 60.000 7.70 0.00 40.10 4.85
1914 2083 8.016301 TGACAGAATTCTGATACATCTTAGCT 57.984 34.615 36.15 13.34 46.59 3.32
1934 2103 8.900511 ACATCAATTATTTCGTGAAATGACAG 57.099 30.769 16.12 6.29 40.83 3.51
1950 2119 8.356657 AGTTTTCACATTCCGAAACATCAATTA 58.643 29.630 0.00 0.00 35.13 1.40
1981 2150 5.885912 AGGTGCAAGTAAATATCGAACCAAT 59.114 36.000 0.00 0.00 0.00 3.16
1982 2151 5.250200 AGGTGCAAGTAAATATCGAACCAA 58.750 37.500 0.00 0.00 0.00 3.67
1984 2153 5.006746 CAGAGGTGCAAGTAAATATCGAACC 59.993 44.000 0.00 0.00 0.00 3.62
1986 2155 5.730550 ACAGAGGTGCAAGTAAATATCGAA 58.269 37.500 0.00 0.00 0.00 3.71
1987 2156 5.339008 ACAGAGGTGCAAGTAAATATCGA 57.661 39.130 0.00 0.00 0.00 3.59
2006 2252 7.656412 AGAGTGCAGTACAGATCATTATACAG 58.344 38.462 0.00 0.00 0.00 2.74
2009 2255 7.503902 ACAGAGAGTGCAGTACAGATCATTATA 59.496 37.037 0.00 0.00 0.00 0.98
2011 2257 5.654209 ACAGAGAGTGCAGTACAGATCATTA 59.346 40.000 0.00 0.00 0.00 1.90
2013 2259 4.022603 ACAGAGAGTGCAGTACAGATCAT 58.977 43.478 0.00 0.00 0.00 2.45
2014 2260 3.425659 ACAGAGAGTGCAGTACAGATCA 58.574 45.455 0.00 0.00 0.00 2.92
2016 2262 3.194542 GGAACAGAGAGTGCAGTACAGAT 59.805 47.826 0.00 0.00 0.00 2.90
2018 2264 2.560542 AGGAACAGAGAGTGCAGTACAG 59.439 50.000 0.00 0.00 0.00 2.74
2023 2269 5.724328 TGTATTTAGGAACAGAGAGTGCAG 58.276 41.667 0.00 0.00 0.00 4.41
2024 2270 5.738619 TGTATTTAGGAACAGAGAGTGCA 57.261 39.130 0.00 0.00 0.00 4.57
2025 2271 6.311690 GTCTTGTATTTAGGAACAGAGAGTGC 59.688 42.308 0.00 0.00 0.00 4.40
2026 2272 6.528423 CGTCTTGTATTTAGGAACAGAGAGTG 59.472 42.308 0.00 0.00 0.00 3.51
2032 2285 7.075741 CCAAAACGTCTTGTATTTAGGAACAG 58.924 38.462 0.20 0.00 0.00 3.16
2045 2298 2.097466 ACTGAACTGCCAAAACGTCTTG 59.903 45.455 0.00 0.00 0.00 3.02
2050 2303 5.099575 AGTTTAAACTGAACTGCCAAAACG 58.900 37.500 19.94 0.00 37.98 3.60
2065 2318 4.850859 AAACGCTTTTGGCAGTTTAAAC 57.149 36.364 10.47 10.47 41.69 2.01
2069 2322 3.851098 TGTAAAACGCTTTTGGCAGTTT 58.149 36.364 0.00 0.00 43.54 2.66
2077 2330 9.233232 CTCTGTTTCTAAATGTAAAACGCTTTT 57.767 29.630 0.00 0.00 36.02 2.27
2081 2334 6.665465 ACCTCTGTTTCTAAATGTAAAACGC 58.335 36.000 0.00 0.00 36.02 4.84
2176 2534 0.809385 CTGCATGTTCTGGAGGCTTG 59.191 55.000 0.00 0.00 39.51 4.01
2199 2557 5.235850 TGGTTTAACAACTAGGCATGAGA 57.764 39.130 0.00 0.00 32.90 3.27
2234 2592 4.654262 TGGTAGGACTTCTCTTCAACTGTT 59.346 41.667 0.00 0.00 0.00 3.16
2435 2793 4.347453 GTTTGTGCTGCCGCCTGG 62.347 66.667 0.00 0.00 38.77 4.45
2724 3083 1.845809 GAAGCACCGAGGCACACAAG 61.846 60.000 1.23 0.00 35.83 3.16
2736 3095 1.661112 GTGCTGAAGTATCGAAGCACC 59.339 52.381 21.54 8.29 44.53 5.01
2850 3211 9.933723 ATATACGTAGTTAGTCCAAAGTGTTTT 57.066 29.630 0.08 0.00 37.78 2.43
2882 3243 8.671028 TGTACTCCAGTTTTACTTTTGAAGTTC 58.329 33.333 0.00 0.00 42.81 3.01
2883 3244 8.570068 TGTACTCCAGTTTTACTTTTGAAGTT 57.430 30.769 0.00 0.00 42.81 2.66
2888 3249 7.936584 TCCAATGTACTCCAGTTTTACTTTTG 58.063 34.615 0.00 0.00 0.00 2.44
2892 3253 6.710744 CAGTTCCAATGTACTCCAGTTTTACT 59.289 38.462 0.00 0.00 0.00 2.24
2894 3255 6.485313 CACAGTTCCAATGTACTCCAGTTTTA 59.515 38.462 0.00 0.00 0.00 1.52
3032 3488 5.412904 GGGACTTTACTTTGAGAGATGTTGG 59.587 44.000 0.00 0.00 0.00 3.77
3057 3514 1.488812 AGGTGTAGTGGTTGAACTGCA 59.511 47.619 0.00 0.00 39.99 4.41
3180 3643 1.003003 TCACTGGATTCCGTTGATGCA 59.997 47.619 0.00 0.00 0.00 3.96
3262 3725 7.147585 TGCAGCTTCTAAGAATAGAGGAAGAAT 60.148 37.037 0.00 0.00 39.29 2.40
3392 3857 2.237643 TGCTTGCTGCCTTTTATGTGA 58.762 42.857 0.00 0.00 42.00 3.58



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

AutoCloner maintained by Alex Coulton.