Multiple sequence alignment - TraesCS4D01G299800

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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 TraesCS4D01G299800 chr4D 100.000 4154 0 0 1 4154 468600187 468604340 0.000000e+00 7672.0
1 TraesCS4D01G299800 chr4B 90.864 4247 232 63 1 4154 588200687 588204870 0.000000e+00 5550.0
2 TraesCS4D01G299800 chr4A 92.440 873 52 9 2605 3471 2942172 2941308 0.000000e+00 1234.0
3 TraesCS4D01G299800 chr4A 93.198 691 35 7 3473 4154 2941278 2940591 0.000000e+00 1005.0
4 TraesCS4D01G299800 chr4A 86.972 852 64 29 8 838 2943575 2942750 0.000000e+00 915.0
5 TraesCS4D01G299800 chr4A 86.425 442 28 10 2077 2518 2942623 2942214 4.900000e-124 455.0
6 TraesCS4D01G299800 chr3B 86.297 686 51 17 8 676 509971337 509971996 0.000000e+00 706.0
7 TraesCS4D01G299800 chr1B 86.277 685 51 20 8 676 186140613 186139956 0.000000e+00 704.0
8 TraesCS4D01G299800 chr7B 85.735 687 54 19 8 676 707546837 707547497 0.000000e+00 686.0
9 TraesCS4D01G299800 chr7B 85.735 687 53 20 8 676 669095746 669096405 0.000000e+00 684.0
10 TraesCS4D01G299800 chr6B 85.714 686 55 23 8 676 54643763 54643104 0.000000e+00 684.0
11 TraesCS4D01G299800 chr6B 85.251 678 61 17 8 676 9466009 9465362 0.000000e+00 662.0
12 TraesCS4D01G299800 chr6B 83.621 116 18 1 1863 1978 495430446 495430560 1.580000e-19 108.0
13 TraesCS4D01G299800 chrUn 85.420 679 62 17 8 676 65800048 65799397 0.000000e+00 671.0
14 TraesCS4D01G299800 chr2B 84.942 684 61 18 8 676 263970136 263969480 0.000000e+00 654.0
15 TraesCS4D01G299800 chr5B 84.493 690 58 25 8 676 534718398 534717737 1.630000e-178 636.0
16 TraesCS4D01G299800 chr5D 80.612 98 19 0 1881 1978 350227347 350227444 4.450000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G299800 chr4D 468600187 468604340 4153 False 7672.00 7672 100.00000 1 4154 1 chr4D.!!$F1 4153
1 TraesCS4D01G299800 chr4B 588200687 588204870 4183 False 5550.00 5550 90.86400 1 4154 1 chr4B.!!$F1 4153
2 TraesCS4D01G299800 chr4A 2940591 2943575 2984 True 902.25 1234 89.75875 8 4154 4 chr4A.!!$R1 4146
3 TraesCS4D01G299800 chr3B 509971337 509971996 659 False 706.00 706 86.29700 8 676 1 chr3B.!!$F1 668
4 TraesCS4D01G299800 chr1B 186139956 186140613 657 True 704.00 704 86.27700 8 676 1 chr1B.!!$R1 668
5 TraesCS4D01G299800 chr7B 707546837 707547497 660 False 686.00 686 85.73500 8 676 1 chr7B.!!$F2 668
6 TraesCS4D01G299800 chr7B 669095746 669096405 659 False 684.00 684 85.73500 8 676 1 chr7B.!!$F1 668
7 TraesCS4D01G299800 chr6B 54643104 54643763 659 True 684.00 684 85.71400 8 676 1 chr6B.!!$R2 668
8 TraesCS4D01G299800 chr6B 9465362 9466009 647 True 662.00 662 85.25100 8 676 1 chr6B.!!$R1 668
9 TraesCS4D01G299800 chrUn 65799397 65800048 651 True 671.00 671 85.42000 8 676 1 chrUn.!!$R1 668
10 TraesCS4D01G299800 chr2B 263969480 263970136 656 True 654.00 654 84.94200 8 676 1 chr2B.!!$R1 668
11 TraesCS4D01G299800 chr5B 534717737 534718398 661 True 636.00 636 84.49300 8 676 1 chr5B.!!$R1 668

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
931 1012 0.109919 TCACACGAGTTGACCGATCG 60.110 55.0 8.51 8.51 42.04 3.69 F
1306 1400 0.030101 CAAGGCGTTTTGCTTTCCGA 59.970 50.0 0.00 0.00 41.57 4.55 F
1605 1713 0.319211 AACATGTGTGTGCTGCATGC 60.319 50.0 11.82 11.82 42.50 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2050 0.604578 TATATTAGTCGGGCACGGGC 59.395 55.000 9.32 0.00 41.39 6.13 R
2541 2693 2.480073 GGCGCTGTGTTTTATGCATCAT 60.480 45.455 7.64 0.00 0.00 2.45 R
3452 3613 1.010350 CCGAAGTATCCGTCCGACG 60.010 63.158 14.15 14.15 42.11 5.12 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
101 102 1.734477 CGCAAGGGACGACACAGAG 60.734 63.158 0.00 0.00 0.00 3.35
110 111 0.809385 ACGACACAGAGACCGTATGG 59.191 55.000 0.00 0.00 42.84 2.74
125 126 4.142403 ACCGTATGGATGCAAAAATCACAG 60.142 41.667 8.33 0.00 39.21 3.66
137 138 1.620822 AATCACAGGAAACAGGTGCC 58.379 50.000 0.00 0.00 37.68 5.01
146 147 5.476945 ACAGGAAACAGGTGCCTTTATTTAG 59.523 40.000 0.00 0.00 0.00 1.85
192 193 2.111384 GTACAGATCAGGCAAGGGAGA 58.889 52.381 0.00 0.00 0.00 3.71
193 194 1.890552 ACAGATCAGGCAAGGGAGAT 58.109 50.000 0.00 0.00 0.00 2.75
194 195 2.203584 ACAGATCAGGCAAGGGAGATT 58.796 47.619 0.00 0.00 0.00 2.40
255 265 1.673808 GCGTACTTGACCTCGGGGAT 61.674 60.000 9.33 0.00 36.25 3.85
353 363 2.505557 GCTCAGGCATGCGCAAAC 60.506 61.111 17.11 9.72 41.24 2.93
363 373 2.730069 CATGCGCAAACACAAGAAAGA 58.270 42.857 17.11 0.00 0.00 2.52
367 378 3.366422 TGCGCAAACACAAGAAAGAAAAC 59.634 39.130 8.16 0.00 0.00 2.43
373 384 4.091453 ACACAAGAAAGAAAACACACGG 57.909 40.909 0.00 0.00 0.00 4.94
635 685 3.610669 CCTCGATCCCGGAGCAGG 61.611 72.222 0.73 5.26 36.24 4.85
681 739 1.302511 GTTTCTTGGAGGCAGGCGA 60.303 57.895 0.00 0.00 0.00 5.54
685 743 3.249189 TTGGAGGCAGGCGAAGGT 61.249 61.111 0.00 0.00 0.00 3.50
686 744 2.754664 CTTGGAGGCAGGCGAAGGTT 62.755 60.000 0.00 0.00 0.00 3.50
870 937 3.846405 TTCTCTGGACCGGCCCACT 62.846 63.158 4.87 0.00 34.97 4.00
914 995 1.762858 TGGACTCGTGGGTGGTTCA 60.763 57.895 0.00 0.00 0.00 3.18
927 1008 0.528901 TGGTTCACACGAGTTGACCG 60.529 55.000 9.09 0.00 34.43 4.79
928 1009 0.249155 GGTTCACACGAGTTGACCGA 60.249 55.000 0.00 0.00 0.00 4.69
929 1010 1.604693 GGTTCACACGAGTTGACCGAT 60.605 52.381 0.00 0.00 0.00 4.18
930 1011 1.719780 GTTCACACGAGTTGACCGATC 59.280 52.381 0.00 0.00 0.00 3.69
931 1012 0.109919 TCACACGAGTTGACCGATCG 60.110 55.000 8.51 8.51 42.04 3.69
932 1013 1.071019 CACACGAGTTGACCGATCGG 61.071 60.000 32.20 32.20 40.67 4.18
933 1014 1.516386 CACGAGTTGACCGATCGGG 60.516 63.158 35.87 19.44 40.67 5.14
934 1015 2.104331 CGAGTTGACCGATCGGGG 59.896 66.667 35.87 14.32 41.60 5.73
935 1016 2.499685 GAGTTGACCGATCGGGGG 59.500 66.667 35.87 13.56 41.60 5.40
936 1017 2.038329 AGTTGACCGATCGGGGGA 59.962 61.111 35.87 18.90 41.60 4.81
937 1018 2.017559 GAGTTGACCGATCGGGGGAG 62.018 65.000 35.87 12.79 41.60 4.30
938 1019 2.762459 TTGACCGATCGGGGGAGG 60.762 66.667 35.87 12.03 41.60 4.30
939 1020 4.853142 TGACCGATCGGGGGAGGG 62.853 72.222 35.87 11.28 41.60 4.30
940 1021 4.534824 GACCGATCGGGGGAGGGA 62.535 72.222 35.87 0.00 41.60 4.20
941 1022 4.541648 ACCGATCGGGGGAGGGAG 62.542 72.222 35.87 9.78 41.60 4.30
942 1023 4.220163 CCGATCGGGGGAGGGAGA 62.220 72.222 26.95 0.00 0.00 3.71
943 1024 2.123425 CGATCGGGGGAGGGAGAA 60.123 66.667 7.38 0.00 0.00 2.87
944 1025 1.760875 CGATCGGGGGAGGGAGAAA 60.761 63.158 7.38 0.00 0.00 2.52
1254 1341 2.572284 GACCCCTCCGTCTTCACG 59.428 66.667 0.00 0.00 46.29 4.35
1291 1385 4.331168 GCACTAGTACTTGCTGAATCAAGG 59.669 45.833 11.53 0.00 45.72 3.61
1292 1386 4.331168 CACTAGTACTTGCTGAATCAAGGC 59.669 45.833 0.00 0.00 45.72 4.35
1296 1390 1.956477 ACTTGCTGAATCAAGGCGTTT 59.044 42.857 8.17 0.00 45.72 3.60
1304 1398 2.438868 ATCAAGGCGTTTTGCTTTCC 57.561 45.000 0.00 0.00 41.57 3.13
1306 1400 0.030101 CAAGGCGTTTTGCTTTCCGA 59.970 50.000 0.00 0.00 41.57 4.55
1311 1405 2.542178 GGCGTTTTGCTTTCCGATTTTT 59.458 40.909 0.00 0.00 45.43 1.94
1318 1412 4.503741 TGCTTTCCGATTTTTCTTCCAG 57.496 40.909 0.00 0.00 0.00 3.86
1319 1413 3.888930 TGCTTTCCGATTTTTCTTCCAGT 59.111 39.130 0.00 0.00 0.00 4.00
1322 1416 3.502123 TCCGATTTTTCTTCCAGTGGT 57.498 42.857 9.54 0.00 0.00 4.16
1323 1417 3.827722 TCCGATTTTTCTTCCAGTGGTT 58.172 40.909 9.54 0.00 0.00 3.67
1324 1418 4.975631 TCCGATTTTTCTTCCAGTGGTTA 58.024 39.130 9.54 0.00 0.00 2.85
1325 1419 5.001232 TCCGATTTTTCTTCCAGTGGTTAG 58.999 41.667 9.54 8.30 0.00 2.34
1327 1421 5.122396 CCGATTTTTCTTCCAGTGGTTAGAG 59.878 44.000 9.54 3.87 0.00 2.43
1337 1431 2.549754 CAGTGGTTAGAGGTTGCTGTTG 59.450 50.000 0.00 0.00 0.00 3.33
1346 1440 3.706086 AGAGGTTGCTGTTGAAAATTGGT 59.294 39.130 0.00 0.00 0.00 3.67
1372 1466 2.028476 CAGGTTCGTGGATTGGTAGTGA 60.028 50.000 0.00 0.00 0.00 3.41
1400 1494 1.589630 CCAGGTCGACGGTGAATCA 59.410 57.895 16.02 0.00 0.00 2.57
1411 1505 4.036567 ACGGTGAATCATGATGCATTTG 57.963 40.909 19.55 13.91 0.00 2.32
1429 1523 2.886862 TGGTGCTTGGTTGTTTGATG 57.113 45.000 0.00 0.00 0.00 3.07
1431 1525 1.130955 GTGCTTGGTTGTTTGATGCG 58.869 50.000 0.00 0.00 0.00 4.73
1439 1533 2.292292 GGTTGTTTGATGCGGTTGTAGT 59.708 45.455 0.00 0.00 0.00 2.73
1444 1538 5.182487 TGTTTGATGCGGTTGTAGTATGAT 58.818 37.500 0.00 0.00 0.00 2.45
1445 1539 5.645929 TGTTTGATGCGGTTGTAGTATGATT 59.354 36.000 0.00 0.00 0.00 2.57
1452 1546 6.521162 TGCGGTTGTAGTATGATTGTCATAT 58.479 36.000 3.26 0.00 40.97 1.78
1454 1548 8.145122 TGCGGTTGTAGTATGATTGTCATATAA 58.855 33.333 3.26 0.00 40.97 0.98
1455 1549 8.984764 GCGGTTGTAGTATGATTGTCATATAAA 58.015 33.333 3.26 0.00 40.97 1.40
1490 1598 6.873076 GCTGCTGCTTAGATAAGAACTATGAT 59.127 38.462 8.53 0.00 35.33 2.45
1545 1653 2.731691 GAAGGCACCAAGCTGGACGA 62.732 60.000 8.91 0.00 40.96 4.20
1546 1654 2.281484 GGCACCAAGCTGGACGAA 60.281 61.111 8.91 0.00 40.96 3.85
1550 1658 1.401539 GCACCAAGCTGGACGAAATTC 60.402 52.381 8.91 0.00 40.96 2.17
1558 1666 1.262950 CTGGACGAAATTCGCAACACA 59.737 47.619 15.90 6.60 45.12 3.72
1559 1667 1.003331 TGGACGAAATTCGCAACACAC 60.003 47.619 15.90 0.00 45.12 3.82
1601 1709 8.633075 ATTATTATTAAACATGTGTGTGCTGC 57.367 30.769 0.00 0.00 38.92 5.25
1602 1710 5.444663 TTATTAAACATGTGTGTGCTGCA 57.555 34.783 0.00 0.00 38.92 4.41
1603 1711 4.524316 ATTAAACATGTGTGTGCTGCAT 57.476 36.364 5.27 0.00 38.92 3.96
1604 1712 2.143008 AAACATGTGTGTGCTGCATG 57.857 45.000 5.27 0.78 43.84 4.06
1605 1713 0.319211 AACATGTGTGTGCTGCATGC 60.319 50.000 11.82 11.82 42.50 4.06
1606 1714 1.799916 CATGTGTGTGCTGCATGCG 60.800 57.895 14.09 9.16 46.63 4.73
1607 1715 2.985117 ATGTGTGTGCTGCATGCGG 61.985 57.895 22.66 22.66 46.63 5.69
1608 1716 3.663176 GTGTGTGCTGCATGCGGT 61.663 61.111 26.79 0.00 46.63 5.68
1648 1756 4.041567 TGAGAGGGCTTGAGAATGTGTTAA 59.958 41.667 0.00 0.00 0.00 2.01
1649 1757 4.327680 AGAGGGCTTGAGAATGTGTTAAC 58.672 43.478 0.00 0.00 0.00 2.01
1650 1758 4.072131 GAGGGCTTGAGAATGTGTTAACA 58.928 43.478 3.59 3.59 41.58 2.41
1664 1772 1.197036 GTTAACAGCGGCCAAGAGAAC 59.803 52.381 2.24 0.00 0.00 3.01
1695 1803 7.856398 ACAGTAAAGAAGATCATATACACGTCG 59.144 37.037 0.00 0.00 0.00 5.12
1758 1866 2.618241 TGAGACACAGGTGAAATTGTGC 59.382 45.455 6.40 0.00 46.59 4.57
1761 1869 3.815401 AGACACAGGTGAAATTGTGCTAC 59.185 43.478 6.40 0.00 46.59 3.58
1765 1873 6.003950 ACACAGGTGAAATTGTGCTACTATT 58.996 36.000 6.40 0.00 46.59 1.73
1801 1909 5.340667 GCTTTGTCGTTTTTCATCTTGCTAG 59.659 40.000 0.00 0.00 0.00 3.42
1868 1976 3.344515 GGCACGGATTTTTAGGTCTTCT 58.655 45.455 0.00 0.00 0.00 2.85
1988 2097 3.497332 CGGAGGGAGTATGTCCTTATGA 58.503 50.000 0.00 0.00 46.06 2.15
2006 2115 8.366401 TCCTTATGAATGATTTTTGAGCAACAA 58.634 29.630 0.00 0.00 36.65 2.83
2079 2216 9.935241 AGCATACAGATATTTACTTGGTCTATG 57.065 33.333 0.00 0.00 0.00 2.23
2122 2259 8.827177 TTGCAAGGGTAAATAGATATTCTACG 57.173 34.615 0.00 0.00 30.79 3.51
2181 2318 6.719370 ACTGGTGCTATTTCCAAGAACAATTA 59.281 34.615 0.00 0.00 33.06 1.40
2185 2322 6.197096 GTGCTATTTCCAAGAACAATTATGCG 59.803 38.462 0.00 0.00 0.00 4.73
2205 2342 2.229543 CGTGTACAGTAACACCCAGCTA 59.770 50.000 0.00 0.00 45.66 3.32
2305 2442 4.133856 CACAAACTGTGCTAGCTGTAAC 57.866 45.455 17.23 6.11 41.89 2.50
2528 2680 8.465273 AACCTTCTTGCCCATAGTTATTTATC 57.535 34.615 0.00 0.00 0.00 1.75
2603 2755 3.004752 ACCTCTGTGACTTTTTGCAGT 57.995 42.857 0.00 0.00 0.00 4.40
2778 2930 8.697846 AACTTGTCATTCATGCATATTTTCAG 57.302 30.769 0.00 0.00 0.00 3.02
2851 3003 6.427853 CGCTCTGGTTGATTGAAATATATGGA 59.572 38.462 0.00 0.00 0.00 3.41
2926 3078 3.518303 ACCCTGTATGTCCCAGTACTTTC 59.482 47.826 0.00 0.00 0.00 2.62
2973 3129 5.789643 AACTTGTTTGCATACAGTCCATT 57.210 34.783 9.95 0.26 0.00 3.16
3054 3210 3.205338 TCAATGGGCGTATTCATGTGAG 58.795 45.455 0.00 0.00 0.00 3.51
3105 3261 4.884164 CCAAGAAACTTGACTGAAGGTCTT 59.116 41.667 12.25 0.00 44.74 3.01
3220 3376 6.809689 TGTAGACCGTCATGTTTTATGTACTG 59.190 38.462 0.40 0.00 0.00 2.74
3390 3549 3.888323 TGCATGAGTAGTTGCTTTTGGAA 59.112 39.130 0.00 0.00 39.60 3.53
3452 3613 6.675987 TGCACCCAAAAATATGAAAAATTGC 58.324 32.000 0.00 0.00 0.00 3.56
3461 3622 0.236187 TGAAAAATTGCGTCGGACGG 59.764 50.000 29.30 13.13 42.82 4.79
3468 3657 0.179156 TTGCGTCGGACGGATACTTC 60.179 55.000 29.30 12.92 42.59 3.01
3471 3660 1.709147 CGTCGGACGGATACTTCGGT 61.709 60.000 22.18 0.00 38.08 4.69
3506 3695 5.840243 TTGATCAAGATAGCAAACATGGG 57.160 39.130 3.38 0.00 0.00 4.00
3511 3700 3.370840 AGATAGCAAACATGGGCTTCA 57.629 42.857 12.95 0.00 41.41 3.02
3547 3737 5.403166 CCTATTGAAATTACGCAATGCCATG 59.597 40.000 0.00 0.00 36.27 3.66
3622 3820 7.035840 ACAACATTCAGCCATCTCATAAATC 57.964 36.000 0.00 0.00 0.00 2.17
3623 3821 6.832384 ACAACATTCAGCCATCTCATAAATCT 59.168 34.615 0.00 0.00 0.00 2.40
3624 3822 7.994911 ACAACATTCAGCCATCTCATAAATCTA 59.005 33.333 0.00 0.00 0.00 1.98
3625 3823 8.843262 CAACATTCAGCCATCTCATAAATCTAA 58.157 33.333 0.00 0.00 0.00 2.10
3626 3824 8.985315 ACATTCAGCCATCTCATAAATCTAAA 57.015 30.769 0.00 0.00 0.00 1.85
3651 3849 4.084328 GCTGGATAATCGATGTACAACAGC 60.084 45.833 17.93 17.93 40.40 4.40
3714 3912 6.014669 ACATGTAGCAGATAAATCCTCTCCTC 60.015 42.308 0.00 0.00 0.00 3.71
3716 3914 5.772672 TGTAGCAGATAAATCCTCTCCTCTC 59.227 44.000 0.00 0.00 0.00 3.20
3717 3915 4.813809 AGCAGATAAATCCTCTCCTCTCA 58.186 43.478 0.00 0.00 0.00 3.27
3724 3922 5.675684 AAATCCTCTCCTCTCAAAGAGTC 57.324 43.478 3.47 0.00 40.72 3.36
3958 4156 3.981071 TTGGTATACAAGCTGCTGACT 57.019 42.857 1.35 0.00 33.18 3.41
3978 4176 4.917385 ACTGGCATACCTGACAAACATTA 58.083 39.130 0.00 0.00 40.83 1.90
3990 4188 7.867403 ACCTGACAAACATTACAAATGTGATTC 59.133 33.333 6.07 4.17 31.80 2.52
3994 4192 9.891828 GACAAACATTACAAATGTGATTCAGTA 57.108 29.630 6.07 0.00 31.80 2.74
4002 4200 9.755804 TTACAAATGTGATTCAGTATGCAAAAA 57.244 25.926 0.00 0.00 34.76 1.94
4031 4229 8.244113 GGAAACTCATACAGGGAAAATAAGTTG 58.756 37.037 0.00 0.00 0.00 3.16
4046 4245 6.840780 AATAAGTTGATAAAACAGGCTGCT 57.159 33.333 15.89 0.00 0.00 4.24
4075 4274 5.560722 TTCTCAAGAAGAACCACCACATA 57.439 39.130 0.00 0.00 39.12 2.29
4101 4300 4.607293 ACCTTCCTCTTTTTCATTTGCC 57.393 40.909 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.733150 GTCCCTTGCGTGGCTAATTC 59.267 55.000 0.00 0.00 0.00 2.17
95 96 1.136891 TGCATCCATACGGTCTCTGTG 59.863 52.381 0.00 0.00 0.00 3.66
101 102 4.142491 TGTGATTTTTGCATCCATACGGTC 60.142 41.667 0.00 0.00 0.00 4.79
110 111 4.687483 CCTGTTTCCTGTGATTTTTGCATC 59.313 41.667 0.00 0.00 0.00 3.91
125 126 5.977489 ACTAAATAAAGGCACCTGTTTCC 57.023 39.130 0.00 0.00 0.00 3.13
137 138 9.362151 TGGGGGAAATGCTTATACTAAATAAAG 57.638 33.333 0.00 0.00 0.00 1.85
146 147 4.693283 GCTTTTGGGGGAAATGCTTATAC 58.307 43.478 0.00 0.00 40.13 1.47
192 193 4.572007 CCATCCATCCATCCATCCATCAAT 60.572 45.833 0.00 0.00 0.00 2.57
193 194 3.245479 CCATCCATCCATCCATCCATCAA 60.245 47.826 0.00 0.00 0.00 2.57
194 195 2.310647 CCATCCATCCATCCATCCATCA 59.689 50.000 0.00 0.00 0.00 3.07
347 357 4.384247 TGTGTTTTCTTTCTTGTGTTTGCG 59.616 37.500 0.00 0.00 0.00 4.85
348 358 5.608146 GTGTGTTTTCTTTCTTGTGTTTGC 58.392 37.500 0.00 0.00 0.00 3.68
349 359 5.164100 CCGTGTGTTTTCTTTCTTGTGTTTG 60.164 40.000 0.00 0.00 0.00 2.93
350 360 4.920927 CCGTGTGTTTTCTTTCTTGTGTTT 59.079 37.500 0.00 0.00 0.00 2.83
353 363 4.091453 ACCGTGTGTTTTCTTTCTTGTG 57.909 40.909 0.00 0.00 0.00 3.33
363 373 2.544903 GCTGCCATTAACCGTGTGTTTT 60.545 45.455 0.00 0.00 38.42 2.43
367 378 1.134487 CGCTGCCATTAACCGTGTG 59.866 57.895 0.00 0.00 0.00 3.82
373 384 1.348594 GTCGCTCGCTGCCATTAAC 59.651 57.895 0.00 0.00 38.78 2.01
421 436 4.087892 TCTTCCTGCCTCTGCCGC 62.088 66.667 0.00 0.00 36.33 6.53
422 437 2.186384 CTCTTCCTGCCTCTGCCG 59.814 66.667 0.00 0.00 36.33 5.69
425 440 1.481772 CCTTCTCTCTTCCTGCCTCTG 59.518 57.143 0.00 0.00 0.00 3.35
426 441 1.864669 CCTTCTCTCTTCCTGCCTCT 58.135 55.000 0.00 0.00 0.00 3.69
427 442 0.177836 GCCTTCTCTCTTCCTGCCTC 59.822 60.000 0.00 0.00 0.00 4.70
428 443 1.612395 CGCCTTCTCTCTTCCTGCCT 61.612 60.000 0.00 0.00 0.00 4.75
429 444 1.153469 CGCCTTCTCTCTTCCTGCC 60.153 63.158 0.00 0.00 0.00 4.85
430 445 1.153469 CCGCCTTCTCTCTTCCTGC 60.153 63.158 0.00 0.00 0.00 4.85
431 446 1.153469 GCCGCCTTCTCTCTTCCTG 60.153 63.158 0.00 0.00 0.00 3.86
432 447 2.716017 CGCCGCCTTCTCTCTTCCT 61.716 63.158 0.00 0.00 0.00 3.36
433 448 2.202810 CGCCGCCTTCTCTCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
434 449 1.226831 CTCGCCGCCTTCTCTCTTC 60.227 63.158 0.00 0.00 0.00 2.87
435 450 2.716017 CCTCGCCGCCTTCTCTCTT 61.716 63.158 0.00 0.00 0.00 2.85
436 451 3.144193 CCTCGCCGCCTTCTCTCT 61.144 66.667 0.00 0.00 0.00 3.10
635 685 3.432588 CACCTGCTGCTGCTGCTC 61.433 66.667 27.67 8.99 40.48 4.26
681 739 2.548547 GCCTTCCTCCCCCAACCTT 61.549 63.158 0.00 0.00 0.00 3.50
685 743 3.646715 CACGCCTTCCTCCCCCAA 61.647 66.667 0.00 0.00 0.00 4.12
783 849 1.737008 GAAGCCTCCAACGGTCGAC 60.737 63.158 7.13 7.13 0.00 4.20
870 937 1.065782 ACTCTCTCACTGAGCGAGCTA 60.066 52.381 21.19 0.00 43.00 3.32
914 995 1.211969 CCGATCGGTCAACTCGTGT 59.788 57.895 26.35 0.00 0.00 4.49
927 1008 2.046009 GCTTTCTCCCTCCCCCGATC 62.046 65.000 0.00 0.00 0.00 3.69
928 1009 2.073101 GCTTTCTCCCTCCCCCGAT 61.073 63.158 0.00 0.00 0.00 4.18
929 1010 2.687566 GCTTTCTCCCTCCCCCGA 60.688 66.667 0.00 0.00 0.00 5.14
930 1011 3.009115 TGCTTTCTCCCTCCCCCG 61.009 66.667 0.00 0.00 0.00 5.73
931 1012 1.925972 ACTGCTTTCTCCCTCCCCC 60.926 63.158 0.00 0.00 0.00 5.40
932 1013 1.301293 CACTGCTTTCTCCCTCCCC 59.699 63.158 0.00 0.00 0.00 4.81
933 1014 1.301293 CCACTGCTTTCTCCCTCCC 59.699 63.158 0.00 0.00 0.00 4.30
934 1015 0.402121 AACCACTGCTTTCTCCCTCC 59.598 55.000 0.00 0.00 0.00 4.30
935 1016 1.528129 CAACCACTGCTTTCTCCCTC 58.472 55.000 0.00 0.00 0.00 4.30
936 1017 0.111253 CCAACCACTGCTTTCTCCCT 59.889 55.000 0.00 0.00 0.00 4.20
937 1018 0.110486 TCCAACCACTGCTTTCTCCC 59.890 55.000 0.00 0.00 0.00 4.30
938 1019 2.087646 GATCCAACCACTGCTTTCTCC 58.912 52.381 0.00 0.00 0.00 3.71
939 1020 1.734465 CGATCCAACCACTGCTTTCTC 59.266 52.381 0.00 0.00 0.00 2.87
940 1021 1.611673 CCGATCCAACCACTGCTTTCT 60.612 52.381 0.00 0.00 0.00 2.52
941 1022 0.804989 CCGATCCAACCACTGCTTTC 59.195 55.000 0.00 0.00 0.00 2.62
942 1023 1.244019 GCCGATCCAACCACTGCTTT 61.244 55.000 0.00 0.00 0.00 3.51
943 1024 1.675641 GCCGATCCAACCACTGCTT 60.676 57.895 0.00 0.00 0.00 3.91
944 1025 2.045926 GCCGATCCAACCACTGCT 60.046 61.111 0.00 0.00 0.00 4.24
1268 1355 4.331168 CCTTGATTCAGCAAGTACTAGTGC 59.669 45.833 10.95 10.95 42.84 4.40
1270 1357 4.508662 GCCTTGATTCAGCAAGTACTAGT 58.491 43.478 0.00 0.00 42.84 2.57
1291 1385 3.489416 AGAAAAATCGGAAAGCAAAACGC 59.511 39.130 0.00 0.00 42.91 4.84
1292 1386 5.332280 GGAAGAAAAATCGGAAAGCAAAACG 60.332 40.000 0.00 0.00 0.00 3.60
1296 1390 4.340950 ACTGGAAGAAAAATCGGAAAGCAA 59.659 37.500 0.00 0.00 37.43 3.91
1304 1398 5.122396 CCTCTAACCACTGGAAGAAAAATCG 59.878 44.000 0.71 0.00 37.43 3.34
1306 1400 5.953571 ACCTCTAACCACTGGAAGAAAAAT 58.046 37.500 0.71 0.00 37.43 1.82
1311 1405 2.038557 GCAACCTCTAACCACTGGAAGA 59.961 50.000 0.71 3.60 37.43 2.87
1318 1412 2.846193 TCAACAGCAACCTCTAACCAC 58.154 47.619 0.00 0.00 0.00 4.16
1319 1413 3.569194 TTCAACAGCAACCTCTAACCA 57.431 42.857 0.00 0.00 0.00 3.67
1322 1416 5.362430 ACCAATTTTCAACAGCAACCTCTAA 59.638 36.000 0.00 0.00 0.00 2.10
1323 1417 4.892934 ACCAATTTTCAACAGCAACCTCTA 59.107 37.500 0.00 0.00 0.00 2.43
1324 1418 3.706086 ACCAATTTTCAACAGCAACCTCT 59.294 39.130 0.00 0.00 0.00 3.69
1325 1419 4.058721 ACCAATTTTCAACAGCAACCTC 57.941 40.909 0.00 0.00 0.00 3.85
1327 1421 4.187694 TCAACCAATTTTCAACAGCAACC 58.812 39.130 0.00 0.00 0.00 3.77
1337 1431 4.917415 CACGAACCTGATCAACCAATTTTC 59.083 41.667 0.00 0.00 0.00 2.29
1346 1440 2.039746 ACCAATCCACGAACCTGATCAA 59.960 45.455 0.00 0.00 0.00 2.57
1379 1473 3.813606 TTCACCGTCGACCTGGGGA 62.814 63.158 10.07 10.07 35.37 4.81
1380 1474 2.573609 GATTCACCGTCGACCTGGGG 62.574 65.000 10.58 7.76 0.00 4.96
1392 1486 4.116961 CACCAAATGCATCATGATTCACC 58.883 43.478 10.32 0.00 0.00 4.02
1411 1505 1.501169 GCATCAAACAACCAAGCACC 58.499 50.000 0.00 0.00 0.00 5.01
1429 1523 8.528917 TTATATGACAATCATACTACAACCGC 57.471 34.615 0.69 0.00 41.62 5.68
1452 1546 9.730705 ATCTAAGCAGCAGCATAAATAGATTTA 57.269 29.630 3.17 0.00 45.49 1.40
1454 1548 9.730705 TTATCTAAGCAGCAGCATAAATAGATT 57.269 29.630 3.17 0.00 45.49 2.40
1455 1549 9.381033 CTTATCTAAGCAGCAGCATAAATAGAT 57.619 33.333 3.17 10.26 45.49 1.98
1457 1551 8.768957 TCTTATCTAAGCAGCAGCATAAATAG 57.231 34.615 3.17 0.00 45.49 1.73
1504 1612 9.595823 CCTTCATAGTTCTTACTCCGAATTTTA 57.404 33.333 0.00 0.00 35.78 1.52
1505 1613 7.065923 GCCTTCATAGTTCTTACTCCGAATTTT 59.934 37.037 0.00 0.00 35.78 1.82
1506 1614 6.539103 GCCTTCATAGTTCTTACTCCGAATTT 59.461 38.462 0.00 0.00 35.78 1.82
1507 1615 6.049790 GCCTTCATAGTTCTTACTCCGAATT 58.950 40.000 0.00 0.00 35.78 2.17
1508 1616 5.128827 TGCCTTCATAGTTCTTACTCCGAAT 59.871 40.000 0.00 0.00 35.78 3.34
1509 1617 4.464951 TGCCTTCATAGTTCTTACTCCGAA 59.535 41.667 0.00 0.00 35.78 4.30
1510 1618 4.021229 TGCCTTCATAGTTCTTACTCCGA 58.979 43.478 0.00 0.00 35.78 4.55
1511 1619 4.113354 GTGCCTTCATAGTTCTTACTCCG 58.887 47.826 0.00 0.00 35.78 4.63
1512 1620 4.081087 TGGTGCCTTCATAGTTCTTACTCC 60.081 45.833 0.00 0.00 35.78 3.85
1513 1621 5.086104 TGGTGCCTTCATAGTTCTTACTC 57.914 43.478 0.00 0.00 35.78 2.59
1514 1622 5.491982 CTTGGTGCCTTCATAGTTCTTACT 58.508 41.667 0.00 0.00 38.44 2.24
1515 1623 4.095036 GCTTGGTGCCTTCATAGTTCTTAC 59.905 45.833 0.00 0.00 35.15 2.34
1516 1624 4.019321 AGCTTGGTGCCTTCATAGTTCTTA 60.019 41.667 0.00 0.00 44.23 2.10
1517 1625 3.084786 GCTTGGTGCCTTCATAGTTCTT 58.915 45.455 0.00 0.00 35.15 2.52
1518 1626 2.307098 AGCTTGGTGCCTTCATAGTTCT 59.693 45.455 0.00 0.00 44.23 3.01
1519 1627 2.421424 CAGCTTGGTGCCTTCATAGTTC 59.579 50.000 0.00 0.00 44.23 3.01
1529 1637 1.244019 ATTTCGTCCAGCTTGGTGCC 61.244 55.000 0.00 0.00 44.23 5.01
1545 1653 2.425312 TCACTTGGTGTGTTGCGAATTT 59.575 40.909 0.00 0.00 46.27 1.82
1546 1654 2.020720 TCACTTGGTGTGTTGCGAATT 58.979 42.857 0.00 0.00 46.27 2.17
1550 1658 0.732571 ACTTCACTTGGTGTGTTGCG 59.267 50.000 0.00 0.00 46.27 4.85
1575 1683 9.729023 GCAGCACACACATGTTTAATAATAATA 57.271 29.630 0.00 0.00 36.72 0.98
1576 1684 8.249638 TGCAGCACACACATGTTTAATAATAAT 58.750 29.630 0.00 0.00 36.72 1.28
1577 1685 7.597386 TGCAGCACACACATGTTTAATAATAA 58.403 30.769 0.00 0.00 36.72 1.40
1583 1691 3.640592 CATGCAGCACACACATGTTTAA 58.359 40.909 0.00 0.00 36.72 1.52
1597 1705 0.946528 TGATAATGACCGCATGCAGC 59.053 50.000 19.57 6.49 40.87 5.25
1598 1706 1.534163 CCTGATAATGACCGCATGCAG 59.466 52.381 19.57 9.32 34.26 4.41
1599 1707 1.134128 ACCTGATAATGACCGCATGCA 60.134 47.619 19.57 0.00 34.26 3.96
1601 1709 2.837498 TGACCTGATAATGACCGCATG 58.163 47.619 0.00 0.00 34.26 4.06
1602 1710 3.558931 TTGACCTGATAATGACCGCAT 57.441 42.857 0.00 0.00 35.92 4.73
1603 1711 3.205338 CATTGACCTGATAATGACCGCA 58.795 45.455 0.00 0.00 36.61 5.69
1604 1712 3.002656 CACATTGACCTGATAATGACCGC 59.997 47.826 0.00 0.00 37.63 5.68
1605 1713 4.441792 TCACATTGACCTGATAATGACCG 58.558 43.478 0.00 0.00 37.63 4.79
1606 1714 5.674525 TCTCACATTGACCTGATAATGACC 58.325 41.667 0.00 0.00 37.63 4.02
1607 1715 5.757320 CCTCTCACATTGACCTGATAATGAC 59.243 44.000 0.00 0.00 37.63 3.06
1608 1716 5.163269 CCCTCTCACATTGACCTGATAATGA 60.163 44.000 0.00 0.00 37.63 2.57
1648 1756 2.357517 CGTTCTCTTGGCCGCTGT 60.358 61.111 0.00 0.00 0.00 4.40
1649 1757 3.793144 GCGTTCTCTTGGCCGCTG 61.793 66.667 0.00 0.00 42.66 5.18
1664 1772 2.876091 TGATCTTCTTTACTGTCGGCG 58.124 47.619 0.00 0.00 0.00 6.46
1695 1803 1.204312 GCCAAGTGCGAAGAACGAC 59.796 57.895 0.00 0.00 45.77 4.34
1757 1865 6.927294 AAGCCAATACAGTTCAATAGTAGC 57.073 37.500 0.00 0.00 0.00 3.58
1758 1866 8.268850 ACAAAGCCAATACAGTTCAATAGTAG 57.731 34.615 0.00 0.00 0.00 2.57
1761 1869 6.128282 ACGACAAAGCCAATACAGTTCAATAG 60.128 38.462 0.00 0.00 0.00 1.73
1765 1873 3.472652 ACGACAAAGCCAATACAGTTCA 58.527 40.909 0.00 0.00 0.00 3.18
1776 1884 3.182372 GCAAGATGAAAAACGACAAAGCC 59.818 43.478 0.00 0.00 0.00 4.35
1801 1909 9.774742 GAGTACCATCATTTATTTCACAGAAAC 57.225 33.333 0.00 0.00 0.00 2.78
1877 1985 7.633193 TGCCACAAAAATTATACGGTTAGAT 57.367 32.000 0.00 0.00 0.00 1.98
1932 2041 1.300634 GGGCACGGGCTTTTAGGTA 59.699 57.895 10.74 0.00 40.87 3.08
1941 2050 0.604578 TATATTAGTCGGGCACGGGC 59.395 55.000 9.32 0.00 41.39 6.13
1944 2053 3.562505 GTCAGTATATTAGTCGGGCACG 58.437 50.000 0.00 0.00 42.74 5.34
1988 2097 6.114767 ACCAAGTTGTTGCTCAAAAATCATT 58.885 32.000 1.45 0.00 37.81 2.57
2006 2115 4.772886 AGAACAGAACTACCAACCAAGT 57.227 40.909 0.00 0.00 0.00 3.16
2122 2259 5.946377 AGTTAGGTTTCCAGATTTGACCATC 59.054 40.000 0.00 0.00 32.81 3.51
2185 2322 2.833631 AGCTGGGTGTTACTGTACAC 57.166 50.000 0.00 10.23 45.99 2.90
2220 2357 7.505585 TCAATACCCCAATTTTAATAGCAGAGG 59.494 37.037 0.00 0.00 0.00 3.69
2541 2693 2.480073 GGCGCTGTGTTTTATGCATCAT 60.480 45.455 7.64 0.00 0.00 2.45
2603 2755 6.209788 AGACGGCCATTAAACCTTTCAATTAA 59.790 34.615 2.24 0.00 0.00 1.40
2778 2930 6.038161 TGTGTTTGTGATATTAGCAGCCATAC 59.962 38.462 0.00 0.00 0.00 2.39
2851 3003 5.723295 CGGGAAATGAAAACTGAAATCCAT 58.277 37.500 0.00 0.00 0.00 3.41
3054 3210 3.574396 AGCCTAGTTCCCTTTTTGCTTTC 59.426 43.478 0.00 0.00 0.00 2.62
3105 3261 2.947652 GAGCCATAAAAGCATCTCAGCA 59.052 45.455 0.00 0.00 36.85 4.41
3220 3376 7.821359 ACTGCAGTATATACATGTCAATGATCC 59.179 37.037 20.16 0.00 37.24 3.36
3452 3613 1.010350 CCGAAGTATCCGTCCGACG 60.010 63.158 14.15 14.15 42.11 5.12
3461 3622 3.885484 CATGGATTGCACCGAAGTATC 57.115 47.619 0.00 0.00 0.00 2.24
3496 3685 3.193267 TGTATTCTGAAGCCCATGTTTGC 59.807 43.478 0.00 0.00 0.00 3.68
3506 3695 6.349300 TCAATAGGGAACTGTATTCTGAAGC 58.651 40.000 0.00 0.00 43.88 3.86
3511 3700 9.326413 CGTAATTTCAATAGGGAACTGTATTCT 57.674 33.333 0.00 0.00 43.88 2.40
3535 3724 1.340889 AGTTTCAACATGGCATTGCGT 59.659 42.857 0.00 0.00 0.00 5.24
3547 3737 6.090628 TCAGCATTTTTGTTGTGAGTTTCAAC 59.909 34.615 0.00 0.00 43.48 3.18
3622 3820 7.889589 TGTACATCGATTATCCAGCATTTAG 57.110 36.000 0.00 0.00 0.00 1.85
3623 3821 7.713073 TGTTGTACATCGATTATCCAGCATTTA 59.287 33.333 0.00 0.00 0.00 1.40
3624 3822 6.542005 TGTTGTACATCGATTATCCAGCATTT 59.458 34.615 0.00 0.00 0.00 2.32
3625 3823 6.054941 TGTTGTACATCGATTATCCAGCATT 58.945 36.000 0.00 0.00 0.00 3.56
3626 3824 5.610398 TGTTGTACATCGATTATCCAGCAT 58.390 37.500 0.00 0.00 0.00 3.79
3714 3912 5.936686 TTGATTCAGCAAGACTCTTTGAG 57.063 39.130 0.00 0.00 35.52 3.02
3716 3914 9.286946 GATTATTTGATTCAGCAAGACTCTTTG 57.713 33.333 0.00 0.00 0.00 2.77
3717 3915 9.017509 TGATTATTTGATTCAGCAAGACTCTTT 57.982 29.630 0.00 0.00 0.00 2.52
3724 3922 6.554419 TCGGTTGATTATTTGATTCAGCAAG 58.446 36.000 0.00 0.00 0.00 4.01
3958 4156 4.657013 TGTAATGTTTGTCAGGTATGCCA 58.343 39.130 1.54 0.00 37.19 4.92
4002 4200 8.893563 TTATTTTCCCTGTATGAGTTTCCATT 57.106 30.769 0.00 0.00 0.00 3.16
4063 4262 4.698780 GGAAGGTAAGTTATGTGGTGGTTC 59.301 45.833 0.00 0.00 0.00 3.62
4066 4265 4.225267 AGAGGAAGGTAAGTTATGTGGTGG 59.775 45.833 0.00 0.00 0.00 4.61
4075 4274 7.210174 GCAAATGAAAAAGAGGAAGGTAAGTT 58.790 34.615 0.00 0.00 0.00 2.66
4101 4300 6.981762 AGAGTTCTTGCTGAATATCAGTTG 57.018 37.500 8.97 1.01 45.94 3.16


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

AutoCloner maintained by Alex Coulton.