Multiple sequence alignment - TraesCS7B01G391400

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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 TraesCS7B01G391400 chr7B 100.000 2816 0 0 1 2816 657934193 657937008 0.000000e+00 5201.0
1 TraesCS7B01G391400 chr7B 77.914 815 151 12 2003 2814 584187694 584186906 5.460000e-132 481.0
2 TraesCS7B01G391400 chr7B 76.736 821 120 38 2000 2814 440820092 440820847 2.630000e-105 392.0
3 TraesCS7B01G391400 chr7B 80.556 216 40 1 2601 2814 729250898 729251113 6.240000e-37 165.0
4 TraesCS7B01G391400 chr7A 85.897 1326 159 19 1498 2816 678591851 678593155 0.000000e+00 1387.0
5 TraesCS7B01G391400 chr7A 91.515 660 38 11 1 657 678581925 678582569 0.000000e+00 893.0
6 TraesCS7B01G391400 chr7A 90.514 506 31 10 1328 1830 678589895 678590386 0.000000e+00 652.0
7 TraesCS7B01G391400 chr7A 76.185 823 181 12 1998 2814 42799154 42799967 1.210000e-113 420.0
8 TraesCS7B01G391400 chr7A 89.441 322 31 1 983 1301 678583589 678583910 1.210000e-108 403.0
9 TraesCS7B01G391400 chr7D 94.146 837 40 5 983 1816 587073386 587074216 0.000000e+00 1266.0
10 TraesCS7B01G391400 chr7D 95.144 659 22 7 1 657 587071490 587072140 0.000000e+00 1031.0
11 TraesCS7B01G391400 chr7D 86.316 95 4 4 900 986 587072949 587073042 8.300000e-16 95.3
12 TraesCS7B01G391400 chr1D 78.750 800 134 20 2017 2810 472399924 472399155 1.160000e-138 503.0
13 TraesCS7B01G391400 chr1D 79.292 734 118 21 2089 2812 400009386 400008677 1.520000e-132 483.0
14 TraesCS7B01G391400 chr5B 78.616 795 135 20 2003 2792 450768876 450768112 7.010000e-136 494.0
15 TraesCS7B01G391400 chr2B 78.145 787 162 8 2030 2812 707607759 707608539 2.520000e-135 492.0
16 TraesCS7B01G391400 chr5D 78.150 746 127 22 2092 2810 464993644 464994380 2.570000e-120 442.0
17 TraesCS7B01G391400 chr2D 77.517 725 152 8 2095 2814 10305016 10304298 2.590000e-115 425.0
18 TraesCS7B01G391400 chr3D 77.534 592 114 15 2212 2794 27957892 27958473 3.470000e-89 339.0
19 TraesCS7B01G391400 chr5A 77.213 531 103 14 2262 2781 585400209 585400732 7.630000e-76 294.0
20 TraesCS7B01G391400 chr1B 82.627 236 36 4 2249 2484 678062150 678062380 1.320000e-48 204.0
21 TraesCS7B01G391400 chr6D 87.302 63 8 0 1355 1417 431070270 431070208 3.890000e-09 73.1
22 TraesCS7B01G391400 chr6B 89.130 46 4 1 1850 1894 12652328 12652373 3.920000e-04 56.5


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 TraesCS7B01G391400 chr7B 657934193 657937008 2815 False 5201.000000 5201 100.000000 1 2816 1 chr7B.!!$F2 2815
1 TraesCS7B01G391400 chr7B 584186906 584187694 788 True 481.000000 481 77.914000 2003 2814 1 chr7B.!!$R1 811
2 TraesCS7B01G391400 chr7B 440820092 440820847 755 False 392.000000 392 76.736000 2000 2814 1 chr7B.!!$F1 814
3 TraesCS7B01G391400 chr7A 678589895 678593155 3260 False 1019.500000 1387 88.205500 1328 2816 2 chr7A.!!$F3 1488
4 TraesCS7B01G391400 chr7A 678581925 678583910 1985 False 648.000000 893 90.478000 1 1301 2 chr7A.!!$F2 1300
5 TraesCS7B01G391400 chr7A 42799154 42799967 813 False 420.000000 420 76.185000 1998 2814 1 chr7A.!!$F1 816
6 TraesCS7B01G391400 chr7D 587071490 587074216 2726 False 797.433333 1266 91.868667 1 1816 3 chr7D.!!$F1 1815
7 TraesCS7B01G391400 chr1D 472399155 472399924 769 True 503.000000 503 78.750000 2017 2810 1 chr1D.!!$R2 793
8 TraesCS7B01G391400 chr1D 400008677 400009386 709 True 483.000000 483 79.292000 2089 2812 1 chr1D.!!$R1 723
9 TraesCS7B01G391400 chr5B 450768112 450768876 764 True 494.000000 494 78.616000 2003 2792 1 chr5B.!!$R1 789
10 TraesCS7B01G391400 chr2B 707607759 707608539 780 False 492.000000 492 78.145000 2030 2812 1 chr2B.!!$F1 782
11 TraesCS7B01G391400 chr5D 464993644 464994380 736 False 442.000000 442 78.150000 2092 2810 1 chr5D.!!$F1 718
12 TraesCS7B01G391400 chr2D 10304298 10305016 718 True 425.000000 425 77.517000 2095 2814 1 chr2D.!!$R1 719
13 TraesCS7B01G391400 chr3D 27957892 27958473 581 False 339.000000 339 77.534000 2212 2794 1 chr3D.!!$F1 582
14 TraesCS7B01G391400 chr5A 585400209 585400732 523 False 294.000000 294 77.213000 2262 2781 1 chr5A.!!$F1 519

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
512 515 0.038166 TTGCCTGAATCTTCGGCCTT 59.962 50.0 17.18 0.0 42.27 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 5360 0.107831 ACGTCTGCTACTGGGCAAAA 59.892 50.0 0.0 0.0 41.94 2.44 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
114 115 1.689273 GCCAGGATACAGAGTACCAGG 59.311 57.143 0.00 0.00 41.41 4.45
219 221 2.203070 GTGTGCCTGCCTATCCGG 60.203 66.667 0.00 0.00 0.00 5.14
394 397 5.680619 TGTTAACAAGGAGCTATGGTATGG 58.319 41.667 5.64 0.00 0.00 2.74
395 398 5.190925 TGTTAACAAGGAGCTATGGTATGGT 59.809 40.000 5.64 0.00 0.00 3.55
396 399 6.384595 TGTTAACAAGGAGCTATGGTATGGTA 59.615 38.462 5.64 0.00 0.00 3.25
397 400 7.071950 TGTTAACAAGGAGCTATGGTATGGTAT 59.928 37.037 5.64 0.00 0.00 2.73
398 401 5.489792 ACAAGGAGCTATGGTATGGTATG 57.510 43.478 0.00 0.00 0.00 2.39
399 402 4.907875 ACAAGGAGCTATGGTATGGTATGT 59.092 41.667 0.00 0.00 0.00 2.29
400 403 5.221722 ACAAGGAGCTATGGTATGGTATGTG 60.222 44.000 0.00 0.00 0.00 3.21
413 416 0.370273 GTATGTGTTCTCCGCAAGCG 59.630 55.000 7.60 7.60 37.07 4.68
435 438 4.201666 CGAAGAGCTATCTTTGTCTTGTGC 60.202 45.833 0.00 0.00 45.98 4.57
491 494 3.058224 GCTGTTGTGTAAATCTGTGTCCC 60.058 47.826 0.00 0.00 0.00 4.46
502 505 1.355381 TCTGTGTCCCATTGCCTGAAT 59.645 47.619 0.00 0.00 0.00 2.57
504 507 1.355381 TGTGTCCCATTGCCTGAATCT 59.645 47.619 0.00 0.00 0.00 2.40
512 515 0.038166 TTGCCTGAATCTTCGGCCTT 59.962 50.000 17.18 0.00 42.27 4.35
513 516 0.677731 TGCCTGAATCTTCGGCCTTG 60.678 55.000 17.18 0.00 42.27 3.61
514 517 1.997928 GCCTGAATCTTCGGCCTTGC 61.998 60.000 0.00 0.21 39.37 4.01
527 530 1.405661 GGCCTTGCTAGTGGTCACTAC 60.406 57.143 6.73 5.57 42.54 2.73
569 573 4.512571 TGAGAATTGTGATGACTGTGTGTG 59.487 41.667 0.00 0.00 0.00 3.82
590 594 1.470098 CTGCCATTCTTTTCACCTCCG 59.530 52.381 0.00 0.00 0.00 4.63
596 600 1.438651 TCTTTTCACCTCCGAATGCG 58.561 50.000 0.00 0.00 37.24 4.73
631 635 7.605691 TGTTCTCATCAGATTCTTCTTCTTTCC 59.394 37.037 0.00 0.00 0.00 3.13
641 648 8.267894 AGATTCTTCTTCTTTCCGGATCAATTA 58.732 33.333 4.15 0.00 0.00 1.40
642 649 8.986929 ATTCTTCTTCTTTCCGGATCAATTAT 57.013 30.769 4.15 0.00 0.00 1.28
643 650 8.438676 TTCTTCTTCTTTCCGGATCAATTATC 57.561 34.615 4.15 0.00 0.00 1.75
657 664 8.547894 CGGATCAATTATCGTCTATGTCAAAAA 58.452 33.333 0.00 0.00 35.21 1.94
705 712 9.533253 AATTCAAGATAACAGTGTTCTTTTTGG 57.467 29.630 12.82 0.00 0.00 3.28
706 713 7.873719 TCAAGATAACAGTGTTCTTTTTGGA 57.126 32.000 12.82 2.02 0.00 3.53
707 714 8.463930 TCAAGATAACAGTGTTCTTTTTGGAT 57.536 30.769 12.82 0.00 0.00 3.41
708 715 8.567948 TCAAGATAACAGTGTTCTTTTTGGATC 58.432 33.333 12.82 7.36 0.00 3.36
709 716 8.352201 CAAGATAACAGTGTTCTTTTTGGATCA 58.648 33.333 12.82 0.00 0.00 2.92
710 717 8.463930 AGATAACAGTGTTCTTTTTGGATCAA 57.536 30.769 12.82 0.00 0.00 2.57
711 718 9.082313 AGATAACAGTGTTCTTTTTGGATCAAT 57.918 29.630 12.82 0.00 0.00 2.57
712 719 9.696917 GATAACAGTGTTCTTTTTGGATCAATT 57.303 29.630 12.82 0.00 0.00 2.32
716 723 9.480053 ACAGTGTTCTTTTTGGATCAATTATTG 57.520 29.630 0.00 0.00 0.00 1.90
717 724 9.480053 CAGTGTTCTTTTTGGATCAATTATTGT 57.520 29.630 4.77 0.00 0.00 2.71
718 725 9.696917 AGTGTTCTTTTTGGATCAATTATTGTC 57.303 29.630 4.77 2.56 0.00 3.18
719 726 9.696917 GTGTTCTTTTTGGATCAATTATTGTCT 57.303 29.630 4.77 0.00 0.00 3.41
762 771 6.839124 ACATTTTGGATCAATTGCTGTCTA 57.161 33.333 0.00 0.00 0.00 2.59
763 772 7.414222 ACATTTTGGATCAATTGCTGTCTAT 57.586 32.000 0.00 0.00 0.00 1.98
775 908 9.108284 TCAATTGCTGTCTATATCAAAATTCGA 57.892 29.630 0.00 0.00 0.00 3.71
776 909 9.720667 CAATTGCTGTCTATATCAAAATTCGAA 57.279 29.630 0.00 0.00 0.00 3.71
800 1587 6.935741 ATAAACCTTTTCCTTTTTGCAACC 57.064 33.333 0.00 0.00 0.00 3.77
816 1603 7.489574 TTTGCAACCAATCCAAAATAAACTC 57.510 32.000 0.00 0.00 0.00 3.01
850 1811 1.852309 TGGCCTCTCTCTCTCTGATCT 59.148 52.381 3.32 0.00 0.00 2.75
857 1818 5.304686 TCTCTCTCTCTGATCTCCCTTAC 57.695 47.826 0.00 0.00 0.00 2.34
877 1838 3.081409 ATCGGAGTTGGGTCCCCG 61.081 66.667 5.13 0.74 43.02 5.73
883 1844 1.305887 AGTTGGGTCCCCGTCCTAG 60.306 63.158 5.13 0.00 39.42 3.02
884 1845 1.611556 GTTGGGTCCCCGTCCTAGT 60.612 63.158 5.13 0.00 39.42 2.57
885 1846 1.305549 TTGGGTCCCCGTCCTAGTC 60.306 63.158 5.13 0.00 39.42 2.59
886 1847 2.832201 GGGTCCCCGTCCTAGTCG 60.832 72.222 0.00 0.00 0.00 4.18
887 1848 2.832201 GGTCCCCGTCCTAGTCGG 60.832 72.222 14.21 14.21 46.49 4.79
895 1856 3.129502 TCCTAGTCGGACGCGGTG 61.130 66.667 12.47 0.00 36.69 4.94
896 1857 3.437795 CCTAGTCGGACGCGGTGT 61.438 66.667 12.47 0.00 33.16 4.16
897 1858 2.564975 CTAGTCGGACGCGGTGTT 59.435 61.111 12.47 0.00 0.00 3.32
898 1859 1.800315 CTAGTCGGACGCGGTGTTG 60.800 63.158 12.47 0.00 0.00 3.33
899 1860 3.902162 TAGTCGGACGCGGTGTTGC 62.902 63.158 12.47 0.00 0.00 4.17
903 1864 4.681978 GGACGCGGTGTTGCTCCT 62.682 66.667 12.47 0.00 32.69 3.69
921 1882 4.020485 GCTCCTCCGCTTTTATATAGGGAA 60.020 45.833 0.00 0.00 0.00 3.97
922 1883 5.725362 CTCCTCCGCTTTTATATAGGGAAG 58.275 45.833 0.00 0.00 0.00 3.46
923 1884 4.530946 TCCTCCGCTTTTATATAGGGAAGG 59.469 45.833 0.00 0.00 0.00 3.46
926 1887 6.110411 TCCGCTTTTATATAGGGAAGGAAG 57.890 41.667 0.00 0.00 0.00 3.46
938 1899 0.949105 GAAGGAAGAGTTCGCGCCAA 60.949 55.000 0.00 0.00 0.00 4.52
939 1900 0.951040 AAGGAAGAGTTCGCGCCAAG 60.951 55.000 0.00 0.00 0.00 3.61
940 1901 2.476499 GAAGAGTTCGCGCCAAGC 59.524 61.111 0.00 0.00 43.95 4.01
953 1921 2.928694 CGCCAAGCAATTTACGTTTCT 58.071 42.857 0.00 0.00 0.00 2.52
1070 2385 4.125695 GCCCTTCTACGCGTCGGT 62.126 66.667 18.63 0.00 0.00 4.69
1323 2641 1.513586 CACCTACTCGTTCGACGCC 60.514 63.158 0.00 0.00 42.21 5.68
1774 4884 0.391528 CACGGTGGCTCATGACATGA 60.392 55.000 17.09 17.09 37.76 3.07
1775 4885 0.543277 ACGGTGGCTCATGACATGAT 59.457 50.000 18.28 0.00 38.85 2.45
1776 4886 1.224075 CGGTGGCTCATGACATGATC 58.776 55.000 18.28 14.05 38.85 2.92
1790 4900 0.177836 ATGATCAATCCGCCGACACA 59.822 50.000 0.00 0.00 0.00 3.72
1816 4926 2.417651 CCTACCGCGTTCTGGATGTAAA 60.418 50.000 4.92 0.00 0.00 2.01
1818 4928 2.006888 ACCGCGTTCTGGATGTAAATG 58.993 47.619 4.92 0.00 0.00 2.32
1824 4934 4.496341 GCGTTCTGGATGTAAATGTGATGG 60.496 45.833 0.00 0.00 0.00 3.51
1830 4940 5.754782 TGGATGTAAATGTGATGGCTACTT 58.245 37.500 0.00 0.00 0.00 2.24
1836 4946 6.539826 TGTAAATGTGATGGCTACTTCATCTG 59.460 38.462 0.00 0.00 41.01 2.90
1950 5060 8.701908 AACACCAAATATACGTATAGAGAGGA 57.298 34.615 19.40 0.00 0.00 3.71
1953 5063 6.377712 ACCAAATATACGTATAGAGAGGAGCC 59.622 42.308 19.40 0.00 0.00 4.70
1954 5064 6.377429 CCAAATATACGTATAGAGAGGAGCCA 59.623 42.308 19.40 0.00 0.00 4.75
1955 5065 7.068839 CCAAATATACGTATAGAGAGGAGCCAT 59.931 40.741 19.40 0.00 0.00 4.40
1956 5066 7.811117 AATATACGTATAGAGAGGAGCCATC 57.189 40.000 19.40 0.00 0.00 3.51
1957 5067 2.428491 ACGTATAGAGAGGAGCCATCG 58.572 52.381 0.00 0.00 0.00 3.84
1958 5068 1.131504 CGTATAGAGAGGAGCCATCGC 59.868 57.143 0.00 0.00 0.00 4.58
1959 5069 1.131504 GTATAGAGAGGAGCCATCGCG 59.868 57.143 0.00 0.00 41.18 5.87
1960 5070 1.872197 ATAGAGAGGAGCCATCGCGC 61.872 60.000 0.00 0.00 41.18 6.86
1978 5088 4.176752 GCGGCCCCTTTCCTCGAT 62.177 66.667 0.00 0.00 0.00 3.59
1982 5092 3.121406 GCCCCTTTCCTCGATCCCC 62.121 68.421 0.00 0.00 0.00 4.81
1992 5102 4.220163 CGATCCCCTCCCTCCCGA 62.220 72.222 0.00 0.00 0.00 5.14
1994 5104 1.152008 GATCCCCTCCCTCCCGATT 60.152 63.158 0.00 0.00 0.00 3.34
2081 5195 4.344865 GGCCTTCCTCCACCGCAA 62.345 66.667 0.00 0.00 0.00 4.85
2086 5200 0.035458 CTTCCTCCACCGCAACTTCT 59.965 55.000 0.00 0.00 0.00 2.85
2093 5207 0.957395 CACCGCAACTTCTGGATGCT 60.957 55.000 0.00 0.00 37.92 3.79
2180 5297 2.124695 GGCCCCTCCATTGTCGAC 60.125 66.667 9.11 9.11 34.01 4.20
2186 5303 1.874019 CTCCATTGTCGACGGCTCG 60.874 63.158 11.62 0.00 41.65 5.03
2237 5365 1.082756 GCTCTGGTCGTGCGTTTTG 60.083 57.895 0.00 0.00 0.00 2.44
2258 5388 1.154016 CAGTAGCAGACGTCACCCG 60.154 63.158 19.50 4.12 44.03 5.28
2340 5470 1.032014 GCCAGTGAAAGCTTGGTTCA 58.968 50.000 0.00 0.00 32.62 3.18
2363 5523 1.300620 CAGCCAGAACCGTCAACGA 60.301 57.895 3.71 0.00 43.02 3.85
2384 5544 1.435577 GACACCCGTGAGCGTTATTT 58.564 50.000 0.96 0.00 36.15 1.40
2453 5615 3.008485 GGAGGAAACCACAGATTCAGACT 59.992 47.826 0.00 0.00 0.00 3.24
2486 5648 0.994247 ATGATGGTGAGGTTCCTGCA 59.006 50.000 0.00 0.00 0.00 4.41
2487 5649 0.036732 TGATGGTGAGGTTCCTGCAC 59.963 55.000 0.00 4.77 0.00 4.57
2547 5714 2.640316 AGTTGGAGGGACAAGTGTTC 57.360 50.000 0.00 0.00 32.99 3.18
2741 5929 1.248101 TGGCGTCGATGACAGAAGGA 61.248 55.000 9.73 0.00 32.09 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 7.145323 TCGTTCTTCTTCCCATTTTTCATTTC 58.855 34.615 0.00 0.00 0.00 2.17
219 221 2.191641 GGGCAGCCATCAGACCTC 59.808 66.667 15.19 0.00 0.00 3.85
394 397 0.370273 CGCTTGCGGAGAACACATAC 59.630 55.000 7.16 0.00 0.00 2.39
395 398 0.245266 TCGCTTGCGGAGAACACATA 59.755 50.000 15.10 0.00 0.00 2.29
396 399 0.602638 TTCGCTTGCGGAGAACACAT 60.603 50.000 15.10 0.00 0.00 3.21
397 400 1.221466 CTTCGCTTGCGGAGAACACA 61.221 55.000 17.46 0.00 30.90 3.72
398 401 0.944311 TCTTCGCTTGCGGAGAACAC 60.944 55.000 21.84 0.00 30.90 3.32
399 402 0.667487 CTCTTCGCTTGCGGAGAACA 60.667 55.000 23.68 5.40 30.90 3.18
400 403 1.960994 GCTCTTCGCTTGCGGAGAAC 61.961 60.000 23.68 17.19 35.14 3.01
413 416 4.934602 AGCACAAGACAAAGATAGCTCTTC 59.065 41.667 0.00 0.00 40.93 2.87
435 438 2.671888 CAGAATATGCAGCCGCTATCAG 59.328 50.000 0.00 0.00 39.64 2.90
491 494 0.383231 GGCCGAAGATTCAGGCAATG 59.617 55.000 21.42 0.00 43.63 2.82
502 505 1.192146 ACCACTAGCAAGGCCGAAGA 61.192 55.000 0.00 0.00 0.00 2.87
504 507 1.295423 GACCACTAGCAAGGCCGAA 59.705 57.895 0.00 0.00 0.00 4.30
527 530 4.584325 TCTCAAATCAACAAAACCAGGAGG 59.416 41.667 0.00 0.00 42.21 4.30
569 573 1.203287 GGAGGTGAAAAGAATGGCAGC 59.797 52.381 0.00 0.00 0.00 5.25
590 594 5.484173 TGAGAACAATATGAACCGCATTC 57.516 39.130 0.00 0.00 38.44 2.67
596 600 8.674263 AGAATCTGATGAGAACAATATGAACC 57.326 34.615 0.00 0.00 0.00 3.62
631 635 7.637709 TTTGACATAGACGATAATTGATCCG 57.362 36.000 0.00 0.00 0.00 4.18
679 686 9.533253 CCAAAAAGAACACTGTTATCTTGAATT 57.467 29.630 10.67 0.00 33.86 2.17
680 687 8.912988 TCCAAAAAGAACACTGTTATCTTGAAT 58.087 29.630 10.67 0.00 33.86 2.57
682 689 7.873719 TCCAAAAAGAACACTGTTATCTTGA 57.126 32.000 10.67 0.00 33.86 3.02
684 691 8.463930 TGATCCAAAAAGAACACTGTTATCTT 57.536 30.769 0.00 0.00 35.00 2.40
685 692 8.463930 TTGATCCAAAAAGAACACTGTTATCT 57.536 30.769 0.00 0.00 0.00 1.98
693 700 9.696917 AGACAATAATTGATCCAAAAAGAACAC 57.303 29.630 0.00 0.00 0.00 3.32
733 740 9.287373 ACAGCAATTGATCCAAAATGTTTATTT 57.713 25.926 10.34 0.00 38.11 1.40
734 741 8.851541 ACAGCAATTGATCCAAAATGTTTATT 57.148 26.923 10.34 0.00 0.00 1.40
735 742 8.316214 AGACAGCAATTGATCCAAAATGTTTAT 58.684 29.630 10.34 0.00 0.00 1.40
736 743 7.669427 AGACAGCAATTGATCCAAAATGTTTA 58.331 30.769 10.34 0.00 0.00 2.01
737 744 6.527423 AGACAGCAATTGATCCAAAATGTTT 58.473 32.000 10.34 0.00 0.00 2.83
738 745 6.105397 AGACAGCAATTGATCCAAAATGTT 57.895 33.333 10.34 0.00 0.00 2.71
739 746 5.733620 AGACAGCAATTGATCCAAAATGT 57.266 34.783 10.34 0.00 0.00 2.71
740 747 9.622004 GATATAGACAGCAATTGATCCAAAATG 57.378 33.333 10.34 0.00 0.00 2.32
741 748 9.358406 TGATATAGACAGCAATTGATCCAAAAT 57.642 29.630 10.34 0.00 0.00 1.82
742 749 8.750515 TGATATAGACAGCAATTGATCCAAAA 57.249 30.769 10.34 0.00 0.00 2.44
743 750 8.750515 TTGATATAGACAGCAATTGATCCAAA 57.249 30.769 10.34 0.00 0.00 3.28
748 755 9.888878 CGAATTTTGATATAGACAGCAATTGAT 57.111 29.630 10.34 0.00 0.00 2.57
750 757 9.720667 TTCGAATTTTGATATAGACAGCAATTG 57.279 29.630 0.00 0.00 0.00 2.32
775 908 7.394641 TGGTTGCAAAAAGGAAAAGGTTTATTT 59.605 29.630 0.00 0.00 0.00 1.40
776 909 6.887002 TGGTTGCAAAAAGGAAAAGGTTTATT 59.113 30.769 0.00 0.00 0.00 1.40
777 910 6.418946 TGGTTGCAAAAAGGAAAAGGTTTAT 58.581 32.000 0.00 0.00 0.00 1.40
779 912 4.657013 TGGTTGCAAAAAGGAAAAGGTTT 58.343 34.783 0.00 0.00 0.00 3.27
782 915 4.275689 GGATTGGTTGCAAAAAGGAAAAGG 59.724 41.667 0.00 0.00 0.00 3.11
783 916 4.880696 TGGATTGGTTGCAAAAAGGAAAAG 59.119 37.500 0.00 0.00 0.00 2.27
795 1582 6.223120 ACAGAGTTTATTTTGGATTGGTTGC 58.777 36.000 0.00 0.00 0.00 4.17
800 1587 6.582295 CGGTGAACAGAGTTTATTTTGGATTG 59.418 38.462 0.00 0.00 0.00 2.67
816 1603 2.551912 GGCCAACACCGGTGAACAG 61.552 63.158 40.21 24.36 0.00 3.16
850 1811 2.108168 CCAACTCCGATCTGTAAGGGA 58.892 52.381 0.00 0.00 0.00 4.20
857 1818 1.522569 GGGACCCAACTCCGATCTG 59.477 63.158 5.33 0.00 0.00 2.90
886 1847 4.681978 AGGAGCAACACCGCGTCC 62.682 66.667 4.92 3.03 36.85 4.79
887 1848 3.112709 GAGGAGCAACACCGCGTC 61.113 66.667 4.92 0.00 36.85 5.19
888 1849 4.681978 GGAGGAGCAACACCGCGT 62.682 66.667 4.92 0.00 36.85 6.01
891 1852 3.883744 AAGCGGAGGAGCAACACCG 62.884 63.158 11.13 11.13 46.74 4.94
892 1853 1.172812 AAAAGCGGAGGAGCAACACC 61.173 55.000 0.00 0.00 40.15 4.16
893 1854 1.519408 TAAAAGCGGAGGAGCAACAC 58.481 50.000 0.00 0.00 40.15 3.32
894 1855 2.489938 ATAAAAGCGGAGGAGCAACA 57.510 45.000 0.00 0.00 40.15 3.33
895 1856 4.691216 CCTATATAAAAGCGGAGGAGCAAC 59.309 45.833 0.00 0.00 40.15 4.17
896 1857 4.262894 CCCTATATAAAAGCGGAGGAGCAA 60.263 45.833 0.00 0.00 40.15 3.91
897 1858 3.260884 CCCTATATAAAAGCGGAGGAGCA 59.739 47.826 0.00 0.00 40.15 4.26
898 1859 3.514309 TCCCTATATAAAAGCGGAGGAGC 59.486 47.826 0.00 0.00 37.41 4.70
899 1860 5.337652 CCTTCCCTATATAAAAGCGGAGGAG 60.338 48.000 0.00 0.00 0.00 3.69
900 1861 4.530946 CCTTCCCTATATAAAAGCGGAGGA 59.469 45.833 0.00 0.00 0.00 3.71
901 1862 4.530946 TCCTTCCCTATATAAAAGCGGAGG 59.469 45.833 0.00 0.00 0.00 4.30
902 1863 5.740290 TCCTTCCCTATATAAAAGCGGAG 57.260 43.478 0.00 0.00 0.00 4.63
903 1864 5.842328 TCTTCCTTCCCTATATAAAAGCGGA 59.158 40.000 0.00 0.00 0.00 5.54
921 1882 1.374758 CTTGGCGCGAACTCTTCCT 60.375 57.895 12.10 0.00 0.00 3.36
922 1883 3.028366 GCTTGGCGCGAACTCTTCC 62.028 63.158 12.10 0.00 0.00 3.46
923 1884 1.841663 TTGCTTGGCGCGAACTCTTC 61.842 55.000 12.10 0.00 43.27 2.87
926 1887 0.387239 AAATTGCTTGGCGCGAACTC 60.387 50.000 12.10 0.00 43.27 3.01
938 1899 5.458779 GCAGAAACAAGAAACGTAAATTGCT 59.541 36.000 0.00 0.00 0.00 3.91
939 1900 5.231147 TGCAGAAACAAGAAACGTAAATTGC 59.769 36.000 0.00 0.00 0.00 3.56
940 1901 6.252441 TGTGCAGAAACAAGAAACGTAAATTG 59.748 34.615 0.00 0.00 0.00 2.32
941 1902 6.326375 TGTGCAGAAACAAGAAACGTAAATT 58.674 32.000 0.00 0.00 0.00 1.82
942 1903 5.885881 TGTGCAGAAACAAGAAACGTAAAT 58.114 33.333 0.00 0.00 0.00 1.40
943 1904 5.298197 TGTGCAGAAACAAGAAACGTAAA 57.702 34.783 0.00 0.00 0.00 2.01
1045 2360 0.179097 GCGTAGAAGGGCTTGGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
1046 2361 1.898154 GCGTAGAAGGGCTTGGAGA 59.102 57.895 0.00 0.00 0.00 3.71
1077 2392 0.247460 CCATGACGAAGAGCCTGTCA 59.753 55.000 0.00 0.00 45.71 3.58
1105 2420 4.803426 GCCGAGCTCCTCCACGTG 62.803 72.222 9.08 9.08 0.00 4.49
1296 2614 0.896019 ACGAGTAGGTGCTCTGCTGT 60.896 55.000 3.42 1.04 38.57 4.40
1301 2619 0.803740 GTCGAACGAGTAGGTGCTCT 59.196 55.000 0.00 0.00 33.55 4.09
1509 2827 1.515020 CCTCTCCTCGCTGACCTTG 59.485 63.158 0.00 0.00 0.00 3.61
1629 4736 4.063230 TCGTCGTCGTCGTCACCG 62.063 66.667 11.41 1.59 38.33 4.94
1673 4783 0.179097 GAGAGCGAAGGTGGTCATCC 60.179 60.000 0.00 0.00 39.88 3.51
1774 4884 0.179100 CTCTGTGTCGGCGGATTGAT 60.179 55.000 7.21 0.00 0.00 2.57
1775 4885 1.215382 CTCTGTGTCGGCGGATTGA 59.785 57.895 7.21 0.00 0.00 2.57
1776 4886 1.078759 GACTCTGTGTCGGCGGATTG 61.079 60.000 7.21 0.00 35.81 2.67
1790 4900 1.313812 CCAGAACGCGGTAGGACTCT 61.314 60.000 12.47 0.00 0.00 3.24
1816 4926 4.767578 ACAGATGAAGTAGCCATCACAT 57.232 40.909 0.00 0.00 42.03 3.21
1818 4928 4.920340 CGATACAGATGAAGTAGCCATCAC 59.080 45.833 0.00 0.00 42.03 3.06
1824 4934 7.881643 ATCATTTCGATACAGATGAAGTAGC 57.118 36.000 0.00 0.00 32.80 3.58
1830 4940 8.722480 AACTTCAATCATTTCGATACAGATGA 57.278 30.769 0.00 0.00 32.51 2.92
1929 5039 6.377429 TGGCTCCTCTCTATACGTATATTTGG 59.623 42.308 15.42 14.16 0.00 3.28
1931 5041 7.012515 CGATGGCTCCTCTCTATACGTATATTT 59.987 40.741 15.42 0.00 0.00 1.40
1936 5046 3.597255 CGATGGCTCCTCTCTATACGTA 58.403 50.000 0.00 0.00 0.00 3.57
1963 5073 2.511403 GGATCGAGGAAAGGGGCC 59.489 66.667 0.00 0.00 0.00 5.80
1970 5080 1.233369 GAGGGAGGGGATCGAGGAA 59.767 63.158 0.00 0.00 0.00 3.36
1978 5088 1.384082 GAAATCGGGAGGGAGGGGA 60.384 63.158 0.00 0.00 0.00 4.81
1982 5092 0.399233 AGGAGGAAATCGGGAGGGAG 60.399 60.000 0.00 0.00 0.00 4.30
1992 5102 1.484240 CAGCGAGGAGAAGGAGGAAAT 59.516 52.381 0.00 0.00 0.00 2.17
1994 5104 0.251832 ACAGCGAGGAGAAGGAGGAA 60.252 55.000 0.00 0.00 0.00 3.36
2027 5138 2.985282 CCGCTTGAGCTTTGCCCA 60.985 61.111 1.07 0.00 39.32 5.36
2075 5189 0.957395 CAGCATCCAGAAGTTGCGGT 60.957 55.000 0.00 0.00 44.46 5.68
2081 5195 0.957395 CCGCAACAGCATCCAGAAGT 60.957 55.000 0.00 0.00 0.00 3.01
2086 5200 2.672651 CCACCGCAACAGCATCCA 60.673 61.111 0.00 0.00 0.00 3.41
2093 5207 2.264480 CGGATCTCCACCGCAACA 59.736 61.111 0.00 0.00 43.74 3.33
2186 5303 3.930012 CCGCTACCCTGCCTAGGC 61.930 72.222 27.71 27.71 43.16 3.93
2233 5360 0.107831 ACGTCTGCTACTGGGCAAAA 59.892 50.000 0.00 0.00 41.94 2.44
2237 5365 1.446272 GTGACGTCTGCTACTGGGC 60.446 63.158 17.92 0.00 0.00 5.36
2258 5388 3.367703 CCTCCATCATCAAGCAAACCAAC 60.368 47.826 0.00 0.00 0.00 3.77
2264 5394 1.918262 ACCTCCTCCATCATCAAGCAA 59.082 47.619 0.00 0.00 0.00 3.91
2340 5470 2.925170 ACGGTTCTGGCTGAGGCT 60.925 61.111 7.74 0.00 38.73 4.58
2384 5544 1.619654 CACAATGCCTCCAACAAGGA 58.380 50.000 0.00 0.00 46.75 3.36
2486 5648 3.713650 CCTCATGGAGGTGACGGT 58.286 61.111 4.08 0.00 44.25 4.83
2547 5714 4.609018 CGCCCAGCCACCTATCCG 62.609 72.222 0.00 0.00 0.00 4.18
2671 5842 0.027979 CGCGCCCATCAAACAGTATG 59.972 55.000 0.00 0.00 46.00 2.39


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

AutoCloner maintained by Alex Coulton.