Multiple sequence alignment - TraesCS6B01G298500

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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 TraesCS6B01G298500 chr6B 100.000 3919 0 0 1 3919 536002455 536006373 0 7238
1 TraesCS6B01G298500 chr6D 92.613 3980 168 49 1 3893 346097732 346101672 0 5605
2 TraesCS6B01G298500 chr6A 89.267 3699 162 98 175 3717 498006048 498009667 0 4414


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 TraesCS6B01G298500 chr6B 536002455 536006373 3918 False 7238 7238 100.000 1 3919 1 chr6B.!!$F1 3918
1 TraesCS6B01G298500 chr6D 346097732 346101672 3940 False 5605 5605 92.613 1 3893 1 chr6D.!!$F1 3892
2 TraesCS6B01G298500 chr6A 498006048 498009667 3619 False 4414 4414 89.267 175 3717 1 chr6A.!!$F1 3542

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
594 610 0.103937 GGAAGCAGCATAGAGAGCGT 59.896 55.0 0.00 0.00 37.01 5.07 F
2313 2444 0.095245 ACATCAATCAACTTCGCGCG 59.905 50.0 26.76 26.76 0.00 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2456 2598 0.039437 TCGAGGTGAGTTGCGAGTTC 60.039 55.0 0.00 0.00 0.0 3.01 R
3426 3604 0.109919 CGCGGTCGATCGATCCATTA 60.110 55.0 24.71 0.27 38.1 1.90 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
76 77 4.477249 TGGGATGCTAACCTACTACTACC 58.523 47.826 0.00 0.00 0.00 3.18
77 78 4.079038 TGGGATGCTAACCTACTACTACCA 60.079 45.833 0.00 0.00 0.00 3.25
99 100 0.461135 AGCGGGCCATTATTTTGCTG 59.539 50.000 4.39 0.00 0.00 4.41
102 103 2.483538 GCGGGCCATTATTTTGCTGAAT 60.484 45.455 4.39 0.00 0.00 2.57
118 119 5.083122 TGCTGAATACCAATTCCAAAAGGA 58.917 37.500 0.00 0.00 40.78 3.36
121 122 6.295292 GCTGAATACCAATTCCAAAAGGAAGT 60.295 38.462 3.15 0.00 40.78 3.01
123 124 8.028652 TGAATACCAATTCCAAAAGGAAGTTT 57.971 30.769 3.15 0.00 40.78 2.66
130 131 8.685427 CCAATTCCAAAAGGAAGTTTGAAAAAT 58.315 29.630 10.58 0.00 40.29 1.82
225 230 1.812686 TTCCCTGACGACGGACCAAG 61.813 60.000 0.00 0.00 0.00 3.61
230 235 0.809385 TGACGACGGACCAAGAGATC 59.191 55.000 0.00 0.00 0.00 2.75
322 328 4.197750 TGCTTTAACCGGTCAGTGTTTAA 58.802 39.130 8.04 0.00 0.00 1.52
355 361 6.587990 CACAAGAATCACGTAGAGAATGACTT 59.412 38.462 0.00 0.00 0.00 3.01
384 395 0.394352 AGCATAAAGGAAGTGGCCCG 60.394 55.000 0.00 0.00 0.00 6.13
417 430 8.334734 AGATATGCAGGCCAATAGAAATATCTT 58.665 33.333 5.01 0.00 34.15 2.40
491 504 2.520968 GGCGGGGCTGGGATATTT 59.479 61.111 0.00 0.00 0.00 1.40
492 505 1.765074 GGCGGGGCTGGGATATTTA 59.235 57.895 0.00 0.00 0.00 1.40
494 507 0.953960 GCGGGGCTGGGATATTTACG 60.954 60.000 0.00 0.00 0.00 3.18
510 523 9.270640 GGATATTTACGAGAGAAGAGTACTGTA 57.729 37.037 0.00 0.00 0.00 2.74
574 590 3.144894 AGCAGGATTATAGGAGAGGGGAA 59.855 47.826 0.00 0.00 0.00 3.97
575 591 3.517500 GCAGGATTATAGGAGAGGGGAAG 59.482 52.174 0.00 0.00 0.00 3.46
576 592 4.100373 CAGGATTATAGGAGAGGGGAAGG 58.900 52.174 0.00 0.00 0.00 3.46
577 593 4.004862 AGGATTATAGGAGAGGGGAAGGA 58.995 47.826 0.00 0.00 0.00 3.36
578 594 4.427406 AGGATTATAGGAGAGGGGAAGGAA 59.573 45.833 0.00 0.00 0.00 3.36
585 601 0.918310 AGAGGGGAAGGAAGCAGCAT 60.918 55.000 0.00 0.00 0.00 3.79
593 609 0.388659 AGGAAGCAGCATAGAGAGCG 59.611 55.000 0.00 0.00 37.01 5.03
594 610 0.103937 GGAAGCAGCATAGAGAGCGT 59.896 55.000 0.00 0.00 37.01 5.07
595 611 1.338337 GGAAGCAGCATAGAGAGCGTA 59.662 52.381 0.00 0.00 37.01 4.42
596 612 2.389998 GAAGCAGCATAGAGAGCGTAC 58.610 52.381 0.00 0.00 37.01 3.67
598 614 1.959985 AGCAGCATAGAGAGCGTACAT 59.040 47.619 0.00 0.00 37.01 2.29
599 615 2.057316 GCAGCATAGAGAGCGTACATG 58.943 52.381 0.00 0.00 37.01 3.21
600 616 2.544694 GCAGCATAGAGAGCGTACATGT 60.545 50.000 2.69 2.69 37.01 3.21
601 617 3.711086 CAGCATAGAGAGCGTACATGTT 58.289 45.455 2.30 0.00 37.01 2.71
603 619 2.797156 GCATAGAGAGCGTACATGTTGG 59.203 50.000 2.30 0.00 0.00 3.77
604 620 3.384668 CATAGAGAGCGTACATGTTGGG 58.615 50.000 2.30 0.00 0.00 4.12
606 622 1.078426 AGAGCGTACATGTTGGGGC 60.078 57.895 2.30 2.71 0.00 5.80
607 623 1.078426 GAGCGTACATGTTGGGGCT 60.078 57.895 2.30 8.00 0.00 5.19
671 693 4.357947 TCTCGCGCGCTGGAAAGT 62.358 61.111 30.48 0.00 0.00 2.66
713 748 6.672593 TCCCTTGGCTAATTGATTGATTAGT 58.327 36.000 6.53 0.00 40.26 2.24
714 749 6.772716 TCCCTTGGCTAATTGATTGATTAGTC 59.227 38.462 3.05 3.05 42.05 2.59
715 750 6.293626 CCCTTGGCTAATTGATTGATTAGTCG 60.294 42.308 5.18 0.00 43.72 4.18
732 778 2.125350 GAGGTCCAGCTCTTGCCG 60.125 66.667 0.00 0.00 40.80 5.69
804 859 4.163649 AGCGCCTAGTTAGATTTTTAGGGT 59.836 41.667 2.29 0.00 34.54 4.34
806 861 4.272748 CGCCTAGTTAGATTTTTAGGGTGC 59.727 45.833 0.00 0.00 34.54 5.01
807 862 4.272748 GCCTAGTTAGATTTTTAGGGTGCG 59.727 45.833 0.00 0.00 34.54 5.34
808 863 4.272748 CCTAGTTAGATTTTTAGGGTGCGC 59.727 45.833 0.00 0.00 31.11 6.09
810 865 1.658994 TAGATTTTTAGGGTGCGCCG 58.341 50.000 10.86 0.00 34.97 6.46
811 866 1.226575 GATTTTTAGGGTGCGCCGC 60.227 57.895 10.86 0.00 34.97 6.53
881 958 2.150014 AAATACCTGCCACGCCCCTT 62.150 55.000 0.00 0.00 0.00 3.95
902 979 0.323725 CATTTCCCTCCACACCCAGG 60.324 60.000 0.00 0.00 0.00 4.45
942 1036 0.107606 TCTCCTCGTCTTCCTCCTCG 60.108 60.000 0.00 0.00 0.00 4.63
968 1065 0.960364 TTCGGGCTCATCCTTTGCAC 60.960 55.000 0.00 0.00 34.39 4.57
974 1071 2.436417 GCTCATCCTTTGCACCTAACA 58.564 47.619 0.00 0.00 0.00 2.41
978 1075 4.326826 TCATCCTTTGCACCTAACAGAAG 58.673 43.478 0.00 0.00 0.00 2.85
985 1082 1.996191 GCACCTAACAGAAGCGAAGAG 59.004 52.381 0.00 0.00 0.00 2.85
998 1095 1.071605 CGAAGAGAGCCTTTCGTTGG 58.928 55.000 0.00 0.00 34.68 3.77
1005 1102 3.364442 CCTTTCGTTGGCATGGCA 58.636 55.556 19.43 19.43 0.00 4.92
1251 1360 0.749454 GGCCCATCTTCAAGACGCAT 60.749 55.000 0.00 0.00 0.00 4.73
1311 1420 1.275657 CGCGAAGTTCGTGCTTGTT 59.724 52.632 24.23 0.00 43.59 2.83
1422 1531 4.803426 GCTCACCTCCGCCGTCTG 62.803 72.222 0.00 0.00 0.00 3.51
1515 1624 2.294078 CGGCTCCTGGGAAGACCTT 61.294 63.158 0.00 0.00 41.11 3.50
1560 1669 2.829741 AGACTGTGAGTGCTTCTTCC 57.170 50.000 0.00 0.00 0.00 3.46
1586 1708 1.471684 CATTCCCACTTGCTCTGCTTC 59.528 52.381 0.00 0.00 0.00 3.86
1612 1734 4.889995 TCTGCTCTGCTCTACTGCTAAATA 59.110 41.667 0.00 0.00 0.00 1.40
1622 1744 6.484977 GCTCTACTGCTAAATAATTGGAGCTT 59.515 38.462 0.00 0.00 39.20 3.74
1626 1748 6.418101 ACTGCTAAATAATTGGAGCTTGAGA 58.582 36.000 0.00 0.00 35.89 3.27
1754 1876 0.325296 TGACGCTGGAGAAGGGGTAT 60.325 55.000 0.00 0.00 43.07 2.73
2107 2238 2.509336 CGACTGACCCGTGCATCC 60.509 66.667 0.00 0.00 0.00 3.51
2108 2239 2.662596 GACTGACCCGTGCATCCA 59.337 61.111 0.00 0.00 0.00 3.41
2128 2259 5.324409 TCCAACAATTAACAGGAAGAGCAT 58.676 37.500 0.00 0.00 0.00 3.79
2296 2427 2.391926 TGGAGTACCAAGGTGAGACA 57.608 50.000 1.07 0.00 43.91 3.41
2297 2428 2.902608 TGGAGTACCAAGGTGAGACAT 58.097 47.619 1.07 0.00 43.91 3.06
2298 2429 2.832129 TGGAGTACCAAGGTGAGACATC 59.168 50.000 1.07 0.00 43.91 3.06
2299 2430 2.832129 GGAGTACCAAGGTGAGACATCA 59.168 50.000 1.07 0.00 35.97 3.07
2301 2432 4.080863 GGAGTACCAAGGTGAGACATCAAT 60.081 45.833 1.07 0.00 34.95 2.57
2302 2433 5.091261 AGTACCAAGGTGAGACATCAATC 57.909 43.478 1.07 0.00 37.14 2.67
2303 2434 4.532126 AGTACCAAGGTGAGACATCAATCA 59.468 41.667 1.07 0.00 37.14 2.57
2306 2437 4.202503 ACCAAGGTGAGACATCAATCAACT 60.203 41.667 0.00 0.00 45.33 3.16
2309 2440 4.248859 AGGTGAGACATCAATCAACTTCG 58.751 43.478 0.00 0.00 40.59 3.79
2310 2441 3.181516 GGTGAGACATCAATCAACTTCGC 60.182 47.826 0.00 0.00 37.14 4.70
2311 2442 2.667969 TGAGACATCAATCAACTTCGCG 59.332 45.455 0.00 0.00 30.61 5.87
2312 2443 1.394917 AGACATCAATCAACTTCGCGC 59.605 47.619 0.00 0.00 0.00 6.86
2313 2444 0.095245 ACATCAATCAACTTCGCGCG 59.905 50.000 26.76 26.76 0.00 6.86
2314 2445 1.060937 ATCAATCAACTTCGCGCGC 59.939 52.632 27.95 23.91 0.00 6.86
2315 2446 2.616776 ATCAATCAACTTCGCGCGCG 62.617 55.000 44.84 44.84 41.35 6.86
2316 2447 4.794241 AATCAACTTCGCGCGCGC 62.794 61.111 45.41 42.65 39.59 6.86
2335 2466 3.091022 CGCGCTTTGGTCGTTTGC 61.091 61.111 5.56 0.00 0.00 3.68
2425 2564 1.755393 AACTGGCTCGGAAAGGACGT 61.755 55.000 0.00 0.00 0.00 4.34
2442 2581 1.447314 GTGCTCCTAACCGAACGGG 60.447 63.158 17.44 0.00 43.62 5.28
2456 2598 2.537401 GAACGGGAATAGACCAACTCG 58.463 52.381 0.00 0.00 0.00 4.18
2478 2620 0.455295 CTCGCAACTCACCTCGACTC 60.455 60.000 0.00 0.00 0.00 3.36
2485 2627 0.742990 CTCACCTCGACTCGCTCTCT 60.743 60.000 0.00 0.00 0.00 3.10
2617 2759 2.623416 ACGATTCGAGGTCAGCATCATA 59.377 45.455 13.95 0.00 0.00 2.15
2621 2767 3.885724 TCGAGGTCAGCATCATAACAA 57.114 42.857 0.00 0.00 0.00 2.83
2628 2774 4.141711 GGTCAGCATCATAACAACCCTCTA 60.142 45.833 0.00 0.00 0.00 2.43
2638 2784 2.973945 ACAACCCTCTATTTGACGAGC 58.026 47.619 0.00 0.00 0.00 5.03
2933 3088 0.769247 CCTGAGCCATCCATCCATCA 59.231 55.000 0.00 0.00 0.00 3.07
3054 3225 1.258445 CGGAGGGGACACTTGTAGCT 61.258 60.000 0.00 0.00 0.00 3.32
3417 3595 4.106925 GCAGGCTGGCAGCTAGGT 62.107 66.667 35.73 17.34 41.99 3.08
3426 3604 3.733337 CTGGCAGCTAGGTCGAATAATT 58.267 45.455 0.00 0.00 0.00 1.40
3440 3618 6.750501 GGTCGAATAATTAATGGATCGATCGA 59.249 38.462 21.86 21.86 40.80 3.59
3441 3619 7.601775 GTCGAATAATTAATGGATCGATCGAC 58.398 38.462 22.06 14.95 45.36 4.20
3510 3688 7.224949 TCTGTATTGTTTGTTACACGTCAATGA 59.775 33.333 14.34 5.57 36.21 2.57
3650 3844 7.664731 TGAGAGTAGTAGTAGTAAGCAACACTT 59.335 37.037 0.00 0.00 42.76 3.16
3707 3901 1.871039 GAAGCAACAAAGTCCACGCTA 59.129 47.619 0.00 0.00 0.00 4.26
3766 3963 1.590665 CGGGGCAAACAATCATGCA 59.409 52.632 0.00 0.00 44.32 3.96
3779 3976 2.360350 ATGCAGGCTTGTGGTCGG 60.360 61.111 0.00 0.00 0.00 4.79
3781 3978 4.329545 GCAGGCTTGTGGTCGGGA 62.330 66.667 0.00 0.00 0.00 5.14
3808 4005 2.095516 GCTCTAGAAACAAAGCCACTGC 60.096 50.000 0.00 0.00 37.95 4.40
3839 4036 1.270041 CGATTCTGGAAGGGCTAGCTC 60.270 57.143 15.72 11.51 0.00 4.09
3849 4046 2.137528 GGCTAGCTCCTCACTCCCC 61.138 68.421 15.72 0.00 0.00 4.81
3908 4105 9.681062 TTATTTTTAGATCAACCACTCTTAGGG 57.319 33.333 0.00 0.00 0.00 3.53
3909 4106 6.697641 TTTTAGATCAACCACTCTTAGGGT 57.302 37.500 0.00 0.00 39.65 4.34
3911 4108 4.828072 AGATCAACCACTCTTAGGGTTC 57.172 45.455 0.00 0.00 45.32 3.62
3912 4109 4.430441 AGATCAACCACTCTTAGGGTTCT 58.570 43.478 0.00 0.00 45.32 3.01
3913 4110 5.590818 AGATCAACCACTCTTAGGGTTCTA 58.409 41.667 0.00 0.00 45.32 2.10
3914 4111 5.422650 AGATCAACCACTCTTAGGGTTCTAC 59.577 44.000 0.00 0.00 45.32 2.59
3915 4112 4.748701 TCAACCACTCTTAGGGTTCTACT 58.251 43.478 0.00 0.00 45.32 2.57
3916 4113 5.895807 TCAACCACTCTTAGGGTTCTACTA 58.104 41.667 0.00 0.00 45.32 1.82
3917 4114 5.950549 TCAACCACTCTTAGGGTTCTACTAG 59.049 44.000 0.00 0.00 45.32 2.57
3918 4115 5.793034 ACCACTCTTAGGGTTCTACTAGA 57.207 43.478 0.00 0.00 32.12 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.543653 GCAAAATAATGGCCCGCTACTG 60.544 50.000 0.00 0.00 0.00 2.74
77 78 1.681264 GCAAAATAATGGCCCGCTACT 59.319 47.619 0.00 0.00 0.00 2.57
136 137 8.792633 TGATTGACGAGATAAAATGTCCTTTTT 58.207 29.630 0.00 0.00 38.09 1.94
137 138 8.335532 TGATTGACGAGATAAAATGTCCTTTT 57.664 30.769 0.00 0.00 40.21 2.27
138 139 7.921786 TGATTGACGAGATAAAATGTCCTTT 57.078 32.000 0.00 0.00 0.00 3.11
139 140 7.921786 TTGATTGACGAGATAAAATGTCCTT 57.078 32.000 0.00 0.00 0.00 3.36
140 141 7.921786 TTTGATTGACGAGATAAAATGTCCT 57.078 32.000 0.00 0.00 0.00 3.85
141 142 8.964420 TTTTTGATTGACGAGATAAAATGTCC 57.036 30.769 0.00 0.00 0.00 4.02
202 207 0.037605 GTCCGTCGTCAGGGAAATGT 60.038 55.000 0.00 0.00 38.33 2.71
225 230 3.995199 TGACAGGTGTTGAACTGATCTC 58.005 45.455 0.00 0.00 38.09 2.75
230 235 2.224079 CGGAATGACAGGTGTTGAACTG 59.776 50.000 0.00 0.00 40.48 3.16
271 276 3.694734 CGTAGAAATGCATGCGGAAAAT 58.305 40.909 14.09 0.00 0.00 1.82
322 328 6.460781 TCTACGTGATTCTTGTGGTAAACAT 58.539 36.000 0.00 0.00 38.99 2.71
355 361 7.067008 GCCACTTCCTTTATGCTTTCTAATGTA 59.933 37.037 0.00 0.00 0.00 2.29
384 395 3.969287 TGGCCTGCATATCTACTGATC 57.031 47.619 3.32 0.00 34.32 2.92
456 469 4.421515 CTCCTGGCCTGCCCACTG 62.422 72.222 3.32 0.00 39.18 3.66
475 488 0.953960 CGTAAATATCCCAGCCCCGC 60.954 60.000 0.00 0.00 0.00 6.13
492 505 9.610705 TTATTGTATACAGTACTCTTCTCTCGT 57.389 33.333 7.54 0.00 0.00 4.18
510 523 8.190784 GCTTGCTTGATTAGTTGGTTATTGTAT 58.809 33.333 0.00 0.00 0.00 2.29
520 536 2.245096 GCACGCTTGCTTGATTAGTTG 58.755 47.619 8.12 0.00 46.17 3.16
574 590 0.388659 CGCTCTCTATGCTGCTTCCT 59.611 55.000 0.00 0.00 0.00 3.36
575 591 0.103937 ACGCTCTCTATGCTGCTTCC 59.896 55.000 0.00 0.00 0.00 3.46
576 592 2.223595 TGTACGCTCTCTATGCTGCTTC 60.224 50.000 0.00 0.00 0.00 3.86
577 593 1.751351 TGTACGCTCTCTATGCTGCTT 59.249 47.619 0.00 0.00 0.00 3.91
578 594 1.393603 TGTACGCTCTCTATGCTGCT 58.606 50.000 0.00 0.00 0.00 4.24
585 601 1.754803 CCCCAACATGTACGCTCTCTA 59.245 52.381 0.00 0.00 0.00 2.43
593 609 0.394352 CCCTCAGCCCCAACATGTAC 60.394 60.000 0.00 0.00 0.00 2.90
594 610 1.570857 CCCCTCAGCCCCAACATGTA 61.571 60.000 0.00 0.00 0.00 2.29
595 611 2.765969 CCCTCAGCCCCAACATGT 59.234 61.111 0.00 0.00 0.00 3.21
596 612 2.043652 CCCCTCAGCCCCAACATG 60.044 66.667 0.00 0.00 0.00 3.21
603 619 4.803908 CCTTTCGCCCCTCAGCCC 62.804 72.222 0.00 0.00 0.00 5.19
604 620 4.803908 CCCTTTCGCCCCTCAGCC 62.804 72.222 0.00 0.00 0.00 4.85
606 622 1.965754 CTCTCCCTTTCGCCCCTCAG 61.966 65.000 0.00 0.00 0.00 3.35
607 623 1.990060 CTCTCCCTTTCGCCCCTCA 60.990 63.158 0.00 0.00 0.00 3.86
671 693 3.881019 AAGGAGCAGTCCCGTCCGA 62.881 63.158 0.00 0.00 45.26 4.55
692 714 7.307632 CCTCGACTAATCAATCAATTAGCCAAG 60.308 40.741 4.06 0.55 41.12 3.61
713 748 2.650116 GGCAAGAGCTGGACCTCGA 61.650 63.158 0.00 0.00 41.70 4.04
714 749 2.125350 GGCAAGAGCTGGACCTCG 60.125 66.667 0.00 0.00 41.70 4.63
715 750 2.125350 CGGCAAGAGCTGGACCTC 60.125 66.667 0.00 0.00 43.60 3.85
732 778 7.915397 ACATCGAATTATTGCACAGTTTAATCC 59.085 33.333 0.00 0.00 0.00 3.01
813 868 4.410400 GTTGGTCTCCGGCCCTGG 62.410 72.222 0.00 0.00 0.00 4.45
832 899 2.819595 TGAGGGAAATGCGAGCGC 60.820 61.111 8.08 8.08 42.35 5.92
881 958 1.076549 GGGTGTGGAGGGAAATGCA 59.923 57.895 0.00 0.00 0.00 3.96
902 979 2.676471 GATGGGTGGTGGTGGTGC 60.676 66.667 0.00 0.00 0.00 5.01
917 994 1.850345 AGGAAGACGAGGAGAGGAGAT 59.150 52.381 0.00 0.00 0.00 2.75
968 1065 2.535331 GCTCTCTTCGCTTCTGTTAGG 58.465 52.381 0.00 0.00 0.00 2.69
974 1071 1.403514 CGAAAGGCTCTCTTCGCTTCT 60.404 52.381 6.86 0.00 33.94 2.85
978 1075 0.440371 CAACGAAAGGCTCTCTTCGC 59.560 55.000 17.19 0.00 33.94 4.70
998 1095 0.384669 GAGGATGAAAGCTGCCATGC 59.615 55.000 10.73 10.73 0.00 4.06
1005 1102 2.093021 GCAGAGGAAGAGGATGAAAGCT 60.093 50.000 0.00 0.00 0.00 3.74
1179 1288 1.652947 TGGGGTTCTTGGAGGAGTAC 58.347 55.000 0.00 0.00 0.00 2.73
1296 1405 3.184581 CCTGAGTAACAAGCACGAACTTC 59.815 47.826 0.00 0.00 0.00 3.01
1308 1417 3.466881 AGGTGCGCCTGAGTAACA 58.533 55.556 20.48 0.00 45.05 2.41
1368 1477 1.281925 GGAAGAAGATGGCCTGGGGA 61.282 60.000 3.32 0.00 0.00 4.81
1407 1516 4.988716 ACCAGACGGCGGAGGTGA 62.989 66.667 17.23 0.00 34.57 4.02
1515 1624 3.454447 TCTCTTGGAAGGTGTTGACTTGA 59.546 43.478 0.00 0.00 0.00 3.02
1560 1669 2.026449 AGAGCAAGTGGGAATGGAAGAG 60.026 50.000 0.00 0.00 0.00 2.85
1586 1708 0.746063 CAGTAGAGCAGAGCAGAGGG 59.254 60.000 0.00 0.00 0.00 4.30
1612 1734 3.522750 AGGATCAGTCTCAAGCTCCAATT 59.477 43.478 0.00 0.00 0.00 2.32
1622 1744 3.007290 CACCAACAGAAGGATCAGTCTCA 59.993 47.826 0.00 0.00 0.00 3.27
1626 1748 2.289072 CGACACCAACAGAAGGATCAGT 60.289 50.000 0.00 0.00 0.00 3.41
1754 1876 0.108520 GGTTCACCGGCATCGAGTTA 60.109 55.000 0.00 0.00 39.00 2.24
2107 2238 4.860907 GCATGCTCTTCCTGTTAATTGTTG 59.139 41.667 11.37 0.00 0.00 3.33
2108 2239 4.082026 GGCATGCTCTTCCTGTTAATTGTT 60.082 41.667 18.92 0.00 0.00 2.83
2294 2425 0.095245 CGCGCGAAGTTGATTGATGT 59.905 50.000 28.94 0.00 0.00 3.06
2295 2426 1.189989 GCGCGCGAAGTTGATTGATG 61.190 55.000 37.18 0.00 0.00 3.07
2296 2427 1.060937 GCGCGCGAAGTTGATTGAT 59.939 52.632 37.18 0.00 0.00 2.57
2297 2428 2.474266 GCGCGCGAAGTTGATTGA 59.526 55.556 37.18 0.00 0.00 2.57
2316 2447 4.659874 AAACGACCAAAGCGCGCG 62.660 61.111 28.44 28.44 0.00 6.86
2317 2448 3.091022 CAAACGACCAAAGCGCGC 61.091 61.111 26.66 26.66 0.00 6.86
2318 2449 3.091022 GCAAACGACCAAAGCGCG 61.091 61.111 0.00 0.00 0.00 6.86
2319 2450 3.091022 CGCAAACGACCAAAGCGC 61.091 61.111 0.00 0.00 43.93 5.92
2346 2477 2.809601 GGACAGCACAGTACGGCG 60.810 66.667 4.80 4.80 34.54 6.46
2349 2480 0.171455 GAGAGGGACAGCACAGTACG 59.829 60.000 0.00 0.00 0.00 3.67
2425 2564 1.186917 TTCCCGTTCGGTTAGGAGCA 61.187 55.000 10.36 0.00 0.00 4.26
2442 2581 2.853003 GCGAGTTCGAGTTGGTCTATTC 59.147 50.000 5.60 0.00 43.02 1.75
2456 2598 0.039437 TCGAGGTGAGTTGCGAGTTC 60.039 55.000 0.00 0.00 0.00 3.01
2485 2627 1.301401 GTACCCTGCACGCACAGAA 60.301 57.895 6.84 0.00 40.25 3.02
2617 2759 3.335579 GCTCGTCAAATAGAGGGTTGTT 58.664 45.455 0.00 0.00 35.19 2.83
2621 2767 1.482593 CAGGCTCGTCAAATAGAGGGT 59.517 52.381 0.00 0.00 35.19 4.34
2628 2774 0.037326 TCGAAGCAGGCTCGTCAAAT 60.037 50.000 0.00 0.00 0.00 2.32
2638 2784 3.126073 TGATCAATCGAATCGAAGCAGG 58.874 45.455 10.12 0.00 39.99 4.85
2933 3088 0.473117 TTTGGGAACGAGGAGGAGGT 60.473 55.000 0.00 0.00 0.00 3.85
3134 3306 3.114606 TCATGGTCCTGGCTGAAGAATA 58.885 45.455 0.00 0.00 0.00 1.75
3417 3595 6.750501 GGTCGATCGATCCATTAATTATTCGA 59.249 38.462 22.50 7.29 39.57 3.71
3426 3604 0.109919 CGCGGTCGATCGATCCATTA 60.110 55.000 24.71 0.27 38.10 1.90
3510 3688 3.070015 CCACAAGAAAGCCATTTCCAGTT 59.930 43.478 0.00 0.00 45.01 3.16
3593 3781 3.452474 AGCATCGAGACAGTTGATTAGC 58.548 45.455 0.00 0.00 0.00 3.09
3635 3829 5.413499 TCGGGAATAAGTGTTGCTTACTAC 58.587 41.667 0.00 0.00 41.93 2.73
3636 3830 5.664294 TCGGGAATAAGTGTTGCTTACTA 57.336 39.130 0.00 0.00 41.93 1.82
3637 3831 4.546829 TCGGGAATAAGTGTTGCTTACT 57.453 40.909 0.00 0.00 41.93 2.24
3684 3878 1.332904 CGTGGACTTTGTTGCTTCGAC 60.333 52.381 0.00 0.00 0.00 4.20
3707 3901 9.962783 GATATTTTATAGAGGTGTACTTCGTGT 57.037 33.333 0.00 0.00 0.00 4.49
3711 3905 8.305317 AGGCGATATTTTATAGAGGTGTACTTC 58.695 37.037 0.00 0.00 0.00 3.01
3717 3911 5.178797 CCCAGGCGATATTTTATAGAGGTG 58.821 45.833 0.00 0.00 0.00 4.00
3718 3912 4.323562 GCCCAGGCGATATTTTATAGAGGT 60.324 45.833 0.00 0.00 0.00 3.85
3719 3913 4.192317 GCCCAGGCGATATTTTATAGAGG 58.808 47.826 0.00 0.00 0.00 3.69
3766 3963 1.002134 CAATCCCGACCACAAGCCT 60.002 57.895 0.00 0.00 0.00 4.58
3779 3976 5.449725 GGCTTTGTTTCTAGAGCATCAATCC 60.450 44.000 0.00 0.28 37.82 3.01
3781 3978 5.012239 TGGCTTTGTTTCTAGAGCATCAAT 58.988 37.500 0.00 0.00 37.82 2.57
3808 4005 1.523258 CAGAATCGCAGAGGCCAGG 60.523 63.158 5.01 0.00 43.63 4.45
3819 4016 0.755686 AGCTAGCCCTTCCAGAATCG 59.244 55.000 12.13 0.00 0.00 3.34
3839 4036 2.122729 TCCACCAGGGGAGTGAGG 59.877 66.667 0.00 0.00 37.42 3.86
3849 4046 3.721706 GGGCTCCACCTCCACCAG 61.722 72.222 0.00 0.00 39.10 4.00
3893 4090 4.748701 AGTAGAACCCTAAGAGTGGTTGA 58.251 43.478 0.00 0.00 44.70 3.18
3894 4091 5.950549 TCTAGTAGAACCCTAAGAGTGGTTG 59.049 44.000 0.00 0.00 44.70 3.77
3896 4093 5.793034 TCTAGTAGAACCCTAAGAGTGGT 57.207 43.478 0.00 0.00 36.06 4.16


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

AutoCloner maintained by Alex Coulton.