Multiple sequence alignment - TraesCS5B01G485000

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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 TraesCS5B01G485000 chr5B 100.000 3749 0 0 1 3749 656467330 656471078 0.000000e+00 6924.0
1 TraesCS5B01G485000 chr5B 91.370 1124 67 14 892 2011 656726042 656727139 0.000000e+00 1511.0
2 TraesCS5B01G485000 chr5B 91.557 687 58 0 2045 2731 656727317 656728003 0.000000e+00 948.0
3 TraesCS5B01G485000 chr5B 88.014 559 44 12 3193 3749 656730051 656730588 1.140000e-179 640.0
4 TraesCS5B01G485000 chr5B 84.333 517 62 9 1 500 656723700 656724214 4.350000e-134 488.0
5 TraesCS5B01G485000 chr5B 84.249 273 30 6 621 880 656724283 656724555 1.730000e-63 254.0
6 TraesCS5B01G485000 chr5B 92.857 56 4 0 2762 2817 250605930 250605875 8.630000e-12 82.4
7 TraesCS5B01G485000 chr5B 94.231 52 2 1 3474 3524 656729424 656729475 1.120000e-10 78.7
8 TraesCS5B01G485000 chr5D 93.456 1085 66 3 892 1976 520805084 520806163 0.000000e+00 1605.0
9 TraesCS5B01G485000 chr5D 91.056 1174 60 20 892 2049 520839233 520840377 0.000000e+00 1544.0
10 TraesCS5B01G485000 chr5D 91.066 929 63 10 1 911 520804099 520805025 0.000000e+00 1238.0
11 TraesCS5B01G485000 chr5D 92.827 711 48 2 2052 2759 520840528 520841238 0.000000e+00 1027.0
12 TraesCS5B01G485000 chr5D 95.385 650 23 3 3100 3749 520841486 520842128 0.000000e+00 1027.0
13 TraesCS5B01G485000 chr5D 88.776 686 65 6 2090 2771 520806331 520807008 0.000000e+00 830.0
14 TraesCS5B01G485000 chr5D 97.479 238 5 1 2816 3052 520841245 520841482 4.510000e-109 405.0
15 TraesCS5B01G485000 chr5D 81.169 154 18 7 2904 3052 495064410 495064263 3.060000e-21 113.0
16 TraesCS5B01G485000 chr5D 91.250 80 7 0 2895 2974 520807197 520807276 3.960000e-20 110.0
17 TraesCS5B01G485000 chr5A 92.735 1115 63 8 877 1976 649364941 649366052 0.000000e+00 1594.0
18 TraesCS5B01G485000 chr5A 89.544 899 70 14 1 880 649363981 649364874 0.000000e+00 1118.0
19 TraesCS5B01G485000 chr5A 90.909 671 58 3 2090 2759 649366187 649366855 0.000000e+00 898.0
20 TraesCS5B01G485000 chr5A 87.786 655 39 13 3100 3749 649367146 649367764 0.000000e+00 728.0
21 TraesCS5B01G485000 chr5A 89.634 164 14 3 2892 3052 649366979 649367142 4.910000e-49 206.0
22 TraesCS5B01G485000 chr5A 81.875 160 18 7 2904 3056 619110673 619110518 1.410000e-24 124.0
23 TraesCS5B01G485000 chr7D 86.364 704 96 0 1127 1830 629497914 629497211 0.000000e+00 769.0
24 TraesCS5B01G485000 chr6D 83.748 683 93 14 1136 1809 85626519 85625846 6.830000e-177 630.0
25 TraesCS5B01G485000 chr6B 82.178 707 103 21 1115 1809 160899141 160899836 1.500000e-163 586.0
26 TraesCS5B01G485000 chr6A 82.102 704 107 17 1115 1809 101858415 101859108 5.400000e-163 584.0
27 TraesCS5B01G485000 chrUn 79.349 707 121 20 1124 1819 95188234 95188926 1.220000e-129 473.0
28 TraesCS5B01G485000 chrUn 78.734 616 119 8 2108 2723 95189130 95189733 5.830000e-108 401.0
29 TraesCS5B01G485000 chr1A 74.441 626 138 16 2107 2721 84729131 84729745 2.240000e-62 250.0
30 TraesCS5B01G485000 chr1B 72.873 623 153 11 2107 2721 142108768 142109382 2.280000e-47 200.0
31 TraesCS5B01G485000 chr1B 86.957 69 6 1 2763 2828 634240438 634240506 1.440000e-09 75.0
32 TraesCS5B01G485000 chr4D 96.364 55 1 1 2763 2817 322663812 322663865 5.160000e-14 89.8
33 TraesCS5B01G485000 chr4D 93.103 58 1 1 2763 2817 486185982 486185925 8.630000e-12 82.4
34 TraesCS5B01G485000 chr4D 87.879 66 6 2 2752 2817 277378611 277378548 4.020000e-10 76.8
35 TraesCS5B01G485000 chr4D 89.062 64 4 2 2757 2817 486185919 486185982 4.020000e-10 76.8
36 TraesCS5B01G485000 chr4A 91.803 61 2 3 2759 2818 702040178 702040120 8.630000e-12 82.4
37 TraesCS5B01G485000 chr7A 90.164 61 4 2 2759 2819 544893884 544893826 1.120000e-10 78.7
38 TraesCS5B01G485000 chr2B 91.379 58 3 2 2763 2818 297463910 297463853 1.120000e-10 78.7


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 TraesCS5B01G485000 chr5B 656467330 656471078 3748 False 6924.000000 6924 100.00000 1 3749 1 chr5B.!!$F1 3748
1 TraesCS5B01G485000 chr5B 656723700 656730588 6888 False 653.283333 1511 88.95900 1 3749 6 chr5B.!!$F2 3748
2 TraesCS5B01G485000 chr5D 520839233 520842128 2895 False 1000.750000 1544 94.18675 892 3749 4 chr5D.!!$F2 2857
3 TraesCS5B01G485000 chr5D 520804099 520807276 3177 False 945.750000 1605 91.13700 1 2974 4 chr5D.!!$F1 2973
4 TraesCS5B01G485000 chr5A 649363981 649367764 3783 False 908.800000 1594 90.12160 1 3749 5 chr5A.!!$F1 3748
5 TraesCS5B01G485000 chr7D 629497211 629497914 703 True 769.000000 769 86.36400 1127 1830 1 chr7D.!!$R1 703
6 TraesCS5B01G485000 chr6D 85625846 85626519 673 True 630.000000 630 83.74800 1136 1809 1 chr6D.!!$R1 673
7 TraesCS5B01G485000 chr6B 160899141 160899836 695 False 586.000000 586 82.17800 1115 1809 1 chr6B.!!$F1 694
8 TraesCS5B01G485000 chr6A 101858415 101859108 693 False 584.000000 584 82.10200 1115 1809 1 chr6A.!!$F1 694
9 TraesCS5B01G485000 chrUn 95188234 95189733 1499 False 437.000000 473 79.04150 1124 2723 2 chrUn.!!$F1 1599
10 TraesCS5B01G485000 chr1A 84729131 84729745 614 False 250.000000 250 74.44100 2107 2721 1 chr1A.!!$F1 614

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
544 562 0.887387 AGATCCTACCTCGAGCTCGC 60.887 60.0 30.97 13.48 39.60 5.03 F
822 850 2.121116 ACGAGCTCATACGTGCATAC 57.879 50.0 15.40 0.00 41.17 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 3108 1.227089 GCAGCTCGGTCATGTCGAT 60.227 57.895 12.56 0.0 36.01 3.59 R
2802 4534 0.106116 ACTGATACTCCCTCCGTCCC 60.106 60.000 0.00 0.0 0.00 4.46 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
44 46 6.651755 ATTGAACTTTGTCAACTTTTGCAG 57.348 33.333 0.00 0.00 40.22 4.41
97 99 4.627611 TCAAGCTCAAATGCTAATCTGC 57.372 40.909 0.00 0.00 43.24 4.26
216 234 6.797033 GTCAAAACGTCAATCGAAATGATCTT 59.203 34.615 7.44 0.86 42.86 2.40
311 329 5.928264 GCTCAAATGTCAATTTTAGGCTTGT 59.072 36.000 0.00 0.00 33.59 3.16
347 365 5.120399 CCAGGCATAACAATTGAATTGCAT 58.880 37.500 17.19 17.24 43.98 3.96
387 405 1.614903 CAACCAAGCTCAATGAAGCCA 59.385 47.619 0.00 0.00 43.56 4.75
402 420 2.998316 AGCCACTCTTGATTCTAGCC 57.002 50.000 0.00 0.00 0.00 3.93
415 433 1.552578 TCTAGCCGCAAACTGGAGTA 58.447 50.000 0.00 0.00 0.00 2.59
442 460 5.988561 AGCTTAATCTCGATTGATCCAGTTC 59.011 40.000 2.52 0.00 32.50 3.01
478 496 2.250031 ACAAGCTTGAATGCCCAATCA 58.750 42.857 32.50 0.00 0.00 2.57
488 506 4.467082 TGAATGCCCAATCATTACTTGCTT 59.533 37.500 0.00 0.00 36.85 3.91
544 562 0.887387 AGATCCTACCTCGAGCTCGC 60.887 60.000 30.97 13.48 39.60 5.03
683 703 8.488651 AACTTGTTCCGTGGAAAGTTATATAG 57.511 34.615 14.22 3.01 35.00 1.31
822 850 2.121116 ACGAGCTCATACGTGCATAC 57.879 50.000 15.40 0.00 41.17 2.39
825 853 2.667137 GAGCTCATACGTGCATACCTC 58.333 52.381 9.40 0.00 34.00 3.85
827 855 3.487372 AGCTCATACGTGCATACCTCTA 58.513 45.455 0.00 0.00 34.00 2.43
828 856 3.889538 AGCTCATACGTGCATACCTCTAA 59.110 43.478 0.00 0.00 34.00 2.10
830 858 4.261656 GCTCATACGTGCATACCTCTAACT 60.262 45.833 0.00 0.00 0.00 2.24
831 859 5.048921 GCTCATACGTGCATACCTCTAACTA 60.049 44.000 0.00 0.00 0.00 2.24
832 860 6.555812 TCATACGTGCATACCTCTAACTAG 57.444 41.667 0.00 0.00 0.00 2.57
906 2437 6.016777 ACTCTTGTTGAGGACATGTTTGATTC 60.017 38.462 0.00 0.00 46.72 2.52
991 2537 4.036518 AGCACCATAGTCTCAGAGGATTT 58.963 43.478 0.00 0.00 0.00 2.17
1017 2566 3.305676 GCGATATGGCTCATGTACTCACT 60.306 47.826 1.96 0.00 0.00 3.41
1021 2570 3.990318 TGGCTCATGTACTCACTATCG 57.010 47.619 0.00 0.00 0.00 2.92
1048 2597 2.353605 CCAGAAGTTCTGCTCTCACTCC 60.354 54.545 24.85 0.00 42.98 3.85
1050 2599 3.761218 CAGAAGTTCTGCTCTCACTCCTA 59.239 47.826 19.55 0.00 37.72 2.94
1060 2609 3.351740 CTCTCACTCCTACTCTGCTTCA 58.648 50.000 0.00 0.00 0.00 3.02
1177 2738 4.314440 GCCACCTGCACCTCGTCA 62.314 66.667 0.00 0.00 40.77 4.35
1714 3276 1.183549 GGACTACTTCCCGAGCTTGA 58.816 55.000 1.22 0.00 38.70 3.02
1865 3427 4.521639 ACATCATCAACAACACAATGAGCT 59.478 37.500 0.00 0.00 32.09 4.09
1874 3436 2.341257 ACACAATGAGCTAGAGCAACG 58.659 47.619 4.01 0.00 45.16 4.10
1921 3483 3.118811 GGTGGATGTTCTCCTCTCTCTTG 60.119 52.174 0.00 0.00 45.21 3.02
1923 3485 4.022603 TGGATGTTCTCCTCTCTCTTGAG 58.977 47.826 0.00 0.00 45.21 3.02
1929 3491 1.815613 CTCCTCTCTCTTGAGCACGAA 59.184 52.381 0.00 0.00 40.03 3.85
1998 3560 9.653287 ATTCTCTGAATTTCGTGACACTTAATA 57.347 29.630 3.68 0.00 0.00 0.98
1999 3561 8.689251 TCTCTGAATTTCGTGACACTTAATAG 57.311 34.615 3.68 0.00 0.00 1.73
2000 3562 8.304596 TCTCTGAATTTCGTGACACTTAATAGT 58.695 33.333 3.68 0.00 34.00 2.12
2001 3563 9.569167 CTCTGAATTTCGTGACACTTAATAGTA 57.431 33.333 3.68 0.00 31.96 1.82
2006 3568 6.897259 TTCGTGACACTTAATAGTATTGCC 57.103 37.500 5.61 0.00 31.96 4.52
2007 3569 5.038683 TCGTGACACTTAATAGTATTGCCG 58.961 41.667 5.61 0.00 31.96 5.69
2011 3573 7.254319 CGTGACACTTAATAGTATTGCCGATTT 60.254 37.037 5.61 0.00 31.96 2.17
2023 3585 5.867903 ATTGCCGATTTCCAATTAATCCA 57.132 34.783 0.00 0.00 0.00 3.41
2026 3588 4.041723 GCCGATTTCCAATTAATCCAACG 58.958 43.478 0.00 0.00 0.00 4.10
2030 3592 6.588373 CCGATTTCCAATTAATCCAACGTTTT 59.412 34.615 0.00 0.00 0.00 2.43
2033 3595 9.150348 GATTTCCAATTAATCCAACGTTTTCAT 57.850 29.630 0.00 0.00 0.00 2.57
2034 3596 7.881643 TTCCAATTAATCCAACGTTTTCATG 57.118 32.000 0.00 0.00 0.00 3.07
2151 3865 2.093973 AGACACGTCATCCATTGTCCTC 60.094 50.000 0.00 0.00 39.39 3.71
2373 4090 2.202770 TGCGACAACGTCAACGGT 60.203 55.556 7.53 0.00 44.95 4.83
2486 4203 1.320344 CCGGAGAGGTTCATGGACGA 61.320 60.000 0.00 0.00 34.51 4.20
2499 4219 2.669569 GACGAGGCCAAAGCAGCA 60.670 61.111 5.01 0.00 42.56 4.41
2542 4262 0.821711 CCAGTTCCTGCCGTTTGGAA 60.822 55.000 0.00 0.00 39.73 3.53
2694 4414 1.669760 GTTTGGGGTGACGATGCGA 60.670 57.895 0.00 0.00 0.00 5.10
2706 4426 0.457853 CGATGCGACGGAAGGAGAAA 60.458 55.000 0.00 0.00 0.00 2.52
2771 4503 3.134458 GCATGTGCATACTACTCCCTTC 58.866 50.000 0.00 0.00 41.59 3.46
2774 4506 2.426024 TGTGCATACTACTCCCTTCGTC 59.574 50.000 0.00 0.00 0.00 4.20
2775 4507 2.029623 TGCATACTACTCCCTTCGTCC 58.970 52.381 0.00 0.00 0.00 4.79
2776 4508 1.340568 GCATACTACTCCCTTCGTCCC 59.659 57.143 0.00 0.00 0.00 4.46
2777 4509 2.662866 CATACTACTCCCTTCGTCCCA 58.337 52.381 0.00 0.00 0.00 4.37
2782 4514 4.098894 ACTACTCCCTTCGTCCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2783 4515 4.533311 ACTACTCCCTTCGTCCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
2784 4516 3.951663 ACTCCCTTCGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
2785 4517 3.329814 ACTCCCTTCGTCCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
2787 4519 2.163613 CCCTTCGTCCCAAAATAAGTGC 59.836 50.000 0.00 0.00 0.00 4.40
2788 4520 2.817258 CCTTCGTCCCAAAATAAGTGCA 59.183 45.455 0.00 0.00 0.00 4.57
2789 4521 3.254657 CCTTCGTCCCAAAATAAGTGCAA 59.745 43.478 0.00 0.00 0.00 4.08
2791 4523 3.745799 TCGTCCCAAAATAAGTGCAAGA 58.254 40.909 0.00 0.00 0.00 3.02
2792 4524 3.500680 TCGTCCCAAAATAAGTGCAAGAC 59.499 43.478 0.00 0.00 0.00 3.01
2793 4525 3.252215 CGTCCCAAAATAAGTGCAAGACA 59.748 43.478 0.00 0.00 0.00 3.41
2808 4570 3.365969 GCAAGACACTTATTTTGGGACGG 60.366 47.826 0.00 0.00 0.00 4.79
3055 6341 5.013547 CCAACAATCCAAAGGGTACACATA 58.986 41.667 0.00 0.00 34.93 2.29
3056 6342 5.478679 CCAACAATCCAAAGGGTACACATAA 59.521 40.000 0.00 0.00 34.93 1.90
3057 6343 6.154363 CCAACAATCCAAAGGGTACACATAAT 59.846 38.462 0.00 0.00 34.93 1.28
3058 6344 6.773976 ACAATCCAAAGGGTACACATAATG 57.226 37.500 0.00 0.00 34.93 1.90
3059 6345 5.656416 ACAATCCAAAGGGTACACATAATGG 59.344 40.000 0.00 0.00 34.93 3.16
3060 6346 5.725551 ATCCAAAGGGTACACATAATGGA 57.274 39.130 11.89 11.89 39.79 3.41
3061 6347 5.522315 TCCAAAGGGTACACATAATGGAA 57.478 39.130 0.00 0.00 33.06 3.53
3062 6348 5.893500 TCCAAAGGGTACACATAATGGAAA 58.106 37.500 0.00 0.00 33.06 3.13
3063 6349 6.498538 TCCAAAGGGTACACATAATGGAAAT 58.501 36.000 0.00 0.00 33.06 2.17
3064 6350 6.379703 TCCAAAGGGTACACATAATGGAAATG 59.620 38.462 0.00 0.00 33.06 2.32
3065 6351 6.154363 CCAAAGGGTACACATAATGGAAATGT 59.846 38.462 0.00 0.00 38.08 2.71
3067 6353 7.875327 AAGGGTACACATAATGGAAATGTAC 57.125 36.000 0.00 4.61 43.11 2.90
3069 6355 6.826741 AGGGTACACATAATGGAAATGTACAC 59.173 38.462 13.18 10.25 46.11 2.90
3070 6356 6.600032 GGGTACACATAATGGAAATGTACACA 59.400 38.462 13.18 0.00 45.42 3.72
3071 6357 7.284489 GGGTACACATAATGGAAATGTACACAT 59.716 37.037 13.18 0.00 45.42 3.21
3072 6358 9.332502 GGTACACATAATGGAAATGTACACATA 57.667 33.333 13.18 0.00 44.78 2.29
3082 6368 9.685276 ATGGAAATGTACACATAATGAAAGAGA 57.315 29.630 0.00 0.00 35.10 3.10
3083 6369 9.166173 TGGAAATGTACACATAATGAAAGAGAG 57.834 33.333 0.00 0.00 35.10 3.20
3128 6414 6.483640 GCTTTCCTATACGAATCCATTCTTGT 59.516 38.462 0.00 0.00 34.69 3.16
3208 6614 5.105351 TGGATCGTCAAACATGATCTAGTGT 60.105 40.000 0.00 0.00 44.37 3.55
3276 6682 1.593006 CGGCCAGCATTACTAAAGACG 59.407 52.381 2.24 0.00 0.00 4.18
3301 6708 5.376854 AACAGACATGAATTAGTTGTGCC 57.623 39.130 0.00 0.00 0.00 5.01
3302 6709 4.397420 ACAGACATGAATTAGTTGTGCCA 58.603 39.130 0.00 0.00 0.00 4.92
3304 6711 5.477984 ACAGACATGAATTAGTTGTGCCAAT 59.522 36.000 0.00 0.00 0.00 3.16
3305 6712 6.032094 CAGACATGAATTAGTTGTGCCAATC 58.968 40.000 0.00 0.00 0.00 2.67
3306 6713 5.126061 AGACATGAATTAGTTGTGCCAATCC 59.874 40.000 0.00 0.00 0.00 3.01
3307 6714 4.160252 ACATGAATTAGTTGTGCCAATCCC 59.840 41.667 0.00 0.00 0.00 3.85
3308 6715 3.096092 TGAATTAGTTGTGCCAATCCCC 58.904 45.455 0.00 0.00 0.00 4.81
3309 6716 1.762708 ATTAGTTGTGCCAATCCCCG 58.237 50.000 0.00 0.00 0.00 5.73
3310 6717 0.402504 TTAGTTGTGCCAATCCCCGT 59.597 50.000 0.00 0.00 0.00 5.28
3438 6847 6.158520 TCTGAGGATGTCAAAATGATTAGGGA 59.841 38.462 0.00 0.00 33.60 4.20
3439 6848 6.359804 TGAGGATGTCAAAATGATTAGGGAG 58.640 40.000 0.00 0.00 29.64 4.30
3440 6849 5.699143 AGGATGTCAAAATGATTAGGGAGG 58.301 41.667 0.00 0.00 0.00 4.30
3450 6860 4.623932 TGATTAGGGAGGTACATGCATC 57.376 45.455 0.00 0.00 0.00 3.91
3533 6965 2.734175 GCCGCTTAAAACAAGGTATGGC 60.734 50.000 0.00 0.00 0.00 4.40
3568 7000 0.253347 TGGGCCTCCCTCATCTTCTT 60.253 55.000 4.53 0.00 45.70 2.52
3730 7162 5.583854 CCTTCATAGTCATCTGTGGACAAAG 59.416 44.000 0.00 0.00 37.74 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 5.402398 AGTCTGCAAAAGTTGACAAAGTTC 58.598 37.500 4.57 0.00 32.41 3.01
26 28 5.391312 AAGTCTGCAAAAGTTGACAAAGT 57.609 34.783 4.57 0.00 32.41 2.66
27 29 7.992180 ATAAAGTCTGCAAAAGTTGACAAAG 57.008 32.000 4.57 0.00 32.41 2.77
44 46 6.568653 GCTTGAGTTCAGGGTTGAATAAAGTC 60.569 42.308 0.00 0.00 44.62 3.01
311 329 6.184068 TGTTATGCCTGGCTATAAACTTTGA 58.816 36.000 21.03 0.00 0.00 2.69
364 382 3.243839 GGCTTCATTGAGCTTGGTTGAAA 60.244 43.478 0.00 0.00 42.32 2.69
368 386 1.615392 GTGGCTTCATTGAGCTTGGTT 59.385 47.619 0.00 0.00 42.32 3.67
387 405 3.003480 GTTTGCGGCTAGAATCAAGAGT 58.997 45.455 0.00 0.00 0.00 3.24
415 433 4.101585 TGGATCAATCGAGATTAAGCTGGT 59.898 41.667 0.00 0.00 0.00 4.00
442 460 1.662629 CTTGTTGCTAGGATCACGCTG 59.337 52.381 0.00 0.00 0.00 5.18
478 496 3.604582 GAGCAGACCTCAAGCAAGTAAT 58.395 45.455 0.00 0.00 40.45 1.89
822 850 5.511363 TCTCTCAGGAAACCTAGTTAGAGG 58.489 45.833 0.00 0.00 42.89 3.69
825 853 6.015350 TGTGTTCTCTCAGGAAACCTAGTTAG 60.015 42.308 0.00 0.00 29.64 2.34
827 855 4.654262 TGTGTTCTCTCAGGAAACCTAGTT 59.346 41.667 0.00 0.00 29.64 2.24
828 856 4.223953 TGTGTTCTCTCAGGAAACCTAGT 58.776 43.478 0.00 0.00 29.64 2.57
830 858 5.825593 ATTGTGTTCTCTCAGGAAACCTA 57.174 39.130 0.00 0.00 29.64 3.08
831 859 4.713792 ATTGTGTTCTCTCAGGAAACCT 57.286 40.909 0.00 0.00 0.00 3.50
832 860 6.431234 ACATAATTGTGTTCTCTCAGGAAACC 59.569 38.462 1.42 0.00 33.85 3.27
991 2537 1.051008 ACATGAGCCATATCGCCTCA 58.949 50.000 0.00 0.00 0.00 3.86
1017 2566 3.024547 CAGAACTTCTGGGGAGACGATA 58.975 50.000 10.57 0.00 40.71 2.92
1021 2570 0.980423 AGCAGAACTTCTGGGGAGAC 59.020 55.000 18.53 2.99 44.43 3.36
1048 2597 4.763874 CGTAGTACGATGAAGCAGAGTAG 58.236 47.826 17.85 0.00 46.05 2.57
1050 2599 2.223294 GCGTAGTACGATGAAGCAGAGT 60.223 50.000 26.29 0.00 46.05 3.24
1060 2609 1.795286 GTAGTAGCGGCGTAGTACGAT 59.205 52.381 26.29 10.54 46.05 3.73
1546 3108 1.227089 GCAGCTCGGTCATGTCGAT 60.227 57.895 12.56 0.00 36.01 3.59
1760 3322 2.099263 TCGTCCCATCTCTTCTTTAGCG 59.901 50.000 0.00 0.00 0.00 4.26
1865 3427 2.233676 TGATCTTCTTGGCGTTGCTCTA 59.766 45.455 0.00 0.00 0.00 2.43
1874 3436 3.932089 GTCTCTGTCTTGATCTTCTTGGC 59.068 47.826 0.00 0.00 0.00 4.52
1921 3483 5.822278 TCTAGTGAGATTGTATTCGTGCTC 58.178 41.667 0.00 0.00 0.00 4.26
1923 3485 5.822278 TCTCTAGTGAGATTGTATTCGTGC 58.178 41.667 0.00 0.00 43.73 5.34
1998 3560 6.549364 TGGATTAATTGGAAATCGGCAATACT 59.451 34.615 0.00 0.00 34.74 2.12
1999 3561 6.744112 TGGATTAATTGGAAATCGGCAATAC 58.256 36.000 0.00 0.00 34.74 1.89
2000 3562 6.968263 TGGATTAATTGGAAATCGGCAATA 57.032 33.333 0.00 0.00 34.74 1.90
2001 3563 5.867903 TGGATTAATTGGAAATCGGCAAT 57.132 34.783 0.00 0.00 34.74 3.56
2002 3564 5.415221 GTTGGATTAATTGGAAATCGGCAA 58.585 37.500 0.00 0.00 34.74 4.52
2003 3565 4.439426 CGTTGGATTAATTGGAAATCGGCA 60.439 41.667 0.00 0.00 34.74 5.69
2006 3568 7.327275 TGAAAACGTTGGATTAATTGGAAATCG 59.673 33.333 0.00 0.00 34.74 3.34
2007 3569 8.527567 TGAAAACGTTGGATTAATTGGAAATC 57.472 30.769 0.00 0.00 33.44 2.17
2011 3573 6.865726 CACATGAAAACGTTGGATTAATTGGA 59.134 34.615 0.00 0.00 0.00 3.53
2023 3585 8.698854 CAATTAATTAGCACACATGAAAACGTT 58.301 29.630 0.00 0.00 0.00 3.99
2086 3800 8.303876 GTCCTGTTTACACATAATGGAATTGTT 58.696 33.333 0.00 0.00 36.99 2.83
2373 4090 3.788145 CCGGCCGGGACCATGTAA 61.788 66.667 37.42 0.00 38.47 2.41
2424 4141 3.682792 CGGGACTCGGTGTCTCTT 58.317 61.111 8.30 0.00 43.84 2.85
2451 4168 3.394836 GGCCAGAACTCCTCCGCT 61.395 66.667 0.00 0.00 0.00 5.52
2499 4219 1.679898 CCTCCCTTTGAAGTCGGCT 59.320 57.895 0.00 0.00 0.00 5.52
2542 4262 4.796495 GCAAATCCTCCGCCCGGT 62.796 66.667 6.61 0.00 36.47 5.28
2682 4402 2.126228 TTCCGTCGCATCGTCACC 60.126 61.111 0.00 0.00 0.00 4.02
2694 4414 1.962100 AGAACGAGTTTCTCCTTCCGT 59.038 47.619 0.00 0.00 40.98 4.69
2755 4479 2.029623 GGACGAAGGGAGTAGTATGCA 58.970 52.381 0.00 0.00 0.00 3.96
2771 4503 3.252215 TGTCTTGCACTTATTTTGGGACG 59.748 43.478 0.00 0.00 0.00 4.79
2785 4517 3.252215 CGTCCCAAAATAAGTGTCTTGCA 59.748 43.478 0.00 0.00 0.00 4.08
2787 4519 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
2788 4520 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2789 4521 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2791 4523 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2792 4524 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2793 4525 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2794 4526 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2795 4527 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2796 4528 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2797 4529 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2798 4530 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
2799 4531 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
2800 4532 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
2802 4534 0.106116 ACTGATACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
2803 4535 1.777941 AACTGATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2804 4536 3.553904 ACTAACTGATACTCCCTCCGTC 58.446 50.000 0.00 0.00 0.00 4.79
2808 4570 5.242171 GCCTCTTACTAACTGATACTCCCTC 59.758 48.000 0.00 0.00 0.00 4.30
2862 4625 2.294512 GGGAAGCATAACTAGGCAATGC 59.705 50.000 14.81 14.81 45.02 3.56
3056 6342 9.685276 TCTCTTTCATTATGTGTACATTTCCAT 57.315 29.630 0.00 0.00 37.76 3.41
3057 6343 9.166173 CTCTCTTTCATTATGTGTACATTTCCA 57.834 33.333 0.00 0.00 37.76 3.53
3058 6344 9.167311 ACTCTCTTTCATTATGTGTACATTTCC 57.833 33.333 0.00 0.00 37.76 3.13
3090 6376 9.661563 TCGTATAGGAAAGCTTTCTTTGATAAA 57.338 29.630 32.28 14.03 42.24 1.40
3091 6377 9.661563 TTCGTATAGGAAAGCTTTCTTTGATAA 57.338 29.630 32.28 18.35 42.24 1.75
3093 6379 8.738645 ATTCGTATAGGAAAGCTTTCTTTGAT 57.261 30.769 32.28 20.91 42.24 2.57
3094 6380 7.280205 GGATTCGTATAGGAAAGCTTTCTTTGA 59.720 37.037 32.28 19.81 42.24 2.69
3095 6381 7.065803 TGGATTCGTATAGGAAAGCTTTCTTTG 59.934 37.037 32.28 18.23 42.24 2.77
3097 6383 6.650120 TGGATTCGTATAGGAAAGCTTTCTT 58.350 36.000 32.28 28.67 37.35 2.52
3098 6384 6.235231 TGGATTCGTATAGGAAAGCTTTCT 57.765 37.500 32.28 22.17 37.35 2.52
3104 6390 7.710907 TCACAAGAATGGATTCGTATAGGAAAG 59.289 37.037 11.60 0.00 41.56 2.62
3155 6441 4.207955 CCCTTAGATTTAGGCCCAGTTTC 58.792 47.826 0.00 0.00 0.00 2.78
3208 6614 3.084039 CACTTAAGCCTCCAATGCAGAA 58.916 45.455 1.29 0.00 0.00 3.02
3276 6682 5.117592 GCACAACTAATTCATGTCTGTTTGC 59.882 40.000 0.00 0.00 0.00 3.68
3450 6860 9.950680 TTCTAAATTGTTTACTTTCTCTTGCTG 57.049 29.630 0.00 0.00 0.00 4.41
3568 7000 1.079681 ACGCCTTTAATGTCCGCGA 60.080 52.632 8.23 0.00 45.41 5.87
3677 7109 3.745799 TCGGGAGCTTTCACACAAATTA 58.254 40.909 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.