Multiple sequence alignment - TraesCS2D01G432300

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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 TraesCS2D01G432300 chr2D 100.000 3200 0 0 1 3200 544615111 544611912 0.000000e+00 5910.0
1 TraesCS2D01G432300 chr2D 85.650 223 20 7 1196 1418 544613679 544613469 1.160000e-54 224.0
2 TraesCS2D01G432300 chr2D 85.650 223 20 7 1433 1643 544613916 544613694 1.160000e-54 224.0
3 TraesCS2D01G432300 chr2B 92.680 1612 93 13 1 1608 650169793 650168203 0.000000e+00 2300.0
4 TraesCS2D01G432300 chr2B 89.507 934 56 18 1558 2452 650168211 650167281 0.000000e+00 1144.0
5 TraesCS2D01G432300 chr2B 89.971 349 34 1 2649 2997 650166893 650166546 1.750000e-122 449.0
6 TraesCS2D01G432300 chr2B 83.103 290 32 6 1367 1643 650168678 650168393 6.850000e-62 248.0
7 TraesCS2D01G432300 chr2B 93.976 83 3 2 3119 3200 650166096 650166015 1.210000e-24 124.0
8 TraesCS2D01G432300 chr2B 100.000 45 0 0 2610 2654 667802115 667802159 2.050000e-12 84.2
9 TraesCS2D01G432300 chr2A 91.816 1564 108 13 762 2311 686842974 686841417 0.000000e+00 2161.0
10 TraesCS2D01G432300 chr2A 82.440 746 82 26 140 843 686843675 686842937 9.820000e-170 606.0
11 TraesCS2D01G432300 chr2A 84.593 344 30 12 2708 3051 686841215 686840895 1.430000e-83 320.0
12 TraesCS2D01G432300 chr2A 84.375 224 21 9 1196 1418 686842299 686842089 1.160000e-49 207.0
13 TraesCS2D01G432300 chr2A 93.243 74 5 0 2649 2722 686841309 686841236 3.370000e-20 110.0
14 TraesCS2D01G432300 chr2A 97.500 40 1 0 691 730 621188586 621188625 5.730000e-08 69.4
15 TraesCS2D01G432300 chr2A 100.000 35 0 0 1 35 686843726 686843692 7.410000e-07 65.8
16 TraesCS2D01G432300 chr1D 91.667 60 5 0 268 327 392950919 392950978 2.050000e-12 84.2
17 TraesCS2D01G432300 chr1D 96.000 50 2 0 2605 2654 286930014 286929965 7.360000e-12 82.4
18 TraesCS2D01G432300 chr1A 80.870 115 15 5 268 375 492270630 492270516 2.050000e-12 84.2
19 TraesCS2D01G432300 chr7D 96.000 50 2 0 2605 2654 58624673 58624722 7.360000e-12 82.4
20 TraesCS2D01G432300 chr7D 96.000 50 2 0 2605 2654 550839679 550839630 7.360000e-12 82.4
21 TraesCS2D01G432300 chr5B 96.000 50 2 0 2605 2654 615005134 615005085 7.360000e-12 82.4
22 TraesCS2D01G432300 chr5B 90.323 62 4 2 2593 2652 290450237 290450298 2.650000e-11 80.5
23 TraesCS2D01G432300 chr4A 96.000 50 2 0 2605 2654 734874288 734874239 7.360000e-12 82.4
24 TraesCS2D01G432300 chr4A 96.000 50 2 0 2605 2654 736112583 736112534 7.360000e-12 82.4
25 TraesCS2D01G432300 chr5A 92.593 54 4 0 2601 2654 523751774 523751721 9.520000e-11 78.7
26 TraesCS2D01G432300 chr3A 88.462 52 5 1 268 319 584127174 584127124 9.580000e-06 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G432300 chr2D 544611912 544615111 3199 True 2119.333333 5910 90.433333 1 3200 3 chr2D.!!$R1 3199
1 TraesCS2D01G432300 chr2B 650166015 650169793 3778 True 853.000000 2300 89.847400 1 3200 5 chr2B.!!$R1 3199
2 TraesCS2D01G432300 chr2A 686840895 686843726 2831 True 578.300000 2161 89.411167 1 3051 6 chr2A.!!$R1 3050


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
97 98 0.246910 TGTACGCGAACATGGCCTAA 59.753 50.0 15.93 0.0 0.00 2.69 F
144 145 1.216064 AGTCAATCTGGCCCATGCTA 58.784 50.0 0.00 0.0 37.74 3.49 F
1093 1186 1.295020 TGGATCCATTCCCCGTCTTT 58.705 50.0 11.44 0.0 44.77 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 1552 1.377725 GACGTACTCCGGGGACTCA 60.378 63.158 9.33 0.00 42.24 3.41 R
2026 2174 2.504681 GTGCAAAATCAGGCGCCG 60.505 61.111 23.20 16.49 34.58 6.46 R
2544 2943 0.243636 CGGGCCAACATTCAGTTTCC 59.756 55.000 4.39 0.00 38.74 3.13 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
49 50 0.545309 ACTAGCAGAGGCCCTGTGAA 60.545 55.000 12.91 0.00 44.71 3.18
57 58 3.809832 CAGAGGCCCTGTGAATTATAACG 59.190 47.826 0.52 0.00 38.10 3.18
67 68 5.795972 TGTGAATTATAACGGACAACCTGA 58.204 37.500 0.00 0.00 0.00 3.86
77 78 4.504858 ACGGACAACCTGATCTTTGTATC 58.495 43.478 7.61 4.24 36.06 2.24
84 85 4.683832 ACCTGATCTTTGTATCTGTACGC 58.316 43.478 0.00 0.00 33.36 4.42
85 86 3.731216 CCTGATCTTTGTATCTGTACGCG 59.269 47.826 3.53 3.53 33.36 6.01
87 88 4.989044 TGATCTTTGTATCTGTACGCGAA 58.011 39.130 15.93 0.00 33.36 4.70
88 89 4.796830 TGATCTTTGTATCTGTACGCGAAC 59.203 41.667 15.93 0.00 33.36 3.95
97 98 0.246910 TGTACGCGAACATGGCCTAA 59.753 50.000 15.93 0.00 0.00 2.69
144 145 1.216064 AGTCAATCTGGCCCATGCTA 58.784 50.000 0.00 0.00 37.74 3.49
164 165 4.534103 GCTAAGAGGAATGGGGAGATGTAT 59.466 45.833 0.00 0.00 0.00 2.29
186 187 8.141909 TGTATAGTTGTGAAGGATAGCACATAC 58.858 37.037 0.00 0.00 43.73 2.39
243 244 7.220030 AGAGAGAGCACTTTAATGACTCAAAA 58.780 34.615 14.08 0.00 31.47 2.44
406 440 3.560896 GCAAGTTTCATTGTGTTGCCATT 59.439 39.130 0.00 0.00 38.03 3.16
440 474 4.947645 TGTCCCAAGCTCAAAGAATTTTG 58.052 39.130 0.00 0.00 44.03 2.44
482 516 1.425066 TCACCCCAAGCTCATTCAAGT 59.575 47.619 0.00 0.00 0.00 3.16
494 528 4.633565 GCTCATTCAAGTTTGGGACTAGAG 59.366 45.833 0.00 0.00 37.72 2.43
496 530 4.019321 TCATTCAAGTTTGGGACTAGAGGG 60.019 45.833 0.00 0.00 37.72 4.30
501 535 2.561526 AGTTTGGGACTAGAGGGGTACC 60.562 54.545 2.17 2.17 43.10 3.34
503 537 5.579676 AGTTTGGGACTAGAGGGGTACCTA 61.580 50.000 12.72 0.00 43.31 3.08
539 573 9.573133 AAACACTTATGCATGAAATAGTTTAGC 57.427 29.630 10.16 0.00 0.00 3.09
592 628 7.088589 AGTTACAAAAGGCTAAGCACATATG 57.911 36.000 0.00 0.00 0.00 1.78
716 760 2.487762 ACGTGTGGCACTTATCATTTGG 59.512 45.455 19.83 0.00 31.34 3.28
717 761 2.731968 CGTGTGGCACTTATCATTTGGC 60.732 50.000 19.83 0.00 36.39 4.52
773 817 3.866356 GTCTTTGGACCCGTACGC 58.134 61.111 10.49 0.00 36.53 4.42
1060 1153 2.215196 GCGTCTCTCCCTAGACTACTG 58.785 57.143 0.00 0.00 43.11 2.74
1061 1154 2.215196 CGTCTCTCCCTAGACTACTGC 58.785 57.143 0.00 0.00 43.11 4.40
1093 1186 1.295020 TGGATCCATTCCCCGTCTTT 58.705 50.000 11.44 0.00 44.77 2.52
1162 1255 3.740397 CCGGAGTACGTGCCGTCA 61.740 66.667 19.95 0.00 45.85 4.35
1207 1300 4.719369 GACCTCGCGCCGTTGACT 62.719 66.667 0.00 0.00 0.00 3.41
1285 1378 3.986006 GTGACGGTCACGGGCAGA 61.986 66.667 23.92 0.00 46.48 4.26
1292 1385 4.293648 TCACGGGCAGACACCACG 62.294 66.667 0.00 0.00 0.00 4.94
1300 1393 2.842462 AGACACCACGCCAGGTCA 60.842 61.111 0.00 0.00 40.77 4.02
1389 1482 1.819288 CGTGGCATCTCCGGAGTATAT 59.181 52.381 30.17 14.64 37.80 0.86
1699 1834 2.507992 CTGGAGCAGCGACCTTCG 60.508 66.667 11.82 0.00 43.89 3.79
1709 1844 2.177778 GACCTTCGTCGTCGGACC 59.822 66.667 1.91 0.00 40.17 4.46
1710 1845 3.333898 GACCTTCGTCGTCGGACCC 62.334 68.421 1.91 0.00 40.17 4.46
1768 1906 2.866523 ATTACTCCCCGTCGGCCTCA 62.867 60.000 5.50 0.00 0.00 3.86
1876 2014 3.591254 GAGGGCGGCGACATATCCC 62.591 68.421 17.61 12.95 37.24 3.85
2068 2217 4.681074 TGTTATCGGATTCATAGGCACA 57.319 40.909 0.00 0.00 0.00 4.57
2070 2219 6.353404 TGTTATCGGATTCATAGGCACATA 57.647 37.500 0.00 0.00 0.00 2.29
2140 2289 3.991773 TGTTAGTAGTTGCCTAACTTGCG 59.008 43.478 10.59 0.00 44.57 4.85
2154 2303 6.459298 GCCTAACTTGCGATACTACTCACTTA 60.459 42.308 0.00 0.00 0.00 2.24
2311 2472 6.705825 AGGTTTACAAATGGCAAATTTCTGAC 59.294 34.615 0.00 0.00 0.00 3.51
2318 2479 9.171877 ACAAATGGCAAATTTCTGACTTTTAAA 57.828 25.926 0.00 0.00 31.72 1.52
2319 2480 9.437045 CAAATGGCAAATTTCTGACTTTTAAAC 57.563 29.630 0.00 0.00 31.72 2.01
2322 2483 6.257630 TGGCAAATTTCTGACTTTTAAACTGC 59.742 34.615 0.00 0.00 0.00 4.40
2325 2486 7.847564 GCAAATTTCTGACTTTTAAACTGCAAG 59.152 33.333 0.00 0.00 42.29 4.01
2326 2487 8.330302 CAAATTTCTGACTTTTAAACTGCAAGG 58.670 33.333 0.00 0.00 39.30 3.61
2328 2489 6.377327 TTCTGACTTTTAAACTGCAAGGAG 57.623 37.500 0.00 0.00 39.30 3.69
2354 2528 1.889454 TCCAATTTGGATGCGGTGC 59.111 52.632 14.24 0.00 42.67 5.01
2363 2537 2.361483 ATGCGGTGCTTGATGGCA 60.361 55.556 0.00 0.00 40.15 4.92
2366 2540 1.517694 GCGGTGCTTGATGGCATTG 60.518 57.895 0.00 0.00 44.34 2.82
2387 2561 4.394729 TGTTTGCCTTCTTATCGGTTCTT 58.605 39.130 0.00 0.00 0.00 2.52
2404 2578 6.206634 TCGGTTCTTGATCTTAGCAAAATGTT 59.793 34.615 0.00 0.00 0.00 2.71
2417 2591 3.597255 CAAAATGTTGCCCATGTATGCA 58.403 40.909 0.00 0.00 32.82 3.96
2446 2620 1.276138 GTGGGGGAGCCAGAAAAATTG 59.724 52.381 0.00 0.00 0.00 2.32
2449 2623 3.245948 TGGGGGAGCCAGAAAAATTGTAT 60.246 43.478 0.00 0.00 0.00 2.29
2450 2624 3.384789 GGGGGAGCCAGAAAAATTGTATC 59.615 47.826 0.00 0.00 0.00 2.24
2451 2625 3.066760 GGGGAGCCAGAAAAATTGTATCG 59.933 47.826 0.00 0.00 0.00 2.92
2452 2626 3.945285 GGGAGCCAGAAAAATTGTATCGA 59.055 43.478 0.00 0.00 0.00 3.59
2454 2628 4.394920 GGAGCCAGAAAAATTGTATCGACA 59.605 41.667 0.00 0.00 0.00 4.35
2455 2629 5.447818 GGAGCCAGAAAAATTGTATCGACAG 60.448 44.000 0.00 0.00 36.76 3.51
2456 2630 4.396166 AGCCAGAAAAATTGTATCGACAGG 59.604 41.667 0.00 0.00 36.76 4.00
2457 2631 4.438744 GCCAGAAAAATTGTATCGACAGGG 60.439 45.833 0.00 0.00 36.76 4.45
2458 2632 4.438744 CCAGAAAAATTGTATCGACAGGGC 60.439 45.833 0.00 0.00 36.76 5.19
2459 2633 4.155826 CAGAAAAATTGTATCGACAGGGCA 59.844 41.667 0.00 0.00 36.76 5.36
2482 2881 9.280174 GGCATATAGTGTTATTAAGCAAGGTTA 57.720 33.333 0.00 0.00 0.00 2.85
2494 2893 2.647802 AGCAAGGTTAAGGAGGGCTAAA 59.352 45.455 0.00 0.00 0.00 1.85
2495 2894 2.753452 GCAAGGTTAAGGAGGGCTAAAC 59.247 50.000 0.00 0.00 0.00 2.01
2497 2896 2.639487 AGGTTAAGGAGGGCTAAACCA 58.361 47.619 5.44 0.00 41.67 3.67
2499 2898 4.377134 AGGTTAAGGAGGGCTAAACCATA 58.623 43.478 5.44 0.00 41.67 2.74
2512 2911 6.254804 GGGCTAAACCATAAAATACGCTTTTG 59.745 38.462 6.57 0.00 42.05 2.44
2517 2916 3.551485 CCATAAAATACGCTTTTGGCAGC 59.449 43.478 6.57 0.00 41.91 5.25
2519 2918 5.449862 CCATAAAATACGCTTTTGGCAGCTA 60.450 40.000 6.57 0.00 41.91 3.32
2520 2919 4.513198 AAAATACGCTTTTGGCAGCTAA 57.487 36.364 0.00 0.00 41.91 3.09
2521 2920 4.513198 AAATACGCTTTTGGCAGCTAAA 57.487 36.364 0.00 0.00 41.91 1.85
2522 2921 4.513198 AATACGCTTTTGGCAGCTAAAA 57.487 36.364 15.21 15.21 41.91 1.52
2562 2961 1.632589 AGGAAACTGAATGTTGGCCC 58.367 50.000 0.00 0.00 41.13 5.80
2566 2965 3.451894 CTGAATGTTGGCCCGGGC 61.452 66.667 38.57 38.57 41.06 6.13
2597 2996 3.145551 CCCTGCCTCTGCCAATGC 61.146 66.667 0.00 0.00 36.33 3.56
2598 2997 3.515286 CCTGCCTCTGCCAATGCG 61.515 66.667 0.00 0.00 41.78 4.73
2613 3012 0.251073 ATGCGGGTGGTAGGTTGTAC 59.749 55.000 0.00 0.00 0.00 2.90
2615 3014 0.108472 GCGGGTGGTAGGTTGTACTC 60.108 60.000 0.00 0.00 0.00 2.59
2616 3015 0.533951 CGGGTGGTAGGTTGTACTCC 59.466 60.000 0.00 0.00 0.00 3.85
2617 3016 0.907486 GGGTGGTAGGTTGTACTCCC 59.093 60.000 0.00 0.00 0.00 4.30
2618 3017 1.554118 GGGTGGTAGGTTGTACTCCCT 60.554 57.143 8.63 8.63 32.93 4.20
2619 3018 1.829849 GGTGGTAGGTTGTACTCCCTC 59.170 57.143 7.11 1.43 32.08 4.30
2620 3019 2.559252 GGTGGTAGGTTGTACTCCCTCT 60.559 54.545 7.11 0.00 32.08 3.69
2621 3020 2.496470 GTGGTAGGTTGTACTCCCTCTG 59.504 54.545 7.11 0.00 32.08 3.35
2622 3021 2.111255 TGGTAGGTTGTACTCCCTCTGT 59.889 50.000 7.11 0.00 32.08 3.41
2623 3022 3.334581 TGGTAGGTTGTACTCCCTCTGTA 59.665 47.826 7.11 0.00 32.08 2.74
2624 3023 4.202706 TGGTAGGTTGTACTCCCTCTGTAA 60.203 45.833 7.11 0.00 32.08 2.41
2626 3025 4.886496 AGGTTGTACTCCCTCTGTAAAC 57.114 45.455 0.00 0.00 0.00 2.01
2627 3026 4.490706 AGGTTGTACTCCCTCTGTAAACT 58.509 43.478 0.00 0.00 0.00 2.66
2628 3027 5.648247 AGGTTGTACTCCCTCTGTAAACTA 58.352 41.667 0.00 0.00 0.00 2.24
2629 3028 6.080009 AGGTTGTACTCCCTCTGTAAACTAA 58.920 40.000 0.00 0.00 0.00 2.24
2631 3030 7.897565 AGGTTGTACTCCCTCTGTAAACTAATA 59.102 37.037 0.00 0.00 0.00 0.98
2638 3037 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2640 3039 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2641 3040 7.808856 CCCTCTGTAAACTAATATAAGAGCGTC 59.191 40.741 0.00 0.00 0.00 5.19
2642 3041 8.569641 CCTCTGTAAACTAATATAAGAGCGTCT 58.430 37.037 0.00 0.00 0.00 4.18
2656 3077 4.300803 AGAGCGTCTAGATCACTACTACG 58.699 47.826 0.00 0.00 37.82 3.51
2661 3082 5.006552 GCGTCTAGATCACTACTACGAGTTT 59.993 44.000 0.00 0.00 36.15 2.66
2665 3086 8.755018 GTCTAGATCACTACTACGAGTTTAGAC 58.245 40.741 0.00 0.00 0.00 2.59
2714 3170 0.467290 GTTGTTTGGCTCCACCTGGA 60.467 55.000 0.00 0.00 43.08 3.86
2722 3178 1.318158 GCTCCACCTGGAAAGCATGG 61.318 60.000 0.00 0.00 44.91 3.66
2744 3200 4.421948 GTGATGTCGGTCAACCTAACTAG 58.578 47.826 0.00 0.00 0.00 2.57
2749 3205 4.828939 TGTCGGTCAACCTAACTAGAAGAA 59.171 41.667 0.00 0.00 0.00 2.52
2752 3208 5.035443 CGGTCAACCTAACTAGAAGAATCG 58.965 45.833 0.00 0.00 0.00 3.34
2759 3215 7.274603 ACCTAACTAGAAGAATCGGATGTAC 57.725 40.000 0.00 0.00 0.00 2.90
2788 3244 7.692291 CGTTGGCAGAATACTTGTAGTTTATTG 59.308 37.037 0.00 0.00 0.00 1.90
2806 3262 9.206870 AGTTTATTGCTTGGTTAAATTCATGTG 57.793 29.630 0.00 0.00 0.00 3.21
2829 3285 3.900966 TGGATCTCATGAACACCTCAG 57.099 47.619 0.00 0.00 37.52 3.35
2835 3291 5.233083 TCTCATGAACACCTCAGAAACAT 57.767 39.130 0.00 0.00 37.52 2.71
2866 3322 3.484649 CCAACAACCGTCGTAATCTATCG 59.515 47.826 0.00 0.00 0.00 2.92
2878 3334 8.927721 CGTCGTAATCTATCGGATATCATATCT 58.072 37.037 4.83 0.00 33.71 1.98
2984 3440 5.492895 TGCGTTTTCAATACTCCCTTGATA 58.507 37.500 0.00 0.00 32.94 2.15
2986 3442 5.353123 GCGTTTTCAATACTCCCTTGATACA 59.647 40.000 0.00 0.00 32.94 2.29
3044 3761 4.325119 TGCGGTTTGGCTGTTAGTTATTA 58.675 39.130 0.00 0.00 0.00 0.98
3051 3768 7.541091 GGTTTGGCTGTTAGTTATTAGCTTTTC 59.459 37.037 0.00 0.00 36.45 2.29
3066 3783 5.757850 AGCTTTTCTTGAAATCACGAGTT 57.242 34.783 0.00 0.00 0.00 3.01
3075 3792 7.203218 TCTTGAAATCACGAGTTCGATGATAT 58.797 34.615 8.72 3.45 43.02 1.63
3082 3799 7.674471 TCACGAGTTCGATGATATAAGAGAT 57.326 36.000 8.72 0.00 43.02 2.75
3106 3823 8.871629 ATTGGACCACACAAACTAAATACATA 57.128 30.769 0.00 0.00 0.00 2.29
3107 3824 7.675962 TGGACCACACAAACTAAATACATAC 57.324 36.000 0.00 0.00 0.00 2.39
3108 3825 7.455058 TGGACCACACAAACTAAATACATACT 58.545 34.615 0.00 0.00 0.00 2.12
3194 3978 6.900568 TGCTTTAAAAATGCATTTATCCCG 57.099 33.333 24.35 13.92 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 7.110155 ACAAAGATCAGGTTGTCCGTTATAAT 58.890 34.615 0.00 0.00 39.05 1.28
57 58 5.491982 ACAGATACAAAGATCAGGTTGTCC 58.508 41.667 11.38 6.83 38.80 4.02
67 68 4.740268 TGTTCGCGTACAGATACAAAGAT 58.260 39.130 14.93 0.00 0.00 2.40
77 78 0.179121 TAGGCCATGTTCGCGTACAG 60.179 55.000 22.78 12.01 0.00 2.74
84 85 1.134699 TCTGAGCTTAGGCCATGTTCG 60.135 52.381 5.01 0.00 39.73 3.95
85 86 2.559440 CTCTGAGCTTAGGCCATGTTC 58.441 52.381 5.01 2.34 39.73 3.18
87 88 0.835941 CCTCTGAGCTTAGGCCATGT 59.164 55.000 5.01 0.00 39.73 3.21
88 89 1.126488 TCCTCTGAGCTTAGGCCATG 58.874 55.000 5.01 0.00 39.73 3.66
97 98 0.043940 ACTCCCCATTCCTCTGAGCT 59.956 55.000 0.00 0.00 0.00 4.09
144 145 5.731924 ACTATACATCTCCCCATTCCTCTT 58.268 41.667 0.00 0.00 0.00 2.85
164 165 5.126545 ACGTATGTGCTATCCTTCACAACTA 59.873 40.000 0.00 0.00 45.03 2.24
243 244 7.665559 TCCTTGTGTAGATAGCATTGTTTCTTT 59.334 33.333 0.00 0.00 0.00 2.52
258 259 6.174720 AGAAACTTCATGTCCTTGTGTAGA 57.825 37.500 0.00 0.00 0.00 2.59
406 440 6.480763 TGAGCTTGGGACATTTGTAGAATTA 58.519 36.000 0.00 0.00 39.30 1.40
454 488 2.152016 GAGCTTGGGGTGAACAGTAAC 58.848 52.381 0.00 0.00 0.00 2.50
469 503 3.837355 AGTCCCAAACTTGAATGAGCTT 58.163 40.909 0.00 0.00 33.03 3.74
482 516 1.726352 AGGTACCCCTCTAGTCCCAAA 59.274 52.381 8.74 0.00 35.62 3.28
494 528 0.684153 TGTGTAGGCGTAGGTACCCC 60.684 60.000 8.74 2.05 0.00 4.95
496 530 2.029110 TGTTTGTGTAGGCGTAGGTACC 60.029 50.000 2.73 2.73 0.00 3.34
501 535 4.201685 GCATAAGTGTTTGTGTAGGCGTAG 60.202 45.833 0.00 0.00 0.00 3.51
503 537 2.482721 GCATAAGTGTTTGTGTAGGCGT 59.517 45.455 0.00 0.00 0.00 5.68
539 573 9.636965 GCTTTCTTTGTTTAAATTGTTTAGCAG 57.363 29.630 0.00 0.00 0.00 4.24
556 590 7.203218 AGCCTTTTGTAACTAAGCTTTCTTTG 58.797 34.615 3.20 0.00 33.85 2.77
614 650 7.277319 GCTAAATACACGAAAAGGCTTAGTACT 59.723 37.037 0.00 0.00 0.00 2.73
625 661 8.673711 AGATGCTAAATGCTAAATACACGAAAA 58.326 29.630 0.00 0.00 43.37 2.29
679 715 0.387929 ACGTGTGACCGTTCTGACAT 59.612 50.000 0.00 0.00 37.96 3.06
1036 1125 3.955101 CTAGGGAGAGACGCCGCG 61.955 72.222 12.14 12.14 0.00 6.46
1222 1315 2.437359 ACGTACTCCGGGGACTCG 60.437 66.667 9.33 12.28 42.24 4.18
1285 1378 2.347490 GATGACCTGGCGTGGTGT 59.653 61.111 6.72 0.00 41.00 4.16
1459 1552 1.377725 GACGTACTCCGGGGACTCA 60.378 63.158 9.33 0.00 42.24 3.41
1709 1844 4.082523 AGGTGTCGATGTGGCGGG 62.083 66.667 0.00 0.00 0.00 6.13
1710 1845 2.509336 GAGGTGTCGATGTGGCGG 60.509 66.667 0.00 0.00 0.00 6.13
1715 1850 2.573869 CCGCAGAGGTGTCGATGT 59.426 61.111 0.00 0.00 34.51 3.06
1717 1852 4.498520 CGCCGCAGAGGTGTCGAT 62.499 66.667 0.00 0.00 45.30 3.59
1859 1997 3.626924 GGGATATGTCGCCGCCCT 61.627 66.667 0.00 0.00 35.86 5.19
1861 1999 3.986006 TCGGGATATGTCGCCGCC 61.986 66.667 12.42 0.00 37.79 6.13
2026 2174 2.504681 GTGCAAAATCAGGCGCCG 60.505 61.111 23.20 16.49 34.58 6.46
2070 2219 9.887629 CAATATCTCATACTATTCCAATCTGCT 57.112 33.333 0.00 0.00 0.00 4.24
2087 2236 5.571791 TGCATGAGGAATCCAATATCTCA 57.428 39.130 0.61 0.00 38.59 3.27
2140 2289 8.604890 GCAAACAGGAAATAAGTGAGTAGTATC 58.395 37.037 0.00 0.00 0.00 2.24
2154 2303 1.000274 GAAGCACGGCAAACAGGAAAT 60.000 47.619 0.00 0.00 0.00 2.17
2278 2430 4.464597 TGCCATTTGTAAACCTGGGAATAC 59.535 41.667 0.00 0.00 31.26 1.89
2283 2435 3.760580 TTTGCCATTTGTAAACCTGGG 57.239 42.857 0.00 0.00 31.26 4.45
2285 2437 6.705381 TCAGAAATTTGCCATTTGTAAACCTG 59.295 34.615 0.00 0.00 31.05 4.00
2292 2453 8.729805 TTAAAAGTCAGAAATTTGCCATTTGT 57.270 26.923 0.00 0.00 0.00 2.83
2311 2472 3.496331 TCCCCTCCTTGCAGTTTAAAAG 58.504 45.455 0.00 0.00 0.00 2.27
2318 2479 1.501582 GATACTCCCCTCCTTGCAGT 58.498 55.000 0.00 0.00 0.00 4.40
2319 2480 0.761802 GGATACTCCCCTCCTTGCAG 59.238 60.000 0.00 0.00 0.00 4.41
2322 2483 4.210331 CAAATTGGATACTCCCCTCCTTG 58.790 47.826 0.00 0.00 35.03 3.61
2325 2486 2.783510 TCCAAATTGGATACTCCCCTCC 59.216 50.000 11.23 0.00 42.67 4.30
2363 2537 5.010282 AGAACCGATAAGAAGGCAAACAAT 58.990 37.500 0.00 0.00 0.00 2.71
2366 2540 4.454504 TCAAGAACCGATAAGAAGGCAAAC 59.545 41.667 0.00 0.00 0.00 2.93
2374 2548 6.465439 TGCTAAGATCAAGAACCGATAAGA 57.535 37.500 0.00 0.00 0.00 2.10
2404 2578 1.076850 CCACCTGCATACATGGGCA 60.077 57.895 8.39 8.39 38.52 5.36
2417 2591 1.923909 GCTCCCCCACTAACCACCT 60.924 63.158 0.00 0.00 0.00 4.00
2446 2620 4.785511 ACACTATATGCCCTGTCGATAC 57.214 45.455 0.00 0.00 0.00 2.24
2449 2623 5.801531 AATAACACTATATGCCCTGTCGA 57.198 39.130 0.00 0.00 0.00 4.20
2450 2624 6.090898 GCTTAATAACACTATATGCCCTGTCG 59.909 42.308 0.00 0.00 0.00 4.35
2451 2625 6.934645 TGCTTAATAACACTATATGCCCTGTC 59.065 38.462 0.00 0.00 0.00 3.51
2452 2626 6.837312 TGCTTAATAACACTATATGCCCTGT 58.163 36.000 0.00 0.00 0.00 4.00
2454 2628 6.942576 CCTTGCTTAATAACACTATATGCCCT 59.057 38.462 0.00 0.00 0.00 5.19
2455 2629 6.715264 ACCTTGCTTAATAACACTATATGCCC 59.285 38.462 0.00 0.00 0.00 5.36
2456 2630 7.745620 ACCTTGCTTAATAACACTATATGCC 57.254 36.000 0.00 0.00 0.00 4.40
2482 2881 5.826208 CGTATTTTATGGTTTAGCCCTCCTT 59.174 40.000 0.00 0.00 36.04 3.36
2483 2882 5.374071 CGTATTTTATGGTTTAGCCCTCCT 58.626 41.667 0.00 0.00 36.04 3.69
2544 2943 0.243636 CGGGCCAACATTCAGTTTCC 59.756 55.000 4.39 0.00 38.74 3.13
2597 2996 0.533951 GGAGTACAACCTACCACCCG 59.466 60.000 0.00 0.00 0.00 5.28
2598 2997 0.907486 GGGAGTACAACCTACCACCC 59.093 60.000 8.59 0.00 35.30 4.61
2613 3012 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2615 3014 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2616 3015 8.569641 AGACGCTCTTATATTAGTTTACAGAGG 58.430 37.037 0.00 0.00 0.00 3.69
2624 3023 9.509956 AGTGATCTAGACGCTCTTATATTAGTT 57.490 33.333 0.00 0.00 0.00 2.24
2629 3028 9.590451 GTAGTAGTGATCTAGACGCTCTTATAT 57.410 37.037 10.41 0.00 0.00 0.86
2631 3030 6.587226 CGTAGTAGTGATCTAGACGCTCTTAT 59.413 42.308 10.41 2.13 33.25 1.73
2633 3032 4.746115 CGTAGTAGTGATCTAGACGCTCTT 59.254 45.833 10.41 5.20 33.25 2.85
2634 3033 4.037803 TCGTAGTAGTGATCTAGACGCTCT 59.962 45.833 10.41 7.61 36.98 4.09
2635 3034 4.297510 TCGTAGTAGTGATCTAGACGCTC 58.702 47.826 10.41 0.00 36.98 5.03
2636 3035 4.202141 ACTCGTAGTAGTGATCTAGACGCT 60.202 45.833 0.00 4.20 36.98 5.07
2637 3036 4.050553 ACTCGTAGTAGTGATCTAGACGC 58.949 47.826 0.00 0.00 36.98 5.19
2638 3037 6.586868 AAACTCGTAGTAGTGATCTAGACG 57.413 41.667 0.00 0.00 37.71 4.18
2640 3039 8.694540 AGTCTAAACTCGTAGTAGTGATCTAGA 58.305 37.037 0.00 0.00 0.00 2.43
2641 3040 8.876275 AGTCTAAACTCGTAGTAGTGATCTAG 57.124 38.462 0.00 0.00 0.00 2.43
2642 3041 9.743057 GTAGTCTAAACTCGTAGTAGTGATCTA 57.257 37.037 0.00 0.00 36.92 1.98
2643 3042 8.477256 AGTAGTCTAAACTCGTAGTAGTGATCT 58.523 37.037 0.00 0.00 36.92 2.75
2644 3043 8.647143 AGTAGTCTAAACTCGTAGTAGTGATC 57.353 38.462 0.00 0.00 36.92 2.92
2672 3093 8.495949 CAACTCAAAACTAAGCTTTCTATTCGA 58.504 33.333 3.20 0.00 0.00 3.71
2714 3170 1.271325 TGACCGACATCACCATGCTTT 60.271 47.619 0.00 0.00 32.57 3.51
2722 3178 3.314541 AGTTAGGTTGACCGACATCAC 57.685 47.619 10.76 0.00 42.08 3.06
2752 3208 0.535335 TCTGCCAACGGAGTACATCC 59.465 55.000 0.00 0.00 45.00 3.51
2759 3215 2.699954 ACAAGTATTCTGCCAACGGAG 58.300 47.619 0.00 0.00 31.21 4.63
2788 3244 6.862209 TCCATACACATGAATTTAACCAAGC 58.138 36.000 0.00 0.00 33.67 4.01
2806 3262 5.069648 TCTGAGGTGTTCATGAGATCCATAC 59.930 44.000 12.38 0.84 34.68 2.39
2808 3264 4.035814 TCTGAGGTGTTCATGAGATCCAT 58.964 43.478 12.38 0.00 34.68 3.41
2829 3285 5.578776 GGTTGTTGGGATTATCGATGTTTC 58.421 41.667 8.54 1.92 0.00 2.78
2835 3291 2.736081 CGACGGTTGTTGGGATTATCGA 60.736 50.000 0.00 0.00 0.00 3.59
2958 3414 2.482721 AGGGAGTATTGAAAACGCAACG 59.517 45.455 0.00 0.00 0.00 4.10
2960 3416 4.138290 TCAAGGGAGTATTGAAAACGCAA 58.862 39.130 0.00 0.00 33.85 4.85
2984 3440 3.567397 AGCTAGGTCGTATCAAGGATGT 58.433 45.455 0.00 0.00 0.00 3.06
2986 3442 3.823873 CTGAGCTAGGTCGTATCAAGGAT 59.176 47.826 16.71 0.00 0.00 3.24
3044 3761 5.559035 CGAACTCGTGATTTCAAGAAAAGCT 60.559 40.000 0.00 0.00 34.32 3.74
3051 3768 5.709011 ATCATCGAACTCGTGATTTCAAG 57.291 39.130 9.76 0.00 37.05 3.02
3062 3779 7.757624 GGTCCAATCTCTTATATCATCGAACTC 59.242 40.741 0.00 0.00 0.00 3.01
3066 3783 6.493458 TGTGGTCCAATCTCTTATATCATCGA 59.507 38.462 0.00 0.00 0.00 3.59
3075 3792 5.304686 AGTTTGTGTGGTCCAATCTCTTA 57.695 39.130 0.00 0.00 0.00 2.10
3082 3799 7.940137 AGTATGTATTTAGTTTGTGTGGTCCAA 59.060 33.333 0.00 0.00 0.00 3.53
3106 3823 7.801716 TCAGTTAAGCATCAAGTTGTTTAGT 57.198 32.000 2.11 0.00 0.00 2.24
3137 3921 9.449719 AAGGATACGTTTGACTATTTTGAGAAT 57.550 29.630 0.00 0.00 46.39 2.40



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

AutoCloner maintained by Alex Coulton.