Multiple sequence alignment - TraesCS2A01G085700

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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 TraesCS2A01G085700 chr2A 100.000 2759 0 0 1 2759 39415210 39412452 0.000000e+00 5096.0
1 TraesCS2A01G085700 chr2A 90.112 1972 132 18 693 2663 39306975 39308884 0.000000e+00 2503.0
2 TraesCS2A01G085700 chr2A 97.033 337 10 0 1 337 18061652 18061988 3.990000e-158 568.0
3 TraesCS2A01G085700 chr2A 95.549 337 15 0 1 337 772038571 772038235 8.690000e-150 540.0
4 TraesCS2A01G085700 chr2A 98.031 254 4 1 333 586 18062019 18062271 9.070000e-120 440.0
5 TraesCS2A01G085700 chr2A 96.327 245 9 0 342 586 772038196 772037952 1.190000e-108 403.0
6 TraesCS2A01G085700 chr2A 91.803 122 9 1 584 705 39293416 39293536 4.730000e-38 169.0
7 TraesCS2A01G085700 chr2D 96.804 1846 54 4 584 2428 35922759 35924600 0.000000e+00 3077.0
8 TraesCS2A01G085700 chr2D 76.285 253 52 8 87 335 640646457 640646209 8.020000e-26 128.0
9 TraesCS2A01G085700 chr2D 94.937 79 4 0 2679 2757 35924777 35924855 1.040000e-24 124.0
10 TraesCS2A01G085700 chr2B 89.963 1335 124 7 1001 2335 61300912 61299588 0.000000e+00 1714.0
11 TraesCS2A01G085700 chr2B 89.064 1143 101 7 955 2095 61495048 61493928 0.000000e+00 1397.0
12 TraesCS2A01G085700 chr2B 90.690 290 25 2 2140 2428 61493394 61493106 4.310000e-103 385.0
13 TraesCS2A01G085700 chr2B 94.091 220 12 1 2538 2757 61299588 61299370 1.580000e-87 333.0
14 TraesCS2A01G085700 chr2B 92.958 142 9 1 2553 2693 61493106 61492965 3.600000e-49 206.0
15 TraesCS2A01G085700 chr2B 94.737 76 4 0 2682 2757 61492926 61492851 4.830000e-23 119.0
16 TraesCS2A01G085700 chr3A 96.736 337 11 0 1 337 745757460 745757796 1.860000e-156 562.0
17 TraesCS2A01G085700 chr3A 98.031 254 4 1 333 586 745757827 745758079 9.070000e-120 440.0
18 TraesCS2A01G085700 chr3A 80.435 92 16 2 244 334 698524602 698524512 4.930000e-08 69.4
19 TraesCS2A01G085700 chr7A 95.846 337 14 0 1 337 403983048 403983384 1.870000e-151 545.0
20 TraesCS2A01G085700 chr7A 97.638 254 5 1 333 586 403983415 403983667 4.220000e-118 435.0
21 TraesCS2A01G085700 chr1B 95.846 337 14 0 1 337 473290018 473290354 1.870000e-151 545.0
22 TraesCS2A01G085700 chr1B 97.244 254 6 1 333 586 473290385 473290637 1.960000e-116 429.0
23 TraesCS2A01G085700 chr1B 85.714 182 18 6 6 186 633845398 633845224 4.690000e-43 185.0
24 TraesCS2A01G085700 chr1B 86.364 88 12 0 250 337 633809083 633808996 2.260000e-16 97.1
25 TraesCS2A01G085700 chr1D 91.837 49 4 0 289 337 205583359 205583407 4.930000e-08 69.4


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 TraesCS2A01G085700 chr2A 39412452 39415210 2758 True 5096.00 5096 100.00000 1 2759 1 chr2A.!!$R1 2758
1 TraesCS2A01G085700 chr2A 39306975 39308884 1909 False 2503.00 2503 90.11200 693 2663 1 chr2A.!!$F2 1970
2 TraesCS2A01G085700 chr2A 18061652 18062271 619 False 504.00 568 97.53200 1 586 2 chr2A.!!$F3 585
3 TraesCS2A01G085700 chr2A 772037952 772038571 619 True 471.50 540 95.93800 1 586 2 chr2A.!!$R2 585
4 TraesCS2A01G085700 chr2D 35922759 35924855 2096 False 1600.50 3077 95.87050 584 2757 2 chr2D.!!$F1 2173
5 TraesCS2A01G085700 chr2B 61299370 61300912 1542 True 1023.50 1714 92.02700 1001 2757 2 chr2B.!!$R1 1756
6 TraesCS2A01G085700 chr2B 61492851 61495048 2197 True 526.75 1397 91.86225 955 2757 4 chr2B.!!$R2 1802
7 TraesCS2A01G085700 chr3A 745757460 745758079 619 False 501.00 562 97.38350 1 586 2 chr3A.!!$F1 585
8 TraesCS2A01G085700 chr7A 403983048 403983667 619 False 490.00 545 96.74200 1 586 2 chr7A.!!$F1 585
9 TraesCS2A01G085700 chr1B 473290018 473290637 619 False 487.00 545 96.54500 1 586 2 chr1B.!!$F1 585

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
619 654 0.259065 TAGGATGGGTCGAGAGCTGT 59.741 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2987 0.249699 CAGTTGTACACTCCGGTGCA 60.25 55.0 0.0 0.0 46.57 4.57 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
176 177 3.956199 CACAGCTCATTATCCACCCAATT 59.044 43.478 0.00 0.00 0.00 2.32
231 232 2.551071 CCCTCAAGAAACCTCCAGTCAC 60.551 54.545 0.00 0.00 0.00 3.67
232 233 2.104792 CCTCAAGAAACCTCCAGTCACA 59.895 50.000 0.00 0.00 0.00 3.58
259 260 2.684881 CGTAAGCTTTGGCAAGATCCAT 59.315 45.455 3.20 0.00 41.70 3.41
270 271 3.181487 GGCAAGATCCATTTTGTACGCAT 60.181 43.478 0.00 0.00 0.00 4.73
440 475 4.526650 TGCATAGGCTGATCGGTCTATAAA 59.473 41.667 24.81 14.87 41.91 1.40
516 551 2.487775 TGTACCTGGTGGCATAATCCT 58.512 47.619 10.23 0.00 36.63 3.24
619 654 0.259065 TAGGATGGGTCGAGAGCTGT 59.741 55.000 0.00 0.00 0.00 4.40
755 790 9.961265 GGTATGCCTTACCTTACATTTTTATTC 57.039 33.333 5.85 0.00 46.07 1.75
843 878 9.388506 CTCAATCTTTATCACTGTTACAGGAAT 57.611 33.333 17.21 11.37 35.51 3.01
965 1000 2.033550 GTGCGGTAGAGATCGAAGACAT 59.966 50.000 0.00 0.00 42.51 3.06
1034 1069 1.570979 TGAGCTCCCTGGATGTAGAGA 59.429 52.381 12.15 0.00 0.00 3.10
1055 1090 1.607756 TCCTGAGCTGCGAAGAGGT 60.608 57.895 0.00 0.00 0.00 3.85
1056 1091 1.188219 TCCTGAGCTGCGAAGAGGTT 61.188 55.000 0.00 0.00 0.00 3.50
1094 1129 5.202004 ACCGACCACTCTGAAGTTATCTAT 58.798 41.667 0.00 0.00 31.71 1.98
1308 1343 5.040635 CGCCAATTTGTTCATATGGTTACC 58.959 41.667 2.13 0.00 33.63 2.85
1368 1403 2.891580 GACCGAGTGGCTAAGGATCATA 59.108 50.000 0.00 0.00 39.70 2.15
1401 1436 2.125147 GCGTGTGATGGCAGCCTA 60.125 61.111 14.15 0.00 0.00 3.93
1407 1442 0.539051 GTGATGGCAGCCTACTCTGT 59.461 55.000 14.15 0.00 36.49 3.41
1821 1871 7.119846 GTCTGAAAGCATCCTACATTGTACTTT 59.880 37.037 8.35 8.35 0.00 2.66
2095 2145 7.329717 ACGGATAGCGATTTGATATTCTTCTTC 59.670 37.037 0.00 0.00 0.00 2.87
2317 2856 2.513897 GGCGCGGTGGAGCTTTAT 60.514 61.111 8.83 0.00 39.15 1.40
2343 2882 6.835488 ACCCTCTTGACATGTATGCATTTTAT 59.165 34.615 3.54 0.00 31.99 1.40
2385 2924 8.190784 CACCTGAAGTGTATTTTCTTTTTCTGT 58.809 33.333 0.00 0.00 41.93 3.41
2426 2966 9.685276 ATGACATGATATACCTTTTTGTCTTGA 57.315 29.630 0.00 0.00 34.55 3.02
2427 2967 9.685276 TGACATGATATACCTTTTTGTCTTGAT 57.315 29.630 0.00 0.00 34.55 2.57
2428 2968 9.941664 GACATGATATACCTTTTTGTCTTGATG 57.058 33.333 0.00 0.00 31.61 3.07
2429 2969 9.685276 ACATGATATACCTTTTTGTCTTGATGA 57.315 29.630 0.00 0.00 0.00 2.92
2437 2977 7.954835 ACCTTTTTGTCTTGATGATTGATTCA 58.045 30.769 0.00 0.00 39.12 2.57
2439 2979 8.869897 CCTTTTTGTCTTGATGATTGATTCATG 58.130 33.333 0.00 0.00 45.29 3.07
2440 2980 9.419297 CTTTTTGTCTTGATGATTGATTCATGT 57.581 29.630 0.00 0.00 45.29 3.21
2441 2981 8.975410 TTTTGTCTTGATGATTGATTCATGTC 57.025 30.769 0.00 0.00 45.29 3.06
2442 2982 7.690952 TTGTCTTGATGATTGATTCATGTCA 57.309 32.000 0.00 5.16 45.29 3.58
2443 2983 7.316544 TGTCTTGATGATTGATTCATGTCAG 57.683 36.000 0.00 0.00 45.29 3.51
2444 2984 6.882678 TGTCTTGATGATTGATTCATGTCAGT 59.117 34.615 0.00 0.00 45.29 3.41
2445 2985 7.392393 TGTCTTGATGATTGATTCATGTCAGTT 59.608 33.333 0.00 0.00 45.29 3.16
2446 2986 8.886719 GTCTTGATGATTGATTCATGTCAGTTA 58.113 33.333 0.00 0.00 45.29 2.24
2447 2987 9.623000 TCTTGATGATTGATTCATGTCAGTTAT 57.377 29.630 0.00 0.00 45.29 1.89
2448 2988 9.665264 CTTGATGATTGATTCATGTCAGTTATG 57.335 33.333 0.00 0.00 45.29 1.90
2449 2989 7.645402 TGATGATTGATTCATGTCAGTTATGC 58.355 34.615 0.00 0.00 45.29 3.14
2450 2990 7.283580 TGATGATTGATTCATGTCAGTTATGCA 59.716 33.333 0.00 0.00 45.29 3.96
2451 2991 6.788243 TGATTGATTCATGTCAGTTATGCAC 58.212 36.000 0.00 0.00 0.00 4.57
2452 2992 5.565592 TTGATTCATGTCAGTTATGCACC 57.434 39.130 0.00 0.00 0.00 5.01
2453 2993 3.622612 TGATTCATGTCAGTTATGCACCG 59.377 43.478 0.00 0.00 0.00 4.94
2454 2994 2.022764 TCATGTCAGTTATGCACCGG 57.977 50.000 0.00 0.00 0.00 5.28
2455 2995 1.552792 TCATGTCAGTTATGCACCGGA 59.447 47.619 9.46 0.00 0.00 5.14
2456 2996 1.935873 CATGTCAGTTATGCACCGGAG 59.064 52.381 9.46 0.00 0.00 4.63
2457 2997 0.973632 TGTCAGTTATGCACCGGAGT 59.026 50.000 9.46 0.00 0.00 3.85
2459 2999 0.973632 TCAGTTATGCACCGGAGTGT 59.026 50.000 9.46 0.00 46.35 3.55
2460 3000 2.094390 GTCAGTTATGCACCGGAGTGTA 60.094 50.000 9.46 0.00 46.35 2.90
2461 3001 2.094390 TCAGTTATGCACCGGAGTGTAC 60.094 50.000 9.46 0.00 46.35 2.90
2462 3002 1.897133 AGTTATGCACCGGAGTGTACA 59.103 47.619 9.46 0.00 46.35 2.90
2463 3003 2.300723 AGTTATGCACCGGAGTGTACAA 59.699 45.455 9.46 0.00 46.35 2.41
2464 3004 2.373540 TATGCACCGGAGTGTACAAC 57.626 50.000 9.46 0.00 46.35 3.32
2465 3005 0.685097 ATGCACCGGAGTGTACAACT 59.315 50.000 9.46 0.00 46.35 3.16
2466 3006 0.249699 TGCACCGGAGTGTACAACTG 60.250 55.000 9.46 0.00 46.35 3.16
2467 3007 1.566018 GCACCGGAGTGTACAACTGC 61.566 60.000 9.46 0.00 46.35 4.40
2474 3014 4.829064 GGAGTGTACAACTGCAAAATCA 57.171 40.909 0.00 0.00 46.06 2.57
2475 3015 4.537015 GGAGTGTACAACTGCAAAATCAC 58.463 43.478 0.00 0.00 46.06 3.06
2476 3016 4.036262 GGAGTGTACAACTGCAAAATCACA 59.964 41.667 0.00 0.00 46.06 3.58
2477 3017 5.278463 GGAGTGTACAACTGCAAAATCACAT 60.278 40.000 0.00 0.00 46.06 3.21
2478 3018 5.762045 AGTGTACAACTGCAAAATCACATC 58.238 37.500 0.00 0.00 37.88 3.06
2479 3019 4.917415 GTGTACAACTGCAAAATCACATCC 59.083 41.667 0.00 0.00 0.00 3.51
2480 3020 4.826733 TGTACAACTGCAAAATCACATCCT 59.173 37.500 0.00 0.00 0.00 3.24
2481 3021 4.247267 ACAACTGCAAAATCACATCCTG 57.753 40.909 0.00 0.00 0.00 3.86
2482 3022 3.638160 ACAACTGCAAAATCACATCCTGT 59.362 39.130 0.00 0.00 0.00 4.00
2483 3023 4.232221 CAACTGCAAAATCACATCCTGTC 58.768 43.478 0.00 0.00 0.00 3.51
2484 3024 2.821969 ACTGCAAAATCACATCCTGTCC 59.178 45.455 0.00 0.00 0.00 4.02
2485 3025 3.087031 CTGCAAAATCACATCCTGTCCT 58.913 45.455 0.00 0.00 0.00 3.85
2486 3026 3.084039 TGCAAAATCACATCCTGTCCTC 58.916 45.455 0.00 0.00 0.00 3.71
2487 3027 3.245016 TGCAAAATCACATCCTGTCCTCT 60.245 43.478 0.00 0.00 0.00 3.69
2488 3028 3.128242 GCAAAATCACATCCTGTCCTCTG 59.872 47.826 0.00 0.00 0.00 3.35
2489 3029 2.706339 AATCACATCCTGTCCTCTGC 57.294 50.000 0.00 0.00 0.00 4.26
2490 3030 1.576577 ATCACATCCTGTCCTCTGCA 58.423 50.000 0.00 0.00 0.00 4.41
2491 3031 0.900421 TCACATCCTGTCCTCTGCAG 59.100 55.000 7.63 7.63 0.00 4.41
2492 3032 0.743701 CACATCCTGTCCTCTGCAGC 60.744 60.000 9.47 0.00 32.93 5.25
2493 3033 1.196766 ACATCCTGTCCTCTGCAGCA 61.197 55.000 9.47 0.00 32.93 4.41
2494 3034 0.462225 CATCCTGTCCTCTGCAGCAG 60.462 60.000 17.10 17.10 32.93 4.24
2495 3035 0.616964 ATCCTGTCCTCTGCAGCAGA 60.617 55.000 23.98 23.98 38.25 4.26
2496 3036 0.833409 TCCTGTCCTCTGCAGCAGAA 60.833 55.000 25.35 9.66 40.18 3.02
2497 3037 0.252479 CCTGTCCTCTGCAGCAGAAT 59.748 55.000 25.35 0.00 40.18 2.40
2498 3038 1.483827 CCTGTCCTCTGCAGCAGAATA 59.516 52.381 25.35 13.70 40.18 1.75
2499 3039 2.093288 CCTGTCCTCTGCAGCAGAATAA 60.093 50.000 25.35 11.23 40.18 1.40
2500 3040 3.603532 CTGTCCTCTGCAGCAGAATAAA 58.396 45.455 25.35 10.88 40.18 1.40
2501 3041 3.603532 TGTCCTCTGCAGCAGAATAAAG 58.396 45.455 25.35 13.38 40.18 1.85
2502 3042 3.261643 TGTCCTCTGCAGCAGAATAAAGA 59.738 43.478 25.35 13.97 40.18 2.52
2503 3043 4.256920 GTCCTCTGCAGCAGAATAAAGAA 58.743 43.478 25.35 1.22 40.18 2.52
2504 3044 4.880696 GTCCTCTGCAGCAGAATAAAGAAT 59.119 41.667 25.35 0.00 40.18 2.40
2505 3045 6.051717 GTCCTCTGCAGCAGAATAAAGAATA 58.948 40.000 25.35 0.00 40.18 1.75
2506 3046 6.540189 GTCCTCTGCAGCAGAATAAAGAATAA 59.460 38.462 25.35 0.00 40.18 1.40
2507 3047 7.066284 GTCCTCTGCAGCAGAATAAAGAATAAA 59.934 37.037 25.35 0.00 40.18 1.40
2508 3048 7.776969 TCCTCTGCAGCAGAATAAAGAATAAAT 59.223 33.333 25.35 0.00 40.18 1.40
2509 3049 8.411683 CCTCTGCAGCAGAATAAAGAATAAATT 58.588 33.333 25.35 0.00 40.18 1.82
2526 3066 9.342308 AGAATAAATTATCTTTTCGGCAGATCA 57.658 29.630 0.00 0.00 32.94 2.92
2529 3069 7.814264 AAATTATCTTTTCGGCAGATCATCT 57.186 32.000 0.00 0.00 32.94 2.90
2530 3070 7.432350 AATTATCTTTTCGGCAGATCATCTC 57.568 36.000 0.00 0.00 32.94 2.75
2531 3071 4.686191 ATCTTTTCGGCAGATCATCTCT 57.314 40.909 0.00 0.00 33.14 3.10
2532 3072 4.052159 TCTTTTCGGCAGATCATCTCTC 57.948 45.455 0.00 0.00 29.16 3.20
2533 3073 3.703556 TCTTTTCGGCAGATCATCTCTCT 59.296 43.478 0.00 0.00 29.16 3.10
2534 3074 3.724508 TTTCGGCAGATCATCTCTCTC 57.275 47.619 0.00 0.00 29.16 3.20
2535 3075 1.614996 TCGGCAGATCATCTCTCTCC 58.385 55.000 0.00 0.00 29.16 3.71
2536 3076 0.602562 CGGCAGATCATCTCTCTCCC 59.397 60.000 0.00 0.00 29.16 4.30
2537 3077 1.822854 CGGCAGATCATCTCTCTCCCT 60.823 57.143 0.00 0.00 29.16 4.20
2538 3078 1.895131 GGCAGATCATCTCTCTCCCTC 59.105 57.143 0.00 0.00 29.16 4.30
2539 3079 2.491455 GGCAGATCATCTCTCTCCCTCT 60.491 54.545 0.00 0.00 29.16 3.69
2540 3080 2.821969 GCAGATCATCTCTCTCCCTCTC 59.178 54.545 0.00 0.00 29.16 3.20
2541 3081 3.499202 GCAGATCATCTCTCTCCCTCTCT 60.499 52.174 0.00 0.00 29.16 3.10
2542 3082 4.330250 CAGATCATCTCTCTCCCTCTCTC 58.670 52.174 0.00 0.00 29.16 3.20
2543 3083 4.042560 CAGATCATCTCTCTCCCTCTCTCT 59.957 50.000 0.00 0.00 29.16 3.10
2544 3084 4.288105 AGATCATCTCTCTCCCTCTCTCTC 59.712 50.000 0.00 0.00 0.00 3.20
2545 3085 2.711009 TCATCTCTCTCCCTCTCTCTCC 59.289 54.545 0.00 0.00 0.00 3.71
2546 3086 1.518367 TCTCTCTCCCTCTCTCTCCC 58.482 60.000 0.00 0.00 0.00 4.30
2547 3087 1.010793 TCTCTCTCCCTCTCTCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
2548 3088 1.421646 CTCTCTCCCTCTCTCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
2549 3089 1.010793 TCTCTCCCTCTCTCTCCCTCT 59.989 57.143 0.00 0.00 0.00 3.69
2550 3090 1.421646 CTCTCCCTCTCTCTCCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
2551 3091 1.010793 TCTCCCTCTCTCTCCCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
2586 3233 9.132521 CTGTGTAAATGGAAAAGCTATGAAAAG 57.867 33.333 0.00 0.00 0.00 2.27
2726 3424 4.082523 TCTCCTTTCGGGCTGCGG 62.083 66.667 0.00 0.00 34.39 5.69
2757 3455 1.341852 GTAGGAGCCCTCGGAGATTTC 59.658 57.143 6.58 0.67 34.61 2.17
2758 3456 0.031616 AGGAGCCCTCGGAGATTTCT 60.032 55.000 6.58 0.00 33.89 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.637229 GGTAGCAGATGGACTAGTTAGCA 59.363 47.826 0.00 0.00 0.00 3.49
231 232 2.076100 TGCCAAAGCTTACGACAGATG 58.924 47.619 0.00 0.00 40.80 2.90
232 233 2.472695 TGCCAAAGCTTACGACAGAT 57.527 45.000 0.00 0.00 40.80 2.90
259 260 6.324042 TCGAATACTCACTATGCGTACAAAA 58.676 36.000 0.00 0.00 35.56 2.44
270 271 6.040955 AGCAAGAATGGATCGAATACTCACTA 59.959 38.462 0.00 0.00 0.00 2.74
440 475 2.039084 GTGATCCACAAGGTCTGAAGGT 59.961 50.000 0.00 0.00 34.08 3.50
516 551 8.225603 AGCTGTGAAAGAATTCTTTAAGTCAA 57.774 30.769 28.83 14.22 45.37 3.18
595 630 2.029470 GCTCTCGACCCATCCTATTGAG 60.029 54.545 0.00 0.00 0.00 3.02
619 654 4.526970 CCAATAGCCTGCCTTCTTTAGAA 58.473 43.478 0.00 0.00 0.00 2.10
755 790 5.816449 TGCATGACCACAGTAATGTAATG 57.184 39.130 0.00 0.00 37.20 1.90
765 800 5.745294 GTGCTAATAAAATGCATGACCACAG 59.255 40.000 0.00 0.00 39.00 3.66
843 878 0.394938 TAGAGCCCGTTGACTTGCAA 59.605 50.000 0.00 0.00 0.00 4.08
1034 1069 0.175302 CTCTTCGCAGCTCAGGACAT 59.825 55.000 0.00 0.00 0.00 3.06
1055 1090 4.343814 TGGTCGGTATCATTATCTCAGCAA 59.656 41.667 0.00 0.00 0.00 3.91
1056 1091 3.895041 TGGTCGGTATCATTATCTCAGCA 59.105 43.478 0.00 0.00 0.00 4.41
1269 1304 2.288025 GCGGTAGTCAAGGTCCCCA 61.288 63.158 0.00 0.00 0.00 4.96
1308 1343 3.384789 TCTGACCATGAAATACCTCCTCG 59.615 47.826 0.00 0.00 0.00 4.63
1368 1403 2.990479 GCGTTCACTCCCTGGGAT 59.010 61.111 17.51 3.78 0.00 3.85
1401 1436 6.041409 CCATCAGGTCAATATGACTACAGAGT 59.959 42.308 10.06 0.00 46.19 3.24
1407 1442 4.284490 GGCTCCATCAGGTCAATATGACTA 59.716 45.833 10.06 0.00 46.19 2.59
1821 1871 3.064207 GACGGAATCTTACTGTGTGCAA 58.936 45.455 0.00 0.00 0.00 4.08
2095 2145 8.738645 ATTTCTACTATACAGCCCAAAAAGAG 57.261 34.615 0.00 0.00 0.00 2.85
2237 2776 5.874261 CACAACAAAACCACCAGAAAGAAAT 59.126 36.000 0.00 0.00 0.00 2.17
2314 2853 6.493189 TGCATACATGTCAAGAGGGTATAA 57.507 37.500 0.00 0.00 0.00 0.98
2317 2856 5.372343 AATGCATACATGTCAAGAGGGTA 57.628 39.130 0.00 0.00 36.36 3.69
2343 2882 3.519107 TCAGGTGATATTCCAGTGCAGAA 59.481 43.478 0.00 0.00 0.00 3.02
2403 2943 9.685276 TCATCAAGACAAAAAGGTATATCATGT 57.315 29.630 0.00 0.00 0.00 3.21
2419 2959 6.882678 ACTGACATGAATCAATCATCAAGACA 59.117 34.615 0.00 0.00 45.91 3.41
2420 2960 7.317842 ACTGACATGAATCAATCATCAAGAC 57.682 36.000 0.00 0.00 45.91 3.01
2421 2961 7.933215 AACTGACATGAATCAATCATCAAGA 57.067 32.000 0.00 0.00 45.91 3.02
2422 2962 9.665264 CATAACTGACATGAATCAATCATCAAG 57.335 33.333 0.00 0.00 45.91 3.02
2424 2964 7.283580 TGCATAACTGACATGAATCAATCATCA 59.716 33.333 0.00 0.00 45.91 3.07
2425 2965 7.590322 GTGCATAACTGACATGAATCAATCATC 59.410 37.037 0.00 0.00 45.91 2.92
2427 2967 6.183360 GGTGCATAACTGACATGAATCAATCA 60.183 38.462 0.00 0.00 43.67 2.57
2428 2968 6.204359 GGTGCATAACTGACATGAATCAATC 58.796 40.000 0.00 0.00 0.00 2.67
2429 2969 5.220912 CGGTGCATAACTGACATGAATCAAT 60.221 40.000 0.00 0.00 37.33 2.57
2430 2970 4.094739 CGGTGCATAACTGACATGAATCAA 59.905 41.667 0.00 0.00 37.33 2.57
2431 2971 3.622612 CGGTGCATAACTGACATGAATCA 59.377 43.478 0.00 0.00 37.33 2.57
2432 2972 3.002656 CCGGTGCATAACTGACATGAATC 59.997 47.826 0.00 0.00 37.33 2.52
2433 2973 2.945008 CCGGTGCATAACTGACATGAAT 59.055 45.455 0.00 0.00 37.33 2.57
2434 2974 2.027653 TCCGGTGCATAACTGACATGAA 60.028 45.455 0.00 0.00 37.33 2.57
2435 2975 1.552792 TCCGGTGCATAACTGACATGA 59.447 47.619 0.00 0.00 37.33 3.07
2436 2976 1.935873 CTCCGGTGCATAACTGACATG 59.064 52.381 0.00 0.00 37.33 3.21
2437 2977 1.555075 ACTCCGGTGCATAACTGACAT 59.445 47.619 0.00 0.00 37.33 3.06
2438 2978 0.973632 ACTCCGGTGCATAACTGACA 59.026 50.000 0.00 0.00 37.33 3.58
2439 2979 1.337823 ACACTCCGGTGCATAACTGAC 60.338 52.381 0.00 0.00 46.57 3.51
2440 2980 0.973632 ACACTCCGGTGCATAACTGA 59.026 50.000 0.00 0.00 46.57 3.41
2441 2981 2.268298 GTACACTCCGGTGCATAACTG 58.732 52.381 0.00 0.00 46.57 3.16
2442 2982 1.897133 TGTACACTCCGGTGCATAACT 59.103 47.619 0.00 0.00 46.57 2.24
2443 2983 2.373540 TGTACACTCCGGTGCATAAC 57.626 50.000 0.00 0.00 46.57 1.89
2444 2984 2.300723 AGTTGTACACTCCGGTGCATAA 59.699 45.455 0.00 0.00 46.57 1.90
2445 2985 1.897133 AGTTGTACACTCCGGTGCATA 59.103 47.619 0.00 0.00 46.57 3.14
2446 2986 0.685097 AGTTGTACACTCCGGTGCAT 59.315 50.000 0.00 0.00 46.57 3.96
2447 2987 0.249699 CAGTTGTACACTCCGGTGCA 60.250 55.000 0.00 0.00 46.57 4.57
2448 2988 1.566018 GCAGTTGTACACTCCGGTGC 61.566 60.000 0.00 0.00 46.57 5.01
2450 2990 0.466543 TTGCAGTTGTACACTCCGGT 59.533 50.000 0.00 0.00 30.92 5.28
2451 2991 1.588674 TTTGCAGTTGTACACTCCGG 58.411 50.000 0.00 0.00 30.92 5.14
2452 2992 3.249799 TGATTTTGCAGTTGTACACTCCG 59.750 43.478 0.00 0.00 30.92 4.63
2453 2993 4.036262 TGTGATTTTGCAGTTGTACACTCC 59.964 41.667 0.00 0.00 30.92 3.85
2454 2994 5.168526 TGTGATTTTGCAGTTGTACACTC 57.831 39.130 0.00 0.00 30.92 3.51
2455 2995 5.278463 GGATGTGATTTTGCAGTTGTACACT 60.278 40.000 0.00 0.00 35.35 3.55
2456 2996 4.917415 GGATGTGATTTTGCAGTTGTACAC 59.083 41.667 0.00 0.00 0.00 2.90
2457 2997 4.826733 AGGATGTGATTTTGCAGTTGTACA 59.173 37.500 0.00 0.00 0.00 2.90
2458 2998 5.156355 CAGGATGTGATTTTGCAGTTGTAC 58.844 41.667 0.00 0.00 0.00 2.90
2459 2999 5.375417 CAGGATGTGATTTTGCAGTTGTA 57.625 39.130 0.00 0.00 0.00 2.41
2460 3000 4.247267 CAGGATGTGATTTTGCAGTTGT 57.753 40.909 0.00 0.00 0.00 3.32
2474 3014 3.118940 CTGCTGCAGAGGACAGGATGT 62.119 57.143 24.88 0.00 43.72 3.06
2475 3015 0.462225 CTGCTGCAGAGGACAGGATG 60.462 60.000 24.88 0.00 34.79 3.51
2476 3016 0.616964 TCTGCTGCAGAGGACAGGAT 60.617 55.000 27.35 0.00 35.39 3.24
2477 3017 0.833409 TTCTGCTGCAGAGGACAGGA 60.833 55.000 28.91 12.58 41.75 3.86
2478 3018 0.252479 ATTCTGCTGCAGAGGACAGG 59.748 55.000 28.91 3.73 41.75 4.00
2479 3019 2.975732 TATTCTGCTGCAGAGGACAG 57.024 50.000 28.91 15.11 41.75 3.51
2480 3020 3.261643 TCTTTATTCTGCTGCAGAGGACA 59.738 43.478 28.91 17.07 41.75 4.02
2481 3021 3.866651 TCTTTATTCTGCTGCAGAGGAC 58.133 45.455 28.91 0.00 41.75 3.85
2482 3022 4.558226 TTCTTTATTCTGCTGCAGAGGA 57.442 40.909 28.91 18.12 41.75 3.71
2483 3023 6.932356 TTATTCTTTATTCTGCTGCAGAGG 57.068 37.500 28.91 18.11 41.75 3.69
2500 3040 9.342308 TGATCTGCCGAAAAGATAATTTATTCT 57.658 29.630 0.00 0.00 34.50 2.40
2503 3043 9.512588 AGATGATCTGCCGAAAAGATAATTTAT 57.487 29.630 0.00 0.00 34.50 1.40
2504 3044 8.908786 AGATGATCTGCCGAAAAGATAATTTA 57.091 30.769 0.00 0.00 34.50 1.40
2505 3045 7.718753 AGAGATGATCTGCCGAAAAGATAATTT 59.281 33.333 0.00 0.00 36.69 1.82
2506 3046 7.222872 AGAGATGATCTGCCGAAAAGATAATT 58.777 34.615 0.00 0.00 36.69 1.40
2507 3047 6.767456 AGAGATGATCTGCCGAAAAGATAAT 58.233 36.000 0.00 0.00 36.69 1.28
2508 3048 6.041409 AGAGAGATGATCTGCCGAAAAGATAA 59.959 38.462 0.00 0.00 38.84 1.75
2509 3049 5.538053 AGAGAGATGATCTGCCGAAAAGATA 59.462 40.000 0.00 0.00 38.84 1.98
2510 3050 4.344679 AGAGAGATGATCTGCCGAAAAGAT 59.655 41.667 0.00 0.00 38.84 2.40
2511 3051 3.703556 AGAGAGATGATCTGCCGAAAAGA 59.296 43.478 0.00 0.00 38.84 2.52
2512 3052 4.050553 GAGAGAGATGATCTGCCGAAAAG 58.949 47.826 0.00 0.00 38.84 2.27
2513 3053 3.181471 GGAGAGAGATGATCTGCCGAAAA 60.181 47.826 0.00 0.00 38.84 2.29
2514 3054 2.363680 GGAGAGAGATGATCTGCCGAAA 59.636 50.000 0.00 0.00 38.84 3.46
2515 3055 1.959985 GGAGAGAGATGATCTGCCGAA 59.040 52.381 0.00 0.00 38.84 4.30
2516 3056 1.614996 GGAGAGAGATGATCTGCCGA 58.385 55.000 0.00 0.00 38.84 5.54
2517 3057 0.602562 GGGAGAGAGATGATCTGCCG 59.397 60.000 0.00 0.00 44.09 5.69
2519 3059 2.821969 GAGAGGGAGAGAGATGATCTGC 59.178 54.545 0.00 0.00 38.84 4.26
2520 3060 4.042560 AGAGAGAGGGAGAGAGATGATCTG 59.957 50.000 0.00 0.00 38.84 2.90
2521 3061 4.246143 AGAGAGAGGGAGAGAGATGATCT 58.754 47.826 0.00 0.00 42.61 2.75
2522 3062 4.566488 GGAGAGAGAGGGAGAGAGATGATC 60.566 54.167 0.00 0.00 0.00 2.92
2523 3063 3.331889 GGAGAGAGAGGGAGAGAGATGAT 59.668 52.174 0.00 0.00 0.00 2.45
2524 3064 2.711009 GGAGAGAGAGGGAGAGAGATGA 59.289 54.545 0.00 0.00 0.00 2.92
2525 3065 2.224867 GGGAGAGAGAGGGAGAGAGATG 60.225 59.091 0.00 0.00 0.00 2.90
2526 3066 2.065799 GGGAGAGAGAGGGAGAGAGAT 58.934 57.143 0.00 0.00 0.00 2.75
2527 3067 1.010793 AGGGAGAGAGAGGGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
2528 3068 1.421646 GAGGGAGAGAGAGGGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
2529 3069 1.010793 AGAGGGAGAGAGAGGGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
2530 3070 1.421646 GAGAGGGAGAGAGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
2531 3071 1.010793 AGAGAGGGAGAGAGAGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
2532 3072 1.522900 AGAGAGGGAGAGAGAGGGAG 58.477 60.000 0.00 0.00 0.00 4.30
2533 3073 1.994399 AAGAGAGGGAGAGAGAGGGA 58.006 55.000 0.00 0.00 0.00 4.20
2534 3074 2.489073 GCTAAGAGAGGGAGAGAGAGGG 60.489 59.091 0.00 0.00 0.00 4.30
2535 3075 2.443255 AGCTAAGAGAGGGAGAGAGAGG 59.557 54.545 0.00 0.00 0.00 3.69
2536 3076 3.864789 AGCTAAGAGAGGGAGAGAGAG 57.135 52.381 0.00 0.00 0.00 3.20
2537 3077 4.277476 CAAAGCTAAGAGAGGGAGAGAGA 58.723 47.826 0.00 0.00 0.00 3.10
2538 3078 3.181476 GCAAAGCTAAGAGAGGGAGAGAG 60.181 52.174 0.00 0.00 0.00 3.20
2539 3079 2.763448 GCAAAGCTAAGAGAGGGAGAGA 59.237 50.000 0.00 0.00 0.00 3.10
2540 3080 2.765699 AGCAAAGCTAAGAGAGGGAGAG 59.234 50.000 0.00 0.00 36.99 3.20
2541 3081 2.499289 CAGCAAAGCTAAGAGAGGGAGA 59.501 50.000 0.00 0.00 36.40 3.71
2542 3082 2.235898 ACAGCAAAGCTAAGAGAGGGAG 59.764 50.000 0.00 0.00 36.40 4.30
2543 3083 2.027745 CACAGCAAAGCTAAGAGAGGGA 60.028 50.000 0.00 0.00 36.40 4.20
2544 3084 2.289945 ACACAGCAAAGCTAAGAGAGGG 60.290 50.000 0.00 0.00 36.40 4.30
2545 3085 3.051081 ACACAGCAAAGCTAAGAGAGG 57.949 47.619 0.00 0.00 36.40 3.69
2546 3086 6.402983 CCATTTACACAGCAAAGCTAAGAGAG 60.403 42.308 0.00 0.00 36.40 3.20
2547 3087 5.412594 CCATTTACACAGCAAAGCTAAGAGA 59.587 40.000 0.00 0.00 36.40 3.10
2548 3088 5.412594 TCCATTTACACAGCAAAGCTAAGAG 59.587 40.000 0.00 0.00 36.40 2.85
2549 3089 5.312895 TCCATTTACACAGCAAAGCTAAGA 58.687 37.500 0.00 0.00 36.40 2.10
2550 3090 5.627499 TCCATTTACACAGCAAAGCTAAG 57.373 39.130 0.00 0.00 36.40 2.18
2551 3091 6.398234 TTTCCATTTACACAGCAAAGCTAA 57.602 33.333 0.00 0.00 36.40 3.09
2586 3233 8.787852 AGAATCAATTCACTAACTCAAGGAAAC 58.212 33.333 5.59 0.00 39.23 2.78
2655 3302 4.644234 TCTTTCAGCTTCATTTGGTGTCAA 59.356 37.500 0.00 0.00 34.86 3.18
2726 3424 1.511768 GCTCCTACCCACGTCTGAC 59.488 63.158 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.