Multiple sequence alignment - TraesCS2D01G213400

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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 TraesCS2D01G213400 chr2D 100.000 2965 0 0 1 2965 174245688 174248652 0.000000e+00 5476.0
1 TraesCS2D01G213400 chr2D 82.114 123 18 1 2795 2913 354956657 354956779 5.230000e-18 102.0
2 TraesCS2D01G213400 chr2A 89.079 2161 146 35 1 2134 173797394 173799491 0.000000e+00 2601.0
3 TraesCS2D01G213400 chr2A 87.650 834 78 12 2132 2963 173839795 173840605 0.000000e+00 946.0
4 TraesCS2D01G213400 chr2B 89.021 1257 107 15 12 1246 222122044 222123291 0.000000e+00 1528.0
5 TraesCS2D01G213400 chr2B 93.804 920 34 8 1273 2184 222123289 222124193 0.000000e+00 1362.0
6 TraesCS2D01G213400 chr2B 88.386 508 55 3 2448 2952 222124198 222124704 2.530000e-170 608.0
7 TraesCS2D01G213400 chr2B 80.851 611 108 8 22 627 162860196 162860802 3.460000e-129 472.0
8 TraesCS2D01G213400 chr7D 82.689 647 98 8 15 650 549700973 549700330 2.000000e-156 562.0
9 TraesCS2D01G213400 chr7D 81.656 616 102 11 25 636 632121445 632120837 4.410000e-138 501.0
10 TraesCS2D01G213400 chr7D 76.857 350 57 13 2557 2890 14781412 14781753 3.040000e-40 176.0
11 TraesCS2D01G213400 chr3A 82.877 584 90 7 44 620 693125034 693124454 1.580000e-142 516.0
12 TraesCS2D01G213400 chr4D 81.090 624 102 9 44 654 417415577 417414957 4.440000e-133 484.0
13 TraesCS2D01G213400 chrUn 80.408 638 109 8 17 643 89533021 89532389 3.460000e-129 472.0
14 TraesCS2D01G213400 chrUn 75.287 348 76 10 2548 2891 82617438 82617779 1.100000e-34 158.0
15 TraesCS2D01G213400 chr5D 80.676 621 107 7 44 653 536240142 536239524 1.240000e-128 470.0
16 TraesCS2D01G213400 chr6D 81.100 582 107 3 45 624 354416325 354416905 2.080000e-126 462.0
17 TraesCS2D01G213400 chr6D 78.652 445 69 12 2480 2913 249453965 249454394 3.770000e-69 272.0
18 TraesCS2D01G213400 chr6B 78.995 438 67 17 2480 2907 337236556 337236978 2.910000e-70 276.0
19 TraesCS2D01G213400 chr6A 80.263 380 60 7 2548 2916 349513111 349512736 3.770000e-69 272.0
20 TraesCS2D01G213400 chr1A 75.893 336 71 8 2554 2883 569140389 569140720 2.360000e-36 163.0
21 TraesCS2D01G213400 chr1D 74.022 358 84 6 2543 2894 474511335 474511689 1.430000e-28 137.0
22 TraesCS2D01G213400 chr5B 78.431 153 27 6 2740 2891 487246725 487246578 8.750000e-16 95.3
23 TraesCS2D01G213400 chr7A 89.091 55 5 1 2553 2607 720841829 720841776 1.910000e-07 67.6


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 TraesCS2D01G213400 chr2D 174245688 174248652 2964 False 5476 5476 100.000000 1 2965 1 chr2D.!!$F1 2964
1 TraesCS2D01G213400 chr2A 173797394 173799491 2097 False 2601 2601 89.079000 1 2134 1 chr2A.!!$F1 2133
2 TraesCS2D01G213400 chr2A 173839795 173840605 810 False 946 946 87.650000 2132 2963 1 chr2A.!!$F2 831
3 TraesCS2D01G213400 chr2B 222122044 222124704 2660 False 1166 1528 90.403667 12 2952 3 chr2B.!!$F2 2940
4 TraesCS2D01G213400 chr2B 162860196 162860802 606 False 472 472 80.851000 22 627 1 chr2B.!!$F1 605
5 TraesCS2D01G213400 chr7D 549700330 549700973 643 True 562 562 82.689000 15 650 1 chr7D.!!$R1 635
6 TraesCS2D01G213400 chr7D 632120837 632121445 608 True 501 501 81.656000 25 636 1 chr7D.!!$R2 611
7 TraesCS2D01G213400 chr3A 693124454 693125034 580 True 516 516 82.877000 44 620 1 chr3A.!!$R1 576
8 TraesCS2D01G213400 chr4D 417414957 417415577 620 True 484 484 81.090000 44 654 1 chr4D.!!$R1 610
9 TraesCS2D01G213400 chrUn 89532389 89533021 632 True 472 472 80.408000 17 643 1 chrUn.!!$R1 626
10 TraesCS2D01G213400 chr5D 536239524 536240142 618 True 470 470 80.676000 44 653 1 chr5D.!!$R1 609
11 TraesCS2D01G213400 chr6D 354416325 354416905 580 False 462 462 81.100000 45 624 1 chr6D.!!$F2 579

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
376 385 0.671781 ACGCTCATGTGTCTTCAGGC 60.672 55.0 0.0 0.0 29.93 4.85 F
1341 1388 0.034186 ACCACATGGCATTCATCCGT 60.034 50.0 0.0 0.0 39.32 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1874 0.313043 AACCCTACACACACGACGAG 59.687 55.0 0.0 0.0 0.0 4.18 R
2396 2465 0.243907 CCACCTCTCGTTGATGTCGT 59.756 55.0 0.0 0.0 0.0 4.34 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
127 130 4.137543 GGCCATAAAGACTTGGTGGATAG 58.862 47.826 18.56 0.00 35.34 2.08
212 216 3.388345 CCTATTTAGGAAGGCGAGACC 57.612 52.381 0.00 0.00 46.63 3.85
254 258 2.185663 ATAAGGTTCTCCCCGCCTAA 57.814 50.000 0.00 0.00 31.43 2.69
264 269 2.666812 CCGCCTAACCCCGTTCTT 59.333 61.111 0.00 0.00 0.00 2.52
317 325 1.300233 GATGTGTCTCGGCGGATCC 60.300 63.158 7.21 0.00 0.00 3.36
327 335 1.160329 CGGCGGATCCATCTTTGGTC 61.160 60.000 13.41 0.00 44.06 4.02
336 344 1.446907 CATCTTTGGTCGAGCTGCTT 58.553 50.000 16.64 0.00 0.00 3.91
342 351 0.898326 TGGTCGAGCTGCTTGGTCTA 60.898 55.000 16.64 6.10 40.75 2.59
352 361 2.993899 CTGCTTGGTCTATTCGTCGTTT 59.006 45.455 0.00 0.00 0.00 3.60
360 369 3.236980 GTCTATTCGTCGTTTGTCTACGC 59.763 47.826 0.00 0.00 41.16 4.42
376 385 0.671781 ACGCTCATGTGTCTTCAGGC 60.672 55.000 0.00 0.00 29.93 4.85
422 434 5.120830 ACTCTTCATCTGCAACGATTGTTAC 59.879 40.000 0.00 0.00 36.28 2.50
443 455 2.244117 CTGGTGCGCTGGTCCTATGT 62.244 60.000 9.73 0.00 0.00 2.29
478 490 3.626670 ACGACTTCCCGACTGTCTATTAG 59.373 47.826 6.21 1.46 0.00 1.73
521 533 1.123928 GAGGAAGGGGTGATGACGAT 58.876 55.000 0.00 0.00 0.00 3.73
524 538 0.815615 GAAGGGGTGATGACGATGGC 60.816 60.000 0.00 0.00 0.00 4.40
525 539 1.561769 AAGGGGTGATGACGATGGCA 61.562 55.000 0.00 0.00 0.00 4.92
741 769 7.867305 TCCAACACTATAACTTTTGTGACAA 57.133 32.000 0.00 0.00 34.81 3.18
929 975 0.742505 ACGTGTCGTCTCCTTGAACA 59.257 50.000 0.00 0.00 33.69 3.18
1012 1059 4.107051 GCGCGATGCACCAGCTTT 62.107 61.111 12.10 0.00 45.45 3.51
1301 1348 3.013921 CCAGGTGTGGCAAAATATACGT 58.986 45.455 0.00 0.00 36.89 3.57
1333 1380 0.530650 GTCGATCGACCACATGGCAT 60.531 55.000 33.06 0.00 39.08 4.40
1334 1381 0.177836 TCGATCGACCACATGGCATT 59.822 50.000 15.15 0.00 39.32 3.56
1335 1382 0.583438 CGATCGACCACATGGCATTC 59.417 55.000 10.26 0.00 39.32 2.67
1336 1383 1.667236 GATCGACCACATGGCATTCA 58.333 50.000 0.00 0.00 39.32 2.57
1337 1384 2.224606 GATCGACCACATGGCATTCAT 58.775 47.619 0.00 0.00 39.32 2.57
1338 1385 1.667236 TCGACCACATGGCATTCATC 58.333 50.000 0.00 0.00 39.32 2.92
1339 1386 0.664761 CGACCACATGGCATTCATCC 59.335 55.000 0.00 0.00 39.32 3.51
1340 1387 0.664761 GACCACATGGCATTCATCCG 59.335 55.000 0.00 0.00 39.32 4.18
1341 1388 0.034186 ACCACATGGCATTCATCCGT 60.034 50.000 0.00 0.00 39.32 4.69
1342 1389 1.105457 CCACATGGCATTCATCCGTT 58.895 50.000 0.00 0.00 32.92 4.44
1343 1390 1.477700 CCACATGGCATTCATCCGTTT 59.522 47.619 0.00 0.00 32.92 3.60
1344 1391 2.480073 CCACATGGCATTCATCCGTTTC 60.480 50.000 0.00 0.00 32.92 2.78
1345 1392 1.750778 ACATGGCATTCATCCGTTTCC 59.249 47.619 0.00 0.00 32.92 3.13
1579 1644 2.334023 AGGATCTTGAGAGGTATGGCC 58.666 52.381 0.00 0.00 37.58 5.36
1580 1645 1.001406 GGATCTTGAGAGGTATGGCCG 59.999 57.143 0.00 0.00 43.70 6.13
1581 1646 1.689273 GATCTTGAGAGGTATGGCCGT 59.311 52.381 1.35 1.35 43.70 5.68
1582 1647 2.447408 TCTTGAGAGGTATGGCCGTA 57.553 50.000 0.00 0.00 43.70 4.02
1583 1648 2.958818 TCTTGAGAGGTATGGCCGTAT 58.041 47.619 8.21 0.00 43.70 3.06
1584 1649 2.628178 TCTTGAGAGGTATGGCCGTATG 59.372 50.000 8.21 0.00 43.70 2.39
1585 1650 1.338107 TGAGAGGTATGGCCGTATGG 58.662 55.000 8.21 0.00 43.70 2.74
1626 1691 7.452880 ACTACAGCTTGCATTCAATTTCTTA 57.547 32.000 0.00 0.00 0.00 2.10
1808 1874 3.853671 CGTTTTGCAACTATGAATGAGCC 59.146 43.478 0.00 0.00 0.00 4.70
1811 1877 2.554142 TGCAACTATGAATGAGCCTCG 58.446 47.619 0.00 0.00 0.00 4.63
1973 2039 4.222886 GTGATGTCGAGTGATCCGATTAG 58.777 47.826 0.00 0.00 38.38 1.73
2029 2095 3.191371 GGAGGCTGAAACCATAACTGTTG 59.809 47.826 2.69 0.00 0.00 3.33
2141 2210 5.006261 CACGTAATCGAAGATTACATGCCAA 59.994 40.000 24.00 0.00 45.12 4.52
2167 2236 9.566432 AAAAATAGAAGGCCTACATAAGAGATG 57.434 33.333 5.16 0.00 0.00 2.90
2170 2239 4.040217 AGAAGGCCTACATAAGAGATGCTG 59.960 45.833 5.16 0.00 0.00 4.41
2179 2248 5.749462 ACATAAGAGATGCTGGCTAGTTTT 58.251 37.500 0.00 0.00 0.00 2.43
2189 2258 0.523519 GGCTAGTTTTGTGAGCTGGC 59.476 55.000 0.00 0.00 36.43 4.85
2198 2267 1.979855 TGTGAGCTGGCTTGCTTTAA 58.020 45.000 0.00 0.00 44.17 1.52
2229 2298 8.621532 TTAGCTTTGTGAATAACAGTTCTGAT 57.378 30.769 6.83 0.00 40.74 2.90
2243 2312 7.825331 ACAGTTCTGATATTATTCCGAGAGA 57.175 36.000 6.83 0.00 0.00 3.10
2244 2313 8.239038 ACAGTTCTGATATTATTCCGAGAGAA 57.761 34.615 6.83 0.00 39.32 2.87
2245 2314 8.696374 ACAGTTCTGATATTATTCCGAGAGAAA 58.304 33.333 6.83 0.00 38.21 2.52
2246 2315 9.534565 CAGTTCTGATATTATTCCGAGAGAAAA 57.465 33.333 0.00 0.00 38.21 2.29
2285 2354 9.597170 CAGTTCTGAGATTATCTTTCAGATTGA 57.403 33.333 12.79 0.00 44.74 2.57
2311 2380 2.040813 CCATCCTTGGATATGTGGAGGG 59.959 54.545 1.37 0.00 46.92 4.30
2312 2381 1.819753 TCCTTGGATATGTGGAGGGG 58.180 55.000 0.00 0.00 0.00 4.79
2315 2384 0.550914 TTGGATATGTGGAGGGGCAC 59.449 55.000 0.00 0.00 0.00 5.01
2344 2413 3.693085 AGATCTTGTCATTGCGCTGAATT 59.307 39.130 9.73 0.00 0.00 2.17
2372 2441 4.734398 TTCCAACAACCCATAATGATGC 57.266 40.909 0.00 0.00 0.00 3.91
2376 2445 5.105392 TCCAACAACCCATAATGATGCTTTC 60.105 40.000 0.00 0.00 0.00 2.62
2379 2448 5.969423 ACAACCCATAATGATGCTTTCAAG 58.031 37.500 0.00 0.00 38.03 3.02
2385 2454 7.092757 ACCCATAATGATGCTTTCAAGGAAAAT 60.093 33.333 0.00 0.00 38.03 1.82
2404 2473 2.920724 TTGTTTCCCTCACGACATCA 57.079 45.000 0.00 0.00 0.00 3.07
2410 2479 0.526211 CCCTCACGACATCAACGAGA 59.474 55.000 0.00 0.00 34.70 4.04
2432 2502 3.202818 AGGTGGCAATGATGACCTATTGA 59.797 43.478 0.00 0.00 33.27 2.57
2434 2504 4.586001 GGTGGCAATGATGACCTATTGAAT 59.414 41.667 0.00 0.00 36.61 2.57
2437 2507 7.039504 GGTGGCAATGATGACCTATTGAATTAT 60.040 37.037 0.00 0.00 36.61 1.28
2447 2517 6.102897 ACCTATTGAATTATGGTCTCTCCG 57.897 41.667 0.00 0.00 39.52 4.63
2448 2518 5.012148 ACCTATTGAATTATGGTCTCTCCGG 59.988 44.000 0.00 0.00 39.52 5.14
2449 2519 5.012148 CCTATTGAATTATGGTCTCTCCGGT 59.988 44.000 0.00 0.00 39.52 5.28
2450 2520 4.402056 TTGAATTATGGTCTCTCCGGTC 57.598 45.455 0.00 0.00 39.52 4.79
2451 2521 3.643237 TGAATTATGGTCTCTCCGGTCT 58.357 45.455 0.00 0.00 39.52 3.85
2452 2522 3.637229 TGAATTATGGTCTCTCCGGTCTC 59.363 47.826 0.00 0.00 39.52 3.36
2453 2523 3.603965 ATTATGGTCTCTCCGGTCTCT 57.396 47.619 0.00 0.00 39.52 3.10
2454 2524 2.642154 TATGGTCTCTCCGGTCTCTC 57.358 55.000 0.00 0.00 39.52 3.20
2455 2525 0.106419 ATGGTCTCTCCGGTCTCTCC 60.106 60.000 0.00 0.88 39.52 3.71
2459 2529 2.291365 GTCTCTCCGGTCTCTCCTTAC 58.709 57.143 0.00 0.00 0.00 2.34
2460 2530 1.914108 TCTCTCCGGTCTCTCCTTACA 59.086 52.381 0.00 0.00 0.00 2.41
2471 2541 3.504906 TCTCTCCTTACATCGACAACGTT 59.495 43.478 0.00 0.00 40.69 3.99
2472 2542 4.022589 TCTCTCCTTACATCGACAACGTTT 60.023 41.667 0.00 0.00 40.69 3.60
2475 2545 4.370049 TCCTTACATCGACAACGTTTGAA 58.630 39.130 0.00 0.00 40.69 2.69
2476 2546 4.809958 TCCTTACATCGACAACGTTTGAAA 59.190 37.500 0.00 0.00 40.69 2.69
2480 2550 3.562141 ACATCGACAACGTTTGAAATGGA 59.438 39.130 0.00 0.00 40.69 3.41
2482 2552 3.199677 TCGACAACGTTTGAAATGGACT 58.800 40.909 0.00 0.00 40.69 3.85
2509 2579 4.236527 AGGACCTTTGAGAGTTTGTGTT 57.763 40.909 0.00 0.00 0.00 3.32
2529 2599 5.008118 GTGTTGCTAGATCTATTGGCTTTCC 59.992 44.000 2.11 0.00 0.00 3.13
2535 2605 5.046288 AGATCTATTGGCTTTCCTTGGAG 57.954 43.478 0.00 0.00 0.00 3.86
2546 2616 1.276622 TCCTTGGAGCTTGGTAGTCC 58.723 55.000 0.00 0.00 0.00 3.85
2633 2703 2.166829 TGTTATGCAACATGGTCCACC 58.833 47.619 0.00 0.00 39.75 4.61
2639 2709 1.826385 CAACATGGTCCACCTTCTCC 58.174 55.000 0.00 0.00 36.82 3.71
2659 2729 0.113776 AACTCTCTGGACCGGTGGTA 59.886 55.000 14.63 0.00 35.25 3.25
2682 2752 1.527034 GATTGCAAGTCTGTCCTGCA 58.473 50.000 4.94 0.00 0.00 4.41
2703 2773 1.598701 GGGCTGATGCTCCAACCAAC 61.599 60.000 1.87 0.00 39.59 3.77
2733 2806 3.877559 AGCGATGTGATCTCATTCCAAA 58.122 40.909 11.38 0.00 0.00 3.28
2735 2808 3.374988 GCGATGTGATCTCATTCCAAACA 59.625 43.478 11.38 0.00 0.00 2.83
2744 2817 5.233083 TCTCATTCCAAACAGTGAGTGAT 57.767 39.130 0.00 0.00 39.22 3.06
2794 2867 1.598130 GAGCGTTTGCAGGTGTCCT 60.598 57.895 0.00 0.00 46.23 3.85
2833 2907 4.652421 TCAGTGCAATTTTCAAGCTTCA 57.348 36.364 0.00 0.00 0.00 3.02
2866 2940 5.006165 CGTACAATCTGAGGAAGAAGAATGC 59.994 44.000 0.00 0.00 38.79 3.56
2868 2942 4.942483 ACAATCTGAGGAAGAAGAATGCTG 59.058 41.667 0.00 0.00 38.79 4.41
2886 2961 8.970020 AGAATGCTGGTATGATTTTCAATGTAA 58.030 29.630 0.00 0.00 0.00 2.41
2887 2962 9.754382 GAATGCTGGTATGATTTTCAATGTAAT 57.246 29.630 0.00 0.00 0.00 1.89
2930 3005 1.732259 CCACTTTGACGGTGCATAGTC 59.268 52.381 15.02 15.02 37.85 2.59
2935 3010 0.687920 TGACGGTGCATAGTCCCAAA 59.312 50.000 17.93 1.47 36.61 3.28
2940 3015 1.463674 GTGCATAGTCCCAAAGGTGG 58.536 55.000 0.00 0.00 45.53 4.61
2952 3027 0.325602 AAAGGTGGCCCGTTAATCGA 59.674 50.000 0.00 0.00 42.86 3.59
2963 3038 2.416836 CCGTTAATCGAGAAGCCAGTCA 60.417 50.000 0.00 0.00 42.86 3.41
2964 3039 3.250744 CGTTAATCGAGAAGCCAGTCAA 58.749 45.455 0.00 0.00 42.86 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.595794 CGGCGGCTACGTGATTTAATT 59.404 47.619 7.61 0.00 43.45 1.40
87 89 2.642254 CGTAAGGCCACCGGAGACA 61.642 63.158 9.46 0.00 0.00 3.41
254 258 2.203294 GCACCACAAGAACGGGGT 60.203 61.111 0.00 0.00 0.00 4.95
317 325 1.129998 CAAGCAGCTCGACCAAAGATG 59.870 52.381 0.00 0.00 33.35 2.90
327 335 1.203928 CGAATAGACCAAGCAGCTCG 58.796 55.000 0.00 0.00 0.00 5.03
336 344 3.928727 AGACAAACGACGAATAGACCA 57.071 42.857 0.00 0.00 0.00 4.02
352 361 2.556622 TGAAGACACATGAGCGTAGACA 59.443 45.455 0.00 0.00 0.00 3.41
360 369 1.277273 TCCAGCCTGAAGACACATGAG 59.723 52.381 0.00 0.00 0.00 2.90
395 407 4.991153 ATCGTTGCAGATGAAGAGTAGA 57.009 40.909 0.00 0.00 0.00 2.59
422 434 1.680522 ATAGGACCAGCGCACCAGAG 61.681 60.000 11.47 0.00 0.00 3.35
443 455 0.892755 AAGTCGTCGTGATAAGGCCA 59.107 50.000 5.01 0.00 0.00 5.36
478 490 0.318699 GAGCCGGGCAAAACTTGTTC 60.319 55.000 23.09 2.30 0.00 3.18
506 518 1.224592 GCCATCGTCATCACCCCTT 59.775 57.895 0.00 0.00 0.00 3.95
512 524 2.511373 GGCGTGCCATCGTCATCA 60.511 61.111 5.89 0.00 35.41 3.07
599 616 3.396260 TGGCAGTACAAGGAACACTAC 57.604 47.619 0.00 0.00 0.00 2.73
701 729 9.911788 ATAGTGTTGGATTCATAGTTCAAAGAT 57.088 29.630 0.00 0.00 0.00 2.40
838 870 2.280186 CGTCCAATAGCGAGGCCC 60.280 66.667 0.00 0.00 0.00 5.80
929 975 5.125097 TCGCTCGAGGTAAGATAAAGAACTT 59.875 40.000 15.58 0.00 0.00 2.66
1040 1087 2.279935 ACTCCGAGAACACTGAGACT 57.720 50.000 1.33 0.00 0.00 3.24
1047 1094 0.450983 CCGTCCTACTCCGAGAACAC 59.549 60.000 1.33 0.00 0.00 3.32
1301 1348 4.463209 GTCGATCGACAAGCAAAATTCAA 58.537 39.130 36.61 0.46 44.02 2.69
1333 1380 5.631512 CGCAAAAATAAAGGAAACGGATGAA 59.368 36.000 0.00 0.00 0.00 2.57
1334 1381 5.157781 CGCAAAAATAAAGGAAACGGATGA 58.842 37.500 0.00 0.00 0.00 2.92
1335 1382 4.201580 GCGCAAAAATAAAGGAAACGGATG 60.202 41.667 0.30 0.00 0.00 3.51
1336 1383 3.924073 GCGCAAAAATAAAGGAAACGGAT 59.076 39.130 0.30 0.00 0.00 4.18
1337 1384 3.243434 TGCGCAAAAATAAAGGAAACGGA 60.243 39.130 8.16 0.00 0.00 4.69
1338 1385 3.053455 TGCGCAAAAATAAAGGAAACGG 58.947 40.909 8.16 0.00 0.00 4.44
1339 1386 3.421698 GCTGCGCAAAAATAAAGGAAACG 60.422 43.478 13.05 0.00 0.00 3.60
1340 1387 3.421698 CGCTGCGCAAAAATAAAGGAAAC 60.422 43.478 13.05 0.00 0.00 2.78
1341 1388 2.728839 CGCTGCGCAAAAATAAAGGAAA 59.271 40.909 13.05 0.00 0.00 3.13
1342 1389 2.287909 ACGCTGCGCAAAAATAAAGGAA 60.288 40.909 23.51 0.00 0.00 3.36
1343 1390 1.268352 ACGCTGCGCAAAAATAAAGGA 59.732 42.857 23.51 0.00 0.00 3.36
1344 1391 1.696988 ACGCTGCGCAAAAATAAAGG 58.303 45.000 23.51 0.00 0.00 3.11
1345 1392 3.459435 CAAACGCTGCGCAAAAATAAAG 58.541 40.909 23.51 0.00 0.00 1.85
1585 1650 5.371115 TGTAGTTTAACAAATGGCTCTGC 57.629 39.130 0.00 0.00 0.00 4.26
1586 1651 5.182001 AGCTGTAGTTTAACAAATGGCTCTG 59.818 40.000 0.00 0.00 0.00 3.35
1626 1691 4.100963 TGCCACAGTCAATATAGACCGAAT 59.899 41.667 0.00 0.00 39.34 3.34
1808 1874 0.313043 AACCCTACACACACGACGAG 59.687 55.000 0.00 0.00 0.00 4.18
1811 1877 2.231964 TCCATAACCCTACACACACGAC 59.768 50.000 0.00 0.00 0.00 4.34
1973 2039 1.227853 AGCACCTCGTGTTCAACCC 60.228 57.895 0.00 0.00 35.75 4.11
2051 2117 3.787785 TGTTCTACAGTTTGCGAGTCAA 58.212 40.909 0.00 0.00 0.00 3.18
2052 2118 3.446310 TGTTCTACAGTTTGCGAGTCA 57.554 42.857 0.00 0.00 0.00 3.41
2053 2119 4.992381 ATTGTTCTACAGTTTGCGAGTC 57.008 40.909 0.00 0.00 0.00 3.36
2054 2120 4.574828 ACAATTGTTCTACAGTTTGCGAGT 59.425 37.500 4.92 0.00 30.77 4.18
2055 2121 5.095691 ACAATTGTTCTACAGTTTGCGAG 57.904 39.130 4.92 0.00 30.77 5.03
2056 2122 5.493133 AACAATTGTTCTACAGTTTGCGA 57.507 34.783 18.13 0.00 31.64 5.10
2141 2210 9.566432 CATCTCTTATGTAGGCCTTCTATTTTT 57.434 33.333 12.58 0.00 0.00 1.94
2158 2227 5.587844 CACAAAACTAGCCAGCATCTCTTAT 59.412 40.000 0.00 0.00 0.00 1.73
2167 2236 1.198637 CAGCTCACAAAACTAGCCAGC 59.801 52.381 0.00 0.00 36.92 4.85
2170 2239 0.523519 GCCAGCTCACAAAACTAGCC 59.476 55.000 0.00 0.00 36.92 3.93
2179 2248 1.979855 TTAAAGCAAGCCAGCTCACA 58.020 45.000 0.51 0.00 45.89 3.58
2189 2258 8.721478 TCACAAAGCTAAGTAGATTAAAGCAAG 58.279 33.333 0.00 0.00 30.76 4.01
2198 2267 9.726438 AACTGTTATTCACAAAGCTAAGTAGAT 57.274 29.630 0.00 0.00 33.87 1.98
2311 2380 4.836125 TGACAAGATCTTCAAAAGTGCC 57.164 40.909 4.57 0.00 0.00 5.01
2312 2381 5.118203 GCAATGACAAGATCTTCAAAAGTGC 59.882 40.000 4.57 8.98 0.00 4.40
2315 2384 4.322804 GCGCAATGACAAGATCTTCAAAAG 59.677 41.667 4.57 0.00 0.00 2.27
2344 2413 8.601047 TCATTATGGGTTGTTGGAATATTTGA 57.399 30.769 0.00 0.00 0.00 2.69
2385 2454 2.875933 GTTGATGTCGTGAGGGAAACAA 59.124 45.455 0.00 0.00 0.00 2.83
2396 2465 0.243907 CCACCTCTCGTTGATGTCGT 59.756 55.000 0.00 0.00 0.00 4.34
2399 2468 0.396435 TTGCCACCTCTCGTTGATGT 59.604 50.000 0.00 0.00 0.00 3.06
2404 2473 1.278985 TCATCATTGCCACCTCTCGTT 59.721 47.619 0.00 0.00 0.00 3.85
2410 2479 3.202818 TCAATAGGTCATCATTGCCACCT 59.797 43.478 6.35 6.35 42.21 4.00
2432 2502 3.892588 GAGAGACCGGAGAGACCATAATT 59.107 47.826 9.46 0.00 38.90 1.40
2434 2504 2.423088 GGAGAGACCGGAGAGACCATAA 60.423 54.545 9.46 0.00 38.90 1.90
2437 2507 1.208844 AGGAGAGACCGGAGAGACCA 61.209 60.000 9.46 0.00 44.74 4.02
2447 2517 3.731264 CGTTGTCGATGTAAGGAGAGACC 60.731 52.174 0.00 0.00 39.71 3.85
2448 2518 3.119919 ACGTTGTCGATGTAAGGAGAGAC 60.120 47.826 0.00 0.00 40.62 3.36
2449 2519 3.079578 ACGTTGTCGATGTAAGGAGAGA 58.920 45.455 0.00 0.00 40.62 3.10
2450 2520 3.489180 ACGTTGTCGATGTAAGGAGAG 57.511 47.619 0.00 0.00 40.62 3.20
2451 2521 3.928727 AACGTTGTCGATGTAAGGAGA 57.071 42.857 0.00 0.00 40.62 3.71
2452 2522 3.985279 TCAAACGTTGTCGATGTAAGGAG 59.015 43.478 0.00 0.00 40.62 3.69
2453 2523 3.979948 TCAAACGTTGTCGATGTAAGGA 58.020 40.909 0.00 0.00 40.62 3.36
2454 2524 4.718858 TTCAAACGTTGTCGATGTAAGG 57.281 40.909 0.00 0.00 40.62 2.69
2455 2525 5.563751 CCATTTCAAACGTTGTCGATGTAAG 59.436 40.000 0.00 0.00 40.62 2.34
2459 2529 3.906008 GTCCATTTCAAACGTTGTCGATG 59.094 43.478 0.00 4.88 40.62 3.84
2460 2530 3.813166 AGTCCATTTCAAACGTTGTCGAT 59.187 39.130 0.00 0.00 40.62 3.59
2471 2541 3.888930 GGTCCTTTGTCAGTCCATTTCAA 59.111 43.478 0.00 0.00 0.00 2.69
2472 2542 3.138283 AGGTCCTTTGTCAGTCCATTTCA 59.862 43.478 0.00 0.00 0.00 2.69
2475 2545 3.884037 AAGGTCCTTTGTCAGTCCATT 57.116 42.857 0.00 0.00 0.00 3.16
2476 2546 3.490348 CAAAGGTCCTTTGTCAGTCCAT 58.510 45.455 29.27 0.00 43.85 3.41
2509 2579 5.371526 CAAGGAAAGCCAATAGATCTAGCA 58.628 41.667 8.70 0.00 36.29 3.49
2529 2599 0.608640 ACGGACTACCAAGCTCCAAG 59.391 55.000 0.00 0.00 35.59 3.61
2535 2605 4.277672 TGATAGATACACGGACTACCAAGC 59.722 45.833 0.00 0.00 35.59 4.01
2546 2616 4.837896 TGCTCTCCTTGATAGATACACG 57.162 45.455 0.00 0.00 0.00 4.49
2639 2709 1.293498 CCACCGGTCCAGAGAGTTG 59.707 63.158 2.59 0.00 0.00 3.16
2659 2729 3.087031 CAGGACAGACTTGCAATCCATT 58.913 45.455 16.39 0.00 31.41 3.16
2682 2752 1.076485 GGTTGGAGCATCAGCCCAT 60.076 57.895 1.67 0.00 43.56 4.00
2703 2773 4.562789 TGAGATCACATCGCTAAAGAAACG 59.437 41.667 0.00 0.00 0.00 3.60
2733 2806 3.334583 ACCGCAATAATCACTCACTGT 57.665 42.857 0.00 0.00 0.00 3.55
2735 2808 8.500753 TTATTAAACCGCAATAATCACTCACT 57.499 30.769 0.00 0.00 0.00 3.41
2744 2817 5.419471 ACCAGGCTTTATTAAACCGCAATAA 59.581 36.000 0.00 0.00 0.00 1.40
2794 2867 7.548097 TGCACTGAACCAACAATAAAGTAAAA 58.452 30.769 0.00 0.00 0.00 1.52
2930 3005 0.613572 ATTAACGGGCCACCTTTGGG 60.614 55.000 4.39 0.00 44.15 4.12
2935 3010 0.974010 TCTCGATTAACGGGCCACCT 60.974 55.000 4.39 0.00 42.91 4.00
2940 3015 0.461339 TGGCTTCTCGATTAACGGGC 60.461 55.000 0.00 0.00 42.91 6.13


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

AutoCloner maintained by Alex Coulton.