Multiple sequence alignment - TraesCS3A01G406300

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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 TraesCS3A01G406300 chr3A 100.000 3020 0 0 1 3020 651503301 651500282 0.000000e+00 5578.0
1 TraesCS3A01G406300 chr3A 83.234 1169 128 35 1331 2475 650195333 650196457 0.000000e+00 1011.0
2 TraesCS3A01G406300 chr3A 82.341 504 69 12 1891 2384 650197202 650196709 1.290000e-113 420.0
3 TraesCS3A01G406300 chr3A 100.000 32 0 0 2945 2976 650197388 650197419 3.250000e-05 60.2
4 TraesCS3A01G406300 chr3B 87.922 2045 178 31 494 2508 679624738 679622733 0.000000e+00 2344.0
5 TraesCS3A01G406300 chr3B 80.114 1227 156 50 1308 2475 678711031 678712228 0.000000e+00 833.0
6 TraesCS3A01G406300 chr3B 95.000 500 22 3 2509 3007 679622626 679622129 0.000000e+00 782.0
7 TraesCS3A01G406300 chr3B 93.662 284 16 2 43 326 679625978 679625697 1.000000e-114 424.0
8 TraesCS3A01G406300 chr3B 87.059 170 14 3 1076 1243 678710861 678711024 5.140000e-43 185.0
9 TraesCS3A01G406300 chr3B 90.647 139 10 3 374 510 679625701 679625564 6.650000e-42 182.0
10 TraesCS3A01G406300 chr3B 81.250 128 17 6 2548 2673 45753841 45753719 2.480000e-16 97.1
11 TraesCS3A01G406300 chr3B 81.250 128 17 6 2548 2673 45823872 45823750 2.480000e-16 97.1
12 TraesCS3A01G406300 chr3B 79.688 128 20 5 2548 2673 45768529 45768406 1.490000e-13 87.9
13 TraesCS3A01G406300 chr3B 79.688 128 20 5 2548 2673 45838670 45838547 1.490000e-13 87.9
14 TraesCS3A01G406300 chr3B 79.688 128 20 5 2548 2673 45875951 45875828 1.490000e-13 87.9
15 TraesCS3A01G406300 chr3B 79.688 128 20 5 2548 2673 45890045 45889922 1.490000e-13 87.9
16 TraesCS3A01G406300 chr3B 79.688 128 20 5 2548 2673 45933757 45933634 1.490000e-13 87.9
17 TraesCS3A01G406300 chr3D 92.851 1175 51 16 363 1532 516194875 516193729 0.000000e+00 1674.0
18 TraesCS3A01G406300 chr3D 88.030 919 66 10 1517 2428 516193712 516192831 0.000000e+00 1048.0
19 TraesCS3A01G406300 chr3D 82.224 1232 131 54 1298 2475 515818996 515820193 0.000000e+00 981.0
20 TraesCS3A01G406300 chr3D 89.780 499 24 13 2509 3007 516192686 516192215 5.530000e-172 614.0
21 TraesCS3A01G406300 chr3D 82.565 499 65 12 1896 2384 515820932 515820446 1.290000e-113 420.0
22 TraesCS3A01G406300 chr3D 91.398 93 8 0 71 163 516195095 516195003 8.790000e-26 128.0
23 TraesCS3A01G406300 chr3D 95.238 42 2 0 2467 2508 516192834 516192793 1.940000e-07 67.6
24 TraesCS3A01G406300 chr3D 97.436 39 0 1 2938 2976 515824797 515824834 6.990000e-07 65.8
25 TraesCS3A01G406300 chr7A 100.000 29 0 0 1686 1714 303967860 303967832 2.000000e-03 54.7
26 TraesCS3A01G406300 chr5A 100.000 28 0 0 1690 1717 275080756 275080783 5.000000e-03 52.8


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 TraesCS3A01G406300 chr3A 651500282 651503301 3019 True 5578.00 5578 100.00000 1 3020 1 chr3A.!!$R2 3019
1 TraesCS3A01G406300 chr3A 650195333 650197419 2086 False 535.60 1011 91.61700 1331 2976 2 chr3A.!!$F1 1645
2 TraesCS3A01G406300 chr3B 679622129 679625978 3849 True 933.00 2344 91.80775 43 3007 4 chr3B.!!$R8 2964
3 TraesCS3A01G406300 chr3B 678710861 678712228 1367 False 509.00 833 83.58650 1076 2475 2 chr3B.!!$F1 1399
4 TraesCS3A01G406300 chr3D 515818996 515820193 1197 False 981.00 981 82.22400 1298 2475 1 chr3D.!!$F1 1177
5 TraesCS3A01G406300 chr3D 516192215 516195095 2880 True 706.32 1674 91.45940 71 3007 5 chr3D.!!$R2 2936

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
325 326 0.107831 ACGTCCAGCCAAGCAAGTTA 59.892 50.0 0.0 0.0 0.00 2.24 F
1879 2787 0.037734 CCCCAACAACTCTGTACCCC 59.962 60.0 0.0 0.0 33.45 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2882 0.098200 CAGCAAGCATCATGTCCACG 59.902 55.0 0.0 0.0 0.0 4.94 R
2915 4517 0.969894 GGATACTCCCTCGGTCATGG 59.030 60.0 0.0 0.0 0.0 3.66 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
17 18 2.606519 TGTCCCGGCAGCCTAGTT 60.607 61.111 10.54 0.00 0.00 2.24
18 19 1.305465 TGTCCCGGCAGCCTAGTTA 60.305 57.895 10.54 0.00 0.00 2.24
19 20 0.689745 TGTCCCGGCAGCCTAGTTAT 60.690 55.000 10.54 0.00 0.00 1.89
20 21 0.468648 GTCCCGGCAGCCTAGTTATT 59.531 55.000 10.54 0.00 0.00 1.40
21 22 1.134189 GTCCCGGCAGCCTAGTTATTT 60.134 52.381 10.54 0.00 0.00 1.40
22 23 1.562475 TCCCGGCAGCCTAGTTATTTT 59.438 47.619 10.54 0.00 0.00 1.82
23 24 1.676006 CCCGGCAGCCTAGTTATTTTG 59.324 52.381 10.54 0.00 0.00 2.44
24 25 2.639065 CCGGCAGCCTAGTTATTTTGA 58.361 47.619 10.54 0.00 0.00 2.69
25 26 2.614057 CCGGCAGCCTAGTTATTTTGAG 59.386 50.000 10.54 0.00 0.00 3.02
26 27 2.614057 CGGCAGCCTAGTTATTTTGAGG 59.386 50.000 10.54 0.00 0.00 3.86
27 28 3.621558 GGCAGCCTAGTTATTTTGAGGT 58.378 45.455 3.29 0.00 0.00 3.85
28 29 3.628032 GGCAGCCTAGTTATTTTGAGGTC 59.372 47.826 3.29 0.00 0.00 3.85
29 30 4.518249 GCAGCCTAGTTATTTTGAGGTCT 58.482 43.478 0.00 0.00 0.00 3.85
30 31 5.396436 GGCAGCCTAGTTATTTTGAGGTCTA 60.396 44.000 3.29 0.00 0.00 2.59
31 32 6.113411 GCAGCCTAGTTATTTTGAGGTCTAA 58.887 40.000 0.00 0.00 0.00 2.10
32 33 6.037281 GCAGCCTAGTTATTTTGAGGTCTAAC 59.963 42.308 0.00 0.00 0.00 2.34
33 34 6.539103 CAGCCTAGTTATTTTGAGGTCTAACC 59.461 42.308 0.00 0.00 38.99 2.85
48 49 5.246307 GGTCTAACCTTGTAGCATGTTCTT 58.754 41.667 0.00 0.00 34.73 2.52
69 70 5.465390 TCTTCCGTATCAAACAGTTCACAAG 59.535 40.000 0.00 0.00 0.00 3.16
122 123 8.539770 AAGTTCTCAGTACTGTGAATGTATTG 57.460 34.615 31.86 4.18 42.57 1.90
124 125 5.419542 TCTCAGTACTGTGAATGTATTGGC 58.580 41.667 22.04 0.00 31.40 4.52
130 131 4.202441 ACTGTGAATGTATTGGCATCTCC 58.798 43.478 0.00 0.00 0.00 3.71
208 209 8.681486 TCCATAATCATGTAAATCAGGTTGAG 57.319 34.615 0.00 0.00 0.00 3.02
222 223 3.803778 CAGGTTGAGTCCAAAAATTGCAC 59.196 43.478 0.00 0.00 33.49 4.57
266 267 4.517285 TCTCCATGCTGTTTCCAGTAATC 58.483 43.478 0.00 0.00 41.02 1.75
267 268 4.019411 TCTCCATGCTGTTTCCAGTAATCA 60.019 41.667 0.00 0.00 41.02 2.57
269 270 5.263599 TCCATGCTGTTTCCAGTAATCATT 58.736 37.500 0.00 0.00 41.02 2.57
270 271 5.716228 TCCATGCTGTTTCCAGTAATCATTT 59.284 36.000 0.00 0.00 41.02 2.32
295 296 3.572255 GGTTCAGGCCAATCTGTTAACAA 59.428 43.478 10.03 1.56 36.25 2.83
322 323 1.597854 TCACGTCCAGCCAAGCAAG 60.598 57.895 0.00 0.00 0.00 4.01
325 326 0.107831 ACGTCCAGCCAAGCAAGTTA 59.892 50.000 0.00 0.00 0.00 2.24
326 327 0.798776 CGTCCAGCCAAGCAAGTTAG 59.201 55.000 0.00 0.00 0.00 2.34
327 328 0.523519 GTCCAGCCAAGCAAGTTAGC 59.476 55.000 0.00 0.00 0.00 3.09
339 340 5.175090 AGCAAGTTAGCTTCAGTTTTGTC 57.825 39.130 0.00 0.00 43.70 3.18
340 341 4.036852 AGCAAGTTAGCTTCAGTTTTGTCC 59.963 41.667 0.00 0.00 43.70 4.02
341 342 4.202010 GCAAGTTAGCTTCAGTTTTGTCCA 60.202 41.667 0.00 0.00 31.49 4.02
342 343 5.507985 GCAAGTTAGCTTCAGTTTTGTCCAT 60.508 40.000 0.00 0.00 31.49 3.41
343 344 6.293955 GCAAGTTAGCTTCAGTTTTGTCCATA 60.294 38.462 0.00 0.00 31.49 2.74
344 345 7.575720 GCAAGTTAGCTTCAGTTTTGTCCATAT 60.576 37.037 0.00 0.00 31.49 1.78
345 346 7.617041 AGTTAGCTTCAGTTTTGTCCATATC 57.383 36.000 0.00 0.00 0.00 1.63
346 347 7.168219 AGTTAGCTTCAGTTTTGTCCATATCA 58.832 34.615 0.00 0.00 0.00 2.15
347 348 7.831193 AGTTAGCTTCAGTTTTGTCCATATCAT 59.169 33.333 0.00 0.00 0.00 2.45
348 349 8.462016 GTTAGCTTCAGTTTTGTCCATATCATT 58.538 33.333 0.00 0.00 0.00 2.57
349 350 7.472334 AGCTTCAGTTTTGTCCATATCATTT 57.528 32.000 0.00 0.00 0.00 2.32
350 351 7.899973 AGCTTCAGTTTTGTCCATATCATTTT 58.100 30.769 0.00 0.00 0.00 1.82
351 352 8.370182 AGCTTCAGTTTTGTCCATATCATTTTT 58.630 29.630 0.00 0.00 0.00 1.94
384 385 5.891551 AGTTGTCCATATCAATTAACACCCC 59.108 40.000 0.00 0.00 0.00 4.95
481 483 5.509163 GGAAAAACTTTACTGCCTTCCTTCC 60.509 44.000 0.00 0.00 0.00 3.46
492 494 1.228429 TTCCTTCCAAAGCCCACCG 60.228 57.895 0.00 0.00 0.00 4.94
497 499 1.618343 CTTCCAAAGCCCACCGATTTT 59.382 47.619 0.00 0.00 0.00 1.82
546 1390 0.873721 GATACGGAGGGAGAGCGTAC 59.126 60.000 0.00 0.00 0.00 3.67
556 1400 2.215196 GGAGAGCGTACAAACACCAAA 58.785 47.619 0.00 0.00 0.00 3.28
557 1401 2.812011 GGAGAGCGTACAAACACCAAAT 59.188 45.455 0.00 0.00 0.00 2.32
559 1403 4.634443 GGAGAGCGTACAAACACCAAATAT 59.366 41.667 0.00 0.00 0.00 1.28
637 1482 3.128242 GTGCTCTGTAGAAGTAGCCGTTA 59.872 47.826 0.00 0.00 33.99 3.18
673 1518 6.294508 GCAGGAAATTAAAGCTTACCACAAGA 60.295 38.462 0.00 0.00 0.00 3.02
717 1562 2.387125 GAAAGAAACACAGGCGCGCA 62.387 55.000 34.42 0.00 0.00 6.09
769 1614 2.868583 CCGGTGCTGAATTCATAGTCAG 59.131 50.000 8.96 0.00 46.51 3.51
774 1619 5.008415 GGTGCTGAATTCATAGTCAGGAATG 59.992 44.000 8.96 0.00 46.01 2.67
805 1650 3.808834 ACTCCTGGGACTTTAAAAGGG 57.191 47.619 3.59 0.00 0.00 3.95
854 1699 1.662629 CATTGCCGGATCATCTATCGC 59.337 52.381 5.05 0.00 35.21 4.58
872 1717 1.311403 CCAGCCCTCCTCTCCTACA 59.689 63.158 0.00 0.00 0.00 2.74
895 1740 5.232838 CACTTTCTGTTCAGGTTGCAAATTC 59.767 40.000 0.00 0.00 0.00 2.17
903 1748 4.637276 TCAGGTTGCAAATTCGTCTTCTA 58.363 39.130 0.00 0.00 0.00 2.10
932 1777 3.090210 TCGTTGGGTAGTGGATAGTGA 57.910 47.619 0.00 0.00 0.00 3.41
934 1779 3.635373 TCGTTGGGTAGTGGATAGTGATC 59.365 47.826 0.00 0.00 0.00 2.92
947 1792 5.758784 TGGATAGTGATCGTAGTAGTGACAG 59.241 44.000 0.00 0.00 32.28 3.51
984 1829 1.623311 TGCAGGATCCTCGTTTCTTGA 59.377 47.619 12.69 0.00 0.00 3.02
1068 1913 3.270000 TCGCTGTCCGACGATTCA 58.730 55.556 0.00 0.00 41.89 2.57
1169 2016 2.853003 GTCGAATTCTCGCTTGTAGGAC 59.147 50.000 3.52 0.00 45.04 3.85
1192 2039 4.455877 CCGATTCTGTTGGTAGAAAAGCTT 59.544 41.667 0.00 0.00 39.87 3.74
1199 2046 9.837907 TTCTGTTGGTAGAAAAGCTTTATGCGC 62.838 40.741 13.10 0.00 39.03 6.09
1354 2205 9.666626 GATCTTGCAGATTTCTGATAGATTTTG 57.333 33.333 18.11 0.49 46.59 2.44
1377 2228 4.999950 GTCATTCAACTCTGTGGACTGAAT 59.000 41.667 0.00 0.00 29.25 2.57
1399 2250 2.438868 AAAGGCTTGCCGTGAATTTC 57.561 45.000 0.00 0.00 0.00 2.17
1422 2273 5.366768 TCCATCCAATCCCTGAACTAGTTAG 59.633 44.000 8.42 6.61 0.00 2.34
1444 2295 3.428862 GCATTATGGGGGAAAACAACTCG 60.429 47.826 0.00 0.00 0.00 4.18
1478 2338 2.549754 ACAAAAATCTCGTGTGCTCCAG 59.450 45.455 0.00 0.00 0.00 3.86
1540 2432 5.590530 ACCTGATCTGATCTGTACAACTC 57.409 43.478 17.82 0.00 0.00 3.01
1756 2656 2.868583 CCATCTGCTCCTAAACATGTCG 59.131 50.000 0.00 0.00 0.00 4.35
1777 2681 2.338984 ACGAGGTGAGACGTTGGC 59.661 61.111 0.00 0.00 39.75 4.52
1816 2720 3.329231 CGCGAAAGTGGACTGCAA 58.671 55.556 0.00 0.00 38.12 4.08
1829 2735 1.268079 GACTGCAAGAAAAGGGACTGC 59.732 52.381 0.00 0.00 36.14 4.40
1879 2787 0.037734 CCCCAACAACTCTGTACCCC 59.962 60.000 0.00 0.00 33.45 4.95
1883 2791 2.125673 CAACTCTGTACCCCGCGG 60.126 66.667 21.04 21.04 0.00 6.46
1923 2861 2.936032 AGTGCCTTCCCCTCACCC 60.936 66.667 0.00 0.00 0.00 4.61
1929 2867 2.285368 TTCCCCTCACCCGCATCT 60.285 61.111 0.00 0.00 0.00 2.90
1944 2882 2.028523 CGCATCTTTCATGACACGTCTC 59.971 50.000 0.00 0.00 0.00 3.36
2020 2961 3.688673 GGACTCTGAAAAGAAGCCATGAG 59.311 47.826 0.00 0.00 0.00 2.90
2049 2995 4.292306 AGGAAGATTGGTGGAGGTGTAAAT 59.708 41.667 0.00 0.00 0.00 1.40
2050 2996 5.016831 GGAAGATTGGTGGAGGTGTAAATT 58.983 41.667 0.00 0.00 0.00 1.82
2052 2998 6.014584 GGAAGATTGGTGGAGGTGTAAATTTT 60.015 38.462 0.00 0.00 0.00 1.82
2053 2999 6.994421 AGATTGGTGGAGGTGTAAATTTTT 57.006 33.333 0.00 0.00 0.00 1.94
2175 3157 7.195839 AGAATGCTGTCAGTCTTAAGAAAAC 57.804 36.000 6.78 6.48 44.30 2.43
2176 3158 5.597813 ATGCTGTCAGTCTTAAGAAAACG 57.402 39.130 6.78 4.31 0.00 3.60
2178 3160 4.873827 TGCTGTCAGTCTTAAGAAAACGTT 59.126 37.500 6.78 0.00 0.00 3.99
2179 3161 5.198274 GCTGTCAGTCTTAAGAAAACGTTG 58.802 41.667 6.78 0.14 0.00 4.10
2180 3162 5.151632 TGTCAGTCTTAAGAAAACGTTGC 57.848 39.130 6.78 0.00 0.00 4.17
2181 3163 4.632251 TGTCAGTCTTAAGAAAACGTTGCA 59.368 37.500 6.78 0.00 0.00 4.08
2182 3164 5.295787 TGTCAGTCTTAAGAAAACGTTGCAT 59.704 36.000 6.78 0.00 0.00 3.96
2215 3197 2.549754 AGAACGCCTCATGTTTCAACTG 59.450 45.455 0.00 0.00 0.00 3.16
2221 3204 0.865111 TCATGTTTCAACTGTCGCCG 59.135 50.000 0.00 0.00 0.00 6.46
2224 3207 1.088306 TGTTTCAACTGTCGCCGTTT 58.912 45.000 0.00 0.00 0.00 3.60
2261 3244 5.010012 TGCTATACGATGATATGATGCCGAT 59.990 40.000 0.00 0.00 0.00 4.18
2328 3315 1.619827 CTCATGATCTCTCCTCTGCCC 59.380 57.143 0.00 0.00 0.00 5.36
2330 3317 0.187117 ATGATCTCTCCTCTGCCCGA 59.813 55.000 0.00 0.00 0.00 5.14
2347 3334 1.478510 CCGACTCAATCTACTGGTGCT 59.521 52.381 0.00 0.00 0.00 4.40
2413 3400 6.694877 ATAGATCTGTAAGTGCGTACTTCA 57.305 37.500 22.53 17.44 43.53 3.02
2448 3435 7.133443 CTTGTAAACAGTACAAGCGTTTTTC 57.867 36.000 12.00 0.00 45.02 2.29
2449 3436 6.179504 TGTAAACAGTACAAGCGTTTTTCA 57.820 33.333 0.00 1.09 34.78 2.69
2450 3437 6.787225 TGTAAACAGTACAAGCGTTTTTCAT 58.213 32.000 0.00 0.00 34.78 2.57
2451 3438 7.917597 TGTAAACAGTACAAGCGTTTTTCATA 58.082 30.769 0.00 0.00 34.78 2.15
2452 3439 8.561212 TGTAAACAGTACAAGCGTTTTTCATAT 58.439 29.630 0.00 0.00 34.78 1.78
2453 3440 9.047871 GTAAACAGTACAAGCGTTTTTCATATC 57.952 33.333 0.00 0.00 34.78 1.63
2462 3451 7.644551 ACAAGCGTTTTTCATATCGTTTTTGTA 59.355 29.630 0.00 0.00 0.00 2.41
2463 3452 7.543127 AGCGTTTTTCATATCGTTTTTGTAC 57.457 32.000 0.00 0.00 0.00 2.90
2498 3487 4.455533 GCCGATTCATAAGCATGTTATGGA 59.544 41.667 19.21 14.86 34.16 3.41
2665 3776 5.183904 CAGAAAATGAAGGAGGTTTACCCAG 59.816 44.000 0.00 0.00 36.42 4.45
2730 4331 6.034683 GCAAGCAATCATCAGAAGATTGTTTC 59.965 38.462 21.02 14.59 46.76 2.78
2895 4497 0.839946 ATGGGTGCACAGGAGGATAC 59.160 55.000 20.43 0.00 0.00 2.24
2901 4503 1.204704 TGCACAGGAGGATACGTTCTG 59.795 52.381 0.00 0.00 46.39 3.02
2915 4517 1.597937 CGTTCTGAGTTGCCAACTTGC 60.598 52.381 12.09 0.18 43.03 4.01
3016 4619 9.777575 AAAACTTTCAGAAAATGCAAATTCAAG 57.222 25.926 14.88 12.05 0.00 3.02
3017 4620 8.496707 AACTTTCAGAAAATGCAAATTCAAGT 57.503 26.923 14.88 12.52 0.00 3.16
3018 4621 8.134905 ACTTTCAGAAAATGCAAATTCAAGTC 57.865 30.769 14.88 0.00 0.00 3.01
3019 4622 7.765360 ACTTTCAGAAAATGCAAATTCAAGTCA 59.235 29.630 14.88 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.468648 AATAACTAGGCTGCCGGGAC 59.531 55.000 13.96 0.00 0.00 4.46
4 5 2.614057 CTCAAAATAACTAGGCTGCCGG 59.386 50.000 13.96 12.76 0.00 6.13
5 6 2.614057 CCTCAAAATAACTAGGCTGCCG 59.386 50.000 13.96 2.09 0.00 5.69
6 7 3.621558 ACCTCAAAATAACTAGGCTGCC 58.378 45.455 11.65 11.65 31.98 4.85
7 8 4.518249 AGACCTCAAAATAACTAGGCTGC 58.482 43.478 0.00 0.00 31.98 5.25
8 9 6.539103 GGTTAGACCTCAAAATAACTAGGCTG 59.461 42.308 0.00 0.00 34.73 4.85
9 10 6.651086 GGTTAGACCTCAAAATAACTAGGCT 58.349 40.000 0.00 0.00 34.73 4.58
10 11 6.922247 GGTTAGACCTCAAAATAACTAGGC 57.078 41.667 0.00 0.00 34.73 3.93
25 26 4.833390 AGAACATGCTACAAGGTTAGACC 58.167 43.478 0.00 0.00 38.99 3.85
26 27 5.351740 GGAAGAACATGCTACAAGGTTAGAC 59.648 44.000 0.00 0.00 0.00 2.59
27 28 5.488341 GGAAGAACATGCTACAAGGTTAGA 58.512 41.667 0.00 0.00 0.00 2.10
28 29 4.330074 CGGAAGAACATGCTACAAGGTTAG 59.670 45.833 0.00 0.00 0.00 2.34
29 30 4.250464 CGGAAGAACATGCTACAAGGTTA 58.750 43.478 0.00 0.00 0.00 2.85
30 31 3.074412 CGGAAGAACATGCTACAAGGTT 58.926 45.455 0.00 0.00 0.00 3.50
31 32 2.038557 ACGGAAGAACATGCTACAAGGT 59.961 45.455 0.00 0.00 0.00 3.50
32 33 2.699954 ACGGAAGAACATGCTACAAGG 58.300 47.619 0.00 0.00 0.00 3.61
33 34 5.109210 TGATACGGAAGAACATGCTACAAG 58.891 41.667 0.00 0.00 0.00 3.16
34 35 5.079689 TGATACGGAAGAACATGCTACAA 57.920 39.130 0.00 0.00 0.00 2.41
35 36 4.729227 TGATACGGAAGAACATGCTACA 57.271 40.909 0.00 0.00 0.00 2.74
36 37 5.350365 TGTTTGATACGGAAGAACATGCTAC 59.650 40.000 0.00 0.00 0.00 3.58
37 38 5.483811 TGTTTGATACGGAAGAACATGCTA 58.516 37.500 0.00 0.00 0.00 3.49
38 39 4.323417 TGTTTGATACGGAAGAACATGCT 58.677 39.130 0.00 0.00 0.00 3.79
39 40 4.154195 ACTGTTTGATACGGAAGAACATGC 59.846 41.667 0.00 0.00 36.57 4.06
40 41 5.862924 ACTGTTTGATACGGAAGAACATG 57.137 39.130 0.00 0.00 36.57 3.21
41 42 5.995282 TGAACTGTTTGATACGGAAGAACAT 59.005 36.000 0.00 0.00 36.57 2.71
48 49 4.062293 CCTTGTGAACTGTTTGATACGGA 58.938 43.478 0.00 0.00 36.57 4.69
69 70 6.346896 ACCGTTCTTCCTCAAGTAATTATCC 58.653 40.000 0.00 0.00 0.00 2.59
103 104 5.159273 TGCCAATACATTCACAGTACTGA 57.841 39.130 29.30 7.59 0.00 3.41
122 123 0.603975 GGATACAAGCGGGAGATGCC 60.604 60.000 0.00 0.00 0.00 4.40
124 125 2.366916 AGAAGGATACAAGCGGGAGATG 59.633 50.000 0.00 0.00 41.41 2.90
130 131 2.866762 GCTACAAGAAGGATACAAGCGG 59.133 50.000 0.00 0.00 41.41 5.52
295 296 0.244994 GCTGGACGTGACAGACTGAT 59.755 55.000 18.20 0.00 38.20 2.90
322 323 7.377766 TGATATGGACAAAACTGAAGCTAAC 57.622 36.000 0.00 0.00 0.00 2.34
325 326 7.472334 AAATGATATGGACAAAACTGAAGCT 57.528 32.000 0.00 0.00 0.00 3.74
326 327 8.538409 AAAAATGATATGGACAAAACTGAAGC 57.462 30.769 0.00 0.00 0.00 3.86
350 351 6.078202 TGATATGGACAACTTTCGCAAAAA 57.922 33.333 0.00 0.00 0.00 1.94
351 352 5.697473 TGATATGGACAACTTTCGCAAAA 57.303 34.783 0.00 0.00 0.00 2.44
352 353 5.697473 TTGATATGGACAACTTTCGCAAA 57.303 34.783 0.00 0.00 0.00 3.68
353 354 5.895636 ATTGATATGGACAACTTTCGCAA 57.104 34.783 0.00 0.00 0.00 4.85
354 355 5.895636 AATTGATATGGACAACTTTCGCA 57.104 34.783 0.00 0.00 0.00 5.10
355 356 7.218204 GTGTTAATTGATATGGACAACTTTCGC 59.782 37.037 0.00 0.00 0.00 4.70
356 357 7.696453 GGTGTTAATTGATATGGACAACTTTCG 59.304 37.037 0.00 0.00 0.00 3.46
357 358 7.973944 GGGTGTTAATTGATATGGACAACTTTC 59.026 37.037 0.00 0.00 0.00 2.62
358 359 7.093509 GGGGTGTTAATTGATATGGACAACTTT 60.094 37.037 0.00 0.00 0.00 2.66
359 360 6.379988 GGGGTGTTAATTGATATGGACAACTT 59.620 38.462 0.00 0.00 0.00 2.66
360 361 5.891551 GGGGTGTTAATTGATATGGACAACT 59.108 40.000 0.00 0.00 0.00 3.16
361 362 5.654650 TGGGGTGTTAATTGATATGGACAAC 59.345 40.000 0.00 0.00 0.00 3.32
384 385 6.564328 AGCTGTCTCTTTGGTTAAAAAGTTG 58.436 36.000 0.00 0.00 38.16 3.16
427 429 5.406175 TCGTTTCGTACCAACAAATTAGAGG 59.594 40.000 4.04 0.00 0.00 3.69
497 499 9.217278 TGCTTACAGTGGTATTTTTCGTATAAA 57.783 29.630 0.00 0.00 0.00 1.40
500 502 6.877322 AGTGCTTACAGTGGTATTTTTCGTAT 59.123 34.615 0.00 0.00 0.00 3.06
556 1400 9.979897 AAGGTGCATGTATAATGTATCCAATAT 57.020 29.630 0.00 0.00 0.00 1.28
557 1401 9.230122 CAAGGTGCATGTATAATGTATCCAATA 57.770 33.333 0.00 0.00 0.00 1.90
559 1403 7.286313 TCAAGGTGCATGTATAATGTATCCAA 58.714 34.615 0.00 0.00 0.00 3.53
569 1413 9.461312 AAGTTATCTTTTCAAGGTGCATGTATA 57.539 29.630 0.00 0.00 0.00 1.47
570 1414 7.944729 AGTTATCTTTTCAAGGTGCATGTAT 57.055 32.000 0.00 0.00 0.00 2.29
673 1518 4.888239 ACGTACAGATTAGCAGTCCTGTAT 59.112 41.667 0.00 0.00 42.05 2.29
717 1562 9.956720 CAGATGTGTTTTCTTCTAAATCTGTTT 57.043 29.630 0.00 0.00 0.00 2.83
754 1599 7.013083 CCTTTCCATTCCTGACTATGAATTCAG 59.987 40.741 14.54 3.71 39.25 3.02
769 1614 3.633986 CAGGAGTATTGCCTTTCCATTCC 59.366 47.826 0.00 0.00 32.12 3.01
774 1619 1.564348 TCCCAGGAGTATTGCCTTTCC 59.436 52.381 0.00 0.00 32.12 3.13
854 1699 1.045911 GTGTAGGAGAGGAGGGCTGG 61.046 65.000 0.00 0.00 0.00 4.85
869 1714 3.879998 TGCAACCTGAACAGAAAGTGTA 58.120 40.909 3.19 0.00 39.03 2.90
872 1717 5.343307 AATTTGCAACCTGAACAGAAAGT 57.657 34.783 0.00 0.00 0.00 2.66
895 1740 6.534079 ACCCAACGAAAGATAATTAGAAGACG 59.466 38.462 0.00 0.00 0.00 4.18
903 1748 6.057321 TCCACTACCCAACGAAAGATAATT 57.943 37.500 0.00 0.00 0.00 1.40
932 1777 3.755378 ACCGAAACTGTCACTACTACGAT 59.245 43.478 0.00 0.00 0.00 3.73
934 1779 3.549299 ACCGAAACTGTCACTACTACG 57.451 47.619 0.00 0.00 0.00 3.51
947 1792 3.244976 CTGCATCAAATCCAACCGAAAC 58.755 45.455 0.00 0.00 0.00 2.78
984 1829 5.122396 GTCAGCCATCTACAAAAGTTTCGAT 59.878 40.000 0.00 0.00 0.00 3.59
1063 1908 5.176590 GCCGTACTGAATCTGAATCTGAATC 59.823 44.000 6.61 0.00 0.00 2.52
1064 1909 5.053145 GCCGTACTGAATCTGAATCTGAAT 58.947 41.667 6.61 0.00 0.00 2.57
1065 1910 4.433615 GCCGTACTGAATCTGAATCTGAA 58.566 43.478 6.61 0.00 0.00 3.02
1066 1911 3.181475 GGCCGTACTGAATCTGAATCTGA 60.181 47.826 6.61 0.00 0.00 3.27
1067 1912 3.126831 GGCCGTACTGAATCTGAATCTG 58.873 50.000 0.00 0.00 0.00 2.90
1068 1913 2.103263 GGGCCGTACTGAATCTGAATCT 59.897 50.000 0.00 0.00 0.00 2.40
1169 2016 4.003648 AGCTTTTCTACCAACAGAATCGG 58.996 43.478 0.00 0.00 34.59 4.18
1192 2039 4.587306 CGCAGAAGATAAAAAGCGCATAA 58.413 39.130 11.47 0.00 38.68 1.90
1199 2046 6.583806 AGAATTGCAACGCAGAAGATAAAAAG 59.416 34.615 0.00 0.00 40.61 2.27
1200 2047 6.363088 CAGAATTGCAACGCAGAAGATAAAAA 59.637 34.615 0.00 0.00 40.61 1.94
1354 2205 3.995199 TCAGTCCACAGAGTTGAATGAC 58.005 45.455 0.00 0.00 29.84 3.06
1377 2228 4.303282 GAAATTCACGGCAAGCCTTTTTA 58.697 39.130 9.73 0.00 0.00 1.52
1399 2250 4.510167 AACTAGTTCAGGGATTGGATGG 57.490 45.455 1.12 0.00 0.00 3.51
1422 2273 3.428862 CGAGTTGTTTTCCCCCATAATGC 60.429 47.826 0.00 0.00 0.00 3.56
1444 2295 6.640907 ACGAGATTTTTGTCTATTGGTTTTGC 59.359 34.615 0.00 0.00 0.00 3.68
1478 2338 0.964358 AAAGACTGCCATGCCAGAGC 60.964 55.000 11.25 2.06 36.67 4.09
1540 2432 5.702670 TCTGCAAAATTCAGGAGTGTTAGAG 59.297 40.000 0.00 0.00 32.63 2.43
1572 2466 2.510613 TCCCTGATTTTCAACGAACCC 58.489 47.619 0.00 0.00 0.00 4.11
1756 2656 1.300697 AACGTCTCACCTCGTTGGC 60.301 57.895 2.29 0.00 46.11 4.52
1777 2681 4.135153 CCGCCTCGTCCTGTCCAG 62.135 72.222 0.00 0.00 0.00 3.86
1816 2720 0.183492 TGCACAGCAGTCCCTTTTCT 59.817 50.000 0.00 0.00 33.32 2.52
1879 2787 1.781429 CTCATTATCTGTCGAACCGCG 59.219 52.381 0.00 0.00 42.69 6.46
1883 2791 3.804873 GCCTTCCTCATTATCTGTCGAAC 59.195 47.826 0.00 0.00 0.00 3.95
1911 2849 1.915078 AAGATGCGGGTGAGGGGAAG 61.915 60.000 0.00 0.00 0.00 3.46
1923 2861 1.995484 AGACGTGTCATGAAAGATGCG 59.005 47.619 0.00 0.00 0.00 4.73
1944 2882 0.098200 CAGCAAGCATCATGTCCACG 59.902 55.000 0.00 0.00 0.00 4.94
2020 2961 1.004745 TCCACCAATCTTCCTGCTTCC 59.995 52.381 0.00 0.00 0.00 3.46
2053 2999 8.556213 ACTCGCATAGATTAAGGTAACAAAAA 57.444 30.769 0.00 0.00 41.41 1.94
2054 3000 8.556213 AACTCGCATAGATTAAGGTAACAAAA 57.444 30.769 0.00 0.00 41.41 2.44
2100 3049 8.893727 GCATCCTCAAGTTACATTAACAAGTAT 58.106 33.333 0.00 0.00 41.07 2.12
2215 3197 1.006832 ATAGCACATCAAACGGCGAC 58.993 50.000 16.62 0.00 0.00 5.19
2221 3204 7.406553 TCGTATAGCAAAATAGCACATCAAAC 58.593 34.615 0.00 0.00 36.85 2.93
2224 3207 6.928492 TCATCGTATAGCAAAATAGCACATCA 59.072 34.615 0.00 0.00 36.85 3.07
2328 3315 2.949451 AGCACCAGTAGATTGAGTCG 57.051 50.000 0.00 0.00 0.00 4.18
2330 3317 5.658634 TCAGATAAGCACCAGTAGATTGAGT 59.341 40.000 0.00 0.00 0.00 3.41
2347 3334 7.170828 GGCGTGTACATTCACATTATCAGATAA 59.829 37.037 5.29 5.29 38.12 1.75
2413 3400 7.045416 TGTACTGTTTACAAGTCAATGTCACT 58.955 34.615 0.00 0.00 34.75 3.41
2452 3439 8.434661 CGGCTAAGTAAATAAGTACAAAAACGA 58.565 33.333 0.00 0.00 0.00 3.85
2453 3440 8.434661 TCGGCTAAGTAAATAAGTACAAAAACG 58.565 33.333 0.00 0.00 0.00 3.60
2462 3451 8.989980 GCTTATGAATCGGCTAAGTAAATAAGT 58.010 33.333 0.00 0.00 31.05 2.24
2463 3452 8.988934 TGCTTATGAATCGGCTAAGTAAATAAG 58.011 33.333 0.00 0.00 0.00 1.73
2498 3487 4.080129 ACAGATCAAATAGCAGTCCATGGT 60.080 41.667 12.58 0.00 43.56 3.55
2545 3640 6.098409 ACCATGATTCACTAGTTACAGGGTAG 59.902 42.308 17.10 0.00 39.88 3.18
2665 3776 6.935208 ACACTTCCAGTAGGACTAAATTGTTC 59.065 38.462 0.00 0.00 45.73 3.18
2730 4331 6.856938 TGATGGTTTCCGTAATTTGTTAAACG 59.143 34.615 0.00 0.00 35.20 3.60
2744 4345 7.730364 AATAATAACTAGCTGATGGTTTCCG 57.270 36.000 0.00 0.00 34.05 4.30
2779 4380 6.708054 AGCATAAAGAGACAACATAGGTATGC 59.292 38.462 0.00 0.00 40.87 3.14
2825 4427 9.758651 AATTAGAAAAACACATTACAGGTTTCC 57.241 29.630 0.00 0.00 33.91 3.13
2895 4497 1.597937 GCAAGTTGGCAACTCAGAACG 60.598 52.381 31.24 16.58 41.91 3.95
2915 4517 0.969894 GGATACTCCCTCGGTCATGG 59.030 60.000 0.00 0.00 0.00 3.66
2994 4597 8.133754 TGACTTGAATTTGCATTTTCTGAAAG 57.866 30.769 2.75 7.84 0.00 2.62


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

AutoCloner maintained by Alex Coulton.