Multiple sequence alignment - TraesCS1A01G053900

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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 TraesCS1A01G053900 chr1A 100.000 2863 0 0 1 2863 35541807 35538945 0.000000e+00 5288.0
1 TraesCS1A01G053900 chr1A 89.234 418 31 9 2184 2597 35489289 35488882 7.080000e-141 510.0
2 TraesCS1A01G053900 chr1A 87.621 412 26 9 1668 2066 35573764 35574163 3.360000e-124 455.0
3 TraesCS1A01G053900 chr1A 83.921 454 35 13 2145 2597 35574957 35575373 1.600000e-107 399.0
4 TraesCS1A01G053900 chr1A 89.925 268 23 4 2597 2863 35488418 35488154 2.730000e-90 342.0
5 TraesCS1A01G053900 chr1A 87.310 197 10 6 2404 2597 35488716 35488532 8.040000e-51 211.0
6 TraesCS1A01G053900 chr1A 97.500 40 1 0 2597 2636 35488766 35488727 5.120000e-08 69.4
7 TraesCS1A01G053900 chr1B 89.462 1319 110 16 1 1311 56136174 56137471 0.000000e+00 1639.0
8 TraesCS1A01G053900 chr1B 87.696 959 75 28 535 1486 56060740 56059818 0.000000e+00 1077.0
9 TraesCS1A01G053900 chr1B 88.303 607 37 11 1555 2133 56059797 56059197 0.000000e+00 697.0
10 TraesCS1A01G053900 chr1B 90.268 298 24 5 2184 2478 56008480 56008185 4.470000e-103 385.0
11 TraesCS1A01G053900 chr1B 89.933 298 25 5 2184 2478 55987225 55986930 2.080000e-101 379.0
12 TraesCS1A01G053900 chr1B 88.291 316 36 1 1 316 56061051 56060737 7.490000e-101 377.0
13 TraesCS1A01G053900 chr1B 88.235 323 24 6 2277 2597 56137507 56137817 9.690000e-100 374.0
14 TraesCS1A01G053900 chr1B 92.887 239 12 3 2185 2421 56059197 56058962 2.730000e-90 342.0
15 TraesCS1A01G053900 chr1D 93.964 613 25 9 580 1184 36320103 36319495 0.000000e+00 917.0
16 TraesCS1A01G053900 chr1D 88.908 595 53 5 1 583 36321816 36321223 0.000000e+00 721.0
17 TraesCS1A01G053900 chr1D 87.269 487 31 12 1605 2076 36319497 36319027 7.030000e-146 527.0
18 TraesCS1A01G053900 chr1D 91.319 288 24 1 1371 1657 36359700 36359987 2.670000e-105 392.0
19 TraesCS1A01G053900 chr1D 90.672 268 23 2 2597 2863 36318039 36317773 3.510000e-94 355.0
20 TraesCS1A01G053900 chr1D 87.361 269 31 3 2597 2863 36360690 36360957 3.580000e-79 305.0
21 TraesCS1A01G053900 chr1D 90.789 228 18 3 2184 2410 36319024 36318799 4.640000e-78 302.0
22 TraesCS1A01G053900 chr1D 86.802 197 11 7 2404 2597 36318340 36318156 3.740000e-49 206.0
23 TraesCS1A01G053900 chr1D 97.561 41 1 0 2597 2637 36318391 36318351 1.420000e-08 71.3
24 TraesCS1A01G053900 chr2A 84.937 239 29 4 2244 2481 711648876 711648644 4.770000e-58 235.0
25 TraesCS1A01G053900 chr4D 81.818 242 40 3 2244 2482 259157956 259157716 1.740000e-47 200.0
26 TraesCS1A01G053900 chr4A 81.328 241 42 2 2244 2481 34265002 34265242 2.910000e-45 193.0
27 TraesCS1A01G053900 chr7B 83.750 80 8 5 2489 2566 418016137 418016061 1.420000e-08 71.3


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 TraesCS1A01G053900 chr1A 35538945 35541807 2862 True 5288.000000 5288 100.000000 1 2863 1 chr1A.!!$R1 2862
1 TraesCS1A01G053900 chr1A 35573764 35575373 1609 False 427.000000 455 85.771000 1668 2597 2 chr1A.!!$F1 929
2 TraesCS1A01G053900 chr1A 35488154 35489289 1135 True 283.100000 510 90.992250 2184 2863 4 chr1A.!!$R2 679
3 TraesCS1A01G053900 chr1B 56136174 56137817 1643 False 1006.500000 1639 88.848500 1 2597 2 chr1B.!!$F1 2596
4 TraesCS1A01G053900 chr1B 56058962 56061051 2089 True 623.250000 1077 89.294250 1 2421 4 chr1B.!!$R3 2420
5 TraesCS1A01G053900 chr1D 36317773 36321816 4043 True 442.757143 917 90.852143 1 2863 7 chr1D.!!$R1 2862
6 TraesCS1A01G053900 chr1D 36359700 36360957 1257 False 348.500000 392 89.340000 1371 2863 2 chr1D.!!$F1 1492

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
32 33 0.042131 AACCCTCGGAGACCACCATA 59.958 55.0 6.58 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 3086 0.034616 AGAGTTGCACCTCTGAGCAC 59.965 55.0 13.66 0.0 40.3 4.4 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
32 33 0.042131 AACCCTCGGAGACCACCATA 59.958 55.000 6.58 0.00 0.00 2.74
100 101 4.960469 AGGATGATGCATTCAAAGGTTCAT 59.040 37.500 0.00 0.00 38.03 2.57
127 128 8.571336 AGTTGATATCTTAGCAAAATATGGTGC 58.429 33.333 3.98 3.22 40.70 5.01
146 147 6.189859 TGGTGCTTATTTCATCTTGATTCCT 58.810 36.000 0.00 0.00 0.00 3.36
163 164 7.860918 TGATTCCTGATGAAGAAGAATGAAG 57.139 36.000 0.00 0.00 36.14 3.02
171 172 3.244215 TGAAGAAGAATGAAGCCACGTCT 60.244 43.478 0.00 0.00 0.00 4.18
172 173 2.693069 AGAAGAATGAAGCCACGTCTG 58.307 47.619 0.00 0.00 0.00 3.51
185 186 3.512680 CCACGTCTGTTGTCTTATCCTC 58.487 50.000 0.00 0.00 0.00 3.71
195 196 3.951663 TGTCTTATCCTCGTCTCACTCA 58.048 45.455 0.00 0.00 0.00 3.41
224 225 0.544357 AGACACCGAGTGATTCCCCA 60.544 55.000 10.46 0.00 36.96 4.96
322 323 3.306088 CGGTGTCTCATGAGGTTAACTGT 60.306 47.826 22.42 0.00 0.00 3.55
325 327 5.179555 GGTGTCTCATGAGGTTAACTGTTTC 59.820 44.000 22.42 0.01 0.00 2.78
354 356 1.933853 GGTGCTCCACTATAACTTGCG 59.066 52.381 0.00 0.00 34.40 4.85
426 428 6.560253 TTCTTCTGTAGGACATTTTTCTGC 57.440 37.500 0.00 0.00 0.00 4.26
427 429 5.003804 TCTTCTGTAGGACATTTTTCTGCC 58.996 41.667 0.00 0.00 0.00 4.85
432 434 0.388520 GGACATTTTTCTGCCGTGCC 60.389 55.000 0.00 0.00 0.00 5.01
450 452 2.760092 TGCCCACTGATTTCATTAAGGC 59.240 45.455 0.00 0.00 38.37 4.35
453 455 4.141869 GCCCACTGATTTCATTAAGGCAAT 60.142 41.667 0.00 0.00 37.80 3.56
509 511 1.063174 GCAAGGAGAAACATAGCGCTG 59.937 52.381 22.90 7.81 0.00 5.18
512 514 3.887621 AGGAGAAACATAGCGCTGTAA 57.112 42.857 22.90 0.00 0.00 2.41
529 531 6.699204 GCGCTGTAATGCTATCATATACATCT 59.301 38.462 0.00 0.00 31.89 2.90
541 552 6.823286 TCATATACATCTGGAAAGGTGGAA 57.177 37.500 0.00 0.00 0.00 3.53
592 1729 2.205342 CAATCCCTAAGAACCCCCAGA 58.795 52.381 0.00 0.00 0.00 3.86
677 1817 3.006217 TCATATCTCCCGAGCACATTCTG 59.994 47.826 0.00 0.00 0.00 3.02
801 1941 7.174413 TCCAATGGAAAATCAAGTACAGATCA 58.826 34.615 0.00 0.00 0.00 2.92
817 1957 3.386726 CAGATCACATGAATTGGGCCATT 59.613 43.478 7.26 0.00 0.00 3.16
818 1958 3.386726 AGATCACATGAATTGGGCCATTG 59.613 43.478 7.26 3.19 0.00 2.82
869 2009 1.507140 AACCTGTTGAGGACTCCACA 58.493 50.000 6.15 6.15 42.93 4.17
876 2016 3.644966 TTGAGGACTCCACAACAAACT 57.355 42.857 3.96 0.00 29.73 2.66
923 2063 8.214721 AGCAAATGTATAAACTTAGAAGAGCC 57.785 34.615 0.00 0.00 0.00 4.70
1129 2271 2.609350 GCAACTAATACAACGTCCGGA 58.391 47.619 0.00 0.00 0.00 5.14
1138 2280 3.116079 ACAACGTCCGGACAGTTTATT 57.884 42.857 32.80 18.92 0.00 1.40
1157 2299 0.473755 TCTTGCAGGTTCTGAAGGCA 59.526 50.000 7.09 7.09 32.44 4.75
1165 2307 0.796927 GTTCTGAAGGCAAGGTACGC 59.203 55.000 0.00 0.00 0.00 4.42
1304 2450 2.037772 ACTAAAGTGCTGGTCTGGAGTG 59.962 50.000 0.00 0.00 0.00 3.51
1305 2451 1.131638 AAAGTGCTGGTCTGGAGTGA 58.868 50.000 0.00 0.00 0.00 3.41
1306 2452 0.394565 AAGTGCTGGTCTGGAGTGAC 59.605 55.000 0.00 0.00 36.31 3.67
1307 2453 0.760567 AGTGCTGGTCTGGAGTGACA 60.761 55.000 0.00 0.00 38.61 3.58
1308 2454 0.106708 GTGCTGGTCTGGAGTGACAA 59.893 55.000 0.00 0.00 38.61 3.18
1309 2455 1.059098 TGCTGGTCTGGAGTGACAAT 58.941 50.000 0.00 0.00 38.61 2.71
1310 2456 1.421268 TGCTGGTCTGGAGTGACAATT 59.579 47.619 0.00 0.00 38.61 2.32
1311 2457 2.158623 TGCTGGTCTGGAGTGACAATTT 60.159 45.455 0.00 0.00 38.61 1.82
1312 2458 2.887152 GCTGGTCTGGAGTGACAATTTT 59.113 45.455 0.00 0.00 38.61 1.82
1313 2459 3.319122 GCTGGTCTGGAGTGACAATTTTT 59.681 43.478 0.00 0.00 38.61 1.94
1331 2477 1.981256 TTTTTGAGGCAGGTCTGGAC 58.019 50.000 0.00 0.00 0.00 4.02
1332 2478 1.140312 TTTTGAGGCAGGTCTGGACT 58.860 50.000 0.00 0.00 0.00 3.85
1333 2479 0.687354 TTTGAGGCAGGTCTGGACTC 59.313 55.000 0.00 0.00 0.00 3.36
1334 2480 0.178921 TTGAGGCAGGTCTGGACTCT 60.179 55.000 0.00 0.00 0.00 3.24
1335 2481 0.902048 TGAGGCAGGTCTGGACTCTG 60.902 60.000 11.89 11.89 34.72 3.35
1336 2482 1.611851 AGGCAGGTCTGGACTCTGG 60.612 63.158 15.51 1.58 33.29 3.86
1337 2483 1.610673 GGCAGGTCTGGACTCTGGA 60.611 63.158 15.51 0.00 33.29 3.86
1338 2484 1.612395 GGCAGGTCTGGACTCTGGAG 61.612 65.000 15.51 0.00 33.29 3.86
1339 2485 0.902516 GCAGGTCTGGACTCTGGAGT 60.903 60.000 2.62 2.62 45.84 3.85
1356 2502 3.843619 TGGAGTGACAATTGGATACCAGA 59.156 43.478 10.83 0.00 33.81 3.86
1357 2503 4.288366 TGGAGTGACAATTGGATACCAGAA 59.712 41.667 10.83 0.00 33.81 3.02
1358 2504 4.878397 GGAGTGACAATTGGATACCAGAAG 59.122 45.833 10.83 0.00 33.81 2.85
1359 2505 5.338381 GGAGTGACAATTGGATACCAGAAGA 60.338 44.000 10.83 0.00 33.81 2.87
1360 2506 5.491982 AGTGACAATTGGATACCAGAAGAC 58.508 41.667 10.83 0.00 33.81 3.01
1361 2507 5.249393 AGTGACAATTGGATACCAGAAGACT 59.751 40.000 10.83 0.00 33.81 3.24
1362 2508 5.940470 GTGACAATTGGATACCAGAAGACTT 59.060 40.000 10.83 0.00 33.81 3.01
1363 2509 6.431234 GTGACAATTGGATACCAGAAGACTTT 59.569 38.462 10.83 0.00 33.81 2.66
1364 2510 6.430925 TGACAATTGGATACCAGAAGACTTTG 59.569 38.462 10.83 0.00 33.81 2.77
1365 2511 5.183904 ACAATTGGATACCAGAAGACTTTGC 59.816 40.000 10.83 0.00 33.81 3.68
1366 2512 4.640771 TTGGATACCAGAAGACTTTGCT 57.359 40.909 0.00 0.00 33.81 3.91
1401 2576 0.813821 GGCTTCTGATGGGAGTTTGC 59.186 55.000 0.00 0.00 0.00 3.68
1438 2613 1.616865 AGCAGTACTTCGTACCTGCAA 59.383 47.619 17.94 0.00 41.18 4.08
1467 2642 2.606108 GCGAAAATGAAAATTCGGCCT 58.394 42.857 0.00 0.00 46.28 5.19
1481 2656 3.112709 GCCTTCCGCTCGACACAC 61.113 66.667 0.00 0.00 0.00 3.82
1509 2684 1.533033 TTCCTCGCCTGTCACCTGA 60.533 57.895 0.00 0.00 0.00 3.86
1532 2707 8.690203 TGATAAAAATTCTGGTGTTCTCTTCA 57.310 30.769 0.00 0.00 0.00 3.02
1571 2746 7.196331 ACAAGTTAGCACTGAATTTCAACTTC 58.804 34.615 8.31 2.11 33.68 3.01
1601 2776 1.379576 AGTCGGGGGTCCTAGTTCG 60.380 63.158 0.00 0.00 0.00 3.95
1666 2842 4.802999 CCTCCAGTTGCTCAAAAGATTTC 58.197 43.478 0.00 0.00 0.00 2.17
1681 2857 6.976934 AAAGATTTCTACCTTTGCTTGGAA 57.023 33.333 0.00 0.00 32.00 3.53
1771 2947 0.803380 CTAATGCAAAAGCCAGCGCC 60.803 55.000 2.29 0.00 34.57 6.53
1826 3028 2.234908 CTCTGAATCCCGTCAAGGTTCT 59.765 50.000 0.00 0.00 38.74 3.01
1833 3035 2.304761 TCCCGTCAAGGTTCTATTTGCT 59.695 45.455 0.00 0.00 38.74 3.91
1878 3084 2.032799 GGTTGACATTGCGTGAGTTCAA 59.967 45.455 0.00 0.00 0.00 2.69
1883 3089 1.980844 CATTGCGTGAGTTCAATGTGC 59.019 47.619 6.75 0.00 42.58 4.57
1884 3090 1.308047 TTGCGTGAGTTCAATGTGCT 58.692 45.000 0.00 0.00 0.00 4.40
1885 3091 0.867746 TGCGTGAGTTCAATGTGCTC 59.132 50.000 0.00 0.00 0.00 4.26
1886 3092 0.867746 GCGTGAGTTCAATGTGCTCA 59.132 50.000 5.69 5.69 36.97 4.26
1887 3093 1.136141 GCGTGAGTTCAATGTGCTCAG 60.136 52.381 9.00 6.11 39.56 3.35
1888 3094 2.407090 CGTGAGTTCAATGTGCTCAGA 58.593 47.619 9.00 0.00 39.56 3.27
1889 3095 2.411069 CGTGAGTTCAATGTGCTCAGAG 59.589 50.000 9.00 0.00 39.56 3.35
1895 3113 1.202794 TCAATGTGCTCAGAGGTGCAA 60.203 47.619 0.00 0.00 44.27 4.08
1939 3157 9.543783 GGAAGAAAATGTTTATAGACGTAGGAT 57.456 33.333 0.00 0.00 0.00 3.24
2047 3265 9.345517 AGTAAAATGACATTCAACATTTCATCG 57.654 29.630 0.05 0.00 43.07 3.84
2084 3302 7.920160 ATGACATTTCTCTTCTTTTCTCTCC 57.080 36.000 0.00 0.00 0.00 3.71
2085 3303 7.072263 TGACATTTCTCTTCTTTTCTCTCCT 57.928 36.000 0.00 0.00 0.00 3.69
2087 3305 8.091449 TGACATTTCTCTTCTTTTCTCTCCTAC 58.909 37.037 0.00 0.00 0.00 3.18
2088 3306 8.201242 ACATTTCTCTTCTTTTCTCTCCTACT 57.799 34.615 0.00 0.00 0.00 2.57
2089 3307 8.655901 ACATTTCTCTTCTTTTCTCTCCTACTT 58.344 33.333 0.00 0.00 0.00 2.24
2090 3308 9.150348 CATTTCTCTTCTTTTCTCTCCTACTTC 57.850 37.037 0.00 0.00 0.00 3.01
2135 3353 1.248486 GCTCCTCCTTTGTCAAACCC 58.752 55.000 0.00 0.00 0.00 4.11
2137 3355 0.841289 TCCTCCTTTGTCAAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2179 4148 2.481952 CCTTGGAGAGAGTTCTTTTGCG 59.518 50.000 0.00 0.00 32.53 4.85
2229 4198 0.463295 CTCTCATGGATTGGCGCAGT 60.463 55.000 10.83 0.00 0.00 4.40
2242 4211 0.730494 GCGCAGTCAAGCAAACCATC 60.730 55.000 0.30 0.00 0.00 3.51
2252 4221 4.461431 TCAAGCAAACCATCGTACTCTCTA 59.539 41.667 0.00 0.00 0.00 2.43
2478 5366 5.998363 GGCTAATAAACCCAGATGAAGGTAG 59.002 44.000 0.00 0.00 34.45 3.18
2489 5377 6.015010 CCCAGATGAAGGTAGTATCTACCAAG 60.015 46.154 22.59 8.20 39.99 3.61
2493 5381 7.839705 AGATGAAGGTAGTATCTACCAAGACAA 59.160 37.037 22.59 7.23 39.99 3.18
2498 5386 7.126733 AGGTAGTATCTACCAAGACAATGACT 58.873 38.462 22.59 0.00 39.99 3.41
2499 5387 8.280084 AGGTAGTATCTACCAAGACAATGACTA 58.720 37.037 22.59 0.00 39.99 2.59
2500 5388 9.080097 GGTAGTATCTACCAAGACAATGACTAT 57.920 37.037 17.75 0.00 37.53 2.12
2501 5389 9.900710 GTAGTATCTACCAAGACAATGACTATG 57.099 37.037 0.00 0.00 33.57 2.23
2502 5390 8.768501 AGTATCTACCAAGACAATGACTATGA 57.231 34.615 0.00 0.00 33.57 2.15
2503 5391 9.201989 AGTATCTACCAAGACAATGACTATGAA 57.798 33.333 0.00 0.00 33.57 2.57
2504 5392 9.469807 GTATCTACCAAGACAATGACTATGAAG 57.530 37.037 0.00 0.00 33.57 3.02
2505 5393 7.482169 TCTACCAAGACAATGACTATGAAGT 57.518 36.000 0.00 0.00 39.21 3.01
2506 5394 7.907389 TCTACCAAGACAATGACTATGAAGTT 58.093 34.615 0.00 0.00 35.56 2.66
2507 5395 6.808008 ACCAAGACAATGACTATGAAGTTG 57.192 37.500 0.00 0.00 35.56 3.16
2508 5396 6.533730 ACCAAGACAATGACTATGAAGTTGA 58.466 36.000 0.00 0.00 35.56 3.18
2610 5615 2.249413 CTCGGTCCAGCTTGCCATCT 62.249 60.000 0.00 0.00 0.00 2.90
2623 5628 3.716195 CATCTGACGGGCCACCCA 61.716 66.667 4.39 0.00 45.83 4.51
2669 5674 2.024414 GAGTCTTGCACAAGTTTGGGT 58.976 47.619 10.05 0.00 39.38 4.51
2706 5712 5.472820 CCTTAGATTTCATCTCCCAATGAGC 59.527 44.000 0.00 0.00 41.18 4.26
2721 5727 0.835276 TGAGCAGGGGATCACATCAG 59.165 55.000 0.00 0.00 33.81 2.90
2744 5750 1.081513 ACTTATACTCCCACCACCCCA 59.918 52.381 0.00 0.00 0.00 4.96
2745 5751 1.768870 CTTATACTCCCACCACCCCAG 59.231 57.143 0.00 0.00 0.00 4.45
2750 5756 0.839946 CTCCCACCACCCCAGAATAG 59.160 60.000 0.00 0.00 0.00 1.73
2756 5762 0.331278 CCACCCCAGAATAGTTGGCA 59.669 55.000 0.00 0.00 34.26 4.92
2790 5796 2.409948 AGATAGTGGGCAGCAGAAAC 57.590 50.000 0.00 0.00 0.00 2.78
2794 5800 1.827789 GTGGGCAGCAGAAACACCA 60.828 57.895 0.00 0.00 0.00 4.17
2818 5824 4.899239 GACTGAGATGCCCCCGCG 62.899 72.222 0.00 0.00 38.08 6.46
2845 5851 4.876107 TCTTATTTGAGGCCGTGAAATCTC 59.124 41.667 11.53 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.104777 TAGGATCTGGAGGGCTGCAT 60.105 55.000 0.50 0.00 0.00 3.96
121 122 6.837568 AGGAATCAAGATGAAATAAGCACCAT 59.162 34.615 0.00 0.00 0.00 3.55
144 145 4.096081 GTGGCTTCATTCTTCTTCATCAGG 59.904 45.833 0.00 0.00 0.00 3.86
146 147 3.686241 CGTGGCTTCATTCTTCTTCATCA 59.314 43.478 0.00 0.00 0.00 3.07
163 164 2.000447 GGATAAGACAACAGACGTGGC 59.000 52.381 0.00 0.00 0.00 5.01
171 172 4.079970 AGTGAGACGAGGATAAGACAACA 58.920 43.478 0.00 0.00 0.00 3.33
172 173 4.156190 TGAGTGAGACGAGGATAAGACAAC 59.844 45.833 0.00 0.00 0.00 3.32
185 186 5.163612 TGTCTGAATTCCTATGAGTGAGACG 60.164 44.000 2.27 0.00 29.73 4.18
195 196 4.023980 TCACTCGGTGTCTGAATTCCTAT 58.976 43.478 2.27 0.00 34.79 2.57
322 323 2.956132 TGGAGCACCCATGAAAAGAAA 58.044 42.857 0.00 0.00 40.82 2.52
354 356 4.519730 ACGTTCTGAGGGTATATAGAGCAC 59.480 45.833 0.00 0.00 0.00 4.40
426 428 1.176527 AATGAAATCAGTGGGCACGG 58.823 50.000 0.00 0.00 36.20 4.94
427 429 3.181497 CCTTAATGAAATCAGTGGGCACG 60.181 47.826 0.00 0.00 36.20 5.34
432 434 6.211587 TGATTGCCTTAATGAAATCAGTGG 57.788 37.500 9.44 0.00 34.86 4.00
450 452 9.139174 GTGGTTTGTAATTAACCTTCATGATTG 57.861 33.333 9.48 0.00 44.32 2.67
453 455 8.356657 CAAGTGGTTTGTAATTAACCTTCATGA 58.643 33.333 9.48 0.00 44.32 3.07
512 514 8.045507 CACCTTTCCAGATGTATATGATAGCAT 58.954 37.037 0.00 0.00 38.54 3.79
529 531 2.517959 CAATCAGCTTCCACCTTTCCA 58.482 47.619 0.00 0.00 0.00 3.53
541 552 0.613012 GAGGGGCAAACCAATCAGCT 60.613 55.000 0.00 0.00 42.91 4.24
572 584 2.205342 TCTGGGGGTTCTTAGGGATTG 58.795 52.381 0.00 0.00 0.00 2.67
609 1748 9.836864 TCAAGAACATTATGATGCTACAGTTAT 57.163 29.630 0.00 0.00 36.72 1.89
616 1755 9.060347 GGAGAATTCAAGAACATTATGATGCTA 57.940 33.333 8.44 0.00 36.72 3.49
677 1817 4.527509 TCTGATCTTCAGTCACAGGAAC 57.472 45.455 4.56 0.00 44.58 3.62
738 1878 1.153086 GAAGGCTGGCGATGGTGAT 60.153 57.895 0.00 0.00 0.00 3.06
801 1941 0.542805 GCCAATGGCCCAATTCATGT 59.457 50.000 14.47 0.00 44.06 3.21
817 1957 1.289694 CCGCTTGCAAAATCAGCCA 59.710 52.632 0.00 0.00 0.00 4.75
818 1958 1.010419 CACCGCTTGCAAAATCAGCC 61.010 55.000 0.00 0.00 0.00 4.85
820 1960 1.010419 GCCACCGCTTGCAAAATCAG 61.010 55.000 0.00 0.00 0.00 2.90
869 2009 6.150976 TGTTCTCTCACACAATTGAGTTTGTT 59.849 34.615 13.59 0.00 43.19 2.83
876 2016 5.034852 TCCTTGTTCTCTCACACAATTGA 57.965 39.130 13.59 0.00 32.50 2.57
885 2025 4.090761 ACATTTGCTCCTTGTTCTCTCA 57.909 40.909 0.00 0.00 0.00 3.27
988 2129 1.003355 ACCACATGTCTTCAGCCCG 60.003 57.895 0.00 0.00 0.00 6.13
1129 2271 5.376625 TCAGAACCTGCAAGAATAAACTGT 58.623 37.500 0.00 0.00 34.07 3.55
1138 2280 0.473755 TGCCTTCAGAACCTGCAAGA 59.526 50.000 0.00 0.00 34.07 3.02
1157 2299 0.535335 ATGACATCGTGGCGTACCTT 59.465 50.000 0.00 0.00 36.63 3.50
1188 2334 1.702182 TGCATTGCCAGAGAAAACCA 58.298 45.000 6.12 0.00 0.00 3.67
1312 2458 1.494721 AGTCCAGACCTGCCTCAAAAA 59.505 47.619 0.00 0.00 0.00 1.94
1313 2459 1.072331 GAGTCCAGACCTGCCTCAAAA 59.928 52.381 8.91 0.00 31.52 2.44
1314 2460 0.687354 GAGTCCAGACCTGCCTCAAA 59.313 55.000 8.91 0.00 31.52 2.69
1315 2461 0.178921 AGAGTCCAGACCTGCCTCAA 60.179 55.000 13.60 0.00 32.75 3.02
1316 2462 0.902048 CAGAGTCCAGACCTGCCTCA 60.902 60.000 13.60 0.00 32.75 3.86
1317 2463 1.612395 CCAGAGTCCAGACCTGCCTC 61.612 65.000 9.49 6.76 32.15 4.70
1318 2464 1.611851 CCAGAGTCCAGACCTGCCT 60.612 63.158 9.49 0.00 32.15 4.75
1319 2465 1.610673 TCCAGAGTCCAGACCTGCC 60.611 63.158 9.49 0.00 32.15 4.85
1320 2466 0.902516 ACTCCAGAGTCCAGACCTGC 60.903 60.000 9.49 0.00 36.92 4.85
1321 2467 0.894141 CACTCCAGAGTCCAGACCTG 59.106 60.000 0.00 8.48 40.20 4.00
1322 2468 0.780637 TCACTCCAGAGTCCAGACCT 59.219 55.000 0.00 0.00 40.20 3.85
1323 2469 0.892063 GTCACTCCAGAGTCCAGACC 59.108 60.000 0.00 0.00 40.20 3.85
1324 2470 1.621992 TGTCACTCCAGAGTCCAGAC 58.378 55.000 0.00 3.85 40.20 3.51
1325 2471 2.381752 TTGTCACTCCAGAGTCCAGA 57.618 50.000 0.00 0.00 40.20 3.86
1326 2472 3.332919 CAATTGTCACTCCAGAGTCCAG 58.667 50.000 0.00 0.00 40.20 3.86
1327 2473 2.038952 CCAATTGTCACTCCAGAGTCCA 59.961 50.000 4.43 0.00 40.20 4.02
1328 2474 2.303022 TCCAATTGTCACTCCAGAGTCC 59.697 50.000 4.43 0.00 40.20 3.85
1329 2475 3.685139 TCCAATTGTCACTCCAGAGTC 57.315 47.619 4.43 0.00 40.20 3.36
1330 2476 4.080863 GGTATCCAATTGTCACTCCAGAGT 60.081 45.833 4.43 0.00 43.61 3.24
1331 2477 4.080919 TGGTATCCAATTGTCACTCCAGAG 60.081 45.833 4.43 0.00 0.00 3.35
1332 2478 3.843619 TGGTATCCAATTGTCACTCCAGA 59.156 43.478 4.43 0.00 0.00 3.86
1333 2479 4.080919 TCTGGTATCCAATTGTCACTCCAG 60.081 45.833 18.95 18.95 40.55 3.86
1334 2480 3.843619 TCTGGTATCCAATTGTCACTCCA 59.156 43.478 4.43 5.72 30.80 3.86
1335 2481 4.487714 TCTGGTATCCAATTGTCACTCC 57.512 45.455 4.43 1.40 30.80 3.85
1336 2482 5.582665 GTCTTCTGGTATCCAATTGTCACTC 59.417 44.000 4.43 0.00 30.80 3.51
1337 2483 5.249393 AGTCTTCTGGTATCCAATTGTCACT 59.751 40.000 4.43 0.00 30.80 3.41
1338 2484 5.491982 AGTCTTCTGGTATCCAATTGTCAC 58.508 41.667 4.43 0.00 30.80 3.67
1339 2485 5.762179 AGTCTTCTGGTATCCAATTGTCA 57.238 39.130 4.43 0.00 30.80 3.58
1438 2613 4.599047 TTTTCATTTTCGCCTCCACATT 57.401 36.364 0.00 0.00 0.00 2.71
1488 2663 1.122019 AGGTGACAGGCGAGGAAGTT 61.122 55.000 0.00 0.00 0.00 2.66
1509 2684 8.697507 ACTGAAGAGAACACCAGAATTTTTAT 57.302 30.769 0.00 0.00 0.00 1.40
1526 2701 1.216710 GGCACCTCGGACTGAAGAG 59.783 63.158 0.00 0.00 0.00 2.85
1532 2707 0.542232 ACTTGTAGGCACCTCGGACT 60.542 55.000 0.00 0.00 0.00 3.85
1571 2746 0.179000 CCCCGACTCCCTGATCAAAG 59.821 60.000 0.00 0.00 0.00 2.77
1878 3084 0.399454 AGTTGCACCTCTGAGCACAT 59.601 50.000 0.00 0.00 41.05 3.21
1880 3086 0.034616 AGAGTTGCACCTCTGAGCAC 59.965 55.000 13.66 0.00 40.30 4.40
1881 3087 0.761187 AAGAGTTGCACCTCTGAGCA 59.239 50.000 15.21 0.00 40.93 4.26
1882 3088 1.155042 CAAGAGTTGCACCTCTGAGC 58.845 55.000 15.21 0.00 40.93 4.26
1895 3113 1.425066 TCCAGGAACCAATGCAAGAGT 59.575 47.619 0.00 0.00 0.00 3.24
1908 3126 7.881232 ACGTCTATAAACATTTTCTTCCAGGAA 59.119 33.333 0.71 0.71 0.00 3.36
1939 3157 8.582657 TGCAAAAATAACCTTAATACTGCCTA 57.417 30.769 0.00 0.00 0.00 3.93
2063 3281 8.201242 AGTAGGAGAGAAAAGAAGAGAAATGT 57.799 34.615 0.00 0.00 0.00 2.71
2076 3294 6.545666 TGTGCATTTTTGAAGTAGGAGAGAAA 59.454 34.615 0.00 0.00 0.00 2.52
2082 3300 4.892934 ACCTTGTGCATTTTTGAAGTAGGA 59.107 37.500 0.00 0.00 0.00 2.94
2083 3301 5.200368 ACCTTGTGCATTTTTGAAGTAGG 57.800 39.130 0.00 0.00 0.00 3.18
2084 3302 7.867403 ACATAACCTTGTGCATTTTTGAAGTAG 59.133 33.333 0.00 0.00 0.00 2.57
2085 3303 7.721402 ACATAACCTTGTGCATTTTTGAAGTA 58.279 30.769 0.00 0.00 0.00 2.24
2087 3305 6.129115 CGACATAACCTTGTGCATTTTTGAAG 60.129 38.462 0.00 0.00 0.00 3.02
2088 3306 5.689514 CGACATAACCTTGTGCATTTTTGAA 59.310 36.000 0.00 0.00 0.00 2.69
2089 3307 5.218885 CGACATAACCTTGTGCATTTTTGA 58.781 37.500 0.00 0.00 0.00 2.69
2090 3308 4.981674 ACGACATAACCTTGTGCATTTTTG 59.018 37.500 0.00 0.00 0.00 2.44
2135 3353 2.323939 TTGGCAAAATAGTTGCGACG 57.676 45.000 0.00 0.00 45.78 5.12
2137 3355 4.021544 AGGAAATTGGCAAAATAGTTGCGA 60.022 37.500 3.01 0.00 45.78 5.10
2166 4135 0.251341 ATGGGGCGCAAAAGAACTCT 60.251 50.000 10.83 0.00 0.00 3.24
2179 4148 2.084546 GTGAGTTTGACTACATGGGGC 58.915 52.381 0.00 0.00 0.00 5.80
2229 4198 3.258372 AGAGAGTACGATGGTTTGCTTGA 59.742 43.478 0.00 0.00 0.00 3.02
2237 4206 3.139850 CGGACATAGAGAGTACGATGGT 58.860 50.000 0.00 0.00 45.96 3.55
2242 4211 1.964552 ACCCGGACATAGAGAGTACG 58.035 55.000 0.73 0.00 42.81 3.67
2252 4221 2.105993 GGAGCCTAATAAACCCGGACAT 59.894 50.000 0.73 0.00 0.00 3.06
2429 5316 7.787424 CCCCCTTATATTTTGGATCCAACTTTA 59.213 37.037 27.04 17.53 35.46 1.85
2448 5335 3.750221 TCTGGGTTTATTAGCCCCCTTA 58.250 45.455 0.76 0.00 44.11 2.69
2472 5360 7.620094 AGTCATTGTCTTGGTAGATACTACCTT 59.380 37.037 22.81 3.44 38.39 3.50
2478 5366 9.469807 CTTCATAGTCATTGTCTTGGTAGATAC 57.530 37.037 0.00 0.00 31.86 2.24
2489 5377 7.856145 AGGAATCAACTTCATAGTCATTGTC 57.144 36.000 0.00 0.00 35.41 3.18
2493 5381 6.825721 GGTCAAGGAATCAACTTCATAGTCAT 59.174 38.462 0.00 0.00 35.41 3.06
2498 5386 7.127186 TGGATAGGTCAAGGAATCAACTTCATA 59.873 37.037 0.00 0.00 35.41 2.15
2499 5387 6.069440 TGGATAGGTCAAGGAATCAACTTCAT 60.069 38.462 0.00 0.00 35.41 2.57
2500 5388 5.250543 TGGATAGGTCAAGGAATCAACTTCA 59.749 40.000 0.00 0.00 35.41 3.02
2501 5389 5.586643 GTGGATAGGTCAAGGAATCAACTTC 59.413 44.000 0.00 0.00 0.00 3.01
2502 5390 5.251700 AGTGGATAGGTCAAGGAATCAACTT 59.748 40.000 0.00 0.00 30.06 2.66
2503 5391 4.785376 AGTGGATAGGTCAAGGAATCAACT 59.215 41.667 0.00 0.00 29.53 3.16
2504 5392 4.878397 CAGTGGATAGGTCAAGGAATCAAC 59.122 45.833 0.00 0.00 0.00 3.18
2505 5393 4.536090 ACAGTGGATAGGTCAAGGAATCAA 59.464 41.667 0.00 0.00 0.00 2.57
2506 5394 4.104086 ACAGTGGATAGGTCAAGGAATCA 58.896 43.478 0.00 0.00 0.00 2.57
2507 5395 4.443598 GGACAGTGGATAGGTCAAGGAATC 60.444 50.000 0.00 0.00 33.26 2.52
2508 5396 3.456277 GGACAGTGGATAGGTCAAGGAAT 59.544 47.826 0.00 0.00 33.26 3.01
2548 5436 2.185387 TCTTGTAACCCTAGGCCTCAC 58.815 52.381 9.68 0.00 0.00 3.51
2549 5437 2.634639 TCTTGTAACCCTAGGCCTCA 57.365 50.000 9.68 0.00 0.00 3.86
2654 5659 2.094286 CAGACAACCCAAACTTGTGCAA 60.094 45.455 0.00 0.00 31.83 4.08
2669 5674 6.003326 TGAAATCTAAGGCATGTTCAGACAA 58.997 36.000 0.00 0.00 39.66 3.18
2706 5712 1.064906 AGTTGCTGATGTGATCCCCTG 60.065 52.381 0.00 0.00 0.00 4.45
2721 5727 2.640184 GGTGGTGGGAGTATAAGTTGC 58.360 52.381 0.00 0.00 0.00 4.17
2767 5773 1.483827 TCTGCTGCCCACTATCTTCAG 59.516 52.381 0.00 0.00 0.00 3.02
2794 5800 2.460669 GGGGCATCTCAGTCCAAAATT 58.539 47.619 0.00 0.00 34.02 1.82
2803 5809 4.598894 CTCGCGGGGGCATCTCAG 62.599 72.222 6.13 0.00 0.00 3.35
2818 5824 2.093658 TCACGGCCTCAAATAAGACCTC 60.094 50.000 0.00 0.00 0.00 3.85
2827 5833 1.438651 CGAGATTTCACGGCCTCAAA 58.561 50.000 0.00 0.00 0.00 2.69
2831 5837 2.125106 GGCGAGATTTCACGGCCT 60.125 61.111 11.79 0.00 46.26 5.19


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

AutoCloner maintained by Alex Coulton.