Multiple sequence alignment - TraesCS2A01G433600

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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 TraesCS2A01G433600 chr2A 100.000 3105 0 0 1 3105 686705714 686702610 0.000000e+00 5734
1 TraesCS2A01G433600 chr2A 85.374 1217 130 35 910 2103 686778270 686777079 0.000000e+00 1218
2 TraesCS2A01G433600 chr2A 83.468 248 17 15 106 347 686778940 686778711 3.140000e-50 209
3 TraesCS2A01G433600 chr2A 87.640 178 22 0 1411 1588 686797549 686797726 1.130000e-49 207
4 TraesCS2A01G433600 chr2A 86.111 180 23 2 1712 1890 686797862 686798040 3.160000e-45 193
5 TraesCS2A01G433600 chr2D 91.187 2746 121 51 440 3101 543848206 543845498 0.000000e+00 3618
6 TraesCS2A01G433600 chr2D 85.131 686 72 22 946 1608 544171648 544170970 0.000000e+00 675
7 TraesCS2A01G433600 chr2D 92.195 410 31 1 1697 2106 544170849 544170441 2.080000e-161 579
8 TraesCS2A01G433600 chr2D 91.803 305 19 2 49 347 543848508 543848204 1.330000e-113 420
9 TraesCS2A01G433600 chr2D 81.847 314 25 21 36 341 544172369 544172080 5.180000e-58 235
10 TraesCS2A01G433600 chr2D 87.079 178 23 0 1411 1588 544259872 544260049 5.250000e-48 202
11 TraesCS2A01G433600 chr2D 85.475 179 26 0 1712 1890 544260178 544260356 1.470000e-43 187
12 TraesCS2A01G433600 chr2D 87.129 101 12 1 343 442 54580749 54580849 2.530000e-21 113
13 TraesCS2A01G433600 chr2B 87.662 2164 125 59 440 2524 649481145 649479045 0.000000e+00 2386
14 TraesCS2A01G433600 chr2B 93.526 587 24 8 2524 3101 649478212 649477631 0.000000e+00 861
15 TraesCS2A01G433600 chr2B 90.751 346 22 4 8 347 649481484 649481143 1.310000e-123 453
16 TraesCS2A01G433600 chr2B 87.640 178 22 0 1411 1588 649670188 649670365 1.130000e-49 207
17 TraesCS2A01G433600 chr6D 83.200 250 41 1 1703 1952 426984491 426984739 8.660000e-56 228
18 TraesCS2A01G433600 chr6D 90.698 86 7 1 357 442 50772015 50771931 2.530000e-21 113
19 TraesCS2A01G433600 chr6B 82.609 253 42 2 1703 1954 642724705 642724956 4.030000e-54 222
20 TraesCS2A01G433600 chr6A 82.400 250 43 1 1703 1952 571683601 571683849 1.880000e-52 217
21 TraesCS2A01G433600 chr4D 88.889 99 11 0 346 444 78845949 78845851 4.200000e-24 122
22 TraesCS2A01G433600 chr4D 86.869 99 13 0 345 443 72581097 72580999 9.100000e-21 111
23 TraesCS2A01G433600 chr5A 87.129 101 11 2 343 442 569720066 569720165 2.530000e-21 113
24 TraesCS2A01G433600 chr5A 86.275 102 12 2 342 442 7654165 7654265 3.270000e-20 110
25 TraesCS2A01G433600 chr5A 86.869 99 11 2 346 443 602651616 602651519 3.270000e-20 110
26 TraesCS2A01G433600 chr7A 85.437 103 12 3 348 448 457605374 457605475 1.520000e-18 104
27 TraesCS2A01G433600 chr5D 85.047 107 11 5 338 443 370119500 370119602 1.520000e-18 104


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 TraesCS2A01G433600 chr2A 686702610 686705714 3104 True 5734.000000 5734 100.000000 1 3105 1 chr2A.!!$R1 3104
1 TraesCS2A01G433600 chr2A 686777079 686778940 1861 True 713.500000 1218 84.421000 106 2103 2 chr2A.!!$R2 1997
2 TraesCS2A01G433600 chr2D 543845498 543848508 3010 True 2019.000000 3618 91.495000 49 3101 2 chr2D.!!$R1 3052
3 TraesCS2A01G433600 chr2D 544170441 544172369 1928 True 496.333333 675 86.391000 36 2106 3 chr2D.!!$R2 2070
4 TraesCS2A01G433600 chr2B 649477631 649481484 3853 True 1233.333333 2386 90.646333 8 3101 3 chr2B.!!$R1 3093

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
653 723 0.025898 CTCGTCTCGTGCATTGCATG 59.974 55.0 22.21 22.21 45.79 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2525 0.196118 AAGTGGAGGAAAGGGGAGGA 59.804 55.0 0.0 0.0 0.0 3.71 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
149 158 1.441016 CCTCAAAGCGCGTTTCTGC 60.441 57.895 9.12 0.00 0.00 4.26
163 173 1.790755 TTCTGCAAGTCGTAATGCGT 58.209 45.000 0.00 0.00 45.47 5.24
195 211 2.846693 CGAGTAACGCCCAATTGAAAC 58.153 47.619 7.12 0.00 34.51 2.78
274 290 1.424493 CCAAATCTGTCTCTCGCCGC 61.424 60.000 0.00 0.00 0.00 6.53
347 367 0.931005 GCTCACGGCTTAGCATGTAC 59.069 55.000 6.53 0.00 38.63 2.90
350 370 1.136305 TCACGGCTTAGCATGTACTCC 59.864 52.381 6.53 0.00 0.00 3.85
351 371 0.464452 ACGGCTTAGCATGTACTCCC 59.536 55.000 6.53 0.00 0.00 4.30
352 372 0.753262 CGGCTTAGCATGTACTCCCT 59.247 55.000 6.53 0.00 0.00 4.20
353 373 1.269831 CGGCTTAGCATGTACTCCCTC 60.270 57.143 6.53 0.00 0.00 4.30
354 374 2.043227 GGCTTAGCATGTACTCCCTCT 58.957 52.381 6.53 0.00 0.00 3.69
355 375 3.231818 GGCTTAGCATGTACTCCCTCTA 58.768 50.000 6.53 0.00 0.00 2.43
356 376 3.835395 GGCTTAGCATGTACTCCCTCTAT 59.165 47.826 6.53 0.00 0.00 1.98
357 377 4.284746 GGCTTAGCATGTACTCCCTCTATT 59.715 45.833 6.53 0.00 0.00 1.73
358 378 5.474825 GCTTAGCATGTACTCCCTCTATTC 58.525 45.833 0.00 0.00 0.00 1.75
359 379 5.245075 GCTTAGCATGTACTCCCTCTATTCT 59.755 44.000 0.00 0.00 0.00 2.40
360 380 6.434652 GCTTAGCATGTACTCCCTCTATTCTA 59.565 42.308 0.00 0.00 0.00 2.10
361 381 7.039644 GCTTAGCATGTACTCCCTCTATTCTAA 60.040 40.741 0.00 0.00 0.00 2.10
362 382 8.777578 TTAGCATGTACTCCCTCTATTCTAAA 57.222 34.615 0.00 0.00 0.00 1.85
363 383 7.676683 AGCATGTACTCCCTCTATTCTAAAA 57.323 36.000 0.00 0.00 0.00 1.52
364 384 8.268878 AGCATGTACTCCCTCTATTCTAAAAT 57.731 34.615 0.00 0.00 0.00 1.82
365 385 9.381038 AGCATGTACTCCCTCTATTCTAAAATA 57.619 33.333 0.00 0.00 0.00 1.40
366 386 9.646427 GCATGTACTCCCTCTATTCTAAAATAG 57.354 37.037 0.00 0.00 43.88 1.73
433 453 7.153217 AGTTGGGTCATCTATTTTAAAACCG 57.847 36.000 1.97 0.00 0.00 4.44
434 454 6.943718 AGTTGGGTCATCTATTTTAAAACCGA 59.056 34.615 1.97 3.29 0.00 4.69
435 455 6.995511 TGGGTCATCTATTTTAAAACCGAG 57.004 37.500 1.97 1.74 0.00 4.63
436 456 5.883673 TGGGTCATCTATTTTAAAACCGAGG 59.116 40.000 1.97 4.90 0.00 4.63
437 457 5.298527 GGGTCATCTATTTTAAAACCGAGGG 59.701 44.000 1.97 0.82 0.00 4.30
438 458 6.117488 GGTCATCTATTTTAAAACCGAGGGA 58.883 40.000 1.97 2.93 0.00 4.20
439 459 6.260271 GGTCATCTATTTTAAAACCGAGGGAG 59.740 42.308 1.97 0.00 0.00 4.30
440 460 6.822170 GTCATCTATTTTAAAACCGAGGGAGT 59.178 38.462 1.97 0.00 0.00 3.85
441 461 7.983484 GTCATCTATTTTAAAACCGAGGGAGTA 59.017 37.037 1.97 0.00 0.00 2.59
447 467 6.916360 TTTAAAACCGAGGGAGTAGAGTTA 57.084 37.500 0.00 0.00 0.00 2.24
457 481 3.532542 GGAGTAGAGTTATGCCAACACC 58.467 50.000 1.64 0.00 0.00 4.16
492 516 6.491394 CACTCCACTTAATTCGTTTGACAAA 58.509 36.000 0.00 0.00 0.00 2.83
510 534 4.106197 ACAAATAGCGAATCTGAGTCGAC 58.894 43.478 28.73 19.42 41.02 4.20
514 538 0.454620 GCGAATCTGAGTCGACGTGT 60.455 55.000 28.73 0.00 41.02 4.49
617 687 1.144565 CGTTGATGCTCAGCTCTCCG 61.145 60.000 0.00 0.00 0.00 4.63
619 689 0.108472 TTGATGCTCAGCTCTCCGTG 60.108 55.000 0.00 0.00 0.00 4.94
646 716 3.264947 GACCTCTCGTCTCGTGCA 58.735 61.111 0.00 0.00 38.57 4.57
647 717 1.803943 GACCTCTCGTCTCGTGCAT 59.196 57.895 0.00 0.00 38.57 3.96
648 718 0.171455 GACCTCTCGTCTCGTGCATT 59.829 55.000 0.00 0.00 38.57 3.56
649 719 0.109086 ACCTCTCGTCTCGTGCATTG 60.109 55.000 0.00 0.00 0.00 2.82
650 720 1.416813 CCTCTCGTCTCGTGCATTGC 61.417 60.000 0.46 0.46 0.00 3.56
651 721 0.733909 CTCTCGTCTCGTGCATTGCA 60.734 55.000 7.38 7.38 35.60 4.08
652 722 0.108662 TCTCGTCTCGTGCATTGCAT 60.109 50.000 15.49 0.00 41.91 3.96
653 723 0.025898 CTCGTCTCGTGCATTGCATG 59.974 55.000 22.21 22.21 45.79 4.06
654 724 0.670239 TCGTCTCGTGCATTGCATGT 60.670 50.000 25.79 0.00 44.84 3.21
742 823 0.166814 GCAACCTAGCAAGCTTGTCG 59.833 55.000 26.55 14.89 0.00 4.35
804 885 1.818060 CAAGGTTGGCATTCGATTCCA 59.182 47.619 0.00 0.00 0.00 3.53
816 897 0.523072 CGATTCCACACTTGCCTTGG 59.477 55.000 0.00 0.00 0.00 3.61
836 917 2.418083 GCCCCCTCCAGCAAATTCG 61.418 63.158 0.00 0.00 0.00 3.34
837 918 1.000896 CCCCCTCCAGCAAATTCGT 60.001 57.895 0.00 0.00 0.00 3.85
838 919 0.611896 CCCCCTCCAGCAAATTCGTT 60.612 55.000 0.00 0.00 0.00 3.85
839 920 0.811281 CCCCTCCAGCAAATTCGTTC 59.189 55.000 0.00 0.00 0.00 3.95
867 948 0.745845 CTCGCCCATTTCCTCACCAG 60.746 60.000 0.00 0.00 0.00 4.00
881 967 0.389166 CACCAGCTTCGTCTCCACTC 60.389 60.000 0.00 0.00 0.00 3.51
882 968 0.540830 ACCAGCTTCGTCTCCACTCT 60.541 55.000 0.00 0.00 0.00 3.24
883 969 0.172352 CCAGCTTCGTCTCCACTCTC 59.828 60.000 0.00 0.00 0.00 3.20
884 970 0.172352 CAGCTTCGTCTCCACTCTCC 59.828 60.000 0.00 0.00 0.00 3.71
900 986 9.480861 CTCCACTCTCCAATATATATACAGGAA 57.519 37.037 13.29 6.68 0.00 3.36
918 1053 1.309499 AACCGCTGACCTCTCTCTCG 61.309 60.000 0.00 0.00 0.00 4.04
972 1107 4.927782 TGTCCCGGCACTGCACAC 62.928 66.667 0.00 0.00 0.00 3.82
994 1137 1.382420 AGCAGCAGGGCTAGCTAGT 60.382 57.895 21.62 0.00 43.70 2.57
1149 1298 2.758979 CACCTACTACTTCATGGACGGT 59.241 50.000 0.00 0.00 0.00 4.83
1304 1453 4.025061 CACCGTCTACGTAAGATCTCGATT 60.025 45.833 10.50 0.00 43.62 3.34
1305 1454 4.210955 ACCGTCTACGTAAGATCTCGATTC 59.789 45.833 10.50 0.00 43.62 2.52
1308 1460 5.116225 CGTCTACGTAAGATCTCGATTCGTA 59.884 44.000 10.50 12.07 43.62 3.43
1314 1479 7.859598 ACGTAAGATCTCGATTCGTAATTAGT 58.140 34.615 10.50 0.00 43.62 2.24
1337 1506 2.380084 CATTAGTGCACCGTACCAGT 57.620 50.000 14.63 0.00 0.00 4.00
1338 1507 1.999735 CATTAGTGCACCGTACCAGTG 59.000 52.381 14.63 6.37 38.30 3.66
1339 1508 0.319083 TTAGTGCACCGTACCAGTGG 59.681 55.000 14.63 7.91 35.71 4.00
1340 1509 2.162338 TAGTGCACCGTACCAGTGGC 62.162 60.000 14.63 0.00 35.71 5.01
1639 1866 6.976349 TCTTTTCTTGCGTGATATGTACGTAT 59.024 34.615 7.33 7.33 43.09 3.06
1642 1869 5.388111 TCTTGCGTGATATGTACGTATAGC 58.612 41.667 7.59 13.15 43.09 2.97
1647 1880 5.003496 GCGTGATATGTACGTATAGCATGTG 59.997 44.000 14.18 4.38 43.09 3.21
1667 1900 0.453390 GGTCGACCGTACCGATCTTT 59.547 55.000 20.85 0.00 38.38 2.52
1677 1910 4.738740 CCGTACCGATCTTTCTGAACATAC 59.261 45.833 0.00 0.00 0.00 2.39
1681 1914 5.655488 ACCGATCTTTCTGAACATACAGAG 58.345 41.667 0.00 0.00 45.63 3.35
2021 2260 1.299926 CGCTACATGGGCTACGTCC 60.300 63.158 0.00 0.00 0.00 4.79
2112 2351 2.978010 CCGCCCGTGAGCAGTTTT 60.978 61.111 0.00 0.00 0.00 2.43
2113 2352 2.556287 CGCCCGTGAGCAGTTTTC 59.444 61.111 0.00 0.00 0.00 2.29
2114 2353 2.556287 GCCCGTGAGCAGTTTTCG 59.444 61.111 0.00 0.00 0.00 3.46
2115 2354 2.251642 GCCCGTGAGCAGTTTTCGT 61.252 57.895 0.00 0.00 0.00 3.85
2116 2355 1.860078 CCCGTGAGCAGTTTTCGTC 59.140 57.895 0.00 0.00 0.00 4.20
2117 2356 1.487231 CCGTGAGCAGTTTTCGTCG 59.513 57.895 0.00 0.00 0.00 5.12
2118 2357 1.213094 CCGTGAGCAGTTTTCGTCGT 61.213 55.000 0.00 0.00 0.00 4.34
2119 2358 0.158928 CGTGAGCAGTTTTCGTCGTC 59.841 55.000 0.00 0.00 0.00 4.20
2120 2359 0.158928 GTGAGCAGTTTTCGTCGTCG 59.841 55.000 0.00 0.00 38.55 5.12
2121 2360 0.248743 TGAGCAGTTTTCGTCGTCGT 60.249 50.000 1.33 0.00 38.33 4.34
2122 2361 0.430110 GAGCAGTTTTCGTCGTCGTC 59.570 55.000 1.33 0.00 38.33 4.20
2123 2362 1.125266 GCAGTTTTCGTCGTCGTCG 59.875 57.895 5.50 5.50 38.33 5.12
2124 2363 1.534811 GCAGTTTTCGTCGTCGTCGT 61.535 55.000 11.41 0.00 38.33 4.34
2125 2364 0.424920 CAGTTTTCGTCGTCGTCGTC 59.575 55.000 11.41 0.00 38.33 4.20
2126 2365 0.988825 AGTTTTCGTCGTCGTCGTCG 60.989 55.000 14.18 14.18 46.06 5.12
2169 2408 3.691342 CGAGGGGGTTGAGCGACA 61.691 66.667 0.00 0.00 0.00 4.35
2170 2409 2.747686 GAGGGGGTTGAGCGACAA 59.252 61.111 0.00 0.00 36.02 3.18
2171 2410 1.299976 GAGGGGGTTGAGCGACAAT 59.700 57.895 3.08 0.00 40.76 2.71
2173 2412 0.322546 AGGGGGTTGAGCGACAATTC 60.323 55.000 3.08 0.47 40.76 2.17
2174 2413 0.608035 GGGGGTTGAGCGACAATTCA 60.608 55.000 3.08 0.00 40.76 2.57
2175 2414 1.463674 GGGGTTGAGCGACAATTCAT 58.536 50.000 3.08 0.00 40.76 2.57
2271 2514 2.159198 CGGGCTTGATTCTTTCATTGGG 60.159 50.000 0.00 0.00 33.34 4.12
2279 2522 6.975196 TGATTCTTTCATTGGGTTTCTGAA 57.025 33.333 0.00 0.00 0.00 3.02
2280 2523 6.748132 TGATTCTTTCATTGGGTTTCTGAAC 58.252 36.000 0.00 0.00 34.96 3.18
2281 2524 4.829064 TCTTTCATTGGGTTTCTGAACG 57.171 40.909 0.00 0.00 36.61 3.95
2282 2525 4.204012 TCTTTCATTGGGTTTCTGAACGT 58.796 39.130 0.00 0.00 36.61 3.99
2355 2604 2.071778 TTTGGCCAGTTTGCTCTTCT 57.928 45.000 5.11 0.00 0.00 2.85
2467 2720 5.862846 CAGGTTTCTGCAGGAATCATCCTTA 60.863 44.000 20.31 0.00 42.89 2.69
2492 2745 2.287308 CGATCCGCTAGAGAAACTCCTG 60.287 54.545 0.00 0.00 0.00 3.86
2495 2750 1.550976 CCGCTAGAGAAACTCCTGGTT 59.449 52.381 0.00 0.00 40.28 3.67
2496 2751 2.758979 CCGCTAGAGAAACTCCTGGTTA 59.241 50.000 0.00 0.00 37.12 2.85
2497 2752 3.181485 CCGCTAGAGAAACTCCTGGTTAG 60.181 52.174 0.00 0.00 37.12 2.34
2498 2753 3.695060 CGCTAGAGAAACTCCTGGTTAGA 59.305 47.826 0.00 0.00 37.12 2.10
2535 3626 1.400846 CTACGCCTACACGTCACATCT 59.599 52.381 0.00 0.00 44.43 2.90
2597 3696 2.049228 CAAACACCGTACGTCTGTCTC 58.951 52.381 15.21 0.00 0.00 3.36
2602 3701 1.067565 ACCGTACGTCTGTCTCGTCTA 60.068 52.381 15.21 0.00 41.72 2.59
2645 3747 1.727511 TAGTATGGCCGACGGAACCG 61.728 60.000 20.50 11.83 46.03 4.44
2660 3762 4.277239 CCGAACAATCAGACGGCA 57.723 55.556 0.00 0.00 38.98 5.69
2739 3847 3.706698 CAGTAGTCCATCACCATGTACG 58.293 50.000 0.00 0.00 0.00 3.67
3093 4201 0.721718 GGAAAACAGAGCATCGACGG 59.278 55.000 0.00 0.00 42.67 4.79
3096 4204 2.163818 AAACAGAGCATCGACGGAAA 57.836 45.000 0.00 0.00 42.67 3.13
3097 4205 1.429463 AACAGAGCATCGACGGAAAC 58.571 50.000 0.00 0.00 42.67 2.78
3100 4208 1.798223 CAGAGCATCGACGGAAACAAA 59.202 47.619 0.00 0.00 42.67 2.83
3101 4209 2.416547 CAGAGCATCGACGGAAACAAAT 59.583 45.455 0.00 0.00 42.67 2.32
3102 4210 3.074412 AGAGCATCGACGGAAACAAATT 58.926 40.909 0.00 0.00 42.67 1.82
3103 4211 3.120199 AGAGCATCGACGGAAACAAATTG 60.120 43.478 0.00 0.00 42.67 2.32
3104 4212 2.552315 AGCATCGACGGAAACAAATTGT 59.448 40.909 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.343465 ACTGGTGAAGTTAGTGTCGGG 59.657 52.381 0.00 0.00 34.57 5.14
30 31 2.814280 ACTGGTGAAGTTAGTGTCGG 57.186 50.000 0.00 0.00 34.57 4.79
31 32 3.979495 GTGTACTGGTGAAGTTAGTGTCG 59.021 47.826 0.00 0.00 40.56 4.35
72 78 4.704057 ACCGGAGTTTAGTAAGGACACTAG 59.296 45.833 9.46 0.00 32.74 2.57
163 173 2.278849 TTACTCGCATCGGGGAACA 58.721 52.632 0.00 0.00 35.34 3.18
177 187 4.216902 GGTTAGTTTCAATTGGGCGTTACT 59.783 41.667 5.42 3.51 0.00 2.24
195 211 2.202570 CGACCGACGCCAGGTTAG 60.203 66.667 0.00 0.00 43.01 2.34
274 290 1.107114 ACTGGTGTATGGAGAGCTCG 58.893 55.000 8.37 0.00 0.00 5.03
407 427 8.085909 CGGTTTTAAAATAGATGACCCAACTTT 58.914 33.333 3.52 0.00 0.00 2.66
408 428 7.449086 TCGGTTTTAAAATAGATGACCCAACTT 59.551 33.333 3.52 0.00 0.00 2.66
409 429 6.943718 TCGGTTTTAAAATAGATGACCCAACT 59.056 34.615 3.52 0.00 0.00 3.16
410 430 7.148355 TCGGTTTTAAAATAGATGACCCAAC 57.852 36.000 3.52 0.00 0.00 3.77
411 431 6.376018 CCTCGGTTTTAAAATAGATGACCCAA 59.624 38.462 3.52 0.00 0.00 4.12
412 432 5.883673 CCTCGGTTTTAAAATAGATGACCCA 59.116 40.000 3.52 0.00 0.00 4.51
413 433 5.298527 CCCTCGGTTTTAAAATAGATGACCC 59.701 44.000 3.52 0.00 0.00 4.46
414 434 6.117488 TCCCTCGGTTTTAAAATAGATGACC 58.883 40.000 3.52 0.00 0.00 4.02
415 435 6.822170 ACTCCCTCGGTTTTAAAATAGATGAC 59.178 38.462 3.52 0.00 0.00 3.06
416 436 6.954232 ACTCCCTCGGTTTTAAAATAGATGA 58.046 36.000 3.52 6.06 0.00 2.92
417 437 8.202137 TCTACTCCCTCGGTTTTAAAATAGATG 58.798 37.037 3.52 4.40 0.00 2.90
418 438 8.315220 TCTACTCCCTCGGTTTTAAAATAGAT 57.685 34.615 3.52 0.00 0.00 1.98
419 439 7.398332 ACTCTACTCCCTCGGTTTTAAAATAGA 59.602 37.037 3.52 6.10 0.00 1.98
420 440 7.554211 ACTCTACTCCCTCGGTTTTAAAATAG 58.446 38.462 3.52 1.90 0.00 1.73
421 441 7.486407 ACTCTACTCCCTCGGTTTTAAAATA 57.514 36.000 3.52 0.00 0.00 1.40
422 442 6.370186 ACTCTACTCCCTCGGTTTTAAAAT 57.630 37.500 3.52 0.00 0.00 1.82
423 443 5.813513 ACTCTACTCCCTCGGTTTTAAAA 57.186 39.130 0.00 0.00 0.00 1.52
424 444 5.813513 AACTCTACTCCCTCGGTTTTAAA 57.186 39.130 0.00 0.00 0.00 1.52
425 445 6.628844 GCATAACTCTACTCCCTCGGTTTTAA 60.629 42.308 0.00 0.00 0.00 1.52
426 446 5.163478 GCATAACTCTACTCCCTCGGTTTTA 60.163 44.000 0.00 0.00 0.00 1.52
427 447 4.382793 GCATAACTCTACTCCCTCGGTTTT 60.383 45.833 0.00 0.00 0.00 2.43
428 448 3.132467 GCATAACTCTACTCCCTCGGTTT 59.868 47.826 0.00 0.00 0.00 3.27
429 449 2.694109 GCATAACTCTACTCCCTCGGTT 59.306 50.000 0.00 0.00 0.00 4.44
430 450 2.308690 GCATAACTCTACTCCCTCGGT 58.691 52.381 0.00 0.00 0.00 4.69
431 451 1.614413 GGCATAACTCTACTCCCTCGG 59.386 57.143 0.00 0.00 0.00 4.63
432 452 2.307768 TGGCATAACTCTACTCCCTCG 58.692 52.381 0.00 0.00 0.00 4.63
433 453 3.451178 TGTTGGCATAACTCTACTCCCTC 59.549 47.826 0.00 0.00 0.00 4.30
434 454 3.197983 GTGTTGGCATAACTCTACTCCCT 59.802 47.826 0.00 0.00 0.00 4.20
435 455 3.532542 GTGTTGGCATAACTCTACTCCC 58.467 50.000 0.00 0.00 0.00 4.30
436 456 3.055385 TGGTGTTGGCATAACTCTACTCC 60.055 47.826 0.00 0.00 0.00 3.85
437 457 4.202245 TGGTGTTGGCATAACTCTACTC 57.798 45.455 0.00 0.00 0.00 2.59
438 458 4.634012 TTGGTGTTGGCATAACTCTACT 57.366 40.909 0.00 0.00 0.00 2.57
439 459 4.760204 AGTTTGGTGTTGGCATAACTCTAC 59.240 41.667 0.00 0.00 0.00 2.59
440 460 4.980573 AGTTTGGTGTTGGCATAACTCTA 58.019 39.130 0.00 0.00 0.00 2.43
441 461 3.832527 AGTTTGGTGTTGGCATAACTCT 58.167 40.909 0.00 0.00 0.00 3.24
447 467 2.493278 GCTCATAGTTTGGTGTTGGCAT 59.507 45.455 0.00 0.00 0.00 4.40
457 481 6.992063 ATTAAGTGGAGTGCTCATAGTTTG 57.008 37.500 1.41 0.00 0.00 2.93
492 516 1.941294 ACGTCGACTCAGATTCGCTAT 59.059 47.619 14.70 0.00 36.40 2.97
510 534 0.895530 ACCTATCCTCACACCACACG 59.104 55.000 0.00 0.00 0.00 4.49
514 538 1.195115 GCTGACCTATCCTCACACCA 58.805 55.000 0.00 0.00 0.00 4.17
617 687 2.229302 ACGAGAGGTCTCTTTGCTACAC 59.771 50.000 5.48 0.00 40.61 2.90
619 689 3.139603 GACGAGAGGTCTCTTTGCTAC 57.860 52.381 5.48 0.00 42.62 3.58
649 719 4.450122 CAGACGCCGTGCACATGC 62.450 66.667 18.64 17.29 42.50 4.06
650 720 4.450122 GCAGACGCCGTGCACATG 62.450 66.667 18.64 8.39 40.86 3.21
662 732 4.452733 CCGTCCCTTCCGGCAGAC 62.453 72.222 1.35 2.83 38.85 3.51
671 752 4.021925 GAGCACTGGCCGTCCCTT 62.022 66.667 0.00 0.00 42.56 3.95
676 757 3.429372 TTTTGGGAGCACTGGCCGT 62.429 57.895 0.00 0.00 42.56 5.68
742 823 2.270986 CCTGCTGCTGGTTTGGGAC 61.271 63.158 16.56 0.00 0.00 4.46
789 870 2.198827 AGTGTGGAATCGAATGCCAA 57.801 45.000 5.92 0.00 32.68 4.52
822 903 1.740025 GAGGAACGAATTTGCTGGAGG 59.260 52.381 0.00 0.00 35.68 4.30
824 905 1.073125 TGGAGGAACGAATTTGCTGGA 59.927 47.619 0.00 0.00 35.68 3.86
836 917 1.330655 TGGGCGAGAGATGGAGGAAC 61.331 60.000 0.00 0.00 0.00 3.62
837 918 0.399091 ATGGGCGAGAGATGGAGGAA 60.399 55.000 0.00 0.00 0.00 3.36
838 919 0.399091 AATGGGCGAGAGATGGAGGA 60.399 55.000 0.00 0.00 0.00 3.71
839 920 0.471617 AAATGGGCGAGAGATGGAGG 59.528 55.000 0.00 0.00 0.00 4.30
867 948 0.603569 TTGGAGAGTGGAGACGAAGC 59.396 55.000 0.00 0.00 0.00 3.86
881 967 6.980978 CAGCGGTTCCTGTATATATATTGGAG 59.019 42.308 0.00 6.89 0.00 3.86
882 968 6.666113 TCAGCGGTTCCTGTATATATATTGGA 59.334 38.462 0.00 10.72 34.47 3.53
883 969 6.757010 GTCAGCGGTTCCTGTATATATATTGG 59.243 42.308 0.00 2.23 34.47 3.16
884 970 6.757010 GGTCAGCGGTTCCTGTATATATATTG 59.243 42.308 0.00 0.00 34.47 1.90
900 986 1.747367 CGAGAGAGAGGTCAGCGGT 60.747 63.158 0.00 0.00 0.00 5.68
918 1053 2.256461 CTTGCTGCTTCCAACGCC 59.744 61.111 0.00 0.00 0.00 5.68
972 1107 2.514128 CTAGCCCTGCTGCTGCTG 60.514 66.667 17.00 15.58 42.77 4.41
1016 1159 1.315257 CCGCAGCTTTGGCCTACAAT 61.315 55.000 3.32 0.00 39.21 2.71
1328 1497 1.667830 CACACAGCCACTGGTACGG 60.668 63.158 0.00 0.00 42.99 4.02
1330 1499 1.507141 GCACACACAGCCACTGGTAC 61.507 60.000 0.00 0.00 35.51 3.34
1333 1502 3.653009 CGCACACACAGCCACTGG 61.653 66.667 0.00 0.00 35.51 4.00
1335 1504 2.588877 GACGCACACACAGCCACT 60.589 61.111 0.00 0.00 0.00 4.00
1336 1505 4.000557 CGACGCACACACAGCCAC 62.001 66.667 0.00 0.00 0.00 5.01
1339 1508 3.702555 GACCGACGCACACACAGC 61.703 66.667 0.00 0.00 0.00 4.40
1340 1509 3.394874 CGACCGACGCACACACAG 61.395 66.667 0.00 0.00 34.51 3.66
1639 1866 0.680601 TACGGTCGACCCACATGCTA 60.681 55.000 28.52 6.79 0.00 3.49
1642 1869 1.153706 GGTACGGTCGACCCACATG 60.154 63.158 28.52 16.36 0.00 3.21
1667 1900 1.810755 ACGTCGCTCTGTATGTTCAGA 59.189 47.619 0.00 0.00 41.40 3.27
1677 1910 1.702886 ATTCAGTTCACGTCGCTCTG 58.297 50.000 0.00 0.00 0.00 3.35
1681 1914 2.298300 CACAAATTCAGTTCACGTCGC 58.702 47.619 0.00 0.00 0.00 5.19
2006 2245 2.579873 GTAGAGGACGTAGCCCATGTA 58.420 52.381 0.00 0.00 0.00 2.29
2021 2260 1.062294 GTCGGTGCAGTAGTCGTAGAG 59.938 57.143 0.00 0.00 36.95 2.43
2106 2345 0.424920 GACGACGACGACGAAAACTG 59.575 55.000 25.15 0.00 42.66 3.16
2123 2362 2.050985 AAACCCGACGACGACGAC 60.051 61.111 20.63 7.02 42.66 4.34
2124 2363 2.051076 CAAACCCGACGACGACGA 60.051 61.111 20.63 0.00 42.66 4.20
2125 2364 3.101428 CCAAACCCGACGACGACG 61.101 66.667 12.66 12.66 42.66 5.12
2126 2365 3.408851 GCCAAACCCGACGACGAC 61.409 66.667 9.28 0.00 42.66 4.34
2156 2395 1.463674 ATGAATTGTCGCTCAACCCC 58.536 50.000 0.00 0.00 38.97 4.95
2170 2409 9.793259 ACTATATCGAACCCAAACAATATGAAT 57.207 29.630 0.00 0.00 0.00 2.57
2174 2413 9.582431 CGATACTATATCGAACCCAAACAATAT 57.418 33.333 11.87 0.00 43.59 1.28
2175 2414 8.579006 ACGATACTATATCGAACCCAAACAATA 58.421 33.333 21.58 0.00 43.59 1.90
2215 2458 5.573282 CGTACCTGTTTCTTCAGATGTACAG 59.427 44.000 0.33 0.00 35.19 2.74
2271 2514 0.685660 AGGGGAGGACGTTCAGAAAC 59.314 55.000 0.00 0.00 0.00 2.78
2279 2522 1.612739 GGAGGAAAGGGGAGGACGT 60.613 63.158 0.00 0.00 0.00 4.34
2280 2523 1.612442 TGGAGGAAAGGGGAGGACG 60.612 63.158 0.00 0.00 0.00 4.79
2281 2524 0.547954 AGTGGAGGAAAGGGGAGGAC 60.548 60.000 0.00 0.00 0.00 3.85
2282 2525 0.196118 AAGTGGAGGAAAGGGGAGGA 59.804 55.000 0.00 0.00 0.00 3.71
2355 2604 1.205655 CTCGACATCTTGAGCCTGGAA 59.794 52.381 0.00 0.00 0.00 3.53
2467 2720 3.543665 AGTTTCTCTAGCGGATCGTAGT 58.456 45.455 0.00 0.00 0.00 2.73
2471 2724 1.950909 AGGAGTTTCTCTAGCGGATCG 59.049 52.381 0.00 0.00 0.00 3.69
2535 3626 1.813178 CTGCTAGGTCGTCTCACTCAA 59.187 52.381 0.00 0.00 0.00 3.02
2645 3747 1.363744 CCTCTGCCGTCTGATTGTTC 58.636 55.000 0.00 0.00 0.00 3.18
2660 3762 2.364842 ATGGACCAGCTCGCCTCT 60.365 61.111 0.00 0.00 0.00 3.69
2881 3989 2.123982 CCTACGGGACCTACGCCT 60.124 66.667 0.00 0.00 34.00 5.52


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

AutoCloner maintained by Alex Coulton.