Multiple sequence alignment - TraesCS3A01G367600

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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 TraesCS3A01G367600 chr3A 100.000 3215 0 0 1 3215 616494242 616491028 0.000000e+00 5938.0
1 TraesCS3A01G367600 chr3A 85.294 170 13 6 1615 1778 32385655 32385492 7.140000e-37 165.0
2 TraesCS3A01G367600 chr3D 91.944 2135 123 20 1 2119 474217811 474215710 0.000000e+00 2944.0
3 TraesCS3A01G367600 chr3D 87.935 978 51 24 2114 3058 474215681 474214738 0.000000e+00 1090.0
4 TraesCS3A01G367600 chr3D 85.882 170 12 6 1615 1778 23195785 23195622 1.530000e-38 171.0
5 TraesCS3A01G367600 chr3D 93.407 91 3 2 3070 3157 474214692 474214602 7.240000e-27 132.0
6 TraesCS3A01G367600 chr3B 93.016 1804 105 12 328 2119 630402775 630400981 0.000000e+00 2614.0
7 TraesCS3A01G367600 chr3B 88.380 611 36 18 2464 3058 630400581 630399990 0.000000e+00 702.0
8 TraesCS3A01G367600 chr3B 87.645 259 20 8 2120 2376 630400945 630400697 1.130000e-74 291.0
9 TraesCS3A01G367600 chr3B 85.882 170 12 6 1615 1778 40908878 40908715 1.530000e-38 171.0
10 TraesCS3A01G367600 chr3B 85.030 167 14 9 3056 3211 630399965 630399799 3.320000e-35 159.0
11 TraesCS3A01G367600 chr3B 97.222 36 1 0 1747 1782 766031802 766031767 9.630000e-06 62.1
12 TraesCS3A01G367600 chr1A 77.479 817 121 43 1076 1842 474451282 474450479 6.370000e-117 431.0
13 TraesCS3A01G367600 chr1A 77.953 254 42 11 1871 2118 24394620 24394865 2.580000e-31 147.0
14 TraesCS3A01G367600 chr1B 77.365 835 110 50 1073 1839 499895916 499896739 3.830000e-114 422.0
15 TraesCS3A01G367600 chr1D 88.583 254 20 4 1595 1842 375646699 375646449 1.870000e-77 300.0
16 TraesCS3A01G367600 chr7A 82.383 193 29 4 1591 1782 16164221 16164033 2.570000e-36 163.0
17 TraesCS3A01G367600 chr4A 82.383 193 29 4 1591 1782 717724320 717724132 2.570000e-36 163.0
18 TraesCS3A01G367600 chr4D 81.538 195 26 7 1928 2118 295104243 295104055 5.560000e-33 152.0
19 TraesCS3A01G367600 chr2A 80.095 211 32 9 1874 2078 37742160 37742366 7.190000e-32 148.0
20 TraesCS3A01G367600 chr6D 80.612 196 27 8 1928 2118 456114368 456114179 1.200000e-29 141.0


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 TraesCS3A01G367600 chr3A 616491028 616494242 3214 True 5938.000000 5938 100.000000 1 3215 1 chr3A.!!$R2 3214
1 TraesCS3A01G367600 chr3D 474214602 474217811 3209 True 1388.666667 2944 91.095333 1 3157 3 chr3D.!!$R2 3156
2 TraesCS3A01G367600 chr3B 630399799 630402775 2976 True 941.500000 2614 88.517750 328 3211 4 chr3B.!!$R3 2883
3 TraesCS3A01G367600 chr1A 474450479 474451282 803 True 431.000000 431 77.479000 1076 1842 1 chr1A.!!$R1 766
4 TraesCS3A01G367600 chr1B 499895916 499896739 823 False 422.000000 422 77.365000 1073 1839 1 chr1B.!!$F1 766

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
417 422 0.596083 CGCTGTCGGATCTCCATGAC 60.596 60.0 0.0 0.0 35.14 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 2403 0.537188 TCGATGGGCTCTTGAGGTTC 59.463 55.0 0.0 0.0 0.0 3.62 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
151 152 8.645814 TGTACACCTACATATCCTAGTTATGG 57.354 38.462 12.20 0.00 32.46 2.74
154 155 8.191534 ACACCTACATATCCTAGTTATGGAAC 57.808 38.462 12.20 0.00 37.13 3.62
198 199 4.439426 CGTCTCTTCAAGGATCGACTCAAT 60.439 45.833 0.00 0.00 0.00 2.57
231 232 4.145052 ACCTCTTCAAGAAAACCATCACC 58.855 43.478 0.00 0.00 0.00 4.02
232 233 3.507622 CCTCTTCAAGAAAACCATCACCC 59.492 47.826 0.00 0.00 0.00 4.61
233 234 3.496331 TCTTCAAGAAAACCATCACCCC 58.504 45.455 0.00 0.00 0.00 4.95
234 235 3.140144 TCTTCAAGAAAACCATCACCCCT 59.860 43.478 0.00 0.00 0.00 4.79
235 236 3.611025 TCAAGAAAACCATCACCCCTT 57.389 42.857 0.00 0.00 0.00 3.95
236 237 3.922375 TCAAGAAAACCATCACCCCTTT 58.078 40.909 0.00 0.00 0.00 3.11
237 238 4.294347 TCAAGAAAACCATCACCCCTTTT 58.706 39.130 0.00 0.00 0.00 2.27
238 239 4.100808 TCAAGAAAACCATCACCCCTTTTG 59.899 41.667 0.00 0.00 0.00 2.44
239 240 2.368548 AGAAAACCATCACCCCTTTTGC 59.631 45.455 0.00 0.00 0.00 3.68
240 241 1.799933 AAACCATCACCCCTTTTGCA 58.200 45.000 0.00 0.00 0.00 4.08
241 242 1.799933 AACCATCACCCCTTTTGCAA 58.200 45.000 0.00 0.00 0.00 4.08
242 243 1.799933 ACCATCACCCCTTTTGCAAA 58.200 45.000 8.05 8.05 0.00 3.68
243 244 2.122768 ACCATCACCCCTTTTGCAAAA 58.877 42.857 22.61 22.61 0.00 2.44
244 245 2.507471 ACCATCACCCCTTTTGCAAAAA 59.493 40.909 23.92 9.84 0.00 1.94
279 280 4.845580 CGGCCACTGCTGCCCTAG 62.846 72.222 2.24 0.00 46.48 3.02
284 285 1.886313 CACTGCTGCCCTAGATGCG 60.886 63.158 0.00 0.00 0.00 4.73
286 287 1.300775 CTGCTGCCCTAGATGCGAG 60.301 63.158 0.00 0.00 0.00 5.03
324 329 2.708861 ACCTTCACATGTTCAGTACCCA 59.291 45.455 0.00 0.00 0.00 4.51
325 330 3.244561 ACCTTCACATGTTCAGTACCCAG 60.245 47.826 0.00 0.00 0.00 4.45
339 344 1.135094 ACCCAGTAGCCATCCAGATG 58.865 55.000 0.40 0.40 38.51 2.90
354 359 1.492176 CAGATGTGGGATGGCCTACTT 59.508 52.381 3.32 0.00 45.26 2.24
356 361 1.490490 GATGTGGGATGGCCTACTTCA 59.510 52.381 3.32 0.00 45.26 3.02
366 371 2.589157 CCTACTTCACCCGGTGCCA 61.589 63.158 13.19 0.92 32.98 4.92
389 394 0.911769 TCCATCGAGCTCATTTGGGT 59.088 50.000 20.50 0.00 0.00 4.51
408 413 3.771160 GTCCCCACGCTGTCGGAT 61.771 66.667 0.00 0.00 40.69 4.18
416 421 1.037579 ACGCTGTCGGATCTCCATGA 61.038 55.000 0.00 0.00 40.69 3.07
417 422 0.596083 CGCTGTCGGATCTCCATGAC 60.596 60.000 0.00 0.00 35.14 3.06
425 430 4.859798 GTCGGATCTCCATGACGATATTTC 59.140 45.833 0.00 0.00 35.90 2.17
427 432 3.614616 GGATCTCCATGACGATATTTCGC 59.385 47.826 5.42 0.00 41.65 4.70
429 434 7.801280 GGATCTCCATGACGATATTTCGCCA 62.801 48.000 5.42 0.91 42.02 5.69
441 446 1.737838 TTTCGCCATCGATTGCTCTT 58.262 45.000 18.21 0.00 45.04 2.85
448 453 3.012518 CCATCGATTGCTCTTTCCTTGT 58.987 45.455 0.00 0.00 0.00 3.16
456 461 5.964958 TTGCTCTTTCCTTGTTATGGAAG 57.035 39.130 0.00 0.00 43.48 3.46
477 482 5.927281 AGATTTGGGATTCCAGAAACATG 57.073 39.130 4.80 0.00 45.04 3.21
487 492 4.572985 TCCAGAAACATGCTTGTCTTTG 57.427 40.909 5.61 0.00 34.06 2.77
503 508 1.676006 CTTTGGCAACGAACTCCACTT 59.324 47.619 0.00 0.00 42.51 3.16
504 509 1.757682 TTGGCAACGAACTCCACTTT 58.242 45.000 0.00 0.00 42.51 2.66
534 539 7.283354 AGGACCAATGTTAGAAATTTAGCTAGC 59.717 37.037 6.62 6.62 0.00 3.42
563 571 9.798885 CTTCACTCTTTGAACTTTATACGAAAG 57.201 33.333 0.00 0.00 39.45 2.62
609 617 1.414181 CCATGGCGTCAATACCTCTCT 59.586 52.381 0.00 0.00 0.00 3.10
647 655 3.850122 ATTGGAAAGCTCGCCTTTTAC 57.150 42.857 6.40 1.62 43.64 2.01
670 678 3.616821 TCGTCTTTGAGTAATGCATTCGG 59.383 43.478 16.86 0.09 0.00 4.30
674 682 5.527582 GTCTTTGAGTAATGCATTCGGGTAT 59.472 40.000 16.86 0.00 0.00 2.73
676 684 4.415881 TGAGTAATGCATTCGGGTATGT 57.584 40.909 16.86 0.00 0.00 2.29
679 687 6.163476 TGAGTAATGCATTCGGGTATGTATC 58.837 40.000 16.86 1.55 30.88 2.24
688 696 1.077334 CGGGTATGTATCCTCTCCCCT 59.923 57.143 0.00 0.00 0.00 4.79
697 705 5.538877 TGTATCCTCTCCCCTTAGTGATTT 58.461 41.667 0.00 0.00 0.00 2.17
706 715 7.010160 TCTCCCCTTAGTGATTTGTCAAAAAT 58.990 34.615 1.31 0.00 0.00 1.82
716 725 9.264719 AGTGATTTGTCAAAAATTCAATTCCTC 57.735 29.630 1.31 0.00 0.00 3.71
804 815 5.319043 ACTATTAGCTAGCACTCTCCTCT 57.681 43.478 18.83 0.00 0.00 3.69
885 896 5.695851 TCCACTTTCTTTTTGCTCATCTC 57.304 39.130 0.00 0.00 0.00 2.75
980 991 1.777941 GGTCCTCCCCTATATAGGCG 58.222 60.000 21.75 14.49 42.26 5.52
1040 1056 4.467084 TCCATTGCTCGCCGTCCC 62.467 66.667 0.00 0.00 0.00 4.46
1326 1360 2.504244 GCCCTCGAGAACGACGTG 60.504 66.667 15.71 0.00 43.81 4.49
1556 1626 5.413833 TGATCTTCTTCTTGTGCTTGGATTC 59.586 40.000 0.00 0.00 0.00 2.52
1562 1632 2.886523 TCTTGTGCTTGGATTCTTGGTG 59.113 45.455 0.00 0.00 0.00 4.17
1589 1666 2.506217 TGATCGCGTTCGTGCTCC 60.506 61.111 5.77 0.00 36.96 4.70
1962 2069 1.739562 GTGAAGCTCGAGCACCAGG 60.740 63.158 36.87 0.00 45.16 4.45
1980 2087 2.434185 GCTCGTTCATGGACGGCA 60.434 61.111 25.81 7.23 42.98 5.69
1981 2088 1.815421 GCTCGTTCATGGACGGCAT 60.815 57.895 25.81 0.00 42.98 4.40
1984 2091 1.745115 CGTTCATGGACGGCATGGT 60.745 57.895 19.23 0.00 39.27 3.55
1986 2093 1.449423 TTCATGGACGGCATGGTCG 60.449 57.895 0.00 0.00 37.82 4.79
2088 2195 4.038080 GGACAAAACAGCGGCGGG 62.038 66.667 9.78 0.00 0.00 6.13
2181 2323 0.954449 TGTCTCTCTCGACCGACACC 60.954 60.000 0.00 0.00 32.00 4.16
2201 2343 0.379669 CAGATGATGGAACGCAAGCC 59.620 55.000 0.00 0.00 45.62 4.35
2220 2362 1.391485 CCAAAACATCTGAGAGCGACG 59.609 52.381 0.00 0.00 0.00 5.12
2261 2403 2.187946 GGTCTGCGTCCATGGAGG 59.812 66.667 26.72 26.72 39.47 4.30
2272 2414 2.191400 TCCATGGAGGAACCTCAAGAG 58.809 52.381 11.44 8.01 45.65 2.85
2339 2482 3.782656 ACCTCCACTGTACCGAAAAAT 57.217 42.857 0.00 0.00 0.00 1.82
2340 2483 4.895668 ACCTCCACTGTACCGAAAAATA 57.104 40.909 0.00 0.00 0.00 1.40
2341 2484 5.431179 ACCTCCACTGTACCGAAAAATAT 57.569 39.130 0.00 0.00 0.00 1.28
2344 2487 7.215085 ACCTCCACTGTACCGAAAAATATATC 58.785 38.462 0.00 0.00 0.00 1.63
2391 2562 2.442272 TCCGGTCAGGAGCTAGCC 60.442 66.667 12.13 2.59 45.98 3.93
2419 2590 2.296190 GGCCTGAAAATTGGTTCGAACT 59.704 45.455 26.32 6.72 0.00 3.01
2420 2591 3.243737 GGCCTGAAAATTGGTTCGAACTT 60.244 43.478 26.32 13.30 0.00 2.66
2421 2592 3.981416 GCCTGAAAATTGGTTCGAACTTC 59.019 43.478 26.32 20.63 0.00 3.01
2422 2593 4.219033 CCTGAAAATTGGTTCGAACTTCG 58.781 43.478 26.32 16.12 42.10 3.79
2454 2625 7.154435 AGCGTTTTCTCTGTCTATTGTACTA 57.846 36.000 0.00 0.00 0.00 1.82
2455 2626 7.251994 AGCGTTTTCTCTGTCTATTGTACTAG 58.748 38.462 0.00 0.00 0.00 2.57
2457 2628 7.218583 GCGTTTTCTCTGTCTATTGTACTAGTC 59.781 40.741 0.00 0.00 0.00 2.59
2458 2629 7.697291 CGTTTTCTCTGTCTATTGTACTAGTCC 59.303 40.741 0.00 0.00 0.00 3.85
2459 2630 8.521176 GTTTTCTCTGTCTATTGTACTAGTCCA 58.479 37.037 0.00 0.00 0.00 4.02
2460 2631 8.645814 TTTCTCTGTCTATTGTACTAGTCCAA 57.354 34.615 3.11 3.11 0.00 3.53
2484 2674 1.369091 GATCCGTCGCCATTGTTGCT 61.369 55.000 0.00 0.00 0.00 3.91
2487 2677 2.877691 GTCGCCATTGTTGCTCCC 59.122 61.111 0.00 0.00 0.00 4.30
2488 2678 1.675641 GTCGCCATTGTTGCTCCCT 60.676 57.895 0.00 0.00 0.00 4.20
2537 2729 4.821589 GGCTTCGCCCTCTCCGTG 62.822 72.222 0.00 0.00 44.06 4.94
2612 2828 3.188048 GGCTTCTCATTAATGCCGATCTG 59.812 47.826 10.76 5.05 33.96 2.90
2796 3012 1.302832 GACTCCCAGTTGGCCAGTG 60.303 63.158 5.11 7.96 29.85 3.66
2813 3033 0.960861 GTGGCCGGGAGAAAGAAAGG 60.961 60.000 2.18 0.00 0.00 3.11
2817 3038 0.253327 CCGGGAGAAAGAAAGGAGGG 59.747 60.000 0.00 0.00 0.00 4.30
2826 3047 5.292815 AGAAAGAAAGGAGGGGAGTATCAT 58.707 41.667 0.00 0.00 36.25 2.45
2852 3073 2.158959 CGTCAATCAGGTCGACGGC 61.159 63.158 9.92 0.00 46.59 5.68
2907 3128 3.444657 GCACGCAGCAGCAATATAC 57.555 52.632 0.82 0.00 44.79 1.47
2908 3129 0.383491 GCACGCAGCAGCAATATACG 60.383 55.000 0.82 0.00 44.79 3.06
2909 3130 0.930310 CACGCAGCAGCAATATACGT 59.070 50.000 0.82 0.00 42.27 3.57
2910 3131 2.124122 CACGCAGCAGCAATATACGTA 58.876 47.619 0.82 0.00 42.27 3.57
2922 3143 7.361885 GCAGCAATATACGTACTGTAGGAGTAT 60.362 40.741 13.87 12.87 39.44 2.12
2923 3144 9.159364 CAGCAATATACGTACTGTAGGAGTATA 57.841 37.037 13.87 14.27 39.44 1.47
2924 3145 9.160496 AGCAATATACGTACTGTAGGAGTATAC 57.840 37.037 13.87 0.00 39.44 1.47
2927 3148 4.408182 ACGTACTGTAGGAGTATACGGT 57.592 45.455 13.87 4.01 45.18 4.83
2930 3153 3.659183 ACTGTAGGAGTATACGGTGGT 57.341 47.619 0.00 0.00 42.38 4.16
2943 3166 0.462047 CGGTGGTATGAGTTGGAGGC 60.462 60.000 0.00 0.00 0.00 4.70
2949 3172 1.622607 TATGAGTTGGAGGCCCACCG 61.623 60.000 0.00 0.00 43.41 4.94
2952 3175 3.319198 GTTGGAGGCCCACCGAGA 61.319 66.667 0.00 0.00 43.41 4.04
3058 3281 0.035343 CCCTTTTCGTCCCCTTCCTC 60.035 60.000 0.00 0.00 0.00 3.71
3059 3282 0.391263 CCTTTTCGTCCCCTTCCTCG 60.391 60.000 0.00 0.00 0.00 4.63
3060 3283 0.391263 CTTTTCGTCCCCTTCCTCGG 60.391 60.000 0.00 0.00 0.00 4.63
3061 3284 2.459202 TTTTCGTCCCCTTCCTCGGC 62.459 60.000 0.00 0.00 0.00 5.54
3191 3463 1.001641 ACTCATCACCCAGCTTGCC 60.002 57.895 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.039784 ACAAAGTACAACATTATTGTGGCAGAT 60.040 33.333 2.58 0.00 35.83 2.90
127 128 8.874744 TCCATAACTAGGATATGTAGGTGTAC 57.125 38.462 13.58 0.00 0.00 2.90
151 152 6.630443 CGAAATCGAAGGAATTGATCATGTTC 59.370 38.462 0.00 4.55 43.02 3.18
154 155 6.018425 AGACGAAATCGAAGGAATTGATCATG 60.018 38.462 10.16 0.00 43.02 3.07
156 157 5.419542 AGACGAAATCGAAGGAATTGATCA 58.580 37.500 10.16 0.00 43.02 2.92
198 199 3.136443 TCTTGAAGAGGTTGCTCTTGGAA 59.864 43.478 0.00 0.00 43.03 3.53
222 223 1.799933 TTGCAAAAGGGGTGATGGTT 58.200 45.000 0.00 0.00 0.00 3.67
247 248 0.394938 GGCCGTTGGGGTGAATTTTT 59.605 50.000 0.00 0.00 38.44 1.94
248 249 0.760945 TGGCCGTTGGGGTGAATTTT 60.761 50.000 0.00 0.00 38.44 1.82
249 250 1.152440 TGGCCGTTGGGGTGAATTT 60.152 52.632 0.00 0.00 38.44 1.82
250 251 1.906333 GTGGCCGTTGGGGTGAATT 60.906 57.895 0.00 0.00 38.44 2.17
251 252 2.282887 GTGGCCGTTGGGGTGAAT 60.283 61.111 0.00 0.00 38.44 2.57
252 253 3.494254 AGTGGCCGTTGGGGTGAA 61.494 61.111 0.00 0.00 38.44 3.18
253 254 4.263572 CAGTGGCCGTTGGGGTGA 62.264 66.667 0.00 0.00 38.44 4.02
272 273 2.444706 AGCCTCGCATCTAGGGCA 60.445 61.111 7.98 0.00 46.23 5.36
273 274 2.341911 GAGCCTCGCATCTAGGGC 59.658 66.667 0.00 0.00 44.38 5.19
275 276 1.112315 ACTGGAGCCTCGCATCTAGG 61.112 60.000 0.00 0.00 37.17 3.02
276 277 0.749649 AACTGGAGCCTCGCATCTAG 59.250 55.000 0.00 0.00 0.00 2.43
277 278 0.461548 CAACTGGAGCCTCGCATCTA 59.538 55.000 0.00 0.00 0.00 1.98
278 279 1.220206 CAACTGGAGCCTCGCATCT 59.780 57.895 0.00 0.00 0.00 2.90
279 280 0.179062 ATCAACTGGAGCCTCGCATC 60.179 55.000 0.00 0.00 0.00 3.91
284 285 0.532573 TCGTCATCAACTGGAGCCTC 59.467 55.000 0.00 0.00 0.00 4.70
286 287 0.741221 GGTCGTCATCAACTGGAGCC 60.741 60.000 0.00 0.00 0.00 4.70
324 329 1.135094 CCCACATCTGGATGGCTACT 58.865 55.000 14.06 0.00 42.91 2.57
325 330 1.131638 TCCCACATCTGGATGGCTAC 58.868 55.000 14.06 0.00 42.91 3.58
339 344 0.107165 GGTGAAGTAGGCCATCCCAC 60.107 60.000 5.01 6.13 35.39 4.61
347 352 2.436115 GCACCGGGTGAAGTAGGC 60.436 66.667 30.65 9.54 35.23 3.93
366 371 1.134280 CAAATGAGCTCGATGGAGGGT 60.134 52.381 9.64 0.00 40.80 4.34
389 394 4.308458 CCGACAGCGTGGGGACAA 62.308 66.667 2.63 0.00 46.06 3.18
425 430 0.305922 GGAAAGAGCAATCGATGGCG 59.694 55.000 18.94 2.30 39.35 5.69
427 432 3.012518 ACAAGGAAAGAGCAATCGATGG 58.987 45.455 0.00 0.00 0.00 3.51
429 434 5.297776 CCATAACAAGGAAAGAGCAATCGAT 59.702 40.000 0.00 0.00 0.00 3.59
441 446 5.898120 TCCCAAATCTTCCATAACAAGGAA 58.102 37.500 0.00 0.00 42.62 3.36
448 453 6.339999 TCTGGAATCCCAAATCTTCCATAA 57.660 37.500 0.00 0.00 45.43 1.90
456 461 4.161001 AGCATGTTTCTGGAATCCCAAATC 59.839 41.667 0.00 0.00 42.98 2.17
477 482 1.065551 AGTTCGTTGCCAAAGACAAGC 59.934 47.619 0.00 0.00 0.00 4.01
487 492 0.317854 GCAAAGTGGAGTTCGTTGCC 60.318 55.000 5.56 0.00 41.66 4.52
503 508 6.418057 AATTTCTAACATTGGTCCTTGCAA 57.582 33.333 0.00 0.00 0.00 4.08
504 509 6.418057 AAATTTCTAACATTGGTCCTTGCA 57.582 33.333 0.00 0.00 0.00 4.08
563 571 4.479786 AAGGCATCCTTCTTAGAGACAC 57.520 45.455 0.00 0.00 40.17 3.67
589 597 1.414181 AGAGAGGTATTGACGCCATGG 59.586 52.381 7.63 7.63 0.00 3.66
631 639 2.067013 ACGAGTAAAAGGCGAGCTTTC 58.933 47.619 0.00 0.00 0.00 2.62
647 655 4.259970 CCGAATGCATTACTCAAAGACGAG 60.260 45.833 12.97 0.00 39.05 4.18
670 678 4.773149 CACTAAGGGGAGAGGATACATACC 59.227 50.000 0.00 0.00 41.41 2.73
674 682 4.834406 ATCACTAAGGGGAGAGGATACA 57.166 45.455 0.00 0.00 41.41 2.29
676 684 5.538877 ACAAATCACTAAGGGGAGAGGATA 58.461 41.667 0.00 0.00 0.00 2.59
679 687 3.519510 TGACAAATCACTAAGGGGAGAGG 59.480 47.826 0.00 0.00 0.00 3.69
716 725 9.663904 CAGACATGTATGAATTATTTTAACCGG 57.336 33.333 15.42 0.00 0.00 5.28
784 795 7.014422 GGTAAAAGAGGAGAGTGCTAGCTAATA 59.986 40.741 17.23 0.00 0.00 0.98
790 801 4.953579 AGAGGTAAAAGAGGAGAGTGCTAG 59.046 45.833 0.00 0.00 0.00 3.42
804 815 4.274147 TCAACCAAGCACAAGAGGTAAAA 58.726 39.130 0.00 0.00 33.15 1.52
885 896 2.045926 CCGTTGGAGGCCTTGAGG 60.046 66.667 6.77 2.71 38.53 3.86
980 991 4.475135 GGAGGTGGAAGGAGGCGC 62.475 72.222 0.00 0.00 0.00 6.53
1326 1360 4.547367 CCGGCCTCGATGAACCCC 62.547 72.222 0.00 0.00 39.00 4.95
1556 1626 1.672881 GATCAGATTTCCGCCACCAAG 59.327 52.381 0.00 0.00 0.00 3.61
1562 1632 1.429148 AACGCGATCAGATTTCCGCC 61.429 55.000 15.93 0.00 44.18 6.13
1589 1666 3.349006 AAGAACAGCCTGCACGCG 61.349 61.111 3.53 3.53 0.00 6.01
1942 2049 3.482783 GGTGCTCGAGCTTCACGC 61.483 66.667 35.27 18.29 42.66 5.34
1962 2069 3.195698 GCCGTCCATGAACGAGCC 61.196 66.667 5.86 0.00 45.37 4.70
2000 2107 1.227205 CATCTGCAGGAGGAGCGAC 60.227 63.158 15.13 0.00 32.51 5.19
2057 2164 4.699522 GTCCTCCGTGCGGGCTTT 62.700 66.667 10.94 0.00 34.94 3.51
2088 2195 1.151668 GCGATGATGGTGATAGGTGC 58.848 55.000 0.00 0.00 0.00 5.01
2160 2302 1.289800 TGTCGGTCGAGAGAGACACG 61.290 60.000 7.74 0.00 39.46 4.49
2201 2343 1.201855 GCGTCGCTCTCAGATGTTTTG 60.202 52.381 10.68 0.00 0.00 2.44
2229 2371 1.801913 GACCTGCACGTACGCTCAG 60.802 63.158 22.80 22.80 0.00 3.35
2261 2403 0.537188 TCGATGGGCTCTTGAGGTTC 59.463 55.000 0.00 0.00 0.00 3.62
2291 2434 2.029970 GTGTGGCGGAATTATGTACACG 59.970 50.000 0.00 0.00 0.00 4.49
2339 2482 8.134202 TCATCGAAGCCTTATTTCAGGATATA 57.866 34.615 0.00 0.00 35.71 0.86
2340 2483 7.009179 TCATCGAAGCCTTATTTCAGGATAT 57.991 36.000 0.00 0.00 35.71 1.63
2341 2484 6.419484 TCATCGAAGCCTTATTTCAGGATA 57.581 37.500 0.00 0.00 35.71 2.59
2344 2487 5.415415 CTTCATCGAAGCCTTATTTCAGG 57.585 43.478 0.00 0.00 32.78 3.86
2391 2562 2.993471 AATTTTCAGGCCGGCGCTG 61.993 57.895 28.82 28.82 34.44 5.18
2421 2592 2.052157 AGAGAAAACGCTCGAACTTCG 58.948 47.619 4.72 4.72 42.10 3.79
2422 2593 2.795470 ACAGAGAAAACGCTCGAACTTC 59.205 45.455 0.00 0.00 39.87 3.01
2423 2594 2.795470 GACAGAGAAAACGCTCGAACTT 59.205 45.455 0.00 0.00 39.87 2.66
2424 2595 2.034812 AGACAGAGAAAACGCTCGAACT 59.965 45.455 0.00 0.00 39.87 3.01
2425 2596 2.395654 AGACAGAGAAAACGCTCGAAC 58.604 47.619 0.00 0.00 39.87 3.95
2426 2597 2.795175 AGACAGAGAAAACGCTCGAA 57.205 45.000 0.00 0.00 39.87 3.71
2427 2598 4.166523 CAATAGACAGAGAAAACGCTCGA 58.833 43.478 0.00 0.00 39.87 4.04
2428 2599 3.921021 ACAATAGACAGAGAAAACGCTCG 59.079 43.478 0.00 0.00 39.87 5.03
2429 2600 6.094061 AGTACAATAGACAGAGAAAACGCTC 58.906 40.000 0.00 0.00 35.11 5.03
2430 2601 6.026947 AGTACAATAGACAGAGAAAACGCT 57.973 37.500 0.00 0.00 0.00 5.07
2431 2602 7.028361 ACTAGTACAATAGACAGAGAAAACGC 58.972 38.462 0.00 0.00 0.00 4.84
2432 2603 7.697291 GGACTAGTACAATAGACAGAGAAAACG 59.303 40.741 0.00 0.00 0.00 3.60
2433 2604 8.521176 TGGACTAGTACAATAGACAGAGAAAAC 58.479 37.037 4.94 0.00 0.00 2.43
2434 2605 8.645814 TGGACTAGTACAATAGACAGAGAAAA 57.354 34.615 4.94 0.00 0.00 2.29
2454 2625 1.471676 GCGACGGATCTCATTTGGACT 60.472 52.381 0.00 0.00 0.00 3.85
2455 2626 0.931005 GCGACGGATCTCATTTGGAC 59.069 55.000 0.00 0.00 0.00 4.02
2457 2628 0.461870 TGGCGACGGATCTCATTTGG 60.462 55.000 0.00 0.00 0.00 3.28
2458 2629 1.586422 ATGGCGACGGATCTCATTTG 58.414 50.000 0.00 0.00 0.00 2.32
2459 2630 1.942657 CAATGGCGACGGATCTCATTT 59.057 47.619 0.00 0.00 29.50 2.32
2460 2631 1.134401 ACAATGGCGACGGATCTCATT 60.134 47.619 0.00 0.00 31.02 2.57
2528 2720 4.803426 GGTGAGCGCACGGAGAGG 62.803 72.222 14.63 0.00 46.09 3.69
2534 2726 1.421485 GATTTCAGGTGAGCGCACG 59.579 57.895 14.63 1.73 46.09 5.34
2535 2727 0.674895 AGGATTTCAGGTGAGCGCAC 60.675 55.000 12.67 12.67 44.39 5.34
2537 2729 1.092345 GGAGGATTTCAGGTGAGCGC 61.092 60.000 0.00 0.00 0.00 5.92
2538 2730 0.250234 TGGAGGATTTCAGGTGAGCG 59.750 55.000 0.00 0.00 0.00 5.03
2539 2731 2.295885 CATGGAGGATTTCAGGTGAGC 58.704 52.381 0.00 0.00 0.00 4.26
2768 2984 3.324930 TGGGAGTCAGCCAGCCAG 61.325 66.667 0.00 0.00 0.00 4.85
2769 2985 3.324930 CTGGGAGTCAGCCAGCCA 61.325 66.667 2.86 0.00 36.60 4.75
2796 3012 0.393132 CTCCTTTCTTTCTCCCGGCC 60.393 60.000 0.00 0.00 0.00 6.13
2799 3015 0.253327 CCCCTCCTTTCTTTCTCCCG 59.747 60.000 0.00 0.00 0.00 5.14
2813 3033 5.368989 ACGAATCAAAATGATACTCCCCTC 58.631 41.667 0.00 0.00 35.76 4.30
2852 3073 4.347453 GGCAAGGCACGGCACTTG 62.347 66.667 15.73 15.73 45.19 3.16
2860 3081 2.785868 CCACTATCAGGCAAGGCAC 58.214 57.895 0.00 0.00 0.00 5.01
2899 3120 8.113062 CGTATACTCCTACAGTACGTATATTGC 58.887 40.741 0.00 0.00 40.60 3.56
2907 3128 3.496130 CCACCGTATACTCCTACAGTACG 59.504 52.174 0.56 0.00 40.60 3.67
2908 3129 4.455606 ACCACCGTATACTCCTACAGTAC 58.544 47.826 0.56 0.00 40.60 2.73
2909 3130 4.778213 ACCACCGTATACTCCTACAGTA 57.222 45.455 0.56 0.00 42.09 2.74
2910 3131 3.659183 ACCACCGTATACTCCTACAGT 57.341 47.619 0.56 0.00 39.41 3.55
2922 3143 2.104967 CCTCCAACTCATACCACCGTA 58.895 52.381 0.00 0.00 0.00 4.02
2923 3144 0.902531 CCTCCAACTCATACCACCGT 59.097 55.000 0.00 0.00 0.00 4.83
2924 3145 0.462047 GCCTCCAACTCATACCACCG 60.462 60.000 0.00 0.00 0.00 4.94
2927 3148 0.548926 TGGGCCTCCAACTCATACCA 60.549 55.000 4.53 0.00 40.73 3.25
2949 3172 4.838486 CGCTCGCTGGTCCGTCTC 62.838 72.222 0.00 0.00 0.00 3.36
2970 3193 1.001378 TGCTTTTCTTTTGGCTCGCTC 60.001 47.619 0.00 0.00 0.00 5.03
2971 3194 1.032014 TGCTTTTCTTTTGGCTCGCT 58.968 45.000 0.00 0.00 0.00 4.93
2972 3195 1.988467 GATGCTTTTCTTTTGGCTCGC 59.012 47.619 0.00 0.00 0.00 5.03
2973 3196 2.982470 GTGATGCTTTTCTTTTGGCTCG 59.018 45.455 0.00 0.00 0.00 5.03
2974 3197 3.981211 TGTGATGCTTTTCTTTTGGCTC 58.019 40.909 0.00 0.00 0.00 4.70
3082 3339 3.567797 GAGGAATGGTGCGAGCGC 61.568 66.667 8.08 8.08 42.35 5.92
3159 3431 1.929836 GATGAGTGGACGAATGAGTGC 59.070 52.381 0.00 0.00 0.00 4.40
3160 3432 2.926200 GTGATGAGTGGACGAATGAGTG 59.074 50.000 0.00 0.00 0.00 3.51
3161 3433 2.093973 GGTGATGAGTGGACGAATGAGT 60.094 50.000 0.00 0.00 0.00 3.41
3162 3434 2.544685 GGTGATGAGTGGACGAATGAG 58.455 52.381 0.00 0.00 0.00 2.90
3163 3435 1.207089 GGGTGATGAGTGGACGAATGA 59.793 52.381 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.