Multiple sequence alignment - TraesCS2B01G110700

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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 TraesCS2B01G110700 chr2B 100.000 3043 0 0 1 3043 72590236 72587194 0.000000e+00 5620
1 TraesCS2B01G110700 chr2B 82.081 346 46 11 9 350 462732293 462732626 6.930000e-72 281
2 TraesCS2B01G110700 chr2B 73.096 814 159 43 1105 1900 692073947 692073176 5.470000e-58 235
3 TraesCS2B01G110700 chr2B 100.000 69 0 0 3211 3279 72587026 72586958 9.550000e-26 128
4 TraesCS2B01G110700 chr2D 92.034 2862 123 44 2 2807 45548981 45546169 0.000000e+00 3925
5 TraesCS2B01G110700 chr2D 93.607 219 13 1 2826 3043 45545853 45545635 3.160000e-85 326
6 TraesCS2B01G110700 chr2D 84.393 346 39 9 9 350 391210861 391211195 3.160000e-85 326
7 TraesCS2B01G110700 chr1D 86.341 1618 174 33 1019 2618 7510039 7511627 0.000000e+00 1720
8 TraesCS2B01G110700 chr1D 80.729 384 59 10 1 380 60186961 60187333 5.350000e-73 285
9 TraesCS2B01G110700 chr1D 84.375 192 18 7 1025 1212 7037788 7037605 9.350000e-41 178
10 TraesCS2B01G110700 chr1B 86.039 1583 179 26 1022 2587 9712685 9711128 0.000000e+00 1661
11 TraesCS2B01G110700 chr1B 79.801 302 48 8 50 350 548276120 548276409 1.190000e-49 207
12 TraesCS2B01G110700 chr4A 85.460 956 119 12 962 1908 727127583 727128527 0.000000e+00 977
13 TraesCS2B01G110700 chr4A 84.270 623 78 13 962 1575 727190836 727190225 1.010000e-164 590
14 TraesCS2B01G110700 chr4A 90.476 315 27 3 1970 2284 727128632 727128943 2.350000e-111 412
15 TraesCS2B01G110700 chr6B 83.569 353 44 8 1 350 508933447 508933788 5.280000e-83 318
16 TraesCS2B01G110700 chr2A 82.152 381 57 8 1 380 145230463 145230833 1.900000e-82 316
17 TraesCS2B01G110700 chr2A 78.816 321 53 13 1106 1420 714022388 714022077 5.550000e-48 202
18 TraesCS2B01G110700 chr5B 79.937 319 61 2 1966 2281 466427728 466427410 7.080000e-57 231
19 TraesCS2B01G110700 chr7D 78.421 380 60 14 2 373 22747008 22746643 9.150000e-56 228
20 TraesCS2B01G110700 chr3B 74.874 398 81 12 427 807 649976911 649976516 2.620000e-36 163
21 TraesCS2B01G110700 chr5D 76.261 337 59 17 1 331 174635652 174635331 3.390000e-35 159


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 TraesCS2B01G110700 chr2B 72586958 72590236 3278 True 2874.0 5620 100.0000 1 3279 2 chr2B.!!$R2 3278
1 TraesCS2B01G110700 chr2B 692073176 692073947 771 True 235.0 235 73.0960 1105 1900 1 chr2B.!!$R1 795
2 TraesCS2B01G110700 chr2D 45545635 45548981 3346 True 2125.5 3925 92.8205 2 3043 2 chr2D.!!$R1 3041
3 TraesCS2B01G110700 chr1D 7510039 7511627 1588 False 1720.0 1720 86.3410 1019 2618 1 chr1D.!!$F1 1599
4 TraesCS2B01G110700 chr1B 9711128 9712685 1557 True 1661.0 1661 86.0390 1022 2587 1 chr1B.!!$R1 1565
5 TraesCS2B01G110700 chr4A 727127583 727128943 1360 False 694.5 977 87.9680 962 2284 2 chr4A.!!$F1 1322
6 TraesCS2B01G110700 chr4A 727190225 727190836 611 True 590.0 590 84.2700 962 1575 1 chr4A.!!$R1 613

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
48 49 0.167470 CAAAGATCTGGCGCACACTG 59.833 55.0 10.83 0.0 0.0 3.66 F
832 873 0.243907 TGAGTTCTAGACACGCCTGC 59.756 55.0 0.00 0.0 0.0 4.85 F
977 1020 0.668096 GTGTTATGTCACGCCACGGA 60.668 55.0 0.00 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1461 0.252103 AGAGACCCGGGTGAGCTTAA 60.252 55.0 36.01 0.0 0.00 1.85 R
2112 2238 1.750341 TTCCGCCTCCTTTGACACGA 61.750 55.0 0.00 0.0 0.00 4.35 R
2849 3286 0.249911 GTGTGTGTGTCCACCTCTCC 60.250 60.0 0.00 0.0 41.09 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
48 49 0.167470 CAAAGATCTGGCGCACACTG 59.833 55.000 10.83 0.00 0.00 3.66
58 59 1.875262 CGCACACTGCAAGGCATAA 59.125 52.632 0.00 0.00 45.36 1.90
86 87 2.341846 TCGGCATGTTTTATCCCCTC 57.658 50.000 0.00 0.00 0.00 4.30
102 103 1.687123 CCCTCATGTAACCGACCTAGG 59.313 57.143 7.41 7.41 37.30 3.02
104 105 2.100916 CCTCATGTAACCGACCTAGGTG 59.899 54.545 22.10 8.62 45.21 4.00
105 106 2.758979 CTCATGTAACCGACCTAGGTGT 59.241 50.000 22.10 9.39 45.21 4.16
106 107 3.949754 CTCATGTAACCGACCTAGGTGTA 59.050 47.826 22.10 3.06 45.21 2.90
122 123 1.401905 GTGTAACCCTACGTACCCTCG 59.598 57.143 0.00 0.00 0.00 4.63
149 150 3.697619 ATATAAGCCGAGGGGTTTAGC 57.302 47.619 4.25 0.00 40.84 3.09
150 151 0.472898 ATAAGCCGAGGGGTTTAGCC 59.527 55.000 4.25 0.00 40.84 3.93
151 152 1.963464 TAAGCCGAGGGGTTTAGCCG 61.963 60.000 4.25 0.00 40.84 5.52
152 153 4.851179 GCCGAGGGGTTTAGCCGG 62.851 72.222 0.00 0.00 42.74 6.13
155 156 3.723922 GAGGGGTTTAGCCGGCCA 61.724 66.667 26.15 6.66 38.44 5.36
168 169 1.348036 GCCGGCCATAGAGGTAGATTT 59.652 52.381 18.11 0.00 40.61 2.17
237 239 9.258629 CCCCATCCATAATCAATACAATACAAT 57.741 33.333 0.00 0.00 0.00 2.71
262 264 1.336609 GCAGGACGTCGAGTTTTACCT 60.337 52.381 9.92 0.00 0.00 3.08
263 265 2.593257 CAGGACGTCGAGTTTTACCTC 58.407 52.381 9.92 0.00 0.00 3.85
283 285 1.248785 TTCGAGAGGGTCCGAACCTG 61.249 60.000 10.61 0.00 45.66 4.00
296 298 3.583966 TCCGAACCTGGGTAAATACTGTT 59.416 43.478 0.00 0.00 0.00 3.16
301 303 6.348213 CGAACCTGGGTAAATACTGTTTCTTG 60.348 42.308 0.00 0.00 0.00 3.02
307 309 8.068892 TGGGTAAATACTGTTTCTTGTTTGTT 57.931 30.769 0.00 0.00 0.00 2.83
319 321 5.666969 TCTTGTTTGTTCTGTTACCATCG 57.333 39.130 0.00 0.00 0.00 3.84
352 354 1.076923 GCTCGGGACCCTCTACTCA 60.077 63.158 9.41 0.00 0.00 3.41
353 355 1.104577 GCTCGGGACCCTCTACTCAG 61.105 65.000 9.41 0.00 0.00 3.35
361 363 1.573376 ACCCTCTACTCAGGATCAGCT 59.427 52.381 0.00 0.00 35.20 4.24
362 364 1.962807 CCCTCTACTCAGGATCAGCTG 59.037 57.143 7.63 7.63 35.20 4.24
363 365 1.962807 CCTCTACTCAGGATCAGCTGG 59.037 57.143 15.13 0.00 35.20 4.85
364 366 2.424091 CCTCTACTCAGGATCAGCTGGA 60.424 54.545 15.13 1.28 35.20 3.86
365 367 3.499338 CTCTACTCAGGATCAGCTGGAT 58.501 50.000 15.13 6.11 39.53 3.41
366 368 3.896888 CTCTACTCAGGATCAGCTGGATT 59.103 47.826 15.13 0.00 36.00 3.01
367 369 3.894427 TCTACTCAGGATCAGCTGGATTC 59.106 47.826 15.13 8.66 36.00 2.52
368 370 2.475155 ACTCAGGATCAGCTGGATTCA 58.525 47.619 15.13 0.00 36.00 2.57
369 371 2.842496 ACTCAGGATCAGCTGGATTCAA 59.158 45.455 15.13 0.00 36.00 2.69
370 372 3.204526 CTCAGGATCAGCTGGATTCAAC 58.795 50.000 15.13 0.00 36.00 3.18
371 373 2.842496 TCAGGATCAGCTGGATTCAACT 59.158 45.455 15.13 0.16 36.00 3.16
372 374 3.118482 TCAGGATCAGCTGGATTCAACTC 60.118 47.826 15.13 0.00 36.00 3.01
373 375 2.172293 AGGATCAGCTGGATTCAACTCC 59.828 50.000 15.13 7.48 36.00 3.85
374 376 2.208431 GATCAGCTGGATTCAACTCCG 58.792 52.381 15.13 0.00 38.21 4.63
375 377 0.391661 TCAGCTGGATTCAACTCCGC 60.392 55.000 15.13 0.00 38.21 5.54
378 380 0.960364 GCTGGATTCAACTCCGCCAA 60.960 55.000 0.00 0.00 38.21 4.52
407 409 1.065358 GGCGAACGTCGAATCTTTGA 58.935 50.000 10.82 0.00 43.74 2.69
416 418 4.809426 ACGTCGAATCTTTGAAGTTTCTGT 59.191 37.500 0.00 5.94 34.25 3.41
444 446 6.796705 TTACTGGCTTGCTAAAACTTAGTC 57.203 37.500 0.00 0.00 0.00 2.59
448 450 2.482721 GCTTGCTAAAACTTAGTCGGCA 59.517 45.455 0.00 0.00 0.00 5.69
451 453 3.585862 TGCTAAAACTTAGTCGGCAGAG 58.414 45.455 0.00 0.00 0.00 3.35
453 455 4.081642 TGCTAAAACTTAGTCGGCAGAGAT 60.082 41.667 0.00 0.00 0.00 2.75
454 456 4.870991 GCTAAAACTTAGTCGGCAGAGATT 59.129 41.667 0.00 0.00 0.00 2.40
455 457 5.351740 GCTAAAACTTAGTCGGCAGAGATTT 59.648 40.000 0.00 0.00 0.00 2.17
456 458 6.128254 GCTAAAACTTAGTCGGCAGAGATTTT 60.128 38.462 3.92 6.01 0.00 1.82
457 459 7.064253 GCTAAAACTTAGTCGGCAGAGATTTTA 59.936 37.037 3.92 6.61 0.00 1.52
458 460 6.723131 AAACTTAGTCGGCAGAGATTTTAC 57.277 37.500 0.00 0.00 0.00 2.01
459 461 4.756502 ACTTAGTCGGCAGAGATTTTACC 58.243 43.478 0.00 0.00 0.00 2.85
460 462 2.295253 AGTCGGCAGAGATTTTACCG 57.705 50.000 0.00 0.00 45.15 4.02
483 485 2.614520 GTCTCAGTCGACTGCATAGCTA 59.385 50.000 35.48 18.61 43.46 3.32
500 502 4.174704 AGCTATTGGATCTTTGCATGGA 57.825 40.909 0.00 0.00 0.00 3.41
505 507 6.432162 GCTATTGGATCTTTGCATGGAGATTA 59.568 38.462 8.57 1.32 32.96 1.75
506 508 7.040201 GCTATTGGATCTTTGCATGGAGATTAA 60.040 37.037 8.57 8.01 32.96 1.40
554 556 3.834231 CCCTCACAACATTCTTTCCCATT 59.166 43.478 0.00 0.00 0.00 3.16
592 594 0.747644 TACCGGTTGCAGCATCCATG 60.748 55.000 15.04 13.52 0.00 3.66
638 657 1.202417 CCCTCGTCGATTGTAGCACAT 60.202 52.381 0.00 0.00 0.00 3.21
640 659 2.479560 CCTCGTCGATTGTAGCACATCA 60.480 50.000 0.00 0.00 0.00 3.07
661 680 0.448990 CACACCGGATGCAACATCTG 59.551 55.000 9.46 9.06 0.00 2.90
691 710 3.738791 TGTTTGTAGCATGTAGTCACACG 59.261 43.478 0.00 0.00 37.54 4.49
700 719 2.309613 TGTAGTCACACGGGTTGTAGT 58.690 47.619 0.00 0.00 35.67 2.73
701 720 2.034939 TGTAGTCACACGGGTTGTAGTG 59.965 50.000 0.00 0.00 43.46 2.74
710 729 2.132762 CGGGTTGTAGTGTCTGTTGTC 58.867 52.381 0.00 0.00 0.00 3.18
744 763 4.111916 CACTCCTTGCAACATTTTTCGTT 58.888 39.130 0.00 0.00 0.00 3.85
751 770 6.035542 CCTTGCAACATTTTTCGTTACTGTTT 59.964 34.615 0.00 0.00 0.00 2.83
763 804 1.167851 TACTGTTTGCAGCATCCAGC 58.832 50.000 17.58 0.00 46.30 4.85
764 805 1.530013 ACTGTTTGCAGCATCCAGCC 61.530 55.000 17.58 0.00 46.30 4.85
811 852 3.696898 GCTGATGTCAGTCTACTAACGG 58.303 50.000 11.35 0.00 45.45 4.44
823 864 6.370994 CAGTCTACTAACGGTTGAGTTCTAGA 59.629 42.308 3.07 0.00 32.59 2.43
832 873 0.243907 TGAGTTCTAGACACGCCTGC 59.756 55.000 0.00 0.00 0.00 4.85
873 914 3.078891 AGTCAAAGGCTTTCTCCATCC 57.921 47.619 10.08 0.00 0.00 3.51
879 920 3.010200 AGGCTTTCTCCATCCAATGTC 57.990 47.619 0.00 0.00 0.00 3.06
897 938 2.542178 TGTCGTCACGGAAAACAATCAG 59.458 45.455 0.00 0.00 0.00 2.90
944 986 4.391830 GTCACATCGCATCCAAAGACTTTA 59.608 41.667 0.00 0.00 0.00 1.85
945 987 5.065218 GTCACATCGCATCCAAAGACTTTAT 59.935 40.000 0.00 0.00 0.00 1.40
946 988 5.294306 TCACATCGCATCCAAAGACTTTATC 59.706 40.000 0.00 0.00 0.00 1.75
948 990 6.479990 CACATCGCATCCAAAGACTTTATCTA 59.520 38.462 0.00 0.00 36.27 1.98
952 994 5.409826 CGCATCCAAAGACTTTATCTATCCC 59.590 44.000 0.00 0.00 36.27 3.85
953 995 6.538263 GCATCCAAAGACTTTATCTATCCCT 58.462 40.000 0.00 0.00 36.27 4.20
954 996 7.001073 GCATCCAAAGACTTTATCTATCCCTT 58.999 38.462 0.00 0.00 36.27 3.95
955 997 7.503902 GCATCCAAAGACTTTATCTATCCCTTT 59.496 37.037 0.00 0.00 36.27 3.11
956 998 8.844244 CATCCAAAGACTTTATCTATCCCTTTG 58.156 37.037 0.00 0.00 36.27 2.77
971 1014 2.350388 CCCTTTGTGTGTTATGTCACGC 60.350 50.000 8.15 8.15 45.47 5.34
977 1020 0.668096 GTGTTATGTCACGCCACGGA 60.668 55.000 0.00 0.00 0.00 4.69
1038 1095 3.686916 AGGTCAACCTTTCAGCTCTAC 57.313 47.619 0.00 0.00 46.09 2.59
1069 1126 0.884514 GGAGCTCAACAAAGGCCTTC 59.115 55.000 20.79 3.97 0.00 3.46
1079 1136 1.406539 CAAAGGCCTTCCCATCATTCG 59.593 52.381 20.79 0.00 35.39 3.34
1200 1267 4.393155 AAGTCCATGGCGCTCGCA 62.393 61.111 16.36 0.00 44.11 5.10
1602 1678 3.073650 GGTGGGAGATGATAGCAAAGGAT 59.926 47.826 0.00 0.00 0.00 3.24
1686 1762 1.746220 CTACTAAGAGAGTGCAGCGGT 59.254 52.381 0.00 0.00 39.39 5.68
2086 2212 5.649395 GGTGATAATCATGGATATGGTGGTG 59.351 44.000 0.00 0.00 34.97 4.17
2091 2217 3.880608 TCATGGATATGGTGGTGGGATA 58.119 45.455 0.00 0.00 34.97 2.59
2212 2338 4.240888 GGAGCAAGATTTTCTTTGAAGCC 58.759 43.478 0.00 0.00 33.78 4.35
2324 2450 7.830940 TTCATGTTATGGATTTGAATGCAAC 57.169 32.000 2.04 0.00 40.19 4.17
2397 2527 8.738645 AAAATGAGTGTTTGACTAACTCTTCT 57.261 30.769 5.95 0.00 39.87 2.85
2444 2578 4.587584 TGTTTCACGGTCATACAGTACA 57.412 40.909 0.00 0.00 0.00 2.90
2486 2621 9.057089 GCTTTTAAACTATAGATGTGTATGCCT 57.943 33.333 6.78 0.00 0.00 4.75
2507 2642 5.295540 GCCTCTGAGGAATTTACAACATCTC 59.704 44.000 27.53 0.00 37.67 2.75
2685 2824 8.082242 GTGTATTTGCTTTTCACTGGATACTTT 58.918 33.333 0.00 0.00 37.61 2.66
2720 2859 1.584724 ATCACCGGGTTCAGATCCTT 58.415 50.000 6.32 0.00 0.00 3.36
2728 2867 2.173569 GGGTTCAGATCCTTACAGGCAT 59.826 50.000 0.00 0.00 34.61 4.40
2786 2926 8.940397 AAATCATCTATTACCCATGGTTAAGG 57.060 34.615 11.73 4.88 37.09 2.69
2823 2963 9.893305 AACTATGTACATAACAAAAACAGAAGC 57.107 29.630 16.17 0.00 42.70 3.86
2838 3275 5.774498 ACAGAAGCAGATATGTATCACGA 57.226 39.130 0.00 0.00 35.17 4.35
2844 3281 4.022762 AGCAGATATGTATCACGACAGGAC 60.023 45.833 0.00 0.00 35.17 3.85
2849 3286 3.145212 TGTATCACGACAGGACGATTG 57.855 47.619 0.00 0.00 37.03 2.67
2850 3287 2.159296 TGTATCACGACAGGACGATTGG 60.159 50.000 0.00 0.00 37.03 3.16
2851 3288 1.182667 ATCACGACAGGACGATTGGA 58.817 50.000 0.00 0.00 37.03 3.53
2878 3315 2.223180 GGACACACACACTTTTCGTTCC 60.223 50.000 0.00 0.00 0.00 3.62
2897 3334 5.881443 CGTTCCAACCCTATAAATGTGGTTA 59.119 40.000 0.00 0.00 39.01 2.85
2955 3392 5.049167 TGTTGCTTTCACAATCAAATCACC 58.951 37.500 0.00 0.00 0.00 4.02
2979 3416 4.874970 ACCACATCACTGCAATTCTTTTC 58.125 39.130 0.00 0.00 0.00 2.29
2998 3436 2.669364 TCTTTTCTTGCGGTAGACGTC 58.331 47.619 7.70 7.70 46.52 4.34
3036 3474 1.080298 GTTGACTTGCCAGGCATGC 60.080 57.895 24.13 9.90 38.13 4.06
3040 3478 1.228644 ACTTGCCAGGCATGCTTGA 60.229 52.632 29.53 9.26 38.76 3.02
3255 3693 3.844090 GGCTGGCTCCTCCTCGTC 61.844 72.222 0.00 0.00 35.26 4.20
3256 3694 4.200283 GCTGGCTCCTCCTCGTCG 62.200 72.222 0.00 0.00 35.26 5.12
3257 3695 3.522731 CTGGCTCCTCCTCGTCGG 61.523 72.222 0.00 0.00 35.26 4.79
3261 3699 3.213402 CTCCTCCTCGTCGGGCTC 61.213 72.222 0.00 0.00 0.00 4.70
3262 3700 4.816984 TCCTCCTCGTCGGGCTCC 62.817 72.222 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.815734 ATCTTGAGTACGTCGTGGGG 59.184 55.000 8.47 0.00 0.00 4.96
48 49 4.726416 CCGATGATTACATTATGCCTTGC 58.274 43.478 0.00 0.00 36.82 4.01
58 59 6.071952 GGGATAAAACATGCCGATGATTACAT 60.072 38.462 0.00 0.00 39.67 2.29
86 87 4.427312 GTTACACCTAGGTCGGTTACATG 58.573 47.826 12.84 0.00 34.29 3.21
102 103 1.401905 CGAGGGTACGTAGGGTTACAC 59.598 57.143 0.00 0.00 0.00 2.90
104 105 1.025041 CCGAGGGTACGTAGGGTTAC 58.975 60.000 0.00 0.00 35.38 2.50
105 106 0.751643 GCCGAGGGTACGTAGGGTTA 60.752 60.000 0.00 0.00 39.36 2.85
106 107 2.054453 GCCGAGGGTACGTAGGGTT 61.054 63.158 0.00 0.00 39.36 4.11
138 139 1.702022 TATGGCCGGCTAAACCCCTC 61.702 60.000 28.56 6.48 33.26 4.30
139 140 1.694882 TATGGCCGGCTAAACCCCT 60.695 57.895 28.56 6.46 33.26 4.79
149 150 5.046591 TGAATAAATCTACCTCTATGGCCGG 60.047 44.000 0.00 0.00 40.22 6.13
150 151 5.869888 GTGAATAAATCTACCTCTATGGCCG 59.130 44.000 0.00 0.00 40.22 6.13
151 152 6.769512 TGTGAATAAATCTACCTCTATGGCC 58.230 40.000 0.00 0.00 40.22 5.36
152 153 8.854614 ATTGTGAATAAATCTACCTCTATGGC 57.145 34.615 0.00 0.00 40.22 4.40
168 169 8.459911 TCTACCTGAAGATCGTATTGTGAATA 57.540 34.615 0.00 0.00 0.00 1.75
199 201 4.938575 ATGGATGGGGTACAAAGTACAA 57.061 40.909 9.27 0.00 0.00 2.41
237 239 0.956633 AACTCGACGTCCTGCTTGTA 59.043 50.000 10.58 0.00 0.00 2.41
238 240 0.104304 AAACTCGACGTCCTGCTTGT 59.896 50.000 10.58 0.00 0.00 3.16
239 241 1.217882 AAAACTCGACGTCCTGCTTG 58.782 50.000 10.58 0.00 0.00 4.01
240 242 2.401351 GTAAAACTCGACGTCCTGCTT 58.599 47.619 10.58 0.00 0.00 3.91
241 243 1.336609 GGTAAAACTCGACGTCCTGCT 60.337 52.381 10.58 0.00 0.00 4.24
245 247 3.240884 GAAGAGGTAAAACTCGACGTCC 58.759 50.000 10.58 0.00 42.31 4.79
262 264 0.964358 GGTTCGGACCCTCTCGAAGA 60.964 60.000 0.00 0.00 44.43 2.87
263 265 1.511768 GGTTCGGACCCTCTCGAAG 59.488 63.158 0.00 0.00 44.43 3.79
274 276 3.175594 ACAGTATTTACCCAGGTTCGGA 58.824 45.455 0.00 0.00 0.00 4.55
283 285 8.410912 AGAACAAACAAGAAACAGTATTTACCC 58.589 33.333 0.00 0.00 0.00 3.69
319 321 1.364626 CGAGCTGGTGATCTTGGCAC 61.365 60.000 0.00 0.00 35.56 5.01
352 354 2.172293 GGAGTTGAATCCAGCTGATCCT 59.828 50.000 17.39 4.18 39.34 3.24
353 355 2.570135 GGAGTTGAATCCAGCTGATCC 58.430 52.381 17.39 5.47 39.34 3.36
361 363 0.109532 TGTTGGCGGAGTTGAATCCA 59.890 50.000 0.00 0.00 39.53 3.41
362 364 1.200020 CTTGTTGGCGGAGTTGAATCC 59.800 52.381 0.00 0.00 35.88 3.01
363 365 1.401539 GCTTGTTGGCGGAGTTGAATC 60.402 52.381 0.00 0.00 0.00 2.52
364 366 0.598065 GCTTGTTGGCGGAGTTGAAT 59.402 50.000 0.00 0.00 0.00 2.57
365 367 0.465460 AGCTTGTTGGCGGAGTTGAA 60.465 50.000 0.00 0.00 37.29 2.69
366 368 0.884704 GAGCTTGTTGGCGGAGTTGA 60.885 55.000 0.00 0.00 37.29 3.18
367 369 1.576421 GAGCTTGTTGGCGGAGTTG 59.424 57.895 0.00 0.00 37.29 3.16
368 370 1.961277 CGAGCTTGTTGGCGGAGTT 60.961 57.895 0.00 0.00 37.29 3.01
369 371 2.357517 CGAGCTTGTTGGCGGAGT 60.358 61.111 0.00 0.00 37.29 3.85
370 372 2.357517 ACGAGCTTGTTGGCGGAG 60.358 61.111 0.00 0.00 37.29 4.63
371 373 2.664851 CACGAGCTTGTTGGCGGA 60.665 61.111 3.02 0.00 37.29 5.54
372 374 3.726517 CCACGAGCTTGTTGGCGG 61.727 66.667 3.02 0.00 37.29 6.13
373 375 4.389576 GCCACGAGCTTGTTGGCG 62.390 66.667 23.34 9.65 38.99 5.69
374 376 4.389576 CGCCACGAGCTTGTTGGC 62.390 66.667 25.83 25.83 40.39 4.52
375 377 2.250939 TTCGCCACGAGCTTGTTGG 61.251 57.895 3.02 10.68 40.39 3.77
395 397 7.971004 AAAACAGAAACTTCAAAGATTCGAC 57.029 32.000 6.99 0.00 41.17 4.20
425 427 3.071479 CCGACTAAGTTTTAGCAAGCCA 58.929 45.455 0.00 0.00 0.00 4.75
440 442 3.018856 TCGGTAAAATCTCTGCCGACTA 58.981 45.455 0.00 0.00 45.26 2.59
444 446 2.159226 AGACTCGGTAAAATCTCTGCCG 60.159 50.000 0.00 0.00 43.32 5.69
448 450 4.095185 CGACTGAGACTCGGTAAAATCTCT 59.905 45.833 17.02 0.00 35.83 3.10
451 453 4.097012 GTCGACTGAGACTCGGTAAAATC 58.903 47.826 17.02 3.66 35.83 2.17
453 455 3.549299 GTCGACTGAGACTCGGTAAAA 57.451 47.619 17.02 3.13 35.83 1.52
483 485 7.289317 ACATTAATCTCCATGCAAAGATCCAAT 59.711 33.333 9.31 9.18 31.03 3.16
500 502 5.815581 TGGTGCTTAGTCCAACATTAATCT 58.184 37.500 0.00 0.00 0.00 2.40
505 507 3.245229 TGGATGGTGCTTAGTCCAACATT 60.245 43.478 3.03 0.00 40.50 2.71
506 508 2.308570 TGGATGGTGCTTAGTCCAACAT 59.691 45.455 3.03 0.00 42.93 2.71
638 657 0.036022 TGTTGCATCCGGTGTGATGA 59.964 50.000 12.69 0.00 43.94 2.92
640 659 1.065199 AGATGTTGCATCCGGTGTGAT 60.065 47.619 12.69 0.00 0.00 3.06
661 680 4.114058 ACATGCTACAAACATCAATGCC 57.886 40.909 0.00 0.00 0.00 4.40
662 681 5.883661 ACTACATGCTACAAACATCAATGC 58.116 37.500 0.00 0.00 0.00 3.56
691 710 2.132762 CGACAACAGACACTACAACCC 58.867 52.381 0.00 0.00 0.00 4.11
700 719 1.732941 ACAAGCAACGACAACAGACA 58.267 45.000 0.00 0.00 0.00 3.41
701 720 2.348591 GCTACAAGCAACGACAACAGAC 60.349 50.000 0.00 0.00 41.89 3.51
726 745 5.040635 ACAGTAACGAAAAATGTTGCAAGG 58.959 37.500 0.00 0.00 34.83 3.61
741 760 1.535028 TGGATGCTGCAAACAGTAACG 59.465 47.619 6.36 0.00 46.30 3.18
742 761 2.669391 GCTGGATGCTGCAAACAGTAAC 60.669 50.000 26.70 14.07 46.30 2.50
744 763 1.167851 GCTGGATGCTGCAAACAGTA 58.832 50.000 26.70 8.74 46.30 2.74
769 810 1.218875 TAGTTGTGGTGTTGCGAGCG 61.219 55.000 0.00 0.00 0.00 5.03
811 852 2.329379 CAGGCGTGTCTAGAACTCAAC 58.671 52.381 0.00 0.00 0.00 3.18
873 914 3.326733 TTGTTTTCCGTGACGACATTG 57.673 42.857 6.54 0.00 0.00 2.82
879 920 1.262950 TGCTGATTGTTTTCCGTGACG 59.737 47.619 0.00 0.00 0.00 4.35
897 938 5.851047 AACAGCATTAAAAAGCAAGATGC 57.149 34.783 0.00 0.00 45.46 3.91
916 958 1.889545 TGGATGCGATGTGACAAACA 58.110 45.000 0.00 0.00 44.79 2.83
917 959 2.987413 TTGGATGCGATGTGACAAAC 57.013 45.000 0.00 0.00 0.00 2.93
944 986 6.823689 GTGACATAACACACAAAGGGATAGAT 59.176 38.462 0.00 0.00 40.11 1.98
945 987 6.170506 GTGACATAACACACAAAGGGATAGA 58.829 40.000 0.00 0.00 40.11 1.98
946 988 5.063438 CGTGACATAACACACAAAGGGATAG 59.937 44.000 0.00 0.00 40.34 2.08
948 990 3.751175 CGTGACATAACACACAAAGGGAT 59.249 43.478 0.00 0.00 40.34 3.85
952 994 2.289274 TGGCGTGACATAACACACAAAG 59.711 45.455 0.00 0.00 40.34 2.77
953 995 2.032302 GTGGCGTGACATAACACACAAA 59.968 45.455 0.00 0.00 40.34 2.83
954 996 1.600013 GTGGCGTGACATAACACACAA 59.400 47.619 0.00 0.00 40.34 3.33
955 997 1.222300 GTGGCGTGACATAACACACA 58.778 50.000 0.00 0.00 40.34 3.72
956 998 0.162933 CGTGGCGTGACATAACACAC 59.837 55.000 0.00 0.00 40.34 3.82
977 1020 2.441822 GATTGCTCTCCGGCGGCTAT 62.442 60.000 23.83 11.83 34.52 2.97
1032 1083 4.698304 AGCTCCGTTCTCATATAGTAGAGC 59.302 45.833 0.00 0.00 0.00 4.09
1036 1093 5.826208 TGTTGAGCTCCGTTCTCATATAGTA 59.174 40.000 12.15 0.00 39.96 1.82
1037 1094 4.645136 TGTTGAGCTCCGTTCTCATATAGT 59.355 41.667 12.15 0.00 39.96 2.12
1038 1095 5.188327 TGTTGAGCTCCGTTCTCATATAG 57.812 43.478 12.15 0.00 39.96 1.31
1069 1126 1.672363 CATGGTGTGTCGAATGATGGG 59.328 52.381 0.00 0.00 0.00 4.00
1079 1136 3.788766 GCGACGCCATGGTGTGTC 61.789 66.667 34.86 25.20 41.29 3.67
1388 1461 0.252103 AGAGACCCGGGTGAGCTTAA 60.252 55.000 36.01 0.00 0.00 1.85
1389 1462 0.683504 GAGAGACCCGGGTGAGCTTA 60.684 60.000 36.01 0.00 0.00 3.09
1662 1738 3.067461 CGCTGCACTCTCTTAGTAGGATT 59.933 47.826 0.00 0.00 35.76 3.01
1686 1762 2.833227 CCCACGGACCCAAAGACA 59.167 61.111 0.00 0.00 0.00 3.41
1912 2031 7.581213 TTGTTATAGTGAAATGGGCTTATGG 57.419 36.000 0.00 0.00 0.00 2.74
2086 2212 2.203195 TGCGGCACTGCATATCCC 60.203 61.111 0.00 0.00 40.62 3.85
2112 2238 1.750341 TTCCGCCTCCTTTGACACGA 61.750 55.000 0.00 0.00 0.00 4.35
2212 2338 3.594603 ATCTTGTAGTCACTGAACCCG 57.405 47.619 0.00 0.00 0.00 5.28
2324 2450 4.695217 AAGGTACCATTTGCATACAACG 57.305 40.909 15.94 0.00 34.87 4.10
2382 2508 7.819900 GCAAGGATAGAAGAAGAGTTAGTCAAA 59.180 37.037 0.00 0.00 0.00 2.69
2418 2548 4.819630 ACTGTATGACCGTGAAACATGTTT 59.180 37.500 23.49 23.49 35.74 2.83
2431 2565 5.965334 CGATTTTGCAATGTACTGTATGACC 59.035 40.000 0.00 0.00 0.00 4.02
2436 2570 3.753797 TGGCGATTTTGCAATGTACTGTA 59.246 39.130 0.00 0.00 36.28 2.74
2444 2578 2.389962 AAGCATGGCGATTTTGCAAT 57.610 40.000 0.00 0.00 38.84 3.56
2486 2621 9.823647 GAATAGAGATGTTGTAAATTCCTCAGA 57.176 33.333 0.00 0.00 0.00 3.27
2685 2824 6.887545 ACCCGGTGATTTTTGTATGAGAAATA 59.112 34.615 0.00 0.00 0.00 1.40
2809 2949 9.013229 TGATACATATCTGCTTCTGTTTTTGTT 57.987 29.630 0.82 0.00 33.88 2.83
2810 2950 8.454106 GTGATACATATCTGCTTCTGTTTTTGT 58.546 33.333 0.82 0.00 33.88 2.83
2811 2951 7.637519 CGTGATACATATCTGCTTCTGTTTTTG 59.362 37.037 0.82 0.00 33.88 2.44
2812 2952 7.549134 TCGTGATACATATCTGCTTCTGTTTTT 59.451 33.333 0.82 0.00 33.88 1.94
2813 2953 7.010552 GTCGTGATACATATCTGCTTCTGTTTT 59.989 37.037 0.82 0.00 33.88 2.43
2814 2954 6.477033 GTCGTGATACATATCTGCTTCTGTTT 59.523 38.462 0.82 0.00 33.88 2.83
2815 2955 5.980116 GTCGTGATACATATCTGCTTCTGTT 59.020 40.000 0.82 0.00 33.88 3.16
2816 2956 5.067805 TGTCGTGATACATATCTGCTTCTGT 59.932 40.000 0.82 0.00 33.88 3.41
2818 2958 5.278709 CCTGTCGTGATACATATCTGCTTCT 60.279 44.000 0.82 0.00 33.88 2.85
2820 2960 4.584743 TCCTGTCGTGATACATATCTGCTT 59.415 41.667 0.82 0.00 33.88 3.91
2821 2961 4.022762 GTCCTGTCGTGATACATATCTGCT 60.023 45.833 0.82 0.00 33.88 4.24
2822 2962 4.230657 GTCCTGTCGTGATACATATCTGC 58.769 47.826 0.82 0.00 33.88 4.26
2823 2963 4.213482 TCGTCCTGTCGTGATACATATCTG 59.787 45.833 0.82 0.00 33.88 2.90
2838 3275 0.898320 CACCTCTCCAATCGTCCTGT 59.102 55.000 0.00 0.00 0.00 4.00
2844 3281 0.608130 TGTGTCCACCTCTCCAATCG 59.392 55.000 0.00 0.00 0.00 3.34
2849 3286 0.249911 GTGTGTGTGTCCACCTCTCC 60.250 60.000 0.00 0.00 41.09 3.71
2850 3287 0.753262 AGTGTGTGTGTCCACCTCTC 59.247 55.000 0.00 0.00 41.09 3.20
2851 3288 1.204146 AAGTGTGTGTGTCCACCTCT 58.796 50.000 0.00 0.00 41.09 3.69
2878 3315 6.419791 TGGTCTAACCACATTTATAGGGTTG 58.580 40.000 5.23 0.00 44.79 3.77
2897 3334 1.107114 CTAGGCATGTCGTCTGGTCT 58.893 55.000 0.00 0.00 0.00 3.85
2905 3342 5.991606 TGGATAGAAAAATCTAGGCATGTCG 59.008 40.000 0.00 0.00 0.00 4.35
2955 3392 3.928727 AGAATTGCAGTGATGTGGTTG 57.071 42.857 0.00 0.00 0.00 3.77
2979 3416 2.673833 AGACGTCTACCGCAAGAAAAG 58.326 47.619 18.46 0.00 41.42 2.27
3210 3648 3.931907 CCAATGACTGGGTAATCCTCA 57.068 47.619 0.00 0.00 42.17 3.86
3238 3676 3.844090 GACGAGGAGGAGCCAGCC 61.844 72.222 0.00 0.00 40.02 4.85
3239 3677 4.200283 CGACGAGGAGGAGCCAGC 62.200 72.222 0.00 0.00 40.02 4.85
3240 3678 3.522731 CCGACGAGGAGGAGCCAG 61.523 72.222 0.00 0.00 45.00 4.85
3244 3682 3.213402 GAGCCCGACGAGGAGGAG 61.213 72.222 0.00 0.00 45.00 3.69
3245 3683 4.816984 GGAGCCCGACGAGGAGGA 62.817 72.222 0.00 0.00 45.00 3.71


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

AutoCloner maintained by Alex Coulton.