Multiple sequence alignment - TraesCS1B01G398700

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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 TraesCS1B01G398700 chr1B 100.000 3026 0 0 1 3026 629939874 629936849 0.000000e+00 5589.0
1 TraesCS1B01G398700 chr1B 81.503 173 29 3 2235 2405 49146426 49146255 4.070000e-29 139.0
2 TraesCS1B01G398700 chr1B 78.075 187 39 2 2221 2405 641636708 641636894 1.910000e-22 117.0
3 TraesCS1B01G398700 chr1B 100.000 38 0 0 502 539 629939410 629939373 1.510000e-08 71.3
4 TraesCS1B01G398700 chr1D 90.522 1878 100 41 583 2418 458483317 458481476 0.000000e+00 2410.0
5 TraesCS1B01G398700 chr1D 89.450 436 39 5 2595 3026 458480875 458480443 7.380000e-151 544.0
6 TraesCS1B01G398700 chr1D 84.211 133 16 5 2221 2350 445264558 445264688 1.140000e-24 124.0
7 TraesCS1B01G398700 chr1D 73.684 266 52 12 2216 2467 405082769 405083030 1.490000e-13 87.9
8 TraesCS1B01G398700 chr1A 87.287 2116 128 62 579 2677 550969528 550967537 0.000000e+00 2287.0
9 TraesCS1B01G398700 chr1A 91.463 328 27 1 2700 3026 550967426 550967099 1.650000e-122 449.0
10 TraesCS1B01G398700 chr7B 87.859 313 9 12 1 284 531437101 531436789 1.040000e-89 340.0
11 TraesCS1B01G398700 chr7B 88.018 217 22 2 285 501 531436715 531436503 1.390000e-63 254.0
12 TraesCS1B01G398700 chr4A 85.942 313 15 9 1 284 456322903 456322591 1.050000e-79 307.0
13 TraesCS1B01G398700 chr4A 85.942 313 15 9 1 284 457555562 457555250 1.050000e-79 307.0
14 TraesCS1B01G398700 chr4A 92.233 206 16 0 285 490 456322516 456322311 2.950000e-75 292.0
15 TraesCS1B01G398700 chr4A 92.233 206 16 0 285 490 457555175 457554970 2.950000e-75 292.0
16 TraesCS1B01G398700 chr4A 87.363 182 22 1 308 489 51132506 51132686 1.100000e-49 207.0
17 TraesCS1B01G398700 chr4A 83.744 203 32 1 285 487 40868909 40868708 1.110000e-44 191.0
18 TraesCS1B01G398700 chr4A 79.821 223 33 10 2221 2437 621887051 621887267 5.230000e-33 152.0
19 TraesCS1B01G398700 chr4A 81.443 194 25 9 2250 2437 621894444 621894632 6.760000e-32 148.0
20 TraesCS1B01G398700 chr4A 89.535 86 1 3 502 579 456322336 456322251 5.340000e-18 102.0
21 TraesCS1B01G398700 chr4A 89.535 86 1 3 502 579 457554995 457554910 5.340000e-18 102.0
22 TraesCS1B01G398700 chr5A 75.301 664 108 35 1379 2026 433567008 433567631 1.790000e-67 267.0
23 TraesCS1B01G398700 chr5D 74.962 663 112 34 1379 2026 332518203 332518826 3.870000e-64 255.0
24 TraesCS1B01G398700 chr5B 81.949 277 42 8 1379 1651 388594623 388594895 8.440000e-56 228.0
25 TraesCS1B01G398700 chrUn 74.729 554 98 32 1280 1812 74554129 74553597 3.060000e-50 209.0
26 TraesCS1B01G398700 chr7D 84.878 205 29 2 285 488 2093254 2093457 3.950000e-49 206.0
27 TraesCS1B01G398700 chr7D 82.857 210 30 6 279 487 545310550 545310346 1.850000e-42 183.0
28 TraesCS1B01G398700 chr2B 84.390 205 29 3 285 488 423908337 423908135 6.620000e-47 198.0
29 TraesCS1B01G398700 chr7A 83.415 205 28 6 285 488 6796414 6796215 5.150000e-43 185.0
30 TraesCS1B01G398700 chr7A 82.128 235 18 5 5 216 127455466 127455233 2.400000e-41 180.0
31 TraesCS1B01G398700 chr6D 72.497 749 142 44 1275 1991 431466125 431466841 1.850000e-42 183.0
32 TraesCS1B01G398700 chr2D 82.589 224 17 11 5 206 42875234 42875457 8.620000e-41 178.0
33 TraesCS1B01G398700 chr2D 73.764 263 56 11 2219 2474 467143905 467143649 1.160000e-14 91.6
34 TraesCS1B01G398700 chr6B 73.105 554 107 28 1280 1812 651420409 651419877 3.120000e-35 159.0
35 TraesCS1B01G398700 chr6B 77.729 229 37 12 2248 2469 166590771 166590992 8.810000e-26 128.0
36 TraesCS1B01G398700 chr6B 76.256 219 40 10 2252 2467 503585594 503585803 4.130000e-19 106.0
37 TraesCS1B01G398700 chr2A 75.197 254 55 8 2219 2467 168839504 168839254 2.470000e-21 113.0


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 TraesCS1B01G398700 chr1B 629936849 629939874 3025 True 2830.150000 5589 100.000000 1 3026 2 chr1B.!!$R2 3025
1 TraesCS1B01G398700 chr1D 458480443 458483317 2874 True 1477.000000 2410 89.986000 583 3026 2 chr1D.!!$R1 2443
2 TraesCS1B01G398700 chr1A 550967099 550969528 2429 True 1368.000000 2287 89.375000 579 3026 2 chr1A.!!$R1 2447
3 TraesCS1B01G398700 chr7B 531436503 531437101 598 True 297.000000 340 87.938500 1 501 2 chr7B.!!$R1 500
4 TraesCS1B01G398700 chr4A 456322251 456322903 652 True 233.666667 307 89.236667 1 579 3 chr4A.!!$R2 578
5 TraesCS1B01G398700 chr4A 457554910 457555562 652 True 233.666667 307 89.236667 1 579 3 chr4A.!!$R3 578
6 TraesCS1B01G398700 chr5A 433567008 433567631 623 False 267.000000 267 75.301000 1379 2026 1 chr5A.!!$F1 647
7 TraesCS1B01G398700 chr5D 332518203 332518826 623 False 255.000000 255 74.962000 1379 2026 1 chr5D.!!$F1 647
8 TraesCS1B01G398700 chrUn 74553597 74554129 532 True 209.000000 209 74.729000 1280 1812 1 chrUn.!!$R1 532

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
865 978 0.107017 CCAGGTCCATGTCCATGTCC 60.107 60.0 6.53 8.14 37.11 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2253 0.453282 CAATGCACACGTACTGCTGC 60.453 55.0 16.09 6.66 35.53 5.25 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
41 42 1.316651 GAAGCCCATGATTCTGAGCC 58.683 55.000 0.00 0.00 34.08 4.70
235 265 6.270000 TCGATATGTCACATTTTCTATCCCCT 59.730 38.462 0.00 0.00 0.00 4.79
380 484 9.619316 TGGATTCGTATTTGAACATAGTTTTTG 57.381 29.630 0.00 0.00 0.00 2.44
403 507 9.681692 TTTGATGATTCTACTTTTTGTGACATG 57.318 29.630 0.00 0.00 0.00 3.21
601 705 2.344025 CTGCTTAACTCGTTGTACCCC 58.656 52.381 0.00 0.00 0.00 4.95
620 724 2.120232 CCGTGAGCATCTGTCGATTAC 58.880 52.381 0.00 0.00 34.92 1.89
700 804 4.192317 GGATTAGTCACAATCTGTCACCC 58.808 47.826 0.00 0.00 35.61 4.61
715 819 1.119684 CACCCCCGTCTGACATCATA 58.880 55.000 8.73 0.00 0.00 2.15
766 870 2.223340 CCTTCCCGATTGCGAATTTCTG 60.223 50.000 0.00 0.00 40.82 3.02
791 895 2.799917 GCGTAATCAGTCTCTTCGCCAT 60.800 50.000 0.00 0.00 36.95 4.40
828 932 1.291184 CGTCGACCAAATCAGCAGCA 61.291 55.000 10.58 0.00 0.00 4.41
857 970 4.082523 CCGCGACCAGGTCCATGT 62.083 66.667 14.46 0.00 0.00 3.21
858 971 2.509336 CGCGACCAGGTCCATGTC 60.509 66.667 14.46 0.00 0.00 3.06
859 972 2.125106 GCGACCAGGTCCATGTCC 60.125 66.667 14.46 0.00 0.00 4.02
860 973 2.954684 GCGACCAGGTCCATGTCCA 61.955 63.158 14.46 0.00 0.00 4.02
861 974 1.907739 CGACCAGGTCCATGTCCAT 59.092 57.895 14.46 0.00 0.00 3.41
862 975 0.462581 CGACCAGGTCCATGTCCATG 60.463 60.000 14.46 0.14 38.51 3.66
863 976 0.620556 GACCAGGTCCATGTCCATGT 59.379 55.000 8.65 3.56 37.11 3.21
864 977 0.620556 ACCAGGTCCATGTCCATGTC 59.379 55.000 6.53 0.13 37.11 3.06
865 978 0.107017 CCAGGTCCATGTCCATGTCC 60.107 60.000 6.53 8.14 37.11 4.02
866 979 0.620030 CAGGTCCATGTCCATGTCCA 59.380 55.000 15.83 0.00 37.11 4.02
867 980 1.004628 CAGGTCCATGTCCATGTCCAA 59.995 52.381 15.83 0.00 37.11 3.53
868 981 1.004745 AGGTCCATGTCCATGTCCAAC 59.995 52.381 15.83 6.31 37.11 3.77
869 982 1.463674 GTCCATGTCCATGTCCAACC 58.536 55.000 6.53 0.00 37.11 3.77
870 983 1.071434 TCCATGTCCATGTCCAACCA 58.929 50.000 6.53 0.00 37.11 3.67
871 984 1.640149 TCCATGTCCATGTCCAACCAT 59.360 47.619 6.53 0.00 37.11 3.55
872 985 2.042842 TCCATGTCCATGTCCAACCATT 59.957 45.455 6.53 0.00 37.11 3.16
873 986 2.428171 CCATGTCCATGTCCAACCATTC 59.572 50.000 6.53 0.00 37.11 2.67
874 987 2.967745 TGTCCATGTCCAACCATTCA 57.032 45.000 0.00 0.00 0.00 2.57
875 988 2.794103 TGTCCATGTCCAACCATTCAG 58.206 47.619 0.00 0.00 0.00 3.02
876 989 1.474077 GTCCATGTCCAACCATTCAGC 59.526 52.381 0.00 0.00 0.00 4.26
889 1002 1.580845 ATTCAGCTCCAACGCAGCAC 61.581 55.000 0.00 0.00 39.56 4.40
922 1035 3.200825 TCCATTTCCTTCTCTAGGCAAGG 59.799 47.826 12.31 12.31 44.37 3.61
934 1050 2.358003 GCAAGGAGCAGACGCAGT 60.358 61.111 0.00 0.00 45.50 4.40
935 1051 1.963338 GCAAGGAGCAGACGCAGTT 60.963 57.895 0.00 0.00 43.21 3.16
936 1052 0.670546 GCAAGGAGCAGACGCAGTTA 60.671 55.000 0.00 0.00 43.21 2.24
937 1053 2.592721 GCAAGGAGCAGACGCAGTTAG 61.593 57.143 0.00 0.00 43.21 2.34
949 1065 1.687494 GCAGTTAGCGCTCCAGTTCG 61.687 60.000 16.34 0.00 0.00 3.95
950 1066 0.388649 CAGTTAGCGCTCCAGTTCGT 60.389 55.000 16.34 0.00 0.00 3.85
953 1069 0.601558 TTAGCGCTCCAGTTCGTTCT 59.398 50.000 16.34 0.00 0.00 3.01
956 1072 1.347817 GCGCTCCAGTTCGTTCTCTG 61.348 60.000 0.00 0.00 0.00 3.35
957 1073 1.347817 CGCTCCAGTTCGTTCTCTGC 61.348 60.000 0.00 0.00 0.00 4.26
961 1077 1.488957 CAGTTCGTTCTCTGCGCAC 59.511 57.895 5.66 0.00 0.00 5.34
1192 1323 2.885644 CGCATGACCCCGTTCTCG 60.886 66.667 0.00 0.00 0.00 4.04
2087 2269 2.664851 GGCAGCAGTACGTGTGCA 60.665 61.111 22.27 0.00 43.82 4.57
2097 2279 3.361644 CAGTACGTGTGCATTGAATTTGC 59.638 43.478 0.00 0.00 40.55 3.68
2106 2288 2.224495 ATTGAATTTGCGCGGGTGGG 62.224 55.000 8.83 0.00 0.00 4.61
2149 2333 7.069085 AGAGGATAATTTGACATGTCCATTTGG 59.931 37.037 22.85 0.00 0.00 3.28
2194 2390 7.769272 TTTTTCAGTGTGTGATTTTCATTCC 57.231 32.000 0.00 0.00 34.17 3.01
2207 2403 9.262358 GTGATTTTCATTCCTAGTACATACTCC 57.738 37.037 0.00 0.00 37.73 3.85
2208 2404 8.988060 TGATTTTCATTCCTAGTACATACTCCA 58.012 33.333 0.00 0.00 37.73 3.86
2382 2607 9.796062 CAATTTTGTGTTGTGAATGCTAATAAC 57.204 29.630 0.00 0.00 0.00 1.89
2446 2765 7.414222 TCAGATAAACCTAATACGTGGAGTT 57.586 36.000 0.00 0.00 0.00 3.01
2447 2766 7.486647 TCAGATAAACCTAATACGTGGAGTTC 58.513 38.462 0.00 0.00 0.00 3.01
2490 2809 3.347216 ACATTCATGGTGTTGCTACCTC 58.653 45.455 0.00 0.00 41.43 3.85
2492 2811 3.788227 TTCATGGTGTTGCTACCTCTT 57.212 42.857 0.00 0.00 41.43 2.85
2493 2812 3.334583 TCATGGTGTTGCTACCTCTTC 57.665 47.619 0.00 0.00 41.43 2.87
2495 2814 2.839486 TGGTGTTGCTACCTCTTCTG 57.161 50.000 0.00 0.00 41.43 3.02
2514 2833 6.326583 TCTTCTGGATTCGGGTTTCTATACAT 59.673 38.462 0.00 0.00 0.00 2.29
2516 2835 5.365605 TCTGGATTCGGGTTTCTATACATGT 59.634 40.000 2.69 2.69 0.00 3.21
2558 2877 4.075910 CACGCGCGTGCACATTCT 62.076 61.111 44.73 14.43 42.97 2.40
2560 2879 2.024868 ACGCGCGTGCACATTCTAA 61.025 52.632 37.37 0.00 42.97 2.10
2562 2881 0.853224 CGCGCGTGCACATTCTAAAG 60.853 55.000 24.19 0.00 42.97 1.85
2565 2884 2.664424 GCGCGTGCACATTCTAAAGAAA 60.664 45.455 17.66 0.00 42.15 2.52
2566 2885 3.155998 CGCGTGCACATTCTAAAGAAAG 58.844 45.455 18.64 0.00 37.61 2.62
2585 2904 5.239525 AGAAAGTGGTGTTGCTACATTTCTC 59.760 40.000 16.65 7.21 34.47 2.87
2588 2907 3.563808 GTGGTGTTGCTACATTTCTCACA 59.436 43.478 3.85 0.00 36.50 3.58
2590 2909 3.058224 GGTGTTGCTACATTTCTCACACC 60.058 47.826 3.85 2.96 36.50 4.16
2591 2910 3.058224 GTGTTGCTACATTTCTCACACCC 60.058 47.826 3.85 0.00 36.50 4.61
2593 2912 3.788227 TGCTACATTTCTCACACCCTT 57.212 42.857 0.00 0.00 0.00 3.95
2602 3253 6.605594 ACATTTCTCACACCCTTTTTAGTTGA 59.394 34.615 0.00 0.00 0.00 3.18
2621 3272 2.147150 GACTCACAACTCTTTCCTGCC 58.853 52.381 0.00 0.00 0.00 4.85
2634 3285 0.036732 TCCTGCCGAACAATTCAGCT 59.963 50.000 0.00 0.00 34.23 4.24
2677 3328 8.463930 TCATCCAAAAAGAAAGTCAACATACT 57.536 30.769 0.00 0.00 0.00 2.12
2731 3470 3.002791 AGCAATGTGTTCTGATGGTACG 58.997 45.455 0.00 0.00 0.00 3.67
2734 3473 4.245660 CAATGTGTTCTGATGGTACGACT 58.754 43.478 0.00 0.00 0.00 4.18
2736 3475 4.696899 TGTGTTCTGATGGTACGACTAG 57.303 45.455 0.00 0.00 0.00 2.57
2769 3508 9.489393 CTTTTTGGAAGAAAAAGAAAAATTCCG 57.511 29.630 12.30 0.00 45.32 4.30
2793 3532 5.234466 ACCAAGTGAAGCAAGAAGTATCT 57.766 39.130 0.00 0.00 37.57 1.98
2878 3617 9.630098 AATGAATATGTTGACACAACTCAATTC 57.370 29.630 14.19 16.72 36.16 2.17
2885 3624 6.974048 TGTTGACACAACTCAATTCAAGAATG 59.026 34.615 14.19 0.00 32.78 2.67
2981 3721 8.133024 TCATCTACAAATTATTTTGGGCACTT 57.867 30.769 13.17 0.00 45.34 3.16
3003 3743 9.922305 CACTTAGCAAAAGTAGCTATGATAAAC 57.078 33.333 12.96 0.00 43.48 2.01
3004 3744 9.110502 ACTTAGCAAAAGTAGCTATGATAAACC 57.889 33.333 12.96 0.00 43.48 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.277273 CTGACACTGGGCTCAGAATCA 59.723 52.381 23.49 20.73 43.49 2.57
41 42 1.735920 GTGCTCGAGCTGACACTGG 60.736 63.158 35.27 0.00 42.66 4.00
123 133 9.699985 GGATCGTATAGTAAATATGTACAGTCG 57.300 37.037 5.84 5.12 0.00 4.18
206 218 7.657761 GGATAGAAAATGTGACATATCGAACCT 59.342 37.037 0.00 0.00 0.00 3.50
208 220 7.095187 GGGGATAGAAAATGTGACATATCGAAC 60.095 40.741 0.00 0.00 0.00 3.95
212 241 9.606631 GATAGGGGATAGAAAATGTGACATATC 57.393 37.037 0.00 0.65 0.00 1.63
291 395 8.740123 TCAGTTAAATCCACTGTCAAACTTTA 57.260 30.769 0.24 0.00 42.12 1.85
295 399 9.959749 TTTTATCAGTTAAATCCACTGTCAAAC 57.040 29.630 0.24 0.00 42.12 2.93
379 483 7.040548 TGCATGTCACAAAAAGTAGAATCATCA 60.041 33.333 0.00 0.00 0.00 3.07
380 484 7.307694 TGCATGTCACAAAAAGTAGAATCATC 58.692 34.615 0.00 0.00 0.00 2.92
459 563 9.063615 ACTACTTTCGTCCTGATTTATTGTTTT 57.936 29.630 0.00 0.00 0.00 2.43
504 608 9.886132 ATTTGTATACTACTTTCGTCCTGATTT 57.114 29.630 4.17 0.00 0.00 2.17
506 610 9.962783 GTATTTGTATACTACTTTCGTCCTGAT 57.037 33.333 4.17 0.00 34.92 2.90
507 611 8.959548 TGTATTTGTATACTACTTTCGTCCTGA 58.040 33.333 4.17 0.00 37.97 3.86
508 612 9.745880 ATGTATTTGTATACTACTTTCGTCCTG 57.254 33.333 4.17 0.00 37.97 3.86
509 613 9.745880 CATGTATTTGTATACTACTTTCGTCCT 57.254 33.333 4.17 0.00 37.97 3.85
510 614 9.525409 ACATGTATTTGTATACTACTTTCGTCC 57.475 33.333 0.00 0.00 37.97 4.79
524 628 9.089601 CGTTGGTAGACATAACATGTATTTGTA 57.910 33.333 0.00 0.00 45.03 2.41
528 632 7.324935 TGTCGTTGGTAGACATAACATGTATT 58.675 34.615 0.00 0.00 45.03 1.89
579 683 2.409975 GGTACAACGAGTTAAGCAGCA 58.590 47.619 0.00 0.00 0.00 4.41
580 684 1.730612 GGGTACAACGAGTTAAGCAGC 59.269 52.381 0.00 0.00 0.00 5.25
581 685 2.344025 GGGGTACAACGAGTTAAGCAG 58.656 52.381 0.00 0.00 0.00 4.24
601 705 2.120232 GGTAATCGACAGATGCTCACG 58.880 52.381 0.00 0.00 37.14 4.35
620 724 4.487714 TCAATAACTAGAGGGCAACTGG 57.512 45.455 0.00 0.00 0.00 4.00
667 771 3.119955 TGTGACTAATCCAACTCGAGTCG 60.120 47.826 20.33 7.73 39.52 4.18
700 804 4.302455 GTTCAGATATGATGTCAGACGGG 58.698 47.826 0.00 0.00 0.00 5.28
715 819 1.290134 GGGAGAGGTTGGGTTCAGAT 58.710 55.000 0.00 0.00 0.00 2.90
766 870 3.060873 GCGAAGAGACTGATTACGCATTC 60.061 47.826 0.00 0.00 43.18 2.67
842 955 2.125106 GGACATGGACCTGGTCGC 60.125 66.667 19.98 13.42 32.65 5.19
857 970 1.355381 AGCTGAATGGTTGGACATGGA 59.645 47.619 0.00 0.00 0.00 3.41
858 971 1.747355 GAGCTGAATGGTTGGACATGG 59.253 52.381 0.00 0.00 0.00 3.66
859 972 1.747355 GGAGCTGAATGGTTGGACATG 59.253 52.381 0.00 0.00 0.00 3.21
860 973 1.355381 TGGAGCTGAATGGTTGGACAT 59.645 47.619 0.00 0.00 0.00 3.06
861 974 0.770499 TGGAGCTGAATGGTTGGACA 59.230 50.000 0.00 0.00 0.00 4.02
862 975 1.541588 GTTGGAGCTGAATGGTTGGAC 59.458 52.381 0.00 0.00 0.00 4.02
863 976 1.881925 CGTTGGAGCTGAATGGTTGGA 60.882 52.381 0.00 0.00 0.00 3.53
864 977 0.523072 CGTTGGAGCTGAATGGTTGG 59.477 55.000 0.00 0.00 0.00 3.77
865 978 0.109597 GCGTTGGAGCTGAATGGTTG 60.110 55.000 0.00 0.00 0.00 3.77
866 979 0.537143 TGCGTTGGAGCTGAATGGTT 60.537 50.000 0.00 0.00 38.13 3.67
867 980 0.957395 CTGCGTTGGAGCTGAATGGT 60.957 55.000 0.00 0.00 38.16 3.55
868 981 1.798735 CTGCGTTGGAGCTGAATGG 59.201 57.895 0.00 0.00 38.16 3.16
869 982 1.136147 GCTGCGTTGGAGCTGAATG 59.864 57.895 2.86 0.00 38.16 2.67
870 983 1.302752 TGCTGCGTTGGAGCTGAAT 60.303 52.632 11.54 0.00 38.16 2.57
871 984 2.110835 TGCTGCGTTGGAGCTGAA 59.889 55.556 11.54 0.00 38.16 3.02
872 985 2.666190 GTGCTGCGTTGGAGCTGA 60.666 61.111 11.54 0.00 38.16 4.26
873 986 2.453773 CTTGTGCTGCGTTGGAGCTG 62.454 60.000 11.54 0.00 37.35 4.24
874 987 2.203195 TTGTGCTGCGTTGGAGCT 60.203 55.556 11.54 0.00 37.35 4.09
875 988 2.253452 CTTGTGCTGCGTTGGAGC 59.747 61.111 3.15 3.15 36.95 4.70
876 989 2.253452 GCTTGTGCTGCGTTGGAG 59.747 61.111 0.00 0.00 36.03 3.86
934 1050 0.601558 AGAACGAACTGGAGCGCTAA 59.398 50.000 11.50 0.00 0.00 3.09
935 1051 0.170561 GAGAACGAACTGGAGCGCTA 59.829 55.000 11.50 0.00 0.00 4.26
936 1052 1.080434 GAGAACGAACTGGAGCGCT 60.080 57.895 11.27 11.27 0.00 5.92
937 1053 1.080434 AGAGAACGAACTGGAGCGC 60.080 57.895 0.00 0.00 0.00 5.92
939 1055 1.347817 CGCAGAGAACGAACTGGAGC 61.348 60.000 0.00 0.00 35.05 4.70
941 1057 1.372997 GCGCAGAGAACGAACTGGA 60.373 57.895 0.30 0.00 35.05 3.86
942 1058 1.664649 TGCGCAGAGAACGAACTGG 60.665 57.895 5.66 0.00 35.05 4.00
943 1059 1.488957 GTGCGCAGAGAACGAACTG 59.511 57.895 12.22 0.00 36.11 3.16
944 1060 2.016704 CGTGCGCAGAGAACGAACT 61.017 57.895 12.22 0.00 39.64 3.01
945 1061 2.465920 CGTGCGCAGAGAACGAAC 59.534 61.111 12.22 0.00 39.64 3.95
1003 1119 1.078143 GCTGCTTGTACAGGGAGGG 60.078 63.158 24.43 5.16 38.16 4.30
1176 1304 3.195698 GCGAGAACGGGGTCATGC 61.196 66.667 0.00 0.00 40.15 4.06
1226 1372 3.800685 TTGACTGGCGTGGTCGTGG 62.801 63.158 0.00 0.00 39.49 4.94
1228 1374 2.029073 CTTGACTGGCGTGGTCGT 59.971 61.111 0.00 0.00 39.49 4.34
1230 1376 3.050275 GCCTTGACTGGCGTGGTC 61.050 66.667 0.00 0.00 43.74 4.02
2070 2252 1.577328 AATGCACACGTACTGCTGCC 61.577 55.000 16.09 0.00 35.53 4.85
2071 2253 0.453282 CAATGCACACGTACTGCTGC 60.453 55.000 16.09 6.66 35.53 5.25
2087 2269 1.215117 CCACCCGCGCAAATTCAAT 59.785 52.632 8.75 0.00 0.00 2.57
2106 2288 3.263425 TCCTCTTCTTATCCAACCACCAC 59.737 47.826 0.00 0.00 0.00 4.16
2111 2295 8.841300 GTCAAATTATCCTCTTCTTATCCAACC 58.159 37.037 0.00 0.00 0.00 3.77
2172 2368 6.713762 AGGAATGAAAATCACACACTGAAA 57.286 33.333 0.00 0.00 30.60 2.69
2174 2370 6.533730 ACTAGGAATGAAAATCACACACTGA 58.466 36.000 0.00 0.00 0.00 3.41
2180 2376 9.817809 GAGTATGTACTAGGAATGAAAATCACA 57.182 33.333 0.00 0.00 36.50 3.58
2185 2381 9.832445 GAATGGAGTATGTACTAGGAATGAAAA 57.168 33.333 0.00 0.00 36.50 2.29
2194 2390 8.928270 AAGAAAACGAATGGAGTATGTACTAG 57.072 34.615 0.00 0.00 36.50 2.57
2207 2403 8.837059 CGTGGAGTAATAAAAAGAAAACGAATG 58.163 33.333 0.00 0.00 0.00 2.67
2208 2404 8.562052 ACGTGGAGTAATAAAAAGAAAACGAAT 58.438 29.630 0.00 0.00 0.00 3.34
2356 2553 9.796062 GTTATTAGCATTCACAACACAAAATTG 57.204 29.630 0.00 0.00 0.00 2.32
2382 2607 9.594478 AAGGTTTGACCAAGTTTATACAAAAAG 57.406 29.630 0.00 0.00 41.95 2.27
2427 2746 8.674263 TTTTTGAACTCCACGTATTAGGTTTA 57.326 30.769 0.00 0.00 0.00 2.01
2471 2790 4.018960 AGAAGAGGTAGCAACACCATGAAT 60.019 41.667 0.00 0.00 41.40 2.57
2490 2809 5.914033 TGTATAGAAACCCGAATCCAGAAG 58.086 41.667 0.00 0.00 0.00 2.85
2492 2811 5.365605 ACATGTATAGAAACCCGAATCCAGA 59.634 40.000 0.00 0.00 0.00 3.86
2493 2812 5.611374 ACATGTATAGAAACCCGAATCCAG 58.389 41.667 0.00 0.00 0.00 3.86
2495 2814 6.289064 AGAACATGTATAGAAACCCGAATCC 58.711 40.000 0.00 0.00 0.00 3.01
2530 2849 0.715551 ACGCGCGTGCATATCATATG 59.284 50.000 37.37 0.00 42.97 1.78
2554 2873 6.770785 TGTAGCAACACCACTTTCTTTAGAAT 59.229 34.615 0.00 0.00 33.54 2.40
2557 2876 6.560253 ATGTAGCAACACCACTTTCTTTAG 57.440 37.500 0.00 0.00 38.78 1.85
2558 2877 6.952773 AATGTAGCAACACCACTTTCTTTA 57.047 33.333 0.00 0.00 38.78 1.85
2560 2879 5.594317 AGAAATGTAGCAACACCACTTTCTT 59.406 36.000 0.00 0.00 37.70 2.52
2562 2881 5.008613 TGAGAAATGTAGCAACACCACTTTC 59.991 40.000 0.00 0.00 38.78 2.62
2565 2884 3.815401 GTGAGAAATGTAGCAACACCACT 59.185 43.478 0.00 0.00 38.78 4.00
2566 2885 3.563808 TGTGAGAAATGTAGCAACACCAC 59.436 43.478 0.00 0.00 38.78 4.16
2585 2904 4.638421 TGTGAGTCAACTAAAAAGGGTGTG 59.362 41.667 0.00 0.00 0.00 3.82
2602 3253 1.541233 CGGCAGGAAAGAGTTGTGAGT 60.541 52.381 0.00 0.00 0.00 3.41
2621 3272 9.988350 AATTTATGTACTTAGCTGAATTGTTCG 57.012 29.630 0.00 0.00 0.00 3.95
2686 3421 6.310960 TGATGGTTTCAAATTATTCGTGACG 58.689 36.000 0.00 0.00 0.00 4.35
2731 3470 6.619801 TCTTCCAAAAAGTTTGAGCTAGTC 57.380 37.500 2.30 0.00 0.00 2.59
2734 3473 8.527810 TCTTTTTCTTCCAAAAAGTTTGAGCTA 58.472 29.630 15.65 0.00 43.81 3.32
2736 3475 7.595311 TCTTTTTCTTCCAAAAAGTTTGAGC 57.405 32.000 15.65 0.00 43.81 4.26
2764 3503 2.851263 TGCTTCACTTGGTACGGAAT 57.149 45.000 0.00 0.00 0.00 3.01
2769 3508 6.166982 AGATACTTCTTGCTTCACTTGGTAC 58.833 40.000 0.00 0.00 0.00 3.34
2805 3544 7.222417 CACTTGCGCCATCATATTTCAAAAATA 59.778 33.333 4.18 0.00 0.00 1.40
2811 3550 3.016031 ACACTTGCGCCATCATATTTCA 58.984 40.909 4.18 0.00 0.00 2.69
2819 3558 3.365832 CATTATGAACACTTGCGCCATC 58.634 45.455 4.18 0.00 0.00 3.51
2885 3624 4.443394 CGTAACCGCTACCAATGACTATTC 59.557 45.833 0.00 0.00 0.00 1.75
2959 3699 7.177568 TGCTAAGTGCCCAAAATAATTTGTAGA 59.822 33.333 2.71 0.00 40.87 2.59
2981 3721 7.570132 TGGGTTTATCATAGCTACTTTTGCTA 58.430 34.615 0.00 0.00 45.49 3.49


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

AutoCloner maintained by Alex Coulton.