Multiple sequence alignment - TraesCS3A01G244300

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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 TraesCS3A01G244300 chr3A 100.000 4026 0 0 1 4026 457486119 457490144 0.000000e+00 7435.0
1 TraesCS3A01G244300 chr3D 95.152 1980 75 9 1315 3279 346311074 346309101 0.000000e+00 3105.0
2 TraesCS3A01G244300 chr3D 91.742 1332 63 22 1 1312 346312422 346311118 0.000000e+00 1807.0
3 TraesCS3A01G244300 chr3D 92.880 309 20 2 3494 3802 346308417 346308111 7.940000e-122 448.0
4 TraesCS3A01G244300 chr3D 85.824 261 14 13 3273 3522 346308761 346308513 5.160000e-64 255.0
5 TraesCS3A01G244300 chr3B 95.524 1698 66 2 1481 3168 445594721 445593024 0.000000e+00 2706.0
6 TraesCS3A01G244300 chr3B 89.521 1336 88 26 1 1312 445596428 445595121 0.000000e+00 1644.0
7 TraesCS3A01G244300 chr3B 91.435 467 28 2 3559 4025 445588752 445588298 7.340000e-177 630.0
8 TraesCS3A01G244300 chr3B 85.799 338 29 12 3166 3503 445592931 445592613 1.390000e-89 340.0
9 TraesCS3A01G244300 chr3B 93.269 104 6 1 1387 1490 445594986 445594884 6.970000e-33 152.0
10 TraesCS3A01G244300 chr1A 100.000 29 0 0 1022 1050 482257160 482257132 2.000000e-03 54.7


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 TraesCS3A01G244300 chr3A 457486119 457490144 4025 False 7435.00 7435 100.0000 1 4026 1 chr3A.!!$F1 4025
1 TraesCS3A01G244300 chr3D 346308111 346312422 4311 True 1403.75 3105 91.3995 1 3802 4 chr3D.!!$R1 3801
2 TraesCS3A01G244300 chr3B 445588298 445596428 8130 True 1094.40 2706 91.1096 1 4025 5 chr3B.!!$R1 4024

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
828 865 0.179215 CGGCAGCTGATGTTTCGTTC 60.179 55.0 20.43 0.0 0.0 3.95 F
1324 1406 0.180406 AACTTCGTGGCCTTGTGAGT 59.820 50.0 3.32 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2623 2911 0.109723 TACGCCTCCAAACCAGCTTT 59.890 50.000 0.00 0.0 0.0 3.51 R
3057 3350 1.745087 GCACATGTACATCAGTTGGGG 59.255 52.381 5.07 0.0 0.0 4.96 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
33 34 5.455056 ACACAGTACTAGGAACTTGTGAG 57.545 43.478 22.13 7.88 45.24 3.51
37 38 5.775701 ACAGTACTAGGAACTTGTGAGATGT 59.224 40.000 0.00 0.00 45.24 3.06
80 81 4.580167 GGTAATGCTGTATGAATTGCTCCA 59.420 41.667 0.00 0.00 0.00 3.86
89 90 8.352201 GCTGTATGAATTGCTCCAAATAACATA 58.648 33.333 0.00 0.00 0.00 2.29
208 210 8.248253 TGATAAAGTGTAAGTTAGCAGATTCGA 58.752 33.333 0.00 0.00 0.00 3.71
236 256 5.978814 TCCAAGCTTGAGAAGGATTAGTAC 58.021 41.667 28.05 0.00 0.00 2.73
237 257 4.806247 CCAAGCTTGAGAAGGATTAGTACG 59.194 45.833 28.05 0.90 0.00 3.67
238 258 5.394224 CCAAGCTTGAGAAGGATTAGTACGA 60.394 44.000 28.05 0.00 0.00 3.43
239 259 6.276847 CAAGCTTGAGAAGGATTAGTACGAT 58.723 40.000 22.31 0.00 0.00 3.73
240 260 6.472686 AGCTTGAGAAGGATTAGTACGATT 57.527 37.500 0.00 0.00 0.00 3.34
241 261 6.508777 AGCTTGAGAAGGATTAGTACGATTC 58.491 40.000 0.00 0.00 0.00 2.52
242 262 5.692654 GCTTGAGAAGGATTAGTACGATTCC 59.307 44.000 8.41 8.41 0.00 3.01
243 263 5.434352 TGAGAAGGATTAGTACGATTCCG 57.566 43.478 10.17 0.00 42.50 4.30
244 264 4.277672 TGAGAAGGATTAGTACGATTCCGG 59.722 45.833 10.17 0.00 40.78 5.14
245 265 4.213513 AGAAGGATTAGTACGATTCCGGT 58.786 43.478 0.00 4.32 40.78 5.28
246 266 4.037684 AGAAGGATTAGTACGATTCCGGTG 59.962 45.833 0.00 0.00 40.78 4.94
247 267 2.035576 AGGATTAGTACGATTCCGGTGC 59.964 50.000 0.00 0.00 40.78 5.01
248 268 2.223876 GGATTAGTACGATTCCGGTGCA 60.224 50.000 0.00 0.00 40.78 4.57
249 269 3.554337 GGATTAGTACGATTCCGGTGCAT 60.554 47.826 0.00 0.00 40.78 3.96
250 270 4.321452 GGATTAGTACGATTCCGGTGCATA 60.321 45.833 0.00 0.00 40.78 3.14
262 282 1.229428 GGTGCATACCATCATCACGG 58.771 55.000 0.00 0.00 46.71 4.94
272 292 1.871676 CATCATCACGGGAATCAGCAG 59.128 52.381 0.00 0.00 0.00 4.24
302 322 4.838152 CATGACGCTCCCCGGTGG 62.838 72.222 0.00 0.82 42.52 4.61
325 345 1.246056 CGTCCAGGTACTCGGACCAA 61.246 60.000 21.26 0.00 46.46 3.67
351 371 2.364961 CTTCCTCTCCCTCGGGGT 59.635 66.667 0.00 0.00 44.74 4.95
586 606 1.264288 GAAGGGCAACACAGAAACGAG 59.736 52.381 0.00 0.00 39.74 4.18
612 632 3.826157 GGATCAATGGTGGAACAAACAGA 59.174 43.478 0.00 0.00 44.16 3.41
677 699 1.672356 GGAGCATTCCACGCACTGT 60.672 57.895 0.00 0.00 43.45 3.55
692 714 0.331954 ACTGTAGGGCGAGGAAGAGA 59.668 55.000 0.00 0.00 0.00 3.10
752 788 1.927838 GGAGAACGAATCGAAGAAGGC 59.072 52.381 10.55 0.00 43.58 4.35
758 794 0.460311 GAATCGAAGAAGGCGGAGGA 59.540 55.000 0.00 0.00 43.58 3.71
828 865 0.179215 CGGCAGCTGATGTTTCGTTC 60.179 55.000 20.43 0.00 0.00 3.95
926 967 1.893919 GACGGCTGAGAAAGGGCTCT 61.894 60.000 0.00 0.00 35.91 4.09
934 975 1.746991 GAAAGGGCTCTGGGCTTCG 60.747 63.158 0.00 0.00 41.46 3.79
1074 1115 2.588856 GGATCTTCCAACCGACCCGG 62.589 65.000 3.58 3.58 44.30 5.73
1257 1298 2.499205 CCGCTCAAGGATACGCCA 59.501 61.111 0.00 0.00 46.39 5.69
1308 1390 2.158943 GCCTCGCTCTTAACCCATAACT 60.159 50.000 0.00 0.00 0.00 2.24
1312 1394 3.194116 TCGCTCTTAACCCATAACTTCGT 59.806 43.478 0.00 0.00 0.00 3.85
1322 1404 2.422597 CATAACTTCGTGGCCTTGTGA 58.577 47.619 3.32 0.00 0.00 3.58
1324 1406 0.180406 AACTTCGTGGCCTTGTGAGT 59.820 50.000 3.32 0.00 0.00 3.41
1332 1414 2.548480 GTGGCCTTGTGAGTGTTACTTC 59.452 50.000 3.32 0.00 0.00 3.01
1333 1415 2.171659 TGGCCTTGTGAGTGTTACTTCA 59.828 45.455 3.32 0.00 0.00 3.02
1357 1439 8.316946 TCAGAATGTGAAGTGATTCTACTGATT 58.683 33.333 0.00 0.00 36.90 2.57
1375 1457 4.119862 TGATTTCCTACTGCGCATACTTC 58.880 43.478 12.24 0.98 0.00 3.01
1378 1460 1.200483 CCTACTGCGCATACTTCACG 58.800 55.000 12.24 0.00 0.00 4.35
1384 1466 3.093574 CTGCGCATACTTCACGATTTTG 58.906 45.455 12.24 0.00 0.00 2.44
1400 1509 7.748683 TCACGATTTTGCATACAGTAAACAATC 59.251 33.333 0.00 0.00 31.28 2.67
1420 1529 2.361119 TCAGTACCATCTGTATGACCGC 59.639 50.000 0.00 0.00 34.84 5.68
1516 1797 8.740369 CAATTGCTAATCTTGAATTCTTAAGCG 58.260 33.333 7.05 0.00 0.00 4.68
1555 1836 4.223320 TCTCGGTTCAAAATGCTTCAAC 57.777 40.909 0.00 0.00 0.00 3.18
1651 1934 1.794701 GCTTGCTGGCTTTGCTAAAAC 59.205 47.619 0.00 0.00 0.00 2.43
1879 2167 3.055530 AGGAGTCTGTTCAGTGGCTTATG 60.056 47.826 0.00 0.00 0.00 1.90
1880 2168 3.265791 GAGTCTGTTCAGTGGCTTATGG 58.734 50.000 0.00 0.00 0.00 2.74
1888 2176 3.808728 TCAGTGGCTTATGGATAACAGC 58.191 45.455 0.00 0.00 0.00 4.40
1897 2185 6.486657 GGCTTATGGATAACAGCAAGAACATA 59.513 38.462 0.00 0.00 30.47 2.29
1900 2188 4.188462 TGGATAACAGCAAGAACATACCG 58.812 43.478 0.00 0.00 0.00 4.02
1948 2236 4.081807 CCGTCCTTAGTAAACAAGCTAGGT 60.082 45.833 0.00 0.00 0.00 3.08
1954 2242 1.463444 GTAAACAAGCTAGGTGGCACG 59.537 52.381 12.17 0.00 34.17 5.34
1956 2244 0.682852 AACAAGCTAGGTGGCACGTA 59.317 50.000 18.03 18.03 34.17 3.57
1969 2257 2.668945 TGGCACGTATGTTCAATACACG 59.331 45.455 0.00 0.00 40.19 4.49
1975 2263 4.082081 ACGTATGTTCAATACACGGGAGAA 60.082 41.667 0.00 0.00 40.19 2.87
2179 2467 3.838903 CAAAAGGTCTGTCTACCCTAGGT 59.161 47.826 8.29 0.00 40.71 3.08
2251 2539 3.334691 CGACTGTAGGAAAGCCATTCAA 58.665 45.455 2.66 0.00 39.98 2.69
2332 2620 2.748132 CGAGAGTCCACATCTAGAGGCT 60.748 54.545 3.87 0.00 0.00 4.58
2430 2718 5.338708 CCCCACTATCAATGTTCAGAGAACT 60.339 44.000 10.79 0.00 0.00 3.01
2515 2803 2.300152 CTGGAGAGTTGTAGCTGGACAA 59.700 50.000 0.00 0.00 36.98 3.18
2590 2878 6.866770 GGAAAGCTAAAGGTTCATTTTGGTAC 59.133 38.462 0.00 0.00 34.26 3.34
2756 3044 4.968626 TGTTGATGTTTCGGATGATTTCG 58.031 39.130 0.00 0.00 0.00 3.46
3057 3350 2.419159 GCATGAAAGGGGCAATTCCTTC 60.419 50.000 0.00 0.00 43.24 3.46
3118 3419 3.547054 AAAGAATGACCGCCGGTATTA 57.453 42.857 9.73 0.00 35.25 0.98
3160 3461 9.762381 TTGTAATTGGGAGGTATATTTTCTTGT 57.238 29.630 0.00 0.00 0.00 3.16
3223 3619 1.000843 CTGCCATCATCATGCCCAATG 59.999 52.381 0.00 0.00 37.66 2.82
3238 3634 3.756434 GCCCAATGCTTAACAACTACAGA 59.244 43.478 0.00 0.00 36.87 3.41
3247 3643 7.667557 TGCTTAACAACTACAGATACAGAACT 58.332 34.615 0.00 0.00 0.00 3.01
3248 3644 8.799367 TGCTTAACAACTACAGATACAGAACTA 58.201 33.333 0.00 0.00 0.00 2.24
3249 3645 9.291664 GCTTAACAACTACAGATACAGAACTAG 57.708 37.037 0.00 0.00 0.00 2.57
3307 4050 8.352942 ACTCTTGTGTGTCTAATTTGAATTTCC 58.647 33.333 0.00 0.00 0.00 3.13
3308 4051 8.231692 TCTTGTGTGTCTAATTTGAATTTCCA 57.768 30.769 0.00 0.00 0.00 3.53
3396 4147 4.970860 AATCCTGGATCCTCACACATAG 57.029 45.455 14.23 0.00 0.00 2.23
3397 4148 2.042464 TCCTGGATCCTCACACATAGC 58.958 52.381 14.23 0.00 0.00 2.97
3398 4149 1.764723 CCTGGATCCTCACACATAGCA 59.235 52.381 14.23 0.00 0.00 3.49
3399 4150 2.224233 CCTGGATCCTCACACATAGCAG 60.224 54.545 14.23 0.00 0.00 4.24
3400 4151 1.764723 TGGATCCTCACACATAGCAGG 59.235 52.381 14.23 0.00 0.00 4.85
3401 4152 2.042464 GGATCCTCACACATAGCAGGA 58.958 52.381 3.84 0.00 39.42 3.86
3402 4153 2.036992 GGATCCTCACACATAGCAGGAG 59.963 54.545 3.84 0.00 38.47 3.69
3403 4154 2.238084 TCCTCACACATAGCAGGAGT 57.762 50.000 0.00 0.00 31.10 3.85
3404 4155 1.827344 TCCTCACACATAGCAGGAGTG 59.173 52.381 0.00 0.00 39.12 3.51
3423 4174 1.003580 TGCAGGACAGAAGGGTTCATC 59.996 52.381 0.00 0.00 0.00 2.92
3456 4207 2.596851 CCAGTCCCACTGTCCCCAG 61.597 68.421 3.07 0.00 44.50 4.45
3477 4228 0.033504 TCTCTGCTGGTGTTCCGTTC 59.966 55.000 0.00 0.00 36.30 3.95
3478 4229 0.034059 CTCTGCTGGTGTTCCGTTCT 59.966 55.000 0.00 0.00 36.30 3.01
3491 4242 1.148310 CCGTTCTGGTTGCTGTACAG 58.852 55.000 18.93 18.93 0.00 2.74
3509 4395 4.680171 ACAGTTATCTTTTGCCGCTTAC 57.320 40.909 0.00 0.00 0.00 2.34
3524 4410 4.143179 GCCGCTTACTGTAAACTTGTAGTG 60.143 45.833 1.46 0.00 0.00 2.74
3534 4420 8.545420 ACTGTAAACTTGTAGTGAACATAAACG 58.455 33.333 0.00 0.00 38.10 3.60
3540 4426 4.827692 TGTAGTGAACATAAACGAGCCAT 58.172 39.130 0.00 0.00 31.43 4.40
3561 4447 6.198591 GCCATTATCGTGTAGACAACTAAGTC 59.801 42.308 0.00 0.00 38.81 3.01
3585 8227 6.310711 TCGTTAATACATGTGTTGTTGCGATA 59.689 34.615 17.19 0.00 39.87 2.92
3665 8307 6.827251 TCAGATAGTTCAGTTCGGTGTATACT 59.173 38.462 4.17 0.00 0.00 2.12
3666 8308 7.338703 TCAGATAGTTCAGTTCGGTGTATACTT 59.661 37.037 4.17 0.00 0.00 2.24
3711 8353 4.672587 TGTTCTTCACACAAGCTAGAGT 57.327 40.909 0.00 0.00 0.00 3.24
3798 8440 4.217334 TCTGATGCGTTCCAATGCTTTTAA 59.783 37.500 5.16 0.00 41.45 1.52
3800 8442 3.019933 TGCGTTCCAATGCTTTTAACC 57.980 42.857 5.16 0.00 41.45 2.85
3814 8456 7.487822 TGCTTTTAACCCATCATTCCATAAA 57.512 32.000 0.00 0.00 0.00 1.40
3833 8475 3.788227 AAGTTTGATGCACTCCCTGTA 57.212 42.857 0.00 0.00 0.00 2.74
3840 8482 3.118038 TGATGCACTCCCTGTATTTACCC 60.118 47.826 0.00 0.00 0.00 3.69
3841 8483 1.562475 TGCACTCCCTGTATTTACCCC 59.438 52.381 0.00 0.00 0.00 4.95
3842 8484 1.844497 GCACTCCCTGTATTTACCCCT 59.156 52.381 0.00 0.00 0.00 4.79
3843 8485 2.421529 GCACTCCCTGTATTTACCCCTG 60.422 54.545 0.00 0.00 0.00 4.45
3844 8486 2.844348 CACTCCCTGTATTTACCCCTGT 59.156 50.000 0.00 0.00 0.00 4.00
3845 8487 2.844348 ACTCCCTGTATTTACCCCTGTG 59.156 50.000 0.00 0.00 0.00 3.66
3846 8488 2.172717 CTCCCTGTATTTACCCCTGTGG 59.827 54.545 0.00 0.00 41.37 4.17
3847 8489 1.409661 CCCTGTATTTACCCCTGTGGC 60.410 57.143 0.00 0.00 37.83 5.01
3848 8490 1.564348 CCTGTATTTACCCCTGTGGCT 59.436 52.381 0.00 0.00 37.83 4.75
3849 8491 2.025321 CCTGTATTTACCCCTGTGGCTT 60.025 50.000 0.00 0.00 37.83 4.35
3850 8492 3.563479 CCTGTATTTACCCCTGTGGCTTT 60.563 47.826 0.00 0.00 37.83 3.51
3864 8506 1.340991 TGGCTTTCCTTGGATGCCTAC 60.341 52.381 24.06 8.37 43.57 3.18
3906 8548 2.035961 TCTCACTGCTGCGTTAACTTCT 59.964 45.455 3.71 0.00 0.00 2.85
3910 8552 1.195448 CTGCTGCGTTAACTTCTGGTG 59.805 52.381 3.71 0.00 0.00 4.17
3921 8563 1.202855 ACTTCTGGTGTCTGCTGCATT 60.203 47.619 1.31 0.00 0.00 3.56
3924 8566 3.354948 TCTGGTGTCTGCTGCATTATT 57.645 42.857 1.31 0.00 0.00 1.40
3929 8571 4.280425 TGGTGTCTGCTGCATTATTTTTCA 59.720 37.500 1.31 0.00 0.00 2.69
3957 8599 5.391097 CGTGGTAGTGTAAAGTCTGAGAGAG 60.391 48.000 0.00 0.00 0.00 3.20
4022 8664 8.635765 TTCATGGCTACCTTTTTATATGGATC 57.364 34.615 0.00 0.00 0.00 3.36
4025 8667 9.685276 CATGGCTACCTTTTTATATGGATCATA 57.315 33.333 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.138276 TCTCACAAGTTCCTAGTACTGTGT 58.862 41.667 5.39 10.87 32.01 3.72
14 15 6.274157 ACATCTCACAAGTTCCTAGTACTG 57.726 41.667 5.39 0.00 0.00 2.74
15 16 6.919775 AACATCTCACAAGTTCCTAGTACT 57.080 37.500 0.00 0.00 0.00 2.73
33 34 6.148480 CCTATGCCAGCACTAGAATAAACATC 59.852 42.308 0.00 0.00 0.00 3.06
37 38 5.630415 ACCTATGCCAGCACTAGAATAAA 57.370 39.130 0.00 0.00 0.00 1.40
89 90 8.471609 TGTGATCTGAAATTGACATGCATTTAT 58.528 29.630 0.00 0.00 0.00 1.40
159 160 9.753674 ATCATTCAAGGTTTAATTTACAGAGGA 57.246 29.630 0.00 0.00 0.00 3.71
194 196 3.118629 TGGATGCTTCGAATCTGCTAACT 60.119 43.478 0.00 0.00 0.00 2.24
195 197 3.198068 TGGATGCTTCGAATCTGCTAAC 58.802 45.455 0.00 0.00 0.00 2.34
243 263 1.229428 CCGTGATGATGGTATGCACC 58.771 55.000 0.00 0.00 46.00 5.01
244 264 1.202639 TCCCGTGATGATGGTATGCAC 60.203 52.381 0.00 0.00 0.00 4.57
245 265 1.127343 TCCCGTGATGATGGTATGCA 58.873 50.000 0.00 0.00 0.00 3.96
246 266 2.254546 TTCCCGTGATGATGGTATGC 57.745 50.000 0.00 0.00 0.00 3.14
247 267 3.999001 CTGATTCCCGTGATGATGGTATG 59.001 47.826 0.00 0.00 0.00 2.39
248 268 3.557898 GCTGATTCCCGTGATGATGGTAT 60.558 47.826 0.00 0.00 0.00 2.73
249 269 2.224281 GCTGATTCCCGTGATGATGGTA 60.224 50.000 0.00 0.00 0.00 3.25
250 270 1.475751 GCTGATTCCCGTGATGATGGT 60.476 52.381 0.00 0.00 0.00 3.55
262 282 3.267860 CGCGGCTCTGCTGATTCC 61.268 66.667 0.00 0.00 37.02 3.01
302 322 0.957395 TCCGAGTACCTGGACGACAC 60.957 60.000 0.00 0.00 0.00 3.67
303 323 0.957395 GTCCGAGTACCTGGACGACA 60.957 60.000 15.94 0.00 44.68 4.35
304 324 1.799383 GTCCGAGTACCTGGACGAC 59.201 63.158 15.94 0.00 44.68 4.34
325 345 1.124477 GGGAGAGGAAGCGGATGGAT 61.124 60.000 0.00 0.00 0.00 3.41
351 371 1.667154 CGGGGATCAGCAAGACGAGA 61.667 60.000 0.00 0.00 0.00 4.04
586 606 2.917933 TGTTCCACCATTGATCCGATC 58.082 47.619 1.01 1.01 0.00 3.69
612 632 0.673644 CAGTCCACCGATTTCCGCTT 60.674 55.000 0.00 0.00 36.84 4.68
625 645 3.059982 CCTCGACCAAGCAGTCCA 58.940 61.111 0.00 0.00 32.91 4.02
665 687 2.345991 GCCCTACAGTGCGTGGAA 59.654 61.111 0.00 0.00 0.00 3.53
677 699 0.464013 CGACTCTCTTCCTCGCCCTA 60.464 60.000 0.00 0.00 0.00 3.53
734 756 1.630148 CGCCTTCTTCGATTCGTTCT 58.370 50.000 5.89 0.00 0.00 3.01
738 760 0.872021 CCTCCGCCTTCTTCGATTCG 60.872 60.000 0.00 0.00 0.00 3.34
741 763 1.395826 CCTCCTCCGCCTTCTTCGAT 61.396 60.000 0.00 0.00 0.00 3.59
815 852 9.778993 ATGAAATGAAATAGAACGAAACATCAG 57.221 29.630 0.00 0.00 0.00 2.90
887 928 3.751175 GTCCGATCCAAAATCAACAGTCA 59.249 43.478 0.00 0.00 0.00 3.41
888 929 3.181520 CGTCCGATCCAAAATCAACAGTC 60.182 47.826 0.00 0.00 0.00 3.51
1074 1115 0.976590 AGGTTCTAGGGAGGCGGAAC 60.977 60.000 0.00 0.00 37.79 3.62
1257 1298 1.227556 GCGCATAACCTCGTCCCAT 60.228 57.895 0.30 0.00 0.00 4.00
1308 1390 0.107410 AACACTCACAAGGCCACGAA 60.107 50.000 5.01 0.00 0.00 3.85
1312 1394 2.171659 TGAAGTAACACTCACAAGGCCA 59.828 45.455 5.01 0.00 0.00 5.36
1332 1414 8.489990 AATCAGTAGAATCACTTCACATTCTG 57.510 34.615 4.73 0.00 39.28 3.02
1333 1415 9.160496 GAAATCAGTAGAATCACTTCACATTCT 57.840 33.333 0.00 0.00 41.35 2.40
1349 1431 3.165058 TGCGCAGTAGGAAATCAGTAG 57.835 47.619 5.66 0.00 0.00 2.57
1357 1439 2.734175 CGTGAAGTATGCGCAGTAGGAA 60.734 50.000 18.32 0.00 0.00 3.36
1375 1457 7.536964 TGATTGTTTACTGTATGCAAAATCGTG 59.463 33.333 0.00 0.00 0.00 4.35
1378 1460 8.970691 ACTGATTGTTTACTGTATGCAAAATC 57.029 30.769 0.00 4.41 0.00 2.17
1384 1466 6.978343 TGGTACTGATTGTTTACTGTATGC 57.022 37.500 0.00 0.00 0.00 3.14
1400 1509 2.100749 TGCGGTCATACAGATGGTACTG 59.899 50.000 0.00 0.00 42.78 2.74
1439 1548 1.273327 GGTGTCCAAAATGAAGCTGGG 59.727 52.381 0.00 0.00 0.00 4.45
1516 1797 9.991388 GAACCGAGATAATGATACTACTCATAC 57.009 37.037 0.00 0.00 34.79 2.39
1723 2011 3.181461 CCCACTTCAACCTATCAGCCTAG 60.181 52.174 0.00 0.00 0.00 3.02
1785 2073 8.455903 TTTCTTAAGATCATCATGGTCAATCC 57.544 34.615 5.89 0.00 27.47 3.01
1879 2167 4.439057 TCGGTATGTTCTTGCTGTTATCC 58.561 43.478 0.00 0.00 0.00 2.59
1880 2168 6.037172 ACATTCGGTATGTTCTTGCTGTTATC 59.963 38.462 0.00 0.00 45.19 1.75
1897 2185 4.134563 ACTGAAAGCAAAGTACATTCGGT 58.865 39.130 0.00 0.00 37.60 4.69
1900 2188 7.138692 AGATGACTGAAAGCAAAGTACATTC 57.861 36.000 0.00 0.00 37.60 2.67
1912 2200 3.601443 AAGGACGGAGATGACTGAAAG 57.399 47.619 0.00 0.00 42.29 2.62
1948 2236 2.668945 CGTGTATTGAACATACGTGCCA 59.331 45.455 0.00 0.00 41.10 4.92
1954 2242 5.172934 TGTTCTCCCGTGTATTGAACATAC 58.827 41.667 0.00 0.00 41.02 2.39
1956 2244 4.253685 CTGTTCTCCCGTGTATTGAACAT 58.746 43.478 7.20 0.00 43.61 2.71
1969 2257 2.784347 CCAAAGAAGTCCTGTTCTCCC 58.216 52.381 0.00 0.00 35.65 4.30
1975 2263 1.133668 AGCTTGCCAAAGAAGTCCTGT 60.134 47.619 0.00 0.00 35.19 4.00
2179 2467 4.393680 GGACCGCAGTTTGTTATCATACAA 59.606 41.667 0.00 0.00 36.30 2.41
2251 2539 4.564782 TGGAGAGCAAGAATTCAGACAT 57.435 40.909 8.44 0.00 0.00 3.06
2320 2608 4.080638 CAGAGGGAAAAAGCCTCTAGATGT 60.081 45.833 0.00 0.00 38.66 3.06
2332 2620 4.543590 TTGCAAAACACAGAGGGAAAAA 57.456 36.364 0.00 0.00 0.00 1.94
2430 2718 4.078537 TGCAACTTCATGGCTAAGCTTTA 58.921 39.130 3.20 0.00 0.00 1.85
2515 2803 4.590222 GGGAATTGGTCATATGCTGGATTT 59.410 41.667 0.00 0.00 0.00 2.17
2590 2878 4.488126 TCTGACTTGAAAAATTGGCTCG 57.512 40.909 0.00 0.00 0.00 5.03
2623 2911 0.109723 TACGCCTCCAAACCAGCTTT 59.890 50.000 0.00 0.00 0.00 3.51
2956 3244 4.016706 AGCCGTGAACCTTCGGGG 62.017 66.667 5.78 0.00 45.85 5.73
3057 3350 1.745087 GCACATGTACATCAGTTGGGG 59.255 52.381 5.07 0.00 0.00 4.96
3118 3419 8.485392 CCCAATTACAAATAAGATCCATTTGGT 58.515 33.333 23.85 15.96 44.20 3.67
3223 3619 9.291664 CTAGTTCTGTATCTGTAGTTGTTAAGC 57.708 37.037 0.00 0.00 0.00 3.09
3248 3644 9.561069 ACTGAACAATCTTTGTATTGAACTACT 57.439 29.630 3.73 0.00 44.59 2.57
3297 4040 7.053316 TGATGAGAAAAGCTGGAAATTCAAA 57.947 32.000 0.00 0.00 0.00 2.69
3301 4044 6.209986 TGTCATGATGAGAAAAGCTGGAAATT 59.790 34.615 0.00 0.00 0.00 1.82
3302 4045 5.713389 TGTCATGATGAGAAAAGCTGGAAAT 59.287 36.000 0.00 0.00 0.00 2.17
3303 4046 5.072055 TGTCATGATGAGAAAAGCTGGAAA 58.928 37.500 0.00 0.00 0.00 3.13
3304 4047 4.654915 TGTCATGATGAGAAAAGCTGGAA 58.345 39.130 0.00 0.00 0.00 3.53
3306 4049 3.377485 CCTGTCATGATGAGAAAAGCTGG 59.623 47.826 0.00 0.00 0.00 4.85
3307 4050 4.008330 ACCTGTCATGATGAGAAAAGCTG 58.992 43.478 0.00 0.00 0.00 4.24
3308 4051 4.260170 GACCTGTCATGATGAGAAAAGCT 58.740 43.478 0.00 0.00 0.00 3.74
3396 4147 0.673022 CTTCTGTCCTGCACTCCTGC 60.673 60.000 0.00 0.00 44.52 4.85
3397 4148 0.036577 CCTTCTGTCCTGCACTCCTG 60.037 60.000 0.00 0.00 0.00 3.86
3398 4149 1.197430 CCCTTCTGTCCTGCACTCCT 61.197 60.000 0.00 0.00 0.00 3.69
3399 4150 1.298014 CCCTTCTGTCCTGCACTCC 59.702 63.158 0.00 0.00 0.00 3.85
3400 4151 0.398318 AACCCTTCTGTCCTGCACTC 59.602 55.000 0.00 0.00 0.00 3.51
3401 4152 0.398318 GAACCCTTCTGTCCTGCACT 59.602 55.000 0.00 0.00 0.00 4.40
3402 4153 0.108585 TGAACCCTTCTGTCCTGCAC 59.891 55.000 0.00 0.00 0.00 4.57
3403 4154 1.003580 GATGAACCCTTCTGTCCTGCA 59.996 52.381 0.00 0.00 0.00 4.41
3404 4155 1.680249 GGATGAACCCTTCTGTCCTGC 60.680 57.143 0.00 0.00 34.48 4.85
3423 4174 0.251354 ACTGGCATAGCAGACACAGG 59.749 55.000 0.00 0.00 0.00 4.00
3456 4207 0.249911 ACGGAACACCAGCAGAGAAC 60.250 55.000 0.00 0.00 0.00 3.01
3469 4220 1.529865 GTACAGCAACCAGAACGGAAC 59.470 52.381 0.00 0.00 38.63 3.62
3477 4228 6.373779 CAAAAGATAACTGTACAGCAACCAG 58.626 40.000 22.90 0.00 0.00 4.00
3478 4229 5.278266 GCAAAAGATAACTGTACAGCAACCA 60.278 40.000 22.90 4.00 0.00 3.67
3491 4242 4.680171 ACAGTAAGCGGCAAAAGATAAC 57.320 40.909 1.45 0.00 0.00 1.89
3509 4395 8.757789 TCGTTTATGTTCACTACAAGTTTACAG 58.242 33.333 0.00 0.00 40.89 2.74
3524 4410 5.006358 ACACGATAATGGCTCGTTTATGTTC 59.994 40.000 0.00 0.00 46.49 3.18
3534 4420 4.683832 AGTTGTCTACACGATAATGGCTC 58.316 43.478 0.00 0.00 0.00 4.70
3540 4426 6.486253 ACGACTTAGTTGTCTACACGATAA 57.514 37.500 0.00 0.00 35.00 1.75
3561 4447 4.703424 TCGCAACAACACATGTATTAACG 58.297 39.130 0.00 0.00 42.99 3.18
3585 8227 5.774690 TGGGAACACTTCAAGATGCTTAAAT 59.225 36.000 0.00 0.00 33.40 1.40
3632 8274 6.045318 CGAACTGAACTATCTGAACATCCAT 58.955 40.000 0.00 0.00 0.00 3.41
3665 8307 5.049818 CCATTTTTGCTTCGCCAACATAAAA 60.050 36.000 0.00 0.00 0.00 1.52
3666 8308 4.450419 CCATTTTTGCTTCGCCAACATAAA 59.550 37.500 0.00 0.00 0.00 1.40
3693 8335 4.280929 TGCTTACTCTAGCTTGTGTGAAGA 59.719 41.667 12.20 0.00 41.76 2.87
3711 8353 3.192844 CCAGACGTAGGAGACTTTGCTTA 59.807 47.826 0.23 0.00 43.67 3.09
3798 8440 6.407299 GCATCAAACTTTATGGAATGATGGGT 60.407 38.462 13.53 0.00 42.60 4.51
3800 8442 6.477688 GTGCATCAAACTTTATGGAATGATGG 59.522 38.462 13.53 0.00 42.60 3.51
3814 8456 4.307032 AATACAGGGAGTGCATCAAACT 57.693 40.909 0.00 0.00 0.00 2.66
3833 8475 1.716503 AGGAAAGCCACAGGGGTAAAT 59.283 47.619 0.00 0.00 46.38 1.40
3840 8482 1.180029 CATCCAAGGAAAGCCACAGG 58.820 55.000 0.00 0.00 36.29 4.00
3841 8483 0.529378 GCATCCAAGGAAAGCCACAG 59.471 55.000 5.82 0.00 36.29 3.66
3842 8484 0.899717 GGCATCCAAGGAAAGCCACA 60.900 55.000 23.22 0.00 43.93 4.17
3843 8485 0.613012 AGGCATCCAAGGAAAGCCAC 60.613 55.000 27.23 10.27 45.63 5.01
3844 8486 0.998928 TAGGCATCCAAGGAAAGCCA 59.001 50.000 27.23 16.00 45.63 4.75
3845 8487 1.064389 AGTAGGCATCCAAGGAAAGCC 60.064 52.381 21.58 21.58 44.45 4.35
3846 8488 2.019984 CAGTAGGCATCCAAGGAAAGC 58.980 52.381 8.01 8.01 0.00 3.51
3847 8489 3.634397 TCAGTAGGCATCCAAGGAAAG 57.366 47.619 0.00 0.00 0.00 2.62
3848 8490 4.526970 GAATCAGTAGGCATCCAAGGAAA 58.473 43.478 0.00 0.00 0.00 3.13
3849 8491 3.117888 GGAATCAGTAGGCATCCAAGGAA 60.118 47.826 0.00 0.00 0.00 3.36
3850 8492 2.439507 GGAATCAGTAGGCATCCAAGGA 59.560 50.000 0.00 0.00 0.00 3.36
3864 8506 6.071784 TGAGATGGTTTTCAACATGGAATCAG 60.072 38.462 0.00 0.00 0.00 2.90
3889 8531 1.202651 ACCAGAAGTTAACGCAGCAGT 60.203 47.619 0.00 0.00 0.00 4.40
3894 8536 2.479837 CAGACACCAGAAGTTAACGCA 58.520 47.619 0.00 0.00 0.00 5.24
3906 8548 4.280425 TGAAAAATAATGCAGCAGACACCA 59.720 37.500 0.00 0.00 0.00 4.17
3921 8563 4.382291 ACACTACCACGTGCTGAAAAATA 58.618 39.130 10.91 0.00 38.45 1.40
3924 8566 2.319136 ACACTACCACGTGCTGAAAA 57.681 45.000 10.91 0.00 38.45 2.29
3929 8571 2.626743 AGACTTTACACTACCACGTGCT 59.373 45.455 10.91 0.00 38.45 4.40
3957 8599 7.086376 TCAGAATCTTAAACTGCAGCAATTTC 58.914 34.615 15.27 11.04 0.00 2.17
3997 8639 8.224025 TGATCCATATAAAAAGGTAGCCATGAA 58.776 33.333 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.