Multiple sequence alignment - TraesCS3B01G464700

Loading Multiple Alignment...

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 TraesCS3B01G464700 chr3B 100.000 4405 0 0 1 4405 707419135 707414731 0.000000e+00 8135.0
1 TraesCS3B01G464700 chr3B 94.009 217 10 3 400 615 92328742 92328956 4.250000e-85 326.0
2 TraesCS3B01G464700 chr3D 92.150 2102 140 17 173 2259 535777684 535775593 0.000000e+00 2944.0
3 TraesCS3B01G464700 chr3D 94.162 1593 64 11 2299 3876 535775598 535774020 0.000000e+00 2399.0
4 TraesCS3B01G464700 chr3D 94.198 293 12 3 3861 4149 535774005 535773714 4.040000e-120 442.0
5 TraesCS3B01G464700 chr3D 90.987 233 5 8 4159 4391 535773620 535773404 2.580000e-77 300.0
6 TraesCS3B01G464700 chr3D 77.419 186 33 5 176 352 509211866 509211681 7.790000e-18 102.0
7 TraesCS3B01G464700 chr3A 94.118 1785 70 14 1815 3568 671021448 671019668 0.000000e+00 2682.0
8 TraesCS3B01G464700 chr3A 89.343 1858 141 30 3 1814 671023396 671021550 0.000000e+00 2281.0
9 TraesCS3B01G464700 chr3A 87.040 679 30 21 3748 4405 671019378 671018737 0.000000e+00 713.0
10 TraesCS3B01G464700 chr3A 93.636 220 11 3 400 618 694364671 694364454 4.250000e-85 326.0
11 TraesCS3B01G464700 chrUn 94.009 217 10 3 400 615 86451475 86451689 4.250000e-85 326.0
12 TraesCS3B01G464700 chrUn 94.009 217 10 3 400 615 86457474 86457688 4.250000e-85 326.0
13 TraesCS3B01G464700 chr4D 94.009 217 10 3 400 615 123434627 123434841 4.250000e-85 326.0
14 TraesCS3B01G464700 chr2D 94.009 217 10 3 400 615 322913530 322913744 4.250000e-85 326.0
15 TraesCS3B01G464700 chr2D 82.278 158 20 7 183 338 640978474 640978323 3.580000e-26 130.0
16 TraesCS3B01G464700 chr2D 92.000 50 4 0 617 666 563306524 563306475 2.200000e-08 71.3
17 TraesCS3B01G464700 chr1D 93.636 220 11 3 400 618 351068552 351068335 4.250000e-85 326.0
18 TraesCS3B01G464700 chr1D 79.444 180 33 4 197 373 442714954 442714776 1.660000e-24 124.0
19 TraesCS3B01G464700 chr1D 92.000 50 4 0 617 666 244392988 244392939 2.200000e-08 71.3
20 TraesCS3B01G464700 chr1D 92.000 50 4 0 617 666 254482574 254482525 2.200000e-08 71.3
21 TraesCS3B01G464700 chr5B 83.333 144 22 2 220 361 701186614 701186757 9.940000e-27 132.0
22 TraesCS3B01G464700 chr5B 82.828 99 15 2 7 103 571181880 571181782 2.180000e-13 87.9
23 TraesCS3B01G464700 chr7B 88.235 102 10 2 3 103 528254645 528254745 2.150000e-23 121.0
24 TraesCS3B01G464700 chr7D 77.778 207 36 10 174 373 75261116 75261319 7.740000e-23 119.0
25 TraesCS3B01G464700 chr2B 81.752 137 22 3 204 338 800988637 800988502 1.300000e-20 111.0
26 TraesCS3B01G464700 chr1A 80.132 151 28 2 220 368 316952657 316952507 1.300000e-20 111.0
27 TraesCS3B01G464700 chr1A 93.617 47 3 0 617 663 554473001 554473047 2.200000e-08 71.3
28 TraesCS3B01G464700 chr6D 92.000 50 4 0 617 666 459928802 459928753 2.200000e-08 71.3
29 TraesCS3B01G464700 chr5D 93.617 47 3 0 617 663 6218604 6218650 2.200000e-08 71.3
30 TraesCS3B01G464700 chr5D 93.617 47 3 0 617 663 483802179 483802225 2.200000e-08 71.3
31 TraesCS3B01G464700 chr4A 81.579 76 12 2 13 87 296355869 296355795 1.320000e-05 62.1


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 TraesCS3B01G464700 chr3B 707414731 707419135 4404 True 8135.00 8135 100.00000 1 4405 1 chr3B.!!$R1 4404
1 TraesCS3B01G464700 chr3D 535773404 535777684 4280 True 1521.25 2944 92.87425 173 4391 4 chr3D.!!$R2 4218
2 TraesCS3B01G464700 chr3A 671018737 671023396 4659 True 1892.00 2682 90.16700 3 4405 3 chr3A.!!$R2 4402

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
385 392 0.390209 GCGCCTTACGTTCCCTTACA 60.390 55.000 0.00 0.00 46.11 2.41 F
1172 1217 1.130561 GCGGTGCCACTATTTCTCAAC 59.869 52.381 0.00 0.00 0.00 3.18 F
1520 1569 1.979308 GTAGGAAGAGGGGATAAGGGC 59.021 57.143 0.00 0.00 0.00 5.19 F
2734 2919 0.032952 CAACCATGGCCTGCATATGC 59.967 55.000 21.09 21.09 42.50 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1641 0.256464 AACCGAAAACCCACCTCACA 59.744 50.0 0.00 0.00 0.00 3.58 R
2715 2900 0.032952 GCATATGCAGGCCATGGTTG 59.967 55.0 22.84 13.36 41.59 3.77 R
3080 3265 0.391597 ACACACGACTTCCGATTGGT 59.608 50.0 0.00 0.00 41.76 3.67 R
4339 4796 0.108138 GAATGGTCCACTCCGGTGAG 60.108 60.0 11.17 1.68 45.61 3.51 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
55 56 4.521256 TGTTTAGGGTTTGTGTTATGCTCC 59.479 41.667 0.00 0.00 0.00 4.70
62 63 2.380084 TGTGTTATGCTCCGGAAGAC 57.620 50.000 5.23 0.00 0.00 3.01
87 88 1.153349 GTGGCGGCTCCCTAAAGAG 60.153 63.158 11.43 0.00 36.92 2.85
104 105 6.101881 CCTAAAGAGGGAATGAGGTTATCCTT 59.898 42.308 0.00 0.00 40.85 3.36
114 115 2.439880 GAGGTTATCCTTGCCTAGCCTT 59.560 50.000 0.00 0.00 45.24 4.35
122 123 4.222847 GCCTAGCCTTCGTCCCGG 62.223 72.222 0.00 0.00 0.00 5.73
123 124 2.758737 CCTAGCCTTCGTCCCGGT 60.759 66.667 0.00 0.00 0.00 5.28
125 126 3.072468 TAGCCTTCGTCCCGGTGG 61.072 66.667 0.00 0.00 0.00 4.61
139 140 1.153881 GGTGGTCCGTCTAAGCGTC 60.154 63.158 0.00 0.00 0.00 5.19
140 141 1.582968 GTGGTCCGTCTAAGCGTCA 59.417 57.895 0.00 0.00 0.00 4.35
153 154 2.509336 CGTCATCGGAGGGTGTGC 60.509 66.667 0.00 0.00 0.00 4.57
170 171 4.946411 CGTAGCTGTATCTCCGGC 57.054 61.111 0.00 0.00 0.00 6.13
171 172 2.332277 CGTAGCTGTATCTCCGGCT 58.668 57.895 0.00 0.00 38.62 5.52
202 208 1.191489 TGGATCCGGTCTTGTCTGCA 61.191 55.000 7.39 0.00 0.00 4.41
248 254 2.640184 TCCGATCTACGCTTCTCTTCA 58.360 47.619 0.00 0.00 41.07 3.02
282 288 1.239347 GTTCTGGTTTGCTGGTCCTC 58.761 55.000 0.00 0.00 0.00 3.71
288 294 0.984995 GTTTGCTGGTCCTCTAGGGT 59.015 55.000 0.00 0.00 36.25 4.34
289 295 1.351350 GTTTGCTGGTCCTCTAGGGTT 59.649 52.381 0.00 0.00 36.25 4.11
297 303 2.570302 GGTCCTCTAGGGTTTTAGCACA 59.430 50.000 0.00 0.00 36.25 4.57
302 308 4.504858 CTCTAGGGTTTTAGCACAACGAT 58.495 43.478 0.00 0.00 0.00 3.73
317 323 5.100259 CACAACGATTTACCGACTGTCTAT 58.900 41.667 6.21 0.00 30.96 1.98
333 339 7.064134 CGACTGTCTATTATAACAAGGTTTGCA 59.936 37.037 6.21 0.00 0.00 4.08
352 359 2.269241 GCTTCAACGAGGGAGGGG 59.731 66.667 0.00 0.00 0.00 4.79
353 360 2.269241 CTTCAACGAGGGAGGGGC 59.731 66.667 0.00 0.00 0.00 5.80
354 361 2.528127 TTCAACGAGGGAGGGGCA 60.528 61.111 0.00 0.00 0.00 5.36
365 372 1.224592 GAGGGGCAATGACGATGGT 59.775 57.895 0.00 0.00 0.00 3.55
374 381 0.810031 ATGACGATGGTGCGCCTTAC 60.810 55.000 18.96 7.79 35.27 2.34
380 387 3.122971 GGTGCGCCTTACGTTCCC 61.123 66.667 9.68 0.00 46.11 3.97
381 388 2.047560 GTGCGCCTTACGTTCCCT 60.048 61.111 4.18 0.00 46.11 4.20
385 392 0.390209 GCGCCTTACGTTCCCTTACA 60.390 55.000 0.00 0.00 46.11 2.41
403 410 2.679082 ACATATAGTCCTCGTTGCCCT 58.321 47.619 0.00 0.00 0.00 5.19
419 426 2.690497 TGCCCTGAAGAATAGAGACGAG 59.310 50.000 0.00 0.00 0.00 4.18
426 433 4.336993 TGAAGAATAGAGACGAGAGGAAGC 59.663 45.833 0.00 0.00 0.00 3.86
498 505 6.073440 GCTACTAAGTCAAAACGTCCAATGAA 60.073 38.462 0.00 0.00 0.00 2.57
504 511 4.447389 GTCAAAACGTCCAATGAAAATGGG 59.553 41.667 0.00 0.00 38.54 4.00
556 565 9.434420 AGCAGCTCTATCAGTTATTTCATTATC 57.566 33.333 0.00 0.00 0.00 1.75
610 619 1.132453 TCACAAGCGGTATCAGTCTCG 59.868 52.381 0.00 0.00 0.00 4.04
651 660 9.442062 TTTAATAGTACATCCCAATAGAGGACA 57.558 33.333 0.00 0.00 35.85 4.02
658 667 5.612688 ACATCCCAATAGAGGACAACCATAT 59.387 40.000 0.00 0.00 35.85 1.78
706 747 9.613428 AACCTTGATGTTTGATAAATAGATCGA 57.387 29.630 0.00 0.00 0.00 3.59
725 766 8.788409 AGATCGAAAGCTTTTCTAACAAAAAG 57.212 30.769 14.05 5.05 45.10 2.27
850 892 1.439679 CTACTCGGGCCAACACTTTC 58.560 55.000 4.39 0.00 0.00 2.62
856 898 1.632589 GGGCCAACACTTTCCTCAAT 58.367 50.000 4.39 0.00 0.00 2.57
947 991 3.764885 CGATAGGAACAGGGCAAAAAG 57.235 47.619 0.00 0.00 0.00 2.27
949 993 3.756434 CGATAGGAACAGGGCAAAAAGAA 59.244 43.478 0.00 0.00 0.00 2.52
953 997 4.769688 AGGAACAGGGCAAAAAGAAAAAG 58.230 39.130 0.00 0.00 0.00 2.27
1079 1123 4.058124 CCAAGCATGTAAGCGAGCTAATA 58.942 43.478 0.00 0.00 40.15 0.98
1172 1217 1.130561 GCGGTGCCACTATTTCTCAAC 59.869 52.381 0.00 0.00 0.00 3.18
1180 1225 5.221402 TGCCACTATTTCTCAACAATTTGCA 60.221 36.000 0.00 0.00 32.17 4.08
1387 1435 2.623416 CGGCTGTCCTTCCTTTTCTTTT 59.377 45.455 0.00 0.00 0.00 2.27
1483 1532 3.257127 GGGTGGGTGAAAATTTCGATTCA 59.743 43.478 0.97 0.00 0.00 2.57
1487 1536 6.090763 GGTGGGTGAAAATTTCGATTCAATTC 59.909 38.462 0.92 0.00 0.00 2.17
1500 1549 4.438200 CGATTCAATTCGGTTAGGGTTTGG 60.438 45.833 0.00 0.00 35.50 3.28
1519 1568 2.090153 TGGTAGGAAGAGGGGATAAGGG 60.090 54.545 0.00 0.00 0.00 3.95
1520 1569 1.979308 GTAGGAAGAGGGGATAAGGGC 59.021 57.143 0.00 0.00 0.00 5.19
1538 1587 3.394606 AGGGCTTTCAAGAAGGAACAGTA 59.605 43.478 0.00 0.00 0.00 2.74
1590 1641 4.178956 ACTTTCATTGGGTGTGGTAACT 57.821 40.909 0.00 0.00 37.61 2.24
1605 1656 2.882761 GGTAACTGTGAGGTGGGTTTTC 59.117 50.000 0.00 0.00 0.00 2.29
1622 1673 4.336153 GGTTTTCGGTTTCTGAAGTTGGTA 59.664 41.667 0.00 0.00 0.00 3.25
1706 1757 2.968574 GAGGGATGACATGAAGGCTCTA 59.031 50.000 0.00 0.00 0.00 2.43
1793 1845 9.713740 GCTAACAACTCTGAAGAATGAATTATG 57.286 33.333 1.07 0.00 0.00 1.90
1929 2102 5.645497 ACAATGCAGAGTTTCTATCCTGTTC 59.355 40.000 0.00 0.00 0.00 3.18
2000 2173 6.913873 TTCTCGTAAAGCAAACTTAACTGT 57.086 33.333 0.00 0.00 34.05 3.55
2057 2230 6.766467 GCATGGCTTTAGTAGGTGTTTACTAT 59.234 38.462 0.00 0.00 36.36 2.12
2421 2603 4.746115 TGAGCATTCTGAAATTTGTGTTGC 59.254 37.500 0.00 0.00 0.00 4.17
2462 2646 2.225091 TGGACTCAAGATGCCATGGTTT 60.225 45.455 14.67 0.16 0.00 3.27
2625 2809 7.461749 AGGAAGAGGTCAGTGATTTTCATTTA 58.538 34.615 0.00 0.00 0.00 1.40
2690 2874 4.937201 TCCAGTGCACATTAGATACGAT 57.063 40.909 21.04 0.00 0.00 3.73
2694 2878 5.523552 CCAGTGCACATTAGATACGATTTGA 59.476 40.000 21.04 0.00 0.00 2.69
2734 2919 0.032952 CAACCATGGCCTGCATATGC 59.967 55.000 21.09 21.09 42.50 3.14
2744 2929 2.928334 CCTGCATATGCCTGTCTTTCT 58.072 47.619 24.54 0.00 41.18 2.52
2826 3011 5.055265 TGTAACAGGATCTGGGACAAAAA 57.945 39.130 0.00 0.00 38.70 1.94
2833 3018 5.188359 CAGGATCTGGGACAAAAATTTGGAT 59.812 40.000 10.38 3.27 42.34 3.41
2954 3139 5.948742 TCTTTCATTTGGGTTGGTTCTTT 57.051 34.783 0.00 0.00 0.00 2.52
3046 3231 1.328680 CAACGCATCCGATCCTTTCTG 59.671 52.381 0.00 0.00 38.29 3.02
3054 3239 4.826274 TCCGATCCTTTCTGATGTCTTT 57.174 40.909 0.00 0.00 0.00 2.52
3079 3264 2.936202 CTTTGGTAGCCCATGTAGCAT 58.064 47.619 7.62 0.00 41.49 3.79
3080 3265 3.747388 GCTTTGGTAGCCCATGTAGCATA 60.747 47.826 7.62 0.00 44.48 3.14
3083 3268 1.697432 GGTAGCCCATGTAGCATACCA 59.303 52.381 18.36 0.00 42.12 3.25
3092 3277 4.380531 CATGTAGCATACCAATCGGAAGT 58.619 43.478 0.00 0.00 42.12 3.01
3095 3280 1.480954 AGCATACCAATCGGAAGTCGT 59.519 47.619 0.00 0.00 40.32 4.34
3131 3316 2.263077 AGCATCGATCTTGAACGTGTC 58.737 47.619 0.00 0.00 0.00 3.67
3141 3326 1.934589 TGAACGTGTCACACTTCAGG 58.065 50.000 14.96 0.00 31.78 3.86
3157 3342 3.650281 TCAGGGAAGCAGCAAATATCA 57.350 42.857 0.00 0.00 0.00 2.15
3221 3406 0.540365 ATGTGGTTGGCCCTGTTCTG 60.540 55.000 0.00 0.00 0.00 3.02
3264 3449 3.935828 TGTATTTGTAGCGCTACATTGCA 59.064 39.130 41.71 35.01 44.54 4.08
3294 3479 3.270027 TCGATGCCACTTGGTAATCTTG 58.730 45.455 0.00 0.00 37.57 3.02
3331 3519 5.593095 AGAATCAATGCGTCTGGTAGTACTA 59.407 40.000 0.00 0.00 0.00 1.82
3332 3520 4.627611 TCAATGCGTCTGGTAGTACTAC 57.372 45.455 22.53 22.53 35.40 2.73
3333 3521 4.267536 TCAATGCGTCTGGTAGTACTACT 58.732 43.478 27.71 7.10 36.36 2.57
3441 3629 9.863845 GAAGGCCTTATCTGATACTAGTATTTC 57.136 37.037 20.54 6.70 0.00 2.17
3487 3675 4.114058 ACATGTATGTGCTGCCAAAATC 57.886 40.909 0.00 0.00 40.03 2.17
3491 3679 2.857592 ATGTGCTGCCAAAATCGATC 57.142 45.000 0.00 0.00 0.00 3.69
3515 3703 1.803334 TTGCCGACGATAAGCTTGTT 58.197 45.000 9.86 0.00 0.00 2.83
3526 3714 2.341846 AAGCTTGTTCGGTCCTTTCA 57.658 45.000 0.00 0.00 0.00 2.69
3533 3721 2.171870 TGTTCGGTCCTTTCAAACCTCT 59.828 45.455 0.00 0.00 33.14 3.69
3568 3756 7.993183 TCACAATAGGGGTGAAAGAGATATTTC 59.007 37.037 0.00 0.00 41.96 2.17
3607 3795 1.195448 CTGCCGATTCAACTGTGTGTC 59.805 52.381 0.00 0.00 0.00 3.67
3611 3799 2.476619 CCGATTCAACTGTGTGTCTGAC 59.523 50.000 0.00 0.00 0.00 3.51
3621 3809 3.768406 TGTGTGTCTGACATTTGTTTGC 58.232 40.909 14.37 0.00 36.78 3.68
3644 3832 4.331108 TGTGCTGTTTGGCTGTTGATATA 58.669 39.130 0.00 0.00 0.00 0.86
3676 3932 6.094742 TGTGCTGCCAAAATCGATCTTATTTA 59.905 34.615 0.00 0.00 0.00 1.40
3686 3942 7.783276 AATCGATCTTATTTATCGTCGACAG 57.217 36.000 17.16 8.67 45.01 3.51
3809 4130 2.310538 TGTGTTGCTCTCTCTCTCACA 58.689 47.619 0.00 0.00 33.06 3.58
3821 4142 3.153130 CTCTCTCACACTCTGGTCAGAA 58.847 50.000 2.13 0.00 36.94 3.02
3856 4177 4.127171 GACCAACGTACTATTCCATGCAT 58.873 43.478 0.00 0.00 0.00 3.96
3942 4293 1.370414 CGACCAAAAAGCAGCACGG 60.370 57.895 0.00 0.00 0.00 4.94
3984 4335 1.523154 GCTGCAAACCACGGATTCCA 61.523 55.000 3.09 0.00 0.00 3.53
4016 4368 2.001872 GCCGAATTGCCAATGGAAAAG 58.998 47.619 2.05 0.00 0.00 2.27
4017 4369 2.620242 CCGAATTGCCAATGGAAAAGG 58.380 47.619 2.05 0.38 0.00 3.11
4026 4378 4.605640 CCAATGGAAAAGGCAAAAGAGA 57.394 40.909 0.00 0.00 0.00 3.10
4028 4380 3.923017 ATGGAAAAGGCAAAAGAGACG 57.077 42.857 0.00 0.00 0.00 4.18
4054 4407 0.251341 AATTGGCACCCTGGACAGAC 60.251 55.000 0.00 0.00 0.00 3.51
4093 4446 1.843368 CACCCATCATCAAGTTGCCT 58.157 50.000 0.00 0.00 0.00 4.75
4098 4451 3.258872 CCCATCATCAAGTTGCCTCAAAA 59.741 43.478 0.00 0.00 0.00 2.44
4240 4690 3.298619 CATGGAGAGAGATCACTCAGGT 58.701 50.000 20.37 1.84 44.79 4.00
4241 4691 3.464720 TGGAGAGAGATCACTCAGGTT 57.535 47.619 20.37 1.49 44.79 3.50
4242 4692 3.360867 TGGAGAGAGATCACTCAGGTTC 58.639 50.000 20.37 9.97 44.79 3.62
4243 4693 3.245407 TGGAGAGAGATCACTCAGGTTCA 60.245 47.826 20.37 4.19 44.79 3.18
4244 4694 3.381272 GGAGAGAGATCACTCAGGTTCAG 59.619 52.174 20.37 0.00 44.79 3.02
4245 4695 4.269183 GAGAGAGATCACTCAGGTTCAGA 58.731 47.826 20.37 0.00 44.79 3.27
4272 4722 0.998145 AGAGGCAGGCAAGGAGATTT 59.002 50.000 0.00 0.00 0.00 2.17
4310 4760 3.735208 CGAAGCATTTTCTCGAGCTAGGA 60.735 47.826 7.81 0.00 36.07 2.94
4336 4793 2.029288 CGGACGCAGCACATGAACT 61.029 57.895 0.00 0.00 0.00 3.01
4337 4794 0.735978 CGGACGCAGCACATGAACTA 60.736 55.000 0.00 0.00 0.00 2.24
4338 4795 0.721718 GGACGCAGCACATGAACTAC 59.278 55.000 0.00 0.00 0.00 2.73
4339 4796 0.721718 GACGCAGCACATGAACTACC 59.278 55.000 0.00 0.00 0.00 3.18
4342 4799 1.672737 CGCAGCACATGAACTACCTCA 60.673 52.381 0.00 0.00 0.00 3.86
4354 4811 1.304713 TACCTCACCGGAGTGGACC 60.305 63.158 24.23 0.00 44.64 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.391312 ACACCTAAAAATGGAGCATGAAC 57.609 39.130 0.00 0.00 0.00 3.18
1 2 6.418057 AAACACCTAAAAATGGAGCATGAA 57.582 33.333 0.00 0.00 0.00 2.57
48 49 1.735376 GCCTCGTCTTCCGGAGCATA 61.735 60.000 3.34 0.00 35.77 3.14
49 50 3.082579 GCCTCGTCTTCCGGAGCAT 62.083 63.158 3.34 0.00 35.77 3.79
55 56 4.796231 CCACCGCCTCGTCTTCCG 62.796 72.222 0.00 0.00 38.13 4.30
99 100 0.466124 GACGAAGGCTAGGCAAGGAT 59.534 55.000 19.70 0.00 0.00 3.24
122 123 0.172803 ATGACGCTTAGACGGACCAC 59.827 55.000 0.00 0.00 37.37 4.16
123 124 0.454600 GATGACGCTTAGACGGACCA 59.545 55.000 0.00 0.00 37.37 4.02
125 126 0.591741 CCGATGACGCTTAGACGGAC 60.592 60.000 0.00 0.00 42.40 4.79
133 134 2.283529 ACACCCTCCGATGACGCTT 61.284 57.895 0.00 0.00 38.29 4.68
139 140 1.226974 CTACGCACACCCTCCGATG 60.227 63.158 0.00 0.00 0.00 3.84
140 141 3.077519 GCTACGCACACCCTCCGAT 62.078 63.158 0.00 0.00 0.00 4.18
153 154 0.039978 CAGCCGGAGATACAGCTACG 60.040 60.000 5.05 0.00 41.85 3.51
158 159 1.000283 GATCCACAGCCGGAGATACAG 60.000 57.143 5.05 0.00 38.83 2.74
162 163 1.406065 CCAGATCCACAGCCGGAGAT 61.406 60.000 5.05 0.00 38.83 2.75
202 208 1.405526 CCAATCGGAGGACACACGAAT 60.406 52.381 0.00 0.00 40.27 3.34
262 268 0.535102 AGGACCAGCAAACCAGAACG 60.535 55.000 0.00 0.00 0.00 3.95
271 277 1.742308 AAACCCTAGAGGACCAGCAA 58.258 50.000 0.00 0.00 39.89 3.91
282 288 5.622770 AAATCGTTGTGCTAAAACCCTAG 57.377 39.130 0.00 0.00 0.00 3.02
288 294 4.751098 AGTCGGTAAATCGTTGTGCTAAAA 59.249 37.500 0.00 0.00 0.00 1.52
289 295 4.150980 CAGTCGGTAAATCGTTGTGCTAAA 59.849 41.667 0.00 0.00 0.00 1.85
297 303 9.455847 GTTATAATAGACAGTCGGTAAATCGTT 57.544 33.333 0.00 0.00 0.00 3.85
302 308 8.752187 ACCTTGTTATAATAGACAGTCGGTAAA 58.248 33.333 0.00 0.00 0.00 2.01
317 323 4.830046 TGAAGCCTGCAAACCTTGTTATAA 59.170 37.500 0.00 0.00 0.00 0.98
333 339 2.294078 CCCTCCCTCGTTGAAGCCT 61.294 63.158 0.00 0.00 0.00 4.58
352 359 2.277501 GCGCACCATCGTCATTGC 60.278 61.111 0.30 0.00 0.00 3.56
353 360 1.647545 AAGGCGCACCATCGTCATTG 61.648 55.000 10.83 0.00 39.06 2.82
354 361 0.107897 TAAGGCGCACCATCGTCATT 60.108 50.000 10.83 0.00 39.06 2.57
365 372 0.390209 GTAAGGGAACGTAAGGCGCA 60.390 55.000 10.83 0.00 46.11 6.09
374 381 4.518211 ACGAGGACTATATGTAAGGGAACG 59.482 45.833 0.00 0.00 0.00 3.95
380 387 4.281182 AGGGCAACGAGGACTATATGTAAG 59.719 45.833 0.00 0.00 37.60 2.34
381 388 4.038763 CAGGGCAACGAGGACTATATGTAA 59.961 45.833 0.00 0.00 37.60 2.41
385 392 2.958818 TCAGGGCAACGAGGACTATAT 58.041 47.619 0.00 0.00 37.60 0.86
403 410 4.336993 GCTTCCTCTCGTCTCTATTCTTCA 59.663 45.833 0.00 0.00 0.00 3.02
419 426 5.956068 ATTTCTTCTTTCACTGCTTCCTC 57.044 39.130 0.00 0.00 0.00 3.71
426 433 8.009974 CCACGTACTTTATTTCTTCTTTCACTG 58.990 37.037 0.00 0.00 0.00 3.66
498 505 2.287584 TGTCCCTCTTGATCCCCATTT 58.712 47.619 0.00 0.00 0.00 2.32
504 511 4.140536 GGATTTCATGTCCCTCTTGATCC 58.859 47.826 0.00 0.00 31.79 3.36
582 591 4.832248 TGATACCGCTTGTGATCTCTTTT 58.168 39.130 0.00 0.00 0.00 2.27
645 654 6.119536 TCCATGTACAAATATGGTTGTCCTC 58.880 40.000 11.96 0.00 43.17 3.71
658 667 9.747898 AGGTTAGAAATTACATCCATGTACAAA 57.252 29.630 0.00 0.00 42.48 2.83
706 747 9.502091 AACCTTTCTTTTTGTTAGAAAAGCTTT 57.498 25.926 5.69 5.69 43.17 3.51
717 758 7.548967 TCGGTCAAATAACCTTTCTTTTTGTT 58.451 30.769 0.00 0.00 37.15 2.83
719 760 7.995463 TTCGGTCAAATAACCTTTCTTTTTG 57.005 32.000 0.00 0.00 37.15 2.44
725 766 7.027778 AGCATATTCGGTCAAATAACCTTTC 57.972 36.000 0.00 0.00 37.15 2.62
774 815 3.838317 GGGAGCAAACTAGGGGAAAAATT 59.162 43.478 0.00 0.00 0.00 1.82
786 827 2.234143 GCTTTTCTCTGGGAGCAAACT 58.766 47.619 0.00 0.00 35.29 2.66
947 991 6.354858 CGGCTTTGCTATGTTTTTCTTTTTC 58.645 36.000 0.00 0.00 0.00 2.29
949 993 4.749598 CCGGCTTTGCTATGTTTTTCTTTT 59.250 37.500 0.00 0.00 0.00 2.27
953 997 3.242518 GACCGGCTTTGCTATGTTTTTC 58.757 45.455 0.00 0.00 0.00 2.29
1102 1147 2.910688 TGAGGGTTAATCGCAGGATC 57.089 50.000 0.00 0.00 30.81 3.36
1158 1203 7.816031 AGAATGCAAATTGTTGAGAAATAGTGG 59.184 33.333 0.00 0.00 36.83 4.00
1159 1204 8.752766 AGAATGCAAATTGTTGAGAAATAGTG 57.247 30.769 0.00 0.00 36.83 2.74
1160 1205 9.768662 AAAGAATGCAAATTGTTGAGAAATAGT 57.231 25.926 0.00 0.00 36.83 2.12
1172 1217 8.790674 CAACAAGAACAAAAAGAATGCAAATTG 58.209 29.630 0.00 0.00 0.00 2.32
1180 1225 5.104982 TCCTGCCAACAAGAACAAAAAGAAT 60.105 36.000 0.00 0.00 0.00 2.40
1387 1435 6.730977 CCATAACCCTAATCCCAAGAGAGATA 59.269 42.308 0.00 0.00 0.00 1.98
1483 1532 3.588396 TCCTACCAAACCCTAACCGAATT 59.412 43.478 0.00 0.00 0.00 2.17
1487 1536 2.568509 TCTTCCTACCAAACCCTAACCG 59.431 50.000 0.00 0.00 0.00 4.44
1500 1549 1.979308 GCCCTTATCCCCTCTTCCTAC 59.021 57.143 0.00 0.00 0.00 3.18
1519 1568 5.123027 CCATCTACTGTTCCTTCTTGAAAGC 59.877 44.000 0.00 0.00 0.00 3.51
1520 1569 6.234177 ACCATCTACTGTTCCTTCTTGAAAG 58.766 40.000 0.00 0.00 0.00 2.62
1538 1587 4.724279 AAACACAACCCTAAGACCATCT 57.276 40.909 0.00 0.00 0.00 2.90
1590 1641 0.256464 AACCGAAAACCCACCTCACA 59.744 50.000 0.00 0.00 0.00 3.58
1605 1656 4.238514 CTCTCTACCAACTTCAGAAACCG 58.761 47.826 0.00 0.00 0.00 4.44
1622 1673 2.044848 TCCTTCTCGCCGCTCTCT 60.045 61.111 0.00 0.00 0.00 3.10
1706 1757 0.333993 ATGAGGAGCCAAACCTGCAT 59.666 50.000 0.00 0.00 37.93 3.96
1757 1808 7.387948 TCTTCAGAGTTGTTAGCCATAGAAAAC 59.612 37.037 0.00 0.00 0.00 2.43
1793 1845 2.234300 TTGGACAGGAAACGACAGAC 57.766 50.000 0.00 0.00 0.00 3.51
1929 2102 8.842358 TTTCTTTGGTCATAACTAACCTAGTG 57.158 34.615 0.00 0.00 39.39 2.74
1975 2148 7.184779 ACAGTTAAGTTTGCTTTACGAGAAAC 58.815 34.615 0.00 0.00 38.74 2.78
2000 2173 3.958147 TCGATCAGAAAGTGGTATGCCTA 59.042 43.478 0.16 0.00 35.27 3.93
2066 2239 8.590204 TGCAAATATTATAGAGACCGGTATTGA 58.410 33.333 7.34 0.00 0.00 2.57
2114 2295 6.770785 ACTTGTAGCTCTGGAATTTTTGTACA 59.229 34.615 0.00 0.00 0.00 2.90
2421 2603 3.571571 CAGACAAATGGAGTGTGCAATG 58.428 45.455 0.00 0.00 0.00 2.82
2462 2646 8.328758 TGATAGCTTTTAGATTCTCAAGGGAAA 58.671 33.333 0.00 0.00 0.00 3.13
2625 2809 8.133024 TGCAACCAGAAATAAATTAACTGGAT 57.867 30.769 23.48 15.21 42.07 3.41
2710 2895 3.530928 ATGCAGGCCATGGTTGTATAT 57.469 42.857 14.67 6.41 31.48 0.86
2711 2896 4.334552 CATATGCAGGCCATGGTTGTATA 58.665 43.478 21.85 21.85 35.34 1.47
2715 2900 0.032952 GCATATGCAGGCCATGGTTG 59.967 55.000 22.84 13.36 41.59 3.77
2725 2910 3.276857 ACAGAAAGACAGGCATATGCAG 58.723 45.455 28.07 21.24 44.36 4.41
2734 2919 4.212214 GCTTGACACTTACAGAAAGACAGG 59.788 45.833 0.00 0.00 38.67 4.00
2736 2921 4.765273 TGCTTGACACTTACAGAAAGACA 58.235 39.130 0.00 0.00 38.67 3.41
2737 2922 5.277538 CCTTGCTTGACACTTACAGAAAGAC 60.278 44.000 0.00 0.00 38.67 3.01
2744 2929 3.569194 TTCCCTTGCTTGACACTTACA 57.431 42.857 0.00 0.00 0.00 2.41
2954 3139 6.554419 CAGGAGAAAATGATAATCGTGCAAA 58.446 36.000 0.00 0.00 0.00 3.68
3046 3231 3.062774 GCTACCAAAGCGAGAAAGACATC 59.937 47.826 0.00 0.00 42.53 3.06
3074 3259 2.691526 ACGACTTCCGATTGGTATGCTA 59.308 45.455 0.00 0.00 41.76 3.49
3076 3261 1.593006 CACGACTTCCGATTGGTATGC 59.407 52.381 0.00 0.00 41.76 3.14
3079 3264 1.614903 ACACACGACTTCCGATTGGTA 59.385 47.619 0.00 0.00 41.76 3.25
3080 3265 0.391597 ACACACGACTTCCGATTGGT 59.608 50.000 0.00 0.00 41.76 3.67
3083 3268 2.165167 TCCTACACACGACTTCCGATT 58.835 47.619 0.00 0.00 41.76 3.34
3092 3277 2.866460 GCTTCAAGCTTCCTACACACGA 60.866 50.000 0.71 0.00 38.45 4.35
3095 3280 2.928801 TGCTTCAAGCTTCCTACACA 57.071 45.000 11.57 0.00 42.97 3.72
3131 3316 0.535780 TGCTGCTTCCCTGAAGTGTG 60.536 55.000 0.00 0.00 41.27 3.82
3141 3326 7.253750 CGTTTTATGTTGATATTTGCTGCTTCC 60.254 37.037 0.00 0.00 0.00 3.46
3157 3342 3.440173 CAGCACCAGATCCGTTTTATGTT 59.560 43.478 0.00 0.00 0.00 2.71
3221 3406 0.534877 TGTGGTGATGGTGCAGTCAC 60.535 55.000 15.06 15.06 43.02 3.67
3264 3449 4.063967 TGGCATCGAAGCGACCGT 62.064 61.111 6.54 0.00 39.18 4.83
3294 3479 6.478344 ACGCATTGATTCTGAGTTCTCTAATC 59.522 38.462 15.05 15.05 0.00 1.75
3332 3520 1.125021 GTTTGACATGAGACACGCGAG 59.875 52.381 15.93 7.88 0.00 5.03
3333 3521 1.136690 GTTTGACATGAGACACGCGA 58.863 50.000 15.93 0.00 0.00 5.87
3441 3629 4.171005 CAATCAATAAAGCAGCACACAGG 58.829 43.478 0.00 0.00 0.00 4.00
3487 3675 0.999406 ATCGTCGGCAAACAAGATCG 59.001 50.000 0.00 0.00 0.00 3.69
3491 3679 1.732259 AGCTTATCGTCGGCAAACAAG 59.268 47.619 0.00 0.00 0.00 3.16
3515 3703 2.043992 TCAGAGGTTTGAAAGGACCGA 58.956 47.619 0.00 0.00 40.89 4.69
3526 3714 7.177392 CCCTATTGTGAAATCTTTCAGAGGTTT 59.823 37.037 5.63 0.00 46.80 3.27
3533 3721 5.886609 TCACCCCTATTGTGAAATCTTTCA 58.113 37.500 1.28 1.28 44.31 2.69
3561 3749 3.129988 AGCAGCACAGCCAAAGAAATATC 59.870 43.478 0.00 0.00 34.23 1.63
3562 3750 3.094572 AGCAGCACAGCCAAAGAAATAT 58.905 40.909 0.00 0.00 34.23 1.28
3563 3751 2.517959 AGCAGCACAGCCAAAGAAATA 58.482 42.857 0.00 0.00 34.23 1.40
3564 3752 1.335145 AGCAGCACAGCCAAAGAAAT 58.665 45.000 0.00 0.00 34.23 2.17
3565 3753 1.113788 AAGCAGCACAGCCAAAGAAA 58.886 45.000 0.00 0.00 34.23 2.52
3568 3756 1.006571 CCAAGCAGCACAGCCAAAG 60.007 57.895 0.00 0.00 34.23 2.77
3607 3795 2.792674 CAGCACAGCAAACAAATGTCAG 59.207 45.455 0.00 0.00 0.00 3.51
3611 3799 3.242478 CCAAACAGCACAGCAAACAAATG 60.242 43.478 0.00 0.00 0.00 2.32
3621 3809 0.740149 TCAACAGCCAAACAGCACAG 59.260 50.000 0.00 0.00 34.23 3.66
3644 3832 3.248125 CGATTTTGGCAGCACAAACAAAT 59.752 39.130 8.16 1.73 39.82 2.32
3699 3955 4.505566 CCATCTTTCAGAGGTTCCAGTGAA 60.506 45.833 0.00 2.97 0.00 3.18
3809 4130 3.498774 ATGCAAACTTCTGACCAGAGT 57.501 42.857 0.00 0.00 38.88 3.24
3821 4142 6.403878 AGTACGTTGGTCTTATATGCAAACT 58.596 36.000 0.00 0.00 0.00 2.66
3856 4177 2.284754 TGCACCACTGCCTTTTGATA 57.715 45.000 0.00 0.00 43.51 2.15
4016 4368 2.358247 TCCGGCGTCTCTTTTGCC 60.358 61.111 6.01 0.00 45.39 4.52
4017 4369 1.503818 TTGTCCGGCGTCTCTTTTGC 61.504 55.000 6.01 0.00 0.00 3.68
4018 4370 1.156736 ATTGTCCGGCGTCTCTTTTG 58.843 50.000 6.01 0.00 0.00 2.44
4019 4371 1.535462 CAATTGTCCGGCGTCTCTTTT 59.465 47.619 6.01 0.00 0.00 2.27
4020 4372 1.156736 CAATTGTCCGGCGTCTCTTT 58.843 50.000 6.01 0.00 0.00 2.52
4023 4375 2.750888 GCCAATTGTCCGGCGTCTC 61.751 63.158 6.01 0.00 38.82 3.36
4054 4407 2.257286 CTGGGCAAGTGGATTTCGCG 62.257 60.000 0.00 0.00 0.00 5.87
4093 4446 2.692557 CTGTGTGATTGGTGGGTTTTGA 59.307 45.455 0.00 0.00 0.00 2.69
4098 4451 0.843309 TCACTGTGTGATTGGTGGGT 59.157 50.000 7.79 0.00 37.67 4.51
4240 4690 2.699321 CCTGCCTCTGATCTGATCTGAA 59.301 50.000 22.29 11.18 36.91 3.02
4241 4691 2.317973 CCTGCCTCTGATCTGATCTGA 58.682 52.381 21.23 21.23 36.12 3.27
4242 4692 1.270412 GCCTGCCTCTGATCTGATCTG 60.270 57.143 17.82 16.82 0.00 2.90
4243 4693 1.050204 GCCTGCCTCTGATCTGATCT 58.950 55.000 17.82 0.00 0.00 2.75
4244 4694 0.757512 TGCCTGCCTCTGATCTGATC 59.242 55.000 10.72 10.72 0.00 2.92
4245 4695 1.141254 CTTGCCTGCCTCTGATCTGAT 59.859 52.381 2.43 0.00 0.00 2.90
4272 4722 2.806745 GCTTCGGCCTGTGCATATCTTA 60.807 50.000 0.00 0.00 40.13 2.10
4310 4760 4.699522 GCTGCGTCCGGAACCCTT 62.700 66.667 5.23 0.00 0.00 3.95
4318 4775 0.735978 TAGTTCATGTGCTGCGTCCG 60.736 55.000 0.00 0.00 0.00 4.79
4319 4776 0.721718 GTAGTTCATGTGCTGCGTCC 59.278 55.000 0.00 0.00 0.00 4.79
4320 4777 0.721718 GGTAGTTCATGTGCTGCGTC 59.278 55.000 0.00 0.00 0.00 5.19
4321 4778 0.321671 AGGTAGTTCATGTGCTGCGT 59.678 50.000 0.00 0.00 0.00 5.24
4322 4779 1.002366 GAGGTAGTTCATGTGCTGCG 58.998 55.000 0.00 0.00 0.00 5.18
4323 4780 1.734465 GTGAGGTAGTTCATGTGCTGC 59.266 52.381 0.00 0.00 0.00 5.25
4324 4781 2.350522 GGTGAGGTAGTTCATGTGCTG 58.649 52.381 0.00 0.00 0.00 4.41
4336 4793 1.304713 GGTCCACTCCGGTGAGGTA 60.305 63.158 17.83 4.40 45.61 3.08
4337 4794 2.603776 GGTCCACTCCGGTGAGGT 60.604 66.667 17.83 3.51 45.61 3.85
4338 4795 1.553690 AATGGTCCACTCCGGTGAGG 61.554 60.000 13.18 13.18 45.61 3.86
4339 4796 0.108138 GAATGGTCCACTCCGGTGAG 60.108 60.000 11.17 1.68 45.61 3.51
4342 4799 2.978824 CGAATGGTCCACTCCGGT 59.021 61.111 0.00 0.00 35.57 5.28


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

AutoCloner maintained by Alex Coulton.