Multiple sequence alignment - TraesCS1A01G198400

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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 TraesCS1A01G198400 chr1A 100.000 4589 0 0 1 4589 356470409 356474997 0.000000e+00 8475
1 TraesCS1A01G198400 chr1B 95.481 3607 138 17 1 3596 387302464 387306056 0.000000e+00 5734
2 TraesCS1A01G198400 chr1B 92.020 1015 50 18 3600 4586 387306097 387307108 0.000000e+00 1397
3 TraesCS1A01G198400 chr1D 94.391 1854 69 16 893 2737 285052518 285054345 0.000000e+00 2815
4 TraesCS1A01G198400 chr1D 96.301 838 27 3 2760 3596 285054416 285055250 0.000000e+00 1373
5 TraesCS1A01G198400 chr1D 93.873 865 38 10 3736 4586 285055385 285056248 0.000000e+00 1290
6 TraesCS1A01G198400 chr1D 90.542 793 51 15 1 781 285051650 285052430 0.000000e+00 1027
7 TraesCS1A01G198400 chr1D 92.593 108 6 1 3595 3702 285055286 285055391 2.210000e-33 154
8 TraesCS1A01G198400 chr1D 85.965 114 13 2 3630 3741 285055466 285055578 8.070000e-23 119


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 TraesCS1A01G198400 chr1A 356470409 356474997 4588 False 8475.000000 8475 100.0000 1 4589 1 chr1A.!!$F1 4588
1 TraesCS1A01G198400 chr1B 387302464 387307108 4644 False 3565.500000 5734 93.7505 1 4586 2 chr1B.!!$F1 4585
2 TraesCS1A01G198400 chr1D 285051650 285056248 4598 False 1129.666667 2815 92.2775 1 4586 6 chr1D.!!$F1 4585

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
332 333 0.957888 GGCAAGGTCTCAGGTGAAGC 60.958 60.000 0.0 0.0 0.0 3.86 F
1410 1434 1.139734 CGGTGGATCACTCAGGTCG 59.860 63.158 0.0 0.0 34.4 4.79 F
2275 2304 0.524180 GTCGCTGCTTATTGGCTTGC 60.524 55.000 0.0 0.0 0.0 4.01 F
3035 3137 1.135972 GGTGAAGTGCGTGCAATAGTG 60.136 52.381 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1925 0.539051 CCTGCTCGGACCAGAAGATT 59.461 55.000 1.85 0.0 32.03 2.40 R
3096 3198 1.068333 GCCATTGTCGCACTGAAATGT 60.068 47.619 0.00 0.0 0.00 2.71 R
3438 3540 1.141665 CACGCTGTCGATGATCCCA 59.858 57.895 0.00 0.0 39.41 4.37 R
4355 4523 0.467384 CCATCCTGATGCCGAAGAGT 59.533 55.000 1.49 0.0 37.49 3.24 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
155 156 3.976490 TAGTGAGGAGGGGCGTGGG 62.976 68.421 0.00 0.00 0.00 4.61
213 214 4.959596 ACATGTTGCAGAGAATGATGAC 57.040 40.909 0.00 0.00 0.00 3.06
216 217 3.402110 TGTTGCAGAGAATGATGACGTT 58.598 40.909 0.00 0.00 0.00 3.99
312 313 3.036819 TGTAGCTGAGAAGGCTGATGAT 58.963 45.455 0.00 0.00 40.52 2.45
332 333 0.957888 GGCAAGGTCTCAGGTGAAGC 60.958 60.000 0.00 0.00 0.00 3.86
354 355 4.439289 GCTAGAAAAGATGGTGTTGATGCC 60.439 45.833 0.00 0.00 0.00 4.40
356 357 2.198827 AAAGATGGTGTTGATGCCGA 57.801 45.000 0.00 0.00 0.00 5.54
480 481 2.165437 AGAAGAGGATGAAGCAGACGAC 59.835 50.000 0.00 0.00 0.00 4.34
498 499 3.186817 ACGACTAGAATCGAATAGCCTCG 59.813 47.826 9.50 2.13 45.13 4.63
509 510 5.641709 TCGAATAGCCTCGATAATGTCATC 58.358 41.667 0.00 0.00 42.69 2.92
518 519 5.510349 CCTCGATAATGTCATCTGATGGTGT 60.510 44.000 17.06 4.03 0.00 4.16
567 568 5.214417 GTTCTTTTGGCAATTTTGGAATGC 58.786 37.500 0.00 0.00 0.00 3.56
574 575 2.553172 GCAATTTTGGAATGCTGGCAAA 59.447 40.909 0.00 0.00 0.00 3.68
575 576 3.365565 GCAATTTTGGAATGCTGGCAAAG 60.366 43.478 0.00 0.00 0.00 2.77
718 728 9.088512 CCAAGATGATTTTACTACTGTGAGTAC 57.911 37.037 0.00 0.00 31.58 2.73
733 746 2.035449 TGAGTACGCTTAAGTGCTGTGT 59.965 45.455 15.92 0.00 37.20 3.72
736 749 3.493503 AGTACGCTTAAGTGCTGTGTTTC 59.506 43.478 15.92 0.00 35.77 2.78
745 758 8.480066 GCTTAAGTGCTGTGTTTCTTAATTTTC 58.520 33.333 4.02 0.00 33.76 2.29
787 800 4.456911 TCTGTGTTGCAATCTCAATTCCTC 59.543 41.667 0.59 0.00 0.00 3.71
795 808 5.100943 GCAATCTCAATTCCTCTTTTGAGC 58.899 41.667 7.60 0.00 45.41 4.26
796 809 5.105837 GCAATCTCAATTCCTCTTTTGAGCT 60.106 40.000 7.60 0.00 45.41 4.09
806 819 6.959639 TCCTCTTTTGAGCTTGTTGTAATT 57.040 33.333 0.00 0.00 44.93 1.40
815 828 7.754069 TGAGCTTGTTGTAATTTCAAACAAG 57.246 32.000 23.00 23.00 36.33 3.16
891 914 1.208293 GGGAAGAAGGCAGTAGTCCTG 59.792 57.143 0.00 0.00 44.53 3.86
1079 1103 2.898840 CAGGCACCGGCAGCTATG 60.899 66.667 17.73 13.18 43.71 2.23
1410 1434 1.139734 CGGTGGATCACTCAGGTCG 59.860 63.158 0.00 0.00 34.40 4.79
1459 1483 5.374921 TCGGTTTGTGTAGGGTTGAATTTA 58.625 37.500 0.00 0.00 0.00 1.40
1460 1484 5.239087 TCGGTTTGTGTAGGGTTGAATTTAC 59.761 40.000 0.00 0.00 0.00 2.01
1461 1485 5.239963 CGGTTTGTGTAGGGTTGAATTTACT 59.760 40.000 0.00 0.00 0.00 2.24
1462 1486 6.238814 CGGTTTGTGTAGGGTTGAATTTACTT 60.239 38.462 0.00 0.00 0.00 2.24
1508 1532 6.489127 TTTGTGGTCTTACATTATTCCACG 57.511 37.500 0.00 0.00 45.43 4.94
1625 1649 7.262772 CACTAATCAAAATCATGACCTGCATT 58.737 34.615 0.00 0.00 34.15 3.56
1626 1650 7.434307 CACTAATCAAAATCATGACCTGCATTC 59.566 37.037 0.00 0.00 34.15 2.67
1654 1682 4.489810 GACTCATCAAGTCGATTCACAGT 58.510 43.478 0.00 0.00 44.79 3.55
1660 1688 6.598064 TCATCAAGTCGATTCACAGTAGTAGA 59.402 38.462 0.00 0.00 29.21 2.59
1742 1770 2.111384 ACTGACACACCTTCAGACTGT 58.889 47.619 6.37 0.00 42.81 3.55
1743 1771 3.068165 CACTGACACACCTTCAGACTGTA 59.932 47.826 6.37 0.00 42.81 2.74
1744 1772 3.704566 ACTGACACACCTTCAGACTGTAA 59.295 43.478 6.37 0.00 42.81 2.41
1750 1778 4.929808 CACACCTTCAGACTGTAATACCAC 59.070 45.833 1.59 0.00 0.00 4.16
1811 1839 8.024285 CCGAATGATACTTTACTGACTATCCTC 58.976 40.741 0.00 0.00 0.00 3.71
1916 1944 0.539051 AATCTTCTGGTCCGAGCAGG 59.461 55.000 23.89 11.55 43.47 4.85
1941 1969 3.302480 CGGAAATCTTATTCTTCACCGCG 60.302 47.826 0.00 0.00 0.00 6.46
1953 1981 2.442212 TCACCGCGTCAACAATTCTA 57.558 45.000 4.92 0.00 0.00 2.10
1994 2023 9.199982 TCTTCGTTGTTACTTCATTAAACTAGG 57.800 33.333 0.00 0.00 0.00 3.02
2066 2095 3.488721 CCAGTGGGTCGTTTCTATACTCG 60.489 52.174 0.00 0.00 0.00 4.18
2275 2304 0.524180 GTCGCTGCTTATTGGCTTGC 60.524 55.000 0.00 0.00 0.00 4.01
2334 2363 2.498167 GAGCACCTTGTTGTCTGTGAT 58.502 47.619 0.00 0.00 0.00 3.06
2545 2575 9.561027 ACTCTTTAGTACTACGCCAATATGGGC 62.561 44.444 11.55 11.55 41.75 5.36
2645 2675 7.744733 TGATGCCTGGAGTTTGTAATGATATA 58.255 34.615 0.00 0.00 0.00 0.86
2667 2697 7.828508 ATATGTTGCACCTTATGAATGATGT 57.171 32.000 0.00 0.00 0.00 3.06
2710 2742 6.456181 GCGTAACATTCATCTCTCTTTCAAGG 60.456 42.308 0.00 0.00 0.00 3.61
2794 2896 5.805728 ACCCTATTGTTAGTTGACTTGGAG 58.194 41.667 0.00 0.00 0.00 3.86
2827 2929 2.714250 AGTTTGGTATGAGTGGTGGGAA 59.286 45.455 0.00 0.00 0.00 3.97
3035 3137 1.135972 GGTGAAGTGCGTGCAATAGTG 60.136 52.381 0.00 0.00 0.00 2.74
3123 3225 2.679837 CAGTGCGACAATGGCTATCTTT 59.320 45.455 0.00 0.00 0.00 2.52
3438 3540 3.068873 GTCCTCTTGAGGCTGTCGATTAT 59.931 47.826 11.61 0.00 0.00 1.28
3589 3691 7.002276 TGTCCCAGACGATGAGATATACTAAA 58.998 38.462 0.00 0.00 34.95 1.85
3590 3692 7.175119 TGTCCCAGACGATGAGATATACTAAAG 59.825 40.741 0.00 0.00 34.95 1.85
3591 3693 6.151312 TCCCAGACGATGAGATATACTAAAGC 59.849 42.308 0.00 0.00 0.00 3.51
3592 3694 6.151985 CCCAGACGATGAGATATACTAAAGCT 59.848 42.308 0.00 0.00 0.00 3.74
3593 3695 7.337184 CCCAGACGATGAGATATACTAAAGCTA 59.663 40.741 0.00 0.00 0.00 3.32
3597 3735 8.343168 ACGATGAGATATACTAAAGCTAGCTT 57.657 34.615 24.42 24.42 37.98 3.74
3670 3808 1.000385 CGTTGCATTTGGTGTGATGGT 60.000 47.619 0.00 0.00 0.00 3.55
3683 3821 2.158827 TGTGATGGTGTAGCTGTTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
3721 3860 3.322828 AGCAAATGAAAGCACATGGAACT 59.677 39.130 0.00 0.00 0.00 3.01
3724 3863 5.695816 GCAAATGAAAGCACATGGAACTTAA 59.304 36.000 0.00 0.00 0.00 1.85
3752 3891 0.393402 TAACCAGCTAGCCTCGTCGA 60.393 55.000 12.13 0.00 0.00 4.20
3760 3908 2.981140 GCTAGCCTCGTCGAATGTATTC 59.019 50.000 2.29 0.00 0.00 1.75
3815 3966 9.998381 GTCAAAAGTTTGTAACACTTGTTTTAC 57.002 29.630 0.00 0.00 39.18 2.01
3816 3967 9.968870 TCAAAAGTTTGTAACACTTGTTTTACT 57.031 25.926 0.00 0.00 39.18 2.24
3827 3984 8.459911 AACACTTGTTTTACTACTAATTGGCT 57.540 30.769 0.00 0.00 33.93 4.75
3948 4113 4.112634 GCAAAGAAGAAACCAAAGGACAC 58.887 43.478 0.00 0.00 0.00 3.67
4036 4204 8.783093 TCCTTTACAAGACACAATAACAATGAG 58.217 33.333 0.00 0.00 0.00 2.90
4088 4256 1.714899 ATTATCACAGCCGCCGCAAC 61.715 55.000 0.00 0.00 37.52 4.17
4138 4306 1.450211 CAACAGTCGGAACCAGGGT 59.550 57.895 0.00 0.00 0.00 4.34
4160 4328 3.723348 GACACGCCGCCTTTGACC 61.723 66.667 0.00 0.00 0.00 4.02
4163 4331 3.315949 ACGCCGCCTTTGACCCTA 61.316 61.111 0.00 0.00 0.00 3.53
4169 4337 4.637771 CCTTTGACCCTAAGGCCG 57.362 61.111 0.00 0.00 36.08 6.13
4215 4383 0.250901 TGAGCTCCCAGTTTTCAGGC 60.251 55.000 12.15 0.00 0.00 4.85
4328 4496 6.015918 TGAACCAATTGTCTGACCCAATATT 58.984 36.000 5.17 0.00 32.40 1.28
4355 4523 3.437624 ATGGTAAGGGCCATGGCA 58.562 55.556 36.56 16.15 46.63 4.92
4445 4613 3.044986 CCATTGCACTGAAAACTTCGTG 58.955 45.455 5.49 6.87 37.30 4.35
4478 4646 2.426024 CCAGATGCCAAGAGGAACATTG 59.574 50.000 0.00 0.00 36.89 2.82
4586 4754 2.339712 GCACGGGCAGCAACAATT 59.660 55.556 3.77 0.00 40.72 2.32
4587 4755 2.023223 GCACGGGCAGCAACAATTG 61.023 57.895 3.77 3.24 40.72 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 3.803231 TGCATTTGTCTTTGTTGTGATGC 59.197 39.130 0.00 0.00 39.15 3.91
213 214 1.864711 TCTTTCAGGAAAGCACGAACG 59.135 47.619 15.26 0.00 45.48 3.95
216 217 2.158957 ACACTCTTTCAGGAAAGCACGA 60.159 45.455 15.26 0.23 45.48 4.35
273 274 5.660417 AGCTACAGAATCATCCTTCTTCTCA 59.340 40.000 0.00 0.00 33.18 3.27
312 313 0.397941 CTTCACCTGAGACCTTGCCA 59.602 55.000 0.00 0.00 0.00 4.92
332 333 4.201851 CGGCATCAACACCATCTTTTCTAG 60.202 45.833 0.00 0.00 0.00 2.43
354 355 2.103934 CTCTTCTCGCCCTGCTCG 59.896 66.667 0.00 0.00 0.00 5.03
356 357 1.610673 TTCCTCTTCTCGCCCTGCT 60.611 57.895 0.00 0.00 0.00 4.24
498 499 6.765036 AGTTGACACCATCAGATGACATTATC 59.235 38.462 12.41 1.84 38.99 1.75
500 501 6.053632 AGTTGACACCATCAGATGACATTA 57.946 37.500 12.41 0.00 38.99 1.90
505 506 4.356405 ACAAGTTGACACCATCAGATGA 57.644 40.909 12.41 0.00 38.99 2.92
507 508 4.637534 GCATACAAGTTGACACCATCAGAT 59.362 41.667 10.54 0.00 38.99 2.90
509 510 4.005650 AGCATACAAGTTGACACCATCAG 58.994 43.478 10.54 0.00 38.99 2.90
518 519 5.555966 TGGATAACACAGCATACAAGTTGA 58.444 37.500 10.54 0.00 0.00 3.18
567 568 5.757850 AAACTCTTACACTTCTTTGCCAG 57.242 39.130 0.00 0.00 0.00 4.85
574 575 6.183360 TGGACAGCTAAAACTCTTACACTTCT 60.183 38.462 0.00 0.00 0.00 2.85
575 576 5.989777 TGGACAGCTAAAACTCTTACACTTC 59.010 40.000 0.00 0.00 0.00 3.01
718 728 3.609103 AAGAAACACAGCACTTAAGCG 57.391 42.857 1.29 0.00 40.15 4.68
745 758 6.709397 ACACAGACAGCAGATAATATTCCATG 59.291 38.462 0.00 0.00 0.00 3.66
787 800 8.655092 TGTTTGAAATTACAACAAGCTCAAAAG 58.345 29.630 0.00 0.00 34.23 2.27
795 808 7.488322 TCCCTCTTGTTTGAAATTACAACAAG 58.512 34.615 20.76 20.76 38.54 3.16
796 809 7.411486 TCCCTCTTGTTTGAAATTACAACAA 57.589 32.000 8.61 8.61 31.46 2.83
806 819 7.396055 TCTTTCTTTTCTTCCCTCTTGTTTGAA 59.604 33.333 0.00 0.00 0.00 2.69
815 828 4.023963 CCGTTGTCTTTCTTTTCTTCCCTC 60.024 45.833 0.00 0.00 0.00 4.30
880 903 3.181474 GGATAACTCACCAGGACTACTGC 60.181 52.174 0.00 0.00 46.14 4.40
1025 1049 2.680352 TGACGGAGAGGGAGGCAC 60.680 66.667 0.00 0.00 0.00 5.01
1106 1130 2.317149 CTTGAGGAGGGGATGCGGTC 62.317 65.000 0.00 0.00 0.00 4.79
1110 1134 1.153005 CAGCTTGAGGAGGGGATGC 60.153 63.158 0.00 0.00 0.00 3.91
1227 1251 4.785453 CCGCTGGCAACTCCTCCC 62.785 72.222 0.00 0.00 35.26 4.30
1236 1260 4.002506 ATGACGTCACCGCTGGCA 62.003 61.111 22.71 0.00 37.70 4.92
1410 1434 1.105759 GGAGTGATGCATTGGGAGGC 61.106 60.000 0.00 0.00 0.00 4.70
1459 1483 4.848357 CATCCCTTGTTGAGATGGTAAGT 58.152 43.478 0.00 0.00 34.94 2.24
1460 1484 3.629398 GCATCCCTTGTTGAGATGGTAAG 59.371 47.826 0.00 0.00 38.25 2.34
1461 1485 3.620488 GCATCCCTTGTTGAGATGGTAA 58.380 45.455 0.00 0.00 38.25 2.85
1462 1486 2.092429 GGCATCCCTTGTTGAGATGGTA 60.092 50.000 0.00 0.00 38.25 3.25
1508 1532 1.327303 TTTGCCCACAAGATGACCAC 58.673 50.000 0.00 0.00 37.04 4.16
1545 1569 9.395707 GTGAATACTATCACGAATCGAATTAGT 57.604 33.333 10.55 13.98 40.23 2.24
1742 1770 7.588169 AGCAAATGGGTTTATAGGTGGTATTA 58.412 34.615 0.00 0.00 0.00 0.98
1743 1771 6.440354 AGCAAATGGGTTTATAGGTGGTATT 58.560 36.000 0.00 0.00 0.00 1.89
1744 1772 6.025793 AGCAAATGGGTTTATAGGTGGTAT 57.974 37.500 0.00 0.00 0.00 2.73
1750 1778 7.653311 GCAGATTTTAGCAAATGGGTTTATAGG 59.347 37.037 0.00 0.00 32.35 2.57
1897 1925 0.539051 CCTGCTCGGACCAGAAGATT 59.461 55.000 1.85 0.00 32.03 2.40
1900 1928 2.581354 CCCTGCTCGGACCAGAAG 59.419 66.667 1.85 0.00 32.03 2.85
1916 1944 3.315470 GGTGAAGAATAAGATTTCCGCCC 59.685 47.826 0.00 0.00 0.00 6.13
1976 2004 9.961265 AACAAAAGCCTAGTTTAATGAAGTAAC 57.039 29.630 0.00 0.00 0.00 2.50
2113 2142 6.803366 AACTTAGGTGTTACCATAGGTAGG 57.197 41.667 0.28 0.00 41.95 3.18
2237 2266 4.613944 CGACCTACTGACACAAACTTACA 58.386 43.478 0.00 0.00 0.00 2.41
2248 2277 2.860735 CAATAAGCAGCGACCTACTGAC 59.139 50.000 0.00 0.00 37.32 3.51
2275 2304 8.865001 GCTAAGAGTTTAATTCGGCTGATATAG 58.135 37.037 0.00 0.00 0.00 1.31
2293 2322 5.694006 GCTCGATGTTGATATTGCTAAGAGT 59.306 40.000 0.00 0.00 0.00 3.24
2361 2390 5.047092 ACAAGCCAATAAGTTGCAAGCTAAT 60.047 36.000 0.00 0.00 31.81 1.73
2368 2397 5.709631 TCTCATAACAAGCCAATAAGTTGCA 59.290 36.000 0.00 0.00 33.90 4.08
2371 2400 7.201767 GCTGATCTCATAACAAGCCAATAAGTT 60.202 37.037 0.00 0.00 0.00 2.66
2466 2495 6.518208 AAGAAACGAGCTAGTGATAGAAGT 57.482 37.500 0.00 0.00 0.00 3.01
2571 2601 3.153919 GAGGGGTCTGTACAAAATGCAA 58.846 45.455 0.00 0.00 0.00 4.08
2572 2602 2.790433 GAGGGGTCTGTACAAAATGCA 58.210 47.619 0.00 0.00 0.00 3.96
2625 2655 8.292448 GCAACATATATCATTACAAACTCCAGG 58.708 37.037 0.00 0.00 0.00 4.45
2645 2675 6.534475 AACATCATTCATAAGGTGCAACAT 57.466 33.333 3.64 0.00 39.98 2.71
2667 2697 9.900710 ATGTTACGCACATATAAACAAGAAAAA 57.099 25.926 0.00 0.00 45.00 1.94
2794 2896 2.861147 ACCAAACTAGAAGAGGGCAC 57.139 50.000 0.00 0.00 0.00 5.01
2827 2929 5.843019 TCCTTTGGACAGGACTATTCTTT 57.157 39.130 0.00 0.00 38.11 2.52
3035 3137 4.580167 TGTATCAACAGATATGCAAAGGCC 59.420 41.667 0.00 0.00 40.13 5.19
3096 3198 1.068333 GCCATTGTCGCACTGAAATGT 60.068 47.619 0.00 0.00 0.00 2.71
3101 3203 1.482182 AGATAGCCATTGTCGCACTGA 59.518 47.619 0.12 0.00 0.00 3.41
3123 3225 2.635714 CTCACCAGCTGCATTACATCA 58.364 47.619 8.66 0.00 0.00 3.07
3438 3540 1.141665 CACGCTGTCGATGATCCCA 59.858 57.895 0.00 0.00 39.41 4.37
3597 3735 4.574421 TCATCTTTGTTTGACGAAAGCTCA 59.426 37.500 0.00 0.00 0.00 4.26
3670 3808 2.095461 TGCCAAAACACAACAGCTACA 58.905 42.857 0.00 0.00 0.00 2.74
3683 3821 2.996249 TGCTTGGTCAAATGCCAAAA 57.004 40.000 9.49 1.56 44.37 2.44
3752 3891 2.821378 TGCTTGCTGTGCAGAATACATT 59.179 40.909 3.02 0.00 40.61 2.71
3760 3908 1.660575 GCAGTTGCTTGCTGTGCAG 60.661 57.895 0.00 0.00 40.61 4.41
3809 3960 6.674066 TGCAACAGCCAATTAGTAGTAAAAC 58.326 36.000 0.00 0.00 0.00 2.43
3815 3966 5.104374 CCAAATGCAACAGCCAATTAGTAG 58.896 41.667 0.00 0.00 0.00 2.57
3816 3967 4.526262 ACCAAATGCAACAGCCAATTAGTA 59.474 37.500 0.00 0.00 0.00 1.82
3818 3969 3.929094 ACCAAATGCAACAGCCAATTAG 58.071 40.909 0.00 0.00 0.00 1.73
3821 3972 3.261390 ACATACCAAATGCAACAGCCAAT 59.739 39.130 0.00 0.00 0.00 3.16
3827 3984 3.234353 TCCCAACATACCAAATGCAACA 58.766 40.909 0.00 0.00 0.00 3.33
3948 4113 5.701029 GGTGCAATCAATAAATTTCACCG 57.299 39.130 0.00 0.00 41.08 4.94
4055 4223 7.201644 CGGCTGTGATAATTGTATCAAGAGTTT 60.202 37.037 0.00 0.00 46.05 2.66
4138 4306 3.469863 AAAGGCGGCGTGTCTCCAA 62.470 57.895 9.37 0.00 0.00 3.53
4142 4310 2.665185 GTCAAAGGCGGCGTGTCT 60.665 61.111 9.37 0.80 0.00 3.41
4149 4317 4.637771 CCTTAGGGTCAAAGGCGG 57.362 61.111 0.00 0.00 37.30 6.13
4160 4328 4.222847 GACCCGCTCGGCCTTAGG 62.223 72.222 0.00 0.00 33.26 2.69
4169 4337 4.154347 CAGCTCTGGGACCCGCTC 62.154 72.222 8.34 0.00 0.00 5.03
4215 4383 3.071580 GGATTGAAGCTCCGGTGAG 57.928 57.895 7.92 0.00 41.84 3.51
4328 4496 1.131638 CCCTTACCATAGCTGCCTCA 58.868 55.000 0.00 0.00 0.00 3.86
4355 4523 0.467384 CCATCCTGATGCCGAAGAGT 59.533 55.000 1.49 0.00 37.49 3.24
4445 4613 1.222936 CATCTGGAGGGAGCACACC 59.777 63.158 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.