Multiple sequence alignment - TraesCS4B01G174000

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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 TraesCS4B01G174000 chr4B 100.000 3642 0 0 1 3642 381372621 381376262 0.000000e+00 6726.0
1 TraesCS4B01G174000 chr4A 91.232 3011 123 41 1 2943 173629231 173632168 0.000000e+00 3967.0
2 TraesCS4B01G174000 chr4A 87.453 534 19 17 3122 3624 173638013 173638529 4.080000e-159 571.0
3 TraesCS4B01G174000 chr4A 84.694 98 3 1 3013 3098 173632307 173632404 1.800000e-13 87.9
4 TraesCS4B01G174000 chr4A 77.931 145 28 4 1229 1371 690886940 690886798 1.800000e-13 87.9
5 TraesCS4B01G174000 chr4A 77.083 144 31 2 1229 1371 691470084 691469942 8.380000e-12 82.4
6 TraesCS4B01G174000 chr4A 97.059 34 1 0 2957 2990 173632206 173632239 1.410000e-04 58.4
7 TraesCS4B01G174000 chr4D 90.476 3045 107 58 1 2962 305139864 305142808 0.000000e+00 3847.0
8 TraesCS4B01G174000 chr4D 87.601 371 17 13 3297 3642 305143352 305143718 1.570000e-108 403.0
9 TraesCS4B01G174000 chr4D 83.636 275 7 13 2957 3195 305142844 305143116 1.320000e-54 224.0
10 TraesCS4B01G174000 chr2D 85.020 247 34 2 1483 1729 417544117 417544360 7.810000e-62 248.0
11 TraesCS4B01G174000 chr2B 84.337 249 32 6 1483 1729 489419049 489419292 1.690000e-58 237.0
12 TraesCS4B01G174000 chr2A 84.362 243 31 6 1489 1729 572615833 572615596 7.860000e-57 231.0
13 TraesCS4B01G174000 chr2A 81.982 222 35 3 1502 1719 625957808 625958028 2.230000e-42 183.0
14 TraesCS4B01G174000 chr5A 82.879 257 33 9 1477 1726 317240005 317239753 1.700000e-53 220.0
15 TraesCS4B01G174000 chr5D 82.490 257 34 9 1477 1726 238073371 238073623 7.920000e-52 215.0
16 TraesCS4B01G174000 chr5B 80.545 257 39 9 1477 1726 267760739 267760487 1.730000e-43 187.0
17 TraesCS4B01G174000 chr7A 80.952 231 41 2 1496 1723 489163235 489163465 2.890000e-41 180.0
18 TraesCS4B01G174000 chr7D 80.426 235 42 3 1493 1723 438368646 438368880 3.740000e-40 176.0
19 TraesCS4B01G174000 chr7D 79.310 145 26 4 1229 1371 34011745 34011603 8.320000e-17 99.0
20 TraesCS4B01G174000 chr7D 78.947 133 24 4 1229 1359 33754653 33754783 1.800000e-13 87.9
21 TraesCS4B01G174000 chr7D 77.931 145 28 4 1229 1371 34077141 34076999 1.800000e-13 87.9
22 TraesCS4B01G174000 chr7B 80.000 235 43 3 1493 1723 455272025 455271791 1.740000e-38 171.0
23 TraesCS4B01G174000 chr7B 78.509 228 42 4 1497 1719 436787584 436787359 3.790000e-30 143.0
24 TraesCS4B01G174000 chr6B 83.696 92 13 2 1194 1284 51580417 51580327 6.480000e-13 86.1
25 TraesCS4B01G174000 chr6A 82.105 95 15 2 1191 1284 30191238 30191145 3.010000e-11 80.5


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 TraesCS4B01G174000 chr4B 381372621 381376262 3641 False 6726.000000 6726 100.000000 1 3642 1 chr4B.!!$F1 3641
1 TraesCS4B01G174000 chr4A 173629231 173632404 3173 False 1371.100000 3967 90.995000 1 3098 3 chr4A.!!$F2 3097
2 TraesCS4B01G174000 chr4A 173638013 173638529 516 False 571.000000 571 87.453000 3122 3624 1 chr4A.!!$F1 502
3 TraesCS4B01G174000 chr4D 305139864 305143718 3854 False 1491.333333 3847 87.237667 1 3642 3 chr4D.!!$F1 3641

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
168 169 0.248784 GGATGCTCATCGCTTTTGGC 60.249 55.0 4.02 0.0 38.69 4.52 F
1768 1836 0.240945 CGCCAAGGTTTGCTTTCGAT 59.759 50.0 0.00 0.0 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2033 1.280421 AGGAAGTCAGTGATGAAGCCC 59.720 52.381 0.00 0.0 0.0 5.19 R
3117 3343 0.035630 AAGGCTGCAGCTTGTAGAGG 60.036 55.000 35.82 0.0 41.7 3.69 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
23 24 1.579429 GCGTCACCATTTCGCCTTT 59.421 52.632 0.00 0.00 43.41 3.11
34 35 5.221441 ACCATTTCGCCTTTCTTTTAAAGCT 60.221 36.000 0.00 0.00 0.00 3.74
43 44 6.385033 CCTTTCTTTTAAAGCTGGAGATGTG 58.615 40.000 0.00 0.00 0.00 3.21
168 169 0.248784 GGATGCTCATCGCTTTTGGC 60.249 55.000 4.02 0.00 38.69 4.52
213 215 4.029418 CGCGTATCTTTGCAGAAAATTGTG 59.971 41.667 0.00 0.00 30.76 3.33
244 246 1.983196 CTCTCTCGATGGCACGTCGT 61.983 60.000 10.01 0.00 39.91 4.34
256 261 1.191647 GCACGTCGTTCCTGTAAACAG 59.808 52.381 0.00 3.02 43.40 3.16
305 310 1.596727 GATGCGGATGAGAAAGCAGAC 59.403 52.381 0.00 0.00 43.20 3.51
333 338 2.878406 GGGACAACCACGGATCAATATG 59.122 50.000 0.00 0.00 39.85 1.78
418 426 9.302345 CTGATCATCCTTTGATTTGATTGAAAG 57.698 33.333 0.00 0.00 45.29 2.62
468 476 2.051345 GTTCTTGCGTTGTGGCCG 60.051 61.111 0.00 0.00 0.00 6.13
471 479 2.652382 TTCTTGCGTTGTGGCCGAGA 62.652 55.000 0.00 0.00 0.00 4.04
491 499 3.937706 AGAGCGGATGAGTTGAATTCTTG 59.062 43.478 7.05 0.00 0.00 3.02
495 503 4.002982 CGGATGAGTTGAATTCTTGTGGA 58.997 43.478 7.05 0.00 0.00 4.02
596 611 9.707957 TGAACTACTACTACTACTACTACTCCT 57.292 37.037 0.00 0.00 0.00 3.69
604 619 8.434589 ACTACTACTACTACTCCTACTATGGG 57.565 42.308 0.00 0.00 0.00 4.00
605 620 8.016054 ACTACTACTACTACTCCTACTATGGGT 58.984 40.741 0.00 0.00 0.00 4.51
606 621 7.704359 ACTACTACTACTCCTACTATGGGTT 57.296 40.000 0.00 0.00 0.00 4.11
623 638 9.831682 ACTATGGGTTTTTATTTAAGGGAGAAA 57.168 29.630 0.00 0.00 0.00 2.52
667 684 4.818417 GTTGTGTCCAACGCATCG 57.182 55.556 0.00 0.00 41.41 3.84
721 738 2.167398 ATTCCACGGGACAGGACACG 62.167 60.000 0.00 0.00 42.75 4.49
762 779 8.133024 AGAAAATACTCTGAATGTGAGAGAGT 57.867 34.615 0.00 0.00 46.45 3.24
763 780 8.592809 AGAAAATACTCTGAATGTGAGAGAGTT 58.407 33.333 6.23 0.00 43.13 3.01
764 781 8.770438 AAAATACTCTGAATGTGAGAGAGTTC 57.230 34.615 6.23 0.00 43.13 3.01
800 821 1.351017 TGTGAGAAAGTTGGGGCCTAG 59.649 52.381 0.84 0.00 0.00 3.02
801 822 0.991920 TGAGAAAGTTGGGGCCTAGG 59.008 55.000 3.67 3.67 0.00 3.02
802 823 0.992695 GAGAAAGTTGGGGCCTAGGT 59.007 55.000 11.31 0.00 0.00 3.08
859 880 5.019785 AGTAATTAGAGTTGCTTACGGGG 57.980 43.478 0.00 0.00 31.08 5.73
867 894 0.887387 TTGCTTACGGGGCACAACTC 60.887 55.000 0.00 0.00 39.55 3.01
976 1020 2.302157 GTGGAGCCTTATATAAGCCGGT 59.698 50.000 15.86 9.49 32.02 5.28
1061 1105 1.541233 CCTCTTTCACACACGCCTCTT 60.541 52.381 0.00 0.00 0.00 2.85
1083 1140 0.916086 TCTTCCTCTCTCTCTCGGCT 59.084 55.000 0.00 0.00 0.00 5.52
1173 1230 2.890847 GATGTCTGAGGCGTCGGTGG 62.891 65.000 14.58 0.00 0.00 4.61
1429 1497 2.279784 GCTTGATCCGAGCCCGAG 60.280 66.667 6.87 0.00 35.00 4.63
1456 1524 3.871594 CGTGGGAATCTTGCCTTACTTAG 59.128 47.826 2.05 0.00 39.72 2.18
1468 1536 2.665052 CCTTACTTAGTCGCGTGTTTCC 59.335 50.000 5.77 0.00 0.00 3.13
1731 1799 2.654079 CCTCGAGGGCAAGCTCACT 61.654 63.158 24.62 0.00 0.00 3.41
1767 1835 1.652012 CGCCAAGGTTTGCTTTCGA 59.348 52.632 0.00 0.00 0.00 3.71
1768 1836 0.240945 CGCCAAGGTTTGCTTTCGAT 59.759 50.000 0.00 0.00 0.00 3.59
1769 1837 1.729149 CGCCAAGGTTTGCTTTCGATC 60.729 52.381 0.00 0.00 0.00 3.69
1792 1860 7.398289 TCCTCCTTCCTGATTCATTATCAAT 57.602 36.000 0.00 0.00 42.56 2.57
1831 1899 4.403585 TCTCTCTGGCTTCATTCATGAG 57.596 45.455 0.00 0.00 38.19 2.90
1844 1916 8.016229 GCTTCATTCATGAGTGCTAAATATGAG 58.984 37.037 13.08 4.16 38.19 2.90
2303 2384 2.184322 GGTTGCGCGGAGATCTCA 59.816 61.111 23.85 0.68 0.00 3.27
2464 2552 6.238130 GGTTCTGGCTCGTTGATTAATTACTC 60.238 42.308 0.00 0.00 0.00 2.59
2466 2554 6.042777 TCTGGCTCGTTGATTAATTACTCAG 58.957 40.000 5.75 0.00 0.00 3.35
2496 2584 3.815401 ACTTAACTTGGTGTGTGATGCTC 59.185 43.478 0.00 0.00 0.00 4.26
2562 2655 0.384669 CTCGGGTCGGATCAGGTTAC 59.615 60.000 0.00 0.00 0.00 2.50
2563 2656 0.033796 TCGGGTCGGATCAGGTTACT 60.034 55.000 0.00 0.00 0.00 2.24
2564 2657 1.212688 TCGGGTCGGATCAGGTTACTA 59.787 52.381 0.00 0.00 0.00 1.82
2565 2658 2.158564 TCGGGTCGGATCAGGTTACTAT 60.159 50.000 0.00 0.00 0.00 2.12
2580 2673 6.207810 CAGGTTACTATCTATCCAGACAGACC 59.792 46.154 0.00 0.00 29.44 3.85
2614 2717 4.287067 CAGGGATTAGCTAGGCATCCTTAA 59.713 45.833 18.30 0.00 34.61 1.85
2615 2718 5.045286 CAGGGATTAGCTAGGCATCCTTAAT 60.045 44.000 18.30 0.00 34.61 1.40
2616 2719 5.190726 AGGGATTAGCTAGGCATCCTTAATC 59.809 44.000 18.30 6.47 33.48 1.75
2617 2720 5.045578 GGGATTAGCTAGGCATCCTTAATCA 60.046 44.000 18.30 0.00 34.79 2.57
2618 2721 6.353429 GGGATTAGCTAGGCATCCTTAATCAT 60.353 42.308 18.30 0.00 34.79 2.45
2619 2722 6.541641 GGATTAGCTAGGCATCCTTAATCATG 59.458 42.308 13.59 0.00 34.79 3.07
2620 2723 4.989875 AGCTAGGCATCCTTAATCATGT 57.010 40.909 0.00 0.00 34.61 3.21
2621 2724 5.316158 AGCTAGGCATCCTTAATCATGTT 57.684 39.130 0.00 0.00 34.61 2.71
2679 2788 7.462571 TCTGTGTGTACATATCACTACAACT 57.537 36.000 14.14 0.00 35.97 3.16
2680 2789 8.570068 TCTGTGTGTACATATCACTACAACTA 57.430 34.615 14.14 0.00 35.97 2.24
2817 2929 2.042404 GATGAGCCAGCCAGCTAGCT 62.042 60.000 12.68 12.68 45.15 3.32
2828 2940 3.393278 AGCCAGCTAGCTCTACTACTAGT 59.607 47.826 16.15 0.00 39.48 2.57
2829 2941 4.594062 AGCCAGCTAGCTCTACTACTAGTA 59.406 45.833 16.15 1.89 39.48 1.82
2898 3023 4.432712 TGACATGTCACTATGTGAATCGG 58.567 43.478 24.56 0.00 44.49 4.18
2925 3051 2.731976 GTGTTCTCTCTGTACCGCTTTG 59.268 50.000 0.00 0.00 0.00 2.77
2932 3058 0.385974 CTGTACCGCTTTGCACTTGC 60.386 55.000 0.00 0.00 42.50 4.01
2950 3076 6.324819 CACTTGCTAATTAATCACTGGGTTG 58.675 40.000 0.00 0.00 0.00 3.77
3010 3207 6.408770 TCTAGCAAGGGGAGATATGAGATA 57.591 41.667 0.00 0.00 0.00 1.98
3011 3208 6.805150 TCTAGCAAGGGGAGATATGAGATAA 58.195 40.000 0.00 0.00 0.00 1.75
3114 3340 5.062683 GTGAACTCGACACATAGACGTACTA 59.937 44.000 0.00 0.00 38.05 1.82
3116 3342 3.868077 ACTCGACACATAGACGTACTACC 59.132 47.826 0.00 0.00 36.76 3.18
3117 3343 3.198068 TCGACACATAGACGTACTACCC 58.802 50.000 0.00 0.00 36.76 3.69
3120 3346 3.549794 ACACATAGACGTACTACCCCTC 58.450 50.000 0.00 0.00 33.62 4.30
3198 3447 0.809241 GTCTCCAAGCGATCCAGCAG 60.809 60.000 0.00 0.00 40.15 4.24
3199 3448 2.124983 TCCAAGCGATCCAGCAGC 60.125 61.111 0.00 0.00 40.15 5.25
3200 3449 2.437180 CCAAGCGATCCAGCAGCA 60.437 61.111 0.00 0.00 40.15 4.41
3252 3501 3.566322 CGTTGATCCTAACCAACCAAACA 59.434 43.478 0.00 0.00 39.42 2.83
3253 3502 4.320202 CGTTGATCCTAACCAACCAAACAG 60.320 45.833 0.00 0.00 39.42 3.16
3254 3503 3.153919 TGATCCTAACCAACCAAACAGC 58.846 45.455 0.00 0.00 0.00 4.40
3255 3504 1.989706 TCCTAACCAACCAAACAGCC 58.010 50.000 0.00 0.00 0.00 4.85
3256 3505 1.215673 TCCTAACCAACCAAACAGCCA 59.784 47.619 0.00 0.00 0.00 4.75
3257 3506 2.035632 CCTAACCAACCAAACAGCCAA 58.964 47.619 0.00 0.00 0.00 4.52
3258 3507 2.223947 CCTAACCAACCAAACAGCCAAC 60.224 50.000 0.00 0.00 0.00 3.77
3259 3508 0.539518 AACCAACCAAACAGCCAACC 59.460 50.000 0.00 0.00 0.00 3.77
3260 3509 0.616111 ACCAACCAAACAGCCAACCA 60.616 50.000 0.00 0.00 0.00 3.67
3261 3510 0.539051 CCAACCAAACAGCCAACCAA 59.461 50.000 0.00 0.00 0.00 3.67
3262 3511 1.473080 CCAACCAAACAGCCAACCAAG 60.473 52.381 0.00 0.00 0.00 3.61
3272 3521 0.759060 GCCAACCAAGAACCAACCCT 60.759 55.000 0.00 0.00 0.00 4.34
3288 3537 4.554363 CTAGCTCGACGCGGGGTG 62.554 72.222 12.47 3.54 45.59 4.61
3320 3764 2.416372 CTTGTCGCTCACACACACGC 62.416 60.000 0.00 0.00 33.41 5.34
3401 3859 3.126073 CGCACAGCATACAGTCACATAT 58.874 45.455 0.00 0.00 0.00 1.78
3437 3900 2.258726 GGAACCGCTTGCTTTCCGT 61.259 57.895 6.98 0.00 29.89 4.69
3448 3911 1.574428 CTTTCCGTTGGACGCAAGG 59.426 57.895 0.00 0.00 40.91 3.61
3449 3912 1.153127 TTTCCGTTGGACGCAAGGT 60.153 52.632 0.00 0.00 40.91 3.50
3517 3992 2.047213 AAACCCGGCCAAGACGAAGA 62.047 55.000 2.24 0.00 35.20 2.87
3631 4113 1.001624 TCATTCATTCAGCTGCGACG 58.998 50.000 9.47 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.938125 GGTACACATCTCCAGCTTTAAAAGA 59.062 40.000 0.00 0.00 0.00 2.52
34 35 1.262417 TCAAGCGGTACACATCTCCA 58.738 50.000 0.00 0.00 0.00 3.86
43 44 2.673368 CCTTTCACTCATCAAGCGGTAC 59.327 50.000 0.00 0.00 0.00 3.34
244 246 3.935818 TGGGTTGTCTGTTTACAGGAA 57.064 42.857 9.82 1.49 43.91 3.36
256 261 3.107642 TCGAGACTTTCTTGGGTTGTC 57.892 47.619 0.00 0.00 0.00 3.18
305 310 2.667199 GTGGTTGTCCCGTTCCCG 60.667 66.667 0.00 0.00 35.15 5.14
333 338 1.526887 CACACATCCAGTTCACGTCAC 59.473 52.381 0.00 0.00 0.00 3.67
418 426 5.995897 AGTAACACTAACCACATCCAGTTTC 59.004 40.000 0.00 0.00 0.00 2.78
468 476 3.791245 AGAATTCAACTCATCCGCTCTC 58.209 45.455 8.44 0.00 0.00 3.20
471 479 3.438087 CACAAGAATTCAACTCATCCGCT 59.562 43.478 8.44 0.00 0.00 5.52
479 487 4.525487 ACATGCATCCACAAGAATTCAACT 59.475 37.500 8.44 0.00 0.00 3.16
491 499 2.165167 CATATCCCCACATGCATCCAC 58.835 52.381 0.00 0.00 0.00 4.02
580 595 8.434589 ACCCATAGTAGGAGTAGTAGTAGTAG 57.565 42.308 0.00 0.00 0.00 2.57
591 606 9.916360 CCTTAAATAAAAACCCATAGTAGGAGT 57.084 33.333 0.00 0.00 0.00 3.85
592 607 9.350951 CCCTTAAATAAAAACCCATAGTAGGAG 57.649 37.037 0.00 0.00 0.00 3.69
593 608 9.071334 TCCCTTAAATAAAAACCCATAGTAGGA 57.929 33.333 0.00 0.00 0.00 2.94
594 609 9.350951 CTCCCTTAAATAAAAACCCATAGTAGG 57.649 37.037 0.00 0.00 0.00 3.18
597 612 9.831682 TTTCTCCCTTAAATAAAAACCCATAGT 57.168 29.630 0.00 0.00 0.00 2.12
787 804 1.625508 CCTCTACCTAGGCCCCAACTT 60.626 57.143 9.30 0.00 0.00 2.66
800 821 3.389329 TGGCTCTTGATTCATCCTCTACC 59.611 47.826 0.00 0.00 0.00 3.18
801 822 4.679373 TGGCTCTTGATTCATCCTCTAC 57.321 45.455 0.00 0.00 0.00 2.59
802 823 5.901413 AATGGCTCTTGATTCATCCTCTA 57.099 39.130 0.00 0.00 0.00 2.43
867 894 3.186047 CCACTTCTTACCGCGCGG 61.186 66.667 44.88 44.88 42.03 6.46
920 954 0.748005 GAGAGAGAGAGAGGCGTGCT 60.748 60.000 0.00 0.00 0.00 4.40
1061 1105 1.488812 CCGAGAGAGAGAGGAAGAGGA 59.511 57.143 0.00 0.00 0.00 3.71
1083 1140 6.407525 GCTAGCTAGAAGAAGAGGAAATGGAA 60.408 42.308 25.15 0.00 0.00 3.53
1173 1230 1.376812 CCACCTCCGCCTGGTTTAC 60.377 63.158 0.00 0.00 35.28 2.01
1429 1497 3.508840 CAAGATTCCCACGGCCGC 61.509 66.667 28.58 6.84 0.00 6.53
1436 1504 4.382685 CGACTAAGTAAGGCAAGATTCCCA 60.383 45.833 0.00 0.00 29.38 4.37
1569 1637 2.269241 GCCTTCCAGTAGCCGCTT 59.731 61.111 0.00 0.00 0.00 4.68
1767 1835 7.398289 TTGATAATGAATCAGGAAGGAGGAT 57.602 36.000 0.00 0.00 45.32 3.24
1768 1836 6.829985 TTGATAATGAATCAGGAAGGAGGA 57.170 37.500 0.00 0.00 45.32 3.71
1769 1837 9.750783 ATAATTGATAATGAATCAGGAAGGAGG 57.249 33.333 0.00 0.00 45.32 4.30
1813 1881 2.355132 GCACTCATGAATGAAGCCAGAG 59.645 50.000 8.65 0.00 36.18 3.35
1831 1899 8.262588 CGCGAATCATATACTCATATTTAGCAC 58.737 37.037 0.00 0.00 0.00 4.40
1844 1916 2.408704 GTCCTGCACGCGAATCATATAC 59.591 50.000 15.93 0.00 0.00 1.47
1961 2033 1.280421 AGGAAGTCAGTGATGAAGCCC 59.720 52.381 0.00 0.00 0.00 5.19
2165 2246 2.444624 CGACATGTCGCCGGAGTTG 61.445 63.158 32.93 6.27 46.50 3.16
2464 2552 6.262273 ACACACCAAGTTAAGTAATCCAACTG 59.738 38.462 0.00 0.00 32.96 3.16
2466 2554 6.261381 TCACACACCAAGTTAAGTAATCCAAC 59.739 38.462 0.00 0.00 0.00 3.77
2496 2584 2.665519 GCATCAGCAAACCACTAACACG 60.666 50.000 0.00 0.00 41.58 4.49
2541 2629 1.038130 AACCTGATCCGACCCGAGAG 61.038 60.000 0.00 0.00 0.00 3.20
2562 2655 4.390264 TGTCGGTCTGTCTGGATAGATAG 58.610 47.826 0.74 0.00 41.88 2.08
2563 2656 4.102681 TCTGTCGGTCTGTCTGGATAGATA 59.897 45.833 0.74 0.00 34.94 1.98
2564 2657 3.117851 TCTGTCGGTCTGTCTGGATAGAT 60.118 47.826 0.74 0.00 34.94 1.98
2565 2658 2.238898 TCTGTCGGTCTGTCTGGATAGA 59.761 50.000 0.00 0.00 0.00 1.98
2580 2673 1.683917 CTAATCCCTGGAGGTCTGTCG 59.316 57.143 0.00 0.00 36.75 4.35
2828 2940 6.070710 TGGTGGTACATGTACATACAAAGCTA 60.071 38.462 31.52 9.21 44.52 3.32
2829 2941 5.183228 GGTGGTACATGTACATACAAAGCT 58.817 41.667 31.52 0.00 44.52 3.74
2898 3023 3.060602 GGTACAGAGAGAACACAAGCAC 58.939 50.000 0.00 0.00 0.00 4.40
2925 3051 4.399303 ACCCAGTGATTAATTAGCAAGTGC 59.601 41.667 0.00 0.00 42.49 4.40
2932 3058 5.440610 AGGAGCAACCCAGTGATTAATTAG 58.559 41.667 0.00 0.00 40.05 1.73
3010 3207 1.663173 CGTCGGCCCAAAACCATTT 59.337 52.632 0.00 0.00 0.00 2.32
3011 3208 2.272447 CCGTCGGCCCAAAACCATT 61.272 57.895 0.00 0.00 0.00 3.16
3114 3340 1.986413 CTGCAGCTTGTAGAGGGGT 59.014 57.895 0.00 0.00 31.36 4.95
3116 3342 1.451028 GGCTGCAGCTTGTAGAGGG 60.451 63.158 35.82 0.00 41.70 4.30
3117 3343 0.035630 AAGGCTGCAGCTTGTAGAGG 60.036 55.000 35.82 0.00 41.70 3.69
3120 3346 3.129871 GAGATAAGGCTGCAGCTTGTAG 58.870 50.000 35.82 0.00 41.70 2.74
3170 3419 0.455295 CGCTTGGAGACACGAGAGAC 60.455 60.000 0.00 0.00 42.67 3.36
3198 3447 0.608640 TCCTTCCTCTCTTCCGTTGC 59.391 55.000 0.00 0.00 0.00 4.17
3199 3448 3.067833 GTTTCCTTCCTCTCTTCCGTTG 58.932 50.000 0.00 0.00 0.00 4.10
3200 3449 2.288886 CGTTTCCTTCCTCTCTTCCGTT 60.289 50.000 0.00 0.00 0.00 4.44
3252 3501 0.759060 GGGTTGGTTCTTGGTTGGCT 60.759 55.000 0.00 0.00 0.00 4.75
3253 3502 0.759060 AGGGTTGGTTCTTGGTTGGC 60.759 55.000 0.00 0.00 0.00 4.52
3254 3503 2.514803 CTAGGGTTGGTTCTTGGTTGG 58.485 52.381 0.00 0.00 0.00 3.77
3255 3504 1.886542 GCTAGGGTTGGTTCTTGGTTG 59.113 52.381 0.00 0.00 0.00 3.77
3256 3505 1.780919 AGCTAGGGTTGGTTCTTGGTT 59.219 47.619 0.00 0.00 0.00 3.67
3257 3506 1.351350 GAGCTAGGGTTGGTTCTTGGT 59.649 52.381 0.00 0.00 0.00 3.67
3258 3507 1.676014 CGAGCTAGGGTTGGTTCTTGG 60.676 57.143 0.00 0.00 0.00 3.61
3259 3508 1.275291 TCGAGCTAGGGTTGGTTCTTG 59.725 52.381 0.00 0.00 0.00 3.02
3260 3509 1.275573 GTCGAGCTAGGGTTGGTTCTT 59.724 52.381 0.00 0.00 0.00 2.52
3261 3510 0.896226 GTCGAGCTAGGGTTGGTTCT 59.104 55.000 0.00 0.00 0.00 3.01
3262 3511 0.458025 CGTCGAGCTAGGGTTGGTTC 60.458 60.000 0.00 0.00 0.00 3.62
3288 3537 1.658114 GACAAGTTTTCGCCCCCAC 59.342 57.895 0.00 0.00 0.00 4.61
3295 3544 1.326245 TGTGTGAGCGACAAGTTTTCG 59.674 47.619 7.06 7.06 35.91 3.46
3389 3840 4.827835 GCCTCACCTCTATATGTGACTGTA 59.172 45.833 0.00 0.00 36.62 2.74
3394 3852 1.613925 GCGCCTCACCTCTATATGTGA 59.386 52.381 0.00 0.00 39.08 3.58
3437 3900 2.904866 GCCACACCTTGCGTCCAA 60.905 61.111 0.00 0.00 0.00 3.53
3490 3965 1.814772 TTGGCCGGGTTTTGATGCAG 61.815 55.000 2.18 0.00 0.00 4.41
3517 3992 1.455383 CCTTTTCCTTGCTGCACCGT 61.455 55.000 0.00 0.00 0.00 4.83
3610 4086 2.031314 CGTCGCAGCTGAATGAATGAAT 59.969 45.455 20.43 0.00 0.00 2.57
3611 4087 1.394572 CGTCGCAGCTGAATGAATGAA 59.605 47.619 20.43 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.