Multiple sequence alignment - TraesCS5A01G205700

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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 TraesCS5A01G205700 chr5A 100.000 3554 0 0 1 3554 415429425 415432978 0.000000e+00 6564
1 TraesCS5A01G205700 chr5A 81.984 1099 134 42 884 1948 429657291 429656223 0.000000e+00 874
2 TraesCS5A01G205700 chr5A 86.667 495 46 11 2011 2492 429656113 429655626 6.760000e-147 531
3 TraesCS5A01G205700 chr5D 90.460 2589 142 38 1 2546 318935232 318932706 0.000000e+00 3315
4 TraesCS5A01G205700 chr5D 86.782 1044 89 21 2546 3554 318893558 318892529 0.000000e+00 1118
5 TraesCS5A01G205700 chr5D 82.422 1115 129 44 881 1959 326903551 326904634 0.000000e+00 911
6 TraesCS5A01G205700 chr5D 80.748 722 119 13 1235 1947 319138528 319137818 2.410000e-151 545
7 TraesCS5A01G205700 chr5D 89.831 413 41 1 1978 2389 326904691 326905103 2.430000e-146 529
8 TraesCS5A01G205700 chr5B 90.983 1841 97 30 768 2562 368787404 368785587 0.000000e+00 2416
9 TraesCS5A01G205700 chr5B 86.673 1043 105 21 2540 3554 368733225 368732189 0.000000e+00 1125
10 TraesCS5A01G205700 chr5B 82.182 1100 133 33 884 1948 379596710 379597781 0.000000e+00 887
11 TraesCS5A01G205700 chr5B 88.941 425 41 3 1971 2389 379597838 379598262 1.460000e-143 520
12 TraesCS5A01G205700 chr5B 82.773 476 29 12 304 777 368788384 368787960 3.350000e-100 375
13 TraesCS5A01G205700 chr5B 90.283 247 20 4 1 245 368788651 368788407 1.590000e-83 320
14 TraesCS5A01G205700 chr7D 88.372 516 59 1 1432 1947 138086557 138086043 1.400000e-173 619
15 TraesCS5A01G205700 chr7D 87.403 516 65 0 1432 1947 138038832 138038317 8.500000e-166 593
16 TraesCS5A01G205700 chr7D 88.081 344 41 0 2017 2360 138038319 138037976 3.300000e-110 409
17 TraesCS5A01G205700 chr7D 87.209 344 44 0 2017 2360 138086045 138085702 3.330000e-105 392
18 TraesCS5A01G205700 chr7D 92.373 118 9 0 1235 1352 138086673 138086556 6.100000e-38 169
19 TraesCS5A01G205700 chr7A 88.178 516 61 0 1432 1947 138012319 138011804 1.810000e-172 616
20 TraesCS5A01G205700 chr7A 88.663 344 39 0 2017 2360 138011806 138011463 1.530000e-113 420
21 TraesCS5A01G205700 chr7A 91.525 118 10 0 1235 1352 138012435 138012318 2.840000e-36 163
22 TraesCS5A01G205700 chr6D 82.883 111 18 1 2250 2360 141930453 141930562 8.120000e-17 99


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 TraesCS5A01G205700 chr5A 415429425 415432978 3553 False 6564.000000 6564 100.000000 1 3554 1 chr5A.!!$F1 3553
1 TraesCS5A01G205700 chr5A 429655626 429657291 1665 True 702.500000 874 84.325500 884 2492 2 chr5A.!!$R1 1608
2 TraesCS5A01G205700 chr5D 318932706 318935232 2526 True 3315.000000 3315 90.460000 1 2546 1 chr5D.!!$R2 2545
3 TraesCS5A01G205700 chr5D 318892529 318893558 1029 True 1118.000000 1118 86.782000 2546 3554 1 chr5D.!!$R1 1008
4 TraesCS5A01G205700 chr5D 326903551 326905103 1552 False 720.000000 911 86.126500 881 2389 2 chr5D.!!$F1 1508
5 TraesCS5A01G205700 chr5D 319137818 319138528 710 True 545.000000 545 80.748000 1235 1947 1 chr5D.!!$R3 712
6 TraesCS5A01G205700 chr5B 368732189 368733225 1036 True 1125.000000 1125 86.673000 2540 3554 1 chr5B.!!$R1 1014
7 TraesCS5A01G205700 chr5B 368785587 368788651 3064 True 1037.000000 2416 88.013000 1 2562 3 chr5B.!!$R2 2561
8 TraesCS5A01G205700 chr5B 379596710 379598262 1552 False 703.500000 887 85.561500 884 2389 2 chr5B.!!$F1 1505
9 TraesCS5A01G205700 chr7D 138037976 138038832 856 True 501.000000 593 87.742000 1432 2360 2 chr7D.!!$R1 928
10 TraesCS5A01G205700 chr7D 138085702 138086673 971 True 393.333333 619 89.318000 1235 2360 3 chr7D.!!$R2 1125
11 TraesCS5A01G205700 chr7A 138011463 138012435 972 True 399.666667 616 89.455333 1235 2360 3 chr7A.!!$R1 1125

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
368 376 0.036952 AGGCCATCACAGTGTCTTCG 60.037 55.0 5.01 0.0 0.00 3.79 F
694 707 0.466189 CCCTGCGACAAATATGGCCT 60.466 55.0 3.32 0.0 0.00 5.19 F
1062 1649 0.527385 AAGAAGCAGAGCGAGCGATC 60.527 55.0 0.00 0.0 37.01 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1782 0.108138 AAGCAGAGTACCGCCATGTC 60.108 55.0 0.00 0.00 0.0 3.06 R
1730 2426 0.469494 TGCATCATCGGGCTGTACAT 59.531 50.0 0.00 0.00 0.0 2.29 R
2943 3734 0.103026 GCCTGAAATCCGATTTGGGC 59.897 55.0 21.62 21.62 39.1 5.36 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
64 66 3.096489 TCTTGCAAAAGAACACATGGC 57.904 42.857 0.00 0.00 0.00 4.40
154 157 4.264352 TGCCCTATCCAAAAGGACAGAATT 60.264 41.667 0.00 0.00 36.08 2.17
165 168 2.806244 AGGACAGAATTCGGACAAAACG 59.194 45.455 12.79 0.00 0.00 3.60
170 173 1.794116 GAATTCGGACAAAACGGACGA 59.206 47.619 0.00 0.00 0.00 4.20
174 177 1.632046 CGGACAAAACGGACGATGGG 61.632 60.000 0.00 0.00 0.00 4.00
208 211 3.071167 AGTTGGCCTAAGAGACGAGTTTT 59.929 43.478 3.32 0.00 0.00 2.43
213 216 5.187186 TGGCCTAAGAGACGAGTTTTAATCT 59.813 40.000 3.32 0.00 0.00 2.40
224 227 4.455877 CGAGTTTTAATCTATGGCCCATCC 59.544 45.833 0.00 0.00 0.00 3.51
236 239 2.311542 TGGCCCATCCACTAAATTGTCT 59.688 45.455 0.00 0.00 40.72 3.41
283 291 5.871524 GGAGATGCCCATATATACGCATATG 59.128 44.000 14.65 0.00 41.85 1.78
285 293 4.687901 TGCCCATATATACGCATATGCT 57.312 40.909 24.56 14.18 37.50 3.79
286 294 4.631131 TGCCCATATATACGCATATGCTC 58.369 43.478 24.56 0.00 37.50 4.26
302 310 0.599060 GCTCGCATCCCTACCTCTAC 59.401 60.000 0.00 0.00 0.00 2.59
315 323 1.451567 CTCTACGAGCACCTCCGGA 60.452 63.158 2.93 2.93 0.00 5.14
346 354 7.855409 CGAGTTAACACAACATTTTGAGATTGA 59.145 33.333 8.61 0.00 36.48 2.57
368 376 0.036952 AGGCCATCACAGTGTCTTCG 60.037 55.000 5.01 0.00 0.00 3.79
374 382 3.057526 CCATCACAGTGTCTTCGTAGTCA 60.058 47.826 0.00 0.00 0.00 3.41
400 408 1.410004 ACGTCTTCTCCCACAGAACA 58.590 50.000 0.00 0.00 36.08 3.18
456 469 3.684103 CACGAGTGCAGTTTTACCAAA 57.316 42.857 0.00 0.00 0.00 3.28
457 470 4.022464 CACGAGTGCAGTTTTACCAAAA 57.978 40.909 0.00 0.00 0.00 2.44
500 513 1.289109 CCAGTTCGCGAATCGTTGGT 61.289 55.000 26.23 1.15 39.67 3.67
501 514 1.342555 CAGTTCGCGAATCGTTGGTA 58.657 50.000 26.23 0.00 39.67 3.25
502 515 1.924524 CAGTTCGCGAATCGTTGGTAT 59.075 47.619 26.23 0.11 39.67 2.73
503 516 2.347452 CAGTTCGCGAATCGTTGGTATT 59.653 45.455 26.23 0.00 39.67 1.89
504 517 2.997986 AGTTCGCGAATCGTTGGTATTT 59.002 40.909 26.23 0.00 39.67 1.40
505 518 3.061697 AGTTCGCGAATCGTTGGTATTTC 59.938 43.478 26.23 6.98 39.67 2.17
506 519 1.928503 TCGCGAATCGTTGGTATTTCC 59.071 47.619 6.20 0.00 39.67 3.13
507 520 1.661617 CGCGAATCGTTGGTATTTCCA 59.338 47.619 0.00 0.00 45.60 3.53
508 521 4.168232 TCGCGAATCGTTGGTATTTCCAA 61.168 43.478 6.20 0.00 44.36 3.53
519 532 4.970711 TGGTATTTCCAACCTCAAACGTA 58.029 39.130 0.00 0.00 44.12 3.57
589 602 2.143925 CGATTCTTTTATCCGCTCCCC 58.856 52.381 0.00 0.00 0.00 4.81
590 603 2.505405 GATTCTTTTATCCGCTCCCCC 58.495 52.381 0.00 0.00 0.00 5.40
617 630 2.010043 GCATTGAATGGGCAGCTTTGG 61.010 52.381 7.35 0.00 0.00 3.28
647 660 1.359848 CAGTGCCCGTAGTGTTCATC 58.640 55.000 0.00 0.00 0.00 2.92
659 672 1.058903 GTTCATCGCTTCGCGGTTC 59.941 57.895 6.13 0.00 45.69 3.62
660 673 1.080093 TTCATCGCTTCGCGGTTCT 60.080 52.632 6.13 0.00 45.69 3.01
661 674 0.669318 TTCATCGCTTCGCGGTTCTT 60.669 50.000 6.13 0.00 45.69 2.52
678 691 4.643334 GGTTCTTTTTAATATGCCGACCCT 59.357 41.667 0.00 0.00 0.00 4.34
687 700 2.746277 GCCGACCCTGCGACAAAT 60.746 61.111 0.00 0.00 0.00 2.32
694 707 0.466189 CCCTGCGACAAATATGGCCT 60.466 55.000 3.32 0.00 0.00 5.19
695 708 0.664761 CCTGCGACAAATATGGCCTG 59.335 55.000 3.32 0.00 0.00 4.85
702 715 3.310774 CGACAAATATGGCCTGACTGAAG 59.689 47.826 3.32 0.00 0.00 3.02
703 716 4.265073 GACAAATATGGCCTGACTGAAGT 58.735 43.478 3.32 0.00 0.00 3.01
704 717 4.265073 ACAAATATGGCCTGACTGAAGTC 58.735 43.478 3.32 3.41 44.97 3.01
743 756 7.169158 TCCATTGATTAACATTTCAGTTCCC 57.831 36.000 0.00 0.00 33.07 3.97
762 775 3.007940 TCCCATCGAAGAAAGAAAGCAGA 59.992 43.478 0.00 0.00 43.58 4.26
809 1387 2.362120 GCAGCAGCAAGGTCCCAT 60.362 61.111 0.00 0.00 41.58 4.00
810 1388 2.707849 GCAGCAGCAAGGTCCCATG 61.708 63.158 0.00 0.00 41.58 3.66
811 1389 1.303888 CAGCAGCAAGGTCCCATGT 60.304 57.895 0.00 0.00 0.00 3.21
812 1390 1.303888 AGCAGCAAGGTCCCATGTG 60.304 57.895 0.00 0.00 0.00 3.21
813 1391 1.604593 GCAGCAAGGTCCCATGTGT 60.605 57.895 0.00 0.00 0.00 3.72
814 1392 1.870055 GCAGCAAGGTCCCATGTGTG 61.870 60.000 0.00 0.00 0.00 3.82
815 1393 0.538057 CAGCAAGGTCCCATGTGTGT 60.538 55.000 0.00 0.00 0.00 3.72
828 1406 1.748950 TGTGTGTGTGTGTGAGCATT 58.251 45.000 0.00 0.00 0.00 3.56
832 1410 2.097304 TGTGTGTGTGTGAGCATTGAAC 59.903 45.455 0.00 0.00 0.00 3.18
844 1422 2.439507 AGCATTGAACTCGGGGATACAT 59.560 45.455 0.00 0.00 39.74 2.29
869 1447 3.775654 GGCCAGGAGTCGACCAGG 61.776 72.222 13.01 10.21 39.22 4.45
910 1488 1.007336 CGTAGTGTCTGACGTTGCCC 61.007 60.000 2.98 0.00 34.39 5.36
915 1493 1.672356 GTCTGACGTTGCCCATGCT 60.672 57.895 0.00 0.00 38.71 3.79
918 1496 2.191354 CTGACGTTGCCCATGCTGTG 62.191 60.000 0.00 0.00 38.71 3.66
988 1571 2.446848 CCATCTCCGGGGCAGTGAT 61.447 63.158 0.00 0.00 0.00 3.06
1031 1617 2.433239 GGAAATCGAAGTACCCCAGCTA 59.567 50.000 0.00 0.00 0.00 3.32
1042 1629 2.213513 CCCAGCTAGAGCCTAGGCC 61.214 68.421 30.42 20.74 43.38 5.19
1055 1642 0.809241 CTAGGCCAAGAAGCAGAGCG 60.809 60.000 5.01 0.00 0.00 5.03
1061 1648 0.805322 CAAGAAGCAGAGCGAGCGAT 60.805 55.000 0.00 0.00 37.01 4.58
1062 1649 0.527385 AAGAAGCAGAGCGAGCGATC 60.527 55.000 0.00 0.00 37.01 3.69
1063 1650 1.226802 GAAGCAGAGCGAGCGATCA 60.227 57.895 10.86 0.00 37.01 2.92
1064 1651 0.597118 GAAGCAGAGCGAGCGATCAT 60.597 55.000 10.86 0.00 37.01 2.45
1065 1652 0.597118 AAGCAGAGCGAGCGATCATC 60.597 55.000 10.86 0.00 37.01 2.92
1066 1653 1.299697 GCAGAGCGAGCGATCATCA 60.300 57.895 10.86 0.00 32.23 3.07
1067 1654 0.666880 GCAGAGCGAGCGATCATCAT 60.667 55.000 10.86 0.00 32.23 2.45
1136 1723 4.124943 TCCGGTCTCCTCTCCCCG 62.125 72.222 0.00 0.00 40.12 5.73
1175 1778 3.227614 GTCTTCCTCTATCCAGTCCCTC 58.772 54.545 0.00 0.00 0.00 4.30
1176 1779 2.178106 TCTTCCTCTATCCAGTCCCTCC 59.822 54.545 0.00 0.00 0.00 4.30
1177 1780 0.861155 TCCTCTATCCAGTCCCTCCC 59.139 60.000 0.00 0.00 0.00 4.30
1178 1781 0.863956 CCTCTATCCAGTCCCTCCCT 59.136 60.000 0.00 0.00 0.00 4.20
1179 1782 1.482177 CCTCTATCCAGTCCCTCCCTG 60.482 61.905 0.00 0.00 0.00 4.45
1180 1783 1.501170 CTCTATCCAGTCCCTCCCTGA 59.499 57.143 0.00 0.00 31.38 3.86
1252 1891 0.969894 ACAGGGTTCAGAAGGACGAG 59.030 55.000 0.00 0.00 0.00 4.18
1360 1999 1.138568 TCGTTCCAGGGTGGGTAAAA 58.861 50.000 0.00 0.00 38.32 1.52
1361 2000 1.706305 TCGTTCCAGGGTGGGTAAAAT 59.294 47.619 0.00 0.00 38.32 1.82
1394 2038 6.843208 ACATATTATCGATGGTCTACGACTG 58.157 40.000 8.54 0.00 41.17 3.51
1407 2077 4.804139 GTCTACGACTGTAATGGTGGATTG 59.196 45.833 0.00 0.00 0.00 2.67
1951 2648 1.132453 GCCGAGCAAATGAAGGTAACC 59.868 52.381 0.00 0.00 37.17 2.85
2006 2752 0.997196 GCGATTGACAAGGGTACGTC 59.003 55.000 0.00 0.00 0.00 4.34
2321 3067 2.604686 AGCGGCTGGAGAGGAACA 60.605 61.111 0.00 0.00 0.00 3.18
2389 3135 0.032678 CATCCGCTTAGTGCTCCGAT 59.967 55.000 0.00 0.00 40.11 4.18
2398 3144 0.935898 AGTGCTCCGATACGTAGACG 59.064 55.000 14.96 14.96 46.33 4.18
2619 3371 2.328099 CCACAAGGTTCTCAGCCGC 61.328 63.158 0.00 0.00 0.00 6.53
2630 3384 0.449388 CTCAGCCGCCTGATGAAAAC 59.551 55.000 0.00 0.00 46.44 2.43
2632 3386 0.962356 CAGCCGCCTGATGAAAACCT 60.962 55.000 0.00 0.00 41.77 3.50
2692 3446 3.927163 TTCCTTCGAACCGCCGAGC 62.927 63.158 0.00 0.00 39.90 5.03
2750 3516 4.379243 CAACCGCCTCGCCACTCT 62.379 66.667 0.00 0.00 0.00 3.24
2751 3517 3.626924 AACCGCCTCGCCACTCTT 61.627 61.111 0.00 0.00 0.00 2.85
2752 3518 3.883744 AACCGCCTCGCCACTCTTG 62.884 63.158 0.00 0.00 0.00 3.02
2758 3524 2.125552 TCGCCACTCTTGCCATCG 60.126 61.111 0.00 0.00 0.00 3.84
2760 3526 3.512516 GCCACTCTTGCCATCGCC 61.513 66.667 0.00 0.00 0.00 5.54
2761 3527 2.270205 CCACTCTTGCCATCGCCT 59.730 61.111 0.00 0.00 0.00 5.52
2764 3546 2.587194 CTCTTGCCATCGCCTCCG 60.587 66.667 0.00 0.00 0.00 4.63
2781 3563 3.237741 GCGGCCATCCCTCTAGCT 61.238 66.667 2.24 0.00 0.00 3.32
2784 3566 2.578714 GGCCATCCCTCTAGCTCCG 61.579 68.421 0.00 0.00 0.00 4.63
2785 3568 1.531840 GCCATCCCTCTAGCTCCGA 60.532 63.158 0.00 0.00 0.00 4.55
2793 3576 2.904866 CTAGCTCCGAGCCTCGCT 60.905 66.667 16.99 3.04 43.77 4.93
2821 3604 3.055719 CCGGCGAACTTGCACCAT 61.056 61.111 9.30 0.00 36.28 3.55
2835 3618 3.873812 CCATCGCCCCACCCCTAC 61.874 72.222 0.00 0.00 0.00 3.18
2841 3624 3.030823 GCCCCACCCCTACCCTAGA 62.031 68.421 0.00 0.00 0.00 2.43
2858 3641 4.472833 CCCTAGAATAGATCATGGGGAAGG 59.527 50.000 0.00 0.00 42.77 3.46
2868 3651 4.111053 GGGGAAGGTTCTCCGGCC 62.111 72.222 0.00 0.00 38.24 6.13
2894 3681 2.300967 CCTCCCCCAGCTGCAACTA 61.301 63.158 8.66 0.00 0.00 2.24
2910 3697 5.497474 TGCAACTATTTCTTCCTTACCTCC 58.503 41.667 0.00 0.00 0.00 4.30
2914 3701 1.354101 TTTCTTCCTTACCTCCGGCA 58.646 50.000 0.00 0.00 0.00 5.69
2920 3707 1.686110 CTTACCTCCGGCACCTCCT 60.686 63.158 0.00 0.00 0.00 3.69
2921 3708 1.229400 TTACCTCCGGCACCTCCTT 60.229 57.895 0.00 0.00 0.00 3.36
2922 3709 0.838987 TTACCTCCGGCACCTCCTTT 60.839 55.000 0.00 0.00 0.00 3.11
2923 3710 0.838987 TACCTCCGGCACCTCCTTTT 60.839 55.000 0.00 0.00 0.00 2.27
2943 3734 4.921470 TTTTCTAGCGAAAATCGACTGG 57.079 40.909 3.61 3.12 43.74 4.00
2952 3743 1.094785 AAATCGACTGGCCCAAATCG 58.905 50.000 10.14 10.14 35.91 3.34
3034 3826 5.941058 TCTATTCGATGGTAGAGAGGTGATC 59.059 44.000 0.00 0.00 0.00 2.92
3068 3860 8.251721 GCACTATTATAGTCGGTGGATATCTTT 58.748 37.037 1.33 0.00 36.76 2.52
3095 3887 5.956068 TCACATGTGATTCGGAAATTTCA 57.044 34.783 24.56 0.00 34.14 2.69
3145 3937 4.586001 CCATTTCATTGATAGGGTGGAAGG 59.414 45.833 0.29 0.00 0.00 3.46
3163 3955 3.214696 AGGAAGTACAAAGTGCAGCTT 57.785 42.857 0.00 0.00 39.52 3.74
3171 3963 1.198637 CAAAGTGCAGCTTCTAGCCAC 59.801 52.381 0.00 0.00 43.77 5.01
3192 3984 2.279659 CGTATACAAGTTGGCGTTACGG 59.720 50.000 6.94 0.00 0.00 4.02
3225 4017 0.985490 GAGGGAGAGGGGTTGCTCAT 60.985 60.000 0.00 0.00 32.83 2.90
3385 4178 4.981674 CGTTGCATTGTTTCCATGTAAACT 59.018 37.500 14.12 0.00 39.57 2.66
3389 4182 6.155827 TGCATTGTTTCCATGTAAACTAAGC 58.844 36.000 14.93 14.93 39.57 3.09
3452 4245 3.865446 CATCACATAACAGGAGAGTGCA 58.135 45.455 0.00 0.00 0.00 4.57
3508 4301 1.227380 GCGAGCTCGGTGATGGAAT 60.227 57.895 35.10 0.00 40.23 3.01
3517 4310 1.526917 GTGATGGAATGGCCCTCCG 60.527 63.158 14.62 0.00 35.55 4.63
3529 4322 1.689582 CCCTCCGGCTAAGGTTCCT 60.690 63.158 6.91 0.00 31.51 3.36
3545 4338 0.033504 TCCTTCCAGAGCGACACAAC 59.966 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 2.211619 ATTTGTTCCGGCGCCATGTG 62.212 55.000 28.98 9.99 0.00 3.21
64 66 1.209127 GGACACATTTGTTCCGGCG 59.791 57.895 0.00 0.00 35.47 6.46
112 115 2.575455 AAAGGGTTGTTGTCCGGCCA 62.575 55.000 2.24 0.00 0.00 5.36
120 123 1.824852 GGATAGGGCAAAGGGTTGTTG 59.175 52.381 0.00 0.00 37.06 3.33
154 157 0.668096 CCATCGTCCGTTTTGTCCGA 60.668 55.000 0.00 0.00 0.00 4.55
170 173 2.355716 CCAACTCCAATACACGACCCAT 60.356 50.000 0.00 0.00 0.00 4.00
174 177 1.084289 GGCCAACTCCAATACACGAC 58.916 55.000 0.00 0.00 0.00 4.34
181 184 2.093447 CGTCTCTTAGGCCAACTCCAAT 60.093 50.000 5.01 0.00 0.00 3.16
250 258 7.995052 ATATATGGGCATCTCCATTGTACTA 57.005 36.000 1.49 0.00 44.55 1.82
260 268 5.349817 GCATATGCGTATATATGGGCATCTC 59.650 44.000 21.48 12.28 44.35 2.75
283 291 0.599060 GTAGAGGTAGGGATGCGAGC 59.401 60.000 0.00 0.00 0.00 5.03
285 293 0.471191 TCGTAGAGGTAGGGATGCGA 59.529 55.000 0.00 0.00 0.00 5.10
286 294 3.016997 TCGTAGAGGTAGGGATGCG 57.983 57.895 0.00 0.00 0.00 4.73
315 323 7.932335 TCAAAATGTTGTGTTAACTCGGTATT 58.068 30.769 7.22 2.91 36.07 1.89
325 333 8.298854 CCTCATCAATCTCAAAATGTTGTGTTA 58.701 33.333 0.00 0.00 36.07 2.41
346 354 1.283347 AGACACTGTGATGGCCTCAT 58.717 50.000 15.86 0.00 35.97 2.90
395 403 6.018262 TCAGATTTTTCGTCGATGTTTGTTCT 60.018 34.615 4.21 1.05 0.00 3.01
400 408 7.979115 TTTTTCAGATTTTTCGTCGATGTTT 57.021 28.000 4.21 0.00 0.00 2.83
476 489 1.464429 CGATTCGCGAACTGGACTCG 61.464 60.000 26.00 23.12 44.57 4.18
500 513 5.806818 TGGATACGTTTGAGGTTGGAAATA 58.193 37.500 0.00 0.00 42.51 1.40
501 514 4.658063 TGGATACGTTTGAGGTTGGAAAT 58.342 39.130 0.00 0.00 42.51 2.17
502 515 4.088056 TGGATACGTTTGAGGTTGGAAA 57.912 40.909 0.00 0.00 42.51 3.13
503 516 3.773418 TGGATACGTTTGAGGTTGGAA 57.227 42.857 0.00 0.00 42.51 3.53
504 517 3.773418 TTGGATACGTTTGAGGTTGGA 57.227 42.857 0.00 0.00 42.51 3.53
505 518 6.693315 ATTATTGGATACGTTTGAGGTTGG 57.307 37.500 0.00 0.00 42.51 3.77
506 519 7.009174 GCAAATTATTGGATACGTTTGAGGTTG 59.991 37.037 0.00 0.00 42.51 3.77
507 520 7.033185 GCAAATTATTGGATACGTTTGAGGTT 58.967 34.615 0.00 0.00 42.51 3.50
508 521 6.405397 GGCAAATTATTGGATACGTTTGAGGT 60.405 38.462 0.00 0.00 42.51 3.85
509 522 5.977129 GGCAAATTATTGGATACGTTTGAGG 59.023 40.000 0.00 0.00 42.51 3.86
510 523 5.977129 GGGCAAATTATTGGATACGTTTGAG 59.023 40.000 0.00 0.00 42.51 3.02
519 532 1.047801 GGCCGGGCAAATTATTGGAT 58.952 50.000 25.33 0.00 37.02 3.41
589 602 1.516892 CCATTCAATGCGGGGTTGG 59.483 57.895 0.00 0.00 0.00 3.77
590 603 1.516892 CCCATTCAATGCGGGGTTG 59.483 57.895 0.00 0.00 36.21 3.77
600 613 0.968405 GACCAAAGCTGCCCATTCAA 59.032 50.000 0.00 0.00 0.00 2.69
617 630 1.586154 CGGGCACTGGGTCATTTGAC 61.586 60.000 1.99 1.99 44.04 3.18
633 646 1.278238 GAAGCGATGAACACTACGGG 58.722 55.000 0.00 0.00 0.00 5.28
634 647 0.914551 CGAAGCGATGAACACTACGG 59.085 55.000 0.00 0.00 0.00 4.02
659 672 3.548014 CGCAGGGTCGGCATATTAAAAAG 60.548 47.826 0.00 0.00 0.00 2.27
660 673 2.356382 CGCAGGGTCGGCATATTAAAAA 59.644 45.455 0.00 0.00 0.00 1.94
661 674 1.944024 CGCAGGGTCGGCATATTAAAA 59.056 47.619 0.00 0.00 0.00 1.52
678 691 1.065491 AGTCAGGCCATATTTGTCGCA 60.065 47.619 5.01 0.00 0.00 5.10
695 708 4.020662 AGGGATTCTTCAGTGACTTCAGTC 60.021 45.833 0.00 0.00 44.97 3.51
709 722 8.613922 AATGTTAATCAATGGAAGGGATTCTT 57.386 30.769 0.00 0.00 38.65 2.52
710 723 8.613922 AAATGTTAATCAATGGAAGGGATTCT 57.386 30.769 0.00 0.00 33.59 2.40
711 724 8.477256 TGAAATGTTAATCAATGGAAGGGATTC 58.523 33.333 0.00 0.00 33.59 2.52
712 725 8.378115 TGAAATGTTAATCAATGGAAGGGATT 57.622 30.769 0.00 0.00 35.57 3.01
713 726 7.620888 ACTGAAATGTTAATCAATGGAAGGGAT 59.379 33.333 0.00 0.00 0.00 3.85
714 727 6.953520 ACTGAAATGTTAATCAATGGAAGGGA 59.046 34.615 0.00 0.00 0.00 4.20
743 756 4.687948 TCTGTCTGCTTTCTTTCTTCGATG 59.312 41.667 0.00 0.00 0.00 3.84
797 1375 0.538057 CACACACATGGGACCTTGCT 60.538 55.000 0.00 0.00 0.00 3.91
798 1376 0.823356 ACACACACATGGGACCTTGC 60.823 55.000 0.00 0.00 31.57 4.01
799 1377 0.953727 CACACACACATGGGACCTTG 59.046 55.000 0.00 2.96 31.57 3.61
800 1378 0.550914 ACACACACACATGGGACCTT 59.449 50.000 0.00 0.00 31.57 3.50
801 1379 0.179020 CACACACACACATGGGACCT 60.179 55.000 0.00 0.00 31.57 3.85
802 1380 0.465460 ACACACACACACATGGGACC 60.465 55.000 0.00 0.00 31.57 4.46
803 1381 0.662619 CACACACACACACATGGGAC 59.337 55.000 0.00 0.00 31.57 4.46
804 1382 0.543749 TCACACACACACACATGGGA 59.456 50.000 0.00 0.00 31.57 4.37
805 1383 0.946528 CTCACACACACACACATGGG 59.053 55.000 0.00 0.00 34.29 4.00
806 1384 0.308684 GCTCACACACACACACATGG 59.691 55.000 0.00 0.00 0.00 3.66
807 1385 1.015868 TGCTCACACACACACACATG 58.984 50.000 0.00 0.00 0.00 3.21
808 1386 1.971481 ATGCTCACACACACACACAT 58.029 45.000 0.00 0.00 0.00 3.21
809 1387 1.401199 CAATGCTCACACACACACACA 59.599 47.619 0.00 0.00 0.00 3.72
810 1388 1.670295 TCAATGCTCACACACACACAC 59.330 47.619 0.00 0.00 0.00 3.82
811 1389 2.035530 TCAATGCTCACACACACACA 57.964 45.000 0.00 0.00 0.00 3.72
812 1390 2.355756 AGTTCAATGCTCACACACACAC 59.644 45.455 0.00 0.00 0.00 3.82
813 1391 2.613595 GAGTTCAATGCTCACACACACA 59.386 45.455 0.00 0.00 33.45 3.72
814 1392 2.348872 CGAGTTCAATGCTCACACACAC 60.349 50.000 0.00 0.00 33.45 3.82
815 1393 1.866601 CGAGTTCAATGCTCACACACA 59.133 47.619 0.00 0.00 33.45 3.72
828 1406 2.184533 ACACATGTATCCCCGAGTTCA 58.815 47.619 0.00 0.00 0.00 3.18
832 1410 2.201732 CGAAACACATGTATCCCCGAG 58.798 52.381 0.00 0.00 0.00 4.63
844 1422 1.070786 GACTCCTGGCCGAAACACA 59.929 57.895 0.00 0.00 0.00 3.72
869 1447 4.273969 CGTATCTCCACTCTTCACCTACTC 59.726 50.000 0.00 0.00 0.00 2.59
910 1488 1.070821 CACTACGTGTCCACAGCATG 58.929 55.000 0.00 0.00 46.00 4.06
988 1571 1.948104 CTCACGAAACTGGGTGTTGA 58.052 50.000 0.00 0.00 39.13 3.18
997 1581 2.069273 CGATTTCCTGCTCACGAAACT 58.931 47.619 0.00 0.00 31.15 2.66
999 1585 2.448926 TCGATTTCCTGCTCACGAAA 57.551 45.000 0.00 0.00 32.82 3.46
1002 1588 1.714794 ACTTCGATTTCCTGCTCACG 58.285 50.000 0.00 0.00 0.00 4.35
1031 1617 0.911525 TGCTTCTTGGCCTAGGCTCT 60.912 55.000 32.18 0.00 41.60 4.09
1042 1629 0.805322 ATCGCTCGCTCTGCTTCTTG 60.805 55.000 0.00 0.00 0.00 3.02
1055 1642 4.694037 TCCATTGATGAATGATGATCGCTC 59.306 41.667 6.45 0.00 41.49 5.03
1061 1648 5.301045 GCCTTTCTCCATTGATGAATGATGA 59.699 40.000 6.45 1.59 41.49 2.92
1062 1649 5.068591 TGCCTTTCTCCATTGATGAATGATG 59.931 40.000 6.45 0.00 41.49 3.07
1063 1650 5.068723 GTGCCTTTCTCCATTGATGAATGAT 59.931 40.000 6.45 0.00 41.49 2.45
1064 1651 4.400251 GTGCCTTTCTCCATTGATGAATGA 59.600 41.667 6.45 0.00 41.49 2.57
1065 1652 4.679662 GTGCCTTTCTCCATTGATGAATG 58.320 43.478 0.00 0.00 39.04 2.67
1066 1653 3.379372 CGTGCCTTTCTCCATTGATGAAT 59.621 43.478 0.00 0.00 0.00 2.57
1067 1654 2.749076 CGTGCCTTTCTCCATTGATGAA 59.251 45.455 0.00 0.00 0.00 2.57
1175 1778 1.144057 GAGTACCGCCATGTCAGGG 59.856 63.158 0.00 0.00 0.00 4.45
1176 1779 0.179100 CAGAGTACCGCCATGTCAGG 60.179 60.000 0.00 0.00 0.00 3.86
1177 1780 0.807667 GCAGAGTACCGCCATGTCAG 60.808 60.000 0.00 0.00 0.00 3.51
1178 1781 1.218047 GCAGAGTACCGCCATGTCA 59.782 57.895 0.00 0.00 0.00 3.58
1179 1782 0.108138 AAGCAGAGTACCGCCATGTC 60.108 55.000 0.00 0.00 0.00 3.06
1180 1783 0.108138 GAAGCAGAGTACCGCCATGT 60.108 55.000 0.00 0.00 0.00 3.21
1252 1891 1.009829 GCACCTTGATCGTCACATCC 58.990 55.000 0.00 0.00 0.00 3.51
1360 1999 8.463930 ACCATCGATAATATGTTTTGGTTGAT 57.536 30.769 0.00 0.00 32.48 2.57
1361 2000 7.773224 AGACCATCGATAATATGTTTTGGTTGA 59.227 33.333 0.00 0.00 36.41 3.18
1394 2038 5.355910 ACGGTAACAATCAATCCACCATTAC 59.644 40.000 0.00 0.00 0.00 1.89
1538 2228 0.537143 TACCCCTTGCTGCAAGTGTG 60.537 55.000 33.16 24.29 39.58 3.82
1543 2233 1.003839 CTCGTACCCCTTGCTGCAA 60.004 57.895 15.16 15.16 0.00 4.08
1730 2426 0.469494 TGCATCATCGGGCTGTACAT 59.531 50.000 0.00 0.00 0.00 2.29
2224 2970 3.197790 CCCGCGAAGTCCAGCATG 61.198 66.667 8.23 0.00 0.00 4.06
2321 3067 1.080974 CGAAGCGGTACCTCACGTT 60.081 57.895 10.90 0.00 0.00 3.99
2619 3371 0.804989 GCCGTCAGGTTTTCATCAGG 59.195 55.000 0.00 0.00 40.50 3.86
2630 3384 2.821366 GCACATCCAGCCGTCAGG 60.821 66.667 0.00 0.00 41.62 3.86
2632 3386 3.932580 GACGCACATCCAGCCGTCA 62.933 63.158 7.09 0.00 36.37 4.35
2748 3514 4.838152 GCGGAGGCGATGGCAAGA 62.838 66.667 1.01 0.00 42.47 3.02
2761 3527 4.533124 TAGAGGGATGGCCGCGGA 62.533 66.667 33.48 9.86 33.83 5.54
2764 3546 3.233259 GAGCTAGAGGGATGGCCGC 62.233 68.421 0.00 0.00 33.83 6.53
2781 3563 1.070786 AAAAACAGCGAGGCTCGGA 59.929 52.632 35.03 0.00 40.84 4.55
2833 3616 5.896530 TCCCCATGATCTATTCTAGGGTA 57.103 43.478 0.00 0.00 37.40 3.69
2835 3618 4.472833 CCTTCCCCATGATCTATTCTAGGG 59.527 50.000 0.00 0.00 38.28 3.53
2841 3624 4.352298 GGAGAACCTTCCCCATGATCTATT 59.648 45.833 0.00 0.00 0.00 1.73
2878 3661 0.704076 AAATAGTTGCAGCTGGGGGA 59.296 50.000 17.12 0.00 0.00 4.81
2884 3671 4.944317 GGTAAGGAAGAAATAGTTGCAGCT 59.056 41.667 8.54 8.54 0.00 4.24
2886 3673 5.586643 GGAGGTAAGGAAGAAATAGTTGCAG 59.413 44.000 0.00 0.00 0.00 4.41
2923 3710 2.671396 GCCAGTCGATTTTCGCTAGAAA 59.329 45.455 0.00 0.00 43.91 2.52
2943 3734 0.103026 GCCTGAAATCCGATTTGGGC 59.897 55.000 21.62 21.62 39.10 5.36
2952 3743 0.389948 ACGTGAGTCGCCTGAAATCC 60.390 55.000 0.00 0.00 44.19 3.01
3034 3826 6.584184 CACCGACTATAATAGTGCTCAGATTG 59.416 42.308 0.00 0.00 39.59 2.67
3073 3865 5.956068 TGAAATTTCCGAATCACATGTGA 57.044 34.783 29.67 29.67 44.59 3.58
3145 3937 4.143009 GCTAGAAGCTGCACTTTGTACTTC 60.143 45.833 1.02 0.00 39.29 3.01
3163 3955 3.429822 GCCAACTTGTATACGTGGCTAGA 60.430 47.826 22.62 0.00 37.90 2.43
3171 3963 2.279659 CCGTAACGCCAACTTGTATACG 59.720 50.000 0.00 0.00 35.65 3.06
3192 3984 0.895530 TCCCTCTGGTCATCGTGAAC 59.104 55.000 0.00 0.00 33.88 3.18
3225 4017 4.686191 AACATGATTTGCTTTGTTGGGA 57.314 36.364 0.00 0.00 31.45 4.37
3385 4178 3.885724 TGACATCATTCTCACGGCTTA 57.114 42.857 0.00 0.00 0.00 3.09
3389 4182 1.600957 GCCATGACATCATTCTCACGG 59.399 52.381 0.00 0.00 33.61 4.94
3517 4310 1.407575 GCTCTGGAAGGAACCTTAGCC 60.408 57.143 12.45 8.83 36.26 3.93
3520 4313 1.549170 GTCGCTCTGGAAGGAACCTTA 59.451 52.381 6.06 0.00 36.26 2.69
3522 4315 0.832135 TGTCGCTCTGGAAGGAACCT 60.832 55.000 0.00 0.00 0.00 3.50
3523 4316 0.670854 GTGTCGCTCTGGAAGGAACC 60.671 60.000 0.00 0.00 0.00 3.62
3525 4318 0.756294 TTGTGTCGCTCTGGAAGGAA 59.244 50.000 0.00 0.00 0.00 3.36
3529 4322 1.300620 CGGTTGTGTCGCTCTGGAA 60.301 57.895 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.