Multiple sequence alignment - TraesCS1A01G109700

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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 TraesCS1A01G109700 chr1A 100.000 3923 0 0 1 3923 108782156 108778234 0.000000e+00 7245.0
1 TraesCS1A01G109700 chr1D 94.584 2308 101 12 661 2965 77453683 77451397 0.000000e+00 3548.0
2 TraesCS1A01G109700 chr1D 89.572 374 31 5 2959 3326 77451357 77450986 5.940000e-128 468.0
3 TraesCS1A01G109700 chr1D 86.555 357 39 6 3370 3720 77450989 77450636 6.150000e-103 385.0
4 TraesCS1A01G109700 chr1B 93.800 2145 98 15 853 2971 121015136 121013001 0.000000e+00 3192.0
5 TraesCS1A01G109700 chr1B 88.919 370 35 6 2959 3326 121012964 121012599 5.980000e-123 451.0
6 TraesCS1A01G109700 chr1B 79.670 364 37 22 3597 3923 121012180 121011817 1.100000e-55 228.0
7 TraesCS1A01G109700 chr1B 88.276 145 12 5 669 813 121015282 121015143 6.740000e-38 169.0
8 TraesCS1A01G109700 chr7A 92.891 2124 108 21 848 2961 477185542 477183452 0.000000e+00 3046.0
9 TraesCS1A01G109700 chr7A 83.946 735 66 20 3238 3923 477183174 477182443 0.000000e+00 656.0
10 TraesCS1A01G109700 chr2B 85.887 1410 165 21 1586 2971 757230798 757232197 0.000000e+00 1471.0
11 TraesCS1A01G109700 chr2B 84.527 433 48 11 3328 3753 757015147 757015567 1.010000e-110 411.0
12 TraesCS1A01G109700 chr2B 89.671 213 20 2 2048 2260 757292621 757292831 1.800000e-68 270.0
13 TraesCS1A01G109700 chr2B 84.959 246 28 4 3518 3754 757452481 757452726 1.410000e-59 241.0
14 TraesCS1A01G109700 chr2B 87.634 186 18 4 2979 3162 757391258 757391440 1.100000e-50 211.0
15 TraesCS1A01G109700 chr2B 81.275 251 38 7 2956 3198 757080464 757080713 1.110000e-45 195.0
16 TraesCS1A01G109700 chr2B 83.544 158 22 2 3344 3501 757391438 757391591 1.140000e-30 145.0
17 TraesCS1A01G109700 chr2B 85.507 69 10 0 3151 3219 757537526 757537594 5.440000e-09 73.1
18 TraesCS1A01G109700 chr2A 86.991 1253 136 16 1739 2971 750330538 750331783 0.000000e+00 1386.0
19 TraesCS1A01G109700 chr2A 92.025 652 50 2 1 651 34087739 34088389 0.000000e+00 915.0
20 TraesCS1A01G109700 chr2A 90.865 613 51 4 2362 2971 750190767 750190157 0.000000e+00 817.0
21 TraesCS1A01G109700 chr2A 79.582 813 101 29 2966 3751 750190113 750189339 4.490000e-144 521.0
22 TraesCS1A01G109700 chr2A 78.323 489 62 21 3151 3621 750331863 750332325 3.860000e-70 276.0
23 TraesCS1A01G109700 chr2A 79.525 337 35 16 3166 3482 750423409 750423731 3.970000e-50 209.0
24 TraesCS1A01G109700 chr2A 81.181 271 39 9 3487 3754 750424459 750424720 1.430000e-49 207.0
25 TraesCS1A01G109700 chr2A 88.148 135 9 4 2842 2971 750334905 750335037 1.890000e-33 154.0
26 TraesCS1A01G109700 chr2D 87.586 725 76 7 1834 2544 619311041 619311765 0.000000e+00 828.0
27 TraesCS1A01G109700 chr2D 86.330 673 70 10 2176 2841 619262268 619262925 0.000000e+00 713.0
28 TraesCS1A01G109700 chr2D 82.996 247 31 5 3519 3754 610756761 610757007 3.070000e-51 213.0
29 TraesCS1A01G109700 chr7D 88.245 621 59 6 2362 2971 498243302 498243919 0.000000e+00 730.0
30 TraesCS1A01G109700 chr7D 79.504 605 84 13 2966 3555 498243962 498244541 1.020000e-105 394.0
31 TraesCS1A01G109700 chr7D 86.076 158 18 2 3344 3501 498284373 498284526 2.420000e-37 167.0
32 TraesCS1A01G109700 chr6B 92.708 96 6 1 556 650 56438652 56438557 1.900000e-28 137.0
33 TraesCS1A01G109700 chr6D 74.479 192 41 7 465 651 8342091 8342279 4.200000e-10 76.8


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 TraesCS1A01G109700 chr1A 108778234 108782156 3922 True 7245.000000 7245 100.000000 1 3923 1 chr1A.!!$R1 3922
1 TraesCS1A01G109700 chr1D 77450636 77453683 3047 True 1467.000000 3548 90.237000 661 3720 3 chr1D.!!$R1 3059
2 TraesCS1A01G109700 chr1B 121011817 121015282 3465 True 1010.000000 3192 87.666250 669 3923 4 chr1B.!!$R1 3254
3 TraesCS1A01G109700 chr7A 477182443 477185542 3099 True 1851.000000 3046 88.418500 848 3923 2 chr7A.!!$R1 3075
4 TraesCS1A01G109700 chr2B 757230798 757232197 1399 False 1471.000000 1471 85.887000 1586 2971 1 chr2B.!!$F3 1385
5 TraesCS1A01G109700 chr2A 34087739 34088389 650 False 915.000000 915 92.025000 1 651 1 chr2A.!!$F1 650
6 TraesCS1A01G109700 chr2A 750189339 750190767 1428 True 669.000000 817 85.223500 2362 3751 2 chr2A.!!$R1 1389
7 TraesCS1A01G109700 chr2A 750330538 750335037 4499 False 605.333333 1386 84.487333 1739 3621 3 chr2A.!!$F2 1882
8 TraesCS1A01G109700 chr2A 750423409 750424720 1311 False 208.000000 209 80.353000 3166 3754 2 chr2A.!!$F3 588
9 TraesCS1A01G109700 chr2D 619311041 619311765 724 False 828.000000 828 87.586000 1834 2544 1 chr2D.!!$F3 710
10 TraesCS1A01G109700 chr2D 619262268 619262925 657 False 713.000000 713 86.330000 2176 2841 1 chr2D.!!$F2 665
11 TraesCS1A01G109700 chr7D 498243302 498244541 1239 False 562.000000 730 83.874500 2362 3555 2 chr7D.!!$F2 1193

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
380 381 0.039527 GCTTGGCGTTGGTAAACCTG 60.040 55.000 0.02 0.0 36.82 4.00 F
1162 1205 0.114168 ATCCATCTCCTCCTCCTCCG 59.886 60.000 0.00 0.0 0.00 4.63 F
1163 1206 1.532794 CCATCTCCTCCTCCTCCGG 60.533 68.421 0.00 0.0 0.00 5.14 F
2076 2147 1.627297 CCTTGGTAGGGGTGCTCTCC 61.627 65.000 0.00 0.0 37.94 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2048 0.817229 TTGACATGCCGTTCTGTGCA 60.817 50.000 0.0 0.0 42.52 4.57 R
2160 2231 1.771854 TCCACTAAAGCAGTCCCAACA 59.228 47.619 0.0 0.0 34.26 3.33 R
2546 2635 2.111043 CCGCATCCGCCTTACCAT 59.889 61.111 0.0 0.0 33.11 3.55 R
3747 4933 1.228862 ACTGGCAAATGGACCCCAC 60.229 57.895 0.0 0.0 35.80 4.61 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
20 21 3.981071 TCCAGAAACAGATGGGTACAG 57.019 47.619 0.00 0.00 37.19 2.74
43 44 2.291153 ACCATGATCAACTTGACCCAGG 60.291 50.000 0.00 0.00 0.00 4.45
49 50 4.042809 TGATCAACTTGACCCAGGTAATGT 59.957 41.667 0.00 0.00 0.00 2.71
66 67 4.884668 AATGTTGTAAGGAGAGTTCGGA 57.115 40.909 0.00 0.00 0.00 4.55
70 71 1.549170 TGTAAGGAGAGTTCGGAAGGC 59.451 52.381 0.00 0.00 0.00 4.35
105 106 2.490903 GAGCTTCCTCAACAACATGCAT 59.509 45.455 0.00 0.00 38.03 3.96
202 203 0.329596 GATGAGGGCAAAGGAGGTGT 59.670 55.000 0.00 0.00 0.00 4.16
204 205 1.440618 TGAGGGCAAAGGAGGTGTAA 58.559 50.000 0.00 0.00 0.00 2.41
205 206 1.992557 TGAGGGCAAAGGAGGTGTAAT 59.007 47.619 0.00 0.00 0.00 1.89
217 218 0.802494 GGTGTAATGGGTGTTGCTCG 59.198 55.000 0.00 0.00 0.00 5.03
230 231 4.606071 GCTCGATCAGCCACTTGT 57.394 55.556 6.02 0.00 43.17 3.16
241 242 1.016653 GCCACTTGTCTTCTCGGAGC 61.017 60.000 0.00 0.00 0.00 4.70
248 249 1.016653 GTCTTCTCGGAGCTTGGTGC 61.017 60.000 0.00 0.00 43.29 5.01
256 257 1.391157 GGAGCTTGGTGCAAACCACA 61.391 55.000 0.00 0.00 46.50 4.17
261 262 0.393132 TTGGTGCAAACCACACGAGA 60.393 50.000 0.00 0.00 46.50 4.04
328 329 2.160022 GCGTTATTTTCGCCAACCTACA 59.840 45.455 0.00 0.00 46.61 2.74
342 343 3.281727 ACCTACAAGGCATACCACATG 57.718 47.619 0.00 0.00 39.63 3.21
357 358 3.450817 ACCACATGTGATATTGGAGACGA 59.549 43.478 27.46 0.00 33.02 4.20
360 361 4.869861 CACATGTGATATTGGAGACGAACA 59.130 41.667 21.64 0.00 0.00 3.18
380 381 0.039527 GCTTGGCGTTGGTAAACCTG 60.040 55.000 0.02 0.00 36.82 4.00
382 383 1.001815 CTTGGCGTTGGTAAACCTGTG 60.002 52.381 0.02 0.00 36.82 3.66
383 384 0.180642 TGGCGTTGGTAAACCTGTGA 59.819 50.000 0.02 0.00 36.82 3.58
414 415 0.249447 CACAGGTCGCTCTGTTGTGA 60.249 55.000 7.57 0.00 44.74 3.58
442 443 7.151308 CCGATACTAGATGAAATTGAAGAGCT 58.849 38.462 0.00 0.00 0.00 4.09
465 466 8.739972 AGCTATCCTTAGTTTTTGGTACATTTG 58.260 33.333 0.00 0.00 39.30 2.32
500 501 6.159293 TGTATCTAGATCAGCTAATTTGCCG 58.841 40.000 8.95 0.00 0.00 5.69
503 504 1.133976 AGATCAGCTAATTTGCCGGCT 60.134 47.619 29.70 9.99 35.23 5.52
522 523 3.176708 GCTCATTTGTGTGCTAAGCATG 58.823 45.455 0.00 0.00 41.91 4.06
543 544 2.875672 GCTTGCTCACTCATGGTAACCA 60.876 50.000 0.00 0.00 38.19 3.67
544 545 3.411446 CTTGCTCACTCATGGTAACCAA 58.589 45.455 0.00 0.00 36.95 3.67
547 548 3.820467 TGCTCACTCATGGTAACCAAAAG 59.180 43.478 0.00 0.00 36.95 2.27
566 567 0.910088 GTTGGCTGGACTCTACCCCT 60.910 60.000 0.00 0.00 0.00 4.79
568 569 0.909610 TGGCTGGACTCTACCCCTTG 60.910 60.000 0.00 0.00 0.00 3.61
575 577 2.904434 GGACTCTACCCCTTGTTCTTGA 59.096 50.000 0.00 0.00 0.00 3.02
600 602 2.084844 GTCTCATTGCAGACTGCCG 58.915 57.895 24.33 12.92 44.23 5.69
628 630 6.646240 TGAATGCCTTTGTTGAATAAAAGCTC 59.354 34.615 8.96 1.45 33.02 4.09
629 631 5.789643 TGCCTTTGTTGAATAAAAGCTCT 57.210 34.783 8.96 0.00 33.02 4.09
641 643 3.990318 AAAAGCTCTCAAAGTTTCCCG 57.010 42.857 0.00 0.00 0.00 5.14
642 644 1.897560 AAGCTCTCAAAGTTTCCCGG 58.102 50.000 0.00 0.00 0.00 5.73
692 694 5.482163 TGATCAGAATATATTGCACCGGA 57.518 39.130 9.46 0.00 0.00 5.14
749 751 3.058293 CAGAACCAATGCATTACACGTGT 60.058 43.478 26.52 26.52 0.00 4.49
750 752 2.987413 ACCAATGCATTACACGTGTG 57.013 45.000 30.83 15.58 0.00 3.82
751 753 1.539388 ACCAATGCATTACACGTGTGG 59.461 47.619 30.83 21.60 34.19 4.17
752 754 1.809547 CCAATGCATTACACGTGTGGA 59.190 47.619 30.83 19.07 34.19 4.02
753 755 2.227626 CCAATGCATTACACGTGTGGAA 59.772 45.455 30.83 18.45 37.88 3.53
754 756 3.233578 CAATGCATTACACGTGTGGAAC 58.766 45.455 30.83 17.37 36.02 3.62
755 757 1.231221 TGCATTACACGTGTGGAACC 58.769 50.000 30.83 14.88 36.02 3.62
756 758 1.231221 GCATTACACGTGTGGAACCA 58.769 50.000 30.83 7.00 36.02 3.67
757 759 1.196808 GCATTACACGTGTGGAACCAG 59.803 52.381 30.83 13.74 36.02 4.00
758 760 2.489971 CATTACACGTGTGGAACCAGT 58.510 47.619 30.83 3.62 36.02 4.00
764 767 1.746787 ACGTGTGGAACCAGTTTTTCC 59.253 47.619 0.00 0.00 42.68 3.13
778 781 3.054802 AGTTTTTCCTGATCTGAGCGGAT 60.055 43.478 2.75 0.00 0.00 4.18
779 782 3.634397 TTTTCCTGATCTGAGCGGATT 57.366 42.857 2.75 0.00 0.00 3.01
805 808 4.406648 TTCCCTGATGTGTATAGTGCTG 57.593 45.455 0.00 0.00 0.00 4.41
809 812 4.993584 CCCTGATGTGTATAGTGCTGATTC 59.006 45.833 0.00 0.00 0.00 2.52
810 813 5.453762 CCCTGATGTGTATAGTGCTGATTCA 60.454 44.000 0.00 0.00 0.00 2.57
812 815 6.709397 CCTGATGTGTATAGTGCTGATTCATT 59.291 38.462 0.00 0.00 0.00 2.57
813 816 7.228108 CCTGATGTGTATAGTGCTGATTCATTT 59.772 37.037 0.00 0.00 0.00 2.32
825 828 4.569564 GCTGATTCATTTTGCAGGAAATCC 59.430 41.667 0.00 0.00 0.00 3.01
826 829 5.726397 CTGATTCATTTTGCAGGAAATCCA 58.274 37.500 1.67 0.00 38.89 3.41
828 831 4.540359 TTCATTTTGCAGGAAATCCAGG 57.460 40.909 1.67 0.00 38.89 4.45
830 833 0.975887 TTTTGCAGGAAATCCAGGCC 59.024 50.000 11.92 0.00 37.66 5.19
831 834 1.250154 TTTGCAGGAAATCCAGGCCG 61.250 55.000 11.92 0.00 37.66 6.13
832 835 3.521796 GCAGGAAATCCAGGCCGC 61.522 66.667 0.00 0.00 38.89 6.53
960 963 4.722700 GCGGCAGGCAGGAAGGAA 62.723 66.667 0.00 0.00 42.87 3.36
988 1020 1.604693 CGAAGGAGCAGTACCAAACGT 60.605 52.381 0.00 0.00 0.00 3.99
1059 1099 2.125952 CACTCGCGATGCCACTCA 60.126 61.111 10.36 0.00 0.00 3.41
1071 1111 1.195115 GCCACTCACTCTCCACCATA 58.805 55.000 0.00 0.00 0.00 2.74
1072 1112 1.134670 GCCACTCACTCTCCACCATAC 60.135 57.143 0.00 0.00 0.00 2.39
1106 1146 2.231380 ACATCCTCCACCACCACCC 61.231 63.158 0.00 0.00 0.00 4.61
1162 1205 0.114168 ATCCATCTCCTCCTCCTCCG 59.886 60.000 0.00 0.00 0.00 4.63
1163 1206 1.532794 CCATCTCCTCCTCCTCCGG 60.533 68.421 0.00 0.00 0.00 5.14
1344 1393 2.507102 CCTGACGCCTACACGCTG 60.507 66.667 0.00 0.00 36.19 5.18
1425 1474 3.011635 GCTCCTGCAGAAGCTCGGA 62.012 63.158 18.89 2.77 42.74 4.55
1426 1475 1.821936 CTCCTGCAGAAGCTCGGAT 59.178 57.895 17.39 0.00 42.74 4.18
1431 1480 2.621338 CTGCAGAAGCTCGGATTACAA 58.379 47.619 8.42 0.00 42.74 2.41
1458 1507 2.516888 CCACACCGTCCACTCCCTT 61.517 63.158 0.00 0.00 0.00 3.95
1563 1612 3.808174 GGAACTCCATGATAAAGGCGTAC 59.192 47.826 0.00 0.00 35.64 3.67
1722 1771 1.679898 GTTGGAGGACTGGGTGAGG 59.320 63.158 0.00 0.00 0.00 3.86
1875 1926 3.209410 CTTGATCACTGGGCAAGTATCC 58.791 50.000 0.00 0.00 36.83 2.59
1913 1967 7.495934 TCGGTCCTCATTTTGAAATAATCTCTC 59.504 37.037 0.00 0.00 0.00 3.20
1935 1998 5.532557 TCATGAATGTAGTCTTATCTGGCG 58.467 41.667 0.00 0.00 0.00 5.69
1967 2030 9.710900 GATCATTTGTCTATGGTGTGTATGATA 57.289 33.333 0.00 0.00 32.19 2.15
1977 2048 4.100344 TGGTGTGTATGATAACGCAGGTAT 59.900 41.667 0.00 0.00 40.35 2.73
2076 2147 1.627297 CCTTGGTAGGGGTGCTCTCC 61.627 65.000 0.00 0.00 37.94 3.71
2160 2231 2.700897 AGGCTTCTACGGCAATGTCTAT 59.299 45.455 0.00 0.00 0.00 1.98
2546 2635 5.455392 TGGGATTTCATTGAGAAGATCCA 57.545 39.130 15.91 6.93 41.11 3.41
2586 2676 2.122901 TTGGGGGCTTTGCTTGCT 60.123 55.556 0.00 0.00 0.00 3.91
2944 3053 2.418976 CACACAACCAGATGCAGATCAG 59.581 50.000 0.00 0.00 0.00 2.90
2961 3070 1.901833 TCAGCCTCAGTATTGCAGTCA 59.098 47.619 0.00 0.00 0.00 3.41
3063 3220 5.210430 TGGATTGCCAAGATGGAATATTGT 58.790 37.500 0.00 0.00 43.70 2.71
3093 3250 4.742012 TCCTTCTCTATGACTGGATACCC 58.258 47.826 0.00 0.00 0.00 3.69
3173 3332 3.129813 CACCATGCTTAGTCATGTGCAAT 59.870 43.478 12.84 0.00 41.60 3.56
3223 3385 6.374333 TGAAAATACCTGATTCAGTTGTAGCC 59.626 38.462 12.54 0.00 0.00 3.93
3292 3494 1.939934 TGGTTTTGCGAGTTGTCAGAG 59.060 47.619 0.00 0.00 0.00 3.35
3300 3502 2.819115 CGAGTTGTCAGAGCATGCTAT 58.181 47.619 22.74 16.22 0.00 2.97
3305 3507 6.810676 CGAGTTGTCAGAGCATGCTATATAAT 59.189 38.462 22.74 3.39 0.00 1.28
3377 3597 6.417258 TCATCTTCTGGCTGAACATATTCAA 58.583 36.000 2.37 0.00 44.28 2.69
3410 3632 8.424133 AGTCTAAAAGAAAAATGAATTGGCACT 58.576 29.630 0.00 0.00 0.00 4.40
3580 4536 6.986817 CCCCTAATTGTCTGTGTAGATTGTAG 59.013 42.308 0.00 0.00 34.94 2.74
3645 4827 7.418337 TGTTCTTACTGCCAGTATCATCTTA 57.582 36.000 5.21 0.00 29.64 2.10
3646 4828 7.265673 TGTTCTTACTGCCAGTATCATCTTAC 58.734 38.462 5.21 0.00 29.64 2.34
3747 4933 9.840427 ACAAACGAAAGAATGAAGGTATAATTG 57.160 29.630 0.00 0.00 0.00 2.32
3760 4965 5.208121 AGGTATAATTGTGGGGTCCATTTG 58.792 41.667 0.00 0.00 35.28 2.32
3764 4969 0.831288 TTGTGGGGTCCATTTGCCAG 60.831 55.000 0.00 0.00 35.28 4.85
3913 6435 6.826231 TGGTTCACAATCTTTGAGTTTCTGTA 59.174 34.615 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.025887 GGGTCAAGTTGATCATGGTCCT 60.026 50.000 17.73 0.00 0.00 3.85
20 21 2.290896 TGGGTCAAGTTGATCATGGTCC 60.291 50.000 17.73 8.01 0.00 4.46
43 44 5.717119 TCCGAACTCTCCTTACAACATTAC 58.283 41.667 0.00 0.00 0.00 1.89
49 50 2.028385 GCCTTCCGAACTCTCCTTACAA 60.028 50.000 0.00 0.00 0.00 2.41
70 71 3.066814 GCTCAAGCAAGGCCAGGG 61.067 66.667 5.01 0.00 41.59 4.45
80 81 1.949525 TGTTGTTGAGGAAGCTCAAGC 59.050 47.619 0.00 0.00 43.08 4.01
105 106 1.771565 CCGTGACCTGGTAGTATGGA 58.228 55.000 0.00 0.00 0.00 3.41
133 134 2.259917 TGATCACTTCCTGCTCTGGAA 58.740 47.619 7.79 7.79 43.16 3.53
202 203 2.905075 CTGATCGAGCAACACCCATTA 58.095 47.619 4.32 0.00 0.00 1.90
204 205 3.465990 CTGATCGAGCAACACCCAT 57.534 52.632 4.32 0.00 0.00 4.00
217 218 2.266554 CGAGAAGACAAGTGGCTGATC 58.733 52.381 0.00 0.00 30.66 2.92
230 231 1.293498 GCACCAAGCTCCGAGAAGA 59.707 57.895 0.00 0.00 41.15 2.87
248 249 0.105964 TCACCCTCTCGTGTGGTTTG 59.894 55.000 5.01 2.45 35.18 2.93
256 257 0.684805 GGGATCAGTCACCCTCTCGT 60.685 60.000 0.00 0.00 42.56 4.18
308 309 4.399978 CTTGTAGGTTGGCGAAAATAACG 58.600 43.478 0.00 0.00 0.00 3.18
328 329 4.828939 CCAATATCACATGTGGTATGCCTT 59.171 41.667 28.07 13.45 37.01 4.35
342 343 3.786635 AGCTGTTCGTCTCCAATATCAC 58.213 45.455 0.00 0.00 0.00 3.06
357 358 1.066454 GTTTACCAACGCCAAGCTGTT 59.934 47.619 0.00 0.00 0.00 3.16
360 361 0.179001 AGGTTTACCAACGCCAAGCT 60.179 50.000 1.13 0.00 38.89 3.74
380 381 0.179215 CTGTGCGGCGAGAATTTCAC 60.179 55.000 12.98 7.93 0.00 3.18
382 383 1.298859 ACCTGTGCGGCGAGAATTTC 61.299 55.000 12.98 0.00 35.61 2.17
383 384 1.298859 GACCTGTGCGGCGAGAATTT 61.299 55.000 12.98 0.00 35.61 1.82
414 415 6.326583 TCTTCAATTTCATCTAGTATCGGGGT 59.673 38.462 0.00 0.00 0.00 4.95
449 450 8.524487 TGTTGAACTACAAATGTACCAAAAACT 58.476 29.630 0.00 0.00 40.36 2.66
465 466 8.356657 AGCTGATCTAGATACATGTTGAACTAC 58.643 37.037 2.30 0.00 0.00 2.73
489 490 2.195922 CAAATGAGCCGGCAAATTAGC 58.804 47.619 31.54 8.86 0.00 3.09
495 496 1.659233 CACACAAATGAGCCGGCAA 59.341 52.632 31.54 17.66 0.00 4.52
500 501 1.541147 TGCTTAGCACACAAATGAGCC 59.459 47.619 1.39 0.00 42.85 4.70
503 504 2.821378 AGCATGCTTAGCACACAAATGA 59.179 40.909 16.30 0.00 43.04 2.57
522 523 1.740025 GGTTACCATGAGTGAGCAAGC 59.260 52.381 0.00 0.00 32.96 4.01
543 544 2.224793 GGGTAGAGTCCAGCCAACTTTT 60.225 50.000 1.58 0.00 33.62 2.27
544 545 1.351350 GGGTAGAGTCCAGCCAACTTT 59.649 52.381 1.58 0.00 33.62 2.66
547 548 0.910088 AGGGGTAGAGTCCAGCCAAC 60.910 60.000 9.07 0.00 35.17 3.77
554 555 2.904434 TCAAGAACAAGGGGTAGAGTCC 59.096 50.000 0.00 0.00 0.00 3.85
566 567 6.369890 GCAATGAGACTACTGATCAAGAACAA 59.630 38.462 0.00 0.00 0.00 2.83
568 569 5.871524 TGCAATGAGACTACTGATCAAGAAC 59.128 40.000 0.00 0.00 0.00 3.01
614 616 7.382488 GGGAAACTTTGAGAGCTTTTATTCAAC 59.618 37.037 0.00 0.00 29.96 3.18
667 669 5.645067 CCGGTGCAATATATTCTGATCATGT 59.355 40.000 0.00 0.00 0.00 3.21
718 720 8.530311 TGTAATGCATTGGTTCTGAATACAAAT 58.470 29.630 22.27 0.00 0.00 2.32
749 751 4.141274 TCAGATCAGGAAAAACTGGTTCCA 60.141 41.667 6.01 0.00 46.01 3.53
750 752 4.398319 TCAGATCAGGAAAAACTGGTTCC 58.602 43.478 0.00 0.00 44.25 3.62
751 753 4.083057 GCTCAGATCAGGAAAAACTGGTTC 60.083 45.833 0.00 0.00 38.98 3.62
752 754 3.823304 GCTCAGATCAGGAAAAACTGGTT 59.177 43.478 0.00 0.00 38.98 3.67
753 755 3.416156 GCTCAGATCAGGAAAAACTGGT 58.584 45.455 0.00 0.00 38.98 4.00
754 756 2.417933 CGCTCAGATCAGGAAAAACTGG 59.582 50.000 0.00 0.00 38.98 4.00
755 757 2.417933 CCGCTCAGATCAGGAAAAACTG 59.582 50.000 0.00 0.00 39.84 3.16
756 758 2.303022 TCCGCTCAGATCAGGAAAAACT 59.697 45.455 0.00 0.00 0.00 2.66
757 759 2.699954 TCCGCTCAGATCAGGAAAAAC 58.300 47.619 0.00 0.00 0.00 2.43
758 760 3.634397 ATCCGCTCAGATCAGGAAAAA 57.366 42.857 0.00 0.00 36.25 1.94
800 803 3.581024 TCCTGCAAAATGAATCAGCAC 57.419 42.857 0.00 0.00 0.00 4.40
805 808 5.114081 CCTGGATTTCCTGCAAAATGAATC 58.886 41.667 1.10 1.33 36.82 2.52
809 812 2.624636 GCCTGGATTTCCTGCAAAATG 58.375 47.619 0.00 0.00 35.51 2.32
810 813 1.556451 GGCCTGGATTTCCTGCAAAAT 59.444 47.619 0.00 0.00 36.59 1.82
812 815 1.250154 CGGCCTGGATTTCCTGCAAA 61.250 55.000 0.00 0.00 36.59 3.68
813 816 1.678635 CGGCCTGGATTTCCTGCAA 60.679 57.895 0.00 0.00 36.59 4.08
825 828 1.160329 GCAACAGTATAGGCGGCCTG 61.160 60.000 31.26 17.21 34.61 4.85
826 829 1.146263 GCAACAGTATAGGCGGCCT 59.854 57.895 26.95 26.95 37.71 5.19
828 831 1.784525 CTAGCAACAGTATAGGCGGC 58.215 55.000 0.00 0.00 0.00 6.53
830 833 2.509052 TGCTAGCAACAGTATAGGCG 57.491 50.000 16.84 0.00 0.00 5.52
831 834 3.134458 CCTTGCTAGCAACAGTATAGGC 58.866 50.000 26.06 0.00 0.00 3.93
832 835 3.134458 GCCTTGCTAGCAACAGTATAGG 58.866 50.000 26.06 22.85 0.00 2.57
869 872 2.079158 CAACATGCCTGTGAGGTAGTG 58.921 52.381 0.00 0.00 37.80 2.74
873 876 0.467844 TTGCAACATGCCTGTGAGGT 60.468 50.000 0.00 0.00 44.23 3.85
875 878 2.512485 TTTTGCAACATGCCTGTGAG 57.488 45.000 0.00 0.00 44.23 3.51
876 879 2.364647 TGATTTTGCAACATGCCTGTGA 59.635 40.909 2.08 0.00 44.23 3.58
877 880 2.756829 TGATTTTGCAACATGCCTGTG 58.243 42.857 2.08 0.00 44.23 3.66
878 881 3.395639 CTTGATTTTGCAACATGCCTGT 58.604 40.909 2.08 0.00 44.23 4.00
879 882 2.739913 CCTTGATTTTGCAACATGCCTG 59.260 45.455 2.08 0.00 44.23 4.85
880 883 2.289819 CCCTTGATTTTGCAACATGCCT 60.290 45.455 2.08 0.00 44.23 4.75
881 884 2.078392 CCCTTGATTTTGCAACATGCC 58.922 47.619 2.08 0.00 44.23 4.40
951 954 1.267121 TCGGTCCTTCTTCCTTCCTG 58.733 55.000 0.00 0.00 0.00 3.86
960 963 0.543174 ACTGCTCCTTCGGTCCTTCT 60.543 55.000 0.00 0.00 0.00 2.85
1059 1099 0.539051 GCTGCTGTATGGTGGAGAGT 59.461 55.000 0.00 0.00 0.00 3.24
1090 1130 2.614013 GGGGTGGTGGTGGAGGAT 60.614 66.667 0.00 0.00 0.00 3.24
1106 1146 2.225596 TGGTTGTACGGGAAGGGGG 61.226 63.158 0.00 0.00 0.00 5.40
1280 1329 1.305718 GAGAGCTGGAGGGAGGTGT 60.306 63.158 0.00 0.00 0.00 4.16
1344 1393 2.110006 GCGAGGAGGAGGAATGGC 59.890 66.667 0.00 0.00 0.00 4.40
1425 1474 1.877443 GTGTGGTCGTGGCTTTGTAAT 59.123 47.619 0.00 0.00 0.00 1.89
1426 1475 1.301423 GTGTGGTCGTGGCTTTGTAA 58.699 50.000 0.00 0.00 0.00 2.41
1431 1480 3.802418 GACGGTGTGGTCGTGGCTT 62.802 63.158 0.00 0.00 41.22 4.35
1458 1507 3.383505 CGAGGTTGGAGTACATGGTGATA 59.616 47.826 0.00 0.00 0.00 2.15
1690 1739 1.909781 CCAACCACCTGCCAAGCAT 60.910 57.895 0.00 0.00 38.13 3.79
1722 1771 3.083997 ACCTCCATCCCCGCAGAC 61.084 66.667 0.00 0.00 0.00 3.51
1875 1926 2.959030 TGAGGACCGAAGTGGATCTATG 59.041 50.000 0.00 0.00 42.00 2.23
1913 1967 4.687948 CCGCCAGATAAGACTACATTCATG 59.312 45.833 0.00 0.00 0.00 3.07
1923 1977 1.227674 CAGGCCCGCCAGATAAGAC 60.228 63.158 8.74 0.00 38.92 3.01
1935 1998 3.152341 CCATAGACAAATGATCAGGCCC 58.848 50.000 0.00 0.00 0.00 5.80
1977 2048 0.817229 TTGACATGCCGTTCTGTGCA 60.817 50.000 0.00 0.00 42.52 4.57
2149 2220 2.684881 CAGTCCCAACATAGACATTGCC 59.315 50.000 0.00 0.00 35.38 4.52
2160 2231 1.771854 TCCACTAAAGCAGTCCCAACA 59.228 47.619 0.00 0.00 34.26 3.33
2546 2635 2.111043 CCGCATCCGCCTTACCAT 59.889 61.111 0.00 0.00 33.11 3.55
2586 2676 2.879002 TTTTGCATTTCCGACAAGCA 57.121 40.000 0.00 0.00 0.00 3.91
2944 3053 2.797156 CGTATGACTGCAATACTGAGGC 59.203 50.000 5.68 0.00 0.00 4.70
2961 3070 4.283722 AGTCACCTCCTTTCTTTCACGTAT 59.716 41.667 0.00 0.00 0.00 3.06
3058 3215 8.677300 GTCATAGAGAAGGAATGCAAAACAATA 58.323 33.333 0.00 0.00 0.00 1.90
3063 3220 5.649395 CCAGTCATAGAGAAGGAATGCAAAA 59.351 40.000 0.00 0.00 0.00 2.44
3093 3250 3.454371 AAATAGACCTGGTTCGATCCG 57.546 47.619 0.00 3.25 0.00 4.18
3244 3406 2.098934 TCCATTGGCGAATTGAAATCGG 59.901 45.455 4.71 0.00 40.54 4.18
3292 3494 8.593492 TCCATATTCGTGATTATATAGCATGC 57.407 34.615 10.51 10.51 0.00 4.06
3344 3559 6.484364 TCAGCCAGAAGATGATACAATGTA 57.516 37.500 0.00 0.00 0.00 2.29
3357 3575 5.879223 AGTCTTGAATATGTTCAGCCAGAAG 59.121 40.000 4.99 0.00 44.62 2.85
3515 4465 5.446260 TCTTACCTGAAGAATTTACCCCC 57.554 43.478 0.00 0.00 41.39 5.40
3595 4777 1.612726 GCTCCTGACCTCTGCAACAAT 60.613 52.381 0.00 0.00 0.00 2.71
3645 4827 5.084818 TGATTGTTCATAGTCACCGATGT 57.915 39.130 0.00 0.00 0.00 3.06
3646 4828 6.609237 ATTGATTGTTCATAGTCACCGATG 57.391 37.500 0.00 0.00 0.00 3.84
3686 4872 8.993121 GTATTTGATTGAAAGAGTTCTGTCTCA 58.007 33.333 1.30 0.00 36.97 3.27
3687 4873 9.213799 AGTATTTGATTGAAAGAGTTCTGTCTC 57.786 33.333 1.30 0.00 34.60 3.36
3747 4933 1.228862 ACTGGCAAATGGACCCCAC 60.229 57.895 0.00 0.00 35.80 4.61
3760 4965 5.705905 ACTTGTACAGGATTTTTAGACTGGC 59.294 40.000 12.54 0.00 35.34 4.85


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

AutoCloner maintained by Alex Coulton.