Multiple sequence alignment - TraesCS4A01G097500

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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 TraesCS4A01G097500 chr4A 100.000 3681 0 0 1 3681 108372896 108376576 0.000000e+00 6798.0
1 TraesCS4A01G097500 chr4B 96.684 2081 59 6 787 2867 440923494 440921424 0.000000e+00 3452.0
2 TraesCS4A01G097500 chr4B 86.970 637 77 6 2866 3498 440921368 440920734 0.000000e+00 712.0
3 TraesCS4A01G097500 chr4B 91.480 223 19 0 3459 3681 440920729 440920507 1.280000e-79 307.0
4 TraesCS4A01G097500 chr4B 87.027 185 24 0 3497 3681 601748171 601748355 3.720000e-50 209.0
5 TraesCS4A01G097500 chr4B 91.463 82 6 1 229 310 440924623 440924543 1.080000e-20 111.0
6 TraesCS4A01G097500 chr4D 96.475 2099 53 4 769 2867 357527653 357525576 0.000000e+00 3446.0
7 TraesCS4A01G097500 chr4D 92.927 509 28 5 183 684 357528162 357527655 0.000000e+00 734.0
8 TraesCS4A01G097500 chr4D 86.727 550 48 2 2866 3415 357525521 357524997 4.090000e-164 588.0
9 TraesCS4A01G097500 chr4D 91.213 239 21 0 3443 3681 357525011 357524773 3.540000e-85 326.0
10 TraesCS4A01G097500 chr4D 81.538 195 14 7 4 198 357528478 357528306 1.380000e-29 141.0
11 TraesCS4A01G097500 chr3B 82.651 513 71 8 2905 3415 810513225 810512729 4.360000e-119 438.0
12 TraesCS4A01G097500 chr1B 85.556 270 33 4 3193 3460 511945071 511944806 1.010000e-70 278.0
13 TraesCS4A01G097500 chr1B 83.333 216 36 0 3200 3415 367838368 367838153 2.240000e-47 200.0
14 TraesCS4A01G097500 chr1B 85.326 184 27 0 3497 3680 367837965 367837782 1.350000e-44 191.0
15 TraesCS4A01G097500 chr1D 91.892 185 15 0 3497 3681 381963773 381963589 3.650000e-65 259.0
16 TraesCS4A01G097500 chr1D 84.865 185 27 1 3497 3681 113674172 113674355 6.280000e-43 185.0
17 TraesCS4A01G097500 chr1D 79.325 237 47 2 3022 3256 1796120 1796356 8.180000e-37 165.0
18 TraesCS4A01G097500 chr2A 87.027 185 24 0 3497 3681 40439338 40439522 3.720000e-50 209.0
19 TraesCS4A01G097500 chr5B 82.667 225 38 1 3192 3415 382319058 382319282 8.060000e-47 198.0
20 TraesCS4A01G097500 chr5B 76.282 312 63 6 2886 3195 16202293 16201991 4.920000e-34 156.0
21 TraesCS4A01G097500 chr5B 79.512 205 40 2 1287 1490 8352161 8352364 1.070000e-30 145.0
22 TraesCS4A01G097500 chr3A 86.022 186 25 1 3497 3681 736150195 736150010 8.060000e-47 198.0
23 TraesCS4A01G097500 chr7A 85.484 186 24 3 3497 3681 648268625 648268442 1.350000e-44 191.0
24 TraesCS4A01G097500 chr5D 81.301 246 36 8 3163 3399 533534148 533533904 1.350000e-44 191.0
25 TraesCS4A01G097500 chr5D 89.362 47 5 0 724 770 8628478 8628524 3.970000e-05 60.2
26 TraesCS4A01G097500 chr7D 76.081 393 63 9 2895 3284 18850230 18849866 3.780000e-40 176.0
27 TraesCS4A01G097500 chr5A 79.888 179 34 2 1287 1464 6422451 6422628 2.980000e-26 130.0
28 TraesCS4A01G097500 chr5A 85.897 78 10 1 2893 2969 3306743 3306820 8.470000e-12 82.4


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 TraesCS4A01G097500 chr4A 108372896 108376576 3680 False 6798.0 6798 100.00000 1 3681 1 chr4A.!!$F1 3680
1 TraesCS4A01G097500 chr4B 440920507 440924623 4116 True 1145.5 3452 91.64925 229 3681 4 chr4B.!!$R1 3452
2 TraesCS4A01G097500 chr4D 357524773 357528478 3705 True 1047.0 3446 89.77600 4 3681 5 chr4D.!!$R1 3677

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
106 107 0.770499 TTTCATGTCTGCCCTCCACA 59.230 50.000 0.00 0.0 0.0 4.17 F
1224 2106 0.106708 TGCACCTAATGGGCGATCTC 59.893 55.000 0.00 0.0 39.1 2.75 F
1368 2250 1.443702 CGACCACATCTTCGCGTCA 60.444 57.895 5.77 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 2402 2.279073 CTAGCCGGACCTCCTCCA 59.721 66.667 5.05 0.00 39.39 3.86 R
2497 3379 0.623723 GAACCCCAGGGCACATTCTA 59.376 55.000 0.00 0.00 39.32 2.10 R
3325 4264 0.692419 ATCTTCTCTGCCCGGGACAT 60.692 55.000 29.31 1.62 0.00 3.06 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
53 54 5.832221 TCTACCTAGGAGCATGCATATAGT 58.168 41.667 21.98 12.01 0.00 2.12
72 73 9.073475 CATATAGTTAGGCTCTTACTTGAGAGT 57.927 37.037 0.00 0.00 44.03 3.24
106 107 0.770499 TTTCATGTCTGCCCTCCACA 59.230 50.000 0.00 0.00 0.00 4.17
107 108 0.994247 TTCATGTCTGCCCTCCACAT 59.006 50.000 0.00 0.00 0.00 3.21
108 109 1.878211 TCATGTCTGCCCTCCACATA 58.122 50.000 0.00 0.00 0.00 2.29
109 110 1.764723 TCATGTCTGCCCTCCACATAG 59.235 52.381 0.00 0.00 0.00 2.23
110 111 1.135094 ATGTCTGCCCTCCACATAGG 58.865 55.000 0.00 0.00 39.47 2.57
115 116 3.281332 GCCCTCCACATAGGCAAAA 57.719 52.632 0.00 0.00 46.34 2.44
116 117 1.555967 GCCCTCCACATAGGCAAAAA 58.444 50.000 0.00 0.00 46.34 1.94
117 118 2.110578 GCCCTCCACATAGGCAAAAAT 58.889 47.619 0.00 0.00 46.34 1.82
118 119 2.159057 GCCCTCCACATAGGCAAAAATG 60.159 50.000 0.00 0.00 46.34 2.32
119 120 2.159057 CCCTCCACATAGGCAAAAATGC 60.159 50.000 0.00 0.00 37.29 3.56
223 383 6.029346 ACTGCTTGTTCCAATTTATTCCAG 57.971 37.500 0.00 0.00 0.00 3.86
258 418 6.527722 CGTAACACTCGCTACCAAAACTATTA 59.472 38.462 0.00 0.00 0.00 0.98
291 451 8.732746 AGTACTTTCACAACTGTAGTTCATTT 57.267 30.769 0.00 0.00 35.83 2.32
319 479 5.968848 TGCGAGAAAATTGTAGTGTGTTTTC 59.031 36.000 0.00 0.00 39.58 2.29
320 480 5.113529 GCGAGAAAATTGTAGTGTGTTTTCG 59.886 40.000 0.00 0.00 42.42 3.46
332 492 1.987770 GTGTTTTCGGCTTGCATGATG 59.012 47.619 3.33 0.00 0.00 3.07
367 529 5.669164 AGGGTGCTTTTTAAGTGTTTCAA 57.331 34.783 0.00 0.00 0.00 2.69
377 539 6.844097 TTTAAGTGTTTCAAAGACCCAACT 57.156 33.333 0.00 0.00 0.00 3.16
378 540 4.718940 AAGTGTTTCAAAGACCCAACTG 57.281 40.909 0.00 0.00 0.00 3.16
486 655 5.408299 GCATAATGAACATACATGCGACCTA 59.592 40.000 14.11 0.00 33.00 3.08
579 777 1.538047 GGAGCACTTGAGCATGGAAA 58.462 50.000 0.00 0.00 36.85 3.13
594 792 6.578023 AGCATGGAAAACTCTGTAGATAGAC 58.422 40.000 0.00 0.00 0.00 2.59
624 1412 6.624352 ATTCGAATATATACATGCATGGGC 57.376 37.500 29.41 8.96 41.68 5.36
672 1554 3.198068 ACATTGTGTGTCAGACTGTCAC 58.802 45.455 21.40 21.40 35.77 3.67
685 1567 6.531948 GTCAGACTGTCACTAATCCATGTTAC 59.468 42.308 10.88 0.00 0.00 2.50
686 1568 6.437477 TCAGACTGTCACTAATCCATGTTACT 59.563 38.462 10.88 0.00 0.00 2.24
687 1569 6.754209 CAGACTGTCACTAATCCATGTTACTC 59.246 42.308 10.88 0.00 0.00 2.59
688 1570 5.978814 ACTGTCACTAATCCATGTTACTCC 58.021 41.667 0.00 0.00 0.00 3.85
689 1571 5.483937 ACTGTCACTAATCCATGTTACTCCA 59.516 40.000 0.00 0.00 0.00 3.86
690 1572 5.730550 TGTCACTAATCCATGTTACTCCAC 58.269 41.667 0.00 0.00 0.00 4.02
691 1573 5.116882 GTCACTAATCCATGTTACTCCACC 58.883 45.833 0.00 0.00 0.00 4.61
692 1574 4.163458 TCACTAATCCATGTTACTCCACCC 59.837 45.833 0.00 0.00 0.00 4.61
693 1575 2.710096 AATCCATGTTACTCCACCCG 57.290 50.000 0.00 0.00 0.00 5.28
694 1576 1.580059 ATCCATGTTACTCCACCCGT 58.420 50.000 0.00 0.00 0.00 5.28
695 1577 0.899720 TCCATGTTACTCCACCCGTC 59.100 55.000 0.00 0.00 0.00 4.79
696 1578 0.902531 CCATGTTACTCCACCCGTCT 59.097 55.000 0.00 0.00 0.00 4.18
697 1579 1.278127 CCATGTTACTCCACCCGTCTT 59.722 52.381 0.00 0.00 0.00 3.01
698 1580 2.498481 CCATGTTACTCCACCCGTCTTA 59.502 50.000 0.00 0.00 0.00 2.10
699 1581 3.134081 CCATGTTACTCCACCCGTCTTAT 59.866 47.826 0.00 0.00 0.00 1.73
700 1582 4.342951 CCATGTTACTCCACCCGTCTTATA 59.657 45.833 0.00 0.00 0.00 0.98
701 1583 5.163385 CCATGTTACTCCACCCGTCTTATAA 60.163 44.000 0.00 0.00 0.00 0.98
702 1584 6.463897 CCATGTTACTCCACCCGTCTTATAAT 60.464 42.308 0.00 0.00 0.00 1.28
703 1585 7.256048 CCATGTTACTCCACCCGTCTTATAATA 60.256 40.741 0.00 0.00 0.00 0.98
704 1586 7.844493 TGTTACTCCACCCGTCTTATAATAT 57.156 36.000 0.00 0.00 0.00 1.28
705 1587 8.938801 TGTTACTCCACCCGTCTTATAATATA 57.061 34.615 0.00 0.00 0.00 0.86
706 1588 9.365906 TGTTACTCCACCCGTCTTATAATATAA 57.634 33.333 0.00 0.00 0.00 0.98
710 1592 7.876582 ACTCCACCCGTCTTATAATATAAAAGC 59.123 37.037 0.00 0.00 0.00 3.51
711 1593 6.869913 TCCACCCGTCTTATAATATAAAAGCG 59.130 38.462 0.00 0.46 0.00 4.68
712 1594 6.647895 CCACCCGTCTTATAATATAAAAGCGT 59.352 38.462 0.00 0.00 0.00 5.07
713 1595 7.172019 CCACCCGTCTTATAATATAAAAGCGTT 59.828 37.037 0.00 0.00 0.00 4.84
714 1596 8.553696 CACCCGTCTTATAATATAAAAGCGTTT 58.446 33.333 2.53 2.53 0.00 3.60
715 1597 9.112725 ACCCGTCTTATAATATAAAAGCGTTTT 57.887 29.630 2.19 1.29 36.67 2.43
716 1598 9.940166 CCCGTCTTATAATATAAAAGCGTTTTT 57.060 29.630 14.50 14.50 39.69 1.94
725 1607 8.447787 AATATAAAAGCGTTTTTGCACTAGTG 57.552 30.769 18.93 18.93 37.12 2.74
726 1608 3.775661 AAAGCGTTTTTGCACTAGTGT 57.224 38.095 23.44 0.00 37.31 3.55
727 1609 4.886247 AAAGCGTTTTTGCACTAGTGTA 57.114 36.364 23.44 17.20 37.31 2.90
728 1610 4.886247 AAGCGTTTTTGCACTAGTGTAA 57.114 36.364 20.78 20.78 37.31 2.41
729 1611 5.432885 AAGCGTTTTTGCACTAGTGTAAT 57.567 34.783 24.35 8.13 35.24 1.89
730 1612 6.548441 AAGCGTTTTTGCACTAGTGTAATA 57.452 33.333 24.35 17.86 35.24 0.98
731 1613 6.737254 AGCGTTTTTGCACTAGTGTAATAT 57.263 33.333 24.35 4.98 35.24 1.28
732 1614 6.772078 AGCGTTTTTGCACTAGTGTAATATC 58.228 36.000 24.35 17.38 35.24 1.63
733 1615 6.370442 AGCGTTTTTGCACTAGTGTAATATCA 59.630 34.615 24.35 10.40 35.24 2.15
734 1616 7.018826 GCGTTTTTGCACTAGTGTAATATCAA 58.981 34.615 24.35 15.31 35.24 2.57
735 1617 7.535940 GCGTTTTTGCACTAGTGTAATATCAAA 59.464 33.333 24.35 19.50 35.24 2.69
736 1618 9.388346 CGTTTTTGCACTAGTGTAATATCAAAA 57.612 29.630 24.35 23.11 35.24 2.44
827 1709 1.006805 CGATGGAGAAGCTAGGCCG 60.007 63.158 0.00 0.00 0.00 6.13
935 1817 1.529226 AAATGAACGCACCGATGGAA 58.471 45.000 0.00 0.00 0.00 3.53
985 1867 5.699458 ACTAAGAACGATAGCTAGCTCTCTC 59.301 44.000 23.26 14.91 42.67 3.20
1024 1906 2.706273 CTCACGTACATGTAGACGAGC 58.294 52.381 24.02 3.82 41.60 5.03
1068 1950 2.622942 AGCTCCACGATCTCTCTTGATC 59.377 50.000 0.00 0.00 39.40 2.92
1124 2006 3.502920 CGCTCCTACTCCGCATTATTAG 58.497 50.000 0.00 0.00 0.00 1.73
1184 2066 2.762459 CCCATCTCCCCCGACGAA 60.762 66.667 0.00 0.00 0.00 3.85
1224 2106 0.106708 TGCACCTAATGGGCGATCTC 59.893 55.000 0.00 0.00 39.10 2.75
1368 2250 1.443702 CGACCACATCTTCGCGTCA 60.444 57.895 5.77 0.00 0.00 4.35
1464 2346 2.437359 CGGAAGGCCAGGAAGCTG 60.437 66.667 5.01 0.00 0.00 4.24
1771 2653 1.540363 GGTTCGAGTTGGTCTGCAAGA 60.540 52.381 0.00 0.00 43.69 3.02
2188 3070 4.348020 AGAGGTAAGGAGGAATGTACCA 57.652 45.455 0.00 0.00 38.80 3.25
2272 3154 2.433318 GAGACACTCCGGCTGCAC 60.433 66.667 0.50 0.00 0.00 4.57
2311 3193 3.769844 TGATTCCACACTTCTCCCTAGAC 59.230 47.826 0.00 0.00 0.00 2.59
2390 3272 2.656646 CACTCGGCAGGCACAGTA 59.343 61.111 0.00 0.00 0.00 2.74
2497 3379 0.757188 TGCCATTTGGGTTTGGACGT 60.757 50.000 0.00 0.00 39.65 4.34
2566 3448 0.398696 TGGCAAACCTCATGTACCGT 59.601 50.000 0.00 0.00 36.63 4.83
2602 3484 1.407437 CCACCCGGATTGAAGGAAGAG 60.407 57.143 0.73 0.00 0.00 2.85
2603 3485 0.912486 ACCCGGATTGAAGGAAGAGG 59.088 55.000 0.73 0.00 0.00 3.69
2620 3502 7.301420 AGGAAGAGGACATAGATATGACTGAA 58.699 38.462 6.84 0.00 37.15 3.02
2831 3713 5.425577 TGCGCACAACTAGACAAATAAAA 57.574 34.783 5.66 0.00 0.00 1.52
2879 3818 8.747666 TGTCGCATTTGTTACTTGAAAATAAAC 58.252 29.630 0.00 0.00 0.00 2.01
2881 3820 7.644551 TCGCATTTGTTACTTGAAAATAAACGT 59.355 29.630 0.00 0.00 0.00 3.99
2882 3821 8.893884 CGCATTTGTTACTTGAAAATAAACGTA 58.106 29.630 0.00 0.00 0.00 3.57
2918 3857 7.400599 TCACTACTGGAATTCTTGTATACGT 57.599 36.000 5.23 0.00 0.00 3.57
2983 3922 3.741344 AGCAAACTCACATACGTCAAGAC 59.259 43.478 0.00 0.00 0.00 3.01
2991 3930 5.008331 TCACATACGTCAAGACTACCTCTT 58.992 41.667 0.00 0.00 40.13 2.85
3039 3978 4.519730 ACAGGATATTGCCGAGAGTAGTAC 59.480 45.833 0.00 0.00 0.00 2.73
3060 3999 0.257328 TGGCAAAAGGGTCACACTCA 59.743 50.000 0.00 0.00 0.00 3.41
3061 4000 1.133513 TGGCAAAAGGGTCACACTCAT 60.134 47.619 0.00 0.00 0.00 2.90
3074 4013 6.038714 GGGTCACACTCATCAAATCCTATTTC 59.961 42.308 0.00 0.00 0.00 2.17
3077 4016 5.887598 CACACTCATCAAATCCTATTTCCCA 59.112 40.000 0.00 0.00 0.00 4.37
3095 4034 1.670406 AAGAGCCAAGCAGCTGTCG 60.670 57.895 16.64 3.85 45.15 4.35
3099 4038 4.081030 CCAAGCAGCTGTCGCACG 62.081 66.667 16.64 0.00 39.10 5.34
3100 4039 4.081030 CAAGCAGCTGTCGCACGG 62.081 66.667 16.64 0.00 39.10 4.94
3247 4186 4.156008 GCGGAAGGACATGTTCAAATAGTT 59.844 41.667 6.96 0.00 0.00 2.24
3267 4206 9.540538 AATAGTTAGATAGTCCAGATGCAGTAT 57.459 33.333 0.00 0.00 0.00 2.12
3311 4250 3.104512 TGTTAAGGAGATGGACCGTCAT 58.895 45.455 16.18 1.15 0.00 3.06
3325 4264 4.215399 GGACCGTCATTTTGAATCTTCACA 59.785 41.667 0.00 0.00 36.83 3.58
3388 4327 2.280797 GATGGATGCCGGCGCTTA 60.281 61.111 23.90 8.98 35.36 3.09
3479 4462 4.471025 TGAGCCATCTTCCTAATCTTCACA 59.529 41.667 0.00 0.00 0.00 3.58
3521 4548 2.447429 TCTCTGGGTATCGAGAGGGAAT 59.553 50.000 14.32 0.00 43.35 3.01
3545 4572 1.101049 CCGGTTTGTGCAGGAAGTGT 61.101 55.000 0.00 0.00 0.00 3.55
3561 4588 1.141053 AGTGTGGGTCCTGTTGTTCTC 59.859 52.381 0.00 0.00 0.00 2.87
3569 4596 3.394719 GTCCTGTTGTTCTCTTGACCTC 58.605 50.000 0.00 0.00 0.00 3.85
3591 4618 4.690748 TCGAAAATTCTCGTGCTCTCAAAT 59.309 37.500 0.37 0.00 39.84 2.32
3596 4623 1.895798 TCTCGTGCTCTCAAATGAGGT 59.104 47.619 10.37 0.00 42.30 3.85
3615 4642 3.188100 ATCGCATGACACGTGCCG 61.188 61.111 17.22 10.80 39.39 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.726438 CCTAGGTAGAAGTAATAAATTGGATGG 57.274 37.037 0.00 0.00 0.00 3.51
23 24 6.075315 TGCATGCTCCTAGGTAGAAGTAATA 58.925 40.000 20.33 0.00 0.00 0.98
31 32 6.537453 AACTATATGCATGCTCCTAGGTAG 57.463 41.667 20.33 12.71 0.00 3.18
53 54 4.463186 GTGGACTCTCAAGTAAGAGCCTAA 59.537 45.833 12.40 0.00 45.56 2.69
97 98 1.555967 TTTTTGCCTATGTGGAGGGC 58.444 50.000 0.00 0.00 45.45 5.19
98 99 2.159057 GCATTTTTGCCTATGTGGAGGG 60.159 50.000 0.00 0.00 37.06 4.30
110 111 3.871006 GCCTACCTTTATGGCATTTTTGC 59.129 43.478 4.78 0.00 45.46 3.68
118 119 5.877491 AGGTTTATAGCCTACCTTTATGGC 58.123 41.667 0.00 0.00 46.42 4.40
157 158 9.886132 TCTTCACCTTGGAAATAGATAGTTTAC 57.114 33.333 0.00 0.00 0.00 2.01
209 369 6.821665 CGAAGGTCTAACTGGAATAAATTGGA 59.178 38.462 0.00 0.00 0.00 3.53
223 383 2.913590 GCGAGTGTTACGAAGGTCTAAC 59.086 50.000 0.00 0.00 0.00 2.34
291 451 5.295787 ACACACTACAATTTTCTCGCAAAGA 59.704 36.000 0.00 0.00 0.00 2.52
319 479 2.523015 GAGAAAACATCATGCAAGCCG 58.477 47.619 0.00 0.00 0.00 5.52
320 480 2.523015 CGAGAAAACATCATGCAAGCC 58.477 47.619 0.00 0.00 0.00 4.35
332 492 2.501261 AGCACCCTTTACCGAGAAAAC 58.499 47.619 0.00 0.00 0.00 2.43
479 648 6.617289 GCATTTTATTTATGCATAGGTCGC 57.383 37.500 6.50 0.24 45.93 5.19
579 777 9.790389 CGAATAAGTTTGTCTATCTACAGAGTT 57.210 33.333 0.00 0.00 33.25 3.01
653 1444 3.827008 AGTGACAGTCTGACACACAAT 57.173 42.857 28.83 12.04 43.56 2.71
672 1554 3.134081 ACGGGTGGAGTAACATGGATTAG 59.866 47.826 0.00 0.00 0.00 1.73
685 1567 7.063074 CGCTTTTATATTATAAGACGGGTGGAG 59.937 40.741 0.00 0.00 0.00 3.86
686 1568 6.869913 CGCTTTTATATTATAAGACGGGTGGA 59.130 38.462 0.00 0.00 0.00 4.02
687 1569 6.647895 ACGCTTTTATATTATAAGACGGGTGG 59.352 38.462 14.14 0.00 0.00 4.61
688 1570 7.647907 ACGCTTTTATATTATAAGACGGGTG 57.352 36.000 14.14 7.11 0.00 4.61
689 1571 8.667076 AAACGCTTTTATATTATAAGACGGGT 57.333 30.769 14.14 10.12 0.00 5.28
690 1572 9.940166 AAAAACGCTTTTATATTATAAGACGGG 57.060 29.630 14.14 9.71 32.85 5.28
699 1581 9.549509 CACTAGTGCAAAAACGCTTTTATATTA 57.450 29.630 10.54 0.00 32.85 0.98
700 1582 8.079809 ACACTAGTGCAAAAACGCTTTTATATT 58.920 29.630 22.90 0.00 32.85 1.28
701 1583 7.590279 ACACTAGTGCAAAAACGCTTTTATAT 58.410 30.769 22.90 0.00 32.85 0.86
702 1584 6.961576 ACACTAGTGCAAAAACGCTTTTATA 58.038 32.000 22.90 0.00 32.85 0.98
703 1585 5.827666 ACACTAGTGCAAAAACGCTTTTAT 58.172 33.333 22.90 0.00 32.85 1.40
704 1586 5.238006 ACACTAGTGCAAAAACGCTTTTA 57.762 34.783 22.90 0.00 32.85 1.52
705 1587 4.104696 ACACTAGTGCAAAAACGCTTTT 57.895 36.364 22.90 0.00 35.02 2.27
706 1588 3.775661 ACACTAGTGCAAAAACGCTTT 57.224 38.095 22.90 0.00 0.00 3.51
707 1589 4.886247 TTACACTAGTGCAAAAACGCTT 57.114 36.364 22.90 1.70 0.00 4.68
708 1590 6.370442 TGATATTACACTAGTGCAAAAACGCT 59.630 34.615 22.90 2.88 0.00 5.07
709 1591 6.539324 TGATATTACACTAGTGCAAAAACGC 58.461 36.000 22.90 6.53 0.00 4.84
710 1592 8.942669 TTTGATATTACACTAGTGCAAAAACG 57.057 30.769 22.90 0.00 0.00 3.60
746 1628 9.790297 ACATGTACTTCCTCCATCCTATAATAT 57.210 33.333 0.00 0.00 0.00 1.28
747 1629 9.256228 GACATGTACTTCCTCCATCCTATAATA 57.744 37.037 0.00 0.00 0.00 0.98
748 1630 7.181125 GGACATGTACTTCCTCCATCCTATAAT 59.819 40.741 0.00 0.00 0.00 1.28
749 1631 6.497259 GGACATGTACTTCCTCCATCCTATAA 59.503 42.308 0.00 0.00 0.00 0.98
750 1632 6.017192 GGACATGTACTTCCTCCATCCTATA 58.983 44.000 0.00 0.00 0.00 1.31
751 1633 4.841246 GGACATGTACTTCCTCCATCCTAT 59.159 45.833 0.00 0.00 0.00 2.57
752 1634 4.223953 GGACATGTACTTCCTCCATCCTA 58.776 47.826 0.00 0.00 0.00 2.94
753 1635 3.041946 GGACATGTACTTCCTCCATCCT 58.958 50.000 0.00 0.00 0.00 3.24
754 1636 2.771943 TGGACATGTACTTCCTCCATCC 59.228 50.000 10.05 0.00 32.55 3.51
755 1637 4.696479 ATGGACATGTACTTCCTCCATC 57.304 45.455 10.05 0.00 37.16 3.51
756 1638 5.467738 TCTATGGACATGTACTTCCTCCAT 58.532 41.667 10.05 13.12 42.99 3.41
757 1639 4.878968 TCTATGGACATGTACTTCCTCCA 58.121 43.478 10.05 6.12 35.49 3.86
758 1640 5.777732 AGATCTATGGACATGTACTTCCTCC 59.222 44.000 10.05 0.00 32.55 4.30
759 1641 6.909550 AGATCTATGGACATGTACTTCCTC 57.090 41.667 10.05 1.55 32.55 3.71
760 1642 6.042552 CCAAGATCTATGGACATGTACTTCCT 59.957 42.308 10.05 0.00 40.56 3.36
761 1643 6.226787 CCAAGATCTATGGACATGTACTTCC 58.773 44.000 10.05 1.65 40.56 3.46
762 1644 6.226787 CCCAAGATCTATGGACATGTACTTC 58.773 44.000 19.56 0.00 40.56 3.01
763 1645 5.455326 GCCCAAGATCTATGGACATGTACTT 60.455 44.000 19.56 5.58 40.56 2.24
764 1646 4.040952 GCCCAAGATCTATGGACATGTACT 59.959 45.833 19.56 0.00 40.56 2.73
765 1647 4.040952 AGCCCAAGATCTATGGACATGTAC 59.959 45.833 19.56 0.00 40.56 2.90
766 1648 4.234550 AGCCCAAGATCTATGGACATGTA 58.765 43.478 19.56 0.00 40.56 2.29
767 1649 3.051581 AGCCCAAGATCTATGGACATGT 58.948 45.455 19.56 0.00 40.56 3.21
803 1685 0.319040 TAGCTTCTCCATCGATGCGC 60.319 55.000 20.25 14.86 38.62 6.09
827 1709 6.147864 TCCTTCAATTATAATTGGCTGTGC 57.852 37.500 29.22 0.00 44.51 4.57
897 1779 4.623932 TTTATAGCCCAAGATCGATGCT 57.376 40.909 0.54 7.60 36.11 3.79
935 1817 0.401738 TGGCTGTGAGGCTTAGCTTT 59.598 50.000 15.65 0.00 41.96 3.51
1073 1955 2.435059 GGGAGAAGAGCACCGCAC 60.435 66.667 0.00 0.00 0.00 5.34
1224 2106 3.217743 GCGAGGGAGACGTAGGGG 61.218 72.222 0.00 0.00 0.00 4.79
1464 2346 2.669569 AGCATGTGCACCGTCACC 60.670 61.111 15.69 0.00 45.16 4.02
1520 2402 2.279073 CTAGCCGGACCTCCTCCA 59.721 66.667 5.05 0.00 39.39 3.86
1883 2765 2.760374 AGTCTTTGTCTTCCTCTTGCG 58.240 47.619 0.00 0.00 0.00 4.85
1890 2772 3.365220 CGTCGATGAAGTCTTTGTCTTCC 59.635 47.826 0.00 0.00 40.10 3.46
2188 3070 0.673644 CGACCATCTCTTGCCCGTTT 60.674 55.000 0.00 0.00 0.00 3.60
2272 3154 2.838225 ATGAGAGGTACCGGCGGG 60.838 66.667 31.78 12.53 40.11 6.13
2311 3193 3.803082 CCATCAACGGTGCAGGCG 61.803 66.667 0.00 0.00 0.00 5.52
2390 3272 6.916360 TTCATTTTCATTTTCCCAGTAGCT 57.084 33.333 0.00 0.00 0.00 3.32
2497 3379 0.623723 GAACCCCAGGGCACATTCTA 59.376 55.000 0.00 0.00 39.32 2.10
2602 3484 7.225538 CCAAACACTTCAGTCATATCTATGTCC 59.774 40.741 0.00 0.00 35.26 4.02
2603 3485 7.981789 TCCAAACACTTCAGTCATATCTATGTC 59.018 37.037 0.00 0.00 35.26 3.06
2620 3502 7.639113 TCTTGAAACTGTTATTCCAAACACT 57.361 32.000 0.00 0.00 35.56 3.55
2831 3713 9.393249 CGACAACATACATAAAAACAATTCACT 57.607 29.630 0.00 0.00 0.00 3.41
2849 3731 5.431420 TCAAGTAACAAATGCGACAACAT 57.569 34.783 0.00 0.00 0.00 2.71
2908 3847 2.479049 CCTGACACCCGACGTATACAAG 60.479 54.545 3.32 0.00 0.00 3.16
2910 3849 1.097232 CCTGACACCCGACGTATACA 58.903 55.000 3.32 0.00 0.00 2.29
2918 3857 2.636412 CGAAGAGCCTGACACCCGA 61.636 63.158 0.00 0.00 0.00 5.14
2991 3930 2.644418 GCGATGTGCTTGTTGCCA 59.356 55.556 0.00 0.00 42.00 4.92
3007 3946 1.798813 GCAATATCCTGTGTTTGCCGC 60.799 52.381 0.00 0.00 38.77 6.53
3039 3978 1.338020 GAGTGTGACCCTTTTGCCAAG 59.662 52.381 0.00 0.00 0.00 3.61
3060 3999 5.143369 GGCTCTTGGGAAATAGGATTTGAT 58.857 41.667 0.00 0.00 0.00 2.57
3061 4000 4.017591 TGGCTCTTGGGAAATAGGATTTGA 60.018 41.667 0.00 0.00 0.00 2.69
3074 4013 2.035312 AGCTGCTTGGCTCTTGGG 59.965 61.111 0.00 0.00 38.24 4.12
3077 4016 1.670406 CGACAGCTGCTTGGCTCTT 60.670 57.895 15.27 0.00 41.00 2.85
3150 4089 1.968493 TCTCGGCAAAGAAGTACCACT 59.032 47.619 0.00 0.00 0.00 4.00
3226 4165 8.738645 ATCTAACTATTTGAACATGTCCTTCC 57.261 34.615 0.00 0.00 0.00 3.46
3247 4186 5.651387 GCATACTGCATCTGGACTATCTA 57.349 43.478 0.00 0.00 44.26 1.98
3267 4206 4.284490 AGGAGTGTAATGAAGACTGAAGCA 59.716 41.667 0.00 0.00 30.33 3.91
3273 4212 6.497259 TCCTTAACAGGAGTGTAATGAAGACT 59.503 38.462 0.00 0.00 45.20 3.24
3307 4246 6.095377 GGGACATGTGAAGATTCAAAATGAC 58.905 40.000 18.99 14.70 39.21 3.06
3311 4250 3.505680 CCGGGACATGTGAAGATTCAAAA 59.494 43.478 1.15 0.00 39.21 2.44
3325 4264 0.692419 ATCTTCTCTGCCCGGGACAT 60.692 55.000 29.31 1.62 0.00 3.06
3450 4389 9.950496 GAAGATTAGGAAGATGGCTCAATAATA 57.050 33.333 0.00 0.00 0.00 0.98
3454 4393 6.060788 GTGAAGATTAGGAAGATGGCTCAAT 58.939 40.000 0.00 0.00 0.00 2.57
3479 4462 4.020485 AGACTAGGTTTACAAGCGGAACAT 60.020 41.667 0.00 0.00 0.00 2.71
3521 4548 1.821759 CCTGCACAAACCGGACACA 60.822 57.895 9.46 0.00 0.00 3.72
3545 4572 2.123589 TCAAGAGAACAACAGGACCCA 58.876 47.619 0.00 0.00 0.00 4.51
3561 4588 3.423645 GCACGAGAATTTTCGAGGTCAAG 60.424 47.826 23.51 6.50 43.03 3.02
3569 4596 4.389664 TTTGAGAGCACGAGAATTTTCG 57.610 40.909 16.10 16.10 45.70 3.46
3596 4623 2.100031 GGCACGTGTCATGCGATGA 61.100 57.895 16.80 0.00 44.37 2.92
3631 4658 1.815613 CAAATATTGCACGTGGGTCCA 59.184 47.619 18.88 3.30 0.00 4.02


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

AutoCloner maintained by Alex Coulton.