Multiple sequence alignment - TraesCS2B01G202700

Loading Multiple Alignment...

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 TraesCS2B01G202700 chr2B 100.000 3679 0 0 1 3679 182568319 182571997 0.000000e+00 6794
1 TraesCS2B01G202700 chr2A 93.968 2039 68 18 758 2782 135884570 135886567 0.000000e+00 3033
2 TraesCS2B01G202700 chr2A 91.203 557 41 5 3131 3679 135886893 135887449 0.000000e+00 750
3 TraesCS2B01G202700 chr2A 91.164 464 22 10 231 690 135883799 135884247 2.430000e-171 612
4 TraesCS2B01G202700 chr2A 96.465 198 7 0 2808 3005 135886559 135886756 9.850000e-86 327
5 TraesCS2B01G202700 chr2A 92.754 69 3 1 3040 3106 135886825 135886893 8.410000e-17 99
6 TraesCS2B01G202700 chr2D 91.142 2066 94 38 1 2023 128962992 128965011 0.000000e+00 2719
7 TraesCS2B01G202700 chr2D 89.838 1358 44 42 2022 3338 128965060 128966364 0.000000e+00 1657
8 TraesCS2B01G202700 chr2D 93.785 354 13 3 3330 3679 128971511 128971859 1.170000e-144 523
9 TraesCS2B01G202700 chr4D 91.026 234 20 1 1076 1308 17743909 17743676 7.670000e-82 315


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 TraesCS2B01G202700 chr2B 182568319 182571997 3678 False 6794.0 6794 100.0000 1 3679 1 chr2B.!!$F1 3678
1 TraesCS2B01G202700 chr2A 135883799 135887449 3650 False 964.2 3033 93.1108 231 3679 5 chr2A.!!$F1 3448
2 TraesCS2B01G202700 chr2D 128962992 128966364 3372 False 2188.0 2719 90.4900 1 3338 2 chr2D.!!$F2 3337

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
232 233 0.169672 CCTTTCTGATGCGTGCAAGG 59.830 55.0 0.79 0.00 0.00 3.61 F
926 1195 0.611896 AATTTGGCCGTCCTTGGAGG 60.612 55.0 0.00 2.63 36.46 4.30 F
1965 2252 0.176910 GCTGTTGCTCCTAGGGTCTC 59.823 60.0 9.46 0.00 36.03 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1790 0.039180 TCGAGTGGTAGGGAAGCTGA 59.961 55.0 0.00 0.00 0.00 4.26 R
2023 2310 0.524862 CCCTGACGCTACGTAACTGT 59.475 55.0 0.00 0.00 41.37 3.55 R
3374 3762 0.168128 GTCAAGATCCCCAAAACGCG 59.832 55.0 3.53 3.53 0.00 6.01 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
39 40 2.946762 GGCACGTCTTCAACAGGC 59.053 61.111 0.00 0.00 0.00 4.85
40 41 1.891919 GGCACGTCTTCAACAGGCA 60.892 57.895 0.00 0.00 0.00 4.75
43 44 1.229428 CACGTCTTCAACAGGCACAT 58.771 50.000 0.00 0.00 0.00 3.21
44 45 1.603802 CACGTCTTCAACAGGCACATT 59.396 47.619 0.00 0.00 0.00 2.71
52 53 6.417930 GTCTTCAACAGGCACATTAAGAAAAC 59.582 38.462 0.00 0.00 0.00 2.43
53 54 4.854399 TCAACAGGCACATTAAGAAAACG 58.146 39.130 0.00 0.00 0.00 3.60
54 55 3.915437 ACAGGCACATTAAGAAAACGG 57.085 42.857 0.00 0.00 0.00 4.44
76 77 5.180492 CGGTGCTGATTTTTGTAAGGACTTA 59.820 40.000 0.00 0.00 32.23 2.24
81 82 7.284489 TGCTGATTTTTGTAAGGACTTAACTGT 59.716 33.333 0.00 0.00 0.00 3.55
95 96 7.550906 AGGACTTAACTGTAATTTCTCATGCTC 59.449 37.037 0.00 0.00 0.00 4.26
104 105 8.437360 TGTAATTTCTCATGCTCGTAAATGAT 57.563 30.769 0.00 0.00 32.56 2.45
105 106 9.541143 TGTAATTTCTCATGCTCGTAAATGATA 57.459 29.630 0.00 0.00 32.56 2.15
197 198 5.338614 CACTTTTGAGTAAAGGGTACACG 57.661 43.478 0.00 0.00 46.16 4.49
198 199 5.051816 CACTTTTGAGTAAAGGGTACACGA 58.948 41.667 0.00 0.00 46.16 4.35
199 200 5.524646 CACTTTTGAGTAAAGGGTACACGAA 59.475 40.000 0.00 0.00 46.16 3.85
200 201 6.204108 CACTTTTGAGTAAAGGGTACACGAAT 59.796 38.462 0.00 0.00 46.16 3.34
201 202 6.204108 ACTTTTGAGTAAAGGGTACACGAATG 59.796 38.462 0.00 0.00 46.16 2.67
222 223 2.488153 GTGCCGTTTAAGCCTTTCTGAT 59.512 45.455 0.00 0.00 0.00 2.90
230 231 0.890542 AGCCTTTCTGATGCGTGCAA 60.891 50.000 0.00 0.00 0.00 4.08
232 233 0.169672 CCTTTCTGATGCGTGCAAGG 59.830 55.000 0.79 0.00 0.00 3.61
243 244 6.898041 TGATGCGTGCAAGGATTATTTATAC 58.102 36.000 8.20 0.00 0.00 1.47
247 248 5.334879 GCGTGCAAGGATTATTTATACCCAG 60.335 44.000 0.79 0.00 0.00 4.45
251 252 6.782000 TGCAAGGATTATTTATACCCAGCAAT 59.218 34.615 0.00 0.00 32.66 3.56
288 294 9.151471 GGTGCGTATAGATACAATCATACAAAT 57.849 33.333 0.89 0.00 32.87 2.32
417 426 2.335369 GCCTCGACACGTCACACT 59.665 61.111 0.00 0.00 0.00 3.55
429 438 1.343465 CGTCACACTTCCCCAAGTACT 59.657 52.381 0.00 0.00 41.24 2.73
430 439 2.609737 CGTCACACTTCCCCAAGTACTC 60.610 54.545 0.00 0.00 41.24 2.59
434 443 1.916181 CACTTCCCCAAGTACTCCCAT 59.084 52.381 0.00 0.00 41.24 4.00
453 462 3.534054 TACCAACCGCGGTCCCAAC 62.534 63.158 34.29 0.00 40.67 3.77
700 719 1.063183 CTCCTCTCCATTCCCATCCC 58.937 60.000 0.00 0.00 0.00 3.85
717 737 4.179599 CCCCTCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
721 741 2.018086 CTCTCCCTCCCTCCCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
738 758 2.044352 TCGCTCGAGGATCCCACA 60.044 61.111 15.58 0.00 0.00 4.17
742 762 3.432051 CTCGAGGATCCCACACGCC 62.432 68.421 8.55 0.00 0.00 5.68
743 763 4.873129 CGAGGATCCCACACGCCG 62.873 72.222 8.55 0.00 0.00 6.46
926 1195 0.611896 AATTTGGCCGTCCTTGGAGG 60.612 55.000 0.00 2.63 36.46 4.30
986 1255 3.118665 GGAATTGCTTGCTCTCTCTCTCT 60.119 47.826 0.00 0.00 0.00 3.10
987 1256 3.806625 ATTGCTTGCTCTCTCTCTCTC 57.193 47.619 0.00 0.00 0.00 3.20
1199 1470 3.536917 CTCCCTCGCCGCCATGTA 61.537 66.667 0.00 0.00 0.00 2.29
1477 1748 2.203523 TCGTCGACCAGGGGAACA 60.204 61.111 10.58 0.00 0.00 3.18
1519 1790 5.195940 AGCAAGGTATACACATGCTTTCAT 58.804 37.500 18.20 2.95 43.06 2.57
1530 1801 3.054139 ACATGCTTTCATCAGCTTCCCTA 60.054 43.478 0.00 0.00 40.79 3.53
1532 1803 2.293170 GCTTTCATCAGCTTCCCTACC 58.707 52.381 0.00 0.00 36.79 3.18
1537 1808 1.115467 ATCAGCTTCCCTACCACTCG 58.885 55.000 0.00 0.00 0.00 4.18
1542 1813 1.404315 GCTTCCCTACCACTCGAACTG 60.404 57.143 0.00 0.00 0.00 3.16
1554 1825 4.688879 CCACTCGAACTGTTTGCTACAATA 59.311 41.667 2.78 0.00 36.02 1.90
1583 1854 2.851263 TTCCCACTGTTCTATTGCGT 57.149 45.000 0.00 0.00 0.00 5.24
1585 1856 2.695359 TCCCACTGTTCTATTGCGTTC 58.305 47.619 0.00 0.00 0.00 3.95
1618 1889 4.970662 TTATTCATTCAGCTGCCTGTTC 57.029 40.909 9.47 0.00 40.09 3.18
1619 1890 2.574006 TTCATTCAGCTGCCTGTTCT 57.426 45.000 9.47 0.00 40.09 3.01
1620 1891 1.817357 TCATTCAGCTGCCTGTTCTG 58.183 50.000 9.47 0.00 40.09 3.02
1621 1892 0.809385 CATTCAGCTGCCTGTTCTGG 59.191 55.000 9.47 0.00 40.09 3.86
1622 1893 0.403271 ATTCAGCTGCCTGTTCTGGT 59.597 50.000 9.47 0.00 40.09 4.00
1623 1894 0.183492 TTCAGCTGCCTGTTCTGGTT 59.817 50.000 9.47 0.00 40.09 3.67
1624 1895 0.535780 TCAGCTGCCTGTTCTGGTTG 60.536 55.000 9.47 0.00 40.09 3.77
1625 1896 1.900498 AGCTGCCTGTTCTGGTTGC 60.900 57.895 0.00 3.32 0.00 4.17
1626 1897 2.924105 GCTGCCTGTTCTGGTTGCC 61.924 63.158 0.00 0.00 0.00 4.52
1822 2093 4.872691 TGCTTTTCTTTTTCGCCAAATTCA 59.127 33.333 0.00 0.00 0.00 2.57
1965 2252 0.176910 GCTGTTGCTCCTAGGGTCTC 59.823 60.000 9.46 0.00 36.03 3.36
2082 2419 4.768130 TCATTATCCGAGCAGCTACTAC 57.232 45.455 0.00 0.00 0.00 2.73
2083 2420 4.399219 TCATTATCCGAGCAGCTACTACT 58.601 43.478 0.00 0.00 0.00 2.57
2084 2421 5.557866 TCATTATCCGAGCAGCTACTACTA 58.442 41.667 0.00 0.00 0.00 1.82
2086 2423 6.489022 TCATTATCCGAGCAGCTACTACTAAA 59.511 38.462 0.00 0.00 0.00 1.85
2087 2424 6.896021 TTATCCGAGCAGCTACTACTAAAT 57.104 37.500 0.00 0.00 0.00 1.40
2088 2425 7.991084 TTATCCGAGCAGCTACTACTAAATA 57.009 36.000 0.00 0.00 0.00 1.40
2089 2426 8.577048 TTATCCGAGCAGCTACTACTAAATAT 57.423 34.615 0.00 0.00 0.00 1.28
2090 2427 9.676861 TTATCCGAGCAGCTACTACTAAATATA 57.323 33.333 0.00 0.00 0.00 0.86
2091 2428 7.991084 TCCGAGCAGCTACTACTAAATATAA 57.009 36.000 0.00 0.00 0.00 0.98
2092 2429 8.041829 TCCGAGCAGCTACTACTAAATATAAG 57.958 38.462 0.00 0.00 0.00 1.73
2215 2556 7.814264 ATATGAAAATGTGACATCTTCTCCC 57.186 36.000 12.34 0.00 0.00 4.30
2321 2662 0.963962 ATGCCAGCAACCAGAACAAG 59.036 50.000 0.00 0.00 0.00 3.16
2426 2770 2.504899 CTGACGATGCGCACGACT 60.505 61.111 29.62 10.05 34.70 4.18
2570 2914 0.179073 GGATAGTGTGCGTCTGCCAT 60.179 55.000 0.00 0.00 41.78 4.40
2658 3002 2.092291 CACATCGTCGTCAACCCCG 61.092 63.158 0.00 0.00 0.00 5.73
2681 3025 2.929592 GCCGTCGGTCTTCTTGTAATGT 60.930 50.000 13.94 0.00 0.00 2.71
2707 3054 2.224077 TGTACCTAGGGGGAGAGATGT 58.776 52.381 14.81 0.00 38.76 3.06
2906 3253 3.573967 TGGATATGCTGCTTCAGTCGATA 59.426 43.478 0.00 0.00 33.43 2.92
2917 3264 2.202703 GTCGATACGCGTGGCCTT 60.203 61.111 24.59 0.58 41.80 4.35
2963 3312 2.115343 AGGAGAAGTCGATTTTGCCC 57.885 50.000 8.47 4.64 0.00 5.36
2985 3334 5.021458 CCTGTTCAGTTACCCCTTACTCTA 58.979 45.833 0.00 0.00 0.00 2.43
3008 3357 0.719465 GCGTATCAACTCCAACACCG 59.281 55.000 0.00 0.00 0.00 4.94
3010 3359 2.671914 GCGTATCAACTCCAACACCGTA 60.672 50.000 0.00 0.00 0.00 4.02
3012 3361 3.612241 CGTATCAACTCCAACACCGTACA 60.612 47.826 0.00 0.00 0.00 2.90
3013 3362 2.983907 TCAACTCCAACACCGTACAA 57.016 45.000 0.00 0.00 0.00 2.41
3015 3364 3.395639 TCAACTCCAACACCGTACAATC 58.604 45.455 0.00 0.00 0.00 2.67
3016 3365 3.135225 CAACTCCAACACCGTACAATCA 58.865 45.455 0.00 0.00 0.00 2.57
3017 3366 3.040147 ACTCCAACACCGTACAATCAG 57.960 47.619 0.00 0.00 0.00 2.90
3019 3368 3.260884 ACTCCAACACCGTACAATCAGAT 59.739 43.478 0.00 0.00 0.00 2.90
3020 3369 4.253685 CTCCAACACCGTACAATCAGATT 58.746 43.478 0.00 0.00 0.00 2.40
3021 3370 4.000325 TCCAACACCGTACAATCAGATTG 59.000 43.478 19.93 19.93 45.59 2.67
3036 3385 7.825681 CAATCAGATTGTGTAATTGGTTGGTA 58.174 34.615 14.28 0.00 35.57 3.25
3037 3386 8.303156 CAATCAGATTGTGTAATTGGTTGGTAA 58.697 33.333 14.28 0.00 35.57 2.85
3091 3474 3.376546 TGGTTTGCAAGGAACAAAAATGC 59.623 39.130 0.00 0.00 38.64 3.56
3098 3481 4.445385 GCAAGGAACAAAAATGCACAGTAG 59.555 41.667 0.00 0.00 37.00 2.57
3100 3483 6.734137 CAAGGAACAAAAATGCACAGTAGTA 58.266 36.000 0.00 0.00 0.00 1.82
3101 3484 6.560253 AGGAACAAAAATGCACAGTAGTAG 57.440 37.500 0.00 0.00 0.00 2.57
3103 3486 6.770785 AGGAACAAAAATGCACAGTAGTAGAA 59.229 34.615 0.00 0.00 0.00 2.10
3105 3488 8.082242 GGAACAAAAATGCACAGTAGTAGAAAT 58.918 33.333 0.00 0.00 0.00 2.17
3112 3495 8.792830 AATGCACAGTAGTAGAAATATGTTGT 57.207 30.769 0.00 0.00 0.00 3.32
3113 3496 7.595311 TGCACAGTAGTAGAAATATGTTGTG 57.405 36.000 0.00 0.00 37.16 3.33
3114 3497 6.593770 TGCACAGTAGTAGAAATATGTTGTGG 59.406 38.462 0.00 0.00 35.27 4.17
3115 3498 6.037172 GCACAGTAGTAGAAATATGTTGTGGG 59.963 42.308 0.00 0.00 35.27 4.61
3116 3499 6.037172 CACAGTAGTAGAAATATGTTGTGGGC 59.963 42.308 0.00 0.00 32.11 5.36
3117 3500 5.234329 CAGTAGTAGAAATATGTTGTGGGCG 59.766 44.000 0.00 0.00 0.00 6.13
3118 3501 4.216411 AGTAGAAATATGTTGTGGGCGT 57.784 40.909 0.00 0.00 0.00 5.68
3119 3502 4.189231 AGTAGAAATATGTTGTGGGCGTC 58.811 43.478 0.00 0.00 0.00 5.19
3120 3503 2.006888 AGAAATATGTTGTGGGCGTCG 58.993 47.619 0.00 0.00 0.00 5.12
3121 3504 1.735571 GAAATATGTTGTGGGCGTCGT 59.264 47.619 0.00 0.00 0.00 4.34
3122 3505 1.365699 AATATGTTGTGGGCGTCGTC 58.634 50.000 0.00 0.00 0.00 4.20
3123 3506 0.248012 ATATGTTGTGGGCGTCGTCA 59.752 50.000 0.00 0.00 0.00 4.35
3124 3507 0.248012 TATGTTGTGGGCGTCGTCAT 59.752 50.000 0.00 0.00 0.00 3.06
3125 3508 1.019278 ATGTTGTGGGCGTCGTCATC 61.019 55.000 0.00 0.00 0.00 2.92
3126 3509 1.374252 GTTGTGGGCGTCGTCATCT 60.374 57.895 0.00 0.00 0.00 2.90
3127 3510 0.949105 GTTGTGGGCGTCGTCATCTT 60.949 55.000 0.00 0.00 0.00 2.40
3128 3511 0.669318 TTGTGGGCGTCGTCATCTTC 60.669 55.000 0.00 0.00 0.00 2.87
3129 3512 2.158959 GTGGGCGTCGTCATCTTCG 61.159 63.158 0.00 0.00 0.00 3.79
3150 3533 8.076781 TCTTCGTCTCCAATATTTCTCTATTCG 58.923 37.037 0.00 0.00 0.00 3.34
3168 3551 9.144747 CTCTATTCGATGACTTCTTTTCAAGAA 57.855 33.333 0.00 0.00 44.82 2.52
3189 3572 2.432756 TGGACCTAGATCCACCCCT 58.567 57.895 0.00 0.00 44.14 4.79
3264 3652 1.895131 ACCAATGAGAATTGTGGTGGC 59.105 47.619 0.00 0.00 42.79 5.01
3275 3663 1.190643 TGTGGTGGCTCATATGTCGA 58.809 50.000 1.90 0.00 0.00 4.20
3421 3809 7.848223 ATTGGTATAACTGGTAAACGGTAAC 57.152 36.000 0.00 0.00 37.84 2.50
3492 3880 3.372206 AGTCGTAGCAATCTGTCATTTGC 59.628 43.478 11.00 11.00 46.68 3.68
3520 3912 3.005791 GCTCTCTCTTCTTATGCTCCTCC 59.994 52.174 0.00 0.00 0.00 4.30
3521 3913 4.214310 CTCTCTCTTCTTATGCTCCTCCA 58.786 47.826 0.00 0.00 0.00 3.86
3527 3919 1.615883 TCTTATGCTCCTCCATCGCTC 59.384 52.381 0.00 0.00 0.00 5.03
3532 3924 1.977293 GCTCCTCCATCGCTCCCTTT 61.977 60.000 0.00 0.00 0.00 3.11
3535 3927 1.341156 CCTCCATCGCTCCCTTTCCT 61.341 60.000 0.00 0.00 0.00 3.36
3552 3944 0.601558 CCTTTCTTGTCCTCGACCGA 59.398 55.000 0.00 0.00 0.00 4.69
3572 3964 3.623703 GAGGGGCGGAGTGGGTTTC 62.624 68.421 0.00 0.00 0.00 2.78
3574 3966 4.735358 GGGCGGAGTGGGTTTCCC 62.735 72.222 0.00 0.00 45.71 3.97
3575 3967 3.647771 GGCGGAGTGGGTTTCCCT 61.648 66.667 6.38 0.00 45.70 4.20
3576 3968 2.434774 GCGGAGTGGGTTTCCCTT 59.565 61.111 6.38 0.00 45.70 3.95
3577 3969 1.971695 GCGGAGTGGGTTTCCCTTG 60.972 63.158 6.38 0.00 45.70 3.61
3578 3970 1.758592 CGGAGTGGGTTTCCCTTGA 59.241 57.895 6.38 0.00 45.70 3.02
3596 3990 2.790433 TGAGGGACTAATGTGTTTGCC 58.210 47.619 0.00 0.00 41.55 4.52
3599 3993 1.202348 GGGACTAATGTGTTTGCCAGC 59.798 52.381 0.00 0.00 0.00 4.85
3603 3997 4.339247 GGACTAATGTGTTTGCCAGCATAT 59.661 41.667 0.00 0.00 0.00 1.78
3617 4011 6.049149 TGCCAGCATATACAAGAAGTAAGTC 58.951 40.000 0.00 0.00 36.05 3.01
3618 4012 5.467063 GCCAGCATATACAAGAAGTAAGTCC 59.533 44.000 0.00 0.00 36.05 3.85
3620 4014 5.992217 CAGCATATACAAGAAGTAAGTCCCC 59.008 44.000 0.00 0.00 36.05 4.81
3621 4015 4.989168 GCATATACAAGAAGTAAGTCCCCG 59.011 45.833 0.00 0.00 36.05 5.73
3638 4032 2.166664 CCCCGAGGAGTTAAGAGAAGTG 59.833 54.545 0.00 0.00 33.47 3.16
3648 4042 4.101741 AGTTAAGAGAAGTGTGCTGGAGTT 59.898 41.667 0.00 0.00 0.00 3.01
3651 4045 4.199432 AGAGAAGTGTGCTGGAGTTATG 57.801 45.455 0.00 0.00 0.00 1.90
3661 4055 3.135348 TGCTGGAGTTATGGAGGAGATTG 59.865 47.826 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.967319 AATGTGCCTGTTGAAGACGT 58.033 45.000 0.00 0.00 0.00 4.34
27 28 5.689383 TTCTTAATGTGCCTGTTGAAGAC 57.311 39.130 0.00 0.00 0.00 3.01
28 29 6.503524 GTTTTCTTAATGTGCCTGTTGAAGA 58.496 36.000 0.00 0.00 0.00 2.87
33 34 3.634910 ACCGTTTTCTTAATGTGCCTGTT 59.365 39.130 0.00 0.00 0.00 3.16
35 36 3.564511 CACCGTTTTCTTAATGTGCCTG 58.435 45.455 0.00 0.00 0.00 4.85
36 37 2.030274 GCACCGTTTTCTTAATGTGCCT 60.030 45.455 0.00 0.00 42.33 4.75
38 39 2.979813 CAGCACCGTTTTCTTAATGTGC 59.020 45.455 4.37 4.37 47.00 4.57
39 40 4.481930 TCAGCACCGTTTTCTTAATGTG 57.518 40.909 0.00 0.00 0.00 3.21
40 41 5.705609 AATCAGCACCGTTTTCTTAATGT 57.294 34.783 0.00 0.00 0.00 2.71
43 44 6.334202 ACAAAAATCAGCACCGTTTTCTTAA 58.666 32.000 0.00 0.00 0.00 1.85
44 45 5.897050 ACAAAAATCAGCACCGTTTTCTTA 58.103 33.333 0.00 0.00 0.00 2.10
52 53 3.502211 AGTCCTTACAAAAATCAGCACCG 59.498 43.478 0.00 0.00 0.00 4.94
53 54 5.453567 AAGTCCTTACAAAAATCAGCACC 57.546 39.130 0.00 0.00 0.00 5.01
54 55 7.591426 CAGTTAAGTCCTTACAAAAATCAGCAC 59.409 37.037 0.00 0.00 0.00 4.40
76 77 7.667043 TTTACGAGCATGAGAAATTACAGTT 57.333 32.000 0.00 0.00 0.00 3.16
131 132 7.959658 TCCAAAATGGTCAAAGATCACATAT 57.040 32.000 0.00 0.00 39.03 1.78
167 168 7.993101 ACCCTTTACTCAAAAGTGTAGAAAAC 58.007 34.615 0.00 0.00 42.68 2.43
174 175 4.812626 CGTGTACCCTTTACTCAAAAGTGT 59.187 41.667 0.00 0.00 42.68 3.55
175 176 5.051816 TCGTGTACCCTTTACTCAAAAGTG 58.948 41.667 0.00 0.00 42.68 3.16
190 191 0.869730 AAACGGCACATTCGTGTACC 59.130 50.000 0.00 0.00 45.50 3.34
196 197 0.802494 AGGCTTAAACGGCACATTCG 59.198 50.000 0.00 0.00 0.00 3.34
197 198 3.057526 AGAAAGGCTTAAACGGCACATTC 60.058 43.478 0.00 0.00 0.00 2.67
198 199 2.890945 AGAAAGGCTTAAACGGCACATT 59.109 40.909 0.00 0.00 0.00 2.71
199 200 2.228822 CAGAAAGGCTTAAACGGCACAT 59.771 45.455 0.00 0.00 0.00 3.21
200 201 1.606668 CAGAAAGGCTTAAACGGCACA 59.393 47.619 0.00 0.00 0.00 4.57
201 202 1.877443 TCAGAAAGGCTTAAACGGCAC 59.123 47.619 0.00 0.00 0.00 5.01
222 223 4.517453 GGGTATAAATAATCCTTGCACGCA 59.483 41.667 0.00 0.00 0.00 5.24
243 244 2.158667 ACCTCCGGTAAATATTGCTGGG 60.159 50.000 0.00 4.57 41.58 4.45
247 248 1.263217 CGCACCTCCGGTAAATATTGC 59.737 52.381 0.00 1.16 32.11 3.56
251 252 4.397420 TCTATACGCACCTCCGGTAAATA 58.603 43.478 0.00 0.00 32.11 1.40
308 314 9.849752 TCCCTCCATACTATACTTCTACTAGTA 57.150 37.037 1.89 1.89 35.25 1.82
311 317 8.381636 GTGTCCCTCCATACTATACTTCTACTA 58.618 40.741 0.00 0.00 0.00 1.82
324 330 1.153429 GTGCGGTGTCCCTCCATAC 60.153 63.158 0.00 0.00 0.00 2.39
326 332 4.082523 CGTGCGGTGTCCCTCCAT 62.083 66.667 0.00 0.00 0.00 3.41
417 426 2.848071 GGTAATGGGAGTACTTGGGGAA 59.152 50.000 0.00 0.00 0.00 3.97
429 438 2.269562 CCGCGGTTGGTAATGGGA 59.730 61.111 19.50 0.00 0.00 4.37
430 439 2.045731 ACCGCGGTTGGTAATGGG 60.046 61.111 28.70 0.00 41.55 4.00
434 443 2.815945 TTGGGACCGCGGTTGGTAA 61.816 57.895 34.65 21.33 44.01 2.85
591 600 7.934120 TCCATTAAACCGAAATTGTTTGGAAAT 59.066 29.630 0.00 0.00 40.45 2.17
593 602 6.817184 TCCATTAAACCGAAATTGTTTGGAA 58.183 32.000 0.00 0.00 40.45 3.53
700 719 4.179599 GGGAGGGAGGGAGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
703 722 2.018086 AGAGGGGAGGGAGGGAGAG 61.018 68.421 0.00 0.00 0.00 3.20
704 723 2.015726 GAGAGGGGAGGGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
706 725 3.430497 CGAGAGGGGAGGGAGGGA 61.430 72.222 0.00 0.00 0.00 4.20
712 732 2.904866 CTCGAGCGAGAGGGGAGG 60.905 72.222 14.28 0.00 44.53 4.30
721 741 2.044352 TGTGGGATCCTCGAGCGA 60.044 61.111 12.58 6.49 0.00 4.93
742 762 4.957684 ATCAGATCCCTGCGCGCG 62.958 66.667 28.44 28.44 40.20 6.86
743 763 2.590007 AATCAGATCCCTGCGCGC 60.590 61.111 27.26 27.26 40.20 6.86
746 766 2.249535 CGGCAATCAGATCCCTGCG 61.250 63.158 0.42 0.00 40.20 5.18
747 767 2.550101 GCGGCAATCAGATCCCTGC 61.550 63.158 0.00 0.00 40.20 4.85
748 768 1.895707 GGCGGCAATCAGATCCCTG 60.896 63.158 3.07 0.00 41.74 4.45
898 1167 1.740025 GACGGCCAAATTCTCAGGAAG 59.260 52.381 2.24 0.00 34.70 3.46
986 1255 3.770040 CCATGTCCGTCCGGCAGA 61.770 66.667 0.00 0.00 34.68 4.26
1045 1316 4.394078 CGCCTTGTCCGACGACGA 62.394 66.667 9.28 0.00 42.37 4.20
1477 1748 2.270205 CGGCATGCTTGAGGAGGT 59.730 61.111 18.92 0.00 0.00 3.85
1519 1790 0.039180 TCGAGTGGTAGGGAAGCTGA 59.961 55.000 0.00 0.00 0.00 4.26
1530 1801 2.159014 TGTAGCAAACAGTTCGAGTGGT 60.159 45.455 2.32 0.00 33.01 4.16
1532 1803 4.732285 ATTGTAGCAAACAGTTCGAGTG 57.268 40.909 0.00 0.00 39.87 3.51
1537 1808 5.343325 GCAAGCTTATTGTAGCAAACAGTTC 59.657 40.000 0.00 0.00 43.68 3.01
1542 1813 6.183360 GGAATTGCAAGCTTATTGTAGCAAAC 60.183 38.462 19.54 16.16 43.97 2.93
1554 1825 1.708341 ACAGTGGGAATTGCAAGCTT 58.292 45.000 4.94 0.00 0.00 3.74
1618 1889 2.037136 CCGAGAGCTTGGCAACCAG 61.037 63.158 0.00 0.00 33.81 4.00
1619 1890 2.032528 CCGAGAGCTTGGCAACCA 59.967 61.111 0.00 0.00 0.00 3.67
1625 1896 2.279784 GGATCGCCGAGAGCTTGG 60.280 66.667 0.00 0.00 40.39 3.61
1626 1897 1.068753 ATGGATCGCCGAGAGCTTG 59.931 57.895 0.00 0.00 40.39 4.01
1715 1986 1.334149 GGCAAAGAACACTCGACTTGC 60.334 52.381 0.00 0.00 36.54 4.01
1822 2093 7.180766 TGCAGAAAAGAATTCCCCATTTCTAAT 59.819 33.333 18.13 3.62 38.04 1.73
1989 2276 8.312896 ACTAAAAGCTTAGAAACTGCTTAGAC 57.687 34.615 13.14 0.00 44.94 2.59
2023 2310 0.524862 CCCTGACGCTACGTAACTGT 59.475 55.000 0.00 0.00 41.37 3.55
2024 2311 0.524862 ACCCTGACGCTACGTAACTG 59.475 55.000 0.00 0.00 41.37 3.16
2291 2632 6.605194 TCTGGTTGCTGGCATTGTTATTATTA 59.395 34.615 0.00 0.00 0.00 0.98
2292 2633 5.421693 TCTGGTTGCTGGCATTGTTATTATT 59.578 36.000 0.00 0.00 0.00 1.40
2293 2634 4.955450 TCTGGTTGCTGGCATTGTTATTAT 59.045 37.500 0.00 0.00 0.00 1.28
2294 2635 4.339748 TCTGGTTGCTGGCATTGTTATTA 58.660 39.130 0.00 0.00 0.00 0.98
2295 2636 3.164268 TCTGGTTGCTGGCATTGTTATT 58.836 40.909 0.00 0.00 0.00 1.40
2296 2637 2.806434 TCTGGTTGCTGGCATTGTTAT 58.194 42.857 0.00 0.00 0.00 1.89
2570 2914 2.281484 GGCGTGAGGAAGTTGCCA 60.281 61.111 0.00 0.00 45.06 4.92
2658 3002 2.807631 TACAAGAAGACCGACGGCGC 62.808 60.000 15.39 6.51 35.83 6.53
2681 3025 0.935942 TCCCCCTAGGTACATTCCGA 59.064 55.000 8.29 0.00 36.75 4.55
2906 3253 3.818121 TTACTGCAAGGCCACGCGT 62.818 57.895 5.58 5.58 39.30 6.01
2917 3264 6.292923 ACCTTACACATTTACAGTTACTGCA 58.707 36.000 12.80 0.00 34.37 4.41
2963 3312 6.600882 TTAGAGTAAGGGGTAACTGAACAG 57.399 41.667 0.00 0.00 0.00 3.16
2985 3334 2.222445 GTGTTGGAGTTGATACGCGTTT 59.778 45.455 20.78 10.40 0.00 3.60
3012 3361 6.916360 ACCAACCAATTACACAATCTGATT 57.084 33.333 0.00 0.00 0.00 2.57
3013 3362 7.669722 ACTTACCAACCAATTACACAATCTGAT 59.330 33.333 0.00 0.00 0.00 2.90
3015 3364 7.083858 CACTTACCAACCAATTACACAATCTG 58.916 38.462 0.00 0.00 0.00 2.90
3016 3365 6.208599 CCACTTACCAACCAATTACACAATCT 59.791 38.462 0.00 0.00 0.00 2.40
3017 3366 6.015772 ACCACTTACCAACCAATTACACAATC 60.016 38.462 0.00 0.00 0.00 2.67
3019 3368 5.202004 ACCACTTACCAACCAATTACACAA 58.798 37.500 0.00 0.00 0.00 3.33
3020 3369 4.794334 ACCACTTACCAACCAATTACACA 58.206 39.130 0.00 0.00 0.00 3.72
3021 3370 6.566376 CGTTACCACTTACCAACCAATTACAC 60.566 42.308 0.00 0.00 0.00 2.90
3022 3371 5.469421 CGTTACCACTTACCAACCAATTACA 59.531 40.000 0.00 0.00 0.00 2.41
3023 3372 5.700373 TCGTTACCACTTACCAACCAATTAC 59.300 40.000 0.00 0.00 0.00 1.89
3025 3374 4.716794 TCGTTACCACTTACCAACCAATT 58.283 39.130 0.00 0.00 0.00 2.32
3026 3375 4.354893 TCGTTACCACTTACCAACCAAT 57.645 40.909 0.00 0.00 0.00 3.16
3027 3376 3.834489 TCGTTACCACTTACCAACCAA 57.166 42.857 0.00 0.00 0.00 3.67
3028 3377 3.387374 TCTTCGTTACCACTTACCAACCA 59.613 43.478 0.00 0.00 0.00 3.67
3029 3378 3.992427 CTCTTCGTTACCACTTACCAACC 59.008 47.826 0.00 0.00 0.00 3.77
3031 3380 4.942761 ACTCTTCGTTACCACTTACCAA 57.057 40.909 0.00 0.00 0.00 3.67
3033 3382 5.754890 TGAAAACTCTTCGTTACCACTTACC 59.245 40.000 0.00 0.00 33.90 2.85
3034 3383 6.833342 TGAAAACTCTTCGTTACCACTTAC 57.167 37.500 0.00 0.00 33.90 2.34
3036 3385 6.053005 TCATGAAAACTCTTCGTTACCACTT 58.947 36.000 0.00 0.00 33.90 3.16
3037 3386 5.607477 TCATGAAAACTCTTCGTTACCACT 58.393 37.500 0.00 0.00 33.90 4.00
3091 3474 6.037172 GCCCACAACATATTTCTACTACTGTG 59.963 42.308 0.00 0.00 33.19 3.66
3098 3481 3.000925 CGACGCCCACAACATATTTCTAC 59.999 47.826 0.00 0.00 0.00 2.59
3100 3483 2.006888 CGACGCCCACAACATATTTCT 58.993 47.619 0.00 0.00 0.00 2.52
3101 3484 1.735571 ACGACGCCCACAACATATTTC 59.264 47.619 0.00 0.00 0.00 2.17
3103 3486 1.338294 TGACGACGCCCACAACATATT 60.338 47.619 0.00 0.00 0.00 1.28
3105 3488 0.248012 ATGACGACGCCCACAACATA 59.752 50.000 0.00 0.00 0.00 2.29
3107 3490 1.666553 GATGACGACGCCCACAACA 60.667 57.895 0.00 0.00 0.00 3.33
3108 3491 0.949105 AAGATGACGACGCCCACAAC 60.949 55.000 0.00 0.00 0.00 3.32
3109 3492 0.669318 GAAGATGACGACGCCCACAA 60.669 55.000 0.00 0.00 0.00 3.33
3110 3493 1.080093 GAAGATGACGACGCCCACA 60.080 57.895 0.00 0.00 0.00 4.17
3111 3494 2.158959 CGAAGATGACGACGCCCAC 61.159 63.158 0.00 0.00 0.00 4.61
3112 3495 2.180769 CGAAGATGACGACGCCCA 59.819 61.111 0.00 0.00 0.00 5.36
3113 3496 1.872679 GACGAAGATGACGACGCCC 60.873 63.158 0.00 0.00 34.70 6.13
3114 3497 0.862283 GAGACGAAGATGACGACGCC 60.862 60.000 0.00 0.00 34.70 5.68
3115 3498 0.862283 GGAGACGAAGATGACGACGC 60.862 60.000 0.00 0.00 34.70 5.19
3116 3499 0.446616 TGGAGACGAAGATGACGACG 59.553 55.000 0.00 0.00 34.70 5.12
3117 3500 2.631418 TTGGAGACGAAGATGACGAC 57.369 50.000 0.00 0.00 34.70 4.34
3118 3501 5.515797 AATATTGGAGACGAAGATGACGA 57.484 39.130 0.00 0.00 34.70 4.20
3119 3502 5.980116 AGAAATATTGGAGACGAAGATGACG 59.020 40.000 0.00 0.00 0.00 4.35
3120 3503 7.206687 AGAGAAATATTGGAGACGAAGATGAC 58.793 38.462 0.00 0.00 0.00 3.06
3121 3504 7.353414 AGAGAAATATTGGAGACGAAGATGA 57.647 36.000 0.00 0.00 0.00 2.92
3122 3505 9.703892 AATAGAGAAATATTGGAGACGAAGATG 57.296 33.333 0.00 0.00 0.00 2.90
3123 3506 9.921637 GAATAGAGAAATATTGGAGACGAAGAT 57.078 33.333 0.00 0.00 0.00 2.40
3124 3507 8.076781 CGAATAGAGAAATATTGGAGACGAAGA 58.923 37.037 0.00 0.00 0.00 2.87
3125 3508 8.076781 TCGAATAGAGAAATATTGGAGACGAAG 58.923 37.037 0.00 0.00 29.74 3.79
3126 3509 7.937649 TCGAATAGAGAAATATTGGAGACGAA 58.062 34.615 0.00 0.00 29.74 3.85
3127 3510 7.506328 TCGAATAGAGAAATATTGGAGACGA 57.494 36.000 0.00 0.00 29.74 4.20
3128 3511 8.023706 TCATCGAATAGAGAAATATTGGAGACG 58.976 37.037 0.00 0.00 34.62 4.18
3129 3512 9.134734 GTCATCGAATAGAGAAATATTGGAGAC 57.865 37.037 0.00 0.00 34.62 3.36
3189 3572 3.587498 TGAAGAGGGAAAGAGAGGAACA 58.413 45.455 0.00 0.00 0.00 3.18
3233 3618 1.211212 TCTCATTGGTGCCTCCTCATG 59.789 52.381 0.00 0.00 37.07 3.07
3234 3619 1.588239 TCTCATTGGTGCCTCCTCAT 58.412 50.000 0.00 0.00 37.07 2.90
3235 3620 1.361204 TTCTCATTGGTGCCTCCTCA 58.639 50.000 0.00 0.00 37.07 3.86
3263 3651 4.264460 AGGAAGGAATCGACATATGAGC 57.736 45.455 10.38 0.00 0.00 4.26
3264 3652 6.582677 AGTAGGAAGGAATCGACATATGAG 57.417 41.667 10.38 3.14 0.00 2.90
3275 3663 4.706962 GCAATGGTTCAAGTAGGAAGGAAT 59.293 41.667 0.00 0.00 0.00 3.01
3374 3762 0.168128 GTCAAGATCCCCAAAACGCG 59.832 55.000 3.53 3.53 0.00 6.01
3406 3794 3.319122 ACTCTTCGTTACCGTTTACCAGT 59.681 43.478 0.00 0.00 35.01 4.00
3415 3803 5.585500 TTCATGAAAACTCTTCGTTACCG 57.415 39.130 5.45 0.00 33.90 4.02
3421 3809 9.398170 ACAACATAAATTCATGAAAACTCTTCG 57.602 29.630 13.09 1.77 0.00 3.79
3431 3819 6.221659 TGCAAAGCACAACATAAATTCATGA 58.778 32.000 0.00 0.00 31.71 3.07
3436 3824 5.609423 TCCTTGCAAAGCACAACATAAATT 58.391 33.333 0.00 0.00 44.44 1.82
3471 3859 3.674423 GCAAATGACAGATTGCTACGAC 58.326 45.455 17.17 0.00 46.42 4.34
3492 3880 4.098349 AGCATAAGAAGAGAGAGCACAGAG 59.902 45.833 0.00 0.00 0.00 3.35
3494 3882 4.362279 GAGCATAAGAAGAGAGAGCACAG 58.638 47.826 0.00 0.00 0.00 3.66
3520 3912 2.409948 AGAAAGGAAAGGGAGCGATG 57.590 50.000 0.00 0.00 0.00 3.84
3521 3913 2.040412 ACAAGAAAGGAAAGGGAGCGAT 59.960 45.455 0.00 0.00 0.00 4.58
3527 3919 2.038557 TCGAGGACAAGAAAGGAAAGGG 59.961 50.000 0.00 0.00 0.00 3.95
3532 3924 0.601558 CGGTCGAGGACAAGAAAGGA 59.398 55.000 0.00 0.00 33.68 3.36
3535 3927 1.958579 TCTTCGGTCGAGGACAAGAAA 59.041 47.619 1.06 0.00 33.23 2.52
3552 3944 4.658786 ACCCACTCCGCCCCTCTT 62.659 66.667 0.00 0.00 0.00 2.85
3574 3966 3.191371 GGCAAACACATTAGTCCCTCAAG 59.809 47.826 0.00 0.00 0.00 3.02
3575 3967 3.153919 GGCAAACACATTAGTCCCTCAA 58.846 45.455 0.00 0.00 0.00 3.02
3576 3968 2.107378 TGGCAAACACATTAGTCCCTCA 59.893 45.455 0.00 0.00 0.00 3.86
3577 3969 2.749621 CTGGCAAACACATTAGTCCCTC 59.250 50.000 0.00 0.00 0.00 4.30
3578 3970 2.795329 CTGGCAAACACATTAGTCCCT 58.205 47.619 0.00 0.00 0.00 4.20
3596 3990 5.992217 GGGGACTTACTTCTTGTATATGCTG 59.008 44.000 0.00 0.00 0.00 4.41
3599 3993 6.401047 TCGGGGACTTACTTCTTGTATATG 57.599 41.667 0.00 0.00 0.00 1.78
3603 3997 3.094572 CCTCGGGGACTTACTTCTTGTA 58.905 50.000 0.00 0.00 33.58 2.41
3617 4011 2.166664 CACTTCTCTTAACTCCTCGGGG 59.833 54.545 0.00 0.00 0.00 5.73
3618 4012 2.826725 ACACTTCTCTTAACTCCTCGGG 59.173 50.000 0.00 0.00 0.00 5.14
3620 4014 3.057174 AGCACACTTCTCTTAACTCCTCG 60.057 47.826 0.00 0.00 0.00 4.63
3621 4015 4.241681 CAGCACACTTCTCTTAACTCCTC 58.758 47.826 0.00 0.00 0.00 3.71
3638 4032 2.111384 TCTCCTCCATAACTCCAGCAC 58.889 52.381 0.00 0.00 0.00 4.40
3648 4042 6.280643 CACACGAATAACAATCTCCTCCATA 58.719 40.000 0.00 0.00 0.00 2.74
3651 4045 3.871594 CCACACGAATAACAATCTCCTCC 59.128 47.826 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.