Multiple sequence alignment - TraesCS3B01G191400

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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 TraesCS3B01G191400 chr3B 100.000 3163 0 0 1 3163 204287620 204284458 0.000000e+00 5842
1 TraesCS3B01G191400 chr3B 90.090 111 6 5 2972 3080 805579403 805579296 4.250000e-29 139
2 TraesCS3B01G191400 chr3D 94.084 2823 111 28 199 2996 142481955 142479164 0.000000e+00 4237
3 TraesCS3B01G191400 chr3D 95.567 203 5 3 1 199 142482492 142482290 3.940000e-84 322
4 TraesCS3B01G191400 chr3A 92.773 2532 116 39 1 2488 161452044 161449536 0.000000e+00 3600
5 TraesCS3B01G191400 chr3A 97.070 512 15 0 2485 2996 161449457 161448946 0.000000e+00 863
6 TraesCS3B01G191400 chr3A 93.407 91 4 1 2994 3084 199541464 199541376 1.980000e-27 134
7 TraesCS3B01G191400 chr6D 87.500 160 19 1 1007 1166 466238555 466238713 1.940000e-42 183
8 TraesCS3B01G191400 chr6D 81.679 131 20 4 1212 1338 3471344 3471214 4.310000e-19 106
9 TraesCS3B01G191400 chr1B 93.458 107 4 2 2985 3090 633092466 633092362 4.220000e-34 156
10 TraesCS3B01G191400 chr7A 94.000 100 3 2 2991 3090 80994169 80994073 7.070000e-32 148
11 TraesCS3B01G191400 chr7A 88.983 118 8 4 2969 3083 374987685 374987570 1.180000e-29 141
12 TraesCS3B01G191400 chr7D 93.878 98 4 1 2986 3083 94261219 94261314 2.540000e-31 147
13 TraesCS3B01G191400 chr1D 93.878 98 4 1 2983 3080 340660028 340660123 2.540000e-31 147
14 TraesCS3B01G191400 chr1D 91.346 104 6 3 2979 3082 10389121 10389021 4.250000e-29 139
15 TraesCS3B01G191400 chr5D 89.381 113 6 4 2969 3081 49290857 49290751 1.530000e-28 137
16 TraesCS3B01G191400 chr6B 83.721 129 16 3 1208 1332 7180081 7180208 1.990000e-22 117
17 TraesCS3B01G191400 chr6A 82.258 124 18 2 1212 1331 2263611 2263488 1.550000e-18 104


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 TraesCS3B01G191400 chr3B 204284458 204287620 3162 True 5842.0 5842 100.0000 1 3163 1 chr3B.!!$R1 3162
1 TraesCS3B01G191400 chr3D 142479164 142482492 3328 True 2279.5 4237 94.8255 1 2996 2 chr3D.!!$R1 2995
2 TraesCS3B01G191400 chr3A 161448946 161452044 3098 True 2231.5 3600 94.9215 1 2996 2 chr3A.!!$R2 2995

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
872 1226 0.607489 CCCTTCTCACACAGCCCAAG 60.607 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2801 3278 2.320681 ACTTCTACACCCCTAGCACA 57.679 50.0 0.0 0.0 0.0 4.57 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
25 26 6.038356 GCAATAGAGATTGTCATTTGTTGGG 58.962 40.000 0.08 0.00 43.82 4.12
191 198 3.093057 ACCGAGATATCTGATGGCTACC 58.907 50.000 10.74 0.00 0.00 3.18
239 581 2.555199 CGAAAGGGGAACATAGCTCTG 58.445 52.381 0.00 0.00 0.00 3.35
291 636 5.047590 AGAGAACTCCACCGTTTTTGTTTTT 60.048 36.000 0.00 0.00 0.00 1.94
416 762 3.637694 AGTTCTCGCTTCTTATCCTACCC 59.362 47.826 0.00 0.00 0.00 3.69
443 795 7.943413 TCTACAGTACGAGTATGATGACTAC 57.057 40.000 0.00 0.00 0.00 2.73
455 807 3.599343 TGATGACTACACTGGATGCAAC 58.401 45.455 0.00 0.00 0.00 4.17
456 808 2.078849 TGACTACACTGGATGCAACG 57.921 50.000 0.00 0.00 0.00 4.10
460 812 1.129251 CTACACTGGATGCAACGCAAG 59.871 52.381 0.00 0.00 43.62 4.01
471 823 1.522806 AACGCAAGGAGTCGCAACA 60.523 52.632 0.00 0.00 46.39 3.33
509 862 8.131100 AGCACAATCAATAGAAATTACGAATGG 58.869 33.333 0.00 0.00 0.00 3.16
518 871 3.899052 AATTACGAATGGAACGAGGGA 57.101 42.857 0.00 0.00 34.70 4.20
563 916 3.458579 CGCGTGAAGTCGTCGGTG 61.459 66.667 0.00 0.00 0.00 4.94
621 974 3.437795 CAGCGAGGCAGGGCAAAG 61.438 66.667 0.00 0.00 0.00 2.77
640 993 3.348236 GCAAGGATATGCGGCAGG 58.652 61.111 9.25 0.00 36.45 4.85
690 1043 3.035576 GCTAGGGTTTTGCGCCGAC 62.036 63.158 4.18 0.00 0.00 4.79
721 1074 0.696501 TCCTCTAAACCCTGGTTGCC 59.303 55.000 1.58 0.00 38.47 4.52
722 1075 0.676782 CCTCTAAACCCTGGTTGCCG 60.677 60.000 1.58 0.00 38.47 5.69
723 1076 1.302993 TCTAAACCCTGGTTGCCGC 60.303 57.895 1.58 0.00 38.47 6.53
774 1127 4.775253 ACAAAAGGGAGAGAGGAGTAGAAG 59.225 45.833 0.00 0.00 0.00 2.85
778 1131 2.358826 GGGAGAGAGGAGTAGAAGGCTT 60.359 54.545 0.00 0.00 0.00 4.35
821 1174 5.008217 CCGTAGAAAACAACAGGATGAAACA 59.992 40.000 0.00 0.00 39.69 2.83
872 1226 0.607489 CCCTTCTCACACAGCCCAAG 60.607 60.000 0.00 0.00 0.00 3.61
924 1278 1.480312 CCACCCACATTGGTTCCTTCA 60.480 52.381 0.00 0.00 36.12 3.02
1047 1412 2.179517 CGCTCGTCCGCTTCTCTT 59.820 61.111 0.00 0.00 0.00 2.85
1222 1591 3.741830 TTCGTTGTGCAGGTCGCCA 62.742 57.895 0.00 0.00 41.33 5.69
1443 1813 7.656542 TGTGTTACGGTGTAATTCAGACAAATA 59.343 33.333 0.00 0.00 0.00 1.40
1498 1889 5.043189 ACAATCCAACTAAAGCTAAACGC 57.957 39.130 0.00 0.00 39.57 4.84
1558 1949 4.168760 GCATAAGAACATTGACTTGCACC 58.831 43.478 0.00 0.00 0.00 5.01
1641 2032 2.472695 TTCCTTCAACACCTGGATCG 57.527 50.000 0.00 0.00 0.00 3.69
1648 2039 4.649088 TCAACACCTGGATCGTACTATG 57.351 45.455 0.00 0.00 0.00 2.23
1786 2178 7.414762 CGAAAGAGACCCACTTTTCTGTTTTTA 60.415 37.037 0.00 0.00 35.94 1.52
1871 2263 7.893302 TGACCACTAAAATATCTCCACCATTTT 59.107 33.333 0.00 0.00 36.25 1.82
2298 2691 3.558418 GGACAACTCGCTGAAACTTTGTA 59.442 43.478 0.00 0.00 0.00 2.41
2339 2732 2.987149 CACCTAGTGTACTGTTTGAGCG 59.013 50.000 0.00 0.00 0.00 5.03
2457 2852 9.739276 TTTTGTTCATATCATAGAGAAACTGGT 57.261 29.630 0.00 0.00 0.00 4.00
2458 2853 9.739276 TTTGTTCATATCATAGAGAAACTGGTT 57.261 29.630 0.00 0.00 0.00 3.67
2459 2854 9.739276 TTGTTCATATCATAGAGAAACTGGTTT 57.261 29.630 0.00 0.00 35.14 3.27
2801 3278 9.857656 AATCATTATGGTTATGTGATGAGAACT 57.142 29.630 0.00 0.00 30.52 3.01
2849 3326 4.881273 TCGCTGGCAAAATGAATACTATGT 59.119 37.500 0.00 0.00 0.00 2.29
2976 3454 6.515272 TGATCCTTTTAATCTTCACTTGGC 57.485 37.500 0.00 0.00 0.00 4.52
2981 3459 6.721208 TCCTTTTAATCTTCACTTGGCAATCT 59.279 34.615 0.00 0.00 0.00 2.40
2996 3474 7.831193 ACTTGGCAATCTCATTTATCTTGTACT 59.169 33.333 0.00 0.00 0.00 2.73
2997 3475 7.792374 TGGCAATCTCATTTATCTTGTACTC 57.208 36.000 0.00 0.00 0.00 2.59
2998 3476 6.767902 TGGCAATCTCATTTATCTTGTACTCC 59.232 38.462 0.00 0.00 0.00 3.85
2999 3477 6.205658 GGCAATCTCATTTATCTTGTACTCCC 59.794 42.308 0.00 0.00 0.00 4.30
3000 3478 6.995091 GCAATCTCATTTATCTTGTACTCCCT 59.005 38.462 0.00 0.00 0.00 4.20
3001 3479 7.172361 GCAATCTCATTTATCTTGTACTCCCTC 59.828 40.741 0.00 0.00 0.00 4.30
3002 3480 6.732896 TCTCATTTATCTTGTACTCCCTCC 57.267 41.667 0.00 0.00 0.00 4.30
3003 3481 5.302059 TCTCATTTATCTTGTACTCCCTCCG 59.698 44.000 0.00 0.00 0.00 4.63
3004 3482 4.960469 TCATTTATCTTGTACTCCCTCCGT 59.040 41.667 0.00 0.00 0.00 4.69
3005 3483 6.131264 TCATTTATCTTGTACTCCCTCCGTA 58.869 40.000 0.00 0.00 0.00 4.02
3006 3484 6.608405 TCATTTATCTTGTACTCCCTCCGTAA 59.392 38.462 0.00 0.00 0.00 3.18
3007 3485 6.855763 TTTATCTTGTACTCCCTCCGTAAA 57.144 37.500 0.00 0.00 0.00 2.01
3008 3486 4.732672 ATCTTGTACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
3009 3487 3.771216 TCTTGTACTCCCTCCGTAAACT 58.229 45.455 0.00 0.00 0.00 2.66
3010 3488 4.922206 TCTTGTACTCCCTCCGTAAACTA 58.078 43.478 0.00 0.00 0.00 2.24
3011 3489 5.324409 TCTTGTACTCCCTCCGTAAACTAA 58.676 41.667 0.00 0.00 0.00 2.24
3012 3490 5.954150 TCTTGTACTCCCTCCGTAAACTAAT 59.046 40.000 0.00 0.00 0.00 1.73
3013 3491 7.118723 TCTTGTACTCCCTCCGTAAACTAATA 58.881 38.462 0.00 0.00 0.00 0.98
3014 3492 7.781693 TCTTGTACTCCCTCCGTAAACTAATAT 59.218 37.037 0.00 0.00 0.00 1.28
3015 3493 8.995027 TTGTACTCCCTCCGTAAACTAATATA 57.005 34.615 0.00 0.00 0.00 0.86
3016 3494 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
3017 3495 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
3018 3496 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
3019 3497 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3020 3498 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3021 3499 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3022 3500 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3023 3501 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3024 3502 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3025 3503 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3057 3535 9.654663 AACTAATTTAGTGATCTAAACGCTCTT 57.345 29.630 9.78 0.00 45.19 2.85
3074 3552 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
3075 3553 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
3076 3554 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
3077 3555 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
3078 3556 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
3084 3562 7.973048 ATTAGTTTACAGAGGGAGTACATCA 57.027 36.000 0.00 0.00 0.00 3.07
3085 3563 7.973048 TTAGTTTACAGAGGGAGTACATCAT 57.027 36.000 0.00 0.00 0.00 2.45
3086 3564 6.875972 AGTTTACAGAGGGAGTACATCATT 57.124 37.500 0.00 0.00 0.00 2.57
3087 3565 6.644347 AGTTTACAGAGGGAGTACATCATTG 58.356 40.000 0.00 0.00 0.00 2.82
3088 3566 6.213600 AGTTTACAGAGGGAGTACATCATTGT 59.786 38.462 0.00 0.00 39.98 2.71
3089 3567 6.620877 TTACAGAGGGAGTACATCATTGTT 57.379 37.500 0.00 0.00 37.28 2.83
3090 3568 4.836825 ACAGAGGGAGTACATCATTGTTG 58.163 43.478 0.00 0.00 37.28 3.33
3091 3569 4.287067 ACAGAGGGAGTACATCATTGTTGT 59.713 41.667 5.73 5.73 37.28 3.32
3092 3570 5.221925 ACAGAGGGAGTACATCATTGTTGTT 60.222 40.000 5.73 0.00 37.28 2.83
3093 3571 5.707298 CAGAGGGAGTACATCATTGTTGTTT 59.293 40.000 5.73 0.00 37.28 2.83
3094 3572 5.940470 AGAGGGAGTACATCATTGTTGTTTC 59.060 40.000 5.73 5.08 37.28 2.78
3095 3573 5.630121 AGGGAGTACATCATTGTTGTTTCA 58.370 37.500 5.73 0.00 37.28 2.69
3096 3574 6.068010 AGGGAGTACATCATTGTTGTTTCAA 58.932 36.000 5.73 0.00 37.28 2.69
3097 3575 6.721208 AGGGAGTACATCATTGTTGTTTCAAT 59.279 34.615 5.73 0.00 38.38 2.57
3098 3576 7.888021 AGGGAGTACATCATTGTTGTTTCAATA 59.112 33.333 5.73 0.00 36.44 1.90
3099 3577 8.519526 GGGAGTACATCATTGTTGTTTCAATAA 58.480 33.333 5.73 0.00 36.44 1.40
3102 3580 9.357652 AGTACATCATTGTTGTTTCAATAATGC 57.642 29.630 19.51 10.40 37.10 3.56
3103 3581 9.357652 GTACATCATTGTTGTTTCAATAATGCT 57.642 29.630 19.51 12.03 37.10 3.79
3104 3582 8.470040 ACATCATTGTTGTTTCAATAATGCTC 57.530 30.769 19.51 0.00 37.10 4.26
3105 3583 7.546667 ACATCATTGTTGTTTCAATAATGCTCC 59.453 33.333 19.51 0.00 37.10 4.70
3106 3584 6.092092 TCATTGTTGTTTCAATAATGCTCCG 58.908 36.000 19.51 4.52 36.44 4.63
3107 3585 5.697473 TTGTTGTTTCAATAATGCTCCGA 57.303 34.783 0.00 0.00 0.00 4.55
3108 3586 5.041951 TGTTGTTTCAATAATGCTCCGAC 57.958 39.130 0.00 0.00 0.00 4.79
3109 3587 4.517075 TGTTGTTTCAATAATGCTCCGACA 59.483 37.500 0.00 0.00 0.00 4.35
3110 3588 4.944962 TGTTTCAATAATGCTCCGACAG 57.055 40.909 0.00 0.00 0.00 3.51
3111 3589 4.574892 TGTTTCAATAATGCTCCGACAGA 58.425 39.130 0.00 0.00 0.00 3.41
3112 3590 4.391830 TGTTTCAATAATGCTCCGACAGAC 59.608 41.667 0.00 0.00 0.00 3.51
3113 3591 3.885724 TCAATAATGCTCCGACAGACA 57.114 42.857 0.00 0.00 0.00 3.41
3114 3592 3.521560 TCAATAATGCTCCGACAGACAC 58.478 45.455 0.00 0.00 0.00 3.67
3115 3593 3.195610 TCAATAATGCTCCGACAGACACT 59.804 43.478 0.00 0.00 0.00 3.55
3116 3594 3.895232 ATAATGCTCCGACAGACACTT 57.105 42.857 0.00 0.00 0.00 3.16
3117 3595 1.800805 AATGCTCCGACAGACACTTG 58.199 50.000 0.00 0.00 0.00 3.16
3118 3596 0.969149 ATGCTCCGACAGACACTTGA 59.031 50.000 0.00 0.00 0.00 3.02
3119 3597 0.750249 TGCTCCGACAGACACTTGAA 59.250 50.000 0.00 0.00 0.00 2.69
3120 3598 1.138069 TGCTCCGACAGACACTTGAAA 59.862 47.619 0.00 0.00 0.00 2.69
3121 3599 2.210116 GCTCCGACAGACACTTGAAAA 58.790 47.619 0.00 0.00 0.00 2.29
3122 3600 2.612212 GCTCCGACAGACACTTGAAAAA 59.388 45.455 0.00 0.00 0.00 1.94
3123 3601 3.251004 GCTCCGACAGACACTTGAAAAAT 59.749 43.478 0.00 0.00 0.00 1.82
3124 3602 4.451096 GCTCCGACAGACACTTGAAAAATA 59.549 41.667 0.00 0.00 0.00 1.40
3125 3603 5.122396 GCTCCGACAGACACTTGAAAAATAT 59.878 40.000 0.00 0.00 0.00 1.28
3126 3604 6.348540 GCTCCGACAGACACTTGAAAAATATT 60.349 38.462 0.00 0.00 0.00 1.28
3127 3605 7.504924 TCCGACAGACACTTGAAAAATATTT 57.495 32.000 0.00 0.00 0.00 1.40
3128 3606 8.610248 TCCGACAGACACTTGAAAAATATTTA 57.390 30.769 0.01 0.00 0.00 1.40
3129 3607 8.500773 TCCGACAGACACTTGAAAAATATTTAC 58.499 33.333 0.01 0.16 0.00 2.01
3130 3608 8.286800 CCGACAGACACTTGAAAAATATTTACA 58.713 33.333 0.01 2.80 0.00 2.41
3131 3609 9.103048 CGACAGACACTTGAAAAATATTTACAC 57.897 33.333 0.01 0.00 0.00 2.90
3132 3610 9.944663 GACAGACACTTGAAAAATATTTACACA 57.055 29.630 0.01 0.03 0.00 3.72
3133 3611 9.950680 ACAGACACTTGAAAAATATTTACACAG 57.049 29.630 0.01 7.96 0.00 3.66
3134 3612 9.398170 CAGACACTTGAAAAATATTTACACAGG 57.602 33.333 0.01 5.65 0.00 4.00
3135 3613 8.082242 AGACACTTGAAAAATATTTACACAGGC 58.918 33.333 0.01 1.22 0.00 4.85
3136 3614 7.951591 ACACTTGAAAAATATTTACACAGGCT 58.048 30.769 0.01 0.00 0.00 4.58
3137 3615 9.073475 ACACTTGAAAAATATTTACACAGGCTA 57.927 29.630 0.01 0.00 0.00 3.93
3138 3616 9.906660 CACTTGAAAAATATTTACACAGGCTAA 57.093 29.630 0.01 0.00 0.00 3.09
3144 3622 8.771920 AAAATATTTACACAGGCTAAAAAGGC 57.228 30.769 0.01 0.00 0.00 4.35
3145 3623 7.475137 AATATTTACACAGGCTAAAAAGGCA 57.525 32.000 1.63 0.00 36.76 4.75
3146 3624 5.799827 ATTTACACAGGCTAAAAAGGCAA 57.200 34.783 1.63 0.00 36.76 4.52
3147 3625 4.846779 TTACACAGGCTAAAAAGGCAAG 57.153 40.909 1.63 0.00 36.76 4.01
3148 3626 2.666317 ACACAGGCTAAAAAGGCAAGT 58.334 42.857 1.63 0.00 36.76 3.16
3149 3627 3.827722 ACACAGGCTAAAAAGGCAAGTA 58.172 40.909 1.63 0.00 36.76 2.24
3150 3628 4.407365 ACACAGGCTAAAAAGGCAAGTAT 58.593 39.130 1.63 0.00 36.76 2.12
3151 3629 4.218417 ACACAGGCTAAAAAGGCAAGTATG 59.782 41.667 1.63 0.00 36.76 2.39
3162 3640 2.010145 GCAAGTATGCGACTCAAGGA 57.990 50.000 0.00 0.00 43.83 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 55 4.321675 GGTTCAAGTTTGTGTGGTCACTTT 60.322 41.667 2.66 0.00 44.14 2.66
173 180 6.471146 ACATTTGGTAGCCATCAGATATCTC 58.529 40.000 1.03 0.00 31.53 2.75
191 198 5.478407 GTTGGGGGAACATCTTAACATTTG 58.522 41.667 0.00 0.00 34.35 2.32
239 581 2.428530 GTCAAATTGATCCCCTTCTGCC 59.571 50.000 0.00 0.00 0.00 4.85
416 762 8.766000 AGTCATCATACTCGTACTGTAGATAG 57.234 38.462 0.00 0.00 0.00 2.08
443 795 1.210931 CCTTGCGTTGCATCCAGTG 59.789 57.895 0.00 0.00 38.76 3.66
455 807 1.664649 TCTGTTGCGACTCCTTGCG 60.665 57.895 5.50 0.00 0.00 4.85
456 808 0.601311 AGTCTGTTGCGACTCCTTGC 60.601 55.000 5.50 0.00 40.04 4.01
460 812 1.011451 GCTCAGTCTGTTGCGACTCC 61.011 60.000 5.50 0.00 42.10 3.85
471 823 1.548357 ATTGTGCTCCCGCTCAGTCT 61.548 55.000 0.00 0.00 40.33 3.24
509 862 0.036388 TGCAGGTGAATCCCTCGTTC 60.036 55.000 0.00 0.00 36.75 3.95
563 916 0.032130 TGAAGGTGATATCGCGCTCC 59.968 55.000 5.56 0.00 0.00 4.70
619 972 1.529244 GCCGCATATCCTTGCCCTT 60.529 57.895 0.00 0.00 39.52 3.95
620 973 2.113986 GCCGCATATCCTTGCCCT 59.886 61.111 0.00 0.00 39.52 5.19
621 974 2.203337 TGCCGCATATCCTTGCCC 60.203 61.111 0.00 0.00 39.52 5.36
640 993 2.022129 CTACGGATTCATCGCGCCC 61.022 63.158 0.00 0.00 0.00 6.13
690 1043 3.369997 GGTTTAGAGGAGGAGAAGCTTGG 60.370 52.174 2.10 0.00 0.00 3.61
749 1102 4.773149 TCTACTCCTCTCTCCCTTTTGTTC 59.227 45.833 0.00 0.00 0.00 3.18
778 1131 1.809619 CCGCCGATCTTTGCTTCGA 60.810 57.895 0.00 0.00 37.55 3.71
803 1156 3.706086 AGCCTGTTTCATCCTGTTGTTTT 59.294 39.130 0.00 0.00 0.00 2.43
804 1157 3.299503 AGCCTGTTTCATCCTGTTGTTT 58.700 40.909 0.00 0.00 0.00 2.83
821 1174 2.901839 TCTTAAACGTTGAGGGTAGCCT 59.098 45.455 14.79 14.79 0.00 4.58
856 1210 1.768275 TCTTCTTGGGCTGTGTGAGAA 59.232 47.619 0.00 0.00 0.00 2.87
872 1226 2.003301 GTCTGCTCGGTCCATTTCTTC 58.997 52.381 0.00 0.00 0.00 2.87
924 1278 1.215655 GCGCTCGAGTCACACAAACT 61.216 55.000 15.13 0.00 0.00 2.66
1187 1552 2.809119 ACGAACAACGCCATACAATCAA 59.191 40.909 0.00 0.00 46.94 2.57
1192 1557 1.261885 CACAACGAACAACGCCATACA 59.738 47.619 0.00 0.00 46.94 2.29
1193 1558 1.945207 CACAACGAACAACGCCATAC 58.055 50.000 0.00 0.00 46.94 2.39
1222 1591 2.881389 CAGAAGCTCGCCTCGACT 59.119 61.111 0.00 0.00 0.00 4.18
1443 1813 7.661536 ATAGGAACACTACTGACATATGTGT 57.338 36.000 14.43 8.57 42.68 3.72
1498 1889 6.771749 ACTATGGTAGGTTACTGCTACTACAG 59.228 42.308 0.00 0.00 43.59 2.74
1516 1907 2.356125 GCACACTGGGATCAACTATGGT 60.356 50.000 0.00 0.00 0.00 3.55
1558 1949 5.768164 ACCAATGTTAACCAAGACTAAGGTG 59.232 40.000 2.48 0.00 38.37 4.00
1641 2032 7.922505 TTTGTGTTTGAAATGCACATAGTAC 57.077 32.000 2.77 0.00 41.86 2.73
1648 2039 8.296799 TCTATTGATTTGTGTTTGAAATGCAC 57.703 30.769 0.00 0.00 0.00 4.57
1902 2294 5.180680 AGGTTTGGTAGTCGTTTAAGATTGC 59.819 40.000 0.00 0.00 0.00 3.56
2483 2878 6.238648 ACTTTTCCAGGGTGTTTCATAGTAG 58.761 40.000 0.00 0.00 0.00 2.57
2750 3227 3.954258 GGTTAATGAAGATGAAGGTGGGG 59.046 47.826 0.00 0.00 0.00 4.96
2801 3278 2.320681 ACTTCTACACCCCTAGCACA 57.679 50.000 0.00 0.00 0.00 4.57
2849 3326 7.118390 CCAAACAAACACATACAAAAGGTCAAA 59.882 33.333 0.00 0.00 0.00 2.69
2864 3341 3.321497 TGCTGACAAACCAAACAAACAC 58.679 40.909 0.00 0.00 0.00 3.32
2951 3429 7.178983 TGCCAAGTGAAGATTAAAAGGATCAAT 59.821 33.333 0.00 0.00 0.00 2.57
2964 3442 7.778853 AGATAAATGAGATTGCCAAGTGAAGAT 59.221 33.333 0.00 0.00 0.00 2.40
2974 3452 6.205658 GGGAGTACAAGATAAATGAGATTGCC 59.794 42.308 0.00 0.00 0.00 4.52
2975 3453 6.995091 AGGGAGTACAAGATAAATGAGATTGC 59.005 38.462 0.00 0.00 0.00 3.56
2976 3454 7.659390 GGAGGGAGTACAAGATAAATGAGATTG 59.341 40.741 0.00 0.00 0.00 2.67
2981 3459 4.960469 ACGGAGGGAGTACAAGATAAATGA 59.040 41.667 0.00 0.00 0.00 2.57
2996 3474 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2997 3475 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2998 3476 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2999 3477 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3031 3509 9.654663 AAGAGCGTTTAGATCACTAAATTAGTT 57.345 29.630 2.41 0.00 46.01 2.24
3048 3526 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
3049 3527 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
3050 3528 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
3051 3529 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
3052 3530 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3058 3536 9.656323 TGATGTACTCCCTCTGTAAACTAATAT 57.344 33.333 0.00 0.00 0.00 1.28
3059 3537 9.656323 ATGATGTACTCCCTCTGTAAACTAATA 57.344 33.333 0.00 0.00 0.00 0.98
3060 3538 7.973048 TGATGTACTCCCTCTGTAAACTAAT 57.027 36.000 0.00 0.00 0.00 1.73
3061 3539 7.973048 ATGATGTACTCCCTCTGTAAACTAA 57.027 36.000 0.00 0.00 0.00 2.24
3062 3540 7.399191 ACAATGATGTACTCCCTCTGTAAACTA 59.601 37.037 0.00 0.00 38.24 2.24
3063 3541 6.213600 ACAATGATGTACTCCCTCTGTAAACT 59.786 38.462 0.00 0.00 38.24 2.66
3064 3542 6.407202 ACAATGATGTACTCCCTCTGTAAAC 58.593 40.000 0.00 0.00 38.24 2.01
3065 3543 6.620877 ACAATGATGTACTCCCTCTGTAAA 57.379 37.500 0.00 0.00 38.24 2.01
3066 3544 6.013725 ACAACAATGATGTACTCCCTCTGTAA 60.014 38.462 0.00 0.00 39.40 2.41
3067 3545 5.483937 ACAACAATGATGTACTCCCTCTGTA 59.516 40.000 0.00 0.00 39.40 2.74
3068 3546 4.287067 ACAACAATGATGTACTCCCTCTGT 59.713 41.667 0.00 0.00 39.40 3.41
3069 3547 4.836825 ACAACAATGATGTACTCCCTCTG 58.163 43.478 0.00 0.00 39.40 3.35
3070 3548 5.505181 AACAACAATGATGTACTCCCTCT 57.495 39.130 0.00 0.00 39.40 3.69
3071 3549 5.705441 TGAAACAACAATGATGTACTCCCTC 59.295 40.000 0.00 0.00 39.40 4.30
3072 3550 5.630121 TGAAACAACAATGATGTACTCCCT 58.370 37.500 0.00 0.00 39.40 4.20
3073 3551 5.957842 TGAAACAACAATGATGTACTCCC 57.042 39.130 0.00 0.00 39.40 4.30
3076 3554 9.357652 GCATTATTGAAACAACAATGATGTACT 57.642 29.630 16.22 0.00 46.37 2.73
3077 3555 9.357652 AGCATTATTGAAACAACAATGATGTAC 57.642 29.630 16.22 9.79 46.37 2.90
3078 3556 9.571810 GAGCATTATTGAAACAACAATGATGTA 57.428 29.630 16.22 0.00 46.37 2.29
3079 3557 7.546667 GGAGCATTATTGAAACAACAATGATGT 59.453 33.333 16.22 11.26 46.37 3.06
3080 3558 7.253850 CGGAGCATTATTGAAACAACAATGATG 60.254 37.037 16.22 16.28 46.86 3.07
3081 3559 6.753279 CGGAGCATTATTGAAACAACAATGAT 59.247 34.615 16.22 11.46 40.15 2.45
3082 3560 6.072230 TCGGAGCATTATTGAAACAACAATGA 60.072 34.615 16.22 1.41 40.15 2.57
3083 3561 6.033831 GTCGGAGCATTATTGAAACAACAATG 59.966 38.462 10.01 10.01 40.15 2.82
3084 3562 6.092748 GTCGGAGCATTATTGAAACAACAAT 58.907 36.000 0.00 0.00 42.17 2.71
3085 3563 5.009110 TGTCGGAGCATTATTGAAACAACAA 59.991 36.000 0.00 0.00 0.00 2.83
3086 3564 4.517075 TGTCGGAGCATTATTGAAACAACA 59.483 37.500 0.00 0.00 0.00 3.33
3087 3565 5.041951 TGTCGGAGCATTATTGAAACAAC 57.958 39.130 0.00 0.00 0.00 3.32
3088 3566 5.000591 TCTGTCGGAGCATTATTGAAACAA 58.999 37.500 0.00 0.00 0.00 2.83
3089 3567 4.391830 GTCTGTCGGAGCATTATTGAAACA 59.608 41.667 0.00 0.00 0.00 2.83
3090 3568 4.391830 TGTCTGTCGGAGCATTATTGAAAC 59.608 41.667 0.00 0.00 0.00 2.78
3091 3569 4.391830 GTGTCTGTCGGAGCATTATTGAAA 59.608 41.667 0.00 0.00 0.00 2.69
3092 3570 3.932710 GTGTCTGTCGGAGCATTATTGAA 59.067 43.478 0.00 0.00 0.00 2.69
3093 3571 3.195610 AGTGTCTGTCGGAGCATTATTGA 59.804 43.478 0.00 0.00 0.00 2.57
3094 3572 3.525537 AGTGTCTGTCGGAGCATTATTG 58.474 45.455 0.00 0.00 0.00 1.90
3095 3573 3.895232 AGTGTCTGTCGGAGCATTATT 57.105 42.857 0.00 0.00 0.00 1.40
3096 3574 3.195610 TCAAGTGTCTGTCGGAGCATTAT 59.804 43.478 0.00 0.00 0.00 1.28
3097 3575 2.560981 TCAAGTGTCTGTCGGAGCATTA 59.439 45.455 0.00 0.00 0.00 1.90
3098 3576 1.344438 TCAAGTGTCTGTCGGAGCATT 59.656 47.619 0.00 0.00 0.00 3.56
3099 3577 0.969149 TCAAGTGTCTGTCGGAGCAT 59.031 50.000 0.00 0.00 0.00 3.79
3100 3578 0.750249 TTCAAGTGTCTGTCGGAGCA 59.250 50.000 0.00 0.00 0.00 4.26
3101 3579 1.865865 TTTCAAGTGTCTGTCGGAGC 58.134 50.000 0.00 0.00 0.00 4.70
3102 3580 6.727824 ATATTTTTCAAGTGTCTGTCGGAG 57.272 37.500 0.00 0.00 0.00 4.63
3103 3581 7.504924 AAATATTTTTCAAGTGTCTGTCGGA 57.495 32.000 0.00 0.00 0.00 4.55
3104 3582 8.286800 TGTAAATATTTTTCAAGTGTCTGTCGG 58.713 33.333 5.91 0.00 0.00 4.79
3105 3583 9.103048 GTGTAAATATTTTTCAAGTGTCTGTCG 57.897 33.333 5.91 0.00 0.00 4.35
3106 3584 9.944663 TGTGTAAATATTTTTCAAGTGTCTGTC 57.055 29.630 5.91 0.00 0.00 3.51
3107 3585 9.950680 CTGTGTAAATATTTTTCAAGTGTCTGT 57.049 29.630 5.91 0.00 0.00 3.41
3108 3586 9.398170 CCTGTGTAAATATTTTTCAAGTGTCTG 57.602 33.333 5.91 0.36 0.00 3.51
3109 3587 8.082242 GCCTGTGTAAATATTTTTCAAGTGTCT 58.918 33.333 5.91 0.00 0.00 3.41
3110 3588 8.082242 AGCCTGTGTAAATATTTTTCAAGTGTC 58.918 33.333 5.91 0.00 0.00 3.67
3111 3589 7.951591 AGCCTGTGTAAATATTTTTCAAGTGT 58.048 30.769 5.91 0.00 0.00 3.55
3112 3590 9.906660 TTAGCCTGTGTAAATATTTTTCAAGTG 57.093 29.630 5.91 0.99 0.00 3.16
3118 3596 9.214957 GCCTTTTTAGCCTGTGTAAATATTTTT 57.785 29.630 5.91 0.00 0.00 1.94
3119 3597 8.371699 TGCCTTTTTAGCCTGTGTAAATATTTT 58.628 29.630 5.91 0.00 0.00 1.82
3120 3598 7.902087 TGCCTTTTTAGCCTGTGTAAATATTT 58.098 30.769 5.89 5.89 0.00 1.40
3121 3599 7.475137 TGCCTTTTTAGCCTGTGTAAATATT 57.525 32.000 0.00 0.00 0.00 1.28
3122 3600 7.178451 ACTTGCCTTTTTAGCCTGTGTAAATAT 59.822 33.333 0.00 0.00 0.00 1.28
3123 3601 6.492087 ACTTGCCTTTTTAGCCTGTGTAAATA 59.508 34.615 0.00 0.00 0.00 1.40
3124 3602 5.304357 ACTTGCCTTTTTAGCCTGTGTAAAT 59.696 36.000 0.00 0.00 0.00 1.40
3125 3603 4.647399 ACTTGCCTTTTTAGCCTGTGTAAA 59.353 37.500 0.00 0.00 0.00 2.01
3126 3604 4.211920 ACTTGCCTTTTTAGCCTGTGTAA 58.788 39.130 0.00 0.00 0.00 2.41
3127 3605 3.827722 ACTTGCCTTTTTAGCCTGTGTA 58.172 40.909 0.00 0.00 0.00 2.90
3128 3606 2.666317 ACTTGCCTTTTTAGCCTGTGT 58.334 42.857 0.00 0.00 0.00 3.72
3129 3607 4.737054 CATACTTGCCTTTTTAGCCTGTG 58.263 43.478 0.00 0.00 0.00 3.66
3130 3608 3.193479 GCATACTTGCCTTTTTAGCCTGT 59.807 43.478 0.00 0.00 43.38 4.00
3131 3609 3.731867 CGCATACTTGCCTTTTTAGCCTG 60.732 47.826 0.00 0.00 46.57 4.85
3132 3610 2.423538 CGCATACTTGCCTTTTTAGCCT 59.576 45.455 0.00 0.00 46.57 4.58
3133 3611 2.422127 TCGCATACTTGCCTTTTTAGCC 59.578 45.455 0.00 0.00 46.57 3.93
3134 3612 3.127030 AGTCGCATACTTGCCTTTTTAGC 59.873 43.478 0.00 0.00 46.57 3.09
3135 3613 4.391830 TGAGTCGCATACTTGCCTTTTTAG 59.608 41.667 0.00 0.00 46.57 1.85
3136 3614 4.320023 TGAGTCGCATACTTGCCTTTTTA 58.680 39.130 0.00 0.00 46.57 1.52
3137 3615 3.146066 TGAGTCGCATACTTGCCTTTTT 58.854 40.909 0.00 0.00 46.57 1.94
3138 3616 2.778299 TGAGTCGCATACTTGCCTTTT 58.222 42.857 0.00 0.00 46.57 2.27
3139 3617 2.472695 TGAGTCGCATACTTGCCTTT 57.527 45.000 0.00 0.00 46.57 3.11
3140 3618 2.350522 CTTGAGTCGCATACTTGCCTT 58.649 47.619 0.00 0.00 46.57 4.35
3141 3619 1.406069 CCTTGAGTCGCATACTTGCCT 60.406 52.381 0.00 0.00 46.57 4.75
3142 3620 1.009829 CCTTGAGTCGCATACTTGCC 58.990 55.000 0.00 0.00 46.57 4.52
3143 3621 2.010145 TCCTTGAGTCGCATACTTGC 57.990 50.000 0.00 0.00 45.78 4.01


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

AutoCloner maintained by Alex Coulton.