Multiple sequence alignment - TraesCS1D01G060800

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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 TraesCS1D01G060800 chr1D 100.000 4460 0 0 1 4460 41159481 41155022 0.000000e+00 8237.0
1 TraesCS1D01G060800 chr1D 81.063 1035 145 29 1313 2311 41302295 41301276 0.000000e+00 778.0
2 TraesCS1D01G060800 chr1D 73.038 586 113 24 1508 2075 41312090 41311532 9.920000e-37 165.0
3 TraesCS1D01G060800 chr1A 92.338 3563 151 49 1 3505 40902402 40898904 0.000000e+00 4955.0
4 TraesCS1D01G060800 chr1A 80.593 1046 147 34 1313 2312 40914148 40913113 0.000000e+00 756.0
5 TraesCS1D01G060800 chr1A 97.692 390 9 0 4071 4460 40898331 40897942 0.000000e+00 671.0
6 TraesCS1D01G060800 chr1A 93.950 281 8 3 3795 4070 40898656 40898380 2.480000e-112 416.0
7 TraesCS1D01G060800 chr1A 97.059 136 4 0 3653 3788 40898846 40898711 3.470000e-56 230.0
8 TraesCS1D01G060800 chr1A 76.699 206 44 2 1566 1770 41151495 41151293 1.310000e-20 111.0
9 TraesCS1D01G060800 chr1A 95.522 67 2 1 3519 3584 40898921 40898855 6.100000e-19 106.0
10 TraesCS1D01G060800 chr1A 98.214 56 0 1 3954 4008 22561924 22561869 3.670000e-16 97.1
11 TraesCS1D01G060800 chr1A 98.214 56 0 1 3954 4008 278522774 278522719 3.670000e-16 97.1
12 TraesCS1D01G060800 chr1B 92.649 3197 157 29 353 3505 60726763 60723601 0.000000e+00 4530.0
13 TraesCS1D01G060800 chr1B 87.392 809 73 13 1 802 60727838 60727052 0.000000e+00 902.0
14 TraesCS1D01G060800 chr1B 81.234 1167 156 30 1313 2431 60965435 60964284 0.000000e+00 883.0
15 TraesCS1D01G060800 chr1B 94.721 341 12 3 4123 4460 60722928 60722591 3.950000e-145 525.0
16 TraesCS1D01G060800 chr1B 72.903 620 119 26 1508 2110 61054286 61053699 7.670000e-38 169.0
17 TraesCS1D01G060800 chr1B 72.481 516 98 25 1594 2107 60593413 60593886 4.680000e-25 126.0
18 TraesCS1D01G060800 chrUn 98.214 56 0 1 3954 4008 217909248 217909193 3.670000e-16 97.1
19 TraesCS1D01G060800 chr6D 98.214 56 0 1 3954 4008 108486789 108486734 3.670000e-16 97.1
20 TraesCS1D01G060800 chr4D 98.214 56 0 1 3954 4008 123447399 123447454 3.670000e-16 97.1
21 TraesCS1D01G060800 chr4B 98.214 56 0 1 3954 4008 209108117 209108062 3.670000e-16 97.1
22 TraesCS1D01G060800 chr4B 98.214 56 0 1 3954 4008 495478132 495478187 3.670000e-16 97.1
23 TraesCS1D01G060800 chr4B 98.214 56 0 1 3954 4008 504212397 504212452 3.670000e-16 97.1
24 TraesCS1D01G060800 chr6B 100.000 35 0 0 4006 4040 247384480 247384514 1.040000e-06 65.8


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 TraesCS1D01G060800 chr1D 41155022 41159481 4459 True 8237.000000 8237 100.000000 1 4460 1 chr1D.!!$R1 4459
1 TraesCS1D01G060800 chr1D 41301276 41302295 1019 True 778.000000 778 81.063000 1313 2311 1 chr1D.!!$R2 998
2 TraesCS1D01G060800 chr1A 40897942 40902402 4460 True 1275.600000 4955 95.312200 1 4460 5 chr1A.!!$R5 4459
3 TraesCS1D01G060800 chr1A 40913113 40914148 1035 True 756.000000 756 80.593000 1313 2312 1 chr1A.!!$R2 999
4 TraesCS1D01G060800 chr1B 60722591 60727838 5247 True 1985.666667 4530 91.587333 1 4460 3 chr1B.!!$R3 4459
5 TraesCS1D01G060800 chr1B 60964284 60965435 1151 True 883.000000 883 81.234000 1313 2431 1 chr1B.!!$R1 1118

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
38 39 0.396974 TAATTGGGCATGGGTCTGGC 60.397 55.0 0.00 0.0 40.76 4.85 F
1003 1754 0.467290 AAACAGAGGCTCCCGCAAAA 60.467 50.0 11.71 0.0 38.10 2.44 F
1476 2268 0.250295 CGGACCAAGACCAAGAAGCA 60.250 55.0 0.00 0.0 0.00 3.91 F
2656 3505 0.111253 CCAGGCCAGAAGGTTTGACT 59.889 55.0 5.01 0.0 37.19 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1863 0.248215 GATCGATGGCAAAACCGCAG 60.248 55.000 0.54 0.0 43.94 5.18 R
2314 3142 0.250252 GCCTTGGCTCATAGCTCTCC 60.250 60.000 4.11 0.0 41.99 3.71 R
3417 4291 0.467290 TTTCTGTGTGGGGACAAGCC 60.467 55.000 0.00 0.0 46.06 4.35 R
3971 4942 1.600957 CCTAGTGGCATGATCAAAGCG 59.399 52.381 14.87 3.8 0.00 4.68 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
38 39 0.396974 TAATTGGGCATGGGTCTGGC 60.397 55.000 0.00 0.00 40.76 4.85
161 162 3.668141 ATGAGGGCATTGTTGTATGGA 57.332 42.857 0.00 0.00 0.00 3.41
165 166 2.509548 AGGGCATTGTTGTATGGAGCTA 59.490 45.455 0.00 0.00 0.00 3.32
340 345 1.751351 TGTTTTCACAACCATTGCCGA 59.249 42.857 0.00 0.00 0.00 5.54
365 370 0.963856 GGTCCGCCCCACCTTAAAAG 60.964 60.000 0.00 0.00 0.00 2.27
390 395 2.125106 CCCTCCGCCACTACTTGC 60.125 66.667 0.00 0.00 0.00 4.01
452 457 2.028130 CAACCAACCAACCAGCTGTTA 58.972 47.619 13.81 0.00 34.69 2.41
498 503 1.429463 GTGGCAGTTTCTACCACGAG 58.571 55.000 3.80 0.00 44.02 4.18
507 512 4.272748 AGTTTCTACCACGAGTTTGCTTTC 59.727 41.667 0.00 0.00 0.00 2.62
511 516 1.134220 ACCACGAGTTTGCTTTCTGGA 60.134 47.619 0.00 0.00 0.00 3.86
514 519 2.221981 CACGAGTTTGCTTTCTGGACTC 59.778 50.000 0.00 0.00 34.78 3.36
585 1317 0.676184 CAATAGCCTAGCGCCTCTGA 59.324 55.000 2.29 0.00 38.78 3.27
642 1375 8.553153 TGGATGGAATTGTACTTAACCTCAATA 58.447 33.333 0.00 0.00 31.54 1.90
645 1378 7.924541 TGGAATTGTACTTAACCTCAATACCT 58.075 34.615 0.00 0.00 31.54 3.08
702 1436 6.422100 CAGAGTGACATCTTTTATATCGGTGG 59.578 42.308 0.00 0.00 0.00 4.61
703 1437 5.057149 AGTGACATCTTTTATATCGGTGGC 58.943 41.667 0.00 0.00 0.00 5.01
710 1444 6.687081 TCTTTTATATCGGTGGCGAAAAAT 57.313 33.333 0.00 0.00 0.00 1.82
743 1477 6.437928 TGCAATGCCATCTTTTTATATCGAC 58.562 36.000 1.53 0.00 0.00 4.20
761 1495 2.618053 GACGGATTGATTCGACTGGTT 58.382 47.619 0.00 0.00 0.00 3.67
906 1640 8.641498 TCATAAGGAAGCAATCTTCTCTTTTT 57.359 30.769 11.24 2.60 46.12 1.94
943 1677 8.752005 ATTGAATGGCATGTTTACAGTACTAT 57.248 30.769 0.00 0.00 0.00 2.12
987 1738 3.323751 AAAAGGCATCTGCATGGAAAC 57.676 42.857 4.33 0.00 44.36 2.78
988 1739 1.927487 AAGGCATCTGCATGGAAACA 58.073 45.000 4.33 0.00 44.36 2.83
989 1740 1.471119 AGGCATCTGCATGGAAACAG 58.529 50.000 4.33 0.00 44.36 3.16
991 1742 1.404391 GGCATCTGCATGGAAACAGAG 59.596 52.381 4.33 1.90 45.55 3.35
992 1743 3.842227 GGCATCTGCATGGAAACAGAGG 61.842 54.545 4.33 7.95 45.55 3.69
998 1749 3.068881 TGGAAACAGAGGCTCCCG 58.931 61.111 11.71 5.36 35.01 5.14
999 1750 2.436824 GGAAACAGAGGCTCCCGC 60.437 66.667 11.71 0.00 0.00 6.13
1000 1751 2.347490 GAAACAGAGGCTCCCGCA 59.653 61.111 11.71 0.00 38.10 5.69
1001 1752 1.302511 GAAACAGAGGCTCCCGCAA 60.303 57.895 11.71 0.00 38.10 4.85
1002 1753 0.889186 GAAACAGAGGCTCCCGCAAA 60.889 55.000 11.71 0.00 38.10 3.68
1003 1754 0.467290 AAACAGAGGCTCCCGCAAAA 60.467 50.000 11.71 0.00 38.10 2.44
1004 1755 0.467290 AACAGAGGCTCCCGCAAAAA 60.467 50.000 11.71 0.00 38.10 1.94
1108 1863 4.452733 CTCCGTCCCCCGCAAGAC 62.453 72.222 0.00 0.00 43.02 3.01
1187 1960 2.045242 CCTCCGTCTCCGTCTCCA 60.045 66.667 0.00 0.00 0.00 3.86
1205 1990 2.045047 TCCACAGAGATCCTTCCTTCCT 59.955 50.000 0.00 0.00 0.00 3.36
1207 1992 3.370315 CCACAGAGATCCTTCCTTCCTTG 60.370 52.174 0.00 0.00 0.00 3.61
1325 2111 2.393768 GGTCACATGGCGTCTGCTG 61.394 63.158 0.00 0.00 42.25 4.41
1476 2268 0.250295 CGGACCAAGACCAAGAAGCA 60.250 55.000 0.00 0.00 0.00 3.91
2173 2983 1.374125 CATTGCCGACGGTGTCAGA 60.374 57.895 16.73 0.00 32.09 3.27
2184 2994 2.601666 TGTCAGAGAGGGCACGCT 60.602 61.111 0.00 0.00 0.00 5.07
2312 3140 1.825281 CGATCCCCTGGAGATGGAGC 61.825 65.000 0.00 0.00 34.05 4.70
2313 3141 0.473501 GATCCCCTGGAGATGGAGCT 60.474 60.000 0.00 0.00 34.05 4.09
2314 3142 0.767446 ATCCCCTGGAGATGGAGCTG 60.767 60.000 0.00 0.00 34.05 4.24
2319 3147 1.042229 CTGGAGATGGAGCTGGAGAG 58.958 60.000 0.00 0.00 0.00 3.20
2337 3165 2.182842 GCTATGAGCCAAGGCCACG 61.183 63.158 5.01 0.00 43.17 4.94
2424 3255 4.760047 GTCGCCGGTGAGCCACAT 62.760 66.667 20.25 0.00 35.86 3.21
2447 3278 0.536687 CGATCCTCAGGCCAATGCAT 60.537 55.000 5.01 0.00 40.13 3.96
2505 3354 0.321475 GCTGCTCCTTCAGTGAAGCT 60.321 55.000 24.85 0.00 38.24 3.74
2656 3505 0.111253 CCAGGCCAGAAGGTTTGACT 59.889 55.000 5.01 0.00 37.19 3.41
2697 3546 0.625849 AGGAAATTGGATGCCGAGGT 59.374 50.000 0.00 0.00 0.00 3.85
2868 3717 0.533032 GAAGCTCTTCAGTAGCCGGT 59.467 55.000 1.90 0.00 41.02 5.28
2869 3718 0.977395 AAGCTCTTCAGTAGCCGGTT 59.023 50.000 1.90 0.00 41.02 4.44
2871 3720 1.066787 AGCTCTTCAGTAGCCGGTTTC 60.067 52.381 1.90 0.00 41.02 2.78
2872 3721 1.066787 GCTCTTCAGTAGCCGGTTTCT 60.067 52.381 1.90 0.00 33.73 2.52
2873 3722 2.611518 CTCTTCAGTAGCCGGTTTCTG 58.388 52.381 17.17 17.17 0.00 3.02
3010 3860 5.916318 TCAATGTTGTTTTTCCTCTTGCAT 58.084 33.333 0.00 0.00 0.00 3.96
3051 3901 5.506982 GGAGGCAATGAAAGAGATTACATGC 60.507 44.000 0.00 0.00 0.00 4.06
3135 3992 7.387673 TCAGGAACTATTGTCAGTTATGTTGTG 59.612 37.037 0.00 0.00 38.86 3.33
3257 4116 6.420008 GCAAAGACATCTAAATTGATGATGCC 59.580 38.462 11.60 4.03 44.71 4.40
3262 4121 8.755977 AGACATCTAAATTGATGATGCCTTTTT 58.244 29.630 11.60 0.00 44.71 1.94
3415 4289 9.561069 AATGATTTTACCAGTCCATGTCTATAC 57.439 33.333 0.00 0.00 0.00 1.47
3417 4291 8.204160 TGATTTTACCAGTCCATGTCTATACAG 58.796 37.037 0.00 0.00 39.49 2.74
3418 4292 6.479972 TTTACCAGTCCATGTCTATACAGG 57.520 41.667 0.00 0.00 39.49 4.00
3502 4376 8.160521 TCATGCAAGCAAGTTTTTAAGTACTA 57.839 30.769 0.00 0.00 0.00 1.82
3503 4377 8.073768 TCATGCAAGCAAGTTTTTAAGTACTAC 58.926 33.333 0.00 0.00 0.00 2.73
3504 4378 7.562454 TGCAAGCAAGTTTTTAAGTACTACT 57.438 32.000 0.00 0.00 0.00 2.57
3505 4379 7.992008 TGCAAGCAAGTTTTTAAGTACTACTT 58.008 30.769 6.68 6.68 41.97 2.24
3506 4380 8.126700 TGCAAGCAAGTTTTTAAGTACTACTTC 58.873 33.333 4.65 2.46 39.51 3.01
3507 4381 7.590322 GCAAGCAAGTTTTTAAGTACTACTTCC 59.410 37.037 4.65 0.00 39.51 3.46
3508 4382 7.741027 AGCAAGTTTTTAAGTACTACTTCCC 57.259 36.000 4.65 1.44 39.51 3.97
3509 4383 7.515586 AGCAAGTTTTTAAGTACTACTTCCCT 58.484 34.615 4.65 3.31 39.51 4.20
3510 4384 7.660617 AGCAAGTTTTTAAGTACTACTTCCCTC 59.339 37.037 4.65 0.00 39.51 4.30
3511 4385 7.443272 GCAAGTTTTTAAGTACTACTTCCCTCA 59.557 37.037 4.65 0.00 39.51 3.86
3512 4386 9.333724 CAAGTTTTTAAGTACTACTTCCCTCAA 57.666 33.333 4.65 0.00 39.51 3.02
3513 4387 9.910267 AAGTTTTTAAGTACTACTTCCCTCAAA 57.090 29.630 4.65 0.00 39.51 2.69
3514 4388 9.910267 AGTTTTTAAGTACTACTTCCCTCAAAA 57.090 29.630 4.65 4.14 39.51 2.44
3589 4465 7.707035 CAGGAACTAGTCAGTTATGTTGTATCC 59.293 40.741 0.00 0.00 45.18 2.59
3593 4469 6.986817 ACTAGTCAGTTATGTTGTATCCATGC 59.013 38.462 0.00 0.00 0.00 4.06
3594 4470 5.744171 AGTCAGTTATGTTGTATCCATGCA 58.256 37.500 0.00 0.00 0.00 3.96
3595 4471 5.586243 AGTCAGTTATGTTGTATCCATGCAC 59.414 40.000 0.00 0.00 0.00 4.57
3596 4472 4.881273 TCAGTTATGTTGTATCCATGCACC 59.119 41.667 0.00 0.00 0.00 5.01
3597 4473 4.639755 CAGTTATGTTGTATCCATGCACCA 59.360 41.667 0.00 0.00 0.00 4.17
3619 4538 8.397906 CACCAGTTTAATGACTATGTTATGTGG 58.602 37.037 0.00 0.00 0.00 4.17
3622 4541 8.946085 CAGTTTAATGACTATGTTATGTGGTGT 58.054 33.333 0.00 0.00 0.00 4.16
3635 4554 8.771920 TGTTATGTGGTGTAAAGACATCTAAG 57.228 34.615 0.00 0.00 37.60 2.18
3638 4557 7.672983 ATGTGGTGTAAAGACATCTAAGTTG 57.327 36.000 0.00 0.00 37.60 3.16
3640 4559 6.704493 TGTGGTGTAAAGACATCTAAGTTGAC 59.296 38.462 0.00 0.00 37.60 3.18
3641 4560 6.147328 GTGGTGTAAAGACATCTAAGTTGACC 59.853 42.308 0.00 0.00 37.60 4.02
3651 4570 8.486210 AGACATCTAAGTTGACCATGCTTTATA 58.514 33.333 0.00 0.00 0.00 0.98
3788 4707 1.280133 AGCAGTCCATGTGTATGCAGT 59.720 47.619 10.74 0.00 39.34 4.40
3789 4708 2.086869 GCAGTCCATGTGTATGCAGTT 58.913 47.619 0.00 0.00 36.88 3.16
3791 4710 3.426695 GCAGTCCATGTGTATGCAGTTTC 60.427 47.826 0.00 0.00 36.88 2.78
3846 4817 6.653526 TCAGTTCATCACAAATTTCACCAT 57.346 33.333 0.00 0.00 0.00 3.55
3847 4818 7.053316 TCAGTTCATCACAAATTTCACCATT 57.947 32.000 0.00 0.00 0.00 3.16
3934 4905 1.906994 GCTACATTTCACACGGCGCA 61.907 55.000 10.83 0.00 0.00 6.09
3971 4942 5.627367 GTGTCAGACATAGCTTACGATCATC 59.373 44.000 6.51 0.00 0.00 2.92
4018 4989 8.920665 CATTTGATTAGGACATCTCTTCGATAC 58.079 37.037 0.00 0.00 0.00 2.24
4031 5002 5.176406 TCTCTTCGATACGGATACAGTAACG 59.824 44.000 6.52 6.52 40.37 3.18
4054 5025 2.120232 CATAGCACGTCAAGATCCGAC 58.880 52.381 3.31 3.31 0.00 4.79
4055 5026 0.454600 TAGCACGTCAAGATCCGACC 59.545 55.000 7.18 0.00 0.00 4.79
4121 5154 6.696148 CAGGATTAATCAATTCAGCAAGAAGC 59.304 38.462 17.07 0.00 40.15 3.86
4179 5296 5.485353 TCAACTTGGAGGTGTCAAGATATCT 59.515 40.000 10.30 0.00 42.94 1.98
4198 5315 8.516234 AGATATCTCGTTACATACATTGACTCC 58.484 37.037 0.00 0.00 0.00 3.85
4244 5362 4.111577 ACATTGATCTAACTGGAGGGGAA 58.888 43.478 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.601419 TTTAGCCGGGTCGACCTCTG 61.601 60.000 32.52 21.78 36.97 3.35
67 68 1.674962 GATCTGGATCAACCTTGCAGC 59.325 52.381 5.79 0.00 39.86 5.25
72 73 2.169352 CGACTGGATCTGGATCAACCTT 59.831 50.000 11.93 0.00 39.54 3.50
126 127 4.017591 TGCCCTCATTTTCCTCCTTTCATA 60.018 41.667 0.00 0.00 0.00 2.15
142 143 2.945440 GCTCCATACAACAATGCCCTCA 60.945 50.000 0.00 0.00 0.00 3.86
161 162 1.709994 GGTTATGCTGGGGCCTAGCT 61.710 60.000 36.90 25.63 41.66 3.32
165 166 2.616893 TGGGTTATGCTGGGGCCT 60.617 61.111 0.84 0.00 37.74 5.19
340 345 2.676265 GGTGGGGCGGACCTTGTAT 61.676 63.158 0.00 0.00 40.03 2.29
365 370 4.849310 TGGCGGAGGGCGCAATAC 62.849 66.667 10.83 0.00 44.92 1.89
390 395 2.286184 CGTCTCAAAACACAAAGGACCG 60.286 50.000 0.00 0.00 0.00 4.79
452 457 3.671740 TCTCCTGTCTATACCTGCTGT 57.328 47.619 0.00 0.00 0.00 4.40
461 466 3.843422 CCACCTCTGATCTCCTGTCTAT 58.157 50.000 0.00 0.00 0.00 1.98
498 503 1.202940 AGGGGAGTCCAGAAAGCAAAC 60.203 52.381 12.30 0.00 38.24 2.93
507 512 2.038557 TCGAAAAAGAAGGGGAGTCCAG 59.961 50.000 12.30 0.00 38.24 3.86
585 1317 0.459899 TGCTAGCGAATCACACCGAT 59.540 50.000 10.77 0.00 35.12 4.18
642 1375 2.297701 CAACAGCTGTGGTTGTTAGGT 58.702 47.619 22.49 0.00 43.23 3.08
645 1378 1.756430 TGCAACAGCTGTGGTTGTTA 58.244 45.000 22.49 6.11 43.23 2.41
702 1436 5.173854 GCATTGCATTCCTACTATTTTTCGC 59.826 40.000 3.15 0.00 0.00 4.70
703 1437 5.687285 GGCATTGCATTCCTACTATTTTTCG 59.313 40.000 11.39 0.00 0.00 3.46
710 1444 4.712051 AGATGGCATTGCATTCCTACTA 57.288 40.909 11.39 0.00 0.00 1.82
731 1465 7.650504 AGTCGAATCAATCCGTCGATATAAAAA 59.349 33.333 0.00 0.00 44.75 1.94
743 1477 6.838198 TTAATAACCAGTCGAATCAATCCG 57.162 37.500 0.00 0.00 0.00 4.18
839 1573 6.017400 CAGGTTTTAGTTGAGAACATGCAT 57.983 37.500 0.00 0.00 29.99 3.96
916 1650 7.895759 AGTACTGTAAACATGCCATTCAATTT 58.104 30.769 0.00 0.00 0.00 1.82
917 1651 7.466746 AGTACTGTAAACATGCCATTCAATT 57.533 32.000 0.00 0.00 0.00 2.32
918 1652 8.752005 ATAGTACTGTAAACATGCCATTCAAT 57.248 30.769 5.39 0.00 0.00 2.57
943 1677 8.806429 TTTTACAGCCTCTGATTTCATCATTA 57.194 30.769 0.29 0.00 38.85 1.90
1005 1756 3.575805 TGGAGCCTCTGTTTCCATTTTT 58.424 40.909 0.00 0.00 36.13 1.94
1006 1757 3.243359 TGGAGCCTCTGTTTCCATTTT 57.757 42.857 0.00 0.00 36.13 1.82
1007 1758 2.978156 TGGAGCCTCTGTTTCCATTT 57.022 45.000 0.00 0.00 36.13 2.32
1008 1759 2.978156 TTGGAGCCTCTGTTTCCATT 57.022 45.000 0.00 0.00 40.48 3.16
1108 1863 0.248215 GATCGATGGCAAAACCGCAG 60.248 55.000 0.54 0.00 43.94 5.18
1187 1960 3.525862 ACAAGGAAGGAAGGATCTCTGT 58.474 45.455 0.00 0.00 0.00 3.41
1193 1978 5.103898 GGGAAGATTACAAGGAAGGAAGGAT 60.104 44.000 0.00 0.00 0.00 3.24
1194 1979 4.227527 GGGAAGATTACAAGGAAGGAAGGA 59.772 45.833 0.00 0.00 0.00 3.36
1205 1990 2.092646 CCATGGACGGGGAAGATTACAA 60.093 50.000 5.56 0.00 0.00 2.41
1207 1992 1.814248 GCCATGGACGGGGAAGATTAC 60.814 57.143 18.40 0.00 0.00 1.89
1564 2374 0.884704 CCTTCACCTTGGACCACACG 60.885 60.000 0.00 0.00 0.00 4.49
1799 2609 2.949909 CGAACGGGGACATGGTGGA 61.950 63.158 0.00 0.00 0.00 4.02
1968 2778 4.003788 CGTCCCTGGTGAAGGCGT 62.004 66.667 0.00 0.00 45.89 5.68
2051 2861 2.659610 GGTGAGCTCGAGCCTGTT 59.340 61.111 32.94 15.61 43.38 3.16
2083 2893 4.003788 CGGGTGAAGGCCGTGAGT 62.004 66.667 0.00 0.00 0.00 3.41
2293 3121 1.825281 GCTCCATCTCCAGGGGATCG 61.825 65.000 0.00 0.00 0.00 3.69
2312 3140 1.070445 CCTTGGCTCATAGCTCTCCAG 59.930 57.143 0.00 0.00 41.99 3.86
2313 3141 1.126488 CCTTGGCTCATAGCTCTCCA 58.874 55.000 0.00 0.00 41.99 3.86
2314 3142 0.250252 GCCTTGGCTCATAGCTCTCC 60.250 60.000 4.11 0.00 41.99 3.71
2319 3147 2.182842 CGTGGCCTTGGCTCATAGC 61.183 63.158 11.71 0.00 41.46 2.97
2337 3165 3.311110 TCTGGTGAGACACGGGCC 61.311 66.667 0.00 0.00 34.83 5.80
2447 3278 1.624813 TGTCATCATCACACCTGCAGA 59.375 47.619 17.39 0.00 0.00 4.26
2460 3291 1.302431 CCGGTGCACCTTGTCATCA 60.302 57.895 32.28 0.00 0.00 3.07
2505 3354 0.895100 GTTGAGGCCACCATTCTGCA 60.895 55.000 5.01 0.00 0.00 4.41
2697 3546 2.494530 GGGGTGCTTGAAAACGCCA 61.495 57.895 8.36 0.00 45.97 5.69
2866 3715 4.600692 AACAAAACCCATAGCAGAAACC 57.399 40.909 0.00 0.00 0.00 3.27
2868 3717 5.363939 CCAAAACAAAACCCATAGCAGAAA 58.636 37.500 0.00 0.00 0.00 2.52
2869 3718 4.202305 CCCAAAACAAAACCCATAGCAGAA 60.202 41.667 0.00 0.00 0.00 3.02
2871 3720 3.556843 CCCCAAAACAAAACCCATAGCAG 60.557 47.826 0.00 0.00 0.00 4.24
2872 3721 2.370189 CCCCAAAACAAAACCCATAGCA 59.630 45.455 0.00 0.00 0.00 3.49
2873 3722 2.290008 CCCCCAAAACAAAACCCATAGC 60.290 50.000 0.00 0.00 0.00 2.97
3010 3860 4.476846 TGCCTCCTCCTATCCAAAATAACA 59.523 41.667 0.00 0.00 0.00 2.41
3051 3901 5.978934 AAACTTGCTTTGCTTGATTTGAG 57.021 34.783 0.00 0.00 0.00 3.02
3415 4289 1.601759 CTGTGTGGGGACAAGCCTG 60.602 63.158 0.00 0.00 46.06 4.85
3417 4291 0.467290 TTTCTGTGTGGGGACAAGCC 60.467 55.000 0.00 0.00 46.06 4.35
3418 4292 1.398692 TTTTCTGTGTGGGGACAAGC 58.601 50.000 0.00 0.00 46.06 4.01
3465 4339 4.633175 TGCTTGCATGATTTGAACATGTT 58.367 34.783 11.78 11.78 44.52 2.71
3522 4396 9.417561 ACAGGCTATCATGTAGTAGTACTTAAA 57.582 33.333 8.40 0.00 0.00 1.52
3523 4397 8.991783 ACAGGCTATCATGTAGTAGTACTTAA 57.008 34.615 8.40 0.00 0.00 1.85
3524 4398 9.722184 CTACAGGCTATCATGTAGTAGTACTTA 57.278 37.037 8.40 0.00 42.50 2.24
3525 4399 7.175293 GCTACAGGCTATCATGTAGTAGTACTT 59.825 40.741 16.95 0.00 46.89 2.24
3526 4400 6.655848 GCTACAGGCTATCATGTAGTAGTACT 59.344 42.308 16.95 8.14 46.89 2.73
3527 4401 6.430308 TGCTACAGGCTATCATGTAGTAGTAC 59.570 42.308 16.95 0.37 46.89 2.73
3528 4402 6.540083 TGCTACAGGCTATCATGTAGTAGTA 58.460 40.000 16.95 2.88 46.89 1.82
3529 4403 5.386060 TGCTACAGGCTATCATGTAGTAGT 58.614 41.667 16.95 0.00 46.89 2.73
3530 4404 5.966742 TGCTACAGGCTATCATGTAGTAG 57.033 43.478 16.95 6.42 46.89 2.57
3531 4405 4.767409 CCTGCTACAGGCTATCATGTAGTA 59.233 45.833 16.95 12.82 46.89 1.82
3532 4406 3.576118 CCTGCTACAGGCTATCATGTAGT 59.424 47.826 16.95 0.00 46.89 2.73
3589 4465 6.441093 ACATAGTCATTAAACTGGTGCATG 57.559 37.500 0.00 0.00 0.00 4.06
3593 4469 8.397906 CCACATAACATAGTCATTAAACTGGTG 58.602 37.037 0.00 0.00 0.00 4.17
3594 4470 8.107095 ACCACATAACATAGTCATTAAACTGGT 58.893 33.333 0.00 0.00 0.00 4.00
3595 4471 8.397906 CACCACATAACATAGTCATTAAACTGG 58.602 37.037 0.00 0.00 0.00 4.00
3596 4472 8.946085 ACACCACATAACATAGTCATTAAACTG 58.054 33.333 0.00 0.00 0.00 3.16
3619 4538 7.624344 GCATGGTCAACTTAGATGTCTTTACAC 60.624 40.741 0.00 0.00 38.78 2.90
3622 4541 6.711277 AGCATGGTCAACTTAGATGTCTTTA 58.289 36.000 0.00 0.00 0.00 1.85
3910 4881 3.259064 GCCGTGTGAAATGTAGCTCTTA 58.741 45.455 0.00 0.00 0.00 2.10
3934 4905 3.509967 TGTCTGACACTACATGGAATCGT 59.490 43.478 6.36 0.00 0.00 3.73
3971 4942 1.600957 CCTAGTGGCATGATCAAAGCG 59.399 52.381 14.87 3.80 0.00 4.68
4004 4975 5.064558 ACTGTATCCGTATCGAAGAGATGT 58.935 41.667 0.00 0.00 43.63 3.06
4018 4989 4.852104 GTGCTATGATCGTTACTGTATCCG 59.148 45.833 0.00 0.00 0.00 4.18
4031 5002 2.983136 CGGATCTTGACGTGCTATGATC 59.017 50.000 0.00 2.28 0.00 2.92
4054 5025 6.480524 TGTTCGTTTCTTATGATGTTCAGG 57.519 37.500 0.00 0.00 0.00 3.86
4055 5026 7.531871 CACTTGTTCGTTTCTTATGATGTTCAG 59.468 37.037 0.00 0.00 0.00 3.02
4121 5154 3.560481 TGCTGTTTGGTTGCAAATGATTG 59.440 39.130 0.00 0.00 39.65 2.67
4179 5296 6.693466 TCTTTGGAGTCAATGTATGTAACGA 58.307 36.000 0.00 0.00 32.28 3.85
4198 5315 4.278170 TGTACAGCCCACTTTGATTCTTTG 59.722 41.667 0.00 0.00 0.00 2.77
4244 5362 4.512571 GCTGAATGTGCAACTCCAATTTTT 59.487 37.500 0.00 0.00 38.04 1.94


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

AutoCloner maintained by Alex Coulton.