Multiple sequence alignment - TraesCS2A01G582300

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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 TraesCS2A01G582300 chr2A 100.000 3965 0 0 1 3965 774577236 774573272 0.000000e+00 7323
1 TraesCS2A01G582300 chr2D 88.335 3892 250 84 183 3953 650319341 650323149 0.000000e+00 4484
2 TraesCS2A01G582300 chr2B 88.052 2059 183 41 1934 3953 786225147 786227181 0.000000e+00 2381
3 TraesCS2A01G582300 chr2B 82.778 2009 173 78 2 1936 786222999 786224908 0.000000e+00 1633
4 TraesCS2A01G582300 chr6A 84.453 521 67 7 2130 2640 27198031 27197515 5.920000e-138 501
5 TraesCS2A01G582300 chrUn 87.705 366 31 9 2709 3065 96707904 96707544 7.930000e-112 414
6 TraesCS2A01G582300 chrUn 83.453 139 18 5 3065 3200 96702250 96702114 1.500000e-24 124
7 TraesCS2A01G582300 chr6B 86.792 371 38 11 2654 3024 47899090 47898731 1.720000e-108 403


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 TraesCS2A01G582300 chr2A 774573272 774577236 3964 True 7323 7323 100.000 1 3965 1 chr2A.!!$R1 3964
1 TraesCS2A01G582300 chr2D 650319341 650323149 3808 False 4484 4484 88.335 183 3953 1 chr2D.!!$F1 3770
2 TraesCS2A01G582300 chr2B 786222999 786227181 4182 False 2007 2381 85.415 2 3953 2 chr2B.!!$F1 3951
3 TraesCS2A01G582300 chr6A 27197515 27198031 516 True 501 501 84.453 2130 2640 1 chr6A.!!$R1 510

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
25 26 0.031585 CATAGCATGCATGTGTGGCC 59.968 55.0 26.79 9.88 0.0 5.36 F
31 32 0.462581 ATGCATGTGTGGCCGTCTAG 60.463 55.0 0.00 0.00 0.0 2.43 F
568 622 0.949588 CGCCTCGTCTCGCCTATCTA 60.950 60.0 0.00 0.00 0.0 1.98 F
2127 2538 0.188342 AAACTGGGACAATGCCACCT 59.812 50.0 0.00 0.00 38.7 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1869 0.675633 GTTGACAATTGGCAGGCAGT 59.324 50.000 14.91 0.00 32.66 4.40 R
1743 1888 3.657634 ACTGCACAGTACAGATGTTCTG 58.342 45.455 15.49 15.49 45.28 3.02 R
2149 2562 0.463295 CATCAGGTGCAGCAGGGTAG 60.463 60.000 19.63 0.63 0.00 3.18 R
3860 4316 0.251474 AGATGTGCCATTGTGCAGGT 60.251 50.000 0.00 0.00 43.02 4.00 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 0.031585 CATAGCATGCATGTGTGGCC 59.968 55.000 26.79 9.88 0.00 5.36
31 32 0.462581 ATGCATGTGTGGCCGTCTAG 60.463 55.000 0.00 0.00 0.00 2.43
62 63 3.369576 GCGGTTCTCCTCTACCTTGATTT 60.370 47.826 0.00 0.00 32.08 2.17
63 64 4.142004 GCGGTTCTCCTCTACCTTGATTTA 60.142 45.833 0.00 0.00 32.08 1.40
73 74 8.483758 TCCTCTACCTTGATTTATGTTTAGTCC 58.516 37.037 0.00 0.00 0.00 3.85
82 83 6.667414 TGATTTATGTTTAGTCCCATGCCTTT 59.333 34.615 0.00 0.00 0.00 3.11
91 92 3.153919 GTCCCATGCCTTTGAACACTTA 58.846 45.455 0.00 0.00 0.00 2.24
93 94 3.826157 TCCCATGCCTTTGAACACTTAAG 59.174 43.478 0.00 0.00 0.00 1.85
94 95 3.826157 CCCATGCCTTTGAACACTTAAGA 59.174 43.478 10.09 0.00 0.00 2.10
95 96 4.321230 CCCATGCCTTTGAACACTTAAGAC 60.321 45.833 10.09 0.00 0.00 3.01
97 98 4.893424 TGCCTTTGAACACTTAAGACAC 57.107 40.909 10.09 0.00 0.00 3.67
98 99 4.523083 TGCCTTTGAACACTTAAGACACT 58.477 39.130 10.09 0.00 0.00 3.55
100 101 4.023963 GCCTTTGAACACTTAAGACACTCC 60.024 45.833 10.09 0.00 0.00 3.85
102 103 5.367945 TTTGAACACTTAAGACACTCCCT 57.632 39.130 10.09 0.00 0.00 4.20
103 104 4.602340 TGAACACTTAAGACACTCCCTC 57.398 45.455 10.09 0.00 0.00 4.30
104 105 3.964688 TGAACACTTAAGACACTCCCTCA 59.035 43.478 10.09 0.00 0.00 3.86
105 106 4.039245 TGAACACTTAAGACACTCCCTCAG 59.961 45.833 10.09 0.00 0.00 3.35
106 107 3.577919 ACACTTAAGACACTCCCTCAGT 58.422 45.455 10.09 0.00 34.67 3.41
107 108 4.737578 ACACTTAAGACACTCCCTCAGTA 58.262 43.478 10.09 0.00 32.21 2.74
109 110 5.601313 ACACTTAAGACACTCCCTCAGTAAA 59.399 40.000 10.09 0.00 32.21 2.01
110 111 6.099269 ACACTTAAGACACTCCCTCAGTAAAA 59.901 38.462 10.09 0.00 32.21 1.52
111 112 6.990349 CACTTAAGACACTCCCTCAGTAAAAA 59.010 38.462 10.09 0.00 32.21 1.94
142 143 6.990798 AGAGCGTTTAGGTAAGTTAGACTTT 58.009 36.000 0.00 0.00 39.51 2.66
160 161 9.787435 TTAGACTTTGTAAACATTCCAGTATGT 57.213 29.630 0.00 0.00 40.37 2.29
218 219 2.582498 GGTGCGATCGACGAAGGG 60.582 66.667 21.57 0.00 45.77 3.95
338 348 4.581093 GGGCCGGGGCTATTCCAC 62.581 72.222 20.88 0.00 41.60 4.02
352 362 4.337555 GCTATTCCACGGACTACTGTAGAA 59.662 45.833 21.01 4.10 37.41 2.10
561 606 4.400109 TGTGTCGCCTCGTCTCGC 62.400 66.667 0.00 0.00 0.00 5.03
568 622 0.949588 CGCCTCGTCTCGCCTATCTA 60.950 60.000 0.00 0.00 0.00 1.98
569 623 1.455248 GCCTCGTCTCGCCTATCTAT 58.545 55.000 0.00 0.00 0.00 1.98
587 641 4.704833 CTGTCTGTGTGGGGCGGG 62.705 72.222 0.00 0.00 0.00 6.13
659 721 3.434319 CATCGGTGGTGCTGTGCC 61.434 66.667 0.00 0.00 0.00 5.01
660 722 4.722700 ATCGGTGGTGCTGTGCCC 62.723 66.667 0.00 0.00 0.00 5.36
663 725 3.064324 GGTGGTGCTGTGCCCATC 61.064 66.667 3.80 0.39 33.13 3.51
664 726 3.064324 GTGGTGCTGTGCCCATCC 61.064 66.667 3.80 0.00 33.13 3.51
665 727 3.259314 TGGTGCTGTGCCCATCCT 61.259 61.111 0.00 0.00 0.00 3.24
846 937 3.379452 TCTCCTCCTCATCCCTTCTTTC 58.621 50.000 0.00 0.00 0.00 2.62
988 1083 3.490348 CTTTTGGAGGAGGAAGAAAGCA 58.510 45.455 0.00 0.00 0.00 3.91
1047 1142 1.069765 CGACCTGCCGCCATTCTAT 59.930 57.895 0.00 0.00 0.00 1.98
1061 1156 2.124445 CTATGGCCAGCAGCAGCA 60.124 61.111 13.05 0.00 46.50 4.41
1062 1157 2.124445 TATGGCCAGCAGCAGCAG 60.124 61.111 13.05 0.00 46.50 4.24
1252 1356 2.373224 TGCAGTTCAACATGGACAACA 58.627 42.857 0.00 0.00 0.00 3.33
1282 1386 1.236616 TTCCTCCATGTTGCAGCACG 61.237 55.000 5.00 0.00 0.00 5.34
1283 1387 2.177531 CTCCATGTTGCAGCACGC 59.822 61.111 5.00 0.00 42.89 5.34
1285 1389 4.764336 CCATGTTGCAGCACGCCG 62.764 66.667 5.00 0.00 41.33 6.46
1293 1397 4.764336 CAGCACGCCGGCAACATG 62.764 66.667 28.98 19.04 35.83 3.21
1305 1409 1.973281 CAACATGGGCGGCTCTGTT 60.973 57.895 18.83 18.83 32.27 3.16
1308 1412 1.377725 CATGGGCGGCTCTGTTTCT 60.378 57.895 9.56 0.00 0.00 2.52
1317 1421 1.743252 CTCTGTTTCTGGCTCGGGC 60.743 63.158 0.00 0.00 37.82 6.13
1318 1422 2.032528 CTGTTTCTGGCTCGGGCA 59.967 61.111 10.74 4.62 40.87 5.36
1319 1423 2.281484 TGTTTCTGGCTCGGGCAC 60.281 61.111 10.74 0.00 40.87 5.01
1455 1559 1.807226 GCATCATCAGCAGCAGCAA 59.193 52.632 3.17 0.00 45.49 3.91
1476 1583 4.923942 CAGATGATGGGCGCGCCT 62.924 66.667 45.23 30.67 36.10 5.52
1587 1694 0.972983 CCGGGAAGAAGCTCTCCTCA 60.973 60.000 0.00 0.00 0.00 3.86
1614 1721 2.094338 CAGTAAACCCTCCGGTCAGTAC 60.094 54.545 0.00 0.00 43.71 2.73
1691 1834 7.857404 ATATATGCACTGTCCTACTTAAGGT 57.143 36.000 7.53 0.00 46.62 3.50
1743 1888 0.675633 ACTGCCTGCCAATTGTCAAC 59.324 50.000 4.43 0.00 0.00 3.18
1748 1893 2.863704 GCCTGCCAATTGTCAACAGAAC 60.864 50.000 4.43 0.00 0.00 3.01
1796 1942 7.495901 TGTAGCAAAGGAATGTTGATTTTTGA 58.504 30.769 0.00 0.00 27.34 2.69
1979 2375 5.274881 CATAGTCTGCAGTTCACTGAAAC 57.725 43.478 14.67 0.57 46.59 2.78
1985 2381 2.163412 TGCAGTTCACTGAAACCACAAC 59.837 45.455 11.29 0.00 46.59 3.32
1989 2385 3.945285 AGTTCACTGAAACCACAACGAAT 59.055 39.130 0.00 0.00 0.00 3.34
2100 2511 1.751351 TCTCCTTCAGAGGTATGCACG 59.249 52.381 0.00 0.00 43.97 5.34
2115 2526 2.519826 CACGCAATGCAAAACTGGG 58.480 52.632 5.91 0.00 0.00 4.45
2120 2531 2.769893 GCAATGCAAAACTGGGACAAT 58.230 42.857 0.00 0.00 38.70 2.71
2121 2532 2.481185 GCAATGCAAAACTGGGACAATG 59.519 45.455 0.00 0.00 38.70 2.82
2127 2538 0.188342 AAACTGGGACAATGCCACCT 59.812 50.000 0.00 0.00 38.70 4.00
2128 2539 1.072266 AACTGGGACAATGCCACCTA 58.928 50.000 0.00 0.00 38.70 3.08
2134 2547 3.245586 TGGGACAATGCCACCTAAATTCT 60.246 43.478 0.00 0.00 30.85 2.40
2138 2551 6.239036 GGGACAATGCCACCTAAATTCTATTC 60.239 42.308 0.00 0.00 0.00 1.75
2149 2562 9.213799 CACCTAAATTCTATTCTATTCCTCTGC 57.786 37.037 0.00 0.00 0.00 4.26
2243 2657 2.815211 GCATTCGCGAGCCAGTCA 60.815 61.111 9.59 0.00 0.00 3.41
2330 2744 4.041444 GCAGATCATCCTCCTTCCTACAAT 59.959 45.833 0.00 0.00 0.00 2.71
2352 2766 1.910671 ACCCTGCCATTTACGAGGTAA 59.089 47.619 0.00 0.00 0.00 2.85
2371 2789 3.988976 AAGCGACCATCCTATATGCAT 57.011 42.857 3.79 3.79 0.00 3.96
2379 2804 6.481313 CGACCATCCTATATGCATATCAAAGG 59.519 42.308 22.33 21.64 0.00 3.11
2381 2806 7.571919 ACCATCCTATATGCATATCAAAGGAG 58.428 38.462 28.36 21.77 36.35 3.69
2399 2824 2.497675 GGAGTGATGCACCTGAGACTTA 59.502 50.000 0.00 0.00 34.49 2.24
2402 2827 5.163405 GGAGTGATGCACCTGAGACTTATAA 60.163 44.000 0.00 0.00 34.49 0.98
2551 2982 1.098050 GGCATGTCATTGGAGGTGTC 58.902 55.000 0.00 0.00 0.00 3.67
2569 3000 1.679977 CCTGGGTGGAGCATTGGTG 60.680 63.158 0.00 0.00 38.35 4.17
2610 3041 7.144661 CAGGTAACAGCAATCTACTAGATCAG 58.855 42.308 0.00 0.00 33.74 2.90
2611 3042 5.923684 GGTAACAGCAATCTACTAGATCAGC 59.076 44.000 12.40 12.40 32.89 4.26
2612 3043 4.599047 ACAGCAATCTACTAGATCAGCC 57.401 45.455 15.03 3.91 36.75 4.85
2620 3051 4.078537 TCTACTAGATCAGCCTCATCTGC 58.921 47.826 0.00 0.00 32.61 4.26
2647 3078 1.003580 TCAGACATGGAACCAAGCTCC 59.996 52.381 0.00 0.00 0.00 4.70
2654 3086 1.034292 GGAACCAAGCTCCTGCATCC 61.034 60.000 0.00 0.00 42.74 3.51
2656 3088 0.323178 AACCAAGCTCCTGCATCCAG 60.323 55.000 0.00 0.00 42.74 3.86
2657 3089 1.203441 ACCAAGCTCCTGCATCCAGA 61.203 55.000 0.00 0.00 41.77 3.86
2659 3091 1.595466 CAAGCTCCTGCATCCAGATC 58.405 55.000 0.00 0.00 41.77 2.75
2661 3093 1.210538 AGCTCCTGCATCCAGATCAA 58.789 50.000 0.00 0.00 41.77 2.57
2662 3094 1.134159 AGCTCCTGCATCCAGATCAAC 60.134 52.381 0.00 0.00 41.77 3.18
2663 3095 1.964552 CTCCTGCATCCAGATCAACC 58.035 55.000 0.00 0.00 41.77 3.77
2665 3097 1.487976 TCCTGCATCCAGATCAACCTC 59.512 52.381 0.00 0.00 41.77 3.85
2666 3098 1.211212 CCTGCATCCAGATCAACCTCA 59.789 52.381 0.00 0.00 41.77 3.86
2668 3100 3.552875 CTGCATCCAGATCAACCTCATT 58.447 45.455 0.00 0.00 41.77 2.57
2669 3101 3.952323 CTGCATCCAGATCAACCTCATTT 59.048 43.478 0.00 0.00 41.77 2.32
2670 3102 3.697542 TGCATCCAGATCAACCTCATTTG 59.302 43.478 0.00 0.00 0.00 2.32
2671 3103 3.490419 GCATCCAGATCAACCTCATTTGC 60.490 47.826 0.00 0.00 0.00 3.68
2672 3104 3.726557 TCCAGATCAACCTCATTTGCT 57.273 42.857 0.00 0.00 0.00 3.91
2675 3107 5.188434 TCCAGATCAACCTCATTTGCTAAG 58.812 41.667 0.00 0.00 0.00 2.18
2677 3109 5.826737 CCAGATCAACCTCATTTGCTAAGAT 59.173 40.000 0.00 0.00 0.00 2.40
2678 3110 6.320672 CCAGATCAACCTCATTTGCTAAGATT 59.679 38.462 0.00 0.00 0.00 2.40
2679 3111 7.416022 CAGATCAACCTCATTTGCTAAGATTC 58.584 38.462 0.00 0.00 0.00 2.52
2689 3128 8.791327 TCATTTGCTAAGATTCAGACATACAA 57.209 30.769 0.00 0.00 0.00 2.41
2694 3133 9.665719 TTGCTAAGATTCAGACATACAACATAA 57.334 29.630 0.00 0.00 0.00 1.90
2754 3193 1.478654 GGGACTTTTGTGCAAGGAGGA 60.479 52.381 0.00 0.00 42.95 3.71
2834 3273 4.415150 CGCTGGGCCAGATGTGGT 62.415 66.667 37.07 0.00 46.96 4.16
2925 3364 4.101585 CCTAGCTCTGGGATATTTGACACA 59.898 45.833 0.00 0.00 32.26 3.72
2992 3431 4.336889 TTTGTCGACACTTCCATCTCTT 57.663 40.909 19.90 0.00 0.00 2.85
3104 3545 1.130955 GGCTGTGTTTTGTTGCATCG 58.869 50.000 0.00 0.00 0.00 3.84
3260 3703 0.245266 ACATACACATGACACGCCGA 59.755 50.000 0.00 0.00 35.96 5.54
3280 3727 0.755079 CGCATGATCTTCCCTGGAGA 59.245 55.000 0.00 0.00 0.00 3.71
3281 3728 1.347050 CGCATGATCTTCCCTGGAGAT 59.653 52.381 0.00 0.00 0.00 2.75
3322 3769 2.223203 GCTTCTTGATGTCATTCTGCGG 60.223 50.000 0.00 0.00 0.00 5.69
3325 3772 3.673902 TCTTGATGTCATTCTGCGGAAA 58.326 40.909 12.96 0.00 34.90 3.13
3338 3789 1.751351 TGCGGAAACAACATTCACCAA 59.249 42.857 0.00 0.00 0.00 3.67
3339 3790 2.223688 TGCGGAAACAACATTCACCAAG 60.224 45.455 0.00 0.00 0.00 3.61
3355 3806 3.813166 CACCAAGTGAATTACCGTTCTGT 59.187 43.478 0.00 0.00 35.23 3.41
3365 3816 0.314302 ACCGTTCTGTTGGAGACGAG 59.686 55.000 0.00 0.00 31.01 4.18
3366 3817 0.388649 CCGTTCTGTTGGAGACGAGG 60.389 60.000 0.00 0.00 31.01 4.63
3371 3822 4.174762 GTTCTGTTGGAGACGAGGAATAC 58.825 47.826 0.00 0.00 0.00 1.89
3372 3823 3.427573 TCTGTTGGAGACGAGGAATACA 58.572 45.455 0.00 0.00 0.00 2.29
3376 3827 4.282449 TGTTGGAGACGAGGAATACAGAAA 59.718 41.667 0.00 0.00 0.00 2.52
3495 3946 3.070446 TGGTGAAGTTCCACTTGATACGT 59.930 43.478 0.00 0.00 38.80 3.57
3513 3964 1.664873 GTTCTCCAAATAGACCGCCC 58.335 55.000 0.00 0.00 0.00 6.13
3540 3991 6.096987 TCTCTGACTTCAAGAACTTGTACAGT 59.903 38.462 13.15 12.86 41.16 3.55
3567 4018 0.306228 CATTGTTGCCGTTCACGTCA 59.694 50.000 0.00 0.00 37.74 4.35
3576 4027 1.003851 CGTTCACGTCAACCTGTTGT 58.996 50.000 9.65 0.00 41.16 3.32
3597 4048 9.554395 TGTTGTCAACTCAGAAATGTTTAGATA 57.446 29.630 16.45 0.00 0.00 1.98
3632 4083 1.225855 TGTGTTTGGAAGCTAGCACG 58.774 50.000 18.83 0.00 0.00 5.34
3644 4095 1.464687 GCTAGCACGCACACAGAAATG 60.465 52.381 10.63 0.00 0.00 2.32
3646 4097 0.534877 AGCACGCACACAGAAATGGA 60.535 50.000 0.00 0.00 0.00 3.41
3649 4100 2.384382 CACGCACACAGAAATGGAAAC 58.616 47.619 0.00 0.00 0.00 2.78
3665 4116 3.634448 TGGAAACAAAGATTTTCGCTGGA 59.366 39.130 0.00 0.00 37.44 3.86
3750 4204 2.363680 CTCATCGCTATCTGGTTCCTGT 59.636 50.000 0.00 0.00 0.00 4.00
3753 4207 0.824109 CGCTATCTGGTTCCTGTCCA 59.176 55.000 0.00 0.00 0.00 4.02
3759 4213 1.915141 CTGGTTCCTGTCCAGCAAAT 58.085 50.000 0.00 0.00 44.46 2.32
3810 4264 4.503741 TCCTAATTGCAGCAGAAAACAC 57.496 40.909 0.00 0.00 0.00 3.32
3815 4270 0.525242 TGCAGCAGAAAACACGCAAC 60.525 50.000 0.00 0.00 0.00 4.17
3940 4396 5.643777 ACTTGCAGCCTAACATAAACTGTAG 59.356 40.000 0.00 0.00 36.98 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.352404 CCGCTCCGAAGACTAGACG 59.648 63.158 0.00 0.00 0.00 4.18
31 32 4.480031 GAGAACCGCTCCGAAGAC 57.520 61.111 0.00 0.00 37.69 3.01
52 53 7.284489 GCATGGGACTAAACATAAATCAAGGTA 59.716 37.037 0.00 0.00 0.00 3.08
62 63 5.186256 TCAAAGGCATGGGACTAAACATA 57.814 39.130 0.00 0.00 0.00 2.29
63 64 4.046286 TCAAAGGCATGGGACTAAACAT 57.954 40.909 0.00 0.00 0.00 2.71
73 74 4.278170 TGTCTTAAGTGTTCAAAGGCATGG 59.722 41.667 1.63 0.00 30.30 3.66
82 83 3.964688 TGAGGGAGTGTCTTAAGTGTTCA 59.035 43.478 1.63 0.00 0.00 3.18
115 116 8.291191 AGTCTAACTTACCTAAACGCTCTTAT 57.709 34.615 0.00 0.00 0.00 1.73
116 117 7.693969 AGTCTAACTTACCTAAACGCTCTTA 57.306 36.000 0.00 0.00 0.00 2.10
117 118 6.587206 AGTCTAACTTACCTAAACGCTCTT 57.413 37.500 0.00 0.00 0.00 2.85
118 119 6.587206 AAGTCTAACTTACCTAAACGCTCT 57.413 37.500 0.00 0.00 36.52 4.09
120 121 6.519382 ACAAAGTCTAACTTACCTAAACGCT 58.481 36.000 0.00 0.00 37.47 5.07
127 128 9.281371 GGAATGTTTACAAAGTCTAACTTACCT 57.719 33.333 0.00 0.00 37.47 3.08
130 131 9.841295 ACTGGAATGTTTACAAAGTCTAACTTA 57.159 29.630 0.00 0.00 37.47 2.24
131 132 8.747538 ACTGGAATGTTTACAAAGTCTAACTT 57.252 30.769 0.00 0.00 40.80 2.66
134 135 9.787435 ACATACTGGAATGTTTACAAAGTCTAA 57.213 29.630 0.00 0.00 36.71 2.10
136 137 9.959721 ATACATACTGGAATGTTTACAAAGTCT 57.040 29.630 3.69 0.00 40.52 3.24
176 177 5.050431 GCCTTGTTTCGCACAATTACAAAAT 60.050 36.000 1.04 0.00 44.72 1.82
177 178 4.268884 GCCTTGTTTCGCACAATTACAAAA 59.731 37.500 1.04 0.00 44.72 2.44
178 179 3.799420 GCCTTGTTTCGCACAATTACAAA 59.201 39.130 1.04 0.00 44.72 2.83
179 180 3.376540 GCCTTGTTTCGCACAATTACAA 58.623 40.909 1.04 0.00 44.72 2.41
180 181 2.603412 CGCCTTGTTTCGCACAATTACA 60.603 45.455 1.04 0.00 44.72 2.41
181 182 1.976045 CGCCTTGTTTCGCACAATTAC 59.024 47.619 1.04 0.00 44.72 1.89
192 193 2.677003 CGATCGCACCGCCTTGTTT 61.677 57.895 0.26 0.00 0.00 2.83
264 269 3.495001 CCTCGAGAAGATATTTTTCGCCC 59.505 47.826 15.71 0.00 0.00 6.13
338 348 1.687123 CCCCCATTCTACAGTAGTCCG 59.313 57.143 7.50 0.00 0.00 4.79
352 362 2.780040 CTCCATCCCAGCCCCCAT 60.780 66.667 0.00 0.00 0.00 4.00
543 588 2.502080 CGAGACGAGGCGACACAC 60.502 66.667 0.00 0.00 0.00 3.82
556 601 4.068599 CACAGACAGATAGATAGGCGAGA 58.931 47.826 0.00 0.00 0.00 4.04
561 606 3.576118 CCCCACACAGACAGATAGATAGG 59.424 52.174 0.00 0.00 0.00 2.57
568 622 2.665000 CGCCCCACACAGACAGAT 59.335 61.111 0.00 0.00 0.00 2.90
569 623 3.625897 CCGCCCCACACAGACAGA 61.626 66.667 0.00 0.00 0.00 3.41
596 650 4.875713 ATGGATGGAACGGCGGCC 62.876 66.667 13.24 9.54 0.00 6.13
597 651 3.279875 GATGGATGGAACGGCGGC 61.280 66.667 13.24 0.00 0.00 6.53
598 652 2.591715 GGATGGATGGAACGGCGG 60.592 66.667 13.24 0.00 0.00 6.13
599 653 1.227943 ATGGATGGATGGAACGGCG 60.228 57.895 4.80 4.80 0.00 6.46
600 654 0.890996 GGATGGATGGATGGAACGGC 60.891 60.000 0.00 0.00 0.00 5.68
601 655 0.473755 TGGATGGATGGATGGAACGG 59.526 55.000 0.00 0.00 0.00 4.44
602 656 2.430465 GATGGATGGATGGATGGAACG 58.570 52.381 0.00 0.00 0.00 3.95
603 657 2.108776 TGGATGGATGGATGGATGGAAC 59.891 50.000 0.00 0.00 0.00 3.62
604 658 2.430963 TGGATGGATGGATGGATGGAA 58.569 47.619 0.00 0.00 0.00 3.53
648 710 3.259314 AGGATGGGCACAGCACCA 61.259 61.111 6.52 0.00 41.76 4.17
659 721 0.990374 GGATGGAGGATGGAGGATGG 59.010 60.000 0.00 0.00 0.00 3.51
660 722 1.629353 CAGGATGGAGGATGGAGGATG 59.371 57.143 0.00 0.00 0.00 3.51
661 723 2.041824 CAGGATGGAGGATGGAGGAT 57.958 55.000 0.00 0.00 0.00 3.24
662 724 3.565979 CAGGATGGAGGATGGAGGA 57.434 57.895 0.00 0.00 0.00 3.71
877 968 4.465446 TCCCTGGCTCCTCCTCCG 62.465 72.222 0.00 0.00 35.26 4.63
878 969 2.445654 CTCCCTGGCTCCTCCTCC 60.446 72.222 0.00 0.00 35.26 4.30
879 970 3.160748 GCTCCCTGGCTCCTCCTC 61.161 72.222 0.00 0.00 35.26 3.71
880 971 3.265708 AAGCTCCCTGGCTCCTCCT 62.266 63.158 0.00 0.00 42.24 3.69
922 1013 0.023732 CATGCACGAACACGATCGAC 59.976 55.000 24.34 8.98 45.48 4.20
1061 1156 4.719106 GGAGGTGCTGCTGCTGCT 62.719 66.667 27.67 11.62 40.48 4.24
1252 1356 2.606826 GGAGGAAGGGGACGTGGT 60.607 66.667 0.00 0.00 0.00 4.16
1289 1393 1.675641 GAAACAGAGCCGCCCATGT 60.676 57.895 0.00 0.00 0.00 3.21
1290 1394 1.377725 AGAAACAGAGCCGCCCATG 60.378 57.895 0.00 0.00 0.00 3.66
1291 1395 1.377725 CAGAAACAGAGCCGCCCAT 60.378 57.895 0.00 0.00 0.00 4.00
1292 1396 2.032528 CAGAAACAGAGCCGCCCA 59.967 61.111 0.00 0.00 0.00 5.36
1293 1397 2.747855 CCAGAAACAGAGCCGCCC 60.748 66.667 0.00 0.00 0.00 6.13
1302 1406 2.281484 GTGCCCGAGCCAGAAACA 60.281 61.111 0.00 0.00 38.69 2.83
1305 1409 4.373116 GTCGTGCCCGAGCCAGAA 62.373 66.667 0.00 0.00 45.26 3.02
1476 1583 2.060383 CGACCCCATCCTCTGCTGA 61.060 63.158 0.00 0.00 0.00 4.26
1563 1670 2.930562 AGCTTCTTCCCGGTGCCT 60.931 61.111 0.00 0.00 0.00 4.75
1587 1694 1.838073 CGGAGGGTTTACTGCTGGGT 61.838 60.000 0.00 0.00 0.00 4.51
1719 1863 3.019564 GACAATTGGCAGGCAGTAGATT 58.980 45.455 6.36 0.00 0.00 2.40
1724 1869 0.675633 GTTGACAATTGGCAGGCAGT 59.324 50.000 14.91 0.00 32.66 4.40
1743 1888 3.657634 ACTGCACAGTACAGATGTTCTG 58.342 45.455 15.49 15.49 45.28 3.02
1769 1914 4.708726 ATCAACATTCCTTTGCTACAGC 57.291 40.909 0.00 0.00 42.50 4.40
1796 1942 8.565896 TGAGCTAATGACACTGTTAAAATCAT 57.434 30.769 0.00 0.00 0.00 2.45
1809 1955 7.337689 ACTGATAAGCAAATTGAGCTAATGACA 59.662 33.333 6.13 3.48 42.53 3.58
1866 2015 6.458210 ACTTTGCATAAAAACTAGCAGCATT 58.542 32.000 0.00 0.00 38.35 3.56
1979 2375 8.459521 TCAGCAATTAATTTTATTCGTTGTGG 57.540 30.769 0.00 0.00 0.00 4.17
2000 2396 6.347644 GCCTGGACAAAATAACAATTTTCAGC 60.348 38.462 0.00 0.00 31.96 4.26
2058 2469 1.486310 GCTGTGATGATGTGGGGAGTA 59.514 52.381 0.00 0.00 0.00 2.59
2100 2511 2.237393 TTGTCCCAGTTTTGCATTGC 57.763 45.000 0.46 0.46 0.00 3.56
2114 2525 6.547510 AGAATAGAATTTAGGTGGCATTGTCC 59.452 38.462 0.00 0.00 0.00 4.02
2115 2526 7.573968 AGAATAGAATTTAGGTGGCATTGTC 57.426 36.000 0.00 0.00 0.00 3.18
2120 2531 8.045720 AGGAATAGAATAGAATTTAGGTGGCA 57.954 34.615 0.00 0.00 0.00 4.92
2121 2532 8.379331 AGAGGAATAGAATAGAATTTAGGTGGC 58.621 37.037 0.00 0.00 0.00 5.01
2128 2539 8.379331 GGGTAGCAGAGGAATAGAATAGAATTT 58.621 37.037 0.00 0.00 0.00 1.82
2134 2547 4.528596 GCAGGGTAGCAGAGGAATAGAATA 59.471 45.833 0.00 0.00 0.00 1.75
2138 2551 2.036992 CAGCAGGGTAGCAGAGGAATAG 59.963 54.545 0.00 0.00 36.85 1.73
2149 2562 0.463295 CATCAGGTGCAGCAGGGTAG 60.463 60.000 19.63 0.63 0.00 3.18
2152 2565 1.001764 TTCATCAGGTGCAGCAGGG 60.002 57.895 19.63 7.28 0.00 4.45
2267 2681 3.148279 GAGACGGACCCCATCGCT 61.148 66.667 0.00 0.00 0.00 4.93
2330 2744 1.910671 ACCTCGTAAATGGCAGGGTTA 59.089 47.619 0.00 0.00 0.00 2.85
2352 2766 4.651045 TGATATGCATATAGGATGGTCGCT 59.349 41.667 19.12 0.00 0.00 4.93
2371 2789 3.519107 TCAGGTGCATCACTCCTTTGATA 59.481 43.478 0.00 0.00 40.37 2.15
2379 2804 2.758736 AAGTCTCAGGTGCATCACTC 57.241 50.000 0.00 0.00 34.40 3.51
2381 2806 5.665459 ACTTATAAGTCTCAGGTGCATCAC 58.335 41.667 12.50 0.00 32.86 3.06
2399 2824 5.372343 TCACATCATGCAGGGTTACTTAT 57.628 39.130 0.00 0.00 0.00 1.73
2402 2827 3.719268 TTCACATCATGCAGGGTTACT 57.281 42.857 0.00 0.00 0.00 2.24
2551 2982 1.679977 CACCAATGCTCCACCCAGG 60.680 63.158 0.00 0.00 39.47 4.45
2569 3000 2.032528 TGCACAGTACTGGCAGCC 59.967 61.111 25.71 3.66 33.85 4.85
2603 3034 4.734266 TCTTAGCAGATGAGGCTGATCTA 58.266 43.478 16.25 0.00 42.62 1.98
2607 3038 3.708121 TGAATCTTAGCAGATGAGGCTGA 59.292 43.478 0.00 0.00 42.62 4.26
2610 3041 4.057432 GTCTGAATCTTAGCAGATGAGGC 58.943 47.826 0.00 0.00 42.51 4.70
2611 3042 5.273674 TGTCTGAATCTTAGCAGATGAGG 57.726 43.478 0.00 0.00 42.51 3.86
2612 3043 5.697178 CCATGTCTGAATCTTAGCAGATGAG 59.303 44.000 0.00 0.00 42.51 2.90
2620 3051 5.065731 GCTTGGTTCCATGTCTGAATCTTAG 59.934 44.000 6.60 0.00 0.00 2.18
2647 3078 2.704464 TGAGGTTGATCTGGATGCAG 57.296 50.000 8.12 8.12 0.00 4.41
2654 3086 6.939132 ATCTTAGCAAATGAGGTTGATCTG 57.061 37.500 0.00 0.00 0.00 2.90
2656 3088 7.281774 TCTGAATCTTAGCAAATGAGGTTGATC 59.718 37.037 0.00 0.00 0.00 2.92
2657 3089 7.066766 GTCTGAATCTTAGCAAATGAGGTTGAT 59.933 37.037 0.00 0.00 0.00 2.57
2659 3091 6.149973 TGTCTGAATCTTAGCAAATGAGGTTG 59.850 38.462 0.00 0.00 0.00 3.77
2661 3093 5.809001 TGTCTGAATCTTAGCAAATGAGGT 58.191 37.500 0.00 0.00 0.00 3.85
2662 3094 6.939132 ATGTCTGAATCTTAGCAAATGAGG 57.061 37.500 0.00 0.00 0.00 3.86
2663 3095 8.429493 TGTATGTCTGAATCTTAGCAAATGAG 57.571 34.615 0.00 0.00 0.00 2.90
2665 3097 8.453320 TGTTGTATGTCTGAATCTTAGCAAATG 58.547 33.333 0.00 0.00 0.00 2.32
2666 3098 8.565896 TGTTGTATGTCTGAATCTTAGCAAAT 57.434 30.769 0.00 0.00 0.00 2.32
2668 3100 9.665719 TTATGTTGTATGTCTGAATCTTAGCAA 57.334 29.630 0.00 0.00 0.00 3.91
2669 3101 9.665719 TTTATGTTGTATGTCTGAATCTTAGCA 57.334 29.630 0.00 0.00 0.00 3.49
2689 3128 8.088365 GCCAAACAGGATTAGAAACTTTTATGT 58.912 33.333 0.00 0.00 41.22 2.29
2694 3133 6.670695 ATGCCAAACAGGATTAGAAACTTT 57.329 33.333 0.00 0.00 41.22 2.66
2754 3193 5.279657 GGCTTTCTTGGACTTTGATTTGGAT 60.280 40.000 0.00 0.00 0.00 3.41
2829 3268 4.314440 GAGCTGGGCGACACCACA 62.314 66.667 0.00 0.00 42.05 4.17
2834 3273 3.695606 GTCCTGAGCTGGGCGACA 61.696 66.667 0.00 0.00 0.00 4.35
2925 3364 6.655003 AGTTGATATCAATGTTGGAACTTCGT 59.345 34.615 20.65 0.00 38.24 3.85
2992 3431 7.341769 TCTTTTTGGGAACAGAAAAATCTCTCA 59.658 33.333 0.00 0.00 43.00 3.27
3038 3477 4.398044 TCTCAAAAACCGAATGGGCTATTC 59.602 41.667 13.07 13.07 41.46 1.75
3126 3567 5.619086 CGGTGAAAGGAAATAACATTTCGCT 60.619 40.000 15.12 2.57 44.64 4.93
3134 3575 6.790285 TTCTACACGGTGAAAGGAAATAAC 57.210 37.500 16.29 0.00 0.00 1.89
3135 3576 7.282675 TGTTTTCTACACGGTGAAAGGAAATAA 59.717 33.333 16.29 8.58 34.29 1.40
3137 3578 5.591067 TGTTTTCTACACGGTGAAAGGAAAT 59.409 36.000 16.29 0.00 34.29 2.17
3142 3585 4.809426 ACTCTGTTTTCTACACGGTGAAAG 59.191 41.667 16.29 11.52 34.29 2.62
3225 3668 6.524734 TGTGTATGTGTCATCTGTTCTTTCT 58.475 36.000 0.00 0.00 0.00 2.52
3226 3669 6.785488 TGTGTATGTGTCATCTGTTCTTTC 57.215 37.500 0.00 0.00 0.00 2.62
3260 3703 0.467384 CTCCAGGGAAGATCATGCGT 59.533 55.000 0.00 0.00 0.00 5.24
3280 3727 4.475016 AGCTGTTGGAGGTTTGAGGTATAT 59.525 41.667 0.00 0.00 0.00 0.86
3281 3728 3.844211 AGCTGTTGGAGGTTTGAGGTATA 59.156 43.478 0.00 0.00 0.00 1.47
3338 3789 4.039973 TCTCCAACAGAACGGTAATTCACT 59.960 41.667 0.00 0.00 0.00 3.41
3339 3790 4.151867 GTCTCCAACAGAACGGTAATTCAC 59.848 45.833 0.00 0.00 30.72 3.18
3349 3800 2.814280 TTCCTCGTCTCCAACAGAAC 57.186 50.000 0.00 0.00 30.72 3.01
3351 3802 3.427573 TGTATTCCTCGTCTCCAACAGA 58.572 45.455 0.00 0.00 0.00 3.41
3355 3806 5.477607 TTTTCTGTATTCCTCGTCTCCAA 57.522 39.130 0.00 0.00 0.00 3.53
3371 3822 8.559536 TGCTCTAACTCAACAGTTTATTTTCTG 58.440 33.333 0.00 0.00 40.16 3.02
3372 3823 8.677148 TGCTCTAACTCAACAGTTTATTTTCT 57.323 30.769 0.00 0.00 40.16 2.52
3376 3827 7.119846 GGTGATGCTCTAACTCAACAGTTTATT 59.880 37.037 0.00 0.00 40.16 1.40
3486 3937 6.830114 GGTCTATTTGGAGAACGTATCAAG 57.170 41.667 0.00 0.00 0.00 3.02
3495 3946 0.544697 GGGGCGGTCTATTTGGAGAA 59.455 55.000 0.00 0.00 0.00 2.87
3513 3964 4.954875 ACAAGTTCTTGAAGTCAGAGAGG 58.045 43.478 17.75 0.00 0.00 3.69
3558 4009 2.004017 TGACAACAGGTTGACGTGAAC 58.996 47.619 18.28 9.59 42.93 3.18
3567 4018 4.949856 ACATTTCTGAGTTGACAACAGGTT 59.050 37.500 20.08 0.00 33.19 3.50
3598 4049 7.856145 TCCAAACACAAATGCACTTATTTTT 57.144 28.000 0.00 0.00 0.00 1.94
3632 4083 4.681744 TCTTTGTTTCCATTTCTGTGTGC 58.318 39.130 0.00 0.00 0.00 4.57
3644 4095 4.237349 TCCAGCGAAAATCTTTGTTTCC 57.763 40.909 0.00 0.00 32.40 3.13
3646 4097 7.084486 GTCTATTCCAGCGAAAATCTTTGTTT 58.916 34.615 0.00 0.00 0.00 2.83
3649 4100 5.355350 AGGTCTATTCCAGCGAAAATCTTTG 59.645 40.000 0.00 0.00 0.00 2.77
3652 4103 4.762289 AGGTCTATTCCAGCGAAAATCT 57.238 40.909 0.00 0.00 0.00 2.40
3654 4105 3.378427 GCAAGGTCTATTCCAGCGAAAAT 59.622 43.478 0.00 0.00 0.00 1.82
3659 4110 2.301505 CGCAAGGTCTATTCCAGCG 58.698 57.895 7.79 7.79 43.40 5.18
3660 4111 2.024176 TTCGCAAGGTCTATTCCAGC 57.976 50.000 0.00 0.00 38.47 4.85
3661 4112 5.567138 ATTTTTCGCAAGGTCTATTCCAG 57.433 39.130 0.00 0.00 38.47 3.86
3662 4113 5.588648 CCTATTTTTCGCAAGGTCTATTCCA 59.411 40.000 0.00 0.00 38.47 3.53
3663 4114 5.820947 TCCTATTTTTCGCAAGGTCTATTCC 59.179 40.000 0.00 0.00 38.47 3.01
3665 4116 7.393515 AGTTTCCTATTTTTCGCAAGGTCTATT 59.606 33.333 0.00 0.00 38.47 1.73
3759 4213 1.976474 GGCGTTCCCCTGCAATCAA 60.976 57.895 0.00 0.00 0.00 2.57
3810 4264 6.409185 GTCTTCAATCTTCATTTATCGTTGCG 59.591 38.462 0.00 0.00 0.00 4.85
3815 4270 7.899974 ACTTCGTCTTCAATCTTCATTTATCG 58.100 34.615 0.00 0.00 0.00 2.92
3860 4316 0.251474 AGATGTGCCATTGTGCAGGT 60.251 50.000 0.00 0.00 43.02 4.00
3901 4357 5.236047 GGCTGCAAGTCTTTAGTATGATGAG 59.764 44.000 0.50 0.00 34.11 2.90
3902 4358 5.118990 GGCTGCAAGTCTTTAGTATGATGA 58.881 41.667 0.50 0.00 34.11 2.92
3903 4359 5.415415 GGCTGCAAGTCTTTAGTATGATG 57.585 43.478 0.50 0.00 34.11 3.07


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

AutoCloner maintained by Alex Coulton.