Multiple sequence alignment - TraesCS1A01G345200

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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 TraesCS1A01G345200 chr1A 100.000 3007 0 0 1 3007 532671330 532674336 0.000000e+00 5553
1 TraesCS1A01G345200 chr1A 85.864 955 102 16 1562 2505 532714218 532715150 0.000000e+00 985
2 TraesCS1A01G345200 chr1A 85.230 914 91 26 573 1468 532713332 532714219 0.000000e+00 900
3 TraesCS1A01G345200 chr1A 90.351 114 10 1 1467 1579 380965107 380964994 6.720000e-32 148
4 TraesCS1A01G345200 chr1A 85.156 128 13 4 434 561 532712980 532713101 3.150000e-25 126
5 TraesCS1A01G345200 chr1D 93.077 1459 83 9 1562 3007 435050686 435052139 0.000000e+00 2119
6 TraesCS1A01G345200 chr1D 92.892 1013 52 8 460 1468 435049691 435050687 0.000000e+00 1454
7 TraesCS1A01G345200 chr1D 88.142 253 9 4 83 332 435048168 435048402 6.350000e-72 281
8 TraesCS1A01G345200 chr1D 95.876 97 4 0 1467 1563 420554542 420554638 1.120000e-34 158
9 TraesCS1A01G345200 chr1D 88.889 99 7 3 359 455 435048401 435048497 5.270000e-23 119
10 TraesCS1A01G345200 chr1D 95.455 66 3 0 1 66 435048110 435048175 4.100000e-19 106
11 TraesCS1A01G345200 chr1B 87.575 1167 94 25 318 1468 588447325 588448456 0.000000e+00 1304
12 TraesCS1A01G345200 chr1B 88.604 702 55 14 1562 2262 588448455 588449132 0.000000e+00 830
13 TraesCS1A01G345200 chr1B 90.090 111 9 2 84 193 588446942 588447051 3.120000e-30 143
14 TraesCS1A01G345200 chr2A 96.000 100 4 0 1470 1569 622459522 622459423 2.400000e-36 163
15 TraesCS1A01G345200 chr2D 95.098 102 5 0 1467 1568 445894980 445894879 8.630000e-36 161
16 TraesCS1A01G345200 chr5B 95.918 98 4 0 1467 1564 474772887 474772790 3.100000e-35 159
17 TraesCS1A01G345200 chr2B 94.231 104 6 0 1467 1570 601206943 601206840 3.100000e-35 159
18 TraesCS1A01G345200 chr7B 93.458 107 5 1 1462 1566 562993059 562993165 1.120000e-34 158
19 TraesCS1A01G345200 chr5D 95.876 97 4 0 1467 1563 202429435 202429531 1.120000e-34 158
20 TraesCS1A01G345200 chr6A 90.435 115 8 3 1467 1581 596589445 596589334 6.720000e-32 148
21 TraesCS1A01G345200 chr7D 85.345 116 12 2 308 423 241179020 241178910 6.810000e-22 115
22 TraesCS1A01G345200 chr3B 90.805 87 7 1 1736 1822 723500646 723500731 6.810000e-22 115
23 TraesCS1A01G345200 chr3D 92.500 80 5 1 1736 1815 546469999 546470077 2.450000e-21 113
24 TraesCS1A01G345200 chr3A 92.500 80 5 1 1736 1815 683240259 683240337 2.450000e-21 113


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 TraesCS1A01G345200 chr1A 532671330 532674336 3006 False 5553.000000 5553 100.000000 1 3007 1 chr1A.!!$F1 3006
1 TraesCS1A01G345200 chr1A 532712980 532715150 2170 False 670.333333 985 85.416667 434 2505 3 chr1A.!!$F2 2071
2 TraesCS1A01G345200 chr1D 435048110 435052139 4029 False 815.800000 2119 91.691000 1 3007 5 chr1D.!!$F2 3006
3 TraesCS1A01G345200 chr1B 588446942 588449132 2190 False 759.000000 1304 88.756333 84 2262 3 chr1B.!!$F1 2178

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
974 2549 0.824109 TTCCTCAGAGCCATACCACG 59.176 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2807 4414 0.25589 GGTGTGAGGGGTATGTGCAT 59.744 55.0 0.0 0.0 0.0 3.96 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
79 80 8.707938 AAAAAGAAAAGAAAACTCATCCACAG 57.292 30.769 0.00 0.00 0.00 3.66
80 81 6.396829 AAGAAAAGAAAACTCATCCACAGG 57.603 37.500 0.00 0.00 0.00 4.00
81 82 4.279420 AGAAAAGAAAACTCATCCACAGGC 59.721 41.667 0.00 0.00 0.00 4.85
82 83 2.957402 AGAAAACTCATCCACAGGCA 57.043 45.000 0.00 0.00 0.00 4.75
143 144 2.880443 ACAATTCCAGTCCACAAGCAT 58.120 42.857 0.00 0.00 0.00 3.79
156 158 3.514645 CACAAGCATGGAATTGCCTTAC 58.485 45.455 0.00 0.00 43.83 2.34
209 211 9.853555 CACTGCAAGAAACAAACCAAATATATA 57.146 29.630 0.00 0.00 37.43 0.86
211 213 8.903570 TGCAAGAAACAAACCAAATATATACG 57.096 30.769 0.00 0.00 0.00 3.06
212 214 8.731605 TGCAAGAAACAAACCAAATATATACGA 58.268 29.630 0.00 0.00 0.00 3.43
213 215 9.730420 GCAAGAAACAAACCAAATATATACGAT 57.270 29.630 0.00 0.00 0.00 3.73
241 243 1.004277 GGTCTTAGGCCATGTCCAACA 59.996 52.381 5.01 0.00 0.00 3.33
431 585 6.537301 CGTTGTAGATGGCCTTACAAATCTTA 59.463 38.462 21.50 5.71 34.70 2.10
439 593 7.214467 TGGCCTTACAAATCTTAACAGAAAG 57.786 36.000 3.32 0.00 30.76 2.62
457 611 5.418209 CAGAAAGCAAATTCATCTCCTTCCT 59.582 40.000 0.00 0.00 0.00 3.36
586 2148 8.352201 GGCATCACAATATAAGACATAAAAGCA 58.648 33.333 0.00 0.00 0.00 3.91
616 2178 2.471264 GCGTCATGATTCATGCGATACG 60.471 50.000 30.07 26.96 41.18 3.06
647 2212 2.440385 TTAGTCTGCGCTGCTGCTGT 62.440 55.000 9.73 5.38 36.97 4.40
651 2222 2.280728 TGCGCTGCTGCTGTTGTA 60.281 55.556 9.73 0.00 36.97 2.41
688 2259 6.604735 AATCCATAAGCATCGTTGACTAAC 57.395 37.500 0.00 0.00 0.00 2.34
712 2283 8.045720 ACCCCAAGTACTTATGATTCATGTAT 57.954 34.615 8.04 0.00 0.00 2.29
735 2309 4.574421 TCACACCAAATATATTCTGCACCG 59.426 41.667 0.00 0.00 0.00 4.94
818 2393 4.815533 TCCTCTCCATCTTTCTGACAAG 57.184 45.455 0.00 0.00 0.00 3.16
834 2409 7.509141 TCTGACAAGATGTTTCTGCATTTTA 57.491 32.000 0.00 0.00 30.72 1.52
836 2411 7.862372 TCTGACAAGATGTTTCTGCATTTTAAC 59.138 33.333 0.00 0.00 30.72 2.01
850 2425 7.596248 TCTGCATTTTAACTCTTGAAAGATTGC 59.404 33.333 0.00 0.00 33.93 3.56
853 2428 7.148689 GCATTTTAACTCTTGAAAGATTGCTGG 60.149 37.037 0.00 0.00 33.93 4.85
856 2431 8.635765 TTTAACTCTTGAAAGATTGCTGGTAT 57.364 30.769 0.00 0.00 33.93 2.73
859 2434 6.479884 ACTCTTGAAAGATTGCTGGTATTCT 58.520 36.000 0.00 0.00 33.93 2.40
922 2497 8.829746 TCTACTCCTCAGGGTATATATAAACGA 58.170 37.037 0.00 0.00 0.00 3.85
938 2513 1.115467 ACGAGCTGCTAGGTATGCTT 58.885 50.000 14.25 0.00 35.76 3.91
946 2521 5.708230 AGCTGCTAGGTATGCTTAGTACTAG 59.292 44.000 0.00 0.00 30.96 2.57
974 2549 0.824109 TTCCTCAGAGCCATACCACG 59.176 55.000 0.00 0.00 0.00 4.94
1053 2628 3.156511 TCTCTCGATGCAATCTGTGAC 57.843 47.619 0.00 0.00 42.58 3.67
1145 2720 3.938963 TCCTCCGAAAATGATAGCACAAC 59.061 43.478 0.00 0.00 0.00 3.32
1239 2814 2.625737 CAAGTGGATGAACAGAGCGAT 58.374 47.619 0.00 0.00 0.00 4.58
1364 2948 4.927978 TCTATAGACTGCAAGGAAGAGC 57.072 45.455 0.00 0.00 39.30 4.09
1400 2984 1.610522 GCTGCAATGGACTCACAAAGT 59.389 47.619 0.00 0.00 42.42 2.66
1466 3050 4.262617 GTTTCGCTTTAGGGGAATCTCTT 58.737 43.478 0.00 0.00 44.41 2.85
1467 3051 5.046159 TGTTTCGCTTTAGGGGAATCTCTTA 60.046 40.000 0.00 0.00 44.41 2.10
1468 3052 4.667519 TCGCTTTAGGGGAATCTCTTAC 57.332 45.455 0.00 0.00 33.87 2.34
1469 3053 4.287552 TCGCTTTAGGGGAATCTCTTACT 58.712 43.478 0.00 0.00 33.87 2.24
1470 3054 4.341520 TCGCTTTAGGGGAATCTCTTACTC 59.658 45.833 0.00 0.00 33.87 2.59
1471 3055 4.501743 CGCTTTAGGGGAATCTCTTACTCC 60.502 50.000 0.00 0.00 0.00 3.85
1476 3060 3.047695 GGGAATCTCTTACTCCCTCCA 57.952 52.381 0.00 0.00 44.81 3.86
1477 3061 3.592865 GGGAATCTCTTACTCCCTCCAT 58.407 50.000 0.00 0.00 44.81 3.41
1478 3062 3.580895 GGGAATCTCTTACTCCCTCCATC 59.419 52.174 0.00 0.00 44.81 3.51
1479 3063 3.580895 GGAATCTCTTACTCCCTCCATCC 59.419 52.174 0.00 0.00 0.00 3.51
1480 3064 2.777459 TCTCTTACTCCCTCCATCCC 57.223 55.000 0.00 0.00 0.00 3.85
1481 3065 1.937350 TCTCTTACTCCCTCCATCCCA 59.063 52.381 0.00 0.00 0.00 4.37
1482 3066 2.317900 TCTCTTACTCCCTCCATCCCAA 59.682 50.000 0.00 0.00 0.00 4.12
1483 3067 3.115390 CTCTTACTCCCTCCATCCCAAA 58.885 50.000 0.00 0.00 0.00 3.28
1484 3068 3.523564 CTCTTACTCCCTCCATCCCAAAA 59.476 47.826 0.00 0.00 0.00 2.44
1485 3069 4.119155 TCTTACTCCCTCCATCCCAAAAT 58.881 43.478 0.00 0.00 0.00 1.82
1486 3070 5.293643 TCTTACTCCCTCCATCCCAAAATA 58.706 41.667 0.00 0.00 0.00 1.40
1487 3071 5.734140 TCTTACTCCCTCCATCCCAAAATAA 59.266 40.000 0.00 0.00 0.00 1.40
1488 3072 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
1489 3073 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
1490 3074 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
1491 3075 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
1492 3076 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
1493 3077 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
1494 3078 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
1495 3079 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
1496 3080 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
1497 3081 6.493166 TCCATCCCAAAATAAGTGTCTCAAT 58.507 36.000 0.00 0.00 0.00 2.57
1498 3082 6.603201 TCCATCCCAAAATAAGTGTCTCAATC 59.397 38.462 0.00 0.00 0.00 2.67
1499 3083 6.604795 CCATCCCAAAATAAGTGTCTCAATCT 59.395 38.462 0.00 0.00 0.00 2.40
1500 3084 7.123247 CCATCCCAAAATAAGTGTCTCAATCTT 59.877 37.037 0.00 0.00 0.00 2.40
1501 3085 9.177608 CATCCCAAAATAAGTGTCTCAATCTTA 57.822 33.333 0.00 0.00 0.00 2.10
1502 3086 8.792830 TCCCAAAATAAGTGTCTCAATCTTAG 57.207 34.615 0.00 0.00 0.00 2.18
1503 3087 8.383175 TCCCAAAATAAGTGTCTCAATCTTAGT 58.617 33.333 0.00 0.00 0.00 2.24
1504 3088 9.667107 CCCAAAATAAGTGTCTCAATCTTAGTA 57.333 33.333 0.00 0.00 0.00 1.82
1540 3124 9.310716 ACTAAAGTTAGTACAAAGTTGAGACAC 57.689 33.333 1.81 0.00 41.92 3.67
1541 3125 9.530633 CTAAAGTTAGTACAAAGTTGAGACACT 57.469 33.333 0.00 0.00 0.00 3.55
1542 3126 8.788325 AAAGTTAGTACAAAGTTGAGACACTT 57.212 30.769 0.00 0.98 38.74 3.16
1543 3127 9.880157 AAAGTTAGTACAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
1549 3133 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
1550 3134 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
1551 3135 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
1552 3136 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
1553 3137 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
1554 3138 3.071479 TGAGACACTTATTTTGGGACGC 58.929 45.455 0.00 0.00 0.00 5.19
1555 3139 3.071479 GAGACACTTATTTTGGGACGCA 58.929 45.455 0.00 0.00 0.00 5.24
1556 3140 3.074412 AGACACTTATTTTGGGACGCAG 58.926 45.455 0.00 0.00 0.00 5.18
1557 3141 2.159382 ACACTTATTTTGGGACGCAGG 58.841 47.619 0.00 0.00 0.00 4.85
1558 3142 1.472480 CACTTATTTTGGGACGCAGGG 59.528 52.381 0.00 0.00 0.00 4.45
1559 3143 1.353022 ACTTATTTTGGGACGCAGGGA 59.647 47.619 0.00 0.00 0.00 4.20
1560 3144 2.017049 CTTATTTTGGGACGCAGGGAG 58.983 52.381 0.00 0.00 0.00 4.30
1693 3277 7.775120 AGTTCTTACTATTTGCCATTCATTGG 58.225 34.615 0.00 0.00 39.81 3.16
1704 3288 4.196626 CCATTCATTGGTCATTTGCACT 57.803 40.909 0.00 0.00 40.99 4.40
1732 3316 4.052159 TGCCAATTGTGTTGATCGTTTT 57.948 36.364 4.43 0.00 0.00 2.43
1823 3407 7.710907 TGCAGATCAAGGTATGTATTCACTTAC 59.289 37.037 0.00 0.00 35.54 2.34
1841 3425 1.283793 CGAAGCAACAGCCAACAGG 59.716 57.895 0.00 0.00 0.00 4.00
1936 3521 2.208431 GAGCTCCGATGAAATGTGGAG 58.792 52.381 0.87 2.78 44.45 3.86
1946 3531 1.207329 GAAATGTGGAGGTACGCTCCT 59.793 52.381 23.01 4.08 41.39 3.69
2021 3607 5.242838 TCATGAATGACTACCCCAAACAAAC 59.757 40.000 0.00 0.00 0.00 2.93
2022 3608 4.798882 TGAATGACTACCCCAAACAAACT 58.201 39.130 0.00 0.00 0.00 2.66
2023 3609 4.582656 TGAATGACTACCCCAAACAAACTG 59.417 41.667 0.00 0.00 0.00 3.16
2064 3650 4.220602 ACATAATTTGTTGGAAGGACCTGC 59.779 41.667 0.00 0.00 39.86 4.85
2072 3658 1.743252 GAAGGACCTGCGGCTCAAG 60.743 63.158 0.00 0.00 0.00 3.02
2086 3672 4.616835 GCGGCTCAAGTTTTCTGAATCATT 60.617 41.667 0.00 0.00 0.00 2.57
2136 3722 7.090808 GTGGACTTTAACCTGAATTTCCATTC 58.909 38.462 0.00 0.00 39.58 2.67
2212 3801 9.624697 GATTGCTTGAACAGTGTCAATAATAAA 57.375 29.630 7.02 1.62 36.92 1.40
2369 3964 7.023171 ACCCTTTACTAATACCACACAATCA 57.977 36.000 0.00 0.00 0.00 2.57
2463 4060 2.224185 TGTTGTAGTGATGACCGCAAGT 60.224 45.455 0.00 0.00 0.00 3.16
2474 4071 1.195900 GACCGCAAGTGCACGAATAAA 59.804 47.619 12.01 0.00 42.21 1.40
2511 4108 9.887629 TTCACGGATGTATTAACCAAGTATTTA 57.112 29.630 0.00 0.00 0.00 1.40
2545 4142 4.011698 GAGTTAAGAAGAGTCGTCTCCCT 58.988 47.826 9.13 5.60 41.26 4.20
2550 4147 4.304048 AGAAGAGTCGTCTCCCTCTTAA 57.696 45.455 2.39 0.00 45.57 1.85
2553 4150 3.349022 AGAGTCGTCTCCCTCTTAACAG 58.651 50.000 6.04 0.00 41.26 3.16
2574 4171 4.033358 CAGAATTAGAGTTGTCACGGCATC 59.967 45.833 0.00 0.00 0.00 3.91
2596 4193 3.165318 CGCGTTCGCATGCAAACC 61.165 61.111 19.57 9.00 34.13 3.27
2622 4219 6.261381 AGAGCTTGGAATTAGTAGTCTACTCG 59.739 42.308 15.94 0.00 40.14 4.18
2643 4240 4.640647 TCGTGCTATATTCTATCGAGGCAT 59.359 41.667 0.00 0.00 0.00 4.40
2644 4241 4.737279 CGTGCTATATTCTATCGAGGCATG 59.263 45.833 0.00 0.00 0.00 4.06
2653 4250 2.898729 ATCGAGGCATGGAACTGTAG 57.101 50.000 0.00 0.00 0.00 2.74
2807 4414 4.360964 GCAAGCCATGTTGCCGCA 62.361 61.111 9.34 0.00 46.00 5.69
2826 4433 0.255890 ATGCACATACCCCTCACACC 59.744 55.000 0.00 0.00 0.00 4.16
2843 4450 2.778850 ACACCACTACAAACCCACCTAA 59.221 45.455 0.00 0.00 0.00 2.69
2848 4455 5.073417 ACCACTACAAACCCACCTAACATTA 59.927 40.000 0.00 0.00 0.00 1.90
2868 4475 1.651240 CGTCGGTCTACGGTGGTCAT 61.651 60.000 0.00 0.00 44.45 3.06
2898 4505 0.597637 CTCGTGGTGCGACAAAGAGT 60.598 55.000 0.00 0.00 45.68 3.24
2908 4515 1.276421 CGACAAAGAGTGGATGGGTCT 59.724 52.381 0.00 0.00 0.00 3.85
2925 4532 0.890683 TCTTTCGTTACTCCCCGGTC 59.109 55.000 0.00 0.00 0.00 4.79
2926 4533 0.893447 CTTTCGTTACTCCCCGGTCT 59.107 55.000 0.00 0.00 0.00 3.85
2957 4564 5.702266 AGGACAAAGGGTTAGCTTTAAGTT 58.298 37.500 0.00 0.00 0.00 2.66
2963 4570 4.572909 AGGGTTAGCTTTAAGTTACCACG 58.427 43.478 0.00 0.00 0.00 4.94
2979 4586 2.125269 CGGTAACCTGAAGCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.519191 TTGAAATCTCACATCTAATCAAAAGGA 57.481 29.630 0.00 0.00 0.00 3.36
17 18 7.312657 TGTTCTATGCTTGAAATCTCACATC 57.687 36.000 0.00 0.00 0.00 3.06
57 58 5.221322 GCCTGTGGATGAGTTTTCTTTTCTT 60.221 40.000 0.00 0.00 0.00 2.52
66 67 2.957402 TTCTGCCTGTGGATGAGTTT 57.043 45.000 0.00 0.00 0.00 2.66
67 68 2.887152 GTTTTCTGCCTGTGGATGAGTT 59.113 45.455 0.00 0.00 0.00 3.01
68 69 2.158623 TGTTTTCTGCCTGTGGATGAGT 60.159 45.455 0.00 0.00 0.00 3.41
69 70 2.507484 TGTTTTCTGCCTGTGGATGAG 58.493 47.619 0.00 0.00 0.00 2.90
70 71 2.655090 TGTTTTCTGCCTGTGGATGA 57.345 45.000 0.00 0.00 0.00 2.92
71 72 3.181477 TGTTTGTTTTCTGCCTGTGGATG 60.181 43.478 0.00 0.00 0.00 3.51
72 73 3.030291 TGTTTGTTTTCTGCCTGTGGAT 58.970 40.909 0.00 0.00 0.00 3.41
73 74 2.426738 CTGTTTGTTTTCTGCCTGTGGA 59.573 45.455 0.00 0.00 0.00 4.02
74 75 2.813061 CTGTTTGTTTTCTGCCTGTGG 58.187 47.619 0.00 0.00 0.00 4.17
75 76 2.195922 GCTGTTTGTTTTCTGCCTGTG 58.804 47.619 0.00 0.00 0.00 3.66
76 77 1.824230 TGCTGTTTGTTTTCTGCCTGT 59.176 42.857 0.00 0.00 0.00 4.00
77 78 2.195922 GTGCTGTTTGTTTTCTGCCTG 58.804 47.619 0.00 0.00 0.00 4.85
78 79 1.202290 CGTGCTGTTTGTTTTCTGCCT 60.202 47.619 0.00 0.00 0.00 4.75
79 80 1.199624 CGTGCTGTTTGTTTTCTGCC 58.800 50.000 0.00 0.00 0.00 4.85
80 81 1.199624 CCGTGCTGTTTGTTTTCTGC 58.800 50.000 0.00 0.00 0.00 4.26
81 82 1.199624 GCCGTGCTGTTTGTTTTCTG 58.800 50.000 0.00 0.00 0.00 3.02
82 83 0.814457 TGCCGTGCTGTTTGTTTTCT 59.186 45.000 0.00 0.00 0.00 2.52
143 144 4.222588 CCCTGATTTTGTAAGGCAATTCCA 59.777 41.667 0.00 0.00 36.89 3.53
156 158 2.091994 AGGATGAGCCTCCCTGATTTTG 60.092 50.000 0.00 0.00 46.97 2.44
218 220 2.398588 TGGACATGGCCTAAGACCTAG 58.601 52.381 21.02 0.00 0.00 3.02
220 222 1.282157 GTTGGACATGGCCTAAGACCT 59.718 52.381 21.02 0.00 0.00 3.85
221 223 1.004277 TGTTGGACATGGCCTAAGACC 59.996 52.381 21.02 0.00 0.00 3.85
222 224 2.489938 TGTTGGACATGGCCTAAGAC 57.510 50.000 21.02 12.57 0.00 3.01
241 243 4.447342 CCTTCCCAAGCGCCCCAT 62.447 66.667 2.29 0.00 0.00 4.00
259 261 1.613255 GCGGGGAAGAAAATCCTGACA 60.613 52.381 0.00 0.00 39.57 3.58
431 585 6.294955 GGAAGGAGATGAATTTGCTTTCTGTT 60.295 38.462 0.00 0.00 0.00 3.16
439 593 2.615912 CCGAGGAAGGAGATGAATTTGC 59.384 50.000 0.00 0.00 0.00 3.68
457 611 5.479375 AGATACAAACTGACTTCTTACCCGA 59.521 40.000 0.00 0.00 0.00 5.14
586 2148 2.289631 TGAATCATGACGCCACAGTTCT 60.290 45.455 0.00 0.00 0.00 3.01
616 2178 2.159517 CGCAGACTAATGGAACTTTGGC 60.160 50.000 0.00 0.00 0.00 4.52
647 2212 6.569127 TGGATTACAATTAGGAGGCTACAA 57.431 37.500 0.00 0.00 0.00 2.41
651 2222 6.183361 TGCTTATGGATTACAATTAGGAGGCT 60.183 38.462 0.00 0.00 0.00 4.58
665 2236 5.527582 GGTTAGTCAACGATGCTTATGGATT 59.472 40.000 0.00 0.00 35.34 3.01
688 2259 8.156820 TGATACATGAATCATAAGTACTTGGGG 58.843 37.037 18.56 7.43 30.92 4.96
712 2283 4.574421 CGGTGCAGAATATATTTGGTGTGA 59.426 41.667 0.00 0.00 0.00 3.58
735 2309 4.137543 CCCTGGGAAGTCATAAATGCTAC 58.862 47.826 7.01 0.00 0.00 3.58
798 2373 4.815533 TCTTGTCAGAAAGATGGAGAGG 57.184 45.455 0.00 0.00 31.19 3.69
805 2380 5.766670 TGCAGAAACATCTTGTCAGAAAGAT 59.233 36.000 0.00 0.00 45.69 2.40
806 2381 5.125356 TGCAGAAACATCTTGTCAGAAAGA 58.875 37.500 0.00 0.00 40.36 2.52
807 2382 5.428496 TGCAGAAACATCTTGTCAGAAAG 57.572 39.130 0.00 0.00 30.76 2.62
809 2384 6.395426 AAATGCAGAAACATCTTGTCAGAA 57.605 33.333 0.00 0.00 30.76 3.02
813 2388 8.078596 AGAGTTAAAATGCAGAAACATCTTGTC 58.921 33.333 0.00 0.00 0.00 3.18
818 2393 8.801715 TTCAAGAGTTAAAATGCAGAAACATC 57.198 30.769 0.00 0.00 0.00 3.06
834 2409 6.944862 AGAATACCAGCAATCTTTCAAGAGTT 59.055 34.615 0.00 0.00 38.66 3.01
836 2411 6.596888 TGAGAATACCAGCAATCTTTCAAGAG 59.403 38.462 0.00 0.00 38.66 2.85
850 2425 6.600822 ACATGGATTTGACTTGAGAATACCAG 59.399 38.462 0.00 0.00 0.00 4.00
853 2428 9.941664 CATTACATGGATTTGACTTGAGAATAC 57.058 33.333 0.00 0.00 0.00 1.89
856 2431 7.665145 TGACATTACATGGATTTGACTTGAGAA 59.335 33.333 0.00 0.00 33.60 2.87
859 2434 7.757941 TTGACATTACATGGATTTGACTTGA 57.242 32.000 0.00 0.00 33.60 3.02
899 2474 6.377712 GCTCGTTTATATATACCCTGAGGAGT 59.622 42.308 0.00 0.00 36.73 3.85
922 2497 4.475345 AGTACTAAGCATACCTAGCAGCT 58.525 43.478 0.00 0.00 39.37 4.24
938 2513 5.525484 TGAGGAATCCTTTGGCTAGTACTA 58.475 41.667 2.09 1.89 31.76 1.82
946 2521 1.387539 GCTCTGAGGAATCCTTTGGC 58.612 55.000 2.09 2.60 31.76 4.52
974 2549 6.757237 TCTTCTGATCTCTGAATTATCTGGC 58.243 40.000 0.00 0.00 34.17 4.85
1053 2628 1.543941 GCGCAATCATCTCCGACTCG 61.544 60.000 0.30 0.00 0.00 4.18
1145 2720 4.874966 CCACTAGGAGATCAAAAGAAGCTG 59.125 45.833 0.00 0.00 36.89 4.24
1239 2814 3.559811 CCACAGGGACTTCATTGTGATGA 60.560 47.826 11.73 0.00 42.61 2.92
1331 2910 7.019774 TGCAGTCTATAGAATCAATTGCAAC 57.980 36.000 0.00 0.00 36.25 4.17
1352 2936 0.394938 TGTTACCGCTCTTCCTTGCA 59.605 50.000 0.00 0.00 0.00 4.08
1364 2948 1.461127 GCAGCTCTTGACTTGTTACCG 59.539 52.381 0.00 0.00 0.00 4.02
1400 2984 9.953565 AGTAACTATCAAACCTTTGCATAGTTA 57.046 29.630 21.30 21.30 42.05 2.24
1440 3024 4.830600 AGATTCCCCTAAAGCGAAACAAAA 59.169 37.500 0.00 0.00 0.00 2.44
1449 3033 4.202377 GGGAGTAAGAGATTCCCCTAAAGC 60.202 50.000 0.00 0.00 46.46 3.51
1466 3050 5.043762 ACTTATTTTGGGATGGAGGGAGTA 58.956 41.667 0.00 0.00 0.00 2.59
1467 3051 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
1468 3052 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
1469 3053 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
1470 3054 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
1471 3055 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
1472 3056 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
1473 3057 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
1474 3058 6.604795 AGATTGAGACACTTATTTTGGGATGG 59.395 38.462 0.00 0.00 0.00 3.51
1475 3059 7.636150 AGATTGAGACACTTATTTTGGGATG 57.364 36.000 0.00 0.00 0.00 3.51
1476 3060 9.401058 CTAAGATTGAGACACTTATTTTGGGAT 57.599 33.333 0.00 0.00 0.00 3.85
1477 3061 8.383175 ACTAAGATTGAGACACTTATTTTGGGA 58.617 33.333 0.00 0.00 0.00 4.37
1478 3062 8.567285 ACTAAGATTGAGACACTTATTTTGGG 57.433 34.615 0.00 0.00 0.00 4.12
1514 3098 9.310716 GTGTCTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
1515 3099 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
1516 3100 9.880157 AAGTGTCTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
1517 3101 8.788325 AAGTGTCTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
1523 3107 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
1524 3108 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
1525 3109 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
1526 3110 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
1527 3111 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
1528 3112 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
1529 3113 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
1530 3114 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
1531 3115 4.612939 GCGTCCCAAAATAAGTGTCTCAAC 60.613 45.833 0.00 0.00 0.00 3.18
1532 3116 3.500680 GCGTCCCAAAATAAGTGTCTCAA 59.499 43.478 0.00 0.00 0.00 3.02
1533 3117 3.071479 GCGTCCCAAAATAAGTGTCTCA 58.929 45.455 0.00 0.00 0.00 3.27
1534 3118 3.071479 TGCGTCCCAAAATAAGTGTCTC 58.929 45.455 0.00 0.00 0.00 3.36
1535 3119 3.074412 CTGCGTCCCAAAATAAGTGTCT 58.926 45.455 0.00 0.00 0.00 3.41
1536 3120 2.161609 CCTGCGTCCCAAAATAAGTGTC 59.838 50.000 0.00 0.00 0.00 3.67
1537 3121 2.159382 CCTGCGTCCCAAAATAAGTGT 58.841 47.619 0.00 0.00 0.00 3.55
1538 3122 1.472480 CCCTGCGTCCCAAAATAAGTG 59.528 52.381 0.00 0.00 0.00 3.16
1539 3123 1.353022 TCCCTGCGTCCCAAAATAAGT 59.647 47.619 0.00 0.00 0.00 2.24
1540 3124 2.017049 CTCCCTGCGTCCCAAAATAAG 58.983 52.381 0.00 0.00 0.00 1.73
1541 3125 1.353022 ACTCCCTGCGTCCCAAAATAA 59.647 47.619 0.00 0.00 0.00 1.40
1542 3126 0.988832 ACTCCCTGCGTCCCAAAATA 59.011 50.000 0.00 0.00 0.00 1.40
1543 3127 0.988832 TACTCCCTGCGTCCCAAAAT 59.011 50.000 0.00 0.00 0.00 1.82
1544 3128 0.988832 ATACTCCCTGCGTCCCAAAA 59.011 50.000 0.00 0.00 0.00 2.44
1545 3129 0.988832 AATACTCCCTGCGTCCCAAA 59.011 50.000 0.00 0.00 0.00 3.28
1546 3130 1.868713 TAATACTCCCTGCGTCCCAA 58.131 50.000 0.00 0.00 0.00 4.12
1547 3131 1.868713 TTAATACTCCCTGCGTCCCA 58.131 50.000 0.00 0.00 0.00 4.37
1548 3132 2.093341 TGTTTAATACTCCCTGCGTCCC 60.093 50.000 0.00 0.00 0.00 4.46
1549 3133 3.255969 TGTTTAATACTCCCTGCGTCC 57.744 47.619 0.00 0.00 0.00 4.79
1550 3134 5.813080 AAATGTTTAATACTCCCTGCGTC 57.187 39.130 0.00 0.00 0.00 5.19
1551 3135 7.554835 TGATAAAATGTTTAATACTCCCTGCGT 59.445 33.333 0.00 0.00 0.00 5.24
1552 3136 7.855904 GTGATAAAATGTTTAATACTCCCTGCG 59.144 37.037 0.00 0.00 0.00 5.18
1553 3137 8.682710 TGTGATAAAATGTTTAATACTCCCTGC 58.317 33.333 0.00 0.00 0.00 4.85
1559 3143 9.019764 GCGCATTGTGATAAAATGTTTAATACT 57.980 29.630 0.30 0.00 37.35 2.12
1560 3144 8.802856 TGCGCATTGTGATAAAATGTTTAATAC 58.197 29.630 5.66 0.00 37.35 1.89
1583 3167 4.488126 TCTTCTCTGTTCCAAAATTGCG 57.512 40.909 0.00 0.00 0.00 4.85
1732 3316 5.592282 TGTGCTTATGTCAACCTGAAAAAGA 59.408 36.000 0.00 0.00 0.00 2.52
1823 3407 1.283793 CCTGTTGGCTGTTGCTTCG 59.716 57.895 0.00 0.00 39.59 3.79
1841 3425 6.033831 CACTGACAACTGAAACATTTGTTCAC 59.966 38.462 8.40 0.00 37.37 3.18
1936 3521 1.525535 TAGGCGAGAGGAGCGTACC 60.526 63.158 0.00 0.00 34.39 3.34
1968 3553 1.773391 CCAGATGGGGGAGCCTGAT 60.773 63.158 0.00 0.00 0.00 2.90
2064 3650 4.691860 ATGATTCAGAAAACTTGAGCCG 57.308 40.909 0.00 0.00 0.00 5.52
2072 3658 6.370593 TGCTACGACAAATGATTCAGAAAAC 58.629 36.000 0.00 0.00 0.00 2.43
2086 3672 3.925379 ACAGATGACAATGCTACGACAA 58.075 40.909 0.00 0.00 0.00 3.18
2136 3722 8.807118 TGGATAAGGAGCTACAATACTGAATAG 58.193 37.037 0.00 0.00 0.00 1.73
2177 3766 6.712095 ACACTGTTCAAGCAATCAAGAATAGA 59.288 34.615 0.00 0.00 34.56 1.98
2212 3801 7.728148 ACAACAAACCCGGTTTAAAATAGAAT 58.272 30.769 15.31 0.00 33.70 2.40
2285 3874 1.680249 GCCACTCTTGATTCTGTCCCC 60.680 57.143 0.00 0.00 0.00 4.81
2288 3877 5.382618 AAATTGCCACTCTTGATTCTGTC 57.617 39.130 0.00 0.00 0.00 3.51
2369 3964 1.014352 GACGGATGCGTTAATTGGCT 58.986 50.000 15.15 0.00 0.00 4.75
2432 4029 7.203910 GGTCATCACTACAACATAGTAGAAGG 58.796 42.308 8.01 0.00 43.24 3.46
2463 4060 6.368243 TGAAAGGTAATACGTTTATTCGTGCA 59.632 34.615 10.55 1.60 43.93 4.57
2474 4071 4.460948 ACATCCGTGAAAGGTAATACGT 57.539 40.909 0.00 0.00 34.96 3.57
2511 4108 4.458295 TCTTCTTAACTCCTCACGTTCGAT 59.542 41.667 0.00 0.00 0.00 3.59
2518 4115 4.456566 AGACGACTCTTCTTAACTCCTCAC 59.543 45.833 0.00 0.00 0.00 3.51
2545 4142 6.866770 CCGTGACAACTCTAATTCTGTTAAGA 59.133 38.462 0.00 0.00 0.00 2.10
2550 4147 3.244078 TGCCGTGACAACTCTAATTCTGT 60.244 43.478 0.00 0.00 0.00 3.41
2553 4150 4.184629 AGATGCCGTGACAACTCTAATTC 58.815 43.478 0.00 0.00 0.00 2.17
2574 4171 1.682867 TTGCATGCGAACGCGACTAG 61.683 55.000 15.93 1.69 45.51 2.57
2596 4193 7.341445 AGTAGACTACTAATTCCAAGCTCTG 57.659 40.000 13.63 0.00 37.23 3.35
2679 4276 6.066054 AGTCTTTTACTTCTTGCTTTCAGC 57.934 37.500 0.00 0.00 37.05 4.26
2760 4367 2.354203 GGCTTGGCCCTCTTATCTATCG 60.354 54.545 0.00 0.00 44.06 2.92
2807 4414 0.255890 GGTGTGAGGGGTATGTGCAT 59.744 55.000 0.00 0.00 0.00 3.96
2826 4433 5.121142 CGTAATGTTAGGTGGGTTTGTAGTG 59.879 44.000 0.00 0.00 0.00 2.74
2843 4450 1.131126 CACCGTAGACCGACGTAATGT 59.869 52.381 0.00 0.00 41.31 2.71
2848 4455 2.281761 ACCACCGTAGACCGACGT 60.282 61.111 0.00 0.00 41.31 4.34
2868 4475 0.323629 CACCACGAGGAAGCCCTTAA 59.676 55.000 5.68 0.00 44.53 1.85
2889 4496 3.425162 AAGACCCATCCACTCTTTGTC 57.575 47.619 0.00 0.00 0.00 3.18
2898 4505 2.235402 GGAGTAACGAAAGACCCATCCA 59.765 50.000 0.00 0.00 0.00 3.41
2908 4515 2.214376 TAGACCGGGGAGTAACGAAA 57.786 50.000 6.32 0.00 0.00 3.46
2925 4532 6.268847 AGCTAACCCTTTGTCCTAGATCATAG 59.731 42.308 0.00 0.00 0.00 2.23
2926 4533 6.143915 AGCTAACCCTTTGTCCTAGATCATA 58.856 40.000 0.00 0.00 0.00 2.15
2957 4564 0.609662 GGCTTCAGGTTACCGTGGTA 59.390 55.000 0.00 0.00 0.00 3.25
2963 4570 2.437895 GCGGGGCTTCAGGTTACC 60.438 66.667 0.00 0.00 0.00 2.85
2970 4577 1.992834 TAGATGTGGCGGGGCTTCA 60.993 57.895 0.00 0.00 0.00 3.02
2974 4581 2.109181 GAGTAGATGTGGCGGGGC 59.891 66.667 0.00 0.00 0.00 5.80
2979 4586 6.116126 AGGATTTAAAGTGAGTAGATGTGGC 58.884 40.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.