Multiple sequence alignment - TraesCS6D01G111000

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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 TraesCS6D01G111000 chr6D 100.000 2951 0 0 1 2951 77685803 77688753 0.000000e+00 5450
1 TraesCS6D01G111000 chr6D 82.123 358 33 8 2046 2378 77757659 77758010 8.060000e-71 278
2 TraesCS6D01G111000 chr6D 89.510 143 14 1 1990 2131 77694728 77694870 2.340000e-41 180
3 TraesCS6D01G111000 chr6D 82.955 176 23 7 2443 2615 77758120 77758291 5.090000e-33 152
4 TraesCS6D01G111000 chr6D 79.464 224 28 9 2210 2420 77694999 77695217 3.070000e-30 143
5 TraesCS6D01G111000 chr6B 90.810 2394 124 26 608 2934 150252748 150255112 0.000000e+00 3114
6 TraesCS6D01G111000 chr6B 90.050 201 19 1 2751 2951 150482961 150483160 2.920000e-65 259
7 TraesCS6D01G111000 chr6B 79.603 353 46 15 2217 2564 150278714 150279045 2.290000e-56 230
8 TraesCS6D01G111000 chr6B 83.843 229 22 9 1998 2211 150287820 150288048 1.390000e-48 204
9 TraesCS6D01G111000 chr6B 78.022 364 30 23 2217 2564 150288092 150288421 1.810000e-42 183
10 TraesCS6D01G111000 chr6A 93.666 1784 65 14 360 2131 93425237 93426984 0.000000e+00 2625
11 TraesCS6D01G111000 chr6A 88.516 775 54 19 2062 2806 93427009 93427778 0.000000e+00 905
12 TraesCS6D01G111000 chr6A 89.109 202 20 2 2751 2951 93459891 93460091 1.760000e-62 250
13 TraesCS6D01G111000 chr6A 80.857 350 38 18 2631 2951 93437266 93437615 6.320000e-62 248
14 TraesCS6D01G111000 chr6A 88.119 202 22 2 2751 2951 93439526 93439726 3.800000e-59 239
15 TraesCS6D01G111000 chr6A 97.541 122 2 1 2824 2945 93435501 93435621 1.070000e-49 207
16 TraesCS6D01G111000 chr6A 85.465 172 17 3 2210 2378 93436990 93437156 3.910000e-39 172


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 TraesCS6D01G111000 chr6D 77685803 77688753 2950 False 5450.0 5450 100.0000 1 2951 1 chr6D.!!$F1 2950
1 TraesCS6D01G111000 chr6D 77757659 77758291 632 False 215.0 278 82.5390 2046 2615 2 chr6D.!!$F3 569
2 TraesCS6D01G111000 chr6B 150252748 150255112 2364 False 3114.0 3114 90.8100 608 2934 1 chr6B.!!$F1 2326
3 TraesCS6D01G111000 chr6A 93425237 93427778 2541 False 1765.0 2625 91.0910 360 2806 2 chr6A.!!$F2 2446
4 TraesCS6D01G111000 chr6A 93435501 93439726 4225 False 216.5 248 87.9955 2210 2951 4 chr6A.!!$F3 741

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
721 732 0.040425 GCCATTAAACGGCGCCATAG 60.040 55.0 28.98 13.29 40.35 2.23 F
1467 1495 0.032117 TCATCCACTCCCAGACCGAT 60.032 55.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 1927 0.268869 TGATGGCCTCCCTGGTATCT 59.731 55.0 3.32 0.00 38.35 1.98 R
2438 2693 0.528470 ACAGAGGTAGCGAGCACTTC 59.472 55.0 0.00 0.43 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 8.474006 AGTTCACAAACTTGGTAAAAATTCAC 57.526 30.769 0.00 0.00 43.28 3.18
74 75 7.274686 AGTTCACAAACTTGGTAAAAATTCACG 59.725 33.333 0.00 0.00 43.28 4.35
75 76 5.517054 TCACAAACTTGGTAAAAATTCACGC 59.483 36.000 0.00 0.00 0.00 5.34
78 79 6.536941 ACAAACTTGGTAAAAATTCACGCATT 59.463 30.769 0.00 0.00 0.00 3.56
79 80 7.065204 ACAAACTTGGTAAAAATTCACGCATTT 59.935 29.630 0.00 0.00 0.00 2.32
80 81 6.523676 ACTTGGTAAAAATTCACGCATTTG 57.476 33.333 0.00 0.00 0.00 2.32
82 83 6.420604 ACTTGGTAAAAATTCACGCATTTGAG 59.579 34.615 0.00 0.00 0.00 3.02
83 84 6.078202 TGGTAAAAATTCACGCATTTGAGA 57.922 33.333 0.00 0.00 0.00 3.27
84 85 6.507900 TGGTAAAAATTCACGCATTTGAGAA 58.492 32.000 0.00 0.00 0.00 2.87
85 86 6.980978 TGGTAAAAATTCACGCATTTGAGAAA 59.019 30.769 0.00 0.00 0.00 2.52
86 87 7.492669 TGGTAAAAATTCACGCATTTGAGAAAA 59.507 29.630 0.00 0.00 0.00 2.29
88 89 6.900568 AAAATTCACGCATTTGAGAAAACA 57.099 29.167 0.00 0.00 0.00 2.83
89 90 5.888412 AATTCACGCATTTGAGAAAACAC 57.112 34.783 0.00 0.00 0.00 3.32
91 92 4.209452 TCACGCATTTGAGAAAACACTC 57.791 40.909 0.00 0.00 37.42 3.51
92 93 2.966708 CACGCATTTGAGAAAACACTCG 59.033 45.455 0.00 0.00 39.49 4.18
93 94 2.032030 ACGCATTTGAGAAAACACTCGG 60.032 45.455 0.00 0.00 39.49 4.63
94 95 2.223144 CGCATTTGAGAAAACACTCGGA 59.777 45.455 0.00 0.00 39.49 4.55
95 96 3.303725 CGCATTTGAGAAAACACTCGGAA 60.304 43.478 0.00 0.00 39.49 4.30
97 98 5.040635 GCATTTGAGAAAACACTCGGAAAA 58.959 37.500 0.00 0.00 39.49 2.29
98 99 5.691754 GCATTTGAGAAAACACTCGGAAAAT 59.308 36.000 0.00 0.00 39.49 1.82
100 101 7.254421 GCATTTGAGAAAACACTCGGAAAATTT 60.254 33.333 0.00 0.00 39.49 1.82
102 103 9.810545 ATTTGAGAAAACACTCGGAAAATTTAA 57.189 25.926 0.00 0.00 39.49 1.52
103 104 8.850454 TTGAGAAAACACTCGGAAAATTTAAG 57.150 30.769 0.00 0.00 39.49 1.85
104 105 7.992008 TGAGAAAACACTCGGAAAATTTAAGT 58.008 30.769 0.00 0.00 39.49 2.24
105 106 8.463607 TGAGAAAACACTCGGAAAATTTAAGTT 58.536 29.630 0.00 0.00 39.49 2.66
150 151 8.961294 TTCACCAATTTTCAAAAGTTCATGAT 57.039 26.923 0.00 0.00 0.00 2.45
152 153 9.393512 TCACCAATTTTCAAAAGTTCATGATTT 57.606 25.926 0.00 0.00 0.00 2.17
186 187 9.796120 AAATCATGAGTTTGAAAAAGTTTACGA 57.204 25.926 1.80 0.00 0.00 3.43
188 189 9.965824 ATCATGAGTTTGAAAAAGTTTACGAAT 57.034 25.926 0.09 0.00 0.00 3.34
189 190 9.796120 TCATGAGTTTGAAAAAGTTTACGAATT 57.204 25.926 0.00 0.00 0.00 2.17
248 249 7.411486 AATAAAACCAAAAACCAAAAAGGGG 57.589 32.000 0.00 0.00 43.89 4.79
250 251 4.659529 AACCAAAAACCAAAAAGGGGAA 57.340 36.364 0.00 0.00 43.89 3.97
252 253 4.594970 ACCAAAAACCAAAAAGGGGAAAG 58.405 39.130 0.00 0.00 43.89 2.62
254 255 5.222151 ACCAAAAACCAAAAAGGGGAAAGAA 60.222 36.000 0.00 0.00 43.89 2.52
256 257 6.176896 CAAAAACCAAAAAGGGGAAAGAAGA 58.823 36.000 0.00 0.00 43.89 2.87
257 258 6.381498 AAAACCAAAAAGGGGAAAGAAGAA 57.619 33.333 0.00 0.00 43.89 2.52
258 259 6.381498 AAACCAAAAAGGGGAAAGAAGAAA 57.619 33.333 0.00 0.00 43.89 2.52
259 260 5.614324 ACCAAAAAGGGGAAAGAAGAAAG 57.386 39.130 0.00 0.00 43.89 2.62
260 261 4.408921 ACCAAAAAGGGGAAAGAAGAAAGG 59.591 41.667 0.00 0.00 43.89 3.11
266 267 6.425210 AAGGGGAAAGAAGAAAGGAAAATG 57.575 37.500 0.00 0.00 0.00 2.32
267 268 5.715921 AGGGGAAAGAAGAAAGGAAAATGA 58.284 37.500 0.00 0.00 0.00 2.57
268 269 6.143206 AGGGGAAAGAAGAAAGGAAAATGAA 58.857 36.000 0.00 0.00 0.00 2.57
269 270 6.615316 AGGGGAAAGAAGAAAGGAAAATGAAA 59.385 34.615 0.00 0.00 0.00 2.69
319 320 2.882927 AAACCAAAAGAGAAACCGGC 57.117 45.000 0.00 0.00 0.00 6.13
321 322 0.106419 ACCAAAAGAGAAACCGGCCA 60.106 50.000 0.00 0.00 0.00 5.36
322 323 1.036707 CCAAAAGAGAAACCGGCCAA 58.963 50.000 0.00 0.00 0.00 4.52
324 325 2.037121 CCAAAAGAGAAACCGGCCAAAT 59.963 45.455 0.00 0.00 0.00 2.32
326 327 4.262249 CCAAAAGAGAAACCGGCCAAATAA 60.262 41.667 0.00 0.00 0.00 1.40
327 328 5.293560 CAAAAGAGAAACCGGCCAAATAAA 58.706 37.500 0.00 0.00 0.00 1.40
328 329 4.514781 AAGAGAAACCGGCCAAATAAAC 57.485 40.909 0.00 0.00 0.00 2.01
329 330 3.763057 AGAGAAACCGGCCAAATAAACT 58.237 40.909 0.00 0.00 0.00 2.66
330 331 4.149598 AGAGAAACCGGCCAAATAAACTT 58.850 39.130 0.00 0.00 0.00 2.66
332 333 5.949952 AGAGAAACCGGCCAAATAAACTTAT 59.050 36.000 0.00 0.00 0.00 1.73
335 336 7.768240 AGAAACCGGCCAAATAAACTTATAAG 58.232 34.615 11.05 11.05 0.00 1.73
336 337 7.612633 AGAAACCGGCCAAATAAACTTATAAGA 59.387 33.333 19.38 0.00 0.00 2.10
337 338 6.937436 ACCGGCCAAATAAACTTATAAGAG 57.063 37.500 19.38 0.00 0.00 2.85
339 340 6.541278 ACCGGCCAAATAAACTTATAAGAGAC 59.459 38.462 19.38 0.00 0.00 3.36
340 341 6.017357 CCGGCCAAATAAACTTATAAGAGACC 60.017 42.308 19.38 6.12 0.00 3.85
341 342 6.540914 CGGCCAAATAAACTTATAAGAGACCA 59.459 38.462 19.38 0.24 0.00 4.02
342 343 7.254795 CGGCCAAATAAACTTATAAGAGACCAG 60.255 40.741 19.38 3.58 0.00 4.00
343 344 7.418408 GCCAAATAAACTTATAAGAGACCAGC 58.582 38.462 19.38 8.09 0.00 4.85
344 345 7.630924 CCAAATAAACTTATAAGAGACCAGCG 58.369 38.462 19.38 1.65 0.00 5.18
345 346 7.254795 CCAAATAAACTTATAAGAGACCAGCGG 60.255 40.741 19.38 6.59 0.00 5.52
346 347 6.726490 ATAAACTTATAAGAGACCAGCGGA 57.274 37.500 19.38 0.00 0.00 5.54
349 350 5.416271 ACTTATAAGAGACCAGCGGAAAA 57.584 39.130 19.38 0.00 0.00 2.29
350 351 5.801380 ACTTATAAGAGACCAGCGGAAAAA 58.199 37.500 19.38 0.00 0.00 1.94
450 451 0.926155 CTTCACGATGCTCATGACGG 59.074 55.000 8.14 0.00 0.00 4.79
460 461 5.557136 CGATGCTCATGACGGAAAAGAATAC 60.557 44.000 0.00 0.00 0.00 1.89
473 474 6.129179 GGAAAAGAATACCATCTGATCCCAA 58.871 40.000 0.00 0.00 32.66 4.12
477 478 5.934781 AGAATACCATCTGATCCCAACTTC 58.065 41.667 0.00 0.00 0.00 3.01
483 484 3.652057 TCTGATCCCAACTTCAATCCC 57.348 47.619 0.00 0.00 0.00 3.85
487 488 1.753903 TCCCAACTTCAATCCCCTGA 58.246 50.000 0.00 0.00 0.00 3.86
495 496 2.268796 TCAATCCCCTGATGTCCTCA 57.731 50.000 0.00 0.00 0.00 3.86
499 500 2.268796 TCCCCTGATGTCCTCAATGA 57.731 50.000 0.00 0.00 32.14 2.57
506 507 4.445879 CCTGATGTCCTCAATGATCATGGT 60.446 45.833 9.46 0.00 32.14 3.55
517 518 2.665165 TGATCATGGTGTTAATGCCCC 58.335 47.619 0.00 0.00 0.00 5.80
533 534 0.400093 CCCCGGGTTCCTCCTTCTAT 60.400 60.000 21.85 0.00 36.25 1.98
551 552 0.749454 ATGCTTTGGATGACGCCCTC 60.749 55.000 0.00 0.00 0.00 4.30
557 558 2.247437 GGATGACGCCCTCGCAATC 61.247 63.158 0.00 0.00 39.84 2.67
563 564 1.522355 CGCCCTCGCAATCTGACAT 60.522 57.895 0.00 0.00 34.03 3.06
568 569 1.791204 CCTCGCAATCTGACATGATCG 59.209 52.381 0.00 0.00 0.00 3.69
575 576 0.103755 TCTGACATGATCGCAGCCTC 59.896 55.000 0.00 0.00 0.00 4.70
581 582 0.388659 ATGATCGCAGCCTCTGAGAC 59.611 55.000 6.17 0.00 42.43 3.36
592 593 1.217689 CCTCTGAGACCTGGAGATCCT 59.782 57.143 6.17 0.00 36.82 3.24
593 594 2.309613 CTCTGAGACCTGGAGATCCTG 58.690 57.143 0.00 0.00 36.82 3.86
594 595 0.752054 CTGAGACCTGGAGATCCTGC 59.248 60.000 0.00 0.00 36.82 4.85
595 596 0.689080 TGAGACCTGGAGATCCTGCC 60.689 60.000 0.00 0.00 36.82 4.85
597 598 0.398381 AGACCTGGAGATCCTGCCTC 60.398 60.000 0.00 0.00 36.82 4.70
599 600 0.252881 ACCTGGAGATCCTGCCTCAA 60.253 55.000 0.00 0.00 36.82 3.02
600 601 0.469070 CCTGGAGATCCTGCCTCAAG 59.531 60.000 0.00 0.00 36.82 3.02
601 602 0.179051 CTGGAGATCCTGCCTCAAGC 60.179 60.000 0.00 0.00 44.14 4.01
617 618 2.434359 GCGTAGTGCCGGAAGCTT 60.434 61.111 5.05 0.00 44.23 3.74
687 698 1.978455 TTGTTCGTGGGAGGTGTGCT 61.978 55.000 0.00 0.00 0.00 4.40
688 699 1.227853 GTTCGTGGGAGGTGTGCTT 60.228 57.895 0.00 0.00 0.00 3.91
690 701 2.709125 TTCGTGGGAGGTGTGCTTCG 62.709 60.000 0.00 0.00 0.00 3.79
693 704 2.426023 GGGAGGTGTGCTTCGTGT 59.574 61.111 0.00 0.00 0.00 4.49
721 732 0.040425 GCCATTAAACGGCGCCATAG 60.040 55.000 28.98 13.29 40.35 2.23
767 783 5.001232 TCCAGCTGACAAGTTTATACAACC 58.999 41.667 17.39 0.00 0.00 3.77
867 887 0.320073 TCCGACCGTTGCGAAATCTT 60.320 50.000 0.00 0.00 0.00 2.40
1467 1495 0.032117 TCATCCACTCCCAGACCGAT 60.032 55.000 0.00 0.00 0.00 4.18
1512 1540 4.760047 GTGCGGCCGGTCATCTGT 62.760 66.667 29.38 0.00 0.00 3.41
1987 2015 1.528542 CGGCGAGGAGATGGAGGTA 60.529 63.158 0.00 0.00 0.00 3.08
1988 2016 0.896019 CGGCGAGGAGATGGAGGTAT 60.896 60.000 0.00 0.00 0.00 2.73
2090 2119 7.147312 TCTTCCTGAATGCAGTTTGTTAAATG 58.853 34.615 0.00 0.00 40.63 2.32
2131 2160 4.510038 AACTGAAACTGGAATGTGCATC 57.490 40.909 0.00 0.00 0.00 3.91
2132 2161 3.489355 ACTGAAACTGGAATGTGCATCA 58.511 40.909 0.00 0.00 0.00 3.07
2134 2163 4.022589 ACTGAAACTGGAATGTGCATCAAG 60.023 41.667 0.00 0.00 0.00 3.02
2135 2164 4.143543 TGAAACTGGAATGTGCATCAAGA 58.856 39.130 0.00 0.00 0.00 3.02
2138 2167 5.733620 AACTGGAATGTGCATCAAGAATT 57.266 34.783 0.00 0.00 0.00 2.17
2140 2169 6.199937 ACTGGAATGTGCATCAAGAATTAC 57.800 37.500 0.00 0.00 0.00 1.89
2141 2170 5.948162 ACTGGAATGTGCATCAAGAATTACT 59.052 36.000 0.00 0.00 0.00 2.24
2150 2294 5.471797 TGCATCAAGAATTACTTTTGTCGGA 59.528 36.000 0.00 0.00 36.61 4.55
2195 2339 7.467539 GCATTGATCTTTCAGGATCTTCTTGAG 60.468 40.741 0.00 0.00 41.72 3.02
2211 2355 8.846943 TCTTCTTGAGTGCAGATTGTTAAATA 57.153 30.769 0.00 0.00 0.00 1.40
2213 2357 9.499585 CTTCTTGAGTGCAGATTGTTAAATATG 57.500 33.333 0.00 0.00 37.92 1.78
2214 2358 8.565896 TCTTGAGTGCAGATTGTTAAATATGT 57.434 30.769 0.00 0.00 37.33 2.29
2215 2359 8.668353 TCTTGAGTGCAGATTGTTAAATATGTC 58.332 33.333 0.00 0.00 37.33 3.06
2231 2413 6.677781 AATATGTCTATGTGGTTCAAACGG 57.322 37.500 0.00 0.00 0.00 4.44
2232 2414 3.478857 TGTCTATGTGGTTCAAACGGT 57.521 42.857 0.00 0.00 0.00 4.83
2233 2415 3.395639 TGTCTATGTGGTTCAAACGGTC 58.604 45.455 0.00 0.00 0.00 4.79
2243 2425 2.940410 GTTCAAACGGTCCTGAAACTGA 59.060 45.455 7.07 0.00 33.52 3.41
2332 2517 6.041751 AGTTCACTACTACACCTAACAAAGCT 59.958 38.462 0.00 0.00 34.56 3.74
2378 2563 1.599797 GGAACAGGGGACAACACGG 60.600 63.158 0.00 0.00 0.00 4.94
2406 2661 1.755179 CCTTCCAATCCACAAGCGAT 58.245 50.000 0.00 0.00 0.00 4.58
2420 2675 2.484062 GCGATCCTCGTTCCCCGTA 61.484 63.158 0.00 0.00 42.81 4.02
2438 2693 2.480419 CGTAGCCACCTCTGTTTTTCTG 59.520 50.000 0.00 0.00 0.00 3.02
2481 2736 7.286087 TGTTCTGTTTGTAGTTACTCACCTCTA 59.714 37.037 0.00 0.00 0.00 2.43
2526 2810 5.939764 AAATCTCTCACCTATACAGCACA 57.060 39.130 0.00 0.00 0.00 4.57
2665 2960 2.027073 GGACTTGTGCGCACGATCA 61.027 57.895 33.22 15.25 0.00 2.92
2671 2967 1.503294 TGTGCGCACGATCAAAAGTA 58.497 45.000 33.22 10.88 0.00 2.24
2696 2992 8.936070 ATTGTAACTTCCAAGTTTTTGTTACC 57.064 30.769 9.92 0.00 46.52 2.85
2709 3005 7.993101 AGTTTTTGTTACCTCCACTACTTTTC 58.007 34.615 0.00 0.00 0.00 2.29
2729 3025 7.488471 ACTTTTCACTAGCATTATCGTAGACAC 59.512 37.037 0.00 0.00 42.51 3.67
2747 3043 3.639538 ACACCGCGTCATATAGATTCAC 58.360 45.455 4.92 0.00 0.00 3.18
2757 3081 6.980978 CGTCATATAGATTCACAGTTTGACCT 59.019 38.462 0.00 0.00 32.26 3.85
2764 3088 9.739276 ATAGATTCACAGTTTGACCTTTATCAA 57.261 29.630 0.00 0.00 36.80 2.57
2765 3089 8.641498 AGATTCACAGTTTGACCTTTATCAAT 57.359 30.769 0.00 0.00 38.37 2.57
2941 3266 8.954950 ACTCATATCATAGCTTGGTATTATGC 57.045 34.615 0.00 0.00 28.65 3.14
2945 3270 9.387257 CATATCATAGCTTGGTATTATGCTTGA 57.613 33.333 0.00 0.00 37.02 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.289675 TGCGTGAATTTTTACCAAGTTTGTG 59.710 36.000 0.00 0.00 0.00 3.33
53 54 5.411781 TGCGTGAATTTTTACCAAGTTTGT 58.588 33.333 0.00 0.00 0.00 2.83
54 55 5.957910 TGCGTGAATTTTTACCAAGTTTG 57.042 34.783 0.00 0.00 0.00 2.93
55 56 7.278868 TCAAATGCGTGAATTTTTACCAAGTTT 59.721 29.630 0.00 0.00 0.00 2.66
56 57 6.758886 TCAAATGCGTGAATTTTTACCAAGTT 59.241 30.769 0.00 0.00 0.00 2.66
58 59 6.640499 TCTCAAATGCGTGAATTTTTACCAAG 59.360 34.615 0.00 0.00 0.00 3.61
61 62 7.401484 TTTCTCAAATGCGTGAATTTTTACC 57.599 32.000 0.00 0.00 0.00 2.85
62 63 8.324567 TGTTTTCTCAAATGCGTGAATTTTTAC 58.675 29.630 0.00 0.00 0.00 2.01
63 64 8.324567 GTGTTTTCTCAAATGCGTGAATTTTTA 58.675 29.630 0.00 0.00 0.00 1.52
65 66 6.534793 AGTGTTTTCTCAAATGCGTGAATTTT 59.465 30.769 0.00 0.00 0.00 1.82
66 67 6.042143 AGTGTTTTCTCAAATGCGTGAATTT 58.958 32.000 0.00 0.00 0.00 1.82
70 71 3.303066 CGAGTGTTTTCTCAAATGCGTGA 60.303 43.478 0.00 0.00 34.46 4.35
72 73 2.032030 CCGAGTGTTTTCTCAAATGCGT 60.032 45.455 0.00 0.00 34.46 5.24
73 74 2.223144 TCCGAGTGTTTTCTCAAATGCG 59.777 45.455 0.00 0.00 34.46 4.73
74 75 3.896648 TCCGAGTGTTTTCTCAAATGC 57.103 42.857 0.00 0.00 34.46 3.56
75 76 7.698836 AATTTTCCGAGTGTTTTCTCAAATG 57.301 32.000 0.00 0.00 34.46 2.32
78 79 8.463607 ACTTAAATTTTCCGAGTGTTTTCTCAA 58.536 29.630 0.00 0.00 34.46 3.02
79 80 7.992008 ACTTAAATTTTCCGAGTGTTTTCTCA 58.008 30.769 0.00 0.00 34.46 3.27
80 81 8.851960 AACTTAAATTTTCCGAGTGTTTTCTC 57.148 30.769 0.00 0.00 0.00 2.87
124 125 8.783833 TCATGAACTTTTGAAAATTGGTGAAA 57.216 26.923 0.00 0.00 0.00 2.69
126 127 8.961294 AATCATGAACTTTTGAAAATTGGTGA 57.039 26.923 0.00 0.00 0.00 4.02
160 161 9.796120 TCGTAAACTTTTTCAAACTCATGATTT 57.204 25.926 0.00 0.00 0.00 2.17
161 162 9.796120 TTCGTAAACTTTTTCAAACTCATGATT 57.204 25.926 0.00 0.00 0.00 2.57
162 163 9.965824 ATTCGTAAACTTTTTCAAACTCATGAT 57.034 25.926 0.00 0.00 0.00 2.45
163 164 9.796120 AATTCGTAAACTTTTTCAAACTCATGA 57.204 25.926 0.00 0.00 0.00 3.07
221 222 9.712305 CCCTTTTTGGTTTTTGGTTTTATTTTT 57.288 25.926 0.00 0.00 0.00 1.94
222 223 8.314751 CCCCTTTTTGGTTTTTGGTTTTATTTT 58.685 29.630 0.00 0.00 0.00 1.82
223 224 7.674348 TCCCCTTTTTGGTTTTTGGTTTTATTT 59.326 29.630 0.00 0.00 0.00 1.40
224 225 7.182760 TCCCCTTTTTGGTTTTTGGTTTTATT 58.817 30.769 0.00 0.00 0.00 1.40
225 226 6.732487 TCCCCTTTTTGGTTTTTGGTTTTAT 58.268 32.000 0.00 0.00 0.00 1.40
226 227 6.135819 TCCCCTTTTTGGTTTTTGGTTTTA 57.864 33.333 0.00 0.00 0.00 1.52
227 228 4.999310 TCCCCTTTTTGGTTTTTGGTTTT 58.001 34.783 0.00 0.00 0.00 2.43
228 229 4.659529 TCCCCTTTTTGGTTTTTGGTTT 57.340 36.364 0.00 0.00 0.00 3.27
230 231 4.289934 TCTTTCCCCTTTTTGGTTTTTGGT 59.710 37.500 0.00 0.00 0.00 3.67
231 232 4.849518 TCTTTCCCCTTTTTGGTTTTTGG 58.150 39.130 0.00 0.00 0.00 3.28
232 233 6.176896 TCTTCTTTCCCCTTTTTGGTTTTTG 58.823 36.000 0.00 0.00 0.00 2.44
233 234 6.381498 TCTTCTTTCCCCTTTTTGGTTTTT 57.619 33.333 0.00 0.00 0.00 1.94
234 235 6.381498 TTCTTCTTTCCCCTTTTTGGTTTT 57.619 33.333 0.00 0.00 0.00 2.43
235 236 6.381498 TTTCTTCTTTCCCCTTTTTGGTTT 57.619 33.333 0.00 0.00 0.00 3.27
237 238 4.408921 CCTTTCTTCTTTCCCCTTTTTGGT 59.591 41.667 0.00 0.00 0.00 3.67
238 239 4.653801 TCCTTTCTTCTTTCCCCTTTTTGG 59.346 41.667 0.00 0.00 0.00 3.28
239 240 5.869649 TCCTTTCTTCTTTCCCCTTTTTG 57.130 39.130 0.00 0.00 0.00 2.44
240 241 6.884472 TTTCCTTTCTTCTTTCCCCTTTTT 57.116 33.333 0.00 0.00 0.00 1.94
241 242 6.884472 TTTTCCTTTCTTCTTTCCCCTTTT 57.116 33.333 0.00 0.00 0.00 2.27
242 243 6.615316 TCATTTTCCTTTCTTCTTTCCCCTTT 59.385 34.615 0.00 0.00 0.00 3.11
243 244 6.143206 TCATTTTCCTTTCTTCTTTCCCCTT 58.857 36.000 0.00 0.00 0.00 3.95
244 245 5.715921 TCATTTTCCTTTCTTCTTTCCCCT 58.284 37.500 0.00 0.00 0.00 4.79
245 246 6.419484 TTCATTTTCCTTTCTTCTTTCCCC 57.581 37.500 0.00 0.00 0.00 4.81
246 247 8.731275 TTTTTCATTTTCCTTTCTTCTTTCCC 57.269 30.769 0.00 0.00 0.00 3.97
299 300 2.159014 GGCCGGTTTCTCTTTTGGTTTT 60.159 45.455 1.90 0.00 0.00 2.43
300 301 1.411246 GGCCGGTTTCTCTTTTGGTTT 59.589 47.619 1.90 0.00 0.00 3.27
301 302 1.037493 GGCCGGTTTCTCTTTTGGTT 58.963 50.000 1.90 0.00 0.00 3.67
302 303 0.106419 TGGCCGGTTTCTCTTTTGGT 60.106 50.000 1.90 0.00 0.00 3.67
304 305 2.880963 TTTGGCCGGTTTCTCTTTTG 57.119 45.000 1.90 0.00 0.00 2.44
305 306 5.069914 AGTTTATTTGGCCGGTTTCTCTTTT 59.930 36.000 1.90 0.00 0.00 2.27
307 308 4.149598 AGTTTATTTGGCCGGTTTCTCTT 58.850 39.130 1.90 0.00 0.00 2.85
308 309 3.763057 AGTTTATTTGGCCGGTTTCTCT 58.237 40.909 1.90 0.00 0.00 3.10
309 310 4.514781 AAGTTTATTTGGCCGGTTTCTC 57.485 40.909 1.90 0.00 0.00 2.87
310 311 7.612633 TCTTATAAGTTTATTTGGCCGGTTTCT 59.387 33.333 12.19 0.00 0.00 2.52
311 312 7.764331 TCTTATAAGTTTATTTGGCCGGTTTC 58.236 34.615 12.19 0.00 0.00 2.78
313 314 7.066645 GTCTCTTATAAGTTTATTTGGCCGGTT 59.933 37.037 12.19 0.00 0.00 4.44
316 317 6.540914 TGGTCTCTTATAAGTTTATTTGGCCG 59.459 38.462 12.19 0.00 0.00 6.13
317 318 7.468768 GCTGGTCTCTTATAAGTTTATTTGGCC 60.469 40.741 12.19 0.00 0.00 5.36
318 319 7.418408 GCTGGTCTCTTATAAGTTTATTTGGC 58.582 38.462 12.19 5.63 0.00 4.52
319 320 7.254795 CCGCTGGTCTCTTATAAGTTTATTTGG 60.255 40.741 12.19 4.03 0.00 3.28
321 322 7.562135 TCCGCTGGTCTCTTATAAGTTTATTT 58.438 34.615 12.19 0.00 0.00 1.40
322 323 7.120923 TCCGCTGGTCTCTTATAAGTTTATT 57.879 36.000 12.19 0.00 0.00 1.40
324 325 6.534475 TTCCGCTGGTCTCTTATAAGTTTA 57.466 37.500 12.19 0.00 0.00 2.01
326 327 5.416271 TTTCCGCTGGTCTCTTATAAGTT 57.584 39.130 12.19 0.00 0.00 2.66
327 328 5.416271 TTTTCCGCTGGTCTCTTATAAGT 57.584 39.130 12.19 0.00 0.00 2.24
349 350 2.142319 GCCATCATGTTTGCGGTTTTT 58.858 42.857 0.00 0.00 0.00 1.94
350 351 1.607767 GGCCATCATGTTTGCGGTTTT 60.608 47.619 0.00 0.00 0.00 2.43
351 352 0.037419 GGCCATCATGTTTGCGGTTT 60.037 50.000 0.00 0.00 0.00 3.27
353 354 1.304381 AGGCCATCATGTTTGCGGT 60.304 52.632 5.01 0.00 0.00 5.68
354 355 1.140161 CAGGCCATCATGTTTGCGG 59.860 57.895 5.01 0.00 0.00 5.69
355 356 1.140161 CCAGGCCATCATGTTTGCG 59.860 57.895 5.01 0.00 0.00 4.85
356 357 1.068127 GATCCAGGCCATCATGTTTGC 59.932 52.381 5.01 0.00 0.00 3.68
400 401 1.002576 TGCTCACAAGTCGCAACATTG 60.003 47.619 0.00 0.00 0.00 2.82
401 402 1.308047 TGCTCACAAGTCGCAACATT 58.692 45.000 0.00 0.00 0.00 2.71
403 404 0.867746 GATGCTCACAAGTCGCAACA 59.132 50.000 0.00 0.00 37.20 3.33
404 405 0.166814 GGATGCTCACAAGTCGCAAC 59.833 55.000 0.00 0.00 37.20 4.17
405 406 0.250252 TGGATGCTCACAAGTCGCAA 60.250 50.000 0.00 0.00 37.20 4.85
406 407 0.250252 TTGGATGCTCACAAGTCGCA 60.250 50.000 0.00 0.00 38.14 5.10
407 408 0.445436 CTTGGATGCTCACAAGTCGC 59.555 55.000 0.00 0.00 39.30 5.19
450 451 6.830838 AGTTGGGATCAGATGGTATTCTTTTC 59.169 38.462 0.00 0.00 0.00 2.29
460 461 3.887716 GGATTGAAGTTGGGATCAGATGG 59.112 47.826 0.00 0.00 0.00 3.51
473 474 2.507471 GAGGACATCAGGGGATTGAAGT 59.493 50.000 0.00 0.00 32.23 3.01
477 478 3.117776 TCATTGAGGACATCAGGGGATTG 60.118 47.826 0.00 0.00 39.68 2.67
483 484 4.072839 CCATGATCATTGAGGACATCAGG 58.927 47.826 5.16 0.00 39.68 3.86
487 488 4.515028 ACACCATGATCATTGAGGACAT 57.485 40.909 15.57 0.52 0.00 3.06
495 496 3.642848 GGGGCATTAACACCATGATCATT 59.357 43.478 5.16 0.00 0.00 2.57
499 500 1.691196 CGGGGCATTAACACCATGAT 58.309 50.000 0.00 0.00 0.00 2.45
506 507 1.000646 GGAACCCGGGGCATTAACA 60.001 57.895 27.92 0.00 0.00 2.41
517 518 1.123928 AGCATAGAAGGAGGAACCCG 58.876 55.000 0.00 0.00 40.05 5.28
533 534 1.377202 GAGGGCGTCATCCAAAGCA 60.377 57.895 1.64 0.00 0.00 3.91
551 552 3.723347 GCGATCATGTCAGATTGCG 57.277 52.632 0.00 0.00 43.40 4.85
557 558 0.104487 AGAGGCTGCGATCATGTCAG 59.896 55.000 0.00 0.00 0.00 3.51
563 564 1.670949 GGTCTCAGAGGCTGCGATCA 61.671 60.000 1.07 0.00 28.08 2.92
568 569 1.958902 CTCCAGGTCTCAGAGGCTGC 61.959 65.000 1.07 0.00 0.00 5.25
575 576 0.752054 GCAGGATCTCCAGGTCTCAG 59.248 60.000 0.00 0.00 38.89 3.35
581 582 0.469070 CTTGAGGCAGGATCTCCAGG 59.531 60.000 0.00 0.00 38.89 4.45
592 593 2.047274 GGCACTACGCTTGAGGCA 60.047 61.111 0.00 0.00 41.91 4.75
593 594 3.188786 CGGCACTACGCTTGAGGC 61.189 66.667 0.00 0.00 41.91 4.70
594 595 2.501223 TTCCGGCACTACGCTTGAGG 62.501 60.000 0.00 0.00 41.91 3.86
595 596 1.078759 CTTCCGGCACTACGCTTGAG 61.079 60.000 0.00 0.00 41.91 3.02
597 598 2.740714 GCTTCCGGCACTACGCTTG 61.741 63.158 0.00 0.00 41.91 4.01
599 600 2.837371 GAAGCTTCCGGCACTACGCT 62.837 60.000 15.97 0.00 44.79 5.07
600 601 2.434359 AAGCTTCCGGCACTACGC 60.434 61.111 0.00 0.00 44.79 4.42
601 602 1.810030 GGAAGCTTCCGGCACTACG 60.810 63.158 29.09 0.00 44.79 3.51
602 603 4.203618 GGAAGCTTCCGGCACTAC 57.796 61.111 29.09 4.53 44.79 2.73
617 618 2.100087 GCTGGTTTTTCCTCGTTTTGGA 59.900 45.455 0.00 0.00 37.07 3.53
628 629 5.366829 AACTGTATAACCGCTGGTTTTTC 57.633 39.130 16.22 8.69 44.33 2.29
687 698 2.303163 ATGGCTTATGCGTACACGAA 57.697 45.000 5.84 0.00 43.02 3.85
688 699 2.303163 AATGGCTTATGCGTACACGA 57.697 45.000 5.84 0.00 43.02 4.35
690 701 4.268522 CGTTTAATGGCTTATGCGTACAC 58.731 43.478 0.00 0.00 40.82 2.90
693 704 2.288458 GCCGTTTAATGGCTTATGCGTA 59.712 45.455 19.93 0.00 46.66 4.42
721 732 2.280186 CAACTCCTATCCGGCGCC 60.280 66.667 19.07 19.07 0.00 6.53
728 739 2.158885 GCTGGACTTCCCAACTCCTATC 60.159 54.545 0.00 0.00 46.07 2.08
755 766 2.095617 GCAAACGCGGGTTGTATAAACT 60.096 45.455 19.33 0.00 36.25 2.66
767 783 4.389576 GACCTGCTGCAAACGCGG 62.390 66.667 12.47 3.34 38.92 6.46
867 887 5.230942 GTGAATTTGAGTTCTTCTCGAGGA 58.769 41.667 13.56 1.83 45.46 3.71
998 1026 2.571757 GCGTCCTCGACACCATCA 59.428 61.111 0.00 0.00 39.71 3.07
1512 1540 3.884774 AAGGTGACCGCCTTGCCA 61.885 61.111 13.51 0.00 46.28 4.92
1581 1609 0.681564 AGATGACGACCTCGAAGGCT 60.682 55.000 0.78 0.00 39.63 4.58
1824 1852 2.181021 GCGTCGTCGATGAAGGGT 59.819 61.111 18.54 0.00 39.71 4.34
1899 1927 0.268869 TGATGGCCTCCCTGGTATCT 59.731 55.000 3.32 0.00 38.35 1.98
2090 2119 8.641499 TCAGTTTCATTGAACCACATAAAAAC 57.359 30.769 0.00 0.00 0.00 2.43
2134 2163 9.878599 CACCATAATATCCGACAAAAGTAATTC 57.121 33.333 0.00 0.00 0.00 2.17
2135 2164 9.621629 TCACCATAATATCCGACAAAAGTAATT 57.378 29.630 0.00 0.00 0.00 1.40
2138 2167 7.709182 CAGTCACCATAATATCCGACAAAAGTA 59.291 37.037 0.00 0.00 0.00 2.24
2140 2169 6.017934 CCAGTCACCATAATATCCGACAAAAG 60.018 42.308 0.00 0.00 0.00 2.27
2141 2170 5.820423 CCAGTCACCATAATATCCGACAAAA 59.180 40.000 0.00 0.00 0.00 2.44
2150 2294 5.573380 ATGCTCACCAGTCACCATAATAT 57.427 39.130 0.00 0.00 0.00 1.28
2195 2339 9.655769 CACATAGACATATTTAACAATCTGCAC 57.344 33.333 0.00 0.00 0.00 4.57
2211 2355 4.000988 GACCGTTTGAACCACATAGACAT 58.999 43.478 0.00 0.00 0.00 3.06
2213 2357 2.740447 GGACCGTTTGAACCACATAGAC 59.260 50.000 0.00 0.00 0.00 2.59
2214 2358 2.635915 AGGACCGTTTGAACCACATAGA 59.364 45.455 0.00 0.00 0.00 1.98
2215 2359 2.742053 CAGGACCGTTTGAACCACATAG 59.258 50.000 0.00 0.00 0.00 2.23
2231 2413 6.331369 TCAATCCAATTTCAGTTTCAGGAC 57.669 37.500 0.00 0.00 0.00 3.85
2232 2414 6.777091 TCTTCAATCCAATTTCAGTTTCAGGA 59.223 34.615 0.00 0.00 0.00 3.86
2233 2415 6.985117 TCTTCAATCCAATTTCAGTTTCAGG 58.015 36.000 0.00 0.00 0.00 3.86
2243 2425 9.893634 TGCATAATTTCATCTTCAATCCAATTT 57.106 25.926 0.00 0.00 0.00 1.82
2332 2517 4.269183 CACCATGGCTTGTAGTAATTCCA 58.731 43.478 13.04 0.00 0.00 3.53
2420 2675 3.217626 CTTCAGAAAAACAGAGGTGGCT 58.782 45.455 0.00 0.00 0.00 4.75
2438 2693 0.528470 ACAGAGGTAGCGAGCACTTC 59.472 55.000 0.00 0.43 0.00 3.01
2481 2736 3.069586 TCAGTTCACAGGAAGTCGTTCAT 59.930 43.478 0.00 0.00 34.43 2.57
2559 2845 6.927381 CCCGGTCGATATACAAGTTAGAAAAT 59.073 38.462 0.00 0.00 0.00 1.82
2622 2916 1.808343 CAACCCAAGCTAAACCGTACC 59.192 52.381 0.00 0.00 0.00 3.34
2626 2921 1.268625 GGTTCAACCCAAGCTAAACCG 59.731 52.381 0.00 0.00 30.04 4.44
2671 2967 8.755028 AGGTAACAAAAACTTGGAAGTTACAAT 58.245 29.630 0.00 0.00 44.19 2.71
2696 2992 7.168302 CGATAATGCTAGTGAAAAGTAGTGGAG 59.832 40.741 0.00 0.00 0.00 3.86
2709 3005 4.219802 CGGTGTCTACGATAATGCTAGTG 58.780 47.826 0.00 0.00 0.00 2.74
2729 3025 3.902150 ACTGTGAATCTATATGACGCGG 58.098 45.455 12.47 0.00 0.00 6.46
2747 3043 7.080099 CAGTGTCATTGATAAAGGTCAAACTG 58.920 38.462 5.38 5.38 41.09 3.16
2757 3081 8.845227 TCACTAAAAAGCAGTGTCATTGATAAA 58.155 29.630 0.00 0.00 43.21 1.40
2764 3088 4.763793 AGCATCACTAAAAAGCAGTGTCAT 59.236 37.500 2.70 0.00 43.21 3.06
2765 3089 4.023792 CAGCATCACTAAAAAGCAGTGTCA 60.024 41.667 2.70 0.00 43.21 3.58
2832 3157 5.184479 TCGAGATTCCATATAACTTACCCCG 59.816 44.000 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.