Multiple sequence alignment - TraesCS2A01G127100

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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 TraesCS2A01G127100 chr2A 100.000 2043 0 0 950 2992 75134769 75136811 0.000000e+00 3773.0
1 TraesCS2A01G127100 chr2A 100.000 596 0 0 1 596 75133820 75134415 0.000000e+00 1101.0
2 TraesCS2A01G127100 chr2D 89.023 1904 124 46 1134 2992 75389632 75391495 0.000000e+00 2279.0
3 TraesCS2A01G127100 chr2D 83.934 610 44 18 3 596 75388710 75389281 4.390000e-148 534.0
4 TraesCS2A01G127100 chr2B 89.289 1055 46 20 1021 2037 115378054 115379079 0.000000e+00 1260.0
5 TraesCS2A01G127100 chr2B 83.660 612 47 20 3 596 115376904 115377480 7.350000e-146 527.0
6 TraesCS2A01G127100 chr2B 86.298 416 26 14 2028 2418 115379198 115379607 9.910000e-115 424.0
7 TraesCS2A01G127100 chr2B 90.476 147 9 2 2851 2992 115379899 115380045 3.940000e-44 189.0
8 TraesCS2A01G127100 chr2B 100.000 34 0 0 950 983 115377563 115377596 2.490000e-06 63.9
9 TraesCS2A01G127100 chr4B 79.545 132 14 5 2444 2563 235395126 235395256 6.870000e-12 82.4
10 TraesCS2A01G127100 chr4D 88.060 67 8 0 2444 2510 258907504 258907570 2.470000e-11 80.5
11 TraesCS2A01G127100 chr4A 79.412 136 11 8 2444 2563 242899483 242899617 2.470000e-11 80.5


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 TraesCS2A01G127100 chr2A 75133820 75136811 2991 False 2437.00 3773 100.0000 1 2992 2 chr2A.!!$F1 2991
1 TraesCS2A01G127100 chr2D 75388710 75391495 2785 False 1406.50 2279 86.4785 3 2992 2 chr2D.!!$F1 2989
2 TraesCS2A01G127100 chr2B 115376904 115380045 3141 False 492.78 1260 89.9446 3 2992 5 chr2B.!!$F1 2989

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
284 312 0.039617 TTCCAAAAGGTTGCGATGCG 60.040 50.0 0.0 0.0 33.01 4.73 F
993 1021 0.107654 CCAGAAATCCCACCCGTCTC 60.108 60.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 1563 0.10852 CGGTACTGTAACCACGCCAT 60.109 55.0 0.00 0.0 39.71 4.40 R
2283 2936 0.17910 TTATGCGCAGAGGACAGAGC 60.179 55.0 18.32 0.0 0.00 4.09 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
34 35 2.650297 GCATTTGTTCGTACGTGAAAGC 59.350 45.455 16.05 10.32 0.00 3.51
36 37 0.230260 TTGTTCGTACGTGAAAGCGC 59.770 50.000 16.05 0.00 34.88 5.92
37 38 1.129209 GTTCGTACGTGAAAGCGCC 59.871 57.895 16.05 0.00 34.88 6.53
46 52 0.651031 GTGAAAGCGCCCGATCTAAC 59.349 55.000 2.29 0.00 0.00 2.34
80 86 1.251251 GTGGTTTTGCTCCTGATGCT 58.749 50.000 0.00 0.00 0.00 3.79
81 87 2.436417 GTGGTTTTGCTCCTGATGCTA 58.564 47.619 0.00 0.00 0.00 3.49
82 88 2.421424 GTGGTTTTGCTCCTGATGCTAG 59.579 50.000 0.00 0.00 0.00 3.42
84 90 2.363683 GTTTTGCTCCTGATGCTAGCT 58.636 47.619 17.23 0.83 37.16 3.32
86 92 1.197812 TTGCTCCTGATGCTAGCTCA 58.802 50.000 17.23 15.15 37.16 4.26
92 108 5.105432 TGCTCCTGATGCTAGCTCATATAAG 60.105 44.000 17.23 3.25 37.16 1.73
129 152 8.876275 ATCCTTATTTTAAAGCATACGTACGA 57.124 30.769 24.41 6.04 0.00 3.43
145 173 0.780002 ACGAACGAACGCACATACAC 59.220 50.000 0.14 0.00 36.70 2.90
162 190 3.619233 ACACAATAACAAAGGTCGTGC 57.381 42.857 0.00 0.00 0.00 5.34
197 225 0.599060 TTGGAAAAATCCGCCGAACC 59.401 50.000 0.00 0.00 0.00 3.62
212 240 3.958147 AACCCCTCGTCTGCATGCG 62.958 63.158 14.09 8.20 0.00 4.73
226 254 0.521867 CATGCGTTCACATCAAGCGG 60.522 55.000 0.00 0.00 0.00 5.52
227 255 0.955428 ATGCGTTCACATCAAGCGGT 60.955 50.000 0.00 0.00 0.00 5.68
228 256 1.154413 GCGTTCACATCAAGCGGTG 60.154 57.895 0.00 0.00 36.36 4.94
229 257 1.497278 CGTTCACATCAAGCGGTGG 59.503 57.895 0.00 0.00 35.74 4.61
230 258 1.875963 GTTCACATCAAGCGGTGGG 59.124 57.895 0.00 0.00 35.74 4.61
231 259 1.971167 TTCACATCAAGCGGTGGGC 60.971 57.895 0.00 0.00 44.05 5.36
232 260 3.443045 CACATCAAGCGGTGGGCC 61.443 66.667 0.00 0.00 45.17 5.80
233 261 3.965258 ACATCAAGCGGTGGGCCA 61.965 61.111 0.00 0.00 45.17 5.36
277 305 5.121611 GCCCGATTAAATTTCCAAAAGGTTG 59.878 40.000 0.00 0.00 34.25 3.77
281 309 6.310224 CGATTAAATTTCCAAAAGGTTGCGAT 59.690 34.615 0.00 0.00 33.01 4.58
284 312 0.039617 TTCCAAAAGGTTGCGATGCG 60.040 50.000 0.00 0.00 33.01 4.73
285 313 1.169661 TCCAAAAGGTTGCGATGCGT 61.170 50.000 0.00 0.00 33.01 5.24
286 314 0.519519 CCAAAAGGTTGCGATGCGTA 59.480 50.000 0.00 0.00 33.01 4.42
287 315 1.602191 CAAAAGGTTGCGATGCGTAC 58.398 50.000 0.00 0.00 0.00 3.67
359 387 2.866726 CGGCCCCAAACCAACCAAG 61.867 63.158 0.00 0.00 0.00 3.61
412 440 0.827368 GTTCCAGCCAAACCAAACCA 59.173 50.000 0.00 0.00 0.00 3.67
414 442 1.573108 TCCAGCCAAACCAAACCAAA 58.427 45.000 0.00 0.00 0.00 3.28
415 443 1.208293 TCCAGCCAAACCAAACCAAAC 59.792 47.619 0.00 0.00 0.00 2.93
416 444 1.662517 CAGCCAAACCAAACCAAACC 58.337 50.000 0.00 0.00 0.00 3.27
417 445 0.544223 AGCCAAACCAAACCAAACCC 59.456 50.000 0.00 0.00 0.00 4.11
418 446 0.253327 GCCAAACCAAACCAAACCCA 59.747 50.000 0.00 0.00 0.00 4.51
419 447 1.133945 GCCAAACCAAACCAAACCCAT 60.134 47.619 0.00 0.00 0.00 4.00
420 448 2.844946 CCAAACCAAACCAAACCCATC 58.155 47.619 0.00 0.00 0.00 3.51
461 489 1.595093 CCACAGAAAATCCACCCCGC 61.595 60.000 0.00 0.00 0.00 6.13
462 490 1.674322 ACAGAAAATCCACCCCGCG 60.674 57.895 0.00 0.00 0.00 6.46
463 491 2.750237 AGAAAATCCACCCCGCGC 60.750 61.111 0.00 0.00 0.00 6.86
464 492 3.822192 GAAAATCCACCCCGCGCC 61.822 66.667 0.00 0.00 0.00 6.53
491 519 1.204062 CAAAGCGCAGTGTACACCG 59.796 57.895 22.28 19.39 0.00 4.94
983 1011 0.526211 GCGAAACACCCCAGAAATCC 59.474 55.000 0.00 0.00 0.00 3.01
985 1013 1.546773 CGAAACACCCCAGAAATCCCA 60.547 52.381 0.00 0.00 0.00 4.37
986 1014 1.893137 GAAACACCCCAGAAATCCCAC 59.107 52.381 0.00 0.00 0.00 4.61
987 1015 0.114364 AACACCCCAGAAATCCCACC 59.886 55.000 0.00 0.00 0.00 4.61
988 1016 1.000359 CACCCCAGAAATCCCACCC 60.000 63.158 0.00 0.00 0.00 4.61
989 1017 2.275418 CCCCAGAAATCCCACCCG 59.725 66.667 0.00 0.00 0.00 5.28
990 1018 2.612493 CCCCAGAAATCCCACCCGT 61.612 63.158 0.00 0.00 0.00 5.28
991 1019 1.077716 CCCAGAAATCCCACCCGTC 60.078 63.158 0.00 0.00 0.00 4.79
992 1020 1.562672 CCCAGAAATCCCACCCGTCT 61.563 60.000 0.00 0.00 0.00 4.18
993 1021 0.107654 CCAGAAATCCCACCCGTCTC 60.108 60.000 0.00 0.00 0.00 3.36
994 1022 0.107654 CAGAAATCCCACCCGTCTCC 60.108 60.000 0.00 0.00 0.00 3.71
995 1023 0.546747 AGAAATCCCACCCGTCTCCA 60.547 55.000 0.00 0.00 0.00 3.86
996 1024 0.392595 GAAATCCCACCCGTCTCCAC 60.393 60.000 0.00 0.00 0.00 4.02
997 1025 1.848886 AAATCCCACCCGTCTCCACC 61.849 60.000 0.00 0.00 0.00 4.61
1002 1439 1.990060 CACCCGTCTCCACCCAGAT 60.990 63.158 0.00 0.00 0.00 2.90
1005 1442 0.464452 CCCGTCTCCACCCAGATAAC 59.536 60.000 0.00 0.00 0.00 1.89
1007 1444 1.191535 CGTCTCCACCCAGATAACCA 58.808 55.000 0.00 0.00 0.00 3.67
1072 1522 0.953960 AAGGTAAGCAAGAACGCCGG 60.954 55.000 0.00 0.00 0.00 6.13
1106 1563 3.905454 ACAGATCTGTGGTGGCCA 58.095 55.556 27.37 0.00 43.11 5.36
1109 1566 0.750546 CAGATCTGTGGTGGCCATGG 60.751 60.000 9.72 7.63 35.28 3.66
1122 1579 3.844911 CCATGGCGTGGTTACAGTA 57.155 52.632 17.89 0.00 43.44 2.74
1123 1580 1.365699 CCATGGCGTGGTTACAGTAC 58.634 55.000 17.89 0.00 43.44 2.73
1124 1581 1.365699 CATGGCGTGGTTACAGTACC 58.634 55.000 0.00 0.00 38.73 3.34
1125 1582 0.108520 ATGGCGTGGTTACAGTACCG 60.109 55.000 0.00 0.00 41.28 4.02
1126 1583 1.177895 TGGCGTGGTTACAGTACCGA 61.178 55.000 0.00 0.00 41.28 4.69
1127 1584 0.174162 GGCGTGGTTACAGTACCGAT 59.826 55.000 0.00 0.00 41.28 4.18
1128 1585 1.553308 GCGTGGTTACAGTACCGATC 58.447 55.000 0.00 0.00 41.28 3.69
1129 1586 1.818850 CGTGGTTACAGTACCGATCG 58.181 55.000 8.51 8.51 41.28 3.69
1131 1588 2.032550 CGTGGTTACAGTACCGATCGAT 59.967 50.000 18.66 0.00 41.28 3.59
1132 1589 3.248363 CGTGGTTACAGTACCGATCGATA 59.752 47.826 18.66 0.00 41.28 2.92
1496 1996 0.969409 AGCAGGTACGGTACACCTCC 60.969 60.000 19.14 1.82 44.81 4.30
1505 2005 1.590147 GTACACCTCCCACCGTCTG 59.410 63.158 0.00 0.00 0.00 3.51
1506 2006 1.154454 TACACCTCCCACCGTCTGT 59.846 57.895 0.00 0.00 0.00 3.41
1507 2007 0.896940 TACACCTCCCACCGTCTGTC 60.897 60.000 0.00 0.00 0.00 3.51
1508 2008 2.603776 ACCTCCCACCGTCTGTCC 60.604 66.667 0.00 0.00 0.00 4.02
1509 2009 2.603473 CCTCCCACCGTCTGTCCA 60.603 66.667 0.00 0.00 0.00 4.02
1510 2010 1.990060 CCTCCCACCGTCTGTCCAT 60.990 63.158 0.00 0.00 0.00 3.41
1511 2011 1.517832 CTCCCACCGTCTGTCCATC 59.482 63.158 0.00 0.00 0.00 3.51
1512 2012 0.972983 CTCCCACCGTCTGTCCATCT 60.973 60.000 0.00 0.00 0.00 2.90
1527 2027 1.112315 CATCTCCTCCTCCTCACCGG 61.112 65.000 0.00 0.00 0.00 5.28
1528 2028 2.305314 ATCTCCTCCTCCTCACCGGG 62.305 65.000 6.32 0.00 0.00 5.73
1548 2048 1.068194 GGCAGAGGTAGTATAGCAGCG 60.068 57.143 0.00 0.00 42.67 5.18
1551 2051 0.244178 GAGGTAGTATAGCAGCGGCC 59.756 60.000 4.82 0.00 42.67 6.13
1771 2271 1.480219 CCGCGCTAGAAGCTAAACGG 61.480 60.000 5.56 1.96 39.60 4.44
1773 2273 1.763200 GCGCTAGAAGCTAAACGGGC 61.763 60.000 0.00 0.00 39.60 6.13
1774 2274 1.152383 CGCTAGAAGCTAAACGGGCC 61.152 60.000 0.00 0.00 39.60 5.80
1775 2275 1.152383 GCTAGAAGCTAAACGGGCCG 61.152 60.000 27.06 27.06 38.45 6.13
1776 2276 0.529992 CTAGAAGCTAAACGGGCCGG 60.530 60.000 31.78 13.56 0.00 6.13
1777 2277 2.582734 TAGAAGCTAAACGGGCCGGC 62.583 60.000 31.78 21.18 0.00 6.13
1943 2455 2.359967 CCTTCCCTCCTCCCGTGTC 61.360 68.421 0.00 0.00 0.00 3.67
1968 2480 3.751479 AATGGGTCAAGAACAAAAGCC 57.249 42.857 0.00 0.00 0.00 4.35
2021 2537 1.338674 TGGTAATCAGGTCCAACGCTG 60.339 52.381 0.00 0.00 0.00 5.18
2053 2697 2.883386 CAAGTGCTTCTCTCTTTTGGCT 59.117 45.455 0.00 0.00 0.00 4.75
2136 2780 6.129179 CCATGAAGGGCTTAAAATAGAAGGA 58.871 40.000 0.00 0.00 0.00 3.36
2143 2787 6.849164 AGGGCTTAAAATAGAAGGAGAGAGAT 59.151 38.462 0.00 0.00 0.00 2.75
2144 2788 7.016170 AGGGCTTAAAATAGAAGGAGAGAGATC 59.984 40.741 0.00 0.00 0.00 2.75
2145 2789 7.202047 GGGCTTAAAATAGAAGGAGAGAGATCA 60.202 40.741 0.00 0.00 0.00 2.92
2146 2790 7.655732 GGCTTAAAATAGAAGGAGAGAGATCAC 59.344 40.741 0.00 0.00 0.00 3.06
2148 2792 9.748708 CTTAAAATAGAAGGAGAGAGATCACTG 57.251 37.037 0.00 0.00 0.00 3.66
2149 2793 7.732222 AAAATAGAAGGAGAGAGATCACTGT 57.268 36.000 0.00 0.00 0.00 3.55
2156 2806 5.271598 AGGAGAGAGATCACTGTCTGATTT 58.728 41.667 15.22 0.00 44.90 2.17
2159 2809 6.357579 AGAGAGATCACTGTCTGATTTTGT 57.642 37.500 0.00 0.00 43.58 2.83
2163 2813 6.594547 AGAGATCACTGTCTGATTTTGTCATG 59.405 38.462 0.00 0.00 39.96 3.07
2164 2814 5.646793 AGATCACTGTCTGATTTTGTCATGG 59.353 40.000 0.00 0.00 39.96 3.66
2173 2823 6.036953 GTCTGATTTTGTCATGGAGAGCTTAG 59.963 42.308 0.00 0.00 35.97 2.18
2253 2904 5.964958 TCAAGAGCTTAAATTGGAAGTGG 57.035 39.130 0.00 0.00 0.00 4.00
2283 2936 0.962489 AAGGTATCCGGCAGAGATCG 59.038 55.000 0.00 0.00 0.00 3.69
2318 2986 4.475944 CGCATAAGAGGAAAACACCTTTG 58.524 43.478 0.00 0.00 40.73 2.77
2334 3002 4.074970 ACCTTTGTTGAGCAAGATACCTG 58.925 43.478 0.00 0.00 38.47 4.00
2355 3023 4.084287 TGTGTACAACAGGTAGTAGAGGG 58.916 47.826 0.00 0.00 33.78 4.30
2380 3048 6.346359 GCAAACAAGAAGCTGCTTTTAGATTG 60.346 38.462 17.10 17.99 0.00 2.67
2391 3059 6.128688 GCTGCTTTTAGATTGATCTCCGATAC 60.129 42.308 0.00 0.00 38.32 2.24
2419 3089 4.978580 GCCTTGTTTGTTTCAGCTTTAGAG 59.021 41.667 0.00 0.00 0.00 2.43
2420 3090 5.221048 GCCTTGTTTGTTTCAGCTTTAGAGA 60.221 40.000 0.00 0.00 0.00 3.10
2421 3091 6.433766 CCTTGTTTGTTTCAGCTTTAGAGAG 58.566 40.000 0.00 0.00 0.00 3.20
2465 3184 1.409064 TCTGGATTCGGACCATTCTCG 59.591 52.381 0.00 0.00 36.79 4.04
2478 3197 0.813184 ATTCTCGGTGCAATTGCCTG 59.187 50.000 26.94 21.25 41.18 4.85
2503 3222 5.133221 AGCATGTCCAAGTTTACTTCAGTT 58.867 37.500 0.00 0.00 33.11 3.16
2558 3277 1.683385 GAAGCTGAAACAAACAGGGCT 59.317 47.619 0.00 0.00 36.09 5.19
2570 3295 1.523258 CAGGGCTCTGCATTCTCCG 60.523 63.158 0.00 0.00 33.86 4.63
2580 3305 0.529555 GCATTCTCCGTGCCTCTCTC 60.530 60.000 0.00 0.00 36.61 3.20
2582 3307 1.066908 CATTCTCCGTGCCTCTCTCTC 59.933 57.143 0.00 0.00 0.00 3.20
2586 3312 0.678366 TCCGTGCCTCTCTCTCTGAC 60.678 60.000 0.00 0.00 0.00 3.51
2603 3330 1.071605 GACTGAGCGGTTCATCACAC 58.928 55.000 0.00 0.00 34.68 3.82
2610 3337 1.715585 GGTTCATCACACGCATCGG 59.284 57.895 0.00 0.00 0.00 4.18
2612 3339 1.075542 GTTCATCACACGCATCGGAA 58.924 50.000 0.00 0.00 0.00 4.30
2630 3357 3.181497 CGGAACTTGGAAATACAGGCATG 60.181 47.826 0.00 0.00 0.00 4.06
2646 3373 2.225963 GGCATGCTACTTGATCATCTGC 59.774 50.000 18.92 0.00 0.00 4.26
2668 3419 3.563479 CCACCATTAGGCCTTGTAAACCT 60.563 47.826 12.58 0.00 39.06 3.50
2705 3456 5.648092 ACCAGTGCCTAATTTTACATGAGAC 59.352 40.000 0.00 0.00 0.00 3.36
2706 3457 5.220662 CCAGTGCCTAATTTTACATGAGACG 60.221 44.000 0.00 0.00 0.00 4.18
2707 3458 5.351465 CAGTGCCTAATTTTACATGAGACGT 59.649 40.000 0.00 0.00 0.00 4.34
2708 3459 5.581085 AGTGCCTAATTTTACATGAGACGTC 59.419 40.000 7.70 7.70 0.00 4.34
2709 3460 5.581085 GTGCCTAATTTTACATGAGACGTCT 59.419 40.000 20.18 20.18 0.00 4.18
2710 3461 6.755141 GTGCCTAATTTTACATGAGACGTCTA 59.245 38.462 20.09 7.62 0.00 2.59
2711 3462 7.277098 GTGCCTAATTTTACATGAGACGTCTAA 59.723 37.037 20.09 12.58 0.00 2.10
2712 3463 7.985184 TGCCTAATTTTACATGAGACGTCTAAT 59.015 33.333 20.09 14.74 0.00 1.73
2713 3464 8.827677 GCCTAATTTTACATGAGACGTCTAATT 58.172 33.333 20.09 19.31 0.00 1.40
2719 3470 9.577110 TTTTACATGAGACGTCTAATTAATCGT 57.423 29.630 20.09 12.54 39.21 3.73
2726 3477 6.311055 GACGTCTAATTAATCGTCTACCCT 57.689 41.667 23.06 2.27 45.69 4.34
2727 3478 7.426929 GACGTCTAATTAATCGTCTACCCTA 57.573 40.000 23.06 0.00 45.69 3.53
2728 3479 7.992754 ACGTCTAATTAATCGTCTACCCTAT 57.007 36.000 8.23 0.00 30.71 2.57
2729 3480 7.814642 ACGTCTAATTAATCGTCTACCCTATG 58.185 38.462 8.23 0.00 30.71 2.23
2758 3509 1.002468 CACCGGTGCTCAAAGAAACAG 60.002 52.381 24.02 0.00 0.00 3.16
2781 3534 7.553044 ACAGTGGTTTATTTATCTAAGCACCTC 59.447 37.037 11.39 0.00 46.11 3.85
2783 3536 6.018180 GTGGTTTATTTATCTAAGCACCTCCG 60.018 42.308 0.00 0.00 41.77 4.63
2786 3539 2.890808 TTATCTAAGCACCTCCGCTG 57.109 50.000 0.00 0.00 42.89 5.18
2806 3559 2.556189 TGAACGCCTTGCATTGTACAAT 59.444 40.909 15.47 15.47 0.00 2.71
2821 3574 7.335055 CATTGTACAATGCCTTGGCTTACAAG 61.335 42.308 30.13 6.38 45.29 3.16
2941 3699 4.866508 TCAACTGTCAGGTAGTACCAAG 57.133 45.455 21.49 13.04 41.95 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153647 AAATGCGTCGCGATCCAGA 60.154 52.632 14.06 0.00 0.00 3.86
1 2 1.011904 CAAATGCGTCGCGATCCAG 60.012 57.895 14.06 5.75 0.00 3.86
34 35 0.659427 TAGTCACGTTAGATCGGGCG 59.341 55.000 0.00 4.74 33.94 6.13
36 37 4.563337 TGAATAGTCACGTTAGATCGGG 57.437 45.455 0.00 0.00 35.37 5.14
37 38 5.154932 GGATGAATAGTCACGTTAGATCGG 58.845 45.833 0.00 0.00 36.31 4.18
46 52 2.579207 ACCACGGATGAATAGTCACG 57.421 50.000 0.00 0.00 36.31 4.35
103 119 9.964303 TCGTACGTATGCTTTAAAATAAGGATA 57.036 29.630 16.05 0.00 37.39 2.59
104 120 8.876275 TCGTACGTATGCTTTAAAATAAGGAT 57.124 30.769 16.05 0.00 39.22 3.24
107 123 8.441313 CGTTCGTACGTATGCTTTAAAATAAG 57.559 34.615 16.05 0.00 42.72 1.73
128 151 2.934107 TTGTGTATGTGCGTTCGTTC 57.066 45.000 0.00 0.00 0.00 3.95
129 152 4.211584 TGTTATTGTGTATGTGCGTTCGTT 59.788 37.500 0.00 0.00 0.00 3.85
132 155 5.567534 CCTTTGTTATTGTGTATGTGCGTTC 59.432 40.000 0.00 0.00 0.00 3.95
133 156 5.009210 ACCTTTGTTATTGTGTATGTGCGTT 59.991 36.000 0.00 0.00 0.00 4.84
134 157 4.517453 ACCTTTGTTATTGTGTATGTGCGT 59.483 37.500 0.00 0.00 0.00 5.24
135 158 5.041951 ACCTTTGTTATTGTGTATGTGCG 57.958 39.130 0.00 0.00 0.00 5.34
136 159 5.086058 CGACCTTTGTTATTGTGTATGTGC 58.914 41.667 0.00 0.00 0.00 4.57
137 160 6.077197 CACGACCTTTGTTATTGTGTATGTG 58.923 40.000 0.00 0.00 0.00 3.21
145 173 4.406069 CATGAGCACGACCTTTGTTATTG 58.594 43.478 0.00 0.00 0.00 1.90
197 225 2.434884 AACGCATGCAGACGAGGG 60.435 61.111 19.57 0.50 0.00 4.30
212 240 1.875963 CCCACCGCTTGATGTGAAC 59.124 57.895 0.00 0.00 34.37 3.18
250 278 5.121611 CCTTTTGGAAATTTAATCGGGCAAC 59.878 40.000 0.00 0.00 44.07 4.17
253 281 4.827692 ACCTTTTGGAAATTTAATCGGGC 58.172 39.130 0.00 0.00 44.07 6.13
254 282 5.121611 GCAACCTTTTGGAAATTTAATCGGG 59.878 40.000 0.00 0.00 44.07 5.14
255 283 5.164002 CGCAACCTTTTGGAAATTTAATCGG 60.164 40.000 0.00 0.00 44.07 4.18
262 290 3.066380 GCATCGCAACCTTTTGGAAATT 58.934 40.909 0.00 0.00 44.07 1.82
263 291 2.687370 GCATCGCAACCTTTTGGAAAT 58.313 42.857 0.00 0.00 44.07 2.17
300 328 1.469126 CTGTCGGTCGTAATTCGCGG 61.469 60.000 6.13 0.00 39.67 6.46
336 364 3.835790 TTGGTTTGGGGCCGAGTCG 62.836 63.158 5.29 5.29 0.00 4.18
404 432 1.047801 GCTGATGGGTTTGGTTTGGT 58.952 50.000 0.00 0.00 0.00 3.67
412 440 1.675641 GTGGAGCGCTGATGGGTTT 60.676 57.895 18.48 0.00 0.00 3.27
414 442 4.101448 GGTGGAGCGCTGATGGGT 62.101 66.667 18.48 0.00 0.00 4.51
501 529 2.003548 GCCAATGGGGAGGAGACCT 61.004 63.158 0.00 0.00 40.01 3.85
983 1011 3.706373 CTGGGTGGAGACGGGTGG 61.706 72.222 0.00 0.00 0.00 4.61
985 1013 0.042131 TTATCTGGGTGGAGACGGGT 59.958 55.000 0.00 0.00 0.00 5.28
986 1014 0.464452 GTTATCTGGGTGGAGACGGG 59.536 60.000 0.00 0.00 0.00 5.28
987 1015 0.464452 GGTTATCTGGGTGGAGACGG 59.536 60.000 0.00 0.00 0.00 4.79
988 1016 1.134788 GTGGTTATCTGGGTGGAGACG 60.135 57.143 0.00 0.00 0.00 4.18
989 1017 1.134788 CGTGGTTATCTGGGTGGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
990 1018 1.191535 CGTGGTTATCTGGGTGGAGA 58.808 55.000 0.00 0.00 0.00 3.71
991 1019 1.137086 CTCGTGGTTATCTGGGTGGAG 59.863 57.143 0.00 0.00 0.00 3.86
992 1020 1.191535 CTCGTGGTTATCTGGGTGGA 58.808 55.000 0.00 0.00 0.00 4.02
993 1021 1.137086 CTCTCGTGGTTATCTGGGTGG 59.863 57.143 0.00 0.00 0.00 4.61
994 1022 2.100197 TCTCTCGTGGTTATCTGGGTG 58.900 52.381 0.00 0.00 0.00 4.61
995 1023 2.526888 TCTCTCGTGGTTATCTGGGT 57.473 50.000 0.00 0.00 0.00 4.51
996 1024 5.730296 AATATCTCTCGTGGTTATCTGGG 57.270 43.478 0.00 0.00 0.00 4.45
997 1025 5.859114 CGAAATATCTCTCGTGGTTATCTGG 59.141 44.000 0.00 0.00 0.00 3.86
998 1026 6.439599 ACGAAATATCTCTCGTGGTTATCTG 58.560 40.000 6.65 0.00 46.01 2.90
999 1027 6.636562 ACGAAATATCTCTCGTGGTTATCT 57.363 37.500 6.65 0.00 46.01 1.98
1044 1492 3.412386 TCTTGCTTACCTTTTCTCTGCC 58.588 45.455 0.00 0.00 0.00 4.85
1072 1522 3.517140 TGCATCGCGGCCAATTCC 61.517 61.111 6.13 0.00 0.00 3.01
1106 1563 0.108520 CGGTACTGTAACCACGCCAT 60.109 55.000 0.00 0.00 39.71 4.40
1109 1566 1.553308 GATCGGTACTGTAACCACGC 58.447 55.000 0.64 0.00 39.71 5.34
1117 1574 6.125327 GATCATCATATCGATCGGTACTGT 57.875 41.667 16.41 0.00 29.21 3.55
1128 1585 4.102035 TCAGCTTCCGATCATCATATCG 57.898 45.455 0.00 0.00 46.51 2.92
1129 1586 5.293814 CCAATCAGCTTCCGATCATCATATC 59.706 44.000 0.00 0.00 0.00 1.63
1131 1588 4.040829 ACCAATCAGCTTCCGATCATCATA 59.959 41.667 0.00 0.00 0.00 2.15
1132 1589 3.181447 ACCAATCAGCTTCCGATCATCAT 60.181 43.478 0.00 0.00 0.00 2.45
1161 1639 1.202348 TGATCACCTCACTACACGCAG 59.798 52.381 0.00 0.00 0.00 5.18
1496 1996 0.972983 AGGAGATGGACAGACGGTGG 60.973 60.000 0.00 0.00 0.00 4.61
1505 2005 1.408969 GTGAGGAGGAGGAGATGGAC 58.591 60.000 0.00 0.00 0.00 4.02
1506 2006 0.263172 GGTGAGGAGGAGGAGATGGA 59.737 60.000 0.00 0.00 0.00 3.41
1507 2007 1.112315 CGGTGAGGAGGAGGAGATGG 61.112 65.000 0.00 0.00 0.00 3.51
1508 2008 1.112315 CCGGTGAGGAGGAGGAGATG 61.112 65.000 0.00 0.00 45.00 2.90
1509 2009 1.231641 CCGGTGAGGAGGAGGAGAT 59.768 63.158 0.00 0.00 45.00 2.75
1510 2010 2.684104 CCGGTGAGGAGGAGGAGA 59.316 66.667 0.00 0.00 45.00 3.71
1511 2011 2.443016 CCCGGTGAGGAGGAGGAG 60.443 72.222 0.00 0.00 45.00 3.69
1512 2012 4.075793 CCCCGGTGAGGAGGAGGA 62.076 72.222 0.00 0.00 45.00 3.71
1527 2027 1.273886 GCTGCTATACTACCTCTGCCC 59.726 57.143 0.00 0.00 0.00 5.36
1528 2028 1.068194 CGCTGCTATACTACCTCTGCC 60.068 57.143 0.00 0.00 0.00 4.85
1559 2059 1.129437 GAGCGATCAAGTTTGCTGGTC 59.871 52.381 0.00 0.00 37.91 4.02
1563 2063 2.462456 TCAGAGCGATCAAGTTTGCT 57.538 45.000 2.38 0.00 41.11 3.91
1565 2065 4.322804 GCAAATTCAGAGCGATCAAGTTTG 59.677 41.667 15.07 15.07 0.00 2.93
1566 2066 4.022935 TGCAAATTCAGAGCGATCAAGTTT 60.023 37.500 2.38 0.00 0.00 2.66
1567 2067 3.503363 TGCAAATTCAGAGCGATCAAGTT 59.497 39.130 2.38 0.00 0.00 2.66
1568 2068 3.076621 TGCAAATTCAGAGCGATCAAGT 58.923 40.909 2.38 0.00 0.00 3.16
1569 2069 3.487042 CCTGCAAATTCAGAGCGATCAAG 60.487 47.826 2.38 0.00 36.19 3.02
1570 2070 2.421073 CCTGCAAATTCAGAGCGATCAA 59.579 45.455 2.38 0.00 36.19 2.57
1571 2071 2.011947 CCTGCAAATTCAGAGCGATCA 58.988 47.619 2.38 0.00 36.19 2.92
1943 2455 4.935352 TTTGTTCTTGACCCATTTCTGG 57.065 40.909 0.00 0.00 42.73 3.86
2021 2537 3.481453 AGAAGCACTTGAGAAAAGGTCC 58.519 45.455 0.00 0.00 0.00 4.46
2074 2718 5.477637 TGAAGAATCATGCACAAAATCAGGA 59.522 36.000 0.00 0.00 0.00 3.86
2136 2780 6.014755 TGACAAAATCAGACAGTGATCTCTCT 60.015 38.462 0.00 0.00 45.89 3.10
2143 2787 4.971939 TCCATGACAAAATCAGACAGTGA 58.028 39.130 0.00 0.00 41.91 3.41
2144 2788 4.999311 TCTCCATGACAAAATCAGACAGTG 59.001 41.667 0.00 0.00 41.91 3.66
2145 2789 5.233083 TCTCCATGACAAAATCAGACAGT 57.767 39.130 0.00 0.00 41.91 3.55
2146 2790 4.094590 GCTCTCCATGACAAAATCAGACAG 59.905 45.833 0.00 0.00 41.91 3.51
2148 2792 4.260170 AGCTCTCCATGACAAAATCAGAC 58.740 43.478 0.00 0.00 41.91 3.51
2149 2793 4.564782 AGCTCTCCATGACAAAATCAGA 57.435 40.909 0.00 0.00 41.91 3.27
2156 2806 3.538591 CATGCTAAGCTCTCCATGACAA 58.461 45.455 12.52 0.00 37.78 3.18
2159 2809 2.401568 TCCATGCTAAGCTCTCCATGA 58.598 47.619 17.18 5.70 37.78 3.07
2163 2813 2.169352 TCACTTCCATGCTAAGCTCTCC 59.831 50.000 6.07 0.00 0.00 3.71
2164 2814 3.533606 TCACTTCCATGCTAAGCTCTC 57.466 47.619 6.07 0.00 0.00 3.20
2173 2823 5.450137 CCTTCTTGATCAATCACTTCCATGC 60.450 44.000 8.96 0.00 36.36 4.06
2217 2867 1.672881 CTCTTGATGGCAAATCGGACC 59.327 52.381 0.00 0.00 32.73 4.46
2253 2904 3.748568 GCCGGATACCTTCTTGATCAATC 59.251 47.826 5.05 1.44 0.00 2.67
2283 2936 0.179100 TTATGCGCAGAGGACAGAGC 60.179 55.000 18.32 0.00 0.00 4.09
2318 2986 4.566004 TGTACACAGGTATCTTGCTCAAC 58.434 43.478 0.00 0.00 0.00 3.18
2334 3002 3.119209 GCCCTCTACTACCTGTTGTACAC 60.119 52.174 0.00 0.00 0.00 2.90
2355 3023 4.610945 TCTAAAAGCAGCTTCTTGTTTGC 58.389 39.130 8.48 0.00 36.83 3.68
2380 3048 1.917872 AGGCCTCTGTATCGGAGATC 58.082 55.000 0.00 0.00 45.12 2.75
2391 3059 2.544486 GCTGAAACAAACAAGGCCTCTG 60.544 50.000 5.23 9.66 0.00 3.35
2448 3167 0.464452 ACCGAGAATGGTCCGAATCC 59.536 55.000 0.00 0.00 37.91 3.01
2465 3184 4.584688 GCTTCAGGCAATTGCACC 57.415 55.556 30.32 15.06 44.36 5.01
2478 3197 5.239525 ACTGAAGTAAACTTGGACATGCTTC 59.760 40.000 0.00 0.00 36.11 3.86
2514 3233 1.955778 TGGCTTCAAATCATATGCGGG 59.044 47.619 0.00 0.00 0.00 6.13
2517 3236 6.292703 GCTTCAATTGGCTTCAAATCATATGC 60.293 38.462 5.42 0.00 33.67 3.14
2527 3246 3.384146 TGTTTCAGCTTCAATTGGCTTCA 59.616 39.130 5.42 2.09 36.59 3.02
2558 3277 1.219124 GAGGCACGGAGAATGCAGA 59.781 57.895 0.00 0.00 45.27 4.26
2570 3295 1.832883 TCAGTCAGAGAGAGAGGCAC 58.167 55.000 0.00 0.00 0.00 5.01
2582 3307 1.337167 TGTGATGAACCGCTCAGTCAG 60.337 52.381 0.00 0.00 37.52 3.51
2586 3312 1.959899 GCGTGTGATGAACCGCTCAG 61.960 60.000 0.00 0.00 41.98 3.35
2603 3330 2.675844 TGTATTTCCAAGTTCCGATGCG 59.324 45.455 0.00 0.00 0.00 4.73
2608 3335 2.432444 TGCCTGTATTTCCAAGTTCCG 58.568 47.619 0.00 0.00 0.00 4.30
2610 3337 3.445096 AGCATGCCTGTATTTCCAAGTTC 59.555 43.478 15.66 0.00 0.00 3.01
2612 3339 3.091633 AGCATGCCTGTATTTCCAAGT 57.908 42.857 15.66 0.00 0.00 3.16
2630 3357 2.216898 GGTGGCAGATGATCAAGTAGC 58.783 52.381 0.00 1.71 0.00 3.58
2646 3373 2.758423 GGTTTACAAGGCCTAATGGTGG 59.242 50.000 5.16 0.00 35.27 4.61
2668 3419 1.110442 CACTGGTGCCAGAAAAACCA 58.890 50.000 23.55 0.00 46.30 3.67
2705 3456 6.746364 GCATAGGGTAGACGATTAATTAGACG 59.254 42.308 10.35 10.35 0.00 4.18
2706 3457 7.600065 TGCATAGGGTAGACGATTAATTAGAC 58.400 38.462 0.00 0.00 0.00 2.59
2707 3458 7.770366 TGCATAGGGTAGACGATTAATTAGA 57.230 36.000 0.00 0.00 0.00 2.10
2708 3459 8.827177 TTTGCATAGGGTAGACGATTAATTAG 57.173 34.615 0.00 0.00 0.00 1.73
2710 3461 9.787435 TTATTTGCATAGGGTAGACGATTAATT 57.213 29.630 0.00 0.00 0.00 1.40
2711 3462 9.436957 CTTATTTGCATAGGGTAGACGATTAAT 57.563 33.333 0.00 0.00 0.00 1.40
2712 3463 7.386848 GCTTATTTGCATAGGGTAGACGATTAA 59.613 37.037 0.00 0.00 0.00 1.40
2713 3464 6.872020 GCTTATTTGCATAGGGTAGACGATTA 59.128 38.462 0.00 0.00 0.00 1.75
2714 3465 5.701290 GCTTATTTGCATAGGGTAGACGATT 59.299 40.000 0.00 0.00 0.00 3.34
2715 3466 5.221641 TGCTTATTTGCATAGGGTAGACGAT 60.222 40.000 0.00 0.00 38.12 3.73
2716 3467 4.100344 TGCTTATTTGCATAGGGTAGACGA 59.900 41.667 0.00 0.00 38.12 4.20
2717 3468 4.211374 GTGCTTATTTGCATAGGGTAGACG 59.789 45.833 0.00 0.00 45.23 4.18
2718 3469 4.515567 GGTGCTTATTTGCATAGGGTAGAC 59.484 45.833 0.00 0.00 45.23 2.59
2719 3470 4.714632 GGTGCTTATTTGCATAGGGTAGA 58.285 43.478 0.00 0.00 45.23 2.59
2720 3471 3.498397 CGGTGCTTATTTGCATAGGGTAG 59.502 47.826 0.00 0.00 45.23 3.18
2721 3472 3.472652 CGGTGCTTATTTGCATAGGGTA 58.527 45.455 0.00 0.00 45.23 3.69
2722 3473 2.297701 CGGTGCTTATTTGCATAGGGT 58.702 47.619 0.00 0.00 45.23 4.34
2723 3474 1.608590 CCGGTGCTTATTTGCATAGGG 59.391 52.381 0.00 0.00 45.23 3.53
2724 3475 2.033299 CACCGGTGCTTATTTGCATAGG 59.967 50.000 24.02 10.11 45.23 2.57
2725 3476 3.338818 CACCGGTGCTTATTTGCATAG 57.661 47.619 24.02 0.00 45.23 2.23
2752 3503 9.556030 GTGCTTAGATAAATAAACCACTGTTTC 57.444 33.333 0.00 0.00 43.50 2.78
2758 3509 6.018180 CGGAGGTGCTTAGATAAATAAACCAC 60.018 42.308 0.00 0.00 0.00 4.16
2786 3539 2.697431 TTGTACAATGCAAGGCGTTC 57.303 45.000 3.59 0.00 35.42 3.95
2812 3565 3.440173 TGCAGCATCTTAACTTGTAAGCC 59.560 43.478 0.00 0.00 0.00 4.35
2958 3716 0.740868 TATCCACTTGCGCTGTGCTC 60.741 55.000 22.35 0.00 46.63 4.26


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

AutoCloner maintained by Alex Coulton.