Multiple sequence alignment - TraesCS2A01G195900

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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 TraesCS2A01G195900 chr2A 100.000 4824 0 0 1 4824 165851719 165846896 0.000000e+00 8909.0
1 TraesCS2A01G195900 chr2D 94.702 4851 164 34 1 4824 155737848 155733064 0.000000e+00 7448.0
2 TraesCS2A01G195900 chr2D 92.982 57 3 1 4084 4139 536535707 536535763 1.110000e-11 82.4
3 TraesCS2A01G195900 chr2B 94.036 4460 156 42 4 4406 213256888 213252482 0.000000e+00 6661.0
4 TraesCS2A01G195900 chr2B 91.743 436 15 10 4410 4824 213252373 213251938 1.930000e-163 586.0
5 TraesCS2A01G195900 chr5D 83.007 153 22 4 1797 1947 231746332 231746482 8.420000e-28 135.0
6 TraesCS2A01G195900 chr5A 83.007 153 22 4 1797 1947 325373840 325373690 8.420000e-28 135.0
7 TraesCS2A01G195900 chr5B 82.353 153 23 4 1797 1947 273719013 273718863 3.920000e-26 130.0
8 TraesCS2A01G195900 chr3A 93.103 58 3 1 4083 4139 477142899 477142956 3.090000e-12 84.2


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 TraesCS2A01G195900 chr2A 165846896 165851719 4823 True 8909.0 8909 100.0000 1 4824 1 chr2A.!!$R1 4823
1 TraesCS2A01G195900 chr2D 155733064 155737848 4784 True 7448.0 7448 94.7020 1 4824 1 chr2D.!!$R1 4823
2 TraesCS2A01G195900 chr2B 213251938 213256888 4950 True 3623.5 6661 92.8895 4 4824 2 chr2B.!!$R1 4820

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
442 444 0.036858 AGAAGAAGAAGAGGCGCCAC 60.037 55.0 31.54 24.27 0.0 5.01 F
1606 1648 0.254178 AAGCCGCACCAATCTCATCT 59.746 50.0 0.00 0.00 0.0 2.90 F
2494 2551 0.032130 GCATTGATGGCATGGCTCTG 59.968 55.0 21.08 10.94 0.0 3.35 F
3100 3157 0.250295 ACTGTGGGTCCAATGTGTCG 60.250 55.0 0.00 0.00 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2080 0.251916 AGAACCATCGCCATTTCGGA 59.748 50.0 0.0 0.0 36.56 4.55 R
3529 3592 0.679505 TGCTCAGTGTAGGCTTCGTT 59.320 50.0 0.0 0.0 0.00 3.85 R
3766 3829 0.105246 TTGGGAGGTTTGGTGGCAAT 60.105 50.0 0.0 0.0 0.00 3.56 R
3966 4029 0.323629 TTTCAGTCCCAAGCCTACCG 59.676 55.0 0.0 0.0 0.00 4.02 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
100 101 4.037222 AGGACAAGAAAACAAAACCCCAT 58.963 39.130 0.00 0.00 0.00 4.00
119 120 5.358922 CCCATTAAATTTACCACTGCCATG 58.641 41.667 0.00 0.00 0.00 3.66
132 133 1.197721 CTGCCATGTTCTTGTTCGGTC 59.802 52.381 0.00 0.00 0.00 4.79
157 158 1.146263 AAGATCGCCCATTCGTCCC 59.854 57.895 0.00 0.00 0.00 4.46
177 178 2.289565 CTTTTAATCAGCCGTCCCCTC 58.710 52.381 0.00 0.00 0.00 4.30
184 185 4.828296 GCCGTCCCCTCTCCGGTA 62.828 72.222 0.00 0.00 43.56 4.02
259 261 2.146061 CCCCTGAGCCTCTCCATCC 61.146 68.421 0.00 0.00 0.00 3.51
264 266 2.607499 CTGAGCCTCTCCATCCATACT 58.393 52.381 0.00 0.00 0.00 2.12
356 358 1.546029 GAAAATCGGGCTGCCTTTTCT 59.454 47.619 25.43 12.90 35.65 2.52
429 431 7.374975 TCCAGTTCCTTTTAGAGAAGAAGAA 57.625 36.000 0.00 0.00 0.00 2.52
432 434 7.934120 CCAGTTCCTTTTAGAGAAGAAGAAGAA 59.066 37.037 0.00 0.00 0.00 2.52
433 435 8.987890 CAGTTCCTTTTAGAGAAGAAGAAGAAG 58.012 37.037 0.00 0.00 0.00 2.85
434 436 8.929487 AGTTCCTTTTAGAGAAGAAGAAGAAGA 58.071 33.333 0.00 0.00 0.00 2.87
435 437 9.203421 GTTCCTTTTAGAGAAGAAGAAGAAGAG 57.797 37.037 0.00 0.00 0.00 2.85
436 438 7.902087 TCCTTTTAGAGAAGAAGAAGAAGAGG 58.098 38.462 0.00 0.00 0.00 3.69
437 439 6.593770 CCTTTTAGAGAAGAAGAAGAAGAGGC 59.406 42.308 0.00 0.00 0.00 4.70
438 440 3.866883 AGAGAAGAAGAAGAAGAGGCG 57.133 47.619 0.00 0.00 0.00 5.52
440 442 1.066502 AGAAGAAGAAGAAGAGGCGCC 60.067 52.381 21.89 21.89 0.00 6.53
441 443 0.687354 AAGAAGAAGAAGAGGCGCCA 59.313 50.000 31.54 0.00 0.00 5.69
442 444 0.036858 AGAAGAAGAAGAGGCGCCAC 60.037 55.000 31.54 24.27 0.00 5.01
443 445 1.355066 GAAGAAGAAGAGGCGCCACG 61.355 60.000 31.54 0.00 0.00 4.94
458 460 2.281070 ACGCATGATGATCCCGGC 60.281 61.111 0.00 0.00 0.00 6.13
462 464 1.303074 CATGATGATCCCGGCCTGG 60.303 63.158 6.92 6.92 37.55 4.45
484 486 7.254227 TGGTTTATCTACACCGAATAATTGC 57.746 36.000 0.00 0.00 35.60 3.56
508 510 6.697892 GCGGATTAGAGTAGTATATTGGCATC 59.302 42.308 0.00 0.00 0.00 3.91
558 560 0.876342 GAATTGTAGCCTCGCCCGAG 60.876 60.000 10.56 10.56 41.63 4.63
565 567 3.905678 CCTCGCCCGAGTAGCCAG 61.906 72.222 15.59 0.00 40.44 4.85
594 596 1.062886 TCTAGGATCCTGTCACCCCTG 60.063 57.143 25.28 3.37 0.00 4.45
648 652 1.268625 GTGGGGTTAAAAACAGCGAGG 59.731 52.381 0.00 0.00 0.00 4.63
665 669 2.799917 CGAGGTTATCTCTGGCTTTCCG 60.800 54.545 0.00 0.00 40.30 4.30
676 680 4.843728 TCTGGCTTTCCGTTGATCTAATT 58.156 39.130 0.00 0.00 34.14 1.40
677 681 4.876107 TCTGGCTTTCCGTTGATCTAATTC 59.124 41.667 0.00 0.00 34.14 2.17
678 682 4.843728 TGGCTTTCCGTTGATCTAATTCT 58.156 39.130 0.00 0.00 34.14 2.40
679 683 5.984725 TGGCTTTCCGTTGATCTAATTCTA 58.015 37.500 0.00 0.00 34.14 2.10
680 684 6.411376 TGGCTTTCCGTTGATCTAATTCTAA 58.589 36.000 0.00 0.00 34.14 2.10
681 685 7.054124 TGGCTTTCCGTTGATCTAATTCTAAT 58.946 34.615 0.00 0.00 34.14 1.73
683 687 7.442666 GGCTTTCCGTTGATCTAATTCTAATCT 59.557 37.037 0.00 0.00 0.00 2.40
684 688 9.477484 GCTTTCCGTTGATCTAATTCTAATCTA 57.523 33.333 0.00 0.00 0.00 1.98
688 692 8.794553 TCCGTTGATCTAATTCTAATCTACTCC 58.205 37.037 0.00 0.00 0.00 3.85
689 693 8.577296 CCGTTGATCTAATTCTAATCTACTCCA 58.423 37.037 0.00 0.00 0.00 3.86
690 694 9.967346 CGTTGATCTAATTCTAATCTACTCCAA 57.033 33.333 0.00 0.00 0.00 3.53
709 713 7.498443 ACTCCAATCTATCTTAACTAAACCCG 58.502 38.462 0.00 0.00 0.00 5.28
718 722 4.465305 TCTTAACTAAACCCGAGCTTAGCT 59.535 41.667 6.37 6.37 43.88 3.32
786 790 1.337703 CTGCTTCCCATCTCTCTCTCG 59.662 57.143 0.00 0.00 0.00 4.04
910 926 3.151022 ACTCCTCCTAGCAGCGCC 61.151 66.667 2.29 0.00 0.00 6.53
977 1001 4.690719 TGCCGCACTGGTTACGGG 62.691 66.667 12.03 0.00 46.97 5.28
1122 1147 2.606449 CCCCACCACCAACAACCT 59.394 61.111 0.00 0.00 0.00 3.50
1125 1150 1.530655 CCACCACCAACAACCTCCC 60.531 63.158 0.00 0.00 0.00 4.30
1127 1152 1.699930 ACCACCAACAACCTCCCCT 60.700 57.895 0.00 0.00 0.00 4.79
1337 1379 4.724602 GCTGACTGCTGACGGCGA 62.725 66.667 16.62 0.00 45.43 5.54
1589 1631 2.125106 GCACCCTCCGCCAGTAAG 60.125 66.667 0.00 0.00 0.00 2.34
1591 1633 3.400054 ACCCTCCGCCAGTAAGCC 61.400 66.667 0.00 0.00 0.00 4.35
1592 1634 4.530857 CCCTCCGCCAGTAAGCCG 62.531 72.222 0.00 0.00 0.00 5.52
1594 1636 4.451150 CTCCGCCAGTAAGCCGCA 62.451 66.667 0.00 0.00 0.00 5.69
1595 1637 4.752879 TCCGCCAGTAAGCCGCAC 62.753 66.667 0.00 0.00 0.00 5.34
1598 1640 2.671619 GCCAGTAAGCCGCACCAA 60.672 61.111 0.00 0.00 0.00 3.67
1599 1641 2.046285 GCCAGTAAGCCGCACCAAT 61.046 57.895 0.00 0.00 0.00 3.16
1600 1642 1.993369 GCCAGTAAGCCGCACCAATC 61.993 60.000 0.00 0.00 0.00 2.67
1601 1643 0.392998 CCAGTAAGCCGCACCAATCT 60.393 55.000 0.00 0.00 0.00 2.40
1602 1644 1.009829 CAGTAAGCCGCACCAATCTC 58.990 55.000 0.00 0.00 0.00 2.75
1603 1645 0.613260 AGTAAGCCGCACCAATCTCA 59.387 50.000 0.00 0.00 0.00 3.27
1606 1648 0.254178 AAGCCGCACCAATCTCATCT 59.746 50.000 0.00 0.00 0.00 2.90
1634 1676 5.595952 AGCCCTCTTTAATGCTCAATAAAGG 59.404 40.000 14.12 7.67 38.85 3.11
1769 1825 0.321671 GGTACAGGCAGAAGCACAGA 59.678 55.000 0.00 0.00 44.61 3.41
1981 2037 1.135489 TCACTGCGTAGGTAAGCTTCG 60.135 52.381 0.00 0.22 0.00 3.79
1997 2053 0.387929 TTCGGCCGATTAGCTACCTG 59.612 55.000 31.56 0.00 0.00 4.00
2003 2059 1.070758 CCGATTAGCTACCTGGCATGT 59.929 52.381 0.10 0.10 34.17 3.21
2008 2064 5.050091 CGATTAGCTACCTGGCATGTAAAAG 60.050 44.000 4.21 0.00 34.17 2.27
2025 2082 4.841443 AAAAGTGTTTTACGGTCCATCC 57.159 40.909 0.00 0.00 0.00 3.51
2050 2107 0.521735 GGCGATGGTTCTGTGGAAAC 59.478 55.000 0.00 0.00 39.45 2.78
2055 2112 3.058914 CGATGGTTCTGTGGAAACTTGAC 60.059 47.826 0.00 0.00 39.70 3.18
2194 2251 2.112279 TGGTCACCTTTGAGTACCCT 57.888 50.000 0.00 0.00 30.10 4.34
2292 2349 3.250744 CCATTTGCAGCTCTTGTGATTG 58.749 45.455 0.00 0.00 0.00 2.67
2295 2352 2.259266 TGCAGCTCTTGTGATTGTGA 57.741 45.000 0.00 0.00 0.00 3.58
2494 2551 0.032130 GCATTGATGGCATGGCTCTG 59.968 55.000 21.08 10.94 0.00 3.35
2498 2555 0.393402 TGATGGCATGGCTCTGTGTC 60.393 55.000 21.08 9.08 0.00 3.67
2500 2557 2.439156 GGCATGGCTCTGTGTCCC 60.439 66.667 12.86 0.00 0.00 4.46
2761 2818 5.525199 GGAATCTTCCTCAGACTACGAATC 58.475 45.833 1.57 0.00 44.11 2.52
2825 2882 4.097741 TCTTTGGTTGAATTCAGTGTGTGG 59.902 41.667 8.41 0.00 0.00 4.17
2899 2956 3.942748 GGGTACGCAACATCTATTTTCCA 59.057 43.478 4.83 0.00 0.00 3.53
2902 2959 6.405397 GGGTACGCAACATCTATTTTCCATTT 60.405 38.462 4.83 0.00 0.00 2.32
3088 3145 1.949525 GCATACTGCCATAACTGTGGG 59.050 52.381 0.00 0.00 39.73 4.61
3100 3157 0.250295 ACTGTGGGTCCAATGTGTCG 60.250 55.000 0.00 0.00 0.00 4.35
3169 3226 4.695993 TGCGCGGAACTGCATGGA 62.696 61.111 8.83 0.00 35.90 3.41
3209 3266 1.094073 CCAAGCTGCCGATGAAGAGG 61.094 60.000 0.00 0.00 0.00 3.69
3391 3448 3.013921 GTGCCCAACCGAGAATTATGAA 58.986 45.455 0.00 0.00 0.00 2.57
3406 3469 6.988580 AGAATTATGAAAGCGATCATCAGTCA 59.011 34.615 10.07 0.00 40.44 3.41
3510 3573 3.554960 CCATCTCTGGACTTCGACAACAA 60.555 47.826 0.00 0.00 46.37 2.83
3526 3589 2.071778 ACAACACCAATGGAGCAAGT 57.928 45.000 6.16 0.00 0.00 3.16
3529 3592 3.181445 ACAACACCAATGGAGCAAGTAGA 60.181 43.478 6.16 0.00 0.00 2.59
3551 3614 1.337260 CGAAGCCTACACTGAGCAAGT 60.337 52.381 0.00 0.00 40.93 3.16
3598 3661 2.409975 CACAATTTCCGTGTACCGACT 58.590 47.619 5.46 0.00 39.56 4.18
3756 3819 8.668510 ATGTTCACAGCCAGAAACTATTATAG 57.331 34.615 0.00 0.00 0.00 1.31
3766 3829 7.500992 CCAGAAACTATTATAGTGGAGCTCAA 58.499 38.462 17.19 0.00 39.39 3.02
3799 3862 3.891366 ACCTCCCAAGAACAAAATCTGTG 59.109 43.478 0.00 0.00 38.67 3.66
3828 3891 1.439228 CCATCGACGCCTGAGATGT 59.561 57.895 0.00 0.00 39.89 3.06
3829 3892 0.179100 CCATCGACGCCTGAGATGTT 60.179 55.000 0.00 0.00 39.89 2.71
3837 3900 0.179189 GCCTGAGATGTTTTTCGCCG 60.179 55.000 0.00 0.00 0.00 6.46
3953 4016 4.274459 GGATTATGCCTGAGCTGTAAACTG 59.726 45.833 0.00 0.00 40.80 3.16
3966 4029 2.878406 TGTAAACTGTCTTCTGCCTTGC 59.122 45.455 0.00 0.00 0.00 4.01
4021 4084 1.276421 TGCCTGAGCTGTAAACTCTCC 59.724 52.381 0.00 0.00 40.80 3.71
4037 4100 1.556911 TCTCCTCTGCCTTGTGAATCC 59.443 52.381 0.00 0.00 0.00 3.01
4071 4134 2.168521 TCTAGGCTGTTGAGTGTATGCC 59.831 50.000 0.00 0.00 40.54 4.40
4094 4157 1.604308 CCCTGATTGGCTGTGTGCA 60.604 57.895 0.00 0.00 45.15 4.57
4095 4158 1.180456 CCCTGATTGGCTGTGTGCAA 61.180 55.000 0.00 0.00 45.15 4.08
4100 4163 0.591170 ATTGGCTGTGTGCAACGTAC 59.409 50.000 0.00 0.00 45.15 3.67
4112 4178 1.153628 AACGTACGATGCAGAGGCC 60.154 57.895 24.41 0.00 40.13 5.19
4282 4353 4.471904 TGATAATAGATGCCGATGTCCC 57.528 45.455 0.00 0.00 0.00 4.46
4317 4388 4.661461 GCAGAAAGCAAAGTGCCC 57.339 55.556 0.00 0.00 46.52 5.36
4335 4406 3.136992 TGCCCAAGCTATGAATCAGATCA 59.863 43.478 0.00 0.00 40.80 2.92
4338 4409 3.744942 CCAAGCTATGAATCAGATCACCG 59.255 47.826 0.00 0.00 30.82 4.94
4390 4461 8.102047 TCAGTCCTATACTAATACAGCCTAGTC 58.898 40.741 0.00 0.00 35.76 2.59
4408 4584 2.017049 GTCCCACATTGACACCTATGC 58.983 52.381 0.00 0.00 32.91 3.14
4603 4797 2.681848 GACCTGTGCAGATCTCATTTGG 59.318 50.000 0.00 0.00 0.00 3.28
4627 4822 1.768077 CCAGGACCAGGGGATCTCC 60.768 68.421 2.22 2.22 0.00 3.71
4693 4888 0.664224 AAGCGGTGGTTAAAACACGG 59.336 50.000 12.12 12.12 39.69 4.94
4720 4915 2.357637 GCTAAAGTGGCTCACAACAACA 59.642 45.455 7.86 0.00 36.74 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 6.909550 AGAACATGGCAGTGGTAAATTTAA 57.090 33.333 0.00 0.00 0.00 1.52
119 120 1.204312 GCGCAGACCGAACAAGAAC 59.796 57.895 0.30 0.00 40.02 3.01
146 147 3.066760 GCTGATTAAAAGGGACGAATGGG 59.933 47.826 0.00 0.00 0.00 4.00
157 158 2.092914 AGAGGGGACGGCTGATTAAAAG 60.093 50.000 0.00 0.00 0.00 2.27
244 246 2.607499 AGTATGGATGGAGAGGCTCAG 58.393 52.381 18.26 0.00 31.08 3.35
254 256 2.285083 TCGCGGAAAAAGTATGGATGG 58.715 47.619 6.13 0.00 0.00 3.51
259 261 0.026285 CGGCTCGCGGAAAAAGTATG 59.974 55.000 6.13 0.00 0.00 2.39
264 266 3.408020 CGACGGCTCGCGGAAAAA 61.408 61.111 6.13 0.00 31.91 1.94
325 327 2.926586 GCCCGATTTTCCAAGAAAGCAC 60.927 50.000 0.00 0.00 0.00 4.40
437 439 2.610694 GGGATCATCATGCGTGGCG 61.611 63.158 5.98 0.00 0.00 5.69
438 440 2.610694 CGGGATCATCATGCGTGGC 61.611 63.158 5.98 0.00 0.00 5.01
440 442 2.610694 GCCGGGATCATCATGCGTG 61.611 63.158 2.18 0.00 0.00 5.34
441 443 2.281070 GCCGGGATCATCATGCGT 60.281 61.111 2.18 0.00 0.00 5.24
442 444 3.052082 GGCCGGGATCATCATGCG 61.052 66.667 2.18 0.00 0.00 4.73
443 445 1.970114 CAGGCCGGGATCATCATGC 60.970 63.158 2.18 0.00 0.00 4.06
444 446 1.303074 CCAGGCCGGGATCATCATG 60.303 63.158 18.42 0.00 0.00 3.07
445 447 1.355718 AACCAGGCCGGGATCATCAT 61.356 55.000 30.18 0.06 40.22 2.45
446 448 1.570857 AAACCAGGCCGGGATCATCA 61.571 55.000 30.18 0.00 40.22 3.07
447 449 0.472471 TAAACCAGGCCGGGATCATC 59.528 55.000 30.18 0.00 40.22 2.92
458 460 7.519970 GCAATTATTCGGTGTAGATAAACCAGG 60.520 40.741 0.26 0.00 36.14 4.45
462 464 6.201425 TCCGCAATTATTCGGTGTAGATAAAC 59.799 38.462 12.76 0.00 45.44 2.01
484 486 6.913132 CGATGCCAATATACTACTCTAATCCG 59.087 42.308 0.00 0.00 0.00 4.18
489 491 5.417894 CACCCGATGCCAATATACTACTCTA 59.582 44.000 0.00 0.00 0.00 2.43
490 492 4.220821 CACCCGATGCCAATATACTACTCT 59.779 45.833 0.00 0.00 0.00 3.24
491 493 4.219944 TCACCCGATGCCAATATACTACTC 59.780 45.833 0.00 0.00 0.00 2.59
492 494 4.157246 TCACCCGATGCCAATATACTACT 58.843 43.478 0.00 0.00 0.00 2.57
493 495 4.495422 CTCACCCGATGCCAATATACTAC 58.505 47.826 0.00 0.00 0.00 2.73
508 510 1.026718 GGTCAAATCAGCCTCACCCG 61.027 60.000 0.00 0.00 0.00 5.28
519 521 3.270027 TCCATCATGACACGGTCAAATC 58.730 45.455 10.17 0.00 45.96 2.17
558 560 2.226912 CCTAGATACTGTCGCTGGCTAC 59.773 54.545 0.00 0.00 0.00 3.58
565 567 3.150767 ACAGGATCCTAGATACTGTCGC 58.849 50.000 15.67 0.00 38.80 5.19
594 596 0.453390 ACTAAGGCTACGTACGCACC 59.547 55.000 16.72 14.24 0.00 5.01
648 652 3.596214 TCAACGGAAAGCCAGAGATAAC 58.404 45.455 0.00 0.00 0.00 1.89
683 687 8.636213 CGGGTTTAGTTAAGATAGATTGGAGTA 58.364 37.037 0.00 0.00 0.00 2.59
684 688 7.343833 TCGGGTTTAGTTAAGATAGATTGGAGT 59.656 37.037 0.00 0.00 0.00 3.85
685 689 7.723324 TCGGGTTTAGTTAAGATAGATTGGAG 58.277 38.462 0.00 0.00 0.00 3.86
686 690 7.664552 TCGGGTTTAGTTAAGATAGATTGGA 57.335 36.000 0.00 0.00 0.00 3.53
687 691 6.424207 GCTCGGGTTTAGTTAAGATAGATTGG 59.576 42.308 0.00 0.00 0.00 3.16
688 692 7.210873 AGCTCGGGTTTAGTTAAGATAGATTG 58.789 38.462 0.00 0.00 0.00 2.67
689 693 7.362802 AGCTCGGGTTTAGTTAAGATAGATT 57.637 36.000 0.00 0.00 0.00 2.40
690 694 6.980416 AGCTCGGGTTTAGTTAAGATAGAT 57.020 37.500 0.00 0.00 0.00 1.98
691 695 6.786967 AAGCTCGGGTTTAGTTAAGATAGA 57.213 37.500 0.00 0.00 0.00 1.98
692 696 6.641723 GCTAAGCTCGGGTTTAGTTAAGATAG 59.358 42.308 18.65 0.00 38.14 2.08
693 697 6.323225 AGCTAAGCTCGGGTTTAGTTAAGATA 59.677 38.462 18.65 0.00 38.14 1.98
698 702 4.813750 AAGCTAAGCTCGGGTTTAGTTA 57.186 40.909 18.65 0.00 38.25 2.24
709 713 1.669604 GCTACCCCAAAGCTAAGCTC 58.330 55.000 0.00 0.00 38.25 4.09
718 722 1.494721 GGATGATGAGGCTACCCCAAA 59.505 52.381 0.00 0.00 35.39 3.28
757 761 2.044551 GGGAAGCAGCCAAGGAGG 60.045 66.667 0.00 0.00 41.84 4.30
786 790 2.598394 ATGGTGTGTGTGGGCAGC 60.598 61.111 0.00 0.00 0.00 5.25
1106 1131 1.530655 GGAGGTTGTTGGTGGTGGG 60.531 63.158 0.00 0.00 0.00 4.61
1107 1132 1.530655 GGGAGGTTGTTGGTGGTGG 60.531 63.158 0.00 0.00 0.00 4.61
1108 1133 1.530655 GGGGAGGTTGTTGGTGGTG 60.531 63.158 0.00 0.00 0.00 4.17
1122 1147 4.465446 CGCAGGAGGAGGAGGGGA 62.465 72.222 0.00 0.00 0.00 4.81
1337 1379 1.454847 TGAAACCAAACCAGCCGCT 60.455 52.632 0.00 0.00 0.00 5.52
1589 1631 0.659957 GAAGATGAGATTGGTGCGGC 59.340 55.000 0.00 0.00 0.00 6.53
1591 1633 2.799412 GCTAGAAGATGAGATTGGTGCG 59.201 50.000 0.00 0.00 0.00 5.34
1592 1634 3.137533 GGCTAGAAGATGAGATTGGTGC 58.862 50.000 0.00 0.00 0.00 5.01
1593 1635 3.390639 AGGGCTAGAAGATGAGATTGGTG 59.609 47.826 0.00 0.00 0.00 4.17
1594 1636 3.645687 GAGGGCTAGAAGATGAGATTGGT 59.354 47.826 0.00 0.00 0.00 3.67
1595 1637 3.903090 AGAGGGCTAGAAGATGAGATTGG 59.097 47.826 0.00 0.00 0.00 3.16
1596 1638 5.549742 AAGAGGGCTAGAAGATGAGATTG 57.450 43.478 0.00 0.00 0.00 2.67
1597 1639 7.682787 TTAAAGAGGGCTAGAAGATGAGATT 57.317 36.000 0.00 0.00 0.00 2.40
1598 1640 7.678837 CATTAAAGAGGGCTAGAAGATGAGAT 58.321 38.462 0.00 0.00 0.00 2.75
1599 1641 6.463614 GCATTAAAGAGGGCTAGAAGATGAGA 60.464 42.308 0.00 0.00 0.00 3.27
1600 1642 5.700373 GCATTAAAGAGGGCTAGAAGATGAG 59.300 44.000 0.00 0.00 0.00 2.90
1601 1643 5.367937 AGCATTAAAGAGGGCTAGAAGATGA 59.632 40.000 0.00 0.00 34.25 2.92
1602 1644 5.619220 AGCATTAAAGAGGGCTAGAAGATG 58.381 41.667 0.00 0.00 34.25 2.90
1603 1645 5.367937 TGAGCATTAAAGAGGGCTAGAAGAT 59.632 40.000 0.00 0.00 36.59 2.40
1606 1648 5.435686 TTGAGCATTAAAGAGGGCTAGAA 57.564 39.130 0.00 0.00 36.59 2.10
1634 1676 4.683832 AGATTGAGCGTACAAGGATACAC 58.316 43.478 0.00 0.00 41.41 2.90
1769 1825 1.005450 ACCGCCCATATGTTCACCTTT 59.995 47.619 1.24 0.00 0.00 3.11
1981 2037 1.301795 GCCAGGTAGCTAATCGGCC 60.302 63.158 14.73 0.00 33.31 6.13
2003 2059 5.945466 GGATGGACCGTAAAACACTTTTA 57.055 39.130 0.00 0.00 34.19 1.52
2018 2075 0.588252 CATCGCCATTTCGGATGGAC 59.412 55.000 18.99 11.01 41.64 4.02
2022 2079 1.134098 AGAACCATCGCCATTTCGGAT 60.134 47.619 0.00 0.00 36.56 4.18
2023 2080 0.251916 AGAACCATCGCCATTTCGGA 59.748 50.000 0.00 0.00 36.56 4.55
2024 2081 0.378257 CAGAACCATCGCCATTTCGG 59.622 55.000 0.00 0.00 38.11 4.30
2025 2082 1.086696 ACAGAACCATCGCCATTTCG 58.913 50.000 0.00 0.00 0.00 3.46
2026 2083 1.133025 CCACAGAACCATCGCCATTTC 59.867 52.381 0.00 0.00 0.00 2.17
2033 2090 3.058914 GTCAAGTTTCCACAGAACCATCG 60.059 47.826 0.00 0.00 0.00 3.84
2050 2107 0.663568 GACACGTCCACCTCGTCAAG 60.664 60.000 0.00 0.00 39.55 3.02
2055 2112 2.209064 AATCCGACACGTCCACCTCG 62.209 60.000 0.00 0.00 0.00 4.63
2210 2267 1.754803 CTTGTAGATCTGCACCGGGTA 59.245 52.381 13.54 0.00 0.00 3.69
2292 2349 2.472695 TCCAACTAGCCACACATCAC 57.527 50.000 0.00 0.00 0.00 3.06
2295 2352 4.151883 ACAATTTCCAACTAGCCACACAT 58.848 39.130 0.00 0.00 0.00 3.21
2498 2555 1.772567 TGTAATCCCCATCCCCGGG 60.773 63.158 15.80 15.80 46.94 5.73
2500 2557 1.454539 GGTGTAATCCCCATCCCCG 59.545 63.158 0.00 0.00 0.00 5.73
2761 2818 3.001634 GCGTGTTACCATCATCATCAGTG 59.998 47.826 0.00 0.00 0.00 3.66
2899 2956 4.337555 GCAGTATCAGCCTCAACATCAAAT 59.662 41.667 0.00 0.00 0.00 2.32
2902 2959 2.236893 TGCAGTATCAGCCTCAACATCA 59.763 45.455 0.00 0.00 0.00 3.07
3088 3145 1.464608 CCACATGACGACACATTGGAC 59.535 52.381 0.00 0.00 34.06 4.02
3100 3157 3.042887 GTCAAAAAGCGAACCACATGAC 58.957 45.455 0.00 0.00 0.00 3.06
3157 3214 2.238521 TCAAACCTTCCATGCAGTTCC 58.761 47.619 0.00 0.00 0.00 3.62
3169 3226 5.634118 TGGAATGTGATCTCTTCAAACCTT 58.366 37.500 0.00 0.00 35.70 3.50
3209 3266 3.128242 CCTGAGTCATGCAAACCAGATTC 59.872 47.826 16.00 7.09 0.00 2.52
3391 3448 2.636830 CCCTTTGACTGATGATCGCTT 58.363 47.619 0.00 0.00 0.00 4.68
3406 3469 3.149005 TGCTTTATGTCGAACCCCTTT 57.851 42.857 0.00 0.00 0.00 3.11
3510 3573 3.412386 GTTCTACTTGCTCCATTGGTGT 58.588 45.455 1.86 0.00 0.00 4.16
3526 3589 2.163815 GCTCAGTGTAGGCTTCGTTCTA 59.836 50.000 0.00 0.00 0.00 2.10
3529 3592 0.679505 TGCTCAGTGTAGGCTTCGTT 59.320 50.000 0.00 0.00 0.00 3.85
3613 3676 2.677524 GGGCTGATTGCTGTGCCA 60.678 61.111 5.21 0.00 46.53 4.92
3624 3687 3.855503 CTTGCTGTGCCAGGGCTGA 62.856 63.158 12.19 0.00 42.51 4.26
3625 3688 3.371063 CTTGCTGTGCCAGGGCTG 61.371 66.667 12.19 3.29 42.51 4.85
3756 3819 0.895100 TGGTGGCAATTGAGCTCCAC 60.895 55.000 19.22 19.22 46.10 4.02
3766 3829 0.105246 TTGGGAGGTTTGGTGGCAAT 60.105 50.000 0.00 0.00 0.00 3.56
3828 3891 3.243101 TGCAGAATTTACACGGCGAAAAA 60.243 39.130 16.62 11.12 0.00 1.94
3829 3892 2.290916 TGCAGAATTTACACGGCGAAAA 59.709 40.909 16.62 11.51 0.00 2.29
3837 3900 3.821033 ACAGTTCCCTGCAGAATTTACAC 59.179 43.478 17.39 1.78 42.81 2.90
3866 3929 8.484799 TCATATCGCATACATAAAGAACGAAAC 58.515 33.333 0.00 0.00 0.00 2.78
3966 4029 0.323629 TTTCAGTCCCAAGCCTACCG 59.676 55.000 0.00 0.00 0.00 4.02
3977 4040 1.503542 CGCAGCCACATTTCAGTCC 59.496 57.895 0.00 0.00 0.00 3.85
4021 4084 2.630158 CTCTGGATTCACAAGGCAGAG 58.370 52.381 0.00 0.00 0.00 3.35
4037 4100 3.900601 ACAGCCTAGAATGGTATCCTCTG 59.099 47.826 0.00 0.00 0.00 3.35
4071 4134 1.377725 ACAGCCAATCAGGGAAGCG 60.378 57.895 0.00 0.00 38.09 4.68
4094 4157 1.153628 GGCCTCTGCATCGTACGTT 60.154 57.895 16.05 3.67 40.13 3.99
4095 4158 2.494918 GGCCTCTGCATCGTACGT 59.505 61.111 16.05 0.00 40.13 3.57
4240 4310 6.339999 TCAAGATATGGGGAGAAAAATCCA 57.660 37.500 0.00 0.00 41.52 3.41
4249 4319 7.222872 GGCATCTATTATCAAGATATGGGGAG 58.777 42.308 0.00 0.00 32.40 4.30
4250 4320 6.183361 CGGCATCTATTATCAAGATATGGGGA 60.183 42.308 0.00 0.00 32.40 4.81
4282 4353 7.430502 GCTTTCTGCATAATTAACTAACAGCAG 59.569 37.037 0.00 0.00 46.94 4.24
4317 4388 4.625028 TCGGTGATCTGATTCATAGCTTG 58.375 43.478 0.00 0.00 0.00 4.01
4335 4406 2.035632 CTTCCAGCTCCTAATCTCGGT 58.964 52.381 0.00 0.00 0.00 4.69
4338 4409 4.892934 TCTTCTCTTCCAGCTCCTAATCTC 59.107 45.833 0.00 0.00 0.00 2.75
4390 4461 2.127271 TGCATAGGTGTCAATGTGGG 57.873 50.000 0.00 0.00 0.00 4.61
4627 4822 1.002134 ACGGAGCCCACATGAAAGG 60.002 57.895 0.00 0.00 0.00 3.11
4720 4915 2.240667 AGCATCATCCTGGCTTTACAGT 59.759 45.455 0.00 0.00 36.75 3.55
4769 4964 3.947868 TCTTCTGGAAAAGAGATGCCTG 58.052 45.455 0.00 0.00 35.91 4.85


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

AutoCloner maintained by Alex Coulton.