Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1165
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7189 original size:177 final size:177
Alignment explanation
Indices: 6888--7360 Score: 605
Period size: 177 Copynumber: 2.7 Consensus size: 177
6878 TATTGGTGGC
* * * * * * * *
6888 AAAGTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAATG-TAGC
1 AAAGTAGATCGAAGATATCAGATCCTATCTTCCTATATTGGTAG-GAAGTAGATCGAA-GAT-GC
* * * * * * *
6951 AGATCCTATCTTCCTATATTGATAG-GAAGT-GGATCCAAG-ATGCAGATCTTGTCTTCCCATAT
63 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGG-TCAAAGAAAGCAGATCTTGTCTTCCCATAT
* *
7013 TGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTATTGGCGT
127 TGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGT
* * *
7064 GAAGTATATCGAAGGTATCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
1 AAAGTAGATCGAAGATATCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
7129 TCTTGTCTTCCCATATTGGTGGCGAAGTAGGTCAAAGAAAGCAGATCTTGTCTTCCCATATTGGT
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGGTCAAAGAAAGCAGATCTTGTCTTCCCATATTGGT
*
7194 GGCGAAGCAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
131 GGCGAAGCAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGT
* * * *
7241 AAAGTAGATCGGAGATATCGGATCCTATCTTCCTATATTGGTAGGAAGTGGACCGAAGATGCAGA
1 AAAGTAGATCGAAGATATCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
* *** *
7306 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATTGCAGAAAGCAGATCTGGTCTTC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGGTCAAAGAAAGCAGATCTTGTCTTC
7361 ATGTATTGGC
Statistics
Matches: 259, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
175 23 0.09
176 55 0.21
177 181 0.70
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (177 bp):
AAAGTAGATCGAAGATATCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
TCTTGTCTTCCCATATTGGTGGCGAAGTAGGTCAAAGAAAGCAGATCTTGTCTTCCCATATTGGT
GGCGAAGCAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGT
Found at i:7192 original size:132 final size:132
Alignment explanation
Indices: 6819--7183 Score: 595
Period size: 132 Copynumber: 2.8 Consensus size: 132
6809 AGGCGTAAAT
* * *
6819 AGATCCTATCTTCCTATATTGGTAGAAAGTGGACCGAAGATGCCGATCTTGTCTTCCCATATTGG
1 AGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
* * *
6884 TGGCAAAGTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATGTA
66 TGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
6949 GC
131 GC
* *
6951 AGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
* *
7016 TGGCGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTATATCGAAGGTA
66 TGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
*
7081 TC
131 GC
*
7083 AGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
* **
7148 TGGCGAAGTAGGTCAAAGAAAGCAGATCTTGTCTTC
66 TGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTC
7184 CCATATTGGT
Statistics
Matches: 215, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 215 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (132 bp):
AGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
TGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
GC
Found at i:7345 original size:132 final size:132
Alignment explanation
Indices: 7108--7529 Score: 537
Period size: 132 Copynumber: 3.2 Consensus size: 132
7098 ATATTGGTAG
* * * * * *
7108 GAAGTAGATCGAAGAT-GCAGATCTTG-TCTTCCCATATTGGTGGCGAAGTAGG-TCAAAGAAAG
1 GAAGTAGATCGAAGATAGCAGATC-CGATCTTCCTATATTGGTAG-GAAGT-GGACCGAAG-ATG
*
7170 CAGATCTTGTCTTCCCATATTGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTGTCTTCATGTAT
62 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTAT
7235 TGGCGT
127 TGGCGT
* * * * *
7241 AAAGTAGATCGGAGATATCGGATCCTATCTTCCTATATTGGTAGGAAGTGGACCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCGATCTTCCTATATTGGTAGGAAGTGGACCGAAGATGCAGA
* * *
7306 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATTGCAGAAAGCAGATCTGGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGC
7371 GT
131 GT
* * * ** * *
7373 GAAGTAGATCAAAGGTAGCAGATCCGGTCTTCCTATATTGGTAGGAAGTGGATTGACGGTGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCGATCTTCCTATATTGGTAGGAAGTGGACCGAAGATGCAGA
* *
7438 TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTTGG
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA-TTGG
*
7503 TGT
130 CGT
7506 GAAGTAGATCGAAGATTA-CAGATC
1 GAAGTAGATCGAAGA-TAGCAGATC
7530 TTGCCTTCCT
Statistics
Matches: 249, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
132 179 0.72
133 48 0.19
134 22 0.09
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (132 bp):
GAAGTAGATCGAAGATAGCAGATCCGATCTTCCTATATTGGTAGGAAGTGGACCGAAGATGCAGA
TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGC
GT
Found at i:7438 original size:309 final size:308
Alignment explanation
Indices: 6863--7544 Score: 1010
Period size: 309 Copynumber: 2.2 Consensus size: 308
6853 CGAAGATGCC
* *
6863 GATCTTGTCTTCCCATATTGGTGGCAAAGTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTG
1 GATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAG-AAACAGATCTTGTCTTCATGTATTG
*
6928 GCGTGAAGTAGATCGAATGTAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATG
65 GCGTAAAGTAGATCGAATGTAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATG
*
6993 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTAT
130 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTGATCTTCATGTAT
* * * *
7058 TGGCGTGAAGTATATCGAAGGTATCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGA
195 TGGCGTGAAGTAGATCAAAGGTAGCAGATCCGATCTTCCTATATTGGTAGGAAGTAGATCGAAGA
* *
7123 TGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGGTCAAAGAAAGCA
260 TGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCA
*
7172 GATCTTGTCTTCCCATATTGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
1 GATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAA-CAGATCTTGTCTTCATGTATTG
* * * *
7237 GCGTAAAGTAGATCGGA-GATATCGGATCCTATCTTCCTATATTGGTAGGAAGTGGA-CCGAAGA
65 GCGTAAAGTAGATCGAATG-TAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCC-AAGA
* *
7300 TGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATTGCAGAAAGCAGATCTGGTCTTCATGT
128 TGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTGATCTTCATGT
* * * *
7365 ATTGGCGTGAAGTAGATCAAAGGTAGCAGATCCGGTCTTCCTATATTGGTAGGAAGTGGATTGAC
193 ATTGGCGTGAAGTAGATCAAAGGTAGCAGATCCGATCTTCCTATATTGGTAGGAAGTAGATCGAA
* *
7430 GGTGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
258 GATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCA
* *** * * * *
7481 GATCTTATCTTCATGTATTTGGT-GTGAAGTAGATCGAAGATTACAGATCTTGCCTTCCTGTATT
1 GATCTTGTCTTCCCATA-TTGGTGGCGAAGTAGATCGAAGA-AACAGATCTTGTCTTCATGTATT
7545 TGGCAGCGAA
Statistics
Matches: 336, Mismatches: 32, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
308 6 0.02
309 324 0.96
310 6 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (308 bp):
GATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAACAGATCTTGTCTTCATGTATTGG
CGTAAAGTAGATCGAATGTAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATGC
AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTGATCTTCATGTATT
GGCGTGAAGTAGATCAAAGGTAGCAGATCCGATCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCA
Found at i:7486 original size:177 final size:177
Alignment explanation
Indices: 6888--7413 Score: 513
Period size: 177 Copynumber: 3.0 Consensus size: 177
6878 TATTGGTGGC
* * * * * * * *
6888 AAAGTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAATG-TAGC
1 AAAGTAGATCGGAGATAGCAGATCCTATCTTCCTATATTGGTAG-GAAGTAGATCGAA-GAT-GC
* * * * * * * * * *
6951 AGATCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAG-ATGCAGATCTTGTCTTCCCATATT
63 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTGGTCTTCACATATT
* * ** *** *
7014 GGTGGCGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTATTGGCGT
128 GGTCGCGAAGCAGATCAAAGAAAGCAGATCCGGTCTTCATATATTGGCGT
* * * * *
7064 GAAGTATATCGAAGGTATCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
1 AAAGTAGATCGGAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
* * *
7129 TCTTGTCTTCCCATATTGGTGGCGAAGTAGGTCAAAGAAAGCAGATCTTGTCTTCCCATATTGGT
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTGGTCTTCACATATTGGT
* * ** *
7194 GGCGAAGCAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
131 CGCGAAGCAGATCAAAGAAAGCAGATCCGGTCTTCATATATTGGCGT
* * * *
7241 AAAGTAGATCGGAGATATCGGATCCTATCTTCCTATATTGGTAGGAAGTGGACCGAAGATGCAGA
1 AAAGTAGATCGGAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
*** **
7306 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATTGCAGAAAGCAGATCTGGTCTTCATGTATTGG-
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTGGTCTTCACATATTGGT
* * ** *
7370 CGTGAAGTAGATCAAAGGTAGCAGATCCGGTCTTCCTATATTGG
131 CGCGAAGCAGATCAAAGAAAGCAGATCCGGTCTTCATATATTGG
7414 TAGGAAGTGG
Statistics
Matches: 298, Mismatches: 48, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
175 23 0.08
176 90 0.30
177 185 0.62
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (177 bp):
AAAGTAGATCGGAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGA
TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTGGTCTTCACATATTGGT
CGCGAAGCAGATCAAAGAAAGCAGATCCGGTCTTCATATATTGGCGT
Found at i:7855 original size:46 final size:46
Alignment explanation
Indices: 7459--7855 Score: 195
Period size: 46 Copynumber: 8.8 Consensus size: 46
7449 CATACTGGTG
* ** * * * * *
7459 GCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTTGG-T
1 GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* * ** * * *
7504 GTGAAGTAGATCGAAGATTACAGATCTTGCCTTCCTGTATTTGGCA
1 GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* * * *
7550 GCGAAGAAGATCGAAGATGGCAGATTTTACCTCCCTG-A-CT-ACA
1 GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* * * ** ** * *
7593 GTGGAGTACATTGAAGCCGATA-ATTCTATCTCCCTGTATTTGGCA
1 GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* * * * *
7638 GTGGAA-TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCA
1 G-CGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* ** ***
7684 GCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTG-A--CCACA
1 GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* * * ** ** * *
7727 GTGGAGTACATTGAAGCCGATA-ATTCTATCTCCCTGTATTTGGCA
1 GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* * * * *
7772 GTGGAA-TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCA
1 G-CGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
* **
7818 GCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGT
1 GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGT
7856 CTACAGTGGA
Statistics
Matches: 249, Mismatches: 90, Indels: 25
0.68 0.25 0.07
Matches are distributed among these distances:
42 24 0.10
43 31 0.12
44 2 0.01
45 71 0.29
46 121 0.49
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (46 bp):
GCGAAGTAGATTGAAGATGGCAGATTTTACCTCCCTGTATTTGGCA
Found at i:7933 original size:134 final size:134
Alignment explanation
Indices: 7494--7922 Score: 700
Period size: 134 Copynumber: 3.2 Consensus size: 134
7484 CTTATCTTCA
* * * *
7494 TGTATTTGG-TGT-GAAGTAGATCGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGA
1 TGTATTTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGC
*
7557 AGATCGAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
65 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
7622 CTCCC
130 CTCCC
7627 TGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCA
1 TGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCA
*
7692 GATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAATTCTATC
66 GATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATC
7757 TCCC
131 TCCC
7761 TGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCA
1 TGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCA
* * *
7826 GATCAAAGATGGCAGATTTTACCTCCCTGTCTACAGTGGAGTACATTGAAGCCAATAACTCTATC
66 GATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATC
7891 TCCC
131 TCCC
** *** *
7895 TACATTCAACAGTGGAATAGAGTGAAGA
1 TGTATTTGGCAGTGGAATAGATTGAAGA
7923 GCACAAATCT
Statistics
Matches: 278, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
133 9 0.03
134 266 0.96
135 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (134 bp):
TGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCA
GATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATC
TCCC
Found at i:9658 original size:20 final size:21
Alignment explanation
Indices: 9626--9685 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
9616 TTATTAATAT
9626 TATAT-TTAGTTATATACCCA
1 TATATCTTAGTTATATACCCA
* *
9646 TATATCTTATTATATATATCCA
1 TATATCTTAGT-TATATACCCA
*
9668 TATATCTTAATATATATA
1 TATATCTTAGT-TATATA
9686 TGTGCATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 5 0.14
21 4 0.11
22 26 0.74
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATCTTAGTTATATACCCA
Found at i:9668 original size:22 final size:22
Alignment explanation
Indices: 9636--9686 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
9626 TATATTTAGT
* *
9636 TATATACCCATATATCTTATTA
1 TATATATCCATATATCTTAATA
9658 TATATATCCATATATCTTAATA
1 TATATATCCATATATCTTAATA
9680 TATATAT
1 TATATAT
9687 GTGCATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATATCCATATATCTTAATA
Found at i:16498 original size:76 final size:74
Alignment explanation
Indices: 16358--16500 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 74
16348 TTTTTAAAAA
* *
16358 AAAAAAATCAACTCATAGTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATAGTGCGAGAGGCGAGTTGAGCCTCAAGACACGCCGAGGTAATTTCAATT
16423 TCTGTTGTC
66 TCTGTTGTC
* * *
16432 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATAGTGCGAGAGGCGAGTTGAGCCTCAAG--ACACGCCGAGGTAATTTCAA
16497 TTTC
64 TTTC
16501 CGTTTTTCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 40 0.65
76 22 0.35
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (74 bp):
AAAAAAATCAACTCATAGTGCGAGAGGCGAGTTGAGCCTCAAGACACGCCGAGGTAATTTCAATT
TCTGTTGTC
Found at i:16637 original size:168 final size:167
Alignment explanation
Indices: 16356--16829 Score: 711
Period size: 168 Copynumber: 2.8 Consensus size: 167
16346 TATTTTTAAA
* *
16356 AAAAAAAAATCAACTCATAGTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
1 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
16421 TTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGA
66 TTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGA
*
16486 GGTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTC
131 GGTATTTTCAATTTCCGTTTTTCAAATTCTGCCTTTC
16523 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
1 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
* *
16588 TTTCTGTTGTCAAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACATGCCG
66 TTTCTGTTGTC-AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCG
*
16653 AGGTATTTTCAATTTCCGTTTTTCAAATTCTGCTTTTC
130 AGGTATTTTCAATTTCCGTTTTTCAAATTCTGCCTTTC
* * * * * * *
16691 --AAAAAAATCGACTCATATTGCGAGAGGTGAGTTAAACCT-TGGCTCACGCGCTGAGCTATTTT
1 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTT
* * * * *
16753 CAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACA
63 CAATTTCTGT-TGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACG
*
16818 CTGAGGTATTTT
127 CCGAGGTATTTT
16830 TTCAATTTAT
Statistics
Matches: 281, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
165 2 0.01
166 36 0.13
167 74 0.26
168 166 0.59
169 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (167 bp):
AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
TTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGA
GGTATTTTCAATTTCCGTTTTTCAAATTCTGCCTTTC
Found at i:16663 original size:77 final size:76
Alignment explanation
Indices: 16504--16910 Score: 256
Period size: 77 Copynumber: 5.1 Consensus size: 76
16494 CAATTTCCGT
*
16504 TTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
1 TTTTCAATTTCTG-CTTTCAAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGA
*
16569 CACGCTGAGGTA
65 CACGCCGAGGTA
* *
16581 ATTTCAATTTCTG-TTGTC-AAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGT
1 TTTTCAATTTCTGCTT-TCAAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-
*
16644 CACATGCCGAGGTA
64 -ACACGCCGAGGTA
* * * *
16658 TTTTCAATTTCCGTTTTTCAAATTCTGCTTTTCAAAAAAATCGACTCATATTGCGAGAGGTGAGT
1 TTTTCAATTTCTG-CTTTC-AA-----------AAAAAAATCAACTCATATTGCGAGAGGCGAGT
* * * * *
16723 TAAACCT-TGGCTCACGCGCTGAGCTA
53 TGAGCCTCAGG-ACACGC-C-GAGGTA
* *
16749 TTTTCAATTTCTGTCTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCA-GA
1 TTTTCAATTTCTG-CTTTCAAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGA
*
16811 TCACACACTGAGGTA
65 -CACGC-C-GAGGTA
* ** * * * * *
16826 TTTTTTCAATTTATATTTTTC--AAAAAAAT-AACGCACATTGCGAGATGTGAGTTGAGCCTCGG
1 --TTTTCAATTTCT-GCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG
*
16888 GTCACACGTCGAGGTA
63 G--ACACGCCGAGGTA
16904 TTTTCAA
1 TTTTCAA
16911 AATCTGTTTT
Statistics
Matches: 265, Mismatches: 37, Indels: 57
0.74 0.10 0.16
Matches are distributed among these distances:
75 44 0.17
76 9 0.03
77 81 0.31
78 35 0.13
79 27 0.10
80 4 0.02
81 1 0.00
89 5 0.02
90 3 0.01
91 56 0.21
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (76 bp):
TTTTCAATTTCTGCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
ACGCCGAGGTA
Found at i:16751 original size:91 final size:91
Alignment explanation
Indices: 16582--16770 Score: 220
Period size: 91 Copynumber: 2.1 Consensus size: 91
16572 GCTGAGGTAA
* * * *
16582 TTTCAATTTCTGTTGTCAAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCAC
1 TTTCAAATTCTGTTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAACCTCAGGTCAC
* * *
16647 ATGCCGAGGTATTTTCAATTTCCGTT
66 ACGCCGAGCTATTTTCAATTTCCGTC
* * * *
16673 TTTCAAATTCTGCTTTTC-AAAAAAATCGACTCATATTGCGAGAGGTGAGTTAAACCT-TGGCTC
1 TTTCAAATTCTG-TTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAACCTCAGG-TC
* * *
16736 ACGCGCTGAGCTATTTTCAATTTCTGTC
64 ACACGCCGAGCTATTTTCAATTTCCGTC
16764 TTTCAAA
1 TTTCAAA
16771 AAAATCAACT
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
90 2 0.02
91 76 0.93
92 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (91 bp):
TTTCAAATTCTGTTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAACCTCAGGTCAC
ACGCCGAGCTATTTTCAATTTCCGTC
Found at i:16923 original size:14 final size:13
Alignment explanation
Indices: 16904--16939 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
16894 CGTCGAGGTA
16904 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
16917 TTTTTCAAATTCTG
1 -TTTTCAAAATCTG
16931 TTTTCAAAA
1 TTTTCAAAA
16940 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:16973 original size:24 final size:24
Alignment explanation
Indices: 16941--16989 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16931 TTTTCAAAAA
16941 TCAACTCATATTGCGAGAAGTGAG
1 TCAACTCATATTGCGAGAAGTGAG
16965 TCAACTCATATTGCGAGAAGTGAG
1 TCAACTCATATTGCGAGAAGTGAG
16989 T
1 T
16990 TGAGCCTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (24 bp):
TCAACTCATATTGCGAGAAGTGAG
Found at i:17102 original size:30 final size:30
Alignment explanation
Indices: 17061--17117 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17051 TCATATTGCG
17061 AGAGGTGAGTTGAG-CTTTTTAATTTCTGCT
1 AGAGGTGAGTTGAGTC-TTTTAATTTCTGCT
*
17091 AGAGTTGAGTTGAGTCTTTTAATTTCT
1 AGAGGTGAGTTGAGTCTTTTAATTTCT
17118 ATTTTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.46
Consensus pattern (30 bp):
AGAGGTGAGTTGAGTCTTTTAATTTCTGCT
Found at i:18291 original size:18 final size:17
Alignment explanation
Indices: 18251--18289 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
18241 CCTAAACGTG
*
18251 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
18268 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
18285 ATTTT
1 ATTTT
18290 TATTGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:18377 original size:13 final size:13
Alignment explanation
Indices: 18342--18370 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18332 TATATACATC
18342 ATAATAAAAATAT
1 ATAATAAAAATAT
18355 ATAATAAAAATAT
1 ATAATAAAAATAT
18368 ATA
1 ATA
18371 TACAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:18384 original size:15 final size:14
Alignment explanation
Indices: 18342--18394 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
18332 TATATACATC
18342 ATAAT-AAAAATAT
1 ATAATAAAAAATAT
18355 ATAATAAAAATATAT
1 ATAATAAAAA-ATAT
18370 ATACA-AAACAAATAT
1 ATA-ATAAA-AAATAT
18385 A-AA-AAAAAAT
1 ATAATAAAAAAT
18395 TTACCTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.11
13 9 0.25
14 5 0.14
15 15 0.42
16 3 0.08
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAATAAAAAATAT
Found at i:18498 original size:11 final size:11
Alignment explanation
Indices: 18479--18513 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
18469 CCCCTTCCCC
18479 CTCCCTTCTCT
1 CTCCCTTCTCT
18490 CTCCCTTCTCT
1 CTCCCTTCTCT
18501 CTTCCC-TCTCT
1 C-TCCCTTCTCT
18512 CT
1 CT
18514 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:19065 original size:11 final size:11
Alignment explanation
Indices: 19041--19083 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
19031 TTCTAATACG
*
19041 TATATATATTA
1 TATATATTTTA
*
19052 TATGTATTTTA
1 TATATATTTTA
* *
19063 TATATATTATG
1 TATATATTTTA
19074 TATATATTTT
1 TATATATTTT
19084 TTAATGCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:20277 original size:9 final size:9
Alignment explanation
Indices: 20263--20287 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20253 ATAAAAAACA
20263 TTATAAATT
1 TTATAAATT
20272 TTATAAATT
1 TTATAAATT
20281 TTATAAA
1 TTATAAA
20288 AAAATAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTATAAATT
Found at i:20505 original size:28 final size:28
Alignment explanation
Indices: 20446--20505 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20436 TTTTATTTTT
* *
20446 TTAACATTTTTACAATATTTTTAGATTG
1 TTAACATTTTTACAATATTTTTAAATTC
* *
20474 TTAATATTTTTATAAT-TTTTTACAATTC
1 TTAACATTTTTACAATATTTTTA-AATTC
20502 TTAA
1 TTAA
20506 AAGATTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (28 bp):
TTAACATTTTTACAATATTTTTAAATTC
Found at i:21389 original size:16 final size:16
Alignment explanation
Indices: 21370--21409 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
21360 ATTACATAAT
21370 ATATAAAAATATTATA
1 ATATAAAAATATTATA
*
21386 ATAT-AAAATTTTATA
1 ATATAAAAATATTATA
21401 A-ATAAAAAT
1 ATATAAAAAT
21410 GGGTCAGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 16 0.73
16 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATATTATA
Found at i:27473 original size:18 final size:18
Alignment explanation
Indices: 27433--27474 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
27423 CATAACTTTT
*
27433 AAAAGTAAAATCTAAATA
1 AAAAGTAAAATCTAAAAA
*
27451 TAAAGTAAAA-CTTAAAAA
1 AAAAGTAAAATC-TAAAAA
27469 AAAAGT
1 AAAAGT
27475 GAATGATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (18 bp):
AAAAGTAAAATCTAAAAA
Found at i:29544 original size:17 final size:17
Alignment explanation
Indices: 29522--29559 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
29512 ATAAATTTTC
29522 AAAGTTTCGGTCGTGAA
1 AAAGTTTCGGTCGTGAA
*
29539 AAAGTTTGGGTCGTGAA
1 AAAGTTTCGGTCGTGAA
29556 AAAG
1 AAAG
29560 ACACTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (17 bp):
AAAGTTTCGGTCGTGAA
Found at i:29830 original size:25 final size:23
Alignment explanation
Indices: 29784--29831 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
29774 GGAGAGATTT
*
29784 TTATTTTATTTAATATATTATAA
1 TTATTTTATTTAATATAATATAA
*
29807 TTATATTTGTTTAATATTAATATAA
1 TTAT-TTTATTTAATA-TAATATAA
29832 AATATTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTTTATTTAATATAATATAA
Found at i:29836 original size:24 final size:24
Alignment explanation
Indices: 29792--29838 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29782 TTTTATTTTA
* *
29792 TTTAATATATTATAATTATATTTG
1 TTTAATATAATATAATAATATTTG
29816 TTTAATATTAATATAA-AATATTT
1 TTTAATA-TAATATAATAATATTT
29839 ATGTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAATATAATATAATAATATTTG
Found at i:31349 original size:17 final size:18
Alignment explanation
Indices: 31322--31366 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
31312 AATAAGACGA
31322 ATCTAAATTA-TTTAGAAT
1 ATCT-AATTATTTTAGAAT
*
31340 ATCTAATTATTTTAGATT
1 ATCTAATTATTTTAGAAT
31358 ATCATAATT
1 ATC-TAATT
31367 TCTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (18 bp):
ATCTAATTATTTTAGAAT
Found at i:31444 original size:32 final size:35
Alignment explanation
Indices: 31380--31445 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 35
31370 TTTTAAAAAC
31380 ATTTTTAACTAGTAAATCTAAATTAGATTATAATT
1 ATTTTTAACTAGTAAATCTAAATTAGATTATAATT
*
31415 ATTTTTAA-T-GT-AATTTAAA-TAGATCTATAAT
1 ATTTTTAACTAGTAAATCTAAATTAGAT-TATAAT
31446 ATAATTAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 5 0.17
32 13 0.45
33 2 0.07
34 1 0.03
35 8 0.28
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (35 bp):
ATTTTTAACTAGTAAATCTAAATTAGATTATAATT
Found at i:32733 original size:16 final size:16
Alignment explanation
Indices: 32712--32780 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
32702 TTTGGTTCGC
32712 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
32728 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
32744 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
*
32761 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
32777 TGTA
1 TGTA
32781 ATAGCTAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:32758 original size:33 final size:32
Alignment explanation
Indices: 32712--32780 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
32702 TTTGGTTCGC
*
32712 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAAAGG
32744 TGTATTGGGATTAGAGGTGTATTGGATTAAAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAAAGG
32777 TGTA
1 TGTA
32781 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAAAGG
Found at i:33037 original size:18 final size:19
Alignment explanation
Indices: 33016--33052 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
33006 TTATTATTAA
33016 ATAT-ATTT-TAATTAAAAT
1 ATATAATTTATAA-TAAAAT
33034 ATATAATTTATAATAAAAT
1 ATATAATTTATAATAAAAT
33053 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 10 0.59
20 3 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATTTATAATAAAAT
Found at i:48658 original size:20 final size:21
Alignment explanation
Indices: 48630--48669 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
48620 ACGAGTTATT
48630 AGTACACTAACAAAA-AAAAA
1 AGTACACTAACAAAATAAAAA
*
48650 AGTATACTAACAAAATAAAA
1 AGTACACTAACAAAATAAAA
48670 GTAATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.68, C:0.12, G:0.05, T:0.15
Consensus pattern (21 bp):
AGTACACTAACAAAATAAAAA
Found at i:51508 original size:16 final size:16
Alignment explanation
Indices: 51487--51536 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
51477 CGAAAATGAT
51487 ATAATAAGTATAATAA
1 ATAATAAGTATAATAA
*
51503 ATAAT-AGTGTAA-AA
1 ATAATAAGTATAATAA
*
51517 A-AATAA-TACAATAA
1 ATAATAAGTATAATAA
51531 ATAATA
1 ATAATA
51537 GGAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 6 0.21
14 7 0.25
15 10 0.36
16 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (16 bp):
ATAATAAGTATAATAA
Found at i:53029 original size:133 final size:132
Alignment explanation
Indices: 52775--53398 Score: 816
Period size: 133 Copynumber: 4.7 Consensus size: 132
52765 GATCTACTGT
* * * *
52775 AATTTGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTGTATGTTTAGCCTACTTCACTCCT
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGTA--TATAGCCTGCTTCACTCCT
* * ** * * * * ** * * *
52840 GCTCAATGAAGATAAGGCTGGTGGCTGAAATCTACTCCATTGCCGATATATAGAGATAAGACTCG
64 GCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCA
52905 CCAA
129 CCAA
* *
52909 AATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTAGTATATAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCT-GTATATAGCCTGCTTCACTCCTG
* *
52974 CTCAGTGAAGATAAGGCTGGTGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAT
65 CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAC
53039 CAA
130 CAA
* * * * * *
53042 AATTCGATCTGCTTCACTTCTGCTCAGTGAATATAAGATCTGGTATTTAGCCTGCTCCACTCCTA
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCT-GTATATAGCCTGCTTCACTCCTG
* * *
53107 CTCAGTGAAGACAAGGCTGATGATTGGAATCTGCTTCATCGCCGGTACGTGGAGATAAGATTCAT
65 CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAC
53172 CAA
130 CAA
* * * *
53175 AATTCGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTGGTTTATAGCCTGCTTCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCT-GTATATAGCCTGCTTCACTCCTG
*
53240 CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATTGCCGGTACGTGGAGATAAGATTCAC
65 CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAC
53305 CAA
130 CAA
* * * *
53308 AATTTGATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCTGCTATATTTAACCTGCTTCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTG-TATA--TAGCCTGCTTCACTCC
*
53373 TGCTCAGTGAAGATAAGACTGATGAT
63 TGCTCAGTGAAGATAAGGCTGATGAT
53399 ATCTGTAATC
Statistics
Matches: 436, Mismatches: 50, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
132 1 0.00
133 354 0.81
134 38 0.09
135 43 0.10
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (132 bp):
AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGTATATAGCCTGCTTCACTCCTGC
TCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACC
AA
Done.