Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 32 of 97
Found at i:13428311 original size:28 final size:30
Alignment explanation
Indices: 13428270--13428329 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
13428260 GTCTATGGGC
*
13428270 AATTTTTCAGTTTT-TGG-GGCAAAAATGT
1 AATTTTTCACTTTTATGGAGGCAAAAATGT
* *
13428298 AATTTTTGACTTTTATGGAGGCAAAAGTGT
1 AATTTTTCACTTTTATGGAGGCAAAAATGT
13428328 AA
1 AA
13428330 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 3 0.11
30 12 0.44
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.40
Consensus pattern (30 bp):
AATTTTTCACTTTTATGGAGGCAAAAATGT
Found at i:13443309 original size:35 final size:33
Alignment explanation
Indices: 13443270--13443365 Score: 93
Period size: 34 Copynumber: 2.8 Consensus size: 33
13443260 CCCCGTTGTG
13443270 GGCTTTATTCATGTGGTATTCTTACCCTTACAATA
1 GGCTTTATTCATGTGGTATTCTTACCC--ACAATA
* * * * * *
13443305 GGCTTAATTTAAGTGCTATTTTTACTCCACGATA
1 GGCTTTATTCATGTGGTATTCTTAC-CCACAATA
* *
13443339 GGCCTTATTCATGTGGTACTCTTACCC
1 GGCTTTATTCATGTGGTATTCTTACCC
13443366 CCCACATTGG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
33 2 0.04
34 23 0.49
35 20 0.43
36 2 0.04
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (33 bp):
GGCTTTATTCATGTGGTATTCTTACCCACAATA
Found at i:13445352 original size:20 final size:20
Alignment explanation
Indices: 13445327--13445365 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13445317 TTTTGGATAG
*
13445327 CAAAGTCTCAATACCTTTTC
1 CAAAGTCTCAAGACCTTTTC
13445347 CAAAGTCTCAAGACCTTTT
1 CAAAGTCTCAAGACCTTTT
13445366 TCTTCTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (20 bp):
CAAAGTCTCAAGACCTTTTC
Found at i:13454854 original size:23 final size:23
Alignment explanation
Indices: 13454826--13454869 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
13454816 CTAATTATCG
13454826 ATATTATATATATATATATATAT
1 ATATTATATATATATATATATAT
* * *
13454849 ATATTATTTTTTTATATATAT
1 ATATTATATATATATATATAT
13454870 TTTCTTCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATTATATATATATATATATAT
Found at i:13462066 original size:19 final size:19
Alignment explanation
Indices: 13462044--13462195 Score: 64
Period size: 18 Copynumber: 7.7 Consensus size: 19
13462034 ATTTTATAAA
13462044 ATTATTTTAATTTTATTTT
1 ATTATTTTAATTTTATTTT
* * * *
13462063 ATTA-TTAAATATTAATTA
1 ATTATTTTAATTTTATTTT
* *
13462081 AAT-TTTTAATTTTAATTT
1 ATTATTTTAATTTTATTTT
*
13462099 AGTTATTTTTAATTAT-TTTT
1 A-TTA-TTTTAATTTTATTTT
*
13462119 A-TA-ATTAATTTATATTTAAAT
1 ATTATTTTAATTT-TATTT---T
13462140 AAGTTATTTTAATTTTATATTT
1 -A-TTATTTTAATTTTAT-TTT
* *
13462162 ATTTTTTTAAATTTGATTATT
1 ATTATTTT-AATTTTATT-TT
*
13462183 ATT-TATTAATTTT
1 ATTATTTTAATTTT
13462196 TATGTTTTTA
Statistics
Matches: 99, Mismatches: 18, Indels: 32
0.66 0.12 0.21
Matches are distributed among these distances:
16 6 0.06
17 1 0.01
18 29 0.29
19 10 0.10
20 14 0.14
21 23 0.23
22 2 0.02
24 5 0.05
25 9 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTTTAATTTTATTTT
Found at i:13464591 original size:45 final size:45
Alignment explanation
Indices: 13464541--13464750 Score: 262
Period size: 45 Copynumber: 4.7 Consensus size: 45
13464531 AATGTTACAC
*
13464541 GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCGTGTCACAA
1 GCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTGTCACAA
* * * * *
13464586 GCCATGTACAAAAACCTATGACAAATCATGGTTAGCATGTTACAC
1 GCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTGTCACAA
* * *
13464631 GCCATGTACAAAAACCTGTGATAAGTCATGGTTAGCGTGTTACAC
1 GCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTGTCACAA
* * *
13464676 GCCAAGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACACAA
1 GCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTG-T-CACAA
**
13464723 --CATGTACAAAAATATGTGACAAGTCATG
1 GCCATGTACAAAAACCTGTGACAAGTCATG
13464751 TACAAAAACT
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
45 139 0.97
46 1 0.01
47 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (45 bp):
GCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTGTCACAA
Found at i:13464685 original size:90 final size:90
Alignment explanation
Indices: 13464532--13464750 Score: 321
Period size: 90 Copynumber: 2.4 Consensus size: 90
13464522 ACACGCTATA
* *
13464532 ATGTTACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCGTGTCACAAGCCATGTACAA
1 ATGTTACACGCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTGTCACAAGCCAAGTACAA
*
13464597 AAACCTATGACAAATCATGGTTAGC
66 AAACCTATGACAAACCATGGTTAGC
* * *
13464622 ATGTTACACGCCATGTACAAAAACCTGTGATAAGTCATGGTTAGCGTGTTACACGCCAAGTACAA
1 ATGTTACACGCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTGTCACAAGCCAAGTACAA
* *
13464687 AAACCTGTGACAAGCCATGGTTAGC
66 AAACCTATGACAAACCATGGTTAGC
* ** **
13464712 TTGTTACACAACATGTACAAAAATATGTGACAAGTCATG
1 ATGTTACACGCCATGTACAAAAACCTGTGACAAGTCATG
13464751 TACAAAAACT
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 115 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (90 bp):
ATGTTACACGCCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTGTCACAAGCCAAGTACAA
AAACCTATGACAAACCATGGTTAGC
Found at i:13464750 original size:24 final size:24
Alignment explanation
Indices: 13464723--13464768 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
13464713 TGTTACACAA
13464723 CATGTACAAAAA-TATGTGACAAGT
1 CATGTACAAAAACT-TGTGACAAGT
13464747 CATGTACAAAAACTTGTGACAA
1 CATGTACAAAAACTTGTGACAA
13464769 ATTATGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (24 bp):
CATGTACAAAAACTTGTGACAAGT
Found at i:13464765 original size:69 final size:69
Alignment explanation
Indices: 13464681--13464819 Score: 197
Period size: 69 Copynumber: 2.0 Consensus size: 69
13464671 TACACGCCAA
* *
13464681 GTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACACAACATGTACAAAAATATGTGACAAG
1 GTACAAAAACCTGTGACAAACCATGGTTAGCTTGTTACACAACATGTACAAAAACATGTGACAAG
13464746 TCAT
66 TCAT
* ** ** * *
13464750 GTACAAAAACTTGTGACAAATTATGGTTAGCTTGTTACACGCCATGTACAAAAACCTGTGATAAG
1 GTACAAAAACCTGTGACAAACCATGGTTAGCTTGTTACACAACATGTACAAAAACATGTGACAAG
13464815 TCAT
66 TCAT
13464819 G
1 G
13464820 GTTAGGTTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (69 bp):
GTACAAAAACCTGTGACAAACCATGGTTAGCTTGTTACACAACATGTACAAAAACATGTGACAAG
TCAT
Found at i:13464848 original size:45 final size:45
Alignment explanation
Indices: 13464747--13464841 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
13464737 TGTGACAAGT
* *
13464747 CATGTACAAAAACTTGTGACAAATTATGGTTAGCTTGTTACACGC
1 CATGTACAAAAACCTGTGACAAATCATGGTTAGCTTGTTACACGC
* * *
13464792 CATGTACAAAAACCTGTGATAAGTCATGGTTAGGTTGTTACACGC
1 CATGTACAAAAACCTGTGACAAATCATGGTTAGCTTGTTACACGC
13464837 CATGT
1 CATGT
13464842 TAAAAAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (45 bp):
CATGTACAAAAACCTGTGACAAATCATGGTTAGCTTGTTACACGC
Found at i:13464859 original size:30 final size:27
Alignment explanation
Indices: 13464825--13464932 Score: 100
Period size: 26 Copynumber: 4.0 Consensus size: 27
13464815 TCATGGTTAG
13464825 GTTGTTACACGCCATGTTAAAAAAAATA
1 GTTGTTACACGCCATGTT-AAAAAAATA
* * * *
13464853 TTGTTGTTACAGGCAATG-TACAAAAACA
1 --GTTGTTACACGCCATGTTAAAAAAATA
13464881 --TGTTACACGCCATGGTT-AAAAAA-A
1 GTTGTTACACGCCAT-GTTAAAAAAATA
13464905 GTTGTTACACGCCATGTTGAAAAAAATA
1 GTTGTTACACGCCATGTT-AAAAAAATA
13464933 TTATTGTTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
24 12 0.19
25 9 0.14
26 14 0.22
27 6 0.09
28 8 0.12
29 1 0.02
30 14 0.22
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (27 bp):
GTTGTTACACGCCATGTTAAAAAAATA
Found at i:13464872 original size:75 final size:76
Alignment explanation
Indices: 13464781--13464943 Score: 193
Period size: 80 Copynumber: 2.1 Consensus size: 76
13464771 TATGGTTAGC
* * * * *
13464781 TTGTTACACGCCATGTACAAAAACCTGTGATAAGTCATGGTT-AGGTTGTTACACGCCATGTTAA
1 TTGTTACACGCAATGTACAAAAACATGTGACAAGCCATGGTTAAAGTTGTTACACGCCATGTTAA
*
13464845 AAAAAATATTG
66 AAAAAATATTA
* * *
13464856 TTGTTACAGGCAATGTACAAAAACATGTTACACGCCATGGTTAAAAAAAGTTGTTACACGCCATG
1 TTGTTACACGCAATGTACAAAAACATGTGACAAGCCATGGTT----AAAGTTGTTACACGCCATG
*
13464921 TTGAAAAAAATATTA
62 TTAAAAAAAATATTA
13464936 TTGTTACA
1 TTGTTACA
13464944 TGACATATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
75 35 0.48
80 38 0.52
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (76 bp):
TTGTTACACGCAATGTACAAAAACATGTGACAAGCCATGGTTAAAGTTGTTACACGCCATGTTAA
AAAAAATATTA
Found at i:13470071 original size:318 final size:317
Alignment explanation
Indices: 13469463--13470097 Score: 862
Period size: 318 Copynumber: 2.0 Consensus size: 317
13469453 AGGTTGTGCA
*
13469463 AGTGACATGATGAGATGCACTAAGTCAACTAACCACTTGGGGGATGATGCTTTTGTTCTAACATA
1 AGTGACATGATCAGATGCACTAAGTCAACTAACCACTTGGGGGATGATGCTTTTGTTCTAACATA
** * * * * *
13469528 ATTAGTAGTTGGAATAGAAGACTTAGGTCTGATTTTGAAGCAATGGTTGGCAGAGTGTCTGAGTT
66 ATTAACAATTGGAATAAAAGACTTAAGTCTGATTTTAAAGCAATGGTTGGCAGAGAGTCTGAGTT
* *
13469593 TATCACAGAACTAATAAACAACCTTGAAGTTGAAATAAGATGAATTCTTGGAAGAATTAGATGGT
131 TATCACAGAACTAACAAACAACCTTGAAGTTGAAATAAGATGAATTCTTGGAAGAATTAGATGAT
* ** *
13469658 GATGAAAATTTGATATTTTGAGGAGGTCAAGGTTGCTTTGGTATACCAGAATGAGAACAAATAAT
196 GAGGAAAACCTAATATTTTGAGGAGGTCAAGGTTGCTTTGGTATACCAGAATGAGAACAAATAAT
** * *
13469723 TTTGGCAGCAAGATAAGTAGAAAGGATGATAATATCAGTTGATGATTCTTGTTTCTT
261 TTTAACAGCAAGATAAGCAGAAAGGATGATAATATCAGTTGATGATTCTTATTTCTT
* * ** *
13469780 AGTGACATGATCAGATGCACCTGAGTCAACTAACCATTTGGGGGATGATGCTTTTGTTCTGGCGT
1 AGTGACATGATCAGATGCA-CTAAGTCAACTAACCACTTGGGGGATGATGCTTTTGTTCTAACAT
* * * *
13469845 GATTAACAATTGGAATAAAAGACTTAAGTTTTATTTTAAAGCAATGCG-TGGTAGAGAGTCTGAG
65 AATTAACAATTGGAATAAAAGACTTAAGTCTGATTTTAAAGCAATG-GTTGGCAGAGAGTCTGAG
* *
13469909 TTTATCACAGAACTGACAAACAACCTTGAAGTTGGAATGAA-ATGAATTCTTGGAAGAATTAGAT
129 TTTATCACAGAACTAACAAACAACCTTGAAGTTGAAAT-AAGATGAATTCTTGGAAGAATTAGAT
** * *
13469973 GATGAGGAAAACCTAATATTTTGAGGAGGTTGAGGTTGCTTTGGTCTACCAGAATGAGAAGAAAT
193 GATGAGGAAAACCTAATATTTTGAGGAGGTCAAGGTTGCTTTGGTATACCAGAATGAGAACAAAT
* ** * * *
13470038 AGTTTTAACAGCAAGATGGGCA-ATAGAGATGATAATATTAGTTGATGTTTCTTATTTCTT
258 AATTTTAACAGCAAGATAAGCAGAAAG-GATGATAATATCAGTTGATGATTCTTATTTCTT
13470098 GATAACTTTT
Statistics
Matches: 275, Mismatches: 39, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
317 21 0.08
318 251 0.91
319 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (317 bp):
AGTGACATGATCAGATGCACTAAGTCAACTAACCACTTGGGGGATGATGCTTTTGTTCTAACATA
ATTAACAATTGGAATAAAAGACTTAAGTCTGATTTTAAAGCAATGGTTGGCAGAGAGTCTGAGTT
TATCACAGAACTAACAAACAACCTTGAAGTTGAAATAAGATGAATTCTTGGAAGAATTAGATGAT
GAGGAAAACCTAATATTTTGAGGAGGTCAAGGTTGCTTTGGTATACCAGAATGAGAACAAATAAT
TTTAACAGCAAGATAAGCAGAAAGGATGATAATATCAGTTGATGATTCTTATTTCTT
Found at i:13471027 original size:27 final size:27
Alignment explanation
Indices: 13470974--13471027 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
13470964 ATATTACAAA
* *
13470974 GATAATATAGTTATCAAAATACTAGTT
1 GATAAGATAGTTATCAAAATACAAGTT
* *
13471001 GATAAGATAGTTATCACAATTCAAGTT
1 GATAAGATAGTTATCAAAATACAAGTT
13471028 TTGATAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (27 bp):
GATAAGATAGTTATCAAAATACAAGTT
Found at i:13471492 original size:24 final size:24
Alignment explanation
Indices: 13471452--13471525 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
13471442 TTTTCGATTT
*
13471452 TGGTTT-GATGTTAGGAATTGTTCA
1 TGGTTTGGA-GTTTGGAATTGTTCA
13471476 TGGTTTGGAGTTTGGAATTGTTCA
1 TGGTTTGGAGTTTGGAATTGTTCA
13471500 TGGTTTGGAGTTTGGAATTGTTCA
1 TGGTTTGGAGTTTGGAATTGTTCA
13471524 TG
1 TG
13471526 ATTGATATGT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.18, C:0.04, G:0.32, T:0.46
Consensus pattern (24 bp):
TGGTTTGGAGTTTGGAATTGTTCA
Found at i:13471748 original size:9 final size:9
Alignment explanation
Indices: 13471712--13471750 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
13471702 TATTTGTAAT
*
13471712 TTAATTGTG
1 TTAAATGTG
13471721 -TAAATGTG
1 TTAAATGTG
*
13471729 TAAAATGTG
1 TTAAATGTG
13471738 TTAAATGTG
1 TTAAATGTG
13471747 TTAA
1 TTAA
13471751 TCGTTATTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.44
Consensus pattern (9 bp):
TTAAATGTG
Found at i:13471968 original size:23 final size:23
Alignment explanation
Indices: 13471938--13471989 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
13471928 CCATATATTG
13471938 ATACGACATGATTAGACATGCGA
1 ATACGACATGATTAGACATGCGA
13471961 ATACGACATGATTAGACATGCGA
1 ATACGACATGATTAGACATGCGA
13471984 ATACGA
1 ATACGA
13471990 ATTGTGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (23 bp):
ATACGACATGATTAGACATGCGA
Found at i:13473107 original size:63 final size:63
Alignment explanation
Indices: 13473003--13473428 Score: 404
Period size: 66 Copynumber: 6.6 Consensus size: 63
13472993 TTTTGCTATC
* * * * *
13473003 AAATTGACATCCAGTTTTGCTATCAATCCATCCATGCATTAGATCCAAGATTGAAAATATTCG
1 AAATTGACATCGAGTTTTGCTATCGATCCATCCATGAATTAGATCCAAGATTGGAAATCTTCG
* * * * *
13473066 AAATTGACATCAAGTTTTGCTATCCATCTATCCGTGAATTAGATCCAAAATTGGAAATCTTCG
1 AAATTGACATCGAGTTTTGCTATCGATCCATCCATGAATTAGATCCAAGATTGGAAATCTTCG
* * * * * * * *
13473129 GAATTGACATTGGGTTTTGCTAT-TAGTCTATCCATGAATTGGATCTAAGATTGGAAATCTTTG
1 AAATTGACATCGAGTTTTGCTATCGA-TCCATCCATGAATTAGATCCAAGATTGGAAATCTTCG
* * * * *
13473192 AAATTAACATCGAGTTTTGTTATCGATCCATCCACGAATCCATGGATCCAAGATTGGAAATCCTC
1 AAATTGACATCGAGTTTTGCTATCGATCCATCCATGAAT---TAGATCCAAGATTGGAAATCTTC
*
13473257 A
63 G
* * * * * * * **
13473258 AAATTGATATTGGGTTTTGCTATTGGTCCATCCATGAACCTTTAAATCCAAGATTGAAAATCCCC
1 AAATTGACATCGAGTTTTGCTATCGATCCATCCATGAA---TTAGATCCAAGATTGGAAATCTTC
13473323 G
63 G
* * * *
13473324 AAATTGACATCAAGTTTTGCTATTGATCCATCCATGAACCCTTGGATCCAAGATTGGAAATCTCC
1 AAATTGACATCGAGTTTTGCTATCGATCCATCCATGAA---TTAGATCCAAGATTGGAAATCTTC
13473389 G
63 G
* *
13473390 GAATTGACATCGAGTTTTGCTATCGATCCATCTATGAAT
1 AAATTGACATCGAGTTTTGCTATCGATCCATCCATGAAT
13473429 CCCCTATTGT
Statistics
Matches: 298, Mismatches: 57, Indels: 16
0.80 0.15 0.04
Matches are distributed among these distances:
62 1 0.00
63 136 0.46
64 1 0.00
66 159 0.53
69 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (63 bp):
AAATTGACATCGAGTTTTGCTATCGATCCATCCATGAATTAGATCCAAGATTGGAAATCTTCG
Found at i:13474707 original size:52 final size:52
Alignment explanation
Indices: 13474646--13474750 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
13474636 TTTTTCAAGA
* *
13474646 GGTGGTGTGGACACAACATTTTTTATATAGAACAAAAGGGATTTTTCTTGTT
1 GGTGGTGTGGACACAACATTTTTTATAAAGAACAAAAAGGATTTTTCTTGTT
*
13474698 GGTGGTGTGGATACAACATTTTTTATAAAGAACAAAAAGGATTTTTCTTGTT
1 GGTGGTGTGGACACAACATTTTTTATAAAGAACAAAAAGGATTTTTCTTGTT
13474750 G
1 G
13474751 ATCAAATCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (52 bp):
GGTGGTGTGGACACAACATTTTTTATAAAGAACAAAAAGGATTTTTCTTGTT
Found at i:13476951 original size:17 final size:15
Alignment explanation
Indices: 13476919--13476952 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
13476909 TTTTAAAGTC
13476919 AAAAAATTAAAAATT
1 AAAAAATTAAAAATT
13476934 AAAAAATATAAAAGATT
1 AAAAAAT-TAAAA-ATT
13476951 AA
1 AA
13476953 GTGTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAAATTAAAAATT
Found at i:13478043 original size:16 final size:18
Alignment explanation
Indices: 13478012--13478044 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
13478002 GTTTTTCCCT
13478012 TTCCAATTTCGATTTTTA
1 TTCCAATTTCGATTTTTA
13478030 TTCC-ATTT-GATTTTT
1 TTCCAATTTCGATTTTT
13478045 CAAATTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.61
Consensus pattern (18 bp):
TTCCAATTTCGATTTTTA
Found at i:13509843 original size:2 final size:2
Alignment explanation
Indices: 13509836--13509860 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13509826 GCTTTGCTAA
13509836 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
13509861 ATTTTCTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13514565 original size:25 final size:25
Alignment explanation
Indices: 13514537--13514587 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
13514527 CGGAACCACG
13514537 TTTTATATATTGATAATGTTAGAAT
1 TTTTATATATTGATAATGTTAGAAT
* *
13514562 TTTTTTTTATTGATAATGTTAGAAT
1 TTTTATATATTGATAATGTTAGAAT
13514587 T
1 T
13514588 GGTATAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (25 bp):
TTTTATATATTGATAATGTTAGAAT
Found at i:13515368 original size:27 final size:29
Alignment explanation
Indices: 13515338--13515409 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
13515328 CATTAAAGTG
*
13515338 TAACAA-AATGTTTTTGAAT-ATGGCGTA
1 TAACAACAATATTTTTGAATCATGGCGTA
** *
13515365 TAACAACAATATTTTTTCATCATGGCGTG
1 TAACAACAATATTTTTGAATCATGGCGTA
*
13515394 TAACAACAATTTTTTT
1 TAACAACAATATTTTT
13515410 TTTCAACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 6 0.16
28 10 0.26
29 22 0.58
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (29 bp):
TAACAACAATATTTTTGAATCATGGCGTA
Found at i:13515406 original size:26 final size:27
Alignment explanation
Indices: 13515335--13515455 Score: 104
Period size: 31 Copynumber: 4.3 Consensus size: 27
13515325 AAGCATTAAA
* *
13515335 GTGTAACAA-AATGTTTTTGAATATGGC
1 GTGTAACAACAAT-TTTTTCAACATGGC
* *
13515362 GTATAACAACAATATTTTTTCATCATGGC
1 GTGTAACAAC-A-ATTTTTTCAACATGGC
13515391 GTGTAACAACAATTTTTTTTTTCAACATGGC
1 GTGTAACAACAA----TTTTTTCAACATGGC
*
13515422 GTGTAACAAC-ATTTTTT-AACCATGGT
1 GTGTAACAACAATTTTTTCAA-CATGGC
13515448 GTGTAACA
1 GTGTAACA
13515456 TGTTTTTGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 17
0.77 0.07 0.17
Matches are distributed among these distances:
25 2 0.03
26 19 0.24
27 9 0.11
28 1 0.01
29 21 0.27
30 3 0.04
31 24 0.30
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (27 bp):
GTGTAACAACAATTTTTTCAACATGGC
Found at i:13515414 original size:31 final size:31
Alignment explanation
Indices: 13515348--13515438 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
13515338 TAACAAAATG
* * * *
13515348 TTTTTGAATATGGCGTATAACAACAA--TAT
1 TTTTTCAACATGGCGTGTAACAACAATTTTT
*
13515377 TTTTTCATCATGGCGTGTAACAACAATTTTT
1 TTTTTCAACATGGCGTGTAACAACAATTTTT
13515408 TTTTTCAACATGGCGTGTAACAAC-ATTTTT
1 TTTTTCAACATGGCGTGTAACAACAATTTTT
13515438 T
1 T
13515439 AACCATGGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
29 22 0.41
30 7 0.13
31 25 0.46
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTTTCAACATGGCGTGTAACAACAATTTTT
Found at i:13515436 original size:29 final size:29
Alignment explanation
Indices: 13515348--13515438 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
13515338 TAACAAAATG
* * * * *
13515348 TTTTTGAATATGGCGTATAACAACAATAT
1 TTTTTCAACATGGCGTGTAACAACATTTT
*
13515377 TTTTTCATCATGGCGTGTAACAACAATTTTT
1 TTTTTCAACATGGCGTGTAACAAC-A-TTTT
13515408 TTTTTCAACATGGCGTGTAACAACATTTT
1 TTTTTCAACATGGCGTGTAACAACATTTT
13515437 TT
1 TT
13515439 AACCATGGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.49
30 2 0.04
31 25 0.47
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTTTCAACATGGCGTGTAACAACATTTT
Found at i:13515462 original size:26 final size:26
Alignment explanation
Indices: 13515348--13515481 Score: 76
Period size: 26 Copynumber: 4.9 Consensus size: 26
13515338 TAACAAAATG
* * *
13515348 TTTTTGAATATGGCGTATAACAACAATAT
1 TTTTTCAACATGGCGTGTAACAAC--T-T
*
13515377 TTTTTCATCATGGCGTGTAACAACAATTTTT
1 TTTTTCAACATGGCGTGTAACAAC-----TT
*
13515408 TTTTTCAACATGGCGTGTAACAACAT
1 TTTTTCAACATGGCGTGTAACAACTT
* **
13515434 TTTTT-AACCATGGTGTGTAACATGTT
1 TTTTTCAA-CATGGCGTGTAACAACTT
* *
13515460 TTTGT-AA-ATGACGTGTAACAAC
1 TTTTTCAACATGGCGTGTAACAAC
13515482 AGTATTTTTT
Statistics
Matches: 84, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
24 11 0.13
25 2 0.02
26 26 0.31
29 20 0.24
31 24 0.29
32 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (26 bp):
TTTTTCAACATGGCGTGTAACAACTT
Found at i:13515507 original size:55 final size:55
Alignment explanation
Indices: 13515447--13515551 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
13515437 TTAACCATGG
* *
13515447 TGTGTAACATGTTTTTGTAAAT-GACGTGTAACAACAGTATTTTTTTTCAATACGA
1 TGTGTAACATGTTTTTGTAAATGGA-GTATAACAACAATATTTTTTTTCAATACGA
*
13515502 TGTGTAACATGTTTTTGTACATGGAGTATAACAACAATATTTTTTTTCAA
1 TGTGTAACATGTTTTTGTAAATGGAGTATAACAACAATATTTTTTTTCAA
13515552 CATGGCATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
55 44 0.96
56 2 0.04
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (55 bp):
TGTGTAACATGTTTTTGTAAATGGAGTATAACAACAATATTTTTTTTCAATACGA
Found at i:13515563 original size:55 final size:55
Alignment explanation
Indices: 13515449--13515565 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 55
13515439 AACCATGGTG
* * * **
13515449 TGTAACATGTTTTTGTAAATGACGTGTAACAACAGTATTTTTTTTCAATACGATG
1 TGTAACATGTTTTTGTAAATGACGTATAACAACAATATTTTTTTTCAACACGACA
* * *
13515504 TGTAACATGTTTTTGTACATGGA-GTATAACAACAATATTTTTTTTCAACATGGCA
1 TGTAACATGTTTTTGTAAAT-GACGTATAACAACAATATTTTTTTTCAACACGACA
13515559 TGTAACA
1 TGTAACA
13515566 ACCTAACCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 51 0.96
56 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (55 bp):
TGTAACATGTTTTTGTAAATGACGTATAACAACAATATTTTTTTTCAACACGACA
Found at i:13515605 original size:24 final size:24
Alignment explanation
Indices: 13515578--13515629 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
13515568 CTAACCATAT
* *
13515578 CGTGCTACATATTTTTGTATATGG
1 CGTGCTACACATTTTTGTACATGG
* *
13515602 CGTGTTACACGTTTTTGTACATGG
1 CGTGCTACACATTTTTGTACATGG
13515626 CGTG
1 CGTG
13515630 TAATAATCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.42
Consensus pattern (24 bp):
CGTGCTACACATTTTTGTACATGG
Found at i:13515897 original size:20 final size:20
Alignment explanation
Indices: 13515850--13515898 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
13515840 ACATTATGAT
13515850 AATATTTTTAAATGTGATAA
1 AATATTTTTAAATGTGATAA
*
13515870 AA-AGTTTTTATGAT-TGATAA
1 AATA-TTTTTA-AATGTGATAA
13515890 AATATTTTT
1 AATATTTTT
13515899 GTAATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
AATATTTTTAAATGTGATAA
Found at i:13519654 original size:111 final size:110
Alignment explanation
Indices: 13519460--13519695 Score: 273
Period size: 111 Copynumber: 2.1 Consensus size: 110
13519450 AAATCGTAAG
* ** * *
13519460 ATGTATCAATACATTTGCCTATGTATTGATACATTTGTCATAGATTTTTATTTTTGGCTATTAGA
1 ATGTATCAATACATTTGCCTATATATTGATACATTCATCATAGAATTTTATTTTTGGCTACTAGA
* *
13519525 AGAAATGTATTGGTAGA-TTTGATGATCTATCGATACATGTCCTTGA
66 AGAAATGTATCGATAGATTTTGA--ATCTATCGATACATGTCCTTGA
*
13519571 ATGTATTAATACATTTGTCC-ATATATTGATACATTCATCATAGGAATTTTA-TTTTGGCTACTA
1 ATGTATCAATACATTTG-CCTATATATTGATACATTCATCATA-GAATTTTATTTTTGGCTACTA
* * * *
13519634 GAA-AGATTGTATCGATAGATTTTGCAATCTATTGATACATGTTCTTGC
64 GAAGA-AATGTATCGATAGATTTTG-AATCTATCGATACATGTCCTTGA
*
13519682 ATGTGTCAATACAT
1 ATGTATCAATACAT
13519696 GGGTGAAAGT
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
110 1 0.01
111 91 0.86
112 13 0.12
113 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (110 bp):
ATGTATCAATACATTTGCCTATATATTGATACATTCATCATAGAATTTTATTTTTGGCTACTAGA
AGAAATGTATCGATAGATTTTGAATCTATCGATACATGTCCTTGA
Found at i:13521580 original size:38 final size:39
Alignment explanation
Indices: 13521538--13521640 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 39
13521528 ATAGTGCCTG
*
13521538 TGTGCACGATGTGAGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGTG-GGGGATGTACACGATGGTGC-CGGATA
* * *
13521576 TGTGCACAATGTGGGAGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGG-GGATGTACACGATGGTGCCGGATA
13521616 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGT-GGGGGATGTACA
13521641 TGAGCAGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
37 2 0.04
38 24 0.44
39 4 0.07
40 21 0.39
41 3 0.06
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGATGTACACGATGGTGCCGGATA
Found at i:13522875 original size:88 final size:88
Alignment explanation
Indices: 13522695--13522875 Score: 335
Period size: 88 Copynumber: 2.1 Consensus size: 88
13522685 TTGGAGGTCG
*
13522695 AGTATTATTTTGTTGTGTGTAGACGAACCTAATGTAAATTGTTAAGATACATGTTGTAGACAATG
1 AGTATTATTTTGTTGTGTATAGACGAACCTAATGTAAATTGTTAAGATACATGTTGTAGACAATG
**
13522760 TATATACACTTGTTTGGTATGNG
66 TATATACACTTGTTTGGTATGCC
13522783 AGTATTATTTTGTTGTGTATAGACGAACCTAATGTAAATTGTTAAGATACATGTTGTAGACAATG
1 AGTATTATTTTGTTGTGTATAGACGAACCTAATGTAAATTGTTAAGATACATGTTGTAGACAATG
13522848 TATATACACTTGTTTGGTATGCC
66 TATATACACTTGTTTGGTATGCC
13522871 AGTAT
1 AGTAT
13522876 GAGATGGCAA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.40
Consensus pattern (88 bp):
AGTATTATTTTGTTGTGTATAGACGAACCTAATGTAAATTGTTAAGATACATGTTGTAGACAATG
TATATACACTTGTTTGGTATGCC
Found at i:13527076 original size:2 final size:2
Alignment explanation
Indices: 13527071--13527096 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13527061 TGTATATAAT
13527071 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
13527097 TAGAAAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13533612 original size:16 final size:17
Alignment explanation
Indices: 13533593--13533624 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13533583 CATTTCTTTC
13533593 TTTATTA-ATTTAAAAT
1 TTTATTATATTTAAAAT
13533609 TTTATTATATTTAAAA
1 TTTATTATATTTAAAA
13533625 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTATATTTAAAAT
Found at i:13539285 original size:2 final size:2
Alignment explanation
Indices: 13539278--13539308 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13539268 ATTTTAATCG
13539278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13539309 ATAACGTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13539434 original size:2 final size:2
Alignment explanation
Indices: 13539427--13539457 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13539417 AAATGGATAN
13539427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13539458 ATAACGTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13539487 original size:149 final size:148
Alignment explanation
Indices: 13539278--13539574 Score: 576
Period size: 149 Copynumber: 2.0 Consensus size: 148
13539268 ATTTTAATCG
13539278 ATATATATATATATATATATATATATATATAATAACGTAGGTGATAGGTGCTAATTAAACTAAAA
1 ATATATATATATATATATATATATATATATAATAACGTAGGTGATAGGTGCTAATTAAACTAAAA
13539343 AGAGAAATAAAAATAAAAAAATGTTAATAAATTAGATTAATAATTTTATTTTAAAACTAATTACA
66 AGAGAAATAAAAATAAAAAAATGTTAATAAATTAGATTAATAATTTTATTTTAAAACTAATTACA
13539408 AATCATGAAAAATGGATA
131 AATCATGAAAAATGGATA
13539426 NATATATATATATATATATATATATATATATAATAACGTAGGTGATAGGTGCTAATTAAACTAAA
1 -ATATATATATATATATATATATATATATATAATAACGTAGGTGATAGGTGCTAATTAAACTAAA
*
13539491 AAGAGAAATAAAAATAAAATAATGTTAATAAATTAGATTAATAATTTTATTTTAAAACTAATTAC
65 AAGAGAAATAAAAATAAAAAAATGTTAATAAATTAGATTAATAATTTTATTTTAAAACTAATTAC
13539556 AAATCATGAAAAATGGATA
130 AAATCATGAAAAATGGATA
13539575 TTTAAAAGAG
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.34
Consensus pattern (148 bp):
ATATATATATATATATATATATATATATATAATAACGTAGGTGATAGGTGCTAATTAAACTAAAA
AGAGAAATAAAAATAAAAAAATGTTAATAAATTAGATTAATAATTTTATTTTAAAACTAATTACA
AATCATGAAAAATGGATA
Found at i:13542366 original size:3 final size:3
Alignment explanation
Indices: 13542358--13542385 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13542348 AATAAAGGGA
13542358 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13542386 TTAGCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13544291 original size:16 final size:17
Alignment explanation
Indices: 13544272--13544305 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
13544262 TAAATATTTA
13544272 AGTG-TAAAAAATATAT
1 AGTGTTAAAAAATATAT
13544288 AGTGTTAAAAAATATAT
1 AGTGTTAAAAAATATAT
13544305 A
1 A
13544306 TAAATACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (17 bp):
AGTGTTAAAAAATATAT
Found at i:13546392 original size:7 final size:7
Alignment explanation
Indices: 13546380--13546405 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13546370 ACATGTTAAC
13546380 GTTGACA
1 GTTGACA
13546387 GTTGACA
1 GTTGACA
13546394 GTTGACA
1 GTTGACA
13546401 GTTGA
1 GTTGA
13546406 AAATGAGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.31
Consensus pattern (7 bp):
GTTGACA
Found at i:13562679 original size:19 final size:20
Alignment explanation
Indices: 13562655--13562694 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
13562645 CCATTTGACT
13562655 TATTGGAGTATGATTT-AAG
1 TATTGGAGTATGATTTGAAG
13562674 TATTGGAGTATGATTTGAAG
1 TATTGGAGTATGATTTGAAG
13562694 T
1 T
13562695 TTAGAAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (20 bp):
TATTGGAGTATGATTTGAAG
Found at i:13570159 original size:233 final size:233
Alignment explanation
Indices: 13569752--13570218 Score: 880
Period size: 233 Copynumber: 2.0 Consensus size: 233
13569742 AAGTTAAGTT
13569752 AACTTGGTTTGGATAATGAGACAATATTATTATAATTCATAATATGATCTAATAATGTGGGTTAG
1 AACTTGGTTTGGATAATGAGACAATATTATTATAATTCATAATATGATCTAATAATGTGGGTTAG
13569817 GTTTTTATAGTCCACATAGCTTAATGCGTATGCCTGTATAAAAAGTCTTAAATCCGATAATGAAT
66 GTTTTTATAGTCCACATAGCTTAATGCGTATGCCTGTATAAAAAGTCTTAAATCCGATAATGAAT
13569882 ATACCTAAAAATTCACTCTATAAAAAGAAGGTTATGTCTCATCTTTTGTCTACCATATTGAATTT
131 ATACCTAAAAATTCACTCTATAAAAAGAAGGTTATGTCTCATCTTTTGTCTACCATATTGAATTT
*
13569947 TTCACCCGTTAAACGCATTGTAGAAAACGAGAAGAAGA
196 TTCACCCGTTAAACGCATTATAGAAAACGAGAAGAAGA
* * *
13569985 AACTTGGTTTGGATAATGAGACAATTTTATTATAATTGATAATATGATTTAATAATGTGGGTTAG
1 AACTTGGTTTGGATAATGAGACAATATTATTATAATTCATAATATGATCTAATAATGTGGGTTAG
*
13570050 GTTTTTATAGTCTACATAGCTTAATGCGTATGCCTGTATAAAAAGTCTTAAATCCGATAATGAAT
66 GTTTTTATAGTCCACATAGCTTAATGCGTATGCCTGTATAAAAAGTCTTAAATCCGATAATGAAT
*
13570115 ATACCTAAAACTTCACTCTATAAAAAGAAGGTTATGTCTCATCTTTTGTCTACCATATTGAATTT
131 ATACCTAAAAATTCACTCTATAAAAAGAAGGTTATGTCTCATCTTTTGTCTACCATATTGAATTT
13570180 TTCACCCGTTAAACGCATTATAGAAAACGAGAAGAAGA
196 TTCACCCGTTAAACGCATTATAGAAAACGAGAAGAAGA
13570218 A
1 A
13570219 CATAGTGTAT
Statistics
Matches: 228, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
233 228 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (233 bp):
AACTTGGTTTGGATAATGAGACAATATTATTATAATTCATAATATGATCTAATAATGTGGGTTAG
GTTTTTATAGTCCACATAGCTTAATGCGTATGCCTGTATAAAAAGTCTTAAATCCGATAATGAAT
ATACCTAAAAATTCACTCTATAAAAAGAAGGTTATGTCTCATCTTTTGTCTACCATATTGAATTT
TTCACCCGTTAAACGCATTATAGAAAACGAGAAGAAGA
Found at i:13571648 original size:16 final size:16
Alignment explanation
Indices: 13571627--13571657 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13571617 TATGGTATTG
13571627 ATATTGACAATTAAAA
1 ATATTGACAATTAAAA
13571643 ATATTGACAATTAAA
1 ATATTGACAATTAAA
13571658 GGGAGCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
ATATTGACAATTAAAA
Found at i:13579582 original size:3 final size:3
Alignment explanation
Indices: 13579574--13579615 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
13579564 GCTTTATTCC
13579574 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
13579616 ATTTCTCCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:13581847 original size:2 final size:2
Alignment explanation
Indices: 13581842--13581874 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13581832 TCTCTCTCTC
*
13581842 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13581875 TTATCTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:13594190 original size:235 final size:232
Alignment explanation
Indices: 13593768--13594233 Score: 632
Period size: 235 Copynumber: 2.0 Consensus size: 232
13593758 TGGTGCTCAT
* * * *
13593768 AAAGTGGGCAATTTTAGGTTTATGTTCGAAGGTTAACATGTTTGCTCTCTTGGACAAAAGCTTGT
1 AAAGTGGGCAATTTTAGGTTTATGTTCAAAGGTTAACATGTTTGCTATCCTGGACAAAAGCTTAT
* **
13593833 CCATACCAATGCGAGGAAAAAAAAGTGAACTTAGATGCAATCTAGGCCTAACACCCATTATTATC
66 CCACACCAATGCGAGGAAAAAAAAGCAAACTTAGATGCAATCTAGGCCTAACACCCATTATTATC
* **
13593898 ATTGCTAAGCTCAAGTTAACAGAAACCCAAAAACACATGGTGTTTAAATAATGCATACTATTTCA
131 ATTACTAAGCTCAAGTTAACAGAAACCCAAAAACACATGGTGTACAAATAATGCATACTATTTCA
* *
13593963 CTCTTCAATCTTTCTTGTTGCTACATCACAAGCTCTA
196 CTCTTCAATCTTTCTTGTGGCAACATCACAAGCTCTA
* * *
13594000 AAAGTGGGCAGTTTTAGG-TTATGTTCAAAAGGTTAACATGTTTATGTTATCCTGGAGAAAAGCT
1 AAAGTGGGCAATTTTAGGTTTATGTTC-AAAGGTTAACATG-TT-TGCTATCCTGGACAAAAGCT
* *
13594064 TATCCACACCAATGTGA-GAAAAGAAAAGCAAACTTTGATGCAATCTAGGCCTAACACCCAATTA
63 TATCCACACCAATGCGAGGAAAA-AAAAGCAAACTTAGATGCAATCTAGGCCTAACACCC-ATTA
* * **** *
13594128 TTATCATTACTAAGCTCGAGTTATA-AGAAACCCTATTTGACATGGTGTACAAATACTGCATACT
126 TTATCATTACTAAGCTCAAGTTA-ACAGAAACCCAAAAACACATGGTGTACAAATAATGCATACT
*
13594192 ATTTCACTCTTCCATCTTTCTTGTGGCAACATCACAAGCTCT
190 ATTTCACTCTTCAATCTTTCTTGTGGCAACATCACAAGCTCT
13594234 GAAATTCCTG
Statistics
Matches: 203, Mismatches: 25, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
231 8 0.04
232 29 0.14
233 7 0.03
234 63 0.31
235 95 0.47
236 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (232 bp):
AAAGTGGGCAATTTTAGGTTTATGTTCAAAGGTTAACATGTTTGCTATCCTGGACAAAAGCTTAT
CCACACCAATGCGAGGAAAAAAAAGCAAACTTAGATGCAATCTAGGCCTAACACCCATTATTATC
ATTACTAAGCTCAAGTTAACAGAAACCCAAAAACACATGGTGTACAAATAATGCATACTATTTCA
CTCTTCAATCTTTCTTGTGGCAACATCACAAGCTCTA
Found at i:13602413 original size:33 final size:33
Alignment explanation
Indices: 13602366--13602480 Score: 117
Period size: 33 Copynumber: 3.4 Consensus size: 33
13602356 ACCTTCTACA
* *
13602366 AGATCAAGCGAAACCCTCACAATGTTTTTTACT
1 AGATCAAGCAAAACCCTCACAATGCTTTTTACT
*
13602399 AGATCAAGCAAAACCCTCACAATGGCTTTTCA-T
1 AGATCAAGCAAAACCCTCACAAT-GCTTTTTACT
* * * *
13602432 GGAAGT-AACCATAACCCTCACAAAGCTTTTTACT
1 AG-A-TCAAGCAAAACCCTCACAATGCTTTTTACT
13602466 AGGATCAAGCAAAAC
1 A-GATCAAGCAAAAC
13602481 TCATGGTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
33 32 0.49
34 31 0.48
35 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.24
Consensus pattern (33 bp):
AGATCAAGCAAAACCCTCACAATGCTTTTTACT
Found at i:13607036 original size:18 final size:18
Alignment explanation
Indices: 13607013--13607065 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
13607003 GTAAGTAAAT
13607013 AAATAAATAACAAATGAA
1 AAATAAATAACAAATGAA
* *
13607031 AAATAAGGTAAC-GATGAA
1 AAATAA-ATAACAAATGAA
13607049 AAA-AAATAA-AAATGAA
1 AAATAAATAACAAATGAA
13607065 A
1 A
13607066 TGAAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 9 0.31
17 2 0.07
18 14 0.48
19 4 0.14
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (18 bp):
AAATAAATAACAAATGAA
Found at i:13607039 original size:35 final size:34
Alignment explanation
Indices: 13607000--13607065 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
13606990 TGACATAAGA
13607000 AAGGTAA-G-TAAATAAATAAATAACAAATGAAAAAT
1 AAGGTAACGATAAA-AAA-AAATAA-AAATGAAAAAT
*
13607035 AAGGTAACGATGAAAAAAAATAAAAATGAAA
1 AAGGTAACGATAAAAAAAAATAAAAATGAAA
13607066 TGAAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 8 0.29
35 13 0.46
36 4 0.14
37 3 0.11
ACGTcount: A:0.67, C:0.03, G:0.14, T:0.17
Consensus pattern (34 bp):
AAGGTAACGATAAAAAAAAATAAAAATGAAAAAT
Found at i:13607294 original size:50 final size:50
Alignment explanation
Indices: 13607234--13607719 Score: 521
Period size: 50 Copynumber: 9.6 Consensus size: 50
13607224 TGTGGTTGAA
* * *
13607234 ACAATTTTAAAAACAATTTGAAAAATAAGAC-ACTCCTCATCCGAGGCTCT
1 ACAACTTTAAAATCAATTTGAAAAATAA-ACAACTCCTCATCCGAGGCTCC
*
13607284 ACAACTTTAAAATC-ATTTAGAAAAATAAACAAC-CCTTCATTCGAGGCTCC
1 ACAACTTTAAAATCAATTT-GAAAAATAAACAACTCC-TCATCCGAGGCTCC
* * ** * * * * *
13607334 ACAAGTATAAAATTGATTTGAAAAATAAATAGCTCATCATTCGAGCCTCC
1 ACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTCC
** * *
13607384 ACAACTTTAAAATTGATTTGTAAAAAAATAAACAACTCTTTATCCGAGGCTCC
1 ACAACTTTAAAATCAATTTG---AAAAATAAACAACTCCTCATCCGAGGCTCC
* *
13607437 ACAACTTTAAAAATTAATTTGAAAAATAAACAACTCCTCACCCGAGGCTCC
1 ACAACTTT-AAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTCC
* * *
13607488 ACAACTTTAAAATCATTTTGAAAAATAAACGACTCCACATCCGAGGCTCC
1 ACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTCC
* * ** *
13607538 ACAACTTTAAAATC-ATTTCAAAAAATAAACAACTCTTCATTTGAGGTTCC
1 ACAACTTTAAAATCAATTT-GAAAAATAAACAACTCCTCATCCGAGGCTCC
* * * **
13607588 ATAACTTTAAAATCAATTGGAAAAATAAACAACTCCTCTCATCTGAAACTCC
1 ACAACTTTAAAATCAATTTGAAAAATAAACAACT-C-CTCATCCGAGGCTCC
* * *
13607640 ACAACTTTAAAATCAATTTAAAAAATAAACAACTCATCATCCGAGGCTTC
1 ACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTCC
*
13607690 ACAACTTTAAAAATCAATTTGAAGAATAAA
1 ACAACTTT-AAAATCAATTTGAAAAATAAA
13607720 TCATTTTGAA
Statistics
Matches: 368, Mismatches: 54, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
49 11 0.03
50 209 0.57
51 64 0.17
52 41 0.11
53 32 0.09
54 11 0.03
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (50 bp):
ACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTCC
Found at i:13607598 original size:204 final size:203
Alignment explanation
Indices: 13607234--13607949 Score: 717
Period size: 204 Copynumber: 3.4 Consensus size: 203
13607224 TGTGGTTGAA
* * *
13607234 ACAATTTTAAAAACAATTTGAAAAATAAGAC-ACTCCTCATCCGAGGC-TCTACAACTTTAAAAT
1 ACAACTTTAAAATCAATTTGAAAAATAA-ACAACTCCTCATCCGAGGCTTCCACAACTTTAAAAT
* * * * *
13607297 CATTTAGAAAAATAAACAAC-CCTTCATTCGAGGCTCCACAAGTATAAAATTGATTTGAAAAATA
65 CATTTTGAAAAATAAACAACTCC-TCATCCGAGGCTCCACAACTTTAAAA-TCATTTGAAAAATA
* * * * *
13607361 AATAGCTCATCATTCGAGCCTCCACAACTTTAAAATTGATTTGTAAAAAAATAAACAACT-CTTT
128 AACAACTCATCATTTGAGGCTCCACAACTTTAAAATTAATTTG-AAAAAAATAAACAACTCCTTT
13607425 ATCCGAGGCTCC
192 ATCCGAGGCTCC
* *
13607437 ACAACTTTAAAAATTAATTTGAAAAATAAACAACTCCTCACCCGAGGC-TCCACAACTTTAAAAT
1 ACAACTTT-AAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTCCACAACTTTAAAAT
* * *
13607501 CATTTTGAAAAATAAACGACTCCACATCCGAGGCTCCACAACTTTAAAATCATTTCAAAAAATAA
65 CATTTTGAAAAATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAATCATTT-GAAAAATAA
* * * * * *
13607566 ACAACTCTTCATTTGAGGTTCCATAACTTTAAAATCAA-TTG-GAAAAATAAACAACTCCTCTCA
129 ACAACTCATCATTTGAGGCTCCACAACTTTAAAATTAATTTGAAAAAAATAAACAACTCCT-TTA
* **
13607629 TCTGAAACTCC
193 TCCGAGGCTCC
* *
13607640 ACAACTTTAAAATCAATTTAAAAAATAAACAACTCATCATCCGAGGCTTCACAACTTTAAAAATC
1 ACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTC-C-AC------AA-C
*
13607705 AATTTGAAGAATAAATCATTTTGAAAAATAAACAACTCCTCATCTGAGGCTCCACAACTTTAAAA
57 --TTT-----A-AAATCATTTTGAAAAATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAA
* * * * *
13607770 TCAATTTGAAAAATAAACAATTCCTCACTTGAGGCTCCACAACTTTAAAAATCAATTTGAAAAAC
114 TC-ATTTGAAAAATAAACAACTCATCATTTGAGGCTCCACAACTTT-AAAATTAATTTGAAAAAA
13607835 ATAAACAACTCCTTGGATCATCCGAGGCTCC
177 ATAAACAACTCCTT---T-ATCCGAGGCTCC
* * ** ** *
13607866 ACAACTTTAAAATCATTTTGAAAAATAAACAACTCCTTATTTGAGGCTTAGACAACTTTAAAAAC
1 ACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTCCACAACTTTAAAATC
* *
13607931 AATTTGAAAAATAAGCAAC
66 ATTTTGAAAAATAAACAAC
13607950 ATCCAGGTGT
Statistics
Matches: 424, Mismatches: 57, Indels: 58
0.79 0.11 0.11
Matches are distributed among these distances:
201 14 0.03
202 37 0.09
203 37 0.09
204 126 0.30
205 4 0.01
209 21 0.05
210 1 0.00
211 2 0.00
212 1 0.00
214 3 0.01
215 3 0.01
217 1 0.00
218 2 0.00
219 1 0.00
220 85 0.20
221 12 0.03
222 4 0.01
223 16 0.04
224 2 0.00
226 52 0.12
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (203 bp):
ACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTCCACAACTTTAAAATC
ATTTTGAAAAATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAATCATTTGAAAAATAAAC
AACTCATCATTTGAGGCTCCACAACTTTAAAATTAATTTGAAAAAAATAAACAACTCCTTTATCC
GAGGCTCC
Found at i:13607722 original size:17 final size:17
Alignment explanation
Indices: 13607700--13607736 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13607690 ACAACTTTAA
*
13607700 AAATCAATTTGAAGAAT
1 AAATCAATTTGAAAAAT
*
13607717 AAATCATTTTGAAAAAT
1 AAATCAATTTGAAAAAT
13607734 AAA
1 AAA
13607737 CAACTCCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (17 bp):
AAATCAATTTGAAAAAT
Found at i:13607761 original size:68 final size:67
Alignment explanation
Indices: 13607649--13607791 Score: 216
Period size: 68 Copynumber: 2.1 Consensus size: 67
13607639 CACAACTTTA
* *
13607649 AAATCAATTTAAAAAATAAACAACTCATCATCCGAGGCTTCACAACTTTAAAAATCAATTTGAAG
1 AAATCAATTTAAAAAATAAACAACTCATCATCCGAGGCTCCACAACTTT-AAAATCAATTTGAAA
13607714 AAT
65 AAT
* * * *
13607717 AAATCATTTTGAAAAATAAACAACTCCTCATCTGAGGCTCCACAACTTTAAAATCAATTTGAAAA
1 AAATCAATTTAAAAAATAAACAACTCATCATCCGAGGCTCCACAACTTTAAAATCAATTTGAAAA
13607782 AT
66 AT
13607784 AAA-CAATT
1 AAATCAATT
13607792 CCTCACTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 4 0.06
67 20 0.29
68 44 0.65
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (67 bp):
AAATCAATTTAAAAAATAAACAACTCATCATCCGAGGCTCCACAACTTTAAAATCAATTTGAAAA
AT
Found at i:13607778 original size:50 final size:50
Alignment explanation
Indices: 13607717--13607949 Score: 279
Period size: 50 Copynumber: 4.5 Consensus size: 50
13607707 TTTGAAGAAT
*
13607717 AAATCATTTTGAAAAATAAACAACTCCTCATCTGAGGCTCCACAACTTTA
1 AAATCAATTTGAAAAATAAACAACTCCTCATCTGAGGCTCCACAACTTTA
*
13607767 AAATCAATTTGAAAAATAAACAATTCCTCA-CTTGAGGCTCCACAACTTTAA
1 AAATCAATTTGAAAAATAAACAACTCCTCATC-TGAGGCTCCACAACTTT-A
*
13607818 AAATCAATTTGAAAAACATAAACAACTCCTTGGATCATCCGAGGCTCCACAACTTTA
1 AAATCAATTTG-AAAA-ATAAACAACTCC-----TCATCTGAGGCTCCACAACTTTA
* * * **
13607875 AAATCATTTTGAAAAATAAACAACTCCTTATTTGAGGCTTAGACAACTTTA
1 AAATCAATTTGAAAAATAAACAACTCCTCATCTGAGGC-TCCACAACTTTA
* *
13607926 AAAACAATTTGAAAAATAAGCAAC
1 AAATCAATTTGAAAAATAAACAAC
13607950 ATCCAGGTGT
Statistics
Matches: 159, Mismatches: 13, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
49 1 0.01
50 53 0.33
51 43 0.27
52 4 0.03
53 11 0.07
55 12 0.08
56 4 0.03
57 11 0.07
58 19 0.12
59 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (50 bp):
AAATCAATTTGAAAAATAAACAACTCCTCATCTGAGGCTCCACAACTTTA
Found at i:13607811 original size:118 final size:120
Alignment explanation
Indices: 13607597--13607830 Score: 357
Period size: 118 Copynumber: 2.0 Consensus size: 120
13607587 CATAACTTTA
13607597 AAATCAATTGGAAAAATAAACAACTCCTCTCATCTGAAACTCCACAACTTTAAAATCAATTTAAA
1 AAATCAATTGGAAAAATAAACAACTCCTCTCATCTGAAACTCCACAACTTTAAAATCAATTTAAA
*
13607662 AAATAAACAACTCATCATCCGAGGCTTCACAACTTTAAAAATCAATTTGAAGAAT
66 AAATAAACAACTCATCATCCGAGGCTCCACAACTTTAAAAATCAATTTGAAGAAT
* * ** *
13607717 AAATCATTTTGAAAAATAAACAACT-C-CTCATCTGAGGCTCCACAACTTTAAAATCAATTTGAA
1 AAATCAATTGGAAAAATAAACAACTCCTCTCATCTGAAACTCCACAACTTTAAAATCAATTTAAA
* * *
13607780 AAATAAACAATTCCTCA-CTTGAGGCTCCACAACTTTAAAAATCAATTTGAA
66 AAATAAACAACTCATCATC-CGAGGCTCCACAACTTTAAAAATCAATTTGAA
13607831 AAACATAAAC
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
117 1 0.01
118 79 0.76
119 1 0.01
120 23 0.22
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (120 bp):
AAATCAATTGGAAAAATAAACAACTCCTCTCATCTGAAACTCCACAACTTTAAAATCAATTTAAA
AAATAAACAACTCATCATCCGAGGCTCCACAACTTTAAAAATCAATTTGAAGAAT
Found at i:13607867 original size:58 final size:54
Alignment explanation
Indices: 13607717--13607949 Score: 256
Period size: 51 Copynumber: 4.4 Consensus size: 54
13607707 TTTGAAGAAT
*
13607717 AAATCATTTTGAAAAATAAACAACT-C--C-TCATCTGAGGCTCCACAACTTTA
1 AAATCAATTTGAAAAATAAACAACTCCTTCATCATCTGAGGCTCCACAACTTTA
*
13607767 AAATCAATTTGAAAAATAAACAATTCC-TCA-C-T-TGAGGCTCCACAACTTTAA
1 AAATCAATTTGAAAAATAAACAACTCCTTCATCATCTGAGGCTCCACAACTTT-A
* *
13607818 AAATCAATTTGAAAAACATAAACAACTCCTTGGATCATCCGAGGCTCCACAACTTTA
1 AAATCAATTTG-AAAA-ATAAACAACTCCTT-CATCATCTGAGGCTCCACAACTTTA
* **
13607875 AAATCATTTTGAAAAATAAACAACTCCTT-AT--T-TGAGGCTTAGACAACTTTA
1 AAATCAATTTGAAAAATAAACAACTCCTTCATCATCTGAGGC-TCCACAACTTTA
* *
13607926 AAAACAATTTGAAAAATAAGCAAC
1 AAATCAATTTGAAAAATAAACAAC
13607950 ATCCAGGTGT
Statistics
Matches: 159, Mismatches: 12, Indels: 23
0.82 0.06 0.12
Matches are distributed among these distances:
50 45 0.28
51 46 0.29
52 6 0.04
53 13 0.08
54 1 0.01
55 15 0.09
56 5 0.03
57 12 0.08
58 16 0.10
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (54 bp):
AAATCAATTTGAAAAATAAACAACTCCTTCATCATCTGAGGCTCCACAACTTTA
Found at i:13607868 original size:108 final size:108
Alignment explanation
Indices: 13607744--13607941 Score: 317
Period size: 108 Copynumber: 1.8 Consensus size: 108
13607734 AAACAACTCC
* * *
13607744 TCATCTGAGGCTCCACAACTTTAAAATCAATTTGAAAAATAAACAATTCCTCACTTGAGGC-TCC
1 TCATCCGAGGCTCCACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCACTTGAGGCTTAC
13607808 ACAACTTTAAAAATCAATTTGAAAAACATAAACAACTCCTTGGA
66 ACAACTTTAAAAA-CAATTTGAAAAACATAAACAACTCCTTGGA
* * * *
13607852 TCATCCGAGGCTCCACAACTTTAAAATCATTTTGAAAAATAAACAACTCCTTATTTGAGGCTTAG
1 TCATCCGAGGCTCCACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCACTTGAGGCTTAC
13607917 ACAACTTTAAAAACAATTTGAAAAA
66 ACAACTTTAAAAACAATTTGAAAAA
13607942 TAAGCAACAT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 68 0.83
109 14 0.17
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.28
Consensus pattern (108 bp):
TCATCCGAGGCTCCACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCACTTGAGGCTTAC
ACAACTTTAAAAACAATTTGAAAAACATAAACAACTCCTTGGA
Found at i:13608768 original size:14 final size:14
Alignment explanation
Indices: 13608749--13608786 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
13608739 TTGAAGCCCC
13608749 TTCTTTTTTTCTTA
1 TTCTTTTTTTCTTA
*
13608763 TTCTTTTTGTCTTA
1 TTCTTTTTTTCTTA
13608777 TAT-TTTTTTT
1 T-TCTTTTTTT
13608787 TGGCATAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 20 0.95
15 1 0.05
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (14 bp):
TTCTTTTTTTCTTA
Found at i:13619983 original size:73 final size:73
Alignment explanation
Indices: 13619844--13620025 Score: 217
Period size: 73 Copynumber: 2.5 Consensus size: 73
13619834 GACAGAATGA
* ** * *
13619844 TCTTAGTCGACTAACTGTGCTT-TTAGTCGACTAAGTTGTCTCTGTTTTTTTATCCCAGTTTATG
1 TCTTAGTCGACTAACT-TGCTTCTTAGTCGACTAAGTTGTCTCTGTTCTTGAATCCAAATTTATG
13619908 GCAGTGA-GC
65 GCAGT-ATGC
* * * *
13619917 TCTTAGTCGACTAACTTCCTTCTTAGTCGATTAAGTTGTTTCTG-TCTTGAAGTCCAAATTTCTG
1 TCTTAGTCGACTAACTTGCTTCTTAGTCGACTAAGTTGTCTCTGTTCTTGAA-TCCAAATTTATG
13619981 GCAGTATGC
65 GCAGTATGC
* *
13619990 TCTTAGTCGACTAACTTGCTTCTTGGTCAACTAAGT
1 TCTTAGTCGACTAACTTGCTTCTTAGTCGACTAAGT
13620026 CTTCTCTATT
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
72 9 0.10
73 84 0.90
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (73 bp):
TCTTAGTCGACTAACTTGCTTCTTAGTCGACTAAGTTGTCTCTGTTCTTGAATCCAAATTTATGG
CAGTATGC
Found at i:13621091 original size:20 final size:20
Alignment explanation
Indices: 13621068--13621108 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
13621058 AATGGTGTGA
13621068 ATGTGGTTTGAATGGGAATG
1 ATGTGGTTTGAATGGGAATG
*
13621088 ATGTGGTTTGGATGGGAATG
1 ATGTGGTTTGAATGGGAATG
13621108 A
1 A
13621109 AGAAAAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (20 bp):
ATGTGGTTTGAATGGGAATG
Found at i:13621505 original size:21 final size:23
Alignment explanation
Indices: 13621460--13621505 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
13621450 TTTGGAGGAA
13621460 TAAGAAAGCTGAAAATTTGTGAGG
1 TAAGAAAGCT-AAAATTTGTGAGG
13621484 TAAGAAAGCT-AAATTT-TGAGG
1 TAAGAAAGCTAAAATTTGTGAGG
13621505 T
1 T
13621506 TATGTTGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
24 10 0.45
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.28
Consensus pattern (23 bp):
TAAGAAAGCTAAAATTTGTGAGG
Found at i:13621690 original size:34 final size:34
Alignment explanation
Indices: 13621645--13621772 Score: 159
Period size: 34 Copynumber: 3.7 Consensus size: 34
13621635 TTGGTTGCTG
*
13621645 AAAATTTGAGCTGTTTGCTGCCAATTTGTGCAAA
1 AAAATTAGAGCTGTTTGCTGCCAATTTGTGCAAA
* * *
13621679 AAAATTGGAGCTGTTTGCTGCCAATTTGTGTAGA
1 AAAATTAGAGCTGTTTGCTGCCAATTTGTGCAAA
** *
13621713 AAAATTAGAGCTGTTTGCTGGTAGTTTGTGCAAA
1 AAAATTAGAGCTGTTTGCTGCCAATTTGTGCAAA
13621747 AAAATTAGACAGCT-TTGTGCTGCCAA
1 AAAATTAG--AGCTGTT-TGCTGCCAA
13621773 AATTGGGAAG
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
34 67 0.85
35 2 0.03
36 10 0.13
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (34 bp):
AAAATTAGAGCTGTTTGCTGCCAATTTGTGCAAA
Found at i:13621917 original size:22 final size:22
Alignment explanation
Indices: 13621889--13621936 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
13621879 GAGAGGTAAG
*
13621889 GAAGAGAGGAAGCCACGGTGGT
1 GAAGAGAGAAAGCCACGGTGGT
13621911 GAAGAGAGAAAGCCACGGTGGT
1 GAAGAGAGAAAGCCACGGTGGT
13621933 GAAG
1 GAAG
13621937 GGGAGGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.44, T:0.08
Consensus pattern (22 bp):
GAAGAGAGAAAGCCACGGTGGT
Found at i:13622070 original size:26 final size:25
Alignment explanation
Indices: 13622011--13622074 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
13622001 AAAAAAAAAT
13622011 AAATAGAAAATAAATGGGCATGACC
1 AAATAGAAAATAAATGGGCATGACC
* *
13622036 AAATAGAAAATAAGTGGGCATGGCC
1 AAATAGAAAATAAATGGGCATGACC
*
13622061 CAATATG-AAATAAA
1 AAATA-GAAAATAAA
13622075 AATAAATGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 33 0.97
26 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.20, T:0.17
Consensus pattern (25 bp):
AAATAGAAAATAAATGGGCATGACC
Found at i:13640922 original size:2 final size:2
Alignment explanation
Indices: 13640915--13640967 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
13640905 NNNNNNNNTC
13640915 TA TA TA TA TA TGA TA TA TA TA TA TA TA TA -A TA TA TA -A TA -A
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13640955 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
13640968 TTTAATTAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13640937 original size:17 final size:16
Alignment explanation
Indices: 13640915--13640967 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
13640905 NNNNNNNNTC
13640915 TATATATATATGATATA
1 TATATATATAT-ATATA
13640932 TATATATATATA-ATA
1 TATATATATATATATA
13640947 TATA-ATA-ATATATA
1 TATATATATATATATA
13640961 TATATAT
1 TATATAT
13640968 TTTAATTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.09
14 10 0.29
15 9 0.26
16 1 0.03
17 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TATATATATATATATA
Found at i:13640973 original size:21 final size:20
Alignment explanation
Indices: 13640915--13640973 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 20
13640905 NNNNNNNNTC
*
13640915 TATATATATATGAT-ATATA
1 TATATATATATTATAATATA
13640934 TATATATATAATATATAATAATA
1 TATATATAT-AT-TATAAT-ATA
*
13640957 TATATATATATTTTAAT
1 TATATATATATTATAAT
13640974 TAACTTATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 7 0.21
22 4 0.12
23 12 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATATATATTATAATATA
Found at i:13642668 original size:18 final size:19
Alignment explanation
Indices: 13642647--13642686 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
13642637 ATAAGGTAAC
*
13642647 AATGGAATAAAATAAAA-A
1 AATGAAATAAAATAAAATA
*
13642665 AATGAAATGAAATAAAATA
1 AATGAAATAAAATAAAATA
13642684 AAT
1 AAT
13642687 AATGAAAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (19 bp):
AATGAAATAAAATAAAATA
Found at i:13642678 original size:23 final size:22
Alignment explanation
Indices: 13642647--13642693 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
13642637 ATAAGGTAAC
*
13642647 AATGGAATAAAATAAAAAAATGA
1 AATGAAATAAAAT-AAAAAATGA
*
13642670 AATGAAATAAAATAAATAATGA
1 AATGAAATAAAATAAAAAATGA
13642692 AA
1 AA
13642694 ACGCATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (22 bp):
AATGAAATAAAATAAAAAATGA
Found at i:13643425 original size:12 final size:12
Alignment explanation
Indices: 13643401--13643432 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
13643391 ATGGCTGGCC
13643401 AAAGGAA-AACA
1 AAAGGAAGAACA
13643412 AAAGGAAGAACA
1 AAAGGAAGAACA
13643424 AAA-GAAGAA
1 AAAGGAAGAA
13643433 AAGAAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAGGAAGAACA
Found at i:13646172 original size:17 final size:18
Alignment explanation
Indices: 13646146--13646179 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13646136 CCTTTAACAT
13646146 AATTCACATT-ATATGGA
1 AATTCACATTCATATGGA
*
13646163 AATTCTCATTCATATGG
1 AATTCACATTCATATGG
13646180 TATGTGGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
AATTCACATTCATATGGA
Found at i:13654900 original size:27 final size:28
Alignment explanation
Indices: 13654842--13654894 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
13654832 CTTTAATTAG
*
13654842 TTAAAGGATGATTGATAAAAAACAGTGT
1 TTAAAGGATGATTGATAAAAAAAAGTGT
13654870 TTAAAGG-TGATTGA-AAACAAAAAGT
1 TTAAAGGATGATTGATAAA-AAAAAGT
13654895 TATTAATCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 13 0.57
28 7 0.30
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (28 bp):
TTAAAGGATGATTGATAAAAAAAAGTGT
Found at i:13659350 original size:30 final size:30
Alignment explanation
Indices: 13659280--13659360 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
13659270 TTTGTAAGGA
*
13659280 CAAAATTATAAAA-TTAAAAGAAAAAGTGG
1 CAAAATTATAAAATTTAAAAAAAAAAGTGG
*
13659309 TCAAAACTATAAAATTTAAAAAAAAGCAAG-GG
1 -CAAAATTATAAAATTTAAAAAAAA--AAGTGG
*
13659341 -AAAATTATAAAATTTTAAAA
1 CAAAATTATAAAATTTAAAAA
13659361 CTTTTGAGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
30 30 0.68
31 9 0.20
32 2 0.05
33 3 0.07
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (30 bp):
CAAAATTATAAAATTTAAAAAAAAAAGTGG
Found at i:13668243 original size:3 final size:3
Alignment explanation
Indices: 13668235--13668278 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
13668225 ATTAGTCTCT
* *
13668235 TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA TTA TGA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13668279 TTCCTTTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13679057 original size:72 final size:73
Alignment explanation
Indices: 13678918--13679064 Score: 244
Period size: 72 Copynumber: 2.0 Consensus size: 73
13678908 CCTAAATAGG
*
13678918 AATCCCCCACCAATGTTCTTTTTCAAGGTGTATTTCGTCACCAAATTGAATTTATCATTTTCTAT
1 AATCCCCCACCAATCTTCTTTTTCAAGGTG-ATTTCGTCACCAAATTGAATTTATCATTTTCTAT
13678983 GAAACCCTA
65 GAAACCCTA
*
13678992 AATCCCCCACCAATCTTCTTTTTCAAGGTG-TTTCGTCACCAGATTGAATTTATCATTTT-TGAT
1 AATCCCCCACCAATCTTCTTTTTCAAGGTGATTTCGTCACCAAATTGAATTTATCATTTTCT-AT
13679055 GAAACCCTA
65 GAAACCCTA
13679064 A
1 A
13679065 GTTTGATTTA
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
71 1 0.01
72 40 0.57
74 29 0.41
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.37
Consensus pattern (73 bp):
AATCCCCCACCAATCTTCTTTTTCAAGGTGATTTCGTCACCAAATTGAATTTATCATTTTCTATG
AAACCCTA
Found at i:13683412 original size:10 final size:10
Alignment explanation
Indices: 13683397--13683429 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13683387 GATGTTTATT
13683397 TGATGAATTA
1 TGATGAATTA
*
13683407 TGATGAATAA
1 TGATGAATTA
13683417 TGATGAATTA
1 TGATGAATTA
13683427 TGA
1 TGA
13683430 GCCTAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (10 bp):
TGATGAATTA
Found at i:13685616 original size:20 final size:18
Alignment explanation
Indices: 13685588--13685630 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
13685578 ATTTGAAACG
*
13685588 AAATTATAAAAGTTTGAATA
1 AAATAATAAAA-TTT-AATA
*
13685608 AAATAATAATATTTAATA
1 AAATAATAAAATTTAATA
13685626 AAATA
1 AAATA
13685631 TTCTATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 3 0.14
20 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AAATAATAAAATTTAATA
Found at i:13685627 original size:18 final size:18
Alignment explanation
Indices: 13685604--13685655 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 18
13685594 TAAAAGTTTG
13685604 AATAAAATAATAATATTT
1 AATAAAATAATAATATTT
**
13685622 AATAAAAT-ATTCTATTT
1 AATAAAATAATAATATTT
*
13685639 AA-AAAA-AACAATATTT
1 AATAAAATAATAATATTT
13685655 A
1 A
13685656 TAGAAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 11 0.39
17 9 0.32
18 8 0.29
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAAATAATAATATTT
Found at i:13686585 original size:13 final size:13
Alignment explanation
Indices: 13686567--13686591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13686557 TTCTAGAAAA
13686567 TTTATAAAATCAT
1 TTTATAAAATCAT
13686580 TTTATAAAATCA
1 TTTATAAAATCA
13686592 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:13695585 original size:2 final size:2
Alignment explanation
Indices: 13695578--13695603 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13695568 GTGAAATTTC
13695578 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13695604 TGAGATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13697966 original size:28 final size:27
Alignment explanation
Indices: 13697932--13697985 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
13697922 TTGACTCAAA
*
13697932 ATAAAAATATAAATAATTAATTAAAATC
1 ATAAAAAAATAAA-AATTAATTAAAATC
* *
13697960 ATAAAAAAATAAAAATTTATTTAAAT
1 ATAAAAAAATAAAAATTAATTAAAAT
13697986 TTTTTTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAAAAAAATAAAAATTAATTAAAATC
Found at i:13706670 original size:73 final size:73
Alignment explanation
Indices: 13706530--13706710 Score: 224
Period size: 73 Copynumber: 2.5 Consensus size: 73
13706520 GAAGAATGCT
* * * * * * *
13706530 CTTAGTCGACTAACTTATGTCTTAGTCGACTAAGTTGTCTCTATTTTCTATTTCTAGTTTTTGAC
1 CTTAGTCGACTAACTTATTTCTTGGTCGACTAAGTTGTCTCTATCTTCAAGTTCTAGTTTCTAAC
13706595 AGTAAG-TA
66 AGT-AGCTA
*
13706603 CTTAGTCGACTAACTTATTTCTTGGTCGACTAAGTTGGT-TCTATCTTGAAGTTC-AGATTTCTA
1 CTTAGTCGACTAACTTATTTCTTGGTCGACTAAGTT-GTCTCTATCTTCAAGTTCTAG-TTTCTA
*
13706666 ACAGTAGCTT
64 ACAGTAGCTA
*
13706676 CTTAGTCGACTAACTTATTCCTTGGTCGACTAAGT
1 CTTAGTCGACTAACTTATTTCTTGGTCGACTAAGT
13706711 CTTTTTTGTT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
72 4 0.04
73 89 0.94
74 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (73 bp):
CTTAGTCGACTAACTTATTTCTTGGTCGACTAAGTTGTCTCTATCTTCAAGTTCTAGTTTCTAAC
AGTAGCTA
Found at i:13712304 original size:21 final size:21
Alignment explanation
Indices: 13712278--13712319 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13712268 AAATAGAAGG
13712278 TTTCTCACTGCAACGAAATTC
1 TTTCTCACTGCAACGAAATTC
* *
13712299 TTTCTCGCTGCAGCGAAATTC
1 TTTCTCACTGCAACGAAATTC
13712320 AGCTGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (21 bp):
TTTCTCACTGCAACGAAATTC
Found at i:13716242 original size:48 final size:48
Alignment explanation
Indices: 13716171--13716268 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
13716161 TGAGCTGAGC
**
13716171 TCTTGAACATGTATCTTTTGAGTGCAGCTCAACCTACAAAACAAATAT
1 TCTTGAACATGTATCTTTTGAGTGCAGCTCAAAATACAAAACAAATAT
* *
13716219 TCTTGAACATGTATCTTTTGAGTGTAGCTCAAAATACAAAATAAATAT
1 TCTTGAACATGTATCTTTTGAGTGCAGCTCAAAATACAAAACAAATAT
13716267 TC
1 TC
13716269 AATTTTTCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (48 bp):
TCTTGAACATGTATCTTTTGAGTGCAGCTCAAAATACAAAACAAATAT
Found at i:13724399 original size:10 final size:10
Alignment explanation
Indices: 13724370--13724465 Score: 54
Period size: 10 Copynumber: 8.9 Consensus size: 10
13724360 TCGTTAAACT
*
13724370 TTGTTTGAAT
1 TTGTTTGAAG
*
13724380 TATTTTTGAAG
1 T-TGTTTGAAG
13724391 TTGTTTGAATGAG
1 TTGTTTG-A--AG
*
13724404 TT-TTTGACG
1 TTGTTTGAAG
13724413 TTGTTTGAATGAG
1 TTGTTTG-A--AG
13724426 TT-TTTGAAG
1 TTGTTTGAAG
13724435 TTGTTTGAATGAG
1 TTGTTTG-A--AG
13724448 TT-TTTGAAG
1 TTGTTTGAAG
13724457 TTGTTTGAA
1 TTGTTTGAA
13724466 TAAGTTTTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 26
0.69 0.05 0.26
Matches are distributed among these distances:
9 11 0.16
10 20 0.29
11 14 0.21
12 12 0.18
13 11 0.16
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.52
Consensus pattern (10 bp):
TTGTTTGAAG
Found at i:13724410 original size:22 final size:22
Alignment explanation
Indices: 13724370--13724477 Score: 175
Period size: 22 Copynumber: 5.0 Consensus size: 22
13724360 TCGTTAAACT
*
13724370 TTGTTTGAATTA-TTTTTGAAG
1 TTGTTTGAATGAGTTTTTGAAG
*
13724391 TTGTTTGAATGAGTTTTTGACG
1 TTGTTTGAATGAGTTTTTGAAG
13724413 TTGTTTGAATGAGTTTTTGAAG
1 TTGTTTGAATGAGTTTTTGAAG
13724435 TTGTTTGAATGAGTTTTTGAAG
1 TTGTTTGAATGAGTTTTTGAAG
*
13724457 TTGTTTGAATAAG-TTTTGAAG
1 TTGTTTGAATGAGTTTTTGAAG
13724478 ATCCCAAGTG
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
21 19 0.23
22 63 0.77
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (22 bp):
TTGTTTGAATGAGTTTTTGAAG
Found at i:13724431 original size:12 final size:13
Alignment explanation
Indices: 13724389--13724471 Score: 64
Period size: 13 Copynumber: 7.3 Consensus size: 13
13724379 TTATTTTTGA
13724389 AGTTGTTTGAATG
1 AGTTGTTTGAATG
13724402 AGTT-TTTG-A--
1 AGTTGTTTGAATG
*
13724411 CGTTGTTTGAATG
1 AGTTGTTTGAATG
13724424 AGTT-TTTG-A--
1 AGTTGTTTGAATG
13724433 AGTTGTTTGAATG
1 AGTTGTTTGAATG
13724446 AGTT-TTTG-A--
1 AGTTGTTTGAATG
*
13724455 AGTTGTTTGAATA
1 AGTTGTTTGAATG
13724468 AGTT
1 AGTT
13724472 TTGAAGATCC
Statistics
Matches: 56, Mismatches: 2, Indels: 24
0.68 0.02 0.29
Matches are distributed among these distances:
9 11 0.20
10 12 0.21
11 6 0.11
12 12 0.21
13 15 0.27
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (13 bp):
AGTTGTTTGAATG
Found at i:13725220 original size:34 final size:35
Alignment explanation
Indices: 13725182--13725282 Score: 102
Period size: 34 Copynumber: 2.9 Consensus size: 35
13725172 ACTTTAGCCT
13725182 TAAAAGGCATTGTAGAAAGGTTATGCTTGAT-CTA
1 TAAAAGGCATTGTAGAAAGGTTATGCTTGATCCTA
* * *
13725216 TAAAAGGCATTGCATTATG-ACGGTTGTGCTTGATCCTT
1 TAAAAGGCATTG---TA-GAAAGGTTATGCTTGATCCTA
13725254 TAAAAAGGCATTGTA-AAA-GTTATGCTTGA
1 T-AAAAGGCATTGTAGAAAGGTTATGCTTGA
13725283 GCCTTGAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
34 22 0.40
35 1 0.02
36 2 0.04
37 15 0.27
38 4 0.07
39 11 0.20
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (35 bp):
TAAAAGGCATTGTAGAAAGGTTATGCTTGATCCTA
Found at i:13737273 original size:26 final size:25
Alignment explanation
Indices: 13737243--13737293 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
13737233 AAAAACCAAG
* *
13737243 AAAATATCGTGAAAACCCAAAGAAAT
1 AAAATAAC-TGAAAACCCAAACAAAT
*
13737269 AAAATAACTTAAAACCCAAACAAAT
1 AAAATAACTGAAAACCCAAACAAAT
13737294 TATTGAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.61, C:0.18, G:0.06, T:0.16
Consensus pattern (25 bp):
AAAATAACTGAAAACCCAAACAAAT
Found at i:13737844 original size:68 final size:67
Alignment explanation
Indices: 13737759--13737889 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 67
13737749 TCAATGAATG
*
13737759 ACACTTGTCATTCAATTGGATATCAATTAAAACAATCTC-AATTTGAACTCACTTTTAATATATA
1 ACACTTGTCATTCAATTGGATATCAATTAAAACAATC-CAAATTTGAACTAAC-TTTAATATATA
13737823 AATC
64 AATC
* ** * *
13737827 ACACTTGTTATTCAATTGGATATCAATTGGAATAGTCCAAATTTGAACTAACTTTAATATATA
1 ACACTTGTCATTCAATTGGATATCAATTAAAACAATCCAAATTTGAACTAACTTTAATATATA
13737890 GTTTATATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 12 0.21
68 44 0.79
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (67 bp):
ACACTTGTCATTCAATTGGATATCAATTAAAACAATCCAAATTTGAACTAACTTTAATATATAAA
TC
Found at i:13738252 original size:14 final size:14
Alignment explanation
Indices: 13738230--13738273 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
13738220 TTAATATAAT
*
13738230 TATTCAATAAGGTA
1 TATTTAATAAGGTA
*
13738244 TATTTAATAAAGTTA
1 TATTTAAT-AAGGTA
*
13738259 TATTTAATGAGGTA
1 TATTTAATAAGGTA
13738273 T
1 T
13738274 TTATTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (14 bp):
TATTTAATAAGGTA
Found at i:13750228 original size:13 final size:13
Alignment explanation
Indices: 13750210--13750234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13750200 TTTCATAAAA
13750210 TTTATAAAATCAT
1 TTTATAAAATCAT
13750223 TTTATAAAATCA
1 TTTATAAAATCA
13750235 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:13754876 original size:20 final size:20
Alignment explanation
Indices: 13754852--13754895 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
13754842 TATATAAATG
13754852 AAAAATATACATTTC-ATATCT
1 AAAAATA-A-ATTTCGATATCT
*
13754873 AAAAATAAATTTCGGTATCT
1 AAAAATAAATTTCGATATCT
13754893 AAA
1 AAA
13754896 TCATCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAATAAATTTCGATATCT
Found at i:13758639 original size:17 final size:17
Alignment explanation
Indices: 13758605--13758644 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
13758595 AAAAGATGGG
*
13758605 TTATGTCACATCAGTAT
1 TTATGTCACATCAATAT
*
13758622 TTATGTCACATTAATAT
1 TTATGTCACATCAATAT
*
13758639 TAATGT
1 TTATGT
13758645 GATTATATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (17 bp):
TTATGTCACATCAATAT
Found at i:13758863 original size:32 final size:33
Alignment explanation
Indices: 13758827--13758891 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
13758817 AAAAACTAAA
* * *
13758827 TTTATAT-TTTTTTTAGAATACAAAGATTAATT
1 TTTATATATATTTTTAAAATACAAAGATCAATT
*
13758859 TTTATATATATTTTTAAAATACACAGATCAATT
1 TTTATATATATTTTTAAAATACAAAGATCAATT
13758892 GCATAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (33 bp):
TTTATATATATTTTTAAAATACAAAGATCAATT
Found at i:13760748 original size:21 final size:20
Alignment explanation
Indices: 13760724--13760764 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
13760714 GTTGAATAAA
*
13760724 AATTTTTTTTTATAAAAAAAT
1 AATTTTATTTTA-AAAAAAAT
13760745 AATTTTATTTTAAAAAAAAT
1 AATTTTATTTTAAAAAAAAT
13760765 TTGCGTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTATTTTAAAAAAAAT
Found at i:13771941 original size:27 final size:27
Alignment explanation
Indices: 13771890--13771941 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
13771880 ATGTCCTGAT
*
13771890 GGTGGAAAATTACAATTTTGCCCCTGG
1 GGTGGAAAATTACAATTTTGACCCTGG
*
13771917 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
13771942 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGG
Found at i:13772012 original size:20 final size:20
Alignment explanation
Indices: 13771987--13772032 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
13771977 CTTCTAAACC
*
13771987 TCAAATCATACTCCAGTAAG
1 TCAAATCATACTCCAATAAG
*
13772007 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
13772027 TCAAAT
1 TCAAAT
13772033 GAGGTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:13774570 original size:85 final size:85
Alignment explanation
Indices: 13774427--13774590 Score: 274
Period size: 85 Copynumber: 1.9 Consensus size: 85
13774417 GAAAAGTATG
*
13774427 AAATTATGGTGTTGGTATATACCCTTGAGCTAATTAGATTGGTCGAGAAATATATATTGTCATTT
1 AAATTATGGTGTTGGTATATACCCTTGACCTAATTAGATTGGTCGAGAAATATATATTGTCATTT
13774492 AATGCATACTTAATTGCATA
66 AATGCATACTTAATTGCATA
* * * *
13774512 AAATTATGGTGTTGGTATATGCCCTTGACCTAATTGGATTGGTTGAGGAATATATATTGTCATTT
1 AAATTATGGTGTTGGTATATACCCTTGACCTAATTAGATTGGTCGAGAAATATATATTGTCATTT
*
13774577 AATGCATTCTTAAT
66 AATGCATACTTAAT
13774591 CACATAACTA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (85 bp):
AAATTATGGTGTTGGTATATACCCTTGACCTAATTAGATTGGTCGAGAAATATATATTGTCATTT
AATGCATACTTAATTGCATA
Found at i:13776309 original size:27 final size:27
Alignment explanation
Indices: 13776278--13776332 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13776268 TCAAAATAAA
13776278 TATAATAAAAATATTTAATTTATTTGT
1 TATAATAAAAATATTTAATTTATTTGT
13776305 TATAATAAAAATATTTAATTTATTTGT
1 TATAATAAAAATATTTAATTTATTTGT
13776332 T
1 T
13776333 TTAAATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (27 bp):
TATAATAAAAATATTTAATTTATTTGT
Found at i:13778128 original size:8 final size:8
Alignment explanation
Indices: 13778115--13778153 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
13778105 TAATAGTGAT
13778115 GATAGTGC
1 GATAGTGC
13778123 GATAGTGC
1 GATAGTGC
13778131 GATAGTGC
1 GATAGTGC
13778139 GATAGTGC
1 GATAGTGC
*
13778147 AATAGTG
1 GATAGTG
13778154 AAGAACAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.36, T:0.26
Consensus pattern (8 bp):
GATAGTGC
Found at i:13793300 original size:22 final size:22
Alignment explanation
Indices: 13793273--13793333 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
13793263 GATCGATTTT
**
13793273 GAGAGGAAGCCATTGTGGTGAA
1 GAGAGGAAGCCACGGTGGTGAA
13793295 GAGAGGAAGCCACGGTGGTGAA
1 GAGAGGAAGCCACGGTGGTGAA
13793317 GAGAGGAAGCCACGGTG
1 GAGAGGAAGCCACGGTG
13793334 TAATACCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.44, T:0.11
Consensus pattern (22 bp):
GAGAGGAAGCCACGGTGGTGAA
Found at i:13793980 original size:11 final size:11
Alignment explanation
Indices: 13793964--13793989 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13793954 TGTTTTGAAG
13793964 AAATAAAAATA
1 AAATAAAAATA
13793975 AAATAAAAATA
1 AAATAAAAATA
13793986 AAAT
1 AAAT
13793990 GGATGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:13794317 original size:26 final size:26
Alignment explanation
Indices: 13794288--13794337 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
13794278 GGTTAGTGAA
13794288 GAAGAAAAATAAAGGA-AGAAAGAAAT
1 GAAGAAAAA-AAAGGAGAGAAAGAAAT
* *
13794314 GAAGAGAAAAAGGGAGAGAAAGAA
1 GAAGAAAAAAAAGGAGAGAAAGAA
13794338 CCGTGAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (26 bp):
GAAGAAAAAAAAGGAGAGAAAGAAAT
Found at i:13794592 original size:33 final size:34
Alignment explanation
Indices: 13794510--13794603 Score: 118
Period size: 34 Copynumber: 2.8 Consensus size: 34
13794500 TGATTTTGGA
* * *
13794510 TGCAAAAAAATTGAAGCTATTTGCTACCAATTTG
1 TGCAGAAAAATTGGAGCTATTTGCTGCCAATTTG
** * *
13794544 TTTAGAAAAATTGGAGTTGTTTGCTGCCAATTTG
1 TGCAGAAAAATTGGAGCTATTTGCTGCCAATTTG
13794578 TGCAG-AAAATTGGAGCTATTTGCTGC
1 TGCAGAAAAATTGGAGCTATTTGCTGC
13794604 AGAAAAATTA
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 19 0.39
34 30 0.61
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (34 bp):
TGCAGAAAAATTGGAGCTATTTGCTGCCAATTTG
Found at i:13794605 original size:23 final size:23
Alignment explanation
Indices: 13794573--13794624 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
13794563 TTTGCTGCCA
*
13794573 ATTTGTGCAG-AAAATTGGAGCT
1 ATTTGTGCAGAAAAATTAGAGCT
13794595 ATTTGCTGCAGAAAAATTAGAGCT
1 ATTTG-TGCAGAAAAATTAGAGCT
*
13794619 GTTTGT
1 ATTTGT
13794625 TGCCAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 6 0.23
24 15 0.58
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.35
Consensus pattern (23 bp):
ATTTGTGCAGAAAAATTAGAGCT
Found at i:13794665 original size:47 final size:47
Alignment explanation
Indices: 13794601--13794690 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
13794591 AGCTATTTGC
* * *
13794601 TGCAGAAAAATTAGAGCTGTTTGTTGCCAATTTGTGCAGAAAAATTG
1 TGCAAAAAAATTAGAGCTGTTTGCTACCAATTTGTGCAGAAAAATTG
*
13794648 TGCAAAAAAATTGGAGCTGTTTGCTACCAATTTGTGCAGAAAA
1 TGCAAAAAAATTAGAGCTGTTTGCTACCAATTTGTGCAGAAAA
13794691 TTGGACAGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (47 bp):
TGCAAAAAAATTAGAGCTGTTTGCTACCAATTTGTGCAGAAAAATTG
Found at i:13794693 original size:33 final size:35
Alignment explanation
Indices: 13794645--13794713 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
13794635 TGCAGAAAAA
13794645 TTGTGCAAAAAAATTGG-AGCTGTT-TGCTACCAAT
1 TTGTGCAAAAAAATTGGAAGCT-TTGTGCTACCAAT
*
13794679 TTGTGC-AGAAAATTGGACAGCTTTGTGCTACCAAT
1 TTGTGCAAAAAAATTGGA-AGCTTTGTGCTACCAAT
13794714 ATTGAGGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 9 0.29
34 8 0.26
35 14 0.45
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (35 bp):
TTGTGCAAAAAAATTGGAAGCTTTGTGCTACCAAT
Found at i:13794840 original size:22 final size:22
Alignment explanation
Indices: 13794794--13794863 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 22
13794784 GAGAGGAAAG
* ** *
13794794 GAAGAGAGAAAGCCATAATGAT
1 GAAGAGAGGAAGCCATGGTGGT
13794816 GAAGAGAGGAAGCCATGGTGGT
1 GAAGAGAGGAAGCCATGGTGGT
*
13794838 GAAAAGAGGAAGCCATGGTGGT
1 GAAGAGAGGAAGCCATGGTGGT
13794860 GAAG
1 GAAG
13794864 GGAAGCCACG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.39, T:0.13
Consensus pattern (22 bp):
GAAGAGAGGAAGCCATGGTGGT
Found at i:13794867 original size:19 final size:21
Alignment explanation
Indices: 13794815--13794871 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 21
13794805 GCCATAATGA
13794815 TGAAGAGAGGAAGCCATGGTGG
1 TGAA-AGAGGAAGCCATGGTGG
13794837 TGAAAAGAGGAAGCCATGGTGG
1 TG-AAAGAGGAAGCCATGGTGG
13794859 TG-AAG-GGAAGCCA
1 TGAAAGAGGAAGCCA
13794872 CGGGCTGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.24
20 3 0.09
22 21 0.62
23 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.42, T:0.12
Consensus pattern (21 bp):
TGAAAGAGGAAGCCATGGTGG
Found at i:13794934 original size:17 final size:17
Alignment explanation
Indices: 13794880--13794947 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
13794870 CACGGGCTGG
*
13794880 AAAGAAAAAAAAATAAGA
1 AAAGAAAAGAAAA-AAGA
*
13794898 AACATGGAAGAGAGAAAAAG-
1 AA-A--GAAAAGA-AAAAAGA
13794918 AAAGAAAAAGAAAAAAGA
1 AAAG-AAAAGAAAAAAGA
13794936 AAAGAAAAGAAA
1 AAAGAAAAGAAA
13794948 TAGAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
17 15 0.37
18 11 0.27
19 2 0.05
20 2 0.05
21 8 0.20
22 3 0.07
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (17 bp):
AAAGAAAAGAAAAAAGA
Found at i:13794978 original size:25 final size:25
Alignment explanation
Indices: 13794950--13795033 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 25
13794940 AAAAGAAATA
13794950 GAAAATAAATGGGCATGACCCAATG
1 GAAAATAAATGGGCATGACCCAATG
* *
13794975 GAAAATAAGTGGGCATGACCCAATA
1 GAAAATAAATGGGCATGACCCAATG
* *
13795000 GAAAATAAGTGGGCATGGCCCAATAG
1 GAAAATAAATGGGCATGACCCAAT-G
13795026 G-AAATAAA
1 GAAAATAAA
13795034 AATAAATGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
25 52 0.98
26 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.25, T:0.15
Consensus pattern (25 bp):
GAAAATAAATGGGCATGACCCAATG
Found at i:13809795 original size:10 final size:10
Alignment explanation
Indices: 13809780--13809808 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
13809770 TTTTCTAGGC
13809780 TCATAATTCA
1 TCATAATTCA
13809790 TCATAATTCA
1 TCATAATTCA
13809800 TCATAATTC
1 TCATAATTC
13809809 CTTAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (10 bp):
TCATAATTCA
Found at i:13815484 original size:19 final size:19
Alignment explanation
Indices: 13815460--13815517 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
13815450 ACTTCTAAAC
13815460 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
13815479 CTCAAATCATACTCTAATAA
1 CTCAAATCATACTCCAAT-A
* *
13815499 GTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
13815518 AGTCAAATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:13815505 original size:20 final size:20
Alignment explanation
Indices: 13815461--13815525 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
13815451 CTTCTAAACC
*
13815461 TCAAATCATACTCCAAT-AC
1 TCAAATCATACTCCAATAAG
*
13815480 TCAAATCATACTCTAATAAG
1 TCAAATCATACTCCAATAAG
*
13815500 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
13815520 TCAAAT
1 TCAAAT
13815526 GGGGTCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 16 0.39
20 25 0.61
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.29
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:13826551 original size:87 final size:84
Alignment explanation
Indices: 13826362--13826532 Score: 227
Period size: 87 Copynumber: 2.0 Consensus size: 84
13826352 AGTAAATGAA
* * * *
13826362 AAATTCATATCATTGGACTTTCAATATATAGAAAGAAAATTGGTTTTATTGAGAACTTAAATTTT
1 AAATTAATATGATTGGACTTTCAATATATAGAAAGAAAATTGGCTTTAGTGAGAACTTAAA---T
* * *
13826427 TTTTTTTTCAAATTTTTCTTTG
63 TATTTTTTCAAAATTTTCTTCG
* *
13826449 AAATTCATATGATTGGACTTTCAATATATAGAAAGAAAATTGGCTTTAGTGAGAACTTTAA-TAT
1 AAATTAATATGATTGGACTTTCAATATATAGAAAGAAAATTGGCTTTAGTGAGAACTTAAATTAT
13826513 TTTTTCAAAATTTTCTTCG
66 TTTTTCAAAATTTTCTTCG
13826532 A
1 A
13826533 TATTTAGAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
83 20 0.26
87 57 0.74
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (84 bp):
AAATTAATATGATTGGACTTTCAATATATAGAAAGAAAATTGGCTTTAGTGAGAACTTAAATTAT
TTTTTCAAAATTTTCTTCG
Found at i:13831895 original size:21 final size:21
Alignment explanation
Indices: 13831862--13831904 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
13831852 TTTTATTAAG
13831862 TTATATTATTTTATGC-TAATT
1 TTATATTATTTTAT-CTTAATT
13831883 TTATATT-TATTTATCTTAATT
1 TTATATTAT-TTTATCTTAATT
13831904 T
1 T
13831905 AGTTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATATTATTTTATCTTAATT
Done.