Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 201 of 345
Found at i:57649214 original size:48 final size:48
Alignment explanation
Indices: 57649135--57649321 Score: 218
Period size: 48 Copynumber: 3.9 Consensus size: 48
57649125 AATTGGGTGA
* *
57649135 TATGTGAGCTAGTGTAAGACCATAT-TCGGAACATGGCATCGGCCACAT
1 TATGAGAGCTAGTGTAAGACCATGTCT-GGAACATGGCATCGGCCACAT
* * * **
57649183 TATGAGAGCTAGTGTAAGACCATTTTTGGAACATGGCATC-GACATTGT
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCA-CAT
* * * *
57649231 TACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCACAT
*
57649279 TATGTGAGCTAGTGTAAGACCATGTCT-GAGACATGGCATCGGC
1 TATGAGAGCTAGTGTAAGACCATGTCTGGA-ACATGGCATCGGC
57649322 ATTTTACCCT
Statistics
Matches: 118, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
47 4 0.03
48 111 0.94
49 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCACAT
Found at i:57649313 original size:96 final size:95
Alignment explanation
Indices: 57649140--57649328 Score: 265
Period size: 96 Copynumber: 2.0 Consensus size: 95
57649130 GGTGATATGT
*
57649140 GAGCTAGTGTAAGACCATATTCGGAACATGGCATCGGCCACATTATGAGAGCTAGTGTAAGACCA
1 GAGCTAGTGTAAGACCATATTCGGAACATGGCATCGGCCACAATATGAGAGCTAGTGTAAGACCA
* *
57649205 TTTTTGGAACATGGCATCGACATTGTTACGA
66 TGTCTGGAACATGGCATCGACATT-TTACGA
* * * *
57649236 GAGCTAGTGTAAGACCAT-GTCTGGGACATGGCATCGGCCTCAATATGTGAGCTAGTGTAAGACC
1 GAGCTAGTGTAAGACCATATTC-GGAACATGGCATCGGCCACAATATGAGAGCTAGTGTAAGACC
*
57649300 ATGTCT-GAGACATGGCATCGGCATTTTAC
65 ATGTCTGGA-ACATGGCATCGACATTTTAC
57649329 CCTTTTGGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
95 8 0.10
96 75 0.90
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (95 bp):
GAGCTAGTGTAAGACCATATTCGGAACATGGCATCGGCCACAATATGAGAGCTAGTGTAAGACCA
TGTCTGGAACATGGCATCGACATTTTACGA
Found at i:57653516 original size:49 final size:49
Alignment explanation
Indices: 57653417--57653688 Score: 201
Period size: 49 Copynumber: 5.7 Consensus size: 49
57653407 AGATGTCGAC
* * * * *
57653417 GCCATGTCTCAGACATGGTCTAACACTGGCTTTCATATAGCGAG-GCCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATCTATC-AGTGCCGAT
* *
57653467 GCCATGTCCCAGACAAGTCTTACACTGGCTCTCATCTATCAGTGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGTGCCGAT
* * * * **
57653516 GCCATGTCCCAGACAGGTCTTACGCT-GAT-ACA-CTA-AAG-GCTAAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGTGCCGAT
* ** *
57653560 GCCATGTCCCAGACAGGTCTTACACTAG-T-TTGTGTATC-GTGAGGCCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGT---GCCGAT
* * * * *
57653609 G-CATGTCCCAGACATGTCTTACACTAGCTCTCGTC--TCAATGCCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGTGCCGAT
*
57653655 G-CATGTCCCAGACATGTCTTACACTGGCTCTCAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCAT
57653689 ACTGTGGCTG
Statistics
Matches: 181, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
44 29 0.16
45 6 0.03
46 40 0.22
47 2 0.01
48 31 0.17
49 56 0.31
50 17 0.09
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGTGCCGAT
Found at i:57653702 original size:92 final size:91
Alignment explanation
Indices: 57653459--57653728 Score: 251
Period size: 92 Copynumber: 2.9 Consensus size: 91
57653449 TCATATAGCG
* * *
57653459 AGGCCGATGCCATGTCCCAGACAAGTCTTACACTGGCTCTCATCTATCAGTGTCGATGCCATGTC
1 AGGCCAATGCCATGTCCCAGACAAGTCTTACACTGGCTCTCA--TATCTGTGGCGATG-CATGTC
* * *
57653524 CCAGACAGGTCTTACGCT-GATACACTAA
63 CCAGACATGTCTTACACTAGCTACACTAA
* * * * ** *
57653552 AGGCTAATGCCATGTCCCAGACAGGTCTTACACTAG-TTTGTGTATCGTGAGGCCGATGCATGTC
1 AGGCCAATGCCATGTCCCAGACAAGTCTTACACTGGCTCT-CATATC-TGTGG-CGATGCATGTC
* * *
57653616 CCAGACATGTCTTACACTAGCTCTCGTCTCA
63 CCAGACATGTCTTACACTAGCT-AC-ACTAA
* * *
57653647 ATGCCAATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATA-CTGTGGCTGATGCATGTCCT
1 AGGCCAATGCCATGTCCCAGACAAGTCTTACACTGGCTCTCATATCTGTGGC-GATGCATGTCCC
*
57653710 AGACATGTCTTACATTAGC
65 AGACATGTCTTACACTAGC
57653729 GCACATATCA
Statistics
Matches: 143, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
91 5 0.03
92 59 0.41
93 40 0.28
94 27 0.19
95 12 0.08
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (91 bp):
AGGCCAATGCCATGTCCCAGACAAGTCTTACACTGGCTCTCATATCTGTGGCGATGCATGTCCCA
GACATGTCTTACACTAGCTACACTAA
Found at i:57653703 original size:46 final size:48
Alignment explanation
Indices: 57653417--57653723 Score: 210
Period size: 46 Copynumber: 6.5 Consensus size: 48
57653407 AGATGTCGAC
* * *
57653417 GCCATGTCTCAGACATGGTCTAACACTGGCTTTCATA-TAGCGAGGCCGAT
1 GCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATACTA--GAGGCCGAT
* * *
57653467 GCCATGTCCCAGACAAGTCTTACACTGGCTCTCAT-CTATCAGTGTCGAT
1 GCCATGTCCCAGACATGTCTTACACTGGCTCTCATACTA-GAG-GCCGAT
* * * * * **
57653516 GCCATGTCCCAGACAGGTCTTACGCT-G--AT-ACACTAAAGGCTAAT
1 GCCATGTCCCAGACATGTCTTACACTGGCTCTCATACTAGAGGCCGAT
* * * **
57653560 GCCATGTCCCAGACAGGTCTTACACTAG-TTTGTGTATCGT-GAGGCCGAT
1 GCCATGTCCCAGACATGTCTTACACTGGCTCT-CATA-C-TAGAGGCCGAT
* * * *
57653609 G-CATGTCCCAGACATGTCTTACACTAGCTCTCGT-CTCA-ATGCCAAT
1 GCCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-AGAGGCCGAT
* *
57653655 G-CATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGAT
1 GCCATGTCCCAGACATGTCTTACACTGGCTCTCATACTAGAGGCCGAT
*
57653701 G-CATGTCCTAGACATGTCTTACA
1 GCCATGTCCCAGACATGTCTTACA
57653724 TTAGCGCACA
Statistics
Matches: 209, Mismatches: 34, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
44 28 0.13
45 5 0.02
46 70 0.33
47 2 0.01
48 31 0.15
49 58 0.28
50 15 0.07
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
GCCATGTCCCAGACATGTCTTACACTGGCTCTCATACTAGAGGCCGAT
Found at i:57655810 original size:23 final size:24
Alignment explanation
Indices: 57655784--57655832 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
57655774 TGCTTCTTGC
*
57655784 AACTTCTTCCAAAACT-GAGGTAA
1 AACTTATTCCAAAACTAGAGGTAA
57655807 AACTTATTCCAAAACTAGGAGGTAA
1 AACTTATTCCAAAACTA-GAGGTAA
57655832 A
1 A
57655833 CCTTGGATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.24
Consensus pattern (24 bp):
AACTTATTCCAAAACTAGAGGTAA
Found at i:57663647 original size:39 final size:39
Alignment explanation
Indices: 57663597--57663723 Score: 200
Period size: 39 Copynumber: 3.3 Consensus size: 39
57663587 TGATATTTGG
* *
57663597 AACAAATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AACATATCCGGACCTGAGGTCCGCAGGCTACGTGCTGGA
57663636 AACATATCCGGACCTGAGGTCCGCAGGCTACGTGCTGGA
1 AACATATCCGGACCTGAGGTCCGCAGGCTACGTGCTGGA
* * *
57663675 AACATATCTGGACCTGATGTCCACAGGCTACGTGCTGGA
1 AACATATCCGGACCTGAGGTCCGCAGGCTACGTGCTGGA
*
57663714 AATATATCCG
1 AACATATCCG
57663724 AGCCTAAAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (39 bp):
AACATATCCGGACCTGAGGTCCGCAGGCTACGTGCTGGA
Found at i:57668820 original size:31 final size:31
Alignment explanation
Indices: 57668779--57668842 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
57668769 CCTTTTCATA
*
57668779 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
57668810 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
57668841 TT
1 TT
57668843 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:57669081 original size:24 final size:24
Alignment explanation
Indices: 57669054--57669224 Score: 265
Period size: 24 Copynumber: 7.2 Consensus size: 24
57669044 GGCGTAGCTT
* *
57669054 CTTTTAATAATTGGGGCAAAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
* *
57669078 CTTTTTATAACTGGAGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
57669102 C-TTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
57669125 CTTTTGATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
57669149 CTTTTGATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
57669173 CTTTTGATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
57669197 C-TTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
57669220 CTTTT
1 CTTTT
57669225 TCACTTCCTC
Statistics
Matches: 137, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
23 43 0.31
24 94 0.69
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAGCC
Found at i:57669116 original size:47 final size:47
Alignment explanation
Indices: 57669056--57669224 Score: 284
Period size: 47 Copynumber: 3.6 Consensus size: 47
57669046 CGTAGCTTCT
* * * *
57669056 TTTAATAATTGGGGCAAAAGCCCTTTTTATAACTGGAGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
57669103 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
*
57669150 TTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
57669198 TTTAATAACTGGGGCATAAGCCCTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTT
57669225 TCACTTCCTC
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
47 69 0.60
48 46 0.40
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
Found at i:57669140 original size:71 final size:72
Alignment explanation
Indices: 57669054--57669225 Score: 276
Period size: 71 Copynumber: 2.4 Consensus size: 72
57669044 GGCGTAGCTT
* *
57669054 CTTTTAATAATTGGGGCAAAAGCCCTTTTTATAACTGGAGCATAAGCCC-TTTAATAACTGGGGC
1 CTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGAGCATAAGCCCTTTTAATAACTGGGGC
57669118 ATAAGCC
66 ATAAGCC
* * * *
57669125 CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGC
1 CTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGAGCATAAGCCCTTTTAATAACTGGGGC
57669190 ATAAGCC
66 ATAAGCC
57669197 C-TTTAATAACTGGGGCATAAGCCCTTTTT
1 CTTTTAATAACTGGGGCATAAGCCCTTTTT
57669226 CACTTCCTCC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
71 70 0.76
72 22 0.24
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (72 bp):
CTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGAGCATAAGCCCTTTTAATAACTGGGGC
ATAAGCC
Found at i:57669296 original size:9 final size:9
Alignment explanation
Indices: 57669282--57669358 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
57669272 ATCTCGTGTG
57669282 CATATCATA
1 CATATCATA
*
57669291 CATATCATGTG
1 CATATCA--TA
57669302 CATATCATA
1 CATATCATA
* *
57669311 CATGTCATGTG
1 CATATCA--TA
57669322 CATATCATA
1 CATATCATA
*
57669331 CATATCATGTG
1 CATATCA--TA
57669342 CATATCATA
1 CATATCATA
57669351 CATATCAT
1 CATATCAT
57669359 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:57669301 original size:20 final size:20
Alignment explanation
Indices: 57669278--57669360 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
57669268 GAACATCTCG
57669278 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
57669298 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
57669318 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
57669338 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
57669358 TGT
1 TGT
57669361 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:57669307 original size:11 final size:11
Alignment explanation
Indices: 57669278--57669349 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
57669268 GAACATCTCG
57669278 TGTGCATATCA
1 TGTGCATATCA
*
57669289 --TACATATCA
1 TGTGCATATCA
57669298 TGTGCATATCA
1 TGTGCATATCA
* *
57669309 --TACATGTCA
1 TGTGCATATCA
57669318 TGTGCATATCA
1 TGTGCATATCA
*
57669329 --TACATATCA
1 TGTGCATATCA
57669338 TGTGCATATCA
1 TGTGCATATCA
57669349 T
1 T
57669350 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:57670687 original size:27 final size:27
Alignment explanation
Indices: 57670667--57671169 Score: 550
Period size: 27 Copynumber: 18.6 Consensus size: 27
57670657 AGGGTATTTT
*
57670667 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57670694 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
57670721 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57670748 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
57670775 -GATAATTATGTAAATC-AGGGGTAAAAT
1 AG-TAATTCTGTAAATCGA-GGGTAAAAC
* * *
57670802 GGTAATTATGTAAAT-TAGGGGTAAAAC
1 AGTAATTCTGTAAATCGA-GGGTAAAAC
* * *
57670829 GGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
57670856 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
57670883 GGTAATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
57670910 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
57670937 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
57670964 AGTAATTTTCTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57670991 AATAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
57671018 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * ** *
57671045 GGTAATTTTACAAATTGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
57671072 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
57671099 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
57671126 AGTAATTCTATAAA-CTGAGGGTAAAAT
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
57671153 GGTAATTCTGTAAATCG
1 AGTAATTCTGTAAATCG
57671170 GGAGTACTTT
Statistics
Matches: 414, Mismatches: 51, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.01
27 404 0.98
28 5 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:57670753 original size:81 final size:81
Alignment explanation
Indices: 57670668--57671169 Score: 609
Period size: 81 Copynumber: 6.2 Consensus size: 81
57670658 GGGTATTTTA
* * *
57670668 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
*
57670733 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAACG
* * ** * *
57670749 GTAATTCTGTAAATCGAGGGTAAAACGATAATTATGTAAATC-AGGGGTAAAATGGTAATTATGT
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGA-GGGTAAAACAGTAATTCTAT
*
57670813 AAAT-TAGGGGTAAAACG
65 AAATCGA-GGGTAAAACG
* ** * *
57670830 GTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGT
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAACAGTAATTCTAT
*
57670894 AAATCGAGGGTAAAATG
65 AAATCGAGGGTAAAACG
* ** * * *
57670911 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTCTA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
* *
57670976 AATCAAGGGTAAAACA
66 AATCGAGGGTAAAACG
* * * *
57670992 ATAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAC
1 GTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTAT
*
57671056 AAATTGAGGGTAAAACG
65 AAATCGAGGGTAAAACG
* * **
57671073 GTAATTCTATAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
*
57671138 AA-CTGAGGGTAAAATG
66 AATC-GAGGGTAAAACG
57671154 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
57671170 GGAGTACTTT
Statistics
Matches: 360, Mismatches: 52, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
80 4 0.01
81 352 0.98
82 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
AATCGAGGGTAAAACG
Found at i:57681051 original size:20 final size:20
Alignment explanation
Indices: 57681026--57681063 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57681016 GTTTATTCGC
*
57681026 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
57681046 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
57681064 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:57684900 original size:43 final size:43
Alignment explanation
Indices: 57684730--57684901 Score: 116
Period size: 43 Copynumber: 4.0 Consensus size: 43
57684720 CATACGATTC
* * * *
57684730 CGATATATGATTTCGTGTAAGACCACATCTTGGATGTTGTCAT
1 CGATATTTGATTACGTGTAAGACCACATCTGGGATGTTGGCAT
* * * * ** *
57684773 CGGT-TTGAGATTTATGTGTAAGACCATATCTGGGACATCGGCAT
1 CGATATT-TGA-TTACGTGTAAGACCACATCTGGGATGTTGGCAT
* * *** **
57684817 CG-TATTTGATTTCCTGTAAGACCTTGTCTGATATAG-TGGCAT
1 CGATATTTGATTACGTGTAAGACCACATCTGGGAT-GTTGGCAT
* *
57684859 CGATATTTGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGATATTTGATTACGTGTAAGACCACATCTGGGATGTTGGCAT
57684902 TGTACGAGTT
Statistics
Matches: 95, Mismatches: 28, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
42 26 0.27
43 40 0.42
44 29 0.31
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
CGATATTTGATTACGTGTAAGACCACATCTGGGATGTTGGCAT
Found at i:57690209 original size:23 final size:23
Alignment explanation
Indices: 57690179--57690229 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
57690169 CATTTCTGAT
57690179 ATTGTAAGATTGTACGGGGTGCC
1 ATTGTAAGATTGTACGGGGTGCC
*
57690202 ATTGTAAGATTGTATGGGGTGCC
1 ATTGTAAGATTGTACGGGGTGCC
57690225 ATTGT
1 ATTGT
57690230 CTATTGTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.33, T:0.35
Consensus pattern (23 bp):
ATTGTAAGATTGTACGGGGTGCC
Found at i:57699422 original size:20 final size:20
Alignment explanation
Indices: 57699389--57699649 Score: 127
Period size: 20 Copynumber: 13.1 Consensus size: 20
57699379 AAGGGTACCA
57699389 AAGTACAAACAGGGGCACGT
1 AAGTACAAACAGGGGCACGT
* * * *
57699409 ATGTGCAAATAGGGGTATCG-
1 AAGTACAAACAGGGGCA-CGT
57699429 AAGTACAAACAGGGGCACGT
1 AAGTACAAACAGGGGCACGT
* * **
57699449 AGGTACAAACAGGGGTACCA
1 AAGTACAAACAGGGGCACGT
* * *
57699469 AAGTACAATCAAGGGCATGT
1 AAGTACAAACAGGGGCACGT
* * * *
57699489 ACGTGCAGACAGGGGTAC-T
1 AAGTACAAACAGGGGCACGT
* * ** *
57699508 AAAGAACAATCAGGCACACAT
1 -AAGTACAAACAGGGGCACGT
* * *
57699529 ATGTGCAAACAGGGGTAC-T
1 AAGTACAAACAGGGGCACGT
*
57699548 AAAGTACAAACAAGGGCACGT
1 -AAGTACAAACAGGGGCACGT
* * * **
57699569 ATGTGCAAACAAGGATACCG-
1 AAGTACAAACAGGGGCA-CGT
* *
57699589 AAGTACAATCAAGGGCACGT
1 AAGTACAAACAGGGGCACGT
* * *
57699609 ATGTGCAAACAGGGGTATCG-
1 AAGTACAAACAGGGGCA-CGT
*
57699629 AAGTACAACCAGGGGCACGT
1 AAGTACAAACAGGGGCACGT
57699649 A
1 A
57699650 TGTGCAAATA
Statistics
Matches: 168, Mismatches: 63, Indels: 20
0.67 0.25 0.08
Matches are distributed among these distances:
19 8 0.05
20 152 0.90
21 8 0.05
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.15
Consensus pattern (20 bp):
AAGTACAAACAGGGGCACGT
Found at i:57699436 original size:40 final size:40
Alignment explanation
Indices: 57699389--57699699 Score: 311
Period size: 40 Copynumber: 7.8 Consensus size: 40
57699379 AAGGGTACCA
*
57699389 AAGTACAAACAGGGGCACGTATGTGCAAATAGGGGTATCG
1 AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATCG
* * * *
57699429 AAGTACAAACAGGGGCACGTAGGTACAAACAGGGGTACCA
1 AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATCG
* * * * * *
57699469 AAGTACAATCAAGGGCATGTACGTGCAGACAGGGGTA-CTA
1 AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATC-G
* * ** * *
57699509 AAGAACAATCAGGCACACATATGTGCAAACAGGGGTA-CTA
1 AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATC-G
* * * *
57699549 AAGTACAAACAAGGGCACGTATGTGCAAACAAGGATACCG
1 AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATCG
* *
57699589 AAGTACAATCAAGGGCACGTATGTGCAAACAGGGGTATCG
1 AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATCG
* * *
57699629 AAGTACAACCAGGGGCACGTATGTGCAAATATGGGTATCG
1 AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATCG
* * * * *
57699669 AACTACAAATAGTGACACATATGTGCAAACA
1 AAGTACAAACAGGGGCACGTATGTGCAAACA
57699700 TTCACTAATT
Statistics
Matches: 226, Mismatches: 43, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
39 1 0.00
40 224 0.99
41 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGTATGTGCAAACAGGGGTATCG
Found at i:57699692 original size:120 final size:119
Alignment explanation
Indices: 57699381--57699699 Score: 363
Period size: 120 Copynumber: 2.7 Consensus size: 119
57699371 ATGCGTTAAA
* *
57699381 GGGTACCAAAGTACAAACAGGGGCACGTATGTGCAAATAGGGGTATCGAAGTACAAACAGGGGCA
1 GGGTACTAAAGTACAAACAGGGGCACGTATGTGCAAATAGGGGTATCGAAGTACAAA-AAGGGCA
* * * * * *
57699446 CGTAGGTACAAACAGGGGTACCAAAGTACAATCAAGGGCATGTACGTGCAGACAG
65 CGTATGTGCAAACAAGGATACCAAAGTACAATCAAGGGCACGTACGTGCAAACAG
* * ** * * *
57699501 GGGTACTAAAGAACAATCAGGCACACATATGTGCAAACAGGGGTA-CTAAAGTACAAACAAGGGC
1 GGGTACTAAAGTACAAACAGGGGCACGTATGTGCAAATAGGGGTATC-GAAGTACAAA-AAGGGC
* *
57699565 ACGTATGTGCAAACAAGGATACCGAAGTACAATCAAGGGCACGTATGTGCAAACAG
64 ACGTATGTGCAAACAAGGATACCAAAGTACAATCAAGGGCACGTACGTGCAAACAG
* * * * * *
57699621 GGGTA-TCGAAGTACAACCAGGGGCACGTATGTGCAAATATGGGTATCGAACTACAAATAGTGAC
1 GGGTACT-AAAGTACAAACAGGGGCACGTATGTGCAAATAGGGGTATCGAAGTACAAAAAG-GGC
*
57699685 ACATATGTGCAAACA
64 ACGTATGTGCAAACA
57699700 TTCACTAATT
Statistics
Matches: 165, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
119 4 0.02
120 160 0.97
121 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.16
Consensus pattern (119 bp):
GGGTACTAAAGTACAAACAGGGGCACGTATGTGCAAATAGGGGTATCGAAGTACAAAAAGGGCAC
GTATGTGCAAACAAGGATACCAAAGTACAATCAAGGGCACGTACGTGCAAACAG
Found at i:57699773 original size:21 final size:21
Alignment explanation
Indices: 57699748--57699790 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
57699738 AATGTAAAAG
57699748 TACAAATAGAAATTCATTCAC
1 TACAAATAGAAATTCATTCAC
57699769 TACAAATAGAAATTCATTCAC
1 TACAAATAGAAATTCATTCAC
57699790 T
1 T
57699791 TATTGGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (21 bp):
TACAAATAGAAATTCATTCAC
Found at i:57702470 original size:29 final size:29
Alignment explanation
Indices: 57702438--57702510 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
57702428 ATTTAAATTC
57702438 GCACACTTAGTGCCATACTTTTCAAGCTT
1 GCACACTTAGTGCCATACTTTTCAAGCTT
57702467 GCACACTTAGTGCCATACTTTTCAAGCTT
1 GCACACTTAGTGCCATACTTTTCAAGCTT
57702496 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
57702511 ATCTTGTCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.32
Consensus pattern (29 bp):
GCACACTTAGTGCCATACTTTTCAAGCTT
Found at i:57705980 original size:19 final size:19
Alignment explanation
Indices: 57705943--57705981 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
57705933 AAAGCCGAAT
**
57705943 TCTTTCTTCTTCTTTTCTC
1 TCTTTCTTCTTCTCATCTC
*
57705962 TCTTTCTTTTTCTCATCTC
1 TCTTTCTTCTTCTCATCTC
57705981 T
1 T
57705982 TCCTTCCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTTTCTTCTTCTCATCTC
Found at i:57713161 original size:40 final size:39
Alignment explanation
Indices: 57713116--57713387 Score: 242
Period size: 40 Copynumber: 6.8 Consensus size: 39
57713106 TAAAGGTACT
* *
57713116 GAAGTACAAACAGAGGCACGTATATGCAAACAGTGGTATC
1 GAAGTACAAACAGGGGCACGTATGTGCAAACAG-GGTATC
* * * **
57713156 AAAGTACAAACAGGTGCACTTA-GCTGCAAACAAGGGTGCC
1 GAAGTACAAACAGGGGCACGTATG-TGCAAAC-AGGGTATC
** *
57713196 GAAGTACAATTAGGGGCACGTATGTGCAAACAAGGGTACC
1 GAAGTACAAACAGGGGCACGTATGTGCAAAC-AGGGTATC
* * * * *
57713236 GAAGTACAATCTGGGGCATC-TAAGTACAAAAAGGGGTATC
1 GAAGTACAAACAGGGGCA-CGTATGTGCAAACA-GGGTATC
* * * *
57713276 GAAGTACAAATAGGGGCATGCATGTGCAAACATGGGTATT
1 GAAGTACAAACAGGGGCACGTATGTGCAAACA-GGGTATC
* *
57713316 GAAGTACAATCAGGGGCACGTATGTGCAAATAGGGGTATC
1 GAAGTACAAACAGGGGCACGTATGTGCAAACA-GGGTATC
** *
57713356 GAAGTACAAACAATGGCACGCATGTGCAAACA
1 GAAGTACAAACAGGGGCACGTATGTGCAAACA
57713388 TTCAATAATT
Statistics
Matches: 185, Mismatches: 41, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
39 1 0.01
40 180 0.97
41 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (39 bp):
GAAGTACAAACAGGGGCACGTATGTGCAAACAGGGTATC
Found at i:57713271 original size:20 final size:20
Alignment explanation
Indices: 57713248--57713365 Score: 69
Period size: 20 Copynumber: 5.9 Consensus size: 20
57713238 AGTACAATCT
*
57713248 GGGGCATCTAAGTACAAAAA
1 GGGGCATCGAAGTACAAAAA
* *
57713268 GGGGTATCGAAGTACAAATA
1 GGGGCATCGAAGTACAAAAA
* * *
57713288 GGGGCAT-GCATGTGCAAACA
1 GGGGCATCG-AAGTACAAAAA
* * * **
57713308 TGGGTATTGAAGTACAATCA
1 GGGGCATCGAAGTACAAAAA
* * *
57713328 GGGGCA-CGTATGTGCAAATA
1 GGGGCATCG-AAGTACAAAAA
*
57713348 GGGGTATCGAAGTACAAA
1 GGGGCATCGAAGTACAAA
57713366 CAATGGCACG
Statistics
Matches: 72, Mismatches: 22, Indels: 8
0.71 0.22 0.08
Matches are distributed among these distances:
19 2 0.03
20 67 0.93
21 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (20 bp):
GGGGCATCGAAGTACAAAAA
Found at i:57714425 original size:21 final size:22
Alignment explanation
Indices: 57714376--57714425 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
57714366 TAAAATTTCT
* *
57714376 TAATAAAATTTCAATACGACCC
1 TAATAAAATCTCAATACGACAC
57714398 TAATAAAATCTC-ATA-GACAC
1 TAATAAAATCTCAATACGACAC
57714418 TAAATAAA
1 T-AATAAA
57714426 TATTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 11 0.44
ACGTcount: A:0.52, C:0.18, G:0.04, T:0.26
Consensus pattern (22 bp):
TAATAAAATCTCAATACGACAC
Found at i:57717529 original size:40 final size:40
Alignment explanation
Indices: 57717443--57717665 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
57717433 TTTTTGGATG
*
57717443 ATATCCGGGCTAAGACCCGAAGGCACTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* * *
57717484 ATATCCGAGTTAAGTCCCGAAGGCATTTGCGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
** *
57717524 ATATCCGGATTAAGTCCCGAAGGCATTTGTGCTAGTGACG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
57717564 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
57717604 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGATTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACT
* *
57717644 ATATCC-GGTTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
57717666 TACTTGGGTT
Statistics
Matches: 162, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 14 0.09
40 125 0.77
41 23 0.14
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:57720680 original size:46 final size:46
Alignment explanation
Indices: 57720627--57720802 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
57720617 TATTTGGGCA
57720627 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
57720673 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATG-TAACTAG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T-G
* * *
57720717 GCATCTAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TC--CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
57720766 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
57720803 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 11, Indels: 22
0.77 0.08 0.16
Matches are distributed among these distances:
42 3 0.03
43 6 0.06
44 3 0.03
46 61 0.56
47 24 0.22
49 3 0.03
50 5 0.05
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:57723471 original size:25 final size:25
Alignment explanation
Indices: 57723443--57723498 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
57723433 TCGTGTCAAT
57723443 TAATTACAATTTCAATCCATTTAAA
1 TAATTACAATTTCAATCCATTTAAA
57723468 TAATTACAATTTCAATCCATTTAAA
1 TAATTACAATTTCAATCCATTTAAA
57723493 TAATTA
1 TAATTA
57723499 AGTCATTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATTACAATTTCAATCCATTTAAA
Found at i:57724360 original size:17 final size:16
Alignment explanation
Indices: 57724338--57724370 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
57724328 TATTTAACCC
57724338 AAATTAAAATTGAATTA
1 AAATTAAAATT-AATTA
57724355 AAATTAAAATTAATTA
1 AAATTAAAATTAATTA
57724371 TATTATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATTAAAATTAATTA
Found at i:57730579 original size:38 final size:35
Alignment explanation
Indices: 57730518--57730635 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 35
57730508 TCAATCATGC
*
57730518 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
*
57730557 ACTGGGCCGAAGCATTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
57730588 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
57730619 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
57730636 ACTGTAAACG
Statistics
Matches: 76, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
31 48 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 13 0.17
39 11 0.14
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:57730632 original size:31 final size:31
Alignment explanation
Indices: 57730541--57730635 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
57730531 CCTTTTCATA
* *
57730541 TTTCATATTTCATAATACTGGGCCGAAGCAT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
57730572 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
57730603 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
57730634 TT
1 TT
57730636 ACTGTAAACG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:57730878 original size:24 final size:24
Alignment explanation
Indices: 57730827--57730969 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
57730817 GCTTTATCAT
*
57730827 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
57730852 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
57730876 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
57730899 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
57730923 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
57730947 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
57730970 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:57730906 original size:47 final size:48
Alignment explanation
Indices: 57730827--57730968 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
57730817 GCTTTATCAT
* *
57730827 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
57730876 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
57730923 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
57730969 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:57730927 original size:71 final size:72
Alignment explanation
Indices: 57730826--57730969 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
57730816 TGCTTTATCA
*
57730826 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
57730891 GCCCTTT
66 GCCCTTT
* * **
57730898 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
57730961 AGCCCTTT
65 AGCCCTTT
57730969 T
1 T
57730970 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:57731044 original size:20 final size:20
Alignment explanation
Indices: 57731019--57731078 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
57731009 TATGATTACC
57731019 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
57731039 TCATGTGCATAGCATACATT
1 TCATGTGCATATCATACATA
57731059 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
57731079 CCGTATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:57731153 original size:25 final size:25
Alignment explanation
Indices: 57731121--57731168 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
57731111 ATACATAAAC
* * *
57731121 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
57731146 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
57731169 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:57732388 original size:27 final size:27
Alignment explanation
Indices: 57732326--57732390 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
57732316 GGGCATATTC
57732326 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
57732353 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
57732380 GTCTTTTTACC
1 GTCATTTTACC
57732391 TTTTAAGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:57732474 original size:27 final size:26
Alignment explanation
Indices: 57732444--57732499 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
57732434 GTAAATCAAC
*
57732444 AAACCAAAGGTATTTC-AGTAATTTTGT
1 AAACCAAAGGTACTTCTA-TAATTTT-T
*
57732471 AAACCAATGGTACTTCTATAATTTTT
1 AAACCAAAGGTACTTCTATAATTTTT
57732497 AAA
1 AAA
57732500 AAGTCAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (26 bp):
AAACCAAAGGTACTTCTATAATTTTT
Found at i:57732540 original size:27 final size:27
Alignment explanation
Indices: 57732452--57732590 Score: 95
Period size: 27 Copynumber: 5.0 Consensus size: 27
57732442 ACAAACCAAA
* * **
57732452 GGTATTTCAGTAATTTTGTAAACCAAT
1 GGTATTTCTGTAATTTTGTAAATCAGG
* * *
57732479 GGTACTTCTATAATTTT-TAAAAAGTCAAG
1 GGTATTTCTGTAATTTTGT--AAA-TCAGG
*
57732508 GGTATTTCTGTAACTTTGTAAATCAGG
1 GGTATTTCTGTAATTTTGTAAATCAGG
** *
57732535 GGTATTT-TGGTAATTTTACAAAT-TGAG
1 GGTATTTCT-GTAATTTTGTAAATCAG-G
*
57732562 GGTATTTCGGTAATTTTGTAAATCGAGG
1 GGTATTTCTGTAATTTTGTAAATC-AGG
57732590 G
1 G
57732591 TAAAACAGTA
Statistics
Matches: 86, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
26 3 0.03
27 56 0.65
28 8 0.09
29 18 0.21
30 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTATTTCTGTAATTTTGTAAATCAGG
Found at i:57732591 original size:27 final size:27
Alignment explanation
Indices: 57732543--57732970 Score: 262
Period size: 27 Copynumber: 15.9 Consensus size: 27
57732533 GGGGTATTTT
* * **
57732543 GGTAATTTTACAAATTGAGGGTATTTC
1 GGTAATTTTATAAATCGAGGGTAAATC
* *
57732570 GGTAATTTTGTAAATCGAGGGTAAAAC
1 GGTAATTTTATAAATCGAGGGTAAATC
* *
57732597 AGTAATTCTATAAATCGAGGGTAAAAT-
1 GGTAATTTTATAAATCGAGGGT-AAATC
* * *
57732624 GGTAATTCTGTAAATCGAGGGTAAAAC
1 GGTAATTTTATAAATCGAGGGTAAATC
* * * *
57732651 GGTAATTCTGTAAGTCGAGGGTAAAAC
1 GGTAATTTTATAAATCGAGGGTAAATC
* *
57732678 GATAATTATT-TAAATC-AGGGGTAAAAC
1 GGTAATT-TTATAAATCGA-GGGTAAATC
* * * * *
57732705 GGTAATTATGTAAATTGTGGGTAAAAC
1 GGTAATTTTATAAATCGAGGGTAAATC
* * *
57732732 GGTAATTCTGTAAGTCGAGGGTAAAAT-
1 GGTAATTTTATAAATCGAGGGT-AAATC
* * *
57732759 GATAATTATGTAAATC-AGGGGTAAAAT-
1 GGTAATTTTATAAATCGA-GGGT-AAATC
* * * *
57732786 GGTAATTATGTAAAT-TAGGGGTAAAAC
1 GGTAATTTTATAAATCGA-GGGTAAATC
*
57732813 GGTAATTCTATAAATCGAGGGTAAAAT-
1 GGTAATTTTATAAATCGAGGGT-AAATC
** * * * *
57732840 AATAATTCTGTAAA-CTGAGGATAAAAC
1 GGTAATTTTATAAATC-GAGGGTAAATC
*
57732867 GGTAATTTTATAAATCGAGGGTAAAAC
1 GGTAATTTTATAAATCGAGGGTAAATC
* * *
57732894 AGTAATTTTACAAATCGAGGGTAAAAC
1 GGTAATTTTATAAATCGAGGGTAAATC
* * ** *
57732921 GATAATTCTATAAATCGAGGGTACTTT
1 GGTAATTTTATAAATCGAGGGTAAATC
* *
57732948 GGTAATTTTACAAGTCGAGGGTA
1 GGTAATTTTATAAATCGAGGGTA
57732971 TTTCAATAAT
Statistics
Matches: 327, Mismatches: 59, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
26 13 0.04
27 302 0.92
28 12 0.04
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (27 bp):
GGTAATTTTATAAATCGAGGGTAAATC
Found at i:57732627 original size:81 final size:81
Alignment explanation
Indices: 57732542--57732970 Score: 436
Period size: 81 Copynumber: 5.3 Consensus size: 81
57732532 AGGGGTATTT
* * *** *
57732542 TGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTGTAAATCGAGGGTAAAAC-AGTAATTCT
1 TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGA-TAATTCT
57732606 ATAAATCGAGGGTAAAA
65 ATAAATCGAGGGTAAAA
* * * * *
57732623 TGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGATAATTATT
1 TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTA
57732688 TAAATC-AGGGGTAAAA
66 TAAATCGA-GGGTAAAA
* * * * * * * * *
57732704 CGGTAATTATGTAAATTGTGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAATGATAATTATG
1 TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTA
57732769 TAAATC-AGGGGTAAAA
66 TAAATCGA-GGGTAAAA
* * * * **
57732785 TGGTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAATAATTCT
1 TGGTAATTTTATAAATCGA-GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCT
* *
57732849 GTAAA-CTGAGGATAAAA
65 ATAAATC-GAGGGTAAAA
* * * **
57732866 CGGTAATTTTATAAATCGAGGGTAAAACAGTAATTTTACAAATCGAGGGTAAAACGATAATTCTA
1 TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTA
***
57732931 TAAATCGAGGGTACTT
66 TAAATCGAGGGTAAAA
* *
57732947 TGGTAATTTTACAAGTCGAGGGTA
1 TGGTAATTTTATAAATCGAGGGTA
57732971 TTTCAATAAT
Statistics
Matches: 299, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
80 2 0.01
81 293 0.98
82 4 0.01
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (81 bp):
TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTA
TAAATCGAGGGTAAAA
Found at i:57732953 original size:54 final size:54
Alignment explanation
Indices: 57732570--57732970 Score: 380
Period size: 54 Copynumber: 7.4 Consensus size: 54
57732560 AGGGTATTTC
* *
57732570 GGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAT
1 GGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
* * * * *
57732624 GGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAAC
1 GGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
* * * * * *
57732678 GATAATTATT-TAAATC-AGGGGTAAAACGGTAATTATGTAAATTGTGGGTAAAAC
1 GGTAATT-TTATAAATCGA-GGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
* * * * * * *
57732732 GGTAATTCTGTAAGTCGAGGGTAAAATGATAATTATGTAAATC-AGGGGTAAAAT
1 GGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGA-GGGTAAAAT
* * *
57732786 GGTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
1 GGTAATTTTATAAATCGA-GGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
** * * * * *
57732840 AATAATTCTGTAAA-CTGAGGATAAAACGGTAATTTTATAAATCGAGGGTAAAAC
1 GGTAATTTTATAAATC-GAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
* * * ***
57732894 AGTAATTTTACAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTACTTT
1 GGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
* *
57732948 GGTAATTTTACAAGTCGAGGGTA
1 GGTAATTTTATAAATCGAGGGTA
57732971 TTTCAATAAT
Statistics
Matches: 291, Mismatches: 46, Indels: 20
0.82 0.13 0.06
Matches are distributed among these distances:
53 3 0.01
54 283 0.97
55 5 0.02
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.29
Consensus pattern (54 bp):
GGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
Found at i:57732980 original size:27 final size:27
Alignment explanation
Indices: 57732868--57733144 Score: 181
Period size: 27 Copynumber: 10.3 Consensus size: 27
57732858 GGATAAAACG
* ***
57732868 GTAATTTTATAAATCGAGGGTAAAACA
1 GTAATTTTACAAATCGAGGGTATTTCA
***
57732895 GTAATTTTACAAATCGAGGGTAAAAC-
1 GTAATTTTACAAATCGAGGGTATTTCA
* * *
57732921 GATAATTCTATAAATCGAGGGTACTTT-G
1 G-TAATTTTACAAATCGAGGGTA-TTTCA
*
57732949 GTAATTTTACAAGTCGAGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
* **
57732976 ATAATTTTACAGGTCGAGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
* * **
57733003 GTAATTTCACAAAT-TAGGGGTATTTTG
1 GTAATTTTACAAATCGA-GGGTATTTCA
* **
57733030 GTAATTTTACAAA-CTAGGGGTATTTTG
1 GTAATTTTACAAATCGA-GGGTATTTCA
* **
57733057 GTAATTTTACAAA-CTAGGGGTATTTTG
1 GTAATTTTACAAATCGA-GGGTATTTCA
* * *
57733084 GTAATTTTATAAACCAAGGGTAATTT-A
1 GTAATTTTACAAATCGAGGGT-ATTTCA
* **
57733111 GTAATTTTACAAAGC-AGGGTATTTTG
1 GTAATTTTACAAATCGAGGGTATTTCA
57733137 GTAATTTT
1 GTAATTTT
57733145 GTAAACCAAA
Statistics
Matches: 215, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.02
26 18 0.08
27 186 0.87
28 7 0.03
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.37
Consensus pattern (27 bp):
GTAATTTTACAAATCGAGGGTATTTCA
Found at i:57741008 original size:69 final size:68
Alignment explanation
Indices: 57740884--57741020 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 68
57740874 TTTTAAGAAA
* *
57740884 ATGTTCCTCTTGGATTTTGGTTTGGATTTCGAAATTCATATCTTTGGTCCTTCTTTGGTTCACTT
1 ATGTTCCTCCTGGATTTTGGTTTGGATTTCGAAATTCATATCTTTGGTCCTTCTTTCGTTCACTT
57740949 GTC
66 GTC
*
57740952 ATGTTCCTCCTGGATTTTGGTTTGGATTTTCGAAATTCATGA-CTTTGGTCCTTCTTTCGTTCGC
1 ATGTTCCTCCTGGATTTTGGTTTGGA-TTTCGAAATTCAT-ATCTTTGGTCCTTCTTTCGTTCAC
57741016 TTGTC
64 TTGTC
57741021 TTCTTCTTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
68 25 0.39
69 38 0.59
70 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (68 bp):
ATGTTCCTCCTGGATTTTGGTTTGGATTTCGAAATTCATATCTTTGGTCCTTCTTTCGTTCACTT
GTC
Found at i:57741137 original size:16 final size:15
Alignment explanation
Indices: 57741111--57741140 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
57741101 TGAAAAAATA
57741111 TAAAAATAACAGAAT
1 TAAAAATAACAGAAT
57741126 TAAAATATAACAGAA
1 TAAAA-ATAACAGAA
57741141 AAAAAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
TAAAAATAACAGAAT
Found at i:57755051 original size:62 final size:64
Alignment explanation
Indices: 57754982--57755105 Score: 189
Period size: 68 Copynumber: 1.9 Consensus size: 64
57754972 TATTAGGGGC
*
57754982 AAAAGTATAATTTTTCC-AT-AATTTTGGGCTAAATTGAATAGAATGATAATTAAATACAGGGA
1 AAAAGTATAATTTTTCCAATGAATTTTAGGCTAAATTGAATAGAATGATAATTAAATACAGGGA
57755044 AAAAGTATAATTTTTCCATAATATGAATTTTAGGCTAAATTGAATAGAATGATAATTAAATA
1 AAAAGTATAATTTTTCC---A-ATGAATTTTAGGCTAAATTGAATAGAATGATAATTAAATA
57755106 AGTTAAATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
62 17 0.31
67 2 0.04
68 36 0.65
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (64 bp):
AAAAGTATAATTTTTCCAATGAATTTTAGGCTAAATTGAATAGAATGATAATTAAATACAGGGA
Found at i:57759193 original size:2 final size:2
Alignment explanation
Indices: 57759188--57759226 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
57759178 AAAAATCTCT
57759188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57759227 TTATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57761147 original size:79 final size:80
Alignment explanation
Indices: 57761011--57761228 Score: 232
Period size: 79 Copynumber: 2.8 Consensus size: 80
57761001 GAATCACGTA
*** * **
57761011 CCTTCGGAAT-TTAA-CCGGATATAACGACTCGCTCAAATGCCTTCGGGACAAAGCCCGG-TTAT
1 CCTTCGG-ATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-T
*
57761073 AGTAACTCGCACGAATG
64 AGTAACTCGCACGAACG
* *
57761090 CCTTCGGGA-CTTAACCCGGGTTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTA
1 CCTTC-GGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTA
*
57761153 TTAACTCGCACGAACG
65 GTAACTCGCACGAACG
** * *
57761169 CCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
57761229 CATCATTCAA
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
78 3 0.03
79 63 0.54
80 50 0.43
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CCTTCGGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAG
TAACTCGCACGAACG
Found at i:57761228 original size:40 final size:39
Alignment explanation
Indices: 57761037--57761228 Score: 190
Period size: 40 Copynumber: 4.8 Consensus size: 39
57761027 GGATATAACG
* ** *
57761037 ACTCGCTCAAATGCCTTCGGGACAAAGCCCGGTTATAGTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
57761077 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* *
57761117 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * *
57761156 ACTCGCACGAACGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
57761196 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
57761229 CATCATTCAA
Statistics
Matches: 126, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 83 0.66
41 10 0.08
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:57769162 original size:79 final size:80
Alignment explanation
Indices: 57769026--57769243 Score: 232
Period size: 79 Copynumber: 2.8 Consensus size: 80
57769016 GAATCACGTA
*** * **
57769026 CCTTCGGAAT-TTAA-CCGGATATAACGACTCGCTCAAATGCCTTCGGGACAAAGCCCGG-TTAT
1 CCTTCGG-ATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-T
*
57769088 AGTAACTCGCACGAATG
64 AGTAACTCGCACGAACG
* *
57769105 CCTTCGGGA-CTTAACCCGGGTTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTA
1 CCTTC-GGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTA
*
57769168 TTAACTCGCACGAACG
65 GTAACTCGCACGAACG
** * *
57769184 CCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
57769244 CATCATTCAA
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
78 3 0.03
79 63 0.54
80 50 0.43
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CCTTCGGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAG
TAACTCGCACGAACG
Found at i:57769243 original size:40 final size:39
Alignment explanation
Indices: 57769052--57769243 Score: 190
Period size: 40 Copynumber: 4.8 Consensus size: 39
57769042 GGATATAACG
* ** *
57769052 ACTCGCTCAAATGCCTTCGGGACAAAGCCCGGTTATAGTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
57769092 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* *
57769132 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * *
57769171 ACTCGCACGAACGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
57769211 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
57769244 CATCATTCAA
Statistics
Matches: 126, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 83 0.66
41 10 0.08
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:57776264 original size:27 final size:28
Alignment explanation
Indices: 57776207--57776276 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
57776197 AAACTTGTAC
*
57776207 AGCACTAAGTGTGCGAGTTTGATCATGT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
57776235 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
57776262 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
57776277 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:57776287 original size:27 final size:27
Alignment explanation
Indices: 57776207--57776288 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
57776197 AAACTTGTAC
* * *
57776207 AGCACTAAGTGTGCGAGTTTGA-TCATGT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
57776235 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
57776262 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
57776289 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:57784156 original size:31 final size:28
Alignment explanation
Indices: 57784118--57784191 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 28
57784108 CATGAGAATG
*
57784118 GCACTAAGTGTGCGGGTTTAAAACTTGTACA
1 GCACTAAGTGTGCGGGTTT-AAACATGT--A
* * *
57784149 GCACTAAGTGTGCGAGTTTGATCATGTA
1 GCACTAAGTGTGCGGGTTTAAACATGTA
57784177 GCACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
57784192 ACTCACTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 15 0.39
30 5 0.13
31 18 0.47
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTTAAACATGTA
Found at i:57787008 original size:37 final size:37
Alignment explanation
Indices: 57786957--57787042 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 37
57786947 TACGAAGTCT
57786957 TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
*
57786994 TACCCGGACGTAATCTCCACACGTAGTCATCGGGTC-
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
*
57787030 TCACCCGAACATA
1 T-ACCCGGACATA
57787043 TTTCTAAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 1 0.02
37 44 0.98
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.21
Consensus pattern (37 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
Found at i:57787183 original size:49 final size:49
Alignment explanation
Indices: 57787091--57787561 Score: 773
Period size: 49 Copynumber: 9.6 Consensus size: 49
57787081 ATTCACATTA
* * * * *
57787091 GCCATTCGGCTTTACCACATATATATATACATTTCACATTCATCACGTCG
1 GCCATTAGGCCTTATCACATATATATACAC-TTTCACATTCATCACATCG
* *
57787141 GCCATTAGGCCTTATCACATATGTATACACTTTCACATTCATCACGTCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
*
57787190 GCCATTAGGCCTTATCACATATATATACATTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
* *
57787239 GCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACGTCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
*
57787288 GCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
* *
57787337 GCCATTAGGCCTTATCACATATATATACACTTTCGCATTCATCACGTCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
57787386 GCCATTAGGCCTTATCACATATAT-TCACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATATAT-ACACTTTCACATTCATCACATCG
*
57787435 GCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
* *
57787484 GCCATTAGGCCTTATCACATATATACACACTTTCGCATTCATCACATCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
57787533 GCCATTAGGCCTTATCACATATATATACA
1 GCCATTAGGCCTTATCACATATATATACA
57787562 TCTCATACAT
Statistics
Matches: 399, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
48 1 0.00
49 373 0.93
50 25 0.06
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
Found at i:57790521 original size:41 final size:41
Alignment explanation
Indices: 57790383--57790523 Score: 148
Period size: 40 Copynumber: 3.5 Consensus size: 41
57790373 GCTCGATTGT
* *
57790383 CTTCGGGACATAGCCCGG-TTATAGTGA-TTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATT-TAGTAACTTCGCACAAATGC
* *
57790423 CTTCGGGACTTAACCC-GATTTTGGTAAC-TCGCACAAATGC
1 CTTCGGGACTTAGCCCGGA-TTTAGTAACTTCGCACAAATGC
* * * *
57790463 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAGGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAACTTCGCACAAATGC
57790504 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGAT
57790524 ACCATTCGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
39 1 0.01
40 50 0.60
41 31 0.37
42 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (41 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTTCGCACAAATGC
Found at i:57791312 original size:40 final size:40
Alignment explanation
Indices: 57791268--57791579 Score: 511
Period size: 40 Copynumber: 7.8 Consensus size: 40
57791258 CCAGCATGAT
* *
57791268 TGCTCTTCGGGACCTAG-CCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCC-GGATACATCACTAGCACGAA
57791308 TGCTCCTT-GGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCT-CTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
57791348 TGCTCTTCGGAACTTAGTCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
57791388 TGCTCTTCGGAACATAGTCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
57791428 TGCTCTTCGGAACTTAGTCTGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
57791468 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
57791508 TGCTCTTCGGAACTTAGTCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
57791548 TGCTCTTCGGAACTTAGTCCGGATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
57791580 CTCAATTCTC
Statistics
Matches: 258, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
39 3 0.01
40 250 0.97
41 5 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:57794532 original size:49 final size:49
Alignment explanation
Indices: 57794476--57794662 Score: 338
Period size: 49 Copynumber: 3.8 Consensus size: 49
57794466 TATGATATAC
57794476 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
57794525 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
* * * *
57794574 ATATGTATGTGATAAGGCCTAAGGGCCGATGTGATGAATGTGGAAGTGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
57794623 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
57794663 CGATATGTAT
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 132 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (49 bp):
ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
Found at i:57794676 original size:44 final size:47
Alignment explanation
Indices: 57794476--57794692 Score: 264
Period size: 49 Copynumber: 4.6 Consensus size: 47
57794466 TATGATATAC
57794476 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT-GAAAATGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTCG--AA-GT
57794525 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT-GAAAATGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTCG--AA-GT
* * *
57794574 ATATGTATGTGATAAGGCCTAAGGGCCGATGTGATGAATGTGGAAGTGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTCGAA--GT
57794623 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG-CG-A-T
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTCGAAGT
* * * *
57794667 ATGTATATGTGGTAAAGCCGAATGGC
1 ATATATATGTGATAAGGCCTAATGGC
57794693 TAATGTGAAT
Statistics
Matches: 157, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
44 23 0.15
47 1 0.01
48 3 0.02
49 129 0.82
50 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTCGAAGT
Found at i:57794792 original size:37 final size:37
Alignment explanation
Indices: 57794741--57794827 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 37
57794731 AACTTGGAAA
57794741 TATGTTCCGGGTACGACCCGATGACTACATGTGGAGAT
1 TATG-TCCGGGTACGACCCGATGACTACATGTGGAGAT
**
57794779 TATGTCCGGGTACGACCCGATGACTATGTGTGGAGAT
1 TATGTCCGGGTACGACCCGATGACTACATGTGGAGAT
57794816 TATGTCCGGGTA
1 TATGTCCGGGTA
57794828 AGACTTCGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 43 0.91
38 4 0.09
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.28
Consensus pattern (37 bp):
TATGTCCGGGTACGACCCGATGACTACATGTGGAGAT
Found at i:57796815 original size:40 final size:40
Alignment explanation
Indices: 57796691--57796802 Score: 188
Period size: 40 Copynumber: 2.8 Consensus size: 40
57796681 GAGAATGGAG
*
57796691 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
57796731 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* * *
57796771 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCA
57796803 ATCATACTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:57797646 original size:40 final size:41
Alignment explanation
Indices: 57797547--57797647 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 41
57797537 TCGAATGGTG
* *
57797547 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 TCCGGGCTAAATCCCGAAGGCATTTGTGCTAAGTGACTAAA
* * * * *
57797588 TCCAGG-TCAATTCTCGAAGGCATTTGTGC-GAGTTACTAAA
1 TCCGGGCT-AAATCCCGAAGGCATTTGTGCTAAGTGACTAAA
57797628 TCCGGGCTAAATCCCGAAGG
1 TCCGGGCTAAATCCCGAAGG
57797648 TACGTGATTC
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 25 0.51
41 24 0.49
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAATCCCGAAGGCATTTGTGCTAAGTGACTAAA
Found at i:57799769 original size:11 final size:11
Alignment explanation
Indices: 57799753--57799795 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
57799743 AGAAAGAATA
57799753 AAAAAAAAAGG
1 AAAAAAAAAGG
** *
57799764 AAAAAATGATG
1 AAAAAAAAAGG
*
57799775 AAAACAAAAGG
1 AAAAAAAAAGG
57799786 AAAAAAAAAG
1 AAAAAAAAAG
57799796 TGTCCATCCT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:57800029 original size:7 final size:7
Alignment explanation
Indices: 57800017--57800048 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
57800007 GTTGTCTTCT
57800017 TGTTTGA
1 TGTTTGA
57800024 TGTTTGA
1 TGTTTGA
57800031 TGTTTGA
1 TGTTTGA
57800038 TGTTTGA
1 TGTTTGA
57800045 TGTT
1 TGTT
57800049 GTGGTGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.59
Consensus pattern (7 bp):
TGTTTGA
Found at i:57800975 original size:27 final size:28
Alignment explanation
Indices: 57800919--57800988 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
57800909 AAATTTGTAC
57800919 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
* *
57800947 AGCACTAGGTGTGCGAG-TTGATTTTAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
57800974 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
57800989 GACTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:57803664 original size:49 final size:49
Alignment explanation
Indices: 57803608--57803794 Score: 329
Period size: 49 Copynumber: 3.8 Consensus size: 49
57803598 TATGATATAC
57803608 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
57803657 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
* * * *
57803706 ATATGTATGTGATAAGGCCTAAGGGCCGATGTGATGAATGTGGAAGTGT
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
*
57803755 ATATATATGTGATAAGGCCTAATGGCTGATGTGATGAATG
1 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
57803795 CGATATGTAT
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 131 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGT
Found at i:57803924 original size:37 final size:37
Alignment explanation
Indices: 57803873--57803959 Score: 156
Period size: 37 Copynumber: 2.3 Consensus size: 37
57803863 AACTTGGAAA
57803873 TATGTTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTACGACCCGATGACTACGTGTGGAGAT
*
57803911 TATGTCCGGGTACGACCCGATGACTATGTGTGGAGAT
1 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
57803948 TATGTCCGGGTA
1 TATGTCCGGGTA
57803960 AGACTTCGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 44 0.92
38 4 0.08
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.28
Consensus pattern (37 bp):
TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
Found at i:57806782 original size:26 final size:28
Alignment explanation
Indices: 57806718--57806786 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
57806708 AAATTTGTAC
57806718 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
57806746 AGCACTAAGTGTGCGAG-TTGATTA-AT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
57806772 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
57806787 GACTCACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 16 0.41
27 6 0.15
28 17 0.44
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:57814695 original size:27 final size:28
Alignment explanation
Indices: 57814638--57814707 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
57814628 AAACTTGTAC
*
57814638 AGCACTAAGTGTGCGAGTTTGATCATGT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
57814666 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
57814693 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
57814708 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:57814718 original size:27 final size:27
Alignment explanation
Indices: 57814638--57814719 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
57814628 AAACTTGTAC
* * *
57814638 AGCACTAAGTGTGCGAGTTTGA-TCATGT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
57814666 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
57814693 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
57814720 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:57827668 original size:25 final size:25
Alignment explanation
Indices: 57827639--57827725 Score: 138
Period size: 25 Copynumber: 3.5 Consensus size: 25
57827629 ACCTTAGTGC
*
57827639 GCTCTATGATTATTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
* *
57827664 GCTCTCTCATTATTTGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
*
57827689 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTCAGT
57827714 GCTCTCTGATTA
1 GCTCTCTGATTA
57827726 GCACATATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:57827728 original size:22 final size:22
Alignment explanation
Indices: 57827650--57827742 Score: 89
Period size: 25 Copynumber: 4.0 Consensus size: 22
57827640 CTCTATGATT
*
57827650 ATTAGCACGTCAGTGCTCTCTC
1 ATTAGCACGTCAGTGCTCTCTG
57827672 ATTATTTGCACGTCAGTGCTCTCTG
1 ATTA---GCACGTCAGTGCTCTCTG
*
57827697 ATTATTAGCACGTTAGTGCTCTCTG
1 ---ATTAGCACGTCAGTGCTCTCTG
*
57827722 ATTAGCACAT-ATGTGCTCTCT
1 ATTAGCACGTCA-GTGCTCTCT
57827743 ATTCATTAGT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
21 1 0.02
22 22 0.36
25 34 0.56
28 4 0.07
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (22 bp):
ATTAGCACGTCAGTGCTCTCTG
Found at i:57837064 original size:5 final size:5
Alignment explanation
Indices: 57837033--57837113 Score: 53
Period size: 5 Copynumber: 15.8 Consensus size: 5
57837023 CCTATTATTT
* *
57837033 TTTTA -TTTA TTCTTA TTTT- TATTTA TTTTA TTTTC TTTTC TTTTGA
1 TTTTA TTTTA TT-TTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTT-A
*
57837079 TTTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
57837114 GAAAGACATA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
3 3 0.05
4 5 0.08
5 35 0.56
6 15 0.24
7 4 0.06
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:57837076 original size:15 final size:15
Alignment explanation
Indices: 57837032--57837113 Score: 78
Period size: 16 Copynumber: 5.3 Consensus size: 15
57837022 TCCTATTATT
57837032 TTTTTATTTATTCTTA
1 TTTTTATTTATT-TTA
57837048 TTTTTATTTATTTTA
1 TTTTTATTTATTTTA
*
57837063 TTTTCT-TTTCTTTTGA
1 TTTT-TATTTATTTT-A
*
57837079 TTTTTATTTTCATTTCA
1 TTTTTA-TTT-ATTTTA
*
57837096 ATTTTA-TTATTTTA
1 TTTTTATTTATTTTA
57837110 TTTT
1 TTTT
57837114 GAAAGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
14 8 0.15
15 17 0.31
16 18 0.33
17 9 0.16
18 3 0.05
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTTTATTTATTTTA
Found at i:57837088 original size:17 final size:16
Alignment explanation
Indices: 57837032--57837103 Score: 51
Period size: 17 Copynumber: 4.5 Consensus size: 16
57837022 TCCTATTATT
*
57837032 TTTTTATTTAT-TCTTA
1 TTTTTATTT-TCTTTTA
*
57837048 TTTTTA-TTTATTTTA
1 TTTTTATTTTCTTTTA
*
57837063 -TTTTCTTTTCTTTTGA
1 TTTTTATTTTCTTTT-A
*
57837079 TTTTTATTTTCATTTCA
1 TTTTTATTTTC-TTTTA
*
57837096 ATTTTATT
1 TTTTTATT
57837104 ATTTTATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.11
15 13 0.29
16 7 0.16
17 17 0.38
18 3 0.07
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTTTATTTTCTTTTA
Found at i:57837114 original size:37 final size:35
Alignment explanation
Indices: 57837025--57837115 Score: 83
Period size: 37 Copynumber: 2.5 Consensus size: 35
57837015 TGAATCCTCC
* * *
57837025 TATTATTTTTTTATTTATTCTTATTTTTATTTATTT
1 TATTATTTTATT-TTGATTCTTATTTTCATTTATTT
* * *
57837061 TATTTTCTTTTCTTTTGATTTTTATTTTCATTTCAATTT
1 TA--TTATTTTATTTTGATTCTTATTTTCATTT--ATTT
57837100 TATTATTTTATTTTGA
1 TATTATTTTATTTTGA
57837116 AAGACATATC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
36 2 0.05
37 28 0.64
38 8 0.18
39 6 0.14
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (35 bp):
TATTATTTTATTTTGATTCTTATTTTCATTTATTT
Found at i:57839981 original size:13 final size:13
Alignment explanation
Indices: 57839965--57839997 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
57839955 TTTTATTAAA
*
57839965 TTAGTTAATTAGT
1 TTAGATAATTAGT
57839978 TTAGATAATTAGT
1 TTAGATAATTAGT
57839991 TTA-ATAA
1 TTAGATAA
57839998 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:57854499 original size:20 final size:18
Alignment explanation
Indices: 57854463--57854499 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
57854453 ATTGTAATTT
57854463 ATATTAATTATAAATAAG
1 ATATTAATTATAAATAAG
57854481 ATATTATATTATGAAATAA
1 ATATTA-ATTAT-AAATAA
57854500 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATTAATTATAAATAAG
Found at i:57854625 original size:3 final size:3
Alignment explanation
Indices: 57854607--57854666 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
57854597 TAAAAGATAT
* * *
57854607 TTA TATA TTA -TA TTA TTA TT- TATA TTA TGA -TA TTG GTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
57854651 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
57854667 AAATTAAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 4 0.09
3 38 0.83
4 4 0.09
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:57854646 original size:20 final size:19
Alignment explanation
Indices: 57854604--57854646 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
57854594 AAGTAAAAGA
* *
57854604 TATTTATATATTATATTAT
1 TATTTATATATGATATTAG
*
57854623 TATTTATATTATGATATTGG
1 TATTTATA-TATGATATTAG
57854643 TATT
1 TATT
57854647 ATTATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
TATTTATATATGATATTAG
Found at i:57855952 original size:25 final size:25
Alignment explanation
Indices: 57855913--57856024 Score: 126
Period size: 25 Copynumber: 4.6 Consensus size: 25
57855903 CCTTAGCGCT
*
57855913 CTCTCTGATTGTTAGCATGTTAGTG
1 CTCTCTGATTATTAGCATGTTAGTG
* *
57855938 CTCTCTTATTATTAGCATGTCAGTG
1 CTCTCTGATTATTAGCATGTTAGTG
* *
57855963 ATCTCTGATTATTAGCACGTTAGTG
1 CTCTCTGATTATTAGCATGTTAGTG
57855988 CTCTCTG--TA-TAGCACT-TTAGTG
1 CTCTCTGATTATTAGCA-TGTTAGTG
57856010 CTCTCTG-TTCATTAG
1 CTCTCTGATT-ATTAG
57856025 TGCATAATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
22 18 0.24
23 3 0.04
24 1 0.01
25 52 0.70
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (25 bp):
CTCTCTGATTATTAGCATGTTAGTG
Found at i:57857359 original size:24 final size:24
Alignment explanation
Indices: 57857326--57857399 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
57857316 AAGTCTGTCT
*
57857326 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
57857350 GGAGAGGATTTAGGAGCTGATCAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
57857374 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
57857398 GG
1 GG
57857400 TGAAATGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.31, C:0.05, G:0.42, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:57858870 original size:27 final size:26
Alignment explanation
Indices: 57858830--57858942 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
57858820 AGGAAGCGTC
*
57858830 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
57858857 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
57858884 CTGGTGGTTCTGCCACGGTTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
57858912 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
57858938 CTGGT
1 CTGGT
57858943 AGCCATGCTG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.11
27 50 0.68
28 15 0.21
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:57858934 original size:54 final size:54
Alignment explanation
Indices: 57858830--57858942 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
57858820 AGGAAGCGTC
*
57858830 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * ** *
57858884 CTGGTGGTTCTGCCACGGTTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
57858938 CTGGT
1 CTGGT
57858943 AGCCATGCTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:57861344 original size:2 final size:2
Alignment explanation
Indices: 57861337--57861365 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57861327 TTGATTTACC
57861337 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 A
57861366 CACCAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57863318 original size:40 final size:40
Alignment explanation
Indices: 57863238--57863458 Score: 320
Period size: 40 Copynumber: 5.5 Consensus size: 40
57863228 ACCCAAGTTT
* * * *
57863238 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * * *
57863277 CTTCGGGTCTTAACCCGGACATAGCAACTCGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
57863317 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
57863357 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
* *
57863397 CTTTGGGTCTTAGCCCGGATATAACAACTCGGACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
57863437 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
57863459 CATTCAAATG
Statistics
Matches: 164, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 10 0.06
40 153 0.93
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:57868431 original size:28 final size:28
Alignment explanation
Indices: 57868399--57868456 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
57868389 GATTGTTTGA
57868399 GAGCCGTCACATCTCGATTTTCTTAACG
1 GAGCCGTCACATCTCGATTTTCTTAACG
57868427 GAGCCGTCACATCTCGATTTTCTTAACG
1 GAGCCGTCACATCTCGATTTTCTTAACG
57868455 GA
1 GA
57868457 ACTAATCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (28 bp):
GAGCCGTCACATCTCGATTTTCTTAACG
Found at i:57871694 original size:14 final size:14
Alignment explanation
Indices: 57871677--57871721 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
57871667 GAAAAAATCA
57871677 AAATAAAAAAAAAG
1 AAATAAAAAAAAAG
*
57871691 AAATAAAAAGAAAAA
1 AAATAAAAA-AAAAG
*
57871706 AAAT-CAAAAAAAG
1 AAATAAAAAAAAAG
57871719 AAA
1 AAA
57871722 GAAAGAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.26
14 12 0.44
15 8 0.30
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (14 bp):
AAATAAAAAAAAAG
Found at i:57871698 original size:10 final size:9
Alignment explanation
Indices: 57871682--57871721 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
57871672 AATCAAAATA
57871682 AAAAAAAAG
1 AAAAAAAAG
57871691 AAATAAAAAG
1 AAA-AAAAAG
*
57871701 AAAAAAAAT
1 AAAAAAAAG
*
57871710 CAAAAAAAG
1 AAAAAAAAG
57871719 AAA
1 AAA
57871722 GAAAGAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.85, C:0.03, G:0.07, T:0.05
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:57871699 original size:20 final size:20
Alignment explanation
Indices: 57871671--57871708 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57871661 GACCTTGAAA
* *
57871671 AAATCAAAATAAAAAAAAAG
1 AAATAAAAAGAAAAAAAAAG
57871691 AAATAAAAAGAAAAAAAA
1 AAATAAAAAGAAAAAAAA
57871709 TCAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (20 bp):
AAATAAAAAGAAAAAAAAAG
Found at i:57871732 original size:20 final size:19
Alignment explanation
Indices: 57871668--57871732 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 19
57871658 TGAGACCTTG
57871668 AAAA-AATCAAAATAAA-AA
1 AAAAGAATCAAAA-AAAGAA
*
57871686 AAAAGAA--ATAAAAAGAA
1 AAAAGAATCAAAAAAAGAA
57871703 AAAA-AATCAAAAAAAGAA
1 AAAAGAATCAAAAAAAGAA
57871721 AGAAAGAATCAA
1 A-AAAGAATCAA
57871733 TCAAAGAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 5 0.13
17 9 0.23
18 14 0.36
19 5 0.13
20 6 0.15
ACGTcount: A:0.80, C:0.05, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAAGAATCAAAAAAAGAA
Found at i:57872943 original size:64 final size:64
Alignment explanation
Indices: 57872859--57873113 Score: 332
Period size: 64 Copynumber: 4.0 Consensus size: 64
57872849 CATTCATAAC
* * * *
57872859 ACATTTAGTTAGGTGCATTTGATTCATTTCGATAATAGCATCCTAATTAATTGACATCAGCATT
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTAATTGACATAAGCATT
** * *
57872923 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCGGCCTAATTATTTGACATCAGCATT
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTAATTGACATAAGCATT
* * *
57872987 ACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATT-ATGTGTCATAAGCATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTAAT-TGACATAAGCATT
* * * * * * *
57873051 ACGTCTAATTAGGAGTATTTGATTCATTTTGATCATAACATCCTAATTATTTGGCATAAGCAT
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTAATTGACATAAGCAT
57873114 GATACATGAA
Statistics
Matches: 170, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
63 1 0.01
64 168 0.99
65 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (64 bp):
ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTAATTGACATAAGCATT
Found at i:57873345 original size:45 final size:44
Alignment explanation
Indices: 57873293--57873392 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 44
57873283 TCATAACAAG
* * *
57873293 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGAT-TGAAGA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATGTG-A-A
*
57873338 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATGGTGAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGAT-GTGAA
57873383 TCTTATCTCC
1 TCTTATCTCC
57873393 ATGTATCGGC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 46 0.94
46 1 0.02
47 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATGTGAA
Found at i:57873656 original size:44 final size:44
Alignment explanation
Indices: 57873608--57873694 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
57873598 AGCCCTAAAC
* **
57873608 CTTATCTCTCTAAGGTAGCAA-GAGAGCAGGTTGAAGATTGAAGT
1 CTTATCTCCCTAAGGTAGCAAGGA-AGCAGACTGAAGATTGAAGT
*
57873652 CTTATCTCCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAG
1 CTTATCTCCCTAAGGTAGCAAGGAAGCAGACTGAAGATTGAAG
57873695 GTTGGAAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 36 0.95
45 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (44 bp):
CTTATCTCCCTAAGGTAGCAAGGAAGCAGACTGAAGATTGAAGT
Found at i:57873818 original size:44 final size:44
Alignment explanation
Indices: 57873756--57873842 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
57873746 GCCTCAAGGC
* **
57873756 CTTATCTCTCTGAGGTAGCAA-GAGAGCAGGTTGAAGATTGAAGT
1 CTTATCTCTCTGAAGTAGCAAGGA-AGCAGACTGAAGATTGAAGT
57873800 CTTATCT-TCCTGAAGTAGCAAGGAAGCAGACTGAAGATTGAAG
1 CTTATCTCT-CTGAAGTAGCAAGGAAGCAGACTGAAGATTGAAG
57873843 ATTGGAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 35 0.92
45 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (44 bp):
CTTATCTCTCTGAAGTAGCAAGGAAGCAGACTGAAGATTGAAGT
Found at i:57873827 original size:148 final size:147
Alignment explanation
Indices: 57873560--57873924 Score: 565
Period size: 148 Copynumber: 2.5 Consensus size: 147
57873550 CGTAGATGAT
** * *
57873560 GAATCTTATCTCCATGTATTGACAATGGAGCAAATTTAAGCCCTAAACCTTATCTCTCTAAGGTA
1 GAATCTTATCTCCATGTACCGACAATGGAGCAAATTTAAGCCCTAAGCCTTATCTCTCTGAGGTA
*
57873625 GCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTCCCTGAGGTAGCAAGGAAGCAGACTGAAGAT
66 GCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTCCCTGAAGTAGCAAGGAAGCAGACTGAAGAT
* * *
57873690 TGAAGGTTGGAAGAGGC
131 TGAAGATTGGAAAAGAC
*
57873707 GAATCTTATCTCCATGTACC-AGCAATGGAGCAGATTTAAG-CCTCAAGGCCTTATCTCTCTGAG
1 GAATCTTATCTCCATGTACCGA-CAATGGAGCAAATTTAAGCCCT-AA-GCCTTATCTCTCTGAG
*
57873770 GTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAAGTAGCAAGGAAGCAGACTGAA
63 GTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTCCCTGAAGTAGCAAGGAAGCAGACTGAA
57873835 GATTGAAGATTGGAAAAGAC
128 GATTGAAGATTGGAAAAGAC
* *
57873855 AAATCTTATCTCCATGTACCGACAATGGAGCAAATTTAAGCCCTAAGCCTTATCT-TCCTGAAGT
1 GAATCTTATCTCCATGTACCGACAATGGAGCAAATTTAAGCCCTAAGCCTTATCTCT-CTGAGGT
57873919 AGCAAG
65 AGCAAG
57873925 GAAACAGACT
Statistics
Matches: 199, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
146 5 0.03
147 58 0.29
148 132 0.66
149 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (147 bp):
GAATCTTATCTCCATGTACCGACAATGGAGCAAATTTAAGCCCTAAGCCTTATCTCTCTGAGGTA
GCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTCCCTGAAGTAGCAAGGAAGCAGACTGAAGAT
TGAAGATTGGAAAAGAC
Found at i:57873886 original size:103 final size:103
Alignment explanation
Indices: 57873800--57874018 Score: 321
Period size: 103 Copynumber: 2.1 Consensus size: 103
57873790 AGATTGAAGT
*
57873800 CTTATCTTCCTGAAGTAGCAAGGAAGCAGACTGAAGATTGAAGATTGGAAAAGACAAATCTTATC
1 CTTATCTTCCTGAAGTAGCAAGGAAACAGACTGAAGATTGAAGATTGGAAAAGACAAATCTTATC
* * *
57873865 TCCATGTACCGACAATGGAGCAAATTTAAGCCCTAAGC
66 TCCATGTACCGACAATGGAGCAGATTGAAGCACTAAGC
*
57873903 CTTATCTTCCTGAAGTAGCAAGGAAACAGACTGAAGATTGAAGATTGGAAAAGGCAAATCTTATC
1 CTTATCTTCCTGAAGTAGCAAGGAAACAGACTGAAGATTGAAGATTGGAAAAGACAAATCTTATC
* * * * * * *
57873968 TCCATGTATCGGCAATTGAGCAGATTTAAGCCCCAAGT
66 TCCATGTACCGACAATGGAGCAGATTGAAGCACTAAGC
*
57874006 GTTATCTTCCTGA
1 CTTATCTTCCTGA
57874019 GATAGTAAGA
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (103 bp):
CTTATCTTCCTGAAGTAGCAAGGAAACAGACTGAAGATTGAAGATTGGAAAAGACAAATCTTATC
TCCATGTACCGACAATGGAGCAGATTGAAGCACTAAGC
Found at i:57877491 original size:26 final size:26
Alignment explanation
Indices: 57877462--57877517 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
57877452 TCCTCTTTGA
57877462 AGCCATATAA-CAGGAAGCTCACAAAG
1 AGCCAT-TAATCAGGAAGCTCACAAAG
**
57877488 AGCCATTAATTGGGAAGCTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
57877514 AGCC
1 AGCC
57877518 TACCAAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.14
Consensus pattern (26 bp):
AGCCATTAATCAGGAAGCTCACAAAG
Found at i:57880374 original size:33 final size:33
Alignment explanation
Indices: 57880312--57880421 Score: 125
Period size: 33 Copynumber: 3.3 Consensus size: 33
57880302 AGTCCTACCA
* * *
57880312 AACACACCAAATGCTCACACGAG-TCAATCCCTCC
1 AACACACC-AATGCTCATAAGAGCT-AATCCATCC
57880346 AACACACCAATGCTCATAAGAGCTAATCCAAT-C
1 AACACACCAATGCTCATAAGAGCTAATCC-ATCC
* * *
57880379 AACACACCAATGCTCATAAAAGCTAATCCAACT
1 AACACACCAATGCTCATAAGAGCTAATCCATCC
57880412 AACACACCAA
1 AACACACCAA
57880422 ACAAAGTGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
32 1 0.01
33 56 0.84
34 10 0.15
ACGTcount: A:0.43, C:0.35, G:0.07, T:0.15
Consensus pattern (33 bp):
AACACACCAATGCTCATAAGAGCTAATCCATCC
Found at i:57885357 original size:18 final size:19
Alignment explanation
Indices: 57885327--57885364 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
57885317 CAGTAGTGGG
*
57885327 CCAAGGTGGTGTTCAGCTA
1 CCAAGGTGGTGTTCAACTA
57885346 CCAAGG-GGTGTTCAACTA
1 CCAAGGTGGTGTTCAACTA
57885364 C
1 C
57885365 TGCCAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (19 bp):
CCAAGGTGGTGTTCAACTA
Found at i:57885370 original size:21 final size:19
Alignment explanation
Indices: 57885326--57885375 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
57885316 CCAGTAGTGG
*
57885326 GCCAAGGTGGTGTTCAGCTA
1 GCCAAGG-GGTGTTCAACTA
57885346 -CCAAGGGGTGTTCAACTA
1 GCCAAGGGGTGTTCAACTA
57885364 CTGCCAAGGGGT
1 --GCCAAGGGGT
57885376 CGTGGGCAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.42
19 6 0.23
21 9 0.35
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (19 bp):
GCCAAGGGGTGTTCAACTA
Found at i:57888705 original size:40 final size:40
Alignment explanation
Indices: 57888601--57888724 Score: 149
Period size: 40 Copynumber: 3.1 Consensus size: 40
57888591 CGAAATTTAA
* * * *
57888601 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
57888641 CCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* *
57888681 CCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
57888721 CCGG
1 CCGG
57888725 GTATTATTCA
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:57893605 original size:29 final size:29
Alignment explanation
Indices: 57893546--57893679 Score: 139
Period size: 29 Copynumber: 4.7 Consensus size: 29
57893536 GTGAGTATGA
* * * *
57893546 ATAT-AAGGTGATTTGGGCCTAACGGGAC
1 ATATAAAGGTGAATTGGGCCTGATGGGCC
*
57893574 ATATAAAGGTGATTTGGGCCTGATGGGCC
1 ATATAAAGGTGAATTGGGCCTGATGGGCC
* ** *
57893603 ATATGAATATGAATTGGGCCTGATGAGCC
1 ATATAAAGGTGAATTGGGCCTGATGGGCC
* *
57893632 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATAAAGGTGAATTGGGCCTGATGGGCC
57893661 ATATAAA--TGAGATTGGGCC
1 ATATAAAGGTGA-ATTGGGCC
57893680 AAGTGGGCTA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
27 3 0.03
28 12 0.13
29 78 0.84
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.27
Consensus pattern (29 bp):
ATATAAAGGTGAATTGGGCCTGATGGGCC
Found at i:57897049 original size:61 final size:61
Alignment explanation
Indices: 57896954--57897245 Score: 241
Period size: 61 Copynumber: 4.8 Consensus size: 61
57896944 CACCAGGAGA
* ** * * *
57896954 AGGAAAGCCTTTATGGCAAGTACTAAATGTAAAGGACATCCTTTGTGGGAAAAATCTGGAT
1 AGGAAAGCCTTTGTGGTGAGTACTAGATGTAAAGGACAACCTTTGTGGCAAAAATCTGGAT
* * * * * * * * *
57897015 AGGAAAGTCTTTTTGGTGAGTACTAGATATAAAGGATAGCCTCTATGGCACAACTCTGGACT
1 AGGAAAGCCTTTGTGGTGAGTACTAGATGTAAAGGACAACCTTTGTGGCAAAAATCTGGA-T
* * * *
57897077 -TGAAAGCCTTTTTGGTAAGTACT-GAATGTAAAGGACAACCTTTGTGGCAAAACTCTGGAT
1 AGGAAAGCCTTTGTGGTGAGTACTAG-ATGTAAAGGACAACCTTTGTGGCAAAAATCTGGAT
* * * * * * * * * *
57897137 AGGAAAGCCTTTGTGATGAGTATTGGATAT-AATGATAGCTTTTGTGGCAAAAATCTAGAC
1 AGGAAAGCCTTTGTGGTGAGTACTAGATGTAAAGGACAACCTTTGTGGCAAAAATCTGGAT
* * *
57897197 AGGAAAGCCTTTGTGGCGAGTA-TTGAATGTAAAGGAAAACCTTTGTGGC
1 AGGAAAGCCTTTGTGGTGAGTACTAG-ATGTAAAGGACAACCTTTGTGGC
57897246 GGCCTCTATT
Statistics
Matches: 182, Mismatches: 43, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
59 2 0.01
60 48 0.26
61 130 0.71
62 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (61 bp):
AGGAAAGCCTTTGTGGTGAGTACTAGATGTAAAGGACAACCTTTGTGGCAAAAATCTGGAT
Found at i:57897238 original size:121 final size:122
Alignment explanation
Indices: 57896954--57897245 Score: 361
Period size: 122 Copynumber: 2.4 Consensus size: 122
57896944 CACCAGGAGA
* * *
57896954 AGGAAAGCCTTTATGGCAAGTACTAAATGTAAAGGACATCCTTTGTGGGAAAAATCTGGATAGGA
1 AGGAAAGCCTTTATGGCAAGTACTGAATGTAAAGGACAACCTTTGTGGCAAAAATCTGGATAGGA
* * * * * *
57897019 AAGTCTTTTTGGTGAGTACTAGATATAAAGGATAGCCTCTATGGCACAACTCTGGAC
66 AAGCCTTTGTGATGAGTACTAGATATAAAGGATAGCCTCTATGGCAAAAATCTAGAC
** * * *
57897076 TTGAAAGCCTTTTTGGTAAGTACTGAATGTAAAGGACAACCTTTGTGGCAAAACTCTGGATAGGA
1 AGGAAAGCCTTTATGGCAAGTACTGAATGTAAAGGACAACCTTTGTGGCAAAAATCTGGATAGGA
* * * * * *
57897141 AAGCCTTTGTGATGAGTATTGGATAT-AATGATAGCTTTTGTGGCAAAAATCTAGAC
66 AAGCCTTTGTGATGAGTACTAGATATAAAGGATAGCCTCTATGGCAAAAATCTAGAC
* * * *
57897197 AGGAAAGCCTTTGTGGCGAGTATTGAATGTAAAGGAAAACCTTTGTGGC
1 AGGAAAGCCTTTATGGCAAGTACTGAATGTAAAGGACAACCTTTGTGGC
57897246 GGCCTCTATT
Statistics
Matches: 143, Mismatches: 27, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
121 65 0.45
122 78 0.55
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (122 bp):
AGGAAAGCCTTTATGGCAAGTACTGAATGTAAAGGACAACCTTTGTGGCAAAAATCTGGATAGGA
AAGCCTTTGTGATGAGTACTAGATATAAAGGATAGCCTCTATGGCAAAAATCTAGAC
Found at i:57897324 original size:29 final size:28
Alignment explanation
Indices: 57897257--57897324 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
57897247 GCCTCTATTT
* *
57897257 AAGAATGCCTTTGTGGTATATCTCTTAA
1 AAGAAAGCCTTTGTGGTAGATCTCTTAA
*
57897285 AGGAAATGCCTTTGTGGT-GATCTCTGTCAA
1 AAGAAA-GCCTTTGTGGTAGATCTCT-T-AA
57897315 AAGAAAGCCT
1 AAGAAAGCCT
57897325 CTGTCGTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 10 0.30
29 16 0.48
30 7 0.21
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (28 bp):
AAGAAAGCCTTTGTGGTAGATCTCTTAA
Found at i:57902976 original size:31 final size:31
Alignment explanation
Indices: 57902941--57903003 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
57902931 AATAAAGTAG
* *
57902941 ATTATATATTATTTTA-ATAATACTATATATT
1 ATTATATATTAATTTATATAATAAT-TATATT
* *
57902972 ATTATTTCTTAATTTATATAATAATTATATT
1 ATTATATATTAATTTATATAATAATTATATT
57903003 A
1 A
57903004 AGAATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTATATATTAATTTATATAATAATTATATT
Found at i:57903360 original size:16 final size:15
Alignment explanation
Indices: 57903303--57903362 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
57903293 GTTACATTTC
*
57903303 TATTCCATTAC-GGT
1 TATTCCATTACAGCT
*
57903317 CTATTCCATTATAGCT
1 -TATTCCATTACAGCT
*
57903333 CTATTCAATTACAGCCT
1 -TATTCCATTACAG-CT
57903350 TATTCCATTACAG
1 TATTCCATTACAG
57903363 TGAACCAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
15 10 0.26
16 26 0.68
17 2 0.05
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (15 bp):
TATTCCATTACAGCT
Found at i:57904900 original size:29 final size:29
Alignment explanation
Indices: 57904868--57905003 Score: 157
Period size: 29 Copynumber: 4.7 Consensus size: 29
57904858 ATACCCTTCG
** * *
57904868 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
57904897 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
57904926 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
57904955 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
57904984 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
57905004 ATCTCGTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 93 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:57905837 original size:143 final size:141
Alignment explanation
Indices: 57905647--57905941 Score: 563
Period size: 143 Copynumber: 2.1 Consensus size: 141
57905637 AAATTCTATA
57905647 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
57905712 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
57905777 GAAGACAACAT
131 GAAAACAACAT
57905788 GCATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
1 GCATGGCCGAATACTCATG--CACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
57905853 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
64 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
57905918 AGGAAAACAACAT
129 AGGAAAACAACAT
57905931 GCATGGCCGAA
1 GCATGGCCGAA
57905942 ATTTAACTCA
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
141 19 0.13
143 132 0.87
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (141 bp):
GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAAACAACAT
Found at i:57907804 original size:21 final size:21
Alignment explanation
Indices: 57907780--57907836 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
57907770 AAACAGGGAC
57907780 ACACGCCCGTGTGGAAGGGTG
1 ACACGCCCGTGTGGAAGGGTG
57907801 ACACGCCCGTGTGGAAGGGTG
1 ACACGCCCGTGTGGAAGGGTG
*
57907822 ACACACCCGTGTGGA
1 ACACGCCCGTGTGGA
57907837 TTTATTTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.26, G:0.39, T:0.14
Consensus pattern (21 bp):
ACACGCCCGTGTGGAAGGGTG
Found at i:57909093 original size:48 final size:48
Alignment explanation
Indices: 57909022--57909256 Score: 260
Period size: 48 Copynumber: 4.9 Consensus size: 48
57909012 AGGGTAAATT
* * * *
57909022 GCCGATGCCATGTCCCAAACATGGTCTTACGCTGGCTCACAT-GTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAAT-GAG
* * *
57909070 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGTTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATGAG
* * * * *
57909118 GCTGATGCCATGTCCCAGACATGATCTTACATTAGCACACAT-ATCA-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATGAG
* * * *
57909164 ACATCGATGCCCTGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
1 GC--CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATGAG
* *
57909214 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
57909257 TCACCCAAAT
Statistics
Matches: 153, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
46 1 0.01
47 2 0.01
48 146 0.95
49 3 0.02
50 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATGAG
Found at i:57909189 original size:96 final size:96
Alignment explanation
Indices: 57909022--57909259 Score: 341
Period size: 96 Copynumber: 2.5 Consensus size: 96
57909012 AGGGTAAATT
* * * * * * ***
57909022 GCCGATGCCATGTCCCAAACATGGTCTTACGCTGGCTCACATGTCGAGGCCGATGCCATGTCCCA
1 GCCGATGCCATGTCCCAAACATGATCTTACACTAGCACACATATCAACATCGATGCCATGTCCCA
*
57909087 GACATGGTCTTACACTAGTTCTCATAATGTG
66 GACATGGTCTTACACTAGCTCTCATAATGTG
* * * *
57909118 GCTGATGCCATGTCCCAGACATGATCTTACATTAGCACACATATCAACATCGATGCCCTGTCCCA
1 GCCGATGCCATGTCCCAAACATGATCTTACACTAGCACACATATCAACATCGATGCCATGTCCCA
57909183 GACATGGTCTTACACTAGCTCTCATAATGTG
66 GACATGGTCTTACACTAGCTCTCATAATGTG
*
57909214 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCA
1 GCCGATGCCATGTCCCAAACATGATCTTACACTAGCACACATATCA
57909260 CCCAAATGTC
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 124 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAAACATGATCTTACACTAGCACACATATCAACATCGATGCCATGTCCCA
GACATGGTCTTACACTAGCTCTCATAATGTG
Found at i:57910707 original size:27 final size:27
Alignment explanation
Indices: 57910670--57910725 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
57910660 TAAGTTGAAC
*
57910670 AAACACATATGTGAAC-TCAGTTTGCCA
1 AAACACATATGCGAACAT-AGTTTGCCA
*
57910697 AAACACTTATGCGAACATAGTTTGCCA
1 AAACACATATGCGAACATAGTTTGCCA
57910724 AA
1 AA
57910726 CATAACTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (27 bp):
AAACACATATGCGAACATAGTTTGCCA
Found at i:57918273 original size:15 final size:15
Alignment explanation
Indices: 57918253--57918284 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
57918243 ATATGTCTTT
57918253 TTCTGTCTATTTCAA
1 TTCTGTCTATTTCAA
57918268 TTCTGTCTATTTCAA
1 TTCTGTCTATTTCAA
57918283 TT
1 TT
57918285 ATCTTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (15 bp):
TTCTGTCTATTTCAA
Found at i:57918649 original size:2 final size:2
Alignment explanation
Indices: 57918637--57918669 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
57918627 TATCAAATTT
*
57918637 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57918670 TTATGTTTGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.