Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3540.1
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: 120867
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.28
Warning! 9975 characters in sequence are not A, C, G, or T
Found at i:3875 original size:14 final size:14
Alignment explanation
Indices: 3856--3887 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3846 CCTCCCTTTG
3856 GTACGATCCTCGGA
1 GTACGATCCTCGGA
3870 GTACGATCCTCGGA
1 GTACGATCCTCGGA
3884 GTAC
1 GTAC
3888 TTCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (14 bp):
GTACGATCCTCGGA
Found at i:8594 original size:14 final size:14
Alignment explanation
Indices: 8575--8606 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
8565 CCTCCCTTTG
8575 GTACGATCCTCGGA
1 GTACGATCCTCGGA
8589 GTACGATCCTCGGA
1 GTACGATCCTCGGA
8603 GTAC
1 GTAC
8607 TTCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (14 bp):
GTACGATCCTCGGA
Found at i:16177 original size:40 final size:40
Alignment explanation
Indices: 16115--16332 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
16105 AAGCCAAGTA
* * * *
16115 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCCAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
16154 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
16194 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
16234 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
16274 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
16314 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
16333 TTATCATCCA
Statistics
Matches: 167, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 13 0.08
40 154 0.92
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39776 original size:28 final size:28
Alignment explanation
Indices: 39731--39794 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
39721 GTCTATGGCT
* *
39731 CGTGTCCCTCACAGGGCCATGACACGCC
1 CGTGTCCCTCACACGGCCAGGACACGCC
* *
39759 CGTGTCCCTCACCCGGCCAGGACACGCG
1 CGTGTCCCTCACACGGCCAGGACACGCC
39787 CGTG-CCCT
1 CGTGTCCCT
39795 AGCCCATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.14, C:0.45, G:0.27, T:0.14
Consensus pattern (28 bp):
CGTGTCCCTCACACGGCCAGGACACGCC
Found at i:40961 original size:48 final size:45
Alignment explanation
Indices: 40753--41061 Score: 173
Period size: 46 Copynumber: 6.6 Consensus size: 45
40743 ATGTCGATGC
* * ***
40753 CATGTCCCAGACATGGTCTTACACTGGCTCATC-CATCAAGTTGATG
1 CATGTCCCAGACATGGTCTTACACTGACACATCTCAT--AGCCAATG
* ** * * *
40799 CCATGTCCCAGACATGGCCTTACACTGACTACCGAAATCGTGGCCGACA-C
1 -CATGTCCCAGACATGGTCTTACACTGAC-A-C-ATCTCATAGCC-A-ATG
* * * * *
40849 CATGTCCCAGACAAGGTCTTACACTAGCTCTCACATATCCGT-GCGAATG
1 CATGTCCCAGACATGGTCTTACACT-G---ACACATCT-CATAGCCAATG
*
40898 TCATGTCCCAGACATGGTCTTACACTGACACCTCT-ATATGTCCCAATG
1 -CATGTCCCAGACATGGTCTTACACTGACACATCTCATA-G--CCAATG
* * *
40946 CCATATCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATG
1 -CATGTCCCAGACATGGTCTTACACTGACACATCTCATAGCCAATG
* * *
40992 CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGA-GGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGAC--ACATCTC-ATAGCCAATG
41038 CATGTCCCAGACAT-GTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
41062 AGCTTTCGTC
Statistics
Matches: 209, Mismatches: 32, Indels: 43
0.74 0.11 0.15
Matches are distributed among these distances:
44 13 0.06
45 13 0.06
46 49 0.23
47 26 0.12
48 39 0.19
49 29 0.14
50 31 0.15
51 7 0.03
52 1 0.00
53 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (45 bp):
CATGTCCCAGACATGGTCTTACACTGACACATCTCATAGCCAATG
Found at i:41035 original size:46 final size:46
Alignment explanation
Indices: 40951--41155 Score: 231
Period size: 46 Copynumber: 4.4 Consensus size: 46
40941 CAATGCCATA
*
40951 TCCCAGACATGGTCTTACACTGAC--ACATCTCGTA-GCCGATGCATG
1 TCCCAGACAT-GTCTTACACTGGCTTACATCTCG-AGGCCGATGCATG
40996 TCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATG
1 TCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATG
* * * * * **
41042 TCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGTGGATGCCATG
1 TCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATG-CATG
* *
41089 TCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATG
1 TCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATG
41136 TCCCAGACATGTCTTACACT
1 TCCCAGACATGTCTTACACT
41156 AGCACACAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
44 12 0.09
45 11 0.08
46 64 0.47
47 28 0.20
48 20 0.15
49 2 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
TCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATG
Found at i:41128 original size:94 final size:94
Alignment explanation
Indices: 40747--41158 Score: 334
Period size: 94 Copynumber: 4.3 Consensus size: 94
40737 GGTATAATGT
* *
40747 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-C-ATCAAGTTGATGCCATGTCCCAG
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCATCTCAATC--GTGGATGCCATGTCCCAG
*
40810 ACATGGCCTTACACTGACTAC-CGA-AATCGTGGC
62 ACATGGTCTTACACTGACT-CTC-ATAATCGTGGC
** * * *
40843 CGACACCATGTCCCAGACAAGGTCTTACACTAGCTC-TCACATATCCGTGCGAATGTCATGTCCC
1 CGA-TGCATGTCCCAGAC-ATGTCTTACACTAGCTCATCTCA-AT-CGTG-G-ATGCCATGTCCC
* *
40907 AGACATGGTCTTACACTGACACCTC-TATAT-GT-CC
60 AGACATGGTCTTACACTGAC-TCTCATA-ATCGTGGC
* * * * * **
40941 CAATGCCATATCCCAGACATGGTCTTACACT-GACACATCTC-GTAGCCGATG-CATGTCCCAGA
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTCATCTCAATCGTGGATGCCATGTCCCAGA
* * *
41003 CAT-GTCTTACACTGGCT-TACAT-CTCGAGGC
63 CATGGTCTTACACTGACTCT-CATAATCGTGGC
*
41033 CGATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAAT-GTGGATGCCATGTCCCAGAC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC--TCATCTCAATCGTGGATGCCATGTCCCAGAC
*
41097 ATGGTCTTACACTGGCTCTCATAAT-GTGGC
64 ATGGTCTTACACTGACTCTCATAATCGTGGC
41127 CGATGCATGTCCCAGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
41159 ACACAAATAA
Statistics
Matches: 254, Mismatches: 34, Indels: 58
0.73 0.10 0.17
Matches are distributed among these distances:
90 13 0.05
91 16 0.06
92 28 0.11
93 29 0.11
94 56 0.22
95 5 0.02
96 31 0.12
97 6 0.02
98 29 0.11
99 38 0.15
100 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (94 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCATCTCAATCGTGGATGCCATGTCCCAGACAT
GGTCTTACACTGACTCTCATAATCGTGGC
Found at i:47723 original size:32 final size:32
Alignment explanation
Indices: 47687--47749 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
47677 GTGTGTTTAC
**
47687 TACCATGCATACTGGCTTACAAATTTTACGTG
1 TACCATGCATACTAACTTACAAATTTTACGTG
*
47719 TACCATGCATACTAACTTGCAAATTTTACGT
1 TACCATGCATACTAACTTACAAATTTTACGT
47750 ACAAGGGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (32 bp):
TACCATGCATACTAACTTACAAATTTTACGTG
Found at i:48714 original size:50 final size:50
Alignment explanation
Indices: 48589--49055 Score: 315
Period size: 50 Copynumber: 9.7 Consensus size: 50
48579 ATCGAGTCGG
* * * * * * *
48589 TGCCATGTCCCAGACATGGTCTTACACTAACTAT-AAAAATCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* *
48638 CGCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* ** * ** * * * *
48688 TGCCATGTCCCATACATTCTCTTACACTAAC-ACCTC-TATACGTGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* * * *
48736 TGCCATGTCCCAGACAT-GTCTTACACTGGC-TT-ACATCTCGAGGCCAA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* * * * * * *
48783 -G-CATGTCCCAGACATGGTCTTACACTAACTAT-AAAAATCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* *
48830 CGCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* ** * ** * * * *
48880 TGCCATGTCCCATACATTCTCTTACACTAAC-ACCTC-TATACGTGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* * * *
48928 TGCCATGTCCCAGACAT-GTCTTACACTGGC-TT-ACATCTCGAGGCCAA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* * * * *
48975 -G-CATGTCCCAGACAT-GTCTTACACTAGC--TCCCGTCTCAATGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
* * *
49020 TGTCATGTCCCAAACATGGTCTTACACTGGCTTTCA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCA
49056 TAATGTGGTC
Statistics
Matches: 321, Mismatches: 83, Indels: 27
0.74 0.19 0.06
Matches are distributed among these distances:
44 1 0.00
45 50 0.16
46 16 0.05
47 57 0.18
48 63 0.20
49 62 0.19
50 72 0.22
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.26
Consensus pattern (50 bp):
TGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAA
Found at i:48747 original size:48 final size:49
Alignment explanation
Indices: 48539--49047 Score: 243
Period size: 49 Copynumber: 10.6 Consensus size: 49
48529 GGTATAATGT
* * * * * * *
48539 CGATGCCATGTCCCAGACATAGCCTTACACTAGCT-CATCCAT-CGAGT
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTCTATACGTGC
* * ** * *
48586 CGGTGCCATGTCCCAGACATGGTCTTACACTAACTA--TAAAAATCGAGGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTCTATA-CG-TGC
* * * * ** * * *
48635 CGACGCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTC-TATACGTGC
* * *
48685 CAATGCCATGTCCCATACATTCTCTTACACTAAC-ACCTCTATACGTGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTCTATACGTGC
** * **
48733 CGATGCCATGTCCCAGACA-TGTCTTACACTGGCTTACATCTCGA-G-GC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAAC-TACCTCTATACGTGC
* * ** * *
48780 C-AAG-CATGTCCCAGACATGGTCTTACACTAACTA--TAAAAATCGAGGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTCTATA-CG-TGC
* * * * ** * * *
48827 CGACGCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTC-TATACGTGC
* * *
48877 CAATGCCATGTCCCATACATTCTCTTACACTAAC-ACCTCTATACGTGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTCTATACGTGC
** * **
48925 CGATGCCATGTCCCAGACA-TGTCTTACACTGGCTTACATCTCGA-G-GC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAAC-TACCTCTATACGTGC
* * *
48972 C-AAG-CATGTCCCAGACA-TGTCTTACACTAGCTCCCGTCTCA-A--TGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTAACTACC-TCT-ATACGTGC
* * *
49017 CGATGTCATGTCCCAAACATGGTCTTACACT
1 CGATGCCATGTCCCAGACATTGTCTTACACT
49048 GGCTTTCATA
Statistics
Matches: 347, Mismatches: 88, Indels: 53
0.71 0.18 0.11
Matches are distributed among these distances:
43 2 0.01
44 2 0.01
45 49 0.14
46 19 0.05
47 74 0.21
48 64 0.18
49 75 0.22
50 58 0.17
51 2 0.01
52 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACATTGTCTTACACTAACTACCTCTATACGTGC
Found at i:48795 original size:45 final size:47
Alignment explanation
Indices: 48543--49052 Score: 308
Period size: 47 Copynumber: 10.7 Consensus size: 47
48533 TAATGTCGAT
* * **
48543 GCCATGTCCCAGACATAGCCTTACACTAGC-T-CATCCATCGA-GTCGGT
1 GCCATGTCCCAGACAT-GTCTTACACTAGCTTACAT-C-TCGAGGCCGAA
* * ** *
48590 GCCATGTCCCAGACATGGTCTTACACTAACTATAAAAATCGAGGCCGAC
1 GCCATGTCCCAGACAT-GTCTTACACTAGCT-TACATCTCGAGGCCGAA
* * * *
48639 GCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGCC-AA
1 GCCATGTCCCAGACAT-GTCTTACACTAGC-TT-ACATCTCGAGGCCGAA
* * * * ** *
48688 TGCCATGTCCCATACATTCTCTTACACTAAC--ACCTCTATACGTGCCGAT
1 -GCCATGTCCCAGACA-TGTCTTACACTAGCTTACATCTCGA-G-GCCGAA
*
48737 GCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCC-AA
1 GCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGGCCGAA
* * ** *
48783 G-CATGTCCCAGACATGGTCTTACACTAACTATAAAAATCGAGGCCGAC
1 GCCATGTCCCAGACAT-GTCTTACACTAGCT-TACATCTCGAGGCCGAA
* * * *
48831 GCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGCC-AA
1 GCCATGTCCCAGACAT-GTCTTACACTAGC-TT-ACATCTCGAGGCCGAA
* * * * ** *
48880 TGCCATGTCCCATACATTCTCTTACACTAAC--ACCTCTATACGTGCCGAT
1 -GCCATGTCCCAGACA-TGTCTTACACTAGCTTACATCTCGA-G-GCCGAA
*
48929 GCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCC-AA
1 GCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGGCCGAA
** * * * *
48975 G-CATGTCCCAGACATGTCTTACACTAGCTCCCGTCTCAATGCCGAT
1 GCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGGCCGAA
* * *
49021 GTCATGTCCCAAACATGGTCTTACACTGGCTT
1 GCCATGTCCCAGACAT-GTCTTACACTAGCTT
49053 TCATAATGTG
Statistics
Matches: 359, Mismatches: 75, Indels: 57
0.73 0.15 0.12
Matches are distributed among these distances:
45 50 0.14
46 28 0.08
47 79 0.22
48 55 0.15
49 76 0.21
50 69 0.19
51 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (47 bp):
GCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGGCCGAA
Found at i:48811 original size:93 final size:96
Alignment explanation
Indices: 48539--49052 Score: 464
Period size: 93 Copynumber: 5.4 Consensus size: 96
48529 GGTATAATGT
* * * ***
48539 CGATGCCATGTCCCAGACATAGCCTTACACTAGC-T-CATCCATCGAGTCGGTGCCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACAT-C-TCGAGGCCAAGCCATGTCCCAG
** *
48602 ACATGGTCTTACACTAACTA--TAAAAATCGAGGC
64 ACATGGTCTTACACTAACTACCTCTAAA-CG-TGC
* * * * *
48635 CGACGCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAATGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC-TT-ACATCTCGAGGCCAA-GCCATGTCCCA
* ** *
48700 TACATTCTCTTACACTAAC-ACCTCTATACGTGC
63 GACATGGTCTTACACTAACTACCTCTAAACGTGC
*
48733 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGCCAAG-CATGTCCCAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACATCTCGAGGCCAAGCCATGTCCCAGAC
** *
48796 ATGGTCTTACACTAACTA--TAAAAATCGAGGC
66 ATGGTCTTACACTAACTACCTCTAAA-CG-TGC
* * * * *
48827 CGACGCCATGTCCGAGACATGGTCTTACACTAGCTTTCACATATCCATGCCAATGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC-TT-ACATCTCGAGGCCAA-GCCATGTCCCA
* ** *
48892 TACATTCTCTTACACTAAC-ACCTCTATACGTGC
63 GACATGGTCTTACACTAACTACCTCTAAACGTGC
*
48925 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGCCAAG-CATGTCCCAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACATCTCGAGGCCAAGCCATGTCCCAGAC
* * *
48988 AT-GTCTTACACTAGCTCCCGTCTCAA--TGC
66 ATGGTCTTACACTAACTACC-TCTAAACGTGC
* * *
49017 CGATGTCATGTCCCAAACATGGTCTTACACTGGCTT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTT
49053 TCATAATGTG
Statistics
Matches: 340, Mismatches: 58, Indels: 43
0.77 0.13 0.10
Matches are distributed among these distances:
92 35 0.10
93 57 0.17
94 27 0.08
95 36 0.11
96 36 0.11
97 36 0.11
98 48 0.14
99 56 0.16
100 9 0.03
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACATCTCGAGGCCAAGCCATGTCCCAGAC
ATGGTCTTACACTAACTACCTCTAAACGTGC
Found at i:48868 original size:192 final size:192
Alignment explanation
Indices: 48539--49000 Score: 813
Period size: 192 Copynumber: 2.4 Consensus size: 192
48529 GGTATAATGT
* * * ***
48539 CGATGCCATGTCCCAGACATAGCCTTACACTAGC-T-CATCCATCGAGTCGGTGCCATGTCCCAG
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTTACAT-C-TCGAGGCCAAG-CATGTCCCAG
48602 ACATGGTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACATGGTCTTACACTA
62 ACATGGTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACATGGTCTTACACTA
48667 GCTTTCACATATCCATGCCAATGCCATGTCCCATACATTCTCTTACACTAACACCTCTATACGTG
127 GCTTTCACATATCCATGCCAATGCCATGTCCCATACATTCTCTTACACTAACACCTCTATACGTG
48732 C
192 C
48733 CGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAAGCATGTCCCAGACAT
1 CGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAAGCATGTCCCAGACAT
48798 GGTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACATGGTCTTACACTAGCTT
66 GGTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACATGGTCTTACACTAGCTT
48863 TCACATATCCATGCCAATGCCATGTCCCATACATTCTCTTACACTAACACCTCTATACGTGC
131 TCACATATCCATGCCAATGCCATGTCCCATACATTCTCTTACACTAACACCTCTATACGTGC
48925 CGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAAGCATGTCCCAGACAT
1 CGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAAGCATGTCCCAGACAT
48990 -GTCTTACACTA
66 GGTCTTACACTA
49001 GCTCCCGTCT
Statistics
Matches: 260, Mismatches: 6, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
191 11 0.04
192 206 0.79
193 18 0.07
194 22 0.08
195 3 0.01
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (192 bp):
CGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAAGCATGTCCCAGACAT
GGTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACATGGTCTTACACTAGCTT
TCACATATCCATGCCAATGCCATGTCCCATACATTCTCTTACACTAACACCTCTATACGTGC
Found at i:48910 original size:99 final size:99
Alignment explanation
Indices: 48589--49000 Score: 435
Period size: 99 Copynumber: 4.3 Consensus size: 99
48579 ATCGAGTCGG
*
48589 TGCCATGTCCCAGACATGGTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACA
1 TGCCATGTCCCAGACATGCTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACA
48654 TGGTCTTACACTAGCTTTCACATATCCATGCCAA
66 TGGTCTTACACTAGCTTTCACATATCCATGCCAA
* * ** * * * *
48688 TGCCATGTCCCATACATTCTCTTACACTAAC-ACCTCTATA-CG-TGCCGATGCCATGTCCCAGA
1 TGCCATGTCCCAGACATGCTCTTACACTAACTA--TAAAAATCGAGGCCGACGCCATGTCCGAGA
* * * *
48750 CAT-GTCTTACACTGGC-TT-ACATCTCGAGGCCAA
64 CATGGTCTTACACTAGCTTTCACATATCCATGCCAA
*
48783 -G-CATGTCCCAGACATGGTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACA
1 TGCCATGTCCCAGACATGCTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACA
48846 TGGTCTTACACTAGCTTTCACATATCCATGCCAA
66 TGGTCTTACACTAGCTTTCACATATCCATGCCAA
* * ** * * * *
48880 TGCCATGTCCCATACATTCTCTTACACTAAC-ACCTCTATA-CG-TGCCGATGCCATGTCCCAGA
1 TGCCATGTCCCAGACATGCTCTTACACTAACTA--TAAAAATCGAGGCCGACGCCATGTCCGAGA
* * * *
48942 CAT-GTCTTACACTGGC-TT-ACATCTCGAGGCCAA
64 CATGGTCTTACACTAGCTTTCACATATCCATGCCAA
48975 -G-CATGTCCCAGACATG-TCTTACACTA
1 TGCCATGTCCCAGACATGCTCTTACACTA
49001 GCTCCCGTCT
Statistics
Matches: 260, Mismatches: 41, Indels: 31
0.78 0.12 0.09
Matches are distributed among these distances:
92 13 0.05
93 40 0.15
94 23 0.09
95 36 0.14
96 6 0.02
97 36 0.14
98 43 0.17
99 57 0.22
100 6 0.02
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (99 bp):
TGCCATGTCCCAGACATGCTCTTACACTAACTATAAAAATCGAGGCCGACGCCATGTCCGAGACA
TGGTCTTACACTAGCTTTCACATATCCATGCCAA
Found at i:59709 original size:43 final size:42
Alignment explanation
Indices: 59611--59735 Score: 128
Period size: 43 Copynumber: 3.0 Consensus size: 42
59601 CATAAAGCTC
* ** *
59611 ATACAATGTC-ATATCCCAGACATGGTCTTACACAAAATCAT
1 ATACAATGTCAATGTCCCAGACATGGTCTTACACGTAATCAA
* *
59652 ATA-ATGATGCCAATGTCCCAGACATGGTTTTACACGTAATCACA
1 ATACA--ATGTCAATGTCCCAGACATGGTCTTACACGTAATCA-A
** *
59696 ATACAATGTCAATGTCCTTGACATGGTCTTACATGTAATC
1 ATACAATGTCAATGTCCCAGACATGGTCTTACACGTAATC
59736 TCATCTCTGT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
40 1 0.01
41 3 0.04
42 4 0.06
43 56 0.82
44 3 0.04
45 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (42 bp):
ATACAATGTCAATGTCCCAGACATGGTCTTACACGTAATCAA
Found at i:59928 original size:35 final size:35
Alignment explanation
Indices: 59862--59928 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
59852 TTCATAGCAG
* **
59862 TTCAATGACAAATAAGCATATATAATTCAATTCAA
1 TTCAATAACAAATAAGCATATATAACACAATTCAA
* * *
59897 TTCAATAATAAATAAGCATTTGTAACACAATT
1 TTCAATAACAAATAAGCATATATAACACAATT
59929 TAAATACGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (35 bp):
TTCAATAACAAATAAGCATATATAACACAATTCAA
Found at i:62450 original size:56 final size:56
Alignment explanation
Indices: 62364--62499 Score: 272
Period size: 56 Copynumber: 2.4 Consensus size: 56
62354 ACAAGGGATG
62364 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
62420 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
62476 ATGGGCAAAACATGTCATGAAACA
1 ATGGGCAAAACATGTCATGAAACA
62500 CCCTCCCCAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 80 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:63874 original size:40 final size:40
Alignment explanation
Indices: 63780--63924 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
63770 TACTCGAATG
*
63780 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
63821 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
63861 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
63901 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
63925 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:79830 original size:43 final size:43
Alignment explanation
Indices: 79726--79869 Score: 141
Period size: 43 Copynumber: 3.3 Consensus size: 43
79716 TATCCCAGAT
* * * *
79726 ATGGTCTTACATGTTATCTCATATCGGTGCCAATAG-CCC-AAC
1 ATGGTCTTACATGTAATCACATAACGATGCCAAT-GTCCCAAAC
* * *
79768 TATGGTCTTAGACGAAATCACATAACGATGCCAATGTCCCAAAC
1 -ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAAAC
* * *
79812 ATGGTCTTACGTGTAATCACA-ATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATA-ACGATGCCAATGTCCCAAAC
*
79855 ATAGTCTTACATGTA
1 ATGGTCTTACATGTA
79870 GCCACATCTC
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
42 2 0.02
43 78 0.94
44 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAAAC
Found at i:97507 original size:43 final size:42
Alignment explanation
Indices: 97460--97567 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
97450 GGATTTTCGA
* * * *
97460 TATCTGTTTTGCGTGTAAGACCATGTCTGGGACATTGGCATCG
1 TATCTGATTT-CGTGTAAGACCATATCTAGGACAGTGGCATCG
*
97503 TATCTGATTTCGTGTAAGACCCTATCTAGGACAGTGGCATCG
1 TATCTGATTTCGTGTAAGACCATATCTAGGACAGTGGCATCG
* * * *
97545 ATGTTTGATTACATGTAAGACCA
1 -TATCTGATTTCGTGTAAGACCA
97568 CGTCTGAGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 28 0.52
43 26 0.48
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (42 bp):
TATCTGATTTCGTGTAAGACCATATCTAGGACAGTGGCATCG
Found at i:97518 original size:42 final size:43
Alignment explanation
Indices: 97456--97573 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
97446 CATAGGATTT
* *
97456 TCGATATCTGTTTTGCGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATCTGATTT-CGTGTAAGACCATGTCTGGGACAGTGGCA
* * *
97500 TCG-TATCTGATTTCGTGTAAGACCCTATCTAGGACAGTGGCA
1 TCGATATCTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCA
* * * * *
97542 TCGATGTTTGATTACATGTAAGACCACGTCTG
1 TCGATATCTGATTTCGTGTAAGACCATGTCTG
97574 AGACGCCGAC
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
42 28 0.47
43 29 0.48
44 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (43 bp):
TCGATATCTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCA
Found at i:99935 original size:18 final size:18
Alignment explanation
Indices: 99909--99949 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
99899 ATAGCCCAAA
*
99909 AAAAAACCCCAATGGCCC
1 AAAAAACCCAAATGGCCC
*
99927 AAAAGACCCAAATGGCCC
1 AAAAAACCCAAATGGCCC
99945 AAAAA
1 AAAAA
99950 CCTAAAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.32, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAAACCCAAATGGCCC
Found at i:101033 original size:5 final size:5
Alignment explanation
Indices: 101023--101062 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
101013 ATGTATTATT
101023 TTTTA TTTTA -TTTA TTTTA -TTTA TTTTA -TTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
101063 ATTATTTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:101038 original size:4 final size:4
Alignment explanation
Indices: 101018--101069 Score: 54
Period size: 4 Copynumber: 12.5 Consensus size: 4
101008 TTTTTATGTA
101018 TTAT TT-T TTATT TTAT TTATT TTAT TTATT TTAT TTATT TTAT TTA-
1 TTAT TTAT TTA-T TTAT TTA-T TTAT TTA-T TTAT TTA-T TTAT TTAT
101064 TTAT TT
1 TTAT TT
101070 CCTTTGTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
3 6 0.14
4 20 0.48
5 16 0.38
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTAT
Found at i:101038 original size:9 final size:9
Alignment explanation
Indices: 100999--101065 Score: 91
Period size: 9 Copynumber: 7.3 Consensus size: 9
100989 CCCTGTCTAA
100999 ATTTT-TTT
1 ATTTTATTT
*
101007 ATTTTTATGT
1 A-TTTTATTT
*
101017 ATTATTTTTT
1 ATT-TTATTT
101027 ATTTTATTT
1 ATTTTATTT
101036 ATTTTATTT
1 ATTTTATTT
101045 ATTTTATTT
1 ATTTTATTT
101054 ATTTTATTT
1 ATTTTATTT
101063 ATT
1 ATT
101066 ATTTCCTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
8 1 0.02
9 41 0.79
10 10 0.19
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.78
Consensus pattern (9 bp):
ATTTTATTT
Found at i:113277 original size:44 final size:44
Alignment explanation
Indices: 113133--113777 Score: 488
Period size: 44 Copynumber: 14.3 Consensus size: 44
113123 ATCCTATGCT
*
113133 CTGAAGTTGCAGTGGGACAGATTGAAGTCATCGTAGCAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAACAGATTGAAG----C-TA-CAAATCTTATCTCC
** * * * *
113183 CCAAAGTTGTAGTGGAGCAGATTGAAACTA-TAATCTTATCTCC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
*
113226 TTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
* * * *
113270 CTGAAGTTGCAGTGGAGCAGATTGAAGTTAGCAAATCTTATTTTC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTA-CAAATCTTATCTCC
* * *
113315 CTGAAGTTGTAGTGGAACAGATTAAAGTTACAAGTTACAAATCTTATTTCC
1 CTGAAGTTGCAGTGGAACAGATT---G----AAGCTACAAATCTTATCTCC
* ** * * *
113366 CTAAAGTTGCAGTAAAATAGATTAAAGCTACAAATCTTATTTCC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
* *
113410 CTGAAGTTACAGTAGAGA-AGATTGAAGCTACAAATCTTATCTCC
1 CTGAAGTTGCAGTGGA-ACAGATTGAAGCTACAAATCTTATCTCC
* * ** * *
113454 CTAAAGGTGCAGTGGAGTAGATTAAAGATAGCAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTA-CAAATCTTATCTCC
* * * *
113499 CTGAAGTTGCAGTAGAATAGATTGAAGCTATAAATCTTTTCTCC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
* * *
113543 CTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCT
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTA-CAAATCTTATCTCC
* * * * * * * * *
113588 CTGAAGTTTCAATAGAGCAGATTAAAACCATAAATCTTATCTCT
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
** * * * *
113632 CAAAAGTTGCAGTGGAGCAGATTAAAGCCATAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
* * * * * *
113676 CTGAAATTACAGT-GAAGTAGATTAAAACTACAAATCTCATCTCC
1 CTGAAGTTGCAGTGGAA-CAGATTGAAGCTACAAATCTTATCTCC
* * * ** * ** * * *
113720 TTG-AGTTGTAGCGGAGTAAATTGAAATTACAATTCCTATATCC
1 CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
113763 CTGAAGTTGCAGTGG
1 CTGAAGTTGCAGTGG
113778 GTTGGAAAGA
Statistics
Matches: 482, Mismatches: 97, Indels: 38
0.78 0.16 0.06
Matches are distributed among these distances:
43 65 0.13
44 249 0.52
45 108 0.22
46 1 0.00
48 1 0.00
50 21 0.04
51 31 0.06
52 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCC
Found at i:113373 original size:51 final size:52
Alignment explanation
Indices: 113294--113398 Score: 140
Period size: 51 Copynumber: 2.0 Consensus size: 52
113284 GAGCAGATTG
* * * ** *
113294 AAGTTAGCAAATCTTATTTTCCTGAAGTTGTAGTGGAACAGATTAAAGTTAC
1 AAGTTAGCAAATCTTATTTCCCTAAAGTTGCAGTAAAACAGATTAAAGCTAC
*
113346 AAGTTA-CAAATCTTATTTCCCTAAAGTTGCAGTAAAATAGATTAAAGCTAC
1 AAGTTAGCAAATCTTATTTCCCTAAAGTTGCAGTAAAACAGATTAAAGCTAC
113397 AA
1 AA
113399 ATCTTATTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 40 0.87
52 6 0.13
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (52 bp):
AAGTTAGCAAATCTTATTTCCCTAAAGTTGCAGTAAAACAGATTAAAGCTAC
Found at i:113525 original size:89 final size:88
Alignment explanation
Indices: 113350--113719 Score: 402
Period size: 89 Copynumber: 4.2 Consensus size: 88
113340 AGTTACAAGT
* ** ** * *
113350 TACAAATCTTATTTCCCTAAAGTTGCAGTAAAATAGATTAAAGCTACAAATCTTATTTCCCTGAA
1 TACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATCTTATCTCCCTGAA
* *
113415 GTTACAGTAGAGA-AGATTGAAGC
66 GTTACAGTAGA-ATAGATTAAAAC
* *
113438 TACAAATCTTATCTCCCTAAAGGTGCAGTGGAGTAGATTAAAGATAGCAAATCTTATCTCCCTGA
1 TACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATA-CAAATCTTATCTCCCTGA
* * *
113503 AGTTGCAGTAGAATAGATTGAAGC
65 AGTTACAGTAGAATAGATTAAAAC
* * * * *
113527 TATAAATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCTCTGA
1 TACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATA-CAAATCTTATCTCCCTGA
* * **
113592 AGTTTCAATAGAGCAGATTAAAAC
65 AGTTACAGTAGAATAGATTAAAAC
* * * * ** *
113616 CATAAATCTTATCTCTCAAAAGTTGCAGTGGAGCAGATTAAAGCCATAAATCTTATCTCCCTGAA
1 TACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATCTTATCTCCCTGAA
*
113681 ATTACAGT-GAAGTAGATTAAAAC
66 GTTACAGTAGAA-TAGATTAAAAC
*
113704 TACAAATCTCATCTCC
1 TACAAATCTTATCTCC
113720 TTGAGTTGTA
Statistics
Matches: 239, Mismatches: 40, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
87 2 0.01
88 85 0.36
89 152 0.64
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (88 bp):
TACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATCTTATCTCCCTGAA
GTTACAGTAGAATAGATTAAAAC
Found at i:113528 original size:133 final size:133
Alignment explanation
Indices: 113166--113719 Score: 558
Period size: 133 Copynumber: 4.1 Consensus size: 133
113156 GAAGTCATCG
* * * * * *
113166 TAGCAAATCTTATCTCCCCAAAGTTGTAGTGGAGCAGATTGAAACTA-TAATCTTATCTCCTTGA
1 TAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACTACAAATCTTATCTCCCTAA
* * *
113230 AGTTGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
66 AGTTGCAGTAGAACAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
*
113295 AGT
131 AGC
* * * * * *
113298 TAGCAAATCTTATTTTCCTGAAGTTGTAGTGGAACAGATTAAAGTTACAAGTTACAAATCTTATT
1 TAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA---AC----TACAAATCTTATC
* * * * *
113363 TCCCTAAAGTTGCAGTAAAATAGATTAAAGCTACAAATCTTATTTCCCTGAAGTTACAGTAGAGA
59 TCCCTAAAGTTGCAGTAGAACAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGC
113428 AGATTGAAGC
124 AGATTGAAGC
* *
113438 TA-CAAATCTTATCTCCCTAAAGGTGCAGTGGAGTAGATTAAAGA-TAGCAAATCTTATCTCCCT
1 TAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA-ACTA-CAAATCTTATCTCCCT
* * * * * *
113501 GAAGTTGCAGTAGAATAGATTGAAGCTATAAATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATT
64 AAAGTTGCAGTAGAACAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT
*
113566 GAAGA
129 GAAGC
* * * * * * * * *
113571 TAGCAAATCTTATCTCTCTGAAGTTTCAATAGAGCAGATTAAAACCATAAATCTTATCTCTCAAA
1 TAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACTACAAATCTTATCTCCCTAA
* * * * * * * *
113636 AGTTGCAGTGGAGCAGATTAAAGCCATAAATCTTATCTCCCTGAAATTACAGTGAAGTAGATTAA
66 AGTTGCAGTAGAACAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
*
113701 AAC
131 AGC
*
113704 TA-CAAATCTCATCTCC
1 TAGCAAATCTTATCTCC
113720 TTGAGTTGTA
Statistics
Matches: 346, Mismatches: 65, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
132 51 0.15
133 149 0.43
134 34 0.10
135 2 0.01
137 1 0.00
139 35 0.10
140 74 0.21
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (133 bp):
TAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACTACAAATCTTATCTCCCTAA
AGTTGCAGTAGAACAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
AGC
Found at i:115742 original size:41 final size:41
Alignment explanation
Indices: 115697--115865 Score: 130
Period size: 41 Copynumber: 4.1 Consensus size: 41
115687 GCACAAACAT
* *
115697 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATTATGAGCACTGGCTCAAAAGC
* * * * *
115738 CCTTC-GAGACCAAGCTCAGATTA-GACCACTGCCTCAAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATGAGCACTGGCTCAAAAGC
** * **
115779 CCTTCGGAACTAAGTTCGGTTATGA-CACTGGCTCTGAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
* ** * *
115819 CCTTCGAAACTAAGTTCGGTTATTAGCACTGGCTCAAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
115860 CCTTCG
1 CCTTCG
115866 AGACCAAGCT
Statistics
Matches: 102, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
40 40 0.39
41 55 0.54
42 7 0.07
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (41 bp):
CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
Found at i:115821 original size:40 final size:41
Alignment explanation
Indices: 115721--115866 Score: 170
Period size: 41 Copynumber: 3.6 Consensus size: 41
115711 CCCGATTCTT
* * * *
115721 AGCACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAGATTA-G
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTC-GGTTATG
* * * *
115762 ACCACTGCCTCAAAGGCCCTTCGGAACTAAGTTCGGTTATG
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTATG
** *
115803 A-CACTGGCTCTGAAGCCCTTCGAAACTAAGTTCGGTTATT
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTATG
115843 AGCACTGGCTCAAAAGCCCTTCGA
1 AGCACTGGCTCAAAAGCCCTTCGA
115867 GACCAAGCTC
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 38 0.44
41 49 0.56
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (41 bp):
AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTATG
Found at i:117166 original size:56 final size:56
Alignment explanation
Indices: 117098--117208 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
117088 TCAAAGGTAA
117098 ATACCGCTCCCATGAACCACTAAACTCAAGGATGCAACATCTCAACATATCCTCGC
1 ATACCGCTCCCATGAACCACTAAACTCAAGGATGCAACATCTCAACATATCCTCGC
* * *
117154 ATACCGTTCCCATGAACCACTAAACTCAAGGATGCAGCATCTCAGCATATCCTCG
1 ATACCGCTCCCATGAACCACTAAACTCAAGGATGCAACATCTCAACATATCCTCG
117209 AGTATCTGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.32, C:0.34, G:0.13, T:0.21
Consensus pattern (56 bp):
ATACCGCTCCCATGAACCACTAAACTCAAGGATGCAACATCTCAACATATCCTCGC
Found at i:117656 original size:50 final size:50
Alignment explanation
Indices: 117592--117692 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
117582 CTTGATGTTC
*
117592 CGCTTTCACTTGTTGACATATTAAACA-CTTCGAAACAAAATCAGAAATGT
1 CGCTTTCACCTGTTGACATATTAAACATC-TCGAAACAAAATCAGAAATGT
* *
117642 CGCTTTCACCTGTTGACATATTAAACATCTCGAAACAAAGTCAGAGATGT
1 CGCTTTCACCTGTTGACATATTAAACATCTCGAAACAAAATCAGAAATGT
117692 C
1 C
117693 TCGCTTCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 46 0.98
51 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (50 bp):
CGCTTTCACCTGTTGACATATTAAACATCTCGAAACAAAATCAGAAATGT
Found at i:118155 original size:40 final size:41
Alignment explanation
Indices: 118100--118182 Score: 141
Period size: 40 Copynumber: 2.0 Consensus size: 41
118090 TGATAGTCAA
*
118100 TGACAAGCTCATAATCTTTTAACAACTCAAGCCAACGT-TT
1 TGACAAGCTCATAATCTTTCAACAACTCAAGCCAACGTCTT
*
118140 TGACAAGCTCGTAATCTTTCAACAACTCAAGCCAACGTCTT
1 TGACAAGCTCATAATCTTTCAACAACTCAAGCCAACGTCTT
118181 TG
1 TG
118183 TCGCAGATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (41 bp):
TGACAAGCTCATAATCTTTCAACAACTCAAGCCAACGTCTT
Done.