Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3216
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: 34804
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:1794 original size:48 final size:48
Alignment explanation
Indices: 1735--2096 Score: 213
Period size: 48 Copynumber: 7.6 Consensus size: 48
1725 GTGTGCTAGC
* **
1735 GTAAGACCATGTTTGGGACATGGTGTCGGCCATAATATGAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATAATATGAGAGCCAGT
* ** *** *
1783 GTAAGATCATGT-TGAAACATGGCATCGAAAAT-ATGGTGAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATAAT-ATGAGAGCCAGT
* * * * * * *
1830 GTAAGACCATGTATGGGACATGGAATCGG-CATTGACATGTGTGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCA-TAATATGAGAGCCAGT
* * * *
1878 GTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATAATATGAGAGCCAGT
* * * * * *
1926 GTAAGACCATGTCTGGGACATGGTATC-GACATTGACATGTG-TCCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCA-TAATATGAGAGCC-AGT
* * ** *
1974 CTAAGACCATGTCTGGGACAT-GCATCAG-CATTGAA-ACAAGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCA-T-AATATGAGAGCCAGT
* * ** * *
2021 GGAAGACCATGTTTGGGACATGGCATCAACC-TCGACATGTA-AGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCAT-AATATG-AGAGCCAGT
* * *
2069 GTAAGACCATGTTTGGAACATGGTATCG
1 GTAAGACCATGTCTGGGACATGGCATCG
2097 ACAATTCACC
Statistics
Matches: 241, Mismatches: 59, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
46 2 0.01
47 73 0.30
48 161 0.67
49 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCCATAATATGAGAGCCAGT
Found at i:1936 original size:96 final size:94
Alignment explanation
Indices: 1819--2091 Score: 316
Period size: 96 Copynumber: 2.9 Consensus size: 94
1809 GAAAATATGG
* *
1819 TGAGAGCCAGTGTAAGACCATGTATGGGACATGGAATCGGCATTGACATGTGTGCTAGTGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTATGGGACATGGAATCGACATTGACATGTGTGCTAGTGTAAGA
1884 CCATGTCTGGGACATGGCATCAGCCACATT-A
66 CCATGTCTGGGACATGGCATCAG---CATTAA
* * * *
1915 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGTATCGACATTGACATGTGTCCTAGTCTAAGA
1 TGAGAGCTAGTGTAAGACCATGTATGGGACATGGAATCGACATTGACATGTGTGCTAGTGTAAGA
1980 CCATGTCTGGGACAT-GCATCAGCATTGAAA
66 CCATGTCTGGGACATGGCATCAGCATT--AA
** * * * * * * ** *
2010 CAAGAGCTAGTGGAAGACCATGTTTGGGACATGGCATCAACCTCGACATGTAAGCCAGTGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTATGGGACATGGAATCGACATTGACATGTGTGCTAGTGTAAGA
* *
2075 CCATGTTTGGAACATGG
66 CCATGTCTGGGACATGG
2092 TATCGACAAT
Statistics
Matches: 152, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
92 4 0.03
95 73 0.48
96 75 0.49
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (94 bp):
TGAGAGCTAGTGTAAGACCATGTATGGGACATGGAATCGACATTGACATGTGTGCTAGTGTAAGA
CCATGTCTGGGACATGGCATCAGCATTAA
Found at i:2005 original size:143 final size:141
Alignment explanation
Indices: 1723--2099 Score: 384
Period size: 143 Copynumber: 2.6 Consensus size: 141
1713 TTTGGGTGAT
* ** * *
1723 ATGTGTGCTAGCGTAAGACCATGTTTGGGACATGGTGTCGGCCATAATATGAGAGCCAGTGTAAG
1 ATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCCA-CATATGAGAGCCAGTGTAAG
* * * * * *
1788 ATCATGTTGAAACATGGCATCGAAAATATGGTGAGAGCCAGTGTAAGACCATGTATGGGACATGG
65 ACCATGTTGGAACATGGTATCG-ACATATGATGAGAGCCAGTCTAAGACCATGTATGGGACATGG
* *
1853 AATCGGCATTGAC
129 AATCAGCATTGAA
* *
1866 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCTAGTGTAAG
1 ATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCCACA-TATGAGAGCCAGTGTAAG
* * * *
1931 ACCATGTCTGGGACATGGTATCGACAT-TGACATGTG-TCCTAGTCTAAGACCATGTCTGGGACA
65 ACCATGT-TGGAACATGGTATCGACATATG--ATGAGAGCC-AGTCTAAGACCATGTATGGGACA
*
1994 T-GCATCAGCATTGAA
126 TGGAATCAGCATTGAA
*** * * * * *
2009 ACAAGAGCTAGTGGAAGACCATGTTTGGGACATGGCATCAACCTCGACATGTA-AGCCAGTGTAA
1 ATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCCAC-ATATG-AGAGCCAGTGTAA
2073 GACCATGTTTGGAACATGGTATCGACA
64 GACCATG-TTGGAACATGGTATCGACA
2100 ATTCACCGCT
Statistics
Matches: 195, Mismatches: 31, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
142 3 0.02
143 152 0.78
144 40 0.21
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (141 bp):
ATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCCACATATGAGAGCCAGTGTAAGA
CCATGTTGGAACATGGTATCGACATATGATGAGAGCCAGTCTAAGACCATGTATGGGACATGGAA
TCAGCATTGAA
Found at i:6726 original size:13 final size:13
Alignment explanation
Indices: 6708--6746 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
6698 ATAGGAATCG
*
6708 AACACGGGCGTGT
1 AACACGGGTGTGT
6721 AACACGGGTGTGT
1 AACACGGGTGTGT
*
6734 CACACGGGTGTGT
1 AACACGGGTGTGT
6747 TCCTGCCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (13 bp):
AACACGGGTGTGT
Found at i:9518 original size:96 final size:95
Alignment explanation
Indices: 9189--9557 Score: 273
Period size: 96 Copynumber: 3.9 Consensus size: 95
9179 GGTGAATTGT
* * * * * *
9189 CGATGCCATGTTCCAATCATGGTCTTACACTGGCTCACATGTCAAGGTCGATGCAATGTCCCAGA
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAATGCCGACGCCATGTCCCAGA
* *
9254 CATGGTCTTACACTAGCTCTCGTCTCAATAT--
66 CATGGTCTTACACTGGCT-T--TCACAATATGC
** ** * * ** *
9285 CGATGCCATG-TCCTGGACATGGTCTTACACTCACTCACATGTCCGA-GTTGATGCCATGTCCCA
1 CGATGCCATGTTCC-AAACATGGTCTTACACTGGCTCACATAT-CAATGCCGACGCCATGTCCCA
* * * ** *
9348 TACATCGTCTTACACTGGCTCTCA-TGTGTGGC
64 GACATGGTCTTACACTGGCTTTCACAATAT-GC
** ** * * * * *
9380 TAATGCCATGCCCCAGACATAGTCTTACACTAGCACACATATCAATGCCGACACCATGTCCCAGA
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAATGCCGACGCCATGTCCCAGA
*
9445 CATGGTCTTACACTGGCTTTCACAACATCGC
66 CATGGTCTTACACTGGCTTTCACAATAT-GC
* * * * *
9476 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATC-GTGGCTGGCGCCATGTCCTAG
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAT-GCCGACGCCATGTCCCAG
*
9540 ACATTGTCTTACACTGGC
65 ACATGGTCTTACACTGGC
9558 ACACATATCA
Statistics
Matches: 211, Mismatches: 53, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
92 2 0.01
93 2 0.01
94 2 0.01
95 68 0.32
96 135 0.64
97 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (95 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAATGCCGACGCCATGTCCCAGA
CATGGTCTTACACTGGCTTTCACAATATGC
Found at i:9532 original size:48 final size:48
Alignment explanation
Indices: 9193--9567 Score: 229
Period size: 48 Copynumber: 7.8 Consensus size: 48
9183 AATTGTCGAT
* * * * * *
9193 GCCATGTTCCA-ATCATGGTCTTACACTGGCTCACATGTCAAGGTCGAT
1 GCCATGTCCCAGA-CATGGTCTTACACTGGCTCTCATATCATGGCCGAC
* * * * ** *
9241 GCAATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAAT-ATCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATC-ATGGCCGAC
** ** * * * ** *
9289 GCCATGTCCTGGACATGGTCTTACACTCACTCACATGTC-CGAGTTGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATG-GCCGAC
* * * * ** *
9337 GCCATGTCCCATACATCGTCTTACACTGGCTCTCATGT-GTGGCTAAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGGCCGAC
* * * * *
9384 GCCATGCCCCAGACATAGTCTTACACTAGCACACATATCAAT-GCCGAC
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATC-ATGGCCGAC
* * * * * *
9432 ACCATGTCCCAGACATGGTCTTACACTGGCTTTCACAACATCGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGGCCGAC
* * * * *
9480 GCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCTGGC
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGGCCGAC
* * * *
9528 GCCATGTCCTAGACATTGTCTTACACTGGCACACATATCA
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCA
9568 CCCAAATGTC
Statistics
Matches: 251, Mismatches: 68, Indels: 16
0.75 0.20 0.05
Matches are distributed among these distances:
47 37 0.15
48 211 0.84
49 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGGCCGAC
Found at i:10519 original size:23 final size:23
Alignment explanation
Indices: 10489--10538 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
10479 AGCTGACCAC
10489 CCCTATTGAAATGGGTTTATTTT
1 CCCTATTGAAATGGGTTTATTTT
10512 CCCTATTGAAATGGGTTTATTTT
1 CCCTATTGAAATGGGTTTATTTT
10535 CCCT
1 CCCT
10539 TTAAAAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (23 bp):
CCCTATTGAAATGGGTTTATTTT
Found at i:11568 original size:48 final size:48
Alignment explanation
Indices: 11491--11767 Score: 234
Period size: 48 Copynumber: 5.8 Consensus size: 48
11481 AGGGTGAATT
* * * * *
11491 GCCGATGCCATGTTCCAAACTTGGTCTTACA-TGGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT-AGCTCACATGTCAAG
* * * *** *
11539 GCCGATGCCATATCCCAGACATGGCCTTACACTAGCTCTCAACCCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
* * * * *
11587 GCCGATGCCATATGCCAAATATGGTCTTACACTAGCTCACATGTTAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
* * * * * ***
11635 GCTGATGCCATGTCCTAGACATGGTCTTACAATGGCTCTCATGTTGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
* * ** * *
11683 GCC-ATGCCATGTCTCAGACATGGTTTTACACTAGCAGACATATCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
* *
11730 GTCGATGCCATGTCCCAGACATGGTCTTAGACTAGCTC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC
11768 TCACAACATC
Statistics
Matches: 174, Mismatches: 53, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
47 33 0.19
48 140 0.80
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
Found at i:11754 original size:143 final size:144
Alignment explanation
Indices: 11494--11767 Score: 322
Period size: 143 Copynumber: 1.9 Consensus size: 144
11484 GTGAATTGCC
*
11494 GATGCCATGTTCCAAACTTGGTCTTACATGGGCTCACATGTCGAGGCCGATGCCATATCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACATGGGCTCACATGTCGAGGCCGATGCCATATCCCAGAC
* * * *
11559 ATGGCCTTACACTAGCTCTCAACCCAATGCCGATGCCATATGCCAAATATGGTCTTACACTAGCT
66 ATGGCCTTACACTAGCACACAACCCAATGCCGATGCCATATCCCAAACATGGTCTTACACTAGCT
11624 CACATGTTAAGGCT
131 CACATGTTAAGGCT
* * * * * *
11638 GATGCCATG-TCCTAGACATGGTCTTACAAT-GGCTCTCATGTTGTGGCC-ATGCCATGTCTCAG
1 GATGCCATGTTCC-AAACATGGTCTTAC-ATGGGCTCACATGTCGAGGCCGATGCCATATCCCAG
** * * * * * *
11700 ACATGGTTTTACACTAGCAGACATA-TCAATGTCGATGCCATGTCCCAGACATGGTCTTAGACTA
64 ACATGGCCTTACACTAGCACACA-ACCCAATGCCGATGCCATATCCCAAACATGGTCTTACACTA
11764 GCTC
128 GCTC
11768 TCACAACATC
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
143 69 0.64
144 37 0.34
145 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (144 bp):
GATGCCATGTTCCAAACATGGTCTTACATGGGCTCACATGTCGAGGCCGATGCCATATCCCAGAC
ATGGCCTTACACTAGCACACAACCCAATGCCGATGCCATATCCCAAACATGGTCTTACACTAGCT
CACATGTTAAGGCT
Found at i:11784 original size:48 final size:47
Alignment explanation
Indices: 11490--11810 Score: 207
Period size: 48 Copynumber: 6.7 Consensus size: 47
11480 TAGGGTGAAT
* * * * * *
11490 TGCCGATGCCATGTTCCAAACTTGGTCTTACA-TGGGCTCACATGTCGA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACT-AGCTCTCATATC-A
* * * *
11538 GGCCGATGCCATATCCCAGACATGGCCTTACACTAGCTCTCA-ACCCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA-TC-A
* * * * * * *
11586 TGCCGATGCCATATGCCAAATATGGTCTTACACTAGCTCACATGTTAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCA
* * * * * * **
11634 GGCTGATGCCATGTCCTAGACATGGTCTTACAATGGCTCTCATGTTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA
* * ***
11681 TGGCC-ATGCCATGTCTCAGACATGGTTTTACACTAGCAGACATATCAA
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC-A
* * * *
11729 TGTCGATGCCATGTCCCAGACATGGTCTTAGACTAGCTCTCACAACA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA
** * *
11776 TCGCCGATGCCATGTTGCAAATATGGTCTTACACT
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACT
11811 GGCACACATA
Statistics
Matches: 204, Mismatches: 61, Indels: 16
0.73 0.22 0.06
Matches are distributed among these distances:
47 36 0.18
48 167 0.82
49 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (47 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA
Found at i:15742 original size:37 final size:36
Alignment explanation
Indices: 15692--15769 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 36
15682 TTATTACGAA
* *
15692 GTCTTACCCGGACATAATCTCCA-ACGAGAGTTATCGG
1 GTCTTACCCGGACAAAATC-CCACACG-GAGTCATCGG
*
15729 GTCTTACCCGGACAAAATCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCACACGGAGTCATCGG
15765 GTCTT
1 GTCTT
15770 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 16 0.43
37 21 0.57
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (36 bp):
GTCTTACCCGGACAAAATCCCACACGGAGTCATCGG
Found at i:15965 original size:47 final size:47
Alignment explanation
Indices: 15887--16507 Score: 986
Period size: 47 Copynumber: 13.4 Consensus size: 47
15877 CCCTTCGGGA
* * * * * * * *
15887 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
15934 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
15981 CTTATCACAT-TATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
16027 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
16072 CTTATCA-ATATATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
16118 CTTATCACACATATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
16165 CTTATCACACATATACACTTTCTCATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
16212 CTTATCACATATATACACTCTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
16259 CTTATCACACATATACA-TTTCACATTCATCACATCGG-TATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
16304 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
16351 CTTATCACATATATACACTTTCACATTCATCACATCGG-TATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
16397 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
16444 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
16491 CTTATTACATATATACA
1 CTTATCACATATATACA
16508 TACTTGGCTG
Statistics
Matches: 541, Mismatches: 26, Indels: 14
0.93 0.04 0.02
Matches are distributed among these distances:
45 67 0.12
46 171 0.32
47 303 0.56
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:15989 original size:22 final size:22
Alignment explanation
Indices: 15962--16036 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
15952 TTTCACATTC
15962 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
**** *** *
15984 ATCACATTATACACTTTCACATT
1 ATCACATCGGCCA-TTAGGCCTT
16007 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
16030 ATCACAT
1 ATCACAT
16037 ATACACTTTC
Statistics
Matches: 35, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
22 16 0.46
23 10 0.29
24 9 0.26
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:16169 original size:93 final size:94
Alignment explanation
Indices: 15887--16507 Score: 986
Period size: 93 Copynumber: 6.7 Consensus size: 94
15877 CCCTTCGGGA
* * * * * * * * * *
15887 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
15952 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCTATTAGGC
*
15981 CTTATCACAT-TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
16043 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCTATTAGGC
* *
16072 CTTATCA-ATATATACACTTTCACATTCATCACATCGACTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
16136 TTTCACATTCATCACATCGACTATTAGGC
66 TTTCACATTCATCACATCGGCTATTAGGC
* *
16165 CTTATCACACATATACACTTTCTCATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
16230 TCTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCTATTAGGC
* *
16259 CTTATCACACATATACA-TTTCACATTCATCACATCGG-TATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
16322 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCTATTAGGC
16351 CTTATCACATATATACACTTTCACATTCATCACATCGG-TATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
16415 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCTATTAGGC
* *
16444 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
16508 TACTTGGCTG
Statistics
Matches: 494, Mismatches: 27, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
90 2 0.00
91 85 0.17
92 68 0.14
93 209 0.42
94 130 0.26
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCTATTAGGC
Found at i:16400 original size:232 final size:231
Alignment explanation
Indices: 15887--16508 Score: 980
Period size: 232 Copynumber: 2.7 Consensus size: 231
15877 CCCTTCGGGA
* * * * * * * * * *
15887 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGG-TATTAGGCCTTATCACATATATACAC
*
15952 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT-TATACACTTTCACATTCATCACATC
65 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
16016 GGCCATTAGGCCTTAT-CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAA
130 GGCCATTAGGCCTTATACACATATACA-TTTCACATTCATCACATCGGCTATTAGGCCTTATCAA
* *
16080 TATATACACTTTCACATTCATCACATCGACTATTAGGC
194 CATATACACTTTCACATTCATCACATCGACCATTAGGC
* * *
16118 CTTATCACACATATACACTTTCACATTCATCACATCGACTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCG-GTATTAGGCCTTATCACATATATACAC
* *
16183 TTTCTCATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTCTCACATTCATCACATC
65 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
16248 GGCTATTAGGCCTTATCACACATATACATTTCACATTCATCACATCGG-TATTAGGCCTTATCAC
130 GGCCATTAGGCCTTAT-ACACATATACATTTCACATTCATCACATCGGCTATTAGGCCTTATCA-
*
16312 ACATATACACTTTCACATTCATCACATCGGCCATTAGGC
193 ACATATACACTTTCACATTCATCACATCGACCATTAGGC
16351 CTTATCACATATATACACTTTCACATTCATCACATCGGTATTAGGCCTTATCACATATATACACT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGTATTAGGCCTTATCACATATATACACT
16416 TTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
66 TTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
*
16481 GCCATTAGGCCTTATTACATATATACAT
131 GCCATTAGGCCTTA-TACACATATACAT
16509 ACTTGGCTGA
Statistics
Matches: 358, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
231 88 0.25
232 167 0.47
233 93 0.26
234 10 0.03
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (231 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGTATTAGGCCTTATCACATATATACACT
TTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
GCCATTAGGCCTTATACACATATACATTTCACATTCATCACATCGGCTATTAGGCCTTATCAACA
TATACACTTTCACATTCATCACATCGACCATTAGGC
Found at i:19568 original size:13 final size:13
Alignment explanation
Indices: 19534--19573 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
19524 ATAGGAATCG
*
19534 AACACGGGCGTGT
1 AACACGGGTGTGT
19547 AACACGGGTGTGT
1 AACACGGGTGTGT
*
19560 CACACGGGTTGTGT
1 AACACGGG-TGTGT
19574 TCCTGCCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.23
Consensus pattern (13 bp):
AACACGGGTGTGT
Found at i:22310 original size:48 final size:48
Alignment explanation
Indices: 22204--22333 Score: 138
Period size: 48 Copynumber: 2.8 Consensus size: 48
22194 ACATATCAAT
* * *
22204 GCCGACACCATGTCCCAGACATGGTCTTACACTGGCTTTCACAACATC
1 GCCGACGCCATGTTCCAGACATGGTCTTACACTGGCTCTCACAACATC
* * * * * *
22252 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTG
1 GCCGACGCCATGTTCCAGACATGGTCTTACACTGGCTCTCACAACATC
* * *
22300 GCTGGCGCCATG-T-CAGACATTGTCTTACACTGGC
1 GCCGACGCCATGTTCCAGACATGGTCTTACACTGGC
22334 ACAACATATC
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
46 19 0.28
47 1 0.01
48 48 0.71
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (48 bp):
GCCGACGCCATGTTCCAGACATGGTCTTACACTGGCTCTCACAACATC
Found at i:23278 original size:21 final size:23
Alignment explanation
Indices: 23243--23290 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
23233 AGCTGACCAC
23243 CCCTATTGAAATGGG-TTATTTT
1 CCCTATTGAAATGGGTTTATTTT
23265 CCCTATTG-AATGGGTTTATTTT
1 CCCTATTGAAATGGGTTTATTTT
23287 CCCT
1 CCCT
23291 TTAAAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (23 bp):
CCCTATTGAAATGGGTTTATTTT
Found at i:28486 original size:37 final size:36
Alignment explanation
Indices: 28414--28491 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 36
28404 CTTATTAGAA
* *
28414 GTCTTACCCGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGACAAAATCTCCACACGAAGTCATCGG
*
28450 GTCTTACCCGGACAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCC-GACAAAATCT-CCACACGAAGTCATCGG
28487 GTCTT
1 GTCTT
28492 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 10 0.27
37 27 0.73
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (36 bp):
GTCTTACCCGACAAAATCTCCACACGAAGTCATCGG
Found at i:28785 original size:47 final size:47
Alignment explanation
Indices: 28609--29232 Score: 956
Period size: 47 Copynumber: 13.4 Consensus size: 47
28599 CGCTTCGGGA
* * * * * * * *
28609 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
28656 C-TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
28702 CTTCTCAC-TATATA-ACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
28747 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
28794 CTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGG-C
* *
28842 CTTATCACACATATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
28889 CTTATCACACATATACACTTTCTCATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
28936 CTTATCACATATATACACTCTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
28983 CTTATCACACATATACAATTTCACATTCATCACATCGGATATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
29030 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
29077 CTTATCACATATATACACTTTCACATTCATCACATC-GCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
29123 CTTATCACATATATACA-TTTCACATTCATCACATCGGCTATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
29168 CTTATCACATATATACACTTTCACATTC-TCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
29214 CTTATTACATATATACACT
1 CTTATCACATATATACACT
29233 ATCTTGGCTG
Statistics
Matches: 539, Mismatches: 31, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
45 88 0.16
46 113 0.21
47 292 0.54
48 46 0.09
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:29076 original size:236 final size:234
Alignment explanation
Indices: 28659--29230 Score: 965
Period size: 236 Copynumber: 2.5 Consensus size: 234
28649 ACTCGGCCTG
* *
28659 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTCTCAC-TATATA-ACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTC
* *
28722 ACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCT
66 ACATTCATCACATCGGCCATTAGGCCTTATTACATATATACAATTTCACATTCATCACATCGGAT
* *
28787 ATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGCCCTTATCACAC
131 ATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGACCATTAGG-CCTTATCACAC
28852 ATATACACTTTCACATTCATCACATCGACTATTAGGCCTTA
195 ATATACACTTTCACATTCATCACATCG-CTATTAGGCCTTA
* * *
28893 TCACACATATACACTTTCTCATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTCTC
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTC
* * *
28958 ACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAATTTCACATTCATCACATCGGAT
66 ACATTCATCACATCGGCCATTAGGCCTTATTACATATATACAATTTCACATTCATCACATCGGAT
* *
29023 ATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
131 ATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGACCATTAGGCCTTATCACACA
29088 TATACACTTTCACATTCATCACATCGCTATTAGGCCTTA
196 TATACACTTTCACATTCATCACATCGCTATTAGGCCTTA
29127 TCACATATATACA-TTTCACATTCATCACATCGGCTATTA-GCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTC
29190 ACATTC-TCACATCGGCCATTAGGCCTTATTACATATATACA
66 ACATTCATCACATCGGCCATTAGGCCTTATTACATATATACA
29231 CTATCTTGGC
Statistics
Matches: 316, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
231 32 0.10
232 29 0.09
233 25 0.08
234 72 0.23
235 43 0.14
236 115 0.36
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (234 bp):
TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTATTACATATATACAATTTCACATTCATCACATCGGAT
ATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGACCATTAGGCCTTATCACACA
TATACACTTTCACATTCATCACATCGCTATTAGGCCTTA
Found at i:34326 original size:91 final size:89
Alignment explanation
Indices: 34194--34668 Score: 407
Period size: 90 Copynumber: 5.2 Consensus size: 89
34184 CCAAGAAGTG
* *
34194 TATATGTGATAA-GCCTAAT-GCCGAAGTGATGATGTGAAAGTGTCATTATAATTTGAAGGCCTA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAAGTGT-A-TAT-ATGTGAAGGCCTA
34257 ATGGCCGAGTGTGAATGTGAAAGTGTA
63 ATGGCCGAGTGTGAATGTGAAAGTGTA
*
34284 TATATTGTGATCAGGCCTAATGG-CGATTGTGATGATG-G-AAGTGTA-ATTATGTGATTAAGGC
1 TATA-TGTGATAAGGCCTAATGGCCGA-TGTGATGATGTGAAAGTGTATA-TATGTG---AAGGC
*
34345 CTACTGG-CGA-TG-G-ATGATGATGAAGTGTAA
60 CTAATGGCCGAGTGTGAATG-TGA--AAGTGT-A
* *
34375 TTATATGT-ATTAGGCCTAATTGGCCGATGTGATGAATGTGAAAGTGTAAATATAGTGATAAGG-
1 -TATATGTGATAAGGCCTAA-TGGCCGATGTGATG-ATGTGAAAGTGTATATAT-GTG--AAGGC
34438 CTAAT-GCCGA-TGTGAATGAAGTGAAAGTGT-
60 CTAATGGCCGAGTGTGAAT---GTGAAAGTGTA
*
34468 TAATATGTGA-AAGG-CTAATGGCCGATGTGA-GAATGTGAAAGTGTATATATGTGATAAGCCTA
1 T-ATATGTGATAAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTGTATATATGTGA-AGGCCT-
*
34530 AATGGCCGATGTGAGAATGTGAAAGTGTA
62 AATGGCCGA-GTGTGAATGTGAAAGTGTA
34559 TATATGTGATAAGG-CTAAATGGCCGATGTGATGAATGATGAAAGTGTATAT-TGTGATCAGGCC
1 TATATGTGATAAGGCCT-AATGGCCGATGTGATG-ATG-TGAAAGTGTATATATGTGA--AGGCC
*
34622 TAATGGCCAATGTGATGAATGTGAAAGCTGTA
61 TAATGGCCGA-GTG-TGAATGTGAAAG-TGTA
34654 TATATGTGA-AAGGCC
1 TATATGTGATAAGGCC
34669 GAGTGGCCAA
Statistics
Matches: 327, Mismatches: 15, Indels: 81
0.77 0.04 0.19
Matches are distributed among these distances:
87 4 0.01
88 11 0.03
89 8 0.02
90 64 0.20
91 62 0.19
92 41 0.13
93 57 0.17
94 50 0.15
95 26 0.08
97 3 0.01
98 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (89 bp):
TATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAAGTGTATATATGTGAAGGCCTAATG
GCCGAGTGTGAATGTGAAAGTGTA
Found at i:34678 original size:47 final size:47
Alignment explanation
Indices: 34194--34668 Score: 513
Period size: 46 Copynumber: 10.3 Consensus size: 47
34184 CCAAGAAGTG
*
34194 TATATGTGATAA-GCCTAAT-GCCGAAGTGATG-ATGTGAAAGTGTCA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-A
*
34239 TTATAATTTG--AAGGCCTAATGGCCGA-GTG-TGAATGTGAAAGTGTA
1 -TAT-ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
*
34284 TATATTGTGATCAGGCCTAATGG-CGATTGTGATG-ATG-G-AAGTGTA
1 TATA-TGTGATAAGGCCTAATGGCCGA-TGTGATGAATGTGAAAGTGTA
*
34329 -ATTATGTGATTAAGGCCTACTGG-CGATG-GATG-ATGATG-AAGTGTAA
1 TA-TATGTGA-TAAGGCCTAATGGCCGATGTGATGAATG-TGAAAGTGT-A
*
34375 TTATATGT-ATTAGGCCTAATTGGCCGATGTGATGAATGTGAAAGTGTA
1 -TATATGTGATAAGGCCTAA-TGGCCGATGTGATGAATGTGAAAGTGTA
*
34423 AATATAGTGATAAGG-CTAAT-GCCGATGTGAATGAA-GTGAAAGTGT-
1 TATAT-GTGATAAGGCCTAATGGCCGATGTG-ATGAATGTGAAAGTGTA
34468 TAATATGTGA-AAGG-CTAATGGCCGATGTGA-GAATGTGAAAGTGTA
1 T-ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
34513 TATATGTGATAA-GCCTAAATGGCCGATGTGA-GAATGTGAAAGTGTA
1 TATATGTGATAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTA
34559 TATATGTGATAAGG-CTAAATGGCCGATGTGATGAATGATGAAAGTGTA
1 TATATGTGATAAGGCCT-AATGGCCGATGTGATGAATG-TGAAAGTGTA
* *
34607 TAT-TGTGATCAGGCCTAATGGCCAATGTGATGAATGTGAAAGCTGTA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG-TGTA
34654 TATATGTGA-AAGGCC
1 TATATGTGATAAGGCC
34669 GAGTGGCCAA
Statistics
Matches: 378, Mismatches: 13, Indels: 75
0.81 0.03 0.16
Matches are distributed among these distances:
43 11 0.03
44 43 0.11
45 64 0.17
46 129 0.34
47 81 0.21
48 36 0.10
49 14 0.04
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
Done.