Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2395
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: 60224
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:2207 original size:42 final size:40
Alignment explanation
Indices: 2034--2224 Score: 174
Period size: 42 Copynumber: 4.7 Consensus size: 40
2024 GATTTTATCC
*
2034 GGCTAAGACCC-AAAGC-ATTTGTGCGAGTTGCTATACCCG
1 GGCTAAGACCCGAAGGCAATTTGTGCGAGTT-CTATACCCG
* * * * * * *
2073 GGTTAAGACTCGAAGGCAATGAATGTGCTAGTTATTTATCCG
1 GGCTAAGACCCGAAGGCAAT--TTGTGCGAGTTCTATACCCG
*
2115 GGCTAAGACCCGAAGGC-ATTTGTGCGAGTTCTGATATCCG
1 GGCTAAGACCCGAAGGCAATTTGTGCGAGTTCT-ATACCCG
*
2155 GGCTATAGACCCG-AGGACAATTTGTGCGAAGTTGCTATACCCA
1 GGCTA-AGACCCGAAGG-CAATTTGTGCG-AGTT-CTATACCCG
*
2198 GGTTAAGACCCGAAGGCAAATTTGTGC
1 GGCTAAGACCCGAAGGC-AATTTGTGC
2225 TGTTTATCAT
Statistics
Matches: 123, Mismatches: 17, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
39 19 0.15
40 18 0.15
41 12 0.10
42 38 0.31
43 34 0.28
44 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
GGCTAAGACCCGAAGGCAATTTGTGCGAGTTCTATACCCG
Found at i:10095 original size:40 final size:40
Alignment explanation
Indices: 10008--10238 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
9998 CATTTGAATG
* * * *
10008 ATATCCGGGCTAAG-TCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
*
10047 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* * * * *
10087 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
* *
10127 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
10167 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* * *
10207 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
10239 TTGTGGTTAT
Statistics
Matches: 166, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 15 0.09
40 147 0.89
41 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
Found at i:10236 original size:120 final size:119
Alignment explanation
Indices: 10008--10258 Score: 407
Period size: 120 Copynumber: 2.1 Consensus size: 119
9998 CATTTGAATG
* * *
10008 ATATCCGGGCTAAGTCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAT
1 ATATCCGGGCTAAGCCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCAT
10073 TTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
66 TTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
10127 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAG-CCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGC
* *
10191 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
64 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
10247 ATATCC-GGCTAA
1 ATATCCGGGCTAA
10259 ATTCCGAAGA
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
119 19 0.16
120 100 0.82
121 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (119 bp):
ATATCCGGGCTAAGCCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCAT
TTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:10254 original size:80 final size:80
Alignment explanation
Indices: 10008--10238 Score: 331
Period size: 80 Copynumber: 2.9 Consensus size: 80
9998 CATTTGAATG
* *
10008 ATATCCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
10072 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGAT
* * *
10087 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
10152 TTTGTGCGAGTTGAT
66 TTTGTGCGAGTTGAT
* * * * *
10167 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTTTATCCGGGCTAAGACCCGAAGGC
*
10231 AATTGTGC
65 ATTTGTGC
10239 TTGTGGTTAT
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 12 0.09
80 121 0.90
81 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGAT
Found at i:18079 original size:40 final size:41
Alignment explanation
Indices: 18020--18250 Score: 294
Period size: 40 Copynumber: 5.8 Consensus size: 41
18010 CATTTGAATG
* * *
18020 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* *
18060 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * * *
18100 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
18140 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
18180 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * *
18220 ATA-CCCGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
18251 TTGTGGTTAT
Statistics
Matches: 167, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
39 27 0.16
40 135 0.81
41 5 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
Found at i:20782 original size:26 final size:26
Alignment explanation
Indices: 20753--20805 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20743 TATACAACAT
20753 AACTTTTCCATTCATCAACAAGTATC
1 AACTTTTCCATTCATCAACAAGTATC
20779 AACTTTTCCATTCATCAACAAGTATC
1 AACTTTTCCATTCATCAACAAGTATC
20805 A
1 A
20806 TAATACACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (26 bp):
AACTTTTCCATTCATCAACAAGTATC
Found at i:21203 original size:46 final size:45
Alignment explanation
Indices: 21071--21203 Score: 132
Period size: 46 Copynumber: 2.9 Consensus size: 45
21061 ATATCTGTGT
*
21071 TGATGCCATGTCACAGACATGGTCTTACACTGACAC-C-TCTCGTAGC
1 TGATG-CATGTCCCAGACAT-GTCTTACACTG-CACTCGTCTCGTAGC
* *
21117 TGATACATGTCCCAGGCATGTCTTACACTGGCTTA-T-GTCTCG-AGGC
1 TGATGCATGTCCCAGACATGTCTTACACT-GC--ACTCGTCTCGTA-GC
21163 TGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTC
1 TGATGCATGTCCCAGACATGTCTTACACT-GCACTCGTCTC
21204 AATGTCGATG
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
44 12 0.16
45 15 0.21
46 46 0.63
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (45 bp):
TGATGCATGTCCCAGACATGTCTTACACTGCACTCGTCTCGTAGC
Found at i:21239 original size:48 final size:45
Alignment explanation
Indices: 21176--21298 Score: 142
Period size: 45 Copynumber: 2.7 Consensus size: 45
21166 TGCATGTCCC
* *
21176 AGACAT-GTCTTACACTAGCACTCGTC-TCAATGTCGATGCCGTCTCCT
1 AGACATGGTCTTACACT-G-ACTC-TCAT-AATGTCGATGCCATCTCAT
*
21223 AGACATGGTCTTACACTGGCTCTCATAATGTCGATGCCATCTCAT
1 AGACATGGTCTTACACTGACTCTCATAATGTCGATGCCATCTCAT
* * *
21268 AGACATGGTCTTAAAATGGCTCTCATAATGT
1 AGACATGGTCTTACACTGACTCTCATAATGT
21299 GGCCTATGCA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
45 48 0.70
46 4 0.06
47 7 0.10
48 10 0.14
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (45 bp):
AGACATGGTCTTACACTGACTCTCATAATGTCGATGCCATCTCAT
Found at i:21258 original size:45 final size:45
Alignment explanation
Indices: 21204--21298 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
21194 CACTCGTCTC
* * * *
21204 AATGTCGATGCCGTCTCCTAGACATGGTCTTACACTGGCTCTCAT
1 AATGTCGATGCCATCTCATAGACATGGTCTTAAAATGGCTCTCAT
21249 AATGTCGATGCCATCTCATAGACATGGTCTTAAAATGGCTCTCAT
1 AATGTCGATGCCATCTCATAGACATGGTCTTAAAATGGCTCTCAT
21294 AATGT
1 AATGT
21299 GGCCTATGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
AATGTCGATGCCATCTCATAGACATGGTCTTAAAATGGCTCTCAT
Found at i:25970 original size:42 final size:41
Alignment explanation
Indices: 25907--26028 Score: 118
Period size: 43 Copynumber: 2.9 Consensus size: 41
25897 TTAGGGTTAC
*
25907 TAAGATTACGTGTAAGGCCATAACTGGGATATGGCATCGAAA
1 TAAGATT-CGTGTAAGACCATAACTGGGATATGGCATCGAAA
* * * *
25949 TAAGACTTCGTGTAAGACCATAGCTGGGCTATTGGCGTCGATA
1 TAAGA-TTCGTGTAAGACCATAACTGGGATA-TGGCATCGAAA
* * * * *
25992 TGAGATCACATGTAAGACCATATCTAGGATATGGCAT
1 TAAGAT-TCGTGTAAGACCATAACTGGGATATGGCAT
26029 TGGTACAGTA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
42 31 0.48
43 34 0.52
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (41 bp):
TAAGATTCGTGTAAGACCATAACTGGGATATGGCATCGAAA
Found at i:27729 original size:48 final size:48
Alignment explanation
Indices: 27606--27927 Score: 265
Period size: 48 Copynumber: 6.7 Consensus size: 48
27596 AGGGTAAGAA
* * * * * * *
27606 GCCGATGCCATGTCCCAGACATGGTCTTACAGTGGCTCTTATATATCG-G
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTAGC-C-CACATATAGAG
* * *
27655 TGCCAATGCCATGTTCCAAACTTGGTCATACACTAGCCCACATATAGAG
1 -GCCGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATAGAG
* * * *
27704 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACC-CATATAAAT
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTAGC-CCACATATAGAG
* * * * *
27752 TCCAATGCCGTGTTCCAAACATGGTCTTACACTAGCTCACATATCA-AT
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATAT-AGAG
* * * * *
27800 GCTGATCCCATGTTCCAAACATGGTTTTACACTAGCTCACATATCGAG
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATAGAG
** * * * * * * * *
27848 G-CGATGCTTTGCTCCAAATATGGTTTTACAATAGCTCTCATATAAAT
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATAGAG
27895 GCCGATGCCATGTTCCAAACATGGTCTTACACT
1 GCCGATGCCATGTTCCAAACATGGTCTTACACT
27928 GGATCACATA
Statistics
Matches: 218, Mismatches: 48, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
47 37 0.17
48 147 0.67
49 5 0.02
50 29 0.13
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATAGAG
Found at i:27793 original size:96 final size:95
Alignment explanation
Indices: 27606--27937 Score: 315
Period size: 96 Copynumber: 3.5 Consensus size: 95
27596 AGGGTAAGAA
* * * * * *
27606 GCCGATGCCATGTCCCAGACATGGTCTTACAGTGGCTCTTATATATCGGTGCCAATGCCATGTTC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTC--ACATATAGATGCCAATGCCATGTTC
* * * *
27671 CAAACTTGGTCATACACTAGCCCACATATAGAG
64 CAAACATGGTCTTACACTAGCTCACATATA-AT
* * * * * *
27704 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACCCATATAAATTCCAATGCCGTGTTCCA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGATGCCAATGCCATGTTCCA
27769 AACATGGTCTTACACTAGCTCACATATCAAT
66 AACATGGTCTTACACTAGCTCACATAT-AAT
* * * * * * * ** *
27800 GCTGATCCCATGTTCCAAACATGGTTTTACACTAGCTCACATATCGA-GGCGATGCTTTGCTCCA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGATGCCAATGCCATGTTCCA
* * * *
27864 AATATGGTTTTACAATAGCTCTCATATAAAT
66 AACATGGTCTTACACTAGCTCACATAT-AAT
* * *
27895 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGATCACATA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATA
27938 ACCCTAGTAT
Statistics
Matches: 194, Mismatches: 39, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
95 75 0.39
96 83 0.43
97 1 0.01
98 35 0.18
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (95 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGATGCCAATGCCATGTTCCA
AACATGGTCTTACACTAGCTCACATATAAT
Found at i:27896 original size:95 final size:95
Alignment explanation
Indices: 27669--27937 Score: 261
Period size: 95 Copynumber: 2.8 Consensus size: 95
27659 AATGCCATGT
* * * * * * * * *
27669 TCCAAACTTGGTCATACACTAGCCCACATATAGAGGCCGATGCCATGTCCCAGACATGGTCTTAC
1 TCCAAACATGGTCTTACAATAGCTCACATATAAATGCCGATCCCATGTTCCAAACATGGTCTTAC
* ** ** * ** *
27734 ACTAGCA-CCCATATAAATTCCAATGCCGTGT
66 ACTAG-ATCACATATCGA-GGCGATGCTTTGC
* * * *
27765 TCCAAACATGGTCTTACACTAGCTCACATATCAATGCTGATCCCATGTTCCAAACATGGTTTTAC
1 TCCAAACATGGTCTTACAATAGCTCACATATAAATGCCGATCCCATGTTCCAAACATGGTCTTAC
*
27830 ACTAGCTCACATATCGAGGCGATGCTTTGC
66 ACTAGATCACATATCGAGGCGATGCTTTGC
* * * *
27860 TCCAAATATGGTTTTACAATAGCTCTCATATAAATGCCGATGCCATGTTCCAAACATGGTCTTAC
1 TCCAAACATGGTCTTACAATAGCTCACATATAAATGCCGATCCCATGTTCCAAACATGGTCTTAC
*
27925 ACTGGATCACATA
66 ACTAGATCACATA
27938 ACCCTAGTAT
Statistics
Matches: 141, Mismatches: 31, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
95 75 0.53
96 66 0.47
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (95 bp):
TCCAAACATGGTCTTACAATAGCTCACATATAAATGCCGATCCCATGTTCCAAACATGGTCTTAC
ACTAGATCACATATCGAGGCGATGCTTTGC
Found at i:27913 original size:143 final size:144
Alignment explanation
Indices: 27606--27937 Score: 380
Period size: 143 Copynumber: 2.3 Consensus size: 144
27596 AGGGTAAGAA
* * * * ** *
27606 GCCGATGCCATGTCCCAGACATGGTCTTACAGTGGCTCTTATATATCGGTGCCAATGCCATGTTC
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTC--ACATATCAATGCCAATCCCATGTTC
* * *
27671 CAAACTTGGTCATACACTAGCCCACATATAGAGGCCGATGCCATGTCCCAGACATGGTCTTACAC
64 CAAACATGGTCATACACTAGCCCACATATAGAGGCCGATGCCATGTCCCAAACATGGTCTTACAA
27736 TAGCACCCATATAAAT
129 TAGCACCCATATAAAT
* * * * **
27752 TCCAATGCCGTGTTCCAAACATGGTCTTACACTAGCTCACATATCAATGCTGATCCCATGTTCCA
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAATGCCAATCCCATGTTCCA
** * * ** * *
27817 AACATGGTTTTACACTAGCTCACATATCGAGG-CGATGCTTTG-CTCCAAATATGGTTTTACAAT
66 AACATGGTCATACACTAGCCCACATATAGAGGCCGATGCCATGTC-CCAAACATGGTCTTACAAT
* *
27880 AGCTCTCATATAAAT
130 AGCACCCATATAAAT
*
27895 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGATCACATA
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATA
27938 ACCCTAGTAT
Statistics
Matches: 154, Mismatches: 31, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
142 1 0.01
143 74 0.48
144 48 0.31
146 31 0.20
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (144 bp):
GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAATGCCAATCCCATGTTCCA
AACATGGTCATACACTAGCCCACATATAGAGGCCGATGCCATGTCCCAAACATGGTCTTACAATA
GCACCCATATAAAT
Found at i:35433 original size:48 final size:48
Alignment explanation
Indices: 35360--35576 Score: 299
Period size: 48 Copynumber: 4.5 Consensus size: 48
35350 CATGTCTTAG
* * *
35360 ACATGGTCTTACACTAGCTCTCATATAAATACCGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCACATATAAATGCTGATGCCATGTTCCAA
* * *
35408 ACATGGTCTTACATTGGCTCACATATCAATGCTGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCACATATAAATGCTGATGCCATGTTCCAA
* ** * * * *
35456 TCATGGTCTTACACTAGCTCACATATCGAGGCAGATGCCATATACCAA
1 ACATGGTCTTACACTAGCTCACATATAAATGCTGATGCCATGTTCCAA
*
35504 ACATGGTCTTACACTAGCTCTCATATAAATGCTGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCACATATAAATGCTGATGCCATGTTCCAA
*
35552 ACATGGTCTTACACTGGCTCACATA
1 ACATGGTCTTACACTAGCTCACATA
35577 ACCCTAGTAT
Statistics
Matches: 145, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 145 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (48 bp):
ACATGGTCTTACACTAGCTCACATATAAATGCTGATGCCATGTTCCAA
Found at i:45414 original size:40 final size:40
Alignment explanation
Indices: 45335--45511 Score: 216
Period size: 40 Copynumber: 4.5 Consensus size: 40
45325 CGGATGATAA
* *
45335 CCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * *
45375 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
* * *
45415 TCGGGCTAAGACCCAAAGGCATTTGTGTGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
45455 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
45495 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
45512 ATACTTGGGT
Statistics
Matches: 115, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 97 0.84
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:52457 original size:40 final size:40
Alignment explanation
Indices: 52390--52514 Score: 155
Period size: 40 Copynumber: 3.1 Consensus size: 40
52380 GGACTAAGAT
** * *
52390 CCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTC
1 CCGAAGGCATTTATGCGAGTTGTTATATCCGGGCTAAGTC
* *
52430 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGAC
1 CCGAAGGCATTTATGCGAGTTG-TTATATCCGGGCTAAGTC
* *
52470 CCGAAGGCATTTGTGCGAGTTGTTATATCC-GGCTAAATC
1 CCGAAGGCATTTATGCGAGTTGTTATATCCGGGCTAAGTC
52509 CCGAAG
1 CCGAAG
52515 ATACTTGGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 15 0.21
40 56 0.77
41 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTATGCGAGTTGTTATATCCGGGCTAAGTC
Found at i:52782 original size:22 final size:22
Alignment explanation
Indices: 52742--52783 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52732 GAATGTGCAT
*
52742 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
52764 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
52784 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Done.