Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1027
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: 86203
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:7295 original size:17 final size:17
Alignment explanation
Indices: 7273--7308 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
7263 TAACGAAATT
7273 ATAATTGAATTGAGAAA
1 ATAATTGAATTGAGAAA
* *
7290 ATAATTTAATTGGGAAA
1 ATAATTGAATTGAGAAA
7307 AT
1 AT
7309 TAAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (17 bp):
ATAATTGAATTGAGAAA
Found at i:7318 original size:18 final size:18
Alignment explanation
Indices: 7268--7318 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
7258 TACTTTAACG
7268 AAATTATAATTGAATTGAGA
1 AAATTA-AATT-AATTGAGA
* *
7288 AAA-TAATTTAATTGGGA
1 AAATTAAATTAATTGAGA
7305 AAATTAAATTAATT
1 AAATTAAATTAATT
7319 TATTTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 10 0.37
18 12 0.44
19 2 0.07
20 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (18 bp):
AAATTAAATTAATTGAGA
Found at i:8734 original size:29 final size:29
Alignment explanation
Indices: 8689--8789 Score: 132
Period size: 29 Copynumber: 3.5 Consensus size: 29
8679 CATGAAATTG
*
8689 GCACTAAGTGTGCGGGTTGAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* *
8718 GCACTAAGTGTGTGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
8747 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
8775 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
8790 ACTTACTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 19 0.31
29 43 0.69
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.31
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:15993 original size:29 final size:29
Alignment explanation
Indices: 15951--16049 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
15941 CATGAAATTG
15951 GCACTAAGTGTGCGGGTTGAAATTGTATA
1 GCACTAAGTGTGCGGGTTGAAATTGTATA
* *
15980 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTGAAATTGTATA
* *
16009 GCACTAAGTGTGCGAGTTCG--ATTATATA
1 GCACTAAGTGTGCGGGTT-GAAATTGTATA
*
16037 ACACTAAGTGTGC
1 GCACTAAGTGTGC
16050 AGACTTACTA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
28 18 0.29
29 44 0.71
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTGAAATTGTATA
Found at i:20276 original size:17 final size:16
Alignment explanation
Indices: 20254--20286 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
20244 AGTGGTGAAG
20254 ATGAGGAAGGAAAGGAA
1 ATGAGGAA-GAAAGGAA
20271 ATGAGGAAGAAAGGAA
1 ATGAGGAAGAAAGGAA
20287 GAAATTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (16 bp):
ATGAGGAAGAAAGGAA
Found at i:21711 original size:24 final size:25
Alignment explanation
Indices: 21683--21732 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
21673 GTAATATTAC
* *
21683 ACATATTTATTTAAT-AATAATAAA
1 ACATATGTAGTTAATGAATAATAAA
*
21707 ACATATGTAGTTAATGAGTAATAAA
1 ACATATGTAGTTAATGAATAATAAA
21732 A
1 A
21733 TAATGTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (25 bp):
ACATATGTAGTTAATGAATAATAAA
Found at i:21842 original size:42 final size:42
Alignment explanation
Indices: 21787--21873 Score: 97
Period size: 42 Copynumber: 2.0 Consensus size: 42
21777 TATATGGTAA
* * *
21787 AATATATAGCATATAATAA-AATTTATAAACAAAGTATATA-AT
1 AATATAAACCATATAATAAGAATATATAAA-AAA-TATATATAT
*
21829 AATATAAACCATATGATAAGTAATATATAAAAAATATATATAT
1 AATATAAACCATATAATAAG-AATATATAAAAAATATATATAT
21872 AA
1 AA
21874 AATGTATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
42 22 0.58
43 7 0.18
44 9 0.24
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (42 bp):
AATATAAACCATATAATAAGAATATATAAAAAATATATATAT
Found at i:21871 original size:15 final size:15
Alignment explanation
Indices: 21851--21888 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21841 ATGATAAGTA
21851 ATATATAAAAAATAT
1 ATATATAAAAAATAT
**
21866 ATATATAAAATGTAT
1 ATATATAAAAAATAT
21881 ATATATAA
1 ATATATAA
21889 TATATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
ATATATAAAAAATAT
Found at i:21906 original size:16 final size:18
Alignment explanation
Indices: 21885--21918 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
21875 ATGTATATAT
21885 ATAATAT-AT-AATAAAA
1 ATAATATAATGAATAAAA
21901 ATAATATAATGAATAAAA
1 ATAATATAATGAATAAAA
21919 CATATATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAATATAATGAATAAAA
Found at i:21909 original size:11 final size:12
Alignment explanation
Indices: 21850--21909 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 12
21840 TATGATAAGT
21850 AATATATA-AAA
1 AATATATATAAA
21861 AATATATATATAA
1 AATATATATA-AA
* *
21874 AATGTATATATAT
1 AATATATATA-AA
21887 AATATATAATAAA
1 AATATAT-ATAAA
21900 AATA-ATATAA
1 AATATATATAA
21910 TGAATAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
11 12 0.29
12 3 0.07
13 24 0.57
14 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
AATATATATAAA
Found at i:22376 original size:30 final size:30
Alignment explanation
Indices: 22318--22377 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
22308 TTATAATAGC
* * *
22318 TATTAGGACTAAATTGAAACAAATATAAAA
1 TATTAGGACCAAATTAAAACAAAAATAAAA
* *
22348 TATTAGGACCGAATTAAAATAAAAATAAAA
1 TATTAGGACCAAATTAAAACAAAAATAAAA
22378 CAAAATTGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.58, C:0.07, G:0.10, T:0.25
Consensus pattern (30 bp):
TATTAGGACCAAATTAAAACAAAAATAAAA
Found at i:24129 original size:220 final size:220
Alignment explanation
Indices: 23686--24227 Score: 823
Period size: 220 Copynumber: 2.4 Consensus size: 220
23676 CTTAGGAATA
* * * * * *
23686 CCAAATTTGTTATCTTTGATTTGCTCTCTTACAATACAGAGACGCCAAATCTGCTATCTTCGATC
1 CCAAATATGTT-TCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAA--T-C-ATCTTAGATC
* * *
23751 TGCTTCATCGTAAACACGTGAAAGCTAAATCTACTATATCTTCGATTTGCTCCTTGTAATAGCAA
61 TGCTTCAGCGTAAACACGTGAAAGCCAAATCTACTATATCTTCGATCTGCTCCTTGTAATAGCAA
23816 GGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCT
126 GGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCT
*
23881 TCGATTTACTCTCCGTCGAATATGGAGATG
191 TCGATCTACTCTCCGTCGAATATGGAGATG
23911 CCAAATATGTTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTT
1 CCAAATATGTTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTT
* *
23976 CAGCGTAAACACGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAATAGCAAGGATG
66 CAGCGTAAACACGTGAAAGCCAAATCTACTATATCTTCGATCTGCTCCTTGTAATAGCAAGGATG
*
24041 CCAAATCATCTTGGATCTACTTCGATGTGAAAACATCCGAAGGTTAGATCTACTATGTCTTCGAT
131 CCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCTTCGAT
* *
24106 CTGCTCTCCGTTGAATATGGAGATG
196 CTACTCTCCGTCGAATATGGAGATG
* * ** *
24131 CCAAATCTATTTCTTCGATTTGTTCTCTGACAATATGGAGATGCCAAATCATCTTGGATCTGCTT
1 CCAAATATGTTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTT
* * * *
24196 CAGCGTAAACACCTGAAGGTCAGATCTACTAT
66 CAGCGTAAACACGTGAAAGCCAAATCTACTAT
24228 GCTTTAGCCT
Statistics
Matches: 292, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
220 247 0.85
221 1 0.00
222 1 0.00
224 33 0.11
225 10 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (220 bp):
CCAAATATGTTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTT
CAGCGTAAACACGTGAAAGCCAAATCTACTATATCTTCGATCTGCTCCTTGTAATAGCAAGGATG
CCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCTTCGAT
CTACTCTCCGTCGAATATGGAGATG
Found at i:28556 original size:18 final size:17
Alignment explanation
Indices: 28531--28565 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28521 CAGATCCAGA
*
28531 GACACTTCACAATCCTG
1 GACACTTCAAAATCCTG
28548 GACATCTTCAAAATCCTG
1 GACA-CTTCAAAATCCTG
28566 AGATTCCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.26
Consensus pattern (17 bp):
GACACTTCAAAATCCTG
Found at i:40087 original size:11 final size:11
Alignment explanation
Indices: 40068--40104 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
40058 AGGATGATAT
40068 TTTTG-GCATG
1 TTTTGAGCATG
40078 TTTTGAGCATG
1 TTTTGAGCATG
*
40089 -TTTGATCATG
1 TTTTGAGCATG
40099 TTTTGA
1 TTTTGA
40105 ATAGGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.51
Consensus pattern (11 bp):
TTTTGAGCATG
Found at i:42047 original size:50 final size:50
Alignment explanation
Indices: 41972--42255 Score: 228
Period size: 50 Copynumber: 5.8 Consensus size: 50
41962 TGATGCTATA
*
41972 GAGATATGAGAGCTAGTGTAAGACCATCTCTGGGACATGGCATCGACCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
* * *
42022 GAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCTTC-AGCT-
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
* * * *
42070 -TGATATGTG-TC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-C
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-CTC
* * * * * * *
42117 GATAGATGAGAGCCAATGTAAAACCATGTCTAGAACATGGCATC-AGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CCTC
* * * * *
42167 AATACAAGAGAG-TCAGTGTAAGACCATGCCTGGGACATGGCATCGA-CT-
1 GAGATATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
** * * * **
42215 TTGATGTGTGAGCCAGTGTAAGACCATGTCCAGGACATGGC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGC
42256 GTTGGCACCT
Statistics
Matches: 182, Mismatches: 41, Indels: 24
0.74 0.17 0.10
Matches are distributed among these distances:
45 28 0.15
46 1 0.01
47 8 0.04
48 34 0.19
49 7 0.04
50 103 0.57
51 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
Found at i:42149 original size:95 final size:97
Alignment explanation
Indices: 41986--42255 Score: 298
Period size: 95 Copynumber: 2.8 Consensus size: 97
41976 TATGAGAGCT
* * * *
41986 AGTGTAAGACCATCTCTGGGACATGGCATCGACCTCGAGATATGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACC-CGATAGATGAGAGCCAGTGTAAGACCATGT
* ** * *
42051 CTAGGACATGGCTTCAG-CTTGAT-A-TGTGTC
65 CTAGGACATGGCATCAGCCTCAATAAGAGAGTC
* * *
42081 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATAGATGAGAGCCAATGTAAAACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-CCGATAGATGAGAGCCAGTGTAAGACCATGT
*
42146 CTAGAACATGGCATCAGCCTCAATACAAGAGAGTC
65 CTAGGACATGGCATCAGCCTCAAT--AAGAGAGTC
* ** *
42181 AGTGTAAGACCATGCCTGGGACATGGCATCGACTTTGAT-G-TGTGAGCCAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-CCGATAGATGAGAGCCAGTGTAAGACCATGT
*
42244 CCAGGACATGGC
65 CTAGGACATGGC
42256 GTTGGCACCT
Statistics
Matches: 146, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
95 71 0.49
96 5 0.03
98 30 0.21
99 2 0.01
100 38 0.26
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (97 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACCCGATAGATGAGAGCCAGTGTAAGACCATGTC
TAGGACATGGCATCAGCCTCAATAAGAGAGTC
Found at i:50008 original size:16 final size:15
Alignment explanation
Indices: 49980--50012 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
49970 AAATTTAGTG
49980 TTTATTTAATTTTATT
1 TTTATTTAATTTT-TT
49996 TTTATTTAATTTTTT
1 TTTATTTAATTTTTT
50011 TT
1 TT
50013 CATATCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTAATTTTTT
Found at i:50719 original size:21 final size:21
Alignment explanation
Indices: 50668--50707 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50658 AGTTACACGG
*
50668 CCTG-TTCACATGGTCGTGTC
1 CCTGCTTCACATAGTCGTGTC
50688 CCTGCTTCACATAGTCGTGT
1 CCTGCTTCACATAGTCGTGT
50708 GCCTCTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.30, G:0.23, T:0.35
Consensus pattern (21 bp):
CCTGCTTCACATAGTCGTGTC
Found at i:51087 original size:4 final size:4
Alignment explanation
Indices: 51078--51105 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
51068 CATTTGACTG
51078 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
51106 TGCATAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:61157 original size:17 final size:17
Alignment explanation
Indices: 61135--61170 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61125 TAACGAAATT
61135 ATAATTGAATTGAGAAA
1 ATAATTGAATTGAGAAA
* *
61152 ATAATTTAATTGGGAAA
1 ATAATTGAATTGAGAAA
61169 AT
1 AT
61171 TAAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (17 bp):
ATAATTGAATTGAGAAA
Found at i:61180 original size:18 final size:18
Alignment explanation
Indices: 61130--61180 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
61120 TACTTTAACG
61130 AAATTATAATTGAATTGAGA
1 AAATTA-AATT-AATTGAGA
* *
61150 AAA-TAATTTAATTGGGA
1 AAATTAAATTAATTGAGA
61167 AAATTAAATTAATT
1 AAATTAAATTAATT
61181 TATTTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 10 0.37
18 12 0.44
19 2 0.07
20 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (18 bp):
AAATTAAATTAATTGAGA
Found at i:62596 original size:29 final size:29
Alignment explanation
Indices: 62551--62651 Score: 132
Period size: 29 Copynumber: 3.5 Consensus size: 29
62541 CATGAAATTG
*
62551 GCACTAAGTGTGCGGGTTGAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* *
62580 GCACTAAGTGTGTGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
62609 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
62637 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
62652 ACTTACTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 19 0.31
29 43 0.69
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.31
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:69860 original size:29 final size:29
Alignment explanation
Indices: 69818--69916 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
69808 CATGAAATTG
69818 GCACTAAGTGTGCGGGTTGAAATTGTATA
1 GCACTAAGTGTGCGGGTTGAAATTGTATA
* *
69847 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTGAAATTGTATA
* *
69876 GCACTAAGTGTGCGAGTTCG--ATTATATA
1 GCACTAAGTGTGCGGGTT-GAAATTGTATA
*
69904 ACACTAAGTGTGC
1 GCACTAAGTGTGC
69917 AGACTTACTA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
28 18 0.29
29 44 0.71
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTGAAATTGTATA
Found at i:74139 original size:17 final size:16
Alignment explanation
Indices: 74117--74149 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
74107 AGTGGTGAAG
74117 ATGAGGAAGGAAAGGAA
1 ATGAGGAA-GAAAGGAA
74134 ATGAGGAAGAAAGGAA
1 ATGAGGAAGAAAGGAA
74150 GAAATTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (16 bp):
ATGAGGAAGAAAGGAA
Found at i:76035 original size:24 final size:25
Alignment explanation
Indices: 76007--76056 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
75997 GTAATATTAC
* *
76007 ACATATTTATTTAAT-AATAATAAA
1 ACATATGTAGTTAATGAATAATAAA
*
76031 ACATATGTAGTTAATGAGTAATAAA
1 ACATATGTAGTTAATGAATAATAAA
76056 A
1 A
76057 TAATGTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (25 bp):
ACATATGTAGTTAATGAATAATAAA
Found at i:76192 original size:14 final size:14
Alignment explanation
Indices: 76175--76232 Score: 61
Period size: 13 Copynumber: 4.4 Consensus size: 14
76165 ATGATAAGTA
76175 ATATATAAAAATAT
1 ATATATAAAAATAT
*
76189 ATATAT-AAAATGT
1 ATATATAAAAATAT
*
76202 ATATA-ATATAATAT
1 ATATATA-AAAATAT
76216 ATA-ATAAAAATA-
1 ATATATAAAAATAT
76228 ATATA
1 ATATA
76233 ATGAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
12 3 0.08
13 18 0.50
14 15 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
ATATATAAAAATAT
Found at i:76204 original size:25 final size:26
Alignment explanation
Indices: 76176--76224 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
76166 TGATAAGTAA
76176 TATATAA-A-AATATATATATAAAATG
1 TATATAATATAATATATA-ATAAAATG
76201 TATATAATATAATATATAATAAAA
1 TATATAATATAATATATAATAAAA
76225 ATAATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
TATATAATATAATATATAATAAAATG
Found at i:76228 original size:16 final size:18
Alignment explanation
Indices: 76209--76242 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
76199 TGTATATAAT
76209 ATAATAT-AT-AATAAAA
1 ATAATATAATGAATAAAA
76225 ATAATATAATGAATAAAA
1 ATAATATAATGAATAAAA
76243 CATATATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAATATAATGAATAAAA
Found at i:76233 original size:14 final size:13
Alignment explanation
Indices: 76175--76234 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
76165 ATGATAAGTA
76175 ATAT-ATAAAAAT
1 ATATAATAAAAAT
*
76187 ATATATATAAAATGT
1 ATATA-ATAAAA-AT
*
76202 ATATAAT-ATAAT
1 ATATAATAAAAAT
76214 ATATAATAAAAAT
1 ATATAATAAAAAT
76227 AATATAAT
1 -ATATAAT
76235 GAATAAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 12 0.31
13 6 0.15
14 15 0.38
15 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
ATATAATAAAAAT
Found at i:77839 original size:220 final size:220
Alignment explanation
Indices: 77396--77937 Score: 816
Period size: 220 Copynumber: 2.4 Consensus size: 220
77386 CTTAGGAATA
* * * * * *
77396 CCAAATTTGTTATCTTTGATTTGCTCTCTTACAATACAGAGACGCCAAATCTGCTATCTTCGATC
1 CCAAATATGTT-TCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAA--T-C-ATCTTAGATC
* * *
77461 TGCTTCATCGTAAACACGTGAAAGCTAAATCTACTATATCTTCGATTTGCTCCTTGTAATAGCAA
61 TGCTTCAGCGTAAACACGTGAAAGCCAAATCTACTATATCTTCGATCTGCTCCTTGTAATAGCAA
77526 GGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCT
126 GGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCT
*
77591 TCGATTTGCTCTCCGTCGAATATGGAGATG
191 TCGATCTGCTCTCCGTCGAATATGGAGATG
77621 CCAAATATGTTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTT
1 CCAAATATGTTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTT
* *
77686 CAGCGTAAACACGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAATAGCAAGGATG
66 CAGCGTAAACACGTGAAAGCCAAATCTACTATATCTTCGATCTGCTCCTTGTAATAGCAAGGATG
*
77751 CCAAATCATCTTGGATCTACTTCGATGTGAAAACATCCGAAGGTTAGATCTACTATGTCTTCGAT
131 CCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCTTCGAT
*
77816 CTGCTCTCCGTTGAATATGGAGATG
196 CTGCTCTCCGTCGAATATGGAGATG
* * ** *
77841 CCAAATCTATTTCTTC-ATTTTGTTCTCTGACAATATGGAGATGCCAAATCATCTTGGATCTGCT
1 CCAAATATGTTTCTTCGA-TTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCT
* * * *
77905 TCAGCGTAAACACCTGAAGGTCAGATCTACTAT
65 TCAGCGTAAACACGTGAAAGCCAAATCTACTAT
77938 GCTTTAGCCT
Statistics
Matches: 292, Mismatches: 24, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
219 1 0.00
220 246 0.84
221 1 0.00
222 1 0.00
224 33 0.11
225 10 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (220 bp):
CCAAATATGTTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTT
CAGCGTAAACACGTGAAAGCCAAATCTACTATATCTTCGATCTGCTCCTTGTAATAGCAAGGATG
CCAAATCATCTTGGATCTACTTCGATGTGAAAAAATCCGAAGGTTAGATCTACTATGTCTTCGAT
CTGCTCTCCGTCGAATATGGAGATG
Found at i:81032 original size:40 final size:40
Alignment explanation
Indices: 80914--81092 Score: 156
Period size: 40 Copynumber: 4.5 Consensus size: 40
80904 TTGAATGCTG
* *
80914 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTA-AGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGA-T-ACTAAT
** * * *
80953 ATCCGGACTAAGAT-CCGAAGG--TATGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCCTTTGTGCGAGATACTAAT
80992 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
* * ** *
81032 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
81072 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
81093 ATTGAATGAG
Statistics
Matches: 117, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
37 1 0.01
38 18 0.15
39 12 0.10
40 85 0.73
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
Found at i:81049 original size:78 final size:81
Alignment explanation
Indices: 80914--81092 Score: 212
Period size: 78 Copynumber: 2.3 Consensus size: 81
80904 TTGAATGCTG
* * *
80914 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTA-T
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
*
80977 -GTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
80992 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
81053 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
81072 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
81093 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
77 2 0.02
78 42 0.48
79 12 0.14
80 32 0.36
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:81093 original size:40 final size:39
Alignment explanation
Indices: 80977--81095 Score: 166
Period size: 40 Copynumber: 3.0 Consensus size: 39
80967 CCGAAGGTAT
* *
80977 GTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTT
1 GTGCGAGTT-TTAATTCCGGGTTAAGTCCCGAAGGCATTC
**
81017 GTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTC
1 GTGCGAG-TTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
*
81057 GTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATT
1 GTGCGAGTTTT-AATTCCGGGTTAAGTCCCGAAGGCATT
81096 GAATGAGTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.03
40 67 0.96
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
GTGCGAGTTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
Found at i:81116 original size:39 final size:38
Alignment explanation
Indices: 80993--81142 Score: 122
Period size: 40 Copynumber: 3.8 Consensus size: 38
80983 GTTATTAATT
* ** * *
80993 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACT-ATA
** * *
81033 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-ATA
*
81072 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAT-A
* *
81112 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
81143 GAGCTATATC
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 32 0.35
40 60 0.65
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTATA
Found at i:85305 original size:32 final size:28
Alignment explanation
Indices: 85228--85291 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
85218 CATATTATTT
* *
85228 TATGTAAATGTTCTCTTTTAAATTTATA
1 TATGTATATATTCTCTTTTAAATTTATA
* *
85256 TATGTATATATTCTCTTTTAAGTTTATT
1 TATGTATATATTCTCTTTTAAATTTATA
85284 TATGTATA
1 TATGTATA
85292 ATTTGGCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (28 bp):
TATGTATATATTCTCTTTTAAATTTATA
Done.