Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4038.1
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: 85607
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Found at i:5870 original size:38 final size:38
Alignment explanation
Indices: 5819--5894 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
5809 TATGGAAGTG
5819 GGAAAGAATAACAATGGACTTTGTGAGTGGGTTACCTT
1 GGAAAGAATAACAATGGACTTTGTGAGTGGGTTACCTT
*
5857 GGAAAGAGTAACAATGGACTTTGTGAGTGGGTTACCTT
1 GGAAAGAATAACAATGGACTTTGTGAGTGGGTTACCTT
5895 TGACACCCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (38 bp):
GGAAAGAATAACAATGGACTTTGTGAGTGGGTTACCTT
Found at i:19017 original size:27 final size:27
Alignment explanation
Indices: 18978--19040 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
18968 CCTACAAAAC
*
18978 CTTCTTCTACATCATCTAAGTAGCCCA
1 CTTCTACTACATCATCTAAGTAGCCCA
* *
19005 CTTCTACTGCATCTTCTAAGTAGCCCA
1 CTTCTACTACATCATCTAAGTAGCCCA
19032 CTTCTACTA
1 CTTCTACTA
19041 ATTTTTCACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.24, C:0.33, G:0.08, T:0.35
Consensus pattern (27 bp):
CTTCTACTACATCATCTAAGTAGCCCA
Found at i:29222 original size:53 final size:53
Alignment explanation
Indices: 29043--29297 Score: 236
Period size: 55 Copynumber: 4.8 Consensus size: 53
29033 ATTAAGGTTT
* * *
29043 AAGGATACCGTGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-G-TTCATAAGGC
* * * * *
29098 AAGGAAATCATGTAAGATCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
29153 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* *
29206 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCAT-AAGGC
* ** * *
29255 AAGGATACCACGTAAGACCATGAAAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
29298 GTACCCACGT
Statistics
Matches: 169, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
49 39 0.23
51 1 0.01
52 8 0.05
53 44 0.26
54 8 0.05
55 65 0.38
56 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:29249 original size:108 final size:110
Alignment explanation
Indices: 29053--29250 Score: 303
Period size: 108 Copynumber: 1.8 Consensus size: 110
29043 AAGGATACCG
* *
29053 TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGATCA
1 TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
*
29118 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* * *
29163 TGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
29225 ATGTCAAGACATGGCAATGGTAAGTT
65 ATGTCAAGACATGGCAATGATAAGTT
29251 TCAAAAGGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.59
109 7 0.09
110 23 0.29
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:29510 original size:16 final size:16
Alignment explanation
Indices: 29489--29519 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29479 ATAAATTTGA
29489 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
29505 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
29520 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:35191 original size:12 final size:12
Alignment explanation
Indices: 35174--35199 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35164 TTCAGATCCG
35174 TCACATGTGATT
1 TCACATGTGATT
35186 TCACATGTGATT
1 TCACATGTGATT
35198 TC
1 TC
35200 TCAGAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (12 bp):
TCACATGTGATT
Found at i:36824 original size:53 final size:53
Alignment explanation
Indices: 36641--36895 Score: 218
Period size: 55 Copynumber: 4.8 Consensus size: 53
36631 ATTAGGGTTT
* * * *
36641 AAGGACACCGTGTAAGACCATGCCAAGGCATGGCAATTCGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-G-TTCATAAGGC
* * * *
36696 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* ** *
36751 AAAGG-TCCCATGTAAGACCATGCCAAGGTATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* * *
36804 AAGGATACCATATAAGACCATGTCAAGACATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCAT-AAGGC
* ** * *
36853 AAGGATACCACGTAAGACCATGAAAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
36896 GTACCCGCAT
Statistics
Matches: 167, Mismatches: 27, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
49 38 0.23
51 1 0.01
52 8 0.05
53 42 0.25
54 7 0.04
55 67 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:36847 original size:108 final size:110
Alignment explanation
Indices: 36651--36848 Score: 294
Period size: 108 Copynumber: 1.8 Consensus size: 110
36641 AAGGACACCG
* *
36651 TGTAAGACCATGCCAAGGCATGGCAATTCGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGCAATTCGTAAGGTTTCTAAGGCAAGGAAACCATATAAGACCA
*
36716 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* * * *
36761 TGTAAGACCATGCCAAGGTATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATATAAGACC
1 TGTAAGACCATGCCAAGGCATGGCAATTCGTAAGGTTTC-TAAGGCAAGGAAACCATATAAGACC
*
36823 ATGTCAAGACATGGCAATGGTAAGTT
65 ATGTCAAGACATGGCAATGATAAGTT
36849 TCAAAAGGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.59
109 6 0.08
110 23 0.29
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGCAATTCGTAAGGTTTCTAAGGCAAGGAAACCATATAAGACCA
TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:37108 original size:16 final size:16
Alignment explanation
Indices: 37087--37117 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37077 ATAAATTTGA
37087 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
37103 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
37118 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:38980 original size:43 final size:43
Alignment explanation
Indices: 38924--39052 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 43
38914 GTTGGTGAAT
*
38924 AATATTATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
* *
38967 GATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGATGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
* *** * *
39010 AATGATATCGGGCTTCAAACCTGGCAGGCGA-AATGCCGGTGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
39052 A
1 A
39053 TGAGTTCAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 11 0.15
43 64 0.85
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (43 bp):
AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
Found at i:45970 original size:43 final size:43
Alignment explanation
Indices: 45889--45990 Score: 114
Period size: 43 Copynumber: 2.4 Consensus size: 43
45879 ATTATCGGGC
* * * *
45889 TTCGATCCTAGCAGGCTATAATGTCGGTGAGATAATATCGAGT
1 TTCGAGCCTAGCAGGCTATAATGCCGATGAAATAATATCGAGT
* * * *
45932 TTCGAGCCTAGTAGGCTATAATGCCGATGAAATGATATCGGGC
1 TTCGAGCCTAGCAGGCTATAATGCCGATGAAATAATATCGAGT
* *
45975 TTCAAGCCTGGCAGGC
1 TTCGAGCCTAGCAGGC
45991 AAAATGCTGG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (43 bp):
TTCGAGCCTAGCAGGCTATAATGCCGATGAAATAATATCGAGT
Found at i:49875 original size:25 final size:23
Alignment explanation
Indices: 49857--49961 Score: 81
Period size: 23 Copynumber: 4.6 Consensus size: 23
49847 TGAGCTGATG
49857 AACAGTAAGCTCTAATGAGCTAA
1 AACAGTAAGCTCTAATGAGCTAA
* * *
49880 AACGGTAAGCTCT-ATCAAGCT-G
1 AACAGTAAGCTCTAAT-GAGCTAA
* *
49902 AACAGTAAGCT-TATACGAGCTGA
1 AACAGTAAGCTCTA-ATGAGCTAA
* * *
49925 AACGGTAGGCTCCAATGAGCTAAA
1 AACAGTAAGCTCTAATGAGCT-AA
*
49949 AATAGTAAGCTCT
1 AACAGTAAGCTCT
49962 TACGAGCTGA
Statistics
Matches: 60, Mismatches: 16, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
21 1 0.02
22 16 0.27
23 32 0.53
24 11 0.18
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (23 bp):
AACAGTAAGCTCTAATGAGCTAA
Found at i:49912 original size:22 final size:22
Alignment explanation
Indices: 49855--49925 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
49845 CCTGAGCTGA
49855 TGAACAGTAAGCTCTAAT-GAGC
1 TGAACAGTAAGCTCT-ATCGAGC
* * *
49877 TAAAACGGTAAGCTCTATCAAGC
1 T-GAACAGTAAGCTCTATCGAGC
49900 TGAACAGTAAGCT-TATACGAGC
1 TGAACAGTAAGCTCTAT-CGAGC
49922 TGAA
1 TGAA
49926 ACGGTAGGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 3 0.08
22 21 0.52
23 16 0.40
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATCGAGC
Found at i:51342 original size:16 final size:15
Alignment explanation
Indices: 51321--51350 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
51311 CAAACATGCT
51321 TTAACACATTATCAAA
1 TTAACACATT-TCAAA
51337 TTAACACATTTCAA
1 TTAACACATTTCAA
51351 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAACACATTTCAAA
Found at i:52975 original size:53 final size:53
Alignment explanation
Indices: 52796--53046 Score: 255
Period size: 55 Copynumber: 4.7 Consensus size: 53
52786 GGGTTTAAGA
52796 ATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGG
1 ATACCATGTAAGACCATGCCAAGGCATGGC-ATTGGTAA-G-TTCATAAGGCAAGG
* * * * *
52851 AAATCATGTAAGACCATGTCAAGGCATGCCATTGATAAGTTACTATAAGGCAAAGG
1 ATACCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTT-C-ATAAGGC-AAGG
*
52907 -T-CTCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGG
1 ATAC-CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGG
* * * *
52959 ATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT-TTAA---AAGG
1 ATACCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGG
* * * * *
53008 ATACCACGTAAGACCATGACAAGTCTTGGCAATGGTAAG
1 ATACCATGTAAGACCATGCCAAGGCATGGCATTGGTAAG
53047 GTACCTGTGT
Statistics
Matches: 169, Mismatches: 20, Indels: 20
0.81 0.10 0.10
Matches are distributed among these distances:
49 39 0.23
52 9 0.05
53 43 0.25
54 9 0.05
55 65 0.38
56 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (53 bp):
ATACCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGG
Found at i:52998 original size:108 final size:110
Alignment explanation
Indices: 52800--52999 Score: 307
Period size: 108 Copynumber: 1.8 Consensus size: 110
52790 TTAAGAATAC
*
52800 CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
* *
52865 CATGTCAAGGCATGCCATTGATAAGTTACTATAAGGCAAAGGTCT
66 CATGTCAAGACATGCCAATGATAAGTTACTATAAGGCAAAGGTCT
* *
52910 CATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGA
1 CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGA
* *
52972 CCATGTCAAGACATGGCAATGGTAAGTT
65 CCATGTCAAGACATGCCAATGATAAGTT
53000 TTAAAAGGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.56
109 7 0.09
110 26 0.32
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (110 bp):
CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
CATGTCAAGACATGCCAATGATAAGTTACTATAAGGCAAAGGTCT
Found at i:53259 original size:16 final size:16
Alignment explanation
Indices: 53238--53268 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53228 ATAAATTTGA
53238 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
53254 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
53269 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:59060 original size:27 final size:27
Alignment explanation
Indices: 59030--59281 Score: 335
Period size: 27 Copynumber: 9.3 Consensus size: 27
59020 CCCTAATTGA
*
59030 TAAAATGACTATTTTACCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
59057 TAAAATGACTGTTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* *
59084 TAAAATG-CTTGTTTTGCCCTTAGGTGG
1 TAAAATGAC-TATTTTGCCCTTATGTGG
* *
59111 TAAAATAACTATTTTACCCTTATAGTGG
1 TAAAATGACTATTTTGCCCTTAT-GTGG
* *
59139 TAACATGACTATTTTGCCCTTATGCGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
59166 TAAAATGACTATTTTGCCCTTATGCGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
59193 TAAAATGAATATTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
** * *
59220 TAAAATGGTTGTTTTGCCATTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
59247 TAAAATGACTATTTTGCCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
59274 TAAGATGA
1 TAAAATGA
59282 TTCGCCCTAT
Statistics
Matches: 198, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 172 0.87
28 25 0.13
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGG
Found at i:62444 original size:21 final size:21
Alignment explanation
Indices: 62418--62459 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
62408 ACACTTAGGA
62418 TAGTTTTTGCT-TTAGTTTTCT
1 TAGTTTTT-CTCTTAGTTTTCT
62439 TAGTTTTTCTCTTAGTTTTCT
1 TAGTTTTTCTCTTAGTTTTCT
62460 CTTCTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.67
Consensus pattern (21 bp):
TAGTTTTTCTCTTAGTTTTCT
Found at i:63963 original size:37 final size:38
Alignment explanation
Indices: 63876--63977 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 38
63866 GTTAAGCTTA
*
63876 ATCACTTTAATATTAAA-TTAATATAATACTTATCAAG
1 ATCACTTTAATATTAAATTTAATATAATACTTAACAAG
* * * * *
63913 ATAAATATT-ATATTAAATTTAATTTAATA-TTAAGATG
1 ATCACT-TTAATATTAAATTTAATATAATACTTAACAAG
*
63950 ATCACTTTAATATTAAA-TTAATAAAATA
1 ATCACTTTAATATTAAATTTAATATAATA
63978 ATATTAATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
36 11 0.21
37 29 0.56
38 12 0.23
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (38 bp):
ATCACTTTAATATTAAATTTAATATAATACTTAACAAG
Found at i:63965 original size:74 final size:74
Alignment explanation
Indices: 63876--64013 Score: 197
Period size: 74 Copynumber: 1.9 Consensus size: 74
63866 GTTAAGCTTA
* * *
63876 ATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTATATTAAATTTAAT-TTAA
1 ATCACTTTAATATTAAATTAATAAAATA-ATATCAAGATAAATATTAAATTAAATTTAATATTAA
63940 TATTAAGATG
65 TATTAAGATG
* * * *
63950 ATCACTTTAATATTAAATTAATAAAATAATATTAATATAAGTATTAAATTTAATTTAATATTAA
1 ATCACTTTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAATTAAATTTAATATTAA
64014 ATCGATTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 25 0.45
74 31 0.55
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (74 bp):
ATCACTTTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAATTAAATTTAATATTAAT
ATTAAGATG
Found at i:64527 original size:15 final size:17
Alignment explanation
Indices: 64496--64528 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
64486 CACTATTTTC
64496 GAAACATAAACAAGAAA
1 GAAACATAAACAAGAAA
64513 GAAA-ATAAA-AAGAAA
1 GAAACATAAACAAGAAA
64528 G
1 G
64529 CTAGGGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAACATAAACAAGAAA
Found at i:70504 original size:47 final size:49
Alignment explanation
Indices: 70388--70752 Score: 382
Period size: 46 Copynumber: 7.8 Consensus size: 49
70378 TGTAACCCGC
* * * *
70388 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGG--G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
70434 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
70484 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
70527 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
70577 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
70620 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
70670 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
70713 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
70753 TCAACCATCC
Statistics
Matches: 267, Mismatches: 22, Indels: 57
0.77 0.06 0.16
Matches are distributed among these distances:
42 6 0.02
43 12 0.04
44 6 0.02
45 6 0.02
46 120 0.45
47 87 0.33
48 7 0.03
49 6 0.02
50 11 0.04
51 6 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:70554 original size:93 final size:93
Alignment explanation
Indices: 70395--70752 Score: 680
Period size: 93 Copynumber: 3.8 Consensus size: 93
70385 CGCCCATAAG
* * * *
70395 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
70460 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
70488 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
70553 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
70581 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
70646 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
70674 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
70739 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
70753 TCAACCATCC
Statistics
Matches: 261, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 261 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:70768 original size:46 final size:45
Alignment explanation
Indices: 70439--70761 Score: 256
Period size: 47 Copynumber: 7.0 Consensus size: 45
70429 CGCATCCATA
70439 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * *
70487 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
70532 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * *
70580 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
70625 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * *
70673 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
70718 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATC
70762 CTAGTGACAT
Statistics
Matches: 222, Mismatches: 24, Indels: 60
0.73 0.08 0.20
Matches are distributed among these distances:
43 2 0.01
44 16 0.07
45 6 0.03
46 88 0.40
47 90 0.41
48 5 0.02
49 12 0.05
50 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTC
Found at i:72063 original size:17 final size:17
Alignment explanation
Indices: 72041--72074 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
72031 ATATTACACA
72041 AGAGAGCACGGGCGTCG
1 AGAGAGCACGGGCGTCG
*
72058 AGAGAGCATGGGCGTCG
1 AGAGAGCACGGGCGTCG
72075 TCAATACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.47, T:0.09
Consensus pattern (17 bp):
AGAGAGCACGGGCGTCG
Found at i:77703 original size:18 final size:19
Alignment explanation
Indices: 77672--77707 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
77662 AAATTTAGTG
*
77672 AATTAATTGAATTATGTTA
1 AATTAAATGAATTATGTTA
77691 AATTAAATG-ATTATGTT
1 AATTAAATGAATTATGTT
77708 GCCAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (19 bp):
AATTAAATGAATTATGTTA
Found at i:82358 original size:18 final size:18
Alignment explanation
Indices: 82332--82368 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
82322 ATTACAACGC
82332 ATAAAAATAACAATCCAA
1 ATAAAAATAACAATCCAA
*
82350 ATAATAATAACAATCCAA
1 ATAAAAATAACAATCCAA
82368 A
1 A
82369 ACAAGTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (18 bp):
ATAAAAATAACAATCCAA
Found at i:83248 original size:28 final size:29
Alignment explanation
Indices: 83215--83299 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 29
83205 CATACATGCA
**
83215 TATGGCCTTTTAGGCCC-AATCACATTCG
1 TATGGCCCATTAGGCCCAAATCACATTCG
* *
83243 TATGGCCCATCAGGCCCAAATCACATTTG
1 TATGGCCCATTAGGCCCAAATCACATTCG
*
83272 TATGGCCCATTAGGCCCAAATCATATTC
1 TATGGCCCATTAGGCCCAAATCACATTC
83300 ATATTCATGC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 14 0.29
29 35 0.71
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (29 bp):
TATGGCCCATTAGGCCCAAATCACATTCG
Done.