Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_202
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: 131923
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:8590 original size:42 final size:42
Alignment explanation
Indices: 8464--8590 Score: 166
Period size: 43 Copynumber: 3.0 Consensus size: 42
8454 CTCAGTACTG
* *
8464 TATCAATGCCATATCCCAGATATGGTCTTACATGTAATCTCG
1 TATCGATGCCATATCCCAGATATGGTCTTACATGTAATCTCA
* *
8506 TATCGATGCCAATAGCCCAGATATGGTCTTACACG-AAGTCTCA
1 TATCGATGCC-ATATCCCAGATATGGTCTTACATGTAA-TCTCA
** *
8549 TATCGATGCCATATCCTTGATATGGTTTTACATGTAATCTCA
1 TATCGATGCCATATCCCAGATATGGTCTTACATGTAATCTCA
8591 ATAACCCTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
42 35 0.48
43 38 0.52
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (42 bp):
TATCGATGCCATATCCCAGATATGGTCTTACATGTAATCTCA
Found at i:13386 original size:20 final size:20
Alignment explanation
Indices: 13361--13399 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13351 AAAATTTCAA
13361 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
13381 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
13400 AATAGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:21016 original size:37 final size:37
Alignment explanation
Indices: 20966--21152 Score: 320
Period size: 37 Copynumber: 5.1 Consensus size: 37
20956 CTTTAGCTCA
* * *
20966 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
21003 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
21040 GACATAATCTTCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
21077 GACATAATCTTCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
21114 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
21151 GA
1 GA
21153 ATATATTTCC
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 145 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:21418 original size:47 final size:47
Alignment explanation
Indices: 21357--21541 Score: 289
Period size: 47 Copynumber: 3.9 Consensus size: 47
21347 TACATATATT
* * * *
21357 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
21404 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
21451 TCACATTGGCCATTTGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
**
21498 TCACATTGGCCATTCGGCCTTATCACATATATGCACATTCACAT
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACAT
21542 CACAATTATC
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 126 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:21477 original size:22 final size:22
Alignment explanation
Indices: 21450--21525 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
21440 GCTCACATTC
21450 ATCACATTGGCCATTTGGCCTT
1 ATCACATTGGCCATTTGGCCTT
* ** *
21472 ATCACATATATG-CATGTTCACATT
1 ATCACAT-T-GGCCAT-TTGGCCTT
*
21496 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTTGGCCTT
21519 ATCACAT
1 ATCACAT
21526 ATATGCACAT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 10 0.25
25 7 0.17
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTTGGCCTT
Found at i:25988 original size:43 final size:42
Alignment explanation
Indices: 25918--26046 Score: 125
Period size: 43 Copynumber: 3.0 Consensus size: 42
25908 CACTCAGTAC
* * * *
25918 CATATCAATGCCATATCCTAGATATGGTCTTACATGTAATCT
1 CATATCGATGCAATAGCCCAGATATGGTCTTACATGTAATCT
* * *
25960 CGTATCGATGCCAATAGCCCAGCTATGGTTTTACATG-AAGTCT
1 CATATCGATG-CAATAGCCCAGATATGGTCTTACATGTAA-TCT
** * * *
26003 CATATCGATGTTATATCCCTGATATGGTCTTACACGTAATCT
1 CATATCGATGCAATAGCCCAGATATGGTCTTACATGTAATCT
26045 CA
1 CA
26047 GTAACCATAA
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
42 34 0.49
43 35 0.51
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (42 bp):
CATATCGATGCAATAGCCCAGATATGGTCTTACATGTAATCT
Found at i:26046 original size:42 final size:43
Alignment explanation
Indices: 25918--26046 Score: 131
Period size: 42 Copynumber: 3.0 Consensus size: 43
25908 CACTCAGTAC
*
25918 CATATCAATGCC-ATAT-CCTAGATATGGTCTTACATGTAATCT
1 CATATCGATGCCAATATCCCT-GATATGGTCTTACATGTAATCT
* * * * *
25960 CGTATCGATGCCAATAGCCCAGCTATGGTTTTACATG-AAGTCT
1 CATATCGATGCCAATATCCCTGATATGGTCTTACATGTAA-TCT
** *
26003 CATATCGATG-TTATATCCCTGATATGGTCTTACACGTAATCT
1 CATATCGATGCCAATATCCCTGATATGGTCTTACATGTAATCT
26045 CA
1 CA
26047 GTAACCATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
42 36 0.52
43 31 0.45
44 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (43 bp):
CATATCGATGCCAATATCCCTGATATGGTCTTACATGTAATCT
Found at i:27761 original size:43 final size:42
Alignment explanation
Indices: 27693--27819 Score: 139
Period size: 43 Copynumber: 3.0 Consensus size: 42
27683 CTCAGTACTG
* * * *
27693 TATCAATGCCATATCCTAGATATGGTCTTACATGTAATCTCG
1 TATCGATGCCATAGCCCAGATATGGTCTTACATGTAATCTCA
* * *
27735 TATCGATTCCAATAGCCCAGCTATGGTCTTACACG-AAGTCTCA
1 TATCGATGCC-ATAGCCCAGATATGGTCTTACATGTAA-TCTCA
* * *
27778 TATCGATGCCATATCCCTGATATGGTCTTTCATGTAATCTCA
1 TATCGATGCCATAGCCCAGATATGGTCTTACATGTAATCTCA
27820 GTAACCCTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 34 0.49
43 35 0.51
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (42 bp):
TATCGATGCCATAGCCCAGATATGGTCTTACATGTAATCTCA
Found at i:27819 original size:42 final size:42
Alignment explanation
Indices: 27693--27819 Score: 141
Period size: 42 Copynumber: 3.0 Consensus size: 42
27683 CTCAGTACTG
* *
27693 TATCAATGCCATAT-CCTAGATATGGTCTTACATGTAATCTCG
1 TATCGATGCCATATCCCT-GATATGGTCTTACATGTAATCTCA
* * * * *
27735 TATCGATTCCAATAGCCCAGCTATGGTCTTACACG-AAGTCTCA
1 TATCGATGCC-ATATCCCTGATATGGTCTTACATGTAA-TCTCA
*
27778 TATCGATGCCATATCCCTGATATGGTCTTTCATGTAATCTCA
1 TATCGATGCCATATCCCTGATATGGTCTTACATGTAATCTCA
27820 GTAACCCTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
42 34 0.50
43 32 0.47
44 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (42 bp):
TATCGATGCCATATCCCTGATATGGTCTTACATGTAATCTCA
Found at i:34170 original size:28 final size:28
Alignment explanation
Indices: 34094--34171 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 28
34084 CTGTAAAAGT
* * *
34094 GATTAGGCCTAATGGGCCATATAGATGT
1 GATTGGGCCTAATGGGCCATATAAATGA
34122 GATTTGGGCCTAATGGGCCATATAAATGA
1 GA-TTGGGCCTAATGGGCCATATAAATGA
* *
34151 GATTGGGCCTAGTGGTCCATA
1 GATTGGGCCTAATGGGCCATA
34172 AGCATGTATG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 19 0.43
29 25 0.57
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (28 bp):
GATTGGGCCTAATGGGCCATATAAATGA
Found at i:35738 original size:39 final size:40
Alignment explanation
Indices: 35581--35752 Score: 242
Period size: 40 Copynumber: 4.3 Consensus size: 40
35571 GCTACTCGTT
* *
35581 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
35621 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
35661 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
35701 CCATTGCCTTCAGG-CTTAGA-CCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTA-ACCCGGATTTAGTAACTCGCA
35740 CAAATGCCTTCGG
1 CAAATGCCTTCGG
35753 ATCTTAGTCC
Statistics
Matches: 120, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 31 0.26
40 87 0.73
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:37003 original size:56 final size:56
Alignment explanation
Indices: 36936--37055 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
36926 TATTAGTTTA
36936 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
36992 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
37048 TTACCCAT
1 TTGCCCAT
37056 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.24, G:0.08, T:0.44
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:43677 original size:39 final size:40
Alignment explanation
Indices: 43527--43744 Score: 273
Period size: 40 Copynumber: 5.5 Consensus size: 40
43517 GCTACTCGTT
* *
43527 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
43567 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
43607 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
43647 CCAATGCCTTCGGG-CTTAACCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
43686 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
43727 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
43745 GCCCAGACAT
Statistics
Matches: 157, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.20
40 110 0.70
41 13 0.08
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:44955 original size:56 final size:56
Alignment explanation
Indices: 44884--45059 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
44874 TATTAGTTTA
44884 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
44940 TTGCCCATGCCTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
44996 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
45052 TTGCCCAT
1 TTGCCCAT
45060 CATCCATTGT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 118 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:46910 original size:27 final size:27
Alignment explanation
Indices: 46879--47106 Score: 258
Period size: 27 Copynumber: 8.4 Consensus size: 27
46869 CCCCAAAATA
** *
46879 GGTAAAATGACTATAATACCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
46906 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
46933 GGTAAAATAACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* ** *
46960 GGCCAAAATGACTATAATGCCCTTGTAAG
1 GG-TAAAATGACCGTAATGCCCCTGT-AG
** * * * * *
46989 GCCAAAATGACTGTAGTTCTCCTTTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
47016 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
47043 GGTAAAATGACCATAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * * *
47070 GGTACAATGACCGTAATACCCATGTAT
1 GGTAAAATGACCGTAATGCCCCTGTAG
47097 GGTAAAATGA
1 GGTAAAATGA
47107 AGATTATGAC
Statistics
Matches: 169, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
27 131 0.78
28 35 0.21
29 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTGTAG
Found at i:47020 original size:83 final size:82
Alignment explanation
Indices: 46882--47104 Score: 261
Period size: 83 Copynumber: 2.7 Consensus size: 82
46872 CAAAATAGGT
* **
46882 AAAATGACTATAATACCCCTGT-AGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACCG
1 AAAATGACTATAATGCCCCTGTAAGGCCAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACCG
46946 TAATGCCCCTGTAGGGCC
66 TAATGCCCCTGTAGGG-C
* * * * * * *
46964 AAAATGACTATAATGCCCTTGTAAGGCCAAAATGACTGTAGTTCTCCTTTAGGGTAAAATGACCG
1 AAAATGACTATAATGCCCCTGTAAGGCCAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACCG
*
47029 TAATGCCCCTGTAGGGT
66 TAATGCCCCTGTAGGGC
* ** * * * *
47046 AAAATGACCATAATGCCCCTGT-AGGGTACAATGACCGTAATACCCATGTATGGTAAAAT
1 AAAATGACTATAATGCCCCTGTAAGGCCAAAATGACCGTAATGCCCCTGTAGGGTAAAAT
47105 GAAGATTATG
Statistics
Matches: 117, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
81 27 0.23
82 40 0.34
83 50 0.43
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (82 bp):
AAAATGACTATAATGCCCCTGTAAGGCCAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACCG
TAATGCCCCTGTAGGGC
Found at i:47293 original size:27 final size:27
Alignment explanation
Indices: 47244--47307 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
47234 TGGAGGAAGT
*
47244 ACTG-TACTGGTGACTATGTCACATTC
1 ACTGTTACTGGTGACTATGCCACATTC
* * *
47270 ACTGTTACTGGTGGCTTTGCCACATTT
1 ACTGTTACTGGTGACTATGCCACATTC
*
47297 ACTGTTTCTGG
1 ACTGTTACTGG
47308 CAGCTATGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (27 bp):
ACTGTTACTGGTGACTATGCCACATTC
Found at i:47321 original size:27 final size:27
Alignment explanation
Indices: 47257--47336 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
47247 GTACTGGTGA
* **
47257 CTATGTCACATTCACTGTTACTGGTGG
1 CTATGCCACATTCACTGTTACTGGCAG
* * *
47284 CTTTGCCACATTTACTGTTTCTGGCAG
1 CTATGCCACATTCACTGTTACTGGCAG
* * *
47311 CTATGCTACATT-ATTATTACTGGCAG
1 CTATGCCACATTCACTGTTACTGGCAG
47337 TTTTGTTGCG
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 11 0.26
27 31 0.74
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (27 bp):
CTATGCCACATTCACTGTTACTGGCAG
Found at i:76925 original size:40 final size:40
Alignment explanation
Indices: 76895--77104 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
76885 GGACTAAGAT
* * * **
76895 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
76935 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
76975 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
77015 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
77055 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
77094 CCGAAGGCATT
1 CCGAAGGCATT
77105 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:84887 original size:40 final size:40
Alignment explanation
Indices: 84857--85066 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
84847 GGACTAAGAT
* * * **
84857 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
84897 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
84937 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
84977 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
85017 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
85056 CCGAAGGCATT
1 CCGAAGGCATT
85067 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:87040 original size:43 final size:42
Alignment explanation
Indices: 86902--87070 Score: 151
Period size: 43 Copynumber: 4.0 Consensus size: 42
86892 ACATAAGGTC
* * * * * *
86902 ATACAATGAC-ATATCCCAGATATGGGCTTACATGTTATCAT
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAA
* * * * * *
86943 ATATCGATGCCACTGTCCCAAGATAGGGTCTTACATGAAATCGA
1 ATA-CAATGCCAATGTCCC-AGACATGGTCTTACATGTAATCAA
* *
86987 TTAACGATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
1 AT-ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA-A
* *
87031 ATACAATGCCAATGTCCCAAACATGGTCTTATATGTAATC
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
87071 CCTACTCGAT
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.03
42 5 0.05
43 59 0.57
44 35 0.34
45 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (42 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAA
Found at i:90266 original size:120 final size:120
Alignment explanation
Indices: 90034--90292 Score: 287
Period size: 120 Copynumber: 2.2 Consensus size: 120
90024 TTGAATGATG
* * *
90034 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
90099 GTACGAGTTACTAAATCCGGACTAAGATCCAAAGGCATTTGTGCGAGTTA-CTAAA
66 GTACGAGTTACTAAATCCGGACTAAGATCCAAAGGCATTTGAACGAG-TAGCTAAA
* * **
90154 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * *
90217 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTACGAGTTACTA-AATCCGGACTAAGAT-CCAAAGGCATTTGAACGAGTAGCTAAA
* *
90274 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
90293 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
119 18 0.15
120 90 0.76
121 10 0.08
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAATCCGGACTAAGATCCAAAGGCATTTGAACGAGTAGCTAAA
Found at i:90273 original size:40 final size:40
Alignment explanation
Indices: 90034--90259 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
90024 TTGAATGATG
* * * *
90034 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
90074 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
90114 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
90154 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
90194 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
90235 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
90260 AACGAGTAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 158 0.93
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:98119 original size:28 final size:28
Alignment explanation
Indices: 98081--98262 Score: 294
Period size: 28 Copynumber: 6.5 Consensus size: 28
98071 TAAATTGTAC
*
98081 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
98109 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
98137 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
98165 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
98193 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
98221 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
98248 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
98263 GACTTAATAT
Statistics
Matches: 147, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
27 24 0.16
28 123 0.84
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:109747 original size:28 final size:28
Alignment explanation
Indices: 109684--109865 Score: 321
Period size: 28 Copynumber: 6.5 Consensus size: 28
109674 ATATTAAGTC
* *
109684 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
109711 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
109739 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
109767 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
109795 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
109823 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
109851 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
109866 GTACAATTTA
Statistics
Matches: 151, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
27 22 0.15
28 129 0.85
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:116178 original size:42 final size:42
Alignment explanation
Indices: 116119--116227 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 42
116109 TTTAATATTG
* * *
116119 AAATATGATTCGCATGTTAATCAT-ACCGACTATGTTGATTAT
1 AAATATGATTTGCATGTTAAGCATGA-CGACTATGTGGATTAT
*
116161 AAATATGATTTGCATGTTAAGCATGACGAGTATGTGGATTAT
1 AAATATGATTTGCATGTTAAGCATGACGACTATGTGGATTAT
* *
116203 AAATTTGAATTGCATGTTAAGCATG
1 AAATATGATTTGCATGTTAAGCATG
116228 CCCATTGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 59 0.98
43 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (42 bp):
AAATATGATTTGCATGTTAAGCATGACGACTATGTGGATTAT
Found at i:116388 original size:48 final size:48
Alignment explanation
Indices: 116317--116433 Score: 171
Period size: 48 Copynumber: 2.4 Consensus size: 48
116307 TTCACTGTAA
116317 TATTGAGTGGCTTGACCACAACATTATTGAGTGGCTTGACCACAATGC
1 TATTGAGTGGCTTGACCACAACATTATTGAGTGGCTTGACCACAATGC
* * * * *
116365 TATTGAGTGGCTTGGCCATAACATTATTGATTGGCTTGGCCACAATGT
1 TATTGAGTGGCTTGACCACAACATTATTGAGTGGCTTGACCACAATGC
* *
116413 TATTGATTGGCTTGTCCACAA
1 TATTGAGTGGCTTGACCACAA
116434 TGTGTAGTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (48 bp):
TATTGAGTGGCTTGACCACAACATTATTGAGTGGCTTGACCACAATGC
Found at i:116434 original size:24 final size:24
Alignment explanation
Indices: 116317--116436 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
116307 TTCACTGTAA
**
116317 TATTGAGTGGCTTGACCACAACAT
1 TATTGAGTGGCTTGACCACAATGT
*
116341 TATTGAGTGGCTTGACCACAATGC
1 TATTGAGTGGCTTGACCACAATGT
* * **
116365 TATTGAGTGGCTTGGCCATAACAT
1 TATTGAGTGGCTTGACCACAATGT
* *
116389 TATTGATTGGCTTGGCCACAATGT
1 TATTGAGTGGCTTGACCACAATGT
* *
116413 TATTGATTGGCTTGTCCACAATGT
1 TATTGAGTGGCTTGACCACAATGT
116437 GTAGTTTTAC
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCACAATGT
Found at i:124388 original size:29 final size:29
Alignment explanation
Indices: 124325--124392 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
124315 TAATCAACCG
124325 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
124354 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
124383 CGCACACTTA
1 CGCACACTTA
124393 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:124505 original size:174 final size:174
Alignment explanation
Indices: 124214--124541 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
124204 AACTCAAGGT
* *
124214 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAGGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
* *
124279 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCACACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
124344 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
124388 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
*
124453 GAAAATATATATTGGGTTCACACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCACACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
124518 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
124542 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCACACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:124533 original size:29 final size:28
Alignment explanation
Indices: 124494--124568 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
124484 CTTAATAATC
124494 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTG-C-TGTACATTTA
*
124524 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCTGTAC-ATTTA
124553 AACCCGCACACTTAGT
1 AACCCGCACACTTAGT
124569 TCCAATCTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 32 0.78
30 3 0.07
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
AACCCGCACACTTAGTGCTGTACATTTA
Done.