Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold681
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: 27627
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:69 original size:23 final size:21
Alignment explanation
Indices: 38--83 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
28 TTTTTTGTTT
38 ATTTTAAAT-ATATAAATTATAA
1 ATTTTAAATGA-ATAAATTA-AA
60 ATTTTAAAATGAATAAATTAAA
1 ATTTT-AAATGAATAAATTAAA
82 AT
1 AT
84 GAAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.41
23 12 0.55
24 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTTAAATGAATAAATTAAA
Found at i:80 original size:14 final size:15
Alignment explanation
Indices: 63--91 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53 ATTATAAATT
63 TTAAAATG-AATAAA
1 TTAAAATGAAATAAA
77 TTAAAATGAAATAAA
1 TTAAAATGAAATAAA
92 ATGTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
TTAAAATGAAATAAA
Found at i:4853 original size:13 final size:13
Alignment explanation
Indices: 4835--4860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4825 AATTTTTTTG
4835 TGTATCGATACAT
1 TGTATCGATACAT
4848 TGTATCGATACAT
1 TGTATCGATACAT
4861 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5809 original size:155 final size:155
Alignment explanation
Indices: 5650--6005 Score: 344
Period size: 156 Copynumber: 2.3 Consensus size: 155
5640 AGTCAACGAC
* * *
5650 ATGCTTTTATGCTAAAGGTGTGA-ATTTAGGATAGGTTCATCTTTTCATGATCATTTT-GAGTCT
1 ATGCTTTTATGCTAAAGGTGT-ACATTTAGGATAGGTTCAACTTTTC-TGATCATTTTAAAGTCC
* * * * *
5713 TTTGGGATTACTGAAATACTTTTATATCGAAAATATACCCCA-AAAGTTTTTTAGTAATTT-TCC
64 TTTAGGATTACCGAAATACTTTCACATCGAAAATATA-CCCATAAAGTATTTTAGTAATTTCT-C
* *
5776 CTAAAACCAAGTCCGATATAGTCACTGGG
127 CTAAAACCAAGTCCGATATAGTCACTAGA
* * * * * *
5805 ATGCTTTTAAG-TCAAAGGTCTACATTTAGGATAAGTTTACCATTTTCTTATCATTTTAAAGTCC
1 ATGCTTTTATGCT-AAAGGTGTACATTTAGGATAGGTTCAAC-TTTTCTGATCATTTTAAAGTCC
* * * ** * * *
5869 TTTAGGTTTACCGAGATACTTTCACATGGAAGGTATACCCATAAGGTATTTTGGTAATTTCTTCT
64 TTTAGGATTACCGAAATACTTTCACATCGAAAATATACCCATAAAGTATTTTAGTAATTTCTCCT
* * * *
5934 ATAATCTAGTCCGATATAGTCATTAGA
129 AAAACCAAGTCCGATATAGTCACTAGA
* * *
5961 ATGTTTTTATGCCAAAGGTGTATATTTAGGATAGGTTCAACTTTT
1 ATGCTTTTATGCTAAAGGTGTACATTTAGGATAGGTTCAACTTTT
6006 TTATTATTTT
Statistics
Matches: 159, Mismatches: 35, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
154 2 0.01
155 49 0.31
156 107 0.67
157 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (155 bp):
ATGCTTTTATGCTAAAGGTGTACATTTAGGATAGGTTCAACTTTTCTGATCATTTTAAAGTCCTT
TAGGATTACCGAAATACTTTCACATCGAAAATATACCCATAAAGTATTTTAGTAATTTCTCCTAA
AACCAAGTCCGATATAGTCACTAGA
Found at i:6080 original size:154 final size:156
Alignment explanation
Indices: 5761--6132 Score: 414
Period size: 154 Copynumber: 2.4 Consensus size: 156
5751 CCCAAAAGTT
* ** * * * *
5761 TTTTAGTAATTT-TCCCTAAAACCAAGTCCGATATAGTCACTGGGATGCTTTTAAGTCAAAGGTC
1 TTTTAGTAATTTCT-TCTAAAATTAAGTCCGATATAGTCATTGGGATGTTTTTATGCCAAAGGTC
* *
5825 TACATTTAGGATAAGTTTACCATTTTCTTATCATTTTAAAGTCCTTTAGGTTTACCGAGATACTT
65 TACATTTAGGATAAGTTCAACATTTTCTTATCATTTTAAAGTCCTTTAGGTTTACCGAGATACTT
*
5890 TCACATGGAAGGTATACCCATAAGGTA
130 TCACATGGAAGGTATACCCATAAGGCA
* * * * *
5917 TTTTGGTAATTTCTTCTATAATCT-AGTCCGATATAGTCATTAGAATGTTTTTATGCCAAAGGTG
1 TTTTAGTAATTTCTTCTAAAAT-TAAGTCCGATATAGTCATTGGGATGTTTTTATGCCAAAGGTC
* * * ** ** *
5981 TATATTTAGGATAGGTTCAAC-TTTT-TTATTATTTTCGAGTCCTTTAAGG-TTATTGAGATATT
65 TACATTTAGGATAAGTTCAACATTTTCTTATCATTTTAAAGTCCTTT-AGGTTTACCGAGATACT
* * *
6043 TTCACGTTGAAGGTATA-CTATAATGGCA
129 TTCACATGGAAGGTATACCCATAA-GGCA
* *
6071 TTTTAGTAATTTCTTCTAAAATTAAGTTCTATATAGTCATTGGGATGTTTTTATGCCAAAGG
1 TTTTAGTAATTTCTTCTAAAATTAAGTCCGATATAGTCATTGGGATGTTTTTATGCCAAAGG
6133 CGTGCGTCTA
Statistics
Matches: 179, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
153 6 0.03
154 99 0.55
155 7 0.04
156 66 0.37
157 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (156 bp):
TTTTAGTAATTTCTTCTAAAATTAAGTCCGATATAGTCATTGGGATGTTTTTATGCCAAAGGTCT
ACATTTAGGATAAGTTCAACATTTTCTTATCATTTTAAAGTCCTTTAGGTTTACCGAGATACTTT
CACATGGAAGGTATACCCATAAGGCA
Found at i:6582 original size:20 final size:20
Alignment explanation
Indices: 6554--6628 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
6544 TTTTACCCAG
6554 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
6574 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
6594 ATGTATCAATATATTCTTCA
1 ATGTATCGATACATTTTTCA
6614 ATGTATCGATACATT
1 ATGTATCGATACATT
6629 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:6614 original size:40 final size:39
Alignment explanation
Indices: 6554--6631 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
6544 TTTTACCCAG
* *
6554 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCAATACATTCTTCAATATATCGATACAT-TATGA
* *
6594 ATGTATCAATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCAATACATTCTTCAATATATCGATACATTATG
6632 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (39 bp):
ATGTATCAATACATTCTTCAATATATCGATACATTATGA
Found at i:7550 original size:20 final size:21
Alignment explanation
Indices: 7513--7551 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
7503 AGCCTTTGAC
**
7513 CATGCATTTTTTTTTATGTTT
1 CATGCATTTTTTAATATGTTT
7534 CATGCA-TTTTTAATATGT
1 CATGCATTTTTTAATATGT
7552 CTAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:13683 original size:14 final size:16
Alignment explanation
Indices: 13652--13698 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
13642 AAAAAAAATC
13652 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
13668 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
13682 AAAATGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
13698 A
1 A
13699 TAAAAAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 13 0.46
17 1 0.04
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:13705 original size:20 final size:21
Alignment explanation
Indices: 13680--13728 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
13670 AATGAAAAGA
13680 AAAAAATGCAA-AAGC-AAAAT
1 AAAAAATGCAACAA-CAAAAAT
* *
13700 AAAAAAGGGAACAACAAAAAT
1 AAAAAATGCAACAACAAAAAT
13721 AAAAAATG
1 AAAAAATG
13729 AGGACATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.08
Consensus pattern (21 bp):
AAAAAATGCAACAACAAAAAT
Found at i:15084 original size:27 final size:27
Alignment explanation
Indices: 15041--15315 Score: 345
Period size: 27 Copynumber: 10.1 Consensus size: 27
15031 TGGCATTATT
*
15041 TTTTAAAGTCCACAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
15069 TTTTAAGTCCACAACTCCGTGGCACAC
1 TTTTAAGTCCACAACTCCGTGGCACCC
15096 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
15123 TTTTAAGTCCACAACTCCGTGGGACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
15150 TTTTAAGTCCATAACTCCGTGGTACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
15177 TTTTAAATCCACAACTCCGTCGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
15204 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* * * * *
15232 TTTGAAATCCACAACTCCGTGGTATCT
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
15259 TTTTTAGTCCATAACTCCGTGGCA-CC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * * *
15285 TTTTAAAGCCCACAAGTCAGTAGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
15313 TTT
1 TTT
15316 CAAAGCACAC
Statistics
Matches: 213, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
26 5 0.02
27 176 0.83
28 32 0.15
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.29
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:15349 original size:32 final size:32
Alignment explanation
Indices: 15295--15769 Score: 452
Period size: 32 Copynumber: 15.5 Consensus size: 32
15285 TTTTAAAGCC
* * *
15295 CACAAGTCAGTAGC-ACCC-TTTCAAAGCACA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
15325 CATAAGTCGGTGGTAGCCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
15355 CACAAGTCGGTGGC-A-TCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
15385 CACAAGTCGATGGC-ACCC-TTTCAAAGCCTA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
15415 CACAAGTCGGTGGCAACTCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
15447 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
15479 CATAAGTTGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
15511 TACAAGTTGGTGGCAACCCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
15543 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
15575 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
15607 CACAAGTCGGTGGC-A-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
15635 CACAAGTCAGTGGC-ACCC-TTTGAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
15663 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * * * *
15691 TATAAGTCAGTGGC-ACTCTTTTTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * * *
15722 CACGAGTTGGTGGCATCTCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
**
15754 CACAAGTTAGTGGCAA
1 CACAAGTCGGTGGCAA
15770 GATTTTTTTT
Statistics
Matches: 379, Mismatches: 54, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
28 74 0.20
29 12 0.03
30 71 0.19
31 18 0.05
32 204 0.54
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:16010 original size:28 final size:28
Alignment explanation
Indices: 15971--16201 Score: 309
Period size: 28 Copynumber: 8.0 Consensus size: 28
15961 CTCTCACTCT
15971 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
15999 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * * *
16027 TTTCAAAGCCCACAAGTTAGTAGTACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
16056 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
16084 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
16112 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
** *
16141 TTTCAAAGCCCACACGAGTTGGTGGCATCTCT
1 TTTCAAAGCCCACA--AGTCAGTGGCA-C-CC
*
16173 TTTCAAAGCCCACACAAGTTAGTGGCACC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACC
16202 ATTTTTTAAA
Statistics
Matches: 184, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
28 106 0.58
29 39 0.21
30 1 0.01
31 10 0.05
32 22 0.12
33 2 0.01
34 4 0.02
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:16072 original size:57 final size:56
Alignment explanation
Indices: 15971--16201 Score: 309
Period size: 57 Copynumber: 4.0 Consensus size: 56
15961 CTCTCACTCT
15971 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * *
16027 TTTCAAAGCCCACAAGTTAGTAGTACTCTTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
16084 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
** * *
16141 TTTCAAAGCCCACACGAGTTGGTGGCATCTCTTTTCAAAGCCCACACAAGTTAGTGGCACC
1 TTTCAAAGCCCACA--AGTCAGTGGCA-C-CCTTTCAAAG-CC-CACAAGTCAGTGGCACC
16202 ATTTTTTAAA
Statistics
Matches: 154, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
56 50 0.32
57 67 0.44
59 9 0.06
60 1 0.01
61 9 0.06
62 3 0.02
63 15 0.10
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (56 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:16094 original size:431 final size:437
Alignment explanation
Indices: 15543--16400 Score: 1446
Period size: 429 Copynumber: 2.0 Consensus size: 437
15533 TGAAAGCCCA
* **
15543 CACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
1 CACAAGTCAGTGGCAACTCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCAC
* * *
15608 ACAAGTCGGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTGAAAGCCCACAAGTCAG
66 ACAAGTCAGTAGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAG
* * *
15673 TGGCACCCTTTCAAAGCCTATAAGTCAGTGGCACTCTTTTTAAAGCCCACACGAGTTGGTGGCAT
131 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGCAT
* *
15738 CTCTTTTCAAAGCCCACACAAGTTAGTGGCAAGATTTTTTTTTAAAAAAAGCCCATGCAAGTCGG
196 CTCTTTTCAAAGCCCACACAAGTTAGTGGCAACA--TTTTTTAAAAAAAAGCCCATGCAAGTCGG
*
15803 TGGCAACCCTTTTCAAATCACCACTGTCTAACATCGCTAGCATTGAATCAGCATATTGGCACCTT
259 TGGCAACCATTTTCAAATCACCACTGTCTAACATCGCTAGCATTGAATCAGCATATTGGCACCTT
15868 TATGAGCCCAATGTCGCTGGCCTTAAATCAACACATTGGTCCACTTTTCCCTTAGTCCAATGTCG
324 TATGAGCCCAATGTCGCTGGCCTTAAATCAACACATTGGTCCACTTTTCCCTTAGTCCAATGTCG
15933 CTAGCCTTGAATTGGCACATTGGCAATCCTCTCA-CTCTTTTCAAAGCC
389 CTAGCCTTGAATTGGCACATTGGCAATCCTCTCATCTCTTTTCAAAGCC
*
15981 CACAAGTCAGTGGC-AC-CCTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-C
1 CACAAGTCAGTGGCAACTCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCAC
* *
16038 ACAAGTTAGTAGTACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
66 ACAAGTCAGTAGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
16103 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGCA
130 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* *
16168 TCTCTTTTCAAAGCCCACACAAGTTAGTGGCACCATTTTTTAAAAAAAAGCCCATGCAAGTTGGT
195 TCTCTTTTCAAAGCCCACACAAGTTAGTGGCAACATTTTTTAAAAAAAAGCCCATGCAAGTCGGT
*
16233 GGCAACCATTTTCAAATCACCACTGTCTGACATCGCTAGCATTGAATCAGCATATTGGCACCTTT
260 GGCAACCATTTTCAAATCACCACTGTCTAACATCGCTAGCATTGAATCAGCATATTGGCACCTTT
* *
16298 ATGAGCCCAATGTCGCTGGCCTTAATTCAGCACATTGGTCCACTTTTCCCTTAGTCCAATGTCGC
325 ATGAGCCCAATGTCGCTGGCCTTAAATCAACACATTGGTCCACTTTTCCCTTAGTCCAATGTCGC
16363 TAGCCTTGAATTGGCACATTGGCAATCCTCTCATCTCT
390 TAGCCTTGAATTGGCACATTGGCAATCCTCTCATCTCT
16401 AAGTCTAGTG
Statistics
Matches: 398, Mismatches: 20, Indels: 12
0.93 0.05 0.03
Matches are distributed among these distances:
429 187 0.47
430 15 0.04
431 146 0.37
432 8 0.02
433 4 0.01
434 12 0.03
435 2 0.01
436 9 0.02
437 2 0.01
438 13 0.03
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (437 bp):
CACAAGTCAGTGGCAACTCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCAC
ACAAGTCAGTAGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAG
TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGCAT
CTCTTTTCAAAGCCCACACAAGTTAGTGGCAACATTTTTTAAAAAAAAGCCCATGCAAGTCGGTG
GCAACCATTTTCAAATCACCACTGTCTAACATCGCTAGCATTGAATCAGCATATTGGCACCTTTA
TGAGCCCAATGTCGCTGGCCTTAAATCAACACATTGGTCCACTTTTCCCTTAGTCCAATGTCGCT
AGCCTTGAATTGGCACATTGGCAATCCTCTCATCTCTTTTCAAAGCC
Found at i:16109 original size:85 final size:85
Alignment explanation
Indices: 15965--16201 Score: 357
Period size: 85 Copynumber: 2.7 Consensus size: 85
15955 GCAATCCTCT
15965 CACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
1 CACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
16030 CAAAGCCCACAAGTTAGTAG
66 CAAAGCCCACAAGTCAGTAG
*
16050 TACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
1 CACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
16115 CAAAGCCCACAAGTCAGTGG
66 CAAAGCCCACAAGTCAGTAG
** * *
16135 CACTCTTTTCAAAGCCCACACGAGTTGGTGGCATCTCTTTTCAAAGCCCACACAAGTTAGTGGCA
1 CACTCTTTTCAAAGCCCACA--AGTCAGTGGCA-C-CCTTTCAAAG-CC-CACAAGTCAGTGGCA
16200 CC
60 CC
16202 ATTTTTTAAA
Statistics
Matches: 138, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
85 101 0.73
87 9 0.07
88 1 0.01
89 9 0.07
90 2 0.01
91 16 0.12
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (85 bp):
CACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
CAAAGCCCACAAGTCAGTAG
Found at i:16789 original size:20 final size:20
Alignment explanation
Indices: 16764--16835 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
16754 TACCTAGATG
16764 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * * *
16784 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATA
* *
16804 TATCGATATATTCTTCAATA
1 TATCGATACATTTTTCAATA
16824 TATCGATACATT
1 TATCGATACATT
16836 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:16821 original size:40 final size:39
Alignment explanation
Indices: 16761--16838 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
16751 TTTTACCTAG
*
16761 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
*
16801 ATGTATCGATATATTCTTCAATATATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
16839 TCTTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:20336 original size:150 final size:149
Alignment explanation
Indices: 20065--20344 Score: 375
Period size: 149 Copynumber: 1.9 Consensus size: 149
20055 AAGTTGTGAC
* * *
20065 ACTTTCATGTCGAAGGTATACCCCAAAAGCATTTTGATAATTTTTTTAGAAGCGAATATGATATT
1 ACTTTCATGTCAAAGGTATACCCCAAAAGCATTTTGATAATTTTTTTAGAACCGAATATGATATA
* *
20130 GTCACGAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCTTTTTATGATCGTTTT
66 GTCACGAGATGCTTTTATGCCAAAGGTGTACATTTAGGATAGGTTCACCATTTTATGATCGTTTT
20195 ATTTTAGAGTTATTGGGAT
131 ATTTTAGAGTTATTGGGAT
* * * * * * *
20214 ACTTTTATGTCAAAGGTATGCCTCAAAGGTATTTT-AGTAATTTTTTTAGAACC-AGGTCTGATA
1 ACTTTCATGTCAAAGGTATACCCCAAAAGCATTTTGA-TAATTTTTTTAGAACCGA-ATATGATA
* * * *
20277 TAGTCACTAGGATGCTTTTATGCCAAATGTGTACATTTAGGATAGGTTCATCATTTTATGATTGT
64 TAGTCACGA-GATGCTTTTATGCCAAAGGTGTACATTTAGGATAGGTTCACCATTTTATGATCGT
20342 TTT
128 TTT
20345 CGAATCCTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
148 2 0.02
149 57 0.51
150 53 0.47
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (149 bp):
ACTTTCATGTCAAAGGTATACCCCAAAAGCATTTTGATAATTTTTTTAGAACCGAATATGATATA
GTCACGAGATGCTTTTATGCCAAAGGTGTACATTTAGGATAGGTTCACCATTTTATGATCGTTTT
ATTTTAGAGTTATTGGGAT
Found at i:23295 original size:11 final size:11
Alignment explanation
Indices: 23279--23303 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23269 TTACTTTGAT
23279 TTTGATTTTAA
1 TTTGATTTTAA
23290 TTTGATTTTAA
1 TTTGATTTTAA
23301 TTT
1 TTT
23304 ATACTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTGATTTTAA
Done.