Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold276
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: 761718
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
File 6 of 6
Found at i:731749 original size:16 final size:16
Alignment explanation
Indices: 731697--731750 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
731687 AACCGGAAGC
*
731697 CGAAATGGCTCGAA-T
1 CGAAATGGCCCGAACT
731712 CTGAAATGGCCC-AACT
1 C-GAAATGGCCCGAACT
*
731728 CAAAATGGCCCGAACT
1 CGAAATGGCCCGAACT
731744 CGAAATG
1 CGAAATG
731751 ATCCGACTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (16 bp):
CGAAATGGCCCGAACT
Found at i:731760 original size:31 final size:31
Alignment explanation
Indices: 731699--731762 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
731689 CCGGAAGCCG
* *
731699 AAATGGCTCGAATCTGAAATGGCCCAACTCA
1 AAATGGCCCGAATCTGAAATGACCCAACTCA
* *
731730 AAATGGCCCGAA-CTCGAAATGATCCGACTCA
1 AAATGGCCCGAATCT-GAAATGACCCAACTCA
731761 AA
1 AA
731763 TGATTTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (31 bp):
AAATGGCCCGAATCTGAAATGACCCAACTCA
Found at i:737733 original size:14 final size:14
Alignment explanation
Indices: 737709--737744 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
737699 CCATTTCATA
737709 TTTTTTCTTTTT-T
1 TTTTTTCTTTTTCT
737722 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
*
737736 TTCTTTCTT
1 TTTTTTCTT
737745 CTTCATCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:739042 original size:32 final size:32
Alignment explanation
Indices: 738993--739307 Score: 506
Period size: 32 Copynumber: 9.8 Consensus size: 32
738983 AAAATGGTGA
* * *
738993 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
739025 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
739057 TTTTAAATGGGTTGCCACCAACTTGTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
739089 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
739121 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
739153 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
739185 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
739217 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
739249 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
739281 TTTGAAATGGGTTGCCACCGATTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
739308 AATTTAAAAG
Statistics
Matches: 265, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
31 1 0.00
32 263 0.99
33 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:739359 original size:27 final size:27
Alignment explanation
Indices: 739293--740139 Score: 1273
Period size: 27 Copynumber: 30.9 Consensus size: 27
739283 TGAAATGGGT
* * * *
739293 TGCCACCGATTTGTGAATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739320 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
739348 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739375 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
739403 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
739431 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739458 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
739486 TGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* *
739514 TGCCACAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739541 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
739568 TGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739595 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
739622 ATGCCATGGAGTTATGGACTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
739650 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739677 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
739704 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
739732 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739759 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
739786 TGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
**
739814 TGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739841 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739868 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
739895 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
739922 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
739949 TACCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
739977 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
740004 TACCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
740032 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
740059 TGCCACAGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
740087 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
740114 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
740140 AAAATGCCAC
Statistics
Matches: 755, Mismatches: 52, Indels: 24
0.91 0.06 0.03
Matches are distributed among these distances:
27 475 0.63
28 280 0.37
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:739362 original size:55 final size:54
Alignment explanation
Indices: 739293--740139 Score: 1273
Period size: 55 Copynumber: 15.5 Consensus size: 54
739283 TGAAATGGGT
* * * *
739293 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
739348 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
* *
739403 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
739458 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGG
* *
739514 TGCCACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
739568 TGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
739622 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
739677 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
739732 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* **
739786 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGG
739841 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
739895 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
739949 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
740004 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
740059 TGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
740114 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
740140 AAAATGCCAC
Statistics
Matches: 737, Mismatches: 45, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
54 240 0.33
55 449 0.61
56 48 0.07
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:739504 original size:82 final size:81
Alignment explanation
Indices: 739293--740139 Score: 1273
Period size: 82 Copynumber: 10.3 Consensus size: 81
739283 TGAAATGGGT
* * * * *
739293 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
739358 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* *
739375 ATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
*
739440 GTTGTGGACTAAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
739458 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTT-AAAAGGGTGCCACGGA
*
739523 GTTATGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
739541 TGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
739606 TGTGGACTTAAAAGGG
66 TGTGGACTTAAAAGGG
* * * *
739622 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
739687 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
*
739704 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
739768 GTTGTGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* *
739786 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
739851 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* *
739868 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
739933 TGTGGACTAAAAAGGG
66 TGTGGACTTAAAAGGG
* * *
739949 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
740014 TTGTGGACTTTAAAAGGG
65 TTGTGGAC-TTAAAAGGG
* * *
740032 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAG
*
740097 TTGTGGACTTAAAAGGA
65 TTGTGGACTTAAAAGGG
*
740114 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
740140 AAAATGCCAC
Statistics
Matches: 707, Mismatches: 47, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
81 118 0.17
82 401 0.57
83 188 0.27
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGG
Found at i:741211 original size:15 final size:15
Alignment explanation
Indices: 741191--741220 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
741181 AGGGTGAAAA
741191 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
741206 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
741221 TTTAGGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GGTTTTTTTTTTTTT
Found at i:741535 original size:36 final size:32
Alignment explanation
Indices: 741494--741559 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 32
741484 CCCTTTTTTA
741494 TTTTGCTTTTGCACTTTTTCTTTTCATTTTTTGTGC
1 TTTTGCTTTTG-ACTTTTT-TTTT--TTTTTTGTGC
741530 TTTTGCTTTTGACTTTTTTTTTTTTTTTGT
1 TTTTGCTTTTGACTTTTTTTTTTTTTTTGT
741560 CATTTTGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 8 0.27
34 4 0.13
35 7 0.23
36 11 0.37
ACGTcount: A:0.05, C:0.12, G:0.11, T:0.73
Consensus pattern (32 bp):
TTTTGCTTTTGACTTTTTTTTTTTTTTTGTGC
Found at i:747992 original size:17 final size:17
Alignment explanation
Indices: 747970--748005 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
747960 CATTTCATAT
* *
747970 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
747987 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
748004 TT
1 TT
748006 CATCTTCCTT
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:753890 original size:43 final size:43
Alignment explanation
Indices: 753829--754177 Score: 398
Period size: 43 Copynumber: 7.9 Consensus size: 43
753819 GATGAAGATA
* * *
753829 CCAATATGCTGATTCAAGGCC-GACAACGTTAGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAG-CGACATTGGACTTAAAGGTG
*
753872 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G--G-TG
* *
753921 CCAATGTGCTAATTCAAGGCC-GACGACATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAG-CGACATTGGACTTAAAGGTG
* *
753964 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
* *
754007 CCAATATGCTGATTCAAGGCCAGTGA-TTTGGACTTAAAGATGAAGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G--G-TG
* * *
754055 CCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
*
754098 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
* * *
754141 CCAATATACTGATTCAAGGCCAGCGATATTAGACTTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
754178 GAAGAAGATG
Statistics
Matches: 267, Mismatches: 23, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
42 8 0.03
43 172 0.64
44 7 0.03
45 2 0.01
46 3 0.01
47 2 0.01
48 32 0.12
49 41 0.15
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (43 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
Found at i:753936 original size:92 final size:90
Alignment explanation
Indices: 753771--754190 Score: 441
Period size: 92 Copynumber: 4.7 Consensus size: 90
753761 CTTAGGAATG
* * * * *** *
753771 TTAAAGATGTCAATATGCTGATTCAAAGCCAACGATATCAAACTTAAAGATGAAGATACCAATAT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAGA-GAAGATGCCAATAT
* * *
753836 GCTGATTCAAGGCC-GACAACGTTAGAC
64 GCTGATTCAAGGCCAG-CGACATTGGAC
*
753863 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAGA-GAAGATGCCAATAT
*
753928 GCTAATTCAAGGCC-GACGACATTGGAC
64 GCTGATTCAAGGCCAG-CGACATTGGAC
753955 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---A-AAGATGCCAATATGC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAGAAGATGCCAATATGC
* *
754016 TGATTCAAGGCCAGTGA-TTTGGAC
66 TGATTCAAGGCCAGCGACATTGGAC
* * * *
754040 TTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAA-AG--G-TGCCA
1 TT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAGAAGATGCCA
*
754101 ATATGCTGATTCAAGGCCAGCGATATTGGAC
60 ATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
754132 TTAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTT-AGAAGAAGATGCCA
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAG-AGAAGATGCCA
754191 CCAACTTGTG
Statistics
Matches: 283, Mismatches: 29, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
85 9 0.03
86 61 0.22
87 5 0.02
88 2 0.01
89 2 0.01
90 7 0.02
91 63 0.22
92 133 0.47
93 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (90 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAGAAGATGCCAATATGC
TGATTCAAGGCCAGCGACATTGGAC
Found at i:754091 original size:134 final size:135
Alignment explanation
Indices: 753829--754190 Score: 579
Period size: 134 Copynumber: 2.7 Consensus size: 135
753819 GATGAAGATA
* ** *
753829 CCAATATGCTGATTCAAGGCC-GACAACGTTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCC
1 CCAATATGCTGATTCAAGGCCAG-CGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCC
753893 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTA
65 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTA
753958 AAGGTG
130 AAGGTG
*
753964 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGCCAATATGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCA
* * **
754029 GTGAT-TTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAA
66 GCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTAA
754093 AGGTG
131 AGGTG
*
754098 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATACTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCA
* *
754163 GCGATATTAGACTT--AGAAGAAGATGCCA
66 GCGATATTGGACTTAAAGATGAAGATGCCA
754191 CCAACTTGTG
Statistics
Matches: 211, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
133 13 0.06
134 128 0.61
135 69 0.33
136 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (135 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCA
GCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTAA
AGGTG
Found at i:754100 original size:91 final size:92
Alignment explanation
Indices: 753870--754182 Score: 339
Period size: 91 Copynumber: 3.5 Consensus size: 92
753860 GACTTAAAGG
* * *
753870 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATT
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A--AAGATGCCAATATGCTGATT
*
753935 CAAGGCC-GACGACATTGGACTT-AA-A-G--G-
60 CAAGGCCAG-CGATATTGGACTTAAAGATGAAGA
*
753962 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
*
754027 CAGTGAT-TTGGACTTAAAGATGAAGA
66 CAGCGATATTGGACTTAAAGATGAAGA
* * * *
754053 TGCCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
754118 CAGCGATATTGGACTT-AA-A-G--G-
66 CAGCGATATTGGACTTAAAGATGAAGA
* * *
754139 TGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
754183 AGATGCCACC
Statistics
Matches: 195, Mismatches: 17, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
85 8 0.04
86 62 0.32
87 6 0.03
88 2 0.01
89 1 0.01
90 2 0.01
91 68 0.35
92 46 0.24
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGATGAAGA
Found at i:754159 original size:21 final size:21
Alignment explanation
Indices: 754092--754159 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
754082 ATTGGACTTA
*
754092 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATACTGATTC
** * *
754113 AA-G-GCCAGCGATATTGGACTTA
1 AAGGTGCCA-ATATACT-GA-TTC
754135 AAGGTGCCAATATACTGATTC
1 AAGGTGCCAATATACTGATTC
754156 AAGG
1 AAGG
754160 CCAGCGATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 10 0.30
22 6 0.18
23 5 0.15
24 4 0.12
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATACTGATTC
Found at i:754315 original size:58 final size:58
Alignment explanation
Indices: 754239--754440 Score: 257
Period size: 58 Copynumber: 3.5 Consensus size: 58
754229 TGTGTTTTTG
* *
754239 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
* * * * *
754297 AAGGGTACCACTAACTTGTGGGC-TTTGAAAGGGGTGCCACCGACTTATGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAA
* * * *
754355 AGGGGTGCCACCGACTTGGGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
* *
754412 AAAGATGCCACTGACTTGT-GGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAA
754441 GGGTGAGGAA
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
56 8 0.07
57 46 0.38
58 63 0.52
59 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (58 bp):
AAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
Found at i:754440 original size:29 final size:29
Alignment explanation
Indices: 754239--754436 Score: 233
Period size: 29 Copynumber: 6.9 Consensus size: 29
754229 TGTGTTTTTG
*
754239 AAGGTTGCCACTGACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA
*
754269 AA-GATGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* *
754297 AAGGGTACCACTAACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* * *
754326 AGGGGTGCCACCGACTTATGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* * *
754355 AGGGGTGCCACCGACTTGGGGGCTTTTG--
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA
*
754383 AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* *
754412 AAAGATGCCACTGACTTGT-GGCTTT
1 AAGGGTGCCACTGACTTGTGGGCTTT
754437 TGAAGGGTGA
Statistics
Matches: 147, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.03
28 33 0.22
29 104 0.71
30 6 0.04
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (29 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGAA
Found at i:755712 original size:15 final size:14
Alignment explanation
Indices: 755694--755739 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
755684 CATCCGGACC
755694 TTTTTTGTTGTTGTT
1 TTTTTTGTTGTT-TT
755709 TTTTTT-TT-TTTT
1 TTTTTTGTTGTTTT
755721 GTTTTTTGTTTGTTTT
1 -TTTTTTG-TTGTTTT
755737 TTT
1 TTT
755740 CCTTGTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 2 0.07
15 11 0.41
16 4 0.15
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
TTTTTTGTTGTTTT
Found at i:755720 original size:21 final size:22
Alignment explanation
Indices: 755694--755739 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
755684 CATCCGGACC
*
755694 TTTTTTG-TTGTTGTTTTTTTT
1 TTTTTTGTTTGTTGTTTGTTTT
*
755715 TTTTTTGTTTTTTGTTTGTTTT
1 TTTTTTGTTTGTTGTTTGTTTT
755737 TTT
1 TTT
755740 CCTTGTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (22 bp):
TTTTTTGTTTGTTGTTTGTTTT
Found at i:755736 original size:18 final size:18
Alignment explanation
Indices: 755696--755738 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
755686 TCCGGACCTT
*
755696 TTTTGTTGTTGTTTTTTTT
1 TTTT-TTGTTGTTTTTTTG
755715 TTTTTTGTT-TTTTGTTTG
1 TTTTTTGTTGTTTT-TTTG
755733 TTTTTT
1 TTTTTT
755739 TCCTTGTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (18 bp):
TTTTTTGTTGTTTTTTTG
Done.