Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold344
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: 528373
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 65855 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:351039 original size:13 final size:13
Alignment explanation
Indices: 351023--351051 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
351013 ATAAATGAAG
351023 TTCATAATTAGTA
1 TTCATAATTAGTA
351036 TTCATAATTAGTA
1 TTCATAATTAGTA
351049 TTC
1 TTC
351052 TAAGTTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (13 bp):
TTCATAATTAGTA
Found at i:373701 original size:29 final size:27
Alignment explanation
Indices: 373652--373710 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
373642 AATCTATCCT
*
373652 TTTTATTTATTTATTTATTATTTAACTAA
1 TTTTATTTATTTAGTTATTATTT--CTAA
*
373681 TTTTATTTATTCTCGTT-TTATTTCTAA
1 TTTTATTTATT-TAGTTATTATTTCTAA
373708 TTT
1 TTT
373711 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
29 17 0.63
30 3 0.11
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTTAGTTATTATTTCTAA
Found at i:373906 original size:10 final size:11
Alignment explanation
Indices: 373891--373930 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
373881 CTTATTCTTT
373891 AAAAAAA-CAA
1 AAAAAAAGCAA
373901 AAAAAAAGCAA
1 AAAAAAAGCAA
*
373912 AAAAAAGCGCAA
1 AAAAAA-AGCAA
373924 AAAAAAA
1 AAAAAAA
373931 AAGAAAGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 7 0.27
11 9 0.35
12 10 0.38
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCAA
Found at i:373944 original size:28 final size:30
Alignment explanation
Indices: 373891--373988 Score: 123
Period size: 30 Copynumber: 3.3 Consensus size: 30
373881 CTTATTCTTT
373891 AAAAAAACAAAA--AAAAAGCAAAAAAAAGCGC
1 AAAAAAA-AAAAGCAAAAAGC--AAAAAAGCGC
* *
373922 AAAAAAAAAAAG-AAAGAG-TAAAAAGCGC
1 AAAAAAAAAAAGCAAAAAGCAAAAAAGCGC
373950 AAAAAAAAAAAGCAAAAAGCAAAAAAGCGC
1 AAAAAAAAAAAGCAAAAAGCAAAAAAGCGC
373980 AAAAAAAAA
1 AAAAAAAAA
373989 GTTGCCTACC
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
28 21 0.35
29 5 0.08
30 22 0.37
31 12 0.20
ACGTcount: A:0.77, C:0.10, G:0.12, T:0.01
Consensus pattern (30 bp):
AAAAAAAAAAAGCAAAAAGCAAAAAAGCGC
Found at i:373945 original size:30 final size:29
Alignment explanation
Indices: 373912--373988 Score: 120
Period size: 28 Copynumber: 2.7 Consensus size: 29
373902 AAAAAAGCAA
*
373912 AAAAAAGCGCAAAAAAAAAAAG-AAAGAG
1 AAAAAAGCGCAAAAAAAAAAAGCAAAAAG
*
373940 TAAAAAGCGCAAAAAAAAAAAGCAAAAAG
1 AAAAAAGCGCAAAAAAAAAAAGCAAAAAG
373969 CAAAAAAGCGCAAAAAAAAA
1 -AAAAAAGCGCAAAAAAAAA
373989 GTTGCCTACC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 21 0.48
29 5 0.11
30 18 0.41
ACGTcount: A:0.74, C:0.10, G:0.14, T:0.01
Consensus pattern (29 bp):
AAAAAAGCGCAAAAAAAAAAAGCAAAAAG
Found at i:373966 original size:22 final size:24
Alignment explanation
Indices: 373926--373969 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
373916 AAGCGCAAAA
*
373926 AAAAAAAGAAAGAGTAAAAAGCGC
1 AAAAAAAGAAAGAGCAAAAAGCGC
373950 AAAAAAA-AAA-AGCAAAAAGC
1 AAAAAAAGAAAGAGCAAAAAGC
373970 AAAAAAGCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
24 7 0.37
ACGTcount: A:0.73, C:0.09, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAAAAAGAAAGAGCAAAAAGCGC
Found at i:383734 original size:41 final size:41
Alignment explanation
Indices: 383665--383935 Score: 242
Period size: 41 Copynumber: 6.5 Consensus size: 41
383655 CATTGAATGT
* * * *
383665 AAGGGGTTGTTAAGTGCAAATTCTCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
* *
383706 AAGGGGTTGCTAATTGCAGATTCCCCGAATCACTTATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
*
383747 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
* * * * * *
383788 AAGGGGTTGCTAAGTGCTGATTCCCTGAATTATTTATTCTAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGA-TCGAA
* * * * *
383830 AAGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATTGTGA
1 AAGGGGTTGCTAAGTGCAGATTCC-CCGAATCAC-TGATCG-AA
* ** * * *
383873 AAGGGGTTGCTATGTGTTGAATCCCCGTATCACTGAAT--AT
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTG-ATCGAA
*
383913 AAGGTGGTTGCTAAGTGCTGATT
1 AAGG-GGTTGCTAAGTGCAGATT
383936 TCACCGAGTA
Statistics
Matches: 189, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
40 4 0.02
41 118 0.62
42 37 0.20
43 30 0.16
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
Found at i:383810 original size:82 final size:83
Alignment explanation
Indices: 383665--383906 Score: 272
Period size: 82 Copynumber: 2.9 Consensus size: 83
383655 CATTGAATGT
* * * * *
383665 AAGGGGTTGTTAAGTGCAAATTCTCCGAATCACTGATCAAAAAGGGGTTGCTAATTGCAGATTCC
1 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
383730 CCGAATCACTTA-TCGAA
66 CCGAATCACTTATTCGAA
383747 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
* * * *
383812 CTGAATTATTTATTCTAA
66 CCGAATCACTTATTCGAA
* ** * * * * * *
383830 AAGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATTGTGAAAGGGGTTGCTATGTGTTGAA
1 AAGGGGTTGCTAAGTGCAAATTCC-CCGAATCAC-TGATCG-AAAAGGGGTTGCTAAGTGCTGAT
*
383894 TCCCCGTATCACT
63 TCCCCGAATCACT
383907 GAATATAAGG
Statistics
Matches: 134, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
82 69 0.51
83 26 0.19
84 11 0.08
85 28 0.21
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (83 bp):
AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
CCGAATCACTTATTCGAA
Found at i:383905 original size:126 final size:124
Alignment explanation
Indices: 383704--383935 Score: 283
Period size: 126 Copynumber: 1.9 Consensus size: 124
383694 TCACTGATCA
*
383704 AAAAGGGGTTGCTAATTGCAGATTCCCCGAATCACTTATCGAAAAGGGGTTGCTAAGTGCAAATT
1 AAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTTATCGAAAAGGGGTTGCTAAGTGCAAATT
383769 CCCCGAATCACTG-ATCGAAAAGG-GGTTGCTAAGTGCTGATTCCCTGAATTATTTATTCT
66 CCCCGAATCACTGAAT--AAAAGGTGGTTGCTAAGTGCTGATTCCCTGAATTATTTATTCT
* * * * * * **
383828 AAAAGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATTGTGAAAGGGGTTGCTATGTGTTG
1 AAAAGGGGTTGCTAAGTGCAGATTCC-CCGAATCACTT-ATCG-AAAAGGGGTTGCTAAGTG-CA
* *
383892 AA-TCCCCGTATCACTGAATATAAGGTGGTTGCTAAGTGCTGATT
62 AATTCCCCGAATCACTGAATAAAAGGTGGTTGCTAAGTGCTGATT
383936 TCACCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
124 26 0.29
125 14 0.15
126 47 0.52
127 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (124 bp):
AAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTTATCGAAAAGGGGTTGCTAAGTGCAAATT
CCCCGAATCACTGAATAAAAGGTGGTTGCTAAGTGCTGATTCCCTGAATTATTTATTCT
Found at i:386207 original size:10 final size:11
Alignment explanation
Indices: 386181--386205 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
386171 CATAGATAGG
386181 TTTTAATGAAT
1 TTTTAATGAAT
386192 TTTTAATGAAT
1 TTTTAATGAAT
386203 TTT
1 TTT
386206 AAAGGTTAAT
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTTAATGAAT
Found at i:394082 original size:30 final size:30
Alignment explanation
Indices: 394024--394082 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
394014 TTTACGAGCC
* *
394024 TAGGGGCAAAATCGTAATTTTGTAAAAGTT
1 TAGGGGCAAAAACGTAATTTTGCAAAAGTT
* *
394054 TAGGGGCAAAAAGGTAATTTTGCCAAAGT
1 TAGGGGCAAAAACGTAATTTTGCAAAAGT
394083 GTGATTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAAACGTAATTTTGCAAAAGTT
Found at i:394456 original size:51 final size:51
Alignment explanation
Indices: 394309--394506 Score: 231
Period size: 51 Copynumber: 3.9 Consensus size: 51
394299 AGTTAAAGTG
* * *
394309 ATGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TG
1 ATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * *
394358 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * *
394409 TTCGATCACATGTGTAGTACTATGTGCAGGCTAGTACGTGTATCGGATGGTA
1 AT-GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * *
394461 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGGA
1 ATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA
394507 CATCATTGAT
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.31
51 82 0.66
52 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (51 bp):
ATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
Found at i:394552 original size:45 final size:45
Alignment explanation
Indices: 394501--394594 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
394491 TACTATGTGA
* * * *
394501 ACCGGACATCATTGATTAGTAAGGTGGTTACTATGTGCTGATTCC
1 ACCGGACATCATTAATTAATAAAGTGGTTACTATGTGCTGAATCC
*
394546 ACCGGACATCATTAATTAATAAAGTGGTTGCTATGTGCTGAATCC
1 ACCGGACATCATTAATTAATAAAGTGGTTACTATGTGCTGAATCC
394591 ACCG
1 ACCG
394595 AGTATCTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (45 bp):
ACCGGACATCATTAATTAATAAAGTGGTTACTATGTGCTGAATCC
Found at i:394665 original size:23 final size:22
Alignment explanation
Indices: 394639--394682 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
394629 AATTGACTAA
394639 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
394662 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
394683 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:397315 original size:127 final size:127
Alignment explanation
Indices: 397066--397308 Score: 450
Period size: 127 Copynumber: 1.9 Consensus size: 127
397056 ATTTCTGTCA
397066 TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTGTTTTAAAAGTCATTATTTGTGAATTTGTTAATT
1 TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTGTTTTAAAAGTCATTATTTGTGAATTTGTTAATT
* *
397131 TTTCATTTTGCTTAAATTTTTTCTGTTCAATTTTCACTTAGCTAATTTTTCAATGTTTGTTG
66 TTGCATTTTGCTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTCAATGTTTGTTG
*
397193 TTCCAAGTTTTTGGTGCCGTTGTCGGGGACTGTTTTAAAAGTCATTATTTGTGAATTTGTTAATT
1 TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTGTTTTAAAAGTCATTATTTGTGAATTTGTTAATT
*
397258 TTGCATTTTGGTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTC
66 TTGCATTTTGCTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTC
397309 TGTGTTTTTT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 112 1.00
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (127 bp):
TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTGTTTTAAAAGTCATTATTTGTGAATTTGTTAATT
TTGCATTTTGCTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTCAATGTTTGTTG
Found at i:400646 original size:55 final size:55
Alignment explanation
Indices: 400587--400752 Score: 126
Period size: 55 Copynumber: 3.0 Consensus size: 55
400577 GGCACACAGG
400587 TGTGTAAGGCCATTTCGAGTGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
1 TGTGTAAGGCCATTTCGAGTGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
* * ** * * * * * * * **
400642 TGTGTGA-CCCAACTCAAAGAGTAACACAAGCATGAG-TCAC-GGCTTG-GCACACAGG-
1 TGTGTAAGGCCATTTC-GAGTGTTACAC-GGCTTG-GCACACGGGCTTGTG-GC-TTGGC
*
400697 TGTGTAAGGCCATTTCGAGTGTTACACGACTTGGCACACGGGCTTGTGGCTTGGC
1 TGTGTAAGGCCATTTCGAGTGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
400752 T
1 T
400753 TGGAACACTA
Statistics
Matches: 74, Mismatches: 27, Indels: 20
0.61 0.22 0.17
Matches are distributed among these distances:
53 1 0.01
54 14 0.19
55 43 0.58
56 15 0.20
57 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (55 bp):
TGTGTAAGGCCATTTCGAGTGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
Found at i:402321 original size:40 final size:40
Alignment explanation
Indices: 402271--402558 Score: 459
Period size: 40 Copynumber: 7.2 Consensus size: 40
402261 ACCGAAATGT
* * * *
402271 AAACAGGGGCACGCAAGTGCAATCAGGGGTACCGAAGAAC
1 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
* * * * *
402311 AAGCAAGGGCACTTAAGTGCAATCAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
402351 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
402391 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
* **
402431 AAACAGGGGCACGTAAGTGTAATCAGGGGTTGCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
*
402471 AAACAAGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
402511 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
402551 AAACAGGG
1 AAACAGGG
402559 TATAATTTAC
Statistics
Matches: 230, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 230 1.00
ACGTcount: A:0.36, C:0.17, G:0.32, T:0.15
Consensus pattern (40 bp):
AAACAGGGGCACGTAAGTGTAATTAGGGGTACCGAAGTAC
Found at i:405352 original size:27 final size:27
Alignment explanation
Indices: 405322--405384 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
405312 TAGGTCTGAC
405322 TTAAAACATGCATTGATGCTGTCCGAA
1 TTAAAACATGCATTGATGCTGTCCGAA
* *
405349 TTAAAACCTGCATTGATGCTGTCCTAA
1 TTAAAACATGCATTGATGCTGTCCGAA
*
405376 TTATAACAT
1 TTAAAACAT
405385 ACTTAATAGA
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:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (27 bp):
TTAAAACATGCATTGATGCTGTCCGAA
Found at i:411122 original size:25 final size:25
Alignment explanation
Indices: 411067--411123 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
411057 ATTTTCCTCC
411067 TAAA-TTTCAATTTTATTTAATTAT
1 TAAATTTTCAATTTTATTTAATTAT
*
411091 TTAATTTTCAA-TTTATTTAATTAT
1 TAAATTTTCAATTTTATTTAATTAT
411115 TAATATTTT
1 TAA-ATTTT
411124 ATACTAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TAAATTTTCAATTTTATTTAATTAT
Found at i:413368 original size:24 final size:23
Alignment explanation
Indices: 413338--413409 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
413328 AATTTTCCTC
*
413338 TTAAATTTTAATTTTATTTAATTA
1 TTAAATTTTAA-TTTATTGAATTA
*
413362 TTTAATTTTCAATTTATTGAATTA
1 TTAAATTTT-AATTTATTGAATTA
413386 TTAATATTTT-ATTCTAATTGAATT
1 TTAA-ATTTTAATT-T-ATTGAATT
413410 TTTGAGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 3 0.07
24 23 0.56
25 15 0.37
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (23 bp):
TTAAATTTTAATTTATTGAATTA
Found at i:416283 original size:18 final size:18
Alignment explanation
Indices: 416260--416346 Score: 59
Period size: 18 Copynumber: 4.7 Consensus size: 18
416250 CAAATACCAA
416260 ATACCAAAATATCAAATG
1 ATACCAAAATATCAAATG
* * *
416278 ATACCAAAATTTCTAATAA
1 ATACCAAAATATCAAAT-G
* *
416297 ATAACCAAAATCTGTAAATG
1 AT-ACCAAAATAT-CAAATG
* *
416317 ATACC-AAATCTCTAATG
1 ATACCAAAATATCAAATG
*
416334 TATAACAAAATAT
1 -ATACCAAAATAT
416347 TTAACAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.08
18 25 0.47
19 10 0.19
20 11 0.21
21 3 0.06
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.28
Consensus pattern (18 bp):
ATACCAAAATATCAAATG
Found at i:416304 original size:38 final size:38
Alignment explanation
Indices: 416258--416346 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
416248 ACCAAATACC
*
416258 AAAT-ACCAAAATAT-CAAATGATACCAAAATTTCTAAT
1 AAATAACCAAAATATGCAAATGATACC-AAATCTCTAAT
* *
416295 AAATAACCAAAATCTGTAAATGATACCAAATCTCTAAT
1 AAATAACCAAAATATGCAAATGATACCAAATCTCTAAT
**
416333 GTATAA-CAAAATAT
1 AAATAACCAAAATAT
416347 TTAACAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
37 11 0.25
38 23 0.52
39 10 0.23
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (38 bp):
AAATAACCAAAATATGCAAATGATACCAAATCTCTAAT
Found at i:417194 original size:247 final size:254
Alignment explanation
Indices: 416682--417194 Score: 675
Period size: 247 Copynumber: 2.0 Consensus size: 254
416672 CGTAAACTAA
* * *
416682 AAAAATTCAATACAACTCTGATCGTTTTTAGATTTAAAATCAACACCCAAAATAATTTTTTTAAA
1 AAAATTTCAATACAACTCTCATC-TTTTTA-ATTCAAAATCAACACCCAAAATAATTTTTTTAAA
* ** * * *
416747 AACATTTTTAAAATTTTTAACACTAAAATCTCTCTATTCAAAAACAAAAAAAATGAAAATTTCTT
64 AAAATTTCGAAAAATTTTAACACTAAAATCTCTCTATT---AAACAAAAAAAACGAAAATTTCTG
*
416812 AAAACTATTTGGCAATGAAGATGAGTAAGAACAACTATAATATGTAAGAGAAGTTAGCAACATAA
126 AAAACTATTTGGCAATGAAGATGAGTAAGAACAACTATAATATGTAAGAGAAGTCAGCAACATAA
* * * * *
416877 ATCGAGAGGAGTTGTTGACTTTTCATTTATATTTTAGTATTTATTACAAATTTCGATATCTTTC
191 ATCAAGAGGAGTAGGTGACTTTTCATTTATATTTCAGTATTCATTACAAATTTCGATATCTTTC
*
416941 AAAATTTCAATACAACTCTCAT-TTTTT-ATTCAAAATCAACACTCAAAATAATTTTTTATAAAA
1 AAAATTTCAATACAACTCTCATCTTTTTAATTCAAAATCAACACCCAAAATAATTTTTT-TAAAA
** *
417004 AAATTTCGAAAAATTTTAACACTAAAATCT-T-T-TT-ATTAAAAAAAACGGAAA-TT-TGAAAA
65 AAATTTCGAAAAATTTTAACACTAAAATCTCTCTATTAAACAAAAAAAACGAAAATTTCTGAAAA
* ** *
417063 CTGTTTGTTAATGAAGATGAGTAAGAACAACTATAATTTGTAAGAGAAGTCAGCAACATAAATCA
130 CTATTTGGCAATGAAGATGAGTAAGAACAACTATAATATGTAAGAGAAGTCAGCAACATAAATCA
* *
417128 AGAGGAGTAGGTGACTTTTCGTTTATATTTCAGTATTCATTACAGAATTTCG-TATCTTTT
195 AGAGGAGTAGGTGACTTTTCATTTATATTTCAGTATTCATTACA-AATTTCGATATCTTTC
417188 AAAATTT
1 AAAATTT
417195 TTACTATTGC
Statistics
Matches: 227, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
247 117 0.52
248 9 0.04
249 13 0.06
253 2 0.01
254 1 0.00
255 29 0.13
256 31 0.14
257 5 0.02
259 20 0.09
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (254 bp):
AAAATTTCAATACAACTCTCATCTTTTTAATTCAAAATCAACACCCAAAATAATTTTTTTAAAAA
AATTTCGAAAAATTTTAACACTAAAATCTCTCTATTAAACAAAAAAAACGAAAATTTCTGAAAAC
TATTTGGCAATGAAGATGAGTAAGAACAACTATAATATGTAAGAGAAGTCAGCAACATAAATCAA
GAGGAGTAGGTGACTTTTCATTTATATTTCAGTATTCATTACAAATTTCGATATCTTTC
Found at i:435819 original size:39 final size:38
Alignment explanation
Indices: 435700--435858 Score: 144
Period size: 38 Copynumber: 4.1 Consensus size: 38
435690 AGTTTAAGTC
* *
435700 TTTACTTATGTCATAATTTGAACATCATTAATATGA-GT
1 TTTAATTATGTCATAATTTGAACATCTTTAATAT-ATGT
* *
435738 TTTAATTATGTCATAATCTGAACATCTTTAATA-AGGATT
1 TTTAATTATGTCATAATTTGAACATCTTTAATATATG--T
* * *
435777 TTTAATTATGTCATAGTTTAGGACATCTTAAATATATGT
1 TTTAATTATGTCATAATTT-GAACATCTTTAATATATGT
* * * *
435816 TTTAAATATGTCTTAGTTT-AGACATCTTTAATACATGT
1 TTTAATTATGTCATAATTTGA-ACATCTTTAATATATGT
435854 CTTTA
1 -TTTA
435859 GTTTAGACCA
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 45 0.45
39 40 0.40
40 12 0.12
41 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (38 bp):
TTTAATTATGTCATAATTTGAACATCTTTAATATATGT
Found at i:435879 original size:27 final size:26
Alignment explanation
Indices: 435817--435880 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
435807 AATATATGTT
*
435817 TTAAAT-ATGTCTTAGTTTAGACATC
1 TTAAATCATGTCTTAGTTTAGACATA
*
435842 TTTAATACATGTCTTTAGTTTAGACCA-A
1 TTAAAT-CATGTC-TTAGTTTAGA-CATA
435870 TTAAATCATGT
1 TTAAATCATGT
435881 TTAAGCTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.16
27 10 0.31
28 15 0.47
29 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (26 bp):
TTAAATCATGTCTTAGTTTAGACATA
Found at i:439436 original size:21 final size:21
Alignment explanation
Indices: 439410--439449 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
439400 TACAACAACA
439410 ATTAGAGCC-ACTCCAAGAATG
1 ATTAGA-CCAACTCCAAGAATG
*
439431 ATTAGACCAACTCGAAGAA
1 ATTAGACCAACTCCAAGAA
439450 AGAAACTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (21 bp):
ATTAGACCAACTCCAAGAATG
Found at i:442920 original size:59 final size:62
Alignment explanation
Indices: 442854--442995 Score: 182
Period size: 63 Copynumber: 2.3 Consensus size: 62
442844 TTTGATTTCA
* *
442854 TACAACATTATTACATGTCTGATTATTT-TAG-T-TAAGTCTATTAATTGTGTCCTATTTTG
1 TACAACATTATTACATGTCTGATTATTTATAGTTCTAAGTCTATTAATGGTGTCCTAGTTTG
* * *
442913 TACAACATTATTACATGTCTGATTGTTTAGTTGTTCTAAGTCTATTAATGGTGTCTTAGTTTG
1 TACAACATTATTACATGTCTGATTATTTA-TAGTTCTAAGTCTATTAATGGTGTCCTAGTTTG
* * *
442976 TACCACATTAATACTTGTCT
1 TACAACATTATTACATGTCT
442996 AAGTCAGATT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
59 27 0.38
61 2 0.03
62 1 0.01
63 41 0.58
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (62 bp):
TACAACATTATTACATGTCTGATTATTTATAGTTCTAAGTCTATTAATGGTGTCCTAGTTTG
Found at i:446746 original size:32 final size:32
Alignment explanation
Indices: 446705--446784 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
446695 TTTGAAGAGT
*
446705 CTTT-GGTGTGAACACTTGGACTTGGACGGTC
1 CTTTGGGTGTGAACACTTGGACTTAGACGGTC
*
446736 TTTTGGGTGTGAACACTTGGACTTAGACGGTC
1 CTTTGGGTGTGAACACTTGGACTTAGACGGTC
446768 CTTTGGGTGTGAACACT
1 CTTTGGGTGTGAACACT
446785 AGGAAGTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 3 0.07
32 42 0.93
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (32 bp):
CTTTGGGTGTGAACACTTGGACTTAGACGGTC
Found at i:446800 original size:32 final size:31
Alignment explanation
Indices: 446705--446813 Score: 105
Period size: 32 Copynumber: 3.5 Consensus size: 31
446695 TTTGAAGAGT
*
446705 CTTTGGTGTGAACACTTGG-ACTTGGACGGTC
1 CTTTGGTGTGAACACTTGGAAC-TGAACGGTC
* *
446736 TTTTGGGTGTGAACACTTGG-ACTTAGACGGTC
1 CTTT-GGTGTGAACACTTGGAACTGA-ACGGTC
* * *
446768 CTTTGGGTGTGAACACTAGGAAGTGAATGGTC
1 CTTT-GGTGTGAACACTTGGAACTGAACGGTC
*
446800 CATTGGTGTGAACA
1 CTTTGGTGTGAACA
446814 AAAGCAGCTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
31 14 0.21
32 49 0.74
33 3 0.05
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (31 bp):
CTTTGGTGTGAACACTTGGAACTGAACGGTC
Found at i:452027 original size:25 final size:24
Alignment explanation
Indices: 451999--452050 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
451989 CTCTTTTGAG
* *
451999 TTAATAAATTCTCTTTGAGATTTTT
1 TTAAGAAATTCTC-TTGAGATTCTT
*
452024 TTAAGAATTTCTCTTGAGATTCTT
1 TTAAGAAATTCTCTTGAGATTCTT
452048 TTA
1 TTA
452051 GAAGAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (24 bp):
TTAAGAAATTCTCTTGAGATTCTT
Found at i:453416 original size:20 final size:20
Alignment explanation
Indices: 453393--453439 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
453383 GGGTTAAAAT
*
453393 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
453413 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
453433 TGAGCTG
1 TGAGCTG
453440 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:463085 original size:21 final size:22
Alignment explanation
Indices: 463040--463085 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
463030 AGAGAAAAAT
*
463040 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
463062 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
463083 AAA
1 AAA
463086 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:472789 original size:53 final size:52
Alignment explanation
Indices: 472731--472853 Score: 126
Period size: 50 Copynumber: 2.4 Consensus size: 52
472721 ATGAATTACG
* *
472731 TAATGCATGACTTTATTAAAAAAATGCAAACTTTAACTAACAT-AGGAGTTATA
1 TAATGCATGACTTTATTAAAAAAATGCAAAC-TTAACTAACATGA-GAGTAACA
* * * ** *
472784 TAATGCATGACATAATT--TATGATGCAATCTTAACTAACATGAGAGTAACA
1 TAATGCATGACTTTATTAAAAAAATGCAAACTTAACTAACATGAGAGTAACA
*
472834 TAATACATGACTTTATTAAA
1 TAATGCATGACTTTATTAAA
472854 TGCAGAACAC
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
50 31 0.56
51 9 0.16
53 15 0.27
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (52 bp):
TAATGCATGACTTTATTAAAAAAATGCAAACTTAACTAACATGAGAGTAACA
Found at i:473398 original size:82 final size:83
Alignment explanation
Indices: 473300--473466 Score: 318
Period size: 82 Copynumber: 2.0 Consensus size: 83
473290 CGAAAAATAA
473300 AAGAAATTGAAAGAAAAAGAGGGCTTGAACGAAAGGAGCAAGAAAAAGAGTGCGAGCAAGAAAAG
1 AAGAAATTG-AAGAAAAAGAGGGCTTGAACGAAAGGAGCAAGAAAAAGAGTGCGAGCAAGAAAAG
473365 AACTTTGAAAATGAGTTTG
65 AACTTTGAAAATGAGTTTG
473384 AAGAAATTG-AGAAAAAGAGGGCTTGAACGAAAGGAGCAAGAAAAAGAGTGCGAGCAAGAAAAGA
1 AAGAAATTGAAGAAAAAGAGGGCTTGAACGAAAGGAGCAAGAAAAAGAGTGCGAGCAAGAAAAGA
473448 ACTTTGAAAATGAGTTTG
66 ACTTTGAAAATGAGTTTG
473466 A
1 A
473467 GAATGAAAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
82 74 0.89
84 9 0.11
ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (83 bp):
AAGAAATTGAAGAAAAAGAGGGCTTGAACGAAAGGAGCAAGAAAAAGAGTGCGAGCAAGAAAAGA
ACTTTGAAAATGAGTTTG
Found at i:478281 original size:14 final size:14
Alignment explanation
Indices: 478254--478294 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
478244 TGGACTGAAT
478254 ATAAAAATTAAAATAA
1 ATAAAAA-T-AAATAA
*
478270 GTAAAAATAAATAA
1 ATAAAAATAAATAA
478284 ATAAAAATAAA
1 ATAAAAATAAA
478295 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 16 0.70
15 1 0.04
16 6 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
ATAAAAATAAATAA
Found at i:480019 original size:26 final size:26
Alignment explanation
Indices: 479990--480049 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
479980 TAGAAGCATG
479990 ATATTCAATTCAAGAAGTTCCTTGAC
1 ATATTCAATTCAAGAAGTTCCTTGAC
480016 ATATTCAATTCAAGAAGTTCCTTGAC
1 ATATTCAATTCAAGAAGTTCCTTGAC
*
480042 GTATTCAA
1 ATATTCAA
480050 GCAACTTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (26 bp):
ATATTCAATTCAAGAAGTTCCTTGAC
Found at i:484542 original size:30 final size:30
Alignment explanation
Indices: 484506--484566 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
484496 ATTTCATGCC
484506 ATTAGACTGATGATGCTGTTAATGTGGCTA
1 ATTAGACTGATGATGCTGTTAATGTGGCTA
484536 ATTAGACTGATGATGCTGTTAATGTGGCTA
1 ATTAGACTGATGATGCTGTTAATGTGGCTA
484566 A
1 A
484567 CTTGTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (30 bp):
ATTAGACTGATGATGCTGTTAATGTGGCTA
Found at i:495471 original size:28 final size:28
Alignment explanation
Indices: 495266--495462 Score: 394
Period size: 28 Copynumber: 7.0 Consensus size: 28
495256 TATAACTAGG
495266 TCACGAGCTAAGAACTTTAAAGAAGCTT
1 TCACGAGCTAAGAACTTTAAAGAAGCTT
495294 TCACGAGCTAAGAACTTTAAAGAAGCTT
1 TCACGAGCTAAGAACTTTAAAGAAGCTT
495322 TCACGAGCTAAGAACTTTAAAGAAGCTT
1 TCACGAGCTAAGAACTTTAAAGAAGCTT
495350 TCACGAGCTAAGAACTTTAAAGAAGCTT
1 TCACGAGCTAAGAACTTTAAAGAAGCTT
495378 TCACGAGCTAAGAACTTTAAAGAAGCTT
1 TCACGAGCTAAGAACTTTAAAGAAGCTT
495406 TCACGAGCTAAGAACTTTAAAGAAGCTT
1 TCACGAGCTAAGAACTTTAAAGAAGCTT
495434 TCACGAGCTAAGAACTTTAAAGAAGCTT
1 TCACGAGCTAAGAACTTTAAAGAAGCTT
495462 T
1 T
495463 GGCAAGCTAT
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 169 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (28 bp):
TCACGAGCTAAGAACTTTAAAGAAGCTT
Done.