Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold129
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: 3652842
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 48564 characters in sequence are not A, C, G, or T
File 23 of 23
Found at i:3553794 original size:12 final size:12
Alignment explanation
Indices: 3553773--3553801 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3553763 ATTTTTTTGA
3553773 TTTT-TTGATTT
1 TTTTATTGATTT
3553784 TTTTATTGATTT
1 TTTTATTGATTT
3553796 TTTTAT
1 TTTTAT
3553802 ATAAGATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTATTGATTT
Found at i:3553796 original size:9 final size:8
Alignment explanation
Indices: 3553732--3553786 Score: 76
Period size: 8 Copynumber: 6.8 Consensus size: 8
3553722 TTCTTTTTCT
*
3553732 TTTTTTTA
1 TTTTTTGA
3553740 TTTTTTGA
1 TTTTTTGA
3553748 -TTTTTGA
1 TTTTTTGA
3553755 TTTTTTTGA
1 -TTTTTTGA
3553764 TTTTTTTGA
1 -TTTTTTGA
3553773 TTTTTTGA
1 TTTTTTGA
3553781 TTTTTT
1 TTTTTT
3553787 TATTGATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
7 7 0.16
8 21 0.48
9 16 0.36
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (8 bp):
TTTTTTGA
Found at i:3566948 original size:13 final size:13
Alignment explanation
Indices: 3566932--3566957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3566922 GACCATGCTT
3566932 TAACATTCTCAAA
1 TAACATTCTCAAA
3566945 TAACATTCTCAAA
1 TAACATTCTCAAA
3566958 CAATTCAAGG
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:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
TAACATTCTCAAA
Found at i:3569259 original size:97 final size:96
Alignment explanation
Indices: 3569084--3569289 Score: 306
Period size: 97 Copynumber: 2.1 Consensus size: 96
3569074 GGATGGAATG
* * *
3569084 TCCCCTCGGAGGAATGGGGTTGGAGTATCCCTGACGATGATAATTTAAGCAAAAATAAGATTTAA
1 TCCCCTCGGAAGAATGGGGTTAGAGTATCACTGACGATGATAATTTAAGCAAAAATAAGATTTAA
3569149 ACCTTGACAAGTTTAAAAATG-GGATCAGAGTA
66 ACCTTGACAAGTTTAAAAATGAGG-TCAGA-TA
* *
3569181 TCCCTTCGGAAGAATGGGGTTAGAGTATCACTGATGATGATAATTTAAGCAAAAATAAGATTTAA
1 TCCCCTCGGAAGAATGGGGTTAGAGTATCACTGACGATGATAATTTAAGCAAAAATAAGATTTAA
* ** *
3569246 ATCTTGATGAGTTTAAAAATGAGGTTAGATA
66 ACCTTGACAAGTTTAAAAATGAGGTCAGATA
3569277 TCCCCTCGGAAGA
1 TCCCCTCGGAAGA
3569290 TGAGGTTGGA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
96 14 0.14
97 82 0.84
98 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (96 bp):
TCCCCTCGGAAGAATGGGGTTAGAGTATCACTGACGATGATAATTTAAGCAAAAATAAGATTTAA
ACCTTGACAAGTTTAAAAATGAGGTCAGATA
Found at i:3571482 original size:17 final size:17
Alignment explanation
Indices: 3571460--3571502 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
3571450 CCTAGAGTAT
3571460 GATGATGAAGAGAAGGC
1 GATGATGAAGAGAAGGC
*
3571477 GATGATGAAGAGAAGGT
1 GATGATGAAGAGAAGGC
*
3571494 AATGATGAA
1 GATGATGAA
3571503 AATGTGACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.37, T:0.16
Consensus pattern (17 bp):
GATGATGAAGAGAAGGC
Found at i:3571806 original size:20 final size:20
Alignment explanation
Indices: 3571769--3571817 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
3571759 AAGGTCTAGT
* *
3571769 ATCGATACATTTACTTATGA
1 ATCGATACACTCACTTATGA
* *
3571789 ATCGATACACTCATTTATGT
1 ATCGATACACTCACTTATGA
*
3571809 ATTGATACA
1 ATCGATACA
3571818 TTAACTTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (20 bp):
ATCGATACACTCACTTATGA
Found at i:3572384 original size:21 final size:21
Alignment explanation
Indices: 3572355--3572408 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3572345 AGCATCTTTT
*
3572355 CATCTAACAAATATATCCTTC
1 CATCCAACAAATATATCCTTC
*
3572376 CATCCAACAAATATATCTTTC
1 CATCCAACAAATATATCCTTC
3572397 CATCCAACAAAT
1 CATCCAACAAAT
3572409 GCATTATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (21 bp):
CATCCAACAAATATATCCTTC
Found at i:3572421 original size:21 final size:21
Alignment explanation
Indices: 3572355--3572424 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
3572345 AGCATCTTTT
* **
3572355 CATCTAACAAATATATCCTTC
1 CATCCAACAAATATATATTTC
*
3572376 CATCCAACAAATATATCTTTC
1 CATCCAACAAATATATATTTC
3572397 CATCCAACAAATGCAT-TATTT-
1 CATCCAACAAAT--ATATATTTC
3572418 CATCCAA
1 CATCCAA
3572425 ATGCATCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 38 0.86
22 4 0.09
23 2 0.05
ACGTcount: A:0.39, C:0.29, G:0.01, T:0.31
Consensus pattern (21 bp):
CATCCAACAAATATATATTTC
Found at i:3573583 original size:3 final size:3
Alignment explanation
Indices: 3573575--3573614 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3573565 CCGAAGTTTG
3573575 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3573615 TAAAAAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3573739 original size:19 final size:19
Alignment explanation
Indices: 3573715--3573754 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3573705 ATATATGACA
*
3573715 TATGTAATGATTTAATTTT
1 TATGTAATAATTTAATTTT
3573734 TATGTAATAATTTAATTTT
1 TATGTAATAATTTAATTTT
3573753 TA
1 TA
3573755 AATCAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TATGTAATAATTTAATTTT
Found at i:3573762 original size:20 final size:20
Alignment explanation
Indices: 3573724--3573768 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
3573714 ATATGTAATG
**
3573724 ATTTAATTTTTATGTAAT-A
1 ATTTAATTTTTAAATAATAA
3573743 ATTTAATTTTTAAATCAATAA
1 ATTTAATTTTTAAAT-AATAA
3573764 ATTTA
1 ATTTA
3573769 GAGTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 3 0.14
21 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTAATTTTTAAATAATAA
Found at i:3574634 original size:44 final size:44
Alignment explanation
Indices: 3574575--3574658 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
3574565 TAATAATTCA
3574575 TATTATATAAATTGAGATATTCGTGTATCATGTCATATTTTAAT
1 TATTATATAAATTGAGATATTCGTGTATCATGTCATATTTTAAT
*
3574619 TATTTTATAAATTGAGATATTCGTGTATCATGTCATATTT
1 TATTATATAAATTGAGATATTCGTGTATCATGTCATATTT
3574659 AAAATATGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (44 bp):
TATTATATAAATTGAGATATTCGTGTATCATGTCATATTTTAAT
Found at i:3577949 original size:29 final size:29
Alignment explanation
Indices: 3577915--3577979 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
3577905 TTCTATATTA
*
3577915 TAAAAATATTATT-TATGTTAATAAAATAT
1 TAAAAATATAATTAT-TGTTAATAAAATAT
* *
3577944 TAAAAATATAATTATTTTTATTAAAATAT
1 TAAAAATATAATTATTGTTAATAAAATAT
3577973 TAAAAAT
1 TAAAAAT
3577980 TATACTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAAAATATAATTATTGTTAATAAAATAT
Found at i:3579530 original size:16 final size:16
Alignment explanation
Indices: 3579507--3579547 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3579497 ATTCAAATAA
3579507 TCAAAATAATATAAAT
1 TCAAAATAATATAAAT
* *
3579523 TTAAAATAATTTAAAT
1 TCAAAATAATATAAAT
3579539 TCAAAATAA
1 TCAAAATAA
3579548 CTTAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
TCAAAATAATATAAAT
Found at i:3579552 original size:16 final size:15
Alignment explanation
Indices: 3579507--3579553 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
3579497 ATTCAAATAA
3579507 TCAAAATAATATAAAT
1 TCAAAATAAT-TAAAT
*
3579523 TTAAAATAATTTAAAT
1 TCAAAATAA-TTAAAT
3579539 TCAAAATAACTTAAA
1 TCAAAATAA-TTAAA
3579554 ATTTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 26 0.96
17 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TCAAAATAATTAAAT
Found at i:3581972 original size:6 final size:6
Alignment explanation
Indices: 3581957--3581990 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3581947 GAAGCAGCAA
*
3581957 CTCT-G CTCTGG CTCTGG CTCTGG CTCTTG CTCTG
1 CTCTGG CTCTGG CTCTGG CTCTGG CTCTGG CTCTG
3581991 CCATGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.38
Consensus pattern (6 bp):
CTCTGG
Found at i:3582240 original size:2 final size:2
Alignment explanation
Indices: 3582233--3582268 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3582223 TATCCGCTTT
* *
3582233 TC TC TC TC TC TT TC TC TC TC CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3582269 GCTCCCTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3582706 original size:17 final size:19
Alignment explanation
Indices: 3582685--3582732 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 19
3582675 CATTCACCCT
3582685 TTTTTTTATTTTATAAA-A
1 TTTTTTTATTTTATAAACA
*
3582703 --TTTTAATTTT-TAAACTA
1 TTTTTTTATTTTATAAAC-A
3582720 TTTTTTTATTTTA
1 TTTTTTTATTTTA
3582733 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
15 4 0.17
16 9 0.39
17 1 0.04
19 9 0.39
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTATTTTATAAACA
Found at i:3582741 original size:28 final size:28
Alignment explanation
Indices: 3582709--3582764 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3582699 AAAATTTTAA
*
3582709 TTTTTAAACTATTT-TTTTATTTTAATAT
1 TTTTTAAACTATTTACTTT-TTTTAATAT
* *
3582737 TTTTTTAATTATTTACTTTTTTTAATAT
1 TTTTTAAACTATTTACTTTTTTTAATAT
3582765 AAATATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTTAAACTATTTACTTTTTTTAATAT
Found at i:3582759 original size:35 final size:34
Alignment explanation
Indices: 3582684--3582759 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
3582674 CCATTCACCC
3582684 TTTTTTTTATTTTATAAAATTTTAATTTTTAAACT
1 TTTTTTTTATTTTATAAAATTTTAATTTTT-AACT
* ***
3582719 ATTTTTTTATTTTAATATTTTTTTAATTATTT-ACT
1 TTTTTTTTATTTT-ATAAAATTTTAATT-TTTAACT
3582754 TTTTTT
1 TTTTTT
3582760 AATATAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
35 20 0.59
36 11 0.32
37 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (34 bp):
TTTTTTTTATTTTATAAAATTTTAATTTTTAACT
Found at i:3584309 original size:121 final size:121
Alignment explanation
Indices: 3584164--3584383 Score: 341
Period size: 121 Copynumber: 1.8 Consensus size: 121
3584154 CTATTGGGGT
* *
3584164 AATTTGTCTTTCTTTGCTTACAAGCATTAATTTTTTTTAAAACTAAAGAAGAAAAGAGAAAGAAA
1 AATTTGTCTTTCTTTACTTACAAGCATTAATTTTTTATAAAACTAAAGAAGAAAAGAGAAAGAAA
3584229 AAAATAAATATGATAATTTGTGTATTTAGTGTTTCCTTTGTAAGTAATTGAAGGGC
66 AAAATAAATATGATAATTTGTGTATTTAGTGTTTCCTTTGTAAGTAATTGAAGGGC
* * * * * *
3584285 AATTTGTTTTTCTTTACTTGCAAGCATTAGTTTTTTATCAAATTAAAGAAGAAAAGAGAAAGAAG
1 AATTTGTCTTTCTTTACTTACAAGCATTAATTTTTTATAAAACTAAAGAAGAAAAGAGAAAGAAA
* * *
3584350 AAAATAGATTTGATAATTTGTGTATTTGGTGTTT
66 AAAATAAATATGATAATTTGTGTATTTAGTGTTT
3584384 GTTTGATTTG
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
121 88 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (121 bp):
AATTTGTCTTTCTTTACTTACAAGCATTAATTTTTTATAAAACTAAAGAAGAAAAGAGAAAGAAA
AAAATAAATATGATAATTTGTGTATTTAGTGTTTCCTTTGTAAGTAATTGAAGGGC
Found at i:3584926 original size:26 final size:27
Alignment explanation
Indices: 3584892--3584945 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
3584882 ATTTTTTAAT
*
3584892 TTTTATATT-ATTGA-ATTAAAAATTA
1 TTTTATATTAAATGACATTAAAAATTA
3584917 TTTTATTATTAAATGATCATTAAAAATTA
1 TTTTA-TATTAAATGA-CATTAAAAATTA
3584946 AAATATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 4 0.17
29 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTTATATTAAATGACATTAAAAATTA
Found at i:3585301 original size:34 final size:32
Alignment explanation
Indices: 3585230--3585366 Score: 118
Period size: 34 Copynumber: 4.1 Consensus size: 32
3585220 AACCTTATAA
* *
3585230 CACTATCTTTTGA-AAGCTAAAATAGAACCTT
1 CACTATCTTTTCACAAGCTAAGATAGAACCTT
*
3585261 C-CTATCTTTTCACAAGGTAAGATAGAATCTCTT
1 CACTATCTTTTCACAAGCTAAGATAGAA-C-CTT
* *
3585294 CACTATCTTTTCACAAGTTAAGATGGAACCTTT
1 CACTATCTTTTCACAAGCTAAGATAGAACC-TT
**
3585327 CTTTTTATCTTTTTCA-AAGGCTAAGATAGAACCTCT
1 C--ACTATC-TTTTCACAA-GCTAAGATAGAACCT-T
3585363 CACT
1 CACT
3585367 TCGAGAATTA
Statistics
Matches: 85, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
30 10 0.12
31 13 0.15
32 2 0.02
33 8 0.09
34 25 0.29
35 7 0.08
36 20 0.24
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (32 bp):
CACTATCTTTTCACAAGCTAAGATAGAACCTT
Found at i:3585732 original size:20 final size:20
Alignment explanation
Indices: 3585703--3585741 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3585693 CTTATATGCT
*
3585703 ATAATGTATCGATACAATTC
1 ATAATATATCGATACAATTC
3585723 ATAATATATCGATACAATT
1 ATAATATATCGATACAATT
3585742 ATAGCCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (20 bp):
ATAATATATCGATACAATTC
Found at i:3585877 original size:13 final size:13
Alignment explanation
Indices: 3585859--3585883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3585849 TACAAAGAAC
3585859 ATGTATCGATACA
1 ATGTATCGATACA
3585872 ATGTATCGATAC
1 ATGTATCGATAC
3585884 TAAATAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3585903 original size:33 final size:32
Alignment explanation
Indices: 3585841--3585904 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
3585831 CATTTTATGG
3585841 TGTATCGATACAAAGAACATGTATCGATACAA
1 TGTATCGATACAAAGAACATGTATCGATACAA
* * *
3585873 TGTATCGATACTAAATAATATGTATTGATACA
1 TGTATCGATAC-AAAGAACATGTATCGATACA
3585905 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAA
Found at i:3587421 original size:11 final size:10
Alignment explanation
Indices: 3587405--3587460 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 10
3587395 TATGAAGAAA
3587405 AAAGAAAGGAG
1 AAAGAAA-GAG
*
3587416 AAAGAAA-TG
1 AAAGAAAGAG
3587425 AAAGAAA-AG
1 AAAGAAAGAG
3587434 --AGAAAGAG
1 AAAGAAAGAG
3587442 AAAGGAAAGAG
1 AAA-GAAAGAG
3587453 AAA-AAAGA
1 AAAGAAAGA
3587461 AAAATTCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 5 0.13
8 2 0.05
9 14 0.36
10 1 0.03
11 17 0.44
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.02
Consensus pattern (10 bp):
AAAGAAAGAG
Found at i:3587432 original size:26 final size:24
Alignment explanation
Indices: 3587402--3587462 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 24
3587392 ATTTATGAAG
3587402 AAAAAAGAAAGGAGAAA-GAAATGAA
1 AAAAAAGAAA-GAGAAAGGAAA-GAA
*
3587427 AGAAAAGAGAAAGAGAAAGGAAAGAG
1 A-AAAA-AGAAAGAGAAAGGAAAGAA
3587453 AAAAAAGAAA
1 AAAAAAGAAA
3587463 AATTCATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 5 0.16
25 5 0.16
26 13 0.41
27 9 0.28
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAAGAGAAAGGAAAGAA
Found at i:3587441 original size:6 final size:6
Alignment explanation
Indices: 3587424--3587455 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3587414 AGAAAGAAAT
3587424 GAAAGA -AAAGA GAAAGA GAAAG- GAAAGA GAAA
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAA
3587456 AAAGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:3597678 original size:24 final size:24
Alignment explanation
Indices: 3597629--3597731 Score: 74
Period size: 24 Copynumber: 4.3 Consensus size: 24
3597619 ATTAAGCATA
3597629 AATATTTATATTTTAATATAATAT
1 AATATTTATATTTTAATATAATAT
3597653 AATA-TTACTATTTT-A-ATAAT-T
1 AATATTTA-TATTTTAATATAATAT
* *
3597674 AATA-ATAAATTATTAATATAATGAAT
1 AATATTTATATT-TTAATATAAT--AT
* *
3597700 ATTATTTATTATTTTAATAGAA-AT
1 AATATTTA-TATTTTAATATAATAT
*
3597724 ATTATTTA
1 AATATTTA
3597732 ATATAATAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
20 3 0.05
21 9 0.14
22 6 0.09
23 9 0.14
24 20 0.31
26 4 0.06
27 10 0.16
28 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (24 bp):
AATATTTATATTTTAATATAATAT
Found at i:3597703 original size:18 final size:19
Alignment explanation
Indices: 3597682--3597747 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 19
3597672 TTAATAATAA
3597682 ATTA-TTAATATAATGAAT
1 ATTATTTAATATAATGAAT
*
3597700 ATTATTTATTATTTTAATAGAAAT
1 ATTATTTA--A-TATAAT-G-AAT
3597724 ATTATTTAATATAAT-AAT
1 ATTATTTAATATAATGAAT
3597742 ATTATT
1 ATTATT
3597748 ATTTTAGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
18 13 0.32
19 3 0.08
21 6 0.15
22 6 0.15
23 1 0.03
24 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
ATTATTTAATATAATGAAT
Found at i:3597741 original size:24 final size:24
Alignment explanation
Indices: 3597697--3597742 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3597687 TAATATAATG
* **
3597697 AATATTATTTATTATTTTAATAGA
1 AATATTATTTAATATAATAATAGA
3597721 AATATTATTTAATATAATAATA
1 AATATTATTTAATATAATAATA
3597743 TTATTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AATATTATTTAATATAATAATAGA
Found at i:3598330 original size:21 final size:21
Alignment explanation
Indices: 3598306--3598373 Score: 55
Period size: 24 Copynumber: 3.0 Consensus size: 21
3598296 ATTTTTTTTT
3598306 AGAAATCTTTACATTTTTCAA
1 AGAAATCTTTACATTTTTCAA
* * * **
3598327 AGAAGTATTATCAAAATTTTTTTA
1 AGAAATCTT-T--ACATTTTTCAA
3598351 AGAAAATCTTTACATTTTTCAA
1 AG-AAATCTTTACATTTTTCAA
3598373 A
1 A
3598374 AGAAGTATTA
Statistics
Matches: 33, Mismatches: 10, Indels: 7
0.66 0.20 0.14
Matches are distributed among these distances:
21 7 0.21
22 10 0.30
24 11 0.33
25 5 0.15
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (21 bp):
AGAAATCTTTACATTTTTCAA
Found at i:3598349 original size:46 final size:48
Alignment explanation
Indices: 3598296--3598393 Score: 166
Period size: 46 Copynumber: 2.1 Consensus size: 48
3598286 TGAGCATCAG
*
3598296 ATTTTTTTTTAG-AAATCTTTACATTTTTC-AAAGAAGTATTATCAAA
1 ATTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAA
3598342 A-TTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAA
1 ATTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAA
3598389 ATTTT
1 ATTTT
3598394 GTTGTTCCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
45 9 0.19
46 18 0.38
47 18 0.38
48 3 0.06
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (48 bp):
ATTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAA
Found at i:3598378 original size:47 final size:45
Alignment explanation
Indices: 3598298--3598393 Score: 165
Period size: 47 Copynumber: 2.1 Consensus size: 45
3598288 AGCATCAGAT
*
3598298 TTTTTTTTAGAAATCTTTACATTTTTCAAAGAAGTATTATCAAAA
1 TTTTTTTAAGAAATCTTTACATTTTTCAAAGAAGTATTATCAAAA
3598343 TTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAAA
1 TTTTTTTAAG-AAATCTTTACATTTTTC-AAAGAAGTATTATCAAAA
3598390 TTTT
1 TTTT
3598394 GTTGTTCCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 9 0.19
46 17 0.35
47 22 0.46
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (45 bp):
TTTTTTTAAGAAATCTTTACATTTTTCAAAGAAGTATTATCAAAA
Found at i:3601694 original size:97 final size:97
Alignment explanation
Indices: 3601559--3601806 Score: 338
Period size: 97 Copynumber: 2.6 Consensus size: 97
3601549 AATTATCTTA
* * * * *
3601559 AAAACTAGAATTCTCACACTCAT-ATTAGGGTATGGTGAACGCCAAACAGTATATAATATGCCTA
1 AAAACTAGTATTCTTACATTCATAATT-GGGTATAGTGAAAGCCAAACAGTATATAATATGCCTA
* * *
3601623 CTGTGTTTTCAATGACTACTCA-TCCATTGTATT
65 CTATATTTTCAATGACTACTCACT-CATTCTATT
* *
3601656 AAAACTAGTATTCTTACATTCATAATTGTGTATAGTGAAAGCCAAACGGTATATAATATGCCTAC
1 AAAACTAGTATTCTTACATTCATAATTGGGTATAGTGAAAGCCAAACAGTATATAATATGCCTAC
3601721 TATATTTTCAATGACTACTCACTCATTCTATT
66 TATATTTTCAATGACTACTCACTCATTCTATT
* * * *
3601753 AAAACTAGTATTCTTACATTCATAATAGGGTACAGTTAAGGCCAAACAGTATAT
1 AAAACTAGTATTCTTACATTCATAATTGGGTATAGTGAAAGCCAAACAGTATAT
3601807 GCCTATCATA
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
97 129 0.97
98 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (97 bp):
AAAACTAGTATTCTTACATTCATAATTGGGTATAGTGAAAGCCAAACAGTATATAATATGCCTAC
TATATTTTCAATGACTACTCACTCATTCTATT
Found at i:3602809 original size:17 final size:18
Alignment explanation
Indices: 3602778--3602817 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
3602768 ACTTAATTTA
3602778 ATTC-AAGTCGAAATATT
1 ATTCTAAGTCGAAATATT
3602795 ATTCTAAGTCG-AATATT
1 ATTCTAAGTCGAAATATT
3602812 ATTCTA
1 ATTCTA
3602818 TTAATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (18 bp):
ATTCTAAGTCGAAATATT
Found at i:3611295 original size:31 final size:32
Alignment explanation
Indices: 3611232--3611310 Score: 115
Period size: 31 Copynumber: 2.4 Consensus size: 32
3611222 TATTGGTAAG
3611232 GAAGGCAAGCAAGTTAACTATCAAAAAAAAAAAA
1 GAAGGCAAGCAAGTTAACTAT--AAAAAAAAAAA
* *
3611266 GAAGGCAAGCAAGTTAACTAT-TAAAAAAAAG
1 GAAGGCAAGCAAGTTAACTATAAAAAAAAAAA
3611297 GAAGGCAAGCAAGT
1 GAAGGCAAGCAAGT
3611311 ACACAACTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 22 0.51
34 21 0.49
ACGTcount: A:0.56, C:0.11, G:0.20, T:0.13
Consensus pattern (32 bp):
GAAGGCAAGCAAGTTAACTATAAAAAAAAAAA
Found at i:3612314 original size:2 final size:2
Alignment explanation
Indices: 3612307--3612347 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3612297 TAAATAAAAG
3612307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3612348 ATCATCCTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3614722 original size:2 final size:2
Alignment explanation
Indices: 3614715--3614755 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3614705 CTAAGAACAA
3614715 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3614756 CCATAAAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3617436 original size:17 final size:18
Alignment explanation
Indices: 3617408--3617441 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3617398 TGTAAAAAAT
*
3617408 ATTTTTACTTTTGAGTTA
1 ATTTTTACTTTTAAGTTA
3617426 ATTTTTA-TTTTAAGTT
1 ATTTTTACTTTTAAGTT
3617442 TTAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65
Consensus pattern (18 bp):
ATTTTTACTTTTAAGTTA
Found at i:3617709 original size:15 final size:14
Alignment explanation
Indices: 3617680--3617706 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3617670 ATAAGTTAAT
3617680 TAAAATATATTTTA
1 TAAAATATATTTTA
3617694 TAAAATATATTTT
1 TAAAATATATTTT
3617707 TATTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAAATATATTTTA
Found at i:3618025 original size:14 final size:14
Alignment explanation
Indices: 3618008--3618035 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3617998 ATAATTATAA
3618008 TTTTATTTAAATTT
1 TTTTATTTAAATTT
3618022 TTTTATTTAAATTT
1 TTTTATTTAAATTT
3618036 AAGTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTTAAATTT
Found at i:3619924 original size:35 final size:35
Alignment explanation
Indices: 3619878--3619948 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
3619868 AATTGAGAAA
3619878 TATTATTTCACACTTAAATCCACACATGAATGGCC
1 TATTATTTCACACTTAAATCCACACATGAATGGCC
**
3619913 TATTATTTCACACTTAAATCCGTACATGAATGGCC
1 TATTATTTCACACTTAAATCCACACATGAATGGCC
3619948 T
1 T
3619949 TACAATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (35 bp):
TATTATTTCACACTTAAATCCACACATGAATGGCC
Found at i:3623855 original size:79 final size:77
Alignment explanation
Indices: 3623688--3623860 Score: 238
Period size: 78 Copynumber: 2.2 Consensus size: 77
3623678 AACAACGGGA
* * * * *
3623688 TTGGAGTATCCCCGATTATGGAAAATCGGTGTTCCGAAAATAAAATGGGGTTGAAATATTCCCTC
1 TTGGAGTAT-CCCGATTATAGAAAATCAGTATTCCGAAAATAAAATGGGATTGAAACATTCCCTC
3623753 GAAAATAACAGGG
65 GAAAATAACAGGG
** * *
3623766 TTGGAGTATCCCTGATTATAGAAAATCAGTATTTTGAAAATAAAATCGGGATTGGAGCATTCCCT
1 TTGGAGTATCCC-GATTATAGAAAATCAGTATTCCGAAAATAAAAT-GGGATTGAAACATTCCCT
3623831 CGAAAATAACAGGG
64 CGAAAATAACAGGG
3623845 TTGGAGTATCCCGATT
1 TTGGAGTATCCCGATT
3623861 GTGAAAAATC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
77 3 0.04
78 41 0.49
79 40 0.48
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (77 bp):
TTGGAGTATCCCGATTATAGAAAATCAGTATTCCGAAAATAAAATGGGATTGAAACATTCCCTCG
AAAATAACAGGG
Found at i:3623935 original size:51 final size:51
Alignment explanation
Indices: 3623842--3623958 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
3623832 GAAAATAACA
* *
3623842 GGGTTGGAGTAT-CCCGATTGTGAAAAATCGATGATTTAGAAAT-AAGACCG
1 GGGTTGGAGTATCCCCAATTGTGAAAAATCAATGATTTAGAAATAAAG-CCG
* * *
3623892 GGGTTGAAGTATCCCCAATTGTGAGAAATCAAT-ATTTTGGAAATAAAGCCG
1 GGGTTGGAGTATCCCCAATTGTGAAAAATCAATGA-TTTAGAAATAAAGCCG
3623943 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
3623959 TCCAAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 12 0.21
51 43 0.74
52 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAATTGTGAAAAATCAATGATTTAGAAATAAAGCCG
Found at i:3623975 original size:28 final size:28
Alignment explanation
Indices: 3623941--3624042 Score: 145
Period size: 28 Copynumber: 3.6 Consensus size: 28
3623931 GAAATAAAGC
*
3623941 CGGGGTTGGAGTATCCCCTCCAAAATAA
1 CGGGGTTGGAGTATCCCCTCGAAAATAA
3623969 CGGGGTTGGAGTAT-CCCT-GATGAAATAA
1 CGGGGTTGGAGTATCCCCTCGA--AAATAA
*
3623997 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCTCGAAAATAA
*
3624025 CGGGATTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
3624043 GATTATGAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
26 1 0.01
27 4 0.06
28 57 0.85
29 4 0.06
30 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAA
Found at i:3626434 original size:33 final size:33
Alignment explanation
Indices: 3626392--3626494 Score: 179
Period size: 33 Copynumber: 3.1 Consensus size: 33
3626382 TACATTGTAA
* *
3626392 AATGTATCGATACAATGAGCAATATATTGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
3626425 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
*
3626458 AATGTATCGATACAATGAGTAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
3626491 AATG
1 AATG
3626495 CAAAATGTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:3626434 original size:53 final size:52
Alignment explanation
Indices: 3626372--3626511 Score: 167
Period size: 53 Copynumber: 2.6 Consensus size: 52
3626362 AAAATGCCTG
* * *
3626372 AATGTATCGATACATTGTAAAATGTATCGATACAATG-AGCAATATATTGA-T
1 AATGTATCGATACAATG-AAAATGTATCGATACAATGTAGCAATACAATGAGT
* * *
3626423 ACAATGTATCGATACAATGAGCAATGTATCGATACAATGTATCGATACAATGAGT
1 --AATGTATCGATACAATGA-AAATGTATCGATACAATGTAGCAATACAATGAGT
3626478 AATGTATCGATACAATGCAAAATGTATCGATACA
1 AATGTATCGATACAATG-AAAATGTATCGATACA
3626512 TCTGGGTAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
52 1 0.01
53 64 0.84
54 10 0.13
55 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (52 bp):
AATGTATCGATACAATGAAAATGTATCGATACAATGTAGCAATACAATGAGT
Found at i:3626441 original size:13 final size:13
Alignment explanation
Indices: 3626420--3626474 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
3626410 GCAATATATT
3626420 GATACAATGTATC
1 GATACAATGTATC
3626433 GATACAATG-A--
1 GATACAATGTATC
3626443 G---CAATGTATC
1 GATACAATGTATC
3626453 GATACAATGTATC
1 GATACAATGTATC
3626466 GATACAATG
1 GATACAATG
3626475 AGTAATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
7 5 0.14
8 1 0.03
10 2 0.06
12 1 0.03
13 27 0.75
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (13 bp):
GATACAATGTATC
Found at i:3626447 original size:20 final size:19
Alignment explanation
Indices: 3626372--3626511 Score: 97
Period size: 20 Copynumber: 7.7 Consensus size: 19
3626362 AAAATGCCTG
* *
3626372 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AC
3626392 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
**
3626412 AA--TAT--AT-TGAT-AC
1 AATGTATCGATACAATGAC
3626425 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
3626445 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
*
3626458 AATGTATCGATACAATGAGT
1 AATGTATCGATACAATGA-C
*
3626478 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
3626498 AATGTATCGATACA
1 AATGTATCGATACA
3626512 TCTGGGTAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 32
0.71 0.06 0.24
Matches are distributed among these distances:
13 13 0.14
14 2 0.02
15 7 0.07
16 2 0.02
17 2 0.02
18 7 0.07
19 3 0.03
20 59 0.61
21 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:3627098 original size:21 final size:21
Alignment explanation
Indices: 3627074--3627115 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3627064 TGATCCATAA
3627074 AGGAAAAGAAAGGAATTCTTT
1 AGGAAAAGAAAGGAATTCTTT
3627095 AGGAAAAGAAAGGAATTCTTT
1 AGGAAAAGAAAGGAATTCTTT
3627116 GTCATGCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.24
Consensus pattern (21 bp):
AGGAAAAGAAAGGAATTCTTT
Found at i:3633407 original size:319 final size:320
Alignment explanation
Indices: 3632792--3633417 Score: 970
Period size: 319 Copynumber: 2.0 Consensus size: 320
3632782 AAATATCTCG
3632792 AAATAAGCATAAGCATAGTGCAGTGTCTCTTTGTGCTTCTATCCATATTAGTTCTTACAATTCAT
1 AAATAAGCATAAGCATAGTGCAGTGTCTCTTTGTGCTTCTATCCATATTAGTTCTTACAATTCAT
* *
3632857 GGTTAATGATCATGAATCTTTAAAAAATGATTCCCATAATTCATTGTGCTTTGGCCAAAGACTTT
66 GGTTAATGATCATGAATCTATAAAAAATGATTCCCATAATTCATTATGCTTTGGCCAAAGACTTT
*
3632922 AATCAAATTAACCATAGTTAAGAATAGATAGGATACATCTCCAATGTCACTTAGAGTGGTGAATT
131 AATCAAATTAACCATAGTTAAGAATAGATAGGATACATCTCCAATGTCACTTAGAATGGTGAATT
* * * * *
3632987 TTCTCTAGATCACCCATTTATCTTTTTATGCTTCATGTCGTATCCAAAATGACCATGCCTTCGAT
196 CTCTCTAGATCACCCATCTATCTTTATATGCTTCATGTCGTACCCAAAATGACCATGCCTTCAAT
* * *
3633052 AACCAAGAAAATGGACCACTTCGTGATGAAATCAAAATATGACACTCCCTATTAGTCCTA
261 AACCAACAAAATGGACCACTTCATGATAAAATCAAAATATGACACTCCCTATTAGTCCTA
* *
3633112 AAATAAGCATAAGCATAGTGCAGTGT-T-TATTGTGTTTCTATCCATGTTAGTTCTTACAATTCA
1 AAATAAGCATAAGCATAGTGCAGTGTCTCT-TTGTGCTTCTATCCATATTAGTTCTTACAATTCA
*
3633175 TGGTTAATGATCATGAATCTATCAAAAATGATTCCCATAATTCATTATGCTTTGGCCAAAGACTT
65 TGGTTAATGATCATGAATCTATAAAAAATGATTCCCATAATTCATTATGCTTTGGCCAAAGACTT
* * * * * ** *
3633240 TAGTCAAATTAACCATAATTTAA-AATAGGTAGGATACATCTTCGATGTTGCTTGGAATGGTGAA
130 TAATCAAATTAACCAT-AGTTAAGAATAGATAGGATACATCTCCAATGTCACTTAGAATGGTGAA
* * * *
3633304 TTCTCTTTAGATCACTCATCTATCTTTATATGTTTCATGTCGTACCCAAAATGACTATGCCTTCA
194 TTCTCTCTAGATCACCCATCTATCTTTATATGCTTCATGTCGTACCCAAAATGACCATGCCTTCA
*
3633369 ATAACCAACAAAGTGGACCACTTCATGATAAAATCAAAATATGACACTC
259 ATAACCAACAAAATGGACCACTTCATGATAAAATCAAAATATGACACTC
3633418 TTTATATAAG
Statistics
Matches: 277, Mismatches: 27, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
318 1 0.00
319 245 0.88
320 31 0.11
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (320 bp):
AAATAAGCATAAGCATAGTGCAGTGTCTCTTTGTGCTTCTATCCATATTAGTTCTTACAATTCAT
GGTTAATGATCATGAATCTATAAAAAATGATTCCCATAATTCATTATGCTTTGGCCAAAGACTTT
AATCAAATTAACCATAGTTAAGAATAGATAGGATACATCTCCAATGTCACTTAGAATGGTGAATT
CTCTCTAGATCACCCATCTATCTTTATATGCTTCATGTCGTACCCAAAATGACCATGCCTTCAAT
AACCAACAAAATGGACCACTTCATGATAAAATCAAAATATGACACTCCCTATTAGTCCTA
Found at i:3636056 original size:23 final size:22
Alignment explanation
Indices: 3636015--3636057 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3636005 TATTGCATTA
*
3636015 GAATGAATAAATGAATTAAAAG
1 GAATGAAGAAATGAATTAAAAG
*
3636037 GAATGAAGGAAATGACTTAAA
1 GAATGAA-GAAATGAATTAAA
3636058 TGAAGAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (22 bp):
GAATGAAGAAATGAATTAAAAG
Found at i:3645119 original size:62 final size:62
Alignment explanation
Indices: 3645046--3645165 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 62
3645036 TAGCCCAACG
** *
3645046 TAGTTTCGAAAACTTGGTTCATTTTAGACCTTGATAACTTCAAAATGTAATAAAACTACTGC
1 TAGTTTCGAAAACTTGGTTCATTGGAGACCTTGATAACCTCAAAATGTAATAAAACTACTGC
* * *
3645108 TAGTTTTGAAAACTTGGTTCATTGGAGACCTTGATGACCTCAAAATGTTATAAAACTA
1 TAGTTTCGAAAACTTGGTTCATTGGAGACCTTGATAACCTCAAAATGTAATAAAACTA
3645166 GTGCCATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (62 bp):
TAGTTTCGAAAACTTGGTTCATTGGAGACCTTGATAACCTCAAAATGTAATAAAACTACTGC
Found at i:3646087 original size:104 final size:106
Alignment explanation
Indices: 3645895--3646101 Score: 296
Period size: 104 Copynumber: 2.0 Consensus size: 106
3645885 GTCGAGTTGG
* *
3645895 TTTTAATTCAGGTTGATTGGGGTTAGGTCATTTCAGCTATTTAGATTTTTTATTCATTTTTAGGT
1 TTTTAATTCAGGTTAATTGGGGTTAGGTCATTTCAGCTACTTAGATTTTTTATTCATTTTTAGGT
***
3645960 TTAGGTCATTTTGGCTTCAGGTCACTTCAGAATCAAGTAAC
66 TTAGGTCATTTCAACTTCAGGTCACTTCAGAATCAAGTAAC
*
3646001 TTTTGATTCAGGTTAATT-GGGTTAGGTCATTTC-GACGT-CTTAGATTTTTTA-TCATTTTTAG
1 TTTTAATTCAGGTTAATTGGGGTTAGGTCATTTCAG-C-TACTTAGATTTTTTATTCATTTTTAG
* *
3646062 GTTTAGGTTATTTCAACTTCGGGTCACTTCAGAATCAAGT
64 GTTTAGGTCATTTCAACTTCAGGTCACTTCAGAATCAAGT
3646102 CATTTCAGTT
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
104 46 0.51
105 28 0.31
106 17 0.19
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (106 bp):
TTTTAATTCAGGTTAATTGGGGTTAGGTCATTTCAGCTACTTAGATTTTTTATTCATTTTTAGGT
TTAGGTCATTTCAACTTCAGGTCACTTCAGAATCAAGTAAC
Found at i:3648103 original size:15 final size:16
Alignment explanation
Indices: 3648083--3648115 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3648073 GCATGATTCT
3648083 TATGCAT-AAATATTA
1 TATGCATGAAATATTA
3648098 TATGCATGGAAATATTA
1 TATGCAT-GAAATATTA
3648115 T
1 T
3648116 GTAAGCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (16 bp):
TATGCATGAAATATTA
Found at i:3648424 original size:31 final size:31
Alignment explanation
Indices: 3648386--3648503 Score: 128
Period size: 31 Copynumber: 3.6 Consensus size: 31
3648376 TATCTTTTGA
*
3648386 AGGCTAAGATAGAGCCTCTCTATTTTTTCAC
1 AGGCTAAGATAGAACCTCTCTATTTTTTCAC
* *
3648417 AGGCTAAGATAGAACCTCCCTATCTTTTCAC
1 AGGCTAAGATAGAACCTCTCTATTTTTTCAC
* * *
3648448 AGGTTAAGATAAAACCTTTCTCCCTATCTTTTTCAA
1 AGGCTAAGATAGAACC--TCT--CTAT-TTTTTCAC
*
3648484 AAGCTAAGATAGAACCTCTC
1 AGGCTAAGATAGAACCTCTC
3648504 AATCACTTCG
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
31 42 0.59
32 1 0.01
33 2 0.03
34 3 0.04
35 4 0.06
36 19 0.27
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.32
Consensus pattern (31 bp):
AGGCTAAGATAGAACCTCTCTATTTTTTCAC
Found at i:3648492 original size:36 final size:35
Alignment explanation
Indices: 3648432--3648500 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
3648422 AAGATAGAAC
* * *
3648432 CTCCCTATCTTTTCACAGGTTAAGATAAAACCTTT
1 CTCCCTATCTTTTCAAAAGCTAAGATAAAACCTTT
*
3648467 CTCCCTATCTTTTTCAAAAGCTAAGATAGAACCT
1 CTCCCTATC-TTTTCAAAAGCTAAGATAAAACCT
3648501 CTCAATCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (35 bp):
CTCCCTATCTTTTCAAAAGCTAAGATAAAACCTTT
Found at i:3648878 original size:20 final size:20
Alignment explanation
Indices: 3648853--3648912 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
3648843 CCATTGGACT
*
3648853 TAATGTATCAATACAATTCA
1 TAATGTATCGATACAATTCA
3648873 TAATGTATCGATACAATTCA
1 TAATGTATCGATACAATTCA
3648893 TAATGTATCGATACAATTCA
1 TAATGTATCGATACAATTCA
3648913 ATATAGCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (20 bp):
TAATGTATCGATACAATTCA
Found at i:3649055 original size:32 final size:33
Alignment explanation
Indices: 3649014--3649078 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3649004 CATTTCATGG
*
3649014 TGTATCGATACAAAG-AACATGTATTGATACAT
1 TGTATCGATACAAAGCAACATGTATCGATACAT
* *
3649046 TGTATCGATACTAAGCAATATGTATCGATACAT
1 TGTATCGATACAAAGCAACATGTATCGATACAT
3649079 CTGGGTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACATGTATCGATACAT
Found at i:3649743 original size:25 final size:27
Alignment explanation
Indices: 3649689--3649747 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 27
3649679 CTCCCCTTAA
3649689 TGAAAGATTTTCTATTTCTCCCTTTGTG
1 TGAAAGA-TTTCTATTTCTCCCTTTGTG
3649717 TGAAAGA-TTCTA-TTCTCCCATTTTGTG
1 TGAAAGATTTCTATTTCTCCC--TTTGTG
3649744 TGAA
1 TGAA
3649748 TTTACCTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.24
26 5 0.17
27 10 0.34
28 7 0.24
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (27 bp):
TGAAAGATTTCTATTTCTCCCTTTGTG
Done.